[2016-04-14T18:22Z] Resource requests: bwa, sambamba, samtools; memory: 2.00, 2.00; cores: 16, 16, 16
[2016-04-14T18:22Z] Configuring 1 jobs to run, using 16 cores each with 32.1g of memory reserved for each job
[2016-04-14T18:22Z] Timing: organize samples
[2016-04-14T18:22Z] multiprocessing: organize_samples
[2016-04-14T18:22Z] Using input YAML configuration: /coldstorage/fastq/160208_SN404_0473_AHHFLHBCXX/sample.yaml
[2016-04-14T18:22Z] Checking sample YAML configuration: /coldstorage/fastq/160208_SN404_0473_AHHFLHBCXX/sample.yaml
[2016-04-14T18:22Z] Testing minimum versions of installed programs
[2016-04-14T18:22Z] Timing: alignment preparation
[2016-04-14T18:22Z] multiprocessing: prep_align_inputs
[2016-04-14T18:22Z] bgzip input file
[2016-04-14T18:23Z] bgzip input file
[2016-04-14T18:25Z] Resource requests: ; memory: 1.00; cores: 1
[2016-04-14T18:25Z] Configuring 2 jobs to run, using 1 cores each with 1.00g of memory reserved for each job
[2016-04-14T18:25Z] bgzip input file
[2016-04-14T18:26Z] bgzip input file
[2016-04-14T18:27Z] Resource requests: ; memory: 1.00; cores: 1
[2016-04-14T18:27Z] Configuring 2 jobs to run, using 1 cores each with 1.00g of memory reserved for each job
[2016-04-14T18:27Z] bgzip input file
[2016-04-14T18:28Z] bgzip input file
[2016-04-14T18:30Z] Resource requests: ; memory: 1.00; cores: 1
[2016-04-14T18:30Z] Configuring 2 jobs to run, using 1 cores each with 1.00g of memory reserved for each job
[2016-04-14T18:30Z] multiprocessing: disambiguate_split
[2016-04-14T18:30Z] Timing: alignment
[2016-04-14T18:30Z] multiprocessing: process_alignment
[2016-04-14T18:30Z] Aligning lane R14-18102_20HHFLHB_HHFLHBCXX with bwa aligner
[2016-04-14T18:30Z] bwa mem alignment from fastq: R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T18:30Z] samblaster: Version 0.1.22
[2016-04-14T18:30Z] samblaster: Inputting from stdin
[2016-04-14T18:30Z] samblaster: Outputting to stdout
[2016-04-14T18:30Z] samblaster: Opening /dev/fd/62 for write.
[2016-04-14T18:30Z] samblaster: Opening /dev/fd/63 for write.
[2016-04-14T18:30Z] [M::mem_pestat] skip orientation FF as there are not enough pairs
[2016-04-14T18:30Z] [M::mem_pestat] analyzing insert size distribution for orientation FR...
[2016-04-14T18:30Z] [M::mem_pestat] (25, 50, 75) percentile: (145, 183, 228)
[2016-04-14T18:30Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 394)
[2016-04-14T18:30Z] [M::mem_pestat] mean and std.dev: (189.47, 60.27)
[2016-04-14T18:30Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 477)
[2016-04-14T18:30Z] [M::mem_pestat] skip orientation RF as there are not enough pairs
[2016-04-14T18:30Z] [M::mem_pestat] skip orientation RR as there are not enough pairs
[2016-04-14T18:31Z] samblaster: Loaded 84 header sequence entries.
[2016-04-14T18:31Z] [M::mem_pestat] skip orientation FF as there are not enough pairs
[2016-04-14T18:31Z] [M::mem_pestat] analyzing insert size distribution for orientation FR...
[2016-04-14T18:31Z] [M::mem_pestat] (25, 50, 75) percentile: (144, 182, 227)
[2016-04-14T18:31Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 393)
[2016-04-14T18:31Z] [M::mem_pestat] mean and std.dev: (188.41, 59.76)
[2016-04-14T18:31Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 476)
[2016-04-14T18:31Z] [M::mem_pestat] skip orientation RF as there are not enough pairs
[2016-04-14T18:31Z] [M::mem_pestat] skip orientation RR as there are not enough pairs
[2016-04-14T18:31Z] [M::mem_pestat] skip orientation FF as there are not enough pairs
[2016-04-14T18:31Z] [M::mem_pestat] analyzing insert size distribution for orientation FR...
[2016-04-14T18:31Z] [M::mem_pestat] (25, 50, 75) percentile: (144, 182, 226)
[2016-04-14T18:31Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 390)
[2016-04-14T18:31Z] [M::mem_pestat] mean and std.dev: (187.53, 59.55)
[2016-04-14T18:31Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 472)
[2016-04-14T18:31Z] [M::mem_pestat] skip orientation RF as there are not enough pairs
[2016-04-14T18:31Z] [M::mem_pestat] skip orientation RR as there are not enough pairs
[2016-04-14T18:31Z] [M::mem_pestat] skip orientation FF as there are not enough pairs
[2016-04-14T18:31Z] [M::mem_pestat] analyzing insert size distribution for orientation FR...
[2016-04-14T18:31Z] [M::mem_pestat] (25, 50, 75) percentile: (143, 181, 224)
[2016-04-14T18:31Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 386)
[2016-04-14T18:31Z] [M::mem_pestat] mean and std.dev: (186.43, 59.09)
[2016-04-14T18:31Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 467)
[2016-04-14T18:31Z] [M::mem_pestat] skip orientation RF as there are not enough pairs
[2016-04-14T18:31Z] [M::mem_pestat] skip orientation RR as there are not enough pairs
[2016-04-14T18:32Z] [M::mem_pestat] skip orientation FF as there are not enough pairs
[2016-04-14T18:32Z] [M::mem_pestat] analyzing insert size distribution for orientation FR...
[2016-04-14T18:32Z] [M::mem_pestat] (25, 50, 75) percentile: (143, 181, 225)
[2016-04-14T18:32Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 389)
[2016-04-14T18:32Z] [M::mem_pestat] mean and std.dev: (186.78, 59.22)
[2016-04-14T18:32Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 471)
[2016-04-14T18:32Z] [M::mem_pestat] analyzing insert size distribution for orientation RF...
[2016-04-14T18:32Z] [M::mem_pestat] (25, 50, 75) percentile: (187, 806, 940)
[2016-04-14T18:32Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 2446)
[2016-04-14T18:32Z] [M::mem_pestat] mean and std.dev: (612.75, 365.44)
[2016-04-14T18:32Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 3199)
[2016-04-14T18:32Z] [M::mem_pestat] skip orientation RR as there are not enough pairs
[2016-04-14T18:32Z] [M::mem_pestat] skip orientation RF
[2016-04-14T18:32Z] [M::mem_pestat] skip orientation FF as there are not enough pairs
[2016-04-14T18:32Z] [M::mem_pestat] analyzing insert size distribution for orientation FR...
[2016-04-14T18:32Z] [M::mem_pestat] (25, 50, 75) percentile: (146, 184, 229)
[2016-04-14T18:32Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 395)
[2016-04-14T18:32Z] [M::mem_pestat] mean and std.dev: (190.05, 60.32)
[2016-04-14T18:32Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 478)
[2016-04-14T18:32Z] [M::mem_pestat] skip orientation RF as there are not enough pairs
[2016-04-14T18:32Z] [M::mem_pestat] skip orientation RR as there are not enough pairs
[2016-04-14T18:32Z] [M::mem_pestat] skip orientation FF as there are not enough pairs
[2016-04-14T18:32Z] [M::mem_pestat] analyzing insert size distribution for orientation FR...
[2016-04-14T18:32Z] [M::mem_pestat] (25, 50, 75) percentile: (145, 183, 228)
[2016-04-14T18:32Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 394)
[2016-04-14T18:32Z] [M::mem_pestat] mean and std.dev: (189.09, 60.15)
[2016-04-14T18:32Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 477)
[2016-04-14T18:32Z] [M::mem_pestat] skip orientation RF as there are not enough pairs
[2016-04-14T18:32Z] [M::mem_pestat] skip orientation RR as there are not enough pairs
[2016-04-14T18:32Z] [M::mem_pestat] skip orientation FF as there are not enough pairs
[2016-04-14T18:32Z] [M::mem_pestat] analyzing insert size distribution for orientation FR...
[2016-04-14T18:32Z] [M::mem_pestat] (25, 50, 75) percentile: (144, 182, 227)
[2016-04-14T18:32Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 393)
[2016-04-14T18:32Z] [M::mem_pestat] mean and std.dev: (188.46, 59.85)
[2016-04-14T18:32Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 476)
[2016-04-14T18:32Z] [M::mem_pestat] skip orientation RF as there are not enough pairs
[2016-04-14T18:32Z] [M::mem_pestat] skip orientation RR as there are not enough pairs
[2016-04-14T18:33Z] [M::mem_pestat] skip orientation FF as there are not enough pairs
[2016-04-14T18:33Z] [M::mem_pestat] analyzing insert size distribution for orientation FR...
[2016-04-14T18:33Z] [M::mem_pestat] (25, 50, 75) percentile: (143, 181, 225)
[2016-04-14T18:33Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 389)
[2016-04-14T18:33Z] [M::mem_pestat] mean and std.dev: (187.01, 59.35)
[2016-04-14T18:33Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 471)
[2016-04-14T18:33Z] [M::mem_pestat] analyzing insert size distribution for orientation RF...
[2016-04-14T18:33Z] [M::mem_pestat] (25, 50, 75) percentile: (109, 832, 939)
[2016-04-14T18:33Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 2599)
[2016-04-14T18:33Z] [M::mem_pestat] mean and std.dev: (634.54, 588.82)
[2016-04-14T18:33Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 3429)
[2016-04-14T18:33Z] [M::mem_pestat] skip orientation RR as there are not enough pairs
[2016-04-14T18:33Z] [M::mem_pestat] skip orientation RF
[2016-04-14T18:33Z] [M::mem_pestat] skip orientation FF as there are not enough pairs
[2016-04-14T18:33Z] [M::mem_pestat] analyzing insert size distribution for orientation FR...
[2016-04-14T18:33Z] [M::mem_pestat] (25, 50, 75) percentile: (144, 181, 226)
[2016-04-14T18:33Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 390)
[2016-04-14T18:33Z] [M::mem_pestat] mean and std.dev: (187.53, 59.37)
[2016-04-14T18:33Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 472)
[2016-04-14T18:33Z] [M::mem_pestat] analyzing insert size distribution for orientation RF...
[2016-04-14T18:33Z] [M::mem_pestat] (25, 50, 75) percentile: (376, 943, 952)
[2016-04-14T18:33Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 2104)
[2016-04-14T18:33Z] [M::mem_pestat] mean and std.dev: (669.56, 390.80)
[2016-04-14T18:33Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 2680)
[2016-04-14T18:33Z] [M::mem_pestat] skip orientation RR as there are not enough pairs
[2016-04-14T18:33Z] [M::mem_pestat] skip orientation RF
[2016-04-14T18:33Z] [M::mem_pestat] skip orientation FF as there are not enough pairs
[2016-04-14T18:33Z] [M::mem_pestat] analyzing insert size distribution for orientation FR...
[2016-04-14T18:33Z] [M::mem_pestat] (25, 50, 75) percentile: (145, 184, 229)
[2016-04-14T18:33Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 397)
[2016-04-14T18:33Z] [M::mem_pestat] mean and std.dev: (189.95, 60.57)
[2016-04-14T18:33Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 481)
[2016-04-14T18:33Z] [M::mem_pestat] analyzing insert size distribution for orientation RF...
[2016-04-14T18:33Z] [M::mem_pestat] (25, 50, 75) percentile: (187, 899, 1001)
[2016-04-14T18:33Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 2629)
[2016-04-14T18:33Z] [M::mem_pestat] mean and std.dev: (614.75, 368.14)
[2016-04-14T18:33Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 3443)
[2016-04-14T18:33Z] [M::mem_pestat] skip orientation RR as there are not enough pairs
[2016-04-14T18:33Z] [M::mem_pestat] skip orientation RF
[2016-04-14T18:33Z] [M::mem_pestat] skip orientation FF as there are not enough pairs
[2016-04-14T18:33Z] [M::mem_pestat] analyzing insert size distribution for orientation FR...
[2016-04-14T18:33Z] [M::mem_pestat] (25, 50, 75) percentile: (145, 183, 228)
[2016-04-14T18:33Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 394)
[2016-04-14T18:33Z] [M::mem_pestat] mean and std.dev: (189.45, 60.35)
[2016-04-14T18:33Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 477)
[2016-04-14T18:33Z] [M::mem_pestat] skip orientation RF as there are not enough pairs
[2016-04-14T18:33Z] [M::mem_pestat] skip orientation RR as there are not enough pairs
[2016-04-14T18:34Z] [M::mem_pestat] skip orientation FF as there are not enough pairs
[2016-04-14T18:34Z] [M::mem_pestat] analyzing insert size distribution for orientation FR...
[2016-04-14T18:34Z] [M::mem_pestat] (25, 50, 75) percentile: (144, 183, 227)
[2016-04-14T18:34Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 393)
[2016-04-14T18:34Z] [M::mem_pestat] mean and std.dev: (188.78, 60.03)
[2016-04-14T18:34Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 476)
[2016-04-14T18:34Z] [M::mem_pestat] analyzing insert size distribution for orientation RF...
[2016-04-14T18:34Z] [M::mem_pestat] (25, 50, 75) percentile: (749, 887, 923)
[2016-04-14T18:34Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (401, 1271)
[2016-04-14T18:34Z] [M::mem_pestat] mean and std.dev: (848.50, 118.02)
[2016-04-14T18:34Z] [M::mem_pestat] low and high boundaries for proper pairs: (227, 1445)
[2016-04-14T18:34Z] [M::mem_pestat] skip orientation RR as there are not enough pairs
[2016-04-14T18:34Z] [M::mem_pestat] skip orientation RF
[2016-04-14T18:34Z] [M::mem_pestat] skip orientation FF as there are not enough pairs
[2016-04-14T18:34Z] [M::mem_pestat] analyzing insert size distribution for orientation FR...
[2016-04-14T18:34Z] [M::mem_pestat] (25, 50, 75) percentile: (144, 182, 226)
[2016-04-14T18:34Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 390)
[2016-04-14T18:34Z] [M::mem_pestat] mean and std.dev: (187.60, 59.73)
[2016-04-14T18:34Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 472)
[2016-04-14T18:34Z] [M::mem_pestat] analyzing insert size distribution for orientation RF...
[2016-04-14T18:34Z] [M::mem_pestat] (25, 50, 75) percentile: (99, 134, 759)
[2016-04-14T18:34Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 2079)
[2016-04-14T18:34Z] [M::mem_pestat] mean and std.dev: (299.85, 338.19)
[2016-04-14T18:34Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 2739)
[2016-04-14T18:34Z] [M::mem_pestat] skip orientation RR as there are not enough pairs
[2016-04-14T18:34Z] [M::mem_pestat] skip orientation RF
[2016-04-14T18:34Z] [M::mem_pestat] skip orientation FF as there are not enough pairs
[2016-04-14T18:34Z] [M::mem_pestat] analyzing insert size distribution for orientation FR...
[2016-04-14T18:34Z] [M::mem_pestat] (25, 50, 75) percentile: (143, 181, 225)
[2016-04-14T18:34Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 389)
[2016-04-14T18:34Z] [M::mem_pestat] mean and std.dev: (186.85, 59.49)
[2016-04-14T18:34Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 471)
[2016-04-14T18:34Z] [M::mem_pestat] skip orientation RF as there are not enough pairs
[2016-04-14T18:34Z] [M::mem_pestat] skip orientation RR as there are not enough pairs
[2016-04-14T18:34Z] [M::mem_pestat] skip orientation FF as there are not enough pairs
[2016-04-14T18:34Z] [M::mem_pestat] analyzing insert size distribution for orientation FR...
[2016-04-14T18:34Z] [M::mem_pestat] (25, 50, 75) percentile: (146, 184, 229)
[2016-04-14T18:34Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 395)
[2016-04-14T18:34Z] [M::mem_pestat] mean and std.dev: (190.14, 60.31)
[2016-04-14T18:34Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 478)
[2016-04-14T18:34Z] [M::mem_pestat] skip orientation RF as there are not enough pairs
[2016-04-14T18:34Z] [M::mem_pestat] skip orientation RR as there are not enough pairs
[2016-04-14T18:35Z] [M::mem_pestat] skip orientation FF as there are not enough pairs
[2016-04-14T18:35Z] [M::mem_pestat] analyzing insert size distribution for orientation FR...
[2016-04-14T18:35Z] [M::mem_pestat] (25, 50, 75) percentile: (145, 183, 228)
[2016-04-14T18:35Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 394)
[2016-04-14T18:35Z] [M::mem_pestat] mean and std.dev: (189.16, 59.96)
[2016-04-14T18:35Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 477)
[2016-04-14T18:35Z] [M::mem_pestat] skip orientation RF as there are not enough pairs
[2016-04-14T18:35Z] [M::mem_pestat] skip orientation RR as there are not enough pairs
[2016-04-14T18:35Z] [M::mem_pestat] skip orientation FF as there are not enough pairs
[2016-04-14T18:35Z] [M::mem_pestat] analyzing insert size distribution for orientation FR...
[2016-04-14T18:35Z] [M::mem_pestat] (25, 50, 75) percentile: (144, 182, 226)
[2016-04-14T18:35Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 390)
[2016-04-14T18:35Z] [M::mem_pestat] mean and std.dev: (188.26, 59.63)
[2016-04-14T18:35Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 472)
[2016-04-14T18:35Z] [M::mem_pestat] skip orientation RF as there are not enough pairs
[2016-04-14T18:35Z] [M::mem_pestat] skip orientation RR as there are not enough pairs
[2016-04-14T18:35Z] [M::mem_pestat] skip orientation FF as there are not enough pairs
[2016-04-14T18:35Z] [M::mem_pestat] analyzing insert size distribution for orientation FR...
[2016-04-14T18:35Z] [M::mem_pestat] (25, 50, 75) percentile: (144, 181, 225)
[2016-04-14T18:35Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 387)
[2016-04-14T18:35Z] [M::mem_pestat] mean and std.dev: (187.24, 59.23)
[2016-04-14T18:35Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 468)
[2016-04-14T18:35Z] [M::mem_pestat] skip orientation RF as there are not enough pairs
[2016-04-14T18:35Z] [M::mem_pestat] skip orientation RR as there are not enough pairs
[2016-04-14T18:36Z] [M::mem_pestat] skip orientation FF as there are not enough pairs
[2016-04-14T18:36Z] [M::mem_pestat] analyzing insert size distribution for orientation FR...
[2016-04-14T18:36Z] [M::mem_pestat] (25, 50, 75) percentile: (144, 182, 226)
[2016-04-14T18:36Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 390)
[2016-04-14T18:36Z] [M::mem_pestat] mean and std.dev: (187.52, 59.24)
[2016-04-14T18:36Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 472)
[2016-04-14T18:36Z] [M::mem_pestat] skip orientation RF as there are not enough pairs
[2016-04-14T18:36Z] [M::mem_pestat] skip orientation RR as there are not enough pairs
[2016-04-14T18:36Z] [M::mem_pestat] skip orientation FF as there are not enough pairs
[2016-04-14T18:36Z] [M::mem_pestat] analyzing insert size distribution for orientation FR...
[2016-04-14T18:36Z] [M::mem_pestat] (25, 50, 75) percentile: (144, 182, 227)
[2016-04-14T18:36Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 393)
[2016-04-14T18:36Z] [M::mem_pestat] mean and std.dev: (188.32, 59.74)
[2016-04-14T18:36Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 476)
[2016-04-14T18:36Z] [M::mem_pestat] skip orientation RF as there are not enough pairs
[2016-04-14T18:36Z] [M::mem_pestat] skip orientation RR as there are not enough pairs
[2016-04-14T18:36Z] [M::mem_pestat] skip orientation FF as there are not enough pairs
[2016-04-14T18:36Z] [M::mem_pestat] analyzing insert size distribution for orientation FR...
[2016-04-14T18:36Z] [M::mem_pestat] (25, 50, 75) percentile: (145, 184, 228)
[2016-04-14T18:36Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 394)
[2016-04-14T18:36Z] [M::mem_pestat] mean and std.dev: (189.60, 60.39)
[2016-04-14T18:36Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 477)
[2016-04-14T18:36Z] [M::mem_pestat] skip orientation RF as there are not enough pairs
[2016-04-14T18:36Z] [M::mem_pestat] skip orientation RR as there are not enough pairs
[2016-04-14T18:36Z] [M::mem_pestat] skip orientation FF as there are not enough pairs
[2016-04-14T18:36Z] [M::mem_pestat] analyzing insert size distribution for orientation FR...
[2016-04-14T18:36Z] [M::mem_pestat] (25, 50, 75) percentile: (144, 183, 227)
[2016-04-14T18:36Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 393)
[2016-04-14T18:36Z] [M::mem_pestat] mean and std.dev: (188.64, 60.01)
[2016-04-14T18:36Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 476)
[2016-04-14T18:36Z] [M::mem_pestat] skip orientation RF as there are not enough pairs
[2016-04-14T18:36Z] [M::mem_pestat] skip orientation RR as there are not enough pairs
[2016-04-14T18:37Z] [M::mem_pestat] skip orientation FF as there are not enough pairs
[2016-04-14T18:37Z] [M::mem_pestat] analyzing insert size distribution for orientation FR...
[2016-04-14T18:37Z] [M::mem_pestat] (25, 50, 75) percentile: (144, 182, 226)
[2016-04-14T18:37Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 390)
[2016-04-14T18:37Z] [M::mem_pestat] mean and std.dev: (187.95, 59.83)
[2016-04-14T18:37Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 472)
[2016-04-14T18:37Z] [M::mem_pestat] analyzing insert size distribution for orientation RF...
[2016-04-14T18:37Z] [M::mem_pestat] (25, 50, 75) percentile: (143, 194, 960)
[2016-04-14T18:37Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 2594)
[2016-04-14T18:37Z] [M::mem_pestat] mean and std.dev: (523.40, 450.04)
[2016-04-14T18:37Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 3411)
[2016-04-14T18:37Z] [M::mem_pestat] skip orientation RR as there are not enough pairs
[2016-04-14T18:37Z] [M::mem_pestat] skip orientation RF
[2016-04-14T18:37Z] [M::mem_pestat] skip orientation FF as there are not enough pairs
[2016-04-14T18:37Z] [M::mem_pestat] analyzing insert size distribution for orientation FR...
[2016-04-14T18:37Z] [M::mem_pestat] (25, 50, 75) percentile: (143, 181, 225)
[2016-04-14T18:37Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 389)
[2016-04-14T18:37Z] [M::mem_pestat] mean and std.dev: (186.66, 59.31)
[2016-04-14T18:37Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 471)
[2016-04-14T18:37Z] [M::mem_pestat] skip orientation RF as there are not enough pairs
[2016-04-14T18:37Z] [M::mem_pestat] skip orientation RR as there are not enough pairs
[2016-04-14T18:37Z] [M::mem_pestat] skip orientation FF as there are not enough pairs
[2016-04-14T18:37Z] [M::mem_pestat] analyzing insert size distribution for orientation FR...
[2016-04-14T18:37Z] [M::mem_pestat] (25, 50, 75) percentile: (143, 181, 225)
[2016-04-14T18:37Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 389)
[2016-04-14T18:37Z] [M::mem_pestat] mean and std.dev: (186.90, 59.29)
[2016-04-14T18:37Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 471)
[2016-04-14T18:37Z] [M::mem_pestat] skip orientation RF as there are not enough pairs
[2016-04-14T18:37Z] [M::mem_pestat] skip orientation RR as there are not enough pairs
[2016-04-14T18:37Z] [M::mem_pestat] skip orientation FF as there are not enough pairs
[2016-04-14T18:37Z] [M::mem_pestat] analyzing insert size distribution for orientation FR...
[2016-04-14T18:37Z] [M::mem_pestat] (25, 50, 75) percentile: (146, 184, 229)
[2016-04-14T18:37Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 395)
[2016-04-14T18:37Z] [M::mem_pestat] mean and std.dev: (190.08, 60.37)
[2016-04-14T18:37Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 478)
[2016-04-14T18:37Z] [M::mem_pestat] skip orientation RF as there are not enough pairs
[2016-04-14T18:37Z] [M::mem_pestat] skip orientation RR as there are not enough pairs
[2016-04-14T18:38Z] [M::mem_pestat] skip orientation FF as there are not enough pairs
[2016-04-14T18:38Z] [M::mem_pestat] analyzing insert size distribution for orientation FR...
[2016-04-14T18:38Z] [M::mem_pestat] (25, 50, 75) percentile: (145, 184, 229)
[2016-04-14T18:38Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 397)
[2016-04-14T18:38Z] [M::mem_pestat] mean and std.dev: (189.77, 60.40)
[2016-04-14T18:38Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 481)
[2016-04-14T18:38Z] [M::mem_pestat] skip orientation RF as there are not enough pairs
[2016-04-14T18:38Z] [M::mem_pestat] skip orientation RR as there are not enough pairs
[2016-04-14T18:38Z] [M::mem_pestat] skip orientation FF as there are not enough pairs
[2016-04-14T18:38Z] [M::mem_pestat] analyzing insert size distribution for orientation FR...
[2016-04-14T18:38Z] [M::mem_pestat] (25, 50, 75) percentile: (145, 183, 228)
[2016-04-14T18:38Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 394)
[2016-04-14T18:38Z] [M::mem_pestat] mean and std.dev: (189.02, 60.22)
[2016-04-14T18:38Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 477)
[2016-04-14T18:38Z] [M::mem_pestat] skip orientation RF as there are not enough pairs
[2016-04-14T18:38Z] [M::mem_pestat] skip orientation RR as there are not enough pairs
[2016-04-14T18:38Z] [M::mem_pestat] skip orientation FF as there are not enough pairs
[2016-04-14T18:38Z] [M::mem_pestat] analyzing insert size distribution for orientation FR...
[2016-04-14T18:38Z] [M::mem_pestat] (25, 50, 75) percentile: (144, 182, 226)
[2016-04-14T18:38Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 390)
[2016-04-14T18:38Z] [M::mem_pestat] mean and std.dev: (187.87, 59.78)
[2016-04-14T18:38Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 472)
[2016-04-14T18:38Z] [M::mem_pestat] skip orientation RF as there are not enough pairs
[2016-04-14T18:38Z] [M::mem_pestat] skip orientation RR as there are not enough pairs
[2016-04-14T18:38Z] [M::mem_pestat] skip orientation FF as there are not enough pairs
[2016-04-14T18:38Z] [M::mem_pestat] analyzing insert size distribution for orientation FR...
[2016-04-14T18:38Z] [M::mem_pestat] (25, 50, 75) percentile: (143, 181, 225)
[2016-04-14T18:38Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 389)
[2016-04-14T18:38Z] [M::mem_pestat] mean and std.dev: (187.14, 59.45)
[2016-04-14T18:38Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 471)
[2016-04-14T18:38Z] [M::mem_pestat] skip orientation RF as there are not enough pairs
[2016-04-14T18:38Z] [M::mem_pestat] skip orientation RR as there are not enough pairs
[2016-04-14T18:39Z] [M::mem_pestat] skip orientation FF as there are not enough pairs
[2016-04-14T18:39Z] [M::mem_pestat] analyzing insert size distribution for orientation FR...
[2016-04-14T18:39Z] [M::mem_pestat] (25, 50, 75) percentile: (145, 183, 228)
[2016-04-14T18:39Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 394)
[2016-04-14T18:39Z] [M::mem_pestat] mean and std.dev: (189.21, 60.07)
[2016-04-14T18:39Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 477)
[2016-04-14T18:39Z] [M::mem_pestat] skip orientation RF as there are not enough pairs
[2016-04-14T18:39Z] [M::mem_pestat] skip orientation RR as there are not enough pairs
[2016-04-14T18:39Z] [M::mem_pestat] skip orientation FF as there are not enough pairs
[2016-04-14T18:39Z] [M::mem_pestat] analyzing insert size distribution for orientation FR...
[2016-04-14T18:39Z] [M::mem_pestat] (25, 50, 75) percentile: (146, 184, 229)
[2016-04-14T18:39Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 395)
[2016-04-14T18:39Z] [M::mem_pestat] mean and std.dev: (190.08, 60.42)
[2016-04-14T18:39Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 478)
[2016-04-14T18:39Z] [M::mem_pestat] skip orientation RF as there are not enough pairs
[2016-04-14T18:39Z] [M::mem_pestat] skip orientation RR as there are not enough pairs
[2016-04-14T18:39Z] [M::mem_pestat] skip orientation FF as there are not enough pairs
[2016-04-14T18:39Z] [M::mem_pestat] analyzing insert size distribution for orientation FR...
[2016-04-14T18:39Z] [M::mem_pestat] (25, 50, 75) percentile: (145, 183, 228)
[2016-04-14T18:39Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 394)
[2016-04-14T18:39Z] [M::mem_pestat] mean and std.dev: (189.28, 60.12)
[2016-04-14T18:39Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 477)
[2016-04-14T18:39Z] [M::mem_pestat] skip orientation RF as there are not enough pairs
[2016-04-14T18:39Z] [M::mem_pestat] skip orientation RR as there are not enough pairs
[2016-04-14T18:39Z] [M::mem_pestat] skip orientation FF as there are not enough pairs
[2016-04-14T18:39Z] [M::mem_pestat] analyzing insert size distribution for orientation FR...
[2016-04-14T18:39Z] [M::mem_pestat] (25, 50, 75) percentile: (144, 183, 227)
[2016-04-14T18:39Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 393)
[2016-04-14T18:39Z] [M::mem_pestat] mean and std.dev: (188.59, 59.98)
[2016-04-14T18:39Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 476)
[2016-04-14T18:39Z] [M::mem_pestat] skip orientation RF as there are not enough pairs
[2016-04-14T18:39Z] [M::mem_pestat] skip orientation RR as there are not enough pairs
[2016-04-14T18:40Z] [M::mem_pestat] skip orientation FF as there are not enough pairs
[2016-04-14T18:40Z] [M::mem_pestat] analyzing insert size distribution for orientation FR...
[2016-04-14T18:40Z] [M::mem_pestat] (25, 50, 75) percentile: (143, 181, 225)
[2016-04-14T18:40Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 389)
[2016-04-14T18:40Z] [M::mem_pestat] mean and std.dev: (187.23, 59.48)
[2016-04-14T18:40Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 471)
[2016-04-14T18:40Z] [M::mem_pestat] skip orientation RF as there are not enough pairs
[2016-04-14T18:40Z] [M::mem_pestat] skip orientation RR as there are not enough pairs
[2016-04-14T18:40Z] [M::mem_pestat] skip orientation FF as there are not enough pairs
[2016-04-14T18:40Z] [M::mem_pestat] analyzing insert size distribution for orientation FR...
[2016-04-14T18:40Z] [M::mem_pestat] (25, 50, 75) percentile: (145, 183, 228)
[2016-04-14T18:40Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 394)
[2016-04-14T18:40Z] [M::mem_pestat] mean and std.dev: (189.33, 60.28)
[2016-04-14T18:40Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 477)
[2016-04-14T18:40Z] [M::mem_pestat] skip orientation RF as there are not enough pairs
[2016-04-14T18:40Z] [M::mem_pestat] skip orientation RR as there are not enough pairs
[2016-04-14T18:40Z] [M::mem_pestat] skip orientation FF as there are not enough pairs
[2016-04-14T18:40Z] [M::mem_pestat] analyzing insert size distribution for orientation FR...
[2016-04-14T18:40Z] [M::mem_pestat] (25, 50, 75) percentile: (145, 183, 228)
[2016-04-14T18:40Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 394)
[2016-04-14T18:40Z] [M::mem_pestat] mean and std.dev: (189.00, 60.11)
[2016-04-14T18:40Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 477)
[2016-04-14T18:40Z] [M::mem_pestat] skip orientation RF as there are not enough pairs
[2016-04-14T18:40Z] [M::mem_pestat] skip orientation RR as there are not enough pairs
[2016-04-14T18:40Z] [M::mem_pestat] skip orientation FF as there are not enough pairs
[2016-04-14T18:40Z] [M::mem_pestat] analyzing insert size distribution for orientation FR...
[2016-04-14T18:40Z] [M::mem_pestat] (25, 50, 75) percentile: (144, 182, 227)
[2016-04-14T18:40Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 393)
[2016-04-14T18:40Z] [M::mem_pestat] mean and std.dev: (188.20, 59.88)
[2016-04-14T18:40Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 476)
[2016-04-14T18:40Z] [M::mem_pestat] skip orientation RF as there are not enough pairs
[2016-04-14T18:40Z] [M::mem_pestat] skip orientation RR as there are not enough pairs
[2016-04-14T18:41Z] [M::mem_pestat] skip orientation FF as there are not enough pairs
[2016-04-14T18:41Z] [M::mem_pestat] analyzing insert size distribution for orientation FR...
[2016-04-14T18:41Z] [M::mem_pestat] (25, 50, 75) percentile: (143, 181, 225)
[2016-04-14T18:41Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 389)
[2016-04-14T18:41Z] [M::mem_pestat] mean and std.dev: (186.93, 59.36)
[2016-04-14T18:41Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 471)
[2016-04-14T18:41Z] [M::mem_pestat] analyzing insert size distribution for orientation RF...
[2016-04-14T18:41Z] [M::mem_pestat] (25, 50, 75) percentile: (221, 907, 951)
[2016-04-14T18:41Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 2411)
[2016-04-14T18:41Z] [M::mem_pestat] mean and std.dev: (596.00, 388.47)
[2016-04-14T18:41Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 3141)
[2016-04-14T18:41Z] [M::mem_pestat] skip orientation RR as there are not enough pairs
[2016-04-14T18:41Z] [M::mem_pestat] skip orientation RF
[2016-04-14T18:41Z] [M::mem_pestat] skip orientation FF as there are not enough pairs
[2016-04-14T18:41Z] [M::mem_pestat] analyzing insert size distribution for orientation FR...
[2016-04-14T18:41Z] [M::mem_pestat] (25, 50, 75) percentile: (143, 181, 225)
[2016-04-14T18:41Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 389)
[2016-04-14T18:41Z] [M::mem_pestat] mean and std.dev: (186.98, 59.21)
[2016-04-14T18:41Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 471)
[2016-04-14T18:41Z] [M::mem_pestat] skip orientation RF as there are not enough pairs
[2016-04-14T18:41Z] [M::mem_pestat] skip orientation RR as there are not enough pairs
[2016-04-14T18:41Z] [M::mem_pestat] skip orientation FF as there are not enough pairs
[2016-04-14T18:41Z] [M::mem_pestat] analyzing insert size distribution for orientation FR...
[2016-04-14T18:41Z] [M::mem_pestat] (25, 50, 75) percentile: (146, 185, 229)
[2016-04-14T18:41Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 395)
[2016-04-14T18:41Z] [M::mem_pestat] mean and std.dev: (190.48, 60.06)
[2016-04-14T18:41Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 478)
[2016-04-14T18:41Z] [M::mem_pestat] skip orientation RF as there are not enough pairs
[2016-04-14T18:41Z] [M::mem_pestat] skip orientation RR as there are not enough pairs
[2016-04-14T18:41Z] [main] Version: 0.7.13-r1126
[2016-04-14T18:41Z] [main] CMD: /mnt/speed/qc/sequencing/bcbio/anaconda/bin/bwa mem -c 250 -M -t 16 -R @RG\tID:R14-18102_kapa-NGv3-PE100-NGv3\tPL:illumina\tPU:R14-18102_20HHFLHB_HHFLHBCXX\tSM:R14-18102_kapa-NGv3-PE100-NGv3 -v 1 /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/bwa/GRCh37.fa /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align_prep/Sample_R14-18102_R1.fastq.gz /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align_prep/Sample_R14-18102_R2.fastq.gz
[2016-04-14T18:41Z] [main] Real time: 685.806 sec; CPU: 8926.212 sec
[2016-04-14T18:41Z] samblaster: Output 102181 discordant read pairs to /dev/fd/62
[2016-04-14T18:41Z] samblaster: Output 73114 split reads to /dev/fd/63
[2016-04-14T18:41Z] samblaster: Marked 2572672 of 32901894 (7.82%) read ids as duplicates using 641948k memory in 1M14S(73.786S) CPU seconds and 11M26S(686S) wall time.
[2016-04-14T18:43Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-sr.bam
[2016-04-14T18:43Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-disc.bam
[2016-04-14T18:43Z] Aligning lane R14-18105_20HHFLHB_HHFLHBCXX with bwa aligner
[2016-04-14T18:43Z] bwa mem alignment from fastq: R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-14T18:43Z] samblaster: Version 0.1.22
[2016-04-14T18:43Z] samblaster: Inputting from stdin
[2016-04-14T18:43Z] samblaster: Outputting to stdout
[2016-04-14T18:43Z] samblaster: Opening /dev/fd/62 for write.
[2016-04-14T18:43Z] samblaster: Opening /dev/fd/63 for write.
[2016-04-14T18:44Z] [M::mem_pestat] skip orientation FF as there are not enough pairs
[2016-04-14T18:44Z] [M::mem_pestat] analyzing insert size distribution for orientation FR...
[2016-04-14T18:44Z] [M::mem_pestat] (25, 50, 75) percentile: (145, 182, 226)
[2016-04-14T18:44Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 388)
[2016-04-14T18:44Z] [M::mem_pestat] mean and std.dev: (187.78, 58.83)
[2016-04-14T18:44Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 469)
[2016-04-14T18:44Z] [M::mem_pestat] analyzing insert size distribution for orientation RF...
[2016-04-14T18:44Z] [M::mem_pestat] (25, 50, 75) percentile: (170, 875, 919)
[2016-04-14T18:44Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 2417)
[2016-04-14T18:44Z] [M::mem_pestat] mean and std.dev: (552.27, 383.38)
[2016-04-14T18:44Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 3166)
[2016-04-14T18:44Z] [M::mem_pestat] skip orientation RR as there are not enough pairs
[2016-04-14T18:44Z] [M::mem_pestat] skip orientation RF
[2016-04-14T18:44Z] samblaster: Loaded 84 header sequence entries.
[2016-04-14T18:44Z] [M::mem_pestat] skip orientation FF as there are not enough pairs
[2016-04-14T18:44Z] [M::mem_pestat] analyzing insert size distribution for orientation FR...
[2016-04-14T18:44Z] [M::mem_pestat] (25, 50, 75) percentile: (145, 183, 226)
[2016-04-14T18:44Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 388)
[2016-04-14T18:44Z] [M::mem_pestat] mean and std.dev: (188.43, 59.14)
[2016-04-14T18:44Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 469)
[2016-04-14T18:44Z] [M::mem_pestat] analyzing insert size distribution for orientation RF...
[2016-04-14T18:44Z] [M::mem_pestat] (25, 50, 75) percentile: (130, 179, 905)
[2016-04-14T18:44Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 2455)
[2016-04-14T18:44Z] [M::mem_pestat] mean and std.dev: (390.64, 370.07)
[2016-04-14T18:44Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 3230)
[2016-04-14T18:44Z] [M::mem_pestat] skip orientation RR as there are not enough pairs
[2016-04-14T18:44Z] [M::mem_pestat] skip orientation RF
[2016-04-14T18:44Z] [M::mem_pestat] skip orientation FF as there are not enough pairs
[2016-04-14T18:44Z] [M::mem_pestat] analyzing insert size distribution for orientation FR...
[2016-04-14T18:44Z] [M::mem_pestat] (25, 50, 75) percentile: (145, 182, 226)
[2016-04-14T18:44Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 388)
[2016-04-14T18:44Z] [M::mem_pestat] mean and std.dev: (187.86, 58.92)
[2016-04-14T18:44Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 469)
[2016-04-14T18:44Z] [M::mem_pestat] skip orientation RF as there are not enough pairs
[2016-04-14T18:44Z] [M::mem_pestat] skip orientation RR as there are not enough pairs
[2016-04-14T18:44Z] [M::mem_pestat] skip orientation FF as there are not enough pairs
[2016-04-14T18:44Z] [M::mem_pestat] analyzing insert size distribution for orientation FR...
[2016-04-14T18:44Z] [M::mem_pestat] (25, 50, 75) percentile: (144, 181, 225)
[2016-04-14T18:44Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 387)
[2016-04-14T18:44Z] [M::mem_pestat] mean and std.dev: (186.89, 58.72)
[2016-04-14T18:44Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 468)
[2016-04-14T18:44Z] [M::mem_pestat] analyzing insert size distribution for orientation RF...
[2016-04-14T18:44Z] [M::mem_pestat] (25, 50, 75) percentile: (147, 155, 915)
[2016-04-14T18:44Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 2451)
[2016-04-14T18:44Z] [M::mem_pestat] mean and std.dev: (366.91, 373.08)
[2016-04-14T18:44Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 3219)
[2016-04-14T18:44Z] [M::mem_pestat] skip orientation RR as there are not enough pairs
[2016-04-14T18:44Z] [M::mem_pestat] skip orientation RF
[2016-04-14T18:45Z] [M::mem_pestat] skip orientation FF as there are not enough pairs
[2016-04-14T18:45Z] [M::mem_pestat] analyzing insert size distribution for orientation FR...
[2016-04-14T18:45Z] [M::mem_pestat] (25, 50, 75) percentile: (143, 180, 223)
[2016-04-14T18:45Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 383)
[2016-04-14T18:45Z] [M::mem_pestat] mean and std.dev: (185.49, 58.30)
[2016-04-14T18:45Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 463)
[2016-04-14T18:45Z] [M::mem_pestat] skip orientation RF as there are not enough pairs
[2016-04-14T18:45Z] [M::mem_pestat] skip orientation RR as there are not enough pairs
[2016-04-14T18:45Z] [M::mem_pestat] skip orientation FF as there are not enough pairs
[2016-04-14T18:45Z] [M::mem_pestat] analyzing insert size distribution for orientation FR...
[2016-04-14T18:45Z] [M::mem_pestat] (25, 50, 75) percentile: (145, 182, 226)
[2016-04-14T18:45Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 388)
[2016-04-14T18:45Z] [M::mem_pestat] mean and std.dev: (188.23, 59.04)
[2016-04-14T18:45Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 469)
[2016-04-14T18:45Z] [M::mem_pestat] skip orientation RF as there are not enough pairs
[2016-04-14T18:45Z] [M::mem_pestat] skip orientation RR as there are not enough pairs
[2016-04-14T18:45Z] [M::mem_pestat] skip orientation FF as there are not enough pairs
[2016-04-14T18:45Z] [M::mem_pestat] analyzing insert size distribution for orientation FR...
[2016-04-14T18:45Z] [M::mem_pestat] (25, 50, 75) percentile: (144, 181, 225)
[2016-04-14T18:45Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 387)
[2016-04-14T18:45Z] [M::mem_pestat] mean and std.dev: (187.27, 58.85)
[2016-04-14T18:45Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 468)
[2016-04-14T18:45Z] [M::mem_pestat] analyzing insert size distribution for orientation RF...
[2016-04-14T18:45Z] [M::mem_pestat] (25, 50, 75) percentile: (22, 173, 808)
[2016-04-14T18:45Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 2380)
[2016-04-14T18:45Z] [M::mem_pestat] mean and std.dev: (255.20, 317.55)
[2016-04-14T18:45Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 3166)
[2016-04-14T18:45Z] [M::mem_pestat] skip orientation RR as there are not enough pairs
[2016-04-14T18:45Z] [M::mem_pestat] skip orientation RF
[2016-04-14T18:45Z] [M::mem_pestat] skip orientation FF as there are not enough pairs
[2016-04-14T18:45Z] [M::mem_pestat] analyzing insert size distribution for orientation FR...
[2016-04-14T18:45Z] [M::mem_pestat] (25, 50, 75) percentile: (143, 181, 224)
[2016-04-14T18:45Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 386)
[2016-04-14T18:45Z] [M::mem_pestat] mean and std.dev: (186.71, 58.75)
[2016-04-14T18:45Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 467)
[2016-04-14T18:45Z] [M::mem_pestat] analyzing insert size distribution for orientation RF...
[2016-04-14T18:45Z] [M::mem_pestat] (25, 50, 75) percentile: (118, 134, 921)
[2016-04-14T18:45Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 2527)
[2016-04-14T18:45Z] [M::mem_pestat] mean and std.dev: (366.20, 426.52)
[2016-04-14T18:45Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 3330)
[2016-04-14T18:45Z] [M::mem_pestat] skip orientation RR as there are not enough pairs
[2016-04-14T18:45Z] [M::mem_pestat] skip orientation RF
[2016-04-14T18:46Z] [M::mem_pestat] skip orientation FF as there are not enough pairs
[2016-04-14T18:46Z] [M::mem_pestat] analyzing insert size distribution for orientation FR...
[2016-04-14T18:46Z] [M::mem_pestat] (25, 50, 75) percentile: (142, 179, 223)
[2016-04-14T18:46Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 385)
[2016-04-14T18:46Z] [M::mem_pestat] mean and std.dev: (185.24, 58.28)
[2016-04-14T18:46Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 466)
[2016-04-14T18:46Z] [M::mem_pestat] analyzing insert size distribution for orientation RF...
[2016-04-14T18:46Z] [M::mem_pestat] (25, 50, 75) percentile: (166, 875, 957)
[2016-04-14T18:46Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 2539)
[2016-04-14T18:46Z] [M::mem_pestat] mean and std.dev: (648.33, 397.50)
[2016-04-14T18:46Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 3330)
[2016-04-14T18:46Z] [M::mem_pestat] skip orientation RR as there are not enough pairs
[2016-04-14T18:46Z] [M::mem_pestat] skip orientation RF
[2016-04-14T18:46Z] [M::mem_pestat] skip orientation FF as there are not enough pairs
[2016-04-14T18:46Z] [M::mem_pestat] analyzing insert size distribution for orientation FR...
[2016-04-14T18:46Z] [M::mem_pestat] (25, 50, 75) percentile: (143, 180, 223)
[2016-04-14T18:46Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 383)
[2016-04-14T18:46Z] [M::mem_pestat] mean and std.dev: (185.41, 58.09)
[2016-04-14T18:46Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 463)
[2016-04-14T18:46Z] [M::mem_pestat] skip orientation RF as there are not enough pairs
[2016-04-14T18:46Z] [M::mem_pestat] skip orientation RR as there are not enough pairs
[2016-04-14T18:46Z] [M::mem_pestat] skip orientation FF as there are not enough pairs
[2016-04-14T18:46Z] [M::mem_pestat] analyzing insert size distribution for orientation FR...
[2016-04-14T18:46Z] [M::mem_pestat] (25, 50, 75) percentile: (144, 182, 225)
[2016-04-14T18:46Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 387)
[2016-04-14T18:46Z] [M::mem_pestat] mean and std.dev: (187.51, 58.75)
[2016-04-14T18:46Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 468)
[2016-04-14T18:46Z] [M::mem_pestat] analyzing insert size distribution for orientation RF...
[2016-04-14T18:46Z] [M::mem_pestat] (25, 50, 75) percentile: (86, 146, 905)
[2016-04-14T18:46Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 2543)
[2016-04-14T18:46Z] [M::mem_pestat] mean and std.dev: (336.58, 566.01)
[2016-04-14T18:46Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 3362)
[2016-04-14T18:46Z] [M::mem_pestat] skip orientation RR as there are not enough pairs
[2016-04-14T18:46Z] [M::mem_pestat] skip orientation RF
[2016-04-14T18:46Z] [M::mem_pestat] skip orientation FF as there are not enough pairs
[2016-04-14T18:46Z] [M::mem_pestat] analyzing insert size distribution for orientation FR...
[2016-04-14T18:46Z] [M::mem_pestat] (25, 50, 75) percentile: (145, 183, 227)
[2016-04-14T18:46Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 391)
[2016-04-14T18:46Z] [M::mem_pestat] mean and std.dev: (188.65, 59.38)
[2016-04-14T18:46Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 473)
[2016-04-14T18:46Z] [M::mem_pestat] skip orientation RF as there are not enough pairs
[2016-04-14T18:46Z] [M::mem_pestat] skip orientation RR as there are not enough pairs
[2016-04-14T18:47Z] [M::mem_pestat] skip orientation FF as there are not enough pairs
[2016-04-14T18:47Z] [M::mem_pestat] analyzing insert size distribution for orientation FR...
[2016-04-14T18:47Z] [M::mem_pestat] (25, 50, 75) percentile: (144, 182, 226)
[2016-04-14T18:47Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 390)
[2016-04-14T18:47Z] [M::mem_pestat] mean and std.dev: (187.75, 59.14)
[2016-04-14T18:47Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 472)
[2016-04-14T18:47Z] [M::mem_pestat] analyzing insert size distribution for orientation RF...
[2016-04-14T18:47Z] [M::mem_pestat] (25, 50, 75) percentile: (146, 209, 844)
[2016-04-14T18:47Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 2240)
[2016-04-14T18:47Z] [M::mem_pestat] mean and std.dev: (366.67, 308.99)
[2016-04-14T18:47Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 2938)
[2016-04-14T18:47Z] [M::mem_pestat] skip orientation RR as there are not enough pairs
[2016-04-14T18:47Z] [M::mem_pestat] skip orientation RF
[2016-04-14T18:47Z] [M::mem_pestat] skip orientation FF as there are not enough pairs
[2016-04-14T18:47Z] [M::mem_pestat] analyzing insert size distribution for orientation FR...
[2016-04-14T18:47Z] [M::mem_pestat] (25, 50, 75) percentile: (144, 181, 225)
[2016-04-14T18:47Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 387)
[2016-04-14T18:47Z] [M::mem_pestat] mean and std.dev: (186.98, 58.74)
[2016-04-14T18:47Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 468)
[2016-04-14T18:47Z] [M::mem_pestat] skip orientation RF as there are not enough pairs
[2016-04-14T18:47Z] [M::mem_pestat] skip orientation RR as there are not enough pairs
[2016-04-14T18:47Z] [M::mem_pestat] skip orientation FF as there are not enough pairs
[2016-04-14T18:47Z] [M::mem_pestat] analyzing insert size distribution for orientation FR...
[2016-04-14T18:47Z] [M::mem_pestat] (25, 50, 75) percentile: (143, 180, 223)
[2016-04-14T18:47Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 383)
[2016-04-14T18:47Z] [M::mem_pestat] mean and std.dev: (185.72, 58.36)
[2016-04-14T18:47Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 463)
[2016-04-14T18:47Z] [M::mem_pestat] skip orientation RF as there are not enough pairs
[2016-04-14T18:47Z] [M::mem_pestat] skip orientation RR as there are not enough pairs
[2016-04-14T18:47Z] [M::mem_pestat] skip orientation FF as there are not enough pairs
[2016-04-14T18:47Z] [M::mem_pestat] analyzing insert size distribution for orientation FR...
[2016-04-14T18:47Z] [M::mem_pestat] (25, 50, 75) percentile: (143, 180, 223)
[2016-04-14T18:47Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 383)
[2016-04-14T18:47Z] [M::mem_pestat] mean and std.dev: (185.39, 58.13)
[2016-04-14T18:47Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 463)
[2016-04-14T18:47Z] [M::mem_pestat] skip orientation RF as there are not enough pairs
[2016-04-14T18:47Z] [M::mem_pestat] skip orientation RR as there are not enough pairs
[2016-04-14T18:48Z] [M::mem_pestat] skip orientation FF as there are not enough pairs
[2016-04-14T18:48Z] [M::mem_pestat] analyzing insert size distribution for orientation FR...
[2016-04-14T18:48Z] [M::mem_pestat] (25, 50, 75) percentile: (144, 182, 225)
[2016-04-14T18:48Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 387)
[2016-04-14T18:48Z] [M::mem_pestat] mean and std.dev: (187.61, 58.80)
[2016-04-14T18:48Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 468)
[2016-04-14T18:48Z] [M::mem_pestat] skip orientation RF as there are not enough pairs
[2016-04-14T18:48Z] [M::mem_pestat] skip orientation RR as there are not enough pairs
[2016-04-14T18:48Z] [M::mem_pestat] skip orientation FF as there are not enough pairs
[2016-04-14T18:48Z] [M::mem_pestat] analyzing insert size distribution for orientation FR...
[2016-04-14T18:48Z] [M::mem_pestat] (25, 50, 75) percentile: (144, 182, 226)
[2016-04-14T18:48Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 390)
[2016-04-14T18:48Z] [M::mem_pestat] mean and std.dev: (187.90, 59.24)
[2016-04-14T18:48Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 472)
[2016-04-14T18:48Z] [M::mem_pestat] skip orientation RF as there are not enough pairs
[2016-04-14T18:48Z] [M::mem_pestat] skip orientation RR as there are not enough pairs
[2016-04-14T18:48Z] [M::mem_pestat] skip orientation FF as there are not enough pairs
[2016-04-14T18:48Z] [M::mem_pestat] analyzing insert size distribution for orientation FR...
[2016-04-14T18:48Z] [M::mem_pestat] (25, 50, 75) percentile: (144, 181, 225)
[2016-04-14T18:48Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 387)
[2016-04-14T18:48Z] [M::mem_pestat] mean and std.dev: (187.01, 58.84)
[2016-04-14T18:48Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 468)
[2016-04-14T18:48Z] [M::mem_pestat] skip orientation RF as there are not enough pairs
[2016-04-14T18:48Z] [M::mem_pestat] skip orientation RR as there are not enough pairs
[2016-04-14T18:49Z] [M::mem_pestat] skip orientation FF as there are not enough pairs
[2016-04-14T18:49Z] [M::mem_pestat] analyzing insert size distribution for orientation FR...
[2016-04-14T18:49Z] [M::mem_pestat] (25, 50, 75) percentile: (143, 180, 224)
[2016-04-14T18:49Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 386)
[2016-04-14T18:49Z] [M::mem_pestat] mean and std.dev: (186.27, 58.57)
[2016-04-14T18:49Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 467)
[2016-04-14T18:49Z] [M::mem_pestat] skip orientation RF as there are not enough pairs
[2016-04-14T18:49Z] [M::mem_pestat] skip orientation RR as there are not enough pairs
[2016-04-14T18:49Z] [M::mem_pestat] skip orientation FF as there are not enough pairs
[2016-04-14T18:49Z] [M::mem_pestat] analyzing insert size distribution for orientation FR...
[2016-04-14T18:49Z] [M::mem_pestat] (25, 50, 75) percentile: (142, 179, 222)
[2016-04-14T18:49Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 382)
[2016-04-14T18:49Z] [M::mem_pestat] mean and std.dev: (184.98, 58.12)
[2016-04-14T18:49Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 462)
[2016-04-14T18:49Z] [M::mem_pestat] analyzing insert size distribution for orientation RF...
[2016-04-14T18:49Z] [M::mem_pestat] (25, 50, 75) percentile: (328, 934, 2627)
[2016-04-14T18:49Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 7225)
[2016-04-14T18:49Z] [M::mem_pestat] mean and std.dev: (1366.42, 1552.68)
[2016-04-14T18:49Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 9524)
[2016-04-14T18:49Z] [M::mem_pestat] skip orientation RR as there are not enough pairs
[2016-04-14T18:49Z] [M::mem_pestat] skip orientation RF
[2016-04-14T18:49Z] [M::mem_pestat] skip orientation FF as there are not enough pairs
[2016-04-14T18:49Z] [M::mem_pestat] analyzing insert size distribution for orientation FR...
[2016-04-14T18:49Z] [M::mem_pestat] (25, 50, 75) percentile: (143, 180, 224)
[2016-04-14T18:49Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 386)
[2016-04-14T18:49Z] [M::mem_pestat] mean and std.dev: (186.10, 58.49)
[2016-04-14T18:49Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 467)
[2016-04-14T18:49Z] [M::mem_pestat] skip orientation RF as there are not enough pairs
[2016-04-14T18:49Z] [M::mem_pestat] skip orientation RR as there are not enough pairs
[2016-04-14T18:49Z] [M::mem_pestat] skip orientation FF as there are not enough pairs
[2016-04-14T18:49Z] [M::mem_pestat] analyzing insert size distribution for orientation FR...
[2016-04-14T18:49Z] [M::mem_pestat] (25, 50, 75) percentile: (145, 182, 226)
[2016-04-14T18:49Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 388)
[2016-04-14T18:49Z] [M::mem_pestat] mean and std.dev: (188.24, 59.22)
[2016-04-14T18:49Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 469)
[2016-04-14T18:49Z] [M::mem_pestat] analyzing insert size distribution for orientation RF...
[2016-04-14T18:49Z] [M::mem_pestat] (25, 50, 75) percentile: (173, 1011, 2683)
[2016-04-14T18:49Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 7703)
[2016-04-14T18:49Z] [M::mem_pestat] mean and std.dev: (1322.67, 1482.71)
[2016-04-14T18:49Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 10213)
[2016-04-14T18:49Z] [M::mem_pestat] skip orientation RR as there are not enough pairs
[2016-04-14T18:49Z] [M::mem_pestat] skip orientation RF
[2016-04-14T18:50Z] [M::mem_pestat] skip orientation FF as there are not enough pairs
[2016-04-14T18:50Z] [M::mem_pestat] analyzing insert size distribution for orientation FR...
[2016-04-14T18:50Z] [M::mem_pestat] (25, 50, 75) percentile: (144, 182, 225)
[2016-04-14T18:50Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 387)
[2016-04-14T18:50Z] [M::mem_pestat] mean and std.dev: (187.55, 59.02)
[2016-04-14T18:50Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 468)
[2016-04-14T18:50Z] [M::mem_pestat] analyzing insert size distribution for orientation RF...
[2016-04-14T18:50Z] [M::mem_pestat] (25, 50, 75) percentile: (122, 180, 829)
[2016-04-14T18:50Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 2243)
[2016-04-14T18:50Z] [M::mem_pestat] mean and std.dev: (362.75, 346.60)
[2016-04-14T18:50Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 2950)
[2016-04-14T18:50Z] [M::mem_pestat] skip orientation RR as there are not enough pairs
[2016-04-14T18:50Z] [M::mem_pestat] skip orientation RF
[2016-04-14T18:50Z] [M::mem_pestat] skip orientation FF as there are not enough pairs
[2016-04-14T18:50Z] [M::mem_pestat] analyzing insert size distribution for orientation FR...
[2016-04-14T18:50Z] [M::mem_pestat] (25, 50, 75) percentile: (144, 181, 224)
[2016-04-14T18:50Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 384)
[2016-04-14T18:50Z] [M::mem_pestat] mean and std.dev: (186.74, 58.69)
[2016-04-14T18:50Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 464)
[2016-04-14T18:50Z] [M::mem_pestat] analyzing insert size distribution for orientation RF...
[2016-04-14T18:50Z] [M::mem_pestat] (25, 50, 75) percentile: (168, 200, 963)
[2016-04-14T18:50Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 2553)
[2016-04-14T18:50Z] [M::mem_pestat] mean and std.dev: (276.22, 284.15)
[2016-04-14T18:50Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 3348)
[2016-04-14T18:50Z] [M::mem_pestat] skip orientation RR as there are not enough pairs
[2016-04-14T18:50Z] [M::mem_pestat] skip orientation RF
[2016-04-14T18:50Z] [M::mem_pestat] skip orientation FF as there are not enough pairs
[2016-04-14T18:50Z] [M::mem_pestat] analyzing insert size distribution for orientation FR...
[2016-04-14T18:50Z] [M::mem_pestat] (25, 50, 75) percentile: (143, 180, 223)
[2016-04-14T18:50Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 383)
[2016-04-14T18:50Z] [M::mem_pestat] mean and std.dev: (185.53, 58.42)
[2016-04-14T18:50Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 463)
[2016-04-14T18:50Z] [M::mem_pestat] analyzing insert size distribution for orientation RF...
[2016-04-14T18:50Z] [M::mem_pestat] (25, 50, 75) percentile: (340, 799, 973)
[2016-04-14T18:50Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 2239)
[2016-04-14T18:50Z] [M::mem_pestat] mean and std.dev: (632.46, 370.14)
[2016-04-14T18:50Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 2872)
[2016-04-14T18:50Z] [M::mem_pestat] skip orientation RR as there are not enough pairs
[2016-04-14T18:50Z] [M::mem_pestat] skip orientation RF
[2016-04-14T18:50Z] [M::mem_pestat] skip orientation FF as there are not enough pairs
[2016-04-14T18:50Z] [M::mem_pestat] analyzing insert size distribution for orientation FR...
[2016-04-14T18:50Z] [M::mem_pestat] (25, 50, 75) percentile: (144, 181, 225)
[2016-04-14T18:50Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 387)
[2016-04-14T18:50Z] [M::mem_pestat] mean and std.dev: (187.17, 58.82)
[2016-04-14T18:50Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 468)
[2016-04-14T18:50Z] [M::mem_pestat] skip orientation RF as there are not enough pairs
[2016-04-14T18:50Z] [M::mem_pestat] skip orientation RR as there are not enough pairs
[2016-04-14T18:51Z] [M::mem_pestat] skip orientation FF as there are not enough pairs
[2016-04-14T18:51Z] [M::mem_pestat] analyzing insert size distribution for orientation FR...
[2016-04-14T18:51Z] [M::mem_pestat] (25, 50, 75) percentile: (145, 182, 226)
[2016-04-14T18:51Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 388)
[2016-04-14T18:51Z] [M::mem_pestat] mean and std.dev: (187.93, 58.92)
[2016-04-14T18:51Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 469)
[2016-04-14T18:51Z] [M::mem_pestat] skip orientation RF as there are not enough pairs
[2016-04-14T18:51Z] [M::mem_pestat] skip orientation RR as there are not enough pairs
[2016-04-14T18:51Z] [M::mem_pestat] skip orientation FF as there are not enough pairs
[2016-04-14T18:51Z] [M::mem_pestat] analyzing insert size distribution for orientation FR...
[2016-04-14T18:51Z] [M::mem_pestat] (25, 50, 75) percentile: (144, 181, 225)
[2016-04-14T18:51Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 387)
[2016-04-14T18:51Z] [M::mem_pestat] mean and std.dev: (187.15, 58.67)
[2016-04-14T18:51Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 468)
[2016-04-14T18:51Z] [M::mem_pestat] skip orientation RF as there are not enough pairs
[2016-04-14T18:51Z] [M::mem_pestat] skip orientation RR as there are not enough pairs
[2016-04-14T18:51Z] [M::mem_pestat] skip orientation FF as there are not enough pairs
[2016-04-14T18:51Z] [M::mem_pestat] analyzing insert size distribution for orientation FR...
[2016-04-14T18:51Z] [M::mem_pestat] (25, 50, 75) percentile: (143, 181, 224)
[2016-04-14T18:51Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 386)
[2016-04-14T18:51Z] [M::mem_pestat] mean and std.dev: (186.35, 58.44)
[2016-04-14T18:51Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 467)
[2016-04-14T18:51Z] [M::mem_pestat] skip orientation RF as there are not enough pairs
[2016-04-14T18:51Z] [M::mem_pestat] skip orientation RR as there are not enough pairs
[2016-04-14T18:51Z] [M::mem_pestat] skip orientation FF as there are not enough pairs
[2016-04-14T18:51Z] [M::mem_pestat] analyzing insert size distribution for orientation FR...
[2016-04-14T18:51Z] [M::mem_pestat] (25, 50, 75) percentile: (143, 179, 222)
[2016-04-14T18:51Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 380)
[2016-04-14T18:51Z] [M::mem_pestat] mean and std.dev: (185.13, 57.79)
[2016-04-14T18:51Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 459)
[2016-04-14T18:51Z] [M::mem_pestat] analyzing insert size distribution for orientation RF...
[2016-04-14T18:51Z] [M::mem_pestat] (25, 50, 75) percentile: (122, 208, 878)
[2016-04-14T18:51Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 2390)
[2016-04-14T18:51Z] [M::mem_pestat] mean and std.dev: (419.07, 373.05)
[2016-04-14T18:51Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 3146)
[2016-04-14T18:51Z] [M::mem_pestat] skip orientation RR as there are not enough pairs
[2016-04-14T18:51Z] [M::mem_pestat] skip orientation RF
[2016-04-14T18:52Z] [M::mem_pestat] skip orientation FF as there are not enough pairs
[2016-04-14T18:52Z] [M::mem_pestat] analyzing insert size distribution for orientation FR...
[2016-04-14T18:52Z] [M::mem_pestat] (25, 50, 75) percentile: (144, 182, 225)
[2016-04-14T18:52Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 387)
[2016-04-14T18:52Z] [M::mem_pestat] mean and std.dev: (187.56, 58.77)
[2016-04-14T18:52Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 468)
[2016-04-14T18:52Z] [M::mem_pestat] analyzing insert size distribution for orientation RF...
[2016-04-14T18:52Z] [M::mem_pestat] (25, 50, 75) percentile: (160, 222, 954)
[2016-04-14T18:52Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 2542)
[2016-04-14T18:52Z] [M::mem_pestat] mean and std.dev: (477.40, 385.21)
[2016-04-14T18:52Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 3336)
[2016-04-14T18:52Z] [M::mem_pestat] skip orientation RR as there are not enough pairs
[2016-04-14T18:52Z] [M::mem_pestat] skip orientation RF
[2016-04-14T18:52Z] [M::mem_pestat] skip orientation FF as there are not enough pairs
[2016-04-14T18:52Z] [M::mem_pestat] analyzing insert size distribution for orientation FR...
[2016-04-14T18:52Z] [M::mem_pestat] (25, 50, 75) percentile: (145, 182, 226)
[2016-04-14T18:52Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 388)
[2016-04-14T18:52Z] [M::mem_pestat] mean and std.dev: (187.88, 58.99)
[2016-04-14T18:52Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 469)
[2016-04-14T18:52Z] [M::mem_pestat] skip orientation RF as there are not enough pairs
[2016-04-14T18:52Z] [M::mem_pestat] skip orientation RR as there are not enough pairs
[2016-04-14T18:52Z] [M::mem_pestat] skip orientation FF as there are not enough pairs
[2016-04-14T18:52Z] [M::mem_pestat] analyzing insert size distribution for orientation FR...
[2016-04-14T18:52Z] [M::mem_pestat] (25, 50, 75) percentile: (144, 181, 225)
[2016-04-14T18:52Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 387)
[2016-04-14T18:52Z] [M::mem_pestat] mean and std.dev: (187.11, 58.72)
[2016-04-14T18:52Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 468)
[2016-04-14T18:52Z] [M::mem_pestat] skip orientation RF as there are not enough pairs
[2016-04-14T18:52Z] [M::mem_pestat] skip orientation RR as there are not enough pairs
[2016-04-14T18:52Z] [M::mem_pestat] skip orientation FF as there are not enough pairs
[2016-04-14T18:52Z] [M::mem_pestat] analyzing insert size distribution for orientation FR...
[2016-04-14T18:52Z] [M::mem_pestat] (25, 50, 75) percentile: (143, 180, 223)
[2016-04-14T18:52Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 383)
[2016-04-14T18:52Z] [M::mem_pestat] mean and std.dev: (186.00, 58.33)
[2016-04-14T18:52Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 463)
[2016-04-14T18:52Z] [M::mem_pestat] skip orientation RF as there are not enough pairs
[2016-04-14T18:52Z] [M::mem_pestat] skip orientation RR as there are not enough pairs
[2016-04-14T18:53Z] [M::mem_pestat] skip orientation FF as there are not enough pairs
[2016-04-14T18:53Z] [M::mem_pestat] analyzing insert size distribution for orientation FR...
[2016-04-14T18:53Z] [M::mem_pestat] (25, 50, 75) percentile: (143, 179, 222)
[2016-04-14T18:53Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 380)
[2016-04-14T18:53Z] [M::mem_pestat] mean and std.dev: (184.99, 57.87)
[2016-04-14T18:53Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 459)
[2016-04-14T18:53Z] [M::mem_pestat] analyzing insert size distribution for orientation RF...
[2016-04-14T18:53Z] [M::mem_pestat] (25, 50, 75) percentile: (174, 197, 850)
[2016-04-14T18:53Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 2202)
[2016-04-14T18:53Z] [M::mem_pestat] mean and std.dev: (407.45, 341.01)
[2016-04-14T18:53Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 2878)
[2016-04-14T18:53Z] [M::mem_pestat] skip orientation RR as there are not enough pairs
[2016-04-14T18:53Z] [M::mem_pestat] skip orientation RF
[2016-04-14T18:53Z] [M::mem_pestat] skip orientation FF as there are not enough pairs
[2016-04-14T18:53Z] [M::mem_pestat] analyzing insert size distribution for orientation FR...
[2016-04-14T18:53Z] [M::mem_pestat] (25, 50, 75) percentile: (144, 182, 225)
[2016-04-14T18:53Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 387)
[2016-04-14T18:53Z] [M::mem_pestat] mean and std.dev: (187.57, 58.73)
[2016-04-14T18:53Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 468)
[2016-04-14T18:53Z] [M::mem_pestat] skip orientation RF as there are not enough pairs
[2016-04-14T18:53Z] [M::mem_pestat] skip orientation RR as there are not enough pairs
[2016-04-14T18:53Z] [M::mem_pestat] skip orientation FF as there are not enough pairs
[2016-04-14T18:53Z] [M::mem_pestat] analyzing insert size distribution for orientation FR...
[2016-04-14T18:53Z] [M::mem_pestat] (25, 50, 75) percentile: (144, 181, 225)
[2016-04-14T18:53Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 387)
[2016-04-14T18:53Z] [M::mem_pestat] mean and std.dev: (187.27, 58.79)
[2016-04-14T18:53Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 468)
[2016-04-14T18:53Z] [M::mem_pestat] skip orientation RF as there are not enough pairs
[2016-04-14T18:53Z] [M::mem_pestat] skip orientation RR as there are not enough pairs
[2016-04-14T18:54Z] [M::mem_pestat] skip orientation FF as there are not enough pairs
[2016-04-14T18:54Z] [M::mem_pestat] analyzing insert size distribution for orientation FR...
[2016-04-14T18:54Z] [M::mem_pestat] (25, 50, 75) percentile: (143, 181, 224)
[2016-04-14T18:54Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 386)
[2016-04-14T18:54Z] [M::mem_pestat] mean and std.dev: (186.37, 58.65)
[2016-04-14T18:54Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 467)
[2016-04-14T18:54Z] [M::mem_pestat] skip orientation RF as there are not enough pairs
[2016-04-14T18:54Z] [M::mem_pestat] skip orientation RR as there are not enough pairs
[2016-04-14T18:54Z] [M::mem_pestat] skip orientation FF as there are not enough pairs
[2016-04-14T18:54Z] [M::mem_pestat] analyzing insert size distribution for orientation FR...
[2016-04-14T18:54Z] [M::mem_pestat] (25, 50, 75) percentile: (143, 180, 223)
[2016-04-14T18:54Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 383)
[2016-04-14T18:54Z] [M::mem_pestat] mean and std.dev: (185.34, 58.17)
[2016-04-14T18:54Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 463)
[2016-04-14T18:54Z] [M::mem_pestat] skip orientation RF as there are not enough pairs
[2016-04-14T18:54Z] [M::mem_pestat] skip orientation RR as there are not enough pairs
[2016-04-14T18:54Z] [M::mem_pestat] skip orientation FF as there are not enough pairs
[2016-04-14T18:54Z] [M::mem_pestat] analyzing insert size distribution for orientation FR...
[2016-04-14T18:54Z] [M::mem_pestat] (25, 50, 75) percentile: (142, 179, 221)
[2016-04-14T18:54Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 379)
[2016-04-14T18:54Z] [M::mem_pestat] mean and std.dev: (184.32, 57.79)
[2016-04-14T18:54Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 458)
[2016-04-14T18:54Z] [M::mem_pestat] analyzing insert size distribution for orientation RF...
[2016-04-14T18:54Z] [M::mem_pestat] (25, 50, 75) percentile: (99, 658, 862)
[2016-04-14T18:54Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 2388)
[2016-04-14T18:54Z] [M::mem_pestat] mean and std.dev: (467.42, 363.03)
[2016-04-14T18:54Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 3151)
[2016-04-14T18:54Z] [M::mem_pestat] skip orientation RR as there are not enough pairs
[2016-04-14T18:54Z] [M::mem_pestat] skip orientation RF
[2016-04-14T18:54Z] [M::mem_pestat] skip orientation FF as there are not enough pairs
[2016-04-14T18:54Z] [M::mem_pestat] analyzing insert size distribution for orientation FR...
[2016-04-14T18:54Z] [M::mem_pestat] (25, 50, 75) percentile: (143, 180, 222)
[2016-04-14T18:54Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 380)
[2016-04-14T18:54Z] [M::mem_pestat] mean and std.dev: (185.46, 57.89)
[2016-04-14T18:54Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 459)
[2016-04-14T18:54Z] [M::mem_pestat] skip orientation RF as there are not enough pairs
[2016-04-14T18:54Z] [M::mem_pestat] skip orientation RR as there are not enough pairs
[2016-04-14T18:54Z] [main] Version: 0.7.13-r1126
[2016-04-14T18:54Z] [main] CMD: /mnt/speed/qc/sequencing/bcbio/anaconda/bin/bwa mem -c 250 -M -t 16 -R @RG\tID:R14-18105_kapa-NGv3-PE100-NGv3\tPL:illumina\tPU:R14-18105_20HHFLHB_HHFLHBCXX\tSM:R14-18105_kapa-NGv3-PE100-NGv3 -v 1 /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/bwa/GRCh37.fa /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align_prep/Sample_R14-18105_R1.fastq.gz /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align_prep/Sample_R14-18105_R2.fastq.gz
[2016-04-14T18:54Z] [main] Real time: 689.230 sec; CPU: 8982.038 sec
[2016-04-14T18:54Z] samblaster: Output 98650 discordant read pairs to /dev/fd/62
[2016-04-14T18:54Z] samblaster: Output 76012 split reads to /dev/fd/63
[2016-04-14T18:54Z] samblaster: Marked 2550708 of 33143451 (7.70%) read ids as duplicates using 647072k memory in 1M14S(73.676S) CPU seconds and 11M29S(689S) wall time.
[2016-04-14T18:56Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-sr.bam
[2016-04-14T18:56Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-disc.bam
[2016-04-14T18:56Z] Aligning lane R14-18106_20HHFLHB_HHFLHBCXX with bwa aligner
[2016-04-14T18:56Z] bwa mem alignment from fastq: R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-14T18:56Z] samblaster: Version 0.1.22
[2016-04-14T18:56Z] samblaster: Inputting from stdin
[2016-04-14T18:56Z] samblaster: Outputting to stdout
[2016-04-14T18:56Z] samblaster: Opening /dev/fd/62 for write.
[2016-04-14T18:56Z] samblaster: Opening /dev/fd/63 for write.
[2016-04-14T18:57Z] [M::mem_pestat] skip orientation FF as there are not enough pairs
[2016-04-14T18:57Z] [M::mem_pestat] analyzing insert size distribution for orientation FR...
[2016-04-14T18:57Z] [M::mem_pestat] (25, 50, 75) percentile: (145, 183, 228)
[2016-04-14T18:57Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 394)
[2016-04-14T18:57Z] [M::mem_pestat] mean and std.dev: (189.40, 60.25)
[2016-04-14T18:57Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 477)
[2016-04-14T18:57Z] [M::mem_pestat] skip orientation RF as there are not enough pairs
[2016-04-14T18:57Z] [M::mem_pestat] skip orientation RR as there are not enough pairs
[2016-04-14T18:57Z] samblaster: Loaded 84 header sequence entries.
[2016-04-14T18:57Z] [M::mem_pestat] skip orientation FF as there are not enough pairs
[2016-04-14T18:57Z] [M::mem_pestat] analyzing insert size distribution for orientation FR...
[2016-04-14T18:57Z] [M::mem_pestat] (25, 50, 75) percentile: (144, 183, 227)
[2016-04-14T18:57Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 393)
[2016-04-14T18:57Z] [M::mem_pestat] mean and std.dev: (188.76, 60.05)
[2016-04-14T18:57Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 476)
[2016-04-14T18:57Z] [M::mem_pestat] skip orientation RF as there are not enough pairs
[2016-04-14T18:57Z] [M::mem_pestat] skip orientation RR as there are not enough pairs
[2016-04-14T18:57Z] [M::mem_pestat] skip orientation FF as there are not enough pairs
[2016-04-14T18:57Z] [M::mem_pestat] analyzing insert size distribution for orientation FR...
[2016-04-14T18:57Z] [M::mem_pestat] (25, 50, 75) percentile: (144, 181, 226)
[2016-04-14T18:57Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 390)
[2016-04-14T18:57Z] [M::mem_pestat] mean and std.dev: (187.71, 59.72)
[2016-04-14T18:57Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 472)
[2016-04-14T18:57Z] [M::mem_pestat] skip orientation RF as there are not enough pairs
[2016-04-14T18:57Z] [M::mem_pestat] skip orientation RR as there are not enough pairs
[2016-04-14T18:57Z] [M::mem_pestat] skip orientation FF as there are not enough pairs
[2016-04-14T18:57Z] [M::mem_pestat] analyzing insert size distribution for orientation FR...
[2016-04-14T18:57Z] [M::mem_pestat] (25, 50, 75) percentile: (143, 181, 225)
[2016-04-14T18:57Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 389)
[2016-04-14T18:57Z] [M::mem_pestat] mean and std.dev: (187.02, 59.20)
[2016-04-14T18:57Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 471)
[2016-04-14T18:57Z] [M::mem_pestat] skip orientation RF as there are not enough pairs
[2016-04-14T18:57Z] [M::mem_pestat] skip orientation RR as there are not enough pairs
[2016-04-14T18:58Z] [M::mem_pestat] skip orientation FF as there are not enough pairs
[2016-04-14T18:58Z] [M::mem_pestat] analyzing insert size distribution for orientation FR...
[2016-04-14T18:58Z] [M::mem_pestat] (25, 50, 75) percentile: (145, 184, 228)
[2016-04-14T18:58Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 394)
[2016-04-14T18:58Z] [M::mem_pestat] mean and std.dev: (189.79, 60.20)
[2016-04-14T18:58Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 477)
[2016-04-14T18:58Z] [M::mem_pestat] analyzing insert size distribution for orientation RF...
[2016-04-14T18:58Z] [M::mem_pestat] (25, 50, 75) percentile: (107, 312, 993)
[2016-04-14T18:58Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 2765)
[2016-04-14T18:58Z] [M::mem_pestat] mean and std.dev: (467.08, 418.92)
[2016-04-14T18:58Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 3651)
[2016-04-14T18:58Z] [M::mem_pestat] skip orientation RR as there are not enough pairs
[2016-04-14T18:58Z] [M::mem_pestat] skip orientation RF
[2016-04-14T18:58Z] [M::mem_pestat] skip orientation FF as there are not enough pairs
[2016-04-14T18:58Z] [M::mem_pestat] analyzing insert size distribution for orientation FR...
[2016-04-14T18:58Z] [M::mem_pestat] (25, 50, 75) percentile: (145, 183, 227)
[2016-04-14T18:58Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 391)
[2016-04-14T18:58Z] [M::mem_pestat] mean and std.dev: (188.96, 59.75)
[2016-04-14T18:58Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 473)
[2016-04-14T18:58Z] [M::mem_pestat] skip orientation RF as there are not enough pairs
[2016-04-14T18:58Z] [M::mem_pestat] skip orientation RR as there are not enough pairs
[2016-04-14T18:58Z] [M::mem_pestat] skip orientation FF as there are not enough pairs
[2016-04-14T18:58Z] [M::mem_pestat] analyzing insert size distribution for orientation FR...
[2016-04-14T18:58Z] [M::mem_pestat] (25, 50, 75) percentile: (144, 182, 226)
[2016-04-14T18:58Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 390)
[2016-04-14T18:58Z] [M::mem_pestat] mean and std.dev: (188.17, 59.44)
[2016-04-14T18:58Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 472)
[2016-04-14T18:58Z] [M::mem_pestat] skip orientation RF as there are not enough pairs
[2016-04-14T18:58Z] [M::mem_pestat] skip orientation RR as there are not enough pairs
[2016-04-14T18:59Z] [M::mem_pestat] skip orientation FF as there are not enough pairs
[2016-04-14T18:59Z] [M::mem_pestat] analyzing insert size distribution for orientation FR...
[2016-04-14T18:59Z] [M::mem_pestat] (25, 50, 75) percentile: (144, 181, 225)
[2016-04-14T18:59Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 387)
[2016-04-14T18:59Z] [M::mem_pestat] mean and std.dev: (187.10, 59.08)
[2016-04-14T18:59Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 468)
[2016-04-14T18:59Z] [M::mem_pestat] skip orientation RF as there are not enough pairs
[2016-04-14T18:59Z] [M::mem_pestat] skip orientation RR as there are not enough pairs
[2016-04-14T18:59Z] [M::mem_pestat] skip orientation FF as there are not enough pairs
[2016-04-14T18:59Z] [M::mem_pestat] analyzing insert size distribution for orientation FR...
[2016-04-14T18:59Z] [M::mem_pestat] (25, 50, 75) percentile: (145, 183, 227)
[2016-04-14T18:59Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 391)
[2016-04-14T18:59Z] [M::mem_pestat] mean and std.dev: (188.61, 59.33)
[2016-04-14T18:59Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 473)
[2016-04-14T18:59Z] [M::mem_pestat] skip orientation RF as there are not enough pairs
[2016-04-14T18:59Z] [M::mem_pestat] skip orientation RR as there are not enough pairs
[2016-04-14T18:59Z] [M::mem_pestat] skip orientation FF as there are not enough pairs
[2016-04-14T18:59Z] [M::mem_pestat] analyzing insert size distribution for orientation FR...
[2016-04-14T18:59Z] [M::mem_pestat] (25, 50, 75) percentile: (145, 183, 228)
[2016-04-14T18:59Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 394)
[2016-04-14T18:59Z] [M::mem_pestat] mean and std.dev: (189.64, 60.31)
[2016-04-14T18:59Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 477)
[2016-04-14T18:59Z] [M::mem_pestat] skip orientation RF as there are not enough pairs
[2016-04-14T18:59Z] [M::mem_pestat] skip orientation RR as there are not enough pairs
[2016-04-14T18:59Z] [M::mem_pestat] skip orientation FF as there are not enough pairs
[2016-04-14T18:59Z] [M::mem_pestat] analyzing insert size distribution for orientation FR...
[2016-04-14T18:59Z] [M::mem_pestat] (25, 50, 75) percentile: (144, 183, 227)
[2016-04-14T18:59Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 393)
[2016-04-14T18:59Z] [M::mem_pestat] mean and std.dev: (188.70, 59.94)
[2016-04-14T18:59Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 476)
[2016-04-14T18:59Z] [M::mem_pestat] analyzing insert size distribution for orientation RF...
[2016-04-14T18:59Z] [M::mem_pestat] (25, 50, 75) percentile: (309, 865, 924)
[2016-04-14T18:59Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 2154)
[2016-04-14T18:59Z] [M::mem_pestat] mean and std.dev: (685.90, 319.71)
[2016-04-14T18:59Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 2769)
[2016-04-14T18:59Z] [M::mem_pestat] skip orientation RR as there are not enough pairs
[2016-04-14T18:59Z] [M::mem_pestat] skip orientation RF
[2016-04-14T19:00Z] [M::mem_pestat] skip orientation FF as there are not enough pairs
[2016-04-14T19:00Z] [M::mem_pestat] analyzing insert size distribution for orientation FR...
[2016-04-14T19:00Z] [M::mem_pestat] (25, 50, 75) percentile: (144, 181, 226)
[2016-04-14T19:00Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 390)
[2016-04-14T19:00Z] [M::mem_pestat] mean and std.dev: (187.60, 59.58)
[2016-04-14T19:00Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 472)
[2016-04-14T19:00Z] [M::mem_pestat] skip orientation RF as there are not enough pairs
[2016-04-14T19:00Z] [M::mem_pestat] skip orientation RR as there are not enough pairs
[2016-04-14T19:00Z] [M::mem_pestat] skip orientation FF as there are not enough pairs
[2016-04-14T19:00Z] [M::mem_pestat] analyzing insert size distribution for orientation FR...
[2016-04-14T19:00Z] [M::mem_pestat] (25, 50, 75) percentile: (143, 181, 225)
[2016-04-14T19:00Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 389)
[2016-04-14T19:00Z] [M::mem_pestat] mean and std.dev: (186.69, 59.26)
[2016-04-14T19:00Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 471)
[2016-04-14T19:00Z] [M::mem_pestat] skip orientation RF as there are not enough pairs
[2016-04-14T19:00Z] [M::mem_pestat] skip orientation RR as there are not enough pairs
[2016-04-14T19:00Z] [M::mem_pestat] skip orientation FF as there are not enough pairs
[2016-04-14T19:00Z] [M::mem_pestat] analyzing insert size distribution for orientation FR...
[2016-04-14T19:00Z] [M::mem_pestat] (25, 50, 75) percentile: (144, 182, 227)
[2016-04-14T19:00Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 393)
[2016-04-14T19:00Z] [M::mem_pestat] mean and std.dev: (188.61, 59.83)
[2016-04-14T19:00Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 476)
[2016-04-14T19:00Z] [M::mem_pestat] analyzing insert size distribution for orientation RF...
[2016-04-14T19:00Z] [M::mem_pestat] (25, 50, 75) percentile: (365, 533, 935)
[2016-04-14T19:00Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 2075)
[2016-04-14T19:00Z] [M::mem_pestat] mean and std.dev: (581.00, 339.13)
[2016-04-14T19:00Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 2645)
[2016-04-14T19:00Z] [M::mem_pestat] skip orientation RR as there are not enough pairs
[2016-04-14T19:00Z] [M::mem_pestat] skip orientation RF
[2016-04-14T19:00Z] [M::mem_pestat] skip orientation FF as there are not enough pairs
[2016-04-14T19:00Z] [M::mem_pestat] analyzing insert size distribution for orientation FR...
[2016-04-14T19:00Z] [M::mem_pestat] (25, 50, 75) percentile: (145, 184, 229)
[2016-04-14T19:00Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 397)
[2016-04-14T19:00Z] [M::mem_pestat] mean and std.dev: (190.08, 60.48)
[2016-04-14T19:00Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 481)
[2016-04-14T19:00Z] [M::mem_pestat] skip orientation RF as there are not enough pairs
[2016-04-14T19:00Z] [M::mem_pestat] skip orientation RR as there are not enough pairs
[2016-04-14T19:01Z] [M::mem_pestat] skip orientation FF as there are not enough pairs
[2016-04-14T19:01Z] [M::mem_pestat] analyzing insert size distribution for orientation FR...
[2016-04-14T19:01Z] [M::mem_pestat] (25, 50, 75) percentile: (145, 183, 228)
[2016-04-14T19:01Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 394)
[2016-04-14T19:01Z] [M::mem_pestat] mean and std.dev: (189.28, 60.11)
[2016-04-14T19:01Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 477)
[2016-04-14T19:01Z] [M::mem_pestat] skip orientation RF as there are not enough pairs
[2016-04-14T19:01Z] [M::mem_pestat] skip orientation RR as there are not enough pairs
[2016-04-14T19:01Z] [M::mem_pestat] skip orientation FF as there are not enough pairs
[2016-04-14T19:01Z] [M::mem_pestat] analyzing insert size distribution for orientation FR...
[2016-04-14T19:01Z] [M::mem_pestat] (25, 50, 75) percentile: (144, 182, 227)
[2016-04-14T19:01Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 393)
[2016-04-14T19:01Z] [M::mem_pestat] mean and std.dev: (188.53, 59.90)
[2016-04-14T19:01Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 476)
[2016-04-14T19:01Z] [M::mem_pestat] analyzing insert size distribution for orientation RF...
[2016-04-14T19:01Z] [M::mem_pestat] (25, 50, 75) percentile: (198, 226, 899)
[2016-04-14T19:01Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 2301)
[2016-04-14T19:01Z] [M::mem_pestat] mean and std.dev: (375.42, 323.04)
[2016-04-14T19:01Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 3002)
[2016-04-14T19:01Z] [M::mem_pestat] skip orientation RR as there are not enough pairs
[2016-04-14T19:01Z] [M::mem_pestat] skip orientation RF
[2016-04-14T19:01Z] [M::mem_pestat] skip orientation FF as there are not enough pairs
[2016-04-14T19:01Z] [M::mem_pestat] analyzing insert size distribution for orientation FR...
[2016-04-14T19:01Z] [M::mem_pestat] (25, 50, 75) percentile: (143, 181, 225)
[2016-04-14T19:01Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 389)
[2016-04-14T19:01Z] [M::mem_pestat] mean and std.dev: (187.10, 59.37)
[2016-04-14T19:01Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 471)
[2016-04-14T19:01Z] [M::mem_pestat] analyzing insert size distribution for orientation RF...
[2016-04-14T19:01Z] [M::mem_pestat] (25, 50, 75) percentile: (80, 174, 843)
[2016-04-14T19:01Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 2369)
[2016-04-14T19:01Z] [M::mem_pestat] mean and std.dev: (342.06, 351.72)
[2016-04-14T19:01Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 3132)
[2016-04-14T19:01Z] [M::mem_pestat] skip orientation RR as there are not enough pairs
[2016-04-14T19:01Z] [M::mem_pestat] skip orientation RF
[2016-04-14T19:01Z] [M::mem_pestat] skip orientation FF as there are not enough pairs
[2016-04-14T19:01Z] [M::mem_pestat] analyzing insert size distribution for orientation FR...
[2016-04-14T19:01Z] [M::mem_pestat] (25, 50, 75) percentile: (144, 182, 227)
[2016-04-14T19:01Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 393)
[2016-04-14T19:01Z] [M::mem_pestat] mean and std.dev: (188.44, 59.61)
[2016-04-14T19:01Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 476)
[2016-04-14T19:01Z] [M::mem_pestat] analyzing insert size distribution for orientation RF...
[2016-04-14T19:01Z] [M::mem_pestat] (25, 50, 75) percentile: (77, 132, 960)
[2016-04-14T19:01Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 2726)
[2016-04-14T19:01Z] [M::mem_pestat] mean and std.dev: (604.77, 712.84)
[2016-04-14T19:01Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 3609)
[2016-04-14T19:01Z] [M::mem_pestat] skip orientation RR as there are not enough pairs
[2016-04-14T19:01Z] [M::mem_pestat] skip orientation RF
[2016-04-14T19:02Z] [M::mem_pestat] skip orientation FF as there are not enough pairs
[2016-04-14T19:02Z] [M::mem_pestat] analyzing insert size distribution for orientation FR...
[2016-04-14T19:02Z] [M::mem_pestat] (25, 50, 75) percentile: (146, 184, 229)
[2016-04-14T19:02Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 395)
[2016-04-14T19:02Z] [M::mem_pestat] mean and std.dev: (190.15, 60.34)
[2016-04-14T19:02Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 478)
[2016-04-14T19:02Z] [M::mem_pestat] skip orientation RF as there are not enough pairs
[2016-04-14T19:02Z] [M::mem_pestat] skip orientation RR as there are not enough pairs
[2016-04-14T19:02Z] [M::mem_pestat] skip orientation FF as there are not enough pairs
[2016-04-14T19:02Z] [M::mem_pestat] analyzing insert size distribution for orientation FR...
[2016-04-14T19:02Z] [M::mem_pestat] (25, 50, 75) percentile: (145, 183, 228)
[2016-04-14T19:02Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 394)
[2016-04-14T19:02Z] [M::mem_pestat] mean and std.dev: (189.36, 60.16)
[2016-04-14T19:02Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 477)
[2016-04-14T19:02Z] [M::mem_pestat] skip orientation RF as there are not enough pairs
[2016-04-14T19:02Z] [M::mem_pestat] skip orientation RR as there are not enough pairs
[2016-04-14T19:02Z] [M::mem_pestat] skip orientation FF as there are not enough pairs
[2016-04-14T19:02Z] [M::mem_pestat] analyzing insert size distribution for orientation FR...
[2016-04-14T19:02Z] [M::mem_pestat] (25, 50, 75) percentile: (145, 183, 227)
[2016-04-14T19:02Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 391)
[2016-04-14T19:02Z] [M::mem_pestat] mean and std.dev: (188.62, 59.70)
[2016-04-14T19:02Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 473)
[2016-04-14T19:02Z] [M::mem_pestat] skip orientation RF as there are not enough pairs
[2016-04-14T19:02Z] [M::mem_pestat] skip orientation RR as there are not enough pairs
[2016-04-14T19:02Z] [M::mem_pestat] skip orientation FF as there are not enough pairs
[2016-04-14T19:02Z] [M::mem_pestat] analyzing insert size distribution for orientation FR...
[2016-04-14T19:02Z] [M::mem_pestat] (25, 50, 75) percentile: (144, 181, 225)
[2016-04-14T19:02Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 387)
[2016-04-14T19:02Z] [M::mem_pestat] mean and std.dev: (187.24, 59.22)
[2016-04-14T19:02Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 468)
[2016-04-14T19:02Z] [M::mem_pestat] skip orientation RF as there are not enough pairs
[2016-04-14T19:02Z] [M::mem_pestat] skip orientation RR as there are not enough pairs
[2016-04-14T19:03Z] [M::mem_pestat] skip orientation FF as there are not enough pairs
[2016-04-14T19:03Z] [M::mem_pestat] analyzing insert size distribution for orientation FR...
[2016-04-14T19:03Z] [M::mem_pestat] (25, 50, 75) percentile: (144, 182, 226)
[2016-04-14T19:03Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 390)
[2016-04-14T19:03Z] [M::mem_pestat] mean and std.dev: (188.06, 59.46)
[2016-04-14T19:03Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 472)
[2016-04-14T19:03Z] [M::mem_pestat] skip orientation RF as there are not enough pairs
[2016-04-14T19:03Z] [M::mem_pestat] skip orientation RR as there are not enough pairs
[2016-04-14T19:03Z] [M::mem_pestat] skip orientation FF as there are not enough pairs
[2016-04-14T19:03Z] [M::mem_pestat] analyzing insert size distribution for orientation FR...
[2016-04-14T19:03Z] [M::mem_pestat] (25, 50, 75) percentile: (145, 183, 228)
[2016-04-14T19:03Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 394)
[2016-04-14T19:03Z] [M::mem_pestat] mean and std.dev: (189.27, 60.13)
[2016-04-14T19:03Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 477)
[2016-04-14T19:03Z] [M::mem_pestat] analyzing insert size distribution for orientation RF...
[2016-04-14T19:03Z] [M::mem_pestat] (25, 50, 75) percentile: (217, 883, 946)
[2016-04-14T19:03Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 2404)
[2016-04-14T19:03Z] [M::mem_pestat] mean and std.dev: (538.62, 364.39)
[2016-04-14T19:03Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 3133)
[2016-04-14T19:03Z] [M::mem_pestat] skip orientation RR as there are not enough pairs
[2016-04-14T19:03Z] [M::mem_pestat] skip orientation RF
[2016-04-14T19:03Z] [M::mem_pestat] skip orientation FF as there are not enough pairs
[2016-04-14T19:03Z] [M::mem_pestat] analyzing insert size distribution for orientation FR...
[2016-04-14T19:03Z] [M::mem_pestat] (25, 50, 75) percentile: (144, 182, 227)
[2016-04-14T19:03Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 393)
[2016-04-14T19:03Z] [M::mem_pestat] mean and std.dev: (188.31, 59.79)
[2016-04-14T19:03Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 476)
[2016-04-14T19:03Z] [M::mem_pestat] skip orientation RF as there are not enough pairs
[2016-04-14T19:03Z] [M::mem_pestat] skip orientation RR as there are not enough pairs
[2016-04-14T19:03Z] [M::mem_pestat] skip orientation FF as there are not enough pairs
[2016-04-14T19:03Z] [M::mem_pestat] analyzing insert size distribution for orientation FR...
[2016-04-14T19:03Z] [M::mem_pestat] (25, 50, 75) percentile: (143, 181, 225)
[2016-04-14T19:03Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 389)
[2016-04-14T19:03Z] [M::mem_pestat] mean and std.dev: (187.28, 59.37)
[2016-04-14T19:03Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 471)
[2016-04-14T19:03Z] [M::mem_pestat] analyzing insert size distribution for orientation RF...
[2016-04-14T19:03Z] [M::mem_pestat] (25, 50, 75) percentile: (198, 867, 2562)
[2016-04-14T19:03Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 7290)
[2016-04-14T19:03Z] [M::mem_pestat] mean and std.dev: (1040.38, 975.41)
[2016-04-14T19:03Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 9654)
[2016-04-14T19:03Z] [M::mem_pestat] skip orientation RR as there are not enough pairs
[2016-04-14T19:03Z] [M::mem_pestat] skip orientation RF
[2016-04-14T19:04Z] [M::mem_pestat] skip orientation FF as there are not enough pairs
[2016-04-14T19:04Z] [M::mem_pestat] analyzing insert size distribution for orientation FR...
[2016-04-14T19:04Z] [M::mem_pestat] (25, 50, 75) percentile: (143, 180, 224)
[2016-04-14T19:04Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 386)
[2016-04-14T19:04Z] [M::mem_pestat] mean and std.dev: (186.57, 59.05)
[2016-04-14T19:04Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 467)
[2016-04-14T19:04Z] [M::mem_pestat] skip orientation RF as there are not enough pairs
[2016-04-14T19:04Z] [M::mem_pestat] skip orientation RR as there are not enough pairs
[2016-04-14T19:04Z] [M::mem_pestat] skip orientation FF as there are not enough pairs
[2016-04-14T19:04Z] [M::mem_pestat] analyzing insert size distribution for orientation FR...
[2016-04-14T19:04Z] [M::mem_pestat] (25, 50, 75) percentile: (145, 184, 228)
[2016-04-14T19:04Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 394)
[2016-04-14T19:04Z] [M::mem_pestat] mean and std.dev: (189.73, 60.11)
[2016-04-14T19:04Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 477)
[2016-04-14T19:04Z] [M::mem_pestat] skip orientation RF as there are not enough pairs
[2016-04-14T19:04Z] [M::mem_pestat] skip orientation RR as there are not enough pairs
[2016-04-14T19:04Z] [M::mem_pestat] skip orientation FF as there are not enough pairs
[2016-04-14T19:04Z] [M::mem_pestat] analyzing insert size distribution for orientation FR...
[2016-04-14T19:04Z] [M::mem_pestat] (25, 50, 75) percentile: (145, 183, 228)
[2016-04-14T19:04Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 394)
[2016-04-14T19:04Z] [M::mem_pestat] mean and std.dev: (189.15, 60.08)
[2016-04-14T19:04Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 477)
[2016-04-14T19:04Z] [M::mem_pestat] analyzing insert size distribution for orientation RF...
[2016-04-14T19:04Z] [M::mem_pestat] (25, 50, 75) percentile: (339, 555, 876)
[2016-04-14T19:04Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 1950)
[2016-04-14T19:04Z] [M::mem_pestat] mean and std.dev: (555.00, 310.52)
[2016-04-14T19:04Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 2487)
[2016-04-14T19:04Z] [M::mem_pestat] skip orientation RR as there are not enough pairs
[2016-04-14T19:04Z] [M::mem_pestat] skip orientation RF
[2016-04-14T19:05Z] [M::mem_pestat] skip orientation FF as there are not enough pairs
[2016-04-14T19:05Z] [M::mem_pestat] analyzing insert size distribution for orientation FR...
[2016-04-14T19:05Z] [M::mem_pestat] (25, 50, 75) percentile: (144, 182, 226)
[2016-04-14T19:05Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 390)
[2016-04-14T19:05Z] [M::mem_pestat] mean and std.dev: (188.11, 59.62)
[2016-04-14T19:05Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 472)
[2016-04-14T19:05Z] [M::mem_pestat] skip orientation RF as there are not enough pairs
[2016-04-14T19:05Z] [M::mem_pestat] skip orientation RR as there are not enough pairs
[2016-04-14T19:05Z] [M::mem_pestat] skip orientation FF as there are not enough pairs
[2016-04-14T19:05Z] [M::mem_pestat] analyzing insert size distribution for orientation FR...
[2016-04-14T19:05Z] [M::mem_pestat] (25, 50, 75) percentile: (143, 181, 225)
[2016-04-14T19:05Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 389)
[2016-04-14T19:05Z] [M::mem_pestat] mean and std.dev: (187.23, 59.40)
[2016-04-14T19:05Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 471)
[2016-04-14T19:05Z] [M::mem_pestat] analyzing insert size distribution for orientation RF...
[2016-04-14T19:05Z] [M::mem_pestat] (25, 50, 75) percentile: (253, 804, 1013)
[2016-04-14T19:05Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 2533)
[2016-04-14T19:05Z] [M::mem_pestat] mean and std.dev: (560.79, 374.25)
[2016-04-14T19:05Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 3293)
[2016-04-14T19:05Z] [M::mem_pestat] skip orientation RR as there are not enough pairs
[2016-04-14T19:05Z] [M::mem_pestat] skip orientation RF
[2016-04-14T19:05Z] [M::mem_pestat] skip orientation FF as there are not enough pairs
[2016-04-14T19:05Z] [M::mem_pestat] analyzing insert size distribution for orientation FR...
[2016-04-14T19:05Z] [M::mem_pestat] (25, 50, 75) percentile: (143, 180, 224)
[2016-04-14T19:05Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 386)
[2016-04-14T19:05Z] [M::mem_pestat] mean and std.dev: (186.18, 59.01)
[2016-04-14T19:05Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 467)
[2016-04-14T19:05Z] [M::mem_pestat] skip orientation RF as there are not enough pairs
[2016-04-14T19:05Z] [M::mem_pestat] skip orientation RR as there are not enough pairs
[2016-04-14T19:05Z] [M::mem_pestat] skip orientation FF as there are not enough pairs
[2016-04-14T19:05Z] [M::mem_pestat] analyzing insert size distribution for orientation FR...
[2016-04-14T19:05Z] [M::mem_pestat] (25, 50, 75) percentile: (144, 182, 227)
[2016-04-14T19:05Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 393)
[2016-04-14T19:05Z] [M::mem_pestat] mean and std.dev: (188.50, 59.81)
[2016-04-14T19:05Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 476)
[2016-04-14T19:05Z] [M::mem_pestat] skip orientation RF as there are not enough pairs
[2016-04-14T19:05Z] [M::mem_pestat] skip orientation RR as there are not enough pairs
[2016-04-14T19:06Z] [M::mem_pestat] skip orientation FF as there are not enough pairs
[2016-04-14T19:06Z] [M::mem_pestat] analyzing insert size distribution for orientation FR...
[2016-04-14T19:06Z] [M::mem_pestat] (25, 50, 75) percentile: (145, 184, 228)
[2016-04-14T19:06Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 394)
[2016-04-14T19:06Z] [M::mem_pestat] mean and std.dev: (189.77, 60.17)
[2016-04-14T19:06Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 477)
[2016-04-14T19:06Z] [M::mem_pestat] skip orientation RF as there are not enough pairs
[2016-04-14T19:06Z] [M::mem_pestat] skip orientation RR as there are not enough pairs
[2016-04-14T19:06Z] [M::mem_pestat] skip orientation FF as there are not enough pairs
[2016-04-14T19:06Z] [M::mem_pestat] analyzing insert size distribution for orientation FR...
[2016-04-14T19:06Z] [M::mem_pestat] (25, 50, 75) percentile: (145, 183, 227)
[2016-04-14T19:06Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 391)
[2016-04-14T19:06Z] [M::mem_pestat] mean and std.dev: (188.95, 59.83)
[2016-04-14T19:06Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 473)
[2016-04-14T19:06Z] [M::mem_pestat] skip orientation RF as there are not enough pairs
[2016-04-14T19:06Z] [M::mem_pestat] skip orientation RR as there are not enough pairs
[2016-04-14T19:06Z] [M::mem_pestat] skip orientation FF as there are not enough pairs
[2016-04-14T19:06Z] [M::mem_pestat] analyzing insert size distribution for orientation FR...
[2016-04-14T19:06Z] [M::mem_pestat] (25, 50, 75) percentile: (144, 182, 226)
[2016-04-14T19:06Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 390)
[2016-04-14T19:06Z] [M::mem_pestat] mean and std.dev: (187.87, 59.49)
[2016-04-14T19:06Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 472)
[2016-04-14T19:06Z] [M::mem_pestat] skip orientation RF as there are not enough pairs
[2016-04-14T19:06Z] [M::mem_pestat] skip orientation RR as there are not enough pairs
[2016-04-14T19:06Z] [M::mem_pestat] skip orientation FF as there are not enough pairs
[2016-04-14T19:06Z] [M::mem_pestat] analyzing insert size distribution for orientation FR...
[2016-04-14T19:06Z] [M::mem_pestat] (25, 50, 75) percentile: (143, 181, 225)
[2016-04-14T19:06Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 389)
[2016-04-14T19:06Z] [M::mem_pestat] mean and std.dev: (187.00, 59.19)
[2016-04-14T19:06Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 471)
[2016-04-14T19:06Z] [M::mem_pestat] skip orientation RF as there are not enough pairs
[2016-04-14T19:06Z] [M::mem_pestat] skip orientation RR as there are not enough pairs
[2016-04-14T19:07Z] [M::mem_pestat] skip orientation FF as there are not enough pairs
[2016-04-14T19:07Z] [M::mem_pestat] analyzing insert size distribution for orientation FR...
[2016-04-14T19:07Z] [M::mem_pestat] (25, 50, 75) percentile: (145, 183, 227)
[2016-04-14T19:07Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 391)
[2016-04-14T19:07Z] [M::mem_pestat] mean and std.dev: (189.00, 59.49)
[2016-04-14T19:07Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 473)
[2016-04-14T19:07Z] [M::mem_pestat] analyzing insert size distribution for orientation RF...
[2016-04-14T19:07Z] [M::mem_pestat] (25, 50, 75) percentile: (123, 298, 978)
[2016-04-14T19:07Z] [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 2688)
[2016-04-14T19:07Z] [M::mem_pestat] mean and std.dev: (440.11, 389.74)
[2016-04-14T19:07Z] [M::mem_pestat] low and high boundaries for proper pairs: (1, 3543)
[2016-04-14T19:07Z] [M::mem_pestat] skip orientation RR as there are not enough pairs
[2016-04-14T19:07Z] [M::mem_pestat] skip orientation RF
[2016-04-14T19:07Z] [main] Version: 0.7.13-r1126
[2016-04-14T19:07Z] [main] CMD: /mnt/speed/qc/sequencing/bcbio/anaconda/bin/bwa mem -c 250 -M -t 16 -R @RG\tID:R14-18106_kapa-NGv3-PE100-NGv3\tPL:illumina\tPU:R14-18106_20HHFLHB_HHFLHBCXX\tSM:R14-18106_kapa-NGv3-PE100-NGv3 -v 1 /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/bwa/GRCh37.fa /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align_prep/Sample_R14-18106_R1.fastq.gz /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align_prep/Sample_R14-18106_R2.fastq.gz
[2016-04-14T19:07Z] [main] Real time: 646.152 sec; CPU: 8398.535 sec
[2016-04-14T19:07Z] samblaster: Output 106990 discordant read pairs to /dev/fd/62
[2016-04-14T19:07Z] samblaster: Output 79436 split reads to /dev/fd/63
[2016-04-14T19:07Z] samblaster: Marked 2273272 of 31048908 (7.32%) read ids as duplicates using 628540k memory in 1M8S(67.923S) CPU seconds and 10M46S(646S) wall time.
[2016-04-14T19:08Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-sr.bam
[2016-04-14T19:08Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-disc.bam
[2016-04-14T19:08Z] Timing: callable regions
[2016-04-14T19:08Z] multiprocessing: prep_samples
[2016-04-14T19:08Z] Prepare cleaned BED file : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T19:08Z] bgzip xgen-exome-research-panel-targets-cols1-2-noChr.bed
[2016-04-14T19:08Z] tabix index xgen-exome-research-panel-targets-cols1-2-noChr.bed.gz
[2016-04-14T19:08Z] Prepare merged BED file : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T19:08Z] bgzip xgen-exome-research-panel-targets-cols1-2-noChr-merged.bed
[2016-04-14T19:08Z] tabix index xgen-exome-research-panel-targets-cols1-2-noChr-merged.bed.gz
[2016-04-14T19:08Z] multiprocessing: postprocess_alignment
[2016-04-14T19:08Z] Resource requests: ; memory: 1.00; cores: 1
[2016-04-14T19:08Z] Configuring 16 jobs to run, using 1 cores each with 1.00g of memory reserved for each job
[2016-04-14T19:08Z] multiprocessing: calc_callable_loci
[2016-04-14T19:08Z] bedtools genomecov: 1 : R14-18102_kapa-NGv3-PE100-NGv3-sort.bam
[2016-04-14T19:08Z] bedtools genomecov: 6 : R14-18102_kapa-NGv3-PE100-NGv3-sort.bam
[2016-04-14T19:08Z] bedtools genomecov: 5 : R14-18102_kapa-NGv3-PE100-NGv3-sort.bam
[2016-04-14T19:08Z] bedtools genomecov: 12 : R14-18102_kapa-NGv3-PE100-NGv3-sort.bam
[2016-04-14T19:08Z] bedtools genomecov: 13 : R14-18102_kapa-NGv3-PE100-NGv3-sort.bam
[2016-04-14T19:08Z] bedtools genomecov: 7 : R14-18102_kapa-NGv3-PE100-NGv3-sort.bam
[2016-04-14T19:08Z] bedtools genomecov: 11 : R14-18102_kapa-NGv3-PE100-NGv3-sort.bam
[2016-04-14T19:08Z] bedtools genomecov: 15 : R14-18102_kapa-NGv3-PE100-NGv3-sort.bam
[2016-04-14T19:08Z] bedtools genomecov: 16 : R14-18102_kapa-NGv3-PE100-NGv3-sort.bam
[2016-04-14T19:08Z] bedtools genomecov: 4 : R14-18102_kapa-NGv3-PE100-NGv3-sort.bam
[2016-04-14T19:08Z] bedtools genomecov: 2 : R14-18102_kapa-NGv3-PE100-NGv3-sort.bam
[2016-04-14T19:08Z] bedtools genomecov: 3 : R14-18102_kapa-NGv3-PE100-NGv3-sort.bam
[2016-04-14T19:08Z] bedtools genomecov: 9 : R14-18102_kapa-NGv3-PE100-NGv3-sort.bam
[2016-04-14T19:08Z] bedtools genomecov: 10 : R14-18102_kapa-NGv3-PE100-NGv3-sort.bam
[2016-04-14T19:08Z] bedtools genomecov: 8 : R14-18102_kapa-NGv3-PE100-NGv3-sort.bam
[2016-04-14T19:08Z] bedtools genomecov: 14 : R14-18102_kapa-NGv3-PE100-NGv3-sort.bam
[2016-04-14T19:10Z] bedtools groupby coverage: 13 : R14-18102_kapa-NGv3-PE100-NGv3-sort.bam
[2016-04-14T19:10Z] bedtools genomecov: 17 : R14-18102_kapa-NGv3-PE100-NGv3-sort.bam
[2016-04-14T19:11Z] bedtools groupby coverage: 14 : R14-18102_kapa-NGv3-PE100-NGv3-sort.bam
[2016-04-14T19:12Z] bedtools genomecov: 18 : R14-18102_kapa-NGv3-PE100-NGv3-sort.bam
[2016-04-14T19:12Z] bedtools groupby coverage: 8 : R14-18102_kapa-NGv3-PE100-NGv3-sort.bam
[2016-04-14T19:12Z] bedtools genomecov: 19 : R14-18102_kapa-NGv3-PE100-NGv3-sort.bam
[2016-04-14T19:12Z] bedtools groupby coverage: 15 : R14-18102_kapa-NGv3-PE100-NGv3-sort.bam
[2016-04-14T19:12Z] bedtools genomecov: 20 : R14-18102_kapa-NGv3-PE100-NGv3-sort.bam
[2016-04-14T19:12Z] bedtools groupby coverage: 4 : R14-18102_kapa-NGv3-PE100-NGv3-sort.bam
[2016-04-14T19:12Z] bedtools genomecov: 21 : R14-18102_kapa-NGv3-PE100-NGv3-sort.bam
[2016-04-14T19:12Z] bedtools groupby coverage: 10 : R14-18102_kapa-NGv3-PE100-NGv3-sort.bam
[2016-04-14T19:13Z] bedtools groupby coverage: 9 : R14-18102_kapa-NGv3-PE100-NGv3-sort.bam
[2016-04-14T19:13Z] bedtools genomecov: 22 : R14-18102_kapa-NGv3-PE100-NGv3-sort.bam
[2016-04-14T19:13Z] bedtools genomecov: X : R14-18102_kapa-NGv3-PE100-NGv3-sort.bam
[2016-04-14T19:13Z] bedtools groupby coverage: 5 : R14-18102_kapa-NGv3-PE100-NGv3-sort.bam
[2016-04-14T19:13Z] bedtools groupby coverage: 16 : R14-18102_kapa-NGv3-PE100-NGv3-sort.bam
[2016-04-14T19:13Z] bedtools groupby coverage: 7 : R14-18102_kapa-NGv3-PE100-NGv3-sort.bam
[2016-04-14T19:13Z] bedtools groupby coverage: 18 : R14-18102_kapa-NGv3-PE100-NGv3-sort.bam
[2016-04-14T19:13Z] bedtools genomecov: Y : R14-18102_kapa-NGv3-PE100-NGv3-sort.bam
[2016-04-14T19:13Z] bedtools groupby coverage: Y : R14-18102_kapa-NGv3-PE100-NGv3-sort.bam
[2016-04-14T19:13Z] bedtools groupby coverage: 21 : R14-18102_kapa-NGv3-PE100-NGv3-sort.bam
[2016-04-14T19:13Z] bedtools groupby coverage: 6 : R14-18102_kapa-NGv3-PE100-NGv3-sort.bam
[2016-04-14T19:14Z] bedtools groupby coverage: 12 : R14-18102_kapa-NGv3-PE100-NGv3-sort.bam
[2016-04-14T19:14Z] bedtools groupby coverage: 3 : R14-18102_kapa-NGv3-PE100-NGv3-sort.bam
[2016-04-14T19:14Z] bedtools groupby coverage: 20 : R14-18102_kapa-NGv3-PE100-NGv3-sort.bam
[2016-04-14T19:14Z] bedtools groupby coverage: 11 : R14-18102_kapa-NGv3-PE100-NGv3-sort.bam
[2016-04-14T19:14Z] bedtools groupby coverage: 22 : R14-18102_kapa-NGv3-PE100-NGv3-sort.bam
[2016-04-14T19:14Z] bedtools groupby coverage: 17 : R14-18102_kapa-NGv3-PE100-NGv3-sort.bam
[2016-04-14T19:14Z] bedtools groupby coverage: 2 : R14-18102_kapa-NGv3-PE100-NGv3-sort.bam
[2016-04-14T19:14Z] bedtools groupby coverage: X : R14-18102_kapa-NGv3-PE100-NGv3-sort.bam
[2016-04-14T19:14Z] bedtools groupby coverage: 19 : R14-18102_kapa-NGv3-PE100-NGv3-sort.bam
[2016-04-14T19:14Z] bedtools groupby coverage: 1 : R14-18102_kapa-NGv3-PE100-NGv3-sort.bam
[2016-04-14T19:14Z] multiprocessing: combine_bed
[2016-04-14T19:15Z] Resource requests: ; memory: 1.00; cores: 1
[2016-04-14T19:15Z] Configuring 16 jobs to run, using 1 cores each with 1.00g of memory reserved for each job
[2016-04-14T19:21Z] Recalibrating ['', 'R14-18102_kapa-NGv3-PE100-NGv3'] with GATK
[2016-04-14T19:21Z] GATK: BaseRecalibrator
[2016-04-14T19:21Z] INFO  12:21:25,829 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T19:21Z] INFO  12:21:25,834 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T19:21Z] INFO  12:21:25,835 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T19:21Z] INFO  12:21:25,835 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T19:21Z] INFO  12:21:25,844 HelpFormatter - Program Args: -T BaseRecalibrator -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/tx/tmphS_R6E/R14-18102_kapa-NGv3-PE100-NGv3-sort.grp -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --knownSites /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bedprep/xgen-exome-research-panel-targets-cols1-2-noChr.bed --interval_set_rule INTERSECTION -nct 16 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-14T19:21Z] INFO  12:21:25,865 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T19:21Z] INFO  12:21:25,866 HelpFormatter - Date/Time: 2016/04/14 12:21:25
[2016-04-14T19:21Z] INFO  12:21:25,866 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T19:21Z] INFO  12:21:25,867 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T19:21Z] INFO  12:21:26,032 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T19:21Z] INFO  12:21:26,207 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T19:21Z] INFO  12:21:26,215 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T19:21Z] INFO  12:21:26,248 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.03
[2016-04-14T19:21Z] INFO  12:21:27,339 IntervalUtils - Processing 38874504 bp from intervals
[2016-04-14T19:21Z] WARN  12:21:27,343 IndexDictionaryUtils - Track knownSites doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T19:21Z] INFO  12:21:27,363 MicroScheduler - Running the GATK in parallel mode with 16 total threads, 16 CPU thread(s) for each of 1 data thread(s), of 16 processors available on this machine
[2016-04-14T19:21Z] INFO  12:21:27,530 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T19:21Z] INFO  12:21:27,961 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T19:21Z] INFO  12:21:27,961 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T19:21Z] INFO  12:21:27,962 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T19:21Z] INFO  12:21:27,962 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T19:21Z] INFO  12:21:28,131 BaseRecalibrator - The covariates being used here:
[2016-04-14T19:21Z] INFO  12:21:28,132 BaseRecalibrator - 	ReadGroupCovariate
[2016-04-14T19:21Z] INFO  12:21:28,132 BaseRecalibrator - 	QualityScoreCovariate
[2016-04-14T19:21Z] INFO  12:21:28,132 BaseRecalibrator - 	ContextCovariate
[2016-04-14T19:21Z] INFO  12:21:28,132 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-14T19:21Z] INFO  12:21:28,133 BaseRecalibrator - 	CycleCovariate
[2016-04-14T19:21Z] INFO  12:21:28,135 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T19:21Z] INFO  12:21:28,701 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T19:21Z] INFO  12:21:58,278 ProgressMeter -       1:9067518    200002.0    30.0 s       2.5 m        0.6%    89.2 m      88.7 m
[2016-04-14T19:22Z] INFO  12:22:28,279 ProgressMeter -      1:19981566    600007.0    60.0 s     100.0 s        1.3%    75.1 m      74.1 m
[2016-04-14T19:22Z] INFO  12:22:58,338 ProgressMeter -      1:33820089   1100014.0    90.0 s      82.0 s        2.2%    67.7 m      66.2 m
[2016-04-14T19:23Z] INFO  12:23:28,376 ProgressMeter -      1:45974608   1500018.0   120.0 s      80.0 s        3.0%    65.7 m      63.7 m
[2016-04-14T19:23Z] INFO  12:23:58,379 ProgressMeter -      1:64732819   1800022.0     2.5 m      83.0 s        3.7%    68.2 m      65.7 m
[2016-04-14T19:24Z] INFO  12:24:28,381 ProgressMeter -      1:91405467   2000024.0     3.0 m      90.0 s        4.3%    70.5 m      67.5 m
[2016-04-14T19:24Z] INFO  12:24:58,382 ProgressMeter -     1:117160071   2400033.0     3.5 m      87.0 s        5.1%    68.1 m      64.6 m
[2016-04-14T19:25Z] INFO  12:25:28,384 ProgressMeter -     1:152327233   2800038.0     4.0 m      85.0 s        5.8%    68.5 m      64.5 m
[2016-04-14T19:25Z] INFO  12:25:58,386 ProgressMeter -     1:162332871   3300047.0     4.5 m      81.0 s        6.9%    65.5 m      61.0 m
[2016-04-14T19:26Z] INFO  12:26:28,387 ProgressMeter -     1:181768005   3600050.0     5.0 m      83.0 s        7.5%    66.4 m      61.4 m
[2016-04-14T19:26Z] INFO  12:26:58,389 ProgressMeter -     1:204286411   3900057.0     5.5 m      84.0 s        8.3%    66.5 m      61.0 m
[2016-04-14T19:27Z] INFO  12:27:28,390 ProgressMeter -     1:223176238   4200060.0     6.0 m      85.0 s        9.0%    66.9 m      60.9 m
[2016-04-14T19:27Z] INFO  12:27:58,429 ProgressMeter -     1:236228382   4600065.0     6.5 m      84.0 s        9.6%    67.6 m      61.1 m
[2016-04-14T19:28Z] INFO  12:28:06,886 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T19:28Z] INFO  12:28:07,316 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T19:28Z] INFO  12:28:29,172 ProgressMeter -      2:11702677   4792310.0     7.0 m      87.0 s       10.3%    68.3 m      61.2 m
[2016-04-14T19:29Z] INFO  12:29:00,242 ProgressMeter -      2:31483774   5192318.0     7.5 m      87.0 s       10.9%    68.9 m      61.4 m
[2016-04-14T19:29Z] INFO  12:29:30,243 ProgressMeter -      2:56611493   5392320.0     8.0 m      89.0 s       11.6%    69.2 m      61.2 m
[2016-04-14T19:30Z] INFO  12:30:00,244 ProgressMeter -      2:75938437   5692324.0     8.5 m      89.0 s       12.3%    69.5 m      61.0 m
[2016-04-14T19:30Z] INFO  12:30:30,245 ProgressMeter -     2:101646177   5992332.0     9.0 m      90.0 s       12.9%    69.9 m      60.9 m
[2016-04-14T19:31Z] INFO  12:31:00,247 ProgressMeter -     2:128065267   6292338.0     9.5 m      90.0 s       13.5%    70.5 m      60.9 m
[2016-04-14T19:31Z] INFO  12:31:30,254 ProgressMeter -     2:152348965   6492341.0    10.0 m      92.0 s       14.0%    71.4 m      61.4 m
[2016-04-14T19:32Z] INFO  12:32:00,752 ProgressMeter -     2:175450305   6792345.0    10.5 m      93.0 s       14.8%    71.3 m      60.7 m
[2016-04-14T19:32Z] INFO  12:32:30,793 ProgressMeter -     2:192288684   7192354.0    11.0 m      92.0 s       15.5%    71.1 m      60.1 m
[2016-04-14T19:33Z] INFO  12:33:01,587 ProgressMeter -     2:217279817   7392356.0    11.6 m      93.0 s       16.2%    71.1 m      59.6 m
[2016-04-14T19:33Z] INFO  12:33:31,588 ProgressMeter -     2:233925374   7792362.0    12.1 m      92.0 s       16.9%    71.2 m      59.2 m
[2016-04-14T19:33Z] INFO  12:33:43,834 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T19:33Z] INFO  12:33:44,141 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T19:34Z] INFO  12:34:02,323 ProgressMeter -       3:9796484   8080829.0    12.6 m      93.0 s       17.5%    71.7 m      59.1 m
[2016-04-14T19:34Z] INFO  12:34:32,324 ProgressMeter -      3:30032820   8380833.0    13.1 m      93.0 s       18.1%    72.3 m      59.2 m
[2016-04-14T19:35Z] INFO  12:35:02,370 ProgressMeter -      3:47049996   8780840.0    13.6 m      92.0 s       18.9%    71.9 m      58.4 m
[2016-04-14T19:35Z] INFO  12:35:32,426 ProgressMeter -      3:54354623   9280846.0    14.1 m      90.0 s       19.8%    71.2 m      57.1 m
[2016-04-14T19:36Z] INFO  12:36:02,428 ProgressMeter -      3:78648104   9380847.0    14.6 m      93.0 s       20.2%    72.2 m      57.6 m
[2016-04-14T19:36Z] INFO  12:36:32,429 ProgressMeter -     3:121616392   9680850.0    15.1 m      93.0 s       20.9%    72.0 m      56.9 m
[2016-04-14T19:37Z] INFO  12:37:02,431 ProgressMeter -     3:134968432   1.0080858E7    15.6 m      92.0 s       21.6%    72.0 m      56.5 m
[2016-04-14T19:37Z] INFO  12:37:32,433 ProgressMeter -     3:156763615   1.0280861E7    16.1 m      93.0 s       22.2%    72.5 m      56.5 m
[2016-04-14T19:38Z] INFO  12:38:02,434 ProgressMeter -     3:185010623   1.0480863E7    16.6 m      94.0 s       22.8%    72.7 m      56.1 m
[2016-04-14T19:38Z] INFO  12:38:14,591 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T19:38Z] INFO  12:38:14,816 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T19:38Z] INFO  12:38:32,460 ProgressMeter -       4:4861728   1.0911554E7    17.1 m      93.0 s       23.6%    72.2 m      55.2 m
[2016-04-14T19:39Z] INFO  12:39:02,946 ProgressMeter -      4:26756585   1.1211557E7    17.6 m      94.0 s       24.1%    72.8 m      55.3 m
[2016-04-14T19:39Z] INFO  12:39:34,460 ProgressMeter -      4:71099906   1.1411561E7    18.1 m      95.0 s       24.8%    72.9 m      54.8 m
[2016-04-14T19:40Z] INFO  12:40:04,462 ProgressMeter -      4:88420766   1.1711565E7    18.6 m      95.0 s       25.4%    73.3 m      54.7 m
[2016-04-14T19:40Z] INFO  12:40:34,508 ProgressMeter -     4:113345218   1.1911567E7    19.1 m      96.0 s       25.9%    73.9 m      54.8 m
[2016-04-14T19:41Z] INFO  12:41:04,514 ProgressMeter -     4:151336665   1.2111569E7    19.6 m      97.0 s       26.6%    73.7 m      54.1 m
[2016-04-14T19:41Z] INFO  12:41:34,516 ProgressMeter -     4:174450443   1.2311571E7    20.1 m      98.0 s       27.0%    74.4 m      54.3 m
[2016-04-14T19:41Z] INFO  12:41:38,423 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T19:41Z] INFO  12:41:38,535 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T19:42Z] INFO  12:42:04,517 ProgressMeter -       5:7851127   1.2509001E7    20.6 m      98.0 s       27.5%    74.8 m      54.2 m
[2016-04-14T19:42Z] INFO  12:42:34,555 ProgressMeter -      5:37396600   1.2709003E7    21.1 m      99.0 s       28.0%    75.3 m      54.2 m
[2016-04-14T19:43Z] INFO  12:43:05,275 ProgressMeter -      5:66460949   1.2909005E7    21.6 m     100.0 s       28.5%    75.8 m      54.2 m
[2016-04-14T19:43Z] INFO  12:43:35,298 ProgressMeter -      5:90678787   1.3209009E7    22.1 m     100.0 s       29.2%    75.8 m      53.7 m
[2016-04-14T19:44Z] INFO  12:44:05,333 ProgressMeter -     5:123984136   1.3409012E7    22.6 m     101.0 s       29.7%    76.3 m      53.7 m
[2016-04-14T19:44Z] INFO  12:44:35,335 ProgressMeter -     5:140581519   1.3809021E7    23.1 m     100.0 s       30.4%    75.9 m      52.8 m
[2016-04-14T19:45Z] INFO  12:45:05,336 ProgressMeter -     5:154203082   1.4109024E7    23.6 m     100.0 s       31.1%    75.8 m      52.2 m
[2016-04-14T19:45Z] INFO  12:45:35,551 ProgressMeter -     5:178043995   1.4509032E7    24.1 m      99.0 s       31.7%    76.0 m      51.9 m
[2016-04-14T19:45Z] INFO  12:45:38,203 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T19:45Z] INFO  12:45:38,396 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T19:46Z] INFO  12:46:05,553 ProgressMeter -      6:18264296   1.4714581E7    24.6 m     100.0 s       32.4%    76.0 m      51.4 m
[2016-04-14T19:46Z] INFO  12:46:35,611 ProgressMeter -      6:32089216   1.5114586E7    25.1 m      99.0 s       33.2%    75.6 m      50.5 m
[2016-04-14T19:47Z] INFO  12:47:05,985 ProgressMeter -      6:43607957   1.5614595E7    25.6 m      98.0 s       34.1%    75.2 m      49.5 m
[2016-04-14T19:47Z] INFO  12:47:36,009 ProgressMeter -      6:69646576   1.58146E7    26.1 m      99.0 s       34.7%    75.4 m      49.2 m
[2016-04-14T19:48Z] INFO  12:48:07,235 ProgressMeter -     6:105850806   1.6114603E7    26.7 m      99.0 s       35.4%    75.4 m      48.7 m
[2016-04-14T19:48Z] INFO  12:48:37,251 ProgressMeter -     6:132272363   1.6414614E7    27.2 m      99.0 s       36.0%    75.4 m      48.2 m
[2016-04-14T19:49Z] INFO  12:49:07,802 ProgressMeter -     6:158094211   1.671462E7    27.7 m      99.0 s       36.7%    75.3 m      47.6 m
[2016-04-14T19:49Z] INFO  12:49:11,651 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T19:49Z] INFO  12:49:11,890 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T19:49Z] INFO  12:49:38,437 ProgressMeter -       7:4307719   1.6911086E7    28.2 m      99.0 s       37.3%    75.6 m      47.4 m
[2016-04-14T19:50Z] INFO  12:50:09,279 ProgressMeter -      7:31829780   1.721109E7    28.7 m     100.0 s       38.0%    75.5 m      46.8 m
[2016-04-14T19:50Z] INFO  12:50:39,280 ProgressMeter -      7:51384378   1.7511093E7    29.2 m     100.0 s       38.4%    75.9 m      46.7 m
[2016-04-14T19:51Z] INFO  12:51:09,281 ProgressMeter -      7:86526978   1.7711095E7    29.7 m     100.0 s       39.0%    76.1 m      46.4 m
[2016-04-14T19:51Z] INFO  12:51:39,283 ProgressMeter -     7:100424693   1.81111E7    30.2 m     100.0 s       39.7%    76.0 m      45.8 m
[2016-04-14T19:52Z] INFO  12:52:09,473 ProgressMeter -     7:116423535   1.8311105E7    30.7 m     100.0 s       40.3%    76.1 m      45.4 m
[2016-04-14T19:52Z] INFO  12:52:40,434 ProgressMeter -     7:140386896   1.8611109E7    31.2 m     100.0 s       41.0%    76.1 m      44.9 m
[2016-04-14T19:53Z] INFO  12:53:02,708 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T19:53Z] INFO  12:53:02,770 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T19:53Z] INFO  12:53:10,470 ProgressMeter -     7:155604841   1.901112E7    31.7 m     100.0 s       41.7%    76.1 m      44.4 m
[2016-04-14T19:53Z] INFO  12:53:40,714 ProgressMeter -      8:17933120   1.9164696E7    32.2 m     100.0 s       42.1%    76.5 m      44.3 m
[2016-04-14T19:54Z] INFO  12:54:10,715 ProgressMeter -      8:39007378   1.94647E7    32.7 m     100.0 s       42.8%    76.4 m      43.7 m
[2016-04-14T19:54Z] INFO  12:54:40,720 ProgressMeter -      8:72987645   1.9764705E7    33.2 m     100.0 s       43.4%    76.5 m      43.3 m
[2016-04-14T19:55Z] INFO  12:55:10,721 ProgressMeter -     8:103424483   1.9964708E7    33.7 m     101.0 s       44.0%    76.6 m      42.9 m
[2016-04-14T19:55Z] INFO  12:55:40,833 ProgressMeter -     8:139153677   2.0164712E7    34.2 m     101.0 s       44.5%    76.8 m      42.6 m
[2016-04-14T19:55Z] INFO  12:55:56,314 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T19:55Z] INFO  12:55:56,462 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T19:56Z] INFO  12:56:10,897 ProgressMeter -       9:5920093   2.0599769E7    34.7 m     101.0 s       45.3%    76.6 m      41.9 m
[2016-04-14T19:56Z] INFO  12:56:41,125 ProgressMeter -      9:35061116   2.0899772E7    35.2 m     101.0 s       45.8%    76.8 m      41.6 m
[2016-04-14T19:57Z] INFO  12:57:11,365 ProgressMeter -      9:79321959   2.1099776E7    35.7 m     101.0 s       46.5%    76.8 m      41.1 m
[2016-04-14T19:57Z] INFO  12:57:41,694 ProgressMeter -     9:100693211   2.139978E7    36.2 m     101.0 s       47.1%    76.8 m      40.6 m
[2016-04-14T19:58Z] INFO  12:58:11,718 ProgressMeter -     9:119460031   2.1699784E7    36.7 m     101.0 s       47.8%    76.8 m      40.1 m
[2016-04-14T19:58Z] INFO  12:58:42,924 ProgressMeter -     9:134322628   2.2099789E7    37.2 m     101.0 s       48.6%    76.7 m      39.4 m
[2016-04-14T19:58Z] INFO  12:58:59,496 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T19:58Z] INFO  12:58:59,659 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T19:59Z] INFO  12:59:13,036 ProgressMeter -      10:5853855   2.2591869E7    37.8 m     100.0 s       49.4%    76.4 m      38.7 m
[2016-04-14T19:59Z] INFO  12:59:43,105 ProgressMeter -     10:34420505   2.2891873E7    38.3 m     100.0 s       50.1%    76.3 m      38.1 m
[2016-04-14T20:00Z] INFO  13:00:13,106 ProgressMeter -     10:62648344   2.3191877E7    38.8 m     100.0 s       50.7%    76.4 m      37.7 m
[2016-04-14T20:00Z] INFO  13:00:43,108 ProgressMeter -     10:82403823   2.3491881E7    39.3 m     100.0 s       51.4%    76.4 m      37.1 m
[2016-04-14T20:01Z] INFO  13:01:13,240 ProgressMeter -    10:102748252   2.3791887E7    39.8 m     100.0 s       52.2%    76.2 m      36.4 m
[2016-04-14T20:01Z] INFO  13:01:43,242 ProgressMeter -    10:121692693   2.4191893E7    40.3 m      99.0 s       52.9%    76.1 m      35.9 m
[2016-04-14T20:02Z] INFO  13:02:00,112 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T20:02Z] INFO  13:02:00,302 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T20:02Z] INFO  13:02:13,479 ProgressMeter -      11:1263317   2.4527493E7    40.8 m      99.0 s       53.6%    76.1 m      35.3 m
[2016-04-14T20:02Z] INFO  13:02:43,707 ProgressMeter -     11:12283330   2.4927499E7    41.3 m      99.0 s       54.4%    75.8 m      34.6 m
[2016-04-14T20:03Z] INFO  13:03:13,889 ProgressMeter -     11:33375095   2.5227502E7    41.8 m      99.0 s       54.9%    76.0 m      34.3 m
[2016-04-14T20:03Z] INFO  13:03:43,924 ProgressMeter -     11:58477743   2.5527506E7    42.3 m      99.0 s       55.6%    75.9 m      33.7 m
[2016-04-14T20:04Z] INFO  13:04:13,925 ProgressMeter -     11:66105310   2.6027514E7    42.8 m      98.0 s       56.6%    75.5 m      32.8 m
[2016-04-14T20:04Z] INFO  13:04:45,134 ProgressMeter -     11:77702315   2.6427519E7    43.3 m      98.0 s       57.4%    75.5 m      32.2 m
[2016-04-14T20:05Z] INFO  13:05:15,967 ProgressMeter -    11:110143392   2.6727529E7    43.8 m      98.0 s       58.1%    75.4 m      31.6 m
[2016-04-14T20:05Z] INFO  13:05:46,040 ProgressMeter -    11:124545269   2.7127536E7    44.3 m      97.0 s       58.8%    75.3 m      31.0 m
[2016-04-14T20:05Z] INFO  13:05:57,100 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T20:05Z] INFO  13:05:57,259 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T20:06Z] INFO  13:06:16,042 ProgressMeter -      12:6500111   2.745846E7    44.8 m      97.0 s       59.5%    75.3 m      30.5 m
[2016-04-14T20:06Z] INFO  13:06:46,623 ProgressMeter -     12:22837507   2.7758466E7    45.3 m      97.0 s       60.2%    75.3 m      30.0 m
[2016-04-14T20:07Z] INFO  13:07:16,677 ProgressMeter -     12:50746091   2.8158474E7    45.8 m      97.0 s       61.1%    75.0 m      29.2 m
[2016-04-14T20:07Z] INFO  13:07:46,684 ProgressMeter -     12:64668745   2.8658483E7    46.3 m      96.0 s       62.1%    74.6 m      28.3 m
[2016-04-14T20:08Z] INFO  13:08:16,685 ProgressMeter -     12:94580189   2.8858486E7    46.8 m      97.0 s       62.6%    74.7 m      27.9 m
[2016-04-14T20:08Z] INFO  13:08:46,971 ProgressMeter -    12:112613598   2.9258492E7    47.3 m      97.0 s       63.4%    74.6 m      27.3 m
[2016-04-14T20:09Z] INFO  13:09:16,972 ProgressMeter -    12:125457252   2.9658497E7    47.8 m      96.0 s       64.1%    74.6 m      26.8 m
[2016-04-14T20:09Z] INFO  13:09:21,784 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T20:09Z] INFO  13:09:21,894 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T20:09Z] INFO  13:09:46,976 ProgressMeter -     13:34410664   2.9899676E7    48.3 m      96.0 s       64.9%    74.5 m      26.2 m
[2016-04-14T20:10Z] INFO  13:10:16,977 ProgressMeter -     13:60453540   3.0199679E7    48.8 m      96.0 s       65.5%    74.6 m      25.7 m
[2016-04-14T20:10Z] INFO  13:10:48,091 ProgressMeter -    13:111134939   3.0399682E7    49.3 m      97.0 s       66.0%    74.7 m      25.4 m
[2016-04-14T20:10Z] INFO  13:10:49,347 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T20:10Z] INFO  13:10:49,476 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T20:11Z] INFO  13:11:18,222 ProgressMeter -     14:25045508   3.0877159E7    49.8 m      96.0 s       66.9%    74.5 m      24.7 m
[2016-04-14T20:11Z] INFO  13:11:48,235 ProgressMeter -     14:55411167   3.1077161E7    50.3 m      97.0 s       67.5%    74.6 m      24.3 m
[2016-04-14T20:12Z] INFO  13:12:18,238 ProgressMeter -     14:73428762   3.1377165E7    50.8 m      97.0 s       68.1%    74.6 m      23.8 m
[2016-04-14T20:12Z] INFO  13:12:48,883 ProgressMeter -     14:96010489   3.1677169E7    51.3 m      97.0 s       68.9%    74.5 m      23.2 m
[2016-04-14T20:13Z] INFO  13:13:04,674 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T20:13Z] INFO  13:13:04,811 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T20:13Z] INFO  13:13:19,067 ProgressMeter -     15:23062298   3.2060881E7    51.9 m      97.0 s       69.5%    74.6 m      22.8 m
[2016-04-14T20:13Z] INFO  13:13:49,707 ProgressMeter -     15:41657748   3.2360886E7    52.4 m      97.0 s       70.1%    74.7 m      22.3 m
[2016-04-14T20:14Z] INFO  13:14:20,771 ProgressMeter -     15:56961104   3.2660889E7    52.9 m      97.0 s       71.0%    74.5 m      21.6 m
[2016-04-14T20:14Z] INFO  13:14:50,773 ProgressMeter -     15:73925564   3.30609E7    53.4 m      96.0 s       71.7%    74.4 m      21.0 m
[2016-04-14T20:15Z] INFO  13:15:20,776 ProgressMeter -     15:90039736   3.3360906E7    53.9 m      96.0 s       72.5%    74.3 m      20.4 m
[2016-04-14T20:15Z] INFO  13:15:29,477 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T20:15Z] INFO  13:15:29,664 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T20:15Z] INFO  13:15:51,409 ProgressMeter -      16:1835585   3.3729429E7    54.4 m      96.0 s       73.2%    74.3 m      19.9 m
[2016-04-14T20:16Z] INFO  13:16:21,412 ProgressMeter -     16:12875249   3.4129434E7    54.9 m      96.0 s       73.9%    74.3 m      19.4 m
[2016-04-14T20:16Z] INFO  13:16:52,358 ProgressMeter -     16:28330336   3.4429441E7    55.4 m      96.0 s       74.6%    74.3 m      18.9 m
[2016-04-14T20:17Z] INFO  13:17:22,648 ProgressMeter -     16:57499944   3.4929449E7    55.9 m      96.0 s       75.5%    74.0 m      18.1 m
[2016-04-14T20:17Z] INFO  13:17:53,319 ProgressMeter -     16:77228781   3.5429454E7    56.4 m      95.0 s       76.5%    73.7 m      17.3 m
[2016-04-14T20:18Z] INFO  13:18:12,973 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T20:18Z] INFO  13:18:13,183 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T20:18Z] INFO  13:18:23,497 ProgressMeter -      17:2226972   3.5829975E7    56.9 m      95.0 s       77.3%    73.6 m      16.7 m
[2016-04-14T20:18Z] INFO  13:18:53,528 ProgressMeter -      17:9929586   3.6329981E7    57.4 m      94.0 s       78.2%    73.4 m      16.0 m
[2016-04-14T20:19Z] INFO  13:19:24,473 ProgressMeter -     17:27076131   3.6729987E7    57.9 m      94.0 s       78.9%    73.4 m      15.5 m
[2016-04-14T20:19Z] INFO  13:19:54,474 ProgressMeter -     17:39928202   3.7229998E7    58.4 m      94.0 s       79.9%    73.1 m      14.7 m
[2016-04-14T20:20Z] INFO  13:20:24,554 ProgressMeter -     17:49245656   3.7730003E7    58.9 m      93.0 s       80.9%    72.9 m      14.0 m
[2016-04-14T20:20Z] INFO  13:20:54,556 ProgressMeter -     17:65850633   3.8030008E7    59.4 m      93.0 s       81.5%    72.9 m      13.5 m
[2016-04-14T20:21Z] INFO  13:21:24,620 ProgressMeter -     17:79687580   3.8630018E7    59.9 m      93.0 s       82.5%    72.7 m      12.7 m
[2016-04-14T20:21Z] INFO  13:21:26,246 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T20:21Z] INFO  13:21:26,324 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T20:21Z] INFO  13:21:54,661 ProgressMeter -     18:24056557   3.8964465E7    60.4 m      93.0 s       83.2%    72.6 m      12.2 m
[2016-04-14T20:22Z] INFO  13:22:24,663 ProgressMeter -     18:54305684   3.9264469E7    60.9 m      93.0 s       83.8%    72.7 m      11.8 m
[2016-04-14T20:22Z] INFO  13:22:45,123 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T20:22Z] INFO  13:22:45,188 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T20:22Z] INFO  13:22:54,665 ProgressMeter -      19:1277276   3.9576881E7    61.4 m      93.0 s       84.5%    72.7 m      11.3 m
[2016-04-14T20:23Z] INFO  13:23:26,404 ProgressMeter -      19:9324650   4.0076888E7    62.0 m      92.0 s       85.5%    72.5 m      10.5 m
[2016-04-14T20:23Z] INFO  13:23:58,927 ProgressMeter -     19:17627302   4.0676897E7    62.5 m      92.0 s       86.6%    72.2 m       9.7 m
[2016-04-14T20:24Z] INFO  13:24:29,767 ProgressMeter -     19:35793633   4.1176904E7    63.0 m      91.0 s       87.3%    72.2 m       9.2 m
[2016-04-14T20:25Z] INFO  13:25:00,882 ProgressMeter -     19:43865547   4.167691E7    63.5 m      91.0 s       88.3%    71.9 m       8.4 m
[2016-04-14T20:25Z] INFO  13:25:30,905 ProgressMeter -     19:50826851   4.2276921E7    64.0 m      90.0 s       89.3%    71.7 m       7.6 m
[2016-04-14T20:26Z] INFO  13:26:01,183 ProgressMeter -     19:57641545   4.2776927E7    64.6 m      90.0 s       90.3%    71.5 m       7.0 m
[2016-04-14T20:26Z] INFO  13:26:05,541 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T20:26Z] INFO  13:26:05,626 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T20:26Z] INFO  13:26:31,211 ProgressMeter -     20:13982969   4.3191946E7    65.1 m      90.0 s       91.0%    71.5 m       6.4 m
[2016-04-14T20:27Z] INFO  13:27:02,357 ProgressMeter -     20:35695669   4.3491952E7    65.6 m      90.0 s       91.7%    71.5 m       5.9 m
[2016-04-14T20:27Z] INFO  13:27:32,359 ProgressMeter -     20:50092159   4.3891956E7    66.1 m      90.0 s       92.4%    71.5 m       5.5 m
[2016-04-14T20:27Z] INFO  13:27:50,869 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T20:27Z] INFO  13:27:50,904 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T20:28Z] INFO  13:28:02,361 ProgressMeter -     21:22907030   4.4218069E7    66.6 m      90.0 s       93.0%    71.6 m       5.0 m
[2016-04-14T20:28Z] INFO  13:28:32,363 ProgressMeter -     21:45855098   4.4518075E7    67.1 m      90.0 s       93.8%    71.5 m       4.5 m
[2016-04-14T20:28Z] INFO  13:28:37,022 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T20:28Z] INFO  13:28:37,204 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T20:29Z] INFO  13:29:02,365 ProgressMeter -     22:25024696   4.4936306E7    67.6 m      90.0 s       94.6%    71.5 m       3.9 m
[2016-04-14T20:29Z] INFO  13:29:32,383 ProgressMeter -     22:38958330   4.5336315E7    68.1 m      90.0 s       95.3%    71.4 m       3.3 m
[2016-04-14T20:30Z] INFO  13:30:00,564 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T20:30Z] INFO  13:30:00,665 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T20:30Z] INFO  13:30:02,534 ProgressMeter -     22:51160452   4.5836322E7    68.6 m      89.0 s       96.1%    71.4 m       2.8 m
[2016-04-14T20:30Z] INFO  13:30:32,536 ProgressMeter -      X:19650081   4.6051252E7    69.1 m      89.0 s       96.5%    71.5 m       2.5 m
[2016-04-14T20:31Z] INFO  13:31:02,590 ProgressMeter -      X:48270297   4.6251254E7    69.6 m      90.0 s       97.1%    71.7 m       2.1 m
[2016-04-14T20:31Z] INFO  13:31:34,834 ProgressMeter -      X:69720768   4.6551258E7    70.1 m      90.0 s       97.7%    71.7 m      97.0 s
[2016-04-14T20:32Z] INFO  13:32:04,870 ProgressMeter -     X:104728386   4.6851262E7    70.6 m      90.0 s       98.4%    71.8 m      69.0 s
[2016-04-14T20:32Z] INFO  13:32:34,872 ProgressMeter -     X:129546862   4.7151265E7    71.1 m      90.0 s       99.0%    71.8 m      44.0 s
[2016-04-14T20:33Z] INFO  13:33:04,879 ProgressMeter -     X:153459224   4.7451268E7    71.6 m      90.0 s       99.6%    71.9 m      17.0 s
[2016-04-14T20:33Z] INFO  13:33:07,594 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T20:33Z] INFO  13:33:07,597 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T20:33Z] INFO  13:33:10,377 BaseRecalibrator - Calculating quantized quality scores...
[2016-04-14T20:33Z] INFO  13:33:10,558 BaseRecalibrator - Writing recalibration report...
[2016-04-14T20:33Z] INFO  13:33:12,009 BaseRecalibrator - ...done!
[2016-04-14T20:33Z] INFO  13:33:12,009 BaseRecalibrator - BaseRecalibrator was able to recalibrate 47569784 reads
[2016-04-14T20:33Z] INFO  13:33:12,011 ProgressMeter -            done   4.7569784E7    71.7 m      90.0 s       99.9%    71.8 m       3.0 s
[2016-04-14T20:33Z] INFO  13:33:12,011 ProgressMeter - Total runtime 4304.05 secs, 71.73 min, 1.20 hours
[2016-04-14T20:33Z] INFO  13:33:12,011 MicroScheduler - 6766651 reads were filtered out during the traversal out of approximately 54348418 total reads (12.45%)
[2016-04-14T20:33Z] INFO  13:33:12,011 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T20:33Z] INFO  13:33:12,012 MicroScheduler -   -> 4295678 reads (7.90% of total) failing DuplicateReadFilter
[2016-04-14T20:33Z] INFO  13:33:12,012 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-14T20:33Z] INFO  13:33:12,012 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T20:33Z] INFO  13:33:12,012 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-14T20:33Z] INFO  13:33:12,012 MicroScheduler -   -> 2470973 reads (4.55% of total) failing MappingQualityZeroFilter
[2016-04-14T20:33Z] INFO  13:33:12,012 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T20:33Z] INFO  13:33:12,013 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-14T20:33Z] INFO  13:33:14,147 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T20:33Z] Resource requests: ; memory: 1.00; cores: 1
[2016-04-14T20:33Z] Configuring 16 jobs to run, using 1 cores each with 1.00g of memory reserved for each job
[2016-04-14T20:33Z] multiprocessing: calc_callable_loci
[2016-04-14T20:33Z] bedtools genomecov: 1 : R14-18105_kapa-NGv3-PE100-NGv3-sort.bam
[2016-04-14T20:33Z] bedtools genomecov: 2 : R14-18105_kapa-NGv3-PE100-NGv3-sort.bam
[2016-04-14T20:33Z] bedtools genomecov: 4 : R14-18105_kapa-NGv3-PE100-NGv3-sort.bam
[2016-04-14T20:33Z] bedtools genomecov: 5 : R14-18105_kapa-NGv3-PE100-NGv3-sort.bam
[2016-04-14T20:33Z] bedtools genomecov: 3 : R14-18105_kapa-NGv3-PE100-NGv3-sort.bam
[2016-04-14T20:33Z] bedtools genomecov: 6 : R14-18105_kapa-NGv3-PE100-NGv3-sort.bam
[2016-04-14T20:33Z] bedtools genomecov: 8 : R14-18105_kapa-NGv3-PE100-NGv3-sort.bam
[2016-04-14T20:33Z] bedtools genomecov: 9 : R14-18105_kapa-NGv3-PE100-NGv3-sort.bam
[2016-04-14T20:33Z] bedtools genomecov: 7 : R14-18105_kapa-NGv3-PE100-NGv3-sort.bam
[2016-04-14T20:33Z] bedtools genomecov: 10 : R14-18105_kapa-NGv3-PE100-NGv3-sort.bam
[2016-04-14T20:33Z] bedtools genomecov: 11 : R14-18105_kapa-NGv3-PE100-NGv3-sort.bam
[2016-04-14T20:33Z] bedtools genomecov: 13 : R14-18105_kapa-NGv3-PE100-NGv3-sort.bam
[2016-04-14T20:33Z] bedtools genomecov: 15 : R14-18105_kapa-NGv3-PE100-NGv3-sort.bam
[2016-04-14T20:33Z] bedtools genomecov: 12 : R14-18105_kapa-NGv3-PE100-NGv3-sort.bam
[2016-04-14T20:33Z] bedtools genomecov: 14 : R14-18105_kapa-NGv3-PE100-NGv3-sort.bam
[2016-04-14T20:33Z] bedtools genomecov: 16 : R14-18105_kapa-NGv3-PE100-NGv3-sort.bam
[2016-04-14T20:34Z] bedtools groupby coverage: 13 : R14-18105_kapa-NGv3-PE100-NGv3-sort.bam
[2016-04-14T20:34Z] bedtools genomecov: 17 : R14-18105_kapa-NGv3-PE100-NGv3-sort.bam
[2016-04-14T20:36Z] bedtools groupby coverage: 14 : R14-18105_kapa-NGv3-PE100-NGv3-sort.bam
[2016-04-14T20:36Z] bedtools genomecov: 18 : R14-18105_kapa-NGv3-PE100-NGv3-sort.bam
[2016-04-14T20:36Z] bedtools groupby coverage: 8 : R14-18105_kapa-NGv3-PE100-NGv3-sort.bam
[2016-04-14T20:36Z] bedtools groupby coverage: 15 : R14-18105_kapa-NGv3-PE100-NGv3-sort.bam
[2016-04-14T20:36Z] bedtools genomecov: 19 : R14-18105_kapa-NGv3-PE100-NGv3-sort.bam
[2016-04-14T20:37Z] bedtools genomecov: 20 : R14-18105_kapa-NGv3-PE100-NGv3-sort.bam
[2016-04-14T20:37Z] bedtools groupby coverage: 4 : R14-18105_kapa-NGv3-PE100-NGv3-sort.bam
[2016-04-14T20:37Z] bedtools genomecov: 21 : R14-18105_kapa-NGv3-PE100-NGv3-sort.bam
[2016-04-14T20:37Z] bedtools groupby coverage: 10 : R14-18105_kapa-NGv3-PE100-NGv3-sort.bam
[2016-04-14T20:37Z] bedtools genomecov: 22 : R14-18105_kapa-NGv3-PE100-NGv3-sort.bam
[2016-04-14T20:37Z] bedtools groupby coverage: 9 : R14-18105_kapa-NGv3-PE100-NGv3-sort.bam
[2016-04-14T20:38Z] bedtools genomecov: X : R14-18105_kapa-NGv3-PE100-NGv3-sort.bam
[2016-04-14T20:38Z] bedtools groupby coverage: 5 : R14-18105_kapa-NGv3-PE100-NGv3-sort.bam
[2016-04-14T20:38Z] bedtools groupby coverage: 16 : R14-18105_kapa-NGv3-PE100-NGv3-sort.bam
[2016-04-14T20:38Z] bedtools groupby coverage: 7 : R14-18105_kapa-NGv3-PE100-NGv3-sort.bam
[2016-04-14T20:38Z] bedtools groupby coverage: 18 : R14-18105_kapa-NGv3-PE100-NGv3-sort.bam
[2016-04-14T20:38Z] bedtools genomecov: Y : R14-18105_kapa-NGv3-PE100-NGv3-sort.bam
[2016-04-14T20:38Z] bedtools groupby coverage: Y : R14-18105_kapa-NGv3-PE100-NGv3-sort.bam
[2016-04-14T20:38Z] bedtools groupby coverage: 21 : R14-18105_kapa-NGv3-PE100-NGv3-sort.bam
[2016-04-14T20:38Z] bedtools groupby coverage: 6 : R14-18105_kapa-NGv3-PE100-NGv3-sort.bam
[2016-04-14T20:38Z] bedtools groupby coverage: 12 : R14-18105_kapa-NGv3-PE100-NGv3-sort.bam
[2016-04-14T20:39Z] bedtools groupby coverage: 3 : R14-18105_kapa-NGv3-PE100-NGv3-sort.bam
[2016-04-14T20:39Z] bedtools groupby coverage: 11 : R14-18105_kapa-NGv3-PE100-NGv3-sort.bam
[2016-04-14T20:39Z] bedtools groupby coverage: 20 : R14-18105_kapa-NGv3-PE100-NGv3-sort.bam
[2016-04-14T20:39Z] bedtools groupby coverage: 22 : R14-18105_kapa-NGv3-PE100-NGv3-sort.bam
[2016-04-14T20:39Z] bedtools groupby coverage: X : R14-18105_kapa-NGv3-PE100-NGv3-sort.bam
[2016-04-14T20:39Z] bedtools groupby coverage: 17 : R14-18105_kapa-NGv3-PE100-NGv3-sort.bam
[2016-04-14T20:39Z] bedtools groupby coverage: 2 : R14-18105_kapa-NGv3-PE100-NGv3-sort.bam
[2016-04-14T20:39Z] bedtools groupby coverage: 19 : R14-18105_kapa-NGv3-PE100-NGv3-sort.bam
[2016-04-14T20:39Z] bedtools groupby coverage: 1 : R14-18105_kapa-NGv3-PE100-NGv3-sort.bam
[2016-04-14T20:39Z] multiprocessing: combine_bed
[2016-04-14T20:40Z] Resource requests: ; memory: 1.00; cores: 1
[2016-04-14T20:40Z] Configuring 16 jobs to run, using 1 cores each with 1.00g of memory reserved for each job
[2016-04-14T20:46Z] Recalibrating ['', 'R14-18105_kapa-NGv3-PE100-NGv3'] with GATK
[2016-04-14T20:46Z] GATK: BaseRecalibrator
[2016-04-14T20:46Z] INFO  13:46:10,997 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T20:46Z] INFO  13:46:10,999 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T20:46Z] INFO  13:46:10,999 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T20:46Z] INFO  13:46:10,999 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T20:46Z] INFO  13:46:11,003 HelpFormatter - Program Args: -T BaseRecalibrator -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/tx/tmpZnpiEZ/R14-18105_kapa-NGv3-PE100-NGv3-sort.grp -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --knownSites /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bedprep/xgen-exome-research-panel-targets-cols1-2-noChr.bed --interval_set_rule INTERSECTION -nct 16 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-14T20:46Z] INFO  13:46:11,015 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T20:46Z] INFO  13:46:11,015 HelpFormatter - Date/Time: 2016/04/14 13:46:10
[2016-04-14T20:46Z] INFO  13:46:11,015 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T20:46Z] INFO  13:46:11,015 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T20:46Z] INFO  13:46:11,151 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T20:46Z] INFO  13:46:11,273 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T20:46Z] INFO  13:46:11,281 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T20:46Z] INFO  13:46:11,313 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.03
[2016-04-14T20:46Z] INFO  13:46:12,221 IntervalUtils - Processing 38874504 bp from intervals
[2016-04-14T20:46Z] WARN  13:46:12,225 IndexDictionaryUtils - Track knownSites doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T20:46Z] INFO  13:46:12,241 MicroScheduler - Running the GATK in parallel mode with 16 total threads, 16 CPU thread(s) for each of 1 data thread(s), of 16 processors available on this machine
[2016-04-14T20:46Z] INFO  13:46:12,344 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T20:46Z] INFO  13:46:12,704 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T20:46Z] INFO  13:46:12,705 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T20:46Z] INFO  13:46:12,705 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T20:46Z] INFO  13:46:12,705 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T20:46Z] INFO  13:46:12,729 BaseRecalibrator - The covariates being used here:
[2016-04-14T20:46Z] INFO  13:46:12,730 BaseRecalibrator - 	ReadGroupCovariate
[2016-04-14T20:46Z] INFO  13:46:12,730 BaseRecalibrator - 	QualityScoreCovariate
[2016-04-14T20:46Z] INFO  13:46:12,730 BaseRecalibrator - 	ContextCovariate
[2016-04-14T20:46Z] INFO  13:46:12,730 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-14T20:46Z] INFO  13:46:12,731 BaseRecalibrator - 	CycleCovariate
[2016-04-14T20:46Z] INFO  13:46:12,733 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T20:46Z] INFO  13:46:13,291 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T20:46Z] INFO  13:46:42,711 ProgressMeter -       1:8398105    200004.0    30.0 s       2.5 m        0.5%    93.2 m      92.7 m
[2016-04-14T20:47Z] INFO  13:47:12,900 ProgressMeter -      1:19431173    600011.0    60.0 s     100.0 s        1.3%    78.7 m      77.7 m
[2016-04-14T20:47Z] INFO  13:47:43,008 ProgressMeter -      1:31538634   1100017.0    90.0 s      82.0 s        2.0%    74.4 m      72.9 m
[2016-04-14T20:48Z] INFO  13:48:13,406 ProgressMeter -      1:43618633   1500022.0   120.0 s      80.0 s        2.8%    71.1 m      69.1 m
[2016-04-14T20:48Z] INFO  13:48:44,724 ProgressMeter -      1:58946765   1800026.0     2.5 m      84.0 s        3.5%    71.8 m      69.3 m
[2016-04-14T20:49Z] INFO  13:49:15,169 ProgressMeter -      1:86842036   2100030.0     3.0 m      86.0 s        4.1%    73.3 m      70.3 m
[2016-04-14T20:49Z] INFO  13:49:45,255 ProgressMeter -     1:110456903   2300036.0     3.5 m      92.0 s        4.8%    73.9 m      70.4 m
[2016-04-14T20:50Z] INFO  13:50:15,256 ProgressMeter -     1:150208128   2700040.0     4.0 m      89.0 s        5.5%    73.2 m      69.2 m
[2016-04-14T20:50Z] INFO  13:50:45,307 ProgressMeter -     1:156897121   3200048.0     4.5 m      85.0 s        6.5%    70.2 m      65.7 m
[2016-04-14T20:51Z] INFO  13:51:15,308 ProgressMeter -     1:173176295   3600052.0     5.0 m      84.0 s        7.2%    69.7 m      64.6 m
[2016-04-14T20:51Z] INFO  13:51:45,309 ProgressMeter -     1:193219916   3900056.0     5.5 m      85.0 s        7.8%    70.8 m      65.3 m
[2016-04-14T20:52Z] INFO  13:52:15,310 ProgressMeter -     1:210334271   4200061.0     6.0 m      86.0 s        8.6%    70.0 m      64.0 m
[2016-04-14T20:52Z] INFO  13:52:45,584 ProgressMeter -     1:228559979   4500067.0     6.5 m      87.0 s        9.3%    70.4 m      63.9 m
[2016-04-14T20:53Z] INFO  13:53:08,825 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T20:53Z] INFO  13:53:09,234 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T20:53Z] INFO  13:53:15,586 ProgressMeter -     1:249212599   4900075.0     7.0 m      86.0 s       10.1%    70.0 m      62.9 m
[2016-04-14T20:53Z] INFO  13:53:45,592 ProgressMeter -      2:27306367   5148516.0     7.5 m      87.0 s       10.7%    70.5 m      63.0 m
[2016-04-14T20:54Z] INFO  13:54:15,640 ProgressMeter -      2:47403691   5548523.0     8.0 m      87.0 s       11.4%    70.6 m      62.6 m
[2016-04-14T20:54Z] INFO  13:54:45,724 ProgressMeter -      2:73152772   5748527.0     8.6 m      89.0 s       12.0%    71.1 m      62.5 m
[2016-04-14T20:55Z] INFO  13:55:15,786 ProgressMeter -      2:99154445   6148538.0     9.1 m      88.0 s       12.8%    70.7 m      61.6 m
[2016-04-14T20:55Z] INFO  13:55:45,814 ProgressMeter -     2:121728169   6448549.0     9.6 m      88.0 s       13.5%    70.9 m      61.3 m
[2016-04-14T20:56Z] INFO  13:56:15,815 ProgressMeter -     2:141986963   6748555.0    10.1 m      89.0 s       14.0%    72.0 m      62.0 m
[2016-04-14T20:56Z] INFO  13:56:46,268 ProgressMeter -     2:171242711   6948557.0    10.6 m      91.0 s       14.6%    72.1 m      61.5 m
[2016-04-14T20:57Z] INFO  13:57:16,345 ProgressMeter -     2:186666101   7248561.0    11.1 m      91.0 s       15.3%    72.1 m      61.1 m
[2016-04-14T20:57Z] INFO  13:57:46,363 ProgressMeter -     2:211515185   7648565.0    11.6 m      90.0 s       16.1%    71.6 m      60.0 m
[2016-04-14T20:58Z] INFO  13:58:16,517 ProgressMeter -     2:232262874   7948570.0    12.1 m      91.0 s       16.8%    71.6 m      59.6 m
[2016-04-14T20:58Z] INFO  13:58:34,038 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T20:58Z] INFO  13:58:34,281 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T20:58Z] INFO  13:58:46,715 ProgressMeter -       3:3221430   8332544.0    12.6 m      90.0 s       17.4%    72.2 m      59.6 m
[2016-04-14T20:59Z] INFO  13:59:16,791 ProgressMeter -      3:21792638   8632547.0    13.1 m      90.0 s       18.0%    72.7 m      59.6 m
[2016-04-14T20:59Z] INFO  13:59:46,807 ProgressMeter -      3:44932106   8932550.0    13.6 m      91.0 s       18.7%    72.6 m      59.0 m
[2016-04-14T21:00Z] INFO  14:00:16,825 ProgressMeter -      3:52566387   9432558.0    14.1 m      89.0 s       19.6%    71.6 m      57.5 m
[2016-04-14T21:00Z] INFO  14:00:46,826 ProgressMeter -      3:70014480   9732562.0    14.6 m      89.0 s       20.1%    72.4 m      57.9 m
[2016-04-14T21:01Z] INFO  14:01:16,883 ProgressMeter -     3:113392253   9932565.0    15.1 m      91.0 s       20.7%    72.7 m      57.7 m
[2016-04-14T21:01Z] INFO  14:01:47,444 ProgressMeter -     3:130748756   1.0232568E7    15.6 m      91.0 s       21.5%    72.5 m      57.0 m
[2016-04-14T21:02Z] INFO  14:02:17,445 ProgressMeter -     3:154834778   1.0532571E7    16.1 m      91.0 s       22.1%    72.7 m      56.6 m
[2016-04-14T21:02Z] INFO  14:02:48,046 ProgressMeter -     3:183511185   1.0732573E7    16.6 m      92.0 s       22.6%    73.3 m      56.7 m
[2016-04-14T21:03Z] INFO  14:03:07,886 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T21:03Z] INFO  14:03:08,020 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T21:03Z] INFO  14:03:18,138 ProgressMeter -        4:951991   1.112911E7    17.1 m      92.0 s       23.3%    73.2 m      56.2 m
[2016-04-14T21:03Z] INFO  14:03:48,149 ProgressMeter -      4:22820524   1.1429113E7    17.6 m      92.0 s       24.0%    73.1 m      55.6 m
[2016-04-14T21:04Z] INFO  14:04:18,151 ProgressMeter -      4:54457775   1.1729116E7    18.1 m      92.0 s       24.6%    73.6 m      55.6 m
[2016-04-14T21:04Z] INFO  14:04:48,287 ProgressMeter -      4:84406241   1.1929122E7    18.6 m      93.0 s       25.3%    73.6 m      55.0 m
[2016-04-14T21:05Z] INFO  14:05:18,288 ProgressMeter -     4:106576778   1.2129128E7    19.1 m      94.0 s       25.7%    74.2 m      55.1 m
[2016-04-14T21:05Z] INFO  14:05:48,290 ProgressMeter -     4:143130188   1.2429132E7    19.6 m      94.0 s       26.4%    74.1 m      54.5 m
[2016-04-14T21:06Z] INFO  14:06:18,291 ProgressMeter -     4:168155355   1.2629135E7    20.1 m      95.0 s       26.9%    74.6 m      54.5 m
[2016-04-14T21:06Z] INFO  14:06:33,597 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T21:06Z] INFO  14:06:33,859 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T21:06Z] INFO  14:06:48,292 ProgressMeter -       5:7414865   1.286802E7    20.6 m      96.0 s       27.5%    74.8 m      54.2 m
[2016-04-14T21:07Z] INFO  14:07:19,267 ProgressMeter -      5:37170190   1.3068022E7    21.1 m      96.0 s       28.0%    75.4 m      54.3 m
[2016-04-14T21:07Z] INFO  14:07:49,268 ProgressMeter -      5:65349819   1.3268024E7    21.6 m      97.0 s       28.5%    75.8 m      54.2 m
[2016-04-14T21:08Z] INFO  14:08:19,270 ProgressMeter -      5:86708789   1.3568028E7    22.1 m      97.0 s       29.1%    76.0 m      53.9 m
[2016-04-14T21:08Z] INFO  14:08:49,336 ProgressMeter -     5:122950115   1.376803E7    22.6 m      98.0 s       29.6%    76.2 m      53.6 m
[2016-04-14T21:09Z] INFO  14:09:19,389 ProgressMeter -     5:140567586   1.4168037E7    23.1 m      97.0 s       30.4%    75.9 m      52.8 m
[2016-04-14T21:09Z] INFO  14:09:49,414 ProgressMeter -     5:154397134   1.4568044E7    23.6 m      97.0 s       31.2%    75.7 m      52.1 m
[2016-04-14T21:10Z] INFO  14:10:18,159 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T21:10Z] INFO  14:10:18,424 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T21:10Z] INFO  14:10:20,494 ProgressMeter -     5:179106163   1.4868047E7    24.1 m      97.0 s       31.8%    75.8 m      51.7 m
[2016-04-14T21:10Z] INFO  14:10:50,496 ProgressMeter -      6:18427846   1.5143965E7    24.6 m      97.0 s       32.4%    76.0 m      51.4 m
[2016-04-14T21:11Z] INFO  14:11:21,884 ProgressMeter -      6:32805924   1.5643974E7    25.2 m      96.0 s       33.3%    75.6 m      50.4 m
[2016-04-14T21:11Z] INFO  14:11:51,885 ProgressMeter -      6:43970923   1.6143982E7    25.7 m      95.0 s       34.1%    75.2 m      49.5 m
[2016-04-14T21:12Z] INFO  14:12:21,887 ProgressMeter -      6:75875391   1.6343985E7    26.2 m      96.0 s       34.8%    75.1 m      48.9 m
[2016-04-14T21:12Z] INFO  14:12:51,947 ProgressMeter -     6:105845836   1.6643988E7    26.7 m      96.0 s       35.4%    75.4 m      48.7 m
[2016-04-14T21:13Z] INFO  14:13:21,949 ProgressMeter -     6:131520654   1.684399E7    27.2 m      96.0 s       36.0%    75.5 m      48.3 m
[2016-04-14T21:13Z] INFO  14:13:52,002 ProgressMeter -     6:155757591   1.7143994E7    27.7 m      96.0 s       36.7%    75.3 m      47.7 m
[2016-04-14T21:14Z] INFO  14:14:02,469 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T21:14Z] INFO  14:14:02,647 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T21:14Z] INFO  14:14:22,004 ProgressMeter -       7:5692153   1.7503542E7    28.2 m      96.0 s       37.4%    75.4 m      47.2 m
[2016-04-14T21:14Z] INFO  14:14:52,521 ProgressMeter -      7:30876318   1.7703544E7    28.7 m      97.0 s       37.9%    75.5 m      46.9 m
[2016-04-14T21:15Z] INFO  14:15:22,523 ProgressMeter -      7:51384348   1.8003547E7    29.2 m      97.0 s       38.4%    75.8 m      46.7 m
[2016-04-14T21:15Z] INFO  14:15:52,554 ProgressMeter -      7:82585360   1.8203551E7    29.7 m      97.0 s       39.0%    76.1 m      46.4 m
[2016-04-14T21:16Z] INFO  14:16:23,093 ProgressMeter -     7:100643703   1.8603556E7    30.2 m      97.0 s       39.8%    75.8 m      45.7 m
[2016-04-14T21:16Z] INFO  14:16:53,095 ProgressMeter -     7:123672955   1.890356E7    30.7 m      97.0 s       40.5%    75.8 m      45.1 m
[2016-04-14T21:17Z] INFO  14:17:23,312 ProgressMeter -     7:144532704   1.9303568E7    31.2 m      96.0 s       41.2%    75.6 m      44.4 m
[2016-04-14T21:17Z] INFO  14:17:40,659 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T21:17Z] INFO  14:17:40,792 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T21:17Z] INFO  14:17:53,314 ProgressMeter -       8:3611574   1.9617701E7    31.7 m      96.0 s       41.8%    75.7 m      44.1 m
[2016-04-14T21:18Z] INFO  14:18:23,318 ProgressMeter -      8:24369728   1.9917707E7    32.2 m      96.0 s       42.4%    75.9 m      43.8 m
[2016-04-14T21:18Z] INFO  14:18:53,319 ProgressMeter -      8:51569674   2.011771E7    32.7 m      97.0 s       43.0%    76.0 m      43.3 m
[2016-04-14T21:19Z] INFO  14:19:23,327 ProgressMeter -      8:77896423   2.0417714E7    33.2 m      97.0 s       43.5%    76.2 m      43.1 m
[2016-04-14T21:19Z] INFO  14:19:53,364 ProgressMeter -     8:104336887   2.0617717E7    33.7 m      98.0 s       44.0%    76.5 m      42.8 m
[2016-04-14T21:20Z] INFO  14:20:23,366 ProgressMeter -     8:133913872   2.0817723E7    34.2 m      98.0 s       44.5%    76.8 m      42.6 m
[2016-04-14T21:20Z] INFO  14:20:40,337 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T21:20Z] INFO  14:20:40,491 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T21:20Z] INFO  14:20:53,367 ProgressMeter -       9:4152263   2.1199917E7    34.7 m      98.0 s       45.2%    76.7 m      42.0 m
[2016-04-14T21:21Z] INFO  14:21:23,369 ProgressMeter -      9:34254451   2.139992E7    35.2 m      98.0 s       45.8%    76.8 m      41.7 m
[2016-04-14T21:21Z] INFO  14:21:53,844 ProgressMeter -      9:77752565   2.1699924E7    35.7 m      98.0 s       46.5%    76.8 m      41.1 m
[2016-04-14T21:22Z] INFO  14:22:23,846 ProgressMeter -      9:97695931   2.1999929E7    36.2 m      98.0 s       47.0%    77.0 m      40.8 m
[2016-04-14T21:22Z] INFO  14:22:53,847 ProgressMeter -     9:117168835   2.2299933E7    36.7 m      98.0 s       47.7%    76.9 m      40.2 m
[2016-04-14T21:23Z] INFO  14:23:23,850 ProgressMeter -     9:131592085   2.2699938E7    37.2 m      98.0 s       48.4%    76.9 m      39.7 m
[2016-04-14T21:23Z] INFO  14:23:49,656 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T21:23Z] INFO  14:23:49,807 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T21:23Z] INFO  14:23:53,899 ProgressMeter -     9:141111438   2.3199943E7    37.7 m      97.0 s       49.3%    76.5 m      38.8 m
[2016-04-14T21:24Z] INFO  14:24:23,901 ProgressMeter -     10:27493498   2.3453343E7    38.2 m      97.0 s       50.0%    76.4 m      38.2 m
[2016-04-14T21:24Z] INFO  14:24:54,573 ProgressMeter -     10:51748751   2.375335E7    38.7 m      97.0 s       50.5%    76.5 m      37.9 m
[2016-04-14T21:25Z] INFO  14:25:24,575 ProgressMeter -     10:75674680   2.4053354E7    39.2 m      97.0 s       51.2%    76.5 m      37.3 m
[2016-04-14T21:25Z] INFO  14:25:54,578 ProgressMeter -     10:95557509   2.4353357E7    39.7 m      97.0 s       51.7%    76.7 m      37.0 m
[2016-04-14T21:26Z] INFO  14:26:24,659 ProgressMeter -    10:112557472   2.4753362E7    40.2 m      97.0 s       52.6%    76.4 m      36.3 m
[2016-04-14T21:26Z] INFO  14:26:46,882 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T21:26Z] INFO  14:26:47,049 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T21:26Z] INFO  14:26:55,348 ProgressMeter -    10:135440325   2.5053368E7    40.7 m      97.0 s       53.3%    76.3 m      35.6 m
[2016-04-14T21:27Z] INFO  14:27:25,403 ProgressMeter -      11:7670826   2.5551816E7    41.2 m      96.0 s       54.1%    76.1 m      34.9 m
[2016-04-14T21:27Z] INFO  14:27:55,507 ProgressMeter -     11:25098992   2.585182E7    41.7 m      96.0 s       54.7%    76.2 m      34.5 m
[2016-04-14T21:28Z] INFO  14:28:26,611 ProgressMeter -     11:55406187   2.6151828E7    42.2 m      96.0 s       55.4%    76.2 m      34.0 m
[2016-04-14T21:28Z] INFO  14:28:56,613 ProgressMeter -     11:65546759   2.6751835E7    42.7 m      95.0 s       56.5%    75.6 m      32.9 m
[2016-04-14T21:29Z] INFO  14:29:26,615 ProgressMeter -     11:74988511   2.715184E7    43.2 m      95.0 s       57.2%    75.5 m      32.3 m
[2016-04-14T21:29Z] INFO  14:29:56,639 ProgressMeter -    11:103270442   2.7451844E7    43.7 m      95.0 s       57.9%    75.5 m      31.7 m
[2016-04-14T21:30Z] INFO  14:30:26,771 ProgressMeter -    11:119599302   2.7851849E7    44.2 m      95.0 s       58.6%    75.4 m      31.2 m
[2016-04-14T21:30Z] INFO  14:30:47,410 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T21:30Z] INFO  14:30:47,549 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T21:30Z] INFO  14:30:56,773 ProgressMeter -      12:3149647   2.8166142E7    44.7 m      95.0 s       59.3%    75.4 m      30.6 m
[2016-04-14T21:31Z] INFO  14:31:26,839 ProgressMeter -     12:15823889   2.8566146E7    45.2 m      95.0 s       60.0%    75.3 m      30.1 m
[2016-04-14T21:31Z] INFO  14:31:56,841 ProgressMeter -     12:44148380   2.8766148E7    45.7 m      95.0 s       60.7%    75.4 m      29.7 m
[2016-04-14T21:32Z] INFO  14:32:27,239 ProgressMeter -     12:56355501   2.9266156E7    46.2 m      94.0 s       61.6%    75.0 m      28.8 m
[2016-04-14T21:32Z] INFO  14:32:57,310 ProgressMeter -     12:72005698   2.9666164E7    46.7 m      94.0 s       62.3%    75.0 m      28.3 m
[2016-04-14T21:33Z] INFO  14:33:27,312 ProgressMeter -    12:104208931   2.9866166E7    47.2 m      94.0 s       63.0%    75.0 m      27.8 m
[2016-04-14T21:33Z] INFO  14:33:57,314 ProgressMeter -    12:121426869   3.0266173E7    47.7 m      94.0 s       63.7%    74.9 m      27.1 m
[2016-04-14T21:34Z] INFO  14:34:17,403 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T21:34Z] INFO  14:34:17,493 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T21:34Z] INFO  14:34:27,385 ProgressMeter -     13:24735103   3.0673018E7    48.2 m      94.0 s       64.5%    74.8 m      26.5 m
[2016-04-14T21:34Z] INFO  14:34:57,404 ProgressMeter -     13:42893413   3.0973021E7    48.7 m      94.0 s       65.1%    74.8 m      26.1 m
[2016-04-14T21:35Z] INFO  14:35:28,748 ProgressMeter -     13:78337325   3.1173025E7    49.3 m      94.0 s       65.6%    75.1 m      25.8 m
[2016-04-14T21:35Z] INFO  14:35:56,770 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T21:35Z] INFO  14:35:56,903 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T21:35Z] INFO  14:35:58,777 ProgressMeter -    13:111274793   3.1273027E7    49.8 m      95.0 s       66.0%    75.3 m      25.6 m
[2016-04-14T21:36Z] INFO  14:36:29,232 ProgressMeter -     14:30194843   3.1770229E7    50.3 m      94.0 s       66.9%    75.2 m      24.9 m
[2016-04-14T21:36Z] INFO  14:36:59,233 ProgressMeter -     14:57735510   3.1970235E7    50.8 m      95.0 s       67.5%    75.2 m      24.4 m
[2016-04-14T21:37Z] INFO  14:37:29,651 ProgressMeter -     14:77278941   3.2370241E7    51.3 m      95.0 s       68.4%    75.0 m      23.7 m
[2016-04-14T21:37Z] INFO  14:37:59,652 ProgressMeter -    14:101347628   3.2670245E7    51.8 m      95.0 s       69.0%    75.0 m      23.2 m
[2016-04-14T21:38Z] INFO  14:38:11,627 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T21:38Z] INFO  14:38:11,770 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T21:38Z] INFO  14:38:29,654 ProgressMeter -     15:30385404   3.3001932E7    52.3 m      95.0 s       69.6%    75.1 m      22.8 m
[2016-04-14T21:38Z] INFO  14:38:59,823 ProgressMeter -     15:43785382   3.3401939E7    52.8 m      94.0 s       70.4%    74.9 m      22.2 m
[2016-04-14T21:39Z] INFO  14:39:29,825 ProgressMeter -     15:60919786   3.370195E7    53.3 m      94.0 s       71.1%    74.9 m      21.6 m
[2016-04-14T21:40Z] INFO  14:40:00,342 ProgressMeter -     15:76005144   3.4101961E7    53.8 m      94.0 s       71.9%    74.8 m      21.0 m
[2016-04-14T21:40Z] INFO  14:40:30,345 ProgressMeter -     15:91432647   3.440197E7    54.3 m      94.0 s       72.6%    74.7 m      20.5 m
[2016-04-14T21:40Z] INFO  14:40:41,674 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T21:40Z] INFO  14:40:41,779 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T21:41Z] INFO  14:41:00,613 ProgressMeter -      16:2317702   3.4915686E7    54.8 m      94.0 s       73.4%    74.7 m      19.9 m
[2016-04-14T21:41Z] INFO  14:41:30,661 ProgressMeter -     16:15982497   3.521569E7    55.3 m      94.0 s       74.0%    74.7 m      19.4 m
[2016-04-14T21:42Z] INFO  14:42:00,727 ProgressMeter -     16:30456777   3.5615695E7    55.8 m      94.0 s       74.9%    74.5 m      18.7 m
[2016-04-14T21:42Z] INFO  14:42:30,813 ProgressMeter -     16:58622855   3.6015701E7    56.3 m      93.0 s       75.7%    74.4 m      18.1 m
[2016-04-14T21:43Z] INFO  14:43:00,936 ProgressMeter -     16:75633899   3.6515713E7    56.8 m      93.0 s       76.5%    74.2 m      17.4 m
[2016-04-14T21:43Z] INFO  14:43:23,760 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T21:43Z] INFO  14:43:23,925 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T21:43Z] INFO  14:43:32,406 ProgressMeter -      17:1992034   3.6920791E7    57.3 m      93.0 s       77.3%    74.2 m      16.9 m
[2016-04-14T21:44Z] INFO  14:44:02,408 ProgressMeter -      17:8793386   3.7420801E7    57.8 m      92.0 s       78.2%    74.0 m      16.2 m
[2016-04-14T21:44Z] INFO  14:44:32,410 ProgressMeter -     17:26939330   3.7820809E7    58.3 m      92.0 s       78.9%    73.9 m      15.6 m
[2016-04-14T21:45Z] INFO  14:45:02,432 ProgressMeter -     17:38936078   3.8320824E7    58.8 m      92.0 s       79.8%    73.7 m      14.9 m
[2016-04-14T21:45Z] INFO  14:45:32,763 ProgressMeter -     17:46894415   3.8820835E7    59.3 m      91.0 s       80.6%    73.6 m      14.2 m
[2016-04-14T21:46Z] INFO  14:46:02,800 ProgressMeter -     17:61950583   3.9120839E7    59.8 m      91.0 s       81.3%    73.6 m      13.7 m
[2016-04-14T21:46Z] INFO  14:46:32,802 ProgressMeter -     17:75208331   3.9620845E7    60.3 m      91.0 s       82.1%    73.5 m      13.1 m
[2016-04-14T21:46Z] INFO  14:46:46,148 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T21:46Z] INFO  14:46:46,268 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T21:47Z] INFO  14:47:03,665 ProgressMeter -      18:8829985   3.995583E7    60.8 m      91.0 s       82.9%    73.4 m      12.6 m
[2016-04-14T21:47Z] INFO  14:47:33,667 ProgressMeter -     18:43532380   4.0255833E7    61.3 m      91.0 s       83.6%    73.4 m      12.1 m
[2016-04-14T21:48Z] INFO  14:48:04,403 ProgressMeter -     18:67345163   4.0555839E7    61.9 m      91.0 s       84.1%    73.6 m      11.7 m
[2016-04-14T21:48Z] INFO  14:48:10,044 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T21:48Z] INFO  14:48:10,188 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T21:48Z] INFO  14:48:37,442 ProgressMeter -      19:4793850   4.098088E7    62.4 m      91.0 s       85.0%    73.4 m      11.0 m
[2016-04-14T21:49Z] INFO  14:49:07,921 ProgressMeter -     19:12691635   4.1580887E7    62.9 m      90.0 s       86.0%    73.2 m      10.3 m
[2016-04-14T21:49Z] INFO  14:49:39,927 ProgressMeter -     19:22379422   4.2180896E7    63.5 m      90.0 s       87.0%    72.9 m       9.5 m
[2016-04-14T21:50Z] INFO  14:50:10,549 ProgressMeter -     19:40030153   4.2680902E7    64.0 m      89.0 s       87.9%    72.8 m       8.8 m
[2016-04-14T21:50Z] INFO  14:50:40,956 ProgressMeter -     19:48343135   4.3280915E7    64.5 m      89.0 s       88.9%    72.5 m       8.0 m
[2016-04-14T21:51Z] INFO  14:51:11,089 ProgressMeter -     19:55866746   4.398093E7    65.0 m      88.0 s       90.0%    72.2 m       7.2 m
[2016-04-14T21:51Z] INFO  14:51:22,127 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T21:51Z] INFO  14:51:22,193 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T21:51Z] INFO  14:51:41,137 ProgressMeter -      20:6759613   4.4427159E7    65.5 m      88.0 s       90.9%    72.0 m       6.5 m
[2016-04-14T21:52Z] INFO  14:52:11,139 ProgressMeter -     20:30527006   4.4627164E7    66.0 m      88.0 s       91.3%    72.2 m       6.3 m
[2016-04-14T21:52Z] INFO  14:52:41,141 ProgressMeter -     20:44462871   4.5027172E7    66.5 m      88.0 s       92.1%    72.2 m       5.7 m
[2016-04-14T21:53Z] INFO  14:53:11,144 ProgressMeter -     20:61828123   4.5427178E7    67.0 m      88.0 s       92.7%    72.2 m       5.2 m
[2016-04-14T21:53Z] INFO  14:53:12,641 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T21:53Z] INFO  14:53:12,707 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T21:53Z] INFO  14:53:41,149 ProgressMeter -     21:37612280   4.5700517E7    67.5 m      88.0 s       93.4%    72.3 m       4.8 m
[2016-04-14T21:54Z] INFO  14:54:03,281 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T21:54Z] INFO  14:54:03,330 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T21:54Z] INFO  14:54:11,153 ProgressMeter -     22:18028374   4.6134571E7    68.0 m      88.0 s       94.0%    72.3 m       4.3 m
[2016-04-14T21:54Z] INFO  14:54:42,290 ProgressMeter -     22:31160372   4.6534577E7    68.5 m      88.0 s       94.9%    72.2 m       3.7 m
[2016-04-14T21:55Z] INFO  14:55:12,590 ProgressMeter -     22:42464580   4.6934583E7    69.0 m      88.0 s       95.6%    72.1 m       3.2 m
[2016-04-14T21:55Z] INFO  14:55:27,193 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T21:55Z] INFO  14:55:27,298 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T21:55Z] INFO  14:55:42,909 ProgressMeter -      X:10535669   4.7304327E7    69.5 m      88.0 s       96.3%    72.2 m       2.7 m
[2016-04-14T21:56Z] INFO  14:56:13,190 ProgressMeter -      X:41075857   4.7404329E7    70.0 m      88.0 s       96.9%    72.2 m       2.2 m
[2016-04-14T21:56Z] INFO  14:56:43,193 ProgressMeter -      X:67751783   4.7704332E7    70.5 m      88.0 s       97.7%    72.2 m     101.0 s
[2016-04-14T21:57Z] INFO  14:57:13,279 ProgressMeter -     X:109561184   4.7904334E7    71.0 m      88.0 s       98.5%    72.0 m      62.0 s
[2016-04-14T21:57Z] INFO  14:57:43,281 ProgressMeter -     X:151143147   4.8004335E7    71.5 m      89.0 s       99.4%    71.9 m      26.0 s
[2016-04-14T21:57Z] INFO  14:57:43,723 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T21:57Z] INFO  14:57:43,729 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T21:57Z] INFO  14:57:54,492 BaseRecalibrator - Calculating quantized quality scores...
[2016-04-14T21:57Z] INFO  14:57:54,641 BaseRecalibrator - Writing recalibration report...
[2016-04-14T21:57Z] INFO  14:57:56,013 BaseRecalibrator - ...done!
[2016-04-14T21:57Z] INFO  14:57:56,014 BaseRecalibrator - BaseRecalibrator was able to recalibrate 48233641 reads
[2016-04-14T21:57Z] INFO  14:57:56,015 ProgressMeter -            done   4.8233641E7    71.7 m      89.0 s      100.0%    71.7 m       0.0 s
[2016-04-14T21:57Z] INFO  14:57:56,016 ProgressMeter - Total runtime 4303.31 secs, 71.72 min, 1.20 hours
[2016-04-14T21:57Z] INFO  14:57:56,016 MicroScheduler - 6746495 reads were filtered out during the traversal out of approximately 54992603 total reads (12.27%)
[2016-04-14T21:57Z] INFO  14:57:56,016 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T21:57Z] INFO  14:57:56,017 MicroScheduler -   -> 4294294 reads (7.81% of total) failing DuplicateReadFilter
[2016-04-14T21:57Z] INFO  14:57:56,017 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-14T21:57Z] INFO  14:57:56,017 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T21:57Z] INFO  14:57:56,017 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-14T21:57Z] INFO  14:57:56,017 MicroScheduler -   -> 2452201 reads (4.46% of total) failing MappingQualityZeroFilter
[2016-04-14T21:57Z] INFO  14:57:56,018 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T21:57Z] INFO  14:57:56,018 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-14T21:57Z] INFO  14:57:58,181 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T21:57Z] Resource requests: ; memory: 1.00; cores: 1
[2016-04-14T21:57Z] Configuring 16 jobs to run, using 1 cores each with 1.00g of memory reserved for each job
[2016-04-14T21:57Z] multiprocessing: calc_callable_loci
[2016-04-14T21:57Z] bedtools genomecov: 9 : R14-18106_kapa-NGv3-PE100-NGv3-sort.bam
[2016-04-14T21:57Z] bedtools genomecov: 12 : R14-18106_kapa-NGv3-PE100-NGv3-sort.bam
[2016-04-14T21:57Z] bedtools genomecov: 13 : R14-18106_kapa-NGv3-PE100-NGv3-sort.bam
[2016-04-14T21:57Z] bedtools genomecov: 11 : R14-18106_kapa-NGv3-PE100-NGv3-sort.bam
[2016-04-14T21:57Z] bedtools genomecov: 14 : R14-18106_kapa-NGv3-PE100-NGv3-sort.bam
[2016-04-14T21:57Z] bedtools genomecov: 4 : R14-18106_kapa-NGv3-PE100-NGv3-sort.bam
[2016-04-14T21:57Z] bedtools genomecov: 15 : R14-18106_kapa-NGv3-PE100-NGv3-sort.bam
[2016-04-14T21:57Z] bedtools genomecov: 5 : R14-18106_kapa-NGv3-PE100-NGv3-sort.bam
[2016-04-14T21:57Z] bedtools genomecov: 16 : R14-18106_kapa-NGv3-PE100-NGv3-sort.bam
[2016-04-14T21:57Z] bedtools genomecov: 2 : R14-18106_kapa-NGv3-PE100-NGv3-sort.bam
[2016-04-14T21:57Z] bedtools genomecov: 1 : R14-18106_kapa-NGv3-PE100-NGv3-sort.bam
[2016-04-14T21:57Z] bedtools genomecov: 3 : R14-18106_kapa-NGv3-PE100-NGv3-sort.bam
[2016-04-14T21:57Z] bedtools genomecov: 6 : R14-18106_kapa-NGv3-PE100-NGv3-sort.bam
[2016-04-14T21:57Z] bedtools genomecov: 10 : R14-18106_kapa-NGv3-PE100-NGv3-sort.bam
[2016-04-14T21:57Z] bedtools genomecov: 7 : R14-18106_kapa-NGv3-PE100-NGv3-sort.bam
[2016-04-14T21:57Z] bedtools genomecov: 8 : R14-18106_kapa-NGv3-PE100-NGv3-sort.bam
[2016-04-14T21:59Z] bedtools groupby coverage: 13 : R14-18106_kapa-NGv3-PE100-NGv3-sort.bam
[2016-04-14T21:59Z] bedtools genomecov: 17 : R14-18106_kapa-NGv3-PE100-NGv3-sort.bam
[2016-04-14T22:01Z] bedtools groupby coverage: 14 : R14-18106_kapa-NGv3-PE100-NGv3-sort.bam
[2016-04-14T22:01Z] bedtools genomecov: 18 : R14-18106_kapa-NGv3-PE100-NGv3-sort.bam
[2016-04-14T22:01Z] bedtools groupby coverage: 8 : R14-18106_kapa-NGv3-PE100-NGv3-sort.bam
[2016-04-14T22:01Z] bedtools groupby coverage: 15 : R14-18106_kapa-NGv3-PE100-NGv3-sort.bam
[2016-04-14T22:01Z] bedtools genomecov: 19 : R14-18106_kapa-NGv3-PE100-NGv3-sort.bam
[2016-04-14T22:01Z] bedtools genomecov: 20 : R14-18106_kapa-NGv3-PE100-NGv3-sort.bam
[2016-04-14T22:01Z] bedtools groupby coverage: 4 : R14-18106_kapa-NGv3-PE100-NGv3-sort.bam
[2016-04-14T22:02Z] bedtools genomecov: 21 : R14-18106_kapa-NGv3-PE100-NGv3-sort.bam
[2016-04-14T22:02Z] bedtools groupby coverage: 10 : R14-18106_kapa-NGv3-PE100-NGv3-sort.bam
[2016-04-14T22:02Z] bedtools groupby coverage: 9 : R14-18106_kapa-NGv3-PE100-NGv3-sort.bam
[2016-04-14T22:02Z] bedtools genomecov: 22 : R14-18106_kapa-NGv3-PE100-NGv3-sort.bam
[2016-04-14T22:02Z] bedtools genomecov: X : R14-18106_kapa-NGv3-PE100-NGv3-sort.bam
[2016-04-14T22:02Z] bedtools groupby coverage: 16 : R14-18106_kapa-NGv3-PE100-NGv3-sort.bam
[2016-04-14T22:02Z] bedtools groupby coverage: 5 : R14-18106_kapa-NGv3-PE100-NGv3-sort.bam
[2016-04-14T22:02Z] bedtools genomecov: Y : R14-18106_kapa-NGv3-PE100-NGv3-sort.bam
[2016-04-14T22:02Z] bedtools groupby coverage: 7 : R14-18106_kapa-NGv3-PE100-NGv3-sort.bam
[2016-04-14T22:02Z] bedtools groupby coverage: Y : R14-18106_kapa-NGv3-PE100-NGv3-sort.bam
[2016-04-14T22:03Z] bedtools groupby coverage: 18 : R14-18106_kapa-NGv3-PE100-NGv3-sort.bam
[2016-04-14T22:03Z] bedtools groupby coverage: 21 : R14-18106_kapa-NGv3-PE100-NGv3-sort.bam
[2016-04-14T22:03Z] bedtools groupby coverage: 6 : R14-18106_kapa-NGv3-PE100-NGv3-sort.bam
[2016-04-14T22:03Z] bedtools groupby coverage: 12 : R14-18106_kapa-NGv3-PE100-NGv3-sort.bam
[2016-04-14T22:03Z] bedtools groupby coverage: 3 : R14-18106_kapa-NGv3-PE100-NGv3-sort.bam
[2016-04-14T22:03Z] bedtools groupby coverage: 11 : R14-18106_kapa-NGv3-PE100-NGv3-sort.bam
[2016-04-14T22:03Z] bedtools groupby coverage: 20 : R14-18106_kapa-NGv3-PE100-NGv3-sort.bam
[2016-04-14T22:03Z] bedtools groupby coverage: 22 : R14-18106_kapa-NGv3-PE100-NGv3-sort.bam
[2016-04-14T22:03Z] bedtools groupby coverage: X : R14-18106_kapa-NGv3-PE100-NGv3-sort.bam
[2016-04-14T22:03Z] bedtools groupby coverage: 17 : R14-18106_kapa-NGv3-PE100-NGv3-sort.bam
[2016-04-14T22:03Z] bedtools groupby coverage: 2 : R14-18106_kapa-NGv3-PE100-NGv3-sort.bam
[2016-04-14T22:03Z] bedtools groupby coverage: 19 : R14-18106_kapa-NGv3-PE100-NGv3-sort.bam
[2016-04-14T22:03Z] bedtools groupby coverage: 1 : R14-18106_kapa-NGv3-PE100-NGv3-sort.bam
[2016-04-14T22:04Z] multiprocessing: combine_bed
[2016-04-14T22:04Z] Resource requests: ; memory: 1.00; cores: 1
[2016-04-14T22:04Z] Configuring 16 jobs to run, using 1 cores each with 1.00g of memory reserved for each job
[2016-04-14T22:10Z] Recalibrating ['', 'R14-18106_kapa-NGv3-PE100-NGv3'] with GATK
[2016-04-14T22:10Z] GATK: BaseRecalibrator
[2016-04-14T22:10Z] INFO  15:10:10,968 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T22:10Z] INFO  15:10:10,970 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T22:10Z] INFO  15:10:10,970 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T22:10Z] INFO  15:10:10,970 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T22:10Z] INFO  15:10:10,974 HelpFormatter - Program Args: -T BaseRecalibrator -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/tx/tmp9t312u/R14-18106_kapa-NGv3-PE100-NGv3-sort.grp -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --knownSites /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bedprep/xgen-exome-research-panel-targets-cols1-2-noChr.bed --interval_set_rule INTERSECTION -nct 16 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-14T22:10Z] INFO  15:10:10,987 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T22:10Z] INFO  15:10:10,987 HelpFormatter - Date/Time: 2016/04/14 15:10:10
[2016-04-14T22:10Z] INFO  15:10:10,987 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T22:10Z] INFO  15:10:10,987 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T22:10Z] INFO  15:10:11,121 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T22:10Z] INFO  15:10:11,245 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T22:10Z] INFO  15:10:11,252 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T22:10Z] INFO  15:10:11,284 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.03
[2016-04-14T22:10Z] INFO  15:10:12,199 IntervalUtils - Processing 38874504 bp from intervals
[2016-04-14T22:10Z] WARN  15:10:12,203 IndexDictionaryUtils - Track knownSites doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T22:10Z] INFO  15:10:12,225 MicroScheduler - Running the GATK in parallel mode with 16 total threads, 16 CPU thread(s) for each of 1 data thread(s), of 16 processors available on this machine
[2016-04-14T22:10Z] INFO  15:10:12,321 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T22:10Z] INFO  15:10:12,959 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T22:10Z] INFO  15:10:12,959 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T22:10Z] INFO  15:10:12,960 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T22:10Z] INFO  15:10:12,960 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T22:10Z] INFO  15:10:12,983 BaseRecalibrator - The covariates being used here:
[2016-04-14T22:10Z] INFO  15:10:12,983 BaseRecalibrator - 	ReadGroupCovariate
[2016-04-14T22:10Z] INFO  15:10:12,984 BaseRecalibrator - 	QualityScoreCovariate
[2016-04-14T22:10Z] INFO  15:10:12,984 BaseRecalibrator - 	ContextCovariate
[2016-04-14T22:10Z] INFO  15:10:12,984 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-14T22:10Z] INFO  15:10:12,984 BaseRecalibrator - 	CycleCovariate
[2016-04-14T22:10Z] INFO  15:10:12,987 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T22:10Z] INFO  15:10:13,561 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T22:10Z] INFO  15:10:42,965 ProgressMeter -       1:8934953    200003.0    30.0 s       2.5 m        0.6%    89.8 m      89.3 m
[2016-04-14T22:11Z] INFO  15:11:12,973 ProgressMeter -      1:20417204    600009.0    60.0 s     100.0 s        1.4%    74.0 m      73.0 m
[2016-04-14T22:11Z] INFO  15:11:42,977 ProgressMeter -      1:33168237   1000017.0    90.0 s      90.0 s        2.2%    69.7 m      68.2 m
[2016-04-14T22:12Z] INFO  15:12:14,097 ProgressMeter -      1:45271854   1400029.0     2.0 m      86.0 s        3.0%    67.6 m      65.6 m
[2016-04-14T22:12Z] INFO  15:12:44,098 ProgressMeter -      1:64011780   1700034.0     2.5 m      88.0 s        3.6%    69.1 m      66.6 m
[2016-04-14T22:13Z] INFO  15:13:14,713 ProgressMeter -      1:89523877   1900036.0     3.0 m      95.0 s        4.2%    71.9 m      68.9 m
[2016-04-14T22:13Z] INFO  15:13:54,714 ProgressMeter -     1:117159995   2300040.0     3.7 m      96.0 s        5.1%    71.7 m      68.0 m
[2016-04-14T22:14Z] INFO  15:14:24,715 ProgressMeter -     1:153275033   2700048.0     4.2 m      93.0 s        5.9%    71.0 m      66.8 m
[2016-04-14T22:14Z] INFO  15:14:54,777 ProgressMeter -     1:161976249   3200057.0     4.7 m      88.0 s        6.9%    68.2 m      63.5 m
[2016-04-14T22:15Z] INFO  15:15:24,806 ProgressMeter -     1:181767993   3500062.0     5.2 m      89.0 s        7.5%    68.8 m      63.7 m
[2016-04-14T22:15Z] INFO  15:15:54,807 ProgressMeter -     1:203055140   3800069.0     5.7 m      89.0 s        8.2%    69.3 m      63.6 m
[2016-04-14T22:16Z] INFO  15:16:25,196 ProgressMeter -     1:225607539   4100075.0     6.2 m      90.0 s        9.1%    68.3 m      62.1 m
[2016-04-14T22:16Z] INFO  15:16:55,274 ProgressMeter -     1:241951329   4500079.0     6.7 m      89.0 s        9.8%    68.6 m      61.9 m
[2016-04-14T22:17Z] INFO  15:17:02,531 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T22:17Z] INFO  15:17:02,971 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T22:17Z] INFO  15:17:25,283 ProgressMeter -      2:16082539   4727009.0     7.2 m      91.0 s       10.3%    69.6 m      62.4 m
[2016-04-14T22:17Z] INFO  15:17:55,284 ProgressMeter -      2:40405662   5127014.0     7.7 m      90.0 s       11.2%    68.8 m      61.1 m
[2016-04-14T22:18Z] INFO  15:18:25,285 ProgressMeter -      2:64812653   5327017.0     8.2 m      92.0 s       11.8%    69.7 m      61.5 m
[2016-04-14T22:18Z] INFO  15:18:55,286 ProgressMeter -      2:87243546   5627021.0     8.7 m      92.0 s       12.5%    69.6 m      60.9 m
[2016-04-14T22:19Z] INFO  15:19:26,313 ProgressMeter -     2:112686826   5927025.0     9.2 m      93.0 s       13.2%    69.6 m      60.4 m
[2016-04-14T22:19Z] INFO  15:19:56,314 ProgressMeter -     2:134060754   6227031.0     9.7 m      93.0 s       13.8%    70.5 m      60.8 m
[2016-04-14T22:20Z] INFO  15:20:26,409 ProgressMeter -     2:166747478   6427035.0    10.2 m      95.0 s       14.4%    70.8 m      60.6 m
[2016-04-14T22:20Z] INFO  15:20:56,443 ProgressMeter -     2:183850986   6827042.0    10.7 m      94.0 s       15.3%    70.2 m      59.4 m
[2016-04-14T22:21Z] INFO  15:21:26,560 ProgressMeter -     2:207174791   7127045.0    11.2 m      94.0 s       16.0%    70.2 m      59.0 m
[2016-04-14T22:21Z] INFO  15:21:56,748 ProgressMeter -     2:228890191   7427048.0    11.7 m      94.0 s       16.7%    70.0 m      58.3 m
[2016-04-14T22:22Z] INFO  15:22:16,687 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T22:22Z] INFO  15:22:16,950 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T22:22Z] INFO  15:22:26,749 ProgressMeter -     2:242841495   7727053.0    12.2 m      94.0 s       17.4%    70.3 m      58.1 m
[2016-04-14T22:22Z] INFO  15:22:57,280 ProgressMeter -      3:25674203   8019227.0    12.7 m      95.0 s       18.0%    70.7 m      58.0 m
[2016-04-14T22:23Z] INFO  15:23:27,302 ProgressMeter -      3:44819668   8319231.0    13.2 m      95.0 s       18.7%    70.8 m      57.6 m
[2016-04-14T22:23Z] INFO  15:23:58,091 ProgressMeter -      3:52519827   8819239.0    13.8 m      93.0 s       19.6%    70.1 m      56.4 m
[2016-04-14T22:24Z] INFO  15:24:28,092 ProgressMeter -      3:69054359   9119245.0    14.3 m      93.0 s       20.1%    71.0 m      56.7 m
[2016-04-14T22:24Z] INFO  15:24:58,853 ProgressMeter -     3:119533889   9319247.0    14.8 m      95.0 s       20.8%    70.8 m      56.1 m
[2016-04-14T22:25Z] INFO  15:25:28,854 ProgressMeter -     3:139297798   9719255.0    15.3 m      94.0 s       21.7%    70.1 m      54.9 m
[2016-04-14T22:25Z] INFO  15:25:58,855 ProgressMeter -     3:164735483   9919257.0    15.8 m      95.0 s       22.3%    70.7 m      54.9 m
[2016-04-14T22:26Z] INFO  15:26:28,981 ProgressMeter -     3:185542774   1.0219267E7    16.3 m      95.0 s       22.8%    71.3 m      55.0 m
[2016-04-14T22:26Z] INFO  15:26:44,699 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T22:26Z] INFO  15:26:44,918 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T22:26Z] INFO  15:26:59,213 ProgressMeter -       4:2702120   1.0557629E7    16.8 m      95.0 s       23.5%    71.3 m      54.5 m
[2016-04-14T22:27Z] INFO  15:27:29,214 ProgressMeter -      4:27010580   1.0757632E7    17.3 m      96.0 s       24.1%    71.6 m      54.3 m
[2016-04-14T22:27Z] INFO  15:27:59,286 ProgressMeter -      4:65275120   1.1057637E7    17.8 m      96.0 s       24.7%    71.9 m      54.1 m
[2016-04-14T22:28Z] INFO  15:28:29,313 ProgressMeter -      4:88536545   1.1257639E7    18.3 m      97.0 s       25.4%    72.0 m      53.7 m
[2016-04-14T22:28Z] INFO  15:28:59,314 ProgressMeter -     4:111554190   1.1457645E7    18.8 m      98.0 s       25.9%    72.6 m      53.8 m
[2016-04-14T22:29Z] INFO  15:29:29,315 ProgressMeter -     4:145061845   1.1757649E7    19.3 m      98.0 s       26.5%    72.7 m      53.5 m
[2016-04-14T22:29Z] INFO  15:29:59,368 ProgressMeter -     4:175896819   1.1957655E7    19.8 m      99.0 s       27.0%    73.1 m      53.3 m
[2016-04-14T22:30Z] INFO  15:30:03,985 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T22:30Z] INFO  15:30:04,324 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T22:30Z] INFO  15:30:29,369 ProgressMeter -       5:9119146   1.210836E7    20.3 m     100.0 s       27.6%    73.6 m      53.3 m
[2016-04-14T22:30Z] INFO  15:30:59,371 ProgressMeter -      5:41510610   1.2408363E7    20.8 m     100.0 s       28.1%    73.8 m      53.1 m
[2016-04-14T22:31Z] INFO  15:31:29,383 ProgressMeter -      5:74491763   1.2608365E7    21.3 m     101.0 s       28.8%    74.0 m      52.7 m
[2016-04-14T22:31Z] INFO  15:31:59,384 ProgressMeter -     5:102530781   1.2808368E7    21.8 m     101.0 s       29.4%    74.1 m      52.4 m
[2016-04-14T22:32Z] INFO  15:32:29,431 ProgressMeter -     5:133861499   1.300837E7    22.3 m     102.0 s       29.9%    74.4 m      52.1 m
[2016-04-14T22:32Z] INFO  15:32:59,446 ProgressMeter -     5:147505359   1.3508378E7    22.8 m     101.0 s       30.8%    73.9 m      51.1 m
[2016-04-14T22:33Z] INFO  15:33:29,448 ProgressMeter -     5:171763357   1.3808383E7    23.3 m     101.0 s       31.5%    73.9 m      50.7 m
[2016-04-14T22:33Z] INFO  15:33:44,793 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T22:33Z] INFO  15:33:44,981 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T22:33Z] INFO  15:33:59,928 ProgressMeter -       6:6654850   1.4148292E7    23.8 m     100.0 s       32.1%    74.1 m      50.3 m
[2016-04-14T22:34Z] INFO  15:34:30,062 ProgressMeter -      6:28219708   1.4448299E7    24.3 m     100.0 s       32.6%    74.4 m      50.1 m
[2016-04-14T22:35Z] INFO  15:35:01,127 ProgressMeter -      6:36566706   1.4848308E7    24.8 m     100.0 s       33.6%    73.8 m      49.0 m
[2016-04-14T22:35Z] INFO  15:35:31,212 ProgressMeter -      6:54254760   1.5248314E7    25.3 m      99.0 s       34.5%    73.4 m      48.1 m
[2016-04-14T22:36Z] INFO  15:36:01,213 ProgressMeter -      6:87966280   1.5448317E7    25.8 m     100.0 s       35.1%    73.6 m      47.8 m
[2016-04-14T22:36Z] INFO  15:36:31,215 ProgressMeter -     6:118556780   1.5748321E7    26.3 m     100.0 s       35.7%    73.6 m      47.3 m
[2016-04-14T22:37Z] INFO  15:37:01,217 ProgressMeter -     6:143382185   1.5948323E7    26.8 m     100.0 s       36.3%    73.9 m      47.1 m
[2016-04-14T22:37Z] INFO  15:37:31,219 ProgressMeter -     6:161771140   1.6248327E7    27.3 m     100.0 s       36.9%    74.0 m      46.7 m
[2016-04-14T22:37Z] INFO  15:37:35,791 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T22:37Z] INFO  15:37:36,008 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T22:38Z] INFO  15:38:01,316 ProgressMeter -      7:11144969   1.6476135E7    27.8 m     101.0 s       37.5%    74.1 m      46.3 m
[2016-04-14T22:38Z] INFO  15:38:31,318 ProgressMeter -      7:35678071   1.6776138E7    28.3 m     101.0 s       38.0%    74.4 m      46.1 m
[2016-04-14T22:39Z] INFO  15:39:02,164 ProgressMeter -      7:66703531   1.697614E7    28.8 m     101.0 s       38.6%    74.7 m      45.8 m
[2016-04-14T22:39Z] INFO  15:39:32,298 ProgressMeter -      7:90339042   1.7176143E7    29.3 m     102.0 s       39.1%    74.9 m      45.6 m
[2016-04-14T22:40Z] INFO  15:40:02,299 ProgressMeter -     7:102038164   1.7576149E7    29.8 m     101.0 s       39.9%    74.7 m      44.9 m
[2016-04-14T22:40Z] INFO  15:40:32,301 ProgressMeter -     7:124532466   1.7876155E7    30.3 m     101.0 s       40.5%    74.9 m      44.6 m
[2016-04-14T22:41Z] INFO  15:41:02,879 ProgressMeter -     7:144532749   1.8176158E7    30.8 m     101.0 s       41.2%    74.7 m      43.9 m
[2016-04-14T22:41Z] INFO  15:41:11,159 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T22:41Z] INFO  15:41:11,418 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T22:41Z] INFO  15:41:33,039 ProgressMeter -       8:4851980   1.8455084E7    31.3 m     101.0 s       41.8%    74.9 m      43.6 m
[2016-04-14T22:42Z] INFO  15:42:04,288 ProgressMeter -      8:26726566   1.875509E7    31.9 m     101.0 s       42.4%    75.1 m      43.2 m
[2016-04-14T22:42Z] INFO  15:42:34,290 ProgressMeter -      8:56436198   1.8955093E7    32.4 m     102.0 s       43.1%    75.1 m      42.7 m
[2016-04-14T22:43Z] INFO  15:43:04,291 ProgressMeter -      8:88885714   1.9155096E7    32.9 m     102.0 s       43.6%    75.3 m      42.4 m
[2016-04-14T22:43Z] INFO  15:43:34,292 ProgressMeter -     8:110986531   1.9355102E7    33.4 m     103.0 s       44.1%    75.6 m      42.2 m
[2016-04-14T22:44Z] INFO  15:44:04,467 ProgressMeter -     8:142222360   1.9555104E7    33.9 m     103.0 s       44.6%    75.9 m      42.0 m
[2016-04-14T22:44Z] INFO  15:44:12,587 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T22:44Z] INFO  15:44:12,732 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T22:44Z] INFO  15:44:35,895 ProgressMeter -       9:8733935   2.0036803E7    34.4 m     102.0 s       45.4%    75.8 m      41.4 m
[2016-04-14T22:45Z] INFO  15:45:05,896 ProgressMeter -      9:35825717   2.0236808E7    34.9 m     103.0 s       46.0%    75.8 m      40.9 m
[2016-04-14T22:45Z] INFO  15:45:35,898 ProgressMeter -      9:84610166   2.0536814E7    35.4 m     103.0 s       46.6%    75.9 m      40.6 m
[2016-04-14T22:46Z] INFO  15:46:05,899 ProgressMeter -     9:102822433   2.083682E7    35.9 m     103.0 s       47.2%    76.0 m      40.1 m
[2016-04-14T22:46Z] INFO  15:46:36,027 ProgressMeter -     9:124921989   2.1136825E7    36.4 m     103.0 s       47.9%    75.9 m      39.5 m
[2016-04-14T22:47Z] INFO  15:47:06,825 ProgressMeter -     9:137328522   2.153683E7    36.9 m     102.0 s       48.8%    75.5 m      38.7 m
[2016-04-14T22:47Z] INFO  15:47:16,886 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T22:47Z] INFO  15:47:16,951 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T22:47Z] INFO  15:47:36,882 ProgressMeter -     10:13933832   2.1957451E7    37.4 m     102.0 s       49.6%    75.4 m      38.0 m
[2016-04-14T22:48Z] INFO  15:48:06,977 ProgressMeter -     10:44873298   2.2257455E7    37.9 m     102.0 s       50.3%    75.4 m      37.5 m
[2016-04-14T22:48Z] INFO  15:48:37,095 ProgressMeter -     10:74034993   2.255746E7    38.4 m     102.0 s       51.1%    75.2 m      36.8 m
[2016-04-14T22:49Z] INFO  15:49:07,097 ProgressMeter -     10:96612722   2.2857464E7    38.9 m     102.0 s       51.8%    75.1 m      36.2 m
[2016-04-14T22:49Z] INFO  15:49:37,886 ProgressMeter -    10:116606019   2.3257469E7    39.4 m     101.0 s       52.7%    74.7 m      35.3 m
[2016-04-14T22:49Z] INFO  15:49:56,805 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T22:49Z] INFO  15:49:56,970 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T22:50Z] INFO  15:50:08,603 ProgressMeter -       11:551314   2.3641509E7    39.9 m     101.0 s       53.4%    74.7 m      34.8 m
[2016-04-14T22:50Z] INFO  15:50:38,604 ProgressMeter -      11:9048983   2.4041522E7    40.4 m     100.0 s       54.2%    74.5 m      34.1 m
[2016-04-14T22:51Z] INFO  15:51:08,867 ProgressMeter -     11:32125979   2.4341525E7    40.9 m     100.0 s       54.8%    74.6 m      33.7 m
[2016-04-14T22:51Z] INFO  15:51:38,868 ProgressMeter -     11:57463402   2.4641528E7    41.4 m     100.0 s       55.6%    74.5 m      33.1 m
[2016-04-14T22:52Z] INFO  15:52:10,548 ProgressMeter -     11:65732052   2.5141536E7    42.0 m     100.0 s       56.5%    74.2 m      32.3 m
[2016-04-14T22:52Z] INFO  15:52:40,549 ProgressMeter -     11:76900481   2.5541543E7    42.5 m      99.0 s       57.3%    74.1 m      31.6 m
[2016-04-14T22:53Z] INFO  15:53:10,550 ProgressMeter -    11:110036147   2.5841548E7    43.0 m      99.0 s       58.1%    73.9 m      31.0 m
[2016-04-14T22:53Z] INFO  15:53:40,637 ProgressMeter -    11:125848258   2.6241554E7    43.5 m      99.0 s       58.9%    73.7 m      30.3 m
[2016-04-14T22:53Z] INFO  15:53:50,996 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T22:53Z] INFO  15:53:51,154 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T22:54Z] INFO  15:54:11,661 ProgressMeter -      12:6969576   2.656034E7    44.0 m      99.0 s       59.6%    73.8 m      29.8 m
[2016-04-14T22:54Z] INFO  15:54:41,663 ProgressMeter -     12:27919704   2.6860345E7    44.5 m      99.0 s       60.3%    73.7 m      29.3 m
[2016-04-14T22:55Z] INFO  15:55:11,665 ProgressMeter -     12:49916638   2.7160349E7    45.0 m      99.0 s       61.0%    73.8 m      28.8 m
[2016-04-14T22:55Z] INFO  15:55:41,823 ProgressMeter -     12:58015527   2.7660358E7    45.5 m      98.0 s       62.0%    73.4 m      27.9 m
[2016-04-14T22:56Z] INFO  15:56:11,825 ProgressMeter -     12:82752532   2.7860361E7    46.0 m      99.0 s       62.5%    73.6 m      27.6 m
[2016-04-14T22:56Z] INFO  15:56:41,828 ProgressMeter -    12:109882329   2.8160365E7    46.5 m      99.0 s       63.2%    73.5 m      27.1 m
[2016-04-14T22:57Z] INFO  15:57:12,190 ProgressMeter -    12:124428940   2.8560369E7    47.0 m      98.0 s       64.1%    73.3 m      26.4 m
[2016-04-14T22:57Z] INFO  15:57:22,939 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T22:57Z] INFO  15:57:23,053 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T22:57Z] INFO  15:57:42,204 ProgressMeter -     13:31903853   2.8920202E7    47.5 m      98.0 s       64.8%    73.3 m      25.8 m
[2016-04-14T22:58Z] INFO  15:58:12,206 ProgressMeter -     13:52603629   2.9120206E7    48.0 m      98.0 s       65.4%    73.4 m      25.4 m
[2016-04-14T22:58Z] INFO  15:58:42,209 ProgressMeter -    13:100992531   2.9320209E7    48.5 m      99.0 s       65.8%    73.6 m      25.1 m
[2016-04-14T22:58Z] INFO  15:58:54,603 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T22:58Z] INFO  15:58:54,657 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T22:59Z] INFO  15:59:13,928 ProgressMeter -     14:23893315   2.9673903E7    49.0 m      99.0 s       66.6%    73.5 m      24.5 m
[2016-04-14T22:59Z] INFO  15:59:43,930 ProgressMeter -     14:48143796   2.9973908E7    49.5 m      99.0 s       67.2%    73.6 m      24.1 m
[2016-04-14T23:00Z] INFO  16:00:13,958 ProgressMeter -     14:69062349   3.0273911E7    50.0 m      99.0 s       67.9%    73.6 m      23.6 m
[2016-04-14T23:00Z] INFO  16:00:44,047 ProgressMeter -     14:91059972   3.0573916E7    50.5 m      99.0 s       68.6%    73.6 m      23.1 m
[2016-04-14T23:01Z] INFO  16:01:05,551 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:01Z] INFO  16:01:05,687 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:01Z] INFO  16:01:14,971 ProgressMeter -     15:22742866   3.1014106E7    51.0 m      98.0 s       69.5%    73.5 m      22.4 m
[2016-04-14T23:01Z] INFO  16:01:44,974 ProgressMeter -     15:42560178   3.1314111E7    51.5 m      98.0 s       70.3%    73.3 m      21.8 m
[2016-04-14T23:02Z] INFO  16:02:15,475 ProgressMeter -     15:59225632   3.1614116E7    52.0 m      98.0 s       71.1%    73.2 m      21.2 m
[2016-04-14T23:02Z] INFO  16:02:46,324 ProgressMeter -     15:76005036   3.2014122E7    52.6 m      98.0 s       71.9%    73.1 m      20.5 m
[2016-04-14T23:03Z] INFO  16:03:16,326 ProgressMeter -     15:91432802   3.2314127E7    53.1 m      98.0 s       72.6%    73.0 m      20.0 m
[2016-04-14T23:03Z] INFO  16:03:25,597 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:03Z] INFO  16:03:25,757 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:03Z] INFO  16:03:46,393 ProgressMeter -      16:3119371   3.2822952E7    53.6 m      97.0 s       73.5%    72.9 m      19.3 m
[2016-04-14T23:04Z] INFO  16:04:16,395 ProgressMeter -     16:19528525   3.3122956E7    54.1 m      97.0 s       74.2%    72.9 m      18.8 m
[2016-04-14T23:04Z] INFO  16:04:46,398 ProgressMeter -     16:31374630   3.3522961E7    54.6 m      97.0 s       75.1%    72.7 m      18.1 m
[2016-04-14T23:05Z] INFO  16:05:16,426 ProgressMeter -     16:66424494   3.3822964E7    55.1 m      97.0 s       75.7%    72.7 m      17.7 m
[2016-04-14T23:05Z] INFO  16:05:47,031 ProgressMeter -     16:76311671   3.4322971E7    55.6 m      97.0 s       76.5%    72.6 m      17.0 m
[2016-04-14T23:06Z] INFO  16:06:05,239 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:06Z] INFO  16:06:05,396 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:06Z] INFO  16:06:17,407 ProgressMeter -      17:2266428   3.463599E7    56.1 m      97.0 s       77.3%    72.5 m      16.5 m
[2016-04-14T23:06Z] INFO  16:06:48,247 ProgressMeter -     17:10370010   3.5135997E7    56.6 m      96.0 s       78.2%    72.3 m      15.7 m
[2016-04-14T23:07Z] INFO  16:07:18,410 ProgressMeter -     17:27581386   3.5536008E7    57.1 m      96.0 s       79.0%    72.3 m      15.2 m
[2016-04-14T23:07Z] INFO  16:07:48,523 ProgressMeter -     17:40344691   3.6036014E7    57.6 m      95.0 s       80.0%    72.0 m      14.4 m
[2016-04-14T23:08Z] INFO  16:08:18,880 ProgressMeter -     17:49825911   3.6536024E7    58.1 m      95.0 s       80.9%    71.8 m      13.7 m
[2016-04-14T23:08Z] INFO  16:08:48,883 ProgressMeter -     17:66551903   3.6836029E7    58.6 m      95.0 s       81.6%    71.8 m      13.2 m
[2016-04-14T23:09Z] INFO  16:09:18,885 ProgressMeter -     17:79687585   3.733604E7    59.1 m      94.0 s       82.5%    71.6 m      12.5 m
[2016-04-14T23:09Z] INFO  16:09:21,095 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:09Z] INFO  16:09:21,210 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:09Z] INFO  16:09:48,889 ProgressMeter -     18:21119945   3.7555957E7    59.6 m      95.0 s       83.2%    71.6 m      12.1 m
[2016-04-14T23:10Z] INFO  16:10:18,964 ProgressMeter -     18:48450539   3.7855966E7    60.1 m      95.0 s       83.8%    71.8 m      11.7 m
[2016-04-14T23:10Z] INFO  16:10:39,870 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:10Z] INFO  16:10:40,006 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:10Z] INFO  16:10:48,967 ProgressMeter -     18:72633028   3.805597E7    60.6 m      95.0 s       84.2%    72.0 m      11.4 m
[2016-04-14T23:11Z] INFO  16:11:19,021 ProgressMeter -      19:5788068   3.8543069E7    61.1 m      95.0 s       85.1%    71.8 m      10.7 m
[2016-04-14T23:11Z] INFO  16:11:49,568 ProgressMeter -     19:13876962   3.9043076E7    61.6 m      94.0 s       86.1%    71.5 m       9.9 m
[2016-04-14T23:12Z] INFO  16:12:20,501 ProgressMeter -     19:23543396   3.9543085E7    62.1 m      94.0 s       87.0%    71.4 m       9.3 m
[2016-04-14T23:12Z] INFO  16:12:50,503 ProgressMeter -     19:40322639   4.0043096E7    62.6 m      93.0 s       87.9%    71.2 m       8.6 m
[2016-04-14T23:13Z] INFO  16:13:21,315 ProgressMeter -     19:48480837   4.0543105E7    63.1 m      93.0 s       88.9%    71.0 m       7.9 m
[2016-04-14T23:13Z] INFO  16:13:51,394 ProgressMeter -     19:54930338   4.1043112E7    63.6 m      93.0 s       89.9%    70.8 m       7.2 m
[2016-04-14T23:14Z] INFO  16:14:04,265 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:14Z] INFO  16:14:04,330 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:14Z] INFO  16:14:21,547 ProgressMeter -      20:4168133   4.1614386E7    64.1 m      92.0 s       90.8%    70.6 m       6.5 m
[2016-04-14T23:14Z] INFO  16:14:51,554 ProgressMeter -     20:31115707   4.1814391E7    64.6 m      92.0 s       91.4%    70.7 m       6.1 m
[2016-04-14T23:15Z] INFO  16:15:21,754 ProgressMeter -     20:45174323   4.2214396E7    65.1 m      92.0 s       92.2%    70.7 m       5.5 m
[2016-04-14T23:15Z] INFO  16:15:46,637 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:15Z] INFO  16:15:46,699 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:15Z] INFO  16:15:51,756 ProgressMeter -     20:62904950   4.26144E7    65.6 m      92.0 s       92.9%    70.6 m       5.0 m
[2016-04-14T23:16Z] INFO  16:16:21,793 ProgressMeter -     21:41684293   4.2896073E7    66.1 m      92.0 s       93.5%    70.7 m       4.6 m
[2016-04-14T23:16Z] INFO  16:16:31,990 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:16Z] INFO  16:16:32,100 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:16Z] INFO  16:16:51,824 ProgressMeter -     22:21567525   4.3294817E7    66.6 m      92.0 s       94.3%    70.6 m       4.0 m
[2016-04-14T23:17Z] INFO  16:17:23,230 ProgressMeter -     22:36710322   4.3694826E7    67.2 m      92.0 s       95.1%    70.6 m       3.5 m
[2016-04-14T23:17Z] INFO  16:17:52,711 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:17Z] INFO  16:17:52,812 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:17Z] INFO  16:17:53,233 ProgressMeter -     22:50658775   4.4094833E7    67.7 m      92.0 s       96.0%    70.5 m       2.9 m
[2016-04-14T23:18Z] INFO  16:18:24,213 ProgressMeter -      X:19973606   4.436951E7    68.2 m      92.0 s       96.6%    70.6 m       2.4 m
[2016-04-14T23:18Z] INFO  16:18:54,215 ProgressMeter -      X:53106165   4.4469511E7    68.7 m      92.0 s       97.3%    70.6 m     112.0 s
[2016-04-14T23:19Z] INFO  16:19:24,441 ProgressMeter -     X:100178109   4.4669514E7    69.2 m      92.0 s       98.2%    70.5 m      76.0 s
[2016-04-14T23:19Z] INFO  16:19:54,444 ProgressMeter -     X:136652241   4.4969517E7    69.7 m      92.0 s       99.2%    70.2 m      33.0 s
[2016-04-14T23:20Z] INFO  16:20:06,222 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:20Z] INFO  16:20:06,228 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:20Z] INFO  16:20:16,198 BaseRecalibrator - Calculating quantized quality scores...
[2016-04-14T23:20Z] INFO  16:20:16,350 BaseRecalibrator - Writing recalibration report...
[2016-04-14T23:20Z] INFO  16:20:17,605 BaseRecalibrator - ...done!
[2016-04-14T23:20Z] INFO  16:20:17,606 BaseRecalibrator - BaseRecalibrator was able to recalibrate 45149312 reads
[2016-04-14T23:20Z] INFO  16:20:17,607 ProgressMeter -            done   4.5149312E7    70.1 m      93.0 s      100.0%    70.1 m       0.0 s
[2016-04-14T23:20Z] INFO  16:20:17,608 ProgressMeter - Total runtime 4204.65 secs, 70.08 min, 1.17 hours
[2016-04-14T23:20Z] INFO  16:20:17,608 MicroScheduler - 6096922 reads were filtered out during the traversal out of approximately 51259518 total reads (11.89%)
[2016-04-14T23:20Z] INFO  16:20:17,608 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:20Z] INFO  16:20:17,608 MicroScheduler -   -> 3805874 reads (7.42% of total) failing DuplicateReadFilter
[2016-04-14T23:20Z] INFO  16:20:17,609 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-14T23:20Z] INFO  16:20:17,609 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:20Z] INFO  16:20:17,609 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-14T23:20Z] INFO  16:20:17,610 MicroScheduler -   -> 2291048 reads (4.47% of total) failing MappingQualityZeroFilter
[2016-04-14T23:20Z] INFO  16:20:17,610 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:20Z] INFO  16:20:17,610 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-14T23:20Z] INFO  16:20:19,953 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:20Z] multiprocessing: combine_sample_regions
[2016-04-14T23:20Z] Identified 203 parallel analysis blocks
Block sizes:
  min: 145275
  5%: 7709077.6
  25%: 15513072.5
  median: 15541927.0
  75%: 15756544.0
  95%: 17873479.4
  99%: 32852337.34
  max: 43695667
Between block sizes:
  min: 281
  5%: 504.4
  25%: 1765.5
  median: 5200.0
  75%: 34422.5
  95%: 227813.5
  99%: 784452.26
  max: 4925057

[2016-04-14T23:20Z] Timing: structural variation initial
[2016-04-14T23:20Z] Timing: hla typing
[2016-04-14T23:20Z] Resource requests: gatk, gatk-haplotype, picard, platypus; memory: 3.50, 3.50, 3.50, 2.00; cores: 1, 1, 1, 16
[2016-04-14T23:20Z] Configuring 16 jobs to run, using 1 cores each with 3.50g of memory reserved for each job
[2016-04-14T23:20Z] Timing: alignment post-processing
[2016-04-14T23:20Z] multiprocessing: piped_bamprep
[2016-04-14T23:20Z] GATK pre-alignment ('1', 15545821, 31186478) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:20Z] GATK pre-alignment ('1', 31187093, 46714270) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:20Z] GATK pre-alignment ('1', 46715671, 62228851) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:20Z] GATK pre-alignment ('1', 62231950, 77749296) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:20Z] GATK pre-alignment ('1', 77752625, 93297674) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:20Z] GATK pre-alignment ('1', 93298945, 108993401) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:20Z] GATK pre-alignment ('1', 108994811, 143767848) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:20Z] GATK pre-alignment ('1', 143897546, 159410511) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:20Z] GATK pre-alignment ('1', 159504867, 175046963) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:20Z] GATK pre-alignment ('1', 175048468, 192127886) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:20Z] GATK pre-alignment ('1', 192128349, 207640257) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:20Z] GATK pre-alignment ('1', 207641871, 223156451) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:20Z] GATK pre-alignment ('1', 223162737, 240072524) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:20Z] GATK pre-alignment ('1', 240255409, 249250621) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:20Z] GATK pre-alignment ('2', 0, 15514844) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:20Z] GATK pre-alignment ('1', 0, 15541927) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:20Z] INFO  16:20:40,046 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:20Z] INFO  16:20:40,050 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:20Z] INFO  16:20:40,050 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:20Z] INFO  16:20:40,051 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:20Z] INFO  16:20:40,056 HelpFormatter - Program Args: -T PrintReads -L 1:77752626-93297674 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/1/tx/tmpbHmUOX/R14-18102_kapa-NGv3-PE100-NGv3-sort-1_77752625_93297674-prep-prealign.bam
[2016-04-14T23:20Z] INFO  16:20:40,097 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:20Z] INFO  16:20:40,098 HelpFormatter - Date/Time: 2016/04/14 16:20:40
[2016-04-14T23:20Z] INFO  16:20:40,098 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:20Z] INFO  16:20:40,099 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:20Z] INFO  16:20:40,293 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:20Z] INFO  16:20:40,302 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:20Z] INFO  16:20:40,308 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:20Z] INFO  16:20:40,309 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:20Z] INFO  16:20:40,310 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:20Z] INFO  16:20:40,326 HelpFormatter - Program Args: -T PrintReads -L 1:62231951-77749296 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/1/tx/tmpvVOgtk/R14-18102_kapa-NGv3-PE100-NGv3-sort-1_62231950_77749296-prep-prealign.bam
[2016-04-14T23:20Z] INFO  16:20:40,344 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:20Z] INFO  16:20:40,344 HelpFormatter - Date/Time: 2016/04/14 16:20:40
[2016-04-14T23:20Z] INFO  16:20:40,344 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:20Z] INFO  16:20:40,345 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:20Z] INFO  16:20:40,356 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:20Z] INFO  16:20:40,360 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:20Z] INFO  16:20:40,361 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:20Z] INFO  16:20:40,362 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:20Z] INFO  16:20:40,396 HelpFormatter - Program Args: -T PrintReads -L 1:93298946-108993401 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/1/tx/tmpeliegb/R14-18102_kapa-NGv3-PE100-NGv3-sort-1_93298945_108993401-prep-prealign.bam
[2016-04-14T23:20Z] INFO  16:20:40,411 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:20Z] INFO  16:20:40,412 HelpFormatter - Date/Time: 2016/04/14 16:20:40
[2016-04-14T23:20Z] INFO  16:20:40,412 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:20Z] INFO  16:20:40,413 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:20Z] INFO  16:20:40,545 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:20Z] INFO  16:20:40,548 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:20Z] INFO  16:20:40,548 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:20Z] INFO  16:20:40,549 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:20Z] INFO  16:20:40,553 HelpFormatter - Program Args: -T PrintReads -L 1:108994812-143767848 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/1/tx/tmpn8s2ke/R14-18102_kapa-NGv3-PE100-NGv3-sort-1_108994811_143767848-prep-prealign.bam
[2016-04-14T23:20Z] INFO  16:20:40,568 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:20Z] INFO  16:20:40,582 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:20Z] INFO  16:20:40,582 HelpFormatter - Date/Time: 2016/04/14 16:20:40
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[2016-04-14T23:20Z] INFO  16:20:40,583 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:20Z] INFO  16:20:40,648 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:20Z] INFO  16:20:40,652 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:20Z] INFO  16:20:40,652 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:20Z] INFO  16:20:40,653 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:20Z] INFO  16:20:40,657 HelpFormatter - Program Args: -T PrintReads -L 1:15545822-31186478 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/1/tx/tmpF9gje5/R14-18102_kapa-NGv3-PE100-NGv3-sort-1_15545821_31186478-prep-prealign.bam
[2016-04-14T23:20Z] INFO  16:20:40,668 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:20Z] INFO  16:20:40,674 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:20Z] INFO  16:20:40,697 HelpFormatter - Date/Time: 2016/04/14 16:20:40
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[2016-04-14T23:20Z] INFO  16:20:40,698 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:20Z] INFO  16:20:40,855 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:20Z] INFO  16:20:40,952 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:20Z] INFO  16:20:40,956 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:20Z] INFO  16:20:40,959 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:20Z] INFO  16:20:40,960 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:20Z] INFO  16:20:40,961 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:20Z] INFO  16:20:40,965 HelpFormatter - Program Args: -T PrintReads -L 1:46715672-62228851 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/1/tx/tmpZkb27r/R14-18102_kapa-NGv3-PE100-NGv3-sort-1_46715671_62228851-prep-prealign.bam
[2016-04-14T23:20Z] INFO  16:20:40,993 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:20Z] INFO  16:20:40,994 HelpFormatter - Date/Time: 2016/04/14 16:20:40
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[2016-04-14T23:20Z] INFO  16:20:41,008 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:20Z] INFO  16:20:41,015 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:20Z] INFO  16:20:41,016 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:20Z] INFO  16:20:41,016 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:20Z] INFO  16:20:41,022 HelpFormatter - Program Args: -T PrintReads -L 1:192128350-207640257 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/1/tx/tmpKL4UjI/R14-18102_kapa-NGv3-PE100-NGv3-sort-1_192128349_207640257-prep-prealign.bam
[2016-04-14T23:20Z] INFO  16:20:41,027 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:20Z] INFO  16:20:41,031 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:20Z] INFO  16:20:41,032 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:20Z] INFO  16:20:41,033 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:20Z] INFO  16:20:41,038 HelpFormatter - Program Args: -T PrintReads -L 1:31187094-46714270 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/1/tx/tmpDATNCb/R14-18102_kapa-NGv3-PE100-NGv3-sort-1_31187093_46714270-prep-prealign.bam
[2016-04-14T23:20Z] INFO  16:20:41,053 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:20Z] INFO  16:20:41,061 HelpFormatter - Date/Time: 2016/04/14 16:20:41
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[2016-04-14T23:20Z] INFO  16:20:41,063 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:20Z] INFO  16:20:41,075 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:20Z] INFO  16:20:41,076 HelpFormatter - Date/Time: 2016/04/14 16:20:41
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[2016-04-14T23:20Z] INFO  16:20:41,077 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:20Z] INFO  16:20:41,077 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:20Z] INFO  16:20:41,078 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:20Z] INFO  16:20:41,078 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:20Z] INFO  16:20:41,079 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:20Z] INFO  16:20:41,084 HelpFormatter - Program Args: -T PrintReads -L 1:159504868-175046963 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/1/tx/tmpjX414m/R14-18102_kapa-NGv3-PE100-NGv3-sort-1_159504867_175046963-prep-prealign.bam
[2016-04-14T23:20Z] INFO  16:20:41,115 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:20Z] INFO  16:20:41,116 HelpFormatter - Date/Time: 2016/04/14 16:20:41
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[2016-04-14T23:20Z] INFO  16:20:41,284 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:20Z] INFO  16:20:41,309 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:20Z] INFO  16:20:41,315 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:20Z] INFO  16:20:41,351 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:20Z] INFO  16:20:41,353 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:20Z] INFO  16:20:41,354 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:20Z] INFO  16:20:41,354 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:20Z] INFO  16:20:41,358 HelpFormatter - Program Args: -T PrintReads -L 1:175048469-192127886 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/1/tx/tmp7EQKh9/R14-18102_kapa-NGv3-PE100-NGv3-sort-1_175048468_192127886-prep-prealign.bam
[2016-04-14T23:20Z] INFO  16:20:41,364 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:20Z] INFO  16:20:41,404 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:20Z] INFO  16:20:41,405 HelpFormatter - Date/Time: 2016/04/14 16:20:41
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[2016-04-14T23:20Z] INFO  16:20:41,406 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:20Z] INFO  16:20:41,428 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:20Z] INFO  16:20:41,442 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:20Z] INFO  16:20:41,443 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:20Z] INFO  16:20:41,444 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:20Z] INFO  16:20:41,449 HelpFormatter - Program Args: -T PrintReads -L 2:1-15514844 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/2/tx/tmpCJWh3U/R14-18102_kapa-NGv3-PE100-NGv3-sort-2_0_15514844-prep-prealign.bam
[2016-04-14T23:20Z] INFO  16:20:41,490 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:20Z] INFO  16:20:41,491 HelpFormatter - Date/Time: 2016/04/14 16:20:41
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[2016-04-14T23:20Z] INFO  16:20:41,497 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:20Z] INFO  16:20:41,560 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:20Z] INFO  16:20:41,564 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:20Z] INFO  16:20:41,565 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:20Z] INFO  16:20:41,566 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:20Z] INFO  16:20:41,571 HelpFormatter - Program Args: -T PrintReads -L 1:143897547-159410511 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/1/tx/tmpg6cvOh/R14-18102_kapa-NGv3-PE100-NGv3-sort-1_143897546_159410511-prep-prealign.bam
[2016-04-14T23:20Z] INFO  16:20:41,612 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:20Z] INFO  16:20:41,614 HelpFormatter - Date/Time: 2016/04/14 16:20:41
[2016-04-14T23:20Z] INFO  16:20:41,614 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:20Z] INFO  16:20:41,619 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:20Z] INFO  16:20:41,615 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:20Z] INFO  16:20:41,744 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:20Z] INFO  16:20:41,745 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:20Z] INFO  16:20:41,747 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:20Z] INFO  16:20:41,748 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:20Z] INFO  16:20:41,748 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:20Z] INFO  16:20:41,748 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:20Z] INFO  16:20:41,748 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:20Z] INFO  16:20:41,749 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:20Z] INFO  16:20:41,753 HelpFormatter - Program Args: -T PrintReads -L 1:1-15541927 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/1/tx/tmpIjTVFL/R14-18102_kapa-NGv3-PE100-NGv3-sort-1_0_15541927-prep-prealign.bam
[2016-04-14T23:20Z] INFO  16:20:41,753 HelpFormatter - Program Args: -T PrintReads -L 1:223162738-240072524 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/1/tx/tmpdq2QkE/R14-18102_kapa-NGv3-PE100-NGv3-sort-1_223162737_240072524-prep-prealign.bam
[2016-04-14T23:20Z] INFO  16:20:41,767 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:20Z] INFO  16:20:41,787 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:20Z] INFO  16:20:41,788 HelpFormatter - Date/Time: 2016/04/14 16:20:41
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[2016-04-14T23:20Z] INFO  16:20:41,789 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:20Z] INFO  16:20:41,801 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:20Z] INFO  16:20:41,803 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:20Z] INFO  16:20:41,804 HelpFormatter - Date/Time: 2016/04/14 16:20:41
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[2016-04-14T23:20Z] INFO  16:20:41,807 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:20Z] INFO  16:20:41,811 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:20Z] INFO  16:20:41,811 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:20Z] INFO  16:20:41,812 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:20Z] INFO  16:20:41,817 HelpFormatter - Program Args: -T PrintReads -L 1:207641872-223156451 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/1/tx/tmpgygEjs/R14-18102_kapa-NGv3-PE100-NGv3-sort-1_207641871_223156451-prep-prealign.bam
[2016-04-14T23:20Z] INFO  16:20:41,846 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:20Z] INFO  16:20:41,847 HelpFormatter - Date/Time: 2016/04/14 16:20:41
[2016-04-14T23:20Z] INFO  16:20:41,848 HelpFormatter - ---------------------------------------------------------------------------------
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[2016-04-14T23:20Z] INFO  16:20:41,855 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-14T23:20Z] INFO  16:20:41,924 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:20Z] INFO  16:20:41,953 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:20Z] INFO  16:20:41,980 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:20Z] INFO  16:20:42,005 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:20Z] INFO  16:20:42,009 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:20Z] INFO  16:20:42,009 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:20Z] INFO  16:20:42,010 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:20Z] INFO  16:20:42,014 HelpFormatter - Program Args: -T PrintReads -L 1:240255410-249250621 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/1/tx/tmp9n3B8K/R14-18102_kapa-NGv3-PE100-NGv3-sort-1_240255409_249250621-prep-prealign.bam
[2016-04-14T23:20Z] INFO  16:20:42,025 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-14T23:20Z] INFO  16:20:42,041 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:20Z] INFO  16:20:42,052 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:20Z] INFO  16:20:42,053 HelpFormatter - Date/Time: 2016/04/14 16:20:42
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[2016-04-14T23:20Z] INFO  16:20:42,054 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:20Z] INFO  16:20:42,080 IntervalUtils - Processing 15545049 bp from intervals
[2016-04-14T23:20Z] INFO  16:20:42,086 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:20Z] INFO  16:20:42,232 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-14T23:20Z] INFO  16:20:42,287 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:20Z] INFO  16:20:42,308 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:20Z] INFO  16:20:42,318 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-14T23:20Z] INFO  16:20:42,337 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:20Z] INFO  16:20:42,362 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:20Z] INFO  16:20:42,429 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:20Z] INFO  16:20:42,418 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-14T23:20Z] INFO  16:20:42,436 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-14T23:20Z] INFO  16:20:42,438 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:20Z] INFO  16:20:42,471 IntervalUtils - Processing 15517346 bp from intervals
[2016-04-14T23:20Z] INFO  16:20:42,494 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:20Z] INFO  16:20:42,503 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:20Z] INFO  16:20:42,513 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-14T23:20Z] INFO  16:20:42,538 IntervalUtils - Processing 34773037 bp from intervals
[2016-04-14T23:20Z] INFO  16:20:42,556 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-14T23:20Z] INFO  16:20:42,569 IntervalUtils - Processing 15694456 bp from intervals
[2016-04-14T23:20Z] INFO  16:20:42,585 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-14T23:20Z] INFO  16:20:42,613 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:20Z] INFO  16:20:42,621 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:20Z] INFO  16:20:42,622 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:20Z] INFO  16:20:42,623 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:20Z] INFO  16:20:42,624 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:20Z] INFO  16:20:42,646 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:20Z] INFO  16:20:42,660 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-14T23:20Z] INFO  16:20:42,689 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:20Z] INFO  16:20:42,686 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:20Z] INFO  16:20:42,728 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:20Z] INFO  16:20:42,735 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:20Z] INFO  16:20:42,744 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:20Z] INFO  16:20:42,765 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:20Z] INFO  16:20:42,780 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.04
[2016-04-14T23:20Z] INFO  16:20:42,794 IntervalUtils - Processing 15542096 bp from intervals
[2016-04-14T23:20Z] INFO  16:20:42,835 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-14T23:20Z] INFO  16:20:42,868 IntervalUtils - Processing 15640657 bp from intervals
[2016-04-14T23:20Z] INFO  16:20:42,920 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-14T23:20Z] INFO  16:20:42,923 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-14T23:20Z] INFO  16:20:42,933 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:20Z] INFO  16:20:42,948 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:20Z] INFO  16:20:42,957 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:20Z] INFO  16:20:42,958 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:20Z] INFO  16:20:42,959 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:20Z] INFO  16:20:42,959 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:20Z] INFO  16:20:42,972 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:20Z] INFO  16:20:42,973 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:20Z] INFO  16:20:42,973 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:20Z] INFO  16:20:42,986 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:20Z] INFO  16:20:42,989 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:20Z] INFO  16:20:43,001 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:20Z] INFO  16:20:43,005 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:20Z] INFO  16:20:43,008 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:20Z] INFO  16:20:43,024 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:20Z] INFO  16:20:43,026 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-14T23:20Z] INFO  16:20:43,027 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:20Z] INFO  16:20:43,028 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:20Z] INFO  16:20:43,029 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:20Z] INFO  16:20:43,036 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:20Z] INFO  16:20:43,039 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:20Z] INFO  16:20:43,044 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:20Z] INFO  16:20:43,076 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:20Z] INFO  16:20:43,090 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-14T23:20Z] INFO  16:20:43,096 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:20Z] INFO  16:20:43,105 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:20Z] INFO  16:20:43,111 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-14T23:20Z] INFO  16:20:43,113 IntervalUtils - Processing 15511908 bp from intervals
[2016-04-14T23:20Z] INFO  16:20:43,129 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-14T23:20Z] INFO  16:20:43,150 IntervalUtils - Processing 15513180 bp from intervals
[2016-04-14T23:20Z] INFO  16:20:43,154 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-14T23:20Z] INFO  16:20:43,167 IntervalUtils - Processing 15527177 bp from intervals
[2016-04-14T23:20Z] INFO  16:20:43,215 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:20Z] INFO  16:20:43,218 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:20Z] INFO  16:20:43,230 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:20Z] INFO  16:20:43,233 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-14T23:20Z] INFO  16:20:43,239 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:20Z] INFO  16:20:43,245 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:20Z] INFO  16:20:43,248 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:20Z] INFO  16:20:43,251 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:20Z] INFO  16:20:43,252 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:20Z] INFO  16:20:43,252 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:20Z] INFO  16:20:43,253 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:20Z] INFO  16:20:43,257 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:20Z] INFO  16:20:43,278 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:20Z] INFO  16:20:43,298 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:20Z] INFO  16:20:43,302 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:20Z] INFO  16:20:43,302 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:20Z] INFO  16:20:43,303 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:20Z] INFO  16:20:43,298 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-14T23:20Z] INFO  16:20:43,308 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:20Z] INFO  16:20:43,303 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:20Z] INFO  16:20:43,333 IntervalUtils - Processing 17079418 bp from intervals
[2016-04-14T23:20Z] INFO  16:20:43,342 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:20Z] INFO  16:20:43,404 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-14T23:20Z] INFO  16:20:43,416 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.11
[2016-04-14T23:20Z] INFO  16:20:43,444 IntervalUtils - Processing 15514844 bp from intervals
[2016-04-14T23:20Z] INFO  16:20:43,466 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:20Z] INFO  16:20:43,467 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:20Z] INFO  16:20:43,467 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:20Z] INFO  16:20:43,468 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:20Z] INFO  16:20:43,469 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:20Z] INFO  16:20:43,475 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:20Z] INFO  16:20:43,484 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:20Z] INFO  16:20:43,484 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:20Z] INFO  16:20:43,484 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:20Z] INFO  16:20:43,489 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:20Z] INFO  16:20:43,490 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:20Z] INFO  16:20:43,499 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:20Z] INFO  16:20:43,500 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:20Z] INFO  16:20:43,522 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.04
[2016-04-14T23:20Z] INFO  16:20:43,524 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:20Z] INFO  16:20:43,535 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:20Z] INFO  16:20:43,535 IntervalUtils - Processing 15512965 bp from intervals
[2016-04-14T23:20Z] INFO  16:20:43,537 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:20Z] INFO  16:20:43,538 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:20Z] INFO  16:20:43,539 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:20Z] INFO  16:20:43,539 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:20Z] INFO  16:20:43,540 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:20Z] INFO  16:20:43,556 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-14T23:20Z] INFO  16:20:43,562 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:20Z] INFO  16:20:43,565 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:20Z] INFO  16:20:43,566 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-14T23:20Z] INFO  16:20:43,569 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-14T23:20Z] INFO  16:20:43,635 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:20Z] INFO  16:20:43,636 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:20Z] INFO  16:20:43,642 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:20Z] INFO  16:20:43,643 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:20Z] INFO  16:20:43,646 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:20Z] INFO  16:20:43,651 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:20Z] INFO  16:20:43,657 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:20Z] INFO  16:20:43,660 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:20Z] INFO  16:20:43,699 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-14T23:20Z] INFO  16:20:43,700 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-14T23:20Z] INFO  16:20:43,705 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-14T23:20Z] INFO  16:20:43,710 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:20Z] INFO  16:20:43,713 IntervalUtils - Processing 16909787 bp from intervals
[2016-04-14T23:20Z] INFO  16:20:43,719 IntervalUtils - Processing 15514580 bp from intervals
[2016-04-14T23:20Z] INFO  16:20:43,721 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-14T23:20Z] INFO  16:20:43,739 IntervalUtils - Processing 15541927 bp from intervals
[2016-04-14T23:20Z] INFO  16:20:43,745 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:20Z] INFO  16:20:43,762 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:20Z] INFO  16:20:43,763 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:20Z] INFO  16:20:43,764 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:20Z] INFO  16:20:43,765 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:20Z] INFO  16:20:43,765 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:20Z] INFO  16:20:43,790 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:20Z] INFO  16:20:43,790 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:20Z] INFO  16:20:43,793 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:20Z] INFO  16:20:43,795 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:20Z] INFO  16:20:43,824 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:20Z] INFO  16:20:43,860 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-14T23:20Z] INFO  16:20:43,881 IntervalUtils - Processing 8995212 bp from intervals
[2016-04-14T23:20Z] INFO  16:20:43,886 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:20Z] INFO  16:20:43,887 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:20Z] INFO  16:20:43,887 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:20Z] INFO  16:20:43,888 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:20Z] INFO  16:20:43,948 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:20Z] INFO  16:20:43,958 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:20Z] INFO  16:20:43,961 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:20Z] INFO  16:20:43,962 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:20Z] INFO  16:20:43,963 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:20Z] INFO  16:20:43,964 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:20Z] INFO  16:20:43,985 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:20Z] INFO  16:20:43,999 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:20Z] INFO  16:20:44,064 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:20Z] INFO  16:20:44,065 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:20Z] INFO  16:20:44,065 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:20Z] INFO  16:20:44,065 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:20Z] INFO  16:20:44,100 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:20Z] INFO  16:20:44,109 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:20Z] INFO  16:20:44,127 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:20Z] INFO  16:20:44,128 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:20Z] INFO  16:20:44,129 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:20Z] INFO  16:20:44,130 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:20Z] INFO  16:20:44,138 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:20Z] INFO  16:20:44,139 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:20Z] INFO  16:20:44,139 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:20Z] INFO  16:20:44,140 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:20Z] INFO  16:20:44,144 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:20Z] INFO  16:20:44,161 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:20Z] INFO  16:20:44,180 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:20Z] INFO  16:20:44,306 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:20Z] INFO  16:20:44,325 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:20Z] INFO  16:20:44,334 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:20Z] INFO  16:20:44,325 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:20Z] INFO  16:20:44,340 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:20Z] INFO  16:20:44,345 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:20Z] INFO  16:20:44,340 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:20Z] INFO  16:20:44,372 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:20Z] INFO  16:20:44,558 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:21Z] INFO  16:21:06,773 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@6834dd3c
[2016-04-14T23:21Z] INFO  16:21:06,854 ProgressMeter -            done    155026.0    22.0 s       2.5 m      100.0%    22.0 s       0.0 s
[2016-04-14T23:21Z] INFO  16:21:06,854 ProgressMeter - Total runtime 22.97 secs, 0.38 min, 0.01 hours
[2016-04-14T23:21Z] INFO  16:21:06,855 MicroScheduler - 154 reads were filtered out during the traversal out of approximately 155180 total reads (0.10%)
[2016-04-14T23:21Z] INFO  16:21:06,855 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:21Z] INFO  16:21:06,856 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:21Z] INFO  16:21:06,856 MicroScheduler -   -> 154 reads (0.10% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:21Z] INFO  16:21:07,192 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@66a8c396
[2016-04-14T23:21Z] INFO  16:21:07,507 ProgressMeter -            done    174042.0    24.0 s       2.4 m      100.0%    24.0 s       0.0 s
[2016-04-14T23:21Z] INFO  16:21:07,508 ProgressMeter - Total runtime 24.89 secs, 0.41 min, 0.01 hours
[2016-04-14T23:21Z] INFO  16:21:07,509 MicroScheduler - 105 reads were filtered out during the traversal out of approximately 174147 total reads (0.06%)
[2016-04-14T23:21Z] INFO  16:21:07,509 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:21Z] INFO  16:21:07,509 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:21Z] INFO  16:21:07,510 MicroScheduler -   -> 105 reads (0.06% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:21Z] INFO  16:21:08,088 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@2db068f5
[2016-04-14T23:21Z] INFO  16:21:08,201 ProgressMeter -            done    183893.0    25.0 s       2.3 m      100.0%    25.0 s       0.0 s
[2016-04-14T23:21Z] INFO  16:21:08,202 ProgressMeter - Total runtime 25.24 secs, 0.42 min, 0.01 hours
[2016-04-14T23:21Z] INFO  16:21:08,203 MicroScheduler - 121 reads were filtered out during the traversal out of approximately 184014 total reads (0.07%)
[2016-04-14T23:21Z] INFO  16:21:08,204 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:21Z] INFO  16:21:08,206 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:21Z] INFO  16:21:08,208 MicroScheduler -   -> 121 reads (0.07% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:21Z] INFO  16:21:08,356 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:21Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-2_0_15514844-prep-prealign.bam
[2016-04-14T23:21Z] INFO  16:21:08,840 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:21Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-1_77752625_93297674-prep-prealign.bam
[2016-04-14T23:21Z] INFO  16:21:08,873 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@769cb63b
[2016-04-14T23:21Z] INFO  16:21:09,005 ProgressMeter -            done    181172.0    26.0 s       2.4 m      100.0%    26.0 s       0.0 s
[2016-04-14T23:21Z] INFO  16:21:09,006 ProgressMeter - Total runtime 26.03 secs, 0.43 min, 0.01 hours
[2016-04-14T23:21Z] INFO  16:21:09,007 MicroScheduler - 144 reads were filtered out during the traversal out of approximately 181316 total reads (0.08%)
[2016-04-14T23:21Z] INFO  16:21:09,008 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:21Z] INFO  16:21:09,009 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:21Z] INFO  16:21:09,010 MicroScheduler -   -> 144 reads (0.08% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:21Z] GATK RealignerTargetCreator: R14-18102_kapa-NGv3-PE100-NGv3-sort-2_0_15514844-prep-prealign.bam 2:1-15514844
[2016-04-14T23:21Z] GATK: RealignerTargetCreator
[2016-04-14T23:21Z] GATK RealignerTargetCreator: R14-18102_kapa-NGv3-PE100-NGv3-sort-1_77752625_93297674-prep-prealign.bam 1:77752626-93297674
[2016-04-14T23:21Z] GATK: RealignerTargetCreator
[2016-04-14T23:21Z] INFO  16:21:09,693 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:21Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-1_93298945_108993401-prep-prealign.bam
[2016-04-14T23:21Z] GATK RealignerTargetCreator: R14-18102_kapa-NGv3-PE100-NGv3-sort-1_93298945_108993401-prep-prealign.bam 1:93298946-108993401
[2016-04-14T23:21Z] GATK: RealignerTargetCreator
[2016-04-14T23:21Z] INFO  16:21:10,564 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:21Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-1_62231950_77749296-prep-prealign.bam
[2016-04-14T23:21Z] GATK RealignerTargetCreator: R14-18102_kapa-NGv3-PE100-NGv3-sort-1_62231950_77749296-prep-prealign.bam 1:62231951-77749296
[2016-04-14T23:21Z] GATK: RealignerTargetCreator
[2016-04-14T23:21Z] INFO  16:21:12,124 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:21Z] INFO  16:21:12,126 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:21Z] INFO  16:21:12,126 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:21Z] INFO  16:21:12,127 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:21Z] INFO  16:21:12,133 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/2/R14-18102_kapa-NGv3-PE100-NGv3-sort-2_0_15514844-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/2/tx/tmp63PhBh/R14-18102_kapa-NGv3-PE100-NGv3-sort-2_0_15514844-prep-prealign-realign.intervals -l INFO -L 2:1-15514844 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-14T23:21Z] INFO  16:21:12,147 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:21Z] INFO  16:21:12,148 HelpFormatter - Date/Time: 2016/04/14 16:21:12
[2016-04-14T23:21Z] INFO  16:21:12,148 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:21Z] INFO  16:21:12,149 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:21Z] INFO  16:21:12,295 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:21Z] INFO  16:21:12,480 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:21Z] INFO  16:21:12,495 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@2d3c117a
[2016-04-14T23:21Z] INFO  16:21:12,496 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:21Z] INFO  16:21:12,497 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:21Z] INFO  16:21:12,497 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:21Z] INFO  16:21:12,502 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/1/R14-18102_kapa-NGv3-PE100-NGv3-sort-1_77752625_93297674-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/1/tx/tmporD2GN/R14-18102_kapa-NGv3-PE100-NGv3-sort-1_77752625_93297674-prep-prealign-realign.intervals -l INFO -L 1:77752626-93297674 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-14T23:21Z] INFO  16:21:12,529 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:21Z] INFO  16:21:12,529 HelpFormatter - Date/Time: 2016/04/14 16:21:12
[2016-04-14T23:21Z] INFO  16:21:12,529 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:21Z] INFO  16:21:12,530 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:21Z] INFO  16:21:12,587 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-14T23:21Z] INFO  16:21:12,607 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:21Z] INFO  16:21:12,667 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-14T23:21Z] INFO  16:21:12,675 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:21Z] INFO  16:21:12,693 ProgressMeter -            done    197913.0    28.0 s       2.4 m       99.8%    28.0 s       0.0 s
[2016-04-14T23:21Z] INFO  16:21:12,694 ProgressMeter - Total runtime 28.37 secs, 0.47 min, 0.01 hours
[2016-04-14T23:21Z] INFO  16:21:12,694 MicroScheduler - 94 reads were filtered out during the traversal out of approximately 198007 total reads (0.05%)
[2016-04-14T23:21Z] INFO  16:21:12,697 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:21Z] INFO  16:21:12,698 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:21Z] INFO  16:21:12,698 MicroScheduler -   -> 94 reads (0.05% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:21Z] INFO  16:21:12,836 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-14T23:21Z] INFO  16:21:12,845 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:21Z] INFO  16:21:12,902 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-14T23:21Z] INFO  16:21:13,033 IntervalUtils - Processing 15514844 bp from intervals
[2016-04-14T23:21Z] WARN  16:21:13,038 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:21Z] INFO  16:21:13,146 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:21Z] INFO  16:21:13,167 IntervalUtils - Processing 15545049 bp from intervals
[2016-04-14T23:21Z] WARN  16:21:13,172 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:21Z] INFO  16:21:13,249 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:21Z] INFO  16:21:13,292 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:21Z] INFO  16:21:13,306 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:21Z] INFO  16:21:13,307 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:21Z] INFO  16:21:13,308 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:21Z] INFO  16:21:13,312 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/1/R14-18102_kapa-NGv3-PE100-NGv3-sort-1_93298945_108993401-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/1/tx/tmp74vErb/R14-18102_kapa-NGv3-PE100-NGv3-sort-1_93298945_108993401-prep-prealign-realign.intervals -l INFO -L 1:93298946-108993401 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-14T23:21Z] INFO  16:21:13,322 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:21Z] INFO  16:21:13,333 HelpFormatter - Date/Time: 2016/04/14 16:21:13
[2016-04-14T23:21Z] INFO  16:21:13,334 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:21Z] INFO  16:21:13,335 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:21Z] INFO  16:21:13,362 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:21Z] INFO  16:21:13,363 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:21Z] INFO  16:21:13,364 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:21Z] INFO  16:21:13,365 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-14T23:21Z] INFO  16:21:13,448 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:21Z] INFO  16:21:13,477 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:21Z] INFO  16:21:13,478 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:21Z] INFO  16:21:13,479 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:21Z] INFO  16:21:13,480 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-14T23:21Z] INFO  16:21:13,487 ProgressMeter -     1:202912801    100001.0    30.0 s       5.0 m       69.5%    43.0 s      13.0 s
[2016-04-14T23:21Z] INFO  16:21:13,589 ProgressMeter -      1:54371978    100003.0    30.0 s       5.0 m       49.4%    60.0 s      30.0 s
[2016-04-14T23:21Z] INFO  16:21:13,638 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-14T23:21Z] INFO  16:21:13,647 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:21Z] INFO  16:21:13,695 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-14T23:21Z] INFO  16:21:13,696 ProgressMeter -     1:113212739    100002.0    30.0 s       5.1 m       12.1%     4.1 m       3.6 m
[2016-04-14T23:21Z] INFO  16:21:13,787 ProgressMeter -     1:185089685    200006.0    30.0 s       2.5 m       58.8%    51.0 s      21.0 s
[2016-04-14T23:21Z] INFO  16:21:13,950 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:21Z] INFO  16:21:13,953 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:21Z] INFO  16:21:13,954 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:21Z] INFO  16:21:13,954 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:21Z] INFO  16:21:13,959 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/1/R14-18102_kapa-NGv3-PE100-NGv3-sort-1_62231950_77749296-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/1/tx/tmpMIKZF1/R14-18102_kapa-NGv3-PE100-NGv3-sort-1_62231950_77749296-prep-prealign-realign.intervals -l INFO -L 1:62231951-77749296 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-14T23:21Z] INFO  16:21:13,981 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:21Z] INFO  16:21:13,981 HelpFormatter - Date/Time: 2016/04/14 16:21:13
[2016-04-14T23:21Z] INFO  16:21:13,981 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:21Z] INFO  16:21:13,982 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:21Z] INFO  16:21:14,022 IntervalUtils - Processing 15694456 bp from intervals
[2016-04-14T23:21Z] WARN  16:21:14,026 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:21Z] INFO  16:21:14,100 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:21Z] INFO  16:21:14,101 ProgressMeter -     1:220331206    200003.0    30.0 s       2.5 m       81.8%    36.0 s       6.0 s
[2016-04-14T23:21Z] INFO  16:21:14,101 ProgressMeter -      1:17087005    100004.0    30.0 s       5.1 m        9.9%     5.1 m       4.6 m
[2016-04-14T23:21Z] INFO  16:21:14,163 ProgressMeter -     1:228564881    100002.0    30.0 s       5.0 m       31.9%    93.0 s      63.0 s
[2016-04-14T23:21Z] INFO  16:21:14,197 ProgressMeter -       1:1896394    100002.0    30.0 s       5.0 m       12.2%     4.1 m       3.6 m
[2016-04-14T23:21Z] INFO  16:21:14,199 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:21Z] INFO  16:21:14,224 ProgressMeter -     1:145788879    100003.0    30.0 s       5.0 m       12.2%     4.1 m       3.6 m
[2016-04-14T23:21Z] INFO  16:21:14,238 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:21Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-1_240255409_249250621-prep-prealign.bam
[2016-04-14T23:21Z] INFO  16:21:14,302 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-14T23:21Z] INFO  16:21:14,306 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:21Z] INFO  16:21:14,307 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:21Z] INFO  16:21:14,308 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:21Z] INFO  16:21:14,309 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-14T23:21Z] INFO  16:21:14,312 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:21Z] INFO  16:21:14,360 ProgressMeter -     1:163044249    100001.0    31.0 s       5.2 m       22.8%     2.3 m     105.0 s
[2016-04-14T23:21Z] INFO  16:21:14,370 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-14T23:21Z] INFO  16:21:14,795 IntervalUtils - Processing 15517346 bp from intervals
[2016-04-14T23:21Z] WARN  16:21:14,801 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:21Z] INFO  16:21:14,914 ProgressMeter -      1:35579910    100001.0    31.0 s       5.2 m       28.3%   109.0 s      78.0 s
[2016-04-14T23:21Z] INFO  16:21:14,943 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:21Z] GATK RealignerTargetCreator: R14-18102_kapa-NGv3-PE100-NGv3-sort-1_240255409_249250621-prep-prealign.bam 1:240255410-249250621
[2016-04-14T23:21Z] GATK: RealignerTargetCreator
[2016-04-14T23:21Z] INFO  16:21:15,131 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:21Z] INFO  16:21:15,132 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:21Z] INFO  16:21:15,133 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:21Z] INFO  16:21:15,134 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-14T23:21Z] INFO  16:21:17,556 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@62add7db
[2016-04-14T23:21Z] INFO  16:21:17,796 ProgressMeter -            done    248187.0    33.0 s       2.3 m       99.7%    33.0 s       0.0 s
[2016-04-14T23:21Z] INFO  16:21:17,796 ProgressMeter - Total runtime 33.73 secs, 0.56 min, 0.01 hours
[2016-04-14T23:21Z] INFO  16:21:17,797 MicroScheduler - 172 reads were filtered out during the traversal out of approximately 248359 total reads (0.07%)
[2016-04-14T23:21Z] INFO  16:21:17,797 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:21Z] INFO  16:21:17,797 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:21Z] INFO  16:21:17,798 MicroScheduler -   -> 172 reads (0.07% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:21Z] INFO  16:21:18,082 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:21Z] INFO  16:21:18,085 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:21Z] INFO  16:21:18,086 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:21Z] INFO  16:21:18,086 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:21Z] INFO  16:21:18,091 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/1/R14-18102_kapa-NGv3-PE100-NGv3-sort-1_240255409_249250621-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/1/tx/tmpdFi_Vu/R14-18102_kapa-NGv3-PE100-NGv3-sort-1_240255409_249250621-prep-prealign-realign.intervals -l INFO -L 1:240255410-249250621 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-14T23:21Z] INFO  16:21:18,123 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:21Z] INFO  16:21:18,124 HelpFormatter - Date/Time: 2016/04/14 16:21:18
[2016-04-14T23:21Z] INFO  16:21:18,125 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:21Z] INFO  16:21:18,125 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:21Z] INFO  16:21:18,202 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:21Z] INFO  16:21:18,367 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-14T23:21Z] INFO  16:21:18,388 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:21Z] INFO  16:21:18,451 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-14T23:21Z] INFO  16:21:18,597 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@66a8c396
[2016-04-14T23:21Z] INFO  16:21:18,803 IntervalUtils - Processing 8995212 bp from intervals
[2016-04-14T23:21Z] WARN  16:21:18,818 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:21Z] INFO  16:21:18,883 ProgressMeter -            done    259553.0    35.0 s       2.3 m       99.0%    35.0 s       0.0 s
[2016-04-14T23:21Z] INFO  16:21:18,883 ProgressMeter - Total runtime 35.12 secs, 0.59 min, 0.01 hours
[2016-04-14T23:21Z] INFO  16:21:18,884 MicroScheduler - 144 reads were filtered out during the traversal out of approximately 259697 total reads (0.06%)
[2016-04-14T23:21Z] INFO  16:21:18,884 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:21Z] INFO  16:21:18,885 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:21Z] INFO  16:21:18,885 MicroScheduler -   -> 144 reads (0.06% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:21Z] INFO  16:21:18,947 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:21Z] INFO  16:21:19,144 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:21Z] INFO  16:21:19,145 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:21Z] INFO  16:21:19,146 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:21Z] INFO  16:21:19,147 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-14T23:21Z] INFO  16:21:19,192 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:21Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-1_207641871_223156451-prep-prealign.bam
[2016-04-14T23:21Z] GATK RealignerTargetCreator: R14-18102_kapa-NGv3-PE100-NGv3-sort-1_207641871_223156451-prep-prealign.bam 1:207641872-223156451
[2016-04-14T23:21Z] GATK: RealignerTargetCreator
[2016-04-14T23:21Z] INFO  16:21:20,297 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:21Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-1_175048468_192127886-prep-prealign.bam
[2016-04-14T23:21Z] GATK RealignerTargetCreator: R14-18102_kapa-NGv3-PE100-NGv3-sort-1_175048468_192127886-prep-prealign.bam 1:175048469-192127886
[2016-04-14T23:21Z] GATK: RealignerTargetCreator
[2016-04-14T23:21Z] INFO  16:21:23,007 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:21Z] INFO  16:21:23,010 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:21Z] INFO  16:21:23,010 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:21Z] INFO  16:21:23,010 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:21Z] INFO  16:21:23,014 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/1/R14-18102_kapa-NGv3-PE100-NGv3-sort-1_207641871_223156451-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/1/tx/tmp1R9zUN/R14-18102_kapa-NGv3-PE100-NGv3-sort-1_207641871_223156451-prep-prealign-realign.intervals -l INFO -L 1:207641872-223156451 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-14T23:21Z] INFO  16:21:23,026 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:21Z] INFO  16:21:23,027 HelpFormatter - Date/Time: 2016/04/14 16:21:23
[2016-04-14T23:21Z] INFO  16:21:23,028 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:21Z] INFO  16:21:23,029 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:21Z] INFO  16:21:23,111 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:21Z] INFO  16:21:23,350 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-14T23:21Z] INFO  16:21:23,360 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:21Z] INFO  16:21:23,423 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-14T23:21Z] INFO  16:21:23,708 IntervalUtils - Processing 15514580 bp from intervals
[2016-04-14T23:21Z] WARN  16:21:23,713 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:21Z] INFO  16:21:23,842 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:21Z] INFO  16:21:24,034 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:21Z] INFO  16:21:24,037 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:21Z] INFO  16:21:24,038 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:21Z] INFO  16:21:24,038 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:21Z] INFO  16:21:24,039 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:21Z] INFO  16:21:24,040 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:21Z] INFO  16:21:24,041 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:21Z] INFO  16:21:24,042 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-14T23:21Z] INFO  16:21:24,043 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/1/R14-18102_kapa-NGv3-PE100-NGv3-sort-1_175048468_192127886-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/1/tx/tmpxdX3_W/R14-18102_kapa-NGv3-PE100-NGv3-sort-1_175048468_192127886-prep-prealign-realign.intervals -l INFO -L 1:175048469-192127886 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-14T23:21Z] INFO  16:21:24,067 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:21Z] INFO  16:21:24,076 HelpFormatter - Date/Time: 2016/04/14 16:21:24
[2016-04-14T23:21Z] INFO  16:21:24,077 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:21Z] INFO  16:21:24,077 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:21Z] INFO  16:21:24,191 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:21Z] INFO  16:21:24,370 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-14T23:21Z] INFO  16:21:24,400 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:21Z] INFO  16:21:24,455 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-14T23:21Z] INFO  16:21:24,768 IntervalUtils - Processing 17079418 bp from intervals
[2016-04-14T23:21Z] WARN  16:21:24,774 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:21Z] INFO  16:21:24,848 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:21Z] INFO  16:21:24,915 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@58e607c7
[2016-04-14T23:21Z] INFO  16:21:25,026 ProgressMeter -            done    302614.0    41.0 s       2.3 m      100.0%    41.0 s       0.0 s
[2016-04-14T23:21Z] INFO  16:21:25,028 ProgressMeter - Total runtime 41.54 secs, 0.69 min, 0.01 hours
[2016-04-14T23:21Z] INFO  16:21:25,029 MicroScheduler - 187 reads were filtered out during the traversal out of approximately 302801 total reads (0.06%)
[2016-04-14T23:21Z] INFO  16:21:25,029 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:21Z] INFO  16:21:25,030 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:21Z] INFO  16:21:25,031 MicroScheduler -   -> 187 reads (0.06% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:21Z] INFO  16:21:25,103 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:21Z] INFO  16:21:25,105 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:21Z] INFO  16:21:25,105 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:21Z] INFO  16:21:25,106 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-14T23:21Z] INFO  16:21:26,763 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:21Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-1_46715671_62228851-prep-prealign.bam
[2016-04-14T23:21Z] GATK RealignerTargetCreator: R14-18102_kapa-NGv3-PE100-NGv3-sort-1_46715671_62228851-prep-prealign.bam 1:46715672-62228851
[2016-04-14T23:21Z] GATK: RealignerTargetCreator
[2016-04-14T23:21Z] INFO  16:21:30,443 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:21Z] INFO  16:21:30,446 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:21Z] INFO  16:21:30,446 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:21Z] INFO  16:21:30,447 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:21Z] INFO  16:21:30,451 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/1/R14-18102_kapa-NGv3-PE100-NGv3-sort-1_46715671_62228851-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/1/tx/tmpEcIX_6/R14-18102_kapa-NGv3-PE100-NGv3-sort-1_46715671_62228851-prep-prealign-realign.intervals -l INFO -L 1:46715672-62228851 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-14T23:21Z] INFO  16:21:30,464 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:21Z] INFO  16:21:30,467 HelpFormatter - Date/Time: 2016/04/14 16:21:30
[2016-04-14T23:21Z] INFO  16:21:30,467 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:21Z] INFO  16:21:30,468 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:21Z] INFO  16:21:30,585 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:21Z] INFO  16:21:30,831 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-14T23:21Z] INFO  16:21:30,842 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:21Z] INFO  16:21:30,895 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-14T23:21Z] INFO  16:21:31,000 ProgressMeter -            done   1.5545049E7    17.0 s       1.0 s      100.0%    17.0 s       0.0 s
[2016-04-14T23:21Z] INFO  16:21:31,001 ProgressMeter - Total runtime 17.52 secs, 0.29 min, 0.00 hours
[2016-04-14T23:21Z] INFO  16:21:31,006 MicroScheduler - 14823 reads were filtered out during the traversal out of approximately 175157 total reads (8.46%)
[2016-04-14T23:21Z] INFO  16:21:31,007 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:21Z] INFO  16:21:31,008 MicroScheduler -   -> 547 reads (0.31% of total) failing BadMateFilter
[2016-04-14T23:21Z] INFO  16:21:31,009 MicroScheduler -   -> 13610 reads (7.77% of total) failing DuplicateReadFilter
[2016-04-14T23:21Z] INFO  16:21:31,010 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-14T23:21Z] INFO  16:21:31,011 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:21Z] INFO  16:21:31,011 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-14T23:21Z] INFO  16:21:31,012 MicroScheduler -   -> 666 reads (0.38% of total) failing MappingQualityZeroFilter
[2016-04-14T23:21Z] INFO  16:21:31,013 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:21Z] INFO  16:21:31,013 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-14T23:21Z] INFO  16:21:31,014 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-14T23:21Z] INFO  16:21:31,016 ProgressMeter -            done   1.5514844E7    17.0 s       1.0 s      100.0%    17.0 s       0.0 s
[2016-04-14T23:21Z] INFO  16:21:31,017 ProgressMeter - Total runtime 17.65 secs, 0.29 min, 0.00 hours
[2016-04-14T23:21Z] INFO  16:21:31,022 MicroScheduler - 13343 reads were filtered out during the traversal out of approximately 155732 total reads (8.57%)
[2016-04-14T23:21Z] INFO  16:21:31,023 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:21Z] INFO  16:21:31,024 MicroScheduler -   -> 560 reads (0.36% of total) failing BadMateFilter
[2016-04-14T23:21Z] INFO  16:21:31,025 MicroScheduler -   -> 12407 reads (7.97% of total) failing DuplicateReadFilter
[2016-04-14T23:21Z] INFO  16:21:31,025 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-14T23:21Z] INFO  16:21:31,026 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:21Z] INFO  16:21:31,027 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-14T23:21Z] INFO  16:21:31,028 MicroScheduler -   -> 376 reads (0.24% of total) failing MappingQualityZeroFilter
[2016-04-14T23:21Z] INFO  16:21:31,028 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:21Z] INFO  16:21:31,029 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-14T23:21Z] INFO  16:21:31,030 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-14T23:21Z] INFO  16:21:31,086 ProgressMeter -            done   1.5694456E7    16.0 s       1.0 s      100.0%    16.0 s       0.0 s
[2016-04-14T23:21Z] INFO  16:21:31,087 ProgressMeter - Total runtime 16.78 secs, 0.28 min, 0.00 hours
[2016-04-14T23:21Z] INFO  16:21:31,091 MicroScheduler - 54138 reads were filtered out during the traversal out of approximately 185107 total reads (29.25%)
[2016-04-14T23:21Z] INFO  16:21:31,091 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:21Z] INFO  16:21:31,092 MicroScheduler -   -> 461 reads (0.25% of total) failing BadMateFilter
[2016-04-14T23:21Z] INFO  16:21:31,092 MicroScheduler -   -> 11484 reads (6.20% of total) failing DuplicateReadFilter
[2016-04-14T23:21Z] INFO  16:21:31,092 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-14T23:21Z] INFO  16:21:31,093 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:21Z] INFO  16:21:31,093 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-14T23:21Z] INFO  16:21:31,093 MicroScheduler -   -> 42193 reads (22.79% of total) failing MappingQualityZeroFilter
[2016-04-14T23:21Z] INFO  16:21:31,094 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:21Z] INFO  16:21:31,094 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-14T23:21Z] INFO  16:21:31,094 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-14T23:21Z] INFO  16:21:31,228 IntervalUtils - Processing 15513180 bp from intervals
[2016-04-14T23:21Z] WARN  16:21:31,235 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:21Z] INFO  16:21:31,322 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:21Z] INFO  16:21:31,549 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:21Z] INFO  16:21:31,550 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:21Z] INFO  16:21:31,551 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:21Z] INFO  16:21:31,552 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-14T23:21Z] INFO  16:21:31,996 ProgressMeter -            done   1.5517346E7    16.0 s       1.0 s      100.0%    16.0 s       0.0 s
[2016-04-14T23:21Z] INFO  16:21:31,998 ProgressMeter - Total runtime 16.87 secs, 0.28 min, 0.00 hours
[2016-04-14T23:21Z] INFO  16:21:32,003 MicroScheduler - 15675 reads were filtered out during the traversal out of approximately 182440 total reads (8.59%)
[2016-04-14T23:21Z] INFO  16:21:32,004 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:21Z] INFO  16:21:32,006 MicroScheduler -   -> 549 reads (0.30% of total) failing BadMateFilter
[2016-04-14T23:21Z] INFO  16:21:32,007 MicroScheduler -   -> 14368 reads (7.88% of total) failing DuplicateReadFilter
[2016-04-14T23:21Z] INFO  16:21:32,007 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-14T23:21Z] INFO  16:21:32,008 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:21Z] INFO  16:21:32,009 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-14T23:21Z] INFO  16:21:32,010 MicroScheduler -   -> 758 reads (0.42% of total) failing MappingQualityZeroFilter
[2016-04-14T23:21Z] INFO  16:21:32,010 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:21Z] INFO  16:21:32,011 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-14T23:21Z] INFO  16:21:32,012 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-14T23:21Z] INFO  16:21:32,518 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:21Z] GATK: realign ('1', 93298945, 108993401) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:21Z] INFO  16:21:32,602 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:21Z] GATK: realign ('1', 77752625, 93297674) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:21Z] INFO  16:21:32,639 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:21Z] GATK: realign ('2', 0, 15514844) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:21Z] INFO  16:21:32,998 ProgressMeter -            done   8995212.0    13.0 s       1.0 s      100.0%    13.0 s       0.0 s
[2016-04-14T23:21Z] INFO  16:21:32,999 ProgressMeter - Total runtime 13.85 secs, 0.23 min, 0.00 hours
[2016-04-14T23:21Z] INFO  16:21:33,003 MicroScheduler - 29288 reads were filtered out during the traversal out of approximately 199336 total reads (14.69%)
[2016-04-14T23:21Z] INFO  16:21:33,004 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:21Z] INFO  16:21:33,004 MicroScheduler -   -> 386 reads (0.19% of total) failing BadMateFilter
[2016-04-14T23:21Z] INFO  16:21:33,005 MicroScheduler -   -> 14958 reads (7.50% of total) failing DuplicateReadFilter
[2016-04-14T23:21Z] INFO  16:21:33,005 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-14T23:21Z] INFO  16:21:33,005 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:21Z] INFO  16:21:33,006 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-14T23:21Z] INFO  16:21:33,006 MicroScheduler -   -> 13944 reads (7.00% of total) failing MappingQualityZeroFilter
[2016-04-14T23:21Z] INFO  16:21:33,006 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:21Z] INFO  16:21:33,006 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-14T23:21Z] INFO  16:21:33,007 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-14T23:21Z] INFO  16:21:33,307 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@58e607c7
[2016-04-14T23:21Z] INFO  16:21:33,496 ProgressMeter -            done    398749.0    50.0 s       2.1 m      100.0%    50.0 s       0.0 s
[2016-04-14T23:21Z] INFO  16:21:33,498 ProgressMeter - Total runtime 50.25 secs, 0.84 min, 0.01 hours
[2016-04-14T23:21Z] INFO  16:21:33,498 MicroScheduler - 182 reads were filtered out during the traversal out of approximately 398931 total reads (0.05%)
[2016-04-14T23:21Z] INFO  16:21:33,499 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:21Z] INFO  16:21:33,500 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:21Z] INFO  16:21:33,501 MicroScheduler -   -> 182 reads (0.05% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:21Z] INFO  16:21:33,516 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:21Z] GATK: realign ('1', 62231950, 77749296) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:21Z] INFO  16:21:34,486 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:21Z] GATK: realign ('1', 240255409, 249250621) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:21Z] INFO  16:21:35,183 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:21Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-1_159504867_175046963-prep-prealign.bam
[2016-04-14T23:21Z] INFO  16:21:35,888 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:21Z] INFO  16:21:35,891 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:21Z] INFO  16:21:35,891 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:21Z] INFO  16:21:35,891 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:21Z] INFO  16:21:35,896 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/1/R14-18102_kapa-NGv3-PE100-NGv3-sort-1_77752625_93297674-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/1/R14-18102_kapa-NGv3-PE100-NGv3-sort-1_77752625_93297674-prep-prealign-realign.intervals -L 1:77752626-93297674 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/1/tx/tmpTa6Msx/R14-18102_kapa-NGv3-PE100-NGv3-sort-1_77752625_93297674-prep.bam
[2016-04-14T23:21Z] INFO  16:21:35,908 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:21Z] INFO  16:21:35,911 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:21Z] INFO  16:21:35,912 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:21Z] INFO  16:21:35,912 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:21Z] INFO  16:21:35,917 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/2/R14-18102_kapa-NGv3-PE100-NGv3-sort-2_0_15514844-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/2/R14-18102_kapa-NGv3-PE100-NGv3-sort-2_0_15514844-prep-prealign-realign.intervals -L 2:1-15514844 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/2/tx/tmpfse1Qb/R14-18102_kapa-NGv3-PE100-NGv3-sort-2_0_15514844-prep.bam
[2016-04-14T23:21Z] INFO  16:21:35,920 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:21Z] INFO  16:21:35,921 HelpFormatter - Date/Time: 2016/04/14 16:21:35
[2016-04-14T23:21Z] INFO  16:21:35,921 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:21Z] INFO  16:21:35,921 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:21Z] INFO  16:21:35,927 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:21Z] INFO  16:21:35,928 HelpFormatter - Date/Time: 2016/04/14 16:21:35
[2016-04-14T23:21Z] INFO  16:21:35,929 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:21Z] INFO  16:21:35,929 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:21Z] INFO  16:21:36,139 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:21Z] INFO  16:21:36,169 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:21Z] INFO  16:21:36,172 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:21Z] INFO  16:21:36,173 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:21Z] INFO  16:21:36,173 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:21Z] INFO  16:21:36,178 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/1/R14-18102_kapa-NGv3-PE100-NGv3-sort-1_93298945_108993401-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/1/R14-18102_kapa-NGv3-PE100-NGv3-sort-1_93298945_108993401-prep-prealign-realign.intervals -L 1:93298946-108993401 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/1/tx/tmp4f1dcJ/R14-18102_kapa-NGv3-PE100-NGv3-sort-1_93298945_108993401-prep.bam
[2016-04-14T23:21Z] INFO  16:21:36,187 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:21Z] INFO  16:21:36,194 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:21Z] INFO  16:21:36,198 HelpFormatter - Date/Time: 2016/04/14 16:21:36
[2016-04-14T23:21Z] INFO  16:21:36,199 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:21Z] INFO  16:21:36,200 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:21Z] INFO  16:21:36,267 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:21Z] INFO  16:21:36,276 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:21Z] INFO  16:21:36,342 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-14T23:21Z] INFO  16:21:36,375 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:21Z] INFO  16:21:36,385 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:21Z] INFO  16:21:36,408 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:21Z] INFO  16:21:36,446 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-14T23:21Z] GATK RealignerTargetCreator: R14-18102_kapa-NGv3-PE100-NGv3-sort-1_159504867_175046963-prep-prealign.bam 1:159504868-175046963
[2016-04-14T23:21Z] GATK: RealignerTargetCreator
[2016-04-14T23:21Z] INFO  16:21:36,539 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:21Z] INFO  16:21:36,543 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:21Z] INFO  16:21:36,546 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:21Z] INFO  16:21:36,547 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:21Z] INFO  16:21:36,547 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:21Z] INFO  16:21:36,548 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:21Z] INFO  16:21:36,552 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/1/R14-18102_kapa-NGv3-PE100-NGv3-sort-1_62231950_77749296-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/1/R14-18102_kapa-NGv3-PE100-NGv3-sort-1_62231950_77749296-prep-prealign-realign.intervals -L 1:62231951-77749296 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/1/tx/tmpgKcFIY/R14-18102_kapa-NGv3-PE100-NGv3-sort-1_62231950_77749296-prep.bam
[2016-04-14T23:21Z] INFO  16:21:36,572 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:21Z] INFO  16:21:36,573 HelpFormatter - Date/Time: 2016/04/14 16:21:36
[2016-04-14T23:21Z] INFO  16:21:36,573 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:21Z] INFO  16:21:36,574 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:21Z] INFO  16:21:36,611 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-14T23:21Z] INFO  16:21:36,766 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@3369d7a
[2016-04-14T23:21Z] INFO  16:21:36,774 IntervalUtils - Processing 15514844 bp from intervals
[2016-04-14T23:21Z] WARN  16:21:36,792 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:21Z] INFO  16:21:36,867 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:21Z] INFO  16:21:36,873 IntervalUtils - Processing 15545049 bp from intervals
[2016-04-14T23:21Z] WARN  16:21:36,879 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:21Z] INFO  16:21:36,877 ProgressMeter -            done    413363.0    53.0 s       2.2 m      100.0%    53.0 s       0.0 s
[2016-04-14T23:21Z] INFO  16:21:36,878 ProgressMeter - Total runtime 53.85 secs, 0.90 min, 0.01 hours
[2016-04-14T23:21Z] INFO  16:21:36,878 MicroScheduler - 212 reads were filtered out during the traversal out of approximately 413575 total reads (0.05%)
[2016-04-14T23:21Z] INFO  16:21:36,879 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:21Z] INFO  16:21:36,879 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:21Z] INFO  16:21:36,879 MicroScheduler -   -> 212 reads (0.05% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:21Z] INFO  16:21:36,882 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:21Z] INFO  16:21:36,946 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:21Z] INFO  16:21:37,006 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:21Z] INFO  16:21:37,017 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:21Z] INFO  16:21:37,030 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@3fbd06f1
[2016-04-14T23:21Z] INFO  16:21:37,061 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:21Z] INFO  16:21:37,062 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:21Z] INFO  16:21:37,063 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:21Z] INFO  16:21:37,063 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:21Z] INFO  16:21:37,077 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-14T23:21Z] INFO  16:21:37,093 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:21Z] INFO  16:21:37,093 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:21Z] INFO  16:21:37,094 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:21Z] INFO  16:21:37,095 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:21Z] INFO  16:21:37,097 IntervalUtils - Processing 15694456 bp from intervals
[2016-04-14T23:21Z] WARN  16:21:37,103 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:21Z] INFO  16:21:37,235 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:21Z] INFO  16:21:37,259 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:21Z] INFO  16:21:37,265 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:21Z] INFO  16:21:37,314 ProgressMeter -            done    412767.0    53.0 s       2.2 m      100.0%    53.0 s       0.0 s
[2016-04-14T23:21Z] INFO  16:21:37,315 ProgressMeter - Total runtime 53.85 secs, 0.90 min, 0.01 hours
[2016-04-14T23:21Z] INFO  16:21:37,315 MicroScheduler - 217 reads were filtered out during the traversal out of approximately 412984 total reads (0.05%)
[2016-04-14T23:21Z] INFO  16:21:37,315 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:21Z] INFO  16:21:37,316 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:21Z] INFO  16:21:37,316 MicroScheduler -   -> 217 reads (0.05% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:21Z] INFO  16:21:37,408 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:21Z] INFO  16:21:37,421 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:21Z] INFO  16:21:37,421 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:21Z] INFO  16:21:37,421 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:21Z] INFO  16:21:37,425 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/1/R14-18102_kapa-NGv3-PE100-NGv3-sort-1_240255409_249250621-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/1/R14-18102_kapa-NGv3-PE100-NGv3-sort-1_240255409_249250621-prep-prealign-realign.intervals -L 1:240255410-249250621 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/1/tx/tmpQu4oLg/R14-18102_kapa-NGv3-PE100-NGv3-sort-1_240255409_249250621-prep.bam
[2016-04-14T23:21Z] INFO  16:21:37,450 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:21Z] INFO  16:21:37,456 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:21Z] INFO  16:21:37,457 HelpFormatter - Date/Time: 2016/04/14 16:21:37
[2016-04-14T23:21Z] INFO  16:21:37,457 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:21Z] INFO  16:21:37,457 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:21Z] INFO  16:21:37,467 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:21Z] INFO  16:21:37,473 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:21Z] INFO  16:21:37,475 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:21Z] INFO  16:21:37,475 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:21Z] INFO  16:21:37,476 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:21Z] INFO  16:21:37,522 IntervalUtils - Processing 15517346 bp from intervals
[2016-04-14T23:21Z] WARN  16:21:37,529 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:21Z] INFO  16:21:37,616 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:21Z] INFO  16:21:37,685 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:21Z] INFO  16:21:37,690 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:21Z] INFO  16:21:37,738 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:21Z] INFO  16:21:37,739 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:21Z] INFO  16:21:37,740 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:21Z] INFO  16:21:37,741 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:21Z] INFO  16:21:37,783 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:21Z] INFO  16:21:37,793 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:21Z] INFO  16:21:37,829 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:21Z] INFO  16:21:37,851 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-14T23:21Z] INFO  16:21:37,932 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:21Z] INFO  16:21:38,133 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:21Z] INFO  16:21:38,160 IntervalUtils - Processing 8995212 bp from intervals
[2016-04-14T23:21Z] WARN  16:21:38,165 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:21Z] INFO  16:21:38,250 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:21Z] INFO  16:21:38,382 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:21Z] INFO  16:21:38,382 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:21Z] INFO  16:21:38,383 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:21Z] INFO  16:21:38,383 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:21Z] INFO  16:21:38,548 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:21Z] INFO  16:21:38,660 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:21Z] INFO  16:21:38,661 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:21Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-1_108994811_143767848-prep-prealign.bam
[2016-04-14T23:21Z] INFO  16:21:38,853 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:21Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-1_192128349_207640257-prep-prealign.bam
[2016-04-14T23:21Z] INFO  16:21:39,612 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:21Z] INFO  16:21:39,616 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:21Z] INFO  16:21:39,616 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:21Z] INFO  16:21:39,617 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:21Z] INFO  16:21:39,622 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/1/R14-18102_kapa-NGv3-PE100-NGv3-sort-1_159504867_175046963-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/1/tx/tmpu4RIkH/R14-18102_kapa-NGv3-PE100-NGv3-sort-1_159504867_175046963-prep-prealign-realign.intervals -l INFO -L 1:159504868-175046963 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-14T23:21Z] INFO  16:21:39,652 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:21Z] INFO  16:21:39,654 HelpFormatter - Date/Time: 2016/04/14 16:21:39
[2016-04-14T23:21Z] INFO  16:21:39,654 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:21Z] INFO  16:21:39,655 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:21Z] INFO  16:21:39,781 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:21Z] INFO  16:21:39,923 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@7e64f359
[2016-04-14T23:21Z] INFO  16:21:40,047 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-14T23:21Z] INFO  16:21:40,057 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:21Z] GATK RealignerTargetCreator: R14-18102_kapa-NGv3-PE100-NGv3-sort-1_108994811_143767848-prep-prealign.bam 1:108994812-143767848
[2016-04-14T23:21Z] GATK: RealignerTargetCreator
[2016-04-14T23:21Z] INFO  16:21:40,124 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-14T23:21Z] INFO  16:21:40,141 ProgressMeter -            done    434166.0    56.0 s       2.1 m      100.0%    56.0 s       0.0 s
[2016-04-14T23:21Z] INFO  16:21:40,142 ProgressMeter - Total runtime 56.00 secs, 0.93 min, 0.02 hours
[2016-04-14T23:21Z] INFO  16:21:40,142 MicroScheduler - 211 reads were filtered out during the traversal out of approximately 434377 total reads (0.05%)
[2016-04-14T23:21Z] INFO  16:21:40,142 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:21Z] INFO  16:21:40,143 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:21Z] INFO  16:21:40,143 MicroScheduler -   -> 211 reads (0.05% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:21Z] GATK RealignerTargetCreator: R14-18102_kapa-NGv3-PE100-NGv3-sort-1_192128349_207640257-prep-prealign.bam 1:192128350-207640257
[2016-04-14T23:21Z] GATK: RealignerTargetCreator
[2016-04-14T23:21Z] INFO  16:21:40,415 IntervalUtils - Processing 15542096 bp from intervals
[2016-04-14T23:21Z] WARN  16:21:40,421 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:21Z] INFO  16:21:40,524 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:21Z] INFO  16:21:40,710 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:21Z] INFO  16:21:40,712 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:21Z] INFO  16:21:40,712 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:21Z] INFO  16:21:40,713 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-14T23:21Z] INFO  16:21:41,543 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:21Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-1_223162737_240072524-prep-prealign.bam
[2016-04-14T23:21Z] INFO  16:21:42,644 ProgressMeter -            done   1.551458E7    18.0 s       1.0 s      100.0%    18.0 s       0.0 s
[2016-04-14T23:21Z] INFO  16:21:42,645 ProgressMeter - Total runtime 18.61 secs, 0.31 min, 0.01 hours
[2016-04-14T23:21Z] INFO  16:21:42,649 MicroScheduler - 28990 reads were filtered out during the traversal out of approximately 249159 total reads (11.64%)
[2016-04-14T23:21Z] INFO  16:21:42,661 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:21Z] INFO  16:21:42,662 MicroScheduler -   -> 718 reads (0.29% of total) failing BadMateFilter
[2016-04-14T23:21Z] INFO  16:21:42,662 MicroScheduler -   -> 19165 reads (7.69% of total) failing DuplicateReadFilter
[2016-04-14T23:21Z] INFO  16:21:42,663 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-14T23:21Z] INFO  16:21:42,664 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:21Z] INFO  16:21:42,664 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-14T23:21Z] INFO  16:21:42,665 MicroScheduler -   -> 9107 reads (3.66% of total) failing MappingQualityZeroFilter
[2016-04-14T23:21Z] INFO  16:21:42,666 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:21Z] INFO  16:21:42,666 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-14T23:21Z] INFO  16:21:42,667 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-14T23:21Z] GATK RealignerTargetCreator: R14-18102_kapa-NGv3-PE100-NGv3-sort-1_223162737_240072524-prep-prealign.bam 1:223162738-240072524
[2016-04-14T23:21Z] GATK: RealignerTargetCreator
[2016-04-14T23:21Z] INFO  16:21:42,996 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:21Z] INFO  16:21:42,999 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:21Z] INFO  16:21:43,000 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:21Z] INFO  16:21:43,000 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:21Z] INFO  16:21:43,005 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/1/R14-18102_kapa-NGv3-PE100-NGv3-sort-1_192128349_207640257-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/1/tx/tmp3rV167/R14-18102_kapa-NGv3-PE100-NGv3-sort-1_192128349_207640257-prep-prealign-realign.intervals -l INFO -L 1:192128350-207640257 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-14T23:21Z] INFO  16:21:43,019 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:21Z] INFO  16:21:43,020 HelpFormatter - Date/Time: 2016/04/14 16:21:42
[2016-04-14T23:21Z] INFO  16:21:43,021 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:21Z] INFO  16:21:43,021 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:21Z] INFO  16:21:43,048 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:21Z] INFO  16:21:43,052 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:21Z] INFO  16:21:43,052 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:21Z] INFO  16:21:43,053 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:21Z] INFO  16:21:43,057 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/1/R14-18102_kapa-NGv3-PE100-NGv3-sort-1_108994811_143767848-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/1/tx/tmpRA5bkR/R14-18102_kapa-NGv3-PE100-NGv3-sort-1_108994811_143767848-prep-prealign-realign.intervals -l INFO -L 1:108994812-143767848 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-14T23:21Z] INFO  16:21:43,068 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:21Z] INFO  16:21:43,080 HelpFormatter - Date/Time: 2016/04/14 16:21:43
[2016-04-14T23:21Z] INFO  16:21:43,081 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:21Z] INFO  16:21:43,082 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:21Z] INFO  16:21:43,164 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:21Z] INFO  16:21:43,219 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:21Z] INFO  16:21:43,395 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-14T23:21Z] INFO  16:21:43,405 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:21Z] INFO  16:21:43,444 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-14T23:21Z] INFO  16:21:43,454 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:21Z] INFO  16:21:43,487 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-14T23:21Z] INFO  16:21:43,493 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.04
[2016-04-14T23:21Z] INFO  16:21:43,747 IntervalUtils - Processing 34773037 bp from intervals
[2016-04-14T23:21Z] WARN  16:21:43,752 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:21Z] INFO  16:21:43,830 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:21Z] INFO  16:21:43,922 IntervalUtils - Processing 15511908 bp from intervals
[2016-04-14T23:21Z] WARN  16:21:43,938 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:21Z] INFO  16:21:44,036 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:21Z] INFO  16:21:44,102 ProgressMeter -      1:22305040    400018.0    60.0 s       2.5 m       43.2%     2.3 m      78.0 s
[2016-04-14T23:21Z] INFO  16:21:44,135 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:21Z] GATK: realign ('1', 207641871, 223156451) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:21Z] INFO  16:21:44,159 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:21Z] INFO  16:21:44,160 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:21Z] INFO  16:21:44,161 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:21Z] INFO  16:21:44,162 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-14T23:21Z] INFO  16:21:44,225 ProgressMeter -     1:149920953    400045.0    60.0 s       2.5 m       38.8%     2.6 m      94.0 s
[2016-04-14T23:21Z] INFO  16:21:44,296 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:21Z] INFO  16:21:44,296 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:21Z] INFO  16:21:44,297 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:21Z] INFO  16:21:44,297 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-14T23:21Z] INFO  16:21:44,916 ProgressMeter -      1:40928443    400005.0    61.0 s       2.6 m       62.7%    97.0 s      36.0 s
[2016-04-14T23:21Z] INFO  16:21:45,096 ProgressMeter -       1:9658615    400010.0    60.0 s       2.5 m       62.1%    96.0 s      36.0 s
[2016-04-14T23:21Z] INFO  16:21:45,776 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:21Z] INFO  16:21:45,780 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:21Z] INFO  16:21:45,781 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:21Z] INFO  16:21:45,781 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:21Z] INFO  16:21:45,786 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/1/R14-18102_kapa-NGv3-PE100-NGv3-sort-1_223162737_240072524-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/1/tx/tmpJU9hch/R14-18102_kapa-NGv3-PE100-NGv3-sort-1_223162737_240072524-prep-prealign-realign.intervals -l INFO -L 1:223162738-240072524 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-14T23:21Z] INFO  16:21:45,804 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:21Z] INFO  16:21:45,804 HelpFormatter - Date/Time: 2016/04/14 16:21:45
[2016-04-14T23:21Z] INFO  16:21:45,804 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:21Z] INFO  16:21:45,804 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:21Z] INFO  16:21:45,938 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:21Z] INFO  16:21:46,170 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-14T23:21Z] INFO  16:21:46,179 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:21Z] INFO  16:21:46,261 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-14T23:21Z] INFO  16:21:46,542 IntervalUtils - Processing 16909787 bp from intervals
[2016-04-14T23:21Z] WARN  16:21:46,548 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:21Z] INFO  16:21:46,655 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:21Z] INFO  16:21:46,710 ProgressMeter -            done   1.7079418E7    21.0 s       1.0 s      100.0%    21.0 s       0.0 s
[2016-04-14T23:21Z] INFO  16:21:46,712 ProgressMeter - Total runtime 21.61 secs, 0.36 min, 0.01 hours
[2016-04-14T23:21Z] INFO  16:21:46,716 MicroScheduler - 21442 reads were filtered out during the traversal out of approximately 261909 total reads (8.19%)
[2016-04-14T23:21Z] INFO  16:21:46,717 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:21Z] INFO  16:21:46,718 MicroScheduler -   -> 645 reads (0.25% of total) failing BadMateFilter
[2016-04-14T23:21Z] INFO  16:21:46,719 MicroScheduler -   -> 20332 reads (7.76% of total) failing DuplicateReadFilter
[2016-04-14T23:21Z] INFO  16:21:46,720 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-14T23:21Z] INFO  16:21:46,721 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:21Z] INFO  16:21:46,721 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-14T23:21Z] INFO  16:21:46,722 MicroScheduler -   -> 465 reads (0.18% of total) failing MappingQualityZeroFilter
[2016-04-14T23:21Z] INFO  16:21:46,723 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:21Z] INFO  16:21:46,724 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-14T23:21Z] INFO  16:21:46,724 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-14T23:21Z] INFO  16:21:46,987 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:21Z] INFO  16:21:46,988 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:21Z] INFO  16:21:46,989 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:21Z] INFO  16:21:46,992 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-14T23:21Z] INFO  16:21:47,121 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:21Z] INFO  16:21:47,125 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:21Z] INFO  16:21:47,126 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:21Z] INFO  16:21:47,127 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:21Z] INFO  16:21:47,132 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/1/R14-18102_kapa-NGv3-PE100-NGv3-sort-1_207641871_223156451-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/1/R14-18102_kapa-NGv3-PE100-NGv3-sort-1_207641871_223156451-prep-prealign-realign.intervals -L 1:207641872-223156451 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/1/tx/tmpYoLDUg/R14-18102_kapa-NGv3-PE100-NGv3-sort-1_207641871_223156451-prep.bam
[2016-04-14T23:21Z] INFO  16:21:47,147 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:21Z] INFO  16:21:47,149 HelpFormatter - Date/Time: 2016/04/14 16:21:47
[2016-04-14T23:21Z] INFO  16:21:47,149 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:21Z] INFO  16:21:47,150 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:21Z] INFO  16:21:47,377 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:21Z] INFO  16:21:47,467 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:21Z] INFO  16:21:47,494 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:21Z] INFO  16:21:47,593 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.10
[2016-04-14T23:21Z] INFO  16:21:47,944 IntervalUtils - Processing 15514580 bp from intervals
[2016-04-14T23:21Z] WARN  16:21:47,949 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:21Z] INFO  16:21:48,035 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:21Z] INFO  16:21:48,074 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:21Z] GATK: realign ('1', 175048468, 192127886) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:21Z] INFO  16:21:48,185 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:21Z] INFO  16:21:48,186 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:21Z] INFO  16:21:48,187 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:21Z] INFO  16:21:48,191 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:21Z] INFO  16:21:48,408 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:21Z] INFO  16:21:48,593 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:21Z] INFO  16:21:50,681 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:21Z] INFO  16:21:50,685 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:21Z] INFO  16:21:50,685 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:21Z] INFO  16:21:50,686 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:21Z] INFO  16:21:50,690 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/1/R14-18102_kapa-NGv3-PE100-NGv3-sort-1_175048468_192127886-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/1/R14-18102_kapa-NGv3-PE100-NGv3-sort-1_175048468_192127886-prep-prealign-realign.intervals -L 1:175048469-192127886 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/1/tx/tmpx9bAV1/R14-18102_kapa-NGv3-PE100-NGv3-sort-1_175048468_192127886-prep.bam
[2016-04-14T23:21Z] INFO  16:21:50,717 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:21Z] INFO  16:21:50,718 HelpFormatter - Date/Time: 2016/04/14 16:21:50
[2016-04-14T23:21Z] INFO  16:21:50,719 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:21Z] INFO  16:21:50,719 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:21Z] INFO  16:21:50,908 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:21Z] INFO  16:21:50,997 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:21Z] INFO  16:21:51,006 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:21Z] INFO  16:21:51,045 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.04
[2016-04-14T23:21Z] INFO  16:21:51,274 ProgressMeter -            done    155026.0    14.0 s      91.0 s      100.0%    14.0 s       0.0 s
[2016-04-14T23:21Z] INFO  16:21:51,275 ProgressMeter - Total runtime 14.21 secs, 0.24 min, 0.00 hours
[2016-04-14T23:21Z] INFO  16:21:51,278 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 155026 total reads (0.00%)
[2016-04-14T23:21Z] INFO  16:21:51,278 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:21Z] INFO  16:21:51,279 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:21Z] INFO  16:21:51,279 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:21Z] INFO  16:21:51,352 IntervalUtils - Processing 17079418 bp from intervals
[2016-04-14T23:21Z] WARN  16:21:51,358 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:21Z] INFO  16:21:51,393 ProgressMeter -            done    174042.0    14.0 s      82.0 s      100.0%    14.0 s       0.0 s
[2016-04-14T23:21Z] INFO  16:21:51,394 ProgressMeter - Total runtime 14.30 secs, 0.24 min, 0.00 hours
[2016-04-14T23:21Z] INFO  16:21:51,398 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 174042 total reads (0.00%)
[2016-04-14T23:21Z] INFO  16:21:51,399 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:21Z] INFO  16:21:51,400 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:21Z] INFO  16:21:51,401 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:21Z] INFO  16:21:51,432 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:21Z] INFO  16:21:51,560 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:21Z] INFO  16:21:51,561 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:21Z] INFO  16:21:51,562 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:21Z] INFO  16:21:51,562 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:21Z] INFO  16:21:51,723 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:21Z] INFO  16:21:51,939 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:21Z] INFO  16:21:51,944 ProgressMeter -            done   1.551318E7    20.0 s       1.0 s      100.0%    20.0 s       0.0 s
[2016-04-14T23:21Z] INFO  16:21:51,945 ProgressMeter - Total runtime 20.40 secs, 0.34 min, 0.01 hours
[2016-04-14T23:21Z] INFO  16:21:51,958 MicroScheduler - 27421 reads were filtered out during the traversal out of approximately 304520 total reads (9.00%)
[2016-04-14T23:21Z] INFO  16:21:51,960 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:21Z] INFO  16:21:51,960 MicroScheduler -   -> 720 reads (0.24% of total) failing BadMateFilter
[2016-04-14T23:21Z] INFO  16:21:51,961 MicroScheduler -   -> 24135 reads (7.93% of total) failing DuplicateReadFilter
[2016-04-14T23:21Z] INFO  16:21:51,962 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-14T23:21Z] INFO  16:21:51,963 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:21Z] INFO  16:21:51,963 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-14T23:21Z] INFO  16:21:51,964 MicroScheduler -   -> 2566 reads (0.84% of total) failing MappingQualityZeroFilter
[2016-04-14T23:21Z] INFO  16:21:51,965 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:21Z] INFO  16:21:51,966 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-14T23:21Z] INFO  16:21:51,967 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-14T23:21Z] INFO  16:21:52,082 ProgressMeter -            done    183893.0    14.0 s      79.0 s      100.0%    14.0 s       0.0 s
[2016-04-14T23:21Z] INFO  16:21:52,083 ProgressMeter - Total runtime 14.61 secs, 0.24 min, 0.00 hours
[2016-04-14T23:21Z] INFO  16:21:52,088 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 183893 total reads (0.00%)
[2016-04-14T23:21Z] INFO  16:21:52,089 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:21Z] INFO  16:21:52,090 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:21Z] INFO  16:21:52,091 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:21Z] INFO  16:21:52,370 ProgressMeter -            done    181172.0    14.0 s      80.0 s      100.0%    14.0 s       0.0 s
[2016-04-14T23:21Z] INFO  16:21:52,371 ProgressMeter - Total runtime 14.63 secs, 0.24 min, 0.00 hours
[2016-04-14T23:21Z] INFO  16:21:52,375 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 181172 total reads (0.00%)
[2016-04-14T23:21Z] INFO  16:21:52,376 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:21Z] INFO  16:21:52,376 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:21Z] INFO  16:21:52,376 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:21Z] INFO  16:21:52,853 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:21Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-2_0_15514844-prep.bam
[2016-04-14T23:21Z] INFO  16:21:52,976 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:21Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-1_77752625_93297674-prep.bam
[2016-04-14T23:21Z] GATK pre-alignment ('2', 15519725, 31133925) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:21Z] GATK pre-alignment ('2', 31135088, 46706841) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:21Z] INFO  16:21:53,611 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:21Z] GATK: realign ('1', 46715671, 62228851) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:21Z] INFO  16:21:53,660 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:21Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-1_93298945_108993401-prep.bam
[2016-04-14T23:21Z] INFO  16:21:53,742 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:21Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-1_62231950_77749296-prep.bam
[2016-04-14T23:21Z] INFO  16:21:53,884 ProgressMeter -            done    197913.0    15.0 s      78.0 s       99.8%    15.0 s       0.0 s
[2016-04-14T23:21Z] INFO  16:21:53,885 ProgressMeter - Total runtime 15.50 secs, 0.26 min, 0.00 hours
[2016-04-14T23:21Z] INFO  16:21:53,889 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 197913 total reads (0.00%)
[2016-04-14T23:21Z] INFO  16:21:53,889 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:21Z] INFO  16:21:53,892 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:21Z] INFO  16:21:53,892 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:21Z] GATK pre-alignment ('2', 46707543, 62228117) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:21Z] GATK pre-alignment ('2', 62362965, 79253295) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:21Z] INFO  16:21:55,724 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:21Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-1_240255409_249250621-prep.bam
[2016-04-14T23:21Z] INFO  16:21:56,229 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:21Z] INFO  16:21:56,232 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:21Z] INFO  16:21:56,233 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:21Z] INFO  16:21:56,234 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:21Z] INFO  16:21:56,238 HelpFormatter - Program Args: -T PrintReads -L 2:15519726-31133925 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/2/tx/tmpwvN1LU/R14-18102_kapa-NGv3-PE100-NGv3-sort-2_15519725_31133925-prep-prealign.bam
[2016-04-14T23:21Z] INFO  16:21:56,267 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:21Z] INFO  16:21:56,268 HelpFormatter - Date/Time: 2016/04/14 16:21:56
[2016-04-14T23:21Z] INFO  16:21:56,268 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:21Z] INFO  16:21:56,269 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:21Z] INFO  16:21:56,412 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:21Z] GATK pre-alignment ('2', 79253838, 95537822) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:21Z] INFO  16:21:56,690 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:21Z] INFO  16:21:56,693 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:21Z] INFO  16:21:56,694 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:21Z] INFO  16:21:56,695 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:21Z] INFO  16:21:56,700 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/1/R14-18102_kapa-NGv3-PE100-NGv3-sort-1_46715671_62228851-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/1/R14-18102_kapa-NGv3-PE100-NGv3-sort-1_46715671_62228851-prep-prealign-realign.intervals -L 1:46715672-62228851 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/1/tx/tmpQxYjqd/R14-18102_kapa-NGv3-PE100-NGv3-sort-1_46715671_62228851-prep.bam
[2016-04-14T23:21Z] INFO  16:21:56,724 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:21Z] INFO  16:21:56,725 HelpFormatter - Date/Time: 2016/04/14 16:21:56
[2016-04-14T23:21Z] INFO  16:21:56,726 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:21Z] INFO  16:21:56,732 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:21Z] INFO  16:21:56,849 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:21Z] INFO  16:21:56,852 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:21Z] INFO  16:21:56,852 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:21Z] INFO  16:21:56,853 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:21Z] INFO  16:21:56,857 HelpFormatter - Program Args: -T PrintReads -L 2:31135089-46706841 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/2/tx/tmpXL4VtC/R14-18102_kapa-NGv3-PE100-NGv3-sort-2_31135088_46706841-prep-prealign.bam
[2016-04-14T23:21Z] INFO  16:21:56,910 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:21Z] INFO  16:21:56,910 HelpFormatter - Date/Time: 2016/04/14 16:21:56
[2016-04-14T23:21Z] INFO  16:21:56,911 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:21Z] INFO  16:21:56,911 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:21Z] INFO  16:21:56,947 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:21Z] INFO  16:21:57,131 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:21Z] INFO  16:21:57,146 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:21Z] INFO  16:21:57,160 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:21Z] INFO  16:21:57,225 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-14T23:21Z] INFO  16:21:57,414 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-14T23:21Z] INFO  16:21:57,432 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:21Z] INFO  16:21:57,436 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:21Z] INFO  16:21:57,437 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:21Z] INFO  16:21:57,437 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:21Z] INFO  16:21:57,443 HelpFormatter - Program Args: -T PrintReads -L 2:62362966-79253295 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/2/tx/tmpLzdCbE/R14-18102_kapa-NGv3-PE100-NGv3-sort-2_62362965_79253295-prep-prealign.bam
[2016-04-14T23:21Z] INFO  16:21:57,477 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:21Z] INFO  16:21:57,478 HelpFormatter - Date/Time: 2016/04/14 16:21:57
[2016-04-14T23:21Z] INFO  16:21:57,479 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:21Z] INFO  16:21:57,479 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:21Z] INFO  16:21:57,497 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:21Z] INFO  16:21:57,501 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:21Z] INFO  16:21:57,501 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:21Z] INFO  16:21:57,502 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:21Z] INFO  16:21:57,508 HelpFormatter - Program Args: -T PrintReads -L 2:46707544-62228117 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/2/tx/tmpySEpxF/R14-18102_kapa-NGv3-PE100-NGv3-sort-2_46707543_62228117-prep-prealign.bam
[2016-04-14T23:21Z] INFO  16:21:57,520 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:21Z] INFO  16:21:57,529 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:21Z] INFO  16:21:57,536 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:21Z] INFO  16:21:57,541 HelpFormatter - Date/Time: 2016/04/14 16:21:57
[2016-04-14T23:21Z] INFO  16:21:57,541 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:21Z] INFO  16:21:57,542 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:21Z] INFO  16:21:57,596 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-14T23:21Z] INFO  16:21:57,610 IntervalUtils - Processing 15614200 bp from intervals
[2016-04-14T23:21Z] INFO  16:21:57,684 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:21Z] INFO  16:21:57,693 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:21Z] INFO  16:21:57,768 IntervalUtils - Processing 15513180 bp from intervals
[2016-04-14T23:21Z] WARN  16:21:57,773 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:21Z] INFO  16:21:57,787 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:21Z] INFO  16:21:57,856 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:21Z] INFO  16:21:57,942 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:21Z] INFO  16:21:57,944 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:21Z] INFO  16:21:57,944 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:21Z] INFO  16:21:57,945 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:21Z] INFO  16:21:57,959 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:21Z] INFO  16:21:58,019 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:21Z] INFO  16:21:58,020 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:21Z] INFO  16:21:58,021 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:21Z] INFO  16:21:58,022 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:21Z] INFO  16:21:58,186 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:21Z] INFO  16:21:58,202 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:21Z] INFO  16:21:58,416 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:21Z] INFO  16:21:58,451 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-14T23:21Z] INFO  16:21:58,530 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:21Z] INFO  16:21:58,547 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:21Z] INFO  16:21:58,647 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.10
[2016-04-14T23:21Z] INFO  16:21:58,673 IntervalUtils - Processing 15571753 bp from intervals
[2016-04-14T23:21Z] INFO  16:21:58,749 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:21Z] INFO  16:21:58,775 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-14T23:21Z] INFO  16:21:58,832 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:21Z] INFO  16:21:58,841 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:21Z] INFO  16:21:58,885 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.04
[2016-04-14T23:21Z] INFO  16:21:58,908 IntervalUtils - Processing 16890330 bp from intervals
[2016-04-14T23:21Z] INFO  16:21:58,916 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-14T23:21Z] INFO  16:21:58,985 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:21Z] INFO  16:21:58,996 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:21Z] INFO  16:21:59,011 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:21Z] INFO  16:21:59,050 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-14T23:21Z] INFO  16:21:59,073 IntervalUtils - Processing 15520574 bp from intervals
[2016-04-14T23:21Z] INFO  16:21:59,110 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:21Z] INFO  16:21:59,111 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:21Z] INFO  16:21:59,112 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:21Z] INFO  16:21:59,112 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:21Z] INFO  16:21:59,126 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:21Z] INFO  16:21:59,153 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:21Z] INFO  16:21:59,260 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:21Z] INFO  16:21:59,326 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:21Z] INFO  16:21:59,326 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:21Z] INFO  16:21:59,327 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:21Z] INFO  16:21:59,327 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:21Z] INFO  16:21:59,362 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:21Z] INFO  16:21:59,476 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:21Z] INFO  16:21:59,477 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:21Z] INFO  16:21:59,478 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:21Z] INFO  16:21:59,479 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:21Z] INFO  16:21:59,500 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:21Z] INFO  16:21:59,555 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:21Z] INFO  16:21:59,557 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:21Z] INFO  16:21:59,558 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:21Z] INFO  16:21:59,558 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:21Z] INFO  16:21:59,562 HelpFormatter - Program Args: -T PrintReads -L 2:79253839-95537822 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/2/tx/tmpg5knDE/R14-18102_kapa-NGv3-PE100-NGv3-sort-2_79253838_95537822-prep-prealign.bam
[2016-04-14T23:21Z] INFO  16:21:59,571 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:21Z] INFO  16:21:59,582 HelpFormatter - Date/Time: 2016/04/14 16:21:59
[2016-04-14T23:21Z] INFO  16:21:59,583 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:21Z] INFO  16:21:59,583 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:21Z] INFO  16:21:59,619 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:21Z] INFO  16:21:59,643 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:21Z] INFO  16:21:59,813 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:22Z] INFO  16:22:00,881 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-14T23:22Z] INFO  16:22:00,984 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:22Z] INFO  16:22:00,994 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:22Z] INFO  16:22:01,060 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-14T23:22Z] INFO  16:22:01,075 IntervalUtils - Processing 16283984 bp from intervals
[2016-04-14T23:22Z] INFO  16:22:01,170 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:22Z] INFO  16:22:01,500 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:22Z] INFO  16:22:01,501 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:22Z] INFO  16:22:01,502 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:22Z] INFO  16:22:01,502 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:22Z] INFO  16:22:01,516 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:22Z] INFO  16:22:01,653 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:22Z] INFO  16:22:03,013 ProgressMeter -            done   1.5542096E7    22.0 s       1.0 s      100.0%    22.0 s       0.0 s
[2016-04-14T23:22Z] INFO  16:22:03,014 ProgressMeter - Total runtime 22.30 secs, 0.37 min, 0.01 hours
[2016-04-14T23:22Z] INFO  16:22:03,018 MicroScheduler - 37268 reads were filtered out during the traversal out of approximately 401229 total reads (9.29%)
[2016-04-14T23:22Z] INFO  16:22:03,020 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:22Z] INFO  16:22:03,020 MicroScheduler -   -> 800 reads (0.20% of total) failing BadMateFilter
[2016-04-14T23:22Z] INFO  16:22:03,021 MicroScheduler -   -> 31203 reads (7.78% of total) failing DuplicateReadFilter
[2016-04-14T23:22Z] INFO  16:22:03,021 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-14T23:22Z] INFO  16:22:03,021 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:22Z] INFO  16:22:03,021 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-14T23:22Z] INFO  16:22:03,022 MicroScheduler -   -> 5265 reads (1.31% of total) failing MappingQualityZeroFilter
[2016-04-14T23:22Z] INFO  16:22:03,022 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:22Z] INFO  16:22:03,022 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-14T23:22Z] INFO  16:22:03,022 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-14T23:22Z] INFO  16:22:04,429 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:22Z] GATK: realign ('1', 159504867, 175046963) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:22Z] INFO  16:22:06,768 ProgressMeter -            done   1.5511908E7    22.0 s       1.0 s      100.0%    22.0 s       0.0 s
[2016-04-14T23:22Z] INFO  16:22:06,769 ProgressMeter - Total runtime 22.47 secs, 0.37 min, 0.01 hours
[2016-04-14T23:22Z] INFO  16:22:06,773 MicroScheduler - 38496 reads were filtered out during the traversal out of approximately 415477 total reads (9.27%)
[2016-04-14T23:22Z] INFO  16:22:06,773 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:22Z] INFO  16:22:06,773 MicroScheduler -   -> 837 reads (0.20% of total) failing BadMateFilter
[2016-04-14T23:22Z] INFO  16:22:06,774 MicroScheduler -   -> 32630 reads (7.85% of total) failing DuplicateReadFilter
[2016-04-14T23:22Z] INFO  16:22:06,774 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-14T23:22Z] INFO  16:22:06,774 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:22Z] INFO  16:22:06,774 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-14T23:22Z] INFO  16:22:06,775 MicroScheduler -   -> 5029 reads (1.21% of total) failing MappingQualityZeroFilter
[2016-04-14T23:22Z] INFO  16:22:06,775 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:22Z] INFO  16:22:06,775 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-14T23:22Z] INFO  16:22:06,775 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-14T23:22Z] INFO  16:22:07,344 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:22Z] INFO  16:22:07,347 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:22Z] INFO  16:22:07,348 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:22Z] INFO  16:22:07,349 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:22Z] INFO  16:22:07,353 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/1/R14-18102_kapa-NGv3-PE100-NGv3-sort-1_159504867_175046963-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/1/R14-18102_kapa-NGv3-PE100-NGv3-sort-1_159504867_175046963-prep-prealign-realign.intervals -L 1:159504868-175046963 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/1/tx/tmpHvSkJW/R14-18102_kapa-NGv3-PE100-NGv3-sort-1_159504867_175046963-prep.bam
[2016-04-14T23:22Z] INFO  16:22:07,363 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:22Z] INFO  16:22:07,365 HelpFormatter - Date/Time: 2016/04/14 16:22:07
[2016-04-14T23:22Z] INFO  16:22:07,366 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:22Z] INFO  16:22:07,366 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:22Z] INFO  16:22:07,563 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:22Z] INFO  16:22:07,681 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:22Z] INFO  16:22:07,711 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:22Z] INFO  16:22:07,780 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-14T23:22Z] INFO  16:22:07,941 ProgressMeter -            done    248187.0    19.0 s      79.0 s       99.7%    19.0 s       0.0 s
[2016-04-14T23:22Z] INFO  16:22:07,941 ProgressMeter - Total runtime 19.76 secs, 0.33 min, 0.01 hours
[2016-04-14T23:22Z] INFO  16:22:07,945 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 248187 total reads (0.00%)
[2016-04-14T23:22Z] INFO  16:22:07,945 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:22Z] INFO  16:22:07,945 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:22Z] INFO  16:22:07,946 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:22Z] INFO  16:22:08,194 IntervalUtils - Processing 15542096 bp from intervals
[2016-04-14T23:22Z] WARN  16:22:08,200 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:22Z] INFO  16:22:08,288 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:22Z] INFO  16:22:08,300 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:22Z] GATK: realign ('1', 192128349, 207640257) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:22Z] INFO  16:22:08,420 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:22Z] INFO  16:22:08,421 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:22Z] INFO  16:22:08,422 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:22Z] INFO  16:22:08,427 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:22Z] INFO  16:22:08,651 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:22Z] INFO  16:22:08,796 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:22Z] INFO  16:22:09,416 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:22Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-1_207641871_223156451-prep.bam
[2016-04-14T23:22Z] INFO  16:22:10,370 ProgressMeter -            done   1.6909787E7    23.0 s       1.0 s      100.0%    23.0 s       0.0 s
[2016-04-14T23:22Z] INFO  16:22:10,371 ProgressMeter - Total runtime 23.38 secs, 0.39 min, 0.01 hours
[2016-04-14T23:22Z] INFO  16:22:10,375 MicroScheduler - 38192 reads were filtered out during the traversal out of approximately 436672 total reads (8.75%)
[2016-04-14T23:22Z] INFO  16:22:10,376 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:22Z] INFO  16:22:10,377 MicroScheduler -   -> 935 reads (0.21% of total) failing BadMateFilter
[2016-04-14T23:22Z] INFO  16:22:10,378 MicroScheduler -   -> 35097 reads (8.04% of total) failing DuplicateReadFilter
[2016-04-14T23:22Z] INFO  16:22:10,378 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-14T23:22Z] INFO  16:22:10,379 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:22Z] INFO  16:22:10,380 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-14T23:22Z] INFO  16:22:10,380 MicroScheduler -   -> 2160 reads (0.49% of total) failing MappingQualityZeroFilter
[2016-04-14T23:22Z] INFO  16:22:10,381 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:22Z] INFO  16:22:10,382 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-14T23:22Z] INFO  16:22:10,382 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-14T23:22Z] GATK pre-alignment ('2', 95538561, 111273222) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:22Z] INFO  16:22:11,067 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:22Z] INFO  16:22:11,079 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:22Z] INFO  16:22:11,080 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:22Z] INFO  16:22:11,080 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:22Z] INFO  16:22:11,084 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/1/R14-18102_kapa-NGv3-PE100-NGv3-sort-1_192128349_207640257-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/1/R14-18102_kapa-NGv3-PE100-NGv3-sort-1_192128349_207640257-prep-prealign-realign.intervals -L 1:192128350-207640257 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/1/tx/tmpm_lEGJ/R14-18102_kapa-NGv3-PE100-NGv3-sort-1_192128349_207640257-prep.bam
[2016-04-14T23:22Z] INFO  16:22:11,095 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:22Z] INFO  16:22:11,096 HelpFormatter - Date/Time: 2016/04/14 16:22:11
[2016-04-14T23:22Z] INFO  16:22:11,096 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:22Z] INFO  16:22:11,097 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:22Z] INFO  16:22:11,264 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:22Z] INFO  16:22:11,351 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:22Z] INFO  16:22:11,378 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:22Z] INFO  16:22:11,437 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-14T23:22Z] INFO  16:22:11,554 ProgressMeter -            done    259553.0    19.0 s      77.0 s       99.0%    19.0 s       0.0 s
[2016-04-14T23:22Z] INFO  16:22:11,557 ProgressMeter - Total runtime 20.00 secs, 0.33 min, 0.01 hours
[2016-04-14T23:22Z] INFO  16:22:11,564 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 259553 total reads (0.00%)
[2016-04-14T23:22Z] INFO  16:22:11,571 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:22Z] INFO  16:22:11,571 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:22Z] INFO  16:22:11,572 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:22Z] INFO  16:22:11,668 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@1b0324a3
[2016-04-14T23:22Z] INFO  16:22:11,734 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:22Z] GATK: realign ('1', 223162737, 240072524) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:22Z] INFO  16:22:11,766 ProgressMeter -            done    711471.0    88.0 s       2.1 m      100.0%    88.0 s       0.0 s
[2016-04-14T23:22Z] INFO  16:22:11,767 ProgressMeter - Total runtime 88.23 secs, 1.47 min, 0.02 hours
[2016-04-14T23:22Z] INFO  16:22:11,767 MicroScheduler - 265 reads were filtered out during the traversal out of approximately 711736 total reads (0.04%)
[2016-04-14T23:22Z] INFO  16:22:11,768 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:22Z] INFO  16:22:11,768 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:22Z] INFO  16:22:11,768 MicroScheduler -   -> 265 reads (0.04% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:22Z] INFO  16:22:11,775 IntervalUtils - Processing 15511908 bp from intervals
[2016-04-14T23:22Z] WARN  16:22:11,790 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:22Z] INFO  16:22:11,894 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:22Z] INFO  16:22:12,018 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:22Z] INFO  16:22:12,019 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:22Z] INFO  16:22:12,020 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:22Z] INFO  16:22:12,020 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:22Z] INFO  16:22:12,196 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:22Z] INFO  16:22:12,343 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:22Z] INFO  16:22:12,886 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:22Z] INFO  16:22:12,917 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:22Z] INFO  16:22:12,922 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:22Z] INFO  16:22:12,923 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:22Z] INFO  16:22:12,923 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:22Z] INFO  16:22:12,930 HelpFormatter - Program Args: -T PrintReads -L 2:95538562-111273222 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/2/tx/tmpnaFj_1/R14-18102_kapa-NGv3-PE100-NGv3-sort-2_95538561_111273222-prep-prealign.bam
[2016-04-14T23:22Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-1_175048468_192127886-prep.bam
[2016-04-14T23:22Z] INFO  16:22:12,940 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:22Z] INFO  16:22:12,941 HelpFormatter - Date/Time: 2016/04/14 16:22:12
[2016-04-14T23:22Z] INFO  16:22:12,942 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:22Z] INFO  16:22:12,942 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:22Z] INFO  16:22:13,116 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:22Z] INFO  16:22:13,145 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:22Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-1_31187093_46714270-prep-prealign.bam
[2016-04-14T23:22Z] GATK pre-alignment ('2', 111281072, 127413888) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:22Z] INFO  16:22:14,103 ProgressMeter -      1:28144576    700021.0    90.0 s       2.2 m       80.6%   111.0 s      21.0 s
[2016-04-14T23:22Z] INFO  16:22:14,182 ProgressMeter -     1:143024369   3.3988357E7    30.0 s       0.0 s       97.9%    30.0 s       0.0 s
[2016-04-14T23:22Z] INFO  16:22:14,226 ProgressMeter -     1:152327072    600049.0    90.0 s       2.5 m       54.3%     2.8 m      75.0 s
[2016-04-14T23:22Z] INFO  16:22:14,368 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-14T23:22Z] INFO  16:22:14,436 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:22Z] INFO  16:22:14,445 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:22Z] INFO  16:22:14,485 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.04
[2016-04-14T23:22Z] INFO  16:22:14,499 IntervalUtils - Processing 15734661 bp from intervals
[2016-04-14T23:22Z] INFO  16:22:14,575 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:22Z] INFO  16:22:14,594 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:22Z] INFO  16:22:14,604 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:22Z] INFO  16:22:14,605 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:22Z] INFO  16:22:14,605 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:22Z] INFO  16:22:14,616 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/1/R14-18102_kapa-NGv3-PE100-NGv3-sort-1_223162737_240072524-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/1/R14-18102_kapa-NGv3-PE100-NGv3-sort-1_223162737_240072524-prep-prealign-realign.intervals -L 1:223162738-240072524 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/1/tx/tmpkMpqHc/R14-18102_kapa-NGv3-PE100-NGv3-sort-1_223162737_240072524-prep.bam
[2016-04-14T23:22Z] INFO  16:22:14,635 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:22Z] INFO  16:22:14,636 HelpFormatter - Date/Time: 2016/04/14 16:22:14
[2016-04-14T23:22Z] INFO  16:22:14,636 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:22Z] INFO  16:22:14,636 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:22Z] INFO  16:22:14,819 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:22Z] INFO  16:22:14,897 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:22Z] INFO  16:22:14,905 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:22Z] INFO  16:22:14,908 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:22Z] INFO  16:22:14,908 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:22Z] INFO  16:22:14,909 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:22Z] INFO  16:22:14,909 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:22Z] INFO  16:22:14,931 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:22Z] INFO  16:22:14,948 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.04
[2016-04-14T23:22Z] INFO  16:22:15,072 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:22Z] INFO  16:22:15,097 ProgressMeter -      1:13496325    700014.0    90.0 s       2.2 m       86.8%   103.0 s      13.0 s
[2016-04-14T23:22Z] INFO  16:22:15,252 IntervalUtils - Processing 16909787 bp from intervals
[2016-04-14T23:22Z] WARN  16:22:15,257 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:22Z] INFO  16:22:15,325 ProgressMeter -            done   3.4773037E7    31.0 s       0.0 s      100.0%    31.0 s       0.0 s
[2016-04-14T23:22Z] INFO  16:22:15,326 ProgressMeter - Total runtime 31.17 secs, 0.52 min, 0.01 hours
[2016-04-14T23:22Z] INFO  16:22:15,330 MicroScheduler - 47627 reads were filtered out during the traversal out of approximately 415580 total reads (11.46%)
[2016-04-14T23:22Z] INFO  16:22:15,342 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:22Z] INFO  16:22:15,343 MicroScheduler -   -> 1015 reads (0.24% of total) failing BadMateFilter
[2016-04-14T23:22Z] INFO  16:22:15,343 MicroScheduler -   -> 32469 reads (7.81% of total) failing DuplicateReadFilter
[2016-04-14T23:22Z] INFO  16:22:15,344 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-14T23:22Z] INFO  16:22:15,344 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:22Z] INFO  16:22:15,345 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-14T23:22Z] INFO  16:22:15,346 MicroScheduler -   -> 14143 reads (3.40% of total) failing MappingQualityZeroFilter
[2016-04-14T23:22Z] INFO  16:22:15,346 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:22Z] INFO  16:22:15,347 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-14T23:22Z] INFO  16:22:15,347 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-14T23:22Z] INFO  16:22:15,366 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:22Z] GATK RealignerTargetCreator: R14-18102_kapa-NGv3-PE100-NGv3-sort-1_31187093_46714270-prep-prealign.bam 1:31187094-46714270
[2016-04-14T23:22Z] GATK: RealignerTargetCreator
[2016-04-14T23:22Z] INFO  16:22:15,480 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:22Z] INFO  16:22:15,481 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:22Z] INFO  16:22:15,481 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:22Z] INFO  16:22:15,482 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:22Z] INFO  16:22:15,685 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:22Z] INFO  16:22:15,907 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:22Z] INFO  16:22:16,831 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:22Z] INFO  16:22:16,834 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:22Z] INFO  16:22:16,835 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:22Z] INFO  16:22:16,835 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:22Z] INFO  16:22:16,840 HelpFormatter - Program Args: -T PrintReads -L 2:111281073-127413888 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/2/tx/tmpduN_87/R14-18102_kapa-NGv3-PE100-NGv3-sort-2_111281072_127413888-prep-prealign.bam
[2016-04-14T23:22Z] INFO  16:22:16,849 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:22Z] INFO  16:22:16,861 HelpFormatter - Date/Time: 2016/04/14 16:22:16
[2016-04-14T23:22Z] INFO  16:22:16,862 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:22Z] INFO  16:22:16,863 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:22Z] INFO  16:22:16,895 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:22Z] GATK: realign ('1', 108994811, 143767848) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:22Z] INFO  16:22:17,062 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:22Z] INFO  16:22:18,256 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-14T23:22Z] INFO  16:22:18,314 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:22Z] INFO  16:22:18,325 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:22Z] INFO  16:22:18,327 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:22Z] INFO  16:22:18,331 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:22Z] INFO  16:22:18,331 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:22Z] INFO  16:22:18,332 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:22Z] INFO  16:22:18,336 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/1/R14-18102_kapa-NGv3-PE100-NGv3-sort-1_31187093_46714270-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/1/tx/tmpPa3y8q/R14-18102_kapa-NGv3-PE100-NGv3-sort-1_31187093_46714270-prep-prealign-realign.intervals -l INFO -L 1:31187094-46714270 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-14T23:22Z] INFO  16:22:18,346 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:22Z] INFO  16:22:18,358 HelpFormatter - Date/Time: 2016/04/14 16:22:18
[2016-04-14T23:22Z] INFO  16:22:18,359 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:22Z] INFO  16:22:18,360 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:22Z] INFO  16:22:18,381 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-14T23:22Z] INFO  16:22:18,397 IntervalUtils - Processing 16132816 bp from intervals
[2016-04-14T23:22Z] INFO  16:22:18,489 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:22Z] INFO  16:22:18,504 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:22Z] INFO  16:22:18,698 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-14T23:22Z] INFO  16:22:18,708 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:22Z] INFO  16:22:18,776 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-14T23:22Z] INFO  16:22:18,832 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:22Z] INFO  16:22:18,832 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:22Z] INFO  16:22:18,833 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:22Z] INFO  16:22:18,833 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:22Z] INFO  16:22:18,859 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:22Z] INFO  16:22:19,017 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:22Z] INFO  16:22:19,216 IntervalUtils - Processing 15527177 bp from intervals
[2016-04-14T23:22Z] WARN  16:22:19,223 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:22Z] INFO  16:22:19,236 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@464274bf
[2016-04-14T23:22Z] INFO  16:22:19,305 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:22Z] INFO  16:22:19,386 ProgressMeter -            done    766170.0    95.0 s       2.1 m      100.0%    95.0 s       0.0 s
[2016-04-14T23:22Z] INFO  16:22:19,386 ProgressMeter - Total runtime 95.26 secs, 1.59 min, 0.03 hours
[2016-04-14T23:22Z] INFO  16:22:19,386 MicroScheduler - 348 reads were filtered out during the traversal out of approximately 766518 total reads (0.05%)
[2016-04-14T23:22Z] INFO  16:22:19,387 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:22Z] INFO  16:22:19,387 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:22Z] INFO  16:22:19,387 MicroScheduler -   -> 348 reads (0.05% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:22Z] INFO  16:22:19,546 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:22Z] INFO  16:22:19,547 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:22Z] INFO  16:22:19,549 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:22Z] INFO  16:22:19,550 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-14T23:22Z] INFO  16:22:19,606 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:22Z] INFO  16:22:19,609 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:22Z] INFO  16:22:19,610 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:22Z] INFO  16:22:19,611 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:22Z] INFO  16:22:19,615 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/1/R14-18102_kapa-NGv3-PE100-NGv3-sort-1_108994811_143767848-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/1/R14-18102_kapa-NGv3-PE100-NGv3-sort-1_108994811_143767848-prep-prealign-realign.intervals -L 1:108994812-143767848 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/1/tx/tmpfnVXOX/R14-18102_kapa-NGv3-PE100-NGv3-sort-1_108994811_143767848-prep.bam
[2016-04-14T23:22Z] INFO  16:22:19,640 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:22Z] INFO  16:22:19,641 HelpFormatter - Date/Time: 2016/04/14 16:22:19
[2016-04-14T23:22Z] INFO  16:22:19,642 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:22Z] INFO  16:22:19,643 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:22Z] INFO  16:22:19,884 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:22Z] INFO  16:22:20,023 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:22Z] INFO  16:22:20,034 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:22Z] INFO  16:22:20,056 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@66ce581b
[2016-04-14T23:22Z] INFO  16:22:20,134 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.10
[2016-04-14T23:22Z] INFO  16:22:20,156 ProgressMeter -            done    791594.0    96.0 s       2.0 m      100.0%    96.0 s       0.0 s
[2016-04-14T23:22Z] INFO  16:22:20,157 ProgressMeter - Total runtime 96.85 secs, 1.61 min, 0.03 hours
[2016-04-14T23:22Z] INFO  16:22:20,157 MicroScheduler - 260 reads were filtered out during the traversal out of approximately 791854 total reads (0.03%)
[2016-04-14T23:22Z] INFO  16:22:20,158 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:22Z] INFO  16:22:20,158 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:22Z] INFO  16:22:20,158 MicroScheduler -   -> 260 reads (0.03% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:22Z] INFO  16:22:20,526 ProgressMeter -            done    302614.0    22.0 s      74.0 s      100.0%    22.0 s       0.0 s
[2016-04-14T23:22Z] INFO  16:22:20,526 ProgressMeter - Total runtime 22.51 secs, 0.38 min, 0.01 hours
[2016-04-14T23:22Z] INFO  16:22:20,530 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 302614 total reads (0.00%)
[2016-04-14T23:22Z] INFO  16:22:20,531 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:22Z] INFO  16:22:20,531 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:22Z] INFO  16:22:20,532 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:22Z] INFO  16:22:20,571 IntervalUtils - Processing 34773037 bp from intervals
[2016-04-14T23:22Z] WARN  16:22:20,588 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:22Z] INFO  16:22:20,709 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:22Z] INFO  16:22:20,833 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:22Z] INFO  16:22:20,835 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:22Z] INFO  16:22:20,835 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:22Z] INFO  16:22:20,836 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:22Z] INFO  16:22:20,928 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:22Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-1_0_15541927-prep-prealign.bam
[2016-04-14T23:22Z] INFO  16:22:21,006 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:22Z] INFO  16:22:21,347 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:22Z] INFO  16:22:21,598 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:22Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-1_15545821_31186478-prep-prealign.bam
[2016-04-14T23:22Z] INFO  16:22:22,060 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:22Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-1_46715671_62228851-prep.bam
[2016-04-14T23:22Z] GATK pre-alignment ('2', 127433207, 143643105) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:22Z] GATK RealignerTargetCreator: R14-18102_kapa-NGv3-PE100-NGv3-sort-1_0_15541927-prep-prealign.bam 1:1-15541927
[2016-04-14T23:22Z] GATK: RealignerTargetCreator
[2016-04-14T23:22Z] INFO  16:22:23,694 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@41fd9d8e
[2016-04-14T23:22Z] GATK RealignerTargetCreator: R14-18102_kapa-NGv3-PE100-NGv3-sort-1_15545821_31186478-prep-prealign.bam 1:15545822-31186478
[2016-04-14T23:22Z] GATK: RealignerTargetCreator
[2016-04-14T23:22Z] INFO  16:22:23,811 ProgressMeter -            done    181160.0    24.0 s       2.2 m      100.0%    24.0 s       0.0 s
[2016-04-14T23:22Z] INFO  16:22:23,811 ProgressMeter - Total runtime 24.33 secs, 0.41 min, 0.01 hours
[2016-04-14T23:22Z] INFO  16:22:23,812 MicroScheduler - 113 reads were filtered out during the traversal out of approximately 181273 total reads (0.06%)
[2016-04-14T23:22Z] INFO  16:22:23,812 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:22Z] INFO  16:22:23,812 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:22Z] INFO  16:22:23,813 MicroScheduler -   -> 113 reads (0.06% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:22Z] INFO  16:22:25,228 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:22Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-2_46707543_62228117-prep-prealign.bam
[2016-04-14T23:22Z] GATK RealignerTargetCreator: R14-18102_kapa-NGv3-PE100-NGv3-sort-2_46707543_62228117-prep-prealign.bam 2:46707544-62228117
[2016-04-14T23:22Z] GATK: RealignerTargetCreator
[2016-04-14T23:22Z] INFO  16:22:26,085 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:22Z] INFO  16:22:26,089 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:22Z] INFO  16:22:26,090 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:22Z] INFO  16:22:26,090 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:22Z] INFO  16:22:26,095 HelpFormatter - Program Args: -T PrintReads -L 2:127433208-143643105 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/2/tx/tmpoYFCbb/R14-18102_kapa-NGv3-PE100-NGv3-sort-2_127433207_143643105-prep-prealign.bam
[2016-04-14T23:22Z] INFO  16:22:26,128 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:22Z] INFO  16:22:26,137 HelpFormatter - Date/Time: 2016/04/14 16:22:26
[2016-04-14T23:22Z] INFO  16:22:26,138 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:22Z] INFO  16:22:26,143 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:22Z] INFO  16:22:26,297 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:22Z] INFO  16:22:26,381 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:22Z] INFO  16:22:26,385 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:22Z] INFO  16:22:26,386 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:22Z] INFO  16:22:26,386 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:22Z] INFO  16:22:26,392 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/1/R14-18102_kapa-NGv3-PE100-NGv3-sort-1_0_15541927-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/1/tx/tmpvwtoc2/R14-18102_kapa-NGv3-PE100-NGv3-sort-1_0_15541927-prep-prealign-realign.intervals -l INFO -L 1:1-15541927 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-14T23:22Z] INFO  16:22:26,408 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:22Z] INFO  16:22:26,420 HelpFormatter - Date/Time: 2016/04/14 16:22:26
[2016-04-14T23:22Z] INFO  16:22:26,421 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:22Z] INFO  16:22:26,421 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:22Z] INFO  16:22:26,609 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:22Z] INFO  16:22:26,859 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-14T23:22Z] INFO  16:22:26,876 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:22Z] INFO  16:22:26,943 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-14T23:22Z] INFO  16:22:27,004 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:22Z] INFO  16:22:27,007 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:22Z] INFO  16:22:27,008 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:22Z] INFO  16:22:27,008 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:22Z] INFO  16:22:27,013 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/1/R14-18102_kapa-NGv3-PE100-NGv3-sort-1_15545821_31186478-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/1/tx/tmpffyMLc/R14-18102_kapa-NGv3-PE100-NGv3-sort-1_15545821_31186478-prep-prealign-realign.intervals -l INFO -L 1:15545822-31186478 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-14T23:22Z] INFO  16:22:27,023 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:22Z] INFO  16:22:27,023 HelpFormatter - Date/Time: 2016/04/14 16:22:27
[2016-04-14T23:22Z] INFO  16:22:27,023 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:22Z] INFO  16:22:27,023 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:22Z] INFO  16:22:27,165 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:22Z] INFO  16:22:27,255 IntervalUtils - Processing 15541927 bp from intervals
[2016-04-14T23:22Z] WARN  16:22:27,261 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:22Z] INFO  16:22:27,392 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:22Z] INFO  16:22:27,436 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-14T23:22Z] INFO  16:22:27,445 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:22Z] INFO  16:22:27,539 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.09
[2016-04-14T23:22Z] INFO  16:22:27,545 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-14T23:22Z] INFO  16:22:27,599 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:22Z] INFO  16:22:27,608 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:22Z] INFO  16:22:27,650 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.04
[2016-04-14T23:22Z] INFO  16:22:27,658 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:22Z] INFO  16:22:27,659 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:22Z] INFO  16:22:27,660 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:22Z] INFO  16:22:27,661 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-14T23:22Z] INFO  16:22:27,665 IntervalUtils - Processing 16209898 bp from intervals
[2016-04-14T23:22Z] INFO  16:22:27,749 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:22Z] INFO  16:22:27,855 IntervalUtils - Processing 15640657 bp from intervals
[2016-04-14T23:22Z] WARN  16:22:27,862 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:22Z] INFO  16:22:28,002 ProgressMeter -      2:26687202    100001.0    30.0 s       5.0 m       71.5%    41.0 s      11.0 s
[2016-04-14T23:22Z] INFO  16:22:28,083 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:22Z] INFO  16:22:28,084 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:22Z] INFO  16:22:28,085 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:22Z] INFO  16:22:28,085 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:22Z] INFO  16:22:28,097 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:22Z] INFO  16:22:28,100 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:22Z] INFO  16:22:28,228 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:22Z] INFO  16:22:28,229 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:22Z] INFO  16:22:28,230 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:22Z] INFO  16:22:28,231 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-14T23:22Z] INFO  16:22:28,316 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:22Z] INFO  16:22:29,096 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:22Z] INFO  16:22:29,098 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:22Z] INFO  16:22:29,099 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:22Z] INFO  16:22:29,099 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:22Z] INFO  16:22:29,103 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/2/R14-18102_kapa-NGv3-PE100-NGv3-sort-2_46707543_62228117-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/2/tx/tmpvH6WE3/R14-18102_kapa-NGv3-PE100-NGv3-sort-2_46707543_62228117-prep-prealign-realign.intervals -l INFO -L 2:46707544-62228117 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-14T23:22Z] INFO  16:22:29,124 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:22Z] INFO  16:22:29,125 HelpFormatter - Date/Time: 2016/04/14 16:22:29
[2016-04-14T23:22Z] INFO  16:22:29,126 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:22Z] INFO  16:22:29,126 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:22Z] INFO  16:22:29,167 ProgressMeter -      2:46605194    200002.0    30.0 s       2.5 m       99.3%    30.0 s       0.0 s
[2016-04-14T23:22Z] INFO  16:22:29,270 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:22Z] INFO  16:22:29,337 ProgressMeter -      2:73677522    200005.0    30.0 s       2.5 m       67.0%    44.0 s      14.0 s
[2016-04-14T23:22Z] INFO  16:22:29,396 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@5fe152b7
[2016-04-14T23:22Z] INFO  16:22:29,508 ProgressMeter -            done    229772.0    30.0 s       2.2 m      100.0%    30.0 s       0.0 s
[2016-04-14T23:22Z] INFO  16:22:29,508 ProgressMeter - Total runtime 30.40 secs, 0.51 min, 0.01 hours
[2016-04-14T23:22Z] INFO  16:22:29,509 MicroScheduler - 2405 reads were filtered out during the traversal out of approximately 232177 total reads (1.04%)
[2016-04-14T23:22Z] INFO  16:22:29,509 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:22Z] INFO  16:22:29,509 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:22Z] INFO  16:22:29,510 MicroScheduler -   -> 2405 reads (1.04% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:22Z] INFO  16:22:29,562 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-14T23:22Z] INFO  16:22:29,573 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:22Z] INFO  16:22:29,649 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-14T23:22Z] INFO  16:22:29,997 IntervalUtils - Processing 15520574 bp from intervals
[2016-04-14T23:22Z] WARN  16:22:30,008 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:22Z] INFO  16:22:30,131 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:22Z] INFO  16:22:30,380 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:22Z] INFO  16:22:30,381 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:22Z] INFO  16:22:30,382 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:22Z] INFO  16:22:30,383 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-14T23:22Z] INFO  16:22:30,879 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:22Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-2_31135088_46706841-prep-prealign.bam
[2016-04-14T23:22Z] INFO  16:22:31,525 ProgressMeter -      2:91843498    200005.0    30.0 s       2.5 m       77.3%    38.0 s       8.0 s
[2016-04-14T23:22Z] GATK RealignerTargetCreator: R14-18102_kapa-NGv3-PE100-NGv3-sort-2_31135088_46706841-prep-prealign.bam 2:31135089-46706841
[2016-04-14T23:22Z] GATK: RealignerTargetCreator
[2016-04-14T23:22Z] INFO  16:22:33,823 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@41fd9d8e
[2016-04-14T23:22Z] INFO  16:22:33,974 ProgressMeter -            done    249843.0    32.0 s       2.2 m      100.0%    32.0 s       0.0 s
[2016-04-14T23:22Z] INFO  16:22:33,974 ProgressMeter - Total runtime 32.47 secs, 0.54 min, 0.01 hours
[2016-04-14T23:22Z] INFO  16:22:33,975 MicroScheduler - 296 reads were filtered out during the traversal out of approximately 250139 total reads (0.12%)
[2016-04-14T23:22Z] INFO  16:22:33,975 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:22Z] INFO  16:22:33,975 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:22Z] INFO  16:22:33,976 MicroScheduler -   -> 296 reads (0.12% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:22Z] INFO  16:22:34,504 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:22Z] INFO  16:22:34,507 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:22Z] INFO  16:22:34,508 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:22Z] INFO  16:22:34,508 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:22Z] INFO  16:22:34,512 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/2/R14-18102_kapa-NGv3-PE100-NGv3-sort-2_31135088_46706841-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/2/tx/tmpzlfjHV/R14-18102_kapa-NGv3-PE100-NGv3-sort-2_31135088_46706841-prep-prealign-realign.intervals -l INFO -L 2:31135089-46706841 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-14T23:22Z] INFO  16:22:34,522 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:22Z] INFO  16:22:34,545 HelpFormatter - Date/Time: 2016/04/14 16:22:34
[2016-04-14T23:22Z] INFO  16:22:34,546 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:22Z] INFO  16:22:34,556 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:22Z] INFO  16:22:34,653 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:22Z] INFO  16:22:34,853 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-14T23:22Z] INFO  16:22:34,863 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:22Z] INFO  16:22:34,930 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-14T23:22Z] INFO  16:22:35,209 IntervalUtils - Processing 15571753 bp from intervals
[2016-04-14T23:22Z] WARN  16:22:35,214 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:22Z] INFO  16:22:35,260 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:22Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-2_79253838_95537822-prep-prealign.bam
[2016-04-14T23:22Z] INFO  16:22:35,312 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:22Z] INFO  16:22:35,527 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:22Z] INFO  16:22:35,532 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:22Z] INFO  16:22:35,534 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:22Z] INFO  16:22:35,535 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-14T23:22Z] INFO  16:22:35,965 ProgressMeter -            done    398749.0    27.0 s      69.0 s      100.0%    27.0 s       0.0 s
[2016-04-14T23:22Z] INFO  16:22:35,966 ProgressMeter - Total runtime 27.55 secs, 0.46 min, 0.01 hours
[2016-04-14T23:22Z] INFO  16:22:35,983 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 398749 total reads (0.00%)
[2016-04-14T23:22Z] INFO  16:22:35,984 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:22Z] INFO  16:22:35,985 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:22Z] INFO  16:22:35,985 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:22Z] GATK RealignerTargetCreator: R14-18102_kapa-NGv3-PE100-NGv3-sort-2_79253838_95537822-prep-prealign.bam 2:79253839-95537822
[2016-04-14T23:22Z] GATK: RealignerTargetCreator
[2016-04-14T23:22Z] INFO  16:22:37,622 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:22Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-1_159504867_175046963-prep.bam
[2016-04-14T23:22Z] INFO  16:22:38,795 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:22Z] INFO  16:22:38,798 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:22Z] INFO  16:22:38,799 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:22Z] INFO  16:22:38,799 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:22Z] INFO  16:22:38,805 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/2/R14-18102_kapa-NGv3-PE100-NGv3-sort-2_79253838_95537822-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/2/tx/tmpSY9K5r/R14-18102_kapa-NGv3-PE100-NGv3-sort-2_79253838_95537822-prep-prealign-realign.intervals -l INFO -L 2:79253839-95537822 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-14T23:22Z] INFO  16:22:38,819 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:22Z] INFO  16:22:38,820 HelpFormatter - Date/Time: 2016/04/14 16:22:38
[2016-04-14T23:22Z] INFO  16:22:38,831 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:22Z] INFO  16:22:38,832 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:22Z] GATK pre-alignment ('2', 143676177, 159195597) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:22Z] INFO  16:22:38,954 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:22Z] INFO  16:22:39,212 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-14T23:22Z] INFO  16:22:39,222 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:22Z] INFO  16:22:39,276 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-14T23:22Z] INFO  16:22:39,655 IntervalUtils - Processing 16283984 bp from intervals
[2016-04-14T23:22Z] WARN  16:22:39,660 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:22Z] INFO  16:22:39,744 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:22Z] INFO  16:22:39,982 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:22Z] INFO  16:22:39,982 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:22Z] INFO  16:22:39,983 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:22Z] INFO  16:22:39,983 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-14T23:22Z] INFO  16:22:40,631 ProgressMeter -            done    412767.0    28.0 s      69.0 s      100.0%    28.0 s       0.0 s
[2016-04-14T23:22Z] INFO  16:22:40,632 ProgressMeter - Total runtime 28.61 secs, 0.48 min, 0.01 hours
[2016-04-14T23:22Z] INFO  16:22:40,635 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 412767 total reads (0.00%)
[2016-04-14T23:22Z] INFO  16:22:40,636 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:22Z] INFO  16:22:40,636 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:22Z] INFO  16:22:40,636 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:22Z] INFO  16:22:41,214 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@7172f77a
[2016-04-14T23:22Z] INFO  16:22:41,298 ProgressMeter -            done    332095.0    41.0 s       2.1 m      100.0%    41.0 s       0.0 s
[2016-04-14T23:22Z] INFO  16:22:41,298 ProgressMeter - Total runtime 41.97 secs, 0.70 min, 0.01 hours
[2016-04-14T23:22Z] INFO  16:22:41,299 MicroScheduler - 170 reads were filtered out during the traversal out of approximately 332265 total reads (0.05%)
[2016-04-14T23:22Z] INFO  16:22:41,299 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:22Z] INFO  16:22:41,299 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:22Z] INFO  16:22:41,300 MicroScheduler -   -> 170 reads (0.05% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:22Z] INFO  16:22:41,695 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:22Z] INFO  16:22:41,698 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:22Z] INFO  16:22:41,699 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:22Z] INFO  16:22:41,700 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:22Z] INFO  16:22:41,704 HelpFormatter - Program Args: -T PrintReads -L 2:143676178-159195597 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/2/tx/tmpgZGH4R/R14-18102_kapa-NGv3-PE100-NGv3-sort-2_143676177_159195597-prep-prealign.bam
[2016-04-14T23:22Z] INFO  16:22:41,715 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:22Z] INFO  16:22:41,716 HelpFormatter - Date/Time: 2016/04/14 16:22:41
[2016-04-14T23:22Z] INFO  16:22:41,717 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:22Z] INFO  16:22:41,717 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:22Z] INFO  16:22:41,906 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:22Z] INFO  16:22:42,297 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:22Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-1_192128349_207640257-prep.bam
[2016-04-14T23:22Z] INFO  16:22:42,767 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:22Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-2_62362965_79253295-prep-prealign.bam
[2016-04-14T23:22Z] INFO  16:22:42,934 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-14T23:22Z] INFO  16:22:42,992 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:22Z] INFO  16:22:43,013 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:22Z] INFO  16:22:43,100 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.09
[2016-04-14T23:22Z] INFO  16:22:43,115 IntervalUtils - Processing 15519420 bp from intervals
[2016-04-14T23:22Z] INFO  16:22:43,196 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:22Z] INFO  16:22:43,520 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:22Z] INFO  16:22:43,520 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:22Z] INFO  16:22:43,521 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:22Z] INFO  16:22:43,521 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:22Z] INFO  16:22:43,552 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:22Z] GATK pre-alignment ('2', 159196753, 174774985) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:22Z] INFO  16:22:43,745 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:22Z] GATK RealignerTargetCreator: R14-18102_kapa-NGv3-PE100-NGv3-sort-2_62362965_79253295-prep-prealign.bam 2:62362966-79253295
[2016-04-14T23:22Z] GATK: RealignerTargetCreator
[2016-04-14T23:22Z] INFO  16:22:44,227 ProgressMeter -     1:155581654    900054.0   120.0 s       2.2 m       75.3%     2.7 m      39.0 s
[2016-04-14T23:22Z] INFO  16:22:44,858 ProgressMeter -            done    434166.0    29.0 s      67.0 s      100.0%    29.0 s       0.0 s
[2016-04-14T23:22Z] INFO  16:22:44,859 ProgressMeter - Total runtime 29.38 secs, 0.49 min, 0.01 hours
[2016-04-14T23:22Z] INFO  16:22:44,874 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 434166 total reads (0.00%)
[2016-04-14T23:22Z] INFO  16:22:44,874 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:22Z] INFO  16:22:44,875 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:22Z] INFO  16:22:44,875 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:22Z] INFO  16:22:44,932 ProgressMeter -      2:97911400    100002.0    30.0 s       5.0 m       15.1%     3.3 m       2.8 m
[2016-04-14T23:22Z] INFO  16:22:46,588 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:22Z] INFO  16:22:46,596 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:22Z] INFO  16:22:46,600 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:22Z] INFO  16:22:46,600 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:22Z] INFO  16:22:46,601 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:22Z] INFO  16:22:46,606 HelpFormatter - Program Args: -T PrintReads -L 2:159196754-174774985 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/2/tx/tmpFc5Ylb/R14-18102_kapa-NGv3-PE100-NGv3-sort-2_159196753_174774985-prep-prealign.bam
[2016-04-14T23:22Z] INFO  16:22:46,616 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:22Z] INFO  16:22:46,628 HelpFormatter - Date/Time: 2016/04/14 16:22:46
[2016-04-14T23:22Z] INFO  16:22:46,629 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:22Z] INFO  16:22:46,630 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:22Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-1_223162737_240072524-prep.bam
[2016-04-14T23:22Z] INFO  16:22:46,782 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:22Z] INFO  16:22:46,785 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:22Z] INFO  16:22:46,786 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:22Z] INFO  16:22:46,786 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:22Z] INFO  16:22:46,791 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/2/R14-18102_kapa-NGv3-PE100-NGv3-sort-2_62362965_79253295-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/2/tx/tmp8W82e5/R14-18102_kapa-NGv3-PE100-NGv3-sort-2_62362965_79253295-prep-prealign-realign.intervals -l INFO -L 2:62362966-79253295 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-14T23:22Z] INFO  16:22:46,800 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:22Z] INFO  16:22:46,809 HelpFormatter - Date/Time: 2016/04/14 16:22:46
[2016-04-14T23:22Z] INFO  16:22:46,809 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:22Z] INFO  16:22:46,810 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:22Z] INFO  16:22:46,812 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:22Z] INFO  16:22:46,897 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:22Z] INFO  16:22:46,978 ProgressMeter -            done   1.5520574E7    16.0 s       1.0 s      100.0%    16.0 s       0.0 s
[2016-04-14T23:22Z] INFO  16:22:46,979 ProgressMeter - Total runtime 16.60 secs, 0.28 min, 0.00 hours
[2016-04-14T23:22Z] INFO  16:22:46,984 MicroScheduler - 15094 reads were filtered out during the traversal out of approximately 182431 total reads (8.27%)
[2016-04-14T23:22Z] INFO  16:22:46,985 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:22Z] INFO  16:22:46,986 MicroScheduler -   -> 516 reads (0.28% of total) failing BadMateFilter
[2016-04-14T23:22Z] INFO  16:22:46,987 MicroScheduler -   -> 14220 reads (7.79% of total) failing DuplicateReadFilter
[2016-04-14T23:22Z] INFO  16:22:46,988 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-14T23:22Z] INFO  16:22:46,989 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:22Z] INFO  16:22:46,990 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-14T23:22Z] INFO  16:22:46,991 MicroScheduler -   -> 358 reads (0.20% of total) failing MappingQualityZeroFilter
[2016-04-14T23:22Z] INFO  16:22:46,992 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:22Z] INFO  16:22:46,993 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-14T23:22Z] INFO  16:22:46,994 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-14T23:22Z] INFO  16:22:47,108 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-14T23:22Z] INFO  16:22:47,118 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:22Z] INFO  16:22:47,172 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-14T23:22Z] INFO  16:22:47,475 IntervalUtils - Processing 16890330 bp from intervals
[2016-04-14T23:22Z] WARN  16:22:47,480 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:22Z] INFO  16:22:47,564 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:22Z] INFO  16:22:47,782 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:22Z] INFO  16:22:47,783 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:22Z] INFO  16:22:47,784 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:22Z] INFO  16:22:47,784 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-14T23:22Z] INFO  16:22:47,918 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-14T23:22Z] INFO  16:22:47,996 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:22Z] INFO  16:22:48,008 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:22Z] GATK pre-alignment ('2', 174777797, 190306304) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:22Z] INFO  16:22:48,072 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-14T23:22Z] INFO  16:22:48,104 IntervalUtils - Processing 15578232 bp from intervals
[2016-04-14T23:22Z] INFO  16:22:48,204 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:22Z] INFO  16:22:48,457 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:22Z] GATK: realign ('2', 46707543, 62228117) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:22Z] INFO  16:22:48,568 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:22Z] INFO  16:22:48,570 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:22Z] INFO  16:22:48,570 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:22Z] INFO  16:22:48,571 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:22Z] INFO  16:22:48,589 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:22Z] INFO  16:22:48,761 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:22Z] INFO  16:22:48,816 ProgressMeter -            done   1.5527177E7    29.0 s       1.0 s      100.0%    29.0 s       0.0 s
[2016-04-14T23:22Z] INFO  16:22:48,817 ProgressMeter - Total runtime 29.27 secs, 0.49 min, 0.01 hours
[2016-04-14T23:22Z] INFO  16:22:48,821 MicroScheduler - 64963 reads were filtered out during the traversal out of approximately 716214 total reads (9.07%)
[2016-04-14T23:22Z] INFO  16:22:48,822 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:22Z] INFO  16:22:48,823 MicroScheduler -   -> 1291 reads (0.18% of total) failing BadMateFilter
[2016-04-14T23:22Z] INFO  16:22:48,823 MicroScheduler -   -> 56969 reads (7.95% of total) failing DuplicateReadFilter
[2016-04-14T23:22Z] INFO  16:22:48,824 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-14T23:22Z] INFO  16:22:48,825 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:22Z] INFO  16:22:48,825 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-14T23:22Z] INFO  16:22:48,826 MicroScheduler -   -> 6703 reads (0.94% of total) failing MappingQualityZeroFilter
[2016-04-14T23:22Z] INFO  16:22:48,826 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:22Z] INFO  16:22:48,827 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-14T23:22Z] INFO  16:22:48,828 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-14T23:22Z] INFO  16:22:48,873 ProgressMeter -     2:127413499    200003.0    30.0 s       2.5 m      100.0%    30.0 s       0.0 s
[2016-04-14T23:22Z] INFO  16:22:48,897 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@7172f77a
[2016-04-14T23:22Z] INFO  16:22:49,060 ProgressMeter -            done    231116.0    30.0 s       2.2 m      100.0%    30.0 s       0.0 s
[2016-04-14T23:22Z] INFO  16:22:49,061 ProgressMeter - Total runtime 30.23 secs, 0.50 min, 0.01 hours
[2016-04-14T23:22Z] INFO  16:22:49,061 MicroScheduler - 137 reads were filtered out during the traversal out of approximately 231253 total reads (0.06%)
[2016-04-14T23:22Z] INFO  16:22:49,062 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:22Z] INFO  16:22:49,062 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:22Z] INFO  16:22:49,062 MicroScheduler -   -> 137 reads (0.06% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:22Z] INFO  16:22:50,328 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:22Z] GATK: realign ('1', 31187093, 46714270) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:22Z] INFO  16:22:50,777 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:22Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-2_111281072_127413888-prep-prealign.bam
[2016-04-14T23:22Z] INFO  16:22:51,097 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:22Z] INFO  16:22:51,100 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:22Z] INFO  16:22:51,101 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:22Z] INFO  16:22:51,101 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:22Z] INFO  16:22:51,106 HelpFormatter - Program Args: -T PrintReads -L 2:174777798-190306304 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/2/tx/tmpo0ZOTo/R14-18102_kapa-NGv3-PE100-NGv3-sort-2_174777797_190306304-prep-prealign.bam
[2016-04-14T23:22Z] INFO  16:22:51,115 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:22Z] INFO  16:22:51,126 HelpFormatter - Date/Time: 2016/04/14 16:22:51
[2016-04-14T23:22Z] INFO  16:22:51,127 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:22Z] INFO  16:22:51,127 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:22Z] INFO  16:22:51,198 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:22Z] INFO  16:22:51,202 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:22Z] INFO  16:22:51,202 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:22Z] INFO  16:22:51,202 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:22Z] INFO  16:22:51,206 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/2/R14-18102_kapa-NGv3-PE100-NGv3-sort-2_46707543_62228117-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/2/R14-18102_kapa-NGv3-PE100-NGv3-sort-2_46707543_62228117-prep-prealign-realign.intervals -L 2:46707544-62228117 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/2/tx/tmpnbGIdl/R14-18102_kapa-NGv3-PE100-NGv3-sort-2_46707543_62228117-prep.bam
[2016-04-14T23:22Z] INFO  16:22:51,218 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:22Z] INFO  16:22:51,226 HelpFormatter - Date/Time: 2016/04/14 16:22:51
[2016-04-14T23:22Z] INFO  16:22:51,226 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:22Z] INFO  16:22:51,227 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:22Z] INFO  16:22:51,274 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:22Z] INFO  16:22:51,407 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:22Z] INFO  16:22:51,522 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:22Z] INFO  16:22:51,532 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:22Z] INFO  16:22:51,582 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-14T23:22Z] GATK RealignerTargetCreator: R14-18102_kapa-NGv3-PE100-NGv3-sort-2_111281072_127413888-prep-prealign.bam 2:111281073-127413888
[2016-04-14T23:22Z] GATK: RealignerTargetCreator
[2016-04-14T23:22Z] INFO  16:22:51,874 ProgressMeter -     1:142727174    400007.0    31.0 s      77.0 s       97.0%    31.0 s       0.0 s
[2016-04-14T23:22Z] INFO  16:22:52,013 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@5fe152b7
[2016-04-14T23:22Z] INFO  16:22:52,024 IntervalUtils - Processing 15520574 bp from intervals
[2016-04-14T23:22Z] WARN  16:22:52,030 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:22Z] INFO  16:22:52,083 ProgressMeter -            done    360327.0    54.0 s       2.5 m      100.0%    54.0 s       0.0 s
[2016-04-14T23:22Z] INFO  16:22:52,084 ProgressMeter - Total runtime 54.14 secs, 0.90 min, 0.02 hours
[2016-04-14T23:22Z] INFO  16:22:52,084 MicroScheduler - 176 reads were filtered out during the traversal out of approximately 360503 total reads (0.05%)
[2016-04-14T23:22Z] INFO  16:22:52,084 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:22Z] INFO  16:22:52,085 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:22Z] INFO  16:22:52,085 MicroScheduler -   -> 176 reads (0.05% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:22Z] INFO  16:22:52,128 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:22Z] INFO  16:22:52,280 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:22Z] INFO  16:22:52,281 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:22Z] INFO  16:22:52,282 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:22Z] INFO  16:22:52,283 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:22Z] INFO  16:22:52,360 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-14T23:22Z] INFO  16:22:52,449 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:22Z] INFO  16:22:52,450 ProgressMeter -            done    413363.0    31.0 s      76.0 s      100.0%    31.0 s       0.0 s
[2016-04-14T23:22Z] INFO  16:22:52,451 ProgressMeter - Total runtime 31.62 secs, 0.53 min, 0.01 hours
[2016-04-14T23:22Z] INFO  16:22:52,454 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 413363 total reads (0.00%)
[2016-04-14T23:22Z] INFO  16:22:52,455 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:22Z] INFO  16:22:52,455 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:22Z] INFO  16:22:52,455 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:22Z] INFO  16:22:52,466 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:22Z] INFO  16:22:52,505 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:22Z] INFO  16:22:52,524 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-14T23:22Z] INFO  16:22:52,552 IntervalUtils - Processing 15528507 bp from intervals
[2016-04-14T23:22Z] INFO  16:22:52,683 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:22Z] INFO  16:22:52,688 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:22Z] INFO  16:22:52,952 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:22Z] INFO  16:22:52,953 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:22Z] INFO  16:22:52,953 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:22Z] INFO  16:22:52,953 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:22Z] INFO  16:22:52,968 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:22Z] INFO  16:22:53,168 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:22Z] INFO  16:22:53,359 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:22Z] INFO  16:22:53,361 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:22Z] INFO  16:22:53,361 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:22Z] INFO  16:22:53,362 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:22Z] INFO  16:22:53,366 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/1/R14-18102_kapa-NGv3-PE100-NGv3-sort-1_31187093_46714270-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/1/R14-18102_kapa-NGv3-PE100-NGv3-sort-1_31187093_46714270-prep-prealign-realign.intervals -L 1:31187094-46714270 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/1/tx/tmp_QaA_A/R14-18102_kapa-NGv3-PE100-NGv3-sort-1_31187093_46714270-prep.bam
[2016-04-14T23:22Z] INFO  16:22:53,374 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:22Z] INFO  16:22:53,375 HelpFormatter - Date/Time: 2016/04/14 16:22:53
[2016-04-14T23:22Z] INFO  16:22:53,376 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:22Z] INFO  16:22:53,377 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:22Z] INFO  16:22:53,524 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:22Z] INFO  16:22:53,570 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:22Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-2_15519725_31133925-prep-prealign.bam
[2016-04-14T23:22Z] INFO  16:22:53,681 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:22Z] INFO  16:22:53,690 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:22Z] INFO  16:22:53,746 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.04
[2016-04-14T23:22Z] INFO  16:22:54,015 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:22Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-1_108994811_143767848-prep.bam
[2016-04-14T23:22Z] INFO  16:22:54,100 IntervalUtils - Processing 15527177 bp from intervals
[2016-04-14T23:22Z] WARN  16:22:54,107 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:22Z] INFO  16:22:54,217 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:22Z] INFO  16:22:54,221 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:22Z] INFO  16:22:54,222 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:22Z] INFO  16:22:54,222 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:22Z] INFO  16:22:54,227 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/2/R14-18102_kapa-NGv3-PE100-NGv3-sort-2_111281072_127413888-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/2/tx/tmpKZ4C1Z/R14-18102_kapa-NGv3-PE100-NGv3-sort-2_111281072_127413888-prep-prealign-realign.intervals -l INFO -L 2:111281073-127413888 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-14T23:22Z] INFO  16:22:54,243 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:22Z] INFO  16:22:54,244 HelpFormatter - Date/Time: 2016/04/14 16:22:54
[2016-04-14T23:22Z] INFO  16:22:54,245 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:22Z] INFO  16:22:54,245 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:22Z] INFO  16:22:54,245 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:22Z] INFO  16:22:54,391 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:22Z] INFO  16:22:54,452 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:22Z] INFO  16:22:54,453 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:22Z] INFO  16:22:54,454 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:22Z] INFO  16:22:54,455 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:22Z] INFO  16:22:54,589 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-14T23:22Z] INFO  16:22:54,598 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:22Z] INFO  16:22:54,610 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:22Z] INFO  16:22:54,647 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-14T23:22Z] INFO  16:22:54,782 ProgressMeter -            done   1.5541927E7    27.0 s       1.0 s      100.0%    27.0 s       0.0 s
[2016-04-14T23:22Z] INFO  16:22:54,783 ProgressMeter - Total runtime 27.12 secs, 0.45 min, 0.01 hours
[2016-04-14T23:22Z] INFO  16:22:54,797 MicroScheduler - 169424 reads were filtered out during the traversal out of approximately 770627 total reads (21.99%)
[2016-04-14T23:22Z] INFO  16:22:54,798 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:22Z] INFO  16:22:54,798 MicroScheduler -   -> 1386 reads (0.18% of total) failing BadMateFilter
[2016-04-14T23:22Z] INFO  16:22:54,799 MicroScheduler -   -> 53263 reads (6.91% of total) failing DuplicateReadFilter
[2016-04-14T23:22Z] INFO  16:22:54,799 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-14T23:22Z] INFO  16:22:54,799 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:22Z] INFO  16:22:54,799 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-14T23:22Z] INFO  16:22:54,800 MicroScheduler -   -> 114775 reads (14.89% of total) failing MappingQualityZeroFilter
[2016-04-14T23:22Z] INFO  16:22:54,800 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:22Z] INFO  16:22:54,800 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-14T23:22Z] INFO  16:22:54,800 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-14T23:22Z] GATK RealignerTargetCreator: R14-18102_kapa-NGv3-PE100-NGv3-sort-2_15519725_31133925-prep-prealign.bam 2:15519726-31133925
[2016-04-14T23:22Z] INFO  16:22:54,803 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:22Z] GATK: RealignerTargetCreator
[2016-04-14T23:22Z] INFO  16:22:54,906 IntervalUtils - Processing 16132816 bp from intervals
[2016-04-14T23:22Z] WARN  16:22:54,911 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:22Z] INFO  16:22:54,992 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:22Z] INFO  16:22:55,188 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:22Z] INFO  16:22:55,190 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:22Z] INFO  16:22:55,190 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:22Z] INFO  16:22:55,191 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-14T23:22Z] GATK pre-alignment ('2', 190313104, 205830046) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:22Z] INFO  16:22:55,552 ProgressMeter -            done   1.5571753E7    20.0 s       1.0 s      100.0%    20.0 s       0.0 s
[2016-04-14T23:22Z] INFO  16:22:55,553 ProgressMeter - Total runtime 20.02 secs, 0.33 min, 0.01 hours
[2016-04-14T23:22Z] INFO  16:22:55,556 MicroScheduler - 23746 reads were filtered out during the traversal out of approximately 231209 total reads (10.27%)
[2016-04-14T23:22Z] INFO  16:22:55,557 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:22Z] INFO  16:22:55,558 MicroScheduler -   -> 2030 reads (0.88% of total) failing BadMateFilter
[2016-04-14T23:22Z] INFO  16:22:55,559 MicroScheduler -   -> 17894 reads (7.74% of total) failing DuplicateReadFilter
[2016-04-14T23:22Z] INFO  16:22:55,559 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-14T23:22Z] INFO  16:22:55,560 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:22Z] INFO  16:22:55,560 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-14T23:22Z] INFO  16:22:55,561 MicroScheduler -   -> 3822 reads (1.65% of total) failing MappingQualityZeroFilter
[2016-04-14T23:22Z] INFO  16:22:55,562 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:22Z] INFO  16:22:55,562 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-14T23:22Z] INFO  16:22:55,563 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-14T23:22Z] INFO  16:22:56,253 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:22Z] GATK: realign ('1', 0, 15541927) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:22Z] INFO  16:22:57,105 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:22Z] GATK: realign ('2', 31135088, 46706841) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:22Z] INFO  16:22:57,151 ProgressMeter -            done   1.6283984E7    17.0 s       1.0 s      100.0%    17.0 s       0.0 s
[2016-04-14T23:22Z] INFO  16:22:57,152 ProgressMeter - Total runtime 17.17 secs, 0.29 min, 0.00 hours
[2016-04-14T23:22Z] INFO  16:22:57,155 MicroScheduler - 86229 reads were filtered out during the traversal out of approximately 251296 total reads (34.31%)
[2016-04-14T23:22Z] INFO  16:22:57,156 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:22Z] INFO  16:22:57,157 MicroScheduler -   -> 645 reads (0.26% of total) failing BadMateFilter
[2016-04-14T23:22Z] INFO  16:22:57,158 MicroScheduler -   -> 14668 reads (5.84% of total) failing DuplicateReadFilter
[2016-04-14T23:22Z] INFO  16:22:57,158 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-14T23:22Z] INFO  16:22:57,159 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:22Z] INFO  16:22:57,160 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-14T23:22Z] INFO  16:22:57,160 MicroScheduler -   -> 70916 reads (28.22% of total) failing MappingQualityZeroFilter
[2016-04-14T23:22Z] INFO  16:22:57,161 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:22Z] INFO  16:22:57,161 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-14T23:22Z] INFO  16:22:57,162 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-14T23:22Z] INFO  16:22:57,606 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:22Z] INFO  16:22:57,625 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:22Z] INFO  16:22:57,625 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:22Z] INFO  16:22:57,626 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:22Z] INFO  16:22:57,630 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/2/R14-18102_kapa-NGv3-PE100-NGv3-sort-2_15519725_31133925-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/2/tx/tmpDmckhE/R14-18102_kapa-NGv3-PE100-NGv3-sort-2_15519725_31133925-prep-prealign-realign.intervals -l INFO -L 2:15519726-31133925 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-14T23:22Z] INFO  16:22:57,650 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:22Z] INFO  16:22:57,651 HelpFormatter - Date/Time: 2016/04/14 16:22:57
[2016-04-14T23:22Z] INFO  16:22:57,651 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:22Z] INFO  16:22:57,651 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:22Z] INFO  16:22:57,784 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:22Z] INFO  16:22:58,055 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-14T23:22Z] INFO  16:22:58,069 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:22Z] INFO  16:22:58,099 ProgressMeter -     2:133019721    200002.0    30.0 s       2.5 m       34.5%    87.0 s      57.0 s
[2016-04-14T23:22Z] INFO  16:22:58,152 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-14T23:22Z] INFO  16:22:58,244 ProgressMeter -      1:29448349   1.3896227E7    30.0 s       2.0 s       88.9%    33.0 s       3.0 s
[2016-04-14T23:22Z] INFO  16:22:58,326 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:22Z] INFO  16:22:58,334 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:22Z] INFO  16:22:58,335 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:22Z] INFO  16:22:58,335 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:22Z] INFO  16:22:58,340 HelpFormatter - Program Args: -T PrintReads -L 2:190313105-205830046 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/2/tx/tmp6ipmnJ/R14-18102_kapa-NGv3-PE100-NGv3-sort-2_190313104_205830046-prep-prealign.bam
[2016-04-14T23:22Z] INFO  16:22:58,378 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:22Z] INFO  16:22:58,383 HelpFormatter - Date/Time: 2016/04/14 16:22:58
[2016-04-14T23:22Z] INFO  16:22:58,384 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:22Z] INFO  16:22:58,384 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:22Z] INFO  16:22:58,417 IntervalUtils - Processing 15614200 bp from intervals
[2016-04-14T23:22Z] WARN  16:22:58,422 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:22Z] INFO  16:22:58,489 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:22Z] INFO  16:22:58,553 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:22Z] INFO  16:22:58,563 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:22Z] GATK: realign ('2', 79253838, 95537822) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:22Z] INFO  16:22:58,665 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:22Z] INFO  16:22:58,666 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:22Z] INFO  16:22:58,667 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:22Z] INFO  16:22:58,667 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-14T23:22Z] INFO  16:22:59,252 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:22Z] INFO  16:22:59,255 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:22Z] INFO  16:22:59,256 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:22Z] INFO  16:22:59,256 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:22Z] INFO  16:22:59,261 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/1/R14-18102_kapa-NGv3-PE100-NGv3-sort-1_0_15541927-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/1/R14-18102_kapa-NGv3-PE100-NGv3-sort-1_0_15541927-prep-prealign-realign.intervals -L 1:1-15541927 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/1/tx/tmpUQClkw/R14-18102_kapa-NGv3-PE100-NGv3-sort-1_0_15541927-prep.bam
[2016-04-14T23:22Z] INFO  16:22:59,302 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:22Z] INFO  16:22:59,308 HelpFormatter - Date/Time: 2016/04/14 16:22:59
[2016-04-14T23:22Z] INFO  16:22:59,309 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:22Z] INFO  16:22:59,309 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:22Z] INFO  16:22:59,598 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:22Z] INFO  16:22:59,743 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:22Z] INFO  16:22:59,752 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:22Z] INFO  16:22:59,764 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-14T23:22Z] INFO  16:22:59,792 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.04
[2016-04-14T23:22Z] INFO  16:22:59,823 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:22Z] INFO  16:22:59,832 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:22Z] INFO  16:22:59,887 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-14T23:22Z] INFO  16:22:59,913 IntervalUtils - Processing 15516942 bp from intervals
[2016-04-14T23:23Z] INFO  16:23:00,072 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:23Z] INFO  16:23:00,170 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:23Z] INFO  16:23:00,173 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:23Z] INFO  16:23:00,174 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:23Z] INFO  16:23:00,174 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:23Z] INFO  16:23:00,179 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/2/R14-18102_kapa-NGv3-PE100-NGv3-sort-2_31135088_46706841-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/2/R14-18102_kapa-NGv3-PE100-NGv3-sort-2_31135088_46706841-prep-prealign-realign.intervals -L 2:31135089-46706841 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/2/tx/tmp1ABv5c/R14-18102_kapa-NGv3-PE100-NGv3-sort-2_31135088_46706841-prep.bam
[2016-04-14T23:23Z] INFO  16:23:00,189 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:23Z] INFO  16:23:00,197 IntervalUtils - Processing 15541927 bp from intervals
[2016-04-14T23:23Z] INFO  16:23:00,200 HelpFormatter - Date/Time: 2016/04/14 16:23:00
[2016-04-14T23:23Z] INFO  16:23:00,201 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:23Z] INFO  16:23:00,202 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:23Z] WARN  16:23:00,202 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:23Z] INFO  16:23:00,297 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:23Z] INFO  16:23:00,406 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:23Z] INFO  16:23:00,407 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:23Z] INFO  16:23:00,408 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:23Z] INFO  16:23:00,408 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:23Z] INFO  16:23:00,414 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:23Z] INFO  16:23:00,421 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:23Z] INFO  16:23:00,467 ProgressMeter -            done   1.5640657E7    32.0 s       2.0 s      100.0%    32.0 s       0.0 s
[2016-04-14T23:23Z] INFO  16:23:00,468 ProgressMeter - Total runtime 32.24 secs, 0.54 min, 0.01 hours
[2016-04-14T23:23Z] INFO  16:23:00,469 MicroScheduler - 87603 reads were filtered out during the traversal out of approximately 796388 total reads (11.00%)
[2016-04-14T23:23Z] INFO  16:23:00,470 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:23Z] INFO  16:23:00,470 MicroScheduler -   -> 1401 reads (0.18% of total) failing BadMateFilter
[2016-04-14T23:23Z] INFO  16:23:00,471 MicroScheduler -   -> 62844 reads (7.89% of total) failing DuplicateReadFilter
[2016-04-14T23:23Z] INFO  16:23:00,477 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-14T23:23Z] INFO  16:23:00,478 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:23Z] INFO  16:23:00,479 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-14T23:23Z] INFO  16:23:00,479 MicroScheduler -   -> 23358 reads (2.93% of total) failing MappingQualityZeroFilter
[2016-04-14T23:23Z] INFO  16:23:00,480 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:23Z] INFO  16:23:00,481 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-14T23:23Z] INFO  16:23:00,482 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-14T23:23Z] INFO  16:23:00,496 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:23Z] INFO  16:23:00,497 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:23Z] INFO  16:23:00,497 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:23Z] INFO  16:23:00,498 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:23Z] INFO  16:23:00,538 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:23Z] INFO  16:23:00,548 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:23Z] INFO  16:23:00,554 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:23Z] INFO  16:23:00,610 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-14T23:23Z] INFO  16:23:00,681 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:23Z] INFO  16:23:00,942 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:23Z] INFO  16:23:01,079 IntervalUtils - Processing 15571753 bp from intervals
[2016-04-14T23:23Z] WARN  16:23:01,097 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:23Z] INFO  16:23:01,212 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:23Z] INFO  16:23:01,378 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:23Z] INFO  16:23:01,379 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:23Z] INFO  16:23:01,380 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:23Z] INFO  16:23:01,381 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:23Z] INFO  16:23:01,425 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:23Z] INFO  16:23:01,428 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:23Z] INFO  16:23:01,429 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:23Z] INFO  16:23:01,429 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:23Z] INFO  16:23:01,434 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/2/R14-18102_kapa-NGv3-PE100-NGv3-sort-2_79253838_95537822-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/2/R14-18102_kapa-NGv3-PE100-NGv3-sort-2_79253838_95537822-prep-prealign-realign.intervals -L 2:79253839-95537822 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/2/tx/tmplu0ksa/R14-18102_kapa-NGv3-PE100-NGv3-sort-2_79253838_95537822-prep.bam
[2016-04-14T23:23Z] INFO  16:23:01,469 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:23Z] INFO  16:23:01,469 HelpFormatter - Date/Time: 2016/04/14 16:23:01
[2016-04-14T23:23Z] INFO  16:23:01,469 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:23Z] INFO  16:23:01,470 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:23Z] INFO  16:23:01,561 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:23Z] INFO  16:23:01,684 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:23Z] INFO  16:23:01,714 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:23Z] INFO  16:23:01,806 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:23Z] INFO  16:23:01,815 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:23Z] INFO  16:23:01,873 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-14T23:23Z] INFO  16:23:02,034 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:23Z] GATK: realign ('1', 15545821, 31186478) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:23Z] INFO  16:23:02,241 IntervalUtils - Processing 16283984 bp from intervals
[2016-04-14T23:23Z] WARN  16:23:02,246 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:23Z] INFO  16:23:02,351 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:23Z] INFO  16:23:02,482 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:23Z] INFO  16:23:02,483 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:23Z] INFO  16:23:02,483 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:23Z] INFO  16:23:02,484 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:23Z] INFO  16:23:02,620 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:23Z] INFO  16:23:02,768 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:23Z] INFO  16:23:04,763 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@41fd9d8e
[2016-04-14T23:23Z] INFO  16:23:04,901 ProgressMeter -            done    121676.0    21.0 s       2.9 m      100.0%    21.0 s       0.0 s
[2016-04-14T23:23Z] INFO  16:23:04,902 ProgressMeter - Total runtime 21.38 secs, 0.36 min, 0.01 hours
[2016-04-14T23:23Z] INFO  16:23:04,902 MicroScheduler - 124 reads were filtered out during the traversal out of approximately 121800 total reads (0.10%)
[2016-04-14T23:23Z] INFO  16:23:04,903 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:23Z] INFO  16:23:04,903 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:23Z] INFO  16:23:04,903 MicroScheduler -   -> 124 reads (0.10% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:23Z] INFO  16:23:04,937 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:23Z] INFO  16:23:04,940 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:23Z] INFO  16:23:04,941 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:23Z] INFO  16:23:04,941 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:23Z] INFO  16:23:04,946 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/1/R14-18102_kapa-NGv3-PE100-NGv3-sort-1_15545821_31186478-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/1/R14-18102_kapa-NGv3-PE100-NGv3-sort-1_15545821_31186478-prep-prealign-realign.intervals -L 1:15545822-31186478 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/1/tx/tmp3E1sHM/R14-18102_kapa-NGv3-PE100-NGv3-sort-1_15545821_31186478-prep.bam
[2016-04-14T23:23Z] INFO  16:23:04,957 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:23Z] INFO  16:23:04,965 HelpFormatter - Date/Time: 2016/04/14 16:23:04
[2016-04-14T23:23Z] INFO  16:23:04,966 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:23Z] INFO  16:23:04,966 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:23Z] INFO  16:23:05,200 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:23Z] INFO  16:23:05,328 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:23Z] INFO  16:23:05,344 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:23Z] INFO  16:23:05,407 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-14T23:23Z] INFO  16:23:05,728 IntervalUtils - Processing 15640657 bp from intervals
[2016-04-14T23:23Z] WARN  16:23:05,745 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:23Z] INFO  16:23:05,850 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:23Z] INFO  16:23:06,028 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:23Z] INFO  16:23:06,029 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:23Z] INFO  16:23:06,029 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:23Z] INFO  16:23:06,030 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:23Z] INFO  16:23:06,239 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:23Z] INFO  16:23:06,426 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:23Z] INFO  16:23:06,433 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:23Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-2_143676177_159195597-prep-prealign.bam
[2016-04-14T23:23Z] GATK RealignerTargetCreator: R14-18102_kapa-NGv3-PE100-NGv3-sort-2_143676177_159195597-prep-prealign.bam 2:143676178-159195597
[2016-04-14T23:23Z] GATK: RealignerTargetCreator
[2016-04-14T23:23Z] INFO  16:23:07,029 ProgressMeter -            done    181160.0    14.0 s      81.0 s      100.0%    14.0 s       0.0 s
[2016-04-14T23:23Z] INFO  16:23:07,029 ProgressMeter - Total runtime 14.75 secs, 0.25 min, 0.00 hours
[2016-04-14T23:23Z] INFO  16:23:07,033 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 181160 total reads (0.00%)
[2016-04-14T23:23Z] INFO  16:23:07,033 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:23Z] INFO  16:23:07,034 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:23Z] INFO  16:23:07,034 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:23Z] INFO  16:23:08,217 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@5fe152b7
[2016-04-14T23:23Z] INFO  16:23:08,419 ProgressMeter -            done    322561.0    40.0 s       2.1 m      100.0%    40.0 s       0.0 s
[2016-04-14T23:23Z] INFO  16:23:08,419 ProgressMeter - Total runtime 40.34 secs, 0.67 min, 0.01 hours
[2016-04-14T23:23Z] INFO  16:23:08,420 MicroScheduler - 184 reads were filtered out during the traversal out of approximately 322745 total reads (0.06%)
[2016-04-14T23:23Z] INFO  16:23:08,420 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:23Z] INFO  16:23:08,420 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:23Z] INFO  16:23:08,421 MicroScheduler -   -> 184 reads (0.06% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:23Z] INFO  16:23:08,650 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:23Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-2_46707543_62228117-prep.bam
[2016-04-14T23:23Z] INFO  16:23:08,924 ProgressMeter -            done   1.689033E7    21.0 s       1.0 s      100.0%    21.0 s       0.0 s
[2016-04-14T23:23Z] INFO  16:23:08,925 ProgressMeter - Total runtime 21.14 secs, 0.35 min, 0.01 hours
[2016-04-14T23:23Z] INFO  16:23:08,929 MicroScheduler - 29807 reads were filtered out during the traversal out of approximately 333948 total reads (8.93%)
[2016-04-14T23:23Z] INFO  16:23:08,930 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:23Z] INFO  16:23:08,931 MicroScheduler -   -> 736 reads (0.22% of total) failing BadMateFilter
[2016-04-14T23:23Z] INFO  16:23:08,931 MicroScheduler -   -> 26653 reads (7.98% of total) failing DuplicateReadFilter
[2016-04-14T23:23Z] INFO  16:23:08,932 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-14T23:23Z] INFO  16:23:08,932 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:23Z] INFO  16:23:08,934 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-14T23:23Z] INFO  16:23:08,934 MicroScheduler -   -> 2418 reads (0.72% of total) failing MappingQualityZeroFilter
[2016-04-14T23:23Z] INFO  16:23:08,935 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:23Z] INFO  16:23:08,935 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-14T23:23Z] INFO  16:23:08,936 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-14T23:23Z] GATK pre-alignment ('2', 205912303, 222290862) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:23Z] INFO  16:23:09,761 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:23Z] INFO  16:23:09,765 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:23Z] INFO  16:23:09,766 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:23Z] INFO  16:23:09,767 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:23Z] INFO  16:23:09,772 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/2/R14-18102_kapa-NGv3-PE100-NGv3-sort-2_143676177_159195597-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/2/tx/tmpbQ7wpn/R14-18102_kapa-NGv3-PE100-NGv3-sort-2_143676177_159195597-prep-prealign-realign.intervals -l INFO -L 2:143676178-159195597 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-14T23:23Z] INFO  16:23:09,773 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:23Z] INFO  16:23:09,781 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:23Z] INFO  16:23:09,782 HelpFormatter - Date/Time: 2016/04/14 16:23:09
[2016-04-14T23:23Z] INFO  16:23:09,782 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:23Z] INFO  16:23:09,782 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:23Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-2_127433207_143643105-prep-prealign.bam
[2016-04-14T23:23Z] INFO  16:23:09,921 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:23Z] INFO  16:23:10,191 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-14T23:23Z] INFO  16:23:10,203 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:23Z] INFO  16:23:10,262 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:23Z] INFO  16:23:10,279 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-14T23:23Z] GATK: realign ('2', 62362965, 79253295) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:23Z] INFO  16:23:10,640 IntervalUtils - Processing 15519420 bp from intervals
[2016-04-14T23:23Z] WARN  16:23:10,645 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:23Z] INFO  16:23:10,714 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:23Z] GATK RealignerTargetCreator: R14-18102_kapa-NGv3-PE100-NGv3-sort-2_127433207_143643105-prep-prealign.bam 2:127433208-143643105
[2016-04-14T23:23Z] GATK: RealignerTargetCreator
[2016-04-14T23:23Z] INFO  16:23:10,865 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@6834dd3c
[2016-04-14T23:23Z] INFO  16:23:10,950 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:23Z] INFO  16:23:10,951 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:23Z] INFO  16:23:10,952 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:23Z] INFO  16:23:10,953 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-14T23:23Z] INFO  16:23:11,035 ProgressMeter -            done   1229850.0     2.5 m     119.0 s      100.0%     2.5 m       0.0 s
[2016-04-14T23:23Z] INFO  16:23:11,036 ProgressMeter - Total runtime 147.07 secs, 2.45 min, 0.04 hours
[2016-04-14T23:23Z] INFO  16:23:11,037 MicroScheduler - 417 reads were filtered out during the traversal out of approximately 1230267 total reads (0.03%)
[2016-04-14T23:23Z] INFO  16:23:11,038 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:23Z] INFO  16:23:11,038 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:23Z] INFO  16:23:11,039 MicroScheduler -   -> 417 reads (0.03% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:23Z] INFO  16:23:11,874 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:23Z] INFO  16:23:11,878 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:23Z] INFO  16:23:11,879 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:23Z] INFO  16:23:11,879 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:23Z] INFO  16:23:11,885 HelpFormatter - Program Args: -T PrintReads -L 2:205912304-222290862 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/2/tx/tmpUUa7lB/R14-18102_kapa-NGv3-PE100-NGv3-sort-2_205912303_222290862-prep-prealign.bam
[2016-04-14T23:23Z] INFO  16:23:11,913 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:23Z] INFO  16:23:11,914 HelpFormatter - Date/Time: 2016/04/14 16:23:11
[2016-04-14T23:23Z] INFO  16:23:11,915 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:23Z] INFO  16:23:11,915 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:23Z] INFO  16:23:12,117 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:23Z] INFO  16:23:12,672 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:23Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-1_143897546_159410511-prep-prealign.bam
[2016-04-14T23:23Z] INFO  16:23:13,286 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:23Z] INFO  16:23:13,290 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:23Z] INFO  16:23:13,290 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:23Z] INFO  16:23:13,291 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:23Z] INFO  16:23:13,296 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/2/R14-18102_kapa-NGv3-PE100-NGv3-sort-2_62362965_79253295-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/2/R14-18102_kapa-NGv3-PE100-NGv3-sort-2_62362965_79253295-prep-prealign-realign.intervals -L 2:62362966-79253295 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/2/tx/tmp2oXk3s/R14-18102_kapa-NGv3-PE100-NGv3-sort-2_62362965_79253295-prep.bam
[2016-04-14T23:23Z] INFO  16:23:13,317 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:23Z] INFO  16:23:13,318 HelpFormatter - Date/Time: 2016/04/14 16:23:13
[2016-04-14T23:23Z] INFO  16:23:13,319 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:23Z] INFO  16:23:13,323 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:23Z] INFO  16:23:13,425 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-14T23:23Z] INFO  16:23:13,497 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:23Z] INFO  16:23:13,506 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:23Z] INFO  16:23:13,550 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:23Z] INFO  16:23:13,557 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-14T23:23Z] INFO  16:23:13,573 IntervalUtils - Processing 16378559 bp from intervals
[2016-04-14T23:23Z] INFO  16:23:13,678 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:23Z] INFO  16:23:13,701 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:23Z] INFO  16:23:13,704 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:23Z] INFO  16:23:13,704 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:23Z] INFO  16:23:13,705 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:23Z] INFO  16:23:13,705 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:23Z] INFO  16:23:13,710 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/2/R14-18102_kapa-NGv3-PE100-NGv3-sort-2_127433207_143643105-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/2/tx/tmphC4Yya/R14-18102_kapa-NGv3-PE100-NGv3-sort-2_127433207_143643105-prep-prealign-realign.intervals -l INFO -L 2:127433208-143643105 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-14T23:23Z] INFO  16:23:13,713 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:23Z] INFO  16:23:13,719 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:23Z] INFO  16:23:13,730 HelpFormatter - Date/Time: 2016/04/14 16:23:13
[2016-04-14T23:23Z] INFO  16:23:13,731 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:23Z] INFO  16:23:13,731 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:23Z] INFO  16:23:13,763 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-14T23:23Z] INFO  16:23:13,862 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:23Z] INFO  16:23:14,019 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:23Z] INFO  16:23:14,020 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:23Z] INFO  16:23:14,020 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:23Z] INFO  16:23:14,020 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:23Z] INFO  16:23:14,046 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:23Z] INFO  16:23:14,090 IntervalUtils - Processing 16890330 bp from intervals
[2016-04-14T23:23Z] WARN  16:23:14,094 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:23Z] INFO  16:23:14,115 ProgressMeter -            done   1.6132816E7    18.0 s       1.0 s      100.0%    18.0 s       0.0 s
[2016-04-14T23:23Z] INFO  16:23:14,116 ProgressMeter - Total runtime 18.93 secs, 0.32 min, 0.01 hours
[2016-04-14T23:23Z] INFO  16:23:14,120 MicroScheduler - 75918 reads were filtered out during the traversal out of approximately 232798 total reads (32.61%)
[2016-04-14T23:23Z] INFO  16:23:14,121 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:23Z] INFO  16:23:14,122 MicroScheduler -   -> 514 reads (0.22% of total) failing BadMateFilter
[2016-04-14T23:23Z] INFO  16:23:14,122 MicroScheduler -   -> 13652 reads (5.86% of total) failing DuplicateReadFilter
[2016-04-14T23:23Z] INFO  16:23:14,123 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-14T23:23Z] INFO  16:23:14,124 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:23Z] INFO  16:23:14,124 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-14T23:23Z] INFO  16:23:14,125 MicroScheduler -   -> 61752 reads (26.53% of total) failing MappingQualityZeroFilter
[2016-04-14T23:23Z] INFO  16:23:14,125 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:23Z] INFO  16:23:14,126 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-14T23:23Z] INFO  16:23:14,126 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-14T23:23Z] INFO  16:23:14,160 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-14T23:23Z] INFO  16:23:14,174 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:23Z] INFO  16:23:14,193 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:23Z] INFO  16:23:14,227 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:23Z] INFO  16:23:14,257 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-14T23:23Z] INFO  16:23:14,333 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:23Z] INFO  16:23:14,335 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:23Z] INFO  16:23:14,335 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:23Z] INFO  16:23:14,336 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:23Z] INFO  16:23:14,512 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:23Z] INFO  16:23:14,602 IntervalUtils - Processing 16209898 bp from intervals
[2016-04-14T23:23Z] WARN  16:23:14,607 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:23Z] INFO  16:23:14,688 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:23Z] INFO  16:23:14,716 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:23Z] INFO  16:23:14,932 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:23Z] INFO  16:23:14,933 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:23Z] INFO  16:23:14,934 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:23Z] INFO  16:23:14,935 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-14T23:23Z] INFO  16:23:15,504 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:23Z] GATK: realign ('2', 111281072, 127413888) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:23Z] INFO  16:23:15,664 ProgressMeter -     2:107104112    300005.0    60.0 s       3.4 m       73.5%    81.0 s      21.0 s
[2016-04-14T23:23Z] GATK RealignerTargetCreator: R14-18102_kapa-NGv3-PE100-NGv3-sort-1_143897546_159410511-prep-prealign.bam 1:143897547-159410511
[2016-04-14T23:23Z] GATK: RealignerTargetCreator
[2016-04-14T23:23Z] INFO  16:23:18,197 ProgressMeter -            done   1.56142E7    19.0 s       1.0 s      100.0%    19.0 s       0.0 s
[2016-04-14T23:23Z] INFO  16:23:18,198 ProgressMeter - Total runtime 19.53 secs, 0.33 min, 0.01 hours
[2016-04-14T23:23Z] INFO  16:23:18,202 MicroScheduler - 30187 reads were filtered out during the traversal out of approximately 362264 total reads (8.33%)
[2016-04-14T23:23Z] INFO  16:23:18,203 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:23Z] INFO  16:23:18,204 MicroScheduler -   -> 848 reads (0.23% of total) failing BadMateFilter
[2016-04-14T23:23Z] INFO  16:23:18,214 MicroScheduler -   -> 28840 reads (7.96% of total) failing DuplicateReadFilter
[2016-04-14T23:23Z] INFO  16:23:18,215 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-14T23:23Z] INFO  16:23:18,215 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:23Z] INFO  16:23:18,215 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-14T23:23Z] INFO  16:23:18,216 MicroScheduler -   -> 499 reads (0.14% of total) failing MappingQualityZeroFilter
[2016-04-14T23:23Z] INFO  16:23:18,216 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:23Z] INFO  16:23:18,216 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-14T23:23Z] INFO  16:23:18,216 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-14T23:23Z] INFO  16:23:18,479 ProgressMeter -            done    229772.0    17.0 s      74.0 s      100.0%    17.0 s       0.0 s
[2016-04-14T23:23Z] INFO  16:23:18,480 ProgressMeter - Total runtime 17.10 secs, 0.29 min, 0.00 hours
[2016-04-14T23:23Z] INFO  16:23:18,484 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 229772 total reads (0.00%)
[2016-04-14T23:23Z] INFO  16:23:18,484 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:23Z] INFO  16:23:18,485 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:23Z] INFO  16:23:18,485 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:23Z] INFO  16:23:18,585 ProgressMeter -     2:170089951    200002.0    30.0 s       2.5 m       69.9%    42.0 s      12.0 s
[2016-04-14T23:23Z] INFO  16:23:18,740 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:23Z] INFO  16:23:18,743 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:23Z] INFO  16:23:18,744 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:23Z] INFO  16:23:18,744 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:23Z] INFO  16:23:18,748 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/2/R14-18102_kapa-NGv3-PE100-NGv3-sort-2_111281072_127413888-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/2/R14-18102_kapa-NGv3-PE100-NGv3-sort-2_111281072_127413888-prep-prealign-realign.intervals -L 2:111281073-127413888 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/2/tx/tmp11QZQL/R14-18102_kapa-NGv3-PE100-NGv3-sort-2_111281072_127413888-prep.bam
[2016-04-14T23:23Z] INFO  16:23:18,758 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:23Z] INFO  16:23:18,759 HelpFormatter - Date/Time: 2016/04/14 16:23:18
[2016-04-14T23:23Z] INFO  16:23:18,759 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:23Z] INFO  16:23:18,760 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:23Z] INFO  16:23:18,989 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:23Z] INFO  16:23:19,088 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:23Z] INFO  16:23:19,098 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:23Z] INFO  16:23:19,174 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-14T23:23Z] INFO  16:23:19,465 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:23Z] INFO  16:23:19,469 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:23Z] INFO  16:23:19,470 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:23Z] INFO  16:23:19,470 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:23Z] INFO  16:23:19,475 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/1/R14-18102_kapa-NGv3-PE100-NGv3-sort-1_143897546_159410511-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/1/tx/tmpVx3ORs/R14-18102_kapa-NGv3-PE100-NGv3-sort-1_143897546_159410511-prep-prealign-realign.intervals -l INFO -L 1:143897547-159410511 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-14T23:23Z] INFO  16:23:19,485 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:23Z] INFO  16:23:19,486 HelpFormatter - Date/Time: 2016/04/14 16:23:19
[2016-04-14T23:23Z] INFO  16:23:19,487 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:23Z] INFO  16:23:19,488 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:23Z] INFO  16:23:19,551 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:23Z] INFO  16:23:19,557 IntervalUtils - Processing 16132816 bp from intervals
[2016-04-14T23:23Z] WARN  16:23:19,563 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:23Z] GATK: realign ('2', 15519725, 31133925) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:23Z] INFO  16:23:19,604 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:23Z] INFO  16:23:19,649 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:23Z] INFO  16:23:19,767 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:23Z] INFO  16:23:19,768 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:23Z] INFO  16:23:19,769 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:23Z] INFO  16:23:19,770 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:23Z] INFO  16:23:19,852 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-14T23:23Z] INFO  16:23:19,872 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:23Z] INFO  16:23:19,938 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:23Z] INFO  16:23:19,944 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-14T23:23Z] INFO  16:23:20,087 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:23Z] INFO  16:23:20,176 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:23Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-2_31135088_46706841-prep.bam
[2016-04-14T23:23Z] INFO  16:23:20,274 IntervalUtils - Processing 15512965 bp from intervals
[2016-04-14T23:23Z] WARN  16:23:20,279 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:23Z] INFO  16:23:20,358 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:23Z] INFO  16:23:20,580 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:23Z] INFO  16:23:20,581 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:23Z] INFO  16:23:20,584 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:23Z] INFO  16:23:20,592 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-14T23:23Z] GATK pre-alignment ('2', 222291154, 237994685) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:23Z] INFO  16:23:21,533 ProgressMeter -            done    249843.0    19.0 s      76.0 s      100.0%    19.0 s       0.0 s
[2016-04-14T23:23Z] INFO  16:23:21,533 ProgressMeter - Total runtime 19.05 secs, 0.32 min, 0.01 hours
[2016-04-14T23:23Z] INFO  16:23:21,537 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 249843 total reads (0.00%)
[2016-04-14T23:23Z] INFO  16:23:21,537 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:23Z] INFO  16:23:21,538 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:23Z] INFO  16:23:21,538 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:23Z] INFO  16:23:22,509 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:23Z] INFO  16:23:22,513 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:23Z] INFO  16:23:22,514 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:23Z] INFO  16:23:22,514 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:23Z] INFO  16:23:22,519 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/2/R14-18102_kapa-NGv3-PE100-NGv3-sort-2_15519725_31133925-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/2/R14-18102_kapa-NGv3-PE100-NGv3-sort-2_15519725_31133925-prep-prealign-realign.intervals -L 2:15519726-31133925 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/2/tx/tmpGDb62P/R14-18102_kapa-NGv3-PE100-NGv3-sort-2_15519725_31133925-prep.bam
[2016-04-14T23:23Z] INFO  16:23:22,539 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:23Z] INFO  16:23:22,540 HelpFormatter - Date/Time: 2016/04/14 16:23:22
[2016-04-14T23:23Z] INFO  16:23:22,540 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:23Z] INFO  16:23:22,541 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:23Z] INFO  16:23:22,735 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:23Z] INFO  16:23:22,865 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:23Z] INFO  16:23:22,875 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:23Z] INFO  16:23:22,940 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-14T23:23Z] INFO  16:23:22,962 ProgressMeter -     2:179596802    200006.0    30.0 s       2.5 m       31.0%    96.0 s      66.0 s
[2016-04-14T23:23Z] INFO  16:23:23,217 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:23Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-2_79253838_95537822-prep.bam
[2016-04-14T23:23Z] INFO  16:23:23,286 IntervalUtils - Processing 15614200 bp from intervals
[2016-04-14T23:23Z] WARN  16:23:23,296 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:23Z] INFO  16:23:23,369 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:23Z] INFO  16:23:23,533 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:23Z] INFO  16:23:23,534 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:23Z] INFO  16:23:23,535 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:23Z] INFO  16:23:23,536 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:23Z] INFO  16:23:23,693 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:23Z] INFO  16:23:23,851 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:23Z] INFO  16:23:24,073 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:23Z] INFO  16:23:24,078 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:23Z] INFO  16:23:24,078 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:23Z] INFO  16:23:24,078 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:23Z] INFO  16:23:24,082 HelpFormatter - Program Args: -T PrintReads -L 2:222291155-237994685 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/2/tx/tmpFAYF5y/R14-18102_kapa-NGv3-PE100-NGv3-sort-2_222291154_237994685-prep-prealign.bam
[2016-04-14T23:23Z] INFO  16:23:24,091 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:23Z] GATK pre-alignment ('2', 237995374, 243199373) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:23Z] INFO  16:23:24,091 HelpFormatter - Date/Time: 2016/04/14 16:23:24
[2016-04-14T23:23Z] INFO  16:23:24,091 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:23Z] INFO  16:23:24,091 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:23Z] INFO  16:23:24,236 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:23Z] INFO  16:23:24,708 ProgressMeter -      1:40030909    300004.0    30.0 s     100.0 s       57.0%    52.0 s      22.0 s
[2016-04-14T23:23Z] INFO  16:23:25,467 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-14T23:23Z] INFO  16:23:25,533 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:23Z] INFO  16:23:25,545 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:23Z] INFO  16:23:25,588 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.04
[2016-04-14T23:23Z] INFO  16:23:25,606 IntervalUtils - Processing 15703531 bp from intervals
[2016-04-14T23:23Z] INFO  16:23:25,687 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:23Z] INFO  16:23:25,976 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:23Z] INFO  16:23:25,977 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:23Z] INFO  16:23:25,978 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:23Z] INFO  16:23:25,979 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:23Z] INFO  16:23:25,994 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:23Z] INFO  16:23:26,122 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:23Z] INFO  16:23:26,689 ProgressMeter -            done   1.551942E7    15.0 s       1.0 s      100.0%    15.0 s       0.0 s
[2016-04-14T23:23Z] INFO  16:23:26,690 ProgressMeter - Total runtime 15.74 secs, 0.26 min, 0.00 hours
[2016-04-14T23:23Z] INFO  16:23:26,694 MicroScheduler - 20089 reads were filtered out during the traversal out of approximately 122401 total reads (16.41%)
[2016-04-14T23:23Z] INFO  16:23:26,695 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:23Z] INFO  16:23:26,696 MicroScheduler -   -> 457 reads (0.37% of total) failing BadMateFilter
[2016-04-14T23:23Z] INFO  16:23:26,696 MicroScheduler -   -> 8905 reads (7.28% of total) failing DuplicateReadFilter
[2016-04-14T23:23Z] INFO  16:23:26,697 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-14T23:23Z] INFO  16:23:26,698 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:23Z] INFO  16:23:26,698 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-14T23:23Z] INFO  16:23:26,699 MicroScheduler -   -> 10727 reads (8.76% of total) failing MappingQualityZeroFilter
[2016-04-14T23:23Z] INFO  16:23:26,699 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:23Z] INFO  16:23:26,700 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-14T23:23Z] INFO  16:23:26,701 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-14T23:23Z] INFO  16:23:26,724 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:23Z] INFO  16:23:26,727 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:23Z] INFO  16:23:26,728 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:23Z] INFO  16:23:26,729 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:23Z] INFO  16:23:26,733 HelpFormatter - Program Args: -T PrintReads -L 2:237995375-243199373 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/2/tx/tmpq9nqcN/R14-18102_kapa-NGv3-PE100-NGv3-sort-2_237995374_243199373-prep-prealign.bam
[2016-04-14T23:23Z] INFO  16:23:26,742 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:23Z] INFO  16:23:26,742 HelpFormatter - Date/Time: 2016/04/14 16:23:26
[2016-04-14T23:23Z] INFO  16:23:26,742 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:23Z] INFO  16:23:26,743 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:23Z] INFO  16:23:26,912 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:23Z] INFO  16:23:27,028 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@41fd9d8e
[2016-04-14T23:23Z] INFO  16:23:27,184 ProgressMeter -            done    296472.0    38.0 s       2.2 m      100.0%    38.0 s       0.0 s
[2016-04-14T23:23Z] INFO  16:23:27,185 ProgressMeter - Total runtime 38.62 secs, 0.64 min, 0.01 hours
[2016-04-14T23:23Z] INFO  16:23:27,186 MicroScheduler - 150 reads were filtered out during the traversal out of approximately 296622 total reads (0.05%)
[2016-04-14T23:23Z] INFO  16:23:27,186 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:23Z] INFO  16:23:27,186 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:23Z] INFO  16:23:27,187 MicroScheduler -   -> 150 reads (0.05% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:23Z] INFO  16:23:27,962 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-14T23:23Z] INFO  16:23:28,016 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:23Z] INFO  16:23:28,026 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:23Z] INFO  16:23:28,062 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.04
[2016-04-14T23:23Z] INFO  16:23:28,082 IntervalUtils - Processing 5203999 bp from intervals
[2016-04-14T23:23Z] INFO  16:23:28,139 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:23Z] GATK: realign ('2', 143676177, 159195597) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:23Z] INFO  16:23:28,177 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:23Z] INFO  16:23:28,426 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:23Z] INFO  16:23:28,427 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:23Z] INFO  16:23:28,428 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:23Z] INFO  16:23:28,428 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:23Z] INFO  16:23:28,442 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:23Z] INFO  16:23:28,495 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:23Z] INFO  16:23:28,575 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:23Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-2_159196753_174774985-prep-prealign.bam
[2016-04-14T23:23Z] GATK RealignerTargetCreator: R14-18102_kapa-NGv3-PE100-NGv3-sort-2_159196753_174774985-prep-prealign.bam 2:159196754-174774985
[2016-04-14T23:23Z] GATK: RealignerTargetCreator
[2016-04-14T23:23Z] INFO  16:23:30,455 ProgressMeter -     2:203820487    200003.0    30.0 s       2.5 m       87.0%    34.0 s       4.0 s
[2016-04-14T23:23Z] INFO  16:23:30,654 ProgressMeter -       1:9416646    400010.0    30.0 s      75.0 s       60.6%    49.0 s      19.0 s
[2016-04-14T23:23Z] INFO  16:23:30,915 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:23Z] INFO  16:23:30,919 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:23Z] INFO  16:23:30,919 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:23Z] INFO  16:23:30,920 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:23Z] INFO  16:23:30,924 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/2/R14-18102_kapa-NGv3-PE100-NGv3-sort-2_143676177_159195597-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/2/R14-18102_kapa-NGv3-PE100-NGv3-sort-2_143676177_159195597-prep-prealign-realign.intervals -L 2:143676178-159195597 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/2/tx/tmpNBHMkE/R14-18102_kapa-NGv3-PE100-NGv3-sort-2_143676177_159195597-prep.bam
[2016-04-14T23:23Z] INFO  16:23:30,933 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:23Z] INFO  16:23:30,934 HelpFormatter - Date/Time: 2016/04/14 16:23:30
[2016-04-14T23:23Z] INFO  16:23:30,935 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:23Z] INFO  16:23:30,935 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:23Z] INFO  16:23:31,133 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:23Z] INFO  16:23:31,297 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:23Z] INFO  16:23:31,307 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:23Z] INFO  16:23:31,363 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-14T23:23Z] INFO  16:23:31,777 IntervalUtils - Processing 15519420 bp from intervals
[2016-04-14T23:23Z] WARN  16:23:31,782 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:23Z] INFO  16:23:31,868 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:23Z] INFO  16:23:31,957 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:23Z] INFO  16:23:31,958 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:23Z] INFO  16:23:31,959 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:23Z] INFO  16:23:31,960 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:23Z] INFO  16:23:32,118 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:23Z] INFO  16:23:32,300 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:23Z] INFO  16:23:32,349 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:23Z] INFO  16:23:32,353 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:23Z] INFO  16:23:32,353 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:23Z] INFO  16:23:32,354 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:23Z] INFO  16:23:32,359 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/2/R14-18102_kapa-NGv3-PE100-NGv3-sort-2_159196753_174774985-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/2/tx/tmpNjMCcu/R14-18102_kapa-NGv3-PE100-NGv3-sort-2_159196753_174774985-prep-prealign-realign.intervals -l INFO -L 2:159196754-174774985 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-14T23:23Z] INFO  16:23:32,369 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:23Z] INFO  16:23:32,369 HelpFormatter - Date/Time: 2016/04/14 16:23:32
[2016-04-14T23:23Z] INFO  16:23:32,369 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:23Z] INFO  16:23:32,370 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:23Z] INFO  16:23:32,479 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:23Z] INFO  16:23:32,688 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-14T23:23Z] INFO  16:23:32,697 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:23Z] INFO  16:23:32,768 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-14T23:23Z] INFO  16:23:33,049 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@41fd9d8e
[2016-04-14T23:23Z] INFO  16:23:33,099 IntervalUtils - Processing 15578232 bp from intervals
[2016-04-14T23:23Z] WARN  16:23:33,104 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:23Z] INFO  16:23:33,261 ProgressMeter -            done    247771.0    32.0 s       2.2 m      100.0%    32.0 s       0.0 s
[2016-04-14T23:23Z] INFO  16:23:33,261 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@7172f77a
[2016-04-14T23:23Z] INFO  16:23:33,262 ProgressMeter - Total runtime 32.86 secs, 0.55 min, 0.01 hours
[2016-04-14T23:23Z] INFO  16:23:33,263 MicroScheduler - 141 reads were filtered out during the traversal out of approximately 247912 total reads (0.06%)
[2016-04-14T23:23Z] INFO  16:23:33,264 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:23Z] INFO  16:23:33,264 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:23Z] INFO  16:23:33,265 MicroScheduler -   -> 141 reads (0.06% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:23Z] INFO  16:23:33,310 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:23Z] INFO  16:23:33,436 ProgressMeter -            done    523828.0    78.0 s       2.5 m      100.0%    78.0 s       0.0 s
[2016-04-14T23:23Z] INFO  16:23:33,436 ProgressMeter - Total runtime 78.53 secs, 1.31 min, 0.02 hours
[2016-04-14T23:23Z] INFO  16:23:33,437 MicroScheduler - 207 reads were filtered out during the traversal out of approximately 524035 total reads (0.04%)
[2016-04-14T23:23Z] INFO  16:23:33,437 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:23Z] INFO  16:23:33,437 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:23Z] INFO  16:23:33,437 MicroScheduler -   -> 207 reads (0.04% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:23Z] INFO  16:23:33,512 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:23Z] INFO  16:23:33,512 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:23Z] INFO  16:23:33,513 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:23Z] INFO  16:23:33,513 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-14T23:23Z] INFO  16:23:34,452 ProgressMeter -            done   1.6209898E7    19.0 s       1.0 s      100.0%    19.0 s       0.0 s
[2016-04-14T23:23Z] INFO  16:23:34,453 ProgressMeter - Total runtime 19.52 secs, 0.33 min, 0.01 hours
[2016-04-14T23:23Z] INFO  16:23:34,458 MicroScheduler - 67151 reads were filtered out during the traversal out of approximately 324352 total reads (20.70%)
[2016-04-14T23:23Z] INFO  16:23:34,459 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:23Z] INFO  16:23:34,460 MicroScheduler -   -> 660 reads (0.20% of total) failing BadMateFilter
[2016-04-14T23:23Z] INFO  16:23:34,461 MicroScheduler -   -> 23690 reads (7.30% of total) failing DuplicateReadFilter
[2016-04-14T23:23Z] INFO  16:23:34,462 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-14T23:23Z] INFO  16:23:34,462 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:23Z] INFO  16:23:34,463 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-14T23:23Z] INFO  16:23:34,464 MicroScheduler -   -> 42801 reads (13.20% of total) failing MappingQualityZeroFilter
[2016-04-14T23:23Z] INFO  16:23:34,465 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:23Z] INFO  16:23:34,465 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-14T23:23Z] INFO  16:23:34,466 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-14T23:23Z] INFO  16:23:34,987 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:23Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-2_95538561_111273222-prep-prealign.bam
[2016-04-14T23:23Z] INFO  16:23:35,101 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:23Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-2_190313104_205830046-prep-prealign.bam
[2016-04-14T23:23Z] INFO  16:23:35,130 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@5fe152b7
[2016-04-14T23:23Z] INFO  16:23:35,370 ProgressMeter -            done    335722.0    42.0 s       2.1 m      100.0%    42.0 s       0.0 s
[2016-04-14T23:23Z] INFO  16:23:35,371 ProgressMeter - Total runtime 42.42 secs, 0.71 min, 0.01 hours
[2016-04-14T23:23Z] INFO  16:23:35,371 MicroScheduler - 171 reads were filtered out during the traversal out of approximately 335893 total reads (0.05%)
[2016-04-14T23:23Z] INFO  16:23:35,372 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:23Z] INFO  16:23:35,372 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:23Z] INFO  16:23:35,372 MicroScheduler -   -> 171 reads (0.05% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:23Z] INFO  16:23:35,732 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:23Z] GATK: realign ('2', 127433207, 143643105) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:23Z] GATK RealignerTargetCreator: R14-18102_kapa-NGv3-PE100-NGv3-sort-2_190313104_205830046-prep-prealign.bam 2:190313105-205830046
[2016-04-14T23:23Z] GATK: RealignerTargetCreator
[2016-04-14T23:23Z] INFO  16:23:36,719 ProgressMeter -            done    332095.0    22.0 s      67.0 s      100.0%    22.0 s       0.0 s
[2016-04-14T23:23Z] INFO  16:23:36,719 ProgressMeter - Total runtime 22.39 secs, 0.37 min, 0.01 hours
[2016-04-14T23:23Z] INFO  16:23:36,723 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 332095 total reads (0.00%)
[2016-04-14T23:23Z] INFO  16:23:36,724 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:23Z] INFO  16:23:36,724 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:23Z] INFO  16:23:36,725 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:23Z] GATK RealignerTargetCreator: R14-18102_kapa-NGv3-PE100-NGv3-sort-2_95538561_111273222-prep-prealign.bam 2:95538562-111273222
[2016-04-14T23:23Z] GATK: RealignerTargetCreator
[2016-04-14T23:23Z] INFO  16:23:36,971 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:23Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-2_174777797_190306304-prep-prealign.bam
[2016-04-14T23:23Z] INFO  16:23:37,697 ProgressMeter -            done    231116.0    17.0 s      77.0 s      100.0%    17.0 s       0.0 s
[2016-04-14T23:23Z] INFO  16:23:37,698 ProgressMeter - Total runtime 17.93 secs, 0.30 min, 0.00 hours
[2016-04-14T23:23Z] INFO  16:23:37,703 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 231116 total reads (0.00%)
[2016-04-14T23:23Z] INFO  16:23:37,706 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:23Z] INFO  16:23:37,707 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:23Z] INFO  16:23:37,708 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:23Z] GATK RealignerTargetCreator: R14-18102_kapa-NGv3-PE100-NGv3-sort-2_174777797_190306304-prep-prealign.bam 2:174777798-190306304
[2016-04-14T23:23Z] GATK: RealignerTargetCreator
[2016-04-14T23:23Z] INFO  16:23:38,357 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:23Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-2_62362965_79253295-prep.bam
[2016-04-14T23:23Z] INFO  16:23:38,521 ProgressMeter -      1:21794977    400018.0    32.0 s      81.0 s       40.0%    80.0 s      48.0 s
[2016-04-14T23:23Z] INFO  16:23:38,612 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:23Z] INFO  16:23:38,616 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:23Z] INFO  16:23:38,616 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:23Z] INFO  16:23:38,617 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:23Z] INFO  16:23:38,621 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/2/R14-18102_kapa-NGv3-PE100-NGv3-sort-2_127433207_143643105-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/2/R14-18102_kapa-NGv3-PE100-NGv3-sort-2_127433207_143643105-prep-prealign-realign.intervals -L 2:127433208-143643105 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/2/tx/tmpuRxR8Y/R14-18102_kapa-NGv3-PE100-NGv3-sort-2_127433207_143643105-prep.bam
[2016-04-14T23:23Z] INFO  16:23:38,631 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:23Z] INFO  16:23:38,631 HelpFormatter - Date/Time: 2016/04/14 16:23:38
[2016-04-14T23:23Z] INFO  16:23:38,631 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:23Z] INFO  16:23:38,632 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:23Z] INFO  16:23:38,856 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:23Z] INFO  16:23:38,934 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:23Z] INFO  16:23:38,938 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:23Z] INFO  16:23:38,938 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:23Z] INFO  16:23:38,939 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:23Z] INFO  16:23:38,943 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/2/R14-18102_kapa-NGv3-PE100-NGv3-sort-2_190313104_205830046-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/2/tx/tmps8GTgm/R14-18102_kapa-NGv3-PE100-NGv3-sort-2_190313104_205830046-prep-prealign-realign.intervals -l INFO -L 2:190313105-205830046 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-14T23:23Z] INFO  16:23:38,959 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:23Z] INFO  16:23:38,967 HelpFormatter - Date/Time: 2016/04/14 16:23:38
[2016-04-14T23:23Z] INFO  16:23:38,968 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:23Z] INFO  16:23:38,969 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:23Z] INFO  16:23:39,030 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:23Z] INFO  16:23:39,041 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:23Z] INFO  16:23:39,092 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-14T23:23Z] INFO  16:23:39,101 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:23Z] INFO  16:23:39,137 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:23Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-2_111281072_127413888-prep.bam
[2016-04-14T23:23Z] INFO  16:23:39,331 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-14T23:23Z] INFO  16:23:39,341 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:23Z] INFO  16:23:39,400 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-14T23:23Z] INFO  16:23:39,464 IntervalUtils - Processing 16209898 bp from intervals
[2016-04-14T23:23Z] WARN  16:23:39,470 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:23Z] INFO  16:23:39,578 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:23Z] INFO  16:23:39,624 ProgressMeter -            done    711471.0    45.0 s      63.0 s      100.0%    45.0 s       0.0 s
[2016-04-14T23:23Z] INFO  16:23:39,624 ProgressMeter - Total runtime 45.17 secs, 0.75 min, 0.01 hours
[2016-04-14T23:23Z] INFO  16:23:39,628 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 711471 total reads (0.00%)
[2016-04-14T23:23Z] INFO  16:23:39,629 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:23Z] INFO  16:23:39,633 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:23Z] INFO  16:23:39,634 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:23Z] GATK pre-alignment ('3', 0, 15512123) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:23Z] INFO  16:23:39,693 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:23Z] INFO  16:23:39,697 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:23Z] INFO  16:23:39,698 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:23Z] INFO  16:23:39,699 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:23Z] INFO  16:23:39,704 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/2/R14-18102_kapa-NGv3-PE100-NGv3-sort-2_95538561_111273222-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/2/tx/tmp3RI5Hq/R14-18102_kapa-NGv3-PE100-NGv3-sort-2_95538561_111273222-prep-prealign-realign.intervals -l INFO -L 2:95538562-111273222 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-14T23:23Z] INFO  16:23:39,714 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:23Z] INFO  16:23:39,719 HelpFormatter - Date/Time: 2016/04/14 16:23:39
[2016-04-14T23:23Z] INFO  16:23:39,720 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:23Z] INFO  16:23:39,720 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:23Z] INFO  16:23:39,732 IntervalUtils - Processing 15516942 bp from intervals
[2016-04-14T23:23Z] WARN  16:23:39,738 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:23Z] INFO  16:23:39,753 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:23Z] INFO  16:23:39,755 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:23Z] INFO  16:23:39,755 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:23Z] INFO  16:23:39,756 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:23Z] INFO  16:23:39,850 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:23Z] INFO  16:23:39,852 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:23Z] INFO  16:23:39,894 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:23Z] INFO  16:23:40,064 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:23Z] INFO  16:23:40,065 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:23Z] INFO  16:23:40,065 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:23Z] INFO  16:23:40,065 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-14T23:23Z] INFO  16:23:40,078 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:23Z] GATK pre-alignment ('3', 15515506, 31574805) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:23Z] INFO  16:23:40,119 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-14T23:23Z] INFO  16:23:40,131 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:23Z] INFO  16:23:40,184 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-14T23:23Z] INFO  16:23:40,533 IntervalUtils - Processing 15734661 bp from intervals
[2016-04-14T23:23Z] WARN  16:23:40,539 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:23Z] INFO  16:23:40,686 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:23Z] INFO  16:23:40,988 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:23Z] INFO  16:23:40,989 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:23Z] INFO  16:23:40,990 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:23Z] INFO  16:23:40,991 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-14T23:23Z] INFO  16:23:41,166 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:23Z] INFO  16:23:41,172 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:23Z] INFO  16:23:41,176 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:23Z] INFO  16:23:41,176 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:23Z] INFO  16:23:41,177 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:23Z] INFO  16:23:41,181 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/2/R14-18102_kapa-NGv3-PE100-NGv3-sort-2_174777797_190306304-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/2/tx/tmpa0oGRf/R14-18102_kapa-NGv3-PE100-NGv3-sort-2_174777797_190306304-prep-prealign-realign.intervals -l INFO -L 2:174777798-190306304 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-14T23:23Z] INFO  16:23:41,198 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:23Z] INFO  16:23:41,199 HelpFormatter - Date/Time: 2016/04/14 16:23:41
[2016-04-14T23:23Z] INFO  16:23:41,200 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:23Z] INFO  16:23:41,200 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:23Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-1_31187093_46714270-prep.bam
[2016-04-14T23:23Z] INFO  16:23:41,340 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:23Z] INFO  16:23:41,616 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-14T23:23Z] INFO  16:23:41,637 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:23Z] INFO  16:23:41,725 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-14T23:23Z] INFO  16:23:42,101 IntervalUtils - Processing 15528507 bp from intervals
[2016-04-14T23:23Z] WARN  16:23:42,141 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:23Z] INFO  16:23:42,228 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:23Z] INFO  16:23:42,499 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:23Z] INFO  16:23:42,501 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:23Z] INFO  16:23:42,502 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:23Z] INFO  16:23:42,502 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-14T23:23Z] INFO  16:23:42,648 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:23Z] INFO  16:23:42,652 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:23Z] INFO  16:23:42,652 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:23Z] INFO  16:23:42,653 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:23Z] INFO  16:23:42,658 HelpFormatter - Program Args: -T PrintReads -L 3:1-15512123 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/3/tx/tmp68Sm1Z/R14-18102_kapa-NGv3-PE100-NGv3-sort-3_0_15512123-prep-prealign.bam
[2016-04-14T23:23Z] INFO  16:23:42,696 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:23Z] INFO  16:23:42,697 HelpFormatter - Date/Time: 2016/04/14 16:23:42
[2016-04-14T23:23Z] INFO  16:23:42,697 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:23Z] INFO  16:23:42,698 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:23Z] INFO  16:23:42,910 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:23Z] INFO  16:23:43,199 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:23Z] INFO  16:23:43,203 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:23Z] INFO  16:23:43,203 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:23Z] INFO  16:23:43,204 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:23Z] INFO  16:23:43,208 HelpFormatter - Program Args: -T PrintReads -L 3:15515507-31574805 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/3/tx/tmptsvHfv/R14-18102_kapa-NGv3-PE100-NGv3-sort-3_15515506_31574805-prep-prealign.bam
[2016-04-14T23:23Z] INFO  16:23:43,220 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:23Z] INFO  16:23:43,221 HelpFormatter - Date/Time: 2016/04/14 16:23:43
[2016-04-14T23:23Z] INFO  16:23:43,221 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:23Z] INFO  16:23:43,222 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:23Z] INFO  16:23:43,424 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:23Z] INFO  16:23:43,505 ProgressMeter -            done    121676.0    11.0 s      94.0 s      100.0%    11.0 s       0.0 s
[2016-04-14T23:23Z] INFO  16:23:43,506 ProgressMeter - Total runtime 11.55 secs, 0.19 min, 0.00 hours
[2016-04-14T23:23Z] INFO  16:23:43,509 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 121676 total reads (0.00%)
[2016-04-14T23:23Z] INFO  16:23:43,510 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:23Z] INFO  16:23:43,510 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:23Z] INFO  16:23:43,510 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:23Z] GATK pre-alignment ('3', 31617887, 47127804) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:23Z] INFO  16:23:43,977 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-14T23:23Z] INFO  16:23:44,035 ProgressMeter -     2:219103470    100002.0    30.0 s       5.0 m       80.5%    37.0 s       7.0 s
[2016-04-14T23:23Z] INFO  16:23:44,044 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:23Z] INFO  16:23:44,053 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:23Z] INFO  16:23:44,103 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-14T23:23Z] INFO  16:23:44,118 IntervalUtils - Processing 15512123 bp from intervals
[2016-04-14T23:23Z] INFO  16:23:44,195 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:23Z] INFO  16:23:44,491 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:23Z] INFO  16:23:44,493 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:23Z] INFO  16:23:44,493 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:23Z] INFO  16:23:44,494 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:23Z] INFO  16:23:44,517 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:23Z] INFO  16:23:44,626 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-14T23:23Z] INFO  16:23:44,653 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:23Z] INFO  16:23:44,689 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:23Z] INFO  16:23:44,699 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:23Z] INFO  16:23:44,764 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-14T23:23Z] INFO  16:23:44,780 IntervalUtils - Processing 16059299 bp from intervals
[2016-04-14T23:23Z] INFO  16:23:44,869 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:23Z] INFO  16:23:45,068 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:23Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-2_143676177_159195597-prep.bam
[2016-04-14T23:23Z] INFO  16:23:45,117 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:23Z] INFO  16:23:45,119 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:23Z] INFO  16:23:45,119 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:23Z] INFO  16:23:45,120 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:23Z] INFO  16:23:45,134 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:23Z] INFO  16:23:45,301 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:23Z] GATK pre-alignment ('3', 47129602, 62648069) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:23Z] INFO  16:23:46,825 ProgressMeter -            done    360327.0    23.0 s      64.0 s      100.0%    23.0 s       0.0 s
[2016-04-14T23:23Z] INFO  16:23:46,826 ProgressMeter - Total runtime 23.29 secs, 0.39 min, 0.01 hours
[2016-04-14T23:23Z] INFO  16:23:46,829 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 360327 total reads (0.00%)
[2016-04-14T23:23Z] INFO  16:23:46,830 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:23Z] INFO  16:23:46,830 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:23Z] INFO  16:23:46,830 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:23Z] INFO  16:23:46,860 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:23Z] INFO  16:23:46,863 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:23Z] INFO  16:23:46,864 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:23Z] INFO  16:23:46,864 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:23Z] INFO  16:23:46,869 HelpFormatter - Program Args: -T PrintReads -L 3:31617888-47127804 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/3/tx/tmpyQv03e/R14-18102_kapa-NGv3-PE100-NGv3-sort-3_31617887_47127804-prep-prealign.bam
[2016-04-14T23:23Z] INFO  16:23:46,878 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:23Z] INFO  16:23:46,889 HelpFormatter - Date/Time: 2016/04/14 16:23:46
[2016-04-14T23:23Z] INFO  16:23:46,890 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:23Z] INFO  16:23:46,891 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:23Z] INFO  16:23:47,071 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:23Z] INFO  16:23:47,532 ProgressMeter -            done    766170.0    47.0 s      61.0 s      100.0%    47.0 s       0.0 s
[2016-04-14T23:23Z] INFO  16:23:47,533 ProgressMeter - Total runtime 47.04 secs, 0.78 min, 0.01 hours
[2016-04-14T23:23Z] INFO  16:23:47,536 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 766170 total reads (0.00%)
[2016-04-14T23:23Z] INFO  16:23:47,537 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:23Z] INFO  16:23:47,537 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:23Z] INFO  16:23:47,537 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:23Z] INFO  16:23:48,180 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-14T23:23Z] INFO  16:23:48,266 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:23Z] INFO  16:23:48,275 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:23Z] INFO  16:23:48,319 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.04
[2016-04-14T23:23Z] INFO  16:23:48,331 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:23Z] INFO  16:23:48,334 IntervalUtils - Processing 15509917 bp from intervals
[2016-04-14T23:23Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-2_15519725_31133925-prep.bam
[2016-04-14T23:23Z] INFO  16:23:48,415 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:23Z] INFO  16:23:48,552 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:23Z] INFO  16:23:48,556 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:23Z] INFO  16:23:48,556 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:23Z] INFO  16:23:48,557 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:23Z] INFO  16:23:48,562 HelpFormatter - Program Args: -T PrintReads -L 3:47129603-62648069 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/3/tx/tmpqPHCn6/R14-18102_kapa-NGv3-PE100-NGv3-sort-3_47129602_62648069-prep-prealign.bam
[2016-04-14T23:23Z] INFO  16:23:48,582 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:23Z] INFO  16:23:48,583 HelpFormatter - Date/Time: 2016/04/14 16:23:48
[2016-04-14T23:23Z] INFO  16:23:48,583 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:23Z] INFO  16:23:48,584 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:23Z] INFO  16:23:48,727 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:23Z] INFO  16:23:48,728 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:23Z] INFO  16:23:48,729 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:23Z] INFO  16:23:48,730 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:23Z] INFO  16:23:48,759 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:23Z] INFO  16:23:48,805 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:23Z] INFO  16:23:48,904 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:23Z] INFO  16:23:49,003 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:23Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-1_0_15541927-prep.bam
[2016-04-14T23:23Z] GATK pre-alignment ('3', 62739115, 78648077) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:23Z] INFO  16:23:49,987 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-14T23:23Z] INFO  16:23:50,047 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:23Z] INFO  16:23:50,056 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:23Z] INFO  16:23:50,102 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-14T23:23Z] INFO  16:23:50,127 IntervalUtils - Processing 15518467 bp from intervals
[2016-04-14T23:23Z] INFO  16:23:50,249 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:23Z] INFO  16:23:50,605 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:23Z] INFO  16:23:50,606 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:23Z] INFO  16:23:50,606 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:23Z] INFO  16:23:50,606 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:23Z] INFO  16:23:50,615 ProgressMeter -     1:156599673   1.2700726E7    30.0 s       2.0 s       81.9%    36.0 s       6.0 s
[2016-04-14T23:23Z] INFO  16:23:50,648 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:23Z] INFO  16:23:50,847 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:23Z] GATK pre-alignment ('3', 78649262, 96533852) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:23Z] INFO  16:23:52,090 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:23Z] INFO  16:23:52,094 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:23Z] INFO  16:23:52,095 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:23Z] INFO  16:23:52,096 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:23Z] INFO  16:23:52,100 HelpFormatter - Program Args: -T PrintReads -L 3:62739116-78648077 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/3/tx/tmp6LlsIc/R14-18102_kapa-NGv3-PE100-NGv3-sort-3_62739115_78648077-prep-prealign.bam
[2016-04-14T23:23Z] INFO  16:23:52,110 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:23Z] INFO  16:23:52,110 HelpFormatter - Date/Time: 2016/04/14 16:23:52
[2016-04-14T23:23Z] INFO  16:23:52,110 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:23Z] INFO  16:23:52,111 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:23Z] INFO  16:23:52,309 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:23Z] INFO  16:23:53,401 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-14T23:23Z] INFO  16:23:53,490 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:23Z] INFO  16:23:53,500 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:23Z] INFO  16:23:53,550 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-14T23:23Z] INFO  16:23:53,573 IntervalUtils - Processing 15908962 bp from intervals
[2016-04-14T23:23Z] INFO  16:23:53,705 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:23Z] INFO  16:23:53,875 ProgressMeter -            done   1.5578232E7    20.0 s       1.0 s      100.0%    20.0 s       0.0 s
[2016-04-14T23:23Z] INFO  16:23:53,877 ProgressMeter - Total runtime 20.36 secs, 0.34 min, 0.01 hours
[2016-04-14T23:23Z] INFO  16:23:53,881 MicroScheduler - 25679 reads were filtered out during the traversal out of approximately 298013 total reads (8.62%)
[2016-04-14T23:23Z] INFO  16:23:53,883 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:23Z] INFO  16:23:53,883 MicroScheduler -   -> 653 reads (0.22% of total) failing BadMateFilter
[2016-04-14T23:23Z] INFO  16:23:53,884 MicroScheduler -   -> 23531 reads (7.90% of total) failing DuplicateReadFilter
[2016-04-14T23:23Z] INFO  16:23:53,885 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-14T23:23Z] INFO  16:23:53,886 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:23Z] INFO  16:23:53,886 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-14T23:23Z] INFO  16:23:53,887 MicroScheduler -   -> 1495 reads (0.50% of total) failing MappingQualityZeroFilter
[2016-04-14T23:23Z] INFO  16:23:53,888 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:23Z] INFO  16:23:53,889 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-14T23:23Z] INFO  16:23:53,889 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-14T23:23Z] INFO  16:23:53,939 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:23Z] INFO  16:23:53,950 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:23Z] INFO  16:23:53,951 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:23Z] INFO  16:23:53,951 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:23Z] INFO  16:23:53,956 HelpFormatter - Program Args: -T PrintReads -L 3:78649263-96533852 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/3/tx/tmpy5tPXE/R14-18102_kapa-NGv3-PE100-NGv3-sort-3_78649262_96533852-prep-prealign.bam
[2016-04-14T23:23Z] INFO  16:23:53,980 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:23Z] INFO  16:23:53,981 HelpFormatter - Date/Time: 2016/04/14 16:23:53
[2016-04-14T23:23Z] INFO  16:23:53,981 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:23Z] INFO  16:23:53,981 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:23Z] INFO  16:23:54,046 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:23Z] INFO  16:23:54,048 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:23Z] INFO  16:23:54,049 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:23Z] INFO  16:23:54,050 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:23Z] INFO  16:23:54,069 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:23Z] INFO  16:23:54,233 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:23Z] INFO  16:23:54,256 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:23Z] INFO  16:23:55,276 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-14T23:23Z] INFO  16:23:55,301 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:23Z] GATK: realign ('2', 159196753, 174774985) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:23Z] INFO  16:23:55,359 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:23Z] INFO  16:23:55,368 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:23Z] INFO  16:23:55,436 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-14T23:23Z] INFO  16:23:55,450 IntervalUtils - Processing 17884590 bp from intervals
[2016-04-14T23:23Z] INFO  16:23:55,545 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:23Z] INFO  16:23:55,784 ProgressMeter -            done   1.5512965E7    35.0 s       2.0 s      100.0%    35.0 s       0.0 s
[2016-04-14T23:23Z] INFO  16:23:55,785 ProgressMeter - Total runtime 35.20 secs, 0.59 min, 0.01 hours
[2016-04-14T23:23Z] INFO  16:23:55,785 MicroScheduler - 373532 reads were filtered out during the traversal out of approximately 1236063 total reads (30.22%)
[2016-04-14T23:23Z] INFO  16:23:55,785 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:23Z] INFO  16:23:55,786 MicroScheduler -   -> 1485 reads (0.12% of total) failing BadMateFilter
[2016-04-14T23:23Z] INFO  16:23:55,786 MicroScheduler -   -> 76843 reads (6.22% of total) failing DuplicateReadFilter
[2016-04-14T23:23Z] INFO  16:23:55,786 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-14T23:23Z] INFO  16:23:55,786 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:23Z] INFO  16:23:55,787 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-14T23:23Z] INFO  16:23:55,787 MicroScheduler -   -> 295204 reads (23.88% of total) failing MappingQualityZeroFilter
[2016-04-14T23:23Z] INFO  16:23:55,787 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:23Z] INFO  16:23:55,787 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-14T23:23Z] INFO  16:23:55,788 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-14T23:23Z] INFO  16:23:55,904 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:23Z] INFO  16:23:55,905 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:23Z] INFO  16:23:55,906 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:23Z] INFO  16:23:55,906 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:23Z] INFO  16:23:55,946 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:23Z] INFO  16:23:56,135 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:23Z] INFO  16:23:56,495 ProgressMeter -     2:234356457    200004.0    30.0 s       2.5 m       76.8%    39.0 s       9.0 s
[2016-04-14T23:23Z] INFO  16:23:56,626 ProgressMeter -            done    791594.0    50.0 s      63.0 s      100.0%    50.0 s       0.0 s
[2016-04-14T23:23Z] INFO  16:23:56,627 ProgressMeter - Total runtime 50.60 secs, 0.84 min, 0.01 hours
[2016-04-14T23:23Z] INFO  16:23:56,631 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 791594 total reads (0.00%)
[2016-04-14T23:23Z] INFO  16:23:56,631 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:23Z] INFO  16:23:56,631 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:23Z] INFO  16:23:56,632 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:23Z] INFO  16:23:57,209 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:23Z] GATK: realign ('1', 143897546, 159410511) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:23Z] INFO  16:23:58,249 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:23Z] INFO  16:23:58,291 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:23Z] INFO  16:23:58,295 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:23Z] INFO  16:23:58,295 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:23Z] INFO  16:23:58,296 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:23Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-1_15545821_31186478-prep.bam
[2016-04-14T23:23Z] INFO  16:23:58,301 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/2/R14-18102_kapa-NGv3-PE100-NGv3-sort-2_159196753_174774985-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/2/R14-18102_kapa-NGv3-PE100-NGv3-sort-2_159196753_174774985-prep-prealign-realign.intervals -L 2:159196754-174774985 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/2/tx/tmpiDmzrR/R14-18102_kapa-NGv3-PE100-NGv3-sort-2_159196753_174774985-prep.bam
[2016-04-14T23:23Z] INFO  16:23:58,311 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:23Z] INFO  16:23:58,312 HelpFormatter - Date/Time: 2016/04/14 16:23:58
[2016-04-14T23:23Z] INFO  16:23:58,313 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:23Z] INFO  16:23:58,313 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:23Z] INFO  16:23:58,442 ProgressMeter -     2:242499725    100002.0    30.0 s       5.0 m       86.6%    34.0 s       4.0 s
[2016-04-14T23:23Z] INFO  16:23:58,590 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:23Z] INFO  16:23:58,715 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:23Z] INFO  16:23:58,739 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:23Z] INFO  16:23:58,820 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-14T23:23Z] INFO  16:23:59,156 IntervalUtils - Processing 15578232 bp from intervals
[2016-04-14T23:23Z] WARN  16:23:59,161 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:23Z] INFO  16:23:59,260 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:23Z] INFO  16:23:59,419 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:23Z] INFO  16:23:59,421 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:23Z] INFO  16:23:59,421 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:23Z] INFO  16:23:59,422 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:23Z] INFO  16:23:59,468 ProgressMeter -            done   1.5516942E7    19.0 s       1.0 s      100.0%    19.0 s       0.0 s
[2016-04-14T23:23Z] INFO  16:23:59,469 ProgressMeter - Total runtime 19.40 secs, 0.32 min, 0.01 hours
[2016-04-14T23:23Z] INFO  16:23:59,473 MicroScheduler - 20874 reads were filtered out during the traversal out of approximately 249669 total reads (8.36%)
[2016-04-14T23:23Z] INFO  16:23:59,474 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:23Z] INFO  16:23:59,475 MicroScheduler -   -> 611 reads (0.24% of total) failing BadMateFilter
[2016-04-14T23:23Z] INFO  16:23:59,476 MicroScheduler -   -> 19532 reads (7.82% of total) failing DuplicateReadFilter
[2016-04-14T23:23Z] INFO  16:23:59,476 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-14T23:23Z] INFO  16:23:59,477 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:23Z] INFO  16:23:59,477 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-14T23:23Z] INFO  16:23:59,478 MicroScheduler -   -> 731 reads (0.29% of total) failing MappingQualityZeroFilter
[2016-04-14T23:23Z] INFO  16:23:59,479 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:23Z] INFO  16:23:59,479 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-14T23:23Z] INFO  16:23:59,480 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-14T23:23Z] INFO  16:23:59,627 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:23Z] INFO  16:23:59,799 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:23Z] INFO  16:23:59,853 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:23Z] INFO  16:23:59,856 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:23Z] INFO  16:23:59,856 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:23Z] INFO  16:23:59,857 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:23Z] INFO  16:23:59,862 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/1/R14-18102_kapa-NGv3-PE100-NGv3-sort-1_143897546_159410511-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/1/R14-18102_kapa-NGv3-PE100-NGv3-sort-1_143897546_159410511-prep-prealign-realign.intervals -L 1:143897547-159410511 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/1/tx/tmpJGpJtY/R14-18102_kapa-NGv3-PE100-NGv3-sort-1_143897546_159410511-prep.bam
[2016-04-14T23:23Z] INFO  16:23:59,875 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:23Z] INFO  16:23:59,882 HelpFormatter - Date/Time: 2016/04/14 16:23:59
[2016-04-14T23:23Z] INFO  16:23:59,883 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:23Z] INFO  16:23:59,884 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:24Z] INFO  16:24:00,139 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:24Z] INFO  16:24:00,242 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:24Z] INFO  16:24:00,261 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:24Z] INFO  16:24:00,328 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-14T23:24Z] INFO  16:24:00,790 IntervalUtils - Processing 15512965 bp from intervals
[2016-04-14T23:24Z] WARN  16:24:00,796 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:24Z] INFO  16:24:00,830 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:24Z] GATK: realign ('2', 190313104, 205830046) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:24Z] GATK pre-alignment ('3', 96585668, 112185230) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:24Z] INFO  16:24:00,906 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:24Z] INFO  16:24:01,096 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:24Z] INFO  16:24:01,109 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:24Z] INFO  16:24:01,110 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:24Z] INFO  16:24:01,111 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:24Z] INFO  16:24:01,364 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:24Z] INFO  16:24:01,638 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:24Z] INFO  16:24:01,683 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@41fd9d8e
[2016-04-14T23:24Z] INFO  16:24:01,794 ProgressMeter -            done    113363.0    16.0 s       2.5 m      100.0%    16.0 s       0.0 s
[2016-04-14T23:24Z] INFO  16:24:01,795 ProgressMeter - Total runtime 16.68 secs, 0.28 min, 0.00 hours
[2016-04-14T23:24Z] INFO  16:24:01,796 MicroScheduler - 101 reads were filtered out during the traversal out of approximately 113464 total reads (0.09%)
[2016-04-14T23:24Z] INFO  16:24:01,796 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:24Z] INFO  16:24:01,796 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:24Z] INFO  16:24:01,797 MicroScheduler -   -> 101 reads (0.09% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:24Z] INFO  16:24:02,258 ProgressMeter -            done   1.5734661E7    21.0 s       1.0 s      100.0%    21.0 s       0.0 s
[2016-04-14T23:24Z] INFO  16:24:02,270 ProgressMeter - Total runtime 21.28 secs, 0.35 min, 0.01 hours
[2016-04-14T23:24Z] INFO  16:24:02,274 MicroScheduler - 135631 reads were filtered out during the traversal out of approximately 527468 total reads (25.71%)
[2016-04-14T23:24Z] INFO  16:24:02,284 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:24Z] INFO  16:24:02,285 MicroScheduler -   -> 825 reads (0.16% of total) failing BadMateFilter
[2016-04-14T23:24Z] INFO  16:24:02,286 MicroScheduler -   -> 34969 reads (6.63% of total) failing DuplicateReadFilter
[2016-04-14T23:24Z] INFO  16:24:02,286 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-14T23:24Z] INFO  16:24:02,287 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:24Z] INFO  16:24:02,287 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-14T23:24Z] INFO  16:24:02,288 MicroScheduler -   -> 99837 reads (18.93% of total) failing MappingQualityZeroFilter
[2016-04-14T23:24Z] INFO  16:24:02,289 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:24Z] INFO  16:24:02,289 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-14T23:24Z] INFO  16:24:02,290 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-14T23:24Z] INFO  16:24:02,496 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@5fe152b7
[2016-04-14T23:24Z] INFO  16:24:02,755 ProgressMeter -            done    213828.0    34.0 s       2.7 m       97.4%    34.0 s       0.0 s
[2016-04-14T23:24Z] INFO  16:24:02,755 ProgressMeter - Total runtime 34.33 secs, 0.57 min, 0.01 hours
[2016-04-14T23:24Z] INFO  16:24:02,756 MicroScheduler - 92 reads were filtered out during the traversal out of approximately 213920 total reads (0.04%)
[2016-04-14T23:24Z] INFO  16:24:02,756 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:24Z] INFO  16:24:02,757 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:24Z] INFO  16:24:02,757 MicroScheduler -   -> 92 reads (0.04% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:24Z] INFO  16:24:03,050 ProgressMeter -            done    322561.0    23.0 s      72.0 s      100.0%    23.0 s       0.0 s
[2016-04-14T23:24Z] INFO  16:24:03,051 ProgressMeter - Total runtime 23.30 secs, 0.39 min, 0.01 hours
[2016-04-14T23:24Z] INFO  16:24:03,056 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 322561 total reads (0.00%)
[2016-04-14T23:24Z] INFO  16:24:03,057 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:24Z] INFO  16:24:03,058 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:24Z] INFO  16:24:03,059 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:24Z] INFO  16:24:03,125 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:24Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-3_15515506_31574805-prep-prealign.bam
[2016-04-14T23:24Z] GATK RealignerTargetCreator: R14-18102_kapa-NGv3-PE100-NGv3-sort-3_15515506_31574805-prep-prealign.bam 3:15515507-31574805
[2016-04-14T23:24Z] GATK: RealignerTargetCreator
[2016-04-14T23:24Z] INFO  16:24:03,692 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:24Z] GATK: realign ('2', 95538561, 111273222) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:24Z] INFO  16:24:03,817 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:24Z] INFO  16:24:03,820 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:24Z] INFO  16:24:03,821 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:24Z] INFO  16:24:03,821 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:24Z] INFO  16:24:03,829 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/2/R14-18102_kapa-NGv3-PE100-NGv3-sort-2_190313104_205830046-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/2/R14-18102_kapa-NGv3-PE100-NGv3-sort-2_190313104_205830046-prep-prealign-realign.intervals -L 2:190313105-205830046 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/2/tx/tmpEgRTVZ/R14-18102_kapa-NGv3-PE100-NGv3-sort-2_190313104_205830046-prep.bam
[2016-04-14T23:24Z] INFO  16:24:03,848 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:24Z] INFO  16:24:03,857 HelpFormatter - Date/Time: 2016/04/14 16:24:03
[2016-04-14T23:24Z] INFO  16:24:03,858 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:24Z] INFO  16:24:03,859 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:24Z] INFO  16:24:03,889 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:24Z] INFO  16:24:03,893 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:24Z] INFO  16:24:03,894 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:24Z] INFO  16:24:03,894 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:24Z] INFO  16:24:03,900 HelpFormatter - Program Args: -T PrintReads -L 3:96585669-112185230 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/3/tx/tmpTGsJ1t/R14-18102_kapa-NGv3-PE100-NGv3-sort-3_96585668_112185230-prep-prealign.bam
[2016-04-14T23:24Z] INFO  16:24:03,915 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:24Z] INFO  16:24:03,916 HelpFormatter - Date/Time: 2016/04/14 16:24:03
[2016-04-14T23:24Z] INFO  16:24:03,916 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:24Z] INFO  16:24:03,916 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:24Z] INFO  16:24:04,025 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@5fe152b7
[2016-04-14T23:24Z] INFO  16:24:04,115 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:24Z] INFO  16:24:04,121 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:24Z] INFO  16:24:04,251 ProgressMeter -            done    401370.0    50.0 s       2.1 m      100.0%    50.0 s       0.0 s
[2016-04-14T23:24Z] INFO  16:24:04,251 ProgressMeter - Total runtime 50.23 secs, 0.84 min, 0.01 hours
[2016-04-14T23:24Z] INFO  16:24:04,252 MicroScheduler - 175 reads were filtered out during the traversal out of approximately 401545 total reads (0.04%)
[2016-04-14T23:24Z] INFO  16:24:04,252 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:24Z] INFO  16:24:04,253 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:24Z] INFO  16:24:04,253 MicroScheduler -   -> 175 reads (0.04% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:24Z] INFO  16:24:04,255 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:24Z] INFO  16:24:04,267 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:24Z] INFO  16:24:04,287 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:24Z] INFO  16:24:04,319 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-14T23:24Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-2_237995374_243199373-prep-prealign.bam
[2016-04-14T23:24Z] INFO  16:24:04,620 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:24Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-2_127433207_143643105-prep.bam
[2016-04-14T23:24Z] INFO  16:24:04,690 ProgressMeter -            done   1.5528507E7    22.0 s       1.0 s      100.0%    22.0 s       0.0 s
[2016-04-14T23:24Z] INFO  16:24:04,690 ProgressMeter - Total runtime 22.19 secs, 0.37 min, 0.01 hours
[2016-04-14T23:24Z] INFO  16:24:04,694 MicroScheduler - 35054 reads were filtered out during the traversal out of approximately 337889 total reads (10.37%)
[2016-04-14T23:24Z] INFO  16:24:04,696 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:24Z] INFO  16:24:04,707 MicroScheduler -   -> 728 reads (0.22% of total) failing BadMateFilter
[2016-04-14T23:24Z] INFO  16:24:04,708 MicroScheduler -   -> 26272 reads (7.78% of total) failing DuplicateReadFilter
[2016-04-14T23:24Z] INFO  16:24:04,709 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-14T23:24Z] INFO  16:24:04,709 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:24Z] INFO  16:24:04,710 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-14T23:24Z] INFO  16:24:04,711 MicroScheduler -   -> 8054 reads (2.38% of total) failing MappingQualityZeroFilter
[2016-04-14T23:24Z] INFO  16:24:04,711 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:24Z] INFO  16:24:04,712 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-14T23:24Z] INFO  16:24:04,713 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-14T23:24Z] INFO  16:24:04,722 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@32d5a4c6
[2016-04-14T23:24Z] INFO  16:24:04,750 IntervalUtils - Processing 15516942 bp from intervals
[2016-04-14T23:24Z] WARN  16:24:04,757 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:24Z] INFO  16:24:04,858 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:24Z] INFO  16:24:05,028 ProgressMeter -            done    310529.0    39.0 s       2.1 m      100.0%    39.0 s       0.0 s
[2016-04-14T23:24Z] INFO  16:24:05,029 ProgressMeter - Total runtime 39.05 secs, 0.65 min, 0.01 hours
[2016-04-14T23:24Z] INFO  16:24:05,029 MicroScheduler - 220 reads were filtered out during the traversal out of approximately 310749 total reads (0.07%)
[2016-04-14T23:24Z] INFO  16:24:05,030 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:24Z] INFO  16:24:05,030 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:24Z] INFO  16:24:05,030 MicroScheduler -   -> 220 reads (0.07% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:24Z] INFO  16:24:05,062 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:24Z] INFO  16:24:05,063 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:24Z] INFO  16:24:05,064 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:24Z] INFO  16:24:05,066 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:24Z] GATK RealignerTargetCreator: R14-18102_kapa-NGv3-PE100-NGv3-sort-2_237995374_243199373-prep-prealign.bam 2:237995375-243199373
[2016-04-14T23:24Z] GATK: RealignerTargetCreator
[2016-04-14T23:24Z] INFO  16:24:05,298 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:24Z] INFO  16:24:05,468 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-14T23:24Z] INFO  16:24:05,546 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@7172f77a
[2016-04-14T23:24Z] INFO  16:24:05,558 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:24Z] INFO  16:24:05,584 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:24Z] INFO  16:24:05,597 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:24Z] INFO  16:24:05,640 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-14T23:24Z] INFO  16:24:05,656 IntervalUtils - Processing 15599562 bp from intervals
[2016-04-14T23:24Z] INFO  16:24:05,690 ProgressMeter -            done     45148.0     9.0 s       3.6 m      100.0%     9.0 s       0.0 s
[2016-04-14T23:24Z] INFO  16:24:05,691 ProgressMeter - Total runtime 9.79 secs, 0.16 min, 0.00 hours
[2016-04-14T23:24Z] INFO  16:24:05,694 MicroScheduler - 80 reads were filtered out during the traversal out of approximately 45228 total reads (0.18%)
[2016-04-14T23:24Z] INFO  16:24:05,695 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:24Z] INFO  16:24:05,695 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:24Z] INFO  16:24:05,696 MicroScheduler -   -> 80 reads (0.18% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:24Z] INFO  16:24:05,739 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:24Z] INFO  16:24:05,744 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:24Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-2_205912303_222290862-prep-prealign.bam
[2016-04-14T23:24Z] GATK pre-alignment ('3', 112188604, 127703121) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:24Z] INFO  16:24:06,027 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:24Z] INFO  16:24:06,028 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:24Z] INFO  16:24:06,029 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:24Z] INFO  16:24:06,030 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:24Z] INFO  16:24:06,063 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:24Z] INFO  16:24:06,171 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:24Z] GATK: realign ('2', 174777797, 190306304) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:24Z] INFO  16:24:06,250 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:24Z] INFO  16:24:06,649 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:24Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-2_222291154_237994685-prep-prealign.bam
[2016-04-14T23:24Z] INFO  16:24:06,765 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:24Z] INFO  16:24:06,769 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:24Z] INFO  16:24:06,770 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:24Z] INFO  16:24:06,770 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:24Z] INFO  16:24:06,776 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/3/R14-18102_kapa-NGv3-PE100-NGv3-sort-3_15515506_31574805-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/3/tx/tmpA2tWMY/R14-18102_kapa-NGv3-PE100-NGv3-sort-3_15515506_31574805-prep-prealign-realign.intervals -l INFO -L 3:15515507-31574805 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-14T23:24Z] INFO  16:24:06,794 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:24Z] INFO  16:24:06,797 HelpFormatter - Date/Time: 2016/04/14 16:24:06
[2016-04-14T23:24Z] INFO  16:24:06,798 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:24Z] INFO  16:24:06,804 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:24Z] INFO  16:24:06,978 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:24Z] INFO  16:24:07,005 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:24Z] INFO  16:24:07,009 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:24Z] INFO  16:24:07,009 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:24Z] INFO  16:24:07,010 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:24Z] INFO  16:24:07,014 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/2/R14-18102_kapa-NGv3-PE100-NGv3-sort-2_95538561_111273222-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/2/R14-18102_kapa-NGv3-PE100-NGv3-sort-2_95538561_111273222-prep-prealign-realign.intervals -L 2:95538562-111273222 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/2/tx/tmpg2MzAi/R14-18102_kapa-NGv3-PE100-NGv3-sort-2_95538561_111273222-prep.bam
[2016-04-14T23:24Z] INFO  16:24:07,037 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:24Z] INFO  16:24:07,038 HelpFormatter - Date/Time: 2016/04/14 16:24:07
[2016-04-14T23:24Z] INFO  16:24:07,038 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:24Z] INFO  16:24:07,046 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:24Z] GATK RealignerTargetCreator: R14-18102_kapa-NGv3-PE100-NGv3-sort-2_205912303_222290862-prep-prealign.bam 2:205912304-222290862
[2016-04-14T23:24Z] GATK: RealignerTargetCreator
[2016-04-14T23:24Z] INFO  16:24:07,106 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:24Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-3_78649262_96533852-prep-prealign.bam
[2016-04-14T23:24Z] INFO  16:24:07,302 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:24Z] INFO  16:24:07,304 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-14T23:24Z] INFO  16:24:07,316 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:24Z] INFO  16:24:07,386 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-14T23:24Z] GATK RealignerTargetCreator: R14-18102_kapa-NGv3-PE100-NGv3-sort-3_78649262_96533852-prep-prealign.bam 3:78649263-96533852
[2016-04-14T23:24Z] GATK: RealignerTargetCreator
[2016-04-14T23:24Z] INFO  16:24:07,494 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:24Z] INFO  16:24:07,512 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:24Z] INFO  16:24:07,619 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.11
[2016-04-14T23:24Z] GATK RealignerTargetCreator: R14-18102_kapa-NGv3-PE100-NGv3-sort-2_222291154_237994685-prep-prealign.bam 2:222291155-237994685
[2016-04-14T23:24Z] GATK: RealignerTargetCreator
[2016-04-14T23:24Z] INFO  16:24:07,813 IntervalUtils - Processing 16059299 bp from intervals
[2016-04-14T23:24Z] WARN  16:24:07,818 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:24Z] INFO  16:24:07,945 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:24Z] INFO  16:24:08,125 IntervalUtils - Processing 15734661 bp from intervals
[2016-04-14T23:24Z] WARN  16:24:08,130 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:24Z] INFO  16:24:08,216 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:24Z] INFO  16:24:08,273 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:24Z] INFO  16:24:08,283 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:24Z] INFO  16:24:08,283 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:24Z] INFO  16:24:08,283 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-14T23:24Z] INFO  16:24:08,438 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:24Z] INFO  16:24:08,447 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:24Z] INFO  16:24:08,448 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:24Z] INFO  16:24:08,449 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:24Z] INFO  16:24:08,650 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:24Z] INFO  16:24:08,834 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:24Z] INFO  16:24:08,900 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:24Z] INFO  16:24:08,904 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:24Z] INFO  16:24:08,904 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:24Z] INFO  16:24:08,905 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:24Z] INFO  16:24:08,909 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/2/R14-18102_kapa-NGv3-PE100-NGv3-sort-2_237995374_243199373-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/2/tx/tmpvLK6H7/R14-18102_kapa-NGv3-PE100-NGv3-sort-2_237995374_243199373-prep-prealign-realign.intervals -l INFO -L 2:237995375-243199373 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-14T23:24Z] INFO  16:24:08,939 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:24Z] INFO  16:24:08,940 HelpFormatter - Date/Time: 2016/04/14 16:24:08
[2016-04-14T23:24Z] INFO  16:24:08,941 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:24Z] INFO  16:24:08,941 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:24Z] INFO  16:24:09,044 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:24Z] INFO  16:24:09,212 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:24Z] INFO  16:24:09,216 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:24Z] INFO  16:24:09,216 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:24Z] INFO  16:24:09,217 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:24Z] INFO  16:24:09,222 HelpFormatter - Program Args: -T PrintReads -L 3:112188605-127703121 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/3/tx/tmpYVufWe/R14-18102_kapa-NGv3-PE100-NGv3-sort-3_112188604_127703121-prep-prealign.bam
[2016-04-14T23:24Z] INFO  16:24:09,236 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:24Z] INFO  16:24:09,237 HelpFormatter - Date/Time: 2016/04/14 16:24:09
[2016-04-14T23:24Z] INFO  16:24:09,238 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:24Z] INFO  16:24:09,238 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:24Z] INFO  16:24:09,272 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-14T23:24Z] INFO  16:24:09,283 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:24Z] INFO  16:24:09,336 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-14T23:24Z] INFO  16:24:09,334 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:24Z] INFO  16:24:09,337 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:24Z] INFO  16:24:09,338 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:24Z] INFO  16:24:09,338 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:24Z] INFO  16:24:09,343 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/2/R14-18102_kapa-NGv3-PE100-NGv3-sort-2_174777797_190306304-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/2/R14-18102_kapa-NGv3-PE100-NGv3-sort-2_174777797_190306304-prep-prealign-realign.intervals -L 2:174777798-190306304 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/2/tx/tmp68360_/R14-18102_kapa-NGv3-PE100-NGv3-sort-2_174777797_190306304-prep.bam
[2016-04-14T23:24Z] INFO  16:24:09,386 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:24Z] INFO  16:24:09,387 HelpFormatter - Date/Time: 2016/04/14 16:24:09
[2016-04-14T23:24Z] INFO  16:24:09,387 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:24Z] INFO  16:24:09,388 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:24Z] INFO  16:24:09,452 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:24Z] INFO  16:24:09,578 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:24Z] INFO  16:24:09,725 IntervalUtils - Processing 5203999 bp from intervals
[2016-04-14T23:24Z] WARN  16:24:09,741 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:24Z] INFO  16:24:09,800 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:24Z] INFO  16:24:09,809 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:24Z] INFO  16:24:09,882 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:24Z] INFO  16:24:09,908 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.09
[2016-04-14T23:24Z] INFO  16:24:10,092 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:24Z] INFO  16:24:10,094 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:24Z] INFO  16:24:10,094 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:24Z] INFO  16:24:10,095 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-14T23:24Z] INFO  16:24:10,347 IntervalUtils - Processing 15528507 bp from intervals
[2016-04-14T23:24Z] WARN  16:24:10,352 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:24Z] INFO  16:24:10,418 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:24Z] INFO  16:24:10,473 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:24Z] INFO  16:24:10,479 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:24Z] INFO  16:24:10,480 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:24Z] INFO  16:24:10,480 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:24Z] INFO  16:24:10,485 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/2/R14-18102_kapa-NGv3-PE100-NGv3-sort-2_205912303_222290862-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/2/tx/tmp3NffYq/R14-18102_kapa-NGv3-PE100-NGv3-sort-2_205912303_222290862-prep-prealign-realign.intervals -l INFO -L 2:205912304-222290862 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-14T23:24Z] INFO  16:24:10,503 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:24Z] INFO  16:24:10,504 HelpFormatter - Date/Time: 2016/04/14 16:24:10
[2016-04-14T23:24Z] INFO  16:24:10,505 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:24Z] INFO  16:24:10,506 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:24Z] INFO  16:24:10,586 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:24Z] INFO  16:24:10,587 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:24Z] INFO  16:24:10,587 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:24Z] INFO  16:24:10,588 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:24Z] INFO  16:24:10,605 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-14T23:24Z] INFO  16:24:10,632 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:24Z] INFO  16:24:10,715 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:24Z] INFO  16:24:10,724 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:24Z] INFO  16:24:10,733 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:24Z] INFO  16:24:10,778 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-14T23:24Z] INFO  16:24:10,781 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:24Z] INFO  16:24:10,784 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:24Z] INFO  16:24:10,785 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:24Z] INFO  16:24:10,785 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:24Z] INFO  16:24:10,790 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/3/R14-18102_kapa-NGv3-PE100-NGv3-sort-3_78649262_96533852-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/3/tx/tmpb1VjZW/R14-18102_kapa-NGv3-PE100-NGv3-sort-3_78649262_96533852-prep-prealign-realign.intervals -l INFO -L 3:78649263-96533852 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-14T23:24Z] INFO  16:24:10,797 IntervalUtils - Processing 15514517 bp from intervals
[2016-04-14T23:24Z] INFO  16:24:10,806 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:24Z] INFO  16:24:10,807 HelpFormatter - Date/Time: 2016/04/14 16:24:10
[2016-04-14T23:24Z] INFO  16:24:10,808 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:24Z] INFO  16:24:10,808 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:24Z] INFO  16:24:10,882 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:24Z] INFO  16:24:10,886 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-14T23:24Z] INFO  16:24:10,892 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:24Z] INFO  16:24:10,896 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:24Z] INFO  16:24:10,970 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-14T23:24Z] INFO  16:24:10,983 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:24Z] INFO  16:24:10,986 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:24Z] INFO  16:24:10,990 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:24Z] INFO  16:24:10,991 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:24Z] INFO  16:24:10,991 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:24Z] INFO  16:24:10,996 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/2/R14-18102_kapa-NGv3-PE100-NGv3-sort-2_222291154_237994685-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/2/tx/tmpYyXSbO/R14-18102_kapa-NGv3-PE100-NGv3-sort-2_222291154_237994685-prep-prealign-realign.intervals -l INFO -L 2:222291155-237994685 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-14T23:24Z] INFO  16:24:11,009 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:24Z] INFO  16:24:11,009 HelpFormatter - Date/Time: 2016/04/14 16:24:10
[2016-04-14T23:24Z] INFO  16:24:11,009 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:24Z] INFO  16:24:11,010 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:24Z] INFO  16:24:11,192 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:24Z] INFO  16:24:11,200 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:24Z] INFO  16:24:11,207 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:24Z] INFO  16:24:11,209 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:24Z] INFO  16:24:11,209 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:24Z] INFO  16:24:11,222 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-14T23:24Z] INFO  16:24:11,238 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:24Z] INFO  16:24:11,264 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:24Z] INFO  16:24:11,326 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.09
[2016-04-14T23:24Z] INFO  16:24:11,397 IntervalUtils - Processing 16378559 bp from intervals
[2016-04-14T23:24Z] WARN  16:24:11,413 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:24Z] INFO  16:24:11,445 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-14T23:24Z] INFO  16:24:11,455 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:24Z] INFO  16:24:11,531 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-14T23:24Z] INFO  16:24:11,550 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:24Z] INFO  16:24:11,579 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:24Z] INFO  16:24:11,693 IntervalUtils - Processing 17884590 bp from intervals
[2016-04-14T23:24Z] WARN  16:24:11,699 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:24Z] INFO  16:24:11,799 IntervalUtils - Processing 15703531 bp from intervals
[2016-04-14T23:24Z] WARN  16:24:11,804 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:24Z] INFO  16:24:11,827 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:24Z] INFO  16:24:11,826 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:24Z] INFO  16:24:11,827 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:24Z] INFO  16:24:11,828 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:24Z] INFO  16:24:11,829 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-14T23:24Z] INFO  16:24:11,887 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:24Z] INFO  16:24:12,095 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:24Z] INFO  16:24:12,097 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:24Z] INFO  16:24:12,098 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:24Z] INFO  16:24:12,099 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-14T23:24Z] INFO  16:24:12,106 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:24Z] INFO  16:24:12,107 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:24Z] INFO  16:24:12,108 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:24Z] INFO  16:24:12,109 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-14T23:24Z] INFO  16:24:14,200 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@5fe152b7
[2016-04-14T23:24Z] INFO  16:24:14,305 ProgressMeter -            done    121321.0    20.0 s       2.8 m      100.0%    20.0 s       0.0 s
[2016-04-14T23:24Z] INFO  16:24:14,305 ProgressMeter - Total runtime 20.26 secs, 0.34 min, 0.01 hours
[2016-04-14T23:24Z] INFO  16:24:14,306 MicroScheduler - 116 reads were filtered out during the traversal out of approximately 121437 total reads (0.10%)
[2016-04-14T23:24Z] INFO  16:24:14,306 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:24Z] INFO  16:24:14,306 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:24Z] INFO  16:24:14,307 MicroScheduler -   -> 116 reads (0.10% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:24Z] INFO  16:24:14,516 ProgressMeter -      3:12983302    200004.0    30.0 s       2.5 m       83.7%    35.0 s       5.0 s
[2016-04-14T23:24Z] INFO  16:24:15,770 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:24Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-3_62739115_78648077-prep-prealign.bam
[2016-04-14T23:24Z] GATK RealignerTargetCreator: R14-18102_kapa-NGv3-PE100-NGv3-sort-3_62739115_78648077-prep-prealign.bam 3:62739116-78648077
[2016-04-14T23:24Z] GATK: RealignerTargetCreator
[2016-04-14T23:24Z] INFO  16:24:18,763 ProgressMeter -      3:39172255    100001.0    30.0 s       5.0 m       48.7%    61.0 s      31.0 s
[2016-04-14T23:24Z] INFO  16:24:18,974 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:24Z] INFO  16:24:18,978 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:24Z] INFO  16:24:18,979 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:24Z] INFO  16:24:18,980 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:24Z] INFO  16:24:18,985 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/3/R14-18102_kapa-NGv3-PE100-NGv3-sort-3_62739115_78648077-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/3/tx/tmpKuMQIh/R14-18102_kapa-NGv3-PE100-NGv3-sort-3_62739115_78648077-prep-prealign-realign.intervals -l INFO -L 3:62739116-78648077 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-14T23:24Z] INFO  16:24:18,996 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:24Z] INFO  16:24:19,004 HelpFormatter - Date/Time: 2016/04/14 16:24:18
[2016-04-14T23:24Z] INFO  16:24:19,015 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:24Z] INFO  16:24:19,016 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:24Z] INFO  16:24:19,112 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:24Z] INFO  16:24:19,335 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-14T23:24Z] INFO  16:24:19,359 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:24Z] INFO  16:24:19,419 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-14T23:24Z] INFO  16:24:19,749 IntervalUtils - Processing 15908962 bp from intervals
[2016-04-14T23:24Z] WARN  16:24:19,754 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:24Z] INFO  16:24:19,887 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:24Z] INFO  16:24:20,058 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:24Z] INFO  16:24:20,059 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:24Z] INFO  16:24:20,060 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:24Z] INFO  16:24:20,061 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-14T23:24Z] INFO  16:24:21,053 ProgressMeter -            done    296472.0    21.0 s      72.0 s      100.0%    21.0 s       0.0 s
[2016-04-14T23:24Z] INFO  16:24:21,053 ProgressMeter - Total runtime 21.63 secs, 0.36 min, 0.01 hours
[2016-04-14T23:24Z] INFO  16:24:21,061 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 296472 total reads (0.00%)
[2016-04-14T23:24Z] INFO  16:24:21,062 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:24Z] INFO  16:24:21,062 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:24Z] INFO  16:24:21,062 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:24Z] INFO  16:24:22,190 ProgressMeter -      3:49147877    100002.0    31.0 s       5.3 m       13.0%     4.0 m       3.5 m
[2016-04-14T23:24Z] INFO  16:24:22,293 ProgressMeter -            done   5203999.0    12.0 s       2.0 s      100.0%    12.0 s       0.0 s
[2016-04-14T23:24Z] INFO  16:24:22,294 ProgressMeter - Total runtime 12.20 secs, 0.20 min, 0.00 hours
[2016-04-14T23:24Z] INFO  16:24:22,298 MicroScheduler - 23013 reads were filtered out during the traversal out of approximately 214972 total reads (10.71%)
[2016-04-14T23:24Z] INFO  16:24:22,299 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:24Z] INFO  16:24:22,299 MicroScheduler -   -> 370 reads (0.17% of total) failing BadMateFilter
[2016-04-14T23:24Z] INFO  16:24:22,299 MicroScheduler -   -> 16879 reads (7.85% of total) failing DuplicateReadFilter
[2016-04-14T23:24Z] INFO  16:24:22,300 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-14T23:24Z] INFO  16:24:22,300 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:24Z] INFO  16:24:22,300 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-14T23:24Z] INFO  16:24:22,301 MicroScheduler -   -> 5764 reads (2.68% of total) failing MappingQualityZeroFilter
[2016-04-14T23:24Z] INFO  16:24:22,301 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:24Z] INFO  16:24:22,301 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-14T23:24Z] INFO  16:24:22,301 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-14T23:24Z] INFO  16:24:22,763 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:24Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-2_159196753_174774985-prep.bam
[2016-04-14T23:24Z] INFO  16:24:23,691 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:24Z] GATK: realign ('2', 237995374, 243199373) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:24Z] GATK pre-alignment ('3', 127770401, 143293035) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:24Z] INFO  16:24:24,175 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@7172f77a
[2016-04-14T23:24Z] INFO  16:24:24,235 ProgressMeter -            done    317231.0    39.0 s       2.1 m      100.0%    39.0 s       0.0 s
[2016-04-14T23:24Z] INFO  16:24:24,236 ProgressMeter - Total runtime 39.74 secs, 0.66 min, 0.01 hours
[2016-04-14T23:24Z] INFO  16:24:24,237 MicroScheduler - 171 reads were filtered out during the traversal out of approximately 317402 total reads (0.05%)
[2016-04-14T23:24Z] INFO  16:24:24,245 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:24Z] INFO  16:24:24,246 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:24Z] INFO  16:24:24,247 MicroScheduler -   -> 171 reads (0.05% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:24Z] INFO  16:24:24,718 ProgressMeter -            done    247771.0    19.0 s      79.0 s      100.0%    19.0 s       0.0 s
[2016-04-14T23:24Z] INFO  16:24:24,719 ProgressMeter - Total runtime 19.66 secs, 0.33 min, 0.01 hours
[2016-04-14T23:24Z] INFO  16:24:24,723 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 247771 total reads (0.00%)
[2016-04-14T23:24Z] INFO  16:24:24,724 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:24Z] INFO  16:24:24,724 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:24Z] INFO  16:24:24,725 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:24Z] INFO  16:24:25,528 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:24Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-3_0_15512123-prep-prealign.bam
[2016-04-14T23:24Z] INFO  16:24:25,637 ProgressMeter -            done   1.6059299E7    17.0 s       1.0 s      100.0%    17.0 s       0.0 s
[2016-04-14T23:24Z] INFO  16:24:25,637 ProgressMeter - Total runtime 17.35 secs, 0.29 min, 0.00 hours
[2016-04-14T23:24Z] INFO  16:24:25,642 MicroScheduler - 10185 reads were filtered out during the traversal out of approximately 114029 total reads (8.93%)
[2016-04-14T23:24Z] INFO  16:24:25,643 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:24Z] INFO  16:24:25,644 MicroScheduler -   -> 506 reads (0.44% of total) failing BadMateFilter
[2016-04-14T23:24Z] INFO  16:24:25,645 MicroScheduler -   -> 9040 reads (7.93% of total) failing DuplicateReadFilter
[2016-04-14T23:24Z] INFO  16:24:25,646 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-14T23:24Z] INFO  16:24:25,646 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:24Z] INFO  16:24:25,647 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-14T23:24Z] INFO  16:24:25,648 MicroScheduler -   -> 639 reads (0.56% of total) failing MappingQualityZeroFilter
[2016-04-14T23:24Z] INFO  16:24:25,649 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:24Z] INFO  16:24:25,649 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-14T23:24Z] INFO  16:24:25,650 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-14T23:24Z] INFO  16:24:26,317 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:24Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-2_190313104_205830046-prep.bam
[2016-04-14T23:24Z] INFO  16:24:26,455 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:24Z] INFO  16:24:26,459 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:24Z] INFO  16:24:26,459 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:24Z] INFO  16:24:26,460 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:24Z] INFO  16:24:26,464 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/2/R14-18102_kapa-NGv3-PE100-NGv3-sort-2_237995374_243199373-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/2/R14-18102_kapa-NGv3-PE100-NGv3-sort-2_237995374_243199373-prep-prealign-realign.intervals -L 2:237995375-243199373 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/2/tx/tmp21GC4u/R14-18102_kapa-NGv3-PE100-NGv3-sort-2_237995374_243199373-prep.bam
[2016-04-14T23:24Z] INFO  16:24:26,475 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:24Z] INFO  16:24:26,476 HelpFormatter - Date/Time: 2016/04/14 16:24:26
[2016-04-14T23:24Z] INFO  16:24:26,476 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:24Z] INFO  16:24:26,474 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:24Z] INFO  16:24:26,478 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:24Z] INFO  16:24:26,478 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:24Z] INFO  16:24:26,479 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:24Z] INFO  16:24:26,483 HelpFormatter - Program Args: -T PrintReads -L 3:127770402-143293035 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/3/tx/tmpER1Jdw/R14-18102_kapa-NGv3-PE100-NGv3-sort-3_127770401_143293035-prep-prealign.bam
[2016-04-14T23:24Z] INFO  16:24:26,476 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:24Z] INFO  16:24:26,492 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:24Z] INFO  16:24:26,492 HelpFormatter - Date/Time: 2016/04/14 16:24:26
[2016-04-14T23:24Z] INFO  16:24:26,492 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:24Z] INFO  16:24:26,493 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:24Z] INFO  16:24:26,663 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:24Z] INFO  16:24:26,675 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:24Z] GATK RealignerTargetCreator: R14-18102_kapa-NGv3-PE100-NGv3-sort-3_0_15512123-prep-prealign.bam 3:1-15512123
[2016-04-14T23:24Z] GATK: RealignerTargetCreator
[2016-04-14T23:24Z] INFO  16:24:26,831 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:24Z] INFO  16:24:26,843 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:24Z] INFO  16:24:26,904 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-14T23:24Z] INFO  16:24:27,016 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:24Z] GATK: realign ('3', 15515506, 31574805) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:24Z] GATK pre-alignment ('3', 143297426, 158963696) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:24Z] INFO  16:24:27,369 IntervalUtils - Processing 5203999 bp from intervals
[2016-04-14T23:24Z] WARN  16:24:27,386 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:24Z] INFO  16:24:27,477 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:24Z] INFO  16:24:27,613 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:24Z] INFO  16:24:27,614 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:24Z] INFO  16:24:27,615 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:24Z] INFO  16:24:27,616 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:24Z] INFO  16:24:27,752 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:24Z] INFO  16:24:27,814 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:24Z] INFO  16:24:27,900 ProgressMeter -            done   1.788459E7    15.0 s       0.0 s      100.0%    15.0 s       0.0 s
[2016-04-14T23:24Z] INFO  16:24:27,901 ProgressMeter - Total runtime 15.80 secs, 0.26 min, 0.00 hours
[2016-04-14T23:24Z] INFO  16:24:27,906 MicroScheduler - 4342 reads were filtered out during the traversal out of approximately 45419 total reads (9.56%)
[2016-04-14T23:24Z] INFO  16:24:27,907 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:24Z] INFO  16:24:27,908 MicroScheduler -   -> 297 reads (0.65% of total) failing BadMateFilter
[2016-04-14T23:24Z] INFO  16:24:27,909 MicroScheduler -   -> 3592 reads (7.91% of total) failing DuplicateReadFilter
[2016-04-14T23:24Z] INFO  16:24:27,909 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-14T23:24Z] INFO  16:24:27,910 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:24Z] INFO  16:24:27,911 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-14T23:24Z] INFO  16:24:27,911 MicroScheduler -   -> 453 reads (1.00% of total) failing MappingQualityZeroFilter
[2016-04-14T23:24Z] INFO  16:24:27,912 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:24Z] INFO  16:24:27,913 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-14T23:24Z] INFO  16:24:27,913 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-14T23:24Z] INFO  16:24:27,984 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-14T23:24Z] INFO  16:24:28,040 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:24Z] INFO  16:24:28,050 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:24Z] INFO  16:24:28,121 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-14T23:24Z] INFO  16:24:28,137 IntervalUtils - Processing 15522634 bp from intervals
[2016-04-14T23:24Z] INFO  16:24:28,227 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:24Z] INFO  16:24:28,600 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:24Z] INFO  16:24:28,603 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:24Z] INFO  16:24:28,604 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:24Z] INFO  16:24:28,604 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:24Z] INFO  16:24:28,618 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:24Z] INFO  16:24:28,770 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:24Z] INFO  16:24:29,272 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:24Z] GATK: realign ('3', 78649262, 96533852) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:24Z] INFO  16:24:29,893 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@41fd9d8e
[2016-04-14T23:24Z] INFO  16:24:29,995 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:24Z] INFO  16:24:29,998 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:24Z] INFO  16:24:29,999 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:24Z] INFO  16:24:30,000 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:24Z] INFO  16:24:30,004 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/3/R14-18102_kapa-NGv3-PE100-NGv3-sort-3_15515506_31574805-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/3/R14-18102_kapa-NGv3-PE100-NGv3-sort-3_15515506_31574805-prep-prealign-realign.intervals -L 3:15515507-31574805 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/3/tx/tmpb61_kO/R14-18102_kapa-NGv3-PE100-NGv3-sort-3_15515506_31574805-prep.bam
[2016-04-14T23:24Z] INFO  16:24:30,013 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:24Z] INFO  16:24:30,014 HelpFormatter - Date/Time: 2016/04/14 16:24:29
[2016-04-14T23:24Z] INFO  16:24:30,014 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:24Z] INFO  16:24:30,015 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:24Z] INFO  16:24:30,038 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:24Z] INFO  16:24:30,042 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:24Z] INFO  16:24:30,043 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:24Z] INFO  16:24:30,043 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:24Z] INFO  16:24:30,048 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/3/R14-18102_kapa-NGv3-PE100-NGv3-sort-3_0_15512123-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/3/tx/tmp9_zJbE/R14-18102_kapa-NGv3-PE100-NGv3-sort-3_0_15512123-prep-prealign-realign.intervals -l INFO -L 3:1-15512123 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-14T23:24Z] INFO  16:24:30,064 ProgressMeter -            done    170309.0    24.0 s       2.4 m      100.0%    24.0 s       0.0 s
[2016-04-14T23:24Z] INFO  16:24:30,065 ProgressMeter - Total runtime 24.04 secs, 0.40 min, 0.01 hours
[2016-04-14T23:24Z] INFO  16:24:30,065 MicroScheduler - 142 reads were filtered out during the traversal out of approximately 170451 total reads (0.08%)
[2016-04-14T23:24Z] INFO  16:24:30,066 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:24Z] INFO  16:24:30,066 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:24Z] INFO  16:24:30,066 MicroScheduler -   -> 142 reads (0.08% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:24Z] INFO  16:24:30,084 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:24Z] INFO  16:24:30,085 HelpFormatter - Date/Time: 2016/04/14 16:24:30
[2016-04-14T23:24Z] INFO  16:24:30,086 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:24Z] INFO  16:24:30,087 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:24Z] INFO  16:24:30,257 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:24Z] INFO  16:24:30,265 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:24Z] INFO  16:24:30,283 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:24Z] INFO  16:24:30,286 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:24Z] INFO  16:24:30,287 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:24Z] INFO  16:24:30,288 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:24Z] INFO  16:24:30,292 HelpFormatter - Program Args: -T PrintReads -L 3:143297427-158963696 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/3/tx/tmpzSmGiH/R14-18102_kapa-NGv3-PE100-NGv3-sort-3_143297426_158963696-prep-prealign.bam
[2016-04-14T23:24Z] INFO  16:24:30,301 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:24Z] INFO  16:24:30,312 HelpFormatter - Date/Time: 2016/04/14 16:24:30
[2016-04-14T23:24Z] INFO  16:24:30,313 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:24Z] INFO  16:24:30,314 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:24Z] INFO  16:24:30,338 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:24Z] INFO  16:24:30,348 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:24Z] INFO  16:24:30,411 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-14T23:24Z] INFO  16:24:30,489 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:24Z] INFO  16:24:30,494 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-14T23:24Z] INFO  16:24:30,504 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:24Z] INFO  16:24:30,581 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-14T23:24Z] INFO  16:24:30,786 IntervalUtils - Processing 16059299 bp from intervals
[2016-04-14T23:24Z] WARN  16:24:30,792 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:24Z] INFO  16:24:30,867 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:24Z] INFO  16:24:30,945 IntervalUtils - Processing 15512123 bp from intervals
[2016-04-14T23:24Z] WARN  16:24:30,950 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:24Z] INFO  16:24:30,968 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:24Z] INFO  16:24:30,969 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:24Z] INFO  16:24:30,970 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:24Z] INFO  16:24:30,971 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:24Z] INFO  16:24:31,031 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:24Z] INFO  16:24:31,276 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:24Z] INFO  16:24:31,278 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:24Z] INFO  16:24:31,278 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:24Z] INFO  16:24:31,279 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-14T23:24Z] INFO  16:24:31,297 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:24Z] INFO  16:24:31,514 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:24Z] INFO  16:24:31,528 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-14T23:24Z] INFO  16:24:31,601 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:24Z] INFO  16:24:31,600 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:24Z] INFO  16:24:31,612 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:24Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-3_96585668_112185230-prep-prealign.bam
[2016-04-14T23:24Z] INFO  16:24:31,667 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-14T23:24Z] INFO  16:24:31,681 IntervalUtils - Processing 15666270 bp from intervals
[2016-04-14T23:24Z] INFO  16:24:31,773 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:24Z] INFO  16:24:32,229 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:24Z] INFO  16:24:32,230 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:24Z] INFO  16:24:32,230 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:24Z] INFO  16:24:32,230 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:24Z] INFO  16:24:32,265 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:24Z] GATK RealignerTargetCreator: R14-18102_kapa-NGv3-PE100-NGv3-sort-3_96585668_112185230-prep-prealign.bam 3:96585669-112185230
[2016-04-14T23:24Z] GATK: RealignerTargetCreator
[2016-04-14T23:24Z] INFO  16:24:32,468 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:24Z] INFO  16:24:32,475 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:24Z] INFO  16:24:32,482 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:24Z] INFO  16:24:32,483 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:24Z] INFO  16:24:32,485 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:24Z] INFO  16:24:32,488 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/3/R14-18102_kapa-NGv3-PE100-NGv3-sort-3_78649262_96533852-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/3/R14-18102_kapa-NGv3-PE100-NGv3-sort-3_78649262_96533852-prep-prealign-realign.intervals -L 3:78649263-96533852 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/3/tx/tmptG1U7W/R14-18102_kapa-NGv3-PE100-NGv3-sort-3_78649262_96533852-prep.bam
[2016-04-14T23:24Z] INFO  16:24:32,510 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:24Z] INFO  16:24:32,511 HelpFormatter - Date/Time: 2016/04/14 16:24:32
[2016-04-14T23:24Z] INFO  16:24:32,511 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:24Z] INFO  16:24:32,512 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:24Z] INFO  16:24:32,790 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:24Z] INFO  16:24:32,944 ProgressMeter -     1:149879436    400045.0    31.0 s      79.0 s       38.6%    80.0 s      49.0 s
[2016-04-14T23:24Z] INFO  16:24:32,964 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:24Z] INFO  16:24:32,986 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:24Z] INFO  16:24:33,068 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-14T23:24Z] INFO  16:24:33,488 IntervalUtils - Processing 17884590 bp from intervals
[2016-04-14T23:24Z] WARN  16:24:33,495 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:24Z] INFO  16:24:33,612 ProgressMeter -            done    335722.0    23.0 s      68.0 s      100.0%    23.0 s       0.0 s
[2016-04-14T23:24Z] INFO  16:24:33,613 ProgressMeter - Total runtime 23.03 secs, 0.38 min, 0.01 hours
[2016-04-14T23:24Z] INFO  16:24:33,617 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 335722 total reads (0.00%)
[2016-04-14T23:24Z] INFO  16:24:33,617 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:24Z] INFO  16:24:33,618 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:24Z] INFO  16:24:33,618 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:24Z] INFO  16:24:33,677 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:24Z] INFO  16:24:33,853 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:24Z] INFO  16:24:33,856 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:24Z] INFO  16:24:33,857 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:24Z] INFO  16:24:33,857 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:24Z] INFO  16:24:34,085 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:24Z] INFO  16:24:34,143 ProgressMeter -            done   1.5703531E7    22.0 s       1.0 s      100.0%    22.0 s       0.0 s
[2016-04-14T23:24Z] INFO  16:24:34,144 ProgressMeter - Total runtime 22.04 secs, 0.37 min, 0.01 hours
[2016-04-14T23:24Z] INFO  16:24:34,147 MicroScheduler - 28735 reads were filtered out during the traversal out of approximately 312665 total reads (9.19%)
[2016-04-14T23:24Z] INFO  16:24:34,148 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:24Z] INFO  16:24:34,148 MicroScheduler -   -> 748 reads (0.24% of total) failing BadMateFilter
[2016-04-14T23:24Z] INFO  16:24:34,148 MicroScheduler -   -> 25233 reads (8.07% of total) failing DuplicateReadFilter
[2016-04-14T23:24Z] INFO  16:24:34,149 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-14T23:24Z] INFO  16:24:34,149 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:24Z] INFO  16:24:34,149 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-14T23:24Z] INFO  16:24:34,149 MicroScheduler -   -> 2754 reads (0.88% of total) failing MappingQualityZeroFilter
[2016-04-14T23:24Z] INFO  16:24:34,150 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:24Z] INFO  16:24:34,150 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-14T23:24Z] INFO  16:24:34,150 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-14T23:24Z] INFO  16:24:34,282 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:24Z] INFO  16:24:35,066 ProgressMeter -            done   1.6378559E7    23.0 s       1.0 s      100.0%    23.0 s       0.0 s
[2016-04-14T23:24Z] INFO  16:24:35,066 ProgressMeter - Total runtime 23.24 secs, 0.39 min, 0.01 hours
[2016-04-14T23:24Z] INFO  16:24:35,070 MicroScheduler - 33458 reads were filtered out during the traversal out of approximately 403711 total reads (8.29%)
[2016-04-14T23:24Z] INFO  16:24:35,071 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:24Z] INFO  16:24:35,072 MicroScheduler -   -> 834 reads (0.21% of total) failing BadMateFilter
[2016-04-14T23:24Z] INFO  16:24:35,072 MicroScheduler -   -> 31980 reads (7.92% of total) failing DuplicateReadFilter
[2016-04-14T23:24Z] INFO  16:24:35,073 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-14T23:24Z] INFO  16:24:35,074 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:24Z] INFO  16:24:35,074 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-14T23:24Z] INFO  16:24:35,075 MicroScheduler -   -> 644 reads (0.16% of total) failing MappingQualityZeroFilter
[2016-04-14T23:24Z] INFO  16:24:35,076 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:24Z] INFO  16:24:35,076 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-14T23:24Z] INFO  16:24:35,077 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-14T23:24Z] INFO  16:24:35,134 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:24Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-2_174777797_190306304-prep.bam
[2016-04-14T23:24Z] INFO  16:24:35,365 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:24Z] INFO  16:24:35,369 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:24Z] INFO  16:24:35,369 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:24Z] INFO  16:24:35,370 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:24Z] INFO  16:24:35,374 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/3/R14-18102_kapa-NGv3-PE100-NGv3-sort-3_96585668_112185230-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/3/tx/tmpvUlBBG/R14-18102_kapa-NGv3-PE100-NGv3-sort-3_96585668_112185230-prep-prealign-realign.intervals -l INFO -L 3:96585669-112185230 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-14T23:24Z] INFO  16:24:35,387 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:24Z] INFO  16:24:35,388 HelpFormatter - Date/Time: 2016/04/14 16:24:35
[2016-04-14T23:24Z] INFO  16:24:35,389 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:24Z] INFO  16:24:35,389 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:24Z] INFO  16:24:35,524 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:24Z] INFO  16:24:35,651 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:24Z] GATK: realign ('2', 222291154, 237994685) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:24Z] INFO  16:24:35,781 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-14T23:24Z] INFO  16:24:35,791 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:24Z] INFO  16:24:35,859 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-14T23:24Z] INFO  16:24:36,131 IntervalUtils - Processing 15599562 bp from intervals
[2016-04-14T23:24Z] WARN  16:24:36,136 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:24Z] GATK pre-alignment ('3', 158970515, 174577240) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:24Z] INFO  16:24:36,254 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:24Z] INFO  16:24:36,447 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:24Z] INFO  16:24:36,448 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:24Z] INFO  16:24:36,449 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:24Z] INFO  16:24:36,450 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-14T23:24Z] INFO  16:24:36,493 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:24Z] GATK: realign ('2', 205912303, 222290862) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:24Z] INFO  16:24:36,701 ProgressMeter -            done   1.5908962E7    16.0 s       1.0 s      100.0%    16.0 s       0.0 s
[2016-04-14T23:24Z] INFO  16:24:36,702 ProgressMeter - Total runtime 16.64 secs, 0.28 min, 0.00 hours
[2016-04-14T23:24Z] INFO  16:24:36,705 MicroScheduler - 13698 reads were filtered out during the traversal out of approximately 121915 total reads (11.24%)
[2016-04-14T23:24Z] INFO  16:24:36,705 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:24Z] INFO  16:24:36,706 MicroScheduler -   -> 471 reads (0.39% of total) failing BadMateFilter
[2016-04-14T23:24Z] INFO  16:24:36,706 MicroScheduler -   -> 9162 reads (7.52% of total) failing DuplicateReadFilter
[2016-04-14T23:24Z] INFO  16:24:36,706 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-14T23:24Z] INFO  16:24:36,708 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:24Z] INFO  16:24:36,709 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-14T23:24Z] INFO  16:24:36,710 MicroScheduler -   -> 4065 reads (3.33% of total) failing MappingQualityZeroFilter
[2016-04-14T23:24Z] INFO  16:24:36,710 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:24Z] INFO  16:24:36,711 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-14T23:24Z] INFO  16:24:36,711 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-14T23:24Z] INFO  16:24:38,162 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:24Z] GATK: realign ('3', 62739115, 78648077) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:24Z] INFO  16:24:38,475 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:24Z] INFO  16:24:38,479 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:24Z] INFO  16:24:38,479 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:24Z] INFO  16:24:38,480 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:24Z] INFO  16:24:38,481 ProgressMeter -     2:108614377    400006.0    30.0 s      75.0 s       83.1%    36.0 s       6.0 s
[2016-04-14T23:24Z] INFO  16:24:38,484 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/2/R14-18102_kapa-NGv3-PE100-NGv3-sort-2_222291154_237994685-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/2/R14-18102_kapa-NGv3-PE100-NGv3-sort-2_222291154_237994685-prep-prealign-realign.intervals -L 2:222291155-237994685 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/2/tx/tmposVTTn/R14-18102_kapa-NGv3-PE100-NGv3-sort-2_222291154_237994685-prep.bam
[2016-04-14T23:24Z] INFO  16:24:38,493 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:24Z] INFO  16:24:38,494 HelpFormatter - Date/Time: 2016/04/14 16:24:38
[2016-04-14T23:24Z] INFO  16:24:38,505 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:24Z] INFO  16:24:38,506 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:24Z] INFO  16:24:38,746 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:24Z] INFO  16:24:38,856 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:24Z] INFO  16:24:38,865 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:24Z] INFO  16:24:38,943 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-14T23:24Z] INFO  16:24:38,952 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:24Z] INFO  16:24:38,955 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:24Z] INFO  16:24:38,956 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:24Z] INFO  16:24:38,957 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:24Z] INFO  16:24:38,961 HelpFormatter - Program Args: -T PrintReads -L 3:158970516-174577240 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/3/tx/tmpJkaBmu/R14-18102_kapa-NGv3-PE100-NGv3-sort-3_158970515_174577240-prep-prealign.bam
[2016-04-14T23:24Z] INFO  16:24:38,978 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:24Z] INFO  16:24:38,978 HelpFormatter - Date/Time: 2016/04/14 16:24:38
[2016-04-14T23:24Z] INFO  16:24:38,978 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:24Z] INFO  16:24:38,979 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:24Z] INFO  16:24:39,210 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:24Z] INFO  16:24:39,308 IntervalUtils - Processing 15703531 bp from intervals
[2016-04-14T23:24Z] WARN  16:24:39,313 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:24Z] INFO  16:24:39,319 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:24Z] INFO  16:24:39,322 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:24Z] INFO  16:24:39,323 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:24Z] INFO  16:24:39,324 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:24Z] INFO  16:24:39,328 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/2/R14-18102_kapa-NGv3-PE100-NGv3-sort-2_205912303_222290862-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/2/R14-18102_kapa-NGv3-PE100-NGv3-sort-2_205912303_222290862-prep-prealign-realign.intervals -L 2:205912304-222290862 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/2/tx/tmptckw0I/R14-18102_kapa-NGv3-PE100-NGv3-sort-2_205912303_222290862-prep.bam
[2016-04-14T23:24Z] INFO  16:24:39,343 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:24Z] INFO  16:24:39,344 HelpFormatter - Date/Time: 2016/04/14 16:24:39
[2016-04-14T23:24Z] INFO  16:24:39,344 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:24Z] INFO  16:24:39,345 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:24Z] INFO  16:24:39,377 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:24Z] INFO  16:24:39,569 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:24Z] INFO  16:24:39,570 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:24Z] INFO  16:24:39,571 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:24Z] INFO  16:24:39,571 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:24Z] INFO  16:24:39,579 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:24Z] INFO  16:24:39,756 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:24Z] INFO  16:24:39,778 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:24Z] INFO  16:24:39,785 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:24Z] INFO  16:24:39,842 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-14T23:24Z] INFO  16:24:40,010 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:24Z] INFO  16:24:40,210 IntervalUtils - Processing 16378559 bp from intervals
[2016-04-14T23:24Z] WARN  16:24:40,216 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:24Z] INFO  16:24:40,252 ProgressMeter -            done     45148.0     6.0 s       2.4 m      100.0%     6.0 s       0.0 s
[2016-04-14T23:24Z] INFO  16:24:40,253 ProgressMeter - Total runtime 6.40 secs, 0.11 min, 0.00 hours
[2016-04-14T23:24Z] INFO  16:24:40,256 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 45148 total reads (0.00%)
[2016-04-14T23:24Z] INFO  16:24:40,257 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:24Z] INFO  16:24:40,257 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:24Z] INFO  16:24:40,257 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:24Z] INFO  16:24:40,296 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-14T23:24Z] INFO  16:24:40,321 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:24Z] INFO  16:24:40,372 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:24Z] INFO  16:24:40,391 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:24Z] INFO  16:24:40,422 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:24Z] INFO  16:24:40,423 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:24Z] INFO  16:24:40,424 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:24Z] INFO  16:24:40,425 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:24Z] INFO  16:24:40,480 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.09
[2016-04-14T23:24Z] INFO  16:24:40,504 IntervalUtils - Processing 15606725 bp from intervals
[2016-04-14T23:24Z] INFO  16:24:40,569 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:24Z] INFO  16:24:40,608 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:24Z] INFO  16:24:40,756 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:24Z] INFO  16:24:40,906 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:24Z] INFO  16:24:40,907 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:24Z] INFO  16:24:40,908 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:24Z] INFO  16:24:40,908 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:24Z] INFO  16:24:40,921 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:24Z] INFO  16:24:41,022 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:24Z] INFO  16:24:41,026 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:24Z] INFO  16:24:41,026 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:24Z] INFO  16:24:41,027 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:24Z] INFO  16:24:41,045 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:24Z] INFO  16:24:41,052 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/3/R14-18102_kapa-NGv3-PE100-NGv3-sort-3_62739115_78648077-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/3/R14-18102_kapa-NGv3-PE100-NGv3-sort-3_62739115_78648077-prep-prealign-realign.intervals -L 3:62739116-78648077 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/3/tx/tmppc_owr/R14-18102_kapa-NGv3-PE100-NGv3-sort-3_62739115_78648077-prep.bam
[2016-04-14T23:24Z] INFO  16:24:41,062 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:24Z] INFO  16:24:41,063 HelpFormatter - Date/Time: 2016/04/14 16:24:41
[2016-04-14T23:24Z] INFO  16:24:41,064 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:24Z] INFO  16:24:41,064 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:24Z] INFO  16:24:41,322 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:24Z] INFO  16:24:41,475 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:24Z] INFO  16:24:41,485 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:24Z] INFO  16:24:41,551 ProgressMeter -            done    113363.0    10.0 s      93.0 s      100.0%    10.0 s       0.0 s
[2016-04-14T23:24Z] INFO  16:24:41,551 ProgressMeter - Total runtime 10.58 secs, 0.18 min, 0.00 hours
[2016-04-14T23:24Z] INFO  16:24:41,556 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-14T23:24Z] INFO  16:24:41,555 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 113363 total reads (0.00%)
[2016-04-14T23:24Z] INFO  16:24:41,555 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:24Z] INFO  16:24:41,555 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:24Z] INFO  16:24:41,556 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:24Z] INFO  16:24:41,614 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:24Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-3_78649262_96533852-prep.bam
[2016-04-14T23:24Z] GATK pre-alignment ('3', 174814579, 190326970) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:24Z] INFO  16:24:41,990 ProgressMeter -     3:122695156    200003.0    30.0 s       2.6 m       67.7%    44.0 s      14.0 s
[2016-04-14T23:24Z] INFO  16:24:42,011 IntervalUtils - Processing 15908962 bp from intervals
[2016-04-14T23:24Z] WARN  16:24:42,016 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:24Z] INFO  16:24:42,082 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:24Z] INFO  16:24:42,140 ProgressMeter -            done    523828.0    33.0 s      64.0 s      100.0%    33.0 s       0.0 s
[2016-04-14T23:24Z] INFO  16:24:42,141 ProgressMeter - Total runtime 33.69 secs, 0.56 min, 0.01 hours
[2016-04-14T23:24Z] INFO  16:24:42,144 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 523828 total reads (0.00%)
[2016-04-14T23:24Z] INFO  16:24:42,145 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:24Z] INFO  16:24:42,145 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:24Z] INFO  16:24:42,146 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:24Z] INFO  16:24:42,313 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:24Z] INFO  16:24:42,314 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:24Z] INFO  16:24:42,314 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:24Z] INFO  16:24:42,314 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:24Z] INFO  16:24:42,487 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:24Z] INFO  16:24:42,704 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:24Z] INFO  16:24:43,610 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:24Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-3_15515506_31574805-prep.bam
[2016-04-14T23:24Z] INFO  16:24:43,734 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:24Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-2_95538561_111273222-prep.bam
[2016-04-14T23:24Z] GATK pre-alignment ('3', 190333063, 198022430) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:24Z] INFO  16:24:44,745 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:24Z] INFO  16:24:44,749 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:24Z] INFO  16:24:44,750 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:24Z] INFO  16:24:44,751 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:24Z] INFO  16:24:44,756 HelpFormatter - Program Args: -T PrintReads -L 3:174814580-190326970 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/3/tx/tmpEP_U3a/R14-18102_kapa-NGv3-PE100-NGv3-sort-3_174814579_190326970-prep-prealign.bam
[2016-04-14T23:24Z] INFO  16:24:44,772 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:24Z] INFO  16:24:44,773 HelpFormatter - Date/Time: 2016/04/14 16:24:44
[2016-04-14T23:24Z] INFO  16:24:44,774 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:24Z] INFO  16:24:44,775 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:24Z] INFO  16:24:44,916 ProgressMeter -            done    213828.0    17.0 s      80.0 s       97.4%    17.0 s       0.0 s
[2016-04-14T23:24Z] INFO  16:24:44,916 ProgressMeter - Total runtime 17.30 secs, 0.29 min, 0.00 hours
[2016-04-14T23:24Z] INFO  16:24:44,920 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 213828 total reads (0.00%)
[2016-04-14T23:24Z] INFO  16:24:44,920 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:24Z] INFO  16:24:44,921 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:24Z] INFO  16:24:44,921 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:24Z] INFO  16:24:44,973 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:24Z] GATK pre-alignment ('4', 0, 15511864) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:24Z] INFO  16:24:46,209 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-14T23:24Z] INFO  16:24:46,301 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:24Z] INFO  16:24:46,312 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:24Z] INFO  16:24:46,377 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-14T23:24Z] INFO  16:24:46,398 IntervalUtils - Processing 15512391 bp from intervals
[2016-04-14T23:24Z] INFO  16:24:46,511 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:24Z] INFO  16:24:46,662 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:24Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-2_237995374_243199373-prep.bam
[2016-04-14T23:24Z] INFO  16:24:46,930 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:24Z] INFO  16:24:46,931 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:24Z] INFO  16:24:46,931 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:24Z] INFO  16:24:46,932 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:24Z] INFO  16:24:46,971 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:24Z] INFO  16:24:47,131 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:24Z] INFO  16:24:47,445 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:24Z] INFO  16:24:47,449 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:24Z] INFO  16:24:47,449 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:24Z] INFO  16:24:47,450 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:24Z] INFO  16:24:47,455 HelpFormatter - Program Args: -T PrintReads -L 3:190333064-198022430 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/3/tx/tmp8bgygx/R14-18102_kapa-NGv3-PE100-NGv3-sort-3_190333063_198022430-prep-prealign.bam
[2016-04-14T23:24Z] INFO  16:24:47,481 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:24Z] INFO  16:24:47,492 HelpFormatter - Date/Time: 2016/04/14 16:24:47
[2016-04-14T23:24Z] INFO  16:24:47,493 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:24Z] INFO  16:24:47,494 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:24Z] GATK pre-alignment ('4', 15512869, 31144471) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:24Z] INFO  16:24:47,667 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:24Z] INFO  16:24:48,176 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@41fd9d8e
[2016-04-14T23:24Z] INFO  16:24:48,306 ProgressMeter -            done    466384.0    59.0 s       2.1 m      100.0%    59.0 s       0.0 s
[2016-04-14T23:24Z] INFO  16:24:48,307 ProgressMeter - Total runtime 59.58 secs, 0.99 min, 0.02 hours
[2016-04-14T23:24Z] INFO  16:24:48,307 MicroScheduler - 210 reads were filtered out during the traversal out of approximately 466594 total reads (0.05%)
[2016-04-14T23:24Z] INFO  16:24:48,308 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:24Z] INFO  16:24:48,308 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:24Z] INFO  16:24:48,308 MicroScheduler -   -> 210 reads (0.05% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:24Z] INFO  16:24:48,862 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:24Z] INFO  16:24:48,865 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:24Z] INFO  16:24:48,866 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:24Z] INFO  16:24:48,866 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:24Z] INFO  16:24:48,866 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-14T23:24Z] INFO  16:24:48,871 HelpFormatter - Program Args: -T PrintReads -L 4:1-15511864 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/4/tx/tmp8B9el9/R14-18102_kapa-NGv3-PE100-NGv3-sort-4_0_15511864-prep-prealign.bam
[2016-04-14T23:24Z] INFO  16:24:48,881 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:24Z] INFO  16:24:48,892 HelpFormatter - Date/Time: 2016/04/14 16:24:48
[2016-04-14T23:24Z] INFO  16:24:48,892 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:24Z] INFO  16:24:48,893 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:24Z] INFO  16:24:48,922 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:24Z] INFO  16:24:48,933 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:24Z] INFO  16:24:48,967 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.03
[2016-04-14T23:24Z] INFO  16:24:48,982 IntervalUtils - Processing 7689367 bp from intervals
[2016-04-14T23:24Z] INFO  16:24:49,051 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:24Z] INFO  16:24:49,117 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:24Z] INFO  16:24:49,310 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:24Z] INFO  16:24:49,311 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:24Z] INFO  16:24:49,312 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:24Z] INFO  16:24:49,312 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:24Z] INFO  16:24:49,326 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:24Z] INFO  16:24:49,437 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:24Z] INFO  16:24:49,724 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:24Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-3_31617887_47127804-prep-prealign.bam
[2016-04-14T23:24Z] INFO  16:24:50,194 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:24Z] INFO  16:24:50,201 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:24Z] INFO  16:24:50,202 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:24Z] INFO  16:24:50,202 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:24Z] INFO  16:24:50,203 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-14T23:24Z] INFO  16:24:50,207 HelpFormatter - Program Args: -T PrintReads -L 4:15512870-31144471 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/4/tx/tmp063Saz/R14-18102_kapa-NGv3-PE100-NGv3-sort-4_15512869_31144471-prep-prealign.bam
[2016-04-14T23:24Z] INFO  16:24:50,220 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:24Z] INFO  16:24:50,221 HelpFormatter - Date/Time: 2016/04/14 16:24:50
[2016-04-14T23:24Z] INFO  16:24:50,221 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:24Z] INFO  16:24:50,221 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:24Z] INFO  16:24:50,257 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:24Z] INFO  16:24:50,266 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:24Z] INFO  16:24:50,304 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.04
[2016-04-14T23:24Z] INFO  16:24:50,318 IntervalUtils - Processing 15511864 bp from intervals
[2016-04-14T23:24Z] INFO  16:24:50,396 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:24Z] INFO  16:24:50,406 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:24Z] INFO  16:24:50,638 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:24Z] INFO  16:24:50,650 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:24Z] INFO  16:24:50,651 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:24Z] INFO  16:24:50,652 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:24Z] INFO  16:24:50,679 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:24Z] INFO  16:24:50,869 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:24Z] GATK RealignerTargetCreator: R14-18102_kapa-NGv3-PE100-NGv3-sort-3_31617887_47127804-prep-prealign.bam 3:31617888-47127804
[2016-04-14T23:24Z] GATK: RealignerTargetCreator
[2016-04-14T23:24Z] INFO  16:24:51,498 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-14T23:24Z] INFO  16:24:51,568 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:24Z] INFO  16:24:51,579 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:24Z] INFO  16:24:51,662 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-14T23:24Z] INFO  16:24:51,681 IntervalUtils - Processing 15631602 bp from intervals
[2016-04-14T23:24Z] INFO  16:24:51,799 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:24Z] INFO  16:24:52,179 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:24Z] INFO  16:24:52,180 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:24Z] INFO  16:24:52,181 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:24Z] INFO  16:24:52,182 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:24Z] INFO  16:24:52,191 ProgressMeter -      3:52257916    400012.0    61.0 s       2.6 m       33.0%     3.1 m       2.1 m
[2016-04-14T23:24Z] INFO  16:24:52,198 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:24Z] INFO  16:24:52,385 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:24Z] INFO  16:24:52,656 ProgressMeter -            done   1.5512123E7    21.0 s       1.0 s      100.0%    21.0 s       0.0 s
[2016-04-14T23:24Z] INFO  16:24:52,658 ProgressMeter - Total runtime 21.38 secs, 0.36 min, 0.01 hours
[2016-04-14T23:24Z] INFO  16:24:52,662 MicroScheduler - 27382 reads were filtered out during the traversal out of approximately 318677 total reads (8.59%)
[2016-04-14T23:24Z] INFO  16:24:52,663 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:24Z] INFO  16:24:52,664 MicroScheduler -   -> 786 reads (0.25% of total) failing BadMateFilter
[2016-04-14T23:24Z] INFO  16:24:52,665 MicroScheduler -   -> 25934 reads (8.14% of total) failing DuplicateReadFilter
[2016-04-14T23:24Z] INFO  16:24:52,665 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-14T23:24Z] INFO  16:24:52,666 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:24Z] INFO  16:24:52,667 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-14T23:24Z] INFO  16:24:52,667 MicroScheduler -   -> 662 reads (0.21% of total) failing MappingQualityZeroFilter
[2016-04-14T23:24Z] INFO  16:24:52,668 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:24Z] INFO  16:24:52,669 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-14T23:24Z] INFO  16:24:52,669 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-14T23:24Z] INFO  16:24:53,790 ProgressMeter -            done   1.5599562E7    17.0 s       1.0 s      100.0%    17.0 s       0.0 s
[2016-04-14T23:24Z] INFO  16:24:53,791 ProgressMeter - Total runtime 17.34 secs, 0.29 min, 0.00 hours
[2016-04-14T23:24Z] INFO  16:24:53,795 MicroScheduler - 14397 reads were filtered out during the traversal out of approximately 171264 total reads (8.41%)
[2016-04-14T23:24Z] INFO  16:24:53,796 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:24Z] INFO  16:24:53,797 MicroScheduler -   -> 493 reads (0.29% of total) failing BadMateFilter
[2016-04-14T23:24Z] INFO  16:24:53,798 MicroScheduler -   -> 13071 reads (7.63% of total) failing DuplicateReadFilter
[2016-04-14T23:24Z] INFO  16:24:53,798 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-14T23:24Z] INFO  16:24:53,799 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:24Z] INFO  16:24:53,799 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-14T23:24Z] INFO  16:24:53,800 MicroScheduler -   -> 833 reads (0.49% of total) failing MappingQualityZeroFilter
[2016-04-14T23:24Z] INFO  16:24:53,801 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:24Z] INFO  16:24:53,801 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-14T23:24Z] INFO  16:24:53,802 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-14T23:24Z] INFO  16:24:54,067 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:24Z] GATK: realign ('3', 0, 15512123) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:24Z] INFO  16:24:54,194 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:24Z] INFO  16:24:54,198 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:24Z] INFO  16:24:54,198 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:24Z] INFO  16:24:54,199 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:24Z] INFO  16:24:54,204 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/3/R14-18102_kapa-NGv3-PE100-NGv3-sort-3_31617887_47127804-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/3/tx/tmpBVJ47k/R14-18102_kapa-NGv3-PE100-NGv3-sort-3_31617887_47127804-prep-prealign-realign.intervals -l INFO -L 3:31617888-47127804 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-14T23:24Z] INFO  16:24:54,217 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:24Z] INFO  16:24:54,218 HelpFormatter - Date/Time: 2016/04/14 16:24:54
[2016-04-14T23:24Z] INFO  16:24:54,219 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:24Z] INFO  16:24:54,219 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:24Z] INFO  16:24:54,314 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:24Z] INFO  16:24:54,509 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-14T23:24Z] INFO  16:24:54,537 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:24Z] INFO  16:24:54,612 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-14T23:24Z] INFO  16:24:54,887 IntervalUtils - Processing 15509917 bp from intervals
[2016-04-14T23:24Z] WARN  16:24:54,893 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:24Z] INFO  16:24:54,970 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:24Z] INFO  16:24:54,992 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@41fd9d8e
[2016-04-14T23:24Z] INFO  16:24:55,094 ProgressMeter -            done    121321.0    12.0 s     105.0 s      100.0%    12.0 s       0.0 s
[2016-04-14T23:24Z] INFO  16:24:55,094 ProgressMeter - Total runtime 12.78 secs, 0.21 min, 0.00 hours
[2016-04-14T23:24Z] INFO  16:24:55,099 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 121321 total reads (0.00%)
[2016-04-14T23:24Z] INFO  16:24:55,099 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:24Z] INFO  16:24:55,100 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:24Z] INFO  16:24:55,100 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:24Z] INFO  16:24:55,101 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:24Z] GATK: realign ('3', 96585668, 112185230) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:24Z] INFO  16:24:55,189 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:24Z] INFO  16:24:55,190 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:24Z] INFO  16:24:55,191 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:24Z] INFO  16:24:55,191 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-14T23:24Z] INFO  16:24:55,245 ProgressMeter -            done    162269.0    23.0 s       2.4 m      100.0%    23.0 s       0.0 s
[2016-04-14T23:24Z] INFO  16:24:55,245 ProgressMeter - Total runtime 23.02 secs, 0.38 min, 0.01 hours
[2016-04-14T23:24Z] INFO  16:24:55,246 MicroScheduler - 106 reads were filtered out during the traversal out of approximately 162375 total reads (0.07%)
[2016-04-14T23:24Z] INFO  16:24:55,246 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:24Z] INFO  16:24:55,246 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:24Z] INFO  16:24:55,247 MicroScheduler -   -> 106 reads (0.07% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:24Z] INFO  16:24:56,686 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:24Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-3_62739115_78648077-prep.bam
[2016-04-14T23:24Z] INFO  16:24:56,763 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:24Z] INFO  16:24:56,766 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:24Z] INFO  16:24:56,767 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:24Z] INFO  16:24:56,767 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:24Z] INFO  16:24:56,772 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/3/R14-18102_kapa-NGv3-PE100-NGv3-sort-3_0_15512123-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/3/R14-18102_kapa-NGv3-PE100-NGv3-sort-3_0_15512123-prep-prealign-realign.intervals -L 3:1-15512123 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/3/tx/tmprTq_yf/R14-18102_kapa-NGv3-PE100-NGv3-sort-3_0_15512123-prep.bam
[2016-04-14T23:24Z] INFO  16:24:56,781 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:24Z] INFO  16:24:56,785 HelpFormatter - Date/Time: 2016/04/14 16:24:56
[2016-04-14T23:24Z] INFO  16:24:56,786 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:24Z] INFO  16:24:56,787 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:24Z] INFO  16:24:56,946 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:24Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-3_143297426_158963696-prep-prealign.bam
[2016-04-14T23:24Z] INFO  16:24:57,014 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:24Z] INFO  16:24:57,038 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@32d5a4c6
[2016-04-14T23:24Z] INFO  16:24:57,106 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:24Z] GATK pre-alignment ('4', 36069528, 52709433) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:24Z] INFO  16:24:57,115 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:24Z] INFO  16:24:57,170 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-14T23:24Z] INFO  16:24:57,209 ProgressMeter -            done    360143.0    46.0 s       2.1 m      100.0%    46.0 s       0.0 s
[2016-04-14T23:24Z] INFO  16:24:57,210 ProgressMeter - Total runtime 46.00 secs, 0.77 min, 0.01 hours
[2016-04-14T23:24Z] INFO  16:24:57,210 MicroScheduler - 187 reads were filtered out during the traversal out of approximately 360330 total reads (0.05%)
[2016-04-14T23:24Z] INFO  16:24:57,211 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:24Z] INFO  16:24:57,211 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:24Z] INFO  16:24:57,211 MicroScheduler -   -> 187 reads (0.05% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:24Z] INFO  16:24:57,549 IntervalUtils - Processing 15512123 bp from intervals
[2016-04-14T23:24Z] GATK RealignerTargetCreator: R14-18102_kapa-NGv3-PE100-NGv3-sort-3_143297426_158963696-prep-prealign.bam 3:143297427-158963696
[2016-04-14T23:24Z] WARN  16:24:57,554 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:24Z] GATK: RealignerTargetCreator
[2016-04-14T23:24Z] INFO  16:24:57,656 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:24Z] INFO  16:24:57,804 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:24Z] INFO  16:24:57,806 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:24Z] INFO  16:24:57,807 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:24Z] INFO  16:24:57,813 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:24Z] INFO  16:24:58,014 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:24Z] INFO  16:24:58,129 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:24Z] INFO  16:24:58,133 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:24Z] INFO  16:24:58,134 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:24Z] INFO  16:24:58,135 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:24Z] INFO  16:24:58,140 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/3/R14-18102_kapa-NGv3-PE100-NGv3-sort-3_96585668_112185230-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/3/R14-18102_kapa-NGv3-PE100-NGv3-sort-3_96585668_112185230-prep-prealign-realign.intervals -L 3:96585669-112185230 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/3/tx/tmpGuEDfU/R14-18102_kapa-NGv3-PE100-NGv3-sort-3_96585668_112185230-prep.bam
[2016-04-14T23:24Z] INFO  16:24:58,177 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:24Z] INFO  16:24:58,178 HelpFormatter - Date/Time: 2016/04/14 16:24:58
[2016-04-14T23:24Z] INFO  16:24:58,178 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:24Z] INFO  16:24:58,178 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:24Z] INFO  16:24:58,332 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:24Z] INFO  16:24:58,500 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:24Z] INFO  16:24:58,637 ProgressMeter -     3:135721686    200003.0    30.0 s       2.5 m       51.2%    58.0 s      28.0 s
[2016-04-14T23:24Z] INFO  16:24:58,662 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:24Z] INFO  16:24:58,672 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:24Z] INFO  16:24:58,744 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-14T23:24Z] INFO  16:24:58,945 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:24Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-3_112188604_127703121-prep-prealign.bam
[2016-04-14T23:24Z] INFO  16:24:59,200 IntervalUtils - Processing 15599562 bp from intervals
[2016-04-14T23:24Z] WARN  16:24:59,205 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:24Z] INFO  16:24:59,327 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:24Z] INFO  16:24:59,449 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:24Z] INFO  16:24:59,450 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:24Z] INFO  16:24:59,451 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:24Z] INFO  16:24:59,452 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:24Z] INFO  16:24:59,615 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:24Z] INFO  16:24:59,790 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:25Z] INFO  16:25:00,158 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:25Z] INFO  16:25:00,161 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:25Z] INFO  16:25:00,162 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:25Z] INFO  16:25:00,162 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:25Z] INFO  16:25:00,167 HelpFormatter - Program Args: -T PrintReads -L 4:36069529-52709433 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/4/tx/tmpGHRu_U/R14-18102_kapa-NGv3-PE100-NGv3-sort-4_36069528_52709433-prep-prealign.bam
[2016-04-14T23:25Z] INFO  16:25:00,176 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:25Z] INFO  16:25:00,177 HelpFormatter - Date/Time: 2016/04/14 16:25:00
[2016-04-14T23:25Z] INFO  16:25:00,178 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:25Z] INFO  16:25:00,178 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:25Z] GATK RealignerTargetCreator: R14-18102_kapa-NGv3-PE100-NGv3-sort-3_112188604_127703121-prep-prealign.bam 3:112188605-127703121
[2016-04-14T23:25Z] GATK: RealignerTargetCreator
[2016-04-14T23:25Z] INFO  16:25:00,375 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:25Z] INFO  16:25:00,762 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:25Z] INFO  16:25:00,765 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:25Z] INFO  16:25:00,765 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:25Z] INFO  16:25:00,765 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:25Z] INFO  16:25:00,780 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/3/R14-18102_kapa-NGv3-PE100-NGv3-sort-3_143297426_158963696-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/3/tx/tmpC_VtL7/R14-18102_kapa-NGv3-PE100-NGv3-sort-3_143297426_158963696-prep-prealign-realign.intervals -l INFO -L 3:143297427-158963696 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-14T23:25Z] INFO  16:25:00,790 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:25Z] INFO  16:25:00,791 HelpFormatter - Date/Time: 2016/04/14 16:25:00
[2016-04-14T23:25Z] INFO  16:25:00,791 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:25Z] INFO  16:25:00,791 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:25Z] INFO  16:25:00,942 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:25Z] INFO  16:25:01,215 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-14T23:25Z] INFO  16:25:01,224 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:25Z] INFO  16:25:01,319 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.09
[2016-04-14T23:25Z] INFO  16:25:01,502 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-14T23:25Z] INFO  16:25:01,591 IntervalUtils - Processing 15666270 bp from intervals
[2016-04-14T23:25Z] INFO  16:25:01,593 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:25Z] WARN  16:25:01,596 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:25Z] INFO  16:25:01,617 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:25Z] INFO  16:25:01,659 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.04
[2016-04-14T23:25Z] INFO  16:25:01,665 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:25Z] INFO  16:25:01,676 IntervalUtils - Processing 16639905 bp from intervals
[2016-04-14T23:25Z] INFO  16:25:01,762 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:25Z] INFO  16:25:01,844 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:25Z] INFO  16:25:01,846 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:25Z] INFO  16:25:01,846 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:25Z] INFO  16:25:01,847 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-14T23:25Z] INFO  16:25:01,870 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@5fe152b7
[2016-04-14T23:25Z] INFO  16:25:02,009 ProgressMeter -            done    127339.0    21.0 s       2.8 m      100.0%    21.0 s       0.0 s
[2016-04-14T23:25Z] INFO  16:25:02,010 ProgressMeter - Total runtime 21.10 secs, 0.35 min, 0.01 hours
[2016-04-14T23:25Z] INFO  16:25:02,011 MicroScheduler - 91 reads were filtered out during the traversal out of approximately 127430 total reads (0.07%)
[2016-04-14T23:25Z] INFO  16:25:02,012 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:25Z] INFO  16:25:02,012 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:25Z] INFO  16:25:02,013 MicroScheduler -   -> 91 reads (0.07% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:25Z] INFO  16:25:02,015 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:25Z] INFO  16:25:02,016 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:25Z] INFO  16:25:02,016 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:25Z] INFO  16:25:02,017 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:25Z] INFO  16:25:02,033 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:25Z] INFO  16:25:02,173 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:25Z] INFO  16:25:02,488 ProgressMeter -            done    310529.0    22.0 s      73.0 s      100.0%    22.0 s       0.0 s
[2016-04-14T23:25Z] INFO  16:25:02,488 ProgressMeter - Total runtime 22.92 secs, 0.38 min, 0.01 hours
[2016-04-14T23:25Z] INFO  16:25:02,491 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 310529 total reads (0.00%)
[2016-04-14T23:25Z] INFO  16:25:02,492 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:25Z] INFO  16:25:02,492 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:25Z] INFO  16:25:02,492 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:25Z] INFO  16:25:02,945 ProgressMeter -     1:155058871    800053.0    61.0 s      77.0 s       71.9%    84.0 s      23.0 s
[2016-04-14T23:25Z] INFO  16:25:03,028 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:25Z] INFO  16:25:03,031 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:25Z] INFO  16:25:03,032 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:25Z] INFO  16:25:03,033 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:25Z] INFO  16:25:03,037 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/3/R14-18102_kapa-NGv3-PE100-NGv3-sort-3_112188604_127703121-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/3/tx/tmpnfTqYD/R14-18102_kapa-NGv3-PE100-NGv3-sort-3_112188604_127703121-prep-prealign-realign.intervals -l INFO -L 3:112188605-127703121 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-14T23:25Z] INFO  16:25:03,059 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:25Z] INFO  16:25:03,061 HelpFormatter - Date/Time: 2016/04/14 16:25:03
[2016-04-14T23:25Z] INFO  16:25:03,065 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:25Z] INFO  16:25:03,066 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:25Z] INFO  16:25:03,184 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:25Z] INFO  16:25:03,383 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-14T23:25Z] INFO  16:25:03,397 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:25Z] INFO  16:25:03,406 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:25Z] INFO  16:25:03,438 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.04
[2016-04-14T23:25Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-3_158970515_174577240-prep-prealign.bam
[2016-04-14T23:25Z] INFO  16:25:03,702 IntervalUtils - Processing 15514517 bp from intervals
[2016-04-14T23:25Z] WARN  16:25:03,714 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:25Z] INFO  16:25:03,798 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:25Z] GATK RealignerTargetCreator: R14-18102_kapa-NGv3-PE100-NGv3-sort-3_158970515_174577240-prep-prealign.bam 3:158970516-174577240
[2016-04-14T23:25Z] GATK: RealignerTargetCreator
[2016-04-14T23:25Z] INFO  16:25:03,982 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:25Z] INFO  16:25:03,994 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:25Z] INFO  16:25:03,994 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:25Z] INFO  16:25:03,994 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:25Z] INFO  16:25:03,995 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-14T23:25Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-2_222291154_237994685-prep.bam
[2016-04-14T23:25Z] GATK pre-alignment ('4', 52709749, 68338393) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:25Z] INFO  16:25:06,772 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:25Z] INFO  16:25:06,775 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:25Z] INFO  16:25:06,775 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:25Z] INFO  16:25:06,775 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:25Z] INFO  16:25:06,779 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/3/R14-18102_kapa-NGv3-PE100-NGv3-sort-3_158970515_174577240-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/3/tx/tmpOPqhZP/R14-18102_kapa-NGv3-PE100-NGv3-sort-3_158970515_174577240-prep-prealign-realign.intervals -l INFO -L 3:158970516-174577240 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-14T23:25Z] INFO  16:25:06,813 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:25Z] INFO  16:25:06,814 HelpFormatter - Date/Time: 2016/04/14 16:25:06
[2016-04-14T23:25Z] INFO  16:25:06,814 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:25Z] INFO  16:25:06,814 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:25Z] INFO  16:25:06,960 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:25Z] INFO  16:25:07,234 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-14T23:25Z] INFO  16:25:07,249 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:25Z] INFO  16:25:07,311 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-14T23:25Z] INFO  16:25:07,600 IntervalUtils - Processing 15606725 bp from intervals
[2016-04-14T23:25Z] WARN  16:25:07,605 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:25Z] INFO  16:25:07,703 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:25Z] INFO  16:25:07,961 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:25Z] INFO  16:25:07,962 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:25Z] INFO  16:25:07,963 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:25Z] INFO  16:25:07,964 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-14T23:25Z] INFO  16:25:08,079 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:25Z] INFO  16:25:08,083 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:25Z] INFO  16:25:08,083 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:25Z] INFO  16:25:08,084 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:25Z] INFO  16:25:08,089 HelpFormatter - Program Args: -T PrintReads -L 4:52709750-68338393 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/4/tx/tmpBFLXSG/R14-18102_kapa-NGv3-PE100-NGv3-sort-4_52709749_68338393-prep-prealign.bam
[2016-04-14T23:25Z] INFO  16:25:08,103 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:25Z] INFO  16:25:08,114 HelpFormatter - Date/Time: 2016/04/14 16:25:08
[2016-04-14T23:25Z] INFO  16:25:08,115 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:25Z] INFO  16:25:08,115 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:25Z] INFO  16:25:08,348 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:25Z] INFO  16:25:09,005 ProgressMeter -            done    401370.0    28.0 s      71.0 s      100.0%    28.0 s       0.0 s
[2016-04-14T23:25Z] INFO  16:25:09,007 ProgressMeter - Total runtime 28.58 secs, 0.48 min, 0.01 hours
[2016-04-14T23:25Z] INFO  16:25:09,011 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 401370 total reads (0.00%)
[2016-04-14T23:25Z] INFO  16:25:09,012 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:25Z] INFO  16:25:09,012 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:25Z] INFO  16:25:09,013 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:25Z] INFO  16:25:09,627 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-14T23:25Z] INFO  16:25:09,695 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:25Z] INFO  16:25:09,704 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:25Z] INFO  16:25:09,776 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-14T23:25Z] INFO  16:25:09,791 IntervalUtils - Processing 15628644 bp from intervals
[2016-04-14T23:25Z] INFO  16:25:09,886 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:25Z] INFO  16:25:10,127 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:25Z] INFO  16:25:10,128 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:25Z] INFO  16:25:10,129 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:25Z] INFO  16:25:10,130 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:25Z] INFO  16:25:10,160 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:25Z] INFO  16:25:10,349 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:25Z] INFO  16:25:10,642 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:25Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-2_205912303_222290862-prep.bam
[2016-04-14T23:25Z] INFO  16:25:11,875 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@41fd9d8e
[2016-04-14T23:25Z] GATK pre-alignment ('4', 68340604, 83852298) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:25Z] INFO  16:25:12,042 ProgressMeter -            done    340882.0    43.0 s       2.1 m      100.0%    43.0 s       0.0 s
[2016-04-14T23:25Z] INFO  16:25:12,043 ProgressMeter - Total runtime 43.44 secs, 0.72 min, 0.01 hours
[2016-04-14T23:25Z] INFO  16:25:12,044 MicroScheduler - 173 reads were filtered out during the traversal out of approximately 341055 total reads (0.05%)
[2016-04-14T23:25Z] INFO  16:25:12,045 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:25Z] INFO  16:25:12,046 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:25Z] INFO  16:25:12,047 MicroScheduler -   -> 173 reads (0.05% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:25Z] INFO  16:25:12,105 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@7172f77a
[2016-04-14T23:25Z] INFO  16:25:12,192 ProgressMeter -            done    114454.0    20.0 s       2.9 m      100.0%    20.0 s       0.0 s
[2016-04-14T23:25Z] INFO  16:25:12,193 ProgressMeter - Total runtime 20.01 secs, 0.33 min, 0.01 hours
[2016-04-14T23:25Z] INFO  16:25:12,193 MicroScheduler - 119 reads were filtered out during the traversal out of approximately 114573 total reads (0.10%)
[2016-04-14T23:25Z] INFO  16:25:12,194 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:25Z] INFO  16:25:12,194 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:25Z] INFO  16:25:12,194 MicroScheduler -   -> 119 reads (0.10% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:25Z] INFO  16:25:13,448 ProgressMeter -            done    170309.0    13.0 s      82.0 s      100.0%    13.0 s       0.0 s
[2016-04-14T23:25Z] INFO  16:25:13,448 ProgressMeter - Total runtime 14.00 secs, 0.23 min, 0.00 hours
[2016-04-14T23:25Z] INFO  16:25:13,452 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 170309 total reads (0.00%)
[2016-04-14T23:25Z] INFO  16:25:13,452 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:25Z] INFO  16:25:13,453 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:25Z] INFO  16:25:13,453 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:25Z] INFO  16:25:13,551 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:25Z] INFO  16:25:13,564 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:25Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-4_15512869_31144471-prep-prealign.bam
[2016-04-14T23:25Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-3_127770401_143293035-prep-prealign.bam
[2016-04-14T23:25Z] GATK RealignerTargetCreator: R14-18102_kapa-NGv3-PE100-NGv3-sort-4_15512869_31144471-prep-prealign.bam 4:15512870-31144471
[2016-04-14T23:25Z] GATK: RealignerTargetCreator
[2016-04-14T23:25Z] INFO  16:25:14,871 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:25Z] INFO  16:25:14,875 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:25Z] INFO  16:25:14,875 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:25Z] INFO  16:25:14,876 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:25Z] INFO  16:25:14,880 HelpFormatter - Program Args: -T PrintReads -L 4:68340605-83852298 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/4/tx/tmpiQ1Tix/R14-18102_kapa-NGv3-PE100-NGv3-sort-4_68340604_83852298-prep-prealign.bam
[2016-04-14T23:25Z] INFO  16:25:14,892 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:25Z] INFO  16:25:14,903 HelpFormatter - Date/Time: 2016/04/14 16:25:14
[2016-04-14T23:25Z] INFO  16:25:14,904 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:25Z] INFO  16:25:14,904 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:25Z] INFO  16:25:14,939 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:25Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-3_96585668_112185230-prep.bam
[2016-04-14T23:25Z] GATK RealignerTargetCreator: R14-18102_kapa-NGv3-PE100-NGv3-sort-3_127770401_143293035-prep-prealign.bam 3:127770402-143293035
[2016-04-14T23:25Z] GATK: RealignerTargetCreator
[2016-04-14T23:25Z] INFO  16:25:15,070 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:25Z] GATK pre-alignment ('4', 83857133, 99393738) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:25Z] INFO  16:25:16,137 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-14T23:25Z] INFO  16:25:16,220 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:25Z] INFO  16:25:16,229 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:25Z] INFO  16:25:16,289 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-14T23:25Z] INFO  16:25:16,337 IntervalUtils - Processing 15511694 bp from intervals
[2016-04-14T23:25Z] INFO  16:25:16,447 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:25Z] INFO  16:25:16,739 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:25Z] INFO  16:25:16,740 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:25Z] INFO  16:25:16,741 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:25Z] INFO  16:25:16,741 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:25Z] INFO  16:25:16,761 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:25Z] INFO  16:25:16,923 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:25Z] INFO  16:25:16,970 ProgressMeter -     3:186256317    200003.0    30.0 s       2.5 m       73.8%    40.0 s      10.0 s
[2016-04-14T23:25Z] INFO  16:25:16,982 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:25Z] INFO  16:25:16,986 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:25Z] INFO  16:25:16,987 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:25Z] INFO  16:25:16,987 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:25Z] INFO  16:25:16,992 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/4/R14-18102_kapa-NGv3-PE100-NGv3-sort-4_15512869_31144471-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/4/tx/tmpiYzo7S/R14-18102_kapa-NGv3-PE100-NGv3-sort-4_15512869_31144471-prep-prealign-realign.intervals -l INFO -L 4:15512870-31144471 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-14T23:25Z] INFO  16:25:17,006 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:25Z] INFO  16:25:17,012 HelpFormatter - Date/Time: 2016/04/14 16:25:16
[2016-04-14T23:25Z] INFO  16:25:17,013 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:25Z] INFO  16:25:17,013 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:25Z] INFO  16:25:17,153 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:25Z] INFO  16:25:17,359 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-14T23:25Z] INFO  16:25:17,372 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:25Z] INFO  16:25:17,427 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-14T23:25Z] INFO  16:25:17,731 IntervalUtils - Processing 15631602 bp from intervals
[2016-04-14T23:25Z] WARN  16:25:17,737 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:25Z] INFO  16:25:17,748 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:25Z] INFO  16:25:17,752 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:25Z] INFO  16:25:17,752 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:25Z] INFO  16:25:17,753 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:25Z] INFO  16:25:17,759 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/3/R14-18102_kapa-NGv3-PE100-NGv3-sort-3_127770401_143293035-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/3/tx/tmpdeNqNN/R14-18102_kapa-NGv3-PE100-NGv3-sort-3_127770401_143293035-prep-prealign-realign.intervals -l INFO -L 3:127770402-143293035 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-14T23:25Z] INFO  16:25:17,774 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:25Z] INFO  16:25:17,775 HelpFormatter - Date/Time: 2016/04/14 16:25:17
[2016-04-14T23:25Z] INFO  16:25:17,776 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:25Z] INFO  16:25:17,777 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:25Z] INFO  16:25:17,863 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:25Z] INFO  16:25:17,945 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:25Z] INFO  16:25:18,066 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:25Z] INFO  16:25:18,068 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:25Z] INFO  16:25:18,069 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:25Z] INFO  16:25:18,069 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-14T23:25Z] INFO  16:25:18,175 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-14T23:25Z] INFO  16:25:18,185 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:25Z] INFO  16:25:18,231 ProgressMeter -            done   1.5509917E7    23.0 s       1.0 s      100.0%    23.0 s       0.0 s
[2016-04-14T23:25Z] INFO  16:25:18,232 ProgressMeter - Total runtime 23.04 secs, 0.38 min, 0.01 hours
[2016-04-14T23:25Z] INFO  16:25:18,237 MicroScheduler - 39986 reads were filtered out during the traversal out of approximately 469081 total reads (8.52%)
[2016-04-14T23:25Z] INFO  16:25:18,237 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-14T23:25Z] INFO  16:25:18,238 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:25Z] INFO  16:25:18,239 MicroScheduler -   -> 965 reads (0.21% of total) failing BadMateFilter
[2016-04-14T23:25Z] INFO  16:25:18,240 MicroScheduler -   -> 37519 reads (8.00% of total) failing DuplicateReadFilter
[2016-04-14T23:25Z] INFO  16:25:18,240 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-14T23:25Z] INFO  16:25:18,241 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:25Z] INFO  16:25:18,242 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-14T23:25Z] INFO  16:25:18,243 MicroScheduler -   -> 1502 reads (0.32% of total) failing MappingQualityZeroFilter
[2016-04-14T23:25Z] INFO  16:25:18,243 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:25Z] INFO  16:25:18,244 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-14T23:25Z] INFO  16:25:18,245 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-14T23:25Z] INFO  16:25:18,252 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:25Z] INFO  16:25:18,256 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:25Z] INFO  16:25:18,256 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:25Z] INFO  16:25:18,257 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:25Z] INFO  16:25:18,261 HelpFormatter - Program Args: -T PrintReads -L 4:83857134-99393738 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/4/tx/tmp_GdimR/R14-18102_kapa-NGv3-PE100-NGv3-sort-4_83857133_99393738-prep-prealign.bam
[2016-04-14T23:25Z] INFO  16:25:18,290 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:25Z] INFO  16:25:18,291 HelpFormatter - Date/Time: 2016/04/14 16:25:18
[2016-04-14T23:25Z] INFO  16:25:18,291 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:25Z] INFO  16:25:18,292 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:25Z] INFO  16:25:18,490 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:25Z] INFO  16:25:18,584 IntervalUtils - Processing 15522634 bp from intervals
[2016-04-14T23:25Z] WARN  16:25:18,590 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:25Z] INFO  16:25:18,694 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:25Z] INFO  16:25:18,761 ProgressMeter -            done   1229850.0    77.0 s      63.0 s      100.0%    77.0 s       0.0 s
[2016-04-14T23:25Z] INFO  16:25:18,762 ProgressMeter - Total runtime 77.65 secs, 1.29 min, 0.02 hours
[2016-04-14T23:25Z] INFO  16:25:18,765 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 1229850 total reads (0.00%)
[2016-04-14T23:25Z] INFO  16:25:18,766 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:25Z] INFO  16:25:18,766 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:25Z] INFO  16:25:18,766 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:25Z] INFO  16:25:18,923 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:25Z] INFO  16:25:18,925 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:25Z] INFO  16:25:18,925 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:25Z] INFO  16:25:18,926 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-14T23:25Z] INFO  16:25:19,259 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@41fd9d8e
[2016-04-14T23:25Z] INFO  16:25:19,345 ProgressMeter -     3:197955408    200010.0    30.0 s       2.5 m       99.1%    30.0 s       0.0 s
[2016-04-14T23:25Z] INFO  16:25:19,485 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-14T23:25Z] INFO  16:25:19,528 ProgressMeter -            done    222214.0    30.0 s       2.3 m       99.1%    30.0 s       0.0 s
[2016-04-14T23:25Z] INFO  16:25:19,528 ProgressMeter - Total runtime 30.22 secs, 0.50 min, 0.01 hours
[2016-04-14T23:25Z] INFO  16:25:19,529 MicroScheduler - 108 reads were filtered out during the traversal out of approximately 222322 total reads (0.05%)
[2016-04-14T23:25Z] INFO  16:25:19,529 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:25Z] INFO  16:25:19,529 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:25Z] INFO  16:25:19,530 MicroScheduler -   -> 108 reads (0.05% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:25Z] INFO  16:25:19,545 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:25Z] INFO  16:25:19,554 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:25Z] INFO  16:25:19,601 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-14T23:25Z] INFO  16:25:19,616 IntervalUtils - Processing 15536605 bp from intervals
[2016-04-14T23:25Z] INFO  16:25:19,650 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:25Z] GATK: realign ('3', 31617887, 47127804) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:25Z] INFO  16:25:19,687 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:25Z] INFO  16:25:19,750 ProgressMeter -            done   1.566627E7    17.0 s       1.0 s      100.0%    17.0 s       0.0 s
[2016-04-14T23:25Z] INFO  16:25:19,750 ProgressMeter - Total runtime 17.90 secs, 0.30 min, 0.00 hours
[2016-04-14T23:25Z] INFO  16:25:19,754 MicroScheduler - 14641 reads were filtered out during the traversal out of approximately 163703 total reads (8.94%)
[2016-04-14T23:25Z] INFO  16:25:19,754 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:25Z] INFO  16:25:19,755 MicroScheduler -   -> 543 reads (0.33% of total) failing BadMateFilter
[2016-04-14T23:25Z] INFO  16:25:19,755 MicroScheduler -   -> 12898 reads (7.88% of total) failing DuplicateReadFilter
[2016-04-14T23:25Z] INFO  16:25:19,755 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-14T23:25Z] INFO  16:25:19,755 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:25Z] INFO  16:25:19,756 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-14T23:25Z] INFO  16:25:19,756 MicroScheduler -   -> 1200 reads (0.73% of total) failing MappingQualityZeroFilter
[2016-04-14T23:25Z] INFO  16:25:19,756 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:25Z] INFO  16:25:19,756 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-14T23:25Z] INFO  16:25:19,757 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-14T23:25Z] INFO  16:25:19,979 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:25Z] INFO  16:25:19,980 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:25Z] INFO  16:25:19,981 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:25Z] INFO  16:25:19,982 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:25Z] INFO  16:25:19,995 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:25Z] INFO  16:25:20,082 ProgressMeter -            done    317231.0    22.0 s      70.0 s      100.0%    22.0 s       0.0 s
[2016-04-14T23:25Z] INFO  16:25:20,083 ProgressMeter - Total runtime 22.28 secs, 0.37 min, 0.01 hours
[2016-04-14T23:25Z] INFO  16:25:20,086 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 317231 total reads (0.00%)
[2016-04-14T23:25Z] INFO  16:25:20,087 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:25Z] INFO  16:25:20,087 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:25Z] INFO  16:25:20,087 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:25Z] INFO  16:25:20,155 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:25Z] INFO  16:25:20,397 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:25Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-1_143897546_159410511-prep.bam
[2016-04-14T23:25Z] INFO  16:25:20,876 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:25Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-3_190333063_198022430-prep-prealign.bam
[2016-04-14T23:25Z] INFO  16:25:21,162 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:25Z] GATK: realign ('3', 143297426, 158963696) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:25Z] INFO  16:25:21,219 ProgressMeter -       4:3037144    100002.0    30.0 s       5.1 m       19.6%     2.6 m       2.1 m
[2016-04-14T23:25Z] GATK RealignerTargetCreator: R14-18102_kapa-NGv3-PE100-NGv3-sort-3_190333063_198022430-prep-prealign.bam 3:190333064-198022430
[2016-04-14T23:25Z] GATK: RealignerTargetCreator
[2016-04-14T23:25Z] INFO  16:25:21,867 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:25Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-3_0_15512123-prep.bam
[2016-04-14T23:25Z] INFO  16:25:21,953 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@41fd9d8e
[2016-04-14T23:25Z] INFO  16:25:22,104 ProgressMeter -            done    745632.0    91.0 s       2.0 m      100.0%    91.0 s       0.0 s
[2016-04-14T23:25Z] INFO  16:25:22,105 ProgressMeter - Total runtime 91.50 secs, 1.52 min, 0.03 hours
[2016-04-14T23:25Z] INFO  16:25:22,106 MicroScheduler - 290 reads were filtered out during the traversal out of approximately 745922 total reads (0.04%)
[2016-04-14T23:25Z] INFO  16:25:22,107 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:25Z] INFO  16:25:22,108 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:25Z] INFO  16:25:22,109 MicroScheduler -   -> 290 reads (0.04% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:25Z] INFO  16:25:22,592 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:25Z] INFO  16:25:22,595 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:25Z] INFO  16:25:22,596 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:25Z] INFO  16:25:22,596 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:25Z] INFO  16:25:22,601 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/3/R14-18102_kapa-NGv3-PE100-NGv3-sort-3_31617887_47127804-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/3/R14-18102_kapa-NGv3-PE100-NGv3-sort-3_31617887_47127804-prep-prealign-realign.intervals -L 3:31617888-47127804 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/3/tx/tmpUXQ_hi/R14-18102_kapa-NGv3-PE100-NGv3-sort-3_31617887_47127804-prep.bam
[2016-04-14T23:25Z] INFO  16:25:22,614 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:25Z] INFO  16:25:22,618 HelpFormatter - Date/Time: 2016/04/14 16:25:22
[2016-04-14T23:25Z] INFO  16:25:22,619 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:25Z] INFO  16:25:22,620 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:25Z] INFO  16:25:22,719 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@5fe152b7
[2016-04-14T23:25Z] INFO  16:25:22,859 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:25Z] GATK pre-alignment ('4', 99397339, 115544957) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:25Z] INFO  16:25:22,956 ProgressMeter -            done    285855.0    36.0 s       2.1 m      100.0%    36.0 s       0.0 s
[2016-04-14T23:25Z] INFO  16:25:22,957 ProgressMeter - Total runtime 36.03 secs, 0.60 min, 0.01 hours
[2016-04-14T23:25Z] INFO  16:25:22,957 MicroScheduler - 126 reads were filtered out during the traversal out of approximately 285981 total reads (0.04%)
[2016-04-14T23:25Z] INFO  16:25:22,957 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:25Z] INFO  16:25:22,958 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:25Z] INFO  16:25:22,958 MicroScheduler -   -> 126 reads (0.04% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:25Z] INFO  16:25:22,981 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:25Z] INFO  16:25:23,005 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:25Z] INFO  16:25:23,083 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-14T23:25Z] INFO  16:25:23,392 IntervalUtils - Processing 15509917 bp from intervals
[2016-04-14T23:25Z] WARN  16:25:23,398 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:25Z] INFO  16:25:23,467 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:25Z] INFO  16:25:23,613 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:25Z] INFO  16:25:23,614 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:25Z] INFO  16:25:23,617 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:25Z] INFO  16:25:23,618 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:25Z] INFO  16:25:23,816 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:25Z] INFO  16:25:23,827 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:25Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-3_47129602_62648069-prep-prealign.bam
[2016-04-14T23:25Z] INFO  16:25:24,054 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:25Z] GATK pre-alignment ('4', 115584857, 134074404) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:25Z] INFO  16:25:24,369 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:25Z] INFO  16:25:24,372 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:25Z] INFO  16:25:24,372 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:25Z] INFO  16:25:24,372 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:25Z] INFO  16:25:24,381 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/3/R14-18102_kapa-NGv3-PE100-NGv3-sort-3_143297426_158963696-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/3/R14-18102_kapa-NGv3-PE100-NGv3-sort-3_143297426_158963696-prep-prealign-realign.intervals -L 3:143297427-158963696 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/3/tx/tmpwqnkCy/R14-18102_kapa-NGv3-PE100-NGv3-sort-3_143297426_158963696-prep.bam
[2016-04-14T23:25Z] INFO  16:25:24,401 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:25Z] INFO  16:25:24,402 HelpFormatter - Date/Time: 2016/04/14 16:25:24
[2016-04-14T23:25Z] INFO  16:25:24,402 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:25Z] INFO  16:25:24,402 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:25Z] INFO  16:25:24,441 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:25Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-3_174814579_190326970-prep-prealign.bam
[2016-04-14T23:25Z] INFO  16:25:24,608 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:25Z] INFO  16:25:24,638 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:25Z] INFO  16:25:24,642 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:25Z] INFO  16:25:24,643 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:25Z] INFO  16:25:24,643 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:25Z] INFO  16:25:24,649 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/3/R14-18102_kapa-NGv3-PE100-NGv3-sort-3_190333063_198022430-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/3/tx/tmpqaJaHh/R14-18102_kapa-NGv3-PE100-NGv3-sort-3_190333063_198022430-prep-prealign-realign.intervals -l INFO -L 3:190333064-198022430 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-14T23:25Z] INFO  16:25:24,678 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:25Z] INFO  16:25:24,679 HelpFormatter - Date/Time: 2016/04/14 16:25:24
[2016-04-14T23:25Z] INFO  16:25:24,679 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:25Z] INFO  16:25:24,680 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:25Z] INFO  16:25:24,788 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:25Z] INFO  16:25:24,810 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:25Z] INFO  16:25:24,813 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:25Z] INFO  16:25:24,898 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-14T23:25Z] INFO  16:25:25,060 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-14T23:25Z] INFO  16:25:25,070 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:25Z] INFO  16:25:25,144 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-14T23:25Z] INFO  16:25:25,372 IntervalUtils - Processing 15666270 bp from intervals
[2016-04-14T23:25Z] WARN  16:25:25,378 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:25Z] INFO  16:25:25,467 IntervalUtils - Processing 7689367 bp from intervals
[2016-04-14T23:25Z] WARN  16:25:25,472 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:25Z] INFO  16:25:25,475 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:25Z] INFO  16:25:25,485 ProgressMeter -            done   1.5606725E7    17.0 s       1.0 s      100.0%    17.0 s       0.0 s
[2016-04-14T23:25Z] INFO  16:25:25,486 ProgressMeter - Total runtime 17.52 secs, 0.29 min, 0.00 hours
[2016-04-14T23:25Z] INFO  16:25:25,494 MicroScheduler - 10859 reads were filtered out during the traversal out of approximately 128420 total reads (8.46%)
[2016-04-14T23:25Z] INFO  16:25:25,495 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:25Z] INFO  16:25:25,497 MicroScheduler -   -> 451 reads (0.35% of total) failing BadMateFilter
[2016-04-14T23:25Z] INFO  16:25:25,499 MicroScheduler -   -> 10030 reads (7.81% of total) failing DuplicateReadFilter
[2016-04-14T23:25Z] GATK RealignerTargetCreator: R14-18102_kapa-NGv3-PE100-NGv3-sort-3_174814579_190326970-prep-prealign.bam 3:174814580-190326970
[2016-04-14T23:25Z] INFO  16:25:25,500 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-14T23:25Z] INFO  16:25:25,500 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:25Z] INFO  16:25:25,501 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-14T23:25Z] GATK: RealignerTargetCreator
[2016-04-14T23:25Z] INFO  16:25:25,502 MicroScheduler -   -> 378 reads (0.29% of total) failing MappingQualityZeroFilter
[2016-04-14T23:25Z] INFO  16:25:25,508 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:25Z] INFO  16:25:25,509 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-14T23:25Z] INFO  16:25:25,509 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-14T23:25Z] INFO  16:25:25,551 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:25Z] INFO  16:25:25,710 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:25Z] INFO  16:25:25,711 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:25Z] INFO  16:25:25,712 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:25Z] INFO  16:25:25,712 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:25Z] INFO  16:25:25,784 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:25Z] INFO  16:25:25,785 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:25Z] INFO  16:25:25,786 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:25Z] INFO  16:25:25,787 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-14T23:25Z] INFO  16:25:25,824 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:25Z] INFO  16:25:25,968 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@32d5a4c6
[2016-04-14T23:25Z] INFO  16:25:25,986 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:25Z] INFO  16:25:26,092 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:25Z] INFO  16:25:26,096 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:25Z] INFO  16:25:26,097 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:25Z] INFO  16:25:26,097 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:25Z] INFO  16:25:26,102 HelpFormatter - Program Args: -T PrintReads -L 4:99397340-115544957 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/4/tx/tmpGylT4M/R14-18102_kapa-NGv3-PE100-NGv3-sort-4_99397339_115544957-prep-prealign.bam
[2016-04-14T23:25Z] INFO  16:25:26,109 ProgressMeter -            done    111796.0    15.0 s       2.4 m       99.8%    15.0 s       0.0 s
[2016-04-14T23:25Z] INFO  16:25:26,109 ProgressMeter - Total runtime 15.98 secs, 0.27 min, 0.00 hours
[2016-04-14T23:25Z] INFO  16:25:26,110 MicroScheduler - 104 reads were filtered out during the traversal out of approximately 111900 total reads (0.09%)
[2016-04-14T23:25Z] INFO  16:25:26,110 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:25Z] INFO  16:25:26,110 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:25Z] INFO  16:25:26,111 MicroScheduler -   -> 104 reads (0.09% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:25Z] INFO  16:25:26,115 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:25Z] INFO  16:25:26,115 HelpFormatter - Date/Time: 2016/04/14 16:25:26
[2016-04-14T23:25Z] INFO  16:25:26,115 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:25Z] INFO  16:25:26,115 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:25Z] INFO  16:25:26,118 ProgressMeter -            done   1.5514517E7    22.0 s       1.0 s      100.0%    22.0 s       0.0 s
[2016-04-14T23:25Z] INFO  16:25:26,119 ProgressMeter - Total runtime 22.13 secs, 0.37 min, 0.01 hours
[2016-04-14T23:25Z] INFO  16:25:26,123 MicroScheduler - 31086 reads were filtered out during the traversal out of approximately 361788 total reads (8.59%)
[2016-04-14T23:25Z] INFO  16:25:26,124 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:25Z] INFO  16:25:26,125 MicroScheduler -   -> 804 reads (0.22% of total) failing BadMateFilter
[2016-04-14T23:25Z] INFO  16:25:26,125 MicroScheduler -   -> 28670 reads (7.92% of total) failing DuplicateReadFilter
[2016-04-14T23:25Z] INFO  16:25:26,126 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-14T23:25Z] INFO  16:25:26,127 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:25Z] INFO  16:25:26,127 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-14T23:25Z] INFO  16:25:26,128 MicroScheduler -   -> 1612 reads (0.45% of total) failing MappingQualityZeroFilter
[2016-04-14T23:25Z] INFO  16:25:26,129 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:25Z] INFO  16:25:26,129 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-14T23:25Z] INFO  16:25:26,130 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-14T23:25Z] INFO  16:25:26,335 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:25Z] GATK RealignerTargetCreator: R14-18102_kapa-NGv3-PE100-NGv3-sort-3_47129602_62648069-prep-prealign.bam 3:47129603-62648069
[2016-04-14T23:25Z] GATK: RealignerTargetCreator
[2016-04-14T23:25Z] INFO  16:25:26,857 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@41fd9d8e
[2016-04-14T23:25Z] INFO  16:25:26,907 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:25Z] GATK: realign ('3', 158970515, 174577240) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:25Z] INFO  16:25:27,175 ProgressMeter -            done    182749.0    25.0 s       2.3 m      100.0%    25.0 s       0.0 s
[2016-04-14T23:25Z] INFO  16:25:27,176 ProgressMeter - Total runtime 25.16 secs, 0.42 min, 0.01 hours
[2016-04-14T23:25Z] INFO  16:25:27,177 MicroScheduler - 434 reads were filtered out during the traversal out of approximately 183183 total reads (0.24%)
[2016-04-14T23:25Z] INFO  16:25:27,177 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:25Z] INFO  16:25:27,177 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:25Z] INFO  16:25:27,178 MicroScheduler -   -> 434 reads (0.24% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:25Z] INFO  16:25:27,218 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:25Z] INFO  16:25:27,222 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:25Z] INFO  16:25:27,223 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:25Z] INFO  16:25:27,223 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:25Z] INFO  16:25:27,231 HelpFormatter - Program Args: -T PrintReads -L 4:115584858-134074404 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/4/tx/tmpuwfZUN/R14-18102_kapa-NGv3-PE100-NGv3-sort-4_115584857_134074404-prep-prealign.bam
[2016-04-14T23:25Z] INFO  16:25:27,270 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:25Z] INFO  16:25:27,271 HelpFormatter - Date/Time: 2016/04/14 16:25:27
[2016-04-14T23:25Z] INFO  16:25:27,282 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:25Z] INFO  16:25:27,283 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:25Z] INFO  16:25:27,540 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:25Z] INFO  16:25:27,684 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-14T23:25Z] INFO  16:25:27,776 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:25Z] INFO  16:25:27,780 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:25Z] INFO  16:25:27,800 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:25Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-4_52709749_68338393-prep-prealign.bam
[2016-04-14T23:25Z] INFO  16:25:27,882 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-14T23:25Z] INFO  16:25:27,907 IntervalUtils - Processing 16147618 bp from intervals
[2016-04-14T23:25Z] INFO  16:25:27,980 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:25Z] INFO  16:25:28,120 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:25Z] GATK: realign ('3', 112188604, 127703121) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:25Z] INFO  16:25:28,261 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:25Z] INFO  16:25:28,262 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:25Z] INFO  16:25:28,263 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:25Z] INFO  16:25:28,264 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:25Z] GATK RealignerTargetCreator: R14-18102_kapa-NGv3-PE100-NGv3-sort-4_52709749_68338393-prep-prealign.bam 4:52709750-68338393
[2016-04-14T23:25Z] INFO  16:25:28,279 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:25Z] GATK: RealignerTargetCreator
[2016-04-14T23:25Z] INFO  16:25:28,434 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:25Z] INFO  16:25:28,527 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-14T23:25Z] INFO  16:25:28,622 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:25Z] INFO  16:25:28,631 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:25Z] INFO  16:25:28,687 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-14T23:25Z] INFO  16:25:28,710 IntervalUtils - Processing 18489547 bp from intervals
[2016-04-14T23:25Z] INFO  16:25:28,810 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:25Z] INFO  16:25:28,960 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:25Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-4_36069528_52709433-prep-prealign.bam
[2016-04-14T23:25Z] INFO  16:25:29,081 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:25Z] INFO  16:25:29,083 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:25Z] INFO  16:25:29,084 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:25Z] INFO  16:25:29,084 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:25Z] INFO  16:25:29,088 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/3/R14-18102_kapa-NGv3-PE100-NGv3-sort-3_174814579_190326970-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/3/tx/tmpDM49TE/R14-18102_kapa-NGv3-PE100-NGv3-sort-3_174814579_190326970-prep-prealign-realign.intervals -l INFO -L 3:174814580-190326970 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-14T23:25Z] INFO  16:25:29,114 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:25Z] INFO  16:25:29,115 HelpFormatter - Date/Time: 2016/04/14 16:25:29
[2016-04-14T23:25Z] INFO  16:25:29,116 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:25Z] INFO  16:25:29,120 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:25Z] INFO  16:25:29,161 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:25Z] INFO  16:25:29,161 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:25Z] INFO  16:25:29,162 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:25Z] INFO  16:25:29,162 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:25Z] INFO  16:25:29,177 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:25Z] INFO  16:25:29,260 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:25Z] INFO  16:25:29,344 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:25Z] INFO  16:25:29,542 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-14T23:25Z] INFO  16:25:29,553 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:25Z] INFO  16:25:29,565 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:25Z] INFO  16:25:29,569 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:25Z] INFO  16:25:29,570 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:25Z] INFO  16:25:29,571 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:25Z] INFO  16:25:29,576 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/3/R14-18102_kapa-NGv3-PE100-NGv3-sort-3_47129602_62648069-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/3/tx/tmpAKYeqY/R14-18102_kapa-NGv3-PE100-NGv3-sort-3_47129602_62648069-prep-prealign-realign.intervals -l INFO -L 3:47129603-62648069 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-14T23:25Z] INFO  16:25:29,606 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:25Z] INFO  16:25:29,615 HelpFormatter - Date/Time: 2016/04/14 16:25:29
[2016-04-14T23:25Z] INFO  16:25:29,616 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:25Z] INFO  16:25:29,617 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:25Z] INFO  16:25:29,649 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.09
[2016-04-14T23:25Z] GATK RealignerTargetCreator: R14-18102_kapa-NGv3-PE100-NGv3-sort-4_36069528_52709433-prep-prealign.bam 4:36069529-52709433
[2016-04-14T23:25Z] GATK: RealignerTargetCreator
[2016-04-14T23:25Z] INFO  16:25:29,761 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:25Z] INFO  16:25:29,900 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:25Z] INFO  16:25:29,902 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:25Z] INFO  16:25:29,903 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:25Z] INFO  16:25:29,903 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:25Z] INFO  16:25:29,907 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/3/R14-18102_kapa-NGv3-PE100-NGv3-sort-3_158970515_174577240-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/3/R14-18102_kapa-NGv3-PE100-NGv3-sort-3_158970515_174577240-prep-prealign-realign.intervals -L 3:158970516-174577240 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/3/tx/tmpYxDEKr/R14-18102_kapa-NGv3-PE100-NGv3-sort-3_158970515_174577240-prep.bam
[2016-04-14T23:25Z] INFO  16:25:29,927 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:25Z] INFO  16:25:29,927 HelpFormatter - Date/Time: 2016/04/14 16:25:29
[2016-04-14T23:25Z] INFO  16:25:29,927 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:25Z] INFO  16:25:29,928 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:25Z] INFO  16:25:29,994 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-14T23:25Z] INFO  16:25:30,013 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:25Z] INFO  16:25:30,033 IntervalUtils - Processing 15512391 bp from intervals
[2016-04-14T23:25Z] WARN  16:25:30,038 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:25Z] INFO  16:25:30,087 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-14T23:25Z] INFO  16:25:30,156 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:25Z] INFO  16:25:30,161 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:25Z] INFO  16:25:30,345 IntervalUtils - Processing 15518467 bp from intervals
[2016-04-14T23:25Z] WARN  16:25:30,350 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:25Z] INFO  16:25:30,357 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:25Z] INFO  16:25:30,368 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:25Z] INFO  16:25:30,411 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:25Z] INFO  16:25:30,412 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:25Z] INFO  16:25:30,413 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:25Z] INFO  16:25:30,413 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-14T23:25Z] INFO  16:25:30,416 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:25Z] INFO  16:25:30,424 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-14T23:25Z] INFO  16:25:30,685 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:25Z] INFO  16:25:30,697 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:25Z] INFO  16:25:30,698 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:25Z] INFO  16:25:30,699 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-14T23:25Z] INFO  16:25:30,978 IntervalUtils - Processing 15606725 bp from intervals
[2016-04-14T23:25Z] WARN  16:25:30,984 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:25Z] INFO  16:25:31,119 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:25Z] INFO  16:25:31,252 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:25Z] INFO  16:25:31,256 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:25Z] INFO  16:25:31,258 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:25Z] INFO  16:25:31,259 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:25Z] INFO  16:25:31,449 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:25Z] INFO  16:25:31,545 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:25Z] INFO  16:25:31,549 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:25Z] INFO  16:25:31,550 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:25Z] INFO  16:25:31,551 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:25Z] INFO  16:25:31,556 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/4/R14-18102_kapa-NGv3-PE100-NGv3-sort-4_52709749_68338393-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/4/tx/tmpVLxBjP/R14-18102_kapa-NGv3-PE100-NGv3-sort-4_52709749_68338393-prep-prealign-realign.intervals -l INFO -L 4:52709750-68338393 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-14T23:25Z] INFO  16:25:31,576 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:25Z] INFO  16:25:31,577 HelpFormatter - Date/Time: 2016/04/14 16:25:31
[2016-04-14T23:25Z] INFO  16:25:31,577 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:25Z] INFO  16:25:31,578 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:25Z] INFO  16:25:31,606 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:25Z] INFO  16:25:31,610 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:25Z] INFO  16:25:31,611 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:25Z] INFO  16:25:31,612 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:25Z] INFO  16:25:31,617 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/3/R14-18102_kapa-NGv3-PE100-NGv3-sort-3_112188604_127703121-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/3/R14-18102_kapa-NGv3-PE100-NGv3-sort-3_112188604_127703121-prep-prealign-realign.intervals -L 3:112188605-127703121 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/3/tx/tmpSOudJu/R14-18102_kapa-NGv3-PE100-NGv3-sort-3_112188604_127703121-prep.bam
[2016-04-14T23:25Z] INFO  16:25:31,637 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:25Z] INFO  16:25:31,639 HelpFormatter - Date/Time: 2016/04/14 16:25:31
[2016-04-14T23:25Z] INFO  16:25:31,639 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:25Z] INFO  16:25:31,645 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:25Z] INFO  16:25:31,693 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:25Z] INFO  16:25:31,716 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:25Z] INFO  16:25:31,893 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:25Z] INFO  16:25:32,039 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-14T23:25Z] INFO  16:25:32,049 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:25Z] INFO  16:25:32,054 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:25Z] INFO  16:25:32,067 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:25Z] INFO  16:25:32,113 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-14T23:25Z] INFO  16:25:32,143 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-14T23:25Z] INFO  16:25:32,509 IntervalUtils - Processing 15628644 bp from intervals
[2016-04-14T23:25Z] WARN  16:25:32,525 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:25Z] INFO  16:25:32,617 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:25Z] INFO  16:25:32,659 IntervalUtils - Processing 15514517 bp from intervals
[2016-04-14T23:25Z] WARN  16:25:32,675 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:25Z] INFO  16:25:32,769 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:25Z] INFO  16:25:32,783 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:25Z] INFO  16:25:32,784 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:25Z] INFO  16:25:32,785 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:25Z] INFO  16:25:32,786 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-14T23:25Z] INFO  16:25:33,000 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:25Z] INFO  16:25:33,012 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:25Z] INFO  16:25:33,013 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:25Z] INFO  16:25:33,014 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:25Z] INFO  16:25:33,082 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:25Z] INFO  16:25:33,085 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:25Z] INFO  16:25:33,086 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:25Z] INFO  16:25:33,086 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:25Z] INFO  16:25:33,091 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/4/R14-18102_kapa-NGv3-PE100-NGv3-sort-4_36069528_52709433-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/4/tx/tmpdRwb3t/R14-18102_kapa-NGv3-PE100-NGv3-sort-4_36069528_52709433-prep-prealign-realign.intervals -l INFO -L 4:36069529-52709433 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-14T23:25Z] INFO  16:25:33,100 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:25Z] INFO  16:25:33,101 HelpFormatter - Date/Time: 2016/04/14 16:25:33
[2016-04-14T23:25Z] INFO  16:25:33,101 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:25Z] INFO  16:25:33,112 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:25Z] INFO  16:25:33,221 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:25Z] INFO  16:25:33,230 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:25Z] INFO  16:25:33,420 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-14T23:25Z] INFO  16:25:33,429 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:25Z] INFO  16:25:33,436 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:25Z] INFO  16:25:33,492 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-14T23:25Z] INFO  16:25:33,784 IntervalUtils - Processing 16639905 bp from intervals
[2016-04-14T23:25Z] WARN  16:25:33,792 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:25Z] INFO  16:25:33,898 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:25Z] INFO  16:25:34,060 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:25Z] INFO  16:25:34,061 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:25Z] INFO  16:25:34,062 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:25Z] INFO  16:25:34,063 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-14T23:25Z] INFO  16:25:34,912 ProgressMeter -            done   1.5631602E7    16.0 s       1.0 s      100.0%    16.0 s       0.0 s
[2016-04-14T23:25Z] INFO  16:25:34,914 ProgressMeter - Total runtime 16.85 secs, 0.28 min, 0.00 hours
[2016-04-14T23:25Z] INFO  16:25:34,918 MicroScheduler - 9724 reads were filtered out during the traversal out of approximately 114997 total reads (8.46%)
[2016-04-14T23:25Z] INFO  16:25:34,919 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:25Z] INFO  16:25:34,919 MicroScheduler -   -> 459 reads (0.40% of total) failing BadMateFilter
[2016-04-14T23:25Z] INFO  16:25:34,920 MicroScheduler -   -> 9029 reads (7.85% of total) failing DuplicateReadFilter
[2016-04-14T23:25Z] INFO  16:25:34,921 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-14T23:25Z] INFO  16:25:34,921 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:25Z] INFO  16:25:34,935 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-14T23:25Z] INFO  16:25:34,935 MicroScheduler -   -> 236 reads (0.21% of total) failing MappingQualityZeroFilter
[2016-04-14T23:25Z] INFO  16:25:34,936 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:25Z] INFO  16:25:34,936 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-14T23:25Z] INFO  16:25:34,937 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-14T23:25Z] INFO  16:25:36,403 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:25Z] GATK: realign ('4', 15512869, 31144471) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:25Z] INFO  16:25:38,865 ProgressMeter -            done   7689367.0    13.0 s       1.0 s      100.0%    13.0 s       0.0 s
[2016-04-14T23:25Z] INFO  16:25:38,866 ProgressMeter - Total runtime 13.08 secs, 0.22 min, 0.00 hours
[2016-04-14T23:25Z] INFO  16:25:38,866 MicroScheduler - 35686 reads were filtered out during the traversal out of approximately 223873 total reads (15.94%)
[2016-04-14T23:25Z] INFO  16:25:38,866 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:25Z] INFO  16:25:38,867 MicroScheduler -   -> 486 reads (0.22% of total) failing BadMateFilter
[2016-04-14T23:25Z] INFO  16:25:38,867 MicroScheduler -   -> 17151 reads (7.66% of total) failing DuplicateReadFilter
[2016-04-14T23:25Z] INFO  16:25:38,867 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-14T23:25Z] INFO  16:25:38,867 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:25Z] INFO  16:25:38,868 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-14T23:25Z] INFO  16:25:38,868 MicroScheduler -   -> 18049 reads (8.06% of total) failing MappingQualityZeroFilter
[2016-04-14T23:25Z] INFO  16:25:38,868 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:25Z] INFO  16:25:38,868 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-14T23:25Z] INFO  16:25:38,869 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-14T23:25Z] INFO  16:25:39,355 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:25Z] INFO  16:25:39,359 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:25Z] INFO  16:25:39,359 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:25Z] INFO  16:25:39,360 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:25Z] INFO  16:25:39,365 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/4/R14-18102_kapa-NGv3-PE100-NGv3-sort-4_15512869_31144471-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/4/R14-18102_kapa-NGv3-PE100-NGv3-sort-4_15512869_31144471-prep-prealign-realign.intervals -L 4:15512870-31144471 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/4/tx/tmpCIx23d/R14-18102_kapa-NGv3-PE100-NGv3-sort-4_15512869_31144471-prep.bam
[2016-04-14T23:25Z] INFO  16:25:39,379 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:25Z] INFO  16:25:39,381 HelpFormatter - Date/Time: 2016/04/14 16:25:39
[2016-04-14T23:25Z] INFO  16:25:39,381 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:25Z] INFO  16:25:39,382 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:25Z] INFO  16:25:39,574 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:25Z] INFO  16:25:39,638 ProgressMeter -            done    162269.0    13.0 s      85.0 s      100.0%    13.0 s       0.0 s
[2016-04-14T23:25Z] INFO  16:25:39,638 ProgressMeter - Total runtime 13.93 secs, 0.23 min, 0.00 hours
[2016-04-14T23:25Z] INFO  16:25:39,642 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 162269 total reads (0.00%)
[2016-04-14T23:25Z] INFO  16:25:39,643 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:25Z] INFO  16:25:39,644 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:25Z] INFO  16:25:39,644 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:25Z] INFO  16:25:39,756 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:25Z] INFO  16:25:39,777 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:25Z] INFO  16:25:39,853 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-14T23:25Z] INFO  16:25:40,129 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:25Z] GATK: realign ('3', 190333063, 198022430) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:25Z] INFO  16:25:40,263 IntervalUtils - Processing 15631602 bp from intervals
[2016-04-14T23:25Z] WARN  16:25:40,269 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:25Z] INFO  16:25:40,387 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:25Z] INFO  16:25:40,505 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:25Z] INFO  16:25:40,506 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:25Z] INFO  16:25:40,507 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:25Z] INFO  16:25:40,508 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:25Z] INFO  16:25:40,655 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:25Z] INFO  16:25:40,853 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:25Z] INFO  16:25:41,164 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:25Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-3_143297426_158963696-prep.bam
[2016-04-14T23:25Z] GATK pre-alignment ('4', 134075461, 150351181) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:25Z] INFO  16:25:42,355 ProgressMeter -            done   1.5522634E7    23.0 s       1.0 s      100.0%    23.0 s       0.0 s
[2016-04-14T23:25Z] INFO  16:25:42,356 ProgressMeter - Total runtime 23.43 secs, 0.39 min, 0.01 hours
[2016-04-14T23:25Z] INFO  16:25:42,360 MicroScheduler - 29701 reads were filtered out during the traversal out of approximately 343161 total reads (8.66%)
[2016-04-14T23:25Z] INFO  16:25:42,360 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:25Z] INFO  16:25:42,361 MicroScheduler -   -> 816 reads (0.24% of total) failing BadMateFilter
[2016-04-14T23:25Z] INFO  16:25:42,361 MicroScheduler -   -> 27442 reads (8.00% of total) failing DuplicateReadFilter
[2016-04-14T23:25Z] INFO  16:25:42,361 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-14T23:25Z] INFO  16:25:42,361 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:25Z] INFO  16:25:42,362 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-14T23:25Z] INFO  16:25:42,362 MicroScheduler -   -> 1443 reads (0.42% of total) failing MappingQualityZeroFilter
[2016-04-14T23:25Z] INFO  16:25:42,362 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:25Z] INFO  16:25:42,362 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-14T23:25Z] INFO  16:25:42,362 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-14T23:25Z] INFO  16:25:43,011 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:25Z] INFO  16:25:43,014 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:25Z] INFO  16:25:43,014 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:25Z] INFO  16:25:43,014 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:25Z] INFO  16:25:43,018 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/3/R14-18102_kapa-NGv3-PE100-NGv3-sort-3_190333063_198022430-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/3/R14-18102_kapa-NGv3-PE100-NGv3-sort-3_190333063_198022430-prep-prealign-realign.intervals -L 3:190333064-198022430 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/3/tx/tmpr0IusV/R14-18102_kapa-NGv3-PE100-NGv3-sort-3_190333063_198022430-prep.bam
[2016-04-14T23:25Z] INFO  16:25:43,027 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:25Z] INFO  16:25:43,028 HelpFormatter - Date/Time: 2016/04/14 16:25:43
[2016-04-14T23:25Z] INFO  16:25:43,028 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:25Z] INFO  16:25:43,028 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:25Z] INFO  16:25:43,057 ProgressMeter -            done    127339.0    11.0 s      92.0 s      100.0%    11.0 s       0.0 s
[2016-04-14T23:25Z] INFO  16:25:43,058 ProgressMeter - Total runtime 11.80 secs, 0.20 min, 0.00 hours
[2016-04-14T23:25Z] INFO  16:25:43,062 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 127339 total reads (0.00%)
[2016-04-14T23:25Z] INFO  16:25:43,063 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:25Z] INFO  16:25:43,064 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:25Z] INFO  16:25:43,064 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:25Z] INFO  16:25:43,247 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:25Z] INFO  16:25:43,347 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:25Z] INFO  16:25:43,357 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:25Z] INFO  16:25:43,418 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-14T23:25Z] INFO  16:25:43,770 IntervalUtils - Processing 7689367 bp from intervals
[2016-04-14T23:25Z] WARN  16:25:43,775 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:25Z] INFO  16:25:43,830 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:25Z] GATK: realign ('3', 127770401, 143293035) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:25Z] INFO  16:25:43,859 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:25Z] INFO  16:25:43,970 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:25Z] INFO  16:25:43,973 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:25Z] INFO  16:25:43,974 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:25Z] INFO  16:25:43,974 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:25Z] INFO  16:25:44,105 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:25Z] INFO  16:25:44,190 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:25Z] INFO  16:25:44,496 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:25Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-3_158970515_174577240-prep.bam
[2016-04-14T23:25Z] INFO  16:25:44,754 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:25Z] INFO  16:25:44,758 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:25Z] INFO  16:25:44,758 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:25Z] INFO  16:25:44,758 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:25Z] INFO  16:25:44,763 HelpFormatter - Program Args: -T PrintReads -L 4:134075462-150351181 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/4/tx/tmpoY0t7r/R14-18102_kapa-NGv3-PE100-NGv3-sort-4_134075461_150351181-prep-prealign.bam
[2016-04-14T23:25Z] INFO  16:25:44,773 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:25Z] INFO  16:25:44,784 HelpFormatter - Date/Time: 2016/04/14 16:25:44
[2016-04-14T23:25Z] INFO  16:25:44,785 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:25Z] INFO  16:25:44,786 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:25Z] GATK pre-alignment ('4', 150354547, 165878648) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:25Z] INFO  16:25:45,030 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:25Z] INFO  16:25:46,308 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-14T23:25Z] INFO  16:25:46,373 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:25Z] INFO  16:25:46,394 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:25Z] INFO  16:25:46,429 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.04
[2016-04-14T23:25Z] INFO  16:25:46,444 IntervalUtils - Processing 16275720 bp from intervals
[2016-04-14T23:25Z] INFO  16:25:46,513 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:25Z] INFO  16:25:46,701 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:25Z] INFO  16:25:46,704 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:25Z] INFO  16:25:46,705 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:25Z] INFO  16:25:46,706 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:25Z] INFO  16:25:46,711 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/3/R14-18102_kapa-NGv3-PE100-NGv3-sort-3_127770401_143293035-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/3/R14-18102_kapa-NGv3-PE100-NGv3-sort-3_127770401_143293035-prep-prealign-realign.intervals -L 3:127770402-143293035 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/3/tx/tmpxta0MF/R14-18102_kapa-NGv3-PE100-NGv3-sort-3_127770401_143293035-prep.bam
[2016-04-14T23:25Z] INFO  16:25:46,726 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:25Z] INFO  16:25:46,726 HelpFormatter - Date/Time: 2016/04/14 16:25:46
[2016-04-14T23:25Z] INFO  16:25:46,727 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:25Z] INFO  16:25:46,727 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:25Z] INFO  16:25:46,764 ProgressMeter -      4:79430041    200002.0    30.0 s       2.5 m       71.5%    41.0 s      11.0 s
[2016-04-14T23:25Z] INFO  16:25:46,839 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:25Z] INFO  16:25:46,839 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:25Z] INFO  16:25:46,840 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:25Z] INFO  16:25:46,840 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:25Z] INFO  16:25:46,853 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:25Z] INFO  16:25:46,943 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:25Z] INFO  16:25:46,992 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:25Z] INFO  16:25:47,063 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:25Z] INFO  16:25:47,072 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:25Z] INFO  16:25:47,144 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-14T23:25Z] INFO  16:25:47,465 IntervalUtils - Processing 15522634 bp from intervals
[2016-04-14T23:25Z] WARN  16:25:47,470 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:25Z] INFO  16:25:47,514 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@41fd9d8e
[2016-04-14T23:25Z] INFO  16:25:47,539 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:25Z] INFO  16:25:47,624 ProgressMeter -            done    165766.0    27.0 s       2.8 m      100.0%    27.0 s       0.0 s
[2016-04-14T23:25Z] INFO  16:25:47,625 ProgressMeter - Total runtime 27.65 secs, 0.46 min, 0.01 hours
[2016-04-14T23:25Z] INFO  16:25:47,626 MicroScheduler - 118 reads were filtered out during the traversal out of approximately 165884 total reads (0.07%)
[2016-04-14T23:25Z] INFO  16:25:47,627 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:25Z] INFO  16:25:47,628 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:25Z] INFO  16:25:47,628 MicroScheduler -   -> 118 reads (0.07% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:25Z] INFO  16:25:47,666 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:25Z] INFO  16:25:47,667 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:25Z] INFO  16:25:47,668 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:25Z] INFO  16:25:47,668 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:25Z] INFO  16:25:47,849 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:25Z] INFO  16:25:47,941 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:25Z] INFO  16:25:47,945 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:25Z] INFO  16:25:47,945 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:25Z] INFO  16:25:47,946 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:25Z] INFO  16:25:47,950 HelpFormatter - Program Args: -T PrintReads -L 4:150354548-165878648 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/4/tx/tmpCYs640/R14-18102_kapa-NGv3-PE100-NGv3-sort-4_150354547_165878648-prep-prealign.bam
[2016-04-14T23:25Z] INFO  16:25:47,960 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:25Z] INFO  16:25:47,960 HelpFormatter - Date/Time: 2016/04/14 16:25:47
[2016-04-14T23:25Z] INFO  16:25:47,961 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:25Z] INFO  16:25:47,962 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:25Z] INFO  16:25:47,998 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:25Z] INFO  16:25:48,156 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:25Z] INFO  16:25:49,157 ProgressMeter -            done   1.5628644E7    16.0 s       1.0 s      100.0%    16.0 s       0.0 s
[2016-04-14T23:25Z] INFO  16:25:49,158 ProgressMeter - Total runtime 16.37 secs, 0.27 min, 0.00 hours
[2016-04-14T23:25Z] INFO  16:25:49,162 MicroScheduler - 9758 reads were filtered out during the traversal out of approximately 112251 total reads (8.69%)
[2016-04-14T23:25Z] INFO  16:25:49,163 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:25Z] INFO  16:25:49,164 MicroScheduler -   -> 452 reads (0.40% of total) failing BadMateFilter
[2016-04-14T23:25Z] INFO  16:25:49,164 MicroScheduler -   -> 8965 reads (7.99% of total) failing DuplicateReadFilter
[2016-04-14T23:25Z] INFO  16:25:49,165 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-14T23:25Z] INFO  16:25:49,166 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:25Z] INFO  16:25:49,166 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-14T23:25Z] INFO  16:25:49,167 MicroScheduler -   -> 341 reads (0.30% of total) failing MappingQualityZeroFilter
[2016-04-14T23:25Z] INFO  16:25:49,167 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:25Z] INFO  16:25:49,168 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-14T23:25Z] INFO  16:25:49,169 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-14T23:25Z] INFO  16:25:49,345 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:25Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-4_83857133_99393738-prep-prealign.bam
[2016-04-14T23:25Z] INFO  16:25:49,406 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-14T23:25Z] INFO  16:25:49,456 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:25Z] INFO  16:25:49,465 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:25Z] INFO  16:25:49,511 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-14T23:25Z] INFO  16:25:49,546 IntervalUtils - Processing 15524101 bp from intervals
[2016-04-14T23:25Z] INFO  16:25:49,637 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:25Z] INFO  16:25:49,878 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:25Z] INFO  16:25:49,879 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:25Z] INFO  16:25:49,879 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:25Z] INFO  16:25:49,880 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:25Z] INFO  16:25:49,898 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:25Z] GATK RealignerTargetCreator: R14-18102_kapa-NGv3-PE100-NGv3-sort-4_83857133_99393738-prep-prealign.bam 4:83857134-99393738
[2016-04-14T23:25Z] GATK: RealignerTargetCreator
[2016-04-14T23:25Z] INFO  16:25:50,024 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:25Z] INFO  16:25:50,557 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:25Z] GATK: realign ('4', 52709749, 68338393) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:25Z] INFO  16:25:50,690 ProgressMeter -            done   1.5512391E7    20.0 s       1.0 s      100.0%    20.0 s       0.0 s
[2016-04-14T23:25Z] INFO  16:25:50,691 ProgressMeter - Total runtime 20.28 secs, 0.34 min, 0.01 hours
[2016-04-14T23:25Z] INFO  16:25:50,696 MicroScheduler - 24852 reads were filtered out during the traversal out of approximately 287721 total reads (8.64%)
[2016-04-14T23:25Z] INFO  16:25:50,697 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:25Z] INFO  16:25:50,698 MicroScheduler -   -> 683 reads (0.24% of total) failing BadMateFilter
[2016-04-14T23:25Z] INFO  16:25:50,699 MicroScheduler -   -> 23336 reads (8.11% of total) failing DuplicateReadFilter
[2016-04-14T23:25Z] INFO  16:25:50,699 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-14T23:25Z] INFO  16:25:50,700 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:25Z] INFO  16:25:50,701 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-14T23:25Z] INFO  16:25:50,702 MicroScheduler -   -> 833 reads (0.29% of total) failing MappingQualityZeroFilter
[2016-04-14T23:25Z] INFO  16:25:50,702 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:25Z] INFO  16:25:50,703 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-14T23:25Z] INFO  16:25:50,704 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-14T23:25Z] INFO  16:25:51,039 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@7172f77a
[2016-04-14T23:25Z] INFO  16:25:51,172 ProgressMeter -            done    278584.0    34.0 s       2.1 m      100.0%    34.0 s       0.0 s
[2016-04-14T23:25Z] INFO  16:25:51,172 ProgressMeter - Total runtime 34.43 secs, 0.57 min, 0.01 hours
[2016-04-14T23:25Z] INFO  16:25:51,173 MicroScheduler - 156 reads were filtered out during the traversal out of approximately 278740 total reads (0.06%)
[2016-04-14T23:25Z] INFO  16:25:51,173 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:25Z] INFO  16:25:51,174 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:25Z] INFO  16:25:51,174 MicroScheduler -   -> 156 reads (0.06% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:25Z] INFO  16:25:51,220 ProgressMeter -       4:9231847    400006.0    60.0 s       2.5 m       59.5%   100.0 s      40.0 s
[2016-04-14T23:25Z] INFO  16:25:51,726 ProgressMeter -            done    114454.0    11.0 s      98.0 s      100.0%    11.0 s       0.0 s
[2016-04-14T23:25Z] INFO  16:25:51,726 ProgressMeter - Total runtime 11.22 secs, 0.19 min, 0.00 hours
[2016-04-14T23:25Z] INFO  16:25:51,730 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 114454 total reads (0.00%)
[2016-04-14T23:25Z] INFO  16:25:51,730 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:25Z] INFO  16:25:51,730 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:25Z] INFO  16:25:51,731 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:25Z] INFO  16:25:52,093 ProgressMeter -            done   1.6639905E7    18.0 s       1.0 s      100.0%    18.0 s       0.0 s
[2016-04-14T23:25Z] INFO  16:25:52,094 ProgressMeter - Total runtime 18.03 secs, 0.30 min, 0.01 hours
[2016-04-14T23:25Z] INFO  16:25:52,099 MicroScheduler - 17812 reads were filtered out during the traversal out of approximately 183904 total reads (9.69%)
[2016-04-14T23:25Z] INFO  16:25:52,105 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:25Z] INFO  16:25:52,108 MicroScheduler -   -> 736 reads (0.40% of total) failing BadMateFilter
[2016-04-14T23:25Z] INFO  16:25:52,108 MicroScheduler -   -> 14044 reads (7.64% of total) failing DuplicateReadFilter
[2016-04-14T23:25Z] INFO  16:25:52,109 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-14T23:25Z] INFO  16:25:52,109 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:25Z] INFO  16:25:52,109 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-14T23:25Z] INFO  16:25:52,109 MicroScheduler -   -> 3032 reads (1.65% of total) failing MappingQualityZeroFilter
[2016-04-14T23:25Z] INFO  16:25:52,110 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:25Z] INFO  16:25:52,110 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-14T23:25Z] INFO  16:25:52,110 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-14T23:25Z] INFO  16:25:52,236 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:25Z] GATK: realign ('3', 174814579, 190326970) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:25Z] INFO  16:25:52,797 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@5fe152b7
[2016-04-14T23:25Z] INFO  16:25:52,846 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:25Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-4_68340604_83852298-prep-prealign.bam
[2016-04-14T23:25Z] INFO  16:25:52,933 ProgressMeter -            done    178257.0    23.0 s       2.2 m      100.0%    23.0 s       0.0 s
[2016-04-14T23:25Z] INFO  16:25:52,933 ProgressMeter - Total runtime 23.77 secs, 0.40 min, 0.01 hours
[2016-04-14T23:25Z] INFO  16:25:52,934 MicroScheduler - 135 reads were filtered out during the traversal out of approximately 178392 total reads (0.08%)
[2016-04-14T23:25Z] INFO  16:25:52,934 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:25Z] INFO  16:25:52,934 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:25Z] INFO  16:25:52,934 MicroScheduler -   -> 135 reads (0.08% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:25Z] INFO  16:25:53,046 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:25Z] INFO  16:25:53,049 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:25Z] INFO  16:25:53,049 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:25Z] INFO  16:25:53,050 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:25Z] INFO  16:25:53,054 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/4/R14-18102_kapa-NGv3-PE100-NGv3-sort-4_83857133_99393738-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/4/tx/tmpljP8Qu/R14-18102_kapa-NGv3-PE100-NGv3-sort-4_83857133_99393738-prep-prealign-realign.intervals -l INFO -L 4:83857134-99393738 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-14T23:25Z] INFO  16:25:53,067 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:25Z] INFO  16:25:53,067 HelpFormatter - Date/Time: 2016/04/14 16:25:53
[2016-04-14T23:25Z] INFO  16:25:53,068 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:25Z] INFO  16:25:53,069 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:25Z] INFO  16:25:53,169 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:25Z] INFO  16:25:53,241 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:25Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-4_15512869_31144471-prep.bam
[2016-04-14T23:25Z] INFO  16:25:53,431 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-14T23:25Z] INFO  16:25:53,444 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:25Z] INFO  16:25:53,532 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:25Z] INFO  16:25:53,535 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:25Z] INFO  16:25:53,529 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-14T23:25Z] INFO  16:25:53,536 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:25Z] INFO  16:25:53,536 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:25Z] INFO  16:25:53,540 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/4/R14-18102_kapa-NGv3-PE100-NGv3-sort-4_52709749_68338393-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/4/R14-18102_kapa-NGv3-PE100-NGv3-sort-4_52709749_68338393-prep-prealign-realign.intervals -L 4:52709750-68338393 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/4/tx/tmpacoX4r/R14-18102_kapa-NGv3-PE100-NGv3-sort-4_52709749_68338393-prep.bam
[2016-04-14T23:25Z] INFO  16:25:53,559 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:25Z] INFO  16:25:53,560 HelpFormatter - Date/Time: 2016/04/14 16:25:53
[2016-04-14T23:25Z] INFO  16:25:53,560 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:25Z] INFO  16:25:53,561 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:25Z] INFO  16:25:53,608 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:25Z] INFO  16:25:53,631 ProgressMeter -      3:46875628    400011.0    30.0 s      75.0 s       98.4%    30.0 s       0.0 s
[2016-04-14T23:25Z] GATK: realign ('4', 36069528, 52709433) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:25Z] GATK pre-alignment ('4', 165889318, 183245405) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:25Z] INFO  16:25:53,755 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:25Z] GATK RealignerTargetCreator: R14-18102_kapa-NGv3-PE100-NGv3-sort-4_68340604_83852298-prep-prealign.bam 4:68340605-83852298
[2016-04-14T23:25Z] GATK: RealignerTargetCreator
[2016-04-14T23:25Z] INFO  16:25:53,912 IntervalUtils - Processing 15536605 bp from intervals
[2016-04-14T23:25Z] WARN  16:25:53,917 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:25Z] INFO  16:25:53,934 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:25Z] INFO  16:25:53,942 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:25Z] INFO  16:25:54,027 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-14T23:25Z] INFO  16:25:54,045 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:25Z] INFO  16:25:54,258 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:25Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-4_115584857_134074404-prep-prealign.bam
[2016-04-14T23:25Z] INFO  16:25:54,334 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:25Z] INFO  16:25:54,346 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:25Z] INFO  16:25:54,347 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:25Z] INFO  16:25:54,348 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-14T23:25Z] INFO  16:25:54,503 IntervalUtils - Processing 15628644 bp from intervals
[2016-04-14T23:25Z] WARN  16:25:54,508 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:25Z] INFO  16:25:54,587 ProgressMeter -            done    466384.0    30.0 s      66.0 s      100.0%    30.0 s       0.0 s
[2016-04-14T23:25Z] INFO  16:25:54,587 ProgressMeter - Total runtime 30.97 secs, 0.52 min, 0.01 hours
[2016-04-14T23:25Z] INFO  16:25:54,591 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 466384 total reads (0.00%)
[2016-04-14T23:25Z] INFO  16:25:54,591 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:25Z] INFO  16:25:54,591 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:25Z] INFO  16:25:54,591 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:25Z] INFO  16:25:54,609 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:25Z] INFO  16:25:54,778 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:25Z] INFO  16:25:54,779 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:25Z] INFO  16:25:54,780 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:25Z] INFO  16:25:54,780 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:25Z] INFO  16:25:54,798 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:25Z] INFO  16:25:54,801 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:25Z] INFO  16:25:54,802 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:25Z] INFO  16:25:54,802 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:25Z] INFO  16:25:54,807 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/3/R14-18102_kapa-NGv3-PE100-NGv3-sort-3_174814579_190326970-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/3/R14-18102_kapa-NGv3-PE100-NGv3-sort-3_174814579_190326970-prep-prealign-realign.intervals -L 3:174814580-190326970 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/3/tx/tmpRBugMt/R14-18102_kapa-NGv3-PE100-NGv3-sort-3_174814579_190326970-prep.bam
[2016-04-14T23:25Z] INFO  16:25:54,827 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:25Z] INFO  16:25:54,828 HelpFormatter - Date/Time: 2016/04/14 16:25:54
[2016-04-14T23:25Z] INFO  16:25:54,828 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:25Z] INFO  16:25:54,829 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:25Z] INFO  16:25:55,004 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:25Z] GATK RealignerTargetCreator: R14-18102_kapa-NGv3-PE100-NGv3-sort-4_115584857_134074404-prep-prealign.bam 4:115584858-134074404
[2016-04-14T23:25Z] GATK: RealignerTargetCreator
[2016-04-14T23:25Z] INFO  16:25:55,044 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:25Z] INFO  16:25:55,144 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:25Z] INFO  16:25:55,235 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:25Z] INFO  16:25:55,264 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:25Z] INFO  16:25:55,348 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@52f3b59
[2016-04-14T23:25Z] INFO  16:25:55,357 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.09
[2016-04-14T23:25Z] INFO  16:25:55,521 ProgressMeter -            done    197626.0    27.0 s       2.3 m      100.0%    27.0 s       0.0 s
[2016-04-14T23:25Z] INFO  16:25:55,522 ProgressMeter - Total runtime 27.26 secs, 0.45 min, 0.01 hours
[2016-04-14T23:25Z] INFO  16:25:55,522 MicroScheduler - 133 reads were filtered out during the traversal out of approximately 197759 total reads (0.07%)
[2016-04-14T23:25Z] INFO  16:25:55,523 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:25Z] INFO  16:25:55,523 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:25Z] INFO  16:25:55,523 MicroScheduler -   -> 133 reads (0.07% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:25Z] INFO  16:25:55,681 IntervalUtils - Processing 15512391 bp from intervals
[2016-04-14T23:25Z] WARN  16:25:55,686 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:25Z] INFO  16:25:55,758 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:25Z] INFO  16:25:55,926 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:25Z] INFO  16:25:55,927 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:25Z] INFO  16:25:55,928 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:25Z] INFO  16:25:55,928 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:25Z] INFO  16:25:56,061 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:25Z] INFO  16:25:56,225 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:25Z] INFO  16:25:56,229 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:25Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-3_31617887_47127804-prep.bam
[2016-04-14T23:25Z] INFO  16:25:56,324 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:25Z] INFO  16:25:56,328 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:25Z] INFO  16:25:56,328 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:25Z] INFO  16:25:56,329 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:25Z] INFO  16:25:56,333 HelpFormatter - Program Args: -T PrintReads -L 4:165889319-183245405 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/4/tx/tmpky5Mat/R14-18102_kapa-NGv3-PE100-NGv3-sort-4_165889318_183245405-prep-prealign.bam
[2016-04-14T23:25Z] INFO  16:25:56,348 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:25Z] INFO  16:25:56,348 HelpFormatter - Date/Time: 2016/04/14 16:25:56
[2016-04-14T23:25Z] INFO  16:25:56,349 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:25Z] INFO  16:25:56,350 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:25Z] INFO  16:25:56,527 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:25Z] INFO  16:25:56,740 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:25Z] INFO  16:25:56,743 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:25Z] INFO  16:25:56,744 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:25Z] INFO  16:25:56,745 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:25Z] INFO  16:25:56,749 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/4/R14-18102_kapa-NGv3-PE100-NGv3-sort-4_36069528_52709433-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/4/R14-18102_kapa-NGv3-PE100-NGv3-sort-4_36069528_52709433-prep-prealign-realign.intervals -L 4:36069529-52709433 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/4/tx/tmpv8lIp7/R14-18102_kapa-NGv3-PE100-NGv3-sort-4_36069528_52709433-prep.bam
[2016-04-14T23:25Z] INFO  16:25:56,790 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:25Z] INFO  16:25:56,791 HelpFormatter - Date/Time: 2016/04/14 16:25:56
[2016-04-14T23:25Z] INFO  16:25:56,792 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:25Z] INFO  16:25:56,792 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:25Z] INFO  16:25:56,865 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:25Z] INFO  16:25:56,869 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:25Z] INFO  16:25:56,869 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:25Z] INFO  16:25:56,870 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:25Z] INFO  16:25:56,875 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/4/R14-18102_kapa-NGv3-PE100-NGv3-sort-4_68340604_83852298-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/4/tx/tmprFCAht/R14-18102_kapa-NGv3-PE100-NGv3-sort-4_68340604_83852298-prep-prealign-realign.intervals -l INFO -L 4:68340605-83852298 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-14T23:25Z] INFO  16:25:56,895 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:25Z] INFO  16:25:56,896 HelpFormatter - Date/Time: 2016/04/14 16:25:56
[2016-04-14T23:25Z] INFO  16:25:56,896 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:25Z] INFO  16:25:56,897 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:25Z] INFO  16:25:56,930 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:25Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-4_99397339_115544957-prep-prealign.bam
[2016-04-14T23:25Z] INFO  16:25:57,045 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:25Z] INFO  16:25:57,051 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:25Z] INFO  16:25:57,187 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:25Z] INFO  16:25:57,198 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:25Z] INFO  16:25:57,263 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-14T23:25Z] INFO  16:25:57,292 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-14T23:25Z] INFO  16:25:57,313 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:25Z] INFO  16:25:57,380 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-14T23:25Z] GATK RealignerTargetCreator: R14-18102_kapa-NGv3-PE100-NGv3-sort-4_99397339_115544957-prep-prealign.bam 4:99397340-115544957
[2016-04-14T23:25Z] GATK: RealignerTargetCreator
[2016-04-14T23:25Z] INFO  16:25:57,588 ProgressMeter -            done    360143.0    24.0 s      68.0 s      100.0%    24.0 s       0.0 s
[2016-04-14T23:25Z] INFO  16:25:57,588 ProgressMeter - Total runtime 24.58 secs, 0.41 min, 0.01 hours
[2016-04-14T23:25Z] INFO  16:25:57,599 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 360143 total reads (0.00%)
[2016-04-14T23:25Z] INFO  16:25:57,600 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:25Z] INFO  16:25:57,600 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:25Z] INFO  16:25:57,600 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:25Z] INFO  16:25:57,601 IntervalUtils - Processing 16639905 bp from intervals
[2016-04-14T23:25Z] WARN  16:25:57,606 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:25Z] GATK pre-alignment ('4', 183267803, 191154276) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:25Z] INFO  16:25:57,682 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:25Z] INFO  16:25:57,798 IntervalUtils - Processing 15511694 bp from intervals
[2016-04-14T23:25Z] WARN  16:25:57,804 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:25Z] INFO  16:25:57,835 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:25Z] INFO  16:25:57,836 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:25Z] INFO  16:25:57,837 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:25Z] INFO  16:25:57,838 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:25Z] INFO  16:25:57,889 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:25Z] INFO  16:25:57,963 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-14T23:25Z] INFO  16:25:58,028 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:25Z] INFO  16:25:58,041 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:25Z] INFO  16:25:58,055 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:25Z] INFO  16:25:58,058 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:25Z] INFO  16:25:58,059 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:25Z] INFO  16:25:58,059 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:25Z] INFO  16:25:58,064 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/4/R14-18102_kapa-NGv3-PE100-NGv3-sort-4_115584857_134074404-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/4/tx/tmpAmYJ9m/R14-18102_kapa-NGv3-PE100-NGv3-sort-4_115584857_134074404-prep-prealign-realign.intervals -l INFO -L 4:115584858-134074404 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-14T23:25Z] INFO  16:25:58,065 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:25Z] INFO  16:25:58,072 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:25Z] INFO  16:25:58,073 HelpFormatter - Date/Time: 2016/04/14 16:25:58
[2016-04-14T23:25Z] INFO  16:25:58,073 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:25Z] INFO  16:25:58,073 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:25Z] INFO  16:25:58,129 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-14T23:25Z] INFO  16:25:58,144 IntervalUtils - Processing 17356087 bp from intervals
[2016-04-14T23:25Z] INFO  16:25:58,152 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:25Z] INFO  16:25:58,153 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:25Z] INFO  16:25:58,154 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:25Z] INFO  16:25:58,155 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-14T23:25Z] INFO  16:25:58,220 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:25Z] INFO  16:25:58,223 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:25Z] INFO  16:25:58,232 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:25Z] INFO  16:25:58,467 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-14T23:25Z] INFO  16:25:58,477 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:25Z] INFO  16:25:58,537 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-14T23:25Z] INFO  16:25:58,589 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:25Z] INFO  16:25:58,591 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:25Z] INFO  16:25:58,591 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:25Z] INFO  16:25:58,592 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:25Z] INFO  16:25:58,617 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:25Z] INFO  16:25:58,815 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:25Z] INFO  16:25:58,944 IntervalUtils - Processing 18489547 bp from intervals
[2016-04-14T23:25Z] WARN  16:25:58,958 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:25Z] INFO  16:25:59,040 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:25Z] INFO  16:25:59,151 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:25Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-3_112188604_127703121-prep.bam
[2016-04-14T23:25Z] INFO  16:25:59,222 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:25Z] INFO  16:25:59,223 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:25Z] INFO  16:25:59,224 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:25Z] INFO  16:25:59,225 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-14T23:26Z] GATK pre-alignment ('5', 0, 15580921) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:26Z] INFO  16:26:00,722 ProgressMeter -      3:62648033   1.550643E7    30.0 s       1.0 s      100.0%    30.0 s       0.0 s
[2016-04-14T23:26Z] INFO  16:26:00,803 ProgressMeter -            done    222214.0    16.0 s      75.0 s       99.1%    16.0 s       0.0 s
[2016-04-14T23:26Z] INFO  16:26:00,803 ProgressMeter - Total runtime 16.83 secs, 0.28 min, 0.00 hours
[2016-04-14T23:26Z] INFO  16:26:00,806 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 222214 total reads (0.00%)
[2016-04-14T23:26Z] INFO  16:26:00,807 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:26Z] INFO  16:26:00,807 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:26Z] INFO  16:26:00,807 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:26Z] INFO  16:26:00,818 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:26Z] INFO  16:26:00,822 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:26Z] INFO  16:26:00,822 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:26Z] INFO  16:26:00,823 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:26Z] INFO  16:26:00,827 HelpFormatter - Program Args: -T PrintReads -L 4:183267804-191154276 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/4/tx/tmpXtsR6i/R14-18102_kapa-NGv3-PE100-NGv3-sort-4_183267803_191154276-prep-prealign.bam
[2016-04-14T23:26Z] INFO  16:26:00,863 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:26Z] INFO  16:26:00,863 HelpFormatter - Date/Time: 2016/04/14 16:26:00
[2016-04-14T23:26Z] INFO  16:26:00,863 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:26Z] INFO  16:26:00,863 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:26Z] INFO  16:26:00,902 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:26Z] INFO  16:26:00,905 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:26Z] INFO  16:26:00,906 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:26Z] INFO  16:26:00,906 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:26Z] INFO  16:26:00,911 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/4/R14-18102_kapa-NGv3-PE100-NGv3-sort-4_99397339_115544957-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/4/tx/tmpTJuFjU/R14-18102_kapa-NGv3-PE100-NGv3-sort-4_99397339_115544957-prep-prealign-realign.intervals -l INFO -L 4:99397340-115544957 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-14T23:26Z] INFO  16:26:00,924 ProgressMeter -            done   1.5518467E7    30.0 s       1.0 s      100.0%    30.0 s       0.0 s
[2016-04-14T23:26Z] INFO  16:26:00,925 ProgressMeter - Total runtime 30.23 secs, 0.50 min, 0.01 hours
[2016-04-14T23:26Z] INFO  16:26:00,930 MicroScheduler - 63690 reads were filtered out during the traversal out of approximately 750240 total reads (8.49%)
[2016-04-14T23:26Z] INFO  16:26:00,931 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:26Z] INFO  16:26:00,932 MicroScheduler -   -> 1428 reads (0.19% of total) failing BadMateFilter
[2016-04-14T23:26Z] INFO  16:26:00,932 MicroScheduler -   -> 60536 reads (8.07% of total) failing DuplicateReadFilter
[2016-04-14T23:26Z] INFO  16:26:00,933 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-14T23:26Z] INFO  16:26:00,934 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:26Z] INFO  16:26:00,934 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-14T23:26Z] INFO  16:26:00,935 MicroScheduler -   -> 1726 reads (0.23% of total) failing MappingQualityZeroFilter
[2016-04-14T23:26Z] INFO  16:26:00,935 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:26Z] INFO  16:26:00,936 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-14T23:26Z] INFO  16:26:00,937 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-14T23:26Z] INFO  16:26:00,943 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:26Z] INFO  16:26:00,944 HelpFormatter - Date/Time: 2016/04/14 16:26:00
[2016-04-14T23:26Z] INFO  16:26:00,945 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:26Z] INFO  16:26:00,945 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:26Z] INFO  16:26:01,070 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:26Z] INFO  16:26:01,105 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:26Z] INFO  16:26:01,323 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-14T23:26Z] INFO  16:26:01,339 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:26Z] INFO  16:26:01,397 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-14T23:26Z] INFO  16:26:01,832 IntervalUtils - Processing 16147618 bp from intervals
[2016-04-14T23:26Z] WARN  16:26:01,847 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:26Z] INFO  16:26:01,975 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:26Z] INFO  16:26:02,225 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:26Z] INFO  16:26:02,227 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:26Z] INFO  16:26:02,227 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:26Z] INFO  16:26:02,228 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-14T23:26Z] INFO  16:26:02,295 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-14T23:26Z] INFO  16:26:02,355 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:26Z] INFO  16:26:02,363 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:26Z] INFO  16:26:02,407 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.04
[2016-04-14T23:26Z] INFO  16:26:02,422 IntervalUtils - Processing 7886473 bp from intervals
[2016-04-14T23:26Z] INFO  16:26:02,451 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:26Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-3_190333063_198022430-prep.bam
[2016-04-14T23:26Z] INFO  16:26:02,504 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:26Z] INFO  16:26:02,590 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:26Z] GATK: realign ('3', 47129602, 62648069) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:26Z] INFO  16:26:02,789 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:26Z] INFO  16:26:02,790 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:26Z] INFO  16:26:02,791 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:26Z] INFO  16:26:02,792 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:26Z] INFO  16:26:02,805 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:26Z] INFO  16:26:02,933 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:26Z] GATK pre-alignment ('5', 15616091, 31267808) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:26Z] INFO  16:26:03,389 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:26Z] INFO  16:26:03,392 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:26Z] INFO  16:26:03,393 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:26Z] INFO  16:26:03,393 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:26Z] INFO  16:26:03,398 HelpFormatter - Program Args: -T PrintReads -L 5:1-15580921 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/5/tx/tmpD0R8Tp/R14-18102_kapa-NGv3-PE100-NGv3-sort-5_0_15580921-prep-prealign.bam
[2016-04-14T23:26Z] INFO  16:26:03,443 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:26Z] INFO  16:26:03,444 HelpFormatter - Date/Time: 2016/04/14 16:26:03
[2016-04-14T23:26Z] INFO  16:26:03,444 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:26Z] INFO  16:26:03,445 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:26Z] INFO  16:26:03,642 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:26Z] INFO  16:26:04,916 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-14T23:26Z] INFO  16:26:04,970 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@6834dd3c
[2016-04-14T23:26Z] INFO  16:26:04,972 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:26Z] INFO  16:26:04,981 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:26Z] INFO  16:26:05,041 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-14T23:26Z] INFO  16:26:05,055 IntervalUtils - Processing 15580921 bp from intervals
[2016-04-14T23:26Z] INFO  16:26:05,178 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:26Z] INFO  16:26:05,248 ProgressMeter -            done    119491.0    18.0 s       2.6 m       99.5%    18.0 s       0.0 s
[2016-04-14T23:26Z] INFO  16:26:05,249 ProgressMeter - Total runtime 18.41 secs, 0.31 min, 0.01 hours
[2016-04-14T23:26Z] INFO  16:26:05,249 MicroScheduler - 104 reads were filtered out during the traversal out of approximately 119595 total reads (0.09%)
[2016-04-14T23:26Z] INFO  16:26:05,250 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:26Z] INFO  16:26:05,250 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:26Z] INFO  16:26:05,250 MicroScheduler -   -> 104 reads (0.09% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:26Z] INFO  16:26:05,516 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:26Z] INFO  16:26:05,518 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:26Z] INFO  16:26:05,519 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:26Z] INFO  16:26:05,519 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:26Z] INFO  16:26:05,534 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:26Z] INFO  16:26:05,601 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:26Z] INFO  16:26:05,604 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:26Z] INFO  16:26:05,605 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:26Z] INFO  16:26:05,605 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:26Z] INFO  16:26:05,610 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/3/R14-18102_kapa-NGv3-PE100-NGv3-sort-3_47129602_62648069-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/3/R14-18102_kapa-NGv3-PE100-NGv3-sort-3_47129602_62648069-prep-prealign-realign.intervals -L 3:47129603-62648069 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/3/tx/tmp21avuU/R14-18102_kapa-NGv3-PE100-NGv3-sort-3_47129602_62648069-prep.bam
[2016-04-14T23:26Z] INFO  16:26:05,634 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:26Z] INFO  16:26:05,635 HelpFormatter - Date/Time: 2016/04/14 16:26:05
[2016-04-14T23:26Z] INFO  16:26:05,639 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:26Z] INFO  16:26:05,640 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:26Z] INFO  16:26:05,696 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:26Z] INFO  16:26:05,868 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:26Z] INFO  16:26:06,028 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:26Z] INFO  16:26:06,046 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:26Z] INFO  16:26:06,148 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.10
[2016-04-14T23:26Z] INFO  16:26:06,344 ProgressMeter -            done    111796.0    11.0 s     103.0 s       99.8%    11.0 s       0.0 s
[2016-04-14T23:26Z] INFO  16:26:06,345 ProgressMeter - Total runtime 11.57 secs, 0.19 min, 0.00 hours
[2016-04-14T23:26Z] INFO  16:26:06,349 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 111796 total reads (0.00%)
[2016-04-14T23:26Z] INFO  16:26:06,349 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:26Z] INFO  16:26:06,349 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:26Z] INFO  16:26:06,350 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:26Z] INFO  16:26:06,348 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:26Z] INFO  16:26:06,353 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:26Z] INFO  16:26:06,353 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:26Z] INFO  16:26:06,354 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:26Z] INFO  16:26:06,358 HelpFormatter - Program Args: -T PrintReads -L 5:15616092-31267808 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/5/tx/tmp8128_r/R14-18102_kapa-NGv3-PE100-NGv3-sort-5_15616091_31267808-prep-prealign.bam
[2016-04-14T23:26Z] INFO  16:26:06,367 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:26Z] INFO  16:26:06,369 HelpFormatter - Date/Time: 2016/04/14 16:26:06
[2016-04-14T23:26Z] INFO  16:26:06,369 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:26Z] INFO  16:26:06,370 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:26Z] INFO  16:26:06,558 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:26Z] INFO  16:26:06,574 IntervalUtils - Processing 15518467 bp from intervals
[2016-04-14T23:26Z] WARN  16:26:06,586 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:26Z] INFO  16:26:06,704 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:26Z] INFO  16:26:06,864 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:26Z] INFO  16:26:06,865 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:26Z] INFO  16:26:06,866 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:26Z] INFO  16:26:06,867 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:26Z] INFO  16:26:06,889 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:26Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-4_134075461_150351181-prep-prealign.bam
[2016-04-14T23:26Z] INFO  16:26:07,068 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:26Z] INFO  16:26:07,211 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:26Z] GATK RealignerTargetCreator: R14-18102_kapa-NGv3-PE100-NGv3-sort-4_134075461_150351181-prep-prealign.bam 4:134075462-150351181
[2016-04-14T23:26Z] GATK: RealignerTargetCreator
[2016-04-14T23:26Z] INFO  16:26:07,645 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-14T23:26Z] INFO  16:26:07,719 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:26Z] INFO  16:26:07,729 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:26Z] INFO  16:26:07,779 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-14T23:26Z] INFO  16:26:07,794 IntervalUtils - Processing 15651717 bp from intervals
[2016-04-14T23:26Z] INFO  16:26:07,887 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:26Z] INFO  16:26:08,026 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:26Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-4_52709749_68338393-prep.bam
[2016-04-14T23:26Z] INFO  16:26:08,261 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:26Z] INFO  16:26:08,261 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:26Z] INFO  16:26:08,262 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:26Z] INFO  16:26:08,262 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:26Z] INFO  16:26:08,282 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:26Z] GATK pre-alignment ('5', 31294068, 49695124) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:26Z] INFO  16:26:08,531 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:26Z] INFO  16:26:10,212 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:26Z] INFO  16:26:10,216 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:26Z] INFO  16:26:10,216 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:26Z] INFO  16:26:10,217 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:26Z] INFO  16:26:10,222 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/4/R14-18102_kapa-NGv3-PE100-NGv3-sort-4_134075461_150351181-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/4/tx/tmpRoClFU/R14-18102_kapa-NGv3-PE100-NGv3-sort-4_134075461_150351181-prep-prealign-realign.intervals -l INFO -L 4:134075462-150351181 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-14T23:26Z] INFO  16:26:10,248 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:26Z] INFO  16:26:10,259 HelpFormatter - Date/Time: 2016/04/14 16:26:10
[2016-04-14T23:26Z] INFO  16:26:10,260 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:26Z] INFO  16:26:10,261 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:26Z] INFO  16:26:10,387 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:26Z] INFO  16:26:10,508 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@5fe152b7
[2016-04-14T23:26Z] INFO  16:26:10,628 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-14T23:26Z] INFO  16:26:10,649 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:26Z] INFO  16:26:10,686 ProgressMeter -            done    149890.0    20.0 s       2.3 m      100.0%    20.0 s       0.0 s
[2016-04-14T23:26Z] INFO  16:26:10,688 ProgressMeter - Total runtime 20.81 secs, 0.35 min, 0.01 hours
[2016-04-14T23:26Z] INFO  16:26:10,688 MicroScheduler - 94 reads were filtered out during the traversal out of approximately 149984 total reads (0.06%)
[2016-04-14T23:26Z] INFO  16:26:10,689 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:26Z] INFO  16:26:10,690 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:26Z] INFO  16:26:10,690 MicroScheduler -   -> 94 reads (0.06% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:26Z] INFO  16:26:10,720 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-14T23:26Z] INFO  16:26:11,003 IntervalUtils - Processing 16275720 bp from intervals
[2016-04-14T23:26Z] WARN  16:26:11,009 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:26Z] INFO  16:26:11,086 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:26Z] INFO  16:26:11,289 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:26Z] INFO  16:26:11,290 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:26Z] INFO  16:26:11,291 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:26Z] INFO  16:26:11,291 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-14T23:26Z] INFO  16:26:11,344 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:26Z] INFO  16:26:11,347 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:26Z] INFO  16:26:11,347 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:26Z] INFO  16:26:11,348 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:26Z] INFO  16:26:11,352 HelpFormatter - Program Args: -T PrintReads -L 5:31294069-49695124 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/5/tx/tmphVaYsR/R14-18102_kapa-NGv3-PE100-NGv3-sort-5_31294068_49695124-prep-prealign.bam
[2016-04-14T23:26Z] INFO  16:26:11,363 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:26Z] INFO  16:26:11,374 HelpFormatter - Date/Time: 2016/04/14 16:26:11
[2016-04-14T23:26Z] INFO  16:26:11,375 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:26Z] INFO  16:26:11,376 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:26Z] INFO  16:26:11,529 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:26Z] INFO  16:26:11,777 ProgressMeter -            done    340882.0    24.0 s      70.0 s      100.0%    24.0 s       0.0 s
[2016-04-14T23:26Z] INFO  16:26:11,777 ProgressMeter - Total runtime 24.11 secs, 0.40 min, 0.01 hours
[2016-04-14T23:26Z] INFO  16:26:11,783 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 340882 total reads (0.00%)
[2016-04-14T23:26Z] INFO  16:26:11,784 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:26Z] INFO  16:26:11,785 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:26Z] INFO  16:26:11,785 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:26Z] INFO  16:26:12,008 ProgressMeter -            done   1.5536605E7    17.0 s       1.0 s      100.0%    17.0 s       0.0 s
[2016-04-14T23:26Z] INFO  16:26:12,009 ProgressMeter - Total runtime 17.66 secs, 0.29 min, 0.00 hours
[2016-04-14T23:26Z] INFO  16:26:12,013 MicroScheduler - 14845 reads were filtered out during the traversal out of approximately 166543 total reads (8.91%)
[2016-04-14T23:26Z] INFO  16:26:12,014 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:26Z] INFO  16:26:12,014 MicroScheduler -   -> 516 reads (0.31% of total) failing BadMateFilter
[2016-04-14T23:26Z] INFO  16:26:12,015 MicroScheduler -   -> 13791 reads (8.28% of total) failing DuplicateReadFilter
[2016-04-14T23:26Z] INFO  16:26:12,016 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-14T23:26Z] INFO  16:26:12,016 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:26Z] INFO  16:26:12,017 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-14T23:26Z] INFO  16:26:12,017 MicroScheduler -   -> 538 reads (0.32% of total) failing MappingQualityZeroFilter
[2016-04-14T23:26Z] INFO  16:26:12,018 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:26Z] INFO  16:26:12,019 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-14T23:26Z] INFO  16:26:12,019 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-14T23:26Z] INFO  16:26:12,034 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:26Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-4_150354547_165878648-prep-prealign.bam
[2016-04-14T23:26Z] GATK RealignerTargetCreator: R14-18102_kapa-NGv3-PE100-NGv3-sort-4_150354547_165878648-prep-prealign.bam 4:150354548-165878648
[2016-04-14T23:26Z] GATK: RealignerTargetCreator
[2016-04-14T23:26Z] INFO  16:26:12,745 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-14T23:26Z] INFO  16:26:12,804 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:26Z] INFO  16:26:12,813 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:26Z] INFO  16:26:12,851 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.04
[2016-04-14T23:26Z] INFO  16:26:12,866 IntervalUtils - Processing 18401056 bp from intervals
[2016-04-14T23:26Z] INFO  16:26:12,995 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:26Z] INFO  16:26:13,367 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:26Z] INFO  16:26:13,369 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:26Z] INFO  16:26:13,369 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:26Z] INFO  16:26:13,370 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:26Z] INFO  16:26:13,393 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:26Z] INFO  16:26:13,406 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:26Z] INFO  16:26:13,409 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:26Z] GATK: realign ('4', 83857133, 99393738) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:26Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-3_127770401_143293035-prep.bam
[2016-04-14T23:26Z] INFO  16:26:13,610 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:26Z] INFO  16:26:14,104 ProgressMeter -            done    182749.0    16.0 s      89.0 s      100.0%    16.0 s       0.0 s
[2016-04-14T23:26Z] INFO  16:26:14,104 ProgressMeter - Total runtime 16.27 secs, 0.27 min, 0.00 hours
[2016-04-14T23:26Z] INFO  16:26:14,108 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 182749 total reads (0.00%)
[2016-04-14T23:26Z] INFO  16:26:14,108 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:26Z] INFO  16:26:14,109 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:26Z] INFO  16:26:14,109 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:26Z] INFO  16:26:14,398 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@32d5a4c6
[2016-04-14T23:26Z] GATK pre-alignment ('5', 49695692, 65288736) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:26Z] INFO  16:26:14,665 ProgressMeter -            done     95852.0    16.0 s       2.8 m      100.0%    16.0 s       0.0 s
[2016-04-14T23:26Z] INFO  16:26:14,665 ProgressMeter - Total runtime 16.07 secs, 0.27 min, 0.00 hours
[2016-04-14T23:26Z] INFO  16:26:14,666 MicroScheduler - 118 reads were filtered out during the traversal out of approximately 95970 total reads (0.12%)
[2016-04-14T23:26Z] INFO  16:26:14,666 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:26Z] INFO  16:26:14,666 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:26Z] INFO  16:26:14,667 MicroScheduler -   -> 118 reads (0.12% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:26Z] INFO  16:26:15,458 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:26Z] INFO  16:26:15,462 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:26Z] INFO  16:26:15,462 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:26Z] INFO  16:26:15,463 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:26Z] INFO  16:26:15,473 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/4/R14-18102_kapa-NGv3-PE100-NGv3-sort-4_150354547_165878648-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/4/tx/tmpw7Kg2N/R14-18102_kapa-NGv3-PE100-NGv3-sort-4_150354547_165878648-prep-prealign-realign.intervals -l INFO -L 4:150354548-165878648 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-14T23:26Z] INFO  16:26:15,497 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:26Z] INFO  16:26:15,497 HelpFormatter - Date/Time: 2016/04/14 16:26:15
[2016-04-14T23:26Z] INFO  16:26:15,497 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:26Z] INFO  16:26:15,498 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:26Z] INFO  16:26:15,630 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:26Z] INFO  16:26:15,725 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:26Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-4_36069528_52709433-prep.bam
[2016-04-14T23:26Z] INFO  16:26:15,905 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-14T23:26Z] INFO  16:26:15,917 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:26Z] INFO  16:26:16,030 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.10
[2016-04-14T23:26Z] INFO  16:26:16,259 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:26Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-4_165889318_183245405-prep-prealign.bam
[2016-04-14T23:26Z] INFO  16:26:16,305 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:26Z] INFO  16:26:16,309 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:26Z] INFO  16:26:16,310 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:26Z] INFO  16:26:16,311 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:26Z] INFO  16:26:16,311 IntervalUtils - Processing 15524101 bp from intervals
[2016-04-14T23:26Z] WARN  16:26:16,316 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:26Z] INFO  16:26:16,316 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/4/R14-18102_kapa-NGv3-PE100-NGv3-sort-4_83857133_99393738-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/4/R14-18102_kapa-NGv3-PE100-NGv3-sort-4_83857133_99393738-prep-prealign-realign.intervals -L 4:83857134-99393738 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/4/tx/tmp2MzV0F/R14-18102_kapa-NGv3-PE100-NGv3-sort-4_83857133_99393738-prep.bam
[2016-04-14T23:26Z] INFO  16:26:16,342 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:26Z] INFO  16:26:16,343 HelpFormatter - Date/Time: 2016/04/14 16:26:16
[2016-04-14T23:26Z] INFO  16:26:16,344 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:26Z] INFO  16:26:16,344 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:26Z] GATK pre-alignment ('5', 65290574, 80809536) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:26Z] INFO  16:26:16,488 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:26Z] INFO  16:26:16,592 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:26Z] INFO  16:26:16,596 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:26Z] INFO  16:26:16,596 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:26Z] INFO  16:26:16,596 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:26Z] INFO  16:26:16,597 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-14T23:26Z] INFO  16:26:16,648 ProgressMeter -            done    285855.0    20.0 s      72.0 s      100.0%    20.0 s       0.0 s
[2016-04-14T23:26Z] INFO  16:26:16,650 ProgressMeter - Total runtime 20.72 secs, 0.35 min, 0.01 hours
[2016-04-14T23:26Z] INFO  16:26:16,654 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 285855 total reads (0.00%)
[2016-04-14T23:26Z] INFO  16:26:16,655 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:26Z] INFO  16:26:16,655 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:26Z] INFO  16:26:16,656 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:26Z] INFO  16:26:16,714 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:26Z] INFO  16:26:16,724 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:26Z] GATK RealignerTargetCreator: R14-18102_kapa-NGv3-PE100-NGv3-sort-4_165889318_183245405-prep-prealign.bam 4:165889319-183245405
[2016-04-14T23:26Z] GATK: RealignerTargetCreator
[2016-04-14T23:26Z] INFO  16:26:16,769 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.04
[2016-04-14T23:26Z] INFO  16:26:17,137 IntervalUtils - Processing 15536605 bp from intervals
[2016-04-14T23:26Z] WARN  16:26:17,153 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:26Z] INFO  16:26:17,312 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:26Z] INFO  16:26:17,478 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:26Z] INFO  16:26:17,486 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@32d5a4c6
[2016-04-14T23:26Z] INFO  16:26:17,498 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:26Z] INFO  16:26:17,499 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:26Z] INFO  16:26:17,500 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:26Z] INFO  16:26:17,539 ProgressMeter -            done   1.5511694E7    19.0 s       1.0 s      100.0%    19.0 s       0.0 s
[2016-04-14T23:26Z] INFO  16:26:17,551 ProgressMeter - Total runtime 19.40 secs, 0.32 min, 0.01 hours
[2016-04-14T23:26Z] INFO  16:26:17,555 MicroScheduler - 26682 reads were filtered out during the traversal out of approximately 280449 total reads (9.51%)
[2016-04-14T23:26Z] INFO  16:26:17,556 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:26Z] INFO  16:26:17,557 MicroScheduler -   -> 691 reads (0.25% of total) failing BadMateFilter
[2016-04-14T23:26Z] INFO  16:26:17,558 MicroScheduler -   -> 22127 reads (7.89% of total) failing DuplicateReadFilter
[2016-04-14T23:26Z] INFO  16:26:17,558 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-14T23:26Z] INFO  16:26:17,559 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:26Z] INFO  16:26:17,560 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-14T23:26Z] INFO  16:26:17,560 MicroScheduler -   -> 3864 reads (1.38% of total) failing MappingQualityZeroFilter
[2016-04-14T23:26Z] INFO  16:26:17,561 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:26Z] INFO  16:26:17,570 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-14T23:26Z] INFO  16:26:17,571 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-14T23:26Z] INFO  16:26:17,575 ProgressMeter -            done     44534.0     9.0 s       3.5 m      100.0%     9.0 s       0.0 s
[2016-04-14T23:26Z] INFO  16:26:17,576 ProgressMeter - Total runtime 9.31 secs, 0.16 min, 0.00 hours
[2016-04-14T23:26Z] INFO  16:26:17,577 MicroScheduler - 76 reads were filtered out during the traversal out of approximately 44610 total reads (0.17%)
[2016-04-14T23:26Z] INFO  16:26:17,578 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:26Z] INFO  16:26:17,579 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:26Z] INFO  16:26:17,579 MicroScheduler -   -> 76 reads (0.17% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:26Z] INFO  16:26:17,680 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:26Z] INFO  16:26:17,780 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:26Z] INFO  16:26:17,785 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:26Z] INFO  16:26:17,785 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:26Z] INFO  16:26:17,786 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:26Z] INFO  16:26:17,790 HelpFormatter - Program Args: -T PrintReads -L 5:49695693-65288736 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/5/tx/tmpXFqneN/R14-18102_kapa-NGv3-PE100-NGv3-sort-5_49695692_65288736-prep-prealign.bam
[2016-04-14T23:26Z] INFO  16:26:17,820 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:26Z] INFO  16:26:17,828 HelpFormatter - Date/Time: 2016/04/14 16:26:17
[2016-04-14T23:26Z] INFO  16:26:17,829 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:26Z] INFO  16:26:17,832 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:26Z] INFO  16:26:17,830 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:26Z] INFO  16:26:18,026 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:26Z] INFO  16:26:18,171 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:26Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-3_174814579_190326970-prep.bam
[2016-04-14T23:26Z] INFO  16:26:18,866 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:26Z] INFO  16:26:18,884 ProgressMeter -            done   1.8489547E7    19.0 s       1.0 s      100.0%    19.0 s       0.0 s
[2016-04-14T23:26Z] INFO  16:26:18,885 ProgressMeter - Total runtime 19.66 secs, 0.33 min, 0.01 hours
[2016-04-14T23:26Z] INFO  16:26:18,889 MicroScheduler - 17073 reads were filtered out during the traversal out of approximately 179428 total reads (9.52%)
[2016-04-14T23:26Z] INFO  16:26:18,889 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:26Z] INFO  16:26:18,889 MicroScheduler -   -> 576 reads (0.32% of total) failing BadMateFilter
[2016-04-14T23:26Z] INFO  16:26:18,890 MicroScheduler -   -> 13745 reads (7.66% of total) failing DuplicateReadFilter
[2016-04-14T23:26Z] INFO  16:26:18,890 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-14T23:26Z] INFO  16:26:18,890 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:26Z] INFO  16:26:18,890 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-14T23:26Z] INFO  16:26:18,891 MicroScheduler -   -> 2752 reads (1.53% of total) failing MappingQualityZeroFilter
[2016-04-14T23:26Z] INFO  16:26:18,891 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:26Z] INFO  16:26:18,891 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-14T23:26Z] INFO  16:26:18,891 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-14T23:26Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-5_15616091_31267808-prep-prealign.bam
[2016-04-14T23:26Z] INFO  16:26:18,901 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:26Z] GATK: realign ('4', 68340604, 83852298) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:26Z] GATK RealignerTargetCreator: R14-18102_kapa-NGv3-PE100-NGv3-sort-5_15616091_31267808-prep-prealign.bam 5:15616092-31267808
[2016-04-14T23:26Z] GATK: RealignerTargetCreator
[2016-04-14T23:26Z] GATK pre-alignment ('5', 80911291, 96430739) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:26Z] INFO  16:26:19,182 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-14T23:26Z] INFO  16:26:19,254 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:26Z] INFO  16:26:19,263 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:26Z] INFO  16:26:19,319 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-14T23:26Z] INFO  16:26:19,334 IntervalUtils - Processing 15593044 bp from intervals
[2016-04-14T23:26Z] INFO  16:26:19,361 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:26Z] INFO  16:26:19,364 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:26Z] INFO  16:26:19,365 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:26Z] INFO  16:26:19,365 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:26Z] INFO  16:26:19,370 HelpFormatter - Program Args: -T PrintReads -L 5:65290575-80809536 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/5/tx/tmprn9i0p/R14-18102_kapa-NGv3-PE100-NGv3-sort-5_65290574_80809536-prep-prealign.bam
[2016-04-14T23:26Z] INFO  16:26:19,386 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:26Z] INFO  16:26:19,395 HelpFormatter - Date/Time: 2016/04/14 16:26:19
[2016-04-14T23:26Z] INFO  16:26:19,395 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:26Z] INFO  16:26:19,396 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:26Z] INFO  16:26:19,405 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:26Z] INFO  16:26:19,534 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:26Z] INFO  16:26:19,646 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:26Z] INFO  16:26:19,660 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:26Z] INFO  16:26:19,661 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:26Z] INFO  16:26:19,662 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:26Z] INFO  16:26:19,666 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/4/R14-18102_kapa-NGv3-PE100-NGv3-sort-4_165889318_183245405-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/4/tx/tmpyA9jrh/R14-18102_kapa-NGv3-PE100-NGv3-sort-4_165889318_183245405-prep-prealign-realign.intervals -l INFO -L 4:165889319-183245405 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-14T23:26Z] INFO  16:26:19,682 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:26Z] INFO  16:26:19,682 HelpFormatter - Date/Time: 2016/04/14 16:26:19
[2016-04-14T23:26Z] INFO  16:26:19,683 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:26Z] INFO  16:26:19,683 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:26Z] INFO  16:26:19,756 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:26Z] INFO  16:26:19,758 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:26Z] INFO  16:26:19,758 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:26Z] INFO  16:26:19,759 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:26Z] INFO  16:26:19,773 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:26Z] INFO  16:26:19,841 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:26Z] INFO  16:26:19,932 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:26Z] INFO  16:26:20,155 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-14T23:26Z] INFO  16:26:20,165 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:26Z] INFO  16:26:20,246 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-14T23:26Z] INFO  16:26:20,547 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:26Z] GATK: realign ('4', 115584857, 134074404) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:26Z] INFO  16:26:20,597 IntervalUtils - Processing 17356087 bp from intervals
[2016-04-14T23:26Z] WARN  16:26:20,613 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:26Z] INFO  16:26:20,630 ProgressMeter -            done   1.6147618E7    18.0 s       1.0 s      100.0%    18.0 s       0.0 s
[2016-04-14T23:26Z] INFO  16:26:20,631 ProgressMeter - Total runtime 18.40 secs, 0.31 min, 0.01 hours
[2016-04-14T23:26Z] INFO  16:26:20,634 MicroScheduler - 16964 reads were filtered out during the traversal out of approximately 198662 total reads (8.54%)
[2016-04-14T23:26Z] INFO  16:26:20,635 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:26Z] INFO  16:26:20,635 MicroScheduler -   -> 607 reads (0.31% of total) failing BadMateFilter
[2016-04-14T23:26Z] INFO  16:26:20,636 MicroScheduler -   -> 15487 reads (7.80% of total) failing DuplicateReadFilter
[2016-04-14T23:26Z] INFO  16:26:20,636 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-14T23:26Z] INFO  16:26:20,636 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:26Z] INFO  16:26:20,636 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-14T23:26Z] INFO  16:26:20,637 MicroScheduler -   -> 870 reads (0.44% of total) failing MappingQualityZeroFilter
[2016-04-14T23:26Z] INFO  16:26:20,637 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:26Z] INFO  16:26:20,637 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-14T23:26Z] INFO  16:26:20,637 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-14T23:26Z] INFO  16:26:20,708 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:26Z] INFO  16:26:20,751 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-14T23:26Z] INFO  16:26:20,828 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:26Z] INFO  16:26:20,847 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:26Z] INFO  16:26:20,915 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-14T23:26Z] INFO  16:26:20,934 IntervalUtils - Processing 15518962 bp from intervals
[2016-04-14T23:26Z] INFO  16:26:20,937 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:26Z] INFO  16:26:20,937 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:26Z] INFO  16:26:20,938 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:26Z] INFO  16:26:20,938 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-14T23:26Z] INFO  16:26:21,082 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:26Z] INFO  16:26:21,221 ProgressMeter -       4:9327109    700166.0    90.0 s       2.2 m       60.1%     2.5 m      59.0 s
[2016-04-14T23:26Z] INFO  16:26:21,511 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:26Z] INFO  16:26:21,512 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:26Z] INFO  16:26:21,513 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:26Z] INFO  16:26:21,513 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:26Z] INFO  16:26:21,549 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:26Z] INFO  16:26:21,688 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:26Z] INFO  16:26:21,787 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:26Z] INFO  16:26:21,790 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:26Z] INFO  16:26:21,791 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:26Z] INFO  16:26:21,791 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:26Z] INFO  16:26:21,796 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/4/R14-18102_kapa-NGv3-PE100-NGv3-sort-4_68340604_83852298-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/4/R14-18102_kapa-NGv3-PE100-NGv3-sort-4_68340604_83852298-prep-prealign-realign.intervals -L 4:68340605-83852298 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/4/tx/tmpmhcjXb/R14-18102_kapa-NGv3-PE100-NGv3-sort-4_68340604_83852298-prep.bam
[2016-04-14T23:26Z] INFO  16:26:21,827 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:26Z] INFO  16:26:21,828 HelpFormatter - Date/Time: 2016/04/14 16:26:21
[2016-04-14T23:26Z] INFO  16:26:21,828 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:26Z] INFO  16:26:21,829 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:26Z] INFO  16:26:22,004 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:26Z] INFO  16:26:22,080 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:26Z] INFO  16:26:22,084 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:26Z] INFO  16:26:22,084 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:26Z] INFO  16:26:22,085 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:26Z] INFO  16:26:22,090 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/5/R14-18102_kapa-NGv3-PE100-NGv3-sort-5_15616091_31267808-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/5/tx/tmpY9Arej/R14-18102_kapa-NGv3-PE100-NGv3-sort-5_15616091_31267808-prep-prealign-realign.intervals -l INFO -L 5:15616092-31267808 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-14T23:26Z] INFO  16:26:22,102 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:26Z] INFO  16:26:22,103 HelpFormatter - Date/Time: 2016/04/14 16:26:22
[2016-04-14T23:26Z] INFO  16:26:22,103 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:26Z] INFO  16:26:22,104 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:26Z] INFO  16:26:22,142 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:26Z] INFO  16:26:22,156 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:26Z] INFO  16:26:22,183 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:26Z] INFO  16:26:22,188 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:26Z] GATK: realign ('4', 99397339, 115544957) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:26Z] INFO  16:26:22,227 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-14T23:26Z] INFO  16:26:22,443 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@5fe152b7
[2016-04-14T23:26Z] INFO  16:26:22,485 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-14T23:26Z] INFO  16:26:22,495 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:26Z] INFO  16:26:22,574 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-14T23:26Z] INFO  16:26:22,631 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:26Z] INFO  16:26:22,634 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:26Z] INFO  16:26:22,635 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:26Z] INFO  16:26:22,635 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:26Z] INFO  16:26:22,640 HelpFormatter - Program Args: -T PrintReads -L 5:80911292-96430739 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/5/tx/tmpOF8vj7/R14-18102_kapa-NGv3-PE100-NGv3-sort-5_80911291_96430739-prep-prealign.bam
[2016-04-14T23:26Z] INFO  16:26:22,649 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:26Z] INFO  16:26:22,660 HelpFormatter - Date/Time: 2016/04/14 16:26:22
[2016-04-14T23:26Z] INFO  16:26:22,661 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:26Z] INFO  16:26:22,662 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:26Z] INFO  16:26:22,684 ProgressMeter -            done    141429.0    19.0 s       2.3 m       98.1%    19.0 s       0.0 s
[2016-04-14T23:26Z] INFO  16:26:22,684 ProgressMeter - Total runtime 19.89 secs, 0.33 min, 0.01 hours
[2016-04-14T23:26Z] INFO  16:26:22,684 MicroScheduler - 80 reads were filtered out during the traversal out of approximately 141509 total reads (0.06%)
[2016-04-14T23:26Z] INFO  16:26:22,685 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:26Z] INFO  16:26:22,685 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:26Z] INFO  16:26:22,685 MicroScheduler -   -> 80 reads (0.06% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:26Z] INFO  16:26:22,734 IntervalUtils - Processing 15511694 bp from intervals
[2016-04-14T23:26Z] WARN  16:26:22,745 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:26Z] INFO  16:26:22,832 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:26Z] INFO  16:26:22,839 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:26Z] INFO  16:26:22,956 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:26Z] INFO  16:26:22,957 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:26Z] INFO  16:26:22,958 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:26Z] INFO  16:26:22,959 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:26Z] INFO  16:26:23,033 IntervalUtils - Processing 15651717 bp from intervals
[2016-04-14T23:26Z] WARN  16:26:23,038 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:26Z] INFO  16:26:23,122 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:26Z] INFO  16:26:23,173 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:26Z] INFO  16:26:23,310 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:26Z] INFO  16:26:23,311 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:26Z] INFO  16:26:23,311 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:26Z] INFO  16:26:23,312 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-14T23:26Z] INFO  16:26:23,501 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:26Z] INFO  16:26:23,625 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:26Z] INFO  16:26:23,628 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:26Z] INFO  16:26:23,629 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:26Z] INFO  16:26:23,630 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:26Z] INFO  16:26:23,634 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/4/R14-18102_kapa-NGv3-PE100-NGv3-sort-4_115584857_134074404-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/4/R14-18102_kapa-NGv3-PE100-NGv3-sort-4_115584857_134074404-prep-prealign-realign.intervals -L 4:115584858-134074404 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/4/tx/tmpSViM9r/R14-18102_kapa-NGv3-PE100-NGv3-sort-4_115584857_134074404-prep.bam
[2016-04-14T23:26Z] INFO  16:26:23,644 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:26Z] INFO  16:26:23,645 HelpFormatter - Date/Time: 2016/04/14 16:26:23
[2016-04-14T23:26Z] INFO  16:26:23,645 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:26Z] INFO  16:26:23,646 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:26Z] INFO  16:26:23,881 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:26Z] INFO  16:26:24,059 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-14T23:26Z] INFO  16:26:24,068 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:26Z] INFO  16:26:24,081 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:26Z] INFO  16:26:24,115 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:26Z] INFO  16:26:24,124 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:26Z] INFO  16:26:24,144 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-14T23:26Z] INFO  16:26:24,179 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-14T23:26Z] INFO  16:26:24,192 IntervalUtils - Processing 15519448 bp from intervals
[2016-04-14T23:26Z] INFO  16:26:24,231 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:26Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-4_183267803_191154276-prep-prealign.bam
[2016-04-14T23:26Z] INFO  16:26:24,287 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:26Z] INFO  16:26:24,474 IntervalUtils - Processing 18489547 bp from intervals
[2016-04-14T23:26Z] WARN  16:26:24,479 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:26Z] INFO  16:26:24,561 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:26Z] INFO  16:26:24,616 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:26Z] INFO  16:26:24,617 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:26Z] INFO  16:26:24,618 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:26Z] INFO  16:26:24,619 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:26Z] INFO  16:26:24,643 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:26Z] GATK RealignerTargetCreator: R14-18102_kapa-NGv3-PE100-NGv3-sort-4_183267803_191154276-prep-prealign.bam 4:183267804-191154276
[2016-04-14T23:26Z] GATK: RealignerTargetCreator
[2016-04-14T23:26Z] INFO  16:26:24,750 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:26Z] INFO  16:26:24,752 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:26Z] INFO  16:26:24,752 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:26Z] INFO  16:26:24,753 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:26Z] INFO  16:26:24,798 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:26Z] INFO  16:26:24,933 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:26Z] INFO  16:26:25,144 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:26Z] INFO  16:26:25,333 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:26Z] INFO  16:26:25,347 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:26Z] INFO  16:26:25,347 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:26Z] INFO  16:26:25,347 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:26Z] INFO  16:26:25,351 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/4/R14-18102_kapa-NGv3-PE100-NGv3-sort-4_99397339_115544957-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/4/R14-18102_kapa-NGv3-PE100-NGv3-sort-4_99397339_115544957-prep-prealign-realign.intervals -L 4:99397340-115544957 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/4/tx/tmp0hqAb_/R14-18102_kapa-NGv3-PE100-NGv3-sort-4_99397339_115544957-prep.bam
[2016-04-14T23:26Z] INFO  16:26:25,368 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:26Z] INFO  16:26:25,368 HelpFormatter - Date/Time: 2016/04/14 16:26:25
[2016-04-14T23:26Z] INFO  16:26:25,368 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:26Z] INFO  16:26:25,369 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:26Z] INFO  16:26:25,608 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:26Z] INFO  16:26:25,727 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:26Z] INFO  16:26:25,736 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:26Z] INFO  16:26:25,804 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-14T23:26Z] INFO  16:26:26,274 IntervalUtils - Processing 16147618 bp from intervals
[2016-04-14T23:26Z] WARN  16:26:26,290 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:26Z] INFO  16:26:26,461 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:26Z] INFO  16:26:26,640 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:26Z] INFO  16:26:26,641 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:26Z] INFO  16:26:26,642 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:26Z] INFO  16:26:26,643 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:26Z] INFO  16:26:26,796 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:26Z] INFO  16:26:26,958 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:26Z] INFO  16:26:27,631 ProgressMeter -            done   1.627572E7    16.0 s       1.0 s      100.0%    16.0 s       0.0 s
[2016-04-14T23:26Z] INFO  16:26:27,632 ProgressMeter - Total runtime 16.34 secs, 0.27 min, 0.00 hours
[2016-04-14T23:26Z] INFO  16:26:27,636 MicroScheduler - 10724 reads were filtered out during the traversal out of approximately 120235 total reads (8.92%)
[2016-04-14T23:26Z] INFO  16:26:27,638 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:26Z] INFO  16:26:27,639 MicroScheduler -   -> 489 reads (0.41% of total) failing BadMateFilter
[2016-04-14T23:26Z] INFO  16:26:27,639 MicroScheduler -   -> 9493 reads (7.90% of total) failing DuplicateReadFilter
[2016-04-14T23:26Z] INFO  16:26:27,640 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-14T23:26Z] INFO  16:26:27,640 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:26Z] INFO  16:26:27,641 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-14T23:26Z] INFO  16:26:27,642 MicroScheduler -   -> 742 reads (0.62% of total) failing MappingQualityZeroFilter
[2016-04-14T23:26Z] INFO  16:26:27,642 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:26Z] INFO  16:26:27,643 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-14T23:26Z] INFO  16:26:27,644 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-14T23:26Z] INFO  16:26:27,738 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:26Z] INFO  16:26:27,741 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:26Z] INFO  16:26:27,742 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:26Z] INFO  16:26:27,764 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:26Z] INFO  16:26:27,769 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/4/R14-18102_kapa-NGv3-PE100-NGv3-sort-4_183267803_191154276-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/4/tx/tmps8jrj_/R14-18102_kapa-NGv3-PE100-NGv3-sort-4_183267803_191154276-prep-prealign-realign.intervals -l INFO -L 4:183267804-191154276 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-14T23:26Z] INFO  16:26:27,789 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:26Z] INFO  16:26:27,790 HelpFormatter - Date/Time: 2016/04/14 16:26:27
[2016-04-14T23:26Z] INFO  16:26:27,791 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:26Z] INFO  16:26:27,791 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:26Z] INFO  16:26:27,940 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:26Z] INFO  16:26:28,196 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-14T23:26Z] INFO  16:26:28,221 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:26Z] INFO  16:26:28,285 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-14T23:26Z] INFO  16:26:28,578 IntervalUtils - Processing 7886473 bp from intervals
[2016-04-14T23:26Z] WARN  16:26:28,583 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:26Z] INFO  16:26:28,731 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:26Z] INFO  16:26:28,936 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:26Z] INFO  16:26:28,937 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:26Z] INFO  16:26:28,938 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:26Z] INFO  16:26:28,939 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-14T23:26Z] INFO  16:26:29,060 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:26Z] GATK: realign ('4', 134075461, 150351181) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:26Z] INFO  16:26:31,842 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:26Z] INFO  16:26:31,856 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:26Z] INFO  16:26:31,857 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:26Z] INFO  16:26:31,858 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:26Z] INFO  16:26:31,863 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/4/R14-18102_kapa-NGv3-PE100-NGv3-sort-4_134075461_150351181-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/4/R14-18102_kapa-NGv3-PE100-NGv3-sort-4_134075461_150351181-prep-prealign-realign.intervals -L 4:134075462-150351181 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/4/tx/tmp127gI4/R14-18102_kapa-NGv3-PE100-NGv3-sort-4_134075461_150351181-prep.bam
[2016-04-14T23:26Z] INFO  16:26:31,875 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:26Z] INFO  16:26:31,905 HelpFormatter - Date/Time: 2016/04/14 16:26:31
[2016-04-14T23:26Z] INFO  16:26:31,905 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:26Z] INFO  16:26:31,905 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:26Z] INFO  16:26:32,163 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:26Z] INFO  16:26:32,246 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:26Z] INFO  16:26:32,256 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:26Z] INFO  16:26:32,299 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.04
[2016-04-14T23:26Z] INFO  16:26:32,685 IntervalUtils - Processing 16275720 bp from intervals
[2016-04-14T23:26Z] WARN  16:26:32,703 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:26Z] INFO  16:26:32,821 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:26Z] INFO  16:26:32,886 ProgressMeter -            done    165766.0    15.0 s      92.0 s      100.0%    15.0 s       0.0 s
[2016-04-14T23:26Z] INFO  16:26:32,887 ProgressMeter - Total runtime 15.39 secs, 0.26 min, 0.00 hours
[2016-04-14T23:26Z] INFO  16:26:32,890 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 165766 total reads (0.00%)
[2016-04-14T23:26Z] INFO  16:26:32,891 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:26Z] INFO  16:26:32,891 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:26Z] INFO  16:26:32,892 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:26Z] INFO  16:26:33,020 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:26Z] INFO  16:26:33,022 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:26Z] INFO  16:26:33,023 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:26Z] INFO  16:26:33,024 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:26Z] INFO  16:26:33,056 ProgressMeter -            done   1.5524101E7    16.0 s       1.0 s      100.0%    16.0 s       0.0 s
[2016-04-14T23:26Z] INFO  16:26:33,057 ProgressMeter - Total runtime 16.46 secs, 0.27 min, 0.00 hours
[2016-04-14T23:26Z] INFO  16:26:33,060 MicroScheduler - 13074 reads were filtered out during the traversal out of approximately 150694 total reads (8.68%)
[2016-04-14T23:26Z] INFO  16:26:33,061 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:26Z] INFO  16:26:33,061 MicroScheduler -   -> 491 reads (0.33% of total) failing BadMateFilter
[2016-04-14T23:26Z] INFO  16:26:33,061 MicroScheduler -   -> 11950 reads (7.93% of total) failing DuplicateReadFilter
[2016-04-14T23:26Z] INFO  16:26:33,062 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-14T23:26Z] INFO  16:26:33,062 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:26Z] INFO  16:26:33,062 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-14T23:26Z] INFO  16:26:33,062 MicroScheduler -   -> 633 reads (0.42% of total) failing MappingQualityZeroFilter
[2016-04-14T23:26Z] INFO  16:26:33,063 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:26Z] INFO  16:26:33,063 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-14T23:26Z] INFO  16:26:33,063 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-14T23:26Z] INFO  16:26:33,195 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:26Z] INFO  16:26:33,400 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:26Z] INFO  16:26:34,370 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@7172f77a
[2016-04-14T23:26Z] INFO  16:26:34,380 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:26Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-4_83857133_99393738-prep.bam
[2016-04-14T23:26Z] INFO  16:26:34,440 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:26Z] INFO  16:26:34,465 ProgressMeter -            done    219480.0    28.0 s       2.2 m      100.0%    28.0 s       0.0 s
[2016-04-14T23:26Z] INFO  16:26:34,466 ProgressMeter - Total runtime 28.95 secs, 0.48 min, 0.01 hours
[2016-04-14T23:26Z] INFO  16:26:34,466 MicroScheduler - 142 reads were filtered out during the traversal out of approximately 219622 total reads (0.06%)
[2016-04-14T23:26Z] INFO  16:26:34,467 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:26Z] INFO  16:26:34,467 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:26Z] INFO  16:26:34,467 MicroScheduler -   -> 142 reads (0.06% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:26Z] GATK: realign ('4', 150354547, 165878648) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:26Z] GATK pre-alignment ('5', 96432513, 112043579) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:26Z] INFO  16:26:36,162 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:26Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-5_0_15580921-prep-prealign.bam
[2016-04-14T23:26Z] GATK RealignerTargetCreator: R14-18102_kapa-NGv3-PE100-NGv3-sort-5_0_15580921-prep-prealign.bam 5:1-15580921
[2016-04-14T23:26Z] GATK: RealignerTargetCreator
[2016-04-14T23:26Z] INFO  16:26:37,209 ProgressMeter -      3:51395436    400012.0    30.0 s      75.0 s       27.5%   109.0 s      79.0 s
[2016-04-14T23:26Z] INFO  16:26:37,343 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:26Z] INFO  16:26:37,346 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:26Z] INFO  16:26:37,347 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:26Z] INFO  16:26:37,347 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:26Z] INFO  16:26:37,352 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/4/R14-18102_kapa-NGv3-PE100-NGv3-sort-4_150354547_165878648-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/4/R14-18102_kapa-NGv3-PE100-NGv3-sort-4_150354547_165878648-prep-prealign-realign.intervals -L 4:150354548-165878648 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/4/tx/tmpLsZR1l/R14-18102_kapa-NGv3-PE100-NGv3-sort-4_150354547_165878648-prep.bam
[2016-04-14T23:26Z] INFO  16:26:37,361 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:26Z] INFO  16:26:37,362 HelpFormatter - Date/Time: 2016/04/14 16:26:37
[2016-04-14T23:26Z] INFO  16:26:37,363 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:26Z] INFO  16:26:37,364 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:26Z] INFO  16:26:37,544 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:26Z] INFO  16:26:37,690 ProgressMeter -            done   1.7356087E7    16.0 s       0.0 s      100.0%    16.0 s       0.0 s
[2016-04-14T23:26Z] INFO  16:26:37,691 ProgressMeter - Total runtime 16.75 secs, 0.28 min, 0.00 hours
[2016-04-14T23:26Z] INFO  16:26:37,695 MicroScheduler - 8789 reads were filtered out during the traversal out of approximately 96186 total reads (9.14%)
[2016-04-14T23:26Z] INFO  16:26:37,696 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:26Z] INFO  16:26:37,696 MicroScheduler -   -> 418 reads (0.43% of total) failing BadMateFilter
[2016-04-14T23:26Z] INFO  16:26:37,697 MicroScheduler -   -> 7688 reads (7.99% of total) failing DuplicateReadFilter
[2016-04-14T23:26Z] INFO  16:26:37,698 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-14T23:26Z] INFO  16:26:37,699 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:26Z] INFO  16:26:37,699 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-14T23:26Z] INFO  16:26:37,700 MicroScheduler -   -> 683 reads (0.71% of total) failing MappingQualityZeroFilter
[2016-04-14T23:26Z] INFO  16:26:37,700 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:26Z] INFO  16:26:37,701 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-14T23:26Z] INFO  16:26:37,702 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-14T23:26Z] INFO  16:26:37,702 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:26Z] INFO  16:26:37,718 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:26Z] INFO  16:26:37,777 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-14T23:26Z] INFO  16:26:37,787 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:26Z] INFO  16:26:37,790 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:26Z] INFO  16:26:37,791 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:26Z] INFO  16:26:37,791 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:26Z] INFO  16:26:37,796 HelpFormatter - Program Args: -T PrintReads -L 5:96432514-112043579 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/5/tx/tmppyBuoZ/R14-18102_kapa-NGv3-PE100-NGv3-sort-5_96432513_112043579-prep-prealign.bam
[2016-04-14T23:26Z] INFO  16:26:37,814 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:26Z] INFO  16:26:37,815 HelpFormatter - Date/Time: 2016/04/14 16:26:37
[2016-04-14T23:26Z] INFO  16:26:37,816 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:26Z] INFO  16:26:37,816 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:26Z] INFO  16:26:37,978 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:26Z] INFO  16:26:38,110 IntervalUtils - Processing 15524101 bp from intervals
[2016-04-14T23:26Z] WARN  16:26:38,115 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:26Z] INFO  16:26:38,178 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:26Z] INFO  16:26:38,296 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:26Z] INFO  16:26:38,297 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:26Z] INFO  16:26:38,297 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:26Z] INFO  16:26:38,298 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:26Z] INFO  16:26:38,463 ProgressMeter -            done   1.5651717E7    15.0 s       0.0 s      100.0%    15.0 s       0.0 s
[2016-04-14T23:26Z] INFO  16:26:38,464 ProgressMeter - Total runtime 15.15 secs, 0.25 min, 0.00 hours
[2016-04-14T23:26Z] INFO  16:26:38,460 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:26Z] INFO  16:26:38,469 MicroScheduler - 5153 reads were filtered out during the traversal out of approximately 45036 total reads (11.44%)
[2016-04-14T23:26Z] INFO  16:26:38,470 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:26Z] INFO  16:26:38,470 MicroScheduler -   -> 323 reads (0.72% of total) failing BadMateFilter
[2016-04-14T23:26Z] INFO  16:26:38,471 MicroScheduler -   -> 3588 reads (7.97% of total) failing DuplicateReadFilter
[2016-04-14T23:26Z] INFO  16:26:38,472 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-14T23:26Z] INFO  16:26:38,472 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:26Z] INFO  16:26:38,473 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-14T23:26Z] INFO  16:26:38,474 MicroScheduler -   -> 1242 reads (2.76% of total) failing MappingQualityZeroFilter
[2016-04-14T23:26Z] INFO  16:26:38,474 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:26Z] INFO  16:26:38,475 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-14T23:26Z] INFO  16:26:38,475 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-14T23:26Z] INFO  16:26:38,603 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:26Z] INFO  16:26:39,045 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:26Z] GATK: realign ('4', 165889318, 183245405) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:26Z] INFO  16:26:39,076 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-14T23:26Z] INFO  16:26:39,145 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:26Z] INFO  16:26:39,156 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:26Z] INFO  16:26:39,228 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-14T23:26Z] INFO  16:26:39,236 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@7172f77a
[2016-04-14T23:26Z] INFO  16:26:39,257 IntervalUtils - Processing 15611066 bp from intervals
[2016-04-14T23:26Z] INFO  16:26:39,382 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:26Z] INFO  16:26:39,421 ProgressMeter -            done    138356.0    19.0 s       2.4 m      100.0%    19.0 s       0.0 s
[2016-04-14T23:26Z] INFO  16:26:39,421 ProgressMeter - Total runtime 19.66 secs, 0.33 min, 0.01 hours
[2016-04-14T23:26Z] INFO  16:26:39,422 MicroScheduler - 99 reads were filtered out during the traversal out of approximately 138455 total reads (0.07%)
[2016-04-14T23:26Z] INFO  16:26:39,422 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:26Z] INFO  16:26:39,422 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:26Z] INFO  16:26:39,423 MicroScheduler -   -> 99 reads (0.07% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:26Z] INFO  16:26:39,503 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:26Z] INFO  16:26:39,507 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:26Z] INFO  16:26:39,507 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:26Z] INFO  16:26:39,508 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:26Z] INFO  16:26:39,512 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/5/R14-18102_kapa-NGv3-PE100-NGv3-sort-5_0_15580921-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/5/tx/tmpmnCVVl/R14-18102_kapa-NGv3-PE100-NGv3-sort-5_0_15580921-prep-prealign-realign.intervals -l INFO -L 5:1-15580921 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-14T23:26Z] INFO  16:26:39,522 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:26Z] INFO  16:26:39,533 HelpFormatter - Date/Time: 2016/04/14 16:26:39
[2016-04-14T23:26Z] INFO  16:26:39,534 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:26Z] INFO  16:26:39,535 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:26Z] INFO  16:26:39,644 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:26Z] INFO  16:26:39,746 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:26Z] INFO  16:26:39,747 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:26Z] INFO  16:26:39,748 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:26Z] INFO  16:26:39,748 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:26Z] INFO  16:26:39,762 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:26Z] INFO  16:26:39,767 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:26Z] GATK: realign ('5', 15616091, 31267808) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:26Z] INFO  16:26:39,869 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-14T23:26Z] INFO  16:26:39,894 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:26Z] INFO  16:26:39,898 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:26Z] INFO  16:26:39,962 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-14T23:26Z] INFO  16:26:40,213 ProgressMeter -            done    178257.0    15.0 s      86.0 s      100.0%    15.0 s       0.0 s
[2016-04-14T23:26Z] INFO  16:26:40,214 ProgressMeter - Total runtime 15.46 secs, 0.26 min, 0.00 hours
[2016-04-14T23:26Z] INFO  16:26:40,217 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 178257 total reads (0.00%)
[2016-04-14T23:26Z] INFO  16:26:40,217 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:26Z] INFO  16:26:40,218 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:26Z] INFO  16:26:40,218 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:26Z] INFO  16:26:40,222 IntervalUtils - Processing 15580921 bp from intervals
[2016-04-14T23:26Z] WARN  16:26:40,226 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:26Z] INFO  16:26:40,332 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:26Z] INFO  16:26:40,541 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:26Z] INFO  16:26:40,542 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:26Z] INFO  16:26:40,542 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:26Z] INFO  16:26:40,543 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-14T23:26Z] INFO  16:26:40,570 ProgressMeter -            done   7886473.0    11.0 s       1.0 s      100.0%    11.0 s       0.0 s
[2016-04-14T23:26Z] INFO  16:26:40,570 ProgressMeter - Total runtime 11.63 secs, 0.19 min, 0.00 hours
[2016-04-14T23:26Z] INFO  16:26:40,574 MicroScheduler - 14207 reads were filtered out during the traversal out of approximately 142329 total reads (9.98%)
[2016-04-14T23:26Z] INFO  16:26:40,574 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:26Z] INFO  16:26:40,574 MicroScheduler -   -> 367 reads (0.26% of total) failing BadMateFilter
[2016-04-14T23:26Z] INFO  16:26:40,575 MicroScheduler -   -> 11138 reads (7.83% of total) failing DuplicateReadFilter
[2016-04-14T23:26Z] INFO  16:26:40,575 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-14T23:26Z] INFO  16:26:40,575 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:26Z] INFO  16:26:40,575 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-14T23:26Z] INFO  16:26:40,576 MicroScheduler -   -> 2702 reads (1.90% of total) failing MappingQualityZeroFilter
[2016-04-14T23:26Z] INFO  16:26:40,576 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:26Z] INFO  16:26:40,576 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-14T23:26Z] INFO  16:26:40,576 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-14T23:26Z] INFO  16:26:40,918 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:26Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-5_49695692_65288736-prep-prealign.bam
[2016-04-14T23:26Z] GATK RealignerTargetCreator: R14-18102_kapa-NGv3-PE100-NGv3-sort-5_49695692_65288736-prep-prealign.bam 5:49695693-65288736
[2016-04-14T23:26Z] GATK: RealignerTargetCreator
[2016-04-14T23:26Z] INFO  16:26:41,610 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:26Z] INFO  16:26:41,613 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:26Z] INFO  16:26:41,614 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:26Z] INFO  16:26:41,615 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:26Z] INFO  16:26:41,629 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/4/R14-18102_kapa-NGv3-PE100-NGv3-sort-4_165889318_183245405-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/4/R14-18102_kapa-NGv3-PE100-NGv3-sort-4_165889318_183245405-prep-prealign-realign.intervals -L 4:165889319-183245405 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/4/tx/tmpiXlsB9/R14-18102_kapa-NGv3-PE100-NGv3-sort-4_165889318_183245405-prep.bam
[2016-04-14T23:26Z] INFO  16:26:41,655 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:26Z] INFO  16:26:41,656 HelpFormatter - Date/Time: 2016/04/14 16:26:41
[2016-04-14T23:26Z] INFO  16:26:41,656 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:26Z] INFO  16:26:41,657 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:26Z] INFO  16:26:41,760 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:26Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-4_115584857_134074404-prep.bam
[2016-04-14T23:26Z] INFO  16:26:41,918 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:26Z] INFO  16:26:42,005 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:26Z] INFO  16:26:42,014 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:26Z] INFO  16:26:42,053 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:26Z] INFO  16:26:42,061 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-14T23:26Z] GATK: realign ('4', 183267803, 191154276) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:26Z] INFO  16:26:42,231 ProgressMeter -            done    197626.0    15.0 s      78.0 s      100.0%    15.0 s       0.0 s
[2016-04-14T23:26Z] INFO  16:26:42,231 ProgressMeter - Total runtime 15.59 secs, 0.26 min, 0.00 hours
[2016-04-14T23:26Z] INFO  16:26:42,234 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 197626 total reads (0.00%)
[2016-04-14T23:26Z] INFO  16:26:42,235 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:26Z] INFO  16:26:42,235 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:26Z] INFO  16:26:42,236 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:26Z] GATK pre-alignment ('5', 112073555, 127595521) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:26Z] INFO  16:26:42,461 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:26Z] INFO  16:26:42,464 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:26Z] INFO  16:26:42,465 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:26Z] INFO  16:26:42,465 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:26Z] INFO  16:26:42,470 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/5/R14-18102_kapa-NGv3-PE100-NGv3-sort-5_15616091_31267808-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/5/R14-18102_kapa-NGv3-PE100-NGv3-sort-5_15616091_31267808-prep-prealign-realign.intervals -L 5:15616092-31267808 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/5/tx/tmpUXqlbA/R14-18102_kapa-NGv3-PE100-NGv3-sort-5_15616091_31267808-prep.bam
[2016-04-14T23:26Z] INFO  16:26:42,496 IntervalUtils - Processing 17356087 bp from intervals
[2016-04-14T23:26Z] WARN  16:26:42,501 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:26Z] INFO  16:26:42,502 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:26Z] INFO  16:26:42,505 HelpFormatter - Date/Time: 2016/04/14 16:26:42
[2016-04-14T23:26Z] INFO  16:26:42,506 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:26Z] INFO  16:26:42,506 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:26Z] INFO  16:26:42,587 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:26Z] INFO  16:26:42,679 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:26Z] INFO  16:26:42,680 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:26Z] INFO  16:26:42,681 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:26Z] INFO  16:26:42,682 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:26Z] INFO  16:26:42,685 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:26Z] INFO  16:26:42,809 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:26Z] INFO  16:26:42,818 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:26Z] INFO  16:26:42,882 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:26Z] INFO  16:26:42,892 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-14T23:26Z] INFO  16:26:43,107 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:26Z] INFO  16:26:43,109 ProgressMeter -            done    278584.0    20.0 s      72.0 s      100.0%    20.0 s       0.0 s
[2016-04-14T23:26Z] INFO  16:26:43,110 ProgressMeter - Total runtime 20.15 secs, 0.34 min, 0.01 hours
[2016-04-14T23:26Z] INFO  16:26:43,113 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 278584 total reads (0.00%)
[2016-04-14T23:26Z] INFO  16:26:43,114 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:26Z] INFO  16:26:43,114 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:26Z] INFO  16:26:43,114 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:26Z] INFO  16:26:43,331 IntervalUtils - Processing 15651717 bp from intervals
[2016-04-14T23:26Z] WARN  16:26:43,336 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:26Z] INFO  16:26:43,396 ProgressMeter -      5:43381957    200002.0    30.0 s       2.5 m       65.7%    45.0 s      15.0 s
[2016-04-14T23:26Z] INFO  16:26:43,400 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:26Z] INFO  16:26:43,505 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:26Z] INFO  16:26:43,506 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:26Z] INFO  16:26:43,507 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:26Z] INFO  16:26:43,508 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:26Z] INFO  16:26:43,676 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:26Z] INFO  16:26:43,833 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:26Z] INFO  16:26:43,835 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:26Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-4_99397339_115544957-prep.bam
[2016-04-14T23:26Z] INFO  16:26:43,932 ProgressMeter -            done    119491.0    10.0 s      91.0 s       99.5%    10.0 s       0.0 s
[2016-04-14T23:26Z] INFO  16:26:43,933 ProgressMeter - Total runtime 10.91 secs, 0.18 min, 0.00 hours
[2016-04-14T23:26Z] INFO  16:26:43,937 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 119491 total reads (0.00%)
[2016-04-14T23:26Z] INFO  16:26:43,938 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:26Z] INFO  16:26:43,938 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:26Z] INFO  16:26:43,939 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:26Z] INFO  16:26:44,495 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:26Z] INFO  16:26:44,497 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:26Z] INFO  16:26:44,498 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:26Z] INFO  16:26:44,498 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:26Z] INFO  16:26:44,502 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/5/R14-18102_kapa-NGv3-PE100-NGv3-sort-5_49695692_65288736-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/5/tx/tmpGU2430/R14-18102_kapa-NGv3-PE100-NGv3-sort-5_49695692_65288736-prep-prealign-realign.intervals -l INFO -L 5:49695693-65288736 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-14T23:26Z] INFO  16:26:44,519 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:26Z] INFO  16:26:44,520 HelpFormatter - Date/Time: 2016/04/14 16:26:44
[2016-04-14T23:26Z] INFO  16:26:44,520 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:26Z] INFO  16:26:44,521 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:26Z] GATK pre-alignment ('5', 127597427, 143191869) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:26Z] INFO  16:26:44,640 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:26Z] INFO  16:26:44,669 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@41fd9d8e
[2016-04-14T23:26Z] INFO  16:26:44,774 ProgressMeter -            done    134208.0    20.0 s       2.5 m      100.0%    20.0 s       0.0 s
[2016-04-14T23:26Z] INFO  16:26:44,774 ProgressMeter - Total runtime 20.16 secs, 0.34 min, 0.01 hours
[2016-04-14T23:26Z] INFO  16:26:44,774 MicroScheduler - 159 reads were filtered out during the traversal out of approximately 134367 total reads (0.12%)
[2016-04-14T23:26Z] INFO  16:26:44,775 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:26Z] INFO  16:26:44,775 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:26Z] INFO  16:26:44,775 MicroScheduler -   -> 159 reads (0.12% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:26Z] INFO  16:26:44,824 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:26Z] INFO  16:26:44,827 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:26Z] INFO  16:26:44,827 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:26Z] INFO  16:26:44,827 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:26Z] INFO  16:26:44,828 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:26Z] INFO  16:26:44,832 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/4/R14-18102_kapa-NGv3-PE100-NGv3-sort-4_183267803_191154276-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/4/R14-18102_kapa-NGv3-PE100-NGv3-sort-4_183267803_191154276-prep-prealign-realign.intervals -L 4:183267804-191154276 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/4/tx/tmpEhIrA7/R14-18102_kapa-NGv3-PE100-NGv3-sort-4_183267803_191154276-prep.bam
[2016-04-14T23:26Z] INFO  16:26:44,838 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-14T23:26Z] INFO  16:26:44,841 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:26Z] INFO  16:26:44,842 HelpFormatter - Date/Time: 2016/04/14 16:26:44
[2016-04-14T23:26Z] INFO  16:26:44,842 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:26Z] INFO  16:26:44,843 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:26Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-4_68340604_83852298-prep.bam
[2016-04-14T23:26Z] INFO  16:26:44,859 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:26Z] INFO  16:26:44,961 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.10
[2016-04-14T23:26Z] INFO  16:26:45,058 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:26Z] INFO  16:26:45,069 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@5fe152b7
[2016-04-14T23:26Z] INFO  16:26:45,172 ProgressMeter -            done    233992.0    31.0 s       2.3 m       99.3%    31.0 s       0.0 s
[2016-04-14T23:26Z] INFO  16:26:45,173 ProgressMeter - Total runtime 31.80 secs, 0.53 min, 0.01 hours
[2016-04-14T23:26Z] INFO  16:26:45,173 MicroScheduler - 133 reads were filtered out during the traversal out of approximately 234125 total reads (0.06%)
[2016-04-14T23:26Z] INFO  16:26:45,174 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:26Z] INFO  16:26:45,174 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:26Z] INFO  16:26:45,174 MicroScheduler -   -> 133 reads (0.06% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:26Z] INFO  16:26:45,221 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:26Z] INFO  16:26:45,240 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:26Z] INFO  16:26:45,313 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-14T23:26Z] INFO  16:26:45,422 IntervalUtils - Processing 15593044 bp from intervals
[2016-04-14T23:26Z] WARN  16:26:45,427 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:26Z] INFO  16:26:45,448 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:26Z] INFO  16:26:45,451 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:26Z] INFO  16:26:45,451 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:26Z] INFO  16:26:45,451 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:26Z] INFO  16:26:45,455 HelpFormatter - Program Args: -T PrintReads -L 5:112073556-127595521 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/5/tx/tmp0mq6Tl/R14-18102_kapa-NGv3-PE100-NGv3-sort-5_112073555_127595521-prep-prealign.bam
[2016-04-14T23:26Z] INFO  16:26:45,474 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:26Z] INFO  16:26:45,475 HelpFormatter - Date/Time: 2016/04/14 16:26:45
[2016-04-14T23:26Z] INFO  16:26:45,475 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:26Z] INFO  16:26:45,475 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:26Z] INFO  16:26:45,528 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:26Z] INFO  16:26:45,569 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:26Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-4_134075461_150351181-prep.bam
[2016-04-14T23:26Z] INFO  16:26:45,673 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:26Z] INFO  16:26:45,694 IntervalUtils - Processing 7886473 bp from intervals
[2016-04-14T23:26Z] WARN  16:26:45,703 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:26Z] INFO  16:26:45,723 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:26Z] INFO  16:26:45,724 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:26Z] INFO  16:26:45,725 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:26Z] INFO  16:26:45,725 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-14T23:26Z] INFO  16:26:45,827 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:26Z] GATK pre-alignment ('5', 143200044, 158710347) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:26Z] INFO  16:26:45,932 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:26Z] INFO  16:26:45,933 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:26Z] INFO  16:26:45,933 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:26Z] INFO  16:26:45,934 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:26Z] INFO  16:26:46,037 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:26Z] GATK pre-alignment ('5', 158711911, 174870102) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:26Z] INFO  16:26:46,125 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:26Z] INFO  16:26:46,315 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:26Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-5_80911291_96430739-prep-prealign.bam
[2016-04-14T23:26Z] INFO  16:26:46,605 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:26Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-5_31294068_49695124-prep-prealign.bam
[2016-04-14T23:26Z] GATK RealignerTargetCreator: R14-18102_kapa-NGv3-PE100-NGv3-sort-5_80911291_96430739-prep-prealign.bam 5:80911292-96430739
[2016-04-14T23:26Z] GATK: RealignerTargetCreator
[2016-04-14T23:26Z] INFO  16:26:46,928 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-14T23:26Z] INFO  16:26:46,973 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:26Z] INFO  16:26:46,982 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:26Z] INFO  16:26:47,043 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-14T23:26Z] INFO  16:26:47,067 IntervalUtils - Processing 15521966 bp from intervals
[2016-04-14T23:26Z] INFO  16:26:47,220 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:26Z] GATK RealignerTargetCreator: R14-18102_kapa-NGv3-PE100-NGv3-sort-5_31294068_49695124-prep-prealign.bam 5:31294069-49695124
[2016-04-14T23:26Z] GATK: RealignerTargetCreator
[2016-04-14T23:26Z] INFO  16:26:47,499 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:26Z] INFO  16:26:47,500 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:26Z] INFO  16:26:47,501 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:26Z] INFO  16:26:47,502 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:26Z] INFO  16:26:47,515 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:26Z] INFO  16:26:47,567 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:26Z] INFO  16:26:47,570 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:26Z] INFO  16:26:47,570 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:26Z] INFO  16:26:47,571 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:26Z] INFO  16:26:47,575 HelpFormatter - Program Args: -T PrintReads -L 5:127597428-143191869 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/5/tx/tmp8J4HLL/R14-18102_kapa-NGv3-PE100-NGv3-sort-5_127597427_143191869-prep-prealign.bam
[2016-04-14T23:26Z] INFO  16:26:47,603 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:26Z] INFO  16:26:47,604 HelpFormatter - Date/Time: 2016/04/14 16:26:47
[2016-04-14T23:26Z] INFO  16:26:47,605 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:26Z] INFO  16:26:47,606 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:26Z] INFO  16:26:47,658 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:26Z] INFO  16:26:47,754 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:26Z] INFO  16:26:48,671 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:26Z] INFO  16:26:48,674 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:26Z] INFO  16:26:48,675 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:26Z] INFO  16:26:48,675 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:26Z] INFO  16:26:48,680 HelpFormatter - Program Args: -T PrintReads -L 5:143200045-158710347 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/5/tx/tmp6D1Rpa/R14-18102_kapa-NGv3-PE100-NGv3-sort-5_143200044_158710347-prep-prealign.bam
[2016-04-14T23:26Z] INFO  16:26:48,715 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:26Z] INFO  16:26:48,715 HelpFormatter - Date/Time: 2016/04/14 16:26:48
[2016-04-14T23:26Z] INFO  16:26:48,715 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:26Z] INFO  16:26:48,716 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:26Z] INFO  16:26:48,873 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:26Z] INFO  16:26:49,014 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-14T23:26Z] INFO  16:26:49,075 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:26Z] INFO  16:26:49,084 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:26Z] INFO  16:26:49,143 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-14T23:26Z] INFO  16:26:49,158 IntervalUtils - Processing 15594442 bp from intervals
[2016-04-14T23:26Z] INFO  16:26:49,235 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:26Z] INFO  16:26:49,235 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:26Z] INFO  16:26:49,239 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:26Z] INFO  16:26:49,239 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:26Z] INFO  16:26:49,240 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:26Z] INFO  16:26:49,245 HelpFormatter - Program Args: -T PrintReads -L 5:158711912-174870102 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/5/tx/tmpQwAV9E/R14-18102_kapa-NGv3-PE100-NGv3-sort-5_158711911_174870102-prep-prealign.bam
[2016-04-14T23:26Z] INFO  16:26:49,275 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:26Z] INFO  16:26:49,277 HelpFormatter - Date/Time: 2016/04/14 16:26:49
[2016-04-14T23:26Z] INFO  16:26:49,277 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:26Z] INFO  16:26:49,278 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:26Z] INFO  16:26:49,476 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:26Z] INFO  16:26:49,544 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@41fd9d8e
[2016-04-14T23:26Z] INFO  16:26:49,622 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:26Z] INFO  16:26:49,623 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:26Z] INFO  16:26:49,623 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:26Z] INFO  16:26:49,623 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:26Z] INFO  16:26:49,661 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:26Z] INFO  16:26:49,678 ProgressMeter -            done   1006933.0   119.0 s     118.0 s      100.0%   119.0 s       0.0 s
[2016-04-14T23:26Z] INFO  16:26:49,679 ProgressMeter - Total runtime 119.03 secs, 1.98 min, 0.03 hours
[2016-04-14T23:26Z] INFO  16:26:49,679 MicroScheduler - 389 reads were filtered out during the traversal out of approximately 1007322 total reads (0.04%)
[2016-04-14T23:26Z] INFO  16:26:49,679 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:26Z] INFO  16:26:49,680 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:26Z] INFO  16:26:49,680 MicroScheduler -   -> 389 reads (0.04% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:26Z] INFO  16:26:49,787 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:26Z] INFO  16:26:49,805 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:26Z] INFO  16:26:49,806 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:26Z] INFO  16:26:49,807 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:26Z] INFO  16:26:49,812 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/5/R14-18102_kapa-NGv3-PE100-NGv3-sort-5_80911291_96430739-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/5/tx/tmplEpc8Q/R14-18102_kapa-NGv3-PE100-NGv3-sort-5_80911291_96430739-prep-prealign-realign.intervals -l INFO -L 5:80911292-96430739 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-14T23:26Z] INFO  16:26:49,819 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:26Z] INFO  16:26:49,824 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:26Z] INFO  16:26:49,825 HelpFormatter - Date/Time: 2016/04/14 16:26:49
[2016-04-14T23:26Z] INFO  16:26:49,825 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:26Z] INFO  16:26:49,826 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:26Z] INFO  16:26:49,964 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:26Z] INFO  16:26:50,218 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-14T23:26Z] INFO  16:26:50,229 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-14T23:26Z] INFO  16:26:50,272 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:26Z] INFO  16:26:50,269 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:26Z] INFO  16:26:50,280 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:26Z] INFO  16:26:50,281 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:26Z] INFO  16:26:50,284 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:26Z] INFO  16:26:50,285 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:26Z] INFO  16:26:50,286 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:26Z] INFO  16:26:50,290 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/5/R14-18102_kapa-NGv3-PE100-NGv3-sort-5_31294068_49695124-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/5/tx/tmpJBzu_l/R14-18102_kapa-NGv3-PE100-NGv3-sort-5_31294068_49695124-prep-prealign-realign.intervals -l INFO -L 5:31294069-49695124 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-14T23:26Z] INFO  16:26:50,309 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:26Z] INFO  16:26:50,310 HelpFormatter - Date/Time: 2016/04/14 16:26:50
[2016-04-14T23:26Z] INFO  16:26:50,311 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:26Z] INFO  16:26:50,311 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:26Z] INFO  16:26:50,326 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-14T23:26Z] INFO  16:26:50,335 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-14T23:26Z] INFO  16:26:50,351 IntervalUtils - Processing 15510303 bp from intervals
[2016-04-14T23:26Z] INFO  16:26:50,411 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:26Z] INFO  16:26:50,458 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:26Z] INFO  16:26:50,620 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-14T23:26Z] INFO  16:26:50,630 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-14T23:26Z] INFO  16:26:50,648 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:26Z] INFO  16:26:50,672 IntervalUtils - Processing 15519448 bp from intervals
[2016-04-14T23:26Z] WARN  16:26:50,677 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:26Z] INFO  16:26:50,714 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:26Z] INFO  16:26:50,723 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:26Z] INFO  16:26:50,736 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.09
[2016-04-14T23:26Z] INFO  16:26:50,744 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:26Z] INFO  16:26:50,766 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.04
[2016-04-14T23:26Z] INFO  16:26:50,777 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:26Z] INFO  16:26:50,778 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:26Z] INFO  16:26:50,782 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:26Z] INFO  16:26:50,782 IntervalUtils - Processing 16158191 bp from intervals
[2016-04-14T23:26Z] INFO  16:26:50,782 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:26Z] INFO  16:26:50,798 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:26Z] INFO  16:26:50,904 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:26Z] INFO  16:26:50,918 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:26Z] INFO  16:26:50,918 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:26Z] INFO  16:26:50,940 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:26Z] INFO  16:26:50,940 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-14T23:26Z] INFO  16:26:50,976 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:26Z] INFO  16:26:51,019 IntervalUtils - Processing 18401056 bp from intervals
[2016-04-14T23:26Z] WARN  16:26:51,024 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:26Z] INFO  16:26:51,096 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:26Z] INFO  16:26:51,140 ProgressMeter -            done     44534.0     7.0 s       2.9 m      100.0%     7.0 s       0.0 s
[2016-04-14T23:26Z] INFO  16:26:51,141 ProgressMeter - Total runtime 7.63 secs, 0.13 min, 0.00 hours
[2016-04-14T23:26Z] INFO  16:26:51,144 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 44534 total reads (0.00%)
[2016-04-14T23:26Z] INFO  16:26:51,145 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:26Z] INFO  16:26:51,146 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:26Z] INFO  16:26:51,146 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:26Z] INFO  16:26:51,283 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:26Z] INFO  16:26:51,284 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:26Z] INFO  16:26:51,285 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:26Z] INFO  16:26:51,285 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-14T23:26Z] INFO  16:26:51,311 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:26Z] INFO  16:26:51,311 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:26Z] INFO  16:26:51,312 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:26Z] INFO  16:26:51,312 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:26Z] INFO  16:26:51,340 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:26Z] INFO  16:26:51,385 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:26Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-4_0_15511864-prep-prealign.bam
[2016-04-14T23:26Z] INFO  16:26:51,554 ProgressMeter -      5:79366615    200004.0    30.0 s       2.5 m       90.7%    33.0 s       3.0 s
[2016-04-14T23:26Z] INFO  16:26:51,637 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:26Z] INFO  16:26:52,128 ProgressMeter -            done    149890.0    13.0 s      92.0 s      100.0%    13.0 s       0.0 s
[2016-04-14T23:26Z] INFO  16:26:52,128 ProgressMeter - Total runtime 13.83 secs, 0.23 min, 0.00 hours
[2016-04-14T23:26Z] INFO  16:26:52,133 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 149890 total reads (0.00%)
[2016-04-14T23:26Z] INFO  16:26:52,134 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:26Z] INFO  16:26:52,135 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:26Z] INFO  16:26:52,135 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:26Z] INFO  16:26:52,568 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:26Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-5_15616091_31267808-prep.bam
[2016-04-14T23:26Z] INFO  16:26:52,624 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@41fd9d8e
[2016-04-14T23:26Z] INFO  16:26:52,808 ProgressMeter -            done     66497.0    13.0 s       3.3 m      100.0%    13.0 s       0.0 s
[2016-04-14T23:26Z] INFO  16:26:52,809 ProgressMeter - Total runtime 13.06 secs, 0.22 min, 0.00 hours
[2016-04-14T23:26Z] INFO  16:26:52,809 MicroScheduler - 86 reads were filtered out during the traversal out of approximately 66583 total reads (0.13%)
[2016-04-14T23:26Z] INFO  16:26:52,809 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:26Z] INFO  16:26:52,810 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:26Z] INFO  16:26:52,810 MicroScheduler -   -> 86 reads (0.13% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:26Z] GATK pre-alignment ('5', 174919106, 180915260) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:26Z] INFO  16:26:53,542 ProgressMeter -            done     95852.0    10.0 s     113.0 s      100.0%    10.0 s       0.0 s
[2016-04-14T23:26Z] INFO  16:26:53,542 ProgressMeter - Total runtime 10.86 secs, 0.18 min, 0.00 hours
[2016-04-14T23:26Z] INFO  16:26:53,547 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 95852 total reads (0.00%)
[2016-04-14T23:26Z] INFO  16:26:53,547 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:26Z] INFO  16:26:53,548 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:26Z] INFO  16:26:53,548 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:26Z] INFO  16:26:53,554 ProgressMeter -            done    745632.0    46.0 s      62.0 s      100.0%    46.0 s       0.0 s
[2016-04-14T23:26Z] INFO  16:26:53,554 ProgressMeter - Total runtime 46.69 secs, 0.78 min, 0.01 hours
[2016-04-14T23:26Z] INFO  16:26:53,558 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 745632 total reads (0.00%)
[2016-04-14T23:26Z] INFO  16:26:53,559 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:26Z] INFO  16:26:53,559 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:26Z] INFO  16:26:53,560 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:26Z] INFO  16:26:53,822 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:26Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-4_150354547_165878648-prep.bam
[2016-04-14T23:26Z] INFO  16:26:54,354 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:26Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-5_96432513_112043579-prep-prealign.bam
[2016-04-14T23:26Z] GATK RealignerTargetCreator: R14-18102_kapa-NGv3-PE100-NGv3-sort-4_0_15511864-prep-prealign.bam 4:1-15511864
[2016-04-14T23:26Z] GATK: RealignerTargetCreator
[2016-04-14T23:26Z] GATK pre-alignment ('6', 0, 15509601) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:26Z] GATK RealignerTargetCreator: R14-18102_kapa-NGv3-PE100-NGv3-sort-5_96432513_112043579-prep-prealign.bam 5:96432514-112043579
[2016-04-14T23:26Z] GATK: RealignerTargetCreator
[2016-04-14T23:26Z] INFO  16:26:54,781 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:26Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-4_165889318_183245405-prep.bam
[2016-04-14T23:26Z] INFO  16:26:55,127 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:26Z] GATK pre-alignment ('6', 15511526, 31080332) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:26Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-3_47129602_62648069-prep.bam
[2016-04-14T23:26Z] INFO  16:26:55,367 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@5fe152b7
[2016-04-14T23:26Z] INFO  16:26:55,533 ProgressMeter -            done    263004.0    34.0 s       2.2 m      100.0%    34.0 s       0.0 s
[2016-04-14T23:26Z] INFO  16:26:55,533 ProgressMeter - Total runtime 34.02 secs, 0.57 min, 0.01 hours
[2016-04-14T23:26Z] INFO  16:26:55,534 MicroScheduler - 162 reads were filtered out during the traversal out of approximately 263166 total reads (0.06%)
[2016-04-14T23:26Z] INFO  16:26:55,534 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:26Z] INFO  16:26:55,535 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:26Z] INFO  16:26:55,535 MicroScheduler -   -> 162 reads (0.06% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:26Z] INFO  16:26:56,229 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:26Z] INFO  16:26:56,234 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:26Z] INFO  16:26:56,234 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:26Z] INFO  16:26:56,235 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:26Z] INFO  16:26:56,240 HelpFormatter - Program Args: -T PrintReads -L 5:174919107-180915260 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/5/tx/tmp_poBMe/R14-18102_kapa-NGv3-PE100-NGv3-sort-5_174919106_180915260-prep-prealign.bam
[2016-04-14T23:26Z] INFO  16:26:56,259 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:26Z] INFO  16:26:56,260 HelpFormatter - Date/Time: 2016/04/14 16:26:56
[2016-04-14T23:26Z] INFO  16:26:56,260 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:26Z] INFO  16:26:56,260 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:26Z] INFO  16:26:56,471 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:26Z] INFO  16:26:56,972 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:26Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-5_65290574_80809536-prep-prealign.bam
[2016-04-14T23:26Z] INFO  16:26:57,434 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:26Z] INFO  16:26:57,439 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:26Z] INFO  16:26:57,439 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:26Z] INFO  16:26:57,440 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:26Z] INFO  16:26:57,446 HelpFormatter - Program Args: -T PrintReads -L 6:1-15509601 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/6/tx/tmpkmlRvf/R14-18102_kapa-NGv3-PE100-NGv3-sort-6_0_15509601-prep-prealign.bam
[2016-04-14T23:26Z] INFO  16:26:57,467 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:26Z] INFO  16:26:57,479 HelpFormatter - Date/Time: 2016/04/14 16:26:57
[2016-04-14T23:26Z] INFO  16:26:57,479 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:26Z] INFO  16:26:57,480 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:26Z] INFO  16:26:57,588 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:26Z] INFO  16:26:57,591 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:26Z] INFO  16:26:57,592 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:26Z] INFO  16:26:57,592 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:26Z] INFO  16:26:57,597 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/4/R14-18102_kapa-NGv3-PE100-NGv3-sort-4_0_15511864-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/4/tx/tmp_zs2ps/R14-18102_kapa-NGv3-PE100-NGv3-sort-4_0_15511864-prep-prealign-realign.intervals -l INFO -L 4:1-15511864 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-14T23:26Z] INFO  16:26:57,606 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-14T23:26Z] INFO  16:26:57,624 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:26Z] INFO  16:26:57,625 HelpFormatter - Date/Time: 2016/04/14 16:26:57
[2016-04-14T23:26Z] INFO  16:26:57,626 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:26Z] INFO  16:26:57,630 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:26Z] INFO  16:26:57,665 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:26Z] INFO  16:26:57,673 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:26Z] INFO  16:26:57,711 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:26Z] INFO  16:26:57,715 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:26Z] INFO  16:26:57,717 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.04
[2016-04-14T23:26Z] INFO  16:26:57,744 IntervalUtils - Processing 5996154 bp from intervals
[2016-04-14T23:26Z] INFO  16:26:57,866 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:26Z] GATK pre-alignment ('6', 31083801, 46593245) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:26Z] INFO  16:26:57,915 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-14T23:26Z] INFO  16:26:57,933 ProgressMeter -            done    141429.0    11.0 s      84.0 s       98.1%    11.0 s       0.0 s
[2016-04-14T23:26Z] INFO  16:26:57,934 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:26Z] INFO  16:26:57,935 ProgressMeter - Total runtime 12.00 secs, 0.20 min, 0.00 hours
[2016-04-14T23:26Z] INFO  16:26:57,939 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 141429 total reads (0.00%)
[2016-04-14T23:26Z] INFO  16:26:57,940 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:26Z] INFO  16:26:57,940 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:26Z] INFO  16:26:57,940 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:26Z] INFO  16:26:57,951 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:26Z] INFO  16:26:57,953 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:26Z] INFO  16:26:57,953 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:26Z] INFO  16:26:57,961 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:26Z] INFO  16:26:57,965 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/5/R14-18102_kapa-NGv3-PE100-NGv3-sort-5_96432513_112043579-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/5/tx/tmp8bmuzl/R14-18102_kapa-NGv3-PE100-NGv3-sort-5_96432513_112043579-prep-prealign-realign.intervals -l INFO -L 5:96432514-112043579 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-14T23:26Z] GATK RealignerTargetCreator: R14-18102_kapa-NGv3-PE100-NGv3-sort-5_65290574_80809536-prep-prealign.bam 5:65290575-80809536
[2016-04-14T23:26Z] GATK: RealignerTargetCreator
[2016-04-14T23:26Z] INFO  16:26:57,984 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-14T23:26Z] INFO  16:26:57,985 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:26Z] INFO  16:26:57,985 HelpFormatter - Date/Time: 2016/04/14 16:26:57
[2016-04-14T23:26Z] INFO  16:26:57,986 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:26Z] INFO  16:26:57,986 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:26Z] INFO  16:26:58,129 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:26Z] INFO  16:26:58,176 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:26Z] INFO  16:26:58,177 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:26Z] INFO  16:26:58,178 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:26Z] INFO  16:26:58,179 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:26Z] INFO  16:26:58,237 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:26Z] INFO  16:26:58,350 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:26Z] INFO  16:26:58,410 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-14T23:26Z] INFO  16:26:58,419 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:26Z] INFO  16:26:58,423 IntervalUtils - Processing 15511864 bp from intervals
[2016-04-14T23:26Z] WARN  16:26:58,431 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:26Z] INFO  16:26:58,504 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-14T23:26Z] INFO  16:26:58,520 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:26Z] INFO  16:26:58,516 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:26Z] INFO  16:26:58,522 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:26Z] INFO  16:26:58,523 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:26Z] INFO  16:26:58,523 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:26Z] INFO  16:26:58,529 HelpFormatter - Program Args: -T PrintReads -L 6:15511527-31080332 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/6/tx/tmp1N8Y5v/R14-18102_kapa-NGv3-PE100-NGv3-sort-6_15511526_31080332-prep-prealign.bam
[2016-04-14T23:26Z] INFO  16:26:58,541 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:26Z] INFO  16:26:58,541 HelpFormatter - Date/Time: 2016/04/14 16:26:58
[2016-04-14T23:26Z] INFO  16:26:58,541 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:26Z] INFO  16:26:58,541 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:26Z] INFO  16:26:58,778 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:26Z] INFO  16:26:58,844 IntervalUtils - Processing 15611066 bp from intervals
[2016-04-14T23:26Z] WARN  16:26:58,849 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:26Z] INFO  16:26:58,865 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:26Z] INFO  16:26:58,866 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:26Z] INFO  16:26:58,867 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:26Z] INFO  16:26:58,867 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-14T23:26Z] INFO  16:26:58,940 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:26Z] INFO  16:26:58,998 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-14T23:26Z] INFO  16:26:59,080 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:26Z] INFO  16:26:59,100 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:26Z] INFO  16:26:59,124 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:26Z] INFO  16:26:59,125 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:26Z] INFO  16:26:59,126 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:26Z] INFO  16:26:59,126 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-14T23:26Z] INFO  16:26:59,165 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-14T23:26Z] INFO  16:26:59,190 IntervalUtils - Processing 15509601 bp from intervals
[2016-04-14T23:26Z] INFO  16:26:59,344 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:26Z] INFO  16:26:59,515 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:26Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-4_183267803_191154276-prep.bam
[2016-04-14T23:26Z] INFO  16:26:59,758 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:26Z] INFO  16:26:59,759 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:26Z] INFO  16:26:59,760 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:26Z] INFO  16:26:59,761 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:26Z] INFO  16:26:59,821 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:26Z] INFO  16:26:59,967 ProgressMeter -            done   1.5580921E7    19.0 s       1.0 s      100.0%    19.0 s       0.0 s
[2016-04-14T23:26Z] INFO  16:26:59,968 ProgressMeter - Total runtime 19.43 secs, 0.32 min, 0.01 hours
[2016-04-14T23:26Z] INFO  16:26:59,972 MicroScheduler - 22688 reads were filtered out during the traversal out of approximately 220578 total reads (10.29%)
[2016-04-14T23:26Z] INFO  16:26:59,982 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:26Z] INFO  16:26:59,983 MicroScheduler -   -> 721 reads (0.33% of total) failing BadMateFilter
[2016-04-14T23:26Z] INFO  16:26:59,984 MicroScheduler -   -> 17733 reads (8.04% of total) failing DuplicateReadFilter
[2016-04-14T23:26Z] INFO  16:26:59,984 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-14T23:26Z] INFO  16:26:59,985 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:26Z] INFO  16:26:59,985 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-14T23:26Z] INFO  16:26:59,986 MicroScheduler -   -> 4234 reads (1.92% of total) failing MappingQualityZeroFilter
[2016-04-14T23:26Z] INFO  16:26:59,987 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:26Z] INFO  16:26:59,987 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-14T23:26Z] INFO  16:26:59,988 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-14T23:26Z] INFO  16:26:59,988 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-14T23:27Z] INFO  16:27:00,034 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:27Z] INFO  16:27:00,052 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:27Z] GATK pre-alignment ('6', 46598699, 62284307) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:27Z] INFO  16:27:00,061 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:27Z] INFO  16:27:00,110 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-14T23:27Z] INFO  16:27:00,128 IntervalUtils - Processing 15568806 bp from intervals
[2016-04-14T23:27Z] INFO  16:27:00,202 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:27Z] INFO  16:27:00,473 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:27Z] INFO  16:27:00,474 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:27Z] INFO  16:27:00,475 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:27Z] INFO  16:27:00,475 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:27Z] INFO  16:27:00,498 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:27Z] INFO  16:27:00,657 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:27Z] INFO  16:27:00,937 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:27Z] INFO  16:27:00,941 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:27Z] INFO  16:27:00,941 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:27Z] INFO  16:27:00,942 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:27Z] INFO  16:27:00,946 HelpFormatter - Program Args: -T PrintReads -L 6:31083802-46593245 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/6/tx/tmp2d7m1d/R14-18102_kapa-NGv3-PE100-NGv3-sort-6_31083801_46593245-prep-prealign.bam
[2016-04-14T23:27Z] INFO  16:27:01,001 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:27Z] INFO  16:27:01,002 HelpFormatter - Date/Time: 2016/04/14 16:27:00
[2016-04-14T23:27Z] INFO  16:27:01,003 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:27Z] INFO  16:27:01,003 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:27Z] INFO  16:27:01,240 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:27Z] INFO  16:27:01,439 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:27Z] INFO  16:27:01,462 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:27Z] INFO  16:27:01,462 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:27Z] INFO  16:27:01,463 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:27Z] INFO  16:27:01,468 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/5/R14-18102_kapa-NGv3-PE100-NGv3-sort-5_65290574_80809536-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/5/tx/tmpxRDMiA/R14-18102_kapa-NGv3-PE100-NGv3-sort-5_65290574_80809536-prep-prealign-realign.intervals -l INFO -L 5:65290575-80809536 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-14T23:27Z] INFO  16:27:01,488 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:27Z] INFO  16:27:01,489 HelpFormatter - Date/Time: 2016/04/14 16:27:01
[2016-04-14T23:27Z] INFO  16:27:01,489 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:27Z] INFO  16:27:01,490 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:27Z] INFO  16:27:01,598 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:27Z] INFO  16:27:01,724 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:27Z] GATK: realign ('5', 0, 15580921) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:27Z] INFO  16:27:01,865 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-14T23:27Z] INFO  16:27:01,875 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:27Z] INFO  16:27:01,966 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.09
[2016-04-14T23:27Z] INFO  16:27:02,420 IntervalUtils - Processing 15518962 bp from intervals
[2016-04-14T23:27Z] WARN  16:27:02,437 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:27Z] INFO  16:27:02,539 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-14T23:27Z] INFO  16:27:02,572 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:27Z] INFO  16:27:02,628 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:27Z] INFO  16:27:02,636 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:27Z] INFO  16:27:02,706 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-14T23:27Z] INFO  16:27:02,728 IntervalUtils - Processing 15509444 bp from intervals
[2016-04-14T23:27Z] INFO  16:27:02,797 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:27Z] INFO  16:27:02,798 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:27Z] INFO  16:27:02,799 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:27Z] INFO  16:27:02,800 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-14T23:27Z] INFO  16:27:02,808 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:27Z] INFO  16:27:03,040 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:27Z] INFO  16:27:03,043 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:27Z] INFO  16:27:03,044 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:27Z] INFO  16:27:03,044 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:27Z] INFO  16:27:03,049 HelpFormatter - Program Args: -T PrintReads -L 6:46598700-62284307 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/6/tx/tmpMFkVOk/R14-18102_kapa-NGv3-PE100-NGv3-sort-6_46598699_62284307-prep-prealign.bam
[2016-04-14T23:27Z] INFO  16:27:03,080 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:27Z] INFO  16:27:03,081 HelpFormatter - Date/Time: 2016/04/14 16:27:03
[2016-04-14T23:27Z] INFO  16:27:03,082 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:27Z] INFO  16:27:03,082 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:27Z] INFO  16:27:03,112 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:27Z] INFO  16:27:03,113 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:27Z] INFO  16:27:03,114 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:27Z] INFO  16:27:03,115 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:27Z] INFO  16:27:03,148 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:27Z] INFO  16:27:03,267 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:27Z] INFO  16:27:03,356 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:27Z] INFO  16:27:04,433 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-14T23:27Z] INFO  16:27:04,497 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:27Z] INFO  16:27:04,506 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:27Z] INFO  16:27:04,594 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.09
[2016-04-14T23:27Z] INFO  16:27:04,618 IntervalUtils - Processing 15685608 bp from intervals
[2016-04-14T23:27Z] INFO  16:27:04,745 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:27Z] INFO  16:27:04,828 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:27Z] INFO  16:27:04,830 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:27Z] INFO  16:27:04,830 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:27Z] INFO  16:27:04,831 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:27Z] INFO  16:27:04,850 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/5/R14-18102_kapa-NGv3-PE100-NGv3-sort-5_0_15580921-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/5/R14-18102_kapa-NGv3-PE100-NGv3-sort-5_0_15580921-prep-prealign-realign.intervals -L 5:1-15580921 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/5/tx/tmpZsVNLy/R14-18102_kapa-NGv3-PE100-NGv3-sort-5_0_15580921-prep.bam
[2016-04-14T23:27Z] INFO  16:27:04,881 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:27Z] INFO  16:27:04,882 HelpFormatter - Date/Time: 2016/04/14 16:27:04
[2016-04-14T23:27Z] INFO  16:27:04,883 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:27Z] INFO  16:27:04,883 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:27Z] INFO  16:27:04,984 ProgressMeter -            done   1.5593044E7    19.0 s       1.0 s      100.0%    19.0 s       0.0 s
[2016-04-14T23:27Z] INFO  16:27:04,985 ProgressMeter - Total runtime 19.26 secs, 0.32 min, 0.01 hours
[2016-04-14T23:27Z] INFO  16:27:05,000 MicroScheduler - 12104 reads were filtered out during the traversal out of approximately 139021 total reads (8.71%)
[2016-04-14T23:27Z] INFO  16:27:05,000 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:27Z] INFO  16:27:05,000 MicroScheduler -   -> 463 reads (0.33% of total) failing BadMateFilter
[2016-04-14T23:27Z] INFO  16:27:05,001 MicroScheduler -   -> 11143 reads (8.02% of total) failing DuplicateReadFilter
[2016-04-14T23:27Z] INFO  16:27:05,001 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-14T23:27Z] INFO  16:27:05,001 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:27Z] INFO  16:27:05,002 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-14T23:27Z] INFO  16:27:05,002 MicroScheduler -   -> 498 reads (0.36% of total) failing MappingQualityZeroFilter
[2016-04-14T23:27Z] INFO  16:27:05,002 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:27Z] INFO  16:27:05,003 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-14T23:27Z] INFO  16:27:05,003 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-14T23:27Z] INFO  16:27:05,081 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:27Z] INFO  16:27:05,096 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:27Z] INFO  16:27:05,097 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:27Z] INFO  16:27:05,098 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:27Z] INFO  16:27:05,099 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:27Z] INFO  16:27:05,112 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:27Z] INFO  16:27:05,157 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:27Z] INFO  16:27:05,166 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:27Z] INFO  16:27:05,232 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-14T23:27Z] INFO  16:27:05,293 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:27Z] INFO  16:27:05,673 IntervalUtils - Processing 15580921 bp from intervals
[2016-04-14T23:27Z] WARN  16:27:05,678 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:27Z] INFO  16:27:05,786 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:27Z] INFO  16:27:05,965 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:27Z] INFO  16:27:05,966 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:27Z] INFO  16:27:05,966 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:27Z] INFO  16:27:05,967 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:27Z] INFO  16:27:06,191 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:27Z] INFO  16:27:06,383 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:27Z] INFO  16:27:06,440 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:27Z] GATK: realign ('5', 49695692, 65288736) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:27Z] INFO  16:27:07,779 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@41fd9d8e
[2016-04-14T23:27Z] INFO  16:27:08,048 ProgressMeter -            done    137900.0    20.0 s       2.5 m      100.0%    20.0 s       0.0 s
[2016-04-14T23:27Z] INFO  16:27:08,049 ProgressMeter - Total runtime 20.55 secs, 0.34 min, 0.01 hours
[2016-04-14T23:27Z] INFO  16:27:08,049 MicroScheduler - 127 reads were filtered out during the traversal out of approximately 138027 total reads (0.09%)
[2016-04-14T23:27Z] INFO  16:27:08,050 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:27Z] INFO  16:27:08,050 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:27Z] INFO  16:27:08,050 MicroScheduler -   -> 127 reads (0.09% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:27Z] INFO  16:27:08,276 ProgressMeter -            done   1.5519448E7    17.0 s       1.0 s      100.0%    17.0 s       0.0 s
[2016-04-14T23:27Z] INFO  16:27:08,277 ProgressMeter - Total runtime 17.36 secs, 0.29 min, 0.00 hours
[2016-04-14T23:27Z] INFO  16:27:08,281 MicroScheduler - 11444 reads were filtered out during the traversal out of approximately 135062 total reads (8.47%)
[2016-04-14T23:27Z] INFO  16:27:08,282 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:27Z] INFO  16:27:08,283 MicroScheduler -   -> 471 reads (0.35% of total) failing BadMateFilter
[2016-04-14T23:27Z] INFO  16:27:08,284 MicroScheduler -   -> 10590 reads (7.84% of total) failing DuplicateReadFilter
[2016-04-14T23:27Z] INFO  16:27:08,284 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-14T23:27Z] INFO  16:27:08,285 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:27Z] INFO  16:27:08,285 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-14T23:27Z] INFO  16:27:08,286 MicroScheduler -   -> 383 reads (0.28% of total) failing MappingQualityZeroFilter
[2016-04-14T23:27Z] INFO  16:27:08,287 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:27Z] INFO  16:27:08,287 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-14T23:27Z] INFO  16:27:08,288 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-14T23:27Z] INFO  16:27:09,442 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:27Z] INFO  16:27:09,446 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:27Z] INFO  16:27:09,447 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:27Z] INFO  16:27:09,447 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:27Z] INFO  16:27:09,452 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/5/R14-18102_kapa-NGv3-PE100-NGv3-sort-5_49695692_65288736-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/5/R14-18102_kapa-NGv3-PE100-NGv3-sort-5_49695692_65288736-prep-prealign-realign.intervals -L 5:49695693-65288736 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/5/tx/tmpaBnVXv/R14-18102_kapa-NGv3-PE100-NGv3-sort-5_49695692_65288736-prep.bam
[2016-04-14T23:27Z] INFO  16:27:09,454 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:27Z] INFO  16:27:09,468 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:27Z] INFO  16:27:09,468 HelpFormatter - Date/Time: 2016/04/14 16:27:09
[2016-04-14T23:27Z] INFO  16:27:09,469 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:27Z] INFO  16:27:09,478 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:27Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-5_112073555_127595521-prep-prealign.bam
[2016-04-14T23:27Z] INFO  16:27:09,631 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:27Z] GATK: realign ('5', 80911291, 96430739) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:27Z] INFO  16:27:09,684 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:27Z] INFO  16:27:09,823 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:27Z] INFO  16:27:09,835 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:27Z] INFO  16:27:09,898 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-14T23:27Z] GATK RealignerTargetCreator: R14-18102_kapa-NGv3-PE100-NGv3-sort-5_112073555_127595521-prep-prealign.bam 5:112073556-127595521
[2016-04-14T23:27Z] GATK: RealignerTargetCreator
[2016-04-14T23:27Z] INFO  16:27:10,346 IntervalUtils - Processing 15593044 bp from intervals
[2016-04-14T23:27Z] WARN  16:27:10,352 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:27Z] INFO  16:27:10,437 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:27Z] INFO  16:27:10,589 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:27Z] INFO  16:27:10,590 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:27Z] INFO  16:27:10,591 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:27Z] INFO  16:27:10,592 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:27Z] INFO  16:27:10,832 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:27Z] INFO  16:27:11,017 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:27Z] INFO  16:27:11,924 ProgressMeter -            done   1.8401056E7    20.0 s       1.0 s      100.0%    20.0 s       0.0 s
[2016-04-14T23:27Z] INFO  16:27:11,925 ProgressMeter - Total runtime 20.64 secs, 0.34 min, 0.01 hours
[2016-04-14T23:27Z] INFO  16:27:11,929 MicroScheduler - 20159 reads were filtered out during the traversal out of approximately 235196 total reads (8.57%)
[2016-04-14T23:27Z] INFO  16:27:11,930 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:27Z] INFO  16:27:11,931 MicroScheduler -   -> 652 reads (0.28% of total) failing BadMateFilter
[2016-04-14T23:27Z] INFO  16:27:11,932 MicroScheduler -   -> 18886 reads (8.03% of total) failing DuplicateReadFilter
[2016-04-14T23:27Z] INFO  16:27:11,932 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-14T23:27Z] INFO  16:27:11,933 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:27Z] INFO  16:27:11,934 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-14T23:27Z] INFO  16:27:11,935 MicroScheduler -   -> 621 reads (0.26% of total) failing MappingQualityZeroFilter
[2016-04-14T23:27Z] INFO  16:27:11,935 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:27Z] INFO  16:27:11,936 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-14T23:27Z] INFO  16:27:11,936 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-14T23:27Z] INFO  16:27:12,695 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:27Z] INFO  16:27:12,698 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:27Z] INFO  16:27:12,698 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:27Z] INFO  16:27:12,698 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:27Z] INFO  16:27:12,702 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/5/R14-18102_kapa-NGv3-PE100-NGv3-sort-5_80911291_96430739-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/5/R14-18102_kapa-NGv3-PE100-NGv3-sort-5_80911291_96430739-prep-prealign-realign.intervals -L 5:80911292-96430739 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/5/tx/tmpn5C1aV/R14-18102_kapa-NGv3-PE100-NGv3-sort-5_80911291_96430739-prep.bam
[2016-04-14T23:27Z] INFO  16:27:12,720 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:27Z] INFO  16:27:12,720 HelpFormatter - Date/Time: 2016/04/14 16:27:12
[2016-04-14T23:27Z] INFO  16:27:12,721 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:27Z] INFO  16:27:12,721 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:27Z] INFO  16:27:13,041 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:27Z] INFO  16:27:13,137 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:27Z] INFO  16:27:13,141 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:27Z] INFO  16:27:13,142 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:27Z] INFO  16:27:13,142 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:27Z] INFO  16:27:13,147 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/5/R14-18102_kapa-NGv3-PE100-NGv3-sort-5_112073555_127595521-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/5/tx/tmpodbfgq/R14-18102_kapa-NGv3-PE100-NGv3-sort-5_112073555_127595521-prep-prealign-realign.intervals -l INFO -L 5:112073556-127595521 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-14T23:27Z] INFO  16:27:13,155 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:27Z] INFO  16:27:13,164 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:27Z] INFO  16:27:13,164 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:27Z] INFO  16:27:13,165 HelpFormatter - Date/Time: 2016/04/14 16:27:13
[2016-04-14T23:27Z] INFO  16:27:13,166 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:27Z] INFO  16:27:13,166 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:27Z] INFO  16:27:13,220 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-14T23:27Z] INFO  16:27:13,284 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:27Z] INFO  16:27:13,374 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:27Z] GATK: realign ('5', 31294068, 49695124) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:27Z] INFO  16:27:13,575 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-14T23:27Z] INFO  16:27:13,587 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:27Z] INFO  16:27:13,595 IntervalUtils - Processing 15519448 bp from intervals
[2016-04-14T23:27Z] WARN  16:27:13,611 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:27Z] INFO  16:27:13,682 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.09
[2016-04-14T23:27Z] INFO  16:27:13,750 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:27Z] INFO  16:27:13,859 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:27Z] INFO  16:27:13,860 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:27Z] INFO  16:27:13,861 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:27Z] INFO  16:27:13,878 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:27Z] INFO  16:27:14,064 IntervalUtils - Processing 15521966 bp from intervals
[2016-04-14T23:27Z] INFO  16:27:14,069 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:27Z] WARN  16:27:14,080 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:27Z] INFO  16:27:14,204 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:27Z] INFO  16:27:14,219 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:27Z] INFO  16:27:14,475 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:27Z] INFO  16:27:14,476 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:27Z] INFO  16:27:14,476 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:27Z] INFO  16:27:14,476 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-14T23:27Z] INFO  16:27:14,664 ProgressMeter -            done   1.5611066E7    15.0 s       0.0 s      100.0%    15.0 s       0.0 s
[2016-04-14T23:27Z] INFO  16:27:14,665 ProgressMeter - Total runtime 15.54 secs, 0.26 min, 0.00 hours
[2016-04-14T23:27Z] INFO  16:27:14,670 MicroScheduler - 6155 reads were filtered out during the traversal out of approximately 67095 total reads (9.17%)
[2016-04-14T23:27Z] INFO  16:27:14,671 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:27Z] INFO  16:27:14,671 MicroScheduler -   -> 382 reads (0.57% of total) failing BadMateFilter
[2016-04-14T23:27Z] INFO  16:27:14,672 MicroScheduler -   -> 5182 reads (7.72% of total) failing DuplicateReadFilter
[2016-04-14T23:27Z] INFO  16:27:14,672 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-14T23:27Z] INFO  16:27:14,673 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:27Z] INFO  16:27:14,673 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-14T23:27Z] INFO  16:27:14,673 MicroScheduler -   -> 591 reads (0.88% of total) failing MappingQualityZeroFilter
[2016-04-14T23:27Z] INFO  16:27:14,673 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:27Z] INFO  16:27:14,674 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-14T23:27Z] INFO  16:27:14,674 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-14T23:27Z] INFO  16:27:14,838 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@5fe152b7
[2016-04-14T23:27Z] INFO  16:27:14,977 ProgressMeter -            done    167280.0    23.0 s       2.4 m      100.0%    23.0 s       0.0 s
[2016-04-14T23:27Z] INFO  16:27:14,978 ProgressMeter - Total runtime 23.67 secs, 0.39 min, 0.01 hours
[2016-04-14T23:27Z] INFO  16:27:14,978 MicroScheduler - 127 reads were filtered out during the traversal out of approximately 167407 total reads (0.08%)
[2016-04-14T23:27Z] INFO  16:27:14,978 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:27Z] INFO  16:27:14,979 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:27Z] INFO  16:27:14,979 MicroScheduler -   -> 127 reads (0.08% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:27Z] INFO  16:27:15,944 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:27Z] INFO  16:27:15,947 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:27Z] INFO  16:27:15,948 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:27Z] INFO  16:27:15,949 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:27Z] INFO  16:27:15,953 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/5/R14-18102_kapa-NGv3-PE100-NGv3-sort-5_31294068_49695124-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/5/R14-18102_kapa-NGv3-PE100-NGv3-sort-5_31294068_49695124-prep-prealign-realign.intervals -L 5:31294069-49695124 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/5/tx/tmpgpDRWh/R14-18102_kapa-NGv3-PE100-NGv3-sort-5_31294068_49695124-prep.bam
[2016-04-14T23:27Z] INFO  16:27:15,963 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:27Z] INFO  16:27:15,963 HelpFormatter - Date/Time: 2016/04/14 16:27:15
[2016-04-14T23:27Z] INFO  16:27:15,963 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:27Z] INFO  16:27:15,963 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:27Z] INFO  16:27:16,159 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:27Z] INFO  16:27:16,296 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:27Z] INFO  16:27:16,305 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:27Z] INFO  16:27:16,344 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.04
[2016-04-14T23:27Z] INFO  16:27:16,647 IntervalUtils - Processing 18401056 bp from intervals
[2016-04-14T23:27Z] WARN  16:27:16,653 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:27Z] INFO  16:27:16,787 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:27Z] INFO  16:27:16,919 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:27Z] INFO  16:27:16,920 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:27Z] INFO  16:27:16,921 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:27Z] INFO  16:27:16,922 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:27Z] INFO  16:27:17,067 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:27Z] INFO  16:27:17,093 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:27Z] INFO  16:27:17,096 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:27Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-5_158711911_174870102-prep-prealign.bam
[2016-04-14T23:27Z] GATK: realign ('5', 96432513, 112043579) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:27Z] INFO  16:27:17,336 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:27Z] GATK RealignerTargetCreator: R14-18102_kapa-NGv3-PE100-NGv3-sort-5_158711911_174870102-prep-prealign.bam 5:158711912-174870102
[2016-04-14T23:27Z] GATK: RealignerTargetCreator
[2016-04-14T23:27Z] INFO  16:27:19,803 ProgressMeter -     5:137722521    100001.0    30.0 s       5.0 m       64.9%    46.0 s      16.0 s
[2016-04-14T23:27Z] INFO  16:27:19,930 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:27Z] INFO  16:27:19,933 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:27Z] INFO  16:27:19,934 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:27Z] INFO  16:27:19,934 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:27Z] INFO  16:27:19,939 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/5/R14-18102_kapa-NGv3-PE100-NGv3-sort-5_96432513_112043579-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/5/R14-18102_kapa-NGv3-PE100-NGv3-sort-5_96432513_112043579-prep-prealign-realign.intervals -L 5:96432514-112043579 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/5/tx/tmpcGJ2vq/R14-18102_kapa-NGv3-PE100-NGv3-sort-5_96432513_112043579-prep.bam
[2016-04-14T23:27Z] INFO  16:27:19,948 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:27Z] INFO  16:27:19,949 HelpFormatter - Date/Time: 2016/04/14 16:27:19
[2016-04-14T23:27Z] INFO  16:27:19,949 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:27Z] INFO  16:27:19,950 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:27Z] INFO  16:27:20,167 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:27Z] INFO  16:27:20,307 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:27Z] INFO  16:27:20,317 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:27Z] INFO  16:27:20,376 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-14T23:27Z] INFO  16:27:20,610 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:27Z] INFO  16:27:20,614 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:27Z] INFO  16:27:20,615 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:27Z] INFO  16:27:20,616 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:27Z] INFO  16:27:20,621 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/5/R14-18102_kapa-NGv3-PE100-NGv3-sort-5_158711911_174870102-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/5/tx/tmp8W1Jqk/R14-18102_kapa-NGv3-PE100-NGv3-sort-5_158711911_174870102-prep-prealign-realign.intervals -l INFO -L 5:158711912-174870102 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-14T23:27Z] INFO  16:27:20,637 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:27Z] INFO  16:27:20,637 HelpFormatter - Date/Time: 2016/04/14 16:27:20
[2016-04-14T23:27Z] INFO  16:27:20,637 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:27Z] INFO  16:27:20,637 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:27Z] INFO  16:27:20,743 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:27Z] INFO  16:27:20,802 ProgressMeter -     5:150847343    200006.0    30.0 s       2.5 m       49.3%    60.0 s      30.0 s
[2016-04-14T23:27Z] INFO  16:27:20,874 IntervalUtils - Processing 15611066 bp from intervals
[2016-04-14T23:27Z] WARN  16:27:20,879 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:27Z] INFO  16:27:20,954 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-14T23:27Z] INFO  16:27:20,964 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:27Z] INFO  16:27:20,979 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:27Z] INFO  16:27:21,010 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-14T23:27Z] INFO  16:27:21,122 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:27Z] INFO  16:27:21,124 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:27Z] INFO  16:27:21,124 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:27Z] INFO  16:27:21,128 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:27Z] INFO  16:27:21,258 IntervalUtils - Processing 16158191 bp from intervals
[2016-04-14T23:27Z] WARN  16:27:21,264 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:27Z] INFO  16:27:21,297 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:27Z] INFO  16:27:21,335 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:27Z] INFO  16:27:21,459 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:27Z] INFO  16:27:21,513 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:27Z] INFO  16:27:21,515 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:27Z] INFO  16:27:21,515 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:27Z] INFO  16:27:21,516 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-14T23:27Z] INFO  16:27:22,157 ProgressMeter -            done   1.5518962E7    19.0 s       1.0 s      100.0%    19.0 s       0.0 s
[2016-04-14T23:27Z] INFO  16:27:22,158 ProgressMeter - Total runtime 19.36 secs, 0.32 min, 0.01 hours
[2016-04-14T23:27Z] INFO  16:27:22,162 MicroScheduler - 43250 reads were filtered out during the traversal out of approximately 264232 total reads (16.37%)
[2016-04-14T23:27Z] INFO  16:27:22,163 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:27Z] INFO  16:27:22,164 MicroScheduler -   -> 630 reads (0.24% of total) failing BadMateFilter
[2016-04-14T23:27Z] INFO  16:27:22,165 MicroScheduler -   -> 18636 reads (7.05% of total) failing DuplicateReadFilter
[2016-04-14T23:27Z] INFO  16:27:22,165 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-14T23:27Z] INFO  16:27:22,166 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:27Z] INFO  16:27:22,167 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-14T23:27Z] INFO  16:27:22,167 MicroScheduler -   -> 23984 reads (9.08% of total) failing MappingQualityZeroFilter
[2016-04-14T23:27Z] INFO  16:27:22,170 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:27Z] INFO  16:27:22,171 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-14T23:27Z] INFO  16:27:22,181 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-14T23:27Z] INFO  16:27:22,304 ProgressMeter -            done    138356.0    11.0 s      84.0 s      100.0%    11.0 s       0.0 s
[2016-04-14T23:27Z] INFO  16:27:22,305 ProgressMeter - Total runtime 11.71 secs, 0.20 min, 0.00 hours
[2016-04-14T23:27Z] INFO  16:27:22,308 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 138356 total reads (0.00%)
[2016-04-14T23:27Z] INFO  16:27:22,309 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:27Z] INFO  16:27:22,309 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:27Z] INFO  16:27:22,309 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:27Z] INFO  16:27:23,675 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:27Z] GATK: realign ('5', 65290574, 80809536) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:27Z] INFO  16:27:23,788 ProgressMeter -            done    219480.0    17.0 s      81.0 s      100.0%    17.0 s       0.0 s
[2016-04-14T23:27Z] INFO  16:27:23,789 ProgressMeter - Total runtime 17.82 secs, 0.30 min, 0.00 hours
[2016-04-14T23:27Z] INFO  16:27:23,793 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 219480 total reads (0.00%)
[2016-04-14T23:27Z] INFO  16:27:23,794 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:27Z] INFO  16:27:23,794 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:27Z] INFO  16:27:23,795 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:27Z] INFO  16:27:23,841 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:27Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-5_49695692_65288736-prep.bam
[2016-04-14T23:27Z] GATK pre-alignment ('6', 62390867, 78173120) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:27Z] INFO  16:27:25,331 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:27Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-5_0_15580921-prep.bam
[2016-04-14T23:27Z] INFO  16:27:25,641 ProgressMeter -            done   1.5511864E7    26.0 s       1.0 s      100.0%    26.0 s       0.0 s
[2016-04-14T23:27Z] INFO  16:27:25,642 ProgressMeter - Total runtime 26.78 secs, 0.45 min, 0.01 hours
[2016-04-14T23:27Z] INFO  16:27:25,642 MicroScheduler - 577599 reads were filtered out during the traversal out of approximately 1009915 total reads (57.19%)
[2016-04-14T23:27Z] INFO  16:27:25,643 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:27Z] INFO  16:27:25,643 MicroScheduler -   -> 1082 reads (0.11% of total) failing BadMateFilter
[2016-04-14T23:27Z] INFO  16:27:25,643 MicroScheduler -   -> 47558 reads (4.71% of total) failing DuplicateReadFilter
[2016-04-14T23:27Z] INFO  16:27:25,644 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-14T23:27Z] INFO  16:27:25,644 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:27Z] INFO  16:27:25,644 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-14T23:27Z] INFO  16:27:25,644 MicroScheduler -   -> 528959 reads (52.38% of total) failing MappingQualityZeroFilter
[2016-04-14T23:27Z] INFO  16:27:25,645 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:27Z] INFO  16:27:25,645 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-14T23:27Z] INFO  16:27:25,645 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-14T23:27Z] INFO  16:27:25,708 ProgressMeter -            done    134208.0    11.0 s      88.0 s      100.0%    11.0 s       0.0 s
[2016-04-14T23:27Z] INFO  16:27:25,708 ProgressMeter - Total runtime 11.85 secs, 0.20 min, 0.00 hours
[2016-04-14T23:27Z] INFO  16:27:25,712 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 134208 total reads (0.00%)
[2016-04-14T23:27Z] INFO  16:27:25,712 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:27Z] INFO  16:27:25,713 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:27Z] INFO  16:27:25,713 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:27Z] GATK pre-alignment ('6', 78400388, 93953258) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:27Z] INFO  16:27:26,397 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:27Z] INFO  16:27:26,400 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:27Z] INFO  16:27:26,401 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:27Z] INFO  16:27:26,401 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:27Z] INFO  16:27:26,406 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/5/R14-18102_kapa-NGv3-PE100-NGv3-sort-5_65290574_80809536-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/5/R14-18102_kapa-NGv3-PE100-NGv3-sort-5_65290574_80809536-prep-prealign-realign.intervals -L 5:65290575-80809536 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/5/tx/tmpYt57zs/R14-18102_kapa-NGv3-PE100-NGv3-sort-5_65290574_80809536-prep.bam
[2016-04-14T23:27Z] INFO  16:27:26,439 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:27Z] INFO  16:27:26,440 HelpFormatter - Date/Time: 2016/04/14 16:27:26
[2016-04-14T23:27Z] INFO  16:27:26,440 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:27Z] INFO  16:27:26,441 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:27Z] INFO  16:27:26,702 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:27Z] INFO  16:27:26,836 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:27Z] INFO  16:27:26,850 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:27Z] INFO  16:27:26,903 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-14T23:27Z] INFO  16:27:27,109 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:27Z] GATK: realign ('4', 0, 15511864) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:27Z] INFO  16:27:27,183 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@7172f77a
[2016-04-14T23:27Z] INFO  16:27:27,219 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:27Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-5_80911291_96430739-prep.bam
[2016-04-14T23:27Z] INFO  16:27:27,282 ProgressMeter -            done    205175.0    27.0 s       2.2 m      100.0%    27.0 s       0.0 s
[2016-04-14T23:27Z] INFO  16:27:27,282 ProgressMeter - Total runtime 27.52 secs, 0.46 min, 0.01 hours
[2016-04-14T23:27Z] INFO  16:27:27,283 MicroScheduler - 161 reads were filtered out during the traversal out of approximately 205336 total reads (0.08%)
[2016-04-14T23:27Z] INFO  16:27:27,283 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:27Z] INFO  16:27:27,283 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:27Z] INFO  16:27:27,284 MicroScheduler -   -> 161 reads (0.08% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:27Z] INFO  16:27:27,352 IntervalUtils - Processing 15518962 bp from intervals
[2016-04-14T23:27Z] WARN  16:27:27,358 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:27Z] INFO  16:27:27,362 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:27Z] INFO  16:27:27,366 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:27Z] INFO  16:27:27,366 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:27Z] INFO  16:27:27,367 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:27Z] INFO  16:27:27,373 HelpFormatter - Program Args: -T PrintReads -L 6:62390868-78173120 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/6/tx/tmppJWFsr/R14-18102_kapa-NGv3-PE100-NGv3-sort-6_62390867_78173120-prep-prealign.bam
[2016-04-14T23:27Z] INFO  16:27:27,387 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:27Z] INFO  16:27:27,387 HelpFormatter - Date/Time: 2016/04/14 16:27:27
[2016-04-14T23:27Z] INFO  16:27:27,387 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:27Z] INFO  16:27:27,387 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:27Z] INFO  16:27:27,456 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:27Z] INFO  16:27:27,589 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:27Z] INFO  16:27:27,609 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:27Z] INFO  16:27:27,611 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:27Z] INFO  16:27:27,611 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:27Z] INFO  16:27:27,612 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:27Z] INFO  16:27:27,762 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:27Z] GATK pre-alignment ('6', 93955015, 109466584) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:27Z] INFO  16:27:27,965 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:27Z] INFO  16:27:28,214 ProgressMeter -     5:179220681    200002.0    30.0 s       2.5 m       71.7%    41.0 s      11.0 s
[2016-04-14T23:27Z] INFO  16:27:28,673 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:27Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-6_0_15509601-prep-prealign.bam
[2016-04-14T23:27Z] INFO  16:27:28,895 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-14T23:27Z] INFO  16:27:28,900 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:27Z] INFO  16:27:28,903 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:27Z] INFO  16:27:28,903 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:27Z] INFO  16:27:28,903 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:27Z] INFO  16:27:28,919 HelpFormatter - Program Args: -T PrintReads -L 6:78400389-93953258 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/6/tx/tmpfMGnSN/R14-18102_kapa-NGv3-PE100-NGv3-sort-6_78400388_93953258-prep-prealign.bam
[2016-04-14T23:27Z] INFO  16:27:28,941 ProgressMeter -            done     66497.0     7.0 s     117.0 s      100.0%     7.0 s       0.0 s
[2016-04-14T23:27Z] INFO  16:27:28,942 ProgressMeter - Total runtime 7.82 secs, 0.13 min, 0.00 hours
[2016-04-14T23:27Z] INFO  16:27:28,946 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 66497 total reads (0.00%)
[2016-04-14T23:27Z] INFO  16:27:28,948 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:27Z] INFO  16:27:28,954 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:27Z] INFO  16:27:28,949 HelpFormatter - Date/Time: 2016/04/14 16:27:28
[2016-04-14T23:27Z] INFO  16:27:28,955 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:27Z] INFO  16:27:28,956 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:27Z] INFO  16:27:28,955 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:27Z] INFO  16:27:28,961 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:27Z] INFO  16:27:28,992 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:27Z] INFO  16:27:29,002 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:27Z] INFO  16:27:29,051 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-14T23:27Z] INFO  16:27:29,066 IntervalUtils - Processing 15782253 bp from intervals
[2016-04-14T23:27Z] INFO  16:27:29,114 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:27Z] INFO  16:27:29,152 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:27Z] GATK RealignerTargetCreator: R14-18102_kapa-NGv3-PE100-NGv3-sort-6_0_15509601-prep-prealign.bam 6:1-15509601
[2016-04-14T23:27Z] GATK: RealignerTargetCreator
[2016-04-14T23:27Z] INFO  16:27:29,501 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:27Z] INFO  16:27:29,502 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:27Z] INFO  16:27:29,503 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:27Z] INFO  16:27:29,504 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:27Z] INFO  16:27:29,531 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:27Z] INFO  16:27:29,709 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:27Z] INFO  16:27:29,931 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:27Z] INFO  16:27:29,935 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:27Z] INFO  16:27:29,936 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:27Z] INFO  16:27:29,936 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:27Z] INFO  16:27:29,941 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/4/R14-18102_kapa-NGv3-PE100-NGv3-sort-4_0_15511864-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/4/R14-18102_kapa-NGv3-PE100-NGv3-sort-4_0_15511864-prep-prealign-realign.intervals -L 4:1-15511864 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/4/tx/tmpHoERVT/R14-18102_kapa-NGv3-PE100-NGv3-sort-4_0_15511864-prep.bam
[2016-04-14T23:27Z] INFO  16:27:29,953 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:27Z] INFO  16:27:29,954 HelpFormatter - Date/Time: 2016/04/14 16:27:29
[2016-04-14T23:27Z] INFO  16:27:29,956 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:27Z] INFO  16:27:29,967 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:27Z] INFO  16:27:30,275 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:27Z] INFO  16:27:30,295 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-14T23:27Z] INFO  16:27:30,359 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:27Z] INFO  16:27:30,383 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:27Z] INFO  16:27:30,406 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:27Z] INFO  16:27:30,416 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:27Z] INFO  16:27:30,440 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-14T23:27Z] INFO  16:27:30,455 IntervalUtils - Processing 15552870 bp from intervals
[2016-04-14T23:27Z] INFO  16:27:30,460 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.04
[2016-04-14T23:27Z] INFO  16:27:30,482 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:27Z] INFO  16:27:30,496 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:27Z] INFO  16:27:30,507 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:27Z] INFO  16:27:30,508 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:27Z] INFO  16:27:30,508 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:27Z] INFO  16:27:30,512 HelpFormatter - Program Args: -T PrintReads -L 6:93955016-109466584 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/6/tx/tmp5A0Sh8/R14-18102_kapa-NGv3-PE100-NGv3-sort-6_93955015_109466584-prep-prealign.bam
[2016-04-14T23:27Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-5_96432513_112043579-prep.bam
[2016-04-14T23:27Z] INFO  16:27:30,529 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:27Z] INFO  16:27:30,530 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:27Z] INFO  16:27:30,531 HelpFormatter - Date/Time: 2016/04/14 16:27:30
[2016-04-14T23:27Z] INFO  16:27:30,531 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:27Z] INFO  16:27:30,531 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:27Z] INFO  16:27:30,627 ProgressMeter -      6:28200606    200002.0    30.0 s       2.5 m       81.5%    36.0 s       6.0 s
[2016-04-14T23:27Z] INFO  16:27:30,728 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:27Z] GATK pre-alignment ('6', 109467960, 124979532) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:27Z] INFO  16:27:30,833 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:27Z] INFO  16:27:30,834 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:27Z] INFO  16:27:30,835 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:27Z] INFO  16:27:30,835 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:27Z] INFO  16:27:30,851 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:27Z] INFO  16:27:30,856 IntervalUtils - Processing 15511864 bp from intervals
[2016-04-14T23:27Z] WARN  16:27:30,861 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:27Z] INFO  16:27:30,955 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:27Z] INFO  16:27:31,127 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:27Z] INFO  16:27:31,144 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:27Z] INFO  16:27:31,145 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:27Z] INFO  16:27:31,146 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:27Z] INFO  16:27:31,147 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:27Z] INFO  16:27:31,374 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:27Z] INFO  16:27:31,412 ProgressMeter -            done   1.5521966E7    16.0 s       1.0 s      100.0%    16.0 s       0.0 s
[2016-04-14T23:27Z] INFO  16:27:31,413 ProgressMeter - Total runtime 16.94 secs, 0.28 min, 0.00 hours
[2016-04-14T23:27Z] INFO  16:27:31,416 MicroScheduler - 11975 reads were filtered out during the traversal out of approximately 138255 total reads (8.66%)
[2016-04-14T23:27Z] INFO  16:27:31,417 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:27Z] INFO  16:27:31,417 MicroScheduler -   -> 572 reads (0.41% of total) failing BadMateFilter
[2016-04-14T23:27Z] INFO  16:27:31,417 MicroScheduler -   -> 11084 reads (8.02% of total) failing DuplicateReadFilter
[2016-04-14T23:27Z] INFO  16:27:31,417 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-14T23:27Z] INFO  16:27:31,418 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:27Z] INFO  16:27:31,418 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-14T23:27Z] INFO  16:27:31,418 MicroScheduler -   -> 319 reads (0.23% of total) failing MappingQualityZeroFilter
[2016-04-14T23:27Z] INFO  16:27:31,418 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:27Z] INFO  16:27:31,419 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-14T23:27Z] INFO  16:27:31,419 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-14T23:27Z] INFO  16:27:31,629 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:27Z] INFO  16:27:31,748 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-14T23:27Z] INFO  16:27:31,841 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:27Z] INFO  16:27:31,851 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:27Z] INFO  16:27:31,901 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-14T23:27Z] INFO  16:27:31,916 IntervalUtils - Processing 15511569 bp from intervals
[2016-04-14T23:27Z] INFO  16:27:31,925 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:27Z] INFO  16:27:31,928 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:27Z] INFO  16:27:31,928 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:27Z] INFO  16:27:31,929 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:27Z] INFO  16:27:31,933 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/6/R14-18102_kapa-NGv3-PE100-NGv3-sort-6_0_15509601-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/6/tx/tmp7t_x3i/R14-18102_kapa-NGv3-PE100-NGv3-sort-6_0_15509601-prep-prealign-realign.intervals -l INFO -L 6:1-15509601 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-14T23:27Z] INFO  16:27:31,942 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:27Z] INFO  16:27:31,950 HelpFormatter - Date/Time: 2016/04/14 16:27:31
[2016-04-14T23:27Z] INFO  16:27:31,951 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:27Z] INFO  16:27:31,953 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:27Z] INFO  16:27:32,009 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:27Z] INFO  16:27:32,071 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:27Z] INFO  16:27:32,278 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-14T23:27Z] INFO  16:27:32,288 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:27Z] INFO  16:27:32,361 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:27Z] INFO  16:27:32,365 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:27Z] INFO  16:27:32,377 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:27Z] INFO  16:27:32,378 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:27Z] INFO  16:27:32,398 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.11
[2016-04-14T23:27Z] INFO  16:27:32,402 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:27Z] INFO  16:27:32,508 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@7172f77a
[2016-04-14T23:27Z] INFO  16:27:32,592 ProgressMeter -            done    196844.0    27.0 s       2.3 m      100.0%    27.0 s       0.0 s
[2016-04-14T23:27Z] INFO  16:27:32,593 ProgressMeter - Total runtime 27.50 secs, 0.46 min, 0.01 hours
[2016-04-14T23:27Z] INFO  16:27:32,593 MicroScheduler - 139 reads were filtered out during the traversal out of approximately 196983 total reads (0.07%)
[2016-04-14T23:27Z] INFO  16:27:32,594 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:27Z] INFO  16:27:32,595 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:27Z] INFO  16:27:32,596 MicroScheduler -   -> 139 reads (0.07% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:27Z] INFO  16:27:32,677 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:27Z] INFO  16:27:32,796 IntervalUtils - Processing 15509601 bp from intervals
[2016-04-14T23:27Z] WARN  16:27:32,802 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:27Z] INFO  16:27:32,807 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:27Z] GATK: realign ('5', 112073555, 127595521) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:27Z] INFO  16:27:32,884 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:27Z] INFO  16:27:33,080 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:27Z] INFO  16:27:33,081 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:27Z] INFO  16:27:33,082 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:27Z] INFO  16:27:33,083 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-14T23:27Z] INFO  16:27:33,149 ProgressMeter -      6:32023677    200007.0    30.0 s       2.5 m        6.1%     8.3 m       7.8 m
[2016-04-14T23:27Z] INFO  16:27:33,553 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:27Z] INFO  16:27:33,556 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:27Z] INFO  16:27:33,556 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:27Z] INFO  16:27:33,557 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:27Z] INFO  16:27:33,561 HelpFormatter - Program Args: -T PrintReads -L 6:109467961-124979532 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/6/tx/tmpKfahm_/R14-18102_kapa-NGv3-PE100-NGv3-sort-6_109467960_124979532-prep-prealign.bam
[2016-04-14T23:27Z] INFO  16:27:33,580 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:27Z] INFO  16:27:33,581 HelpFormatter - Date/Time: 2016/04/14 16:27:33
[2016-04-14T23:27Z] INFO  16:27:33,582 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:27Z] INFO  16:27:33,582 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:27Z] INFO  16:27:33,774 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:27Z] INFO  16:27:33,909 ProgressMeter -            done    233992.0    16.0 s      72.0 s       99.3%    16.0 s       0.0 s
[2016-04-14T23:27Z] INFO  16:27:33,910 ProgressMeter - Total runtime 16.99 secs, 0.28 min, 0.00 hours
[2016-04-14T23:27Z] INFO  16:27:33,910 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@41fd9d8e
[2016-04-14T23:27Z] INFO  16:27:33,914 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 233992 total reads (0.00%)
[2016-04-14T23:27Z] INFO  16:27:33,915 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:27Z] INFO  16:27:33,916 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:27Z] INFO  16:27:33,916 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:27Z] INFO  16:27:34,051 ProgressMeter -            done    324130.0    43.0 s       2.2 m      100.0%    43.0 s       0.0 s
[2016-04-14T23:27Z] INFO  16:27:34,052 ProgressMeter - Total runtime 43.27 secs, 0.72 min, 0.01 hours
[2016-04-14T23:27Z] INFO  16:27:34,053 MicroScheduler - 138 reads were filtered out during the traversal out of approximately 324268 total reads (0.04%)
[2016-04-14T23:27Z] INFO  16:27:34,054 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:27Z] INFO  16:27:34,054 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:27Z] INFO  16:27:34,055 MicroScheduler -   -> 138 reads (0.04% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:27Z] INFO  16:27:34,078 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:27Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-6_46598699_62284307-prep-prealign.bam
[2016-04-14T23:27Z] GATK RealignerTargetCreator: R14-18102_kapa-NGv3-PE100-NGv3-sort-6_46598699_62284307-prep-prealign.bam 6:46598700-62284307
[2016-04-14T23:27Z] GATK: RealignerTargetCreator
[2016-04-14T23:27Z] INFO  16:27:34,984 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-14T23:27Z] INFO  16:27:35,069 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:27Z] INFO  16:27:35,093 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:27Z] INFO  16:27:35,141 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-14T23:27Z] INFO  16:27:35,162 IntervalUtils - Processing 15511572 bp from intervals
[2016-04-14T23:27Z] INFO  16:27:35,249 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:27Z] INFO  16:27:35,540 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:27Z] INFO  16:27:35,558 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:27Z] INFO  16:27:35,559 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:27Z] INFO  16:27:35,560 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:27Z] INFO  16:27:35,561 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:27Z] INFO  16:27:35,575 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:27Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-5_143200044_158710347-prep-prealign.bam
[2016-04-14T23:27Z] INFO  16:27:35,634 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:27Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-5_31294068_49695124-prep.bam
[2016-04-14T23:27Z] INFO  16:27:35,742 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:27Z] INFO  16:27:35,753 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:27Z] INFO  16:27:35,756 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:27Z] INFO  16:27:35,757 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:27Z] INFO  16:27:35,757 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:27Z] INFO  16:27:35,762 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/5/R14-18102_kapa-NGv3-PE100-NGv3-sort-5_112073555_127595521-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/5/R14-18102_kapa-NGv3-PE100-NGv3-sort-5_112073555_127595521-prep-prealign-realign.intervals -L 5:112073556-127595521 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/5/tx/tmpRNQcsf/R14-18102_kapa-NGv3-PE100-NGv3-sort-5_112073555_127595521-prep.bam
[2016-04-14T23:27Z] INFO  16:27:35,789 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:27Z] INFO  16:27:35,790 HelpFormatter - Date/Time: 2016/04/14 16:27:35
[2016-04-14T23:27Z] INFO  16:27:35,790 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:27Z] INFO  16:27:35,790 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:27Z] INFO  16:27:35,981 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:27Z] INFO  16:27:36,166 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:27Z] INFO  16:27:36,175 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:27Z] INFO  16:27:36,237 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-14T23:27Z] GATK pre-alignment ('6', 125112484, 142397186) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:27Z] INFO  16:27:36,567 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@32d5a4c6
[2016-04-14T23:27Z] GATK RealignerTargetCreator: R14-18102_kapa-NGv3-PE100-NGv3-sort-5_143200044_158710347-prep-prealign.bam 5:143200045-158710347
[2016-04-14T23:27Z] GATK: RealignerTargetCreator
[2016-04-14T23:27Z] INFO  16:27:36,692 ProgressMeter -            done    299937.0    38.0 s       2.1 m       98.0%    38.0 s       0.0 s
[2016-04-14T23:27Z] INFO  16:27:36,692 ProgressMeter - Total runtime 38.51 secs, 0.64 min, 0.01 hours
[2016-04-14T23:27Z] INFO  16:27:36,693 MicroScheduler - 101 reads were filtered out during the traversal out of approximately 300038 total reads (0.03%)
[2016-04-14T23:27Z] INFO  16:27:36,693 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:27Z] INFO  16:27:36,693 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:27Z] INFO  16:27:36,694 MicroScheduler -   -> 101 reads (0.03% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:27Z] INFO  16:27:36,758 IntervalUtils - Processing 15521966 bp from intervals
[2016-04-14T23:27Z] WARN  16:27:36,774 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:27Z] INFO  16:27:36,906 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:27Z] INFO  16:27:37,105 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:27Z] INFO  16:27:37,118 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:27Z] INFO  16:27:37,119 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:27Z] INFO  16:27:37,120 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:27Z] INFO  16:27:37,328 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:27Z] INFO  16:27:37,551 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:27Z] INFO  16:27:37,930 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:27Z] INFO  16:27:37,932 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:27Z] INFO  16:27:37,932 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:27Z] INFO  16:27:37,932 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:27Z] INFO  16:27:37,936 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/6/R14-18102_kapa-NGv3-PE100-NGv3-sort-6_46598699_62284307-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/6/tx/tmptV9rFS/R14-18102_kapa-NGv3-PE100-NGv3-sort-6_46598699_62284307-prep-prealign-realign.intervals -l INFO -L 6:46598700-62284307 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-14T23:27Z] INFO  16:27:37,960 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:27Z] INFO  16:27:37,961 HelpFormatter - Date/Time: 2016/04/14 16:27:37
[2016-04-14T23:27Z] INFO  16:27:37,961 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:27Z] INFO  16:27:37,961 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:27Z] INFO  16:27:38,031 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:27Z] INFO  16:27:38,281 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-14T23:27Z] INFO  16:27:38,287 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:27Z] INFO  16:27:38,290 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:27Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-5_174919106_180915260-prep-prealign.bam
[2016-04-14T23:27Z] INFO  16:27:38,358 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-14T23:27Z] INFO  16:27:38,714 IntervalUtils - Processing 15685608 bp from intervals
[2016-04-14T23:27Z] WARN  16:27:38,730 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:27Z] INFO  16:27:38,841 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:27Z] INFO  16:27:39,038 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:27Z] INFO  16:27:39,038 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:27Z] INFO  16:27:39,039 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:27Z] INFO  16:27:39,039 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-14T23:27Z] GATK RealignerTargetCreator: R14-18102_kapa-NGv3-PE100-NGv3-sort-5_174919106_180915260-prep-prealign.bam 5:174919107-180915260
[2016-04-14T23:27Z] GATK: RealignerTargetCreator
[2016-04-14T23:27Z] INFO  16:27:39,453 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:27Z] INFO  16:27:39,456 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:27Z] INFO  16:27:39,457 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:27Z] INFO  16:27:39,457 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:27Z] INFO  16:27:39,462 HelpFormatter - Program Args: -T PrintReads -L 6:125112485-142397186 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/6/tx/tmpJhlbVM/R14-18102_kapa-NGv3-PE100-NGv3-sort-6_125112484_142397186-prep-prealign.bam
[2016-04-14T23:27Z] INFO  16:27:39,481 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:27Z] INFO  16:27:39,482 HelpFormatter - Date/Time: 2016/04/14 16:27:39
[2016-04-14T23:27Z] INFO  16:27:39,483 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:27Z] INFO  16:27:39,483 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:27Z] INFO  16:27:39,625 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:27Z] INFO  16:27:39,628 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:27Z] INFO  16:27:39,629 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:27Z] INFO  16:27:39,629 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:27Z] INFO  16:27:39,633 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/5/R14-18102_kapa-NGv3-PE100-NGv3-sort-5_143200044_158710347-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/5/tx/tmp2qlA4S/R14-18102_kapa-NGv3-PE100-NGv3-sort-5_143200044_158710347-prep-prealign-realign.intervals -l INFO -L 5:143200045-158710347 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-14T23:27Z] INFO  16:27:39,642 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:27Z] INFO  16:27:39,642 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:27Z] INFO  16:27:39,643 HelpFormatter - Date/Time: 2016/04/14 16:27:39
[2016-04-14T23:27Z] INFO  16:27:39,643 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:27Z] INFO  16:27:39,643 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:27Z] INFO  16:27:39,785 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:27Z] INFO  16:27:39,999 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-14T23:27Z] INFO  16:27:40,019 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:27Z] INFO  16:27:40,091 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-14T23:27Z] INFO  16:27:40,235 ProgressMeter -            done   1.6158191E7    18.0 s       1.0 s      100.0%    18.0 s       0.0 s
[2016-04-14T23:27Z] INFO  16:27:40,236 ProgressMeter - Total runtime 18.72 secs, 0.31 min, 0.01 hours
[2016-04-14T23:27Z] INFO  16:27:40,240 MicroScheduler - 14311 reads were filtered out during the traversal out of approximately 168567 total reads (8.49%)
[2016-04-14T23:27Z] INFO  16:27:40,241 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:27Z] INFO  16:27:40,242 MicroScheduler -   -> 565 reads (0.34% of total) failing BadMateFilter
[2016-04-14T23:27Z] INFO  16:27:40,242 MicroScheduler -   -> 13337 reads (7.91% of total) failing DuplicateReadFilter
[2016-04-14T23:27Z] INFO  16:27:40,243 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-14T23:27Z] INFO  16:27:40,244 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:27Z] INFO  16:27:40,244 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-14T23:27Z] INFO  16:27:40,245 MicroScheduler -   -> 409 reads (0.24% of total) failing MappingQualityZeroFilter
[2016-04-14T23:27Z] INFO  16:27:40,245 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:27Z] INFO  16:27:40,246 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-14T23:27Z] INFO  16:27:40,247 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-14T23:27Z] INFO  16:27:40,459 IntervalUtils - Processing 15510303 bp from intervals
[2016-04-14T23:27Z] WARN  16:27:40,473 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:27Z] INFO  16:27:40,552 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:27Z] INFO  16:27:40,763 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-14T23:27Z] INFO  16:27:40,833 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:27Z] INFO  16:27:40,834 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:27Z] INFO  16:27:40,834 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:27Z] INFO  16:27:40,835 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-14T23:27Z] INFO  16:27:40,848 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:27Z] INFO  16:27:40,874 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:27Z] INFO  16:27:40,930 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-14T23:27Z] INFO  16:27:40,947 IntervalUtils - Processing 17284702 bp from intervals
[2016-04-14T23:27Z] INFO  16:27:41,062 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:27Z] INFO  16:27:41,426 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:27Z] INFO  16:27:41,428 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:27Z] INFO  16:27:41,428 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:27Z] INFO  16:27:41,429 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:27Z] INFO  16:27:41,456 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:27Z] INFO  16:27:41,569 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:27Z] GATK: realign ('5', 158711911, 174870102) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:27Z] INFO  16:27:41,638 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:27Z] INFO  16:27:42,278 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:27Z] INFO  16:27:42,281 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:27Z] INFO  16:27:42,282 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:27Z] INFO  16:27:42,282 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:27Z] INFO  16:27:42,287 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/5/R14-18102_kapa-NGv3-PE100-NGv3-sort-5_174919106_180915260-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/5/tx/tmpD86JEx/R14-18102_kapa-NGv3-PE100-NGv3-sort-5_174919106_180915260-prep-prealign-realign.intervals -l INFO -L 5:174919107-180915260 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-14T23:27Z] INFO  16:27:42,302 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:27Z] INFO  16:27:42,303 HelpFormatter - Date/Time: 2016/04/14 16:27:42
[2016-04-14T23:27Z] INFO  16:27:42,303 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:27Z] INFO  16:27:42,304 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:27Z] INFO  16:27:42,405 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:27Z] INFO  16:27:42,688 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-14T23:27Z] INFO  16:27:42,709 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:27Z] INFO  16:27:42,786 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-14T23:27Z] INFO  16:27:43,091 IntervalUtils - Processing 5996154 bp from intervals
[2016-04-14T23:27Z] WARN  16:27:43,096 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:27Z] INFO  16:27:43,218 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:27Z] INFO  16:27:43,455 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:27Z] INFO  16:27:43,456 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:27Z] INFO  16:27:43,457 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:27Z] INFO  16:27:43,457 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-14T23:27Z] INFO  16:27:44,749 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:27Z] INFO  16:27:44,766 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:27Z] INFO  16:27:44,767 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:27Z] INFO  16:27:44,767 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:27Z] INFO  16:27:44,771 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/5/R14-18102_kapa-NGv3-PE100-NGv3-sort-5_158711911_174870102-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/5/R14-18102_kapa-NGv3-PE100-NGv3-sort-5_158711911_174870102-prep-prealign-realign.intervals -L 5:158711912-174870102 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/5/tx/tmpOJFnr_/R14-18102_kapa-NGv3-PE100-NGv3-sort-5_158711911_174870102-prep.bam
[2016-04-14T23:27Z] INFO  16:27:44,787 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:27Z] INFO  16:27:44,788 HelpFormatter - Date/Time: 2016/04/14 16:27:44
[2016-04-14T23:27Z] INFO  16:27:44,788 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:27Z] INFO  16:27:44,789 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:27Z] INFO  16:27:44,979 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:27Z] INFO  16:27:45,116 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:27Z] INFO  16:27:45,136 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:27Z] INFO  16:27:45,219 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-14T23:27Z] INFO  16:27:45,524 IntervalUtils - Processing 16158191 bp from intervals
[2016-04-14T23:27Z] WARN  16:27:45,529 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:27Z] INFO  16:27:45,598 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:27Z] INFO  16:27:45,726 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:27Z] INFO  16:27:45,727 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:27Z] INFO  16:27:45,728 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:27Z] INFO  16:27:45,729 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:27Z] INFO  16:27:45,933 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:27Z] INFO  16:27:46,152 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:27Z] INFO  16:27:47,116 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@7172f77a
[2016-04-14T23:27Z] INFO  16:27:47,174 ProgressMeter -            done    263004.0    19.0 s      74.0 s      100.0%    19.0 s       0.0 s
[2016-04-14T23:27Z] INFO  16:27:47,175 ProgressMeter - Total runtime 19.56 secs, 0.33 min, 0.01 hours
[2016-04-14T23:27Z] INFO  16:27:47,178 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 263004 total reads (0.00%)
[2016-04-14T23:27Z] INFO  16:27:47,179 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:27Z] INFO  16:27:47,179 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:27Z] INFO  16:27:47,179 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:27Z] INFO  16:27:47,237 ProgressMeter -            done    378887.0    46.0 s       2.1 m      100.0%    46.0 s       0.0 s
[2016-04-14T23:27Z] INFO  16:27:47,242 ProgressMeter - Total runtime 46.77 secs, 0.78 min, 0.01 hours
[2016-04-14T23:27Z] INFO  16:27:47,243 MicroScheduler - 195 reads were filtered out during the traversal out of approximately 379082 total reads (0.05%)
[2016-04-14T23:27Z] INFO  16:27:47,243 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:27Z] INFO  16:27:47,243 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:27Z] INFO  16:27:47,244 MicroScheduler -   -> 195 reads (0.05% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:27Z] INFO  16:27:47,571 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@7172f77a
[2016-04-14T23:27Z] INFO  16:27:47,695 ProgressMeter -            done    126981.0    18.0 s       2.4 m      100.0%    18.0 s       0.0 s
[2016-04-14T23:27Z] INFO  16:27:47,696 ProgressMeter - Total runtime 18.19 secs, 0.30 min, 0.01 hours
[2016-04-14T23:27Z] INFO  16:27:47,702 MicroScheduler - 113 reads were filtered out during the traversal out of approximately 127094 total reads (0.09%)
[2016-04-14T23:27Z] INFO  16:27:47,705 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:27Z] INFO  16:27:47,706 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:27Z] INFO  16:27:47,707 MicroScheduler -   -> 113 reads (0.09% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:27Z] INFO  16:27:48,556 ProgressMeter -            done    137900.0    11.0 s      82.0 s      100.0%    11.0 s       0.0 s
[2016-04-14T23:27Z] INFO  16:27:48,556 ProgressMeter - Total runtime 11.44 secs, 0.19 min, 0.00 hours
[2016-04-14T23:27Z] INFO  16:27:48,560 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 137900 total reads (0.00%)
[2016-04-14T23:27Z] INFO  16:27:48,561 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:27Z] INFO  16:27:48,561 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:27Z] INFO  16:27:48,562 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:27Z] INFO  16:27:48,565 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:27Z] INFO  16:27:48,572 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:27Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-5_65290574_80809536-prep.bam
[2016-04-14T23:27Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-6_15511526_31080332-prep-prealign.bam
[2016-04-14T23:27Z] INFO  16:27:49,137 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:27Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-6_62390867_78173120-prep-prealign.bam
[2016-04-14T23:27Z] GATK pre-alignment ('6', 142399691, 157963777) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:27Z] GATK RealignerTargetCreator: R14-18102_kapa-NGv3-PE100-NGv3-sort-6_62390867_78173120-prep-prealign.bam 6:62390868-78173120
[2016-04-14T23:27Z] GATK: RealignerTargetCreator
[2016-04-14T23:27Z] INFO  16:27:49,805 ProgressMeter -     5:140554085    400010.0    60.0 s       2.5 m       83.1%    72.0 s      12.0 s
[2016-04-14T23:27Z] GATK RealignerTargetCreator: R14-18102_kapa-NGv3-PE100-NGv3-sort-6_15511526_31080332-prep-prealign.bam 6:15511527-31080332
[2016-04-14T23:27Z] GATK: RealignerTargetCreator
[2016-04-14T23:27Z] INFO  16:27:50,112 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:27Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-5_112073555_127595521-prep.bam
[2016-04-14T23:27Z] GATK pre-alignment ('6', 158013810, 171115067) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:27Z] INFO  16:27:51,764 ProgressMeter -            done   1.5509601E7    18.0 s       1.0 s      100.0%    18.0 s       0.0 s
[2016-04-14T23:27Z] INFO  16:27:51,765 ProgressMeter - Total runtime 18.68 secs, 0.31 min, 0.01 hours
[2016-04-14T23:27Z] INFO  16:27:51,780 MicroScheduler - 25038 reads were filtered out during the traversal out of approximately 206533 total reads (12.12%)
[2016-04-14T23:27Z] INFO  16:27:51,781 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:27Z] INFO  16:27:51,781 MicroScheduler -   -> 630 reads (0.31% of total) failing BadMateFilter
[2016-04-14T23:27Z] INFO  16:27:51,781 MicroScheduler -   -> 15891 reads (7.69% of total) failing DuplicateReadFilter
[2016-04-14T23:27Z] INFO  16:27:51,782 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-14T23:27Z] INFO  16:27:51,782 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:27Z] INFO  16:27:51,782 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-14T23:27Z] INFO  16:27:51,782 MicroScheduler -   -> 8517 reads (4.12% of total) failing MappingQualityZeroFilter
[2016-04-14T23:27Z] INFO  16:27:51,782 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:27Z] INFO  16:27:51,783 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-14T23:27Z] INFO  16:27:51,783 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-14T23:27Z] INFO  16:27:52,055 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@5fe152b7
[2016-04-14T23:27Z] INFO  16:27:52,192 ProgressMeter -            done    115290.0    19.0 s       2.9 m      100.0%    19.0 s       0.0 s
[2016-04-14T23:27Z] INFO  16:27:52,192 ProgressMeter - Total runtime 19.83 secs, 0.33 min, 0.01 hours
[2016-04-14T23:27Z] INFO  16:27:52,193 MicroScheduler - 100 reads were filtered out during the traversal out of approximately 115390 total reads (0.09%)
[2016-04-14T23:27Z] INFO  16:27:52,193 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:27Z] INFO  16:27:52,193 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:27Z] INFO  16:27:52,194 MicroScheduler -   -> 100 reads (0.09% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:27Z] INFO  16:27:52,342 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:27Z] INFO  16:27:52,356 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:27Z] INFO  16:27:52,357 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:27Z] INFO  16:27:52,358 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:27Z] INFO  16:27:52,362 HelpFormatter - Program Args: -T PrintReads -L 6:142399692-157963777 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/6/tx/tmpR97Pki/R14-18102_kapa-NGv3-PE100-NGv3-sort-6_142399691_157963777-prep-prealign.bam
[2016-04-14T23:27Z] INFO  16:27:52,381 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:27Z] INFO  16:27:52,381 HelpFormatter - Date/Time: 2016/04/14 16:27:52
[2016-04-14T23:27Z] INFO  16:27:52,381 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:27Z] INFO  16:27:52,381 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:27Z] INFO  16:27:52,441 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:27Z] INFO  16:27:52,444 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:27Z] INFO  16:27:52,444 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:27Z] INFO  16:27:52,445 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:27Z] INFO  16:27:52,449 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/6/R14-18102_kapa-NGv3-PE100-NGv3-sort-6_62390867_78173120-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/6/tx/tmpmrz83n/R14-18102_kapa-NGv3-PE100-NGv3-sort-6_62390867_78173120-prep-prealign-realign.intervals -l INFO -L 6:62390868-78173120 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-14T23:27Z] INFO  16:27:52,464 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:27Z] INFO  16:27:52,465 HelpFormatter - Date/Time: 2016/04/14 16:27:52
[2016-04-14T23:27Z] INFO  16:27:52,466 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:27Z] INFO  16:27:52,467 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:27Z] INFO  16:27:52,543 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:27Z] INFO  16:27:52,554 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:27Z] INFO  16:27:52,591 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:27Z] INFO  16:27:52,594 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:27Z] INFO  16:27:52,595 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:27Z] INFO  16:27:52,595 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:27Z] INFO  16:27:52,600 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/6/R14-18102_kapa-NGv3-PE100-NGv3-sort-6_15511526_31080332-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/6/tx/tmpHgdWpN/R14-18102_kapa-NGv3-PE100-NGv3-sort-6_15511526_31080332-prep-prealign-realign.intervals -l INFO -L 6:15511527-31080332 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-14T23:27Z] INFO  16:27:52,623 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:27Z] INFO  16:27:52,638 HelpFormatter - Date/Time: 2016/04/14 16:27:52
[2016-04-14T23:27Z] INFO  16:27:52,639 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:27Z] INFO  16:27:52,639 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:27Z] INFO  16:27:52,754 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:27Z] INFO  16:27:52,755 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-14T23:27Z] INFO  16:27:52,764 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:27Z] INFO  16:27:52,858 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.09
[2016-04-14T23:27Z] INFO  16:27:52,951 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-14T23:27Z] INFO  16:27:52,983 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:27Z] INFO  16:27:53,053 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-14T23:27Z] INFO  16:27:53,132 IntervalUtils - Processing 15782253 bp from intervals
[2016-04-14T23:27Z] WARN  16:27:53,137 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:27Z] INFO  16:27:53,215 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:27Z] INFO  16:27:53,231 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:27Z] GATK: realign ('6', 0, 15509601) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:27Z] INFO  16:27:53,333 IntervalUtils - Processing 15568806 bp from intervals
[2016-04-14T23:27Z] WARN  16:27:53,338 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:27Z] INFO  16:27:53,413 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:27Z] INFO  16:27:53,414 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:27Z] INFO  16:27:53,414 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:27Z] INFO  16:27:53,414 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-14T23:27Z] INFO  16:27:53,414 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:27Z] INFO  16:27:53,551 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:27Z] INFO  16:27:53,554 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:27Z] INFO  16:27:53,554 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:27Z] INFO  16:27:53,554 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:27Z] INFO  16:27:53,558 HelpFormatter - Program Args: -T PrintReads -L 6:158013811-171115067 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/6/tx/tmp6cpy_D/R14-18102_kapa-NGv3-PE100-NGv3-sort-6_158013810_171115067-prep-prealign.bam
[2016-04-14T23:27Z] INFO  16:27:53,569 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:27Z] INFO  16:27:53,569 HelpFormatter - Date/Time: 2016/04/14 16:27:53
[2016-04-14T23:27Z] INFO  16:27:53,570 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:27Z] INFO  16:27:53,570 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:27Z] INFO  16:27:53,599 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-14T23:27Z] INFO  16:27:53,615 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:27Z] INFO  16:27:53,617 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:27Z] INFO  16:27:53,617 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:27Z] INFO  16:27:53,618 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-14T23:27Z] INFO  16:27:53,659 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:27Z] INFO  16:27:53,667 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:27Z] INFO  16:27:53,675 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:27Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-6_93955015_109466584-prep-prealign.bam
[2016-04-14T23:27Z] INFO  16:27:53,713 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-14T23:27Z] INFO  16:27:53,726 IntervalUtils - Processing 15564086 bp from intervals
[2016-04-14T23:27Z] INFO  16:27:53,758 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:27Z] INFO  16:27:53,813 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:27Z] GATK RealignerTargetCreator: R14-18102_kapa-NGv3-PE100-NGv3-sort-6_93955015_109466584-prep-prealign.bam 6:93955016-109466584
[2016-04-14T23:27Z] GATK: RealignerTargetCreator
[2016-04-14T23:27Z] INFO  16:27:54,188 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:27Z] INFO  16:27:54,189 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:27Z] INFO  16:27:54,190 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:27Z] INFO  16:27:54,191 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:27Z] INFO  16:27:54,227 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:27Z] INFO  16:27:54,420 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:27Z] INFO  16:27:55,124 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-14T23:27Z] INFO  16:27:55,188 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:27Z] INFO  16:27:55,198 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:27Z] INFO  16:27:55,245 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-14T23:27Z] INFO  16:27:55,260 IntervalUtils - Processing 13101257 bp from intervals
[2016-04-14T23:27Z] INFO  16:27:55,343 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:27Z] INFO  16:27:55,654 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:27Z] INFO  16:27:55,656 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:27Z] INFO  16:27:55,657 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:27Z] INFO  16:27:55,657 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:27Z] INFO  16:27:55,674 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:27Z] INFO  16:27:55,853 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:27Z] INFO  16:27:56,101 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@41fd9d8e
[2016-04-14T23:27Z] INFO  16:27:56,258 ProgressMeter -            done    158680.0    25.0 s       2.7 m      100.0%    25.0 s       0.0 s
[2016-04-14T23:27Z] INFO  16:27:56,258 ProgressMeter - Total runtime 25.42 secs, 0.42 min, 0.01 hours
[2016-04-14T23:27Z] INFO  16:27:56,259 MicroScheduler - 116 reads were filtered out during the traversal out of approximately 158796 total reads (0.07%)
[2016-04-14T23:27Z] INFO  16:27:56,259 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:27Z] INFO  16:27:56,259 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:27Z] INFO  16:27:56,259 MicroScheduler -   -> 116 reads (0.07% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:27Z] INFO  16:27:56,259 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:27Z] INFO  16:27:56,262 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:27Z] INFO  16:27:56,262 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:27Z] INFO  16:27:56,262 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:27Z] INFO  16:27:56,267 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/6/R14-18102_kapa-NGv3-PE100-NGv3-sort-6_0_15509601-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/6/R14-18102_kapa-NGv3-PE100-NGv3-sort-6_0_15509601-prep-prealign-realign.intervals -L 6:1-15509601 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/6/tx/tmpYYPbel/R14-18102_kapa-NGv3-PE100-NGv3-sort-6_0_15509601-prep.bam
[2016-04-14T23:27Z] INFO  16:27:56,279 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:27Z] INFO  16:27:56,291 HelpFormatter - Date/Time: 2016/04/14 16:27:56
[2016-04-14T23:27Z] INFO  16:27:56,291 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:27Z] INFO  16:27:56,292 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:27Z] INFO  16:27:56,301 ProgressMeter -            done   1.5685608E7    17.0 s       1.0 s      100.0%    17.0 s       0.0 s
[2016-04-14T23:27Z] INFO  16:27:56,302 ProgressMeter - Total runtime 17.26 secs, 0.29 min, 0.00 hours
[2016-04-14T23:27Z] INFO  16:27:56,307 MicroScheduler - 17373 reads were filtered out during the traversal out of approximately 198038 total reads (8.77%)
[2016-04-14T23:27Z] INFO  16:27:56,308 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:27Z] INFO  16:27:56,309 MicroScheduler -   -> 598 reads (0.30% of total) failing BadMateFilter
[2016-04-14T23:27Z] INFO  16:27:56,310 MicroScheduler -   -> 15671 reads (7.91% of total) failing DuplicateReadFilter
[2016-04-14T23:27Z] INFO  16:27:56,310 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-14T23:27Z] INFO  16:27:56,311 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:27Z] INFO  16:27:56,312 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-14T23:27Z] INFO  16:27:56,312 MicroScheduler -   -> 1104 reads (0.56% of total) failing MappingQualityZeroFilter
[2016-04-14T23:27Z] INFO  16:27:56,313 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:27Z] INFO  16:27:56,314 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-14T23:27Z] INFO  16:27:56,315 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-14T23:27Z] INFO  16:27:56,548 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:27Z] INFO  16:27:56,677 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:27Z] INFO  16:27:56,687 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:27Z] INFO  16:27:56,729 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.04
[2016-04-14T23:27Z] INFO  16:27:56,892 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:27Z] INFO  16:27:56,894 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:27Z] INFO  16:27:56,895 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:27Z] INFO  16:27:56,895 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:27Z] INFO  16:27:56,899 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/6/R14-18102_kapa-NGv3-PE100-NGv3-sort-6_93955015_109466584-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/6/tx/tmpEP8SYl/R14-18102_kapa-NGv3-PE100-NGv3-sort-6_93955015_109466584-prep-prealign-realign.intervals -l INFO -L 6:93955016-109466584 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-14T23:27Z] INFO  16:27:56,911 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:27Z] INFO  16:27:56,922 HelpFormatter - Date/Time: 2016/04/14 16:27:56
[2016-04-14T23:27Z] INFO  16:27:56,923 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:27Z] INFO  16:27:56,924 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:27Z] INFO  16:27:57,006 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:27Z] INFO  16:27:57,140 IntervalUtils - Processing 15509601 bp from intervals
[2016-04-14T23:27Z] WARN  16:27:57,144 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:27Z] INFO  16:27:57,180 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-14T23:27Z] INFO  16:27:57,200 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:27Z] INFO  16:27:57,240 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:27Z] INFO  16:27:57,254 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-14T23:27Z] INFO  16:27:57,410 ProgressMeter -            done   5996154.0    13.0 s       2.0 s      100.0%    13.0 s       0.0 s
[2016-04-14T23:27Z] INFO  16:27:57,411 ProgressMeter - Total runtime 13.96 secs, 0.23 min, 0.00 hours
[2016-04-14T23:27Z] INFO  16:27:57,413 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:27Z] INFO  16:27:57,414 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:27Z] INFO  16:27:57,415 MicroScheduler - 39648 reads were filtered out during the traversal out of approximately 301625 total reads (13.14%)
[2016-04-14T23:27Z] INFO  16:27:57,416 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:27Z] INFO  16:27:57,417 MicroScheduler -   -> 555 reads (0.18% of total) failing BadMateFilter
[2016-04-14T23:27Z] INFO  16:27:57,417 MicroScheduler -   -> 23141 reads (7.67% of total) failing DuplicateReadFilter
[2016-04-14T23:27Z] INFO  16:27:57,414 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:27Z] INFO  16:27:57,418 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-14T23:27Z] INFO  16:27:57,414 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:27Z] INFO  16:27:57,418 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:27Z] INFO  16:27:57,419 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-14T23:27Z] INFO  16:27:57,430 MicroScheduler -   -> 15952 reads (5.29% of total) failing MappingQualityZeroFilter
[2016-04-14T23:27Z] INFO  16:27:57,431 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:27Z] INFO  16:27:57,432 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-14T23:27Z] INFO  16:27:57,433 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-14T23:27Z] INFO  16:27:57,599 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:27Z] INFO  16:27:57,621 IntervalUtils - Processing 15511569 bp from intervals
[2016-04-14T23:27Z] WARN  16:27:57,626 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:27Z] INFO  16:27:57,669 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:27Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-6_78400388_93953258-prep-prealign.bam
[2016-04-14T23:27Z] INFO  16:27:57,756 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:27Z] INFO  16:27:57,783 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:27Z] GATK: realign ('6', 46598699, 62284307) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:27Z] INFO  16:27:57,842 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:27Z] INFO  16:27:57,952 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:27Z] INFO  16:27:57,953 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:27Z] INFO  16:27:57,954 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:27Z] INFO  16:27:57,955 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-14T23:27Z] GATK RealignerTargetCreator: R14-18102_kapa-NGv3-PE100-NGv3-sort-6_78400388_93953258-prep-prealign.bam 6:78400389-93953258
[2016-04-14T23:27Z] GATK: RealignerTargetCreator
[2016-04-14T23:27Z] INFO  16:27:58,878 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:27Z] GATK: realign ('5', 174919106, 180915260) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:27Z] INFO  16:27:59,255 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@41fd9d8e
[2016-04-14T23:27Z] INFO  16:27:59,383 ProgressMeter -            done    167280.0    13.0 s      81.0 s      100.0%    13.0 s       0.0 s
[2016-04-14T23:27Z] INFO  16:27:59,384 ProgressMeter - Total runtime 13.66 secs, 0.23 min, 0.00 hours
[2016-04-14T23:27Z] INFO  16:27:59,387 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 167280 total reads (0.00%)
[2016-04-14T23:27Z] INFO  16:27:59,387 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:27Z] INFO  16:27:59,388 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:27Z] INFO  16:27:59,388 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:27Z] INFO  16:27:59,463 ProgressMeter -            done    182205.0    23.0 s       2.2 m      100.0%    23.0 s       0.0 s
[2016-04-14T23:27Z] INFO  16:27:59,464 ProgressMeter - Total runtime 23.90 secs, 0.40 min, 0.01 hours
[2016-04-14T23:27Z] INFO  16:27:59,464 MicroScheduler - 130 reads were filtered out during the traversal out of approximately 182335 total reads (0.07%)
[2016-04-14T23:27Z] INFO  16:27:59,465 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:27Z] INFO  16:27:59,465 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:27Z] INFO  16:27:59,465 MicroScheduler -   -> 130 reads (0.07% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:28Z] INFO  16:28:00,751 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:28Z] INFO  16:28:00,753 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:28Z] INFO  16:28:00,754 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:28Z] INFO  16:28:00,754 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:28Z] INFO  16:28:00,758 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/6/R14-18102_kapa-NGv3-PE100-NGv3-sort-6_46598699_62284307-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/6/R14-18102_kapa-NGv3-PE100-NGv3-sort-6_46598699_62284307-prep-prealign-realign.intervals -L 6:46598700-62284307 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/6/tx/tmp33mqCz/R14-18102_kapa-NGv3-PE100-NGv3-sort-6_46598699_62284307-prep.bam
[2016-04-14T23:28Z] INFO  16:28:00,767 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:28Z] INFO  16:28:00,767 HelpFormatter - Date/Time: 2016/04/14 16:28:00
[2016-04-14T23:28Z] INFO  16:28:00,767 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:28Z] INFO  16:28:00,767 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:28Z] INFO  16:28:00,800 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:28Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-5_158711911_174870102-prep.bam
[2016-04-14T23:28Z] INFO  16:28:00,856 ProgressMeter -            done   1.5510303E7    20.0 s       1.0 s      100.0%    20.0 s       0.0 s
[2016-04-14T23:28Z] INFO  16:28:00,857 ProgressMeter - Total runtime 20.02 secs, 0.33 min, 0.01 hours
[2016-04-14T23:28Z] INFO  16:28:00,861 MicroScheduler - 27500 reads were filtered out during the traversal out of approximately 326585 total reads (8.42%)
[2016-04-14T23:28Z] INFO  16:28:00,861 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:28Z] INFO  16:28:00,862 MicroScheduler -   -> 747 reads (0.23% of total) failing BadMateFilter
[2016-04-14T23:28Z] INFO  16:28:00,862 MicroScheduler -   -> 25979 reads (7.95% of total) failing DuplicateReadFilter
[2016-04-14T23:28Z] INFO  16:28:00,862 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-14T23:28Z] INFO  16:28:00,863 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:28Z] INFO  16:28:00,863 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-14T23:28Z] INFO  16:28:00,863 MicroScheduler -   -> 774 reads (0.24% of total) failing MappingQualityZeroFilter
[2016-04-14T23:28Z] INFO  16:28:00,863 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:28Z] INFO  16:28:00,863 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-14T23:28Z] INFO  16:28:00,864 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-14T23:28Z] INFO  16:28:00,888 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:28Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-6_109467960_124979532-prep-prealign.bam
[2016-04-14T23:28Z] INFO  16:28:00,959 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:28Z] INFO  16:28:00,973 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:28Z] INFO  16:28:00,976 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:28Z] INFO  16:28:00,976 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:28Z] INFO  16:28:00,976 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:28Z] INFO  16:28:00,981 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/6/R14-18102_kapa-NGv3-PE100-NGv3-sort-6_78400388_93953258-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/6/tx/tmpudM6t2/R14-18102_kapa-NGv3-PE100-NGv3-sort-6_78400388_93953258-prep-prealign-realign.intervals -l INFO -L 6:78400389-93953258 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-14T23:28Z] INFO  16:28:00,991 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:28Z] INFO  16:28:01,000 HelpFormatter - Date/Time: 2016/04/14 16:28:00
[2016-04-14T23:28Z] INFO  16:28:01,000 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:28Z] INFO  16:28:01,000 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:28Z] INFO  16:28:01,080 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:28Z] INFO  16:28:01,103 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:28Z] INFO  16:28:01,151 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:28Z] INFO  16:28:01,189 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-14T23:28Z] INFO  16:28:01,246 ProgressMeter -       4:6590788    300004.0    30.0 s     100.0 s       42.5%    70.0 s      40.0 s
[2016-04-14T23:28Z] GATK pre-alignment ('7', 0, 15584548) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:28Z] INFO  16:28:01,410 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-14T23:28Z] INFO  16:28:01,419 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:28Z] INFO  16:28:01,460 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.04
[2016-04-14T23:28Z] GATK RealignerTargetCreator: R14-18102_kapa-NGv3-PE100-NGv3-sort-6_109467960_124979532-prep-prealign.bam 6:109467961-124979532
[2016-04-14T23:28Z] GATK: RealignerTargetCreator
[2016-04-14T23:28Z] INFO  16:28:01,636 IntervalUtils - Processing 15685608 bp from intervals
[2016-04-14T23:28Z] WARN  16:28:01,652 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:28Z] INFO  16:28:01,727 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:28Z] INFO  16:28:01,835 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:28Z] INFO  16:28:01,836 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:28Z] INFO  16:28:01,837 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:28Z] INFO  16:28:01,837 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:28Z] INFO  16:28:01,855 IntervalUtils - Processing 15552870 bp from intervals
[2016-04-14T23:28Z] WARN  16:28:01,865 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:28Z] INFO  16:28:01,946 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:28Z] INFO  16:28:01,963 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:28Z] INFO  16:28:01,968 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:28Z] INFO  16:28:01,972 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:28Z] INFO  16:28:01,972 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:28Z] INFO  16:28:01,972 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:28Z] INFO  16:28:01,977 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/5/R14-18102_kapa-NGv3-PE100-NGv3-sort-5_174919106_180915260-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/5/R14-18102_kapa-NGv3-PE100-NGv3-sort-5_174919106_180915260-prep-prealign-realign.intervals -L 5:174919107-180915260 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/5/tx/tmpCpCCL5/R14-18102_kapa-NGv3-PE100-NGv3-sort-5_174919106_180915260-prep.bam
[2016-04-14T23:28Z] INFO  16:28:01,986 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:28Z] INFO  16:28:01,987 HelpFormatter - Date/Time: 2016/04/14 16:28:01
[2016-04-14T23:28Z] INFO  16:28:01,987 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:28Z] INFO  16:28:01,988 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:28Z] INFO  16:28:02,038 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:28Z] GATK: realign ('5', 143200044, 158710347) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:28Z] INFO  16:28:02,111 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:28Z] INFO  16:28:02,184 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:28Z] INFO  16:28:02,255 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:28Z] INFO  16:28:02,267 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:28Z] INFO  16:28:02,268 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:28Z] INFO  16:28:02,269 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-14T23:28Z] INFO  16:28:02,324 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:28Z] INFO  16:28:02,334 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:28Z] INFO  16:28:02,395 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-14T23:28Z] INFO  16:28:02,797 IntervalUtils - Processing 5996154 bp from intervals
[2016-04-14T23:28Z] WARN  16:28:02,802 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:28Z] INFO  16:28:02,886 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:28Z] INFO  16:28:03,009 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:28Z] INFO  16:28:03,022 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:28Z] INFO  16:28:03,023 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:28Z] INFO  16:28:03,023 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:28Z] INFO  16:28:03,150 ProgressMeter -      6:36043681    400009.0    60.0 s       2.5 m       32.0%     3.1 m       2.1 m
[2016-04-14T23:28Z] INFO  16:28:03,151 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:28Z] INFO  16:28:03,248 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:28Z] INFO  16:28:04,154 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:28Z] INFO  16:28:04,158 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:28Z] INFO  16:28:04,158 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:28Z] INFO  16:28:04,159 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:28Z] INFO  16:28:04,163 HelpFormatter - Program Args: -T PrintReads -L 7:1-15584548 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/7/tx/tmpFzxuxl/R14-18102_kapa-NGv3-PE100-NGv3-sort-7_0_15584548-prep-prealign.bam
[2016-04-14T23:28Z] INFO  16:28:04,174 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:28Z] INFO  16:28:04,174 HelpFormatter - Date/Time: 2016/04/14 16:28:04
[2016-04-14T23:28Z] INFO  16:28:04,175 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:28Z] INFO  16:28:04,175 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:28Z] INFO  16:28:04,452 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:28Z] INFO  16:28:04,688 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:28Z] INFO  16:28:04,692 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:28Z] INFO  16:28:04,692 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:28Z] INFO  16:28:04,693 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:28Z] INFO  16:28:04,697 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/6/R14-18102_kapa-NGv3-PE100-NGv3-sort-6_109467960_124979532-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/6/tx/tmpBh9S0n/R14-18102_kapa-NGv3-PE100-NGv3-sort-6_109467960_124979532-prep-prealign-realign.intervals -l INFO -L 6:109467961-124979532 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-14T23:28Z] INFO  16:28:04,727 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:28Z] INFO  16:28:04,728 HelpFormatter - Date/Time: 2016/04/14 16:28:04
[2016-04-14T23:28Z] INFO  16:28:04,729 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:28Z] INFO  16:28:04,729 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:28Z] INFO  16:28:04,809 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:28Z] INFO  16:28:04,978 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-14T23:28Z] INFO  16:28:05,004 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:28Z] INFO  16:28:05,069 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-14T23:28Z] INFO  16:28:05,252 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:28Z] INFO  16:28:05,255 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:28Z] INFO  16:28:05,256 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:28Z] INFO  16:28:05,257 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:28Z] INFO  16:28:05,261 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/5/R14-18102_kapa-NGv3-PE100-NGv3-sort-5_143200044_158710347-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/5/R14-18102_kapa-NGv3-PE100-NGv3-sort-5_143200044_158710347-prep-prealign-realign.intervals -L 5:143200045-158710347 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/5/tx/tmp1dy_7L/R14-18102_kapa-NGv3-PE100-NGv3-sort-5_143200044_158710347-prep.bam
[2016-04-14T23:28Z] INFO  16:28:05,281 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:28Z] INFO  16:28:05,282 HelpFormatter - Date/Time: 2016/04/14 16:28:05
[2016-04-14T23:28Z] INFO  16:28:05,282 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:28Z] INFO  16:28:05,283 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:28Z] INFO  16:28:05,398 IntervalUtils - Processing 15511572 bp from intervals
[2016-04-14T23:28Z] WARN  16:28:05,411 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:28Z] INFO  16:28:05,547 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:28Z] INFO  16:28:05,552 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:28Z] INFO  16:28:05,695 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:28Z] INFO  16:28:05,698 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-14T23:28Z] INFO  16:28:05,705 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:28Z] INFO  16:28:05,747 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.04
[2016-04-14T23:28Z] INFO  16:28:05,773 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:28Z] INFO  16:28:05,783 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:28Z] INFO  16:28:05,814 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:28Z] INFO  16:28:05,815 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:28Z] INFO  16:28:05,816 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:28Z] INFO  16:28:05,817 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-14T23:28Z] INFO  16:28:05,842 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-14T23:28Z] INFO  16:28:05,860 IntervalUtils - Processing 15584548 bp from intervals
[2016-04-14T23:28Z] INFO  16:28:05,948 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:28Z] INFO  16:28:06,145 IntervalUtils - Processing 15510303 bp from intervals
[2016-04-14T23:28Z] WARN  16:28:06,150 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:28Z] INFO  16:28:06,220 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:28Z] INFO  16:28:06,245 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:28Z] INFO  16:28:06,246 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:28Z] INFO  16:28:06,247 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:28Z] INFO  16:28:06,247 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:28Z] INFO  16:28:06,266 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:28Z] INFO  16:28:06,354 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:28Z] INFO  16:28:06,355 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:28Z] INFO  16:28:06,355 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:28Z] INFO  16:28:06,355 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:28Z] INFO  16:28:06,419 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:28Z] INFO  16:28:06,498 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:28Z] INFO  16:28:06,647 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:28Z] INFO  16:28:09,738 ProgressMeter -            done   1.5782253E7    16.0 s       1.0 s      100.0%    16.0 s       0.0 s
[2016-04-14T23:28Z] INFO  16:28:09,740 ProgressMeter - Total runtime 16.33 secs, 0.27 min, 0.00 hours
[2016-04-14T23:28Z] INFO  16:28:09,744 MicroScheduler - 12279 reads were filtered out during the traversal out of approximately 127809 total reads (9.61%)
[2016-04-14T23:28Z] INFO  16:28:09,745 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:28Z] INFO  16:28:09,746 MicroScheduler -   -> 442 reads (0.35% of total) failing BadMateFilter
[2016-04-14T23:28Z] INFO  16:28:09,747 MicroScheduler -   -> 10036 reads (7.85% of total) failing DuplicateReadFilter
[2016-04-14T23:28Z] INFO  16:28:09,747 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-14T23:28Z] INFO  16:28:09,748 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:28Z] INFO  16:28:09,748 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-14T23:28Z] INFO  16:28:09,749 MicroScheduler -   -> 1801 reads (1.41% of total) failing MappingQualityZeroFilter
[2016-04-14T23:28Z] INFO  16:28:09,750 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:28Z] INFO  16:28:09,750 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-14T23:28Z] INFO  16:28:09,750 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-14T23:28Z] INFO  16:28:09,797 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@41fd9d8e
[2016-04-14T23:28Z] INFO  16:28:09,998 ProgressMeter -            done    212698.0    28.0 s       2.2 m      100.0%    28.0 s       0.0 s
[2016-04-14T23:28Z] INFO  16:28:09,999 ProgressMeter - Total runtime 28.57 secs, 0.48 min, 0.01 hours
[2016-04-14T23:28Z] INFO  16:28:10,000 MicroScheduler - 158 reads were filtered out during the traversal out of approximately 212856 total reads (0.07%)
[2016-04-14T23:28Z] INFO  16:28:10,000 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:28Z] INFO  16:28:10,000 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:28Z] INFO  16:28:10,001 MicroScheduler -   -> 158 reads (0.07% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:28Z] INFO  16:28:10,911 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:28Z] GATK: realign ('6', 62390867, 78173120) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:28Z] INFO  16:28:11,129 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:28Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-6_125112484_142397186-prep-prealign.bam
[2016-04-14T23:28Z] GATK RealignerTargetCreator: R14-18102_kapa-NGv3-PE100-NGv3-sort-6_125112484_142397186-prep-prealign.bam 6:125112485-142397186
[2016-04-14T23:28Z] GATK: RealignerTargetCreator
[2016-04-14T23:28Z] INFO  16:28:13,126 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@7172f77a
[2016-04-14T23:28Z] INFO  16:28:13,380 ProgressMeter -            done    686317.0    83.0 s       2.0 m      100.0%    83.0 s       0.0 s
[2016-04-14T23:28Z] INFO  16:28:13,380 ProgressMeter - Total runtime 83.76 secs, 1.40 min, 0.02 hours
[2016-04-14T23:28Z] INFO  16:28:13,381 MicroScheduler - 233 reads were filtered out during the traversal out of approximately 686550 total reads (0.03%)
[2016-04-14T23:28Z] INFO  16:28:13,381 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:28Z] INFO  16:28:13,381 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:28Z] INFO  16:28:13,382 MicroScheduler -   -> 233 reads (0.03% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:28Z] INFO  16:28:13,734 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:28Z] INFO  16:28:13,737 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:28Z] INFO  16:28:13,738 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:28Z] INFO  16:28:13,738 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:28Z] INFO  16:28:13,743 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/6/R14-18102_kapa-NGv3-PE100-NGv3-sort-6_62390867_78173120-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/6/R14-18102_kapa-NGv3-PE100-NGv3-sort-6_62390867_78173120-prep-prealign-realign.intervals -L 6:62390868-78173120 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/6/tx/tmpEOjcDK/R14-18102_kapa-NGv3-PE100-NGv3-sort-6_62390867_78173120-prep.bam
[2016-04-14T23:28Z] INFO  16:28:13,754 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:28Z] INFO  16:28:13,754 HelpFormatter - Date/Time: 2016/04/14 16:28:13
[2016-04-14T23:28Z] INFO  16:28:13,754 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:28Z] INFO  16:28:13,754 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:28Z] INFO  16:28:13,985 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:28Z] INFO  16:28:14,101 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:28Z] INFO  16:28:14,111 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:28Z] INFO  16:28:14,176 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-14T23:28Z] INFO  16:28:14,522 IntervalUtils - Processing 15782253 bp from intervals
[2016-04-14T23:28Z] WARN  16:28:14,528 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:28Z] INFO  16:28:14,611 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:28Z] INFO  16:28:14,671 ProgressMeter -            done   1.5511569E7    16.0 s       1.0 s      100.0%    16.0 s       0.0 s
[2016-04-14T23:28Z] INFO  16:28:14,672 ProgressMeter - Total runtime 16.72 secs, 0.28 min, 0.00 hours
[2016-04-14T23:28Z] INFO  16:28:14,676 MicroScheduler - 10207 reads were filtered out during the traversal out of approximately 115807 total reads (8.81%)
[2016-04-14T23:28Z] INFO  16:28:14,677 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:28Z] INFO  16:28:14,677 MicroScheduler -   -> 453 reads (0.39% of total) failing BadMateFilter
[2016-04-14T23:28Z] INFO  16:28:14,678 MicroScheduler -   -> 8853 reads (7.64% of total) failing DuplicateReadFilter
[2016-04-14T23:28Z] INFO  16:28:14,678 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-14T23:28Z] INFO  16:28:14,678 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:28Z] INFO  16:28:14,678 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-14T23:28Z] INFO  16:28:14,679 MicroScheduler -   -> 901 reads (0.78% of total) failing MappingQualityZeroFilter
[2016-04-14T23:28Z] INFO  16:28:14,679 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:28Z] INFO  16:28:14,679 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-14T23:28Z] INFO  16:28:14,681 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-14T23:28Z] INFO  16:28:14,738 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:28Z] INFO  16:28:14,739 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:28Z] INFO  16:28:14,740 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:28Z] INFO  16:28:14,741 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:28Z] INFO  16:28:14,752 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:28Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-5_127597427_143191869-prep-prealign.bam
[2016-04-14T23:28Z] INFO  16:28:14,874 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:28Z] INFO  16:28:14,878 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:28Z] INFO  16:28:14,879 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:28Z] INFO  16:28:14,880 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:28Z] INFO  16:28:14,885 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/6/R14-18102_kapa-NGv3-PE100-NGv3-sort-6_125112484_142397186-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/6/tx/tmpNOzGKd/R14-18102_kapa-NGv3-PE100-NGv3-sort-6_125112484_142397186-prep-prealign-realign.intervals -l INFO -L 6:125112485-142397186 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-14T23:28Z] INFO  16:28:14,894 ProgressMeter -            done    205175.0    17.0 s      85.0 s      100.0%    17.0 s       0.0 s
[2016-04-14T23:28Z] INFO  16:28:14,894 ProgressMeter - Total runtime 17.48 secs, 0.29 min, 0.00 hours
[2016-04-14T23:28Z] INFO  16:28:14,898 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 205175 total reads (0.00%)
[2016-04-14T23:28Z] INFO  16:28:14,898 ProgressMeter -            done   1.5568806E7    21.0 s       1.0 s      100.0%    21.0 s       0.0 s
[2016-04-14T23:28Z] INFO  16:28:14,899 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:28Z] INFO  16:28:14,899 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:28Z] INFO  16:28:14,899 ProgressMeter - Total runtime 21.28 secs, 0.35 min, 0.01 hours
[2016-04-14T23:28Z] INFO  16:28:14,899 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:28Z] INFO  16:28:14,903 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:28Z] INFO  16:28:14,903 MicroScheduler - 36680 reads were filtered out during the traversal out of approximately 381102 total reads (9.62%)
[2016-04-14T23:28Z] INFO  16:28:14,905 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:28Z] INFO  16:28:14,899 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:28Z] INFO  16:28:14,905 HelpFormatter - Date/Time: 2016/04/14 16:28:14
[2016-04-14T23:28Z] INFO  16:28:14,905 MicroScheduler -   -> 886 reads (0.23% of total) failing BadMateFilter
[2016-04-14T23:28Z] INFO  16:28:14,906 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:28Z] INFO  16:28:14,906 MicroScheduler -   -> 30419 reads (7.98% of total) failing DuplicateReadFilter
[2016-04-14T23:28Z] INFO  16:28:14,906 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:28Z] INFO  16:28:14,907 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-14T23:28Z] INFO  16:28:14,907 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:28Z] INFO  16:28:14,908 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-14T23:28Z] INFO  16:28:14,909 MicroScheduler -   -> 5375 reads (1.41% of total) failing MappingQualityZeroFilter
[2016-04-14T23:28Z] INFO  16:28:14,909 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:28Z] INFO  16:28:14,910 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-14T23:28Z] INFO  16:28:14,910 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-14T23:28Z] INFO  16:28:15,021 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:28Z] INFO  16:28:15,085 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:28Z] INFO  16:28:15,242 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-14T23:28Z] INFO  16:28:15,255 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:28Z] INFO  16:28:15,309 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-14T23:28Z] INFO  16:28:15,590 IntervalUtils - Processing 17284702 bp from intervals
[2016-04-14T23:28Z] WARN  16:28:15,595 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:28Z] INFO  16:28:15,675 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:28Z] INFO  16:28:15,892 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:28Z] INFO  16:28:15,893 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:28Z] INFO  16:28:15,894 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:28Z] INFO  16:28:15,895 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-14T23:28Z] INFO  16:28:15,948 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:28Z] GATK: realign ('6', 93955015, 109466584) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:28Z] INFO  16:28:16,282 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:28Z] GATK: realign ('6', 15511526, 31080332) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:28Z] INFO  16:28:16,447 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:28Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-6_0_15509601-prep.bam
[2016-04-14T23:28Z] INFO  16:28:16,567 ProgressMeter -            done    196844.0    14.0 s      74.0 s      100.0%    14.0 s       0.0 s
[2016-04-14T23:28Z] INFO  16:28:16,568 ProgressMeter - Total runtime 14.73 secs, 0.25 min, 0.00 hours
[2016-04-14T23:28Z] INFO  16:28:16,573 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 196844 total reads (0.00%)
[2016-04-14T23:28Z] INFO  16:28:16,574 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:28Z] INFO  16:28:16,575 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:28Z] INFO  16:28:16,576 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:28Z] GATK pre-alignment ('7', 15599765, 31117713) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:28Z] GATK RealignerTargetCreator: R14-18102_kapa-NGv3-PE100-NGv3-sort-5_127597427_143191869-prep-prealign.bam 5:127597428-143191869
[2016-04-14T23:28Z] GATK: RealignerTargetCreator
[2016-04-14T23:28Z] INFO  16:28:18,607 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:28Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-6_46598699_62284307-prep.bam
[2016-04-14T23:28Z] INFO  16:28:18,664 ProgressMeter -            done   1.555287E7    16.0 s       1.0 s      100.0%    16.0 s       0.0 s
[2016-04-14T23:28Z] INFO  16:28:18,665 ProgressMeter - Total runtime 16.40 secs, 0.27 min, 0.00 hours
[2016-04-14T23:28Z] INFO  16:28:18,670 MicroScheduler - 13514 reads were filtered out during the traversal out of approximately 159187 total reads (8.49%)
[2016-04-14T23:28Z] INFO  16:28:18,671 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:28Z] INFO  16:28:18,672 MicroScheduler -   -> 517 reads (0.32% of total) failing BadMateFilter
[2016-04-14T23:28Z] INFO  16:28:18,672 MicroScheduler -   -> 12438 reads (7.81% of total) failing DuplicateReadFilter
[2016-04-14T23:28Z] INFO  16:28:18,673 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-14T23:28Z] INFO  16:28:18,674 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:28Z] INFO  16:28:18,674 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-14T23:28Z] INFO  16:28:18,675 MicroScheduler -   -> 559 reads (0.35% of total) failing MappingQualityZeroFilter
[2016-04-14T23:28Z] INFO  16:28:18,676 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:28Z] INFO  16:28:18,676 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-14T23:28Z] INFO  16:28:18,677 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-14T23:28Z] INFO  16:28:18,899 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:28Z] INFO  16:28:18,902 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:28Z] INFO  16:28:18,903 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:28Z] INFO  16:28:18,903 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:28Z] INFO  16:28:18,908 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/6/R14-18102_kapa-NGv3-PE100-NGv3-sort-6_93955015_109466584-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/6/R14-18102_kapa-NGv3-PE100-NGv3-sort-6_93955015_109466584-prep-prealign-realign.intervals -L 6:93955016-109466584 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/6/tx/tmpW8VGxC/R14-18102_kapa-NGv3-PE100-NGv3-sort-6_93955015_109466584-prep.bam
[2016-04-14T23:28Z] INFO  16:28:18,944 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:28Z] INFO  16:28:18,952 HelpFormatter - Date/Time: 2016/04/14 16:28:18
[2016-04-14T23:28Z] INFO  16:28:18,953 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:28Z] INFO  16:28:18,953 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:28Z] INFO  16:28:19,174 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:28Z] INFO  16:28:19,333 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:28Z] INFO  16:28:19,342 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:28Z] GATK pre-alignment ('7', 31120227, 47317818) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:28Z] INFO  16:28:19,424 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-14T23:28Z] INFO  16:28:19,475 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:28Z] INFO  16:28:19,479 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:28Z] INFO  16:28:19,479 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:28Z] INFO  16:28:19,480 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:28Z] INFO  16:28:19,484 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/6/R14-18102_kapa-NGv3-PE100-NGv3-sort-6_15511526_31080332-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/6/R14-18102_kapa-NGv3-PE100-NGv3-sort-6_15511526_31080332-prep-prealign-realign.intervals -L 6:15511527-31080332 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/6/tx/tmp9yNIcY/R14-18102_kapa-NGv3-PE100-NGv3-sort-6_15511526_31080332-prep.bam
[2016-04-14T23:28Z] INFO  16:28:19,499 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:28Z] INFO  16:28:19,500 HelpFormatter - Date/Time: 2016/04/14 16:28:19
[2016-04-14T23:28Z] INFO  16:28:19,501 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:28Z] INFO  16:28:19,501 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:28Z] INFO  16:28:19,823 IntervalUtils - Processing 15511569 bp from intervals
[2016-04-14T23:28Z] WARN  16:28:19,828 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:28Z] INFO  16:28:19,864 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:28Z] INFO  16:28:19,908 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:28Z] INFO  16:28:20,038 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:28Z] INFO  16:28:20,040 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:28Z] INFO  16:28:20,040 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:28Z] INFO  16:28:20,041 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:28Z] INFO  16:28:20,055 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:28Z] INFO  16:28:20,076 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:28Z] INFO  16:28:20,132 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:28Z] INFO  16:28:20,148 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:28Z] INFO  16:28:20,152 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:28Z] INFO  16:28:20,152 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:28Z] INFO  16:28:20,153 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:28Z] INFO  16:28:20,158 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/5/R14-18102_kapa-NGv3-PE100-NGv3-sort-5_127597427_143191869-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/5/tx/tmpo42c4h/R14-18102_kapa-NGv3-PE100-NGv3-sort-5_127597427_143191869-prep-prealign-realign.intervals -l INFO -L 5:127597428-143191869 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-14T23:28Z] INFO  16:28:20,167 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.09
[2016-04-14T23:28Z] INFO  16:28:20,169 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:28Z] INFO  16:28:20,170 HelpFormatter - Date/Time: 2016/04/14 16:28:20
[2016-04-14T23:28Z] GATK: realign ('6', 78400388, 93953258) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:28Z] INFO  16:28:20,170 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:28Z] INFO  16:28:20,180 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:28Z] INFO  16:28:20,194 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:28Z] INFO  16:28:20,276 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:28Z] INFO  16:28:20,279 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:28Z] INFO  16:28:20,283 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:28Z] INFO  16:28:20,283 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:28Z] INFO  16:28:20,284 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:28Z] INFO  16:28:20,288 HelpFormatter - Program Args: -T PrintReads -L 7:15599766-31117713 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/7/tx/tmpKZ8RAh/R14-18102_kapa-NGv3-PE100-NGv3-sort-7_15599765_31117713-prep-prealign.bam
[2016-04-14T23:28Z] INFO  16:28:20,333 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:28Z] INFO  16:28:20,334 HelpFormatter - Date/Time: 2016/04/14 16:28:20
[2016-04-14T23:28Z] INFO  16:28:20,334 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:28Z] INFO  16:28:20,335 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:28Z] INFO  16:28:20,376 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:28Z] INFO  16:28:20,492 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-14T23:28Z] INFO  16:28:20,511 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:28Z] INFO  16:28:20,548 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:28Z] INFO  16:28:20,583 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-14T23:28Z] INFO  16:28:20,666 IntervalUtils - Processing 15568806 bp from intervals
[2016-04-14T23:28Z] WARN  16:28:20,682 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:28Z] INFO  16:28:20,756 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:28Z] INFO  16:28:20,933 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:28Z] INFO  16:28:20,934 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:28Z] INFO  16:28:20,935 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:28Z] INFO  16:28:20,936 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:28Z] INFO  16:28:21,024 IntervalUtils - Processing 15594442 bp from intervals
[2016-04-14T23:28Z] WARN  16:28:21,041 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:28Z] INFO  16:28:21,132 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:28Z] INFO  16:28:21,150 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:28Z] INFO  16:28:21,395 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:28Z] INFO  16:28:21,446 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:28Z] INFO  16:28:21,447 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:28Z] INFO  16:28:21,448 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:28Z] INFO  16:28:21,449 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-14T23:28Z] INFO  16:28:21,659 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-14T23:28Z] INFO  16:28:21,723 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:28Z] INFO  16:28:21,732 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:28Z] INFO  16:28:21,778 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-14T23:28Z] INFO  16:28:21,793 IntervalUtils - Processing 15517948 bp from intervals
[2016-04-14T23:28Z] INFO  16:28:21,914 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:28Z] INFO  16:28:22,224 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:28Z] INFO  16:28:22,225 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:28Z] INFO  16:28:22,225 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:28Z] INFO  16:28:22,225 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:28Z] INFO  16:28:22,256 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:28Z] INFO  16:28:22,384 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:28Z] INFO  16:28:22,397 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:28Z] INFO  16:28:22,397 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:28Z] INFO  16:28:22,398 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:28Z] INFO  16:28:22,402 HelpFormatter - Program Args: -T PrintReads -L 7:31120228-47317818 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/7/tx/tmprECk_D/R14-18102_kapa-NGv3-PE100-NGv3-sort-7_31120227_47317818-prep-prealign.bam
[2016-04-14T23:28Z] INFO  16:28:22,406 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:28Z] INFO  16:28:22,419 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:28Z] INFO  16:28:22,419 HelpFormatter - Date/Time: 2016/04/14 16:28:22
[2016-04-14T23:28Z] INFO  16:28:22,419 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:28Z] INFO  16:28:22,419 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:28Z] INFO  16:28:22,663 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:28Z] INFO  16:28:23,055 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:28Z] INFO  16:28:23,059 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:28Z] INFO  16:28:23,059 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:28Z] INFO  16:28:23,059 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:28Z] INFO  16:28:23,064 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/6/R14-18102_kapa-NGv3-PE100-NGv3-sort-6_78400388_93953258-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/6/R14-18102_kapa-NGv3-PE100-NGv3-sort-6_78400388_93953258-prep-prealign-realign.intervals -L 6:78400389-93953258 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/6/tx/tmpV6jfdE/R14-18102_kapa-NGv3-PE100-NGv3-sort-6_78400388_93953258-prep.bam
[2016-04-14T23:28Z] INFO  16:28:23,077 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:28Z] INFO  16:28:23,081 HelpFormatter - Date/Time: 2016/04/14 16:28:23
[2016-04-14T23:28Z] INFO  16:28:23,082 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:28Z] INFO  16:28:23,083 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:28Z] INFO  16:28:23,229 ProgressMeter -            done   1.5511572E7    17.0 s       1.0 s      100.0%    17.0 s       0.0 s
[2016-04-14T23:28Z] INFO  16:28:23,230 ProgressMeter - Total runtime 17.41 secs, 0.29 min, 0.00 hours
[2016-04-14T23:28Z] INFO  16:28:23,228 ProgressMeter -            done    299937.0    20.0 s      67.0 s       98.0%    20.0 s       0.0 s
[2016-04-14T23:28Z] INFO  16:28:23,229 ProgressMeter - Total runtime 20.21 secs, 0.34 min, 0.01 hours
[2016-04-14T23:28Z] INFO  16:28:23,233 MicroScheduler - 15321 reads were filtered out during the traversal out of approximately 182904 total reads (8.38%)
[2016-04-14T23:28Z] INFO  16:28:23,234 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:28Z] INFO  16:28:23,234 MicroScheduler -   -> 561 reads (0.31% of total) failing BadMateFilter
[2016-04-14T23:28Z] INFO  16:28:23,234 MicroScheduler -   -> 14273 reads (7.80% of total) failing DuplicateReadFilter
[2016-04-14T23:28Z] INFO  16:28:23,234 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 299937 total reads (0.00%)
[2016-04-14T23:28Z] INFO  16:28:23,235 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-14T23:28Z] INFO  16:28:23,235 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:28Z] INFO  16:28:23,235 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:28Z] INFO  16:28:23,235 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-14T23:28Z] INFO  16:28:23,235 MicroScheduler -   -> 487 reads (0.27% of total) failing MappingQualityZeroFilter
[2016-04-14T23:28Z] INFO  16:28:23,236 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:28Z] INFO  16:28:23,236 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:28Z] INFO  16:28:23,236 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-14T23:28Z] INFO  16:28:23,237 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:28Z] INFO  16:28:23,236 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-14T23:28Z] INFO  16:28:23,321 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:28Z] INFO  16:28:23,463 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:28Z] INFO  16:28:23,474 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:28Z] INFO  16:28:23,544 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-14T23:28Z] INFO  16:28:23,758 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-14T23:28Z] INFO  16:28:23,855 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:28Z] INFO  16:28:23,875 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:28Z] INFO  16:28:23,921 IntervalUtils - Processing 15552870 bp from intervals
[2016-04-14T23:28Z] WARN  16:28:23,926 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:28Z] INFO  16:28:23,952 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-14T23:28Z] INFO  16:28:23,982 IntervalUtils - Processing 16197591 bp from intervals
[2016-04-14T23:28Z] INFO  16:28:24,045 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:28Z] INFO  16:28:24,120 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:28Z] INFO  16:28:24,227 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:28Z] INFO  16:28:24,228 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:28Z] INFO  16:28:24,229 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:28Z] INFO  16:28:24,231 ProgressMeter -     6:153316453    200003.0    30.0 s       2.5 m       70.1%    42.0 s      12.0 s
[2016-04-14T23:28Z] INFO  16:28:24,234 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:28Z] INFO  16:28:24,430 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:28Z] INFO  16:28:24,507 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:28Z] INFO  16:28:24,508 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:28Z] INFO  16:28:24,508 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:28Z] INFO  16:28:24,509 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:28Z] INFO  16:28:24,561 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:28Z] INFO  16:28:24,644 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:28Z] INFO  16:28:24,731 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:28Z] INFO  16:28:24,853 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:28Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-5_174919106_180915260-prep.bam
[2016-04-14T23:28Z] INFO  16:28:24,960 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:28Z] GATK: realign ('6', 109467960, 124979532) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:28Z] INFO  16:28:25,678 ProgressMeter -     6:170592226    200003.0    30.0 s       2.5 m       96.0%    31.0 s       1.0 s
[2016-04-14T23:28Z] GATK pre-alignment ('7', 47319761, 63093154) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:28Z] INFO  16:28:27,319 ProgressMeter -            done    126981.0    12.0 s      99.0 s      100.0%    12.0 s       0.0 s
[2016-04-14T23:28Z] INFO  16:28:27,319 ProgressMeter - Total runtime 12.58 secs, 0.21 min, 0.00 hours
[2016-04-14T23:28Z] INFO  16:28:27,323 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 126981 total reads (0.00%)
[2016-04-14T23:28Z] INFO  16:28:27,323 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:28Z] INFO  16:28:27,323 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:28Z] INFO  16:28:27,324 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:28Z] INFO  16:28:27,350 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@41fd9d8e
[2016-04-14T23:28Z] INFO  16:28:27,489 ProgressMeter -            done    240843.0    31.0 s       2.2 m       98.7%    31.0 s       0.0 s
[2016-04-14T23:28Z] INFO  16:28:27,489 ProgressMeter - Total runtime 31.83 secs, 0.53 min, 0.01 hours
[2016-04-14T23:28Z] INFO  16:28:27,490 MicroScheduler - 146 reads were filtered out during the traversal out of approximately 240989 total reads (0.06%)
[2016-04-14T23:28Z] INFO  16:28:27,490 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:28Z] INFO  16:28:27,490 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:28Z] INFO  16:28:27,491 MicroScheduler -   -> 146 reads (0.06% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:28Z] INFO  16:28:27,856 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:28Z] INFO  16:28:27,860 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:28Z] INFO  16:28:27,861 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:28Z] INFO  16:28:27,861 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:28Z] INFO  16:28:27,874 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/6/R14-18102_kapa-NGv3-PE100-NGv3-sort-6_109467960_124979532-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/6/R14-18102_kapa-NGv3-PE100-NGv3-sort-6_109467960_124979532-prep-prealign-realign.intervals -L 6:109467961-124979532 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/6/tx/tmp9xoCjp/R14-18102_kapa-NGv3-PE100-NGv3-sort-6_109467960_124979532-prep.bam
[2016-04-14T23:28Z] INFO  16:28:27,890 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:28Z] INFO  16:28:27,901 HelpFormatter - Date/Time: 2016/04/14 16:28:27
[2016-04-14T23:28Z] INFO  16:28:27,902 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:28Z] INFO  16:28:27,903 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:28Z] INFO  16:28:28,042 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@41fd9d8e
[2016-04-14T23:28Z] INFO  16:28:28,124 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:28Z] INFO  16:28:28,213 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:28Z] INFO  16:28:28,223 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:28Z] INFO  16:28:28,267 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.04
[2016-04-14T23:28Z] INFO  16:28:28,278 ProgressMeter -            done    324130.0    21.0 s      67.0 s      100.0%    21.0 s       0.0 s
[2016-04-14T23:28Z] INFO  16:28:28,278 ProgressMeter - Total runtime 21.92 secs, 0.37 min, 0.01 hours
[2016-04-14T23:28Z] INFO  16:28:28,282 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 324130 total reads (0.00%)
[2016-04-14T23:28Z] INFO  16:28:28,283 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:28Z] INFO  16:28:28,283 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:28Z] INFO  16:28:28,286 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:28Z] INFO  16:28:28,289 ProgressMeter -            done    256244.0    34.0 s       2.2 m      100.0%    34.0 s       0.0 s
[2016-04-14T23:28Z] INFO  16:28:28,291 ProgressMeter - Total runtime 34.10 secs, 0.57 min, 0.01 hours
[2016-04-14T23:28Z] INFO  16:28:28,292 MicroScheduler - 148 reads were filtered out during the traversal out of approximately 256392 total reads (0.06%)
[2016-04-14T23:28Z] INFO  16:28:28,292 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:28Z] INFO  16:28:28,293 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:28Z] INFO  16:28:28,294 MicroScheduler -   -> 148 reads (0.06% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:28Z] INFO  16:28:28,550 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:28Z] INFO  16:28:28,553 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:28Z] INFO  16:28:28,553 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:28Z] INFO  16:28:28,554 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:28Z] INFO  16:28:28,558 HelpFormatter - Program Args: -T PrintReads -L 7:47319762-63093154 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/7/tx/tmpWo2LiT/R14-18102_kapa-NGv3-PE100-NGv3-sort-7_47319761_63093154-prep-prealign.bam
[2016-04-14T23:28Z] INFO  16:28:28,569 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:28Z] INFO  16:28:28,574 HelpFormatter - Date/Time: 2016/04/14 16:28:28
[2016-04-14T23:28Z] INFO  16:28:28,575 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:28Z] INFO  16:28:28,576 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:28Z] INFO  16:28:28,682 IntervalUtils - Processing 15511572 bp from intervals
[2016-04-14T23:28Z] WARN  16:28:28,688 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:28Z] INFO  16:28:28,729 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:28Z] INFO  16:28:28,768 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:28Z] INFO  16:28:28,775 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:28Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-6_158013810_171115067-prep-prealign.bam
[2016-04-14T23:28Z] INFO  16:28:28,899 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:28Z] INFO  16:28:28,908 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:28Z] INFO  16:28:28,909 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:28Z] INFO  16:28:28,910 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:28Z] INFO  16:28:28,910 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:28Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-6_62390867_78173120-prep.bam
[2016-04-14T23:28Z] INFO  16:28:29,078 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:28Z] INFO  16:28:29,229 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:28Z] GATK pre-alignment ('7', 63095909, 78636522) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:28Z] GATK RealignerTargetCreator: R14-18102_kapa-NGv3-PE100-NGv3-sort-6_158013810_171115067-prep-prealign.bam 6:158013811-171115067
[2016-04-14T23:28Z] GATK: RealignerTargetCreator
[2016-04-14T23:28Z] INFO  16:28:29,736 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:28Z] INFO  16:28:29,774 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-14T23:28Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-6_142399691_157963777-prep-prealign.bam
[2016-04-14T23:28Z] INFO  16:28:29,829 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:28Z] INFO  16:28:29,838 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:28Z] INFO  16:28:29,880 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:28Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-5_143200044_158710347-prep.bam
[2016-04-14T23:28Z] INFO  16:28:29,913 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-14T23:28Z] INFO  16:28:29,939 IntervalUtils - Processing 15773393 bp from intervals
[2016-04-14T23:28Z] INFO  16:28:30,007 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:28Z] INFO  16:28:30,389 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:28Z] INFO  16:28:30,390 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:28Z] INFO  16:28:30,391 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:28Z] INFO  16:28:30,391 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:28Z] INFO  16:28:30,405 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:28Z] INFO  16:28:30,549 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:28Z] GATK RealignerTargetCreator: R14-18102_kapa-NGv3-PE100-NGv3-sort-6_142399691_157963777-prep-prealign.bam 6:142399692-157963777
[2016-04-14T23:28Z] GATK: RealignerTargetCreator
[2016-04-14T23:28Z] GATK pre-alignment ('7', 79082334, 94740703) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:28Z] INFO  16:28:31,635 ProgressMeter -      4:13369796    900204.0    60.0 s      67.0 s       86.2%    69.0 s       9.0 s
[2016-04-14T23:28Z] INFO  16:28:32,023 ProgressMeter -            done    115290.0    11.0 s     103.0 s      100.0%    11.0 s       0.0 s
[2016-04-14T23:28Z] INFO  16:28:32,023 ProgressMeter - Total runtime 11.98 secs, 0.20 min, 0.00 hours
[2016-04-14T23:28Z] INFO  16:28:32,027 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 115290 total reads (0.00%)
[2016-04-14T23:28Z] INFO  16:28:32,028 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:28Z] INFO  16:28:32,028 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:28Z] INFO  16:28:32,029 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:28Z] INFO  16:28:32,177 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:28Z] INFO  16:28:32,181 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:28Z] INFO  16:28:32,181 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:28Z] INFO  16:28:32,182 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:28Z] INFO  16:28:32,195 HelpFormatter - Program Args: -T PrintReads -L 7:63095910-78636522 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/7/tx/tmp_JibRL/R14-18102_kapa-NGv3-PE100-NGv3-sort-7_63095909_78636522-prep-prealign.bam
[2016-04-14T23:28Z] INFO  16:28:32,233 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:28Z] INFO  16:28:32,233 HelpFormatter - Date/Time: 2016/04/14 16:28:32
[2016-04-14T23:28Z] INFO  16:28:32,233 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:28Z] INFO  16:28:32,233 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:28Z] INFO  16:28:32,408 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:28Z] INFO  16:28:32,412 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:28Z] INFO  16:28:32,413 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:28Z] INFO  16:28:32,414 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:28Z] INFO  16:28:32,415 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:28Z] INFO  16:28:32,419 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/6/R14-18102_kapa-NGv3-PE100-NGv3-sort-6_158013810_171115067-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/6/tx/tmpZBJSoc/R14-18102_kapa-NGv3-PE100-NGv3-sort-6_158013810_171115067-prep-prealign-realign.intervals -l INFO -L 6:158013811-171115067 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-14T23:28Z] INFO  16:28:32,430 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:28Z] INFO  16:28:32,434 HelpFormatter - Date/Time: 2016/04/14 16:28:32
[2016-04-14T23:28Z] INFO  16:28:32,435 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:28Z] INFO  16:28:32,436 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:28Z] INFO  16:28:32,490 ProgressMeter -            done   1006933.0    61.0 s      60.0 s      100.0%    61.0 s       0.0 s
[2016-04-14T23:28Z] INFO  16:28:32,490 ProgressMeter - Total runtime 61.35 secs, 1.02 min, 0.02 hours
[2016-04-14T23:28Z] INFO  16:28:32,494 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 1006933 total reads (0.00%)
[2016-04-14T23:28Z] INFO  16:28:32,495 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:28Z] INFO  16:28:32,495 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:28Z] INFO  16:28:32,495 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:28Z] INFO  16:28:32,552 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:28Z] INFO  16:28:32,785 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-14T23:28Z] INFO  16:28:32,794 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:28Z] INFO  16:28:32,862 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-14T23:28Z] INFO  16:28:33,151 ProgressMeter -      6:43160842    700014.0    90.0 s       2.1 m       77.9%   115.0 s      25.0 s
[2016-04-14T23:28Z] INFO  16:28:33,198 IntervalUtils - Processing 13101257 bp from intervals
[2016-04-14T23:28Z] WARN  16:28:33,204 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:28Z] INFO  16:28:33,287 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:28Z] INFO  16:28:33,374 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:28Z] INFO  16:28:33,377 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:28Z] INFO  16:28:33,377 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:28Z] INFO  16:28:33,378 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:28Z] INFO  16:28:33,383 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/6/R14-18102_kapa-NGv3-PE100-NGv3-sort-6_142399691_157963777-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/6/tx/tmp6FK8N0/R14-18102_kapa-NGv3-PE100-NGv3-sort-6_142399691_157963777-prep-prealign-realign.intervals -l INFO -L 6:142399692-157963777 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-14T23:28Z] INFO  16:28:33,403 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:28Z] INFO  16:28:33,404 HelpFormatter - Date/Time: 2016/04/14 16:28:33
[2016-04-14T23:28Z] INFO  16:28:33,405 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:28Z] INFO  16:28:33,405 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:28Z] INFO  16:28:33,516 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:28Z] INFO  16:28:33,517 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:28Z] INFO  16:28:33,518 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:28Z] INFO  16:28:33,519 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-14T23:28Z] INFO  16:28:33,520 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:28Z] INFO  16:28:33,546 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-14T23:28Z] INFO  16:28:33,610 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:28Z] INFO  16:28:33,626 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:28Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-6_93955015_109466584-prep.bam
[2016-04-14T23:28Z] INFO  16:28:33,635 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:28Z] INFO  16:28:33,674 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.04
[2016-04-14T23:28Z] INFO  16:28:33,689 IntervalUtils - Processing 15540613 bp from intervals
[2016-04-14T23:28Z] INFO  16:28:33,727 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-14T23:28Z] INFO  16:28:33,737 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:28Z] INFO  16:28:33,758 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:28Z] INFO  16:28:33,797 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-14T23:28Z] INFO  16:28:33,893 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:28Z] INFO  16:28:33,896 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:28Z] INFO  16:28:33,897 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:28Z] INFO  16:28:33,897 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:28Z] INFO  16:28:33,902 HelpFormatter - Program Args: -T PrintReads -L 7:79082335-94740703 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/7/tx/tmp8CxlTP/R14-18102_kapa-NGv3-PE100-NGv3-sort-7_79082334_94740703-prep-prealign.bam
[2016-04-14T23:28Z] INFO  16:28:33,913 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:28Z] INFO  16:28:33,914 HelpFormatter - Date/Time: 2016/04/14 16:28:33
[2016-04-14T23:28Z] INFO  16:28:33,925 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:28Z] INFO  16:28:33,926 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:28Z] INFO  16:28:34,037 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:28Z] INFO  16:28:34,038 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:28Z] INFO  16:28:34,039 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:28Z] INFO  16:28:34,040 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:28Z] GATK pre-alignment ('7', 94750023, 110303777) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:28Z] INFO  16:28:34,098 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:28Z] INFO  16:28:34,103 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:28Z] INFO  16:28:34,117 IntervalUtils - Processing 15564086 bp from intervals
[2016-04-14T23:28Z] WARN  16:28:34,128 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:28Z] INFO  16:28:34,138 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:28Z] INFO  16:28:34,193 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:28Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-4_0_15511864-prep.bam
[2016-04-14T23:28Z] INFO  16:28:34,255 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:28Z] INFO  16:28:34,407 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:28Z] INFO  16:28:34,408 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:28Z] INFO  16:28:34,409 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:28Z] INFO  16:28:34,409 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-14T23:28Z] INFO  16:28:34,757 ProgressMeter -            done   1.7284702E7    18.0 s       1.0 s      100.0%    18.0 s       0.0 s
[2016-04-14T23:28Z] INFO  16:28:34,759 ProgressMeter - Total runtime 18.87 secs, 0.31 min, 0.01 hours
[2016-04-14T23:28Z] INFO  16:28:34,763 MicroScheduler - 23988 reads were filtered out during the traversal out of approximately 214536 total reads (11.18%)
[2016-04-14T23:28Z] INFO  16:28:34,783 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:28Z] INFO  16:28:34,784 MicroScheduler -   -> 678 reads (0.32% of total) failing BadMateFilter
[2016-04-14T23:28Z] INFO  16:28:34,785 MicroScheduler -   -> 16452 reads (7.67% of total) failing DuplicateReadFilter
[2016-04-14T23:28Z] INFO  16:28:34,785 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-14T23:28Z] INFO  16:28:34,786 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:28Z] INFO  16:28:34,787 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-14T23:28Z] INFO  16:28:34,788 MicroScheduler -   -> 6858 reads (3.20% of total) failing MappingQualityZeroFilter
[2016-04-14T23:28Z] INFO  16:28:34,799 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:28Z] INFO  16:28:34,800 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-14T23:28Z] INFO  16:28:34,801 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-14T23:28Z] INFO  16:28:35,303 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-14T23:28Z] INFO  16:28:35,367 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:28Z] INFO  16:28:35,376 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:28Z] INFO  16:28:35,425 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-14T23:28Z] INFO  16:28:35,439 IntervalUtils - Processing 15658369 bp from intervals
[2016-04-14T23:28Z] INFO  16:28:35,511 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:28Z] INFO  16:28:35,969 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:28Z] INFO  16:28:35,970 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:28Z] INFO  16:28:35,971 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:28Z] INFO  16:28:35,972 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:28Z] INFO  16:28:35,999 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:28Z] INFO  16:28:36,196 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:28Z] INFO  16:28:36,266 ProgressMeter -       7:6194101    200003.0    30.0 s       2.5 m       39.7%    75.0 s      45.0 s
[2016-04-14T23:28Z] INFO  16:28:36,344 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:28Z] GATK: realign ('6', 125112484, 142397186) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:28Z] GATK pre-alignment ('7', 110526648, 126079222) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:28Z] INFO  16:28:37,408 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:28Z] INFO  16:28:37,411 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:28Z] INFO  16:28:37,412 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:28Z] INFO  16:28:37,413 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:28Z] INFO  16:28:37,417 HelpFormatter - Program Args: -T PrintReads -L 7:94750024-110303777 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/7/tx/tmpqI9xWO/R14-18102_kapa-NGv3-PE100-NGv3-sort-7_94750023_110303777-prep-prealign.bam
[2016-04-14T23:28Z] INFO  16:28:37,426 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:28Z] INFO  16:28:37,427 HelpFormatter - Date/Time: 2016/04/14 16:28:37
[2016-04-14T23:28Z] INFO  16:28:37,428 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:28Z] INFO  16:28:37,428 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:28Z] INFO  16:28:37,649 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:28Z] INFO  16:28:37,715 ProgressMeter -            done    158680.0    13.0 s      84.0 s      100.0%    13.0 s       0.0 s
[2016-04-14T23:28Z] INFO  16:28:37,716 ProgressMeter - Total runtime 13.49 secs, 0.22 min, 0.00 hours
[2016-04-14T23:28Z] INFO  16:28:37,719 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 158680 total reads (0.00%)
[2016-04-14T23:28Z] INFO  16:28:37,720 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:28Z] INFO  16:28:37,721 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:28Z] INFO  16:28:37,721 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:28Z] INFO  16:28:38,806 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-14T23:28Z] INFO  16:28:38,874 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:28Z] INFO  16:28:38,883 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:28Z] INFO  16:28:38,952 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-14T23:28Z] INFO  16:28:38,967 IntervalUtils - Processing 15553754 bp from intervals
[2016-04-14T23:28Z] INFO  16:28:39,054 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:28Z] INFO  16:28:39,091 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:28Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-6_78400388_93953258-prep.bam
[2016-04-14T23:28Z] INFO  16:28:39,441 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:28Z] INFO  16:28:39,442 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:28Z] INFO  16:28:39,443 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:28Z] INFO  16:28:39,443 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:28Z] INFO  16:28:39,468 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:28Z] INFO  16:28:39,574 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:28Z] INFO  16:28:39,577 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:28Z] INFO  16:28:39,578 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:28Z] INFO  16:28:39,579 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:28Z] INFO  16:28:39,583 HelpFormatter - Program Args: -T PrintReads -L 7:110526649-126079222 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/7/tx/tmpTjC2xQ/R14-18102_kapa-NGv3-PE100-NGv3-sort-7_110526648_126079222-prep-prealign.bam
[2016-04-14T23:28Z] INFO  16:28:39,592 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:28Z] INFO  16:28:39,593 HelpFormatter - Date/Time: 2016/04/14 16:28:39
[2016-04-14T23:28Z] INFO  16:28:39,594 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:28Z] INFO  16:28:39,594 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:28Z] GATK pre-alignment ('7', 126086124, 141619620) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:28Z] INFO  16:28:39,638 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:28Z] INFO  16:28:39,693 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:28Z] INFO  16:28:39,696 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:28Z] INFO  16:28:39,696 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:28Z] INFO  16:28:39,696 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:28Z] INFO  16:28:39,701 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/6/R14-18102_kapa-NGv3-PE100-NGv3-sort-6_125112484_142397186-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/6/R14-18102_kapa-NGv3-PE100-NGv3-sort-6_125112484_142397186-prep-prealign-realign.intervals -L 6:125112485-142397186 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/6/tx/tmpInC7NH/R14-18102_kapa-NGv3-PE100-NGv3-sort-6_125112484_142397186-prep.bam
[2016-04-14T23:28Z] INFO  16:28:39,710 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:28Z] INFO  16:28:39,722 HelpFormatter - Date/Time: 2016/04/14 16:28:39
[2016-04-14T23:28Z] INFO  16:28:39,723 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:28Z] INFO  16:28:39,724 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:28Z] INFO  16:28:39,829 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:28Z] INFO  16:28:39,959 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:28Z] INFO  16:28:40,120 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:28Z] INFO  16:28:40,130 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:28Z] INFO  16:28:40,208 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-14T23:28Z] INFO  16:28:40,619 IntervalUtils - Processing 17284702 bp from intervals
[2016-04-14T23:28Z] WARN  16:28:40,635 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:28Z] INFO  16:28:40,748 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:28Z] INFO  16:28:40,926 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:28Z] INFO  16:28:40,938 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:28Z] INFO  16:28:40,939 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:28Z] INFO  16:28:40,939 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:28Z] INFO  16:28:41,118 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:28Z] INFO  16:28:41,133 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-14T23:28Z] INFO  16:28:41,201 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:28Z] INFO  16:28:41,210 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:28Z] INFO  16:28:41,281 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-14T23:28Z] INFO  16:28:41,310 IntervalUtils - Processing 15552574 bp from intervals
[2016-04-14T23:28Z] INFO  16:28:41,348 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:28Z] INFO  16:28:41,481 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:28Z] INFO  16:28:41,938 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:28Z] INFO  16:28:41,951 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:28Z] INFO  16:28:41,952 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:28Z] INFO  16:28:41,952 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:28Z] INFO  16:28:41,975 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:28Z] INFO  16:28:42,171 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:28Z] INFO  16:28:42,628 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:28Z] INFO  16:28:42,632 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:28Z] INFO  16:28:42,632 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:28Z] INFO  16:28:42,633 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:28Z] INFO  16:28:42,638 HelpFormatter - Program Args: -T PrintReads -L 7:126086125-141619620 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/7/tx/tmpMZzCbz/R14-18102_kapa-NGv3-PE100-NGv3-sort-7_126086124_141619620-prep-prealign.bam
[2016-04-14T23:28Z] INFO  16:28:42,649 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:28Z] INFO  16:28:42,650 HelpFormatter - Date/Time: 2016/04/14 16:28:42
[2016-04-14T23:28Z] INFO  16:28:42,650 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:28Z] INFO  16:28:42,650 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:28Z] INFO  16:28:42,826 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:28Z] INFO  16:28:43,617 ProgressMeter -            done    182205.0    14.0 s      80.0 s      100.0%    14.0 s       0.0 s
[2016-04-14T23:28Z] INFO  16:28:43,617 ProgressMeter - Total runtime 14.71 secs, 0.25 min, 0.00 hours
[2016-04-14T23:28Z] INFO  16:28:43,621 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 182205 total reads (0.00%)
[2016-04-14T23:28Z] INFO  16:28:43,621 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:28Z] INFO  16:28:43,621 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:28Z] INFO  16:28:43,622 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:28Z] INFO  16:28:43,796 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-14T23:28Z] INFO  16:28:43,879 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:28Z] INFO  16:28:43,889 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:28Z] INFO  16:28:43,951 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-14T23:28Z] INFO  16:28:43,966 IntervalUtils - Processing 15533496 bp from intervals
[2016-04-14T23:28Z] INFO  16:28:44,047 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:28Z] INFO  16:28:44,398 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:28Z] INFO  16:28:44,398 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:28Z] INFO  16:28:44,399 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:28Z] INFO  16:28:44,399 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:28Z] INFO  16:28:44,423 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:28Z] INFO  16:28:44,599 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:28Z] INFO  16:28:45,238 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:28Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-6_109467960_124979532-prep.bam
[2016-04-14T23:28Z] INFO  16:28:45,908 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@7172f77a
[2016-04-14T23:28Z] GATK pre-alignment ('7', 141629903, 157151331) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:28Z] INFO  16:28:45,997 ProgressMeter -            done    322336.0    39.0 s       2.1 m      100.0%    39.0 s       0.0 s
[2016-04-14T23:28Z] INFO  16:28:45,998 ProgressMeter - Total runtime 39.75 secs, 0.66 min, 0.01 hours
[2016-04-14T23:28Z] INFO  16:28:45,998 MicroScheduler - 192 reads were filtered out during the traversal out of approximately 322528 total reads (0.06%)
[2016-04-14T23:28Z] INFO  16:28:45,999 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:28Z] INFO  16:28:45,999 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:28Z] INFO  16:28:45,999 MicroScheduler -   -> 192 reads (0.06% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:28Z] INFO  16:28:46,928 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@32d5a4c6
[2016-04-14T23:28Z] INFO  16:28:47,081 ProgressMeter -            done    880352.0   103.0 s     118.0 s      100.0%   103.0 s       0.0 s
[2016-04-14T23:28Z] INFO  16:28:47,082 ProgressMeter - Total runtime 103.97 secs, 1.73 min, 0.03 hours
[2016-04-14T23:28Z] INFO  16:28:47,083 MicroScheduler - 357 reads were filtered out during the traversal out of approximately 880709 total reads (0.04%)
[2016-04-14T23:28Z] INFO  16:28:47,084 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:28Z] INFO  16:28:47,096 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:28Z] INFO  16:28:47,097 MicroScheduler -   -> 357 reads (0.04% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:28Z] INFO  16:28:47,664 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:28Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-7_0_15584548-prep-prealign.bam
[2016-04-14T23:28Z] INFO  16:28:48,317 ProgressMeter -            done    378887.0    27.0 s      72.0 s      100.0%    27.0 s       0.0 s
[2016-04-14T23:28Z] INFO  16:28:48,317 ProgressMeter - Total runtime 27.38 secs, 0.46 min, 0.01 hours
[2016-04-14T23:28Z] INFO  16:28:48,321 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 378887 total reads (0.00%)
[2016-04-14T23:28Z] INFO  16:28:48,322 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:28Z] INFO  16:28:48,322 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:28Z] INFO  16:28:48,323 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:28Z] INFO  16:28:48,451 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:28Z] INFO  16:28:48,455 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:28Z] INFO  16:28:48,456 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:28Z] INFO  16:28:48,457 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:28Z] INFO  16:28:48,463 HelpFormatter - Program Args: -T PrintReads -L 7:141629904-157151331 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/7/tx/tmpYEPHSX/R14-18102_kapa-NGv3-PE100-NGv3-sort-7_141629903_157151331-prep-prealign.bam
[2016-04-14T23:28Z] INFO  16:28:48,474 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:28Z] INFO  16:28:48,475 HelpFormatter - Date/Time: 2016/04/14 16:28:48
[2016-04-14T23:28Z] INFO  16:28:48,476 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:28Z] INFO  16:28:48,477 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:28Z] INFO  16:28:48,498 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@41fd9d8e
[2016-04-14T23:28Z] INFO  16:28:48,542 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:28Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-6_31083801_46593245-prep-prealign.bam
[2016-04-14T23:28Z] INFO  16:28:48,621 ProgressMeter -            done    202937.0    26.0 s       2.2 m      100.0%    26.0 s       0.0 s
[2016-04-14T23:28Z] INFO  16:28:48,621 ProgressMeter - Total runtime 26.40 secs, 0.44 min, 0.01 hours
[2016-04-14T23:28Z] INFO  16:28:48,622 MicroScheduler - 140 reads were filtered out during the traversal out of approximately 203077 total reads (0.07%)
[2016-04-14T23:28Z] INFO  16:28:48,622 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:28Z] INFO  16:28:48,622 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:28Z] INFO  16:28:48,623 MicroScheduler -   -> 140 reads (0.07% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:28Z] INFO  16:28:48,664 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:28Z] GATK RealignerTargetCreator: R14-18102_kapa-NGv3-PE100-NGv3-sort-7_0_15584548-prep-prealign.bam 7:1-15584548
[2016-04-14T23:28Z] GATK: RealignerTargetCreator
[2016-04-14T23:28Z] INFO  16:28:49,182 ProgressMeter -            done   1.5594442E7    27.0 s       1.0 s      100.0%    27.0 s       0.0 s
[2016-04-14T23:28Z] INFO  16:28:49,194 ProgressMeter - Total runtime 27.75 secs, 0.46 min, 0.01 hours
[2016-04-14T23:28Z] INFO  16:28:49,196 MicroScheduler - 76910 reads were filtered out during the traversal out of approximately 690660 total reads (11.14%)
[2016-04-14T23:28Z] INFO  16:28:49,196 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:28Z] INFO  16:28:49,197 MicroScheduler -   -> 1263 reads (0.18% of total) failing BadMateFilter
[2016-04-14T23:28Z] INFO  16:28:49,198 MicroScheduler -   -> 58276 reads (8.44% of total) failing DuplicateReadFilter
[2016-04-14T23:28Z] INFO  16:28:49,199 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-14T23:28Z] INFO  16:28:49,199 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:28Z] INFO  16:28:49,199 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-14T23:28Z] INFO  16:28:49,200 MicroScheduler -   -> 17371 reads (2.52% of total) failing MappingQualityZeroFilter
[2016-04-14T23:28Z] INFO  16:28:49,200 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:28Z] INFO  16:28:49,200 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-14T23:28Z] INFO  16:28:49,200 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-14T23:28Z] INFO  16:28:49,623 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-14T23:28Z] INFO  16:28:49,694 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:28Z] INFO  16:28:49,705 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:28Z] INFO  16:28:49,771 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-14T23:28Z] INFO  16:28:49,788 IntervalUtils - Processing 15521428 bp from intervals
[2016-04-14T23:28Z] INFO  16:28:49,878 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:28Z] INFO  16:28:49,987 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:28Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-6_15511526_31080332-prep.bam
[2016-04-14T23:28Z] INFO  16:28:50,153 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:28Z] INFO  16:28:50,176 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:28Z] INFO  16:28:50,178 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:28Z] INFO  16:28:50,179 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:28Z] INFO  16:28:50,179 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:28Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-7_15599765_31117713-prep-prealign.bam
[2016-04-14T23:28Z] INFO  16:28:50,200 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:28Z] INFO  16:28:50,385 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:28Z] INFO  16:28:50,552 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:28Z] GATK: realign ('5', 127597427, 143191869) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:28Z] GATK RealignerTargetCreator: R14-18102_kapa-NGv3-PE100-NGv3-sort-7_15599765_31117713-prep-prealign.bam 7:15599766-31117713
[2016-04-14T23:28Z] GATK: RealignerTargetCreator
[2016-04-14T23:28Z] GATK pre-alignment ('7', 157155854, 159138663) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:28Z] GATK RealignerTargetCreator: R14-18102_kapa-NGv3-PE100-NGv3-sort-6_31083801_46593245-prep-prealign.bam 6:31083802-46593245
[2016-04-14T23:28Z] GATK: RealignerTargetCreator
[2016-04-14T23:28Z] INFO  16:28:51,991 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:28Z] INFO  16:28:51,994 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:28Z] INFO  16:28:51,995 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:28Z] INFO  16:28:51,995 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:28Z] INFO  16:28:52,000 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/7/R14-18102_kapa-NGv3-PE100-NGv3-sort-7_0_15584548-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/7/tx/tmpshdHrv/R14-18102_kapa-NGv3-PE100-NGv3-sort-7_0_15584548-prep-prealign-realign.intervals -l INFO -L 7:1-15584548 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-14T23:28Z] INFO  16:28:52,027 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:28Z] INFO  16:28:52,033 HelpFormatter - Date/Time: 2016/04/14 16:28:51
[2016-04-14T23:28Z] INFO  16:28:52,040 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:28Z] INFO  16:28:52,041 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:28Z] INFO  16:28:52,141 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:28Z] INFO  16:28:52,260 ProgressMeter -            done   1.3101257E7    18.0 s       1.0 s      100.0%    18.0 s       0.0 s
[2016-04-14T23:28Z] INFO  16:28:52,261 ProgressMeter - Total runtime 18.74 secs, 0.31 min, 0.01 hours
[2016-04-14T23:28Z] INFO  16:28:52,266 MicroScheduler - 32029 reads were filtered out during the traversal out of approximately 242892 total reads (13.19%)
[2016-04-14T23:28Z] INFO  16:28:52,267 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:28Z] INFO  16:28:52,267 MicroScheduler -   -> 616 reads (0.25% of total) failing BadMateFilter
[2016-04-14T23:28Z] INFO  16:28:52,268 MicroScheduler -   -> 18397 reads (7.57% of total) failing DuplicateReadFilter
[2016-04-14T23:28Z] INFO  16:28:52,269 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-14T23:28Z] INFO  16:28:52,269 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:28Z] INFO  16:28:52,270 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-14T23:28Z] INFO  16:28:52,270 MicroScheduler -   -> 13016 reads (5.36% of total) failing MappingQualityZeroFilter
[2016-04-14T23:28Z] INFO  16:28:52,271 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:28Z] INFO  16:28:52,272 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-14T23:28Z] INFO  16:28:52,272 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-14T23:28Z] INFO  16:28:52,314 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-14T23:28Z] INFO  16:28:52,334 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:28Z] INFO  16:28:52,388 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-14T23:28Z] INFO  16:28:52,796 IntervalUtils - Processing 15584548 bp from intervals
[2016-04-14T23:28Z] WARN  16:28:52,801 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:28Z] INFO  16:28:52,902 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:28Z] INFO  16:28:53,072 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:28Z] INFO  16:28:53,074 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:28Z] INFO  16:28:53,074 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:28Z] INFO  16:28:53,075 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-14T23:28Z] INFO  16:28:53,636 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:28Z] INFO  16:28:53,639 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:28Z] INFO  16:28:53,640 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:28Z] INFO  16:28:53,640 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:28Z] INFO  16:28:53,645 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/5/R14-18102_kapa-NGv3-PE100-NGv3-sort-5_127597427_143191869-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/5/R14-18102_kapa-NGv3-PE100-NGv3-sort-5_127597427_143191869-prep-prealign-realign.intervals -L 5:127597428-143191869 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/5/tx/tmpsS16Kz/R14-18102_kapa-NGv3-PE100-NGv3-sort-5_127597427_143191869-prep.bam
[2016-04-14T23:28Z] INFO  16:28:53,666 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:28Z] INFO  16:28:53,677 HelpFormatter - Date/Time: 2016/04/14 16:28:53
[2016-04-14T23:28Z] INFO  16:28:53,678 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:28Z] INFO  16:28:53,679 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:28Z] INFO  16:28:53,821 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:28Z] GATK: realign ('6', 158013810, 171115067) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:28Z] INFO  16:28:53,935 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:28Z] INFO  16:28:54,057 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:28Z] INFO  16:28:54,067 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:28Z] INFO  16:28:54,065 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:28Z] INFO  16:28:54,068 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:28Z] INFO  16:28:54,069 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:28Z] INFO  16:28:54,069 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:28Z] INFO  16:28:54,074 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/7/R14-18102_kapa-NGv3-PE100-NGv3-sort-7_15599765_31117713-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/7/tx/tmpABqaji/R14-18102_kapa-NGv3-PE100-NGv3-sort-7_15599765_31117713-prep-prealign-realign.intervals -l INFO -L 7:15599766-31117713 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-14T23:28Z] INFO  16:28:54,114 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:28Z] INFO  16:28:54,115 HelpFormatter - Date/Time: 2016/04/14 16:28:54
[2016-04-14T23:28Z] INFO  16:28:54,115 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:28Z] INFO  16:28:54,116 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:28Z] INFO  16:28:54,127 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-14T23:28Z] INFO  16:28:54,186 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:28Z] INFO  16:28:54,189 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:28Z] INFO  16:28:54,190 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:28Z] INFO  16:28:54,190 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:28Z] INFO  16:28:54,195 HelpFormatter - Program Args: -T PrintReads -L 7:157155855-159138663 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/7/tx/tmp9aIImy/R14-18102_kapa-NGv3-PE100-NGv3-sort-7_157155854_159138663-prep-prealign.bam
[2016-04-14T23:28Z] INFO  16:28:54,203 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:28Z] INFO  16:28:54,203 HelpFormatter - Date/Time: 2016/04/14 16:28:54
[2016-04-14T23:28Z] INFO  16:28:54,203 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:28Z] INFO  16:28:54,203 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:28Z] INFO  16:28:54,246 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:28Z] INFO  16:28:54,417 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:28Z] INFO  16:28:54,454 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:28Z] INFO  16:28:54,457 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:28Z] INFO  16:28:54,458 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:28Z] INFO  16:28:54,458 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:28Z] INFO  16:28:54,463 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/6/R14-18102_kapa-NGv3-PE100-NGv3-sort-6_31083801_46593245-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/6/tx/tmpYSy5Gr/R14-18102_kapa-NGv3-PE100-NGv3-sort-6_31083801_46593245-prep-prealign-realign.intervals -l INFO -L 6:31083802-46593245 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-14T23:28Z] INFO  16:28:54,492 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:28Z] INFO  16:28:54,493 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-14T23:28Z] INFO  16:28:54,495 HelpFormatter - Date/Time: 2016/04/14 16:28:54
[2016-04-14T23:28Z] INFO  16:28:54,495 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:28Z] INFO  16:28:54,495 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:28Z] INFO  16:28:54,509 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:28Z] INFO  16:28:54,527 IntervalUtils - Processing 15594442 bp from intervals
[2016-04-14T23:28Z] WARN  16:28:54,532 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:28Z] INFO  16:28:54,560 ProgressMeter -      7:44685115    200003.0    30.0 s       2.5 m       83.7%    35.0 s       5.0 s
[2016-04-14T23:28Z] INFO  16:28:54,580 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-14T23:28Z] INFO  16:28:54,635 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:28Z] INFO  16:28:54,643 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:28Z] INFO  16:28:54,841 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-14T23:28Z] INFO  16:28:54,856 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:28Z] INFO  16:28:54,857 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:28Z] INFO  16:28:54,857 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:28Z] INFO  16:28:54,858 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:28Z] INFO  16:28:54,860 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:28Z] INFO  16:28:54,918 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-14T23:28Z] INFO  16:28:54,962 IntervalUtils - Processing 15517948 bp from intervals
[2016-04-14T23:28Z] WARN  16:28:54,968 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:28Z] INFO  16:28:55,061 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:28Z] INFO  16:28:55,066 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:28Z] INFO  16:28:55,159 ProgressMeter -            done   1.5564086E7    20.0 s       1.0 s      100.0%    20.0 s       0.0 s
[2016-04-14T23:28Z] INFO  16:28:55,160 ProgressMeter - Total runtime 20.75 secs, 0.35 min, 0.01 hours
[2016-04-14T23:28Z] INFO  16:28:55,164 MicroScheduler - 23414 reads were filtered out during the traversal out of approximately 257991 total reads (9.08%)
[2016-04-14T23:28Z] INFO  16:28:55,175 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:28Z] INFO  16:28:55,177 MicroScheduler -   -> 646 reads (0.25% of total) failing BadMateFilter
[2016-04-14T23:28Z] INFO  16:28:55,177 MicroScheduler -   -> 19892 reads (7.71% of total) failing DuplicateReadFilter
[2016-04-14T23:28Z] INFO  16:28:55,178 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-14T23:28Z] INFO  16:28:55,178 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:28Z] INFO  16:28:55,179 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-14T23:28Z] INFO  16:28:55,179 MicroScheduler -   -> 2876 reads (1.11% of total) failing MappingQualityZeroFilter
[2016-04-14T23:28Z] INFO  16:28:55,180 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:28Z] INFO  16:28:55,181 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-14T23:28Z] INFO  16:28:55,181 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-14T23:28Z] INFO  16:28:55,277 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:28Z] INFO  16:28:55,279 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:28Z] INFO  16:28:55,280 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:28Z] INFO  16:28:55,281 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:28Z] INFO  16:28:55,282 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-14T23:28Z] INFO  16:28:55,287 IntervalUtils - Processing 15509444 bp from intervals
[2016-04-14T23:28Z] WARN  16:28:55,292 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:28Z] INFO  16:28:55,403 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:28Z] INFO  16:28:55,611 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:28Z] INFO  16:28:55,612 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:28Z] INFO  16:28:55,613 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:28Z] INFO  16:28:55,614 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-14T23:28Z] INFO  16:28:55,616 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-14T23:28Z] INFO  16:28:55,675 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:28Z] INFO  16:28:55,684 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:28Z] INFO  16:28:55,726 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.04
[2016-04-14T23:28Z] INFO  16:28:55,765 IntervalUtils - Processing 1982809 bp from intervals
[2016-04-14T23:28Z] INFO  16:28:55,861 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:28Z] INFO  16:28:56,074 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:28Z] INFO  16:28:56,075 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:28Z] INFO  16:28:56,076 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:28Z] INFO  16:28:56,076 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:28Z] INFO  16:28:56,090 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:28Z] INFO  16:28:56,112 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:28Z] INFO  16:28:56,755 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:28Z] GATK: realign ('6', 142399691, 157963777) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:28Z] INFO  16:28:56,956 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:28Z] INFO  16:28:56,960 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:28Z] INFO  16:28:56,960 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:28Z] INFO  16:28:56,961 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:28Z] INFO  16:28:56,965 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/6/R14-18102_kapa-NGv3-PE100-NGv3-sort-6_158013810_171115067-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/6/R14-18102_kapa-NGv3-PE100-NGv3-sort-6_158013810_171115067-prep-prealign-realign.intervals -L 6:158013811-171115067 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/6/tx/tmpYYULAT/R14-18102_kapa-NGv3-PE100-NGv3-sort-6_158013810_171115067-prep.bam
[2016-04-14T23:28Z] INFO  16:28:56,974 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:28Z] INFO  16:28:56,975 HelpFormatter - Date/Time: 2016/04/14 16:28:56
[2016-04-14T23:28Z] INFO  16:28:56,976 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:28Z] INFO  16:28:56,977 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:28Z] INFO  16:28:57,185 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:28Z] INFO  16:28:57,333 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:28Z] INFO  16:28:57,346 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:28Z] INFO  16:28:57,413 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-14T23:28Z] INFO  16:28:57,665 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@7172f77a
[2016-04-14T23:28Z] INFO  16:28:57,758 IntervalUtils - Processing 13101257 bp from intervals
[2016-04-14T23:28Z] WARN  16:28:57,763 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:28Z] INFO  16:28:57,844 ProgressMeter -            done    161635.0    27.0 s       2.8 m      100.0%    27.0 s       0.0 s
[2016-04-14T23:28Z] INFO  16:28:57,844 ProgressMeter - Total runtime 27.45 secs, 0.46 min, 0.01 hours
[2016-04-14T23:28Z] INFO  16:28:57,844 MicroScheduler - 175 reads were filtered out during the traversal out of approximately 161810 total reads (0.11%)
[2016-04-14T23:28Z] INFO  16:28:57,845 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:28Z] INFO  16:28:57,845 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:28Z] INFO  16:28:57,845 MicroScheduler -   -> 175 reads (0.11% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:28Z] INFO  16:28:57,877 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:28Z] INFO  16:28:57,932 ProgressMeter -            done    212698.0    16.0 s      79.0 s      100.0%    16.0 s       0.0 s
[2016-04-14T23:28Z] INFO  16:28:57,933 ProgressMeter - Total runtime 17.00 secs, 0.28 min, 0.00 hours
[2016-04-14T23:28Z] INFO  16:28:57,937 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 212698 total reads (0.00%)
[2016-04-14T23:28Z] INFO  16:28:57,937 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:28Z] INFO  16:28:57,938 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:28Z] INFO  16:28:57,938 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:28Z] INFO  16:28:58,008 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:28Z] INFO  16:28:58,009 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:28Z] INFO  16:28:58,010 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:28Z] INFO  16:28:58,010 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:28Z] INFO  16:28:58,171 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:28Z] INFO  16:28:58,338 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:28Z] INFO  16:28:58,969 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@41fd9d8e
[2016-04-14T23:28Z] INFO  16:28:59,073 ProgressMeter -            done    174316.0    23.0 s       2.2 m      100.0%    23.0 s       0.0 s
[2016-04-14T23:28Z] INFO  16:28:59,073 ProgressMeter - Total runtime 23.10 secs, 0.39 min, 0.01 hours
[2016-04-14T23:28Z] INFO  16:28:59,073 MicroScheduler - 120 reads were filtered out during the traversal out of approximately 174436 total reads (0.07%)
[2016-04-14T23:28Z] INFO  16:28:59,074 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:28Z] INFO  16:28:59,074 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:28Z] INFO  16:28:59,074 MicroScheduler -   -> 120 reads (0.07% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:28Z] INFO  16:28:59,348 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:28Z] INFO  16:28:59,352 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:28Z] INFO  16:28:59,352 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:28Z] INFO  16:28:59,353 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:28Z] INFO  16:28:59,358 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:28Z] INFO  16:28:59,357 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/6/R14-18102_kapa-NGv3-PE100-NGv3-sort-6_142399691_157963777-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/6/R14-18102_kapa-NGv3-PE100-NGv3-sort-6_142399691_157963777-prep-prealign-realign.intervals -L 6:142399692-157963777 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/6/tx/tmpnsKN5G/R14-18102_kapa-NGv3-PE100-NGv3-sort-6_142399691_157963777-prep.bam
[2016-04-14T23:28Z] INFO  16:28:59,383 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:28Z] INFO  16:28:59,384 HelpFormatter - Date/Time: 2016/04/14 16:28:59
[2016-04-14T23:28Z] INFO  16:28:59,385 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:28Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-7_47319761_63093154-prep-prealign.bam
[2016-04-14T23:28Z] INFO  16:28:59,385 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:28Z] INFO  16:28:59,486 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:28Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-6_125112484_142397186-prep.bam
[2016-04-14T23:28Z] INFO  16:28:59,598 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@41fd9d8e
[2016-04-14T23:28Z] INFO  16:28:59,605 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:28Z] INFO  16:28:59,711 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:28Z] INFO  16:28:59,720 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:28Z] INFO  16:28:59,769 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-14T23:28Z] INFO  16:28:59,781 ProgressMeter -            done    120903.0    17.0 s       2.5 m      100.0%    17.0 s       0.0 s
[2016-04-14T23:28Z] INFO  16:28:59,786 ProgressMeter - Total runtime 17.84 secs, 0.30 min, 0.00 hours
[2016-04-14T23:28Z] INFO  16:28:59,788 MicroScheduler - 110 reads were filtered out during the traversal out of approximately 121013 total reads (0.09%)
[2016-04-14T23:28Z] INFO  16:28:59,789 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:28Z] INFO  16:28:59,790 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:28Z] INFO  16:28:59,791 MicroScheduler -   -> 110 reads (0.09% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:29Z] GATK RealignerTargetCreator: R14-18102_kapa-NGv3-PE100-NGv3-sort-7_47319761_63093154-prep-prealign.bam 7:47319762-63093154
[2016-04-14T23:29Z] GATK: RealignerTargetCreator
[2016-04-14T23:29Z] INFO  16:29:00,104 IntervalUtils - Processing 15564086 bp from intervals
[2016-04-14T23:29Z] WARN  16:29:00,108 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:29Z] INFO  16:29:00,175 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:29Z] GATK pre-alignment ('8', 0, 15517156) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:29Z] INFO  16:29:00,308 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:29Z] INFO  16:29:00,316 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:29Z] INFO  16:29:00,317 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:29Z] INFO  16:29:00,318 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:29Z] INFO  16:29:00,380 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@7172f77a
[2016-04-14T23:29Z] INFO  16:29:00,474 ProgressMeter -            done    264097.0    35.0 s       2.3 m      100.0%    35.0 s       0.0 s
[2016-04-14T23:29Z] INFO  16:29:00,475 ProgressMeter - Total runtime 35.97 secs, 0.60 min, 0.01 hours
[2016-04-14T23:29Z] INFO  16:29:00,475 MicroScheduler - 139 reads were filtered out during the traversal out of approximately 264236 total reads (0.05%)
[2016-04-14T23:29Z] INFO  16:29:00,475 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:29Z] INFO  16:29:00,475 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:29Z] INFO  16:29:00,476 MicroScheduler -   -> 139 reads (0.05% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:29Z] INFO  16:29:00,483 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:29Z] INFO  16:29:00,512 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:29Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-7_79082334_94740703-prep-prealign.bam
[2016-04-14T23:29Z] INFO  16:29:00,663 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:29Z] INFO  16:29:01,116 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:29Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-7_110526648_126079222-prep-prealign.bam
[2016-04-14T23:29Z] GATK RealignerTargetCreator: R14-18102_kapa-NGv3-PE100-NGv3-sort-7_79082334_94740703-prep-prealign.bam 7:79082335-94740703
[2016-04-14T23:29Z] GATK: RealignerTargetCreator
[2016-04-14T23:29Z] GATK RealignerTargetCreator: R14-18102_kapa-NGv3-PE100-NGv3-sort-7_110526648_126079222-prep-prealign.bam 7:110526649-126079222
[2016-04-14T23:29Z] GATK: RealignerTargetCreator
[2016-04-14T23:29Z] INFO  16:29:02,021 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:29Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-7_31120227_47317818-prep-prealign.bam
[2016-04-14T23:29Z] INFO  16:29:02,556 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@41fd9d8e
[2016-04-14T23:29Z] INFO  16:29:02,696 ProgressMeter -            done     28996.0     6.0 s       3.8 m       89.9%     6.0 s       0.0 s
[2016-04-14T23:29Z] INFO  16:29:02,697 ProgressMeter - Total runtime 6.62 secs, 0.11 min, 0.00 hours
[2016-04-14T23:29Z] INFO  16:29:02,698 MicroScheduler - 28 reads were filtered out during the traversal out of approximately 29024 total reads (0.10%)
[2016-04-14T23:29Z] INFO  16:29:02,698 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:29Z] INFO  16:29:02,699 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:29Z] INFO  16:29:02,700 MicroScheduler -   -> 28 reads (0.10% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:29Z] INFO  16:29:02,804 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:29Z] INFO  16:29:02,808 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:29Z] INFO  16:29:02,809 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:29Z] INFO  16:29:02,809 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:29Z] INFO  16:29:02,814 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/7/R14-18102_kapa-NGv3-PE100-NGv3-sort-7_47319761_63093154-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/7/tx/tmpPqOVTW/R14-18102_kapa-NGv3-PE100-NGv3-sort-7_47319761_63093154-prep-prealign-realign.intervals -l INFO -L 7:47319762-63093154 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-14T23:29Z] INFO  16:29:02,844 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:29Z] INFO  16:29:02,845 HelpFormatter - Date/Time: 2016/04/14 16:29:02
[2016-04-14T23:29Z] INFO  16:29:02,846 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:29Z] INFO  16:29:02,846 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:29Z] GATK RealignerTargetCreator: R14-18102_kapa-NGv3-PE100-NGv3-sort-7_31120227_47317818-prep-prealign.bam 7:31120228-47317818
[2016-04-14T23:29Z] GATK: RealignerTargetCreator
[2016-04-14T23:29Z] INFO  16:29:02,926 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:29Z] INFO  16:29:03,117 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-14T23:29Z] INFO  16:29:03,126 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:29Z] INFO  16:29:03,207 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-14T23:29Z] INFO  16:29:03,273 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:29Z] INFO  16:29:03,277 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:29Z] INFO  16:29:03,277 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:29Z] INFO  16:29:03,278 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:29Z] INFO  16:29:03,282 HelpFormatter - Program Args: -T PrintReads -L 8:1-15517156 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/8/tx/tmp22Z2pY/R14-18102_kapa-NGv3-PE100-NGv3-sort-8_0_15517156-prep-prealign.bam
[2016-04-14T23:29Z] INFO  16:29:03,292 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:29Z] INFO  16:29:03,298 HelpFormatter - Date/Time: 2016/04/14 16:29:03
[2016-04-14T23:29Z] INFO  16:29:03,299 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:29Z] INFO  16:29:03,299 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:29Z] INFO  16:29:03,512 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:29Z] INFO  16:29:03,549 IntervalUtils - Processing 15773393 bp from intervals
[2016-04-14T23:29Z] WARN  16:29:03,555 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:29Z] INFO  16:29:03,677 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:29Z] INFO  16:29:03,904 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:29Z] INFO  16:29:03,905 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:29Z] INFO  16:29:03,906 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:29Z] INFO  16:29:03,907 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-14T23:29Z] INFO  16:29:04,099 ProgressMeter -      7:73639057    200003.0    30.0 s       2.5 m       67.8%    44.0 s      14.0 s
[2016-04-14T23:29Z] INFO  16:29:04,140 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:29Z] INFO  16:29:04,144 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:29Z] INFO  16:29:04,144 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:29Z] INFO  16:29:04,145 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:29Z] INFO  16:29:04,151 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/7/R14-18102_kapa-NGv3-PE100-NGv3-sort-7_79082334_94740703-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/7/tx/tmpeSTbUz/R14-18102_kapa-NGv3-PE100-NGv3-sort-7_79082334_94740703-prep-prealign-realign.intervals -l INFO -L 7:79082335-94740703 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-14T23:29Z] INFO  16:29:04,170 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:29Z] INFO  16:29:04,171 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:29Z] INFO  16:29:04,172 HelpFormatter - Date/Time: 2016/04/14 16:29:04
[2016-04-14T23:29Z] INFO  16:29:04,173 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:29Z] INFO  16:29:04,174 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:29Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-7_157155854_159138663-prep-prealign.bam
[2016-04-14T23:29Z] INFO  16:29:04,342 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:29Z] GATK RealignerTargetCreator: R14-18102_kapa-NGv3-PE100-NGv3-sort-7_157155854_159138663-prep-prealign.bam 7:157155855-159138663
[2016-04-14T23:29Z] GATK: RealignerTargetCreator
[2016-04-14T23:29Z] INFO  16:29:04,573 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-14T23:29Z] INFO  16:29:04,586 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:29Z] INFO  16:29:04,630 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:29Z] INFO  16:29:04,633 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:29Z] INFO  16:29:04,634 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:29Z] INFO  16:29:04,634 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:29Z] INFO  16:29:04,639 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/7/R14-18102_kapa-NGv3-PE100-NGv3-sort-7_110526648_126079222-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/7/tx/tmpmo89nR/R14-18102_kapa-NGv3-PE100-NGv3-sort-7_110526648_126079222-prep-prealign-realign.intervals -l INFO -L 7:110526649-126079222 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-14T23:29Z] INFO  16:29:04,656 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:29Z] INFO  16:29:04,663 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-14T23:29Z] INFO  16:29:04,667 HelpFormatter - Date/Time: 2016/04/14 16:29:04
[2016-04-14T23:29Z] INFO  16:29:04,668 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:29Z] INFO  16:29:04,669 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:29Z] INFO  16:29:04,823 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:29Z] INFO  16:29:04,845 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-14T23:29Z] INFO  16:29:04,919 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:29Z] INFO  16:29:04,928 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:29Z] INFO  16:29:05,029 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.10
[2016-04-14T23:29Z] INFO  16:29:05,059 IntervalUtils - Processing 15517156 bp from intervals
[2016-04-14T23:29Z] INFO  16:29:05,097 IntervalUtils - Processing 15658369 bp from intervals
[2016-04-14T23:29Z] WARN  16:29:05,102 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:29Z] INFO  16:29:05,135 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-14T23:29Z] INFO  16:29:05,146 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:29Z] INFO  16:29:05,170 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:29Z] INFO  16:29:05,200 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:29Z] INFO  16:29:05,223 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-14T23:29Z] INFO  16:29:05,421 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:29Z] INFO  16:29:05,423 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:29Z] INFO  16:29:05,423 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:29Z] INFO  16:29:05,424 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-14T23:29Z] INFO  16:29:05,511 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:29Z] INFO  16:29:05,513 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:29Z] INFO  16:29:05,518 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:29Z] INFO  16:29:05,519 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:29Z] INFO  16:29:05,539 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:29Z] INFO  16:29:05,633 IntervalUtils - Processing 15552574 bp from intervals
[2016-04-14T23:29Z] WARN  16:29:05,652 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:29Z] INFO  16:29:05,700 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:29Z] INFO  16:29:05,752 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:29Z] INFO  16:29:05,795 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:29Z] INFO  16:29:05,798 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:29Z] INFO  16:29:05,798 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:29Z] INFO  16:29:05,799 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:29Z] INFO  16:29:05,803 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/7/R14-18102_kapa-NGv3-PE100-NGv3-sort-7_31120227_47317818-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/7/tx/tmpU6iIBO/R14-18102_kapa-NGv3-PE100-NGv3-sort-7_31120227_47317818-prep-prealign-realign.intervals -l INFO -L 7:31120228-47317818 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-14T23:29Z] INFO  16:29:05,812 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:29Z] INFO  16:29:05,813 HelpFormatter - Date/Time: 2016/04/14 16:29:05
[2016-04-14T23:29Z] INFO  16:29:05,813 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:29Z] INFO  16:29:05,814 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:29Z] INFO  16:29:05,924 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:29Z] INFO  16:29:06,041 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:29Z] INFO  16:29:06,042 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:29Z] INFO  16:29:06,043 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:29Z] INFO  16:29:06,044 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-14T23:29Z] INFO  16:29:06,131 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-14T23:29Z] INFO  16:29:06,151 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:29Z] INFO  16:29:06,209 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-14T23:29Z] INFO  16:29:06,475 IntervalUtils - Processing 16197591 bp from intervals
[2016-04-14T23:29Z] WARN  16:29:06,480 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:29Z] INFO  16:29:06,604 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:29Z] INFO  16:29:06,869 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:29Z] INFO  16:29:06,881 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:29Z] INFO  16:29:06,882 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:29Z] INFO  16:29:06,882 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-14T23:29Z] INFO  16:29:07,621 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:29Z] INFO  16:29:07,631 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:29Z] INFO  16:29:07,632 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:29Z] INFO  16:29:07,632 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:29Z] INFO  16:29:07,637 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/7/R14-18102_kapa-NGv3-PE100-NGv3-sort-7_157155854_159138663-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/7/tx/tmposdDH_/R14-18102_kapa-NGv3-PE100-NGv3-sort-7_157155854_159138663-prep-prealign-realign.intervals -l INFO -L 7:157155855-159138663 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-14T23:29Z] INFO  16:29:07,650 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:29Z] INFO  16:29:07,651 HelpFormatter - Date/Time: 2016/04/14 16:29:07
[2016-04-14T23:29Z] INFO  16:29:07,662 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:29Z] INFO  16:29:07,663 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:29Z] INFO  16:29:07,779 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:29Z] INFO  16:29:08,022 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-14T23:29Z] INFO  16:29:08,040 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:29Z] INFO  16:29:08,106 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-14T23:29Z] INFO  16:29:08,404 IntervalUtils - Processing 1982809 bp from intervals
[2016-04-14T23:29Z] WARN  16:29:08,421 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:29Z] INFO  16:29:08,568 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:29Z] INFO  16:29:08,772 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:29Z] INFO  16:29:08,774 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:29Z] INFO  16:29:08,774 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:29Z] INFO  16:29:08,775 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-14T23:29Z] INFO  16:29:10,193 ProgressMeter -      7:99910693    100001.0    30.0 s       5.1 m       33.2%    90.0 s      60.0 s
[2016-04-14T23:29Z] INFO  16:29:13,294 ProgressMeter -            done   1982809.0     4.0 s       2.0 s      100.0%     4.0 s       0.0 s
[2016-04-14T23:29Z] INFO  16:29:13,295 ProgressMeter - Total runtime 4.52 secs, 0.08 min, 0.00 hours
[2016-04-14T23:29Z] INFO  16:29:13,326 MicroScheduler - 2697 reads were filtered out during the traversal out of approximately 29119 total reads (9.26%)
[2016-04-14T23:29Z] INFO  16:29:13,327 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:29Z] INFO  16:29:13,327 MicroScheduler -   -> 106 reads (0.36% of total) failing BadMateFilter
[2016-04-14T23:29Z] INFO  16:29:13,328 MicroScheduler -   -> 2287 reads (7.85% of total) failing DuplicateReadFilter
[2016-04-14T23:29Z] INFO  16:29:13,329 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-14T23:29Z] INFO  16:29:13,329 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:29Z] INFO  16:29:13,330 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-14T23:29Z] INFO  16:29:13,331 MicroScheduler -   -> 304 reads (1.04% of total) failing MappingQualityZeroFilter
[2016-04-14T23:29Z] INFO  16:29:13,331 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:29Z] INFO  16:29:13,332 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-14T23:29Z] INFO  16:29:13,332 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-14T23:29Z] INFO  16:29:14,093 ProgressMeter -            done   1.5584548E7    21.0 s       1.0 s      100.0%    21.0 s       0.0 s
[2016-04-14T23:29Z] INFO  16:29:14,095 ProgressMeter - Total runtime 21.02 secs, 0.35 min, 0.01 hours
[2016-04-14T23:29Z] INFO  16:29:14,099 MicroScheduler - 42684 reads were filtered out during the traversal out of approximately 324192 total reads (13.17%)
[2016-04-14T23:29Z] INFO  16:29:14,100 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:29Z] INFO  16:29:14,100 MicroScheduler -   -> 819 reads (0.25% of total) failing BadMateFilter
[2016-04-14T23:29Z] INFO  16:29:14,101 MicroScheduler -   -> 24472 reads (7.55% of total) failing DuplicateReadFilter
[2016-04-14T23:29Z] INFO  16:29:14,101 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-14T23:29Z] INFO  16:29:14,102 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:29Z] INFO  16:29:14,102 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-14T23:29Z] INFO  16:29:14,102 MicroScheduler -   -> 17393 reads (5.37% of total) failing MappingQualityZeroFilter
[2016-04-14T23:29Z] INFO  16:29:14,102 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:29Z] INFO  16:29:14,102 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-14T23:29Z] INFO  16:29:14,103 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-14T23:29Z] INFO  16:29:14,169 ProgressMeter -            done   1.5517948E7    18.0 s       1.0 s      100.0%    18.0 s       0.0 s
[2016-04-14T23:29Z] INFO  16:29:14,171 ProgressMeter - Total runtime 18.89 secs, 0.31 min, 0.01 hours
[2016-04-14T23:29Z] INFO  16:29:14,175 MicroScheduler - 17685 reads were filtered out during the traversal out of approximately 204069 total reads (8.67%)
[2016-04-14T23:29Z] INFO  16:29:14,176 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:29Z] INFO  16:29:14,177 MicroScheduler -   -> 623 reads (0.31% of total) failing BadMateFilter
[2016-04-14T23:29Z] INFO  16:29:14,177 MicroScheduler -   -> 15726 reads (7.71% of total) failing DuplicateReadFilter
[2016-04-14T23:29Z] INFO  16:29:14,178 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-14T23:29Z] INFO  16:29:14,178 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:29Z] INFO  16:29:14,179 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-14T23:29Z] INFO  16:29:14,180 MicroScheduler -   -> 1336 reads (0.65% of total) failing MappingQualityZeroFilter
[2016-04-14T23:29Z] INFO  16:29:14,180 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:29Z] INFO  16:29:14,181 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-14T23:29Z] INFO  16:29:14,181 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-14T23:29Z] INFO  16:29:14,413 ProgressMeter -     7:136700625    200003.0    30.0 s       2.5 m       68.3%    43.0 s      13.0 s
[2016-04-14T23:29Z] INFO  16:29:14,717 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:29Z] GATK: realign ('7', 157155854, 159138663) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:29Z] INFO  16:29:15,498 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:29Z] GATK: realign ('7', 15599765, 31117713) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:29Z] INFO  16:29:15,542 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:29Z] GATK: realign ('7', 0, 15584548) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:29Z] INFO  16:29:16,126 ProgressMeter -            done    240843.0    18.0 s      75.0 s       98.7%    18.0 s       0.0 s
[2016-04-14T23:29Z] INFO  16:29:16,127 ProgressMeter - Total runtime 18.12 secs, 0.30 min, 0.01 hours
[2016-04-14T23:29Z] INFO  16:29:16,130 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 240843 total reads (0.00%)
[2016-04-14T23:29Z] INFO  16:29:16,131 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:29Z] INFO  16:29:16,131 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:29Z] INFO  16:29:16,134 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:29Z] INFO  16:29:17,517 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:29Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-6_158013810_171115067-prep.bam
[2016-04-14T23:29Z] INFO  16:29:17,592 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:29Z] INFO  16:29:17,605 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:29Z] INFO  16:29:17,606 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:29Z] INFO  16:29:17,607 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:29Z] INFO  16:29:17,611 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/7/R14-18102_kapa-NGv3-PE100-NGv3-sort-7_157155854_159138663-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/7/R14-18102_kapa-NGv3-PE100-NGv3-sort-7_157155854_159138663-prep-prealign-realign.intervals -L 7:157155855-159138663 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/7/tx/tmpJUnF6Z/R14-18102_kapa-NGv3-PE100-NGv3-sort-7_157155854_159138663-prep.bam
[2016-04-14T23:29Z] INFO  16:29:17,637 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:29Z] INFO  16:29:17,638 HelpFormatter - Date/Time: 2016/04/14 16:29:17
[2016-04-14T23:29Z] INFO  16:29:17,638 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:29Z] INFO  16:29:17,639 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:29Z] INFO  16:29:17,835 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:29Z] INFO  16:29:17,969 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:29Z] INFO  16:29:17,981 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:29Z] INFO  16:29:18,045 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-14T23:29Z] INFO  16:29:18,154 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:29Z] INFO  16:29:18,158 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:29Z] INFO  16:29:18,158 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:29Z] INFO  16:29:18,158 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:29Z] INFO  16:29:18,162 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/7/R14-18102_kapa-NGv3-PE100-NGv3-sort-7_15599765_31117713-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/7/R14-18102_kapa-NGv3-PE100-NGv3-sort-7_15599765_31117713-prep-prealign-realign.intervals -L 7:15599766-31117713 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/7/tx/tmpkmymbV/R14-18102_kapa-NGv3-PE100-NGv3-sort-7_15599765_31117713-prep.bam
[2016-04-14T23:29Z] INFO  16:29:18,181 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:29Z] INFO  16:29:18,182 HelpFormatter - Date/Time: 2016/04/14 16:29:18
[2016-04-14T23:29Z] INFO  16:29:18,182 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:29Z] INFO  16:29:18,183 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:29Z] GATK pre-alignment ('8', 15519664, 31030618) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:29Z] INFO  16:29:18,346 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:29Z] INFO  16:29:18,350 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:29Z] INFO  16:29:18,350 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:29Z] INFO  16:29:18,351 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:29Z] INFO  16:29:18,355 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/7/R14-18102_kapa-NGv3-PE100-NGv3-sort-7_0_15584548-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/7/R14-18102_kapa-NGv3-PE100-NGv3-sort-7_0_15584548-prep-prealign-realign.intervals -L 7:1-15584548 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/7/tx/tmpkrDyFh/R14-18102_kapa-NGv3-PE100-NGv3-sort-7_0_15584548-prep.bam
[2016-04-14T23:29Z] INFO  16:29:18,371 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:29Z] INFO  16:29:18,378 HelpFormatter - Date/Time: 2016/04/14 16:29:18
[2016-04-14T23:29Z] INFO  16:29:18,379 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:29Z] INFO  16:29:18,379 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:29Z] INFO  16:29:18,433 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:29Z] INFO  16:29:18,493 IntervalUtils - Processing 1982809 bp from intervals
[2016-04-14T23:29Z] WARN  16:29:18,498 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:29Z] INFO  16:29:18,550 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:29Z] INFO  16:29:18,592 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:29Z] INFO  16:29:18,593 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:29Z] INFO  16:29:18,602 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:29Z] INFO  16:29:18,632 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:29Z] INFO  16:29:18,641 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:29Z] INFO  16:29:18,647 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.04
[2016-04-14T23:29Z] INFO  16:29:18,666 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:29Z] INFO  16:29:18,667 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:29Z] INFO  16:29:18,667 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:29Z] INFO  16:29:18,668 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:29Z] INFO  16:29:18,685 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.04
[2016-04-14T23:29Z] INFO  16:29:18,727 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:29Z] INFO  16:29:18,769 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:29Z] INFO  16:29:19,074 IntervalUtils - Processing 15584548 bp from intervals
[2016-04-14T23:29Z] WARN  16:29:19,079 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:29Z] INFO  16:29:19,133 IntervalUtils - Processing 15517948 bp from intervals
[2016-04-14T23:29Z] WARN  16:29:19,139 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:29Z] INFO  16:29:19,166 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:29Z] INFO  16:29:19,235 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:29Z] INFO  16:29:19,244 ProgressMeter -            done    256244.0    18.0 s      73.0 s      100.0%    18.0 s       0.0 s
[2016-04-14T23:29Z] INFO  16:29:19,245 ProgressMeter - Total runtime 18.93 secs, 0.32 min, 0.01 hours
[2016-04-14T23:29Z] INFO  16:29:19,250 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 256244 total reads (0.00%)
[2016-04-14T23:29Z] INFO  16:29:19,251 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:29Z] INFO  16:29:19,251 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:29Z] INFO  16:29:19,252 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:29Z] INFO  16:29:19,252 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:29Z] INFO  16:29:19,252 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:29Z] INFO  16:29:19,253 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:29Z] INFO  16:29:19,254 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:29Z] INFO  16:29:19,427 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:29Z] INFO  16:29:19,428 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:29Z] INFO  16:29:19,430 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:29Z] INFO  16:29:19,431 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:29Z] INFO  16:29:19,431 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:29Z] INFO  16:29:19,570 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:29Z] INFO  16:29:19,607 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:29Z] INFO  16:29:19,787 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:29Z] INFO  16:29:20,030 ProgressMeter -            done   1.5773393E7    16.0 s       1.0 s      100.0%    16.0 s       0.0 s
[2016-04-14T23:29Z] INFO  16:29:20,031 ProgressMeter - Total runtime 16.13 secs, 0.27 min, 0.00 hours
[2016-04-14T23:29Z] INFO  16:29:20,036 MicroScheduler - 30387 reads were filtered out during the traversal out of approximately 162172 total reads (18.74%)
[2016-04-14T23:29Z] INFO  16:29:20,037 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:29Z] INFO  16:29:20,037 MicroScheduler -   -> 472 reads (0.29% of total) failing BadMateFilter
[2016-04-14T23:29Z] INFO  16:29:20,038 MicroScheduler -   -> 11443 reads (7.06% of total) failing DuplicateReadFilter
[2016-04-14T23:29Z] INFO  16:29:20,039 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-14T23:29Z] INFO  16:29:20,039 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:29Z] INFO  16:29:20,040 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-14T23:29Z] INFO  16:29:20,041 MicroScheduler -   -> 18472 reads (11.39% of total) failing MappingQualityZeroFilter
[2016-04-14T23:29Z] INFO  16:29:20,041 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:29Z] INFO  16:29:20,042 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-14T23:29Z] INFO  16:29:20,043 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-14T23:29Z] INFO  16:29:20,357 ProgressMeter -     7:147092679    100006.0    30.0 s       5.0 m       35.2%    85.0 s      55.0 s
[2016-04-14T23:29Z] INFO  16:29:20,808 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:29Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-6_142399691_157963777-prep.bam
[2016-04-14T23:29Z] INFO  16:29:21,173 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:29Z] INFO  16:29:21,176 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:29Z] INFO  16:29:21,177 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:29Z] INFO  16:29:21,177 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:29Z] INFO  16:29:21,182 HelpFormatter - Program Args: -T PrintReads -L 8:15519665-31030618 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/8/tx/tmpdQPgU_/R14-18102_kapa-NGv3-PE100-NGv3-sort-8_15519664_31030618-prep-prealign.bam
[2016-04-14T23:29Z] INFO  16:29:21,204 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:29Z] INFO  16:29:21,205 HelpFormatter - Date/Time: 2016/04/14 16:29:21
[2016-04-14T23:29Z] INFO  16:29:21,205 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:29Z] INFO  16:29:21,206 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:29Z] INFO  16:29:21,403 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:29Z] INFO  16:29:21,486 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:29Z] GATK: realign ('7', 47319761, 63093154) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:29Z] GATK pre-alignment ('8', 31496910, 48001429) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:29Z] INFO  16:29:21,906 ProgressMeter -            done   1.5552574E7    15.0 s       1.0 s      100.0%    15.0 s       0.0 s
[2016-04-14T23:29Z] INFO  16:29:21,907 ProgressMeter - Total runtime 15.87 secs, 0.26 min, 0.00 hours
[2016-04-14T23:29Z] INFO  16:29:21,910 MicroScheduler - 10183 reads were filtered out during the traversal out of approximately 121678 total reads (8.37%)
[2016-04-14T23:29Z] INFO  16:29:21,911 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:29Z] INFO  16:29:21,911 MicroScheduler -   -> 458 reads (0.38% of total) failing BadMateFilter
[2016-04-14T23:29Z] INFO  16:29:21,923 MicroScheduler -   -> 9483 reads (7.79% of total) failing DuplicateReadFilter
[2016-04-14T23:29Z] INFO  16:29:21,923 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-14T23:29Z] INFO  16:29:21,923 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:29Z] INFO  16:29:21,924 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-14T23:29Z] INFO  16:29:21,924 MicroScheduler -   -> 242 reads (0.20% of total) failing MappingQualityZeroFilter
[2016-04-14T23:29Z] INFO  16:29:21,924 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:29Z] INFO  16:29:21,924 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-14T23:29Z] INFO  16:29:21,924 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-14T23:29Z] INFO  16:29:22,189 ProgressMeter -            done   1.5658369E7    16.0 s       1.0 s      100.0%    16.0 s       0.0 s
[2016-04-14T23:29Z] INFO  16:29:22,190 ProgressMeter - Total runtime 16.77 secs, 0.28 min, 0.00 hours
[2016-04-14T23:29Z] INFO  16:29:22,194 MicroScheduler - 14547 reads were filtered out during the traversal out of approximately 175501 total reads (8.29%)
[2016-04-14T23:29Z] INFO  16:29:22,195 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:29Z] INFO  16:29:22,196 MicroScheduler -   -> 562 reads (0.32% of total) failing BadMateFilter
[2016-04-14T23:29Z] INFO  16:29:22,197 MicroScheduler -   -> 13609 reads (7.75% of total) failing DuplicateReadFilter
[2016-04-14T23:29Z] INFO  16:29:22,197 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-14T23:29Z] INFO  16:29:22,198 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:29Z] INFO  16:29:22,198 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-14T23:29Z] INFO  16:29:22,198 MicroScheduler -   -> 376 reads (0.21% of total) failing MappingQualityZeroFilter
[2016-04-14T23:29Z] INFO  16:29:22,198 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:29Z] INFO  16:29:22,198 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-14T23:29Z] INFO  16:29:22,199 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-14T23:29Z] INFO  16:29:22,437 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@41fd9d8e
[2016-04-14T23:29Z] INFO  16:29:22,542 ProgressMeter -            done    396454.0    48.0 s       2.0 m      100.0%    48.0 s       0.0 s
[2016-04-14T23:29Z] INFO  16:29:22,542 ProgressMeter - Total runtime 48.50 secs, 0.81 min, 0.01 hours
[2016-04-14T23:29Z] INFO  16:29:22,542 MicroScheduler - 232 reads were filtered out during the traversal out of approximately 396686 total reads (0.06%)
[2016-04-14T23:29Z] INFO  16:29:22,543 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:29Z] INFO  16:29:22,543 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:29Z] INFO  16:29:22,543 MicroScheduler -   -> 232 reads (0.06% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:29Z] INFO  16:29:22,575 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-14T23:29Z] INFO  16:29:22,646 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:29Z] INFO  16:29:22,662 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:29Z] INFO  16:29:22,719 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-14T23:29Z] INFO  16:29:22,733 IntervalUtils - Processing 15510954 bp from intervals
[2016-04-14T23:29Z] INFO  16:29:22,830 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:29Z] INFO  16:29:23,080 ProgressMeter -            done     28996.0     4.0 s       2.5 m       89.9%     4.0 s       0.0 s
[2016-04-14T23:29Z] INFO  16:29:23,082 ProgressMeter - Total runtime 4.41 secs, 0.07 min, 0.00 hours
[2016-04-14T23:29Z] INFO  16:29:23,086 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 28996 total reads (0.00%)
[2016-04-14T23:29Z] INFO  16:29:23,089 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:29Z] INFO  16:29:23,090 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:29Z] INFO  16:29:23,091 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:29Z] INFO  16:29:23,163 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:29Z] INFO  16:29:23,164 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:29Z] INFO  16:29:23,165 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:29Z] INFO  16:29:23,165 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:29Z] INFO  16:29:23,197 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:29Z] INFO  16:29:23,303 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:29Z] GATK: realign ('7', 110526648, 126079222) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:29Z] INFO  16:29:23,344 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:29Z] INFO  16:29:23,655 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:29Z] GATK: realign ('7', 79082334, 94740703) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:29Z] INFO  16:29:23,832 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:29Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-7_63095909_78636522-prep-prealign.bam
[2016-04-14T23:29Z] INFO  16:29:24,252 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:29Z] INFO  16:29:24,256 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:29Z] INFO  16:29:24,257 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:29Z] INFO  16:29:24,257 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:29Z] INFO  16:29:24,262 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/7/R14-18102_kapa-NGv3-PE100-NGv3-sort-7_47319761_63093154-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/7/R14-18102_kapa-NGv3-PE100-NGv3-sort-7_47319761_63093154-prep-prealign-realign.intervals -L 7:47319762-63093154 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/7/tx/tmp71YIgf/R14-18102_kapa-NGv3-PE100-NGv3-sort-7_47319761_63093154-prep.bam
[2016-04-14T23:29Z] INFO  16:29:24,274 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:29Z] INFO  16:29:24,285 HelpFormatter - Date/Time: 2016/04/14 16:29:24
[2016-04-14T23:29Z] INFO  16:29:24,286 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:29Z] INFO  16:29:24,286 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:29Z] INFO  16:29:24,413 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:29Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-7_157155854_159138663-prep.bam
[2016-04-14T23:29Z] INFO  16:29:24,529 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:29Z] INFO  16:29:24,532 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:29Z] INFO  16:29:24,533 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:29Z] INFO  16:29:24,533 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:29Z] INFO  16:29:24,538 HelpFormatter - Program Args: -T PrintReads -L 8:31496911-48001429 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/8/tx/tmp2dK99o/R14-18102_kapa-NGv3-PE100-NGv3-sort-8_31496910_48001429-prep-prealign.bam
[2016-04-14T23:29Z] INFO  16:29:24,556 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:29Z] INFO  16:29:24,557 HelpFormatter - Date/Time: 2016/04/14 16:29:24
[2016-04-14T23:29Z] INFO  16:29:24,557 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:29Z] INFO  16:29:24,558 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:29Z] INFO  16:29:24,571 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:29Z] GATK pre-alignment ('8', 48003022, 63659688) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:29Z] INFO  16:29:24,712 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:29Z] INFO  16:29:24,721 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:29Z] INFO  16:29:24,766 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.04
[2016-04-14T23:29Z] INFO  16:29:24,832 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:29Z] INFO  16:29:25,310 IntervalUtils - Processing 15773393 bp from intervals
[2016-04-14T23:29Z] WARN  16:29:25,314 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:29Z] GATK RealignerTargetCreator: R14-18102_kapa-NGv3-PE100-NGv3-sort-7_63095909_78636522-prep-prealign.bam 7:63095910-78636522
[2016-04-14T23:29Z] GATK: RealignerTargetCreator
[2016-04-14T23:29Z] INFO  16:29:25,406 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:29Z] INFO  16:29:25,412 ProgressMeter -            done   1.5509444E7    29.0 s       1.0 s      100.0%    29.0 s       0.0 s
[2016-04-14T23:29Z] INFO  16:29:25,412 ProgressMeter - Total runtime 29.80 secs, 0.50 min, 0.01 hours
[2016-04-14T23:29Z] INFO  16:29:25,416 MicroScheduler - 116326 reads were filtered out during the traversal out of approximately 886018 total reads (13.13%)
[2016-04-14T23:29Z] INFO  16:29:25,417 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:29Z] INFO  16:29:25,417 MicroScheduler -   -> 1590 reads (0.18% of total) failing BadMateFilter
[2016-04-14T23:29Z] INFO  16:29:25,418 MicroScheduler -   -> 67585 reads (7.63% of total) failing DuplicateReadFilter
[2016-04-14T23:29Z] INFO  16:29:25,418 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-14T23:29Z] INFO  16:29:25,418 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:29Z] INFO  16:29:25,418 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-14T23:29Z] INFO  16:29:25,419 MicroScheduler -   -> 47151 reads (5.32% of total) failing MappingQualityZeroFilter
[2016-04-14T23:29Z] INFO  16:29:25,419 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:29Z] INFO  16:29:25,419 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-14T23:29Z] INFO  16:29:25,420 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-14T23:29Z] INFO  16:29:25,566 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:29Z] INFO  16:29:25,566 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:29Z] INFO  16:29:25,567 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:29Z] INFO  16:29:25,567 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:29Z] INFO  16:29:25,723 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:29Z] INFO  16:29:25,981 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:29Z] INFO  16:29:26,190 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-14T23:29Z] INFO  16:29:26,213 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@7172f77a
[2016-04-14T23:29Z] INFO  16:29:26,275 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:29Z] INFO  16:29:26,284 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:29Z] INFO  16:29:26,366 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-14T23:29Z] INFO  16:29:26,377 ProgressMeter -            done    335925.0    41.0 s       2.1 m      100.0%    41.0 s       0.0 s
[2016-04-14T23:29Z] INFO  16:29:26,378 ProgressMeter - Total runtime 41.98 secs, 0.70 min, 0.01 hours
[2016-04-14T23:29Z] INFO  16:29:26,378 MicroScheduler - 180 reads were filtered out during the traversal out of approximately 336105 total reads (0.05%)
[2016-04-14T23:29Z] INFO  16:29:26,379 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:29Z] INFO  16:29:26,379 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:29Z] INFO  16:29:26,379 MicroScheduler -   -> 180 reads (0.05% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:29Z] INFO  16:29:26,386 IntervalUtils - Processing 16504519 bp from intervals
[2016-04-14T23:29Z] INFO  16:29:26,427 ProgressMeter -            done   1.6197591E7    19.0 s       1.0 s      100.0%    19.0 s       0.0 s
[2016-04-14T23:29Z] INFO  16:29:26,429 ProgressMeter - Total runtime 19.55 secs, 0.33 min, 0.01 hours
[2016-04-14T23:29Z] INFO  16:29:26,433 MicroScheduler - 33029 reads were filtered out during the traversal out of approximately 265869 total reads (12.42%)
[2016-04-14T23:29Z] INFO  16:29:26,434 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:29Z] INFO  16:29:26,434 MicroScheduler -   -> 693 reads (0.26% of total) failing BadMateFilter
[2016-04-14T23:29Z] INFO  16:29:26,435 MicroScheduler -   -> 20721 reads (7.79% of total) failing DuplicateReadFilter
[2016-04-14T23:29Z] INFO  16:29:26,436 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-14T23:29Z] INFO  16:29:26,436 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:29Z] INFO  16:29:26,437 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-14T23:29Z] INFO  16:29:26,437 MicroScheduler -   -> 11615 reads (4.37% of total) failing MappingQualityZeroFilter
[2016-04-14T23:29Z] INFO  16:29:26,438 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:29Z] INFO  16:29:26,439 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-14T23:29Z] INFO  16:29:26,440 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-14T23:29Z] INFO  16:29:26,460 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:29Z] INFO  16:29:26,477 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:29Z] INFO  16:29:26,481 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:29Z] INFO  16:29:26,482 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:29Z] INFO  16:29:26,482 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:29Z] INFO  16:29:26,487 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/7/R14-18102_kapa-NGv3-PE100-NGv3-sort-7_110526648_126079222-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/7/R14-18102_kapa-NGv3-PE100-NGv3-sort-7_110526648_126079222-prep-prealign-realign.intervals -L 7:110526649-126079222 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/7/tx/tmprAavKN/R14-18102_kapa-NGv3-PE100-NGv3-sort-7_110526648_126079222-prep.bam
[2016-04-14T23:29Z] INFO  16:29:26,510 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:29Z] INFO  16:29:26,515 HelpFormatter - Date/Time: 2016/04/14 16:29:26
[2016-04-14T23:29Z] INFO  16:29:26,516 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:29Z] INFO  16:29:26,516 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:29Z] INFO  16:29:26,591 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:29Z] INFO  16:29:26,594 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:29Z] INFO  16:29:26,594 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:29Z] INFO  16:29:26,594 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:29Z] INFO  16:29:26,598 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/7/R14-18102_kapa-NGv3-PE100-NGv3-sort-7_79082334_94740703-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/7/R14-18102_kapa-NGv3-PE100-NGv3-sort-7_79082334_94740703-prep-prealign-realign.intervals -L 7:79082335-94740703 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/7/tx/tmph8Uiqe/R14-18102_kapa-NGv3-PE100-NGv3-sort-7_79082334_94740703-prep.bam
[2016-04-14T23:29Z] INFO  16:29:26,615 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:29Z] INFO  16:29:26,616 HelpFormatter - Date/Time: 2016/04/14 16:29:26
[2016-04-14T23:29Z] INFO  16:29:26,616 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:29Z] INFO  16:29:26,617 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:29Z] INFO  16:29:26,729 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:29Z] INFO  16:29:26,743 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:29Z] INFO  16:29:26,745 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:29Z] INFO  16:29:26,745 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:29Z] INFO  16:29:26,751 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:29Z] INFO  16:29:26,773 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:29Z] INFO  16:29:26,840 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:29Z] INFO  16:29:26,854 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:29Z] INFO  16:29:26,868 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:29Z] INFO  16:29:26,948 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-14T23:29Z] INFO  16:29:26,957 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:29Z] INFO  16:29:26,997 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:29Z] GATK: realign ('6', 31083801, 46593245) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:29Z] INFO  16:29:27,065 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:29Z] INFO  16:29:27,085 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:29Z] INFO  16:29:27,163 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-14T23:29Z] INFO  16:29:27,344 IntervalUtils - Processing 15552574 bp from intervals
[2016-04-14T23:29Z] WARN  16:29:27,356 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:29Z] INFO  16:29:27,510 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:29Z] INFO  16:29:27,541 IntervalUtils - Processing 15658369 bp from intervals
[2016-04-14T23:29Z] WARN  16:29:27,546 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:29Z] INFO  16:29:27,629 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:29Z] INFO  16:29:27,664 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:29Z] INFO  16:29:27,665 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:29Z] INFO  16:29:27,665 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:29Z] INFO  16:29:27,666 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:29Z] INFO  16:29:27,749 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:29Z] INFO  16:29:27,750 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:29Z] INFO  16:29:27,751 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:29Z] INFO  16:29:27,752 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:29Z] INFO  16:29:27,756 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:29Z] INFO  16:29:27,760 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:29Z] INFO  16:29:27,760 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:29Z] INFO  16:29:27,761 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:29Z] INFO  16:29:27,765 HelpFormatter - Program Args: -T PrintReads -L 8:48003023-63659688 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/8/tx/tmp22cG5t/R14-18102_kapa-NGv3-PE100-NGv3-sort-8_48003022_63659688-prep-prealign.bam
[2016-04-14T23:29Z] INFO  16:29:27,792 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:29Z] INFO  16:29:27,792 HelpFormatter - Date/Time: 2016/04/14 16:29:27
[2016-04-14T23:29Z] INFO  16:29:27,792 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:29Z] INFO  16:29:27,792 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:29Z] INFO  16:29:27,847 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:29Z] INFO  16:29:27,868 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:29Z] INFO  16:29:27,885 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:29Z] INFO  16:29:27,902 ProgressMeter -     5:140481933    400010.0    33.0 s      82.0 s       82.6%    39.0 s       6.0 s
[2016-04-14T23:29Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-7_126086124_141619620-prep-prealign.bam
[2016-04-14T23:29Z] INFO  16:29:27,996 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:29Z] INFO  16:29:28,022 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:29Z] INFO  16:29:28,032 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:29Z] INFO  16:29:28,168 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:29Z] INFO  16:29:28,172 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:29Z] INFO  16:29:28,172 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:29Z] INFO  16:29:28,173 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:29Z] INFO  16:29:28,178 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/7/R14-18102_kapa-NGv3-PE100-NGv3-sort-7_63095909_78636522-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/7/tx/tmpmA5Y2F/R14-18102_kapa-NGv3-PE100-NGv3-sort-7_63095909_78636522-prep-prealign-realign.intervals -l INFO -L 7:63095910-78636522 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-14T23:29Z] INFO  16:29:28,187 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:29Z] INFO  16:29:28,188 HelpFormatter - Date/Time: 2016/04/14 16:29:28
[2016-04-14T23:29Z] INFO  16:29:28,189 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:29Z] INFO  16:29:28,189 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:29Z] INFO  16:29:28,260 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:29Z] GATK: realign ('7', 31120227, 47317818) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:29Z] INFO  16:29:28,337 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:29Z] INFO  16:29:28,600 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-14T23:29Z] INFO  16:29:28,620 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:29Z] INFO  16:29:28,670 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-14T23:29Z] GATK RealignerTargetCreator: R14-18102_kapa-NGv3-PE100-NGv3-sort-7_126086124_141619620-prep-prealign.bam 7:126086125-141619620
[2016-04-14T23:29Z] GATK: RealignerTargetCreator
[2016-04-14T23:29Z] INFO  16:29:29,036 IntervalUtils - Processing 15540613 bp from intervals
[2016-04-14T23:29Z] WARN  16:29:29,041 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:29Z] INFO  16:29:29,177 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:29Z] INFO  16:29:29,219 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-14T23:29Z] INFO  16:29:29,275 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:29Z] INFO  16:29:29,284 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:29Z] INFO  16:29:29,341 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-14T23:29Z] INFO  16:29:29,366 IntervalUtils - Processing 15656666 bp from intervals
[2016-04-14T23:29Z] INFO  16:29:29,479 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:29Z] INFO  16:29:29,491 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:29Z] INFO  16:29:29,492 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:29Z] INFO  16:29:29,492 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-14T23:29Z] INFO  16:29:29,501 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:29Z] INFO  16:29:29,843 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:29Z] INFO  16:29:29,845 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:29Z] INFO  16:29:29,845 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:29Z] INFO  16:29:29,846 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:29Z] INFO  16:29:29,852 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:29Z] INFO  16:29:29,855 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:29Z] INFO  16:29:29,856 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:29Z] INFO  16:29:29,856 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:29Z] INFO  16:29:29,860 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:29Z] INFO  16:29:29,861 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/6/R14-18102_kapa-NGv3-PE100-NGv3-sort-6_31083801_46593245-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/6/R14-18102_kapa-NGv3-PE100-NGv3-sort-6_31083801_46593245-prep-prealign-realign.intervals -L 6:31083802-46593245 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/6/tx/tmpWTfc3x/R14-18102_kapa-NGv3-PE100-NGv3-sort-6_31083801_46593245-prep.bam
[2016-04-14T23:29Z] INFO  16:29:29,874 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:29Z] INFO  16:29:29,875 HelpFormatter - Date/Time: 2016/04/14 16:29:29
[2016-04-14T23:29Z] INFO  16:29:29,875 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:29Z] INFO  16:29:29,886 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:29Z] INFO  16:29:29,995 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:29Z] INFO  16:29:30,132 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:29Z] INFO  16:29:30,283 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:29Z] INFO  16:29:30,303 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:29Z] INFO  16:29:30,357 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-14T23:29Z] INFO  16:29:30,814 IntervalUtils - Processing 15509444 bp from intervals
[2016-04-14T23:29Z] WARN  16:29:30,819 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:29Z] INFO  16:29:30,989 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:29Z] INFO  16:29:31,193 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:29Z] INFO  16:29:31,205 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:29Z] INFO  16:29:31,206 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:29Z] INFO  16:29:31,207 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:29Z] INFO  16:29:31,390 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:29Z] INFO  16:29:31,387 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:29Z] INFO  16:29:31,391 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:29Z] INFO  16:29:31,391 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:29Z] INFO  16:29:31,392 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:29Z] INFO  16:29:31,396 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/7/R14-18102_kapa-NGv3-PE100-NGv3-sort-7_31120227_47317818-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/7/R14-18102_kapa-NGv3-PE100-NGv3-sort-7_31120227_47317818-prep-prealign-realign.intervals -L 7:31120228-47317818 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/7/tx/tmprnFjQh/R14-18102_kapa-NGv3-PE100-NGv3-sort-7_31120227_47317818-prep.bam
[2016-04-14T23:29Z] INFO  16:29:31,423 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:29Z] INFO  16:29:31,424 HelpFormatter - Date/Time: 2016/04/14 16:29:31
[2016-04-14T23:29Z] INFO  16:29:31,424 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:29Z] INFO  16:29:31,425 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:29Z] INFO  16:29:31,579 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:29Z] INFO  16:29:31,637 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:29Z] INFO  16:29:31,793 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:29Z] INFO  16:29:31,813 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:29Z] INFO  16:29:31,823 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:29Z] INFO  16:29:31,826 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:29Z] INFO  16:29:31,827 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:29Z] INFO  16:29:31,828 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:29Z] INFO  16:29:31,832 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/7/R14-18102_kapa-NGv3-PE100-NGv3-sort-7_126086124_141619620-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/7/tx/tmphEAPJ7/R14-18102_kapa-NGv3-PE100-NGv3-sort-7_126086124_141619620-prep-prealign-realign.intervals -l INFO -L 7:126086125-141619620 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-14T23:29Z] INFO  16:29:31,866 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:29Z] INFO  16:29:31,866 HelpFormatter - Date/Time: 2016/04/14 16:29:31
[2016-04-14T23:29Z] INFO  16:29:31,866 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:29Z] INFO  16:29:31,867 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:29Z] INFO  16:29:31,893 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-14T23:29Z] INFO  16:29:32,000 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:29Z] INFO  16:29:32,216 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-14T23:29Z] INFO  16:29:32,240 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:29Z] INFO  16:29:32,244 IntervalUtils - Processing 16197591 bp from intervals
[2016-04-14T23:29Z] WARN  16:29:32,249 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:29Z] INFO  16:29:32,310 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-14T23:29Z] INFO  16:29:32,376 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:29Z] INFO  16:29:32,565 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:29Z] INFO  16:29:32,566 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:29Z] INFO  16:29:32,567 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:29Z] INFO  16:29:32,579 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:29Z] INFO  16:29:32,706 IntervalUtils - Processing 15533496 bp from intervals
[2016-04-14T23:29Z] WARN  16:29:32,711 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:29Z] INFO  16:29:32,775 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:29Z] INFO  16:29:32,840 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:29Z] INFO  16:29:33,039 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:29Z] INFO  16:29:33,177 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:29Z] INFO  16:29:33,178 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:29Z] INFO  16:29:33,179 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:29Z] INFO  16:29:33,180 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-14T23:29Z] INFO  16:29:35,542 ProgressMeter -      8:11058199    100001.0    30.0 s       5.0 m       71.3%    42.0 s      12.0 s
[2016-04-14T23:29Z] INFO  16:29:36,672 ProgressMeter -            done    202937.0    17.0 s      84.0 s      100.0%    17.0 s       0.0 s
[2016-04-14T23:29Z] INFO  16:29:36,672 ProgressMeter - Total runtime 17.24 secs, 0.29 min, 0.00 hours
[2016-04-14T23:29Z] INFO  16:29:36,677 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 202937 total reads (0.00%)
[2016-04-14T23:29Z] INFO  16:29:36,677 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:29Z] INFO  16:29:36,678 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:29Z] INFO  16:29:36,678 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:29Z] INFO  16:29:38,063 ProgressMeter -            done    686317.0    43.0 s      62.0 s      100.0%    43.0 s       0.0 s
[2016-04-14T23:29Z] INFO  16:29:38,064 ProgressMeter - Total runtime 43.21 secs, 0.72 min, 0.01 hours
[2016-04-14T23:29Z] INFO  16:29:38,067 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 686317 total reads (0.00%)
[2016-04-14T23:29Z] INFO  16:29:38,068 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:29Z] INFO  16:29:38,068 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:29Z] INFO  16:29:38,068 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:29Z] INFO  16:29:38,182 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:29Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-7_15599765_31117713-prep.bam
[2016-04-14T23:29Z] GATK pre-alignment ('8', 63775819, 79510770) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:29Z] INFO  16:29:39,438 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:29Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-5_127597427_143191869-prep.bam
[2016-04-14T23:29Z] INFO  16:29:39,480 ProgressMeter -            done    161635.0    13.0 s      86.0 s      100.0%    13.0 s       0.0 s
[2016-04-14T23:29Z] INFO  16:29:39,480 ProgressMeter - Total runtime 13.91 secs, 0.23 min, 0.00 hours
[2016-04-14T23:29Z] INFO  16:29:39,483 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 161635 total reads (0.00%)
[2016-04-14T23:29Z] INFO  16:29:39,484 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:29Z] INFO  16:29:39,484 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:29Z] INFO  16:29:39,484 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:29Z] INFO  16:29:40,195 ProgressMeter -     7:100807122    400004.0    60.0 s       2.5 m       38.9%     2.6 m      94.0 s
[2016-04-14T23:29Z] INFO  16:29:40,349 ProgressMeter -            done    120903.0    12.0 s     104.0 s      100.0%    12.0 s       0.0 s
[2016-04-14T23:29Z] INFO  16:29:40,351 ProgressMeter - Total runtime 12.69 secs, 0.21 min, 0.00 hours
[2016-04-14T23:29Z] INFO  16:29:40,355 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 120903 total reads (0.00%)
[2016-04-14T23:29Z] INFO  16:29:40,356 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:29Z] INFO  16:29:40,357 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:29Z] INFO  16:29:40,358 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:29Z] INFO  16:29:40,988 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:29Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-7_47319761_63093154-prep.bam
[2016-04-14T23:29Z] GATK pre-alignment ('8', 79513976, 95140568) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:29Z] INFO  16:29:41,586 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:29Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-7_110526648_126079222-prep.bam
[2016-04-14T23:29Z] GATK pre-alignment ('8', 95142853, 110655419) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:29Z] INFO  16:29:41,723 ProgressMeter -            done    174316.0    13.0 s      80.0 s      100.0%    13.0 s       0.0 s
[2016-04-14T23:29Z] INFO  16:29:41,724 ProgressMeter - Total runtime 13.97 secs, 0.23 min, 0.00 hours
[2016-04-14T23:29Z] INFO  16:29:41,739 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 174316 total reads (0.00%)
[2016-04-14T23:29Z] INFO  16:29:41,741 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:29Z] INFO  16:29:41,742 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:29Z] INFO  16:29:41,743 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:29Z] INFO  16:29:41,901 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:29Z] INFO  16:29:41,904 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:29Z] INFO  16:29:41,905 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:29Z] INFO  16:29:41,905 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:29Z] INFO  16:29:41,910 HelpFormatter - Program Args: -T PrintReads -L 8:63775820-79510770 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/8/tx/tmpFrAqB3/R14-18102_kapa-NGv3-PE100-NGv3-sort-8_63775819_79510770-prep-prealign.bam
[2016-04-14T23:29Z] INFO  16:29:41,924 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:29Z] INFO  16:29:41,925 HelpFormatter - Date/Time: 2016/04/14 16:29:41
[2016-04-14T23:29Z] INFO  16:29:41,926 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:29Z] INFO  16:29:41,926 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:29Z] GATK pre-alignment ('8', 110656864, 126194498) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:29Z] INFO  16:29:42,107 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:29Z] INFO  16:29:42,471 ProgressMeter -            done    322336.0    23.0 s      72.0 s      100.0%    23.0 s       0.0 s
[2016-04-14T23:29Z] INFO  16:29:42,471 ProgressMeter - Total runtime 23.22 secs, 0.39 min, 0.01 hours
[2016-04-14T23:29Z] INFO  16:29:42,475 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 322336 total reads (0.00%)
[2016-04-14T23:29Z] INFO  16:29:42,477 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:29Z] INFO  16:29:42,478 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:29Z] INFO  16:29:42,479 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:29Z] INFO  16:29:43,163 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-14T23:29Z] INFO  16:29:43,266 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:29Z] INFO  16:29:43,277 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:29Z] INFO  16:29:43,352 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-14T23:29Z] INFO  16:29:43,372 IntervalUtils - Processing 15734951 bp from intervals
[2016-04-14T23:29Z] INFO  16:29:43,424 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:29Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-7_79082334_94740703-prep.bam
[2016-04-14T23:29Z] INFO  16:29:43,469 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:29Z] INFO  16:29:43,797 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:29Z] INFO  16:29:43,809 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:29Z] INFO  16:29:43,810 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:29Z] INFO  16:29:43,811 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:29Z] INFO  16:29:43,834 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:29Z] INFO  16:29:43,977 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:29Z] GATK pre-alignment ('8', 126369460, 141889736) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:29Z] INFO  16:29:44,132 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:29Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-7_0_15584548-prep.bam
[2016-04-14T23:29Z] INFO  16:29:44,553 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:29Z] INFO  16:29:44,556 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:29Z] INFO  16:29:44,557 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:29Z] INFO  16:29:44,557 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:29Z] INFO  16:29:44,562 HelpFormatter - Program Args: -T PrintReads -L 8:95142854-110655419 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/8/tx/tmpxd5K6m/R14-18102_kapa-NGv3-PE100-NGv3-sort-8_95142853_110655419-prep-prealign.bam
[2016-04-14T23:29Z] INFO  16:29:44,573 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:29Z] INFO  16:29:44,577 HelpFormatter - Date/Time: 2016/04/14 16:29:44
[2016-04-14T23:29Z] INFO  16:29:44,578 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:29Z] INFO  16:29:44,579 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:29Z] INFO  16:29:44,607 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:29Z] INFO  16:29:44,610 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:29Z] INFO  16:29:44,610 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:29Z] INFO  16:29:44,610 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:29Z] INFO  16:29:44,614 HelpFormatter - Program Args: -T PrintReads -L 8:79513977-95140568 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/8/tx/tmpimETp7/R14-18102_kapa-NGv3-PE100-NGv3-sort-8_79513976_95140568-prep-prealign.bam
[2016-04-14T23:29Z] INFO  16:29:44,654 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:29Z] INFO  16:29:44,661 HelpFormatter - Date/Time: 2016/04/14 16:29:44
[2016-04-14T23:29Z] INFO  16:29:44,662 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:29Z] INFO  16:29:44,662 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:29Z] INFO  16:29:44,767 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:29Z] INFO  16:29:44,894 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:29Z] INFO  16:29:45,277 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:29Z] INFO  16:29:45,280 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:29Z] INFO  16:29:45,281 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:29Z] INFO  16:29:45,281 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:29Z] INFO  16:29:45,286 HelpFormatter - Program Args: -T PrintReads -L 8:110656865-126194498 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/8/tx/tmpy5nQ8c/R14-18102_kapa-NGv3-PE100-NGv3-sort-8_110656864_126194498-prep-prealign.bam
[2016-04-14T23:29Z] INFO  16:29:45,297 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:29Z] INFO  16:29:45,298 HelpFormatter - Date/Time: 2016/04/14 16:29:45
[2016-04-14T23:29Z] INFO  16:29:45,298 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:29Z] INFO  16:29:45,299 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:29Z] GATK pre-alignment ('8', 141900641, 146364022) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:29Z] INFO  16:29:45,477 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:29Z] INFO  16:29:46,202 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-14T23:29Z] INFO  16:29:46,219 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-14T23:29Z] INFO  16:29:46,298 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:29Z] INFO  16:29:46,307 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:29Z] INFO  16:29:46,312 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:29Z] INFO  16:29:46,321 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:29Z] INFO  16:29:46,366 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.04
[2016-04-14T23:29Z] INFO  16:29:46,390 IntervalUtils - Processing 15626592 bp from intervals
[2016-04-14T23:29Z] INFO  16:29:46,395 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.09
[2016-04-14T23:29Z] INFO  16:29:46,410 IntervalUtils - Processing 15512566 bp from intervals
[2016-04-14T23:29Z] INFO  16:29:46,411 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@7172f77a
[2016-04-14T23:29Z] INFO  16:29:46,466 ProgressMeter -            done    309294.0    40.0 s       2.2 m      100.0%    40.0 s       0.0 s
[2016-04-14T23:29Z] INFO  16:29:46,467 ProgressMeter - Total runtime 40.95 secs, 0.68 min, 0.01 hours
[2016-04-14T23:29Z] INFO  16:29:46,468 MicroScheduler - 293 reads were filtered out during the traversal out of approximately 309587 total reads (0.09%)
[2016-04-14T23:29Z] INFO  16:29:46,469 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:29Z] INFO  16:29:46,469 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:29Z] INFO  16:29:46,470 MicroScheduler -   -> 293 reads (0.09% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:29Z] INFO  16:29:46,513 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:29Z] INFO  16:29:46,509 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:29Z] INFO  16:29:46,801 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-14T23:29Z] INFO  16:29:46,871 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:29Z] INFO  16:29:46,871 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:29Z] INFO  16:29:46,872 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:29Z] INFO  16:29:46,873 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:29Z] INFO  16:29:46,874 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:29Z] INFO  16:29:46,880 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:29Z] INFO  16:29:46,888 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:29Z] INFO  16:29:46,893 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:29Z] INFO  16:29:46,893 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:29Z] INFO  16:29:46,893 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:29Z] INFO  16:29:46,894 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:29Z] INFO  16:29:46,932 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:29Z] INFO  16:29:46,932 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-14T23:29Z] INFO  16:29:46,966 IntervalUtils - Processing 15537634 bp from intervals
[2016-04-14T23:29Z] INFO  16:29:47,037 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:29Z] INFO  16:29:47,040 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:29Z] INFO  16:29:47,041 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:29Z] INFO  16:29:47,041 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:29Z] INFO  16:29:47,044 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:29Z] INFO  16:29:47,046 HelpFormatter - Program Args: -T PrintReads -L 8:126369461-141889736 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/8/tx/tmpYdEmrU/R14-18102_kapa-NGv3-PE100-NGv3-sort-8_126369460_141889736-prep-prealign.bam
[2016-04-14T23:29Z] INFO  16:29:47,074 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:29Z] INFO  16:29:47,077 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:29Z] INFO  16:29:47,078 HelpFormatter - Date/Time: 2016/04/14 16:29:47
[2016-04-14T23:29Z] INFO  16:29:47,078 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:29Z] INFO  16:29:47,079 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:29Z] INFO  16:29:47,103 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:29Z] INFO  16:29:47,253 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:29Z] INFO  16:29:47,311 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:29Z] INFO  16:29:47,312 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:29Z] INFO  16:29:47,313 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:29Z] INFO  16:29:47,313 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:29Z] INFO  16:29:47,341 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:29Z] INFO  16:29:47,596 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:29Z] INFO  16:29:47,858 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:29Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-8_0_15517156-prep-prealign.bam
[2016-04-14T23:29Z] INFO  16:29:48,275 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:29Z] INFO  16:29:48,278 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:29Z] INFO  16:29:48,279 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:29Z] INFO  16:29:48,280 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:29Z] INFO  16:29:48,284 HelpFormatter - Program Args: -T PrintReads -L 8:141900642-146364022 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/8/tx/tmp_wTM9U/R14-18102_kapa-NGv3-PE100-NGv3-sort-8_141900641_146364022-prep-prealign.bam
[2016-04-14T23:29Z] INFO  16:29:48,301 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-14T23:29Z] INFO  16:29:48,302 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:29Z] INFO  16:29:48,303 HelpFormatter - Date/Time: 2016/04/14 16:29:48
[2016-04-14T23:29Z] INFO  16:29:48,304 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:29Z] INFO  16:29:48,310 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:29Z] INFO  16:29:48,357 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:29Z] INFO  16:29:48,376 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:29Z] INFO  16:29:48,436 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-14T23:29Z] INFO  16:29:48,451 IntervalUtils - Processing 15520276 bp from intervals
[2016-04-14T23:29Z] INFO  16:29:48,485 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:29Z] INFO  16:29:48,574 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:29Z] GATK RealignerTargetCreator: R14-18102_kapa-NGv3-PE100-NGv3-sort-8_0_15517156-prep-prealign.bam 8:1-15517156
[2016-04-14T23:29Z] GATK: RealignerTargetCreator
[2016-04-14T23:29Z] INFO  16:29:48,907 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@7172f77a
[2016-04-14T23:29Z] INFO  16:29:49,026 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:29Z] INFO  16:29:49,037 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:29Z] INFO  16:29:49,037 ProgressMeter -            done    138456.0    19.0 s       2.3 m      100.0%    19.0 s       0.0 s
[2016-04-14T23:29Z] INFO  16:29:49,037 ProgressMeter - Total runtime 19.19 secs, 0.32 min, 0.01 hours
[2016-04-14T23:29Z] INFO  16:29:49,038 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:29Z] INFO  16:29:49,037 MicroScheduler - 105 reads were filtered out during the traversal out of approximately 138561 total reads (0.08%)
[2016-04-14T23:29Z] INFO  16:29:49,038 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:29Z] INFO  16:29:49,038 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:29Z] INFO  16:29:49,038 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:29Z] INFO  16:29:49,038 MicroScheduler -   -> 105 reads (0.08% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:29Z] INFO  16:29:49,052 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:29Z] INFO  16:29:49,274 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:29Z] INFO  16:29:49,594 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-14T23:29Z] INFO  16:29:49,669 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:29Z] INFO  16:29:49,685 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:29Z] INFO  16:29:49,728 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.04
[2016-04-14T23:29Z] INFO  16:29:49,753 IntervalUtils - Processing 4463381 bp from intervals
[2016-04-14T23:29Z] INFO  16:29:49,859 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:29Z] INFO  16:29:50,183 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:29Z] INFO  16:29:50,184 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:29Z] INFO  16:29:50,184 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:29Z] INFO  16:29:50,184 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:29Z] INFO  16:29:50,224 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:29Z] INFO  16:29:50,290 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:29Z] INFO  16:29:50,383 ProgressMeter -     7:151791664    300013.0    60.0 s       3.3 m       65.5%    91.0 s      31.0 s
[2016-04-14T23:29Z] INFO  16:29:50,514 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:29Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-8_48003022_63659688-prep-prealign.bam
[2016-04-14T23:29Z] INFO  16:29:51,133 ProgressMeter -            done   1.5540613E7    21.0 s       1.0 s      100.0%    21.0 s       0.0 s
[2016-04-14T23:29Z] INFO  16:29:51,134 ProgressMeter - Total runtime 21.64 secs, 0.36 min, 0.01 hours
[2016-04-14T23:29Z] GATK RealignerTargetCreator: R14-18102_kapa-NGv3-PE100-NGv3-sort-8_48003022_63659688-prep-prealign.bam 8:48003023-63659688
[2016-04-14T23:29Z] GATK: RealignerTargetCreator
[2016-04-14T23:29Z] INFO  16:29:51,146 MicroScheduler - 129330 reads were filtered out during the traversal out of approximately 398924 total reads (32.42%)
[2016-04-14T23:29Z] INFO  16:29:51,158 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:29Z] INFO  16:29:51,159 MicroScheduler -   -> 702 reads (0.18% of total) failing BadMateFilter
[2016-04-14T23:29Z] INFO  16:29:51,159 MicroScheduler -   -> 23552 reads (5.90% of total) failing DuplicateReadFilter
[2016-04-14T23:29Z] INFO  16:29:51,160 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-14T23:29Z] INFO  16:29:51,161 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:29Z] INFO  16:29:51,161 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-14T23:29Z] INFO  16:29:51,162 MicroScheduler -   -> 105076 reads (26.34% of total) failing MappingQualityZeroFilter
[2016-04-14T23:29Z] INFO  16:29:51,162 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:29Z] INFO  16:29:51,163 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-14T23:29Z] INFO  16:29:51,164 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-14T23:29Z] INFO  16:29:51,856 ProgressMeter -            done    264097.0    19.0 s      73.0 s      100.0%    19.0 s       0.0 s
[2016-04-14T23:29Z] INFO  16:29:51,857 ProgressMeter - Total runtime 19.29 secs, 0.32 min, 0.01 hours
[2016-04-14T23:29Z] INFO  16:29:51,860 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 264097 total reads (0.00%)
[2016-04-14T23:29Z] INFO  16:29:51,861 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:29Z] INFO  16:29:51,861 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:29Z] INFO  16:29:51,861 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:29Z] INFO  16:29:52,014 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:29Z] INFO  16:29:52,028 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:29Z] INFO  16:29:52,028 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:29Z] INFO  16:29:52,029 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:29Z] INFO  16:29:52,037 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/8/R14-18102_kapa-NGv3-PE100-NGv3-sort-8_0_15517156-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/8/tx/tmplCQpsX/R14-18102_kapa-NGv3-PE100-NGv3-sort-8_0_15517156-prep-prealign-realign.intervals -l INFO -L 8:1-15517156 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-14T23:29Z] INFO  16:29:52,060 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:29Z] INFO  16:29:52,060 HelpFormatter - Date/Time: 2016/04/14 16:29:52
[2016-04-14T23:29Z] INFO  16:29:52,068 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:29Z] INFO  16:29:52,068 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:29Z] INFO  16:29:52,183 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:29Z] INFO  16:29:52,402 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-14T23:29Z] INFO  16:29:52,412 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:29Z] INFO  16:29:52,455 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.04
[2016-04-14T23:29Z] INFO  16:29:52,459 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@7172f77a
[2016-04-14T23:29Z] INFO  16:29:52,500 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:29Z] GATK: realign ('7', 63095909, 78636522) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:29Z] INFO  16:29:52,572 ProgressMeter -            done    182259.0    25.0 s       2.4 m      100.0%    25.0 s       0.0 s
[2016-04-14T23:29Z] INFO  16:29:52,573 ProgressMeter - Total runtime 25.83 secs, 0.43 min, 0.01 hours
[2016-04-14T23:29Z] INFO  16:29:52,573 MicroScheduler - 135 reads were filtered out during the traversal out of approximately 182394 total reads (0.07%)
[2016-04-14T23:29Z] INFO  16:29:52,574 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:29Z] INFO  16:29:52,574 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:29Z] INFO  16:29:52,574 MicroScheduler -   -> 135 reads (0.07% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:29Z] INFO  16:29:52,744 IntervalUtils - Processing 15517156 bp from intervals
[2016-04-14T23:29Z] WARN  16:29:52,749 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:29Z] INFO  16:29:52,840 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:29Z] INFO  16:29:53,043 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:29Z] INFO  16:29:53,044 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:29Z] INFO  16:29:53,045 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:29Z] INFO  16:29:53,045 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-14T23:29Z] INFO  16:29:53,197 ProgressMeter -      8:25101314    200002.0    30.0 s       2.5 m       61.8%    48.0 s      18.0 s
[2016-04-14T23:29Z] INFO  16:29:53,291 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:29Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-7_31120227_47317818-prep.bam
[2016-04-14T23:29Z] INFO  16:29:53,535 ProgressMeter -            done   1.5533496E7    20.0 s       1.0 s      100.0%    20.0 s       0.0 s
[2016-04-14T23:29Z] INFO  16:29:53,536 ProgressMeter - Total runtime 20.36 secs, 0.34 min, 0.01 hours
[2016-04-14T23:29Z] INFO  16:29:53,541 MicroScheduler - 29330 reads were filtered out during the traversal out of approximately 337601 total reads (8.69%)
[2016-04-14T23:29Z] INFO  16:29:53,542 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:29Z] INFO  16:29:53,543 MicroScheduler -   -> 767 reads (0.23% of total) failing BadMateFilter
[2016-04-14T23:29Z] INFO  16:29:53,543 MicroScheduler -   -> 26696 reads (7.91% of total) failing DuplicateReadFilter
[2016-04-14T23:29Z] INFO  16:29:53,544 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-14T23:29Z] INFO  16:29:53,545 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:29Z] INFO  16:29:53,545 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-14T23:29Z] INFO  16:29:53,546 MicroScheduler -   -> 1867 reads (0.55% of total) failing MappingQualityZeroFilter
[2016-04-14T23:29Z] INFO  16:29:53,546 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:29Z] INFO  16:29:53,547 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-14T23:29Z] INFO  16:29:53,548 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-14T23:29Z] INFO  16:29:53,977 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:29Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-8_31496910_48001429-prep-prealign.bam
[2016-04-14T23:29Z] INFO  16:29:54,008 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:29Z] INFO  16:29:54,012 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:29Z] INFO  16:29:54,012 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:29Z] INFO  16:29:54,013 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:29Z] INFO  16:29:54,017 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/8/R14-18102_kapa-NGv3-PE100-NGv3-sort-8_48003022_63659688-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/8/tx/tmpdFrUo7/R14-18102_kapa-NGv3-PE100-NGv3-sort-8_48003022_63659688-prep-prealign-realign.intervals -l INFO -L 8:48003023-63659688 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-14T23:29Z] INFO  16:29:54,044 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:29Z] INFO  16:29:54,044 HelpFormatter - Date/Time: 2016/04/14 16:29:54
[2016-04-14T23:29Z] INFO  16:29:54,044 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:29Z] INFO  16:29:54,045 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:29Z] INFO  16:29:54,194 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:29Z] GATK pre-alignment ('9', 0, 15510186) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:29Z] INFO  16:29:54,430 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-14T23:29Z] INFO  16:29:54,439 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:29Z] INFO  16:29:54,509 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-14T23:29Z] GATK RealignerTargetCreator: R14-18102_kapa-NGv3-PE100-NGv3-sort-8_31496910_48001429-prep-prealign.bam 8:31496911-48001429
[2016-04-14T23:29Z] GATK: RealignerTargetCreator
[2016-04-14T23:29Z] INFO  16:29:54,772 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:29Z] GATK: realign ('7', 126086124, 141619620) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:29Z] INFO  16:29:54,830 IntervalUtils - Processing 15656666 bp from intervals
[2016-04-14T23:29Z] WARN  16:29:54,835 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:29Z] INFO  16:29:54,908 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:29Z] INFO  16:29:55,157 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:29Z] INFO  16:29:55,159 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:29Z] INFO  16:29:55,160 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:29Z] INFO  16:29:55,178 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-14T23:29Z] INFO  16:29:55,410 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:29Z] INFO  16:29:55,415 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:29Z] INFO  16:29:55,415 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:29Z] INFO  16:29:55,416 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:29Z] INFO  16:29:55,422 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/7/R14-18102_kapa-NGv3-PE100-NGv3-sort-7_63095909_78636522-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/7/R14-18102_kapa-NGv3-PE100-NGv3-sort-7_63095909_78636522-prep-prealign-realign.intervals -L 7:63095910-78636522 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/7/tx/tmpNkTxeN/R14-18102_kapa-NGv3-PE100-NGv3-sort-7_63095909_78636522-prep.bam
[2016-04-14T23:29Z] INFO  16:29:55,432 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:29Z] INFO  16:29:55,432 HelpFormatter - Date/Time: 2016/04/14 16:29:55
[2016-04-14T23:29Z] INFO  16:29:55,432 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:29Z] INFO  16:29:55,433 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:29Z] INFO  16:29:55,677 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:29Z] INFO  16:29:55,796 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:29Z] INFO  16:29:55,814 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:29Z] INFO  16:29:55,865 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-14T23:29Z] INFO  16:29:56,362 IntervalUtils - Processing 15540613 bp from intervals
[2016-04-14T23:29Z] WARN  16:29:56,368 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:29Z] INFO  16:29:56,505 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:29Z] INFO  16:29:56,666 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:29Z] INFO  16:29:56,667 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:29Z] INFO  16:29:56,667 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:29Z] INFO  16:29:56,668 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:29Z] INFO  16:29:56,882 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:29Z] INFO  16:29:57,069 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:29Z] INFO  16:29:57,527 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:29Z] INFO  16:29:57,530 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:29Z] INFO  16:29:57,530 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:29Z] INFO  16:29:57,530 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:29Z] INFO  16:29:57,535 HelpFormatter - Program Args: -T PrintReads -L 9:1-15510186 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/9/tx/tmpwLvI9Y/R14-18102_kapa-NGv3-PE100-NGv3-sort-9_0_15510186-prep-prealign.bam
[2016-04-14T23:29Z] INFO  16:29:57,552 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:29Z] INFO  16:29:57,553 HelpFormatter - Date/Time: 2016/04/14 16:29:57
[2016-04-14T23:29Z] INFO  16:29:57,554 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:29Z] INFO  16:29:57,554 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:29Z] INFO  16:29:57,718 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:29Z] INFO  16:29:57,721 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:29Z] INFO  16:29:57,722 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:29Z] INFO  16:29:57,722 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:29Z] INFO  16:29:57,727 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/8/R14-18102_kapa-NGv3-PE100-NGv3-sort-8_31496910_48001429-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/8/tx/tmpQSuOqB/R14-18102_kapa-NGv3-PE100-NGv3-sort-8_31496910_48001429-prep-prealign-realign.intervals -l INFO -L 8:31496911-48001429 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-14T23:29Z] INFO  16:29:57,744 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:29Z] INFO  16:29:57,745 HelpFormatter - Date/Time: 2016/04/14 16:29:57
[2016-04-14T23:29Z] INFO  16:29:57,745 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:29Z] INFO  16:29:57,745 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:29Z] INFO  16:29:57,779 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:29Z] INFO  16:29:57,786 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:29Z] INFO  16:29:57,789 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:29Z] INFO  16:29:57,789 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:29Z] INFO  16:29:57,790 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:29Z] INFO  16:29:57,794 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/7/R14-18102_kapa-NGv3-PE100-NGv3-sort-7_126086124_141619620-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/7/R14-18102_kapa-NGv3-PE100-NGv3-sort-7_126086124_141619620-prep-prealign-realign.intervals -L 7:126086125-141619620 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/7/tx/tmpMaBA4o/R14-18102_kapa-NGv3-PE100-NGv3-sort-7_126086124_141619620-prep.bam
[2016-04-14T23:29Z] INFO  16:29:57,804 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:29Z] INFO  16:29:57,805 HelpFormatter - Date/Time: 2016/04/14 16:29:57
[2016-04-14T23:29Z] INFO  16:29:57,805 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:29Z] INFO  16:29:57,806 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:29Z] INFO  16:29:57,867 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:29Z] INFO  16:29:58,022 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@41fd9d8e
[2016-04-14T23:29Z] INFO  16:29:58,060 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:29Z] INFO  16:29:58,152 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-14T23:29Z] INFO  16:29:58,185 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:29Z] INFO  16:29:58,216 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:29Z] INFO  16:29:58,220 ProgressMeter -            done    456560.0    68.0 s       2.5 m      100.0%    68.0 s       0.0 s
[2016-04-14T23:29Z] INFO  16:29:58,221 ProgressMeter - Total runtime 68.04 secs, 1.13 min, 0.02 hours
[2016-04-14T23:29Z] INFO  16:29:58,221 MicroScheduler - 196 reads were filtered out during the traversal out of approximately 456756 total reads (0.04%)
[2016-04-14T23:29Z] INFO  16:29:58,221 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:29Z] INFO  16:29:58,222 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:29Z] INFO  16:29:58,222 MicroScheduler -   -> 196 reads (0.04% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:29Z] INFO  16:29:58,253 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:29Z] INFO  16:29:58,273 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.09
[2016-04-14T23:29Z] INFO  16:29:58,319 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-14T23:29Z] INFO  16:29:58,558 IntervalUtils - Processing 16504519 bp from intervals
[2016-04-14T23:29Z] WARN  16:29:58,563 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:29Z] INFO  16:29:58,664 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:29Z] INFO  16:29:58,700 IntervalUtils - Processing 15533496 bp from intervals
[2016-04-14T23:29Z] WARN  16:29:58,705 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:29Z] INFO  16:29:58,820 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:29Z] INFO  16:29:58,830 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:29Z] INFO  16:29:58,831 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:29Z] INFO  16:29:58,832 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:29Z] INFO  16:29:58,832 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-14T23:29Z] INFO  16:29:58,920 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-14T23:29Z] INFO  16:29:58,970 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:29Z] INFO  16:29:58,971 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:29Z] INFO  16:29:58,971 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:29Z] INFO  16:29:58,972 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:29Z] INFO  16:29:58,980 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:29Z] INFO  16:29:58,989 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:29Z] INFO  16:29:59,040 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-14T23:29Z] INFO  16:29:59,055 IntervalUtils - Processing 15510186 bp from intervals
[2016-04-14T23:29Z] INFO  16:29:59,133 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:29Z] INFO  16:29:59,159 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:29Z] INFO  16:29:59,288 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:29Z] INFO  16:29:59,491 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:29Z] INFO  16:29:59,492 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:29Z] INFO  16:29:59,493 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:29Z] INFO  16:29:59,494 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:29Z] INFO  16:29:59,519 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:29Z] INFO  16:29:59,670 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:29Z] INFO  16:29:59,823 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:29Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-7_141629903_157151331-prep-prealign.bam
[2016-04-14T23:30Z] GATK RealignerTargetCreator: R14-18102_kapa-NGv3-PE100-NGv3-sort-7_141629903_157151331-prep-prealign.bam 7:141629904-157151331
[2016-04-14T23:30Z] GATK: RealignerTargetCreator
[2016-04-14T23:30Z] INFO  16:30:01,487 ProgressMeter -      6:33690752    300008.0    30.0 s     100.0 s       16.8%     3.0 m       2.5 m
[2016-04-14T23:30Z] INFO  16:30:01,847 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@5fe152b7
[2016-04-14T23:30Z] INFO  16:30:01,939 ProgressMeter -            done    101200.0    15.0 s       2.5 m       98.9%    15.0 s       0.0 s
[2016-04-14T23:30Z] INFO  16:30:01,940 ProgressMeter - Total runtime 15.07 secs, 0.25 min, 0.00 hours
[2016-04-14T23:30Z] INFO  16:30:01,940 MicroScheduler - 118 reads were filtered out during the traversal out of approximately 101318 total reads (0.12%)
[2016-04-14T23:30Z] INFO  16:30:01,940 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:30Z] INFO  16:30:01,941 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:30Z] INFO  16:30:01,941 MicroScheduler -   -> 118 reads (0.12% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:30Z] INFO  16:30:03,504 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:30Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-8_79513976_95140568-prep-prealign.bam
[2016-04-14T23:30Z] GATK RealignerTargetCreator: R14-18102_kapa-NGv3-PE100-NGv3-sort-8_79513976_95140568-prep-prealign.bam 8:79513977-95140568
[2016-04-14T23:30Z] GATK: RealignerTargetCreator
[2016-04-14T23:30Z] INFO  16:30:04,070 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:30Z] INFO  16:30:04,073 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:30Z] INFO  16:30:04,074 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:30Z] INFO  16:30:04,074 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:30Z] INFO  16:30:04,079 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/7/R14-18102_kapa-NGv3-PE100-NGv3-sort-7_141629903_157151331-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/7/tx/tmpTlnsKp/R14-18102_kapa-NGv3-PE100-NGv3-sort-7_141629903_157151331-prep-prealign-realign.intervals -l INFO -L 7:141629904-157151331 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-14T23:30Z] INFO  16:30:04,088 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:30Z] INFO  16:30:04,088 HelpFormatter - Date/Time: 2016/04/14 16:30:04
[2016-04-14T23:30Z] INFO  16:30:04,089 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:30Z] INFO  16:30:04,089 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:30Z] INFO  16:30:04,225 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:30Z] INFO  16:30:04,457 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-14T23:30Z] INFO  16:30:04,466 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:30Z] INFO  16:30:04,519 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-14T23:30Z] INFO  16:30:04,776 IntervalUtils - Processing 15521428 bp from intervals
[2016-04-14T23:30Z] WARN  16:30:04,782 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:30Z] INFO  16:30:04,860 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:30Z] INFO  16:30:05,076 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:30Z] INFO  16:30:05,078 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:30Z] INFO  16:30:05,078 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:30Z] INFO  16:30:05,079 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-14T23:30Z] INFO  16:30:06,643 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:30Z] INFO  16:30:06,647 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:30Z] INFO  16:30:06,648 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:30Z] INFO  16:30:06,648 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:30Z] INFO  16:30:06,653 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/8/R14-18102_kapa-NGv3-PE100-NGv3-sort-8_79513976_95140568-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/8/tx/tmpvka8p2/R14-18102_kapa-NGv3-PE100-NGv3-sort-8_79513976_95140568-prep-prealign-realign.intervals -l INFO -L 8:79513977-95140568 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-14T23:30Z] INFO  16:30:06,685 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:30Z] INFO  16:30:06,698 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@7172f77a
[2016-04-14T23:30Z] INFO  16:30:06,707 HelpFormatter - Date/Time: 2016/04/14 16:30:06
[2016-04-14T23:30Z] INFO  16:30:06,707 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:30Z] INFO  16:30:06,707 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:30Z] INFO  16:30:06,819 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:30Z] INFO  16:30:06,838 ProgressMeter -            done    146037.0    23.0 s       2.6 m      100.0%    23.0 s       0.0 s
[2016-04-14T23:30Z] INFO  16:30:06,838 ProgressMeter - Total runtime 23.03 secs, 0.38 min, 0.01 hours
[2016-04-14T23:30Z] INFO  16:30:06,839 MicroScheduler - 101 reads were filtered out during the traversal out of approximately 146138 total reads (0.07%)
[2016-04-14T23:30Z] INFO  16:30:06,839 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:30Z] INFO  16:30:06,839 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:30Z] INFO  16:30:06,839 MicroScheduler -   -> 101 reads (0.07% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:30Z] INFO  16:30:06,956 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@41fd9d8e
[2016-04-14T23:30Z] INFO  16:30:07,067 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-14T23:30Z] INFO  16:30:07,077 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:30Z] INFO  16:30:07,115 ProgressMeter -            done    121022.0    18.0 s       2.5 m      100.0%    18.0 s       0.0 s
[2016-04-14T23:30Z] INFO  16:30:07,115 ProgressMeter - Total runtime 18.08 secs, 0.30 min, 0.01 hours
[2016-04-14T23:30Z] INFO  16:30:07,116 MicroScheduler - 111 reads were filtered out during the traversal out of approximately 121133 total reads (0.09%)
[2016-04-14T23:30Z] INFO  16:30:07,116 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:30Z] INFO  16:30:07,116 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:30Z] INFO  16:30:07,117 MicroScheduler -   -> 111 reads (0.09% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:30Z] INFO  16:30:07,136 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-14T23:30Z] INFO  16:30:07,446 IntervalUtils - Processing 15626592 bp from intervals
[2016-04-14T23:30Z] WARN  16:30:07,451 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:30Z] INFO  16:30:07,532 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:30Z] INFO  16:30:07,739 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@7172f77a
[2016-04-14T23:30Z] INFO  16:30:07,744 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:30Z] INFO  16:30:07,746 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:30Z] INFO  16:30:07,746 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:30Z] INFO  16:30:07,747 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-14T23:30Z] INFO  16:30:07,780 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@7172f77a
[2016-04-14T23:30Z] INFO  16:30:07,870 ProgressMeter -            done    140677.0    20.0 s       2.4 m      100.0%    20.0 s       0.0 s
[2016-04-14T23:30Z] INFO  16:30:07,870 ProgressMeter - Total runtime 20.56 secs, 0.34 min, 0.01 hours
[2016-04-14T23:30Z] INFO  16:30:07,871 MicroScheduler - 114 reads were filtered out during the traversal out of approximately 140791 total reads (0.08%)
[2016-04-14T23:30Z] INFO  16:30:07,871 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:30Z] INFO  16:30:07,871 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:30Z] INFO  16:30:07,871 MicroScheduler -   -> 114 reads (0.08% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:30Z] INFO  16:30:07,889 ProgressMeter -            done    346268.0    44.0 s       2.2 m      100.0%    44.0 s       0.0 s
[2016-04-14T23:30Z] INFO  16:30:07,890 ProgressMeter - Total runtime 44.73 secs, 0.75 min, 0.01 hours
[2016-04-14T23:30Z] INFO  16:30:07,890 MicroScheduler - 181 reads were filtered out during the traversal out of approximately 346449 total reads (0.05%)
[2016-04-14T23:30Z] INFO  16:30:07,891 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:30Z] INFO  16:30:07,891 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:30Z] INFO  16:30:07,891 MicroScheduler -   -> 181 reads (0.05% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:30Z] INFO  16:30:07,927 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@7172f77a
[2016-04-14T23:30Z] INFO  16:30:08,101 ProgressMeter -            done    722781.0    88.0 s       2.0 m      100.0%    88.0 s       0.0 s
[2016-04-14T23:30Z] INFO  16:30:08,102 ProgressMeter - Total runtime 88.66 secs, 1.48 min, 0.02 hours
[2016-04-14T23:30Z] INFO  16:30:08,103 MicroScheduler - 436 reads were filtered out during the traversal out of approximately 723217 total reads (0.06%)
[2016-04-14T23:30Z] INFO  16:30:08,104 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:30Z] INFO  16:30:08,105 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:30Z] INFO  16:30:08,106 MicroScheduler -   -> 436 reads (0.06% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:30Z] INFO  16:30:08,173 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:30Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-8_63775819_79510770-prep-prealign.bam
[2016-04-14T23:30Z] INFO  16:30:08,368 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:30Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-8_126369460_141889736-prep-prealign.bam
[2016-04-14T23:30Z] GATK RealignerTargetCreator: R14-18102_kapa-NGv3-PE100-NGv3-sort-8_63775819_79510770-prep-prealign.bam 8:63775820-79510770
[2016-04-14T23:30Z] GATK: RealignerTargetCreator
[2016-04-14T23:30Z] GATK RealignerTargetCreator: R14-18102_kapa-NGv3-PE100-NGv3-sort-8_126369460_141889736-prep-prealign.bam 8:126369461-141889736
[2016-04-14T23:30Z] GATK: RealignerTargetCreator
[2016-04-14T23:30Z] INFO  16:30:09,155 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:30Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-8_110656864_126194498-prep-prealign.bam
[2016-04-14T23:30Z] INFO  16:30:09,188 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:30Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-8_15519664_31030618-prep-prealign.bam
[2016-04-14T23:30Z] INFO  16:30:09,596 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:30Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-7_94750023_110303777-prep-prealign.bam
[2016-04-14T23:30Z] GATK RealignerTargetCreator: R14-18102_kapa-NGv3-PE100-NGv3-sort-8_110656864_126194498-prep-prealign.bam 8:110656865-126194498
[2016-04-14T23:30Z] GATK: RealignerTargetCreator
[2016-04-14T23:30Z] GATK RealignerTargetCreator: R14-18102_kapa-NGv3-PE100-NGv3-sort-8_15519664_31030618-prep-prealign.bam 8:15519665-31030618
[2016-04-14T23:30Z] GATK: RealignerTargetCreator
[2016-04-14T23:30Z] INFO  16:30:11,832 ProgressMeter -            done   1.5656666E7    16.0 s       1.0 s      100.0%    16.0 s       0.0 s
[2016-04-14T23:30Z] INFO  16:30:11,832 ProgressMeter - Total runtime 16.67 secs, 0.28 min, 0.00 hours
[2016-04-14T23:30Z] INFO  16:30:11,836 MicroScheduler - 12069 reads were filtered out during the traversal out of approximately 138864 total reads (8.69%)
[2016-04-14T23:30Z] INFO  16:30:11,836 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:30Z] INFO  16:30:11,836 MicroScheduler -   -> 466 reads (0.34% of total) failing BadMateFilter
[2016-04-14T23:30Z] INFO  16:30:11,837 MicroScheduler -   -> 10891 reads (7.84% of total) failing DuplicateReadFilter
[2016-04-14T23:30Z] INFO  16:30:11,837 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-14T23:30Z] INFO  16:30:11,837 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:30Z] INFO  16:30:11,837 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-14T23:30Z] INFO  16:30:11,838 MicroScheduler -   -> 712 reads (0.51% of total) failing MappingQualityZeroFilter
[2016-04-14T23:30Z] INFO  16:30:11,838 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:30Z] INFO  16:30:11,838 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-14T23:30Z] INFO  16:30:11,838 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-14T23:30Z] INFO  16:30:11,837 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:30Z] INFO  16:30:11,841 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:30Z] INFO  16:30:11,841 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:30Z] INFO  16:30:11,842 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:30Z] INFO  16:30:11,846 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/8/R14-18102_kapa-NGv3-PE100-NGv3-sort-8_126369460_141889736-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/8/tx/tmp_HVQI7/R14-18102_kapa-NGv3-PE100-NGv3-sort-8_126369460_141889736-prep-prealign-realign.intervals -l INFO -L 8:126369461-141889736 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-14T23:30Z] INFO  16:30:11,856 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:30Z] INFO  16:30:11,868 HelpFormatter - Date/Time: 2016/04/14 16:30:11
[2016-04-14T23:30Z] INFO  16:30:11,869 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:30Z] INFO  16:30:11,870 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:30Z] INFO  16:30:12,014 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:30Z] INFO  16:30:12,156 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:30Z] INFO  16:30:12,159 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:30Z] INFO  16:30:12,159 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:30Z] INFO  16:30:12,159 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:30Z] INFO  16:30:12,164 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/8/R14-18102_kapa-NGv3-PE100-NGv3-sort-8_63775819_79510770-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/8/tx/tmpOU3Tf7/R14-18102_kapa-NGv3-PE100-NGv3-sort-8_63775819_79510770-prep-prealign-realign.intervals -l INFO -L 8:63775820-79510770 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-14T23:30Z] INFO  16:30:12,191 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:30Z] INFO  16:30:12,192 HelpFormatter - Date/Time: 2016/04/14 16:30:12
[2016-04-14T23:30Z] INFO  16:30:12,192 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:30Z] INFO  16:30:12,192 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:30Z] GATK RealignerTargetCreator: R14-18102_kapa-NGv3-PE100-NGv3-sort-7_94750023_110303777-prep-prealign.bam 7:94750024-110303777
[2016-04-14T23:30Z] GATK: RealignerTargetCreator
[2016-04-14T23:30Z] INFO  16:30:12,274 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-14T23:30Z] INFO  16:30:12,285 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:30Z] INFO  16:30:12,372 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.09
[2016-04-14T23:30Z] INFO  16:30:12,381 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:30Z] INFO  16:30:12,658 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-14T23:30Z] INFO  16:30:12,668 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:30Z] INFO  16:30:12,671 ProgressMeter -            done   1.5517156E7    19.0 s       1.0 s      100.0%    19.0 s       0.0 s
[2016-04-14T23:30Z] INFO  16:30:12,672 ProgressMeter - Total runtime 19.63 secs, 0.33 min, 0.01 hours
[2016-04-14T23:30Z] INFO  16:30:12,683 MicroScheduler - 108709 reads were filtered out during the traversal out of approximately 310873 total reads (34.97%)
[2016-04-14T23:30Z] INFO  16:30:12,685 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:30Z] INFO  16:30:12,685 MicroScheduler -   -> 563 reads (0.18% of total) failing BadMateFilter
[2016-04-14T23:30Z] INFO  16:30:12,686 MicroScheduler -   -> 18446 reads (5.93% of total) failing DuplicateReadFilter
[2016-04-14T23:30Z] INFO  16:30:12,687 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-14T23:30Z] INFO  16:30:12,687 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:30Z] INFO  16:30:12,688 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-14T23:30Z] INFO  16:30:12,688 MicroScheduler -   -> 89700 reads (28.85% of total) failing MappingQualityZeroFilter
[2016-04-14T23:30Z] INFO  16:30:12,688 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:30Z] INFO  16:30:12,688 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-14T23:30Z] INFO  16:30:12,689 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-14T23:30Z] INFO  16:30:12,694 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:30Z] INFO  16:30:12,697 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:30Z] INFO  16:30:12,697 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:30Z] INFO  16:30:12,697 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:30Z] INFO  16:30:12,701 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/8/R14-18102_kapa-NGv3-PE100-NGv3-sort-8_110656864_126194498-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/8/tx/tmpPfZcDt/R14-18102_kapa-NGv3-PE100-NGv3-sort-8_110656864_126194498-prep-prealign-realign.intervals -l INFO -L 8:110656865-126194498 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-14T23:30Z] INFO  16:30:12,711 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:30Z] INFO  16:30:12,711 HelpFormatter - Date/Time: 2016/04/14 16:30:12
[2016-04-14T23:30Z] INFO  16:30:12,712 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:30Z] INFO  16:30:12,712 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:30Z] INFO  16:30:12,730 IntervalUtils - Processing 15520276 bp from intervals
[2016-04-14T23:30Z] WARN  16:30:12,736 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:30Z] INFO  16:30:12,741 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-14T23:30Z] INFO  16:30:12,860 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:30Z] INFO  16:30:12,875 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:30Z] INFO  16:30:13,190 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:30Z] INFO  16:30:13,191 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:30Z] INFO  16:30:13,191 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:30Z] INFO  16:30:13,192 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-14T23:30Z] INFO  16:30:13,197 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-14T23:30Z] INFO  16:30:13,198 IntervalUtils - Processing 15734951 bp from intervals
[2016-04-14T23:30Z] INFO  16:30:13,209 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:30Z] WARN  16:30:13,215 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:30Z] INFO  16:30:13,286 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-14T23:30Z] INFO  16:30:13,305 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:30Z] GATK: realign ('8', 48003022, 63659688) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:30Z] INFO  16:30:13,357 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:30Z] INFO  16:30:13,361 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:30Z] INFO  16:30:13,361 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:30Z] INFO  16:30:13,362 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:30Z] INFO  16:30:13,366 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:30Z] INFO  16:30:13,372 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/8/R14-18102_kapa-NGv3-PE100-NGv3-sort-8_15519664_31030618-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/8/tx/tmpUtC8FZ/R14-18102_kapa-NGv3-PE100-NGv3-sort-8_15519664_31030618-prep-prealign-realign.intervals -l INFO -L 8:15519665-31030618 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-14T23:30Z] INFO  16:30:13,382 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:30Z] INFO  16:30:13,383 HelpFormatter - Date/Time: 2016/04/14 16:30:13
[2016-04-14T23:30Z] INFO  16:30:13,384 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:30Z] INFO  16:30:13,385 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:30Z] INFO  16:30:13,488 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:30Z] INFO  16:30:13,583 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:30Z] INFO  16:30:13,584 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:30Z] INFO  16:30:13,585 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:30Z] INFO  16:30:13,585 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-14T23:30Z] INFO  16:30:13,702 IntervalUtils - Processing 15537634 bp from intervals
[2016-04-14T23:30Z] WARN  16:30:13,708 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:30Z] INFO  16:30:13,783 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-14T23:30Z] INFO  16:30:13,791 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:30Z] INFO  16:30:13,797 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:30Z] INFO  16:30:13,885 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.09
[2016-04-14T23:30Z] INFO  16:30:13,988 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:30Z] GATK: realign ('8', 0, 15517156) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:30Z] INFO  16:30:14,076 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:30Z] INFO  16:30:14,077 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:30Z] INFO  16:30:14,078 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:30Z] INFO  16:30:14,078 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-14T23:30Z] INFO  16:30:14,202 IntervalUtils - Processing 15510954 bp from intervals
[2016-04-14T23:30Z] WARN  16:30:14,208 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:30Z] INFO  16:30:14,311 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:30Z] INFO  16:30:14,464 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@7172f77a
[2016-04-14T23:30Z] INFO  16:30:14,649 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:30Z] INFO  16:30:14,650 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:30Z] INFO  16:30:14,651 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:30Z] INFO  16:30:14,652 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-14T23:30Z] INFO  16:30:14,659 ProgressMeter -            done    203490.0    27.0 s       2.3 m      100.0%    27.0 s       0.0 s
[2016-04-14T23:30Z] INFO  16:30:14,660 ProgressMeter - Total runtime 27.77 secs, 0.46 min, 0.01 hours
[2016-04-14T23:30Z] INFO  16:30:14,660 MicroScheduler - 127 reads were filtered out during the traversal out of approximately 203617 total reads (0.06%)
[2016-04-14T23:30Z] INFO  16:30:14,660 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:30Z] INFO  16:30:14,661 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:30Z] INFO  16:30:14,661 MicroScheduler -   -> 127 reads (0.06% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:30Z] INFO  16:30:15,259 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:30Z] INFO  16:30:15,262 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:30Z] INFO  16:30:15,263 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:30Z] INFO  16:30:15,263 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:30Z] INFO  16:30:15,268 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/7/R14-18102_kapa-NGv3-PE100-NGv3-sort-7_94750023_110303777-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/7/tx/tmptOGYAC/R14-18102_kapa-NGv3-PE100-NGv3-sort-7_94750023_110303777-prep-prealign-realign.intervals -l INFO -L 7:94750024-110303777 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-14T23:30Z] INFO  16:30:15,288 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:30Z] INFO  16:30:15,289 HelpFormatter - Date/Time: 2016/04/14 16:30:15
[2016-04-14T23:30Z] INFO  16:30:15,289 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:30Z] INFO  16:30:15,290 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:30Z] INFO  16:30:15,437 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:30Z] INFO  16:30:15,684 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-14T23:30Z] INFO  16:30:15,693 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:30Z] INFO  16:30:15,770 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-14T23:30Z] INFO  16:30:16,073 IntervalUtils - Processing 15553754 bp from intervals
[2016-04-14T23:30Z] WARN  16:30:16,089 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:30Z] INFO  16:30:16,189 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:30Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-8_95142853_110655419-prep-prealign.bam
[2016-04-14T23:30Z] INFO  16:30:16,215 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:30Z] INFO  16:30:16,307 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:30Z] INFO  16:30:16,310 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:30Z] INFO  16:30:16,311 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:30Z] INFO  16:30:16,312 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:30Z] INFO  16:30:16,316 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/8/R14-18102_kapa-NGv3-PE100-NGv3-sort-8_48003022_63659688-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/8/R14-18102_kapa-NGv3-PE100-NGv3-sort-8_48003022_63659688-prep-prealign-realign.intervals -L 8:48003023-63659688 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/8/tx/tmp_KKawz/R14-18102_kapa-NGv3-PE100-NGv3-sort-8_48003022_63659688-prep.bam
[2016-04-14T23:30Z] INFO  16:30:16,339 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:30Z] INFO  16:30:16,339 HelpFormatter - Date/Time: 2016/04/14 16:30:16
[2016-04-14T23:30Z] INFO  16:30:16,339 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:30Z] INFO  16:30:16,339 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:30Z] INFO  16:30:16,473 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:30Z] INFO  16:30:16,475 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:30Z] INFO  16:30:16,475 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:30Z] INFO  16:30:16,476 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-14T23:30Z] INFO  16:30:16,531 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:30Z] INFO  16:30:16,687 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:30Z] INFO  16:30:16,696 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:30Z] INFO  16:30:16,754 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-14T23:30Z] INFO  16:30:16,793 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:30Z] INFO  16:30:16,797 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:30Z] INFO  16:30:16,797 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:30Z] INFO  16:30:16,798 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:30Z] INFO  16:30:16,802 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/8/R14-18102_kapa-NGv3-PE100-NGv3-sort-8_0_15517156-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/8/R14-18102_kapa-NGv3-PE100-NGv3-sort-8_0_15517156-prep-prealign-realign.intervals -L 8:1-15517156 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/8/tx/tmpQbHEoH/R14-18102_kapa-NGv3-PE100-NGv3-sort-8_0_15517156-prep.bam
[2016-04-14T23:30Z] INFO  16:30:16,815 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:30Z] INFO  16:30:16,816 HelpFormatter - Date/Time: 2016/04/14 16:30:16
[2016-04-14T23:30Z] INFO  16:30:16,816 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:30Z] INFO  16:30:16,816 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:30Z] GATK RealignerTargetCreator: R14-18102_kapa-NGv3-PE100-NGv3-sort-8_95142853_110655419-prep-prealign.bam 8:95142854-110655419
[2016-04-14T23:30Z] GATK: RealignerTargetCreator
[2016-04-14T23:30Z] INFO  16:30:17,015 ProgressMeter -            done   1.6504519E7    18.0 s       1.0 s      100.0%    18.0 s       0.0 s
[2016-04-14T23:30Z] INFO  16:30:17,016 ProgressMeter - Total runtime 18.19 secs, 0.30 min, 0.01 hours
[2016-04-14T23:30Z] INFO  16:30:17,020 MicroScheduler - 16309 reads were filtered out during the traversal out of approximately 183727 total reads (8.88%)
[2016-04-14T23:30Z] INFO  16:30:17,022 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:30Z] INFO  16:30:17,022 MicroScheduler -   -> 568 reads (0.31% of total) failing BadMateFilter
[2016-04-14T23:30Z] INFO  16:30:17,023 MicroScheduler -   -> 14581 reads (7.94% of total) failing DuplicateReadFilter
[2016-04-14T23:30Z] INFO  16:30:17,024 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-14T23:30Z] INFO  16:30:17,024 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:30Z] INFO  16:30:17,025 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-14T23:30Z] INFO  16:30:17,026 MicroScheduler -   -> 1160 reads (0.63% of total) failing MappingQualityZeroFilter
[2016-04-14T23:30Z] INFO  16:30:17,026 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:30Z] INFO  16:30:17,027 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-14T23:30Z] INFO  16:30:17,027 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-14T23:30Z] INFO  16:30:17,088 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:30Z] INFO  16:30:17,213 IntervalUtils - Processing 15656666 bp from intervals
[2016-04-14T23:30Z] INFO  16:30:17,222 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:30Z] WARN  16:30:17,228 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:30Z] INFO  16:30:17,235 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:30Z] INFO  16:30:17,303 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:30Z] INFO  16:30:17,305 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-14T23:30Z] INFO  16:30:17,426 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:30Z] INFO  16:30:17,427 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:30Z] INFO  16:30:17,428 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:30Z] INFO  16:30:17,428 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:30Z] INFO  16:30:17,622 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:30Z] INFO  16:30:17,758 IntervalUtils - Processing 15517156 bp from intervals
[2016-04-14T23:30Z] WARN  16:30:17,787 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:30Z] INFO  16:30:17,816 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:30Z] INFO  16:30:17,892 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:30Z] INFO  16:30:18,076 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:30Z] INFO  16:30:18,078 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:30Z] INFO  16:30:18,078 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:30Z] INFO  16:30:18,079 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:30Z] INFO  16:30:18,253 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:30Z] INFO  16:30:18,411 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:30Z] INFO  16:30:18,470 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:30Z] GATK: realign ('8', 31496910, 48001429) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:30Z] INFO  16:30:20,039 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:30Z] INFO  16:30:20,043 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:30Z] INFO  16:30:20,044 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:30Z] INFO  16:30:20,044 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:30Z] INFO  16:30:20,049 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/8/R14-18102_kapa-NGv3-PE100-NGv3-sort-8_95142853_110655419-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/8/tx/tmpXkp13X/R14-18102_kapa-NGv3-PE100-NGv3-sort-8_95142853_110655419-prep-prealign-realign.intervals -l INFO -L 8:95142854-110655419 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-14T23:30Z] INFO  16:30:20,086 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:30Z] INFO  16:30:20,087 HelpFormatter - Date/Time: 2016/04/14 16:30:20
[2016-04-14T23:30Z] INFO  16:30:20,087 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:30Z] INFO  16:30:20,088 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:30Z] INFO  16:30:20,222 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:30Z] INFO  16:30:20,445 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-14T23:30Z] INFO  16:30:20,454 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:30Z] INFO  16:30:20,482 ProgressMeter -     8:144994884    100001.0    30.0 s       5.0 m       69.3%    43.0 s      13.0 s
[2016-04-14T23:30Z] INFO  16:30:20,515 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-14T23:30Z] INFO  16:30:20,795 IntervalUtils - Processing 15512566 bp from intervals
[2016-04-14T23:30Z] WARN  16:30:20,800 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:30Z] INFO  16:30:20,871 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:30Z] INFO  16:30:21,041 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:30Z] INFO  16:30:21,043 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:30Z] INFO  16:30:21,044 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:30Z] INFO  16:30:21,044 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-14T23:30Z] INFO  16:30:21,364 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:30Z] INFO  16:30:21,367 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:30Z] INFO  16:30:21,368 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:30Z] INFO  16:30:21,368 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:30Z] INFO  16:30:21,373 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/8/R14-18102_kapa-NGv3-PE100-NGv3-sort-8_31496910_48001429-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/8/R14-18102_kapa-NGv3-PE100-NGv3-sort-8_31496910_48001429-prep-prealign-realign.intervals -L 8:31496911-48001429 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/8/tx/tmpLfSFoU/R14-18102_kapa-NGv3-PE100-NGv3-sort-8_31496910_48001429-prep.bam
[2016-04-14T23:30Z] INFO  16:30:21,388 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:30Z] INFO  16:30:21,389 HelpFormatter - Date/Time: 2016/04/14 16:30:21
[2016-04-14T23:30Z] INFO  16:30:21,389 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:30Z] INFO  16:30:21,389 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:30Z] INFO  16:30:21,612 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:30Z] INFO  16:30:21,742 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:30Z] INFO  16:30:21,753 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:30Z] INFO  16:30:21,814 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-14T23:30Z] INFO  16:30:22,268 IntervalUtils - Processing 16504519 bp from intervals
[2016-04-14T23:30Z] WARN  16:30:22,274 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:30Z] INFO  16:30:22,373 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:30Z] INFO  16:30:22,519 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:30Z] INFO  16:30:22,521 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:30Z] INFO  16:30:22,522 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:30Z] INFO  16:30:22,523 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:30Z] INFO  16:30:22,703 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:30Z] INFO  16:30:22,853 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:30Z] INFO  16:30:23,645 ProgressMeter -            done    396454.0    26.0 s      68.0 s      100.0%    26.0 s       0.0 s
[2016-04-14T23:30Z] INFO  16:30:23,646 ProgressMeter - Total runtime 26.98 secs, 0.45 min, 0.01 hours
[2016-04-14T23:30Z] INFO  16:30:23,649 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 396454 total reads (0.00%)
[2016-04-14T23:30Z] INFO  16:30:23,650 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:30Z] INFO  16:30:23,651 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:30Z] INFO  16:30:23,651 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:30Z] INFO  16:30:23,947 ProgressMeter -            done    335925.0    24.0 s      74.0 s      100.0%    24.0 s       0.0 s
[2016-04-14T23:30Z] INFO  16:30:23,948 ProgressMeter - Total runtime 24.98 secs, 0.42 min, 0.01 hours
[2016-04-14T23:30Z] INFO  16:30:23,951 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 335925 total reads (0.00%)
[2016-04-14T23:30Z] INFO  16:30:23,952 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:30Z] INFO  16:30:23,952 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:30Z] INFO  16:30:23,952 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:30Z] INFO  16:30:24,034 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@7172f77a
[2016-04-14T23:30Z] INFO  16:30:24,118 ProgressMeter -            done    180070.0    24.0 s       2.3 m      100.0%    24.0 s       0.0 s
[2016-04-14T23:30Z] INFO  16:30:24,118 ProgressMeter - Total runtime 24.63 secs, 0.41 min, 0.01 hours
[2016-04-14T23:30Z] INFO  16:30:24,119 MicroScheduler - 134 reads were filtered out during the traversal out of approximately 180204 total reads (0.07%)
[2016-04-14T23:30Z] INFO  16:30:24,119 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:30Z] INFO  16:30:24,119 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:30Z] INFO  16:30:24,120 MicroScheduler -   -> 134 reads (0.07% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:30Z] INFO  16:30:24,175 ProgressMeter -            done   1.5626592E7    16.0 s       1.0 s      100.0%    16.0 s       0.0 s
[2016-04-14T23:30Z] INFO  16:30:24,176 ProgressMeter - Total runtime 16.43 secs, 0.27 min, 0.00 hours
[2016-04-14T23:30Z] INFO  16:30:24,180 MicroScheduler - 8885 reads were filtered out during the traversal out of approximately 101844 total reads (8.72%)
[2016-04-14T23:30Z] INFO  16:30:24,181 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:30Z] INFO  16:30:24,182 MicroScheduler -   -> 461 reads (0.45% of total) failing BadMateFilter
[2016-04-14T23:30Z] INFO  16:30:24,183 MicroScheduler -   -> 7806 reads (7.66% of total) failing DuplicateReadFilter
[2016-04-14T23:30Z] INFO  16:30:24,183 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-14T23:30Z] INFO  16:30:24,184 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:30Z] INFO  16:30:24,190 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-14T23:30Z] INFO  16:30:24,191 MicroScheduler -   -> 618 reads (0.61% of total) failing MappingQualityZeroFilter
[2016-04-14T23:30Z] INFO  16:30:24,192 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:30Z] INFO  16:30:24,192 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-14T23:30Z] INFO  16:30:24,193 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-14T23:30Z] INFO  16:30:25,178 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:30Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-7_63095909_78636522-prep.bam
[2016-04-14T23:30Z] INFO  16:30:25,315 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:30Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-7_126086124_141619620-prep.bam
[2016-04-14T23:30Z] INFO  16:30:25,439 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:30Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-9_0_15510186-prep-prealign.bam
[2016-04-14T23:30Z] INFO  16:30:25,572 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:30Z] GATK: realign ('8', 79513976, 95140568) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:30Z] GATK RealignerTargetCreator: R14-18102_kapa-NGv3-PE100-NGv3-sort-9_0_15510186-prep-prealign.bam 9:1-15510186
[2016-04-14T23:30Z] GATK: RealignerTargetCreator
[2016-04-14T23:30Z] GATK pre-alignment ('9', 15564086, 32405601) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:30Z] GATK pre-alignment ('9', 32407258, 65506776) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:30Z] INFO  16:30:27,081 ProgressMeter -            done   1.5521428E7    22.0 s       1.0 s      100.0%    22.0 s       0.0 s
[2016-04-14T23:30Z] INFO  16:30:27,082 ProgressMeter - Total runtime 22.00 secs, 0.37 min, 0.01 hours
[2016-04-14T23:30Z] INFO  16:30:27,087 MicroScheduler - 100796 reads were filtered out during the traversal out of approximately 460813 total reads (21.87%)
[2016-04-14T23:30Z] INFO  16:30:27,099 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:30Z] INFO  16:30:27,100 MicroScheduler -   -> 872 reads (0.19% of total) failing BadMateFilter
[2016-04-14T23:30Z] INFO  16:30:27,101 MicroScheduler -   -> 31644 reads (6.87% of total) failing DuplicateReadFilter
[2016-04-14T23:30Z] INFO  16:30:27,102 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-14T23:30Z] INFO  16:30:27,103 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:30Z] INFO  16:30:27,103 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-14T23:30Z] INFO  16:30:27,104 MicroScheduler -   -> 68280 reads (14.82% of total) failing MappingQualityZeroFilter
[2016-04-14T23:30Z] INFO  16:30:27,105 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:30Z] INFO  16:30:27,106 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-14T23:30Z] INFO  16:30:27,106 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-14T23:30Z] INFO  16:30:28,186 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:30Z] INFO  16:30:28,196 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:30Z] INFO  16:30:28,197 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:30Z] INFO  16:30:28,197 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:30Z] INFO  16:30:28,212 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/8/R14-18102_kapa-NGv3-PE100-NGv3-sort-8_79513976_95140568-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/8/R14-18102_kapa-NGv3-PE100-NGv3-sort-8_79513976_95140568-prep-prealign-realign.intervals -L 8:79513977-95140568 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/8/tx/tmpwOuLVh/R14-18102_kapa-NGv3-PE100-NGv3-sort-8_79513976_95140568-prep.bam
[2016-04-14T23:30Z] INFO  16:30:28,228 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:30Z] INFO  16:30:28,229 HelpFormatter - Date/Time: 2016/04/14 16:30:28
[2016-04-14T23:30Z] INFO  16:30:28,230 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:30Z] INFO  16:30:28,230 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:30Z] INFO  16:30:28,425 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:30Z] INFO  16:30:28,544 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:30Z] INFO  16:30:28,571 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:30Z] INFO  16:30:28,580 ProgressMeter -            done    880352.0    57.0 s      65.0 s      100.0%    57.0 s       0.0 s
[2016-04-14T23:30Z] INFO  16:30:28,585 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:30Z] INFO  16:30:28,592 ProgressMeter - Total runtime 57.39 secs, 0.96 min, 0.02 hours
[2016-04-14T23:30Z] GATK: realign ('7', 141629903, 157151331) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:30Z] INFO  16:30:28,597 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 880352 total reads (0.00%)
[2016-04-14T23:30Z] INFO  16:30:28,598 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:30Z] INFO  16:30:28,598 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:30Z] INFO  16:30:28,599 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:30Z] INFO  16:30:28,674 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.09
[2016-04-14T23:30Z] INFO  16:30:29,097 IntervalUtils - Processing 15626592 bp from intervals
[2016-04-14T23:30Z] INFO  16:30:29,101 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:30Z] INFO  16:30:29,104 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:30Z] INFO  16:30:29,105 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:30Z] INFO  16:30:29,105 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:30Z] INFO  16:30:29,110 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/9/R14-18102_kapa-NGv3-PE100-NGv3-sort-9_0_15510186-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/9/tx/tmpHWBUsD/R14-18102_kapa-NGv3-PE100-NGv3-sort-9_0_15510186-prep-prealign-realign.intervals -l INFO -L 9:1-15510186 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-14T23:30Z] WARN  16:30:29,115 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:30Z] INFO  16:30:29,161 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:30Z] INFO  16:30:29,162 HelpFormatter - Date/Time: 2016/04/14 16:30:29
[2016-04-14T23:30Z] INFO  16:30:29,162 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:30Z] INFO  16:30:29,162 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:30Z] INFO  16:30:29,167 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:30Z] INFO  16:30:29,170 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:30Z] INFO  16:30:29,171 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:30Z] INFO  16:30:29,171 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:30Z] INFO  16:30:29,176 HelpFormatter - Program Args: -T PrintReads -L 9:15564087-32405601 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/9/tx/tmpnvue2g/R14-18102_kapa-NGv3-PE100-NGv3-sort-9_15564086_32405601-prep-prealign.bam
[2016-04-14T23:30Z] INFO  16:30:29,190 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:30Z] INFO  16:30:29,191 HelpFormatter - Date/Time: 2016/04/14 16:30:29
[2016-04-14T23:30Z] INFO  16:30:29,192 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:30Z] INFO  16:30:29,192 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:30Z] INFO  16:30:29,212 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:30Z] INFO  16:30:29,308 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:30Z] INFO  16:30:29,368 ProgressMeter -            done   1.5520276E7    16.0 s       1.0 s      100.0%    16.0 s       0.0 s
[2016-04-14T23:30Z] INFO  16:30:29,368 ProgressMeter - Total runtime 16.18 secs, 0.27 min, 0.00 hours
[2016-04-14T23:30Z] INFO  16:30:29,372 MicroScheduler - 10498 reads were filtered out during the traversal out of approximately 121953 total reads (8.61%)
[2016-04-14T23:30Z] INFO  16:30:29,385 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:30Z] INFO  16:30:29,386 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:30Z] INFO  16:30:29,387 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:30Z] INFO  16:30:29,388 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:30Z] INFO  16:30:29,390 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:30Z] INFO  16:30:29,394 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:30Z] INFO  16:30:29,395 MicroScheduler -   -> 496 reads (0.41% of total) failing BadMateFilter
[2016-04-14T23:30Z] INFO  16:30:29,396 MicroScheduler -   -> 9748 reads (7.99% of total) failing DuplicateReadFilter
[2016-04-14T23:30Z] INFO  16:30:29,397 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-14T23:30Z] INFO  16:30:29,398 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:30Z] INFO  16:30:29,398 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-14T23:30Z] INFO  16:30:29,399 MicroScheduler -   -> 254 reads (0.21% of total) failing MappingQualityZeroFilter
[2016-04-14T23:30Z] INFO  16:30:29,399 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:30Z] INFO  16:30:29,400 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-14T23:30Z] INFO  16:30:29,401 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-14T23:30Z] INFO  16:30:29,520 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-14T23:30Z] INFO  16:30:29,529 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:30Z] INFO  16:30:29,561 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:30Z] INFO  16:30:29,614 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-14T23:30Z] INFO  16:30:29,704 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:30Z] INFO  16:30:29,756 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:30Z] INFO  16:30:29,759 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:30Z] INFO  16:30:29,759 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:30Z] INFO  16:30:29,760 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:30Z] INFO  16:30:29,764 HelpFormatter - Program Args: -T PrintReads -L 9:32407259-65506776 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/9/tx/tmpgWWNs3/R14-18102_kapa-NGv3-PE100-NGv3-sort-9_32407258_65506776-prep-prealign.bam
[2016-04-14T23:30Z] INFO  16:30:29,779 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:30Z] INFO  16:30:29,787 HelpFormatter - Date/Time: 2016/04/14 16:30:29
[2016-04-14T23:30Z] INFO  16:30:29,787 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:30Z] INFO  16:30:29,788 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:30Z] INFO  16:30:30,030 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:30Z] INFO  16:30:30,039 IntervalUtils - Processing 15510186 bp from intervals
[2016-04-14T23:30Z] WARN  16:30:30,044 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:30Z] INFO  16:30:30,120 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:30Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-6_31083801_46593245-prep.bam
[2016-04-14T23:30Z] INFO  16:30:30,208 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:30Z] INFO  16:30:30,425 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:30Z] INFO  16:30:30,426 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:30Z] INFO  16:30:30,426 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:30Z] INFO  16:30:30,427 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-14T23:30Z] INFO  16:30:30,455 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-14T23:30Z] INFO  16:30:30,509 ProgressMeter -            done    138456.0    13.0 s      94.0 s      100.0%    13.0 s       0.0 s
[2016-04-14T23:30Z] INFO  16:30:30,509 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:30Z] INFO  16:30:30,509 ProgressMeter - Total runtime 13.08 secs, 0.22 min, 0.00 hours
[2016-04-14T23:30Z] INFO  16:30:30,513 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 138456 total reads (0.00%)
[2016-04-14T23:30Z] INFO  16:30:30,513 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:30Z] INFO  16:30:30,513 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:30Z] INFO  16:30:30,514 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:30Z] INFO  16:30:30,518 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:30Z] INFO  16:30:30,552 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.03
[2016-04-14T23:30Z] INFO  16:30:30,581 IntervalUtils - Processing 16841515 bp from intervals
[2016-04-14T23:30Z] INFO  16:30:30,707 ProgressMeter -            done   1.5734951E7    17.0 s       1.0 s      100.0%    17.0 s       0.0 s
[2016-04-14T23:30Z] INFO  16:30:30,708 ProgressMeter - Total runtime 17.12 secs, 0.29 min, 0.00 hours
[2016-04-14T23:30Z] INFO  16:30:30,712 MicroScheduler - 12620 reads were filtered out during the traversal out of approximately 146522 total reads (8.61%)
[2016-04-14T23:30Z] INFO  16:30:30,713 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:30Z] INFO  16:30:30,714 MicroScheduler -   -> 528 reads (0.36% of total) failing BadMateFilter
[2016-04-14T23:30Z] INFO  16:30:30,715 MicroScheduler -   -> 11623 reads (7.93% of total) failing DuplicateReadFilter
[2016-04-14T23:30Z] INFO  16:30:30,716 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-14T23:30Z] INFO  16:30:30,716 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:30Z] INFO  16:30:30,717 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-14T23:30Z] INFO  16:30:30,718 MicroScheduler -   -> 469 reads (0.32% of total) failing MappingQualityZeroFilter
[2016-04-14T23:30Z] INFO  16:30:30,719 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:30Z] INFO  16:30:30,719 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-14T23:30Z] INFO  16:30:30,720 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-14T23:30Z] INFO  16:30:30,725 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:30Z] INFO  16:30:30,732 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:30Z] GATK: realign ('8', 126369460, 141889736) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:30Z] INFO  16:30:31,131 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-14T23:30Z] INFO  16:30:31,142 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:30Z] INFO  16:30:31,143 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:30Z] INFO  16:30:31,144 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:30Z] INFO  16:30:31,145 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:30Z] INFO  16:30:31,168 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:30Z] INFO  16:30:31,189 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:30Z] INFO  16:30:31,198 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:30Z] INFO  16:30:31,268 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-14T23:30Z] INFO  16:30:31,283 IntervalUtils - Processing 33099518 bp from intervals
[2016-04-14T23:30Z] INFO  16:30:31,363 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:30Z] INFO  16:30:31,380 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:30Z] INFO  16:30:31,451 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:30Z] INFO  16:30:31,455 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:30Z] INFO  16:30:31,455 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:30Z] INFO  16:30:31,456 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:30Z] INFO  16:30:31,461 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/7/R14-18102_kapa-NGv3-PE100-NGv3-sort-7_141629903_157151331-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/7/R14-18102_kapa-NGv3-PE100-NGv3-sort-7_141629903_157151331-prep-prealign-realign.intervals -L 7:141629904-157151331 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/7/tx/tmpw_RGo3/R14-18102_kapa-NGv3-PE100-NGv3-sort-7_141629903_157151331-prep.bam
[2016-04-14T23:30Z] INFO  16:30:31,472 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:30Z] INFO  16:30:31,473 HelpFormatter - Date/Time: 2016/04/14 16:30:31
[2016-04-14T23:30Z] INFO  16:30:31,473 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:30Z] INFO  16:30:31,473 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:30Z] INFO  16:30:31,762 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:30Z] INFO  16:30:31,768 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:30Z] INFO  16:30:31,770 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:30Z] INFO  16:30:31,770 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:30Z] INFO  16:30:31,774 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:30Z] INFO  16:30:31,801 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:30Z] INFO  16:30:31,904 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:30Z] INFO  16:30:31,914 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:30Z] INFO  16:30:31,963 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-14T23:30Z] INFO  16:30:32,133 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:30Z] INFO  16:30:32,235 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:30Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-8_48003022_63659688-prep.bam
[2016-04-14T23:30Z] INFO  16:30:32,304 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:30Z] GATK: realign ('8', 63775819, 79510770) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:30Z] INFO  16:30:32,352 IntervalUtils - Processing 15521428 bp from intervals
[2016-04-14T23:30Z] WARN  16:30:32,357 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:30Z] INFO  16:30:32,423 ProgressMeter -            done   1.5537634E7    18.0 s       1.0 s      100.0%    18.0 s       0.0 s
[2016-04-14T23:30Z] INFO  16:30:32,424 ProgressMeter - Total runtime 18.35 secs, 0.31 min, 0.01 hours
[2016-04-14T23:30Z] INFO  16:30:32,428 MicroScheduler - 11713 reads were filtered out during the traversal out of approximately 141269 total reads (8.29%)
[2016-04-14T23:30Z] INFO  16:30:32,429 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:30Z] INFO  16:30:32,430 MicroScheduler -   -> 430 reads (0.30% of total) failing BadMateFilter
[2016-04-14T23:30Z] INFO  16:30:32,431 MicroScheduler -   -> 11057 reads (7.83% of total) failing DuplicateReadFilter
[2016-04-14T23:30Z] INFO  16:30:32,431 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-14T23:30Z] INFO  16:30:32,432 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:30Z] INFO  16:30:32,432 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-14T23:30Z] INFO  16:30:32,433 MicroScheduler -   -> 226 reads (0.16% of total) failing MappingQualityZeroFilter
[2016-04-14T23:30Z] INFO  16:30:32,434 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:30Z] INFO  16:30:32,434 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-14T23:30Z] INFO  16:30:32,435 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-14T23:30Z] INFO  16:30:32,441 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:30Z] INFO  16:30:32,595 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:30Z] INFO  16:30:32,596 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:30Z] INFO  16:30:32,596 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:30Z] INFO  16:30:32,596 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:30Z] GATK pre-alignment ('9', 65507205, 82187750) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:30Z] INFO  16:30:32,871 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:30Z] INFO  16:30:33,108 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:30Z] GATK pre-alignment ('9', 82188172, 97717561) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:30Z] INFO  16:30:33,714 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:30Z] INFO  16:30:33,717 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:30Z] INFO  16:30:33,718 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:30Z] INFO  16:30:33,719 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:30Z] INFO  16:30:33,723 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/8/R14-18102_kapa-NGv3-PE100-NGv3-sort-8_126369460_141889736-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/8/R14-18102_kapa-NGv3-PE100-NGv3-sort-8_126369460_141889736-prep-prealign-realign.intervals -L 8:126369461-141889736 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/8/tx/tmpMdDHbN/R14-18102_kapa-NGv3-PE100-NGv3-sort-8_126369460_141889736-prep.bam
[2016-04-14T23:30Z] INFO  16:30:33,732 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:30Z] INFO  16:30:33,733 HelpFormatter - Date/Time: 2016/04/14 16:30:33
[2016-04-14T23:30Z] INFO  16:30:33,734 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:30Z] INFO  16:30:33,735 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:30Z] INFO  16:30:34,027 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:30Z] INFO  16:30:34,170 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:30Z] GATK: realign ('8', 110656864, 126194498) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:30Z] INFO  16:30:34,247 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:30Z] INFO  16:30:34,279 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:30Z] INFO  16:30:34,374 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.09
[2016-04-14T23:30Z] INFO  16:30:34,850 IntervalUtils - Processing 15520276 bp from intervals
[2016-04-14T23:30Z] WARN  16:30:34,856 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:30Z] INFO  16:30:34,949 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:30Z] INFO  16:30:35,116 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:30Z] INFO  16:30:35,117 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:30Z] INFO  16:30:35,118 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:30Z] INFO  16:30:35,119 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:30Z] INFO  16:30:35,169 ProgressMeter -            done   1.5510954E7    20.0 s       1.0 s      100.0%    20.0 s       0.0 s
[2016-04-14T23:30Z] INFO  16:30:35,170 ProgressMeter - Total runtime 20.52 secs, 0.34 min, 0.01 hours
[2016-04-14T23:30Z] INFO  16:30:35,181 MicroScheduler - 29487 reads were filtered out during the traversal out of approximately 349735 total reads (8.43%)
[2016-04-14T23:30Z] INFO  16:30:35,183 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:30Z] INFO  16:30:35,183 MicroScheduler -   -> 828 reads (0.24% of total) failing BadMateFilter
[2016-04-14T23:30Z] INFO  16:30:35,184 MicroScheduler -   -> 27120 reads (7.75% of total) failing DuplicateReadFilter
[2016-04-14T23:30Z] INFO  16:30:35,185 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-14T23:30Z] INFO  16:30:35,186 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:30Z] INFO  16:30:35,186 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-14T23:30Z] INFO  16:30:35,187 MicroScheduler -   -> 1539 reads (0.44% of total) failing MappingQualityZeroFilter
[2016-04-14T23:30Z] INFO  16:30:35,187 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:30Z] INFO  16:30:35,188 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-14T23:30Z] INFO  16:30:35,189 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-14T23:30Z] INFO  16:30:35,265 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:30Z] INFO  16:30:35,417 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:30Z] INFO  16:30:35,420 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:30Z] INFO  16:30:35,420 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:30Z] INFO  16:30:35,420 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:30Z] INFO  16:30:35,427 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/8/R14-18102_kapa-NGv3-PE100-NGv3-sort-8_63775819_79510770-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/8/R14-18102_kapa-NGv3-PE100-NGv3-sort-8_63775819_79510770-prep-prealign-realign.intervals -L 8:63775820-79510770 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/8/tx/tmpV_k1gN/R14-18102_kapa-NGv3-PE100-NGv3-sort-8_63775819_79510770-prep.bam
[2016-04-14T23:30Z] INFO  16:30:35,454 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:30Z] INFO  16:30:35,456 HelpFormatter - Date/Time: 2016/04/14 16:30:35
[2016-04-14T23:30Z] INFO  16:30:35,456 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:30Z] INFO  16:30:35,457 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:30Z] INFO  16:30:35,458 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:30Z] INFO  16:30:35,655 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:30Z] INFO  16:30:35,819 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:30Z] INFO  16:30:35,839 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:30Z] INFO  16:30:35,907 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-14T23:30Z] INFO  16:30:36,150 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:30Z] INFO  16:30:36,154 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:30Z] INFO  16:30:36,154 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:30Z] INFO  16:30:36,155 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:30Z] INFO  16:30:36,160 HelpFormatter - Program Args: -T PrintReads -L 9:65507206-82187750 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/9/tx/tmppj2jqw/R14-18102_kapa-NGv3-PE100-NGv3-sort-9_65507205_82187750-prep-prealign.bam
[2016-04-14T23:30Z] INFO  16:30:36,173 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:30Z] INFO  16:30:36,174 HelpFormatter - Date/Time: 2016/04/14 16:30:36
[2016-04-14T23:30Z] INFO  16:30:36,175 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:30Z] INFO  16:30:36,176 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:30Z] INFO  16:30:36,233 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:30Z] INFO  16:30:36,237 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:30Z] INFO  16:30:36,237 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:30Z] INFO  16:30:36,238 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:30Z] INFO  16:30:36,258 HelpFormatter - Program Args: -T PrintReads -L 9:82188173-97717561 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/9/tx/tmp4dWay6/R14-18102_kapa-NGv3-PE100-NGv3-sort-9_82188172_97717561-prep-prealign.bam
[2016-04-14T23:30Z] INFO  16:30:36,274 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:30Z] INFO  16:30:36,274 HelpFormatter - Date/Time: 2016/04/14 16:30:36
[2016-04-14T23:30Z] INFO  16:30:36,274 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:30Z] INFO  16:30:36,275 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:30Z] INFO  16:30:36,306 IntervalUtils - Processing 15734951 bp from intervals
[2016-04-14T23:30Z] WARN  16:30:36,310 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:30Z] INFO  16:30:36,415 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:30Z] INFO  16:30:36,435 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:30Z] INFO  16:30:36,439 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:30Z] INFO  16:30:36,561 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:30Z] INFO  16:30:36,562 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:30Z] INFO  16:30:36,562 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:30Z] INFO  16:30:36,574 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:30Z] INFO  16:30:36,701 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:30Z] INFO  16:30:36,721 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:30Z] GATK: realign ('8', 15519664, 31030618) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:30Z] INFO  16:30:36,936 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:30Z] INFO  16:30:37,020 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:30Z] INFO  16:30:37,023 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:30Z] INFO  16:30:37,023 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:30Z] INFO  16:30:37,024 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:30Z] INFO  16:30:37,028 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/8/R14-18102_kapa-NGv3-PE100-NGv3-sort-8_110656864_126194498-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/8/R14-18102_kapa-NGv3-PE100-NGv3-sort-8_110656864_126194498-prep-prealign-realign.intervals -L 8:110656865-126194498 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/8/tx/tmpZn8Lg0/R14-18102_kapa-NGv3-PE100-NGv3-sort-8_110656864_126194498-prep.bam
[2016-04-14T23:30Z] INFO  16:30:37,043 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:30Z] INFO  16:30:37,044 HelpFormatter - Date/Time: 2016/04/14 16:30:37
[2016-04-14T23:30Z] INFO  16:30:37,044 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:30Z] INFO  16:30:37,044 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:30Z] INFO  16:30:37,240 ProgressMeter -            done    182259.0    14.0 s      80.0 s      100.0%    14.0 s       0.0 s
[2016-04-14T23:30Z] INFO  16:30:37,241 ProgressMeter - Total runtime 14.72 secs, 0.25 min, 0.00 hours
[2016-04-14T23:30Z] INFO  16:30:37,244 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 182259 total reads (0.00%)
[2016-04-14T23:30Z] INFO  16:30:37,245 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:30Z] INFO  16:30:37,245 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:30Z] INFO  16:30:37,245 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:30Z] INFO  16:30:37,321 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:30Z] INFO  16:30:37,464 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:30Z] INFO  16:30:37,473 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:30Z] INFO  16:30:37,487 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-14T23:30Z] INFO  16:30:37,535 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-14T23:30Z] INFO  16:30:37,582 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:30Z] INFO  16:30:37,591 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:30Z] INFO  16:30:37,643 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-14T23:30Z] INFO  16:30:37,669 IntervalUtils - Processing 15529389 bp from intervals
[2016-04-14T23:30Z] INFO  16:30:37,748 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:30Z] INFO  16:30:37,761 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-14T23:30Z] INFO  16:30:37,843 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@32d5a4c6
[2016-04-14T23:30Z] INFO  16:30:37,863 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:30Z] INFO  16:30:37,872 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:30Z] INFO  16:30:37,930 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-14T23:30Z] INFO  16:30:37,951 IntervalUtils - Processing 16680545 bp from intervals
[2016-04-14T23:30Z] INFO  16:30:37,983 ProgressMeter -            done    378277.0    47.0 s       2.1 m       98.1%    47.0 s       0.0 s
[2016-04-14T23:30Z] INFO  16:30:37,984 ProgressMeter - Total runtime 47.80 secs, 0.80 min, 0.01 hours
[2016-04-14T23:30Z] INFO  16:30:37,985 MicroScheduler - 168 reads were filtered out during the traversal out of approximately 378445 total reads (0.04%)
[2016-04-14T23:30Z] INFO  16:30:37,997 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:30Z] INFO  16:30:37,998 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:30Z] INFO  16:30:37,998 IntervalUtils - Processing 15537634 bp from intervals
[2016-04-14T23:30Z] INFO  16:30:37,998 MicroScheduler -   -> 168 reads (0.04% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:30Z] WARN  16:30:38,003 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:30Z] INFO  16:30:38,035 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:30Z] INFO  16:30:38,041 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:30Z] INFO  16:30:38,043 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:30Z] INFO  16:30:38,043 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:30Z] INFO  16:30:38,044 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:30Z] INFO  16:30:38,059 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:30Z] INFO  16:30:38,123 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:30Z] INFO  16:30:38,247 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:30Z] INFO  16:30:38,268 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:30Z] INFO  16:30:38,269 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:30Z] INFO  16:30:38,270 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:30Z] INFO  16:30:38,270 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:30Z] INFO  16:30:38,335 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:30Z] INFO  16:30:38,342 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:30Z] INFO  16:30:38,343 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:30Z] INFO  16:30:38,344 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:30Z] INFO  16:30:38,377 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:30Z] INFO  16:30:38,433 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:30Z] INFO  16:30:38,583 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:30Z] INFO  16:30:38,587 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:30Z] INFO  16:30:38,792 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:30Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-8_31496910_48001429-prep.bam
[2016-04-14T23:30Z] INFO  16:30:39,022 ProgressMeter -            done    101200.0     9.0 s      95.0 s       98.9%     9.0 s       0.0 s
[2016-04-14T23:30Z] INFO  16:30:39,023 ProgressMeter - Total runtime 9.64 secs, 0.16 min, 0.00 hours
[2016-04-14T23:30Z] INFO  16:30:39,026 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 101200 total reads (0.00%)
[2016-04-14T23:30Z] INFO  16:30:39,026 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:30Z] INFO  16:30:39,027 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:30Z] INFO  16:30:39,027 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:30Z] GATK pre-alignment ('9', 97718189, 113228306) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:30Z] INFO  16:30:39,495 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:30Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-8_141900641_146364022-prep-prealign.bam
[2016-04-14T23:30Z] INFO  16:30:39,593 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:30Z] INFO  16:30:39,596 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:30Z] INFO  16:30:39,597 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:30Z] INFO  16:30:39,597 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:30Z] INFO  16:30:39,602 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/8/R14-18102_kapa-NGv3-PE100-NGv3-sort-8_15519664_31030618-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/8/R14-18102_kapa-NGv3-PE100-NGv3-sort-8_15519664_31030618-prep-prealign-realign.intervals -L 8:15519665-31030618 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/8/tx/tmpRAq8ag/R14-18102_kapa-NGv3-PE100-NGv3-sort-8_15519664_31030618-prep.bam
[2016-04-14T23:30Z] INFO  16:30:39,632 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:30Z] INFO  16:30:39,641 HelpFormatter - Date/Time: 2016/04/14 16:30:39
[2016-04-14T23:30Z] INFO  16:30:39,642 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:30Z] INFO  16:30:39,642 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:30Z] INFO  16:30:39,957 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:30Z] INFO  16:30:40,109 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:30Z] INFO  16:30:40,118 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:30Z] INFO  16:30:40,127 ProgressMeter -            done   1.5512566E7    19.0 s       1.0 s      100.0%    19.0 s       0.0 s
[2016-04-14T23:30Z] INFO  16:30:40,128 ProgressMeter - Total runtime 19.09 secs, 0.32 min, 0.01 hours
[2016-04-14T23:30Z] INFO  16:30:40,141 MicroScheduler - 17399 reads were filtered out during the traversal out of approximately 205363 total reads (8.47%)
[2016-04-14T23:30Z] INFO  16:30:40,142 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:30Z] INFO  16:30:40,142 MicroScheduler -   -> 606 reads (0.30% of total) failing BadMateFilter
[2016-04-14T23:30Z] INFO  16:30:40,143 MicroScheduler -   -> 16350 reads (7.96% of total) failing DuplicateReadFilter
[2016-04-14T23:30Z] INFO  16:30:40,144 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-14T23:30Z] INFO  16:30:40,144 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:30Z] INFO  16:30:40,145 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-14T23:30Z] INFO  16:30:40,145 MicroScheduler -   -> 443 reads (0.22% of total) failing MappingQualityZeroFilter
[2016-04-14T23:30Z] INFO  16:30:40,146 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:30Z] INFO  16:30:40,147 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-14T23:30Z] INFO  16:30:40,147 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-14T23:30Z] INFO  16:30:40,238 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.12
[2016-04-14T23:30Z] INFO  16:30:40,555 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:30Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-8_79513976_95140568-prep.bam
[2016-04-14T23:30Z] INFO  16:30:40,734 IntervalUtils - Processing 15510954 bp from intervals
[2016-04-14T23:30Z] WARN  16:30:40,747 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:30Z] INFO  16:30:40,819 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:30Z] GATK RealignerTargetCreator: R14-18102_kapa-NGv3-PE100-NGv3-sort-8_141900641_146364022-prep-prealign.bam 8:141900642-146364022
[2016-04-14T23:30Z] GATK: RealignerTargetCreator
[2016-04-14T23:30Z] INFO  16:30:40,863 ProgressMeter -            done    309294.0    22.0 s      73.0 s      100.0%    22.0 s       0.0 s
[2016-04-14T23:30Z] INFO  16:30:40,864 ProgressMeter - Total runtime 22.79 secs, 0.38 min, 0.01 hours
[2016-04-14T23:30Z] INFO  16:30:40,867 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 309294 total reads (0.00%)
[2016-04-14T23:30Z] INFO  16:30:40,867 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:30Z] INFO  16:30:40,868 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:30Z] INFO  16:30:40,868 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:30Z] INFO  16:30:40,916 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:30Z] INFO  16:30:40,917 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:30Z] INFO  16:30:40,918 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:30Z] INFO  16:30:40,919 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:30Z] GATK pre-alignment ('9', 113231219, 129089575) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:30Z] INFO  16:30:41,124 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:30Z] INFO  16:30:41,326 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:30Z] INFO  16:30:41,664 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:30Z] GATK: realign ('8', 95142853, 110655419) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:30Z] INFO  16:30:42,358 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:30Z] INFO  16:30:42,361 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:30Z] INFO  16:30:42,362 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:30Z] INFO  16:30:42,362 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:30Z] INFO  16:30:42,367 HelpFormatter - Program Args: -T PrintReads -L 9:97718190-113228306 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/9/tx/tmpphSqxI/R14-18102_kapa-NGv3-PE100-NGv3-sort-9_97718189_113228306-prep-prealign.bam
[2016-04-14T23:30Z] INFO  16:30:42,376 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:30Z] INFO  16:30:42,388 HelpFormatter - Date/Time: 2016/04/14 16:30:42
[2016-04-14T23:30Z] INFO  16:30:42,389 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:30Z] INFO  16:30:42,389 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:30Z] INFO  16:30:42,553 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:30Z] INFO  16:30:42,622 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:30Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-8_0_15517156-prep.bam
[2016-04-14T23:30Z] GATK pre-alignment ('9', 129097484, 141213431) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:30Z] INFO  16:30:43,788 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-14T23:30Z] INFO  16:30:43,869 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:30Z] INFO  16:30:43,878 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:30Z] INFO  16:30:43,865 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:30Z] INFO  16:30:43,901 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:30Z] INFO  16:30:43,901 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:30Z] INFO  16:30:43,901 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:30Z] INFO  16:30:43,905 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/8/R14-18102_kapa-NGv3-PE100-NGv3-sort-8_141900641_146364022-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/8/tx/tmpBetFNV/R14-18102_kapa-NGv3-PE100-NGv3-sort-8_141900641_146364022-prep-prealign-realign.intervals -l INFO -L 8:141900642-146364022 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-14T23:30Z] INFO  16:30:43,924 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:30Z] INFO  16:30:43,925 HelpFormatter - Date/Time: 2016/04/14 16:30:43
[2016-04-14T23:30Z] INFO  16:30:43,925 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:30Z] INFO  16:30:43,925 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:30Z] INFO  16:30:43,931 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-14T23:30Z] INFO  16:30:43,945 IntervalUtils - Processing 15510117 bp from intervals
[2016-04-14T23:30Z] INFO  16:30:44,024 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:30Z] INFO  16:30:44,069 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:30Z] INFO  16:30:44,157 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:30Z] INFO  16:30:44,161 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:30Z] INFO  16:30:44,161 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:30Z] INFO  16:30:44,162 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:30Z] INFO  16:30:44,166 HelpFormatter - Program Args: -T PrintReads -L 9:113231220-129089575 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/9/tx/tmpsSR7yL/R14-18102_kapa-NGv3-PE100-NGv3-sort-9_113231219_129089575-prep-prealign.bam
[2016-04-14T23:30Z] INFO  16:30:44,181 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:30Z] INFO  16:30:44,182 HelpFormatter - Date/Time: 2016/04/14 16:30:44
[2016-04-14T23:30Z] INFO  16:30:44,182 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:30Z] INFO  16:30:44,182 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:30Z] INFO  16:30:44,280 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:30Z] INFO  16:30:44,281 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:30Z] INFO  16:30:44,282 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:30Z] INFO  16:30:44,283 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:30Z] INFO  16:30:44,290 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-14T23:30Z] INFO  16:30:44,296 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:30Z] INFO  16:30:44,300 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:30Z] INFO  16:30:44,342 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.04
[2016-04-14T23:30Z] INFO  16:30:44,394 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:30Z] INFO  16:30:44,445 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:30Z] INFO  16:30:44,454 ProgressMeter -            done   1.5553754E7    27.0 s       1.0 s      100.0%    27.0 s       0.0 s
[2016-04-14T23:30Z] INFO  16:30:44,455 ProgressMeter - Total runtime 27.98 secs, 0.47 min, 0.01 hours
[2016-04-14T23:30Z] INFO  16:30:44,455 MicroScheduler - 186222 reads were filtered out during the traversal out of approximately 727088 total reads (25.61%)
[2016-04-14T23:30Z] INFO  16:30:44,456 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:30Z] INFO  16:30:44,456 MicroScheduler -   -> 1184 reads (0.16% of total) failing BadMateFilter
[2016-04-14T23:30Z] INFO  16:30:44,456 MicroScheduler -   -> 50096 reads (6.89% of total) failing DuplicateReadFilter
[2016-04-14T23:30Z] INFO  16:30:44,457 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-14T23:30Z] INFO  16:30:44,457 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:30Z] INFO  16:30:44,457 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-14T23:30Z] INFO  16:30:44,457 MicroScheduler -   -> 134942 reads (18.56% of total) failing MappingQualityZeroFilter
[2016-04-14T23:30Z] INFO  16:30:44,458 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:30Z] INFO  16:30:44,458 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-14T23:30Z] INFO  16:30:44,458 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-14T23:30Z] INFO  16:30:44,589 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:30Z] INFO  16:30:44,592 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:30Z] INFO  16:30:44,592 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:30Z] INFO  16:30:44,593 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:30Z] INFO  16:30:44,598 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/8/R14-18102_kapa-NGv3-PE100-NGv3-sort-8_95142853_110655419-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/8/R14-18102_kapa-NGv3-PE100-NGv3-sort-8_95142853_110655419-prep-prealign-realign.intervals -L 8:95142854-110655419 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/8/tx/tmp1YuMv6/R14-18102_kapa-NGv3-PE100-NGv3-sort-8_95142853_110655419-prep.bam
[2016-04-14T23:30Z] INFO  16:30:44,618 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:30Z] INFO  16:30:44,619 HelpFormatter - Date/Time: 2016/04/14 16:30:44
[2016-04-14T23:30Z] INFO  16:30:44,619 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:30Z] INFO  16:30:44,620 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:30Z] INFO  16:30:44,648 IntervalUtils - Processing 4463381 bp from intervals
[2016-04-14T23:30Z] WARN  16:30:44,654 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:30Z] INFO  16:30:44,763 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:30Z] INFO  16:30:44,878 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:30Z] INFO  16:30:44,921 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:30Z] INFO  16:30:44,922 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:30Z] INFO  16:30:44,923 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:30Z] INFO  16:30:44,923 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-14T23:30Z] INFO  16:30:45,014 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:30Z] INFO  16:30:45,028 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:30Z] INFO  16:30:45,087 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-14T23:30Z] INFO  16:30:45,485 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-14T23:30Z] INFO  16:30:45,512 IntervalUtils - Processing 15512566 bp from intervals
[2016-04-14T23:30Z] WARN  16:30:45,517 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:30Z] INFO  16:30:45,583 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:30Z] INFO  16:30:45,594 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:30Z] INFO  16:30:45,637 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:30Z] INFO  16:30:45,643 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-14T23:30Z] INFO  16:30:45,659 IntervalUtils - Processing 15858356 bp from intervals
[2016-04-14T23:30Z] INFO  16:30:45,741 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:30Z] INFO  16:30:45,780 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:30Z] INFO  16:30:45,781 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:30Z] INFO  16:30:45,782 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:30Z] INFO  16:30:45,783 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:30Z] INFO  16:30:45,872 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:30Z] GATK: realign ('7', 94750023, 110303777) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:30Z] INFO  16:30:45,951 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:30Z] INFO  16:30:46,098 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:30Z] INFO  16:30:46,163 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:30Z] INFO  16:30:46,164 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:30Z] INFO  16:30:46,164 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:30Z] INFO  16:30:46,164 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:30Z] INFO  16:30:46,201 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:30Z] INFO  16:30:46,449 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:30Z] INFO  16:30:46,607 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:30Z] INFO  16:30:46,611 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:30Z] INFO  16:30:46,611 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:30Z] INFO  16:30:46,611 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:30Z] INFO  16:30:46,615 HelpFormatter - Program Args: -T PrintReads -L 9:129097485-141213431 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/9/tx/tmpBPqFkR/R14-18102_kapa-NGv3-PE100-NGv3-sort-9_129097484_141213431-prep-prealign.bam
[2016-04-14T23:30Z] INFO  16:30:46,632 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:30Z] INFO  16:30:46,632 HelpFormatter - Date/Time: 2016/04/14 16:30:46
[2016-04-14T23:30Z] INFO  16:30:46,633 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:30Z] INFO  16:30:46,633 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:30Z] INFO  16:30:46,874 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:30Z] INFO  16:30:47,162 ProgressMeter -            done   1.5510186E7    16.0 s       1.0 s      100.0%    16.0 s       0.0 s
[2016-04-14T23:30Z] INFO  16:30:47,163 ProgressMeter - Total runtime 16.74 secs, 0.28 min, 0.00 hours
[2016-04-14T23:30Z] INFO  16:30:47,167 MicroScheduler - 23939 reads were filtered out during the traversal out of approximately 180699 total reads (13.25%)
[2016-04-14T23:30Z] INFO  16:30:47,180 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:30Z] INFO  16:30:47,181 MicroScheduler -   -> 558 reads (0.31% of total) failing BadMateFilter
[2016-04-14T23:30Z] INFO  16:30:47,181 MicroScheduler -   -> 14060 reads (7.78% of total) failing DuplicateReadFilter
[2016-04-14T23:30Z] INFO  16:30:47,182 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-14T23:30Z] INFO  16:30:47,183 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:30Z] INFO  16:30:47,183 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-14T23:30Z] INFO  16:30:47,184 MicroScheduler -   -> 9321 reads (5.16% of total) failing MappingQualityZeroFilter
[2016-04-14T23:30Z] INFO  16:30:47,184 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:30Z] INFO  16:30:47,185 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-14T23:30Z] INFO  16:30:47,186 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-14T23:30Z] INFO  16:30:48,230 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-14T23:30Z] INFO  16:30:48,290 ProgressMeter -            done    121022.0    13.0 s     108.0 s      100.0%    13.0 s       0.0 s
[2016-04-14T23:30Z] INFO  16:30:48,291 ProgressMeter - Total runtime 13.17 secs, 0.22 min, 0.00 hours
[2016-04-14T23:30Z] INFO  16:30:48,294 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 121022 total reads (0.00%)
[2016-04-14T23:30Z] INFO  16:30:48,295 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:30Z] INFO  16:30:48,295 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:30Z] INFO  16:30:48,295 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:30Z] INFO  16:30:48,307 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:30Z] INFO  16:30:48,316 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:30Z] INFO  16:30:48,350 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.03
[2016-04-14T23:30Z] INFO  16:30:48,365 IntervalUtils - Processing 12115947 bp from intervals
[2016-04-14T23:30Z] INFO  16:30:48,438 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:30Z] INFO  16:30:48,634 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:30Z] GATK: realign ('9', 0, 15510186) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:30Z] INFO  16:30:48,778 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:30Z] INFO  16:30:48,782 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:30Z] INFO  16:30:48,782 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:30Z] INFO  16:30:48,783 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:30Z] INFO  16:30:48,787 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/7/R14-18102_kapa-NGv3-PE100-NGv3-sort-7_94750023_110303777-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/7/R14-18102_kapa-NGv3-PE100-NGv3-sort-7_94750023_110303777-prep-prealign-realign.intervals -L 7:94750024-110303777 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/7/tx/tmpyXMpQD/R14-18102_kapa-NGv3-PE100-NGv3-sort-7_94750023_110303777-prep.bam
[2016-04-14T23:30Z] INFO  16:30:48,797 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:30Z] INFO  16:30:48,808 HelpFormatter - Date/Time: 2016/04/14 16:30:48
[2016-04-14T23:30Z] INFO  16:30:48,809 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:30Z] INFO  16:30:48,810 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:30Z] INFO  16:30:48,836 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:30Z] INFO  16:30:48,837 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:30Z] INFO  16:30:48,838 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:30Z] INFO  16:30:48,839 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:30Z] INFO  16:30:48,865 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:30Z] INFO  16:30:48,978 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:30Z] INFO  16:30:49,009 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:30Z] INFO  16:30:49,213 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:30Z] INFO  16:30:49,225 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:30Z] INFO  16:30:49,315 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-14T23:30Z] INFO  16:30:49,671 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:30Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-8_126369460_141889736-prep.bam
[2016-04-14T23:30Z] INFO  16:30:49,739 IntervalUtils - Processing 15553754 bp from intervals
[2016-04-14T23:30Z] INFO  16:30:49,742 ProgressMeter -            done    146037.0    13.0 s      90.0 s      100.0%    13.0 s       0.0 s
[2016-04-14T23:30Z] INFO  16:30:49,742 ProgressMeter - Total runtime 13.18 secs, 0.22 min, 0.00 hours
[2016-04-14T23:30Z] INFO  16:30:49,746 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 146037 total reads (0.00%)
[2016-04-14T23:30Z] INFO  16:30:49,746 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:30Z] INFO  16:30:49,746 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:30Z] INFO  16:30:49,747 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:30Z] WARN  16:30:49,753 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:30Z] INFO  16:30:49,844 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:30Z] INFO  16:30:50,044 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:30Z] INFO  16:30:50,046 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:30Z] INFO  16:30:50,046 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:30Z] INFO  16:30:50,047 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:30Z] GATK pre-alignment ('10', 0, 15559243) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:30Z] INFO  16:30:50,236 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:30Z] INFO  16:30:50,428 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:30Z] INFO  16:30:51,253 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:30Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-8_63775819_79510770-prep.bam
[2016-04-14T23:30Z] INFO  16:30:51,400 ProgressMeter -            done    140677.0    13.0 s      93.0 s      100.0%    13.0 s       0.0 s
[2016-04-14T23:30Z] INFO  16:30:51,400 ProgressMeter - Total runtime 13.13 secs, 0.22 min, 0.00 hours
[2016-04-14T23:30Z] INFO  16:30:51,403 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 140677 total reads (0.00%)
[2016-04-14T23:30Z] INFO  16:30:51,404 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:30Z] INFO  16:30:51,404 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:30Z] INFO  16:30:51,404 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:30Z] INFO  16:30:51,522 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:30Z] INFO  16:30:51,529 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:30Z] INFO  16:30:51,530 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:30Z] INFO  16:30:51,530 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:30Z] INFO  16:30:51,535 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/9/R14-18102_kapa-NGv3-PE100-NGv3-sort-9_0_15510186-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/9/R14-18102_kapa-NGv3-PE100-NGv3-sort-9_0_15510186-prep-prealign-realign.intervals -L 9:1-15510186 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/9/tx/tmpO17Tus/R14-18102_kapa-NGv3-PE100-NGv3-sort-9_0_15510186-prep.bam
[2016-04-14T23:30Z] INFO  16:30:51,564 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:30Z] INFO  16:30:51,572 HelpFormatter - Date/Time: 2016/04/14 16:30:51
[2016-04-14T23:30Z] INFO  16:30:51,573 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:30Z] INFO  16:30:51,573 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:30Z] INFO  16:30:51,824 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:30Z] GATK pre-alignment ('10', 15561288, 31134502) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:30Z] INFO  16:30:51,962 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:30Z] INFO  16:30:51,985 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:30Z] INFO  16:30:52,046 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-14T23:30Z] INFO  16:30:52,450 IntervalUtils - Processing 15510186 bp from intervals
[2016-04-14T23:30Z] WARN  16:30:52,455 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:30Z] INFO  16:30:52,529 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:30Z] INFO  16:30:52,645 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:30Z] INFO  16:30:52,646 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:30Z] INFO  16:30:52,646 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:30Z] INFO  16:30:52,647 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:30Z] INFO  16:30:52,761 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:30Z] INFO  16:30:52,931 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:30Z] INFO  16:30:53,089 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:30Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-8_110656864_126194498-prep.bam
[2016-04-14T23:30Z] INFO  16:30:53,141 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:30Z] INFO  16:30:53,144 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:30Z] INFO  16:30:53,145 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:30Z] INFO  16:30:53,146 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:30Z] INFO  16:30:53,150 HelpFormatter - Program Args: -T PrintReads -L 10:1-15559243 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/10/tx/tmpIOsp0g/R14-18102_kapa-NGv3-PE100-NGv3-sort-10_0_15559243-prep-prealign.bam
[2016-04-14T23:30Z] INFO  16:30:53,162 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:30Z] INFO  16:30:53,173 HelpFormatter - Date/Time: 2016/04/14 16:30:53
[2016-04-14T23:30Z] INFO  16:30:53,174 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:30Z] INFO  16:30:53,175 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:30Z] INFO  16:30:53,363 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:30Z] GATK pre-alignment ('10', 31137459, 46960129) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:30Z] INFO  16:30:54,391 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@7172f77a
[2016-04-14T23:30Z] INFO  16:30:54,499 ProgressMeter -            done    126175.0    23.0 s       3.1 m      100.0%    23.0 s       0.0 s
[2016-04-14T23:30Z] INFO  16:30:54,499 ProgressMeter - Total runtime 23.36 secs, 0.39 min, 0.01 hours
[2016-04-14T23:30Z] INFO  16:30:54,500 MicroScheduler - 96 reads were filtered out during the traversal out of approximately 126271 total reads (0.08%)
[2016-04-14T23:30Z] INFO  16:30:54,500 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:30Z] INFO  16:30:54,501 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:30Z] INFO  16:30:54,501 MicroScheduler -   -> 96 reads (0.08% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:30Z] INFO  16:30:54,508 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-14T23:30Z] INFO  16:30:54,560 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:30Z] INFO  16:30:54,580 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:30Z] INFO  16:30:54,646 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-14T23:30Z] INFO  16:30:54,673 IntervalUtils - Processing 15559243 bp from intervals
[2016-04-14T23:30Z] INFO  16:30:54,756 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:30Z] INFO  16:30:54,754 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:30Z] INFO  16:30:54,757 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:30Z] INFO  16:30:54,758 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:30Z] INFO  16:30:54,758 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:30Z] INFO  16:30:54,763 HelpFormatter - Program Args: -T PrintReads -L 10:15561289-31134502 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/10/tx/tmpUvgzex/R14-18102_kapa-NGv3-PE100-NGv3-sort-10_15561288_31134502-prep-prealign.bam
[2016-04-14T23:30Z] INFO  16:30:54,782 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:30Z] INFO  16:30:54,792 HelpFormatter - Date/Time: 2016/04/14 16:30:54
[2016-04-14T23:30Z] INFO  16:30:54,793 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:30Z] INFO  16:30:54,793 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:30Z] INFO  16:30:55,047 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:30Z] INFO  16:30:55,072 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:30Z] INFO  16:30:55,072 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:30Z] INFO  16:30:55,073 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:30Z] INFO  16:30:55,073 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:30Z] INFO  16:30:55,096 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:30Z] INFO  16:30:55,288 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:30Z] INFO  16:30:56,044 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:30Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-9_15564086_32405601-prep-prealign.bam
[2016-04-14T23:30Z] INFO  16:30:56,166 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-14T23:30Z] INFO  16:30:56,244 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:30Z] INFO  16:30:56,254 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:30Z] INFO  16:30:56,292 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.04
[2016-04-14T23:30Z] INFO  16:30:56,306 IntervalUtils - Processing 15573214 bp from intervals
[2016-04-14T23:30Z] INFO  16:30:56,407 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:30Z] INFO  16:30:56,451 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:30Z] INFO  16:30:56,454 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:30Z] INFO  16:30:56,455 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:30Z] INFO  16:30:56,455 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:30Z] INFO  16:30:56,460 HelpFormatter - Program Args: -T PrintReads -L 10:31137460-46960129 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/10/tx/tmpM2fBp5/R14-18102_kapa-NGv3-PE100-NGv3-sort-10_31137459_46960129-prep-prealign.bam
[2016-04-14T23:30Z] INFO  16:30:56,473 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:30Z] INFO  16:30:56,474 HelpFormatter - Date/Time: 2016/04/14 16:30:56
[2016-04-14T23:30Z] INFO  16:30:56,475 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:30Z] INFO  16:30:56,475 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:30Z] GATK RealignerTargetCreator: R14-18102_kapa-NGv3-PE100-NGv3-sort-9_15564086_32405601-prep-prealign.bam 9:15564087-32405601
[2016-04-14T23:30Z] GATK: RealignerTargetCreator
[2016-04-14T23:30Z] INFO  16:30:56,691 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:30Z] INFO  16:30:56,780 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:30Z] INFO  16:30:56,781 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:30Z] INFO  16:30:56,782 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:30Z] INFO  16:30:56,783 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:30Z] INFO  16:30:56,797 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:30Z] INFO  16:30:56,969 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:30Z] INFO  16:30:57,937 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-14T23:30Z] INFO  16:30:58,005 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:30Z] INFO  16:30:58,014 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:30Z] INFO  16:30:58,068 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-14T23:30Z] INFO  16:30:58,093 IntervalUtils - Processing 15822670 bp from intervals
[2016-04-14T23:30Z] INFO  16:30:58,179 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:30Z] INFO  16:30:58,558 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:30Z] INFO  16:30:58,559 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:30Z] INFO  16:30:58,559 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:30Z] INFO  16:30:58,559 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:30Z] INFO  16:30:58,593 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:30Z] INFO  16:30:58,758 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:30Z] INFO  16:30:59,233 ProgressMeter -            done   4463381.0    14.0 s       3.0 s      100.0%    14.0 s       0.0 s
[2016-04-14T23:30Z] INFO  16:30:59,234 ProgressMeter - Total runtime 14.31 secs, 0.24 min, 0.00 hours
[2016-04-14T23:30Z] INFO  16:30:59,235 MicroScheduler - 40860 reads were filtered out during the traversal out of approximately 380191 total reads (10.75%)
[2016-04-14T23:30Z] INFO  16:30:59,236 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:30Z] INFO  16:30:59,236 MicroScheduler -   -> 730 reads (0.19% of total) failing BadMateFilter
[2016-04-14T23:30Z] INFO  16:30:59,237 MicroScheduler -   -> 31262 reads (8.22% of total) failing DuplicateReadFilter
[2016-04-14T23:30Z] INFO  16:30:59,238 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-14T23:30Z] INFO  16:30:59,238 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:30Z] INFO  16:30:59,239 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-14T23:30Z] INFO  16:30:59,239 MicroScheduler -   -> 8868 reads (2.33% of total) failing MappingQualityZeroFilter
[2016-04-14T23:30Z] INFO  16:30:59,240 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:30Z] INFO  16:30:59,241 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-14T23:30Z] INFO  16:30:59,241 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-14T23:30Z] INFO  16:30:59,750 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:30Z] INFO  16:30:59,754 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:30Z] INFO  16:30:59,754 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:30Z] INFO  16:30:59,755 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:30Z] INFO  16:30:59,759 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/9/R14-18102_kapa-NGv3-PE100-NGv3-sort-9_15564086_32405601-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/9/tx/tmpvTimNy/R14-18102_kapa-NGv3-PE100-NGv3-sort-9_15564086_32405601-prep-prealign-realign.intervals -l INFO -L 9:15564087-32405601 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-14T23:30Z] INFO  16:30:59,775 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:30Z] INFO  16:30:59,776 HelpFormatter - Date/Time: 2016/04/14 16:30:59
[2016-04-14T23:30Z] INFO  16:30:59,776 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:30Z] INFO  16:30:59,777 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:30Z] INFO  16:30:59,883 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:31Z] INFO  16:31:00,089 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-14T23:31Z] INFO  16:31:00,101 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:31Z] INFO  16:31:00,158 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-14T23:31Z] INFO  16:31:00,549 IntervalUtils - Processing 16841515 bp from intervals
[2016-04-14T23:31Z] WARN  16:31:00,554 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:31Z] INFO  16:31:00,711 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:31Z] INFO  16:31:00,775 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:31Z] GATK: realign ('8', 141900641, 146364022) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:31Z] INFO  16:31:00,873 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:31Z] INFO  16:31:00,874 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:31Z] INFO  16:31:00,874 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:31Z] INFO  16:31:00,874 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-14T23:31Z] INFO  16:31:01,807 ProgressMeter -      9:35704627    100002.0    30.0 s       5.0 m       10.0%     5.0 m       4.5 m
[2016-04-14T23:31Z] INFO  16:31:03,158 ProgressMeter -            done    203490.0    17.0 s      85.0 s      100.0%    17.0 s       0.0 s
[2016-04-14T23:31Z] INFO  16:31:03,158 ProgressMeter - Total runtime 17.38 secs, 0.29 min, 0.00 hours
[2016-04-14T23:31Z] INFO  16:31:03,161 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 203490 total reads (0.00%)
[2016-04-14T23:31Z] INFO  16:31:03,162 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:31Z] INFO  16:31:03,162 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:31Z] INFO  16:31:03,162 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:31Z] INFO  16:31:03,492 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:31Z] INFO  16:31:03,496 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:31Z] INFO  16:31:03,497 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:31Z] INFO  16:31:03,497 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:31Z] INFO  16:31:03,502 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/8/R14-18102_kapa-NGv3-PE100-NGv3-sort-8_141900641_146364022-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/8/R14-18102_kapa-NGv3-PE100-NGv3-sort-8_141900641_146364022-prep-prealign-realign.intervals -L 8:141900642-146364022 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/8/tx/tmpxNdtxC/R14-18102_kapa-NGv3-PE100-NGv3-sort-8_141900641_146364022-prep.bam
[2016-04-14T23:31Z] INFO  16:31:03,522 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:31Z] INFO  16:31:03,523 HelpFormatter - Date/Time: 2016/04/14 16:31:03
[2016-04-14T23:31Z] INFO  16:31:03,523 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:31Z] INFO  16:31:03,524 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:31Z] INFO  16:31:03,527 ProgressMeter -     7:156799169    400014.0    30.0 s      77.0 s       97.7%    30.0 s       0.0 s
[2016-04-14T23:31Z] INFO  16:31:03,786 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:31Z] INFO  16:31:03,879 ProgressMeter -            done    456560.0    31.0 s      68.0 s      100.0%    31.0 s       0.0 s
[2016-04-14T23:31Z] INFO  16:31:03,879 ProgressMeter - Total runtime 31.28 secs, 0.52 min, 0.01 hours
[2016-04-14T23:31Z] INFO  16:31:03,883 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 456560 total reads (0.00%)
[2016-04-14T23:31Z] INFO  16:31:03,884 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:31Z] INFO  16:31:03,884 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:31Z] INFO  16:31:03,884 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:31Z] INFO  16:31:03,900 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:31Z] INFO  16:31:03,910 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:31Z] INFO  16:31:03,960 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-14T23:31Z] INFO  16:31:04,304 IntervalUtils - Processing 4463381 bp from intervals
[2016-04-14T23:31Z] WARN  16:31:04,309 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:31Z] INFO  16:31:04,390 ProgressMeter -            done    346268.0    23.0 s      67.0 s      100.0%    23.0 s       0.0 s
[2016-04-14T23:31Z] INFO  16:31:04,391 ProgressMeter - Total runtime 23.47 secs, 0.39 min, 0.01 hours
[2016-04-14T23:31Z] INFO  16:31:04,395 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 346268 total reads (0.00%)
[2016-04-14T23:31Z] INFO  16:31:04,395 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:31Z] INFO  16:31:04,395 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:31Z] INFO  16:31:04,396 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:31Z] INFO  16:31:04,464 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:31Z] INFO  16:31:04,555 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:31Z] INFO  16:31:04,556 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:31Z] INFO  16:31:04,557 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:31Z] INFO  16:31:04,558 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:31Z] INFO  16:31:04,589 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:31Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-8_95142853_110655419-prep.bam
[2016-04-14T23:31Z] INFO  16:31:04,668 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:31Z] INFO  16:31:04,718 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:31Z] GATK pre-alignment ('10', 46960410, 62493077) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:31Z] INFO  16:31:05,557 ProgressMeter -            done    180070.0    12.0 s      71.0 s      100.0%    12.0 s       0.0 s
[2016-04-14T23:31Z] INFO  16:31:05,557 ProgressMeter - Total runtime 12.91 secs, 0.22 min, 0.00 hours
[2016-04-14T23:31Z] INFO  16:31:05,560 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 180070 total reads (0.00%)
[2016-04-14T23:31Z] INFO  16:31:05,561 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:31Z] INFO  16:31:05,561 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:31Z] INFO  16:31:05,561 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:31Z] INFO  16:31:05,689 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:31Z] INFO  16:31:05,713 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:31Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-8_15519664_31030618-prep.bam
[2016-04-14T23:31Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-7_141629903_157151331-prep.bam
[2016-04-14T23:31Z] GATK pre-alignment ('10', 62539923, 78084243) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:31Z] INFO  16:31:07,256 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:31Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-9_0_15510186-prep.bam
[2016-04-14T23:31Z] GATK pre-alignment ('10', 78316966, 93841258) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:31Z] GATK pre-alignment ('10', 93851586, 111625070) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:31Z] INFO  16:31:08,052 ProgressMeter -      9:95050594    200004.0    30.0 s       2.5 m       82.8%    36.0 s       6.0 s
[2016-04-14T23:31Z] INFO  16:31:08,116 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:31Z] INFO  16:31:08,121 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:31Z] INFO  16:31:08,121 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:31Z] INFO  16:31:08,122 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:31Z] INFO  16:31:08,128 HelpFormatter - Program Args: -T PrintReads -L 10:46960411-62493077 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/10/tx/tmp2m9Xul/R14-18102_kapa-NGv3-PE100-NGv3-sort-10_46960410_62493077-prep-prealign.bam
[2016-04-14T23:31Z] INFO  16:31:08,147 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:31Z] INFO  16:31:08,158 HelpFormatter - Date/Time: 2016/04/14 16:31:08
[2016-04-14T23:31Z] INFO  16:31:08,159 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:31Z] INFO  16:31:08,159 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:31Z] INFO  16:31:08,385 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:31Z] INFO  16:31:08,918 ProgressMeter -      9:80921300    200004.0    30.0 s       2.5 m       92.4%    32.0 s       2.0 s
[2016-04-14T23:31Z] INFO  16:31:09,138 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@6834dd3c
[2016-04-14T23:31Z] INFO  16:31:09,251 ProgressMeter -            done    238003.0    30.0 s       2.2 m      100.0%    30.0 s       0.0 s
[2016-04-14T23:31Z] INFO  16:31:09,252 ProgressMeter - Total runtime 30.91 secs, 0.52 min, 0.01 hours
[2016-04-14T23:31Z] INFO  16:31:09,253 MicroScheduler - 169 reads were filtered out during the traversal out of approximately 238172 total reads (0.07%)
[2016-04-14T23:31Z] INFO  16:31:09,253 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:31Z] INFO  16:31:09,253 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:31Z] INFO  16:31:09,254 MicroScheduler -   -> 169 reads (0.07% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:31Z] INFO  16:31:09,322 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:31Z] INFO  16:31:09,325 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:31Z] INFO  16:31:09,325 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:31Z] INFO  16:31:09,326 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:31Z] INFO  16:31:09,330 HelpFormatter - Program Args: -T PrintReads -L 10:62539924-78084243 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/10/tx/tmpjSPHIA/R14-18102_kapa-NGv3-PE100-NGv3-sort-10_62539923_78084243-prep-prealign.bam
[2016-04-14T23:31Z] INFO  16:31:09,339 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:31Z] INFO  16:31:09,340 HelpFormatter - Date/Time: 2016/04/14 16:31:09
[2016-04-14T23:31Z] INFO  16:31:09,340 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:31Z] INFO  16:31:09,341 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:31Z] INFO  16:31:09,510 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-14T23:31Z] INFO  16:31:09,515 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:31Z] INFO  16:31:09,576 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:31Z] INFO  16:31:09,585 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:31Z] INFO  16:31:09,619 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.03
[2016-04-14T23:31Z] INFO  16:31:09,634 IntervalUtils - Processing 15532667 bp from intervals
[2016-04-14T23:31Z] INFO  16:31:09,704 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:31Z] INFO  16:31:10,049 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:31Z] INFO  16:31:10,050 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:31Z] INFO  16:31:10,051 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:31Z] INFO  16:31:10,052 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:31Z] INFO  16:31:10,075 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:31Z] INFO  16:31:10,179 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:31Z] INFO  16:31:10,183 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:31Z] INFO  16:31:10,183 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:31Z] INFO  16:31:10,184 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:31Z] INFO  16:31:10,189 HelpFormatter - Program Args: -T PrintReads -L 10:78316967-93841258 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/10/tx/tmpfMZG_0/R14-18102_kapa-NGv3-PE100-NGv3-sort-10_78316966_93841258-prep-prealign.bam
[2016-04-14T23:31Z] INFO  16:31:10,237 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:31Z] INFO  16:31:10,243 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:31Z] INFO  16:31:10,245 HelpFormatter - Date/Time: 2016/04/14 16:31:10
[2016-04-14T23:31Z] INFO  16:31:10,245 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:31Z] INFO  16:31:10,246 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:31Z] INFO  16:31:10,424 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:31Z] INFO  16:31:10,646 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-14T23:31Z] INFO  16:31:10,700 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:31Z] INFO  16:31:10,713 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:31Z] INFO  16:31:10,752 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.04
[2016-04-14T23:31Z] INFO  16:31:10,760 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:31Z] INFO  16:31:10,767 IntervalUtils - Processing 15544320 bp from intervals
[2016-04-14T23:31Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-9_65507205_82187750-prep-prealign.bam
[2016-04-14T23:31Z] INFO  16:31:10,840 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:31Z] INFO  16:31:10,843 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:31Z] INFO  16:31:10,844 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:31Z] INFO  16:31:10,845 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:31Z] INFO  16:31:10,849 HelpFormatter - Program Args: -T PrintReads -L 10:93851587-111625070 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/10/tx/tmp9iMeDa/R14-18102_kapa-NGv3-PE100-NGv3-sort-10_93851586_111625070-prep-prealign.bam
[2016-04-14T23:31Z] INFO  16:31:10,858 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:31Z] INFO  16:31:10,863 HelpFormatter - Date/Time: 2016/04/14 16:31:10
[2016-04-14T23:31Z] INFO  16:31:10,864 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:31Z] INFO  16:31:10,865 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:31Z] INFO  16:31:10,886 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:31Z] INFO  16:31:11,031 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:31Z] INFO  16:31:11,166 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:31Z] INFO  16:31:11,167 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:31Z] INFO  16:31:11,168 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:31Z] INFO  16:31:11,168 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:31Z] INFO  16:31:11,182 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:31Z] INFO  16:31:11,325 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:31Z] INFO  16:31:11,569 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-14T23:31Z] INFO  16:31:11,624 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:31Z] INFO  16:31:11,634 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:31Z] GATK RealignerTargetCreator: R14-18102_kapa-NGv3-PE100-NGv3-sort-9_65507205_82187750-prep-prealign.bam 9:65507206-82187750
[2016-04-14T23:31Z] GATK: RealignerTargetCreator
[2016-04-14T23:31Z] INFO  16:31:11,698 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-14T23:31Z] INFO  16:31:11,712 IntervalUtils - Processing 15524292 bp from intervals
[2016-04-14T23:31Z] INFO  16:31:11,822 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:31Z] INFO  16:31:12,163 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:31Z] INFO  16:31:12,164 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:31Z] INFO  16:31:12,165 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:31Z] INFO  16:31:12,166 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:31Z] INFO  16:31:12,179 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:31Z] INFO  16:31:12,191 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-14T23:31Z] INFO  16:31:12,249 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:31Z] INFO  16:31:12,258 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:31Z] INFO  16:31:12,303 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-14T23:31Z] INFO  16:31:12,319 IntervalUtils - Processing 17773484 bp from intervals
[2016-04-14T23:31Z] INFO  16:31:12,361 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:31Z] INFO  16:31:12,395 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:31Z] INFO  16:31:12,780 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:31Z] INFO  16:31:12,782 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:31Z] INFO  16:31:12,783 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:31Z] INFO  16:31:12,783 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:31Z] INFO  16:31:12,808 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:31Z] INFO  16:31:13,018 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:31Z] INFO  16:31:14,310 ProgressMeter -     9:111625539    200003.0    30.0 s       2.5 m       89.7%    33.0 s       3.0 s
[2016-04-14T23:31Z] INFO  16:31:14,776 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:31Z] INFO  16:31:14,780 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:31Z] INFO  16:31:14,781 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:31Z] INFO  16:31:14,781 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:31Z] INFO  16:31:14,786 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/9/R14-18102_kapa-NGv3-PE100-NGv3-sort-9_65507205_82187750-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/9/tx/tmpG8B6xi/R14-18102_kapa-NGv3-PE100-NGv3-sort-9_65507205_82187750-prep-prealign-realign.intervals -l INFO -L 9:65507206-82187750 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-14T23:31Z] INFO  16:31:14,796 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:31Z] INFO  16:31:14,807 HelpFormatter - Date/Time: 2016/04/14 16:31:14
[2016-04-14T23:31Z] INFO  16:31:14,808 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:31Z] INFO  16:31:14,809 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:31Z] INFO  16:31:14,941 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:31Z] INFO  16:31:15,190 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-14T23:31Z] INFO  16:31:15,200 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:31Z] INFO  16:31:15,276 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-14T23:31Z] INFO  16:31:15,573 IntervalUtils - Processing 16680545 bp from intervals
[2016-04-14T23:31Z] WARN  16:31:15,579 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:31Z] INFO  16:31:15,705 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:31Z] INFO  16:31:15,921 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:31Z] INFO  16:31:15,922 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:31Z] INFO  16:31:15,923 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:31Z] INFO  16:31:15,924 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-14T23:31Z] INFO  16:31:16,191 ProgressMeter -     9:123943918    200004.0    30.0 s       2.5 m       67.6%    44.0 s      14.0 s
[2016-04-14T23:31Z] INFO  16:31:17,757 ProgressMeter -            done   1.6841515E7    16.0 s       1.0 s      100.0%    16.0 s       0.0 s
[2016-04-14T23:31Z] INFO  16:31:17,759 ProgressMeter - Total runtime 16.89 secs, 0.28 min, 0.00 hours
[2016-04-14T23:31Z] INFO  16:31:17,779 MicroScheduler - 13232 reads were filtered out during the traversal out of approximately 127363 total reads (10.39%)
[2016-04-14T23:31Z] INFO  16:31:17,795 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:31Z] INFO  16:31:17,795 MicroScheduler -   -> 463 reads (0.36% of total) failing BadMateFilter
[2016-04-14T23:31Z] INFO  16:31:17,795 MicroScheduler -   -> 10019 reads (7.87% of total) failing DuplicateReadFilter
[2016-04-14T23:31Z] INFO  16:31:17,796 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-14T23:31Z] INFO  16:31:17,796 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:31Z] INFO  16:31:17,796 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-14T23:31Z] INFO  16:31:17,796 MicroScheduler -   -> 2750 reads (2.16% of total) failing MappingQualityZeroFilter
[2016-04-14T23:31Z] INFO  16:31:17,797 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:31Z] INFO  16:31:17,797 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-14T23:31Z] INFO  16:31:17,797 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-14T23:31Z] INFO  16:31:18,110 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@41fd9d8e
[2016-04-14T23:31Z] INFO  16:31:18,219 ProgressMeter -            done    326222.0    40.0 s       2.1 m      100.0%    40.0 s       0.0 s
[2016-04-14T23:31Z] INFO  16:31:18,219 ProgressMeter - Total runtime 40.18 secs, 0.67 min, 0.01 hours
[2016-04-14T23:31Z] INFO  16:31:18,220 MicroScheduler - 192 reads were filtered out during the traversal out of approximately 326414 total reads (0.06%)
[2016-04-14T23:31Z] INFO  16:31:18,220 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:31Z] INFO  16:31:18,220 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:31Z] INFO  16:31:18,220 MicroScheduler -   -> 192 reads (0.06% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:31Z] INFO  16:31:18,863 ProgressMeter -     9:131784681    200004.0    30.0 s       2.5 m       22.2%     2.3 m     105.0 s
[2016-04-14T23:31Z] INFO  16:31:19,140 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:31Z] GATK: realign ('9', 15564086, 32405601) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:31Z] INFO  16:31:19,574 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:31Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-9_82188172_97717561-prep-prealign.bam
[2016-04-14T23:31Z] INFO  16:31:20,093 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@41fd9d8e
[2016-04-14T23:31Z] INFO  16:31:20,249 ProgressMeter -            done    299640.0    35.0 s     120.0 s      100.0%    35.0 s       0.0 s
[2016-04-14T23:31Z] INFO  16:31:20,250 ProgressMeter - Total runtime 35.97 secs, 0.60 min, 0.01 hours
[2016-04-14T23:31Z] INFO  16:31:20,250 MicroScheduler - 161 reads were filtered out during the traversal out of approximately 299801 total reads (0.05%)
[2016-04-14T23:31Z] INFO  16:31:20,251 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:31Z] INFO  16:31:20,251 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:31Z] INFO  16:31:20,251 MicroScheduler -   -> 161 reads (0.05% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:31Z] GATK RealignerTargetCreator: R14-18102_kapa-NGv3-PE100-NGv3-sort-9_82188172_97717561-prep-prealign.bam 9:82188173-97717561
[2016-04-14T23:31Z] GATK: RealignerTargetCreator
[2016-04-14T23:31Z] INFO  16:31:21,685 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:31Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-9_97718189_113228306-prep-prealign.bam
[2016-04-14T23:31Z] INFO  16:31:21,960 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:31Z] INFO  16:31:21,963 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:31Z] INFO  16:31:21,963 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:31Z] INFO  16:31:21,964 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:31Z] INFO  16:31:21,977 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/9/R14-18102_kapa-NGv3-PE100-NGv3-sort-9_15564086_32405601-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/9/R14-18102_kapa-NGv3-PE100-NGv3-sort-9_15564086_32405601-prep-prealign-realign.intervals -L 9:15564087-32405601 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/9/tx/tmpq4SDAE/R14-18102_kapa-NGv3-PE100-NGv3-sort-9_15564086_32405601-prep.bam
[2016-04-14T23:31Z] INFO  16:31:22,012 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:31Z] INFO  16:31:22,013 HelpFormatter - Date/Time: 2016/04/14 16:31:21
[2016-04-14T23:31Z] INFO  16:31:22,014 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:31Z] INFO  16:31:22,014 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:31Z] INFO  16:31:22,146 ProgressMeter -     7:100684883    400004.0    32.0 s      80.0 s       38.2%    83.0 s      51.0 s
[2016-04-14T23:31Z] INFO  16:31:22,242 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:31Z] INFO  16:31:22,357 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:31Z] INFO  16:31:22,366 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:31Z] INFO  16:31:22,421 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-14T23:31Z] GATK RealignerTargetCreator: R14-18102_kapa-NGv3-PE100-NGv3-sort-9_97718189_113228306-prep-prealign.bam 9:97718190-113228306
[2016-04-14T23:31Z] GATK: RealignerTargetCreator
[2016-04-14T23:31Z] INFO  16:31:22,922 IntervalUtils - Processing 16841515 bp from intervals
[2016-04-14T23:31Z] WARN  16:31:22,928 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:31Z] INFO  16:31:23,052 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:31Z] INFO  16:31:23,243 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:31Z] INFO  16:31:23,245 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:31Z] INFO  16:31:23,246 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:31Z] INFO  16:31:23,251 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:31Z] INFO  16:31:23,252 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@52f3b59
[2016-04-14T23:31Z] INFO  16:31:23,325 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:31Z] INFO  16:31:23,328 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:31Z] INFO  16:31:23,329 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:31Z] INFO  16:31:23,329 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:31Z] INFO  16:31:23,334 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/9/R14-18102_kapa-NGv3-PE100-NGv3-sort-9_82188172_97717561-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/9/tx/tmpLGQelp/R14-18102_kapa-NGv3-PE100-NGv3-sort-9_82188172_97717561-prep-prealign-realign.intervals -l INFO -L 9:82188173-97717561 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-14T23:31Z] INFO  16:31:23,354 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:31Z] INFO  16:31:23,366 HelpFormatter - Date/Time: 2016/04/14 16:31:23
[2016-04-14T23:31Z] INFO  16:31:23,367 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:31Z] INFO  16:31:23,368 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:31Z] INFO  16:31:23,382 ProgressMeter -            done    202099.0    26.0 s       2.2 m      100.0%    26.0 s       0.0 s
[2016-04-14T23:31Z] INFO  16:31:23,382 ProgressMeter - Total runtime 26.60 secs, 0.44 min, 0.01 hours
[2016-04-14T23:31Z] INFO  16:31:23,383 MicroScheduler - 141 reads were filtered out during the traversal out of approximately 202240 total reads (0.07%)
[2016-04-14T23:31Z] INFO  16:31:23,383 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:31Z] INFO  16:31:23,384 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:31Z] INFO  16:31:23,384 MicroScheduler -   -> 141 reads (0.07% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:31Z] INFO  16:31:23,447 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:31Z] INFO  16:31:23,473 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:31Z] INFO  16:31:23,657 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:31Z] INFO  16:31:23,754 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-14T23:31Z] INFO  16:31:23,764 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:31Z] INFO  16:31:23,832 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-14T23:31Z] INFO  16:31:24,136 IntervalUtils - Processing 15529389 bp from intervals
[2016-04-14T23:31Z] WARN  16:31:24,141 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:31Z] INFO  16:31:24,214 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:31Z] INFO  16:31:24,252 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@41fd9d8e
[2016-04-14T23:31Z] INFO  16:31:24,344 ProgressMeter -            done    223828.0    29.0 s       2.2 m      100.0%    29.0 s       0.0 s
[2016-04-14T23:31Z] INFO  16:31:24,345 ProgressMeter - Total runtime 29.27 secs, 0.49 min, 0.01 hours
[2016-04-14T23:31Z] INFO  16:31:24,346 MicroScheduler - 159 reads were filtered out during the traversal out of approximately 223987 total reads (0.07%)
[2016-04-14T23:31Z] INFO  16:31:24,347 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:31Z] INFO  16:31:24,348 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:31Z] INFO  16:31:24,348 MicroScheduler -   -> 159 reads (0.07% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:31Z] INFO  16:31:24,457 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:31Z] INFO  16:31:24,469 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:31Z] INFO  16:31:24,470 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:31Z] INFO  16:31:24,470 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-14T23:31Z] INFO  16:31:24,865 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:31Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-10_15561288_31134502-prep-prealign.bam
[2016-04-14T23:31Z] GATK RealignerTargetCreator: R14-18102_kapa-NGv3-PE100-NGv3-sort-10_15561288_31134502-prep-prealign.bam 10:15561289-31134502
[2016-04-14T23:31Z] GATK: RealignerTargetCreator
[2016-04-14T23:31Z] INFO  16:31:25,609 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:31Z] INFO  16:31:25,612 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:31Z] INFO  16:31:25,612 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:31Z] INFO  16:31:25,613 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:31Z] INFO  16:31:25,629 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/9/R14-18102_kapa-NGv3-PE100-NGv3-sort-9_97718189_113228306-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/9/tx/tmpS5d8r1/R14-18102_kapa-NGv3-PE100-NGv3-sort-9_97718189_113228306-prep-prealign-realign.intervals -l INFO -L 9:97718190-113228306 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-14T23:31Z] INFO  16:31:25,642 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:31Z] INFO  16:31:25,642 HelpFormatter - Date/Time: 2016/04/14 16:31:25
[2016-04-14T23:31Z] INFO  16:31:25,643 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:31Z] INFO  16:31:25,643 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:31Z] INFO  16:31:25,737 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:31Z] INFO  16:31:25,822 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:31Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-10_0_15559243-prep-prealign.bam
[2016-04-14T23:31Z] INFO  16:31:25,930 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-14T23:31Z] INFO  16:31:25,939 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:31Z] INFO  16:31:26,015 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-14T23:31Z] INFO  16:31:26,093 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@7172f77a
[2016-04-14T23:31Z] INFO  16:31:26,214 ProgressMeter -            done    207883.0    27.0 s       2.2 m      100.0%    27.0 s       0.0 s
[2016-04-14T23:31Z] INFO  16:31:26,214 ProgressMeter - Total runtime 27.66 secs, 0.46 min, 0.01 hours
[2016-04-14T23:31Z] INFO  16:31:26,215 MicroScheduler - 551 reads were filtered out during the traversal out of approximately 208434 total reads (0.26%)
[2016-04-14T23:31Z] INFO  16:31:26,215 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:31Z] INFO  16:31:26,215 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:31Z] INFO  16:31:26,216 MicroScheduler -   -> 551 reads (0.26% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:31Z] INFO  16:31:26,321 IntervalUtils - Processing 15510117 bp from intervals
[2016-04-14T23:31Z] WARN  16:31:26,326 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:31Z] INFO  16:31:26,515 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:31Z] INFO  16:31:26,648 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:31Z] INFO  16:31:26,650 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:31Z] GATK RealignerTargetCreator: R14-18102_kapa-NGv3-PE100-NGv3-sort-10_0_15559243-prep-prealign.bam 10:1-15559243
[2016-04-14T23:31Z] INFO  16:31:26,651 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:31Z] INFO  16:31:26,652 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-14T23:31Z] GATK: RealignerTargetCreator
[2016-04-14T23:31Z] INFO  16:31:27,655 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:31Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-10_31137459_46960129-prep-prealign.bam
[2016-04-14T23:31Z] GATK RealignerTargetCreator: R14-18102_kapa-NGv3-PE100-NGv3-sort-10_31137459_46960129-prep-prealign.bam 10:31137460-46960129
[2016-04-14T23:31Z] GATK: RealignerTargetCreator
[2016-04-14T23:31Z] INFO  16:31:28,376 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:31Z] INFO  16:31:28,379 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:31Z] INFO  16:31:28,380 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:31Z] INFO  16:31:28,381 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:31Z] INFO  16:31:28,385 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/10/R14-18102_kapa-NGv3-PE100-NGv3-sort-10_15561288_31134502-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/10/tx/tmpBayR2n/R14-18102_kapa-NGv3-PE100-NGv3-sort-10_15561288_31134502-prep-prealign-realign.intervals -l INFO -L 10:15561289-31134502 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-14T23:31Z] INFO  16:31:28,411 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:31Z] INFO  16:31:28,412 HelpFormatter - Date/Time: 2016/04/14 16:31:28
[2016-04-14T23:31Z] INFO  16:31:28,412 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:31Z] INFO  16:31:28,413 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:31Z] INFO  16:31:28,514 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:31Z] INFO  16:31:28,746 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@41fd9d8e
[2016-04-14T23:31Z] INFO  16:31:28,778 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-14T23:31Z] INFO  16:31:28,802 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:31Z] INFO  16:31:28,870 ProgressMeter -            done    351620.0    42.0 s       2.0 m      100.0%    42.0 s       0.0 s
[2016-04-14T23:31Z] INFO  16:31:28,871 ProgressMeter - Total runtime 42.71 secs, 0.71 min, 0.01 hours
[2016-04-14T23:31Z] INFO  16:31:28,871 MicroScheduler - 168 reads were filtered out during the traversal out of approximately 351788 total reads (0.05%)
[2016-04-14T23:31Z] INFO  16:31:28,872 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:31Z] INFO  16:31:28,872 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:31Z] INFO  16:31:28,872 MicroScheduler -   -> 168 reads (0.05% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:31Z] INFO  16:31:28,892 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.09
[2016-04-14T23:31Z] INFO  16:31:29,318 IntervalUtils - Processing 15573214 bp from intervals
[2016-04-14T23:31Z] WARN  16:31:29,324 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:31Z] INFO  16:31:29,424 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:31Z] INFO  16:31:29,579 ProgressMeter -            done    378277.0    25.0 s      66.0 s       98.1%    25.0 s       0.0 s
[2016-04-14T23:31Z] INFO  16:31:29,580 ProgressMeter - Total runtime 25.02 secs, 0.42 min, 0.01 hours
[2016-04-14T23:31Z] INFO  16:31:29,583 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 378277 total reads (0.00%)
[2016-04-14T23:31Z] INFO  16:31:29,584 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:31Z] INFO  16:31:29,584 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:31Z] INFO  16:31:29,584 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:31Z] INFO  16:31:29,651 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:31Z] INFO  16:31:29,652 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:31Z] INFO  16:31:29,653 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:31Z] INFO  16:31:29,653 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-14T23:31Z] INFO  16:31:29,786 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:31Z] INFO  16:31:29,789 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:31Z] INFO  16:31:29,790 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:31Z] INFO  16:31:29,790 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:31Z] INFO  16:31:29,794 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/10/R14-18102_kapa-NGv3-PE100-NGv3-sort-10_0_15559243-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/10/tx/tmpUlINOO/R14-18102_kapa-NGv3-PE100-NGv3-sort-10_0_15559243-prep-prealign-realign.intervals -l INFO -L 10:1-15559243 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-14T23:31Z] INFO  16:31:29,812 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:31Z] INFO  16:31:29,813 HelpFormatter - Date/Time: 2016/04/14 16:31:29
[2016-04-14T23:31Z] INFO  16:31:29,814 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:31Z] INFO  16:31:29,814 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:31Z] INFO  16:31:29,921 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:31Z] INFO  16:31:30,146 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-14T23:31Z] INFO  16:31:30,155 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:31Z] INFO  16:31:30,221 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-14T23:31Z] INFO  16:31:30,498 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:31Z] INFO  16:31:30,511 IntervalUtils - Processing 15559243 bp from intervals
[2016-04-14T23:31Z] WARN  16:31:30,517 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:31Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-9_113231219_129089575-prep-prealign.bam
[2016-04-14T23:31Z] INFO  16:31:30,620 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:31Z] INFO  16:31:30,898 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:31Z] INFO  16:31:30,900 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:31Z] INFO  16:31:30,901 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:31Z] INFO  16:31:30,902 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-14T23:31Z] INFO  16:31:31,001 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:31Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-8_141900641_146364022-prep.bam
[2016-04-14T23:31Z] INFO  16:31:31,241 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:31Z] INFO  16:31:31,244 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:31Z] INFO  16:31:31,244 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:31Z] INFO  16:31:31,245 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:31Z] INFO  16:31:31,249 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/10/R14-18102_kapa-NGv3-PE100-NGv3-sort-10_31137459_46960129-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/10/tx/tmpEBd3IR/R14-18102_kapa-NGv3-PE100-NGv3-sort-10_31137459_46960129-prep-prealign-realign.intervals -l INFO -L 10:31137460-46960129 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-14T23:31Z] INFO  16:31:31,259 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:31Z] INFO  16:31:31,269 HelpFormatter - Date/Time: 2016/04/14 16:31:31
[2016-04-14T23:31Z] INFO  16:31:31,270 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:31Z] INFO  16:31:31,271 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:31Z] INFO  16:31:31,346 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@7172f77a
[2016-04-14T23:31Z] INFO  16:31:31,386 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:31Z] INFO  16:31:31,469 ProgressMeter -            done    485974.0    59.0 s       2.0 m      100.0%    59.0 s       0.0 s
[2016-04-14T23:31Z] INFO  16:31:31,470 ProgressMeter - Total runtime 59.70 secs, 1.00 min, 0.02 hours
[2016-04-14T23:31Z] INFO  16:31:31,470 MicroScheduler - 232 reads were filtered out during the traversal out of approximately 486206 total reads (0.05%)
[2016-04-14T23:31Z] INFO  16:31:31,471 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:31Z] INFO  16:31:31,471 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:31Z] INFO  16:31:31,471 MicroScheduler -   -> 232 reads (0.05% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:31Z] INFO  16:31:31,602 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-14T23:31Z] INFO  16:31:31,616 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:31Z] INFO  16:31:31,685 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-14T23:31Z] GATK RealignerTargetCreator: R14-18102_kapa-NGv3-PE100-NGv3-sort-9_113231219_129089575-prep-prealign.bam 9:113231220-129089575
[2016-04-14T23:31Z] GATK: RealignerTargetCreator
[2016-04-14T23:31Z] INFO  16:31:31,987 IntervalUtils - Processing 15822670 bp from intervals
[2016-04-14T23:31Z] WARN  16:31:32,003 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:31Z] INFO  16:31:32,114 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:31Z] GATK pre-alignment ('10', 111628371, 127265443) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:31Z] INFO  16:31:32,351 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:31Z] INFO  16:31:32,351 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:31Z] INFO  16:31:32,352 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:31Z] INFO  16:31:32,352 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-14T23:31Z] INFO  16:31:32,810 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:31Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-9_32407258_65506776-prep-prealign.bam
[2016-04-14T23:31Z] INFO  16:31:34,413 ProgressMeter -            done   1.6680545E7    18.0 s       1.0 s      100.0%    18.0 s       0.0 s
[2016-04-14T23:31Z] INFO  16:31:34,415 ProgressMeter - Total runtime 18.49 secs, 0.31 min, 0.01 hours
[2016-04-14T23:31Z] INFO  16:31:34,419 MicroScheduler - 90087 reads were filtered out during the traversal out of approximately 239009 total reads (37.69%)
[2016-04-14T23:31Z] INFO  16:31:34,420 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:31Z] INFO  16:31:34,420 MicroScheduler -   -> 524 reads (0.22% of total) failing BadMateFilter
[2016-04-14T23:31Z] INFO  16:31:34,421 MicroScheduler -   -> 13180 reads (5.51% of total) failing DuplicateReadFilter
[2016-04-14T23:31Z] INFO  16:31:34,422 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-14T23:31Z] INFO  16:31:34,422 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:31Z] INFO  16:31:34,423 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-14T23:31Z] INFO  16:31:34,423 MicroScheduler -   -> 76383 reads (31.96% of total) failing MappingQualityZeroFilter
[2016-04-14T23:31Z] INFO  16:31:34,424 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:31Z] INFO  16:31:34,425 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-14T23:31Z] INFO  16:31:34,425 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-14T23:31Z] GATK RealignerTargetCreator: R14-18102_kapa-NGv3-PE100-NGv3-sort-9_32407258_65506776-prep-prealign.bam 9:32407259-65506776
[2016-04-14T23:31Z] GATK: RealignerTargetCreator
[2016-04-14T23:31Z] INFO  16:31:34,615 ProgressMeter -            done    126175.0    11.0 s      90.0 s      100.0%    11.0 s       0.0 s
[2016-04-14T23:31Z] INFO  16:31:34,616 ProgressMeter - Total runtime 11.37 secs, 0.19 min, 0.00 hours
[2016-04-14T23:31Z] INFO  16:31:34,619 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 126175 total reads (0.00%)
[2016-04-14T23:31Z] INFO  16:31:34,620 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:31Z] INFO  16:31:34,620 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:31Z] INFO  16:31:34,620 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:31Z] INFO  16:31:34,742 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:31Z] INFO  16:31:34,745 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:31Z] INFO  16:31:34,745 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:31Z] INFO  16:31:34,746 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:31Z] INFO  16:31:34,751 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/9/R14-18102_kapa-NGv3-PE100-NGv3-sort-9_113231219_129089575-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/9/tx/tmpsIJj3A/R14-18102_kapa-NGv3-PE100-NGv3-sort-9_113231219_129089575-prep-prealign-realign.intervals -l INFO -L 9:113231220-129089575 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-14T23:31Z] INFO  16:31:34,761 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:31Z] INFO  16:31:34,769 HelpFormatter - Date/Time: 2016/04/14 16:31:34
[2016-04-14T23:31Z] INFO  16:31:34,770 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:31Z] INFO  16:31:34,771 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:31Z] INFO  16:31:34,902 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:31Z] INFO  16:31:35,158 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-14T23:31Z] INFO  16:31:35,169 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:31Z] INFO  16:31:35,219 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-14T23:31Z] INFO  16:31:35,259 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:31Z] INFO  16:31:35,263 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:31Z] INFO  16:31:35,264 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:31Z] INFO  16:31:35,264 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:31Z] INFO  16:31:35,269 HelpFormatter - Program Args: -T PrintReads -L 10:111628372-127265443 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/10/tx/tmpsGXeMu/R14-18102_kapa-NGv3-PE100-NGv3-sort-10_111628371_127265443-prep-prealign.bam
[2016-04-14T23:31Z] INFO  16:31:35,295 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:31Z] INFO  16:31:35,296 HelpFormatter - Date/Time: 2016/04/14 16:31:35
[2016-04-14T23:31Z] INFO  16:31:35,297 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:31Z] INFO  16:31:35,297 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:31Z] INFO  16:31:35,508 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:31Z] INFO  16:31:35,636 IntervalUtils - Processing 15858356 bp from intervals
[2016-04-14T23:31Z] WARN  16:31:35,642 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:31Z] INFO  16:31:35,723 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:31Z] INFO  16:31:35,780 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:31Z] GATK: realign ('9', 65507205, 82187750) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:31Z] INFO  16:31:35,906 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:31Z] INFO  16:31:35,907 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:31Z] INFO  16:31:35,908 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:31Z] INFO  16:31:35,909 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-14T23:31Z] INFO  16:31:36,142 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:31Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-9_15564086_32405601-prep.bam
[2016-04-14T23:31Z] INFO  16:31:36,225 ProgressMeter -            done    722781.0    46.0 s      63.0 s      100.0%    46.0 s       0.0 s
[2016-04-14T23:31Z] INFO  16:31:36,226 ProgressMeter - Total runtime 46.18 secs, 0.77 min, 0.01 hours
[2016-04-14T23:31Z] INFO  16:31:36,230 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 722781 total reads (0.00%)
[2016-04-14T23:31Z] INFO  16:31:36,231 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:31Z] INFO  16:31:36,231 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:31Z] INFO  16:31:36,232 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:31Z] GATK pre-alignment ('10', 127328721, 135534747) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:31Z] INFO  16:31:36,726 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-14T23:31Z] INFO  16:31:36,794 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:31Z] INFO  16:31:36,806 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:31Z] INFO  16:31:36,867 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-14T23:31Z] INFO  16:31:36,884 IntervalUtils - Processing 15637072 bp from intervals
[2016-04-14T23:31Z] INFO  16:31:36,991 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:31Z] INFO  16:31:37,539 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:31Z] INFO  16:31:37,540 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:31Z] INFO  16:31:37,541 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:31Z] INFO  16:31:37,542 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:31Z] INFO  16:31:37,571 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:31Z] INFO  16:31:37,655 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:31Z] INFO  16:31:37,660 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:31Z] INFO  16:31:37,660 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:31Z] INFO  16:31:37,661 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:31Z] INFO  16:31:37,666 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/9/R14-18102_kapa-NGv3-PE100-NGv3-sort-9_32407258_65506776-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/9/tx/tmpucdyWz/R14-18102_kapa-NGv3-PE100-NGv3-sort-9_32407258_65506776-prep-prealign-realign.intervals -l INFO -L 9:32407259-65506776 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-14T23:31Z] INFO  16:31:37,686 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:31Z] INFO  16:31:37,687 HelpFormatter - Date/Time: 2016/04/14 16:31:37
[2016-04-14T23:31Z] INFO  16:31:37,688 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:31Z] INFO  16:31:37,688 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:31Z] INFO  16:31:37,746 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:31Z] INFO  16:31:37,853 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:31Z] INFO  16:31:38,136 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-14T23:31Z] INFO  16:31:38,153 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:31Z] INFO  16:31:38,222 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:31Z] INFO  16:31:38,261 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.11
[2016-04-14T23:31Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-7_94750023_110303777-prep.bam
[2016-04-14T23:31Z] INFO  16:31:38,653 IntervalUtils - Processing 33099518 bp from intervals
[2016-04-14T23:31Z] WARN  16:31:38,663 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:31Z] INFO  16:31:38,763 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:31Z] INFO  16:31:38,766 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:31Z] INFO  16:31:38,766 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:31Z] INFO  16:31:38,766 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:31Z] INFO  16:31:38,770 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/9/R14-18102_kapa-NGv3-PE100-NGv3-sort-9_65507205_82187750-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/9/R14-18102_kapa-NGv3-PE100-NGv3-sort-9_65507205_82187750-prep-prealign-realign.intervals -L 9:65507206-82187750 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/9/tx/tmpMwQn9S/R14-18102_kapa-NGv3-PE100-NGv3-sort-9_65507205_82187750-prep.bam
[2016-04-14T23:31Z] INFO  16:31:38,789 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:31Z] INFO  16:31:38,796 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:31Z] INFO  16:31:38,797 HelpFormatter - Date/Time: 2016/04/14 16:31:38
[2016-04-14T23:31Z] INFO  16:31:38,797 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:31Z] INFO  16:31:38,797 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:31Z] INFO  16:31:39,038 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:31Z] INFO  16:31:39,039 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:31Z] INFO  16:31:39,040 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:31Z] INFO  16:31:39,041 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-14T23:31Z] INFO  16:31:39,083 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:31Z] INFO  16:31:39,197 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:31Z] INFO  16:31:39,206 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:31Z] INFO  16:31:39,266 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-14T23:31Z] INFO  16:31:39,518 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:31Z] INFO  16:31:39,521 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:31Z] INFO  16:31:39,522 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:31Z] INFO  16:31:39,523 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:31Z] INFO  16:31:39,527 HelpFormatter - Program Args: -T PrintReads -L 10:127328722-135534747 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/10/tx/tmpyojs02/R14-18102_kapa-NGv3-PE100-NGv3-sort-10_127328721_135534747-prep-prealign.bam
[2016-04-14T23:31Z] INFO  16:31:39,565 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:31Z] INFO  16:31:39,565 HelpFormatter - Date/Time: 2016/04/14 16:31:39
[2016-04-14T23:31Z] INFO  16:31:39,566 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:31Z] INFO  16:31:39,567 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:31Z] INFO  16:31:39,685 IntervalUtils - Processing 16680545 bp from intervals
[2016-04-14T23:31Z] WARN  16:31:39,689 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:31Z] INFO  16:31:39,783 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:31Z] INFO  16:31:39,800 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:31Z] INFO  16:31:40,003 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:31Z] INFO  16:31:40,004 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:31Z] INFO  16:31:40,005 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:31Z] INFO  16:31:40,006 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:31Z] INFO  16:31:40,098 ProgressMeter -     10:51226077    200002.0    30.0 s       2.5 m       27.5%   109.0 s      79.0 s
[2016-04-14T23:31Z] INFO  16:31:40,159 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:31Z] INFO  16:31:40,383 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:31Z] GATK pre-alignment ('11', 0, 15994658) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:31Z] INFO  16:31:41,014 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-14T23:31Z] INFO  16:31:41,092 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:31Z] INFO  16:31:41,100 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:31Z] INFO  16:31:41,165 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-14T23:31Z] INFO  16:31:41,180 IntervalUtils - Processing 8206026 bp from intervals
[2016-04-14T23:31Z] INFO  16:31:41,257 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:31Z] INFO  16:31:41,568 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:31Z] INFO  16:31:41,569 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:31Z] INFO  16:31:41,569 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:31Z] INFO  16:31:41,570 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:31Z] INFO  16:31:41,595 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:31Z] INFO  16:31:41,681 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:31Z] INFO  16:31:41,841 ProgressMeter -     10:73053217    100001.0    30.0 s       5.1 m       67.6%    44.0 s      14.0 s
[2016-04-14T23:31Z] INFO  16:31:42,181 ProgressMeter -     10:93258082    200003.0    30.0 s       2.5 m       96.2%    31.0 s       1.0 s
[2016-04-14T23:31Z] INFO  16:31:43,166 ProgressMeter -    10:100022611    100003.0    30.0 s       5.1 m       34.7%    86.0 s      56.0 s
[2016-04-14T23:31Z] INFO  16:31:43,361 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@7172f77a
[2016-04-14T23:31Z] INFO  16:31:43,446 ProgressMeter -            done    249556.0    31.0 s       2.1 m      100.0%    31.0 s       0.0 s
[2016-04-14T23:31Z] INFO  16:31:43,447 ProgressMeter - Total runtime 31.28 secs, 0.52 min, 0.01 hours
[2016-04-14T23:31Z] INFO  16:31:43,448 MicroScheduler - 159 reads were filtered out during the traversal out of approximately 249715 total reads (0.06%)
[2016-04-14T23:31Z] INFO  16:31:43,449 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:31Z] INFO  16:31:43,449 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:31Z] INFO  16:31:43,450 MicroScheduler -   -> 159 reads (0.06% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:31Z] INFO  16:31:43,628 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:31Z] INFO  16:31:43,631 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:31Z] INFO  16:31:43,632 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:31Z] INFO  16:31:43,632 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:31Z] INFO  16:31:43,637 HelpFormatter - Program Args: -T PrintReads -L 11:1-15994658 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/11/tx/tmpiCVFwR/R14-18102_kapa-NGv3-PE100-NGv3-sort-11_0_15994658-prep-prealign.bam
[2016-04-14T23:31Z] INFO  16:31:43,655 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:31Z] INFO  16:31:43,656 HelpFormatter - Date/Time: 2016/04/14 16:31:43
[2016-04-14T23:31Z] INFO  16:31:43,656 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:31Z] INFO  16:31:43,657 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:31Z] INFO  16:31:43,800 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:31Z] INFO  16:31:44,834 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-14T23:31Z] INFO  16:31:44,858 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:31Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-10_78316966_93841258-prep-prealign.bam
[2016-04-14T23:31Z] INFO  16:31:44,908 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:31Z] INFO  16:31:44,918 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:31Z] INFO  16:31:44,969 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-14T23:31Z] INFO  16:31:44,987 IntervalUtils - Processing 15994658 bp from intervals
[2016-04-14T23:31Z] INFO  16:31:45,096 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:31Z] INFO  16:31:45,514 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:31Z] INFO  16:31:45,515 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:31Z] INFO  16:31:45,515 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:31Z] INFO  16:31:45,516 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:31Z] INFO  16:31:45,543 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:31Z] GATK RealignerTargetCreator: R14-18102_kapa-NGv3-PE100-NGv3-sort-10_78316966_93841258-prep-prealign.bam 10:78316967-93841258
[2016-04-14T23:31Z] GATK: RealignerTargetCreator
[2016-04-14T23:31Z] INFO  16:31:45,767 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:31Z] INFO  16:31:45,975 ProgressMeter -            done   1.5529389E7    21.0 s       1.0 s      100.0%    21.0 s       0.0 s
[2016-04-14T23:31Z] INFO  16:31:45,976 ProgressMeter - Total runtime 21.51 secs, 0.36 min, 0.01 hours
[2016-04-14T23:31Z] INFO  16:31:45,981 MicroScheduler - 54018 reads were filtered out during the traversal out of approximately 327973 total reads (16.47%)
[2016-04-14T23:31Z] INFO  16:31:45,993 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:31Z] INFO  16:31:45,994 MicroScheduler -   -> 749 reads (0.23% of total) failing BadMateFilter
[2016-04-14T23:31Z] INFO  16:31:45,995 MicroScheduler -   -> 24506 reads (7.47% of total) failing DuplicateReadFilter
[2016-04-14T23:31Z] INFO  16:31:45,995 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-14T23:31Z] INFO  16:31:45,996 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:31Z] INFO  16:31:45,997 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-14T23:31Z] INFO  16:31:45,998 MicroScheduler -   -> 28763 reads (8.77% of total) failing MappingQualityZeroFilter
[2016-04-14T23:31Z] INFO  16:31:45,998 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:31Z] INFO  16:31:45,999 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-14T23:31Z] INFO  16:31:46,000 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-14T23:31Z] INFO  16:31:47,668 ProgressMeter -            done   1.5510117E7    21.0 s       1.0 s      100.0%    21.0 s       0.0 s
[2016-04-14T23:31Z] INFO  16:31:47,669 ProgressMeter - Total runtime 21.02 secs, 0.35 min, 0.01 hours
[2016-04-14T23:31Z] INFO  16:31:47,673 MicroScheduler - 30019 reads were filtered out during the traversal out of approximately 301478 total reads (9.96%)
[2016-04-14T23:31Z] INFO  16:31:47,674 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:31Z] INFO  16:31:47,675 MicroScheduler -   -> 720 reads (0.24% of total) failing BadMateFilter
[2016-04-14T23:31Z] INFO  16:31:47,675 MicroScheduler -   -> 23676 reads (7.85% of total) failing DuplicateReadFilter
[2016-04-14T23:31Z] INFO  16:31:47,676 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-14T23:31Z] INFO  16:31:47,677 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:31Z] INFO  16:31:47,677 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-14T23:31Z] INFO  16:31:47,678 MicroScheduler -   -> 5623 reads (1.87% of total) failing MappingQualityZeroFilter
[2016-04-14T23:31Z] INFO  16:31:47,678 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:31Z] INFO  16:31:47,679 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-14T23:31Z] INFO  16:31:47,680 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-14T23:31Z] INFO  16:31:47,720 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:31Z] GATK: realign ('9', 82188172, 97717561) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:31Z] INFO  16:31:48,629 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:31Z] INFO  16:31:48,633 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:31Z] INFO  16:31:48,633 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:31Z] INFO  16:31:48,634 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:31Z] INFO  16:31:48,639 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/10/R14-18102_kapa-NGv3-PE100-NGv3-sort-10_78316966_93841258-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/10/tx/tmpTgsUoP/R14-18102_kapa-NGv3-PE100-NGv3-sort-10_78316966_93841258-prep-prealign-realign.intervals -l INFO -L 10:78316967-93841258 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-14T23:31Z] INFO  16:31:48,672 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:31Z] INFO  16:31:48,673 HelpFormatter - Date/Time: 2016/04/14 16:31:48
[2016-04-14T23:31Z] INFO  16:31:48,674 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:31Z] INFO  16:31:48,677 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:31Z] INFO  16:31:48,801 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:31Z] INFO  16:31:48,921 ProgressMeter -            done   1.5573214E7    19.0 s       1.0 s      100.0%    19.0 s       0.0 s
[2016-04-14T23:31Z] INFO  16:31:48,922 ProgressMeter - Total runtime 19.27 secs, 0.32 min, 0.01 hours
[2016-04-14T23:31Z] INFO  16:31:48,935 MicroScheduler - 19918 reads were filtered out during the traversal out of approximately 203646 total reads (9.78%)
[2016-04-14T23:31Z] INFO  16:31:48,935 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:31Z] INFO  16:31:48,936 MicroScheduler -   -> 605 reads (0.30% of total) failing BadMateFilter
[2016-04-14T23:31Z] INFO  16:31:48,936 MicroScheduler -   -> 15984 reads (7.85% of total) failing DuplicateReadFilter
[2016-04-14T23:31Z] INFO  16:31:48,936 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-14T23:31Z] INFO  16:31:48,936 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:31Z] INFO  16:31:48,937 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-14T23:31Z] INFO  16:31:48,937 MicroScheduler -   -> 3329 reads (1.63% of total) failing MappingQualityZeroFilter
[2016-04-14T23:31Z] INFO  16:31:48,937 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:31Z] INFO  16:31:48,937 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-14T23:31Z] INFO  16:31:48,938 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-14T23:31Z] INFO  16:31:48,972 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-14T23:31Z] INFO  16:31:48,982 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:31Z] INFO  16:31:49,011 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:31Z] GATK: realign ('9', 97718189, 113228306) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:31Z] INFO  16:31:49,055 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-14T23:31Z] INFO  16:31:49,342 ProgressMeter -     9:137013716    400010.0    60.0 s       2.5 m       65.3%    91.0 s      31.0 s
[2016-04-14T23:31Z] INFO  16:31:49,359 IntervalUtils - Processing 15524292 bp from intervals
[2016-04-14T23:31Z] WARN  16:31:49,363 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:31Z] INFO  16:31:49,458 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:31Z] INFO  16:31:49,680 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:31Z] INFO  16:31:49,682 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:31Z] INFO  16:31:49,693 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:31Z] INFO  16:31:49,694 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-14T23:31Z] INFO  16:31:50,080 ProgressMeter -            done   1.582267E7    17.0 s       1.0 s      100.0%    17.0 s       0.0 s
[2016-04-14T23:31Z] INFO  16:31:50,081 ProgressMeter - Total runtime 17.73 secs, 0.30 min, 0.00 hours
[2016-04-14T23:31Z] INFO  16:31:50,086 MicroScheduler - 51883 reads were filtered out during the traversal out of approximately 209357 total reads (24.78%)
[2016-04-14T23:31Z] INFO  16:31:50,087 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:31Z] INFO  16:31:50,088 MicroScheduler -   -> 942 reads (0.45% of total) failing BadMateFilter
[2016-04-14T23:31Z] INFO  16:31:50,088 MicroScheduler -   -> 13798 reads (6.59% of total) failing DuplicateReadFilter
[2016-04-14T23:31Z] INFO  16:31:50,089 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-14T23:31Z] INFO  16:31:50,090 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:31Z] INFO  16:31:50,091 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-14T23:31Z] INFO  16:31:50,091 MicroScheduler -   -> 37143 reads (17.74% of total) failing MappingQualityZeroFilter
[2016-04-14T23:31Z] INFO  16:31:50,092 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:31Z] INFO  16:31:50,093 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-14T23:31Z] INFO  16:31:50,094 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-14T23:31Z] INFO  16:31:50,322 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:31Z] INFO  16:31:50,326 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:31Z] INFO  16:31:50,326 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:31Z] INFO  16:31:50,327 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:31Z] INFO  16:31:50,332 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/9/R14-18102_kapa-NGv3-PE100-NGv3-sort-9_82188172_97717561-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/9/R14-18102_kapa-NGv3-PE100-NGv3-sort-9_82188172_97717561-prep-prealign-realign.intervals -L 9:82188173-97717561 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/9/tx/tmpdz7vkn/R14-18102_kapa-NGv3-PE100-NGv3-sort-9_82188172_97717561-prep.bam
[2016-04-14T23:31Z] INFO  16:31:50,363 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:31Z] INFO  16:31:50,364 HelpFormatter - Date/Time: 2016/04/14 16:31:50
[2016-04-14T23:31Z] INFO  16:31:50,365 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:31Z] INFO  16:31:50,365 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:31Z] INFO  16:31:50,365 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:31Z] GATK: realign ('10', 15561288, 31134502) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:31Z] INFO  16:31:50,624 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:31Z] INFO  16:31:50,741 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:31Z] INFO  16:31:50,778 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:31Z] INFO  16:31:50,866 ProgressMeter -            done   1.5559243E7    19.0 s       1.0 s      100.0%    19.0 s       0.0 s
[2016-04-14T23:31Z] INFO  16:31:50,866 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.09
[2016-04-14T23:31Z] INFO  16:31:50,867 ProgressMeter - Total runtime 19.97 secs, 0.33 min, 0.01 hours
[2016-04-14T23:31Z] INFO  16:31:50,871 MicroScheduler - 21535 reads were filtered out during the traversal out of approximately 225001 total reads (9.57%)
[2016-04-14T23:31Z] INFO  16:31:50,872 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:31Z] INFO  16:31:50,873 MicroScheduler -   -> 712 reads (0.32% of total) failing BadMateFilter
[2016-04-14T23:31Z] INFO  16:31:50,873 MicroScheduler -   -> 17634 reads (7.84% of total) failing DuplicateReadFilter
[2016-04-14T23:31Z] INFO  16:31:50,874 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-14T23:31Z] INFO  16:31:50,874 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:31Z] INFO  16:31:50,875 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-14T23:31Z] INFO  16:31:50,876 MicroScheduler -   -> 3189 reads (1.42% of total) failing MappingQualityZeroFilter
[2016-04-14T23:31Z] INFO  16:31:50,876 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:31Z] INFO  16:31:50,877 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-14T23:31Z] INFO  16:31:50,877 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-14T23:31Z] INFO  16:31:51,270 IntervalUtils - Processing 15529389 bp from intervals
[2016-04-14T23:31Z] WARN  16:31:51,275 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:31Z] INFO  16:31:51,383 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:31Z] INFO  16:31:51,491 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:31Z] GATK: realign ('10', 31137459, 46960129) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:31Z] INFO  16:31:51,539 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:31Z] INFO  16:31:51,541 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:31Z] INFO  16:31:51,542 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:31Z] INFO  16:31:51,543 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:31Z] INFO  16:31:51,661 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:31Z] INFO  16:31:51,665 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:31Z] INFO  16:31:51,665 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:31Z] INFO  16:31:51,666 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:31Z] INFO  16:31:51,670 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/9/R14-18102_kapa-NGv3-PE100-NGv3-sort-9_97718189_113228306-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/9/R14-18102_kapa-NGv3-PE100-NGv3-sort-9_97718189_113228306-prep-prealign-realign.intervals -L 9:97718190-113228306 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/9/tx/tmplgVZVf/R14-18102_kapa-NGv3-PE100-NGv3-sort-9_97718189_113228306-prep.bam
[2016-04-14T23:31Z] INFO  16:31:51,680 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:31Z] INFO  16:31:51,680 HelpFormatter - Date/Time: 2016/04/14 16:31:51
[2016-04-14T23:31Z] INFO  16:31:51,681 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:31Z] INFO  16:31:51,681 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:31Z] INFO  16:31:51,767 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:31Z] INFO  16:31:51,875 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:31Z] INFO  16:31:51,941 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:31Z] INFO  16:31:52,036 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:31Z] INFO  16:31:52,045 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:31Z] INFO  16:31:52,108 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-14T23:31Z] INFO  16:31:52,439 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:31Z] GATK: realign ('10', 0, 15559243) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:31Z] INFO  16:31:52,457 IntervalUtils - Processing 15510117 bp from intervals
[2016-04-14T23:31Z] WARN  16:31:52,471 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:31Z] INFO  16:31:52,604 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:31Z] INFO  16:31:52,699 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:31Z] INFO  16:31:52,700 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:31Z] INFO  16:31:52,701 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:31Z] INFO  16:31:52,702 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:31Z] INFO  16:31:52,875 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:31Z] INFO  16:31:53,038 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:31Z] INFO  16:31:53,504 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:31Z] INFO  16:31:53,508 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:31Z] INFO  16:31:53,509 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:31Z] INFO  16:31:53,509 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:31Z] INFO  16:31:53,514 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/10/R14-18102_kapa-NGv3-PE100-NGv3-sort-10_15561288_31134502-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/10/R14-18102_kapa-NGv3-PE100-NGv3-sort-10_15561288_31134502-prep-prealign-realign.intervals -L 10:15561289-31134502 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/10/tx/tmpYA0yMe/R14-18102_kapa-NGv3-PE100-NGv3-sort-10_15561288_31134502-prep.bam
[2016-04-14T23:31Z] INFO  16:31:53,528 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:31Z] INFO  16:31:53,529 HelpFormatter - Date/Time: 2016/04/14 16:31:53
[2016-04-14T23:31Z] INFO  16:31:53,530 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:31Z] INFO  16:31:53,530 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:31Z] INFO  16:31:53,814 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:31Z] INFO  16:31:53,959 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:31Z] INFO  16:31:53,985 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:31Z] INFO  16:31:54,067 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-14T23:31Z] INFO  16:31:54,457 IntervalUtils - Processing 15573214 bp from intervals
[2016-04-14T23:31Z] WARN  16:31:54,470 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:31Z] INFO  16:31:54,592 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:31Z] INFO  16:31:54,631 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:31Z] INFO  16:31:54,633 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:31Z] INFO  16:31:54,634 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:31Z] INFO  16:31:54,634 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:31Z] INFO  16:31:54,638 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/10/R14-18102_kapa-NGv3-PE100-NGv3-sort-10_31137459_46960129-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/10/R14-18102_kapa-NGv3-PE100-NGv3-sort-10_31137459_46960129-prep-prealign-realign.intervals -L 10:31137460-46960129 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/10/tx/tmpwAV3hU/R14-18102_kapa-NGv3-PE100-NGv3-sort-10_31137459_46960129-prep.bam
[2016-04-14T23:31Z] INFO  16:31:54,648 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:31Z] INFO  16:31:54,649 HelpFormatter - Date/Time: 2016/04/14 16:31:54
[2016-04-14T23:31Z] INFO  16:31:54,650 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:31Z] INFO  16:31:54,650 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:31Z] INFO  16:31:54,819 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:31Z] INFO  16:31:54,820 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:31Z] INFO  16:31:54,821 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:31Z] INFO  16:31:54,822 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:31Z] INFO  16:31:54,880 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:31Z] INFO  16:31:55,021 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:31Z] INFO  16:31:55,032 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:31Z] INFO  16:31:55,044 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:31Z] INFO  16:31:55,108 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-14T23:31Z] INFO  16:31:55,146 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@41fd9d8e
[2016-04-14T23:31Z] INFO  16:31:55,197 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:31Z] INFO  16:31:55,290 ProgressMeter -            done    359171.0    45.0 s       2.1 m      100.0%    45.0 s       0.0 s
[2016-04-14T23:31Z] INFO  16:31:55,291 ProgressMeter - Total runtime 45.24 secs, 0.75 min, 0.01 hours
[2016-04-14T23:31Z] INFO  16:31:55,291 MicroScheduler - 162 reads were filtered out during the traversal out of approximately 359333 total reads (0.05%)
[2016-04-14T23:31Z] INFO  16:31:55,291 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:31Z] INFO  16:31:55,292 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:31Z] INFO  16:31:55,292 MicroScheduler -   -> 162 reads (0.05% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:31Z] INFO  16:31:55,483 IntervalUtils - Processing 15822670 bp from intervals
[2016-04-14T23:31Z] WARN  16:31:55,515 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:31Z] INFO  16:31:55,533 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:31Z] INFO  16:31:55,544 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:31Z] INFO  16:31:55,545 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:31Z] INFO  16:31:55,546 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:31Z] INFO  16:31:55,552 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/10/R14-18102_kapa-NGv3-PE100-NGv3-sort-10_0_15559243-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/10/R14-18102_kapa-NGv3-PE100-NGv3-sort-10_0_15559243-prep-prealign-realign.intervals -L 10:1-15559243 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/10/tx/tmp5rdMxo/R14-18102_kapa-NGv3-PE100-NGv3-sort-10_0_15559243-prep.bam
[2016-04-14T23:31Z] INFO  16:31:55,571 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:31Z] INFO  16:31:55,572 HelpFormatter - Date/Time: 2016/04/14 16:31:55
[2016-04-14T23:31Z] INFO  16:31:55,573 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:31Z] INFO  16:31:55,574 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:31Z] INFO  16:31:55,615 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:31Z] INFO  16:31:55,721 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:31Z] INFO  16:31:55,722 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:31Z] INFO  16:31:55,723 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:31Z] INFO  16:31:55,724 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:31Z] INFO  16:31:55,745 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:31Z] INFO  16:31:55,853 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:31Z] INFO  16:31:55,867 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:31Z] INFO  16:31:55,909 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:31Z] INFO  16:31:55,913 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-14T23:31Z] INFO  16:31:56,085 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:31Z] INFO  16:31:56,349 IntervalUtils - Processing 15559243 bp from intervals
[2016-04-14T23:31Z] WARN  16:31:56,365 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:31Z] INFO  16:31:56,471 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:31Z] INFO  16:31:56,566 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:31Z] INFO  16:31:56,567 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:31Z] INFO  16:31:56,567 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:31Z] INFO  16:31:56,568 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:31Z] INFO  16:31:56,711 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:31Z] INFO  16:31:56,742 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:31Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-10_46960410_62493077-prep-prealign.bam
[2016-04-14T23:31Z] INFO  16:31:56,902 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:31Z] INFO  16:31:57,486 ProgressMeter -            done   1.5858356E7    21.0 s       1.0 s      100.0%    21.0 s       0.0 s
[2016-04-14T23:31Z] INFO  16:31:57,487 ProgressMeter - Total runtime 21.58 secs, 0.36 min, 0.01 hours
[2016-04-14T23:31Z] INFO  16:31:57,490 MicroScheduler - 30796 reads were filtered out during the traversal out of approximately 353000 total reads (8.72%)
[2016-04-14T23:31Z] INFO  16:31:57,491 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:31Z] INFO  16:31:57,491 MicroScheduler -   -> 797 reads (0.23% of total) failing BadMateFilter
[2016-04-14T23:31Z] INFO  16:31:57,491 MicroScheduler -   -> 27829 reads (7.88% of total) failing DuplicateReadFilter
[2016-04-14T23:31Z] INFO  16:31:57,492 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-14T23:31Z] INFO  16:31:57,492 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:31Z] INFO  16:31:57,492 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-14T23:31Z] INFO  16:31:57,492 MicroScheduler -   -> 2170 reads (0.61% of total) failing MappingQualityZeroFilter
[2016-04-14T23:31Z] INFO  16:31:57,493 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:31Z] INFO  16:31:57,493 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-14T23:31Z] INFO  16:31:57,493 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-14T23:31Z] GATK RealignerTargetCreator: R14-18102_kapa-NGv3-PE100-NGv3-sort-10_46960410_62493077-prep-prealign.bam 10:46960411-62493077
[2016-04-14T23:31Z] GATK: RealignerTargetCreator
[2016-04-14T23:31Z] INFO  16:31:58,920 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:31Z] GATK: realign ('9', 113231219, 129089575) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:31Z] INFO  16:31:58,979 ProgressMeter -            done    238003.0    18.0 s      79.0 s      100.0%    18.0 s       0.0 s
[2016-04-14T23:31Z] INFO  16:31:58,980 ProgressMeter - Total runtime 18.98 secs, 0.32 min, 0.01 hours
[2016-04-14T23:31Z] INFO  16:31:58,984 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 238003 total reads (0.00%)
[2016-04-14T23:31Z] INFO  16:31:58,985 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:31Z] INFO  16:31:58,986 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:31Z] INFO  16:31:58,986 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:32Z] INFO  16:32:00,524 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:32Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-9_65507205_82187750-prep.bam
[2016-04-14T23:32Z] INFO  16:32:00,943 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:32Z] INFO  16:32:00,947 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:32Z] INFO  16:32:00,948 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:32Z] INFO  16:32:00,948 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:32Z] INFO  16:32:00,953 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/10/R14-18102_kapa-NGv3-PE100-NGv3-sort-10_46960410_62493077-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/10/tx/tmpEs7U28/R14-18102_kapa-NGv3-PE100-NGv3-sort-10_46960410_62493077-prep-prealign-realign.intervals -l INFO -L 10:46960411-62493077 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-14T23:32Z] INFO  16:32:00,973 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:32Z] INFO  16:32:00,980 HelpFormatter - Date/Time: 2016/04/14 16:32:00
[2016-04-14T23:32Z] INFO  16:32:00,980 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:32Z] INFO  16:32:00,981 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:32Z] INFO  16:32:01,072 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:32Z] INFO  16:32:01,273 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-14T23:32Z] INFO  16:32:01,282 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:32Z] INFO  16:32:01,337 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-14T23:32Z] GATK pre-alignment ('11', 16007749, 31531554) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:32Z] INFO  16:32:01,637 IntervalUtils - Processing 15532667 bp from intervals
[2016-04-14T23:32Z] WARN  16:32:01,641 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:32Z] INFO  16:32:01,722 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:32Z] INFO  16:32:01,934 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:32Z] INFO  16:32:01,935 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:32Z] INFO  16:32:01,936 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:32Z] INFO  16:32:01,937 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-14T23:32Z] INFO  16:32:02,074 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:32Z] INFO  16:32:02,078 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:32Z] INFO  16:32:02,078 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:32Z] INFO  16:32:02,079 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:32Z] INFO  16:32:02,084 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/9/R14-18102_kapa-NGv3-PE100-NGv3-sort-9_113231219_129089575-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/9/R14-18102_kapa-NGv3-PE100-NGv3-sort-9_113231219_129089575-prep-prealign-realign.intervals -L 9:113231220-129089575 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/9/tx/tmpkkYjV0/R14-18102_kapa-NGv3-PE100-NGv3-sort-9_113231219_129089575-prep.bam
[2016-04-14T23:32Z] INFO  16:32:02,094 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:32Z] INFO  16:32:02,101 HelpFormatter - Date/Time: 2016/04/14 16:32:02
[2016-04-14T23:32Z] INFO  16:32:02,101 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:32Z] INFO  16:32:02,101 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:32Z] INFO  16:32:02,281 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:32Z] INFO  16:32:02,390 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:32Z] INFO  16:32:02,399 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:32Z] INFO  16:32:02,460 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-14T23:32Z] INFO  16:32:02,876 IntervalUtils - Processing 15858356 bp from intervals
[2016-04-14T23:32Z] WARN  16:32:02,881 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:32Z] INFO  16:32:02,960 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:32Z] INFO  16:32:03,102 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:32Z] INFO  16:32:03,103 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:32Z] INFO  16:32:03,104 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:32Z] INFO  16:32:03,105 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:32Z] INFO  16:32:03,295 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:32Z] INFO  16:32:03,480 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:32Z] INFO  16:32:04,496 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:32Z] INFO  16:32:04,499 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:32Z] INFO  16:32:04,499 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:32Z] INFO  16:32:04,500 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:32Z] INFO  16:32:04,504 HelpFormatter - Program Args: -T PrintReads -L 11:16007750-31531554 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/11/tx/tmp3Rsdcs/R14-18102_kapa-NGv3-PE100-NGv3-sort-11_16007749_31531554-prep-prealign.bam
[2016-04-14T23:32Z] INFO  16:32:04,531 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:32Z] INFO  16:32:04,538 HelpFormatter - Date/Time: 2016/04/14 16:32:04
[2016-04-14T23:32Z] INFO  16:32:04,539 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:32Z] INFO  16:32:04,540 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:32Z] INFO  16:32:04,709 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:32Z] INFO  16:32:04,805 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@5fe152b7
[2016-04-14T23:32Z] INFO  16:32:04,984 ProgressMeter -            done    175852.0    23.0 s       2.2 m       99.5%    23.0 s       0.0 s
[2016-04-14T23:32Z] INFO  16:32:04,986 ProgressMeter - Total runtime 23.42 secs, 0.39 min, 0.01 hours
[2016-04-14T23:32Z] INFO  16:32:04,986 MicroScheduler - 148 reads were filtered out during the traversal out of approximately 176000 total reads (0.08%)
[2016-04-14T23:32Z] INFO  16:32:04,987 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:32Z] INFO  16:32:04,988 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:32Z] INFO  16:32:04,989 MicroScheduler -   -> 148 reads (0.08% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:32Z] INFO  16:32:05,169 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@7172f77a
[2016-04-14T23:32Z] INFO  16:32:05,247 ProgressMeter -            done    359648.0    54.0 s       2.5 m      100.0%    54.0 s       0.0 s
[2016-04-14T23:32Z] INFO  16:32:05,248 ProgressMeter - Total runtime 54.08 secs, 0.90 min, 0.02 hours
[2016-04-14T23:32Z] INFO  16:32:05,249 MicroScheduler - 161 reads were filtered out during the traversal out of approximately 359809 total reads (0.04%)
[2016-04-14T23:32Z] INFO  16:32:05,250 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:32Z] INFO  16:32:05,250 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:32Z] INFO  16:32:05,250 MicroScheduler -   -> 161 reads (0.04% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:32Z] INFO  16:32:05,897 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-14T23:32Z] INFO  16:32:05,964 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:32Z] INFO  16:32:05,973 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:32Z] INFO  16:32:06,008 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.03
[2016-04-14T23:32Z] INFO  16:32:06,021 IntervalUtils - Processing 15523805 bp from intervals
[2016-04-14T23:32Z] INFO  16:32:06,093 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:32Z] INFO  16:32:06,370 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:32Z] INFO  16:32:06,371 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:32Z] INFO  16:32:06,372 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:32Z] INFO  16:32:06,373 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:32Z] INFO  16:32:06,389 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:32Z] INFO  16:32:06,524 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:32Z] INFO  16:32:06,602 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:32Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-10_127328721_135534747-prep-prealign.bam
[2016-04-14T23:32Z] INFO  16:32:06,635 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:32Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-10_62539923_78084243-prep-prealign.bam
[2016-04-14T23:32Z] GATK RealignerTargetCreator: R14-18102_kapa-NGv3-PE100-NGv3-sort-10_127328721_135534747-prep-prealign.bam 10:127328722-135534747
[2016-04-14T23:32Z] GATK: RealignerTargetCreator
[2016-04-14T23:32Z] INFO  16:32:07,557 ProgressMeter -    10:124092625    200005.0    30.0 s       2.5 m       79.7%    37.0 s       7.0 s
[2016-04-14T23:32Z] GATK RealignerTargetCreator: R14-18102_kapa-NGv3-PE100-NGv3-sort-10_62539923_78084243-prep-prealign.bam 10:62539924-78084243
[2016-04-14T23:32Z] GATK: RealignerTargetCreator
[2016-04-14T23:32Z] INFO  16:32:08,255 ProgressMeter -            done   3.3099518E7    29.0 s       0.0 s      100.0%    29.0 s       0.0 s
[2016-04-14T23:32Z] INFO  16:32:08,255 ProgressMeter - Total runtime 29.22 secs, 0.49 min, 0.01 hours
[2016-04-14T23:32Z] INFO  16:32:08,259 MicroScheduler - 159459 reads were filtered out during the traversal out of approximately 488421 total reads (32.65%)
[2016-04-14T23:32Z] INFO  16:32:08,271 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:32Z] INFO  16:32:08,271 MicroScheduler -   -> 709 reads (0.15% of total) failing BadMateFilter
[2016-04-14T23:32Z] INFO  16:32:08,272 MicroScheduler -   -> 29234 reads (5.99% of total) failing DuplicateReadFilter
[2016-04-14T23:32Z] INFO  16:32:08,273 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-14T23:32Z] INFO  16:32:08,273 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:32Z] INFO  16:32:08,274 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-14T23:32Z] INFO  16:32:08,275 MicroScheduler -   -> 129516 reads (26.52% of total) failing MappingQualityZeroFilter
[2016-04-14T23:32Z] INFO  16:32:08,276 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:32Z] INFO  16:32:08,276 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-14T23:32Z] INFO  16:32:08,277 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-14T23:32Z] INFO  16:32:09,661 ProgressMeter -            done   1.5524292E7    19.0 s       1.0 s      100.0%    19.0 s       0.0 s
[2016-04-14T23:32Z] INFO  16:32:09,662 ProgressMeter - Total runtime 19.98 secs, 0.33 min, 0.01 hours
[2016-04-14T23:32Z] INFO  16:32:09,668 MicroScheduler - 42688 reads were filtered out during the traversal out of approximately 250957 total reads (17.01%)
[2016-04-14T23:32Z] INFO  16:32:09,669 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:32Z] INFO  16:32:09,670 MicroScheduler -   -> 617 reads (0.25% of total) failing BadMateFilter
[2016-04-14T23:32Z] INFO  16:32:09,670 MicroScheduler -   -> 18136 reads (7.23% of total) failing DuplicateReadFilter
[2016-04-14T23:32Z] INFO  16:32:09,671 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-14T23:32Z] INFO  16:32:09,672 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:32Z] INFO  16:32:09,672 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-14T23:32Z] INFO  16:32:09,673 MicroScheduler -   -> 23935 reads (9.54% of total) failing MappingQualityZeroFilter
[2016-04-14T23:32Z] INFO  16:32:09,673 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:32Z] INFO  16:32:09,674 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-14T23:32Z] INFO  16:32:09,675 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-14T23:32Z] INFO  16:32:09,788 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:32Z] GATK: realign ('9', 32407258, 65506776) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:32Z] INFO  16:32:10,049 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:32Z] INFO  16:32:10,052 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:32Z] INFO  16:32:10,052 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:32Z] INFO  16:32:10,052 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:32Z] INFO  16:32:10,056 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/10/R14-18102_kapa-NGv3-PE100-NGv3-sort-10_127328721_135534747-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/10/tx/tmpoM49He/R14-18102_kapa-NGv3-PE100-NGv3-sort-10_127328721_135534747-prep-prealign-realign.intervals -l INFO -L 10:127328722-135534747 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-14T23:32Z] INFO  16:32:10,075 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:32Z] INFO  16:32:10,076 HelpFormatter - Date/Time: 2016/04/14 16:32:10
[2016-04-14T23:32Z] INFO  16:32:10,076 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:32Z] INFO  16:32:10,077 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:32Z] INFO  16:32:10,206 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:32Z] INFO  16:32:10,432 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-14T23:32Z] INFO  16:32:10,452 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:32Z] INFO  16:32:10,516 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-14T23:32Z] INFO  16:32:10,582 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:32Z] INFO  16:32:10,586 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:32Z] INFO  16:32:10,587 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:32Z] INFO  16:32:10,587 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:32Z] INFO  16:32:10,592 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/10/R14-18102_kapa-NGv3-PE100-NGv3-sort-10_62539923_78084243-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/10/tx/tmpvCctcj/R14-18102_kapa-NGv3-PE100-NGv3-sort-10_62539923_78084243-prep-prealign-realign.intervals -l INFO -L 10:62539924-78084243 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-14T23:32Z] INFO  16:32:10,623 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:32Z] INFO  16:32:10,624 HelpFormatter - Date/Time: 2016/04/14 16:32:10
[2016-04-14T23:32Z] INFO  16:32:10,624 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:32Z] INFO  16:32:10,629 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:32Z] INFO  16:32:10,732 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:32Z] INFO  16:32:10,861 IntervalUtils - Processing 8206026 bp from intervals
[2016-04-14T23:32Z] WARN  16:32:10,866 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:32Z] INFO  16:32:10,940 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-14T23:32Z] INFO  16:32:10,945 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:32Z] INFO  16:32:10,949 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:32Z] INFO  16:32:10,993 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.04
[2016-04-14T23:32Z] INFO  16:32:11,101 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:32Z] INFO  16:32:11,102 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:32Z] INFO  16:32:11,103 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:32Z] INFO  16:32:11,104 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-14T23:32Z] INFO  16:32:11,137 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:32Z] GATK: realign ('10', 78316966, 93841258) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:32Z] INFO  16:32:11,256 IntervalUtils - Processing 15544320 bp from intervals
[2016-04-14T23:32Z] WARN  16:32:11,261 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:32Z] INFO  16:32:11,356 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:32Z] INFO  16:32:11,495 ProgressMeter -            done    202099.0    16.0 s      82.0 s      100.0%    16.0 s       0.0 s
[2016-04-14T23:32Z] INFO  16:32:11,495 ProgressMeter - Total runtime 16.67 secs, 0.28 min, 0.00 hours
[2016-04-14T23:32Z] INFO  16:32:11,499 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 202099 total reads (0.00%)
[2016-04-14T23:32Z] INFO  16:32:11,499 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:32Z] INFO  16:32:11,499 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:32Z] INFO  16:32:11,500 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:32Z] INFO  16:32:11,551 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:32Z] INFO  16:32:11,552 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:32Z] INFO  16:32:11,553 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:32Z] INFO  16:32:11,553 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-14T23:32Z] INFO  16:32:12,448 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:32Z] INFO  16:32:12,451 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:32Z] INFO  16:32:12,452 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:32Z] INFO  16:32:12,452 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:32Z] INFO  16:32:12,457 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/9/R14-18102_kapa-NGv3-PE100-NGv3-sort-9_32407258_65506776-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/9/R14-18102_kapa-NGv3-PE100-NGv3-sort-9_32407258_65506776-prep-prealign-realign.intervals -L 9:32407259-65506776 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/9/tx/tmp4Z7jv5/R14-18102_kapa-NGv3-PE100-NGv3-sort-9_32407258_65506776-prep.bam
[2016-04-14T23:32Z] INFO  16:32:12,491 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:32Z] INFO  16:32:12,507 HelpFormatter - Date/Time: 2016/04/14 16:32:12
[2016-04-14T23:32Z] INFO  16:32:12,507 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:32Z] INFO  16:32:12,507 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:32Z] INFO  16:32:12,734 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:32Z] INFO  16:32:12,750 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:32Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-10_15561288_31134502-prep.bam
[2016-04-14T23:32Z] INFO  16:32:12,873 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:32Z] INFO  16:32:12,881 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:32Z] INFO  16:32:12,949 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-14T23:32Z] INFO  16:32:13,167 ProgressMeter -    10:106214085    400007.0    60.0 s       2.5 m       69.6%    86.0 s      26.0 s
[2016-04-14T23:32Z] INFO  16:32:13,210 ProgressMeter -            done    326222.0    21.0 s      66.0 s      100.0%    21.0 s       0.0 s
[2016-04-14T23:32Z] INFO  16:32:13,211 ProgressMeter - Total runtime 21.67 secs, 0.36 min, 0.01 hours
[2016-04-14T23:32Z] INFO  16:32:13,215 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 326222 total reads (0.00%)
[2016-04-14T23:32Z] INFO  16:32:13,215 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:32Z] INFO  16:32:13,216 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:32Z] INFO  16:32:13,216 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:32Z] INFO  16:32:13,334 IntervalUtils - Processing 33099518 bp from intervals
[2016-04-14T23:32Z] WARN  16:32:13,339 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:32Z] INFO  16:32:13,419 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:32Z] GATK pre-alignment ('11', 31541602, 47074069) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:32Z] INFO  16:32:13,533 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:32Z] INFO  16:32:13,534 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:32Z] INFO  16:32:13,534 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:32Z] INFO  16:32:13,535 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:32Z] INFO  16:32:13,663 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:32Z] INFO  16:32:13,964 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:32Z] INFO  16:32:14,231 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:32Z] INFO  16:32:14,235 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:32Z] INFO  16:32:14,236 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:32Z] INFO  16:32:14,236 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:32Z] INFO  16:32:14,242 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/10/R14-18102_kapa-NGv3-PE100-NGv3-sort-10_78316966_93841258-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/10/R14-18102_kapa-NGv3-PE100-NGv3-sort-10_78316966_93841258-prep-prealign-realign.intervals -L 10:78316967-93841258 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/10/tx/tmphnHD6C/R14-18102_kapa-NGv3-PE100-NGv3-sort-10_78316966_93841258-prep.bam
[2016-04-14T23:32Z] INFO  16:32:14,252 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:32Z] INFO  16:32:14,263 HelpFormatter - Date/Time: 2016/04/14 16:32:14
[2016-04-14T23:32Z] INFO  16:32:14,264 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:32Z] INFO  16:32:14,264 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:32Z] INFO  16:32:14,383 ProgressMeter -            done    223828.0    17.0 s      79.0 s      100.0%    17.0 s       0.0 s
[2016-04-14T23:32Z] INFO  16:32:14,384 ProgressMeter - Total runtime 17.82 secs, 0.30 min, 0.00 hours
[2016-04-14T23:32Z] INFO  16:32:14,388 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 223828 total reads (0.00%)
[2016-04-14T23:32Z] INFO  16:32:14,389 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:32Z] INFO  16:32:14,390 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:32Z] INFO  16:32:14,391 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:32Z] INFO  16:32:14,449 ProgressMeter -            done    299640.0    21.0 s      72.0 s      100.0%    21.0 s       0.0 s
[2016-04-14T23:32Z] INFO  16:32:14,450 ProgressMeter - Total runtime 21.75 secs, 0.36 min, 0.01 hours
[2016-04-14T23:32Z] INFO  16:32:14,453 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 299640 total reads (0.00%)
[2016-04-14T23:32Z] INFO  16:32:14,454 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:32Z] INFO  16:32:14,454 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:32Z] INFO  16:32:14,454 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:32Z] INFO  16:32:14,530 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:32Z] INFO  16:32:14,740 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:32Z] INFO  16:32:14,756 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:32Z] INFO  16:32:14,820 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-14T23:32Z] INFO  16:32:15,018 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:32Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-9_82188172_97717561-prep.bam
[2016-04-14T23:32Z] INFO  16:32:15,148 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@5fe152b7
[2016-04-14T23:32Z] INFO  16:32:15,198 IntervalUtils - Processing 15524292 bp from intervals
[2016-04-14T23:32Z] WARN  16:32:15,203 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:32Z] INFO  16:32:15,298 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:32Z] INFO  16:32:15,339 ProgressMeter -            done    504811.0    62.0 s       2.1 m      100.0%    62.0 s       0.0 s
[2016-04-14T23:32Z] INFO  16:32:15,340 ProgressMeter - Total runtime 62.56 secs, 1.04 min, 0.02 hours
[2016-04-14T23:32Z] INFO  16:32:15,340 MicroScheduler - 208 reads were filtered out during the traversal out of approximately 505019 total reads (0.04%)
[2016-04-14T23:32Z] INFO  16:32:15,341 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:32Z] INFO  16:32:15,341 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:32Z] INFO  16:32:15,342 MicroScheduler -   -> 208 reads (0.04% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:32Z] INFO  16:32:15,461 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:32Z] INFO  16:32:15,462 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:32Z] INFO  16:32:15,462 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:32Z] INFO  16:32:15,462 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:32Z] INFO  16:32:15,664 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:32Z] INFO  16:32:15,753 ProgressMeter -      11:1093405    100002.0    30.0 s       5.0 m        6.8%     7.3 m       6.8 m
[2016-04-14T23:32Z] INFO  16:32:15,828 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:32Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-9_97718189_113228306-prep.bam
[2016-04-14T23:32Z] INFO  16:32:15,890 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:32Z] INFO  16:32:15,943 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@5fe152b7
[2016-04-14T23:32Z] INFO  16:32:16,058 ProgressMeter -            done    207883.0    20.0 s      97.0 s      100.0%    20.0 s       0.0 s
[2016-04-14T23:32Z] INFO  16:32:16,059 ProgressMeter - Total runtime 20.34 secs, 0.34 min, 0.01 hours
[2016-04-14T23:32Z] INFO  16:32:16,062 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 207883 total reads (0.00%)
[2016-04-14T23:32Z] INFO  16:32:16,063 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:32Z] INFO  16:32:16,063 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:32Z] INFO  16:32:16,064 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:32Z] INFO  16:32:16,116 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:32Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-10_0_15559243-prep.bam
[2016-04-14T23:32Z] INFO  16:32:16,155 ProgressMeter -            done    305977.0    38.0 s       2.1 m      100.0%    38.0 s       0.0 s
[2016-04-14T23:32Z] INFO  16:32:16,155 ProgressMeter - Total runtime 38.62 secs, 0.64 min, 0.01 hours
[2016-04-14T23:32Z] INFO  16:32:16,156 MicroScheduler - 152 reads were filtered out during the traversal out of approximately 306129 total reads (0.05%)
[2016-04-14T23:32Z] INFO  16:32:16,156 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:32Z] INFO  16:32:16,157 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:32Z] INFO  16:32:16,157 MicroScheduler -   -> 152 reads (0.05% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:32Z] GATK pre-alignment ('11', 47158866, 62678572) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:32Z] INFO  16:32:16,551 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:32Z] INFO  16:32:16,555 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:32Z] INFO  16:32:16,556 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:32Z] INFO  16:32:16,557 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:32Z] INFO  16:32:16,562 HelpFormatter - Program Args: -T PrintReads -L 11:31541603-47074069 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/11/tx/tmp0gFcbU/R14-18102_kapa-NGv3-PE100-NGv3-sort-11_31541602_47074069-prep-prealign.bam
[2016-04-14T23:32Z] INFO  16:32:16,603 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:32Z] INFO  16:32:16,605 HelpFormatter - Date/Time: 2016/04/14 16:32:16
[2016-04-14T23:32Z] INFO  16:32:16,606 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:32Z] INFO  16:32:16,607 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:32Z] INFO  16:32:16,761 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:32Z] INFO  16:32:16,950 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:32Z] GATK pre-alignment ('11', 62744265, 78270665) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:32Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-10_93851586_111625070-prep-prealign.bam
[2016-04-14T23:32Z] GATK pre-alignment ('11', 78277177, 93796886) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:32Z] INFO  16:32:17,424 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:32Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-10_111628371_127265443-prep-prealign.bam
[2016-04-14T23:32Z] INFO  16:32:17,558 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:32Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-10_31137459_46960129-prep.bam
[2016-04-14T23:32Z] INFO  16:32:17,985 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-14T23:32Z] INFO  16:32:18,110 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:32Z] INFO  16:32:18,120 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:32Z] INFO  16:32:18,188 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-14T23:32Z] INFO  16:32:18,221 IntervalUtils - Processing 15532467 bp from intervals
[2016-04-14T23:32Z] INFO  16:32:18,309 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:32Z] GATK pre-alignment ('11', 93797496, 109964158) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:32Z] GATK RealignerTargetCreator: R14-18102_kapa-NGv3-PE100-NGv3-sort-10_111628371_127265443-prep-prealign.bam 10:111628372-127265443
[2016-04-14T23:32Z] GATK: RealignerTargetCreator
[2016-04-14T23:32Z] INFO  16:32:18,598 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:32Z] INFO  16:32:18,599 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:32Z] INFO  16:32:18,600 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:32Z] INFO  16:32:18,601 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:32Z] INFO  16:32:18,618 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:32Z] INFO  16:32:18,824 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:32Z] GATK RealignerTargetCreator: R14-18102_kapa-NGv3-PE100-NGv3-sort-10_93851586_111625070-prep-prealign.bam 10:93851587-111625070
[2016-04-14T23:32Z] GATK: RealignerTargetCreator
[2016-04-14T23:32Z] INFO  16:32:19,351 ProgressMeter -     9:140146429    700014.0    90.0 s       2.2 m       91.2%    98.0 s       8.0 s
[2016-04-14T23:32Z] INFO  16:32:19,589 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:32Z] INFO  16:32:19,593 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:32Z] INFO  16:32:19,594 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:32Z] INFO  16:32:19,594 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:32Z] INFO  16:32:19,600 HelpFormatter - Program Args: -T PrintReads -L 11:47158867-62678572 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/11/tx/tmpBR_1sy/R14-18102_kapa-NGv3-PE100-NGv3-sort-11_47158866_62678572-prep-prealign.bam
[2016-04-14T23:32Z] INFO  16:32:19,611 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:32Z] INFO  16:32:19,622 HelpFormatter - Date/Time: 2016/04/14 16:32:19
[2016-04-14T23:32Z] INFO  16:32:19,623 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:32Z] INFO  16:32:19,624 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:32Z] INFO  16:32:19,816 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:32Z] INFO  16:32:20,244 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:32Z] INFO  16:32:20,258 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:32Z] INFO  16:32:20,259 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:32Z] INFO  16:32:20,260 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:32Z] INFO  16:32:20,264 HelpFormatter - Program Args: -T PrintReads -L 11:62744266-78270665 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/11/tx/tmpC5Rh5B/R14-18102_kapa-NGv3-PE100-NGv3-sort-11_62744265_78270665-prep-prealign.bam
[2016-04-14T23:32Z] INFO  16:32:20,283 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:32Z] INFO  16:32:20,284 HelpFormatter - Date/Time: 2016/04/14 16:32:20
[2016-04-14T23:32Z] INFO  16:32:20,284 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:32Z] INFO  16:32:20,285 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:32Z] INFO  16:32:20,356 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:32Z] INFO  16:32:20,360 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:32Z] INFO  16:32:20,361 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:32Z] INFO  16:32:20,361 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:32Z] INFO  16:32:20,366 HelpFormatter - Program Args: -T PrintReads -L 11:78277178-93796886 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/11/tx/tmpekBkmW/R14-18102_kapa-NGv3-PE100-NGv3-sort-11_78277177_93796886-prep-prealign.bam
[2016-04-14T23:32Z] INFO  16:32:20,398 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:32Z] INFO  16:32:20,404 HelpFormatter - Date/Time: 2016/04/14 16:32:20
[2016-04-14T23:32Z] INFO  16:32:20,405 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:32Z] INFO  16:32:20,406 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:32Z] INFO  16:32:20,524 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:32Z] INFO  16:32:20,632 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:32Z] INFO  16:32:20,913 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-14T23:32Z] INFO  16:32:21,011 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:32Z] INFO  16:32:21,020 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:32Z] INFO  16:32:21,078 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-14T23:32Z] INFO  16:32:21,102 IntervalUtils - Processing 15519706 bp from intervals
[2016-04-14T23:32Z] INFO  16:32:21,271 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:32Z] INFO  16:32:21,297 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:32Z] INFO  16:32:21,300 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:32Z] INFO  16:32:21,301 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:32Z] INFO  16:32:21,301 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:32Z] INFO  16:32:21,316 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/10/R14-18102_kapa-NGv3-PE100-NGv3-sort-10_111628371_127265443-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/10/tx/tmpAvOE4K/R14-18102_kapa-NGv3-PE100-NGv3-sort-10_111628371_127265443-prep-prealign-realign.intervals -l INFO -L 10:111628372-127265443 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-14T23:32Z] INFO  16:32:21,354 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:32Z] INFO  16:32:21,360 HelpFormatter - Date/Time: 2016/04/14 16:32:21
[2016-04-14T23:32Z] INFO  16:32:21,361 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:32Z] INFO  16:32:21,362 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:32Z] INFO  16:32:21,514 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:32Z] INFO  16:32:21,571 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:32Z] INFO  16:32:21,572 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:32Z] INFO  16:32:21,573 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:32Z] INFO  16:32:21,573 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:32Z] INFO  16:32:21,574 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:32Z] INFO  16:32:21,574 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:32Z] INFO  16:32:21,575 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:32Z] INFO  16:32:21,575 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:32Z] INFO  16:32:21,580 HelpFormatter - Program Args: -T PrintReads -L 11:93797497-109964158 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/11/tx/tmpvowFJc/R14-18102_kapa-NGv3-PE100-NGv3-sort-11_93797496_109964158-prep-prealign.bam
[2016-04-14T23:32Z] INFO  16:32:21,603 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:32Z] INFO  16:32:21,608 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:32Z] INFO  16:32:21,627 HelpFormatter - Date/Time: 2016/04/14 16:32:21
[2016-04-14T23:32Z] INFO  16:32:21,628 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:32Z] INFO  16:32:21,629 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:32Z] INFO  16:32:21,763 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-14T23:32Z] INFO  16:32:21,774 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:32Z] INFO  16:32:21,772 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:32Z] INFO  16:32:21,779 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-14T23:32Z] INFO  16:32:21,849 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:32Z] INFO  16:32:21,859 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:32Z] INFO  16:32:21,867 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:32Z] INFO  16:32:21,874 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.10
[2016-04-14T23:32Z] INFO  16:32:21,930 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-14T23:32Z] INFO  16:32:21,963 IntervalUtils - Processing 15526400 bp from intervals
[2016-04-14T23:32Z] INFO  16:32:21,988 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-14T23:32Z] INFO  16:32:22,033 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:32Z] INFO  16:32:22,036 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:32Z] INFO  16:32:22,037 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:32Z] INFO  16:32:22,038 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:32Z] INFO  16:32:22,042 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/10/R14-18102_kapa-NGv3-PE100-NGv3-sort-10_93851586_111625070-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/10/tx/tmp7bUJe2/R14-18102_kapa-NGv3-PE100-NGv3-sort-10_93851586_111625070-prep-prealign-realign.intervals -l INFO -L 10:93851587-111625070 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-14T23:32Z] INFO  16:32:22,048 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:32Z] INFO  16:32:22,073 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:32Z] INFO  16:32:22,072 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:32Z] INFO  16:32:22,073 HelpFormatter - Date/Time: 2016/04/14 16:32:22
[2016-04-14T23:32Z] INFO  16:32:22,074 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:32Z] INFO  16:32:22,074 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:32Z] INFO  16:32:22,093 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:32Z] INFO  16:32:22,140 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-14T23:32Z] INFO  16:32:22,171 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:32Z] INFO  16:32:22,176 IntervalUtils - Processing 15519709 bp from intervals
[2016-04-14T23:32Z] INFO  16:32:22,283 IntervalUtils - Processing 15637072 bp from intervals
[2016-04-14T23:32Z] WARN  16:32:22,299 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:32Z] INFO  16:32:22,322 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:32Z] INFO  16:32:22,370 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:32Z] INFO  16:32:22,372 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-14T23:32Z] INFO  16:32:22,382 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:32Z] INFO  16:32:22,396 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:32Z] INFO  16:32:22,397 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:32Z] INFO  16:32:22,398 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:32Z] INFO  16:32:22,399 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:32Z] INFO  16:32:22,417 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:32Z] INFO  16:32:22,457 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-14T23:32Z] INFO  16:32:22,622 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:32Z] INFO  16:32:22,624 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:32Z] INFO  16:32:22,625 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:32Z] INFO  16:32:22,625 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-14T23:32Z] INFO  16:32:22,646 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:32Z] INFO  16:32:22,647 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:32Z] INFO  16:32:22,648 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:32Z] INFO  16:32:22,648 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:32Z] INFO  16:32:22,647 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:32Z] INFO  16:32:22,688 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:32Z] INFO  16:32:22,782 IntervalUtils - Processing 17773484 bp from intervals
[2016-04-14T23:32Z] WARN  16:32:22,798 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:32Z] INFO  16:32:22,885 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:32Z] INFO  16:32:22,885 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:32Z] INFO  16:32:22,967 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-14T23:32Z] INFO  16:32:23,026 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:32Z] INFO  16:32:23,036 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:32Z] INFO  16:32:23,077 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.04
[2016-04-14T23:32Z] INFO  16:32:23,079 ProgressMeter -            done   1.5532667E7    21.0 s       1.0 s      100.0%    21.0 s       0.0 s
[2016-04-14T23:32Z] INFO  16:32:23,080 ProgressMeter - Total runtime 21.14 secs, 0.35 min, 0.01 hours
[2016-04-14T23:32Z] INFO  16:32:23,084 MicroScheduler - 128562 reads were filtered out during the traversal out of approximately 361487 total reads (35.56%)
[2016-04-14T23:32Z] INFO  16:32:23,090 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:32Z] INFO  16:32:23,091 MicroScheduler -   -> 597 reads (0.17% of total) failing BadMateFilter
[2016-04-14T23:32Z] INFO  16:32:23,091 IntervalUtils - Processing 16166662 bp from intervals
[2016-04-14T23:32Z] INFO  16:32:23,091 MicroScheduler -   -> 21661 reads (5.99% of total) failing DuplicateReadFilter
[2016-04-14T23:32Z] INFO  16:32:23,092 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-14T23:32Z] INFO  16:32:23,093 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:32Z] INFO  16:32:23,093 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-14T23:32Z] INFO  16:32:23,094 MicroScheduler -   -> 106304 reads (29.41% of total) failing MappingQualityZeroFilter
[2016-04-14T23:32Z] INFO  16:32:23,094 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:32Z] INFO  16:32:23,095 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-14T23:32Z] INFO  16:32:23,096 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-14T23:32Z] INFO  16:32:23,184 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:32Z] INFO  16:32:23,194 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:32Z] INFO  16:32:23,195 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:32Z] INFO  16:32:23,207 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:32Z] INFO  16:32:23,208 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-14T23:32Z] INFO  16:32:23,443 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:32Z] INFO  16:32:23,444 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:32Z] INFO  16:32:23,444 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:32Z] INFO  16:32:23,445 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:32Z] INFO  16:32:23,472 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:32Z] INFO  16:32:23,725 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:32Z] INFO  16:32:24,427 ProgressMeter -            done   8206026.0    13.0 s       1.0 s      100.0%    13.0 s       0.0 s
[2016-04-14T23:32Z] INFO  16:32:24,428 ProgressMeter - Total runtime 13.33 secs, 0.22 min, 0.00 hours
[2016-04-14T23:32Z] INFO  16:32:24,433 MicroScheduler - 16297 reads were filtered out during the traversal out of approximately 176954 total reads (9.21%)
[2016-04-14T23:32Z] INFO  16:32:24,434 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:32Z] INFO  16:32:24,434 MicroScheduler -   -> 486 reads (0.27% of total) failing BadMateFilter
[2016-04-14T23:32Z] INFO  16:32:24,435 MicroScheduler -   -> 14234 reads (8.04% of total) failing DuplicateReadFilter
[2016-04-14T23:32Z] INFO  16:32:24,435 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-14T23:32Z] INFO  16:32:24,436 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:32Z] INFO  16:32:24,437 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-14T23:32Z] INFO  16:32:24,437 MicroScheduler -   -> 1577 reads (0.89% of total) failing MappingQualityZeroFilter
[2016-04-14T23:32Z] INFO  16:32:24,438 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:32Z] INFO  16:32:24,438 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-14T23:32Z] INFO  16:32:24,449 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-14T23:32Z] INFO  16:32:24,766 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:32Z] GATK: realign ('10', 46960410, 62493077) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:32Z] INFO  16:32:25,954 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:32Z] GATK: realign ('10', 127328721, 135534747) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:32Z] INFO  16:32:26,818 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@7172f77a
[2016-04-14T23:32Z] INFO  16:32:27,016 ProgressMeter -            done    828757.0    98.0 s     118.0 s       99.3%    98.0 s       0.0 s
[2016-04-14T23:32Z] INFO  16:32:27,016 ProgressMeter - Total runtime 98.18 secs, 1.64 min, 0.03 hours
[2016-04-14T23:32Z] INFO  16:32:27,017 MicroScheduler - 430 reads were filtered out during the traversal out of approximately 829187 total reads (0.05%)
[2016-04-14T23:32Z] INFO  16:32:27,017 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:32Z] INFO  16:32:27,018 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:32Z] INFO  16:32:27,018 MicroScheduler -   -> 430 reads (0.05% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:32Z] INFO  16:32:27,842 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:32Z] INFO  16:32:27,845 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:32Z] INFO  16:32:27,846 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:32Z] INFO  16:32:27,846 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:32Z] INFO  16:32:27,851 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/10/R14-18102_kapa-NGv3-PE100-NGv3-sort-10_46960410_62493077-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/10/R14-18102_kapa-NGv3-PE100-NGv3-sort-10_46960410_62493077-prep-prealign-realign.intervals -L 10:46960411-62493077 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/10/tx/tmps9cr7V/R14-18102_kapa-NGv3-PE100-NGv3-sort-10_46960410_62493077-prep.bam
[2016-04-14T23:32Z] INFO  16:32:27,861 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:32Z] INFO  16:32:27,872 HelpFormatter - Date/Time: 2016/04/14 16:32:27
[2016-04-14T23:32Z] INFO  16:32:27,873 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:32Z] INFO  16:32:27,874 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:32Z] INFO  16:32:28,088 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:32Z] INFO  16:32:28,188 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:32Z] INFO  16:32:28,197 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:32Z] INFO  16:32:28,243 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.04
[2016-04-14T23:32Z] INFO  16:32:28,450 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:32Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-9_129097484_141213431-prep-prealign.bam
[2016-04-14T23:32Z] INFO  16:32:28,563 IntervalUtils - Processing 15532667 bp from intervals
[2016-04-14T23:32Z] WARN  16:32:28,567 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:32Z] INFO  16:32:28,648 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:32Z] INFO  16:32:28,696 ProgressMeter -            done    351620.0    25.0 s      72.0 s      100.0%    25.0 s       0.0 s
[2016-04-14T23:32Z] INFO  16:32:28,696 ProgressMeter - Total runtime 25.59 secs, 0.43 min, 0.01 hours
[2016-04-14T23:32Z] INFO  16:32:28,700 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 351620 total reads (0.00%)
[2016-04-14T23:32Z] INFO  16:32:28,700 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:32Z] INFO  16:32:28,700 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:32Z] INFO  16:32:28,701 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:32Z] INFO  16:32:28,799 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:32Z] INFO  16:32:28,800 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:32Z] INFO  16:32:28,800 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:32Z] INFO  16:32:28,801 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:32Z] INFO  16:32:28,963 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:32Z] INFO  16:32:29,119 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:32Z] INFO  16:32:29,123 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:32Z] INFO  16:32:29,123 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:32Z] INFO  16:32:29,124 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:32Z] INFO  16:32:29,129 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/10/R14-18102_kapa-NGv3-PE100-NGv3-sort-10_127328721_135534747-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/10/R14-18102_kapa-NGv3-PE100-NGv3-sort-10_127328721_135534747-prep-prealign-realign.intervals -L 10:127328722-135534747 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/10/tx/tmp0DUFo7/R14-18102_kapa-NGv3-PE100-NGv3-sort-10_127328721_135534747-prep.bam
[2016-04-14T23:32Z] INFO  16:32:29,156 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:32Z] INFO  16:32:29,156 HelpFormatter - Date/Time: 2016/04/14 16:32:29
[2016-04-14T23:32Z] INFO  16:32:29,157 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:32Z] INFO  16:32:29,157 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:32Z] INFO  16:32:29,190 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:32Z] INFO  16:32:29,358 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:32Z] INFO  16:32:29,540 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:32Z] INFO  16:32:29,553 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:32Z] INFO  16:32:29,623 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-14T23:32Z] INFO  16:32:30,088 IntervalUtils - Processing 8206026 bp from intervals
[2016-04-14T23:32Z] WARN  16:32:30,093 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:32Z] INFO  16:32:30,195 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:32Z] INFO  16:32:30,258 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:32Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-9_113231219_129089575-prep.bam
[2016-04-14T23:32Z] INFO  16:32:30,314 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:32Z] INFO  16:32:30,315 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:32Z] INFO  16:32:30,316 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:32Z] INFO  16:32:30,316 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:32Z] INFO  16:32:30,451 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:32Z] INFO  16:32:30,526 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:32Z] GATK RealignerTargetCreator: R14-18102_kapa-NGv3-PE100-NGv3-sort-9_129097484_141213431-prep-prealign.bam 9:129097485-141213431
[2016-04-14T23:32Z] GATK: RealignerTargetCreator
[2016-04-14T23:32Z] GATK pre-alignment ('11', 110001730, 125514538) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:32Z] INFO  16:32:33,789 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:32Z] INFO  16:32:33,793 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:32Z] INFO  16:32:33,794 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:32Z] INFO  16:32:33,795 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:32Z] INFO  16:32:33,800 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/9/R14-18102_kapa-NGv3-PE100-NGv3-sort-9_129097484_141213431-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/9/tx/tmpPeE9Zy/R14-18102_kapa-NGv3-PE100-NGv3-sort-9_129097484_141213431-prep-prealign-realign.intervals -l INFO -L 9:129097485-141213431 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-14T23:32Z] INFO  16:32:33,806 ProgressMeter -            done   1.554432E7    22.0 s       1.0 s      100.0%    22.0 s       0.0 s
[2016-04-14T23:32Z] INFO  16:32:33,807 ProgressMeter - Total runtime 22.26 secs, 0.37 min, 0.01 hours
[2016-04-14T23:32Z] INFO  16:32:33,812 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:32Z] INFO  16:32:33,813 HelpFormatter - Date/Time: 2016/04/14 16:32:33
[2016-04-14T23:32Z] INFO  16:32:33,812 MicroScheduler - 35426 reads were filtered out during the traversal out of approximately 361609 total reads (9.80%)
[2016-04-14T23:32Z] INFO  16:32:33,814 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:32Z] INFO  16:32:33,813 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:32Z] INFO  16:32:33,814 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:32Z] INFO  16:32:33,814 MicroScheduler -   -> 808 reads (0.22% of total) failing BadMateFilter
[2016-04-14T23:32Z] INFO  16:32:33,815 MicroScheduler -   -> 28567 reads (7.90% of total) failing DuplicateReadFilter
[2016-04-14T23:32Z] INFO  16:32:33,816 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-14T23:32Z] INFO  16:32:33,816 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:32Z] INFO  16:32:33,817 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-14T23:32Z] INFO  16:32:33,818 MicroScheduler -   -> 6051 reads (1.67% of total) failing MappingQualityZeroFilter
[2016-04-14T23:32Z] INFO  16:32:33,819 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:32Z] INFO  16:32:33,819 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-14T23:32Z] INFO  16:32:33,820 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-14T23:32Z] INFO  16:32:33,945 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:32Z] INFO  16:32:34,164 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@41fd9d8e
[2016-04-14T23:32Z] INFO  16:32:34,231 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-14T23:32Z] INFO  16:32:34,243 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:32Z] INFO  16:32:34,270 ProgressMeter -            done    204189.0    27.0 s       2.3 m      100.0%    27.0 s       0.0 s
[2016-04-14T23:32Z] INFO  16:32:34,270 ProgressMeter - Total runtime 27.90 secs, 0.46 min, 0.01 hours
[2016-04-14T23:32Z] INFO  16:32:34,271 MicroScheduler - 130 reads were filtered out during the traversal out of approximately 204319 total reads (0.06%)
[2016-04-14T23:32Z] INFO  16:32:34,271 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:32Z] INFO  16:32:34,272 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:32Z] INFO  16:32:34,272 MicroScheduler -   -> 130 reads (0.06% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:32Z] INFO  16:32:34,319 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-14T23:32Z] INFO  16:32:34,344 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:32Z] INFO  16:32:34,349 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:32Z] INFO  16:32:34,349 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:32Z] INFO  16:32:34,350 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:32Z] INFO  16:32:34,357 HelpFormatter - Program Args: -T PrintReads -L 11:110001731-125514538 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/11/tx/tmpcrMbNQ/R14-18102_kapa-NGv3-PE100-NGv3-sort-11_110001730_125514538-prep-prealign.bam
[2016-04-14T23:32Z] INFO  16:32:34,379 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:32Z] INFO  16:32:34,382 HelpFormatter - Date/Time: 2016/04/14 16:32:34
[2016-04-14T23:32Z] INFO  16:32:34,383 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:32Z] INFO  16:32:34,384 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:32Z] INFO  16:32:34,642 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:32Z] INFO  16:32:34,685 IntervalUtils - Processing 12115947 bp from intervals
[2016-04-14T23:32Z] WARN  16:32:34,690 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:32Z] INFO  16:32:34,772 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:32Z] INFO  16:32:34,999 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:32Z] INFO  16:32:35,000 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:32Z] INFO  16:32:35,001 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:32Z] INFO  16:32:35,002 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-14T23:32Z] INFO  16:32:35,210 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:32Z] GATK: realign ('10', 62539923, 78084243) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:32Z] INFO  16:32:35,644 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-14T23:32Z] INFO  16:32:35,675 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:32Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-11_16007749_31531554-prep-prealign.bam
[2016-04-14T23:32Z] INFO  16:32:35,724 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:32Z] INFO  16:32:35,744 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:32Z] INFO  16:32:35,829 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.09
[2016-04-14T23:32Z] INFO  16:32:35,853 IntervalUtils - Processing 15512808 bp from intervals
[2016-04-14T23:32Z] INFO  16:32:35,984 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:32Z] INFO  16:32:36,320 ProgressMeter -            done    249556.0    20.0 s      83.0 s      100.0%    20.0 s       0.0 s
[2016-04-14T23:32Z] INFO  16:32:36,321 ProgressMeter - Total runtime 20.86 secs, 0.35 min, 0.01 hours
[2016-04-14T23:32Z] INFO  16:32:36,325 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 249556 total reads (0.00%)
[2016-04-14T23:32Z] INFO  16:32:36,330 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:32Z] INFO  16:32:36,331 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:32Z] INFO  16:32:36,332 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:32Z] INFO  16:32:36,332 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:32Z] INFO  16:32:36,333 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:32Z] INFO  16:32:36,334 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:32Z] INFO  16:32:36,335 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:32Z] INFO  16:32:36,360 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:32Z] GATK RealignerTargetCreator: R14-18102_kapa-NGv3-PE100-NGv3-sort-11_16007749_31531554-prep-prealign.bam 11:16007750-31531554
[2016-04-14T23:32Z] GATK: RealignerTargetCreator
[2016-04-14T23:32Z] INFO  16:32:36,538 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:32Z] INFO  16:32:37,896 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:32Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-10_78316966_93841258-prep.bam
[2016-04-14T23:32Z] INFO  16:32:38,128 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:32Z] INFO  16:32:38,131 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:32Z] INFO  16:32:38,132 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:32Z] INFO  16:32:38,132 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:32Z] INFO  16:32:38,137 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/10/R14-18102_kapa-NGv3-PE100-NGv3-sort-10_62539923_78084243-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/10/R14-18102_kapa-NGv3-PE100-NGv3-sort-10_62539923_78084243-prep-prealign-realign.intervals -L 10:62539924-78084243 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/10/tx/tmp8Ud_t0/R14-18102_kapa-NGv3-PE100-NGv3-sort-10_62539923_78084243-prep.bam
[2016-04-14T23:32Z] INFO  16:32:38,148 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:32Z] INFO  16:32:38,175 HelpFormatter - Date/Time: 2016/04/14 16:32:38
[2016-04-14T23:32Z] INFO  16:32:38,175 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:32Z] INFO  16:32:38,175 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:32Z] INFO  16:32:38,388 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:32Z] INFO  16:32:38,463 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:32Z] INFO  16:32:38,472 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:32Z] INFO  16:32:38,517 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.04
[2016-04-14T23:32Z] GATK pre-alignment ('11', 125523640, 135006516) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:32Z] INFO  16:32:38,903 IntervalUtils - Processing 15544320 bp from intervals
[2016-04-14T23:32Z] WARN  16:32:38,908 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:32Z] INFO  16:32:38,990 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:32Z] INFO  16:32:39,122 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:32Z] INFO  16:32:39,123 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:32Z] INFO  16:32:39,124 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:32Z] INFO  16:32:39,124 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:32Z] INFO  16:32:39,312 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:32Z] INFO  16:32:39,415 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:32Z] INFO  16:32:39,419 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:32Z] INFO  16:32:39,419 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:32Z] INFO  16:32:39,420 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:32Z] INFO  16:32:39,424 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/11/R14-18102_kapa-NGv3-PE100-NGv3-sort-11_16007749_31531554-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/11/tx/tmpWYXBvm/R14-18102_kapa-NGv3-PE100-NGv3-sort-11_16007749_31531554-prep-prealign-realign.intervals -l INFO -L 11:16007750-31531554 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-14T23:32Z] INFO  16:32:39,436 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:32Z] INFO  16:32:39,436 HelpFormatter - Date/Time: 2016/04/14 16:32:39
[2016-04-14T23:32Z] INFO  16:32:39,436 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:32Z] INFO  16:32:39,437 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:32Z] INFO  16:32:39,482 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:32Z] INFO  16:32:39,575 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:32Z] INFO  16:32:39,758 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-14T23:32Z] INFO  16:32:39,768 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:32Z] INFO  16:32:39,832 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-14T23:32Z] INFO  16:32:40,088 IntervalUtils - Processing 15523805 bp from intervals
[2016-04-14T23:32Z] WARN  16:32:40,093 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:32Z] INFO  16:32:40,178 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:32Z] INFO  16:32:40,388 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:32Z] INFO  16:32:40,389 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:32Z] INFO  16:32:40,389 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:32Z] INFO  16:32:40,390 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-14T23:32Z] INFO  16:32:41,266 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:32Z] INFO  16:32:41,269 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:32Z] INFO  16:32:41,270 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:32Z] INFO  16:32:41,270 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:32Z] INFO  16:32:41,275 HelpFormatter - Program Args: -T PrintReads -L 11:125523641-135006516 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/11/tx/tmpystEEn/R14-18102_kapa-NGv3-PE100-NGv3-sort-11_125523640_135006516-prep-prealign.bam
[2016-04-14T23:32Z] INFO  16:32:41,293 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:32Z] INFO  16:32:41,294 HelpFormatter - Date/Time: 2016/04/14 16:32:41
[2016-04-14T23:32Z] INFO  16:32:41,294 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:32Z] INFO  16:32:41,295 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:32Z] INFO  16:32:41,470 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:32Z] INFO  16:32:42,529 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-14T23:32Z] INFO  16:32:42,579 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:32Z] INFO  16:32:42,589 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:32Z] INFO  16:32:42,648 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-14T23:32Z] INFO  16:32:42,664 IntervalUtils - Processing 9482876 bp from intervals
[2016-04-14T23:32Z] INFO  16:32:42,764 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:32Z] INFO  16:32:43,113 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:32Z] INFO  16:32:43,115 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:32Z] INFO  16:32:43,115 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:32Z] INFO  16:32:43,116 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:32Z] INFO  16:32:43,132 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:32Z] INFO  16:32:43,264 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:32Z] INFO  16:32:43,568 ProgressMeter -            done   1.5637072E7    20.0 s       1.0 s      100.0%    20.0 s       0.0 s
[2016-04-14T23:32Z] INFO  16:32:43,569 ProgressMeter - Total runtime 20.95 secs, 0.35 min, 0.01 hours
[2016-04-14T23:32Z] INFO  16:32:43,572 MicroScheduler - 35377 reads were filtered out during the traversal out of approximately 307914 total reads (11.49%)
[2016-04-14T23:32Z] INFO  16:32:43,574 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:32Z] INFO  16:32:43,574 MicroScheduler -   -> 779 reads (0.25% of total) failing BadMateFilter
[2016-04-14T23:32Z] INFO  16:32:43,575 MicroScheduler -   -> 23779 reads (7.72% of total) failing DuplicateReadFilter
[2016-04-14T23:32Z] INFO  16:32:43,575 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-14T23:32Z] INFO  16:32:43,575 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:32Z] INFO  16:32:43,575 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-14T23:32Z] INFO  16:32:43,575 MicroScheduler -   -> 10819 reads (3.51% of total) failing MappingQualityZeroFilter
[2016-04-14T23:32Z] INFO  16:32:43,576 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:32Z] INFO  16:32:43,576 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-14T23:32Z] INFO  16:32:43,576 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-14T23:32Z] INFO  16:32:44,367 ProgressMeter -            done    175852.0    14.0 s      79.0 s       99.5%    14.0 s       0.0 s
[2016-04-14T23:32Z] INFO  16:32:44,367 ProgressMeter - Total runtime 14.05 secs, 0.23 min, 0.00 hours
[2016-04-14T23:32Z] INFO  16:32:44,371 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 175852 total reads (0.00%)
[2016-04-14T23:32Z] INFO  16:32:44,371 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:32Z] INFO  16:32:44,371 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:32Z] INFO  16:32:44,371 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:32Z] INFO  16:32:45,085 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:32Z] GATK: realign ('10', 111628371, 127265443) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:32Z] INFO  16:32:45,172 ProgressMeter -            done    485974.0    31.0 s      65.0 s      100.0%    31.0 s       0.0 s
[2016-04-14T23:32Z] INFO  16:32:45,174 ProgressMeter - Total runtime 31.64 secs, 0.53 min, 0.01 hours
[2016-04-14T23:32Z] INFO  16:32:45,178 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 485974 total reads (0.00%)
[2016-04-14T23:32Z] INFO  16:32:45,180 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:32Z] INFO  16:32:45,180 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:32Z] INFO  16:32:45,181 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:32Z] INFO  16:32:45,790 ProgressMeter -      11:5624572    400067.0    60.0 s       2.5 m       35.2%     2.8 m     110.0 s
[2016-04-14T23:32Z] INFO  16:32:46,015 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:32Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-10_127328721_135534747-prep.bam
[2016-04-14T23:32Z] GATK pre-alignment ('12', 0, 15637181) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:32Z] INFO  16:32:46,991 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:32Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-9_32407258_65506776-prep.bam
[2016-04-14T23:32Z] INFO  16:32:47,531 ProgressMeter -            done   1.7773484E7    24.0 s       1.0 s      100.0%    24.0 s       0.0 s
[2016-04-14T23:32Z] INFO  16:32:47,532 ProgressMeter - Total runtime 24.34 secs, 0.41 min, 0.01 hours
[2016-04-14T23:32Z] INFO  16:32:47,538 MicroScheduler - 42528 reads were filtered out during the traversal out of approximately 508233 total reads (8.37%)
[2016-04-14T23:32Z] INFO  16:32:47,539 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:32Z] INFO  16:32:47,540 MicroScheduler -   -> 1127 reads (0.22% of total) failing BadMateFilter
[2016-04-14T23:32Z] INFO  16:32:47,541 MicroScheduler -   -> 39935 reads (7.86% of total) failing DuplicateReadFilter
[2016-04-14T23:32Z] INFO  16:32:47,542 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-14T23:32Z] INFO  16:32:47,543 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:32Z] INFO  16:32:47,544 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-14T23:32Z] INFO  16:32:47,544 MicroScheduler -   -> 1466 reads (0.29% of total) failing MappingQualityZeroFilter
[2016-04-14T23:32Z] INFO  16:32:47,545 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:32Z] INFO  16:32:47,546 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-14T23:32Z] INFO  16:32:47,547 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-14T23:32Z] INFO  16:32:47,958 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:32Z] INFO  16:32:47,961 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:32Z] INFO  16:32:47,962 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:32Z] INFO  16:32:47,963 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:32Z] INFO  16:32:47,967 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/10/R14-18102_kapa-NGv3-PE100-NGv3-sort-10_111628371_127265443-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/10/R14-18102_kapa-NGv3-PE100-NGv3-sort-10_111628371_127265443-prep-prealign-realign.intervals -L 10:111628372-127265443 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/10/tx/tmp1KkzdV/R14-18102_kapa-NGv3-PE100-NGv3-sort-10_111628371_127265443-prep.bam
[2016-04-14T23:32Z] INFO  16:32:47,987 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:32Z] INFO  16:32:47,987 HelpFormatter - Date/Time: 2016/04/14 16:32:47
[2016-04-14T23:32Z] INFO  16:32:47,987 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:32Z] INFO  16:32:47,988 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:32Z] INFO  16:32:48,190 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:32Z] INFO  16:32:48,304 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:32Z] INFO  16:32:48,313 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:32Z] INFO  16:32:48,354 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.04
[2016-04-14T23:32Z] INFO  16:32:48,622 ProgressMeter -     11:46772875    200002.0    30.0 s       2.5 m       98.1%    30.0 s       0.0 s
[2016-04-14T23:32Z] GATK pre-alignment ('12', 15650178, 31231471) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:32Z] INFO  16:32:48,834 IntervalUtils - Processing 15637072 bp from intervals
[2016-04-14T23:32Z] WARN  16:32:48,839 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:32Z] INFO  16:32:48,894 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:32Z] GATK: realign ('10', 93851586, 111625070) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:32Z] INFO  16:32:48,917 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:32Z] INFO  16:32:48,977 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@41fd9d8e
[2016-04-14T23:32Z] INFO  16:32:49,081 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:32Z] INFO  16:32:49,082 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:32Z] INFO  16:32:49,082 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:32Z] INFO  16:32:49,083 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:32Z] INFO  16:32:49,152 ProgressMeter -            done    183470.0    25.0 s       2.3 m      100.0%    25.0 s       0.0 s
[2016-04-14T23:32Z] INFO  16:32:49,153 ProgressMeter - Total runtime 25.71 secs, 0.43 min, 0.01 hours
[2016-04-14T23:32Z] INFO  16:32:49,153 MicroScheduler - 110 reads were filtered out during the traversal out of approximately 183580 total reads (0.06%)
[2016-04-14T23:32Z] INFO  16:32:49,153 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:32Z] INFO  16:32:49,154 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:32Z] INFO  16:32:49,154 MicroScheduler -   -> 110 reads (0.06% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:32Z] INFO  16:32:49,266 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:32Z] INFO  16:32:49,271 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:32Z] INFO  16:32:49,271 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:32Z] INFO  16:32:49,271 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:32Z] INFO  16:32:49,275 HelpFormatter - Program Args: -T PrintReads -L 12:1-15637181 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/12/tx/tmp7cvXo0/R14-18102_kapa-NGv3-PE100-NGv3-sort-12_0_15637181-prep-prealign.bam
[2016-04-14T23:32Z] INFO  16:32:49,289 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:32Z] INFO  16:32:49,290 HelpFormatter - Date/Time: 2016/04/14 16:32:49
[2016-04-14T23:32Z] INFO  16:32:49,290 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:32Z] INFO  16:32:49,290 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:32Z] INFO  16:32:49,331 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:32Z] INFO  16:32:49,425 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@7172f77a
[2016-04-14T23:32Z] INFO  16:32:49,454 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:32Z] INFO  16:32:49,563 ProgressMeter -            done    193112.0    26.0 s       2.3 m      100.0%    26.0 s       0.0 s
[2016-04-14T23:32Z] INFO  16:32:49,563 ProgressMeter - Total runtime 26.92 secs, 0.45 min, 0.01 hours
[2016-04-14T23:32Z] INFO  16:32:49,564 MicroScheduler - 127 reads were filtered out during the traversal out of approximately 193239 total reads (0.07%)
[2016-04-14T23:32Z] INFO  16:32:49,564 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:32Z] INFO  16:32:49,564 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:32Z] INFO  16:32:49,565 MicroScheduler -   -> 127 reads (0.07% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:32Z] INFO  16:32:49,590 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:32Z] INFO  16:32:50,234 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@41fd9d8e
[2016-04-14T23:32Z] INFO  16:32:50,373 ProgressMeter -            done    237430.0    31.0 s       2.2 m      100.0%    31.0 s       0.0 s
[2016-04-14T23:32Z] INFO  16:32:50,373 ProgressMeter - Total runtime 31.77 secs, 0.53 min, 0.01 hours
[2016-04-14T23:32Z] INFO  16:32:50,374 MicroScheduler - 178 reads were filtered out during the traversal out of approximately 237608 total reads (0.07%)
[2016-04-14T23:32Z] INFO  16:32:50,374 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:32Z] INFO  16:32:50,375 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:32Z] INFO  16:32:50,375 MicroScheduler -   -> 178 reads (0.07% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:32Z] INFO  16:32:50,442 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:32Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-11_93797496_109964158-prep-prealign.bam
[2016-04-14T23:32Z] INFO  16:32:50,678 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-14T23:32Z] INFO  16:32:50,776 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:32Z] INFO  16:32:50,785 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:32Z] INFO  16:32:50,876 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.09
[2016-04-14T23:32Z] INFO  16:32:50,912 IntervalUtils - Processing 15637181 bp from intervals
[2016-04-14T23:32Z] INFO  16:32:51,049 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:32Z] GATK RealignerTargetCreator: R14-18102_kapa-NGv3-PE100-NGv3-sort-11_93797496_109964158-prep-prealign.bam 11:93797497-109964158
[2016-04-14T23:32Z] GATK: RealignerTargetCreator
[2016-04-14T23:32Z] INFO  16:32:51,147 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:32Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-11_78277177_93796886-prep-prealign.bam
[2016-04-14T23:32Z] INFO  16:32:51,322 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:32Z] INFO  16:32:51,323 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:32Z] INFO  16:32:51,324 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:32Z] INFO  16:32:51,324 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:32Z] INFO  16:32:51,349 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:32Z] INFO  16:32:51,535 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:32Z] INFO  16:32:51,589 ProgressMeter -     11:57413849    200006.0    30.0 s       2.5 m       66.1%    45.0 s      15.0 s
[2016-04-14T23:32Z] INFO  16:32:51,698 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:32Z] INFO  16:32:51,702 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:32Z] INFO  16:32:51,702 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:32Z] INFO  16:32:51,703 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:32Z] INFO  16:32:51,707 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/10/R14-18102_kapa-NGv3-PE100-NGv3-sort-10_93851586_111625070-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/10/R14-18102_kapa-NGv3-PE100-NGv3-sort-10_93851586_111625070-prep-prealign-realign.intervals -L 10:93851587-111625070 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/10/tx/tmpRGyZVy/R14-18102_kapa-NGv3-PE100-NGv3-sort-10_93851586_111625070-prep.bam
[2016-04-14T23:32Z] INFO  16:32:51,725 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:32Z] INFO  16:32:51,726 HelpFormatter - Date/Time: 2016/04/14 16:32:51
[2016-04-14T23:32Z] INFO  16:32:51,727 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:32Z] INFO  16:32:51,727 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:32Z] INFO  16:32:51,756 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:32Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-11_31541602_47074069-prep-prealign.bam
[2016-04-14T23:32Z] GATK RealignerTargetCreator: R14-18102_kapa-NGv3-PE100-NGv3-sort-11_78277177_93796886-prep-prealign.bam 11:78277178-93796886
[2016-04-14T23:32Z] GATK: RealignerTargetCreator
[2016-04-14T23:32Z] INFO  16:32:51,874 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:32Z] INFO  16:32:51,878 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:32Z] INFO  16:32:51,879 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:32Z] INFO  16:32:51,879 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:32Z] INFO  16:32:51,884 HelpFormatter - Program Args: -T PrintReads -L 12:15650179-31231471 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/12/tx/tmpYVwato/R14-18102_kapa-NGv3-PE100-NGv3-sort-12_15650178_31231471-prep-prealign.bam
[2016-04-14T23:32Z] INFO  16:32:51,908 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:32Z] INFO  16:32:51,908 HelpFormatter - Date/Time: 2016/04/14 16:32:51
[2016-04-14T23:32Z] INFO  16:32:51,908 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:32Z] INFO  16:32:51,908 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:32Z] INFO  16:32:51,996 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:32Z] INFO  16:32:52,088 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:32Z] INFO  16:32:52,137 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:32Z] INFO  16:32:52,145 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:32Z] INFO  16:32:52,225 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-14T23:32Z] INFO  16:32:52,437 ProgressMeter -     11:64884564    200007.0    30.0 s       2.5 m       13.8%     3.6 m       3.1 m
[2016-04-14T23:32Z] INFO  16:32:52,600 IntervalUtils - Processing 17773484 bp from intervals
[2016-04-14T23:32Z] GATK RealignerTargetCreator: R14-18102_kapa-NGv3-PE100-NGv3-sort-11_31541602_47074069-prep-prealign.bam 11:31541603-47074069
[2016-04-14T23:32Z] WARN  16:32:52,607 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:32Z] GATK: RealignerTargetCreator
[2016-04-14T23:32Z] INFO  16:32:52,705 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:32Z] INFO  16:32:52,738 ProgressMeter -            done    359171.0    23.0 s      66.0 s      100.0%    23.0 s       0.0 s
[2016-04-14T23:32Z] INFO  16:32:52,738 ProgressMeter - Total runtime 23.94 secs, 0.40 min, 0.01 hours
[2016-04-14T23:32Z] INFO  16:32:52,742 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 359171 total reads (0.00%)
[2016-04-14T23:32Z] INFO  16:32:52,743 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:32Z] INFO  16:32:52,743 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:32Z] INFO  16:32:52,744 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:32Z] INFO  16:32:52,978 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:32Z] INFO  16:32:52,979 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:32Z] INFO  16:32:52,979 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:32Z] INFO  16:32:52,980 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:32Z] INFO  16:32:53,284 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-14T23:32Z] INFO  16:32:53,311 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:32Z] INFO  16:32:53,355 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:32Z] INFO  16:32:53,379 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:32Z] INFO  16:32:53,460 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-14T23:32Z] INFO  16:32:53,478 IntervalUtils - Processing 15581293 bp from intervals
[2016-04-14T23:32Z] INFO  16:32:53,535 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:32Z] INFO  16:32:53,587 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:32Z] INFO  16:32:53,901 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:32Z] INFO  16:32:53,902 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:32Z] INFO  16:32:53,903 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:32Z] INFO  16:32:53,904 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:32Z] INFO  16:32:53,926 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:32Z] INFO  16:32:53,987 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:32Z] INFO  16:32:53,989 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:32Z] INFO  16:32:53,989 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:32Z] INFO  16:32:53,989 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:32Z] INFO  16:32:54,001 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/11/R14-18102_kapa-NGv3-PE100-NGv3-sort-11_93797496_109964158-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/11/tx/tmpUCMUYp/R14-18102_kapa-NGv3-PE100-NGv3-sort-11_93797496_109964158-prep-prealign-realign.intervals -l INFO -L 11:93797497-109964158 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-14T23:32Z] INFO  16:32:54,011 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:32Z] INFO  16:32:54,012 HelpFormatter - Date/Time: 2016/04/14 16:32:53
[2016-04-14T23:32Z] INFO  16:32:54,013 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:32Z] INFO  16:32:54,013 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:32Z] INFO  16:32:54,118 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:32Z] INFO  16:32:54,156 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:32Z] INFO  16:32:54,314 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:32Z] INFO  16:32:54,352 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-14T23:32Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-10_46960410_62493077-prep.bam
[2016-04-14T23:32Z] INFO  16:32:54,361 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:32Z] INFO  16:32:54,403 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.04
[2016-04-14T23:32Z] INFO  16:32:54,668 IntervalUtils - Processing 16166662 bp from intervals
[2016-04-14T23:32Z] WARN  16:32:54,683 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:32Z] INFO  16:32:54,754 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:32Z] INFO  16:32:54,768 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:32Z] INFO  16:32:54,769 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:32Z] INFO  16:32:54,770 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:32Z] INFO  16:32:54,775 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/11/R14-18102_kapa-NGv3-PE100-NGv3-sort-11_78277177_93796886-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/11/tx/tmptWawjl/R14-18102_kapa-NGv3-PE100-NGv3-sort-11_78277177_93796886-prep-prealign-realign.intervals -l INFO -L 11:78277178-93796886 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-14T23:32Z] INFO  16:32:54,795 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:32Z] INFO  16:32:54,806 HelpFormatter - Date/Time: 2016/04/14 16:32:54
[2016-04-14T23:32Z] INFO  16:32:54,807 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:32Z] INFO  16:32:54,808 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:32Z] INFO  16:32:54,825 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:32Z] INFO  16:32:54,946 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:32Z] INFO  16:32:54,984 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:32Z] INFO  16:32:54,986 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:32Z] INFO  16:32:54,986 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:32Z] INFO  16:32:54,987 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-14T23:32Z] INFO  16:32:55,179 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-14T23:32Z] INFO  16:32:55,200 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:32Z] INFO  16:32:55,253 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-14T23:32Z] GATK pre-alignment ('12', 31236746, 46754992) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:32Z] INFO  16:32:55,645 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:32Z] INFO  16:32:55,648 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:32Z] INFO  16:32:55,649 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:32Z] INFO  16:32:55,648 IntervalUtils - Processing 15519709 bp from intervals
[2016-04-14T23:32Z] INFO  16:32:55,649 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:32Z] INFO  16:32:55,654 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/11/R14-18102_kapa-NGv3-PE100-NGv3-sort-11_31541602_47074069-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/11/tx/tmpTkQnRd/R14-18102_kapa-NGv3-PE100-NGv3-sort-11_31541602_47074069-prep-prealign-realign.intervals -l INFO -L 11:31541603-47074069 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-14T23:32Z] WARN  16:32:55,653 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:32Z] INFO  16:32:55,684 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:32Z] INFO  16:32:55,685 HelpFormatter - Date/Time: 2016/04/14 16:32:55
[2016-04-14T23:32Z] INFO  16:32:55,686 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:32Z] INFO  16:32:55,686 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:32Z] INFO  16:32:55,802 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:32Z] INFO  16:32:55,824 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:32Z] INFO  16:32:55,989 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:32Z] INFO  16:32:55,990 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:32Z] INFO  16:32:55,991 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:32Z] INFO  16:32:55,991 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-14T23:32Z] INFO  16:32:56,096 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-14T23:32Z] INFO  16:32:56,115 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:32Z] INFO  16:32:56,194 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-14T23:32Z] INFO  16:32:56,485 IntervalUtils - Processing 15532467 bp from intervals
[2016-04-14T23:32Z] WARN  16:32:56,490 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:32Z] INFO  16:32:56,557 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:32Z] INFO  16:32:56,728 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:32Z] INFO  16:32:56,729 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:32Z] INFO  16:32:56,730 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:32Z] INFO  16:32:56,731 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-14T23:32Z] INFO  16:32:58,648 ProgressMeter -            done   1.5523805E7    18.0 s       1.0 s      100.0%    18.0 s       0.0 s
[2016-04-14T23:32Z] INFO  16:32:58,649 ProgressMeter - Total runtime 18.26 secs, 0.30 min, 0.01 hours
[2016-04-14T23:32Z] INFO  16:32:58,654 MicroScheduler - 17842 reads were filtered out during the traversal out of approximately 205724 total reads (8.67%)
[2016-04-14T23:32Z] INFO  16:32:58,655 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:32Z] INFO  16:32:58,655 MicroScheduler -   -> 590 reads (0.29% of total) failing BadMateFilter
[2016-04-14T23:32Z] INFO  16:32:58,656 MicroScheduler -   -> 16420 reads (7.98% of total) failing DuplicateReadFilter
[2016-04-14T23:32Z] INFO  16:32:58,657 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-14T23:32Z] INFO  16:32:58,657 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:32Z] INFO  16:32:58,658 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-14T23:32Z] INFO  16:32:58,659 MicroScheduler -   -> 832 reads (0.40% of total) failing MappingQualityZeroFilter
[2016-04-14T23:32Z] INFO  16:32:58,659 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:32Z] INFO  16:32:58,660 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-14T23:32Z] INFO  16:32:58,660 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-14T23:32Z] INFO  16:32:58,741 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:32Z] INFO  16:32:58,745 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:32Z] INFO  16:32:58,745 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:32Z] INFO  16:32:58,746 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:32Z] INFO  16:32:58,750 HelpFormatter - Program Args: -T PrintReads -L 12:31236747-46754992 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/12/tx/tmpVa_2d_/R14-18102_kapa-NGv3-PE100-NGv3-sort-12_31236746_46754992-prep-prealign.bam
[2016-04-14T23:32Z] INFO  16:32:58,765 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:32Z] INFO  16:32:58,766 HelpFormatter - Date/Time: 2016/04/14 16:32:58
[2016-04-14T23:32Z] INFO  16:32:58,767 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:32Z] INFO  16:32:58,767 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:32Z] INFO  16:32:58,968 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:33Z] INFO  16:33:00,146 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:33Z] GATK: realign ('11', 16007749, 31531554) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:33Z] INFO  16:33:00,213 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-14T23:33Z] INFO  16:33:00,287 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:33Z] INFO  16:33:00,296 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:33Z] INFO  16:33:00,348 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-14T23:33Z] INFO  16:33:00,373 IntervalUtils - Processing 15518246 bp from intervals
[2016-04-14T23:33Z] INFO  16:33:00,474 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:33Z] INFO  16:33:00,772 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:33Z] INFO  16:33:00,773 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:33Z] INFO  16:33:00,773 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:33Z] INFO  16:33:00,773 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:33Z] INFO  16:33:00,805 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:33Z] INFO  16:33:00,943 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:33Z] INFO  16:33:02,520 ProgressMeter -            done    359648.0    23.0 s      65.0 s      100.0%    23.0 s       0.0 s
[2016-04-14T23:33Z] INFO  16:33:02,520 ProgressMeter - Total runtime 23.40 secs, 0.39 min, 0.01 hours
[2016-04-14T23:33Z] INFO  16:33:02,524 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 359648 total reads (0.00%)
[2016-04-14T23:33Z] INFO  16:33:02,525 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:33Z] INFO  16:33:02,525 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:33Z] INFO  16:33:02,525 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:33Z] INFO  16:33:02,543 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:33Z] INFO  16:33:02,549 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:33Z] INFO  16:33:02,550 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:33Z] INFO  16:33:02,550 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:33Z] INFO  16:33:02,555 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/11/R14-18102_kapa-NGv3-PE100-NGv3-sort-11_16007749_31531554-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/11/R14-18102_kapa-NGv3-PE100-NGv3-sort-11_16007749_31531554-prep-prealign-realign.intervals -L 11:16007750-31531554 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/11/tx/tmpKcYlzQ/R14-18102_kapa-NGv3-PE100-NGv3-sort-11_16007749_31531554-prep.bam
[2016-04-14T23:33Z] INFO  16:33:02,565 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:33Z] INFO  16:33:02,565 HelpFormatter - Date/Time: 2016/04/14 16:33:02
[2016-04-14T23:33Z] INFO  16:33:02,565 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:33Z] INFO  16:33:02,566 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:33Z] INFO  16:33:02,795 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:33Z] INFO  16:33:02,910 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:33Z] INFO  16:33:02,926 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:33Z] INFO  16:33:02,980 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-14T23:33Z] INFO  16:33:03,414 IntervalUtils - Processing 15523805 bp from intervals
[2016-04-14T23:33Z] WARN  16:33:03,425 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:33Z] INFO  16:33:03,499 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:33Z] INFO  16:33:03,606 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:33Z] INFO  16:33:03,607 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:33Z] INFO  16:33:03,608 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:33Z] INFO  16:33:03,608 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:33Z] INFO  16:33:03,753 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:33Z] INFO  16:33:03,953 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:33Z] INFO  16:33:04,232 ProgressMeter -            done   1.2115947E7    29.0 s       2.0 s      100.0%    29.0 s       0.0 s
[2016-04-14T23:33Z] INFO  16:33:04,233 ProgressMeter - Total runtime 29.23 secs, 0.49 min, 0.01 hours
[2016-04-14T23:33Z] INFO  16:33:04,237 MicroScheduler - 77085 reads were filtered out during the traversal out of approximately 834182 total reads (9.24%)
[2016-04-14T23:33Z] INFO  16:33:04,238 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:33Z] INFO  16:33:04,238 MicroScheduler -   -> 1591 reads (0.19% of total) failing BadMateFilter
[2016-04-14T23:33Z] INFO  16:33:04,238 MicroScheduler -   -> 66632 reads (7.99% of total) failing DuplicateReadFilter
[2016-04-14T23:33Z] INFO  16:33:04,239 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-14T23:33Z] INFO  16:33:04,239 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:33Z] INFO  16:33:04,239 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-14T23:33Z] INFO  16:33:04,240 MicroScheduler -   -> 8862 reads (1.06% of total) failing MappingQualityZeroFilter
[2016-04-14T23:33Z] INFO  16:33:04,240 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:33Z] INFO  16:33:04,240 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-14T23:33Z] INFO  16:33:04,240 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-14T23:33Z] INFO  16:33:04,243 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:33Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-10_62539923_78084243-prep.bam
[2016-04-14T23:33Z] GATK pre-alignment ('12', 46756066, 62654284) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:33Z] INFO  16:33:05,630 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:33Z] GATK: realign ('9', 129097484, 141213431) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:33Z] INFO  16:33:07,380 ProgressMeter -    11:117301721    100002.0    31.0 s       5.2 m       47.1%    65.0 s      34.0 s
[2016-04-14T23:33Z] INFO  16:33:08,314 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:33Z] INFO  16:33:08,340 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:33Z] INFO  16:33:08,340 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:33Z] INFO  16:33:08,341 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:33Z] INFO  16:33:08,346 HelpFormatter - Program Args: -T PrintReads -L 12:46756067-62654284 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/12/tx/tmpQCSA2n/R14-18102_kapa-NGv3-PE100-NGv3-sort-12_46756066_62654284-prep-prealign.bam
[2016-04-14T23:33Z] INFO  16:33:08,357 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:33Z] INFO  16:33:08,358 HelpFormatter - Date/Time: 2016/04/14 16:33:08
[2016-04-14T23:33Z] INFO  16:33:08,359 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:33Z] INFO  16:33:08,359 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:33Z] INFO  16:33:08,428 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:33Z] INFO  16:33:08,432 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:33Z] INFO  16:33:08,432 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:33Z] INFO  16:33:08,433 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:33Z] INFO  16:33:08,438 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/9/R14-18102_kapa-NGv3-PE100-NGv3-sort-9_129097484_141213431-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/9/R14-18102_kapa-NGv3-PE100-NGv3-sort-9_129097484_141213431-prep-prealign-realign.intervals -L 9:129097485-141213431 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/9/tx/tmpc3GNEg/R14-18102_kapa-NGv3-PE100-NGv3-sort-9_129097484_141213431-prep.bam
[2016-04-14T23:33Z] INFO  16:33:08,447 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:33Z] INFO  16:33:08,448 HelpFormatter - Date/Time: 2016/04/14 16:33:08
[2016-04-14T23:33Z] INFO  16:33:08,448 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:33Z] INFO  16:33:08,449 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:33Z] INFO  16:33:08,622 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:33Z] INFO  16:33:08,632 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:33Z] INFO  16:33:08,729 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:33Z] INFO  16:33:08,740 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:33Z] INFO  16:33:08,818 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-14T23:33Z] INFO  16:33:09,330 IntervalUtils - Processing 12115947 bp from intervals
[2016-04-14T23:33Z] WARN  16:33:09,336 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:33Z] INFO  16:33:09,426 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:33Z] INFO  16:33:09,620 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-14T23:33Z] INFO  16:33:09,627 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:33Z] INFO  16:33:09,628 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:33Z] INFO  16:33:09,628 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:33Z] INFO  16:33:09,628 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:33Z] INFO  16:33:09,686 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:33Z] INFO  16:33:09,705 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:33Z] INFO  16:33:09,769 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-14T23:33Z] INFO  16:33:09,799 IntervalUtils - Processing 15898218 bp from intervals
[2016-04-14T23:33Z] INFO  16:33:09,809 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:33Z] INFO  16:33:09,893 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:33Z] INFO  16:33:09,931 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:33Z] INFO  16:33:10,216 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:33Z] INFO  16:33:10,217 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:33Z] INFO  16:33:10,218 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:33Z] INFO  16:33:10,219 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:33Z] INFO  16:33:10,234 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:33Z] INFO  16:33:10,449 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:33Z] INFO  16:33:10,970 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@41fd9d8e
[2016-04-14T23:33Z] INFO  16:33:11,185 ProgressMeter -            done    172005.0    28.0 s       2.7 m       99.2%    28.0 s       0.0 s
[2016-04-14T23:33Z] INFO  16:33:11,185 ProgressMeter - Total runtime 28.07 secs, 0.47 min, 0.01 hours
[2016-04-14T23:33Z] INFO  16:33:11,186 MicroScheduler - 101 reads were filtered out during the traversal out of approximately 172106 total reads (0.06%)
[2016-04-14T23:33Z] INFO  16:33:11,186 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:33Z] INFO  16:33:11,186 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:33Z] INFO  16:33:11,187 MicroScheduler -   -> 101 reads (0.06% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:33Z] INFO  16:33:12,670 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:33Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-11_125523640_135006516-prep-prealign.bam
[2016-04-14T23:33Z] INFO  16:33:12,813 ProgressMeter -            done   1.6166662E7    17.0 s       1.0 s      100.0%    17.0 s       0.0 s
[2016-04-14T23:33Z] INFO  16:33:12,814 ProgressMeter - Total runtime 17.83 secs, 0.30 min, 0.00 hours
[2016-04-14T23:33Z] INFO  16:33:12,818 MicroScheduler - 15499 reads were filtered out during the traversal out of approximately 184501 total reads (8.40%)
[2016-04-14T23:33Z] INFO  16:33:12,819 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:33Z] INFO  16:33:12,820 MicroScheduler -   -> 578 reads (0.31% of total) failing BadMateFilter
[2016-04-14T23:33Z] INFO  16:33:12,821 MicroScheduler -   -> 14386 reads (7.80% of total) failing DuplicateReadFilter
[2016-04-14T23:33Z] INFO  16:33:12,821 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-14T23:33Z] INFO  16:33:12,822 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:33Z] INFO  16:33:12,823 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-14T23:33Z] INFO  16:33:12,823 MicroScheduler -   -> 535 reads (0.29% of total) failing MappingQualityZeroFilter
[2016-04-14T23:33Z] INFO  16:33:12,824 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:33Z] INFO  16:33:12,824 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-14T23:33Z] INFO  16:33:12,825 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-14T23:33Z] INFO  16:33:13,076 ProgressMeter -            done    305977.0    23.0 s      78.0 s      100.0%    23.0 s       0.0 s
[2016-04-14T23:33Z] INFO  16:33:13,077 ProgressMeter - Total runtime 24.00 secs, 0.40 min, 0.01 hours
[2016-04-14T23:33Z] INFO  16:33:13,081 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 305977 total reads (0.00%)
[2016-04-14T23:33Z] INFO  16:33:13,083 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:33Z] INFO  16:33:13,083 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:33Z] INFO  16:33:13,084 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:33Z] INFO  16:33:13,197 ProgressMeter -            done   1.5519709E7    17.0 s       1.0 s      100.0%    17.0 s       0.0 s
[2016-04-14T23:33Z] INFO  16:33:13,209 ProgressMeter - Total runtime 17.22 secs, 0.29 min, 0.00 hours
[2016-04-14T23:33Z] INFO  16:33:13,213 MicroScheduler - 46433 reads were filtered out during the traversal out of approximately 194173 total reads (23.91%)
[2016-04-14T23:33Z] INFO  16:33:13,214 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:33Z] INFO  16:33:13,215 MicroScheduler -   -> 601 reads (0.31% of total) failing BadMateFilter
[2016-04-14T23:33Z] INFO  16:33:13,216 MicroScheduler -   -> 13263 reads (6.83% of total) failing DuplicateReadFilter
[2016-04-14T23:33Z] INFO  16:33:13,217 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-14T23:33Z] INFO  16:33:13,217 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:33Z] INFO  16:33:13,218 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-14T23:33Z] INFO  16:33:13,218 MicroScheduler -   -> 32569 reads (16.77% of total) failing MappingQualityZeroFilter
[2016-04-14T23:33Z] INFO  16:33:13,219 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:33Z] INFO  16:33:13,220 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-14T23:33Z] INFO  16:33:13,220 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-14T23:33Z] GATK RealignerTargetCreator: R14-18102_kapa-NGv3-PE100-NGv3-sort-11_125523640_135006516-prep-prealign.bam 11:125523641-135006516
[2016-04-14T23:33Z] GATK: RealignerTargetCreator
[2016-04-14T23:33Z] INFO  16:33:14,091 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:33Z] GATK: realign ('11', 93797496, 109964158) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:33Z] INFO  16:33:14,705 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:33Z] GATK: realign ('11', 78277177, 93796886) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:33Z] INFO  16:33:14,813 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:33Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-10_111628371_127265443-prep.bam
[2016-04-14T23:33Z] INFO  16:33:15,791 ProgressMeter -     11:10823603    700073.0    90.0 s       2.1 m       67.7%     2.2 m      42.0 s
[2016-04-14T23:33Z] GATK pre-alignment ('12', 62687959, 78225484) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:33Z] INFO  16:33:15,934 ProgressMeter -            done   1.5532467E7    19.0 s       1.0 s      100.0%    19.0 s       0.0 s
[2016-04-14T23:33Z] INFO  16:33:15,934 ProgressMeter - Total runtime 19.21 secs, 0.32 min, 0.01 hours
[2016-04-14T23:33Z] INFO  16:33:15,938 MicroScheduler - 20533 reads were filtered out during the traversal out of approximately 239250 total reads (8.58%)
[2016-04-14T23:33Z] INFO  16:33:15,938 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:33Z] INFO  16:33:15,939 MicroScheduler -   -> 650 reads (0.27% of total) failing BadMateFilter
[2016-04-14T23:33Z] INFO  16:33:15,939 MicroScheduler -   -> 19309 reads (8.07% of total) failing DuplicateReadFilter
[2016-04-14T23:33Z] INFO  16:33:15,939 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-14T23:33Z] INFO  16:33:15,939 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:33Z] INFO  16:33:15,940 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-14T23:33Z] INFO  16:33:15,940 MicroScheduler -   -> 574 reads (0.24% of total) failing MappingQualityZeroFilter
[2016-04-14T23:33Z] INFO  16:33:15,940 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:33Z] INFO  16:33:15,940 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-14T23:33Z] INFO  16:33:15,941 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-14T23:33Z] INFO  16:33:16,234 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@5fe152b7
[2016-04-14T23:33Z] INFO  16:33:16,301 ProgressMeter -            done    159952.0    22.0 s       2.3 m      100.0%    22.0 s       0.0 s
[2016-04-14T23:33Z] INFO  16:33:16,301 ProgressMeter - Total runtime 22.40 secs, 0.37 min, 0.01 hours
[2016-04-14T23:33Z] INFO  16:33:16,302 MicroScheduler - 119 reads were filtered out during the traversal out of approximately 160071 total reads (0.07%)
[2016-04-14T23:33Z] INFO  16:33:16,302 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:33Z] INFO  16:33:16,302 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:33Z] INFO  16:33:16,303 MicroScheduler -   -> 119 reads (0.07% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:33Z] INFO  16:33:16,585 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:33Z] INFO  16:33:16,589 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:33Z] INFO  16:33:16,589 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:33Z] INFO  16:33:16,590 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:33Z] INFO  16:33:16,594 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/11/R14-18102_kapa-NGv3-PE100-NGv3-sort-11_125523640_135006516-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/11/tx/tmpiq8J_I/R14-18102_kapa-NGv3-PE100-NGv3-sort-11_125523640_135006516-prep-prealign-realign.intervals -l INFO -L 11:125523641-135006516 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-14T23:33Z] INFO  16:33:16,603 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:33Z] INFO  16:33:16,604 HelpFormatter - Date/Time: 2016/04/14 16:33:16
[2016-04-14T23:33Z] INFO  16:33:16,605 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:33Z] INFO  16:33:16,606 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:33Z] INFO  16:33:16,745 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:33Z] INFO  16:33:17,002 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-14T23:33Z] INFO  16:33:17,012 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:33Z] INFO  16:33:17,060 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-14T23:33Z] INFO  16:33:17,078 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:33Z] INFO  16:33:17,081 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:33Z] INFO  16:33:17,082 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:33Z] INFO  16:33:17,083 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:33Z] INFO  16:33:17,087 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/11/R14-18102_kapa-NGv3-PE100-NGv3-sort-11_93797496_109964158-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/11/R14-18102_kapa-NGv3-PE100-NGv3-sort-11_93797496_109964158-prep-prealign-realign.intervals -L 11:93797497-109964158 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/11/tx/tmp_GydWv/R14-18102_kapa-NGv3-PE100-NGv3-sort-11_93797496_109964158-prep.bam
[2016-04-14T23:33Z] INFO  16:33:17,099 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:33Z] INFO  16:33:17,100 HelpFormatter - Date/Time: 2016/04/14 16:33:17
[2016-04-14T23:33Z] INFO  16:33:17,100 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:33Z] INFO  16:33:17,101 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:33Z] INFO  16:33:17,236 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:33Z] GATK: realign ('11', 31541602, 47074069) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:33Z] INFO  16:33:17,310 IntervalUtils - Processing 9482876 bp from intervals
[2016-04-14T23:33Z] WARN  16:33:17,315 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:33Z] INFO  16:33:17,347 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:33Z] INFO  16:33:17,398 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:33Z] INFO  16:33:17,479 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:33Z] INFO  16:33:17,488 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:33Z] INFO  16:33:17,573 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-14T23:33Z] INFO  16:33:17,635 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:33Z] INFO  16:33:17,636 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:33Z] INFO  16:33:17,637 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:33Z] INFO  16:33:17,638 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-14T23:33Z] INFO  16:33:17,758 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:33Z] INFO  16:33:17,760 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:33Z] INFO  16:33:17,761 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:33Z] INFO  16:33:17,761 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:33Z] INFO  16:33:17,765 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/11/R14-18102_kapa-NGv3-PE100-NGv3-sort-11_78277177_93796886-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/11/R14-18102_kapa-NGv3-PE100-NGv3-sort-11_78277177_93796886-prep-prealign-realign.intervals -L 11:78277178-93796886 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/11/tx/tmpm1b7Y2/R14-18102_kapa-NGv3-PE100-NGv3-sort-11_78277177_93796886-prep.bam
[2016-04-14T23:33Z] INFO  16:33:17,775 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:33Z] INFO  16:33:17,781 HelpFormatter - Date/Time: 2016/04/14 16:33:17
[2016-04-14T23:33Z] INFO  16:33:17,782 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:33Z] INFO  16:33:17,788 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:33Z] INFO  16:33:17,803 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:33Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-12_15650178_31231471-prep-prealign.bam
[2016-04-14T23:33Z] INFO  16:33:17,985 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:33Z] INFO  16:33:17,982 IntervalUtils - Processing 16166662 bp from intervals
[2016-04-14T23:33Z] WARN  16:33:17,987 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:33Z] INFO  16:33:18,057 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:33Z] INFO  16:33:18,150 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:33Z] INFO  16:33:18,159 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:33Z] INFO  16:33:18,203 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:33Z] INFO  16:33:18,204 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:33Z] INFO  16:33:18,204 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:33Z] INFO  16:33:18,205 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:33Z] INFO  16:33:18,227 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-14T23:33Z] INFO  16:33:18,352 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:33Z] GATK RealignerTargetCreator: R14-18102_kapa-NGv3-PE100-NGv3-sort-12_15650178_31231471-prep-prealign.bam 12:15650179-31231471
[2016-04-14T23:33Z] GATK: RealignerTargetCreator
[2016-04-14T23:33Z] INFO  16:33:18,549 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:33Z] INFO  16:33:18,687 IntervalUtils - Processing 15519709 bp from intervals
[2016-04-14T23:33Z] WARN  16:33:18,693 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:33Z] INFO  16:33:18,788 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:33Z] INFO  16:33:18,901 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:33Z] INFO  16:33:18,902 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:33Z] INFO  16:33:18,903 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:33Z] INFO  16:33:18,904 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:33Z] INFO  16:33:18,983 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:33Z] INFO  16:33:18,987 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:33Z] INFO  16:33:18,988 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:33Z] INFO  16:33:18,989 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:33Z] INFO  16:33:18,998 HelpFormatter - Program Args: -T PrintReads -L 12:62687960-78225484 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/12/tx/tmpyZQNws/R14-18102_kapa-NGv3-PE100-NGv3-sort-12_62687959_78225484-prep-prealign.bam
[2016-04-14T23:33Z] INFO  16:33:19,009 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:33Z] INFO  16:33:19,010 HelpFormatter - Date/Time: 2016/04/14 16:33:18
[2016-04-14T23:33Z] INFO  16:33:19,010 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:33Z] INFO  16:33:19,011 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:33Z] INFO  16:33:19,103 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:33Z] INFO  16:33:19,201 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:33Z] INFO  16:33:19,256 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:33Z] INFO  16:33:20,035 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:33Z] INFO  16:33:20,038 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:33Z] INFO  16:33:20,039 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:33Z] INFO  16:33:20,039 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:33Z] INFO  16:33:20,044 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/11/R14-18102_kapa-NGv3-PE100-NGv3-sort-11_31541602_47074069-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/11/R14-18102_kapa-NGv3-PE100-NGv3-sort-11_31541602_47074069-prep-prealign-realign.intervals -L 11:31541603-47074069 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/11/tx/tmpfEHeyb/R14-18102_kapa-NGv3-PE100-NGv3-sort-11_31541602_47074069-prep.bam
[2016-04-14T23:33Z] INFO  16:33:20,073 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:33Z] INFO  16:33:20,074 HelpFormatter - Date/Time: 2016/04/14 16:33:20
[2016-04-14T23:33Z] INFO  16:33:20,074 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:33Z] INFO  16:33:20,079 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:33Z] INFO  16:33:20,339 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-14T23:33Z] INFO  16:33:20,341 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:33Z] INFO  16:33:20,395 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:33Z] INFO  16:33:20,404 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:33Z] INFO  16:33:20,459 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-14T23:33Z] INFO  16:33:20,473 IntervalUtils - Processing 15537525 bp from intervals
[2016-04-14T23:33Z] INFO  16:33:20,490 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:33Z] INFO  16:33:20,499 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:33Z] INFO  16:33:20,542 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:33Z] INFO  16:33:20,590 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.09
[2016-04-14T23:33Z] INFO  16:33:20,910 ProgressMeter -            done    204189.0    17.0 s      84.0 s      100.0%    17.0 s       0.0 s
[2016-04-14T23:33Z] INFO  16:33:20,910 ProgressMeter - Total runtime 17.30 secs, 0.29 min, 0.00 hours
[2016-04-14T23:33Z] INFO  16:33:20,914 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 204189 total reads (0.00%)
[2016-04-14T23:33Z] INFO  16:33:20,914 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:33Z] INFO  16:33:20,915 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:33Z] INFO  16:33:20,915 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:33Z] INFO  16:33:20,929 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:33Z] INFO  16:33:20,930 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:33Z] INFO  16:33:20,931 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:33Z] INFO  16:33:20,932 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:33Z] INFO  16:33:20,972 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:33Z] INFO  16:33:21,014 IntervalUtils - Processing 15532467 bp from intervals
[2016-04-14T23:33Z] WARN  16:33:21,023 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:33Z] INFO  16:33:21,092 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:33Z] INFO  16:33:21,116 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:33Z] INFO  16:33:21,200 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:33Z] INFO  16:33:21,201 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:33Z] INFO  16:33:21,202 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:33Z] INFO  16:33:21,203 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:33Z] INFO  16:33:21,337 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:33Z] INFO  16:33:21,339 ProgressMeter -      12:6173347    100001.0    30.0 s       5.0 m       39.5%    75.0 s      45.0 s
[2016-04-14T23:33Z] INFO  16:33:21,528 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:33Z] INFO  16:33:21,641 ProgressMeter -     11:62396372    500009.0    60.0 s     120.0 s       98.2%    61.0 s       1.0 s
[2016-04-14T23:33Z] INFO  16:33:21,688 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:33Z] INFO  16:33:21,692 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:33Z] INFO  16:33:21,692 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:33Z] INFO  16:33:21,693 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:33Z] INFO  16:33:21,698 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/12/R14-18102_kapa-NGv3-PE100-NGv3-sort-12_15650178_31231471-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/12/tx/tmpt4MRYQ/R14-18102_kapa-NGv3-PE100-NGv3-sort-12_15650178_31231471-prep-prealign-realign.intervals -l INFO -L 12:15650179-31231471 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-14T23:33Z] INFO  16:33:21,722 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:33Z] INFO  16:33:21,723 HelpFormatter - Date/Time: 2016/04/14 16:33:21
[2016-04-14T23:33Z] INFO  16:33:21,723 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:33Z] INFO  16:33:21,724 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:33Z] INFO  16:33:21,842 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:33Z] INFO  16:33:22,028 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-14T23:33Z] INFO  16:33:22,037 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:33Z] INFO  16:33:22,096 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-14T23:33Z] INFO  16:33:22,335 IntervalUtils - Processing 15581293 bp from intervals
[2016-04-14T23:33Z] INFO  16:33:22,339 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:33Z] WARN  16:33:22,341 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:33Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-11_16007749_31531554-prep.bam
[2016-04-14T23:33Z] INFO  16:33:22,420 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:33Z] INFO  16:33:22,557 ProgressMeter -     11:67168574    400012.0    60.0 s       2.5 m       28.5%     3.5 m       2.5 m
[2016-04-14T23:33Z] INFO  16:33:22,630 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:33Z] INFO  16:33:22,630 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:33Z] INFO  16:33:22,631 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:33Z] INFO  16:33:22,631 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-14T23:33Z] INFO  16:33:22,850 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@52f3b59
[2016-04-14T23:33Z] INFO  16:33:22,973 ProgressMeter -            done    804510.0    97.0 s       2.0 m      100.0%    97.0 s       0.0 s
[2016-04-14T23:33Z] INFO  16:33:22,974 ProgressMeter - Total runtime 97.46 secs, 1.62 min, 0.03 hours
[2016-04-14T23:33Z] INFO  16:33:22,974 MicroScheduler - 508 reads were filtered out during the traversal out of approximately 805018 total reads (0.06%)
[2016-04-14T23:33Z] INFO  16:33:22,974 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:33Z] INFO  16:33:22,975 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:33Z] INFO  16:33:22,975 MicroScheduler -   -> 508 reads (0.06% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:33Z] INFO  16:33:22,999 ProgressMeter -    10:104491934    400007.0    30.0 s      75.0 s       59.9%    50.0 s      20.0 s
[2016-04-14T23:33Z] GATK pre-alignment ('12', 78334098, 93863131) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:33Z] INFO  16:33:24,415 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:33Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-11_0_15994658-prep-prealign.bam
[2016-04-14T23:33Z] INFO  16:33:25,727 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:33Z] INFO  16:33:25,731 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:33Z] INFO  16:33:25,731 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:33Z] INFO  16:33:25,732 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:33Z] INFO  16:33:25,737 HelpFormatter - Program Args: -T PrintReads -L 12:78334099-93863131 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/12/tx/tmpQ5j5kH/R14-18102_kapa-NGv3-PE100-NGv3-sort-12_78334098_93863131-prep-prealign.bam
[2016-04-14T23:33Z] INFO  16:33:25,747 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:33Z] INFO  16:33:25,756 HelpFormatter - Date/Time: 2016/04/14 16:33:25
[2016-04-14T23:33Z] INFO  16:33:25,757 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:33Z] INFO  16:33:25,757 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:33Z] INFO  16:33:25,960 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:33Z] INFO  16:33:26,497 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@41fd9d8e
[2016-04-14T23:33Z] INFO  16:33:26,626 ProgressMeter -            done    192367.0    25.0 s       2.2 m      100.0%    25.0 s       0.0 s
[2016-04-14T23:33Z] INFO  16:33:26,627 ProgressMeter - Total runtime 25.85 secs, 0.43 min, 0.01 hours
[2016-04-14T23:33Z] INFO  16:33:26,627 MicroScheduler - 158 reads were filtered out during the traversal out of approximately 192525 total reads (0.08%)
[2016-04-14T23:33Z] INFO  16:33:26,627 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:33Z] INFO  16:33:26,628 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:33Z] INFO  16:33:26,628 MicroScheduler -   -> 158 reads (0.08% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:33Z] INFO  16:33:26,899 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@7172f77a
[2016-04-14T23:33Z] INFO  16:33:27,017 ProgressMeter -            done    557151.0    65.0 s     117.0 s      100.0%    65.0 s       0.0 s
[2016-04-14T23:33Z] INFO  16:33:27,017 ProgressMeter - Total runtime 65.44 secs, 1.09 min, 0.02 hours
[2016-04-14T23:33Z] INFO  16:33:27,018 MicroScheduler - 329 reads were filtered out during the traversal out of approximately 557480 total reads (0.06%)
[2016-04-14T23:33Z] INFO  16:33:27,018 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:33Z] INFO  16:33:27,018 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:33Z] INFO  16:33:27,019 MicroScheduler -   -> 329 reads (0.06% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:33Z] INFO  16:33:27,031 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-14T23:33Z] INFO  16:33:27,080 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:33Z] INFO  16:33:27,089 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:33Z] GATK RealignerTargetCreator: R14-18102_kapa-NGv3-PE100-NGv3-sort-11_0_15994658-prep-prealign.bam 11:1-15994658
[2016-04-14T23:33Z] GATK: RealignerTargetCreator
[2016-04-14T23:33Z] INFO  16:33:27,124 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.03
[2016-04-14T23:33Z] INFO  16:33:27,141 IntervalUtils - Processing 15529033 bp from intervals
[2016-04-14T23:33Z] INFO  16:33:27,220 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:33Z] INFO  16:33:27,446 ProgressMeter -            done    504811.0    34.0 s      68.0 s      100.0%    34.0 s       0.0 s
[2016-04-14T23:33Z] INFO  16:33:27,447 ProgressMeter - Total runtime 34.47 secs, 0.57 min, 0.01 hours
[2016-04-14T23:33Z] INFO  16:33:27,451 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 504811 total reads (0.00%)
[2016-04-14T23:33Z] INFO  16:33:27,451 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:33Z] INFO  16:33:27,452 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:33Z] INFO  16:33:27,452 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:33Z] INFO  16:33:27,460 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:33Z] INFO  16:33:27,461 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:33Z] INFO  16:33:27,462 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:33Z] INFO  16:33:27,463 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:33Z] INFO  16:33:27,496 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:33Z] INFO  16:33:27,682 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:33Z] INFO  16:33:28,148 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:33Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-12_31236746_46754992-prep-prealign.bam
[2016-04-14T23:33Z] INFO  16:33:28,497 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:33Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-11_47158866_62678572-prep-prealign.bam
[2016-04-14T23:33Z] GATK RealignerTargetCreator: R14-18102_kapa-NGv3-PE100-NGv3-sort-12_31236746_46754992-prep-prealign.bam 12:31236747-46754992
[2016-04-14T23:33Z] GATK: RealignerTargetCreator
[2016-04-14T23:33Z] INFO  16:33:29,198 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:33Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-10_93851586_111625070-prep.bam
[2016-04-14T23:33Z] INFO  16:33:29,840 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:33Z] INFO  16:33:29,843 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:33Z] INFO  16:33:29,844 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:33Z] INFO  16:33:29,844 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:33Z] INFO  16:33:29,849 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/11/R14-18102_kapa-NGv3-PE100-NGv3-sort-11_0_15994658-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/11/tx/tmpsKPss4/R14-18102_kapa-NGv3-PE100-NGv3-sort-11_0_15994658-prep-prealign-realign.intervals -l INFO -L 11:1-15994658 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-14T23:33Z] INFO  16:33:29,860 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:33Z] INFO  16:33:29,860 HelpFormatter - Date/Time: 2016/04/14 16:33:29
[2016-04-14T23:33Z] INFO  16:33:29,860 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:33Z] INFO  16:33:29,861 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:33Z] INFO  16:33:29,972 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:33Z] INFO  16:33:30,242 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-14T23:33Z] INFO  16:33:30,252 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:33Z] GATK RealignerTargetCreator: R14-18102_kapa-NGv3-PE100-NGv3-sort-11_47158866_62678572-prep-prealign.bam 11:47158867-62678572
[2016-04-14T23:33Z] GATK: RealignerTargetCreator
[2016-04-14T23:33Z] INFO  16:33:30,336 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-14T23:33Z] INFO  16:33:30,536 ProgressMeter -            done   9482876.0    12.0 s       1.0 s      100.0%    12.0 s       0.0 s
[2016-04-14T23:33Z] INFO  16:33:30,537 ProgressMeter - Total runtime 12.90 secs, 0.22 min, 0.00 hours
[2016-04-14T23:33Z] INFO  16:33:30,541 MicroScheduler - 14997 reads were filtered out during the traversal out of approximately 172564 total reads (8.69%)
[2016-04-14T23:33Z] INFO  16:33:30,542 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:33Z] INFO  16:33:30,543 MicroScheduler -   -> 436 reads (0.25% of total) failing BadMateFilter
[2016-04-14T23:33Z] INFO  16:33:30,544 MicroScheduler -   -> 13690 reads (7.93% of total) failing DuplicateReadFilter
[2016-04-14T23:33Z] INFO  16:33:30,544 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-14T23:33Z] INFO  16:33:30,545 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:33Z] INFO  16:33:30,546 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-14T23:33Z] INFO  16:33:30,546 MicroScheduler -   -> 871 reads (0.50% of total) failing MappingQualityZeroFilter
[2016-04-14T23:33Z] INFO  16:33:30,547 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:33Z] INFO  16:33:30,547 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-14T23:33Z] INFO  16:33:30,548 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-14T23:33Z] INFO  16:33:30,683 IntervalUtils - Processing 15994658 bp from intervals
[2016-04-14T23:33Z] WARN  16:33:30,688 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:33Z] INFO  16:33:30,780 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:33Z] GATK pre-alignment ('12', 93870729, 109490566) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:33Z] INFO  16:33:31,083 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:33Z] INFO  16:33:31,096 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:33Z] INFO  16:33:31,107 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:33Z] INFO  16:33:31,108 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-14T23:33Z] INFO  16:33:31,459 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:33Z] INFO  16:33:31,463 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:33Z] INFO  16:33:31,463 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:33Z] INFO  16:33:31,464 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:33Z] INFO  16:33:31,468 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/12/R14-18102_kapa-NGv3-PE100-NGv3-sort-12_31236746_46754992-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/12/tx/tmpyG6_tS/R14-18102_kapa-NGv3-PE100-NGv3-sort-12_31236746_46754992-prep-prealign-realign.intervals -l INFO -L 12:31236747-46754992 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-14T23:33Z] INFO  16:33:31,490 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:33Z] INFO  16:33:31,490 HelpFormatter - Date/Time: 2016/04/14 16:33:31
[2016-04-14T23:33Z] INFO  16:33:31,490 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:33Z] INFO  16:33:31,490 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:33Z] INFO  16:33:31,654 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:33Z] INFO  16:33:31,899 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-14T23:33Z] INFO  16:33:31,909 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:33Z] INFO  16:33:31,981 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-14T23:33Z] INFO  16:33:31,993 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:33Z] GATK: realign ('11', 125523640, 135006516) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:33Z] INFO  16:33:32,268 IntervalUtils - Processing 15518246 bp from intervals
[2016-04-14T23:33Z] WARN  16:33:32,273 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:33Z] INFO  16:33:32,360 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:33Z] INFO  16:33:32,537 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:33Z] INFO  16:33:32,540 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:33Z] INFO  16:33:32,540 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:33Z] INFO  16:33:32,541 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-14T23:33Z] INFO  16:33:33,171 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:33Z] INFO  16:33:33,175 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:33Z] INFO  16:33:33,175 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:33Z] INFO  16:33:33,176 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:33Z] INFO  16:33:33,181 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/11/R14-18102_kapa-NGv3-PE100-NGv3-sort-11_47158866_62678572-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/11/tx/tmpt12Bxm/R14-18102_kapa-NGv3-PE100-NGv3-sort-11_47158866_62678572-prep-prealign-realign.intervals -l INFO -L 11:47158867-62678572 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-14T23:33Z] INFO  16:33:33,210 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:33Z] INFO  16:33:33,211 HelpFormatter - Date/Time: 2016/04/14 16:33:33
[2016-04-14T23:33Z] INFO  16:33:33,212 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:33Z] INFO  16:33:33,213 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:33Z] INFO  16:33:33,337 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:33Z] INFO  16:33:33,570 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-14T23:33Z] INFO  16:33:33,580 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:33Z] INFO  16:33:33,634 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-14T23:33Z] INFO  16:33:33,637 ProgressMeter -            done    183470.0    15.0 s      84.0 s      100.0%    15.0 s       0.0 s
[2016-04-14T23:33Z] INFO  16:33:33,638 ProgressMeter - Total runtime 15.43 secs, 0.26 min, 0.00 hours
[2016-04-14T23:33Z] INFO  16:33:33,642 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 183470 total reads (0.00%)
[2016-04-14T23:33Z] INFO  16:33:33,643 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:33Z] INFO  16:33:33,644 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:33Z] INFO  16:33:33,645 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:33Z] INFO  16:33:33,816 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:33Z] INFO  16:33:33,819 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:33Z] INFO  16:33:33,820 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:33Z] INFO  16:33:33,820 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:33Z] INFO  16:33:33,825 HelpFormatter - Program Args: -T PrintReads -L 12:93870730-109490566 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/12/tx/tmpoK4awk/R14-18102_kapa-NGv3-PE100-NGv3-sort-12_93870729_109490566-prep-prealign.bam
[2016-04-14T23:33Z] INFO  16:33:33,839 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:33Z] INFO  16:33:33,840 HelpFormatter - Date/Time: 2016/04/14 16:33:33
[2016-04-14T23:33Z] INFO  16:33:33,841 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:33Z] INFO  16:33:33,841 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:33Z] INFO  16:33:33,943 IntervalUtils - Processing 15519706 bp from intervals
[2016-04-14T23:33Z] WARN  16:33:33,949 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:33Z] INFO  16:33:34,021 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:33Z] INFO  16:33:34,057 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:33Z] INFO  16:33:34,315 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:33Z] INFO  16:33:34,315 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:33Z] INFO  16:33:34,316 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:33Z] INFO  16:33:34,316 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-14T23:33Z] INFO  16:33:34,364 ProgressMeter -            done    193112.0    15.0 s      80.0 s      100.0%    15.0 s       0.0 s
[2016-04-14T23:33Z] INFO  16:33:34,365 ProgressMeter - Total runtime 15.46 secs, 0.26 min, 0.00 hours
[2016-04-14T23:33Z] INFO  16:33:34,368 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 193112 total reads (0.00%)
[2016-04-14T23:33Z] INFO  16:33:34,369 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:33Z] INFO  16:33:34,370 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:33Z] INFO  16:33:34,370 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:33Z] INFO  16:33:35,088 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:33Z] INFO  16:33:35,102 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:33Z] INFO  16:33:35,103 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:33Z] INFO  16:33:35,104 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:33Z] INFO  16:33:35,108 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/11/R14-18102_kapa-NGv3-PE100-NGv3-sort-11_125523640_135006516-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/11/R14-18102_kapa-NGv3-PE100-NGv3-sort-11_125523640_135006516-prep-prealign-realign.intervals -L 11:125523641-135006516 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/11/tx/tmphjrKeW/R14-18102_kapa-NGv3-PE100-NGv3-sort-11_125523640_135006516-prep.bam
[2016-04-14T23:33Z] INFO  16:33:35,120 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:33Z] INFO  16:33:35,121 HelpFormatter - Date/Time: 2016/04/14 16:33:35
[2016-04-14T23:33Z] INFO  16:33:35,121 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:33Z] INFO  16:33:35,122 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:33Z] INFO  16:33:35,145 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-14T23:33Z] INFO  16:33:35,212 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:33Z] INFO  16:33:35,231 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:33Z] INFO  16:33:35,305 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-14T23:33Z] INFO  16:33:35,313 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:33Z] INFO  16:33:35,339 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:33Z] INFO  16:33:35,341 IntervalUtils - Processing 15619837 bp from intervals
[2016-04-14T23:33Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-11_93797496_109964158-prep.bam
[2016-04-14T23:33Z] INFO  16:33:35,451 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:33Z] INFO  16:33:35,452 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:33Z] INFO  16:33:35,460 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:33Z] INFO  16:33:35,512 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-14T23:33Z] INFO  16:33:35,791 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:33Z] INFO  16:33:35,803 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:33Z] INFO  16:33:35,803 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:33Z] INFO  16:33:35,803 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:33Z] INFO  16:33:35,828 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:33Z] INFO  16:33:35,861 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:33Z] INFO  16:33:35,877 IntervalUtils - Processing 9482876 bp from intervals
[2016-04-14T23:33Z] WARN  16:33:35,882 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:33Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-11_78277177_93796886-prep.bam
[2016-04-14T23:33Z] INFO  16:33:35,973 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:33Z] INFO  16:33:36,034 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:33Z] GATK pre-alignment ('12', 109494486, 125263132) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:33Z] INFO  16:33:36,105 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:33Z] INFO  16:33:36,105 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:33Z] INFO  16:33:36,106 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:33Z] INFO  16:33:36,106 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:33Z] INFO  16:33:36,235 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:33Z] INFO  16:33:36,332 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:33Z] GATK pre-alignment ('12', 125267228, 133851895) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:33Z] INFO  16:33:37,868 ProgressMeter -    11:121429659    300006.0    61.0 s       3.4 m       73.7%    82.0 s      21.0 s
[2016-04-14T23:33Z] INFO  16:33:38,866 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:33Z] INFO  16:33:38,870 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:33Z] INFO  16:33:38,871 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:33Z] INFO  16:33:38,872 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:33Z] INFO  16:33:38,877 HelpFormatter - Program Args: -T PrintReads -L 12:109494487-125263132 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/12/tx/tmpSoOf7O/R14-18102_kapa-NGv3-PE100-NGv3-sort-12_109494486_125263132-prep-prealign.bam
[2016-04-14T23:33Z] INFO  16:33:38,892 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:33Z] INFO  16:33:38,893 HelpFormatter - Date/Time: 2016/04/14 16:33:38
[2016-04-14T23:33Z] INFO  16:33:38,894 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:33Z] INFO  16:33:38,894 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:33Z] INFO  16:33:39,121 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:33Z] INFO  16:33:39,230 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:33Z] INFO  16:33:39,234 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:33Z] INFO  16:33:39,235 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:33Z] INFO  16:33:39,235 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:33Z] INFO  16:33:39,241 HelpFormatter - Program Args: -T PrintReads -L 12:125267229-133851895 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/12/tx/tmpiok8D1/R14-18102_kapa-NGv3-PE100-NGv3-sort-12_125267228_133851895-prep-prealign.bam
[2016-04-14T23:33Z] INFO  16:33:39,254 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:33Z] INFO  16:33:39,254 HelpFormatter - Date/Time: 2016/04/14 16:33:39
[2016-04-14T23:33Z] INFO  16:33:39,254 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:33Z] INFO  16:33:39,254 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:33Z] INFO  16:33:39,464 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:33Z] INFO  16:33:39,511 ProgressMeter -            done    237430.0    18.0 s      77.0 s      100.0%    18.0 s       0.0 s
[2016-04-14T23:33Z] INFO  16:33:39,512 ProgressMeter - Total runtime 18.31 secs, 0.31 min, 0.01 hours
[2016-04-14T23:33Z] INFO  16:33:39,515 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 237430 total reads (0.00%)
[2016-04-14T23:33Z] INFO  16:33:39,516 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:33Z] INFO  16:33:39,516 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:33Z] INFO  16:33:39,517 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:33Z] INFO  16:33:39,813 ProgressMeter -     9:136066921    400010.0    30.0 s      75.0 s       57.5%    52.0 s      22.0 s
[2016-04-14T23:33Z] INFO  16:33:40,106 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-14T23:33Z] INFO  16:33:40,167 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:33Z] INFO  16:33:40,177 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:33Z] INFO  16:33:40,224 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-14T23:33Z] INFO  16:33:40,249 IntervalUtils - Processing 15768646 bp from intervals
[2016-04-14T23:33Z] INFO  16:33:40,259 ProgressMeter -     12:50356058    100001.0    30.0 s       5.0 m       22.6%     2.2 m     102.0 s
[2016-04-14T23:33Z] INFO  16:33:40,387 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:33Z] INFO  16:33:40,406 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-14T23:33Z] INFO  16:33:40,412 ProgressMeter -            done   1.5581293E7    17.0 s       1.0 s      100.0%    17.0 s       0.0 s
[2016-04-14T23:33Z] INFO  16:33:40,412 ProgressMeter - Total runtime 17.78 secs, 0.30 min, 0.00 hours
[2016-04-14T23:33Z] INFO  16:33:40,416 MicroScheduler - 13728 reads were filtered out during the traversal out of approximately 160758 total reads (8.54%)
[2016-04-14T23:33Z] INFO  16:33:40,416 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:33Z] INFO  16:33:40,417 MicroScheduler -   -> 523 reads (0.33% of total) failing BadMateFilter
[2016-04-14T23:33Z] INFO  16:33:40,417 MicroScheduler -   -> 12611 reads (7.84% of total) failing DuplicateReadFilter
[2016-04-14T23:33Z] INFO  16:33:40,417 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-14T23:33Z] INFO  16:33:40,417 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:33Z] INFO  16:33:40,418 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-14T23:33Z] INFO  16:33:40,418 MicroScheduler -   -> 594 reads (0.37% of total) failing MappingQualityZeroFilter
[2016-04-14T23:33Z] INFO  16:33:40,418 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:33Z] INFO  16:33:40,418 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-14T23:33Z] INFO  16:33:40,419 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-14T23:33Z] INFO  16:33:40,470 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:33Z] INFO  16:33:40,479 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:33Z] INFO  16:33:40,523 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.04
[2016-04-14T23:33Z] INFO  16:33:40,537 IntervalUtils - Processing 8584667 bp from intervals
[2016-04-14T23:33Z] INFO  16:33:40,608 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:33Z] INFO  16:33:40,704 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:33Z] INFO  16:33:40,705 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:33Z] INFO  16:33:40,706 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:33Z] INFO  16:33:40,707 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:33Z] INFO  16:33:40,720 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:33Z] INFO  16:33:40,849 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:33Z] INFO  16:33:40,926 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:33Z] INFO  16:33:40,927 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:33Z] INFO  16:33:40,928 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:33Z] INFO  16:33:40,929 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:33Z] INFO  16:33:40,953 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:33Z] INFO  16:33:41,014 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:33Z] INFO  16:33:41,036 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:33Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-11_31541602_47074069-prep.bam
[2016-04-14T23:33Z] INFO  16:33:41,693 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:33Z] GATK: realign ('12', 15650178, 31231471) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:33Z] GATK pre-alignment ('13', 0, 19748299) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:33Z] INFO  16:33:44,343 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@41fd9d8e
[2016-04-14T23:33Z] INFO  16:33:44,512 ProgressMeter -            done     96606.0    17.0 s       2.9 m      100.0%    17.0 s       0.0 s
[2016-04-14T23:33Z] INFO  16:33:44,512 ProgressMeter - Total runtime 17.05 secs, 0.28 min, 0.00 hours
[2016-04-14T23:33Z] INFO  16:33:44,513 MicroScheduler - 101 reads were filtered out during the traversal out of approximately 96707 total reads (0.10%)
[2016-04-14T23:33Z] INFO  16:33:44,513 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:33Z] INFO  16:33:44,513 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:33Z] INFO  16:33:44,514 MicroScheduler -   -> 101 reads (0.10% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:33Z] INFO  16:33:44,586 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:33Z] INFO  16:33:44,590 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:33Z] INFO  16:33:44,590 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:33Z] INFO  16:33:44,591 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:33Z] INFO  16:33:44,596 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/12/R14-18102_kapa-NGv3-PE100-NGv3-sort-12_15650178_31231471-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/12/R14-18102_kapa-NGv3-PE100-NGv3-sort-12_15650178_31231471-prep-prealign-realign.intervals -L 12:15650179-31231471 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/12/tx/tmp74wZdH/R14-18102_kapa-NGv3-PE100-NGv3-sort-12_15650178_31231471-prep.bam
[2016-04-14T23:33Z] INFO  16:33:44,616 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:33Z] INFO  16:33:44,617 HelpFormatter - Date/Time: 2016/04/14 16:33:44
[2016-04-14T23:33Z] INFO  16:33:44,618 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:33Z] INFO  16:33:44,619 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:33Z] INFO  16:33:44,705 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:33Z] INFO  16:33:44,709 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:33Z] INFO  16:33:44,710 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:33Z] INFO  16:33:44,710 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:33Z] INFO  16:33:44,715 HelpFormatter - Program Args: -T PrintReads -L 13:1-19748299 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/13/tx/tmpH1OMbh/R14-18102_kapa-NGv3-PE100-NGv3-sort-13_0_19748299-prep-prealign.bam
[2016-04-14T23:33Z] INFO  16:33:44,747 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:33Z] INFO  16:33:44,748 HelpFormatter - Date/Time: 2016/04/14 16:33:44
[2016-04-14T23:33Z] INFO  16:33:44,748 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:33Z] INFO  16:33:44,753 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:33Z] INFO  16:33:44,828 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:33Z] INFO  16:33:44,895 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:33Z] INFO  16:33:44,947 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:33Z] INFO  16:33:44,957 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:33Z] INFO  16:33:44,997 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.04
[2016-04-14T23:33Z] INFO  16:33:45,317 IntervalUtils - Processing 15581293 bp from intervals
[2016-04-14T23:33Z] WARN  16:33:45,323 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:33Z] INFO  16:33:45,420 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:33Z] INFO  16:33:45,619 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:33Z] INFO  16:33:45,620 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:33Z] INFO  16:33:45,620 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:33Z] INFO  16:33:45,620 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:33Z] INFO  16:33:45,847 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:33Z] INFO  16:33:46,003 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@41fd9d8e
[2016-04-14T23:33Z] INFO  16:33:46,041 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:33Z] INFO  16:33:46,049 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:33Z] INFO  16:33:46,053 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-14T23:33Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-12_78334098_93863131-prep-prealign.bam
[2016-04-14T23:33Z] INFO  16:33:46,124 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:33Z] INFO  16:33:46,133 ProgressMeter -            done    178263.0    25.0 s       2.4 m      100.0%    25.0 s       0.0 s
[2016-04-14T23:33Z] INFO  16:33:46,134 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:33Z] INFO  16:33:46,133 ProgressMeter - Total runtime 25.20 secs, 0.42 min, 0.01 hours
[2016-04-14T23:33Z] INFO  16:33:46,134 MicroScheduler - 135 reads were filtered out during the traversal out of approximately 178398 total reads (0.08%)
[2016-04-14T23:33Z] INFO  16:33:46,134 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:33Z] INFO  16:33:46,135 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:33Z] INFO  16:33:46,135 MicroScheduler -   -> 135 reads (0.08% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:33Z] INFO  16:33:46,215 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-14T23:33Z] INFO  16:33:46,237 IntervalUtils - Processing 19748299 bp from intervals
[2016-04-14T23:33Z] INFO  16:33:46,363 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:33Z] GATK RealignerTargetCreator: R14-18102_kapa-NGv3-PE100-NGv3-sort-12_78334098_93863131-prep-prealign.bam 12:78334099-93863131
[2016-04-14T23:33Z] GATK: RealignerTargetCreator
[2016-04-14T23:33Z] INFO  16:33:46,992 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:33Z] INFO  16:33:46,993 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:33Z] INFO  16:33:46,994 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:33Z] INFO  16:33:46,995 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:33Z] INFO  16:33:47,008 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:33Z] INFO  16:33:47,015 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:33Z] INFO  16:33:48,076 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:33Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-12_62687959_78225484-prep-prealign.bam
[2016-04-14T23:33Z] GATK RealignerTargetCreator: R14-18102_kapa-NGv3-PE100-NGv3-sort-12_62687959_78225484-prep-prealign.bam 12:62687960-78225484
[2016-04-14T23:33Z] GATK: RealignerTargetCreator
[2016-04-14T23:33Z] INFO  16:33:49,349 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:33Z] INFO  16:33:49,353 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:33Z] INFO  16:33:49,353 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:33Z] INFO  16:33:49,353 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:33Z] INFO  16:33:49,357 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/12/R14-18102_kapa-NGv3-PE100-NGv3-sort-12_78334098_93863131-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/12/tx/tmpu1tvJR/R14-18102_kapa-NGv3-PE100-NGv3-sort-12_78334098_93863131-prep-prealign-realign.intervals -l INFO -L 12:78334099-93863131 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-14T23:33Z] INFO  16:33:49,377 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:33Z] INFO  16:33:49,378 HelpFormatter - Date/Time: 2016/04/14 16:33:49
[2016-04-14T23:33Z] INFO  16:33:49,378 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:33Z] INFO  16:33:49,378 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:33Z] INFO  16:33:49,439 ProgressMeter -            done    172005.0    13.0 s      77.0 s       99.2%    13.0 s       0.0 s
[2016-04-14T23:33Z] INFO  16:33:49,440 ProgressMeter - Total runtime 13.33 secs, 0.22 min, 0.00 hours
[2016-04-14T23:33Z] INFO  16:33:49,444 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 172005 total reads (0.00%)
[2016-04-14T23:33Z] INFO  16:33:49,445 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:33Z] INFO  16:33:49,445 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:33Z] INFO  16:33:49,446 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:33Z] INFO  16:33:49,490 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:33Z] INFO  16:33:49,730 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-14T23:33Z] INFO  16:33:49,740 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:33Z] INFO  16:33:49,781 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@32d5a4c6
[2016-04-14T23:33Z] INFO  16:33:49,792 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-14T23:33Z] INFO  16:33:49,819 ProgressMeter -            done      6932.0     2.0 s       6.8 m      100.0%     2.0 s       0.0 s
[2016-04-14T23:33Z] INFO  16:33:49,820 ProgressMeter - Total runtime 2.83 secs, 0.05 min, 0.00 hours
[2016-04-14T23:33Z] INFO  16:33:49,821 MicroScheduler - 6 reads were filtered out during the traversal out of approximately 6938 total reads (0.09%)
[2016-04-14T23:33Z] INFO  16:33:49,822 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:33Z] INFO  16:33:49,823 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:33Z] INFO  16:33:49,824 MicroScheduler -   -> 6 reads (0.09% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:33Z] INFO  16:33:50,137 IntervalUtils - Processing 15529033 bp from intervals
[2016-04-14T23:33Z] WARN  16:33:50,142 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:33Z] INFO  16:33:50,225 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:33Z] INFO  16:33:50,270 ProgressMeter -            done   1.5518246E7    17.0 s       1.0 s      100.0%    17.0 s       0.0 s
[2016-04-14T23:33Z] INFO  16:33:50,270 ProgressMeter - Total runtime 17.73 secs, 0.30 min, 0.00 hours
[2016-04-14T23:33Z] INFO  16:33:50,275 MicroScheduler - 18400 reads were filtered out during the traversal out of approximately 194096 total reads (9.48%)
[2016-04-14T23:33Z] INFO  16:33:50,275 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:33Z] INFO  16:33:50,276 MicroScheduler -   -> 512 reads (0.26% of total) failing BadMateFilter
[2016-04-14T23:33Z] INFO  16:33:50,276 MicroScheduler -   -> 15789 reads (8.13% of total) failing DuplicateReadFilter
[2016-04-14T23:33Z] INFO  16:33:50,276 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-14T23:33Z] INFO  16:33:50,277 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:33Z] INFO  16:33:50,277 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-14T23:33Z] INFO  16:33:50,277 MicroScheduler -   -> 2099 reads (1.08% of total) failing MappingQualityZeroFilter
[2016-04-14T23:33Z] INFO  16:33:50,278 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:33Z] INFO  16:33:50,278 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-14T23:33Z] INFO  16:33:50,278 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-14T23:33Z] INFO  16:33:50,405 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:33Z] INFO  16:33:50,406 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:33Z] INFO  16:33:50,407 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:33Z] INFO  16:33:50,408 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-14T23:33Z] INFO  16:33:51,003 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:33Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-11_125523640_135006516-prep.bam
[2016-04-14T23:33Z] INFO  16:33:51,199 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:33Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-13_0_19748299-prep-prealign.bam
[2016-04-14T23:33Z] GATK RealignerTargetCreator: R14-18102_kapa-NGv3-PE100-NGv3-sort-13_0_19748299-prep-prealign.bam 13:1-19748299
[2016-04-14T23:33Z] GATK: RealignerTargetCreator
[2016-04-14T23:33Z] INFO  16:33:51,341 ProgressMeter -      12:9004894    300006.0    60.0 s       3.3 m       57.6%   104.0 s      44.0 s
[2016-04-14T23:33Z] INFO  16:33:51,345 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:33Z] INFO  16:33:51,347 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:33Z] INFO  16:33:51,347 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:33Z] INFO  16:33:51,348 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:33Z] INFO  16:33:51,351 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/12/R14-18102_kapa-NGv3-PE100-NGv3-sort-12_62687959_78225484-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/12/tx/tmp4DXEK2/R14-18102_kapa-NGv3-PE100-NGv3-sort-12_62687959_78225484-prep-prealign-realign.intervals -l INFO -L 12:62687960-78225484 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-14T23:33Z] INFO  16:33:51,382 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:33Z] INFO  16:33:51,382 HelpFormatter - Date/Time: 2016/04/14 16:33:51
[2016-04-14T23:33Z] INFO  16:33:51,383 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:33Z] INFO  16:33:51,384 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:33Z] INFO  16:33:51,520 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:33Z] GATK pre-alignment ('13', 19751066, 35517251) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:33Z] INFO  16:33:51,665 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:33Z] GATK: realign ('12', 31236746, 46754992) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:33Z] INFO  16:33:51,793 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-14T23:33Z] INFO  16:33:51,809 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:33Z] INFO  16:33:51,913 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.10
[2016-04-14T23:33Z] INFO  16:33:52,264 IntervalUtils - Processing 15537525 bp from intervals
[2016-04-14T23:33Z] WARN  16:33:52,270 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:33Z] INFO  16:33:52,375 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:33Z] INFO  16:33:52,573 ProgressMeter -     11:72539557    700016.0    90.0 s       2.1 m       63.1%     2.4 m      52.0 s
[2016-04-14T23:33Z] INFO  16:33:52,656 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:33Z] INFO  16:33:52,657 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:33Z] INFO  16:33:52,658 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:33Z] INFO  16:33:52,658 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-14T23:33Z] INFO  16:33:53,545 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@5fe152b7
[2016-04-14T23:33Z] INFO  16:33:53,705 ProgressMeter -            done    510059.0    77.0 s       2.5 m      100.0%    77.0 s       0.0 s
[2016-04-14T23:33Z] INFO  16:33:53,716 ProgressMeter - Total runtime 77.38 secs, 1.29 min, 0.02 hours
[2016-04-14T23:33Z] INFO  16:33:53,718 MicroScheduler - 239 reads were filtered out during the traversal out of approximately 510298 total reads (0.05%)
[2016-04-14T23:33Z] INFO  16:33:53,719 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:33Z] INFO  16:33:53,719 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:33Z] INFO  16:33:53,720 MicroScheduler -   -> 239 reads (0.05% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:33Z] INFO  16:33:54,253 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:33Z] INFO  16:33:54,257 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:33Z] INFO  16:33:54,257 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:33Z] INFO  16:33:54,258 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:33Z] INFO  16:33:54,263 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/13/R14-18102_kapa-NGv3-PE100-NGv3-sort-13_0_19748299-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/13/tx/tmp3CGeny/R14-18102_kapa-NGv3-PE100-NGv3-sort-13_0_19748299-prep-prealign-realign.intervals -l INFO -L 13:1-19748299 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-14T23:33Z] INFO  16:33:54,273 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:33Z] INFO  16:33:54,280 HelpFormatter - Date/Time: 2016/04/14 16:33:54
[2016-04-14T23:33Z] INFO  16:33:54,280 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:33Z] INFO  16:33:54,280 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:33Z] INFO  16:33:54,411 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:33Z] INFO  16:33:54,459 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:33Z] INFO  16:33:54,462 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:33Z] INFO  16:33:54,462 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:33Z] INFO  16:33:54,463 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:33Z] INFO  16:33:54,467 HelpFormatter - Program Args: -T PrintReads -L 13:19751067-35517251 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/13/tx/tmpg9vWZ6/R14-18102_kapa-NGv3-PE100-NGv3-sort-13_19751066_35517251-prep-prealign.bam
[2016-04-14T23:33Z] INFO  16:33:54,477 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:33Z] INFO  16:33:54,478 HelpFormatter - Date/Time: 2016/04/14 16:33:54
[2016-04-14T23:33Z] INFO  16:33:54,478 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:33Z] INFO  16:33:54,478 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:33Z] INFO  16:33:54,639 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:33Z] INFO  16:33:54,667 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-14T23:33Z] INFO  16:33:54,678 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:33Z] INFO  16:33:54,676 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:33Z] INFO  16:33:54,679 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:33Z] INFO  16:33:54,682 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:33Z] INFO  16:33:54,683 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:33Z] INFO  16:33:54,688 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/12/R14-18102_kapa-NGv3-PE100-NGv3-sort-12_31236746_46754992-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/12/R14-18102_kapa-NGv3-PE100-NGv3-sort-12_31236746_46754992-prep-prealign-realign.intervals -L 12:31236747-46754992 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/12/tx/tmpmYWmVy/R14-18102_kapa-NGv3-PE100-NGv3-sort-12_31236746_46754992-prep.bam
[2016-04-14T23:33Z] INFO  16:33:54,719 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:33Z] INFO  16:33:54,719 HelpFormatter - Date/Time: 2016/04/14 16:33:54
[2016-04-14T23:33Z] INFO  16:33:54,719 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:33Z] INFO  16:33:54,720 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:33Z] INFO  16:33:54,746 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-14T23:33Z] INFO  16:33:54,921 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:33Z] INFO  16:33:54,990 IntervalUtils - Processing 19748299 bp from intervals
[2016-04-14T23:33Z] INFO  16:33:54,995 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:33Z] WARN  16:33:54,995 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:33Z] INFO  16:33:55,004 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:33Z] INFO  16:33:55,048 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.04
[2016-04-14T23:33Z] INFO  16:33:55,068 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:33Z] INFO  16:33:55,355 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:33Z] INFO  16:33:55,356 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:33Z] INFO  16:33:55,356 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:33Z] INFO  16:33:55,357 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-14T23:33Z] INFO  16:33:55,430 IntervalUtils - Processing 15518246 bp from intervals
[2016-04-14T23:33Z] INFO  16:33:55,434 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:33Z] WARN  16:33:55,446 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:33Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-11_110001730_125514538-prep-prealign.bam
[2016-04-14T23:33Z] INFO  16:33:55,533 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:33Z] INFO  16:33:55,635 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-14T23:33Z] INFO  16:33:55,687 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:33Z] INFO  16:33:55,691 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:33Z] INFO  16:33:55,692 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:33Z] INFO  16:33:55,693 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:33Z] INFO  16:33:55,694 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:33Z] INFO  16:33:55,698 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:33Z] INFO  16:33:55,753 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-14T23:33Z] INFO  16:33:55,769 IntervalUtils - Processing 15766185 bp from intervals
[2016-04-14T23:33Z] INFO  16:33:55,851 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:33Z] INFO  16:33:55,865 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:33Z] INFO  16:33:56,048 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:33Z] INFO  16:33:56,197 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:33Z] INFO  16:33:56,198 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:33Z] INFO  16:33:56,198 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:33Z] INFO  16:33:56,199 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:33Z] INFO  16:33:56,222 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:33Z] INFO  16:33:56,385 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:33Z] GATK RealignerTargetCreator: R14-18102_kapa-NGv3-PE100-NGv3-sort-11_110001730_125514538-prep-prealign.bam 11:110001731-125514538
[2016-04-14T23:33Z] GATK: RealignerTargetCreator
[2016-04-14T23:33Z] INFO  16:33:58,798 ProgressMeter -            done    159952.0    13.0 s      82.0 s      100.0%    13.0 s       0.0 s
[2016-04-14T23:33Z] INFO  16:33:58,799 ProgressMeter - Total runtime 13.18 secs, 0.22 min, 0.00 hours
[2016-04-14T23:33Z] INFO  16:33:58,803 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 159952 total reads (0.00%)
[2016-04-14T23:33Z] INFO  16:33:58,804 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:33Z] INFO  16:33:58,804 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:33Z] INFO  16:33:58,804 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:33Z] INFO  16:33:59,565 ProgressMeter -            done   1.5519706E7    25.0 s       1.0 s      100.0%    25.0 s       0.0 s
[2016-04-14T23:33Z] INFO  16:33:59,567 ProgressMeter - Total runtime 25.25 secs, 0.42 min, 0.01 hours
[2016-04-14T23:33Z] INFO  16:33:59,572 MicroScheduler - 63371 reads were filtered out during the traversal out of approximately 561659 total reads (11.28%)
[2016-04-14T23:33Z] INFO  16:33:59,573 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:33Z] INFO  16:33:59,574 MicroScheduler -   -> 1076 reads (0.19% of total) failing BadMateFilter
[2016-04-14T23:33Z] INFO  16:33:59,575 MicroScheduler -   -> 44174 reads (7.86% of total) failing DuplicateReadFilter
[2016-04-14T23:33Z] INFO  16:33:59,576 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-14T23:33Z] INFO  16:33:59,576 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:33Z] INFO  16:33:59,577 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-14T23:33Z] INFO  16:33:59,578 MicroScheduler -   -> 18121 reads (3.23% of total) failing MappingQualityZeroFilter
[2016-04-14T23:33Z] INFO  16:33:59,578 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:33Z] INFO  16:33:59,578 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-14T23:33Z] INFO  16:33:59,578 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-14T23:33Z] INFO  16:33:59,648 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:33Z] INFO  16:33:59,653 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:33Z] INFO  16:33:59,654 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:33Z] INFO  16:33:59,654 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:33Z] INFO  16:33:59,660 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/11/R14-18102_kapa-NGv3-PE100-NGv3-sort-11_110001730_125514538-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/11/tx/tmpfcqSVP/R14-18102_kapa-NGv3-PE100-NGv3-sort-11_110001730_125514538-prep-prealign-realign.intervals -l INFO -L 11:110001731-125514538 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-14T23:33Z] INFO  16:33:59,697 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:33Z] INFO  16:33:59,702 HelpFormatter - Date/Time: 2016/04/14 16:33:59
[2016-04-14T23:33Z] INFO  16:33:59,703 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:33Z] INFO  16:33:59,703 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:33Z] INFO  16:33:59,810 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:34Z] INFO  16:34:00,037 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-14T23:34Z] INFO  16:34:00,057 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:34Z] INFO  16:34:00,109 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-14T23:34Z] INFO  16:34:00,129 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:34Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-12_15650178_31231471-prep.bam
[2016-04-14T23:34Z] INFO  16:34:00,430 IntervalUtils - Processing 15512808 bp from intervals
[2016-04-14T23:34Z] WARN  16:34:00,437 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:34Z] INFO  16:34:00,619 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:34Z] GATK pre-alignment ('13', 35615069, 51287376) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:34Z] INFO  16:34:00,857 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:34Z] INFO  16:34:00,858 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:34Z] INFO  16:34:00,859 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:34Z] INFO  16:34:00,860 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-14T23:34Z] INFO  16:34:00,914 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:34Z] GATK: realign ('11', 47158866, 62678572) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:34Z] INFO  16:34:01,126 ProgressMeter -     11:15994617   1.5958016E7    30.0 s       1.0 s      100.0%    30.0 s       0.0 s
[2016-04-14T23:34Z] INFO  16:34:01,368 ProgressMeter -            done    828757.0    51.0 s      62.0 s       99.3%    51.0 s       0.0 s
[2016-04-14T23:34Z] INFO  16:34:01,368 ProgressMeter - Total runtime 51.74 secs, 0.86 min, 0.01 hours
[2016-04-14T23:34Z] INFO  16:34:01,372 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 828757 total reads (0.00%)
[2016-04-14T23:34Z] INFO  16:34:01,373 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:34Z] INFO  16:34:01,373 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:34Z] INFO  16:34:01,373 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:34Z] INFO  16:34:01,414 ProgressMeter -            done   1.5994658E7    30.0 s       1.0 s      100.0%    30.0 s       0.0 s
[2016-04-14T23:34Z] INFO  16:34:01,415 ProgressMeter - Total runtime 30.32 secs, 0.51 min, 0.01 hours
[2016-04-14T23:34Z] INFO  16:34:01,416 MicroScheduler - 92752 reads were filtered out during the traversal out of approximately 808527 total reads (11.47%)
[2016-04-14T23:34Z] INFO  16:34:01,416 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:34Z] INFO  16:34:01,417 MicroScheduler -   -> 1618 reads (0.20% of total) failing BadMateFilter
[2016-04-14T23:34Z] INFO  16:34:01,418 MicroScheduler -   -> 68441 reads (8.46% of total) failing DuplicateReadFilter
[2016-04-14T23:34Z] INFO  16:34:01,418 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-14T23:34Z] INFO  16:34:01,419 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:34Z] INFO  16:34:01,419 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-14T23:34Z] INFO  16:34:01,420 MicroScheduler -   -> 22693 reads (2.81% of total) failing MappingQualityZeroFilter
[2016-04-14T23:34Z] INFO  16:34:01,421 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:34Z] INFO  16:34:01,421 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-14T23:34Z] INFO  16:34:01,422 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-14T23:34Z] INFO  16:34:03,122 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:34Z] INFO  16:34:03,125 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:34Z] GATK: realign ('11', 0, 15994658) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:34Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-9_129097484_141213431-prep.bam
[2016-04-14T23:34Z] INFO  16:34:03,476 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:34Z] INFO  16:34:03,480 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:34Z] INFO  16:34:03,480 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:34Z] INFO  16:34:03,481 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:34Z] INFO  16:34:03,486 HelpFormatter - Program Args: -T PrintReads -L 13:35615070-51287376 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/13/tx/tmpTU766H/R14-18102_kapa-NGv3-PE100-NGv3-sort-13_35615069_51287376-prep-prealign.bam
[2016-04-14T23:34Z] INFO  16:34:03,497 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:34Z] INFO  16:34:03,498 HelpFormatter - Date/Time: 2016/04/14 16:34:03
[2016-04-14T23:34Z] INFO  16:34:03,498 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:34Z] INFO  16:34:03,499 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:34Z] INFO  16:34:03,665 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:34Z] INFO  16:34:03,769 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:34Z] INFO  16:34:03,772 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:34Z] INFO  16:34:03,773 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:34Z] INFO  16:34:03,773 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:34Z] INFO  16:34:03,778 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/11/R14-18102_kapa-NGv3-PE100-NGv3-sort-11_47158866_62678572-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/11/R14-18102_kapa-NGv3-PE100-NGv3-sort-11_47158866_62678572-prep-prealign-realign.intervals -L 11:47158867-62678572 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/11/tx/tmpABuWA8/R14-18102_kapa-NGv3-PE100-NGv3-sort-11_47158866_62678572-prep.bam
[2016-04-14T23:34Z] INFO  16:34:03,807 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:34Z] INFO  16:34:03,807 HelpFormatter - Date/Time: 2016/04/14 16:34:03
[2016-04-14T23:34Z] INFO  16:34:03,807 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:34Z] INFO  16:34:03,807 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:34Z] INFO  16:34:04,106 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:34Z] INFO  16:34:04,260 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:34Z] INFO  16:34:04,276 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:34Z] INFO  16:34:04,342 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-14T23:34Z] INFO  16:34:04,721 IntervalUtils - Processing 15519706 bp from intervals
[2016-04-14T23:34Z] WARN  16:34:04,735 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:34Z] INFO  16:34:04,845 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:34Z] INFO  16:34:04,845 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-14T23:34Z] INFO  16:34:04,904 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:34Z] INFO  16:34:04,913 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:34Z] INFO  16:34:04,944 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:34Z] INFO  16:34:04,945 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:34Z] INFO  16:34:04,945 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:34Z] INFO  16:34:04,946 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:34Z] INFO  16:34:04,954 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.04
[2016-04-14T23:34Z] INFO  16:34:04,969 IntervalUtils - Processing 15672307 bp from intervals
[2016-04-14T23:34Z] INFO  16:34:05,048 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:34Z] INFO  16:34:05,072 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:34Z] INFO  16:34:05,223 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:34Z] INFO  16:34:05,344 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:34Z] INFO  16:34:05,351 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:34Z] INFO  16:34:05,353 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:34Z] INFO  16:34:05,353 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:34Z] INFO  16:34:05,383 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:34Z] GATK pre-alignment ('13', 51396767, 67205543) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:34Z] INFO  16:34:05,552 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:34Z] INFO  16:34:05,818 ProgressMeter -    12:107048143    200004.0    30.0 s       2.5 m       84.4%    35.0 s       5.0 s
[2016-04-14T23:34Z] INFO  16:34:05,907 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:34Z] INFO  16:34:05,910 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:34Z] INFO  16:34:05,911 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:34Z] INFO  16:34:05,911 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:34Z] INFO  16:34:05,916 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/11/R14-18102_kapa-NGv3-PE100-NGv3-sort-11_0_15994658-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/11/R14-18102_kapa-NGv3-PE100-NGv3-sort-11_0_15994658-prep-prealign-realign.intervals -L 11:1-15994658 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/11/tx/tmpxrfiwB/R14-18102_kapa-NGv3-PE100-NGv3-sort-11_0_15994658-prep.bam
[2016-04-14T23:34Z] INFO  16:34:05,934 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:34Z] INFO  16:34:05,935 HelpFormatter - Date/Time: 2016/04/14 16:34:05
[2016-04-14T23:34Z] INFO  16:34:05,936 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:34Z] INFO  16:34:05,936 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:34Z] INFO  16:34:06,151 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:34Z] INFO  16:34:06,288 ProgressMeter -            done   1.5529033E7    15.0 s       1.0 s      100.0%    15.0 s       0.0 s
[2016-04-14T23:34Z] INFO  16:34:06,289 ProgressMeter - Total runtime 15.88 secs, 0.26 min, 0.00 hours
[2016-04-14T23:34Z] INFO  16:34:06,293 MicroScheduler - 8266 reads were filtered out during the traversal out of approximately 96894 total reads (8.53%)
[2016-04-14T23:34Z] INFO  16:34:06,294 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:34Z] INFO  16:34:06,294 MicroScheduler -   -> 438 reads (0.45% of total) failing BadMateFilter
[2016-04-14T23:34Z] INFO  16:34:06,295 MicroScheduler -   -> 7479 reads (7.72% of total) failing DuplicateReadFilter
[2016-04-14T23:34Z] INFO  16:34:06,296 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-14T23:34Z] INFO  16:34:06,296 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:34Z] INFO  16:34:06,297 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-14T23:34Z] INFO  16:34:06,298 MicroScheduler -   -> 349 reads (0.36% of total) failing MappingQualityZeroFilter
[2016-04-14T23:34Z] INFO  16:34:06,298 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:34Z] INFO  16:34:06,299 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-14T23:34Z] INFO  16:34:06,299 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-14T23:34Z] INFO  16:34:06,302 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:34Z] INFO  16:34:06,332 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:34Z] INFO  16:34:06,417 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-14T23:34Z] INFO  16:34:06,920 ProgressMeter -            done   1.9748299E7    11.0 s       0.0 s      100.0%    11.0 s       0.0 s
[2016-04-14T23:34Z] INFO  16:34:06,921 ProgressMeter - Total runtime 11.57 secs, 0.19 min, 0.00 hours
[2016-04-14T23:34Z] INFO  16:34:06,924 MicroScheduler - 828 reads were filtered out during the traversal out of approximately 6995 total reads (11.84%)
[2016-04-14T23:34Z] INFO  16:34:06,925 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:34Z] INFO  16:34:06,931 IntervalUtils - Processing 15994658 bp from intervals
[2016-04-14T23:34Z] INFO  16:34:06,937 MicroScheduler -   -> 31 reads (0.44% of total) failing BadMateFilter
[2016-04-14T23:34Z] INFO  16:34:06,937 MicroScheduler -   -> 510 reads (7.29% of total) failing DuplicateReadFilter
[2016-04-14T23:34Z] INFO  16:34:06,938 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-14T23:34Z] INFO  16:34:06,939 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:34Z] INFO  16:34:06,939 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-14T23:34Z] INFO  16:34:06,940 MicroScheduler -   -> 287 reads (4.10% of total) failing MappingQualityZeroFilter
[2016-04-14T23:34Z] INFO  16:34:06,941 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:34Z] INFO  16:34:06,941 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-14T23:34Z] INFO  16:34:06,942 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-14T23:34Z] WARN  16:34:06,944 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:34Z] INFO  16:34:07,056 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:34Z] INFO  16:34:07,203 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:34Z] INFO  16:34:07,204 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:34Z] INFO  16:34:07,204 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:34Z] INFO  16:34:07,207 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:34Z] INFO  16:34:07,387 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:34Z] INFO  16:34:07,557 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:34Z] INFO  16:34:07,787 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:34Z] GATK: realign ('12', 78334098, 93863131) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:34Z] INFO  16:34:08,139 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:34Z] INFO  16:34:08,142 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:34Z] INFO  16:34:08,143 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:34Z] INFO  16:34:08,144 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:34Z] INFO  16:34:08,148 HelpFormatter - Program Args: -T PrintReads -L 13:51396768-67205543 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/13/tx/tmpMBwnqS/R14-18102_kapa-NGv3-PE100-NGv3-sort-13_51396767_67205543-prep-prealign.bam
[2016-04-14T23:34Z] INFO  16:34:08,158 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:34Z] INFO  16:34:08,165 HelpFormatter - Date/Time: 2016/04/14 16:34:08
[2016-04-14T23:34Z] INFO  16:34:08,166 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:34Z] INFO  16:34:08,166 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:34Z] INFO  16:34:08,348 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:34Z] INFO  16:34:08,363 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:34Z] GATK: realign ('13', 0, 19748299) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:34Z] INFO  16:34:09,598 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-14T23:34Z] INFO  16:34:09,671 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:34Z] INFO  16:34:09,680 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:34Z] INFO  16:34:09,728 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-14T23:34Z] INFO  16:34:09,742 IntervalUtils - Processing 15808776 bp from intervals
[2016-04-14T23:34Z] INFO  16:34:09,834 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:34Z] INFO  16:34:09,993 ProgressMeter -            done   1.5537525E7    17.0 s       1.0 s      100.0%    17.0 s       0.0 s
[2016-04-14T23:34Z] INFO  16:34:09,994 ProgressMeter - Total runtime 17.34 secs, 0.29 min, 0.00 hours
[2016-04-14T23:34Z] INFO  16:34:09,998 MicroScheduler - 15286 reads were filtered out during the traversal out of approximately 179131 total reads (8.53%)
[2016-04-14T23:34Z] INFO  16:34:09,999 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:34Z] INFO  16:34:09,999 MicroScheduler -   -> 586 reads (0.33% of total) failing BadMateFilter
[2016-04-14T23:34Z] INFO  16:34:10,000 MicroScheduler -   -> 13986 reads (7.81% of total) failing DuplicateReadFilter
[2016-04-14T23:34Z] INFO  16:34:10,001 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-14T23:34Z] INFO  16:34:10,001 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:34Z] INFO  16:34:10,002 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-14T23:34Z] INFO  16:34:10,002 MicroScheduler -   -> 714 reads (0.40% of total) failing MappingQualityZeroFilter
[2016-04-14T23:34Z] INFO  16:34:10,003 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:34Z] INFO  16:34:10,004 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-14T23:34Z] INFO  16:34:10,004 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-14T23:34Z] INFO  16:34:10,128 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:34Z] INFO  16:34:10,129 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:34Z] INFO  16:34:10,129 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:34Z] INFO  16:34:10,129 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:34Z] INFO  16:34:10,154 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:34Z] INFO  16:34:10,260 ProgressMeter -     12:53682212    400006.0    60.0 s       2.5 m       43.6%     2.3 m      77.0 s
[2016-04-14T23:34Z] INFO  16:34:10,310 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:34Z] INFO  16:34:10,656 ProgressMeter -            done    192367.0    14.0 s      77.0 s      100.0%    14.0 s       0.0 s
[2016-04-14T23:34Z] INFO  16:34:10,657 ProgressMeter - Total runtime 14.96 secs, 0.25 min, 0.00 hours
[2016-04-14T23:34Z] INFO  16:34:10,660 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 192367 total reads (0.00%)
[2016-04-14T23:34Z] INFO  16:34:10,660 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:34Z] INFO  16:34:10,661 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:34Z] INFO  16:34:10,661 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:34Z] INFO  16:34:10,740 ProgressMeter -    12:113313529    100001.0    30.0 s       5.0 m       24.2%     2.1 m      93.0 s
[2016-04-14T23:34Z] INFO  16:34:10,805 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:34Z] INFO  16:34:10,809 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:34Z] INFO  16:34:10,809 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:34Z] INFO  16:34:10,810 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:34Z] INFO  16:34:10,814 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/12/R14-18102_kapa-NGv3-PE100-NGv3-sort-12_78334098_93863131-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/12/R14-18102_kapa-NGv3-PE100-NGv3-sort-12_78334098_93863131-prep-prealign-realign.intervals -L 12:78334099-93863131 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/12/tx/tmpUN96JN/R14-18102_kapa-NGv3-PE100-NGv3-sort-12_78334098_93863131-prep.bam
[2016-04-14T23:34Z] INFO  16:34:10,841 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:34Z] INFO  16:34:10,842 HelpFormatter - Date/Time: 2016/04/14 16:34:10
[2016-04-14T23:34Z] INFO  16:34:10,843 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:34Z] INFO  16:34:10,843 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:34Z] INFO  16:34:10,958 ProgressMeter -    12:133352965    100003.0    30.0 s       5.0 m       94.2%    31.0 s       1.0 s
[2016-04-14T23:34Z] INFO  16:34:10,999 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:34Z] INFO  16:34:11,076 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:34Z] INFO  16:34:11,085 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:34Z] INFO  16:34:11,129 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.04
[2016-04-14T23:34Z] INFO  16:34:11,435 IntervalUtils - Processing 15529033 bp from intervals
[2016-04-14T23:34Z] WARN  16:34:11,441 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:34Z] INFO  16:34:11,462 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:34Z] INFO  16:34:11,465 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:34Z] INFO  16:34:11,466 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:34Z] INFO  16:34:11,466 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:34Z] INFO  16:34:11,471 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/13/R14-18102_kapa-NGv3-PE100-NGv3-sort-13_0_19748299-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/13/R14-18102_kapa-NGv3-PE100-NGv3-sort-13_0_19748299-prep-prealign-realign.intervals -L 13:1-19748299 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/13/tx/tmpo9gGil/R14-18102_kapa-NGv3-PE100-NGv3-sort-13_0_19748299-prep.bam
[2016-04-14T23:34Z] INFO  16:34:11,485 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:34Z] INFO  16:34:11,486 HelpFormatter - Date/Time: 2016/04/14 16:34:11
[2016-04-14T23:34Z] INFO  16:34:11,487 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:34Z] INFO  16:34:11,487 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:34Z] INFO  16:34:11,508 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:34Z] INFO  16:34:11,594 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:34Z] INFO  16:34:11,595 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@41fd9d8e
[2016-04-14T23:34Z] INFO  16:34:11,630 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:34Z] INFO  16:34:11,642 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:34Z] GATK: realign ('12', 62687959, 78225484) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:34Z] INFO  16:34:11,643 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:34Z] INFO  16:34:11,643 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:34Z] INFO  16:34:11,700 ProgressMeter -            done    279447.0    35.0 s       2.1 m      100.0%    35.0 s       0.0 s
[2016-04-14T23:34Z] INFO  16:34:11,701 ProgressMeter - Total runtime 35.90 secs, 0.60 min, 0.01 hours
[2016-04-14T23:34Z] INFO  16:34:11,701 MicroScheduler - 157 reads were filtered out during the traversal out of approximately 279604 total reads (0.06%)
[2016-04-14T23:34Z] INFO  16:34:11,701 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:34Z] INFO  16:34:11,702 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:34Z] INFO  16:34:11,702 MicroScheduler -   -> 157 reads (0.06% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:34Z] INFO  16:34:11,714 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:34Z] INFO  16:34:11,741 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@7172f77a
[2016-04-14T23:34Z] INFO  16:34:11,794 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:34Z] INFO  16:34:11,827 ProgressMeter -            done    905434.0   109.0 s     120.0 s      100.0%   109.0 s       0.0 s
[2016-04-14T23:34Z] INFO  16:34:11,827 ProgressMeter - Total runtime 109.43 secs, 1.82 min, 0.03 hours
[2016-04-14T23:34Z] INFO  16:34:11,828 MicroScheduler - 363 reads were filtered out during the traversal out of approximately 905797 total reads (0.04%)
[2016-04-14T23:34Z] INFO  16:34:11,828 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:34Z] INFO  16:34:11,830 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:34Z] INFO  16:34:11,830 MicroScheduler -   -> 363 reads (0.04% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:34Z] INFO  16:34:11,842 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:34Z] INFO  16:34:11,852 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:34Z] INFO  16:34:11,907 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-14T23:34Z] INFO  16:34:11,964 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:34Z] INFO  16:34:12,263 IntervalUtils - Processing 19748299 bp from intervals
[2016-04-14T23:34Z] WARN  16:34:12,268 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:34Z] INFO  16:34:12,331 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:34Z] INFO  16:34:12,407 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:34Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-12_31236746_46754992-prep.bam
[2016-04-14T23:34Z] INFO  16:34:12,470 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@7172f77a
[2016-04-14T23:34Z] INFO  16:34:12,522 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:34Z] INFO  16:34:12,523 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:34Z] INFO  16:34:12,524 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:34Z] INFO  16:34:12,525 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:34Z] INFO  16:34:12,557 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:34Z] INFO  16:34:12,564 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:34Z] INFO  16:34:12,589 ProgressMeter -            done    560719.0    81.0 s       2.4 m      100.0%    81.0 s       0.0 s
[2016-04-14T23:34Z] INFO  16:34:12,596 ProgressMeter - Total runtime 81.27 secs, 1.35 min, 0.02 hours
[2016-04-14T23:34Z] INFO  16:34:12,596 MicroScheduler - 230 reads were filtered out during the traversal out of approximately 560949 total reads (0.04%)
[2016-04-14T23:34Z] INFO  16:34:12,596 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:34Z] INFO  16:34:12,597 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:34Z] INFO  16:34:12,597 MicroScheduler -   -> 230 reads (0.04% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:34Z] INFO  16:34:13,009 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:34Z] GATK pre-alignment ('13', 67477635, 84455642) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:34Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-12_93870729_109490566-prep-prealign.bam
[2016-04-14T23:34Z] INFO  16:34:13,340 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:34Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-11_62744265_78270665-prep-prealign.bam
[2016-04-14T23:34Z] GATK RealignerTargetCreator: R14-18102_kapa-NGv3-PE100-NGv3-sort-12_93870729_109490566-prep-prealign.bam 12:93870730-109490566
[2016-04-14T23:34Z] GATK: RealignerTargetCreator
[2016-04-14T23:34Z] INFO  16:34:14,112 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:34Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-12_0_15637181-prep-prealign.bam
[2016-04-14T23:34Z] INFO  16:34:14,428 ProgressMeter -            done      6932.0     1.0 s       4.6 m      100.0%     1.0 s       0.0 s
[2016-04-14T23:34Z] INFO  16:34:14,429 ProgressMeter - Total runtime 1.91 secs, 0.03 min, 0.00 hours
[2016-04-14T23:34Z] INFO  16:34:14,433 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 6932 total reads (0.00%)
[2016-04-14T23:34Z] INFO  16:34:14,433 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:34Z] INFO  16:34:14,434 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:34Z] INFO  16:34:14,434 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:34Z] INFO  16:34:14,639 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@41fd9d8e
[2016-04-14T23:34Z] INFO  16:34:14,637 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:34Z] INFO  16:34:14,640 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:34Z] INFO  16:34:14,641 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:34Z] INFO  16:34:14,641 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:34Z] INFO  16:34:14,646 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/12/R14-18102_kapa-NGv3-PE100-NGv3-sort-12_62687959_78225484-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/12/R14-18102_kapa-NGv3-PE100-NGv3-sort-12_62687959_78225484-prep-prealign-realign.intervals -L 12:62687960-78225484 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/12/tx/tmpqwmBJB/R14-18102_kapa-NGv3-PE100-NGv3-sort-12_62687959_78225484-prep.bam
[2016-04-14T23:34Z] INFO  16:34:14,665 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:34Z] INFO  16:34:14,669 HelpFormatter - Date/Time: 2016/04/14 16:34:14
[2016-04-14T23:34Z] INFO  16:34:14,670 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:34Z] INFO  16:34:14,675 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:34Z] INFO  16:34:14,797 ProgressMeter -            done    207191.0    33.0 s       2.7 m       99.5%    33.0 s       0.0 s
[2016-04-14T23:34Z] INFO  16:34:14,798 ProgressMeter - Total runtime 33.87 secs, 0.56 min, 0.01 hours
[2016-04-14T23:34Z] INFO  16:34:14,798 MicroScheduler - 160 reads were filtered out during the traversal out of approximately 207351 total reads (0.08%)
[2016-04-14T23:34Z] INFO  16:34:14,799 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:34Z] INFO  16:34:14,799 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:34Z] INFO  16:34:14,799 MicroScheduler -   -> 160 reads (0.08% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:34Z] INFO  16:34:14,909 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:34Z] INFO  16:34:15,065 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:34Z] INFO  16:34:15,077 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:34Z] INFO  16:34:15,149 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-14T23:34Z] INFO  16:34:15,644 IntervalUtils - Processing 15537525 bp from intervals
[2016-04-14T23:34Z] WARN  16:34:15,663 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:34Z] INFO  16:34:15,758 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:34Z] GATK RealignerTargetCreator: R14-18102_kapa-NGv3-PE100-NGv3-sort-12_0_15637181-prep-prealign.bam 12:1-15637181
[2016-04-14T23:34Z] GATK: RealignerTargetCreator
[2016-04-14T23:34Z] INFO  16:34:15,926 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:34Z] INFO  16:34:15,943 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:34Z] INFO  16:34:15,943 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:34Z] INFO  16:34:15,944 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:34Z] INFO  16:34:16,040 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:34Z] INFO  16:34:16,043 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:34Z] INFO  16:34:16,044 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:34Z] INFO  16:34:16,044 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:34Z] INFO  16:34:16,049 HelpFormatter - Program Args: -T PrintReads -L 13:67477636-84455642 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/13/tx/tmpCoaSGH/R14-18102_kapa-NGv3-PE100-NGv3-sort-13_67477635_84455642-prep-prealign.bam
[2016-04-14T23:34Z] INFO  16:34:16,081 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:34Z] INFO  16:34:16,081 HelpFormatter - Date/Time: 2016/04/14 16:34:16
[2016-04-14T23:34Z] INFO  16:34:16,082 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:34Z] INFO  16:34:16,082 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:34Z] INFO  16:34:16,097 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:34Z] INFO  16:34:16,101 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:34Z] GATK RealignerTargetCreator: R14-18102_kapa-NGv3-PE100-NGv3-sort-11_62744265_78270665-prep-prealign.bam 11:62744266-78270665
[2016-04-14T23:34Z] GATK: RealignerTargetCreator
[2016-04-14T23:34Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-13_0_19748299-prep.bam
[2016-04-14T23:34Z] INFO  16:34:16,227 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:34Z] GATK pre-alignment ('13', 86368117, 101881935) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:34Z] INFO  16:34:16,269 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:34Z] INFO  16:34:16,325 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:34Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-12_125267228_133851895-prep-prealign.bam
[2016-04-14T23:34Z] GATK RealignerTargetCreator: R14-18102_kapa-NGv3-PE100-NGv3-sort-12_125267228_133851895-prep-prealign.bam 12:125267229-133851895
[2016-04-14T23:34Z] GATK: RealignerTargetCreator
[2016-04-14T23:34Z] INFO  16:34:17,353 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:34Z] INFO  16:34:17,356 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:34Z] INFO  16:34:17,357 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:34Z] INFO  16:34:17,357 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:34Z] INFO  16:34:17,361 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/12/R14-18102_kapa-NGv3-PE100-NGv3-sort-12_93870729_109490566-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/12/tx/tmpF8mUUe/R14-18102_kapa-NGv3-PE100-NGv3-sort-12_93870729_109490566-prep-prealign-realign.intervals -l INFO -L 12:93870730-109490566 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-14T23:34Z] INFO  16:34:17,372 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:34Z] INFO  16:34:17,383 HelpFormatter - Date/Time: 2016/04/14 16:34:17
[2016-04-14T23:34Z] INFO  16:34:17,384 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:34Z] INFO  16:34:17,384 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:34Z] INFO  16:34:17,530 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:34Z] INFO  16:34:17,552 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-14T23:34Z] INFO  16:34:17,658 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:34Z] INFO  16:34:17,676 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:34Z] INFO  16:34:17,710 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.03
[2016-04-14T23:34Z] INFO  16:34:17,736 IntervalUtils - Processing 16978007 bp from intervals
[2016-04-14T23:34Z] INFO  16:34:17,749 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-14T23:34Z] INFO  16:34:17,784 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:34Z] INFO  16:34:17,809 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:34Z] INFO  16:34:17,857 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-14T23:34Z] INFO  16:34:18,068 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:34Z] INFO  16:34:18,069 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:34Z] INFO  16:34:18,070 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:34Z] INFO  16:34:18,070 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:34Z] INFO  16:34:18,086 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:34Z] INFO  16:34:18,247 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:34Z] INFO  16:34:18,263 IntervalUtils - Processing 15619837 bp from intervals
[2016-04-14T23:34Z] WARN  16:34:18,269 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:34Z] INFO  16:34:18,367 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:34Z] INFO  16:34:18,566 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:34Z] INFO  16:34:18,567 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:34Z] INFO  16:34:18,568 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:34Z] INFO  16:34:18,569 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-14T23:34Z] INFO  16:34:18,990 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:34Z] INFO  16:34:18,994 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:34Z] INFO  16:34:18,994 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:34Z] INFO  16:34:18,995 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:34Z] INFO  16:34:18,999 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/12/R14-18102_kapa-NGv3-PE100-NGv3-sort-12_0_15637181-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/12/tx/tmpreEori/R14-18102_kapa-NGv3-PE100-NGv3-sort-12_0_15637181-prep-prealign-realign.intervals -l INFO -L 12:1-15637181 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-14T23:34Z] INFO  16:34:19,009 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:34Z] INFO  16:34:19,017 HelpFormatter - Date/Time: 2016/04/14 16:34:18
[2016-04-14T23:34Z] INFO  16:34:19,017 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:34Z] INFO  16:34:19,017 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:34Z] INFO  16:34:19,122 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:34Z] INFO  16:34:19,276 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:34Z] INFO  16:34:19,280 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:34Z] INFO  16:34:19,280 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:34Z] INFO  16:34:19,281 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:34Z] INFO  16:34:19,286 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/11/R14-18102_kapa-NGv3-PE100-NGv3-sort-11_62744265_78270665-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/11/tx/tmpmQOeLT/R14-18102_kapa-NGv3-PE100-NGv3-sort-11_62744265_78270665-prep-prealign-realign.intervals -l INFO -L 11:62744266-78270665 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-14T23:34Z] INFO  16:34:19,295 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:34Z] INFO  16:34:19,306 HelpFormatter - Date/Time: 2016/04/14 16:34:19
[2016-04-14T23:34Z] INFO  16:34:19,307 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:34Z] INFO  16:34:19,308 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:34Z] INFO  16:34:19,377 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-14T23:34Z] INFO  16:34:19,391 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:34Z] INFO  16:34:19,400 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:34Z] INFO  16:34:19,403 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:34Z] INFO  16:34:19,404 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:34Z] INFO  16:34:19,404 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:34Z] INFO  16:34:19,409 HelpFormatter - Program Args: -T PrintReads -L 13:86368118-101881935 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/13/tx/tmpbQGMHM/R14-18102_kapa-NGv3-PE100-NGv3-sort-13_86368117_101881935-prep-prealign.bam
[2016-04-14T23:34Z] INFO  16:34:19,439 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:34Z] INFO  16:34:19,440 HelpFormatter - Date/Time: 2016/04/14 16:34:19
[2016-04-14T23:34Z] INFO  16:34:19,441 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:34Z] INFO  16:34:19,441 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:34Z] INFO  16:34:19,445 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:34Z] INFO  16:34:19,478 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.09
[2016-04-14T23:34Z] INFO  16:34:19,674 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:34Z] INFO  16:34:19,725 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-14T23:34Z] INFO  16:34:19,739 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:34Z] INFO  16:34:19,814 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-14T23:34Z] INFO  16:34:19,953 IntervalUtils - Processing 15637181 bp from intervals
[2016-04-14T23:34Z] WARN  16:34:19,957 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:34Z] INFO  16:34:20,078 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:34Z] INFO  16:34:20,081 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:34Z] INFO  16:34:20,082 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:34Z] INFO  16:34:20,082 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:34Z] INFO  16:34:20,087 IntervalUtils - Processing 15526400 bp from intervals
[2016-04-14T23:34Z] INFO  16:34:20,087 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/12/R14-18102_kapa-NGv3-PE100-NGv3-sort-12_125267228_133851895-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/12/tx/tmpH8eOZq/R14-18102_kapa-NGv3-PE100-NGv3-sort-12_125267228_133851895-prep-prealign-realign.intervals -l INFO -L 12:125267229-133851895 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-14T23:34Z] WARN  16:34:20,092 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:34Z] INFO  16:34:20,093 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:34Z] INFO  16:34:20,096 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:34Z] INFO  16:34:20,107 HelpFormatter - Date/Time: 2016/04/14 16:34:20
[2016-04-14T23:34Z] INFO  16:34:20,108 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:34Z] INFO  16:34:20,109 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:34Z] INFO  16:34:20,206 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:34Z] INFO  16:34:20,215 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:34Z] INFO  16:34:20,360 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:34Z] INFO  16:34:20,361 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:34Z] INFO  16:34:20,361 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:34Z] INFO  16:34:20,364 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-14T23:34Z] INFO  16:34:20,398 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-14T23:34Z] INFO  16:34:20,436 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:34Z] INFO  16:34:20,478 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:34Z] INFO  16:34:20,480 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:34Z] INFO  16:34:20,480 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:34Z] INFO  16:34:20,481 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-14T23:34Z] INFO  16:34:20,495 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-14T23:34Z] INFO  16:34:20,736 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-14T23:34Z] INFO  16:34:20,803 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:34Z] INFO  16:34:20,806 IntervalUtils - Processing 8584667 bp from intervals
[2016-04-14T23:34Z] WARN  16:34:20,810 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:34Z] INFO  16:34:20,812 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:34Z] INFO  16:34:20,865 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-14T23:34Z] INFO  16:34:20,879 IntervalUtils - Processing 15513818 bp from intervals
[2016-04-14T23:34Z] INFO  16:34:20,914 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:34Z] INFO  16:34:20,950 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:34Z] INFO  16:34:21,123 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:34Z] INFO  16:34:21,124 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:34Z] INFO  16:34:21,125 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:34Z] INFO  16:34:21,125 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-14T23:34Z] INFO  16:34:21,278 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:34Z] INFO  16:34:21,293 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:34Z] INFO  16:34:21,294 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:34Z] INFO  16:34:21,294 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:34Z] INFO  16:34:21,320 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:34Z] INFO  16:34:21,513 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:34Z] INFO  16:34:21,723 ProgressMeter -            done     96606.0    10.0 s     104.0 s      100.0%    10.0 s       0.0 s
[2016-04-14T23:34Z] INFO  16:34:21,724 ProgressMeter - Total runtime 10.08 secs, 0.17 min, 0.00 hours
[2016-04-14T23:34Z] INFO  16:34:21,727 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 96606 total reads (0.00%)
[2016-04-14T23:34Z] INFO  16:34:21,728 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:34Z] INFO  16:34:21,729 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:34Z] INFO  16:34:21,730 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:34Z] INFO  16:34:23,559 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:34Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-12_78334098_93863131-prep.bam
[2016-04-14T23:34Z] GATK pre-alignment ('13', 101890105, 115169878) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:34Z] INFO  16:34:25,336 ProgressMeter -            done   1.5512808E7    24.0 s       1.0 s      100.0%    24.0 s       0.0 s
[2016-04-14T23:34Z] INFO  16:34:25,337 ProgressMeter - Total runtime 24.48 secs, 0.41 min, 0.01 hours
[2016-04-14T23:34Z] INFO  16:34:25,340 MicroScheduler - 45670 reads were filtered out during the traversal out of approximately 513437 total reads (8.89%)
[2016-04-14T23:34Z] INFO  16:34:25,341 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:34Z] INFO  16:34:25,342 MicroScheduler -   -> 1013 reads (0.20% of total) failing BadMateFilter
[2016-04-14T23:34Z] INFO  16:34:25,343 MicroScheduler -   -> 40778 reads (7.94% of total) failing DuplicateReadFilter
[2016-04-14T23:34Z] INFO  16:34:25,343 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-14T23:34Z] INFO  16:34:25,344 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:34Z] INFO  16:34:25,344 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-14T23:34Z] INFO  16:34:25,345 MicroScheduler -   -> 3879 reads (0.76% of total) failing MappingQualityZeroFilter
[2016-04-14T23:34Z] INFO  16:34:25,346 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:34Z] INFO  16:34:25,346 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-14T23:34Z] INFO  16:34:25,347 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-14T23:34Z] INFO  16:34:26,589 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:34Z] INFO  16:34:26,593 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:34Z] INFO  16:34:26,593 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:34Z] INFO  16:34:26,593 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:34Z] INFO  16:34:26,597 HelpFormatter - Program Args: -T PrintReads -L 13:101890106-115169878 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/13/tx/tmpHGswXW/R14-18102_kapa-NGv3-PE100-NGv3-sort-13_101890105_115169878-prep-prealign.bam
[2016-04-14T23:34Z] INFO  16:34:26,607 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:34Z] INFO  16:34:26,608 HelpFormatter - Date/Time: 2016/04/14 16:34:26
[2016-04-14T23:34Z] INFO  16:34:26,609 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:34Z] INFO  16:34:26,609 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:34Z] INFO  16:34:26,632 ProgressMeter -     13:29856134    100001.0    30.0 s       5.1 m       64.1%    46.0 s      16.0 s
[2016-04-14T23:34Z] INFO  16:34:26,760 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:34Z] INFO  16:34:26,765 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:34Z] GATK: realign ('11', 110001730, 125514538) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:34Z] INFO  16:34:27,843 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-14T23:34Z] INFO  16:34:27,910 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:34Z] INFO  16:34:27,931 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:34Z] INFO  16:34:27,981 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-14T23:34Z] INFO  16:34:27,996 IntervalUtils - Processing 13279773 bp from intervals
[2016-04-14T23:34Z] INFO  16:34:28,077 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:34Z] INFO  16:34:28,319 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:34Z] INFO  16:34:28,320 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:34Z] INFO  16:34:28,321 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:34Z] INFO  16:34:28,322 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:34Z] INFO  16:34:28,335 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:34Z] INFO  16:34:28,539 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:34Z] INFO  16:34:29,670 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@32d5a4c6
[2016-04-14T23:34Z] INFO  16:34:29,685 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:34Z] INFO  16:34:29,688 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:34Z] INFO  16:34:29,689 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:34Z] INFO  16:34:29,689 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:34Z] INFO  16:34:29,694 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/11/R14-18102_kapa-NGv3-PE100-NGv3-sort-11_110001730_125514538-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/11/R14-18102_kapa-NGv3-PE100-NGv3-sort-11_110001730_125514538-prep-prealign-realign.intervals -L 11:110001731-125514538 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/11/tx/tmpxGKrNs/R14-18102_kapa-NGv3-PE100-NGv3-sort-11_110001730_125514538-prep.bam
[2016-04-14T23:34Z] INFO  16:34:29,716 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:34Z] INFO  16:34:29,717 HelpFormatter - Date/Time: 2016/04/14 16:34:29
[2016-04-14T23:34Z] INFO  16:34:29,718 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:34Z] INFO  16:34:29,719 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:34Z] INFO  16:34:29,807 ProgressMeter -            done    115562.0    19.0 s       2.8 m      100.0%    19.0 s       0.0 s
[2016-04-14T23:34Z] INFO  16:34:29,808 ProgressMeter - Total runtime 19.68 secs, 0.33 min, 0.01 hours
[2016-04-14T23:34Z] INFO  16:34:29,809 MicroScheduler - 115 reads were filtered out during the traversal out of approximately 115677 total reads (0.10%)
[2016-04-14T23:34Z] INFO  16:34:29,810 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:34Z] INFO  16:34:29,811 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:34Z] INFO  16:34:29,811 MicroScheduler -   -> 115 reads (0.10% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:34Z] INFO  16:34:29,962 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:34Z] INFO  16:34:30,123 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:34Z] INFO  16:34:30,137 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:34Z] INFO  16:34:30,195 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-14T23:34Z] INFO  16:34:30,514 IntervalUtils - Processing 15512808 bp from intervals
[2016-04-14T23:34Z] WARN  16:34:30,520 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:34Z] INFO  16:34:30,619 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:34Z] INFO  16:34:30,786 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:34Z] INFO  16:34:30,787 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:34Z] INFO  16:34:30,788 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:34Z] INFO  16:34:30,789 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:34Z] INFO  16:34:30,954 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:34Z] INFO  16:34:30,998 ProgressMeter -            done    178263.0    15.0 s      84.0 s      100.0%    15.0 s       0.0 s
[2016-04-14T23:34Z] INFO  16:34:30,999 ProgressMeter - Total runtime 15.06 secs, 0.25 min, 0.00 hours
[2016-04-14T23:34Z] INFO  16:34:31,003 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 178263 total reads (0.00%)
[2016-04-14T23:34Z] INFO  16:34:31,004 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:34Z] INFO  16:34:31,005 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:34Z] INFO  16:34:31,005 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:34Z] INFO  16:34:31,090 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:34Z] INFO  16:34:31,150 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:34Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-13_51396767_67205543-prep-prealign.bam
[2016-04-14T23:34Z] GATK RealignerTargetCreator: R14-18102_kapa-NGv3-PE100-NGv3-sort-13_51396767_67205543-prep-prealign.bam 13:51396768-67205543
[2016-04-14T23:34Z] GATK: RealignerTargetCreator
[2016-04-14T23:34Z] INFO  16:34:31,770 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@32d5a4c6
[2016-04-14T23:34Z] INFO  16:34:31,890 ProgressMeter -            done     92784.0    13.0 s       2.5 m      100.0%    13.0 s       0.0 s
[2016-04-14T23:34Z] INFO  16:34:31,891 ProgressMeter - Total runtime 13.82 secs, 0.23 min, 0.00 hours
[2016-04-14T23:34Z] INFO  16:34:31,891 MicroScheduler - 96 reads were filtered out during the traversal out of approximately 92880 total reads (0.10%)
[2016-04-14T23:34Z] INFO  16:34:31,891 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:34Z] INFO  16:34:31,892 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:34Z] INFO  16:34:31,892 MicroScheduler -   -> 96 reads (0.10% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:34Z] INFO  16:34:32,463 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:34Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-12_62687959_78225484-prep.bam
[2016-04-14T23:34Z] GATK pre-alignment ('14', 0, 19378574) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:34Z] INFO  16:34:33,165 ProgressMeter -            done   8584667.0    12.0 s       1.0 s      100.0%    12.0 s       0.0 s
[2016-04-14T23:34Z] INFO  16:34:33,165 ProgressMeter - Total runtime 12.04 secs, 0.20 min, 0.00 hours
[2016-04-14T23:34Z] INFO  16:34:33,166 MicroScheduler - 28207 reads were filtered out during the traversal out of approximately 208355 total reads (13.54%)
[2016-04-14T23:34Z] INFO  16:34:33,167 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:34Z] INFO  16:34:33,168 MicroScheduler -   -> 470 reads (0.23% of total) failing BadMateFilter
[2016-04-14T23:34Z] INFO  16:34:33,176 MicroScheduler -   -> 16110 reads (7.73% of total) failing DuplicateReadFilter
[2016-04-14T23:34Z] INFO  16:34:33,176 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-14T23:34Z] INFO  16:34:33,177 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:34Z] INFO  16:34:33,177 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-14T23:34Z] INFO  16:34:33,177 MicroScheduler -   -> 11627 reads (5.58% of total) failing MappingQualityZeroFilter
[2016-04-14T23:34Z] INFO  16:34:33,177 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:34Z] INFO  16:34:33,178 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-14T23:34Z] INFO  16:34:33,178 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-14T23:34Z] INFO  16:34:33,308 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:34Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-13_67477635_84455642-prep-prealign.bam
[2016-04-14T23:34Z] GATK RealignerTargetCreator: R14-18102_kapa-NGv3-PE100-NGv3-sort-13_67477635_84455642-prep-prealign.bam 13:67477636-84455642
[2016-04-14T23:34Z] GATK: RealignerTargetCreator
[2016-04-14T23:34Z] INFO  16:34:34,018 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:34Z] INFO  16:34:34,036 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:34Z] INFO  16:34:34,036 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:34Z] INFO  16:34:34,036 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:34Z] INFO  16:34:34,041 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/13/R14-18102_kapa-NGv3-PE100-NGv3-sort-13_51396767_67205543-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/13/tx/tmpZKlNNQ/R14-18102_kapa-NGv3-PE100-NGv3-sort-13_51396767_67205543-prep-prealign-realign.intervals -l INFO -L 13:51396768-67205543 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-14T23:34Z] INFO  16:34:34,072 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:34Z] INFO  16:34:34,072 HelpFormatter - Date/Time: 2016/04/14 16:34:34
[2016-04-14T23:34Z] INFO  16:34:34,073 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:34Z] INFO  16:34:34,073 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:34Z] INFO  16:34:34,204 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:34Z] INFO  16:34:34,473 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-14T23:34Z] INFO  16:34:34,482 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:34Z] INFO  16:34:34,557 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-14T23:34Z] INFO  16:34:34,737 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:34Z] INFO  16:34:34,757 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@41fd9d8e
[2016-04-14T23:34Z] GATK: realign ('12', 125267228, 133851895) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:34Z] INFO  16:34:34,813 IntervalUtils - Processing 15808776 bp from intervals
[2016-04-14T23:34Z] WARN  16:34:34,818 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:34Z] INFO  16:34:34,858 ProgressMeter -            done    231379.0    29.0 s       2.1 m      100.0%    29.0 s       0.0 s
[2016-04-14T23:34Z] INFO  16:34:34,859 ProgressMeter - Total runtime 29.51 secs, 0.49 min, 0.01 hours
[2016-04-14T23:34Z] INFO  16:34:34,859 MicroScheduler - 127 reads were filtered out during the traversal out of approximately 231506 total reads (0.05%)
[2016-04-14T23:34Z] INFO  16:34:34,859 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:34Z] INFO  16:34:34,860 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:34Z] INFO  16:34:34,860 MicroScheduler -   -> 127 reads (0.05% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:34Z] INFO  16:34:34,885 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:34Z] INFO  16:34:35,087 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:34Z] INFO  16:34:35,088 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:34Z] INFO  16:34:35,089 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:34Z] INFO  16:34:35,089 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-14T23:34Z] INFO  16:34:35,423 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@5fe152b7
[2016-04-14T23:34Z] INFO  16:34:35,541 ProgressMeter -            done    256845.0    39.0 s       2.6 m      100.0%    39.0 s       0.0 s
[2016-04-14T23:34Z] INFO  16:34:35,542 ProgressMeter - Total runtime 39.34 secs, 0.66 min, 0.01 hours
[2016-04-14T23:34Z] INFO  16:34:35,542 MicroScheduler - 157 reads were filtered out during the traversal out of approximately 257002 total reads (0.06%)
[2016-04-14T23:34Z] INFO  16:34:35,542 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:34Z] INFO  16:34:35,543 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:34Z] INFO  16:34:35,543 MicroScheduler -   -> 157 reads (0.06% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:34Z] INFO  16:34:35,662 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:34Z] INFO  16:34:35,664 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:34Z] INFO  16:34:35,665 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:34Z] INFO  16:34:35,665 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:34Z] INFO  16:34:35,669 HelpFormatter - Program Args: -T PrintReads -L 14:1-19378574 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/14/tx/tmpAWE916/R14-18102_kapa-NGv3-PE100-NGv3-sort-14_0_19378574-prep-prealign.bam
[2016-04-14T23:34Z] INFO  16:34:35,691 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:34Z] INFO  16:34:35,692 HelpFormatter - Date/Time: 2016/04/14 16:34:35
[2016-04-14T23:34Z] INFO  16:34:35,692 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:34Z] INFO  16:34:35,692 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:34Z] INFO  16:34:35,894 ProgressMeter -     11:62294689    400008.0    30.0 s      77.0 s       97.5%    30.0 s       0.0 s
[2016-04-14T23:34Z] INFO  16:34:35,914 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:34Z] INFO  16:34:36,251 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:34Z] INFO  16:34:36,257 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:34Z] INFO  16:34:36,260 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:34Z] INFO  16:34:36,261 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:34Z] INFO  16:34:36,262 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:34Z] INFO  16:34:36,266 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/13/R14-18102_kapa-NGv3-PE100-NGv3-sort-13_67477635_84455642-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/13/tx/tmpcii_6j/R14-18102_kapa-NGv3-PE100-NGv3-sort-13_67477635_84455642-prep-prealign-realign.intervals -l INFO -L 13:67477636-84455642 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-14T23:34Z] INFO  16:34:36,275 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:34Z] INFO  16:34:36,276 HelpFormatter - Date/Time: 2016/04/14 16:34:36
[2016-04-14T23:34Z] INFO  16:34:36,283 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:34Z] INFO  16:34:36,284 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:34Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-13_35615069_51287376-prep-prealign.bam
[2016-04-14T23:34Z] INFO  16:34:36,396 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:34Z] INFO  16:34:36,607 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-14T23:34Z] INFO  16:34:36,660 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:34Z] INFO  16:34:36,761 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.10
[2016-04-14T23:34Z] INFO  16:34:36,924 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-14T23:34Z] GATK RealignerTargetCreator: R14-18102_kapa-NGv3-PE100-NGv3-sort-13_35615069_51287376-prep-prealign.bam 13:35615070-51287376
[2016-04-14T23:34Z] GATK: RealignerTargetCreator
[2016-04-14T23:34Z] INFO  16:34:36,977 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:34Z] INFO  16:34:36,986 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:34Z] INFO  16:34:37,019 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.03
[2016-04-14T23:34Z] INFO  16:34:37,034 IntervalUtils - Processing 19378574 bp from intervals
[2016-04-14T23:34Z] INFO  16:34:37,087 IntervalUtils - Processing 16978007 bp from intervals
[2016-04-14T23:34Z] WARN  16:34:37,092 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:34Z] INFO  16:34:37,100 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:34Z] INFO  16:34:37,106 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:34Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-13_19751066_35517251-prep-prealign.bam
[2016-04-14T23:34Z] INFO  16:34:37,188 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:34Z] INFO  16:34:37,233 ProgressMeter -      11:1651652    300065.0    30.0 s     100.0 s       10.3%     4.8 m       4.3 m
[2016-04-14T23:34Z] INFO  16:34:37,467 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:34Z] INFO  16:34:37,479 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:34Z] INFO  16:34:37,480 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:34Z] INFO  16:34:37,480 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-14T23:34Z] INFO  16:34:37,518 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:34Z] INFO  16:34:37,520 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:34Z] INFO  16:34:37,520 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:34Z] INFO  16:34:37,521 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:34Z] INFO  16:34:37,538 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:34Z] INFO  16:34:37,542 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:34Z] INFO  16:34:37,617 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:34Z] INFO  16:34:37,620 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:34Z] INFO  16:34:37,621 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:34Z] INFO  16:34:37,622 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:34Z] INFO  16:34:37,626 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/12/R14-18102_kapa-NGv3-PE100-NGv3-sort-12_125267228_133851895-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/12/R14-18102_kapa-NGv3-PE100-NGv3-sort-12_125267228_133851895-prep-prealign-realign.intervals -L 12:125267229-133851895 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/12/tx/tmpuoNbio/R14-18102_kapa-NGv3-PE100-NGv3-sort-12_125267228_133851895-prep.bam
[2016-04-14T23:34Z] INFO  16:34:37,651 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:34Z] INFO  16:34:37,651 HelpFormatter - Date/Time: 2016/04/14 16:34:37
[2016-04-14T23:34Z] INFO  16:34:37,651 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:34Z] INFO  16:34:37,652 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:34Z] INFO  16:34:37,722 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@7172f77a
[2016-04-14T23:34Z] INFO  16:34:37,856 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:34Z] INFO  16:34:37,925 ProgressMeter -            done    114409.0    16.0 s       2.4 m      100.0%    16.0 s       0.0 s
[2016-04-14T23:34Z] INFO  16:34:37,925 ProgressMeter - Total runtime 16.63 secs, 0.28 min, 0.00 hours
[2016-04-14T23:34Z] INFO  16:34:37,925 MicroScheduler - 110 reads were filtered out during the traversal out of approximately 114519 total reads (0.10%)
[2016-04-14T23:34Z] INFO  16:34:37,926 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:34Z] INFO  16:34:37,926 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:34Z] INFO  16:34:37,926 MicroScheduler -   -> 110 reads (0.10% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:34Z] INFO  16:34:37,943 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:34Z] INFO  16:34:37,943 ProgressMeter -            done   1.5619837E7    19.0 s       1.0 s      100.0%    19.0 s       0.0 s
[2016-04-14T23:34Z] INFO  16:34:37,944 ProgressMeter - Total runtime 19.38 secs, 0.32 min, 0.01 hours
[2016-04-14T23:34Z] INFO  16:34:37,948 MicroScheduler - 24945 reads were filtered out during the traversal out of approximately 281428 total reads (8.86%)
[2016-04-14T23:34Z] INFO  16:34:37,949 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:34Z] INFO  16:34:37,950 MicroScheduler -   -> 670 reads (0.24% of total) failing BadMateFilter
[2016-04-14T23:34Z] INFO  16:34:37,951 MicroScheduler -   -> 22429 reads (7.97% of total) failing DuplicateReadFilter
[2016-04-14T23:34Z] INFO  16:34:37,951 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-14T23:34Z] INFO  16:34:37,952 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:34Z] INFO  16:34:37,952 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-14T23:34Z] INFO  16:34:37,953 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:34Z] INFO  16:34:37,952 MicroScheduler -   -> 1846 reads (0.66% of total) failing MappingQualityZeroFilter
[2016-04-14T23:34Z] INFO  16:34:37,953 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:34Z] INFO  16:34:37,953 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-14T23:34Z] INFO  16:34:37,953 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-14T23:34Z] GATK RealignerTargetCreator: R14-18102_kapa-NGv3-PE100-NGv3-sort-13_19751066_35517251-prep-prealign.bam 13:19751067-35517251
[2016-04-14T23:34Z] GATK: RealignerTargetCreator
[2016-04-14T23:34Z] INFO  16:34:37,996 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.04
[2016-04-14T23:34Z] INFO  16:34:38,299 IntervalUtils - Processing 8584667 bp from intervals
[2016-04-14T23:34Z] WARN  16:34:38,304 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:34Z] INFO  16:34:38,369 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:34Z] INFO  16:34:38,492 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:34Z] INFO  16:34:38,504 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:34Z] INFO  16:34:38,505 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:34Z] INFO  16:34:38,506 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:34Z] INFO  16:34:38,646 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:34Z] INFO  16:34:38,788 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:34Z] INFO  16:34:39,484 ProgressMeter -            done    557151.0    34.0 s      61.0 s      100.0%    34.0 s       0.0 s
[2016-04-14T23:34Z] INFO  16:34:39,484 ProgressMeter - Total runtime 34.54 secs, 0.58 min, 0.01 hours
[2016-04-14T23:34Z] INFO  16:34:39,488 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 557151 total reads (0.00%)
[2016-04-14T23:34Z] INFO  16:34:39,488 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:34Z] INFO  16:34:39,489 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:34Z] INFO  16:34:39,489 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:34Z] INFO  16:34:39,495 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@41fd9d8e
[2016-04-14T23:34Z] INFO  16:34:39,517 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:34Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-13_86368117_101881935-prep-prealign.bam
[2016-04-14T23:34Z] INFO  16:34:39,550 ProgressMeter -            done      3259.0     2.0 s      10.4 m      100.0%     2.0 s       0.0 s
[2016-04-14T23:34Z] INFO  16:34:39,549 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:34Z] INFO  16:34:39,551 ProgressMeter - Total runtime 2.03 secs, 0.03 min, 0.00 hours
[2016-04-14T23:34Z] INFO  16:34:39,552 MicroScheduler - 7 reads were filtered out during the traversal out of approximately 3266 total reads (0.21%)
[2016-04-14T23:34Z] INFO  16:34:39,553 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:34Z] INFO  16:34:39,554 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:34Z] INFO  16:34:39,555 MicroScheduler -   -> 7 reads (0.21% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:34Z] INFO  16:34:39,559 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:34Z] INFO  16:34:39,563 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:34Z] INFO  16:34:39,564 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:34Z] INFO  16:34:39,564 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:34Z] INFO  16:34:39,570 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/13/R14-18102_kapa-NGv3-PE100-NGv3-sort-13_35615069_51287376-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/13/tx/tmp92Sam0/R14-18102_kapa-NGv3-PE100-NGv3-sort-13_35615069_51287376-prep-prealign-realign.intervals -l INFO -L 13:35615070-51287376 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-14T23:34Z] GATK: realign ('12', 93870729, 109490566) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:34Z] INFO  16:34:39,590 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:34Z] INFO  16:34:39,591 HelpFormatter - Date/Time: 2016/04/14 16:34:39
[2016-04-14T23:34Z] INFO  16:34:39,592 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:34Z] INFO  16:34:39,593 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:34Z] INFO  16:34:39,742 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:34Z] INFO  16:34:39,912 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-14T23:34Z] INFO  16:34:39,921 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:34Z] INFO  16:34:39,979 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-14T23:34Z] GATK RealignerTargetCreator: R14-18102_kapa-NGv3-PE100-NGv3-sort-13_86368117_101881935-prep-prealign.bam 13:86368118-101881935
[2016-04-14T23:34Z] GATK: RealignerTargetCreator
[2016-04-14T23:34Z] INFO  16:34:40,261 ProgressMeter -     12:57430793    700010.0    90.0 s       2.1 m       67.1%     2.2 m      44.0 s
[2016-04-14T23:34Z] INFO  16:34:40,344 IntervalUtils - Processing 15672307 bp from intervals
[2016-04-14T23:34Z] WARN  16:34:40,349 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:34Z] INFO  16:34:40,426 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:34Z] INFO  16:34:40,741 ProgressMeter -    12:121416523    300008.0    60.0 s       3.3 m       75.6%    79.0 s      19.0 s
[2016-04-14T23:34Z] INFO  16:34:40,733 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:34Z] INFO  16:34:40,743 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:34Z] INFO  16:34:40,744 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:34Z] INFO  16:34:40,745 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-14T23:34Z] INFO  16:34:40,874 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:34Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-14_0_19378574-prep-prealign.bam
[2016-04-14T23:34Z] GATK RealignerTargetCreator: R14-18102_kapa-NGv3-PE100-NGv3-sort-14_0_19378574-prep-prealign.bam 14:1-19378574
[2016-04-14T23:34Z] GATK: RealignerTargetCreator
[2016-04-14T23:34Z] INFO  16:34:40,992 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:34Z] INFO  16:34:40,996 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:34Z] INFO  16:34:40,996 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:34Z] INFO  16:34:40,997 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:34Z] INFO  16:34:41,001 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/13/R14-18102_kapa-NGv3-PE100-NGv3-sort-13_19751066_35517251-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/13/tx/tmpRl1Q9O/R14-18102_kapa-NGv3-PE100-NGv3-sort-13_19751066_35517251-prep-prealign-realign.intervals -l INFO -L 13:19751067-35517251 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-14T23:34Z] INFO  16:34:41,021 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:34Z] INFO  16:34:41,022 HelpFormatter - Date/Time: 2016/04/14 16:34:40
[2016-04-14T23:34Z] INFO  16:34:41,022 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:34Z] INFO  16:34:41,023 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:34Z] INFO  16:34:41,119 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:34Z] INFO  16:34:41,153 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:34Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-11_47158866_62678572-prep.bam
[2016-04-14T23:34Z] INFO  16:34:41,399 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-14T23:34Z] INFO  16:34:41,427 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:34Z] INFO  16:34:41,506 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-14T23:34Z] INFO  16:34:42,016 IntervalUtils - Processing 15766185 bp from intervals
[2016-04-14T23:34Z] WARN  16:34:42,028 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:34Z] INFO  16:34:42,147 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:34Z] INFO  16:34:42,425 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:34Z] INFO  16:34:42,426 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:34Z] INFO  16:34:42,427 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:34Z] INFO  16:34:42,428 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-14T23:34Z] INFO  16:34:42,731 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:34Z] INFO  16:34:42,733 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:34Z] INFO  16:34:42,734 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:34Z] INFO  16:34:42,734 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:34Z] INFO  16:34:42,738 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/12/R14-18102_kapa-NGv3-PE100-NGv3-sort-12_93870729_109490566-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/12/R14-18102_kapa-NGv3-PE100-NGv3-sort-12_93870729_109490566-prep-prealign-realign.intervals -L 12:93870730-109490566 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/12/tx/tmp83O0HM/R14-18102_kapa-NGv3-PE100-NGv3-sort-12_93870729_109490566-prep.bam
[2016-04-14T23:34Z] INFO  16:34:42,748 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:34Z] INFO  16:34:42,749 HelpFormatter - Date/Time: 2016/04/14 16:34:42
[2016-04-14T23:34Z] INFO  16:34:42,750 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:34Z] INFO  16:34:42,750 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:34Z] GATK pre-alignment ('14', 19553416, 35066851) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:34Z] INFO  16:34:42,906 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:34Z] INFO  16:34:42,917 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:34Z] INFO  16:34:42,918 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:34Z] INFO  16:34:42,918 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:34Z] INFO  16:34:42,923 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/13/R14-18102_kapa-NGv3-PE100-NGv3-sort-13_86368117_101881935-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/13/tx/tmpu_L59J/R14-18102_kapa-NGv3-PE100-NGv3-sort-13_86368117_101881935-prep-prealign-realign.intervals -l INFO -L 13:86368118-101881935 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-14T23:34Z] INFO  16:34:42,940 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:34Z] INFO  16:34:42,941 HelpFormatter - Date/Time: 2016/04/14 16:34:42
[2016-04-14T23:34Z] INFO  16:34:42,942 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:34Z] INFO  16:34:42,943 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:34Z] INFO  16:34:42,956 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:34Z] INFO  16:34:43,083 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:34Z] INFO  16:34:43,105 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:34Z] INFO  16:34:43,118 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:34Z] INFO  16:34:43,183 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-14T23:34Z] INFO  16:34:43,352 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-14T23:34Z] INFO  16:34:43,362 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:34Z] INFO  16:34:43,436 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-14T23:34Z] INFO  16:34:43,507 IntervalUtils - Processing 15619837 bp from intervals
[2016-04-14T23:34Z] WARN  16:34:43,521 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:34Z] INFO  16:34:43,606 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:34Z] INFO  16:34:43,777 IntervalUtils - Processing 15513818 bp from intervals
[2016-04-14T23:34Z] WARN  16:34:43,781 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:34Z] INFO  16:34:43,801 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:34Z] INFO  16:34:43,804 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:34Z] INFO  16:34:43,805 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:34Z] INFO  16:34:43,806 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:34Z] INFO  16:34:43,810 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/14/R14-18102_kapa-NGv3-PE100-NGv3-sort-14_0_19378574-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/14/tx/tmp6WcTgi/R14-18102_kapa-NGv3-PE100-NGv3-sort-14_0_19378574-prep-prealign-realign.intervals -l INFO -L 14:1-19378574 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-14T23:34Z] INFO  16:34:43,826 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:34Z] INFO  16:34:43,827 HelpFormatter - Date/Time: 2016/04/14 16:34:43
[2016-04-14T23:34Z] INFO  16:34:43,827 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:34Z] INFO  16:34:43,828 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:34Z] INFO  16:34:43,845 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:34Z] INFO  16:34:43,858 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:34Z] INFO  16:34:43,859 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:34Z] INFO  16:34:43,859 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:34Z] INFO  16:34:43,865 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:34Z] INFO  16:34:43,979 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:34Z] INFO  16:34:44,068 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:34Z] INFO  16:34:44,113 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:34Z] INFO  16:34:44,114 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:34Z] INFO  16:34:44,115 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:34Z] INFO  16:34:44,116 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-14T23:34Z] INFO  16:34:44,193 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-14T23:34Z] INFO  16:34:44,214 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:34Z] INFO  16:34:44,233 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:34Z] INFO  16:34:44,261 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-14T23:34Z] INFO  16:34:44,553 IntervalUtils - Processing 19378574 bp from intervals
[2016-04-14T23:34Z] WARN  16:34:44,560 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:34Z] INFO  16:34:44,558 ProgressMeter -            done   1.5637181E7    24.0 s       1.0 s      100.0%    24.0 s       0.0 s
[2016-04-14T23:34Z] INFO  16:34:44,560 ProgressMeter - Total runtime 24.20 secs, 0.40 min, 0.01 hours
[2016-04-14T23:34Z] INFO  16:34:44,564 MicroScheduler - 59958 reads were filtered out during the traversal out of approximately 563749 total reads (10.64%)
[2016-04-14T23:34Z] INFO  16:34:44,570 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:34Z] INFO  16:34:44,571 MicroScheduler -   -> 1113 reads (0.20% of total) failing BadMateFilter
[2016-04-14T23:34Z] INFO  16:34:44,572 MicroScheduler -   -> 43838 reads (7.78% of total) failing DuplicateReadFilter
[2016-04-14T23:34Z] INFO  16:34:44,572 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-14T23:34Z] INFO  16:34:44,573 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:34Z] INFO  16:34:44,574 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-14T23:34Z] INFO  16:34:44,576 MicroScheduler -   -> 15007 reads (2.66% of total) failing MappingQualityZeroFilter
[2016-04-14T23:34Z] INFO  16:34:44,576 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:34Z] INFO  16:34:44,577 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-14T23:34Z] INFO  16:34:44,578 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-14T23:34Z] INFO  16:34:44,700 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:34Z] INFO  16:34:45,044 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:34Z] INFO  16:34:45,045 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:34Z] INFO  16:34:45,046 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:34Z] INFO  16:34:45,047 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-14T23:34Z] INFO  16:34:45,901 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:34Z] INFO  16:34:45,903 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:34Z] INFO  16:34:45,904 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:34Z] INFO  16:34:45,904 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:34Z] INFO  16:34:45,908 HelpFormatter - Program Args: -T PrintReads -L 14:19553417-35066851 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/14/tx/tmpQ3dtqy/R14-18102_kapa-NGv3-PE100-NGv3-sort-14_19553416_35066851-prep-prealign.bam
[2016-04-14T23:34Z] INFO  16:34:45,931 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:34Z] INFO  16:34:45,932 HelpFormatter - Date/Time: 2016/04/14 16:34:45
[2016-04-14T23:34Z] INFO  16:34:45,932 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:34Z] INFO  16:34:45,932 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:34Z] INFO  16:34:46,097 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:34Z] INFO  16:34:46,954 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:34Z] GATK: realign ('12', 0, 15637181) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:34Z] INFO  16:34:47,023 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-14T23:34Z] INFO  16:34:47,082 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:34Z] INFO  16:34:47,093 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:34Z] INFO  16:34:47,152 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-14T23:34Z] INFO  16:34:47,169 IntervalUtils - Processing 15513435 bp from intervals
[2016-04-14T23:34Z] INFO  16:34:47,283 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:34Z] INFO  16:34:47,724 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:34Z] INFO  16:34:47,728 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:34Z] INFO  16:34:47,729 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:34Z] INFO  16:34:47,729 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:34Z] INFO  16:34:47,755 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:34Z] INFO  16:34:47,934 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:34Z] INFO  16:34:49,555 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:34Z] INFO  16:34:49,558 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:34Z] INFO  16:34:49,559 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:34Z] INFO  16:34:49,559 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:34Z] INFO  16:34:49,564 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/12/R14-18102_kapa-NGv3-PE100-NGv3-sort-12_0_15637181-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/12/R14-18102_kapa-NGv3-PE100-NGv3-sort-12_0_15637181-prep-prealign-realign.intervals -L 12:1-15637181 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/12/tx/tmpr59d6s/R14-18102_kapa-NGv3-PE100-NGv3-sort-12_0_15637181-prep.bam
[2016-04-14T23:34Z] INFO  16:34:49,574 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:34Z] INFO  16:34:49,575 HelpFormatter - Date/Time: 2016/04/14 16:34:49
[2016-04-14T23:34Z] INFO  16:34:49,576 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:34Z] INFO  16:34:49,576 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:34Z] INFO  16:34:49,766 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:34Z] INFO  16:34:49,902 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:34Z] INFO  16:34:49,912 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:34Z] INFO  16:34:49,980 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-14T23:34Z] INFO  16:34:50,343 IntervalUtils - Processing 15637181 bp from intervals
[2016-04-14T23:34Z] WARN  16:34:50,348 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:34Z] INFO  16:34:50,429 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:34Z] INFO  16:34:50,501 ProgressMeter -     11:77916921   1.5161655E7    30.0 s       1.0 s       97.7%    30.0 s       0.0 s
[2016-04-14T23:34Z] INFO  16:34:50,573 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:34Z] INFO  16:34:50,574 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:34Z] INFO  16:34:50,575 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:34Z] INFO  16:34:50,576 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:34Z] INFO  16:34:50,768 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:34Z] INFO  16:34:50,938 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:34Z] INFO  16:34:51,465 ProgressMeter -            done   1.55264E7    30.0 s       1.0 s      100.0%    30.0 s       0.0 s
[2016-04-14T23:34Z] INFO  16:34:51,466 ProgressMeter - Total runtime 30.99 secs, 0.52 min, 0.01 hours
[2016-04-14T23:34Z] INFO  16:34:51,470 MicroScheduler - 80295 reads were filtered out during the traversal out of approximately 910732 total reads (8.82%)
[2016-04-14T23:34Z] INFO  16:34:51,470 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:34Z] INFO  16:34:51,470 MicroScheduler -   -> 1731 reads (0.19% of total) failing BadMateFilter
[2016-04-14T23:34Z] INFO  16:34:51,471 MicroScheduler -   -> 73109 reads (8.03% of total) failing DuplicateReadFilter
[2016-04-14T23:34Z] INFO  16:34:51,471 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-14T23:34Z] INFO  16:34:51,471 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:34Z] INFO  16:34:51,471 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-14T23:34Z] INFO  16:34:51,472 MicroScheduler -   -> 5455 reads (0.60% of total) failing MappingQualityZeroFilter
[2016-04-14T23:34Z] INFO  16:34:51,472 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:34Z] INFO  16:34:51,472 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-14T23:34Z] INFO  16:34:51,472 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-14T23:34Z] INFO  16:34:51,721 ProgressMeter -            done   1.5808776E7    16.0 s       1.0 s      100.0%    16.0 s       0.0 s
[2016-04-14T23:34Z] INFO  16:34:51,722 ProgressMeter - Total runtime 16.63 secs, 0.28 min, 0.00 hours
[2016-04-14T23:34Z] INFO  16:34:51,727 MicroScheduler - 40367 reads were filtered out during the traversal out of approximately 116533 total reads (34.64%)
[2016-04-14T23:34Z] INFO  16:34:51,728 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:34Z] INFO  16:34:51,729 MicroScheduler -   -> 375 reads (0.32% of total) failing BadMateFilter
[2016-04-14T23:34Z] INFO  16:34:51,730 MicroScheduler -   -> 6541 reads (5.61% of total) failing DuplicateReadFilter
[2016-04-14T23:34Z] INFO  16:34:51,731 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-14T23:34Z] INFO  16:34:51,732 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:34Z] INFO  16:34:51,732 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-14T23:34Z] INFO  16:34:51,733 MicroScheduler -   -> 33451 reads (28.71% of total) failing MappingQualityZeroFilter
[2016-04-14T23:34Z] INFO  16:34:51,734 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:34Z] INFO  16:34:51,735 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-14T23:34Z] INFO  16:34:51,735 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-14T23:34Z] INFO  16:34:52,978 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:34Z] GATK: realign ('11', 62744265, 78270665) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:34Z] INFO  16:34:53,072 ProgressMeter -            done   1.6978007E7    15.0 s       0.0 s      100.0%    15.0 s       0.0 s
[2016-04-14T23:34Z] INFO  16:34:53,073 ProgressMeter - Total runtime 15.59 secs, 0.26 min, 0.00 hours
[2016-04-14T23:34Z] INFO  16:34:53,077 MicroScheduler - 8307 reads were filtered out during the traversal out of approximately 93546 total reads (8.88%)
[2016-04-14T23:34Z] INFO  16:34:53,078 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:34Z] INFO  16:34:53,079 MicroScheduler -   -> 401 reads (0.43% of total) failing BadMateFilter
[2016-04-14T23:34Z] INFO  16:34:53,080 MicroScheduler -   -> 7332 reads (7.84% of total) failing DuplicateReadFilter
[2016-04-14T23:34Z] INFO  16:34:53,080 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-14T23:34Z] INFO  16:34:53,081 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:34Z] INFO  16:34:53,082 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-14T23:34Z] INFO  16:34:53,082 MicroScheduler -   -> 574 reads (0.61% of total) failing MappingQualityZeroFilter
[2016-04-14T23:34Z] INFO  16:34:53,083 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:34Z] INFO  16:34:53,083 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-14T23:34Z] INFO  16:34:53,084 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-14T23:34Z] INFO  16:34:53,974 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:34Z] GATK: realign ('13', 51396767, 67205543) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:34Z] INFO  16:34:54,452 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:34Z] GATK: realign ('13', 67477635, 84455642) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:34Z] INFO  16:34:54,831 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@5fe152b7
[2016-04-14T23:34Z] INFO  16:34:54,938 ProgressMeter -            done    867741.0   104.0 s     120.0 s      100.0%   104.0 s       0.0 s
[2016-04-14T23:34Z] INFO  16:34:54,939 ProgressMeter - Total runtime 104.72 secs, 1.75 min, 0.03 hours
[2016-04-14T23:34Z] INFO  16:34:54,939 MicroScheduler - 332 reads were filtered out during the traversal out of approximately 868073 total reads (0.04%)
[2016-04-14T23:34Z] INFO  16:34:54,940 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:34Z] INFO  16:34:54,942 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:34Z] INFO  16:34:54,943 MicroScheduler -   -> 332 reads (0.04% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:34Z] INFO  16:34:55,139 ProgressMeter -            done   1.9378574E7    10.0 s       0.0 s      100.0%    10.0 s       0.0 s
[2016-04-14T23:34Z] INFO  16:34:55,140 ProgressMeter - Total runtime 10.10 secs, 0.17 min, 0.00 hours
[2016-04-14T23:34Z] INFO  16:34:55,158 MicroScheduler - 1334 reads were filtered out during the traversal out of approximately 3259 total reads (40.93%)
[2016-04-14T23:34Z] INFO  16:34:55,159 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:34Z] INFO  16:34:55,160 MicroScheduler -   -> 16 reads (0.49% of total) failing BadMateFilter
[2016-04-14T23:34Z] INFO  16:34:55,160 MicroScheduler -   -> 210 reads (6.44% of total) failing DuplicateReadFilter
[2016-04-14T23:34Z] INFO  16:34:55,161 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-14T23:34Z] INFO  16:34:55,162 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:34Z] INFO  16:34:55,162 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-14T23:34Z] INFO  16:34:55,163 MicroScheduler -   -> 1108 reads (34.00% of total) failing MappingQualityZeroFilter
[2016-04-14T23:34Z] INFO  16:34:55,164 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:34Z] INFO  16:34:55,168 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-14T23:34Z] INFO  16:34:55,169 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-14T23:34Z] INFO  16:34:56,049 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:34Z] INFO  16:34:56,052 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:34Z] INFO  16:34:56,053 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:34Z] INFO  16:34:56,053 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:34Z] INFO  16:34:56,058 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/11/R14-18102_kapa-NGv3-PE100-NGv3-sort-11_62744265_78270665-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/11/R14-18102_kapa-NGv3-PE100-NGv3-sort-11_62744265_78270665-prep-prealign-realign.intervals -L 11:62744266-78270665 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/11/tx/tmp57SAxj/R14-18102_kapa-NGv3-PE100-NGv3-sort-11_62744265_78270665-prep.bam
[2016-04-14T23:34Z] INFO  16:34:56,069 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:34Z] INFO  16:34:56,070 HelpFormatter - Date/Time: 2016/04/14 16:34:56
[2016-04-14T23:34Z] INFO  16:34:56,071 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:34Z] INFO  16:34:56,071 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:34Z] INFO  16:34:56,365 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:34Z] INFO  16:34:56,499 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:34Z] INFO  16:34:56,508 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:34Z] INFO  16:34:56,551 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.04
[2016-04-14T23:34Z] INFO  16:34:56,585 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:34Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-12_46756066_62654284-prep-prealign.bam
[2016-04-14T23:34Z] INFO  16:34:56,794 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:34Z] INFO  16:34:56,798 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:34Z] INFO  16:34:56,799 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:34Z] INFO  16:34:56,799 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:34Z] INFO  16:34:56,804 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/13/R14-18102_kapa-NGv3-PE100-NGv3-sort-13_51396767_67205543-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/13/R14-18102_kapa-NGv3-PE100-NGv3-sort-13_51396767_67205543-prep-prealign-realign.intervals -L 13:51396768-67205543 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/13/tx/tmpGR87u1/R14-18102_kapa-NGv3-PE100-NGv3-sort-13_51396767_67205543-prep.bam
[2016-04-14T23:34Z] INFO  16:34:56,823 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:34Z] INFO  16:34:56,824 HelpFormatter - Date/Time: 2016/04/14 16:34:56
[2016-04-14T23:34Z] INFO  16:34:56,824 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:34Z] INFO  16:34:56,824 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:34Z] INFO  16:34:56,938 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:34Z] GATK: realign ('14', 0, 19378574) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:34Z] INFO  16:34:56,968 IntervalUtils - Processing 15526400 bp from intervals
[2016-04-14T23:34Z] WARN  16:34:56,973 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:34Z] INFO  16:34:57,045 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:34Z] INFO  16:34:57,058 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:34Z] INFO  16:34:57,065 ProgressMeter -            done    207191.0    18.0 s      89.0 s       99.5%    18.0 s       0.0 s
[2016-04-14T23:34Z] INFO  16:34:57,065 ProgressMeter - Total runtime 18.56 secs, 0.31 min, 0.01 hours
[2016-04-14T23:34Z] INFO  16:34:57,068 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 207191 total reads (0.00%)
[2016-04-14T23:34Z] INFO  16:34:57,069 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:34Z] INFO  16:34:57,069 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:34Z] INFO  16:34:57,069 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:34Z] INFO  16:34:57,201 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:34Z] INFO  16:34:57,211 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:34Z] INFO  16:34:57,254 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:34Z] INFO  16:34:57,255 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:34Z] INFO  16:34:57,255 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:34Z] INFO  16:34:57,255 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:34Z] INFO  16:34:57,285 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-14T23:34Z] INFO  16:34:57,330 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:34Z] INFO  16:34:57,334 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:34Z] INFO  16:34:57,334 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:34Z] INFO  16:34:57,335 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:34Z] INFO  16:34:57,340 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/13/R14-18102_kapa-NGv3-PE100-NGv3-sort-13_67477635_84455642-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/13/R14-18102_kapa-NGv3-PE100-NGv3-sort-13_67477635_84455642-prep-prealign-realign.intervals -L 13:67477636-84455642 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/13/tx/tmpl9h8zm/R14-18102_kapa-NGv3-PE100-NGv3-sort-13_67477635_84455642-prep.bam
[2016-04-14T23:34Z] INFO  16:34:57,373 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:34Z] INFO  16:34:57,374 HelpFormatter - Date/Time: 2016/04/14 16:34:57
[2016-04-14T23:34Z] INFO  16:34:57,375 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:34Z] INFO  16:34:57,375 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:34Z] INFO  16:34:57,503 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:34Z] INFO  16:34:57,643 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:34Z] INFO  16:34:57,698 IntervalUtils - Processing 15808776 bp from intervals
[2016-04-14T23:34Z] WARN  16:34:57,714 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:34Z] INFO  16:34:57,737 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:34Z] INFO  16:34:57,776 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:34Z] INFO  16:34:57,797 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:34Z] INFO  16:34:57,833 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:34Z] INFO  16:34:57,864 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-14T23:34Z] INFO  16:34:57,964 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:34Z] INFO  16:34:57,965 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:34Z] INFO  16:34:57,966 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:34Z] INFO  16:34:57,967 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:34Z] INFO  16:34:58,142 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:34Z] INFO  16:34:58,241 IntervalUtils - Processing 16978007 bp from intervals
[2016-04-14T23:34Z] WARN  16:34:58,257 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:34Z] INFO  16:34:58,309 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:34Z] INFO  16:34:58,328 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:34Z] INFO  16:34:58,466 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:34Z] INFO  16:34:58,467 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:34Z] INFO  16:34:58,468 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:34Z] INFO  16:34:58,469 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:34Z] INFO  16:34:58,617 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:34Z] INFO  16:34:58,619 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:34Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-12_125267228_133851895-prep.bam
[2016-04-14T23:34Z] INFO  16:34:58,815 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:34Z] INFO  16:34:58,817 ProgressMeter -            done   1.5513818E7    14.0 s       0.0 s      100.0%    14.0 s       0.0 s
[2016-04-14T23:34Z] INFO  16:34:58,818 ProgressMeter - Total runtime 14.70 secs, 0.25 min, 0.00 hours
[2016-04-14T23:34Z] INFO  16:34:58,823 MicroScheduler - 9960 reads were filtered out during the traversal out of approximately 115345 total reads (8.63%)
[2016-04-14T23:34Z] INFO  16:34:58,824 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:34Z] INFO  16:34:58,824 MicroScheduler -   -> 459 reads (0.40% of total) failing BadMateFilter
[2016-04-14T23:34Z] INFO  16:34:58,825 MicroScheduler -   -> 9252 reads (8.02% of total) failing DuplicateReadFilter
[2016-04-14T23:34Z] INFO  16:34:58,826 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-14T23:34Z] INFO  16:34:58,827 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:34Z] INFO  16:34:58,827 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-14T23:34Z] INFO  16:34:58,828 MicroScheduler -   -> 249 reads (0.22% of total) failing MappingQualityZeroFilter
[2016-04-14T23:34Z] INFO  16:34:58,829 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:34Z] INFO  16:34:58,829 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-14T23:34Z] INFO  16:34:58,830 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-14T23:34Z] INFO  16:34:58,898 ProgressMeter -    13:114502339    100001.0    30.0 s       5.1 m       95.0%    31.0 s       1.0 s
[2016-04-14T23:34Z] INFO  16:34:59,026 ProgressMeter -            done   1.5672307E7    18.0 s       1.0 s      100.0%    18.0 s       0.0 s
[2016-04-14T23:34Z] INFO  16:34:59,026 ProgressMeter - Total runtime 18.28 secs, 0.30 min, 0.01 hours
[2016-04-14T23:34Z] INFO  16:34:59,030 MicroScheduler - 20289 reads were filtered out during the traversal out of approximately 233166 total reads (8.70%)
[2016-04-14T23:34Z] INFO  16:34:59,031 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:34Z] INFO  16:34:59,031 MicroScheduler -   -> 606 reads (0.26% of total) failing BadMateFilter
[2016-04-14T23:34Z] INFO  16:34:59,032 MicroScheduler -   -> 18379 reads (7.88% of total) failing DuplicateReadFilter
[2016-04-14T23:34Z] INFO  16:34:59,033 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-14T23:34Z] INFO  16:34:59,033 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:34Z] INFO  16:34:59,034 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-14T23:34Z] INFO  16:34:59,034 MicroScheduler -   -> 1304 reads (0.56% of total) failing MappingQualityZeroFilter
[2016-04-14T23:34Z] INFO  16:34:59,035 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:34Z] INFO  16:34:59,036 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-14T23:34Z] INFO  16:34:59,036 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-14T23:34Z] GATK RealignerTargetCreator: R14-18102_kapa-NGv3-PE100-NGv3-sort-12_46756066_62654284-prep-prealign.bam 12:46756067-62654284
[2016-04-14T23:34Z] GATK: RealignerTargetCreator
[2016-04-14T23:34Z] GATK pre-alignment ('14', 35072553, 50583270) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:34Z] INFO  16:34:59,616 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:34Z] INFO  16:34:59,618 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:34Z] INFO  16:34:59,618 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:34Z] INFO  16:34:59,619 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:34Z] INFO  16:34:59,623 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/14/R14-18102_kapa-NGv3-PE100-NGv3-sort-14_0_19378574-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/14/R14-18102_kapa-NGv3-PE100-NGv3-sort-14_0_19378574-prep-prealign-realign.intervals -L 14:1-19378574 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/14/tx/tmpAlcMag/R14-18102_kapa-NGv3-PE100-NGv3-sort-14_0_19378574-prep.bam
[2016-04-14T23:34Z] INFO  16:34:59,633 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:34Z] INFO  16:34:59,634 HelpFormatter - Date/Time: 2016/04/14 16:34:59
[2016-04-14T23:34Z] INFO  16:34:59,635 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:34Z] INFO  16:34:59,635 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:34Z] INFO  16:34:59,933 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:35Z] INFO  16:35:00,177 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:35Z] INFO  16:35:00,200 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:35Z] INFO  16:35:00,302 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.10
[2016-04-14T23:35Z] INFO  16:35:00,433 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:35Z] GATK: realign ('13', 35615069, 51287376) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:35Z] INFO  16:35:00,488 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:35Z] GATK: realign ('13', 86368117, 101881935) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:35Z] INFO  16:35:00,696 IntervalUtils - Processing 19378574 bp from intervals
[2016-04-14T23:35Z] WARN  16:35:00,701 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:35Z] INFO  16:35:00,805 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:35Z] INFO  16:35:00,984 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:35Z] INFO  16:35:00,985 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:35Z] INFO  16:35:00,986 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:35Z] INFO  16:35:00,986 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:35Z] INFO  16:35:01,047 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:35Z] INFO  16:35:01,050 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:35Z] INFO  16:35:01,601 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@41fd9d8e
[2016-04-14T23:35Z] INFO  16:35:01,766 ProgressMeter -            done   1.5766185E7    19.0 s       1.0 s      100.0%    19.0 s       0.0 s
[2016-04-14T23:35Z] INFO  16:35:01,767 ProgressMeter - Total runtime 19.34 secs, 0.32 min, 0.01 hours
[2016-04-14T23:35Z] INFO  16:35:01,770 MicroScheduler - 23412 reads were filtered out during the traversal out of approximately 257936 total reads (9.08%)
[2016-04-14T23:35Z] INFO  16:35:01,770 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:35Z] INFO  16:35:01,771 MicroScheduler -   -> 734 reads (0.28% of total) failing BadMateFilter
[2016-04-14T23:35Z] INFO  16:35:01,771 MicroScheduler -   -> 20370 reads (7.90% of total) failing DuplicateReadFilter
[2016-04-14T23:35Z] INFO  16:35:01,771 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-14T23:35Z] INFO  16:35:01,772 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:35Z] INFO  16:35:01,772 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-14T23:35Z] INFO  16:35:01,772 MicroScheduler -   -> 2308 reads (0.89% of total) failing MappingQualityZeroFilter
[2016-04-14T23:35Z] INFO  16:35:01,772 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:35Z] INFO  16:35:01,772 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-14T23:35Z] INFO  16:35:01,773 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-14T23:35Z] INFO  16:35:01,816 ProgressMeter -            done    211543.0    33.0 s       2.6 m       99.4%    33.0 s       0.0 s
[2016-04-14T23:35Z] INFO  16:35:01,817 ProgressMeter - Total runtime 33.50 secs, 0.56 min, 0.01 hours
[2016-04-14T23:35Z] INFO  16:35:01,817 MicroScheduler - 142 reads were filtered out during the traversal out of approximately 211685 total reads (0.07%)
[2016-04-14T23:35Z] INFO  16:35:01,817 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:35Z] INFO  16:35:01,818 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:35Z] INFO  16:35:01,818 MicroScheduler -   -> 142 reads (0.07% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:35Z] INFO  16:35:02,105 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:35Z] INFO  16:35:02,109 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:35Z] INFO  16:35:02,109 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:35Z] INFO  16:35:02,110 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:35Z] INFO  16:35:02,114 HelpFormatter - Program Args: -T PrintReads -L 14:35072554-50583270 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/14/tx/tmpatvsnj/R14-18102_kapa-NGv3-PE100-NGv3-sort-14_35072553_50583270-prep-prealign.bam
[2016-04-14T23:35Z] INFO  16:35:02,124 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:35Z] INFO  16:35:02,135 HelpFormatter - Date/Time: 2016/04/14 16:35:02
[2016-04-14T23:35Z] INFO  16:35:02,136 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:35Z] INFO  16:35:02,137 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:35Z] INFO  16:35:02,204 ProgressMeter -            done      3259.0     1.0 s       6.2 m      100.0%     1.0 s       0.0 s
[2016-04-14T23:35Z] INFO  16:35:02,206 ProgressMeter - Total runtime 1.22 secs, 0.02 min, 0.00 hours
[2016-04-14T23:35Z] INFO  16:35:02,210 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 3259 total reads (0.00%)
[2016-04-14T23:35Z] INFO  16:35:02,211 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:35Z] INFO  16:35:02,212 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:35Z] INFO  16:35:02,212 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:35Z] INFO  16:35:02,237 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:35Z] INFO  16:35:02,240 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:35Z] INFO  16:35:02,241 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:35Z] INFO  16:35:02,241 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:35Z] INFO  16:35:02,246 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/12/R14-18102_kapa-NGv3-PE100-NGv3-sort-12_46756066_62654284-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/12/tx/tmp9NaBqE/R14-18102_kapa-NGv3-PE100-NGv3-sort-12_46756066_62654284-prep-prealign-realign.intervals -l INFO -L 12:46756067-62654284 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-14T23:35Z] INFO  16:35:02,279 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:35Z] INFO  16:35:02,280 HelpFormatter - Date/Time: 2016/04/14 16:35:02
[2016-04-14T23:35Z] INFO  16:35:02,280 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:35Z] INFO  16:35:02,285 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:35Z] INFO  16:35:02,296 ProgressMeter -    11:124623761    400007.0    31.0 s      78.0 s       94.3%    32.0 s       1.0 s
[2016-04-14T23:35Z] INFO  16:35:02,360 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:35Z] INFO  16:35:02,362 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:35Z] INFO  16:35:02,556 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-14T23:35Z] INFO  16:35:02,568 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:35Z] INFO  16:35:02,621 ProgressMeter -            done    804510.0    55.0 s      68.0 s      100.0%    55.0 s       0.0 s
[2016-04-14T23:35Z] INFO  16:35:02,622 ProgressMeter - Total runtime 55.42 secs, 0.92 min, 0.02 hours
[2016-04-14T23:35Z] INFO  16:35:02,625 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 804510 total reads (0.00%)
[2016-04-14T23:35Z] INFO  16:35:02,626 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:35Z] INFO  16:35:02,626 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:35Z] INFO  16:35:02,626 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:35Z] INFO  16:35:02,654 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.09
[2016-04-14T23:35Z] INFO  16:35:02,999 IntervalUtils - Processing 15898218 bp from intervals
[2016-04-14T23:35Z] WARN  16:35:03,004 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:35Z] INFO  16:35:03,114 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:35Z] INFO  16:35:03,142 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:35Z] GATK: realign ('13', 19751066, 35517251) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:35Z] INFO  16:35:03,359 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:35Z] INFO  16:35:03,360 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:35Z] INFO  16:35:03,361 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:35Z] INFO  16:35:03,371 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-14T23:35Z] INFO  16:35:03,428 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:35Z] INFO  16:35:03,439 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:35Z] INFO  16:35:03,442 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:35Z] INFO  16:35:03,443 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:35Z] INFO  16:35:03,443 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:35Z] INFO  16:35:03,448 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/13/R14-18102_kapa-NGv3-PE100-NGv3-sort-13_86368117_101881935-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/13/R14-18102_kapa-NGv3-PE100-NGv3-sort-13_86368117_101881935-prep-prealign-realign.intervals -L 13:86368118-101881935 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/13/tx/tmpfd1VtP/R14-18102_kapa-NGv3-PE100-NGv3-sort-13_86368117_101881935-prep.bam
[2016-04-14T23:35Z] INFO  16:35:03,457 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:35Z] INFO  16:35:03,457 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:35Z] INFO  16:35:03,461 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:35Z] INFO  16:35:03,461 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:35Z] INFO  16:35:03,462 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:35Z] INFO  16:35:03,463 HelpFormatter - Date/Time: 2016/04/14 16:35:03
[2016-04-14T23:35Z] INFO  16:35:03,464 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:35Z] INFO  16:35:03,464 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:35Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-13_101890105_115169878-prep-prealign.bam
[2016-04-14T23:35Z] INFO  16:35:03,467 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/13/R14-18102_kapa-NGv3-PE100-NGv3-sort-13_35615069_51287376-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/13/R14-18102_kapa-NGv3-PE100-NGv3-sort-13_35615069_51287376-prep-prealign-realign.intervals -L 13:35615070-51287376 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/13/tx/tmpd7kQbX/R14-18102_kapa-NGv3-PE100-NGv3-sort-13_35615069_51287376-prep.bam
[2016-04-14T23:35Z] INFO  16:35:03,483 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-14T23:35Z] INFO  16:35:03,488 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:35Z] INFO  16:35:03,489 HelpFormatter - Date/Time: 2016/04/14 16:35:03
[2016-04-14T23:35Z] INFO  16:35:03,489 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:35Z] INFO  16:35:03,490 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:35Z] INFO  16:35:03,545 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:35Z] INFO  16:35:03,554 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:35Z] INFO  16:35:03,614 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-14T23:35Z] INFO  16:35:03,628 IntervalUtils - Processing 15510717 bp from intervals
[2016-04-14T23:35Z] INFO  16:35:03,734 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:35Z] INFO  16:35:03,762 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:35Z] INFO  16:35:03,762 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:35Z] INFO  16:35:03,850 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:35Z] INFO  16:35:03,862 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:35Z] INFO  16:35:03,880 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:35Z] INFO  16:35:03,913 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:35Z] INFO  16:35:03,926 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:35Z] INFO  16:35:03,949 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.09
[2016-04-14T23:35Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-14_0_19378574-prep.bam
[2016-04-14T23:35Z] INFO  16:35:04,010 ProgressMeter -            done    279447.0    20.0 s      72.0 s      100.0%    20.0 s       0.0 s
[2016-04-14T23:35Z] INFO  16:35:04,011 ProgressMeter - Total runtime 20.15 secs, 0.34 min, 0.01 hours
[2016-04-14T23:35Z] INFO  16:35:04,014 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 279447 total reads (0.00%)
[2016-04-14T23:35Z] INFO  16:35:04,014 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:35Z] INFO  16:35:04,014 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:35Z] INFO  16:35:04,015 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:35Z] INFO  16:35:04,033 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.12
[2016-04-14T23:35Z] GATK pre-alignment ('14', 50585061, 66096324) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:35Z] GATK RealignerTargetCreator: R14-18102_kapa-NGv3-PE100-NGv3-sort-13_101890105_115169878-prep-prealign.bam 13:101890106-115169878
[2016-04-14T23:35Z] GATK: RealignerTargetCreator
[2016-04-14T23:35Z] INFO  16:35:04,082 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:35Z] INFO  16:35:04,083 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:35Z] INFO  16:35:04,084 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:35Z] INFO  16:35:04,085 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:35Z] INFO  16:35:04,083 ProgressMeter -            done    510059.0    33.0 s      65.0 s      100.0%    33.0 s       0.0 s
[2016-04-14T23:35Z] INFO  16:35:04,083 ProgressMeter - Total runtime 33.30 secs, 0.55 min, 0.01 hours
[2016-04-14T23:35Z] INFO  16:35:04,087 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 510059 total reads (0.00%)
[2016-04-14T23:35Z] INFO  16:35:04,088 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:35Z] INFO  16:35:04,088 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:35Z] INFO  16:35:04,088 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:35Z] INFO  16:35:04,107 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:35Z] INFO  16:35:04,240 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:35Z] INFO  16:35:04,451 IntervalUtils - Processing 15672307 bp from intervals
[2016-04-14T23:35Z] WARN  16:35:04,466 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:35Z] INFO  16:35:04,481 IntervalUtils - Processing 15513818 bp from intervals
[2016-04-14T23:35Z] WARN  16:35:04,487 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:35Z] INFO  16:35:04,545 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:35Z] INFO  16:35:04,613 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:35Z] INFO  16:35:04,620 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:35Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-11_0_15994658-prep.bam
[2016-04-14T23:35Z] INFO  16:35:04,704 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:35Z] INFO  16:35:04,705 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:35Z] INFO  16:35:04,706 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:35Z] INFO  16:35:04,707 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:35Z] INFO  16:35:04,734 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:35Z] INFO  16:35:04,735 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:35Z] INFO  16:35:04,736 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:35Z] INFO  16:35:04,736 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:35Z] INFO  16:35:04,886 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:35Z] INFO  16:35:04,888 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:35Z] INFO  16:35:05,045 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:35Z] INFO  16:35:05,057 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:35Z] INFO  16:35:05,569 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:35Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-12_93870729_109490566-prep.bam
[2016-04-14T23:35Z] INFO  16:35:05,799 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:35Z] INFO  16:35:05,821 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:35Z] INFO  16:35:05,828 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:35Z] INFO  16:35:05,829 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:35Z] INFO  16:35:05,829 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:35Z] INFO  16:35:05,833 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/13/R14-18102_kapa-NGv3-PE100-NGv3-sort-13_19751066_35517251-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/13/R14-18102_kapa-NGv3-PE100-NGv3-sort-13_19751066_35517251-prep-prealign-realign.intervals -L 13:19751067-35517251 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/13/tx/tmp4ewVlN/R14-18102_kapa-NGv3-PE100-NGv3-sort-13_19751066_35517251-prep.bam
[2016-04-14T23:35Z] INFO  16:35:05,847 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:35Z] INFO  16:35:05,855 HelpFormatter - Date/Time: 2016/04/14 16:35:05
[2016-04-14T23:35Z] INFO  16:35:05,856 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:35Z] INFO  16:35:05,856 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:35Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-11_110001730_125514538-prep.bam
[2016-04-14T23:35Z] INFO  16:35:06,081 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:35Z] INFO  16:35:06,180 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:35Z] INFO  16:35:06,189 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:35Z] INFO  16:35:06,254 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-14T23:35Z] INFO  16:35:06,615 IntervalUtils - Processing 15766185 bp from intervals
[2016-04-14T23:35Z] WARN  16:35:06,620 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:35Z] INFO  16:35:06,683 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:35Z] GATK pre-alignment ('14', 66135960, 81646674) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:35Z] INFO  16:35:06,893 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:35Z] INFO  16:35:06,894 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:35Z] INFO  16:35:06,895 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:35Z] INFO  16:35:06,896 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:35Z] INFO  16:35:07,086 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:35Z] INFO  16:35:07,203 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:35Z] INFO  16:35:07,206 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:35Z] INFO  16:35:07,207 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:35Z] INFO  16:35:07,207 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:35Z] INFO  16:35:07,212 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/13/R14-18102_kapa-NGv3-PE100-NGv3-sort-13_101890105_115169878-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/13/tx/tmpae0uKc/R14-18102_kapa-NGv3-PE100-NGv3-sort-13_101890105_115169878-prep-prealign-realign.intervals -l INFO -L 13:101890106-115169878 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-14T23:35Z] INFO  16:35:07,229 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:35Z] INFO  16:35:07,241 HelpFormatter - Date/Time: 2016/04/14 16:35:07
[2016-04-14T23:35Z] INFO  16:35:07,241 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:35Z] INFO  16:35:07,241 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:35Z] INFO  16:35:07,258 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:35Z] GATK pre-alignment ('14', 81651874, 97299968) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:35Z] INFO  16:35:07,366 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:35Z] INFO  16:35:07,531 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:35Z] INFO  16:35:07,534 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:35Z] INFO  16:35:07,534 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:35Z] INFO  16:35:07,535 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:35Z] INFO  16:35:07,540 HelpFormatter - Program Args: -T PrintReads -L 14:50585062-66096324 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/14/tx/tmpvayRq7/R14-18102_kapa-NGv3-PE100-NGv3-sort-14_50585061_66096324-prep-prealign.bam
[2016-04-14T23:35Z] INFO  16:35:07,550 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:35Z] INFO  16:35:07,551 HelpFormatter - Date/Time: 2016/04/14 16:35:07
[2016-04-14T23:35Z] INFO  16:35:07,552 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:35Z] INFO  16:35:07,552 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:35Z] GATK pre-alignment ('14', 97304098, 107349540) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:35Z] INFO  16:35:07,571 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-14T23:35Z] INFO  16:35:07,580 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:35Z] INFO  16:35:07,619 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.04
[2016-04-14T23:35Z] INFO  16:35:07,632 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@7172f77a
[2016-04-14T23:35Z] INFO  16:35:07,773 ProgressMeter -            done    599937.0    87.0 s       2.4 m      100.0%    87.0 s       0.0 s
[2016-04-14T23:35Z] INFO  16:35:07,774 ProgressMeter - Total runtime 87.07 secs, 1.45 min, 0.02 hours
[2016-04-14T23:35Z] INFO  16:35:07,774 MicroScheduler - 215 reads were filtered out during the traversal out of approximately 600152 total reads (0.04%)
[2016-04-14T23:35Z] INFO  16:35:07,775 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:35Z] INFO  16:35:07,775 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:35Z] INFO  16:35:07,775 MicroScheduler -   -> 215 reads (0.04% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:35Z] INFO  16:35:07,798 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:35Z] INFO  16:35:08,057 IntervalUtils - Processing 13279773 bp from intervals
[2016-04-14T23:35Z] WARN  16:35:08,063 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:35Z] INFO  16:35:08,219 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:35Z] INFO  16:35:08,307 ProgressMeter -            done     92784.0     9.0 s     106.0 s      100.0%     9.0 s       0.0 s
[2016-04-14T23:35Z] INFO  16:35:08,308 ProgressMeter - Total runtime 9.84 secs, 0.16 min, 0.00 hours
[2016-04-14T23:35Z] INFO  16:35:08,312 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 92784 total reads (0.00%)
[2016-04-14T23:35Z] INFO  16:35:08,314 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:35Z] INFO  16:35:08,314 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:35Z] INFO  16:35:08,315 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:35Z] INFO  16:35:08,630 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:35Z] INFO  16:35:08,632 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:35Z] INFO  16:35:08,633 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:35Z] INFO  16:35:08,634 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-14T23:35Z] INFO  16:35:09,112 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-14T23:35Z] INFO  16:35:09,166 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:35Z] INFO  16:35:09,175 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:35Z] INFO  16:35:09,200 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:35Z] INFO  16:35:09,213 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.04
[2016-04-14T23:35Z] INFO  16:35:09,229 IntervalUtils - Processing 15511263 bp from intervals
[2016-04-14T23:35Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-12_109494486_125263132-prep-prealign.bam
[2016-04-14T23:35Z] INFO  16:35:09,316 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:35Z] INFO  16:35:09,641 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:35Z] INFO  16:35:09,653 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:35Z] INFO  16:35:09,654 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:35Z] INFO  16:35:09,655 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:35Z] INFO  16:35:09,682 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:35Z] INFO  16:35:09,849 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:35Z] INFO  16:35:09,877 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:35Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-13_67477635_84455642-prep.bam
[2016-04-14T23:35Z] INFO  16:35:09,911 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:35Z] INFO  16:35:09,914 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:35Z] INFO  16:35:09,915 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:35Z] INFO  16:35:09,916 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:35Z] INFO  16:35:09,920 HelpFormatter - Program Args: -T PrintReads -L 14:66135961-81646674 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/14/tx/tmpgvN19i/R14-18102_kapa-NGv3-PE100-NGv3-sort-14_66135960_81646674-prep-prealign.bam
[2016-04-14T23:35Z] INFO  16:35:09,953 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:35Z] INFO  16:35:09,963 HelpFormatter - Date/Time: 2016/04/14 16:35:09
[2016-04-14T23:35Z] INFO  16:35:09,964 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:35Z] INFO  16:35:09,964 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:35Z] INFO  16:35:10,129 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:35Z] GATK pre-alignment ('15', 0, 20740485) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:35Z] INFO  16:35:10,391 ProgressMeter -            done    115562.0    12.0 s     107.0 s      100.0%    12.0 s       0.0 s
[2016-04-14T23:35Z] INFO  16:35:10,391 ProgressMeter - Total runtime 12.43 secs, 0.21 min, 0.00 hours
[2016-04-14T23:35Z] INFO  16:35:10,395 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 115562 total reads (0.00%)
[2016-04-14T23:35Z] INFO  16:35:10,395 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:35Z] INFO  16:35:10,395 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:35Z] INFO  16:35:10,396 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:35Z] INFO  16:35:10,474 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:35Z] INFO  16:35:10,479 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:35Z] INFO  16:35:10,479 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:35Z] INFO  16:35:10,480 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:35Z] INFO  16:35:10,486 HelpFormatter - Program Args: -T PrintReads -L 14:81651875-97299968 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/14/tx/tmp_zm9wM/R14-18102_kapa-NGv3-PE100-NGv3-sort-14_81651874_97299968-prep-prealign.bam
[2016-04-14T23:35Z] INFO  16:35:10,496 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:35Z] INFO  16:35:10,507 HelpFormatter - Date/Time: 2016/04/14 16:35:10
[2016-04-14T23:35Z] INFO  16:35:10,508 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:35Z] INFO  16:35:10,509 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:35Z] INFO  16:35:10,707 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:35Z] INFO  16:35:10,711 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:35Z] INFO  16:35:10,711 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:35Z] INFO  16:35:10,712 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:35Z] INFO  16:35:10,716 HelpFormatter - Program Args: -T PrintReads -L 14:97304099-107349540 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/14/tx/tmpZBMb_Q/R14-18102_kapa-NGv3-PE100-NGv3-sort-14_97304098_107349540-prep-prealign.bam
[2016-04-14T23:35Z] INFO  16:35:10,744 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:35Z] INFO  16:35:10,747 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:35Z] INFO  16:35:10,744 HelpFormatter - Date/Time: 2016/04/14 16:35:10
[2016-04-14T23:35Z] INFO  16:35:10,745 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:35Z] INFO  16:35:10,745 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:35Z] INFO  16:35:10,943 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:35Z] GATK RealignerTargetCreator: R14-18102_kapa-NGv3-PE100-NGv3-sort-12_109494486_125263132-prep-prealign.bam 12:109494487-125263132
[2016-04-14T23:35Z] GATK: RealignerTargetCreator
[2016-04-14T23:35Z] INFO  16:35:11,620 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-14T23:35Z] INFO  16:35:11,670 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:35Z] INFO  16:35:11,679 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:35Z] INFO  16:35:11,728 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-14T23:35Z] INFO  16:35:11,742 IntervalUtils - Processing 15510714 bp from intervals
[2016-04-14T23:35Z] INFO  16:35:11,814 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:35Z] INFO  16:35:11,904 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:35Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-13_51396767_67205543-prep.bam
[2016-04-14T23:35Z] INFO  16:35:12,173 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-14T23:35Z] INFO  16:35:12,227 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-14T23:35Z] INFO  16:35:12,249 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:35Z] INFO  16:35:12,250 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:35Z] INFO  16:35:12,269 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:35Z] INFO  16:35:12,281 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:35Z] INFO  16:35:12,282 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:35Z] INFO  16:35:12,282 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:35Z] INFO  16:35:12,282 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:35Z] INFO  16:35:12,290 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:35Z] INFO  16:35:12,316 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:35Z] INFO  16:35:12,324 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-14T23:35Z] INFO  16:35:12,338 IntervalUtils - Processing 15648094 bp from intervals
[2016-04-14T23:35Z] INFO  16:35:12,340 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-14T23:35Z] INFO  16:35:12,355 IntervalUtils - Processing 10045442 bp from intervals
[2016-04-14T23:35Z] INFO  16:35:12,418 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:35Z] GATK pre-alignment ('15', 20741621, 36872162) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:35Z] INFO  16:35:12,445 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:35Z] INFO  16:35:12,534 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:35Z] INFO  16:35:12,701 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:35Z] INFO  16:35:12,702 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:35Z] INFO  16:35:12,703 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:35Z] INFO  16:35:12,703 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:35Z] INFO  16:35:12,716 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:35Z] INFO  16:35:12,736 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:35Z] INFO  16:35:12,737 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:35Z] INFO  16:35:12,738 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:35Z] INFO  16:35:12,739 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:35Z] INFO  16:35:12,755 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:35Z] INFO  16:35:12,818 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:35Z] INFO  16:35:12,935 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:35Z] INFO  16:35:13,348 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:35Z] INFO  16:35:13,351 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:35Z] INFO  16:35:13,352 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:35Z] INFO  16:35:13,352 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:35Z] INFO  16:35:13,356 HelpFormatter - Program Args: -T PrintReads -L 15:1-20740485 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/15/tx/tmp7J__YC/R14-18102_kapa-NGv3-PE100-NGv3-sort-15_0_20740485-prep-prealign.bam
[2016-04-14T23:35Z] INFO  16:35:13,365 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:35Z] INFO  16:35:13,376 HelpFormatter - Date/Time: 2016/04/14 16:35:13
[2016-04-14T23:35Z] INFO  16:35:13,377 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:35Z] INFO  16:35:13,378 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:35Z] INFO  16:35:13,596 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:35Z] INFO  16:35:14,366 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:35Z] INFO  16:35:14,369 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:35Z] INFO  16:35:14,369 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:35Z] INFO  16:35:14,369 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:35Z] INFO  16:35:14,373 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/12/R14-18102_kapa-NGv3-PE100-NGv3-sort-12_109494486_125263132-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/12/tx/tmpaOgAKM/R14-18102_kapa-NGv3-PE100-NGv3-sort-12_109494486_125263132-prep-prealign-realign.intervals -l INFO -L 12:109494487-125263132 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-14T23:35Z] INFO  16:35:14,399 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:35Z] INFO  16:35:14,399 HelpFormatter - Date/Time: 2016/04/14 16:35:14
[2016-04-14T23:35Z] INFO  16:35:14,399 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:35Z] INFO  16:35:14,400 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:35Z] INFO  16:35:14,589 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:35Z] INFO  16:35:14,928 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-14T23:35Z] INFO  16:35:14,938 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:35Z] INFO  16:35:15,021 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-14T23:35Z] INFO  16:35:15,089 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-14T23:35Z] INFO  16:35:15,162 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:35Z] INFO  16:35:15,171 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:35Z] INFO  16:35:15,213 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.04
[2016-04-14T23:35Z] INFO  16:35:15,228 IntervalUtils - Processing 20740485 bp from intervals
[2016-04-14T23:35Z] INFO  16:35:15,323 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:35Z] INFO  16:35:15,383 IntervalUtils - Processing 15768646 bp from intervals
[2016-04-14T23:35Z] WARN  16:35:15,388 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:35Z] INFO  16:35:15,468 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:35Z] INFO  16:35:15,471 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:35Z] INFO  16:35:15,472 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:35Z] INFO  16:35:15,472 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:35Z] INFO  16:35:15,477 HelpFormatter - Program Args: -T PrintReads -L 15:20741622-36872162 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/15/tx/tmpfMf3ds/R14-18102_kapa-NGv3-PE100-NGv3-sort-15_20741621_36872162-prep-prealign.bam
[2016-04-14T23:35Z] INFO  16:35:15,520 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:35Z] INFO  16:35:15,521 HelpFormatter - Date/Time: 2016/04/14 16:35:15
[2016-04-14T23:35Z] INFO  16:35:15,521 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:35Z] INFO  16:35:15,521 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:35Z] INFO  16:35:15,571 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:35Z] INFO  16:35:15,689 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:35Z] INFO  16:35:15,691 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:35Z] INFO  16:35:15,691 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:35Z] INFO  16:35:15,692 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:35Z] INFO  16:35:15,704 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:35Z] INFO  16:35:15,705 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:35Z] INFO  16:35:15,706 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:35Z] INFO  16:35:15,706 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-14T23:35Z] INFO  16:35:15,716 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:35Z] INFO  16:35:15,722 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:35Z] INFO  16:35:15,767 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:35Z] INFO  16:35:16,893 ProgressMeter -            done    114409.0    12.0 s     106.0 s      100.0%    12.0 s       0.0 s
[2016-04-14T23:35Z] INFO  16:35:16,894 ProgressMeter - Total runtime 12.16 secs, 0.20 min, 0.00 hours
[2016-04-14T23:35Z] INFO  16:35:16,897 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 114409 total reads (0.00%)
[2016-04-14T23:35Z] INFO  16:35:16,898 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:35Z] INFO  16:35:16,898 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:35Z] INFO  16:35:16,898 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:35Z] INFO  16:35:16,920 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-14T23:35Z] INFO  16:35:17,014 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:35Z] INFO  16:35:17,023 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:35Z] INFO  16:35:17,092 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-14T23:35Z] INFO  16:35:17,107 IntervalUtils - Processing 16130541 bp from intervals
[2016-04-14T23:35Z] INFO  16:35:17,184 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:35Z] INFO  16:35:17,466 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:35Z] INFO  16:35:17,467 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:35Z] INFO  16:35:17,468 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:35Z] INFO  16:35:17,468 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:35Z] INFO  16:35:17,482 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:35Z] INFO  16:35:17,629 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:35Z] INFO  16:35:18,252 ProgressMeter -     14:21992684    100003.0    30.0 s       5.1 m       15.7%     3.2 m       2.7 m
[2016-04-14T23:35Z] INFO  16:35:18,502 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:35Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-13_86368117_101881935-prep.bam
[2016-04-14T23:35Z] GATK pre-alignment ('15', 36887086, 52402170) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:35Z] INFO  16:35:20,633 ProgressMeter -      12:9086477    300006.0    30.0 s     100.0 s       58.1%    51.0 s      21.0 s
[2016-04-14T23:35Z] INFO  16:35:21,075 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@32d5a4c6
[2016-04-14T23:35Z] INFO  16:35:21,113 ProgressMeter -            done     22538.0     5.0 s       4.0 m      100.0%     5.0 s       0.0 s
[2016-04-14T23:35Z] INFO  16:35:21,114 ProgressMeter - Total runtime 5.42 secs, 0.09 min, 0.00 hours
[2016-04-14T23:35Z] INFO  16:35:21,115 MicroScheduler - 15 reads were filtered out during the traversal out of approximately 22553 total reads (0.07%)
[2016-04-14T23:35Z] INFO  16:35:21,115 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:35Z] INFO  16:35:21,115 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:35Z] INFO  16:35:21,116 MicroScheduler -   -> 15 reads (0.07% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:35Z] INFO  16:35:21,806 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:35Z] INFO  16:35:21,810 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:35Z] INFO  16:35:21,810 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:35Z] INFO  16:35:21,811 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:35Z] INFO  16:35:21,816 HelpFormatter - Program Args: -T PrintReads -L 15:36887087-52402170 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/15/tx/tmpzwKz1b/R14-18102_kapa-NGv3-PE100-NGv3-sort-15_36887086_52402170-prep-prealign.bam
[2016-04-14T23:35Z] INFO  16:35:21,825 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:35Z] INFO  16:35:21,826 HelpFormatter - Date/Time: 2016/04/14 16:35:21
[2016-04-14T23:35Z] INFO  16:35:21,826 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:35Z] INFO  16:35:21,827 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:35Z] INFO  16:35:21,984 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:35Z] INFO  16:35:22,586 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:35Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-15_0_20740485-prep-prealign.bam
[2016-04-14T23:35Z] GATK RealignerTargetCreator: R14-18102_kapa-NGv3-PE100-NGv3-sort-15_0_20740485-prep-prealign.bam 15:1-20740485
[2016-04-14T23:35Z] GATK: RealignerTargetCreator
[2016-04-14T23:35Z] INFO  16:35:23,028 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-14T23:35Z] INFO  16:35:23,111 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:35Z] INFO  16:35:23,123 ProgressMeter -            done    231379.0    18.0 s      79.0 s      100.0%    18.0 s       0.0 s
[2016-04-14T23:35Z] INFO  16:35:23,125 ProgressMeter - Total runtime 18.42 secs, 0.31 min, 0.01 hours
[2016-04-14T23:35Z] INFO  16:35:23,129 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 231379 total reads (0.00%)
[2016-04-14T23:35Z] INFO  16:35:23,126 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:35Z] INFO  16:35:23,130 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:35Z] INFO  16:35:23,131 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:35Z] INFO  16:35:23,132 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:35Z] INFO  16:35:23,181 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-14T23:35Z] INFO  16:35:23,218 IntervalUtils - Processing 15515084 bp from intervals
[2016-04-14T23:35Z] INFO  16:35:23,312 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:35Z] INFO  16:35:23,626 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:35Z] INFO  16:35:23,627 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:35Z] INFO  16:35:23,628 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:35Z] INFO  16:35:23,629 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:35Z] INFO  16:35:23,662 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:35Z] INFO  16:35:23,834 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:35Z] INFO  16:35:24,610 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:35Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-13_35615069_51287376-prep.bam
[2016-04-14T23:35Z] GATK pre-alignment ('15', 52404364, 67923265) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:35Z] INFO  16:35:25,493 ProgressMeter -            done    256845.0    18.0 s      72.0 s      100.0%    18.0 s       0.0 s
[2016-04-14T23:35Z] INFO  16:35:25,494 ProgressMeter - Total runtime 18.60 secs, 0.31 min, 0.01 hours
[2016-04-14T23:35Z] INFO  16:35:25,499 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 256845 total reads (0.00%)
[2016-04-14T23:35Z] INFO  16:35:25,500 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:35Z] INFO  16:35:25,500 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:35Z] INFO  16:35:25,501 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:35Z] INFO  16:35:25,814 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:35Z] INFO  16:35:25,818 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:35Z] INFO  16:35:25,819 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:35Z] INFO  16:35:25,819 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:35Z] INFO  16:35:25,825 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/15/R14-18102_kapa-NGv3-PE100-NGv3-sort-15_0_20740485-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/15/tx/tmpI5pexG/R14-18102_kapa-NGv3-PE100-NGv3-sort-15_0_20740485-prep-prealign-realign.intervals -l INFO -L 15:1-20740485 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-14T23:35Z] INFO  16:35:25,835 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:35Z] INFO  16:35:25,835 HelpFormatter - Date/Time: 2016/04/14 16:35:25
[2016-04-14T23:35Z] INFO  16:35:25,836 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:35Z] INFO  16:35:25,836 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:35Z] INFO  16:35:25,891 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@7172f77a
[2016-04-14T23:35Z] INFO  16:35:25,906 ProgressMeter -            done   1.3279773E7    17.0 s       1.0 s      100.0%    17.0 s       0.0 s
[2016-04-14T23:35Z] INFO  16:35:25,907 ProgressMeter - Total runtime 17.28 secs, 0.29 min, 0.00 hours
[2016-04-14T23:35Z] INFO  16:35:25,911 MicroScheduler - 17973 reads were filtered out during the traversal out of approximately 213027 total reads (8.44%)
[2016-04-14T23:35Z] INFO  16:35:25,911 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:35Z] INFO  16:35:25,912 MicroScheduler -   -> 603 reads (0.28% of total) failing BadMateFilter
[2016-04-14T23:35Z] INFO  16:35:25,912 MicroScheduler -   -> 16858 reads (7.91% of total) failing DuplicateReadFilter
[2016-04-14T23:35Z] INFO  16:35:25,912 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-14T23:35Z] INFO  16:35:25,912 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:35Z] INFO  16:35:25,913 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-14T23:35Z] INFO  16:35:25,914 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:35Z] INFO  16:35:25,913 MicroScheduler -   -> 512 reads (0.24% of total) failing MappingQualityZeroFilter
[2016-04-14T23:35Z] INFO  16:35:25,913 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:35Z] INFO  16:35:25,913 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-14T23:35Z] INFO  16:35:25,914 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-14T23:35Z] INFO  16:35:25,963 ProgressMeter -            done    126949.0    21.0 s       2.9 m      100.0%    21.0 s       0.0 s
[2016-04-14T23:35Z] INFO  16:35:25,964 ProgressMeter - Total runtime 21.88 secs, 0.36 min, 0.01 hours
[2016-04-14T23:35Z] INFO  16:35:25,965 MicroScheduler - 115 reads were filtered out during the traversal out of approximately 127064 total reads (0.09%)
[2016-04-14T23:35Z] INFO  16:35:25,966 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:35Z] INFO  16:35:25,967 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:35Z] INFO  16:35:25,968 MicroScheduler -   -> 115 reads (0.09% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:35Z] INFO  16:35:26,172 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-14T23:35Z] INFO  16:35:26,194 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:35Z] INFO  16:35:26,249 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-14T23:35Z] INFO  16:35:26,500 IntervalUtils - Processing 20740485 bp from intervals
[2016-04-14T23:35Z] WARN  16:35:26,505 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:35Z] INFO  16:35:26,587 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:35Z] INFO  16:35:26,835 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:35Z] INFO  16:35:26,836 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:35Z] INFO  16:35:26,836 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:35Z] INFO  16:35:26,837 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-14T23:35Z] INFO  16:35:26,960 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:35Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-13_19751066_35517251-prep.bam
[2016-04-14T23:35Z] INFO  16:35:27,259 ProgressMeter -     11:66454557    400012.0    30.0 s      75.0 s       23.9%     2.1 m      95.0 s
[2016-04-14T23:35Z] INFO  16:35:27,313 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:35Z] GATK: realign ('13', 101890105, 115169878) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:35Z] INFO  16:35:27,512 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:35Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-14_35072553_50583270-prep-prealign.bam
[2016-04-14T23:35Z] INFO  16:35:27,743 ProgressMeter -            done    560719.0    37.0 s      66.0 s      100.0%    37.0 s       0.0 s
[2016-04-14T23:35Z] INFO  16:35:27,744 ProgressMeter - Total runtime 37.17 secs, 0.62 min, 0.01 hours
[2016-04-14T23:35Z] INFO  16:35:27,748 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 560719 total reads (0.00%)
[2016-04-14T23:35Z] INFO  16:35:27,749 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:35Z] INFO  16:35:27,749 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:35Z] INFO  16:35:27,749 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:35Z] GATK pre-alignment ('15', 67932890, 83447639) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:35Z] GATK RealignerTargetCreator: R14-18102_kapa-NGv3-PE100-NGv3-sort-14_35072553_50583270-prep-prealign.bam 14:35072554-50583270
[2016-04-14T23:35Z] GATK: RealignerTargetCreator
[2016-04-14T23:35Z] INFO  16:35:28,191 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:35Z] INFO  16:35:28,196 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:35Z] INFO  16:35:28,196 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:35Z] INFO  16:35:28,197 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:35Z] INFO  16:35:28,202 HelpFormatter - Program Args: -T PrintReads -L 15:52404365-67923265 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/15/tx/tmpTmZfg_/R14-18102_kapa-NGv3-PE100-NGv3-sort-15_52404364_67923265-prep-prealign.bam
[2016-04-14T23:35Z] INFO  16:35:28,216 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:35Z] INFO  16:35:28,217 HelpFormatter - Date/Time: 2016/04/14 16:35:28
[2016-04-14T23:35Z] INFO  16:35:28,218 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:35Z] INFO  16:35:28,218 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:35Z] INFO  16:35:28,414 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:35Z] INFO  16:35:29,387 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:35Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-12_0_15637181-prep.bam
[2016-04-14T23:35Z] INFO  16:35:29,589 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-14T23:35Z] INFO  16:35:29,680 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:35Z] INFO  16:35:29,692 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:35Z] INFO  16:35:29,760 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-14T23:35Z] INFO  16:35:29,800 IntervalUtils - Processing 15518901 bp from intervals
[2016-04-14T23:35Z] INFO  16:35:29,902 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:35Z] INFO  16:35:30,182 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:35Z] INFO  16:35:30,183 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:35Z] INFO  16:35:30,184 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:35Z] INFO  16:35:30,185 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:35Z] INFO  16:35:30,222 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:35Z] INFO  16:35:30,219 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:35Z] INFO  16:35:30,234 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:35Z] INFO  16:35:30,235 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:35Z] INFO  16:35:30,236 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:35Z] INFO  16:35:30,242 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/13/R14-18102_kapa-NGv3-PE100-NGv3-sort-13_101890105_115169878-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/13/R14-18102_kapa-NGv3-PE100-NGv3-sort-13_101890105_115169878-prep-prealign-realign.intervals -L 13:101890106-115169878 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/13/tx/tmptBR6yb/R14-18102_kapa-NGv3-PE100-NGv3-sort-13_101890105_115169878-prep.bam
[2016-04-14T23:35Z] INFO  16:35:30,263 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:35Z] INFO  16:35:30,264 HelpFormatter - Date/Time: 2016/04/14 16:35:30
[2016-04-14T23:35Z] INFO  16:35:30,265 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:35Z] INFO  16:35:30,265 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:35Z] INFO  16:35:30,502 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:35Z] INFO  16:35:30,513 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:35Z] INFO  16:35:30,645 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:35Z] INFO  16:35:30,661 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:35Z] INFO  16:35:30,751 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.09
[2016-04-14T23:35Z] INFO  16:35:31,022 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:35Z] INFO  16:35:31,026 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:35Z] INFO  16:35:31,027 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:35Z] INFO  16:35:31,028 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:35Z] INFO  16:35:31,039 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/14/R14-18102_kapa-NGv3-PE100-NGv3-sort-14_35072553_50583270-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/14/tx/tmpn83IDq/R14-18102_kapa-NGv3-PE100-NGv3-sort-14_35072553_50583270-prep-prealign-realign.intervals -l INFO -L 14:35072554-50583270 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-14T23:35Z] INFO  16:35:31,067 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:35Z] INFO  16:35:31,068 HelpFormatter - Date/Time: 2016/04/14 16:35:31
[2016-04-14T23:35Z] INFO  16:35:31,068 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:35Z] INFO  16:35:31,069 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:35Z] INFO  16:35:31,110 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:35Z] INFO  16:35:31,114 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:35Z] INFO  16:35:31,115 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:35Z] INFO  16:35:31,115 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:35Z] INFO  16:35:31,120 HelpFormatter - Program Args: -T PrintReads -L 15:67932891-83447639 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/15/tx/tmpZs_OzL/R14-18102_kapa-NGv3-PE100-NGv3-sort-15_67932890_83447639-prep-prealign.bam
[2016-04-14T23:35Z] INFO  16:35:31,137 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:35Z] INFO  16:35:31,138 HelpFormatter - Date/Time: 2016/04/14 16:35:31
[2016-04-14T23:35Z] INFO  16:35:31,138 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:35Z] INFO  16:35:31,139 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:35Z] INFO  16:35:31,193 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:35Z] INFO  16:35:31,251 IntervalUtils - Processing 13279773 bp from intervals
[2016-04-14T23:35Z] WARN  16:35:31,268 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:35Z] INFO  16:35:31,333 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:35Z] INFO  16:35:31,356 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:35Z] GATK pre-alignment ('15', 83448996, 98982979) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:35Z] INFO  16:35:31,458 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-14T23:35Z] INFO  16:35:31,481 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:35Z] INFO  16:35:31,515 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:35Z] INFO  16:35:31,516 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:35Z] INFO  16:35:31,517 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:35Z] INFO  16:35:31,518 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:35Z] INFO  16:35:31,545 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-14T23:35Z] INFO  16:35:31,739 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:35Z] INFO  16:35:31,905 IntervalUtils - Processing 15510717 bp from intervals
[2016-04-14T23:35Z] WARN  16:35:31,923 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:35Z] INFO  16:35:31,952 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:35Z] INFO  16:35:32,025 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:35Z] INFO  16:35:32,353 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:35Z] INFO  16:35:32,355 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:35Z] INFO  16:35:32,356 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:35Z] INFO  16:35:32,356 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-14T23:35Z] INFO  16:35:32,547 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-14T23:35Z] INFO  16:35:32,617 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:35Z] INFO  16:35:32,638 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:35Z] INFO  16:35:32,682 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.04
[2016-04-14T23:35Z] INFO  16:35:32,697 IntervalUtils - Processing 15514749 bp from intervals
[2016-04-14T23:35Z] INFO  16:35:32,770 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:35Z] INFO  16:35:33,111 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:35Z] INFO  16:35:33,112 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:35Z] INFO  16:35:33,116 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:35Z] INFO  16:35:33,116 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:35Z] INFO  16:35:33,151 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:35Z] INFO  16:35:33,344 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:35Z] INFO  16:35:33,392 ProgressMeter -     12:61602857   1.483139E7    30.0 s       2.0 s       93.4%    32.0 s       2.0 s
[2016-04-14T23:35Z] INFO  16:35:34,362 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:35Z] INFO  16:35:34,365 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:35Z] INFO  16:35:34,365 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:35Z] INFO  16:35:34,366 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:35Z] INFO  16:35:34,371 HelpFormatter - Program Args: -T PrintReads -L 15:83448997-98982979 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/15/tx/tmpuKsmiA/R14-18102_kapa-NGv3-PE100-NGv3-sort-15_83448996_98982979-prep-prealign.bam
[2016-04-14T23:35Z] INFO  16:35:34,379 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:35Z] INFO  16:35:34,380 HelpFormatter - Date/Time: 2016/04/14 16:35:34
[2016-04-14T23:35Z] INFO  16:35:34,381 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:35Z] INFO  16:35:34,381 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:35Z] INFO  16:35:34,510 ProgressMeter -            done   1.5898218E7    31.0 s       1.0 s      100.0%    31.0 s       0.0 s
[2016-04-14T23:35Z] INFO  16:35:34,511 ProgressMeter - Total runtime 31.15 secs, 0.52 min, 0.01 hours
[2016-04-14T23:35Z] INFO  16:35:34,515 MicroScheduler - 81511 reads were filtered out during the traversal out of approximately 872443 total reads (9.34%)
[2016-04-14T23:35Z] INFO  16:35:34,516 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:35Z] INFO  16:35:34,516 MicroScheduler -   -> 1612 reads (0.18% of total) failing BadMateFilter
[2016-04-14T23:35Z] INFO  16:35:34,517 MicroScheduler -   -> 69098 reads (7.92% of total) failing DuplicateReadFilter
[2016-04-14T23:35Z] INFO  16:35:34,518 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-14T23:35Z] INFO  16:35:34,518 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:35Z] INFO  16:35:34,519 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-14T23:35Z] INFO  16:35:34,519 MicroScheduler -   -> 10801 reads (1.24% of total) failing MappingQualityZeroFilter
[2016-04-14T23:35Z] INFO  16:35:34,520 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:35Z] INFO  16:35:34,521 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-14T23:35Z] INFO  16:35:34,522 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-14T23:35Z] INFO  16:35:34,592 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:35Z] INFO  16:35:35,627 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-14T23:35Z] INFO  16:35:35,686 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:35Z] INFO  16:35:35,695 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:35Z] INFO  16:35:35,743 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-14T23:35Z] INFO  16:35:35,758 IntervalUtils - Processing 15533983 bp from intervals
[2016-04-14T23:35Z] INFO  16:35:35,849 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:35Z] INFO  16:35:36,019 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:35Z] GATK: realign ('12', 46756066, 62654284) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:35Z] INFO  16:35:36,089 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:35Z] INFO  16:35:36,090 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:35Z] INFO  16:35:36,091 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:35Z] INFO  16:35:36,092 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:35Z] INFO  16:35:36,139 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:35Z] INFO  16:35:36,281 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:35Z] INFO  16:35:38,558 ProgressMeter -            done   2.0740485E7    11.0 s       0.0 s      100.0%    11.0 s       0.0 s
[2016-04-14T23:35Z] INFO  16:35:38,559 ProgressMeter - Total runtime 11.72 secs, 0.20 min, 0.00 hours
[2016-04-14T23:35Z] INFO  16:35:38,563 MicroScheduler - 10045 reads were filtered out during the traversal out of approximately 22708 total reads (44.24%)
[2016-04-14T23:35Z] INFO  16:35:38,564 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:35Z] INFO  16:35:38,564 MicroScheduler -   -> 39 reads (0.17% of total) failing BadMateFilter
[2016-04-14T23:35Z] INFO  16:35:38,565 MicroScheduler -   -> 1071 reads (4.72% of total) failing DuplicateReadFilter
[2016-04-14T23:35Z] INFO  16:35:38,566 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-14T23:35Z] INFO  16:35:38,566 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:35Z] INFO  16:35:38,567 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-14T23:35Z] INFO  16:35:38,568 MicroScheduler -   -> 8935 reads (39.35% of total) failing MappingQualityZeroFilter
[2016-04-14T23:35Z] INFO  16:35:38,568 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:35Z] INFO  16:35:38,569 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-14T23:35Z] INFO  16:35:38,570 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-14T23:35Z] INFO  16:35:39,096 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:35Z] INFO  16:35:39,100 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:35Z] INFO  16:35:39,100 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:35Z] INFO  16:35:39,101 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:35Z] INFO  16:35:39,106 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/12/R14-18102_kapa-NGv3-PE100-NGv3-sort-12_46756066_62654284-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/12/R14-18102_kapa-NGv3-PE100-NGv3-sort-12_46756066_62654284-prep-prealign-realign.intervals -L 12:46756067-62654284 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/12/tx/tmpsSlRUK/R14-18102_kapa-NGv3-PE100-NGv3-sort-12_46756066_62654284-prep.bam
[2016-04-14T23:35Z] INFO  16:35:39,116 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:35Z] INFO  16:35:39,127 HelpFormatter - Date/Time: 2016/04/14 16:35:39
[2016-04-14T23:35Z] INFO  16:35:39,128 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:35Z] INFO  16:35:39,129 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:35Z] INFO  16:35:39,325 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:35Z] INFO  16:35:39,400 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:35Z] INFO  16:35:39,410 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:35Z] INFO  16:35:39,474 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-14T23:35Z] INFO  16:35:39,673 ProgressMeter -     14:63856475    200003.0    30.0 s       2.5 m       85.6%    35.0 s       5.0 s
[2016-04-14T23:35Z] INFO  16:35:39,828 IntervalUtils - Processing 15898218 bp from intervals
[2016-04-14T23:35Z] WARN  16:35:39,833 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:35Z] INFO  16:35:39,898 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:35Z] INFO  16:35:39,930 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:35Z] GATK: realign ('15', 0, 20740485) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:35Z] INFO  16:35:40,032 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:35Z] INFO  16:35:40,033 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:35Z] INFO  16:35:40,033 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:35Z] INFO  16:35:40,034 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:35Z] INFO  16:35:40,223 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:35Z] INFO  16:35:40,426 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:35Z] INFO  16:35:42,517 ProgressMeter -     14:74417162    200002.0    30.0 s       2.5 m       53.4%    56.0 s      26.0 s
[2016-04-14T23:35Z] INFO  16:35:42,595 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:35Z] INFO  16:35:42,599 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:35Z] INFO  16:35:42,599 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:35Z] INFO  16:35:42,600 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:35Z] INFO  16:35:42,604 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/15/R14-18102_kapa-NGv3-PE100-NGv3-sort-15_0_20740485-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/15/R14-18102_kapa-NGv3-PE100-NGv3-sort-15_0_20740485-prep-prealign-realign.intervals -L 15:1-20740485 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/15/tx/tmp10zzAj/R14-18102_kapa-NGv3-PE100-NGv3-sort-15_0_20740485-prep.bam
[2016-04-14T23:35Z] INFO  16:35:42,624 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:35Z] INFO  16:35:42,625 HelpFormatter - Date/Time: 2016/04/14 16:35:42
[2016-04-14T23:35Z] INFO  16:35:42,626 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:35Z] INFO  16:35:42,626 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:35Z] INFO  16:35:42,720 ProgressMeter -    14:105180853    200003.0    30.0 s       2.5 m       78.4%    38.0 s       8.0 s
[2016-04-14T23:35Z] INFO  16:35:42,769 ProgressMeter -     14:96782880    200006.0    30.0 s       2.5 m       96.7%    31.0 s       1.0 s
[2016-04-14T23:35Z] INFO  16:35:42,827 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:35Z] INFO  16:35:42,946 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:35Z] INFO  16:35:42,956 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:35Z] INFO  16:35:43,003 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-14T23:35Z] INFO  16:35:43,462 IntervalUtils - Processing 20740485 bp from intervals
[2016-04-14T23:35Z] WARN  16:35:43,467 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:35Z] INFO  16:35:43,605 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:35Z] INFO  16:35:43,621 ProgressMeter -            done   1.5768646E7    27.0 s       1.0 s      100.0%    27.0 s       0.0 s
[2016-04-14T23:35Z] INFO  16:35:43,622 ProgressMeter - Total runtime 27.92 secs, 0.47 min, 0.01 hours
[2016-04-14T23:35Z] INFO  16:35:43,626 MicroScheduler - 50908 reads were filtered out during the traversal out of approximately 602892 total reads (8.44%)
[2016-04-14T23:35Z] INFO  16:35:43,627 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:35Z] INFO  16:35:43,628 MicroScheduler -   -> 1265 reads (0.21% of total) failing BadMateFilter
[2016-04-14T23:35Z] INFO  16:35:43,629 MicroScheduler -   -> 48345 reads (8.02% of total) failing DuplicateReadFilter
[2016-04-14T23:35Z] INFO  16:35:43,629 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-14T23:35Z] INFO  16:35:43,630 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:35Z] INFO  16:35:43,631 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-14T23:35Z] INFO  16:35:43,631 MicroScheduler -   -> 1298 reads (0.22% of total) failing MappingQualityZeroFilter
[2016-04-14T23:35Z] INFO  16:35:43,632 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:35Z] INFO  16:35:43,633 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-14T23:35Z] INFO  16:35:43,633 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-14T23:35Z] INFO  16:35:43,776 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:35Z] INFO  16:35:43,777 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:35Z] INFO  16:35:43,778 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:35Z] INFO  16:35:43,779 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:35Z] INFO  16:35:43,779 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@41fd9d8e
[2016-04-14T23:35Z] INFO  16:35:43,808 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:35Z] INFO  16:35:43,826 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:35Z] INFO  16:35:43,909 ProgressMeter -            done    247045.0    31.0 s       2.1 m      100.0%    31.0 s       0.0 s
[2016-04-14T23:35Z] INFO  16:35:43,910 ProgressMeter - Total runtime 31.17 secs, 0.52 min, 0.01 hours
[2016-04-14T23:35Z] INFO  16:35:43,911 MicroScheduler - 153 reads were filtered out during the traversal out of approximately 247198 total reads (0.06%)
[2016-04-14T23:35Z] INFO  16:35:43,911 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:35Z] INFO  16:35:43,911 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:35Z] INFO  16:35:43,912 MicroScheduler -   -> 153 reads (0.06% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:35Z] INFO  16:35:44,986 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:35Z] GATK: realign ('12', 109494486, 125263132) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:35Z] INFO  16:35:45,399 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:35Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-14_81651874_97299968-prep-prealign.bam
[2016-04-14T23:35Z] GATK RealignerTargetCreator: R14-18102_kapa-NGv3-PE100-NGv3-sort-14_81651874_97299968-prep-prealign.bam 14:81651875-97299968
[2016-04-14T23:35Z] GATK: RealignerTargetCreator
[2016-04-14T23:35Z] INFO  16:35:47,285 ProgressMeter -            done     22538.0     3.0 s       2.6 m      100.0%     3.0 s       0.0 s
[2016-04-14T23:35Z] INFO  16:35:47,286 ProgressMeter - Total runtime 3.51 secs, 0.06 min, 0.00 hours
[2016-04-14T23:35Z] INFO  16:35:47,290 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 22538 total reads (0.00%)
[2016-04-14T23:35Z] INFO  16:35:47,290 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:35Z] INFO  16:35:47,291 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:35Z] INFO  16:35:47,291 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:35Z] INFO  16:35:47,475 ProgressMeter -     15:28506074    200003.0    30.0 s       2.5 m       48.1%    62.0 s      32.0 s
[2016-04-14T23:35Z] INFO  16:35:47,815 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:35Z] INFO  16:35:47,818 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:35Z] INFO  16:35:47,819 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:35Z] INFO  16:35:47,820 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:35Z] INFO  16:35:47,825 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/12/R14-18102_kapa-NGv3-PE100-NGv3-sort-12_109494486_125263132-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/12/R14-18102_kapa-NGv3-PE100-NGv3-sort-12_109494486_125263132-prep-prealign-realign.intervals -L 12:109494487-125263132 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/12/tx/tmpV3VdAo/R14-18102_kapa-NGv3-PE100-NGv3-sort-12_109494486_125263132-prep.bam
[2016-04-14T23:35Z] INFO  16:35:47,836 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:35Z] INFO  16:35:47,846 HelpFormatter - Date/Time: 2016/04/14 16:35:47
[2016-04-14T23:35Z] INFO  16:35:47,847 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:35Z] INFO  16:35:47,847 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:35Z] INFO  16:35:48,154 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:35Z] INFO  16:35:48,271 ProgressMeter -            done   1.5510717E7    15.0 s       1.0 s      100.0%    15.0 s       0.0 s
[2016-04-14T23:35Z] INFO  16:35:48,272 ProgressMeter - Total runtime 15.92 secs, 0.27 min, 0.00 hours
[2016-04-14T23:35Z] INFO  16:35:48,277 MicroScheduler - 12777 reads were filtered out during the traversal out of approximately 127746 total reads (10.00%)
[2016-04-14T23:35Z] INFO  16:35:48,278 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:35Z] INFO  16:35:48,279 MicroScheduler -   -> 511 reads (0.40% of total) failing BadMateFilter
[2016-04-14T23:35Z] INFO  16:35:48,280 MicroScheduler -   -> 10014 reads (7.84% of total) failing DuplicateReadFilter
[2016-04-14T23:35Z] INFO  16:35:48,280 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-14T23:35Z] INFO  16:35:48,281 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:35Z] INFO  16:35:48,282 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-14T23:35Z] INFO  16:35:48,283 MicroScheduler -   -> 2252 reads (1.76% of total) failing MappingQualityZeroFilter
[2016-04-14T23:35Z] INFO  16:35:48,283 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:35Z] INFO  16:35:48,284 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-14T23:35Z] INFO  16:35:48,285 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-14T23:35Z] INFO  16:35:48,322 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@41fd9d8e
[2016-04-14T23:35Z] INFO  16:35:48,315 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:35Z] INFO  16:35:48,336 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:35Z] INFO  16:35:48,387 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-14T23:35Z] INFO  16:35:48,457 ProgressMeter -            done    295217.0    38.0 s       2.2 m      100.0%    38.0 s       0.0 s
[2016-04-14T23:35Z] INFO  16:35:48,457 ProgressMeter - Total runtime 38.80 secs, 0.65 min, 0.01 hours
[2016-04-14T23:35Z] INFO  16:35:48,458 MicroScheduler - 164 reads were filtered out during the traversal out of approximately 295381 total reads (0.06%)
[2016-04-14T23:35Z] INFO  16:35:48,458 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:35Z] INFO  16:35:48,459 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:35Z] INFO  16:35:48,459 MicroScheduler -   -> 164 reads (0.06% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:35Z] INFO  16:35:48,754 IntervalUtils - Processing 15768646 bp from intervals
[2016-04-14T23:35Z] WARN  16:35:48,759 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:35Z] INFO  16:35:48,759 ProgressMeter -            done    211543.0    17.0 s      81.0 s       99.4%    17.0 s       0.0 s
[2016-04-14T23:35Z] INFO  16:35:48,760 ProgressMeter - Total runtime 17.24 secs, 0.29 min, 0.00 hours
[2016-04-14T23:35Z] INFO  16:35:48,764 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 211543 total reads (0.00%)
[2016-04-14T23:35Z] INFO  16:35:48,765 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:35Z] INFO  16:35:48,765 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:35Z] INFO  16:35:48,765 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:35Z] INFO  16:35:48,766 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:35Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-15_0_20740485-prep.bam
[2016-04-14T23:35Z] INFO  16:35:48,832 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:35Z] GATK pre-alignment ('15', 98984299, 102531392) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:35Z] INFO  16:35:48,967 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:35Z] INFO  16:35:48,968 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:35Z] INFO  16:35:48,969 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:35Z] INFO  16:35:48,970 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:35Z] INFO  16:35:48,981 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:35Z] INFO  16:35:48,985 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:35Z] INFO  16:35:48,985 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:35Z] INFO  16:35:48,986 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:35Z] INFO  16:35:48,990 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/14/R14-18102_kapa-NGv3-PE100-NGv3-sort-14_81651874_97299968-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/14/tx/tmpqfIuFq/R14-18102_kapa-NGv3-PE100-NGv3-sort-14_81651874_97299968-prep-prealign-realign.intervals -l INFO -L 14:81651875-97299968 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-14T23:35Z] INFO  16:35:49,002 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:35Z] INFO  16:35:49,003 HelpFormatter - Date/Time: 2016/04/14 16:35:48
[2016-04-14T23:35Z] INFO  16:35:49,003 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:35Z] INFO  16:35:49,004 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:35Z] INFO  16:35:49,108 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:35Z] INFO  16:35:49,121 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:35Z] INFO  16:35:49,278 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:35Z] INFO  16:35:49,309 ProgressMeter -     14:24686397    300005.0    61.0 s       3.4 m       33.1%     3.1 m       2.1 m
[2016-04-14T23:35Z] INFO  16:35:49,358 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-14T23:35Z] INFO  16:35:49,370 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:35Z] INFO  16:35:49,459 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.09
[2016-04-14T23:35Z] INFO  16:35:49,718 IntervalUtils - Processing 15648094 bp from intervals
[2016-04-14T23:35Z] WARN  16:35:49,724 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:35Z] INFO  16:35:49,789 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:35Z] INFO  16:35:49,812 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:35Z] INFO  16:35:49,813 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:35Z] GATK: realign ('14', 35072553, 50583270) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:35Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-14_50585061_66096324-prep-prealign.bam
[2016-04-14T23:35Z] INFO  16:35:50,098 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:35Z] INFO  16:35:50,100 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:35Z] INFO  16:35:50,101 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:35Z] INFO  16:35:50,102 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-14T23:35Z] INFO  16:35:50,164 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:35Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-13_101890105_115169878-prep.bam
[2016-04-14T23:35Z] GATK RealignerTargetCreator: R14-18102_kapa-NGv3-PE100-NGv3-sort-14_50585061_66096324-prep-prealign.bam 14:50585062-66096324
[2016-04-14T23:35Z] GATK: RealignerTargetCreator
[2016-04-14T23:35Z] GATK pre-alignment ('16', 0, 15528616) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:35Z] INFO  16:35:51,914 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:35Z] INFO  16:35:51,918 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:35Z] INFO  16:35:51,919 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:35Z] INFO  16:35:51,920 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:35Z] INFO  16:35:51,925 HelpFormatter - Program Args: -T PrintReads -L 15:98984300-102531392 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/15/tx/tmprqNLvt/R14-18102_kapa-NGv3-PE100-NGv3-sort-15_98984299_102531392-prep-prealign.bam
[2016-04-14T23:35Z] INFO  16:35:51,945 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:35Z] INFO  16:35:51,946 HelpFormatter - Date/Time: 2016/04/14 16:35:51
[2016-04-14T23:35Z] INFO  16:35:51,947 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:35Z] INFO  16:35:51,947 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:35Z] INFO  16:35:52,218 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:35Z] INFO  16:35:53,144 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:35Z] INFO  16:35:53,147 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:35Z] INFO  16:35:53,148 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:35Z] INFO  16:35:53,148 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:35Z] INFO  16:35:53,153 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/14/R14-18102_kapa-NGv3-PE100-NGv3-sort-14_35072553_50583270-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/14/R14-18102_kapa-NGv3-PE100-NGv3-sort-14_35072553_50583270-prep-prealign-realign.intervals -L 14:35072554-50583270 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/14/tx/tmpkG_27F/R14-18102_kapa-NGv3-PE100-NGv3-sort-14_35072553_50583270-prep.bam
[2016-04-14T23:35Z] INFO  16:35:53,165 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:35Z] INFO  16:35:53,166 HelpFormatter - Date/Time: 2016/04/14 16:35:53
[2016-04-14T23:35Z] INFO  16:35:53,166 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:35Z] INFO  16:35:53,167 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:35Z] INFO  16:35:53,352 ProgressMeter -            done    905434.0    56.0 s      61.0 s      100.0%    56.0 s       0.0 s
[2016-04-14T23:35Z] INFO  16:35:53,353 ProgressMeter - Total runtime 56.10 secs, 0.93 min, 0.02 hours
[2016-04-14T23:35Z] INFO  16:35:53,357 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 905434 total reads (0.00%)
[2016-04-14T23:35Z] INFO  16:35:53,357 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:35Z] INFO  16:35:53,357 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:35Z] INFO  16:35:53,358 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:35Z] INFO  16:35:53,417 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:35Z] INFO  16:35:53,489 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-14T23:35Z] INFO  16:35:53,497 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@7172f77a
[2016-04-14T23:35Z] INFO  16:35:53,549 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:35Z] INFO  16:35:53,551 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:35Z] INFO  16:35:53,558 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:35Z] INFO  16:35:53,560 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:35Z] INFO  16:35:53,579 ProgressMeter -            done    329348.0    40.0 s       2.1 m       99.3%    40.0 s       0.0 s
[2016-04-14T23:35Z] INFO  16:35:53,580 ProgressMeter - Total runtime 40.88 secs, 0.68 min, 0.01 hours
[2016-04-14T23:35Z] INFO  16:35:53,580 MicroScheduler - 323 reads were filtered out during the traversal out of approximately 329671 total reads (0.10%)
[2016-04-14T23:35Z] INFO  16:35:53,580 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:35Z] INFO  16:35:53,581 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:35Z] INFO  16:35:53,581 MicroScheduler -   -> 323 reads (0.10% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:35Z] INFO  16:35:53,602 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.04
[2016-04-14T23:35Z] INFO  16:35:53,602 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.04
[2016-04-14T23:35Z] INFO  16:35:53,628 IntervalUtils - Processing 3547093 bp from intervals
[2016-04-14T23:35Z] INFO  16:35:53,750 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:35Z] INFO  16:35:53,987 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:35Z] INFO  16:35:53,988 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:35Z] INFO  16:35:53,989 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:35Z] INFO  16:35:53,990 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:35Z] INFO  16:35:54,030 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:35Z] INFO  16:35:54,055 IntervalUtils - Processing 15510717 bp from intervals
[2016-04-14T23:35Z] WARN  16:35:54,060 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:35Z] INFO  16:35:54,092 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:35Z] INFO  16:35:54,172 ProgressMeter -     15:42137041    100001.0    30.0 s       5.1 m       33.8%    88.0 s      58.0 s
[2016-04-14T23:35Z] INFO  16:35:54,177 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:35Z] INFO  16:35:54,277 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:35Z] INFO  16:35:54,278 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:35Z] INFO  16:35:54,279 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:35Z] INFO  16:35:54,280 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:35Z] INFO  16:35:54,385 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:35Z] INFO  16:35:54,388 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:35Z] INFO  16:35:54,389 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:35Z] INFO  16:35:54,389 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:35Z] INFO  16:35:54,393 HelpFormatter - Program Args: -T PrintReads -L 16:1-15528616 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/16/tx/tmpWSQdkk/R14-18102_kapa-NGv3-PE100-NGv3-sort-16_0_15528616-prep-prealign.bam
[2016-04-14T23:35Z] INFO  16:35:54,406 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:35Z] INFO  16:35:54,408 HelpFormatter - Date/Time: 2016/04/14 16:35:54
[2016-04-14T23:35Z] INFO  16:35:54,409 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:35Z] INFO  16:35:54,414 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:35Z] INFO  16:35:54,463 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:35Z] INFO  16:35:54,525 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:35Z] INFO  16:35:54,528 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:35Z] INFO  16:35:54,529 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:35Z] INFO  16:35:54,529 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:35Z] INFO  16:35:54,533 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/14/R14-18102_kapa-NGv3-PE100-NGv3-sort-14_50585061_66096324-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/14/tx/tmpIvC2M3/R14-18102_kapa-NGv3-PE100-NGv3-sort-14_50585061_66096324-prep-prealign-realign.intervals -l INFO -L 14:50585062-66096324 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-14T23:35Z] INFO  16:35:54,559 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:35Z] INFO  16:35:54,560 HelpFormatter - Date/Time: 2016/04/14 16:35:54
[2016-04-14T23:35Z] INFO  16:35:54,561 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:35Z] INFO  16:35:54,565 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:35Z] INFO  16:35:54,610 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:35Z] INFO  16:35:54,649 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:35Z] INFO  16:35:54,657 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:35Z] INFO  16:35:54,870 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-14T23:35Z] INFO  16:35:54,880 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:35Z] INFO  16:35:54,959 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-14T23:35Z] INFO  16:35:54,963 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:35Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-11_62744265_78270665-prep.bam
[2016-04-14T23:35Z] INFO  16:35:55,106 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:35Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-14_97304098_107349540-prep-prealign.bam
[2016-04-14T23:35Z] INFO  16:35:55,278 IntervalUtils - Processing 15511263 bp from intervals
[2016-04-14T23:35Z] WARN  16:35:55,360 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:35Z] INFO  16:35:55,489 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:35Z] INFO  16:35:55,670 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:35Z] INFO  16:35:55,671 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:35Z] INFO  16:35:55,672 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:35Z] INFO  16:35:55,673 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-14T23:35Z] INFO  16:35:55,920 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-14T23:35Z] INFO  16:35:55,988 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:35Z] INFO  16:35:55,999 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:35Z] INFO  16:35:56,064 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-14T23:35Z] INFO  16:35:56,078 IntervalUtils - Processing 15528616 bp from intervals
[2016-04-14T23:35Z] INFO  16:35:56,165 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:35Z] GATK RealignerTargetCreator: R14-18102_kapa-NGv3-PE100-NGv3-sort-14_97304098_107349540-prep-prealign.bam 14:97304099-107349540
[2016-04-14T23:35Z] GATK: RealignerTargetCreator
[2016-04-14T23:35Z] INFO  16:35:56,446 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:35Z] INFO  16:35:56,448 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:35Z] INFO  16:35:56,448 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:35Z] INFO  16:35:56,449 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:35Z] INFO  16:35:56,465 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:35Z] INFO  16:35:56,620 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:35Z] GATK pre-alignment ('16', 15596122, 31106473) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:35Z] INFO  16:35:59,076 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:35Z] INFO  16:35:59,079 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:35Z] INFO  16:35:59,080 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:35Z] INFO  16:35:59,080 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:35Z] INFO  16:35:59,085 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/14/R14-18102_kapa-NGv3-PE100-NGv3-sort-14_97304098_107349540-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/14/tx/tmpqfYQ7M/R14-18102_kapa-NGv3-PE100-NGv3-sort-14_97304098_107349540-prep-prealign-realign.intervals -l INFO -L 14:97304099-107349540 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-14T23:35Z] INFO  16:35:59,094 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:35Z] INFO  16:35:59,095 HelpFormatter - Date/Time: 2016/04/14 16:35:59
[2016-04-14T23:35Z] INFO  16:35:59,095 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:35Z] INFO  16:35:59,095 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:35Z] INFO  16:35:59,223 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:35Z] INFO  16:35:59,484 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-14T23:35Z] INFO  16:35:59,504 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:35Z] INFO  16:35:59,584 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-14T23:36Z] INFO  16:36:00,022 IntervalUtils - Processing 10045442 bp from intervals
[2016-04-14T23:36Z] WARN  16:36:00,027 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:36Z] INFO  16:36:00,119 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@41fd9d8e
[2016-04-14T23:36Z] INFO  16:36:00,121 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:36Z] INFO  16:36:00,219 ProgressMeter -     15:63353879    100001.0    30.0 s       5.0 m       70.6%    42.0 s      12.0 s
[2016-04-14T23:36Z] INFO  16:36:00,261 ProgressMeter -            done    384040.0    47.0 s       2.1 m       99.8%    47.0 s       0.0 s
[2016-04-14T23:36Z] INFO  16:36:00,262 ProgressMeter - Total runtime 47.98 secs, 0.80 min, 0.01 hours
[2016-04-14T23:36Z] INFO  16:36:00,262 MicroScheduler - 224 reads were filtered out during the traversal out of approximately 384264 total reads (0.06%)
[2016-04-14T23:36Z] INFO  16:36:00,262 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:36Z] INFO  16:36:00,263 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:36Z] INFO  16:36:00,263 MicroScheduler -   -> 224 reads (0.06% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:36Z] INFO  16:36:00,403 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:36Z] INFO  16:36:00,415 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:36Z] INFO  16:36:00,416 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:36Z] INFO  16:36:00,417 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-14T23:36Z] INFO  16:36:00,824 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:36Z] INFO  16:36:00,828 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:36Z] INFO  16:36:00,829 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:36Z] INFO  16:36:00,829 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:36Z] INFO  16:36:00,834 HelpFormatter - Program Args: -T PrintReads -L 16:15596123-31106473 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/16/tx/tmpIYF6zt/R14-18102_kapa-NGv3-PE100-NGv3-sort-16_15596122_31106473-prep-prealign.bam
[2016-04-14T23:36Z] INFO  16:36:00,850 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:36Z] INFO  16:36:00,851 HelpFormatter - Date/Time: 2016/04/14 16:36:00
[2016-04-14T23:36Z] INFO  16:36:00,852 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:36Z] INFO  16:36:00,853 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:36Z] INFO  16:36:01,043 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:36Z] INFO  16:36:01,718 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:36Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-14_66135960_81646674-prep-prealign.bam
[2016-04-14T23:36Z] INFO  16:36:02,183 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-14T23:36Z] INFO  16:36:02,277 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:36Z] INFO  16:36:02,292 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:36Z] INFO  16:36:02,359 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-14T23:36Z] INFO  16:36:02,391 IntervalUtils - Processing 15510351 bp from intervals
[2016-04-14T23:36Z] INFO  16:36:02,524 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:36Z] INFO  16:36:02,814 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:36Z] INFO  16:36:02,815 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:36Z] INFO  16:36:02,816 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:36Z] INFO  16:36:02,817 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:36Z] INFO  16:36:02,855 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:36Z] GATK RealignerTargetCreator: R14-18102_kapa-NGv3-PE100-NGv3-sort-14_66135960_81646674-prep-prealign.bam 14:66135961-81646674
[2016-04-14T23:36Z] GATK: RealignerTargetCreator
[2016-04-14T23:36Z] INFO  16:36:03,105 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:36Z] INFO  16:36:03,308 ProgressMeter -     15:74495493    200002.0    30.0 s       2.5 m       42.3%    70.0 s      40.0 s
[2016-04-14T23:36Z] INFO  16:36:05,646 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:36Z] INFO  16:36:05,650 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:36Z] INFO  16:36:05,650 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:36Z] INFO  16:36:05,651 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:36Z] INFO  16:36:05,655 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/14/R14-18102_kapa-NGv3-PE100-NGv3-sort-14_66135960_81646674-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/14/tx/tmpS93UIz/R14-18102_kapa-NGv3-PE100-NGv3-sort-14_66135960_81646674-prep-prealign-realign.intervals -l INFO -L 14:66135961-81646674 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-14T23:36Z] INFO  16:36:05,673 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:36Z] INFO  16:36:05,674 HelpFormatter - Date/Time: 2016/04/14 16:36:05
[2016-04-14T23:36Z] INFO  16:36:05,675 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:36Z] INFO  16:36:05,675 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:36Z] INFO  16:36:05,780 ProgressMeter -            done    126949.0    11.0 s      90.0 s      100.0%    11.0 s       0.0 s
[2016-04-14T23:36Z] INFO  16:36:05,781 ProgressMeter - Total runtime 11.50 secs, 0.19 min, 0.00 hours
[2016-04-14T23:36Z] INFO  16:36:05,785 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 126949 total reads (0.00%)
[2016-04-14T23:36Z] INFO  16:36:05,785 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:36Z] INFO  16:36:05,785 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:36Z] INFO  16:36:05,786 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:36Z] INFO  16:36:05,793 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:36Z] INFO  16:36:05,829 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@41fd9d8e
[2016-04-14T23:36Z] INFO  16:36:05,921 ProgressMeter -            done    510672.0    78.0 s       2.6 m      100.0%    78.0 s       0.0 s
[2016-04-14T23:36Z] INFO  16:36:05,921 ProgressMeter - Total runtime 78.19 secs, 1.30 min, 0.02 hours
[2016-04-14T23:36Z] INFO  16:36:05,922 MicroScheduler - 209 reads were filtered out during the traversal out of approximately 510881 total reads (0.04%)
[2016-04-14T23:36Z] INFO  16:36:05,922 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:36Z] INFO  16:36:05,923 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:36Z] INFO  16:36:05,923 MicroScheduler -   -> 209 reads (0.04% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:36Z] INFO  16:36:05,985 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-14T23:36Z] INFO  16:36:05,999 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:36Z] INFO  16:36:06,062 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-14T23:36Z] INFO  16:36:06,100 ProgressMeter -     15:90380971    200002.0    30.0 s       2.5 m       44.6%    67.0 s      37.0 s
[2016-04-14T23:36Z] INFO  16:36:06,357 IntervalUtils - Processing 15510714 bp from intervals
[2016-04-14T23:36Z] WARN  16:36:06,363 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:36Z] INFO  16:36:06,484 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:36Z] INFO  16:36:06,663 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:36Z] INFO  16:36:06,664 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:36Z] INFO  16:36:06,665 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:36Z] INFO  16:36:06,665 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-14T23:36Z] INFO  16:36:07,183 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:36Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-14_35072553_50583270-prep.bam
[2016-04-14T23:36Z] INFO  16:36:07,300 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@41fd9d8e
[2016-04-14T23:36Z] INFO  16:36:07,347 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:36Z] INFO  16:36:07,376 ProgressMeter -            done     85493.0    13.0 s       2.6 m       99.6%    13.0 s       0.0 s
[2016-04-14T23:36Z] INFO  16:36:07,376 ProgressMeter - Total runtime 13.39 secs, 0.22 min, 0.00 hours
[2016-04-14T23:36Z] INFO  16:36:07,377 MicroScheduler - 52 reads were filtered out during the traversal out of approximately 85545 total reads (0.06%)
[2016-04-14T23:36Z] INFO  16:36:07,377 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:36Z] INFO  16:36:07,377 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:36Z] INFO  16:36:07,378 MicroScheduler -   -> 52 reads (0.06% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:36Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-14_19553416_35066851-prep-prealign.bam
[2016-04-14T23:36Z] GATK pre-alignment ('16', 31120544, 46629582) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:36Z] INFO  16:36:08,806 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:36Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-15_98984299_102531392-prep-prealign.bam
[2016-04-14T23:36Z] GATK RealignerTargetCreator: R14-18102_kapa-NGv3-PE100-NGv3-sort-14_19553416_35066851-prep-prealign.bam 14:19553417-35066851
[2016-04-14T23:36Z] GATK: RealignerTargetCreator
[2016-04-14T23:36Z] GATK RealignerTargetCreator: R14-18102_kapa-NGv3-PE100-NGv3-sort-15_98984299_102531392-prep-prealign.bam 15:98984300-102531392
[2016-04-14T23:36Z] GATK: RealignerTargetCreator
[2016-04-14T23:36Z] INFO  16:36:10,046 ProgressMeter -     12:53457022    400006.0    30.0 s      75.0 s       42.1%    71.0 s      41.0 s
[2016-04-14T23:36Z] INFO  16:36:10,768 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:36Z] INFO  16:36:10,771 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:36Z] INFO  16:36:10,772 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:36Z] INFO  16:36:10,773 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:36Z] INFO  16:36:10,777 HelpFormatter - Program Args: -T PrintReads -L 16:31120545-46629582 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/16/tx/tmpEOtv1Z/R14-18102_kapa-NGv3-PE100-NGv3-sort-16_31120544_46629582-prep-prealign.bam
[2016-04-14T23:36Z] INFO  16:36:10,787 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:36Z] INFO  16:36:10,797 HelpFormatter - Date/Time: 2016/04/14 16:36:10
[2016-04-14T23:36Z] INFO  16:36:10,798 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:36Z] INFO  16:36:10,799 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:36Z] INFO  16:36:10,802 ProgressMeter -            done   1.5648094E7    20.0 s       1.0 s      100.0%    20.0 s       0.0 s
[2016-04-14T23:36Z] INFO  16:36:10,803 ProgressMeter - Total runtime 20.70 secs, 0.35 min, 0.01 hours
[2016-04-14T23:36Z] INFO  16:36:10,807 MicroScheduler - 20674 reads were filtered out during the traversal out of approximately 248396 total reads (8.32%)
[2016-04-14T23:36Z] INFO  16:36:10,808 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:36Z] INFO  16:36:10,809 MicroScheduler -   -> 669 reads (0.27% of total) failing BadMateFilter
[2016-04-14T23:36Z] INFO  16:36:10,810 MicroScheduler -   -> 19468 reads (7.84% of total) failing DuplicateReadFilter
[2016-04-14T23:36Z] INFO  16:36:10,810 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-14T23:36Z] INFO  16:36:10,811 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:36Z] INFO  16:36:10,812 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-14T23:36Z] INFO  16:36:10,812 MicroScheduler -   -> 537 reads (0.22% of total) failing MappingQualityZeroFilter
[2016-04-14T23:36Z] INFO  16:36:10,813 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:36Z] INFO  16:36:10,814 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-14T23:36Z] INFO  16:36:10,814 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-14T23:36Z] INFO  16:36:11,041 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:36Z] INFO  16:36:12,009 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:36Z] INFO  16:36:12,012 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:36Z] INFO  16:36:12,013 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:36Z] INFO  16:36:12,013 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:36Z] INFO  16:36:12,018 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/14/R14-18102_kapa-NGv3-PE100-NGv3-sort-14_19553416_35066851-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/14/tx/tmp_XBZxg/R14-18102_kapa-NGv3-PE100-NGv3-sort-14_19553416_35066851-prep-prealign-realign.intervals -l INFO -L 14:19553417-35066851 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-14T23:36Z] INFO  16:36:12,028 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:36Z] INFO  16:36:12,039 HelpFormatter - Date/Time: 2016/04/14 16:36:12
[2016-04-14T23:36Z] INFO  16:36:12,039 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:36Z] INFO  16:36:12,040 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:36Z] INFO  16:36:12,062 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:36Z] INFO  16:36:12,071 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-14T23:36Z] GATK: realign ('14', 81651874, 97299968) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:36Z] INFO  16:36:12,131 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:36Z] INFO  16:36:12,150 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:36Z] INFO  16:36:12,155 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:36Z] INFO  16:36:12,207 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-14T23:36Z] INFO  16:36:12,222 IntervalUtils - Processing 15509038 bp from intervals
[2016-04-14T23:36Z] INFO  16:36:12,254 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:36Z] INFO  16:36:12,257 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:36Z] INFO  16:36:12,258 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:36Z] INFO  16:36:12,259 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:36Z] INFO  16:36:12,263 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/15/R14-18102_kapa-NGv3-PE100-NGv3-sort-15_98984299_102531392-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/15/tx/tmpmWlotD/R14-18102_kapa-NGv3-PE100-NGv3-sort-15_98984299_102531392-prep-prealign-realign.intervals -l INFO -L 15:98984300-102531392 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-14T23:36Z] INFO  16:36:12,288 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:36Z] INFO  16:36:12,288 HelpFormatter - Date/Time: 2016/04/14 16:36:12
[2016-04-14T23:36Z] INFO  16:36:12,288 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:36Z] INFO  16:36:12,289 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:36Z] INFO  16:36:12,307 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:36Z] INFO  16:36:12,381 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:36Z] INFO  16:36:12,410 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-14T23:36Z] INFO  16:36:12,420 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:36Z] INFO  16:36:12,483 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-14T23:36Z] INFO  16:36:12,650 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:36Z] INFO  16:36:12,651 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:36Z] INFO  16:36:12,651 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:36Z] INFO  16:36:12,652 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:36Z] INFO  16:36:12,653 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-14T23:36Z] INFO  16:36:12,663 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:36Z] INFO  16:36:12,676 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:36Z] INFO  16:36:12,706 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.04
[2016-04-14T23:36Z] INFO  16:36:12,782 IntervalUtils - Processing 15513435 bp from intervals
[2016-04-14T23:36Z] WARN  16:36:12,787 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:36Z] INFO  16:36:12,798 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:36Z] INFO  16:36:12,918 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:36Z] INFO  16:36:12,944 IntervalUtils - Processing 3547093 bp from intervals
[2016-04-14T23:36Z] WARN  16:36:12,949 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:36Z] INFO  16:36:13,022 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:36Z] INFO  16:36:13,105 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:36Z] INFO  16:36:13,106 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:36Z] INFO  16:36:13,107 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:36Z] INFO  16:36:13,108 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-14T23:36Z] INFO  16:36:13,214 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:36Z] INFO  16:36:13,246 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:36Z] INFO  16:36:13,247 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:36Z] INFO  16:36:13,248 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-14T23:36Z] INFO  16:36:15,044 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:36Z] INFO  16:36:15,047 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:36Z] INFO  16:36:15,048 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:36Z] INFO  16:36:15,049 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:36Z] INFO  16:36:15,053 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/14/R14-18102_kapa-NGv3-PE100-NGv3-sort-14_81651874_97299968-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/14/R14-18102_kapa-NGv3-PE100-NGv3-sort-14_81651874_97299968-prep-prealign-realign.intervals -L 14:81651875-97299968 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/14/tx/tmpwMKts3/R14-18102_kapa-NGv3-PE100-NGv3-sort-14_81651874_97299968-prep.bam
[2016-04-14T23:36Z] INFO  16:36:15,062 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:36Z] INFO  16:36:15,073 HelpFormatter - Date/Time: 2016/04/14 16:36:15
[2016-04-14T23:36Z] INFO  16:36:15,074 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:36Z] INFO  16:36:15,075 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:36Z] INFO  16:36:15,257 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:36Z] INFO  16:36:15,368 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:36Z] INFO  16:36:15,377 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:36Z] INFO  16:36:15,438 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-14T23:36Z] INFO  16:36:15,822 IntervalUtils - Processing 15648094 bp from intervals
[2016-04-14T23:36Z] WARN  16:36:15,827 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:36Z] INFO  16:36:15,911 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:36Z] INFO  16:36:16,046 ProgressMeter -            done   1.5511263E7    20.0 s       1.0 s      100.0%    20.0 s       0.0 s
[2016-04-14T23:36Z] INFO  16:36:16,046 ProgressMeter - Total runtime 20.38 secs, 0.34 min, 0.01 hours
[2016-04-14T23:36Z] INFO  16:36:16,050 MicroScheduler - 25017 reads were filtered out during the traversal out of approximately 296693 total reads (8.43%)
[2016-04-14T23:36Z] INFO  16:36:16,051 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:36Z] INFO  16:36:16,052 MicroScheduler -   -> 741 reads (0.25% of total) failing BadMateFilter
[2016-04-14T23:36Z] INFO  16:36:16,052 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:36Z] INFO  16:36:16,052 MicroScheduler -   -> 23679 reads (7.98% of total) failing DuplicateReadFilter
[2016-04-14T23:36Z] INFO  16:36:16,053 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-14T23:36Z] INFO  16:36:16,054 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:36Z] INFO  16:36:16,054 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-14T23:36Z] INFO  16:36:16,055 MicroScheduler -   -> 597 reads (0.20% of total) failing MappingQualityZeroFilter
[2016-04-14T23:36Z] INFO  16:36:16,056 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:36Z] INFO  16:36:16,056 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-14T23:36Z] INFO  16:36:16,056 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:36Z] INFO  16:36:16,057 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:36Z] INFO  16:36:16,057 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-14T23:36Z] INFO  16:36:16,058 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:36Z] INFO  16:36:16,206 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:36Z] INFO  16:36:16,427 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:36Z] INFO  16:36:17,367 ProgressMeter -            done   1.0045442E7    16.0 s       1.0 s      100.0%    16.0 s       0.0 s
[2016-04-14T23:36Z] INFO  16:36:17,368 ProgressMeter - Total runtime 16.95 secs, 0.28 min, 0.00 hours
[2016-04-14T23:36Z] INFO  16:36:17,371 MicroScheduler - 29298 reads were filtered out during the traversal out of approximately 330934 total reads (8.85%)
[2016-04-14T23:36Z] INFO  16:36:17,372 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:36Z] INFO  16:36:17,372 MicroScheduler -   -> 787 reads (0.24% of total) failing BadMateFilter
[2016-04-14T23:36Z] INFO  16:36:17,373 MicroScheduler -   -> 27276 reads (8.24% of total) failing DuplicateReadFilter
[2016-04-14T23:36Z] INFO  16:36:17,373 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-14T23:36Z] INFO  16:36:17,373 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:36Z] INFO  16:36:17,373 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-14T23:36Z] INFO  16:36:17,374 MicroScheduler -   -> 1235 reads (0.37% of total) failing MappingQualityZeroFilter
[2016-04-14T23:36Z] INFO  16:36:17,374 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:36Z] INFO  16:36:17,374 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-14T23:36Z] INFO  16:36:17,374 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-14T23:36Z] INFO  16:36:17,419 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:36Z] GATK: realign ('14', 50585061, 66096324) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:36Z] INFO  16:36:17,607 ProgressMeter -     15:34640455    400007.0    60.0 s       2.5 m       86.2%    69.0 s       9.0 s
[2016-04-14T23:36Z] INFO  16:36:18,690 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@41fd9d8e
[2016-04-14T23:36Z] INFO  16:36:18,770 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:36Z] INFO  16:36:18,801 ProgressMeter -            done    339405.0    42.0 s       2.1 m      100.0%    42.0 s       0.0 s
[2016-04-14T23:36Z] GATK: realign ('14', 97304098, 107349540) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:36Z] INFO  16:36:18,802 ProgressMeter - Total runtime 42.71 secs, 0.71 min, 0.01 hours
[2016-04-14T23:36Z] INFO  16:36:18,803 MicroScheduler - 150 reads were filtered out during the traversal out of approximately 339555 total reads (0.04%)
[2016-04-14T23:36Z] INFO  16:36:18,803 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:36Z] INFO  16:36:18,804 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:36Z] INFO  16:36:18,805 MicroScheduler -   -> 150 reads (0.04% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:36Z] INFO  16:36:20,086 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:36Z] INFO  16:36:20,091 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:36Z] INFO  16:36:20,091 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:36Z] INFO  16:36:20,092 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:36Z] INFO  16:36:20,096 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/14/R14-18102_kapa-NGv3-PE100-NGv3-sort-14_50585061_66096324-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/14/R14-18102_kapa-NGv3-PE100-NGv3-sort-14_50585061_66096324-prep-prealign-realign.intervals -L 14:50585062-66096324 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/14/tx/tmpLdc2qX/R14-18102_kapa-NGv3-PE100-NGv3-sort-14_50585061_66096324-prep.bam
[2016-04-14T23:36Z] INFO  16:36:20,109 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:36Z] INFO  16:36:20,110 HelpFormatter - Date/Time: 2016/04/14 16:36:20
[2016-04-14T23:36Z] INFO  16:36:20,110 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:36Z] INFO  16:36:20,110 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:36Z] INFO  16:36:20,200 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:36Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-15_83448996_98982979-prep-prealign.bam
[2016-04-14T23:36Z] INFO  16:36:20,299 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:36Z] INFO  16:36:20,439 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:36Z] INFO  16:36:20,448 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:36Z] INFO  16:36:20,511 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-14T23:36Z] INFO  16:36:20,600 ProgressMeter -            done   3547093.0     7.0 s       2.0 s      100.0%     7.0 s       0.0 s
[2016-04-14T23:36Z] INFO  16:36:20,601 ProgressMeter - Total runtime 7.36 secs, 0.12 min, 0.00 hours
[2016-04-14T23:36Z] INFO  16:36:20,605 MicroScheduler - 12568 reads were filtered out during the traversal out of approximately 86309 total reads (14.56%)
[2016-04-14T23:36Z] INFO  16:36:20,606 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:36Z] INFO  16:36:20,607 MicroScheduler -   -> 204 reads (0.24% of total) failing BadMateFilter
[2016-04-14T23:36Z] INFO  16:36:20,607 MicroScheduler -   -> 6280 reads (7.28% of total) failing DuplicateReadFilter
[2016-04-14T23:36Z] INFO  16:36:20,608 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-14T23:36Z] INFO  16:36:20,609 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:36Z] INFO  16:36:20,609 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-14T23:36Z] INFO  16:36:20,610 MicroScheduler -   -> 6084 reads (7.05% of total) failing MappingQualityZeroFilter
[2016-04-14T23:36Z] INFO  16:36:20,610 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:36Z] INFO  16:36:20,611 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-14T23:36Z] INFO  16:36:20,612 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-14T23:36Z] INFO  16:36:20,844 IntervalUtils - Processing 15511263 bp from intervals
[2016-04-14T23:36Z] WARN  16:36:20,850 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:36Z] INFO  16:36:20,917 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:36Z] INFO  16:36:21,038 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:36Z] INFO  16:36:21,039 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:36Z] INFO  16:36:21,040 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:36Z] INFO  16:36:21,041 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:36Z] INFO  16:36:21,207 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:36Z] INFO  16:36:21,227 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@7172f77a
[2016-04-14T23:36Z] INFO  16:36:21,276 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@32d5a4c6
[2016-04-14T23:36Z] INFO  16:36:21,352 ProgressMeter -            done    356017.0    51.0 s       2.4 m      100.0%    51.0 s       0.0 s
[2016-04-14T23:36Z] INFO  16:36:21,352 ProgressMeter - Total runtime 51.17 secs, 0.85 min, 0.01 hours
[2016-04-14T23:36Z] INFO  16:36:21,353 MicroScheduler - 185 reads were filtered out during the traversal out of approximately 356202 total reads (0.05%)
[2016-04-14T23:36Z] INFO  16:36:21,353 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:36Z] INFO  16:36:21,354 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:36Z] INFO  16:36:21,354 MicroScheduler -   -> 185 reads (0.05% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:36Z] INFO  16:36:21,359 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:36Z] INFO  16:36:21,379 ProgressMeter -            done    524432.0    63.0 s       2.0 m      100.0%    63.0 s       0.0 s
[2016-04-14T23:36Z] INFO  16:36:21,379 ProgressMeter - Total runtime 63.91 secs, 1.07 min, 0.02 hours
[2016-04-14T23:36Z] INFO  16:36:21,380 MicroScheduler - 215 reads were filtered out during the traversal out of approximately 524647 total reads (0.04%)
[2016-04-14T23:36Z] INFO  16:36:21,380 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:36Z] INFO  16:36:21,381 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:36Z] INFO  16:36:21,381 MicroScheduler -   -> 215 reads (0.04% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:36Z] GATK RealignerTargetCreator: R14-18102_kapa-NGv3-PE100-NGv3-sort-15_83448996_98982979-prep-prealign.bam 15:83448997-98982979
[2016-04-14T23:36Z] GATK: RealignerTargetCreator
[2016-04-14T23:36Z] INFO  16:36:21,721 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:36Z] INFO  16:36:21,724 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:36Z] INFO  16:36:21,725 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:36Z] INFO  16:36:21,725 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:36Z] INFO  16:36:21,730 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/14/R14-18102_kapa-NGv3-PE100-NGv3-sort-14_97304098_107349540-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/14/R14-18102_kapa-NGv3-PE100-NGv3-sort-14_97304098_107349540-prep-prealign-realign.intervals -L 14:97304099-107349540 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/14/tx/tmp8TGq_5/R14-18102_kapa-NGv3-PE100-NGv3-sort-14_97304098_107349540-prep.bam
[2016-04-14T23:36Z] INFO  16:36:21,762 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:36Z] INFO  16:36:21,763 HelpFormatter - Date/Time: 2016/04/14 16:36:21
[2016-04-14T23:36Z] INFO  16:36:21,764 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:36Z] INFO  16:36:21,764 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:36Z] INFO  16:36:21,947 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:36Z] INFO  16:36:22,066 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:36Z] INFO  16:36:22,075 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:36Z] INFO  16:36:22,116 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:36Z] GATK: realign ('15', 98984299, 102531392) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:36Z] INFO  16:36:22,148 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-14T23:36Z] INFO  16:36:22,668 IntervalUtils - Processing 10045442 bp from intervals
[2016-04-14T23:36Z] WARN  16:36:22,673 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:36Z] INFO  16:36:22,689 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:36Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-15_52404364_67923265-prep-prealign.bam
[2016-04-14T23:36Z] INFO  16:36:22,763 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:36Z] INFO  16:36:22,891 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:36Z] INFO  16:36:22,899 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:36Z] INFO  16:36:22,902 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:36Z] INFO  16:36:22,903 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:36Z] INFO  16:36:22,948 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:36Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-15_20741621_36872162-prep-prealign.bam
[2016-04-14T23:36Z] INFO  16:36:23,028 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:36Z] INFO  16:36:23,121 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:36Z] INFO  16:36:23,252 ProgressMeter -    12:122958856    400009.0    34.0 s      85.0 s       85.4%    39.0 s       5.0 s
[2016-04-14T23:36Z] GATK RealignerTargetCreator: R14-18102_kapa-NGv3-PE100-NGv3-sort-15_52404364_67923265-prep-prealign.bam 15:52404365-67923265
[2016-04-14T23:36Z] GATK: RealignerTargetCreator
[2016-04-14T23:36Z] INFO  16:36:23,989 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:36Z] INFO  16:36:23,991 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:36Z] INFO  16:36:23,991 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:36Z] INFO  16:36:23,991 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:36Z] INFO  16:36:23,996 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/15/R14-18102_kapa-NGv3-PE100-NGv3-sort-15_83448996_98982979-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/15/tx/tmpWOhXoj/R14-18102_kapa-NGv3-PE100-NGv3-sort-15_83448996_98982979-prep-prealign-realign.intervals -l INFO -L 15:83448997-98982979 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-14T23:36Z] INFO  16:36:24,014 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:36Z] INFO  16:36:24,015 HelpFormatter - Date/Time: 2016/04/14 16:36:23
[2016-04-14T23:36Z] INFO  16:36:24,016 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:36Z] INFO  16:36:24,016 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:36Z] INFO  16:36:24,173 ProgressMeter -     15:44069078    300004.0    60.0 s       3.4 m       46.3%     2.2 m      69.0 s
[2016-04-14T23:36Z] INFO  16:36:24,193 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:36Z] INFO  16:36:24,488 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-14T23:36Z] INFO  16:36:24,513 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:36Z] INFO  16:36:24,593 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-14T23:36Z] GATK RealignerTargetCreator: R14-18102_kapa-NGv3-PE100-NGv3-sort-15_20741621_36872162-prep-prealign.bam 15:20741622-36872162
[2016-04-14T23:36Z] GATK: RealignerTargetCreator
[2016-04-14T23:36Z] INFO  16:36:24,870 IntervalUtils - Processing 15533983 bp from intervals
[2016-04-14T23:36Z] WARN  16:36:24,876 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:36Z] INFO  16:36:24,973 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:36Z] INFO  16:36:24,992 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:36Z] INFO  16:36:24,996 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:36Z] INFO  16:36:24,996 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:36Z] INFO  16:36:24,997 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:36Z] INFO  16:36:25,002 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/15/R14-18102_kapa-NGv3-PE100-NGv3-sort-15_98984299_102531392-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/15/R14-18102_kapa-NGv3-PE100-NGv3-sort-15_98984299_102531392-prep-prealign-realign.intervals -L 15:98984300-102531392 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/15/tx/tmptGxVv4/R14-18102_kapa-NGv3-PE100-NGv3-sort-15_98984299_102531392-prep.bam
[2016-04-14T23:36Z] INFO  16:36:25,022 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:36Z] INFO  16:36:25,023 HelpFormatter - Date/Time: 2016/04/14 16:36:24
[2016-04-14T23:36Z] INFO  16:36:25,024 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:36Z] INFO  16:36:25,025 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:36Z] INFO  16:36:25,168 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:36Z] INFO  16:36:25,169 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:36Z] INFO  16:36:25,170 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:36Z] INFO  16:36:25,171 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-14T23:36Z] INFO  16:36:25,213 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:36Z] INFO  16:36:25,339 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:36Z] INFO  16:36:25,350 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:36Z] INFO  16:36:25,433 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-14T23:36Z] INFO  16:36:25,790 IntervalUtils - Processing 3547093 bp from intervals
[2016-04-14T23:36Z] WARN  16:36:25,794 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:36Z] INFO  16:36:25,877 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:36Z] INFO  16:36:25,960 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:36Z] INFO  16:36:25,961 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:36Z] INFO  16:36:25,961 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:36Z] INFO  16:36:25,962 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:36Z] INFO  16:36:26,053 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:36Z] INFO  16:36:26,091 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:36Z] INFO  16:36:26,468 ProgressMeter -      16:1507521    200002.0    30.0 s       2.5 m        9.7%     5.2 m       4.7 m
[2016-04-14T23:36Z] INFO  16:36:26,540 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:36Z] INFO  16:36:26,543 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:36Z] INFO  16:36:26,543 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:36Z] INFO  16:36:26,544 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:36Z] INFO  16:36:26,548 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/15/R14-18102_kapa-NGv3-PE100-NGv3-sort-15_52404364_67923265-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/15/tx/tmpcwRWd0/R14-18102_kapa-NGv3-PE100-NGv3-sort-15_52404364_67923265-prep-prealign-realign.intervals -l INFO -L 15:52404365-67923265 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-14T23:36Z] INFO  16:36:26,568 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:36Z] INFO  16:36:26,568 HelpFormatter - Date/Time: 2016/04/14 16:36:26
[2016-04-14T23:36Z] INFO  16:36:26,569 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:36Z] INFO  16:36:26,569 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:36Z] INFO  16:36:26,717 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:36Z] INFO  16:36:26,929 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-14T23:36Z] INFO  16:36:26,939 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:36Z] INFO  16:36:27,007 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-14T23:36Z] INFO  16:36:27,347 IntervalUtils - Processing 15518901 bp from intervals
[2016-04-14T23:36Z] WARN  16:36:27,356 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:36Z] INFO  16:36:27,468 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:36Z] INFO  16:36:27,628 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:36Z] INFO  16:36:27,629 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:36Z] INFO  16:36:27,630 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:36Z] INFO  16:36:27,631 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-14T23:36Z] INFO  16:36:27,746 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:36Z] INFO  16:36:27,750 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:36Z] INFO  16:36:27,750 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:36Z] INFO  16:36:27,751 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:36Z] INFO  16:36:27,755 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/15/R14-18102_kapa-NGv3-PE100-NGv3-sort-15_20741621_36872162-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/15/tx/tmpMs3RpN/R14-18102_kapa-NGv3-PE100-NGv3-sort-15_20741621_36872162-prep-prealign-realign.intervals -l INFO -L 15:20741622-36872162 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-14T23:36Z] INFO  16:36:27,765 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:36Z] INFO  16:36:27,776 HelpFormatter - Date/Time: 2016/04/14 16:36:27
[2016-04-14T23:36Z] INFO  16:36:27,777 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:36Z] INFO  16:36:27,778 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:36Z] INFO  16:36:27,893 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:36Z] INFO  16:36:28,175 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-14T23:36Z] INFO  16:36:28,185 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:36Z] INFO  16:36:28,283 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.10
[2016-04-14T23:36Z] INFO  16:36:28,521 ProgressMeter -            done   1.5510714E7    21.0 s       1.0 s      100.0%    21.0 s       0.0 s
[2016-04-14T23:36Z] INFO  16:36:28,522 ProgressMeter - Total runtime 21.86 secs, 0.36 min, 0.01 hours
[2016-04-14T23:36Z] INFO  16:36:28,525 MicroScheduler - 34227 reads were filtered out during the traversal out of approximately 386581 total reads (8.85%)
[2016-04-14T23:36Z] INFO  16:36:28,526 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:36Z] INFO  16:36:28,526 MicroScheduler -   -> 949 reads (0.25% of total) failing BadMateFilter
[2016-04-14T23:36Z] INFO  16:36:28,526 MicroScheduler -   -> 30774 reads (7.96% of total) failing DuplicateReadFilter
[2016-04-14T23:36Z] INFO  16:36:28,527 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-14T23:36Z] INFO  16:36:28,527 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:36Z] INFO  16:36:28,527 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-14T23:36Z] INFO  16:36:28,527 MicroScheduler -   -> 2504 reads (0.65% of total) failing MappingQualityZeroFilter
[2016-04-14T23:36Z] INFO  16:36:28,528 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:36Z] INFO  16:36:28,528 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-14T23:36Z] INFO  16:36:28,528 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-14T23:36Z] INFO  16:36:28,571 IntervalUtils - Processing 16130541 bp from intervals
[2016-04-14T23:36Z] WARN  16:36:28,576 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:36Z] INFO  16:36:28,641 ProgressMeter -            done    599937.0    39.0 s      66.0 s      100.0%    39.0 s       0.0 s
[2016-04-14T23:36Z] INFO  16:36:28,641 ProgressMeter - Total runtime 39.67 secs, 0.66 min, 0.01 hours
[2016-04-14T23:36Z] INFO  16:36:28,645 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 599937 total reads (0.00%)
[2016-04-14T23:36Z] INFO  16:36:28,645 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:36Z] INFO  16:36:28,646 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:36Z] INFO  16:36:28,646 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:36Z] INFO  16:36:28,646 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:36Z] INFO  16:36:28,883 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:36Z] INFO  16:36:28,884 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:36Z] INFO  16:36:28,884 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:36Z] INFO  16:36:28,884 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-14T23:36Z] INFO  16:36:29,675 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@41fd9d8e
[2016-04-14T23:36Z] INFO  16:36:29,741 ProgressMeter -            done    115619.0    17.0 s       2.5 m      100.0%    17.0 s       0.0 s
[2016-04-14T23:36Z] INFO  16:36:29,742 ProgressMeter - Total runtime 17.09 secs, 0.28 min, 0.00 hours
[2016-04-14T23:36Z] INFO  16:36:29,742 MicroScheduler - 140 reads were filtered out during the traversal out of approximately 115759 total reads (0.12%)
[2016-04-14T23:36Z] INFO  16:36:29,742 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:36Z] INFO  16:36:29,743 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:36Z] INFO  16:36:29,743 MicroScheduler -   -> 140 reads (0.12% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:36Z] INFO  16:36:29,866 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:36Z] GATK: realign ('14', 66135960, 81646674) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:36Z] INFO  16:36:31,000 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:36Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-12_109494486_125263132-prep.bam
[2016-04-14T23:36Z] INFO  16:36:31,207 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:36Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-16_31120544_46629582-prep-prealign.bam
[2016-04-14T23:36Z] GATK RealignerTargetCreator: R14-18102_kapa-NGv3-PE100-NGv3-sort-16_31120544_46629582-prep-prealign.bam 16:31120545-46629582
[2016-04-14T23:36Z] GATK: RealignerTargetCreator
[2016-04-14T23:36Z] INFO  16:36:32,835 ProgressMeter -     16:18911450    100001.0    30.0 s       5.0 m       21.4%     2.3 m     110.0 s
[2016-04-14T23:36Z] INFO  16:36:32,842 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:36Z] INFO  16:36:32,846 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:36Z] INFO  16:36:32,847 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:36Z] INFO  16:36:32,848 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:36Z] INFO  16:36:32,853 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/14/R14-18102_kapa-NGv3-PE100-NGv3-sort-14_66135960_81646674-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/14/R14-18102_kapa-NGv3-PE100-NGv3-sort-14_66135960_81646674-prep-prealign-realign.intervals -L 14:66135961-81646674 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/14/tx/tmpTbF6Gs/R14-18102_kapa-NGv3-PE100-NGv3-sort-14_66135960_81646674-prep.bam
[2016-04-14T23:36Z] INFO  16:36:32,864 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:36Z] INFO  16:36:32,865 HelpFormatter - Date/Time: 2016/04/14 16:36:32
[2016-04-14T23:36Z] INFO  16:36:32,866 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:36Z] INFO  16:36:32,867 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:36Z] GATK pre-alignment ('16', 46633742, 64982002) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:36Z] INFO  16:36:33,065 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:36Z] INFO  16:36:33,108 ProgressMeter -            done    867741.0    53.0 s      61.0 s      100.0%    53.0 s       0.0 s
[2016-04-14T23:36Z] INFO  16:36:33,108 ProgressMeter - Total runtime 53.08 secs, 0.88 min, 0.01 hours
[2016-04-14T23:36Z] INFO  16:36:33,112 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 867741 total reads (0.00%)
[2016-04-14T23:36Z] INFO  16:36:33,113 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:36Z] INFO  16:36:33,113 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:36Z] INFO  16:36:33,113 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:36Z] INFO  16:36:33,189 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:36Z] INFO  16:36:33,201 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:36Z] INFO  16:36:33,254 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-14T23:36Z] INFO  16:36:33,581 IntervalUtils - Processing 15510714 bp from intervals
[2016-04-14T23:36Z] WARN  16:36:33,586 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:36Z] INFO  16:36:33,672 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:36Z] INFO  16:36:33,781 ProgressMeter -     15:81426830    400004.0    60.0 s       2.5 m       87.0%    68.0 s       8.0 s
[2016-04-14T23:36Z] INFO  16:36:33,844 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:36Z] INFO  16:36:33,845 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:36Z] INFO  16:36:33,846 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:36Z] INFO  16:36:33,846 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:36Z] INFO  16:36:34,013 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:36Z] INFO  16:36:34,065 ProgressMeter -            done     85493.0     8.0 s      94.0 s       99.6%     8.0 s       0.0 s
[2016-04-14T23:36Z] INFO  16:36:34,066 ProgressMeter - Total runtime 8.11 secs, 0.14 min, 0.00 hours
[2016-04-14T23:36Z] INFO  16:36:34,069 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 85493 total reads (0.00%)
[2016-04-14T23:36Z] INFO  16:36:34,069 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:36Z] INFO  16:36:34,070 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:36Z] INFO  16:36:34,070 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:36Z] INFO  16:36:34,161 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:36Z] INFO  16:36:34,210 ProgressMeter -            done    247045.0    18.0 s      73.0 s      100.0%    18.0 s       0.0 s
[2016-04-14T23:36Z] INFO  16:36:34,210 ProgressMeter - Total runtime 18.15 secs, 0.30 min, 0.01 hours
[2016-04-14T23:36Z] INFO  16:36:34,214 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 247045 total reads (0.00%)
[2016-04-14T23:36Z] INFO  16:36:34,214 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:36Z] INFO  16:36:34,214 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:36Z] INFO  16:36:34,215 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:36Z] INFO  16:36:34,525 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:36Z] INFO  16:36:34,529 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:36Z] INFO  16:36:34,530 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:36Z] INFO  16:36:34,531 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:36Z] INFO  16:36:34,536 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/16/R14-18102_kapa-NGv3-PE100-NGv3-sort-16_31120544_46629582-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/16/tx/tmpK_gSzv/R14-18102_kapa-NGv3-PE100-NGv3-sort-16_31120544_46629582-prep-prealign-realign.intervals -l INFO -L 16:31120545-46629582 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-14T23:36Z] INFO  16:36:34,556 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:36Z] INFO  16:36:34,565 HelpFormatter - Date/Time: 2016/04/14 16:36:34
[2016-04-14T23:36Z] INFO  16:36:34,565 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:36Z] INFO  16:36:34,565 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:36Z] INFO  16:36:34,686 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:36Z] INFO  16:36:34,808 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:36Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-12_46756066_62654284-prep.bam
[2016-04-14T23:36Z] INFO  16:36:34,870 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-14T23:36Z] INFO  16:36:34,880 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:36Z] INFO  16:36:34,920 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.04
[2016-04-14T23:36Z] INFO  16:36:35,177 IntervalUtils - Processing 15509038 bp from intervals
[2016-04-14T23:36Z] WARN  16:36:35,182 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:36Z] INFO  16:36:35,269 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:36Z] INFO  16:36:35,426 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:36Z] INFO  16:36:35,427 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:36Z] INFO  16:36:35,428 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:36Z] INFO  16:36:35,429 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-14T23:36Z] INFO  16:36:35,544 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:36Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-14_81651874_97299968-prep.bam
[2016-04-14T23:36Z] INFO  16:36:35,679 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:36Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-15_98984299_102531392-prep.bam
[2016-04-14T23:36Z] GATK pre-alignment ('16', 64982511, 80574976) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:36Z] INFO  16:36:36,138 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:36Z] INFO  16:36:36,142 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:36Z] INFO  16:36:36,143 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:36Z] INFO  16:36:36,143 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:36Z] INFO  16:36:36,148 HelpFormatter - Program Args: -T PrintReads -L 16:46633743-64982002 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/16/tx/tmprhT_hU/R14-18102_kapa-NGv3-PE100-NGv3-sort-16_46633742_64982002-prep-prealign.bam
[2016-04-14T23:36Z] INFO  16:36:36,168 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:36Z] INFO  16:36:36,176 HelpFormatter - Date/Time: 2016/04/14 16:36:36
[2016-04-14T23:36Z] INFO  16:36:36,176 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:36Z] INFO  16:36:36,176 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:36Z] INFO  16:36:36,345 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:36Z] GATK pre-alignment ('16', 80575258, 90354753) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:36Z] INFO  16:36:37,598 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-14T23:36Z] INFO  16:36:37,668 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:36Z] INFO  16:36:37,677 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:36Z] INFO  16:36:37,705 ProgressMeter -            done   1.5513435E7    24.0 s       1.0 s      100.0%    24.0 s       0.0 s
[2016-04-14T23:36Z] INFO  16:36:37,706 ProgressMeter - Total runtime 24.60 secs, 0.41 min, 0.01 hours
[2016-04-14T23:36Z] INFO  16:36:37,707 MicroScheduler - 67203 reads were filtered out during the traversal out of approximately 513756 total reads (13.08%)
[2016-04-14T23:36Z] INFO  16:36:37,708 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:36Z] INFO  16:36:37,708 MicroScheduler -   -> 975 reads (0.19% of total) failing BadMateFilter
[2016-04-14T23:36Z] INFO  16:36:37,708 MicroScheduler -   -> 39114 reads (7.61% of total) failing DuplicateReadFilter
[2016-04-14T23:36Z] INFO  16:36:37,708 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-14T23:36Z] INFO  16:36:37,709 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:36Z] INFO  16:36:37,709 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-14T23:36Z] INFO  16:36:37,709 MicroScheduler -   -> 27114 reads (5.28% of total) failing MappingQualityZeroFilter
[2016-04-14T23:36Z] GATK pre-alignment ('17', 0, 15511002) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:36Z] INFO  16:36:37,709 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:36Z] INFO  16:36:37,710 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-14T23:36Z] INFO  16:36:37,710 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-14T23:36Z] INFO  16:36:37,731 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-14T23:36Z] INFO  16:36:37,746 IntervalUtils - Processing 18348260 bp from intervals
[2016-04-14T23:36Z] INFO  16:36:37,831 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:36Z] INFO  16:36:38,132 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:36Z] INFO  16:36:38,133 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:36Z] INFO  16:36:38,134 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:36Z] INFO  16:36:38,135 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:36Z] INFO  16:36:38,150 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:36Z] INFO  16:36:38,317 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:36Z] INFO  16:36:39,047 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:36Z] INFO  16:36:39,051 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:36Z] INFO  16:36:39,052 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:36Z] INFO  16:36:39,052 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:36Z] INFO  16:36:39,057 HelpFormatter - Program Args: -T PrintReads -L 16:64982512-80574976 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/16/tx/tmp1vXL7O/R14-18102_kapa-NGv3-PE100-NGv3-sort-16_64982511_80574976-prep-prealign.bam
[2016-04-14T23:36Z] INFO  16:36:39,079 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:36Z] INFO  16:36:39,080 HelpFormatter - Date/Time: 2016/04/14 16:36:39
[2016-04-14T23:36Z] INFO  16:36:39,081 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:36Z] INFO  16:36:39,085 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:36Z] INFO  16:36:39,274 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:36Z] INFO  16:36:39,287 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:36Z] INFO  16:36:39,287 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:36Z] INFO  16:36:39,287 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:36Z] INFO  16:36:39,288 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:36Z] INFO  16:36:39,292 HelpFormatter - Program Args: -T PrintReads -L 16:80575259-90354753 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/16/tx/tmpXGawlu/R14-18102_kapa-NGv3-PE100-NGv3-sort-16_80575258_90354753-prep-prealign.bam
[2016-04-14T23:36Z] INFO  16:36:39,313 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:36Z] INFO  16:36:39,314 HelpFormatter - Date/Time: 2016/04/14 16:36:39
[2016-04-14T23:36Z] INFO  16:36:39,314 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:36Z] INFO  16:36:39,320 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:36Z] INFO  16:36:39,474 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:36Z] INFO  16:36:39,495 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:36Z] GATK: realign ('14', 19553416, 35066851) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:36Z] INFO  16:36:40,209 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:36Z] INFO  16:36:40,212 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:36Z] INFO  16:36:40,213 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:36Z] INFO  16:36:40,213 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:36Z] INFO  16:36:40,218 HelpFormatter - Program Args: -T PrintReads -L 17:1-15511002 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/17/tx/tmpWBFO1C/R14-18102_kapa-NGv3-PE100-NGv3-sort-17_0_15511002-prep-prealign.bam
[2016-04-14T23:36Z] INFO  16:36:40,240 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:36Z] INFO  16:36:40,241 HelpFormatter - Date/Time: 2016/04/14 16:36:40
[2016-04-14T23:36Z] INFO  16:36:40,241 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:36Z] INFO  16:36:40,241 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:36Z] INFO  16:36:40,449 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:36Z] INFO  16:36:40,606 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-14T23:36Z] INFO  16:36:40,675 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-14T23:36Z] INFO  16:36:40,687 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:36Z] INFO  16:36:40,696 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:36Z] INFO  16:36:40,743 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:36Z] INFO  16:36:40,753 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:36Z] INFO  16:36:40,768 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-14T23:36Z] INFO  16:36:40,804 IntervalUtils - Processing 15592465 bp from intervals
[2016-04-14T23:36Z] INFO  16:36:40,833 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-14T23:36Z] INFO  16:36:40,859 IntervalUtils - Processing 9779495 bp from intervals
[2016-04-14T23:36Z] INFO  16:36:40,874 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:36Z] INFO  16:36:40,999 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:36Z] INFO  16:36:41,194 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:36Z] INFO  16:36:41,206 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:36Z] INFO  16:36:41,207 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:36Z] INFO  16:36:41,208 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:36Z] INFO  16:36:41,239 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:36Z] INFO  16:36:41,336 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:36Z] INFO  16:36:41,337 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:36Z] INFO  16:36:41,337 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:36Z] INFO  16:36:41,338 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:36Z] INFO  16:36:41,379 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:36Z] INFO  16:36:41,397 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:36Z] INFO  16:36:41,482 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:36Z] INFO  16:36:41,567 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-14T23:36Z] INFO  16:36:41,625 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:36Z] INFO  16:36:41,634 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:36Z] INFO  16:36:41,685 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-14T23:36Z] INFO  16:36:41,700 IntervalUtils - Processing 15511002 bp from intervals
[2016-04-14T23:36Z] INFO  16:36:41,774 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:36Z] INFO  16:36:41,999 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@41fd9d8e
[2016-04-14T23:36Z] INFO  16:36:42,163 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:36Z] INFO  16:36:42,166 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:36Z] INFO  16:36:42,175 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:36Z] INFO  16:36:42,177 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:36Z] INFO  16:36:42,189 ProgressMeter -            done    295217.0    21.0 s      71.0 s      100.0%    21.0 s       0.0 s
[2016-04-14T23:36Z] INFO  16:36:42,189 ProgressMeter - Total runtime 21.15 secs, 0.35 min, 0.01 hours
[2016-04-14T23:36Z] INFO  16:36:42,190 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:36Z] INFO  16:36:42,192 ProgressMeter -            done    566407.0    69.0 s       2.0 m      100.0%    69.0 s       0.0 s
[2016-04-14T23:36Z] INFO  16:36:42,192 ProgressMeter - Total runtime 69.08 secs, 1.15 min, 0.02 hours
[2016-04-14T23:36Z] INFO  16:36:42,193 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 295217 total reads (0.00%)
[2016-04-14T23:36Z] INFO  16:36:42,193 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:36Z] INFO  16:36:42,193 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:36Z] INFO  16:36:42,194 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:36Z] INFO  16:36:42,193 MicroScheduler - 237 reads were filtered out during the traversal out of approximately 566644 total reads (0.04%)
[2016-04-14T23:36Z] INFO  16:36:42,193 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:36Z] INFO  16:36:42,193 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:36Z] INFO  16:36:42,194 MicroScheduler -   -> 237 reads (0.04% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:36Z] INFO  16:36:42,348 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:36Z] INFO  16:36:42,484 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:36Z] INFO  16:36:42,487 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:36Z] INFO  16:36:42,488 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:36Z] INFO  16:36:42,489 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:36Z] INFO  16:36:42,493 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/14/R14-18102_kapa-NGv3-PE100-NGv3-sort-14_19553416_35066851-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/14/R14-18102_kapa-NGv3-PE100-NGv3-sort-14_19553416_35066851-prep-prealign-realign.intervals -L 14:19553417-35066851 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/14/tx/tmpCjd8W6/R14-18102_kapa-NGv3-PE100-NGv3-sort-14_19553416_35066851-prep.bam
[2016-04-14T23:36Z] INFO  16:36:42,525 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:36Z] INFO  16:36:42,526 HelpFormatter - Date/Time: 2016/04/14 16:36:42
[2016-04-14T23:36Z] INFO  16:36:42,526 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:36Z] INFO  16:36:42,526 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:36Z] INFO  16:36:42,740 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:36Z] INFO  16:36:42,907 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:36Z] INFO  16:36:42,917 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:36Z] INFO  16:36:42,990 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-14T23:36Z] INFO  16:36:43,441 IntervalUtils - Processing 15513435 bp from intervals
[2016-04-14T23:36Z] WARN  16:36:43,446 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:36Z] INFO  16:36:43,530 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:36Z] INFO  16:36:43,691 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:36Z] INFO  16:36:43,728 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:36Z] INFO  16:36:43,729 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:36Z] INFO  16:36:43,730 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:36Z] INFO  16:36:43,730 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:36Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-14_50585061_66096324-prep.bam
[2016-04-14T23:36Z] INFO  16:36:43,914 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:36Z] INFO  16:36:44,078 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:36Z] INFO  16:36:44,466 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:36Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-15_67932890_83447639-prep-prealign.bam
[2016-04-14T23:36Z] GATK pre-alignment ('17', 15515955, 31039213) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:36Z] INFO  16:36:45,089 ProgressMeter -            done    329348.0    22.0 s      67.0 s       99.3%    22.0 s       0.0 s
[2016-04-14T23:36Z] INFO  16:36:45,090 ProgressMeter - Total runtime 22.19 secs, 0.37 min, 0.01 hours
[2016-04-14T23:36Z] INFO  16:36:45,093 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 329348 total reads (0.00%)
[2016-04-14T23:36Z] INFO  16:36:45,094 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:36Z] INFO  16:36:45,094 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:36Z] INFO  16:36:45,094 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:36Z] INFO  16:36:45,296 ProgressMeter -            done   1.5533983E7    20.0 s       1.0 s      100.0%    20.0 s       0.0 s
[2016-04-14T23:36Z] INFO  16:36:45,297 ProgressMeter - Total runtime 20.13 secs, 0.34 min, 0.01 hours
[2016-04-14T23:36Z] INFO  16:36:45,298 MicroScheduler - 58253 reads were filtered out during the traversal out of approximately 341677 total reads (17.05%)
[2016-04-14T23:36Z] INFO  16:36:45,299 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:36Z] INFO  16:36:45,299 MicroScheduler -   -> 732 reads (0.21% of total) failing BadMateFilter
[2016-04-14T23:36Z] INFO  16:36:45,300 MicroScheduler -   -> 24723 reads (7.24% of total) failing DuplicateReadFilter
[2016-04-14T23:36Z] INFO  16:36:45,301 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-14T23:36Z] INFO  16:36:45,301 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:36Z] INFO  16:36:45,302 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-14T23:36Z] INFO  16:36:45,303 MicroScheduler -   -> 32798 reads (9.60% of total) failing MappingQualityZeroFilter
[2016-04-14T23:36Z] INFO  16:36:45,303 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:36Z] INFO  16:36:45,304 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-14T23:36Z] INFO  16:36:45,304 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-14T23:36Z] GATK RealignerTargetCreator: R14-18102_kapa-NGv3-PE100-NGv3-sort-15_67932890_83447639-prep-prealign.bam 15:67932891-83447639
[2016-04-14T23:36Z] GATK: RealignerTargetCreator
[2016-04-14T23:36Z] INFO  16:36:46,599 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:36Z] GATK: realign ('15', 83448996, 98982979) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:36Z] INFO  16:36:46,633 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:36Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-14_97304098_107349540-prep.bam
[2016-04-14T23:36Z] GATK pre-alignment ('17', 31048040, 46607237) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:36Z] INFO  16:36:47,887 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:36Z] INFO  16:36:47,889 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:36Z] INFO  16:36:47,889 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:36Z] INFO  16:36:47,889 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:36Z] INFO  16:36:47,894 HelpFormatter - Program Args: -T PrintReads -L 17:15515956-31039213 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/17/tx/tmp2Y1LVy/R14-18102_kapa-NGv3-PE100-NGv3-sort-17_15515955_31039213-prep-prealign.bam
[2016-04-14T23:36Z] INFO  16:36:47,904 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:36Z] INFO  16:36:47,905 HelpFormatter - Date/Time: 2016/04/14 16:36:47
[2016-04-14T23:36Z] INFO  16:36:47,909 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:36Z] INFO  16:36:47,910 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:36Z] INFO  16:36:48,103 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:36Z] INFO  16:36:48,178 ProgressMeter -            done   1.5518901E7    20.0 s       1.0 s      100.0%    20.0 s       0.0 s
[2016-04-14T23:36Z] INFO  16:36:48,179 ProgressMeter - Total runtime 20.55 secs, 0.34 min, 0.01 hours
[2016-04-14T23:36Z] INFO  16:36:48,183 MicroScheduler - 30245 reads were filtered out during the traversal out of approximately 358380 total reads (8.44%)
[2016-04-14T23:36Z] INFO  16:36:48,184 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:36Z] INFO  16:36:48,185 MicroScheduler -   -> 847 reads (0.24% of total) failing BadMateFilter
[2016-04-14T23:36Z] INFO  16:36:48,185 MicroScheduler -   -> 28613 reads (7.98% of total) failing DuplicateReadFilter
[2016-04-14T23:36Z] INFO  16:36:48,186 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-14T23:36Z] INFO  16:36:48,187 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:36Z] INFO  16:36:48,187 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-14T23:36Z] INFO  16:36:48,188 MicroScheduler -   -> 785 reads (0.22% of total) failing MappingQualityZeroFilter
[2016-04-14T23:36Z] INFO  16:36:48,188 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:36Z] INFO  16:36:48,190 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-14T23:36Z] INFO  16:36:48,190 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-14T23:36Z] INFO  16:36:49,101 ProgressMeter -            done   1.5509038E7    13.0 s       0.0 s      100.0%    13.0 s       0.0 s
[2016-04-14T23:36Z] INFO  16:36:49,102 ProgressMeter - Total runtime 13.68 secs, 0.23 min, 0.00 hours
[2016-04-14T23:36Z] INFO  16:36:49,106 MicroScheduler - 33169 reads were filtered out during the traversal out of approximately 116655 total reads (28.43%)
[2016-04-14T23:36Z] INFO  16:36:49,107 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:36Z] INFO  16:36:49,108 MicroScheduler -   -> 364 reads (0.31% of total) failing BadMateFilter
[2016-04-14T23:36Z] INFO  16:36:49,109 MicroScheduler -   -> 7276 reads (6.24% of total) failing DuplicateReadFilter
[2016-04-14T23:36Z] INFO  16:36:49,109 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-14T23:36Z] INFO  16:36:49,110 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:36Z] INFO  16:36:49,110 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-14T23:36Z] INFO  16:36:49,111 MicroScheduler -   -> 25529 reads (21.88% of total) failing MappingQualityZeroFilter
[2016-04-14T23:36Z] INFO  16:36:49,112 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:36Z] INFO  16:36:49,112 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-14T23:36Z] INFO  16:36:49,113 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-14T23:36Z] INFO  16:36:49,163 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:36Z] INFO  16:36:49,167 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:36Z] INFO  16:36:49,168 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:36Z] INFO  16:36:49,168 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:36Z] INFO  16:36:49,173 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/15/R14-18102_kapa-NGv3-PE100-NGv3-sort-15_67932890_83447639-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/15/tx/tmppv_O2L/R14-18102_kapa-NGv3-PE100-NGv3-sort-15_67932890_83447639-prep-prealign-realign.intervals -l INFO -L 15:67932891-83447639 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-14T23:36Z] INFO  16:36:49,208 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-14T23:36Z] INFO  16:36:49,210 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:36Z] INFO  16:36:49,213 HelpFormatter - Date/Time: 2016/04/14 16:36:49
[2016-04-14T23:36Z] INFO  16:36:49,213 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:36Z] INFO  16:36:49,214 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:36Z] INFO  16:36:49,274 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:36Z] INFO  16:36:49,288 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:36Z] INFO  16:36:49,322 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:36Z] INFO  16:36:49,327 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.04
[2016-04-14T23:36Z] INFO  16:36:49,347 IntervalUtils - Processing 15523258 bp from intervals
[2016-04-14T23:36Z] INFO  16:36:49,420 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:36Z] INFO  16:36:49,531 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-14T23:36Z] INFO  16:36:49,551 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:36Z] INFO  16:36:49,598 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-14T23:36Z] INFO  16:36:49,611 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:36Z] GATK: realign ('15', 52404364, 67923265) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:36Z] INFO  16:36:49,764 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:36Z] INFO  16:36:49,765 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:36Z] INFO  16:36:49,766 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:36Z] INFO  16:36:49,767 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:36Z] INFO  16:36:49,794 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:36Z] INFO  16:36:49,987 IntervalUtils - Processing 15514749 bp from intervals
[2016-04-14T23:36Z] WARN  16:36:49,992 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:36Z] INFO  16:36:50,005 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@5fe152b7
[2016-04-14T23:36Z] INFO  16:36:50,067 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:36Z] INFO  16:36:50,070 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:36Z] INFO  16:36:50,073 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:36Z] INFO  16:36:50,074 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:36Z] INFO  16:36:50,074 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:36Z] INFO  16:36:50,079 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/15/R14-18102_kapa-NGv3-PE100-NGv3-sort-15_83448996_98982979-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/15/R14-18102_kapa-NGv3-PE100-NGv3-sort-15_83448996_98982979-prep-prealign-realign.intervals -L 15:83448997-98982979 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/15/tx/tmplrmQtD/R14-18102_kapa-NGv3-PE100-NGv3-sort-15_83448996_98982979-prep.bam
[2016-04-14T23:36Z] INFO  16:36:50,092 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:36Z] INFO  16:36:50,093 HelpFormatter - Date/Time: 2016/04/14 16:36:50
[2016-04-14T23:36Z] INFO  16:36:50,094 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:36Z] INFO  16:36:50,094 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:36Z] INFO  16:36:50,100 ProgressMeter -            done    594648.0    86.0 s       2.4 m      100.0%    86.0 s       0.0 s
[2016-04-14T23:36Z] INFO  16:36:50,101 ProgressMeter - Total runtime 86.47 secs, 1.44 min, 0.02 hours
[2016-04-14T23:36Z] INFO  16:36:50,101 MicroScheduler - 265 reads were filtered out during the traversal out of approximately 594913 total reads (0.04%)
[2016-04-14T23:36Z] INFO  16:36:50,101 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:36Z] INFO  16:36:50,102 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:36Z] INFO  16:36:50,102 MicroScheduler -   -> 265 reads (0.04% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:36Z] INFO  16:36:50,181 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:36Z] INFO  16:36:50,299 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:36Z] INFO  16:36:50,334 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:36Z] INFO  16:36:50,335 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:36Z] INFO  16:36:50,336 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:36Z] INFO  16:36:50,337 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-14T23:36Z] INFO  16:36:50,405 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:36Z] INFO  16:36:50,414 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:36Z] INFO  16:36:50,460 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.04
[2016-04-14T23:36Z] INFO  16:36:50,475 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:36Z] GATK: realign ('16', 31120544, 46629582) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:36Z] INFO  16:36:50,821 IntervalUtils - Processing 15533983 bp from intervals
[2016-04-14T23:36Z] WARN  16:36:50,826 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:36Z] INFO  16:36:50,840 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:36Z] INFO  16:36:50,844 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:36Z] INFO  16:36:50,844 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:36Z] INFO  16:36:50,845 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:36Z] INFO  16:36:50,849 HelpFormatter - Program Args: -T PrintReads -L 17:31048041-46607237 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/17/tx/tmp76YbNh/R14-18102_kapa-NGv3-PE100-NGv3-sort-17_31048040_46607237-prep-prealign.bam
[2016-04-14T23:36Z] INFO  16:36:50,861 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:36Z] INFO  16:36:50,885 HelpFormatter - Date/Time: 2016/04/14 16:36:50
[2016-04-14T23:36Z] INFO  16:36:50,885 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:36Z] INFO  16:36:50,886 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:36Z] INFO  16:36:50,902 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:36Z] INFO  16:36:51,055 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:36Z] INFO  16:36:51,056 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:36Z] INFO  16:36:51,057 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:36Z] INFO  16:36:51,058 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:36Z] INFO  16:36:51,062 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:36Z] INFO  16:36:51,277 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:36Z] INFO  16:36:51,486 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:36Z] INFO  16:36:51,515 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:36Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-15_36887086_52402170-prep-prealign.bam
[2016-04-14T23:36Z] INFO  16:36:51,721 ProgressMeter -            done   1.6130541E7    22.0 s       1.0 s      100.0%    22.0 s       0.0 s
[2016-04-14T23:36Z] INFO  16:36:51,722 ProgressMeter - Total runtime 22.84 secs, 0.38 min, 0.01 hours
[2016-04-14T23:36Z] INFO  16:36:51,726 MicroScheduler - 238613 reads were filtered out during the traversal out of approximately 527840 total reads (45.21%)
[2016-04-14T23:36Z] INFO  16:36:51,727 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:36Z] INFO  16:36:51,727 MicroScheduler -   -> 690 reads (0.13% of total) failing BadMateFilter
[2016-04-14T23:36Z] INFO  16:36:51,728 MicroScheduler -   -> 24843 reads (4.71% of total) failing DuplicateReadFilter
[2016-04-14T23:36Z] INFO  16:36:51,729 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-14T23:36Z] INFO  16:36:51,729 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:36Z] INFO  16:36:51,730 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-14T23:36Z] INFO  16:36:51,731 MicroScheduler -   -> 213080 reads (40.37% of total) failing MappingQualityZeroFilter
[2016-04-14T23:36Z] INFO  16:36:51,731 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:36Z] INFO  16:36:51,732 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-14T23:36Z] INFO  16:36:51,732 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-14T23:36Z] INFO  16:36:52,242 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-14T23:36Z] INFO  16:36:52,299 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:36Z] INFO  16:36:52,308 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:36Z] INFO  16:36:52,357 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-14T23:36Z] INFO  16:36:52,382 IntervalUtils - Processing 15559197 bp from intervals
[2016-04-14T23:36Z] INFO  16:36:52,458 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:36Z] INFO  16:36:52,703 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:36Z] INFO  16:36:52,707 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:36Z] INFO  16:36:52,707 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:36Z] INFO  16:36:52,708 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:36Z] INFO  16:36:52,713 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/15/R14-18102_kapa-NGv3-PE100-NGv3-sort-15_52404364_67923265-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/15/R14-18102_kapa-NGv3-PE100-NGv3-sort-15_52404364_67923265-prep-prealign-realign.intervals -L 15:52404365-67923265 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/15/tx/tmp_2i4TO/R14-18102_kapa-NGv3-PE100-NGv3-sort-15_52404364_67923265-prep.bam
[2016-04-14T23:36Z] INFO  16:36:52,741 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:36Z] INFO  16:36:52,748 HelpFormatter - Date/Time: 2016/04/14 16:36:52
[2016-04-14T23:36Z] INFO  16:36:52,749 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:36Z] INFO  16:36:52,749 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:36Z] INFO  16:36:52,828 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:36Z] INFO  16:36:52,829 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:36Z] INFO  16:36:52,830 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:36Z] INFO  16:36:52,841 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:36Z] INFO  16:36:52,901 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:36Z] INFO  16:36:52,915 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:36Z] INFO  16:36:53,025 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:36Z] INFO  16:36:53,035 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:36Z] INFO  16:36:53,085 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-14T23:36Z] INFO  16:36:53,161 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:36Z] INFO  16:36:53,283 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:36Z] GATK: realign ('15', 20741621, 36872162) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:36Z] INFO  16:36:53,426 IntervalUtils - Processing 15518901 bp from intervals
[2016-04-14T23:36Z] WARN  16:36:53,431 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:36Z] GATK RealignerTargetCreator: R14-18102_kapa-NGv3-PE100-NGv3-sort-15_36887086_52402170-prep-prealign.bam 15:36887087-52402170
[2016-04-14T23:36Z] GATK: RealignerTargetCreator
[2016-04-14T23:36Z] INFO  16:36:53,523 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:36Z] INFO  16:36:53,525 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:36Z] INFO  16:36:53,525 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:36Z] INFO  16:36:53,526 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:36Z] INFO  16:36:53,529 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/16/R14-18102_kapa-NGv3-PE100-NGv3-sort-16_31120544_46629582-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/16/R14-18102_kapa-NGv3-PE100-NGv3-sort-16_31120544_46629582-prep-prealign-realign.intervals -L 16:31120545-46629582 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/16/tx/tmpKSFUfV/R14-18102_kapa-NGv3-PE100-NGv3-sort-16_31120544_46629582-prep.bam
[2016-04-14T23:36Z] INFO  16:36:53,540 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:36Z] INFO  16:36:53,545 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:36Z] INFO  16:36:53,546 HelpFormatter - Date/Time: 2016/04/14 16:36:53
[2016-04-14T23:36Z] INFO  16:36:53,546 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:36Z] INFO  16:36:53,547 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:36Z] INFO  16:36:53,719 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:36Z] INFO  16:36:53,720 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:36Z] INFO  16:36:53,721 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:36Z] INFO  16:36:53,722 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:36Z] INFO  16:36:53,792 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:36Z] INFO  16:36:53,952 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:36Z] INFO  16:36:53,973 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:36Z] INFO  16:36:53,984 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:36Z] INFO  16:36:54,063 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-14T23:36Z] INFO  16:36:54,248 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:36Z] INFO  16:36:54,541 IntervalUtils - Processing 15509038 bp from intervals
[2016-04-14T23:36Z] WARN  16:36:54,547 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:36Z] INFO  16:36:54,623 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:36Z] INFO  16:36:54,792 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:36Z] INFO  16:36:54,793 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:36Z] INFO  16:36:54,794 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:36Z] INFO  16:36:54,794 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:36Z] INFO  16:36:54,890 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:36Z] INFO  16:36:55,043 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:36Z] INFO  16:36:56,469 ProgressMeter -      16:3306504    400006.0    60.0 s       2.5 m       21.3%     4.7 m       3.7 m
[2016-04-14T23:36Z] INFO  16:36:56,515 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:36Z] INFO  16:36:56,518 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:36Z] INFO  16:36:56,519 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:36Z] INFO  16:36:56,520 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:36Z] INFO  16:36:56,524 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/15/R14-18102_kapa-NGv3-PE100-NGv3-sort-15_36887086_52402170-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/15/tx/tmpZz1SsG/R14-18102_kapa-NGv3-PE100-NGv3-sort-15_36887086_52402170-prep-prealign-realign.intervals -l INFO -L 15:36887087-52402170 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-14T23:36Z] INFO  16:36:56,535 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:36Z] INFO  16:36:56,546 HelpFormatter - Date/Time: 2016/04/14 16:36:56
[2016-04-14T23:36Z] INFO  16:36:56,547 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:36Z] INFO  16:36:56,548 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:36Z] INFO  16:36:56,641 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:36Z] INFO  16:36:56,645 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:36Z] INFO  16:36:56,646 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:36Z] INFO  16:36:56,646 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:36Z] INFO  16:36:56,651 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/15/R14-18102_kapa-NGv3-PE100-NGv3-sort-15_20741621_36872162-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/15/R14-18102_kapa-NGv3-PE100-NGv3-sort-15_20741621_36872162-prep-prealign-realign.intervals -L 15:20741622-36872162 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/15/tx/tmph7jUBX/R14-18102_kapa-NGv3-PE100-NGv3-sort-15_20741621_36872162-prep.bam
[2016-04-14T23:36Z] INFO  16:36:56,658 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:36Z] INFO  16:36:56,661 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:36Z] INFO  16:36:56,661 HelpFormatter - Date/Time: 2016/04/14 16:36:56
[2016-04-14T23:36Z] INFO  16:36:56,661 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:36Z] INFO  16:36:56,662 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:36Z] INFO  16:36:56,896 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-14T23:36Z] INFO  16:36:56,928 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:36Z] INFO  16:36:56,929 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:36Z] INFO  16:36:57,021 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.09
[2016-04-14T23:36Z] INFO  16:36:57,028 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:36Z] INFO  16:36:57,038 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:36Z] INFO  16:36:57,096 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-14T23:36Z] INFO  16:36:57,365 IntervalUtils - Processing 15515084 bp from intervals
[2016-04-14T23:36Z] WARN  16:36:57,371 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:36Z] INFO  16:36:57,479 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:36Z] INFO  16:36:57,525 IntervalUtils - Processing 16130541 bp from intervals
[2016-04-14T23:36Z] WARN  16:36:57,531 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:36Z] INFO  16:36:57,663 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:36Z] INFO  16:36:57,664 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:36Z] INFO  16:36:57,666 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:36Z] INFO  16:36:57,666 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:36Z] INFO  16:36:57,667 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-14T23:36Z] INFO  16:36:57,785 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:36Z] INFO  16:36:57,786 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:36Z] INFO  16:36:57,787 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:36Z] INFO  16:36:57,788 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:36Z] INFO  16:36:57,991 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:36Z] INFO  16:36:58,205 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:37Z] INFO  16:37:01,406 ProgressMeter -            done    384040.0    27.0 s      71.0 s       99.8%    27.0 s       0.0 s
[2016-04-14T23:37Z] INFO  16:37:01,407 ProgressMeter - Total runtime 27.56 secs, 0.46 min, 0.01 hours
[2016-04-14T23:37Z] INFO  16:37:01,411 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 384040 total reads (0.00%)
[2016-04-14T23:37Z] INFO  16:37:01,424 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:37Z] INFO  16:37:01,425 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:37Z] INFO  16:37:01,425 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:37Z] INFO  16:37:02,843 ProgressMeter -     16:22543873    400005.0    60.0 s       2.5 m       44.8%     2.2 m      73.0 s
[2016-04-14T23:37Z] INFO  16:37:02,943 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:37Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-14_66135960_81646674-prep.bam
[2016-04-14T23:37Z] GATK pre-alignment ('17', 46607689, 62121560) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:37Z] INFO  16:37:04,380 ProgressMeter -            done    115619.0     9.0 s      82.0 s      100.0%     9.0 s       0.0 s
[2016-04-14T23:37Z] INFO  16:37:04,381 ProgressMeter - Total runtime 9.59 secs, 0.16 min, 0.00 hours
[2016-04-14T23:37Z] INFO  16:37:04,385 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 115619 total reads (0.00%)
[2016-04-14T23:37Z] INFO  16:37:04,387 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:37Z] INFO  16:37:04,388 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:37Z] INFO  16:37:04,389 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:37Z] INFO  16:37:05,927 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:37Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-16_31120544_46629582-prep.bam
[2016-04-14T23:37Z] GATK pre-alignment ('17', 62122219, 77705154) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:37Z] INFO  16:37:06,764 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:37Z] INFO  16:37:06,768 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:37Z] INFO  16:37:06,769 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:37Z] INFO  16:37:06,770 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:37Z] INFO  16:37:06,776 HelpFormatter - Program Args: -T PrintReads -L 17:46607690-62121560 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/17/tx/tmpBcqZFb/R14-18102_kapa-NGv3-PE100-NGv3-sort-17_46607689_62121560-prep-prealign.bam
[2016-04-14T23:37Z] INFO  16:37:06,787 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:37Z] INFO  16:37:06,807 HelpFormatter - Date/Time: 2016/04/14 16:37:06
[2016-04-14T23:37Z] INFO  16:37:06,808 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:37Z] INFO  16:37:06,809 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:37Z] INFO  16:37:07,037 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:37Z] INFO  16:37:08,151 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-14T23:37Z] INFO  16:37:08,154 ProgressMeter -     16:57060123    200003.0    30.0 s       2.5 m       56.8%    52.0 s      22.0 s
[2016-04-14T23:37Z] INFO  16:37:08,208 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:37Z] INFO  16:37:08,218 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:37Z] INFO  16:37:08,276 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-14T23:37Z] INFO  16:37:08,292 IntervalUtils - Processing 15513871 bp from intervals
[2016-04-14T23:37Z] INFO  16:37:08,385 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:37Z] INFO  16:37:08,759 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:37Z] INFO  16:37:08,760 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:37Z] INFO  16:37:08,761 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:37Z] INFO  16:37:08,762 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:37Z] INFO  16:37:08,793 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:37Z] INFO  16:37:08,952 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:37Z] INFO  16:37:08,989 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:37Z] INFO  16:37:08,992 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:37Z] INFO  16:37:08,993 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:37Z] INFO  16:37:08,993 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:37Z] INFO  16:37:08,998 HelpFormatter - Program Args: -T PrintReads -L 17:62122220-77705154 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/17/tx/tmpzqaeLk/R14-18102_kapa-NGv3-PE100-NGv3-sort-17_62122219_77705154-prep-prealign.bam
[2016-04-14T23:37Z] INFO  16:37:09,013 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:37Z] INFO  16:37:09,014 HelpFormatter - Date/Time: 2016/04/14 16:37:08
[2016-04-14T23:37Z] INFO  16:37:09,015 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:37Z] INFO  16:37:09,016 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:37Z] INFO  16:37:09,218 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:37Z] INFO  16:37:10,295 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-14T23:37Z] INFO  16:37:10,373 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:37Z] INFO  16:37:10,384 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:37Z] INFO  16:37:10,430 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-14T23:37Z] INFO  16:37:10,472 IntervalUtils - Processing 15582935 bp from intervals
[2016-04-14T23:37Z] INFO  16:37:10,622 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:37Z] INFO  16:37:11,036 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:37Z] INFO  16:37:11,037 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:37Z] INFO  16:37:11,037 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:37Z] INFO  16:37:11,038 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:37Z] INFO  16:37:11,062 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:37Z] INFO  16:37:11,190 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:37Z] INFO  16:37:11,235 ProgressMeter -     16:67995679    100002.0    30.0 s       5.0 m       19.3%     2.6 m       2.1 m
[2016-04-14T23:37Z] INFO  16:37:11,612 ProgressMeter -     16:88724026    200002.0    30.0 s       2.5 m       83.3%    36.0 s       6.0 s
[2016-04-14T23:37Z] INFO  16:37:12,188 ProgressMeter -      17:3379648    100001.0    30.0 s       5.0 m       21.8%     2.3 m     107.0 s
[2016-04-14T23:37Z] INFO  16:37:13,829 ProgressMeter -            done    339405.0    22.0 s      67.0 s      100.0%    22.0 s       0.0 s
[2016-04-14T23:37Z] INFO  16:37:13,830 ProgressMeter - Total runtime 22.77 secs, 0.38 min, 0.01 hours
[2016-04-14T23:37Z] INFO  16:37:13,834 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 339405 total reads (0.00%)
[2016-04-14T23:37Z] INFO  16:37:13,835 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:37Z] INFO  16:37:13,835 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:37Z] INFO  16:37:13,835 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:37Z] INFO  16:37:15,135 ProgressMeter -     14:31364723    400006.0    31.0 s      78.0 s       76.1%    40.0 s       9.0 s
[2016-04-14T23:37Z] INFO  16:37:15,870 ProgressMeter -            done   1.5514749E7    25.0 s       1.0 s      100.0%    25.0 s       0.0 s
[2016-04-14T23:37Z] INFO  16:37:15,872 ProgressMeter - Total runtime 25.54 secs, 0.43 min, 0.01 hours
[2016-04-14T23:37Z] INFO  16:37:15,876 MicroScheduler - 133494 reads were filtered out during the traversal out of approximately 571026 total reads (23.38%)
[2016-04-14T23:37Z] INFO  16:37:15,877 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:37Z] INFO  16:37:15,878 MicroScheduler -   -> 1044 reads (0.18% of total) failing BadMateFilter
[2016-04-14T23:37Z] INFO  16:37:15,879 MicroScheduler -   -> 38676 reads (6.77% of total) failing DuplicateReadFilter
[2016-04-14T23:37Z] INFO  16:37:15,879 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-14T23:37Z] INFO  16:37:15,880 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:37Z] INFO  16:37:15,880 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-14T23:37Z] INFO  16:37:15,881 MicroScheduler -   -> 93774 reads (16.42% of total) failing MappingQualityZeroFilter
[2016-04-14T23:37Z] INFO  16:37:15,882 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:37Z] INFO  16:37:15,882 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-14T23:37Z] INFO  16:37:15,883 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-14T23:37Z] INFO  16:37:16,530 ProgressMeter -            done    510672.0    32.0 s      64.0 s      100.0%    32.0 s       0.0 s
[2016-04-14T23:37Z] INFO  16:37:16,530 ProgressMeter - Total runtime 32.80 secs, 0.55 min, 0.01 hours
[2016-04-14T23:37Z] INFO  16:37:16,534 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 510672 total reads (0.00%)
[2016-04-14T23:37Z] INFO  16:37:16,535 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:37Z] INFO  16:37:16,536 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:37Z] INFO  16:37:16,537 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:37Z] INFO  16:37:16,579 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:37Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-15_83448996_98982979-prep.bam
[2016-04-14T23:37Z] INFO  16:37:17,305 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:37Z] GATK: realign ('15', 67932890, 83447639) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:37Z] GATK pre-alignment ('17', 77707305, 81195210) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:37Z] INFO  16:37:18,148 ProgressMeter -            done    356017.0    24.0 s      68.0 s      100.0%    24.0 s       0.0 s
[2016-04-14T23:37Z] INFO  16:37:18,149 ProgressMeter - Total runtime 24.43 secs, 0.41 min, 0.01 hours
[2016-04-14T23:37Z] INFO  16:37:18,153 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 356017 total reads (0.00%)
[2016-04-14T23:37Z] INFO  16:37:18,153 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:37Z] INFO  16:37:18,154 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:37Z] INFO  16:37:18,154 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:37Z] INFO  16:37:18,244 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:37Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-14_19553416_35066851-prep.bam
[2016-04-14T23:37Z] INFO  16:37:19,661 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:37Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-15_52404364_67923265-prep.bam
[2016-04-14T23:37Z] INFO  16:37:19,780 ProgressMeter -     17:18566076    200006.0    30.0 s       2.5 m       19.6%     2.5 m       2.0 m
[2016-04-14T23:37Z] GATK pre-alignment ('18', 0, 18531348) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:37Z] INFO  16:37:20,107 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:37Z] INFO  16:37:20,111 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:37Z] INFO  16:37:20,111 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:37Z] INFO  16:37:20,112 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:37Z] INFO  16:37:20,116 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/15/R14-18102_kapa-NGv3-PE100-NGv3-sort-15_67932890_83447639-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/15/R14-18102_kapa-NGv3-PE100-NGv3-sort-15_67932890_83447639-prep-prealign-realign.intervals -L 15:67932891-83447639 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/15/tx/tmpFBky0J/R14-18102_kapa-NGv3-PE100-NGv3-sort-15_67932890_83447639-prep.bam
[2016-04-14T23:37Z] INFO  16:37:20,129 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:37Z] INFO  16:37:20,129 HelpFormatter - Date/Time: 2016/04/14 16:37:20
[2016-04-14T23:37Z] INFO  16:37:20,129 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:37Z] INFO  16:37:20,130 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:37Z] INFO  16:37:20,353 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:37Z] INFO  16:37:20,485 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:37Z] INFO  16:37:20,487 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:37Z] INFO  16:37:20,487 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:37Z] INFO  16:37:20,488 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:37Z] INFO  16:37:20,492 HelpFormatter - Program Args: -T PrintReads -L 17:77707306-81195210 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/17/tx/tmpF2u38G/R14-18102_kapa-NGv3-PE100-NGv3-sort-17_77707305_81195210-prep-prealign.bam
[2016-04-14T23:37Z] INFO  16:37:20,508 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:37Z] INFO  16:37:20,517 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:37Z] INFO  16:37:20,522 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:37Z] INFO  16:37:20,523 HelpFormatter - Date/Time: 2016/04/14 16:37:20
[2016-04-14T23:37Z] INFO  16:37:20,524 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:37Z] INFO  16:37:20,524 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:37Z] INFO  16:37:20,569 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-14T23:37Z] INFO  16:37:20,686 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:37Z] GATK pre-alignment ('18', 18533538, 34081962) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:37Z] INFO  16:37:20,937 IntervalUtils - Processing 15514749 bp from intervals
[2016-04-14T23:37Z] WARN  16:37:20,942 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:37Z] INFO  16:37:21,011 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:37Z] INFO  16:37:21,133 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:37Z] INFO  16:37:21,134 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:37Z] INFO  16:37:21,135 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:37Z] INFO  16:37:21,136 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:37Z] INFO  16:37:21,257 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:37Z] INFO  16:37:21,435 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:37Z] INFO  16:37:22,039 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-14T23:37Z] INFO  16:37:22,131 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:37Z] INFO  16:37:22,140 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:37Z] INFO  16:37:22,193 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-14T23:37Z] INFO  16:37:22,208 IntervalUtils - Processing 3487905 bp from intervals
[2016-04-14T23:37Z] INFO  16:37:22,291 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:37Z] INFO  16:37:22,407 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@41fd9d8e
[2016-04-14T23:37Z] INFO  16:37:22,544 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:37Z] INFO  16:37:22,545 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:37Z] INFO  16:37:22,546 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:37Z] INFO  16:37:22,546 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:37Z] INFO  16:37:22,549 ProgressMeter -            done   1.5515084E7    24.0 s       1.0 s      100.0%    24.0 s       0.0 s
[2016-04-14T23:37Z] INFO  16:37:22,549 ProgressMeter - Total runtime 24.88 secs, 0.41 min, 0.01 hours
[2016-04-14T23:37Z] INFO  16:37:22,552 MicroScheduler - 81541 reads were filtered out during the traversal out of approximately 598234 total reads (13.63%)
[2016-04-14T23:37Z] INFO  16:37:22,553 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:37Z] INFO  16:37:22,553 MicroScheduler -   -> 1170 reads (0.20% of total) failing BadMateFilter
[2016-04-14T23:37Z] INFO  16:37:22,553 MicroScheduler -   -> 44893 reads (7.50% of total) failing DuplicateReadFilter
[2016-04-14T23:37Z] INFO  16:37:22,553 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-14T23:37Z] INFO  16:37:22,554 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:37Z] INFO  16:37:22,554 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-14T23:37Z] INFO  16:37:22,554 MicroScheduler -   -> 35478 reads (5.93% of total) failing MappingQualityZeroFilter
[2016-04-14T23:37Z] INFO  16:37:22,554 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:37Z] INFO  16:37:22,555 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-14T23:37Z] INFO  16:37:22,555 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-14T23:37Z] INFO  16:37:22,560 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:37Z] INFO  16:37:22,599 ProgressMeter -            done    359302.0    44.0 s       2.1 m      100.0%    44.0 s       0.0 s
[2016-04-14T23:37Z] INFO  16:37:22,602 ProgressMeter - Total runtime 44.47 secs, 0.74 min, 0.01 hours
[2016-04-14T23:37Z] INFO  16:37:22,602 MicroScheduler - 204 reads were filtered out during the traversal out of approximately 359506 total reads (0.06%)
[2016-04-14T23:37Z] INFO  16:37:22,602 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:37Z] INFO  16:37:22,603 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:37Z] INFO  16:37:22,603 MicroScheduler -   -> 204 reads (0.06% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:37Z] INFO  16:37:22,608 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:37Z] INFO  16:37:22,878 ProgressMeter -     17:35310632    200002.0    30.0 s       2.5 m       27.4%   109.0 s      79.0 s
[2016-04-14T23:37Z] INFO  16:37:22,964 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:37Z] INFO  16:37:22,968 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:37Z] INFO  16:37:22,968 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:37Z] INFO  16:37:22,969 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:37Z] INFO  16:37:22,974 HelpFormatter - Program Args: -T PrintReads -L 18:1-18531348 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/18/tx/tmpneMlpd/R14-18102_kapa-NGv3-PE100-NGv3-sort-18_0_18531348-prep-prealign.bam
[2016-04-14T23:37Z] INFO  16:37:22,983 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:37Z] INFO  16:37:22,988 HelpFormatter - Date/Time: 2016/04/14 16:37:22
[2016-04-14T23:37Z] INFO  16:37:22,989 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:37Z] INFO  16:37:22,990 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:37Z] INFO  16:37:23,183 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:37Z] INFO  16:37:23,734 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:37Z] INFO  16:37:23,737 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:37Z] INFO  16:37:23,738 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:37Z] INFO  16:37:23,738 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:37Z] INFO  16:37:23,743 HelpFormatter - Program Args: -T PrintReads -L 18:18533539-34081962 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/18/tx/tmpjQuK7Y/R14-18102_kapa-NGv3-PE100-NGv3-sort-18_18533538_34081962-prep-prealign.bam
[2016-04-14T23:37Z] INFO  16:37:23,752 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:37Z] INFO  16:37:23,753 HelpFormatter - Date/Time: 2016/04/14 16:37:23
[2016-04-14T23:37Z] INFO  16:37:23,754 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:37Z] INFO  16:37:23,754 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:37Z] INFO  16:37:23,928 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:37Z] INFO  16:37:24,016 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:37Z] GATK: realign ('15', 36887086, 52402170) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:37Z] INFO  16:37:24,126 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:37Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-16_46633742_64982002-prep-prealign.bam
[2016-04-14T23:37Z] INFO  16:37:24,268 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-14T23:37Z] INFO  16:37:24,332 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:37Z] INFO  16:37:24,342 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:37Z] INFO  16:37:24,377 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.03
[2016-04-14T23:37Z] INFO  16:37:24,392 IntervalUtils - Processing 18531348 bp from intervals
[2016-04-14T23:37Z] INFO  16:37:24,464 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:37Z] INFO  16:37:24,791 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:37Z] INFO  16:37:24,792 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:37Z] INFO  16:37:24,792 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:37Z] INFO  16:37:24,793 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:37Z] INFO  16:37:24,820 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:37Z] INFO  16:37:25,015 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-14T23:37Z] INFO  16:37:25,046 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:37Z] INFO  16:37:25,078 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:37Z] INFO  16:37:25,087 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:37Z] INFO  16:37:25,136 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-14T23:37Z] INFO  16:37:25,151 IntervalUtils - Processing 15548424 bp from intervals
[2016-04-14T23:37Z] INFO  16:37:25,238 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:37Z] GATK RealignerTargetCreator: R14-18102_kapa-NGv3-PE100-NGv3-sort-16_46633742_64982002-prep-prealign.bam 16:46633743-64982002
[2016-04-14T23:37Z] GATK: RealignerTargetCreator
[2016-04-14T23:37Z] INFO  16:37:25,582 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:37Z] INFO  16:37:25,583 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:37Z] INFO  16:37:25,583 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:37Z] INFO  16:37:25,584 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:37Z] INFO  16:37:25,608 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:37Z] INFO  16:37:25,842 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:37Z] INFO  16:37:26,554 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@7172f77a
[2016-04-14T23:37Z] INFO  16:37:26,693 ProgressMeter -            done    362290.0    45.0 s       2.1 m       98.8%    45.0 s       0.0 s
[2016-04-14T23:37Z] INFO  16:37:26,693 ProgressMeter - Total runtime 45.36 secs, 0.76 min, 0.01 hours
[2016-04-14T23:37Z] INFO  16:37:26,694 MicroScheduler - 167 reads were filtered out during the traversal out of approximately 362457 total reads (0.05%)
[2016-04-14T23:37Z] INFO  16:37:26,694 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:37Z] INFO  16:37:26,695 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:37Z] INFO  16:37:26,695 MicroScheduler -   -> 167 reads (0.05% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:37Z] INFO  16:37:26,805 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:37Z] INFO  16:37:26,808 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:37Z] INFO  16:37:26,809 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:37Z] INFO  16:37:26,809 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:37Z] INFO  16:37:26,814 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/15/R14-18102_kapa-NGv3-PE100-NGv3-sort-15_36887086_52402170-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/15/R14-18102_kapa-NGv3-PE100-NGv3-sort-15_36887086_52402170-prep-prealign-realign.intervals -L 15:36887087-52402170 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/15/tx/tmp6s46ze/R14-18102_kapa-NGv3-PE100-NGv3-sort-15_36887086_52402170-prep.bam
[2016-04-14T23:37Z] INFO  16:37:26,835 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:37Z] INFO  16:37:26,846 HelpFormatter - Date/Time: 2016/04/14 16:37:26
[2016-04-14T23:37Z] INFO  16:37:26,847 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:37Z] INFO  16:37:26,848 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:37Z] INFO  16:37:27,096 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:37Z] INFO  16:37:27,215 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:37Z] INFO  16:37:27,235 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:37Z] INFO  16:37:27,307 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-14T23:37Z] INFO  16:37:27,754 IntervalUtils - Processing 15515084 bp from intervals
[2016-04-14T23:37Z] WARN  16:37:27,760 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:37Z] INFO  16:37:27,792 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:37Z] INFO  16:37:27,795 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:37Z] INFO  16:37:27,795 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:37Z] INFO  16:37:27,795 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:37Z] INFO  16:37:27,804 ProgressMeter -     16:12036102    700010.0    91.0 s       2.2 m       77.5%   117.0 s      26.0 s
[2016-04-14T23:37Z] INFO  16:37:27,808 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/16/R14-18102_kapa-NGv3-PE100-NGv3-sort-16_46633742_64982002-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/16/tx/tmp0NYMnU/R14-18102_kapa-NGv3-PE100-NGv3-sort-16_46633742_64982002-prep-prealign-realign.intervals -l INFO -L 16:46633743-64982002 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-14T23:37Z] INFO  16:37:27,831 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:37Z] INFO  16:37:27,832 HelpFormatter - Date/Time: 2016/04/14 16:37:27
[2016-04-14T23:37Z] INFO  16:37:27,832 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:37Z] INFO  16:37:27,832 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:37Z] INFO  16:37:27,840 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:37Z] INFO  16:37:27,854 ProgressMeter -     15:33765719    400007.0    30.0 s      75.0 s       80.7%    37.0 s       7.0 s
[2016-04-14T23:37Z] INFO  16:37:27,966 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:37Z] INFO  16:37:27,967 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:37Z] INFO  16:37:27,968 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:37Z] INFO  16:37:27,969 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:37Z] INFO  16:37:27,973 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:37Z] INFO  16:37:28,197 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:37Z] INFO  16:37:28,270 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:37Z] INFO  16:37:28,274 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-14T23:37Z] INFO  16:37:28,285 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:37Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-16_80575258_90354753-prep-prealign.bam
[2016-04-14T23:37Z] INFO  16:37:28,382 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:37Z] INFO  16:37:28,385 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.10
[2016-04-14T23:37Z] INFO  16:37:28,669 IntervalUtils - Processing 18348260 bp from intervals
[2016-04-14T23:37Z] WARN  16:37:28,674 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:37Z] INFO  16:37:28,771 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:37Z] INFO  16:37:28,954 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:37Z] INFO  16:37:28,954 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:37Z] INFO  16:37:28,955 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:37Z] INFO  16:37:28,955 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-14T23:37Z] GATK RealignerTargetCreator: R14-18102_kapa-NGv3-PE100-NGv3-sort-16_80575258_90354753-prep-prealign.bam 16:80575259-90354753
[2016-04-14T23:37Z] GATK: RealignerTargetCreator
[2016-04-14T23:37Z] INFO  16:37:30,758 ProgressMeter -            done    524432.0    32.0 s      62.0 s      100.0%    32.0 s       0.0 s
[2016-04-14T23:37Z] INFO  16:37:30,759 ProgressMeter - Total runtime 32.97 secs, 0.55 min, 0.01 hours
[2016-04-14T23:37Z] INFO  16:37:30,764 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 524432 total reads (0.00%)
[2016-04-14T23:37Z] INFO  16:37:30,764 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:37Z] INFO  16:37:30,764 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:37Z] INFO  16:37:30,765 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:37Z] INFO  16:37:32,298 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:37Z] INFO  16:37:32,345 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:37Z] INFO  16:37:32,349 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:37Z] INFO  16:37:32,349 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:37Z] INFO  16:37:32,350 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:37Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-15_20741621_36872162-prep.bam
[2016-04-14T23:37Z] INFO  16:37:32,354 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/16/R14-18102_kapa-NGv3-PE100-NGv3-sort-16_80575258_90354753-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/16/tx/tmpZngjDk/R14-18102_kapa-NGv3-PE100-NGv3-sort-16_80575258_90354753-prep-prealign-realign.intervals -l INFO -L 16:80575259-90354753 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-14T23:37Z] INFO  16:37:32,368 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:37Z] INFO  16:37:32,370 HelpFormatter - Date/Time: 2016/04/14 16:37:32
[2016-04-14T23:37Z] INFO  16:37:32,370 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:37Z] INFO  16:37:32,371 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:37Z] INFO  16:37:32,465 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:37Z] INFO  16:37:32,634 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-14T23:37Z] INFO  16:37:32,652 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:37Z] INFO  16:37:32,733 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-14T23:37Z] INFO  16:37:32,845 ProgressMeter -     16:28669878    700010.0    90.0 s       2.1 m       84.3%   106.0 s      16.0 s
[2016-04-14T23:37Z] INFO  16:37:33,096 IntervalUtils - Processing 9779495 bp from intervals
[2016-04-14T23:37Z] WARN  16:37:33,102 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:37Z] INFO  16:37:33,256 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:37Z] INFO  16:37:33,371 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:37Z] INFO  16:37:33,372 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:37Z] INFO  16:37:33,372 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:37Z] INFO  16:37:33,373 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-14T23:37Z] GATK pre-alignment ('18', 34092400, 49867248) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:37Z] INFO  16:37:36,762 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:37Z] INFO  16:37:36,766 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:37Z] INFO  16:37:36,767 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:37Z] INFO  16:37:36,767 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:37Z] INFO  16:37:36,773 HelpFormatter - Program Args: -T PrintReads -L 18:34092401-49867248 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/18/tx/tmpkKkJQc/R14-18102_kapa-NGv3-PE100-NGv3-sort-18_34092400_49867248-prep-prealign.bam
[2016-04-14T23:37Z] INFO  16:37:36,803 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:37Z] INFO  16:37:36,804 HelpFormatter - Date/Time: 2016/04/14 16:37:36
[2016-04-14T23:37Z] INFO  16:37:36,804 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:37Z] INFO  16:37:36,804 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:37Z] INFO  16:37:36,990 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:37Z] INFO  16:37:38,219 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-14T23:37Z] INFO  16:37:38,308 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:37Z] INFO  16:37:38,319 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:37Z] INFO  16:37:38,398 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-14T23:37Z] INFO  16:37:38,425 IntervalUtils - Processing 15774848 bp from intervals
[2016-04-14T23:37Z] INFO  16:37:38,510 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:37Z] INFO  16:37:38,792 ProgressMeter -     17:53392811    100001.0    30.0 s       5.0 m       43.7%    68.0 s      38.0 s
[2016-04-14T23:37Z] INFO  16:37:38,810 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:37Z] INFO  16:37:38,811 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:37Z] INFO  16:37:38,812 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:37Z] INFO  16:37:38,813 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:37Z] INFO  16:37:38,826 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:37Z] INFO  16:37:39,002 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:37Z] INFO  16:37:41,236 ProgressMeter -     16:72056299    400006.0    60.0 s       2.5 m       45.4%     2.2 m      72.0 s
[2016-04-14T23:37Z] INFO  16:37:41,740 ProgressMeter -     17:72205396    100002.0    30.0 s       5.1 m       64.7%    46.0 s      16.0 s
[2016-04-14T23:37Z] INFO  16:37:42,189 ProgressMeter -      17:5404002    300007.0    60.0 s       3.3 m       34.8%     2.9 m     112.0 s
[2016-04-14T23:37Z] INFO  16:37:43,237 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@7172f77a
[2016-04-14T23:37Z] INFO  16:37:43,298 ProgressMeter -            done    910120.0   106.0 s     117.0 s      100.0%   106.0 s       0.0 s
[2016-04-14T23:37Z] INFO  16:37:43,299 ProgressMeter - Total runtime 106.85 secs, 1.78 min, 0.03 hours
[2016-04-14T23:37Z] INFO  16:37:43,299 MicroScheduler - 411 reads were filtered out during the traversal out of approximately 910531 total reads (0.05%)
[2016-04-14T23:37Z] INFO  16:37:43,300 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:37Z] INFO  16:37:43,301 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:37Z] INFO  16:37:43,301 MicroScheduler -   -> 411 reads (0.05% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:37Z] INFO  16:37:44,842 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:37Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-16_0_15528616-prep-prealign.bam
[2016-04-14T23:37Z] GATK RealignerTargetCreator: R14-18102_kapa-NGv3-PE100-NGv3-sort-16_0_15528616-prep-prealign.bam 16:1-15528616
[2016-04-14T23:37Z] GATK: RealignerTargetCreator
[2016-04-14T23:37Z] INFO  16:37:49,781 ProgressMeter -     17:27277162    400009.0    60.0 s       2.5 m       75.8%    79.0 s      19.0 s
[2016-04-14T23:37Z] INFO  16:37:50,348 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:37Z] INFO  16:37:50,351 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:37Z] INFO  16:37:50,352 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:37Z] INFO  16:37:50,353 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:37Z] INFO  16:37:50,357 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/16/R14-18102_kapa-NGv3-PE100-NGv3-sort-16_0_15528616-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/16/tx/tmpe6lewc/R14-18102_kapa-NGv3-PE100-NGv3-sort-16_0_15528616-prep-prealign-realign.intervals -l INFO -L 16:1-15528616 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-14T23:37Z] INFO  16:37:50,373 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:37Z] INFO  16:37:50,374 HelpFormatter - Date/Time: 2016/04/14 16:37:50
[2016-04-14T23:37Z] INFO  16:37:50,374 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:37Z] INFO  16:37:50,375 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:37Z] INFO  16:37:50,518 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:37Z] INFO  16:37:50,757 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-14T23:37Z] INFO  16:37:50,767 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:37Z] INFO  16:37:50,842 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-14T23:37Z] INFO  16:37:51,037 ProgressMeter -            done   1.834826E7    22.0 s       1.0 s      100.0%    22.0 s       0.0 s
[2016-04-14T23:37Z] INFO  16:37:51,038 ProgressMeter - Total runtime 22.08 secs, 0.37 min, 0.01 hours
[2016-04-14T23:37Z] INFO  16:37:51,042 MicroScheduler - 32552 reads were filtered out during the traversal out of approximately 361701 total reads (9.00%)
[2016-04-14T23:37Z] INFO  16:37:51,043 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:37Z] INFO  16:37:51,045 MicroScheduler -   -> 898 reads (0.25% of total) failing BadMateFilter
[2016-04-14T23:37Z] INFO  16:37:51,046 MicroScheduler -   -> 28919 reads (8.00% of total) failing DuplicateReadFilter
[2016-04-14T23:37Z] INFO  16:37:51,046 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-14T23:37Z] INFO  16:37:51,047 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:37Z] INFO  16:37:51,047 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-14T23:37Z] INFO  16:37:51,048 MicroScheduler -   -> 2735 reads (0.76% of total) failing MappingQualityZeroFilter
[2016-04-14T23:37Z] INFO  16:37:51,049 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:37Z] INFO  16:37:51,049 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-14T23:37Z] INFO  16:37:51,050 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-14T23:37Z] INFO  16:37:51,166 IntervalUtils - Processing 15528616 bp from intervals
[2016-04-14T23:37Z] WARN  16:37:51,172 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:37Z] INFO  16:37:51,251 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:37Z] INFO  16:37:51,484 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:37Z] INFO  16:37:51,485 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:37Z] INFO  16:37:51,486 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:37Z] INFO  16:37:51,487 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-14T23:37Z] INFO  16:37:51,759 ProgressMeter -     15:79056407    400004.0    30.0 s      76.0 s       71.7%    41.0 s      11.0 s
[2016-04-14T23:37Z] INFO  16:37:52,034 ProgressMeter -            done   9779495.0    18.0 s       1.0 s      100.0%    18.0 s       0.0 s
[2016-04-14T23:37Z] INFO  16:37:52,034 ProgressMeter - Total runtime 18.66 secs, 0.31 min, 0.01 hours
[2016-04-14T23:37Z] INFO  16:37:52,035 MicroScheduler - 34267 reads were filtered out during the traversal out of approximately 364492 total reads (9.40%)
[2016-04-14T23:37Z] INFO  16:37:52,036 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:37Z] INFO  16:37:52,036 MicroScheduler -   -> 862 reads (0.24% of total) failing BadMateFilter
[2016-04-14T23:37Z] INFO  16:37:52,036 MicroScheduler -   -> 29593 reads (8.12% of total) failing DuplicateReadFilter
[2016-04-14T23:37Z] INFO  16:37:52,037 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-14T23:37Z] INFO  16:37:52,037 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:37Z] INFO  16:37:52,037 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-14T23:37Z] INFO  16:37:52,038 MicroScheduler -   -> 3812 reads (1.05% of total) failing MappingQualityZeroFilter
[2016-04-14T23:37Z] INFO  16:37:52,038 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:37Z] INFO  16:37:52,038 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-14T23:37Z] INFO  16:37:52,038 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-14T23:37Z] INFO  16:37:52,570 ProgressMeter -     17:80201436    200004.0    30.0 s       2.5 m       71.5%    41.0 s      11.0 s
[2016-04-14T23:37Z] INFO  16:37:52,604 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:37Z] GATK: realign ('16', 46633742, 64982002) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:37Z] INFO  16:37:52,951 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@5fe152b7
[2016-04-14T23:37Z] INFO  16:37:53,029 ProgressMeter -            done    201173.0    27.0 s       2.3 m       99.2%    27.0 s       0.0 s
[2016-04-14T23:37Z] INFO  16:37:53,029 ProgressMeter - Total runtime 27.45 secs, 0.46 min, 0.01 hours
[2016-04-14T23:37Z] INFO  16:37:53,030 MicroScheduler - 135 reads were filtered out during the traversal out of approximately 201308 total reads (0.07%)
[2016-04-14T23:37Z] INFO  16:37:53,030 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:37Z] INFO  16:37:53,030 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:37Z] INFO  16:37:53,031 MicroScheduler -   -> 135 reads (0.07% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:37Z] INFO  16:37:53,265 ProgressMeter -     17:38978866    400004.0    60.0 s       2.5 m       51.0%   117.0 s      57.0 s
[2016-04-14T23:37Z] INFO  16:37:53,536 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:37Z] GATK: realign ('16', 80575258, 90354753) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:37Z] INFO  16:37:54,470 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:37Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-18_18533538_34081962-prep-prealign.bam
[2016-04-14T23:37Z] INFO  16:37:54,809 ProgressMeter -     18:13826824    200009.0    30.0 s       2.5 m       74.6%    40.0 s      10.0 s
[2016-04-14T23:37Z] GATK RealignerTargetCreator: R14-18102_kapa-NGv3-PE100-NGv3-sort-18_18533538_34081962-prep-prealign.bam 18:18533539-34081962
[2016-04-14T23:37Z] GATK: RealignerTargetCreator
[2016-04-14T23:37Z] INFO  16:37:55,240 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:37Z] INFO  16:37:55,244 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:37Z] INFO  16:37:55,244 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:37Z] INFO  16:37:55,245 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:37Z] INFO  16:37:55,249 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/16/R14-18102_kapa-NGv3-PE100-NGv3-sort-16_46633742_64982002-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/16/R14-18102_kapa-NGv3-PE100-NGv3-sort-16_46633742_64982002-prep-prealign-realign.intervals -L 16:46633743-64982002 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/16/tx/tmpYtqsic/R14-18102_kapa-NGv3-PE100-NGv3-sort-16_46633742_64982002-prep.bam
[2016-04-14T23:37Z] INFO  16:37:55,261 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:37Z] INFO  16:37:55,261 HelpFormatter - Date/Time: 2016/04/14 16:37:55
[2016-04-14T23:37Z] INFO  16:37:55,261 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:37Z] INFO  16:37:55,262 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:37Z] INFO  16:37:55,444 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:37Z] INFO  16:37:55,554 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:37Z] INFO  16:37:55,564 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:37Z] INFO  16:37:55,621 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-14T23:37Z] INFO  16:37:55,952 IntervalUtils - Processing 18348260 bp from intervals
[2016-04-14T23:37Z] WARN  16:37:55,957 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:37Z] INFO  16:37:56,039 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:37Z] INFO  16:37:56,170 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:37Z] INFO  16:37:56,171 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:37Z] INFO  16:37:56,172 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:37Z] INFO  16:37:56,173 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:37Z] INFO  16:37:56,206 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:37Z] INFO  16:37:56,210 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:37Z] INFO  16:37:56,211 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:37Z] INFO  16:37:56,211 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:37Z] INFO  16:37:56,218 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/16/R14-18102_kapa-NGv3-PE100-NGv3-sort-16_80575258_90354753-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/16/R14-18102_kapa-NGv3-PE100-NGv3-sort-16_80575258_90354753-prep-prealign-realign.intervals -L 16:80575259-90354753 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/16/tx/tmphZRY48/R14-18102_kapa-NGv3-PE100-NGv3-sort-16_80575258_90354753-prep.bam
[2016-04-14T23:37Z] INFO  16:37:56,239 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:37Z] INFO  16:37:56,241 HelpFormatter - Date/Time: 2016/04/14 16:37:56
[2016-04-14T23:37Z] INFO  16:37:56,241 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:37Z] INFO  16:37:56,242 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:37Z] INFO  16:37:56,345 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:37Z] INFO  16:37:56,452 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:37Z] INFO  16:37:56,502 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:37Z] INFO  16:37:56,630 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:37Z] INFO  16:37:56,652 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:37Z] INFO  16:37:56,735 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-14T23:37Z] INFO  16:37:57,056 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@7172f77a
[2016-04-14T23:37Z] INFO  16:37:57,130 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@7172f77a
[2016-04-14T23:37Z] INFO  16:37:57,190 ProgressMeter -            done    638190.0    75.0 s     119.0 s      100.0%    75.0 s       0.0 s
[2016-04-14T23:37Z] INFO  16:37:57,190 ProgressMeter - Total runtime 75.98 secs, 1.27 min, 0.02 hours
[2016-04-14T23:37Z] INFO  16:37:57,191 MicroScheduler - 228 reads were filtered out during the traversal out of approximately 638418 total reads (0.04%)
[2016-04-14T23:37Z] INFO  16:37:57,191 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:37Z] INFO  16:37:57,191 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:37Z] INFO  16:37:57,192 MicroScheduler -   -> 228 reads (0.04% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:37Z] INFO  16:37:57,199 IntervalUtils - Processing 9779495 bp from intervals
[2016-04-14T23:37Z] WARN  16:37:57,215 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:37Z] INFO  16:37:57,219 ProgressMeter -            done    261415.0    32.0 s       2.1 m      100.0%    32.0 s       0.0 s
[2016-04-14T23:37Z] INFO  16:37:57,220 ProgressMeter - Total runtime 32.43 secs, 0.54 min, 0.01 hours
[2016-04-14T23:37Z] INFO  16:37:57,221 MicroScheduler - 161 reads were filtered out during the traversal out of approximately 261576 total reads (0.06%)
[2016-04-14T23:37Z] INFO  16:37:57,222 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:37Z] INFO  16:37:57,222 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:37Z] INFO  16:37:57,223 MicroScheduler -   -> 161 reads (0.06% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:37Z] INFO  16:37:57,365 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:37Z] INFO  16:37:57,521 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:37Z] INFO  16:37:57,522 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:37Z] INFO  16:37:57,523 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:37Z] INFO  16:37:57,523 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:37Z] INFO  16:37:57,657 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:37Z] INFO  16:37:57,754 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:37Z] INFO  16:37:58,020 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@41fd9d8e
[2016-04-14T23:37Z] INFO  16:37:58,023 ProgressMeter -            done    566407.0    36.0 s      65.0 s      100.0%    36.0 s       0.0 s
[2016-04-14T23:37Z] INFO  16:37:58,024 ProgressMeter - Total runtime 36.89 secs, 0.61 min, 0.01 hours
[2016-04-14T23:37Z] INFO  16:37:58,028 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 566407 total reads (0.00%)
[2016-04-14T23:37Z] INFO  16:37:58,028 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:37Z] INFO  16:37:58,028 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:37Z] INFO  16:37:58,029 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:37Z] INFO  16:37:58,089 ProgressMeter -            done    288621.0    35.0 s       2.1 m       98.0%    35.0 s       0.0 s
[2016-04-14T23:37Z] INFO  16:37:58,090 ProgressMeter - Total runtime 35.55 secs, 0.59 min, 0.01 hours
[2016-04-14T23:37Z] INFO  16:37:58,091 MicroScheduler - 89 reads were filtered out during the traversal out of approximately 288710 total reads (0.03%)
[2016-04-14T23:37Z] INFO  16:37:58,091 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:37Z] INFO  16:37:58,091 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:37Z] INFO  16:37:58,091 MicroScheduler -   -> 89 reads (0.03% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:37Z] INFO  16:37:58,222 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:37Z] INFO  16:37:58,225 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:37Z] INFO  16:37:58,226 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:37Z] INFO  16:37:58,227 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:37Z] INFO  16:37:58,232 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/18/R14-18102_kapa-NGv3-PE100-NGv3-sort-18_18533538_34081962-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/18/tx/tmpYi5nVa/R14-18102_kapa-NGv3-PE100-NGv3-sort-18_18533538_34081962-prep-prealign-realign.intervals -l INFO -L 18:18533539-34081962 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-14T23:37Z] INFO  16:37:58,263 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:37Z] INFO  16:37:58,264 HelpFormatter - Date/Time: 2016/04/14 16:37:58
[2016-04-14T23:37Z] INFO  16:37:58,265 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:37Z] INFO  16:37:58,265 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:37Z] INFO  16:37:58,360 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:37Z] INFO  16:37:58,542 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-14T23:37Z] INFO  16:37:58,552 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:37Z] INFO  16:37:58,569 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:37Z] INFO  16:37:58,594 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.04
[2016-04-14T23:37Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-16_64982511_80574976-prep-prealign.bam
[2016-04-14T23:37Z] INFO  16:37:58,686 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:37Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-18_0_18531348-prep-prealign.bam
[2016-04-14T23:37Z] INFO  16:37:58,835 ProgressMeter -     15:48461040    400008.0    30.0 s      77.0 s       74.6%    40.0 s      10.0 s
[2016-04-14T23:37Z] INFO  16:37:58,998 IntervalUtils - Processing 15548424 bp from intervals
[2016-04-14T23:37Z] WARN  16:37:59,014 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:37Z] INFO  16:37:59,107 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:37Z] INFO  16:37:59,384 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:37Z] INFO  16:37:59,386 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:37Z] INFO  16:37:59,386 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:37Z] INFO  16:37:59,387 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-14T23:37Z] INFO  16:37:59,510 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:37Z] INFO  16:37:59,536 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:37Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-15_67932890_83447639-prep.bam
[2016-04-14T23:37Z] GATK RealignerTargetCreator: R14-18102_kapa-NGv3-PE100-NGv3-sort-18_0_18531348-prep-prealign.bam 18:1-18531348
[2016-04-14T23:37Z] GATK: RealignerTargetCreator
[2016-04-14T23:37Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-17_77707305_81195210-prep-prealign.bam
[2016-04-14T23:38Z] GATK RealignerTargetCreator: R14-18102_kapa-NGv3-PE100-NGv3-sort-17_77707305_81195210-prep-prealign.bam 17:77707306-81195210
[2016-04-14T23:38Z] GATK: RealignerTargetCreator
[2016-04-14T23:38Z] GATK RealignerTargetCreator: R14-18102_kapa-NGv3-PE100-NGv3-sort-16_64982511_80574976-prep-prealign.bam 16:64982512-80574976
[2016-04-14T23:38Z] GATK: RealignerTargetCreator
[2016-04-14T23:38Z] GATK pre-alignment ('18', 50278423, 66344430) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:38Z] INFO  16:38:02,585 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:38Z] INFO  16:38:02,589 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:38Z] INFO  16:38:02,590 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:38Z] INFO  16:38:02,591 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:38Z] INFO  16:38:02,597 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/18/R14-18102_kapa-NGv3-PE100-NGv3-sort-18_0_18531348-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/18/tx/tmpu9gSf3/R14-18102_kapa-NGv3-PE100-NGv3-sort-18_0_18531348-prep-prealign-realign.intervals -l INFO -L 18:1-18531348 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-14T23:38Z] INFO  16:38:02,611 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:38Z] INFO  16:38:02,612 HelpFormatter - Date/Time: 2016/04/14 16:38:02
[2016-04-14T23:38Z] INFO  16:38:02,612 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:38Z] INFO  16:38:02,612 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:38Z] INFO  16:38:02,733 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:38Z] INFO  16:38:02,917 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-14T23:38Z] INFO  16:38:02,927 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:38Z] INFO  16:38:03,022 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.09
[2016-04-14T23:38Z] INFO  16:38:03,206 ProgressMeter -     16:30235942    900016.0   120.0 s       2.2 m       94.4%     2.1 m       7.0 s
[2016-04-14T23:38Z] INFO  16:38:03,332 IntervalUtils - Processing 18531348 bp from intervals
[2016-04-14T23:38Z] WARN  16:38:03,337 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:38Z] INFO  16:38:03,403 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:38Z] INFO  16:38:03,484 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:38Z] INFO  16:38:03,487 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:38Z] INFO  16:38:03,488 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:38Z] INFO  16:38:03,488 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:38Z] INFO  16:38:03,493 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/17/R14-18102_kapa-NGv3-PE100-NGv3-sort-17_77707305_81195210-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/17/tx/tmpUEhxuw/R14-18102_kapa-NGv3-PE100-NGv3-sort-17_77707305_81195210-prep-prealign-realign.intervals -l INFO -L 17:77707306-81195210 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-14T23:38Z] INFO  16:38:03,524 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:38Z] INFO  16:38:03,525 HelpFormatter - Date/Time: 2016/04/14 16:38:03
[2016-04-14T23:38Z] INFO  16:38:03,526 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:38Z] INFO  16:38:03,531 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:38Z] INFO  16:38:03,641 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:38Z] INFO  16:38:03,646 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:38Z] INFO  16:38:03,647 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:38Z] INFO  16:38:03,648 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-14T23:38Z] INFO  16:38:03,665 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:38Z] INFO  16:38:03,834 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:38Z] INFO  16:38:03,847 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:38Z] INFO  16:38:03,848 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:38Z] INFO  16:38:03,848 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:38Z] INFO  16:38:03,852 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/16/R14-18102_kapa-NGv3-PE100-NGv3-sort-16_64982511_80574976-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/16/tx/tmpzrMnAS/R14-18102_kapa-NGv3-PE100-NGv3-sort-16_64982511_80574976-prep-prealign-realign.intervals -l INFO -L 16:64982512-80574976 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-14T23:38Z] INFO  16:38:03,859 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:38Z] INFO  16:38:03,860 HelpFormatter - Date/Time: 2016/04/14 16:38:03
[2016-04-14T23:38Z] INFO  16:38:03,861 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:38Z] INFO  16:38:03,861 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:38Z] INFO  16:38:03,892 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-14T23:38Z] INFO  16:38:03,910 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:38Z] INFO  16:38:03,970 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-14T23:38Z] INFO  16:38:03,973 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:38Z] INFO  16:38:04,023 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@41fd9d8e
[2016-04-14T23:38Z] INFO  16:38:04,124 ProgressMeter -            done    617571.0    74.0 s     120.0 s      100.0%    74.0 s       0.0 s
[2016-04-14T23:38Z] INFO  16:38:04,132 ProgressMeter - Total runtime 74.37 secs, 1.24 min, 0.02 hours
[2016-04-14T23:38Z] INFO  16:38:04,132 MicroScheduler - 287 reads were filtered out during the traversal out of approximately 617858 total reads (0.05%)
[2016-04-14T23:38Z] INFO  16:38:04,132 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:38Z] INFO  16:38:04,133 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:38Z] INFO  16:38:04,144 MicroScheduler -   -> 287 reads (0.05% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:38Z] INFO  16:38:04,226 IntervalUtils - Processing 3487905 bp from intervals
[2016-04-14T23:38Z] WARN  16:38:04,231 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:38Z] INFO  16:38:04,249 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-14T23:38Z] INFO  16:38:04,270 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:38Z] INFO  16:38:04,332 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:38Z] INFO  16:38:04,335 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:38Z] INFO  16:38:04,336 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:38Z] INFO  16:38:04,336 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:38Z] INFO  16:38:04,341 HelpFormatter - Program Args: -T PrintReads -L 18:50278424-66344430 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/18/tx/tmpy0JBZ6/R14-18102_kapa-NGv3-PE100-NGv3-sort-18_50278423_66344430-prep-prealign.bam
[2016-04-14T23:38Z] INFO  16:38:04,349 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-14T23:38Z] INFO  16:38:04,367 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:38Z] INFO  16:38:04,367 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:38Z] INFO  16:38:04,367 HelpFormatter - Date/Time: 2016/04/14 16:38:04
[2016-04-14T23:38Z] INFO  16:38:04,367 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:38Z] INFO  16:38:04,368 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:38Z] INFO  16:38:04,535 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:38Z] INFO  16:38:04,579 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:38Z] INFO  16:38:04,581 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:38Z] INFO  16:38:04,581 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:38Z] INFO  16:38:04,582 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-14T23:38Z] INFO  16:38:04,684 IntervalUtils - Processing 15592465 bp from intervals
[2016-04-14T23:38Z] WARN  16:38:04,689 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:38Z] INFO  16:38:04,850 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:38Z] INFO  16:38:05,036 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:38Z] INFO  16:38:05,048 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:38Z] INFO  16:38:05,049 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:38Z] INFO  16:38:05,050 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-14T23:38Z] INFO  16:38:05,504 ProgressMeter -            done    594648.0    37.0 s      63.0 s      100.0%    37.0 s       0.0 s
[2016-04-14T23:38Z] INFO  16:38:05,505 ProgressMeter - Total runtime 37.54 secs, 0.63 min, 0.01 hours
[2016-04-14T23:38Z] INFO  16:38:05,509 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 594648 total reads (0.00%)
[2016-04-14T23:38Z] INFO  16:38:05,510 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:38Z] INFO  16:38:05,511 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:38Z] INFO  16:38:05,512 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:38Z] INFO  16:38:05,691 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:38Z] INFO  16:38:05,694 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-14T23:38Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-17_15515955_31039213-prep-prealign.bam
[2016-04-14T23:38Z] INFO  16:38:05,772 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:38Z] INFO  16:38:05,780 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:38Z] INFO  16:38:05,842 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-14T23:38Z] INFO  16:38:05,860 IntervalUtils - Processing 16066007 bp from intervals
[2016-04-14T23:38Z] INFO  16:38:05,957 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:38Z] INFO  16:38:06,346 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:38Z] INFO  16:38:06,347 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:38Z] INFO  16:38:06,348 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:38Z] INFO  16:38:06,348 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:38Z] INFO  16:38:06,362 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:38Z] INFO  16:38:06,542 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:38Z] INFO  16:38:07,178 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:38Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-15_36887086_52402170-prep.bam
[2016-04-14T23:38Z] GATK RealignerTargetCreator: R14-18102_kapa-NGv3-PE100-NGv3-sort-17_15515955_31039213-prep-prealign.bam 17:15515956-31039213
[2016-04-14T23:38Z] GATK: RealignerTargetCreator
[2016-04-14T23:38Z] INFO  16:38:08,793 ProgressMeter -     17:60483940    300003.0    60.0 s       3.3 m       89.4%    67.0 s       7.0 s
[2016-04-14T23:38Z] INFO  16:38:08,853 ProgressMeter -     18:44773695    100002.0    30.0 s       5.0 m       67.7%    44.0 s      14.0 s
[2016-04-14T23:38Z] GATK pre-alignment ('18', 66346699, 78077248) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:38Z] INFO  16:38:10,563 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:38Z] INFO  16:38:10,567 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:38Z] INFO  16:38:10,568 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:38Z] INFO  16:38:10,568 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:38Z] INFO  16:38:10,573 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/17/R14-18102_kapa-NGv3-PE100-NGv3-sort-17_15515955_31039213-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/17/tx/tmphRu1MT/R14-18102_kapa-NGv3-PE100-NGv3-sort-17_15515955_31039213-prep-prealign-realign.intervals -l INFO -L 17:15515956-31039213 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-14T23:38Z] INFO  16:38:10,603 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:38Z] INFO  16:38:10,604 HelpFormatter - Date/Time: 2016/04/14 16:38:10
[2016-04-14T23:38Z] INFO  16:38:10,604 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:38Z] INFO  16:38:10,605 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:38Z] INFO  16:38:10,720 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:38Z] INFO  16:38:10,924 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-14T23:38Z] INFO  16:38:10,935 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:38Z] INFO  16:38:11,009 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-14T23:38Z] INFO  16:38:11,429 IntervalUtils - Processing 15523258 bp from intervals
[2016-04-14T23:38Z] WARN  16:38:11,447 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:38Z] INFO  16:38:11,532 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:38Z] INFO  16:38:11,741 ProgressMeter -     17:74035928    300004.0    60.0 s       3.4 m       76.5%    78.0 s      18.0 s
[2016-04-14T23:38Z] INFO  16:38:11,751 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:38Z] INFO  16:38:11,752 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:38Z] INFO  16:38:11,753 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:38Z] INFO  16:38:11,754 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-14T23:38Z] INFO  16:38:11,966 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:38Z] INFO  16:38:11,970 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:38Z] INFO  16:38:11,970 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:38Z] INFO  16:38:11,971 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:38Z] INFO  16:38:11,976 HelpFormatter - Program Args: -T PrintReads -L 18:66346700-78077248 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/18/tx/tmpmM3ULB/R14-18102_kapa-NGv3-PE100-NGv3-sort-18_66346699_78077248-prep-prealign.bam
[2016-04-14T23:38Z] INFO  16:38:11,985 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:38Z] INFO  16:38:11,988 HelpFormatter - Date/Time: 2016/04/14 16:38:11
[2016-04-14T23:38Z] INFO  16:38:11,989 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:38Z] INFO  16:38:11,989 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:38Z] INFO  16:38:12,189 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:38Z] INFO  16:38:12,190 ProgressMeter -      17:7727338    600015.0    90.0 s       2.5 m       49.8%     3.0 m      90.0 s
[2016-04-14T23:38Z] INFO  16:38:13,266 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-14T23:38Z] INFO  16:38:13,374 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:38Z] INFO  16:38:13,383 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:38Z] INFO  16:38:13,439 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-14T23:38Z] INFO  16:38:13,454 IntervalUtils - Processing 11730549 bp from intervals
[2016-04-14T23:38Z] INFO  16:38:13,548 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:38Z] INFO  16:38:13,809 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:38Z] INFO  16:38:13,811 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:38Z] INFO  16:38:13,812 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:38Z] INFO  16:38:13,812 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:38Z] INFO  16:38:13,830 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:38Z] INFO  16:38:14,052 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:38Z] INFO  16:38:16,077 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@32d5a4c6
[2016-04-14T23:38Z] INFO  16:38:16,257 ProgressMeter -            done    249059.0    37.0 s       2.5 m      100.0%    37.0 s       0.0 s
[2016-04-14T23:38Z] INFO  16:38:16,257 ProgressMeter - Total runtime 37.45 secs, 0.62 min, 0.01 hours
[2016-04-14T23:38Z] INFO  16:38:16,258 MicroScheduler - 144 reads were filtered out during the traversal out of approximately 249203 total reads (0.06%)
[2016-04-14T23:38Z] INFO  16:38:16,258 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:38Z] INFO  16:38:16,258 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:38Z] INFO  16:38:16,259 MicroScheduler -   -> 144 reads (0.06% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:38Z] INFO  16:38:16,262 ProgressMeter -            done   3487905.0    11.0 s       3.0 s      100.0%    11.0 s       0.0 s
[2016-04-14T23:38Z] INFO  16:38:16,263 ProgressMeter - Total runtime 11.68 secs, 0.19 min, 0.00 hours
[2016-04-14T23:38Z] INFO  16:38:16,267 MicroScheduler - 24733 reads were filtered out during the traversal out of approximately 290291 total reads (8.52%)
[2016-04-14T23:38Z] INFO  16:38:16,267 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:38Z] INFO  16:38:16,267 MicroScheduler -   -> 502 reads (0.17% of total) failing BadMateFilter
[2016-04-14T23:38Z] INFO  16:38:16,268 MicroScheduler -   -> 23652 reads (8.15% of total) failing DuplicateReadFilter
[2016-04-14T23:38Z] INFO  16:38:16,268 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-14T23:38Z] INFO  16:38:16,268 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:38Z] INFO  16:38:16,269 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-14T23:38Z] INFO  16:38:16,269 MicroScheduler -   -> 579 reads (0.20% of total) failing MappingQualityZeroFilter
[2016-04-14T23:38Z] INFO  16:38:16,269 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:38Z] INFO  16:38:16,270 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-14T23:38Z] INFO  16:38:16,270 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-14T23:38Z] INFO  16:38:17,668 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:38Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-18_34092400_49867248-prep-prealign.bam
[2016-04-14T23:38Z] INFO  16:38:17,716 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:38Z] GATK: realign ('17', 77707305, 81195210) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:38Z] INFO  16:38:17,751 ProgressMeter -            done   1.5548424E7    18.0 s       1.0 s      100.0%    18.0 s       0.0 s
[2016-04-14T23:38Z] INFO  16:38:17,752 ProgressMeter - Total runtime 18.37 secs, 0.31 min, 0.01 hours
[2016-04-14T23:38Z] INFO  16:38:17,756 MicroScheduler - 17696 reads were filtered out during the traversal out of approximately 202867 total reads (8.72%)
[2016-04-14T23:38Z] INFO  16:38:17,757 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:38Z] INFO  16:38:17,757 MicroScheduler -   -> 638 reads (0.31% of total) failing BadMateFilter
[2016-04-14T23:38Z] INFO  16:38:17,757 MicroScheduler -   -> 16177 reads (7.97% of total) failing DuplicateReadFilter
[2016-04-14T23:38Z] INFO  16:38:17,758 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-14T23:38Z] INFO  16:38:17,758 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:38Z] INFO  16:38:17,758 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-14T23:38Z] INFO  16:38:17,758 MicroScheduler -   -> 881 reads (0.43% of total) failing MappingQualityZeroFilter
[2016-04-14T23:38Z] INFO  16:38:17,759 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:38Z] INFO  16:38:17,759 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-14T23:38Z] INFO  16:38:17,759 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-14T23:38Z] GATK RealignerTargetCreator: R14-18102_kapa-NGv3-PE100-NGv3-sort-18_34092400_49867248-prep-prealign.bam 18:34092401-49867248
[2016-04-14T23:38Z] GATK: RealignerTargetCreator
[2016-04-14T23:38Z] INFO  16:38:19,104 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:38Z] GATK: realign ('18', 18533538, 34081962) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:38Z] INFO  16:38:19,229 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@7172f77a
[2016-04-14T23:38Z] INFO  16:38:19,289 ProgressMeter -            done   1167959.0     2.3 m     116.0 s      100.0%     2.3 m       0.0 s
[2016-04-14T23:38Z] INFO  16:38:19,290 ProgressMeter - Total runtime 136.47 secs, 2.27 min, 0.04 hours
[2016-04-14T23:38Z] INFO  16:38:19,290 MicroScheduler - 416 reads were filtered out during the traversal out of approximately 1168375 total reads (0.04%)
[2016-04-14T23:38Z] INFO  16:38:19,291 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:38Z] INFO  16:38:19,291 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:38Z] INFO  16:38:19,291 MicroScheduler -   -> 416 reads (0.04% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:38Z] INFO  16:38:20,082 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:38Z] INFO  16:38:20,085 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:38Z] INFO  16:38:20,086 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:38Z] INFO  16:38:20,087 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:38Z] INFO  16:38:20,091 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/17/R14-18102_kapa-NGv3-PE100-NGv3-sort-17_77707305_81195210-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/17/R14-18102_kapa-NGv3-PE100-NGv3-sort-17_77707305_81195210-prep-prealign-realign.intervals -L 17:77707306-81195210 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/17/tx/tmpRDeyR6/R14-18102_kapa-NGv3-PE100-NGv3-sort-17_77707305_81195210-prep.bam
[2016-04-14T23:38Z] INFO  16:38:20,102 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:38Z] INFO  16:38:20,103 HelpFormatter - Date/Time: 2016/04/14 16:38:20
[2016-04-14T23:38Z] INFO  16:38:20,103 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:38Z] INFO  16:38:20,104 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:38Z] INFO  16:38:20,354 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:38Z] INFO  16:38:20,469 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:38Z] INFO  16:38:20,478 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:38Z] INFO  16:38:20,540 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-14T23:38Z] INFO  16:38:20,676 ProgressMeter -            done    359302.0    24.0 s      68.0 s      100.0%    24.0 s       0.0 s
[2016-04-14T23:38Z] INFO  16:38:20,676 ProgressMeter - Total runtime 24.50 secs, 0.41 min, 0.01 hours
[2016-04-14T23:38Z] INFO  16:38:20,680 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 359302 total reads (0.00%)
[2016-04-14T23:38Z] INFO  16:38:20,680 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:38Z] INFO  16:38:20,680 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:38Z] INFO  16:38:20,681 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:38Z] INFO  16:38:20,788 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:38Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-16_15596122_31106473-prep-prealign.bam
[2016-04-14T23:38Z] INFO  16:38:20,894 IntervalUtils - Processing 3487905 bp from intervals
[2016-04-14T23:38Z] WARN  16:38:20,899 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:38Z] INFO  16:38:20,975 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:38Z] INFO  16:38:21,045 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:38Z] INFO  16:38:21,046 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:38Z] INFO  16:38:21,047 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:38Z] INFO  16:38:21,048 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:38Z] INFO  16:38:21,116 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:38Z] INFO  16:38:21,119 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:38Z] INFO  16:38:21,120 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:38Z] INFO  16:38:21,120 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:38Z] INFO  16:38:21,130 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/18/R14-18102_kapa-NGv3-PE100-NGv3-sort-18_34092400_49867248-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/18/tx/tmpUiW4uR/R14-18102_kapa-NGv3-PE100-NGv3-sort-18_34092400_49867248-prep-prealign-realign.intervals -l INFO -L 18:34092401-49867248 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-14T23:38Z] INFO  16:38:21,144 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:38Z] INFO  16:38:21,145 HelpFormatter - Date/Time: 2016/04/14 16:38:21
[2016-04-14T23:38Z] INFO  16:38:21,146 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:38Z] INFO  16:38:21,146 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:38Z] INFO  16:38:21,159 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:38Z] INFO  16:38:21,207 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:38Z] INFO  16:38:21,252 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:38Z] INFO  16:38:21,501 ProgressMeter -     16:14991277   1.4974976E7    30.0 s       2.0 s       96.5%    31.0 s       1.0 s
[2016-04-14T23:38Z] INFO  16:38:21,521 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-14T23:38Z] INFO  16:38:21,542 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:38Z] INFO  16:38:21,591 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-14T23:38Z] INFO  16:38:21,887 IntervalUtils - Processing 15774848 bp from intervals
[2016-04-14T23:38Z] WARN  16:38:21,893 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:38Z] INFO  16:38:21,977 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:38Z] INFO  16:38:22,059 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:38Z] INFO  16:38:22,062 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:38Z] INFO  16:38:22,063 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:38Z] INFO  16:38:22,063 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:38Z] INFO  16:38:22,067 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/18/R14-18102_kapa-NGv3-PE100-NGv3-sort-18_18533538_34081962-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/18/R14-18102_kapa-NGv3-PE100-NGv3-sort-18_18533538_34081962-prep-prealign-realign.intervals -L 18:18533539-34081962 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/18/tx/tmps_HeZ9/R14-18102_kapa-NGv3-PE100-NGv3-sort-18_18533538_34081962-prep.bam
[2016-04-14T23:38Z] INFO  16:38:22,075 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:38Z] INFO  16:38:22,076 HelpFormatter - Date/Time: 2016/04/14 16:38:22
[2016-04-14T23:38Z] INFO  16:38:22,077 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:38Z] INFO  16:38:22,077 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:38Z] INFO  16:38:22,123 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@41fd9d8e
[2016-04-14T23:38Z] INFO  16:38:22,211 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:38Z] INFO  16:38:22,213 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:38Z] INFO  16:38:22,214 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:38Z] INFO  16:38:22,215 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-14T23:38Z] INFO  16:38:22,244 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:38Z] INFO  16:38:22,252 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:38Z] INFO  16:38:22,252 ProgressMeter -            done    507581.0    73.0 s       2.4 m      100.0%    73.0 s       0.0 s
[2016-04-14T23:38Z] INFO  16:38:22,253 ProgressMeter - Total runtime 73.49 secs, 1.22 min, 0.02 hours
[2016-04-14T23:38Z] INFO  16:38:22,253 MicroScheduler - 225 reads were filtered out during the traversal out of approximately 507806 total reads (0.04%)
[2016-04-14T23:38Z] INFO  16:38:22,253 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:38Z] INFO  16:38:22,254 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:38Z] INFO  16:38:22,254 MicroScheduler -   -> 225 reads (0.04% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:38Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-16_46633742_64982002-prep.bam
[2016-04-14T23:38Z] INFO  16:38:22,382 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:38Z] INFO  16:38:22,391 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:38Z] INFO  16:38:22,435 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.04
[2016-04-14T23:38Z] INFO  16:38:22,788 IntervalUtils - Processing 15548424 bp from intervals
[2016-04-14T23:38Z] WARN  16:38:22,794 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:38Z] INFO  16:38:22,918 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:38Z] INFO  16:38:23,108 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:38Z] INFO  16:38:23,109 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:38Z] INFO  16:38:23,110 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:38Z] INFO  16:38:23,111 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:38Z] INFO  16:38:23,256 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:38Z] INFO  16:38:23,520 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:38Z] GATK pre-alignment ('19', 0, 15509577) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:38Z] INFO  16:38:23,702 ProgressMeter -            done   1.5528616E7    32.0 s       2.0 s      100.0%    32.0 s       0.0 s
[2016-04-14T23:38Z] INFO  16:38:23,702 ProgressMeter - Total runtime 32.22 secs, 0.54 min, 0.01 hours
[2016-04-14T23:38Z] INFO  16:38:23,706 MicroScheduler - 171639 reads were filtered out during the traversal out of approximately 914899 total reads (18.76%)
[2016-04-14T23:38Z] INFO  16:38:23,707 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:38Z] INFO  16:38:23,707 MicroScheduler -   -> 1581 reads (0.17% of total) failing BadMateFilter
[2016-04-14T23:38Z] INFO  16:38:23,708 MicroScheduler -   -> 66455 reads (7.26% of total) failing DuplicateReadFilter
[2016-04-14T23:38Z] INFO  16:38:23,708 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-14T23:38Z] INFO  16:38:23,709 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:38Z] INFO  16:38:23,710 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-14T23:38Z] INFO  16:38:23,710 MicroScheduler -   -> 103603 reads (11.32% of total) failing MappingQualityZeroFilter
[2016-04-14T23:38Z] INFO  16:38:23,711 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:38Z] INFO  16:38:23,711 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-14T23:38Z] INFO  16:38:23,712 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-14T23:38Z] INFO  16:38:23,845 ProgressMeter -     17:40936127    700011.0    91.0 s       2.2 m       63.6%     2.4 m      52.0 s
[2016-04-14T23:38Z] INFO  16:38:23,873 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:38Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-17_46607689_62121560-prep-prealign.bam
[2016-04-14T23:38Z] INFO  16:38:24,162 ProgressMeter -            done   1.8531348E7    20.0 s       1.0 s      100.0%    20.0 s       0.0 s
[2016-04-14T23:38Z] INFO  16:38:24,162 ProgressMeter - Total runtime 20.52 secs, 0.34 min, 0.01 hours
[2016-04-14T23:38Z] INFO  16:38:24,165 MicroScheduler - 31407 reads were filtered out during the traversal out of approximately 262588 total reads (11.96%)
[2016-04-14T23:38Z] INFO  16:38:24,166 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:38Z] INFO  16:38:24,166 MicroScheduler -   -> 775 reads (0.30% of total) failing BadMateFilter
[2016-04-14T23:38Z] INFO  16:38:24,166 MicroScheduler -   -> 20294 reads (7.73% of total) failing DuplicateReadFilter
[2016-04-14T23:38Z] INFO  16:38:24,167 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-14T23:38Z] INFO  16:38:24,167 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:38Z] INFO  16:38:24,167 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-14T23:38Z] INFO  16:38:24,167 MicroScheduler -   -> 10338 reads (3.94% of total) failing MappingQualityZeroFilter
[2016-04-14T23:38Z] INFO  16:38:24,168 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:38Z] INFO  16:38:24,168 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-14T23:38Z] INFO  16:38:24,169 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-14T23:38Z] GATK RealignerTargetCreator: R14-18102_kapa-NGv3-PE100-NGv3-sort-16_15596122_31106473-prep-prealign.bam 16:15596123-31106473
[2016-04-14T23:38Z] GATK: RealignerTargetCreator
[2016-04-14T23:38Z] INFO  16:38:25,056 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:38Z] GATK: realign ('16', 0, 15528616) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:38Z] INFO  16:38:25,203 ProgressMeter -            done    362290.0    27.0 s      76.0 s       98.8%    27.0 s       0.0 s
[2016-04-14T23:38Z] INFO  16:38:25,204 ProgressMeter - Total runtime 27.68 secs, 0.46 min, 0.01 hours
[2016-04-14T23:38Z] INFO  16:38:25,207 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 362290 total reads (0.00%)
[2016-04-14T23:38Z] INFO  16:38:25,207 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:38Z] INFO  16:38:25,208 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:38Z] INFO  16:38:25,208 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:38Z] GATK RealignerTargetCreator: R14-18102_kapa-NGv3-PE100-NGv3-sort-17_46607689_62121560-prep-prealign.bam 17:46607690-62121560
[2016-04-14T23:38Z] GATK: RealignerTargetCreator
[2016-04-14T23:38Z] INFO  16:38:25,612 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:38Z] GATK: realign ('18', 0, 18531348) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:38Z] INFO  16:38:26,257 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:38Z] INFO  16:38:26,260 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:38Z] INFO  16:38:26,261 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:38Z] INFO  16:38:26,261 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:38Z] INFO  16:38:26,266 HelpFormatter - Program Args: -T PrintReads -L 19:1-15509577 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/19/tx/tmpm8QRET/R14-18102_kapa-NGv3-PE100-NGv3-sort-19_0_15509577-prep-prealign.bam
[2016-04-14T23:38Z] INFO  16:38:26,276 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:38Z] INFO  16:38:26,277 HelpFormatter - Date/Time: 2016/04/14 16:38:26
[2016-04-14T23:38Z] INFO  16:38:26,278 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:38Z] INFO  16:38:26,278 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:38Z] INFO  16:38:26,501 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:38Z] INFO  16:38:26,568 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@41fd9d8e
[2016-04-14T23:38Z] INFO  16:38:26,651 ProgressMeter -            done    150730.0    20.0 s       2.2 m      100.0%    20.0 s       0.0 s
[2016-04-14T23:38Z] INFO  16:38:26,652 ProgressMeter - Total runtime 20.30 secs, 0.34 min, 0.01 hours
[2016-04-14T23:38Z] INFO  16:38:26,652 MicroScheduler - 116 reads were filtered out during the traversal out of approximately 150846 total reads (0.08%)
[2016-04-14T23:38Z] INFO  16:38:26,653 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:38Z] INFO  16:38:26,654 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:38Z] INFO  16:38:26,654 MicroScheduler -   -> 116 reads (0.08% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:38Z] INFO  16:38:26,843 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:38Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-16_80575258_90354753-prep.bam
[2016-04-14T23:38Z] INFO  16:38:27,114 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:38Z] INFO  16:38:27,117 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:38Z] INFO  16:38:27,117 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:38Z] INFO  16:38:27,118 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:38Z] INFO  16:38:27,122 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/16/R14-18102_kapa-NGv3-PE100-NGv3-sort-16_15596122_31106473-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/16/tx/tmpbSBzjP/R14-18102_kapa-NGv3-PE100-NGv3-sort-16_15596122_31106473-prep-prealign-realign.intervals -l INFO -L 16:15596123-31106473 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-14T23:38Z] INFO  16:38:27,141 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:38Z] INFO  16:38:27,141 HelpFormatter - Date/Time: 2016/04/14 16:38:27
[2016-04-14T23:38Z] INFO  16:38:27,141 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:38Z] INFO  16:38:27,142 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:38Z] INFO  16:38:27,251 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:38Z] INFO  16:38:27,517 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-14T23:38Z] INFO  16:38:27,526 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:38Z] INFO  16:38:27,575 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-14T23:38Z] INFO  16:38:27,593 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-14T23:38Z] INFO  16:38:27,610 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:38Z] INFO  16:38:27,613 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:38Z] INFO  16:38:27,614 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:38Z] INFO  16:38:27,614 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:38Z] INFO  16:38:27,619 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/16/R14-18102_kapa-NGv3-PE100-NGv3-sort-16_0_15528616-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/16/R14-18102_kapa-NGv3-PE100-NGv3-sort-16_0_15528616-prep-prealign-realign.intervals -L 16:1-15528616 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/16/tx/tmpX7P_P2/R14-18102_kapa-NGv3-PE100-NGv3-sort-16_0_15528616-prep.bam
[2016-04-14T23:38Z] INFO  16:38:27,631 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:38Z] INFO  16:38:27,640 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:38Z] INFO  16:38:27,654 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:38Z] INFO  16:38:27,663 HelpFormatter - Date/Time: 2016/04/14 16:38:27
[2016-04-14T23:38Z] INFO  16:38:27,664 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:38Z] INFO  16:38:27,665 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:38Z] INFO  16:38:27,714 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-14T23:38Z] INFO  16:38:27,728 IntervalUtils - Processing 15509577 bp from intervals
[2016-04-14T23:38Z] INFO  16:38:27,841 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:38Z] INFO  16:38:27,905 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:38Z] INFO  16:38:27,958 IntervalUtils - Processing 15510351 bp from intervals
[2016-04-14T23:38Z] WARN  16:38:27,963 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:38Z] INFO  16:38:28,033 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:38Z] INFO  16:38:28,085 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:38Z] GATK pre-alignment ('19', 15510112, 31025906) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:38Z] INFO  16:38:28,094 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:38Z] INFO  16:38:28,095 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:38Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-18_50278423_66344430-prep-prealign.bam
[2016-04-14T23:38Z] INFO  16:38:28,172 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-14T23:38Z] INFO  16:38:28,200 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:38Z] INFO  16:38:28,200 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:38Z] INFO  16:38:28,201 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:38Z] INFO  16:38:28,201 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:38Z] INFO  16:38:28,217 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:38Z] INFO  16:38:28,236 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:38Z] INFO  16:38:28,237 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:38Z] INFO  16:38:28,238 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:38Z] INFO  16:38:28,239 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-14T23:38Z] INFO  16:38:28,301 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:38Z] INFO  16:38:28,305 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:38Z] INFO  16:38:28,305 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:38Z] INFO  16:38:28,306 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:38Z] INFO  16:38:28,311 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/17/R14-18102_kapa-NGv3-PE100-NGv3-sort-17_46607689_62121560-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/17/tx/tmp2rbBko/R14-18102_kapa-NGv3-PE100-NGv3-sort-17_46607689_62121560-prep-prealign-realign.intervals -l INFO -L 17:46607690-62121560 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-14T23:38Z] INFO  16:38:28,323 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:38Z] INFO  16:38:28,323 HelpFormatter - Date/Time: 2016/04/14 16:38:28
[2016-04-14T23:38Z] INFO  16:38:28,323 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:38Z] INFO  16:38:28,323 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:38Z] INFO  16:38:28,389 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:38Z] INFO  16:38:28,459 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:38Z] INFO  16:38:28,463 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:38Z] INFO  16:38:28,463 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:38Z] INFO  16:38:28,464 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:38Z] INFO  16:38:28,468 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/18/R14-18102_kapa-NGv3-PE100-NGv3-sort-18_0_18531348-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/18/R14-18102_kapa-NGv3-PE100-NGv3-sort-18_0_18531348-prep-prealign-realign.intervals -L 18:1-18531348 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/18/tx/tmpBmj5EL/R14-18102_kapa-NGv3-PE100-NGv3-sort-18_0_18531348-prep.bam
[2016-04-14T23:38Z] INFO  16:38:28,469 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:38Z] INFO  16:38:28,501 IntervalUtils - Processing 15528616 bp from intervals
[2016-04-14T23:38Z] WARN  16:38:28,506 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:38Z] INFO  16:38:28,528 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:38Z] INFO  16:38:28,529 HelpFormatter - Date/Time: 2016/04/14 16:38:28
[2016-04-14T23:38Z] INFO  16:38:28,530 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:38Z] INFO  16:38:28,530 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:38Z] INFO  16:38:28,587 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:38Z] GATK RealignerTargetCreator: R14-18102_kapa-NGv3-PE100-NGv3-sort-18_50278423_66344430-prep-prealign.bam 18:50278424-66344430
[2016-04-14T23:38Z] GATK: RealignerTargetCreator
[2016-04-14T23:38Z] INFO  16:38:28,725 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:38Z] INFO  16:38:28,735 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-14T23:38Z] INFO  16:38:28,738 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:38Z] INFO  16:38:28,740 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:38Z] INFO  16:38:28,740 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:38Z] INFO  16:38:28,741 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:38Z] INFO  16:38:28,757 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:38Z] INFO  16:38:28,812 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-14T23:38Z] INFO  16:38:28,880 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:38Z] INFO  16:38:28,889 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:38Z] INFO  16:38:28,925 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:38Z] INFO  16:38:28,951 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-14T23:38Z] INFO  16:38:29,119 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:38Z] INFO  16:38:29,135 IntervalUtils - Processing 15513871 bp from intervals
[2016-04-14T23:38Z] WARN  16:38:29,140 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:38Z] INFO  16:38:29,243 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:38Z] INFO  16:38:29,283 IntervalUtils - Processing 18531348 bp from intervals
[2016-04-14T23:38Z] WARN  16:38:29,288 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:38Z] INFO  16:38:29,358 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:38Z] INFO  16:38:29,514 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:38Z] INFO  16:38:29,515 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:38Z] INFO  16:38:29,516 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:38Z] INFO  16:38:29,528 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:38Z] INFO  16:38:29,560 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:38Z] INFO  16:38:29,560 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:38Z] INFO  16:38:29,561 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:38Z] INFO  16:38:29,561 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-14T23:38Z] INFO  16:38:29,785 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:38Z] INFO  16:38:29,984 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:38Z] INFO  16:38:31,127 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:38Z] INFO  16:38:31,131 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:38Z] INFO  16:38:31,131 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:38Z] INFO  16:38:31,132 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:38Z] INFO  16:38:31,159 HelpFormatter - Program Args: -T PrintReads -L 19:15510113-31025906 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/19/tx/tmphK51Lg/R14-18102_kapa-NGv3-PE100-NGv3-sort-19_15510112_31025906-prep-prealign.bam
[2016-04-14T23:38Z] INFO  16:38:31,168 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:38Z] INFO  16:38:31,179 HelpFormatter - Date/Time: 2016/04/14 16:38:31
[2016-04-14T23:38Z] INFO  16:38:31,180 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:38Z] INFO  16:38:31,181 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:38Z] INFO  16:38:31,394 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:38Z] INFO  16:38:31,607 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:38Z] INFO  16:38:31,611 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:38Z] INFO  16:38:31,612 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:38Z] INFO  16:38:31,612 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:38Z] INFO  16:38:31,617 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/18/R14-18102_kapa-NGv3-PE100-NGv3-sort-18_50278423_66344430-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/18/tx/tmpDFuVua/R14-18102_kapa-NGv3-PE100-NGv3-sort-18_50278423_66344430-prep-prealign-realign.intervals -l INFO -L 18:50278424-66344430 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-14T23:38Z] INFO  16:38:31,635 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:38Z] INFO  16:38:31,636 HelpFormatter - Date/Time: 2016/04/14 16:38:31
[2016-04-14T23:38Z] INFO  16:38:31,636 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:38Z] INFO  16:38:31,637 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:38Z] INFO  16:38:31,746 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:38Z] INFO  16:38:31,981 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-14T23:38Z] INFO  16:38:31,998 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:38Z] INFO  16:38:32,083 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-14T23:38Z] INFO  16:38:32,465 IntervalUtils - Processing 16066007 bp from intervals
[2016-04-14T23:38Z] WARN  16:38:32,471 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:38Z] INFO  16:38:32,560 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:38Z] INFO  16:38:32,599 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-14T23:38Z] INFO  16:38:32,672 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:38Z] INFO  16:38:32,692 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:38Z] INFO  16:38:32,736 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.04
[2016-04-14T23:38Z] INFO  16:38:32,743 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:38Z] INFO  16:38:32,744 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:38Z] INFO  16:38:32,745 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:38Z] INFO  16:38:32,746 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-14T23:38Z] INFO  16:38:32,750 IntervalUtils - Processing 15515794 bp from intervals
[2016-04-14T23:38Z] INFO  16:38:32,832 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:38Z] INFO  16:38:33,143 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:38Z] INFO  16:38:33,145 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:38Z] INFO  16:38:33,145 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:38Z] INFO  16:38:33,146 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:38Z] INFO  16:38:33,177 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:38Z] INFO  16:38:33,219 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@41fd9d8e
[2016-04-14T23:38Z] INFO  16:38:33,318 ProgressMeter -            done    129890.0    19.0 s       2.5 m       99.4%    19.0 s       0.0 s
[2016-04-14T23:38Z] INFO  16:38:33,319 ProgressMeter - Total runtime 19.51 secs, 0.33 min, 0.01 hours
[2016-04-14T23:38Z] INFO  16:38:33,319 MicroScheduler - 95 reads were filtered out during the traversal out of approximately 129985 total reads (0.07%)
[2016-04-14T23:38Z] INFO  16:38:33,320 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:38Z] INFO  16:38:33,320 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:38Z] INFO  16:38:33,320 MicroScheduler -   -> 95 reads (0.07% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:38Z] INFO  16:38:33,342 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:38Z] INFO  16:38:33,932 ProgressMeter -            done   1.5592465E7    28.0 s       1.0 s      100.0%    28.0 s       0.0 s
[2016-04-14T23:38Z] INFO  16:38:33,934 ProgressMeter - Total runtime 28.89 secs, 0.48 min, 0.01 hours
[2016-04-14T23:38Z] INFO  16:38:33,938 MicroScheduler - 95193 reads were filtered out during the traversal out of approximately 641782 total reads (14.83%)
[2016-04-14T23:38Z] INFO  16:38:33,939 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:38Z] INFO  16:38:33,940 MicroScheduler -   -> 1235 reads (0.19% of total) failing BadMateFilter
[2016-04-14T23:38Z] INFO  16:38:33,941 MicroScheduler -   -> 48636 reads (7.58% of total) failing DuplicateReadFilter
[2016-04-14T23:38Z] INFO  16:38:33,942 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-14T23:38Z] INFO  16:38:33,942 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:38Z] INFO  16:38:33,943 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-14T23:38Z] INFO  16:38:33,944 MicroScheduler -   -> 45322 reads (7.06% of total) failing MappingQualityZeroFilter
[2016-04-14T23:38Z] INFO  16:38:33,944 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:38Z] INFO  16:38:33,945 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-14T23:38Z] INFO  16:38:33,945 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-14T23:38Z] INFO  16:38:34,933 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:38Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-18_66346699_78077248-prep-prealign.bam
[2016-04-14T23:38Z] GATK RealignerTargetCreator: R14-18102_kapa-NGv3-PE100-NGv3-sort-18_66346699_78077248-prep-prealign.bam 18:66346700-78077248
[2016-04-14T23:38Z] GATK: RealignerTargetCreator
[2016-04-14T23:38Z] INFO  16:38:35,424 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:38Z] GATK: realign ('16', 64982511, 80574976) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:38Z] INFO  16:38:37,864 ProgressMeter -            done   1.5523258E7    26.0 s       1.0 s      100.0%    26.0 s       0.0 s
[2016-04-14T23:38Z] INFO  16:38:37,865 ProgressMeter - Total runtime 26.11 secs, 0.44 min, 0.01 hours
[2016-04-14T23:38Z] INFO  16:38:37,869 MicroScheduler - 81942 reads were filtered out during the traversal out of approximately 622023 total reads (13.17%)
[2016-04-14T23:38Z] INFO  16:38:37,870 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:38Z] INFO  16:38:37,871 MicroScheduler -   -> 1118 reads (0.18% of total) failing BadMateFilter
[2016-04-14T23:38Z] INFO  16:38:37,871 MicroScheduler -   -> 47524 reads (7.64% of total) failing DuplicateReadFilter
[2016-04-14T23:38Z] INFO  16:38:37,872 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-14T23:38Z] INFO  16:38:37,872 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:38Z] INFO  16:38:37,873 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-14T23:38Z] INFO  16:38:37,874 MicroScheduler -   -> 33300 reads (5.35% of total) failing MappingQualityZeroFilter
[2016-04-14T23:38Z] INFO  16:38:37,874 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:38Z] INFO  16:38:37,875 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-14T23:38Z] INFO  16:38:37,875 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-14T23:38Z] INFO  16:38:38,039 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@7172f77a
[2016-04-14T23:38Z] INFO  16:38:38,068 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:38Z] INFO  16:38:38,072 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:38Z] INFO  16:38:38,072 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:38Z] INFO  16:38:38,073 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:38Z] INFO  16:38:38,077 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/18/R14-18102_kapa-NGv3-PE100-NGv3-sort-18_66346699_78077248-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/18/tx/tmpp2eP3e/R14-18102_kapa-NGv3-PE100-NGv3-sort-18_66346699_78077248-prep-prealign-realign.intervals -l INFO -L 18:66346700-78077248 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-14T23:38Z] INFO  16:38:38,099 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:38Z] INFO  16:38:38,108 HelpFormatter - Date/Time: 2016/04/14 16:38:38
[2016-04-14T23:38Z] INFO  16:38:38,109 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:38Z] INFO  16:38:38,109 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:38Z] INFO  16:38:38,189 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:38Z] INFO  16:38:38,238 ProgressMeter -            done    593504.0    87.0 s       2.4 m      100.0%    87.0 s       0.0 s
[2016-04-14T23:38Z] INFO  16:38:38,239 ProgressMeter - Total runtime 87.20 secs, 1.45 min, 0.02 hours
[2016-04-14T23:38Z] INFO  16:38:38,239 MicroScheduler - 253 reads were filtered out during the traversal out of approximately 593757 total reads (0.04%)
[2016-04-14T23:38Z] INFO  16:38:38,239 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:38Z] INFO  16:38:38,240 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:38Z] INFO  16:38:38,240 MicroScheduler -   -> 253 reads (0.04% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:38Z] INFO  16:38:38,415 ProgressMeter -            done   1.5774848E7    16.0 s       1.0 s      100.0%    16.0 s       0.0 s
[2016-04-14T23:38Z] INFO  16:38:38,420 ProgressMeter - Total runtime 16.21 secs, 0.27 min, 0.00 hours
[2016-04-14T23:38Z] INFO  16:38:38,420 MicroScheduler - 88491 reads were filtered out during the traversal out of approximately 250256 total reads (35.36%)
[2016-04-14T23:38Z] INFO  16:38:38,421 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:38Z] INFO  16:38:38,425 MicroScheduler -   -> 624 reads (0.25% of total) failing BadMateFilter
[2016-04-14T23:38Z] INFO  16:38:38,426 MicroScheduler -   -> 15055 reads (6.02% of total) failing DuplicateReadFilter
[2016-04-14T23:38Z] INFO  16:38:38,427 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-14T23:38Z] INFO  16:38:38,427 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:38Z] INFO  16:38:38,428 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-14T23:38Z] INFO  16:38:38,429 MicroScheduler -   -> 72812 reads (29.10% of total) failing MappingQualityZeroFilter
[2016-04-14T23:38Z] INFO  16:38:38,429 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:38Z] INFO  16:38:38,430 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-14T23:38Z] INFO  16:38:38,432 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-14T23:38Z] INFO  16:38:38,447 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-14T23:38Z] INFO  16:38:38,449 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:38Z] INFO  16:38:38,453 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:38Z] INFO  16:38:38,454 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:38Z] INFO  16:38:38,454 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:38Z] INFO  16:38:38,459 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/16/R14-18102_kapa-NGv3-PE100-NGv3-sort-16_64982511_80574976-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/16/R14-18102_kapa-NGv3-PE100-NGv3-sort-16_64982511_80574976-prep-prealign-realign.intervals -L 16:64982512-80574976 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/16/tx/tmpbhM68m/R14-18102_kapa-NGv3-PE100-NGv3-sort-16_64982511_80574976-prep.bam
[2016-04-14T23:38Z] INFO  16:38:38,474 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:38Z] INFO  16:38:38,476 HelpFormatter - Date/Time: 2016/04/14 16:38:38
[2016-04-14T23:38Z] INFO  16:38:38,476 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:38Z] INFO  16:38:38,477 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:38Z] INFO  16:38:38,479 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:38Z] INFO  16:38:38,557 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-14T23:38Z] INFO  16:38:38,674 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:38Z] INFO  16:38:38,812 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:38Z] INFO  16:38:38,823 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:38Z] INFO  16:38:38,875 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-14T23:38Z] INFO  16:38:38,913 IntervalUtils - Processing 11730549 bp from intervals
[2016-04-14T23:38Z] WARN  16:38:38,919 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:38Z] INFO  16:38:39,003 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:38Z] INFO  16:38:39,227 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:38Z] INFO  16:38:39,252 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:38Z] INFO  16:38:39,252 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:38Z] INFO  16:38:39,253 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-14T23:38Z] INFO  16:38:39,321 IntervalUtils - Processing 15592465 bp from intervals
[2016-04-14T23:38Z] WARN  16:38:39,327 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:38Z] INFO  16:38:39,327 ProgressMeter -            done    201173.0    16.0 s      80.0 s       99.2%    16.0 s       0.0 s
[2016-04-14T23:38Z] INFO  16:38:39,327 ProgressMeter - Total runtime 16.22 secs, 0.27 min, 0.00 hours
[2016-04-14T23:38Z] INFO  16:38:39,332 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 201173 total reads (0.00%)
[2016-04-14T23:38Z] INFO  16:38:39,332 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:38Z] INFO  16:38:39,333 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:38Z] INFO  16:38:39,333 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:38Z] INFO  16:38:39,382 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:38Z] GATK: realign ('17', 15515955, 31039213) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:38Z] INFO  16:38:39,446 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:38Z] INFO  16:38:39,592 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:38Z] INFO  16:38:39,593 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:38Z] INFO  16:38:39,594 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:38Z] INFO  16:38:39,594 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:38Z] INFO  16:38:39,611 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:38Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-17_62122219_77705154-prep-prealign.bam
[2016-04-14T23:38Z] INFO  16:38:39,789 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:38Z] INFO  16:38:39,940 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:38Z] INFO  16:38:39,953 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:38Z] GATK: realign ('18', 34092400, 49867248) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:38Z] INFO  16:38:40,815 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:38Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-18_18533538_34081962-prep.bam
[2016-04-14T23:38Z] GATK pre-alignment ('19', 31038849, 46627578) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:38Z] GATK RealignerTargetCreator: R14-18102_kapa-NGv3-PE100-NGv3-sort-17_62122219_77705154-prep-prealign.bam 17:62122220-77705154
[2016-04-14T23:38Z] GATK: RealignerTargetCreator
[2016-04-14T23:38Z] INFO  16:38:42,191 ProgressMeter -     17:11881842    800020.0   120.0 s       2.5 m       76.6%     2.6 m      36.0 s
[2016-04-14T23:38Z] INFO  16:38:42,296 ProgressMeter -            done    288621.0    21.0 s      73.0 s       98.0%    21.0 s       0.0 s
[2016-04-14T23:38Z] INFO  16:38:42,297 ProgressMeter - Total runtime 21.25 secs, 0.35 min, 0.01 hours
[2016-04-14T23:38Z] INFO  16:38:42,301 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 288621 total reads (0.00%)
[2016-04-14T23:38Z] INFO  16:38:42,301 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:38Z] INFO  16:38:42,302 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:38Z] INFO  16:38:42,302 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:38Z] INFO  16:38:42,527 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:38Z] INFO  16:38:42,552 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:38Z] INFO  16:38:42,552 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:38Z] INFO  16:38:42,553 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:38Z] INFO  16:38:42,557 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/17/R14-18102_kapa-NGv3-PE100-NGv3-sort-17_15515955_31039213-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/17/R14-18102_kapa-NGv3-PE100-NGv3-sort-17_15515955_31039213-prep-prealign-realign.intervals -L 17:15515956-31039213 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/17/tx/tmpsUhpyK/R14-18102_kapa-NGv3-PE100-NGv3-sort-17_15515955_31039213-prep.bam
[2016-04-14T23:38Z] INFO  16:38:42,577 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:38Z] INFO  16:38:42,577 HelpFormatter - Date/Time: 2016/04/14 16:38:42
[2016-04-14T23:38Z] INFO  16:38:42,578 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:38Z] INFO  16:38:42,578 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:38Z] INFO  16:38:42,805 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:38Z] INFO  16:38:42,808 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:38Z] INFO  16:38:42,808 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:38Z] INFO  16:38:42,808 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:38Z] INFO  16:38:42,819 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:38Z] INFO  16:38:42,831 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/18/R14-18102_kapa-NGv3-PE100-NGv3-sort-18_34092400_49867248-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/18/R14-18102_kapa-NGv3-PE100-NGv3-sort-18_34092400_49867248-prep-prealign-realign.intervals -L 18:34092401-49867248 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/18/tx/tmpOSB9UU/R14-18102_kapa-NGv3-PE100-NGv3-sort-18_34092400_49867248-prep.bam
[2016-04-14T23:38Z] INFO  16:38:42,851 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:38Z] INFO  16:38:42,851 HelpFormatter - Date/Time: 2016/04/14 16:38:42
[2016-04-14T23:38Z] INFO  16:38:42,852 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:38Z] INFO  16:38:42,852 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:38Z] INFO  16:38:42,948 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:38Z] INFO  16:38:42,957 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:38Z] INFO  16:38:43,021 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-14T23:38Z] INFO  16:38:43,101 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:38Z] INFO  16:38:43,250 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:38Z] INFO  16:38:43,261 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:38Z] INFO  16:38:43,323 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-14T23:38Z] INFO  16:38:43,487 IntervalUtils - Processing 15523258 bp from intervals
[2016-04-14T23:38Z] WARN  16:38:43,501 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:38Z] INFO  16:38:43,638 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:38Z] INFO  16:38:43,638 IntervalUtils - Processing 15774848 bp from intervals
[2016-04-14T23:38Z] WARN  16:38:43,643 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:38Z] INFO  16:38:43,752 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:38Z] INFO  16:38:43,818 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:38Z] INFO  16:38:43,819 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:38Z] INFO  16:38:43,820 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:38Z] INFO  16:38:43,821 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:38Z] INFO  16:38:43,870 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:38Z] INFO  16:38:43,871 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:38Z] INFO  16:38:43,872 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:38Z] INFO  16:38:43,873 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:38Z] INFO  16:38:43,987 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:38Z] INFO  16:38:44,031 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:38Z] INFO  16:38:44,095 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:38Z] INFO  16:38:44,144 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:38Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-17_77707305_81195210-prep.bam
[2016-04-14T23:38Z] INFO  16:38:44,173 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:38Z] INFO  16:38:44,243 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:38Z] INFO  16:38:44,247 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:38Z] INFO  16:38:44,247 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:38Z] INFO  16:38:44,248 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:38Z] INFO  16:38:44,253 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/17/R14-18102_kapa-NGv3-PE100-NGv3-sort-17_62122219_77705154-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/17/tx/tmpDPaowt/R14-18102_kapa-NGv3-PE100-NGv3-sort-17_62122219_77705154-prep-prealign-realign.intervals -l INFO -L 17:62122220-77705154 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-14T23:38Z] INFO  16:38:44,294 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:38Z] INFO  16:38:44,300 HelpFormatter - Date/Time: 2016/04/14 16:38:44
[2016-04-14T23:38Z] INFO  16:38:44,301 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:38Z] INFO  16:38:44,302 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:38Z] INFO  16:38:44,421 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:38Z] INFO  16:38:44,543 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:38Z] INFO  16:38:44,547 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:38Z] INFO  16:38:44,547 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:38Z] INFO  16:38:44,548 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:38Z] INFO  16:38:44,553 HelpFormatter - Program Args: -T PrintReads -L 19:31038850-46627578 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/19/tx/tmpCbmHKM/R14-18102_kapa-NGv3-PE100-NGv3-sort-19_31038849_46627578-prep-prealign.bam
[2016-04-14T23:38Z] INFO  16:38:44,562 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:38Z] INFO  16:38:44,573 HelpFormatter - Date/Time: 2016/04/14 16:38:44
[2016-04-14T23:38Z] INFO  16:38:44,574 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:38Z] INFO  16:38:44,575 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:38Z] INFO  16:38:44,725 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-14T23:38Z] INFO  16:38:44,747 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:38Z] INFO  16:38:44,773 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:38Z] INFO  16:38:44,844 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.10
[2016-04-14T23:38Z] GATK pre-alignment ('19', 46627881, 59128983) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:38Z] INFO  16:38:45,369 IntervalUtils - Processing 15582935 bp from intervals
[2016-04-14T23:38Z] WARN  16:38:45,386 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:38Z] INFO  16:38:45,549 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:38Z] INFO  16:38:45,865 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:38Z] INFO  16:38:45,866 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:38Z] INFO  16:38:45,867 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:38Z] INFO  16:38:45,868 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-14T23:38Z] INFO  16:38:46,011 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-14T23:38Z] INFO  16:38:46,111 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:38Z] INFO  16:38:46,120 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:38Z] INFO  16:38:46,157 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.04
[2016-04-14T23:38Z] INFO  16:38:46,185 IntervalUtils - Processing 15588729 bp from intervals
[2016-04-14T23:38Z] INFO  16:38:46,275 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:38Z] INFO  16:38:46,545 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:38Z] INFO  16:38:46,546 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:38Z] INFO  16:38:46,547 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:38Z] INFO  16:38:46,548 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:38Z] INFO  16:38:46,565 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:38Z] INFO  16:38:46,735 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:38Z] INFO  16:38:47,434 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@7172f77a
[2016-04-14T23:38Z] INFO  16:38:47,552 ProgressMeter -            done    885930.0     2.1 m       2.4 m      100.0%     2.1 m       0.0 s
[2016-04-14T23:38Z] INFO  16:38:47,558 ProgressMeter - Total runtime 125.39 secs, 2.09 min, 0.03 hours
[2016-04-14T23:38Z] INFO  16:38:47,559 MicroScheduler - 403 reads were filtered out during the traversal out of approximately 886333 total reads (0.05%)
[2016-04-14T23:38Z] INFO  16:38:47,560 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:38Z] INFO  16:38:47,560 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:38Z] INFO  16:38:47,561 MicroScheduler -   -> 403 reads (0.05% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:38Z] INFO  16:38:48,728 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:38Z] INFO  16:38:48,738 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:38Z] INFO  16:38:48,739 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:38Z] INFO  16:38:48,742 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:38Z] INFO  16:38:48,746 HelpFormatter - Program Args: -T PrintReads -L 19:46627882-59128983 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/19/tx/tmpzLabUx/R14-18102_kapa-NGv3-PE100-NGv3-sort-19_46627881_59128983-prep-prealign.bam
[2016-04-14T23:38Z] INFO  16:38:48,759 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:38Z] INFO  16:38:48,759 HelpFormatter - Date/Time: 2016/04/14 16:38:48
[2016-04-14T23:38Z] INFO  16:38:48,760 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:38Z] INFO  16:38:48,760 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:38Z] INFO  16:38:48,942 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:38Z] INFO  16:38:49,111 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:38Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-17_0_15511002-prep-prealign.bam
[2016-04-14T23:38Z] INFO  16:38:50,088 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-14T23:38Z] INFO  16:38:50,166 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:38Z] INFO  16:38:50,177 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:38Z] INFO  16:38:50,258 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-14T23:38Z] INFO  16:38:50,263 ProgressMeter -            done    261415.0    20.0 s      79.0 s      100.0%    20.0 s       0.0 s
[2016-04-14T23:38Z] INFO  16:38:50,263 ProgressMeter - Total runtime 20.75 secs, 0.35 min, 0.01 hours
[2016-04-14T23:38Z] INFO  16:38:50,267 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 261415 total reads (0.00%)
[2016-04-14T23:38Z] INFO  16:38:50,269 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:38Z] INFO  16:38:50,270 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:38Z] INFO  16:38:50,270 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:38Z] INFO  16:38:50,275 IntervalUtils - Processing 12501102 bp from intervals
[2016-04-14T23:38Z] INFO  16:38:50,390 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:38Z] INFO  16:38:50,567 ProgressMeter -            done   1.6066007E7    17.0 s       1.0 s      100.0%    17.0 s       0.0 s
[2016-04-14T23:38Z] INFO  16:38:50,568 ProgressMeter - Total runtime 17.82 secs, 0.30 min, 0.00 hours
[2016-04-14T23:38Z] INFO  16:38:50,572 MicroScheduler - 12858 reads were filtered out during the traversal out of approximately 151934 total reads (8.46%)
[2016-04-14T23:38Z] INFO  16:38:50,572 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:38Z] INFO  16:38:50,572 MicroScheduler -   -> 525 reads (0.35% of total) failing BadMateFilter
[2016-04-14T23:38Z] INFO  16:38:50,573 MicroScheduler -   -> 11972 reads (7.88% of total) failing DuplicateReadFilter
[2016-04-14T23:38Z] INFO  16:38:50,573 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-14T23:38Z] INFO  16:38:50,573 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:38Z] INFO  16:38:50,573 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-14T23:38Z] INFO  16:38:50,574 MicroScheduler -   -> 361 reads (0.24% of total) failing MappingQualityZeroFilter
[2016-04-14T23:38Z] INFO  16:38:50,574 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:38Z] INFO  16:38:50,574 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-14T23:38Z] INFO  16:38:50,574 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-14T23:38Z] INFO  16:38:50,686 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:38Z] INFO  16:38:50,688 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:38Z] INFO  16:38:50,689 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:38Z] INFO  16:38:50,689 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:38Z] INFO  16:38:50,705 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:38Z] INFO  16:38:50,868 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:38Z] INFO  16:38:52,090 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:38Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-18_0_18531348-prep.bam
[2016-04-14T23:38Z] INFO  16:38:52,120 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:38Z] GATK: realign ('18', 50278423, 66344430) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:38Z] GATK RealignerTargetCreator: R14-18102_kapa-NGv3-PE100-NGv3-sort-17_0_15511002-prep-prealign.bam 17:1-15511002
[2016-04-14T23:38Z] GATK: RealignerTargetCreator
[2016-04-14T23:38Z] INFO  16:38:52,878 ProgressMeter -            done   1.1730549E7    13.0 s       1.0 s      100.0%    13.0 s       0.0 s
[2016-04-14T23:38Z] INFO  16:38:52,879 ProgressMeter - Total runtime 13.63 secs, 0.23 min, 0.00 hours
[2016-04-14T23:38Z] INFO  16:38:52,884 MicroScheduler - 11767 reads were filtered out during the traversal out of approximately 130696 total reads (9.00%)
[2016-04-14T23:38Z] INFO  16:38:52,885 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:38Z] INFO  16:38:52,886 MicroScheduler -   -> 424 reads (0.32% of total) failing BadMateFilter
[2016-04-14T23:38Z] INFO  16:38:52,886 MicroScheduler -   -> 10588 reads (8.10% of total) failing DuplicateReadFilter
[2016-04-14T23:38Z] INFO  16:38:52,887 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-14T23:38Z] INFO  16:38:52,887 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:38Z] INFO  16:38:52,887 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-14T23:38Z] INFO  16:38:52,888 MicroScheduler -   -> 755 reads (0.58% of total) failing MappingQualityZeroFilter
[2016-04-14T23:38Z] INFO  16:38:52,888 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:38Z] INFO  16:38:52,889 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-14T23:38Z] INFO  16:38:52,889 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-14T23:38Z] GATK pre-alignment ('20', 0, 15843471) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:38Z] INFO  16:38:53,847 ProgressMeter -     17:44116256   1000017.0     2.0 m       2.0 m       84.0%     2.4 m      23.0 s
[2016-04-14T23:38Z] INFO  16:38:54,201 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:38Z] GATK: realign ('18', 66346699, 78077248) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:38Z] INFO  16:38:54,961 ProgressMeter -            done   1.5513871E7    25.0 s       1.0 s      100.0%    25.0 s       0.0 s
[2016-04-14T23:38Z] INFO  16:38:54,962 ProgressMeter - Total runtime 25.40 secs, 0.42 min, 0.01 hours
[2016-04-14T23:38Z] INFO  16:38:54,965 MicroScheduler - 57928 reads were filtered out during the traversal out of approximately 510618 total reads (11.34%)
[2016-04-14T23:38Z] INFO  16:38:54,966 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:38Z] INFO  16:38:54,966 MicroScheduler -   -> 1031 reads (0.20% of total) failing BadMateFilter
[2016-04-14T23:38Z] INFO  16:38:54,966 MicroScheduler -   -> 39713 reads (7.78% of total) failing DuplicateReadFilter
[2016-04-14T23:38Z] INFO  16:38:54,967 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-14T23:38Z] INFO  16:38:54,967 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:38Z] INFO  16:38:54,967 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-14T23:38Z] INFO  16:38:54,967 MicroScheduler -   -> 17184 reads (3.37% of total) failing MappingQualityZeroFilter
[2016-04-14T23:38Z] INFO  16:38:54,968 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:38Z] INFO  16:38:54,968 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-14T23:38Z] INFO  16:38:54,968 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-14T23:38Z] INFO  16:38:55,147 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:38Z] INFO  16:38:55,149 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:38Z] INFO  16:38:55,149 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:38Z] INFO  16:38:55,150 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:38Z] INFO  16:38:55,154 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/18/R14-18102_kapa-NGv3-PE100-NGv3-sort-18_50278423_66344430-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/18/R14-18102_kapa-NGv3-PE100-NGv3-sort-18_50278423_66344430-prep-prealign-realign.intervals -L 18:50278424-66344430 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/18/tx/tmpPuA214/R14-18102_kapa-NGv3-PE100-NGv3-sort-18_50278423_66344430-prep.bam
[2016-04-14T23:38Z] INFO  16:38:55,176 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:38Z] INFO  16:38:55,177 HelpFormatter - Date/Time: 2016/04/14 16:38:55
[2016-04-14T23:38Z] INFO  16:38:55,177 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:38Z] INFO  16:38:55,178 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:38Z] INFO  16:38:55,379 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:38Z] INFO  16:38:55,471 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:38Z] INFO  16:38:55,474 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:38Z] INFO  16:38:55,475 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:38Z] INFO  16:38:55,476 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:38Z] INFO  16:38:55,480 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/17/R14-18102_kapa-NGv3-PE100-NGv3-sort-17_0_15511002-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/17/tx/tmpG6odRV/R14-18102_kapa-NGv3-PE100-NGv3-sort-17_0_15511002-prep-prealign-realign.intervals -l INFO -L 17:1-15511002 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-14T23:38Z] INFO  16:38:55,490 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:38Z] INFO  16:38:55,498 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:38Z] INFO  16:38:55,501 HelpFormatter - Date/Time: 2016/04/14 16:38:55
[2016-04-14T23:38Z] INFO  16:38:55,502 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:38Z] INFO  16:38:55,503 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:38Z] INFO  16:38:55,517 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:38Z] INFO  16:38:55,577 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-14T23:38Z] INFO  16:38:55,589 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:38Z] INFO  16:38:55,784 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:38Z] INFO  16:38:55,787 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:38Z] INFO  16:38:55,787 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:38Z] INFO  16:38:55,787 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:38Z] INFO  16:38:55,829 HelpFormatter - Program Args: -T PrintReads -L 20:1-15843471 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/20/tx/tmpHPY8o6/R14-18102_kapa-NGv3-PE100-NGv3-sort-20_0_15843471-prep-prealign.bam
[2016-04-14T23:38Z] INFO  16:38:55,838 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-14T23:38Z] INFO  16:38:55,848 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:38Z] INFO  16:38:55,849 HelpFormatter - Date/Time: 2016/04/14 16:38:55
[2016-04-14T23:38Z] INFO  16:38:55,850 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:38Z] INFO  16:38:55,850 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:38Z] INFO  16:38:55,850 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:38Z] INFO  16:38:55,941 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-14T23:38Z] INFO  16:38:55,961 IntervalUtils - Processing 16066007 bp from intervals
[2016-04-14T23:38Z] WARN  16:38:55,972 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:38Z] INFO  16:38:56,068 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:38Z] INFO  16:38:56,110 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:38Z] INFO  16:38:56,251 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:38Z] INFO  16:38:56,252 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:38Z] INFO  16:38:56,253 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:38Z] INFO  16:38:56,254 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:38Z] INFO  16:38:56,343 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:38Z] GATK: realign ('17', 46607689, 62121560) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:38Z] INFO  16:38:56,369 IntervalUtils - Processing 15511002 bp from intervals
[2016-04-14T23:38Z] WARN  16:38:56,375 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:38Z] INFO  16:38:56,467 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:38Z] INFO  16:38:56,471 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:38Z] INFO  16:38:56,660 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:38Z] INFO  16:38:56,731 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:38Z] INFO  16:38:56,732 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:38Z] INFO  16:38:56,733 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:38Z] INFO  16:38:56,734 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-14T23:38Z] INFO  16:38:57,216 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-14T23:38Z] INFO  16:38:57,292 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:38Z] INFO  16:38:57,296 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:38Z] INFO  16:38:57,296 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:38Z] INFO  16:38:57,297 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:38Z] INFO  16:38:57,301 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/18/R14-18102_kapa-NGv3-PE100-NGv3-sort-18_66346699_78077248-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/18/R14-18102_kapa-NGv3-PE100-NGv3-sort-18_66346699_78077248-prep-prealign-realign.intervals -L 18:66346700-78077248 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/18/tx/tmpu_D_mc/R14-18102_kapa-NGv3-PE100-NGv3-sort-18_66346699_78077248-prep.bam
[2016-04-14T23:38Z] INFO  16:38:57,302 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:38Z] INFO  16:38:57,312 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:38Z] INFO  16:38:57,315 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:38Z] INFO  16:38:57,316 HelpFormatter - Date/Time: 2016/04/14 16:38:57
[2016-04-14T23:38Z] INFO  16:38:57,317 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:38Z] INFO  16:38:57,317 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:38Z] INFO  16:38:57,369 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-14T23:38Z] INFO  16:38:57,386 IntervalUtils - Processing 15843471 bp from intervals
[2016-04-14T23:38Z] INFO  16:38:57,457 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:38Z] INFO  16:38:57,604 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:38Z] INFO  16:38:57,685 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:38Z] INFO  16:38:57,686 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:38Z] INFO  16:38:57,687 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:38Z] INFO  16:38:57,688 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:38Z] INFO  16:38:57,702 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:38Z] INFO  16:38:57,792 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:38Z] INFO  16:38:57,801 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:38Z] INFO  16:38:57,853 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:38Z] INFO  16:38:57,866 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-14T23:38Z] INFO  16:38:58,252 ProgressMeter -     16:30664165   1.5058342E7    30.0 s       1.0 s       97.1%    30.0 s       0.0 s
[2016-04-14T23:38Z] INFO  16:38:58,369 IntervalUtils - Processing 11730549 bp from intervals
[2016-04-14T23:38Z] WARN  16:38:58,396 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:38Z] INFO  16:38:58,491 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:38Z] INFO  16:38:58,690 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:38Z] INFO  16:38:58,691 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:38Z] INFO  16:38:58,692 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:38Z] INFO  16:38:58,692 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:38Z] INFO  16:38:58,755 ProgressMeter -      16:2511342    300003.0    30.0 s     100.0 s       16.2%     3.1 m       2.6 m
[2016-04-14T23:38Z] INFO  16:38:58,792 ProgressMeter -      19:1508487    100001.0    30.0 s       5.1 m        9.7%     5.1 m       4.6 m
[2016-04-14T23:38Z] INFO  16:38:58,905 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:38Z] INFO  16:38:59,023 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:38Z] INFO  16:38:59,954 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:38Z] INFO  16:38:59,957 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:38Z] INFO  16:38:59,958 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:38Z] INFO  16:38:59,958 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:38Z] INFO  16:38:59,963 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/17/R14-18102_kapa-NGv3-PE100-NGv3-sort-17_46607689_62121560-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/17/R14-18102_kapa-NGv3-PE100-NGv3-sort-17_46607689_62121560-prep-prealign-realign.intervals -L 17:46607690-62121560 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/17/tx/tmpvYMexM/R14-18102_kapa-NGv3-PE100-NGv3-sort-17_46607689_62121560-prep.bam
[2016-04-14T23:38Z] INFO  16:38:59,983 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:38Z] INFO  16:38:59,984 HelpFormatter - Date/Time: 2016/04/14 16:38:59
[2016-04-14T23:38Z] INFO  16:38:59,985 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:38Z] INFO  16:38:59,985 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:39Z] INFO  16:39:00,169 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:39Z] INFO  16:39:00,302 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:39Z] INFO  16:39:00,311 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:39Z] INFO  16:39:00,352 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.04
[2016-04-14T23:39Z] INFO  16:39:00,806 IntervalUtils - Processing 15513871 bp from intervals
[2016-04-14T23:39Z] WARN  16:39:00,822 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:39Z] INFO  16:39:00,889 ProgressMeter -            done   1.5510351E7    32.0 s       2.0 s      100.0%    32.0 s       0.0 s
[2016-04-14T23:39Z] INFO  16:39:00,890 ProgressMeter - Total runtime 32.65 secs, 0.54 min, 0.01 hours
[2016-04-14T23:39Z] INFO  16:39:00,891 MicroScheduler - 558639 reads were filtered out during the traversal out of approximately 1174658 total reads (47.56%)
[2016-04-14T23:39Z] INFO  16:39:00,892 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:39Z] INFO  16:39:00,893 MicroScheduler -   -> 1237 reads (0.11% of total) failing BadMateFilter
[2016-04-14T23:39Z] INFO  16:39:00,894 MicroScheduler -   -> 55260 reads (4.70% of total) failing DuplicateReadFilter
[2016-04-14T23:39Z] INFO  16:39:00,894 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-14T23:39Z] INFO  16:39:00,895 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:39Z] INFO  16:39:00,895 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-14T23:39Z] INFO  16:39:00,896 MicroScheduler -   -> 502142 reads (42.75% of total) failing MappingQualityZeroFilter
[2016-04-14T23:39Z] INFO  16:39:00,897 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:39Z] INFO  16:39:00,897 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-14T23:39Z] INFO  16:39:00,898 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-14T23:39Z] INFO  16:39:00,940 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:39Z] INFO  16:39:01,143 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:39Z] INFO  16:39:01,144 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:39Z] INFO  16:39:01,145 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:39Z] INFO  16:39:01,146 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:39Z] INFO  16:39:01,367 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:39Z] INFO  16:39:01,527 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:39Z] INFO  16:39:02,347 ProgressMeter -            done    249059.0    18.0 s      74.0 s      100.0%    18.0 s       0.0 s
[2016-04-14T23:39Z] INFO  16:39:02,347 ProgressMeter - Total runtime 18.48 secs, 0.31 min, 0.01 hours
[2016-04-14T23:39Z] INFO  16:39:02,351 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 249059 total reads (0.00%)
[2016-04-14T23:39Z] INFO  16:39:02,352 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:39Z] INFO  16:39:02,352 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:39Z] INFO  16:39:02,352 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:39Z] INFO  16:39:03,820 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:39Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-18_34092400_49867248-prep.bam
[2016-04-14T23:39Z] INFO  16:39:03,868 ProgressMeter -     19:17766838    200004.0    30.0 s       2.6 m       14.5%     3.4 m       2.9 m
[2016-04-14T23:39Z] GATK pre-alignment ('20', 15866408, 31376818) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:39Z] INFO  16:39:05,196 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@7172f77a
[2016-04-14T23:39Z] INFO  16:39:05,339 ProgressMeter -            done   1132563.0     2.2 m     116.0 s      100.0%     2.2 m       0.0 s
[2016-04-14T23:39Z] INFO  16:39:05,339 ProgressMeter - Total runtime 132.51 secs, 2.21 min, 0.04 hours
[2016-04-14T23:39Z] INFO  16:39:05,340 MicroScheduler - 450 reads were filtered out during the traversal out of approximately 1133013 total reads (0.04%)
[2016-04-14T23:39Z] INFO  16:39:05,341 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:39Z] INFO  16:39:05,341 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:39Z] INFO  16:39:05,342 MicroScheduler -   -> 450 reads (0.04% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:39Z] INFO  16:39:05,457 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:39Z] GATK: realign ('16', 15596122, 31106473) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:39Z] INFO  16:39:06,757 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:39Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-17_31048040_46607237-prep-prealign.bam
[2016-04-14T23:39Z] INFO  16:39:07,515 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:39Z] INFO  16:39:07,519 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:39Z] INFO  16:39:07,520 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:39Z] INFO  16:39:07,520 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:39Z] INFO  16:39:07,525 HelpFormatter - Program Args: -T PrintReads -L 20:15866409-31376818 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/20/tx/tmp92j9n0/R14-18102_kapa-NGv3-PE100-NGv3-sort-20_15866408_31376818-prep-prealign.bam
[2016-04-14T23:39Z] INFO  16:39:07,563 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:39Z] INFO  16:39:07,564 HelpFormatter - Date/Time: 2016/04/14 16:39:07
[2016-04-14T23:39Z] INFO  16:39:07,564 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:39Z] INFO  16:39:07,564 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:39Z] INFO  16:39:07,810 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:39Z] INFO  16:39:08,322 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:39Z] INFO  16:39:08,325 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:39Z] INFO  16:39:08,325 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:39Z] INFO  16:39:08,326 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:39Z] INFO  16:39:08,331 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/16/R14-18102_kapa-NGv3-PE100-NGv3-sort-16_15596122_31106473-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/16/R14-18102_kapa-NGv3-PE100-NGv3-sort-16_15596122_31106473-prep-prealign-realign.intervals -L 16:15596123-31106473 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/16/tx/tmpfELb6H/R14-18102_kapa-NGv3-PE100-NGv3-sort-16_15596122_31106473-prep.bam
[2016-04-14T23:39Z] INFO  16:39:08,354 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:39Z] INFO  16:39:08,354 HelpFormatter - Date/Time: 2016/04/14 16:39:08
[2016-04-14T23:39Z] INFO  16:39:08,354 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:39Z] INFO  16:39:08,354 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:39Z] INFO  16:39:08,566 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:39Z] INFO  16:39:08,633 ProgressMeter -            done    150730.0    12.0 s      82.0 s      100.0%    12.0 s       0.0 s
[2016-04-14T23:39Z] INFO  16:39:08,633 ProgressMeter - Total runtime 12.38 secs, 0.21 min, 0.00 hours
[2016-04-14T23:39Z] INFO  16:39:08,638 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 150730 total reads (0.00%)
[2016-04-14T23:39Z] INFO  16:39:08,639 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:39Z] INFO  16:39:08,639 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:39Z] INFO  16:39:08,639 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:39Z] INFO  16:39:08,668 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:39Z] INFO  16:39:08,677 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:39Z] INFO  16:39:08,730 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-14T23:39Z] INFO  16:39:09,037 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-14T23:39Z] INFO  16:39:09,120 IntervalUtils - Processing 15510351 bp from intervals
[2016-04-14T23:39Z] WARN  16:39:09,125 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:39Z] INFO  16:39:09,146 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:39Z] INFO  16:39:09,154 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:39Z] INFO  16:39:09,191 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:39Z] INFO  16:39:09,215 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-14T23:39Z] INFO  16:39:09,235 IntervalUtils - Processing 15510410 bp from intervals
[2016-04-14T23:39Z] INFO  16:39:09,321 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:39Z] INFO  16:39:09,329 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:39Z] INFO  16:39:09,333 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:39Z] INFO  16:39:09,336 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:39Z] INFO  16:39:09,336 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:39Z] INFO  16:39:09,544 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:39Z] INFO  16:39:09,570 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:39Z] INFO  16:39:09,571 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:39Z] INFO  16:39:09,572 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:39Z] INFO  16:39:09,573 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:39Z] INFO  16:39:09,589 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:39Z] INFO  16:39:09,699 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:39Z] INFO  16:39:09,825 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:39Z] INFO  16:39:10,248 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:39Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-18_50278423_66344430-prep.bam
[2016-04-14T23:39Z] INFO  16:39:10,348 ProgressMeter -            done    129890.0    11.0 s      89.0 s       99.4%    11.0 s       0.0 s
[2016-04-14T23:39Z] INFO  16:39:10,349 ProgressMeter - Total runtime 11.66 secs, 0.19 min, 0.00 hours
[2016-04-14T23:39Z] INFO  16:39:10,353 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 129890 total reads (0.00%)
[2016-04-14T23:39Z] INFO  16:39:10,353 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:39Z] INFO  16:39:10,354 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:39Z] INFO  16:39:10,366 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:39Z] INFO  16:39:10,384 ProgressMeter -            done   1.5582935E7    24.0 s       1.0 s      100.0%    24.0 s       0.0 s
[2016-04-14T23:39Z] INFO  16:39:10,385 ProgressMeter - Total runtime 24.52 secs, 0.41 min, 0.01 hours
[2016-04-14T23:39Z] INFO  16:39:10,390 MicroScheduler - 53508 reads were filtered out during the traversal out of approximately 597269 total reads (8.96%)
[2016-04-14T23:39Z] INFO  16:39:10,391 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:39Z] INFO  16:39:10,392 MicroScheduler -   -> 1242 reads (0.21% of total) failing BadMateFilter
[2016-04-14T23:39Z] INFO  16:39:10,393 MicroScheduler -   -> 47939 reads (8.03% of total) failing DuplicateReadFilter
[2016-04-14T23:39Z] INFO  16:39:10,394 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-14T23:39Z] INFO  16:39:10,394 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:39Z] INFO  16:39:10,395 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-14T23:39Z] INFO  16:39:10,396 MicroScheduler -   -> 4327 reads (0.72% of total) failing MappingQualityZeroFilter
[2016-04-14T23:39Z] INFO  16:39:10,396 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:39Z] INFO  16:39:10,397 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-14T23:39Z] INFO  16:39:10,398 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-14T23:39Z] GATK RealignerTargetCreator: R14-18102_kapa-NGv3-PE100-NGv3-sort-17_31048040_46607237-prep-prealign.bam 17:31048041-46607237
[2016-04-14T23:39Z] GATK: RealignerTargetCreator
[2016-04-14T23:39Z] GATK pre-alignment ('20', 31379406, 47242465) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:39Z] INFO  16:39:11,726 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:39Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-18_66346699_78077248-prep.bam
[2016-04-14T23:39Z] INFO  16:39:11,812 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:39Z] GATK: realign ('17', 62122219, 77705154) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:39Z] GATK pre-alignment ('20', 47244085, 62830269) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:39Z] INFO  16:39:13,262 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:39Z] INFO  16:39:13,266 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:39Z] INFO  16:39:13,267 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:39Z] INFO  16:39:13,268 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:39Z] INFO  16:39:13,273 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/17/R14-18102_kapa-NGv3-PE100-NGv3-sort-17_31048040_46607237-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/17/tx/tmpp_Fc0T/R14-18102_kapa-NGv3-PE100-NGv3-sort-17_31048040_46607237-prep-prealign-realign.intervals -l INFO -L 17:31048041-46607237 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-14T23:39Z] INFO  16:39:13,284 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:39Z] INFO  16:39:13,295 HelpFormatter - Date/Time: 2016/04/14 16:39:13
[2016-04-14T23:39Z] INFO  16:39:13,296 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:39Z] INFO  16:39:13,297 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:39Z] INFO  16:39:13,513 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:39Z] INFO  16:39:13,572 ProgressMeter -     16:71669984    400006.0    33.0 s      84.0 s       42.9%    76.0 s      43.0 s
[2016-04-14T23:39Z] INFO  16:39:13,773 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-14T23:39Z] INFO  16:39:13,783 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:39Z] INFO  16:39:13,836 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-14T23:39Z] INFO  16:39:14,113 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:39Z] INFO  16:39:14,116 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:39Z] INFO  16:39:14,117 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:39Z] INFO  16:39:14,118 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:39Z] INFO  16:39:14,118 IntervalUtils - Processing 15559197 bp from intervals
[2016-04-14T23:39Z] INFO  16:39:14,122 HelpFormatter - Program Args: -T PrintReads -L 20:31379407-47242465 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/20/tx/tmpsZWcpc/R14-18102_kapa-NGv3-PE100-NGv3-sort-20_31379406_47242465-prep-prealign.bam
[2016-04-14T23:39Z] WARN  16:39:14,123 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:39Z] INFO  16:39:14,136 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:39Z] INFO  16:39:14,137 HelpFormatter - Date/Time: 2016/04/14 16:39:14
[2016-04-14T23:39Z] INFO  16:39:14,138 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:39Z] INFO  16:39:14,138 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:39Z] INFO  16:39:14,256 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:39Z] INFO  16:39:14,304 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:39Z] INFO  16:39:14,489 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:39Z] INFO  16:39:14,490 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:39Z] INFO  16:39:14,491 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:39Z] INFO  16:39:14,492 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-14T23:39Z] INFO  16:39:14,786 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:39Z] INFO  16:39:14,790 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:39Z] INFO  16:39:14,791 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:39Z] INFO  16:39:14,791 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:39Z] INFO  16:39:14,796 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/17/R14-18102_kapa-NGv3-PE100-NGv3-sort-17_62122219_77705154-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/17/R14-18102_kapa-NGv3-PE100-NGv3-sort-17_62122219_77705154-prep-prealign-realign.intervals -L 17:62122220-77705154 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/17/tx/tmp3kKEqp/R14-18102_kapa-NGv3-PE100-NGv3-sort-17_62122219_77705154-prep.bam
[2016-04-14T23:39Z] INFO  16:39:14,806 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:39Z] INFO  16:39:14,807 HelpFormatter - Date/Time: 2016/04/14 16:39:14
[2016-04-14T23:39Z] INFO  16:39:14,807 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:39Z] INFO  16:39:14,808 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:39Z] INFO  16:39:14,850 ProgressMeter -     17:27022360    400009.0    31.0 s      77.0 s       74.1%    41.0 s      10.0 s
[2016-04-14T23:39Z] INFO  16:39:15,024 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:39Z] INFO  16:39:15,192 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:39Z] INFO  16:39:15,212 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:39Z] INFO  16:39:15,230 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:39Z] INFO  16:39:15,234 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:39Z] INFO  16:39:15,234 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:39Z] INFO  16:39:15,235 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:39Z] INFO  16:39:15,239 HelpFormatter - Program Args: -T PrintReads -L 20:47244086-62830269 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/20/tx/tmpIFT0pl/R14-18102_kapa-NGv3-PE100-NGv3-sort-20_47244085_62830269-prep-prealign.bam
[2016-04-14T23:39Z] INFO  16:39:15,247 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:39Z] INFO  16:39:15,256 HelpFormatter - Date/Time: 2016/04/14 16:39:15
[2016-04-14T23:39Z] INFO  16:39:15,257 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:39Z] INFO  16:39:15,257 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:39Z] INFO  16:39:15,291 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-14T23:39Z] INFO  16:39:15,414 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-14T23:39Z] INFO  16:39:15,468 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:39Z] INFO  16:39:15,524 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:39Z] INFO  16:39:15,533 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:39Z] INFO  16:39:15,592 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-14T23:39Z] INFO  16:39:15,619 IntervalUtils - Processing 15863059 bp from intervals
[2016-04-14T23:39Z] INFO  16:39:15,724 IntervalUtils - Processing 15582935 bp from intervals
[2016-04-14T23:39Z] WARN  16:39:15,740 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:39Z] INFO  16:39:15,768 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:39Z] INFO  16:39:15,889 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:39Z] INFO  16:39:16,017 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:39Z] INFO  16:39:16,018 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:39Z] INFO  16:39:16,019 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:39Z] INFO  16:39:16,020 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:39Z] INFO  16:39:16,033 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:39Z] INFO  16:39:16,124 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:39Z] INFO  16:39:16,137 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:39Z] INFO  16:39:16,138 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:39Z] INFO  16:39:16,139 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:39Z] INFO  16:39:16,239 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:39Z] INFO  16:39:16,408 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:39Z] INFO  16:39:16,555 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-14T23:39Z] INFO  16:39:16,564 ProgressMeter -     19:36229432    200005.0    30.0 s       2.5 m       33.3%    90.0 s      60.0 s
[2016-04-14T23:39Z] INFO  16:39:16,627 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:39Z] INFO  16:39:16,636 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:39Z] INFO  16:39:16,656 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:39Z] INFO  16:39:16,677 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.04
[2016-04-14T23:39Z] INFO  16:39:16,691 IntervalUtils - Processing 15586184 bp from intervals
[2016-04-14T23:39Z] INFO  16:39:16,787 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:39Z] INFO  16:39:17,112 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:39Z] INFO  16:39:17,133 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:39Z] INFO  16:39:17,134 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:39Z] INFO  16:39:17,134 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:39Z] INFO  16:39:17,154 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:39Z] INFO  16:39:17,374 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:39Z] INFO  16:39:21,036 ProgressMeter -     19:49230286    100001.0    30.0 s       5.1 m       20.8%     2.4 m     114.0 s
[2016-04-14T23:39Z] INFO  16:39:21,535 ProgressMeter -            done    638190.0    41.0 s      65.0 s      100.0%    41.0 s       0.0 s
[2016-04-14T23:39Z] INFO  16:39:21,536 ProgressMeter - Total runtime 41.94 secs, 0.70 min, 0.01 hours
[2016-04-14T23:39Z] INFO  16:39:21,540 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 638190 total reads (0.00%)
[2016-04-14T23:39Z] INFO  16:39:21,540 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:39Z] INFO  16:39:21,541 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:39Z] INFO  16:39:21,541 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:39Z] INFO  16:39:22,884 ProgressMeter -            done    617571.0    39.0 s      63.0 s      100.0%    39.0 s       0.0 s
[2016-04-14T23:39Z] INFO  16:39:22,884 ProgressMeter - Total runtime 39.06 secs, 0.65 min, 0.01 hours
[2016-04-14T23:39Z] INFO  16:39:22,888 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 617571 total reads (0.00%)
[2016-04-14T23:39Z] INFO  16:39:22,889 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:39Z] INFO  16:39:22,890 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:39Z] INFO  16:39:22,890 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:39Z] INFO  16:39:23,049 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:39Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-16_64982511_80574976-prep.bam
[2016-04-14T23:39Z] INFO  16:39:24,413 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:39Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-17_15515955_31039213-prep.bam
[2016-04-14T23:39Z] GATK pre-alignment ('20', 62831244, 63025520) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:39Z] GATK pre-alignment ('21', 0, 15517120) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:39Z] INFO  16:39:26,748 ProgressMeter -     17:12656049   1.2648448E7    30.0 s       2.0 s       81.6%    36.0 s       6.0 s
[2016-04-14T23:39Z] INFO  16:39:27,165 ProgressMeter -            done    910120.0    58.0 s      64.0 s      100.0%    58.0 s       0.0 s
[2016-04-14T23:39Z] INFO  16:39:27,166 ProgressMeter - Total runtime 58.43 secs, 0.97 min, 0.02 hours
[2016-04-14T23:39Z] INFO  16:39:27,170 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 910120 total reads (0.00%)
[2016-04-14T23:39Z] INFO  16:39:27,170 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:39Z] INFO  16:39:27,171 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:39Z] INFO  16:39:27,171 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:39Z] INFO  16:39:28,098 ProgressMeter -      20:3781236    100002.0    30.0 s       5.1 m       23.9%     2.1 m      95.0 s
[2016-04-14T23:39Z] INFO  16:39:28,836 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:39Z] INFO  16:39:28,839 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:39Z] INFO  16:39:28,840 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:39Z] INFO  16:39:28,840 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:39Z] INFO  16:39:28,851 HelpFormatter - Program Args: -T PrintReads -L 20:62831245-63025520 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/20/tx/tmpI3LZJ4/R14-18102_kapa-NGv3-PE100-NGv3-sort-20_62831244_63025520-prep-prealign.bam
[2016-04-14T23:39Z] INFO  16:39:28,852 ProgressMeter -      19:3740887    300004.0    60.0 s       3.4 m       24.1%     4.1 m       3.1 m
[2016-04-14T23:39Z] INFO  16:39:28,859 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:39Z] INFO  16:39:28,860 HelpFormatter - Date/Time: 2016/04/14 16:39:28
[2016-04-14T23:39Z] INFO  16:39:28,860 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:39Z] INFO  16:39:28,861 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:39Z] INFO  16:39:28,933 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:39Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-16_0_15528616-prep.bam
[2016-04-14T23:39Z] INFO  16:39:29,042 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:39Z] INFO  16:39:29,587 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:39Z] INFO  16:39:29,590 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:39Z] INFO  16:39:29,591 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:39Z] INFO  16:39:29,591 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:39Z] INFO  16:39:29,596 HelpFormatter - Program Args: -T PrintReads -L 21:1-15517120 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/21/tx/tmpeux9z2/R14-18102_kapa-NGv3-PE100-NGv3-sort-21_0_15517120-prep-prealign.bam
[2016-04-14T23:39Z] INFO  16:39:29,605 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:39Z] INFO  16:39:29,605 HelpFormatter - Date/Time: 2016/04/14 16:39:29
[2016-04-14T23:39Z] INFO  16:39:29,617 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:39Z] INFO  16:39:29,618 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:39Z] INFO  16:39:29,793 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:39Z] INFO  16:39:30,205 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-14T23:39Z] INFO  16:39:30,260 ProgressMeter -            done   1.5511002E7    33.0 s       2.0 s      100.0%    33.0 s       0.0 s
[2016-04-14T23:39Z] INFO  16:39:30,262 ProgressMeter - Total runtime 33.53 secs, 0.56 min, 0.01 hours
[2016-04-14T23:39Z] INFO  16:39:30,262 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:39Z] INFO  16:39:30,267 MicroScheduler - 83097 reads were filtered out during the traversal out of approximately 890913 total reads (9.33%)
[2016-04-14T23:39Z] INFO  16:39:30,268 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:39Z] INFO  16:39:30,269 MicroScheduler -   -> 1693 reads (0.19% of total) failing BadMateFilter
[2016-04-14T23:39Z] INFO  16:39:30,269 MicroScheduler -   -> 71302 reads (8.00% of total) failing DuplicateReadFilter
[2016-04-14T23:39Z] INFO  16:39:30,270 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-14T23:39Z] INFO  16:39:30,271 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:39Z] INFO  16:39:30,272 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-14T23:39Z] INFO  16:39:30,272 MicroScheduler -   -> 10102 reads (1.13% of total) failing MappingQualityZeroFilter
[2016-04-14T23:39Z] INFO  16:39:30,273 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:39Z] INFO  16:39:30,273 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:39Z] INFO  16:39:30,274 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-14T23:39Z] INFO  16:39:30,274 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-14T23:39Z] INFO  16:39:30,320 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-14T23:39Z] INFO  16:39:30,347 IntervalUtils - Processing 194276 bp from intervals
[2016-04-14T23:39Z] INFO  16:39:30,488 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:39Z] INFO  16:39:30,627 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:39Z] INFO  16:39:30,627 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:39Z] INFO  16:39:30,628 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:39Z] INFO  16:39:30,628 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:39Z] INFO  16:39:30,664 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:39Z] INFO  16:39:30,669 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:39Z] INFO  16:39:30,708 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-14T23:39Z] INFO  16:39:30,763 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:39Z] INFO  16:39:30,772 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:39Z] INFO  16:39:30,808 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.04
[2016-04-14T23:39Z] INFO  16:39:30,824 IntervalUtils - Processing 15517120 bp from intervals
[2016-04-14T23:39Z] INFO  16:39:30,897 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:39Z] INFO  16:39:31,160 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:39Z] INFO  16:39:31,161 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:39Z] INFO  16:39:31,162 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:39Z] INFO  16:39:31,163 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:39Z] INFO  16:39:31,180 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:39Z] INFO  16:39:31,265 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:39Z] INFO  16:39:31,771 ProgressMeter -     17:61557881    400007.0    30.0 s      76.0 s       96.4%    31.0 s       1.0 s
[2016-04-14T23:39Z] INFO  16:39:31,870 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:39Z] GATK: realign ('17', 0, 15511002) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:39Z] GATK pre-alignment ('21', 15524893, 31045484) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:39Z] INFO  16:39:33,751 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@41fd9d8e
[2016-04-14T23:39Z] INFO  16:39:33,825 ProgressMeter -            done      8224.0     3.0 s       6.5 m       66.0%     4.0 s       1.0 s
[2016-04-14T23:39Z] INFO  16:39:33,826 ProgressMeter - Total runtime 3.20 secs, 0.05 min, 0.00 hours
[2016-04-14T23:39Z] INFO  16:39:33,827 MicroScheduler - 6 reads were filtered out during the traversal out of approximately 8230 total reads (0.07%)
[2016-04-14T23:39Z] INFO  16:39:33,828 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:39Z] INFO  16:39:33,828 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:39Z] INFO  16:39:33,829 MicroScheduler -   -> 6 reads (0.07% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:39Z] INFO  16:39:33,870 ProgressMeter -     19:22155236    400008.0    60.0 s       2.5 m       42.8%     2.3 m      80.0 s
[2016-04-14T23:39Z] INFO  16:39:33,992 ProgressMeter -            done    507581.0    32.0 s      64.0 s      100.0%    32.0 s       0.0 s
[2016-04-14T23:39Z] INFO  16:39:33,993 ProgressMeter - Total runtime 32.85 secs, 0.55 min, 0.01 hours
[2016-04-14T23:39Z] INFO  16:39:33,996 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 507581 total reads (0.00%)
[2016-04-14T23:39Z] INFO  16:39:33,997 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:39Z] INFO  16:39:33,997 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:39Z] INFO  16:39:33,997 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:39Z] INFO  16:39:34,798 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:39Z] INFO  16:39:34,801 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:39Z] INFO  16:39:34,801 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:39Z] INFO  16:39:34,801 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:39Z] INFO  16:39:34,805 HelpFormatter - Program Args: -T PrintReads -L 21:15524894-31045484 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/21/tx/tmps4GVah/R14-18102_kapa-NGv3-PE100-NGv3-sort-21_15524893_31045484-prep-prealign.bam
[2016-04-14T23:39Z] INFO  16:39:34,825 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:39Z] INFO  16:39:34,826 HelpFormatter - Date/Time: 2016/04/14 16:39:34
[2016-04-14T23:39Z] INFO  16:39:34,826 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:39Z] INFO  16:39:34,826 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:39Z] INFO  16:39:35,019 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:39Z] INFO  16:39:35,023 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:39Z] INFO  16:39:35,024 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:39Z] INFO  16:39:35,024 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:39Z] INFO  16:39:35,028 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/17/R14-18102_kapa-NGv3-PE100-NGv3-sort-17_0_15511002-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/17/R14-18102_kapa-NGv3-PE100-NGv3-sort-17_0_15511002-prep-prealign-realign.intervals -L 17:1-15511002 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/17/tx/tmpxqDk3K/R14-18102_kapa-NGv3-PE100-NGv3-sort-17_0_15511002-prep.bam
[2016-04-14T23:39Z] INFO  16:39:35,029 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:39Z] INFO  16:39:35,039 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:39Z] INFO  16:39:35,040 HelpFormatter - Date/Time: 2016/04/14 16:39:35
[2016-04-14T23:39Z] INFO  16:39:35,040 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:39Z] INFO  16:39:35,041 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:39Z] INFO  16:39:35,203 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:39Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-20_62831244_63025520-prep-prealign.bam
[2016-04-14T23:39Z] INFO  16:39:35,272 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:39Z] GATK RealignerTargetCreator: R14-18102_kapa-NGv3-PE100-NGv3-sort-20_62831244_63025520-prep-prealign.bam 20:62831245-63025520
[2016-04-14T23:39Z] GATK: RealignerTargetCreator
[2016-04-14T23:39Z] INFO  16:39:35,471 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:39Z] INFO  16:39:35,481 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:39Z] INFO  16:39:35,559 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-14T23:39Z] INFO  16:39:35,604 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:39Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-17_46607689_62121560-prep.bam
[2016-04-14T23:39Z] INFO  16:39:35,960 IntervalUtils - Processing 15511002 bp from intervals
[2016-04-14T23:39Z] WARN  16:39:35,966 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:39Z] INFO  16:39:35,982 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-14T23:39Z] INFO  16:39:36,040 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:39Z] INFO  16:39:36,049 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:39Z] INFO  16:39:36,053 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:39Z] INFO  16:39:36,083 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.03
[2016-04-14T23:39Z] INFO  16:39:36,109 IntervalUtils - Processing 15520591 bp from intervals
[2016-04-14T23:39Z] INFO  16:39:36,224 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:39Z] INFO  16:39:36,287 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:39Z] INFO  16:39:36,288 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:39Z] INFO  16:39:36,289 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:39Z] INFO  16:39:36,290 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:39Z] INFO  16:39:36,472 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:39Z] INFO  16:39:36,473 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:39Z] INFO  16:39:36,474 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:39Z] INFO  16:39:36,475 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:39Z] INFO  16:39:36,488 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:39Z] INFO  16:39:36,554 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:39Z] INFO  16:39:36,640 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:39Z] INFO  16:39:36,777 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:39Z] GATK pre-alignment ('21', 31062047, 46591599) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:39Z] INFO  16:39:38,389 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:39Z] INFO  16:39:38,393 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:39Z] INFO  16:39:38,394 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:39Z] INFO  16:39:38,394 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:39Z] INFO  16:39:38,400 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/20/R14-18102_kapa-NGv3-PE100-NGv3-sort-20_62831244_63025520-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/20/tx/tmpob_rF7/R14-18102_kapa-NGv3-PE100-NGv3-sort-20_62831244_63025520-prep-prealign-realign.intervals -l INFO -L 20:62831245-63025520 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-14T23:39Z] INFO  16:39:38,410 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:39Z] INFO  16:39:38,417 HelpFormatter - Date/Time: 2016/04/14 16:39:38
[2016-04-14T23:39Z] INFO  16:39:38,418 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:39Z] INFO  16:39:38,418 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:39Z] INFO  16:39:38,606 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:39Z] INFO  16:39:38,842 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-14T23:39Z] INFO  16:39:38,854 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:39Z] INFO  16:39:38,926 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-14T23:39Z] INFO  16:39:39,202 IntervalUtils - Processing 194276 bp from intervals
[2016-04-14T23:39Z] WARN  16:39:39,207 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:39Z] INFO  16:39:39,280 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:39Z] INFO  16:39:39,306 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:39Z] INFO  16:39:39,307 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:39Z] INFO  16:39:39,308 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:39Z] INFO  16:39:39,308 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-14T23:39Z] INFO  16:39:39,592 ProgressMeter -     20:31123624    200004.0    30.0 s       2.5 m       98.4%    30.0 s       0.0 s
[2016-04-14T23:39Z] INFO  16:39:39,653 ProgressMeter -     16:22149658    400005.0    30.0 s      75.0 s       42.3%    71.0 s      41.0 s
[2016-04-14T23:39Z] INFO  16:39:39,948 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@7172f77a
[2016-04-14T23:39Z] INFO  16:39:40,001 ProgressMeter -            done     38243.0     8.0 s       3.9 m      100.0%     8.0 s       0.0 s
[2016-04-14T23:39Z] INFO  16:39:40,002 ProgressMeter - Total runtime 8.84 secs, 0.15 min, 0.00 hours
[2016-04-14T23:39Z] INFO  16:39:40,003 MicroScheduler - 110 reads were filtered out during the traversal out of approximately 38353 total reads (0.29%)
[2016-04-14T23:39Z] INFO  16:39:40,004 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:39Z] INFO  16:39:40,005 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:39Z] INFO  16:39:40,005 MicroScheduler -   -> 110 reads (0.29% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:39Z] INFO  16:39:40,045 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@41fd9d8e
[2016-04-14T23:39Z] INFO  16:39:40,109 ProgressMeter -            done    241470.0    30.0 s       2.1 m      100.0%    30.0 s       0.0 s
[2016-04-14T23:39Z] INFO  16:39:40,109 ProgressMeter - Total runtime 30.54 secs, 0.51 min, 0.01 hours
[2016-04-14T23:39Z] INFO  16:39:40,110 MicroScheduler - 162 reads were filtered out during the traversal out of approximately 241632 total reads (0.07%)
[2016-04-14T23:39Z] INFO  16:39:40,110 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:39Z] INFO  16:39:40,110 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:39Z] INFO  16:39:40,111 MicroScheduler -   -> 162 reads (0.07% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:39Z] INFO  16:39:40,408 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:39Z] INFO  16:39:40,411 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:39Z] INFO  16:39:40,412 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:39Z] INFO  16:39:40,413 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:39Z] INFO  16:39:40,418 HelpFormatter - Program Args: -T PrintReads -L 21:31062048-46591599 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/21/tx/tmpgqD3mU/R14-18102_kapa-NGv3-PE100-NGv3-sort-21_31062047_46591599-prep-prealign.bam
[2016-04-14T23:39Z] INFO  16:39:40,441 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:39Z] INFO  16:39:40,442 HelpFormatter - Date/Time: 2016/04/14 16:39:40
[2016-04-14T23:39Z] INFO  16:39:40,442 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:39Z] INFO  16:39:40,442 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:39Z] INFO  16:39:40,707 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:39Z] INFO  16:39:41,015 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@5fe152b7
[2016-04-14T23:39Z] INFO  16:39:41,122 ProgressMeter -            done    294844.0    43.0 s       2.5 m      100.0%    43.0 s       0.0 s
[2016-04-14T23:39Z] INFO  16:39:41,123 ProgressMeter - Total runtime 43.44 secs, 0.72 min, 0.01 hours
[2016-04-14T23:39Z] INFO  16:39:41,124 MicroScheduler - 143 reads were filtered out during the traversal out of approximately 294987 total reads (0.05%)
[2016-04-14T23:39Z] INFO  16:39:41,125 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:39Z] INFO  16:39:41,126 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:39Z] INFO  16:39:41,126 MicroScheduler -   -> 143 reads (0.05% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:39Z] INFO  16:39:41,413 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:39Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-21_0_15517120-prep-prealign.bam
[2016-04-14T23:39Z] INFO  16:39:41,584 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:39Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-20_15866408_31376818-prep-prealign.bam
[2016-04-14T23:39Z] GATK RealignerTargetCreator: R14-18102_kapa-NGv3-PE100-NGv3-sort-21_0_15517120-prep-prealign.bam 21:1-15517120
[2016-04-14T23:39Z] GATK: RealignerTargetCreator
[2016-04-14T23:39Z] INFO  16:39:41,713 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-14T23:39Z] INFO  16:39:41,778 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:39Z] INFO  16:39:41,787 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:39Z] INFO  16:39:41,829 ProgressMeter -            done    194276.0     2.0 s      12.0 s      100.0%     2.0 s       0.0 s
[2016-04-14T23:39Z] INFO  16:39:41,829 ProgressMeter - Total runtime 2.52 secs, 0.04 min, 0.00 hours
[2016-04-14T23:39Z] INFO  16:39:41,828 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.04
[2016-04-14T23:39Z] INFO  16:39:41,833 MicroScheduler - 987 reads were filtered out during the traversal out of approximately 8224 total reads (12.00%)
[2016-04-14T23:39Z] INFO  16:39:41,834 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:39Z] INFO  16:39:41,834 MicroScheduler -   -> 7 reads (0.09% of total) failing BadMateFilter
[2016-04-14T23:39Z] INFO  16:39:41,835 MicroScheduler -   -> 582 reads (7.08% of total) failing DuplicateReadFilter
[2016-04-14T23:39Z] INFO  16:39:41,835 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-14T23:39Z] INFO  16:39:41,835 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:39Z] INFO  16:39:41,835 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-14T23:39Z] INFO  16:39:41,836 MicroScheduler -   -> 398 reads (4.84% of total) failing MappingQualityZeroFilter
[2016-04-14T23:39Z] INFO  16:39:41,836 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:39Z] INFO  16:39:41,836 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-14T23:39Z] INFO  16:39:41,836 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-14T23:39Z] INFO  16:39:41,841 IntervalUtils - Processing 15529552 bp from intervals
[2016-04-14T23:39Z] INFO  16:39:41,964 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:39Z] INFO  16:39:42,244 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:39Z] INFO  16:39:42,244 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:39Z] INFO  16:39:42,245 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:39Z] INFO  16:39:42,245 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:39Z] INFO  16:39:42,280 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:39Z] INFO  16:39:42,445 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:39Z] GATK RealignerTargetCreator: R14-18102_kapa-NGv3-PE100-NGv3-sort-20_15866408_31376818-prep-prealign.bam 20:15866409-31376818
[2016-04-14T23:39Z] GATK: RealignerTargetCreator
[2016-04-14T23:39Z] INFO  16:39:42,583 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@32d5a4c6
[2016-04-14T23:39Z] INFO  16:39:42,659 ProgressMeter -            done    558759.0    69.0 s       2.1 m      100.0%    69.0 s       0.0 s
[2016-04-14T23:39Z] INFO  16:39:42,660 ProgressMeter - Total runtime 69.52 secs, 1.16 min, 0.02 hours
[2016-04-14T23:39Z] INFO  16:39:42,660 MicroScheduler - 336 reads were filtered out during the traversal out of approximately 559095 total reads (0.06%)
[2016-04-14T23:39Z] INFO  16:39:42,660 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:39Z] INFO  16:39:42,661 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:39Z] INFO  16:39:42,661 MicroScheduler -   -> 336 reads (0.06% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:39Z] INFO  16:39:42,717 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:39Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-20_0_15843471-prep-prealign.bam
[2016-04-14T23:39Z] INFO  16:39:43,261 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:39Z] GATK: realign ('20', 62831244, 63025520) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:39Z] GATK RealignerTargetCreator: R14-18102_kapa-NGv3-PE100-NGv3-sort-20_0_15843471-prep-prealign.bam 20:1-15843471
[2016-04-14T23:39Z] GATK: RealignerTargetCreator
[2016-04-14T23:39Z] INFO  16:39:44,089 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:39Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-19_15510112_31025906-prep-prealign.bam
[2016-04-14T23:39Z] INFO  16:39:44,512 ProgressMeter -     17:44407941   1.33526E7    30.0 s       2.0 s       85.9%    34.0 s       4.0 s
[2016-04-14T23:39Z] INFO  16:39:44,634 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:39Z] INFO  16:39:44,642 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:39Z] INFO  16:39:44,643 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:39Z] INFO  16:39:44,643 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:39Z] INFO  16:39:44,647 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/21/R14-18102_kapa-NGv3-PE100-NGv3-sort-21_0_15517120-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/21/tx/tmpG_2uVf/R14-18102_kapa-NGv3-PE100-NGv3-sort-21_0_15517120-prep-prealign-realign.intervals -l INFO -L 21:1-15517120 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-14T23:39Z] INFO  16:39:44,689 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:39Z] INFO  16:39:44,689 HelpFormatter - Date/Time: 2016/04/14 16:39:44
[2016-04-14T23:39Z] INFO  16:39:44,689 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:39Z] INFO  16:39:44,689 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:39Z] INFO  16:39:44,785 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:39Z] INFO  16:39:44,988 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-14T23:39Z] INFO  16:39:44,998 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:39Z] INFO  16:39:45,053 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-14T23:39Z] INFO  16:39:45,245 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:39Z] INFO  16:39:45,250 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:39Z] INFO  16:39:45,250 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:39Z] INFO  16:39:45,251 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:39Z] INFO  16:39:45,273 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/20/R14-18102_kapa-NGv3-PE100-NGv3-sort-20_15866408_31376818-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/20/tx/tmp6xXTSI/R14-18102_kapa-NGv3-PE100-NGv3-sort-20_15866408_31376818-prep-prealign-realign.intervals -l INFO -L 20:15866409-31376818 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-14T23:39Z] INFO  16:39:45,290 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:39Z] INFO  16:39:45,293 HelpFormatter - Date/Time: 2016/04/14 16:39:45
[2016-04-14T23:39Z] INFO  16:39:45,305 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:39Z] INFO  16:39:45,306 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:39Z] INFO  16:39:45,330 IntervalUtils - Processing 15517120 bp from intervals
[2016-04-14T23:39Z] WARN  16:39:45,336 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:39Z] INFO  16:39:45,409 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:39Z] INFO  16:39:45,446 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:39Z] INFO  16:39:45,610 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:39Z] INFO  16:39:45,611 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:39Z] INFO  16:39:45,612 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:39Z] INFO  16:39:45,613 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-14T23:39Z] INFO  16:39:45,685 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-14T23:39Z] INFO  16:39:45,697 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:39Z] INFO  16:39:45,773 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-14T23:39Z] GATK RealignerTargetCreator: R14-18102_kapa-NGv3-PE100-NGv3-sort-19_15510112_31025906-prep-prealign.bam 19:15510113-31025906
[2016-04-14T23:39Z] GATK: RealignerTargetCreator
[2016-04-14T23:39Z] INFO  16:39:46,163 IntervalUtils - Processing 15510410 bp from intervals
[2016-04-14T23:39Z] INFO  16:39:46,166 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:39Z] INFO  16:39:46,169 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:39Z] INFO  16:39:46,170 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:39Z] INFO  16:39:46,171 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:39Z] INFO  16:39:46,176 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/20/R14-18102_kapa-NGv3-PE100-NGv3-sort-20_62831244_63025520-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/20/R14-18102_kapa-NGv3-PE100-NGv3-sort-20_62831244_63025520-prep-prealign-realign.intervals -L 20:62831245-63025520 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/20/tx/tmpOJnAB4/R14-18102_kapa-NGv3-PE100-NGv3-sort-20_62831244_63025520-prep.bam
[2016-04-14T23:39Z] WARN  16:39:46,180 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:39Z] INFO  16:39:46,186 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:39Z] INFO  16:39:46,198 HelpFormatter - Date/Time: 2016/04/14 16:39:46
[2016-04-14T23:39Z] INFO  16:39:46,199 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:39Z] INFO  16:39:46,199 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:39Z] INFO  16:39:46,297 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:39Z] INFO  16:39:46,418 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:39Z] INFO  16:39:46,451 ProgressMeter -     20:35414191    200002.0    30.0 s       2.5 m       25.4%   117.0 s      87.0 s
[2016-04-14T23:39Z] INFO  16:39:46,499 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:39Z] INFO  16:39:46,501 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:39Z] INFO  16:39:46,502 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:39Z] INFO  16:39:46,503 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-14T23:39Z] INFO  16:39:46,581 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:39Z] INFO  16:39:46,591 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:39Z] INFO  16:39:46,660 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-14T23:39Z] INFO  16:39:46,712 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:39Z] INFO  16:39:46,716 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:39Z] INFO  16:39:46,716 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:39Z] INFO  16:39:46,717 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:39Z] INFO  16:39:46,721 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/20/R14-18102_kapa-NGv3-PE100-NGv3-sort-20_0_15843471-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/20/tx/tmpLlipL0/R14-18102_kapa-NGv3-PE100-NGv3-sort-20_0_15843471-prep-prealign-realign.intervals -l INFO -L 20:1-15843471 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-14T23:39Z] INFO  16:39:46,734 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:39Z] INFO  16:39:46,735 HelpFormatter - Date/Time: 2016/04/14 16:39:46
[2016-04-14T23:39Z] INFO  16:39:46,735 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:39Z] INFO  16:39:46,736 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:39Z] INFO  16:39:46,810 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:39Z] INFO  16:39:46,844 ProgressMeter -     19:39361664    400008.0    60.0 s       2.5 m       53.4%   112.0 s      52.0 s
[2016-04-14T23:39Z] INFO  16:39:47,001 IntervalUtils - Processing 194276 bp from intervals
[2016-04-14T23:39Z] WARN  16:39:47,006 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:39Z] INFO  16:39:47,055 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-14T23:39Z] INFO  16:39:47,070 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:39Z] INFO  16:39:47,086 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:39Z] INFO  16:39:47,137 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:39Z] INFO  16:39:47,137 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:39Z] INFO  16:39:47,138 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:39Z] INFO  16:39:47,138 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:39Z] INFO  16:39:47,161 ProgressMeter -     20:57876658    200004.0    30.0 s       2.5 m       68.2%    43.0 s      13.0 s
[2016-04-14T23:39Z] INFO  16:39:47,169 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.10
[2016-04-14T23:39Z] INFO  16:39:47,180 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:39Z] INFO  16:39:47,193 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:39Z] INFO  16:39:47,441 IntervalUtils - Processing 15843471 bp from intervals
[2016-04-14T23:39Z] WARN  16:39:47,446 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:39Z] INFO  16:39:47,530 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:39Z] INFO  16:39:47,714 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:39Z] INFO  16:39:47,714 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:39Z] INFO  16:39:47,715 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:39Z] INFO  16:39:47,715 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-14T23:39Z] INFO  16:39:48,655 ProgressMeter -     17:74527762    400006.0    32.0 s      81.0 s       79.6%    40.0 s       8.0 s
[2016-04-14T23:39Z] INFO  16:39:48,859 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:39Z] INFO  16:39:48,863 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:39Z] INFO  16:39:48,863 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:39Z] INFO  16:39:48,864 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:39Z] INFO  16:39:48,868 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/19/R14-18102_kapa-NGv3-PE100-NGv3-sort-19_15510112_31025906-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/19/tx/tmp81hK9J/R14-18102_kapa-NGv3-PE100-NGv3-sort-19_15510112_31025906-prep-prealign-realign.intervals -l INFO -L 19:15510113-31025906 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-14T23:39Z] INFO  16:39:48,873 ProgressMeter -            done   1.5559197E7    34.0 s       2.0 s      100.0%    34.0 s       0.0 s
[2016-04-14T23:39Z] INFO  16:39:48,874 ProgressMeter - Total runtime 34.38 secs, 0.57 min, 0.01 hours
[2016-04-14T23:39Z] INFO  16:39:48,878 MicroScheduler - 266756 reads were filtered out during the traversal out of approximately 1141675 total reads (23.37%)
[2016-04-14T23:39Z] INFO  16:39:48,878 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:39Z] INFO  16:39:48,878 MicroScheduler -   -> 1717 reads (0.15% of total) failing BadMateFilter
[2016-04-14T23:39Z] INFO  16:39:48,879 MicroScheduler -   -> 78605 reads (6.89% of total) failing DuplicateReadFilter
[2016-04-14T23:39Z] INFO  16:39:48,879 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-14T23:39Z] INFO  16:39:48,879 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:39Z] INFO  16:39:48,879 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-14T23:39Z] INFO  16:39:48,880 MicroScheduler -   -> 186434 reads (16.33% of total) failing MappingQualityZeroFilter
[2016-04-14T23:39Z] INFO  16:39:48,880 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:39Z] INFO  16:39:48,881 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-14T23:39Z] INFO  16:39:48,881 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-14T23:39Z] INFO  16:39:48,884 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:39Z] INFO  16:39:48,885 HelpFormatter - Date/Time: 2016/04/14 16:39:48
[2016-04-14T23:39Z] INFO  16:39:48,886 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:39Z] INFO  16:39:48,886 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:39Z] INFO  16:39:49,035 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:39Z] INFO  16:39:49,262 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-14T23:39Z] INFO  16:39:49,275 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:39Z] INFO  16:39:49,274 ProgressMeter -            done      8224.0     2.0 s       4.3 m       66.0%     3.0 s       1.0 s
[2016-04-14T23:39Z] INFO  16:39:49,275 ProgressMeter - Total runtime 2.14 secs, 0.04 min, 0.00 hours
[2016-04-14T23:39Z] INFO  16:39:49,278 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 8224 total reads (0.00%)
[2016-04-14T23:39Z] INFO  16:39:49,278 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:39Z] INFO  16:39:49,279 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:39Z] INFO  16:39:49,279 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:39Z] INFO  16:39:49,337 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-14T23:39Z] INFO  16:39:49,634 IntervalUtils - Processing 15515794 bp from intervals
[2016-04-14T23:39Z] WARN  16:39:49,639 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:39Z] INFO  16:39:49,736 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:39Z] INFO  16:39:49,946 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:39Z] INFO  16:39:49,947 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:39Z] INFO  16:39:49,948 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:39Z] INFO  16:39:49,948 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-14T23:39Z] INFO  16:39:49,967 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@41fd9d8e
[2016-04-14T23:39Z] INFO  16:39:50,071 ProgressMeter -            done     71661.0    13.0 s       3.2 m      100.0%    13.0 s       0.0 s
[2016-04-14T23:39Z] INFO  16:39:50,072 ProgressMeter - Total runtime 13.60 secs, 0.23 min, 0.00 hours
[2016-04-14T23:39Z] INFO  16:39:50,072 MicroScheduler - 86 reads were filtered out during the traversal out of approximately 71747 total reads (0.12%)
[2016-04-14T23:39Z] INFO  16:39:50,072 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:39Z] INFO  16:39:50,073 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:39Z] INFO  16:39:50,073 MicroScheduler -   -> 86 reads (0.12% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:39Z] INFO  16:39:50,293 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:39Z] GATK: realign ('17', 31048040, 46607237) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:39Z] INFO  16:39:50,608 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:39Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-20_62831244_63025520-prep.bam
[2016-04-14T23:39Z] GATK pre-alignment ('21', 46595644, 48129895) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:39Z] INFO  16:39:51,037 ProgressMeter -     19:51159611    400007.0    60.0 s       2.5 m       36.3%     2.8 m     105.0 s
[2016-04-14T23:39Z] INFO  16:39:51,465 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:39Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-21_15524893_31045484-prep-prealign.bam
[2016-04-14T23:39Z] GATK RealignerTargetCreator: R14-18102_kapa-NGv3-PE100-NGv3-sort-21_15524893_31045484-prep-prealign.bam 21:15524894-31045484
[2016-04-14T23:39Z] GATK: RealignerTargetCreator
[2016-04-14T23:39Z] INFO  16:39:53,305 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:39Z] INFO  16:39:53,309 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:39Z] INFO  16:39:53,309 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:39Z] INFO  16:39:53,310 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:39Z] INFO  16:39:53,314 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/17/R14-18102_kapa-NGv3-PE100-NGv3-sort-17_31048040_46607237-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/17/R14-18102_kapa-NGv3-PE100-NGv3-sort-17_31048040_46607237-prep-prealign-realign.intervals -L 17:31048041-46607237 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/17/tx/tmp0M8DUr/R14-18102_kapa-NGv3-PE100-NGv3-sort-17_31048040_46607237-prep.bam
[2016-04-14T23:39Z] INFO  16:39:53,324 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:39Z] INFO  16:39:53,325 HelpFormatter - Date/Time: 2016/04/14 16:39:53
[2016-04-14T23:39Z] INFO  16:39:53,326 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:39Z] INFO  16:39:53,326 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:39Z] INFO  16:39:53,636 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:39Z] INFO  16:39:53,639 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:39Z] INFO  16:39:53,643 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:39Z] INFO  16:39:53,645 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:39Z] INFO  16:39:53,646 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:39Z] INFO  16:39:53,651 HelpFormatter - Program Args: -T PrintReads -L 21:46595645-48129895 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/21/tx/tmpv9wz1O/R14-18102_kapa-NGv3-PE100-NGv3-sort-21_46595644_48129895-prep-prealign.bam
[2016-04-14T23:39Z] INFO  16:39:53,675 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:39Z] INFO  16:39:53,676 HelpFormatter - Date/Time: 2016/04/14 16:39:53
[2016-04-14T23:39Z] INFO  16:39:53,676 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:39Z] INFO  16:39:53,676 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:39Z] INFO  16:39:53,769 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:39Z] INFO  16:39:53,779 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:39Z] INFO  16:39:53,822 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.04
[2016-04-14T23:39Z] INFO  16:39:53,908 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:39Z] INFO  16:39:54,131 IntervalUtils - Processing 15559197 bp from intervals
[2016-04-14T23:39Z] WARN  16:39:54,136 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:39Z] INFO  16:39:54,249 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:39Z] INFO  16:39:54,401 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:39Z] INFO  16:39:54,403 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:39Z] INFO  16:39:54,403 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:39Z] INFO  16:39:54,404 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:39Z] INFO  16:39:54,635 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:39Z] INFO  16:39:54,804 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:39Z] INFO  16:39:54,808 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:39Z] INFO  16:39:54,809 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:39Z] INFO  16:39:54,809 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:39Z] INFO  16:39:54,814 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/21/R14-18102_kapa-NGv3-PE100-NGv3-sort-21_15524893_31045484-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/21/tx/tmpPb_XNC/R14-18102_kapa-NGv3-PE100-NGv3-sort-21_15524893_31045484-prep-prealign-realign.intervals -l INFO -L 21:15524894-31045484 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-14T23:39Z] INFO  16:39:54,824 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:39Z] INFO  16:39:54,828 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:39Z] INFO  16:39:54,837 HelpFormatter - Date/Time: 2016/04/14 16:39:54
[2016-04-14T23:39Z] INFO  16:39:54,838 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:39Z] INFO  16:39:54,839 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:39Z] INFO  16:39:54,972 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:39Z] INFO  16:39:55,011 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-14T23:39Z] INFO  16:39:55,093 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:39Z] INFO  16:39:55,102 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:39Z] INFO  16:39:55,146 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.04
[2016-04-14T23:39Z] INFO  16:39:55,163 IntervalUtils - Processing 1534251 bp from intervals
[2016-04-14T23:39Z] INFO  16:39:55,168 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-14T23:39Z] INFO  16:39:55,188 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:39Z] INFO  16:39:55,234 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:39Z] INFO  16:39:55,262 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-14T23:39Z] INFO  16:39:55,314 ProgressMeter -            done    593504.0    39.0 s      66.0 s      100.0%    39.0 s       0.0 s
[2016-04-14T23:39Z] INFO  16:39:55,315 ProgressMeter - Total runtime 39.18 secs, 0.65 min, 0.01 hours
[2016-04-14T23:39Z] INFO  16:39:55,318 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 593504 total reads (0.00%)
[2016-04-14T23:39Z] INFO  16:39:55,319 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:39Z] INFO  16:39:55,319 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:39Z] INFO  16:39:55,320 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:39Z] INFO  16:39:55,445 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:39Z] INFO  16:39:55,445 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:39Z] INFO  16:39:55,446 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:39Z] INFO  16:39:55,446 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:39Z] INFO  16:39:55,473 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:39Z] INFO  16:39:55,495 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:39Z] INFO  16:39:55,583 IntervalUtils - Processing 15520591 bp from intervals
[2016-04-14T23:39Z] WARN  16:39:55,589 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:39Z] INFO  16:39:55,728 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:39Z] INFO  16:39:55,915 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:39Z] INFO  16:39:55,916 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:39Z] INFO  16:39:55,917 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:39Z] INFO  16:39:55,918 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-14T23:39Z] INFO  16:39:55,998 ProgressMeter -            done   1.551712E7    10.0 s       0.0 s      100.0%    10.0 s       0.0 s
[2016-04-14T23:39Z] INFO  16:39:55,999 ProgressMeter - Total runtime 10.39 secs, 0.17 min, 0.00 hours
[2016-04-14T23:39Z] INFO  16:39:56,003 MicroScheduler - 11820 reads were filtered out during the traversal out of approximately 38286 total reads (30.87%)
[2016-04-14T23:39Z] INFO  16:39:56,003 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:39Z] INFO  16:39:56,004 MicroScheduler -   -> 188 reads (0.49% of total) failing BadMateFilter
[2016-04-14T23:39Z] INFO  16:39:56,004 MicroScheduler -   -> 2376 reads (6.21% of total) failing DuplicateReadFilter
[2016-04-14T23:39Z] INFO  16:39:56,004 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-14T23:39Z] INFO  16:39:56,005 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:39Z] INFO  16:39:56,005 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-14T23:39Z] INFO  16:39:56,005 MicroScheduler -   -> 9256 reads (24.18% of total) failing MappingQualityZeroFilter
[2016-04-14T23:39Z] INFO  16:39:56,006 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:39Z] INFO  16:39:56,006 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-14T23:39Z] INFO  16:39:56,006 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-14T23:39Z] INFO  16:39:57,107 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:39Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-17_62122219_77705154-prep.bam
[2016-04-14T23:39Z] INFO  16:39:58,363 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:39Z] GATK: realign ('21', 0, 15517120) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:39Z] INFO  16:39:58,853 ProgressMeter -      19:6375401    500006.0    90.0 s       3.0 m       41.1%     3.6 m       2.1 m
[2016-04-14T23:39Z] GATK pre-alignment ('22', 0, 16258303) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:40Z] INFO  16:40:01,336 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:40Z] INFO  16:40:01,339 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:40Z] INFO  16:40:01,339 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:40Z] INFO  16:40:01,339 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:40Z] INFO  16:40:01,354 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/21/R14-18102_kapa-NGv3-PE100-NGv3-sort-21_0_15517120-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/21/R14-18102_kapa-NGv3-PE100-NGv3-sort-21_0_15517120-prep-prealign-realign.intervals -L 21:1-15517120 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/21/tx/tmpumraVj/R14-18102_kapa-NGv3-PE100-NGv3-sort-21_0_15517120-prep.bam
[2016-04-14T23:40Z] INFO  16:40:01,374 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:40Z] INFO  16:40:01,374 HelpFormatter - Date/Time: 2016/04/14 16:40:01
[2016-04-14T23:40Z] INFO  16:40:01,375 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:40Z] INFO  16:40:01,375 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:40Z] INFO  16:40:01,646 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:40Z] INFO  16:40:01,793 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:40Z] INFO  16:40:01,805 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:40Z] INFO  16:40:01,873 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-14T23:40Z] INFO  16:40:02,319 IntervalUtils - Processing 15517120 bp from intervals
[2016-04-14T23:40Z] WARN  16:40:02,324 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:40Z] INFO  16:40:02,403 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:40Z] INFO  16:40:02,497 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:40Z] INFO  16:40:02,500 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:40Z] INFO  16:40:02,501 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:40Z] INFO  16:40:02,502 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:40Z] INFO  16:40:02,506 HelpFormatter - Program Args: -T PrintReads -L 22:1-16258303 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/22/tx/tmpHEGpBR/R14-18102_kapa-NGv3-PE100-NGv3-sort-22_0_16258303-prep-prealign.bam
[2016-04-14T23:40Z] INFO  16:40:02,515 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:40Z] INFO  16:40:02,515 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:40Z] INFO  16:40:02,516 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:40Z] INFO  16:40:02,516 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:40Z] INFO  16:40:02,516 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:40Z] INFO  16:40:02,527 HelpFormatter - Date/Time: 2016/04/14 16:40:02
[2016-04-14T23:40Z] INFO  16:40:02,528 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:40Z] INFO  16:40:02,529 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:40Z] INFO  16:40:02,549 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:40Z] INFO  16:40:02,593 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:40Z] INFO  16:40:02,679 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:40Z] INFO  16:40:03,651 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-14T23:40Z] INFO  16:40:03,730 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:40Z] INFO  16:40:03,745 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:40Z] INFO  16:40:03,800 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-14T23:40Z] INFO  16:40:03,814 IntervalUtils - Processing 16258303 bp from intervals
[2016-04-14T23:40Z] INFO  16:40:03,893 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:40Z] INFO  16:40:04,235 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:40Z] INFO  16:40:04,236 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:40Z] INFO  16:40:04,237 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:40Z] INFO  16:40:04,237 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:40Z] INFO  16:40:04,256 ProgressMeter -            done   1.551041E7    17.0 s       1.0 s      100.0%    17.0 s       0.0 s
[2016-04-14T23:40Z] INFO  16:40:04,257 ProgressMeter - Total runtime 17.76 secs, 0.30 min, 0.00 hours
[2016-04-14T23:40Z] INFO  16:40:04,260 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:40Z] INFO  16:40:04,261 MicroScheduler - 21482 reads were filtered out during the traversal out of approximately 243132 total reads (8.84%)
[2016-04-14T23:40Z] INFO  16:40:04,262 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:40Z] INFO  16:40:04,262 MicroScheduler -   -> 611 reads (0.25% of total) failing BadMateFilter
[2016-04-14T23:40Z] INFO  16:40:04,263 MicroScheduler -   -> 19528 reads (8.03% of total) failing DuplicateReadFilter
[2016-04-14T23:40Z] INFO  16:40:04,263 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-14T23:40Z] INFO  16:40:04,263 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:40Z] INFO  16:40:04,263 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:40Z] INFO  16:40:04,263 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-14T23:40Z] INFO  16:40:04,264 MicroScheduler -   -> 1343 reads (0.55% of total) failing MappingQualityZeroFilter
[2016-04-14T23:40Z] INFO  16:40:04,264 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:40Z] INFO  16:40:04,264 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-14T23:40Z] INFO  16:40:04,264 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-14T23:40Z] INFO  16:40:05,801 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:40Z] GATK: realign ('20', 15866408, 31376818) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:40Z] INFO  16:40:06,943 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@5fe152b7
[2016-04-14T23:40Z] INFO  16:40:06,975 ProgressMeter -            done      6650.0     2.0 s       6.9 m      100.0%     2.0 s       0.0 s
[2016-04-14T23:40Z] INFO  16:40:06,977 ProgressMeter - Total runtime 2.74 secs, 0.05 min, 0.00 hours
[2016-04-14T23:40Z] INFO  16:40:06,978 MicroScheduler - 2 reads were filtered out during the traversal out of approximately 6652 total reads (0.03%)
[2016-04-14T23:40Z] INFO  16:40:06,979 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:40Z] INFO  16:40:06,979 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:40Z] INFO  16:40:06,980 MicroScheduler -   -> 2 reads (0.03% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:40Z] INFO  16:40:07,377 ProgressMeter -            done     38243.0     4.0 s       2.1 m      100.0%     4.0 s       0.0 s
[2016-04-14T23:40Z] INFO  16:40:07,377 ProgressMeter - Total runtime 4.86 secs, 0.08 min, 0.00 hours
[2016-04-14T23:40Z] INFO  16:40:07,381 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 38243 total reads (0.00%)
[2016-04-14T23:40Z] INFO  16:40:07,381 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:40Z] INFO  16:40:07,382 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:40Z] INFO  16:40:07,382 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:40Z] INFO  16:40:07,599 ProgressMeter -            done   1.5843471E7    19.0 s       1.0 s      100.0%    19.0 s       0.0 s
[2016-04-14T23:40Z] INFO  16:40:07,600 ProgressMeter - Total runtime 19.89 secs, 0.33 min, 0.01 hours
[2016-04-14T23:40Z] INFO  16:40:07,604 MicroScheduler - 25779 reads were filtered out during the traversal out of approximately 297417 total reads (8.67%)
[2016-04-14T23:40Z] INFO  16:40:07,605 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:40Z] INFO  16:40:07,606 MicroScheduler -   -> 756 reads (0.25% of total) failing BadMateFilter
[2016-04-14T23:40Z] INFO  16:40:07,607 MicroScheduler -   -> 23902 reads (8.04% of total) failing DuplicateReadFilter
[2016-04-14T23:40Z] INFO  16:40:07,607 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-14T23:40Z] INFO  16:40:07,608 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:40Z] INFO  16:40:07,609 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-14T23:40Z] INFO  16:40:07,609 MicroScheduler -   -> 1121 reads (0.38% of total) failing MappingQualityZeroFilter
[2016-04-14T23:40Z] INFO  16:40:07,610 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:40Z] INFO  16:40:07,611 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-14T23:40Z] INFO  16:40:07,611 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-14T23:40Z] INFO  16:40:08,248 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:40Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-22_0_16258303-prep-prealign.bam
[2016-04-14T23:40Z] INFO  16:40:08,336 ProgressMeter -      17:6331859    400012.0    32.0 s      80.0 s       40.8%    78.0 s      46.0 s
[2016-04-14T23:40Z] GATK RealignerTargetCreator: R14-18102_kapa-NGv3-PE100-NGv3-sort-22_0_16258303-prep-prealign.bam 22:1-16258303
[2016-04-14T23:40Z] GATK: RealignerTargetCreator
[2016-04-14T23:40Z] INFO  16:40:08,424 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:40Z] INFO  16:40:08,427 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:40Z] INFO  16:40:08,428 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:40Z] INFO  16:40:08,428 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:40Z] INFO  16:40:08,433 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/20/R14-18102_kapa-NGv3-PE100-NGv3-sort-20_15866408_31376818-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/20/R14-18102_kapa-NGv3-PE100-NGv3-sort-20_15866408_31376818-prep-prealign-realign.intervals -L 20:15866409-31376818 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/20/tx/tmpqIvml0/R14-18102_kapa-NGv3-PE100-NGv3-sort-20_15866408_31376818-prep.bam
[2016-04-14T23:40Z] INFO  16:40:08,444 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:40Z] INFO  16:40:08,455 HelpFormatter - Date/Time: 2016/04/14 16:40:08
[2016-04-14T23:40Z] INFO  16:40:08,456 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:40Z] INFO  16:40:08,457 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:40Z] INFO  16:40:08,624 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:40Z] INFO  16:40:08,743 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:40Z] INFO  16:40:08,753 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:40Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-21_0_15517120-prep.bam
[2016-04-14T23:40Z] INFO  16:40:08,763 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:40Z] INFO  16:40:08,822 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-14T23:40Z] GATK pre-alignment ('22', 16266928, 31795711) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:40Z] INFO  16:40:09,097 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:40Z] GATK: realign ('20', 0, 15843471) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:40Z] INFO  16:40:09,179 IntervalUtils - Processing 15510410 bp from intervals
[2016-04-14T23:40Z] WARN  16:40:09,208 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:40Z] INFO  16:40:09,363 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:40Z] INFO  16:40:09,501 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:40Z] INFO  16:40:09,503 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:40Z] INFO  16:40:09,503 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:40Z] INFO  16:40:09,504 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:40Z] INFO  16:40:09,654 ProgressMeter -     16:30214805    900016.0    60.0 s      67.0 s       94.3%    63.0 s       3.0 s
[2016-04-14T23:40Z] INFO  16:40:09,669 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:40Z] INFO  16:40:09,908 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:40Z] INFO  16:40:10,775 ProgressMeter -            done   1.5520591E7    14.0 s       0.0 s      100.0%    14.0 s       0.0 s
[2016-04-14T23:40Z] INFO  16:40:10,775 ProgressMeter - Total runtime 14.86 secs, 0.25 min, 0.00 hours
[2016-04-14T23:40Z] INFO  16:40:10,779 MicroScheduler - 6504 reads were filtered out during the traversal out of approximately 72063 total reads (9.03%)
[2016-04-14T23:40Z] INFO  16:40:10,786 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:40Z] INFO  16:40:10,787 MicroScheduler -   -> 375 reads (0.52% of total) failing BadMateFilter
[2016-04-14T23:40Z] INFO  16:40:10,787 MicroScheduler -   -> 5783 reads (8.02% of total) failing DuplicateReadFilter
[2016-04-14T23:40Z] INFO  16:40:10,788 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-14T23:40Z] INFO  16:40:10,789 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:40Z] INFO  16:40:10,789 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-14T23:40Z] INFO  16:40:10,790 MicroScheduler -   -> 346 reads (0.48% of total) failing MappingQualityZeroFilter
[2016-04-14T23:40Z] INFO  16:40:10,791 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:40Z] INFO  16:40:10,791 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-14T23:40Z] INFO  16:40:10,792 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-14T23:40Z] INFO  16:40:11,184 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:40Z] INFO  16:40:11,188 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:40Z] INFO  16:40:11,188 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:40Z] INFO  16:40:11,189 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:40Z] INFO  16:40:11,194 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/22/R14-18102_kapa-NGv3-PE100-NGv3-sort-22_0_16258303-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/22/tx/tmpaWKi2T/R14-18102_kapa-NGv3-PE100-NGv3-sort-22_0_16258303-prep-prealign-realign.intervals -l INFO -L 22:1-16258303 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-14T23:40Z] INFO  16:40:11,203 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:40Z] INFO  16:40:11,203 HelpFormatter - Date/Time: 2016/04/14 16:40:11
[2016-04-14T23:40Z] INFO  16:40:11,203 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:40Z] INFO  16:40:11,204 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:40Z] INFO  16:40:11,354 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:40Z] INFO  16:40:11,592 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-14T23:40Z] INFO  16:40:11,613 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:40Z] INFO  16:40:11,672 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@5fe152b7
[2016-04-14T23:40Z] INFO  16:40:11,697 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-14T23:40Z] INFO  16:40:11,781 ProgressMeter -            done    451351.0    54.0 s       2.0 m      100.0%    54.0 s       0.0 s
[2016-04-14T23:40Z] INFO  16:40:11,782 ProgressMeter - Total runtime 54.66 secs, 0.91 min, 0.02 hours
[2016-04-14T23:40Z] INFO  16:40:11,783 MicroScheduler - 234 reads were filtered out during the traversal out of approximately 451585 total reads (0.05%)
[2016-04-14T23:40Z] INFO  16:40:11,783 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:40Z] INFO  16:40:11,784 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:40Z] INFO  16:40:11,785 MicroScheduler -   -> 234 reads (0.05% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:40Z] INFO  16:40:11,896 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@7172f77a
[2016-04-14T23:40Z] INFO  16:40:11,988 ProgressMeter -            done    108991.0    16.0 s       2.5 m       97.0%    16.0 s       0.0 s
[2016-04-14T23:40Z] INFO  16:40:11,989 ProgressMeter - Total runtime 16.54 secs, 0.28 min, 0.00 hours
[2016-04-14T23:40Z] INFO  16:40:11,990 MicroScheduler - 61 reads were filtered out during the traversal out of approximately 109052 total reads (0.06%)
[2016-04-14T23:40Z] INFO  16:40:11,990 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:40Z] INFO  16:40:11,990 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:40Z] INFO  16:40:11,991 MicroScheduler -   -> 61 reads (0.06% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:40Z] INFO  16:40:12,033 IntervalUtils - Processing 16258303 bp from intervals
[2016-04-14T23:40Z] WARN  16:40:12,038 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:40Z] INFO  16:40:12,058 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:40Z] GATK: realign ('21', 15524893, 31045484) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:40Z] INFO  16:40:12,118 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:40Z] INFO  16:40:12,303 ProgressMeter -     21:40560597    100001.0    30.0 s       5.0 m       61.2%    49.0 s      19.0 s
[2016-04-14T23:40Z] INFO  16:40:12,309 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:40Z] INFO  16:40:12,313 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:40Z] INFO  16:40:12,313 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:40Z] INFO  16:40:12,314 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:40Z] INFO  16:40:12,319 HelpFormatter - Program Args: -T PrintReads -L 22:16266929-31795711 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/22/tx/tmphlE9Ys/R14-18102_kapa-NGv3-PE100-NGv3-sort-22_16266928_31795711-prep-prealign.bam
[2016-04-14T23:40Z] INFO  16:40:12,332 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:40Z] INFO  16:40:12,333 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:40Z] INFO  16:40:12,337 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:40Z] INFO  16:40:12,338 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:40Z] INFO  16:40:12,339 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:40Z] INFO  16:40:12,343 HelpFormatter - Date/Time: 2016/04/14 16:40:12
[2016-04-14T23:40Z] INFO  16:40:12,343 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/20/R14-18102_kapa-NGv3-PE100-NGv3-sort-20_0_15843471-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/20/R14-18102_kapa-NGv3-PE100-NGv3-sort-20_0_15843471-prep-prealign-realign.intervals -L 20:1-15843471 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/20/tx/tmp15Ml62/R14-18102_kapa-NGv3-PE100-NGv3-sort-20_0_15843471-prep.bam
[2016-04-14T23:40Z] INFO  16:40:12,344 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:40Z] INFO  16:40:12,345 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:40Z] INFO  16:40:12,351 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:40Z] INFO  16:40:12,352 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:40Z] INFO  16:40:12,353 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:40Z] INFO  16:40:12,354 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-14T23:40Z] INFO  16:40:12,355 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:40Z] INFO  16:40:12,366 HelpFormatter - Date/Time: 2016/04/14 16:40:12
[2016-04-14T23:40Z] INFO  16:40:12,367 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:40Z] INFO  16:40:12,368 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:40Z] INFO  16:40:12,516 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:40Z] INFO  16:40:12,570 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:40Z] INFO  16:40:12,659 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:40Z] INFO  16:40:12,668 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:40Z] INFO  16:40:12,712 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.04
[2016-04-14T23:40Z] INFO  16:40:13,120 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:40Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-20_47244085_62830269-prep-prealign.bam
[2016-04-14T23:40Z] INFO  16:40:13,228 IntervalUtils - Processing 15843471 bp from intervals
[2016-04-14T23:40Z] WARN  16:40:13,234 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:40Z] INFO  16:40:13,315 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:40Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-21_46595644_48129895-prep-prealign.bam
[2016-04-14T23:40Z] INFO  16:40:13,370 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:40Z] INFO  16:40:13,519 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:40Z] INFO  16:40:13,521 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:40Z] INFO  16:40:13,522 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:40Z] INFO  16:40:13,523 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:40Z] INFO  16:40:13,773 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:40Z] GATK RealignerTargetCreator: R14-18102_kapa-NGv3-PE100-NGv3-sort-21_46595644_48129895-prep-prealign.bam 21:46595645-48129895
[2016-04-14T23:40Z] GATK: RealignerTargetCreator
[2016-04-14T23:40Z] INFO  16:40:13,830 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-14T23:40Z] INFO  16:40:13,911 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:40Z] INFO  16:40:13,920 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:40Z] INFO  16:40:13,927 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:40Z] INFO  16:40:13,960 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.04
[2016-04-14T23:40Z] INFO  16:40:13,974 IntervalUtils - Processing 15528783 bp from intervals
[2016-04-14T23:40Z] INFO  16:40:14,068 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:40Z] INFO  16:40:14,350 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:40Z] INFO  16:40:14,351 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:40Z] INFO  16:40:14,352 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:40Z] INFO  16:40:14,353 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:40Z] INFO  16:40:14,367 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:40Z] GATK RealignerTargetCreator: R14-18102_kapa-NGv3-PE100-NGv3-sort-20_47244085_62830269-prep-prealign.bam 20:47244086-62830269
[2016-04-14T23:40Z] GATK: RealignerTargetCreator
[2016-04-14T23:40Z] INFO  16:40:14,578 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:40Z] INFO  16:40:14,870 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:40Z] INFO  16:40:14,873 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:40Z] INFO  16:40:14,874 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:40Z] INFO  16:40:14,875 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:40Z] INFO  16:40:14,879 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/21/R14-18102_kapa-NGv3-PE100-NGv3-sort-21_15524893_31045484-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/21/R14-18102_kapa-NGv3-PE100-NGv3-sort-21_15524893_31045484-prep-prealign-realign.intervals -L 21:15524894-31045484 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/21/tx/tmpvazBRn/R14-18102_kapa-NGv3-PE100-NGv3-sort-21_15524893_31045484-prep.bam
[2016-04-14T23:40Z] INFO  16:40:14,901 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:40Z] INFO  16:40:14,912 HelpFormatter - Date/Time: 2016/04/14 16:40:14
[2016-04-14T23:40Z] INFO  16:40:14,913 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:40Z] INFO  16:40:14,914 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:40Z] INFO  16:40:15,105 ProgressMeter -            done   1.5515794E7    25.0 s       1.0 s      100.0%    25.0 s       0.0 s
[2016-04-14T23:40Z] INFO  16:40:15,106 ProgressMeter - Total runtime 25.16 secs, 0.42 min, 0.01 hours
[2016-04-14T23:40Z] INFO  16:40:15,109 MicroScheduler - 53329 reads were filtered out during the traversal out of approximately 561952 total reads (9.49%)
[2016-04-14T23:40Z] INFO  16:40:15,109 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:40Z] INFO  16:40:15,110 MicroScheduler -   -> 1268 reads (0.23% of total) failing BadMateFilter
[2016-04-14T23:40Z] INFO  16:40:15,110 MicroScheduler -   -> 45403 reads (8.08% of total) failing DuplicateReadFilter
[2016-04-14T23:40Z] INFO  16:40:15,110 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-14T23:40Z] INFO  16:40:15,110 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:40Z] INFO  16:40:15,111 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-14T23:40Z] INFO  16:40:15,111 MicroScheduler -   -> 6658 reads (1.18% of total) failing MappingQualityZeroFilter
[2016-04-14T23:40Z] INFO  16:40:15,111 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:40Z] INFO  16:40:15,111 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-14T23:40Z] INFO  16:40:15,112 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-14T23:40Z] INFO  16:40:15,144 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:40Z] INFO  16:40:15,289 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:40Z] INFO  16:40:15,309 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:40Z] INFO  16:40:15,398 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.09
[2016-04-14T23:40Z] INFO  16:40:15,792 IntervalUtils - Processing 15520591 bp from intervals
[2016-04-14T23:40Z] WARN  16:40:15,797 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:40Z] INFO  16:40:15,875 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:40Z] INFO  16:40:16,022 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:40Z] INFO  16:40:16,023 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:40Z] INFO  16:40:16,024 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:40Z] INFO  16:40:16,024 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:40Z] INFO  16:40:16,247 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:40Z] INFO  16:40:16,423 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:40Z] INFO  16:40:16,452 ProgressMeter -     20:44676103    400004.0    60.0 s       2.5 m       83.8%    71.0 s      11.0 s
[2016-04-14T23:40Z] INFO  16:40:16,495 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:40Z] GATK: realign ('19', 15510112, 31025906) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:40Z] INFO  16:40:16,675 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:40Z] INFO  16:40:16,679 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:40Z] INFO  16:40:16,679 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:40Z] INFO  16:40:16,680 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:40Z] INFO  16:40:16,685 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/21/R14-18102_kapa-NGv3-PE100-NGv3-sort-21_46595644_48129895-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/21/tx/tmpSQMGuB/R14-18102_kapa-NGv3-PE100-NGv3-sort-21_46595644_48129895-prep-prealign-realign.intervals -l INFO -L 21:46595645-48129895 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-14T23:40Z] INFO  16:40:16,694 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:40Z] INFO  16:40:16,705 HelpFormatter - Date/Time: 2016/04/14 16:40:16
[2016-04-14T23:40Z] INFO  16:40:16,706 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:40Z] INFO  16:40:16,707 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:40Z] INFO  16:40:16,845 ProgressMeter -     19:41807642    700012.0    90.0 s       2.1 m       69.1%     2.2 m      40.0 s
[2016-04-14T23:40Z] INFO  16:40:16,853 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:40Z] INFO  16:40:16,863 ProgressMeter -            done   1167959.0    67.0 s      57.0 s      100.0%    67.0 s       0.0 s
[2016-04-14T23:40Z] INFO  16:40:16,864 ProgressMeter - Total runtime 67.53 secs, 1.13 min, 0.02 hours
[2016-04-14T23:40Z] INFO  16:40:16,867 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 1167959 total reads (0.00%)
[2016-04-14T23:40Z] INFO  16:40:16,868 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:40Z] INFO  16:40:16,869 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:40Z] INFO  16:40:16,870 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:40Z] INFO  16:40:17,078 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-14T23:40Z] INFO  16:40:17,088 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:40Z] INFO  16:40:17,181 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.09
[2016-04-14T23:40Z] INFO  16:40:17,420 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:40Z] INFO  16:40:17,423 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:40Z] INFO  16:40:17,424 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:40Z] INFO  16:40:17,425 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:40Z] INFO  16:40:17,429 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/20/R14-18102_kapa-NGv3-PE100-NGv3-sort-20_47244085_62830269-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/20/tx/tmpQD9D_O/R14-18102_kapa-NGv3-PE100-NGv3-sort-20_47244085_62830269-prep-prealign-realign.intervals -l INFO -L 20:47244086-62830269 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-14T23:40Z] INFO  16:40:17,442 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:40Z] INFO  16:40:17,443 HelpFormatter - Date/Time: 2016/04/14 16:40:17
[2016-04-14T23:40Z] INFO  16:40:17,454 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:40Z] INFO  16:40:17,455 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:40Z] INFO  16:40:17,615 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:40Z] INFO  16:40:17,626 IntervalUtils - Processing 1534251 bp from intervals
[2016-04-14T23:40Z] WARN  16:40:17,643 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:40Z] INFO  16:40:17,793 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:40Z] INFO  16:40:17,868 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-14T23:40Z] INFO  16:40:17,878 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:40Z] INFO  16:40:17,941 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-14T23:40Z] INFO  16:40:17,943 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:40Z] INFO  16:40:17,944 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:40Z] INFO  16:40:17,945 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:40Z] INFO  16:40:17,946 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-14T23:40Z] INFO  16:40:18,333 IntervalUtils - Processing 15586184 bp from intervals
[2016-04-14T23:40Z] WARN  16:40:18,338 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:40Z] INFO  16:40:18,448 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:40Z] INFO  16:40:18,494 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:40Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-16_15596122_31106473-prep.bam
[2016-04-14T23:40Z] INFO  16:40:18,723 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:40Z] INFO  16:40:18,724 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:40Z] INFO  16:40:18,725 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:40Z] INFO  16:40:18,726 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-14T23:40Z] INFO  16:40:19,300 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:40Z] INFO  16:40:19,303 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:40Z] INFO  16:40:19,304 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:40Z] INFO  16:40:19,304 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:40Z] INFO  16:40:19,309 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/19/R14-18102_kapa-NGv3-PE100-NGv3-sort-19_15510112_31025906-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/19/R14-18102_kapa-NGv3-PE100-NGv3-sort-19_15510112_31025906-prep-prealign-realign.intervals -L 19:15510113-31025906 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/19/tx/tmpySm_IR/R14-18102_kapa-NGv3-PE100-NGv3-sort-19_15510112_31025906-prep.bam
[2016-04-14T23:40Z] INFO  16:40:19,329 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:40Z] INFO  16:40:19,330 HelpFormatter - Date/Time: 2016/04/14 16:40:19
[2016-04-14T23:40Z] INFO  16:40:19,331 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:40Z] INFO  16:40:19,331 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:40Z] INFO  16:40:19,566 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:40Z] INFO  16:40:19,739 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:40Z] INFO  16:40:19,748 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:40Z] INFO  16:40:19,812 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-14T23:40Z] INFO  16:40:20,299 IntervalUtils - Processing 15515794 bp from intervals
[2016-04-14T23:40Z] WARN  16:40:20,315 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:40Z] INFO  16:40:20,418 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:40Z] INFO  16:40:20,545 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:40Z] INFO  16:40:20,546 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:40Z] INFO  16:40:20,547 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:40Z] INFO  16:40:20,547 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:40Z] INFO  16:40:20,724 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:40Z] INFO  16:40:20,897 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:40Z] INFO  16:40:21,038 ProgressMeter -     19:54408108    700015.0    90.0 s       2.2 m       62.2%     2.4 m      54.0 s
[2016-04-14T23:40Z] INFO  16:40:21,866 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@5fe152b7
[2016-04-14T23:40Z] INFO  16:40:21,975 ProgressMeter -            done    555571.0    65.0 s     118.0 s      100.0%    65.0 s       0.0 s
[2016-04-14T23:40Z] INFO  16:40:21,975 ProgressMeter - Total runtime 65.96 secs, 1.10 min, 0.02 hours
[2016-04-14T23:40Z] INFO  16:40:21,976 MicroScheduler - 238 reads were filtered out during the traversal out of approximately 555809 total reads (0.04%)
[2016-04-14T23:40Z] INFO  16:40:21,976 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:40Z] INFO  16:40:21,976 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:40Z] INFO  16:40:21,977 MicroScheduler -   -> 238 reads (0.04% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:40Z] GATK pre-alignment ('22', 31796605, 47308085) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:40Z] INFO  16:40:22,234 ProgressMeter -            done   1.6258303E7     9.0 s       0.0 s      100.0%     9.0 s       0.0 s
[2016-04-14T23:40Z] INFO  16:40:22,235 ProgressMeter - Total runtime 9.88 secs, 0.16 min, 0.00 hours
[2016-04-14T23:40Z] INFO  16:40:22,239 MicroScheduler - 4338 reads were filtered out during the traversal out of approximately 6650 total reads (65.23%)
[2016-04-14T23:40Z] INFO  16:40:22,240 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:40Z] INFO  16:40:22,241 MicroScheduler -   -> 1 reads (0.02% of total) failing BadMateFilter
[2016-04-14T23:40Z] INFO  16:40:22,242 MicroScheduler -   -> 248 reads (3.73% of total) failing DuplicateReadFilter
[2016-04-14T23:40Z] INFO  16:40:22,253 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-14T23:40Z] INFO  16:40:22,254 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:40Z] INFO  16:40:22,254 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-14T23:40Z] INFO  16:40:22,255 MicroScheduler -   -> 4089 reads (61.49% of total) failing MappingQualityZeroFilter
[2016-04-14T23:40Z] INFO  16:40:22,256 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:40Z] INFO  16:40:22,256 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-14T23:40Z] INFO  16:40:22,257 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-14T23:40Z] INFO  16:40:23,588 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:40Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-20_31379406_47242465-prep-prealign.bam
[2016-04-14T23:40Z] INFO  16:40:23,698 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:40Z] GATK: realign ('22', 0, 16258303) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:40Z] INFO  16:40:23,739 ProgressMeter -            done     71661.0     7.0 s     107.0 s      100.0%     7.0 s       0.0 s
[2016-04-14T23:40Z] INFO  16:40:23,740 ProgressMeter - Total runtime 7.72 secs, 0.13 min, 0.00 hours
[2016-04-14T23:40Z] INFO  16:40:23,743 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 71661 total reads (0.00%)
[2016-04-14T23:40Z] INFO  16:40:23,744 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:40Z] INFO  16:40:23,744 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:40Z] INFO  16:40:23,745 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:40Z] INFO  16:40:24,665 ProgressMeter -            done   1534251.0     6.0 s       4.0 s      100.0%     6.0 s       0.0 s
[2016-04-14T23:40Z] INFO  16:40:24,666 ProgressMeter - Total runtime 6.72 secs, 0.11 min, 0.00 hours
[2016-04-14T23:40Z] INFO  16:40:24,671 MicroScheduler - 9224 reads were filtered out during the traversal out of approximately 109485 total reads (8.42%)
[2016-04-14T23:40Z] INFO  16:40:24,672 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:40Z] INFO  16:40:24,672 MicroScheduler -   -> 212 reads (0.19% of total) failing BadMateFilter
[2016-04-14T23:40Z] INFO  16:40:24,672 MicroScheduler -   -> 8849 reads (8.08% of total) failing DuplicateReadFilter
[2016-04-14T23:40Z] INFO  16:40:24,673 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-14T23:40Z] INFO  16:40:24,673 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:40Z] INFO  16:40:24,673 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-14T23:40Z] INFO  16:40:24,674 MicroScheduler -   -> 163 reads (0.15% of total) failing MappingQualityZeroFilter
[2016-04-14T23:40Z] INFO  16:40:24,674 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:40Z] INFO  16:40:24,674 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-14T23:40Z] INFO  16:40:24,675 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-14T23:40Z] INFO  16:40:24,823 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:40Z] INFO  16:40:24,841 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:40Z] INFO  16:40:24,847 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:40Z] INFO  16:40:24,848 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:40Z] INFO  16:40:24,853 HelpFormatter - Program Args: -T PrintReads -L 22:31796606-47308085 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/22/tx/tmpDhpyNe/R14-18102_kapa-NGv3-PE100-NGv3-sort-22_31796605_47308085-prep-prealign.bam
[2016-04-14T23:40Z] INFO  16:40:24,878 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:40Z] INFO  16:40:24,879 HelpFormatter - Date/Time: 2016/04/14 16:40:24
[2016-04-14T23:40Z] INFO  16:40:24,880 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:40Z] INFO  16:40:24,880 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:40Z] INFO  16:40:25,091 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:40Z] INFO  16:40:25,170 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:40Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-21_15524893_31045484-prep.bam
[2016-04-14T23:40Z] GATK RealignerTargetCreator: R14-18102_kapa-NGv3-PE100-NGv3-sort-20_31379406_47242465-prep-prealign.bam 20:31379407-47242465
[2016-04-14T23:40Z] GATK: RealignerTargetCreator
[2016-04-14T23:40Z] GATK pre-alignment ('22', 47309229, 51304566) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:40Z] INFO  16:40:26,038 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:40Z] GATK: realign ('21', 46595644, 48129895) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:40Z] INFO  16:40:26,311 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-14T23:40Z] INFO  16:40:26,381 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:40Z] INFO  16:40:26,392 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:40Z] INFO  16:40:26,474 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-14T23:40Z] INFO  16:40:26,491 IntervalUtils - Processing 15511480 bp from intervals
[2016-04-14T23:40Z] INFO  16:40:26,583 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:40Z] INFO  16:40:26,676 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:40Z] INFO  16:40:26,679 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:40Z] INFO  16:40:26,680 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:40Z] INFO  16:40:26,681 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:40Z] INFO  16:40:26,685 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/22/R14-18102_kapa-NGv3-PE100-NGv3-sort-22_0_16258303-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/22/R14-18102_kapa-NGv3-PE100-NGv3-sort-22_0_16258303-prep-prealign-realign.intervals -L 22:1-16258303 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/22/tx/tmpFJXbc6/R14-18102_kapa-NGv3-PE100-NGv3-sort-22_0_16258303-prep.bam
[2016-04-14T23:40Z] INFO  16:40:26,694 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:40Z] INFO  16:40:26,705 HelpFormatter - Date/Time: 2016/04/14 16:40:26
[2016-04-14T23:40Z] INFO  16:40:26,706 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:40Z] INFO  16:40:26,707 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:40Z] INFO  16:40:26,880 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:40Z] INFO  16:40:26,912 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:40Z] INFO  16:40:26,913 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:40Z] INFO  16:40:26,913 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:40Z] INFO  16:40:26,913 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:40Z] INFO  16:40:26,953 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:40Z] INFO  16:40:27,016 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:40Z] INFO  16:40:27,025 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:40Z] INFO  16:40:27,088 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-14T23:40Z] INFO  16:40:27,134 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:40Z] INFO  16:40:27,309 ProgressMeter -     17:38546339    400004.0    32.0 s      82.0 s       48.2%    66.0 s      34.0 s
[2016-04-14T23:40Z] INFO  16:40:27,466 IntervalUtils - Processing 16258303 bp from intervals
[2016-04-14T23:40Z] WARN  16:40:27,481 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:40Z] INFO  16:40:27,561 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:40Z] INFO  16:40:27,798 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:40Z] INFO  16:40:27,798 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:40Z] INFO  16:40:27,799 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:40Z] INFO  16:40:27,799 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:40Z] INFO  16:40:27,830 ProgressMeter -            done    241470.0    18.0 s      75.0 s      100.0%    18.0 s       0.0 s
[2016-04-14T23:40Z] INFO  16:40:27,830 ProgressMeter - Total runtime 18.33 secs, 0.31 min, 0.01 hours
[2016-04-14T23:40Z] INFO  16:40:27,837 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 241470 total reads (0.00%)
[2016-04-14T23:40Z] INFO  16:40:27,838 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:40Z] INFO  16:40:27,838 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:40Z] INFO  16:40:27,838 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:40Z] INFO  16:40:27,849 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:40Z] INFO  16:40:27,852 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:40Z] INFO  16:40:27,991 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:40Z] INFO  16:40:27,994 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:40Z] INFO  16:40:27,994 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:40Z] INFO  16:40:27,994 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:40Z] INFO  16:40:27,998 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/20/R14-18102_kapa-NGv3-PE100-NGv3-sort-20_31379406_47242465-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/20/tx/tmpb1HZ_O/R14-18102_kapa-NGv3-PE100-NGv3-sort-20_31379406_47242465-prep-prealign-realign.intervals -l INFO -L 20:31379407-47242465 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-14T23:40Z] INFO  16:40:28,018 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:40Z] INFO  16:40:28,018 HelpFormatter - Date/Time: 2016/04/14 16:40:27
[2016-04-14T23:40Z] INFO  16:40:28,018 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:40Z] INFO  16:40:28,019 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:40Z] INFO  16:40:28,164 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:40Z] INFO  16:40:28,369 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:40Z] INFO  16:40:28,372 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:40Z] INFO  16:40:28,372 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:40Z] INFO  16:40:28,372 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:40Z] INFO  16:40:28,376 HelpFormatter - Program Args: -T PrintReads -L 22:47309230-51304566 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/22/tx/tmp0MtE_k/R14-18102_kapa-NGv3-PE100-NGv3-sort-22_47309229_51304566-prep-prealign.bam
[2016-04-14T23:40Z] INFO  16:40:28,399 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:40Z] INFO  16:40:28,402 HelpFormatter - Date/Time: 2016/04/14 16:40:28
[2016-04-14T23:40Z] INFO  16:40:28,403 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:40Z] INFO  16:40:28,403 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:40Z] INFO  16:40:28,405 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-14T23:40Z] INFO  16:40:28,414 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:40Z] INFO  16:40:28,454 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.04
[2016-04-14T23:40Z] INFO  16:40:28,623 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:40Z] INFO  16:40:28,757 IntervalUtils - Processing 15863059 bp from intervals
[2016-04-14T23:40Z] WARN  16:40:28,762 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:40Z] INFO  16:40:28,878 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:40Z] INFO  16:40:29,043 ProgressMeter -      19:8591344    700009.0   120.0 s       2.9 m       55.4%     3.6 m      96.0 s
[2016-04-14T23:40Z] INFO  16:40:29,057 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:40Z] INFO  16:40:29,058 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:40Z] INFO  16:40:29,059 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:40Z] INFO  16:40:29,060 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-14T23:40Z] INFO  16:40:29,222 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:40Z] INFO  16:40:29,225 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:40Z] INFO  16:40:29,226 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:40Z] INFO  16:40:29,226 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:40Z] INFO  16:40:29,231 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/21/R14-18102_kapa-NGv3-PE100-NGv3-sort-21_46595644_48129895-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/21/R14-18102_kapa-NGv3-PE100-NGv3-sort-21_46595644_48129895-prep-prealign-realign.intervals -L 21:46595645-48129895 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/21/tx/tmptpdD3p/R14-18102_kapa-NGv3-PE100-NGv3-sort-21_46595644_48129895-prep.bam
[2016-04-14T23:40Z] INFO  16:40:29,259 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:40Z] INFO  16:40:29,260 HelpFormatter - Date/Time: 2016/04/14 16:40:29
[2016-04-14T23:40Z] INFO  16:40:29,260 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:40Z] INFO  16:40:29,261 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:40Z] INFO  16:40:29,364 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:40Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-20_15866408_31376818-prep.bam
[2016-04-14T23:40Z] INFO  16:40:29,455 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:40Z] INFO  16:40:29,568 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:40Z] INFO  16:40:29,589 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:40Z] INFO  16:40:29,647 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-14T23:40Z] INFO  16:40:29,721 ProgressMeter -            done      6650.0     1.0 s       4.8 m      100.0%     1.0 s       0.0 s
[2016-04-14T23:40Z] INFO  16:40:29,721 ProgressMeter - Total runtime 1.92 secs, 0.03 min, 0.00 hours
[2016-04-14T23:40Z] INFO  16:40:29,725 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 6650 total reads (0.00%)
[2016-04-14T23:40Z] INFO  16:40:29,725 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:40Z] INFO  16:40:29,725 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:40Z] INFO  16:40:29,726 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:40Z] INFO  16:40:29,873 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-14T23:40Z] INFO  16:40:29,973 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:40Z] INFO  16:40:29,983 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:40Z] INFO  16:40:29,984 IntervalUtils - Processing 1534251 bp from intervals
[2016-04-14T23:40Z] WARN  16:40:29,989 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:40Z] INFO  16:40:30,025 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.04
[2016-04-14T23:40Z] INFO  16:40:30,041 IntervalUtils - Processing 3995337 bp from intervals
[2016-04-14T23:40Z] INFO  16:40:30,058 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:40Z] INFO  16:40:30,115 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:40Z] INFO  16:40:30,116 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:40Z] INFO  16:40:30,117 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:40Z] INFO  16:40:30,121 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:40Z] INFO  16:40:30,163 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:40Z] INFO  16:40:30,203 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:40Z] INFO  16:40:30,233 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:40Z] GATK pre-alignment ('X', 0, 15509380) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:40Z] INFO  16:40:30,373 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:40Z] INFO  16:40:30,374 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:40Z] INFO  16:40:30,375 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:40Z] INFO  16:40:30,375 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:40Z] INFO  16:40:30,389 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:40Z] INFO  16:40:30,432 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:40Z] INFO  16:40:30,657 ProgressMeter -            done    885930.0    54.0 s      61.0 s      100.0%    54.0 s       0.0 s
[2016-04-14T23:40Z] INFO  16:40:30,657 ProgressMeter - Total runtime 54.37 secs, 0.91 min, 0.02 hours
[2016-04-14T23:40Z] INFO  16:40:30,661 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 885930 total reads (0.00%)
[2016-04-14T23:40Z] INFO  16:40:30,662 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:40Z] INFO  16:40:30,662 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:40Z] INFO  16:40:30,662 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:40Z] INFO  16:40:31,215 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:40Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-22_0_16258303-prep.bam
[2016-04-14T23:40Z] GATK pre-alignment ('X', 15518899, 31090070) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:40Z] INFO  16:40:32,672 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:40Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-17_0_15511002-prep.bam
[2016-04-14T23:40Z] INFO  16:40:33,313 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:40Z] INFO  16:40:33,317 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:40Z] INFO  16:40:33,317 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:40Z] INFO  16:40:33,318 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:40Z] INFO  16:40:33,323 HelpFormatter - Program Args: -T PrintReads -L X:1-15509380 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/X/tx/tmpAxf5lk/R14-18102_kapa-NGv3-PE100-NGv3-sort-X_0_15509380-prep-prealign.bam
[2016-04-14T23:40Z] INFO  16:40:33,332 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:40Z] INFO  16:40:33,333 HelpFormatter - Date/Time: 2016/04/14 16:40:33
[2016-04-14T23:40Z] INFO  16:40:33,333 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:40Z] INFO  16:40:33,334 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:40Z] INFO  16:40:33,528 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:40Z] INFO  16:40:34,023 ProgressMeter -            done    294844.0    20.0 s      69.0 s      100.0%    20.0 s       0.0 s
[2016-04-14T23:40Z] INFO  16:40:34,024 ProgressMeter - Total runtime 20.50 secs, 0.34 min, 0.01 hours
[2016-04-14T23:40Z] INFO  16:40:34,027 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 294844 total reads (0.00%)
[2016-04-14T23:40Z] INFO  16:40:34,028 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:40Z] INFO  16:40:34,028 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:40Z] INFO  16:40:34,031 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:40Z] INFO  16:40:34,451 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:40Z] INFO  16:40:34,455 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:40Z] INFO  16:40:34,456 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:40Z] INFO  16:40:34,456 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:40Z] INFO  16:40:34,462 HelpFormatter - Program Args: -T PrintReads -L X:15518900-31090070 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/X/tx/tmpKvRXkc/R14-18102_kapa-NGv3-PE100-NGv3-sort-X_15518899_31090070-prep-prealign.bam
[2016-04-14T23:40Z] INFO  16:40:34,498 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:40Z] INFO  16:40:34,499 HelpFormatter - Date/Time: 2016/04/14 16:40:34
[2016-04-14T23:40Z] INFO  16:40:34,499 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:40Z] INFO  16:40:34,500 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:40Z] INFO  16:40:34,708 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:40Z] INFO  16:40:34,768 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-14T23:40Z] INFO  16:40:34,842 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:40Z] INFO  16:40:34,851 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:40Z] INFO  16:40:34,891 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.04
[2016-04-14T23:40Z] INFO  16:40:34,905 IntervalUtils - Processing 15509380 bp from intervals
[2016-04-14T23:40Z] INFO  16:40:34,989 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:40Z] INFO  16:40:35,212 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:40Z] INFO  16:40:35,213 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:40Z] INFO  16:40:35,214 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:40Z] INFO  16:40:35,215 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:40Z] INFO  16:40:35,228 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:40Z] INFO  16:40:35,426 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:40Z] GATK pre-alignment ('X', 31139949, 46696637) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:40Z] INFO  16:40:35,840 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-14T23:40Z] INFO  16:40:35,895 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:40Z] INFO  16:40:35,904 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:40Z] INFO  16:40:35,957 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-14T23:40Z] INFO  16:40:35,977 IntervalUtils - Processing 15571171 bp from intervals
[2016-04-14T23:40Z] INFO  16:40:35,980 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:40Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-20_0_15843471-prep.bam
[2016-04-14T23:40Z] INFO  16:40:36,078 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:40Z] INFO  16:40:36,380 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:40Z] INFO  16:40:36,381 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:40Z] INFO  16:40:36,382 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:40Z] INFO  16:40:36,383 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:40Z] INFO  16:40:36,399 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:40Z] INFO  16:40:36,548 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:40Z] GATK pre-alignment ('X', 46712910, 62570698) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:40Z] INFO  16:40:36,986 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@7172f77a
[2016-04-14T23:40Z] INFO  16:40:37,083 ProgressMeter -            done    460481.0    54.0 s     119.0 s      100.0%    54.0 s       0.0 s
[2016-04-14T23:40Z] INFO  16:40:37,084 ProgressMeter - Total runtime 54.84 secs, 0.91 min, 0.02 hours
[2016-04-14T23:40Z] INFO  16:40:37,084 MicroScheduler - 218 reads were filtered out during the traversal out of approximately 460699 total reads (0.05%)
[2016-04-14T23:40Z] INFO  16:40:37,084 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:40Z] INFO  16:40:37,085 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:40Z] INFO  16:40:37,085 MicroScheduler -   -> 218 reads (0.05% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:40Z] INFO  16:40:38,508 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:40Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-21_31062047_46591599-prep-prealign.bam
[2016-04-14T23:40Z] INFO  16:40:38,619 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:40Z] INFO  16:40:38,623 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:40Z] INFO  16:40:38,624 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:40Z] INFO  16:40:38,624 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:40Z] INFO  16:40:38,630 HelpFormatter - Program Args: -T PrintReads -L X:31139950-46696637 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/X/tx/tmpXAIGZa/R14-18102_kapa-NGv3-PE100-NGv3-sort-X_31139949_46696637-prep-prealign.bam
[2016-04-14T23:40Z] INFO  16:40:38,644 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:40Z] INFO  16:40:38,645 HelpFormatter - Date/Time: 2016/04/14 16:40:38
[2016-04-14T23:40Z] INFO  16:40:38,646 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:40Z] INFO  16:40:38,646 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:40Z] INFO  16:40:38,832 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:40Z] INFO  16:40:39,579 ProgressMeter -            done    108991.0     9.0 s      86.0 s       97.0%     9.0 s       0.0 s
[2016-04-14T23:40Z] INFO  16:40:39,579 ProgressMeter - Total runtime 9.46 secs, 0.16 min, 0.00 hours
[2016-04-14T23:40Z] INFO  16:40:39,583 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 108991 total reads (0.00%)
[2016-04-14T23:40Z] INFO  16:40:39,583 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:40Z] INFO  16:40:39,583 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:40Z] INFO  16:40:39,584 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:40Z] INFO  16:40:39,602 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:40Z] INFO  16:40:39,612 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:40Z] INFO  16:40:39,612 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:40Z] INFO  16:40:39,612 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:40Z] INFO  16:40:39,616 HelpFormatter - Program Args: -T PrintReads -L X:46712911-62570698 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/X/tx/tmpaySMYA/R14-18102_kapa-NGv3-PE100-NGv3-sort-X_46712910_62570698-prep-prealign.bam
[2016-04-14T23:40Z] INFO  16:40:39,625 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:40Z] INFO  16:40:39,626 HelpFormatter - Date/Time: 2016/04/14 16:40:39
[2016-04-14T23:40Z] INFO  16:40:39,626 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:40Z] INFO  16:40:39,626 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:40Z] INFO  16:40:39,830 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:40Z] INFO  16:40:39,835 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-14T23:40Z] GATK RealignerTargetCreator: R14-18102_kapa-NGv3-PE100-NGv3-sort-21_31062047_46591599-prep-prealign.bam 21:31062048-46591599
[2016-04-14T23:40Z] GATK: RealignerTargetCreator
[2016-04-14T23:40Z] INFO  16:40:39,913 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:40Z] INFO  16:40:39,928 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:40Z] INFO  16:40:39,969 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.04
[2016-04-14T23:40Z] INFO  16:40:39,984 IntervalUtils - Processing 15556688 bp from intervals
[2016-04-14T23:40Z] INFO  16:40:40,068 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:40Z] INFO  16:40:40,327 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:40Z] INFO  16:40:40,328 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:40Z] INFO  16:40:40,329 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:40Z] INFO  16:40:40,330 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:40Z] INFO  16:40:40,361 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:40Z] INFO  16:40:40,525 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:40Z] INFO  16:40:40,757 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-14T23:40Z] INFO  16:40:40,838 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:40Z] INFO  16:40:40,852 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:40Z] INFO  16:40:40,893 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:40Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-21_46595644_48129895-prep.bam
[2016-04-14T23:40Z] INFO  16:40:40,921 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-14T23:40Z] INFO  16:40:40,935 IntervalUtils - Processing 15857788 bp from intervals
[2016-04-14T23:40Z] INFO  16:40:41,013 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:40Z] INFO  16:40:41,311 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:40Z] INFO  16:40:41,313 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:40Z] INFO  16:40:41,318 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:40Z] INFO  16:40:41,320 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:40Z] GATK pre-alignment ('X', 62857907, 78427545) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:40Z] INFO  16:40:41,348 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:40Z] INFO  16:40:41,506 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:40Z] INFO  16:40:43,176 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:40Z] INFO  16:40:43,180 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:40Z] INFO  16:40:43,180 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:40Z] INFO  16:40:43,181 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:40Z] INFO  16:40:43,186 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/21/R14-18102_kapa-NGv3-PE100-NGv3-sort-21_31062047_46591599-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/21/tx/tmp6eZLX3/R14-18102_kapa-NGv3-PE100-NGv3-sort-21_31062047_46591599-prep-prealign-realign.intervals -l INFO -L 21:31062048-46591599 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-14T23:40Z] INFO  16:40:43,196 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:40Z] INFO  16:40:43,208 HelpFormatter - Date/Time: 2016/04/14 16:40:43
[2016-04-14T23:40Z] INFO  16:40:43,209 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:40Z] INFO  16:40:43,210 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:40Z] INFO  16:40:43,310 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:40Z] INFO  16:40:43,508 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-14T23:40Z] INFO  16:40:43,528 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:40Z] INFO  16:40:43,580 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-14T23:40Z] INFO  16:40:43,683 ProgressMeter -            done   1.5586184E7    24.0 s       1.0 s      100.0%    24.0 s       0.0 s
[2016-04-14T23:40Z] INFO  16:40:43,684 ProgressMeter - Total runtime 24.96 secs, 0.42 min, 0.01 hours
[2016-04-14T23:40Z] INFO  16:40:43,688 MicroScheduler - 39054 reads were filtered out during the traversal out of approximately 453959 total reads (8.60%)
[2016-04-14T23:40Z] INFO  16:40:43,689 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:40Z] INFO  16:40:43,690 MicroScheduler -   -> 1123 reads (0.25% of total) failing BadMateFilter
[2016-04-14T23:40Z] INFO  16:40:43,691 MicroScheduler -   -> 37046 reads (8.16% of total) failing DuplicateReadFilter
[2016-04-14T23:40Z] INFO  16:40:43,691 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-14T23:40Z] INFO  16:40:43,692 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:40Z] INFO  16:40:43,693 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-14T23:40Z] INFO  16:40:43,693 MicroScheduler -   -> 885 reads (0.19% of total) failing MappingQualityZeroFilter
[2016-04-14T23:40Z] INFO  16:40:43,694 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:40Z] INFO  16:40:43,695 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-14T23:40Z] INFO  16:40:43,695 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-14T23:40Z] INFO  16:40:43,934 IntervalUtils - Processing 15529552 bp from intervals
[2016-04-14T23:40Z] WARN  16:40:43,939 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:40Z] INFO  16:40:44,011 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:40Z] INFO  16:40:44,014 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:40Z] INFO  16:40:44,015 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:40Z] INFO  16:40:44,015 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:40Z] INFO  16:40:44,020 HelpFormatter - Program Args: -T PrintReads -L X:62857908-78427545 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/X/tx/tmpC9NIgv/R14-18102_kapa-NGv3-PE100-NGv3-sort-X_62857907_78427545-prep-prealign.bam
[2016-04-14T23:40Z] INFO  16:40:44,029 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:40Z] INFO  16:40:44,029 HelpFormatter - Date/Time: 2016/04/14 16:40:44
[2016-04-14T23:40Z] INFO  16:40:44,029 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:40Z] INFO  16:40:44,030 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:40Z] INFO  16:40:44,055 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:40Z] INFO  16:40:44,214 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:40Z] INFO  16:40:44,226 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:40Z] INFO  16:40:44,228 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:40Z] INFO  16:40:44,229 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:40Z] INFO  16:40:44,230 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-14T23:40Z] INFO  16:40:44,368 ProgressMeter -     22:20079629    200002.0    30.0 s       2.5 m       24.6%     2.0 m      92.0 s
[2016-04-14T23:40Z] INFO  16:40:45,177 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:40Z] GATK: realign ('20', 47244085, 62830269) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:40Z] INFO  16:40:45,257 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-14T23:40Z] INFO  16:40:45,317 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:40Z] INFO  16:40:45,326 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:40Z] INFO  16:40:45,389 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-14T23:40Z] INFO  16:40:45,415 IntervalUtils - Processing 15569638 bp from intervals
[2016-04-14T23:40Z] INFO  16:40:45,530 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:40Z] INFO  16:40:45,825 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:40Z] INFO  16:40:45,826 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:40Z] INFO  16:40:45,827 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:40Z] INFO  16:40:45,828 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:40Z] INFO  16:40:45,842 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:40Z] INFO  16:40:45,986 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:40Z] INFO  16:40:47,540 ProgressMeter -     19:44732783   1000016.0   120.0 s     120.0 s       87.8%     2.3 m      16.0 s
[2016-04-14T23:40Z] INFO  16:40:48,090 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:40Z] INFO  16:40:48,107 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:40Z] INFO  16:40:48,108 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:40Z] INFO  16:40:48,108 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:40Z] INFO  16:40:48,112 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/20/R14-18102_kapa-NGv3-PE100-NGv3-sort-20_47244085_62830269-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/20/R14-18102_kapa-NGv3-PE100-NGv3-sort-20_47244085_62830269-prep-prealign-realign.intervals -L 20:47244086-62830269 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/20/tx/tmpLvp4tx/R14-18102_kapa-NGv3-PE100-NGv3-sort-20_47244085_62830269-prep.bam
[2016-04-14T23:40Z] INFO  16:40:48,122 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:40Z] INFO  16:40:48,122 HelpFormatter - Date/Time: 2016/04/14 16:40:48
[2016-04-14T23:40Z] INFO  16:40:48,123 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:40Z] INFO  16:40:48,123 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:40Z] INFO  16:40:48,337 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:40Z] INFO  16:40:48,490 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:40Z] INFO  16:40:48,500 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:40Z] INFO  16:40:48,557 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-14T23:40Z] INFO  16:40:48,936 IntervalUtils - Processing 15586184 bp from intervals
[2016-04-14T23:40Z] WARN  16:40:48,941 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:40Z] INFO  16:40:49,024 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:40Z] INFO  16:40:49,132 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:40Z] INFO  16:40:49,133 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:40Z] INFO  16:40:49,134 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:40Z] INFO  16:40:49,135 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:40Z] INFO  16:40:49,340 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:40Z] INFO  16:40:49,558 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:40Z] INFO  16:40:50,552 ProgressMeter -     19:19756778    400008.0    30.0 s      75.0 s       27.4%   109.0 s      79.0 s
[2016-04-14T23:40Z] INFO  16:40:51,075 ProgressMeter -     19:56307504   1000019.0   120.0 s     120.0 s       77.4%     2.6 m      34.0 s
[2016-04-14T23:40Z] INFO  16:40:51,503 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@32d5a4c6
[2016-04-14T23:40Z] INFO  16:40:51,597 ProgressMeter -            done    150990.0    21.0 s       2.3 m       97.9%    21.0 s       0.0 s
[2016-04-14T23:40Z] INFO  16:40:51,598 ProgressMeter - Total runtime 21.22 secs, 0.35 min, 0.01 hours
[2016-04-14T23:40Z] INFO  16:40:51,598 MicroScheduler - 68 reads were filtered out during the traversal out of approximately 151058 total reads (0.05%)
[2016-04-14T23:40Z] INFO  16:40:51,599 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:40Z] INFO  16:40:51,599 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:40Z] INFO  16:40:51,599 MicroScheduler -   -> 68 reads (0.05% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:40Z] INFO  16:40:53,130 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:40Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-22_47309229_51304566-prep-prealign.bam
[2016-04-14T23:40Z] GATK RealignerTargetCreator: R14-18102_kapa-NGv3-PE100-NGv3-sort-22_47309229_51304566-prep-prealign.bam 22:47309230-51304566
[2016-04-14T23:40Z] GATK: RealignerTargetCreator
[2016-04-14T23:40Z] INFO  16:40:54,198 ProgressMeter -            done   1.5863059E7    25.0 s       1.0 s      100.0%    25.0 s       0.0 s
[2016-04-14T23:40Z] INFO  16:40:54,199 ProgressMeter - Total runtime 25.14 secs, 0.42 min, 0.01 hours
[2016-04-14T23:40Z] INFO  16:40:54,203 MicroScheduler - 46454 reads were filtered out during the traversal out of approximately 558839 total reads (8.31%)
[2016-04-14T23:40Z] INFO  16:40:54,205 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:40Z] INFO  16:40:54,205 MicroScheduler -   -> 1125 reads (0.20% of total) failing BadMateFilter
[2016-04-14T23:40Z] INFO  16:40:54,206 MicroScheduler -   -> 44550 reads (7.97% of total) failing DuplicateReadFilter
[2016-04-14T23:40Z] INFO  16:40:54,207 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-14T23:40Z] INFO  16:40:54,207 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:40Z] INFO  16:40:54,208 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-14T23:40Z] INFO  16:40:54,209 MicroScheduler -   -> 779 reads (0.14% of total) failing MappingQualityZeroFilter
[2016-04-14T23:40Z] INFO  16:40:54,209 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:40Z] INFO  16:40:54,210 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-14T23:40Z] INFO  16:40:54,210 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-14T23:40Z] INFO  16:40:55,565 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:40Z] GATK: realign ('20', 31379406, 47242465) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:40Z] INFO  16:40:56,206 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:40Z] INFO  16:40:56,209 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:40Z] INFO  16:40:56,210 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:40Z] INFO  16:40:56,210 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:40Z] INFO  16:40:56,215 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/22/R14-18102_kapa-NGv3-PE100-NGv3-sort-22_47309229_51304566-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/22/tx/tmplbqQqT/R14-18102_kapa-NGv3-PE100-NGv3-sort-22_47309229_51304566-prep-prealign-realign.intervals -l INFO -L 22:47309230-51304566 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-14T23:40Z] INFO  16:40:56,240 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:40Z] INFO  16:40:56,251 HelpFormatter - Date/Time: 2016/04/14 16:40:56
[2016-04-14T23:40Z] INFO  16:40:56,252 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:40Z] INFO  16:40:56,252 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:40Z] INFO  16:40:56,388 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:40Z] INFO  16:40:56,620 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-14T23:40Z] INFO  16:40:56,642 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:40Z] INFO  16:40:56,712 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-14T23:40Z] INFO  16:40:56,931 ProgressMeter -     22:38202187    200004.0    30.0 s       2.5 m       41.3%    72.0 s      42.0 s
[2016-04-14T23:40Z] INFO  16:40:57,050 ProgressMeter -            done    558759.0    36.0 s      65.0 s      100.0%    36.0 s       0.0 s
[2016-04-14T23:40Z] INFO  16:40:57,050 ProgressMeter - Total runtime 36.50 secs, 0.61 min, 0.01 hours
[2016-04-14T23:40Z] INFO  16:40:57,054 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 558759 total reads (0.00%)
[2016-04-14T23:40Z] INFO  16:40:57,054 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:40Z] INFO  16:40:57,054 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:40Z] INFO  16:40:57,054 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:40Z] INFO  16:40:57,067 IntervalUtils - Processing 3995337 bp from intervals
[2016-04-14T23:40Z] WARN  16:40:57,073 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:40Z] INFO  16:40:57,145 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:40Z] INFO  16:40:57,208 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:40Z] INFO  16:40:57,210 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:40Z] INFO  16:40:57,211 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:40Z] INFO  16:40:57,211 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-14T23:40Z] INFO  16:40:58,103 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:40Z] INFO  16:40:58,107 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:40Z] INFO  16:40:58,107 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:40Z] INFO  16:40:58,108 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:40Z] INFO  16:40:58,114 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/20/R14-18102_kapa-NGv3-PE100-NGv3-sort-20_31379406_47242465-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/20/R14-18102_kapa-NGv3-PE100-NGv3-sort-20_31379406_47242465-prep-prealign-realign.intervals -L 20:31379407-47242465 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/20/tx/tmpHXrx5u/R14-18102_kapa-NGv3-PE100-NGv3-sort-20_31379406_47242465-prep.bam
[2016-04-14T23:40Z] INFO  16:40:58,125 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:40Z] INFO  16:40:58,136 HelpFormatter - Date/Time: 2016/04/14 16:40:58
[2016-04-14T23:40Z] INFO  16:40:58,137 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:40Z] INFO  16:40:58,137 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:40Z] INFO  16:40:58,395 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:40Z] INFO  16:40:58,461 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:40Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-19_15510112_31025906-prep.bam
[2016-04-14T23:40Z] INFO  16:40:58,564 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:40Z] INFO  16:40:58,586 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:40Z] INFO  16:40:58,692 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.10
[2016-04-14T23:40Z] INFO  16:40:59,044 ProgressMeter -     19:10664908   1000014.0     2.5 m       2.5 m       68.8%     3.6 m      68.0 s
[2016-04-14T23:40Z] INFO  16:40:59,142 IntervalUtils - Processing 15863059 bp from intervals
[2016-04-14T23:40Z] WARN  16:40:59,148 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:40Z] INFO  16:40:59,223 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:40Z] INFO  16:40:59,346 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:40Z] INFO  16:40:59,347 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:40Z] INFO  16:40:59,347 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:40Z] INFO  16:40:59,347 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:40Z] INFO  16:40:59,530 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:40Z] INFO  16:40:59,679 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:41Z] GATK pre-alignment ('X', 78616585, 95940189) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:41Z] INFO  16:41:00,555 ProgressMeter -     17:46050986   1100020.0    66.0 s      60.0 s       96.4%    68.0 s       2.0 s
[2016-04-14T23:41Z] INFO  16:41:01,200 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@7172f77a
[2016-04-14T23:41Z] INFO  16:41:01,282 ProgressMeter -            done    151563.0    20.0 s       2.3 m      100.0%    20.0 s       0.0 s
[2016-04-14T23:41Z] INFO  16:41:01,283 ProgressMeter - Total runtime 20.95 secs, 0.35 min, 0.01 hours
[2016-04-14T23:41Z] INFO  16:41:01,283 MicroScheduler - 127 reads were filtered out during the traversal out of approximately 151690 total reads (0.08%)
[2016-04-14T23:41Z] INFO  16:41:01,283 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:41Z] INFO  16:41:01,284 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:41Z] INFO  16:41:01,284 MicroScheduler -   -> 127 reads (0.08% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:41Z] INFO  16:41:01,576 ProgressMeter -            done   1132563.0    67.0 s      59.0 s      100.0%    67.0 s       0.0 s
[2016-04-14T23:41Z] INFO  16:41:01,577 ProgressMeter - Total runtime 67.17 secs, 1.12 min, 0.02 hours
[2016-04-14T23:41Z] INFO  16:41:01,581 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 1132563 total reads (0.00%)
[2016-04-14T23:41Z] INFO  16:41:01,582 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:41Z] INFO  16:41:01,582 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:41Z] INFO  16:41:01,582 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:41Z] INFO  16:41:02,132 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@32d5a4c6
[2016-04-14T23:41Z] INFO  16:41:02,179 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@41fd9d8e
[2016-04-14T23:41Z] INFO  16:41:02,211 ProgressMeter -            done    193111.0    25.0 s       2.2 m      100.0%    25.0 s       0.0 s
[2016-04-14T23:41Z] INFO  16:41:02,212 ProgressMeter - Total runtime 25.83 secs, 0.43 min, 0.01 hours
[2016-04-14T23:41Z] INFO  16:41:02,213 MicroScheduler - 142 reads were filtered out during the traversal out of approximately 193253 total reads (0.07%)
[2016-04-14T23:41Z] INFO  16:41:02,213 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:41Z] INFO  16:41:02,214 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:41Z] INFO  16:41:02,215 MicroScheduler -   -> 142 reads (0.07% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:41Z] INFO  16:41:02,243 ProgressMeter -            done    207102.0    27.0 s       2.2 m      100.0%    27.0 s       0.0 s
[2016-04-14T23:41Z] INFO  16:41:02,244 ProgressMeter - Total runtime 27.03 secs, 0.45 min, 0.01 hours
[2016-04-14T23:41Z] INFO  16:41:02,244 MicroScheduler - 176 reads were filtered out during the traversal out of approximately 207278 total reads (0.08%)
[2016-04-14T23:41Z] INFO  16:41:02,244 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:41Z] INFO  16:41:02,245 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:41Z] INFO  16:41:02,245 MicroScheduler -   -> 176 reads (0.08% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:41Z] INFO  16:41:02,982 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:41Z] INFO  16:41:03,019 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:41Z] INFO  16:41:03,023 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:41Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-X_31139949_46696637-prep-prealign.bam
[2016-04-14T23:41Z] INFO  16:41:03,024 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:41Z] INFO  16:41:03,024 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:41Z] INFO  16:41:03,029 HelpFormatter - Program Args: -T PrintReads -L X:78616586-95940189 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/X/tx/tmpY8MCQK/R14-18102_kapa-NGv3-PE100-NGv3-sort-X_78616585_95940189-prep-prealign.bam
[2016-04-14T23:41Z] INFO  16:41:03,050 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:41Z] INFO  16:41:03,051 HelpFormatter - Date/Time: 2016/04/14 16:41:03
[2016-04-14T23:41Z] INFO  16:41:03,052 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:41Z] INFO  16:41:03,052 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:41Z] INFO  16:41:03,225 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:41Z] INFO  16:41:03,308 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:41Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-17_31048040_46607237-prep.bam
[2016-04-14T23:41Z] INFO  16:41:03,521 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:41Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-X_15518899_31090070-prep-prealign.bam
[2016-04-14T23:41Z] INFO  16:41:03,574 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:41Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-X_0_15509380-prep-prealign.bam
[2016-04-14T23:41Z] GATK RealignerTargetCreator: R14-18102_kapa-NGv3-PE100-NGv3-sort-X_31139949_46696637-prep-prealign.bam X:31139950-46696637
[2016-04-14T23:41Z] GATK: RealignerTargetCreator
[2016-04-14T23:41Z] GATK RealignerTargetCreator: R14-18102_kapa-NGv3-PE100-NGv3-sort-X_15518899_31090070-prep-prealign.bam X:15518900-31090070
[2016-04-14T23:41Z] GATK: RealignerTargetCreator
[2016-04-14T23:41Z] INFO  16:41:04,382 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-14T23:41Z] INFO  16:41:04,397 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@41fd9d8e
[2016-04-14T23:41Z] GATK RealignerTargetCreator: R14-18102_kapa-NGv3-PE100-NGv3-sort-X_0_15509380-prep-prealign.bam X:1-15509380
[2016-04-14T23:41Z] GATK: RealignerTargetCreator
[2016-04-14T23:41Z] INFO  16:41:04,449 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:41Z] INFO  16:41:04,460 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:41Z] INFO  16:41:04,517 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-14T23:41Z] INFO  16:41:04,535 IntervalUtils - Processing 17323604 bp from intervals
[2016-04-14T23:41Z] INFO  16:41:04,542 ProgressMeter -            done   1179943.0     2.3 m     116.0 s      100.0%     2.3 m       0.0 s
[2016-04-14T23:41Z] INFO  16:41:04,543 ProgressMeter - Total runtime 138.00 secs, 2.30 min, 0.04 hours
[2016-04-14T23:41Z] INFO  16:41:04,544 MicroScheduler - 505 reads were filtered out during the traversal out of approximately 1180448 total reads (0.04%)
[2016-04-14T23:41Z] INFO  16:41:04,544 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:41Z] INFO  16:41:04,545 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:41Z] INFO  16:41:04,545 MicroScheduler -   -> 505 reads (0.04% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:41Z] INFO  16:41:04,659 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:41Z] INFO  16:41:04,955 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:41Z] INFO  16:41:04,956 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:41Z] INFO  16:41:04,957 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:41Z] INFO  16:41:04,958 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:41Z] INFO  16:41:05,001 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:41Z] INFO  16:41:05,178 ProgressMeter -            done   1.5529552E7    20.0 s       1.0 s      100.0%    20.0 s       0.0 s
[2016-04-14T23:41Z] INFO  16:41:05,178 ProgressMeter - Total runtime 20.95 secs, 0.35 min, 0.01 hours
[2016-04-14T23:41Z] INFO  16:41:05,196 MicroScheduler - 42443 reads were filtered out during the traversal out of approximately 462677 total reads (9.17%)
[2016-04-14T23:41Z] INFO  16:41:05,197 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:41Z] INFO  16:41:05,198 MicroScheduler -   -> 1019 reads (0.22% of total) failing BadMateFilter
[2016-04-14T23:41Z] INFO  16:41:05,198 MicroScheduler -   -> 37861 reads (8.18% of total) failing DuplicateReadFilter
[2016-04-14T23:41Z] INFO  16:41:05,199 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-14T23:41Z] INFO  16:41:05,200 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:41Z] INFO  16:41:05,200 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-14T23:41Z] INFO  16:41:05,201 MicroScheduler -   -> 3563 reads (0.77% of total) failing MappingQualityZeroFilter
[2016-04-14T23:41Z] INFO  16:41:05,202 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:41Z] INFO  16:41:05,202 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-14T23:41Z] INFO  16:41:05,203 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-14T23:41Z] INFO  16:41:05,212 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:41Z] INFO  16:41:06,162 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:41Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-19_31038849_46627578-prep-prealign.bam
[2016-04-14T23:41Z] INFO  16:41:06,710 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:41Z] INFO  16:41:06,714 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:41Z] INFO  16:41:06,714 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:41Z] INFO  16:41:06,715 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:41Z] INFO  16:41:06,719 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/X/R14-18102_kapa-NGv3-PE100-NGv3-sort-X_31139949_46696637-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/X/tx/tmp5inP5_/R14-18102_kapa-NGv3-PE100-NGv3-sort-X_31139949_46696637-prep-prealign-realign.intervals -l INFO -L X:31139950-46696637 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-14T23:41Z] INFO  16:41:06,744 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:41Z] INFO  16:41:06,745 HelpFormatter - Date/Time: 2016/04/14 16:41:06
[2016-04-14T23:41Z] INFO  16:41:06,746 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:41Z] INFO  16:41:06,752 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:41Z] INFO  16:41:06,880 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:41Z] INFO  16:41:06,895 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:41Z] INFO  16:41:06,898 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:41Z] INFO  16:41:06,899 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:41Z] INFO  16:41:06,899 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:41Z] INFO  16:41:06,904 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/X/R14-18102_kapa-NGv3-PE100-NGv3-sort-X_15518899_31090070-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/X/tx/tmpB61i2T/R14-18102_kapa-NGv3-PE100-NGv3-sort-X_15518899_31090070-prep-prealign-realign.intervals -l INFO -L X:15518900-31090070 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-14T23:41Z] INFO  16:41:06,914 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:41Z] INFO  16:41:06,915 HelpFormatter - Date/Time: 2016/04/14 16:41:06
[2016-04-14T23:41Z] INFO  16:41:06,915 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:41Z] INFO  16:41:06,916 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:41Z] INFO  16:41:06,945 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:41Z] GATK: realign ('21', 31062047, 46591599) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:41Z] INFO  16:41:07,009 ProgressMeter -            done   3995337.0     9.0 s       2.0 s      100.0%     9.0 s       0.0 s
[2016-04-14T23:41Z] INFO  16:41:07,009 ProgressMeter - Total runtime 9.80 secs, 0.16 min, 0.00 hours
[2016-04-14T23:41Z] INFO  16:41:07,013 MicroScheduler - 14043 reads were filtered out during the traversal out of approximately 152459 total reads (9.21%)
[2016-04-14T23:41Z] INFO  16:41:07,014 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:41Z] INFO  16:41:07,014 MicroScheduler -   -> 371 reads (0.24% of total) failing BadMateFilter
[2016-04-14T23:41Z] INFO  16:41:07,014 MicroScheduler -   -> 12319 reads (8.08% of total) failing DuplicateReadFilter
[2016-04-14T23:41Z] INFO  16:41:07,015 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-14T23:41Z] INFO  16:41:07,015 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:41Z] INFO  16:41:07,015 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-14T23:41Z] INFO  16:41:07,015 MicroScheduler -   -> 1353 reads (0.89% of total) failing MappingQualityZeroFilter
[2016-04-14T23:41Z] INFO  16:41:07,015 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:41Z] INFO  16:41:07,016 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-14T23:41Z] INFO  16:41:07,016 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-14T23:41Z] INFO  16:41:07,037 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:41Z] INFO  16:41:07,177 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-14T23:41Z] INFO  16:41:07,186 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:41Z] INFO  16:41:07,250 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-14T23:41Z] INFO  16:41:07,310 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-14T23:41Z] INFO  16:41:07,320 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:41Z] GATK pre-alignment ('X', 95990756, 111698889) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:41Z] INFO  16:41:07,437 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.12
[2016-04-14T23:41Z] INFO  16:41:07,528 IntervalUtils - Processing 15556688 bp from intervals
[2016-04-14T23:41Z] WARN  16:41:07,534 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:41Z] INFO  16:41:07,636 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:41Z] INFO  16:41:07,640 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:41Z] INFO  16:41:07,644 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:41Z] INFO  16:41:07,644 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:41Z] INFO  16:41:07,645 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:41Z] INFO  16:41:07,650 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/X/R14-18102_kapa-NGv3-PE100-NGv3-sort-X_0_15509380-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/X/tx/tmpUkti0L/R14-18102_kapa-NGv3-PE100-NGv3-sort-X_0_15509380-prep-prealign-realign.intervals -l INFO -L X:1-15509380 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-14T23:41Z] INFO  16:41:07,663 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:41Z] INFO  16:41:07,674 HelpFormatter - Date/Time: 2016/04/14 16:41:07
[2016-04-14T23:41Z] INFO  16:41:07,675 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:41Z] INFO  16:41:07,676 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:41Z] INFO  16:41:07,785 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:41Z] INFO  16:41:07,792 IntervalUtils - Processing 15571171 bp from intervals
[2016-04-14T23:41Z] WARN  16:41:07,797 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:41Z] INFO  16:41:07,836 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:41Z] INFO  16:41:07,837 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:41Z] INFO  16:41:07,838 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:41Z] INFO  16:41:07,839 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-14T23:41Z] INFO  16:41:07,945 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:41Z] INFO  16:41:08,037 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-14T23:41Z] INFO  16:41:08,046 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:41Z] INFO  16:41:08,122 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-14T23:41Z] INFO  16:41:08,177 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:41Z] INFO  16:41:08,178 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:41Z] INFO  16:41:08,179 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:41Z] INFO  16:41:08,180 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-14T23:41Z] INFO  16:41:08,420 IntervalUtils - Processing 15509380 bp from intervals
[2016-04-14T23:41Z] WARN  16:41:08,432 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:41Z] INFO  16:41:08,554 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:41Z] INFO  16:41:08,609 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:41Z] GATK: realign ('22', 47309229, 51304566) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:41Z] INFO  16:41:08,799 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:41Z] INFO  16:41:08,800 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:41Z] INFO  16:41:08,801 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:41Z] INFO  16:41:08,802 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-14T23:41Z] INFO  16:41:09,887 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:41Z] INFO  16:41:09,890 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:41Z] INFO  16:41:09,891 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:41Z] INFO  16:41:09,892 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:41Z] INFO  16:41:09,896 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/21/R14-18102_kapa-NGv3-PE100-NGv3-sort-21_31062047_46591599-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/21/R14-18102_kapa-NGv3-PE100-NGv3-sort-21_31062047_46591599-prep-prealign-realign.intervals -L 21:31062048-46591599 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/21/tx/tmpKfmanZ/R14-18102_kapa-NGv3-PE100-NGv3-sort-21_31062047_46591599-prep.bam
[2016-04-14T23:41Z] INFO  16:41:09,907 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:41Z] INFO  16:41:09,908 HelpFormatter - Date/Time: 2016/04/14 16:41:09
[2016-04-14T23:41Z] INFO  16:41:09,909 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:41Z] INFO  16:41:09,909 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:41Z] INFO  16:41:10,112 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:41Z] GATK RealignerTargetCreator: R14-18102_kapa-NGv3-PE100-NGv3-sort-19_31038849_46627578-prep-prealign.bam 19:31038850-46627578
[2016-04-14T23:41Z] GATK: RealignerTargetCreator
[2016-04-14T23:41Z] INFO  16:41:10,301 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:41Z] INFO  16:41:10,324 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:41Z] INFO  16:41:10,401 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-14T23:41Z] INFO  16:41:10,430 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:41Z] INFO  16:41:10,433 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:41Z] INFO  16:41:10,434 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:41Z] INFO  16:41:10,435 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:41Z] INFO  16:41:10,440 HelpFormatter - Program Args: -T PrintReads -L X:95990757-111698889 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/X/tx/tmpY0tijL/R14-18102_kapa-NGv3-PE100-NGv3-sort-X_95990756_111698889-prep-prealign.bam
[2016-04-14T23:41Z] INFO  16:41:10,450 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:41Z] INFO  16:41:10,455 HelpFormatter - Date/Time: 2016/04/14 16:41:10
[2016-04-14T23:41Z] INFO  16:41:10,456 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:41Z] INFO  16:41:10,457 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:41Z] INFO  16:41:10,678 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:41Z] INFO  16:41:10,863 IntervalUtils - Processing 15529552 bp from intervals
[2016-04-14T23:41Z] WARN  16:41:10,868 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:41Z] INFO  16:41:10,947 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:41Z] INFO  16:41:11,060 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:41Z] INFO  16:41:11,062 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:41Z] INFO  16:41:11,084 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:41Z] INFO  16:41:11,085 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:41Z] INFO  16:41:11,302 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:41Z] INFO  16:41:11,336 ProgressMeter -      X:49040452    100001.0    30.0 s       5.0 m       14.7%     3.4 m       2.9 m
[2016-04-14T23:41Z] INFO  16:41:11,570 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:41Z] INFO  16:41:11,630 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:41Z] INFO  16:41:11,633 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:41Z] INFO  16:41:11,634 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:41Z] INFO  16:41:11,635 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:41Z] INFO  16:41:11,640 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/22/R14-18102_kapa-NGv3-PE100-NGv3-sort-22_47309229_51304566-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/22/R14-18102_kapa-NGv3-PE100-NGv3-sort-22_47309229_51304566-prep-prealign-realign.intervals -L 22:47309230-51304566 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/22/tx/tmpCWTQfE/R14-18102_kapa-NGv3-PE100-NGv3-sort-22_47309229_51304566-prep.bam
[2016-04-14T23:41Z] INFO  16:41:11,657 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:41Z] INFO  16:41:11,658 HelpFormatter - Date/Time: 2016/04/14 16:41:11
[2016-04-14T23:41Z] INFO  16:41:11,659 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:41Z] INFO  16:41:11,659 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:41Z] INFO  16:41:11,946 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-14T23:41Z] INFO  16:41:11,962 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:41Z] INFO  16:41:12,046 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:41Z] INFO  16:41:12,055 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:41Z] INFO  16:41:12,097 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:41Z] INFO  16:41:12,108 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-14T23:41Z] INFO  16:41:12,113 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:41Z] INFO  16:41:12,137 IntervalUtils - Processing 15708133 bp from intervals
[2016-04-14T23:41Z] INFO  16:41:12,172 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-14T23:41Z] INFO  16:41:12,223 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:41Z] INFO  16:41:12,474 IntervalUtils - Processing 3995337 bp from intervals
[2016-04-14T23:41Z] WARN  16:41:12,479 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:41Z] INFO  16:41:12,544 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:41Z] INFO  16:41:12,594 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:41Z] INFO  16:41:12,597 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:41Z] INFO  16:41:12,598 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:41Z] INFO  16:41:12,599 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:41Z] INFO  16:41:12,612 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:41Z] INFO  16:41:12,625 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:41Z] INFO  16:41:12,626 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:41Z] INFO  16:41:12,626 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:41Z] INFO  16:41:12,627 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:41Z] INFO  16:41:12,745 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:41Z] INFO  16:41:12,764 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:41Z] INFO  16:41:12,788 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:41Z] INFO  16:41:13,334 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:41Z] INFO  16:41:13,337 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:41Z] INFO  16:41:13,338 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:41Z] INFO  16:41:13,339 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:41Z] INFO  16:41:13,343 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/19/R14-18102_kapa-NGv3-PE100-NGv3-sort-19_31038849_46627578-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/19/tx/tmpmxWEpL/R14-18102_kapa-NGv3-PE100-NGv3-sort-19_31038849_46627578-prep-prealign-realign.intervals -l INFO -L 19:31038850-46627578 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-14T23:41Z] INFO  16:41:13,359 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:41Z] INFO  16:41:13,360 HelpFormatter - Date/Time: 2016/04/14 16:41:13
[2016-04-14T23:41Z] INFO  16:41:13,361 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:41Z] INFO  16:41:13,362 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:41Z] INFO  16:41:13,510 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:41Z] INFO  16:41:13,727 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-14T23:41Z] INFO  16:41:13,737 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:41Z] INFO  16:41:13,799 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-14T23:41Z] INFO  16:41:14,147 IntervalUtils - Processing 15588729 bp from intervals
[2016-04-14T23:41Z] WARN  16:41:14,152 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:41Z] INFO  16:41:14,233 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:41Z] INFO  16:41:14,369 ProgressMeter -     22:24573513    400004.0    60.0 s       2.5 m       53.5%   112.0 s      52.0 s
[2016-04-14T23:41Z] INFO  16:41:14,464 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:41Z] INFO  16:41:14,468 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:41Z] INFO  16:41:14,469 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:41Z] INFO  16:41:14,470 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-14T23:41Z] INFO  16:41:15,880 ProgressMeter -      X:70757988    100001.0    30.0 s       5.0 m       50.7%    59.0 s      29.0 s
[2016-04-14T23:41Z] INFO  16:41:16,476 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@7172f77a
[2016-04-14T23:41Z] INFO  16:41:16,555 ProgressMeter -            done     66712.0    11.0 s       2.9 m      100.0%    11.0 s       0.0 s
[2016-04-14T23:41Z] INFO  16:41:16,556 ProgressMeter - Total runtime 11.60 secs, 0.19 min, 0.00 hours
[2016-04-14T23:41Z] INFO  16:41:16,556 MicroScheduler - 98 reads were filtered out during the traversal out of approximately 66810 total reads (0.15%)
[2016-04-14T23:41Z] INFO  16:41:16,557 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:41Z] INFO  16:41:16,557 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:41Z] INFO  16:41:16,557 MicroScheduler -   -> 98 reads (0.15% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:41Z] INFO  16:41:17,835 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:41Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-X_78616585_95940189-prep-prealign.bam
[2016-04-14T23:41Z] GATK RealignerTargetCreator: R14-18102_kapa-NGv3-PE100-NGv3-sort-X_78616585_95940189-prep-prealign.bam X:78616586-95940189
[2016-04-14T23:41Z] GATK: RealignerTargetCreator
[2016-04-14T23:41Z] INFO  16:41:19,716 ProgressMeter -            done    451351.0    30.0 s      67.0 s      100.0%    30.0 s       0.0 s
[2016-04-14T23:41Z] INFO  16:41:19,717 ProgressMeter - Total runtime 30.58 secs, 0.51 min, 0.01 hours
[2016-04-14T23:41Z] INFO  16:41:19,721 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 451351 total reads (0.00%)
[2016-04-14T23:41Z] INFO  16:41:19,721 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:41Z] INFO  16:41:19,722 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:41Z] INFO  16:41:19,722 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:41Z] INFO  16:41:20,894 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:41Z] INFO  16:41:20,898 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:41Z] INFO  16:41:20,898 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:41Z] INFO  16:41:20,899 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:41Z] INFO  16:41:20,904 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/X/R14-18102_kapa-NGv3-PE100-NGv3-sort-X_78616585_95940189-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/X/tx/tmpSaN5lZ/R14-18102_kapa-NGv3-PE100-NGv3-sort-X_78616585_95940189-prep-prealign-realign.intervals -l INFO -L X:78616586-95940189 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-14T23:41Z] INFO  16:41:20,940 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:41Z] INFO  16:41:20,941 HelpFormatter - Date/Time: 2016/04/14 16:41:20
[2016-04-14T23:41Z] INFO  16:41:20,941 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:41Z] INFO  16:41:20,942 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:41Z] INFO  16:41:21,037 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@32d5a4c6
[2016-04-14T23:41Z] INFO  16:41:21,076 ProgressMeter -     19:59084022   1300026.0     2.5 m     115.0 s       99.6%     2.5 m       0.0 s
[2016-04-14T23:41Z] INFO  16:41:21,099 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:41Z] INFO  16:41:21,169 ProgressMeter -            done   1302696.0     2.5 m     115.0 s       99.6%     2.5 m       0.0 s
[2016-04-14T23:41Z] INFO  16:41:21,180 ProgressMeter - Total runtime 150.49 secs, 2.51 min, 0.04 hours
[2016-04-14T23:41Z] INFO  16:41:21,189 MicroScheduler - 445 reads were filtered out during the traversal out of approximately 1303141 total reads (0.03%)
[2016-04-14T23:41Z] INFO  16:41:21,190 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:41Z] INFO  16:41:21,191 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:41Z] INFO  16:41:21,191 MicroScheduler -   -> 445 reads (0.03% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:41Z] INFO  16:41:21,314 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-14T23:41Z] INFO  16:41:21,326 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:41Z] INFO  16:41:21,380 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-14T23:41Z] INFO  16:41:21,503 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:41Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-20_47244085_62830269-prep.bam
[2016-04-14T23:41Z] INFO  16:41:21,757 IntervalUtils - Processing 17323604 bp from intervals
[2016-04-14T23:41Z] WARN  16:41:21,764 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:41Z] INFO  16:41:21,849 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:41Z] INFO  16:41:22,055 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:41Z] INFO  16:41:22,056 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:41Z] INFO  16:41:22,057 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:41Z] INFO  16:41:22,058 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-14T23:41Z] INFO  16:41:22,846 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:41Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-19_46627881_59128983-prep-prealign.bam
[2016-04-14T23:41Z] GATK pre-alignment ('X', 111874647, 128581278) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:41Z] INFO  16:41:24,182 ProgressMeter -            done   1.5556688E7    16.0 s       1.0 s      100.0%    16.0 s       0.0 s
[2016-04-14T23:41Z] INFO  16:41:24,182 ProgressMeter - Total runtime 16.34 secs, 0.27 min, 0.00 hours
[2016-04-14T23:41Z] INFO  16:41:24,186 MicroScheduler - 13465 reads were filtered out during the traversal out of approximately 152327 total reads (8.84%)
[2016-04-14T23:41Z] INFO  16:41:24,188 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:41Z] INFO  16:41:24,188 MicroScheduler -   -> 564 reads (0.37% of total) failing BadMateFilter
[2016-04-14T23:41Z] INFO  16:41:24,189 MicroScheduler -   -> 12058 reads (7.92% of total) failing DuplicateReadFilter
[2016-04-14T23:41Z] INFO  16:41:24,190 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-14T23:41Z] INFO  16:41:24,191 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:41Z] INFO  16:41:24,192 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-14T23:41Z] INFO  16:41:24,192 MicroScheduler -   -> 843 reads (0.55% of total) failing MappingQualityZeroFilter
[2016-04-14T23:41Z] INFO  16:41:24,193 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:41Z] INFO  16:41:24,194 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-14T23:41Z] INFO  16:41:24,195 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-14T23:41Z] INFO  16:41:24,568 ProgressMeter -            done    150990.0    11.0 s      79.0 s       97.9%    11.0 s       0.0 s
[2016-04-14T23:41Z] INFO  16:41:24,569 ProgressMeter - Total runtime 11.94 secs, 0.20 min, 0.00 hours
[2016-04-14T23:41Z] INFO  16:41:24,573 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 150990 total reads (0.00%)
[2016-04-14T23:41Z] INFO  16:41:24,574 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:41Z] INFO  16:41:24,575 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:41Z] INFO  16:41:24,576 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:41Z] INFO  16:41:25,430 ProgressMeter -            done   1.5571171E7    17.0 s       1.0 s      100.0%    17.0 s       0.0 s
[2016-04-14T23:41Z] INFO  16:41:25,431 ProgressMeter - Total runtime 17.25 secs, 0.29 min, 0.00 hours
[2016-04-14T23:41Z] INFO  16:41:25,436 MicroScheduler - 17784 reads were filtered out during the traversal out of approximately 194387 total reads (9.15%)
[2016-04-14T23:41Z] INFO  16:41:25,437 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:41Z] INFO  16:41:25,438 MicroScheduler -   -> 564 reads (0.29% of total) failing BadMateFilter
[2016-04-14T23:41Z] INFO  16:41:25,438 MicroScheduler -   -> 15399 reads (7.92% of total) failing DuplicateReadFilter
[2016-04-14T23:41Z] INFO  16:41:25,439 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-14T23:41Z] INFO  16:41:25,440 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:41Z] INFO  16:41:25,441 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-14T23:41Z] INFO  16:41:25,441 MicroScheduler -   -> 1821 reads (0.94% of total) failing MappingQualityZeroFilter
[2016-04-14T23:41Z] INFO  16:41:25,442 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:41Z] INFO  16:41:25,443 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-14T23:41Z] INFO  16:41:25,443 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-14T23:41Z] INFO  16:41:25,683 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:41Z] GATK: realign ('X', 31139949, 46696637) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:41Z] INFO  16:41:26,090 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:41Z] INFO  16:41:26,104 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:41Z] INFO  16:41:26,105 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:41Z] INFO  16:41:26,106 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:41Z] INFO  16:41:26,112 HelpFormatter - Program Args: -T PrintReads -L X:111874648-128581278 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/X/tx/tmppKZvjH/R14-18102_kapa-NGv3-PE100-NGv3-sort-X_111874647_128581278-prep-prealign.bam
[2016-04-14T23:41Z] INFO  16:41:26,131 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:41Z] INFO  16:41:26,131 HelpFormatter - Date/Time: 2016/04/14 16:41:26
[2016-04-14T23:41Z] INFO  16:41:26,132 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:41Z] INFO  16:41:26,132 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:41Z] INFO  16:41:26,307 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:41Z] INFO  16:41:26,353 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:41Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-22_47309229_51304566-prep.bam
[2016-04-14T23:41Z] INFO  16:41:26,904 ProgressMeter -            done   1.550938E7    18.0 s       1.0 s      100.0%    18.0 s       0.0 s
[2016-04-14T23:41Z] INFO  16:41:26,904 ProgressMeter - Total runtime 18.10 secs, 0.30 min, 0.01 hours
[2016-04-14T23:41Z] INFO  16:41:26,907 MicroScheduler - 25586 reads were filtered out during the traversal out of approximately 208673 total reads (12.26%)
[2016-04-14T23:41Z] INFO  16:41:26,908 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:41Z] INFO  16:41:26,909 MicroScheduler -   -> 586 reads (0.28% of total) failing BadMateFilter
[2016-04-14T23:41Z] INFO  16:41:26,910 MicroScheduler -   -> 16326 reads (7.82% of total) failing DuplicateReadFilter
[2016-04-14T23:41Z] INFO  16:41:26,910 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-14T23:41Z] INFO  16:41:26,911 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:41Z] INFO  16:41:26,912 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-14T23:41Z] INFO  16:41:26,912 MicroScheduler -   -> 8674 reads (4.16% of total) failing MappingQualityZeroFilter
[2016-04-14T23:41Z] INFO  16:41:26,913 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:41Z] INFO  16:41:26,913 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-14T23:41Z] INFO  16:41:26,914 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-14T23:41Z] GATK pre-alignment ('X', 128582278, 144329181) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:41Z] INFO  16:41:27,316 ProgressMeter -     22:42606740    400006.0    60.0 s       2.5 m       69.7%    86.0 s      26.0 s
[2016-04-14T23:41Z] INFO  16:41:27,339 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-14T23:41Z] GATK RealignerTargetCreator: R14-18102_kapa-NGv3-PE100-NGv3-sort-19_46627881_59128983-prep-prealign.bam 19:46627882-59128983
[2016-04-14T23:41Z] GATK: RealignerTargetCreator
[2016-04-14T23:41Z] INFO  16:41:27,411 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:41Z] INFO  16:41:27,421 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:41Z] INFO  16:41:27,469 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-14T23:41Z] INFO  16:41:27,483 IntervalUtils - Processing 16706631 bp from intervals
[2016-04-14T23:41Z] INFO  16:41:27,559 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:41Z] INFO  16:41:27,809 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:41Z] GATK: realign ('X', 15518899, 31090070) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:41Z] INFO  16:41:27,957 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:41Z] INFO  16:41:27,958 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:41Z] INFO  16:41:27,958 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:41Z] INFO  16:41:27,958 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:41Z] INFO  16:41:28,002 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:41Z] INFO  16:41:28,190 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:41Z] INFO  16:41:28,202 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:41Z] GATK: realign ('X', 0, 15509380) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:41Z] INFO  16:41:28,282 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:41Z] INFO  16:41:28,285 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:41Z] INFO  16:41:28,286 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:41Z] INFO  16:41:28,287 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:41Z] INFO  16:41:28,292 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/X/R14-18102_kapa-NGv3-PE100-NGv3-sort-X_31139949_46696637-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/X/R14-18102_kapa-NGv3-PE100-NGv3-sort-X_31139949_46696637-prep-prealign-realign.intervals -L X:31139950-46696637 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/X/tx/tmpU7VlTY/R14-18102_kapa-NGv3-PE100-NGv3-sort-X_31139949_46696637-prep.bam
[2016-04-14T23:41Z] INFO  16:41:28,310 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:41Z] INFO  16:41:28,310 HelpFormatter - Date/Time: 2016/04/14 16:41:28
[2016-04-14T23:41Z] INFO  16:41:28,310 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:41Z] INFO  16:41:28,311 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:41Z] INFO  16:41:28,600 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:41Z] INFO  16:41:28,745 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:41Z] INFO  16:41:28,754 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:41Z] INFO  16:41:28,841 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.09
[2016-04-14T23:41Z] INFO  16:41:29,046 ProgressMeter -     19:12826276   1200017.0     3.0 m       2.5 m       82.7%     3.6 m      37.0 s
[2016-04-14T23:41Z] INFO  16:41:29,349 IntervalUtils - Processing 15556688 bp from intervals
[2016-04-14T23:41Z] WARN  16:41:29,354 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:41Z] INFO  16:41:29,418 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:41Z] INFO  16:41:29,574 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:41Z] INFO  16:41:29,578 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:41Z] INFO  16:41:29,579 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:41Z] INFO  16:41:29,579 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:41Z] INFO  16:41:29,660 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:41Z] INFO  16:41:29,798 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:41Z] INFO  16:41:29,900 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:41Z] INFO  16:41:29,904 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:41Z] INFO  16:41:29,905 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:41Z] INFO  16:41:29,905 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:41Z] INFO  16:41:29,910 HelpFormatter - Program Args: -T PrintReads -L X:128582279-144329181 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/X/tx/tmpsoINfq/R14-18102_kapa-NGv3-PE100-NGv3-sort-X_128582278_144329181-prep-prealign.bam
[2016-04-14T23:41Z] INFO  16:41:29,920 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:41Z] INFO  16:41:29,930 HelpFormatter - Date/Time: 2016/04/14 16:41:29
[2016-04-14T23:41Z] INFO  16:41:29,931 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:41Z] INFO  16:41:29,931 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:41Z] INFO  16:41:30,142 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:41Z] INFO  16:41:30,195 ProgressMeter -     20:44453454    400004.0    30.0 s      77.0 s       82.4%    36.0 s       6.0 s
[2016-04-14T23:41Z] INFO  16:41:30,290 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:41Z] INFO  16:41:30,294 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:41Z] INFO  16:41:30,294 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:41Z] INFO  16:41:30,295 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:41Z] INFO  16:41:30,300 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/19/R14-18102_kapa-NGv3-PE100-NGv3-sort-19_46627881_59128983-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/19/tx/tmpAexRLl/R14-18102_kapa-NGv3-PE100-NGv3-sort-19_46627881_59128983-prep-prealign-realign.intervals -l INFO -L 19:46627882-59128983 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-14T23:41Z] INFO  16:41:30,315 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:41Z] INFO  16:41:30,316 HelpFormatter - Date/Time: 2016/04/14 16:41:30
[2016-04-14T23:41Z] INFO  16:41:30,316 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:41Z] INFO  16:41:30,317 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:41Z] INFO  16:41:30,471 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:41Z] INFO  16:41:30,658 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-14T23:41Z] INFO  16:41:30,679 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:41Z] INFO  16:41:30,705 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:41Z] INFO  16:41:30,709 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:41Z] INFO  16:41:30,709 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:41Z] INFO  16:41:30,710 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:41Z] INFO  16:41:30,715 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/X/R14-18102_kapa-NGv3-PE100-NGv3-sort-X_15518899_31090070-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/X/R14-18102_kapa-NGv3-PE100-NGv3-sort-X_15518899_31090070-prep-prealign-realign.intervals -L X:15518900-31090070 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/X/tx/tmp3rLjza/R14-18102_kapa-NGv3-PE100-NGv3-sort-X_15518899_31090070-prep.bam
[2016-04-14T23:41Z] INFO  16:41:30,743 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-14T23:41Z] INFO  16:41:30,747 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:41Z] INFO  16:41:30,748 HelpFormatter - Date/Time: 2016/04/14 16:41:30
[2016-04-14T23:41Z] INFO  16:41:30,749 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:41Z] INFO  16:41:30,749 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:41Z] INFO  16:41:30,943 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:41Z] INFO  16:41:31,046 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:41Z] INFO  16:41:31,052 IntervalUtils - Processing 12501102 bp from intervals
[2016-04-14T23:41Z] WARN  16:41:31,057 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:41Z] INFO  16:41:31,066 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:41Z] INFO  16:41:31,140 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:41Z] INFO  16:41:31,144 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-14T23:41Z] INFO  16:41:31,291 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:41Z] INFO  16:41:31,295 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:41Z] INFO  16:41:31,295 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:41Z] INFO  16:41:31,296 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:41Z] INFO  16:41:31,300 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/X/R14-18102_kapa-NGv3-PE100-NGv3-sort-X_0_15509380-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/X/R14-18102_kapa-NGv3-PE100-NGv3-sort-X_0_15509380-prep-prealign-realign.intervals -L X:1-15509380 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/X/tx/tmpTYKjsZ/R14-18102_kapa-NGv3-PE100-NGv3-sort-X_0_15509380-prep.bam
[2016-04-14T23:41Z] INFO  16:41:31,321 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-14T23:41Z] INFO  16:41:31,330 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:41Z] INFO  16:41:31,331 HelpFormatter - Date/Time: 2016/04/14 16:41:31
[2016-04-14T23:41Z] INFO  16:41:31,332 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:41Z] INFO  16:41:31,332 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:41Z] INFO  16:41:31,345 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:41Z] INFO  16:41:31,352 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:41Z] INFO  16:41:31,353 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:41Z] INFO  16:41:31,353 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-14T23:41Z] INFO  16:41:31,373 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:41Z] INFO  16:41:31,382 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:41Z] INFO  16:41:31,468 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.09
[2016-04-14T23:41Z] INFO  16:41:31,497 IntervalUtils - Processing 15746903 bp from intervals
[2016-04-14T23:41Z] INFO  16:41:31,505 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:41Z] INFO  16:41:31,525 IntervalUtils - Processing 15571171 bp from intervals
[2016-04-14T23:41Z] WARN  16:41:31,530 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:41Z] INFO  16:41:31,578 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:41Z] INFO  16:41:31,587 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:41Z] INFO  16:41:31,596 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:41Z] INFO  16:41:31,635 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:41Z] INFO  16:41:31,653 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-14T23:41Z] INFO  16:41:31,774 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:41Z] INFO  16:41:31,775 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:41Z] INFO  16:41:31,775 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:41Z] INFO  16:41:31,775 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:41Z] INFO  16:41:31,886 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:41Z] INFO  16:41:31,900 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:41Z] INFO  16:41:31,901 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:41Z] INFO  16:41:31,902 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:41Z] INFO  16:41:31,903 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:41Z] INFO  16:41:31,919 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:41Z] INFO  16:41:32,015 IntervalUtils - Processing 15509380 bp from intervals
[2016-04-14T23:41Z] WARN  16:41:32,020 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:41Z] INFO  16:41:32,058 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:41Z] INFO  16:41:32,077 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:41Z] INFO  16:41:32,095 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:41Z] INFO  16:41:32,208 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:41Z] INFO  16:41:32,208 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:41Z] INFO  16:41:32,209 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:41Z] INFO  16:41:32,209 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:41Z] INFO  16:41:32,360 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:41Z] INFO  16:41:32,506 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:41Z] INFO  16:41:33,792 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@5fe152b7
[2016-04-14T23:41Z] INFO  16:41:33,950 ProgressMeter -            done    304892.0    48.0 s       2.6 m      100.0%    48.0 s       0.0 s
[2016-04-14T23:41Z] INFO  16:41:33,950 ProgressMeter - Total runtime 48.12 secs, 0.80 min, 0.01 hours
[2016-04-14T23:41Z] INFO  16:41:33,950 MicroScheduler - 165 reads were filtered out during the traversal out of approximately 305057 total reads (0.05%)
[2016-04-14T23:41Z] INFO  16:41:33,951 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:41Z] INFO  16:41:33,951 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:41Z] INFO  16:41:33,951 MicroScheduler -   -> 165 reads (0.05% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:41Z] INFO  16:41:34,507 ProgressMeter -            done    555571.0    35.0 s      63.0 s      100.0%    35.0 s       0.0 s
[2016-04-14T23:41Z] INFO  16:41:34,508 ProgressMeter - Total runtime 35.16 secs, 0.59 min, 0.01 hours
[2016-04-14T23:41Z] INFO  16:41:34,511 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 555571 total reads (0.00%)
[2016-04-14T23:41Z] INFO  16:41:34,511 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:41Z] INFO  16:41:34,512 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:41Z] INFO  16:41:34,512 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:41Z] INFO  16:41:35,308 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:41Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-X_62857907_78427545-prep-prealign.bam
[2016-04-14T23:41Z] INFO  16:41:36,181 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:41Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-20_31379406_47242465-prep.bam
[2016-04-14T23:41Z] GATK RealignerTargetCreator: R14-18102_kapa-NGv3-PE100-NGv3-sort-X_62857907_78427545-prep-prealign.bam X:62857908-78427545
[2016-04-14T23:41Z] GATK: RealignerTargetCreator
[2016-04-14T23:41Z] INFO  16:41:37,199 ProgressMeter -            done   1.7323604E7    15.0 s       0.0 s      100.0%    15.0 s       0.0 s
[2016-04-14T23:41Z] INFO  16:41:37,200 ProgressMeter - Total runtime 15.14 secs, 0.25 min, 0.00 hours
[2016-04-14T23:41Z] INFO  16:41:37,205 MicroScheduler - 7213 reads were filtered out during the traversal out of approximately 66975 total reads (10.77%)
[2016-04-14T23:41Z] INFO  16:41:37,206 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:41Z] INFO  16:41:37,207 MicroScheduler -   -> 354 reads (0.53% of total) failing BadMateFilter
[2016-04-14T23:41Z] INFO  16:41:37,207 MicroScheduler -   -> 5350 reads (7.99% of total) failing DuplicateReadFilter
[2016-04-14T23:41Z] INFO  16:41:37,208 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-14T23:41Z] INFO  16:41:37,209 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:41Z] INFO  16:41:37,210 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-14T23:41Z] INFO  16:41:37,211 MicroScheduler -   -> 1509 reads (2.25% of total) failing MappingQualityZeroFilter
[2016-04-14T23:41Z] INFO  16:41:37,211 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:41Z] INFO  16:41:37,212 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-14T23:41Z] INFO  16:41:37,213 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-14T23:41Z] GATK pre-alignment ('X', 144337190, 155270560) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:41Z] INFO  16:41:38,879 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:41Z] GATK: realign ('X', 78616585, 95940189) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:41Z] INFO  16:41:39,078 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:41Z] INFO  16:41:39,081 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:41Z] INFO  16:41:39,081 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:41Z] INFO  16:41:39,082 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:41Z] INFO  16:41:39,087 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/X/R14-18102_kapa-NGv3-PE100-NGv3-sort-X_62857907_78427545-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/X/tx/tmp_G1sfv/R14-18102_kapa-NGv3-PE100-NGv3-sort-X_62857907_78427545-prep-prealign-realign.intervals -l INFO -L X:62857908-78427545 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-14T23:41Z] INFO  16:41:39,106 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:41Z] INFO  16:41:39,107 HelpFormatter - Date/Time: 2016/04/14 16:41:39
[2016-04-14T23:41Z] INFO  16:41:39,107 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:41Z] INFO  16:41:39,108 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:41Z] INFO  16:41:39,233 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:41Z] INFO  16:41:39,436 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-14T23:41Z] INFO  16:41:39,461 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:41Z] INFO  16:41:39,544 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-14T23:41Z] INFO  16:41:39,841 ProgressMeter -            done    460481.0    28.0 s      62.0 s      100.0%    28.0 s       0.0 s
[2016-04-14T23:41Z] INFO  16:41:39,842 ProgressMeter - Total runtime 28.78 secs, 0.48 min, 0.01 hours
[2016-04-14T23:41Z] INFO  16:41:39,845 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 460481 total reads (0.00%)
[2016-04-14T23:41Z] INFO  16:41:39,846 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:41Z] INFO  16:41:39,846 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:41Z] INFO  16:41:39,846 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:41Z] INFO  16:41:39,863 IntervalUtils - Processing 15569638 bp from intervals
[2016-04-14T23:41Z] WARN  16:41:39,868 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:41Z] INFO  16:41:39,948 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:41Z] INFO  16:41:40,148 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:41Z] INFO  16:41:40,149 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:41Z] INFO  16:41:40,149 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:41Z] INFO  16:41:40,150 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-14T23:41Z] INFO  16:41:40,974 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:41Z] INFO  16:41:40,981 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:41Z] INFO  16:41:40,981 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:41Z] INFO  16:41:40,981 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:41Z] INFO  16:41:40,985 HelpFormatter - Program Args: -T PrintReads -L X:144337191-155270560 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/X/tx/tmpYadHrj/R14-18102_kapa-NGv3-PE100-NGv3-sort-X_144337190_155270560-prep-prealign.bam
[2016-04-14T23:41Z] INFO  16:41:41,003 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:41Z] INFO  16:41:41,003 HelpFormatter - Date/Time: 2016/04/14 16:41:40
[2016-04-14T23:41Z] INFO  16:41:41,003 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:41Z] INFO  16:41:41,003 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:41Z] INFO  16:41:41,194 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:41Z] INFO  16:41:41,309 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:41Z] INFO  16:41:41,312 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:41Z] INFO  16:41:41,313 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:41Z] INFO  16:41:41,313 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:41Z] INFO  16:41:41,318 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/X/R14-18102_kapa-NGv3-PE100-NGv3-sort-X_78616585_95940189-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/X/R14-18102_kapa-NGv3-PE100-NGv3-sort-X_78616585_95940189-prep-prealign-realign.intervals -L X:78616586-95940189 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/X/tx/tmpjd30k1/R14-18102_kapa-NGv3-PE100-NGv3-sort-X_78616585_95940189-prep.bam
[2016-04-14T23:41Z] INFO  16:41:41,327 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:41Z] INFO  16:41:41,335 HelpFormatter - Date/Time: 2016/04/14 16:41:41
[2016-04-14T23:41Z] INFO  16:41:41,336 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:41Z] INFO  16:41:41,337 ProgressMeter -      X:50377812    300019.0    60.0 s       3.3 m       23.1%     4.3 m       3.3 m
[2016-04-14T23:41Z] INFO  16:41:41,337 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:41Z] INFO  16:41:41,426 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:41Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-21_31062047_46591599-prep.bam
[2016-04-14T23:41Z] INFO  16:41:41,534 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:41Z] INFO  16:41:41,646 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:41Z] INFO  16:41:41,655 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:41Z] INFO  16:41:41,707 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-14T23:41Z] INFO  16:41:41,743 ProgressMeter -            done    151563.0    12.0 s      80.0 s      100.0%    12.0 s       0.0 s
[2016-04-14T23:41Z] INFO  16:41:41,744 ProgressMeter - Total runtime 12.17 secs, 0.20 min, 0.00 hours
[2016-04-14T23:41Z] INFO  16:41:41,747 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 151563 total reads (0.00%)
[2016-04-14T23:41Z] INFO  16:41:41,748 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:41Z] INFO  16:41:41,748 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:41Z] INFO  16:41:41,748 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:41Z] INFO  16:41:42,105 IntervalUtils - Processing 17323604 bp from intervals
[2016-04-14T23:41Z] WARN  16:41:42,110 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:41Z] INFO  16:41:42,189 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:41Z] INFO  16:41:42,306 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:41Z] INFO  16:41:42,307 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:41Z] INFO  16:41:42,308 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:41Z] INFO  16:41:42,309 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:41Z] INFO  16:41:42,372 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-14T23:41Z] INFO  16:41:42,410 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:41Z] INFO  16:41:42,464 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:41Z] INFO  16:41:42,480 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:41Z] INFO  16:41:42,538 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-14T23:41Z] INFO  16:41:42,557 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:41Z] INFO  16:41:42,563 IntervalUtils - Processing 10933370 bp from intervals
[2016-04-14T23:41Z] INFO  16:41:42,618 ProgressMeter -     X:107224426    200004.0    30.0 s       2.5 m       71.5%    41.0 s      11.0 s
[2016-04-14T23:41Z] INFO  16:41:42,655 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:41Z] GATK pre-alignment ('Y', 0, 15522993) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:41Z] INFO  16:41:42,958 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:41Z] INFO  16:41:42,959 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:41Z] INFO  16:41:42,960 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:41Z] INFO  16:41:42,961 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:41Z] INFO  16:41:42,992 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:41Z] INFO  16:41:43,185 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:41Z] INFO  16:41:43,313 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:41Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-X_31139949_46696637-prep.bam
[2016-04-14T23:41Z] GATK pre-alignment ('Y', 15526614, 59222281) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:41Z] INFO  16:41:44,395 ProgressMeter -     22:31658816    700010.0    90.0 s       2.1 m       99.1%    90.0 s       0.0 s
[2016-04-14T23:41Z] INFO  16:41:44,492 ProgressMeter -     19:43979657   1.2935807E7    30.0 s       2.0 s       83.0%    36.0 s       6.0 s
[2016-04-14T23:41Z] INFO  16:41:45,554 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:41Z] INFO  16:41:45,558 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:41Z] INFO  16:41:45,558 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:41Z] INFO  16:41:45,559 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:41Z] INFO  16:41:45,563 HelpFormatter - Program Args: -T PrintReads -L Y:1-15522993 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/Y/tx/tmpGRypyN/R14-18102_kapa-NGv3-PE100-NGv3-sort-Y_0_15522993-prep-prealign.bam
[2016-04-14T23:41Z] INFO  16:41:45,577 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:41Z] INFO  16:41:45,578 HelpFormatter - Date/Time: 2016/04/14 16:41:45
[2016-04-14T23:41Z] INFO  16:41:45,578 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:41Z] INFO  16:41:45,578 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:41Z] INFO  16:41:45,645 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@5fe152b7
[2016-04-14T23:41Z] INFO  16:41:45,706 ProgressMeter -            done    779542.0    91.0 s     117.0 s      100.0%    91.0 s       0.0 s
[2016-04-14T23:41Z] INFO  16:41:45,706 ProgressMeter - Total runtime 91.36 secs, 1.52 min, 0.03 hours
[2016-04-14T23:41Z] INFO  16:41:45,707 MicroScheduler - 303 reads were filtered out during the traversal out of approximately 779845 total reads (0.04%)
[2016-04-14T23:41Z] INFO  16:41:45,707 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:41Z] INFO  16:41:45,708 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:41Z] INFO  16:41:45,708 MicroScheduler -   -> 303 reads (0.04% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:41Z] INFO  16:41:45,782 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:41Z] INFO  16:41:45,836 ProgressMeter -            done    193111.0    14.0 s      72.0 s      100.0%    14.0 s       0.0 s
[2016-04-14T23:41Z] INFO  16:41:45,837 ProgressMeter - Total runtime 14.06 secs, 0.23 min, 0.00 hours
[2016-04-14T23:41Z] INFO  16:41:45,840 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 193111 total reads (0.00%)
[2016-04-14T23:41Z] INFO  16:41:45,840 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:41Z] INFO  16:41:45,841 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:41Z] INFO  16:41:45,841 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:41Z] INFO  16:41:46,048 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@41fd9d8e
[2016-04-14T23:41Z] INFO  16:41:46,178 ProgressMeter -            done    651637.0    79.0 s       2.0 m      100.0%    79.0 s       0.0 s
[2016-04-14T23:41Z] INFO  16:41:46,179 ProgressMeter - Total runtime 79.27 secs, 1.32 min, 0.02 hours
[2016-04-14T23:41Z] INFO  16:41:46,180 MicroScheduler - 278 reads were filtered out during the traversal out of approximately 651915 total reads (0.04%)
[2016-04-14T23:41Z] INFO  16:41:46,181 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:41Z] INFO  16:41:46,181 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:41Z] INFO  16:41:46,182 MicroScheduler -   -> 278 reads (0.04% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:41Z] INFO  16:41:46,617 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:41Z] INFO  16:41:46,620 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:41Z] INFO  16:41:46,621 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:41Z] INFO  16:41:46,622 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:41Z] INFO  16:41:46,627 HelpFormatter - Program Args: -T PrintReads -L Y:15526615-59222281 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/Y/tx/tmpkKzvBq/R14-18102_kapa-NGv3-PE100-NGv3-sort-Y_15526614_59222281-prep-prealign.bam
[2016-04-14T23:41Z] INFO  16:41:46,635 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:41Z] INFO  16:41:46,646 HelpFormatter - Date/Time: 2016/04/14 16:41:46
[2016-04-14T23:41Z] INFO  16:41:46,647 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:41Z] INFO  16:41:46,647 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:41Z] INFO  16:41:46,799 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:41Z] INFO  16:41:46,838 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-14T23:41Z] INFO  16:41:46,919 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:41Z] INFO  16:41:46,928 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:41Z] INFO  16:41:46,983 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-14T23:41Z] INFO  16:41:47,008 IntervalUtils - Processing 15522993 bp from intervals
[2016-04-14T23:41Z] INFO  16:41:47,103 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:41Z] INFO  16:41:47,221 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:41Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-22_16266928_31795711-prep-prealign.bam
[2016-04-14T23:41Z] INFO  16:41:47,341 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:41Z] INFO  16:41:47,341 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:41Z] INFO  16:41:47,342 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:41Z] INFO  16:41:47,342 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:41Z] INFO  16:41:47,351 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:41Z] INFO  16:41:47,355 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:41Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-X_15518899_31090070-prep.bam
[2016-04-14T23:41Z] INFO  16:41:47,461 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:41Z] INFO  16:41:47,497 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:41Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-22_31796605_47308085-prep-prealign.bam
[2016-04-14T23:41Z] INFO  16:41:47,772 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-14T23:41Z] INFO  16:41:47,838 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:41Z] INFO  16:41:47,848 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:41Z] INFO  16:41:47,926 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-14T23:41Z] INFO  16:41:47,943 IntervalUtils - Processing 43695667 bp from intervals
[2016-04-14T23:41Z] INFO  16:41:47,985 ProgressMeter -            done    207102.0    15.0 s      76.0 s      100.0%    15.0 s       0.0 s
[2016-04-14T23:41Z] INFO  16:41:47,985 ProgressMeter - Total runtime 15.78 secs, 0.26 min, 0.00 hours
[2016-04-14T23:41Z] INFO  16:41:47,989 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 207102 total reads (0.00%)
[2016-04-14T23:41Z] INFO  16:41:47,990 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:41Z] INFO  16:41:47,990 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:41Z] INFO  16:41:47,991 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:41Z] GATK pre-alignment ('Y', 59228291, 59373566) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:41Z] INFO  16:41:48,028 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:41Z] INFO  16:41:48,313 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:41Z] INFO  16:41:48,313 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:41Z] INFO  16:41:48,314 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:41Z] INFO  16:41:48,314 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:41Z] INFO  16:41:48,343 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:41Z] INFO  16:41:48,700 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:41Z] INFO  16:41:49,636 ProgressMeter -            done     66712.0     7.0 s     109.0 s      100.0%     7.0 s       0.0 s
[2016-04-14T23:41Z] INFO  16:41:49,636 ProgressMeter - Total runtime 7.33 secs, 0.12 min, 0.00 hours
[2016-04-14T23:41Z] INFO  16:41:49,641 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 66712 total reads (0.00%)
[2016-04-14T23:41Z] INFO  16:41:49,642 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:41Z] INFO  16:41:49,642 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:41Z] INFO  16:41:49,643 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:41Z] INFO  16:41:49,643 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:41Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-X_0_15509380-prep.bam
[2016-04-14T23:41Z] GATK RealignerTargetCreator: R14-18102_kapa-NGv3-PE100-NGv3-sort-22_16266928_31795711-prep-prealign.bam 22:16266929-31795711
[2016-04-14T23:41Z] GATK: RealignerTargetCreator
[2016-04-14T23:41Z] GATK RealignerTargetCreator: R14-18102_kapa-NGv3-PE100-NGv3-sort-22_31796605_47308085-prep-prealign.bam 22:31796606-47308085
[2016-04-14T23:41Z] GATK: RealignerTargetCreator
[2016-04-14T23:41Z] INFO  16:41:50,440 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@41fd9d8e
[2016-04-14T23:41Z] Select unmapped reads
[2016-04-14T23:41Z] INFO  16:41:50,488 ProgressMeter -            done      5611.0     3.0 s       9.3 m       99.3%     3.0 s       0.0 s
[2016-04-14T23:41Z] INFO  16:41:50,489 ProgressMeter - Total runtime 3.15 secs, 0.05 min, 0.00 hours
[2016-04-14T23:41Z] INFO  16:41:50,489 MicroScheduler - 126 reads were filtered out during the traversal out of approximately 5737 total reads (2.20%)
[2016-04-14T23:41Z] INFO  16:41:50,489 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:41Z] INFO  16:41:50,490 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:41Z] INFO  16:41:50,490 MicroScheduler -   -> 126 reads (2.20% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:41Z] INFO  16:41:50,639 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@41fd9d8e
[2016-04-14T23:41Z] INFO  16:41:50,828 ProgressMeter -            done    298244.0    38.0 s       2.1 m      100.0%    38.0 s       0.0 s
[2016-04-14T23:41Z] INFO  16:41:50,829 ProgressMeter - Total runtime 38.23 secs, 0.64 min, 0.01 hours
[2016-04-14T23:41Z] INFO  16:41:50,829 MicroScheduler - 164 reads were filtered out during the traversal out of approximately 298408 total reads (0.05%)
[2016-04-14T23:41Z] INFO  16:41:50,830 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:41Z] INFO  16:41:50,830 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:41Z] INFO  16:41:50,830 MicroScheduler -   -> 164 reads (0.05% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:41Z] INFO  16:41:50,989 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@119dc1fb
[2016-04-14T23:41Z] INFO  16:41:51,050 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:41Z] INFO  16:41:51,053 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:41Z] INFO  16:41:51,053 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:41Z] INFO  16:41:51,053 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:41Z] INFO  16:41:51,062 HelpFormatter - Program Args: -T PrintReads -L Y:59228292-59373566 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18102_kapa-NGv3-PE100-NGv3/R14-18102_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/Y/tx/tmpX82Hgg/R14-18102_kapa-NGv3-PE100-NGv3-sort-Y_59228291_59373566-prep-prealign.bam
[2016-04-14T23:41Z] INFO  16:41:51,072 ProgressMeter -            done      3116.0     2.0 s      14.8 m       99.5%     2.0 s       0.0 s
[2016-04-14T23:41Z] INFO  16:41:51,073 ProgressMeter - Total runtime 2.76 secs, 0.05 min, 0.00 hours
[2016-04-14T23:41Z] INFO  16:41:51,074 MicroScheduler - 51 reads were filtered out during the traversal out of approximately 3167 total reads (1.61%)
[2016-04-14T23:41Z] INFO  16:41:51,074 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:41Z] INFO  16:41:51,074 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:41Z] INFO  16:41:51,075 MicroScheduler -   -> 51 reads (1.61% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:41Z] INFO  16:41:51,089 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:41Z] INFO  16:41:51,090 HelpFormatter - Date/Time: 2016/04/14 16:41:51
[2016-04-14T23:41Z] INFO  16:41:51,091 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:41Z] INFO  16:41:51,097 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:41Z] INFO  16:41:51,248 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:41Z] INFO  16:41:51,277 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:41Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-X_78616585_95940189-prep.bam
[2016-04-14T23:41Z] Select unanalyzed reads
[2016-04-14T23:41Z] INFO  16:41:52,008 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:41Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-Y_0_15522993-prep-prealign.bam
[2016-04-14T23:41Z] GATK RealignerTargetCreator: R14-18102_kapa-NGv3-PE100-NGv3-sort-Y_0_15522993-prep-prealign.bam Y:1-15522993
[2016-04-14T23:41Z] GATK: RealignerTargetCreator
[2016-04-14T23:41Z] INFO  16:41:52,143 ProgressMeter -            done   1.5588729E7    37.0 s       2.0 s      100.0%    37.0 s       0.0 s
[2016-04-14T23:41Z] INFO  16:41:52,144 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:41Z] INFO  16:41:52,144 ProgressMeter - Total runtime 37.68 secs, 0.63 min, 0.01 hours
[2016-04-14T23:41Z] INFO  16:41:52,152 MicroScheduler - 126681 reads were filtered out during the traversal out of approximately 1186795 total reads (10.67%)
[2016-04-14T23:41Z] INFO  16:41:52,154 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:41Z] INFO  16:41:52,155 MicroScheduler -   -> 1982 reads (0.17% of total) failing BadMateFilter
[2016-04-14T23:41Z] INFO  16:41:52,156 MicroScheduler -   -> 93944 reads (7.92% of total) failing DuplicateReadFilter
[2016-04-14T23:41Z] INFO  16:41:52,157 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-14T23:41Z] INFO  16:41:52,170 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:41Z] INFO  16:41:52,170 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-14T23:41Z] INFO  16:41:52,170 MicroScheduler -   -> 30755 reads (2.59% of total) failing MappingQualityZeroFilter
[2016-04-14T23:41Z] INFO  16:41:52,171 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:41Z] INFO  16:41:52,171 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-14T23:41Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-X_95990756_111698889-prep-prealign.bam
[2016-04-14T23:41Z] INFO  16:41:52,174 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-14T23:41Z] INFO  16:41:52,386 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:41Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-Y_15526614_59222281-prep-prealign.bam
[2016-04-14T23:41Z] INFO  16:41:52,451 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-14T23:41Z] GATK RealignerTargetCreator: R14-18102_kapa-NGv3-PE100-NGv3-sort-Y_15526614_59222281-prep-prealign.bam Y:15526615-59222281
[2016-04-14T23:41Z] GATK: RealignerTargetCreator
[2016-04-14T23:41Z] INFO  16:41:52,545 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:41Z] INFO  16:41:52,555 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:41Z] INFO  16:41:52,602 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-14T23:41Z] INFO  16:41:52,619 IntervalUtils - Processing 145275 bp from intervals
[2016-04-14T23:41Z] INFO  16:41:52,753 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:41Z] INFO  16:41:52,980 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:41Z] INFO  16:41:52,980 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:41Z] INFO  16:41:52,981 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:41Z] INFO  16:41:52,981 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:41Z] INFO  16:41:53,009 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:41Z] INFO  16:41:53,010 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:41Z] INFO  16:41:53,021 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@32d5a4c6
[2016-04-14T23:41Z] INFO  16:41:53,035 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:41Z] INFO  16:41:53,039 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:41Z] INFO  16:41:53,039 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:41Z] INFO  16:41:53,039 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:41Z] INFO  16:41:53,044 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/22/R14-18102_kapa-NGv3-PE100-NGv3-sort-22_16266928_31795711-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/22/tx/tmpOhEy6g/R14-18102_kapa-NGv3-PE100-NGv3-sort-22_16266928_31795711-prep-prealign-realign.intervals -l INFO -L 22:16266929-31795711 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-14T23:41Z] INFO  16:41:53,062 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:41Z] INFO  16:41:53,062 HelpFormatter - Date/Time: 2016/04/14 16:41:53
[2016-04-14T23:41Z] INFO  16:41:53,063 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:41Z] INFO  16:41:53,063 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:41Z] INFO  16:41:53,071 ProgressMeter -            done         0.0     0.0 s      24.8 h      100.0%     0.0 s       0.0 s
[2016-04-14T23:41Z] INFO  16:41:53,072 ProgressMeter - Total runtime 0.09 secs, 0.00 min, 0.00 hours
[2016-04-14T23:41Z] INFO  16:41:53,178 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:41Z] INFO  16:41:53,225 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:41Z] INFO  16:41:53,228 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:41Z] INFO  16:41:53,228 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:41Z] INFO  16:41:53,228 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:41Z] INFO  16:41:53,233 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/22/R14-18102_kapa-NGv3-PE100-NGv3-sort-22_31796605_47308085-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/22/tx/tmpmdp58W/R14-18102_kapa-NGv3-PE100-NGv3-sort-22_31796605_47308085-prep-prealign-realign.intervals -l INFO -L 22:31796606-47308085 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-14T23:41Z] INFO  16:41:53,273 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:41Z] INFO  16:41:53,274 HelpFormatter - Date/Time: 2016/04/14 16:41:53
[2016-04-14T23:41Z] INFO  16:41:53,274 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:41Z] INFO  16:41:53,275 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:41Z] INFO  16:41:53,399 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:41Z] GATK RealignerTargetCreator: R14-18102_kapa-NGv3-PE100-NGv3-sort-X_95990756_111698889-prep-prealign.bam X:95990757-111698889
[2016-04-14T23:41Z] GATK: RealignerTargetCreator
[2016-04-14T23:41Z] INFO  16:41:53,446 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-14T23:41Z] INFO  16:41:53,457 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:41Z] INFO  16:41:53,546 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.09
[2016-04-14T23:41Z] INFO  16:41:53,658 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-14T23:41Z] INFO  16:41:53,669 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:41Z] INFO  16:41:53,723 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-14T23:41Z] INFO  16:41:53,739 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:41Z] GATK: realign ('19', 31038849, 46627578) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:41Z] INFO  16:41:53,857 IntervalUtils - Processing 15528783 bp from intervals
[2016-04-14T23:41Z] WARN  16:41:53,863 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:41Z] INFO  16:41:53,957 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:41Z] INFO  16:41:54,022 IntervalUtils - Processing 15511480 bp from intervals
[2016-04-14T23:41Z] WARN  16:41:54,028 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:41Z] INFO  16:41:54,157 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:41Z] INFO  16:41:54,296 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:41Z] INFO  16:41:54,297 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:41Z] INFO  16:41:54,298 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:41Z] INFO  16:41:54,298 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-14T23:41Z] INFO  16:41:54,464 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:41Z] INFO  16:41:54,464 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:41Z] INFO  16:41:54,465 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:41Z] INFO  16:41:54,466 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-14T23:41Z] INFO  16:41:54,503 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:41Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-Y_59228291_59373566-prep-prealign.bam
[2016-04-14T23:41Z] GATK RealignerTargetCreator: R14-18102_kapa-NGv3-PE100-NGv3-sort-Y_59228291_59373566-prep-prealign.bam Y:59228292-59373566
[2016-04-14T23:41Z] GATK: RealignerTargetCreator
[2016-04-14T23:41Z] INFO  16:41:54,931 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:41Z] INFO  16:41:54,934 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:41Z] INFO  16:41:54,935 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:41Z] INFO  16:41:54,935 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:41Z] INFO  16:41:54,940 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/Y/R14-18102_kapa-NGv3-PE100-NGv3-sort-Y_0_15522993-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/Y/tx/tmpiP8vD1/R14-18102_kapa-NGv3-PE100-NGv3-sort-Y_0_15522993-prep-prealign-realign.intervals -l INFO -L Y:1-15522993 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-14T23:41Z] INFO  16:41:54,950 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:41Z] INFO  16:41:54,961 HelpFormatter - Date/Time: 2016/04/14 16:41:54
[2016-04-14T23:41Z] INFO  16:41:54,962 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:41Z] INFO  16:41:54,962 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:41Z] INFO  16:41:55,068 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:41Z] INFO  16:41:55,298 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-14T23:41Z] INFO  16:41:55,307 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:41Z] INFO  16:41:55,351 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.04
[2016-04-14T23:41Z] INFO  16:41:55,446 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:41Z] INFO  16:41:55,449 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:41Z] INFO  16:41:55,450 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:41Z] INFO  16:41:55,451 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:41Z] INFO  16:41:55,455 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/Y/R14-18102_kapa-NGv3-PE100-NGv3-sort-Y_15526614_59222281-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/Y/tx/tmpaPLqzB/R14-18102_kapa-NGv3-PE100-NGv3-sort-Y_15526614_59222281-prep-prealign-realign.intervals -l INFO -L Y:15526615-59222281 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-14T23:41Z] INFO  16:41:55,464 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:41Z] INFO  16:41:55,464 HelpFormatter - Date/Time: 2016/04/14 16:41:55
[2016-04-14T23:41Z] INFO  16:41:55,464 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:41Z] INFO  16:41:55,465 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:41Z] INFO  16:41:55,612 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:41Z] INFO  16:41:55,640 IntervalUtils - Processing 15522993 bp from intervals
[2016-04-14T23:41Z] WARN  16:41:55,645 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:41Z] INFO  16:41:55,758 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:41Z] INFO  16:41:55,796 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@7172f77a
[2016-04-14T23:41Z] INFO  16:41:55,847 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-14T23:41Z] INFO  16:41:55,856 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:41Z] INFO  16:41:55,899 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:41Z] INFO  16:41:55,900 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:41Z] INFO  16:41:55,901 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:41Z] INFO  16:41:55,902 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-14T23:41Z] INFO  16:41:55,934 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-14T23:41Z] INFO  16:41:55,944 ProgressMeter -            done    208199.0    27.0 s       2.2 m      100.0%    27.0 s       0.0 s
[2016-04-14T23:41Z] INFO  16:41:55,944 ProgressMeter - Total runtime 27.99 secs, 0.47 min, 0.01 hours
[2016-04-14T23:41Z] INFO  16:41:55,944 MicroScheduler - 159 reads were filtered out during the traversal out of approximately 208358 total reads (0.08%)
[2016-04-14T23:41Z] INFO  16:41:55,945 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:41Z] INFO  16:41:55,945 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:41Z] INFO  16:41:55,946 MicroScheduler -   -> 159 reads (0.08% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:41Z] INFO  16:41:56,180 IntervalUtils - Processing 43695667 bp from intervals
[2016-04-14T23:41Z] WARN  16:41:56,185 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:41Z] INFO  16:41:56,267 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:41Z] INFO  16:41:56,381 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:41Z] INFO  16:41:56,384 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:41Z] INFO  16:41:56,385 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:41Z] INFO  16:41:56,385 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:41Z] INFO  16:41:56,390 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/X/R14-18102_kapa-NGv3-PE100-NGv3-sort-X_95990756_111698889-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/X/tx/tmpeWSu83/R14-18102_kapa-NGv3-PE100-NGv3-sort-X_95990756_111698889-prep-prealign-realign.intervals -l INFO -L X:95990757-111698889 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-14T23:41Z] INFO  16:41:56,399 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:41Z] INFO  16:41:56,400 HelpFormatter - Date/Time: 2016/04/14 16:41:56
[2016-04-14T23:41Z] INFO  16:41:56,401 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:41Z] INFO  16:41:56,402 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:41Z] INFO  16:41:56,431 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:41Z] INFO  16:41:56,432 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:41Z] INFO  16:41:56,432 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:41Z] INFO  16:41:56,432 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-14T23:41Z] INFO  16:41:56,519 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:41Z] INFO  16:41:56,677 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:41Z] INFO  16:41:56,681 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:41Z] INFO  16:41:56,681 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:41Z] INFO  16:41:56,682 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:41Z] INFO  16:41:56,686 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/19/R14-18102_kapa-NGv3-PE100-NGv3-sort-19_31038849_46627578-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/19/R14-18102_kapa-NGv3-PE100-NGv3-sort-19_31038849_46627578-prep-prealign-realign.intervals -L 19:31038850-46627578 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/19/tx/tmpiKp66I/R14-18102_kapa-NGv3-PE100-NGv3-sort-19_31038849_46627578-prep.bam
[2016-04-14T23:41Z] INFO  16:41:56,702 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:41Z] INFO  16:41:56,704 HelpFormatter - Date/Time: 2016/04/14 16:41:56
[2016-04-14T23:41Z] INFO  16:41:56,704 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:41Z] INFO  16:41:56,705 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:41Z] INFO  16:41:56,762 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-14T23:41Z] INFO  16:41:56,797 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:41Z] INFO  16:41:56,890 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.09
[2016-04-14T23:41Z] INFO  16:41:56,939 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:41Z] INFO  16:41:57,113 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:41Z] INFO  16:41:57,128 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:41Z] INFO  16:41:57,209 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-14T23:41Z] INFO  16:41:57,322 IntervalUtils - Processing 15708133 bp from intervals
[2016-04-14T23:41Z] WARN  16:41:57,328 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:41Z] INFO  16:41:57,422 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:41Z] INFO  16:41:57,442 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:41Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-X_111874647_128581278-prep-prealign.bam
[2016-04-14T23:41Z] INFO  16:41:57,644 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:41Z] INFO  16:41:57,648 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:41Z] INFO  16:41:57,649 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:41Z] INFO  16:41:57,649 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:41Z] INFO  16:41:57,654 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/Y/R14-18102_kapa-NGv3-PE100-NGv3-sort-Y_59228291_59373566-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/Y/tx/tmpjVzIMP/R14-18102_kapa-NGv3-PE100-NGv3-sort-Y_59228291_59373566-prep-prealign-realign.intervals -l INFO -L Y:59228292-59373566 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-14T23:41Z] INFO  16:41:57,662 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:41Z] INFO  16:41:57,663 HelpFormatter - Date/Time: 2016/04/14 16:41:57
[2016-04-14T23:41Z] INFO  16:41:57,664 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:41Z] INFO  16:41:57,666 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:41Z] INFO  16:41:57,712 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:41Z] INFO  16:41:57,713 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:41Z] INFO  16:41:57,714 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:41Z] INFO  16:41:57,715 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-14T23:41Z] INFO  16:41:57,788 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:41Z] INFO  16:41:57,811 IntervalUtils - Processing 15588729 bp from intervals
[2016-04-14T23:41Z] WARN  16:41:57,816 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:41Z] INFO  16:41:57,910 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:41Z] INFO  16:41:57,961 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-14T23:41Z] INFO  16:41:57,970 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:41Z] INFO  16:41:57,979 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@5fe152b7
[2016-04-14T23:41Z] INFO  16:41:58,011 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.04
[2016-04-14T23:41Z] INFO  16:41:58,089 ProgressMeter -            done   1464552.0     3.5 m       2.4 m      100.0%     3.5 m       0.0 s
[2016-04-14T23:41Z] INFO  16:41:58,090 ProgressMeter - Total runtime 209.89 secs, 3.50 min, 0.06 hours
[2016-04-14T23:41Z] INFO  16:41:58,091 MicroScheduler - 595 reads were filtered out during the traversal out of approximately 1465147 total reads (0.04%)
[2016-04-14T23:41Z] INFO  16:41:58,092 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:41Z] INFO  16:41:58,092 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:41Z] INFO  16:41:58,093 MicroScheduler -   -> 595 reads (0.04% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:41Z] INFO  16:41:58,112 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:41Z] INFO  16:41:58,114 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:41Z] INFO  16:41:58,114 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:41Z] INFO  16:41:58,115 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:41Z] GATK RealignerTargetCreator: R14-18102_kapa-NGv3-PE100-NGv3-sort-X_111874647_128581278-prep-prealign.bam X:111874648-128581278
[2016-04-14T23:41Z] GATK: RealignerTargetCreator
[2016-04-14T23:41Z] INFO  16:41:58,297 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:41Z] INFO  16:41:58,446 IntervalUtils - Processing 145275 bp from intervals
[2016-04-14T23:41Z] WARN  16:41:58,451 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:41Z] INFO  16:41:58,502 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:41Z] INFO  16:41:58,518 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:41Z] INFO  16:41:58,556 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:41Z] INFO  16:41:58,557 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:41Z] INFO  16:41:58,564 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:41Z] INFO  16:41:58,565 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-14T23:41Z] INFO  16:41:59,059 ProgressMeter -            done   1.5569638E7    18.0 s       1.0 s      100.0%    18.0 s       0.0 s
[2016-04-14T23:41Z] INFO  16:41:59,060 ProgressMeter - Total runtime 18.91 secs, 0.32 min, 0.01 hours
[2016-04-14T23:41Z] INFO  16:41:59,064 MicroScheduler - 45955 reads were filtered out during the traversal out of approximately 307097 total reads (14.96%)
[2016-04-14T23:41Z] INFO  16:41:59,065 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:41Z] INFO  16:41:59,065 MicroScheduler -   -> 669 reads (0.22% of total) failing BadMateFilter
[2016-04-14T23:41Z] INFO  16:41:59,066 MicroScheduler -   -> 22995 reads (7.49% of total) failing DuplicateReadFilter
[2016-04-14T23:41Z] INFO  16:41:59,066 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-14T23:41Z] INFO  16:41:59,067 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:41Z] INFO  16:41:59,068 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-14T23:41Z] INFO  16:41:59,068 MicroScheduler -   -> 22291 reads (7.26% of total) failing MappingQualityZeroFilter
[2016-04-14T23:41Z] INFO  16:41:59,069 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:41Z] INFO  16:41:59,069 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-14T23:41Z] INFO  16:41:59,070 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-14T23:41Z] INFO  16:41:59,372 ProgressMeter -            done    145275.0     0.0 s       5.0 s       99.9%     0.0 s       0.0 s
[2016-04-14T23:41Z] INFO  16:41:59,373 ProgressMeter - Total runtime 0.82 secs, 0.01 min, 0.00 hours
[2016-04-14T23:41Z] INFO  16:41:59,578 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:41Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-19_0_15509577-prep-prealign.bam
[2016-04-14T23:42Z] INFO  16:42:00,303 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:42Z] GATK: realign ('X', 62857907, 78427545) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:42Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-noanalysis-prep.bam
[2016-04-14T23:42Z] INFO  16:42:00,644 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:42Z] GATK: realign ('Y', 59228291, 59373566) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:42Z] GATK pre-alignment ('1', 0, 15541927) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-14T23:42Z] INFO  16:42:01,217 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:42Z] INFO  16:42:01,220 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:42Z] INFO  16:42:01,220 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:42Z] INFO  16:42:01,220 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:42Z] INFO  16:42:01,224 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/X/R14-18102_kapa-NGv3-PE100-NGv3-sort-X_111874647_128581278-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/X/tx/tmpsMguHY/R14-18102_kapa-NGv3-PE100-NGv3-sort-X_111874647_128581278-prep-prealign-realign.intervals -l INFO -L X:111874648-128581278 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-14T23:42Z] INFO  16:42:01,248 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:42Z] INFO  16:42:01,248 HelpFormatter - Date/Time: 2016/04/14 16:42:01
[2016-04-14T23:42Z] INFO  16:42:01,248 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:42Z] INFO  16:42:01,249 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:42Z] INFO  16:42:01,375 ProgressMeter -     19:55963261   9323479.0    30.0 s       3.0 s       74.7%    40.0 s      10.0 s
[2016-04-14T23:42Z] INFO  16:42:01,420 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:42Z] INFO  16:42:01,649 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-14T23:42Z] INFO  16:42:01,671 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:42Z] INFO  16:42:01,738 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-14T23:42Z] INFO  16:42:01,944 ProgressMeter -     X:140984513    200002.0    30.0 s       2.5 m       78.8%    38.0 s       8.0 s
[2016-04-14T23:42Z] INFO  16:42:02,083 IntervalUtils - Processing 16706631 bp from intervals
[2016-04-14T23:42Z] WARN  16:42:02,089 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:42Z] INFO  16:42:02,172 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:42Z] INFO  16:42:02,385 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:42Z] INFO  16:42:02,387 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:42Z] INFO  16:42:02,388 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:42Z] INFO  16:42:02,388 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-14T23:42Z] INFO  16:42:03,151 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:42Z] INFO  16:42:03,154 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:42Z] INFO  16:42:03,155 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:42Z] INFO  16:42:03,155 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:42Z] INFO  16:42:03,159 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/X/R14-18102_kapa-NGv3-PE100-NGv3-sort-X_62857907_78427545-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/X/R14-18102_kapa-NGv3-PE100-NGv3-sort-X_62857907_78427545-prep-prealign-realign.intervals -L X:62857908-78427545 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/X/tx/tmpremH__/R14-18102_kapa-NGv3-PE100-NGv3-sort-X_62857907_78427545-prep.bam
[2016-04-14T23:42Z] INFO  16:42:03,176 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:42Z] INFO  16:42:03,177 HelpFormatter - Date/Time: 2016/04/14 16:42:03
[2016-04-14T23:42Z] INFO  16:42:03,178 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:42Z] INFO  16:42:03,178 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:42Z] INFO  16:42:03,417 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:42Z] INFO  16:42:03,460 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@5fe152b7
[2016-04-14T23:42Z] INFO  16:42:03,543 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:42Z] INFO  16:42:03,552 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:42Z] INFO  16:42:03,609 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-14T23:42Z] INFO  16:42:03,685 ProgressMeter -            done    239516.0    31.0 s       2.2 m      100.0%    31.0 s       0.0 s
[2016-04-14T23:42Z] INFO  16:42:03,686 ProgressMeter - Total runtime 31.78 secs, 0.53 min, 0.01 hours
[2016-04-14T23:42Z] INFO  16:42:03,686 MicroScheduler - 139 reads were filtered out during the traversal out of approximately 239655 total reads (0.06%)
[2016-04-14T23:42Z] INFO  16:42:03,687 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:42Z] INFO  16:42:03,687 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:42Z] INFO  16:42:03,688 MicroScheduler -   -> 139 reads (0.06% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:42Z] INFO  16:42:03,732 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:42Z] INFO  16:42:03,735 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:42Z] INFO  16:42:03,735 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:42Z] INFO  16:42:03,735 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:42Z] INFO  16:42:03,739 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/Y/R14-18102_kapa-NGv3-PE100-NGv3-sort-Y_59228291_59373566-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/Y/R14-18102_kapa-NGv3-PE100-NGv3-sort-Y_59228291_59373566-prep-prealign-realign.intervals -L Y:59228292-59373566 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/Y/tx/tmpsucJ8D/R14-18102_kapa-NGv3-PE100-NGv3-sort-Y_59228291_59373566-prep.bam
[2016-04-14T23:42Z] INFO  16:42:03,773 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:42Z] INFO  16:42:03,774 HelpFormatter - Date/Time: 2016/04/14 16:42:03
[2016-04-14T23:42Z] INFO  16:42:03,774 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:42Z] INFO  16:42:03,774 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:42Z] INFO  16:42:03,864 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:42Z] INFO  16:42:03,867 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:42Z] INFO  16:42:03,868 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:42Z] INFO  16:42:03,868 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:42Z] INFO  16:42:03,873 HelpFormatter - Program Args: -T PrintReads -L 1:1-15541927 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/1/tx/tmpoE5MJl/R14-18105_kapa-NGv3-PE100-NGv3-sort-1_0_15541927-prep-prealign.bam
[2016-04-14T23:42Z] INFO  16:42:03,893 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:42Z] INFO  16:42:03,894 HelpFormatter - Date/Time: 2016/04/14 16:42:03
[2016-04-14T23:42Z] INFO  16:42:03,895 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:42Z] INFO  16:42:03,895 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:42Z] INFO  16:42:04,045 IntervalUtils - Processing 15569638 bp from intervals
[2016-04-14T23:42Z] WARN  16:42:04,051 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:42Z] INFO  16:42:04,073 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:42Z] INFO  16:42:04,122 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:42Z] INFO  16:42:04,147 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:42Z] INFO  16:42:04,194 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:42Z] INFO  16:42:04,210 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:42Z] INFO  16:42:04,263 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-14T23:42Z] INFO  16:42:04,317 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:42Z] INFO  16:42:04,319 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:42Z] INFO  16:42:04,319 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:42Z] INFO  16:42:04,320 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:42Z] INFO  16:42:04,373 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:42Z] GATK RealignerTargetCreator: R14-18102_kapa-NGv3-PE100-NGv3-sort-19_0_15509577-prep-prealign.bam 19:1-15509577
[2016-04-14T23:42Z] GATK: RealignerTargetCreator
[2016-04-14T23:42Z] INFO  16:42:04,547 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:42Z] INFO  16:42:04,789 IntervalUtils - Processing 145275 bp from intervals
[2016-04-14T23:42Z] WARN  16:42:04,803 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:42Z] INFO  16:42:04,931 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:42Z] INFO  16:42:04,950 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:42Z] INFO  16:42:04,978 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:42Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-X_128582278_144329181-prep-prealign.bam
[2016-04-14T23:42Z] INFO  16:42:04,979 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:42Z] INFO  16:42:04,979 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:42Z] INFO  16:42:04,979 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:42Z] INFO  16:42:05,025 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:42Z] INFO  16:42:05,026 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:42Z] INFO  16:42:05,096 ProgressMeter -            done         0.0     0.0 s      32.5 h      100.0%     0.0 s       0.0 s
[2016-04-14T23:42Z] INFO  16:42:05,097 ProgressMeter - Total runtime 0.12 secs, 0.00 min, 0.00 hours
[2016-04-14T23:42Z] INFO  16:42:05,310 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-14T23:42Z] INFO  16:42:05,391 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:42Z] INFO  16:42:05,400 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:42Z] INFO  16:42:05,467 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-14T23:42Z] INFO  16:42:05,493 IntervalUtils - Processing 15541927 bp from intervals
[2016-04-14T23:42Z] INFO  16:42:05,609 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:42Z] GATK RealignerTargetCreator: R14-18102_kapa-NGv3-PE100-NGv3-sort-X_128582278_144329181-prep-prealign.bam X:128582279-144329181
[2016-04-14T23:42Z] GATK: RealignerTargetCreator
[2016-04-14T23:42Z] INFO  16:42:05,884 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:42Z] INFO  16:42:05,884 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:42Z] INFO  16:42:05,885 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:42Z] INFO  16:42:05,885 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:42Z] INFO  16:42:05,903 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:42Z] INFO  16:42:06,061 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:42Z] INFO  16:42:06,474 ProgressMeter -            done   1.5522993E7    10.0 s       0.0 s      100.0%    10.0 s       0.0 s
[2016-04-14T23:42Z] INFO  16:42:06,475 ProgressMeter - Total runtime 10.57 secs, 0.18 min, 0.00 hours
[2016-04-14T23:42Z] INFO  16:42:06,478 MicroScheduler - 3274 reads were filtered out during the traversal out of approximately 5616 total reads (58.30%)
[2016-04-14T23:42Z] INFO  16:42:06,479 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:42Z] INFO  16:42:06,480 MicroScheduler -   -> 192 reads (3.42% of total) failing BadMateFilter
[2016-04-14T23:42Z] INFO  16:42:06,481 MicroScheduler -   -> 195 reads (3.47% of total) failing DuplicateReadFilter
[2016-04-14T23:42Z] INFO  16:42:06,481 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-14T23:42Z] INFO  16:42:06,482 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:42Z] INFO  16:42:06,482 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-14T23:42Z] INFO  16:42:06,483 MicroScheduler -   -> 2887 reads (51.41% of total) failing MappingQualityZeroFilter
[2016-04-14T23:42Z] INFO  16:42:06,484 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:42Z] INFO  16:42:06,484 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-14T23:42Z] INFO  16:42:06,484 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-14T23:42Z] INFO  16:42:06,574 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:42Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-Y_59228291_59373566-prep.bam
[2016-04-14T23:42Z] GATK pre-alignment ('1', 15545821, 31186478) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-14T23:42Z] INFO  16:42:06,997 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@5fe152b7
[2016-04-14T23:42Z] INFO  16:42:07,130 ProgressMeter -            done    583221.0    85.0 s       2.5 m      100.0%    85.0 s       0.0 s
[2016-04-14T23:42Z] INFO  16:42:07,131 ProgressMeter - Total runtime 85.82 secs, 1.43 min, 0.02 hours
[2016-04-14T23:42Z] INFO  16:42:07,131 MicroScheduler - 254 reads were filtered out during the traversal out of approximately 583475 total reads (0.04%)
[2016-04-14T23:42Z] INFO  16:42:07,132 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:42Z] INFO  16:42:07,132 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:42Z] INFO  16:42:07,132 MicroScheduler -   -> 254 reads (0.04% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:42Z] INFO  16:42:07,297 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:42Z] INFO  16:42:07,309 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:42Z] INFO  16:42:07,310 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:42Z] INFO  16:42:07,311 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:42Z] INFO  16:42:07,325 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/19/R14-18102_kapa-NGv3-PE100-NGv3-sort-19_0_15509577-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/19/tx/tmpLMG6VB/R14-18102_kapa-NGv3-PE100-NGv3-sort-19_0_15509577-prep-prealign-realign.intervals -l INFO -L 19:1-15509577 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-14T23:42Z] INFO  16:42:07,339 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:42Z] INFO  16:42:07,340 HelpFormatter - Date/Time: 2016/04/14 16:42:07
[2016-04-14T23:42Z] INFO  16:42:07,340 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:42Z] INFO  16:42:07,340 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:42Z] INFO  16:42:07,452 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:42Z] INFO  16:42:07,730 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-14T23:42Z] INFO  16:42:07,740 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:42Z] INFO  16:42:07,796 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-14T23:42Z] INFO  16:42:07,892 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:42Z] GATK: realign ('Y', 0, 15522993) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:42Z] INFO  16:42:08,096 IntervalUtils - Processing 15509577 bp from intervals
[2016-04-14T23:42Z] WARN  16:42:08,101 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:42Z] INFO  16:42:08,172 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:42Z] INFO  16:42:08,401 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:42Z] INFO  16:42:08,402 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:42Z] INFO  16:42:08,403 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:42Z] INFO  16:42:08,404 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-14T23:42Z] INFO  16:42:08,618 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:42Z] INFO  16:42:08,620 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:42Z] INFO  16:42:08,620 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:42Z] INFO  16:42:08,620 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:42Z] INFO  16:42:08,636 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/X/R14-18102_kapa-NGv3-PE100-NGv3-sort-X_128582278_144329181-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/X/tx/tmpdz3Ndq/R14-18102_kapa-NGv3-PE100-NGv3-sort-X_128582278_144329181-prep-prealign-realign.intervals -l INFO -L X:128582279-144329181 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-14T23:42Z] INFO  16:42:08,647 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:42Z] INFO  16:42:08,671 HelpFormatter - Date/Time: 2016/04/14 16:42:08
[2016-04-14T23:42Z] INFO  16:42:08,671 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:42Z] INFO  16:42:08,671 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:42Z] INFO  16:42:08,761 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:42Z] INFO  16:42:09,023 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-14T23:42Z] INFO  16:42:09,035 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:42Z] INFO  16:42:09,113 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-14T23:42Z] INFO  16:42:09,267 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:42Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-X_46712910_62570698-prep-prealign.bam
[2016-04-14T23:42Z] INFO  16:42:09,338 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:42Z] INFO  16:42:09,342 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:42Z] INFO  16:42:09,343 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:42Z] INFO  16:42:09,344 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:42Z] INFO  16:42:09,349 HelpFormatter - Program Args: -T PrintReads -L 1:15545822-31186478 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/1/tx/tmpcOyEVm/R14-18105_kapa-NGv3-PE100-NGv3-sort-1_15545821_31186478-prep-prealign.bam
[2016-04-14T23:42Z] INFO  16:42:09,367 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:42Z] INFO  16:42:09,368 HelpFormatter - Date/Time: 2016/04/14 16:42:09
[2016-04-14T23:42Z] INFO  16:42:09,368 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:42Z] INFO  16:42:09,368 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:42Z] INFO  16:42:09,567 IntervalUtils - Processing 15746903 bp from intervals
[2016-04-14T23:42Z] WARN  16:42:09,573 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:42Z] INFO  16:42:09,639 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:42Z] INFO  16:42:09,658 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:42Z] INFO  16:42:09,861 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:42Z] INFO  16:42:09,863 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:42Z] INFO  16:42:09,863 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:42Z] INFO  16:42:09,864 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-14T23:42Z] INFO  16:42:10,650 ProgressMeter -            done   1.2501102E7    39.0 s       3.0 s      100.0%    39.0 s       0.0 s
[2016-04-14T23:42Z] INFO  16:42:10,651 ProgressMeter - Total runtime 39.30 secs, 0.65 min, 0.01 hours
[2016-04-14T23:42Z] INFO  16:42:10,666 MicroScheduler - 149669 reads were filtered out during the traversal out of approximately 1309397 total reads (11.43%)
[2016-04-14T23:42Z] INFO  16:42:10,666 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:42Z] INFO  16:42:10,667 MicroScheduler -   -> 2196 reads (0.17% of total) failing BadMateFilter
[2016-04-14T23:42Z] INFO  16:42:10,667 MicroScheduler -   -> 103368 reads (7.89% of total) failing DuplicateReadFilter
[2016-04-14T23:42Z] INFO  16:42:10,667 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-14T23:42Z] INFO  16:42:10,668 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:42Z] INFO  16:42:10,668 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-14T23:42Z] INFO  16:42:10,668 MicroScheduler -   -> 44105 reads (3.37% of total) failing MappingQualityZeroFilter
[2016-04-14T23:42Z] INFO  16:42:10,668 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:42Z] INFO  16:42:10,669 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-14T23:42Z] INFO  16:42:10,669 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-14T23:42Z] INFO  16:42:10,833 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:42Z] INFO  16:42:10,835 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:42Z] INFO  16:42:10,836 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:42Z] INFO  16:42:10,836 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:42Z] INFO  16:42:10,852 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/Y/R14-18102_kapa-NGv3-PE100-NGv3-sort-Y_0_15522993-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/Y/R14-18102_kapa-NGv3-PE100-NGv3-sort-Y_0_15522993-prep-prealign-realign.intervals -L Y:1-15522993 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/Y/tx/tmpSweFoY/R14-18102_kapa-NGv3-PE100-NGv3-sort-Y_0_15522993-prep.bam
[2016-04-14T23:42Z] INFO  16:42:10,872 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:42Z] INFO  16:42:10,872 HelpFormatter - Date/Time: 2016/04/14 16:42:10
[2016-04-14T23:42Z] INFO  16:42:10,873 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:42Z] INFO  16:42:10,873 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:42Z] INFO  16:42:10,887 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-14T23:42Z] INFO  16:42:10,958 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:42Z] INFO  16:42:10,969 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:42Z] INFO  16:42:11,017 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-14T23:42Z] INFO  16:42:11,034 IntervalUtils - Processing 15640657 bp from intervals
[2016-04-14T23:42Z] INFO  16:42:11,141 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:42Z] INFO  16:42:11,216 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:42Z] GATK RealignerTargetCreator: R14-18102_kapa-NGv3-PE100-NGv3-sort-X_46712910_62570698-prep-prealign.bam X:46712911-62570698
[2016-04-14T23:42Z] GATK: RealignerTargetCreator
[2016-04-14T23:42Z] INFO  16:42:11,375 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:42Z] INFO  16:42:11,386 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:42Z] INFO  16:42:11,448 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-14T23:42Z] INFO  16:42:11,492 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:42Z] INFO  16:42:11,493 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:42Z] INFO  16:42:11,494 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:42Z] INFO  16:42:11,494 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:42Z] INFO  16:42:11,524 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:42Z] INFO  16:42:11,794 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:42Z] INFO  16:42:11,877 IntervalUtils - Processing 15522993 bp from intervals
[2016-04-14T23:42Z] WARN  16:42:11,894 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:42Z] INFO  16:42:11,980 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:42Z] INFO  16:42:12,072 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:42Z] INFO  16:42:12,073 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:42Z] INFO  16:42:12,074 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:42Z] INFO  16:42:12,074 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:42Z] INFO  16:42:12,108 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:42Z] INFO  16:42:12,197 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:42Z] GATK: realign ('19', 46627881, 59128983) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:42Z] INFO  16:42:12,210 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:42Z] INFO  16:42:12,982 ProgressMeter -     X:153201072    200002.0    30.0 s       2.5 m       81.1%    37.0 s       7.0 s
[2016-04-14T23:42Z] INFO  16:42:14,481 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:42Z] INFO  16:42:14,485 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:42Z] INFO  16:42:14,485 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:42Z] INFO  16:42:14,486 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:42Z] INFO  16:42:14,491 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/X/R14-18102_kapa-NGv3-PE100-NGv3-sort-X_46712910_62570698-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/X/tx/tmp5saxey/R14-18102_kapa-NGv3-PE100-NGv3-sort-X_46712910_62570698-prep-prealign-realign.intervals -l INFO -L X:46712911-62570698 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-14T23:42Z] INFO  16:42:14,501 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:42Z] INFO  16:42:14,508 HelpFormatter - Date/Time: 2016/04/14 16:42:14
[2016-04-14T23:42Z] INFO  16:42:14,509 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:42Z] INFO  16:42:14,510 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:42Z] INFO  16:42:14,611 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:42Z] INFO  16:42:14,842 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-14T23:42Z] INFO  16:42:14,852 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:42Z] INFO  16:42:14,904 ProgressMeter -            done      5611.0     2.0 s       8.4 m       99.3%     2.0 s       0.0 s
[2016-04-14T23:42Z] INFO  16:42:14,905 ProgressMeter - Total runtime 2.83 secs, 0.05 min, 0.00 hours
[2016-04-14T23:42Z] INFO  16:42:14,908 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 5611 total reads (0.00%)
[2016-04-14T23:42Z] INFO  16:42:14,909 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:42Z] INFO  16:42:14,910 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:42Z] INFO  16:42:14,910 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:42Z] INFO  16:42:14,941 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.09
[2016-04-14T23:42Z] INFO  16:42:15,061 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:42Z] INFO  16:42:15,064 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:42Z] INFO  16:42:15,065 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:42Z] INFO  16:42:15,066 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:42Z] INFO  16:42:15,072 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/19/R14-18102_kapa-NGv3-PE100-NGv3-sort-19_46627881_59128983-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/19/R14-18102_kapa-NGv3-PE100-NGv3-sort-19_46627881_59128983-prep-prealign-realign.intervals -L 19:46627882-59128983 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/19/tx/tmpol84zl/R14-18102_kapa-NGv3-PE100-NGv3-sort-19_46627881_59128983-prep.bam
[2016-04-14T23:42Z] INFO  16:42:15,082 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:42Z] INFO  16:42:15,087 HelpFormatter - Date/Time: 2016/04/14 16:42:15
[2016-04-14T23:42Z] INFO  16:42:15,088 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:42Z] INFO  16:42:15,088 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:42Z] INFO  16:42:15,206 IntervalUtils - Processing 15857788 bp from intervals
[2016-04-14T23:42Z] WARN  16:42:15,211 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:42Z] INFO  16:42:15,272 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:42Z] INFO  16:42:15,281 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:42Z] INFO  16:42:15,422 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:42Z] INFO  16:42:15,431 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:42Z] INFO  16:42:15,446 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:42Z] INFO  16:42:15,447 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:42Z] INFO  16:42:15,448 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:42Z] INFO  16:42:15,449 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-14T23:42Z] INFO  16:42:15,491 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-14T23:42Z] INFO  16:42:15,512 ProgressMeter -            done   1.5708133E7    17.0 s       1.0 s      100.0%    17.0 s       0.0 s
[2016-04-14T23:42Z] INFO  16:42:15,513 ProgressMeter - Total runtime 17.80 secs, 0.30 min, 0.00 hours
[2016-04-14T23:42Z] INFO  16:42:15,520 MicroScheduler - 49919 reads were filtered out during the traversal out of approximately 299946 total reads (16.64%)
[2016-04-14T23:42Z] INFO  16:42:15,533 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:42Z] INFO  16:42:15,534 MicroScheduler -   -> 641 reads (0.21% of total) failing BadMateFilter
[2016-04-14T23:42Z] INFO  16:42:15,534 MicroScheduler -   -> 21631 reads (7.21% of total) failing DuplicateReadFilter
[2016-04-14T23:42Z] INFO  16:42:15,535 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-14T23:42Z] INFO  16:42:15,535 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:42Z] INFO  16:42:15,536 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-14T23:42Z] INFO  16:42:15,537 MicroScheduler -   -> 27647 reads (9.22% of total) failing MappingQualityZeroFilter
[2016-04-14T23:42Z] INFO  16:42:15,537 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:42Z] INFO  16:42:15,538 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-14T23:42Z] INFO  16:42:15,539 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-14T23:42Z] INFO  16:42:15,810 IntervalUtils - Processing 12501102 bp from intervals
[2016-04-14T23:42Z] WARN  16:42:15,826 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:42Z] INFO  16:42:15,915 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:42Z] INFO  16:42:16,058 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:42Z] INFO  16:42:16,059 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:42Z] INFO  16:42:16,059 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:42Z] INFO  16:42:16,060 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:42Z] INFO  16:42:16,210 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:42Z] INFO  16:42:16,302 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:42Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-Y_0_15522993-prep.bam
[2016-04-14T23:42Z] INFO  16:42:16,339 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:42Z] GATK pre-alignment ('1', 31187093, 46714270) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-14T23:42Z] INFO  16:42:17,034 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:42Z] GATK: realign ('X', 95990756, 111698889) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:42Z] INFO  16:42:19,086 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:42Z] INFO  16:42:19,089 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:42Z] INFO  16:42:19,090 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:42Z] INFO  16:42:19,090 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:42Z] INFO  16:42:19,095 HelpFormatter - Program Args: -T PrintReads -L 1:31187094-46714270 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/1/tx/tmpabIYZt/R14-18105_kapa-NGv3-PE100-NGv3-sort-1_31187093_46714270-prep-prealign.bam
[2016-04-14T23:42Z] INFO  16:42:19,104 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:42Z] INFO  16:42:19,105 HelpFormatter - Date/Time: 2016/04/14 16:42:19
[2016-04-14T23:42Z] INFO  16:42:19,105 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:42Z] INFO  16:42:19,106 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:42Z] INFO  16:42:19,338 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:42Z] INFO  16:42:19,751 ProgressMeter -            done   4.3695667E7    23.0 s       0.0 s      100.0%    23.0 s       0.0 s
[2016-04-14T23:42Z] INFO  16:42:19,752 ProgressMeter - Total runtime 23.32 secs, 0.39 min, 0.01 hours
[2016-04-14T23:42Z] INFO  16:42:19,757 MicroScheduler - 1864 reads were filtered out during the traversal out of approximately 3125 total reads (59.65%)
[2016-04-14T23:42Z] INFO  16:42:19,758 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:42Z] INFO  16:42:19,758 MicroScheduler -   -> 43 reads (1.38% of total) failing BadMateFilter
[2016-04-14T23:42Z] INFO  16:42:19,759 MicroScheduler -   -> 117 reads (3.74% of total) failing DuplicateReadFilter
[2016-04-14T23:42Z] INFO  16:42:19,760 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-14T23:42Z] INFO  16:42:19,760 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:42Z] INFO  16:42:19,761 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-14T23:42Z] INFO  16:42:19,762 MicroScheduler -   -> 1704 reads (54.53% of total) failing MappingQualityZeroFilter
[2016-04-14T23:42Z] INFO  16:42:19,763 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:42Z] INFO  16:42:19,763 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-14T23:42Z] INFO  16:42:19,764 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-14T23:42Z] INFO  16:42:19,869 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:42Z] INFO  16:42:19,872 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:42Z] INFO  16:42:19,873 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:42Z] INFO  16:42:19,873 ProgressMeter -            done   1.6706631E7    17.0 s       1.0 s      100.0%    17.0 s       0.0 s
[2016-04-14T23:42Z] INFO  16:42:19,873 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:42Z] INFO  16:42:19,873 ProgressMeter - Total runtime 17.49 secs, 0.29 min, 0.00 hours
[2016-04-14T23:42Z] INFO  16:42:19,877 MicroScheduler - 62332 reads were filtered out during the traversal out of approximately 209698 total reads (29.72%)
[2016-04-14T23:42Z] INFO  16:42:19,878 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:42Z] INFO  16:42:19,878 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/X/R14-18102_kapa-NGv3-PE100-NGv3-sort-X_95990756_111698889-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/X/R14-18102_kapa-NGv3-PE100-NGv3-sort-X_95990756_111698889-prep-prealign-realign.intervals -L X:95990757-111698889 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/X/tx/tmpwiTOn0/R14-18102_kapa-NGv3-PE100-NGv3-sort-X_95990756_111698889-prep.bam
[2016-04-14T23:42Z] INFO  16:42:19,878 MicroScheduler -   -> 541 reads (0.26% of total) failing BadMateFilter
[2016-04-14T23:42Z] INFO  16:42:19,879 MicroScheduler -   -> 13014 reads (6.21% of total) failing DuplicateReadFilter
[2016-04-14T23:42Z] INFO  16:42:19,880 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-14T23:42Z] INFO  16:42:19,880 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:42Z] INFO  16:42:19,881 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-14T23:42Z] INFO  16:42:19,881 MicroScheduler -   -> 48777 reads (23.26% of total) failing MappingQualityZeroFilter
[2016-04-14T23:42Z] INFO  16:42:19,882 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:42Z] INFO  16:42:19,883 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-14T23:42Z] INFO  16:42:19,883 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-14T23:42Z] INFO  16:42:19,896 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:42Z] INFO  16:42:19,907 HelpFormatter - Date/Time: 2016/04/14 16:42:19
[2016-04-14T23:42Z] INFO  16:42:19,908 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:42Z] INFO  16:42:19,908 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:42Z] INFO  16:42:20,143 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:42Z] INFO  16:42:20,253 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:42Z] INFO  16:42:20,262 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:42Z] INFO  16:42:20,312 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-14T23:42Z] INFO  16:42:20,437 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-14T23:42Z] INFO  16:42:20,504 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:42Z] INFO  16:42:20,515 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:42Z] INFO  16:42:20,557 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.04
[2016-04-14T23:42Z] INFO  16:42:20,572 IntervalUtils - Processing 15527177 bp from intervals
[2016-04-14T23:42Z] INFO  16:42:20,638 IntervalUtils - Processing 15708133 bp from intervals
[2016-04-14T23:42Z] WARN  16:42:20,644 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:42Z] INFO  16:42:20,669 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:42Z] INFO  16:42:20,730 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:42Z] INFO  16:42:20,860 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:42Z] INFO  16:42:20,861 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:42Z] INFO  16:42:20,862 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:42Z] INFO  16:42:20,863 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:42Z] INFO  16:42:20,930 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:42Z] INFO  16:42:20,949 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:42Z] INFO  16:42:20,950 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:42Z] INFO  16:42:20,951 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:42Z] INFO  16:42:20,952 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:42Z] INFO  16:42:20,966 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:42Z] INFO  16:42:21,062 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:42Z] GATK: realign ('Y', 15526614, 59222281) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:42Z] INFO  16:42:21,098 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:42Z] INFO  16:42:21,122 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:42Z] INFO  16:42:21,159 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:42Z] GATK: realign ('X', 111874647, 128581278) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:42Z] INFO  16:42:21,771 ProgressMeter -            done   1.551148E7    27.0 s       1.0 s      100.0%    27.0 s       0.0 s
[2016-04-14T23:42Z] INFO  16:42:21,772 ProgressMeter - Total runtime 27.31 secs, 0.46 min, 0.01 hours
[2016-04-14T23:42Z] INFO  16:42:21,776 MicroScheduler - 60264 reads were filtered out during the traversal out of approximately 654985 total reads (9.20%)
[2016-04-14T23:42Z] INFO  16:42:21,777 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:42Z] INFO  16:42:21,778 MicroScheduler -   -> 1368 reads (0.21% of total) failing BadMateFilter
[2016-04-14T23:42Z] INFO  16:42:21,779 MicroScheduler -   -> 52603 reads (8.03% of total) failing DuplicateReadFilter
[2016-04-14T23:42Z] INFO  16:42:21,779 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-14T23:42Z] INFO  16:42:21,780 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:42Z] INFO  16:42:21,781 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-14T23:42Z] INFO  16:42:21,781 MicroScheduler -   -> 6293 reads (0.96% of total) failing MappingQualityZeroFilter
[2016-04-14T23:42Z] INFO  16:42:21,782 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:42Z] INFO  16:42:21,782 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-14T23:42Z] INFO  16:42:21,783 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-14T23:42Z] INFO  16:42:23,181 ProgressMeter -            done   1.5528783E7    28.0 s       1.0 s      100.0%    28.0 s       0.0 s
[2016-04-14T23:42Z] INFO  16:42:23,182 ProgressMeter - Total runtime 28.88 secs, 0.48 min, 0.01 hours
[2016-04-14T23:42Z] INFO  16:42:23,186 MicroScheduler - 160276 reads were filtered out during the traversal out of approximately 783802 total reads (20.45%)
[2016-04-14T23:42Z] INFO  16:42:23,187 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:42Z] INFO  16:42:23,187 MicroScheduler -   -> 1304 reads (0.17% of total) failing BadMateFilter
[2016-04-14T23:42Z] INFO  16:42:23,188 MicroScheduler -   -> 55760 reads (7.11% of total) failing DuplicateReadFilter
[2016-04-14T23:42Z] INFO  16:42:23,188 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-14T23:42Z] INFO  16:42:23,188 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:42Z] INFO  16:42:23,189 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-14T23:42Z] INFO  16:42:23,189 MicroScheduler -   -> 103212 reads (13.17% of total) failing MappingQualityZeroFilter
[2016-04-14T23:42Z] INFO  16:42:23,189 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:42Z] INFO  16:42:23,189 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-14T23:42Z] INFO  16:42:23,190 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-14T23:42Z] INFO  16:42:23,417 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:42Z] GATK: realign ('22', 31796605, 47308085) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:42Z] INFO  16:42:24,208 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:42Z] INFO  16:42:24,211 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:42Z] INFO  16:42:24,212 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:42Z] INFO  16:42:24,212 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:42Z] INFO  16:42:24,217 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/Y/R14-18102_kapa-NGv3-PE100-NGv3-sort-Y_15526614_59222281-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/Y/R14-18102_kapa-NGv3-PE100-NGv3-sort-Y_15526614_59222281-prep-prealign-realign.intervals -L Y:15526615-59222281 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/Y/tx/tmp_u8fd1/R14-18102_kapa-NGv3-PE100-NGv3-sort-Y_15526614_59222281-prep.bam
[2016-04-14T23:42Z] INFO  16:42:24,227 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:42Z] INFO  16:42:24,238 HelpFormatter - Date/Time: 2016/04/14 16:42:24
[2016-04-14T23:42Z] INFO  16:42:24,239 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:42Z] INFO  16:42:24,240 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:42Z] INFO  16:42:24,265 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:42Z] INFO  16:42:24,269 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:42Z] INFO  16:42:24,269 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:42Z] INFO  16:42:24,270 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:42Z] INFO  16:42:24,275 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/X/R14-18102_kapa-NGv3-PE100-NGv3-sort-X_111874647_128581278-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/X/R14-18102_kapa-NGv3-PE100-NGv3-sort-X_111874647_128581278-prep-prealign-realign.intervals -L X:111874648-128581278 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/X/tx/tmp2LzRhj/R14-18102_kapa-NGv3-PE100-NGv3-sort-X_111874647_128581278-prep.bam
[2016-04-14T23:42Z] INFO  16:42:24,302 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:42Z] INFO  16:42:24,303 HelpFormatter - Date/Time: 2016/04/14 16:42:24
[2016-04-14T23:42Z] INFO  16:42:24,304 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:42Z] INFO  16:42:24,304 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:42Z] INFO  16:42:24,462 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:42Z] INFO  16:42:24,503 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:42Z] GATK: realign ('22', 16266928, 31795711) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:42Z] INFO  16:42:24,518 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:42Z] INFO  16:42:24,566 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:42Z] INFO  16:42:24,576 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:42Z] INFO  16:42:24,637 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-14T23:42Z] INFO  16:42:24,644 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:42Z] INFO  16:42:24,657 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:42Z] INFO  16:42:24,723 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-14T23:42Z] INFO  16:42:24,981 IntervalUtils - Processing 43695667 bp from intervals
[2016-04-14T23:42Z] WARN  16:42:24,986 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:42Z] INFO  16:42:25,065 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:42Z] INFO  16:42:25,159 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:42Z] INFO  16:42:25,160 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:42Z] INFO  16:42:25,161 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:42Z] INFO  16:42:25,162 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:42Z] INFO  16:42:25,209 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:42Z] INFO  16:42:25,217 IntervalUtils - Processing 16706631 bp from intervals
[2016-04-14T23:42Z] WARN  16:42:25,244 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:42Z] INFO  16:42:25,314 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:42Z] INFO  16:42:25,460 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:42Z] INFO  16:42:25,490 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:42Z] INFO  16:42:25,491 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:42Z] INFO  16:42:25,492 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:42Z] INFO  16:42:25,493 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:42Z] INFO  16:42:25,611 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:42Z] INFO  16:42:25,808 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:42Z] INFO  16:42:26,065 ProgressMeter -            done    304892.0    21.0 s      71.0 s      100.0%    21.0 s       0.0 s
[2016-04-14T23:42Z] INFO  16:42:26,067 ProgressMeter - Total runtime 21.75 secs, 0.36 min, 0.01 hours
[2016-04-14T23:42Z] INFO  16:42:26,072 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 304892 total reads (0.00%)
[2016-04-14T23:42Z] INFO  16:42:26,074 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:42Z] INFO  16:42:26,074 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:42Z] INFO  16:42:26,075 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:42Z] INFO  16:42:26,119 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:42Z] INFO  16:42:26,124 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:42Z] INFO  16:42:26,124 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:42Z] INFO  16:42:26,125 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:42Z] INFO  16:42:26,131 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/22/R14-18102_kapa-NGv3-PE100-NGv3-sort-22_31796605_47308085-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/22/R14-18102_kapa-NGv3-PE100-NGv3-sort-22_31796605_47308085-prep-prealign-realign.intervals -L 22:31796606-47308085 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/22/tx/tmpL3HsZc/R14-18102_kapa-NGv3-PE100-NGv3-sort-22_31796605_47308085-prep.bam
[2016-04-14T23:42Z] INFO  16:42:26,157 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:42Z] INFO  16:42:26,168 HelpFormatter - Date/Time: 2016/04/14 16:42:26
[2016-04-14T23:42Z] INFO  16:42:26,170 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:42Z] INFO  16:42:26,170 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:42Z] INFO  16:42:26,470 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:42Z] INFO  16:42:26,574 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:42Z] INFO  16:42:26,596 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:42Z] INFO  16:42:26,704 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.11
[2016-04-14T23:42Z] INFO  16:42:26,934 ProgressMeter -            done      3116.0     1.0 s       9.5 m       99.5%     1.0 s       0.0 s
[2016-04-14T23:42Z] INFO  16:42:26,935 ProgressMeter - Total runtime 1.77 secs, 0.03 min, 0.00 hours
[2016-04-14T23:42Z] INFO  16:42:26,939 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 3116 total reads (0.00%)
[2016-04-14T23:42Z] INFO  16:42:26,939 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:42Z] INFO  16:42:26,940 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:42Z] INFO  16:42:26,940 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:42Z] INFO  16:42:27,135 IntervalUtils - Processing 15511480 bp from intervals
[2016-04-14T23:42Z] WARN  16:42:27,140 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:42Z] INFO  16:42:27,241 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:42Z] INFO  16:42:27,371 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:42Z] INFO  16:42:27,374 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:42Z] INFO  16:42:27,374 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:42Z] INFO  16:42:27,375 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:42Z] INFO  16:42:27,379 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/22/R14-18102_kapa-NGv3-PE100-NGv3-sort-22_16266928_31795711-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/22/R14-18102_kapa-NGv3-PE100-NGv3-sort-22_16266928_31795711-prep-prealign-realign.intervals -L 22:16266929-31795711 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/22/tx/tmpD99t6O/R14-18102_kapa-NGv3-PE100-NGv3-sort-22_16266928_31795711-prep.bam
[2016-04-14T23:42Z] INFO  16:42:27,412 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:42Z] INFO  16:42:27,412 HelpFormatter - Date/Time: 2016/04/14 16:42:27
[2016-04-14T23:42Z] INFO  16:42:27,413 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:42Z] INFO  16:42:27,414 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:42Z] INFO  16:42:27,429 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:42Z] INFO  16:42:27,430 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:42Z] INFO  16:42:27,431 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:42Z] INFO  16:42:27,432 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:42Z] INFO  16:42:27,625 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:42Z] INFO  16:42:27,665 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:42Z] INFO  16:42:27,774 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:42Z] INFO  16:42:27,784 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:42Z] INFO  16:42:27,821 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:42Z] INFO  16:42:27,829 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.04
[2016-04-14T23:42Z] INFO  16:42:27,865 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:42Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-X_62857907_78427545-prep.bam
[2016-04-14T23:42Z] INFO  16:42:28,181 IntervalUtils - Processing 15528783 bp from intervals
[2016-04-14T23:42Z] WARN  16:42:28,187 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:42Z] INFO  16:42:28,195 ProgressMeter -            done   1.5746903E7    18.0 s       1.0 s      100.0%    18.0 s       0.0 s
[2016-04-14T23:42Z] INFO  16:42:28,195 ProgressMeter - Total runtime 18.33 secs, 0.31 min, 0.01 hours
[2016-04-14T23:42Z] INFO  16:42:28,195 MicroScheduler - 55156 reads were filtered out during the traversal out of approximately 243752 total reads (22.63%)
[2016-04-14T23:42Z] INFO  16:42:28,196 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:42Z] INFO  16:42:28,196 MicroScheduler -   -> 539 reads (0.22% of total) failing BadMateFilter
[2016-04-14T23:42Z] INFO  16:42:28,196 MicroScheduler -   -> 16604 reads (6.81% of total) failing DuplicateReadFilter
[2016-04-14T23:42Z] INFO  16:42:28,196 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-14T23:42Z] INFO  16:42:28,197 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:42Z] INFO  16:42:28,197 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-14T23:42Z] INFO  16:42:28,197 MicroScheduler -   -> 38013 reads (15.59% of total) failing MappingQualityZeroFilter
[2016-04-14T23:42Z] INFO  16:42:28,197 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:42Z] INFO  16:42:28,198 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-14T23:42Z] INFO  16:42:28,198 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-14T23:42Z] INFO  16:42:28,253 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:42Z] INFO  16:42:28,292 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:42Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-Y_15526614_59222281-prep.bam
[2016-04-14T23:42Z] INFO  16:42:28,393 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:42Z] GATK pre-alignment ('1', 46715671, 62228851) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-14T23:42Z] INFO  16:42:28,394 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:42Z] INFO  16:42:28,395 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:42Z] INFO  16:42:28,396 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:42Z] INFO  16:42:28,626 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:42Z] INFO  16:42:28,810 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:42Z] INFO  16:42:28,950 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@7172f77a
[2016-04-14T23:42Z] GATK pre-alignment ('1', 62231950, 77749296) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-14T23:42Z] INFO  16:42:29,254 ProgressMeter -            done    370973.0    46.0 s       2.1 m       99.9%    46.0 s       0.0 s
[2016-04-14T23:42Z] INFO  16:42:29,254 ProgressMeter - Total runtime 46.29 secs, 0.77 min, 0.01 hours
[2016-04-14T23:42Z] INFO  16:42:29,255 MicroScheduler - 197 reads were filtered out during the traversal out of approximately 371170 total reads (0.05%)
[2016-04-14T23:42Z] INFO  16:42:29,255 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:42Z] INFO  16:42:29,255 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:42Z] INFO  16:42:29,256 MicroScheduler -   -> 197 reads (0.05% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:42Z] INFO  16:42:29,804 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:42Z] GATK: realign ('X', 128582278, 144329181) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:42Z] INFO  16:42:29,885 ProgressMeter -     19:38989848    400008.0    31.0 s      79.0 s       51.0%    60.0 s      29.0 s
[2016-04-14T23:42Z] INFO  16:42:30,632 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:42Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-X_144337190_155270560-prep-prealign.bam
[2016-04-14T23:42Z] INFO  16:42:31,526 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:42Z] INFO  16:42:31,529 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:42Z] INFO  16:42:31,530 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:42Z] INFO  16:42:31,531 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:42Z] INFO  16:42:31,535 HelpFormatter - Program Args: -T PrintReads -L 1:46715672-62228851 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/1/tx/tmpgWWXY3/R14-18105_kapa-NGv3-PE100-NGv3-sort-1_46715671_62228851-prep-prealign.bam
[2016-04-14T23:42Z] INFO  16:42:31,548 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:42Z] INFO  16:42:31,548 HelpFormatter - Date/Time: 2016/04/14 16:42:31
[2016-04-14T23:42Z] INFO  16:42:31,548 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:42Z] INFO  16:42:31,549 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:42Z] INFO  16:42:31,731 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:42Z] INFO  16:42:31,885 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:42Z] INFO  16:42:31,889 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:42Z] INFO  16:42:31,890 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:42Z] INFO  16:42:31,890 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:42Z] INFO  16:42:31,895 HelpFormatter - Program Args: -T PrintReads -L 1:62231951-77749296 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/1/tx/tmpmWeONv/R14-18105_kapa-NGv3-PE100-NGv3-sort-1_62231950_77749296-prep-prealign.bam
[2016-04-14T23:42Z] INFO  16:42:31,914 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:42Z] INFO  16:42:31,915 HelpFormatter - Date/Time: 2016/04/14 16:42:31
[2016-04-14T23:42Z] INFO  16:42:31,916 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:42Z] INFO  16:42:31,916 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:42Z] GATK RealignerTargetCreator: R14-18102_kapa-NGv3-PE100-NGv3-sort-X_144337190_155270560-prep-prealign.bam X:144337191-155270560
[2016-04-14T23:42Z] GATK: RealignerTargetCreator
[2016-04-14T23:42Z] INFO  16:42:32,111 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:42Z] INFO  16:42:32,525 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:42Z] INFO  16:42:32,528 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:42Z] INFO  16:42:32,529 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:42Z] INFO  16:42:32,529 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:42Z] INFO  16:42:32,534 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/X/R14-18102_kapa-NGv3-PE100-NGv3-sort-X_128582278_144329181-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/X/R14-18102_kapa-NGv3-PE100-NGv3-sort-X_128582278_144329181-prep-prealign-realign.intervals -L X:128582279-144329181 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/X/tx/tmpGjhmFW/R14-18102_kapa-NGv3-PE100-NGv3-sort-X_128582278_144329181-prep.bam
[2016-04-14T23:42Z] INFO  16:42:32,571 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:42Z] INFO  16:42:32,572 HelpFormatter - Date/Time: 2016/04/14 16:42:32
[2016-04-14T23:42Z] INFO  16:42:32,573 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:42Z] INFO  16:42:32,573 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:42Z] INFO  16:42:32,922 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:42Z] INFO  16:42:32,945 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-14T23:42Z] INFO  16:42:33,011 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:42Z] INFO  16:42:33,020 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:42Z] INFO  16:42:33,079 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-14T23:42Z] INFO  16:42:33,088 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:42Z] INFO  16:42:33,093 IntervalUtils - Processing 15513180 bp from intervals
[2016-04-14T23:42Z] INFO  16:42:33,097 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:42Z] INFO  16:42:33,185 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-14T23:42Z] INFO  16:42:33,195 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.10
[2016-04-14T23:42Z] INFO  16:42:33,205 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:42Z] INFO  16:42:33,243 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:42Z] INFO  16:42:33,252 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:42Z] INFO  16:42:33,297 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.04
[2016-04-14T23:42Z] INFO  16:42:33,315 IntervalUtils - Processing 15517346 bp from intervals
[2016-04-14T23:42Z] INFO  16:42:33,427 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:42Z] INFO  16:42:33,428 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:42Z] INFO  16:42:33,428 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:42Z] INFO  16:42:33,428 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:42Z] INFO  16:42:33,429 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:42Z] INFO  16:42:33,468 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:42Z] INFO  16:42:33,628 IntervalUtils - Processing 15746903 bp from intervals
[2016-04-14T23:42Z] WARN  16:42:33,633 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:42Z] INFO  16:42:33,641 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:42Z] INFO  16:42:33,642 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:42Z] INFO  16:42:33,642 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:42Z] INFO  16:42:33,642 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:42Z] INFO  16:42:33,664 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:42Z] INFO  16:42:33,727 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:42Z] INFO  16:42:33,764 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:42Z] INFO  16:42:33,835 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:42Z] INFO  16:42:33,930 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:42Z] INFO  16:42:33,931 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:42Z] INFO  16:42:33,932 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:42Z] INFO  16:42:33,937 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:42Z] INFO  16:42:34,052 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:42Z] INFO  16:42:34,206 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:42Z] INFO  16:42:34,792 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:42Z] INFO  16:42:34,796 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:42Z] INFO  16:42:34,796 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:42Z] INFO  16:42:34,797 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:42Z] INFO  16:42:34,802 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/X/R14-18102_kapa-NGv3-PE100-NGv3-sort-X_144337190_155270560-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/X/tx/tmpizPgDZ/R14-18102_kapa-NGv3-PE100-NGv3-sort-X_144337190_155270560-prep-prealign-realign.intervals -l INFO -L X:144337191-155270560 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-14T23:42Z] INFO  16:42:34,811 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:42Z] INFO  16:42:34,812 HelpFormatter - Date/Time: 2016/04/14 16:42:34
[2016-04-14T23:42Z] INFO  16:42:34,813 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:42Z] INFO  16:42:34,813 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:42Z] INFO  16:42:34,907 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:42Z] INFO  16:42:35,122 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-14T23:42Z] INFO  16:42:35,134 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:42Z] INFO  16:42:35,184 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-14T23:42Z] INFO  16:42:35,616 IntervalUtils - Processing 10933370 bp from intervals
[2016-04-14T23:42Z] WARN  16:42:35,621 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:42Z] INFO  16:42:35,725 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:42Z] INFO  16:42:35,899 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:42Z] INFO  16:42:35,900 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:42Z] INFO  16:42:35,901 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:42Z] INFO  16:42:35,901 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-14T23:42Z] INFO  16:42:35,902 ProgressMeter -       1:1886401    200005.0    30.0 s       2.5 m       12.1%     4.1 m       3.6 m
[2016-04-14T23:42Z] INFO  16:42:36,264 ProgressMeter -            done   1.5857788E7    20.0 s       1.0 s      100.0%    20.0 s       0.0 s
[2016-04-14T23:42Z] INFO  16:42:36,265 ProgressMeter - Total runtime 20.82 secs, 0.35 min, 0.01 hours
[2016-04-14T23:42Z] INFO  16:42:36,265 MicroScheduler - 222031 reads were filtered out during the traversal out of approximately 587000 total reads (37.82%)
[2016-04-14T23:42Z] INFO  16:42:36,266 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:42Z] INFO  16:42:36,267 MicroScheduler -   -> 777 reads (0.13% of total) failing BadMateFilter
[2016-04-14T23:42Z] INFO  16:42:36,267 MicroScheduler -   -> 32756 reads (5.58% of total) failing DuplicateReadFilter
[2016-04-14T23:42Z] INFO  16:42:36,268 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-14T23:42Z] INFO  16:42:36,269 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:42Z] INFO  16:42:36,269 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-14T23:42Z] INFO  16:42:36,270 MicroScheduler -   -> 188498 reads (32.11% of total) failing MappingQualityZeroFilter
[2016-04-14T23:42Z] INFO  16:42:36,270 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:42Z] INFO  16:42:36,271 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-14T23:42Z] INFO  16:42:36,272 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-14T23:42Z] INFO  16:42:37,867 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:42Z] GATK: realign ('X', 46712910, 62570698) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:42Z] INFO  16:42:38,418 ProgressMeter -      19:9742897   9732096.0    30.0 s       3.0 s       62.8%    47.0 s      17.0 s
[2016-04-14T23:42Z] INFO  16:42:40,548 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:42Z] INFO  16:42:40,552 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:42Z] INFO  16:42:40,553 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:42Z] INFO  16:42:40,553 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:42Z] INFO  16:42:40,558 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/X/R14-18102_kapa-NGv3-PE100-NGv3-sort-X_46712910_62570698-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/X/R14-18102_kapa-NGv3-PE100-NGv3-sort-X_46712910_62570698-prep-prealign-realign.intervals -L X:46712911-62570698 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/X/tx/tmpZnuzKc/R14-18102_kapa-NGv3-PE100-NGv3-sort-X_46712910_62570698-prep.bam
[2016-04-14T23:42Z] INFO  16:42:40,578 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:42Z] INFO  16:42:40,579 HelpFormatter - Date/Time: 2016/04/14 16:42:40
[2016-04-14T23:42Z] INFO  16:42:40,580 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:42Z] INFO  16:42:40,580 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:42Z] INFO  16:42:40,771 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:42Z] INFO  16:42:40,880 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:42Z] INFO  16:42:40,890 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:42Z] INFO  16:42:40,936 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.04
[2016-04-14T23:42Z] INFO  16:42:41,315 IntervalUtils - Processing 15857788 bp from intervals
[2016-04-14T23:42Z] WARN  16:42:41,321 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:42Z] INFO  16:42:41,424 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:42Z] INFO  16:42:41,527 ProgressMeter -      1:17274842    200005.0    30.0 s       2.5 m       11.1%     4.5 m       4.0 m
[2016-04-14T23:42Z] INFO  16:42:41,563 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:42Z] INFO  16:42:41,564 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:42Z] INFO  16:42:41,564 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:42Z] INFO  16:42:41,565 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:42Z] INFO  16:42:41,654 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:42Z] INFO  16:42:41,803 ProgressMeter -            done    298244.0    20.0 s      70.0 s      100.0%    20.0 s       0.0 s
[2016-04-14T23:42Z] INFO  16:42:41,803 ProgressMeter - Total runtime 20.94 secs, 0.35 min, 0.01 hours
[2016-04-14T23:42Z] INFO  16:42:41,807 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 298244 total reads (0.00%)
[2016-04-14T23:42Z] INFO  16:42:41,807 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:42Z] INFO  16:42:41,807 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:42Z] INFO  16:42:41,802 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:42Z] INFO  16:42:41,808 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:42Z] INFO  16:42:42,547 ProgressMeter -            done    208199.0    17.0 s      81.0 s      100.0%    17.0 s       0.0 s
[2016-04-14T23:42Z] INFO  16:42:42,547 ProgressMeter - Total runtime 17.06 secs, 0.28 min, 0.00 hours
[2016-04-14T23:42Z] INFO  16:42:42,551 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 208199 total reads (0.00%)
[2016-04-14T23:42Z] INFO  16:42:42,551 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:42Z] INFO  16:42:42,551 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:42Z] INFO  16:42:42,552 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:42Z] INFO  16:42:43,224 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:42Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-X_95990756_111698889-prep.bam
[2016-04-14T23:42Z] INFO  16:42:44,016 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:42Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-X_111874647_128581278-prep.bam
[2016-04-14T23:42Z] GATK pre-alignment ('1', 77752625, 93297674) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-14T23:42Z] GATK pre-alignment ('1', 93298945, 108993401) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-14T23:42Z] INFO  16:42:46,657 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:42Z] INFO  16:42:46,660 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:42Z] INFO  16:42:46,661 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:42Z] INFO  16:42:46,661 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:42Z] INFO  16:42:46,666 HelpFormatter - Program Args: -T PrintReads -L 1:77752626-93297674 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/1/tx/tmpYFUgx4/R14-18105_kapa-NGv3-PE100-NGv3-sort-1_77752625_93297674-prep-prealign.bam
[2016-04-14T23:42Z] INFO  16:42:46,681 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:42Z] INFO  16:42:46,682 HelpFormatter - Date/Time: 2016/04/14 16:42:46
[2016-04-14T23:42Z] INFO  16:42:46,683 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:42Z] INFO  16:42:46,683 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:42Z] INFO  16:42:46,847 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:42Z] INFO  16:42:47,224 ProgressMeter -     19:50826693    400007.0    31.0 s      77.0 s       33.6%    92.0 s      61.0 s
[2016-04-14T23:42Z] INFO  16:42:47,680 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:42Z] INFO  16:42:47,705 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:42Z] INFO  16:42:47,706 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:42Z] INFO  16:42:47,706 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:42Z] INFO  16:42:47,711 HelpFormatter - Program Args: -T PrintReads -L 1:93298946-108993401 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/1/tx/tmpEIHtQ_/R14-18105_kapa-NGv3-PE100-NGv3-sort-1_93298945_108993401-prep-prealign.bam
[2016-04-14T23:42Z] INFO  16:42:47,720 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:42Z] INFO  16:42:47,731 HelpFormatter - Date/Time: 2016/04/14 16:42:47
[2016-04-14T23:42Z] INFO  16:42:47,732 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:42Z] INFO  16:42:47,733 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:42Z] INFO  16:42:47,903 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:42Z] INFO  16:42:47,916 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-14T23:42Z] INFO  16:42:47,991 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:42Z] INFO  16:42:48,000 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:42Z] INFO  16:42:48,046 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-14T23:42Z] INFO  16:42:48,060 IntervalUtils - Processing 15545049 bp from intervals
[2016-04-14T23:42Z] INFO  16:42:48,144 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:42Z] INFO  16:42:48,387 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:42Z] INFO  16:42:48,388 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:42Z] INFO  16:42:48,388 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:42Z] INFO  16:42:48,389 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:42Z] INFO  16:42:48,401 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:42Z] INFO  16:42:48,614 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:42Z] INFO  16:42:48,921 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-14T23:42Z] INFO  16:42:48,988 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:42Z] INFO  16:42:48,998 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:42Z] INFO  16:42:49,041 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.04
[2016-04-14T23:42Z] INFO  16:42:49,065 IntervalUtils - Processing 15694456 bp from intervals
[2016-04-14T23:42Z] INFO  16:42:49,190 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:42Z] INFO  16:42:49,415 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:42Z] INFO  16:42:49,416 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:42Z] INFO  16:42:49,417 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:42Z] INFO  16:42:49,418 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:42Z] INFO  16:42:49,432 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:42Z] INFO  16:42:49,622 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:42Z] INFO  16:42:51,273 ProgressMeter -            done    239516.0    17.0 s      72.0 s      100.0%    17.0 s       0.0 s
[2016-04-14T23:42Z] INFO  16:42:51,273 ProgressMeter - Total runtime 17.34 secs, 0.29 min, 0.00 hours
[2016-04-14T23:42Z] INFO  16:42:51,277 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 239516 total reads (0.00%)
[2016-04-14T23:42Z] INFO  16:42:51,278 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:42Z] INFO  16:42:51,279 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:42Z] INFO  16:42:51,279 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:42Z] INFO  16:42:51,931 ProgressMeter -            done   1.093337E7    16.0 s       1.0 s      100.0%    16.0 s       0.0 s
[2016-04-14T23:42Z] INFO  16:42:51,932 ProgressMeter - Total runtime 16.03 secs, 0.27 min, 0.00 hours
[2016-04-14T23:42Z] INFO  16:42:51,935 MicroScheduler - 87316 reads were filtered out during the traversal out of approximately 372823 total reads (23.42%)
[2016-04-14T23:42Z] INFO  16:42:51,936 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:42Z] INFO  16:42:51,937 MicroScheduler -   -> 676 reads (0.18% of total) failing BadMateFilter
[2016-04-14T23:42Z] INFO  16:42:51,938 MicroScheduler -   -> 25658 reads (6.88% of total) failing DuplicateReadFilter
[2016-04-14T23:42Z] INFO  16:42:51,939 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-14T23:42Z] INFO  16:42:51,939 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:42Z] INFO  16:42:51,940 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-14T23:42Z] INFO  16:42:51,941 MicroScheduler -   -> 60982 reads (16.36% of total) failing MappingQualityZeroFilter
[2016-04-14T23:42Z] INFO  16:42:51,941 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:42Z] INFO  16:42:51,942 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-14T23:42Z] INFO  16:42:51,942 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-14T23:42Z] INFO  16:42:52,036 ProgressMeter -      1:34208947    100001.0    31.0 s       5.2 m       19.5%     2.7 m       2.1 m
[2016-04-14T23:42Z] INFO  16:42:52,622 ProgressMeter -            done   1.5509577E7    44.0 s       2.0 s      100.0%    44.0 s       0.0 s
[2016-04-14T23:42Z] INFO  16:42:52,624 ProgressMeter - Total runtime 44.22 secs, 0.74 min, 0.01 hours
[2016-04-14T23:42Z] INFO  16:42:52,628 MicroScheduler - 138202 reads were filtered out during the traversal out of approximately 1472870 total reads (9.38%)
[2016-04-14T23:42Z] INFO  16:42:52,629 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:42Z] INFO  16:42:52,630 MicroScheduler -   -> 2820 reads (0.19% of total) failing BadMateFilter
[2016-04-14T23:42Z] INFO  16:42:52,630 MicroScheduler -   -> 118318 reads (8.03% of total) failing DuplicateReadFilter
[2016-04-14T23:42Z] INFO  16:42:52,631 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-14T23:42Z] INFO  16:42:52,632 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:42Z] INFO  16:42:52,632 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-14T23:42Z] INFO  16:42:52,633 MicroScheduler -   -> 17064 reads (1.16% of total) failing MappingQualityZeroFilter
[2016-04-14T23:42Z] INFO  16:42:52,633 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:42Z] INFO  16:42:52,634 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-14T23:42Z] INFO  16:42:52,634 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-14T23:42Z] INFO  16:42:52,724 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:42Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-X_128582278_144329181-prep.bam
[2016-04-14T23:42Z] INFO  16:42:53,329 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:42Z] GATK: realign ('X', 144337190, 155270560) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:42Z] GATK pre-alignment ('1', 108994811, 143767848) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-14T23:42Z] INFO  16:42:54,000 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:42Z] GATK: realign ('19', 0, 15509577) : R14-18102_kapa-NGv3-PE100-NGv3
[2016-04-14T23:42Z] INFO  16:42:56,041 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:42Z] INFO  16:42:56,044 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:42Z] INFO  16:42:56,045 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:42Z] INFO  16:42:56,045 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:42Z] INFO  16:42:56,050 HelpFormatter - Program Args: -T PrintReads -L 1:108994812-143767848 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/1/tx/tmpuWZecy/R14-18105_kapa-NGv3-PE100-NGv3-sort-1_108994811_143767848-prep-prealign.bam
[2016-04-14T23:42Z] INFO  16:42:56,070 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:42Z] INFO  16:42:56,070 HelpFormatter - Date/Time: 2016/04/14 16:42:56
[2016-04-14T23:42Z] INFO  16:42:56,070 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:42Z] INFO  16:42:56,070 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:42Z] INFO  16:42:56,328 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:42Z] INFO  16:42:56,516 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:42Z] INFO  16:42:56,520 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:42Z] INFO  16:42:56,521 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:42Z] INFO  16:42:56,522 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:42Z] INFO  16:42:56,526 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/X/R14-18102_kapa-NGv3-PE100-NGv3-sort-X_144337190_155270560-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/X/R14-18102_kapa-NGv3-PE100-NGv3-sort-X_144337190_155270560-prep-prealign-realign.intervals -L X:144337191-155270560 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/X/tx/tmpIDwrLF/R14-18102_kapa-NGv3-PE100-NGv3-sort-X_144337190_155270560-prep.bam
[2016-04-14T23:42Z] INFO  16:42:56,538 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:42Z] INFO  16:42:56,553 HelpFormatter - Date/Time: 2016/04/14 16:42:56
[2016-04-14T23:42Z] INFO  16:42:56,554 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:42Z] INFO  16:42:56,555 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:42Z] INFO  16:42:56,793 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:42Z] INFO  16:42:56,796 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:42Z] INFO  16:42:56,796 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:42Z] INFO  16:42:56,797 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:42Z] INFO  16:42:56,801 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/19/R14-18102_kapa-NGv3-PE100-NGv3-sort-19_0_15509577-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/19/R14-18102_kapa-NGv3-PE100-NGv3-sort-19_0_15509577-prep-prealign-realign.intervals -L 19:1-15509577 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/19/tx/tmpXRd78I/R14-18102_kapa-NGv3-PE100-NGv3-sort-19_0_15509577-prep.bam
[2016-04-14T23:42Z] INFO  16:42:56,812 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:42Z] INFO  16:42:56,821 HelpFormatter - Date/Time: 2016/04/14 16:42:56
[2016-04-14T23:42Z] INFO  16:42:56,822 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:42Z] INFO  16:42:56,822 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:42Z] INFO  16:42:56,838 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:42Z] INFO  16:42:56,962 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:42Z] INFO  16:42:56,972 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:42Z] INFO  16:42:57,046 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-14T23:42Z] INFO  16:42:57,097 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:42Z] INFO  16:42:57,222 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:42Z] INFO  16:42:57,232 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:42Z] INFO  16:42:57,299 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-14T23:42Z] INFO  16:42:57,428 IntervalUtils - Processing 10933370 bp from intervals
[2016-04-14T23:42Z] INFO  16:42:57,435 ProgressMeter -     22:41633740    300005.0    30.0 s     100.0 s       63.4%    47.0 s      17.0 s
[2016-04-14T23:42Z] WARN  16:42:57,436 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:42Z] INFO  16:42:57,467 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-14T23:42Z] INFO  16:42:57,536 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:42Z] INFO  16:42:57,545 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:42Z] INFO  16:42:57,577 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:42Z] INFO  16:42:57,618 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-14T23:42Z] INFO  16:42:57,636 IntervalUtils - Processing 15509577 bp from intervals
[2016-04-14T23:42Z] INFO  16:42:57,639 IntervalUtils - Processing 34773037 bp from intervals
[2016-04-14T23:42Z] WARN  16:42:57,641 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:42Z] INFO  16:42:57,668 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:42Z] INFO  16:42:57,670 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:42Z] INFO  16:42:57,670 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:42Z] INFO  16:42:57,671 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:42Z] INFO  16:42:57,733 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:42Z] INFO  16:42:57,733 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:42Z] INFO  16:42:57,788 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:42Z] INFO  16:42:57,901 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:42Z] INFO  16:42:57,953 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:42Z] INFO  16:42:57,954 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:42Z] INFO  16:42:57,955 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:42Z] INFO  16:42:57,956 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:42Z] INFO  16:42:58,016 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:42Z] INFO  16:42:58,017 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:42Z] INFO  16:42:58,017 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:42Z] INFO  16:42:58,017 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:42Z] INFO  16:42:58,052 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:42Z] INFO  16:42:58,164 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:42Z] INFO  16:42:58,304 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:42Z] INFO  16:42:58,372 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:42Z] INFO  16:42:58,410 ProgressMeter -     22:23605823    400004.0    30.0 s      75.0 s       47.3%    63.0 s      33.0 s
[2016-04-14T23:43Z] INFO  16:43:01,296 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@41fd9d8e
[2016-04-14T23:43Z] INFO  16:43:01,400 ProgressMeter -            done    184618.0    27.0 s       2.5 m      100.0%    27.0 s       0.0 s
[2016-04-14T23:43Z] INFO  16:43:01,401 ProgressMeter - Total runtime 27.76 secs, 0.46 min, 0.01 hours
[2016-04-14T23:43Z] INFO  16:43:01,401 MicroScheduler - 142 reads were filtered out during the traversal out of approximately 184760 total reads (0.08%)
[2016-04-14T23:43Z] INFO  16:43:01,401 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:43Z] INFO  16:43:01,402 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:43Z] INFO  16:43:01,402 MicroScheduler -   -> 142 reads (0.08% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:43Z] INFO  16:43:02,490 ProgressMeter -     19:45323875   1000016.0    64.0 s      64.0 s       91.6%    69.0 s       5.0 s
[2016-04-14T23:43Z] INFO  16:43:02,791 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:43Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-1_62231950_77749296-prep-prealign.bam
[2016-04-14T23:43Z] GATK RealignerTargetCreator: R14-18105_kapa-NGv3-PE100-NGv3-sort-1_62231950_77749296-prep-prealign.bam 1:62231951-77749296
[2016-04-14T23:43Z] GATK: RealignerTargetCreator
[2016-04-14T23:43Z] INFO  16:43:03,460 ProgressMeter -      1:55197231    200004.0    30.0 s       2.5 m       54.7%    54.0 s      24.0 s
[2016-04-14T23:43Z] INFO  16:43:06,173 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:43Z] INFO  16:43:06,176 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:43Z] INFO  16:43:06,176 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:43Z] INFO  16:43:06,177 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:43Z] INFO  16:43:06,182 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/1/R14-18105_kapa-NGv3-PE100-NGv3-sort-1_62231950_77749296-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/1/tx/tmpYF97R8/R14-18105_kapa-NGv3-PE100-NGv3-sort-1_62231950_77749296-prep-prealign-realign.intervals -l INFO -L 1:62231951-77749296 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-14T23:43Z] INFO  16:43:06,202 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:43Z] INFO  16:43:06,203 HelpFormatter - Date/Time: 2016/04/14 16:43:06
[2016-04-14T23:43Z] INFO  16:43:06,203 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:43Z] INFO  16:43:06,208 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:43Z] INFO  16:43:06,293 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:43Z] INFO  16:43:06,480 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-14T23:43Z] INFO  16:43:06,500 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:43Z] INFO  16:43:06,568 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-14T23:43Z] INFO  16:43:06,694 ProgressMeter -            done    651637.0    39.0 s      60.0 s      100.0%    39.0 s       0.0 s
[2016-04-14T23:43Z] INFO  16:43:06,694 ProgressMeter - Total runtime 39.26 secs, 0.65 min, 0.01 hours
[2016-04-14T23:43Z] INFO  16:43:06,698 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 651637 total reads (0.00%)
[2016-04-14T23:43Z] INFO  16:43:06,698 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:43Z] INFO  16:43:06,699 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:43Z] INFO  16:43:06,699 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:43Z] INFO  16:43:06,926 IntervalUtils - Processing 15517346 bp from intervals
[2016-04-14T23:43Z] WARN  16:43:06,931 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:43Z] INFO  16:43:07,000 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:43Z] INFO  16:43:07,062 ProgressMeter -      1:10367196    400008.0    61.0 s       2.5 m       66.7%    91.0 s      30.0 s
[2016-04-14T23:43Z] INFO  16:43:07,166 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:43Z] INFO  16:43:07,167 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:43Z] INFO  16:43:07,168 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:43Z] INFO  16:43:07,168 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-14T23:43Z] INFO  16:43:08,084 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:43Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-22_31796605_47308085-prep.bam
[2016-04-14T23:43Z] INFO  16:43:08,661 ProgressMeter -            done   1179943.0    70.0 s      59.0 s      100.0%    70.0 s       0.0 s
[2016-04-14T23:43Z] INFO  16:43:08,662 ProgressMeter - Total runtime 70.55 secs, 1.18 min, 0.02 hours
[2016-04-14T23:43Z] INFO  16:43:08,666 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 1179943 total reads (0.00%)
[2016-04-14T23:43Z] INFO  16:43:08,668 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:43Z] INFO  16:43:08,668 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:43Z] INFO  16:43:08,669 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:43Z] INFO  16:43:10,157 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@7172f77a
[2016-04-14T23:43Z] INFO  16:43:10,230 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:43Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-19_31038849_46627578-prep.bam
[2016-04-14T23:43Z] INFO  16:43:10,332 ProgressMeter -            done    310314.0    36.0 s     118.0 s      100.0%    36.0 s       0.0 s
[2016-04-14T23:43Z] INFO  16:43:10,333 ProgressMeter - Total runtime 36.91 secs, 0.62 min, 0.01 hours
[2016-04-14T23:43Z] INFO  16:43:10,333 MicroScheduler - 168 reads were filtered out during the traversal out of approximately 310482 total reads (0.05%)
[2016-04-14T23:43Z] INFO  16:43:10,334 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:43Z] INFO  16:43:10,334 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:43Z] INFO  16:43:10,334 MicroScheduler -   -> 168 reads (0.05% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:43Z] GATK pre-alignment ('1', 143897546, 159410511) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-14T23:43Z] INFO  16:43:11,587 ProgressMeter -      1:23406151    400007.0    60.0 s       2.5 m       50.3%   119.0 s      59.0 s
[2016-04-14T23:43Z] INFO  16:43:11,740 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:43Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-1_46715671_62228851-prep-prealign.bam
[2016-04-14T23:43Z] INFO  16:43:12,325 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@7172f77a
[2016-04-14T23:43Z] INFO  16:43:12,511 ProgressMeter -            done    175559.0    23.0 s       2.2 m      100.0%    23.0 s       0.0 s
[2016-04-14T23:43Z] INFO  16:43:12,512 ProgressMeter - Total runtime 23.10 secs, 0.38 min, 0.01 hours
[2016-04-14T23:43Z] INFO  16:43:12,513 MicroScheduler - 132 reads were filtered out during the traversal out of approximately 175691 total reads (0.08%)
[2016-04-14T23:43Z] INFO  16:43:12,514 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:43Z] INFO  16:43:12,515 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:43Z] INFO  16:43:12,516 MicroScheduler -   -> 132 reads (0.08% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:43Z] GATK RealignerTargetCreator: R14-18105_kapa-NGv3-PE100-NGv3-sort-1_46715671_62228851-prep-prealign.bam 1:46715672-62228851
[2016-04-14T23:43Z] GATK: RealignerTargetCreator
[2016-04-14T23:43Z] INFO  16:43:12,994 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:43Z] INFO  16:43:12,998 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:43Z] INFO  16:43:12,998 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:43Z] INFO  16:43:12,999 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:43Z] INFO  16:43:13,004 HelpFormatter - Program Args: -T PrintReads -L 1:143897547-159410511 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/1/tx/tmpft7kg1/R14-18105_kapa-NGv3-PE100-NGv3-sort-1_143897546_159410511-prep-prealign.bam
[2016-04-14T23:43Z] INFO  16:43:13,014 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:43Z] INFO  16:43:13,015 HelpFormatter - Date/Time: 2016/04/14 16:43:12
[2016-04-14T23:43Z] INFO  16:43:13,015 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:43Z] INFO  16:43:13,015 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:43Z] INFO  16:43:13,179 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:43Z] INFO  16:43:13,524 ProgressMeter -      X:54328368    400024.0    31.0 s      79.0 s       48.0%    64.0 s      33.0 s
[2016-04-14T23:43Z] INFO  16:43:14,128 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:43Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-1_93298945_108993401-prep-prealign.bam
[2016-04-14T23:43Z] INFO  16:43:14,378 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-14T23:43Z] GATK pre-alignment ('1', 159504867, 175046963) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-14T23:43Z] INFO  16:43:14,440 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:43Z] INFO  16:43:14,450 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:43Z] INFO  16:43:14,482 ProgressMeter -            done    779542.0    46.0 s      59.0 s      100.0%    46.0 s       0.0 s
[2016-04-14T23:43Z] INFO  16:43:14,484 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.03
[2016-04-14T23:43Z] INFO  16:43:14,483 ProgressMeter - Total runtime 46.09 secs, 0.77 min, 0.01 hours
[2016-04-14T23:43Z] INFO  16:43:14,488 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 779542 total reads (0.00%)
[2016-04-14T23:43Z] INFO  16:43:14,489 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:43Z] INFO  16:43:14,489 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:43Z] INFO  16:43:14,489 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:43Z] INFO  16:43:14,500 IntervalUtils - Processing 15512965 bp from intervals
[2016-04-14T23:43Z] INFO  16:43:14,569 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:43Z] INFO  16:43:14,896 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:43Z] INFO  16:43:14,897 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:43Z] INFO  16:43:14,898 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:43Z] INFO  16:43:14,899 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:43Z] GATK RealignerTargetCreator: R14-18105_kapa-NGv3-PE100-NGv3-sort-1_93298945_108993401-prep-prealign.bam 1:93298946-108993401
[2016-04-14T23:43Z] GATK: RealignerTargetCreator
[2016-04-14T23:43Z] INFO  16:43:14,937 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:43Z] INFO  16:43:15,122 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:43Z] INFO  16:43:15,570 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:43Z] INFO  16:43:15,573 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:43Z] INFO  16:43:15,573 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:43Z] INFO  16:43:15,573 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:43Z] INFO  16:43:15,577 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/1/R14-18105_kapa-NGv3-PE100-NGv3-sort-1_46715671_62228851-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/1/tx/tmpxxJCC8/R14-18105_kapa-NGv3-PE100-NGv3-sort-1_46715671_62228851-prep-prealign-realign.intervals -l INFO -L 1:46715672-62228851 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-14T23:43Z] INFO  16:43:15,592 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:43Z] INFO  16:43:15,593 HelpFormatter - Date/Time: 2016/04/14 16:43:15
[2016-04-14T23:43Z] INFO  16:43:15,593 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:43Z] INFO  16:43:15,594 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:43Z] INFO  16:43:15,703 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:43Z] INFO  16:43:15,933 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-14T23:43Z] INFO  16:43:15,965 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:43Z] INFO  16:43:16,056 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.09
[2016-04-14T23:43Z] INFO  16:43:16,347 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@7172f77a
[2016-04-14T23:43Z] INFO  16:43:16,364 IntervalUtils - Processing 15513180 bp from intervals
[2016-04-14T23:43Z] WARN  16:43:16,369 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:43Z] INFO  16:43:16,437 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:43Z] INFO  16:43:16,446 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:43Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-22_16266928_31795711-prep.bam
[2016-04-14T23:43Z] INFO  16:43:16,492 ProgressMeter -            done    583221.0    34.0 s      59.0 s      100.0%    34.0 s       0.0 s
[2016-04-14T23:43Z] INFO  16:43:16,492 ProgressMeter - Total runtime 34.93 secs, 0.58 min, 0.01 hours
[2016-04-14T23:43Z] INFO  16:43:16,496 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 583221 total reads (0.00%)
[2016-04-14T23:43Z] INFO  16:43:16,496 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:43Z] INFO  16:43:16,496 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:43Z] INFO  16:43:16,497 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:43Z] INFO  16:43:16,498 ProgressMeter -            done    176456.0    28.0 s       2.7 m      100.0%    28.0 s       0.0 s
[2016-04-14T23:43Z] INFO  16:43:16,498 ProgressMeter - Total runtime 28.11 secs, 0.47 min, 0.01 hours
[2016-04-14T23:43Z] INFO  16:43:16,499 MicroScheduler - 117 reads were filtered out during the traversal out of approximately 176573 total reads (0.07%)
[2016-04-14T23:43Z] INFO  16:43:16,500 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:43Z] INFO  16:43:16,500 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:43Z] INFO  16:43:16,500 MicroScheduler -   -> 117 reads (0.07% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:43Z] INFO  16:43:16,659 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:43Z] INFO  16:43:16,660 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:43Z] INFO  16:43:16,661 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:43Z] INFO  16:43:16,662 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-14T23:43Z] INFO  16:43:17,346 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:43Z] INFO  16:43:17,349 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:43Z] INFO  16:43:17,350 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:43Z] INFO  16:43:17,350 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:43Z] INFO  16:43:17,354 HelpFormatter - Program Args: -T PrintReads -L 1:159504868-175046963 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/1/tx/tmplBzOnK/R14-18105_kapa-NGv3-PE100-NGv3-sort-1_159504867_175046963-prep-prealign.bam
[2016-04-14T23:43Z] INFO  16:43:17,366 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:43Z] INFO  16:43:17,366 HelpFormatter - Date/Time: 2016/04/14 16:43:17
[2016-04-14T23:43Z] INFO  16:43:17,366 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:43Z] INFO  16:43:17,366 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:43Z] INFO  16:43:17,596 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:43Z] INFO  16:43:17,840 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:43Z] INFO  16:43:17,868 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:43Z] INFO  16:43:17,871 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:43Z] INFO  16:43:17,872 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:43Z] INFO  16:43:17,872 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:43Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-1_77752625_93297674-prep-prealign.bam
[2016-04-14T23:43Z] INFO  16:43:17,877 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/1/R14-18105_kapa-NGv3-PE100-NGv3-sort-1_93298945_108993401-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/1/tx/tmppYjT0Z/R14-18105_kapa-NGv3-PE100-NGv3-sort-1_93298945_108993401-prep-prealign-realign.intervals -l INFO -L 1:93298946-108993401 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-14T23:43Z] INFO  16:43:17,888 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:43Z] INFO  16:43:17,889 HelpFormatter - Date/Time: 2016/04/14 16:43:17
[2016-04-14T23:43Z] INFO  16:43:17,890 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:43Z] INFO  16:43:17,890 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:43Z] INFO  16:43:17,967 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:43Z] INFO  16:43:18,005 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:43Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-X_46712910_62570698-prep.bam
[2016-04-14T23:43Z] INFO  16:43:18,178 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-14T23:43Z] INFO  16:43:18,188 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:43Z] INFO  16:43:18,239 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-14T23:43Z] GATK RealignerTargetCreator: R14-18105_kapa-NGv3-PE100-NGv3-sort-1_77752625_93297674-prep-prealign.bam 1:77752626-93297674
[2016-04-14T23:43Z] GATK: RealignerTargetCreator
[2016-04-14T23:43Z] INFO  16:43:18,561 IntervalUtils - Processing 15694456 bp from intervals
[2016-04-14T23:43Z] WARN  16:43:18,580 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:43Z] INFO  16:43:18,673 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:43Z] INFO  16:43:18,777 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-14T23:43Z] INFO  16:43:18,856 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:43Z] INFO  16:43:18,866 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:43Z] INFO  16:43:18,891 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:43Z] INFO  16:43:18,892 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:43Z] INFO  16:43:18,893 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:43Z] INFO  16:43:18,894 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-14T23:43Z] INFO  16:43:18,934 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-14T23:43Z] INFO  16:43:18,951 IntervalUtils - Processing 15542096 bp from intervals
[2016-04-14T23:43Z] INFO  16:43:19,049 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:43Z] GATK pre-alignment ('1', 175048468, 192127886) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-14T23:43Z] INFO  16:43:19,283 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:43Z] INFO  16:43:19,285 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:43Z] INFO  16:43:19,286 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:43Z] INFO  16:43:19,286 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:43Z] INFO  16:43:19,301 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:43Z] INFO  16:43:19,632 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:43Z] GATK pre-alignment ('1', 192128349, 207640257) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-14T23:43Z] INFO  16:43:20,293 ProgressMeter -     19:56466351   1000019.0    64.0 s      64.0 s       78.7%    81.0 s      17.0 s
[2016-04-14T23:43Z] INFO  16:43:21,267 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:43Z] INFO  16:43:21,269 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:43Z] INFO  16:43:21,270 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:43Z] INFO  16:43:21,270 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:43Z] INFO  16:43:21,284 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/1/R14-18105_kapa-NGv3-PE100-NGv3-sort-1_77752625_93297674-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/1/tx/tmpMd8VhB/R14-18105_kapa-NGv3-PE100-NGv3-sort-1_77752625_93297674-prep-prealign-realign.intervals -l INFO -L 1:77752626-93297674 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-14T23:43Z] INFO  16:43:21,298 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:43Z] INFO  16:43:21,299 HelpFormatter - Date/Time: 2016/04/14 16:43:21
[2016-04-14T23:43Z] INFO  16:43:21,299 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:43Z] INFO  16:43:21,300 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:43Z] INFO  16:43:21,475 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:43Z] INFO  16:43:21,740 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-14T23:43Z] INFO  16:43:21,750 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:43Z] INFO  16:43:21,790 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.04
[2016-04-14T23:43Z] INFO  16:43:22,015 IntervalUtils - Processing 15545049 bp from intervals
[2016-04-14T23:43Z] WARN  16:43:22,021 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:43Z] INFO  16:43:22,038 ProgressMeter -      1:39946794    400004.0    61.0 s       2.5 m       56.4%   108.0 s      47.0 s
[2016-04-14T23:43Z] INFO  16:43:22,076 ProgressMeter -            done    370973.0    24.0 s      65.0 s       99.9%    24.0 s       0.0 s
[2016-04-14T23:43Z] INFO  16:43:22,077 ProgressMeter - Total runtime 24.41 secs, 0.41 min, 0.01 hours
[2016-04-14T23:43Z] INFO  16:43:22,080 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 370973 total reads (0.00%)
[2016-04-14T23:43Z] INFO  16:43:22,081 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:43Z] INFO  16:43:22,081 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:43Z] INFO  16:43:22,081 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:43Z] INFO  16:43:22,092 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:43Z] INFO  16:43:22,326 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:43Z] INFO  16:43:22,328 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:43Z] INFO  16:43:22,329 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:43Z] INFO  16:43:22,329 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-14T23:43Z] INFO  16:43:22,332 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:43Z] INFO  16:43:22,335 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:43Z] INFO  16:43:22,335 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:43Z] INFO  16:43:22,336 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:43Z] INFO  16:43:22,340 HelpFormatter - Program Args: -T PrintReads -L 1:175048469-192127886 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/1/tx/tmpb9P7es/R14-18105_kapa-NGv3-PE100-NGv3-sort-1_175048468_192127886-prep-prealign.bam
[2016-04-14T23:43Z] INFO  16:43:22,359 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:43Z] INFO  16:43:22,360 HelpFormatter - Date/Time: 2016/04/14 16:43:22
[2016-04-14T23:43Z] INFO  16:43:22,360 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:43Z] INFO  16:43:22,361 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:43Z] INFO  16:43:22,520 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:43Z] INFO  16:43:22,891 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:43Z] INFO  16:43:22,894 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:43Z] INFO  16:43:22,895 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:43Z] INFO  16:43:22,895 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:43Z] INFO  16:43:22,900 HelpFormatter - Program Args: -T PrintReads -L 1:192128350-207640257 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/1/tx/tmpsIsYF6/R14-18105_kapa-NGv3-PE100-NGv3-sort-1_192128349_207640257-prep-prealign.bam
[2016-04-14T23:43Z] INFO  16:43:22,914 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:43Z] INFO  16:43:22,915 HelpFormatter - Date/Time: 2016/04/14 16:43:22
[2016-04-14T23:43Z] INFO  16:43:22,915 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:43Z] INFO  16:43:22,916 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:43Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-nochrom-prep.bam
[2016-04-14T23:43Z] INFO  16:43:23,181 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:43Z] GATK pre-alignment ('1', 207641871, 223156451) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-14T23:43Z] INFO  16:43:23,463 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:43Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-X_144337190_155270560-prep.bam
[2016-04-14T23:43Z] INFO  16:43:23,567 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-14T23:43Z] INFO  16:43:23,642 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:43Z] INFO  16:43:23,650 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:43Z] INFO  16:43:23,686 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.04
[2016-04-14T23:43Z] INFO  16:43:23,700 IntervalUtils - Processing 17079418 bp from intervals
[2016-04-14T23:43Z] INFO  16:43:23,819 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:43Z] INFO  16:43:23,981 ProgressMeter -            done   1.5517346E7    16.0 s       1.0 s      100.0%    16.0 s       0.0 s
[2016-04-14T23:43Z] INFO  16:43:23,982 ProgressMeter - Total runtime 16.81 secs, 0.28 min, 0.00 hours
[2016-04-14T23:43Z] INFO  16:43:23,986 MicroScheduler - 15975 reads were filtered out during the traversal out of approximately 185781 total reads (8.60%)
[2016-04-14T23:43Z] INFO  16:43:23,987 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:43Z] INFO  16:43:23,988 MicroScheduler -   -> 530 reads (0.29% of total) failing BadMateFilter
[2016-04-14T23:43Z] INFO  16:43:23,988 MicroScheduler -   -> 14667 reads (7.89% of total) failing DuplicateReadFilter
[2016-04-14T23:43Z] INFO  16:43:23,989 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-14T23:43Z] INFO  16:43:23,990 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:43Z] INFO  16:43:23,990 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-14T23:43Z] INFO  16:43:23,991 MicroScheduler -   -> 778 reads (0.42% of total) failing MappingQualityZeroFilter
[2016-04-14T23:43Z] INFO  16:43:23,991 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:43Z] INFO  16:43:23,992 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-14T23:43Z] INFO  16:43:23,992 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-14T23:43Z] INFO  16:43:24,054 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:43Z] INFO  16:43:24,055 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:43Z] INFO  16:43:24,056 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:43Z] INFO  16:43:24,057 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:43Z] INFO  16:43:24,091 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:43Z] INFO  16:43:24,222 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:43Z] INFO  16:43:24,354 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-14T23:43Z] INFO  16:43:24,423 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:43Z] INFO  16:43:24,432 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:43Z] INFO  16:43:24,477 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.04
[2016-04-14T23:43Z] INFO  16:43:24,499 IntervalUtils - Processing 15511908 bp from intervals
[2016-04-14T23:43Z] INFO  16:43:24,585 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:43Z] INFO  16:43:24,846 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:43Z] INFO  16:43:24,847 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:43Z] INFO  16:43:24,848 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:43Z] INFO  16:43:24,849 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:43Z] INFO  16:43:24,862 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:43Z] GATK pre-alignment ('1', 223162737, 240072524) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-14T23:43Z] INFO  16:43:25,037 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:43Z] INFO  16:43:25,426 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:43Z] GATK: realign ('1', 62231950, 77749296) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-14T23:43Z] INFO  16:43:26,189 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:43Z] INFO  16:43:26,192 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:43Z] INFO  16:43:26,193 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:43Z] INFO  16:43:26,194 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:43Z] INFO  16:43:26,199 HelpFormatter - Program Args: -T PrintReads -L 1:207641872-223156451 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/1/tx/tmpF4Te0R/R14-18105_kapa-NGv3-PE100-NGv3-sort-1_207641871_223156451-prep-prealign.bam
[2016-04-14T23:43Z] INFO  16:43:26,235 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:43Z] INFO  16:43:26,236 HelpFormatter - Date/Time: 2016/04/14 16:43:26
[2016-04-14T23:43Z] INFO  16:43:26,237 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:43Z] INFO  16:43:26,237 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:43Z] INFO  16:43:26,423 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:43Z] INFO  16:43:27,638 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-14T23:43Z] INFO  16:43:27,726 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:43Z] INFO  16:43:27,735 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:43Z] INFO  16:43:27,786 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-14T23:43Z] INFO  16:43:27,802 IntervalUtils - Processing 15514580 bp from intervals
[2016-04-14T23:43Z] INFO  16:43:27,877 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:43Z] INFO  16:43:27,882 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:43Z] INFO  16:43:27,886 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:43Z] INFO  16:43:27,886 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:43Z] INFO  16:43:27,887 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:43Z] INFO  16:43:27,892 HelpFormatter - Program Args: -T PrintReads -L 1:223162738-240072524 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/1/tx/tmpBIl4Ua/R14-18105_kapa-NGv3-PE100-NGv3-sort-1_223162737_240072524-prep-prealign.bam
[2016-04-14T23:43Z] INFO  16:43:27,900 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:43Z] INFO  16:43:27,900 HelpFormatter - Date/Time: 2016/04/14 16:43:27
[2016-04-14T23:43Z] INFO  16:43:27,901 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:43Z] INFO  16:43:27,901 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:43Z] INFO  16:43:28,077 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:43Z] INFO  16:43:28,105 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:43Z] INFO  16:43:28,106 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:43Z] INFO  16:43:28,107 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:43Z] INFO  16:43:28,108 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:43Z] INFO  16:43:28,131 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:43Z] INFO  16:43:28,288 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:43Z] INFO  16:43:28,383 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:43Z] INFO  16:43:28,387 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:43Z] INFO  16:43:28,387 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:43Z] INFO  16:43:28,388 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:43Z] INFO  16:43:28,392 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/1/R14-18105_kapa-NGv3-PE100-NGv3-sort-1_62231950_77749296-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/1/R14-18105_kapa-NGv3-PE100-NGv3-sort-1_62231950_77749296-prep-prealign-realign.intervals -L 1:62231951-77749296 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/1/tx/tmpnecWPz/R14-18105_kapa-NGv3-PE100-NGv3-sort-1_62231950_77749296-prep.bam
[2016-04-14T23:43Z] INFO  16:43:28,402 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:43Z] INFO  16:43:28,412 HelpFormatter - Date/Time: 2016/04/14 16:43:28
[2016-04-14T23:43Z] INFO  16:43:28,413 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:43Z] INFO  16:43:28,413 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:43Z] INFO  16:43:28,595 ProgressMeter -     1:111969190    100002.0    30.0 s       5.1 m        8.6%     5.8 m       5.3 m
[2016-04-14T23:43Z] INFO  16:43:28,600 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:43Z] INFO  16:43:28,708 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:43Z] INFO  16:43:28,718 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:43Z] INFO  16:43:28,784 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-14T23:43Z] INFO  16:43:29,244 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-14T23:43Z] INFO  16:43:29,258 IntervalUtils - Processing 15517346 bp from intervals
[2016-04-14T23:43Z] WARN  16:43:29,263 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:43Z] INFO  16:43:29,286 ProgressMeter -      19:3909748    300004.0    31.0 s     104.0 s       25.2%     2.0 m      91.0 s
[2016-04-14T23:43Z] INFO  16:43:29,312 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:43Z] INFO  16:43:29,321 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:43Z] INFO  16:43:29,354 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:43Z] INFO  16:43:29,377 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-14T23:43Z] INFO  16:43:29,402 IntervalUtils - Processing 16909787 bp from intervals
[2016-04-14T23:43Z] INFO  16:43:29,465 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:43Z] INFO  16:43:29,467 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:43Z] INFO  16:43:29,467 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:43Z] INFO  16:43:29,468 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:43Z] INFO  16:43:29,490 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:43Z] INFO  16:43:29,696 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:43Z] INFO  16:43:29,823 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:43Z] INFO  16:43:29,824 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:43Z] INFO  16:43:29,824 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:43Z] INFO  16:43:29,824 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:43Z] INFO  16:43:29,857 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:43Z] INFO  16:43:29,880 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:43Z] INFO  16:43:30,067 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:43Z] INFO  16:43:32,451 ProgressMeter -            done   1302696.0    76.0 s      58.0 s       99.6%    76.0 s       0.0 s
[2016-04-14T23:43Z] INFO  16:43:32,452 ProgressMeter - Total runtime 76.39 secs, 1.27 min, 0.02 hours
[2016-04-14T23:43Z] INFO  16:43:32,455 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 1302696 total reads (0.00%)
[2016-04-14T23:43Z] INFO  16:43:32,456 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:43Z] INFO  16:43:32,456 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:43Z] INFO  16:43:32,456 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:43Z] INFO  16:43:34,093 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:43Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-19_46627881_59128983-prep.bam
[2016-04-14T23:43Z] INFO  16:43:35,820 ProgressMeter -            done   1.5694456E7    16.0 s       1.0 s      100.0%    16.0 s       0.0 s
[2016-04-14T23:43Z] INFO  16:43:35,820 ProgressMeter - Total runtime 16.93 secs, 0.28 min, 0.00 hours
[2016-04-14T23:43Z] INFO  16:43:35,824 MicroScheduler - 44237 reads were filtered out during the traversal out of approximately 176646 total reads (25.04%)
[2016-04-14T23:43Z] INFO  16:43:35,824 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:43Z] INFO  16:43:35,824 MicroScheduler -   -> 394 reads (0.22% of total) failing BadMateFilter
[2016-04-14T23:43Z] INFO  16:43:35,825 MicroScheduler -   -> 11183 reads (6.33% of total) failing DuplicateReadFilter
[2016-04-14T23:43Z] INFO  16:43:35,826 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-14T23:43Z] INFO  16:43:35,826 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:43Z] INFO  16:43:35,826 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-14T23:43Z] INFO  16:43:35,826 MicroScheduler -   -> 32660 reads (18.49% of total) failing MappingQualityZeroFilter
[2016-04-14T23:43Z] INFO  16:43:35,827 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:43Z] INFO  16:43:35,827 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-14T23:43Z] INFO  16:43:35,827 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-14T23:43Z] INFO  16:43:37,005 ProgressMeter -            done   1.551318E7    20.0 s       1.0 s      100.0%    20.0 s       0.0 s
[2016-04-14T23:43Z] INFO  16:43:37,006 ProgressMeter - Total runtime 20.35 secs, 0.34 min, 0.01 hours
[2016-04-14T23:43Z] INFO  16:43:37,012 MicroScheduler - 27680 reads were filtered out during the traversal out of approximately 312308 total reads (8.86%)
[2016-04-14T23:43Z] INFO  16:43:37,013 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:43Z] INFO  16:43:37,013 MicroScheduler -   -> 724 reads (0.23% of total) failing BadMateFilter
[2016-04-14T23:43Z] INFO  16:43:37,014 MicroScheduler -   -> 24302 reads (7.78% of total) failing DuplicateReadFilter
[2016-04-14T23:43Z] INFO  16:43:37,014 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-14T23:43Z] INFO  16:43:37,014 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:43Z] INFO  16:43:37,015 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-14T23:43Z] INFO  16:43:37,015 MicroScheduler -   -> 2654 reads (0.85% of total) failing MappingQualityZeroFilter
[2016-04-14T23:43Z] INFO  16:43:37,015 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:43Z] INFO  16:43:37,016 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-14T23:43Z] INFO  16:43:37,016 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-14T23:43Z] INFO  16:43:37,095 ProgressMeter -      1:13646179    700016.0    91.0 s       2.2 m       87.8%   103.0 s      12.0 s
[2016-04-14T23:43Z] INFO  16:43:37,298 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:43Z] GATK: realign ('1', 93298945, 108993401) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-14T23:43Z] INFO  16:43:38,531 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:43Z] GATK: realign ('1', 46715671, 62228851) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-14T23:43Z] GATK pre-alignment ('1', 240255409, 249250621) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-14T23:43Z] INFO  16:43:39,502 ProgressMeter -            done   1.5545049E7    17.0 s       1.0 s      100.0%    17.0 s       0.0 s
[2016-04-14T23:43Z] INFO  16:43:39,503 ProgressMeter - Total runtime 17.18 secs, 0.29 min, 0.00 hours
[2016-04-14T23:43Z] INFO  16:43:39,508 MicroScheduler - 14546 reads were filtered out during the traversal out of approximately 177591 total reads (8.19%)
[2016-04-14T23:43Z] INFO  16:43:39,510 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:43Z] INFO  16:43:39,510 MicroScheduler -   -> 510 reads (0.29% of total) failing BadMateFilter
[2016-04-14T23:43Z] INFO  16:43:39,511 MicroScheduler -   -> 13407 reads (7.55% of total) failing DuplicateReadFilter
[2016-04-14T23:43Z] INFO  16:43:39,512 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-14T23:43Z] INFO  16:43:39,513 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:43Z] INFO  16:43:39,514 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-14T23:43Z] INFO  16:43:39,514 MicroScheduler -   -> 629 reads (0.35% of total) failing MappingQualityZeroFilter
[2016-04-14T23:43Z] INFO  16:43:39,515 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:43Z] INFO  16:43:39,516 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-14T23:43Z] INFO  16:43:39,516 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-14T23:43Z] INFO  16:43:40,072 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:43Z] INFO  16:43:40,086 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:43Z] INFO  16:43:40,087 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:43Z] INFO  16:43:40,087 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:43Z] INFO  16:43:40,093 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/1/R14-18105_kapa-NGv3-PE100-NGv3-sort-1_93298945_108993401-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/1/R14-18105_kapa-NGv3-PE100-NGv3-sort-1_93298945_108993401-prep-prealign-realign.intervals -L 1:93298946-108993401 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/1/tx/tmpJbFP7X/R14-18105_kapa-NGv3-PE100-NGv3-sort-1_93298945_108993401-prep.bam
[2016-04-14T23:43Z] INFO  16:43:40,123 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:43Z] INFO  16:43:40,124 HelpFormatter - Date/Time: 2016/04/14 16:43:40
[2016-04-14T23:43Z] INFO  16:43:40,125 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:43Z] INFO  16:43:40,125 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:43Z] INFO  16:43:40,149 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@41fd9d8e
[2016-04-14T23:43Z] INFO  16:43:40,237 ProgressMeter -            done    815768.0    94.0 s     115.0 s      100.0%    94.0 s       0.0 s
[2016-04-14T23:43Z] INFO  16:43:40,238 ProgressMeter - Total runtime 94.35 secs, 1.57 min, 0.03 hours
[2016-04-14T23:43Z] INFO  16:43:40,238 MicroScheduler - 314 reads were filtered out during the traversal out of approximately 816082 total reads (0.04%)
[2016-04-14T23:43Z] INFO  16:43:40,239 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:43Z] INFO  16:43:40,239 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:43Z] INFO  16:43:40,240 MicroScheduler -   -> 314 reads (0.04% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:43Z] INFO  16:43:40,368 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:43Z] INFO  16:43:40,458 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:43Z] INFO  16:43:40,469 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:43Z] INFO  16:43:40,530 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-14T23:43Z] INFO  16:43:40,885 IntervalUtils - Processing 15694456 bp from intervals
[2016-04-14T23:43Z] WARN  16:43:40,890 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:43Z] INFO  16:43:41,022 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:43Z] INFO  16:43:41,041 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:43Z] GATK: realign ('1', 77752625, 93297674) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-14T23:43Z] INFO  16:43:41,117 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:43Z] INFO  16:43:41,118 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:43Z] INFO  16:43:41,118 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:43Z] INFO  16:43:41,119 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:43Z] INFO  16:43:41,266 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:43Z] INFO  16:43:41,402 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:43Z] INFO  16:43:41,533 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:43Z] INFO  16:43:41,536 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:43Z] INFO  16:43:41,536 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:43Z] INFO  16:43:41,536 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:43Z] INFO  16:43:41,540 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/1/R14-18105_kapa-NGv3-PE100-NGv3-sort-1_46715671_62228851-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/1/R14-18105_kapa-NGv3-PE100-NGv3-sort-1_46715671_62228851-prep-prealign-realign.intervals -L 1:46715672-62228851 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/1/tx/tmpObHv2N/R14-18105_kapa-NGv3-PE100-NGv3-sort-1_46715671_62228851-prep.bam
[2016-04-14T23:43Z] INFO  16:43:41,560 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:43Z] INFO  16:43:41,561 HelpFormatter - Date/Time: 2016/04/14 16:43:41
[2016-04-14T23:43Z] INFO  16:43:41,562 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:43Z] INFO  16:43:41,562 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:43Z] INFO  16:43:41,561 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:43Z] INFO  16:43:41,564 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:43Z] INFO  16:43:41,564 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:43Z] INFO  16:43:41,565 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:43Z] INFO  16:43:41,569 HelpFormatter - Program Args: -T PrintReads -L 1:240255410-249250621 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/1/tx/tmpoAvrfO/R14-18105_kapa-NGv3-PE100-NGv3-sort-1_240255409_249250621-prep-prealign.bam
[2016-04-14T23:43Z] INFO  16:43:41,588 ProgressMeter -      1:28537145    700011.0    90.0 s       2.1 m       83.1%   108.0 s      18.0 s
[2016-04-14T23:43Z] INFO  16:43:41,588 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:43Z] INFO  16:43:41,589 HelpFormatter - Date/Time: 2016/04/14 16:43:41
[2016-04-14T23:43Z] INFO  16:43:41,589 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:43Z] INFO  16:43:41,589 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:43Z] INFO  16:43:41,704 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:43Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-1_0_15541927-prep-prealign.bam
[2016-04-14T23:43Z] INFO  16:43:41,780 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:43Z] INFO  16:43:41,823 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:43Z] INFO  16:43:41,961 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:43Z] INFO  16:43:41,971 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:43Z] INFO  16:43:42,053 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-14T23:43Z] INFO  16:43:42,417 IntervalUtils - Processing 15513180 bp from intervals
[2016-04-14T23:43Z] WARN  16:43:42,423 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:43Z] INFO  16:43:42,536 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:43Z] INFO  16:43:42,733 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:43Z] INFO  16:43:42,734 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:43Z] INFO  16:43:42,746 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:43Z] INFO  16:43:42,747 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:43Z] INFO  16:43:42,884 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-14T23:43Z] INFO  16:43:42,927 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:43Z] INFO  16:43:42,946 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:43Z] INFO  16:43:42,955 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:43Z] INFO  16:43:42,957 ProgressMeter -            done    184618.0    13.0 s      73.0 s      100.0%    13.0 s       0.0 s
[2016-04-14T23:43Z] INFO  16:43:42,958 ProgressMeter - Total runtime 13.49 secs, 0.22 min, 0.00 hours
[2016-04-14T23:43Z] INFO  16:43:42,962 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 184618 total reads (0.00%)
[2016-04-14T23:43Z] INFO  16:43:42,963 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:43Z] INFO  16:43:42,964 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:43Z] INFO  16:43:42,964 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:43Z] INFO  16:43:42,990 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.04
[2016-04-14T23:43Z] INFO  16:43:43,005 IntervalUtils - Processing 8995212 bp from intervals
[2016-04-14T23:43Z] INFO  16:43:43,075 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:43Z] INFO  16:43:43,113 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:43Z] INFO  16:43:43,356 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:43Z] INFO  16:43:43,357 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:43Z] INFO  16:43:43,357 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:43Z] INFO  16:43:43,357 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:43Z] INFO  16:43:43,370 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:43Z] INFO  16:43:43,481 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:43Z] INFO  16:43:43,628 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:43Z] INFO  16:43:43,631 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:43Z] INFO  16:43:43,632 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:43Z] INFO  16:43:43,632 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:43Z] INFO  16:43:43,637 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/1/R14-18105_kapa-NGv3-PE100-NGv3-sort-1_77752625_93297674-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/1/R14-18105_kapa-NGv3-PE100-NGv3-sort-1_77752625_93297674-prep-prealign-realign.intervals -L 1:77752626-93297674 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/1/tx/tmp_p2zxy/R14-18105_kapa-NGv3-PE100-NGv3-sort-1_77752625_93297674-prep.bam
[2016-04-14T23:43Z] INFO  16:43:43,654 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:43Z] INFO  16:43:43,655 HelpFormatter - Date/Time: 2016/04/14 16:43:43
[2016-04-14T23:43Z] INFO  16:43:43,655 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:43Z] INFO  16:43:43,656 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:43Z] INFO  16:43:43,908 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:43Z] INFO  16:43:44,103 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:43Z] INFO  16:43:44,113 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:43Z] INFO  16:43:44,195 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-14T23:43Z] GATK RealignerTargetCreator: R14-18105_kapa-NGv3-PE100-NGv3-sort-1_0_15541927-prep-prealign.bam 1:1-15541927
[2016-04-14T23:43Z] GATK: RealignerTargetCreator
[2016-04-14T23:43Z] INFO  16:43:44,503 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:43Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-1_62231950_77749296-prep.bam
[2016-04-14T23:43Z] INFO  16:43:44,706 IntervalUtils - Processing 15545049 bp from intervals
[2016-04-14T23:43Z] WARN  16:43:44,721 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:43Z] INFO  16:43:44,803 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:43Z] INFO  16:43:44,906 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:43Z] INFO  16:43:44,907 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:43Z] INFO  16:43:44,908 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:43Z] INFO  16:43:44,909 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:43Z] INFO  16:43:45,082 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:43Z] INFO  16:43:45,227 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:43Z] GATK pre-alignment ('2', 0, 15514844) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-14T23:43Z] INFO  16:43:46,036 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@41fd9d8e
[2016-04-14T23:43Z] INFO  16:43:46,120 ProgressMeter -     1:145477358    100001.0    31.0 s       5.2 m       10.2%     5.1 m       4.6 m
[2016-04-14T23:43Z] INFO  16:43:46,128 ProgressMeter -            done    798011.0    94.0 s     118.0 s      100.0%    94.0 s       0.0 s
[2016-04-14T23:43Z] INFO  16:43:46,129 ProgressMeter - Total runtime 94.64 secs, 1.58 min, 0.03 hours
[2016-04-14T23:43Z] INFO  16:43:46,129 MicroScheduler - 287 reads were filtered out during the traversal out of approximately 798298 total reads (0.04%)
[2016-04-14T23:43Z] INFO  16:43:46,129 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:43Z] INFO  16:43:46,130 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:43Z] INFO  16:43:46,130 MicroScheduler -   -> 287 reads (0.04% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:43Z] INFO  16:43:47,274 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:43Z] INFO  16:43:47,278 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:43Z] INFO  16:43:47,279 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:43Z] INFO  16:43:47,279 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:43Z] INFO  16:43:47,284 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/1/R14-18105_kapa-NGv3-PE100-NGv3-sort-1_0_15541927-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/1/tx/tmpLjwAG2/R14-18105_kapa-NGv3-PE100-NGv3-sort-1_0_15541927-prep-prealign-realign.intervals -l INFO -L 1:1-15541927 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-14T23:43Z] INFO  16:43:47,304 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:43Z] INFO  16:43:47,305 HelpFormatter - Date/Time: 2016/04/14 16:43:47
[2016-04-14T23:43Z] INFO  16:43:47,305 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:43Z] INFO  16:43:47,305 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:43Z] INFO  16:43:47,431 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:43Z] INFO  16:43:47,657 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:43Z] INFO  16:43:47,663 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-14T23:43Z] INFO  16:43:47,673 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:43Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-1_15545821_31186478-prep-prealign.bam
[2016-04-14T23:43Z] INFO  16:43:47,731 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-14T23:43Z] INFO  16:43:47,982 IntervalUtils - Processing 15541927 bp from intervals
[2016-04-14T23:43Z] WARN  16:43:47,988 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:43Z] INFO  16:43:48,074 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:43Z] INFO  16:43:48,100 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:43Z] INFO  16:43:48,104 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:43Z] INFO  16:43:48,105 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:43Z] INFO  16:43:48,105 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:43Z] INFO  16:43:48,110 HelpFormatter - Program Args: -T PrintReads -L 2:1-15514844 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/2/tx/tmpkfcTYQ/R14-18105_kapa-NGv3-PE100-NGv3-sort-2_0_15514844-prep-prealign.bam
[2016-04-14T23:43Z] INFO  16:43:48,119 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:43Z] INFO  16:43:48,120 HelpFormatter - Date/Time: 2016/04/14 16:43:48
[2016-04-14T23:43Z] INFO  16:43:48,120 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:43Z] INFO  16:43:48,121 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:43Z] INFO  16:43:48,326 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:43Z] INFO  16:43:48,367 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:43Z] INFO  16:43:48,368 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:43Z] INFO  16:43:48,369 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:43Z] INFO  16:43:48,370 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-14T23:43Z] INFO  16:43:49,305 ProgressMeter -     1:164769055    200003.0    30.0 s       2.5 m       33.9%    88.0 s      58.0 s
[2016-04-14T23:43Z] INFO  16:43:49,466 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-14T23:43Z] INFO  16:43:49,518 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:43Z] INFO  16:43:49,527 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:43Z] INFO  16:43:49,561 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.03
[2016-04-14T23:43Z] INFO  16:43:49,576 IntervalUtils - Processing 15514844 bp from intervals
[2016-04-14T23:43Z] INFO  16:43:49,645 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:43Z] INFO  16:43:49,936 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:43Z] INFO  16:43:49,937 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:43Z] INFO  16:43:49,938 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:43Z] INFO  16:43:49,939 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:43Z] INFO  16:43:49,980 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:43Z] INFO  16:43:50,120 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:43Z] GATK RealignerTargetCreator: R14-18105_kapa-NGv3-PE100-NGv3-sort-1_15545821_31186478-prep-prealign.bam 1:15545822-31186478
[2016-04-14T23:43Z] GATK: RealignerTargetCreator
[2016-04-14T23:43Z] INFO  16:43:52,102 ProgressMeter -      1:44595194    600007.0    91.0 s       2.5 m       86.4%   105.0 s      14.0 s
[2016-04-14T23:43Z] INFO  16:43:53,219 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:43Z] INFO  16:43:53,223 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:43Z] INFO  16:43:53,223 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:43Z] INFO  16:43:53,224 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:43Z] INFO  16:43:53,229 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/1/R14-18105_kapa-NGv3-PE100-NGv3-sort-1_15545821_31186478-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/1/tx/tmpKOvpPA/R14-18105_kapa-NGv3-PE100-NGv3-sort-1_15545821_31186478-prep-prealign-realign.intervals -l INFO -L 1:15545822-31186478 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-14T23:43Z] INFO  16:43:53,238 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:43Z] INFO  16:43:53,239 HelpFormatter - Date/Time: 2016/04/14 16:43:53
[2016-04-14T23:43Z] INFO  16:43:53,239 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:43Z] INFO  16:43:53,240 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:43Z] INFO  16:43:53,351 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:43Z] INFO  16:43:53,558 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-14T23:43Z] INFO  16:43:53,580 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:43Z] INFO  16:43:53,623 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.04
[2016-04-14T23:43Z] INFO  16:43:53,949 IntervalUtils - Processing 15640657 bp from intervals
[2016-04-14T23:43Z] WARN  16:43:53,955 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:43Z] INFO  16:43:54,063 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:43Z] INFO  16:43:54,081 ProgressMeter -     1:186099736    200003.0    30.0 s       2.5 m       64.7%    46.0 s      16.0 s
[2016-04-14T23:43Z] INFO  16:43:54,345 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:43Z] INFO  16:43:54,346 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:43Z] INFO  16:43:54,347 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:43Z] INFO  16:43:54,348 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-14T23:43Z] INFO  16:43:54,865 ProgressMeter -     1:203152094    200003.0    30.0 s       2.5 m       71.1%    42.0 s      12.0 s
[2016-04-14T23:43Z] INFO  16:43:55,485 ProgressMeter -            done    175559.0    14.0 s      81.0 s      100.0%    14.0 s       0.0 s
[2016-04-14T23:43Z] INFO  16:43:55,486 ProgressMeter - Total runtime 14.37 secs, 0.24 min, 0.00 hours
[2016-04-14T23:43Z] INFO  16:43:55,489 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 175559 total reads (0.00%)
[2016-04-14T23:43Z] INFO  16:43:55,490 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:43Z] INFO  16:43:55,490 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:43Z] INFO  16:43:55,490 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:43Z] INFO  16:43:57,141 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@41fd9d8e
[2016-04-14T23:43Z] INFO  16:43:57,172 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:43Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-1_93298945_108993401-prep.bam
[2016-04-14T23:43Z] INFO  16:43:57,345 ProgressMeter -            done    264533.0    33.0 s       2.1 m      100.0%    33.0 s       0.0 s
[2016-04-14T23:43Z] INFO  16:43:57,346 ProgressMeter - Total runtime 33.29 secs, 0.55 min, 0.01 hours
[2016-04-14T23:43Z] INFO  16:43:57,346 MicroScheduler - 158 reads were filtered out during the traversal out of approximately 264691 total reads (0.06%)
[2016-04-14T23:43Z] INFO  16:43:57,346 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:43Z] INFO  16:43:57,347 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:43Z] INFO  16:43:57,347 MicroScheduler -   -> 158 reads (0.06% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:43Z] GATK pre-alignment ('2', 15519725, 31133925) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-14T23:43Z] INFO  16:43:58,145 ProgressMeter -     1:220440480    200003.0    30.0 s       2.5 m       82.5%    36.0 s       6.0 s
[2016-04-14T23:43Z] INFO  16:43:58,596 ProgressMeter -     1:120611666    300005.0    60.0 s       3.4 m       33.4%     3.0 m     119.0 s
[2016-04-14T23:43Z] INFO  16:43:58,688 ProgressMeter -            done    176456.0    13.0 s      78.0 s      100.0%    13.0 s       0.0 s
[2016-04-14T23:43Z] INFO  16:43:58,688 ProgressMeter - Total runtime 13.78 secs, 0.23 min, 0.00 hours
[2016-04-14T23:43Z] INFO  16:43:58,693 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 176456 total reads (0.00%)
[2016-04-14T23:43Z] INFO  16:43:58,694 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:43Z] INFO  16:43:58,694 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:43Z] INFO  16:43:58,695 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:43Z] INFO  16:43:58,770 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:43Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-1_175048468_192127886-prep-prealign.bam
[2016-04-14T23:43Z] GATK RealignerTargetCreator: R14-18105_kapa-NGv3-PE100-NGv3-sort-1_175048468_192127886-prep-prealign.bam 1:175048469-192127886
[2016-04-14T23:43Z] GATK: RealignerTargetCreator
[2016-04-14T23:44Z] INFO  16:44:00,269 ProgressMeter -     1:228560438    200005.0    30.0 s       2.5 m       31.9%    93.0 s      63.0 s
[2016-04-14T23:44Z] INFO  16:44:00,444 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:44Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-1_77752625_93297674-prep.bam
[2016-04-14T23:44Z] INFO  16:44:00,648 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:44Z] INFO  16:44:00,668 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:44Z] INFO  16:44:00,669 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:44Z] INFO  16:44:00,670 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:44Z] INFO  16:44:00,675 HelpFormatter - Program Args: -T PrintReads -L 2:15519726-31133925 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/2/tx/tmpCKGaJn/R14-18105_kapa-NGv3-PE100-NGv3-sort-2_15519725_31133925-prep-prealign.bam
[2016-04-14T23:44Z] INFO  16:44:00,684 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:44Z] INFO  16:44:00,684 HelpFormatter - Date/Time: 2016/04/14 16:44:00
[2016-04-14T23:44Z] INFO  16:44:00,684 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:44Z] INFO  16:44:00,685 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:44Z] INFO  16:44:00,853 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:44Z] GATK pre-alignment ('2', 31135088, 46706841) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-14T23:44Z] INFO  16:44:01,297 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@41fd9d8e
[2016-04-14T23:44Z] INFO  16:44:01,533 ProgressMeter -            done    264105.0    33.0 s       2.1 m      100.0%    33.0 s       0.0 s
[2016-04-14T23:44Z] INFO  16:44:01,533 ProgressMeter - Total runtime 33.43 secs, 0.56 min, 0.01 hours
[2016-04-14T23:44Z] INFO  16:44:01,534 MicroScheduler - 215 reads were filtered out during the traversal out of approximately 264320 total reads (0.08%)
[2016-04-14T23:44Z] INFO  16:44:01,534 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:44Z] INFO  16:44:01,534 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:44Z] INFO  16:44:01,535 MicroScheduler -   -> 215 reads (0.08% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:44Z] INFO  16:44:01,925 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-14T23:44Z] INFO  16:44:02,005 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:44Z] INFO  16:44:02,022 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:44Z] INFO  16:44:02,029 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@7172f77a
[2016-04-14T23:44Z] INFO  16:44:02,083 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-14T23:44Z] INFO  16:44:02,102 IntervalUtils - Processing 15614200 bp from intervals
[2016-04-14T23:44Z] INFO  16:44:02,216 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:44Z] INFO  16:44:02,233 ProgressMeter -            done    420538.0    64.0 s       2.5 m      100.0%    64.0 s       0.0 s
[2016-04-14T23:44Z] INFO  16:44:02,234 ProgressMeter - Total runtime 64.22 secs, 1.07 min, 0.02 hours
[2016-04-14T23:44Z] INFO  16:44:02,234 MicroScheduler - 245 reads were filtered out during the traversal out of approximately 420783 total reads (0.06%)
[2016-04-14T23:44Z] INFO  16:44:02,235 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:44Z] INFO  16:44:02,235 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:44Z] INFO  16:44:02,235 MicroScheduler -   -> 245 reads (0.06% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:44Z] INFO  16:44:02,358 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:44Z] INFO  16:44:02,362 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:44Z] INFO  16:44:02,363 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:44Z] INFO  16:44:02,364 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:44Z] INFO  16:44:02,369 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/1/R14-18105_kapa-NGv3-PE100-NGv3-sort-1_175048468_192127886-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/1/tx/tmpF0ujgJ/R14-18105_kapa-NGv3-PE100-NGv3-sort-1_175048468_192127886-prep-prealign-realign.intervals -l INFO -L 1:175048469-192127886 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-14T23:44Z] INFO  16:44:02,380 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:44Z] INFO  16:44:02,381 HelpFormatter - Date/Time: 2016/04/14 16:44:02
[2016-04-14T23:44Z] INFO  16:44:02,382 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:44Z] INFO  16:44:02,382 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:44Z] INFO  16:44:02,452 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:44Z] INFO  16:44:02,453 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:44Z] INFO  16:44:02,454 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:44Z] INFO  16:44:02,455 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:44Z] INFO  16:44:02,469 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:44Z] INFO  16:44:02,506 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:44Z] INFO  16:44:02,693 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:44Z] INFO  16:44:02,700 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-14T23:44Z] INFO  16:44:02,732 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:44Z] INFO  16:44:02,803 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-14T23:44Z] INFO  16:44:02,857 ProgressMeter -     19:10506915    900012.0    64.0 s      72.0 s       67.7%    94.0 s      30.0 s
[2016-04-14T23:44Z] INFO  16:44:03,104 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:44Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-1_207641871_223156451-prep-prealign.bam
[2016-04-14T23:44Z] INFO  16:44:03,222 IntervalUtils - Processing 17079418 bp from intervals
[2016-04-14T23:44Z] WARN  16:44:03,227 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:44Z] INFO  16:44:03,319 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:44Z] INFO  16:44:03,560 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:44Z] INFO  16:44:03,561 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:44Z] INFO  16:44:03,562 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:44Z] INFO  16:44:03,563 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-14T23:44Z] INFO  16:44:03,704 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:44Z] INFO  16:44:03,702 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:44Z] INFO  16:44:03,720 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:44Z] INFO  16:44:03,721 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:44Z] INFO  16:44:03,722 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:44Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-1_108994811_143767848-prep-prealign.bam
[2016-04-14T23:44Z] INFO  16:44:03,727 HelpFormatter - Program Args: -T PrintReads -L 2:31135089-46706841 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/2/tx/tmpzQjbvx/R14-18105_kapa-NGv3-PE100-NGv3-sort-2_31135088_46706841-prep-prealign.bam
[2016-04-14T23:44Z] INFO  16:44:03,757 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:44Z] INFO  16:44:03,758 HelpFormatter - Date/Time: 2016/04/14 16:44:03
[2016-04-14T23:44Z] INFO  16:44:03,758 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:44Z] INFO  16:44:03,759 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:44Z] INFO  16:44:03,910 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:44Z] GATK RealignerTargetCreator: R14-18105_kapa-NGv3-PE100-NGv3-sort-1_207641871_223156451-prep-prealign.bam 1:207641872-223156451
[2016-04-14T23:44Z] GATK: RealignerTargetCreator
[2016-04-14T23:44Z] INFO  16:44:04,352 ProgressMeter -            done    310314.0    21.0 s      69.0 s      100.0%    21.0 s       0.0 s
[2016-04-14T23:44Z] INFO  16:44:04,353 ProgressMeter - Total runtime 21.62 secs, 0.36 min, 0.01 hours
[2016-04-14T23:44Z] INFO  16:44:04,356 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 310314 total reads (0.00%)
[2016-04-14T23:44Z] INFO  16:44:04,357 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:44Z] INFO  16:44:04,357 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:44Z] INFO  16:44:04,357 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:44Z] INFO  16:44:04,650 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@41fd9d8e
[2016-04-14T23:44Z] INFO  16:44:04,752 ProgressMeter -            done    732024.0   103.0 s       2.4 m      100.0%   103.0 s       0.0 s
[2016-04-14T23:44Z] INFO  16:44:04,753 ProgressMeter - Total runtime 103.80 secs, 1.73 min, 0.03 hours
[2016-04-14T23:44Z] INFO  16:44:04,754 MicroScheduler - 257 reads were filtered out during the traversal out of approximately 732281 total reads (0.04%)
[2016-04-14T23:44Z] INFO  16:44:04,754 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:44Z] INFO  16:44:04,755 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:44Z] INFO  16:44:04,756 MicroScheduler -   -> 257 reads (0.04% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:44Z] INFO  16:44:04,911 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-14T23:44Z] GATK RealignerTargetCreator: R14-18105_kapa-NGv3-PE100-NGv3-sort-1_108994811_143767848-prep-prealign.bam 1:108994812-143767848
[2016-04-14T23:44Z] GATK: RealignerTargetCreator
[2016-04-14T23:44Z] INFO  16:44:04,978 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:44Z] INFO  16:44:04,998 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:44Z] INFO  16:44:05,038 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.04
[2016-04-14T23:44Z] INFO  16:44:05,062 IntervalUtils - Processing 15571753 bp from intervals
[2016-04-14T23:44Z] INFO  16:44:05,134 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:44Z] INFO  16:44:05,493 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:44Z] INFO  16:44:05,493 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:44Z] INFO  16:44:05,509 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:44Z] INFO  16:44:05,509 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:44Z] INFO  16:44:05,534 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:44Z] INFO  16:44:05,659 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:44Z] INFO  16:44:06,072 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:44Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-1_46715671_62228851-prep.bam
[2016-04-14T23:44Z] INFO  16:44:06,172 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:44Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-1_31187093_46714270-prep-prealign.bam
[2016-04-14T23:44Z] INFO  16:44:06,603 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:44Z] INFO  16:44:06,607 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:44Z] INFO  16:44:06,608 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:44Z] INFO  16:44:06,608 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:44Z] INFO  16:44:06,613 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/1/R14-18105_kapa-NGv3-PE100-NGv3-sort-1_207641871_223156451-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/1/tx/tmp_rnSRt/R14-18105_kapa-NGv3-PE100-NGv3-sort-1_207641871_223156451-prep-prealign-realign.intervals -l INFO -L 1:207641872-223156451 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-14T23:44Z] INFO  16:44:06,627 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:44Z] INFO  16:44:06,628 HelpFormatter - Date/Time: 2016/04/14 16:44:06
[2016-04-14T23:44Z] INFO  16:44:06,628 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:44Z] INFO  16:44:06,628 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:44Z] INFO  16:44:06,774 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:44Z] INFO  16:44:07,014 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-14T23:44Z] INFO  16:44:07,023 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:44Z] INFO  16:44:07,077 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-14T23:44Z] GATK pre-alignment ('2', 46707543, 62228117) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-14T23:44Z] INFO  16:44:07,371 IntervalUtils - Processing 15514580 bp from intervals
[2016-04-14T23:44Z] WARN  16:44:07,376 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:44Z] INFO  16:44:07,481 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:44Z] INFO  16:44:07,757 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:44Z] INFO  16:44:07,758 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:44Z] INFO  16:44:07,758 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:44Z] INFO  16:44:07,769 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-14T23:44Z] INFO  16:44:08,134 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:44Z] INFO  16:44:08,137 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:44Z] INFO  16:44:08,138 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:44Z] INFO  16:44:08,138 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:44Z] INFO  16:44:08,144 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/1/R14-18105_kapa-NGv3-PE100-NGv3-sort-1_108994811_143767848-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/1/tx/tmpiPfpIl/R14-18105_kapa-NGv3-PE100-NGv3-sort-1_108994811_143767848-prep-prealign-realign.intervals -l INFO -L 1:108994812-143767848 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-14T23:44Z] INFO  16:44:08,161 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:44Z] INFO  16:44:08,161 HelpFormatter - Date/Time: 2016/04/14 16:44:08
[2016-04-14T23:44Z] INFO  16:44:08,162 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:44Z] INFO  16:44:08,162 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:44Z] INFO  16:44:08,206 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@5fe152b7
[2016-04-14T23:44Z] INFO  16:44:08,306 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:44Z] GATK RealignerTargetCreator: R14-18105_kapa-NGv3-PE100-NGv3-sort-1_31187093_46714270-prep-prealign.bam 1:31187094-46714270
[2016-04-14T23:44Z] GATK: RealignerTargetCreator
[2016-04-14T23:44Z] INFO  16:44:08,395 ProgressMeter -            done    402876.0    49.0 s       2.0 m      100.0%    49.0 s       0.0 s
[2016-04-14T23:44Z] INFO  16:44:08,396 ProgressMeter - Total runtime 49.11 secs, 0.82 min, 0.01 hours
[2016-04-14T23:44Z] INFO  16:44:08,397 MicroScheduler - 196 reads were filtered out during the traversal out of approximately 403072 total reads (0.05%)
[2016-04-14T23:44Z] INFO  16:44:08,398 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:44Z] INFO  16:44:08,398 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:44Z] INFO  16:44:08,399 MicroScheduler -   -> 196 reads (0.05% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:44Z] INFO  16:44:08,534 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-14T23:44Z] INFO  16:44:08,547 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:44Z] INFO  16:44:08,603 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-14T23:44Z] INFO  16:44:08,940 IntervalUtils - Processing 34773037 bp from intervals
[2016-04-14T23:44Z] WARN  16:44:08,950 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:44Z] INFO  16:44:09,021 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:44Z] INFO  16:44:09,212 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:44Z] INFO  16:44:09,213 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:44Z] INFO  16:44:09,214 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:44Z] INFO  16:44:09,214 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-14T23:44Z] INFO  16:44:09,923 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:44Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-1_159504867_175046963-prep-prealign.bam
[2016-04-14T23:44Z] INFO  16:44:10,090 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:44Z] INFO  16:44:10,093 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:44Z] INFO  16:44:10,094 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:44Z] INFO  16:44:10,095 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:44Z] INFO  16:44:10,099 HelpFormatter - Program Args: -T PrintReads -L 2:46707544-62228117 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/2/tx/tmpvhS4z0/R14-18105_kapa-NGv3-PE100-NGv3-sort-2_46707543_62228117-prep-prealign.bam
[2016-04-14T23:44Z] INFO  16:44:10,114 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:44Z] INFO  16:44:10,115 HelpFormatter - Date/Time: 2016/04/14 16:44:10
[2016-04-14T23:44Z] INFO  16:44:10,116 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:44Z] INFO  16:44:10,117 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:44Z] INFO  16:44:10,352 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:44Z] INFO  16:44:10,742 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@5fe152b7
[2016-04-14T23:44Z] INFO  16:44:10,973 ProgressMeter -            done    201016.0    27.0 s       2.3 m       99.8%    27.0 s       0.0 s
[2016-04-14T23:44Z] INFO  16:44:10,974 ProgressMeter - Total runtime 27.62 secs, 0.46 min, 0.01 hours
[2016-04-14T23:44Z] INFO  16:44:10,974 MicroScheduler - 117 reads were filtered out during the traversal out of approximately 201133 total reads (0.06%)
[2016-04-14T23:44Z] INFO  16:44:10,974 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:44Z] INFO  16:44:10,975 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:44Z] INFO  16:44:10,975 MicroScheduler -   -> 117 reads (0.06% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:44Z] GATK RealignerTargetCreator: R14-18105_kapa-NGv3-PE100-NGv3-sort-1_159504867_175046963-prep-prealign.bam 1:159504868-175046963
[2016-04-14T23:44Z] GATK: RealignerTargetCreator
[2016-04-14T23:44Z] INFO  16:44:11,468 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:44Z] INFO  16:44:11,470 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:44Z] INFO  16:44:11,471 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:44Z] INFO  16:44:11,471 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:44Z] INFO  16:44:11,487 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/1/R14-18105_kapa-NGv3-PE100-NGv3-sort-1_31187093_46714270-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/1/tx/tmpjXmhsM/R14-18105_kapa-NGv3-PE100-NGv3-sort-1_31187093_46714270-prep-prealign-realign.intervals -l INFO -L 1:31187094-46714270 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-14T23:44Z] INFO  16:44:11,501 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@5fe152b7
[2016-04-14T23:44Z] INFO  16:44:11,516 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:44Z] INFO  16:44:11,517 HelpFormatter - Date/Time: 2016/04/14 16:44:11
[2016-04-14T23:44Z] INFO  16:44:11,517 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:44Z] INFO  16:44:11,517 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:44Z] INFO  16:44:11,526 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-14T23:44Z] INFO  16:44:11,578 ProgressMeter -            done    160602.0    21.0 s       2.2 m       99.9%    21.0 s       0.0 s
[2016-04-14T23:44Z] INFO  16:44:11,579 ProgressMeter - Total runtime 21.64 secs, 0.36 min, 0.01 hours
[2016-04-14T23:44Z] INFO  16:44:11,579 MicroScheduler - 144 reads were filtered out during the traversal out of approximately 160746 total reads (0.09%)
[2016-04-14T23:44Z] INFO  16:44:11,579 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:44Z] INFO  16:44:11,580 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:44Z] INFO  16:44:11,580 MicroScheduler -   -> 144 reads (0.09% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:44Z] INFO  16:44:11,582 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:44Z] INFO  16:44:11,601 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:44Z] INFO  16:44:11,632 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:44Z] INFO  16:44:11,676 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-14T23:44Z] INFO  16:44:11,714 IntervalUtils - Processing 15520574 bp from intervals
[2016-04-14T23:44Z] INFO  16:44:11,838 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:44Z] INFO  16:44:11,846 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-14T23:44Z] INFO  16:44:11,856 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:44Z] INFO  16:44:11,925 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-14T23:44Z] INFO  16:44:12,145 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:44Z] INFO  16:44:12,146 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:44Z] INFO  16:44:12,147 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:44Z] INFO  16:44:12,147 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:44Z] INFO  16:44:12,162 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:44Z] INFO  16:44:12,169 IntervalUtils - Processing 15527177 bp from intervals
[2016-04-14T23:44Z] WARN  16:44:12,174 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:44Z] INFO  16:44:12,241 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:44Z] INFO  16:44:12,299 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:44Z] INFO  16:44:12,313 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:44Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-1_240255409_249250621-prep-prealign.bam
[2016-04-14T23:44Z] INFO  16:44:12,432 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:44Z] INFO  16:44:12,433 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:44Z] INFO  16:44:12,434 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:44Z] INFO  16:44:12,434 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-14T23:44Z] INFO  16:44:12,974 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:44Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-2_0_15514844-prep-prealign.bam
[2016-04-14T23:44Z] GATK RealignerTargetCreator: R14-18105_kapa-NGv3-PE100-NGv3-sort-1_240255409_249250621-prep-prealign.bam 1:240255410-249250621
[2016-04-14T23:44Z] GATK: RealignerTargetCreator
[2016-04-14T23:44Z] GATK RealignerTargetCreator: R14-18105_kapa-NGv3-PE100-NGv3-sort-2_0_15514844-prep-prealign.bam 2:1-15514844
[2016-04-14T23:44Z] GATK: RealignerTargetCreator
[2016-04-14T23:44Z] INFO  16:44:13,962 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@41fd9d8e
[2016-04-14T23:44Z] INFO  16:44:14,144 ProgressMeter -            done    422334.0    49.0 s     116.0 s      100.0%    49.0 s       0.0 s
[2016-04-14T23:44Z] INFO  16:44:14,144 ProgressMeter - Total runtime 49.30 secs, 0.82 min, 0.01 hours
[2016-04-14T23:44Z] INFO  16:44:14,145 MicroScheduler - 278 reads were filtered out during the traversal out of approximately 422612 total reads (0.07%)
[2016-04-14T23:44Z] INFO  16:44:14,145 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:44Z] INFO  16:44:14,145 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:44Z] INFO  16:44:14,146 MicroScheduler -   -> 278 reads (0.07% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:44Z] INFO  16:44:14,351 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:44Z] INFO  16:44:14,354 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:44Z] INFO  16:44:14,354 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:44Z] INFO  16:44:14,354 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:44Z] INFO  16:44:14,358 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/1/R14-18105_kapa-NGv3-PE100-NGv3-sort-1_159504867_175046963-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/1/tx/tmpwQq3Wv/R14-18105_kapa-NGv3-PE100-NGv3-sort-1_159504867_175046963-prep-prealign-realign.intervals -l INFO -L 1:159504868-175046963 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-14T23:44Z] INFO  16:44:14,386 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:44Z] INFO  16:44:14,387 HelpFormatter - Date/Time: 2016/04/14 16:44:14
[2016-04-14T23:44Z] INFO  16:44:14,387 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:44Z] INFO  16:44:14,387 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:44Z] INFO  16:44:14,499 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:44Z] INFO  16:44:14,765 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-14T23:44Z] INFO  16:44:14,774 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:44Z] INFO  16:44:14,824 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-14T23:44Z] INFO  16:44:15,098 IntervalUtils - Processing 15542096 bp from intervals
[2016-04-14T23:44Z] WARN  16:44:15,103 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:44Z] INFO  16:44:15,193 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:44Z] INFO  16:44:15,392 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:44Z] INFO  16:44:15,392 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:44Z] INFO  16:44:15,393 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:44Z] INFO  16:44:15,393 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-14T23:44Z] INFO  16:44:15,596 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:44Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-1_192128349_207640257-prep-prealign.bam
[2016-04-14T23:44Z] INFO  16:44:15,989 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:44Z] INFO  16:44:15,992 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:44Z] INFO  16:44:15,993 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:44Z] INFO  16:44:15,994 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:44Z] INFO  16:44:15,998 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/1/R14-18105_kapa-NGv3-PE100-NGv3-sort-1_240255409_249250621-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/1/tx/tmp51G1F3/R14-18105_kapa-NGv3-PE100-NGv3-sort-1_240255409_249250621-prep-prealign-realign.intervals -l INFO -L 1:240255410-249250621 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-14T23:44Z] INFO  16:44:16,008 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:44Z] INFO  16:44:16,013 HelpFormatter - Date/Time: 2016/04/14 16:44:15
[2016-04-14T23:44Z] INFO  16:44:16,013 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:44Z] INFO  16:44:16,014 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:44Z] INFO  16:44:16,115 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:44Z] INFO  16:44:16,261 ProgressMeter -     1:148806282    300009.0    61.0 s       3.4 m       31.6%     3.2 m       2.2 m
[2016-04-14T23:44Z] INFO  16:44:16,327 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-14T23:44Z] INFO  16:44:16,354 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:44Z] INFO  16:44:16,405 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:44Z] INFO  16:44:16,408 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-14T23:44Z] INFO  16:44:16,408 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:44Z] INFO  16:44:16,408 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:44Z] INFO  16:44:16,408 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:44Z] INFO  16:44:16,412 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/2/R14-18105_kapa-NGv3-PE100-NGv3-sort-2_0_15514844-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/2/tx/tmpjUasHX/R14-18105_kapa-NGv3-PE100-NGv3-sort-2_0_15514844-prep-prealign-realign.intervals -l INFO -L 2:1-15514844 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-14T23:44Z] INFO  16:44:16,429 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:44Z] INFO  16:44:16,430 HelpFormatter - Date/Time: 2016/04/14 16:44:16
[2016-04-14T23:44Z] INFO  16:44:16,431 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:44Z] INFO  16:44:16,431 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:44Z] INFO  16:44:16,589 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:44Z] INFO  16:44:16,669 IntervalUtils - Processing 8995212 bp from intervals
[2016-04-14T23:44Z] WARN  16:44:16,678 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:44Z] INFO  16:44:16,774 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:44Z] INFO  16:44:16,820 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-14T23:44Z] INFO  16:44:16,835 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:44Z] INFO  16:44:16,907 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-14T23:44Z] GATK RealignerTargetCreator: R14-18105_kapa-NGv3-PE100-NGv3-sort-1_192128349_207640257-prep-prealign.bam 1:192128350-207640257
[2016-04-14T23:44Z] GATK: RealignerTargetCreator
[2016-04-14T23:44Z] INFO  16:44:16,989 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:44Z] INFO  16:44:17,001 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:44Z] INFO  16:44:17,002 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:44Z] INFO  16:44:17,003 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-14T23:44Z] INFO  16:44:17,269 IntervalUtils - Processing 15514844 bp from intervals
[2016-04-14T23:44Z] WARN  16:44:17,275 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:44Z] INFO  16:44:17,421 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:44Z] INFO  16:44:17,607 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:44Z] INFO  16:44:17,608 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:44Z] INFO  16:44:17,609 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:44Z] INFO  16:44:17,610 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-14T23:44Z] INFO  16:44:17,883 ProgressMeter -            done   1.5541927E7    29.0 s       1.0 s      100.0%    29.0 s       0.0 s
[2016-04-14T23:44Z] INFO  16:44:17,883 ProgressMeter - Total runtime 29.51 secs, 0.49 min, 0.01 hours
[2016-04-14T23:44Z] INFO  16:44:17,887 MicroScheduler - 184842 reads were filtered out during the traversal out of approximately 820297 total reads (22.53%)
[2016-04-14T23:44Z] INFO  16:44:17,887 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:44Z] INFO  16:44:17,887 MicroScheduler -   -> 1217 reads (0.15% of total) failing BadMateFilter
[2016-04-14T23:44Z] INFO  16:44:17,888 MicroScheduler -   -> 55649 reads (6.78% of total) failing DuplicateReadFilter
[2016-04-14T23:44Z] INFO  16:44:17,888 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-14T23:44Z] INFO  16:44:17,888 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:44Z] INFO  16:44:17,888 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-14T23:44Z] INFO  16:44:17,889 MicroScheduler -   -> 127976 reads (15.60% of total) failing MappingQualityZeroFilter
[2016-04-14T23:44Z] INFO  16:44:17,889 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:44Z] INFO  16:44:17,889 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-14T23:44Z] INFO  16:44:17,889 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-14T23:44Z] INFO  16:44:19,217 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:44Z] GATK: realign ('1', 0, 15541927) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-14T23:44Z] INFO  16:44:19,973 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:44Z] INFO  16:44:19,976 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:44Z] INFO  16:44:19,976 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:44Z] INFO  16:44:19,976 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:44Z] INFO  16:44:19,980 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/1/R14-18105_kapa-NGv3-PE100-NGv3-sort-1_192128349_207640257-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/1/tx/tmpEkT948/R14-18105_kapa-NGv3-PE100-NGv3-sort-1_192128349_207640257-prep-prealign-realign.intervals -l INFO -L 1:192128350-207640257 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-14T23:44Z] INFO  16:44:19,993 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:44Z] INFO  16:44:19,994 HelpFormatter - Date/Time: 2016/04/14 16:44:19
[2016-04-14T23:44Z] INFO  16:44:19,994 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:44Z] INFO  16:44:20,006 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:44Z] INFO  16:44:20,111 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:44Z] INFO  16:44:20,330 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-14T23:44Z] INFO  16:44:20,339 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:44Z] INFO  16:44:20,412 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-14T23:44Z] INFO  16:44:20,766 IntervalUtils - Processing 15511908 bp from intervals
[2016-04-14T23:44Z] WARN  16:44:20,772 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:44Z] INFO  16:44:20,941 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:44Z] INFO  16:44:21,184 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:44Z] INFO  16:44:21,186 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:44Z] INFO  16:44:21,187 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:44Z] INFO  16:44:21,187 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-14T23:44Z] INFO  16:44:22,083 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:44Z] INFO  16:44:22,087 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:44Z] INFO  16:44:22,087 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:44Z] INFO  16:44:22,088 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:44Z] INFO  16:44:22,092 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/1/R14-18105_kapa-NGv3-PE100-NGv3-sort-1_0_15541927-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/1/R14-18105_kapa-NGv3-PE100-NGv3-sort-1_0_15541927-prep-prealign-realign.intervals -L 1:1-15541927 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/1/tx/tmpxnt0Gh/R14-18105_kapa-NGv3-PE100-NGv3-sort-1_0_15541927-prep.bam
[2016-04-14T23:44Z] INFO  16:44:22,131 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:44Z] INFO  16:44:22,131 HelpFormatter - Date/Time: 2016/04/14 16:44:22
[2016-04-14T23:44Z] INFO  16:44:22,131 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:44Z] INFO  16:44:22,132 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:44Z] INFO  16:44:22,296 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:44Z] INFO  16:44:22,392 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:44Z] INFO  16:44:22,401 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:44Z] INFO  16:44:22,457 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-14T23:44Z] INFO  16:44:22,827 IntervalUtils - Processing 15541927 bp from intervals
[2016-04-14T23:44Z] WARN  16:44:22,831 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:44Z] INFO  16:44:22,958 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:44Z] INFO  16:44:23,089 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:44Z] INFO  16:44:23,090 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:44Z] INFO  16:44:23,090 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:44Z] INFO  16:44:23,090 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:44Z] INFO  16:44:23,256 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:44Z] INFO  16:44:23,397 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:44Z] INFO  16:44:23,881 ProgressMeter -            done   1464552.0    85.0 s      58.0 s      100.0%    85.0 s       0.0 s
[2016-04-14T23:44Z] INFO  16:44:23,881 ProgressMeter - Total runtime 85.93 secs, 1.43 min, 0.02 hours
[2016-04-14T23:44Z] INFO  16:44:23,885 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 1464552 total reads (0.00%)
[2016-04-14T23:44Z] INFO  16:44:23,886 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:44Z] INFO  16:44:23,886 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:44Z] INFO  16:44:23,886 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:44Z] INFO  16:44:24,361 ProgressMeter -      1:31136101   1.5583779E7    30.0 s       1.0 s       99.7%    30.0 s       0.0 s
[2016-04-14T23:44Z] INFO  16:44:24,785 ProgressMeter -            done   1.7079418E7    21.0 s       1.0 s      100.0%    21.0 s       0.0 s
[2016-04-14T23:44Z] INFO  16:44:24,787 ProgressMeter - Total runtime 21.23 secs, 0.35 min, 0.01 hours
[2016-04-14T23:44Z] INFO  16:44:24,792 MicroScheduler - 21906 reads were filtered out during the traversal out of approximately 266845 total reads (8.21%)
[2016-04-14T23:44Z] INFO  16:44:24,792 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:44Z] INFO  16:44:24,792 MicroScheduler -   -> 605 reads (0.23% of total) failing BadMateFilter
[2016-04-14T23:44Z] INFO  16:44:24,793 MicroScheduler -   -> 20896 reads (7.83% of total) failing DuplicateReadFilter
[2016-04-14T23:44Z] INFO  16:44:24,793 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-14T23:44Z] INFO  16:44:24,793 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:44Z] INFO  16:44:24,794 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-14T23:44Z] INFO  16:44:24,794 MicroScheduler -   -> 405 reads (0.15% of total) failing MappingQualityZeroFilter
[2016-04-14T23:44Z] INFO  16:44:24,794 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:44Z] INFO  16:44:24,795 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-14T23:44Z] INFO  16:44:24,795 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-14T23:44Z] INFO  16:44:25,175 ProgressMeter -            done   1.5640657E7    30.0 s       1.0 s      100.0%    30.0 s       0.0 s
[2016-04-14T23:44Z] INFO  16:44:25,177 ProgressMeter - Total runtime 30.83 secs, 0.51 min, 0.01 hours
[2016-04-14T23:44Z] INFO  16:44:25,178 MicroScheduler - 86421 reads were filtered out during the traversal out of approximately 802617 total reads (10.77%)
[2016-04-14T23:44Z] INFO  16:44:25,179 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:44Z] INFO  16:44:25,180 MicroScheduler -   -> 1261 reads (0.16% of total) failing BadMateFilter
[2016-04-14T23:44Z] INFO  16:44:25,186 MicroScheduler -   -> 62930 reads (7.84% of total) failing DuplicateReadFilter
[2016-04-14T23:44Z] INFO  16:44:25,187 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-14T23:44Z] INFO  16:44:25,188 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:44Z] INFO  16:44:25,189 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-14T23:44Z] INFO  16:44:25,190 MicroScheduler -   -> 22230 reads (2.77% of total) failing MappingQualityZeroFilter
[2016-04-14T23:44Z] INFO  16:44:25,191 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:44Z] INFO  16:44:25,192 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-14T23:44Z] INFO  16:44:25,193 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-14T23:44Z] INFO  16:44:25,405 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@41fd9d8e
[2016-04-14T23:44Z] INFO  16:44:25,455 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:44Z] Index BAM file: R14-18102_kapa-NGv3-PE100-NGv3-sort-19_0_15509577-prep.bam
[2016-04-14T23:44Z] INFO  16:44:25,589 ProgressMeter -            done    445426.0    55.0 s       2.1 m      100.0%    55.0 s       0.0 s
[2016-04-14T23:44Z] INFO  16:44:25,591 ProgressMeter - Total runtime 55.77 secs, 0.93 min, 0.02 hours
[2016-04-14T23:44Z] INFO  16:44:25,592 MicroScheduler - 228 reads were filtered out during the traversal out of approximately 445654 total reads (0.05%)
[2016-04-14T23:44Z] INFO  16:44:25,593 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:44Z] INFO  16:44:25,594 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:44Z] INFO  16:44:25,595 MicroScheduler -   -> 228 reads (0.05% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:44Z] INFO  16:44:26,104 ProgressMeter -            done   1.551458E7    18.0 s       1.0 s      100.0%    18.0 s       0.0 s
[2016-04-14T23:44Z] INFO  16:44:26,105 ProgressMeter - Total runtime 18.35 secs, 0.31 min, 0.01 hours
[2016-04-14T23:44Z] INFO  16:44:26,110 MicroScheduler - 38008 reads were filtered out during the traversal out of approximately 265196 total reads (14.33%)
[2016-04-14T23:44Z] INFO  16:44:26,112 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:44Z] INFO  16:44:26,112 MicroScheduler -   -> 719 reads (0.27% of total) failing BadMateFilter
[2016-04-14T23:44Z] INFO  16:44:26,113 MicroScheduler -   -> 19656 reads (7.41% of total) failing DuplicateReadFilter
[2016-04-14T23:44Z] INFO  16:44:26,114 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-14T23:44Z] INFO  16:44:26,114 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:44Z] INFO  16:44:26,114 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-14T23:44Z] INFO  16:44:26,115 MicroScheduler -   -> 17633 reads (6.65% of total) failing MappingQualityZeroFilter
[2016-04-14T23:44Z] INFO  16:44:26,115 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:44Z] INFO  16:44:26,115 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-14T23:44Z] INFO  16:44:26,116 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-14T23:44Z] INFO  16:44:26,161 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:44Z] GATK: realign ('1', 175048468, 192127886) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-14T23:44Z] INFO  16:44:26,490 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:44Z] GATK: realign ('1', 15545821, 31186478) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-14T23:44Z] INFO  16:44:27,131 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:44Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-1_223162737_240072524-prep-prealign.bam
[2016-04-14T23:44Z] INFO  16:44:27,592 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:44Z] GATK: realign ('1', 207641871, 223156451) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-14T23:44Z] GATK RealignerTargetCreator: R14-18105_kapa-NGv3-PE100-NGv3-sort-1_223162737_240072524-prep-prealign.bam 1:223162738-240072524
[2016-04-14T23:44Z] GATK: RealignerTargetCreator
[2016-04-14T23:44Z] INFO  16:44:29,159 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:44Z] INFO  16:44:29,164 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:44Z] INFO  16:44:29,165 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:44Z] INFO  16:44:29,165 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:44Z] INFO  16:44:29,171 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/1/R14-18105_kapa-NGv3-PE100-NGv3-sort-1_175048468_192127886-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/1/R14-18105_kapa-NGv3-PE100-NGv3-sort-1_175048468_192127886-prep-prealign-realign.intervals -L 1:175048469-192127886 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/1/tx/tmpEewIGH/R14-18105_kapa-NGv3-PE100-NGv3-sort-1_175048468_192127886-prep.bam
[2016-04-14T23:44Z] INFO  16:44:29,193 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:44Z] INFO  16:44:29,193 HelpFormatter - Date/Time: 2016/04/14 16:44:29
[2016-04-14T23:44Z] INFO  16:44:29,194 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:44Z] INFO  16:44:29,194 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:44Z] INFO  16:44:29,445 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:44Z] INFO  16:44:29,596 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:44Z] INFO  16:44:29,592 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:44Z] INFO  16:44:29,607 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:44Z] INFO  16:44:29,608 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:44Z] INFO  16:44:29,608 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:44Z] INFO  16:44:29,608 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:44Z] INFO  16:44:29,614 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/1/R14-18105_kapa-NGv3-PE100-NGv3-sort-1_15545821_31186478-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/1/R14-18105_kapa-NGv3-PE100-NGv3-sort-1_15545821_31186478-prep-prealign-realign.intervals -L 1:15545822-31186478 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/1/tx/tmp2IJ_8c/R14-18105_kapa-NGv3-PE100-NGv3-sort-1_15545821_31186478-prep.bam
[2016-04-14T23:44Z] INFO  16:44:29,634 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:44Z] INFO  16:44:29,634 HelpFormatter - Date/Time: 2016/04/14 16:44:29
[2016-04-14T23:44Z] INFO  16:44:29,635 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:44Z] INFO  16:44:29,635 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:44Z] INFO  16:44:29,678 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-14T23:44Z] INFO  16:44:29,842 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:44Z] INFO  16:44:29,949 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:44Z] INFO  16:44:29,967 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:44Z] INFO  16:44:30,011 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.04
[2016-04-14T23:44Z] INFO  16:44:30,095 IntervalUtils - Processing 17079418 bp from intervals
[2016-04-14T23:44Z] WARN  16:44:30,112 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:44Z] INFO  16:44:30,214 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:44Z] INFO  16:44:30,433 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:44Z] INFO  16:44:30,434 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:44Z] INFO  16:44:30,445 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:44Z] INFO  16:44:30,446 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:44Z] INFO  16:44:30,465 IntervalUtils - Processing 15640657 bp from intervals
[2016-04-14T23:44Z] WARN  16:44:30,470 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:44Z] INFO  16:44:30,547 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:44Z] GATK pre-alignment ('2', 62362965, 79253295) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-14T23:44Z] INFO  16:44:30,690 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:44Z] INFO  16:44:30,775 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:44Z] INFO  16:44:30,778 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:44Z] INFO  16:44:30,779 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:44Z] INFO  16:44:30,779 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:44Z] INFO  16:44:30,789 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:44Z] INFO  16:44:30,790 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:44Z] INFO  16:44:30,791 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:44Z] INFO  16:44:30,806 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/1/R14-18105_kapa-NGv3-PE100-NGv3-sort-1_207641871_223156451-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/1/R14-18105_kapa-NGv3-PE100-NGv3-sort-1_207641871_223156451-prep-prealign-realign.intervals -L 1:207641872-223156451 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/1/tx/tmpV4YNB1/R14-18105_kapa-NGv3-PE100-NGv3-sort-1_207641871_223156451-prep.bam
[2016-04-14T23:44Z] INFO  16:44:30,806 ProgressMeter -            done   8995212.0    13.0 s       1.0 s      100.0%    13.0 s       0.0 s
[2016-04-14T23:44Z] INFO  16:44:30,806 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:44Z] INFO  16:44:30,806 ProgressMeter - Total runtime 13.81 secs, 0.23 min, 0.00 hours
[2016-04-14T23:44Z] INFO  16:44:30,811 MicroScheduler - 29252 reads were filtered out during the traversal out of approximately 202455 total reads (14.45%)
[2016-04-14T23:44Z] INFO  16:44:30,812 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:44Z] INFO  16:44:30,812 MicroScheduler -   -> 414 reads (0.20% of total) failing BadMateFilter
[2016-04-14T23:44Z] INFO  16:44:30,813 MicroScheduler -   -> 14922 reads (7.37% of total) failing DuplicateReadFilter
[2016-04-14T23:44Z] INFO  16:44:30,816 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:44Z] INFO  16:44:30,816 HelpFormatter - Date/Time: 2016/04/14 16:44:30
[2016-04-14T23:44Z] INFO  16:44:30,817 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:44Z] INFO  16:44:30,817 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:44Z] INFO  16:44:30,822 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-14T23:44Z] INFO  16:44:30,823 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:44Z] INFO  16:44:30,823 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-14T23:44Z] INFO  16:44:30,823 MicroScheduler -   -> 13916 reads (6.87% of total) failing MappingQualityZeroFilter
[2016-04-14T23:44Z] INFO  16:44:30,823 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:44Z] INFO  16:44:30,824 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-14T23:44Z] INFO  16:44:30,824 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-14T23:44Z] INFO  16:44:30,862 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:44Z] INFO  16:44:31,009 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:44Z] INFO  16:44:31,056 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:44Z] INFO  16:44:31,158 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:44Z] INFO  16:44:31,168 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:44Z] INFO  16:44:31,173 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:44Z] INFO  16:44:31,225 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-14T23:44Z] INFO  16:44:31,423 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:44Z] INFO  16:44:31,426 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:44Z] INFO  16:44:31,427 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:44Z] INFO  16:44:31,427 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:44Z] INFO  16:44:31,432 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/1/R14-18105_kapa-NGv3-PE100-NGv3-sort-1_223162737_240072524-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/1/tx/tmpxjlZoU/R14-18105_kapa-NGv3-PE100-NGv3-sort-1_223162737_240072524-prep-prealign-realign.intervals -l INFO -L 1:223162738-240072524 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-14T23:44Z] INFO  16:44:31,479 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:44Z] INFO  16:44:31,480 HelpFormatter - Date/Time: 2016/04/14 16:44:31
[2016-04-14T23:44Z] INFO  16:44:31,480 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:44Z] INFO  16:44:31,480 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:44Z] INFO  16:44:31,562 IntervalUtils - Processing 15514580 bp from intervals
[2016-04-14T23:44Z] WARN  16:44:31,578 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:44Z] INFO  16:44:31,587 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:44Z] INFO  16:44:31,713 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:44Z] INFO  16:44:31,777 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-14T23:44Z] INFO  16:44:31,788 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:44Z] INFO  16:44:31,857 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-14T23:44Z] INFO  16:44:31,958 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:44Z] INFO  16:44:31,959 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:44Z] INFO  16:44:31,959 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:44Z] INFO  16:44:31,960 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:44Z] INFO  16:44:32,174 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:44Z] INFO  16:44:32,246 IntervalUtils - Processing 16909787 bp from intervals
[2016-04-14T23:44Z] WARN  16:44:32,252 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:44Z] INFO  16:44:32,334 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:44Z] INFO  16:44:32,335 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:44Z] GATK: realign ('1', 240255409, 249250621) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-14T23:44Z] INFO  16:44:32,426 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:44Z] INFO  16:44:32,494 ProgressMeter -      2:26700206    100001.0    30.0 s       5.0 m       71.6%    41.0 s      11.0 s
[2016-04-14T23:44Z] INFO  16:44:32,699 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:44Z] INFO  16:44:32,700 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:44Z] INFO  16:44:32,701 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:44Z] INFO  16:44:32,702 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-14T23:44Z] INFO  16:44:33,211 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:44Z] INFO  16:44:33,214 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:44Z] INFO  16:44:33,215 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:44Z] INFO  16:44:33,215 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:44Z] INFO  16:44:33,220 HelpFormatter - Program Args: -T PrintReads -L 2:62362966-79253295 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/2/tx/tmpGkf2kE/R14-18105_kapa-NGv3-PE100-NGv3-sort-2_62362965_79253295-prep-prealign.bam
[2016-04-14T23:44Z] INFO  16:44:33,229 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:44Z] INFO  16:44:33,230 HelpFormatter - Date/Time: 2016/04/14 16:44:33
[2016-04-14T23:44Z] INFO  16:44:33,231 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:44Z] INFO  16:44:33,231 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:44Z] INFO  16:44:33,447 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:44Z] INFO  16:44:34,008 ProgressMeter -            done   1.5514844E7    16.0 s       1.0 s      100.0%    16.0 s       0.0 s
[2016-04-14T23:44Z] INFO  16:44:34,009 ProgressMeter - Total runtime 16.40 secs, 0.27 min, 0.00 hours
[2016-04-14T23:44Z] INFO  16:44:34,014 MicroScheduler - 13493 reads were filtered out during the traversal out of approximately 161305 total reads (8.36%)
[2016-04-14T23:44Z] INFO  16:44:34,021 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:44Z] INFO  16:44:34,022 MicroScheduler -   -> 476 reads (0.30% of total) failing BadMateFilter
[2016-04-14T23:44Z] INFO  16:44:34,023 MicroScheduler -   -> 12701 reads (7.87% of total) failing DuplicateReadFilter
[2016-04-14T23:44Z] INFO  16:44:34,023 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-14T23:44Z] INFO  16:44:34,024 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:44Z] INFO  16:44:34,025 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-14T23:44Z] INFO  16:44:34,025 MicroScheduler -   -> 316 reads (0.20% of total) failing MappingQualityZeroFilter
[2016-04-14T23:44Z] INFO  16:44:34,026 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:44Z] INFO  16:44:34,027 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-14T23:44Z] INFO  16:44:34,027 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-14T23:44Z] INFO  16:44:34,754 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-14T23:44Z] INFO  16:44:34,814 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:44Z] INFO  16:44:34,842 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:44Z] INFO  16:44:34,895 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-14T23:44Z] INFO  16:44:34,920 IntervalUtils - Processing 16890330 bp from intervals
[2016-04-14T23:44Z] INFO  16:44:34,991 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:44Z] INFO  16:44:35,297 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:44Z] INFO  16:44:35,299 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:44Z] INFO  16:44:35,300 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:44Z] INFO  16:44:35,300 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:44Z] INFO  16:44:35,329 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:44Z] INFO  16:44:35,465 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:44Z] INFO  16:44:35,471 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:44Z] GATK: realign ('2', 0, 15514844) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-14T23:44Z] INFO  16:44:35,498 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:44Z] INFO  16:44:35,501 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:44Z] INFO  16:44:35,501 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:44Z] INFO  16:44:35,502 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:44Z] INFO  16:44:35,506 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/1/R14-18105_kapa-NGv3-PE100-NGv3-sort-1_240255409_249250621-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/1/R14-18105_kapa-NGv3-PE100-NGv3-sort-1_240255409_249250621-prep-prealign-realign.intervals -L 1:240255410-249250621 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/1/tx/tmpCtLVBl/R14-18105_kapa-NGv3-PE100-NGv3-sort-1_240255409_249250621-prep.bam
[2016-04-14T23:44Z] INFO  16:44:35,527 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:44Z] INFO  16:44:35,528 HelpFormatter - Date/Time: 2016/04/14 16:44:35
[2016-04-14T23:44Z] INFO  16:44:35,528 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:44Z] INFO  16:44:35,528 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:44Z] INFO  16:44:35,661 ProgressMeter -      2:43726119    100001.0    30.0 s       5.0 m       80.9%    37.0 s       7.0 s
[2016-04-14T23:44Z] INFO  16:44:35,826 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:44Z] INFO  16:44:35,985 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:44Z] INFO  16:44:36,009 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:44Z] INFO  16:44:36,100 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.09
[2016-04-14T23:44Z] INFO  16:44:36,474 IntervalUtils - Processing 8995212 bp from intervals
[2016-04-14T23:44Z] WARN  16:44:36,480 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:44Z] INFO  16:44:36,551 ProgressMeter -            done   1.5542096E7    21.0 s       1.0 s      100.0%    21.0 s       0.0 s
[2016-04-14T23:44Z] INFO  16:44:36,551 ProgressMeter - Total runtime 21.16 secs, 0.35 min, 0.01 hours
[2016-04-14T23:44Z] INFO  16:44:36,556 MicroScheduler - 36224 reads were filtered out during the traversal out of approximately 405467 total reads (8.93%)
[2016-04-14T23:44Z] INFO  16:44:36,556 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:44Z] INFO  16:44:36,557 MicroScheduler -   -> 754 reads (0.19% of total) failing BadMateFilter
[2016-04-14T23:44Z] INFO  16:44:36,557 MicroScheduler -   -> 31729 reads (7.83% of total) failing DuplicateReadFilter
[2016-04-14T23:44Z] INFO  16:44:36,557 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-14T23:44Z] INFO  16:44:36,557 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:44Z] INFO  16:44:36,558 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-14T23:44Z] INFO  16:44:36,558 MicroScheduler -   -> 3741 reads (0.92% of total) failing MappingQualityZeroFilter
[2016-04-14T23:44Z] INFO  16:44:36,558 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:44Z] INFO  16:44:36,559 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-14T23:44Z] INFO  16:44:36,559 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-14T23:44Z] INFO  16:44:36,575 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:44Z] INFO  16:44:36,696 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:44Z] INFO  16:44:36,698 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:44Z] INFO  16:44:36,698 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:44Z] INFO  16:44:36,699 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:44Z] INFO  16:44:36,885 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:44Z] INFO  16:44:37,003 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:44Z] INFO  16:44:38,040 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@7172f77a
[2016-04-14T23:44Z] INFO  16:44:38,125 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:44Z] GATK: realign ('1', 159504867, 175046963) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-14T23:44Z] INFO  16:44:38,152 ProgressMeter -            done    184947.0    26.0 s       2.3 m      100.0%    26.0 s       0.0 s
[2016-04-14T23:44Z] INFO  16:44:38,153 ProgressMeter - Total runtime 26.01 secs, 0.43 min, 0.01 hours
[2016-04-14T23:44Z] INFO  16:44:38,153 MicroScheduler - 129 reads were filtered out during the traversal out of approximately 185076 total reads (0.07%)
[2016-04-14T23:44Z] INFO  16:44:38,153 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:44Z] INFO  16:44:38,154 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:44Z] INFO  16:44:38,154 MicroScheduler -   -> 129 reads (0.07% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:44Z] INFO  16:44:38,523 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:44Z] INFO  16:44:38,527 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:44Z] INFO  16:44:38,527 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:44Z] INFO  16:44:38,528 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:44Z] INFO  16:44:38,532 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/2/R14-18105_kapa-NGv3-PE100-NGv3-sort-2_0_15514844-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/2/R14-18105_kapa-NGv3-PE100-NGv3-sort-2_0_15514844-prep-prealign-realign.intervals -L 2:1-15514844 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/2/tx/tmpM8oYN5/R14-18105_kapa-NGv3-PE100-NGv3-sort-2_0_15514844-prep.bam
[2016-04-14T23:44Z] INFO  16:44:38,548 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:44Z] INFO  16:44:38,549 HelpFormatter - Date/Time: 2016/04/14 16:44:38
[2016-04-14T23:44Z] INFO  16:44:38,550 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:44Z] INFO  16:44:38,550 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:44Z] INFO  16:44:38,635 ProgressMeter -            done   3.4773037E7    29.0 s       0.0 s      100.0%    29.0 s       0.0 s
[2016-04-14T23:44Z] INFO  16:44:38,636 ProgressMeter - Total runtime 29.42 secs, 0.49 min, 0.01 hours
[2016-04-14T23:44Z] INFO  16:44:38,644 MicroScheduler - 47433 reads were filtered out during the traversal out of approximately 422731 total reads (11.22%)
[2016-04-14T23:44Z] INFO  16:44:38,645 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:44Z] INFO  16:44:38,645 MicroScheduler -   -> 1014 reads (0.24% of total) failing BadMateFilter
[2016-04-14T23:44Z] INFO  16:44:38,657 MicroScheduler -   -> 32366 reads (7.66% of total) failing DuplicateReadFilter
[2016-04-14T23:44Z] INFO  16:44:38,657 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-14T23:44Z] INFO  16:44:38,657 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:44Z] INFO  16:44:38,657 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-14T23:44Z] INFO  16:44:38,658 MicroScheduler -   -> 14053 reads (3.32% of total) failing MappingQualityZeroFilter
[2016-04-14T23:44Z] INFO  16:44:38,658 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:44Z] INFO  16:44:38,658 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-14T23:44Z] INFO  16:44:38,658 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-14T23:44Z] INFO  16:44:38,784 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:44Z] INFO  16:44:38,932 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:44Z] INFO  16:44:38,941 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:44Z] INFO  16:44:38,993 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-14T23:44Z] INFO  16:44:39,395 IntervalUtils - Processing 15514844 bp from intervals
[2016-04-14T23:44Z] WARN  16:44:39,400 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:44Z] INFO  16:44:39,479 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:44Z] INFO  16:44:39,600 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:44Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-2_46707543_62228117-prep-prealign.bam
[2016-04-14T23:44Z] INFO  16:44:39,644 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:44Z] INFO  16:44:39,645 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:44Z] INFO  16:44:39,646 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:44Z] INFO  16:44:39,647 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:44Z] INFO  16:44:39,821 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:44Z] INFO  16:44:39,968 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:44Z] INFO  16:44:40,054 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:44Z] GATK: realign ('1', 108994811, 143767848) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-14T23:44Z] GATK RealignerTargetCreator: R14-18105_kapa-NGv3-PE100-NGv3-sort-2_46707543_62228117-prep-prealign.bam 2:46707544-62228117
[2016-04-14T23:44Z] GATK: RealignerTargetCreator
[2016-04-14T23:44Z] INFO  16:44:40,857 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:44Z] INFO  16:44:40,860 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:44Z] INFO  16:44:40,861 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:44Z] INFO  16:44:40,862 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:44Z] INFO  16:44:40,867 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/1/R14-18105_kapa-NGv3-PE100-NGv3-sort-1_159504867_175046963-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/1/R14-18105_kapa-NGv3-PE100-NGv3-sort-1_159504867_175046963-prep-prealign-realign.intervals -L 1:159504868-175046963 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/1/tx/tmpoJzjGr/R14-18105_kapa-NGv3-PE100-NGv3-sort-1_159504867_175046963-prep.bam
[2016-04-14T23:44Z] INFO  16:44:40,895 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:44Z] INFO  16:44:40,906 HelpFormatter - Date/Time: 2016/04/14 16:44:40
[2016-04-14T23:44Z] INFO  16:44:40,907 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:44Z] INFO  16:44:40,908 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:44Z] INFO  16:44:41,126 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:44Z] INFO  16:44:41,312 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:44Z] INFO  16:44:41,321 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:44Z] INFO  16:44:41,368 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.04
[2016-04-14T23:44Z] INFO  16:44:41,774 IntervalUtils - Processing 15542096 bp from intervals
[2016-04-14T23:44Z] WARN  16:44:41,789 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:44Z] INFO  16:44:41,892 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:44Z] INFO  16:44:42,039 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:44Z] INFO  16:44:42,041 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:44Z] INFO  16:44:42,041 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:44Z] INFO  16:44:42,042 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:44Z] INFO  16:44:42,177 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:44Z] INFO  16:44:42,273 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@7172f77a
[2016-04-14T23:44Z] INFO  16:44:42,339 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:44Z] INFO  16:44:42,376 ProgressMeter -            done    233877.0    36.0 s       2.6 m      100.0%    36.0 s       0.0 s
[2016-04-14T23:44Z] INFO  16:44:42,377 ProgressMeter - Total runtime 36.88 secs, 0.61 min, 0.01 hours
[2016-04-14T23:44Z] INFO  16:44:42,378 MicroScheduler - 2237 reads were filtered out during the traversal out of approximately 236114 total reads (0.95%)
[2016-04-14T23:44Z] INFO  16:44:42,379 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:44Z] INFO  16:44:42,380 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:44Z] INFO  16:44:42,380 MicroScheduler -   -> 2237 reads (0.95% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:44Z] INFO  16:44:42,441 ProgressMeter -            done   1.5527177E7    30.0 s       1.0 s      100.0%    30.0 s       0.0 s
[2016-04-14T23:44Z] INFO  16:44:42,442 ProgressMeter - Total runtime 30.01 secs, 0.50 min, 0.01 hours
[2016-04-14T23:44Z] INFO  16:44:42,447 MicroScheduler - 66833 reads were filtered out during the traversal out of approximately 736908 total reads (9.07%)
[2016-04-14T23:44Z] INFO  16:44:42,448 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:44Z] INFO  16:44:42,449 MicroScheduler -   -> 1255 reads (0.17% of total) failing BadMateFilter
[2016-04-14T23:44Z] INFO  16:44:42,450 MicroScheduler -   -> 58471 reads (7.93% of total) failing DuplicateReadFilter
[2016-04-14T23:44Z] INFO  16:44:42,451 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-14T23:44Z] INFO  16:44:42,451 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:44Z] INFO  16:44:42,452 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-14T23:44Z] INFO  16:44:42,453 MicroScheduler -   -> 7107 reads (0.96% of total) failing MappingQualityZeroFilter
[2016-04-14T23:44Z] INFO  16:44:42,454 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:44Z] INFO  16:44:42,454 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-14T23:44Z] INFO  16:44:42,455 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-14T23:44Z] INFO  16:44:43,248 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:44Z] INFO  16:44:43,252 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:44Z] INFO  16:44:43,252 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:44Z] INFO  16:44:43,253 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:44Z] INFO  16:44:43,258 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/1/R14-18105_kapa-NGv3-PE100-NGv3-sort-1_108994811_143767848-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/1/R14-18105_kapa-NGv3-PE100-NGv3-sort-1_108994811_143767848-prep-prealign-realign.intervals -L 1:108994812-143767848 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/1/tx/tmpjI0RPd/R14-18105_kapa-NGv3-PE100-NGv3-sort-1_108994811_143767848-prep.bam
[2016-04-14T23:44Z] INFO  16:44:43,271 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:44Z] INFO  16:44:43,272 HelpFormatter - Date/Time: 2016/04/14 16:44:43
[2016-04-14T23:44Z] INFO  16:44:43,272 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:44Z] INFO  16:44:43,272 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:44Z] INFO  16:44:43,355 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:44Z] INFO  16:44:43,358 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:44Z] INFO  16:44:43,359 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:44Z] INFO  16:44:43,359 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:44Z] INFO  16:44:43,364 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/2/R14-18105_kapa-NGv3-PE100-NGv3-sort-2_46707543_62228117-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/2/tx/tmpqiKSqU/R14-18105_kapa-NGv3-PE100-NGv3-sort-2_46707543_62228117-prep-prealign-realign.intervals -l INFO -L 2:46707544-62228117 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-14T23:44Z] INFO  16:44:43,380 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:44Z] INFO  16:44:43,391 HelpFormatter - Date/Time: 2016/04/14 16:44:43
[2016-04-14T23:44Z] INFO  16:44:43,392 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:44Z] INFO  16:44:43,393 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:44Z] INFO  16:44:43,489 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:44Z] INFO  16:44:43,611 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:44Z] INFO  16:44:43,751 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-14T23:44Z] INFO  16:44:43,761 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:44Z] INFO  16:44:43,761 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:44Z] INFO  16:44:43,771 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:44Z] INFO  16:44:43,800 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.04
[2016-04-14T23:44Z] INFO  16:44:43,812 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.04
[2016-04-14T23:44Z] INFO  16:44:43,823 ProgressMeter -            done   1.5511908E7    22.0 s       1.0 s      100.0%    22.0 s       0.0 s
[2016-04-14T23:44Z] INFO  16:44:43,824 ProgressMeter - Total runtime 22.64 secs, 0.38 min, 0.01 hours
[2016-04-14T23:44Z] INFO  16:44:43,828 MicroScheduler - 39131 reads were filtered out during the traversal out of approximately 425034 total reads (9.21%)
[2016-04-14T23:44Z] INFO  16:44:43,829 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:44Z] INFO  16:44:43,830 MicroScheduler -   -> 832 reads (0.20% of total) failing BadMateFilter
[2016-04-14T23:44Z] INFO  16:44:43,830 MicroScheduler -   -> 33191 reads (7.81% of total) failing DuplicateReadFilter
[2016-04-14T23:44Z] INFO  16:44:43,831 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-14T23:44Z] INFO  16:44:43,831 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:44Z] INFO  16:44:43,832 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-14T23:44Z] INFO  16:44:43,833 MicroScheduler -   -> 5108 reads (1.20% of total) failing MappingQualityZeroFilter
[2016-04-14T23:44Z] INFO  16:44:43,833 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:44Z] INFO  16:44:43,834 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-14T23:44Z] INFO  16:44:43,834 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-14T23:44Z] INFO  16:44:43,995 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:44Z] INFO  16:44:44,010 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:44Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-2_31135088_46706841-prep-prealign.bam
[2016-04-14T23:44Z] GATK: realign ('1', 31187093, 46714270) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-14T23:44Z] INFO  16:44:44,088 IntervalUtils - Processing 15520574 bp from intervals
[2016-04-14T23:44Z] WARN  16:44:44,093 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:44Z] INFO  16:44:44,163 IntervalUtils - Processing 34773037 bp from intervals
[2016-04-14T23:44Z] WARN  16:44:44,177 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:44Z] INFO  16:44:44,214 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:44Z] INFO  16:44:44,273 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:44Z] INFO  16:44:44,419 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:44Z] INFO  16:44:44,420 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:44Z] INFO  16:44:44,420 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:44Z] INFO  16:44:44,421 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-14T23:44Z] INFO  16:44:44,492 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:44Z] INFO  16:44:44,492 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:44Z] INFO  16:44:44,493 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:44Z] INFO  16:44:44,493 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:44Z] INFO  16:44:44,675 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:44Z] GATK RealignerTargetCreator: R14-18105_kapa-NGv3-PE100-NGv3-sort-2_31135088_46706841-prep-prealign.bam 2:31135089-46706841
[2016-04-14T23:44Z] GATK: RealignerTargetCreator
[2016-04-14T23:44Z] INFO  16:44:45,052 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:44Z] INFO  16:44:45,209 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:44Z] GATK: realign ('1', 192128349, 207640257) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-14T23:44Z] INFO  16:44:46,262 ProgressMeter -     1:151554219    500012.0    91.0 s       3.0 m       49.4%     3.1 m      93.0 s
[2016-04-14T23:44Z] INFO  16:44:47,150 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:44Z] INFO  16:44:47,154 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:44Z] INFO  16:44:47,154 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:44Z] INFO  16:44:47,155 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:44Z] INFO  16:44:47,160 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/1/R14-18105_kapa-NGv3-PE100-NGv3-sort-1_31187093_46714270-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/1/R14-18105_kapa-NGv3-PE100-NGv3-sort-1_31187093_46714270-prep-prealign-realign.intervals -L 1:31187094-46714270 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/1/tx/tmpgvwwjT/R14-18105_kapa-NGv3-PE100-NGv3-sort-1_31187093_46714270-prep.bam
[2016-04-14T23:44Z] INFO  16:44:47,171 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:44Z] INFO  16:44:47,172 HelpFormatter - Date/Time: 2016/04/14 16:44:47
[2016-04-14T23:44Z] INFO  16:44:47,173 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:44Z] INFO  16:44:47,173 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:44Z] INFO  16:44:47,390 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:44Z] INFO  16:44:47,499 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:44Z] INFO  16:44:47,509 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:44Z] INFO  16:44:47,569 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-14T23:44Z] INFO  16:44:47,632 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:44Z] INFO  16:44:47,646 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:44Z] INFO  16:44:47,647 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:44Z] INFO  16:44:47,648 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:44Z] INFO  16:44:47,653 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/2/R14-18105_kapa-NGv3-PE100-NGv3-sort-2_31135088_46706841-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/2/tx/tmpmsasyF/R14-18105_kapa-NGv3-PE100-NGv3-sort-2_31135088_46706841-prep-prealign-realign.intervals -l INFO -L 2:31135089-46706841 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-14T23:44Z] INFO  16:44:47,672 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:44Z] INFO  16:44:47,672 HelpFormatter - Date/Time: 2016/04/14 16:44:47
[2016-04-14T23:44Z] INFO  16:44:47,672 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:44Z] INFO  16:44:47,673 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:44Z] INFO  16:44:47,828 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:44Z] INFO  16:44:48,010 IntervalUtils - Processing 15527177 bp from intervals
[2016-04-14T23:44Z] WARN  16:44:48,015 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:44Z] INFO  16:44:48,068 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-14T23:44Z] INFO  16:44:48,079 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:44Z] INFO  16:44:48,082 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:44Z] INFO  16:44:48,136 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-14T23:44Z] INFO  16:44:48,247 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:44Z] INFO  16:44:48,248 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:44Z] INFO  16:44:48,248 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:44Z] INFO  16:44:48,249 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:44Z] INFO  16:44:48,378 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:44Z] INFO  16:44:48,381 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:44Z] INFO  16:44:48,381 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:44Z] INFO  16:44:48,381 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:44Z] INFO  16:44:48,396 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/1/R14-18105_kapa-NGv3-PE100-NGv3-sort-1_192128349_207640257-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/1/R14-18105_kapa-NGv3-PE100-NGv3-sort-1_192128349_207640257-prep-prealign-realign.intervals -L 1:192128350-207640257 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/1/tx/tmpX73siM/R14-18105_kapa-NGv3-PE100-NGv3-sort-1_192128349_207640257-prep.bam
[2016-04-14T23:44Z] INFO  16:44:48,423 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:44Z] INFO  16:44:48,423 HelpFormatter - Date/Time: 2016/04/14 16:44:48
[2016-04-14T23:44Z] INFO  16:44:48,424 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:44Z] INFO  16:44:48,424 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:44Z] INFO  16:44:48,452 IntervalUtils - Processing 15571753 bp from intervals
[2016-04-14T23:44Z] WARN  16:44:48,457 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:44Z] INFO  16:44:48,470 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:44Z] INFO  16:44:48,540 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:44Z] INFO  16:44:48,586 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:44Z] INFO  16:44:48,628 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:44Z] INFO  16:44:48,769 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:44Z] INFO  16:44:48,786 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:44Z] INFO  16:44:48,787 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:44Z] INFO  16:44:48,789 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:44Z] INFO  16:44:48,789 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:44Z] INFO  16:44:48,790 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-14T23:44Z] INFO  16:44:48,885 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.10
[2016-04-14T23:44Z] INFO  16:44:49,225 IntervalUtils - Processing 15511908 bp from intervals
[2016-04-14T23:44Z] WARN  16:44:49,230 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:44Z] INFO  16:44:49,300 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:44Z] INFO  16:44:49,508 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:44Z] INFO  16:44:49,510 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:44Z] INFO  16:44:49,511 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:44Z] INFO  16:44:49,512 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:44Z] INFO  16:44:49,727 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:44Z] INFO  16:44:49,938 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:44Z] INFO  16:44:50,143 ProgressMeter -            done    264533.0    19.0 s      74.0 s      100.0%    19.0 s       0.0 s
[2016-04-14T23:44Z] INFO  16:44:50,143 ProgressMeter - Total runtime 19.71 secs, 0.33 min, 0.01 hours
[2016-04-14T23:44Z] INFO  16:44:50,147 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 264533 total reads (0.00%)
[2016-04-14T23:44Z] INFO  16:44:50,148 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:44Z] INFO  16:44:50,148 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:44Z] INFO  16:44:50,149 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:44Z] INFO  16:44:51,771 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:44Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-1_175048468_192127886-prep.bam
[2016-04-14T23:44Z] INFO  16:44:51,988 ProgressMeter -            done    264105.0    20.0 s      75.0 s      100.0%    20.0 s       0.0 s
[2016-04-14T23:44Z] INFO  16:44:51,989 ProgressMeter - Total runtime 20.03 secs, 0.33 min, 0.01 hours
[2016-04-14T23:44Z] INFO  16:44:51,993 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 264105 total reads (0.00%)
[2016-04-14T23:44Z] INFO  16:44:51,994 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:44Z] INFO  16:44:51,995 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:44Z] INFO  16:44:51,996 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:44Z] INFO  16:44:52,537 ProgressMeter -            done    201016.0    15.0 s      78.0 s       99.8%    15.0 s       0.0 s
[2016-04-14T23:44Z] INFO  16:44:52,537 ProgressMeter - Total runtime 15.84 secs, 0.26 min, 0.00 hours
[2016-04-14T23:44Z] INFO  16:44:52,542 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 201016 total reads (0.00%)
[2016-04-14T23:44Z] INFO  16:44:52,542 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:44Z] INFO  16:44:52,542 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:44Z] INFO  16:44:52,543 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:44Z] GATK pre-alignment ('2', 79253838, 95537822) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-14T23:44Z] INFO  16:44:53,488 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:44Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-1_207641871_223156451-prep.bam
[2016-04-14T23:44Z] INFO  16:44:53,808 ProgressMeter -       1:7723829    400008.0    30.0 s      76.0 s       49.7%    60.0 s      30.0 s
[2016-04-14T23:44Z] INFO  16:44:53,948 ProgressMeter -            done    160602.0    14.0 s      89.0 s       99.9%    14.0 s       0.0 s
[2016-04-14T23:44Z] INFO  16:44:53,948 ProgressMeter - Total runtime 14.30 secs, 0.24 min, 0.00 hours
[2016-04-14T23:44Z] INFO  16:44:53,952 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 160602 total reads (0.00%)
[2016-04-14T23:44Z] INFO  16:44:53,952 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:44Z] INFO  16:44:53,952 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:44Z] INFO  16:44:53,953 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:44Z] INFO  16:44:54,109 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:44Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-1_240255409_249250621-prep.bam
[2016-04-14T23:44Z] GATK pre-alignment ('2', 95538561, 111273222) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-14T23:44Z] GATK pre-alignment ('2', 111281072, 127413888) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-14T23:44Z] INFO  16:44:55,046 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@5fe152b7
[2016-04-14T23:44Z] INFO  16:44:55,120 ProgressMeter -            done    370225.0    52.0 s       2.4 m      100.0%    52.0 s       0.0 s
[2016-04-14T23:44Z] INFO  16:44:55,121 ProgressMeter - Total runtime 52.67 secs, 0.88 min, 0.01 hours
[2016-04-14T23:44Z] INFO  16:44:55,121 MicroScheduler - 175 reads were filtered out during the traversal out of approximately 370400 total reads (0.05%)
[2016-04-14T23:44Z] INFO  16:44:55,121 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:44Z] INFO  16:44:55,122 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:44Z] INFO  16:44:55,122 MicroScheduler -   -> 175 reads (0.05% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:44Z] INFO  16:44:55,435 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:44Z] INFO  16:44:55,439 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:44Z] INFO  16:44:55,440 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:44Z] INFO  16:44:55,441 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:44Z] INFO  16:44:55,446 HelpFormatter - Program Args: -T PrintReads -L 2:79253839-95537822 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/2/tx/tmpt9oG7t/R14-18105_kapa-NGv3-PE100-NGv3-sort-2_79253838_95537822-prep-prealign.bam
[2016-04-14T23:44Z] INFO  16:44:55,455 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:44Z] INFO  16:44:55,474 HelpFormatter - Date/Time: 2016/04/14 16:44:55
[2016-04-14T23:44Z] INFO  16:44:55,475 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:44Z] INFO  16:44:55,475 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:44Z] INFO  16:44:55,632 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:44Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-2_0_15514844-prep.bam
[2016-04-14T23:44Z] INFO  16:44:55,666 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:44Z] GATK pre-alignment ('2', 127433207, 143643105) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-14T23:44Z] INFO  16:44:56,521 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:44Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-2_15519725_31133925-prep-prealign.bam
[2016-04-14T23:44Z] INFO  16:44:56,900 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-14T23:44Z] INFO  16:44:56,941 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:44Z] INFO  16:44:56,945 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:44Z] INFO  16:44:56,945 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:44Z] INFO  16:44:56,946 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:44Z] INFO  16:44:56,956 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:44Z] INFO  16:44:56,956 HelpFormatter - Program Args: -T PrintReads -L 2:95538562-111273222 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/2/tx/tmpQuGyCp/R14-18105_kapa-NGv3-PE100-NGv3-sort-2_95538561_111273222-prep-prealign.bam
[2016-04-14T23:44Z] INFO  16:44:56,964 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:44Z] INFO  16:44:56,965 HelpFormatter - Date/Time: 2016/04/14 16:44:56
[2016-04-14T23:44Z] INFO  16:44:56,966 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:44Z] INFO  16:44:56,966 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:44Z] INFO  16:44:56,966 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:44Z] INFO  16:44:57,015 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-14T23:44Z] INFO  16:44:57,037 IntervalUtils - Processing 16283984 bp from intervals
[2016-04-14T23:44Z] INFO  16:44:57,121 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:44Z] INFO  16:44:57,193 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:44Z] INFO  16:44:57,449 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:44Z] INFO  16:44:57,450 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:44Z] INFO  16:44:57,451 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:44Z] INFO  16:44:57,452 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:44Z] INFO  16:44:57,485 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:44Z] INFO  16:44:57,624 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:44Z] INFO  16:44:57,814 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:44Z] INFO  16:44:57,818 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:44Z] INFO  16:44:57,818 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:44Z] INFO  16:44:57,819 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:44Z] GATK RealignerTargetCreator: R14-18105_kapa-NGv3-PE100-NGv3-sort-2_15519725_31133925-prep-prealign.bam 2:15519726-31133925
[2016-04-14T23:44Z] GATK: RealignerTargetCreator
[2016-04-14T23:44Z] INFO  16:44:57,832 HelpFormatter - Program Args: -T PrintReads -L 2:111281073-127413888 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/2/tx/tmprE247B/R14-18105_kapa-NGv3-PE100-NGv3-sort-2_111281072_127413888-prep-prealign.bam
[2016-04-14T23:44Z] INFO  16:44:57,871 ProgressMeter -            done   1.6909787E7    25.0 s       1.0 s      100.0%    25.0 s       0.0 s
[2016-04-14T23:44Z] INFO  16:44:57,872 ProgressMeter - Total runtime 25.17 secs, 0.42 min, 0.01 hours
[2016-04-14T23:44Z] INFO  16:44:57,876 MicroScheduler - 38919 reads were filtered out during the traversal out of approximately 447977 total reads (8.69%)
[2016-04-14T23:44Z] INFO  16:44:57,876 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:44Z] INFO  16:44:57,876 MicroScheduler -   -> 969 reads (0.22% of total) failing BadMateFilter
[2016-04-14T23:44Z] INFO  16:44:57,877 MicroScheduler -   -> 35706 reads (7.97% of total) failing DuplicateReadFilter
[2016-04-14T23:44Z] INFO  16:44:57,877 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-14T23:44Z] INFO  16:44:57,877 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:44Z] INFO  16:44:57,877 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-14T23:44Z] INFO  16:44:57,878 MicroScheduler -   -> 2244 reads (0.50% of total) failing MappingQualityZeroFilter
[2016-04-14T23:44Z] INFO  16:44:57,878 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:44Z] INFO  16:44:57,876 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:44Z] INFO  16:44:57,876 HelpFormatter - Date/Time: 2016/04/14 16:44:57
[2016-04-14T23:44Z] INFO  16:44:57,878 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-14T23:44Z] INFO  16:44:57,879 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-14T23:44Z] INFO  16:44:57,876 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:44Z] INFO  16:44:57,876 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:44Z] INFO  16:44:58,065 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:44Z] INFO  16:44:58,233 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-14T23:44Z] INFO  16:44:58,325 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:44Z] INFO  16:44:58,333 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:44Z] INFO  16:44:58,366 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.03
[2016-04-14T23:44Z] INFO  16:44:58,380 IntervalUtils - Processing 15734661 bp from intervals
[2016-04-14T23:44Z] INFO  16:44:58,486 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:44Z] INFO  16:44:58,800 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:44Z] INFO  16:44:58,802 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:44Z] INFO  16:44:58,802 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:44Z] INFO  16:44:58,803 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:44Z] INFO  16:44:58,816 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:44Z] INFO  16:44:59,025 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:44Z] INFO  16:44:59,160 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:44Z] INFO  16:44:59,207 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-14T23:44Z] GATK: realign ('1', 223162737, 240072524) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-14T23:44Z] INFO  16:44:59,268 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:44Z] INFO  16:44:59,272 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:44Z] INFO  16:44:59,273 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:44Z] INFO  16:44:59,273 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:44Z] INFO  16:44:59,279 HelpFormatter - Program Args: -T PrintReads -L 2:127433208-143643105 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/2/tx/tmpOgWOBL/R14-18105_kapa-NGv3-PE100-NGv3-sort-2_127433207_143643105-prep-prealign.bam
[2016-04-14T23:44Z] INFO  16:44:59,288 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:44Z] INFO  16:44:59,299 HelpFormatter - Date/Time: 2016/04/14 16:44:59
[2016-04-14T23:44Z] INFO  16:44:59,300 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:44Z] INFO  16:44:59,301 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:44Z] INFO  16:44:59,302 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:44Z] INFO  16:44:59,319 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:44Z] INFO  16:44:59,366 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-14T23:44Z] INFO  16:44:59,390 IntervalUtils - Processing 16132816 bp from intervals
[2016-04-14T23:44Z] INFO  16:44:59,475 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:44Z] INFO  16:44:59,501 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:44Z] INFO  16:44:59,847 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:44Z] INFO  16:44:59,848 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:44Z] INFO  16:44:59,849 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:44Z] INFO  16:44:59,850 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:44Z] INFO  16:44:59,862 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:45Z] INFO  16:45:00,025 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:45Z] INFO  16:45:00,408 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:45Z] INFO  16:45:00,411 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:45Z] INFO  16:45:00,412 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:45Z] INFO  16:45:00,413 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:45Z] INFO  16:45:00,417 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/2/R14-18105_kapa-NGv3-PE100-NGv3-sort-2_15519725_31133925-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/2/tx/tmp6HoeOU/R14-18105_kapa-NGv3-PE100-NGv3-sort-2_15519725_31133925-prep-prealign-realign.intervals -l INFO -L 2:15519726-31133925 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-14T23:45Z] INFO  16:45:00,434 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:45Z] INFO  16:45:00,442 HelpFormatter - Date/Time: 2016/04/14 16:45:00
[2016-04-14T23:45Z] INFO  16:45:00,443 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:45Z] INFO  16:45:00,454 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:45Z] INFO  16:45:00,545 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-14T23:45Z] INFO  16:45:00,596 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:45Z] INFO  16:45:00,629 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:45Z] INFO  16:45:00,638 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:45Z] INFO  16:45:00,698 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-14T23:45Z] INFO  16:45:00,713 IntervalUtils - Processing 16209898 bp from intervals
[2016-04-14T23:45Z] INFO  16:45:00,789 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:45Z] INFO  16:45:00,897 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-14T23:45Z] INFO  16:45:00,906 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:45Z] INFO  16:45:00,991 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-14T23:45Z] INFO  16:45:01,119 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:45Z] INFO  16:45:01,119 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:45Z] INFO  16:45:01,120 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:45Z] INFO  16:45:01,120 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:45Z] INFO  16:45:01,139 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:45Z] INFO  16:45:01,286 ProgressMeter -            done   1.5520574E7    16.0 s       1.0 s      100.0%    16.0 s       0.0 s
[2016-04-14T23:45Z] INFO  16:45:01,287 ProgressMeter - Total runtime 16.87 secs, 0.28 min, 0.00 hours
[2016-04-14T23:45Z] INFO  16:45:01,287 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:45Z] INFO  16:45:01,291 MicroScheduler - 15271 reads were filtered out during the traversal out of approximately 186219 total reads (8.20%)
[2016-04-14T23:45Z] INFO  16:45:01,293 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:45Z] INFO  16:45:01,293 MicroScheduler -   -> 508 reads (0.27% of total) failing BadMateFilter
[2016-04-14T23:45Z] INFO  16:45:01,294 MicroScheduler -   -> 14408 reads (7.74% of total) failing DuplicateReadFilter
[2016-04-14T23:45Z] INFO  16:45:01,295 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-14T23:45Z] INFO  16:45:01,295 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:45Z] INFO  16:45:01,296 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-14T23:45Z] INFO  16:45:01,296 MicroScheduler -   -> 355 reads (0.19% of total) failing MappingQualityZeroFilter
[2016-04-14T23:45Z] INFO  16:45:01,297 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:45Z] INFO  16:45:01,298 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-14T23:45Z] INFO  16:45:01,298 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-14T23:45Z] INFO  16:45:01,300 IntervalUtils - Processing 15614200 bp from intervals
[2016-04-14T23:45Z] WARN  16:45:01,306 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:45Z] INFO  16:45:01,377 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:45Z] INFO  16:45:01,435 ProgressMeter -      1:21887659    300006.0    30.0 s     102.0 s       40.5%    73.0 s      43.0 s
[2016-04-14T23:45Z] INFO  16:45:01,608 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:45Z] INFO  16:45:01,609 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:45Z] INFO  16:45:01,610 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:45Z] INFO  16:45:01,610 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-14T23:45Z] INFO  16:45:01,812 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:45Z] INFO  16:45:01,816 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:45Z] INFO  16:45:01,817 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:45Z] INFO  16:45:01,817 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:45Z] INFO  16:45:01,822 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/1/R14-18105_kapa-NGv3-PE100-NGv3-sort-1_223162737_240072524-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/1/R14-18105_kapa-NGv3-PE100-NGv3-sort-1_223162737_240072524-prep-prealign-realign.intervals -L 1:223162738-240072524 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/1/tx/tmplX1TMo/R14-18105_kapa-NGv3-PE100-NGv3-sort-1_223162737_240072524-prep.bam
[2016-04-14T23:45Z] INFO  16:45:01,849 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:45Z] INFO  16:45:01,850 HelpFormatter - Date/Time: 2016/04/14 16:45:01
[2016-04-14T23:45Z] INFO  16:45:01,850 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:45Z] INFO  16:45:01,851 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:45Z] INFO  16:45:02,131 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:45Z] INFO  16:45:02,283 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:45Z] INFO  16:45:02,299 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:45Z] INFO  16:45:02,359 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-14T23:45Z] INFO  16:45:02,714 IntervalUtils - Processing 16909787 bp from intervals
[2016-04-14T23:45Z] WARN  16:45:02,720 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:45Z] INFO  16:45:02,792 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:45Z] INFO  16:45:02,863 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:45Z] GATK: realign ('2', 46707543, 62228117) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-14T23:45Z] INFO  16:45:02,950 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:45Z] INFO  16:45:02,951 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:45Z] INFO  16:45:02,965 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:45Z] INFO  16:45:02,976 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:45Z] INFO  16:45:03,162 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:45Z] INFO  16:45:03,365 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:45Z] INFO  16:45:05,322 ProgressMeter -      2:73716931    200003.0    30.0 s       2.5 m       67.2%    44.0 s      14.0 s
[2016-04-14T23:45Z] INFO  16:45:05,857 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:45Z] INFO  16:45:05,860 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:45Z] INFO  16:45:05,861 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:45Z] INFO  16:45:05,861 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:45Z] INFO  16:45:05,866 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/2/R14-18105_kapa-NGv3-PE100-NGv3-sort-2_46707543_62228117-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/2/R14-18105_kapa-NGv3-PE100-NGv3-sort-2_46707543_62228117-prep-prealign-realign.intervals -L 2:46707544-62228117 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/2/tx/tmp8Gx1Dh/R14-18105_kapa-NGv3-PE100-NGv3-sort-2_46707543_62228117-prep.bam
[2016-04-14T23:45Z] INFO  16:45:05,876 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:45Z] INFO  16:45:05,887 HelpFormatter - Date/Time: 2016/04/14 16:45:05
[2016-04-14T23:45Z] INFO  16:45:05,888 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:45Z] INFO  16:45:05,889 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:45Z] INFO  16:45:06,119 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:45Z] INFO  16:45:06,196 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:45Z] INFO  16:45:06,205 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:45Z] INFO  16:45:06,269 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-14T23:45Z] INFO  16:45:06,570 IntervalUtils - Processing 15520574 bp from intervals
[2016-04-14T23:45Z] WARN  16:45:06,575 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:45Z] INFO  16:45:06,688 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:45Z] INFO  16:45:06,827 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:45Z] INFO  16:45:06,843 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:45Z] INFO  16:45:06,844 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:45Z] INFO  16:45:06,844 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:45Z] INFO  16:45:07,030 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:45Z] INFO  16:45:07,228 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:45Z] INFO  16:45:07,405 ProgressMeter -            done   1.5571753E7    18.0 s       1.0 s      100.0%    18.0 s       0.0 s
[2016-04-14T23:45Z] INFO  16:45:07,406 ProgressMeter - Total runtime 18.62 secs, 0.31 min, 0.01 hours
[2016-04-14T23:45Z] INFO  16:45:07,410 MicroScheduler - 22817 reads were filtered out during the traversal out of approximately 235323 total reads (9.70%)
[2016-04-14T23:45Z] INFO  16:45:07,412 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:45Z] INFO  16:45:07,412 MicroScheduler -   -> 1775 reads (0.75% of total) failing BadMateFilter
[2016-04-14T23:45Z] INFO  16:45:07,413 MicroScheduler -   -> 17851 reads (7.59% of total) failing DuplicateReadFilter
[2016-04-14T23:45Z] INFO  16:45:07,414 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-14T23:45Z] INFO  16:45:07,414 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:45Z] INFO  16:45:07,415 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-14T23:45Z] INFO  16:45:07,415 MicroScheduler -   -> 3191 reads (1.36% of total) failing MappingQualityZeroFilter
[2016-04-14T23:45Z] INFO  16:45:07,416 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:45Z] INFO  16:45:07,417 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-14T23:45Z] INFO  16:45:07,417 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-14T23:45Z] INFO  16:45:08,755 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:45Z] GATK: realign ('2', 31135088, 46706841) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-14T23:45Z] INFO  16:45:09,440 ProgressMeter -            done    402876.0    27.0 s      68.0 s      100.0%    27.0 s       0.0 s
[2016-04-14T23:45Z] INFO  16:45:09,440 ProgressMeter - Total runtime 27.40 secs, 0.46 min, 0.01 hours
[2016-04-14T23:45Z] INFO  16:45:09,444 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 402876 total reads (0.00%)
[2016-04-14T23:45Z] INFO  16:45:09,445 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:45Z] INFO  16:45:09,445 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:45Z] INFO  16:45:09,445 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:45Z] INFO  16:45:11,139 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:45Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-1_159504867_175046963-prep.bam
[2016-04-14T23:45Z] INFO  16:45:11,690 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:45Z] INFO  16:45:11,693 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:45Z] INFO  16:45:11,694 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:45Z] INFO  16:45:11,694 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:45Z] INFO  16:45:11,699 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/2/R14-18105_kapa-NGv3-PE100-NGv3-sort-2_31135088_46706841-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/2/R14-18105_kapa-NGv3-PE100-NGv3-sort-2_31135088_46706841-prep-prealign-realign.intervals -L 2:31135089-46706841 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/2/tx/tmpHnHgJK/R14-18105_kapa-NGv3-PE100-NGv3-sort-2_31135088_46706841-prep.bam
[2016-04-14T23:45Z] INFO  16:45:11,718 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:45Z] INFO  16:45:11,719 HelpFormatter - Date/Time: 2016/04/14 16:45:11
[2016-04-14T23:45Z] INFO  16:45:11,720 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:45Z] INFO  16:45:11,720 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:45Z] INFO  16:45:11,976 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:45Z] INFO  16:45:12,137 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:45Z] INFO  16:45:12,147 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:45Z] INFO  16:45:12,203 ProgressMeter -            done    815768.0    49.0 s      60.0 s      100.0%    49.0 s       0.0 s
[2016-04-14T23:45Z] INFO  16:45:12,204 ProgressMeter - Total runtime 49.11 secs, 0.82 min, 0.01 hours
[2016-04-14T23:45Z] INFO  16:45:12,208 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 815768 total reads (0.00%)
[2016-04-14T23:45Z] INFO  16:45:12,209 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:45Z] INFO  16:45:12,209 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:45Z] INFO  16:45:12,209 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:45Z] INFO  16:45:12,210 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-14T23:45Z] GATK pre-alignment ('2', 143676177, 159195597) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-14T23:45Z] INFO  16:45:12,677 IntervalUtils - Processing 15571753 bp from intervals
[2016-04-14T23:45Z] WARN  16:45:12,692 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:45Z] INFO  16:45:12,774 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:45Z] INFO  16:45:12,893 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:45Z] INFO  16:45:12,894 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:45Z] INFO  16:45:12,895 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:45Z] INFO  16:45:12,896 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:45Z] INFO  16:45:13,042 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:45Z] INFO  16:45:13,203 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:45Z] INFO  16:45:13,721 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:45Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-1_0_15541927-prep.bam
[2016-04-14T23:45Z] INFO  16:45:15,309 ProgressMeter -     1:121485434    400006.0    30.0 s      77.0 s       35.9%    83.0 s      53.0 s
[2016-04-14T23:45Z] INFO  16:45:15,441 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:45Z] INFO  16:45:15,443 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:45Z] INFO  16:45:15,444 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:45Z] INFO  16:45:15,444 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:45Z] INFO  16:45:15,448 HelpFormatter - Program Args: -T PrintReads -L 2:143676178-159195597 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/2/tx/tmpLaFMDb/R14-18105_kapa-NGv3-PE100-NGv3-sort-2_143676177_159195597-prep-prealign.bam
[2016-04-14T23:45Z] INFO  16:45:15,460 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:45Z] INFO  16:45:15,461 HelpFormatter - Date/Time: 2016/04/14 16:45:15
[2016-04-14T23:45Z] INFO  16:45:15,461 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:45Z] INFO  16:45:15,462 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:45Z] INFO  16:45:15,650 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:45Z] INFO  16:45:16,263 ProgressMeter -     1:153643390    700014.0     2.0 m       2.9 m       62.8%     3.2 m      71.0 s
[2016-04-14T23:45Z] GATK pre-alignment ('2', 159196753, 174774985) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-14T23:45Z] INFO  16:45:16,611 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-14T23:45Z] INFO  16:45:16,679 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:45Z] INFO  16:45:16,689 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:45Z] INFO  16:45:16,751 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-14T23:45Z] INFO  16:45:16,777 IntervalUtils - Processing 15519420 bp from intervals
[2016-04-14T23:45Z] INFO  16:45:16,947 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:45Z] INFO  16:45:17,109 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@32d5a4c6
[2016-04-14T23:45Z] INFO  16:45:17,232 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:45Z] INFO  16:45:17,233 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:45Z] INFO  16:45:17,232 ProgressMeter -            done    341130.0    41.0 s       2.0 m      100.0%    41.0 s       0.0 s
[2016-04-14T23:45Z] INFO  16:45:17,233 ProgressMeter - Total runtime 41.93 secs, 0.70 min, 0.01 hours
[2016-04-14T23:45Z] INFO  16:45:17,233 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:45Z] INFO  16:45:17,233 MicroScheduler - 186 reads were filtered out during the traversal out of approximately 341316 total reads (0.05%)
[2016-04-14T23:45Z] INFO  16:45:17,234 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:45Z] INFO  16:45:17,234 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:45Z] INFO  16:45:17,234 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:45Z] INFO  16:45:17,234 MicroScheduler -   -> 186 reads (0.05% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:45Z] INFO  16:45:17,248 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:45Z] INFO  16:45:17,342 ProgressMeter -            done    420538.0    32.0 s      78.0 s      100.0%    32.0 s       0.0 s
[2016-04-14T23:45Z] INFO  16:45:17,343 ProgressMeter - Total runtime 32.85 secs, 0.55 min, 0.01 hours
[2016-04-14T23:45Z] INFO  16:45:17,346 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 420538 total reads (0.00%)
[2016-04-14T23:45Z] INFO  16:45:17,347 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:45Z] INFO  16:45:17,347 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:45Z] INFO  16:45:17,347 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:45Z] INFO  16:45:17,385 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:45Z] INFO  16:45:18,368 ProgressMeter -            done    422334.0    28.0 s      68.0 s      100.0%    28.0 s       0.0 s
[2016-04-14T23:45Z] INFO  16:45:18,369 ProgressMeter - Total runtime 28.86 secs, 0.48 min, 0.01 hours
[2016-04-14T23:45Z] INFO  16:45:18,373 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 422334 total reads (0.00%)
[2016-04-14T23:45Z] INFO  16:45:18,374 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:45Z] INFO  16:45:18,375 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:45Z] INFO  16:45:18,375 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:45Z] INFO  16:45:18,537 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:45Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-2_62362965_79253295-prep-prealign.bam
[2016-04-14T23:45Z] INFO  16:45:18,900 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:45Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-1_108994811_143767848-prep.bam
[2016-04-14T23:45Z] INFO  16:45:19,051 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:45Z] INFO  16:45:19,055 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:45Z] INFO  16:45:19,055 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:45Z] INFO  16:45:19,056 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:45Z] INFO  16:45:19,061 HelpFormatter - Program Args: -T PrintReads -L 2:159196754-174774985 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/2/tx/tmpsZt3kW/R14-18105_kapa-NGv3-PE100-NGv3-sort-2_159196753_174774985-prep-prealign.bam
[2016-04-14T23:45Z] INFO  16:45:19,075 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:45Z] INFO  16:45:19,076 HelpFormatter - Date/Time: 2016/04/14 16:45:19
[2016-04-14T23:45Z] INFO  16:45:19,077 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:45Z] INFO  16:45:19,077 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:45Z] INFO  16:45:19,246 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:45Z] INFO  16:45:19,600 ProgressMeter -      1:40365634    400004.0    31.0 s      78.0 s       59.1%    52.0 s      21.0 s
[2016-04-14T23:45Z] GATK RealignerTargetCreator: R14-18105_kapa-NGv3-PE100-NGv3-sort-2_62362965_79253295-prep-prealign.bam 2:62362966-79253295
[2016-04-14T23:45Z] GATK: RealignerTargetCreator
[2016-04-14T23:45Z] INFO  16:45:19,833 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:45Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-1_192128349_207640257-prep.bam
[2016-04-14T23:45Z] GATK pre-alignment ('2', 174777797, 190306304) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-14T23:45Z] INFO  16:45:20,383 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-14T23:45Z] INFO  16:45:20,455 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:45Z] INFO  16:45:20,470 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:45Z] INFO  16:45:20,519 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-14T23:45Z] INFO  16:45:20,537 IntervalUtils - Processing 15578232 bp from intervals
[2016-04-14T23:45Z] INFO  16:45:20,626 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:45Z] INFO  16:45:21,076 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:45Z] INFO  16:45:21,077 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:45Z] INFO  16:45:21,078 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:45Z] INFO  16:45:21,078 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:45Z] INFO  16:45:21,107 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:45Z] GATK pre-alignment ('2', 190313104, 205830046) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-14T23:45Z] INFO  16:45:21,264 ProgressMeter -            done    184947.0    14.0 s      77.0 s      100.0%    14.0 s       0.0 s
[2016-04-14T23:45Z] INFO  16:45:21,282 ProgressMeter - Total runtime 14.44 secs, 0.24 min, 0.00 hours
[2016-04-14T23:45Z] INFO  16:45:21,286 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 184947 total reads (0.00%)
[2016-04-14T23:45Z] INFO  16:45:21,286 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:45Z] INFO  16:45:21,287 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:45Z] INFO  16:45:21,287 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:45Z] INFO  16:45:21,463 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:45Z] INFO  16:45:21,731 ProgressMeter -            done    798011.0    50.0 s      63.0 s      100.0%    50.0 s       0.0 s
[2016-04-14T23:45Z] INFO  16:45:21,731 ProgressMeter - Total runtime 50.94 secs, 0.85 min, 0.01 hours
[2016-04-14T23:45Z] INFO  16:45:21,735 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 798011 total reads (0.00%)
[2016-04-14T23:45Z] INFO  16:45:21,735 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:45Z] INFO  16:45:21,736 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:45Z] INFO  16:45:21,736 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:45Z] INFO  16:45:22,519 ProgressMeter -            done   1.56142E7    20.0 s       1.0 s      100.0%    20.0 s       0.0 s
[2016-04-14T23:45Z] INFO  16:45:22,521 ProgressMeter - Total runtime 20.91 secs, 0.35 min, 0.01 hours
[2016-04-14T23:45Z] INFO  16:45:22,524 MicroScheduler - 30354 reads were filtered out during the traversal out of approximately 372125 total reads (8.16%)
[2016-04-14T23:45Z] INFO  16:45:22,525 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:45Z] INFO  16:45:22,526 MicroScheduler -   -> 746 reads (0.20% of total) failing BadMateFilter
[2016-04-14T23:45Z] INFO  16:45:22,527 MicroScheduler -   -> 29135 reads (7.83% of total) failing DuplicateReadFilter
[2016-04-14T23:45Z] INFO  16:45:22,527 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-14T23:45Z] INFO  16:45:22,528 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:45Z] INFO  16:45:22,528 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-14T23:45Z] INFO  16:45:22,529 MicroScheduler -   -> 473 reads (0.13% of total) failing MappingQualityZeroFilter
[2016-04-14T23:45Z] INFO  16:45:22,529 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:45Z] INFO  16:45:22,530 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-14T23:45Z] INFO  16:45:22,531 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-14T23:45Z] INFO  16:45:22,606 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:45Z] INFO  16:45:22,611 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:45Z] INFO  16:45:22,612 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:45Z] INFO  16:45:22,612 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:45Z] INFO  16:45:22,618 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/2/R14-18105_kapa-NGv3-PE100-NGv3-sort-2_62362965_79253295-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/2/tx/tmpVpjEAz/R14-18105_kapa-NGv3-PE100-NGv3-sort-2_62362965_79253295-prep-prealign-realign.intervals -l INFO -L 2:62362966-79253295 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-14T23:45Z] INFO  16:45:22,639 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:45Z] INFO  16:45:22,640 HelpFormatter - Date/Time: 2016/04/14 16:45:22
[2016-04-14T23:45Z] INFO  16:45:22,641 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:45Z] INFO  16:45:22,642 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:45Z] INFO  16:45:22,832 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:45Z] INFO  16:45:22,858 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:45Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-2_46707543_62228117-prep.bam
[2016-04-14T23:45Z] INFO  16:45:23,086 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-14T23:45Z] INFO  16:45:23,096 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:45Z] INFO  16:45:23,126 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:45Z] INFO  16:45:23,140 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:45Z] INFO  16:45:23,141 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:45Z] INFO  16:45:23,142 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:45Z] INFO  16:45:23,147 HelpFormatter - Program Args: -T PrintReads -L 2:174777798-190306304 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/2/tx/tmp_03jEY/R14-18105_kapa-NGv3-PE100-NGv3-sort-2_174777797_190306304-prep-prealign.bam
[2016-04-14T23:45Z] INFO  16:45:23,160 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-14T23:45Z] INFO  16:45:23,186 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:45Z] INFO  16:45:23,187 HelpFormatter - Date/Time: 2016/04/14 16:45:23
[2016-04-14T23:45Z] INFO  16:45:23,188 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:45Z] INFO  16:45:23,188 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:45Z] INFO  16:45:23,430 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:45Z] INFO  16:45:23,445 IntervalUtils - Processing 16890330 bp from intervals
[2016-04-14T23:45Z] WARN  16:45:23,450 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:45Z] GATK pre-alignment ('2', 205912303, 222290862) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-14T23:45Z] INFO  16:45:23,550 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:45Z] INFO  16:45:23,561 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:45Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-1_15545821_31186478-prep.bam
[2016-04-14T23:45Z] INFO  16:45:23,745 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:45Z] INFO  16:45:23,745 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:45Z] INFO  16:45:23,746 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:45Z] INFO  16:45:23,746 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-14T23:45Z] INFO  16:45:23,786 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:45Z] INFO  16:45:23,789 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:45Z] INFO  16:45:23,789 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:45Z] INFO  16:45:23,789 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:45Z] INFO  16:45:23,790 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:45Z] INFO  16:45:23,794 HelpFormatter - Program Args: -T PrintReads -L 2:190313105-205830046 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/2/tx/tmpniVH_M/R14-18105_kapa-NGv3-PE100-NGv3-sort-2_190313104_205830046-prep-prealign.bam
[2016-04-14T23:45Z] GATK: realign ('2', 15519725, 31133925) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-14T23:45Z] INFO  16:45:23,817 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:45Z] INFO  16:45:23,818 HelpFormatter - Date/Time: 2016/04/14 16:45:23
[2016-04-14T23:45Z] INFO  16:45:23,819 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:45Z] INFO  16:45:23,819 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:45Z] INFO  16:45:23,977 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:45Z] INFO  16:45:24,533 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-14T23:45Z] INFO  16:45:24,621 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:45Z] INFO  16:45:24,640 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:45Z] INFO  16:45:24,714 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-14T23:45Z] INFO  16:45:24,739 IntervalUtils - Processing 15528507 bp from intervals
[2016-04-14T23:45Z] INFO  16:45:24,861 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:45Z] INFO  16:45:25,155 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-14T23:45Z] INFO  16:45:25,223 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:45Z] INFO  16:45:25,232 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:45Z] INFO  16:45:25,273 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.04
[2016-04-14T23:45Z] INFO  16:45:25,295 IntervalUtils - Processing 15516942 bp from intervals
[2016-04-14T23:45Z] INFO  16:45:25,300 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:45Z] INFO  16:45:25,301 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:45Z] INFO  16:45:25,301 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:45Z] INFO  16:45:25,302 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:45Z] INFO  16:45:25,340 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:45Z] INFO  16:45:25,422 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:45Z] INFO  16:45:25,517 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:45Z] INFO  16:45:25,778 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:45Z] INFO  16:45:25,779 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:45Z] INFO  16:45:25,780 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:45Z] INFO  16:45:25,780 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:45Z] INFO  16:45:25,796 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:45Z] INFO  16:45:25,945 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:45Z] GATK pre-alignment ('2', 222291154, 237994685) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-14T23:45Z] INFO  16:45:26,884 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:45Z] INFO  16:45:26,888 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:45Z] INFO  16:45:26,888 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:45Z] INFO  16:45:26,889 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:45Z] INFO  16:45:26,893 HelpFormatter - Program Args: -T PrintReads -L 2:205912304-222290862 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/2/tx/tmpnBGLEJ/R14-18105_kapa-NGv3-PE100-NGv3-sort-2_205912303_222290862-prep-prealign.bam
[2016-04-14T23:45Z] INFO  16:45:26,913 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:45Z] INFO  16:45:26,914 HelpFormatter - Date/Time: 2016/04/14 16:45:26
[2016-04-14T23:45Z] INFO  16:45:26,915 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:45Z] INFO  16:45:26,915 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:45Z] INFO  16:45:27,121 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:45Z] INFO  16:45:27,321 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:45Z] INFO  16:45:27,323 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:45Z] INFO  16:45:27,324 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:45Z] INFO  16:45:27,324 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:45Z] INFO  16:45:27,339 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/2/R14-18105_kapa-NGv3-PE100-NGv3-sort-2_15519725_31133925-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/2/R14-18105_kapa-NGv3-PE100-NGv3-sort-2_15519725_31133925-prep-prealign-realign.intervals -L 2:15519726-31133925 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/2/tx/tmpofGoYy/R14-18105_kapa-NGv3-PE100-NGv3-sort-2_15519725_31133925-prep.bam
[2016-04-14T23:45Z] INFO  16:45:27,368 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:45Z] INFO  16:45:27,369 HelpFormatter - Date/Time: 2016/04/14 16:45:27
[2016-04-14T23:45Z] INFO  16:45:27,370 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:45Z] INFO  16:45:27,370 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:45Z] INFO  16:45:27,481 ProgressMeter -      2:91777917    200003.0    30.0 s       2.5 m       76.9%    39.0 s       9.0 s
[2016-04-14T23:45Z] INFO  16:45:27,603 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:45Z] INFO  16:45:27,749 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:45Z] INFO  16:45:27,784 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:45Z] INFO  16:45:27,873 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.09
[2016-04-14T23:45Z] INFO  16:45:28,328 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-14T23:45Z] INFO  16:45:28,380 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:45Z] INFO  16:45:28,389 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:45Z] INFO  16:45:28,425 IntervalUtils - Processing 15614200 bp from intervals
[2016-04-14T23:45Z] WARN  16:45:28,430 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:45Z] INFO  16:45:28,448 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-14T23:45Z] INFO  16:45:28,462 IntervalUtils - Processing 16378559 bp from intervals
[2016-04-14T23:45Z] INFO  16:45:28,525 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:45Z] INFO  16:45:28,528 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:45Z] INFO  16:45:28,711 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:45Z] INFO  16:45:28,723 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:45Z] INFO  16:45:28,724 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:45Z] INFO  16:45:28,724 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:45Z] INFO  16:45:28,786 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:45Z] INFO  16:45:28,787 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:45Z] INFO  16:45:28,787 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:45Z] INFO  16:45:28,788 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:45Z] INFO  16:45:28,829 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:45Z] INFO  16:45:28,877 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:45Z] INFO  16:45:29,004 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:45Z] INFO  16:45:29,030 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:45Z] INFO  16:45:29,345 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:45Z] INFO  16:45:29,352 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:45Z] INFO  16:45:29,352 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:45Z] INFO  16:45:29,352 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:45Z] INFO  16:45:29,363 HelpFormatter - Program Args: -T PrintReads -L 2:222291155-237994685 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/2/tx/tmpUVMdVH/R14-18105_kapa-NGv3-PE100-NGv3-sort-2_222291154_237994685-prep-prealign.bam
[2016-04-14T23:45Z] INFO  16:45:29,376 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:45Z] INFO  16:45:29,376 HelpFormatter - Date/Time: 2016/04/14 16:45:29
[2016-04-14T23:45Z] INFO  16:45:29,377 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:45Z] INFO  16:45:29,377 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:45Z] INFO  16:45:29,598 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:45Z] INFO  16:45:29,865 ProgressMeter -     2:125192166    200002.0    30.0 s       2.5 m       86.2%    34.0 s       4.0 s
[2016-04-14T23:45Z] INFO  16:45:29,912 ProgressMeter -      2:97875443    100001.0    31.0 s       5.2 m       14.9%     3.5 m       3.0 m
[2016-04-14T23:45Z] INFO  16:45:30,348 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@41fd9d8e
[2016-04-14T23:45Z] INFO  16:45:30,500 ProgressMeter -            done    254330.0    33.0 s       2.2 m      100.0%    33.0 s       0.0 s
[2016-04-14T23:45Z] INFO  16:45:30,507 ProgressMeter - Total runtime 33.06 secs, 0.55 min, 0.01 hours
[2016-04-14T23:45Z] INFO  16:45:30,507 MicroScheduler - 362 reads were filtered out during the traversal out of approximately 254692 total reads (0.14%)
[2016-04-14T23:45Z] INFO  16:45:30,508 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:45Z] INFO  16:45:30,508 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:45Z] INFO  16:45:30,508 MicroScheduler -   -> 362 reads (0.14% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:45Z] INFO  16:45:30,562 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@5fe152b7
[2016-04-14T23:45Z] INFO  16:45:30,685 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-14T23:45Z] INFO  16:45:30,775 ProgressMeter -            done    238517.0    30.0 s       2.2 m      100.0%    30.0 s       0.0 s
[2016-04-14T23:45Z] INFO  16:45:30,780 ProgressMeter - Total runtime 30.93 secs, 0.52 min, 0.01 hours
[2016-04-14T23:45Z] INFO  16:45:30,781 MicroScheduler - 165 reads were filtered out during the traversal out of approximately 238682 total reads (0.07%)
[2016-04-14T23:45Z] INFO  16:45:30,781 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:45Z] INFO  16:45:30,781 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:45Z] INFO  16:45:30,782 MicroScheduler -   -> 165 reads (0.07% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:45Z] INFO  16:45:30,794 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:45Z] INFO  16:45:30,804 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:45Z] INFO  16:45:30,856 ProgressMeter -            done    233877.0    17.0 s      76.0 s      100.0%    17.0 s       0.0 s
[2016-04-14T23:45Z] INFO  16:45:30,857 ProgressMeter - Total runtime 17.96 secs, 0.30 min, 0.00 hours
[2016-04-14T23:45Z] INFO  16:45:30,860 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 233877 total reads (0.00%)
[2016-04-14T23:45Z] INFO  16:45:30,861 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:45Z] INFO  16:45:30,861 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:45Z] INFO  16:45:30,861 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:45Z] INFO  16:45:30,888 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-14T23:45Z] INFO  16:45:30,908 IntervalUtils - Processing 15703531 bp from intervals
[2016-04-14T23:45Z] INFO  16:45:31,031 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:45Z] INFO  16:45:31,213 ProgressMeter -     2:132249612    200004.0    30.0 s       2.5 m       29.7%   100.0 s      70.0 s
[2016-04-14T23:45Z] INFO  16:45:31,314 ProgressMeter -            done    445426.0    28.0 s      63.0 s      100.0%    28.0 s       0.0 s
[2016-04-14T23:45Z] INFO  16:45:31,315 ProgressMeter - Total runtime 28.36 secs, 0.47 min, 0.01 hours
[2016-04-14T23:45Z] INFO  16:45:31,318 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 445426 total reads (0.00%)
[2016-04-14T23:45Z] INFO  16:45:31,319 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:45Z] INFO  16:45:31,319 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:45Z] INFO  16:45:31,319 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:45Z] INFO  16:45:31,377 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:45Z] INFO  16:45:31,378 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:45Z] INFO  16:45:31,387 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:45Z] INFO  16:45:31,388 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:45Z] INFO  16:45:31,411 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:45Z] INFO  16:45:31,624 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:45Z] INFO  16:45:31,882 ProgressMeter -            done    732024.0    43.0 s      59.0 s      100.0%    43.0 s       0.0 s
[2016-04-14T23:45Z] INFO  16:45:31,883 ProgressMeter - Total runtime 43.64 secs, 0.73 min, 0.01 hours
[2016-04-14T23:45Z] INFO  16:45:31,887 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 732024 total reads (0.00%)
[2016-04-14T23:45Z] INFO  16:45:31,888 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:45Z] INFO  16:45:31,889 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:45Z] INFO  16:45:31,889 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:45Z] INFO  16:45:31,901 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:45Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-2_79253838_95537822-prep-prealign.bam
[2016-04-14T23:45Z] INFO  16:45:32,132 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:45Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-2_111281072_127413888-prep-prealign.bam
[2016-04-14T23:45Z] INFO  16:45:32,266 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:45Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-2_31135088_46706841-prep.bam
[2016-04-14T23:45Z] GATK RealignerTargetCreator: R14-18105_kapa-NGv3-PE100-NGv3-sort-2_79253838_95537822-prep-prealign.bam 2:79253839-95537822
[2016-04-14T23:45Z] GATK: RealignerTargetCreator
[2016-04-14T23:45Z] INFO  16:45:32,876 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:45Z] GATK RealignerTargetCreator: R14-18105_kapa-NGv3-PE100-NGv3-sort-2_111281072_127413888-prep-prealign.bam 2:111281073-127413888
[2016-04-14T23:45Z] GATK: RealignerTargetCreator
[2016-04-14T23:45Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-1_223162737_240072524-prep.bam
[2016-04-14T23:45Z] GATK pre-alignment ('2', 237995374, 243199373) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-14T23:45Z] INFO  16:45:33,504 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:45Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-1_31187093_46714270-prep.bam
[2016-04-14T23:45Z] GATK pre-alignment ('3', 0, 15512123) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-14T23:45Z] GATK pre-alignment ('3', 15515506, 31574805) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-14T23:45Z] INFO  16:45:35,948 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:45Z] INFO  16:45:35,952 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:45Z] INFO  16:45:35,953 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:45Z] INFO  16:45:35,954 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:45Z] INFO  16:45:35,959 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/2/R14-18105_kapa-NGv3-PE100-NGv3-sort-2_111281072_127413888-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/2/tx/tmpcH95jh/R14-18105_kapa-NGv3-PE100-NGv3-sort-2_111281072_127413888-prep-prealign-realign.intervals -l INFO -L 2:111281073-127413888 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-14T23:45Z] INFO  16:45:35,970 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:45Z] INFO  16:45:35,981 HelpFormatter - Date/Time: 2016/04/14 16:45:35
[2016-04-14T23:45Z] INFO  16:45:35,982 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:45Z] INFO  16:45:35,983 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:45Z] INFO  16:45:36,016 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:45Z] INFO  16:45:36,021 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:45Z] INFO  16:45:36,021 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:45Z] INFO  16:45:36,022 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:45Z] INFO  16:45:36,028 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/2/R14-18105_kapa-NGv3-PE100-NGv3-sort-2_79253838_95537822-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/2/tx/tmpYQMiyC/R14-18105_kapa-NGv3-PE100-NGv3-sort-2_79253838_95537822-prep-prealign-realign.intervals -l INFO -L 2:79253839-95537822 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-14T23:45Z] INFO  16:45:36,037 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:45Z] INFO  16:45:36,038 HelpFormatter - Date/Time: 2016/04/14 16:45:36
[2016-04-14T23:45Z] INFO  16:45:36,039 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:45Z] INFO  16:45:36,040 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:45Z] INFO  16:45:36,138 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:45Z] INFO  16:45:36,200 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:45Z] INFO  16:45:36,380 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-14T23:45Z] INFO  16:45:36,391 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:45Z] INFO  16:45:36,393 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:45Z] INFO  16:45:36,397 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:45Z] INFO  16:45:36,397 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:45Z] INFO  16:45:36,398 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:45Z] INFO  16:45:36,403 HelpFormatter - Program Args: -T PrintReads -L 2:237995375-243199373 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/2/tx/tmpIfhZ3y/R14-18105_kapa-NGv3-PE100-NGv3-sort-2_237995374_243199373-prep-prealign.bam
[2016-04-14T23:45Z] INFO  16:45:36,432 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:45Z] INFO  16:45:36,433 HelpFormatter - Date/Time: 2016/04/14 16:45:36
[2016-04-14T23:45Z] INFO  16:45:36,433 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:45Z] INFO  16:45:36,433 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:45Z] INFO  16:45:36,457 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-14T23:45Z] INFO  16:45:36,478 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-14T23:45Z] INFO  16:45:36,489 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:45Z] INFO  16:45:36,577 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.09
[2016-04-14T23:45Z] INFO  16:45:36,671 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:45Z] INFO  16:45:36,797 IntervalUtils - Processing 16132816 bp from intervals
[2016-04-14T23:45Z] WARN  16:45:36,802 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:45Z] INFO  16:45:36,902 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:45Z] INFO  16:45:37,028 IntervalUtils - Processing 16283984 bp from intervals
[2016-04-14T23:45Z] WARN  16:45:37,033 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:45Z] INFO  16:45:37,113 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:45Z] INFO  16:45:37,238 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:45Z] INFO  16:45:37,239 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:45Z] INFO  16:45:37,239 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:45Z] INFO  16:45:37,240 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-14T23:45Z] INFO  16:45:37,330 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:45Z] INFO  16:45:37,331 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:45Z] INFO  16:45:37,332 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:45Z] INFO  16:45:37,332 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-14T23:45Z] INFO  16:45:37,459 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@5fe152b7
[2016-04-14T23:45Z] INFO  16:45:37,545 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:45Z] INFO  16:45:37,549 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:45Z] INFO  16:45:37,549 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:45Z] INFO  16:45:37,550 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:45Z] INFO  16:45:37,554 HelpFormatter - Program Args: -T PrintReads -L 3:1-15512123 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/3/tx/tmp8ys_tZ/R14-18105_kapa-NGv3-PE100-NGv3-sort-3_0_15512123-prep-prealign.bam
[2016-04-14T23:45Z] INFO  16:45:37,563 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:45Z] INFO  16:45:37,564 HelpFormatter - Date/Time: 2016/04/14 16:45:37
[2016-04-14T23:45Z] INFO  16:45:37,565 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:45Z] INFO  16:45:37,565 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:45Z] INFO  16:45:37,669 ProgressMeter -            done    124003.0    20.0 s       2.7 m      100.0%    20.0 s       0.0 s
[2016-04-14T23:45Z] INFO  16:45:37,670 ProgressMeter - Total runtime 20.44 secs, 0.34 min, 0.01 hours
[2016-04-14T23:45Z] INFO  16:45:37,671 MicroScheduler - 126 reads were filtered out during the traversal out of approximately 124129 total reads (0.10%)
[2016-04-14T23:45Z] INFO  16:45:37,671 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:45Z] INFO  16:45:37,671 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:45Z] INFO  16:45:37,672 MicroScheduler -   -> 126 reads (0.10% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:45Z] INFO  16:45:37,762 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:45Z] INFO  16:45:38,092 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-14T23:45Z] INFO  16:45:38,161 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:45Z] INFO  16:45:38,173 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:45Z] INFO  16:45:38,214 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.04
[2016-04-14T23:45Z] INFO  16:45:38,232 IntervalUtils - Processing 5203999 bp from intervals
[2016-04-14T23:45Z] INFO  16:45:38,333 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:45Z] INFO  16:45:38,536 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:45Z] INFO  16:45:38,540 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:45Z] INFO  16:45:38,541 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:45Z] INFO  16:45:38,542 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:45Z] INFO  16:45:38,547 HelpFormatter - Program Args: -T PrintReads -L 3:15515507-31574805 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/3/tx/tmpDt8wwb/R14-18105_kapa-NGv3-PE100-NGv3-sort-3_15515506_31574805-prep-prealign.bam
[2016-04-14T23:45Z] INFO  16:45:38,558 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:45Z] INFO  16:45:38,562 HelpFormatter - Date/Time: 2016/04/14 16:45:38
[2016-04-14T23:45Z] INFO  16:45:38,563 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:45Z] INFO  16:45:38,563 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:45Z] INFO  16:45:38,687 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:45Z] INFO  16:45:38,688 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:45Z] INFO  16:45:38,689 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:45Z] INFO  16:45:38,689 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:45Z] INFO  16:45:38,715 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:45Z] INFO  16:45:38,779 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:45Z] INFO  16:45:38,820 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:45Z] INFO  16:45:39,002 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-14T23:45Z] INFO  16:45:39,075 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:45Z] INFO  16:45:39,084 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:45Z] INFO  16:45:39,138 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-14T23:45Z] INFO  16:45:39,151 IntervalUtils - Processing 15512123 bp from intervals
[2016-04-14T23:45Z] INFO  16:45:39,229 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:45Z] INFO  16:45:39,376 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:45Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-2_143676177_159195597-prep-prealign.bam
[2016-04-14T23:45Z] INFO  16:45:39,581 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:45Z] INFO  16:45:39,582 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:45Z] INFO  16:45:39,583 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:45Z] INFO  16:45:39,583 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:45Z] INFO  16:45:39,596 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:45Z] INFO  16:45:39,724 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:45Z] GATK RealignerTargetCreator: R14-18105_kapa-NGv3-PE100-NGv3-sort-2_143676177_159195597-prep-prealign.bam 2:143676178-159195597
[2016-04-14T23:45Z] GATK: RealignerTargetCreator
[2016-04-14T23:45Z] INFO  16:45:40,021 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-14T23:45Z] INFO  16:45:40,087 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:45Z] INFO  16:45:40,097 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:45Z] INFO  16:45:40,138 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.04
[2016-04-14T23:45Z] INFO  16:45:40,152 IntervalUtils - Processing 16059299 bp from intervals
[2016-04-14T23:45Z] INFO  16:45:40,258 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:45Z] INFO  16:45:40,548 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:45Z] INFO  16:45:40,549 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:45Z] INFO  16:45:40,550 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:45Z] INFO  16:45:40,551 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:45Z] INFO  16:45:40,573 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:45Z] INFO  16:45:40,733 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:45Z] INFO  16:45:42,828 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:45Z] INFO  16:45:42,831 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:45Z] INFO  16:45:42,832 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:45Z] INFO  16:45:42,832 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:45Z] INFO  16:45:42,837 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/2/R14-18105_kapa-NGv3-PE100-NGv3-sort-2_143676177_159195597-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/2/tx/tmpXr8dfF/R14-18105_kapa-NGv3-PE100-NGv3-sort-2_143676177_159195597-prep-prealign-realign.intervals -l INFO -L 2:143676178-159195597 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-14T23:45Z] INFO  16:45:42,856 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:45Z] INFO  16:45:42,856 HelpFormatter - Date/Time: 2016/04/14 16:45:42
[2016-04-14T23:45Z] INFO  16:45:42,857 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:45Z] INFO  16:45:42,857 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:45Z] INFO  16:45:42,968 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:45Z] INFO  16:45:43,172 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-14T23:45Z] INFO  16:45:43,182 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:45Z] INFO  16:45:43,240 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-14T23:45Z] INFO  16:45:43,584 IntervalUtils - Processing 15519420 bp from intervals
[2016-04-14T23:45Z] WARN  16:45:43,590 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:45Z] INFO  16:45:43,690 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:45Z] INFO  16:45:43,931 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:45Z] INFO  16:45:43,932 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:45Z] INFO  16:45:43,932 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:45Z] INFO  16:45:43,933 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-14T23:45Z] INFO  16:45:44,079 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@5fe152b7
[2016-04-14T23:45Z] INFO  16:45:44,253 ProgressMeter -            done    329163.0    43.0 s       2.2 m      100.0%    43.0 s       0.0 s
[2016-04-14T23:45Z] INFO  16:45:44,254 ProgressMeter - Total runtime 43.13 secs, 0.72 min, 0.01 hours
[2016-04-14T23:45Z] INFO  16:45:44,254 MicroScheduler - 185 reads were filtered out during the traversal out of approximately 329348 total reads (0.06%)
[2016-04-14T23:45Z] INFO  16:45:44,255 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:45Z] INFO  16:45:44,255 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:45Z] INFO  16:45:44,256 MicroScheduler -   -> 185 reads (0.06% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:45Z] INFO  16:45:45,885 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:45Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-2_127433207_143643105-prep-prealign.bam
[2016-04-14T23:45Z] INFO  16:45:46,283 ProgressMeter -     1:155291864    900017.0     2.5 m       2.8 m       73.5%     3.4 m      54.0 s
[2016-04-14T23:45Z] GATK RealignerTargetCreator: R14-18105_kapa-NGv3-PE100-NGv3-sort-2_127433207_143643105-prep-prealign.bam 2:127433208-143643105
[2016-04-14T23:45Z] GATK: RealignerTargetCreator
[2016-04-14T23:45Z] INFO  16:45:47,734 ProgressMeter -            done   1.689033E7    23.0 s       1.0 s      100.0%    23.0 s       0.0 s
[2016-04-14T23:45Z] INFO  16:45:47,735 ProgressMeter - Total runtime 23.99 secs, 0.40 min, 0.01 hours
[2016-04-14T23:45Z] INFO  16:45:47,739 MicroScheduler - 29765 reads were filtered out during the traversal out of approximately 342902 total reads (8.68%)
[2016-04-14T23:45Z] INFO  16:45:47,739 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:45Z] INFO  16:45:47,739 MicroScheduler -   -> 676 reads (0.20% of total) failing BadMateFilter
[2016-04-14T23:45Z] INFO  16:45:47,740 MicroScheduler -   -> 27049 reads (7.89% of total) failing DuplicateReadFilter
[2016-04-14T23:45Z] INFO  16:45:47,740 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-14T23:45Z] INFO  16:45:47,740 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:45Z] INFO  16:45:47,740 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-14T23:45Z] INFO  16:45:47,741 MicroScheduler -   -> 2040 reads (0.59% of total) failing MappingQualityZeroFilter
[2016-04-14T23:45Z] INFO  16:45:47,741 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:45Z] INFO  16:45:47,741 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-14T23:45Z] INFO  16:45:47,741 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-14T23:45Z] INFO  16:45:49,130 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:45Z] GATK: realign ('2', 62362965, 79253295) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-14T23:45Z] INFO  16:45:49,560 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:45Z] INFO  16:45:49,563 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:45Z] INFO  16:45:49,563 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:45Z] INFO  16:45:49,563 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:45Z] INFO  16:45:49,574 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/2/R14-18105_kapa-NGv3-PE100-NGv3-sort-2_127433207_143643105-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/2/tx/tmpvuHXfz/R14-18105_kapa-NGv3-PE100-NGv3-sort-2_127433207_143643105-prep-prealign-realign.intervals -l INFO -L 2:127433208-143643105 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-14T23:45Z] INFO  16:45:49,582 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:45Z] INFO  16:45:49,583 HelpFormatter - Date/Time: 2016/04/14 16:45:49
[2016-04-14T23:45Z] INFO  16:45:49,583 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:45Z] INFO  16:45:49,584 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:45Z] INFO  16:45:49,697 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:45Z] INFO  16:45:49,960 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-14T23:45Z] INFO  16:45:49,971 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:45Z] INFO  16:45:50,029 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-14T23:45Z] INFO  16:45:50,493 IntervalUtils - Processing 16209898 bp from intervals
[2016-04-14T23:45Z] WARN  16:45:50,499 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:45Z] INFO  16:45:50,618 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:45Z] INFO  16:45:50,844 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:45Z] INFO  16:45:50,845 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:45Z] INFO  16:45:50,846 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:45Z] INFO  16:45:50,847 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-14T23:45Z] INFO  16:45:51,518 ProgressMeter -     2:169745928    100002.0    30.0 s       5.1 m       67.7%    44.0 s      14.0 s
[2016-04-14T23:45Z] INFO  16:45:51,718 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:45Z] INFO  16:45:51,722 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:45Z] INFO  16:45:51,722 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:45Z] INFO  16:45:51,723 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:45Z] INFO  16:45:51,728 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/2/R14-18105_kapa-NGv3-PE100-NGv3-sort-2_62362965_79253295-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/2/R14-18105_kapa-NGv3-PE100-NGv3-sort-2_62362965_79253295-prep-prealign-realign.intervals -L 2:62362966-79253295 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/2/tx/tmpT0mRnX/R14-18105_kapa-NGv3-PE100-NGv3-sort-2_62362965_79253295-prep.bam
[2016-04-14T23:45Z] INFO  16:45:51,739 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:45Z] INFO  16:45:51,750 HelpFormatter - Date/Time: 2016/04/14 16:45:51
[2016-04-14T23:45Z] INFO  16:45:51,751 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:45Z] INFO  16:45:51,752 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:45Z] INFO  16:45:51,965 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:45Z] INFO  16:45:52,108 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:45Z] INFO  16:45:52,117 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:45Z] INFO  16:45:52,177 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-14T23:45Z] INFO  16:45:52,489 IntervalUtils - Processing 16890330 bp from intervals
[2016-04-14T23:45Z] WARN  16:45:52,504 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:45Z] INFO  16:45:52,574 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:45Z] INFO  16:45:52,691 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:45Z] INFO  16:45:52,692 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:45Z] INFO  16:45:52,692 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:45Z] INFO  16:45:52,693 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:45Z] INFO  16:45:52,893 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:45Z] INFO  16:45:53,055 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:45Z] INFO  16:45:53,461 ProgressMeter -            done    370225.0    24.0 s      66.0 s      100.0%    24.0 s       0.0 s
[2016-04-14T23:45Z] INFO  16:45:53,462 ProgressMeter - Total runtime 24.74 secs, 0.41 min, 0.01 hours
[2016-04-14T23:45Z] INFO  16:45:53,466 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 370225 total reads (0.00%)
[2016-04-14T23:45Z] INFO  16:45:53,466 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:45Z] INFO  16:45:53,467 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:45Z] INFO  16:45:53,467 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:45Z] INFO  16:45:54,942 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:45Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-2_15519725_31133925-prep.bam
[2016-04-14T23:45Z] INFO  16:45:55,187 ProgressMeter -            done   1.6132816E7    17.0 s       1.0 s      100.0%    17.0 s       0.0 s
[2016-04-14T23:45Z] INFO  16:45:55,188 ProgressMeter - Total runtime 17.95 secs, 0.30 min, 0.00 hours
[2016-04-14T23:45Z] INFO  16:45:55,193 MicroScheduler - 77882 reads were filtered out during the traversal out of approximately 240340 total reads (32.40%)
[2016-04-14T23:45Z] INFO  16:45:55,194 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:45Z] INFO  16:45:55,195 MicroScheduler -   -> 467 reads (0.19% of total) failing BadMateFilter
[2016-04-14T23:45Z] INFO  16:45:55,195 MicroScheduler -   -> 14204 reads (5.91% of total) failing DuplicateReadFilter
[2016-04-14T23:45Z] INFO  16:45:55,196 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-14T23:45Z] INFO  16:45:55,197 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:45Z] INFO  16:45:55,197 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-14T23:45Z] INFO  16:45:55,198 MicroScheduler -   -> 63211 reads (26.30% of total) failing MappingQualityZeroFilter
[2016-04-14T23:45Z] INFO  16:45:55,198 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:45Z] INFO  16:45:55,199 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-14T23:45Z] INFO  16:45:55,200 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-14T23:45Z] INFO  16:45:55,331 ProgressMeter -     2:179610736    200003.0    30.0 s       2.5 m       31.1%    96.0 s      66.0 s
[2016-04-14T23:45Z] INFO  16:45:55,623 ProgressMeter -            done   1.6283984E7    18.0 s       1.0 s      100.0%    18.0 s       0.0 s
[2016-04-14T23:45Z] INFO  16:45:55,624 ProgressMeter - Total runtime 18.29 secs, 0.30 min, 0.01 hours
[2016-04-14T23:45Z] INFO  16:45:55,628 MicroScheduler - 87208 reads were filtered out during the traversal out of approximately 256017 total reads (34.06%)
[2016-04-14T23:45Z] INFO  16:45:55,630 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:45Z] INFO  16:45:55,636 MicroScheduler -   -> 669 reads (0.26% of total) failing BadMateFilter
[2016-04-14T23:45Z] INFO  16:45:55,637 MicroScheduler -   -> 14765 reads (5.77% of total) failing DuplicateReadFilter
[2016-04-14T23:45Z] INFO  16:45:55,637 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-14T23:45Z] INFO  16:45:55,638 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:45Z] INFO  16:45:55,639 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-14T23:45Z] INFO  16:45:55,639 MicroScheduler -   -> 71774 reads (28.03% of total) failing MappingQualityZeroFilter
[2016-04-14T23:45Z] INFO  16:45:55,640 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:45Z] INFO  16:45:55,640 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-14T23:45Z] INFO  16:45:55,641 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-14T23:45Z] INFO  16:45:55,800 ProgressMeter -     2:202254173    100003.0    30.0 s       5.0 m       77.0%    38.0 s       8.0 s
[2016-04-14T23:45Z] GATK pre-alignment ('3', 31617887, 47127804) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-14T23:45Z] INFO  16:45:56,461 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:45Z] GATK: realign ('2', 111281072, 127413888) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-14T23:45Z] INFO  16:45:56,710 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@32d5a4c6
[2016-04-14T23:45Z] INFO  16:45:56,830 ProgressMeter -            done    115016.0    16.0 s       2.4 m      100.0%    16.0 s       0.0 s
[2016-04-14T23:45Z] INFO  16:45:56,830 ProgressMeter - Total runtime 16.28 secs, 0.27 min, 0.00 hours
[2016-04-14T23:45Z] INFO  16:45:56,831 MicroScheduler - 120 reads were filtered out during the traversal out of approximately 115136 total reads (0.10%)
[2016-04-14T23:45Z] INFO  16:45:56,831 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:45Z] INFO  16:45:56,831 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:45Z] INFO  16:45:56,832 MicroScheduler -   -> 120 reads (0.10% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:45Z] INFO  16:45:57,073 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:45Z] GATK: realign ('2', 79253838, 95537822) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-14T23:45Z] INFO  16:45:58,610 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:45Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-3_15515506_31574805-prep-prealign.bam
[2016-04-14T23:45Z] INFO  16:45:58,808 ProgressMeter -     2:219140824    200006.0    30.0 s       2.5 m       80.8%    37.0 s       7.0 s
[2016-04-14T23:45Z] INFO  16:45:58,958 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:45Z] INFO  16:45:58,960 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:45Z] INFO  16:45:58,961 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:45Z] INFO  16:45:58,961 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:45Z] INFO  16:45:58,965 HelpFormatter - Program Args: -T PrintReads -L 3:31617888-47127804 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/3/tx/tmpyR0S2G/R14-18105_kapa-NGv3-PE100-NGv3-sort-3_31617887_47127804-prep-prealign.bam
[2016-04-14T23:45Z] INFO  16:45:58,987 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:45Z] INFO  16:45:58,998 HelpFormatter - Date/Time: 2016/04/14 16:45:58
[2016-04-14T23:45Z] INFO  16:45:58,999 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:45Z] INFO  16:45:59,000 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:45Z] GATK RealignerTargetCreator: R14-18105_kapa-NGv3-PE100-NGv3-sort-3_15515506_31574805-prep-prealign.bam 3:15515507-31574805
[2016-04-14T23:45Z] GATK: RealignerTargetCreator
[2016-04-14T23:45Z] INFO  16:45:59,204 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:45Z] INFO  16:45:59,273 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:45Z] INFO  16:45:59,276 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:45Z] INFO  16:45:59,277 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:45Z] INFO  16:45:59,277 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:45Z] INFO  16:45:59,282 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/2/R14-18105_kapa-NGv3-PE100-NGv3-sort-2_111281072_127413888-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/2/R14-18105_kapa-NGv3-PE100-NGv3-sort-2_111281072_127413888-prep-prealign-realign.intervals -L 2:111281073-127413888 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/2/tx/tmp9wKdWi/R14-18105_kapa-NGv3-PE100-NGv3-sort-2_111281072_127413888-prep.bam
[2016-04-14T23:45Z] INFO  16:45:59,294 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:45Z] INFO  16:45:59,295 HelpFormatter - Date/Time: 2016/04/14 16:45:59
[2016-04-14T23:45Z] INFO  16:45:59,296 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:45Z] INFO  16:45:59,296 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:45Z] INFO  16:45:59,490 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:45Z] INFO  16:45:59,638 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:45Z] INFO  16:45:59,648 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:45Z] INFO  16:45:59,721 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-14T23:46Z] INFO  16:46:00,232 ProgressMeter -            done   1.551942E7    16.0 s       1.0 s      100.0%    16.0 s       0.0 s
[2016-04-14T23:46Z] INFO  16:46:00,234 ProgressMeter - Total runtime 16.30 secs, 0.27 min, 0.00 hours
[2016-04-14T23:46Z] INFO  16:46:00,238 MicroScheduler - 20434 reads were filtered out during the traversal out of approximately 124708 total reads (16.39%)
[2016-04-14T23:46Z] INFO  16:46:00,239 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:46Z] INFO  16:46:00,239 MicroScheduler -   -> 414 reads (0.33% of total) failing BadMateFilter
[2016-04-14T23:46Z] INFO  16:46:00,240 MicroScheduler -   -> 8957 reads (7.18% of total) failing DuplicateReadFilter
[2016-04-14T23:46Z] INFO  16:46:00,241 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-14T23:46Z] INFO  16:46:00,241 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:46Z] INFO  16:46:00,242 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-14T23:46Z] INFO  16:46:00,243 MicroScheduler -   -> 11063 reads (8.87% of total) failing MappingQualityZeroFilter
[2016-04-14T23:46Z] INFO  16:46:00,243 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:46Z] INFO  16:46:00,244 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-14T23:46Z] INFO  16:46:00,244 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-14T23:46Z] INFO  16:46:00,284 IntervalUtils - Processing 16132816 bp from intervals
[2016-04-14T23:46Z] WARN  16:46:00,290 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:46Z] INFO  16:46:00,321 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:46Z] INFO  16:46:00,325 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:46Z] INFO  16:46:00,325 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:46Z] INFO  16:46:00,326 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:46Z] INFO  16:46:00,331 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/2/R14-18105_kapa-NGv3-PE100-NGv3-sort-2_79253838_95537822-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/2/R14-18105_kapa-NGv3-PE100-NGv3-sort-2_79253838_95537822-prep-prealign-realign.intervals -L 2:79253839-95537822 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/2/tx/tmp46Z4__/R14-18105_kapa-NGv3-PE100-NGv3-sort-2_79253838_95537822-prep.bam
[2016-04-14T23:46Z] INFO  16:46:00,351 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:46Z] INFO  16:46:00,352 HelpFormatter - Date/Time: 2016/04/14 16:46:00
[2016-04-14T23:46Z] INFO  16:46:00,353 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:46Z] INFO  16:46:00,353 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:46Z] INFO  16:46:00,359 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:46Z] INFO  16:46:00,394 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-14T23:46Z] INFO  16:46:00,401 ProgressMeter -     2:107429497    400005.0    61.0 s       2.6 m       75.6%    80.0 s      19.0 s
[2016-04-14T23:46Z] INFO  16:46:00,494 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:46Z] INFO  16:46:00,515 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:46Z] INFO  16:46:00,545 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:46Z] INFO  16:46:00,546 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:46Z] INFO  16:46:00,547 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:46Z] INFO  16:46:00,547 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:46Z] INFO  16:46:00,589 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:46Z] INFO  16:46:00,594 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-14T23:46Z] INFO  16:46:00,616 IntervalUtils - Processing 15509917 bp from intervals
[2016-04-14T23:46Z] INFO  16:46:00,697 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:46Z] INFO  16:46:00,699 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:46Z] INFO  16:46:00,721 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:46Z] INFO  16:46:00,731 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:46Z] INFO  16:46:00,801 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-14T23:46Z] INFO  16:46:00,872 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:46Z] INFO  16:46:01,000 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:46Z] INFO  16:46:01,001 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:46Z] INFO  16:46:01,007 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:46Z] INFO  16:46:01,008 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:46Z] INFO  16:46:01,027 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:46Z] INFO  16:46:01,189 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:46Z] INFO  16:46:01,211 IntervalUtils - Processing 16283984 bp from intervals
[2016-04-14T23:46Z] WARN  16:46:01,216 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:46Z] INFO  16:46:01,287 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:46Z] INFO  16:46:01,386 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:46Z] INFO  16:46:01,387 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:46Z] INFO  16:46:01,388 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:46Z] INFO  16:46:01,389 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:46Z] INFO  16:46:01,410 ProgressMeter -     2:233759507    200002.0    30.0 s       2.5 m       73.0%    41.0 s      11.0 s
[2016-04-14T23:46Z] INFO  16:46:01,550 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:46Z] INFO  16:46:01,700 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:46Z] INFO  16:46:01,853 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:46Z] INFO  16:46:01,857 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:46Z] INFO  16:46:01,857 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:46Z] INFO  16:46:01,857 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:46Z] INFO  16:46:01,861 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/3/R14-18105_kapa-NGv3-PE100-NGv3-sort-3_15515506_31574805-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/3/tx/tmpoViwAP/R14-18105_kapa-NGv3-PE100-NGv3-sort-3_15515506_31574805-prep-prealign-realign.intervals -l INFO -L 3:15515507-31574805 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-14T23:46Z] INFO  16:46:01,855 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:46Z] INFO  16:46:01,871 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:46Z] INFO  16:46:01,872 HelpFormatter - Date/Time: 2016/04/14 16:46:01
[2016-04-14T23:46Z] INFO  16:46:01,872 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:46Z] INFO  16:46:01,873 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:46Z] GATK: realign ('2', 143676177, 159195597) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-14T23:46Z] INFO  16:46:01,981 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:46Z] INFO  16:46:02,242 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-14T23:46Z] INFO  16:46:02,264 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:46Z] INFO  16:46:02,321 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-14T23:46Z] INFO  16:46:02,741 IntervalUtils - Processing 16059299 bp from intervals
[2016-04-14T23:46Z] WARN  16:46:02,747 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:46Z] INFO  16:46:02,869 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:46Z] INFO  16:46:03,132 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:46Z] INFO  16:46:03,133 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:46Z] INFO  16:46:03,134 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:46Z] INFO  16:46:03,135 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-14T23:46Z] INFO  16:46:04,798 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:46Z] INFO  16:46:04,801 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:46Z] INFO  16:46:04,802 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:46Z] INFO  16:46:04,802 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:46Z] INFO  16:46:04,807 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/2/R14-18105_kapa-NGv3-PE100-NGv3-sort-2_143676177_159195597-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/2/R14-18105_kapa-NGv3-PE100-NGv3-sort-2_143676177_159195597-prep-prealign-realign.intervals -L 2:143676178-159195597 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/2/tx/tmpNEhP0m/R14-18105_kapa-NGv3-PE100-NGv3-sort-2_143676177_159195597-prep.bam
[2016-04-14T23:46Z] INFO  16:46:04,824 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:46Z] INFO  16:46:04,827 HelpFormatter - Date/Time: 2016/04/14 16:46:04
[2016-04-14T23:46Z] INFO  16:46:04,828 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:46Z] INFO  16:46:04,828 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:46Z] INFO  16:46:05,042 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:46Z] INFO  16:46:05,070 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@41fd9d8e
[2016-04-14T23:46Z] INFO  16:46:05,185 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:46Z] INFO  16:46:05,202 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:46Z] INFO  16:46:05,257 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-14T23:46Z] INFO  16:46:05,360 ProgressMeter -            done    251871.0    39.0 s       2.6 m      100.0%    39.0 s       0.0 s
[2016-04-14T23:46Z] INFO  16:46:05,360 ProgressMeter - Total runtime 39.58 secs, 0.66 min, 0.01 hours
[2016-04-14T23:46Z] INFO  16:46:05,361 MicroScheduler - 152 reads were filtered out during the traversal out of approximately 252023 total reads (0.06%)
[2016-04-14T23:46Z] INFO  16:46:05,361 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:46Z] INFO  16:46:05,361 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:46Z] INFO  16:46:05,362 MicroScheduler -   -> 152 reads (0.06% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:46Z] INFO  16:46:05,697 IntervalUtils - Processing 15519420 bp from intervals
[2016-04-14T23:46Z] WARN  16:46:05,715 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:46Z] INFO  16:46:05,838 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:46Z] INFO  16:46:06,050 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:46Z] INFO  16:46:06,052 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:46Z] INFO  16:46:06,053 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:46Z] INFO  16:46:06,054 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:46Z] INFO  16:46:06,281 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:46Z] INFO  16:46:06,558 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:46Z] INFO  16:46:06,646 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@41fd9d8e
[2016-04-14T23:46Z] INFO  16:46:06,796 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:46Z] INFO  16:46:06,828 ProgressMeter -            done    299067.0    45.0 s       2.5 m      100.0%    45.0 s       0.0 s
[2016-04-14T23:46Z] INFO  16:46:06,828 ProgressMeter - Total runtime 45.75 secs, 0.76 min, 0.01 hours
[2016-04-14T23:46Z] INFO  16:46:06,828 MicroScheduler - 152 reads were filtered out during the traversal out of approximately 299219 total reads (0.05%)
[2016-04-14T23:46Z] INFO  16:46:06,829 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:46Z] INFO  16:46:06,829 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:46Z] INFO  16:46:06,829 MicroScheduler -   -> 152 reads (0.05% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:46Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-2_190313104_205830046-prep-prealign.bam
[2016-04-14T23:46Z] GATK RealignerTargetCreator: R14-18105_kapa-NGv3-PE100-NGv3-sort-2_190313104_205830046-prep-prealign.bam 2:190313105-205830046
[2016-04-14T23:46Z] GATK: RealignerTargetCreator
[2016-04-14T23:46Z] INFO  16:46:07,730 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@41fd9d8e
[2016-04-14T23:46Z] INFO  16:46:07,828 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@41fd9d8e
[2016-04-14T23:46Z] INFO  16:46:07,956 ProgressMeter -            done    221869.0    29.0 s       2.2 m       97.4%    29.0 s       0.0 s
[2016-04-14T23:46Z] INFO  16:46:07,956 ProgressMeter - Total runtime 29.27 secs, 0.49 min, 0.01 hours
[2016-04-14T23:46Z] INFO  16:46:07,956 MicroScheduler - 104 reads were filtered out during the traversal out of approximately 221973 total reads (0.05%)
[2016-04-14T23:46Z] INFO  16:46:07,957 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:46Z] INFO  16:46:07,957 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:46Z] INFO  16:46:07,957 MicroScheduler -   -> 104 reads (0.05% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:46Z] INFO  16:46:08,181 ProgressMeter -            done    340829.0    42.0 s       2.1 m      100.0%    42.0 s       0.0 s
[2016-04-14T23:46Z] INFO  16:46:08,182 ProgressMeter - Total runtime 42.88 secs, 0.71 min, 0.01 hours
[2016-04-14T23:46Z] INFO  16:46:08,182 MicroScheduler - 249 reads were filtered out during the traversal out of approximately 341078 total reads (0.07%)
[2016-04-14T23:46Z] INFO  16:46:08,183 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:46Z] INFO  16:46:08,183 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:46Z] INFO  16:46:08,183 MicroScheduler -   -> 249 reads (0.07% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:46Z] INFO  16:46:08,531 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:46Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-2_159196753_174774985-prep-prealign.bam
[2016-04-14T23:46Z] INFO  16:46:09,590 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:46Z] INFO  16:46:09,597 ProgressMeter -      3:12613792    200004.0    30.0 s       2.5 m       81.3%    36.0 s       6.0 s
[2016-04-14T23:46Z] INFO  16:46:09,618 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:46Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-2_237995374_243199373-prep-prealign.bam
[2016-04-14T23:46Z] GATK RealignerTargetCreator: R14-18105_kapa-NGv3-PE100-NGv3-sort-2_159196753_174774985-prep-prealign.bam 2:159196754-174774985
[2016-04-14T23:46Z] GATK: RealignerTargetCreator
[2016-04-14T23:46Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-2_174777797_190306304-prep-prealign.bam
[2016-04-14T23:46Z] GATK RealignerTargetCreator: R14-18105_kapa-NGv3-PE100-NGv3-sort-2_237995374_243199373-prep-prealign.bam 2:237995375-243199373
[2016-04-14T23:46Z] GATK: RealignerTargetCreator
[2016-04-14T23:46Z] INFO  16:46:10,630 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:46Z] INFO  16:46:10,634 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:46Z] INFO  16:46:10,635 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:46Z] INFO  16:46:10,635 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:46Z] INFO  16:46:10,641 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/2/R14-18105_kapa-NGv3-PE100-NGv3-sort-2_190313104_205830046-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/2/tx/tmp7C4i3p/R14-18105_kapa-NGv3-PE100-NGv3-sort-2_190313104_205830046-prep-prealign-realign.intervals -l INFO -L 2:190313105-205830046 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-14T23:46Z] INFO  16:46:10,651 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:46Z] INFO  16:46:10,652 HelpFormatter - Date/Time: 2016/04/14 16:46:10
[2016-04-14T23:46Z] INFO  16:46:10,652 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:46Z] INFO  16:46:10,652 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:46Z] INFO  16:46:10,779 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:46Z] GATK RealignerTargetCreator: R14-18105_kapa-NGv3-PE100-NGv3-sort-2_174777797_190306304-prep-prealign.bam 2:174777798-190306304
[2016-04-14T23:46Z] GATK: RealignerTargetCreator
[2016-04-14T23:46Z] INFO  16:46:10,978 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-14T23:46Z] INFO  16:46:10,990 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:46Z] INFO  16:46:11,060 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-14T23:46Z] INFO  16:46:11,383 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@5fe152b7
[2016-04-14T23:46Z] INFO  16:46:11,433 ProgressMeter -            done   1.6209898E7    20.0 s       1.0 s      100.0%    20.0 s       0.0 s
[2016-04-14T23:46Z] INFO  16:46:11,434 ProgressMeter - Total runtime 20.59 secs, 0.34 min, 0.01 hours
[2016-04-14T23:46Z] INFO  16:46:11,438 MicroScheduler - 67376 reads were filtered out during the traversal out of approximately 331063 total reads (20.35%)
[2016-04-14T23:46Z] INFO  16:46:11,439 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:46Z] INFO  16:46:11,439 MicroScheduler -   -> 696 reads (0.21% of total) failing BadMateFilter
[2016-04-14T23:46Z] INFO  16:46:11,439 MicroScheduler -   -> 23194 reads (7.01% of total) failing DuplicateReadFilter
[2016-04-14T23:46Z] INFO  16:46:11,440 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-14T23:46Z] INFO  16:46:11,440 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:46Z] INFO  16:46:11,440 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-14T23:46Z] INFO  16:46:11,441 MicroScheduler -   -> 43486 reads (13.14% of total) failing MappingQualityZeroFilter
[2016-04-14T23:46Z] INFO  16:46:11,441 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:46Z] INFO  16:46:11,441 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-14T23:46Z] INFO  16:46:11,441 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-14T23:46Z] INFO  16:46:11,461 IntervalUtils - Processing 15516942 bp from intervals
[2016-04-14T23:46Z] WARN  16:46:11,488 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:46Z] INFO  16:46:11,639 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:46Z] INFO  16:46:11,781 ProgressMeter -            done    321932.0    40.0 s       2.1 m      100.0%    40.0 s       0.0 s
[2016-04-14T23:46Z] INFO  16:46:11,783 ProgressMeter - Total runtime 40.40 secs, 0.67 min, 0.01 hours
[2016-04-14T23:46Z] INFO  16:46:11,784 MicroScheduler - 219 reads were filtered out during the traversal out of approximately 322151 total reads (0.07%)
[2016-04-14T23:46Z] INFO  16:46:11,784 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:46Z] INFO  16:46:11,785 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:46Z] INFO  16:46:11,786 MicroScheduler -   -> 219 reads (0.07% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:46Z] INFO  16:46:11,892 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:46Z] INFO  16:46:11,894 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:46Z] INFO  16:46:11,895 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:46Z] INFO  16:46:11,898 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-14T23:46Z] INFO  16:46:12,569 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:46Z] INFO  16:46:12,573 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:46Z] INFO  16:46:12,573 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:46Z] INFO  16:46:12,574 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:46Z] INFO  16:46:12,579 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/2/R14-18105_kapa-NGv3-PE100-NGv3-sort-2_159196753_174774985-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/2/tx/tmpmjkgYO/R14-18105_kapa-NGv3-PE100-NGv3-sort-2_159196753_174774985-prep-prealign-realign.intervals -l INFO -L 2:159196754-174774985 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-14T23:46Z] INFO  16:46:12,591 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:46Z] INFO  16:46:12,591 HelpFormatter - Date/Time: 2016/04/14 16:46:12
[2016-04-14T23:46Z] INFO  16:46:12,591 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:46Z] INFO  16:46:12,592 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:46Z] INFO  16:46:12,762 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:46Z] INFO  16:46:12,966 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-14T23:46Z] INFO  16:46:12,977 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:46Z] INFO  16:46:12,994 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:46Z] GATK: realign ('2', 127433207, 143643105) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-14T23:46Z] INFO  16:46:13,074 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.10
[2016-04-14T23:46Z] INFO  16:46:13,264 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:46Z] INFO  16:46:13,267 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:46Z] INFO  16:46:13,268 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:46Z] INFO  16:46:13,268 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:46Z] INFO  16:46:13,273 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/2/R14-18105_kapa-NGv3-PE100-NGv3-sort-2_237995374_243199373-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/2/tx/tmp2QUZ4t/R14-18105_kapa-NGv3-PE100-NGv3-sort-2_237995374_243199373-prep-prealign-realign.intervals -l INFO -L 2:237995375-243199373 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-14T23:46Z] INFO  16:46:13,300 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:46Z] INFO  16:46:13,301 HelpFormatter - Date/Time: 2016/04/14 16:46:13
[2016-04-14T23:46Z] INFO  16:46:13,301 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:46Z] INFO  16:46:13,302 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:46Z] INFO  16:46:13,308 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:46Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-2_222291154_237994685-prep-prealign.bam
[2016-04-14T23:46Z] INFO  16:46:13,386 IntervalUtils - Processing 15578232 bp from intervals
[2016-04-14T23:46Z] WARN  16:46:13,392 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:46Z] INFO  16:46:13,402 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:46Z] INFO  16:46:13,517 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:46Z] INFO  16:46:13,622 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-14T23:46Z] INFO  16:46:13,645 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:46Z] INFO  16:46:13,711 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-14T23:46Z] INFO  16:46:13,769 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:46Z] INFO  16:46:13,773 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:46Z] INFO  16:46:13,773 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:46Z] INFO  16:46:13,774 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:46Z] INFO  16:46:13,778 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/2/R14-18105_kapa-NGv3-PE100-NGv3-sort-2_174777797_190306304-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/2/tx/tmpvHWJ6Y/R14-18105_kapa-NGv3-PE100-NGv3-sort-2_174777797_190306304-prep-prealign-realign.intervals -l INFO -L 2:174777798-190306304 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-14T23:46Z] INFO  16:46:13,791 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:46Z] INFO  16:46:13,791 HelpFormatter - Date/Time: 2016/04/14 16:46:13
[2016-04-14T23:46Z] INFO  16:46:13,792 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:46Z] INFO  16:46:13,792 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:46Z] INFO  16:46:13,813 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:46Z] INFO  16:46:13,814 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:46Z] INFO  16:46:13,815 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:46Z] INFO  16:46:13,816 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-14T23:46Z] INFO  16:46:13,937 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:46Z] INFO  16:46:14,081 IntervalUtils - Processing 5203999 bp from intervals
[2016-04-14T23:46Z] WARN  16:46:14,086 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:46Z] INFO  16:46:14,167 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:46Z] INFO  16:46:14,182 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-14T23:46Z] INFO  16:46:14,191 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:46Z] INFO  16:46:14,239 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-14T23:46Z] INFO  16:46:14,328 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:46Z] INFO  16:46:14,329 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:46Z] INFO  16:46:14,330 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:46Z] INFO  16:46:14,331 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-14T23:46Z] GATK RealignerTargetCreator: R14-18105_kapa-NGv3-PE100-NGv3-sort-2_222291154_237994685-prep-prealign.bam 2:222291155-237994685
[2016-04-14T23:46Z] GATK: RealignerTargetCreator
[2016-04-14T23:46Z] INFO  16:46:14,555 IntervalUtils - Processing 15528507 bp from intervals
[2016-04-14T23:46Z] WARN  16:46:14,560 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:46Z] INFO  16:46:14,645 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:46Z] INFO  16:46:14,856 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:46Z] INFO  16:46:14,856 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:46Z] INFO  16:46:14,857 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:46Z] INFO  16:46:14,857 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-14T23:46Z] INFO  16:46:14,918 ProgressMeter -            done    341130.0    22.0 s      65.0 s      100.0%    22.0 s       0.0 s
[2016-04-14T23:46Z] INFO  16:46:14,918 ProgressMeter - Total runtime 22.23 secs, 0.37 min, 0.01 hours
[2016-04-14T23:46Z] INFO  16:46:14,922 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 341130 total reads (0.00%)
[2016-04-14T23:46Z] INFO  16:46:14,922 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:46Z] INFO  16:46:14,923 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:46Z] INFO  16:46:14,923 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:46Z] INFO  16:46:15,932 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:46Z] INFO  16:46:15,935 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:46Z] INFO  16:46:15,936 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:46Z] INFO  16:46:15,936 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:46Z] INFO  16:46:15,941 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/2/R14-18105_kapa-NGv3-PE100-NGv3-sort-2_127433207_143643105-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/2/R14-18105_kapa-NGv3-PE100-NGv3-sort-2_127433207_143643105-prep-prealign-realign.intervals -L 2:127433208-143643105 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/2/tx/tmpcRGLpD/R14-18105_kapa-NGv3-PE100-NGv3-sort-2_127433207_143643105-prep.bam
[2016-04-14T23:46Z] INFO  16:46:15,964 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:46Z] INFO  16:46:15,965 HelpFormatter - Date/Time: 2016/04/14 16:46:15
[2016-04-14T23:46Z] INFO  16:46:15,965 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:46Z] INFO  16:46:15,965 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:46Z] INFO  16:46:16,251 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:46Z] INFO  16:46:16,284 ProgressMeter -     1:157668478   1200021.0     3.0 m       2.5 m       88.8%     3.4 m      22.0 s
[2016-04-14T23:46Z] INFO  16:46:16,288 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:46Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-2_62362965_79253295-prep.bam
[2016-04-14T23:46Z] INFO  16:46:16,432 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:46Z] INFO  16:46:16,442 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:46Z] INFO  16:46:16,491 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-14T23:46Z] INFO  16:46:16,861 IntervalUtils - Processing 16209898 bp from intervals
[2016-04-14T23:46Z] WARN  16:46:16,866 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:46Z] INFO  16:46:16,933 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:46Z] INFO  16:46:17,040 ProgressMeter -            done    124003.0    10.0 s      88.0 s      100.0%    10.0 s       0.0 s
[2016-04-14T23:46Z] INFO  16:46:17,041 ProgressMeter - Total runtime 10.99 secs, 0.18 min, 0.00 hours
[2016-04-14T23:46Z] INFO  16:46:17,045 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 124003 total reads (0.00%)
[2016-04-14T23:46Z] INFO  16:46:17,046 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:46Z] INFO  16:46:17,047 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:46Z] INFO  16:46:17,048 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:46Z] INFO  16:46:17,100 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:46Z] INFO  16:46:17,101 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:46Z] INFO  16:46:17,102 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:46Z] INFO  16:46:17,103 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:46Z] INFO  16:46:17,230 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:46Z] INFO  16:46:17,366 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@7172f77a
[2016-04-14T23:46Z] INFO  16:46:17,381 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:46Z] GATK pre-alignment ('3', 47129602, 62648069) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-14T23:46Z] INFO  16:46:17,492 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:46Z] INFO  16:46:17,495 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:46Z] INFO  16:46:17,496 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:46Z] INFO  16:46:17,497 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:46Z] INFO  16:46:17,501 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/2/R14-18105_kapa-NGv3-PE100-NGv3-sort-2_222291154_237994685-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/2/tx/tmpHfXYQf/R14-18105_kapa-NGv3-PE100-NGv3-sort-2_222291154_237994685-prep-prealign-realign.intervals -l INFO -L 2:222291155-237994685 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-14T23:46Z] INFO  16:46:17,514 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:46Z] INFO  16:46:17,515 HelpFormatter - Date/Time: 2016/04/14 16:46:17
[2016-04-14T23:46Z] INFO  16:46:17,515 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:46Z] INFO  16:46:17,515 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:46Z] INFO  16:46:17,591 ProgressMeter -            done    534760.0    78.0 s       2.5 m      100.0%    78.0 s       0.0 s
[2016-04-14T23:46Z] INFO  16:46:17,592 ProgressMeter - Total runtime 78.79 secs, 1.31 min, 0.02 hours
[2016-04-14T23:46Z] INFO  16:46:17,592 MicroScheduler - 223 reads were filtered out during the traversal out of approximately 534983 total reads (0.04%)
[2016-04-14T23:46Z] INFO  16:46:17,593 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:46Z] INFO  16:46:17,593 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:46Z] INFO  16:46:17,593 MicroScheduler -   -> 223 reads (0.04% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:46Z] INFO  16:46:17,653 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:46Z] INFO  16:46:17,965 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-14T23:46Z] INFO  16:46:17,988 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:46Z] INFO  16:46:17,992 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@41fd9d8e
[2016-04-14T23:46Z] INFO  16:46:18,105 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.12
[2016-04-14T23:46Z] INFO  16:46:18,255 ProgressMeter -            done    412696.0    49.0 s     119.0 s      100.0%    49.0 s       0.0 s
[2016-04-14T23:46Z] INFO  16:46:18,256 ProgressMeter - Total runtime 49.47 secs, 0.82 min, 0.01 hours
[2016-04-14T23:46Z] INFO  16:46:18,256 MicroScheduler - 214 reads were filtered out during the traversal out of approximately 412910 total reads (0.05%)
[2016-04-14T23:46Z] INFO  16:46:18,257 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:46Z] INFO  16:46:18,257 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:46Z] INFO  16:46:18,257 MicroScheduler -   -> 214 reads (0.05% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:46Z] INFO  16:46:18,348 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:46Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-2_143676177_159195597-prep.bam
[2016-04-14T23:46Z] INFO  16:46:18,418 IntervalUtils - Processing 15703531 bp from intervals
[2016-04-14T23:46Z] WARN  16:46:18,424 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:46Z] INFO  16:46:18,552 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:46Z] INFO  16:46:18,786 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:46Z] INFO  16:46:18,787 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:46Z] INFO  16:46:18,788 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:46Z] INFO  16:46:18,789 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-14T23:46Z] GATK pre-alignment ('3', 62739115, 78648077) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-14T23:46Z] INFO  16:46:19,182 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:46Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-2_95538561_111273222-prep-prealign.bam
[2016-04-14T23:46Z] INFO  16:46:19,630 ProgressMeter -            done    238517.0    19.0 s      80.0 s      100.0%    19.0 s       0.0 s
[2016-04-14T23:46Z] INFO  16:46:19,631 ProgressMeter - Total runtime 19.08 secs, 0.32 min, 0.01 hours
[2016-04-14T23:46Z] INFO  16:46:19,634 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 238517 total reads (0.00%)
[2016-04-14T23:46Z] INFO  16:46:19,634 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:46Z] INFO  16:46:19,635 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:46Z] INFO  16:46:19,635 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:46Z] INFO  16:46:19,719 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:46Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-2_205912303_222290862-prep-prealign.bam
[2016-04-14T23:46Z] INFO  16:46:20,245 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:46Z] INFO  16:46:20,249 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:46Z] INFO  16:46:20,250 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:46Z] INFO  16:46:20,251 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:46Z] INFO  16:46:20,257 HelpFormatter - Program Args: -T PrintReads -L 3:47129603-62648069 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/3/tx/tmps2v5cW/R14-18105_kapa-NGv3-PE100-NGv3-sort-3_47129602_62648069-prep-prealign.bam
[2016-04-14T23:46Z] INFO  16:46:20,266 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:46Z] INFO  16:46:20,267 HelpFormatter - Date/Time: 2016/04/14 16:46:20
[2016-04-14T23:46Z] INFO  16:46:20,280 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:46Z] INFO  16:46:20,281 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:46Z] INFO  16:46:20,456 ProgressMeter -            done   1.6059299E7    17.0 s       1.0 s      100.0%    17.0 s       0.0 s
[2016-04-14T23:46Z] INFO  16:46:20,458 ProgressMeter - Total runtime 17.32 secs, 0.29 min, 0.00 hours
[2016-04-14T23:46Z] INFO  16:46:20,473 MicroScheduler - 10069 reads were filtered out during the traversal out of approximately 115663 total reads (8.71%)
[2016-04-14T23:46Z] INFO  16:46:20,483 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:46Z] INFO  16:46:20,484 MicroScheduler -   -> 474 reads (0.41% of total) failing BadMateFilter
[2016-04-14T23:46Z] INFO  16:46:20,484 MicroScheduler -   -> 9000 reads (7.78% of total) failing DuplicateReadFilter
[2016-04-14T23:46Z] INFO  16:46:20,484 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-14T23:46Z] INFO  16:46:20,485 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:46Z] INFO  16:46:20,485 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-14T23:46Z] INFO  16:46:20,485 MicroScheduler -   -> 595 reads (0.51% of total) failing MappingQualityZeroFilter
[2016-04-14T23:46Z] INFO  16:46:20,485 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:46Z] INFO  16:46:20,486 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-14T23:46Z] INFO  16:46:20,486 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-14T23:46Z] INFO  16:46:20,527 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:46Z] INFO  16:46:20,806 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@41fd9d8e
[2016-04-14T23:46Z] INFO  16:46:20,888 ProgressMeter -            done    325382.0    41.0 s       2.1 m      100.0%    41.0 s       0.0 s
[2016-04-14T23:46Z] INFO  16:46:20,888 ProgressMeter - Total runtime 41.31 secs, 0.69 min, 0.01 hours
[2016-04-14T23:46Z] INFO  16:46:20,889 MicroScheduler - 175 reads were filtered out during the traversal out of approximately 325557 total reads (0.05%)
[2016-04-14T23:46Z] INFO  16:46:20,889 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:46Z] INFO  16:46:20,889 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:46Z] INFO  16:46:20,890 MicroScheduler -   -> 175 reads (0.05% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:46Z] INFO  16:46:21,092 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:46Z] GATK RealignerTargetCreator: R14-18105_kapa-NGv3-PE100-NGv3-sort-2_95538561_111273222-prep-prealign.bam 2:95538562-111273222
[2016-04-14T23:46Z] GATK: RealignerTargetCreator
[2016-04-14T23:46Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-2_111281072_127413888-prep.bam
[2016-04-14T23:46Z] INFO  16:46:21,169 ProgressMeter -            done    254330.0    19.0 s      77.0 s      100.0%    19.0 s       0.0 s
[2016-04-14T23:46Z] INFO  16:46:21,170 ProgressMeter - Total runtime 19.78 secs, 0.33 min, 0.01 hours
[2016-04-14T23:46Z] INFO  16:46:21,174 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 254330 total reads (0.00%)
[2016-04-14T23:46Z] INFO  16:46:21,174 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:46Z] INFO  16:46:21,175 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:46Z] INFO  16:46:21,175 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:46Z] GATK RealignerTargetCreator: R14-18105_kapa-NGv3-PE100-NGv3-sort-2_205912303_222290862-prep-prealign.bam 2:205912304-222290862
[2016-04-14T23:46Z] GATK: RealignerTargetCreator
[2016-04-14T23:46Z] INFO  16:46:21,584 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:46Z] INFO  16:46:21,588 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:46Z] INFO  16:46:21,589 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:46Z] INFO  16:46:21,590 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:46Z] INFO  16:46:21,595 HelpFormatter - Program Args: -T PrintReads -L 3:62739116-78648077 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/3/tx/tmp0Tl1_l/R14-18105_kapa-NGv3-PE100-NGv3-sort-3_62739115_78648077-prep-prealign.bam
[2016-04-14T23:46Z] INFO  16:46:21,615 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:46Z] INFO  16:46:21,616 HelpFormatter - Date/Time: 2016/04/14 16:46:21
[2016-04-14T23:46Z] INFO  16:46:21,616 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:46Z] INFO  16:46:21,617 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:46Z] INFO  16:46:21,649 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-14T23:46Z] INFO  16:46:21,705 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:46Z] INFO  16:46:21,714 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:46Z] INFO  16:46:21,763 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-14T23:46Z] INFO  16:46:21,778 IntervalUtils - Processing 15518467 bp from intervals
[2016-04-14T23:46Z] INFO  16:46:21,801 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:46Z] INFO  16:46:21,885 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:46Z] INFO  16:46:21,919 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:46Z] GATK: realign ('3', 15515506, 31574805) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-14T23:46Z] GATK pre-alignment ('3', 78649262, 96533852) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-14T23:46Z] INFO  16:46:22,196 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:46Z] INFO  16:46:22,197 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:46Z] INFO  16:46:22,197 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:46Z] INFO  16:46:22,197 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:46Z] INFO  16:46:22,212 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:46Z] INFO  16:46:22,356 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:46Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-3_0_15512123-prep-prealign.bam
[2016-04-14T23:46Z] INFO  16:46:22,408 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:46Z] INFO  16:46:22,686 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:46Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-2_79253838_95537822-prep.bam
[2016-04-14T23:46Z] INFO  16:46:23,054 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-14T23:46Z] INFO  16:46:23,124 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:46Z] INFO  16:46:23,147 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:46Z] GATK RealignerTargetCreator: R14-18105_kapa-NGv3-PE100-NGv3-sort-3_0_15512123-prep-prealign.bam 3:1-15512123
[2016-04-14T23:46Z] GATK: RealignerTargetCreator
[2016-04-14T23:46Z] INFO  16:46:23,195 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-14T23:46Z] INFO  16:46:23,210 IntervalUtils - Processing 15908962 bp from intervals
[2016-04-14T23:46Z] INFO  16:46:23,304 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:46Z] GATK pre-alignment ('3', 96585668, 112185230) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-14T23:46Z] INFO  16:46:23,612 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:46Z] INFO  16:46:23,613 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:46Z] INFO  16:46:23,614 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:46Z] INFO  16:46:23,615 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:46Z] INFO  16:46:23,629 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:46Z] INFO  16:46:23,818 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:46Z] INFO  16:46:24,268 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:46Z] INFO  16:46:24,272 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:46Z] INFO  16:46:24,272 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:46Z] INFO  16:46:24,273 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:46Z] INFO  16:46:24,277 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/2/R14-18105_kapa-NGv3-PE100-NGv3-sort-2_95538561_111273222-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/2/tx/tmpWEVl1R/R14-18105_kapa-NGv3-PE100-NGv3-sort-2_95538561_111273222-prep-prealign-realign.intervals -l INFO -L 2:95538562-111273222 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-14T23:46Z] INFO  16:46:24,289 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:46Z] INFO  16:46:24,289 HelpFormatter - Date/Time: 2016/04/14 16:46:24
[2016-04-14T23:46Z] INFO  16:46:24,289 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:46Z] INFO  16:46:24,290 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:46Z] INFO  16:46:24,292 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:46Z] INFO  16:46:24,296 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:46Z] INFO  16:46:24,296 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:46Z] INFO  16:46:24,297 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:46Z] INFO  16:46:24,301 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/2/R14-18105_kapa-NGv3-PE100-NGv3-sort-2_205912303_222290862-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/2/tx/tmpVni4JR/R14-18105_kapa-NGv3-PE100-NGv3-sort-2_205912303_222290862-prep-prealign-realign.intervals -l INFO -L 2:205912304-222290862 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-14T23:46Z] INFO  16:46:24,324 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:46Z] INFO  16:46:24,325 HelpFormatter - Date/Time: 2016/04/14 16:46:24
[2016-04-14T23:46Z] INFO  16:46:24,325 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:46Z] INFO  16:46:24,330 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:46Z] INFO  16:46:24,437 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:46Z] INFO  16:46:24,474 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:46Z] INFO  16:46:24,730 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-14T23:46Z] INFO  16:46:24,731 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-14T23:46Z] INFO  16:46:24,741 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:46Z] INFO  16:46:24,759 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:46Z] INFO  16:46:24,813 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-14T23:46Z] INFO  16:46:24,823 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-14T23:46Z] INFO  16:46:24,988 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:46Z] INFO  16:46:24,991 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:46Z] INFO  16:46:24,992 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:46Z] INFO  16:46:24,992 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:46Z] INFO  16:46:24,997 HelpFormatter - Program Args: -T PrintReads -L 3:78649263-96533852 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/3/tx/tmp3OD7WK/R14-18105_kapa-NGv3-PE100-NGv3-sort-3_78649262_96533852-prep-prealign.bam
[2016-04-14T23:46Z] INFO  16:46:25,038 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:46Z] INFO  16:46:25,043 HelpFormatter - Date/Time: 2016/04/14 16:46:24
[2016-04-14T23:46Z] INFO  16:46:25,044 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:46Z] INFO  16:46:25,052 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:46Z] INFO  16:46:25,119 IntervalUtils - Processing 15734661 bp from intervals
[2016-04-14T23:46Z] WARN  16:46:25,124 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:46Z] INFO  16:46:25,190 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:46Z] INFO  16:46:25,231 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:46Z] INFO  16:46:25,245 IntervalUtils - Processing 16378559 bp from intervals
[2016-04-14T23:46Z] INFO  16:46:25,246 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@41fd9d8e
[2016-04-14T23:46Z] WARN  16:46:25,250 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:46Z] INFO  16:46:25,332 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:46Z] INFO  16:46:25,452 ProgressMeter -            done   1277936.0     3.2 m       2.5 m      100.0%     3.2 m       0.0 s
[2016-04-14T23:46Z] INFO  16:46:25,453 ProgressMeter - Total runtime 190.56 secs, 3.18 min, 0.05 hours
[2016-04-14T23:46Z] INFO  16:46:25,453 MicroScheduler - 430 reads were filtered out during the traversal out of approximately 1278366 total reads (0.03%)
[2016-04-14T23:46Z] INFO  16:46:25,454 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:46Z] INFO  16:46:25,454 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:46Z] INFO  16:46:25,454 MicroScheduler -   -> 430 reads (0.03% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:46Z] INFO  16:46:25,536 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:46Z] INFO  16:46:25,538 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:46Z] INFO  16:46:25,539 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:46Z] INFO  16:46:25,539 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-14T23:46Z] INFO  16:46:25,573 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:46Z] INFO  16:46:25,575 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:46Z] INFO  16:46:25,576 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:46Z] INFO  16:46:25,576 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:46Z] INFO  16:46:25,580 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/3/R14-18105_kapa-NGv3-PE100-NGv3-sort-3_15515506_31574805-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/3/R14-18105_kapa-NGv3-PE100-NGv3-sort-3_15515506_31574805-prep-prealign-realign.intervals -L 3:15515507-31574805 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/3/tx/tmpAxwbz8/R14-18105_kapa-NGv3-PE100-NGv3-sort-3_15515506_31574805-prep.bam
[2016-04-14T23:46Z] INFO  16:46:25,621 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:46Z] INFO  16:46:25,622 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:46Z] INFO  16:46:25,622 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:46Z] INFO  16:46:25,622 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-14T23:46Z] INFO  16:46:25,622 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:46Z] INFO  16:46:25,623 HelpFormatter - Date/Time: 2016/04/14 16:46:25
[2016-04-14T23:46Z] INFO  16:46:25,623 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:46Z] INFO  16:46:25,623 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:46Z] INFO  16:46:25,855 ProgressMeter -            done   5203999.0    11.0 s       2.0 s      100.0%    11.0 s       0.0 s
[2016-04-14T23:46Z] INFO  16:46:25,856 ProgressMeter - Total runtime 11.53 secs, 0.19 min, 0.00 hours
[2016-04-14T23:46Z] INFO  16:46:25,860 MicroScheduler - 23391 reads were filtered out during the traversal out of approximately 223022 total reads (10.49%)
[2016-04-14T23:46Z] INFO  16:46:25,860 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:46Z] INFO  16:46:25,861 MicroScheduler -   -> 409 reads (0.18% of total) failing BadMateFilter
[2016-04-14T23:46Z] INFO  16:46:25,862 MicroScheduler -   -> 17138 reads (7.68% of total) failing DuplicateReadFilter
[2016-04-14T23:46Z] INFO  16:46:25,862 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-14T23:46Z] INFO  16:46:25,863 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:46Z] INFO  16:46:25,863 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-14T23:46Z] INFO  16:46:25,864 MicroScheduler -   -> 5844 reads (2.62% of total) failing MappingQualityZeroFilter
[2016-04-14T23:46Z] INFO  16:46:25,865 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:46Z] INFO  16:46:25,865 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-14T23:46Z] INFO  16:46:25,866 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-14T23:46Z] INFO  16:46:25,872 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:46Z] INFO  16:46:26,024 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:46Z] INFO  16:46:26,033 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:46Z] INFO  16:46:26,095 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-14T23:46Z] INFO  16:46:26,134 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:46Z] INFO  16:46:26,137 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:46Z] INFO  16:46:26,138 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:46Z] INFO  16:46:26,139 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:46Z] INFO  16:46:26,143 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/3/R14-18105_kapa-NGv3-PE100-NGv3-sort-3_0_15512123-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/3/tx/tmpJWx9SV/R14-18105_kapa-NGv3-PE100-NGv3-sort-3_0_15512123-prep-prealign-realign.intervals -l INFO -L 3:1-15512123 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-14T23:46Z] INFO  16:46:26,151 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:46Z] INFO  16:46:26,152 HelpFormatter - Date/Time: 2016/04/14 16:46:26
[2016-04-14T23:46Z] INFO  16:46:26,153 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:46Z] INFO  16:46:26,154 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:46Z] INFO  16:46:26,273 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:46Z] INFO  16:46:26,438 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-14T23:46Z] INFO  16:46:26,489 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:46Z] INFO  16:46:26,492 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:46Z] INFO  16:46:26,493 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:46Z] INFO  16:46:26,493 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:46Z] INFO  16:46:26,494 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:46Z] INFO  16:46:26,498 HelpFormatter - Program Args: -T PrintReads -L 3:96585669-112185230 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/3/tx/tmpDqW_PC/R14-18105_kapa-NGv3-PE100-NGv3-sort-3_96585668_112185230-prep-prealign.bam
[2016-04-14T23:46Z] INFO  16:46:26,503 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:46Z] INFO  16:46:26,513 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-14T23:46Z] INFO  16:46:26,508 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:46Z] INFO  16:46:26,513 HelpFormatter - Date/Time: 2016/04/14 16:46:26
[2016-04-14T23:46Z] INFO  16:46:26,514 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:46Z] INFO  16:46:26,514 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:46Z] INFO  16:46:26,523 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:46Z] INFO  16:46:26,556 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-14T23:46Z] INFO  16:46:26,556 IntervalUtils - Processing 16059299 bp from intervals
[2016-04-14T23:46Z] WARN  16:46:26,561 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:46Z] INFO  16:46:26,570 IntervalUtils - Processing 17884590 bp from intervals
[2016-04-14T23:46Z] INFO  16:46:26,599 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-14T23:46Z] INFO  16:46:26,657 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:46Z] INFO  16:46:26,663 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:46Z] INFO  16:46:26,685 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:46Z] INFO  16:46:26,804 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:46Z] INFO  16:46:26,806 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:46Z] INFO  16:46:26,806 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:46Z] INFO  16:46:26,807 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:46Z] INFO  16:46:26,868 IntervalUtils - Processing 15512123 bp from intervals
[2016-04-14T23:46Z] WARN  16:46:26,873 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:46Z] INFO  16:46:26,908 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:46Z] INFO  16:46:26,954 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:46Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-1_143897546_159410511-prep-prealign.bam
[2016-04-14T23:46Z] INFO  16:46:26,986 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:46Z] INFO  16:46:26,986 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:46Z] INFO  16:46:26,987 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:46Z] INFO  16:46:26,987 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:46Z] INFO  16:46:27,011 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:46Z] INFO  16:46:27,028 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:46Z] INFO  16:46:27,174 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:46Z] INFO  16:46:27,193 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:46Z] INFO  16:46:27,194 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:46Z] INFO  16:46:27,194 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:46Z] INFO  16:46:27,195 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-14T23:46Z] INFO  16:46:27,211 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:46Z] INFO  16:46:27,389 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:46Z] GATK: realign ('2', 237995374, 243199373) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-14T23:46Z] INFO  16:46:27,797 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-14T23:46Z] INFO  16:46:27,876 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:46Z] INFO  16:46:27,886 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:46Z] INFO  16:46:27,931 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-14T23:46Z] INFO  16:46:27,947 IntervalUtils - Processing 15599562 bp from intervals
[2016-04-14T23:46Z] INFO  16:46:28,018 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:46Z] INFO  16:46:28,399 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:46Z] INFO  16:46:28,400 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:46Z] INFO  16:46:28,401 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:46Z] INFO  16:46:28,401 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:46Z] INFO  16:46:28,415 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:46Z] INFO  16:46:28,613 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:46Z] INFO  16:46:30,438 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:46Z] INFO  16:46:30,441 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:46Z] INFO  16:46:30,442 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:46Z] INFO  16:46:30,442 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:46Z] INFO  16:46:30,447 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/2/R14-18105_kapa-NGv3-PE100-NGv3-sort-2_237995374_243199373-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/2/R14-18105_kapa-NGv3-PE100-NGv3-sort-2_237995374_243199373-prep-prealign-realign.intervals -L 2:237995375-243199373 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/2/tx/tmpw_WwxK/R14-18105_kapa-NGv3-PE100-NGv3-sort-2_237995374_243199373-prep.bam
[2016-04-14T23:46Z] INFO  16:46:30,479 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:46Z] INFO  16:46:30,480 HelpFormatter - Date/Time: 2016/04/14 16:46:30
[2016-04-14T23:46Z] INFO  16:46:30,480 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:46Z] INFO  16:46:30,481 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:46Z] GATK RealignerTargetCreator: R14-18105_kapa-NGv3-PE100-NGv3-sort-1_143897546_159410511-prep-prealign.bam 1:143897547-159410511
[2016-04-14T23:46Z] INFO  16:46:30,755 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:46Z] GATK: RealignerTargetCreator
[2016-04-14T23:46Z] INFO  16:46:30,858 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:46Z] INFO  16:46:30,867 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:46Z] INFO  16:46:30,920 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-14T23:46Z] INFO  16:46:31,218 IntervalUtils - Processing 5203999 bp from intervals
[2016-04-14T23:46Z] WARN  16:46:31,223 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:46Z] INFO  16:46:31,328 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:46Z] INFO  16:46:31,393 ProgressMeter -            done   1.5516942E7    19.0 s       1.0 s      100.0%    19.0 s       0.0 s
[2016-04-14T23:46Z] INFO  16:46:31,395 ProgressMeter - Total runtime 19.50 secs, 0.33 min, 0.01 hours
[2016-04-14T23:46Z] INFO  16:46:31,399 MicroScheduler - 21134 reads were filtered out during the traversal out of approximately 253838 total reads (8.33%)
[2016-04-14T23:46Z] INFO  16:46:31,400 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:46Z] INFO  16:46:31,401 MicroScheduler -   -> 624 reads (0.25% of total) failing BadMateFilter
[2016-04-14T23:46Z] INFO  16:46:31,402 MicroScheduler -   -> 19860 reads (7.82% of total) failing DuplicateReadFilter
[2016-04-14T23:46Z] INFO  16:46:31,402 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-14T23:46Z] INFO  16:46:31,403 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:46Z] INFO  16:46:31,403 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-14T23:46Z] INFO  16:46:31,404 MicroScheduler -   -> 650 reads (0.26% of total) failing MappingQualityZeroFilter
[2016-04-14T23:46Z] INFO  16:46:31,405 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:46Z] INFO  16:46:31,405 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-14T23:46Z] INFO  16:46:31,406 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-14T23:46Z] INFO  16:46:31,446 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:46Z] INFO  16:46:31,447 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:46Z] INFO  16:46:31,448 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:46Z] INFO  16:46:31,453 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:46Z] INFO  16:46:31,526 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:46Z] INFO  16:46:31,576 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:46Z] INFO  16:46:32,162 ProgressMeter -      3:39150596    100001.0    31.0 s       5.2 m       48.6%    63.0 s      32.0 s
[2016-04-14T23:46Z] INFO  16:46:32,756 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:46Z] GATK: realign ('2', 190313104, 205830046) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-14T23:46Z] INFO  16:46:33,766 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:46Z] INFO  16:46:33,769 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:46Z] INFO  16:46:33,770 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:46Z] INFO  16:46:33,771 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:46Z] INFO  16:46:33,775 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/1/R14-18105_kapa-NGv3-PE100-NGv3-sort-1_143897546_159410511-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/1/tx/tmpVdYUdp/R14-18105_kapa-NGv3-PE100-NGv3-sort-1_143897546_159410511-prep-prealign-realign.intervals -l INFO -L 1:143897547-159410511 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-14T23:46Z] INFO  16:46:33,784 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:46Z] INFO  16:46:33,785 HelpFormatter - Date/Time: 2016/04/14 16:46:33
[2016-04-14T23:46Z] INFO  16:46:33,786 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:46Z] INFO  16:46:33,786 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:46Z] INFO  16:46:33,877 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:46Z] INFO  16:46:33,997 ProgressMeter -            done   1.5578232E7    20.0 s       1.0 s      100.0%    20.0 s       0.0 s
[2016-04-14T23:46Z] INFO  16:46:33,998 ProgressMeter - Total runtime 20.18 secs, 0.34 min, 0.01 hours
[2016-04-14T23:46Z] INFO  16:46:34,014 MicroScheduler - 25357 reads were filtered out during the traversal out of approximately 300602 total reads (8.44%)
[2016-04-14T23:46Z] INFO  16:46:34,015 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:46Z] INFO  16:46:34,016 MicroScheduler -   -> 686 reads (0.23% of total) failing BadMateFilter
[2016-04-14T23:46Z] INFO  16:46:34,016 MicroScheduler -   -> 23276 reads (7.74% of total) failing DuplicateReadFilter
[2016-04-14T23:46Z] INFO  16:46:34,017 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-14T23:46Z] INFO  16:46:34,017 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:46Z] INFO  16:46:34,018 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-14T23:46Z] INFO  16:46:34,019 MicroScheduler -   -> 1395 reads (0.46% of total) failing MappingQualityZeroFilter
[2016-04-14T23:46Z] INFO  16:46:34,019 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:46Z] INFO  16:46:34,020 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-14T23:46Z] INFO  16:46:34,021 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-14T23:46Z] INFO  16:46:34,062 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-14T23:46Z] INFO  16:46:34,074 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:46Z] INFO  16:46:34,130 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-14T23:46Z] INFO  16:46:34,400 IntervalUtils - Processing 15512965 bp from intervals
[2016-04-14T23:46Z] WARN  16:46:34,406 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:46Z] INFO  16:46:34,481 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:46Z] INFO  16:46:34,786 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:46Z] INFO  16:46:34,787 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:46Z] INFO  16:46:34,788 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:46Z] INFO  16:46:34,788 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-14T23:46Z] INFO  16:46:35,373 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:46Z] GATK: realign ('2', 159196753, 174774985) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-14T23:46Z] INFO  16:46:35,608 ProgressMeter -            done   1.5528507E7    20.0 s       1.0 s      100.0%    20.0 s       0.0 s
[2016-04-14T23:46Z] INFO  16:46:35,609 ProgressMeter - Total runtime 20.75 secs, 0.35 min, 0.01 hours
[2016-04-14T23:46Z] INFO  16:46:35,613 MicroScheduler - 34491 reads were filtered out during the traversal out of approximately 342884 total reads (10.06%)
[2016-04-14T23:46Z] INFO  16:46:35,614 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:46Z] INFO  16:46:35,615 MicroScheduler -   -> 668 reads (0.19% of total) failing BadMateFilter
[2016-04-14T23:46Z] INFO  16:46:35,616 MicroScheduler -   -> 26703 reads (7.79% of total) failing DuplicateReadFilter
[2016-04-14T23:46Z] INFO  16:46:35,616 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-14T23:46Z] INFO  16:46:35,617 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:46Z] INFO  16:46:35,617 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-14T23:46Z] INFO  16:46:35,618 MicroScheduler -   -> 7120 reads (2.08% of total) failing MappingQualityZeroFilter
[2016-04-14T23:46Z] INFO  16:46:35,619 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:46Z] INFO  16:46:35,619 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-14T23:46Z] INFO  16:46:35,620 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-14T23:46Z] INFO  16:46:35,687 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:46Z] INFO  16:46:35,691 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:46Z] INFO  16:46:35,692 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:46Z] INFO  16:46:35,692 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:46Z] INFO  16:46:35,698 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/2/R14-18105_kapa-NGv3-PE100-NGv3-sort-2_190313104_205830046-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/2/R14-18105_kapa-NGv3-PE100-NGv3-sort-2_190313104_205830046-prep-prealign-realign.intervals -L 2:190313105-205830046 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/2/tx/tmpblYNte/R14-18105_kapa-NGv3-PE100-NGv3-sort-2_190313104_205830046-prep.bam
[2016-04-14T23:46Z] INFO  16:46:35,716 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:46Z] INFO  16:46:35,717 HelpFormatter - Date/Time: 2016/04/14 16:46:35
[2016-04-14T23:46Z] INFO  16:46:35,718 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:46Z] INFO  16:46:35,718 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:46Z] INFO  16:46:36,039 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:46Z] INFO  16:46:36,042 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@5fe152b7
[2016-04-14T23:46Z] INFO  16:46:36,173 ProgressMeter -            done     46461.0     9.0 s       3.3 m      100.0%     9.0 s       0.0 s
[2016-04-14T23:46Z] INFO  16:46:36,174 ProgressMeter - Total runtime 9.19 secs, 0.15 min, 0.00 hours
[2016-04-14T23:46Z] INFO  16:46:36,174 MicroScheduler - 103 reads were filtered out during the traversal out of approximately 46564 total reads (0.22%)
[2016-04-14T23:46Z] INFO  16:46:36,175 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:46Z] INFO  16:46:36,175 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:46Z] INFO  16:46:36,175 MicroScheduler -   -> 103 reads (0.22% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:46Z] INFO  16:46:36,279 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:46Z] INFO  16:46:36,318 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:46Z] INFO  16:46:36,427 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.11
[2016-04-14T23:46Z] INFO  16:46:36,940 IntervalUtils - Processing 15516942 bp from intervals
[2016-04-14T23:46Z] WARN  16:46:36,944 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:46Z] INFO  16:46:37,062 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:46Z] INFO  16:46:37,198 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:46Z] INFO  16:46:37,197 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:46Z] INFO  16:46:37,200 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:46Z] INFO  16:46:37,201 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:46Z] INFO  16:46:37,202 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:46Z] GATK: realign ('2', 174777797, 190306304) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-14T23:46Z] INFO  16:46:37,333 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:46Z] INFO  16:46:37,529 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:46Z] INFO  16:46:37,603 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:46Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-3_78649262_96533852-prep-prealign.bam
[2016-04-14T23:46Z] GATK RealignerTargetCreator: R14-18105_kapa-NGv3-PE100-NGv3-sort-3_78649262_96533852-prep-prealign.bam 3:78649263-96533852
[2016-04-14T23:46Z] GATK: RealignerTargetCreator
[2016-04-14T23:46Z] INFO  16:46:38,004 ProgressMeter -            done    115016.0    11.0 s      97.0 s      100.0%    11.0 s       0.0 s
[2016-04-14T23:46Z] INFO  16:46:38,005 ProgressMeter - Total runtime 11.20 secs, 0.19 min, 0.00 hours
[2016-04-14T23:46Z] INFO  16:46:38,008 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 115016 total reads (0.00%)
[2016-04-14T23:46Z] INFO  16:46:38,009 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:46Z] INFO  16:46:38,009 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:46Z] INFO  16:46:38,009 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:46Z] INFO  16:46:38,287 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:46Z] INFO  16:46:38,290 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:46Z] INFO  16:46:38,291 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:46Z] INFO  16:46:38,291 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:46Z] INFO  16:46:38,296 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/2/R14-18105_kapa-NGv3-PE100-NGv3-sort-2_159196753_174774985-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/2/R14-18105_kapa-NGv3-PE100-NGv3-sort-2_159196753_174774985-prep-prealign-realign.intervals -L 2:159196754-174774985 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/2/tx/tmpAlTy_9/R14-18105_kapa-NGv3-PE100-NGv3-sort-2_159196753_174774985-prep.bam
[2016-04-14T23:46Z] INFO  16:46:38,316 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:46Z] INFO  16:46:38,317 HelpFormatter - Date/Time: 2016/04/14 16:46:38
[2016-04-14T23:46Z] INFO  16:46:38,318 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:46Z] INFO  16:46:38,318 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:46Z] INFO  16:46:38,526 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:46Z] INFO  16:46:38,648 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:46Z] INFO  16:46:38,656 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:46Z] INFO  16:46:38,727 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-14T23:46Z] INFO  16:46:39,169 IntervalUtils - Processing 15578232 bp from intervals
[2016-04-14T23:46Z] WARN  16:46:39,174 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:46Z] INFO  16:46:39,273 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:46Z] INFO  16:46:39,413 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:46Z] INFO  16:46:39,415 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:46Z] INFO  16:46:39,415 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:46Z] INFO  16:46:39,416 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:46Z] INFO  16:46:39,441 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:46Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-3_15515506_31574805-prep.bam
[2016-04-14T23:46Z] INFO  16:46:39,596 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:46Z] INFO  16:46:39,748 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:46Z] INFO  16:46:39,913 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:46Z] INFO  16:46:39,917 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:46Z] INFO  16:46:39,917 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:46Z] INFO  16:46:39,918 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:46Z] INFO  16:46:39,923 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/2/R14-18105_kapa-NGv3-PE100-NGv3-sort-2_174777797_190306304-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/2/R14-18105_kapa-NGv3-PE100-NGv3-sort-2_174777797_190306304-prep-prealign-realign.intervals -L 2:174777798-190306304 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/2/tx/tmpdaPOaX/R14-18105_kapa-NGv3-PE100-NGv3-sort-2_174777797_190306304-prep.bam
[2016-04-14T23:46Z] INFO  16:46:39,934 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:46Z] GATK pre-alignment ('3', 112188604, 127703121) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-14T23:46Z] INFO  16:46:39,938 HelpFormatter - Date/Time: 2016/04/14 16:46:39
[2016-04-14T23:46Z] INFO  16:46:39,939 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:46Z] INFO  16:46:39,941 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:46Z] INFO  16:46:40,186 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:46Z] INFO  16:46:40,316 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:46Z] INFO  16:46:40,326 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:46Z] INFO  16:46:40,387 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-14T23:46Z] INFO  16:46:40,481 ProgressMeter -            done    329163.0    23.0 s      71.0 s      100.0%    23.0 s       0.0 s
[2016-04-14T23:46Z] INFO  16:46:40,482 ProgressMeter - Total runtime 23.38 secs, 0.39 min, 0.01 hours
[2016-04-14T23:46Z] INFO  16:46:40,485 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 329163 total reads (0.00%)
[2016-04-14T23:46Z] INFO  16:46:40,486 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:46Z] INFO  16:46:40,486 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:46Z] INFO  16:46:40,486 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:46Z] INFO  16:46:40,575 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:46Z] INFO  16:46:40,579 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:46Z] INFO  16:46:40,579 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:46Z] INFO  16:46:40,580 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:46Z] INFO  16:46:40,585 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/3/R14-18105_kapa-NGv3-PE100-NGv3-sort-3_78649262_96533852-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/3/tx/tmptBVBu8/R14-18105_kapa-NGv3-PE100-NGv3-sort-3_78649262_96533852-prep-prealign-realign.intervals -l INFO -L 3:78649263-96533852 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-14T23:46Z] INFO  16:46:40,611 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:46Z] INFO  16:46:40,612 HelpFormatter - Date/Time: 2016/04/14 16:46:40
[2016-04-14T23:46Z] INFO  16:46:40,613 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:46Z] INFO  16:46:40,613 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:46Z] INFO  16:46:40,744 IntervalUtils - Processing 15528507 bp from intervals
[2016-04-14T23:46Z] INFO  16:46:40,745 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:46Z] WARN  16:46:40,749 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:46Z] INFO  16:46:40,833 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:46Z] INFO  16:46:41,017 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:46Z] INFO  16:46:41,018 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:46Z] INFO  16:46:41,019 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:46Z] INFO  16:46:41,025 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-14T23:46Z] INFO  16:46:41,030 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:46Z] INFO  16:46:41,034 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:46Z] INFO  16:46:41,103 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-14T23:46Z] INFO  16:46:41,190 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:46Z] INFO  16:46:41,354 IntervalUtils - Processing 17884590 bp from intervals
[2016-04-14T23:46Z] WARN  16:46:41,359 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:46Z] INFO  16:46:41,363 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:46Z] INFO  16:46:41,522 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:46Z] INFO  16:46:41,665 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:46Z] INFO  16:46:41,666 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:46Z] INFO  16:46:41,667 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:46Z] INFO  16:46:41,668 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-14T23:46Z] INFO  16:46:41,964 ProgressMeter -            done   1.5703531E7    23.0 s       1.0 s      100.0%    23.0 s       0.0 s
[2016-04-14T23:46Z] INFO  16:46:41,965 ProgressMeter - Total runtime 23.18 secs, 0.39 min, 0.01 hours
[2016-04-14T23:46Z] INFO  16:46:41,969 MicroScheduler - 29978 reads were filtered out during the traversal out of approximately 324199 total reads (9.25%)
[2016-04-14T23:46Z] INFO  16:46:41,970 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:46Z] INFO  16:46:41,971 MicroScheduler -   -> 735 reads (0.23% of total) failing BadMateFilter
[2016-04-14T23:46Z] INFO  16:46:41,972 MicroScheduler -   -> 25787 reads (7.95% of total) failing DuplicateReadFilter
[2016-04-14T23:46Z] INFO  16:46:41,973 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-14T23:46Z] INFO  16:46:41,973 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:46Z] INFO  16:46:41,974 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-14T23:46Z] INFO  16:46:41,975 MicroScheduler -   -> 3456 reads (1.07% of total) failing MappingQualityZeroFilter
[2016-04-14T23:46Z] INFO  16:46:41,975 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:46Z] INFO  16:46:41,976 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-14T23:46Z] INFO  16:46:41,977 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-14T23:46Z] INFO  16:46:42,161 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:46Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-2_127433207_143643105-prep.bam
[2016-04-14T23:46Z] INFO  16:46:42,537 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@41fd9d8e
[2016-04-14T23:46Z] INFO  16:46:42,672 ProgressMeter -            done    129658.0    19.0 s       2.4 m      100.0%    19.0 s       0.0 s
[2016-04-14T23:46Z] INFO  16:46:42,673 ProgressMeter - Total runtime 19.06 secs, 0.32 min, 0.01 hours
[2016-04-14T23:46Z] INFO  16:46:42,673 MicroScheduler - 109 reads were filtered out during the traversal out of approximately 129767 total reads (0.08%)
[2016-04-14T23:46Z] INFO  16:46:42,673 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:46Z] INFO  16:46:42,674 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:46Z] INFO  16:46:42,674 MicroScheduler -   -> 109 reads (0.08% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:46Z] INFO  16:46:42,811 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:46Z] INFO  16:46:42,814 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:46Z] INFO  16:46:42,815 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:46Z] INFO  16:46:42,816 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:46Z] INFO  16:46:42,820 HelpFormatter - Program Args: -T PrintReads -L 3:112188605-127703121 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/3/tx/tmpxY4JO8/R14-18105_kapa-NGv3-PE100-NGv3-sort-3_112188604_127703121-prep-prealign.bam
[2016-04-14T23:46Z] INFO  16:46:42,836 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:46Z] INFO  16:46:42,837 HelpFormatter - Date/Time: 2016/04/14 16:46:42
[2016-04-14T23:46Z] INFO  16:46:42,838 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:46Z] INFO  16:46:42,838 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:46Z] INFO  16:46:43,042 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:46Z] INFO  16:46:43,290 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:46Z] GATK pre-alignment ('3', 127770401, 143293035) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-14T23:46Z] GATK: realign ('2', 222291154, 237994685) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-14T23:46Z] INFO  16:46:44,074 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-14T23:46Z] INFO  16:46:44,074 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:46Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-3_62739115_78648077-prep-prealign.bam
[2016-04-14T23:46Z] INFO  16:46:44,159 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:46Z] INFO  16:46:44,169 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:46Z] INFO  16:46:44,251 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-14T23:46Z] INFO  16:46:44,276 IntervalUtils - Processing 15514517 bp from intervals
[2016-04-14T23:46Z] INFO  16:46:44,369 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:46Z] GATK RealignerTargetCreator: R14-18105_kapa-NGv3-PE100-NGv3-sort-3_62739115_78648077-prep-prealign.bam 3:62739116-78648077
[2016-04-14T23:46Z] GATK: RealignerTargetCreator
[2016-04-14T23:46Z] INFO  16:46:44,758 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:46Z] INFO  16:46:44,759 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:46Z] INFO  16:46:44,760 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:46Z] INFO  16:46:44,760 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:46Z] INFO  16:46:44,785 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:46Z] INFO  16:46:45,007 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:46Z] INFO  16:46:46,160 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:46Z] INFO  16:46:46,163 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:46Z] INFO  16:46:46,164 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:46Z] INFO  16:46:46,165 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:46Z] INFO  16:46:46,169 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/2/R14-18105_kapa-NGv3-PE100-NGv3-sort-2_222291154_237994685-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/2/R14-18105_kapa-NGv3-PE100-NGv3-sort-2_222291154_237994685-prep-prealign-realign.intervals -L 2:222291155-237994685 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/2/tx/tmpFLfv8e/R14-18105_kapa-NGv3-PE100-NGv3-sort-2_222291154_237994685-prep.bam
[2016-04-14T23:46Z] INFO  16:46:46,178 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:46Z] INFO  16:46:46,179 HelpFormatter - Date/Time: 2016/04/14 16:46:46
[2016-04-14T23:46Z] INFO  16:46:46,179 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:46Z] INFO  16:46:46,179 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:46Z] INFO  16:46:46,340 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:46Z] INFO  16:46:46,353 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:46Z] INFO  16:46:46,357 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:46Z] INFO  16:46:46,357 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:46Z] INFO  16:46:46,358 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:46Z] INFO  16:46:46,362 HelpFormatter - Program Args: -T PrintReads -L 3:127770402-143293035 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/3/tx/tmpq_FmYk/R14-18105_kapa-NGv3-PE100-NGv3-sort-3_127770401_143293035-prep-prealign.bam
[2016-04-14T23:46Z] INFO  16:46:46,375 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:46Z] INFO  16:46:46,376 HelpFormatter - Date/Time: 2016/04/14 16:46:46
[2016-04-14T23:46Z] INFO  16:46:46,376 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:46Z] INFO  16:46:46,377 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:46Z] INFO  16:46:46,482 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:46Z] INFO  16:46:46,491 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:46Z] INFO  16:46:46,532 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:46Z] INFO  16:46:46,565 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-14T23:46Z] INFO  16:46:47,027 IntervalUtils - Processing 15703531 bp from intervals
[2016-04-14T23:46Z] WARN  16:46:47,033 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:46Z] INFO  16:46:47,135 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:46Z] INFO  16:46:47,158 ProgressMeter -            done    221869.0    15.0 s      70.0 s       97.4%    15.0 s       0.0 s
[2016-04-14T23:46Z] INFO  16:46:47,159 ProgressMeter - Total runtime 15.71 secs, 0.26 min, 0.00 hours
[2016-04-14T23:46Z] INFO  16:46:47,163 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 221869 total reads (0.00%)
[2016-04-14T23:46Z] INFO  16:46:47,174 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:46Z] INFO  16:46:47,176 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:46Z] INFO  16:46:47,176 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:46Z] INFO  16:46:47,292 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:46Z] INFO  16:46:47,293 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:46Z] INFO  16:46:47,294 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:46Z] INFO  16:46:47,294 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:46Z] INFO  16:46:47,428 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:46Z] INFO  16:46:47,580 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:46Z] INFO  16:46:47,584 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:46Z] INFO  16:46:47,584 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:46Z] INFO  16:46:47,585 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:46Z] INFO  16:46:47,589 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/3/R14-18105_kapa-NGv3-PE100-NGv3-sort-3_62739115_78648077-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/3/tx/tmpKHV5u6/R14-18105_kapa-NGv3-PE100-NGv3-sort-3_62739115_78648077-prep-prealign-realign.intervals -l INFO -L 3:62739116-78648077 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-14T23:46Z] INFO  16:46:47,592 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:46Z] INFO  16:46:47,603 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:46Z] INFO  16:46:47,614 HelpFormatter - Date/Time: 2016/04/14 16:46:47
[2016-04-14T23:46Z] INFO  16:46:47,615 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:46Z] INFO  16:46:47,616 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:46Z] INFO  16:46:47,671 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-14T23:46Z] INFO  16:46:47,705 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:46Z] INFO  16:46:47,731 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:46Z] INFO  16:46:47,740 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:46Z] INFO  16:46:47,776 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.04
[2016-04-14T23:46Z] INFO  16:46:47,790 IntervalUtils - Processing 15522634 bp from intervals
[2016-04-14T23:46Z] INFO  16:46:47,807 ProgressMeter -            done   1.5512123E7    20.0 s       1.0 s      100.0%    20.0 s       0.0 s
[2016-04-14T23:46Z] INFO  16:46:47,808 ProgressMeter - Total runtime 20.61 secs, 0.34 min, 0.01 hours
[2016-04-14T23:46Z] INFO  16:46:47,813 MicroScheduler - 27455 reads were filtered out during the traversal out of approximately 326890 total reads (8.40%)
[2016-04-14T23:46Z] INFO  16:46:47,814 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:46Z] INFO  16:46:47,815 MicroScheduler -   -> 747 reads (0.23% of total) failing BadMateFilter
[2016-04-14T23:46Z] INFO  16:46:47,815 MicroScheduler -   -> 26083 reads (7.98% of total) failing DuplicateReadFilter
[2016-04-14T23:46Z] INFO  16:46:47,816 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-14T23:46Z] INFO  16:46:47,817 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:46Z] INFO  16:46:47,817 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-14T23:46Z] INFO  16:46:47,818 MicroScheduler -   -> 625 reads (0.19% of total) failing MappingQualityZeroFilter
[2016-04-14T23:46Z] INFO  16:46:47,818 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:46Z] INFO  16:46:47,819 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-14T23:46Z] INFO  16:46:47,821 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-14T23:46Z] INFO  16:46:47,866 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:46Z] INFO  16:46:47,934 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-14T23:46Z] INFO  16:46:47,944 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:46Z] INFO  16:46:47,998 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-14T23:46Z] INFO  16:46:48,267 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:46Z] INFO  16:46:48,268 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:46Z] INFO  16:46:48,269 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:46Z] INFO  16:46:48,269 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:46Z] INFO  16:46:48,275 ProgressMeter -            done   1.6378559E7    22.0 s       1.0 s      100.0%    22.0 s       0.0 s
[2016-04-14T23:46Z] INFO  16:46:48,276 ProgressMeter - Total runtime 22.65 secs, 0.38 min, 0.01 hours
[2016-04-14T23:46Z] INFO  16:46:48,280 MicroScheduler - 34393 reads were filtered out during the traversal out of approximately 415240 total reads (8.28%)
[2016-04-14T23:46Z] INFO  16:46:48,292 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:46Z] INFO  16:46:48,293 MicroScheduler -   -> 865 reads (0.21% of total) failing BadMateFilter
[2016-04-14T23:46Z] INFO  16:46:48,293 MicroScheduler -   -> 33045 reads (7.96% of total) failing DuplicateReadFilter
[2016-04-14T23:46Z] INFO  16:46:48,294 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-14T23:46Z] INFO  16:46:48,295 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:46Z] INFO  16:46:48,295 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-14T23:46Z] INFO  16:46:48,295 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:46Z] INFO  16:46:48,296 MicroScheduler -   -> 483 reads (0.12% of total) failing MappingQualityZeroFilter
[2016-04-14T23:46Z] INFO  16:46:48,296 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:46Z] INFO  16:46:48,297 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-14T23:46Z] INFO  16:46:48,298 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-14T23:46Z] INFO  16:46:48,397 IntervalUtils - Processing 15908962 bp from intervals
[2016-04-14T23:46Z] WARN  16:46:48,402 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:46Z] INFO  16:46:48,511 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:46Z] INFO  16:46:48,591 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:46Z] INFO  16:46:48,653 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:46Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-2_237995374_243199373-prep.bam
[2016-04-14T23:46Z] INFO  16:46:48,786 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:46Z] INFO  16:46:48,787 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:46Z] INFO  16:46:48,787 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:46Z] INFO  16:46:48,788 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-14T23:46Z] INFO  16:46:49,208 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:46Z] GATK: realign ('3', 0, 15512123) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-14T23:46Z] GATK pre-alignment ('3', 143297426, 158963696) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-14T23:46Z] INFO  16:46:49,630 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:46Z] INFO  16:46:49,671 ProgressMeter -            done   1.5734661E7    24.0 s       1.0 s      100.0%    24.0 s       0.0 s
[2016-04-14T23:46Z] INFO  16:46:49,672 ProgressMeter - Total runtime 24.13 secs, 0.40 min, 0.01 hours
[2016-04-14T23:46Z] INFO  16:46:49,675 MicroScheduler - 138417 reads were filtered out during the traversal out of approximately 538428 total reads (25.71%)
[2016-04-14T23:46Z] INFO  16:46:49,676 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:46Z] INFO  16:46:49,676 MicroScheduler -   -> 743 reads (0.14% of total) failing BadMateFilter
[2016-04-14T23:46Z] INFO  16:46:49,676 MicroScheduler -   -> 35068 reads (6.51% of total) failing DuplicateReadFilter
[2016-04-14T23:46Z] INFO  16:46:49,676 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-14T23:46Z] INFO  16:46:49,677 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:46Z] INFO  16:46:49,677 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-14T23:46Z] GATK: realign ('2', 205912303, 222290862) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-14T23:46Z] INFO  16:46:49,677 MicroScheduler -   -> 102606 reads (19.06% of total) failing MappingQualityZeroFilter
[2016-04-14T23:46Z] INFO  16:46:49,677 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:46Z] INFO  16:46:49,677 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-14T23:46Z] INFO  16:46:49,678 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-14T23:46Z] INFO  16:46:51,036 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:46Z] GATK: realign ('2', 95538561, 111273222) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-14T23:46Z] INFO  16:46:51,359 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@41fd9d8e
[2016-04-14T23:46Z] INFO  16:46:51,502 ProgressMeter -            done    172993.0    23.0 s       2.2 m      100.0%    23.0 s       0.0 s
[2016-04-14T23:46Z] INFO  16:46:51,502 ProgressMeter - Total runtime 23.10 secs, 0.39 min, 0.01 hours
[2016-04-14T23:46Z] INFO  16:46:51,503 MicroScheduler - 139 reads were filtered out during the traversal out of approximately 173132 total reads (0.08%)
[2016-04-14T23:46Z] INFO  16:46:51,503 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:46Z] INFO  16:46:51,504 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:46Z] INFO  16:46:51,505 MicroScheduler -   -> 139 reads (0.08% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:46Z] INFO  16:46:52,213 ProgressMeter -      3:49149728    200002.0    30.0 s       2.5 m       13.0%     3.8 m       3.3 m
[2016-04-14T23:46Z] INFO  16:46:52,324 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:46Z] INFO  16:46:52,327 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:46Z] INFO  16:46:52,328 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:46Z] INFO  16:46:52,328 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:46Z] INFO  16:46:52,333 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/3/R14-18105_kapa-NGv3-PE100-NGv3-sort-3_0_15512123-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/3/R14-18105_kapa-NGv3-PE100-NGv3-sort-3_0_15512123-prep-prealign-realign.intervals -L 3:1-15512123 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/3/tx/tmp5mWA6Y/R14-18105_kapa-NGv3-PE100-NGv3-sort-3_0_15512123-prep.bam
[2016-04-14T23:46Z] INFO  16:46:52,343 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:46Z] INFO  16:46:52,353 HelpFormatter - Date/Time: 2016/04/14 16:46:52
[2016-04-14T23:46Z] INFO  16:46:52,354 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:46Z] INFO  16:46:52,355 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:46Z] INFO  16:46:52,545 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:46Z] INFO  16:46:52,548 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:46Z] INFO  16:46:52,549 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:46Z] INFO  16:46:52,549 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:46Z] INFO  16:46:52,554 HelpFormatter - Program Args: -T PrintReads -L 3:143297427-158963696 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/3/tx/tmpBvzWdQ/R14-18105_kapa-NGv3-PE100-NGv3-sort-3_143297426_158963696-prep-prealign.bam
[2016-04-14T23:46Z] INFO  16:46:52,572 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:46Z] INFO  16:46:52,583 HelpFormatter - Date/Time: 2016/04/14 16:46:52
[2016-04-14T23:46Z] INFO  16:46:52,584 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:46Z] INFO  16:46:52,585 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:46Z] INFO  16:46:52,653 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:46Z] INFO  16:46:52,757 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:46Z] INFO  16:46:52,816 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:46Z] INFO  16:46:52,829 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:46Z] INFO  16:46:52,885 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-14T23:46Z] INFO  16:46:53,023 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:46Z] INFO  16:46:53,026 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:46Z] INFO  16:46:53,027 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:46Z] INFO  16:46:53,027 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:46Z] INFO  16:46:53,032 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/2/R14-18105_kapa-NGv3-PE100-NGv3-sort-2_205912303_222290862-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/2/R14-18105_kapa-NGv3-PE100-NGv3-sort-2_205912303_222290862-prep-prealign-realign.intervals -L 2:205912304-222290862 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/2/tx/tmpmh9k3L/R14-18105_kapa-NGv3-PE100-NGv3-sort-2_205912303_222290862-prep.bam
[2016-04-14T23:46Z] INFO  16:46:53,042 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:46Z] INFO  16:46:53,042 HelpFormatter - Date/Time: 2016/04/14 16:46:53
[2016-04-14T23:46Z] INFO  16:46:53,043 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:46Z] INFO  16:46:53,044 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:46Z] INFO  16:46:53,076 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:46Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-3_96585668_112185230-prep-prealign.bam
[2016-04-14T23:46Z] INFO  16:46:53,201 IntervalUtils - Processing 15512123 bp from intervals
[2016-04-14T23:46Z] WARN  16:46:53,206 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:46Z] INFO  16:46:53,292 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:46Z] INFO  16:46:53,295 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:46Z] INFO  16:46:53,419 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:46Z] INFO  16:46:53,420 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:46Z] INFO  16:46:53,421 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:46Z] INFO  16:46:53,422 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:46Z] INFO  16:46:53,468 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:46Z] INFO  16:46:53,478 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:46Z] INFO  16:46:53,542 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-14T23:46Z] INFO  16:46:53,610 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:46Z] GATK RealignerTargetCreator: R14-18105_kapa-NGv3-PE100-NGv3-sort-3_96585668_112185230-prep-prealign.bam 3:96585669-112185230
[2016-04-14T23:46Z] GATK: RealignerTargetCreator
[2016-04-14T23:46Z] INFO  16:46:53,795 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:46Z] INFO  16:46:53,924 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:46Z] INFO  16:46:53,928 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:46Z] INFO  16:46:53,928 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:46Z] INFO  16:46:53,929 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:46Z] INFO  16:46:53,934 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/2/R14-18105_kapa-NGv3-PE100-NGv3-sort-2_95538561_111273222-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/2/R14-18105_kapa-NGv3-PE100-NGv3-sort-2_95538561_111273222-prep-prealign-realign.intervals -L 2:95538562-111273222 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/2/tx/tmpPoiV7V/R14-18105_kapa-NGv3-PE100-NGv3-sort-2_95538561_111273222-prep.bam
[2016-04-14T23:46Z] INFO  16:46:53,939 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-14T23:46Z] INFO  16:46:53,944 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:46Z] INFO  16:46:53,949 HelpFormatter - Date/Time: 2016/04/14 16:46:53
[2016-04-14T23:46Z] INFO  16:46:53,950 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:46Z] INFO  16:46:53,951 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:46Z] INFO  16:46:53,962 IntervalUtils - Processing 16378559 bp from intervals
[2016-04-14T23:46Z] WARN  16:46:53,967 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:46Z] INFO  16:46:54,016 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:46Z] INFO  16:46:54,036 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:46Z] INFO  16:46:54,046 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:46Z] INFO  16:46:54,098 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-14T23:46Z] INFO  16:46:54,113 IntervalUtils - Processing 15666270 bp from intervals
[2016-04-14T23:46Z] INFO  16:46:54,198 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:46Z] INFO  16:46:54,226 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:46Z] INFO  16:46:54,227 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:46Z] INFO  16:46:54,228 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:46Z] INFO  16:46:54,228 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:46Z] INFO  16:46:54,277 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:46Z] INFO  16:46:54,344 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:46Z] INFO  16:46:54,357 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:46Z] INFO  16:46:54,432 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-14T23:46Z] INFO  16:46:54,439 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:46Z] INFO  16:46:54,620 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:46Z] INFO  16:46:54,620 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:46Z] INFO  16:46:54,621 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:46Z] INFO  16:46:54,621 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:46Z] INFO  16:46:54,636 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:46Z] INFO  16:46:54,645 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:46Z] INFO  16:46:54,779 IntervalUtils - Processing 15734661 bp from intervals
[2016-04-14T23:46Z] WARN  16:46:54,794 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:46Z] INFO  16:46:54,865 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:46Z] INFO  16:46:54,888 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:46Z] INFO  16:46:55,019 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:46Z] INFO  16:46:55,019 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:46Z] INFO  16:46:55,020 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:46Z] INFO  16:46:55,020 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:46Z] INFO  16:46:55,174 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:46Z] INFO  16:46:55,362 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:46Z] INFO  16:46:56,789 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:46Z] INFO  16:46:56,792 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:46Z] INFO  16:46:56,793 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:46Z] INFO  16:46:56,794 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:46Z] INFO  16:46:56,799 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/3/R14-18105_kapa-NGv3-PE100-NGv3-sort-3_96585668_112185230-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/3/tx/tmp7pAQrG/R14-18105_kapa-NGv3-PE100-NGv3-sort-3_96585668_112185230-prep-prealign-realign.intervals -l INFO -L 3:96585669-112185230 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-14T23:46Z] INFO  16:46:56,812 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:46Z] INFO  16:46:56,812 HelpFormatter - Date/Time: 2016/04/14 16:46:56
[2016-04-14T23:46Z] INFO  16:46:56,812 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:46Z] INFO  16:46:56,812 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:46Z] INFO  16:46:56,921 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:46Z] INFO  16:46:56,978 ProgressMeter -            done   1.788459E7    15.0 s       0.0 s      100.0%    15.0 s       0.0 s
[2016-04-14T23:46Z] INFO  16:46:56,979 ProgressMeter - Total runtime 15.31 secs, 0.26 min, 0.00 hours
[2016-04-14T23:46Z] INFO  16:46:56,984 MicroScheduler - 4502 reads were filtered out during the traversal out of approximately 46774 total reads (9.63%)
[2016-04-14T23:46Z] INFO  16:46:56,985 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:46Z] INFO  16:46:56,986 MicroScheduler -   -> 316 reads (0.68% of total) failing BadMateFilter
[2016-04-14T23:46Z] INFO  16:46:56,986 MicroScheduler -   -> 3666 reads (7.84% of total) failing DuplicateReadFilter
[2016-04-14T23:46Z] INFO  16:46:56,987 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-14T23:46Z] INFO  16:46:56,988 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:46Z] INFO  16:46:56,988 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-14T23:46Z] INFO  16:46:56,989 MicroScheduler -   -> 520 reads (1.11% of total) failing MappingQualityZeroFilter
[2016-04-14T23:46Z] INFO  16:46:56,990 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:46Z] INFO  16:46:56,990 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-14T23:46Z] INFO  16:46:56,991 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-14T23:46Z] INFO  16:46:57,089 ProgressMeter -            done    251871.0    19.0 s      78.0 s      100.0%    19.0 s       0.0 s
[2016-04-14T23:46Z] INFO  16:46:57,090 ProgressMeter - Total runtime 19.89 secs, 0.33 min, 0.01 hours
[2016-04-14T23:46Z] INFO  16:46:57,094 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 251871 total reads (0.00%)
[2016-04-14T23:46Z] INFO  16:46:57,096 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:46Z] INFO  16:46:57,097 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:46Z] INFO  16:46:57,098 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:46Z] INFO  16:46:57,149 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-14T23:46Z] INFO  16:46:57,160 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:46Z] INFO  16:46:57,202 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.04
[2016-04-14T23:46Z] INFO  16:46:57,484 IntervalUtils - Processing 15599562 bp from intervals
[2016-04-14T23:46Z] WARN  16:46:57,490 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:46Z] INFO  16:46:57,596 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:46Z] INFO  16:46:57,800 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:46Z] INFO  16:46:57,801 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:46Z] INFO  16:46:57,802 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:46Z] INFO  16:46:57,802 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-14T23:46Z] INFO  16:46:58,317 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:46Z] GATK: realign ('3', 78649262, 96533852) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-14T23:46Z] INFO  16:46:58,447 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:46Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-2_190313104_205830046-prep.bam
[2016-04-14T23:46Z] GATK pre-alignment ('3', 158970515, 174577240) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-14T23:47Z] INFO  16:47:00,146 ProgressMeter -            done    299067.0    20.0 s      69.0 s      100.0%    20.0 s       0.0 s
[2016-04-14T23:47Z] INFO  16:47:00,147 ProgressMeter - Total runtime 20.73 secs, 0.35 min, 0.01 hours
[2016-04-14T23:47Z] INFO  16:47:00,151 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 299067 total reads (0.00%)
[2016-04-14T23:47Z] INFO  16:47:00,152 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:47Z] INFO  16:47:00,152 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:47Z] INFO  16:47:00,153 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:47Z] INFO  16:47:01,330 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@7172f77a
[2016-04-14T23:47Z] INFO  16:47:01,393 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:47Z] INFO  16:47:01,396 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:47Z] INFO  16:47:01,397 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:47Z] INFO  16:47:01,397 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:47Z] INFO  16:47:01,402 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/3/R14-18105_kapa-NGv3-PE100-NGv3-sort-3_78649262_96533852-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/3/R14-18105_kapa-NGv3-PE100-NGv3-sort-3_78649262_96533852-prep-prealign-realign.intervals -L 3:78649263-96533852 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/3/tx/tmpjq2FWv/R14-18105_kapa-NGv3-PE100-NGv3-sort-3_78649262_96533852-prep.bam
[2016-04-14T23:47Z] INFO  16:47:01,412 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:47Z] INFO  16:47:01,413 HelpFormatter - Date/Time: 2016/04/14 16:47:01
[2016-04-14T23:47Z] INFO  16:47:01,423 ProgressMeter -            done    479559.0    60.0 s       2.1 m      100.0%    60.0 s       0.0 s
[2016-04-14T23:47Z] INFO  16:47:01,424 ProgressMeter - Total runtime 60.42 secs, 1.01 min, 0.02 hours
[2016-04-14T23:47Z] INFO  16:47:01,424 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:47Z] INFO  16:47:01,425 MicroScheduler - 197 reads were filtered out during the traversal out of approximately 479756 total reads (0.04%)
[2016-04-14T23:47Z] INFO  16:47:01,425 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:47Z] INFO  16:47:01,426 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:47Z] INFO  16:47:01,426 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:47Z] INFO  16:47:01,427 MicroScheduler -   -> 197 reads (0.04% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:47Z] INFO  16:47:01,659 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:47Z] INFO  16:47:01,745 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:47Z] INFO  16:47:01,754 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:47Z] INFO  16:47:01,773 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:47Z] INFO  16:47:01,807 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-14T23:47Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-2_159196753_174774985-prep.bam
[2016-04-14T23:47Z] INFO  16:47:02,191 IntervalUtils - Processing 17884590 bp from intervals
[2016-04-14T23:47Z] WARN  16:47:02,196 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:47Z] INFO  16:47:02,291 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:47Z] INFO  16:47:02,324 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:47Z] INFO  16:47:02,328 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:47Z] INFO  16:47:02,328 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:47Z] INFO  16:47:02,329 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:47Z] INFO  16:47:02,334 HelpFormatter - Program Args: -T PrintReads -L 3:158970516-174577240 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/3/tx/tmpGNXZbL/R14-18105_kapa-NGv3-PE100-NGv3-sort-3_158970515_174577240-prep-prealign.bam
[2016-04-14T23:47Z] INFO  16:47:02,343 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:47Z] INFO  16:47:02,344 HelpFormatter - Date/Time: 2016/04/14 16:47:02
[2016-04-14T23:47Z] INFO  16:47:02,344 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:47Z] INFO  16:47:02,345 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:47Z] INFO  16:47:02,382 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:47Z] INFO  16:47:02,383 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:47Z] INFO  16:47:02,384 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:47Z] INFO  16:47:02,385 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:47Z] INFO  16:47:02,517 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:47Z] INFO  16:47:02,527 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:47Z] INFO  16:47:02,694 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:47Z] GATK pre-alignment ('3', 174814579, 190326970) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-14T23:47Z] INFO  16:47:02,967 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:47Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-3_31617887_47127804-prep-prealign.bam
[2016-04-14T23:47Z] INFO  16:47:03,685 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-14T23:47Z] INFO  16:47:03,730 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:47Z] INFO  16:47:03,740 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:47Z] INFO  16:47:03,796 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-14T23:47Z] INFO  16:47:03,809 IntervalUtils - Processing 15606725 bp from intervals
[2016-04-14T23:47Z] INFO  16:47:03,876 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:47Z] INFO  16:47:04,205 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:47Z] INFO  16:47:04,205 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:47Z] INFO  16:47:04,205 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:47Z] INFO  16:47:04,206 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:47Z] INFO  16:47:04,220 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:47Z] INFO  16:47:04,379 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:47Z] GATK RealignerTargetCreator: R14-18105_kapa-NGv3-PE100-NGv3-sort-3_31617887_47127804-prep-prealign.bam 3:31617888-47127804
[2016-04-14T23:47Z] GATK: RealignerTargetCreator
[2016-04-14T23:47Z] INFO  16:47:04,819 ProgressMeter -     1:155718337   1.181599E7    30.0 s       2.0 s       76.2%    39.0 s       9.0 s
[2016-04-14T23:47Z] INFO  16:47:04,908 ProgressMeter -            done    340829.0    23.0 s      70.0 s      100.0%    23.0 s       0.0 s
[2016-04-14T23:47Z] INFO  16:47:04,909 ProgressMeter - Total runtime 23.89 secs, 0.40 min, 0.01 hours
[2016-04-14T23:47Z] INFO  16:47:04,913 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 340829 total reads (0.00%)
[2016-04-14T23:47Z] INFO  16:47:04,914 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:47Z] INFO  16:47:04,914 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:47Z] INFO  16:47:04,915 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:47Z] INFO  16:47:05,118 ProgressMeter -            done   1.5908962E7    16.0 s       1.0 s      100.0%    16.0 s       0.0 s
[2016-04-14T23:47Z] INFO  16:47:05,120 ProgressMeter - Total runtime 16.33 secs, 0.27 min, 0.00 hours
[2016-04-14T23:47Z] INFO  16:47:05,124 MicroScheduler - 15014 reads were filtered out during the traversal out of approximately 130227 total reads (11.53%)
[2016-04-14T23:47Z] INFO  16:47:05,125 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:47Z] INFO  16:47:05,126 MicroScheduler -   -> 460 reads (0.35% of total) failing BadMateFilter
[2016-04-14T23:47Z] INFO  16:47:05,127 MicroScheduler -   -> 9995 reads (7.68% of total) failing DuplicateReadFilter
[2016-04-14T23:47Z] INFO  16:47:05,128 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-14T23:47Z] INFO  16:47:05,128 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:47Z] INFO  16:47:05,129 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-14T23:47Z] INFO  16:47:05,130 MicroScheduler -   -> 4559 reads (3.50% of total) failing MappingQualityZeroFilter
[2016-04-14T23:47Z] INFO  16:47:05,131 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:47Z] INFO  16:47:05,131 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-14T23:47Z] INFO  16:47:05,132 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-14T23:47Z] INFO  16:47:05,664 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:47Z] INFO  16:47:05,668 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:47Z] INFO  16:47:05,669 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:47Z] INFO  16:47:05,669 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:47Z] INFO  16:47:05,674 HelpFormatter - Program Args: -T PrintReads -L 3:174814580-190326970 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/3/tx/tmpmCTqda/R14-18105_kapa-NGv3-PE100-NGv3-sort-3_174814579_190326970-prep-prealign.bam
[2016-04-14T23:47Z] INFO  16:47:05,697 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:47Z] INFO  16:47:05,698 HelpFormatter - Date/Time: 2016/04/14 16:47:05
[2016-04-14T23:47Z] INFO  16:47:05,698 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:47Z] INFO  16:47:05,703 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:47Z] INFO  16:47:05,864 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:47Z] INFO  16:47:06,556 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:47Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-2_174777797_190306304-prep.bam
[2016-04-14T23:47Z] INFO  16:47:06,653 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:47Z] GATK: realign ('3', 62739115, 78648077) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-14T23:47Z] INFO  16:47:06,845 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-14T23:47Z] INFO  16:47:06,946 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:47Z] INFO  16:47:06,968 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:47Z] INFO  16:47:07,065 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.10
[2016-04-14T23:47Z] INFO  16:47:07,083 IntervalUtils - Processing 15512391 bp from intervals
[2016-04-14T23:47Z] INFO  16:47:07,170 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:47Z] INFO  16:47:07,454 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:47Z] INFO  16:47:07,455 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:47Z] INFO  16:47:07,456 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:47Z] INFO  16:47:07,457 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:47Z] INFO  16:47:07,473 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:47Z] INFO  16:47:07,635 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:47Z] INFO  16:47:07,639 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:47Z] INFO  16:47:07,639 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:47Z] INFO  16:47:07,640 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:47Z] INFO  16:47:07,644 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/3/R14-18105_kapa-NGv3-PE100-NGv3-sort-3_31617887_47127804-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/3/tx/tmppqoQsZ/R14-18105_kapa-NGv3-PE100-NGv3-sort-3_31617887_47127804-prep-prealign-realign.intervals -l INFO -L 3:31617888-47127804 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-14T23:47Z] INFO  16:47:07,654 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:47Z] INFO  16:47:07,654 HelpFormatter - Date/Time: 2016/04/14 16:47:07
[2016-04-14T23:47Z] INFO  16:47:07,655 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:47Z] INFO  16:47:07,655 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:47Z] GATK pre-alignment ('3', 190333063, 198022430) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-14T23:47Z] INFO  16:47:07,702 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:47Z] INFO  16:47:07,791 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:47Z] INFO  16:47:08,010 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-14T23:47Z] INFO  16:47:08,019 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:47Z] INFO  16:47:08,107 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.09
[2016-04-14T23:47Z] INFO  16:47:08,474 IntervalUtils - Processing 15509917 bp from intervals
[2016-04-14T23:47Z] WARN  16:47:08,480 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:47Z] INFO  16:47:08,565 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:47Z] INFO  16:47:08,912 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:47Z] INFO  16:47:08,913 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:47Z] INFO  16:47:08,914 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:47Z] INFO  16:47:08,915 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-14T23:47Z] INFO  16:47:09,330 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:47Z] INFO  16:47:09,333 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:47Z] INFO  16:47:09,334 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:47Z] INFO  16:47:09,335 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:47Z] INFO  16:47:09,339 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/3/R14-18105_kapa-NGv3-PE100-NGv3-sort-3_62739115_78648077-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/3/R14-18105_kapa-NGv3-PE100-NGv3-sort-3_62739115_78648077-prep-prealign-realign.intervals -L 3:62739116-78648077 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/3/tx/tmpwu8I70/R14-18105_kapa-NGv3-PE100-NGv3-sort-3_62739115_78648077-prep.bam
[2016-04-14T23:47Z] INFO  16:47:09,354 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:47Z] INFO  16:47:09,355 HelpFormatter - Date/Time: 2016/04/14 16:47:09
[2016-04-14T23:47Z] INFO  16:47:09,356 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:47Z] INFO  16:47:09,356 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:47Z] INFO  16:47:09,437 ProgressMeter -            done     46461.0     7.0 s       2.5 m      100.0%     7.0 s       0.0 s
[2016-04-14T23:47Z] INFO  16:47:09,438 ProgressMeter - Total runtime 7.06 secs, 0.12 min, 0.00 hours
[2016-04-14T23:47Z] INFO  16:47:09,442 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 46461 total reads (0.00%)
[2016-04-14T23:47Z] INFO  16:47:09,450 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:47Z] INFO  16:47:09,451 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:47Z] INFO  16:47:09,451 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:47Z] INFO  16:47:09,612 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:47Z] INFO  16:47:09,730 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:47Z] INFO  16:47:09,740 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:47Z] INFO  16:47:09,816 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-14T23:47Z] INFO  16:47:09,860 ProgressMeter -            done    321932.0    22.0 s      70.0 s      100.0%    22.0 s       0.0 s
[2016-04-14T23:47Z] INFO  16:47:09,861 ProgressMeter - Total runtime 22.57 secs, 0.38 min, 0.01 hours
[2016-04-14T23:47Z] INFO  16:47:09,865 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 321932 total reads (0.00%)
[2016-04-14T23:47Z] INFO  16:47:09,866 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:47Z] INFO  16:47:09,867 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:47Z] INFO  16:47:09,867 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:47Z] INFO  16:47:10,245 IntervalUtils - Processing 15908962 bp from intervals
[2016-04-14T23:47Z] WARN  16:47:10,250 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:47Z] INFO  16:47:10,330 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:47Z] INFO  16:47:10,476 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:47Z] INFO  16:47:10,477 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:47Z] INFO  16:47:10,478 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:47Z] INFO  16:47:10,479 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:47Z] INFO  16:47:10,665 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:47Z] INFO  16:47:10,670 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:47Z] INFO  16:47:10,673 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:47Z] INFO  16:47:10,674 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:47Z] INFO  16:47:10,674 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:47Z] INFO  16:47:10,679 HelpFormatter - Program Args: -T PrintReads -L 3:190333064-198022430 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/3/tx/tmpoF3xXc/R14-18105_kapa-NGv3-PE100-NGv3-sort-3_190333063_198022430-prep-prealign.bam
[2016-04-14T23:47Z] INFO  16:47:10,696 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:47Z] INFO  16:47:10,696 HelpFormatter - Date/Time: 2016/04/14 16:47:10
[2016-04-14T23:47Z] INFO  16:47:10,696 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:47Z] INFO  16:47:10,697 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:47Z] INFO  16:47:10,865 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:47Z] INFO  16:47:10,882 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:47Z] INFO  16:47:10,897 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:47Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-3_78649262_96533852-prep.bam
[2016-04-14T23:47Z] GATK pre-alignment ('4', 0, 15511864) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-14T23:47Z] INFO  16:47:11,364 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:47Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-2_222291154_237994685-prep.bam
[2016-04-14T23:47Z] INFO  16:47:12,010 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-14T23:47Z] INFO  16:47:12,098 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:47Z] INFO  16:47:12,132 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:47Z] INFO  16:47:12,193 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-14T23:47Z] INFO  16:47:12,211 IntervalUtils - Processing 7689367 bp from intervals
[2016-04-14T23:47Z] INFO  16:47:12,305 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:47Z] GATK pre-alignment ('4', 15512869, 31144471) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-14T23:47Z] INFO  16:47:12,622 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:47Z] INFO  16:47:12,623 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:47Z] INFO  16:47:12,624 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:47Z] INFO  16:47:12,625 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:47Z] INFO  16:47:12,638 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:47Z] INFO  16:47:12,737 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:47Z] INFO  16:47:13,087 ProgressMeter -            done   1.5512965E7    38.0 s       2.0 s      100.0%    38.0 s       0.0 s
[2016-04-14T23:47Z] INFO  16:47:13,088 ProgressMeter - Total runtime 38.30 secs, 0.64 min, 0.01 hours
[2016-04-14T23:47Z] INFO  16:47:13,089 MicroScheduler - 393565 reads were filtered out during the traversal out of approximately 1284441 total reads (30.64%)
[2016-04-14T23:47Z] INFO  16:47:13,090 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:47Z] INFO  16:47:13,091 MicroScheduler -   -> 1387 reads (0.11% of total) failing BadMateFilter
[2016-04-14T23:47Z] INFO  16:47:13,091 MicroScheduler -   -> 77893 reads (6.06% of total) failing DuplicateReadFilter
[2016-04-14T23:47Z] INFO  16:47:13,092 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-14T23:47Z] INFO  16:47:13,092 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:47Z] INFO  16:47:13,093 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-14T23:47Z] INFO  16:47:13,094 MicroScheduler -   -> 314285 reads (24.47% of total) failing MappingQualityZeroFilter
[2016-04-14T23:47Z] INFO  16:47:13,094 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:47Z] INFO  16:47:13,095 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-14T23:47Z] INFO  16:47:13,095 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-14T23:47Z] INFO  16:47:13,884 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:47Z] INFO  16:47:13,887 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:47Z] INFO  16:47:13,887 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:47Z] INFO  16:47:13,887 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:47Z] INFO  16:47:13,891 HelpFormatter - Program Args: -T PrintReads -L 4:1-15511864 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/4/tx/tmpPgJdcP/R14-18105_kapa-NGv3-PE100-NGv3-sort-4_0_15511864-prep-prealign.bam
[2016-04-14T23:47Z] INFO  16:47:13,914 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:47Z] INFO  16:47:13,915 HelpFormatter - Date/Time: 2016/04/14 16:47:13
[2016-04-14T23:47Z] INFO  16:47:13,915 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:47Z] INFO  16:47:13,916 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:47Z] INFO  16:47:14,123 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:47Z] INFO  16:47:14,497 ProgressMeter -            done   1.5599562E7    16.0 s       1.0 s      100.0%    16.0 s       0.0 s
[2016-04-14T23:47Z] INFO  16:47:14,498 ProgressMeter - Total runtime 16.70 secs, 0.28 min, 0.00 hours
[2016-04-14T23:47Z] INFO  16:47:14,502 MicroScheduler - 14870 reads were filtered out during the traversal out of approximately 173944 total reads (8.55%)
[2016-04-14T23:47Z] INFO  16:47:14,503 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:47Z] INFO  16:47:14,504 MicroScheduler -   -> 541 reads (0.31% of total) failing BadMateFilter
[2016-04-14T23:47Z] INFO  16:47:14,505 MicroScheduler -   -> 13551 reads (7.79% of total) failing DuplicateReadFilter
[2016-04-14T23:47Z] INFO  16:47:14,505 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-14T23:47Z] INFO  16:47:14,506 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:47Z] INFO  16:47:14,507 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-14T23:47Z] INFO  16:47:14,507 MicroScheduler -   -> 778 reads (0.45% of total) failing MappingQualityZeroFilter
[2016-04-14T23:47Z] INFO  16:47:14,508 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:47Z] INFO  16:47:14,508 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-14T23:47Z] INFO  16:47:14,509 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-14T23:47Z] INFO  16:47:14,581 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:47Z] GATK: realign ('1', 143897546, 159410511) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-14T23:47Z] INFO  16:47:14,793 ProgressMeter -     3:123010289    200005.0    30.0 s       2.5 m       69.8%    43.0 s      13.0 s
[2016-04-14T23:47Z] INFO  16:47:15,314 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-14T23:47Z] INFO  16:47:15,384 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:47Z] INFO  16:47:15,393 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:47Z] INFO  16:47:15,413 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:47Z] INFO  16:47:15,416 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:47Z] INFO  16:47:15,417 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:47Z] INFO  16:47:15,418 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:47Z] INFO  16:47:15,422 HelpFormatter - Program Args: -T PrintReads -L 4:15512870-31144471 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/4/tx/tmpYveGeW/R14-18105_kapa-NGv3-PE100-NGv3-sort-4_15512869_31144471-prep-prealign.bam
[2016-04-14T23:47Z] INFO  16:47:15,438 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:47Z] INFO  16:47:15,439 HelpFormatter - Date/Time: 2016/04/14 16:47:15
[2016-04-14T23:47Z] INFO  16:47:15,439 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:47Z] INFO  16:47:15,440 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:47Z] INFO  16:47:15,446 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-14T23:47Z] INFO  16:47:15,471 IntervalUtils - Processing 15511864 bp from intervals
[2016-04-14T23:47Z] INFO  16:47:15,552 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:47Z] INFO  16:47:15,593 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:47Z] INFO  16:47:15,851 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:47Z] INFO  16:47:15,852 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:47Z] INFO  16:47:15,853 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:47Z] INFO  16:47:15,854 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:47Z] INFO  16:47:15,886 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:47Z] INFO  16:47:16,025 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:47Z] INFO  16:47:16,045 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:47Z] GATK: realign ('3', 96585668, 112185230) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-14T23:47Z] INFO  16:47:16,230 ProgressMeter -            done    325382.0    22.0 s      70.0 s      100.0%    22.0 s       0.0 s
[2016-04-14T23:47Z] INFO  16:47:16,230 ProgressMeter - Total runtime 22.81 secs, 0.38 min, 0.01 hours
[2016-04-14T23:47Z] INFO  16:47:16,234 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 325382 total reads (0.00%)
[2016-04-14T23:47Z] INFO  16:47:16,234 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:47Z] INFO  16:47:16,234 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:47Z] INFO  16:47:16,235 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:47Z] INFO  16:47:16,259 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@7172f77a
[2016-04-14T23:47Z] INFO  16:47:16,476 ProgressMeter -            done    164558.0    21.0 s       2.2 m      100.0%    21.0 s       0.0 s
[2016-04-14T23:47Z] INFO  16:47:16,477 ProgressMeter - Total runtime 21.86 secs, 0.36 min, 0.01 hours
[2016-04-14T23:47Z] INFO  16:47:16,477 MicroScheduler - 145 reads were filtered out during the traversal out of approximately 164703 total reads (0.09%)
[2016-04-14T23:47Z] INFO  16:47:16,477 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:47Z] INFO  16:47:16,478 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:47Z] INFO  16:47:16,478 MicroScheduler -   -> 145 reads (0.09% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:47Z] INFO  16:47:16,661 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-14T23:47Z] INFO  16:47:16,735 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:47Z] INFO  16:47:16,749 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:47Z] INFO  16:47:16,852 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.10
[2016-04-14T23:47Z] INFO  16:47:16,886 IntervalUtils - Processing 15631602 bp from intervals
[2016-04-14T23:47Z] INFO  16:47:17,033 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:47Z] INFO  16:47:17,318 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:47Z] INFO  16:47:17,319 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:47Z] INFO  16:47:17,319 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:47Z] INFO  16:47:17,320 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:47Z] INFO  16:47:17,348 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:47Z] INFO  16:47:17,483 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:47Z] INFO  16:47:17,487 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:47Z] INFO  16:47:17,487 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:47Z] INFO  16:47:17,488 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:47Z] INFO  16:47:17,492 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/1/R14-18105_kapa-NGv3-PE100-NGv3-sort-1_143897546_159410511-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/1/R14-18105_kapa-NGv3-PE100-NGv3-sort-1_143897546_159410511-prep-prealign-realign.intervals -L 1:143897547-159410511 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/1/tx/tmpPjVUW4/R14-18105_kapa-NGv3-PE100-NGv3-sort-1_143897546_159410511-prep.bam
[2016-04-14T23:47Z] INFO  16:47:17,495 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:47Z] INFO  16:47:17,514 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:47Z] INFO  16:47:17,515 HelpFormatter - Date/Time: 2016/04/14 16:47:17
[2016-04-14T23:47Z] INFO  16:47:17,516 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:47Z] INFO  16:47:17,520 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:47Z] INFO  16:47:17,746 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:47Z] INFO  16:47:17,911 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:47Z] INFO  16:47:17,920 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:47Z] INFO  16:47:17,951 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:47Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-3_0_15512123-prep.bam
[2016-04-14T23:47Z] INFO  16:47:18,011 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.09
[2016-04-14T23:47Z] INFO  16:47:18,011 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:47Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-3_143297426_158963696-prep-prealign.bam
[2016-04-14T23:47Z] INFO  16:47:18,291 ProgressMeter -     3:136045773    200004.0    30.0 s       2.5 m       53.3%    56.0 s      26.0 s
[2016-04-14T23:47Z] INFO  16:47:18,408 IntervalUtils - Processing 15512965 bp from intervals
[2016-04-14T23:47Z] WARN  16:47:18,413 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:47Z] INFO  16:47:18,534 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:47Z] GATK RealignerTargetCreator: R14-18105_kapa-NGv3-PE100-NGv3-sort-3_143297426_158963696-prep-prealign.bam 3:143297427-158963696
[2016-04-14T23:47Z] GATK: RealignerTargetCreator
[2016-04-14T23:47Z] INFO  16:47:18,717 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:47Z] INFO  16:47:18,718 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:47Z] INFO  16:47:18,719 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:47Z] INFO  16:47:18,720 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:47Z] INFO  16:47:18,871 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:47Z] INFO  16:47:18,875 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:47Z] INFO  16:47:18,875 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:47Z] INFO  16:47:18,876 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:47Z] INFO  16:47:18,881 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/3/R14-18105_kapa-NGv3-PE100-NGv3-sort-3_96585668_112185230-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/3/R14-18105_kapa-NGv3-PE100-NGv3-sort-3_96585668_112185230-prep-prealign-realign.intervals -L 3:96585669-112185230 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/3/tx/tmp0BjgDw/R14-18105_kapa-NGv3-PE100-NGv3-sort-3_96585668_112185230-prep.bam
[2016-04-14T23:47Z] INFO  16:47:18,906 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:47Z] INFO  16:47:18,908 HelpFormatter - Date/Time: 2016/04/14 16:47:18
[2016-04-14T23:47Z] INFO  16:47:18,908 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:47Z] INFO  16:47:18,912 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:47Z] INFO  16:47:18,937 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:47Z] GATK pre-alignment ('4', 36069528, 52709433) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-14T23:47Z] INFO  16:47:19,117 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:47Z] INFO  16:47:19,173 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:47Z] INFO  16:47:19,293 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:47Z] INFO  16:47:19,303 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:47Z] INFO  16:47:19,352 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-14T23:47Z] INFO  16:47:19,854 IntervalUtils - Processing 15599562 bp from intervals
[2016-04-14T23:47Z] WARN  16:47:19,870 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:47Z] INFO  16:47:19,967 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:47Z] INFO  16:47:20,117 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:47Z] INFO  16:47:20,118 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:47Z] INFO  16:47:20,118 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:47Z] INFO  16:47:20,119 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:47Z] INFO  16:47:20,312 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:47Z] INFO  16:47:20,516 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:47Z] INFO  16:47:21,987 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:47Z] INFO  16:47:21,990 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:47Z] INFO  16:47:21,991 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:47Z] INFO  16:47:21,991 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:47Z] INFO  16:47:21,996 HelpFormatter - Program Args: -T PrintReads -L 4:36069529-52709433 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/4/tx/tmpWYKufE/R14-18105_kapa-NGv3-PE100-NGv3-sort-4_36069528_52709433-prep-prealign.bam
[2016-04-14T23:47Z] INFO  16:47:22,016 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:47Z] INFO  16:47:22,016 HelpFormatter - Date/Time: 2016/04/14 16:47:21
[2016-04-14T23:47Z] INFO  16:47:22,016 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:47Z] INFO  16:47:22,016 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:47Z] INFO  16:47:22,198 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:47Z] INFO  16:47:22,249 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@41fd9d8e
[2016-04-14T23:47Z] INFO  16:47:22,262 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:47Z] INFO  16:47:22,265 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:47Z] INFO  16:47:22,266 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:47Z] INFO  16:47:22,266 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:47Z] INFO  16:47:22,271 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/3/R14-18105_kapa-NGv3-PE100-NGv3-sort-3_143297426_158963696-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/3/tx/tmp6zPKb9/R14-18105_kapa-NGv3-PE100-NGv3-sort-3_143297426_158963696-prep-prealign-realign.intervals -l INFO -L 3:143297427-158963696 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-14T23:47Z] INFO  16:47:22,315 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:47Z] INFO  16:47:22,315 HelpFormatter - Date/Time: 2016/04/14 16:47:22
[2016-04-14T23:47Z] INFO  16:47:22,315 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:47Z] INFO  16:47:22,316 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:47Z] INFO  16:47:22,373 ProgressMeter -            done    412696.0    28.0 s      68.0 s      100.0%    28.0 s       0.0 s
[2016-04-14T23:47Z] INFO  16:47:22,373 ProgressMeter - Total runtime 28.15 secs, 0.47 min, 0.01 hours
[2016-04-14T23:47Z] INFO  16:47:22,377 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 412696 total reads (0.00%)
[2016-04-14T23:47Z] INFO  16:47:22,377 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:47Z] INFO  16:47:22,377 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:47Z] INFO  16:47:22,378 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:47Z] INFO  16:47:22,429 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:47Z] INFO  16:47:22,456 ProgressMeter -            done    130910.0    18.0 s       2.3 m      100.0%    18.0 s       0.0 s
[2016-04-14T23:47Z] INFO  16:47:22,457 ProgressMeter - Total runtime 18.25 secs, 0.30 min, 0.01 hours
[2016-04-14T23:47Z] INFO  16:47:22,457 MicroScheduler - 107 reads were filtered out during the traversal out of approximately 131017 total reads (0.08%)
[2016-04-14T23:47Z] INFO  16:47:22,457 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:47Z] INFO  16:47:22,458 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:47Z] INFO  16:47:22,458 MicroScheduler -   -> 107 reads (0.08% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:47Z] INFO  16:47:22,551 ProgressMeter -            done    129658.0    12.0 s      93.0 s      100.0%    12.0 s       0.0 s
[2016-04-14T23:47Z] INFO  16:47:22,551 ProgressMeter - Total runtime 12.07 secs, 0.20 min, 0.00 hours
[2016-04-14T23:47Z] INFO  16:47:22,555 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 129658 total reads (0.00%)
[2016-04-14T23:47Z] INFO  16:47:22,555 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:47Z] INFO  16:47:22,556 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:47Z] INFO  16:47:22,556 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:47Z] INFO  16:47:22,661 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-14T23:47Z] INFO  16:47:22,673 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:47Z] INFO  16:47:22,756 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-14T23:47Z] INFO  16:47:22,946 ProgressMeter -      3:52257495    400004.0    60.0 s       2.5 m       33.0%     3.0 m       2.0 m
[2016-04-14T23:47Z] INFO  16:47:23,150 IntervalUtils - Processing 15666270 bp from intervals
[2016-04-14T23:47Z] WARN  16:47:23,157 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:47Z] INFO  16:47:23,305 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-14T23:47Z] INFO  16:47:23,305 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:47Z] INFO  16:47:23,376 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:47Z] INFO  16:47:23,395 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:47Z] INFO  16:47:23,434 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.04
[2016-04-14T23:47Z] INFO  16:47:23,448 IntervalUtils - Processing 16639905 bp from intervals
[2016-04-14T23:47Z] INFO  16:47:23,517 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:47Z] INFO  16:47:23,531 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:47Z] INFO  16:47:23,533 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:47Z] INFO  16:47:23,533 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:47Z] INFO  16:47:23,534 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-14T23:47Z] INFO  16:47:23,849 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:47Z] INFO  16:47:23,850 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:47Z] INFO  16:47:23,851 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:47Z] INFO  16:47:23,852 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:47Z] INFO  16:47:23,896 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:47Z] INFO  16:47:24,019 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:47Z] INFO  16:47:24,034 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:47Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-2_205912303_222290862-prep.bam
[2016-04-14T23:47Z] INFO  16:47:24,108 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:47Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-3_158970515_174577240-prep-prealign.bam
[2016-04-14T23:47Z] INFO  16:47:24,194 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:47Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-3_62739115_78648077-prep.bam
[2016-04-14T23:47Z] GATK RealignerTargetCreator: R14-18105_kapa-NGv3-PE100-NGv3-sort-3_158970515_174577240-prep-prealign.bam 3:158970516-174577240
[2016-04-14T23:47Z] GATK: RealignerTargetCreator
[2016-04-14T23:47Z] GATK pre-alignment ('4', 52709749, 68338393) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-14T23:47Z] INFO  16:47:25,144 ProgressMeter -     2:109109177    400005.0    30.0 s      75.0 s       86.2%    34.0 s       4.0 s
[2016-04-14T23:47Z] GATK pre-alignment ('4', 68340604, 83852298) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-14T23:47Z] INFO  16:47:27,644 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:47Z] INFO  16:47:27,647 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:47Z] INFO  16:47:27,647 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:47Z] INFO  16:47:27,647 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:47Z] INFO  16:47:27,651 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/3/R14-18105_kapa-NGv3-PE100-NGv3-sort-3_158970515_174577240-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/3/tx/tmpv478ak/R14-18105_kapa-NGv3-PE100-NGv3-sort-3_158970515_174577240-prep-prealign-realign.intervals -l INFO -L 3:158970516-174577240 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-14T23:47Z] INFO  16:47:27,674 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:47Z] INFO  16:47:27,675 HelpFormatter - Date/Time: 2016/04/14 16:47:27
[2016-04-14T23:47Z] INFO  16:47:27,675 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:47Z] INFO  16:47:27,675 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:47Z] INFO  16:47:27,683 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:47Z] INFO  16:47:27,687 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:47Z] INFO  16:47:27,688 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:47Z] INFO  16:47:27,688 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:47Z] INFO  16:47:27,693 HelpFormatter - Program Args: -T PrintReads -L 4:52709750-68338393 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/4/tx/tmppwrkTD/R14-18105_kapa-NGv3-PE100-NGv3-sort-4_52709749_68338393-prep-prealign.bam
[2016-04-14T23:47Z] INFO  16:47:27,706 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:47Z] INFO  16:47:27,706 HelpFormatter - Date/Time: 2016/04/14 16:47:27
[2016-04-14T23:47Z] INFO  16:47:27,707 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:47Z] INFO  16:47:27,707 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:47Z] INFO  16:47:27,797 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:47Z] INFO  16:47:27,903 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:47Z] INFO  16:47:28,028 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-14T23:47Z] INFO  16:47:28,054 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:47Z] INFO  16:47:28,081 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:47Z] INFO  16:47:28,084 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:47Z] INFO  16:47:28,085 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:47Z] INFO  16:47:28,085 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:47Z] INFO  16:47:28,090 HelpFormatter - Program Args: -T PrintReads -L 4:68340605-83852298 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/4/tx/tmpoe_Y64/R14-18105_kapa-NGv3-PE100-NGv3-sort-4_68340604_83852298-prep-prealign.bam
[2016-04-14T23:47Z] INFO  16:47:28,099 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:47Z] INFO  16:47:28,100 HelpFormatter - Date/Time: 2016/04/14 16:47:28
[2016-04-14T23:47Z] INFO  16:47:28,101 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:47Z] INFO  16:47:28,101 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:47Z] INFO  16:47:28,140 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.09
[2016-04-14T23:47Z] INFO  16:47:28,277 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:47Z] INFO  16:47:28,281 ProgressMeter -            done    534760.0    33.0 s      62.0 s      100.0%    33.0 s       0.0 s
[2016-04-14T23:47Z] INFO  16:47:28,282 ProgressMeter - Total runtime 33.26 secs, 0.55 min, 0.01 hours
[2016-04-14T23:47Z] INFO  16:47:28,286 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 534760 total reads (0.00%)
[2016-04-14T23:47Z] INFO  16:47:28,286 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:47Z] INFO  16:47:28,286 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:47Z] INFO  16:47:28,287 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:47Z] INFO  16:47:28,443 IntervalUtils - Processing 15606725 bp from intervals
[2016-04-14T23:47Z] WARN  16:47:28,448 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:47Z] INFO  16:47:28,543 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:47Z] INFO  16:47:28,700 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:47Z] INFO  16:47:28,701 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:47Z] INFO  16:47:28,702 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:47Z] INFO  16:47:28,702 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-14T23:47Z] INFO  16:47:28,996 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-14T23:47Z] INFO  16:47:29,069 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:47Z] INFO  16:47:29,078 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:47Z] INFO  16:47:29,119 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.04
[2016-04-14T23:47Z] INFO  16:47:29,133 IntervalUtils - Processing 15628644 bp from intervals
[2016-04-14T23:47Z] INFO  16:47:29,270 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:47Z] INFO  16:47:29,302 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-14T23:47Z] INFO  16:47:29,378 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:47Z] INFO  16:47:29,393 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:47Z] INFO  16:47:29,471 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-14T23:47Z] INFO  16:47:29,486 IntervalUtils - Processing 15511694 bp from intervals
[2016-04-14T23:47Z] INFO  16:47:29,557 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:47Z] INFO  16:47:29,576 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:47Z] INFO  16:47:29,577 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:47Z] INFO  16:47:29,577 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:47Z] INFO  16:47:29,577 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:47Z] INFO  16:47:29,577 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@5fe152b7
[2016-04-14T23:47Z] INFO  16:47:29,598 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:47Z] INFO  16:47:29,711 ProgressMeter -            done    369074.0    44.0 s       2.0 m      100.0%    44.0 s       0.0 s
[2016-04-14T23:47Z] INFO  16:47:29,712 ProgressMeter - Total runtime 44.95 secs, 0.75 min, 0.01 hours
[2016-04-14T23:47Z] INFO  16:47:29,712 MicroScheduler - 209 reads were filtered out during the traversal out of approximately 369283 total reads (0.06%)
[2016-04-14T23:47Z] INFO  16:47:29,712 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:47Z] INFO  16:47:29,713 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:47Z] INFO  16:47:29,713 MicroScheduler -   -> 209 reads (0.06% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:47Z] INFO  16:47:29,776 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:47Z] INFO  16:47:29,809 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:47Z] INFO  16:47:29,847 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:47Z] INFO  16:47:29,848 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:47Z] INFO  16:47:29,849 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:47Z] INFO  16:47:29,850 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:47Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-2_95538561_111273222-prep.bam
[2016-04-14T23:47Z] INFO  16:47:29,865 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:47Z] INFO  16:47:30,036 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:47Z] INFO  16:47:31,052 ProgressMeter -            done   1.5509917E7    22.0 s       1.0 s      100.0%    22.0 s       0.0 s
[2016-04-14T23:47Z] INFO  16:47:31,052 ProgressMeter - Total runtime 22.14 secs, 0.37 min, 0.01 hours
[2016-04-14T23:47Z] INFO  16:47:31,056 MicroScheduler - 40714 reads were filtered out during the traversal out of approximately 482432 total reads (8.44%)
[2016-04-14T23:47Z] INFO  16:47:31,057 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:47Z] INFO  16:47:31,058 MicroScheduler -   -> 906 reads (0.19% of total) failing BadMateFilter
[2016-04-14T23:47Z] INFO  16:47:31,058 MicroScheduler -   -> 38571 reads (8.00% of total) failing DuplicateReadFilter
[2016-04-14T23:47Z] INFO  16:47:31,059 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-14T23:47Z] INFO  16:47:31,060 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:47Z] INFO  16:47:31,060 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-14T23:47Z] INFO  16:47:31,061 MicroScheduler -   -> 1237 reads (0.26% of total) failing MappingQualityZeroFilter
[2016-04-14T23:47Z] INFO  16:47:31,062 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:47Z] INFO  16:47:31,062 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-14T23:47Z] INFO  16:47:31,063 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-14T23:47Z] INFO  16:47:31,197 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:47Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-3_112188604_127703121-prep-prealign.bam
[2016-04-14T23:47Z] INFO  16:47:31,301 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@5fe152b7
[2016-04-14T23:47Z] INFO  16:47:31,527 ProgressMeter -            done    346261.0    43.0 s       2.1 m      100.0%    43.0 s       0.0 s
[2016-04-14T23:47Z] INFO  16:47:31,528 ProgressMeter - Total runtime 43.26 secs, 0.72 min, 0.01 hours
[2016-04-14T23:47Z] INFO  16:47:31,528 MicroScheduler - 199 reads were filtered out during the traversal out of approximately 346460 total reads (0.06%)
[2016-04-14T23:47Z] INFO  16:47:31,529 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:47Z] INFO  16:47:31,529 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:47Z] INFO  16:47:31,529 MicroScheduler -   -> 199 reads (0.06% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:47Z] GATK pre-alignment ('4', 83857133, 99393738) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-14T23:47Z] GATK RealignerTargetCreator: R14-18105_kapa-NGv3-PE100-NGv3-sort-3_112188604_127703121-prep-prealign.bam 3:112188605-127703121
[2016-04-14T23:47Z] GATK: RealignerTargetCreator
[2016-04-14T23:47Z] INFO  16:47:32,663 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:47Z] GATK: realign ('3', 31617887, 47127804) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-14T23:47Z] INFO  16:47:32,966 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:47Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-3_127770401_143293035-prep-prealign.bam
[2016-04-14T23:47Z] INFO  16:47:33,747 ProgressMeter -            done    172993.0    13.0 s      78.0 s      100.0%    13.0 s       0.0 s
[2016-04-14T23:47Z] INFO  16:47:33,748 ProgressMeter - Total runtime 13.63 secs, 0.23 min, 0.00 hours
[2016-04-14T23:47Z] INFO  16:47:33,752 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 172993 total reads (0.00%)
[2016-04-14T23:47Z] INFO  16:47:33,753 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:47Z] INFO  16:47:33,754 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:47Z] INFO  16:47:33,754 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:47Z] INFO  16:47:34,121 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:47Z] INFO  16:47:34,124 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:47Z] INFO  16:47:34,124 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:47Z] INFO  16:47:34,124 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:47Z] INFO  16:47:34,128 HelpFormatter - Program Args: -T PrintReads -L 4:83857134-99393738 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/4/tx/tmpWp0iRs/R14-18105_kapa-NGv3-PE100-NGv3-sort-4_83857133_99393738-prep-prealign.bam
[2016-04-14T23:47Z] INFO  16:47:34,137 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:47Z] INFO  16:47:34,137 HelpFormatter - Date/Time: 2016/04/14 16:47:34
[2016-04-14T23:47Z] INFO  16:47:34,137 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:47Z] INFO  16:47:34,138 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:47Z] GATK RealignerTargetCreator: R14-18105_kapa-NGv3-PE100-NGv3-sort-3_127770401_143293035-prep-prealign.bam 3:127770402-143293035
[2016-04-14T23:47Z] GATK: RealignerTargetCreator
[2016-04-14T23:47Z] INFO  16:47:34,344 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:47Z] INFO  16:47:34,938 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:47Z] INFO  16:47:34,941 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:47Z] INFO  16:47:34,942 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:47Z] INFO  16:47:34,942 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:47Z] INFO  16:47:34,947 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/3/R14-18105_kapa-NGv3-PE100-NGv3-sort-3_112188604_127703121-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/3/tx/tmpGLMGx_/R14-18105_kapa-NGv3-PE100-NGv3-sort-3_112188604_127703121-prep-prealign-realign.intervals -l INFO -L 3:112188605-127703121 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-14T23:47Z] INFO  16:47:34,972 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:47Z] INFO  16:47:34,973 HelpFormatter - Date/Time: 2016/04/14 16:47:34
[2016-04-14T23:47Z] INFO  16:47:34,973 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:47Z] INFO  16:47:34,973 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:47Z] INFO  16:47:35,120 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:47Z] INFO  16:47:35,301 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-14T23:47Z] INFO  16:47:35,312 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:47Z] INFO  16:47:35,317 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:47Z] INFO  16:47:35,318 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:47Z] INFO  16:47:35,322 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:47Z] INFO  16:47:35,322 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:47Z] INFO  16:47:35,323 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:47Z] INFO  16:47:35,327 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/3/R14-18105_kapa-NGv3-PE100-NGv3-sort-3_31617887_47127804-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/3/R14-18105_kapa-NGv3-PE100-NGv3-sort-3_31617887_47127804-prep-prealign-realign.intervals -L 3:31617888-47127804 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/3/tx/tmpC1BH0x/R14-18105_kapa-NGv3-PE100-NGv3-sort-3_31617887_47127804-prep.bam
[2016-04-14T23:47Z] INFO  16:47:35,341 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:47Z] INFO  16:47:35,342 HelpFormatter - Date/Time: 2016/04/14 16:47:35
[2016-04-14T23:47Z] INFO  16:47:35,342 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:47Z] INFO  16:47:35,343 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:47Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-3_96585668_112185230-prep.bam
[2016-04-14T23:47Z] INFO  16:47:35,387 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-14T23:47Z] INFO  16:47:35,416 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-14T23:47Z] INFO  16:47:35,478 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:47Z] INFO  16:47:35,490 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:47Z] INFO  16:47:35,525 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.03
[2016-04-14T23:47Z] INFO  16:47:35,529 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:47Z] INFO  16:47:35,538 IntervalUtils - Processing 15536605 bp from intervals
[2016-04-14T23:47Z] INFO  16:47:35,654 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:47Z] INFO  16:47:35,674 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:47Z] INFO  16:47:35,677 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:47Z] INFO  16:47:35,700 IntervalUtils - Processing 15514517 bp from intervals
[2016-04-14T23:47Z] WARN  16:47:35,710 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:47Z] INFO  16:47:35,765 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.09
[2016-04-14T23:47Z] INFO  16:47:35,796 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:47Z] GATK pre-alignment ('4', 99397339, 115544957) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-14T23:47Z] INFO  16:47:35,992 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:47Z] INFO  16:47:35,992 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:47Z] INFO  16:47:35,993 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:47Z] INFO  16:47:36,003 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:47Z] INFO  16:47:36,006 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:47Z] INFO  16:47:36,007 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:47Z] INFO  16:47:36,008 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:47Z] INFO  16:47:36,008 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-14T23:47Z] INFO  16:47:36,020 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:47Z] INFO  16:47:36,195 IntervalUtils - Processing 15509917 bp from intervals
[2016-04-14T23:47Z] WARN  16:47:36,211 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:47Z] INFO  16:47:36,226 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:47Z] INFO  16:47:36,389 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:47Z] INFO  16:47:36,605 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:47Z] INFO  16:47:36,606 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:47Z] INFO  16:47:36,607 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:47Z] INFO  16:47:36,607 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:47Z] INFO  16:47:36,894 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:47Z] INFO  16:47:36,911 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:47Z] INFO  16:47:36,915 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:47Z] INFO  16:47:36,915 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:47Z] INFO  16:47:36,916 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:47Z] INFO  16:47:36,921 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/3/R14-18105_kapa-NGv3-PE100-NGv3-sort-3_127770401_143293035-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/3/tx/tmpHHnPte/R14-18105_kapa-NGv3-PE100-NGv3-sort-3_127770401_143293035-prep-prealign-realign.intervals -l INFO -L 3:127770402-143293035 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-14T23:47Z] INFO  16:47:36,938 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:47Z] INFO  16:47:36,939 HelpFormatter - Date/Time: 2016/04/14 16:47:36
[2016-04-14T23:47Z] INFO  16:47:36,939 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:47Z] INFO  16:47:36,943 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:47Z] INFO  16:47:37,053 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:47Z] INFO  16:47:37,107 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:47Z] INFO  16:47:37,286 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-14T23:47Z] INFO  16:47:37,298 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:47Z] INFO  16:47:37,367 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-14T23:47Z] INFO  16:47:37,489 ProgressMeter -     3:184299461    100001.0    30.0 s       5.0 m       61.1%    49.0 s      19.0 s
[2016-04-14T23:47Z] INFO  16:47:37,545 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@41fd9d8e
[2016-04-14T23:47Z] INFO  16:47:37,599 IntervalUtils - Processing 15522634 bp from intervals
[2016-04-14T23:47Z] WARN  16:47:37,604 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:47Z] INFO  16:47:37,617 ProgressMeter -            done    117024.0    20.0 s       2.9 m      100.0%    20.0 s       0.0 s
[2016-04-14T23:47Z] INFO  16:47:37,618 ProgressMeter - Total runtime 20.30 secs, 0.34 min, 0.01 hours
[2016-04-14T23:47Z] INFO  16:47:37,618 MicroScheduler - 125 reads were filtered out during the traversal out of approximately 117149 total reads (0.11%)
[2016-04-14T23:47Z] INFO  16:47:37,619 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:47Z] INFO  16:47:37,619 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:47Z] INFO  16:47:37,619 MicroScheduler -   -> 125 reads (0.11% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:47Z] INFO  16:47:37,673 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:47Z] INFO  16:47:37,893 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:47Z] INFO  16:47:37,894 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:47Z] INFO  16:47:37,895 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:47Z] INFO  16:47:37,895 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-14T23:47Z] INFO  16:47:39,014 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:47Z] INFO  16:47:39,018 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:47Z] INFO  16:47:39,018 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:47Z] INFO  16:47:39,019 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:47Z] INFO  16:47:39,024 HelpFormatter - Program Args: -T PrintReads -L 4:99397340-115544957 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/4/tx/tmp8S5Ey7/R14-18105_kapa-NGv3-PE100-NGv3-sort-4_99397339_115544957-prep-prealign.bam
[2016-04-14T23:47Z] INFO  16:47:39,052 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:47Z] INFO  16:47:39,053 HelpFormatter - Date/Time: 2016/04/14 16:47:39
[2016-04-14T23:47Z] INFO  16:47:39,053 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:47Z] INFO  16:47:39,054 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:47Z] INFO  16:47:39,202 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:47Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-4_15512869_31144471-prep-prealign.bam
[2016-04-14T23:47Z] INFO  16:47:39,243 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:47Z] GATK RealignerTargetCreator: R14-18105_kapa-NGv3-PE100-NGv3-sort-4_15512869_31144471-prep-prealign.bam 4:15512870-31144471
[2016-04-14T23:47Z] GATK: RealignerTargetCreator
[2016-04-14T23:47Z] INFO  16:47:40,317 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-14T23:47Z] INFO  16:47:40,389 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:47Z] INFO  16:47:40,398 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:47Z] INFO  16:47:40,435 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.04
[2016-04-14T23:47Z] INFO  16:47:40,451 IntervalUtils - Processing 16147618 bp from intervals
[2016-04-14T23:47Z] INFO  16:47:40,532 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:47Z] INFO  16:47:40,738 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@41fd9d8e
[2016-04-14T23:47Z] INFO  16:47:40,886 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:47Z] INFO  16:47:40,887 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:47Z] INFO  16:47:40,888 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:47Z] INFO  16:47:40,889 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:47Z] INFO  16:47:40,904 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:47Z] INFO  16:47:41,027 ProgressMeter -            done    213942.0    28.0 s       2.2 m       99.1%    28.0 s       0.0 s
[2016-04-14T23:47Z] INFO  16:47:41,028 ProgressMeter - Total runtime 28.40 secs, 0.47 min, 0.01 hours
[2016-04-14T23:47Z] INFO  16:47:41,028 MicroScheduler - 120 reads were filtered out during the traversal out of approximately 214062 total reads (0.06%)
[2016-04-14T23:47Z] INFO  16:47:41,028 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:47Z] INFO  16:47:41,029 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:47Z] INFO  16:47:41,029 MicroScheduler -   -> 120 reads (0.06% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:47Z] INFO  16:47:41,063 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:47Z] INFO  16:47:41,133 ProgressMeter -            done   1.566627E7    17.0 s       1.0 s      100.0%    17.0 s       0.0 s
[2016-04-14T23:47Z] INFO  16:47:41,134 ProgressMeter - Total runtime 17.60 secs, 0.29 min, 0.00 hours
[2016-04-14T23:47Z] INFO  16:47:41,138 MicroScheduler - 14595 reads were filtered out during the traversal out of approximately 165888 total reads (8.80%)
[2016-04-14T23:47Z] INFO  16:47:41,140 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:47Z] INFO  16:47:41,140 MicroScheduler -   -> 474 reads (0.29% of total) failing BadMateFilter
[2016-04-14T23:47Z] INFO  16:47:41,141 MicroScheduler -   -> 12920 reads (7.79% of total) failing DuplicateReadFilter
[2016-04-14T23:47Z] INFO  16:47:41,142 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-14T23:47Z] INFO  16:47:41,143 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:47Z] INFO  16:47:41,143 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-14T23:47Z] INFO  16:47:41,144 MicroScheduler -   -> 1201 reads (0.72% of total) failing MappingQualityZeroFilter
[2016-04-14T23:47Z] INFO  16:47:41,145 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:47Z] INFO  16:47:41,145 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-14T23:47Z] INFO  16:47:41,146 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-14T23:47Z] INFO  16:47:42,320 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:47Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-3_190333063_198022430-prep-prealign.bam
[2016-04-14T23:47Z] INFO  16:47:42,481 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:47Z] GATK: realign ('3', 143297426, 158963696) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-14T23:47Z] INFO  16:47:42,745 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:47Z] INFO  16:47:42,748 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:47Z] INFO  16:47:42,749 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:47Z] INFO  16:47:42,750 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:47Z] INFO  16:47:42,755 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/4/R14-18105_kapa-NGv3-PE100-NGv3-sort-4_15512869_31144471-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/4/tx/tmpn6u91v/R14-18105_kapa-NGv3-PE100-NGv3-sort-4_15512869_31144471-prep-prealign-realign.intervals -l INFO -L 4:15512870-31144471 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-14T23:47Z] INFO  16:47:42,765 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:47Z] INFO  16:47:42,766 HelpFormatter - Date/Time: 2016/04/14 16:47:42
[2016-04-14T23:47Z] INFO  16:47:42,767 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:47Z] INFO  16:47:42,767 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:47Z] INFO  16:47:42,869 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:47Z] GATK RealignerTargetCreator: R14-18105_kapa-NGv3-PE100-NGv3-sort-3_190333063_198022430-prep-prealign.bam 3:190333064-198022430
[2016-04-14T23:47Z] GATK: RealignerTargetCreator
[2016-04-14T23:47Z] INFO  16:47:43,091 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-14T23:47Z] INFO  16:47:43,104 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:47Z] INFO  16:47:43,163 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-14T23:47Z] INFO  16:47:43,484 IntervalUtils - Processing 15631602 bp from intervals
[2016-04-14T23:47Z] WARN  16:47:43,490 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:47Z] INFO  16:47:43,667 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:47Z] INFO  16:47:43,809 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:47Z] INFO  16:47:43,811 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:47Z] INFO  16:47:43,811 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:47Z] INFO  16:47:43,812 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-14T23:47Z] INFO  16:47:44,878 ProgressMeter -            done   1.5606725E7    16.0 s       1.0 s      100.0%    16.0 s       0.0 s
[2016-04-14T23:47Z] INFO  16:47:44,890 ProgressMeter - Total runtime 16.19 secs, 0.27 min, 0.00 hours
[2016-04-14T23:47Z] INFO  16:47:44,894 MicroScheduler - 10936 reads were filtered out during the traversal out of approximately 131904 total reads (8.29%)
[2016-04-14T23:47Z] INFO  16:47:44,895 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:47Z] INFO  16:47:44,895 MicroScheduler -   -> 447 reads (0.34% of total) failing BadMateFilter
[2016-04-14T23:47Z] INFO  16:47:44,895 MicroScheduler -   -> 10179 reads (7.72% of total) failing DuplicateReadFilter
[2016-04-14T23:47Z] INFO  16:47:44,896 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-14T23:47Z] INFO  16:47:44,896 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:47Z] INFO  16:47:44,896 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-14T23:47Z] INFO  16:47:44,896 MicroScheduler -   -> 310 reads (0.24% of total) failing MappingQualityZeroFilter
[2016-04-14T23:47Z] INFO  16:47:44,897 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:47Z] INFO  16:47:44,897 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-14T23:47Z] INFO  16:47:44,897 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-14T23:47Z] INFO  16:47:45,491 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:47Z] INFO  16:47:45,494 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:47Z] INFO  16:47:45,495 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:47Z] INFO  16:47:45,495 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:47Z] INFO  16:47:45,500 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/3/R14-18105_kapa-NGv3-PE100-NGv3-sort-3_143297426_158963696-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/3/R14-18105_kapa-NGv3-PE100-NGv3-sort-3_143297426_158963696-prep-prealign-realign.intervals -L 3:143297427-158963696 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/3/tx/tmpHsNMgL/R14-18105_kapa-NGv3-PE100-NGv3-sort-3_143297426_158963696-prep.bam
[2016-04-14T23:47Z] INFO  16:47:45,517 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:47Z] INFO  16:47:45,519 HelpFormatter - Date/Time: 2016/04/14 16:47:45
[2016-04-14T23:47Z] INFO  16:47:45,519 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:47Z] INFO  16:47:45,520 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:47Z] INFO  16:47:45,789 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:47Z] INFO  16:47:45,881 ProgressMeter -       4:3076600    200004.0    30.0 s       2.5 m       19.8%     2.5 m       2.0 m
[2016-04-14T23:47Z] INFO  16:47:45,921 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:47Z] INFO  16:47:45,930 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:47Z] INFO  16:47:46,000 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-14T23:47Z] INFO  16:47:46,232 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:47Z] INFO  16:47:46,250 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:47Z] INFO  16:47:46,253 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:47Z] INFO  16:47:46,254 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:47Z] INFO  16:47:46,254 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:47Z] INFO  16:47:46,259 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/3/R14-18105_kapa-NGv3-PE100-NGv3-sort-3_190333063_198022430-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/3/tx/tmpcFl2QA/R14-18105_kapa-NGv3-PE100-NGv3-sort-3_190333063_198022430-prep-prealign-realign.intervals -l INFO -L 3:190333064-198022430 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-14T23:47Z] GATK: realign ('3', 158970515, 174577240) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-14T23:47Z] INFO  16:47:46,274 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:47Z] INFO  16:47:46,275 HelpFormatter - Date/Time: 2016/04/14 16:47:46
[2016-04-14T23:47Z] INFO  16:47:46,276 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:47Z] INFO  16:47:46,277 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:47Z] INFO  16:47:46,406 IntervalUtils - Processing 15666270 bp from intervals
[2016-04-14T23:47Z] WARN  16:47:46,411 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:47Z] INFO  16:47:46,416 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:47Z] INFO  16:47:46,484 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:47Z] INFO  16:47:46,616 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@7172f77a
[2016-04-14T23:47Z] INFO  16:47:46,621 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:47Z] INFO  16:47:46,622 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:47Z] INFO  16:47:46,623 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:47Z] INFO  16:47:46,624 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:47Z] INFO  16:47:46,642 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-14T23:47Z] INFO  16:47:46,651 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:47Z] INFO  16:47:46,734 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-14T23:47Z] INFO  16:47:46,776 ProgressMeter -            done    113894.0    17.0 s       2.5 m       99.8%    17.0 s       0.0 s
[2016-04-14T23:47Z] INFO  16:47:46,777 ProgressMeter - Total runtime 17.20 secs, 0.29 min, 0.00 hours
[2016-04-14T23:47Z] INFO  16:47:46,777 MicroScheduler - 122 reads were filtered out during the traversal out of approximately 114016 total reads (0.11%)
[2016-04-14T23:47Z] INFO  16:47:46,778 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:47Z] INFO  16:47:46,778 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:47Z] INFO  16:47:46,778 MicroScheduler -   -> 122 reads (0.11% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:47Z] INFO  16:47:46,799 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:47Z] INFO  16:47:46,989 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:47Z] INFO  16:47:47,068 IntervalUtils - Processing 7689367 bp from intervals
[2016-04-14T23:47Z] WARN  16:47:47,073 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:47Z] INFO  16:47:47,200 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:47Z] INFO  16:47:47,392 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:47Z] INFO  16:47:47,393 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:47Z] INFO  16:47:47,394 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:47Z] INFO  16:47:47,395 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-14T23:47Z] INFO  16:47:48,309 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:47Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-4_52709749_68338393-prep-prealign.bam
[2016-04-14T23:47Z] GATK RealignerTargetCreator: R14-18105_kapa-NGv3-PE100-NGv3-sort-4_52709749_68338393-prep-prealign.bam 4:52709750-68338393
[2016-04-14T23:47Z] GATK: RealignerTargetCreator
[2016-04-14T23:47Z] INFO  16:47:48,848 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:47Z] INFO  16:47:48,852 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:47Z] INFO  16:47:48,852 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:47Z] INFO  16:47:48,853 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:47Z] INFO  16:47:48,857 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/3/R14-18105_kapa-NGv3-PE100-NGv3-sort-3_158970515_174577240-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/3/R14-18105_kapa-NGv3-PE100-NGv3-sort-3_158970515_174577240-prep-prealign-realign.intervals -L 3:158970516-174577240 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/3/tx/tmpCk8En4/R14-18105_kapa-NGv3-PE100-NGv3-sort-3_158970515_174577240-prep.bam
[2016-04-14T23:47Z] INFO  16:47:48,902 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:47Z] INFO  16:47:48,906 HelpFormatter - Date/Time: 2016/04/14 16:47:48
[2016-04-14T23:47Z] INFO  16:47:48,907 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:47Z] INFO  16:47:48,907 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:47Z] INFO  16:47:49,072 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:47Z] INFO  16:47:49,205 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:47Z] INFO  16:47:49,216 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:47Z] INFO  16:47:49,284 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-14T23:47Z] INFO  16:47:49,598 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@41fd9d8e
[2016-04-14T23:47Z] INFO  16:47:49,693 ProgressMeter -            done    187687.0    25.0 s       2.3 m      100.0%    25.0 s       0.0 s
[2016-04-14T23:47Z] INFO  16:47:49,694 ProgressMeter - Total runtime 25.84 secs, 0.43 min, 0.01 hours
[2016-04-14T23:47Z] INFO  16:47:49,695 MicroScheduler - 487 reads were filtered out during the traversal out of approximately 188174 total reads (0.26%)
[2016-04-14T23:47Z] INFO  16:47:49,696 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:47Z] INFO  16:47:49,697 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:47Z] INFO  16:47:49,697 MicroScheduler -   -> 487 reads (0.26% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:47Z] INFO  16:47:49,715 IntervalUtils - Processing 15606725 bp from intervals
[2016-04-14T23:47Z] WARN  16:47:49,720 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:47Z] INFO  16:47:49,812 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:47Z] INFO  16:47:49,914 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:47Z] INFO  16:47:49,915 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:47Z] INFO  16:47:49,916 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:47Z] INFO  16:47:49,916 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:47Z] INFO  16:47:50,073 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:47Z] INFO  16:47:50,211 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:47Z] INFO  16:47:50,230 ProgressMeter -     1:149899793    400011.0    31.0 s      78.0 s       38.7%    80.0 s      49.0 s
[2016-04-14T23:47Z] INFO  16:47:50,525 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@41fd9d8e
[2016-04-14T23:47Z] INFO  16:47:50,702 ProgressMeter -            done    290383.0    43.0 s       2.5 m      100.0%    43.0 s       0.0 s
[2016-04-14T23:47Z] INFO  16:47:50,703 ProgressMeter - Total runtime 43.25 secs, 0.72 min, 0.01 hours
[2016-04-14T23:47Z] INFO  16:47:50,704 MicroScheduler - 167 reads were filtered out during the traversal out of approximately 290550 total reads (0.06%)
[2016-04-14T23:47Z] INFO  16:47:50,705 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:47Z] INFO  16:47:50,706 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:47Z] INFO  16:47:50,706 MicroScheduler -   -> 167 reads (0.06% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:47Z] INFO  16:47:51,183 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:47Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-4_36069528_52709433-prep-prealign.bam
[2016-04-14T23:47Z] INFO  16:47:51,603 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:47Z] INFO  16:47:51,606 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:47Z] INFO  16:47:51,607 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:47Z] INFO  16:47:51,607 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:47Z] INFO  16:47:51,612 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/4/R14-18105_kapa-NGv3-PE100-NGv3-sort-4_52709749_68338393-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/4/tx/tmp_mRndC/R14-18105_kapa-NGv3-PE100-NGv3-sort-4_52709749_68338393-prep-prealign-realign.intervals -l INFO -L 4:52709750-68338393 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-14T23:47Z] INFO  16:47:51,631 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:47Z] INFO  16:47:51,632 HelpFormatter - Date/Time: 2016/04/14 16:47:51
[2016-04-14T23:47Z] INFO  16:47:51,633 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:47Z] INFO  16:47:51,633 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:47Z] INFO  16:47:51,729 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:47Z] INFO  16:47:51,906 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-14T23:47Z] INFO  16:47:51,919 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:47Z] GATK RealignerTargetCreator: R14-18105_kapa-NGv3-PE100-NGv3-sort-4_36069528_52709433-prep-prealign.bam 4:36069529-52709433
[2016-04-14T23:47Z] GATK: RealignerTargetCreator
[2016-04-14T23:47Z] INFO  16:47:51,993 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-14T23:47Z] INFO  16:47:52,107 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:47Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-3_174814579_190326970-prep-prealign.bam
[2016-04-14T23:47Z] INFO  16:47:52,309 IntervalUtils - Processing 15628644 bp from intervals
[2016-04-14T23:47Z] WARN  16:47:52,314 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:47Z] INFO  16:47:52,392 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:47Z] INFO  16:47:52,551 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:47Z] INFO  16:47:52,552 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:47Z] INFO  16:47:52,557 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:47Z] INFO  16:47:52,558 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-14T23:47Z] INFO  16:47:52,961 ProgressMeter -      3:62535580    700008.0    90.0 s       2.2 m       99.3%    90.0 s       0.0 s
[2016-04-14T23:47Z] GATK RealignerTargetCreator: R14-18105_kapa-NGv3-PE100-NGv3-sort-3_174814579_190326970-prep-prealign.bam 3:174814580-190326970
[2016-04-14T23:47Z] GATK: RealignerTargetCreator
[2016-04-14T23:47Z] INFO  16:47:53,170 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@41fd9d8e
[2016-04-14T23:47Z] INFO  16:47:53,292 ProgressMeter -            done    767511.0    91.0 s     118.0 s      100.0%    91.0 s       0.0 s
[2016-04-14T23:47Z] INFO  16:47:53,293 ProgressMeter - Total runtime 91.10 secs, 1.52 min, 0.03 hours
[2016-04-14T23:47Z] INFO  16:47:53,293 MicroScheduler - 319 reads were filtered out during the traversal out of approximately 767830 total reads (0.04%)
[2016-04-14T23:47Z] INFO  16:47:53,293 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:47Z] INFO  16:47:53,294 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:47Z] INFO  16:47:53,294 MicroScheduler -   -> 319 reads (0.04% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:47Z] INFO  16:47:54,559 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:47Z] INFO  16:47:54,562 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:47Z] INFO  16:47:54,563 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:47Z] INFO  16:47:54,563 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:47Z] INFO  16:47:54,569 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/4/R14-18105_kapa-NGv3-PE100-NGv3-sort-4_36069528_52709433-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/4/tx/tmphrUZGB/R14-18105_kapa-NGv3-PE100-NGv3-sort-4_36069528_52709433-prep-prealign-realign.intervals -l INFO -L 4:36069529-52709433 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-14T23:47Z] INFO  16:47:54,579 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:47Z] INFO  16:47:54,583 HelpFormatter - Date/Time: 2016/04/14 16:47:54
[2016-04-14T23:47Z] INFO  16:47:54,584 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:47Z] INFO  16:47:54,584 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:47Z] INFO  16:47:54,622 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:47Z] INFO  16:47:54,667 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:47Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-3_47129602_62648069-prep-prealign.bam
[2016-04-14T23:47Z] INFO  16:47:54,873 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-14T23:47Z] INFO  16:47:54,883 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:47Z] INFO  16:47:54,962 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-14T23:47Z] INFO  16:47:55,240 IntervalUtils - Processing 16639905 bp from intervals
[2016-04-14T23:47Z] WARN  16:47:55,245 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:47Z] INFO  16:47:55,324 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:47Z] INFO  16:47:55,526 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:47Z] INFO  16:47:55,527 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:47Z] INFO  16:47:55,528 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:47Z] INFO  16:47:55,529 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-14T23:47Z] INFO  16:47:55,890 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:47Z] INFO  16:47:55,894 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:47Z] INFO  16:47:55,894 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:47Z] INFO  16:47:55,895 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:47Z] INFO  16:47:55,899 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/3/R14-18105_kapa-NGv3-PE100-NGv3-sort-3_174814579_190326970-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/3/tx/tmpMMviyO/R14-18105_kapa-NGv3-PE100-NGv3-sort-3_174814579_190326970-prep-prealign-realign.intervals -l INFO -L 3:174814580-190326970 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-14T23:47Z] INFO  16:47:55,918 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:47Z] INFO  16:47:55,924 HelpFormatter - Date/Time: 2016/04/14 16:47:55
[2016-04-14T23:47Z] INFO  16:47:55,924 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:47Z] INFO  16:47:55,925 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:47Z] INFO  16:47:56,070 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:47Z] INFO  16:47:56,342 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-14T23:47Z] INFO  16:47:56,351 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:47Z] INFO  16:47:56,439 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.09
[2016-04-14T23:47Z] INFO  16:47:56,752 ProgressMeter -            done   1.5514517E7    20.0 s       1.0 s      100.0%    20.0 s       0.0 s
[2016-04-14T23:47Z] INFO  16:47:56,753 ProgressMeter - Total runtime 20.75 secs, 0.35 min, 0.01 hours
[2016-04-14T23:47Z] INFO  16:47:56,760 MicroScheduler - 31625 reads were filtered out during the traversal out of approximately 370703 total reads (8.53%)
[2016-04-14T23:47Z] INFO  16:47:56,760 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:47Z] INFO  16:47:56,760 MicroScheduler -   -> 775 reads (0.21% of total) failing BadMateFilter
[2016-04-14T23:47Z] INFO  16:47:56,761 MicroScheduler -   -> 29205 reads (7.88% of total) failing DuplicateReadFilter
[2016-04-14T23:47Z] INFO  16:47:56,761 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-14T23:47Z] INFO  16:47:56,761 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:47Z] INFO  16:47:56,761 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-14T23:47Z] INFO  16:47:56,762 MicroScheduler -   -> 1645 reads (0.44% of total) failing MappingQualityZeroFilter
[2016-04-14T23:47Z] INFO  16:47:56,762 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:47Z] INFO  16:47:56,762 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-14T23:47Z] INFO  16:47:56,762 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-14T23:47Z] INFO  16:47:56,781 IntervalUtils - Processing 15512391 bp from intervals
[2016-04-14T23:47Z] WARN  16:47:56,787 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:47Z] INFO  16:47:56,870 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:47Z] INFO  16:47:57,091 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:47Z] INFO  16:47:57,093 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:47Z] INFO  16:47:57,094 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:47Z] INFO  16:47:57,095 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-14T23:47Z] GATK RealignerTargetCreator: R14-18105_kapa-NGv3-PE100-NGv3-sort-3_47129602_62648069-prep-prealign.bam 3:47129603-62648069
[2016-04-14T23:47Z] GATK: RealignerTargetCreator
[2016-04-14T23:47Z] INFO  16:47:58,069 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:47Z] GATK: realign ('3', 112188604, 127703121) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-14T23:48Z] INFO  16:48:00,053 ProgressMeter -            done   1.5631602E7    16.0 s       1.0 s      100.0%    16.0 s       0.0 s
[2016-04-14T23:48Z] INFO  16:48:00,054 ProgressMeter - Total runtime 16.24 secs, 0.27 min, 0.00 hours
[2016-04-14T23:48Z] INFO  16:48:00,057 MicroScheduler - 9904 reads were filtered out during the traversal out of approximately 117535 total reads (8.43%)
[2016-04-14T23:48Z] INFO  16:48:00,058 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:48Z] INFO  16:48:00,058 MicroScheduler -   -> 474 reads (0.40% of total) failing BadMateFilter
[2016-04-14T23:48Z] INFO  16:48:00,058 MicroScheduler -   -> 9221 reads (7.85% of total) failing DuplicateReadFilter
[2016-04-14T23:48Z] INFO  16:48:00,058 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-14T23:48Z] INFO  16:48:00,059 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:48Z] INFO  16:48:00,059 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-14T23:48Z] INFO  16:48:00,059 MicroScheduler -   -> 209 reads (0.18% of total) failing MappingQualityZeroFilter
[2016-04-14T23:48Z] INFO  16:48:00,059 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:48Z] INFO  16:48:00,060 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-14T23:48Z] INFO  16:48:00,060 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-14T23:48Z] INFO  16:48:00,129 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:48Z] INFO  16:48:00,133 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:48Z] INFO  16:48:00,134 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:48Z] INFO  16:48:00,134 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:48Z] INFO  16:48:00,139 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/3/R14-18105_kapa-NGv3-PE100-NGv3-sort-3_47129602_62648069-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/3/tx/tmpYh7TIQ/R14-18105_kapa-NGv3-PE100-NGv3-sort-3_47129602_62648069-prep-prealign-realign.intervals -l INFO -L 3:47129603-62648069 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-14T23:48Z] INFO  16:48:00,150 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:48Z] INFO  16:48:00,152 HelpFormatter - Date/Time: 2016/04/14 16:48:00
[2016-04-14T23:48Z] INFO  16:48:00,158 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:48Z] INFO  16:48:00,159 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:48Z] INFO  16:48:00,216 ProgressMeter -            done    164558.0    13.0 s      82.0 s      100.0%    13.0 s       0.0 s
[2016-04-14T23:48Z] INFO  16:48:00,216 ProgressMeter - Total runtime 13.59 secs, 0.23 min, 0.00 hours
[2016-04-14T23:48Z] INFO  16:48:00,220 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 164558 total reads (0.00%)
[2016-04-14T23:48Z] INFO  16:48:00,220 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:48Z] INFO  16:48:00,220 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:48Z] INFO  16:48:00,221 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:48Z] INFO  16:48:00,273 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:48Z] INFO  16:48:00,447 ProgressMeter -            done   7689367.0    13.0 s       1.0 s      100.0%    13.0 s       0.0 s
[2016-04-14T23:48Z] INFO  16:48:00,448 ProgressMeter - Total runtime 13.06 secs, 0.22 min, 0.00 hours
[2016-04-14T23:48Z] INFO  16:48:00,448 MicroScheduler - 34503 reads were filtered out during the traversal out of approximately 215502 total reads (16.01%)
[2016-04-14T23:48Z] INFO  16:48:00,449 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:48Z] INFO  16:48:00,449 MicroScheduler -   -> 412 reads (0.19% of total) failing BadMateFilter
[2016-04-14T23:48Z] INFO  16:48:00,449 MicroScheduler -   -> 15869 reads (7.36% of total) failing DuplicateReadFilter
[2016-04-14T23:48Z] INFO  16:48:00,449 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-14T23:48Z] INFO  16:48:00,450 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:48Z] INFO  16:48:00,450 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-14T23:48Z] INFO  16:48:00,450 MicroScheduler -   -> 18222 reads (8.46% of total) failing MappingQualityZeroFilter
[2016-04-14T23:48Z] INFO  16:48:00,450 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:48Z] INFO  16:48:00,451 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-14T23:48Z] INFO  16:48:00,451 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-14T23:48Z] INFO  16:48:00,486 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-14T23:48Z] INFO  16:48:00,496 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:48Z] INFO  16:48:00,562 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-14T23:48Z] INFO  16:48:00,753 ProgressMeter -            done   1.5522634E7    22.0 s       1.0 s      100.0%    22.0 s       0.0 s
[2016-04-14T23:48Z] INFO  16:48:00,753 ProgressMeter - Total runtime 22.86 secs, 0.38 min, 0.01 hours
[2016-04-14T23:48Z] INFO  16:48:00,757 MicroScheduler - 29687 reads were filtered out during the traversal out of approximately 348524 total reads (8.52%)
[2016-04-14T23:48Z] INFO  16:48:00,759 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:48Z] INFO  16:48:00,760 MicroScheduler -   -> 797 reads (0.23% of total) failing BadMateFilter
[2016-04-14T23:48Z] INFO  16:48:00,760 MicroScheduler -   -> 27465 reads (7.88% of total) failing DuplicateReadFilter
[2016-04-14T23:48Z] INFO  16:48:00,761 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-14T23:48Z] INFO  16:48:00,761 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:48Z] INFO  16:48:00,761 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-14T23:48Z] INFO  16:48:00,762 MicroScheduler -   -> 1425 reads (0.41% of total) failing MappingQualityZeroFilter
[2016-04-14T23:48Z] INFO  16:48:00,762 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:48Z] INFO  16:48:00,762 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-14T23:48Z] INFO  16:48:00,762 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-14T23:48Z] INFO  16:48:00,918 IntervalUtils - Processing 15518467 bp from intervals
[2016-04-14T23:48Z] WARN  16:48:00,924 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:48Z] INFO  16:48:01,032 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:48Z] INFO  16:48:01,067 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:48Z] INFO  16:48:01,071 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:48Z] INFO  16:48:01,072 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:48Z] INFO  16:48:01,073 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:48Z] INFO  16:48:01,078 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/3/R14-18105_kapa-NGv3-PE100-NGv3-sort-3_112188604_127703121-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/3/R14-18105_kapa-NGv3-PE100-NGv3-sort-3_112188604_127703121-prep-prealign-realign.intervals -L 3:112188605-127703121 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/3/tx/tmppFb5xN/R14-18105_kapa-NGv3-PE100-NGv3-sort-3_112188604_127703121-prep.bam
[2016-04-14T23:48Z] INFO  16:48:01,082 ProgressMeter -      4:77255282    100001.0    31.0 s       5.2 m       57.5%    53.0 s      22.0 s
[2016-04-14T23:48Z] INFO  16:48:01,090 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:48Z] INFO  16:48:01,095 HelpFormatter - Date/Time: 2016/04/14 16:48:01
[2016-04-14T23:48Z] INFO  16:48:01,099 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:48Z] INFO  16:48:01,100 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:48Z] INFO  16:48:01,327 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:48Z] INFO  16:48:01,336 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:48Z] INFO  16:48:01,337 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:48Z] INFO  16:48:01,338 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:48Z] INFO  16:48:01,339 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-14T23:48Z] INFO  16:48:01,448 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:48Z] INFO  16:48:01,459 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:48Z] INFO  16:48:01,535 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-14T23:48Z] INFO  16:48:01,582 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:48Z] GATK: realign ('4', 15512869, 31144471) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-14T23:48Z] INFO  16:48:01,856 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:48Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-3_143297426_158963696-prep.bam
[2016-04-14T23:48Z] INFO  16:48:01,909 IntervalUtils - Processing 15514517 bp from intervals
[2016-04-14T23:48Z] WARN  16:48:01,914 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:48Z] INFO  16:48:01,928 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:48Z] GATK: realign ('3', 190333063, 198022430) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-14T23:48Z] INFO  16:48:02,004 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:48Z] INFO  16:48:02,118 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:48Z] INFO  16:48:02,119 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:48Z] INFO  16:48:02,120 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:48Z] INFO  16:48:02,121 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:48Z] INFO  16:48:02,186 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:48Z] GATK: realign ('3', 127770401, 143293035) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-14T23:48Z] INFO  16:48:02,204 ProgressMeter -            done    130910.0    12.0 s      93.0 s      100.0%    12.0 s       0.0 s
[2016-04-14T23:48Z] INFO  16:48:02,205 ProgressMeter - Total runtime 12.29 secs, 0.20 min, 0.00 hours
[2016-04-14T23:48Z] INFO  16:48:02,209 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 130910 total reads (0.00%)
[2016-04-14T23:48Z] INFO  16:48:02,210 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:48Z] INFO  16:48:02,210 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:48Z] INFO  16:48:02,211 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:48Z] INFO  16:48:02,260 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:48Z] GATK pre-alignment ('4', 115584857, 134074404) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-14T23:48Z] INFO  16:48:02,416 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:48Z] INFO  16:48:02,567 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@52f3b59
[2016-04-14T23:48Z] INFO  16:48:02,695 ProgressMeter -            done    169724.0    26.0 s       2.6 m      100.0%    26.0 s       0.0 s
[2016-04-14T23:48Z] INFO  16:48:02,696 ProgressMeter - Total runtime 26.70 secs, 0.45 min, 0.01 hours
[2016-04-14T23:48Z] INFO  16:48:02,696 MicroScheduler - 111 reads were filtered out during the traversal out of approximately 169835 total reads (0.07%)
[2016-04-14T23:48Z] INFO  16:48:02,697 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:48Z] INFO  16:48:02,697 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:48Z] INFO  16:48:02,697 MicroScheduler -   -> 111 reads (0.07% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:48Z] INFO  16:48:03,796 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:48Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-3_158970515_174577240-prep.bam
[2016-04-14T23:48Z] GATK pre-alignment ('4', 134075461, 150351181) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-14T23:48Z] INFO  16:48:04,332 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:48Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-4_83857133_99393738-prep-prealign.bam
[2016-04-14T23:48Z] INFO  16:48:04,565 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:48Z] INFO  16:48:04,575 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:48Z] INFO  16:48:04,576 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:48Z] INFO  16:48:04,576 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:48Z] INFO  16:48:04,580 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/4/R14-18105_kapa-NGv3-PE100-NGv3-sort-4_15512869_31144471-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/4/R14-18105_kapa-NGv3-PE100-NGv3-sort-4_15512869_31144471-prep-prealign-realign.intervals -L 4:15512870-31144471 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/4/tx/tmpGK1JEN/R14-18105_kapa-NGv3-PE100-NGv3-sort-4_15512869_31144471-prep.bam
[2016-04-14T23:48Z] INFO  16:48:04,589 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:48Z] INFO  16:48:04,590 HelpFormatter - Date/Time: 2016/04/14 16:48:04
[2016-04-14T23:48Z] INFO  16:48:04,590 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:48Z] INFO  16:48:04,591 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:48Z] INFO  16:48:04,854 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:48Z] GATK RealignerTargetCreator: R14-18105_kapa-NGv3-PE100-NGv3-sort-4_83857133_99393738-prep-prealign.bam 4:83857134-99393738
[2016-04-14T23:48Z] GATK: RealignerTargetCreator
[2016-04-14T23:48Z] INFO  16:48:05,087 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:48Z] INFO  16:48:05,098 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:48Z] INFO  16:48:05,193 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.09
[2016-04-14T23:48Z] INFO  16:48:05,193 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:48Z] INFO  16:48:05,197 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:48Z] INFO  16:48:05,197 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:48Z] INFO  16:48:05,198 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:48Z] INFO  16:48:05,202 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/3/R14-18105_kapa-NGv3-PE100-NGv3-sort-3_190333063_198022430-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/3/R14-18105_kapa-NGv3-PE100-NGv3-sort-3_190333063_198022430-prep-prealign-realign.intervals -L 3:190333064-198022430 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/3/tx/tmpZLV1vM/R14-18105_kapa-NGv3-PE100-NGv3-sort-3_190333063_198022430-prep.bam
[2016-04-14T23:48Z] INFO  16:48:05,235 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:48Z] INFO  16:48:05,236 HelpFormatter - Date/Time: 2016/04/14 16:48:05
[2016-04-14T23:48Z] INFO  16:48:05,237 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:48Z] INFO  16:48:05,237 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:48Z] INFO  16:48:05,352 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:48Z] INFO  16:48:05,355 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:48Z] INFO  16:48:05,356 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:48Z] INFO  16:48:05,356 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:48Z] INFO  16:48:05,361 HelpFormatter - Program Args: -T PrintReads -L 4:115584858-134074404 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/4/tx/tmpaQKdBL/R14-18105_kapa-NGv3-PE100-NGv3-sort-4_115584857_134074404-prep-prealign.bam
[2016-04-14T23:48Z] INFO  16:48:05,373 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:48Z] INFO  16:48:05,385 HelpFormatter - Date/Time: 2016/04/14 16:48:05
[2016-04-14T23:48Z] INFO  16:48:05,386 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:48Z] INFO  16:48:05,387 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:48Z] INFO  16:48:05,485 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:48Z] INFO  16:48:05,497 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:48Z] INFO  16:48:05,498 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:48Z] INFO  16:48:05,498 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:48Z] INFO  16:48:05,503 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/3/R14-18105_kapa-NGv3-PE100-NGv3-sort-3_127770401_143293035-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/3/R14-18105_kapa-NGv3-PE100-NGv3-sort-3_127770401_143293035-prep-prealign-realign.intervals -L 3:127770402-143293035 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/3/tx/tmpid_UOE/R14-18105_kapa-NGv3-PE100-NGv3-sort-3_127770401_143293035-prep.bam
[2016-04-14T23:48Z] INFO  16:48:05,514 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:48Z] INFO  16:48:05,530 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:48Z] INFO  16:48:05,531 HelpFormatter - Date/Time: 2016/04/14 16:48:05
[2016-04-14T23:48Z] INFO  16:48:05,532 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:48Z] INFO  16:48:05,533 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:48Z] INFO  16:48:05,577 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:48Z] INFO  16:48:05,630 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:48Z] INFO  16:48:05,652 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:48Z] INFO  16:48:05,690 IntervalUtils - Processing 15631602 bp from intervals
[2016-04-14T23:48Z] WARN  16:48:05,695 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:48Z] INFO  16:48:05,711 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-14T23:48Z] INFO  16:48:05,781 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:48Z] INFO  16:48:05,786 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:48Z] INFO  16:48:05,914 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:48Z] INFO  16:48:05,916 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:48Z] INFO  16:48:05,916 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:48Z] INFO  16:48:05,917 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:48Z] INFO  16:48:05,965 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:48Z] INFO  16:48:05,982 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:48Z] INFO  16:48:06,052 IntervalUtils - Processing 7689367 bp from intervals
[2016-04-14T23:48Z] WARN  16:48:06,057 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:48Z] INFO  16:48:06,068 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.09
[2016-04-14T23:48Z] INFO  16:48:06,085 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:48Z] INFO  16:48:06,180 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:48Z] INFO  16:48:06,299 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:48Z] INFO  16:48:06,337 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:48Z] INFO  16:48:06,349 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:48Z] INFO  16:48:06,350 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:48Z] INFO  16:48:06,350 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:48Z] INFO  16:48:06,486 IntervalUtils - Processing 15522634 bp from intervals
[2016-04-14T23:48Z] WARN  16:48:06,491 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:48Z] INFO  16:48:06,500 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:48Z] INFO  16:48:06,558 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:48Z] INFO  16:48:06,577 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:48Z] INFO  16:48:06,720 ProgressMeter -      3:46967075    400005.0    30.0 s      75.0 s       99.0%    30.0 s       0.0 s
[2016-04-14T23:48Z] INFO  16:48:06,782 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:48Z] INFO  16:48:06,782 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:48Z] INFO  16:48:06,783 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:48Z] INFO  16:48:06,783 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:48Z] INFO  16:48:06,823 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-14T23:48Z] INFO  16:48:06,900 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:48Z] INFO  16:48:06,909 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:48Z] INFO  16:48:06,956 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:48Z] INFO  16:48:06,961 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-14T23:48Z] INFO  16:48:06,976 IntervalUtils - Processing 18489547 bp from intervals
[2016-04-14T23:48Z] INFO  16:48:07,061 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:48Z] INFO  16:48:07,113 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:48Z] INFO  16:48:07,130 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@7172f77a
[2016-04-14T23:48Z] INFO  16:48:07,290 ProgressMeter -            done    200724.0    26.0 s       2.2 m      100.0%    26.0 s       0.0 s
[2016-04-14T23:48Z] INFO  16:48:07,291 ProgressMeter - Total runtime 26.40 secs, 0.44 min, 0.01 hours
[2016-04-14T23:48Z] INFO  16:48:07,291 MicroScheduler - 173 reads were filtered out during the traversal out of approximately 200897 total reads (0.09%)
[2016-04-14T23:48Z] INFO  16:48:07,292 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:48Z] INFO  16:48:07,292 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:48Z] INFO  16:48:07,292 MicroScheduler -   -> 173 reads (0.09% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:48Z] INFO  16:48:07,432 ProgressMeter -            done    479559.0    30.0 s      64.0 s      100.0%    30.0 s       0.0 s
[2016-04-14T23:48Z] INFO  16:48:07,433 ProgressMeter - Total runtime 30.83 secs, 0.51 min, 0.01 hours
[2016-04-14T23:48Z] INFO  16:48:07,440 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 479559 total reads (0.00%)
[2016-04-14T23:48Z] INFO  16:48:07,442 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:48Z] INFO  16:48:07,442 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:48Z] INFO  16:48:07,442 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:48Z] INFO  16:48:07,458 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:48Z] INFO  16:48:07,459 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:48Z] INFO  16:48:07,460 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:48Z] INFO  16:48:07,461 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:48Z] INFO  16:48:07,496 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:48Z] INFO  16:48:07,531 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:48Z] INFO  16:48:07,534 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:48Z] INFO  16:48:07,535 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:48Z] INFO  16:48:07,536 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:48Z] INFO  16:48:07,540 HelpFormatter - Program Args: -T PrintReads -L 4:134075462-150351181 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/4/tx/tmpNjYR2z/R14-18105_kapa-NGv3-PE100-NGv3-sort-4_134075461_150351181-prep-prealign.bam
[2016-04-14T23:48Z] INFO  16:48:07,556 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:48Z] INFO  16:48:07,557 HelpFormatter - Date/Time: 2016/04/14 16:48:07
[2016-04-14T23:48Z] INFO  16:48:07,558 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:48Z] INFO  16:48:07,559 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:48Z] INFO  16:48:07,586 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:48Z] INFO  16:48:07,590 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:48Z] INFO  16:48:07,590 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:48Z] INFO  16:48:07,591 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:48Z] INFO  16:48:07,595 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/4/R14-18105_kapa-NGv3-PE100-NGv3-sort-4_83857133_99393738-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/4/tx/tmpjol5XF/R14-18105_kapa-NGv3-PE100-NGv3-sort-4_83857133_99393738-prep-prealign-realign.intervals -l INFO -L 4:83857134-99393738 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-14T23:48Z] INFO  16:48:07,605 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:48Z] INFO  16:48:07,617 HelpFormatter - Date/Time: 2016/04/14 16:48:07
[2016-04-14T23:48Z] INFO  16:48:07,618 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:48Z] INFO  16:48:07,619 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:48Z] INFO  16:48:07,751 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:48Z] INFO  16:48:07,757 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:48Z] INFO  16:48:07,761 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:48Z] INFO  16:48:08,043 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-14T23:48Z] INFO  16:48:08,064 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:48Z] INFO  16:48:08,138 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-14T23:48Z] INFO  16:48:08,542 ProgressMeter -            done   1.5628644E7    15.0 s       1.0 s      100.0%    15.0 s       0.0 s
[2016-04-14T23:48Z] INFO  16:48:08,543 ProgressMeter - Total runtime 15.99 secs, 0.27 min, 0.00 hours
[2016-04-14T23:48Z] INFO  16:48:08,547 MicroScheduler - 9566 reads were filtered out during the traversal out of approximately 114325 total reads (8.37%)
[2016-04-14T23:48Z] INFO  16:48:08,547 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:48Z] INFO  16:48:08,547 MicroScheduler -   -> 444 reads (0.39% of total) failing BadMateFilter
[2016-04-14T23:48Z] INFO  16:48:08,548 MicroScheduler -   -> 8864 reads (7.75% of total) failing DuplicateReadFilter
[2016-04-14T23:48Z] INFO  16:48:08,548 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-14T23:48Z] INFO  16:48:08,548 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:48Z] INFO  16:48:08,549 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-14T23:48Z] INFO  16:48:08,549 MicroScheduler -   -> 258 reads (0.23% of total) failing MappingQualityZeroFilter
[2016-04-14T23:48Z] INFO  16:48:08,549 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:48Z] INFO  16:48:08,549 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-14T23:48Z] INFO  16:48:08,550 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-14T23:48Z] INFO  16:48:08,633 IntervalUtils - Processing 15536605 bp from intervals
[2016-04-14T23:48Z] WARN  16:48:08,642 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:48Z] INFO  16:48:08,717 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:48Z] INFO  16:48:08,721 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:48Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-4_99397339_115544957-prep-prealign.bam
[2016-04-14T23:48Z] INFO  16:48:08,935 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:48Z] INFO  16:48:08,936 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:48Z] INFO  16:48:08,937 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:48Z] INFO  16:48:08,938 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-14T23:48Z] INFO  16:48:08,983 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-14T23:48Z] INFO  16:48:09,041 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:48Z] INFO  16:48:09,051 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:48Z] INFO  16:48:09,088 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.04
[2016-04-14T23:48Z] INFO  16:48:09,115 IntervalUtils - Processing 16275720 bp from intervals
[2016-04-14T23:48Z] INFO  16:48:09,203 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:48Z] INFO  16:48:09,206 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:48Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-3_31617887_47127804-prep.bam
[2016-04-14T23:48Z] GATK RealignerTargetCreator: R14-18105_kapa-NGv3-PE100-NGv3-sort-4_99397339_115544957-prep-prealign.bam 4:99397340-115544957
[2016-04-14T23:48Z] GATK: RealignerTargetCreator
[2016-04-14T23:48Z] INFO  16:48:09,555 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:48Z] INFO  16:48:09,556 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:48Z] INFO  16:48:09,557 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:48Z] INFO  16:48:09,558 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:48Z] INFO  16:48:09,587 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:48Z] INFO  16:48:09,881 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:48Z] INFO  16:48:10,015 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:48Z] GATK: realign ('4', 52709749, 68338393) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-14T23:48Z] GATK pre-alignment ('4', 150354547, 165878648) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-14T23:48Z] INFO  16:48:12,301 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:48Z] INFO  16:48:12,305 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:48Z] INFO  16:48:12,305 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:48Z] INFO  16:48:12,306 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:48Z] INFO  16:48:12,310 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/4/R14-18105_kapa-NGv3-PE100-NGv3-sort-4_99397339_115544957-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/4/tx/tmpoLnksP/R14-18105_kapa-NGv3-PE100-NGv3-sort-4_99397339_115544957-prep-prealign-realign.intervals -l INFO -L 4:99397340-115544957 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-14T23:48Z] INFO  16:48:12,320 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:48Z] INFO  16:48:12,324 HelpFormatter - Date/Time: 2016/04/14 16:48:12
[2016-04-14T23:48Z] INFO  16:48:12,325 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:48Z] INFO  16:48:12,325 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:48Z] INFO  16:48:12,437 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:48Z] INFO  16:48:12,663 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-14T23:48Z] INFO  16:48:12,672 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:48Z] INFO  16:48:12,741 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@41fd9d8e
[2016-04-14T23:48Z] INFO  16:48:12,750 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-14T23:48Z] INFO  16:48:12,921 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:48Z] INFO  16:48:12,924 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:48Z] INFO  16:48:12,925 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:48Z] INFO  16:48:12,925 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:48Z] INFO  16:48:12,930 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/4/R14-18105_kapa-NGv3-PE100-NGv3-sort-4_52709749_68338393-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/4/R14-18105_kapa-NGv3-PE100-NGv3-sort-4_52709749_68338393-prep-prealign-realign.intervals -L 4:52709750-68338393 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/4/tx/tmpfcmjGC/R14-18105_kapa-NGv3-PE100-NGv3-sort-4_52709749_68338393-prep.bam
[2016-04-14T23:48Z] INFO  16:48:12,947 ProgressMeter -            done    277042.0    43.0 s       2.6 m      100.0%    43.0 s       0.0 s
[2016-04-14T23:48Z] INFO  16:48:12,948 ProgressMeter - Total runtime 43.10 secs, 0.72 min, 0.01 hours
[2016-04-14T23:48Z] INFO  16:48:12,948 MicroScheduler - 147 reads were filtered out during the traversal out of approximately 277189 total reads (0.05%)
[2016-04-14T23:48Z] INFO  16:48:12,949 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:48Z] INFO  16:48:12,949 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:48Z] INFO  16:48:12,949 MicroScheduler -   -> 147 reads (0.05% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:48Z] INFO  16:48:12,961 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:48Z] INFO  16:48:12,962 HelpFormatter - Date/Time: 2016/04/14 16:48:12
[2016-04-14T23:48Z] INFO  16:48:12,962 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:48Z] INFO  16:48:12,967 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:48Z] INFO  16:48:13,076 IntervalUtils - Processing 16147618 bp from intervals
[2016-04-14T23:48Z] WARN  16:48:13,081 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:48Z] INFO  16:48:13,197 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:48Z] INFO  16:48:13,219 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:48Z] INFO  16:48:13,348 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:48Z] INFO  16:48:13,357 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:48Z] INFO  16:48:13,425 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-14T23:48Z] INFO  16:48:13,468 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:48Z] INFO  16:48:13,469 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:48Z] INFO  16:48:13,470 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:48Z] INFO  16:48:13,471 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-14T23:48Z] INFO  16:48:13,813 IntervalUtils - Processing 15628644 bp from intervals
[2016-04-14T23:48Z] WARN  16:48:13,818 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:48Z] INFO  16:48:13,906 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:48Z] INFO  16:48:14,055 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:48Z] INFO  16:48:14,064 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:48Z] INFO  16:48:14,064 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:48Z] INFO  16:48:14,075 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:48Z] INFO  16:48:14,076 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:48Z] INFO  16:48:14,076 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:48Z] INFO  16:48:14,077 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:48Z] INFO  16:48:14,077 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:48Z] INFO  16:48:14,081 HelpFormatter - Program Args: -T PrintReads -L 4:150354548-165878648 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/4/tx/tmplullDJ/R14-18105_kapa-NGv3-PE100-NGv3-sort-4_150354547_165878648-prep-prealign.bam
[2016-04-14T23:48Z] INFO  16:48:14,109 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:48Z] INFO  16:48:14,110 HelpFormatter - Date/Time: 2016/04/14 16:48:14
[2016-04-14T23:48Z] INFO  16:48:14,110 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:48Z] INFO  16:48:14,111 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:48Z] INFO  16:48:14,233 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:48Z] INFO  16:48:14,313 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:48Z] INFO  16:48:14,373 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:48Z] INFO  16:48:14,461 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:48Z] INFO  16:48:14,469 ProgressMeter -            done   1.6639905E7    18.0 s       1.0 s      100.0%    18.0 s       0.0 s
[2016-04-14T23:48Z] INFO  16:48:14,470 ProgressMeter - Total runtime 18.94 secs, 0.32 min, 0.01 hours
[2016-04-14T23:48Z] INFO  16:48:14,473 MicroScheduler - 18275 reads were filtered out during the traversal out of approximately 188844 total reads (9.68%)
[2016-04-14T23:48Z] INFO  16:48:14,474 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:48Z] INFO  16:48:14,474 MicroScheduler -   -> 721 reads (0.38% of total) failing BadMateFilter
[2016-04-14T23:48Z] INFO  16:48:14,474 MicroScheduler -   -> 14564 reads (7.71% of total) failing DuplicateReadFilter
[2016-04-14T23:48Z] INFO  16:48:14,482 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-14T23:48Z] INFO  16:48:14,483 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:48Z] INFO  16:48:14,483 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-14T23:48Z] INFO  16:48:14,484 MicroScheduler -   -> 2990 reads (1.58% of total) failing MappingQualityZeroFilter
[2016-04-14T23:48Z] INFO  16:48:14,495 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:48Z] INFO  16:48:14,496 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-14T23:48Z] INFO  16:48:14,497 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-14T23:48Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-4_68340604_83852298-prep-prealign.bam
[2016-04-14T23:48Z] GATK RealignerTargetCreator: R14-18105_kapa-NGv3-PE100-NGv3-sort-4_68340604_83852298-prep-prealign.bam 4:68340605-83852298
[2016-04-14T23:48Z] GATK: RealignerTargetCreator
[2016-04-14T23:48Z] INFO  16:48:15,339 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-14T23:48Z] INFO  16:48:15,404 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:48Z] INFO  16:48:15,413 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:48Z] INFO  16:48:15,472 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-14T23:48Z] INFO  16:48:15,499 IntervalUtils - Processing 15524101 bp from intervals
[2016-04-14T23:48Z] INFO  16:48:15,651 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:48Z] INFO  16:48:15,987 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:48Z] INFO  16:48:15,988 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:48Z] INFO  16:48:15,988 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:48Z] INFO  16:48:15,989 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:48Z] INFO  16:48:16,010 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:48Z] INFO  16:48:16,032 ProgressMeter -       4:9237310    400006.0    60.0 s       2.5 m       59.5%   100.0 s      40.0 s
[2016-04-14T23:48Z] INFO  16:48:16,133 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:48Z] GATK: realign ('4', 36069528, 52709433) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-14T23:48Z] INFO  16:48:16,184 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:48Z] INFO  16:48:17,495 ProgressMeter -            done   1.5512391E7    20.0 s       1.0 s      100.0%    20.0 s       0.0 s
[2016-04-14T23:48Z] INFO  16:48:17,496 ProgressMeter - Total runtime 20.40 secs, 0.34 min, 0.01 hours
[2016-04-14T23:48Z] INFO  16:48:17,516 MicroScheduler - 24037 reads were filtered out during the traversal out of approximately 292374 total reads (8.22%)
[2016-04-14T23:48Z] INFO  16:48:17,520 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:48Z] INFO  16:48:17,521 MicroScheduler -   -> 630 reads (0.22% of total) failing BadMateFilter
[2016-04-14T23:48Z] INFO  16:48:17,521 MicroScheduler -   -> 22547 reads (7.71% of total) failing DuplicateReadFilter
[2016-04-14T23:48Z] INFO  16:48:17,522 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-14T23:48Z] INFO  16:48:17,523 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:48Z] INFO  16:48:17,523 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-14T23:48Z] INFO  16:48:17,524 MicroScheduler -   -> 860 reads (0.29% of total) failing MappingQualityZeroFilter
[2016-04-14T23:48Z] INFO  16:48:17,524 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:48Z] INFO  16:48:17,525 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-14T23:48Z] INFO  16:48:17,526 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-14T23:48Z] INFO  16:48:17,824 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:48Z] INFO  16:48:17,829 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:48Z] INFO  16:48:17,830 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:48Z] INFO  16:48:17,831 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:48Z] INFO  16:48:17,836 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/4/R14-18105_kapa-NGv3-PE100-NGv3-sort-4_68340604_83852298-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/4/tx/tmp__946f/R14-18105_kapa-NGv3-PE100-NGv3-sort-4_68340604_83852298-prep-prealign-realign.intervals -l INFO -L 4:68340605-83852298 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-14T23:48Z] INFO  16:48:17,851 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:48Z] INFO  16:48:17,852 HelpFormatter - Date/Time: 2016/04/14 16:48:17
[2016-04-14T23:48Z] INFO  16:48:17,852 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:48Z] INFO  16:48:17,852 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:48Z] INFO  16:48:17,925 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:48Z] INFO  16:48:18,149 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-14T23:48Z] INFO  16:48:18,172 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:48Z] INFO  16:48:18,212 ProgressMeter -            done    117024.0    12.0 s     105.0 s      100.0%    12.0 s       0.0 s
[2016-04-14T23:48Z] INFO  16:48:18,213 ProgressMeter - Total runtime 12.30 secs, 0.20 min, 0.00 hours
[2016-04-14T23:48Z] INFO  16:48:18,217 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 117024 total reads (0.00%)
[2016-04-14T23:48Z] INFO  16:48:18,218 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:48Z] INFO  16:48:18,219 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:48Z] INFO  16:48:18,220 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:48Z] INFO  16:48:18,260 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.09
[2016-04-14T23:48Z] INFO  16:48:18,591 IntervalUtils - Processing 15511694 bp from intervals
[2016-04-14T23:48Z] WARN  16:48:18,606 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:48Z] INFO  16:48:18,695 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:48Z] INFO  16:48:18,898 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:48Z] INFO  16:48:18,911 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:48Z] INFO  16:48:18,912 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:48Z] INFO  16:48:18,913 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:48Z] INFO  16:48:18,913 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-14T23:48Z] GATK: realign ('3', 174814579, 190326970) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-14T23:48Z] INFO  16:48:18,988 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:48Z] INFO  16:48:18,991 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:48Z] INFO  16:48:18,991 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:48Z] INFO  16:48:18,991 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:48Z] INFO  16:48:18,995 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/4/R14-18105_kapa-NGv3-PE100-NGv3-sort-4_36069528_52709433-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/4/R14-18105_kapa-NGv3-PE100-NGv3-sort-4_36069528_52709433-prep-prealign-realign.intervals -L 4:36069529-52709433 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/4/tx/tmpR2ddkY/R14-18105_kapa-NGv3-PE100-NGv3-sort-4_36069528_52709433-prep.bam
[2016-04-14T23:48Z] INFO  16:48:19,017 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:48Z] INFO  16:48:19,017 HelpFormatter - Date/Time: 2016/04/14 16:48:18
[2016-04-14T23:48Z] INFO  16:48:19,017 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:48Z] INFO  16:48:19,018 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:48Z] INFO  16:48:19,208 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:48Z] INFO  16:48:19,324 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:48Z] INFO  16:48:19,333 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:48Z] INFO  16:48:19,394 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-14T23:48Z] INFO  16:48:19,658 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:48Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-4_15512869_31144471-prep.bam
[2016-04-14T23:48Z] INFO  16:48:19,805 IntervalUtils - Processing 16639905 bp from intervals
[2016-04-14T23:48Z] WARN  16:48:19,812 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:48Z] INFO  16:48:19,943 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:48Z] INFO  16:48:20,140 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:48Z] INFO  16:48:20,141 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:48Z] INFO  16:48:20,142 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:48Z] INFO  16:48:20,143 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:48Z] GATK pre-alignment ('4', 165889318, 183245405) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-14T23:48Z] INFO  16:48:20,231 ProgressMeter -     1:155001734    900017.0    61.0 s      68.0 s       71.6%    85.0 s      24.0 s
[2016-04-14T23:48Z] INFO  16:48:20,290 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:48Z] INFO  16:48:20,501 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:48Z] INFO  16:48:21,594 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:48Z] INFO  16:48:21,597 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:48Z] INFO  16:48:21,598 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:48Z] INFO  16:48:21,599 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:48Z] INFO  16:48:21,603 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/3/R14-18105_kapa-NGv3-PE100-NGv3-sort-3_174814579_190326970-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/3/R14-18105_kapa-NGv3-PE100-NGv3-sort-3_174814579_190326970-prep-prealign-realign.intervals -L 3:174814580-190326970 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/3/tx/tmp7ulIrz/R14-18105_kapa-NGv3-PE100-NGv3-sort-3_174814579_190326970-prep.bam
[2016-04-14T23:48Z] INFO  16:48:21,634 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:48Z] INFO  16:48:21,635 HelpFormatter - Date/Time: 2016/04/14 16:48:21
[2016-04-14T23:48Z] INFO  16:48:21,635 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:48Z] INFO  16:48:21,640 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:48Z] INFO  16:48:21,825 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:48Z] INFO  16:48:21,944 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:48Z] INFO  16:48:21,963 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:48Z] INFO  16:48:22,047 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-14T23:48Z] INFO  16:48:22,426 IntervalUtils - Processing 15512391 bp from intervals
[2016-04-14T23:48Z] WARN  16:48:22,438 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:48Z] INFO  16:48:22,571 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:48Z] INFO  16:48:22,713 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:48Z] INFO  16:48:22,715 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:48Z] INFO  16:48:22,715 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:48Z] INFO  16:48:22,716 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:48Z] INFO  16:48:22,796 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:48Z] INFO  16:48:22,799 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:48Z] INFO  16:48:22,799 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:48Z] INFO  16:48:22,799 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:48Z] INFO  16:48:22,803 HelpFormatter - Program Args: -T PrintReads -L 4:165889319-183245405 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/4/tx/tmpe39aDk/R14-18105_kapa-NGv3-PE100-NGv3-sort-4_165889318_183245405-prep-prealign.bam
[2016-04-14T23:48Z] INFO  16:48:22,830 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:48Z] INFO  16:48:22,830 HelpFormatter - Date/Time: 2016/04/14 16:48:22
[2016-04-14T23:48Z] INFO  16:48:22,830 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:48Z] INFO  16:48:22,831 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:48Z] INFO  16:48:22,833 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:48Z] INFO  16:48:23,006 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:48Z] INFO  16:48:23,020 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:48Z] INFO  16:48:23,672 ProgressMeter -            done    213942.0    17.0 s      80.0 s       99.1%    17.0 s       0.0 s
[2016-04-14T23:48Z] INFO  16:48:23,672 ProgressMeter - Total runtime 17.32 secs, 0.29 min, 0.00 hours
[2016-04-14T23:48Z] INFO  16:48:23,677 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 213942 total reads (0.00%)
[2016-04-14T23:48Z] INFO  16:48:23,677 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:48Z] INFO  16:48:23,678 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:48Z] INFO  16:48:23,678 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:48Z] INFO  16:48:24,189 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-14T23:48Z] INFO  16:48:24,257 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:48Z] INFO  16:48:24,268 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:48Z] INFO  16:48:24,342 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-14T23:48Z] INFO  16:48:24,360 IntervalUtils - Processing 17356087 bp from intervals
[2016-04-14T23:48Z] INFO  16:48:24,444 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:48Z] INFO  16:48:24,781 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:48Z] INFO  16:48:24,782 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:48Z] INFO  16:48:24,782 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:48Z] INFO  16:48:24,782 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:48Z] INFO  16:48:24,821 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:48Z] INFO  16:48:25,029 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:48Z] INFO  16:48:25,183 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:48Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-3_190333063_198022430-prep.bam
[2016-04-14T23:48Z] INFO  16:48:25,463 ProgressMeter -            done    113894.0    11.0 s      99.0 s       99.8%    11.0 s       0.0 s
[2016-04-14T23:48Z] INFO  16:48:25,464 ProgressMeter - Total runtime 11.39 secs, 0.19 min, 0.00 hours
[2016-04-14T23:48Z] INFO  16:48:25,468 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 113894 total reads (0.00%)
[2016-04-14T23:48Z] INFO  16:48:25,469 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:48Z] INFO  16:48:25,469 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:48Z] INFO  16:48:25,470 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:48Z] GATK pre-alignment ('4', 183267803, 191154276) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-14T23:48Z] INFO  16:48:26,184 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@32d5a4c6
[2016-04-14T23:48Z] INFO  16:48:26,375 ProgressMeter -            done    121586.0    16.0 s       2.3 m       98.9%    16.0 s       0.0 s
[2016-04-14T23:48Z] INFO  16:48:26,376 ProgressMeter - Total runtime 16.82 secs, 0.28 min, 0.00 hours
[2016-04-14T23:48Z] INFO  16:48:26,376 MicroScheduler - 123 reads were filtered out during the traversal out of approximately 121709 total reads (0.10%)
[2016-04-14T23:48Z] INFO  16:48:26,376 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:48Z] INFO  16:48:26,377 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:48Z] INFO  16:48:26,377 MicroScheduler -   -> 123 reads (0.10% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:48Z] INFO  16:48:26,492 ProgressMeter -            done   1.5536605E7    17.0 s       1.0 s      100.0%    17.0 s       0.0 s
[2016-04-14T23:48Z] INFO  16:48:26,492 ProgressMeter - Total runtime 17.56 secs, 0.29 min, 0.00 hours
[2016-04-14T23:48Z] INFO  16:48:26,496 MicroScheduler - 14936 reads were filtered out during the traversal out of approximately 170525 total reads (8.76%)
[2016-04-14T23:48Z] INFO  16:48:26,497 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:48Z] INFO  16:48:26,497 MicroScheduler -   -> 474 reads (0.28% of total) failing BadMateFilter
[2016-04-14T23:48Z] INFO  16:48:26,497 MicroScheduler -   -> 13953 reads (8.18% of total) failing DuplicateReadFilter
[2016-04-14T23:48Z] INFO  16:48:26,498 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-14T23:48Z] INFO  16:48:26,498 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:48Z] INFO  16:48:26,498 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-14T23:48Z] INFO  16:48:26,498 MicroScheduler -   -> 509 reads (0.30% of total) failing MappingQualityZeroFilter
[2016-04-14T23:48Z] INFO  16:48:26,499 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:48Z] INFO  16:48:26,499 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-14T23:48Z] INFO  16:48:26,499 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-14T23:48Z] INFO  16:48:26,849 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:48Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-4_52709749_68338393-prep.bam
[2016-04-14T23:48Z] INFO  16:48:26,895 ProgressMeter -            done    369074.0    24.0 s      67.0 s      100.0%    24.0 s       0.0 s
[2016-04-14T23:48Z] INFO  16:48:26,896 ProgressMeter - Total runtime 24.78 secs, 0.41 min, 0.01 hours
[2016-04-14T23:48Z] INFO  16:48:26,899 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 369074 total reads (0.00%)
[2016-04-14T23:48Z] INFO  16:48:26,900 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:48Z] INFO  16:48:26,900 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:48Z] INFO  16:48:26,900 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:48Z] GATK pre-alignment ('5', 0, 15580921) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-14T23:48Z] INFO  16:48:27,953 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:48Z] INFO  16:48:27,956 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:48Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-4_134075461_150351181-prep-prealign.bam
[2016-04-14T23:48Z] GATK: realign ('4', 83857133, 99393738) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-14T23:48Z] GATK RealignerTargetCreator: R14-18105_kapa-NGv3-PE100-NGv3-sort-4_134075461_150351181-prep-prealign.bam 4:134075462-150351181
[2016-04-14T23:48Z] GATK: RealignerTargetCreator
[2016-04-14T23:48Z] INFO  16:48:28,481 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:48Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-3_112188604_127703121-prep.bam
[2016-04-14T23:48Z] INFO  16:48:28,746 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:48Z] INFO  16:48:28,749 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:48Z] INFO  16:48:28,749 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:48Z] INFO  16:48:28,750 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:48Z] INFO  16:48:28,754 HelpFormatter - Program Args: -T PrintReads -L 4:183267804-191154276 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/4/tx/tmpaOmxKF/R14-18105_kapa-NGv3-PE100-NGv3-sort-4_183267803_191154276-prep-prealign.bam
[2016-04-14T23:48Z] INFO  16:48:28,774 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:48Z] INFO  16:48:28,774 HelpFormatter - Date/Time: 2016/04/14 16:48:28
[2016-04-14T23:48Z] INFO  16:48:28,775 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:48Z] INFO  16:48:28,775 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:48Z] INFO  16:48:28,923 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:48Z] GATK pre-alignment ('5', 15616091, 31267808) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-14T23:48Z] INFO  16:48:29,980 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-14T23:48Z] INFO  16:48:30,050 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:48Z] INFO  16:48:30,049 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:48Z] INFO  16:48:30,052 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:48Z] INFO  16:48:30,053 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:48Z] INFO  16:48:30,053 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:48Z] INFO  16:48:30,058 HelpFormatter - Program Args: -T PrintReads -L 5:1-15580921 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/5/tx/tmph1BQHH/R14-18105_kapa-NGv3-PE100-NGv3-sort-5_0_15580921-prep-prealign.bam
[2016-04-14T23:48Z] INFO  16:48:30,058 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:48Z] INFO  16:48:30,067 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:48Z] INFO  16:48:30,067 HelpFormatter - Date/Time: 2016/04/14 16:48:30
[2016-04-14T23:48Z] INFO  16:48:30,068 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:48Z] INFO  16:48:30,069 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:48Z] INFO  16:48:30,122 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-14T23:48Z] INFO  16:48:30,144 IntervalUtils - Processing 7886473 bp from intervals
[2016-04-14T23:48Z] INFO  16:48:30,216 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:48Z] INFO  16:48:30,275 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:48Z] INFO  16:48:30,518 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:48Z] INFO  16:48:30,519 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:48Z] INFO  16:48:30,520 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:48Z] INFO  16:48:30,521 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:48Z] INFO  16:48:30,541 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:48Z] INFO  16:48:30,612 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:48Z] INFO  16:48:31,048 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:48Z] INFO  16:48:31,051 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:48Z] INFO  16:48:31,051 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:48Z] INFO  16:48:31,052 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:48Z] INFO  16:48:31,056 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/4/R14-18105_kapa-NGv3-PE100-NGv3-sort-4_83857133_99393738-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/4/R14-18105_kapa-NGv3-PE100-NGv3-sort-4_83857133_99393738-prep-prealign-realign.intervals -L 4:83857134-99393738 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/4/tx/tmpXXo3WW/R14-18105_kapa-NGv3-PE100-NGv3-sort-4_83857133_99393738-prep.bam
[2016-04-14T23:48Z] INFO  16:48:31,067 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:48Z] INFO  16:48:31,068 HelpFormatter - Date/Time: 2016/04/14 16:48:31
[2016-04-14T23:48Z] INFO  16:48:31,068 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:48Z] INFO  16:48:31,080 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:48Z] INFO  16:48:31,220 ProgressMeter -            done    346261.0    24.0 s      70.0 s      100.0%    24.0 s       0.0 s
[2016-04-14T23:48Z] INFO  16:48:31,220 ProgressMeter - Total runtime 24.44 secs, 0.41 min, 0.01 hours
[2016-04-14T23:48Z] INFO  16:48:31,224 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 346261 total reads (0.00%)
[2016-04-14T23:48Z] INFO  16:48:31,224 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:48Z] INFO  16:48:31,224 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:48Z] INFO  16:48:31,225 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:48Z] INFO  16:48:31,297 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:48Z] INFO  16:48:31,370 ProgressMeter -      3:62648033   1.550643E7    30.0 s       1.0 s      100.0%    30.0 s       0.0 s
[2016-04-14T23:48Z] INFO  16:48:31,432 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:48Z] INFO  16:48:31,441 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:48Z] INFO  16:48:31,453 ProgressMeter -            done   1.5518467E7    30.0 s       1.0 s      100.0%    30.0 s       0.0 s
[2016-04-14T23:48Z] INFO  16:48:31,454 ProgressMeter - Total runtime 30.12 secs, 0.50 min, 0.01 hours
[2016-04-14T23:48Z] INFO  16:48:31,458 MicroScheduler - 64553 reads were filtered out during the traversal out of approximately 772146 total reads (8.36%)
[2016-04-14T23:48Z] INFO  16:48:31,458 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:48Z] INFO  16:48:31,458 MicroScheduler -   -> 1405 reads (0.18% of total) failing BadMateFilter
[2016-04-14T23:48Z] INFO  16:48:31,459 MicroScheduler -   -> 61620 reads (7.98% of total) failing DuplicateReadFilter
[2016-04-14T23:48Z] INFO  16:48:31,459 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-14T23:48Z] INFO  16:48:31,459 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:48Z] INFO  16:48:31,460 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-14T23:48Z] INFO  16:48:31,460 MicroScheduler -   -> 1528 reads (0.20% of total) failing MappingQualityZeroFilter
[2016-04-14T23:48Z] INFO  16:48:31,460 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:48Z] INFO  16:48:31,460 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-14T23:48Z] INFO  16:48:31,461 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-14T23:48Z] INFO  16:48:31,530 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-14T23:48Z] INFO  16:48:31,529 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:48Z] INFO  16:48:31,532 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:48Z] INFO  16:48:31,533 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:48Z] INFO  16:48:31,534 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:48Z] INFO  16:48:31,538 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/4/R14-18105_kapa-NGv3-PE100-NGv3-sort-4_134075461_150351181-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/4/tx/tmp1c2Crf/R14-18105_kapa-NGv3-PE100-NGv3-sort-4_134075461_150351181-prep-prealign-realign.intervals -l INFO -L 4:134075462-150351181 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-14T23:48Z] INFO  16:48:31,552 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.11
[2016-04-14T23:48Z] INFO  16:48:31,558 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:48Z] INFO  16:48:31,566 HelpFormatter - Date/Time: 2016/04/14 16:48:31
[2016-04-14T23:48Z] INFO  16:48:31,567 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:48Z] INFO  16:48:31,568 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:48Z] INFO  16:48:31,598 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:48Z] INFO  16:48:31,623 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:48Z] INFO  16:48:31,691 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-14T23:48Z] INFO  16:48:31,698 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:48Z] INFO  16:48:31,705 IntervalUtils - Processing 15580921 bp from intervals
[2016-04-14T23:48Z] INFO  16:48:31,800 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:48Z] INFO  16:48:31,932 ProgressMeter -            done   1.6147618E7    18.0 s       1.0 s      100.0%    18.0 s       0.0 s
[2016-04-14T23:48Z] INFO  16:48:31,933 ProgressMeter - Total runtime 18.46 secs, 0.31 min, 0.01 hours
[2016-04-14T23:48Z] INFO  16:48:31,937 MicroScheduler - 16953 reads were filtered out during the traversal out of approximately 201899 total reads (8.40%)
[2016-04-14T23:48Z] INFO  16:48:31,938 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:48Z] INFO  16:48:31,938 MicroScheduler -   -> 636 reads (0.32% of total) failing BadMateFilter
[2016-04-14T23:48Z] INFO  16:48:31,939 MicroScheduler -   -> 15582 reads (7.72% of total) failing DuplicateReadFilter
[2016-04-14T23:48Z] INFO  16:48:31,940 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-14T23:48Z] INFO  16:48:31,940 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:48Z] INFO  16:48:31,948 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-14T23:48Z] INFO  16:48:31,949 IntervalUtils - Processing 15536605 bp from intervals
[2016-04-14T23:48Z] INFO  16:48:31,949 MicroScheduler -   -> 735 reads (0.36% of total) failing MappingQualityZeroFilter
[2016-04-14T23:48Z] WARN  16:48:31,954 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:48Z] INFO  16:48:31,954 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:48Z] INFO  16:48:31,954 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-14T23:48Z] INFO  16:48:31,954 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-14T23:48Z] INFO  16:48:31,961 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-14T23:48Z] INFO  16:48:31,983 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:48Z] INFO  16:48:32,043 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-14T23:48Z] INFO  16:48:32,053 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:48Z] INFO  16:48:32,097 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@41fd9d8e
[2016-04-14T23:48Z] INFO  16:48:32,116 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:48Z] INFO  16:48:32,118 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:48Z] INFO  16:48:32,118 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:48Z] INFO  16:48:32,119 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:48Z] INFO  16:48:32,132 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:48Z] INFO  16:48:32,175 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:48Z] INFO  16:48:32,176 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:48Z] INFO  16:48:32,177 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:48Z] INFO  16:48:32,177 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:48Z] INFO  16:48:32,280 ProgressMeter -            done    181084.0    24.0 s       2.3 m      100.0%    24.0 s       0.0 s
[2016-04-14T23:48Z] INFO  16:48:32,281 ProgressMeter - Total runtime 24.82 secs, 0.41 min, 0.01 hours
[2016-04-14T23:48Z] INFO  16:48:32,282 MicroScheduler - 152 reads were filtered out during the traversal out of approximately 181236 total reads (0.08%)
[2016-04-14T23:48Z] INFO  16:48:32,282 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:48Z] INFO  16:48:32,283 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:48Z] INFO  16:48:32,283 MicroScheduler -   -> 152 reads (0.08% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:48Z] INFO  16:48:32,289 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:48Z] INFO  16:48:32,343 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:48Z] INFO  16:48:32,434 IntervalUtils - Processing 16275720 bp from intervals
[2016-04-14T23:48Z] WARN  16:48:32,439 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:48Z] INFO  16:48:32,515 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:48Z] INFO  16:48:32,559 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:48Z] INFO  16:48:32,750 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:48Z] INFO  16:48:32,751 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:48Z] INFO  16:48:32,752 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:48Z] INFO  16:48:32,753 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-14T23:48Z] INFO  16:48:32,815 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:48Z] INFO  16:48:32,818 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:48Z] INFO  16:48:32,819 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:48Z] INFO  16:48:32,819 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:48Z] INFO  16:48:32,823 HelpFormatter - Program Args: -T PrintReads -L 5:15616092-31267808 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/5/tx/tmpFbvXmK/R14-18105_kapa-NGv3-PE100-NGv3-sort-5_15616091_31267808-prep-prealign.bam
[2016-04-14T23:48Z] INFO  16:48:32,845 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:48Z] INFO  16:48:32,846 HelpFormatter - Date/Time: 2016/04/14 16:48:32
[2016-04-14T23:48Z] INFO  16:48:32,846 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:48Z] INFO  16:48:32,847 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:48Z] INFO  16:48:32,913 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:48Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-3_127770401_143293035-prep.bam
[2016-04-14T23:48Z] INFO  16:48:32,997 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:48Z] INFO  16:48:33,050 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:48Z] GATK: realign ('3', 47129602, 62648069) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-14T23:48Z] INFO  16:48:33,381 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:48Z] GATK: realign ('4', 99397339, 115544957) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-14T23:48Z] INFO  16:48:33,604 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:48Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-4_115584857_134074404-prep-prealign.bam
[2016-04-14T23:48Z] GATK pre-alignment ('5', 31294068, 49695124) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-14T23:48Z] INFO  16:48:34,323 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-14T23:48Z] GATK RealignerTargetCreator: R14-18105_kapa-NGv3-PE100-NGv3-sort-4_115584857_134074404-prep-prealign.bam 4:115584858-134074404
[2016-04-14T23:48Z] GATK: RealignerTargetCreator
[2016-04-14T23:48Z] INFO  16:48:34,426 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:48Z] INFO  16:48:34,448 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:48Z] INFO  16:48:34,531 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-14T23:48Z] INFO  16:48:34,586 IntervalUtils - Processing 15651717 bp from intervals
[2016-04-14T23:48Z] INFO  16:48:34,695 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:48Z] INFO  16:48:34,976 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:48Z] INFO  16:48:34,979 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:48Z] INFO  16:48:34,991 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:48Z] INFO  16:48:34,992 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:48Z] INFO  16:48:35,015 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:48Z] INFO  16:48:35,224 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:48Z] INFO  16:48:36,180 ProgressMeter -            done    187687.0    16.0 s      85.0 s      100.0%    16.0 s       0.0 s
[2016-04-14T23:48Z] INFO  16:48:36,181 ProgressMeter - Total runtime 16.04 secs, 0.27 min, 0.00 hours
[2016-04-14T23:48Z] INFO  16:48:36,185 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 187687 total reads (0.00%)
[2016-04-14T23:48Z] INFO  16:48:36,187 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:48Z] INFO  16:48:36,188 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:48Z] INFO  16:48:36,188 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:48Z] INFO  16:48:36,288 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:48Z] INFO  16:48:36,292 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:48Z] INFO  16:48:36,292 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:48Z] INFO  16:48:36,293 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:48Z] INFO  16:48:36,298 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/3/R14-18105_kapa-NGv3-PE100-NGv3-sort-3_47129602_62648069-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/3/R14-18105_kapa-NGv3-PE100-NGv3-sort-3_47129602_62648069-prep-prealign-realign.intervals -L 3:47129603-62648069 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/3/tx/tmpKeSp64/R14-18105_kapa-NGv3-PE100-NGv3-sort-3_47129602_62648069-prep.bam
[2016-04-14T23:48Z] INFO  16:48:36,326 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:48Z] INFO  16:48:36,327 HelpFormatter - Date/Time: 2016/04/14 16:48:36
[2016-04-14T23:48Z] INFO  16:48:36,328 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:48Z] INFO  16:48:36,328 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:48Z] INFO  16:48:36,545 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:48Z] INFO  16:48:36,546 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:48Z] INFO  16:48:36,549 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:48Z] INFO  16:48:36,550 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:48Z] INFO  16:48:36,551 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:48Z] INFO  16:48:36,555 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/4/R14-18105_kapa-NGv3-PE100-NGv3-sort-4_99397339_115544957-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/4/R14-18105_kapa-NGv3-PE100-NGv3-sort-4_99397339_115544957-prep-prealign-realign.intervals -L 4:99397340-115544957 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/4/tx/tmpKFKycZ/R14-18105_kapa-NGv3-PE100-NGv3-sort-4_99397339_115544957-prep.bam
[2016-04-14T23:48Z] INFO  16:48:36,588 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:48Z] INFO  16:48:36,589 HelpFormatter - Date/Time: 2016/04/14 16:48:36
[2016-04-14T23:48Z] INFO  16:48:36,589 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:48Z] INFO  16:48:36,590 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:48Z] INFO  16:48:36,687 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:48Z] INFO  16:48:36,706 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:48Z] INFO  16:48:36,734 ProgressMeter -            done   1277936.0    78.0 s      61.0 s      100.0%    78.0 s       0.0 s
[2016-04-14T23:48Z] INFO  16:48:36,734 ProgressMeter - Total runtime 78.02 secs, 1.30 min, 0.02 hours
[2016-04-14T23:48Z] INFO  16:48:36,738 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 1277936 total reads (0.00%)
[2016-04-14T23:48Z] INFO  16:48:36,738 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:48Z] INFO  16:48:36,738 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:48Z] INFO  16:48:36,739 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:48Z] INFO  16:48:36,767 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-14T23:48Z] INFO  16:48:36,880 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:48Z] INFO  16:48:37,041 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:48Z] INFO  16:48:37,049 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:48Z] INFO  16:48:37,090 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:48Z] INFO  16:48:37,094 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:48Z] INFO  16:48:37,094 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:48Z] INFO  16:48:37,095 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:48Z] INFO  16:48:37,095 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.04
[2016-04-14T23:48Z] INFO  16:48:37,099 HelpFormatter - Program Args: -T PrintReads -L 5:31294069-49695124 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/5/tx/tmpYLCqCG/R14-18105_kapa-NGv3-PE100-NGv3-sort-5_31294068_49695124-prep-prealign.bam
[2016-04-14T23:48Z] INFO  16:48:37,118 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:48Z] INFO  16:48:37,119 HelpFormatter - Date/Time: 2016/04/14 16:48:37
[2016-04-14T23:48Z] INFO  16:48:37,120 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:48Z] INFO  16:48:37,120 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:48Z] INFO  16:48:37,261 IntervalUtils - Processing 15518467 bp from intervals
[2016-04-14T23:48Z] WARN  16:48:37,266 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:48Z] INFO  16:48:37,330 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:48Z] INFO  16:48:37,357 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:48Z] INFO  16:48:37,400 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:48Z] INFO  16:48:37,403 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:48Z] INFO  16:48:37,404 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:48Z] INFO  16:48:37,405 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:48Z] INFO  16:48:37,409 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/4/R14-18105_kapa-NGv3-PE100-NGv3-sort-4_115584857_134074404-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/4/tx/tmpLx5iMi/R14-18105_kapa-NGv3-PE100-NGv3-sort-4_115584857_134074404-prep-prealign-realign.intervals -l INFO -L 4:115584858-134074404 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-14T23:48Z] INFO  16:48:37,448 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:48Z] INFO  16:48:37,449 HelpFormatter - Date/Time: 2016/04/14 16:48:37
[2016-04-14T23:48Z] INFO  16:48:37,450 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:48Z] INFO  16:48:37,450 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:48Z] INFO  16:48:37,464 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@41fd9d8e
[2016-04-14T23:48Z] INFO  16:48:37,499 IntervalUtils - Processing 16147618 bp from intervals
[2016-04-14T23:48Z] WARN  16:48:37,504 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:48Z] INFO  16:48:37,529 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:48Z] INFO  16:48:37,530 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:48Z] INFO  16:48:37,531 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:48Z] INFO  16:48:37,532 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:48Z] INFO  16:48:37,581 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:48Z] INFO  16:48:37,670 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:48Z] INFO  16:48:37,670 ProgressMeter -            done    152066.0    21.0 s       2.4 m      100.0%    21.0 s       0.0 s
[2016-04-14T23:48Z] INFO  16:48:37,671 ProgressMeter - Total runtime 21.68 secs, 0.36 min, 0.01 hours
[2016-04-14T23:48Z] INFO  16:48:37,671 MicroScheduler - 105 reads were filtered out during the traversal out of approximately 152171 total reads (0.07%)
[2016-04-14T23:48Z] INFO  16:48:37,672 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:48Z] INFO  16:48:37,672 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:48Z] INFO  16:48:37,672 MicroScheduler -   -> 105 reads (0.07% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:48Z] INFO  16:48:37,736 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:48Z] INFO  16:48:37,747 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:48Z] INFO  16:48:37,748 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:48Z] INFO  16:48:37,749 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:48Z] INFO  16:48:37,750 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:48Z] INFO  16:48:37,882 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:48Z] INFO  16:48:37,919 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-14T23:48Z] INFO  16:48:37,933 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:48Z] INFO  16:48:37,943 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:48Z] INFO  16:48:38,000 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-14T23:48Z] INFO  16:48:38,110 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:48Z] INFO  16:48:38,374 IntervalUtils - Processing 18489547 bp from intervals
[2016-04-14T23:48Z] WARN  16:48:38,379 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:48Z] INFO  16:48:38,447 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-14T23:48Z] INFO  16:48:38,468 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:48Z] INFO  16:48:38,504 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:48Z] INFO  16:48:38,513 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:48Z] INFO  16:48:38,565 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-14T23:48Z] INFO  16:48:38,580 IntervalUtils - Processing 18401056 bp from intervals
[2016-04-14T23:48Z] INFO  16:48:38,615 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:48Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-1_143897546_159410511-prep.bam
[2016-04-14T23:48Z] INFO  16:48:38,667 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:48Z] INFO  16:48:38,668 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:48Z] INFO  16:48:38,669 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:48Z] INFO  16:48:38,670 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-14T23:48Z] INFO  16:48:38,704 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:48Z] INFO  16:48:38,848 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:48Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-4_36069528_52709433-prep.bam
[2016-04-14T23:48Z] INFO  16:48:39,022 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:48Z] INFO  16:48:39,022 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:48Z] INFO  16:48:39,023 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:48Z] INFO  16:48:39,023 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:48Z] INFO  16:48:39,057 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:48Z] INFO  16:48:39,242 ProgressMeter -            done   1.5511694E7    20.0 s       1.0 s      100.0%    20.0 s       0.0 s
[2016-04-14T23:48Z] INFO  16:48:39,243 ProgressMeter - Total runtime 20.33 secs, 0.34 min, 0.01 hours
[2016-04-14T23:48Z] INFO  16:48:39,247 MicroScheduler - 25370 reads were filtered out during the traversal out of approximately 278836 total reads (9.10%)
[2016-04-14T23:48Z] INFO  16:48:39,248 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:48Z] INFO  16:48:39,249 MicroScheduler -   -> 682 reads (0.24% of total) failing BadMateFilter
[2016-04-14T23:48Z] INFO  16:48:39,250 MicroScheduler -   -> 21422 reads (7.68% of total) failing DuplicateReadFilter
[2016-04-14T23:48Z] INFO  16:48:39,250 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-14T23:48Z] INFO  16:48:39,251 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:48Z] INFO  16:48:39,251 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-14T23:48Z] INFO  16:48:39,252 MicroScheduler -   -> 3266 reads (1.17% of total) failing MappingQualityZeroFilter
[2016-04-14T23:48Z] INFO  16:48:39,253 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:48Z] INFO  16:48:39,253 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-14T23:48Z] INFO  16:48:39,254 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-14T23:48Z] INFO  16:48:39,315 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:48Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-4_150354547_165878648-prep-prealign.bam
[2016-04-14T23:48Z] INFO  16:48:39,355 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:48Z] GATK pre-alignment ('5', 49695692, 65288736) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-14T23:48Z] GATK RealignerTargetCreator: R14-18105_kapa-NGv3-PE100-NGv3-sort-4_150354547_165878648-prep-prealign.bam 4:150354548-165878648
[2016-04-14T23:48Z] GATK: RealignerTargetCreator
[2016-04-14T23:48Z] INFO  16:48:40,577 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:48Z] GATK: realign ('4', 68340604, 83852298) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-14T23:48Z] GATK pre-alignment ('5', 65290574, 80809536) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-14T23:48Z] INFO  16:48:42,426 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@7172f77a
[2016-04-14T23:48Z] INFO  16:48:42,613 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:48Z] INFO  16:48:42,616 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:48Z] INFO  16:48:42,617 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:48Z] INFO  16:48:42,617 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:48Z] INFO  16:48:42,622 HelpFormatter - Program Args: -T PrintReads -L 5:49695693-65288736 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/5/tx/tmpJ7N0B1/R14-18105_kapa-NGv3-PE100-NGv3-sort-5_49695692_65288736-prep-prealign.bam
[2016-04-14T23:48Z] INFO  16:48:42,634 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:48Z] INFO  16:48:42,642 ProgressMeter -            done     96279.0    17.0 s       3.1 m      100.0%    17.0 s       0.0 s
[2016-04-14T23:48Z] INFO  16:48:42,643 ProgressMeter - Total runtime 17.86 secs, 0.30 min, 0.00 hours
[2016-04-14T23:48Z] INFO  16:48:42,643 MicroScheduler - 115 reads were filtered out during the traversal out of approximately 96394 total reads (0.12%)
[2016-04-14T23:48Z] INFO  16:48:42,643 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:48Z] INFO  16:48:42,644 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:48Z] INFO  16:48:42,644 MicroScheduler -   -> 115 reads (0.12% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:48Z] INFO  16:48:42,645 HelpFormatter - Date/Time: 2016/04/14 16:48:42
[2016-04-14T23:48Z] INFO  16:48:42,646 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:48Z] INFO  16:48:42,646 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:48Z] INFO  16:48:42,741 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:48Z] INFO  16:48:42,744 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:48Z] INFO  16:48:42,745 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:48Z] INFO  16:48:42,745 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:48Z] INFO  16:48:42,749 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/4/R14-18105_kapa-NGv3-PE100-NGv3-sort-4_150354547_165878648-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/4/tx/tmpk5IHEO/R14-18105_kapa-NGv3-PE100-NGv3-sort-4_150354547_165878648-prep-prealign-realign.intervals -l INFO -L 4:150354548-165878648 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-14T23:48Z] INFO  16:48:42,762 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:48Z] INFO  16:48:42,763 HelpFormatter - Date/Time: 2016/04/14 16:48:42
[2016-04-14T23:48Z] INFO  16:48:42,763 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:48Z] INFO  16:48:42,764 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:48Z] INFO  16:48:42,846 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:48Z] INFO  16:48:42,880 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:48Z] INFO  16:48:43,180 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-14T23:48Z] INFO  16:48:43,188 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:48Z] INFO  16:48:43,234 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.04
[2016-04-14T23:48Z] INFO  16:48:43,462 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:48Z] INFO  16:48:43,465 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:48Z] INFO  16:48:43,466 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:48Z] INFO  16:48:43,466 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:48Z] INFO  16:48:43,471 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/4/R14-18105_kapa-NGv3-PE100-NGv3-sort-4_68340604_83852298-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/4/R14-18105_kapa-NGv3-PE100-NGv3-sort-4_68340604_83852298-prep-prealign-realign.intervals -L 4:68340605-83852298 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/4/tx/tmpllr5D3/R14-18105_kapa-NGv3-PE100-NGv3-sort-4_68340604_83852298-prep.bam
[2016-04-14T23:48Z] INFO  16:48:43,482 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:48Z] INFO  16:48:43,483 HelpFormatter - Date/Time: 2016/04/14 16:48:43
[2016-04-14T23:48Z] INFO  16:48:43,483 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:48Z] INFO  16:48:43,484 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:48Z] INFO  16:48:43,493 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@7172f77a
[2016-04-14T23:48Z] INFO  16:48:43,578 ProgressMeter -            done     45555.0     8.0 s       3.1 m      100.0%     8.0 s       0.0 s
[2016-04-14T23:48Z] INFO  16:48:43,580 ProgressMeter - Total runtime 8.60 secs, 0.14 min, 0.00 hours
[2016-04-14T23:48Z] INFO  16:48:43,580 MicroScheduler - 94 reads were filtered out during the traversal out of approximately 45649 total reads (0.21%)
[2016-04-14T23:48Z] INFO  16:48:43,581 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:48Z] INFO  16:48:43,582 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:48Z] INFO  16:48:43,582 IntervalUtils - Processing 15524101 bp from intervals
[2016-04-14T23:48Z] INFO  16:48:43,582 MicroScheduler -   -> 94 reads (0.21% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:48Z] WARN  16:48:43,587 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:48Z] INFO  16:48:43,680 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:48Z] INFO  16:48:43,681 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:48Z] INFO  16:48:43,864 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:48Z] INFO  16:48:43,875 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:48Z] INFO  16:48:43,921 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.04
[2016-04-14T23:48Z] INFO  16:48:43,953 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:48Z] INFO  16:48:43,953 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:48Z] INFO  16:48:43,954 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:48Z] INFO  16:48:43,954 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-14T23:48Z] INFO  16:48:44,092 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-14T23:48Z] INFO  16:48:44,097 ProgressMeter -            done    290383.0    21.0 s      73.0 s      100.0%    21.0 s       0.0 s
[2016-04-14T23:48Z] INFO  16:48:44,098 ProgressMeter - Total runtime 21.38 secs, 0.36 min, 0.01 hours
[2016-04-14T23:48Z] INFO  16:48:44,101 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 290383 total reads (0.00%)
[2016-04-14T23:48Z] INFO  16:48:44,102 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:48Z] INFO  16:48:44,102 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:48Z] INFO  16:48:44,102 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:48Z] INFO  16:48:44,143 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:48Z] INFO  16:48:44,149 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:48Z] INFO  16:48:44,158 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:48Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-4_165889318_183245405-prep-prealign.bam
[2016-04-14T23:48Z] INFO  16:48:44,214 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-14T23:48Z] INFO  16:48:44,235 IntervalUtils - Processing 15593044 bp from intervals
[2016-04-14T23:48Z] INFO  16:48:44,299 IntervalUtils - Processing 15511694 bp from intervals
[2016-04-14T23:48Z] WARN  16:48:44,314 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:48Z] INFO  16:48:44,374 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:48Z] INFO  16:48:44,392 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:48Z] GATK RealignerTargetCreator: R14-18105_kapa-NGv3-PE100-NGv3-sort-4_165889318_183245405-prep-prealign.bam 4:165889319-183245405
[2016-04-14T23:48Z] GATK: RealignerTargetCreator
[2016-04-14T23:48Z] INFO  16:48:44,553 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:48Z] INFO  16:48:44,565 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:48Z] INFO  16:48:44,566 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:48Z] INFO  16:48:44,567 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:48Z] INFO  16:48:44,629 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:48Z] INFO  16:48:44,630 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:48Z] INFO  16:48:44,631 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:48Z] INFO  16:48:44,632 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:48Z] INFO  16:48:44,655 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:48Z] INFO  16:48:44,778 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:48Z] INFO  16:48:44,917 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:48Z] INFO  16:48:44,933 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:48Z] INFO  16:48:44,958 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:48Z] INFO  16:48:44,963 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:48Z] INFO  16:48:44,963 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:48Z] INFO  16:48:44,964 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:48Z] INFO  16:48:44,968 HelpFormatter - Program Args: -T PrintReads -L 5:65290575-80809536 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/5/tx/tmpfukqaP/R14-18105_kapa-NGv3-PE100-NGv3-sort-5_65290574_80809536-prep-prealign.bam
[2016-04-14T23:48Z] INFO  16:48:44,978 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:48Z] INFO  16:48:44,979 HelpFormatter - Date/Time: 2016/04/14 16:48:44
[2016-04-14T23:48Z] INFO  16:48:44,980 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:48Z] INFO  16:48:44,980 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:48Z] INFO  16:48:45,027 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:48Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-5_15616091_31267808-prep-prealign.bam
[2016-04-14T23:48Z] INFO  16:48:45,138 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:48Z] GATK RealignerTargetCreator: R14-18105_kapa-NGv3-PE100-NGv3-sort-5_15616091_31267808-prep-prealign.bam 5:15616092-31267808
[2016-04-14T23:48Z] GATK: RealignerTargetCreator
[2016-04-14T23:48Z] INFO  16:48:45,714 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:48Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-3_174814579_190326970-prep.bam
[2016-04-14T23:48Z] INFO  16:48:46,037 ProgressMeter -       4:9355623    700030.0    90.0 s       2.1 m       60.3%     2.5 m      59.0 s
[2016-04-14T23:48Z] INFO  16:48:46,403 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-14T23:48Z] INFO  16:48:46,467 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:48Z] INFO  16:48:46,476 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:48Z] INFO  16:48:46,560 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-14T23:48Z] INFO  16:48:46,587 IntervalUtils - Processing 15518962 bp from intervals
[2016-04-14T23:48Z] INFO  16:48:46,737 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:48Z] GATK pre-alignment ('5', 80911291, 96430739) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-14T23:48Z] INFO  16:48:47,208 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:48Z] INFO  16:48:47,220 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:48Z] INFO  16:48:47,221 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:48Z] INFO  16:48:47,221 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:48Z] INFO  16:48:47,252 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:48Z] INFO  16:48:47,439 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:48Z] INFO  16:48:47,487 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:48Z] INFO  16:48:47,490 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:48Z] INFO  16:48:47,491 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:48Z] INFO  16:48:47,491 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:48Z] INFO  16:48:47,496 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/4/R14-18105_kapa-NGv3-PE100-NGv3-sort-4_165889318_183245405-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/4/tx/tmpryUXFI/R14-18105_kapa-NGv3-PE100-NGv3-sort-4_165889318_183245405-prep-prealign-realign.intervals -l INFO -L 4:165889319-183245405 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-14T23:48Z] INFO  16:48:47,505 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:48Z] INFO  16:48:47,505 HelpFormatter - Date/Time: 2016/04/14 16:48:47
[2016-04-14T23:48Z] INFO  16:48:47,505 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:48Z] INFO  16:48:47,505 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:48Z] INFO  16:48:47,612 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:48Z] INFO  16:48:47,799 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-14T23:48Z] INFO  16:48:47,809 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:48Z] INFO  16:48:47,853 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.04
[2016-04-14T23:48Z] INFO  16:48:48,220 IntervalUtils - Processing 17356087 bp from intervals
[2016-04-14T23:48Z] WARN  16:48:48,225 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:48Z] INFO  16:48:48,365 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:48Z] INFO  16:48:48,409 ProgressMeter -            done    169724.0    16.0 s      95.0 s      100.0%    16.0 s       0.0 s
[2016-04-14T23:48Z] INFO  16:48:48,410 ProgressMeter - Total runtime 16.23 secs, 0.27 min, 0.00 hours
[2016-04-14T23:48Z] INFO  16:48:48,414 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 169724 total reads (0.00%)
[2016-04-14T23:48Z] INFO  16:48:48,415 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:48Z] INFO  16:48:48,416 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:48Z] INFO  16:48:48,433 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:48Z] INFO  16:48:48,487 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:48Z] INFO  16:48:48,492 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:48Z] INFO  16:48:48,493 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:48Z] INFO  16:48:48,493 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:48Z] INFO  16:48:48,498 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/5/R14-18105_kapa-NGv3-PE100-NGv3-sort-5_15616091_31267808-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/5/tx/tmpIHlDqJ/R14-18105_kapa-NGv3-PE100-NGv3-sort-5_15616091_31267808-prep-prealign-realign.intervals -l INFO -L 5:15616092-31267808 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-14T23:48Z] INFO  16:48:48,508 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:48Z] INFO  16:48:48,508 HelpFormatter - Date/Time: 2016/04/14 16:48:48
[2016-04-14T23:48Z] INFO  16:48:48,508 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:48Z] INFO  16:48:48,509 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:48Z] INFO  16:48:48,532 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:48Z] INFO  16:48:48,533 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:48Z] INFO  16:48:48,533 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:48Z] INFO  16:48:48,534 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-14T23:48Z] INFO  16:48:48,622 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:48Z] INFO  16:48:48,902 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-14T23:48Z] INFO  16:48:48,913 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:48Z] INFO  16:48:49,003 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.09
[2016-04-14T23:48Z] INFO  16:48:49,412 IntervalUtils - Processing 15651717 bp from intervals
[2016-04-14T23:48Z] WARN  16:48:49,417 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:48Z] INFO  16:48:49,489 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:48Z] INFO  16:48:49,628 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:48Z] INFO  16:48:49,629 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:48Z] INFO  16:48:49,630 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:48Z] INFO  16:48:49,631 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-14T23:48Z] INFO  16:48:49,785 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:48Z] INFO  16:48:49,788 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:48Z] INFO  16:48:49,789 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:48Z] INFO  16:48:49,789 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:48Z] INFO  16:48:49,794 HelpFormatter - Program Args: -T PrintReads -L 5:80911292-96430739 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/5/tx/tmpTVzgfe/R14-18105_kapa-NGv3-PE100-NGv3-sort-5_80911291_96430739-prep-prealign.bam
[2016-04-14T23:48Z] INFO  16:48:49,824 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:48Z] INFO  16:48:49,825 HelpFormatter - Date/Time: 2016/04/14 16:48:49
[2016-04-14T23:48Z] INFO  16:48:49,826 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:48Z] INFO  16:48:49,827 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:48Z] INFO  16:48:50,001 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:48Z] INFO  16:48:50,055 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:48Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-4_83857133_99393738-prep.bam
[2016-04-14T23:48Z] INFO  16:48:50,093 ProgressMeter -            done   1.627572E7    17.0 s       1.0 s      100.0%    17.0 s       0.0 s
[2016-04-14T23:48Z] INFO  16:48:50,093 ProgressMeter - Total runtime 17.34 secs, 0.29 min, 0.00 hours
[2016-04-14T23:48Z] INFO  16:48:50,097 MicroScheduler - 10689 reads were filtered out during the traversal out of approximately 122301 total reads (8.74%)
[2016-04-14T23:48Z] INFO  16:48:50,097 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:48Z] INFO  16:48:50,098 MicroScheduler -   -> 450 reads (0.37% of total) failing BadMateFilter
[2016-04-14T23:48Z] INFO  16:48:50,098 MicroScheduler -   -> 9490 reads (7.76% of total) failing DuplicateReadFilter
[2016-04-14T23:48Z] INFO  16:48:50,098 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-14T23:48Z] INFO  16:48:50,098 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:48Z] INFO  16:48:50,099 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-14T23:48Z] INFO  16:48:50,099 MicroScheduler -   -> 749 reads (0.61% of total) failing MappingQualityZeroFilter
[2016-04-14T23:48Z] INFO  16:48:50,099 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:48Z] INFO  16:48:50,099 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-14T23:48Z] INFO  16:48:50,100 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-14T23:48Z] GATK pre-alignment ('5', 96432513, 112043579) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-14T23:48Z] INFO  16:48:51,044 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-14T23:48Z] INFO  16:48:51,149 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:48Z] INFO  16:48:51,169 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:48Z] INFO  16:48:51,240 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-14T23:48Z] INFO  16:48:51,254 IntervalUtils - Processing 15519448 bp from intervals
[2016-04-14T23:48Z] INFO  16:48:51,372 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:48Z] INFO  16:48:51,535 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:48Z] GATK: realign ('4', 134075461, 150351181) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-14T23:48Z] INFO  16:48:51,671 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:48Z] INFO  16:48:51,672 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:48Z] INFO  16:48:51,673 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:48Z] INFO  16:48:51,674 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:48Z] INFO  16:48:51,696 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:48Z] INFO  16:48:51,845 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:48Z] INFO  16:48:53,487 ProgressMeter -            done    200724.0    15.0 s      78.0 s      100.0%    15.0 s       0.0 s
[2016-04-14T23:48Z] INFO  16:48:53,488 ProgressMeter - Total runtime 15.74 secs, 0.26 min, 0.00 hours
[2016-04-14T23:48Z] INFO  16:48:53,491 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 200724 total reads (0.00%)
[2016-04-14T23:48Z] INFO  16:48:53,492 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:48Z] INFO  16:48:53,492 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:48Z] INFO  16:48:53,493 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:48Z] INFO  16:48:53,856 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:48Z] INFO  16:48:53,860 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:48Z] INFO  16:48:53,860 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:48Z] INFO  16:48:53,861 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:48Z] INFO  16:48:53,866 HelpFormatter - Program Args: -T PrintReads -L 5:96432514-112043579 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/5/tx/tmpHaf8_l/R14-18105_kapa-NGv3-PE100-NGv3-sort-5_96432513_112043579-prep-prealign.bam
[2016-04-14T23:48Z] INFO  16:48:53,897 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:48Z] INFO  16:48:53,898 HelpFormatter - Date/Time: 2016/04/14 16:48:53
[2016-04-14T23:48Z] INFO  16:48:53,899 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:48Z] INFO  16:48:53,899 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:48Z] INFO  16:48:54,116 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:48Z] INFO  16:48:54,584 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:48Z] INFO  16:48:54,587 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:48Z] INFO  16:48:54,588 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:48Z] INFO  16:48:54,589 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:48Z] INFO  16:48:54,593 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/4/R14-18105_kapa-NGv3-PE100-NGv3-sort-4_134075461_150351181-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/4/R14-18105_kapa-NGv3-PE100-NGv3-sort-4_134075461_150351181-prep-prealign-realign.intervals -L 4:134075462-150351181 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/4/tx/tmpfQooK6/R14-18105_kapa-NGv3-PE100-NGv3-sort-4_134075461_150351181-prep.bam
[2016-04-14T23:48Z] INFO  16:48:54,603 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:48Z] INFO  16:48:54,604 HelpFormatter - Date/Time: 2016/04/14 16:48:54
[2016-04-14T23:48Z] INFO  16:48:54,604 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:48Z] INFO  16:48:54,605 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:48Z] INFO  16:48:54,846 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:48Z] INFO  16:48:54,968 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:48Z] INFO  16:48:54,978 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:48Z] INFO  16:48:55,045 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-14T23:48Z] INFO  16:48:55,065 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:48Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-4_99397339_115544957-prep.bam
[2016-04-14T23:48Z] INFO  16:48:55,133 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-14T23:48Z] INFO  16:48:55,204 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:48Z] INFO  16:48:55,214 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:48Z] INFO  16:48:55,279 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-14T23:48Z] INFO  16:48:55,296 IntervalUtils - Processing 15611066 bp from intervals
[2016-04-14T23:48Z] INFO  16:48:55,410 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:48Z] INFO  16:48:55,462 IntervalUtils - Processing 16275720 bp from intervals
[2016-04-14T23:48Z] WARN  16:48:55,478 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:48Z] INFO  16:48:55,561 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:48Z] INFO  16:48:55,698 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@32d5a4c6
[2016-04-14T23:48Z] INFO  16:48:55,755 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:48Z] INFO  16:48:55,756 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:48Z] INFO  16:48:55,756 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:48Z] INFO  16:48:55,757 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:48Z] INFO  16:48:55,760 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:48Z] INFO  16:48:55,761 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:48Z] INFO  16:48:55,761 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:48Z] INFO  16:48:55,762 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:48Z] GATK pre-alignment ('5', 112073555, 127595521) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-14T23:48Z] INFO  16:48:55,787 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:48Z] INFO  16:48:55,902 ProgressMeter -            done    145401.0    25.0 s       2.9 m       97.4%    25.0 s       0.0 s
[2016-04-14T23:48Z] INFO  16:48:55,902 ProgressMeter - Total runtime 25.38 secs, 0.42 min, 0.01 hours
[2016-04-14T23:48Z] INFO  16:48:55,903 MicroScheduler - 75 reads were filtered out during the traversal out of approximately 145476 total reads (0.05%)
[2016-04-14T23:48Z] INFO  16:48:55,909 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:48Z] INFO  16:48:55,909 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:48Z] INFO  16:48:55,910 MicroScheduler -   -> 75 reads (0.05% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:48Z] INFO  16:48:55,938 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:48Z] INFO  16:48:55,950 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:48Z] INFO  16:48:56,102 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:48Z] INFO  16:48:57,478 ProgressMeter -            done   1.8489547E7    18.0 s       1.0 s      100.0%    18.0 s       0.0 s
[2016-04-14T23:48Z] INFO  16:48:57,479 ProgressMeter - Total runtime 18.81 secs, 0.31 min, 0.01 hours
[2016-04-14T23:48Z] INFO  16:48:57,483 MicroScheduler - 17528 reads were filtered out during the traversal out of approximately 182309 total reads (9.61%)
[2016-04-14T23:48Z] INFO  16:48:57,483 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:48Z] INFO  16:48:57,484 MicroScheduler -   -> 559 reads (0.31% of total) failing BadMateFilter
[2016-04-14T23:48Z] INFO  16:48:57,484 MicroScheduler -   -> 14082 reads (7.72% of total) failing DuplicateReadFilter
[2016-04-14T23:48Z] INFO  16:48:57,484 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-14T23:48Z] INFO  16:48:57,484 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:48Z] INFO  16:48:57,485 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-14T23:48Z] INFO  16:48:57,485 MicroScheduler -   -> 2887 reads (1.58% of total) failing MappingQualityZeroFilter
[2016-04-14T23:48Z] INFO  16:48:57,485 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:48Z] INFO  16:48:57,485 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-14T23:48Z] INFO  16:48:57,485 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-14T23:48Z] INFO  16:48:57,526 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:48Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-4_183267803_191154276-prep-prealign.bam
[2016-04-14T23:48Z] INFO  16:48:57,888 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@41fd9d8e
[2016-04-14T23:48Z] INFO  16:48:57,982 ProgressMeter -            done    903910.0   102.0 s     112.0 s      100.0%   102.0 s       0.0 s
[2016-04-14T23:48Z] INFO  16:48:57,982 ProgressMeter - Total runtime 102.13 secs, 1.70 min, 0.03 hours
[2016-04-14T23:48Z] INFO  16:48:57,982 MicroScheduler - 353 reads were filtered out during the traversal out of approximately 904263 total reads (0.04%)
[2016-04-14T23:48Z] INFO  16:48:57,983 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:48Z] INFO  16:48:57,983 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:48Z] INFO  16:48:57,983 MicroScheduler -   -> 353 reads (0.04% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:48Z] GATK RealignerTargetCreator: R14-18105_kapa-NGv3-PE100-NGv3-sort-4_183267803_191154276-prep-prealign.bam 4:183267804-191154276
[2016-04-14T23:48Z] GATK: RealignerTargetCreator
[2016-04-14T23:48Z] INFO  16:48:58,588 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:48Z] INFO  16:48:58,592 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:48Z] INFO  16:48:58,592 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:48Z] INFO  16:48:58,593 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:48Z] INFO  16:48:58,597 HelpFormatter - Program Args: -T PrintReads -L 5:112073556-127595521 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/5/tx/tmpsYmr14/R14-18105_kapa-NGv3-PE100-NGv3-sort-5_112073555_127595521-prep-prealign.bam
[2016-04-14T23:48Z] INFO  16:48:58,622 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:48Z] INFO  16:48:58,623 HelpFormatter - Date/Time: 2016/04/14 16:48:58
[2016-04-14T23:48Z] INFO  16:48:58,624 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:48Z] INFO  16:48:58,624 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:48Z] INFO  16:48:58,795 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:48Z] INFO  16:48:58,946 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:48Z] GATK: realign ('4', 115584857, 134074404) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-14T23:48Z] INFO  16:48:59,391 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:48Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-4_0_15511864-prep-prealign.bam
[2016-04-14T23:48Z] INFO  16:48:59,878 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-14T23:48Z] INFO  16:48:59,950 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:48Z] INFO  16:48:59,959 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:49Z] INFO  16:49:00,005 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-14T23:49Z] INFO  16:49:00,023 IntervalUtils - Processing 15521966 bp from intervals
[2016-04-14T23:49Z] INFO  16:49:00,167 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:49Z] INFO  16:49:00,464 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:49Z] INFO  16:49:00,465 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:49Z] INFO  16:49:00,466 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:49Z] INFO  16:49:00,467 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:49Z] INFO  16:49:00,481 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:49Z] INFO  16:49:00,620 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:49Z] INFO  16:49:01,018 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:49Z] INFO  16:49:01,021 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:49Z] INFO  16:49:01,021 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:49Z] INFO  16:49:01,022 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:49Z] INFO  16:49:01,027 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/4/R14-18105_kapa-NGv3-PE100-NGv3-sort-4_183267803_191154276-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/4/tx/tmp_kBQXw/R14-18105_kapa-NGv3-PE100-NGv3-sort-4_183267803_191154276-prep-prealign-realign.intervals -l INFO -L 4:183267804-191154276 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-14T23:49Z] INFO  16:49:01,036 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:49Z] INFO  16:49:01,039 HelpFormatter - Date/Time: 2016/04/14 16:49:01
[2016-04-14T23:49Z] INFO  16:49:01,041 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:49Z] INFO  16:49:01,042 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:49Z] INFO  16:49:01,194 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:49Z] INFO  16:49:01,479 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-14T23:49Z] INFO  16:49:01,491 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:49Z] INFO  16:49:01,554 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-14T23:49Z] INFO  16:49:01,820 ProgressMeter -            done   1.5524101E7    17.0 s       1.0 s      100.0%    17.0 s       0.0 s
[2016-04-14T23:49Z] INFO  16:49:01,821 ProgressMeter - Total runtime 17.87 secs, 0.30 min, 0.00 hours
[2016-04-14T23:49Z] INFO  16:49:01,824 MicroScheduler - 13073 reads were filtered out during the traversal out of approximately 152798 total reads (8.56%)
[2016-04-14T23:49Z] INFO  16:49:01,825 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:49Z] INFO  16:49:01,825 MicroScheduler -   -> 511 reads (0.33% of total) failing BadMateFilter
[2016-04-14T23:49Z] INFO  16:49:01,825 MicroScheduler -   -> 11993 reads (7.85% of total) failing DuplicateReadFilter
[2016-04-14T23:49Z] INFO  16:49:01,826 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-14T23:49Z] INFO  16:49:01,826 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:49Z] INFO  16:49:01,826 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-14T23:49Z] INFO  16:49:01,826 MicroScheduler -   -> 569 reads (0.37% of total) failing MappingQualityZeroFilter
[2016-04-14T23:49Z] INFO  16:49:01,827 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:49Z] INFO  16:49:01,827 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-14T23:49Z] INFO  16:49:01,827 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-14T23:49Z] INFO  16:49:01,944 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:49Z] INFO  16:49:01,949 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:49Z] INFO  16:49:01,949 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:49Z] INFO  16:49:01,949 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:49Z] INFO  16:49:01,954 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/4/R14-18105_kapa-NGv3-PE100-NGv3-sort-4_115584857_134074404-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/4/R14-18105_kapa-NGv3-PE100-NGv3-sort-4_115584857_134074404-prep-prealign-realign.intervals -L 4:115584858-134074404 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/4/tx/tmpJPEGGC/R14-18105_kapa-NGv3-PE100-NGv3-sort-4_115584857_134074404-prep.bam
[2016-04-14T23:49Z] INFO  16:49:01,975 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:49Z] INFO  16:49:01,976 HelpFormatter - Date/Time: 2016/04/14 16:49:01
[2016-04-14T23:49Z] INFO  16:49:01,977 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:49Z] INFO  16:49:01,977 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:49Z] INFO  16:49:02,014 IntervalUtils - Processing 7886473 bp from intervals
[2016-04-14T23:49Z] WARN  16:49:02,020 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:49Z] INFO  16:49:02,123 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@41fd9d8e
[2016-04-14T23:49Z] GATK RealignerTargetCreator: R14-18105_kapa-NGv3-PE100-NGv3-sort-4_0_15511864-prep-prealign.bam 4:1-15511864
[2016-04-14T23:49Z] GATK: RealignerTargetCreator
[2016-04-14T23:49Z] INFO  16:49:02,150 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:49Z] INFO  16:49:02,152 ProgressMeter -      5:15580929    200005.0    30.0 s       2.5 m      100.0%    30.0 s       0.0 s
[2016-04-14T23:49Z] INFO  16:49:02,222 ProgressMeter -            done    227103.0    30.0 s       2.2 m      100.0%    30.0 s       0.0 s
[2016-04-14T23:49Z] INFO  16:49:02,222 ProgressMeter - Total runtime 30.10 secs, 0.50 min, 0.01 hours
[2016-04-14T23:49Z] INFO  16:49:02,223 MicroScheduler - 182 reads were filtered out during the traversal out of approximately 227285 total reads (0.08%)
[2016-04-14T23:49Z] INFO  16:49:02,223 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:49Z] INFO  16:49:02,224 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:49Z] INFO  16:49:02,224 MicroScheduler -   -> 182 reads (0.08% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:49Z] INFO  16:49:02,252 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:49Z] INFO  16:49:02,365 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:49Z] INFO  16:49:02,366 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:49Z] INFO  16:49:02,366 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:49Z] INFO  16:49:02,366 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-14T23:49Z] INFO  16:49:02,422 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:49Z] INFO  16:49:02,442 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:49Z] INFO  16:49:02,558 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.12
[2016-04-14T23:49Z] INFO  16:49:02,970 IntervalUtils - Processing 18489547 bp from intervals
[2016-04-14T23:49Z] WARN  16:49:02,975 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:49Z] INFO  16:49:03,041 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:49Z] INFO  16:49:03,195 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:49Z] INFO  16:49:03,208 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:49Z] INFO  16:49:03,210 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:49Z] INFO  16:49:03,210 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:49Z] INFO  16:49:03,211 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:49Z] GATK: realign ('4', 150354547, 165878648) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-14T23:49Z] INFO  16:49:03,496 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:49Z] INFO  16:49:03,564 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:49Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-5_0_15580921-prep-prealign.bam
[2016-04-14T23:49Z] INFO  16:49:03,668 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:49Z] GATK RealignerTargetCreator: R14-18105_kapa-NGv3-PE100-NGv3-sort-5_0_15580921-prep-prealign.bam 5:1-15580921
[2016-04-14T23:49Z] GATK: RealignerTargetCreator
[2016-04-14T23:49Z] INFO  16:49:04,644 ProgressMeter -            done   1.5651717E7    15.0 s       0.0 s      100.0%    15.0 s       0.0 s
[2016-04-14T23:49Z] INFO  16:49:04,645 ProgressMeter - Total runtime 15.02 secs, 0.25 min, 0.00 hours
[2016-04-14T23:49Z] INFO  16:49:04,648 MicroScheduler - 5181 reads were filtered out during the traversal out of approximately 46092 total reads (11.24%)
[2016-04-14T23:49Z] INFO  16:49:04,649 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:49Z] INFO  16:49:04,649 MicroScheduler -   -> 305 reads (0.66% of total) failing BadMateFilter
[2016-04-14T23:49Z] INFO  16:49:04,650 MicroScheduler -   -> 3583 reads (7.77% of total) failing DuplicateReadFilter
[2016-04-14T23:49Z] INFO  16:49:04,650 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-14T23:49Z] INFO  16:49:04,651 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:49Z] INFO  16:49:04,651 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-14T23:49Z] INFO  16:49:04,651 MicroScheduler -   -> 1293 reads (2.81% of total) failing MappingQualityZeroFilter
[2016-04-14T23:49Z] INFO  16:49:04,651 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:49Z] INFO  16:49:04,651 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-14T23:49Z] INFO  16:49:04,652 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-14T23:49Z] INFO  16:49:04,897 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:49Z] INFO  16:49:04,900 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:49Z] INFO  16:49:04,901 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:49Z] INFO  16:49:04,902 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:49Z] INFO  16:49:04,906 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/4/R14-18105_kapa-NGv3-PE100-NGv3-sort-4_0_15511864-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/4/tx/tmpxkedXU/R14-18105_kapa-NGv3-PE100-NGv3-sort-4_0_15511864-prep-prealign-realign.intervals -l INFO -L 4:1-15511864 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-14T23:49Z] INFO  16:49:04,913 ProgressMeter -            done    277042.0    20.0 s      73.0 s      100.0%    20.0 s       0.0 s
[2016-04-14T23:49Z] INFO  16:49:04,914 ProgressMeter - Total runtime 20.35 secs, 0.34 min, 0.01 hours
[2016-04-14T23:49Z] INFO  16:49:04,917 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 277042 total reads (0.00%)
[2016-04-14T23:49Z] INFO  16:49:04,918 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:49Z] INFO  16:49:04,918 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:49Z] INFO  16:49:04,918 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:49Z] INFO  16:49:04,929 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:49Z] INFO  16:49:04,931 HelpFormatter - Date/Time: 2016/04/14 16:49:04
[2016-04-14T23:49Z] INFO  16:49:04,931 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:49Z] INFO  16:49:04,932 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:49Z] INFO  16:49:05,066 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:49Z] INFO  16:49:05,285 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@6834dd3c
[2016-04-14T23:49Z] INFO  16:49:05,286 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-14T23:49Z] INFO  16:49:05,296 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:49Z] INFO  16:49:05,361 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-14T23:49Z] INFO  16:49:05,433 ProgressMeter -            done    140505.0    20.0 s       2.5 m      100.0%    20.0 s       0.0 s
[2016-04-14T23:49Z] INFO  16:49:05,433 ProgressMeter - Total runtime 20.80 secs, 0.35 min, 0.01 hours
[2016-04-14T23:49Z] INFO  16:49:05,434 MicroScheduler - 137 reads were filtered out during the traversal out of approximately 140642 total reads (0.10%)
[2016-04-14T23:49Z] INFO  16:49:05,434 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:49Z] INFO  16:49:05,434 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:49Z] INFO  16:49:05,435 MicroScheduler -   -> 137 reads (0.10% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:49Z] INFO  16:49:05,599 IntervalUtils - Processing 15511864 bp from intervals
[2016-04-14T23:49Z] WARN  16:49:05,604 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:49Z] INFO  16:49:05,706 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:49Z] INFO  16:49:05,910 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:49Z] INFO  16:49:05,911 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:49Z] INFO  16:49:05,912 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:49Z] INFO  16:49:05,912 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-14T23:49Z] INFO  16:49:05,936 ProgressMeter -            done   1.7356087E7    17.0 s       1.0 s      100.0%    17.0 s       0.0 s
[2016-04-14T23:49Z] INFO  16:49:05,938 ProgressMeter - Total runtime 17.41 secs, 0.29 min, 0.00 hours
[2016-04-14T23:49Z] INFO  16:49:05,941 MicroScheduler - 8565 reads were filtered out during the traversal out of approximately 96634 total reads (8.86%)
[2016-04-14T23:49Z] INFO  16:49:05,943 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:49Z] INFO  16:49:05,944 MicroScheduler -   -> 476 reads (0.49% of total) failing BadMateFilter
[2016-04-14T23:49Z] INFO  16:49:05,944 MicroScheduler -   -> 7404 reads (7.66% of total) failing DuplicateReadFilter
[2016-04-14T23:49Z] INFO  16:49:05,944 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-14T23:49Z] INFO  16:49:05,945 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:49Z] INFO  16:49:05,945 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-14T23:49Z] INFO  16:49:05,945 MicroScheduler -   -> 685 reads (0.71% of total) failing MappingQualityZeroFilter
[2016-04-14T23:49Z] INFO  16:49:05,945 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:49Z] INFO  16:49:05,946 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-14T23:49Z] INFO  16:49:05,946 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-14T23:49Z] INFO  16:49:06,076 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:49Z] INFO  16:49:06,079 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:49Z] INFO  16:49:06,080 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:49Z] INFO  16:49:06,080 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:49Z] INFO  16:49:06,085 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/4/R14-18105_kapa-NGv3-PE100-NGv3-sort-4_150354547_165878648-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/4/R14-18105_kapa-NGv3-PE100-NGv3-sort-4_150354547_165878648-prep-prealign-realign.intervals -L 4:150354548-165878648 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/4/tx/tmpQrsoGu/R14-18105_kapa-NGv3-PE100-NGv3-sort-4_150354547_165878648-prep.bam
[2016-04-14T23:49Z] INFO  16:49:06,095 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:49Z] INFO  16:49:06,096 HelpFormatter - Date/Time: 2016/04/14 16:49:06
[2016-04-14T23:49Z] INFO  16:49:06,096 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:49Z] INFO  16:49:06,097 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:49Z] INFO  16:49:06,187 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:49Z] GATK: realign ('5', 15616091, 31267808) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-14T23:49Z] INFO  16:49:06,279 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:49Z] INFO  16:49:06,422 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:49Z] INFO  16:49:06,430 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:49Z] INFO  16:49:06,440 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:49Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-4_68340604_83852298-prep.bam
[2016-04-14T23:49Z] INFO  16:49:06,508 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-14T23:49Z] INFO  16:49:06,767 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:49Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-5_49695692_65288736-prep-prealign.bam
[2016-04-14T23:49Z] INFO  16:49:06,837 IntervalUtils - Processing 15524101 bp from intervals
[2016-04-14T23:49Z] WARN  16:49:06,842 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:49Z] INFO  16:49:06,950 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:49Z] INFO  16:49:07,033 ProgressMeter -            done    121586.0    11.0 s      92.0 s       98.9%    11.0 s       0.0 s
[2016-04-14T23:49Z] INFO  16:49:07,033 ProgressMeter - Total runtime 11.28 secs, 0.19 min, 0.00 hours
[2016-04-14T23:49Z] INFO  16:49:07,037 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 121586 total reads (0.00%)
[2016-04-14T23:49Z] INFO  16:49:07,037 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:49Z] INFO  16:49:07,038 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:49Z] INFO  16:49:07,038 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:49Z] INFO  16:49:07,071 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:49Z] INFO  16:49:07,072 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:49Z] INFO  16:49:07,073 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:49Z] INFO  16:49:07,074 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:49Z] INFO  16:49:07,213 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:49Z] INFO  16:49:07,240 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:49Z] GATK: realign ('4', 165889318, 183245405) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-14T23:49Z] GATK RealignerTargetCreator: R14-18105_kapa-NGv3-PE100-NGv3-sort-5_49695692_65288736-prep-prealign.bam 5:49695693-65288736
[2016-04-14T23:49Z] GATK: RealignerTargetCreator
[2016-04-14T23:49Z] INFO  16:49:07,336 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:49Z] INFO  16:49:07,338 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:49Z] INFO  16:49:07,339 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:49Z] INFO  16:49:07,339 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:49Z] INFO  16:49:07,343 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/5/R14-18105_kapa-NGv3-PE100-NGv3-sort-5_0_15580921-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/5/tx/tmpJIOefw/R14-18105_kapa-NGv3-PE100-NGv3-sort-5_0_15580921-prep-prealign-realign.intervals -l INFO -L 5:1-15580921 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-14T23:49Z] INFO  16:49:07,351 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:49Z] INFO  16:49:07,352 HelpFormatter - Date/Time: 2016/04/14 16:49:07
[2016-04-14T23:49Z] INFO  16:49:07,352 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:49Z] INFO  16:49:07,353 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:49Z] INFO  16:49:07,388 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:49Z] GATK pre-alignment ('5', 127597427, 143191869) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-14T23:49Z] INFO  16:49:07,495 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:49Z] INFO  16:49:07,741 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-14T23:49Z] INFO  16:49:07,751 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:49Z] INFO  16:49:07,823 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-14T23:49Z] INFO  16:49:07,886 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@7172f77a
[2016-04-14T23:49Z] INFO  16:49:08,086 ProgressMeter -            done     67730.0    12.0 s       3.0 m      100.0%    12.0 s       0.0 s
[2016-04-14T23:49Z] INFO  16:49:08,087 ProgressMeter - Total runtime 12.33 secs, 0.21 min, 0.00 hours
[2016-04-14T23:49Z] INFO  16:49:08,087 MicroScheduler - 119 reads were filtered out during the traversal out of approximately 67849 total reads (0.18%)
[2016-04-14T23:49Z] INFO  16:49:08,087 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:49Z] INFO  16:49:08,088 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:49Z] INFO  16:49:08,088 MicroScheduler -   -> 119 reads (0.18% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:49Z] INFO  16:49:08,144 IntervalUtils - Processing 15580921 bp from intervals
[2016-04-14T23:49Z] WARN  16:49:08,149 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:49Z] INFO  16:49:08,223 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:49Z] INFO  16:49:08,481 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:49Z] INFO  16:49:08,482 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:49Z] INFO  16:49:08,482 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:49Z] INFO  16:49:08,483 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-14T23:49Z] INFO  16:49:08,777 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:49Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-4_134075461_150351181-prep.bam
[2016-04-14T23:49Z] INFO  16:49:09,038 ProgressMeter -      5:41941401    200002.0    30.0 s       2.5 m       57.9%    51.0 s      21.0 s
[2016-04-14T23:49Z] INFO  16:49:09,276 ProgressMeter -      3:51423671    400004.0    31.0 s      79.0 s       27.7%   112.0 s      81.0 s
[2016-04-14T23:49Z] GATK pre-alignment ('5', 143200044, 158710347) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-14T23:49Z] INFO  16:49:09,307 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:49Z] INFO  16:49:09,310 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:49Z] INFO  16:49:09,310 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:49Z] INFO  16:49:09,310 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:49Z] INFO  16:49:09,314 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/5/R14-18105_kapa-NGv3-PE100-NGv3-sort-5_15616091_31267808-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/5/R14-18105_kapa-NGv3-PE100-NGv3-sort-5_15616091_31267808-prep-prealign-realign.intervals -L 5:15616092-31267808 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/5/tx/tmpYS0hes/R14-18105_kapa-NGv3-PE100-NGv3-sort-5_15616091_31267808-prep.bam
[2016-04-14T23:49Z] INFO  16:49:09,330 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:49Z] INFO  16:49:09,331 HelpFormatter - Date/Time: 2016/04/14 16:49:09
[2016-04-14T23:49Z] INFO  16:49:09,331 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:49Z] INFO  16:49:09,331 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:49Z] INFO  16:49:09,491 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:49Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-5_96432513_112043579-prep-prealign.bam
[2016-04-14T23:49Z] INFO  16:49:09,535 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:49Z] INFO  16:49:09,723 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:49Z] INFO  16:49:09,745 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:49Z] GATK RealignerTargetCreator: R14-18105_kapa-NGv3-PE100-NGv3-sort-5_96432513_112043579-prep-prealign.bam 5:96432514-112043579
[2016-04-14T23:49Z] GATK: RealignerTargetCreator
[2016-04-14T23:49Z] INFO  16:49:09,813 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-14T23:49Z] INFO  16:49:10,349 IntervalUtils - Processing 15651717 bp from intervals
[2016-04-14T23:49Z] WARN  16:49:10,366 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:49Z] INFO  16:49:10,527 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:49Z] INFO  16:49:10,671 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:49Z] INFO  16:49:10,683 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:49Z] INFO  16:49:10,684 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:49Z] INFO  16:49:10,685 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:49Z] INFO  16:49:10,767 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:49Z] INFO  16:49:10,771 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:49Z] INFO  16:49:10,771 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:49Z] INFO  16:49:10,772 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:49Z] INFO  16:49:10,776 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/4/R14-18105_kapa-NGv3-PE100-NGv3-sort-4_165889318_183245405-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/4/R14-18105_kapa-NGv3-PE100-NGv3-sort-4_165889318_183245405-prep-prealign-realign.intervals -L 4:165889319-183245405 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/4/tx/tmp4vuQVz/R14-18105_kapa-NGv3-PE100-NGv3-sort-4_165889318_183245405-prep.bam
[2016-04-14T23:49Z] INFO  16:49:10,794 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:49Z] INFO  16:49:10,795 HelpFormatter - Date/Time: 2016/04/14 16:49:10
[2016-04-14T23:49Z] INFO  16:49:10,795 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:49Z] INFO  16:49:10,796 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:49Z] INFO  16:49:10,849 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:49Z] INFO  16:49:10,913 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:49Z] INFO  16:49:10,917 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:49Z] INFO  16:49:10,917 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:49Z] INFO  16:49:10,918 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:49Z] INFO  16:49:10,922 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/5/R14-18105_kapa-NGv3-PE100-NGv3-sort-5_49695692_65288736-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/5/tx/tmpCrUDgH/R14-18105_kapa-NGv3-PE100-NGv3-sort-5_49695692_65288736-prep-prealign-realign.intervals -l INFO -L 5:49695693-65288736 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-14T23:49Z] INFO  16:49:10,936 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:49Z] INFO  16:49:10,936 HelpFormatter - Date/Time: 2016/04/14 16:49:10
[2016-04-14T23:49Z] INFO  16:49:10,936 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:49Z] INFO  16:49:10,936 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:49Z] INFO  16:49:10,931 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:49Z] INFO  16:49:10,961 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:49Z] INFO  16:49:10,961 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:49Z] INFO  16:49:10,962 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:49Z] INFO  16:49:10,967 HelpFormatter - Program Args: -T PrintReads -L 5:127597428-143191869 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/5/tx/tmp60IpXD/R14-18105_kapa-NGv3-PE100-NGv3-sort-5_127597427_143191869-prep-prealign.bam
[2016-04-14T23:49Z] INFO  16:49:10,979 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:49Z] INFO  16:49:10,990 HelpFormatter - Date/Time: 2016/04/14 16:49:10
[2016-04-14T23:49Z] INFO  16:49:10,991 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:49Z] INFO  16:49:10,992 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:49Z] INFO  16:49:11,002 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:49Z] INFO  16:49:11,012 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:49Z] INFO  16:49:11,061 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:49Z] INFO  16:49:11,146 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:49Z] INFO  16:49:11,169 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:49Z] INFO  16:49:11,181 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:49Z] INFO  16:49:11,251 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-14T23:49Z] INFO  16:49:11,300 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-14T23:49Z] INFO  16:49:11,323 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:49Z] INFO  16:49:11,380 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-14T23:49Z] INFO  16:49:11,661 IntervalUtils - Processing 17356087 bp from intervals
[2016-04-14T23:49Z] WARN  16:49:11,679 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:49Z] INFO  16:49:11,764 IntervalUtils - Processing 15593044 bp from intervals
[2016-04-14T23:49Z] WARN  16:49:11,778 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:49Z] INFO  16:49:11,791 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:49Z] INFO  16:49:11,891 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:49Z] INFO  16:49:11,921 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:49Z] INFO  16:49:11,922 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:49Z] INFO  16:49:11,923 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:49Z] INFO  16:49:11,924 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:49Z] INFO  16:49:12,142 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:49Z] INFO  16:49:12,178 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:49Z] INFO  16:49:12,179 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:49Z] INFO  16:49:12,179 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:49Z] INFO  16:49:12,190 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-14T23:49Z] INFO  16:49:12,359 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:49Z] INFO  16:49:12,458 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:49Z] INFO  16:49:12,462 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:49Z] INFO  16:49:12,462 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:49Z] INFO  16:49:12,463 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:49Z] INFO  16:49:12,468 HelpFormatter - Program Args: -T PrintReads -L 5:143200045-158710347 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/5/tx/tmpKjX8kd/R14-18105_kapa-NGv3-PE100-NGv3-sort-5_143200044_158710347-prep-prealign.bam
[2016-04-14T23:49Z] INFO  16:49:12,478 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:49Z] INFO  16:49:12,484 HelpFormatter - Date/Time: 2016/04/14 16:49:12
[2016-04-14T23:49Z] INFO  16:49:12,485 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:49Z] INFO  16:49:12,485 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:49Z] INFO  16:49:12,489 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-14T23:49Z] INFO  16:49:12,557 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:49Z] INFO  16:49:12,566 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:49Z] INFO  16:49:12,566 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@41fd9d8e
[2016-04-14T23:49Z] INFO  16:49:12,615 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-14T23:49Z] INFO  16:49:12,629 IntervalUtils - Processing 15594442 bp from intervals
[2016-04-14T23:49Z] INFO  16:49:12,671 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:49Z] INFO  16:49:12,674 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:49Z] INFO  16:49:12,675 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:49Z] INFO  16:49:12,676 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:49Z] INFO  16:49:12,680 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/5/R14-18105_kapa-NGv3-PE100-NGv3-sort-5_96432513_112043579-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/5/tx/tmp9eX_dZ/R14-18105_kapa-NGv3-PE100-NGv3-sort-5_96432513_112043579-prep-prealign-realign.intervals -l INFO -L 5:96432514-112043579 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-14T23:49Z] INFO  16:49:12,685 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@7172f77a
[2016-04-14T23:49Z] INFO  16:49:12,685 ProgressMeter -            done    237647.0    33.0 s       2.4 m      100.0%    33.0 s       0.0 s
[2016-04-14T23:49Z] INFO  16:49:12,686 ProgressMeter - Total runtime 33.66 secs, 0.56 min, 0.01 hours
[2016-04-14T23:49Z] INFO  16:49:12,686 MicroScheduler - 151 reads were filtered out during the traversal out of approximately 237798 total reads (0.06%)
[2016-04-14T23:49Z] INFO  16:49:12,686 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:49Z] INFO  16:49:12,687 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:49Z] INFO  16:49:12,689 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:49Z] INFO  16:49:12,687 MicroScheduler -   -> 151 reads (0.06% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:49Z] INFO  16:49:12,695 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:49Z] INFO  16:49:12,695 HelpFormatter - Date/Time: 2016/04/14 16:49:12
[2016-04-14T23:49Z] INFO  16:49:12,696 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:49Z] INFO  16:49:12,697 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:49Z] INFO  16:49:12,697 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:49Z] INFO  16:49:12,848 ProgressMeter -            done    137496.0    21.0 s       2.6 m      100.0%    21.0 s       0.0 s
[2016-04-14T23:49Z] INFO  16:49:12,849 ProgressMeter - Total runtime 21.18 secs, 0.35 min, 0.01 hours
[2016-04-14T23:49Z] INFO  16:49:12,849 MicroScheduler - 175 reads were filtered out during the traversal out of approximately 137671 total reads (0.13%)
[2016-04-14T23:49Z] INFO  16:49:12,850 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:49Z] INFO  16:49:12,850 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:49Z] INFO  16:49:12,850 MicroScheduler -   -> 175 reads (0.13% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:49Z] INFO  16:49:12,851 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:49Z] INFO  16:49:13,092 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:49Z] INFO  16:49:13,093 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:49Z] INFO  16:49:13,094 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:49Z] INFO  16:49:13,095 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:49Z] INFO  16:49:13,117 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-14T23:49Z] INFO  16:49:13,126 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:49Z] INFO  16:49:13,129 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:49Z] INFO  16:49:13,181 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-14T23:49Z] INFO  16:49:13,373 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:49Z] INFO  16:49:13,577 IntervalUtils - Processing 15611066 bp from intervals
[2016-04-14T23:49Z] WARN  16:49:13,604 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:49Z] INFO  16:49:13,741 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:49Z] INFO  16:49:13,925 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-14T23:49Z] INFO  16:49:14,009 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:49Z] INFO  16:49:14,018 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:49Z] INFO  16:49:14,021 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:49Z] INFO  16:49:14,022 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:49Z] INFO  16:49:14,023 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:49Z] INFO  16:49:14,024 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-14T23:49Z] INFO  16:49:14,085 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-14T23:49Z] INFO  16:49:14,099 IntervalUtils - Processing 15510303 bp from intervals
[2016-04-14T23:49Z] INFO  16:49:14,186 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:49Z] INFO  16:49:14,229 ProgressMeter -            done   7886473.0    11.0 s       1.0 s      100.0%    11.0 s       0.0 s
[2016-04-14T23:49Z] INFO  16:49:14,230 ProgressMeter - Total runtime 11.86 secs, 0.20 min, 0.00 hours
[2016-04-14T23:49Z] INFO  16:49:14,234 MicroScheduler - 14560 reads were filtered out during the traversal out of approximately 146310 total reads (9.95%)
[2016-04-14T23:49Z] INFO  16:49:14,235 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:49Z] INFO  16:49:14,235 MicroScheduler -   -> 367 reads (0.25% of total) failing BadMateFilter
[2016-04-14T23:49Z] INFO  16:49:14,236 MicroScheduler -   -> 11470 reads (7.84% of total) failing DuplicateReadFilter
[2016-04-14T23:49Z] INFO  16:49:14,237 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-14T23:49Z] INFO  16:49:14,237 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:49Z] INFO  16:49:14,238 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-14T23:49Z] INFO  16:49:14,239 MicroScheduler -   -> 2723 reads (1.86% of total) failing MappingQualityZeroFilter
[2016-04-14T23:49Z] INFO  16:49:14,239 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:49Z] INFO  16:49:14,240 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-14T23:49Z] INFO  16:49:14,240 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-14T23:49Z] INFO  16:49:14,273 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:49Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-5_31294068_49695124-prep-prealign.bam
[2016-04-14T23:49Z] INFO  16:49:14,401 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:49Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-5_80911291_96430739-prep-prealign.bam
[2016-04-14T23:49Z] INFO  16:49:14,493 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:49Z] INFO  16:49:14,494 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:49Z] INFO  16:49:14,495 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:49Z] INFO  16:49:14,496 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:49Z] INFO  16:49:14,510 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:49Z] INFO  16:49:14,731 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:49Z] GATK RealignerTargetCreator: R14-18105_kapa-NGv3-PE100-NGv3-sort-5_80911291_96430739-prep-prealign.bam 5:80911292-96430739
[2016-04-14T23:49Z] GATK: RealignerTargetCreator
[2016-04-14T23:49Z] GATK RealignerTargetCreator: R14-18105_kapa-NGv3-PE100-NGv3-sort-5_31294068_49695124-prep-prealign.bam 5:31294069-49695124
[2016-04-14T23:49Z] GATK: RealignerTargetCreator
[2016-04-14T23:49Z] INFO  16:49:15,684 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:49Z] GATK: realign ('4', 183267803, 191154276) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-14T23:49Z] INFO  16:49:17,251 ProgressMeter -      5:79378284    200004.0    30.0 s       2.5 m       90.8%    33.0 s       3.0 s
[2016-04-14T23:49Z] INFO  16:49:18,122 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:49Z] INFO  16:49:18,125 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:49Z] INFO  16:49:18,125 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:49Z] INFO  16:49:18,126 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:49Z] INFO  16:49:18,131 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/5/R14-18105_kapa-NGv3-PE100-NGv3-sort-5_80911291_96430739-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/5/tx/tmp9tX9ff/R14-18105_kapa-NGv3-PE100-NGv3-sort-5_80911291_96430739-prep-prealign-realign.intervals -l INFO -L 5:80911292-96430739 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-14T23:49Z] INFO  16:49:18,141 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:49Z] INFO  16:49:18,141 HelpFormatter - Date/Time: 2016/04/14 16:49:18
[2016-04-14T23:49Z] INFO  16:49:18,141 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:49Z] INFO  16:49:18,141 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:49Z] INFO  16:49:18,272 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:49Z] INFO  16:49:18,509 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-14T23:49Z] INFO  16:49:18,518 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:49Z] INFO  16:49:18,526 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:49Z] INFO  16:49:18,533 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:49Z] INFO  16:49:18,534 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:49Z] INFO  16:49:18,534 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:49Z] INFO  16:49:18,539 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/4/R14-18105_kapa-NGv3-PE100-NGv3-sort-4_183267803_191154276-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/4/R14-18105_kapa-NGv3-PE100-NGv3-sort-4_183267803_191154276-prep-prealign-realign.intervals -L 4:183267804-191154276 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/4/tx/tmp6idbpv/R14-18105_kapa-NGv3-PE100-NGv3-sort-4_183267803_191154276-prep.bam
[2016-04-14T23:49Z] INFO  16:49:18,555 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:49Z] INFO  16:49:18,555 HelpFormatter - Date/Time: 2016/04/14 16:49:18
[2016-04-14T23:49Z] INFO  16:49:18,555 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:49Z] INFO  16:49:18,555 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:49Z] INFO  16:49:18,570 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-14T23:49Z] INFO  16:49:18,578 ProgressMeter -            done     45555.0     7.0 s       2.9 m      100.0%     7.0 s       0.0 s
[2016-04-14T23:49Z] INFO  16:49:18,579 ProgressMeter - Total runtime 7.90 secs, 0.13 min, 0.00 hours
[2016-04-14T23:49Z] INFO  16:49:18,583 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 45555 total reads (0.00%)
[2016-04-14T23:49Z] INFO  16:49:18,583 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:49Z] INFO  16:49:18,584 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:49Z] INFO  16:49:18,584 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:49Z] INFO  16:49:18,795 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:49Z] INFO  16:49:18,884 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:49Z] INFO  16:49:18,894 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:49Z] INFO  16:49:18,962 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-14T23:49Z] INFO  16:49:18,975 ProgressMeter -            done    181084.0    15.0 s      87.0 s      100.0%    15.0 s       0.0 s
[2016-04-14T23:49Z] INFO  16:49:18,975 ProgressMeter - Total runtime 15.77 secs, 0.26 min, 0.00 hours
[2016-04-14T23:49Z] INFO  16:49:18,976 IntervalUtils - Processing 15519448 bp from intervals
[2016-04-14T23:49Z] INFO  16:49:18,979 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 181084 total reads (0.00%)
[2016-04-14T23:49Z] INFO  16:49:18,979 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:49Z] INFO  16:49:18,979 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:49Z] INFO  16:49:18,980 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:49Z] INFO  16:49:18,977 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:49Z] INFO  16:49:18,981 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:49Z] INFO  16:49:18,981 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:49Z] INFO  16:49:18,982 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:49Z] WARN  16:49:18,982 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:49Z] INFO  16:49:18,987 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/5/R14-18105_kapa-NGv3-PE100-NGv3-sort-5_31294068_49695124-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/5/tx/tmpYhvDcS/R14-18105_kapa-NGv3-PE100-NGv3-sort-5_31294068_49695124-prep-prealign-realign.intervals -l INFO -L 5:31294069-49695124 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-14T23:49Z] INFO  16:49:18,998 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:49Z] INFO  16:49:19,009 HelpFormatter - Date/Time: 2016/04/14 16:49:18
[2016-04-14T23:49Z] INFO  16:49:19,010 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:49Z] INFO  16:49:19,011 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:49Z] INFO  16:49:19,127 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:49Z] INFO  16:49:19,187 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:49Z] INFO  16:49:19,317 IntervalUtils - Processing 7886473 bp from intervals
[2016-04-14T23:49Z] WARN  16:49:19,322 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:49Z] INFO  16:49:19,354 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:49Z] INFO  16:49:19,356 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:49Z] INFO  16:49:19,357 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:49Z] INFO  16:49:19,358 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-14T23:49Z] INFO  16:49:19,421 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:49Z] INFO  16:49:19,429 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-14T23:49Z] INFO  16:49:19,451 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:49Z] INFO  16:49:19,516 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-14T23:49Z] INFO  16:49:19,535 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:49Z] INFO  16:49:19,536 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:49Z] INFO  16:49:19,537 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:49Z] INFO  16:49:19,538 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:49Z] INFO  16:49:19,746 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:49Z] INFO  16:49:19,789 IntervalUtils - Processing 18401056 bp from intervals
[2016-04-14T23:49Z] WARN  16:49:19,794 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:49Z] INFO  16:49:19,888 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:49Z] INFO  16:49:20,020 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:49Z] INFO  16:49:20,156 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:49Z] INFO  16:49:20,157 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:49Z] INFO  16:49:20,158 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:49Z] INFO  16:49:20,158 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-14T23:49Z] INFO  16:49:20,454 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:49Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-4_115584857_134074404-prep.bam
[2016-04-14T23:49Z] INFO  16:49:20,623 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:49Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-5_15616091_31267808-prep.bam
[2016-04-14T23:49Z] GATK pre-alignment ('5', 158711911, 174870102) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-14T23:49Z] INFO  16:49:21,021 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@41fd9d8e
[2016-04-14T23:49Z] INFO  16:49:21,194 ProgressMeter -            done    271595.0    33.0 s       2.1 m      100.0%    33.0 s       0.0 s
[2016-04-14T23:49Z] INFO  16:49:21,195 ProgressMeter - Total runtime 33.98 secs, 0.57 min, 0.01 hours
[2016-04-14T23:49Z] INFO  16:49:21,195 MicroScheduler - 150 reads were filtered out during the traversal out of approximately 271745 total reads (0.06%)
[2016-04-14T23:49Z] INFO  16:49:21,196 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:49Z] INFO  16:49:21,196 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:49Z] INFO  16:49:21,197 MicroScheduler -   -> 150 reads (0.06% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:49Z] GATK pre-alignment ('5', 174919106, 180915260) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-14T23:49Z] INFO  16:49:21,943 ProgressMeter -            done    152066.0    14.0 s      97.0 s      100.0%    14.0 s       0.0 s
[2016-04-14T23:49Z] INFO  16:49:21,945 ProgressMeter - Total runtime 14.87 secs, 0.25 min, 0.00 hours
[2016-04-14T23:49Z] INFO  16:49:21,960 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 152066 total reads (0.00%)
[2016-04-14T23:49Z] INFO  16:49:21,961 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:49Z] INFO  16:49:21,962 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:49Z] INFO  16:49:21,963 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:49Z] INFO  16:49:22,071 ProgressMeter -            done     96279.0    10.0 s     105.0 s      100.0%    10.0 s       0.0 s
[2016-04-14T23:49Z] INFO  16:49:22,072 ProgressMeter - Total runtime 10.15 secs, 0.17 min, 0.00 hours
[2016-04-14T23:49Z] INFO  16:49:22,076 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 96279 total reads (0.00%)
[2016-04-14T23:49Z] INFO  16:49:22,076 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:49Z] INFO  16:49:22,077 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:49Z] INFO  16:49:22,077 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:49Z] INFO  16:49:22,730 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@5fe152b7
[2016-04-14T23:49Z] INFO  16:49:22,891 ProgressMeter -            done    141065.0    22.0 s       2.6 m      100.0%    22.0 s       0.0 s
[2016-04-14T23:49Z] INFO  16:49:22,891 ProgressMeter - Total runtime 22.43 secs, 0.37 min, 0.01 hours
[2016-04-14T23:49Z] INFO  16:49:22,891 MicroScheduler - 137 reads were filtered out during the traversal out of approximately 141202 total reads (0.10%)
[2016-04-14T23:49Z] INFO  16:49:22,892 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:49Z] INFO  16:49:22,892 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:49Z] INFO  16:49:22,892 MicroScheduler -   -> 137 reads (0.10% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:49Z] INFO  16:49:23,092 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:49Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-5_65290574_80809536-prep-prealign.bam
[2016-04-14T23:49Z] INFO  16:49:23,546 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:49Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-4_150354547_165878648-prep.bam
[2016-04-14T23:49Z] INFO  16:49:23,602 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:49Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-4_165889318_183245405-prep.bam
[2016-04-14T23:49Z] INFO  16:49:23,792 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:49Z] INFO  16:49:23,795 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:49Z] INFO  16:49:23,796 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:49Z] INFO  16:49:23,796 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:49Z] INFO  16:49:23,801 HelpFormatter - Program Args: -T PrintReads -L 5:158711912-174870102 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/5/tx/tmpGEDIar/R14-18105_kapa-NGv3-PE100-NGv3-sort-5_158711911_174870102-prep-prealign.bam
[2016-04-14T23:49Z] INFO  16:49:23,809 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:49Z] INFO  16:49:23,819 HelpFormatter - Date/Time: 2016/04/14 16:49:23
[2016-04-14T23:49Z] INFO  16:49:23,820 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:49Z] INFO  16:49:23,820 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:49Z] GATK RealignerTargetCreator: R14-18105_kapa-NGv3-PE100-NGv3-sort-5_65290574_80809536-prep-prealign.bam 5:65290575-80809536
[2016-04-14T23:49Z] GATK: RealignerTargetCreator
[2016-04-14T23:49Z] INFO  16:49:23,977 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:49Z] GATK pre-alignment ('6', 0, 15509601) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-14T23:49Z] INFO  16:49:24,103 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:49Z] GATK pre-alignment ('6', 15511526, 31080332) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-14T23:49Z] INFO  16:49:24,107 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:49Z] INFO  16:49:24,108 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:49Z] INFO  16:49:24,108 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:49Z] INFO  16:49:24,115 HelpFormatter - Program Args: -T PrintReads -L 5:174919107-180915260 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/5/tx/tmpoBwE9y/R14-18105_kapa-NGv3-PE100-NGv3-sort-5_174919106_180915260-prep-prealign.bam
[2016-04-14T23:49Z] INFO  16:49:24,128 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:49Z] INFO  16:49:24,129 HelpFormatter - Date/Time: 2016/04/14 16:49:24
[2016-04-14T23:49Z] INFO  16:49:24,129 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:49Z] INFO  16:49:24,129 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:49Z] INFO  16:49:24,345 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:49Z] INFO  16:49:24,578 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:49Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-5_112073555_127595521-prep-prealign.bam
[2016-04-14T23:49Z] INFO  16:49:24,858 ProgressMeter -            done    767511.0    47.0 s      61.0 s      100.0%    47.0 s       0.0 s
[2016-04-14T23:49Z] INFO  16:49:24,860 ProgressMeter - Total runtime 47.33 secs, 0.79 min, 0.01 hours
[2016-04-14T23:49Z] INFO  16:49:24,871 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 767511 total reads (0.00%)
[2016-04-14T23:49Z] INFO  16:49:24,873 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:49Z] INFO  16:49:24,874 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:49Z] INFO  16:49:24,875 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:49Z] GATK RealignerTargetCreator: R14-18105_kapa-NGv3-PE100-NGv3-sort-5_112073555_127595521-prep-prealign.bam 5:112073556-127595521
[2016-04-14T23:49Z] GATK: RealignerTargetCreator
[2016-04-14T23:49Z] INFO  16:49:25,310 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-14T23:49Z] INFO  16:49:25,407 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:49Z] INFO  16:49:25,418 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:49Z] INFO  16:49:25,482 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-14T23:49Z] INFO  16:49:25,500 IntervalUtils - Processing 16158191 bp from intervals
[2016-04-14T23:49Z] INFO  16:49:25,547 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-14T23:49Z] INFO  16:49:25,605 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:49Z] INFO  16:49:25,625 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:49Z] INFO  16:49:25,645 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:49Z] INFO  16:49:25,704 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-14T23:49Z] INFO  16:49:25,726 IntervalUtils - Processing 5996154 bp from intervals
[2016-04-14T23:49Z] INFO  16:49:25,831 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:49Z] INFO  16:49:25,919 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:49Z] INFO  16:49:25,921 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:49Z] INFO  16:49:25,921 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:49Z] INFO  16:49:25,922 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:49Z] INFO  16:49:25,957 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:49Z] INFO  16:49:26,175 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:49Z] INFO  16:49:26,207 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:49Z] INFO  16:49:26,208 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:49Z] INFO  16:49:26,209 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:49Z] INFO  16:49:26,209 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:49Z] INFO  16:49:26,235 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:49Z] INFO  16:49:26,293 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:49Z] INFO  16:49:26,582 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:49Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-3_47129602_62648069-prep.bam
[2016-04-14T23:49Z] INFO  16:49:27,212 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:49Z] INFO  16:49:27,215 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:49Z] INFO  16:49:27,216 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:49Z] INFO  16:49:27,216 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:49Z] INFO  16:49:27,221 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/5/R14-18105_kapa-NGv3-PE100-NGv3-sort-5_65290574_80809536-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/5/tx/tmpLLQ2Jh/R14-18105_kapa-NGv3-PE100-NGv3-sort-5_65290574_80809536-prep-prealign-realign.intervals -l INFO -L 5:65290575-80809536 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-14T23:49Z] INFO  16:49:27,267 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:49Z] INFO  16:49:27,268 HelpFormatter - Date/Time: 2016/04/14 16:49:27
[2016-04-14T23:49Z] INFO  16:49:27,269 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:49Z] INFO  16:49:27,269 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:49Z] INFO  16:49:27,335 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:49Z] INFO  16:49:27,338 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:49Z] INFO  16:49:27,338 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:49Z] INFO  16:49:27,339 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:49Z] INFO  16:49:27,343 HelpFormatter - Program Args: -T PrintReads -L 6:15511527-31080332 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/6/tx/tmpDev6RM/R14-18105_kapa-NGv3-PE100-NGv3-sort-6_15511526_31080332-prep-prealign.bam
[2016-04-14T23:49Z] INFO  16:49:27,351 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:49Z] INFO  16:49:27,362 HelpFormatter - Date/Time: 2016/04/14 16:49:27
[2016-04-14T23:49Z] INFO  16:49:27,363 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:49Z] INFO  16:49:27,363 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:49Z] INFO  16:49:27,384 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:49Z] INFO  16:49:27,463 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:49Z] INFO  16:49:27,466 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:49Z] INFO  16:49:27,467 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:49Z] INFO  16:49:27,467 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:49Z] INFO  16:49:27,472 HelpFormatter - Program Args: -T PrintReads -L 6:1-15509601 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/6/tx/tmpmfHArH/R14-18105_kapa-NGv3-PE100-NGv3-sort-6_0_15509601-prep-prealign.bam
[2016-04-14T23:49Z] INFO  16:49:27,485 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:49Z] INFO  16:49:27,486 HelpFormatter - Date/Time: 2016/04/14 16:49:27
[2016-04-14T23:49Z] INFO  16:49:27,487 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:49Z] INFO  16:49:27,487 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:49Z] INFO  16:49:27,533 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:49Z] INFO  16:49:27,632 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-14T23:49Z] INFO  16:49:27,642 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:49Z] INFO  16:49:27,704 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-14T23:49Z] INFO  16:49:27,711 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:49Z] INFO  16:49:27,987 IntervalUtils - Processing 15518962 bp from intervals
[2016-04-14T23:49Z] WARN  16:49:27,993 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:49Z] INFO  16:49:28,061 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:49Z] INFO  16:49:28,064 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:49Z] INFO  16:49:28,065 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:49Z] INFO  16:49:28,065 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:49Z] INFO  16:49:28,070 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/5/R14-18105_kapa-NGv3-PE100-NGv3-sort-5_112073555_127595521-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/5/tx/tmpq7qaH8/R14-18105_kapa-NGv3-PE100-NGv3-sort-5_112073555_127595521-prep-prealign-realign.intervals -l INFO -L 5:112073556-127595521 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-14T23:49Z] INFO  16:49:28,076 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:49Z] INFO  16:49:28,095 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:49Z] INFO  16:49:28,096 HelpFormatter - Date/Time: 2016/04/14 16:49:28
[2016-04-14T23:49Z] INFO  16:49:28,096 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:49Z] INFO  16:49:28,103 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:49Z] INFO  16:49:28,269 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:49Z] INFO  16:49:28,287 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:49Z] INFO  16:49:28,288 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:49Z] INFO  16:49:28,289 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:49Z] INFO  16:49:28,290 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-14T23:49Z] INFO  16:49:28,501 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-14T23:49Z] INFO  16:49:28,511 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:49Z] INFO  16:49:28,574 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-14T23:49Z] INFO  16:49:28,741 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-14T23:49Z] INFO  16:49:28,824 IntervalUtils - Processing 15521966 bp from intervals
[2016-04-14T23:49Z] WARN  16:49:28,829 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:49Z] INFO  16:49:28,838 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:49Z] INFO  16:49:28,848 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:49Z] INFO  16:49:28,881 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.03
[2016-04-14T23:49Z] INFO  16:49:28,895 IntervalUtils - Processing 15568806 bp from intervals
[2016-04-14T23:49Z] INFO  16:49:28,904 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-14T23:49Z] INFO  16:49:28,926 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:49Z] INFO  16:49:28,970 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:49Z] INFO  16:49:28,972 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:49Z] INFO  16:49:28,981 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:49Z] INFO  16:49:28,983 ProgressMeter -            done   1.5580921E7    20.0 s       1.0 s      100.0%    20.0 s       0.0 s
[2016-04-14T23:49Z] INFO  16:49:28,984 ProgressMeter - Total runtime 20.50 secs, 0.34 min, 0.01 hours
[2016-04-14T23:49Z] INFO  16:49:28,989 MicroScheduler - 23302 reads were filtered out during the traversal out of approximately 228323 total reads (10.21%)
[2016-04-14T23:49Z] INFO  16:49:28,990 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:49Z] INFO  16:49:28,991 MicroScheduler -   -> 625 reads (0.27% of total) failing BadMateFilter
[2016-04-14T23:49Z] INFO  16:49:28,992 MicroScheduler -   -> 18053 reads (7.91% of total) failing DuplicateReadFilter
[2016-04-14T23:49Z] INFO  16:49:28,993 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-14T23:49Z] INFO  16:49:28,993 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:49Z] INFO  16:49:28,994 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-14T23:49Z] INFO  16:49:28,995 MicroScheduler -   -> 4624 reads (2.03% of total) failing MappingQualityZeroFilter
[2016-04-14T23:49Z] INFO  16:49:28,996 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:49Z] INFO  16:49:28,997 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-14T23:49Z] INFO  16:49:28,997 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-14T23:49Z] INFO  16:49:29,031 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-14T23:49Z] INFO  16:49:29,046 IntervalUtils - Processing 15509601 bp from intervals
[2016-04-14T23:49Z] INFO  16:49:29,125 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:49Z] INFO  16:49:29,130 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:49Z] INFO  16:49:29,131 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:49Z] INFO  16:49:29,131 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-14T23:49Z] GATK pre-alignment ('6', 31083801, 46593245) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-14T23:49Z] INFO  16:49:29,141 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:49Z] INFO  16:49:29,241 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:49Z] INFO  16:49:29,242 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:49Z] INFO  16:49:29,242 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:49Z] INFO  16:49:29,243 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:49Z] INFO  16:49:29,265 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:49Z] INFO  16:49:29,408 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:49Z] INFO  16:49:29,458 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:49Z] INFO  16:49:29,460 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:49Z] INFO  16:49:29,461 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:49Z] INFO  16:49:29,461 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:49Z] INFO  16:49:29,495 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:49Z] INFO  16:49:29,696 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:49Z] INFO  16:49:29,950 ProgressMeter -            done   1.5593044E7    17.0 s       1.0 s      100.0%    17.0 s       0.0 s
[2016-04-14T23:49Z] INFO  16:49:29,951 ProgressMeter - Total runtime 17.77 secs, 0.30 min, 0.00 hours
[2016-04-14T23:49Z] INFO  16:49:29,954 MicroScheduler - 11947 reads were filtered out during the traversal out of approximately 141108 total reads (8.47%)
[2016-04-14T23:49Z] INFO  16:49:29,955 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:49Z] INFO  16:49:29,955 MicroScheduler -   -> 468 reads (0.33% of total) failing BadMateFilter
[2016-04-14T23:49Z] INFO  16:49:29,955 MicroScheduler -   -> 11020 reads (7.81% of total) failing DuplicateReadFilter
[2016-04-14T23:49Z] INFO  16:49:29,965 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-14T23:49Z] INFO  16:49:29,966 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:49Z] INFO  16:49:29,966 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-14T23:49Z] INFO  16:49:29,966 MicroScheduler -   -> 459 reads (0.33% of total) failing MappingQualityZeroFilter
[2016-04-14T23:49Z] INFO  16:49:29,967 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:49Z] INFO  16:49:29,967 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-14T23:49Z] INFO  16:49:29,967 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-14T23:49Z] INFO  16:49:30,292 ProgressMeter -            done   1.5611066E7    16.0 s       1.0 s      100.0%    16.0 s       0.0 s
[2016-04-14T23:49Z] INFO  16:49:30,293 ProgressMeter - Total runtime 16.27 secs, 0.27 min, 0.00 hours
[2016-04-14T23:49Z] INFO  16:49:30,296 MicroScheduler - 6053 reads were filtered out during the traversal out of approximately 68370 total reads (8.85%)
[2016-04-14T23:49Z] INFO  16:49:30,296 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:49Z] INFO  16:49:30,297 MicroScheduler -   -> 353 reads (0.52% of total) failing BadMateFilter
[2016-04-14T23:49Z] INFO  16:49:30,297 MicroScheduler -   -> 5062 reads (7.40% of total) failing DuplicateReadFilter
[2016-04-14T23:49Z] INFO  16:49:30,297 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-14T23:49Z] INFO  16:49:30,298 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:49Z] INFO  16:49:30,298 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-14T23:49Z] INFO  16:49:30,298 MicroScheduler -   -> 638 reads (0.93% of total) failing MappingQualityZeroFilter
[2016-04-14T23:49Z] INFO  16:49:30,298 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:49Z] INFO  16:49:30,299 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-14T23:49Z] INFO  16:49:30,299 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-14T23:49Z] INFO  16:49:30,332 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:49Z] GATK: realign ('5', 0, 15580921) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-14T23:49Z] INFO  16:49:31,440 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:49Z] GATK: realign ('5', 49695692, 65288736) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-14T23:49Z] INFO  16:49:31,811 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:49Z] GATK: realign ('5', 96432513, 112043579) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-14T23:49Z] INFO  16:49:31,910 ProgressMeter -            done   1.5511864E7    25.0 s       1.0 s      100.0%    25.0 s       0.0 s
[2016-04-14T23:49Z] INFO  16:49:31,910 ProgressMeter - Total runtime 26.00 secs, 0.43 min, 0.01 hours
[2016-04-14T23:49Z] INFO  16:49:31,911 MicroScheduler - 464399 reads were filtered out during the traversal out of approximately 906715 total reads (51.22%)
[2016-04-14T23:49Z] INFO  16:49:31,911 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:49Z] INFO  16:49:31,911 MicroScheduler -   -> 1028 reads (0.11% of total) failing BadMateFilter
[2016-04-14T23:49Z] INFO  16:49:31,911 MicroScheduler -   -> 43829 reads (4.83% of total) failing DuplicateReadFilter
[2016-04-14T23:49Z] INFO  16:49:31,912 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-14T23:49Z] INFO  16:49:31,915 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:49Z] INFO  16:49:31,916 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-14T23:49Z] INFO  16:49:31,916 MicroScheduler -   -> 419542 reads (46.27% of total) failing MappingQualityZeroFilter
[2016-04-14T23:49Z] INFO  16:49:31,917 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:49Z] INFO  16:49:31,917 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-14T23:49Z] INFO  16:49:31,918 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-14T23:49Z] INFO  16:49:32,242 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:49Z] INFO  16:49:32,246 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:49Z] INFO  16:49:32,246 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:49Z] INFO  16:49:32,247 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:49Z] INFO  16:49:32,251 HelpFormatter - Program Args: -T PrintReads -L 6:31083802-46593245 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/6/tx/tmpq0M_f6/R14-18105_kapa-NGv3-PE100-NGv3-sort-6_31083801_46593245-prep-prealign.bam
[2016-04-14T23:49Z] INFO  16:49:32,261 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:49Z] INFO  16:49:32,262 HelpFormatter - Date/Time: 2016/04/14 16:49:32
[2016-04-14T23:49Z] INFO  16:49:32,262 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:49Z] INFO  16:49:32,262 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:49Z] INFO  16:49:32,517 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:49Z] INFO  16:49:33,019 ProgressMeter -            done    145401.0    13.0 s      92.0 s       97.4%    13.0 s       0.0 s
[2016-04-14T23:49Z] INFO  16:49:33,019 ProgressMeter - Total runtime 13.48 secs, 0.22 min, 0.00 hours
[2016-04-14T23:49Z] INFO  16:49:33,023 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 145401 total reads (0.00%)
[2016-04-14T23:49Z] INFO  16:49:33,023 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:49Z] INFO  16:49:33,024 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:49Z] INFO  16:49:33,024 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:49Z] INFO  16:49:33,040 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:49Z] INFO  16:49:33,044 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:49Z] INFO  16:49:33,044 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:49Z] INFO  16:49:33,045 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:49Z] INFO  16:49:33,050 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/5/R14-18105_kapa-NGv3-PE100-NGv3-sort-5_0_15580921-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/5/R14-18105_kapa-NGv3-PE100-NGv3-sort-5_0_15580921-prep-prealign-realign.intervals -L 5:1-15580921 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/5/tx/tmphqgWbZ/R14-18105_kapa-NGv3-PE100-NGv3-sort-5_0_15580921-prep.bam
[2016-04-14T23:49Z] INFO  16:49:33,080 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:49Z] INFO  16:49:33,080 HelpFormatter - Date/Time: 2016/04/14 16:49:33
[2016-04-14T23:49Z] INFO  16:49:33,081 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:49Z] INFO  16:49:33,086 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:49Z] INFO  16:49:33,342 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:49Z] INFO  16:49:33,432 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:49Z] INFO  16:49:33,474 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:49Z] INFO  16:49:33,485 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:49Z] GATK: realign ('4', 0, 15511864) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-14T23:49Z] INFO  16:49:33,567 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-14T23:49Z] INFO  16:49:33,672 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-14T23:49Z] INFO  16:49:33,733 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:49Z] INFO  16:49:33,742 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:49Z] INFO  16:49:33,781 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.04
[2016-04-14T23:49Z] INFO  16:49:33,795 IntervalUtils - Processing 15509444 bp from intervals
[2016-04-14T23:49Z] INFO  16:49:33,867 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:49Z] INFO  16:49:33,935 IntervalUtils - Processing 15580921 bp from intervals
[2016-04-14T23:49Z] WARN  16:49:33,950 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:49Z] INFO  16:49:34,029 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:49Z] INFO  16:49:34,145 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:49Z] INFO  16:49:34,146 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:49Z] INFO  16:49:34,147 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:49Z] INFO  16:49:34,147 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:49Z] INFO  16:49:34,169 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:49Z] INFO  16:49:34,188 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:49Z] INFO  16:49:34,189 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:49Z] INFO  16:49:34,190 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:49Z] INFO  16:49:34,191 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:49Z] INFO  16:49:34,305 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:49Z] INFO  16:49:34,377 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:49Z] INFO  16:49:34,532 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:49Z] INFO  16:49:34,629 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:49Z] INFO  16:49:34,632 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:49Z] INFO  16:49:34,633 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:49Z] INFO  16:49:34,633 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:49Z] INFO  16:49:34,637 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/5/R14-18105_kapa-NGv3-PE100-NGv3-sort-5_49695692_65288736-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/5/R14-18105_kapa-NGv3-PE100-NGv3-sort-5_49695692_65288736-prep-prealign-realign.intervals -L 5:49695693-65288736 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/5/tx/tmpt9NQJ5/R14-18105_kapa-NGv3-PE100-NGv3-sort-5_49695692_65288736-prep.bam
[2016-04-14T23:49Z] INFO  16:49:34,647 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:49Z] INFO  16:49:34,642 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:49Z] INFO  16:49:34,660 HelpFormatter - Date/Time: 2016/04/14 16:49:34
[2016-04-14T23:49Z] INFO  16:49:34,661 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:49Z] INFO  16:49:34,661 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:49Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-4_183267803_191154276-prep.bam
[2016-04-14T23:49Z] INFO  16:49:34,891 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:49Z] INFO  16:49:35,047 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:49Z] INFO  16:49:35,056 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:49Z] INFO  16:49:35,073 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:49Z] INFO  16:49:35,076 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:49Z] INFO  16:49:35,077 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:49Z] INFO  16:49:35,078 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:49Z] INFO  16:49:35,082 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/5/R14-18105_kapa-NGv3-PE100-NGv3-sort-5_96432513_112043579-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/5/R14-18105_kapa-NGv3-PE100-NGv3-sort-5_96432513_112043579-prep-prealign-realign.intervals -L 5:96432514-112043579 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/5/tx/tmpOzifty/R14-18105_kapa-NGv3-PE100-NGv3-sort-5_96432513_112043579-prep.bam
[2016-04-14T23:49Z] INFO  16:49:35,107 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:49Z] INFO  16:49:35,109 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-14T23:49Z] INFO  16:49:35,115 HelpFormatter - Date/Time: 2016/04/14 16:49:35
[2016-04-14T23:49Z] INFO  16:49:35,117 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:49Z] INFO  16:49:35,117 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:49Z] GATK pre-alignment ('6', 46598699, 62284307) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-14T23:49Z] INFO  16:49:35,389 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:49Z] INFO  16:49:35,489 IntervalUtils - Processing 15593044 bp from intervals
[2016-04-14T23:49Z] WARN  16:49:35,495 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:49Z] INFO  16:49:35,511 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:49Z] INFO  16:49:35,521 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:49Z] INFO  16:49:35,575 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-14T23:49Z] INFO  16:49:35,614 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:49Z] INFO  16:49:35,778 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:49Z] INFO  16:49:35,798 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:49Z] INFO  16:49:35,799 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:49Z] INFO  16:49:35,800 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:49Z] INFO  16:49:35,981 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:49Z] INFO  16:49:36,063 IntervalUtils - Processing 15611066 bp from intervals
[2016-04-14T23:49Z] WARN  16:49:36,068 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:49Z] INFO  16:49:36,198 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:49Z] INFO  16:49:36,210 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:49Z] INFO  16:49:36,397 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:49Z] INFO  16:49:36,398 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:49Z] INFO  16:49:36,408 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:49Z] INFO  16:49:36,408 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:49Z] INFO  16:49:36,543 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:49Z] INFO  16:49:36,618 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:49Z] INFO  16:49:36,621 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:49Z] INFO  16:49:36,621 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:49Z] INFO  16:49:36,622 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:49Z] INFO  16:49:36,627 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/4/R14-18105_kapa-NGv3-PE100-NGv3-sort-4_0_15511864-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/4/R14-18105_kapa-NGv3-PE100-NGv3-sort-4_0_15511864-prep-prealign-realign.intervals -L 4:1-15511864 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/4/tx/tmpQPP75G/R14-18105_kapa-NGv3-PE100-NGv3-sort-4_0_15511864-prep.bam
[2016-04-14T23:49Z] INFO  16:49:36,643 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:49Z] INFO  16:49:36,643 HelpFormatter - Date/Time: 2016/04/14 16:49:36
[2016-04-14T23:49Z] INFO  16:49:36,643 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:49Z] INFO  16:49:36,643 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:49Z] INFO  16:49:36,719 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:49Z] INFO  16:49:36,933 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:49Z] INFO  16:49:37,070 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:49Z] INFO  16:49:37,080 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:49Z] INFO  16:49:37,161 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-14T23:49Z] INFO  16:49:37,540 ProgressMeter -            done   1.5519448E7    18.0 s       1.0 s      100.0%    18.0 s       0.0 s
[2016-04-14T23:49Z] INFO  16:49:37,541 ProgressMeter - Total runtime 18.19 secs, 0.30 min, 0.01 hours
[2016-04-14T23:49Z] INFO  16:49:37,546 MicroScheduler - 11491 reads were filtered out during the traversal out of approximately 138475 total reads (8.30%)
[2016-04-14T23:49Z] INFO  16:49:37,547 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:49Z] INFO  16:49:37,547 MicroScheduler -   -> 443 reads (0.32% of total) failing BadMateFilter
[2016-04-14T23:49Z] INFO  16:49:37,548 MicroScheduler -   -> 10731 reads (7.75% of total) failing DuplicateReadFilter
[2016-04-14T23:49Z] INFO  16:49:37,549 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-14T23:49Z] INFO  16:49:37,549 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:49Z] INFO  16:49:37,550 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-14T23:49Z] INFO  16:49:37,551 MicroScheduler -   -> 317 reads (0.23% of total) failing MappingQualityZeroFilter
[2016-04-14T23:49Z] INFO  16:49:37,551 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:49Z] INFO  16:49:37,552 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-14T23:49Z] INFO  16:49:37,552 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-14T23:49Z] INFO  16:49:37,731 IntervalUtils - Processing 15511864 bp from intervals
[2016-04-14T23:49Z] WARN  16:49:37,737 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:49Z] INFO  16:49:37,828 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:49Z] INFO  16:49:37,932 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:49Z] INFO  16:49:37,933 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:49Z] INFO  16:49:37,934 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:49Z] INFO  16:49:37,935 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:49Z] INFO  16:49:38,156 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:49Z] INFO  16:49:38,285 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:49Z] INFO  16:49:38,449 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:49Z] INFO  16:49:38,453 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:49Z] INFO  16:49:38,453 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:49Z] INFO  16:49:38,454 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:49Z] INFO  16:49:38,459 HelpFormatter - Program Args: -T PrintReads -L 6:46598700-62284307 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/6/tx/tmpH3zE7I/R14-18105_kapa-NGv3-PE100-NGv3-sort-6_46598699_62284307-prep-prealign.bam
[2016-04-14T23:49Z] INFO  16:49:38,468 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:49Z] INFO  16:49:38,480 HelpFormatter - Date/Time: 2016/04/14 16:49:38
[2016-04-14T23:49Z] INFO  16:49:38,481 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:49Z] INFO  16:49:38,482 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:49Z] INFO  16:49:38,709 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:49Z] INFO  16:49:38,964 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:49Z] GATK: realign ('5', 80911291, 96430739) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-14T23:49Z] INFO  16:49:39,976 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-14T23:49Z] INFO  16:49:40,045 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:49Z] INFO  16:49:40,057 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:49Z] INFO  16:49:40,097 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.04
[2016-04-14T23:49Z] INFO  16:49:40,119 IntervalUtils - Processing 15685608 bp from intervals
[2016-04-14T23:49Z] INFO  16:49:40,229 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:49Z] INFO  16:49:40,534 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:49Z] INFO  16:49:40,535 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:49Z] INFO  16:49:40,536 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:49Z] INFO  16:49:40,536 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:49Z] INFO  16:49:40,565 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:49Z] INFO  16:49:40,735 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:49Z] INFO  16:49:41,152 ProgressMeter -            done   1.8401056E7    20.0 s       1.0 s      100.0%    20.0 s       0.0 s
[2016-04-14T23:49Z] INFO  16:49:41,154 ProgressMeter - Total runtime 21.00 secs, 0.35 min, 0.01 hours
[2016-04-14T23:49Z] INFO  16:49:41,158 MicroScheduler - 19601 reads were filtered out during the traversal out of approximately 238939 total reads (8.20%)
[2016-04-14T23:49Z] INFO  16:49:41,158 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:49Z] INFO  16:49:41,158 MicroScheduler -   -> 600 reads (0.25% of total) failing BadMateFilter
[2016-04-14T23:49Z] INFO  16:49:41,159 MicroScheduler -   -> 18455 reads (7.72% of total) failing DuplicateReadFilter
[2016-04-14T23:49Z] INFO  16:49:41,159 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-14T23:49Z] INFO  16:49:41,159 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:49Z] INFO  16:49:41,160 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-14T23:49Z] INFO  16:49:41,160 MicroScheduler -   -> 546 reads (0.23% of total) failing MappingQualityZeroFilter
[2016-04-14T23:49Z] INFO  16:49:41,168 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:49Z] INFO  16:49:41,168 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-14T23:49Z] INFO  16:49:41,168 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-14T23:49Z] INFO  16:49:41,911 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:49Z] INFO  16:49:41,914 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:49Z] INFO  16:49:41,915 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:49Z] INFO  16:49:41,915 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:49Z] INFO  16:49:41,920 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/5/R14-18105_kapa-NGv3-PE100-NGv3-sort-5_80911291_96430739-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/5/R14-18105_kapa-NGv3-PE100-NGv3-sort-5_80911291_96430739-prep-prealign-realign.intervals -L 5:80911292-96430739 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/5/tx/tmptxOutz/R14-18105_kapa-NGv3-PE100-NGv3-sort-5_80911291_96430739-prep.bam
[2016-04-14T23:49Z] INFO  16:49:41,929 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:49Z] INFO  16:49:41,930 HelpFormatter - Date/Time: 2016/04/14 16:49:41
[2016-04-14T23:49Z] INFO  16:49:41,931 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:49Z] INFO  16:49:41,932 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:49Z] INFO  16:49:42,222 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:49Z] INFO  16:49:42,354 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:49Z] INFO  16:49:42,364 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:49Z] INFO  16:49:42,429 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-14T23:49Z] INFO  16:49:42,739 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:49Z] GATK: realign ('5', 31294068, 49695124) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-14T23:49Z] INFO  16:49:42,857 IntervalUtils - Processing 15519448 bp from intervals
[2016-04-14T23:49Z] WARN  16:49:42,862 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:49Z] INFO  16:49:42,974 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:49Z] INFO  16:49:43,121 ProgressMeter -     5:137667587    200002.0    30.0 s       2.5 m       64.6%    46.0 s      16.0 s
[2016-04-14T23:49Z] INFO  16:49:43,123 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:49Z] INFO  16:49:43,124 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:49Z] INFO  16:49:43,125 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:49Z] INFO  16:49:43,126 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:49Z] INFO  16:49:43,301 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:49Z] INFO  16:49:43,427 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:49Z] INFO  16:49:43,949 ProgressMeter -            done     67730.0     7.0 s     111.0 s      100.0%     7.0 s       0.0 s
[2016-04-14T23:49Z] INFO  16:49:43,949 ProgressMeter - Total runtime 7.55 secs, 0.13 min, 0.00 hours
[2016-04-14T23:49Z] INFO  16:49:43,953 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 67730 total reads (0.00%)
[2016-04-14T23:49Z] INFO  16:49:43,953 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:49Z] INFO  16:49:43,954 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:49Z] INFO  16:49:43,954 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:49Z] INFO  16:49:44,516 ProgressMeter -     5:150838417    200004.0    30.0 s       2.5 m       49.2%    60.0 s      30.0 s
[2016-04-14T23:49Z] INFO  16:49:45,380 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:49Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-5_96432513_112043579-prep.bam
[2016-04-14T23:49Z] INFO  16:49:45,489 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:49Z] INFO  16:49:45,492 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:49Z] INFO  16:49:45,492 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:49Z] INFO  16:49:45,492 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:49Z] INFO  16:49:45,496 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/5/R14-18105_kapa-NGv3-PE100-NGv3-sort-5_31294068_49695124-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/5/R14-18105_kapa-NGv3-PE100-NGv3-sort-5_31294068_49695124-prep-prealign-realign.intervals -L 5:31294069-49695124 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/5/tx/tmpJpshQm/R14-18105_kapa-NGv3-PE100-NGv3-sort-5_31294068_49695124-prep.bam
[2016-04-14T23:49Z] INFO  16:49:45,541 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:49Z] INFO  16:49:45,541 HelpFormatter - Date/Time: 2016/04/14 16:49:45
[2016-04-14T23:49Z] INFO  16:49:45,541 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:49Z] INFO  16:49:45,542 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:49Z] GATK pre-alignment ('6', 62390867, 78173120) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-14T23:49Z] INFO  16:49:45,744 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:49Z] INFO  16:49:45,866 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:49Z] INFO  16:49:45,878 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:49Z] INFO  16:49:45,938 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-14T23:49Z] INFO  16:49:45,999 ProgressMeter -            done   1.5521966E7    16.0 s       1.0 s      100.0%    16.0 s       0.0 s
[2016-04-14T23:49Z] INFO  16:49:46,000 ProgressMeter - Total runtime 16.87 secs, 0.28 min, 0.00 hours
[2016-04-14T23:49Z] INFO  16:49:46,004 MicroScheduler - 11827 reads were filtered out during the traversal out of approximately 141484 total reads (8.36%)
[2016-04-14T23:49Z] INFO  16:49:46,005 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:49Z] INFO  16:49:46,005 MicroScheduler -   -> 542 reads (0.38% of total) failing BadMateFilter
[2016-04-14T23:49Z] INFO  16:49:46,006 MicroScheduler -   -> 11072 reads (7.83% of total) failing DuplicateReadFilter
[2016-04-14T23:49Z] INFO  16:49:46,007 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-14T23:49Z] INFO  16:49:46,007 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:49Z] INFO  16:49:46,008 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-14T23:49Z] INFO  16:49:46,008 MicroScheduler -   -> 213 reads (0.15% of total) failing MappingQualityZeroFilter
[2016-04-14T23:49Z] INFO  16:49:46,009 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:49Z] INFO  16:49:46,009 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-14T23:49Z] INFO  16:49:46,010 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-14T23:49Z] INFO  16:49:46,305 IntervalUtils - Processing 18401056 bp from intervals
[2016-04-14T23:49Z] WARN  16:49:46,320 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:49Z] INFO  16:49:46,391 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:49Z] INFO  16:49:46,495 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:49Z] INFO  16:49:46,496 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:49Z] INFO  16:49:46,497 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:49Z] INFO  16:49:46,497 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:49Z] INFO  16:49:46,689 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:49Z] INFO  16:49:46,903 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:49Z] INFO  16:49:47,424 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:49Z] GATK: realign ('5', 112073555, 127595521) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-14T23:49Z] INFO  16:49:47,769 ProgressMeter -            done    140505.0    11.0 s      85.0 s      100.0%    11.0 s       0.0 s
[2016-04-14T23:49Z] INFO  16:49:47,769 ProgressMeter - Total runtime 11.97 secs, 0.20 min, 0.00 hours
[2016-04-14T23:49Z] INFO  16:49:47,772 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 140505 total reads (0.00%)
[2016-04-14T23:49Z] INFO  16:49:47,773 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:49Z] INFO  16:49:47,773 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:49Z] INFO  16:49:47,773 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:49Z] INFO  16:49:48,447 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:49Z] INFO  16:49:48,451 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:49Z] INFO  16:49:48,451 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:49Z] INFO  16:49:48,452 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:49Z] INFO  16:49:48,457 HelpFormatter - Program Args: -T PrintReads -L 6:62390868-78173120 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/6/tx/tmpY8XIko/R14-18105_kapa-NGv3-PE100-NGv3-sort-6_62390867_78173120-prep-prealign.bam
[2016-04-14T23:49Z] INFO  16:49:48,470 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:49Z] INFO  16:49:48,471 HelpFormatter - Date/Time: 2016/04/14 16:49:48
[2016-04-14T23:49Z] INFO  16:49:48,472 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:49Z] INFO  16:49:48,472 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:49Z] INFO  16:49:48,702 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:49Z] INFO  16:49:48,764 ProgressMeter -            done   1.5518962E7    20.0 s       1.0 s      100.0%    20.0 s       0.0 s
[2016-04-14T23:49Z] INFO  16:49:48,764 ProgressMeter - Total runtime 20.48 secs, 0.34 min, 0.01 hours
[2016-04-14T23:49Z] INFO  16:49:48,768 MicroScheduler - 44767 reads were filtered out during the traversal out of approximately 272803 total reads (16.41%)
[2016-04-14T23:49Z] INFO  16:49:48,768 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:49Z] INFO  16:49:48,769 MicroScheduler -   -> 575 reads (0.21% of total) failing BadMateFilter
[2016-04-14T23:49Z] INFO  16:49:48,769 MicroScheduler -   -> 18984 reads (6.96% of total) failing DuplicateReadFilter
[2016-04-14T23:49Z] INFO  16:49:48,769 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-14T23:49Z] INFO  16:49:48,769 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:49Z] INFO  16:49:48,770 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-14T23:49Z] INFO  16:49:48,770 MicroScheduler -   -> 25208 reads (9.24% of total) failing MappingQualityZeroFilter
[2016-04-14T23:49Z] INFO  16:49:48,770 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:49Z] INFO  16:49:48,770 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-14T23:49Z] INFO  16:49:48,771 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-14T23:49Z] INFO  16:49:49,483 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:49Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-5_49695692_65288736-prep.bam
[2016-04-14T23:49Z] INFO  16:49:49,789 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@32d5a4c6
[2016-04-14T23:49Z] INFO  16:49:49,814 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-14T23:49Z] INFO  16:49:49,903 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:49Z] INFO  16:49:49,913 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:49Z] INFO  16:49:49,986 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-14T23:49Z] INFO  16:49:49,993 ProgressMeter -            done    172041.0    24.0 s       2.3 m      100.0%    24.0 s       0.0 s
[2016-04-14T23:49Z] INFO  16:49:49,994 ProgressMeter - Total runtime 24.07 secs, 0.40 min, 0.01 hours
[2016-04-14T23:49Z] INFO  16:49:49,994 MicroScheduler - 158 reads were filtered out during the traversal out of approximately 172199 total reads (0.09%)
[2016-04-14T23:49Z] INFO  16:49:49,997 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:49Z] INFO  16:49:49,998 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:49Z] INFO  16:49:49,998 MicroScheduler -   -> 158 reads (0.09% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:49Z] INFO  16:49:50,002 IntervalUtils - Processing 15782253 bp from intervals
[2016-04-14T23:49Z] GATK pre-alignment ('6', 78400388, 93953258) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-14T23:49Z] INFO  16:49:50,085 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:49Z] INFO  16:49:50,224 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:49Z] GATK: realign ('5', 65290574, 80809536) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-14T23:49Z] INFO  16:49:50,269 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:49Z] INFO  16:49:50,272 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:49Z] INFO  16:49:50,273 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:49Z] INFO  16:49:50,273 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:49Z] INFO  16:49:50,278 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/5/R14-18105_kapa-NGv3-PE100-NGv3-sort-5_112073555_127595521-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/5/R14-18105_kapa-NGv3-PE100-NGv3-sort-5_112073555_127595521-prep-prealign-realign.intervals -L 5:112073556-127595521 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/5/tx/tmpkYyW4U/R14-18105_kapa-NGv3-PE100-NGv3-sort-5_112073555_127595521-prep.bam
[2016-04-14T23:49Z] INFO  16:49:50,302 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:49Z] INFO  16:49:50,304 HelpFormatter - Date/Time: 2016/04/14 16:49:50
[2016-04-14T23:49Z] INFO  16:49:50,304 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:49Z] INFO  16:49:50,305 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:49Z] INFO  16:49:50,381 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:49Z] INFO  16:49:50,383 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:49Z] INFO  16:49:50,383 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:49Z] INFO  16:49:50,384 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:49Z] INFO  16:49:50,402 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:49Z] INFO  16:49:50,517 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:49Z] INFO  16:49:50,568 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:49Z] INFO  16:49:50,663 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:49Z] INFO  16:49:50,678 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:49Z] INFO  16:49:50,760 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-14T23:49Z] INFO  16:49:51,154 IntervalUtils - Processing 15521966 bp from intervals
[2016-04-14T23:49Z] WARN  16:49:51,170 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:49Z] INFO  16:49:51,294 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:49Z] INFO  16:49:51,414 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:49Z] INFO  16:49:51,415 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:49Z] INFO  16:49:51,416 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:49Z] INFO  16:49:51,417 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:49Z] INFO  16:49:51,484 ProgressMeter -            done    227103.0    17.0 s      76.0 s      100.0%    17.0 s       0.0 s
[2016-04-14T23:49Z] INFO  16:49:51,484 ProgressMeter - Total runtime 17.30 secs, 0.29 min, 0.00 hours
[2016-04-14T23:49Z] INFO  16:49:51,488 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 227103 total reads (0.00%)
[2016-04-14T23:49Z] INFO  16:49:51,489 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:49Z] INFO  16:49:51,489 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:49Z] INFO  16:49:51,490 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:49Z] INFO  16:49:51,501 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:49Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-5_158711911_174870102-prep-prealign.bam
[2016-04-14T23:49Z] INFO  16:49:51,592 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:49Z] INFO  16:49:51,768 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:49Z] GATK RealignerTargetCreator: R14-18105_kapa-NGv3-PE100-NGv3-sort-5_158711911_174870102-prep-prealign.bam 5:158711912-174870102
[2016-04-14T23:49Z] GATK: RealignerTargetCreator
[2016-04-14T23:49Z] INFO  16:49:52,861 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:49Z] INFO  16:49:52,864 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:49Z] INFO  16:49:52,865 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:49Z] INFO  16:49:52,865 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:49Z] INFO  16:49:52,870 HelpFormatter - Program Args: -T PrintReads -L 6:78400389-93953258 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/6/tx/tmpCo6dug/R14-18105_kapa-NGv3-PE100-NGv3-sort-6_78400388_93953258-prep-prealign.bam
[2016-04-14T23:49Z] INFO  16:49:52,889 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:49Z] INFO  16:49:52,889 HelpFormatter - Date/Time: 2016/04/14 16:49:52
[2016-04-14T23:49Z] INFO  16:49:52,889 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:49Z] INFO  16:49:52,890 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:49Z] INFO  16:49:53,080 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:49Z] INFO  16:49:53,084 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:49Z] INFO  16:49:53,084 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:49Z] INFO  16:49:53,085 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:49Z] INFO  16:49:53,089 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/5/R14-18105_kapa-NGv3-PE100-NGv3-sort-5_65290574_80809536-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/5/R14-18105_kapa-NGv3-PE100-NGv3-sort-5_65290574_80809536-prep-prealign-realign.intervals -L 5:65290575-80809536 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/5/tx/tmp0_z0j9/R14-18105_kapa-NGv3-PE100-NGv3-sort-5_65290574_80809536-prep.bam
[2016-04-14T23:49Z] INFO  16:49:53,091 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:49Z] INFO  16:49:53,099 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:49Z] INFO  16:49:53,111 HelpFormatter - Date/Time: 2016/04/14 16:49:53
[2016-04-14T23:49Z] INFO  16:49:53,112 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:49Z] INFO  16:49:53,113 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:49Z] INFO  16:49:53,397 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:49Z] INFO  16:49:53,481 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:49Z] INFO  16:49:53,487 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:49Z] INFO  16:49:53,497 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:49Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-5_0_15580921-prep.bam
[2016-04-14T23:49Z] INFO  16:49:53,551 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-14T23:49Z] INFO  16:49:53,972 ProgressMeter -            done    137496.0    10.0 s      78.0 s      100.0%    10.0 s       0.0 s
[2016-04-14T23:49Z] INFO  16:49:53,973 ProgressMeter - Total runtime 10.85 secs, 0.18 min, 0.00 hours
[2016-04-14T23:49Z] INFO  16:49:53,977 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 137496 total reads (0.00%)
[2016-04-14T23:49Z] INFO  16:49:53,977 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:49Z] INFO  16:49:53,977 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:49Z] INFO  16:49:53,978 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:49Z] INFO  16:49:54,002 IntervalUtils - Processing 15518962 bp from intervals
[2016-04-14T23:49Z] WARN  16:49:54,007 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:49Z] INFO  16:49:54,091 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:49Z] INFO  16:49:54,189 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-14T23:49Z] GATK pre-alignment ('6', 93955015, 109466584) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-14T23:49Z] INFO  16:49:54,271 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:49Z] INFO  16:49:54,279 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:49Z] INFO  16:49:54,293 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:49Z] INFO  16:49:54,294 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:49Z] INFO  16:49:54,295 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:49Z] INFO  16:49:54,296 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:49Z] INFO  16:49:54,321 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.04
[2016-04-14T23:49Z] INFO  16:49:54,345 IntervalUtils - Processing 15552870 bp from intervals
[2016-04-14T23:49Z] INFO  16:49:54,417 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:49Z] INFO  16:49:54,470 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:49Z] INFO  16:49:54,676 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:49Z] INFO  16:49:54,715 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:49Z] INFO  16:49:54,716 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:49Z] INFO  16:49:54,717 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:49Z] INFO  16:49:54,717 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:49Z] INFO  16:49:54,729 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:49Z] INFO  16:49:54,907 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:49Z] INFO  16:49:54,999 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:49Z] INFO  16:49:55,002 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:49Z] INFO  16:49:55,003 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:49Z] INFO  16:49:55,003 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:49Z] INFO  16:49:55,008 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/5/R14-18105_kapa-NGv3-PE100-NGv3-sort-5_158711911_174870102-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/5/tx/tmp09ujXn/R14-18105_kapa-NGv3-PE100-NGv3-sort-5_158711911_174870102-prep-prealign-realign.intervals -l INFO -L 5:158711912-174870102 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-14T23:49Z] INFO  16:49:55,017 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:49Z] INFO  16:49:55,018 HelpFormatter - Date/Time: 2016/04/14 16:49:54
[2016-04-14T23:49Z] INFO  16:49:55,018 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:49Z] INFO  16:49:55,019 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:49Z] INFO  16:49:55,164 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:49Z] INFO  16:49:55,389 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-14T23:49Z] INFO  16:49:55,398 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:49Z] INFO  16:49:55,444 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.04
[2016-04-14T23:49Z] INFO  16:49:55,630 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:49Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-5_80911291_96430739-prep.bam
[2016-04-14T23:49Z] INFO  16:49:55,761 IntervalUtils - Processing 16158191 bp from intervals
[2016-04-14T23:49Z] WARN  16:49:55,767 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:49Z] INFO  16:49:55,931 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:49Z] INFO  16:49:56,026 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:49Z] INFO  16:49:56,028 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:49Z] INFO  16:49:56,028 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:49Z] INFO  16:49:56,029 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-14T23:49Z] GATK pre-alignment ('6', 109467960, 124979532) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-14T23:49Z] INFO  16:49:56,239 ProgressMeter -     5:179227287    200002.0    30.0 s       2.5 m       71.8%    41.0 s      11.0 s
[2016-04-14T23:49Z] INFO  16:49:56,788 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@41fd9d8e
[2016-04-14T23:49Z] INFO  16:49:56,925 ProgressMeter -            done    331111.0    42.0 s       2.1 m      100.0%    42.0 s       0.0 s
[2016-04-14T23:49Z] INFO  16:49:56,926 ProgressMeter - Total runtime 42.43 secs, 0.71 min, 0.01 hours
[2016-04-14T23:49Z] INFO  16:49:56,927 MicroScheduler - 192 reads were filtered out during the traversal out of approximately 331303 total reads (0.06%)
[2016-04-14T23:49Z] INFO  16:49:56,931 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:49Z] INFO  16:49:56,932 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:49Z] INFO  16:49:56,932 MicroScheduler -   -> 192 reads (0.06% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:49Z] INFO  16:49:57,199 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:49Z] INFO  16:49:57,203 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:49Z] INFO  16:49:57,203 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:49Z] INFO  16:49:57,204 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:49Z] INFO  16:49:57,209 HelpFormatter - Program Args: -T PrintReads -L 6:93955016-109466584 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/6/tx/tmp2b8XD9/R14-18105_kapa-NGv3-PE100-NGv3-sort-6_93955015_109466584-prep-prealign.bam
[2016-04-14T23:49Z] INFO  16:49:57,220 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:49Z] INFO  16:49:57,220 HelpFormatter - Date/Time: 2016/04/14 16:49:57
[2016-04-14T23:49Z] INFO  16:49:57,221 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:49Z] INFO  16:49:57,221 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:49Z] INFO  16:49:57,436 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:49Z] INFO  16:49:58,247 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:49Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-5_143200044_158710347-prep-prealign.bam
[2016-04-14T23:49Z] INFO  16:49:58,549 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@41fd9d8e
[2016-04-14T23:49Z] INFO  16:49:58,609 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-14T23:49Z] INFO  16:49:58,614 ProgressMeter -            done    213819.0    29.0 s       2.3 m      100.0%    29.0 s       0.0 s
[2016-04-14T23:49Z] INFO  16:49:58,615 ProgressMeter - Total runtime 29.16 secs, 0.49 min, 0.01 hours
[2016-04-14T23:49Z] INFO  16:49:58,616 MicroScheduler - 128 reads were filtered out during the traversal out of approximately 213947 total reads (0.06%)
[2016-04-14T23:49Z] INFO  16:49:58,617 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:49Z] INFO  16:49:58,617 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:49Z] INFO  16:49:58,618 MicroScheduler -   -> 128 reads (0.06% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:49Z] INFO  16:49:58,671 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:49Z] INFO  16:49:58,680 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:49Z] INFO  16:49:58,753 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-14T23:49Z] INFO  16:49:58,767 IntervalUtils - Processing 15511569 bp from intervals
[2016-04-14T23:49Z] INFO  16:49:58,841 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:49Z] INFO  16:49:59,127 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:49Z] INFO  16:49:59,128 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:49Z] INFO  16:49:59,129 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:49Z] INFO  16:49:59,130 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:49Z] INFO  16:49:59,153 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:49Z] INFO  16:49:59,223 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:49Z] INFO  16:49:59,227 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:49Z] INFO  16:49:59,228 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:49Z] INFO  16:49:59,228 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:49Z] INFO  16:49:59,233 HelpFormatter - Program Args: -T PrintReads -L 6:109467961-124979532 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/6/tx/tmpE9jZ0u/R14-18105_kapa-NGv3-PE100-NGv3-sort-6_109467960_124979532-prep-prealign.bam
[2016-04-14T23:49Z] GATK RealignerTargetCreator: R14-18105_kapa-NGv3-PE100-NGv3-sort-5_143200044_158710347-prep-prealign.bam 5:143200045-158710347
[2016-04-14T23:49Z] GATK: RealignerTargetCreator
[2016-04-14T23:49Z] INFO  16:49:59,260 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:49Z] INFO  16:49:59,261 HelpFormatter - Date/Time: 2016/04/14 16:49:59
[2016-04-14T23:49Z] INFO  16:49:59,272 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:49Z] INFO  16:49:59,273 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:49Z] INFO  16:49:59,289 ProgressMeter -      6:28120976    200003.0    30.0 s       2.5 m       81.0%    37.0 s       7.0 s
[2016-04-14T23:49Z] INFO  16:49:59,317 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:49Z] INFO  16:49:59,468 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:50Z] INFO  16:50:00,133 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:50Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-6_0_15509601-prep-prealign.bam
[2016-04-14T23:50Z] INFO  16:50:00,705 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-14T23:50Z] INFO  16:50:00,770 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:50Z] INFO  16:50:00,780 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:50Z] INFO  16:50:00,872 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.09
[2016-04-14T23:50Z] INFO  16:50:00,898 IntervalUtils - Processing 15511572 bp from intervals
[2016-04-14T23:50Z] GATK RealignerTargetCreator: R14-18105_kapa-NGv3-PE100-NGv3-sort-6_0_15509601-prep-prealign.bam 6:1-15509601
[2016-04-14T23:50Z] GATK: RealignerTargetCreator
[2016-04-14T23:50Z] INFO  16:50:00,987 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:50Z] INFO  16:50:01,325 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:50Z] INFO  16:50:01,326 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:50Z] INFO  16:50:01,326 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:50Z] INFO  16:50:01,326 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:50Z] INFO  16:50:01,355 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:50Z] INFO  16:50:01,569 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:50Z] INFO  16:50:02,394 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:50Z] INFO  16:50:02,401 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:50Z] INFO  16:50:02,402 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:50Z] INFO  16:50:02,403 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:50Z] INFO  16:50:02,407 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/5/R14-18105_kapa-NGv3-PE100-NGv3-sort-5_143200044_158710347-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/5/tx/tmpATrvN2/R14-18105_kapa-NGv3-PE100-NGv3-sort-5_143200044_158710347-prep-prealign-realign.intervals -l INFO -L 5:143200045-158710347 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-14T23:50Z] INFO  16:50:02,417 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:50Z] INFO  16:50:02,418 HelpFormatter - Date/Time: 2016/04/14 16:50:02
[2016-04-14T23:50Z] INFO  16:50:02,419 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:50Z] INFO  16:50:02,419 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:50Z] INFO  16:50:02,518 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:50Z] INFO  16:50:02,766 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-14T23:50Z] INFO  16:50:02,776 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:50Z] INFO  16:50:02,869 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.09
[2016-04-14T23:50Z] INFO  16:50:03,229 IntervalUtils - Processing 15510303 bp from intervals
[2016-04-14T23:50Z] WARN  16:50:03,235 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:50Z] INFO  16:50:03,375 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:50Z] INFO  16:50:03,583 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:50Z] INFO  16:50:03,584 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:50Z] INFO  16:50:03,585 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:50Z] INFO  16:50:03,585 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-14T23:50Z] INFO  16:50:03,675 ProgressMeter -            done    141065.0    12.0 s      86.0 s      100.0%    12.0 s       0.0 s
[2016-04-14T23:50Z] INFO  16:50:03,676 ProgressMeter - Total runtime 12.26 secs, 0.20 min, 0.00 hours
[2016-04-14T23:50Z] INFO  16:50:03,680 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 141065 total reads (0.00%)
[2016-04-14T23:50Z] INFO  16:50:03,681 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:50Z] INFO  16:50:03,682 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:50Z] INFO  16:50:03,682 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:50Z] INFO  16:50:03,809 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:50Z] INFO  16:50:03,813 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:50Z] INFO  16:50:03,813 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:50Z] INFO  16:50:03,814 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:50Z] INFO  16:50:03,819 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/6/R14-18105_kapa-NGv3-PE100-NGv3-sort-6_0_15509601-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/6/tx/tmpJOsAvB/R14-18105_kapa-NGv3-PE100-NGv3-sort-6_0_15509601-prep-prealign-realign.intervals -l INFO -L 6:1-15509601 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-14T23:50Z] INFO  16:50:03,850 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:50Z] INFO  16:50:03,851 HelpFormatter - Date/Time: 2016/04/14 16:50:03
[2016-04-14T23:50Z] INFO  16:50:03,851 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:50Z] INFO  16:50:03,851 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:50Z] INFO  16:50:03,852 ProgressMeter -            done    237647.0    17.0 s      73.0 s      100.0%    17.0 s       0.0 s
[2016-04-14T23:50Z] INFO  16:50:03,853 ProgressMeter - Total runtime 17.36 secs, 0.29 min, 0.00 hours
[2016-04-14T23:50Z] INFO  16:50:03,857 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 237647 total reads (0.00%)
[2016-04-14T23:50Z] INFO  16:50:03,857 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:50Z] INFO  16:50:03,858 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:50Z] INFO  16:50:03,858 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:50Z] INFO  16:50:03,953 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:50Z] INFO  16:50:04,073 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@7172f77a
[2016-04-14T23:50Z] INFO  16:50:04,153 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-14T23:50Z] INFO  16:50:04,170 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:50Z] INFO  16:50:04,248 ProgressMeter -            done    308109.0    38.0 s       2.1 m       99.8%    38.0 s       0.0 s
[2016-04-14T23:50Z] INFO  16:50:04,249 ProgressMeter - Total runtime 38.04 secs, 0.63 min, 0.01 hours
[2016-04-14T23:50Z] INFO  16:50:04,250 MicroScheduler - 101 reads were filtered out during the traversal out of approximately 308210 total reads (0.03%)
[2016-04-14T23:50Z] INFO  16:50:04,250 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:50Z] INFO  16:50:04,250 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:50Z] INFO  16:50:04,251 MicroScheduler -   -> 101 reads (0.03% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:50Z] INFO  16:50:04,253 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-14T23:50Z] INFO  16:50:04,285 ProgressMeter -      6:32063604    200005.0    30.0 s       2.5 m        6.3%     7.9 m       7.4 m
[2016-04-14T23:50Z] INFO  16:50:04,496 IntervalUtils - Processing 15509601 bp from intervals
[2016-04-14T23:50Z] WARN  16:50:04,501 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:50Z] INFO  16:50:04,599 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:50Z] INFO  16:50:04,795 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:50Z] INFO  16:50:04,796 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:50Z] INFO  16:50:04,797 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:50Z] INFO  16:50:04,798 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-14T23:50Z] INFO  16:50:05,285 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:50Z] INFO  16:50:05,303 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:50Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-5_112073555_127595521-prep.bam
[2016-04-14T23:50Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-5_31294068_49695124-prep.bam
[2016-04-14T23:50Z] INFO  16:50:05,715 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:50Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-5_174919106_180915260-prep-prealign.bam
[2016-04-14T23:50Z] GATK pre-alignment ('6', 125112484, 142397186) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-14T23:50Z] GATK pre-alignment ('6', 142399691, 157963777) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-14T23:50Z] GATK RealignerTargetCreator: R14-18105_kapa-NGv3-PE100-NGv3-sort-5_174919106_180915260-prep-prealign.bam 5:174919107-180915260
[2016-04-14T23:50Z] GATK: RealignerTargetCreator
[2016-04-14T23:50Z] INFO  16:50:07,337 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@5fe152b7
[2016-04-14T23:50Z] INFO  16:50:07,473 ProgressMeter -            done    197998.0    26.0 s       2.3 m      100.0%    26.0 s       0.0 s
[2016-04-14T23:50Z] INFO  16:50:07,473 ProgressMeter - Total runtime 26.94 secs, 0.45 min, 0.01 hours
[2016-04-14T23:50Z] INFO  16:50:07,474 MicroScheduler - 122 reads were filtered out during the traversal out of approximately 198120 total reads (0.06%)
[2016-04-14T23:50Z] INFO  16:50:07,475 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:50Z] INFO  16:50:07,475 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:50Z] INFO  16:50:07,476 MicroScheduler -   -> 122 reads (0.06% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:50Z] INFO  16:50:08,545 ProgressMeter -       4:9213066    300005.0    30.0 s     102.0 s       59.4%    50.0 s      20.0 s
[2016-04-14T23:50Z] INFO  16:50:08,866 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:50Z] INFO  16:50:08,869 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:50Z] INFO  16:50:08,870 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:50Z] INFO  16:50:08,870 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:50Z] INFO  16:50:08,875 HelpFormatter - Program Args: -T PrintReads -L 6:125112485-142397186 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/6/tx/tmpozCw6B/R14-18105_kapa-NGv3-PE100-NGv3-sort-6_125112484_142397186-prep-prealign.bam
[2016-04-14T23:50Z] INFO  16:50:08,877 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:50Z] INFO  16:50:08,884 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:50Z] INFO  16:50:08,885 HelpFormatter - Date/Time: 2016/04/14 16:50:08
[2016-04-14T23:50Z] INFO  16:50:08,886 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:50Z] INFO  16:50:08,886 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:50Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-6_46598699_62284307-prep-prealign.bam
[2016-04-14T23:50Z] INFO  16:50:09,067 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:50Z] INFO  16:50:09,207 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:50Z] INFO  16:50:09,210 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:50Z] INFO  16:50:09,211 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:50Z] INFO  16:50:09,211 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:50Z] INFO  16:50:09,216 HelpFormatter - Program Args: -T PrintReads -L 6:142399692-157963777 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/6/tx/tmpEX2AW3/R14-18105_kapa-NGv3-PE100-NGv3-sort-6_142399691_157963777-prep-prealign.bam
[2016-04-14T23:50Z] INFO  16:50:09,234 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:50Z] INFO  16:50:09,235 HelpFormatter - Date/Time: 2016/04/14 16:50:09
[2016-04-14T23:50Z] INFO  16:50:09,236 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:50Z] INFO  16:50:09,236 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:50Z] INFO  16:50:09,417 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:50Z] GATK RealignerTargetCreator: R14-18105_kapa-NGv3-PE100-NGv3-sort-6_46598699_62284307-prep-prealign.bam 6:46598700-62284307
[2016-04-14T23:50Z] GATK: RealignerTargetCreator
[2016-04-14T23:50Z] INFO  16:50:09,881 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:50Z] INFO  16:50:09,884 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:50Z] INFO  16:50:09,885 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:50Z] INFO  16:50:09,885 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:50Z] INFO  16:50:09,890 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/5/R14-18105_kapa-NGv3-PE100-NGv3-sort-5_174919106_180915260-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/5/tx/tmpMp4rX8/R14-18105_kapa-NGv3-PE100-NGv3-sort-5_174919106_180915260-prep-prealign-realign.intervals -l INFO -L 5:174919107-180915260 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-14T23:50Z] INFO  16:50:09,909 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:50Z] INFO  16:50:09,910 HelpFormatter - Date/Time: 2016/04/14 16:50:09
[2016-04-14T23:50Z] INFO  16:50:09,911 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:50Z] INFO  16:50:09,911 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:50Z] INFO  16:50:10,019 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:50Z] INFO  16:50:10,154 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-14T23:50Z] INFO  16:50:10,221 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:50Z] INFO  16:50:10,229 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:50Z] INFO  16:50:10,230 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-14T23:50Z] INFO  16:50:10,240 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:50Z] INFO  16:50:10,268 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.04
[2016-04-14T23:50Z] INFO  16:50:10,293 IntervalUtils - Processing 17284702 bp from intervals
[2016-04-14T23:50Z] INFO  16:50:10,303 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-14T23:50Z] INFO  16:50:10,368 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:50Z] INFO  16:50:10,584 IntervalUtils - Processing 5996154 bp from intervals
[2016-04-14T23:50Z] WARN  16:50:10,589 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:50Z] INFO  16:50:10,663 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-14T23:50Z] INFO  16:50:10,675 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:50Z] INFO  16:50:10,709 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:50Z] INFO  16:50:10,709 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:50Z] INFO  16:50:10,710 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:50Z] INFO  16:50:10,710 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:50Z] INFO  16:50:10,727 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:50Z] INFO  16:50:10,735 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:50Z] INFO  16:50:10,736 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:50Z] INFO  16:50:10,777 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.04
[2016-04-14T23:50Z] INFO  16:50:10,791 IntervalUtils - Processing 15564086 bp from intervals
[2016-04-14T23:50Z] INFO  16:50:10,851 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:50Z] INFO  16:50:10,852 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:50Z] INFO  16:50:10,853 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:50Z] INFO  16:50:10,854 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-14T23:50Z] INFO  16:50:10,864 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:50Z] INFO  16:50:10,882 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:50Z] INFO  16:50:11,185 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:50Z] INFO  16:50:11,186 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:50Z] INFO  16:50:11,187 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:50Z] INFO  16:50:11,188 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:50Z] INFO  16:50:11,201 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:50Z] INFO  16:50:11,360 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:50Z] INFO  16:50:12,259 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:50Z] INFO  16:50:12,262 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:50Z] INFO  16:50:12,263 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:50Z] INFO  16:50:12,263 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:50Z] INFO  16:50:12,268 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/6/R14-18105_kapa-NGv3-PE100-NGv3-sort-6_46598699_62284307-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/6/tx/tmpo5w_O0/R14-18105_kapa-NGv3-PE100-NGv3-sort-6_46598699_62284307-prep-prealign-realign.intervals -l INFO -L 6:46598700-62284307 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-14T23:50Z] INFO  16:50:12,278 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:50Z] INFO  16:50:12,289 HelpFormatter - Date/Time: 2016/04/14 16:50:12
[2016-04-14T23:50Z] INFO  16:50:12,290 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:50Z] INFO  16:50:12,291 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:50Z] INFO  16:50:12,424 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:50Z] INFO  16:50:12,627 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-14T23:50Z] INFO  16:50:12,637 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:50Z] INFO  16:50:12,716 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-14T23:50Z] INFO  16:50:13,059 IntervalUtils - Processing 15685608 bp from intervals
[2016-04-14T23:50Z] WARN  16:50:13,075 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:50Z] INFO  16:50:13,122 ProgressMeter -     5:140559408    400013.0    60.0 s       2.5 m       83.1%    72.0 s      12.0 s
[2016-04-14T23:50Z] INFO  16:50:13,308 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:50Z] INFO  16:50:13,334 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@41fd9d8e
[2016-04-14T23:50Z] INFO  16:50:13,469 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:50Z] INFO  16:50:13,470 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:50Z] INFO  16:50:13,475 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:50Z] INFO  16:50:13,475 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-14T23:50Z] INFO  16:50:13,552 ProgressMeter -            done    129871.0    23.0 s       3.0 m      100.0%    23.0 s       0.0 s
[2016-04-14T23:50Z] INFO  16:50:13,552 ProgressMeter - Total runtime 23.17 secs, 0.39 min, 0.01 hours
[2016-04-14T23:50Z] INFO  16:50:13,553 MicroScheduler - 117 reads were filtered out during the traversal out of approximately 129988 total reads (0.09%)
[2016-04-14T23:50Z] INFO  16:50:13,553 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:50Z] INFO  16:50:13,553 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:50Z] INFO  16:50:13,554 MicroScheduler -   -> 117 reads (0.09% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:50Z] INFO  16:50:13,606 ProgressMeter -            done    271595.0    19.0 s      71.0 s      100.0%    19.0 s       0.0 s
[2016-04-14T23:50Z] INFO  16:50:13,606 ProgressMeter - Total runtime 19.31 secs, 0.32 min, 0.01 hours
[2016-04-14T23:50Z] INFO  16:50:13,610 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 271595 total reads (0.00%)
[2016-04-14T23:50Z] INFO  16:50:13,611 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:50Z] INFO  16:50:13,611 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:50Z] INFO  16:50:13,611 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:50Z] INFO  16:50:13,797 ProgressMeter -            done   1.6158191E7    17.0 s       1.0 s      100.0%    17.0 s       0.0 s
[2016-04-14T23:50Z] INFO  16:50:13,798 ProgressMeter - Total runtime 17.77 secs, 0.30 min, 0.00 hours
[2016-04-14T23:50Z] INFO  16:50:13,802 MicroScheduler - 14931 reads were filtered out during the traversal out of approximately 173322 total reads (8.61%)
[2016-04-14T23:50Z] INFO  16:50:13,803 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:50Z] INFO  16:50:13,804 MicroScheduler -   -> 572 reads (0.33% of total) failing BadMateFilter
[2016-04-14T23:50Z] INFO  16:50:13,804 MicroScheduler -   -> 13840 reads (7.99% of total) failing DuplicateReadFilter
[2016-04-14T23:50Z] INFO  16:50:13,805 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-14T23:50Z] INFO  16:50:13,805 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:50Z] INFO  16:50:13,806 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-14T23:50Z] INFO  16:50:13,807 MicroScheduler -   -> 519 reads (0.30% of total) failing MappingQualityZeroFilter
[2016-04-14T23:50Z] INFO  16:50:13,807 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:50Z] INFO  16:50:13,808 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-14T23:50Z] INFO  16:50:13,809 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-14T23:50Z] INFO  16:50:15,118 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:50Z] INFO  16:50:15,141 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:50Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-6_62390867_78173120-prep-prealign.bam
[2016-04-14T23:50Z] INFO  16:50:15,179 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:50Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-5_65290574_80809536-prep.bam
[2016-04-14T23:50Z] GATK: realign ('5', 158711911, 174870102) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-14T23:50Z] GATK RealignerTargetCreator: R14-18105_kapa-NGv3-PE100-NGv3-sort-6_62390867_78173120-prep-prealign.bam 6:62390868-78173120
[2016-04-14T23:50Z] GATK: RealignerTargetCreator
[2016-04-14T23:50Z] INFO  16:50:15,948 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@7172f77a
[2016-04-14T23:50Z] GATK pre-alignment ('6', 158013810, 171115067) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-14T23:50Z] INFO  16:50:16,112 ProgressMeter -            done    117862.0    16.0 s       2.4 m      100.0%    16.0 s       0.0 s
[2016-04-14T23:50Z] INFO  16:50:16,112 ProgressMeter - Total runtime 16.98 secs, 0.28 min, 0.00 hours
[2016-04-14T23:50Z] INFO  16:50:16,113 MicroScheduler - 109 reads were filtered out during the traversal out of approximately 117971 total reads (0.09%)
[2016-04-14T23:50Z] INFO  16:50:16,113 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:50Z] INFO  16:50:16,113 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:50Z] INFO  16:50:16,114 MicroScheduler -   -> 109 reads (0.09% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:50Z] INFO  16:50:16,416 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@41fd9d8e
[2016-04-14T23:50Z] INFO  16:50:16,498 ProgressMeter -            done    161655.0    21.0 s       2.2 m      100.0%    21.0 s       0.0 s
[2016-04-14T23:50Z] INFO  16:50:16,499 ProgressMeter - Total runtime 21.78 secs, 0.36 min, 0.01 hours
[2016-04-14T23:50Z] INFO  16:50:16,500 MicroScheduler - 112 reads were filtered out during the traversal out of approximately 161767 total reads (0.07%)
[2016-04-14T23:50Z] INFO  16:50:16,501 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:50Z] INFO  16:50:16,501 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:50Z] INFO  16:50:16,502 MicroScheduler -   -> 112 reads (0.07% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:50Z] INFO  16:50:17,564 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@41fd9d8e
[2016-04-14T23:50Z] INFO  16:50:17,631 ProgressMeter -            done    387349.0    48.0 s       2.1 m      100.0%    48.0 s       0.0 s
[2016-04-14T23:50Z] INFO  16:50:17,632 ProgressMeter - Total runtime 48.39 secs, 0.81 min, 0.01 hours
[2016-04-14T23:50Z] INFO  16:50:17,633 MicroScheduler - 198 reads were filtered out during the traversal out of approximately 387547 total reads (0.05%)
[2016-04-14T23:50Z] INFO  16:50:17,634 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:50Z] INFO  16:50:17,635 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:50Z] INFO  16:50:17,635 MicroScheduler -   -> 198 reads (0.05% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:50Z] INFO  16:50:17,660 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:50Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-6_93955015_109466584-prep-prealign.bam
[2016-04-14T23:50Z] GATK RealignerTargetCreator: R14-18105_kapa-NGv3-PE100-NGv3-sort-6_93955015_109466584-prep-prealign.bam 6:93955016-109466584
[2016-04-14T23:50Z] GATK: RealignerTargetCreator
[2016-04-14T23:50Z] INFO  16:50:18,199 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:50Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-6_78400388_93953258-prep-prealign.bam
[2016-04-14T23:50Z] INFO  16:50:18,514 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:50Z] INFO  16:50:18,517 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:50Z] INFO  16:50:18,518 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:50Z] INFO  16:50:18,518 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:50Z] INFO  16:50:18,523 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/5/R14-18105_kapa-NGv3-PE100-NGv3-sort-5_158711911_174870102-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/5/R14-18105_kapa-NGv3-PE100-NGv3-sort-5_158711911_174870102-prep-prealign-realign.intervals -L 5:158711912-174870102 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/5/tx/tmpH5AGk8/R14-18105_kapa-NGv3-PE100-NGv3-sort-5_158711911_174870102-prep.bam
[2016-04-14T23:50Z] INFO  16:50:18,552 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:50Z] INFO  16:50:18,553 HelpFormatter - Date/Time: 2016/04/14 16:50:18
[2016-04-14T23:50Z] INFO  16:50:18,553 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:50Z] INFO  16:50:18,554 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:50Z] INFO  16:50:18,622 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:50Z] INFO  16:50:18,625 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:50Z] INFO  16:50:18,626 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:50Z] INFO  16:50:18,627 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:50Z] INFO  16:50:18,631 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/6/R14-18105_kapa-NGv3-PE100-NGv3-sort-6_62390867_78173120-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/6/tx/tmpLPi7gc/R14-18105_kapa-NGv3-PE100-NGv3-sort-6_62390867_78173120-prep-prealign-realign.intervals -l INFO -L 6:62390868-78173120 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-14T23:50Z] INFO  16:50:18,648 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:50Z] INFO  16:50:18,649 HelpFormatter - Date/Time: 2016/04/14 16:50:18
[2016-04-14T23:50Z] INFO  16:50:18,649 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:50Z] INFO  16:50:18,649 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:50Z] INFO  16:50:18,765 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:50Z] INFO  16:50:18,781 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:50Z] GATK RealignerTargetCreator: R14-18105_kapa-NGv3-PE100-NGv3-sort-6_78400388_93953258-prep-prealign.bam 6:78400389-93953258
[2016-04-14T23:50Z] GATK: RealignerTargetCreator
[2016-04-14T23:50Z] INFO  16:50:18,887 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:50Z] INFO  16:50:18,902 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:50Z] INFO  16:50:18,977 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-14T23:50Z] INFO  16:50:19,007 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:50Z] INFO  16:50:19,011 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:50Z] INFO  16:50:19,012 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:50Z] INFO  16:50:19,012 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:50Z] INFO  16:50:19,017 HelpFormatter - Program Args: -T PrintReads -L 6:158013811-171115067 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/6/tx/tmpCsD9AX/R14-18105_kapa-NGv3-PE100-NGv3-sort-6_158013810_171115067-prep-prealign.bam
[2016-04-14T23:50Z] INFO  16:50:19,026 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-14T23:50Z] INFO  16:50:19,032 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:50Z] INFO  16:50:19,033 HelpFormatter - Date/Time: 2016/04/14 16:50:19
[2016-04-14T23:50Z] INFO  16:50:19,033 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:50Z] INFO  16:50:19,034 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:50Z] INFO  16:50:19,048 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:50Z] INFO  16:50:19,130 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-14T23:50Z] INFO  16:50:19,140 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:50Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-6_15511526_31080332-prep-prealign.bam
[2016-04-14T23:50Z] INFO  16:50:19,273 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:50Z] INFO  16:50:19,417 IntervalUtils - Processing 15782253 bp from intervals
[2016-04-14T23:50Z] WARN  16:50:19,422 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:50Z] INFO  16:50:19,464 IntervalUtils - Processing 16158191 bp from intervals
[2016-04-14T23:50Z] WARN  16:50:19,470 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:50Z] INFO  16:50:19,513 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:50Z] INFO  16:50:19,600 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:50Z] INFO  16:50:19,804 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:50Z] INFO  16:50:19,810 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:50Z] INFO  16:50:19,811 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:50Z] INFO  16:50:19,812 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:50Z] INFO  16:50:19,813 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-14T23:50Z] INFO  16:50:19,814 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:50Z] INFO  16:50:19,819 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:50Z] INFO  16:50:19,821 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:50Z] INFO  16:50:20,027 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:50Z] INFO  16:50:20,239 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:50Z] INFO  16:50:20,454 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-14T23:50Z] INFO  16:50:20,537 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:50Z] INFO  16:50:20,551 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:50Z] INFO  16:50:20,610 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-14T23:50Z] INFO  16:50:20,627 IntervalUtils - Processing 13101257 bp from intervals
[2016-04-14T23:50Z] GATK RealignerTargetCreator: R14-18105_kapa-NGv3-PE100-NGv3-sort-6_15511526_31080332-prep-prealign.bam 6:15511527-31080332
[2016-04-14T23:50Z] GATK: RealignerTargetCreator
[2016-04-14T23:50Z] INFO  16:50:20,759 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:50Z] INFO  16:50:20,904 IndelRealigner - Not attempting realignment in interval 4:9270105-9270477 because there are too many reads.
[2016-04-14T23:50Z] INFO  16:50:21,091 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:50Z] INFO  16:50:21,094 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:50Z] INFO  16:50:21,095 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:50Z] INFO  16:50:21,095 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:50Z] INFO  16:50:21,100 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/6/R14-18105_kapa-NGv3-PE100-NGv3-sort-6_93955015_109466584-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/6/tx/tmpgBchAU/R14-18105_kapa-NGv3-PE100-NGv3-sort-6_93955015_109466584-prep-prealign-realign.intervals -l INFO -L 6:93955016-109466584 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-14T23:50Z] INFO  16:50:21,110 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:50Z] INFO  16:50:21,121 HelpFormatter - Date/Time: 2016/04/14 16:50:21
[2016-04-14T23:50Z] INFO  16:50:21,122 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:50Z] INFO  16:50:21,123 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:50Z] INFO  16:50:21,163 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:50Z] INFO  16:50:21,165 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:50Z] INFO  16:50:21,166 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:50Z] INFO  16:50:21,166 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:50Z] INFO  16:50:21,183 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:50Z] INFO  16:50:21,239 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:50Z] INFO  16:50:21,435 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:50Z] INFO  16:50:21,532 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-14T23:50Z] INFO  16:50:21,558 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:50Z] INFO  16:50:21,599 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:50Z] INFO  16:50:21,602 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:50Z] INFO  16:50:21,603 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:50Z] INFO  16:50:21,604 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:50Z] INFO  16:50:21,608 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/6/R14-18105_kapa-NGv3-PE100-NGv3-sort-6_78400388_93953258-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/6/tx/tmpVF8YHU/R14-18105_kapa-NGv3-PE100-NGv3-sort-6_78400388_93953258-prep-prealign-realign.intervals -l INFO -L 6:78400389-93953258 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-14T23:50Z] INFO  16:50:21,619 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:50Z] INFO  16:50:21,620 HelpFormatter - Date/Time: 2016/04/14 16:50:21
[2016-04-14T23:50Z] INFO  16:50:21,620 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:50Z] INFO  16:50:21,621 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:50Z] INFO  16:50:21,651 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.09
[2016-04-14T23:50Z] INFO  16:50:21,753 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:50Z] INFO  16:50:22,041 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-14T23:50Z] INFO  16:50:22,051 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:50Z] INFO  16:50:22,075 IntervalUtils - Processing 15511569 bp from intervals
[2016-04-14T23:50Z] WARN  16:50:22,080 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:50Z] INFO  16:50:22,093 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.04
[2016-04-14T23:50Z] INFO  16:50:22,179 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:50Z] INFO  16:50:22,334 IntervalUtils - Processing 15552870 bp from intervals
[2016-04-14T23:50Z] WARN  16:50:22,339 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:50Z] INFO  16:50:22,386 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:50Z] INFO  16:50:22,387 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:50Z] INFO  16:50:22,388 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:50Z] INFO  16:50:22,388 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-14T23:50Z] INFO  16:50:22,418 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:50Z] INFO  16:50:22,641 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:50Z] INFO  16:50:22,643 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:50Z] INFO  16:50:22,644 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:50Z] INFO  16:50:22,644 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-14T23:50Z] INFO  16:50:23,550 ProgressMeter -            done   1.5509601E7    18.0 s       1.0 s      100.0%    18.0 s       0.0 s
[2016-04-14T23:50Z] INFO  16:50:23,550 ProgressMeter - Total runtime 18.75 secs, 0.31 min, 0.01 hours
[2016-04-14T23:50Z] INFO  16:50:23,554 MicroScheduler - 26383 reads were filtered out during the traversal out of approximately 215148 total reads (12.26%)
[2016-04-14T23:50Z] INFO  16:50:23,554 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:50Z] INFO  16:50:23,555 MicroScheduler -   -> 552 reads (0.26% of total) failing BadMateFilter
[2016-04-14T23:50Z] INFO  16:50:23,555 MicroScheduler -   -> 16609 reads (7.72% of total) failing DuplicateReadFilter
[2016-04-14T23:50Z] INFO  16:50:23,555 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-14T23:50Z] INFO  16:50:23,556 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:50Z] INFO  16:50:23,556 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-14T23:50Z] INFO  16:50:23,556 MicroScheduler -   -> 9222 reads (4.29% of total) failing MappingQualityZeroFilter
[2016-04-14T23:50Z] INFO  16:50:23,556 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:50Z] INFO  16:50:23,556 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-14T23:50Z] INFO  16:50:23,557 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-14T23:50Z] INFO  16:50:23,745 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:50Z] INFO  16:50:23,749 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:50Z] INFO  16:50:23,749 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:50Z] INFO  16:50:23,750 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:50Z] INFO  16:50:23,754 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/6/R14-18105_kapa-NGv3-PE100-NGv3-sort-6_15511526_31080332-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/6/tx/tmpj9LsTg/R14-18105_kapa-NGv3-PE100-NGv3-sort-6_15511526_31080332-prep-prealign-realign.intervals -l INFO -L 6:15511527-31080332 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-14T23:50Z] INFO  16:50:23,764 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:50Z] INFO  16:50:23,765 HelpFormatter - Date/Time: 2016/04/14 16:50:23
[2016-04-14T23:50Z] INFO  16:50:23,765 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:50Z] INFO  16:50:23,766 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:50Z] INFO  16:50:23,854 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:50Z] INFO  16:50:24,069 ProgressMeter -            done   5996154.0    13.0 s       2.0 s      100.0%    13.0 s       0.0 s
[2016-04-14T23:50Z] INFO  16:50:24,070 ProgressMeter - Total runtime 13.22 secs, 0.22 min, 0.00 hours
[2016-04-14T23:50Z] INFO  16:50:24,070 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-14T23:50Z] INFO  16:50:24,075 MicroScheduler - 41123 reads were filtered out during the traversal out of approximately 309892 total reads (13.27%)
[2016-04-14T23:50Z] INFO  16:50:24,076 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:50Z] INFO  16:50:24,077 MicroScheduler -   -> 525 reads (0.17% of total) failing BadMateFilter
[2016-04-14T23:50Z] INFO  16:50:24,077 MicroScheduler -   -> 23446 reads (7.57% of total) failing DuplicateReadFilter
[2016-04-14T23:50Z] INFO  16:50:24,078 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-14T23:50Z] INFO  16:50:24,079 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:50Z] INFO  16:50:24,079 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-14T23:50Z] INFO  16:50:24,080 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:50Z] INFO  16:50:24,079 MicroScheduler -   -> 17152 reads (5.53% of total) failing MappingQualityZeroFilter
[2016-04-14T23:50Z] INFO  16:50:24,079 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:50Z] INFO  16:50:24,080 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-14T23:50Z] INFO  16:50:24,080 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-14T23:50Z] INFO  16:50:24,163 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-14T23:50Z] INFO  16:50:24,476 IntervalUtils - Processing 15568806 bp from intervals
[2016-04-14T23:50Z] WARN  16:50:24,492 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:50Z] INFO  16:50:24,574 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:50Z] INFO  16:50:24,818 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:50Z] INFO  16:50:24,819 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:50Z] INFO  16:50:24,820 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:50Z] INFO  16:50:24,821 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-14T23:50Z] INFO  16:50:24,938 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:50Z] GATK: realign ('6', 0, 15509601) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-14T23:50Z] INFO  16:50:25,428 ProgressMeter -            done   1.5510303E7    21.0 s       1.0 s      100.0%    21.0 s       0.0 s
[2016-04-14T23:50Z] INFO  16:50:25,429 ProgressMeter - Total runtime 21.85 secs, 0.36 min, 0.01 hours
[2016-04-14T23:50Z] INFO  16:50:25,433 MicroScheduler - 27670 reads were filtered out during the traversal out of approximately 333638 total reads (8.29%)
[2016-04-14T23:50Z] INFO  16:50:25,434 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:50Z] INFO  16:50:25,435 MicroScheduler -   -> 713 reads (0.21% of total) failing BadMateFilter
[2016-04-14T23:50Z] INFO  16:50:25,436 MicroScheduler -   -> 26315 reads (7.89% of total) failing DuplicateReadFilter
[2016-04-14T23:50Z] INFO  16:50:25,436 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-14T23:50Z] INFO  16:50:25,436 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:50Z] INFO  16:50:25,437 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-14T23:50Z] INFO  16:50:25,437 MicroScheduler -   -> 642 reads (0.19% of total) failing MappingQualityZeroFilter
[2016-04-14T23:50Z] INFO  16:50:25,437 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:50Z] INFO  16:50:25,437 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-14T23:50Z] INFO  16:50:25,438 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-14T23:50Z] INFO  16:50:25,528 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:50Z] GATK: realign ('5', 174919106, 180915260) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-14T23:50Z] INFO  16:50:27,075 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@5fe152b7
[2016-04-14T23:50Z] INFO  16:50:27,094 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:50Z] GATK: realign ('5', 143200044, 158710347) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-14T23:50Z] INFO  16:50:27,247 ProgressMeter -            done    186385.0    25.0 s       2.3 m      100.0%    25.0 s       0.0 s
[2016-04-14T23:50Z] INFO  16:50:27,248 ProgressMeter - Total runtime 25.92 secs, 0.43 min, 0.01 hours
[2016-04-14T23:50Z] INFO  16:50:27,249 MicroScheduler - 149 reads were filtered out during the traversal out of approximately 186534 total reads (0.08%)
[2016-04-14T23:50Z] INFO  16:50:27,250 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:50Z] INFO  16:50:27,251 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:50Z] INFO  16:50:27,251 MicroScheduler -   -> 149 reads (0.08% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:50Z] INFO  16:50:27,742 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:50Z] INFO  16:50:27,746 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:50Z] INFO  16:50:27,746 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:50Z] INFO  16:50:27,747 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:50Z] INFO  16:50:27,751 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/6/R14-18105_kapa-NGv3-PE100-NGv3-sort-6_0_15509601-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/6/R14-18105_kapa-NGv3-PE100-NGv3-sort-6_0_15509601-prep-prealign-realign.intervals -L 6:1-15509601 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/6/tx/tmpGPbtal/R14-18105_kapa-NGv3-PE100-NGv3-sort-6_0_15509601-prep.bam
[2016-04-14T23:50Z] INFO  16:50:27,774 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:50Z] INFO  16:50:27,775 HelpFormatter - Date/Time: 2016/04/14 16:50:27
[2016-04-14T23:50Z] INFO  16:50:27,775 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:50Z] INFO  16:50:27,776 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:50Z] INFO  16:50:28,033 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:50Z] INFO  16:50:28,171 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:50Z] INFO  16:50:28,181 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:50Z] INFO  16:50:28,267 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.09
[2016-04-14T23:50Z] INFO  16:50:28,465 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:50Z] INFO  16:50:28,468 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:50Z] INFO  16:50:28,468 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:50Z] INFO  16:50:28,468 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:50Z] INFO  16:50:28,472 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/5/R14-18105_kapa-NGv3-PE100-NGv3-sort-5_174919106_180915260-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/5/R14-18105_kapa-NGv3-PE100-NGv3-sort-5_174919106_180915260-prep-prealign-realign.intervals -L 5:174919107-180915260 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/5/tx/tmpp3Ds9j/R14-18105_kapa-NGv3-PE100-NGv3-sort-5_174919106_180915260-prep.bam
[2016-04-14T23:50Z] INFO  16:50:28,496 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:50Z] INFO  16:50:28,497 HelpFormatter - Date/Time: 2016/04/14 16:50:28
[2016-04-14T23:50Z] INFO  16:50:28,497 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:50Z] INFO  16:50:28,498 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:50Z] INFO  16:50:28,672 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:50Z] INFO  16:50:28,693 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:50Z] INFO  16:50:28,698 IntervalUtils - Processing 15509601 bp from intervals
[2016-04-14T23:50Z] WARN  16:50:28,713 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:50Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-6_109467960_124979532-prep-prealign.bam
[2016-04-14T23:50Z] INFO  16:50:28,796 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:50Z] INFO  16:50:28,859 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:50Z] INFO  16:50:28,873 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:50Z] INFO  16:50:28,901 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:50Z] INFO  16:50:28,911 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:50Z] INFO  16:50:28,911 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:50Z] INFO  16:50:28,912 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:50Z] INFO  16:50:28,948 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-14T23:50Z] INFO  16:50:29,102 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:50Z] INFO  16:50:29,258 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:50Z] INFO  16:50:29,306 IntervalUtils - Processing 5996154 bp from intervals
[2016-04-14T23:50Z] WARN  16:50:29,312 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:50Z] INFO  16:50:29,384 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:50Z] GATK RealignerTargetCreator: R14-18105_kapa-NGv3-PE100-NGv3-sort-6_109467960_124979532-prep-prealign.bam 6:109467961-124979532
[2016-04-14T23:50Z] GATK: RealignerTargetCreator
[2016-04-14T23:50Z] INFO  16:50:29,485 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:50Z] INFO  16:50:29,486 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:50Z] INFO  16:50:29,487 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:50Z] INFO  16:50:29,488 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:50Z] INFO  16:50:29,589 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:50Z] INFO  16:50:29,651 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:50Z] INFO  16:50:29,813 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:50Z] INFO  16:50:29,816 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:50Z] INFO  16:50:29,817 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:50Z] INFO  16:50:29,818 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:50Z] INFO  16:50:29,822 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/5/R14-18105_kapa-NGv3-PE100-NGv3-sort-5_143200044_158710347-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/5/R14-18105_kapa-NGv3-PE100-NGv3-sort-5_143200044_158710347-prep-prealign-realign.intervals -L 5:143200045-158710347 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/5/tx/tmpTZ8FLh/R14-18105_kapa-NGv3-PE100-NGv3-sort-5_143200044_158710347-prep.bam
[2016-04-14T23:50Z] INFO  16:50:29,865 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:50Z] INFO  16:50:29,865 HelpFormatter - Date/Time: 2016/04/14 16:50:29
[2016-04-14T23:50Z] INFO  16:50:29,866 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:50Z] INFO  16:50:29,867 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:50Z] INFO  16:50:30,068 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:50Z] INFO  16:50:30,233 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:50Z] INFO  16:50:30,243 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:50Z] INFO  16:50:30,314 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-14T23:50Z] INFO  16:50:30,754 IntervalUtils - Processing 15510303 bp from intervals
[2016-04-14T23:50Z] WARN  16:50:30,760 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:50Z] INFO  16:50:30,851 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:50Z] INFO  16:50:30,910 ProgressMeter -            done   1.5685608E7    17.0 s       1.0 s      100.0%    17.0 s       0.0 s
[2016-04-14T23:50Z] INFO  16:50:30,912 ProgressMeter - Total runtime 17.44 secs, 0.29 min, 0.00 hours
[2016-04-14T23:50Z] INFO  16:50:30,916 MicroScheduler - 16908 reads were filtered out during the traversal out of approximately 199194 total reads (8.49%)
[2016-04-14T23:50Z] INFO  16:50:30,917 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:50Z] INFO  16:50:30,917 MicroScheduler -   -> 565 reads (0.28% of total) failing BadMateFilter
[2016-04-14T23:50Z] INFO  16:50:30,918 MicroScheduler -   -> 15353 reads (7.71% of total) failing DuplicateReadFilter
[2016-04-14T23:50Z] INFO  16:50:30,919 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-14T23:50Z] INFO  16:50:30,919 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:50Z] INFO  16:50:30,920 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-14T23:50Z] INFO  16:50:30,921 MicroScheduler -   -> 990 reads (0.50% of total) failing MappingQualityZeroFilter
[2016-04-14T23:50Z] INFO  16:50:30,921 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:50Z] INFO  16:50:30,922 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-14T23:50Z] INFO  16:50:30,922 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-14T23:50Z] INFO  16:50:31,050 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:50Z] INFO  16:50:31,050 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:50Z] INFO  16:50:31,051 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:50Z] INFO  16:50:31,051 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:50Z] INFO  16:50:31,204 ProgressMeter -            done    903910.0    53.0 s      58.0 s      100.0%    53.0 s       0.0 s
[2016-04-14T23:50Z] INFO  16:50:31,205 ProgressMeter - Total runtime 53.27 secs, 0.89 min, 0.01 hours
[2016-04-14T23:50Z] INFO  16:50:31,215 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 903910 total reads (0.00%)
[2016-04-14T23:50Z] INFO  16:50:31,216 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:50Z] INFO  16:50:31,217 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:50Z] INFO  16:50:31,218 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:50Z] INFO  16:50:31,218 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:50Z] INFO  16:50:31,465 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:50Z] INFO  16:50:31,963 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:50Z] INFO  16:50:31,965 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:50Z] INFO  16:50:31,966 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:50Z] INFO  16:50:31,966 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:50Z] INFO  16:50:31,992 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/6/R14-18105_kapa-NGv3-PE100-NGv3-sort-6_109467960_124979532-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/6/tx/tmpar7zWE/R14-18105_kapa-NGv3-PE100-NGv3-sort-6_109467960_124979532-prep-prealign-realign.intervals -l INFO -L 6:109467961-124979532 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-14T23:50Z] INFO  16:50:32,000 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:50Z] INFO  16:50:32,000 HelpFormatter - Date/Time: 2016/04/14 16:50:31
[2016-04-14T23:50Z] INFO  16:50:32,000 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:50Z] INFO  16:50:32,001 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:50Z] INFO  16:50:32,092 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:50Z] INFO  16:50:32,286 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-14T23:50Z] INFO  16:50:32,308 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:50Z] INFO  16:50:32,312 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:50Z] GATK: realign ('6', 46598699, 62284307) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-14T23:50Z] INFO  16:50:32,366 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-14T23:50Z] INFO  16:50:32,634 IntervalUtils - Processing 15511572 bp from intervals
[2016-04-14T23:50Z] WARN  16:50:32,640 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:50Z] INFO  16:50:32,724 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:50Z] INFO  16:50:32,745 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:50Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-4_0_15511864-prep.bam
[2016-04-14T23:50Z] INFO  16:50:33,017 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:50Z] INFO  16:50:33,019 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:50Z] INFO  16:50:33,019 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:50Z] INFO  16:50:33,020 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-14T23:50Z] INFO  16:50:34,286 ProgressMeter -      6:36179226    400007.0    60.0 s       2.5 m       32.9%     3.0 m       2.0 m
[2016-04-14T23:50Z] INFO  16:50:34,689 ProgressMeter -            done    172041.0    14.0 s      86.0 s      100.0%    14.0 s       0.0 s
[2016-04-14T23:50Z] INFO  16:50:34,689 ProgressMeter - Total runtime 14.88 secs, 0.25 min, 0.00 hours
[2016-04-14T23:50Z] INFO  16:50:34,693 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 172041 total reads (0.00%)
[2016-04-14T23:50Z] INFO  16:50:34,695 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:50Z] INFO  16:50:34,696 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:50Z] INFO  16:50:34,697 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:50Z] GATK pre-alignment ('7', 0, 15584548) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-14T23:50Z] INFO  16:50:35,469 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:50Z] INFO  16:50:35,472 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:50Z] INFO  16:50:35,472 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:50Z] INFO  16:50:35,472 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:50Z] INFO  16:50:35,477 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/6/R14-18105_kapa-NGv3-PE100-NGv3-sort-6_46598699_62284307-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/6/R14-18105_kapa-NGv3-PE100-NGv3-sort-6_46598699_62284307-prep-prealign-realign.intervals -L 6:46598700-62284307 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/6/tx/tmpdn1iMy/R14-18105_kapa-NGv3-PE100-NGv3-sort-6_46598699_62284307-prep.bam
[2016-04-14T23:50Z] INFO  16:50:35,499 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:50Z] INFO  16:50:35,500 HelpFormatter - Date/Time: 2016/04/14 16:50:35
[2016-04-14T23:50Z] INFO  16:50:35,501 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:50Z] INFO  16:50:35,502 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:50Z] INFO  16:50:35,738 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:50Z] INFO  16:50:35,941 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:50Z] INFO  16:50:35,952 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:50Z] INFO  16:50:36,016 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-14T23:50Z] INFO  16:50:36,046 ProgressMeter -            done   1.5782253E7    16.0 s       1.0 s      100.0%    16.0 s       0.0 s
[2016-04-14T23:50Z] INFO  16:50:36,047 ProgressMeter - Total runtime 16.24 secs, 0.27 min, 0.00 hours
[2016-04-14T23:50Z] INFO  16:50:36,052 MicroScheduler - 12313 reads were filtered out during the traversal out of approximately 130735 total reads (9.42%)
[2016-04-14T23:50Z] INFO  16:50:36,066 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:50Z] INFO  16:50:36,067 MicroScheduler -   -> 448 reads (0.34% of total) failing BadMateFilter
[2016-04-14T23:50Z] INFO  16:50:36,067 MicroScheduler -   -> 10080 reads (7.71% of total) failing DuplicateReadFilter
[2016-04-14T23:50Z] INFO  16:50:36,068 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-14T23:50Z] INFO  16:50:36,069 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:50Z] INFO  16:50:36,069 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-14T23:50Z] INFO  16:50:36,070 MicroScheduler -   -> 1785 reads (1.37% of total) failing MappingQualityZeroFilter
[2016-04-14T23:50Z] INFO  16:50:36,071 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:50Z] INFO  16:50:36,071 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-14T23:50Z] INFO  16:50:36,072 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-14T23:50Z] INFO  16:50:36,276 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:50Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-5_158711911_174870102-prep.bam
[2016-04-14T23:50Z] INFO  16:50:36,341 IntervalUtils - Processing 15685608 bp from intervals
[2016-04-14T23:50Z] WARN  16:50:36,347 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:50Z] INFO  16:50:36,465 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:50Z] INFO  16:50:36,588 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:50Z] INFO  16:50:36,589 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:50Z] INFO  16:50:36,589 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:50Z] INFO  16:50:36,589 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:50Z] INFO  16:50:36,798 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:50Z] INFO  16:50:36,948 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:50Z] GATK pre-alignment ('7', 15599765, 31117713) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-14T23:50Z] INFO  16:50:37,129 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@7172f77a
[2016-04-14T23:50Z] INFO  16:50:37,292 ProgressMeter -            done    716044.0    84.0 s     117.0 s      100.0%    84.0 s       0.0 s
[2016-04-14T23:50Z] INFO  16:50:37,293 ProgressMeter - Total runtime 84.20 secs, 1.40 min, 0.02 hours
[2016-04-14T23:50Z] INFO  16:50:37,293 MicroScheduler - 268 reads were filtered out during the traversal out of approximately 716312 total reads (0.04%)
[2016-04-14T23:50Z] INFO  16:50:37,294 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:50Z] INFO  16:50:37,294 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:50Z] INFO  16:50:37,295 MicroScheduler -   -> 268 reads (0.04% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:50Z] INFO  16:50:37,660 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:50Z] GATK: realign ('6', 62390867, 78173120) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-14T23:50Z] INFO  16:50:38,199 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:50Z] INFO  16:50:38,203 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:50Z] INFO  16:50:38,203 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:50Z] INFO  16:50:38,204 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:50Z] INFO  16:50:38,209 HelpFormatter - Program Args: -T PrintReads -L 7:1-15584548 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/7/tx/tmpm9pRYD/R14-18105_kapa-NGv3-PE100-NGv3-sort-7_0_15584548-prep-prealign.bam
[2016-04-14T23:50Z] INFO  16:50:38,228 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:50Z] INFO  16:50:38,229 HelpFormatter - Date/Time: 2016/04/14 16:50:38
[2016-04-14T23:50Z] INFO  16:50:38,229 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:50Z] INFO  16:50:38,230 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:50Z] INFO  16:50:38,431 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:50Z] INFO  16:50:38,643 ProgressMeter -            done   1.5511569E7    16.0 s       1.0 s      100.0%    16.0 s       0.0 s
[2016-04-14T23:50Z] INFO  16:50:38,644 ProgressMeter - Total runtime 16.26 secs, 0.27 min, 0.00 hours
[2016-04-14T23:50Z] INFO  16:50:38,649 MicroScheduler - 10638 reads were filtered out during the traversal out of approximately 118370 total reads (8.99%)
[2016-04-14T23:50Z] INFO  16:50:38,650 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:50Z] INFO  16:50:38,650 MicroScheduler -   -> 446 reads (0.38% of total) failing BadMateFilter
[2016-04-14T23:50Z] INFO  16:50:38,651 MicroScheduler -   -> 9098 reads (7.69% of total) failing DuplicateReadFilter
[2016-04-14T23:50Z] INFO  16:50:38,652 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-14T23:50Z] INFO  16:50:38,652 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:50Z] INFO  16:50:38,653 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-14T23:50Z] INFO  16:50:38,654 MicroScheduler -   -> 1094 reads (0.92% of total) failing MappingQualityZeroFilter
[2016-04-14T23:50Z] INFO  16:50:38,654 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:50Z] INFO  16:50:38,655 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-14T23:50Z] INFO  16:50:38,655 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-14T23:50Z] INFO  16:50:38,776 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:50Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-5_127597427_143191869-prep-prealign.bam
[2016-04-14T23:50Z] INFO  16:50:39,474 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-14T23:50Z] INFO  16:50:39,556 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:50Z] INFO  16:50:39,565 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:50Z] INFO  16:50:39,608 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.04
[2016-04-14T23:50Z] INFO  16:50:39,622 IntervalUtils - Processing 15584548 bp from intervals
[2016-04-14T23:50Z] INFO  16:50:39,697 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:50Z] INFO  16:50:39,730 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:50Z] INFO  16:50:39,733 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:50Z] INFO  16:50:39,734 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:50Z] INFO  16:50:39,734 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:50Z] INFO  16:50:39,739 HelpFormatter - Program Args: -T PrintReads -L 7:15599766-31117713 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/7/tx/tmpYDeEui/R14-18105_kapa-NGv3-PE100-NGv3-sort-7_15599765_31117713-prep-prealign.bam
[2016-04-14T23:50Z] INFO  16:50:39,769 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:50Z] INFO  16:50:39,770 HelpFormatter - Date/Time: 2016/04/14 16:50:39
[2016-04-14T23:50Z] INFO  16:50:39,771 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:50Z] INFO  16:50:39,771 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:50Z] INFO  16:50:39,941 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:50Z] INFO  16:50:40,069 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:50Z] GATK: realign ('6', 93955015, 109466584) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-14T23:50Z] INFO  16:50:40,196 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:50Z] INFO  16:50:40,198 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:50Z] INFO  16:50:40,198 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:50Z] INFO  16:50:40,199 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:50Z] INFO  16:50:40,227 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:50Z] INFO  16:50:40,299 ProgressMeter -            done   1.555287E7    17.0 s       1.0 s      100.0%    17.0 s       0.0 s
[2016-04-14T23:50Z] INFO  16:50:40,299 ProgressMeter - Total runtime 17.66 secs, 0.29 min, 0.00 hours
[2016-04-14T23:50Z] INFO  16:50:40,304 MicroScheduler - 13533 reads were filtered out during the traversal out of approximately 162137 total reads (8.35%)
[2016-04-14T23:50Z] INFO  16:50:40,305 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:50Z] INFO  16:50:40,309 MicroScheduler -   -> 484 reads (0.30% of total) failing BadMateFilter
[2016-04-14T23:50Z] INFO  16:50:40,310 MicroScheduler -   -> 12504 reads (7.71% of total) failing DuplicateReadFilter
[2016-04-14T23:50Z] INFO  16:50:40,310 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-14T23:50Z] INFO  16:50:40,311 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:50Z] INFO  16:50:40,312 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-14T23:50Z] INFO  16:50:40,312 MicroScheduler -   -> 545 reads (0.34% of total) failing MappingQualityZeroFilter
[2016-04-14T23:50Z] INFO  16:50:40,313 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:50Z] INFO  16:50:40,314 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-14T23:50Z] INFO  16:50:40,314 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-14T23:50Z] INFO  16:50:40,315 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:50Z] INFO  16:50:40,319 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:50Z] INFO  16:50:40,319 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:50Z] INFO  16:50:40,320 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:50Z] INFO  16:50:40,325 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/6/R14-18105_kapa-NGv3-PE100-NGv3-sort-6_62390867_78173120-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/6/R14-18105_kapa-NGv3-PE100-NGv3-sort-6_62390867_78173120-prep-prealign-realign.intervals -L 6:62390868-78173120 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/6/tx/tmpibqAe2/R14-18105_kapa-NGv3-PE100-NGv3-sort-6_62390867_78173120-prep.bam
[2016-04-14T23:50Z] INFO  16:50:40,341 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:50Z] INFO  16:50:40,349 HelpFormatter - Date/Time: 2016/04/14 16:50:40
[2016-04-14T23:50Z] INFO  16:50:40,350 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:50Z] INFO  16:50:40,350 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:50Z] INFO  16:50:40,392 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:50Z] INFO  16:50:40,588 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:50Z] INFO  16:50:40,737 ProgressMeter -     6:139094934    200003.0    30.0 s       2.5 m       80.9%    37.0 s       7.0 s
[2016-04-14T23:50Z] INFO  16:50:40,770 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:50Z] INFO  16:50:40,784 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:50Z] INFO  16:50:40,861 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-14T23:50Z] GATK RealignerTargetCreator: R14-18105_kapa-NGv3-PE100-NGv3-sort-5_127597427_143191869-prep-prealign.bam 5:127597428-143191869
[2016-04-14T23:50Z] GATK: RealignerTargetCreator
[2016-04-14T23:50Z] INFO  16:50:41,049 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-14T23:50Z] INFO  16:50:41,116 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:50Z] INFO  16:50:41,126 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:50Z] INFO  16:50:41,162 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.04
[2016-04-14T23:50Z] INFO  16:50:41,177 IntervalUtils - Processing 15517948 bp from intervals
[2016-04-14T23:50Z] INFO  16:50:41,213 ProgressMeter -     6:152809531    200005.0    30.0 s       2.5 m       66.9%    44.0 s      14.0 s
[2016-04-14T23:50Z] INFO  16:50:41,250 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:50Z] INFO  16:50:41,348 IntervalUtils - Processing 15782253 bp from intervals
[2016-04-14T23:50Z] WARN  16:50:41,354 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:50Z] INFO  16:50:41,452 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:50Z] INFO  16:50:41,537 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:50Z] INFO  16:50:41,537 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:50Z] INFO  16:50:41,538 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:50Z] INFO  16:50:41,538 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:50Z] INFO  16:50:41,537 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:50Z] INFO  16:50:41,538 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:50Z] INFO  16:50:41,539 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:50Z] INFO  16:50:41,539 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:50Z] INFO  16:50:41,554 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:50Z] INFO  16:50:41,645 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:50Z] GATK: realign ('6', 78400388, 93953258) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-14T23:50Z] INFO  16:50:41,720 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:50Z] INFO  16:50:41,775 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:50Z] INFO  16:50:41,922 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:50Z] INFO  16:50:42,969 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@32d5a4c6
[2016-04-14T23:50Z] INFO  16:50:43,151 ProgressMeter -            done    218927.0    32.0 s       2.5 m      100.0%    32.0 s       0.0 s
[2016-04-14T23:50Z] INFO  16:50:43,152 ProgressMeter - Total runtime 32.44 secs, 0.54 min, 0.01 hours
[2016-04-14T23:50Z] INFO  16:50:43,152 MicroScheduler - 189 reads were filtered out during the traversal out of approximately 219116 total reads (0.09%)
[2016-04-14T23:50Z] INFO  16:50:43,153 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:50Z] INFO  16:50:43,153 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:50Z] INFO  16:50:43,153 MicroScheduler -   -> 189 reads (0.09% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:50Z] INFO  16:50:43,231 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:50Z] INFO  16:50:43,234 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:50Z] INFO  16:50:43,235 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:50Z] INFO  16:50:43,236 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:50Z] INFO  16:50:43,240 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/6/R14-18105_kapa-NGv3-PE100-NGv3-sort-6_93955015_109466584-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/6/R14-18105_kapa-NGv3-PE100-NGv3-sort-6_93955015_109466584-prep-prealign-realign.intervals -L 6:93955016-109466584 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/6/tx/tmpQ3iPLp/R14-18105_kapa-NGv3-PE100-NGv3-sort-6_93955015_109466584-prep.bam
[2016-04-14T23:50Z] INFO  16:50:43,258 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:50Z] INFO  16:50:43,259 HelpFormatter - Date/Time: 2016/04/14 16:50:43
[2016-04-14T23:50Z] INFO  16:50:43,259 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:50Z] INFO  16:50:43,260 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:50Z] INFO  16:50:43,473 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:50Z] INFO  16:50:43,639 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:50Z] INFO  16:50:43,659 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:50Z] INFO  16:50:43,729 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-14T23:50Z] INFO  16:50:44,105 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:50Z] INFO  16:50:44,108 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:50Z] INFO  16:50:44,109 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:50Z] INFO  16:50:44,109 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:50Z] INFO  16:50:44,114 IntervalUtils - Processing 15511569 bp from intervals
[2016-04-14T23:50Z] INFO  16:50:44,114 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/5/R14-18105_kapa-NGv3-PE100-NGv3-sort-5_127597427_143191869-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/5/tx/tmpAcMfjE/R14-18105_kapa-NGv3-PE100-NGv3-sort-5_127597427_143191869-prep-prealign-realign.intervals -l INFO -L 5:127597428-143191869 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-14T23:50Z] WARN  16:50:44,119 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:50Z] INFO  16:50:44,125 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:50Z] INFO  16:50:44,125 HelpFormatter - Date/Time: 2016/04/14 16:50:44
[2016-04-14T23:50Z] INFO  16:50:44,126 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:50Z] INFO  16:50:44,126 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:50Z] INFO  16:50:44,185 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:50Z] INFO  16:50:44,206 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:50Z] INFO  16:50:44,287 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:50Z] INFO  16:50:44,288 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:50Z] INFO  16:50:44,289 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:50Z] INFO  16:50:44,290 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:50Z] INFO  16:50:44,388 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-14T23:50Z] INFO  16:50:44,398 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:50Z] INFO  16:50:44,436 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:50Z] INFO  16:50:44,481 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-14T23:50Z] INFO  16:50:44,590 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:50Z] INFO  16:50:44,673 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:50Z] INFO  16:50:44,676 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:50Z] INFO  16:50:44,677 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:50Z] INFO  16:50:44,677 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:50Z] INFO  16:50:44,682 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/6/R14-18105_kapa-NGv3-PE100-NGv3-sort-6_78400388_93953258-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/6/R14-18105_kapa-NGv3-PE100-NGv3-sort-6_78400388_93953258-prep-prealign-realign.intervals -L 6:78400389-93953258 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/6/tx/tmpGah_eA/R14-18105_kapa-NGv3-PE100-NGv3-sort-6_78400388_93953258-prep.bam
[2016-04-14T23:50Z] INFO  16:50:44,690 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:50Z] INFO  16:50:44,691 HelpFormatter - Date/Time: 2016/04/14 16:50:44
[2016-04-14T23:50Z] INFO  16:50:44,692 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:50Z] INFO  16:50:44,692 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:50Z] INFO  16:50:44,812 IntervalUtils - Processing 15594442 bp from intervals
[2016-04-14T23:50Z] WARN  16:50:44,817 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:50Z] INFO  16:50:44,887 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:50Z] INFO  16:50:44,894 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:50Z] INFO  16:50:44,912 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:50Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-6_125112484_142397186-prep-prealign.bam
[2016-04-14T23:50Z] INFO  16:50:45,008 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:50Z] INFO  16:50:45,018 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:50Z] INFO  16:50:45,071 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:50Z] INFO  16:50:45,072 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:50Z] INFO  16:50:45,073 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:50Z] INFO  16:50:45,073 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-14T23:50Z] INFO  16:50:45,074 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-14T23:50Z] INFO  16:50:45,415 IntervalUtils - Processing 15552870 bp from intervals
[2016-04-14T23:50Z] WARN  16:50:45,420 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:50Z] INFO  16:50:45,497 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:50Z] GATK RealignerTargetCreator: R14-18105_kapa-NGv3-PE100-NGv3-sort-6_125112484_142397186-prep-prealign.bam 6:125112485-142397186
[2016-04-14T23:50Z] GATK: RealignerTargetCreator
[2016-04-14T23:50Z] INFO  16:50:45,642 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:50Z] INFO  16:50:45,644 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:50Z] INFO  16:50:45,644 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:50Z] INFO  16:50:45,645 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:50Z] INFO  16:50:45,829 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@5fe152b7
[2016-04-14T23:50Z] INFO  16:50:45,866 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:50Z] INFO  16:50:46,029 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:50Z] INFO  16:50:46,029 ProgressMeter -            done    261517.0    34.0 s       2.2 m      100.0%    34.0 s       0.0 s
[2016-04-14T23:50Z] INFO  16:50:46,029 ProgressMeter - Total runtime 34.84 secs, 0.58 min, 0.01 hours
[2016-04-14T23:50Z] INFO  16:50:46,030 MicroScheduler - 120 reads were filtered out during the traversal out of approximately 261637 total reads (0.05%)
[2016-04-14T23:50Z] INFO  16:50:46,030 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:50Z] INFO  16:50:46,031 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:50Z] INFO  16:50:46,031 MicroScheduler -   -> 120 reads (0.05% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:50Z] INFO  16:50:46,239 ProgressMeter -            done    213819.0    17.0 s      81.0 s      100.0%    17.0 s       0.0 s
[2016-04-14T23:50Z] INFO  16:50:46,240 ProgressMeter - Total runtime 17.33 secs, 0.29 min, 0.00 hours
[2016-04-14T23:50Z] INFO  16:50:46,243 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 213819 total reads (0.00%)
[2016-04-14T23:50Z] INFO  16:50:46,244 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:50Z] INFO  16:50:46,245 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:50Z] INFO  16:50:46,245 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:50Z] INFO  16:50:46,376 ProgressMeter -            done   1.5568806E7    21.0 s       1.0 s      100.0%    21.0 s       0.0 s
[2016-04-14T23:50Z] INFO  16:50:46,377 ProgressMeter - Total runtime 21.56 secs, 0.36 min, 0.01 hours
[2016-04-14T23:50Z] INFO  16:50:46,381 MicroScheduler - 37069 reads were filtered out during the traversal out of approximately 389544 total reads (9.52%)
[2016-04-14T23:50Z] INFO  16:50:46,383 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:50Z] INFO  16:50:46,384 MicroScheduler -   -> 881 reads (0.23% of total) failing BadMateFilter
[2016-04-14T23:50Z] INFO  16:50:46,395 MicroScheduler -   -> 30634 reads (7.86% of total) failing DuplicateReadFilter
[2016-04-14T23:50Z] INFO  16:50:46,396 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-14T23:50Z] INFO  16:50:46,397 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:50Z] INFO  16:50:46,398 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-14T23:50Z] INFO  16:50:46,398 MicroScheduler -   -> 5554 reads (1.43% of total) failing MappingQualityZeroFilter
[2016-04-14T23:50Z] INFO  16:50:46,399 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:50Z] INFO  16:50:46,399 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-14T23:50Z] INFO  16:50:46,400 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-14T23:50Z] INFO  16:50:47,529 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:50Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-6_142399691_157963777-prep-prealign.bam
[2016-04-14T23:50Z] INFO  16:50:47,980 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:50Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-6_0_15509601-prep.bam
[2016-04-14T23:50Z] INFO  16:50:48,058 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:50Z] GATK: realign ('6', 15511526, 31080332) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-14T23:50Z] INFO  16:50:48,318 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:50Z] INFO  16:50:48,321 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:50Z] INFO  16:50:48,322 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:50Z] INFO  16:50:48,323 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:50Z] INFO  16:50:48,327 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/6/R14-18105_kapa-NGv3-PE100-NGv3-sort-6_125112484_142397186-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/6/tx/tmpD0qiYV/R14-18105_kapa-NGv3-PE100-NGv3-sort-6_125112484_142397186-prep-prealign-realign.intervals -l INFO -L 6:125112485-142397186 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-14T23:50Z] INFO  16:50:48,336 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:50Z] INFO  16:50:48,347 HelpFormatter - Date/Time: 2016/04/14 16:50:48
[2016-04-14T23:50Z] INFO  16:50:48,348 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:50Z] INFO  16:50:48,349 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:50Z] GATK RealignerTargetCreator: R14-18105_kapa-NGv3-PE100-NGv3-sort-6_142399691_157963777-prep-prealign.bam 6:142399692-157963777
[2016-04-14T23:50Z] GATK: RealignerTargetCreator
[2016-04-14T23:50Z] INFO  16:50:48,483 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:50Z] INFO  16:50:48,699 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-14T23:50Z] INFO  16:50:48,708 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:50Z] GATK pre-alignment ('7', 31120227, 47317818) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-14T23:50Z] INFO  16:50:48,784 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-14T23:50Z] INFO  16:50:49,085 IntervalUtils - Processing 17284702 bp from intervals
[2016-04-14T23:50Z] WARN  16:50:49,090 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:50Z] INFO  16:50:49,167 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:50Z] INFO  16:50:49,366 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:50Z] INFO  16:50:49,367 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:50Z] INFO  16:50:49,367 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:50Z] INFO  16:50:49,368 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-14T23:50Z] INFO  16:50:51,075 ProgressMeter -            done    308109.0    21.0 s      70.0 s       99.8%    21.0 s       0.0 s
[2016-04-14T23:50Z] INFO  16:50:51,075 ProgressMeter - Total runtime 21.59 secs, 0.36 min, 0.01 hours
[2016-04-14T23:50Z] INFO  16:50:51,079 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 308109 total reads (0.00%)
[2016-04-14T23:50Z] INFO  16:50:51,079 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:50Z] INFO  16:50:51,080 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:50Z] INFO  16:50:51,080 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:50Z] INFO  16:50:51,094 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:50Z] INFO  16:50:51,107 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:50Z] INFO  16:50:51,107 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:50Z] INFO  16:50:51,107 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:50Z] INFO  16:50:51,111 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/6/R14-18105_kapa-NGv3-PE100-NGv3-sort-6_15511526_31080332-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/6/R14-18105_kapa-NGv3-PE100-NGv3-sort-6_15511526_31080332-prep-prealign-realign.intervals -L 6:15511527-31080332 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/6/tx/tmpIZsNDP/R14-18105_kapa-NGv3-PE100-NGv3-sort-6_15511526_31080332-prep.bam
[2016-04-14T23:50Z] INFO  16:50:51,122 ProgressMeter -            done   1.5511572E7    18.0 s       1.0 s      100.0%    18.0 s       0.0 s
[2016-04-14T23:50Z] INFO  16:50:51,122 ProgressMeter - Total runtime 18.10 secs, 0.30 min, 0.01 hours
[2016-04-14T23:50Z] INFO  16:50:51,125 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:50Z] INFO  16:50:51,125 HelpFormatter - Date/Time: 2016/04/14 16:50:51
[2016-04-14T23:50Z] INFO  16:50:51,125 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:50Z] INFO  16:50:51,126 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:50Z] INFO  16:50:51,128 MicroScheduler - 15368 reads were filtered out during the traversal out of approximately 187077 total reads (8.21%)
[2016-04-14T23:50Z] INFO  16:50:51,129 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:50Z] INFO  16:50:51,129 MicroScheduler -   -> 572 reads (0.31% of total) failing BadMateFilter
[2016-04-14T23:50Z] INFO  16:50:51,130 MicroScheduler -   -> 14355 reads (7.67% of total) failing DuplicateReadFilter
[2016-04-14T23:50Z] INFO  16:50:51,131 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-14T23:50Z] INFO  16:50:51,131 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:50Z] INFO  16:50:51,132 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-14T23:50Z] INFO  16:50:51,133 MicroScheduler -   -> 441 reads (0.24% of total) failing MappingQualityZeroFilter
[2016-04-14T23:50Z] INFO  16:50:51,134 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:50Z] INFO  16:50:51,134 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-14T23:50Z] INFO  16:50:51,135 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-14T23:50Z] INFO  16:50:51,187 ProgressMeter -     6:170062635    200009.0    30.0 s       2.5 m       92.0%    32.0 s       2.0 s
[2016-04-14T23:50Z] INFO  16:50:51,323 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:50Z] INFO  16:50:51,468 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:50Z] INFO  16:50:51,471 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:50Z] INFO  16:50:51,472 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:50Z] INFO  16:50:51,472 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:50Z] INFO  16:50:51,477 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/6/R14-18105_kapa-NGv3-PE100-NGv3-sort-6_142399691_157963777-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/6/tx/tmpcuE1_q/R14-18105_kapa-NGv3-PE100-NGv3-sort-6_142399691_157963777-prep-prealign-realign.intervals -l INFO -L 6:142399692-157963777 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-14T23:50Z] INFO  16:50:51,482 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:50Z] INFO  16:50:51,493 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:50Z] INFO  16:50:51,499 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:50Z] INFO  16:50:51,501 HelpFormatter - Date/Time: 2016/04/14 16:50:51
[2016-04-14T23:50Z] INFO  16:50:51,501 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:50Z] INFO  16:50:51,501 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:50Z] INFO  16:50:51,580 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-14T23:50Z] INFO  16:50:51,620 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:50Z] INFO  16:50:51,762 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:50Z] INFO  16:50:51,765 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:50Z] INFO  16:50:51,766 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:50Z] INFO  16:50:51,766 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:50Z] INFO  16:50:51,771 HelpFormatter - Program Args: -T PrintReads -L 7:31120228-47317818 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/7/tx/tmpZkXqiY/R14-18105_kapa-NGv3-PE100-NGv3-sort-7_31120227_47317818-prep-prealign.bam
[2016-04-14T23:50Z] INFO  16:50:51,789 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:50Z] INFO  16:50:51,789 HelpFormatter - Date/Time: 2016/04/14 16:50:51
[2016-04-14T23:50Z] INFO  16:50:51,790 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:50Z] INFO  16:50:51,791 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:50Z] INFO  16:50:51,819 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-14T23:50Z] INFO  16:50:51,828 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:50Z] INFO  16:50:51,874 IntervalUtils - Processing 15568806 bp from intervals
[2016-04-14T23:50Z] WARN  16:50:51,879 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:50Z] INFO  16:50:51,886 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-14T23:50Z] INFO  16:50:51,973 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:50Z] INFO  16:50:51,985 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:50Z] INFO  16:50:52,128 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:50Z] INFO  16:50:52,129 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:50Z] INFO  16:50:52,130 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:50Z] INFO  16:50:52,130 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:50Z] INFO  16:50:52,286 IntervalUtils - Processing 15564086 bp from intervals
[2016-04-14T23:50Z] WARN  16:50:52,292 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:50Z] INFO  16:50:52,313 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:50Z] INFO  16:50:52,315 ProgressMeter -            done    197998.0    15.0 s      79.0 s      100.0%    15.0 s       0.0 s
[2016-04-14T23:50Z] INFO  16:50:52,315 ProgressMeter - Total runtime 15.73 secs, 0.26 min, 0.00 hours
[2016-04-14T23:50Z] INFO  16:50:52,319 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 197998 total reads (0.00%)
[2016-04-14T23:50Z] INFO  16:50:52,320 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:50Z] INFO  16:50:52,320 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:50Z] INFO  16:50:52,320 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:50Z] INFO  16:50:52,376 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:50Z] INFO  16:50:52,440 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:50Z] GATK: realign ('6', 109467960, 124979532) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-14T23:50Z] INFO  16:50:52,499 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:50Z] INFO  16:50:52,546 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:50Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-5_174919106_180915260-prep.bam
[2016-04-14T23:50Z] INFO  16:50:52,609 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:50Z] INFO  16:50:52,610 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:50Z] INFO  16:50:52,611 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:50Z] INFO  16:50:52,612 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-14T23:50Z] INFO  16:50:53,046 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-14T23:50Z] INFO  16:50:53,154 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:50Z] INFO  16:50:53,163 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:50Z] INFO  16:50:53,233 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-14T23:50Z] INFO  16:50:53,261 IntervalUtils - Processing 16197591 bp from intervals
[2016-04-14T23:50Z] INFO  16:50:53,400 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:50Z] INFO  16:50:53,593 ProgressMeter -            done    331111.0    22.0 s      68.0 s      100.0%    22.0 s       0.0 s
[2016-04-14T23:50Z] INFO  16:50:53,594 ProgressMeter - Total runtime 22.54 secs, 0.38 min, 0.01 hours
[2016-04-14T23:50Z] INFO  16:50:53,597 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 331111 total reads (0.00%)
[2016-04-14T23:50Z] INFO  16:50:53,598 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:50Z] INFO  16:50:53,598 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:50Z] INFO  16:50:53,598 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:50Z] GATK pre-alignment ('7', 47319761, 63093154) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-14T23:50Z] INFO  16:50:53,743 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:50Z] INFO  16:50:53,744 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:50Z] INFO  16:50:53,745 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:50Z] INFO  16:50:53,745 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:50Z] INFO  16:50:53,771 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:50Z] INFO  16:50:53,833 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:50Z] INFO  16:50:53,837 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@41fd9d8e
[2016-04-14T23:50Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-6_46598699_62284307-prep.bam
[2016-04-14T23:50Z] INFO  16:50:53,940 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:50Z] INFO  16:50:54,019 ProgressMeter -            done    248730.0    32.0 s       2.2 m       98.7%    32.0 s       0.0 s
[2016-04-14T23:50Z] INFO  16:50:54,021 ProgressMeter - Total runtime 32.86 secs, 0.55 min, 0.01 hours
[2016-04-14T23:50Z] INFO  16:50:54,023 MicroScheduler - 145 reads were filtered out during the traversal out of approximately 248875 total reads (0.06%)
[2016-04-14T23:50Z] INFO  16:50:54,027 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:50Z] INFO  16:50:54,028 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:50Z] INFO  16:50:54,028 MicroScheduler -   -> 145 reads (0.06% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:50Z] GATK pre-alignment ('7', 63095909, 78636522) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-14T23:50Z] INFO  16:50:54,682 ProgressMeter -            done    129871.0    13.0 s     101.0 s      100.0%    13.0 s       0.0 s
[2016-04-14T23:50Z] INFO  16:50:54,683 ProgressMeter - Total runtime 13.14 secs, 0.22 min, 0.00 hours
[2016-04-14T23:50Z] INFO  16:50:54,687 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 129871 total reads (0.00%)
[2016-04-14T23:50Z] INFO  16:50:54,689 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:50Z] INFO  16:50:54,690 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:50Z] INFO  16:50:54,691 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:50Z] INFO  16:50:55,033 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:50Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-5_143200044_158710347-prep.bam
[2016-04-14T23:50Z] INFO  16:50:55,186 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:50Z] INFO  16:50:55,189 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:50Z] INFO  16:50:55,190 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:50Z] INFO  16:50:55,190 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:50Z] INFO  16:50:55,195 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/6/R14-18105_kapa-NGv3-PE100-NGv3-sort-6_109467960_124979532-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/6/R14-18105_kapa-NGv3-PE100-NGv3-sort-6_109467960_124979532-prep-prealign-realign.intervals -L 6:109467961-124979532 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/6/tx/tmpSSqXrV/R14-18105_kapa-NGv3-PE100-NGv3-sort-6_109467960_124979532-prep.bam
[2016-04-14T23:50Z] INFO  16:50:55,223 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:50Z] INFO  16:50:55,224 HelpFormatter - Date/Time: 2016/04/14 16:50:55
[2016-04-14T23:50Z] INFO  16:50:55,224 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:50Z] INFO  16:50:55,225 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:50Z] INFO  16:50:55,282 ProgressMeter -            done    117862.0    10.0 s      93.0 s      100.0%    10.0 s       0.0 s
[2016-04-14T23:50Z] INFO  16:50:55,282 ProgressMeter - Total runtime 10.99 secs, 0.18 min, 0.00 hours
[2016-04-14T23:50Z] INFO  16:50:55,287 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 117862 total reads (0.00%)
[2016-04-14T23:50Z] INFO  16:50:55,288 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:50Z] INFO  16:50:55,289 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:50Z] INFO  16:50:55,289 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:50Z] INFO  16:50:55,412 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:50Z] INFO  16:50:55,520 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:50Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-6_158013810_171115067-prep-prealign.bam
[2016-04-14T23:50Z] INFO  16:50:55,592 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:50Z] INFO  16:50:55,608 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:50Z] INFO  16:50:55,676 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-14T23:50Z] INFO  16:50:55,992 IntervalUtils - Processing 15511572 bp from intervals
[2016-04-14T23:50Z] WARN  16:50:55,997 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:50Z] INFO  16:50:56,132 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:50Z] GATK pre-alignment ('7', 79082334, 94740703) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-14T23:50Z] GATK RealignerTargetCreator: R14-18105_kapa-NGv3-PE100-NGv3-sort-6_158013810_171115067-prep-prealign.bam 6:158013811-171115067
[2016-04-14T23:50Z] GATK: RealignerTargetCreator
[2016-04-14T23:50Z] INFO  16:50:56,250 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:50Z] INFO  16:50:56,252 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:50Z] INFO  16:50:56,253 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:50Z] INFO  16:50:56,253 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:50Z] INFO  16:50:56,383 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:50Z] INFO  16:50:56,396 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:50Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-6_62390867_78173120-prep.bam
[2016-04-14T23:50Z] INFO  16:50:56,545 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:50Z] INFO  16:50:56,646 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:50Z] INFO  16:50:56,649 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:50Z] INFO  16:50:56,649 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:50Z] INFO  16:50:56,649 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:50Z] INFO  16:50:56,653 HelpFormatter - Program Args: -T PrintReads -L 7:47319762-63093154 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/7/tx/tmpraJLSY/R14-18105_kapa-NGv3-PE100-NGv3-sort-7_47319761_63093154-prep-prealign.bam
[2016-04-14T23:50Z] INFO  16:50:56,662 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:50Z] INFO  16:50:56,663 HelpFormatter - Date/Time: 2016/04/14 16:50:56
[2016-04-14T23:50Z] INFO  16:50:56,663 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:50Z] INFO  16:50:56,664 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:50Z] GATK pre-alignment ('7', 94750023, 110303777) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-14T23:50Z] INFO  16:50:56,883 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:50Z] INFO  16:50:56,951 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:50Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-6_93955015_109466584-prep.bam
[2016-04-14T23:50Z] GATK pre-alignment ('7', 110526648, 126079222) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-14T23:50Z] INFO  16:50:57,569 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:50Z] INFO  16:50:57,571 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:50Z] INFO  16:50:57,571 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:50Z] INFO  16:50:57,571 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:50Z] INFO  16:50:57,581 HelpFormatter - Program Args: -T PrintReads -L 7:63095910-78636522 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/7/tx/tmpmkDmMa/R14-18105_kapa-NGv3-PE100-NGv3-sort-7_63095909_78636522-prep-prealign.bam
[2016-04-14T23:50Z] INFO  16:50:57,592 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:50Z] INFO  16:50:57,597 HelpFormatter - Date/Time: 2016/04/14 16:50:57
[2016-04-14T23:50Z] INFO  16:50:57,598 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:50Z] INFO  16:50:57,598 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:50Z] INFO  16:50:57,826 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:50Z] INFO  16:50:58,111 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-14T23:50Z] INFO  16:50:58,166 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:50Z] INFO  16:50:58,175 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:50Z] INFO  16:50:58,224 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-14T23:50Z] INFO  16:50:58,238 IntervalUtils - Processing 15773393 bp from intervals
[2016-04-14T23:50Z] INFO  16:50:58,310 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:50Z] INFO  16:50:58,603 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:50Z] INFO  16:50:58,605 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:50Z] INFO  16:50:58,605 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:50Z] INFO  16:50:58,606 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:50Z] INFO  16:50:58,641 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:50Z] INFO  16:50:58,805 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:50Z] INFO  16:50:59,037 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:50Z] INFO  16:50:59,040 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:50Z] INFO  16:50:59,040 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:50Z] INFO  16:50:59,041 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:50Z] INFO  16:50:59,045 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-14T23:50Z] INFO  16:50:59,045 HelpFormatter - Program Args: -T PrintReads -L 7:79082335-94740703 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/7/tx/tmpHad_Jl/R14-18105_kapa-NGv3-PE100-NGv3-sort-7_79082334_94740703-prep-prealign.bam
[2016-04-14T23:50Z] INFO  16:50:59,055 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:50Z] INFO  16:50:59,056 HelpFormatter - Date/Time: 2016/04/14 16:50:59
[2016-04-14T23:50Z] INFO  16:50:59,057 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:50Z] INFO  16:50:59,057 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:50Z] INFO  16:50:59,095 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:50Z] INFO  16:50:59,104 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:50Z] INFO  16:50:59,139 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.03
[2016-04-14T23:50Z] INFO  16:50:59,153 IntervalUtils - Processing 15540613 bp from intervals
[2016-04-14T23:50Z] INFO  16:50:59,238 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:50Z] INFO  16:50:59,245 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:50Z] INFO  16:50:59,248 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:50Z] INFO  16:50:59,248 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:50Z] INFO  16:50:59,248 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:50Z] INFO  16:50:59,253 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/6/R14-18105_kapa-NGv3-PE100-NGv3-sort-6_158013810_171115067-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/6/tx/tmpvYW9Pg/R14-18105_kapa-NGv3-PE100-NGv3-sort-6_158013810_171115067-prep-prealign-realign.intervals -l INFO -L 6:158013811-171115067 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-14T23:50Z] INFO  16:50:59,257 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:50Z] INFO  16:50:59,266 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:50Z] INFO  16:50:59,266 HelpFormatter - Date/Time: 2016/04/14 16:50:59
[2016-04-14T23:50Z] INFO  16:50:59,266 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:50Z] INFO  16:50:59,267 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:50Z] INFO  16:50:59,373 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:50Z] INFO  16:50:59,418 ProgressMeter -            done    161655.0    13.0 s      85.0 s      100.0%    13.0 s       0.0 s
[2016-04-14T23:50Z] INFO  16:50:59,430 ProgressMeter - Total runtime 13.78 secs, 0.23 min, 0.00 hours
[2016-04-14T23:50Z] INFO  16:50:59,435 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 161655 total reads (0.00%)
[2016-04-14T23:50Z] INFO  16:50:59,436 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:50Z] INFO  16:50:59,436 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:50Z] INFO  16:50:59,437 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:50Z] INFO  16:50:59,585 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:50Z] INFO  16:50:59,587 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:50Z] INFO  16:50:59,587 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:50Z] INFO  16:50:59,588 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:50Z] INFO  16:50:59,602 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-14T23:50Z] INFO  16:50:59,608 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:50Z] INFO  16:50:59,612 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:50Z] INFO  16:50:59,674 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-14T23:50Z] INFO  16:50:59,833 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:50Z] INFO  16:50:59,920 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:50Z] INFO  16:50:59,923 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:50Z] INFO  16:50:59,924 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:50Z] INFO  16:50:59,925 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:50Z] INFO  16:50:59,930 HelpFormatter - Program Args: -T PrintReads -L 7:94750024-110303777 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/7/tx/tmp7zqqJs/R14-18105_kapa-NGv3-PE100-NGv3-sort-7_94750023_110303777-prep-prealign.bam
[2016-04-14T23:50Z] INFO  16:50:59,945 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:50Z] INFO  16:50:59,946 HelpFormatter - Date/Time: 2016/04/14 16:50:59
[2016-04-14T23:50Z] INFO  16:50:59,947 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:50Z] INFO  16:50:59,947 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:51Z] INFO  16:51:00,118 IntervalUtils - Processing 13101257 bp from intervals
[2016-04-14T23:51Z] WARN  16:51:00,143 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:51Z] INFO  16:51:00,253 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:51Z] INFO  16:51:00,282 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:51Z] INFO  16:51:00,329 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-14T23:51Z] INFO  16:51:00,337 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:51Z] INFO  16:51:00,341 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:51Z] INFO  16:51:00,342 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:51Z] INFO  16:51:00,342 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:51Z] INFO  16:51:00,348 HelpFormatter - Program Args: -T PrintReads -L 7:110526649-126079222 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/7/tx/tmpMW580Q/R14-18105_kapa-NGv3-PE100-NGv3-sort-7_110526648_126079222-prep-prealign.bam
[2016-04-14T23:51Z] INFO  16:51:00,360 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:51Z] INFO  16:51:00,361 HelpFormatter - Date/Time: 2016/04/14 16:51:00
[2016-04-14T23:51Z] INFO  16:51:00,362 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:51Z] INFO  16:51:00,363 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:51Z] INFO  16:51:00,406 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:51Z] INFO  16:51:00,418 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:51Z] INFO  16:51:00,492 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-14T23:51Z] INFO  16:51:00,509 IntervalUtils - Processing 15658369 bp from intervals
[2016-04-14T23:51Z] INFO  16:51:00,546 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:51Z] INFO  16:51:00,580 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:51Z] INFO  16:51:00,582 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:51Z] INFO  16:51:00,582 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:51Z] INFO  16:51:00,583 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-14T23:51Z] INFO  16:51:00,635 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:51Z] INFO  16:51:00,948 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:51Z] INFO  16:51:00,949 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:51Z] INFO  16:51:00,949 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:51Z] INFO  16:51:00,950 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:51Z] INFO  16:51:00,964 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:51Z] INFO  16:51:01,062 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:51Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-6_78400388_93953258-prep.bam
[2016-04-14T23:51Z] INFO  16:51:01,144 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:51Z] INFO  16:51:01,635 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-14T23:51Z] GATK pre-alignment ('7', 126086124, 141619620) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-14T23:51Z] INFO  16:51:01,734 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:51Z] INFO  16:51:01,742 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:51Z] INFO  16:51:01,761 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-14T23:51Z] INFO  16:51:01,793 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-14T23:51Z] INFO  16:51:01,808 IntervalUtils - Processing 15552574 bp from intervals
[2016-04-14T23:51Z] INFO  16:51:01,832 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:51Z] INFO  16:51:01,841 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:51Z] INFO  16:51:01,907 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-14T23:51Z] INFO  16:51:01,924 IntervalUtils - Processing 15553754 bp from intervals
[2016-04-14T23:51Z] INFO  16:51:01,935 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:51Z] INFO  16:51:02,010 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:51Z] INFO  16:51:02,282 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:51Z] INFO  16:51:02,283 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:51Z] INFO  16:51:02,284 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:51Z] INFO  16:51:02,285 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:51Z] INFO  16:51:02,300 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:51Z] INFO  16:51:02,400 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:51Z] INFO  16:51:02,402 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:51Z] INFO  16:51:02,402 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:51Z] INFO  16:51:02,403 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:51Z] INFO  16:51:02,430 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:51Z] INFO  16:51:02,470 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:51Z] INFO  16:51:02,626 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:51Z] INFO  16:51:04,287 ProgressMeter -      6:43139578    700010.0    90.0 s       2.1 m       77.7%   115.0 s      25.0 s
[2016-04-14T23:51Z] INFO  16:51:04,515 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:51Z] INFO  16:51:04,518 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:51Z] INFO  16:51:04,519 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:51Z] INFO  16:51:04,519 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:51Z] INFO  16:51:04,524 HelpFormatter - Program Args: -T PrintReads -L 7:126086125-141619620 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/7/tx/tmpnPZEeT/R14-18105_kapa-NGv3-PE100-NGv3-sort-7_126086124_141619620-prep-prealign.bam
[2016-04-14T23:51Z] INFO  16:51:04,534 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:51Z] INFO  16:51:04,534 HelpFormatter - Date/Time: 2016/04/14 16:51:04
[2016-04-14T23:51Z] INFO  16:51:04,534 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:51Z] INFO  16:51:04,535 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:51Z] INFO  16:51:04,725 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:51Z] INFO  16:51:05,926 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-14T23:51Z] INFO  16:51:05,990 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:51Z] INFO  16:51:06,004 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:51Z] INFO  16:51:06,075 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-14T23:51Z] INFO  16:51:06,100 IntervalUtils - Processing 15533496 bp from intervals
[2016-04-14T23:51Z] INFO  16:51:06,194 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:51Z] INFO  16:51:06,569 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:51Z] INFO  16:51:06,578 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:51Z] INFO  16:51:06,578 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:51Z] INFO  16:51:06,579 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:51Z] INFO  16:51:06,608 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:51Z] INFO  16:51:06,744 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:51Z] INFO  16:51:08,220 ProgressMeter -            done   1.7284702E7    18.0 s       1.0 s      100.0%    18.0 s       0.0 s
[2016-04-14T23:51Z] INFO  16:51:08,221 ProgressMeter - Total runtime 18.85 secs, 0.31 min, 0.01 hours
[2016-04-14T23:51Z] INFO  16:51:08,225 MicroScheduler - 25822 reads were filtered out during the traversal out of approximately 220982 total reads (11.69%)
[2016-04-14T23:51Z] INFO  16:51:08,226 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:51Z] INFO  16:51:08,227 MicroScheduler -   -> 627 reads (0.28% of total) failing BadMateFilter
[2016-04-14T23:51Z] INFO  16:51:08,228 MicroScheduler -   -> 16895 reads (7.65% of total) failing DuplicateReadFilter
[2016-04-14T23:51Z] INFO  16:51:08,228 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-14T23:51Z] INFO  16:51:08,229 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:51Z] INFO  16:51:08,230 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-14T23:51Z] INFO  16:51:08,230 MicroScheduler -   -> 8300 reads (3.76% of total) failing MappingQualityZeroFilter
[2016-04-14T23:51Z] INFO  16:51:08,231 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:51Z] INFO  16:51:08,231 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-14T23:51Z] INFO  16:51:08,232 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-14T23:51Z] INFO  16:51:09,711 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:51Z] GATK: realign ('6', 125112484, 142397186) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-14T23:51Z] INFO  16:51:10,935 ProgressMeter -       7:5410529    100002.0    30.0 s       5.1 m       34.7%    86.0 s      56.0 s
[2016-04-14T23:51Z] INFO  16:51:11,542 ProgressMeter -      7:30119143    100004.0    30.0 s       5.0 m       93.6%    32.0 s       2.0 s
[2016-04-14T23:51Z] INFO  16:51:11,982 ProgressMeter -            done    186385.0    15.0 s      84.0 s      100.0%    15.0 s       0.0 s
[2016-04-14T23:51Z] INFO  16:51:11,983 ProgressMeter - Total runtime 15.73 secs, 0.26 min, 0.00 hours
[2016-04-14T23:51Z] INFO  16:51:11,986 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 186385 total reads (0.00%)
[2016-04-14T23:51Z] INFO  16:51:11,987 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:51Z] INFO  16:51:11,987 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:51Z] INFO  16:51:11,987 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:51Z] INFO  16:51:12,541 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:51Z] INFO  16:51:12,555 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:51Z] INFO  16:51:12,555 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:51Z] INFO  16:51:12,555 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:51Z] INFO  16:51:12,559 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/6/R14-18105_kapa-NGv3-PE100-NGv3-sort-6_125112484_142397186-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/6/R14-18105_kapa-NGv3-PE100-NGv3-sort-6_125112484_142397186-prep-prealign-realign.intervals -L 6:125112485-142397186 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/6/tx/tmpdeFP_J/R14-18105_kapa-NGv3-PE100-NGv3-sort-6_125112484_142397186-prep.bam
[2016-04-14T23:51Z] INFO  16:51:12,572 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:51Z] INFO  16:51:12,573 HelpFormatter - Date/Time: 2016/04/14 16:51:12
[2016-04-14T23:51Z] INFO  16:51:12,574 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:51Z] INFO  16:51:12,574 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:51Z] INFO  16:51:12,794 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:51Z] INFO  16:51:12,909 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:51Z] INFO  16:51:12,920 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:51Z] INFO  16:51:12,958 ProgressMeter -            done   1.5564086E7    20.0 s       1.0 s      100.0%    20.0 s       0.0 s
[2016-04-14T23:51Z] INFO  16:51:12,968 ProgressMeter - Total runtime 20.35 secs, 0.34 min, 0.01 hours
[2016-04-14T23:51Z] INFO  16:51:12,973 MicroScheduler - 23844 reads were filtered out during the traversal out of approximately 263384 total reads (9.05%)
[2016-04-14T23:51Z] INFO  16:51:12,974 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:51Z] INFO  16:51:12,975 MicroScheduler -   -> 652 reads (0.25% of total) failing BadMateFilter
[2016-04-14T23:51Z] INFO  16:51:12,976 MicroScheduler -   -> 20436 reads (7.76% of total) failing DuplicateReadFilter
[2016-04-14T23:51Z] INFO  16:51:12,976 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-14T23:51Z] INFO  16:51:12,977 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:51Z] INFO  16:51:12,977 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-14T23:51Z] INFO  16:51:12,977 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-14T23:51Z] INFO  16:51:12,978 MicroScheduler -   -> 2756 reads (1.05% of total) failing MappingQualityZeroFilter
[2016-04-14T23:51Z] INFO  16:51:12,979 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:51Z] INFO  16:51:12,979 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-14T23:51Z] INFO  16:51:12,979 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-14T23:51Z] INFO  16:51:13,332 IntervalUtils - Processing 17284702 bp from intervals
[2016-04-14T23:51Z] WARN  16:51:13,341 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:51Z] INFO  16:51:13,429 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:51Z] INFO  16:51:13,539 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:51Z] INFO  16:51:13,540 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:51Z] INFO  16:51:13,541 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:51Z] INFO  16:51:13,541 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:51Z] INFO  16:51:13,574 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:51Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-6_109467960_124979532-prep.bam
[2016-04-14T23:51Z] INFO  16:51:13,765 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:51Z] INFO  16:51:13,887 ProgressMeter -            done   1.5594442E7    28.0 s       1.0 s      100.0%    28.0 s       0.0 s
[2016-04-14T23:51Z] INFO  16:51:13,888 ProgressMeter - Total runtime 28.82 secs, 0.48 min, 0.01 hours
[2016-04-14T23:51Z] INFO  16:51:13,889 MicroScheduler - 80208 reads were filtered out during the traversal out of approximately 720888 total reads (11.13%)
[2016-04-14T23:51Z] INFO  16:51:13,891 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:51Z] INFO  16:51:13,891 MicroScheduler -   -> 1165 reads (0.16% of total) failing BadMateFilter
[2016-04-14T23:51Z] INFO  16:51:13,892 MicroScheduler -   -> 60477 reads (8.39% of total) failing DuplicateReadFilter
[2016-04-14T23:51Z] INFO  16:51:13,893 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-14T23:51Z] INFO  16:51:13,894 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:51Z] INFO  16:51:13,894 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-14T23:51Z] INFO  16:51:13,895 MicroScheduler -   -> 18566 reads (2.58% of total) failing MappingQualityZeroFilter
[2016-04-14T23:51Z] INFO  16:51:13,896 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:51Z] INFO  16:51:13,897 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-14T23:51Z] INFO  16:51:13,897 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-14T23:51Z] INFO  16:51:14,049 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:51Z] GATK pre-alignment ('7', 141629903, 157151331) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-14T23:51Z] INFO  16:51:14,337 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:51Z] GATK: realign ('6', 142399691, 157963777) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-14T23:51Z] INFO  16:51:15,290 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:51Z] GATK: realign ('5', 127597427, 143191869) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-14T23:51Z] INFO  16:51:15,636 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@7172f77a
[2016-04-14T23:51Z] INFO  16:51:15,715 ProgressMeter -            done    208285.0    34.0 s       2.7 m      100.0%    34.0 s       0.0 s
[2016-04-14T23:51Z] INFO  16:51:15,715 ProgressMeter - Total runtime 34.18 secs, 0.57 min, 0.01 hours
[2016-04-14T23:51Z] INFO  16:51:15,716 MicroScheduler - 181 reads were filtered out during the traversal out of approximately 208466 total reads (0.09%)
[2016-04-14T23:51Z] INFO  16:51:15,716 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:51Z] INFO  16:51:15,716 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:51Z] INFO  16:51:15,717 MicroScheduler -   -> 181 reads (0.09% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:51Z] INFO  16:51:17,043 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:51Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-7_15599765_31117713-prep-prealign.bam
[2016-04-14T23:51Z] INFO  16:51:17,292 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:51Z] INFO  16:51:17,296 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:51Z] INFO  16:51:17,296 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:51Z] INFO  16:51:17,297 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:51Z] INFO  16:51:17,302 HelpFormatter - Program Args: -T PrintReads -L 7:141629904-157151331 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/7/tx/tmpz38I9q/R14-18105_kapa-NGv3-PE100-NGv3-sort-7_141629903_157151331-prep-prealign.bam
[2016-04-14T23:51Z] INFO  16:51:17,318 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:51Z] INFO  16:51:17,319 HelpFormatter - Date/Time: 2016/04/14 16:51:17
[2016-04-14T23:51Z] INFO  16:51:17,320 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:51Z] INFO  16:51:17,320 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:51Z] INFO  16:51:17,510 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:51Z] INFO  16:51:17,635 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:51Z] INFO  16:51:17,638 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:51Z] INFO  16:51:17,639 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:51Z] INFO  16:51:17,639 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:51Z] INFO  16:51:17,644 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/6/R14-18105_kapa-NGv3-PE100-NGv3-sort-6_142399691_157963777-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/6/R14-18105_kapa-NGv3-PE100-NGv3-sort-6_142399691_157963777-prep-prealign-realign.intervals -L 6:142399692-157963777 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/6/tx/tmpdodott/R14-18105_kapa-NGv3-PE100-NGv3-sort-6_142399691_157963777-prep.bam
[2016-04-14T23:51Z] INFO  16:51:17,672 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:51Z] INFO  16:51:17,672 HelpFormatter - Date/Time: 2016/04/14 16:51:17
[2016-04-14T23:51Z] INFO  16:51:17,672 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:51Z] INFO  16:51:17,673 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:51Z] GATK RealignerTargetCreator: R14-18105_kapa-NGv3-PE100-NGv3-sort-7_15599765_31117713-prep-prealign.bam 7:15599766-31117713
[2016-04-14T23:51Z] GATK: RealignerTargetCreator
[2016-04-14T23:51Z] INFO  16:51:17,862 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:51Z] INFO  16:51:17,947 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:51Z] INFO  16:51:17,956 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:51Z] INFO  16:51:18,022 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-14T23:51Z] INFO  16:51:18,094 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:51Z] INFO  16:51:18,098 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:51Z] INFO  16:51:18,100 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:51Z] INFO  16:51:18,100 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:51Z] INFO  16:51:18,106 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/5/R14-18105_kapa-NGv3-PE100-NGv3-sort-5_127597427_143191869-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/5/R14-18105_kapa-NGv3-PE100-NGv3-sort-5_127597427_143191869-prep-prealign-realign.intervals -L 5:127597428-143191869 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/5/tx/tmp9Pwlwr/R14-18105_kapa-NGv3-PE100-NGv3-sort-5_127597427_143191869-prep.bam
[2016-04-14T23:51Z] INFO  16:51:18,119 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:51Z] INFO  16:51:18,132 HelpFormatter - Date/Time: 2016/04/14 16:51:18
[2016-04-14T23:51Z] INFO  16:51:18,132 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:51Z] INFO  16:51:18,132 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:51Z] INFO  16:51:18,403 IntervalUtils - Processing 15564086 bp from intervals
[2016-04-14T23:51Z] WARN  16:51:18,408 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:51Z] INFO  16:51:18,455 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:51Z] INFO  16:51:18,481 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:51Z] INFO  16:51:18,585 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:51Z] INFO  16:51:18,586 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:51Z] INFO  16:51:18,586 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:51Z] INFO  16:51:18,587 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:51Z] INFO  16:51:18,603 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:51Z] INFO  16:51:18,614 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:51Z] INFO  16:51:18,703 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.09
[2016-04-14T23:51Z] INFO  16:51:18,771 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:51Z] INFO  16:51:18,795 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-14T23:51Z] INFO  16:51:18,807 ProgressMeter -            done    387349.0    26.0 s      68.0 s      100.0%    26.0 s       0.0 s
[2016-04-14T23:51Z] INFO  16:51:18,807 ProgressMeter - Total runtime 26.68 secs, 0.44 min, 0.01 hours
[2016-04-14T23:51Z] INFO  16:51:18,811 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 387349 total reads (0.00%)
[2016-04-14T23:51Z] INFO  16:51:18,812 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:51Z] INFO  16:51:18,812 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:51Z] INFO  16:51:18,812 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:51Z] INFO  16:51:18,860 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:51Z] INFO  16:51:18,884 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:51Z] INFO  16:51:18,942 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-14T23:51Z] INFO  16:51:18,957 IntervalUtils - Processing 15521428 bp from intervals
[2016-04-14T23:51Z] INFO  16:51:18,966 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:51Z] INFO  16:51:19,028 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@7172f77a
[2016-04-14T23:51Z] INFO  16:51:19,062 IntervalUtils - Processing 15594442 bp from intervals
[2016-04-14T23:51Z] WARN  16:51:19,067 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:51Z] INFO  16:51:19,082 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:51Z] INFO  16:51:19,139 ProgressMeter -            done    886903.0   104.0 s     118.0 s      100.0%   104.0 s       0.0 s
[2016-04-14T23:51Z] INFO  16:51:19,143 ProgressMeter - Total runtime 105.00 secs, 1.75 min, 0.03 hours
[2016-04-14T23:51Z] INFO  16:51:19,143 MicroScheduler - 324 reads were filtered out during the traversal out of approximately 887227 total reads (0.04%)
[2016-04-14T23:51Z] INFO  16:51:19,150 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:51Z] INFO  16:51:19,144 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:51Z] INFO  16:51:19,154 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:51Z] INFO  16:51:19,154 MicroScheduler -   -> 324 reads (0.04% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:51Z] INFO  16:51:19,321 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:51Z] INFO  16:51:19,341 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:51Z] INFO  16:51:19,342 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:51Z] INFO  16:51:19,342 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:51Z] INFO  16:51:19,500 ProgressMeter -            done   1.3101257E7    18.0 s       1.0 s      100.0%    18.0 s       0.0 s
[2016-04-14T23:51Z] INFO  16:51:19,501 ProgressMeter - Total runtime 18.92 secs, 0.32 min, 0.01 hours
[2016-04-14T23:51Z] INFO  16:51:19,506 MicroScheduler - 32726 reads were filtered out during the traversal out of approximately 250774 total reads (13.05%)
[2016-04-14T23:51Z] INFO  16:51:19,507 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:51Z] INFO  16:51:19,508 MicroScheduler -   -> 530 reads (0.21% of total) failing BadMateFilter
[2016-04-14T23:51Z] INFO  16:51:19,509 MicroScheduler -   -> 18925 reads (7.55% of total) failing DuplicateReadFilter
[2016-04-14T23:51Z] INFO  16:51:19,509 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-14T23:51Z] INFO  16:51:19,512 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:51Z] INFO  16:51:19,513 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-14T23:51Z] INFO  16:51:19,513 MicroScheduler -   -> 13271 reads (5.29% of total) failing MappingQualityZeroFilter
[2016-04-14T23:51Z] INFO  16:51:19,513 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:51Z] INFO  16:51:19,513 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-14T23:51Z] INFO  16:51:19,514 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-14T23:51Z] INFO  16:51:19,528 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:51Z] INFO  16:51:19,529 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:51Z] INFO  16:51:19,529 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:51Z] INFO  16:51:19,529 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:51Z] INFO  16:51:19,539 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:51Z] INFO  16:51:19,551 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:51Z] INFO  16:51:19,691 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:51Z] INFO  16:51:19,710 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:51Z] INFO  16:51:20,255 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@7172f77a
[2016-04-14T23:51Z] INFO  16:51:20,352 ProgressMeter -            done    123055.0    18.0 s       2.4 m      100.0%    18.0 s       0.0 s
[2016-04-14T23:51Z] INFO  16:51:20,352 ProgressMeter - Total runtime 18.07 secs, 0.30 min, 0.01 hours
[2016-04-14T23:51Z] INFO  16:51:20,352 MicroScheduler - 118 reads were filtered out during the traversal out of approximately 123173 total reads (0.10%)
[2016-04-14T23:51Z] INFO  16:51:20,353 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:51Z] INFO  16:51:20,353 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:51Z] INFO  16:51:20,353 MicroScheduler -   -> 118 reads (0.10% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:51Z] INFO  16:51:20,358 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:51Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-6_15511526_31080332-prep.bam
[2016-04-14T23:51Z] INFO  16:51:20,736 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:51Z] INFO  16:51:20,738 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:51Z] INFO  16:51:20,739 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:51Z] INFO  16:51:20,739 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:51Z] INFO  16:51:20,758 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/7/R14-18105_kapa-NGv3-PE100-NGv3-sort-7_15599765_31117713-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/7/tx/tmp2pxby_/R14-18105_kapa-NGv3-PE100-NGv3-sort-7_15599765_31117713-prep-prealign-realign.intervals -l INFO -L 7:15599766-31117713 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-14T23:51Z] INFO  16:51:20,792 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:51Z] INFO  16:51:20,794 HelpFormatter - Date/Time: 2016/04/14 16:51:20
[2016-04-14T23:51Z] INFO  16:51:20,795 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:51Z] INFO  16:51:20,795 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:51Z] INFO  16:51:20,866 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:51Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-6_31083801_46593245-prep-prealign.bam
[2016-04-14T23:51Z] INFO  16:51:20,953 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:51Z] INFO  16:51:21,014 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:51Z] GATK: realign ('6', 158013810, 171115067) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-14T23:51Z] INFO  16:51:21,226 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-14T23:51Z] INFO  16:51:21,240 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:51Z] INFO  16:51:21,300 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-14T23:51Z] GATK pre-alignment ('7', 157155854, 159138663) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-14T23:51Z] INFO  16:51:21,654 IntervalUtils - Processing 15517948 bp from intervals
[2016-04-14T23:51Z] WARN  16:51:21,659 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:51Z] INFO  16:51:21,728 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:51Z] INFO  16:51:21,781 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:51Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-7_110526648_126079222-prep-prealign.bam
[2016-04-14T23:51Z] INFO  16:51:21,944 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:51Z] INFO  16:51:21,956 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:51Z] INFO  16:51:21,957 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:51Z] INFO  16:51:21,958 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-14T23:51Z] GATK RealignerTargetCreator: R14-18105_kapa-NGv3-PE100-NGv3-sort-7_110526648_126079222-prep-prealign.bam 7:110526649-126079222
[2016-04-14T23:51Z] GATK: RealignerTargetCreator
[2016-04-14T23:51Z] INFO  16:51:22,399 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@32d5a4c6
[2016-04-14T23:51Z] INFO  16:51:22,507 ProgressMeter -            done    164246.0    23.0 s       2.4 m      100.0%    23.0 s       0.0 s
[2016-04-14T23:51Z] INFO  16:51:22,508 ProgressMeter - Total runtime 23.90 secs, 0.40 min, 0.01 hours
[2016-04-14T23:51Z] INFO  16:51:22,508 MicroScheduler - 166 reads were filtered out during the traversal out of approximately 164412 total reads (0.10%)
[2016-04-14T23:51Z] INFO  16:51:22,509 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:51Z] INFO  16:51:22,509 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:51Z] INFO  16:51:22,509 MicroScheduler -   -> 166 reads (0.10% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:51Z] GATK RealignerTargetCreator: R14-18105_kapa-NGv3-PE100-NGv3-sort-6_31083801_46593245-prep-prealign.bam 6:31083802-46593245
[2016-04-14T23:51Z] GATK: RealignerTargetCreator
[2016-04-14T23:51Z] INFO  16:51:23,770 ProgressMeter -      7:44797837    200004.0    30.0 s       2.5 m       84.4%    35.0 s       5.0 s
[2016-04-14T23:51Z] INFO  16:51:23,848 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:51Z] INFO  16:51:23,850 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:51Z] INFO  16:51:23,850 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:51Z] INFO  16:51:23,851 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:51Z] INFO  16:51:23,865 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/6/R14-18105_kapa-NGv3-PE100-NGv3-sort-6_158013810_171115067-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/6/R14-18105_kapa-NGv3-PE100-NGv3-sort-6_158013810_171115067-prep-prealign-realign.intervals -L 6:158013811-171115067 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/6/tx/tmpuAb9_N/R14-18105_kapa-NGv3-PE100-NGv3-sort-6_158013810_171115067-prep.bam
[2016-04-14T23:51Z] INFO  16:51:23,882 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:51Z] INFO  16:51:23,882 HelpFormatter - Date/Time: 2016/04/14 16:51:23
[2016-04-14T23:51Z] INFO  16:51:23,883 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:51Z] INFO  16:51:23,883 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:51Z] INFO  16:51:24,143 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:51Z] INFO  16:51:24,171 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:51Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-7_47319761_63093154-prep-prealign.bam
[2016-04-14T23:51Z] INFO  16:51:24,319 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:51Z] INFO  16:51:24,328 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:51Z] INFO  16:51:24,404 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-14T23:51Z] INFO  16:51:24,500 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:51Z] INFO  16:51:24,504 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:51Z] INFO  16:51:24,505 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:51Z] INFO  16:51:24,505 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:51Z] INFO  16:51:24,511 HelpFormatter - Program Args: -T PrintReads -L 7:157155855-159138663 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/7/tx/tmpb6Frxc/R14-18105_kapa-NGv3-PE100-NGv3-sort-7_157155854_159138663-prep-prealign.bam
[2016-04-14T23:51Z] INFO  16:51:24,542 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:51Z] INFO  16:51:24,543 HelpFormatter - Date/Time: 2016/04/14 16:51:24
[2016-04-14T23:51Z] INFO  16:51:24,544 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:51Z] INFO  16:51:24,544 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:51Z] GATK RealignerTargetCreator: R14-18105_kapa-NGv3-PE100-NGv3-sort-7_47319761_63093154-prep-prealign.bam 7:47319762-63093154
[2016-04-14T23:51Z] GATK: RealignerTargetCreator
[2016-04-14T23:51Z] INFO  16:51:24,782 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:51Z] INFO  16:51:24,860 IntervalUtils - Processing 13101257 bp from intervals
[2016-04-14T23:51Z] WARN  16:51:24,865 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:51Z] INFO  16:51:24,958 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:51Z] INFO  16:51:25,018 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:51Z] INFO  16:51:25,021 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:51Z] INFO  16:51:25,022 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:51Z] INFO  16:51:25,022 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:51Z] INFO  16:51:25,027 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/7/R14-18105_kapa-NGv3-PE100-NGv3-sort-7_110526648_126079222-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/7/tx/tmpMzR6Lo/R14-18105_kapa-NGv3-PE100-NGv3-sort-7_110526648_126079222-prep-prealign-realign.intervals -l INFO -L 7:110526649-126079222 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-14T23:51Z] INFO  16:51:25,065 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:51Z] INFO  16:51:25,066 HelpFormatter - Date/Time: 2016/04/14 16:51:25
[2016-04-14T23:51Z] INFO  16:51:25,066 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:51Z] INFO  16:51:25,066 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:51Z] INFO  16:51:25,083 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@41fd9d8e
[2016-04-14T23:51Z] INFO  16:51:25,135 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:51Z] INFO  16:51:25,136 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:51Z] INFO  16:51:25,137 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:51Z] INFO  16:51:25,138 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:51Z] INFO  16:51:25,178 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:51Z] INFO  16:51:25,234 ProgressMeter -            done    176801.0    24.0 s       2.3 m       98.7%    24.0 s       0.0 s
[2016-04-14T23:51Z] INFO  16:51:25,235 ProgressMeter - Total runtime 24.29 secs, 0.40 min, 0.01 hours
[2016-04-14T23:51Z] INFO  16:51:25,235 MicroScheduler - 159 reads were filtered out during the traversal out of approximately 176960 total reads (0.09%)
[2016-04-14T23:51Z] INFO  16:51:25,236 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:51Z] INFO  16:51:25,236 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:51Z] INFO  16:51:25,236 MicroScheduler -   -> 159 reads (0.09% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:51Z] INFO  16:51:25,346 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:51Z] INFO  16:51:25,394 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-14T23:51Z] INFO  16:51:25,410 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:51Z] INFO  16:51:25,456 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-14T23:51Z] INFO  16:51:25,575 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:51Z] INFO  16:51:25,757 IntervalUtils - Processing 15552574 bp from intervals
[2016-04-14T23:51Z] WARN  16:51:25,762 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:51Z] INFO  16:51:25,840 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:51Z] INFO  16:51:26,068 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:51Z] INFO  16:51:26,069 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:51Z] INFO  16:51:26,070 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:51Z] INFO  16:51:26,070 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-14T23:51Z] INFO  16:51:26,134 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-14T23:51Z] INFO  16:51:26,194 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:51Z] INFO  16:51:26,203 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:51Z] INFO  16:51:26,254 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-14T23:51Z] INFO  16:51:26,283 IntervalUtils - Processing 1982809 bp from intervals
[2016-04-14T23:51Z] INFO  16:51:26,349 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:51Z] INFO  16:51:26,563 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:51Z] INFO  16:51:26,564 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:51Z] INFO  16:51:26,564 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:51Z] INFO  16:51:26,564 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:51Z] INFO  16:51:26,587 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:51Z] INFO  16:51:26,610 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:51Z] INFO  16:51:26,695 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:51Z] INFO  16:51:26,698 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:51Z] INFO  16:51:26,699 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:51Z] INFO  16:51:26,699 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:51Z] INFO  16:51:26,704 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/6/R14-18105_kapa-NGv3-PE100-NGv3-sort-6_31083801_46593245-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/6/tx/tmpSAbKJ1/R14-18105_kapa-NGv3-PE100-NGv3-sort-6_31083801_46593245-prep-prealign-realign.intervals -l INFO -L 6:31083802-46593245 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-14T23:51Z] INFO  16:51:26,722 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:51Z] INFO  16:51:26,723 HelpFormatter - Date/Time: 2016/04/14 16:51:26
[2016-04-14T23:51Z] INFO  16:51:26,724 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:51Z] INFO  16:51:26,724 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:51Z] INFO  16:51:26,814 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:51Z] INFO  16:51:26,865 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:51Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-7_79082334_94740703-prep-prealign.bam
[2016-04-14T23:51Z] INFO  16:51:27,077 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-14T23:51Z] INFO  16:51:27,098 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:51Z] INFO  16:51:27,179 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-14T23:51Z] INFO  16:51:27,318 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:51Z] INFO  16:51:27,320 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:51Z] INFO  16:51:27,320 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:51Z] INFO  16:51:27,320 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:51Z] INFO  16:51:27,324 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/7/R14-18105_kapa-NGv3-PE100-NGv3-sort-7_47319761_63093154-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/7/tx/tmpXiN2jA/R14-18105_kapa-NGv3-PE100-NGv3-sort-7_47319761_63093154-prep-prealign-realign.intervals -l INFO -L 7:47319762-63093154 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-14T23:51Z] INFO  16:51:27,333 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:51Z] INFO  16:51:27,341 HelpFormatter - Date/Time: 2016/04/14 16:51:27
[2016-04-14T23:51Z] INFO  16:51:27,342 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:51Z] INFO  16:51:27,350 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:51Z] INFO  16:51:27,459 IntervalUtils - Processing 15509444 bp from intervals
[2016-04-14T23:51Z] WARN  16:51:27,464 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:51Z] GATK RealignerTargetCreator: R14-18105_kapa-NGv3-PE100-NGv3-sort-7_79082334_94740703-prep-prealign.bam 7:79082335-94740703
[2016-04-14T23:51Z] GATK: RealignerTargetCreator
[2016-04-14T23:51Z] INFO  16:51:27,499 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:51Z] INFO  16:51:27,539 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:51Z] INFO  16:51:27,750 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-14T23:51Z] INFO  16:51:27,759 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:51Z] INFO  16:51:27,817 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-14T23:51Z] INFO  16:51:27,832 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:51Z] INFO  16:51:27,833 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:51Z] INFO  16:51:27,834 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:51Z] INFO  16:51:27,834 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-14T23:51Z] INFO  16:51:28,195 IntervalUtils - Processing 15773393 bp from intervals
[2016-04-14T23:51Z] WARN  16:51:28,200 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:51Z] INFO  16:51:28,327 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:51Z] INFO  16:51:28,568 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:51Z] INFO  16:51:28,570 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:51Z] INFO  16:51:28,570 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:51Z] INFO  16:51:28,571 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-14T23:51Z] INFO  16:51:29,023 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@41fd9d8e
[2016-04-14T23:51Z] INFO  16:51:29,125 ProgressMeter -            done    270277.0    35.0 s       2.2 m      100.0%    35.0 s       0.0 s
[2016-04-14T23:51Z] INFO  16:51:29,125 ProgressMeter - Total runtime 35.38 secs, 0.59 min, 0.01 hours
[2016-04-14T23:51Z] INFO  16:51:29,126 MicroScheduler - 164 reads were filtered out during the traversal out of approximately 270441 total reads (0.06%)
[2016-04-14T23:51Z] INFO  16:51:29,126 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:51Z] INFO  16:51:29,126 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:51Z] INFO  16:51:29,126 MicroScheduler -   -> 164 reads (0.06% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:51Z] INFO  16:51:29,612 ProgressMeter -      7:73475561    200003.0    30.0 s       2.5 m       66.8%    44.0 s      14.0 s
[2016-04-14T23:51Z] INFO  16:51:30,614 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:51Z] INFO  16:51:30,617 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:51Z] INFO  16:51:30,618 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:51Z] INFO  16:51:30,618 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:51Z] INFO  16:51:30,623 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/7/R14-18105_kapa-NGv3-PE100-NGv3-sort-7_79082334_94740703-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/7/tx/tmpojo61A/R14-18105_kapa-NGv3-PE100-NGv3-sort-7_79082334_94740703-prep-prealign-realign.intervals -l INFO -L 7:79082335-94740703 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-14T23:51Z] INFO  16:51:30,634 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:51Z] INFO  16:51:30,634 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:51Z] INFO  16:51:30,635 HelpFormatter - Date/Time: 2016/04/14 16:51:30
[2016-04-14T23:51Z] INFO  16:51:30,635 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:51Z] INFO  16:51:30,636 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:51Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-7_31120227_47317818-prep-prealign.bam
[2016-04-14T23:51Z] INFO  16:51:30,738 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:51Z] INFO  16:51:30,977 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-14T23:51Z] INFO  16:51:30,988 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:51Z] INFO  16:51:31,063 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-14T23:51Z] INFO  16:51:31,234 ProgressMeter -            done    218927.0    17.0 s      80.0 s      100.0%    17.0 s       0.0 s
[2016-04-14T23:51Z] INFO  16:51:31,235 ProgressMeter - Total runtime 17.70 secs, 0.29 min, 0.00 hours
[2016-04-14T23:51Z] INFO  16:51:31,239 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 218927 total reads (0.00%)
[2016-04-14T23:51Z] INFO  16:51:31,240 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:51Z] INFO  16:51:31,241 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:51Z] INFO  16:51:31,241 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:51Z] INFO  16:51:31,370 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@7172f77a
[2016-04-14T23:51Z] INFO  16:51:31,425 IntervalUtils - Processing 15658369 bp from intervals
[2016-04-14T23:51Z] WARN  16:51:31,431 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:51Z] INFO  16:51:31,451 ProgressMeter -            done    335286.0    51.0 s       2.5 m      100.0%    51.0 s       0.0 s
[2016-04-14T23:51Z] INFO  16:51:31,452 ProgressMeter - Total runtime 51.25 secs, 0.85 min, 0.01 hours
[2016-04-14T23:51Z] INFO  16:51:31,453 MicroScheduler - 227 reads were filtered out during the traversal out of approximately 335513 total reads (0.07%)
[2016-04-14T23:51Z] INFO  16:51:31,453 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:51Z] INFO  16:51:31,453 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:51Z] INFO  16:51:31,454 MicroScheduler -   -> 227 reads (0.07% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:51Z] INFO  16:51:31,534 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:51Z] GATK RealignerTargetCreator: R14-18105_kapa-NGv3-PE100-NGv3-sort-7_31120227_47317818-prep-prealign.bam 7:31120228-47317818
[2016-04-14T23:51Z] GATK: RealignerTargetCreator
[2016-04-14T23:51Z] INFO  16:51:31,811 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:51Z] INFO  16:51:31,812 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:51Z] INFO  16:51:31,812 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:51Z] INFO  16:51:31,813 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-14T23:51Z] INFO  16:51:32,633 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:51Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-6_125112484_142397186-prep.bam
[2016-04-14T23:51Z] INFO  16:51:32,967 ProgressMeter -      7:99906745    200003.0    30.0 s       2.5 m       33.2%    90.0 s      60.0 s
[2016-04-14T23:51Z] INFO  16:51:33,056 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:51Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-7_0_15584548-prep-prealign.bam
[2016-04-14T23:51Z] INFO  16:51:33,189 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@5fe152b7
[2016-04-14T23:51Z] INFO  16:51:33,372 ProgressMeter -            done     29452.0     6.0 s       3.9 m       94.3%     6.0 s       0.0 s
[2016-04-14T23:51Z] INFO  16:51:33,373 ProgressMeter - Total runtime 6.81 secs, 0.11 min, 0.00 hours
[2016-04-14T23:51Z] INFO  16:51:33,373 MicroScheduler - 21 reads were filtered out during the traversal out of approximately 29473 total reads (0.07%)
[2016-04-14T23:51Z] INFO  16:51:33,374 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:51Z] INFO  16:51:33,374 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:51Z] INFO  16:51:33,374 MicroScheduler -   -> 21 reads (0.07% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:51Z] GATK pre-alignment ('8', 0, 15517156) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-14T23:51Z] GATK RealignerTargetCreator: R14-18105_kapa-NGv3-PE100-NGv3-sort-7_0_15584548-prep-prealign.bam 7:1-15584548
[2016-04-14T23:51Z] GATK: RealignerTargetCreator
[2016-04-14T23:51Z] INFO  16:51:34,252 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:51Z] INFO  16:51:34,256 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:51Z] INFO  16:51:34,257 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:51Z] INFO  16:51:34,258 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:51Z] INFO  16:51:34,264 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/7/R14-18105_kapa-NGv3-PE100-NGv3-sort-7_31120227_47317818-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/7/tx/tmptKI9VA/R14-18105_kapa-NGv3-PE100-NGv3-sort-7_31120227_47317818-prep-prealign-realign.intervals -l INFO -L 7:31120228-47317818 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-14T23:51Z] INFO  16:51:34,289 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:51Z] INFO  16:51:34,289 HelpFormatter - Date/Time: 2016/04/14 16:51:34
[2016-04-14T23:51Z] INFO  16:51:34,290 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:51Z] INFO  16:51:34,290 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:51Z] INFO  16:51:34,438 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:51Z] INFO  16:51:34,628 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-14T23:51Z] INFO  16:51:34,640 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:51Z] INFO  16:51:34,647 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:51Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-7_157155854_159138663-prep-prealign.bam
[2016-04-14T23:51Z] INFO  16:51:34,718 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-14T23:51Z] GATK RealignerTargetCreator: R14-18105_kapa-NGv3-PE100-NGv3-sort-7_157155854_159138663-prep-prealign.bam 7:157155855-159138663
[2016-04-14T23:51Z] GATK: RealignerTargetCreator
[2016-04-14T23:51Z] INFO  16:51:35,121 IntervalUtils - Processing 16197591 bp from intervals
[2016-04-14T23:51Z] WARN  16:51:35,126 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:51Z] INFO  16:51:35,269 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:51Z] INFO  16:51:35,459 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:51Z] INFO  16:51:35,460 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:51Z] INFO  16:51:35,461 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:51Z] INFO  16:51:35,462 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-14T23:51Z] INFO  16:51:36,167 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:51Z] INFO  16:51:36,171 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:51Z] INFO  16:51:36,172 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:51Z] INFO  16:51:36,172 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:51Z] INFO  16:51:36,177 HelpFormatter - Program Args: -T PrintReads -L 8:1-15517156 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/8/tx/tmp5tV5Ll/R14-18105_kapa-NGv3-PE100-NGv3-sort-8_0_15517156-prep-prealign.bam
[2016-04-14T23:51Z] INFO  16:51:36,209 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:51Z] INFO  16:51:36,220 HelpFormatter - Date/Time: 2016/04/14 16:51:36
[2016-04-14T23:51Z] INFO  16:51:36,221 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:51Z] INFO  16:51:36,222 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:51Z] INFO  16:51:36,457 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:51Z] INFO  16:51:37,038 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:51Z] INFO  16:51:37,042 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:51Z] INFO  16:51:37,043 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:51Z] INFO  16:51:37,043 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:51Z] INFO  16:51:37,048 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/7/R14-18105_kapa-NGv3-PE100-NGv3-sort-7_0_15584548-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/7/tx/tmpYmyVh4/R14-18105_kapa-NGv3-PE100-NGv3-sort-7_0_15584548-prep-prealign-realign.intervals -l INFO -L 7:1-15584548 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-14T23:51Z] INFO  16:51:37,078 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:51Z] INFO  16:51:37,079 HelpFormatter - Date/Time: 2016/04/14 16:51:37
[2016-04-14T23:51Z] INFO  16:51:37,079 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:51Z] INFO  16:51:37,080 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:51Z] INFO  16:51:37,214 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:51Z] INFO  16:51:37,254 ProgressMeter -     7:135329910    200003.0    30.0 s       2.6 m       59.5%    50.0 s      20.0 s
[2016-04-14T23:51Z] INFO  16:51:37,469 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-14T23:51Z] INFO  16:51:37,476 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-14T23:51Z] INFO  16:51:37,486 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:51Z] INFO  16:51:37,521 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:51Z] INFO  16:51:37,530 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:51Z] INFO  16:51:37,547 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-14T23:51Z] INFO  16:51:37,573 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.04
[2016-04-14T23:51Z] INFO  16:51:37,593 IntervalUtils - Processing 15517156 bp from intervals
[2016-04-14T23:51Z] INFO  16:51:37,707 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:51Z] INFO  16:51:37,829 IntervalUtils - Processing 15584548 bp from intervals
[2016-04-14T23:51Z] WARN  16:51:37,835 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:51Z] INFO  16:51:37,908 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:51Z] INFO  16:51:37,944 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:51Z] INFO  16:51:37,947 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:51Z] INFO  16:51:37,947 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:51Z] INFO  16:51:37,948 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:51Z] INFO  16:51:37,953 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/7/R14-18105_kapa-NGv3-PE100-NGv3-sort-7_157155854_159138663-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/7/tx/tmpkmIuxe/R14-18105_kapa-NGv3-PE100-NGv3-sort-7_157155854_159138663-prep-prealign-realign.intervals -l INFO -L 7:157155855-159138663 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-14T23:51Z] INFO  16:51:37,962 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:51Z] INFO  16:51:37,963 HelpFormatter - Date/Time: 2016/04/14 16:51:37
[2016-04-14T23:51Z] INFO  16:51:37,964 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:51Z] INFO  16:51:37,965 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:51Z] INFO  16:51:38,046 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:51Z] INFO  16:51:38,047 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:51Z] INFO  16:51:38,048 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:51Z] INFO  16:51:38,048 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:51Z] INFO  16:51:38,081 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:51Z] INFO  16:51:38,084 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:51Z] INFO  16:51:38,143 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:51Z] INFO  16:51:38,145 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:51Z] INFO  16:51:38,145 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:51Z] INFO  16:51:38,146 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-14T23:51Z] INFO  16:51:38,247 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:51Z] INFO  16:51:38,344 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-14T23:51Z] INFO  16:51:38,353 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:51Z] INFO  16:51:38,397 ProgressMeter -            done    261517.0    19.0 s      75.0 s      100.0%    19.0 s       0.0 s
[2016-04-14T23:51Z] INFO  16:51:38,398 ProgressMeter - Total runtime 19.81 secs, 0.33 min, 0.01 hours
[2016-04-14T23:51Z] INFO  16:51:38,401 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 261517 total reads (0.00%)
[2016-04-14T23:51Z] INFO  16:51:38,401 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:51Z] INFO  16:51:38,402 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:51Z] INFO  16:51:38,402 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:51Z] INFO  16:51:38,426 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-14T23:51Z] INFO  16:51:38,841 IntervalUtils - Processing 1982809 bp from intervals
[2016-04-14T23:51Z] WARN  16:51:38,861 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:51Z] INFO  16:51:39,011 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:51Z] INFO  16:51:39,139 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:51Z] INFO  16:51:39,140 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:51Z] INFO  16:51:39,141 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:51Z] INFO  16:51:39,142 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-14T23:51Z] INFO  16:51:39,738 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:51Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-6_142399691_157963777-prep.bam
[2016-04-14T23:51Z] GATK pre-alignment ('8', 15519664, 31030618) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-14T23:51Z] INFO  16:51:40,992 ProgressMeter -            done   1.5517948E7    19.0 s       1.0 s      100.0%    19.0 s       0.0 s
[2016-04-14T23:51Z] INFO  16:51:40,994 ProgressMeter - Total runtime 19.04 secs, 0.32 min, 0.01 hours
[2016-04-14T23:51Z] INFO  16:51:40,998 MicroScheduler - 18393 reads were filtered out during the traversal out of approximately 209357 total reads (8.79%)
[2016-04-14T23:51Z] INFO  16:51:40,999 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:51Z] INFO  16:51:40,999 MicroScheduler -   -> 618 reads (0.30% of total) failing BadMateFilter
[2016-04-14T23:51Z] INFO  16:51:41,000 MicroScheduler -   -> 16349 reads (7.81% of total) failing DuplicateReadFilter
[2016-04-14T23:51Z] INFO  16:51:41,001 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-14T23:51Z] INFO  16:51:41,001 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:51Z] INFO  16:51:41,002 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-14T23:51Z] INFO  16:51:41,003 MicroScheduler -   -> 1426 reads (0.68% of total) failing MappingQualityZeroFilter
[2016-04-14T23:51Z] INFO  16:51:41,003 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:51Z] INFO  16:51:41,004 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-14T23:51Z] INFO  16:51:41,004 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-14T23:51Z] INFO  16:51:42,390 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:51Z] INFO  16:51:42,408 ProgressMeter -            done   1.5552574E7    16.0 s       1.0 s      100.0%    16.0 s       0.0 s
[2016-04-14T23:51Z] INFO  16:51:42,409 ProgressMeter - Total runtime 16.34 secs, 0.27 min, 0.00 hours
[2016-04-14T23:51Z] INFO  16:51:42,414 MicroScheduler - 10403 reads were filtered out during the traversal out of approximately 123761 total reads (8.41%)
[2016-04-14T23:51Z] INFO  16:51:42,415 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:51Z] INFO  16:51:42,416 MicroScheduler -   -> 474 reads (0.38% of total) failing BadMateFilter
[2016-04-14T23:51Z] INFO  16:51:42,416 MicroScheduler -   -> 9711 reads (7.85% of total) failing DuplicateReadFilter
[2016-04-14T23:51Z] INFO  16:51:42,417 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-14T23:51Z] INFO  16:51:42,417 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:51Z] INFO  16:51:42,417 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-14T23:51Z] INFO  16:51:42,418 MicroScheduler -   -> 218 reads (0.18% of total) failing MappingQualityZeroFilter
[2016-04-14T23:51Z] INFO  16:51:42,418 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:51Z] INFO  16:51:42,418 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-14T23:51Z] INFO  16:51:42,418 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-14T23:51Z] GATK: realign ('7', 15599765, 31117713) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-14T23:51Z] INFO  16:51:43,542 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:51Z] INFO  16:51:43,546 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:51Z] INFO  16:51:43,546 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:51Z] INFO  16:51:43,547 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:51Z] INFO  16:51:43,553 HelpFormatter - Program Args: -T PrintReads -L 8:15519665-31030618 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/8/tx/tmp5E2Fwf/R14-18105_kapa-NGv3-PE100-NGv3-sort-8_15519664_31030618-prep-prealign.bam
[2016-04-14T23:51Z] INFO  16:51:43,588 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:51Z] INFO  16:51:43,589 HelpFormatter - Date/Time: 2016/04/14 16:51:43
[2016-04-14T23:51Z] INFO  16:51:43,589 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:51Z] INFO  16:51:43,590 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:51Z] INFO  16:51:43,716 ProgressMeter -            done   1982809.0     4.0 s       2.0 s      100.0%     4.0 s       0.0 s
[2016-04-14T23:51Z] INFO  16:51:43,717 ProgressMeter - Total runtime 4.58 secs, 0.08 min, 0.00 hours
[2016-04-14T23:51Z] INFO  16:51:43,721 MicroScheduler - 2709 reads were filtered out during the traversal out of approximately 29588 total reads (9.16%)
[2016-04-14T23:51Z] INFO  16:51:43,722 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:51Z] INFO  16:51:43,722 MicroScheduler -   -> 79 reads (0.27% of total) failing BadMateFilter
[2016-04-14T23:51Z] INFO  16:51:43,723 MicroScheduler -   -> 2290 reads (7.74% of total) failing DuplicateReadFilter
[2016-04-14T23:51Z] INFO  16:51:43,724 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-14T23:51Z] INFO  16:51:43,724 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:51Z] INFO  16:51:43,725 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-14T23:51Z] INFO  16:51:43,725 MicroScheduler -   -> 340 reads (1.15% of total) failing MappingQualityZeroFilter
[2016-04-14T23:51Z] INFO  16:51:43,726 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:51Z] INFO  16:51:43,727 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-14T23:51Z] INFO  16:51:43,727 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-14T23:51Z] INFO  16:51:43,734 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:51Z] INFO  16:51:43,755 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:51Z] GATK: realign ('7', 110526648, 126079222) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-14T23:51Z] INFO  16:51:44,434 ProgressMeter -            done    248730.0    19.0 s      77.0 s       98.7%    19.0 s       0.0 s
[2016-04-14T23:51Z] INFO  16:51:44,434 ProgressMeter - Total runtime 19.30 secs, 0.32 min, 0.01 hours
[2016-04-14T23:51Z] INFO  16:51:44,438 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 248730 total reads (0.00%)
[2016-04-14T23:51Z] INFO  16:51:44,439 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:51Z] INFO  16:51:44,439 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:51Z] INFO  16:51:44,439 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:51Z] INFO  16:51:44,778 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-14T23:51Z] INFO  16:51:44,826 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:51Z] INFO  16:51:44,840 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:51Z] INFO  16:51:44,843 ProgressMeter -            done   1.5773393E7    16.0 s       1.0 s      100.0%    16.0 s       0.0 s
[2016-04-14T23:51Z] INFO  16:51:44,844 ProgressMeter - Total runtime 16.27 secs, 0.27 min, 0.00 hours
[2016-04-14T23:51Z] INFO  16:51:44,848 MicroScheduler - 29522 reads were filtered out during the traversal out of approximately 164921 total reads (17.90%)
[2016-04-14T23:51Z] INFO  16:51:44,848 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:51Z] INFO  16:51:44,849 MicroScheduler -   -> 466 reads (0.28% of total) failing BadMateFilter
[2016-04-14T23:51Z] INFO  16:51:44,849 MicroScheduler -   -> 11469 reads (6.95% of total) failing DuplicateReadFilter
[2016-04-14T23:51Z] INFO  16:51:44,849 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-14T23:51Z] INFO  16:51:44,850 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:51Z] INFO  16:51:44,850 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-14T23:51Z] INFO  16:51:44,850 MicroScheduler -   -> 17587 reads (10.66% of total) failing MappingQualityZeroFilter
[2016-04-14T23:51Z] INFO  16:51:44,850 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:51Z] INFO  16:51:44,851 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-14T23:51Z] INFO  16:51:44,851 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-14T23:51Z] INFO  16:51:44,905 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-14T23:51Z] INFO  16:51:44,947 IntervalUtils - Processing 15510954 bp from intervals
[2016-04-14T23:51Z] INFO  16:51:45,037 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:51Z] INFO  16:51:45,040 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:51Z] INFO  16:51:45,041 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:51Z] INFO  16:51:45,041 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:51Z] INFO  16:51:45,046 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/7/R14-18105_kapa-NGv3-PE100-NGv3-sort-7_15599765_31117713-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/7/R14-18105_kapa-NGv3-PE100-NGv3-sort-7_15599765_31117713-prep-prealign-realign.intervals -L 7:15599766-31117713 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/7/tx/tmpU0S_eV/R14-18105_kapa-NGv3-PE100-NGv3-sort-7_15599765_31117713-prep.bam
[2016-04-14T23:51Z] INFO  16:51:45,064 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:51Z] INFO  16:51:45,064 HelpFormatter - Date/Time: 2016/04/14 16:51:45
[2016-04-14T23:51Z] INFO  16:51:45,065 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:51Z] INFO  16:51:45,065 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:51Z] INFO  16:51:45,070 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:51Z] INFO  16:51:45,098 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:51Z] GATK: realign ('7', 157155854, 159138663) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-14T23:51Z] INFO  16:51:45,262 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:51Z] INFO  16:51:45,363 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:51Z] INFO  16:51:45,363 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:51Z] INFO  16:51:45,364 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:51Z] INFO  16:51:45,364 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:51Z] INFO  16:51:45,389 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:51Z] INFO  16:51:45,414 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:51Z] INFO  16:51:45,434 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:51Z] INFO  16:51:45,528 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.09
[2016-04-14T23:51Z] INFO  16:51:45,540 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:51Z] INFO  16:51:45,807 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:51Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-6_158013810_171115067-prep.bam
[2016-04-14T23:51Z] INFO  16:51:45,895 IntervalUtils - Processing 15517948 bp from intervals
[2016-04-14T23:51Z] WARN  16:51:45,911 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:51Z] INFO  16:51:46,043 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:51Z] INFO  16:51:46,127 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:51Z] INFO  16:51:46,128 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:51Z] INFO  16:51:46,129 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:51Z] INFO  16:51:46,130 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:51Z] INFO  16:51:46,270 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:51Z] INFO  16:51:46,281 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:51Z] GATK: realign ('7', 47319761, 63093154) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-14T23:51Z] INFO  16:51:46,433 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:51Z] INFO  16:51:46,461 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:51Z] INFO  16:51:46,464 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:51Z] INFO  16:51:46,464 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:51Z] INFO  16:51:46,465 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:51Z] INFO  16:51:46,469 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/7/R14-18105_kapa-NGv3-PE100-NGv3-sort-7_110526648_126079222-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/7/R14-18105_kapa-NGv3-PE100-NGv3-sort-7_110526648_126079222-prep-prealign-realign.intervals -L 7:110526649-126079222 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/7/tx/tmpeSf92y/R14-18105_kapa-NGv3-PE100-NGv3-sort-7_110526648_126079222-prep.bam
[2016-04-14T23:51Z] INFO  16:51:46,479 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:51Z] INFO  16:51:46,490 HelpFormatter - Date/Time: 2016/04/14 16:51:46
[2016-04-14T23:51Z] INFO  16:51:46,491 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:51Z] INFO  16:51:46,492 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:51Z] GATK pre-alignment ('8', 31496910, 48001429) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-14T23:51Z] INFO  16:51:46,730 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:51Z] INFO  16:51:46,938 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:51Z] INFO  16:51:46,949 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:51Z] INFO  16:51:47,028 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-14T23:51Z] INFO  16:51:47,497 IntervalUtils - Processing 15552574 bp from intervals
[2016-04-14T23:51Z] WARN  16:51:47,503 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:51Z] INFO  16:51:47,653 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:51Z] INFO  16:51:47,813 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:51Z] INFO  16:51:47,814 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:51Z] INFO  16:51:47,815 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:51Z] INFO  16:51:47,816 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:51Z] INFO  16:51:48,037 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:51Z] INFO  16:51:48,041 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:51Z] INFO  16:51:48,042 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:51Z] INFO  16:51:48,042 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:51Z] INFO  16:51:48,046 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:51Z] INFO  16:51:48,047 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/7/R14-18105_kapa-NGv3-PE100-NGv3-sort-7_157155854_159138663-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/7/R14-18105_kapa-NGv3-PE100-NGv3-sort-7_157155854_159138663-prep-prealign-realign.intervals -L 7:157155855-159138663 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/7/tx/tmphdXsbU/R14-18105_kapa-NGv3-PE100-NGv3-sort-7_157155854_159138663-prep.bam
[2016-04-14T23:51Z] INFO  16:51:48,062 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:51Z] INFO  16:51:48,062 HelpFormatter - Date/Time: 2016/04/14 16:51:48
[2016-04-14T23:51Z] INFO  16:51:48,063 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:51Z] INFO  16:51:48,063 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:51Z] INFO  16:51:48,149 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@32d5a4c6
[2016-04-14T23:51Z] INFO  16:51:48,215 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:51Z] INFO  16:51:48,282 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:51Z] INFO  16:51:48,331 ProgressMeter -            done    396794.0    48.0 s       2.0 m      100.0%    48.0 s       0.0 s
[2016-04-14T23:51Z] INFO  16:51:48,332 ProgressMeter - Total runtime 48.75 secs, 0.81 min, 0.01 hours
[2016-04-14T23:51Z] INFO  16:51:48,332 MicroScheduler - 262 reads were filtered out during the traversal out of approximately 397056 total reads (0.07%)
[2016-04-14T23:51Z] INFO  16:51:48,333 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:51Z] INFO  16:51:48,333 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:51Z] INFO  16:51:48,333 MicroScheduler -   -> 262 reads (0.07% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:51Z] INFO  16:51:48,420 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:51Z] INFO  16:51:48,435 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:51Z] INFO  16:51:48,490 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-14T23:51Z] INFO  16:51:48,894 IntervalUtils - Processing 1982809 bp from intervals
[2016-04-14T23:51Z] WARN  16:51:48,900 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:51Z] INFO  16:51:49,021 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:51Z] INFO  16:51:49,075 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:51Z] INFO  16:51:49,077 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:51Z] INFO  16:51:49,077 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:51Z] INFO  16:51:49,078 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:51Z] INFO  16:51:49,102 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:51Z] INFO  16:51:49,105 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:51Z] INFO  16:51:49,106 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:51Z] INFO  16:51:49,106 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:51Z] INFO  16:51:49,111 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/7/R14-18105_kapa-NGv3-PE100-NGv3-sort-7_47319761_63093154-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/7/R14-18105_kapa-NGv3-PE100-NGv3-sort-7_47319761_63093154-prep-prealign-realign.intervals -L 7:47319762-63093154 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/7/tx/tmpuJx2Ib/R14-18105_kapa-NGv3-PE100-NGv3-sort-7_47319761_63093154-prep.bam
[2016-04-14T23:51Z] INFO  16:51:49,127 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:51Z] INFO  16:51:49,128 HelpFormatter - Date/Time: 2016/04/14 16:51:49
[2016-04-14T23:51Z] INFO  16:51:49,129 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:51Z] INFO  16:51:49,129 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:51Z] INFO  16:51:49,147 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:51Z] INFO  16:51:49,176 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:51Z] INFO  16:51:49,306 ProgressMeter -            done   1.5658369E7    17.0 s       1.0 s      100.0%    17.0 s       0.0 s
[2016-04-14T23:51Z] INFO  16:51:49,307 ProgressMeter - Total runtime 17.50 secs, 0.29 min, 0.00 hours
[2016-04-14T23:51Z] INFO  16:51:49,311 MicroScheduler - 14647 reads were filtered out during the traversal out of approximately 177897 total reads (8.23%)
[2016-04-14T23:51Z] INFO  16:51:49,312 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:51Z] INFO  16:51:49,313 MicroScheduler -   -> 513 reads (0.29% of total) failing BadMateFilter
[2016-04-14T23:51Z] INFO  16:51:49,314 MicroScheduler -   -> 13687 reads (7.69% of total) failing DuplicateReadFilter
[2016-04-14T23:51Z] INFO  16:51:49,314 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-14T23:51Z] INFO  16:51:49,315 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:51Z] INFO  16:51:49,316 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-14T23:51Z] INFO  16:51:49,316 MicroScheduler -   -> 447 reads (0.25% of total) failing MappingQualityZeroFilter
[2016-04-14T23:51Z] INFO  16:51:49,317 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:51Z] INFO  16:51:49,317 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-14T23:51Z] INFO  16:51:49,318 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-14T23:51Z] INFO  16:51:49,421 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:51Z] INFO  16:51:49,527 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@5fe152b7
[2016-04-14T23:51Z] INFO  16:51:49,552 ProgressMeter -     7:148876161    200005.0    30.0 s       2.5 m       46.7%    64.0 s      34.0 s
[2016-04-14T23:51Z] INFO  16:51:49,558 ProgressMeter -     5:140308525    400013.0    30.0 s      75.0 s       81.5%    36.0 s       6.0 s
[2016-04-14T23:51Z] INFO  16:51:49,568 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:51Z] INFO  16:51:49,588 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:51Z] INFO  16:51:49,609 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:51Z] INFO  16:51:49,612 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:51Z] INFO  16:51:49,613 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:51Z] INFO  16:51:49,613 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:51Z] INFO  16:51:49,617 HelpFormatter - Program Args: -T PrintReads -L 8:31496911-48001429 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/8/tx/tmpZPI1M9/R14-18105_kapa-NGv3-PE100-NGv3-sort-8_31496910_48001429-prep-prealign.bam
[2016-04-14T23:51Z] INFO  16:51:49,626 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:51Z] INFO  16:51:49,630 HelpFormatter - Date/Time: 2016/04/14 16:51:49
[2016-04-14T23:51Z] INFO  16:51:49,630 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:51Z] INFO  16:51:49,633 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:51Z] INFO  16:51:49,640 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-14T23:51Z] INFO  16:51:49,750 ProgressMeter -            done    344751.0    43.0 s       2.1 m      100.0%    43.0 s       0.0 s
[2016-04-14T23:51Z] INFO  16:51:49,751 ProgressMeter - Total runtime 43.18 secs, 0.72 min, 0.01 hours
[2016-04-14T23:51Z] INFO  16:51:49,751 MicroScheduler - 201 reads were filtered out during the traversal out of approximately 344952 total reads (0.06%)
[2016-04-14T23:51Z] INFO  16:51:49,751 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:51Z] INFO  16:51:49,752 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:51Z] INFO  16:51:49,752 MicroScheduler -   -> 201 reads (0.06% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:51Z] INFO  16:51:49,831 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:51Z] INFO  16:51:49,882 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:51Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-7_63095909_78636522-prep-prealign.bam
[2016-04-14T23:51Z] INFO  16:51:50,037 IntervalUtils - Processing 15773393 bp from intervals
[2016-04-14T23:51Z] WARN  16:51:50,042 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:51Z] INFO  16:51:50,120 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:51Z] INFO  16:51:50,243 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:51Z] INFO  16:51:50,244 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:51Z] INFO  16:51:50,244 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:51Z] INFO  16:51:50,245 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:51Z] INFO  16:51:50,428 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:51Z] INFO  16:51:50,607 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:51Z] INFO  16:51:50,675 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:51Z] GATK: realign ('7', 79082334, 94740703) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-14T23:51Z] INFO  16:51:50,807 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-14T23:51Z] INFO  16:51:50,897 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:51Z] INFO  16:51:50,906 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:51Z] INFO  16:51:50,940 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.03
[2016-04-14T23:51Z] INFO  16:51:50,954 IntervalUtils - Processing 16504519 bp from intervals
[2016-04-14T23:51Z] INFO  16:51:51,022 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:51Z] GATK RealignerTargetCreator: R14-18105_kapa-NGv3-PE100-NGv3-sort-7_63095909_78636522-prep-prealign.bam 7:63095910-78636522
[2016-04-14T23:51Z] GATK: RealignerTargetCreator
[2016-04-14T23:51Z] INFO  16:51:51,251 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:51Z] INFO  16:51:51,252 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:51Z] INFO  16:51:51,252 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:51Z] INFO  16:51:51,252 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:51Z] INFO  16:51:51,257 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:51Z] INFO  16:51:51,266 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:51Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-7_126086124_141619620-prep-prealign.bam
[2016-04-14T23:51Z] INFO  16:51:51,403 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:51Z] GATK RealignerTargetCreator: R14-18105_kapa-NGv3-PE100-NGv3-sort-7_126086124_141619620-prep-prealign.bam 7:126086125-141619620
[2016-04-14T23:51Z] GATK: RealignerTargetCreator
[2016-04-14T23:51Z] INFO  16:51:53,643 ProgressMeter -            done     29452.0     4.0 s       2.6 m       94.3%     4.0 s       0.0 s
[2016-04-14T23:51Z] INFO  16:51:53,644 ProgressMeter - Total runtime 4.57 secs, 0.08 min, 0.00 hours
[2016-04-14T23:51Z] INFO  16:51:53,648 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 29452 total reads (0.00%)
[2016-04-14T23:51Z] INFO  16:51:53,648 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:51Z] INFO  16:51:53,648 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:51Z] INFO  16:51:53,649 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:51Z] INFO  16:51:53,789 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:51Z] INFO  16:51:53,792 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:51Z] INFO  16:51:53,793 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:51Z] INFO  16:51:53,794 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:51Z] INFO  16:51:53,798 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/7/R14-18105_kapa-NGv3-PE100-NGv3-sort-7_79082334_94740703-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/7/R14-18105_kapa-NGv3-PE100-NGv3-sort-7_79082334_94740703-prep-prealign-realign.intervals -L 7:79082335-94740703 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/7/tx/tmppLOupX/R14-18105_kapa-NGv3-PE100-NGv3-sort-7_79082334_94740703-prep.bam
[2016-04-14T23:51Z] INFO  16:51:53,824 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:51Z] INFO  16:51:53,824 HelpFormatter - Date/Time: 2016/04/14 16:51:53
[2016-04-14T23:51Z] INFO  16:51:53,824 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:51Z] INFO  16:51:53,825 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:51Z] INFO  16:51:54,090 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:51Z] INFO  16:51:54,181 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:51Z] INFO  16:51:54,184 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:51Z] INFO  16:51:54,184 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:51Z] INFO  16:51:54,185 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:51Z] INFO  16:51:54,189 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/7/R14-18105_kapa-NGv3-PE100-NGv3-sort-7_63095909_78636522-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/7/tx/tmp6IkRNK/R14-18105_kapa-NGv3-PE100-NGv3-sort-7_63095909_78636522-prep-prealign-realign.intervals -l INFO -L 7:63095910-78636522 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-14T23:51Z] INFO  16:51:54,208 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:51Z] INFO  16:51:54,209 HelpFormatter - Date/Time: 2016/04/14 16:51:54
[2016-04-14T23:51Z] INFO  16:51:54,209 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:51Z] INFO  16:51:54,210 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:51Z] INFO  16:51:54,233 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:51Z] INFO  16:51:54,255 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:51Z] INFO  16:51:54,303 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-14T23:51Z] INFO  16:51:54,345 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:51Z] INFO  16:51:54,607 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-14T23:51Z] INFO  16:51:54,617 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:51Z] INFO  16:51:54,628 IntervalUtils - Processing 15658369 bp from intervals
[2016-04-14T23:51Z] WARN  16:51:54,633 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:51Z] INFO  16:51:54,679 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-14T23:51Z] INFO  16:51:54,711 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:51Z] INFO  16:51:54,762 ProgressMeter -            done   1.6197591E7    19.0 s       1.0 s      100.0%    19.0 s       0.0 s
[2016-04-14T23:51Z] INFO  16:51:54,764 ProgressMeter - Total runtime 19.30 secs, 0.32 min, 0.01 hours
[2016-04-14T23:51Z] INFO  16:51:54,768 MicroScheduler - 33562 reads were filtered out during the traversal out of approximately 272090 total reads (12.33%)
[2016-04-14T23:51Z] INFO  16:51:54,769 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:51Z] INFO  16:51:54,770 MicroScheduler -   -> 650 reads (0.24% of total) failing BadMateFilter
[2016-04-14T23:51Z] INFO  16:51:54,770 MicroScheduler -   -> 20654 reads (7.59% of total) failing DuplicateReadFilter
[2016-04-14T23:51Z] INFO  16:51:54,771 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-14T23:51Z] INFO  16:51:54,772 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:51Z] INFO  16:51:54,772 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-14T23:51Z] INFO  16:51:54,773 MicroScheduler -   -> 12258 reads (4.51% of total) failing MappingQualityZeroFilter
[2016-04-14T23:51Z] INFO  16:51:54,774 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:51Z] INFO  16:51:54,774 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-14T23:51Z] INFO  16:51:54,775 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-14T23:51Z] INFO  16:51:54,824 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:51Z] INFO  16:51:54,836 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:51Z] INFO  16:51:54,837 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:51Z] INFO  16:51:54,837 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:51Z] INFO  16:51:55,019 IntervalUtils - Processing 15540613 bp from intervals
[2016-04-14T23:51Z] INFO  16:51:55,019 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:51Z] WARN  16:51:55,024 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:51Z] INFO  16:51:55,096 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:51Z] INFO  16:51:55,168 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:51Z] INFO  16:51:55,291 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:51Z] INFO  16:51:55,299 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:51Z] INFO  16:51:55,300 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:51Z] INFO  16:51:55,302 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:51Z] INFO  16:51:55,303 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-14T23:51Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-7_157155854_159138663-prep.bam
[2016-04-14T23:51Z] GATK pre-alignment ('8', 48003022, 63659688) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-14T23:51Z] INFO  16:51:55,510 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:51Z] INFO  16:51:55,514 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:51Z] INFO  16:51:55,514 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:51Z] INFO  16:51:55,515 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:51Z] INFO  16:51:55,519 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/7/R14-18105_kapa-NGv3-PE100-NGv3-sort-7_126086124_141619620-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/7/tx/tmpg9Of5v/R14-18105_kapa-NGv3-PE100-NGv3-sort-7_126086124_141619620-prep-prealign-realign.intervals -l INFO -L 7:126086125-141619620 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-14T23:51Z] INFO  16:51:55,535 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:51Z] INFO  16:51:55,539 HelpFormatter - Date/Time: 2016/04/14 16:51:55
[2016-04-14T23:51Z] INFO  16:51:55,540 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:51Z] INFO  16:51:55,541 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:51Z] INFO  16:51:55,657 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:51Z] INFO  16:51:55,950 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-14T23:51Z] INFO  16:51:55,960 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:51Z] INFO  16:51:56,024 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-14T23:51Z] INFO  16:51:56,312 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:51Z] GATK: realign ('7', 31120227, 47317818) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-14T23:51Z] INFO  16:51:56,408 IntervalUtils - Processing 15533496 bp from intervals
[2016-04-14T23:51Z] WARN  16:51:56,424 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:51Z] INFO  16:51:56,571 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:51Z] INFO  16:51:56,861 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:51Z] INFO  16:51:56,874 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:51Z] INFO  16:51:56,875 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:51Z] INFO  16:51:56,876 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-14T23:51Z] INFO  16:51:57,854 ProgressMeter -      6:44222517   1.3136615E7    30.0 s       2.0 s       84.7%    35.0 s       5.0 s
[2016-04-14T23:51Z] INFO  16:51:57,934 ProgressMeter -            done   1.5584548E7    19.0 s       1.0 s      100.0%    19.0 s       0.0 s
[2016-04-14T23:51Z] INFO  16:51:57,935 ProgressMeter - Total runtime 19.79 secs, 0.33 min, 0.01 hours
[2016-04-14T23:51Z] INFO  16:51:57,939 MicroScheduler - 43643 reads were filtered out during the traversal out of approximately 337151 total reads (12.94%)
[2016-04-14T23:51Z] INFO  16:51:57,939 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:51Z] INFO  16:51:57,940 MicroScheduler -   -> 804 reads (0.24% of total) failing BadMateFilter
[2016-04-14T23:51Z] INFO  16:51:57,940 MicroScheduler -   -> 25110 reads (7.45% of total) failing DuplicateReadFilter
[2016-04-14T23:51Z] INFO  16:51:57,940 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-14T23:51Z] INFO  16:51:57,941 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:51Z] INFO  16:51:57,943 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-14T23:51Z] INFO  16:51:57,944 MicroScheduler -   -> 17729 reads (5.26% of total) failing MappingQualityZeroFilter
[2016-04-14T23:51Z] INFO  16:51:57,944 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:51Z] INFO  16:51:57,945 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-14T23:51Z] INFO  16:51:57,946 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-14T23:51Z] INFO  16:51:58,474 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:51Z] INFO  16:51:58,476 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:51Z] INFO  16:51:58,476 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:51Z] INFO  16:51:58,477 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:51Z] INFO  16:51:58,481 HelpFormatter - Program Args: -T PrintReads -L 8:48003023-63659688 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/8/tx/tmpOuqASl/R14-18105_kapa-NGv3-PE100-NGv3-sort-8_48003022_63659688-prep-prealign.bam
[2016-04-14T23:51Z] INFO  16:51:58,511 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:51Z] INFO  16:51:58,511 HelpFormatter - Date/Time: 2016/04/14 16:51:58
[2016-04-14T23:51Z] INFO  16:51:58,511 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:51Z] INFO  16:51:58,512 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:51Z] INFO  16:51:58,758 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:51Z] INFO  16:51:59,338 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:51Z] GATK: realign ('7', 0, 15584548) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-14T23:51Z] INFO  16:51:59,556 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:51Z] INFO  16:51:59,560 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:51Z] INFO  16:51:59,561 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:51Z] INFO  16:51:59,562 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:51Z] INFO  16:51:59,567 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/7/R14-18105_kapa-NGv3-PE100-NGv3-sort-7_31120227_47317818-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/7/R14-18105_kapa-NGv3-PE100-NGv3-sort-7_31120227_47317818-prep-prealign-realign.intervals -L 7:31120228-47317818 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/7/tx/tmpn9uWNH/R14-18105_kapa-NGv3-PE100-NGv3-sort-7_31120227_47317818-prep.bam
[2016-04-14T23:51Z] INFO  16:51:59,578 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:51Z] INFO  16:51:59,578 HelpFormatter - Date/Time: 2016/04/14 16:51:59
[2016-04-14T23:51Z] INFO  16:51:59,578 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:51Z] INFO  16:51:59,579 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:51Z] INFO  16:51:59,792 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:51Z] INFO  16:51:59,815 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-14T23:51Z] INFO  16:51:59,896 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:51Z] INFO  16:51:59,903 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:51Z] INFO  16:51:59,913 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:51Z] INFO  16:51:59,923 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:51Z] INFO  16:51:59,953 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.04
[2016-04-14T23:51Z] INFO  16:51:59,979 IntervalUtils - Processing 15656666 bp from intervals
[2016-04-14T23:52Z] INFO  16:52:00,007 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-14T23:52Z] INFO  16:52:00,053 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:52Z] INFO  16:52:00,410 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:52Z] INFO  16:52:00,411 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:52Z] INFO  16:52:00,411 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:52Z] INFO  16:52:00,411 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:52Z] INFO  16:52:00,452 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:52Z] INFO  16:52:00,468 IntervalUtils - Processing 16197591 bp from intervals
[2016-04-14T23:52Z] WARN  16:52:00,483 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:52Z] INFO  16:52:00,557 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:52Z] INFO  16:52:00,634 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:52Z] INFO  16:52:00,735 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:52Z] INFO  16:52:00,737 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:52Z] INFO  16:52:00,737 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:52Z] INFO  16:52:00,738 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:52Z] INFO  16:52:00,958 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:52Z] INFO  16:52:01,004 ProgressMeter -            done   1.5509444E7    33.0 s       2.0 s      100.0%    33.0 s       0.0 s
[2016-04-14T23:52Z] INFO  16:52:01,005 ProgressMeter - Total runtime 33.17 secs, 0.55 min, 0.01 hours
[2016-04-14T23:52Z] INFO  16:52:01,008 MicroScheduler - 103999 reads were filtered out during the traversal out of approximately 892401 total reads (11.65%)
[2016-04-14T23:52Z] INFO  16:52:01,009 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:52Z] INFO  16:52:01,010 MicroScheduler -   -> 1468 reads (0.16% of total) failing BadMateFilter
[2016-04-14T23:52Z] INFO  16:52:01,011 MicroScheduler -   -> 67037 reads (7.51% of total) failing DuplicateReadFilter
[2016-04-14T23:52Z] INFO  16:52:01,011 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-14T23:52Z] INFO  16:52:01,012 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:52Z] INFO  16:52:01,013 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-14T23:52Z] INFO  16:52:01,013 MicroScheduler -   -> 35494 reads (3.98% of total) failing MappingQualityZeroFilter
[2016-04-14T23:52Z] INFO  16:52:01,014 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:52Z] INFO  16:52:01,014 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-14T23:52Z] INFO  16:52:01,015 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-14T23:52Z] INFO  16:52:01,133 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:52Z] INFO  16:52:01,458 ProgressMeter -            done    123055.0    13.0 s     110.0 s      100.0%    13.0 s       0.0 s
[2016-04-14T23:52Z] INFO  16:52:01,458 ProgressMeter - Total runtime 13.64 secs, 0.23 min, 0.00 hours
[2016-04-14T23:52Z] INFO  16:52:01,461 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 123055 total reads (0.00%)
[2016-04-14T23:52Z] INFO  16:52:01,462 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:52Z] INFO  16:52:01,462 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:52Z] INFO  16:52:01,462 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:52Z] INFO  16:52:02,065 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:52Z] INFO  16:52:02,068 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:52Z] INFO  16:52:02,069 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:52Z] INFO  16:52:02,069 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:52Z] INFO  16:52:02,074 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/7/R14-18105_kapa-NGv3-PE100-NGv3-sort-7_0_15584548-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/7/R14-18105_kapa-NGv3-PE100-NGv3-sort-7_0_15584548-prep-prealign-realign.intervals -L 7:1-15584548 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/7/tx/tmppK6ywB/R14-18105_kapa-NGv3-PE100-NGv3-sort-7_0_15584548-prep.bam
[2016-04-14T23:52Z] INFO  16:52:02,099 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:52Z] INFO  16:52:02,110 HelpFormatter - Date/Time: 2016/04/14 16:52:02
[2016-04-14T23:52Z] INFO  16:52:02,111 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:52Z] INFO  16:52:02,112 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:52Z] INFO  16:52:02,352 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:52Z] INFO  16:52:02,452 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:52Z] INFO  16:52:02,461 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:52Z] INFO  16:52:02,504 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.04
[2016-04-14T23:52Z] INFO  16:52:02,549 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:52Z] GATK: realign ('6', 31083801, 46593245) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-14T23:52Z] INFO  16:52:02,810 IntervalUtils - Processing 15584548 bp from intervals
[2016-04-14T23:52Z] WARN  16:52:02,815 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:52Z] INFO  16:52:02,894 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:52Z] INFO  16:52:03,026 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:52Z] INFO  16:52:03,027 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:52Z] INFO  16:52:03,028 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:52Z] INFO  16:52:03,029 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:52Z] INFO  16:52:03,171 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:52Z] INFO  16:52:03,185 ProgressMeter -     7:101896542    400006.0    60.0 s       2.5 m       45.9%     2.2 m      70.0 s
[2016-04-14T23:52Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-7_110526648_126079222-prep.bam
[2016-04-14T23:52Z] INFO  16:52:03,214 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:52Z] INFO  16:52:03,215 ProgressMeter -            done    716044.0    43.0 s      61.0 s      100.0%    43.0 s       0.0 s
[2016-04-14T23:52Z] INFO  16:52:03,216 ProgressMeter - Total runtime 43.88 secs, 0.73 min, 0.01 hours
[2016-04-14T23:52Z] INFO  16:52:03,220 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 716044 total reads (0.00%)
[2016-04-14T23:52Z] INFO  16:52:03,220 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:52Z] INFO  16:52:03,220 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:52Z] INFO  16:52:03,221 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:52Z] INFO  16:52:03,439 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:52Z] GATK pre-alignment ('8', 63775819, 79510770) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-14T23:52Z] INFO  16:52:03,881 ProgressMeter -            done    208285.0    17.0 s      85.0 s      100.0%    17.0 s       0.0 s
[2016-04-14T23:52Z] INFO  16:52:03,883 ProgressMeter - Total runtime 17.75 secs, 0.30 min, 0.00 hours
[2016-04-14T23:52Z] INFO  16:52:03,887 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 208285 total reads (0.00%)
[2016-04-14T23:52Z] INFO  16:52:03,888 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:52Z] INFO  16:52:03,889 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:52Z] INFO  16:52:03,890 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:52Z] INFO  16:52:04,355 ProgressMeter -            done    164246.0    14.0 s      85.0 s      100.0%    14.0 s       0.0 s
[2016-04-14T23:52Z] INFO  16:52:04,356 ProgressMeter - Total runtime 14.11 secs, 0.24 min, 0.00 hours
[2016-04-14T23:52Z] INFO  16:52:04,360 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 164246 total reads (0.00%)
[2016-04-14T23:52Z] INFO  16:52:04,361 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:52Z] INFO  16:52:04,362 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:52Z] INFO  16:52:04,362 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:52Z] INFO  16:52:04,938 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:52Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-5_127597427_143191869-prep.bam
[2016-04-14T23:52Z] INFO  16:52:05,316 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:52Z] INFO  16:52:05,320 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:52Z] INFO  16:52:05,321 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:52Z] INFO  16:52:05,321 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:52Z] INFO  16:52:05,327 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/6/R14-18105_kapa-NGv3-PE100-NGv3-sort-6_31083801_46593245-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/6/R14-18105_kapa-NGv3-PE100-NGv3-sort-6_31083801_46593245-prep-prealign-realign.intervals -L 6:31083802-46593245 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/6/tx/tmpEO4eC4/R14-18105_kapa-NGv3-PE100-NGv3-sort-6_31083801_46593245-prep.bam
[2016-04-14T23:52Z] INFO  16:52:05,347 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:52Z] INFO  16:52:05,348 HelpFormatter - Date/Time: 2016/04/14 16:52:05
[2016-04-14T23:52Z] INFO  16:52:05,349 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:52Z] INFO  16:52:05,349 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:52Z] INFO  16:52:05,560 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:52Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-7_15599765_31117713-prep.bam
[2016-04-14T23:52Z] INFO  16:52:05,610 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:52Z] INFO  16:52:05,755 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:52Z] INFO  16:52:05,764 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:52Z] INFO  16:52:05,819 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-14T23:52Z] INFO  16:52:05,926 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:52Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-7_47319761_63093154-prep.bam
[2016-04-14T23:52Z] INFO  16:52:06,168 IntervalUtils - Processing 15509444 bp from intervals
[2016-04-14T23:52Z] WARN  16:52:06,183 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:52Z] GATK pre-alignment ('8', 79513976, 95140568) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-14T23:52Z] INFO  16:52:06,310 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:52Z] INFO  16:52:06,332 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:52Z] INFO  16:52:06,336 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:52Z] INFO  16:52:06,336 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:52Z] INFO  16:52:06,336 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:52Z] INFO  16:52:06,341 HelpFormatter - Program Args: -T PrintReads -L 8:63775820-79510770 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/8/tx/tmpK0qiVy/R14-18105_kapa-NGv3-PE100-NGv3-sort-8_63775819_79510770-prep-prealign.bam
[2016-04-14T23:52Z] INFO  16:52:06,365 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:52Z] INFO  16:52:06,366 HelpFormatter - Date/Time: 2016/04/14 16:52:06
[2016-04-14T23:52Z] INFO  16:52:06,366 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:52Z] INFO  16:52:06,366 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:52Z] INFO  16:52:06,504 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:52Z] INFO  16:52:06,505 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:52Z] INFO  16:52:06,506 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:52Z] INFO  16:52:06,507 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:52Z] INFO  16:52:06,545 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:52Z] GATK pre-alignment ('8', 95142853, 110655419) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-14T23:52Z] INFO  16:52:06,700 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:52Z] INFO  16:52:06,872 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:52Z] GATK pre-alignment ('8', 110656864, 126194498) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-14T23:52Z] INFO  16:52:07,765 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-14T23:52Z] INFO  16:52:07,895 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:52Z] INFO  16:52:07,914 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:52Z] INFO  16:52:07,972 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-14T23:52Z] INFO  16:52:07,987 IntervalUtils - Processing 15734951 bp from intervals
[2016-04-14T23:52Z] INFO  16:52:08,111 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:52Z] INFO  16:52:08,463 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:52Z] INFO  16:52:08,464 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:52Z] INFO  16:52:08,465 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:52Z] INFO  16:52:08,466 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:52Z] INFO  16:52:08,481 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:52Z] INFO  16:52:08,763 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:52Z] INFO  16:52:08,918 ProgressMeter -       8:8234430    100005.0    30.0 s       5.1 m       53.1%    56.0 s      26.0 s
[2016-04-14T23:52Z] INFO  16:52:09,605 ProgressMeter -            done    176801.0    14.0 s      83.0 s       98.7%    14.0 s       0.0 s
[2016-04-14T23:52Z] INFO  16:52:09,606 ProgressMeter - Total runtime 14.77 secs, 0.25 min, 0.00 hours
[2016-04-14T23:52Z] INFO  16:52:09,610 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 176801 total reads (0.00%)
[2016-04-14T23:52Z] INFO  16:52:09,611 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:52Z] INFO  16:52:09,612 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:52Z] INFO  16:52:09,613 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:52Z] INFO  16:52:09,674 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:52Z] INFO  16:52:09,678 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:52Z] INFO  16:52:09,678 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:52Z] INFO  16:52:09,679 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:52Z] INFO  16:52:09,684 HelpFormatter - Program Args: -T PrintReads -L 8:79513977-95140568 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/8/tx/tmpPNNiDQ/R14-18105_kapa-NGv3-PE100-NGv3-sort-8_79513976_95140568-prep-prealign.bam
[2016-04-14T23:52Z] INFO  16:52:09,699 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:52Z] INFO  16:52:09,700 HelpFormatter - Date/Time: 2016/04/14 16:52:09
[2016-04-14T23:52Z] INFO  16:52:09,701 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:52Z] INFO  16:52:09,702 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:52Z] INFO  16:52:09,829 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:52Z] INFO  16:52:09,832 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:52Z] INFO  16:52:09,832 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:52Z] INFO  16:52:09,832 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:52Z] INFO  16:52:09,836 HelpFormatter - Program Args: -T PrintReads -L 8:95142854-110655419 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/8/tx/tmpxUuJSZ/R14-18105_kapa-NGv3-PE100-NGv3-sort-8_95142853_110655419-prep-prealign.bam
[2016-04-14T23:52Z] INFO  16:52:09,855 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:52Z] INFO  16:52:09,856 HelpFormatter - Date/Time: 2016/04/14 16:52:09
[2016-04-14T23:52Z] INFO  16:52:09,856 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:52Z] INFO  16:52:09,856 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:52Z] INFO  16:52:09,943 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:52Z] INFO  16:52:10,017 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:52Z] INFO  16:52:10,255 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:52Z] INFO  16:52:10,258 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:52Z] INFO  16:52:10,259 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:52Z] INFO  16:52:10,260 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:52Z] INFO  16:52:10,264 HelpFormatter - Program Args: -T PrintReads -L 8:110656865-126194498 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/8/tx/tmpSYvJmx/R14-18105_kapa-NGv3-PE100-NGv3-sort-8_110656864_126194498-prep-prealign.bam
[2016-04-14T23:52Z] INFO  16:52:10,273 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:52Z] INFO  16:52:10,279 HelpFormatter - Date/Time: 2016/04/14 16:52:10
[2016-04-14T23:52Z] INFO  16:52:10,280 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:52Z] INFO  16:52:10,280 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:52Z] INFO  16:52:10,451 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:52Z] INFO  16:52:11,053 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-14T23:52Z] INFO  16:52:11,117 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:52Z] INFO  16:52:11,126 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:52Z] INFO  16:52:11,163 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:52Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-7_79082334_94740703-prep.bam
[2016-04-14T23:52Z] INFO  16:52:11,190 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-14T23:52Z] INFO  16:52:11,195 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-14T23:52Z] INFO  16:52:11,204 IntervalUtils - Processing 15512566 bp from intervals
[2016-04-14T23:52Z] INFO  16:52:11,265 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:52Z] INFO  16:52:11,274 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:52Z] INFO  16:52:11,287 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:52Z] INFO  16:52:11,311 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.04
[2016-04-14T23:52Z] INFO  16:52:11,326 IntervalUtils - Processing 15626592 bp from intervals
[2016-04-14T23:52Z] INFO  16:52:11,416 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:52Z] INFO  16:52:11,587 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-14T23:52Z] INFO  16:52:11,640 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:52Z] INFO  16:52:11,641 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:52Z] INFO  16:52:11,642 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:52Z] INFO  16:52:11,642 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:52Z] INFO  16:52:11,642 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:52Z] INFO  16:52:11,651 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:52Z] INFO  16:52:11,657 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:52Z] INFO  16:52:11,703 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-14T23:52Z] INFO  16:52:11,713 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:52Z] INFO  16:52:11,713 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:52Z] INFO  16:52:11,714 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:52Z] INFO  16:52:11,714 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:52Z] INFO  16:52:11,717 IntervalUtils - Processing 15537634 bp from intervals
[2016-04-14T23:52Z] INFO  16:52:11,742 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:52Z] INFO  16:52:11,799 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:52Z] INFO  16:52:11,808 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:52Z] GATK pre-alignment ('8', 126369460, 141889736) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-14T23:52Z] INFO  16:52:11,914 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:52Z] INFO  16:52:12,042 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:52Z] INFO  16:52:12,043 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:52Z] INFO  16:52:12,044 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:52Z] INFO  16:52:12,045 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:52Z] INFO  16:52:12,058 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:52Z] INFO  16:52:12,206 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:52Z] INFO  16:52:14,663 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:52Z] INFO  16:52:14,667 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:52Z] INFO  16:52:14,667 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:52Z] INFO  16:52:14,668 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:52Z] INFO  16:52:14,673 HelpFormatter - Program Args: -T PrintReads -L 8:126369461-141889736 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/8/tx/tmpVX3zoS/R14-18105_kapa-NGv3-PE100-NGv3-sort-8_126369460_141889736-prep-prealign.bam
[2016-04-14T23:52Z] INFO  16:52:14,686 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:52Z] INFO  16:52:14,686 HelpFormatter - Date/Time: 2016/04/14 16:52:14
[2016-04-14T23:52Z] INFO  16:52:14,687 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:52Z] INFO  16:52:14,687 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:52Z] INFO  16:52:14,897 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:52Z] INFO  16:52:14,959 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@41fd9d8e
[2016-04-14T23:52Z] INFO  16:52:15,185 ProgressMeter -            done    475121.0    55.0 s     117.0 s      100.0%    55.0 s       0.0 s
[2016-04-14T23:52Z] INFO  16:52:15,185 ProgressMeter - Total runtime 55.66 secs, 0.93 min, 0.02 hours
[2016-04-14T23:52Z] INFO  16:52:15,185 MicroScheduler - 230 reads were filtered out during the traversal out of approximately 475351 total reads (0.05%)
[2016-04-14T23:52Z] INFO  16:52:15,186 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:52Z] INFO  16:52:15,186 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:52Z] INFO  16:52:15,186 MicroScheduler -   -> 230 reads (0.05% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:52Z] INFO  16:52:15,379 ProgressMeter -      8:23059311    100001.0    30.0 s       5.0 m       48.6%    61.0 s      31.0 s
[2016-04-14T23:52Z] INFO  16:52:15,933 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-14T23:52Z] INFO  16:52:16,014 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:52Z] INFO  16:52:16,023 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:52Z] INFO  16:52:16,120 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.10
[2016-04-14T23:52Z] INFO  16:52:16,134 IntervalUtils - Processing 15520276 bp from intervals
[2016-04-14T23:52Z] INFO  16:52:16,214 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:52Z] INFO  16:52:16,472 ProgressMeter -            done   1.5540613E7    21.0 s       1.0 s      100.0%    21.0 s       0.0 s
[2016-04-14T23:52Z] INFO  16:52:16,473 ProgressMeter - Total runtime 21.17 secs, 0.35 min, 0.01 hours
[2016-04-14T23:52Z] INFO  16:52:16,477 MicroScheduler - 121249 reads were filtered out during the traversal out of approximately 399084 total reads (30.38%)
[2016-04-14T23:52Z] INFO  16:52:16,478 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:52Z] INFO  16:52:16,478 MicroScheduler -   -> 668 reads (0.17% of total) failing BadMateFilter
[2016-04-14T23:52Z] INFO  16:52:16,479 MicroScheduler -   -> 24377 reads (6.11% of total) failing DuplicateReadFilter
[2016-04-14T23:52Z] INFO  16:52:16,479 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-14T23:52Z] INFO  16:52:16,479 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:52Z] INFO  16:52:16,479 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-14T23:52Z] INFO  16:52:16,480 MicroScheduler -   -> 96204 reads (24.11% of total) failing MappingQualityZeroFilter
[2016-04-14T23:52Z] INFO  16:52:16,480 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:52Z] INFO  16:52:16,480 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-14T23:52Z] INFO  16:52:16,480 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-14T23:52Z] INFO  16:52:16,497 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:52Z] INFO  16:52:16,498 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:52Z] INFO  16:52:16,499 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:52Z] INFO  16:52:16,500 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:52Z] INFO  16:52:16,515 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:52Z] INFO  16:52:16,554 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:52Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-7_141629903_157151331-prep-prealign.bam
[2016-04-14T23:52Z] INFO  16:52:16,707 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:52Z] INFO  16:52:17,835 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:52Z] GATK: realign ('7', 63095909, 78636522) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-14T23:52Z] GATK RealignerTargetCreator: R14-18105_kapa-NGv3-PE100-NGv3-sort-7_141629903_157151331-prep-prealign.bam 7:141629904-157151331
[2016-04-14T23:52Z] GATK: RealignerTargetCreator
[2016-04-14T23:52Z] INFO  16:52:18,815 ProgressMeter -            done   1.5533496E7    21.0 s       1.0 s      100.0%    21.0 s       0.0 s
[2016-04-14T23:52Z] INFO  16:52:18,816 ProgressMeter - Total runtime 21.94 secs, 0.37 min, 0.01 hours
[2016-04-14T23:52Z] INFO  16:52:18,819 MicroScheduler - 29876 reads were filtered out during the traversal out of approximately 346469 total reads (8.62%)
[2016-04-14T23:52Z] INFO  16:52:18,820 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:52Z] INFO  16:52:18,820 MicroScheduler -   -> 800 reads (0.23% of total) failing BadMateFilter
[2016-04-14T23:52Z] INFO  16:52:18,820 MicroScheduler -   -> 27153 reads (7.84% of total) failing DuplicateReadFilter
[2016-04-14T23:52Z] INFO  16:52:18,820 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-14T23:52Z] INFO  16:52:18,821 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:52Z] INFO  16:52:18,821 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-14T23:52Z] INFO  16:52:18,821 MicroScheduler -   -> 1923 reads (0.56% of total) failing MappingQualityZeroFilter
[2016-04-14T23:52Z] INFO  16:52:18,821 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:52Z] INFO  16:52:18,822 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-14T23:52Z] INFO  16:52:18,822 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-14T23:52Z] INFO  16:52:19,036 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@7172f77a
[2016-04-14T23:52Z] INFO  16:52:19,148 ProgressMeter -            done    141838.0    18.0 s       2.2 m      100.0%    18.0 s       0.0 s
[2016-04-14T23:52Z] INFO  16:52:19,149 ProgressMeter - Total runtime 18.74 secs, 0.31 min, 0.01 hours
[2016-04-14T23:52Z] INFO  16:52:19,149 MicroScheduler - 116 reads were filtered out during the traversal out of approximately 141954 total reads (0.08%)
[2016-04-14T23:52Z] INFO  16:52:19,150 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:52Z] INFO  16:52:19,150 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:52Z] INFO  16:52:19,150 MicroScheduler -   -> 116 reads (0.08% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:52Z] INFO  16:52:19,439 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@32d5a4c6
[2016-04-14T23:52Z] INFO  16:52:19,570 ProgressMeter -            done    188813.0    28.0 s       2.5 m      100.0%    28.0 s       0.0 s
[2016-04-14T23:52Z] INFO  16:52:19,571 ProgressMeter - Total runtime 28.32 secs, 0.47 min, 0.01 hours
[2016-04-14T23:52Z] INFO  16:52:19,572 MicroScheduler - 207 reads were filtered out during the traversal out of approximately 189020 total reads (0.11%)
[2016-04-14T23:52Z] INFO  16:52:19,572 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:52Z] INFO  16:52:19,573 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:52Z] INFO  16:52:19,573 MicroScheduler -   -> 207 reads (0.11% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:52Z] INFO  16:52:20,231 ProgressMeter -            done    270277.0    19.0 s      72.0 s      100.0%    19.0 s       0.0 s
[2016-04-14T23:52Z] INFO  16:52:20,232 ProgressMeter - Total runtime 19.50 secs, 0.32 min, 0.01 hours
[2016-04-14T23:52Z] INFO  16:52:20,236 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 270277 total reads (0.00%)
[2016-04-14T23:52Z] INFO  16:52:20,236 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:52Z] INFO  16:52:20,236 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:52Z] INFO  16:52:20,237 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:52Z] INFO  16:52:20,427 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:52Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-8_48003022_63659688-prep-prealign.bam
[2016-04-14T23:52Z] WARN  16:52:20,747 StorageService - Encountered 1 Internal Server error(s), will retry in 50ms
[2016-04-14T23:52Z] WARN  16:52:20,798 RestStorageService - Error Response: PUT '/Ffuux4s4YRbs8PIaLVLnEMVtYWmeaDlh.report.xml.gz' -- ResponseCode: 500, ResponseStatus: Internal Server Error, Request Headers: [Content-Length: 430, Content-MD5: F7vMf9ncNB0bo8n/CaquEQ==, Content-Type: application/octet-stream, x-amz-meta-md5-hash: 17bbcc7fd9dc341d1ba3c9ff09aaae11, Date: Thu, 14 Apr 2016 23:52:19 GMT, Authorization: AWS AKIAI22FBBJ37D5X62OQ:1IDeufTjlGjqvzU2p2x1qHN4idI=, User-Agent: JetS3t/0.8.1 (Linux/2.6.32-504.1.3.el6.x86_64; amd64; en; JVM 1.7.0_91), Host: broad.gsa.gatk.run.reports.s3.amazonaws.com, Expect: 100-continue], Response Headers: [x-amz-request-id: 5062401A9112D455, x-amz-id-2: ovEvwrfEhVektWZvY/HYpWQKAbYwpvrEiFVR9vDVnHjCKfzhvlz0LLFU9k2hkMPv2VaynKr9mGw=, Content-Type: application/xml, Transfer-Encoding: chunked, Date: Thu, 14 Apr 2016 23:52:19 GMT, Connection: close, Server: AmazonS3]
[2016-04-14T23:52Z] INFO  16:52:20,820 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:52Z] INFO  16:52:20,824 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:52Z] INFO  16:52:20,824 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:52Z] INFO  16:52:20,825 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:52Z] INFO  16:52:20,830 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/7/R14-18105_kapa-NGv3-PE100-NGv3-sort-7_141629903_157151331-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/7/tx/tmpHzYz_6/R14-18105_kapa-NGv3-PE100-NGv3-sort-7_141629903_157151331-prep-prealign-realign.intervals -l INFO -L 7:141629904-157151331 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-14T23:52Z] INFO  16:52:20,846 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:52Z] INFO  16:52:20,847 HelpFormatter - Date/Time: 2016/04/14 16:52:20
[2016-04-14T23:52Z] INFO  16:52:20,847 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:52Z] INFO  16:52:20,847 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:52Z] INFO  16:52:20,939 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:52Z] INFO  16:52:20,946 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:52Z] INFO  16:52:20,946 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:52Z] INFO  16:52:20,947 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:52Z] INFO  16:52:20,952 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/7/R14-18105_kapa-NGv3-PE100-NGv3-sort-7_63095909_78636522-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/7/R14-18105_kapa-NGv3-PE100-NGv3-sort-7_63095909_78636522-prep-prealign-realign.intervals -L 7:63095910-78636522 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/7/tx/tmp6aVhz5/R14-18105_kapa-NGv3-PE100-NGv3-sort-7_63095909_78636522-prep.bam
[2016-04-14T23:52Z] INFO  16:52:20,960 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:52Z] INFO  16:52:20,975 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:52Z] INFO  16:52:20,988 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:52Z] INFO  16:52:20,989 HelpFormatter - Date/Time: 2016/04/14 16:52:20
[2016-04-14T23:52Z] INFO  16:52:20,990 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:52Z] INFO  16:52:20,991 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:52Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-8_31496910_48001429-prep-prealign.bam
[2016-04-14T23:52Z] GATK RealignerTargetCreator: R14-18105_kapa-NGv3-PE100-NGv3-sort-8_48003022_63659688-prep-prealign.bam 8:48003023-63659688
[2016-04-14T23:52Z] GATK: RealignerTargetCreator
[2016-04-14T23:52Z] INFO  16:52:21,150 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-14T23:52Z] WARN  16:52:21,157 RepeatableRequestEntity - Repeating transmission of 430 bytes
[2016-04-14T23:52Z] INFO  16:52:21,158 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:52Z] INFO  16:52:21,161 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:52Z] INFO  16:52:21,234 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-14T23:52Z] INFO  16:52:21,268 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:52Z] GATK: realign ('7', 126086124, 141619620) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-14T23:52Z] INFO  16:52:21,329 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:52Z] INFO  16:52:21,339 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:52Z] INFO  16:52:21,401 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-14T23:52Z] INFO  16:52:21,534 IntervalUtils - Processing 15521428 bp from intervals
[2016-04-14T23:52Z] WARN  16:52:21,540 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:52Z] INFO  16:52:21,620 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:52Z] INFO  16:52:21,639 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:52Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-7_31120227_47317818-prep.bam
[2016-04-14T23:52Z] INFO  16:52:21,746 IntervalUtils - Processing 15540613 bp from intervals
[2016-04-14T23:52Z] WARN  16:52:21,752 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:52Z] GATK RealignerTargetCreator: R14-18105_kapa-NGv3-PE100-NGv3-sort-8_31496910_48001429-prep-prealign.bam 8:31496911-48001429
[2016-04-14T23:52Z] GATK: RealignerTargetCreator
[2016-04-14T23:52Z] INFO  16:52:21,877 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:52Z] INFO  16:52:21,890 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:52Z] INFO  16:52:21,894 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:52Z] INFO  16:52:21,895 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:52Z] INFO  16:52:21,896 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-14T23:52Z] INFO  16:52:21,999 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:52Z] INFO  16:52:22,000 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:52Z] INFO  16:52:22,001 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:52Z] INFO  16:52:22,001 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:52Z] INFO  16:52:22,186 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:52Z] INFO  16:52:22,339 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:52Z] GATK pre-alignment ('8', 141900641, 146364022) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-14T23:52Z] INFO  16:52:23,591 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:52Z] INFO  16:52:23,594 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:52Z] INFO  16:52:23,595 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:52Z] INFO  16:52:23,596 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:52Z] INFO  16:52:23,600 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/8/R14-18105_kapa-NGv3-PE100-NGv3-sort-8_48003022_63659688-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/8/tx/tmpvhuvIk/R14-18105_kapa-NGv3-PE100-NGv3-sort-8_48003022_63659688-prep-prealign-realign.intervals -l INFO -L 8:48003023-63659688 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-14T23:52Z] INFO  16:52:23,630 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:52Z] INFO  16:52:23,631 HelpFormatter - Date/Time: 2016/04/14 16:52:23
[2016-04-14T23:52Z] INFO  16:52:23,631 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:52Z] INFO  16:52:23,632 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:52Z] INFO  16:52:23,743 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:52Z] INFO  16:52:23,944 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-14T23:52Z] INFO  16:52:23,954 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:52Z] INFO  16:52:24,023 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-14T23:52Z] INFO  16:52:24,363 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:52Z] INFO  16:52:24,369 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:52Z] INFO  16:52:24,369 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:52Z] INFO  16:52:24,370 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:52Z] INFO  16:52:24,374 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/7/R14-18105_kapa-NGv3-PE100-NGv3-sort-7_126086124_141619620-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/7/R14-18105_kapa-NGv3-PE100-NGv3-sort-7_126086124_141619620-prep-prealign-realign.intervals -L 7:126086125-141619620 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/7/tx/tmp5M6pwz/R14-18105_kapa-NGv3-PE100-NGv3-sort-7_126086124_141619620-prep.bam
[2016-04-14T23:52Z] INFO  16:52:24,394 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:52Z] INFO  16:52:24,395 HelpFormatter - Date/Time: 2016/04/14 16:52:24
[2016-04-14T23:52Z] INFO  16:52:24,395 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:52Z] INFO  16:52:24,395 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:52Z] INFO  16:52:24,428 IntervalUtils - Processing 15656666 bp from intervals
[2016-04-14T23:52Z] WARN  16:52:24,435 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:52Z] INFO  16:52:24,514 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:52Z] INFO  16:52:24,638 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:52Z] INFO  16:52:24,739 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:52Z] INFO  16:52:24,740 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:52Z] INFO  16:52:24,741 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:52Z] INFO  16:52:24,742 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-14T23:52Z] INFO  16:52:24,773 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:52Z] INFO  16:52:24,782 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:52Z] INFO  16:52:24,844 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:52Z] INFO  16:52:24,848 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:52Z] INFO  16:52:24,848 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:52Z] INFO  16:52:24,849 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:52Z] INFO  16:52:24,854 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/8/R14-18105_kapa-NGv3-PE100-NGv3-sort-8_31496910_48001429-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/8/tx/tmpidxiTa/R14-18105_kapa-NGv3-PE100-NGv3-sort-8_31496910_48001429-prep-prealign-realign.intervals -l INFO -L 8:31496911-48001429 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-14T23:52Z] INFO  16:52:24,858 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-14T23:52Z] INFO  16:52:24,862 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:52Z] INFO  16:52:24,863 HelpFormatter - Date/Time: 2016/04/14 16:52:24
[2016-04-14T23:52Z] INFO  16:52:24,863 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:52Z] INFO  16:52:24,863 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:52Z] INFO  16:52:24,982 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:52Z] INFO  16:52:25,196 IntervalUtils - Processing 15533496 bp from intervals
[2016-04-14T23:52Z] WARN  16:52:25,210 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:52Z] INFO  16:52:25,250 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-14T23:52Z] INFO  16:52:25,270 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:52Z] INFO  16:52:25,285 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:52Z] INFO  16:52:25,333 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-14T23:52Z] INFO  16:52:25,418 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:52Z] INFO  16:52:25,419 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:52Z] INFO  16:52:25,420 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:52Z] INFO  16:52:25,421 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:52Z] INFO  16:52:25,571 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:52Z] INFO  16:52:25,557 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:52Z] INFO  16:52:25,572 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:52Z] INFO  16:52:25,573 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:52Z] INFO  16:52:25,573 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:52Z] INFO  16:52:25,577 IntervalUtils - Processing 16504519 bp from intervals
[2016-04-14T23:52Z] INFO  16:52:25,577 HelpFormatter - Program Args: -T PrintReads -L 8:141900642-146364022 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/8/tx/tmpmGVNcz/R14-18105_kapa-NGv3-PE100-NGv3-sort-8_141900641_146364022-prep-prealign.bam
[2016-04-14T23:52Z] WARN  16:52:25,582 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:52Z] INFO  16:52:25,589 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:52Z] INFO  16:52:25,589 HelpFormatter - Date/Time: 2016/04/14 16:52:25
[2016-04-14T23:52Z] INFO  16:52:25,589 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:52Z] INFO  16:52:25,590 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:52Z] INFO  16:52:25,681 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:52Z] INFO  16:52:25,734 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:52Z] INFO  16:52:25,797 ProgressMeter -            done    335286.0    22.0 s      67.0 s      100.0%    22.0 s       0.0 s
[2016-04-14T23:52Z] INFO  16:52:25,798 ProgressMeter - Total runtime 22.77 secs, 0.38 min, 0.01 hours
[2016-04-14T23:52Z] INFO  16:52:25,801 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 335286 total reads (0.00%)
[2016-04-14T23:52Z] INFO  16:52:25,802 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:52Z] INFO  16:52:25,802 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:52Z] INFO  16:52:25,802 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:52Z] INFO  16:52:25,831 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:52Z] INFO  16:52:25,930 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:52Z] INFO  16:52:25,942 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:52Z] INFO  16:52:25,943 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:52Z] INFO  16:52:25,944 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-14T23:52Z] INFO  16:52:26,685 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@41fd9d8e
[2016-04-14T23:52Z] INFO  16:52:26,799 ProgressMeter -            done    102684.0    15.0 s       2.4 m      100.0%    15.0 s       0.0 s
[2016-04-14T23:52Z] INFO  16:52:26,800 ProgressMeter - Total runtime 15.09 secs, 0.25 min, 0.00 hours
[2016-04-14T23:52Z] INFO  16:52:26,801 MicroScheduler - 137 reads were filtered out during the traversal out of approximately 102821 total reads (0.13%)
[2016-04-14T23:52Z] INFO  16:52:26,802 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:52Z] INFO  16:52:26,803 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:52Z] INFO  16:52:26,803 MicroScheduler -   -> 137 reads (0.13% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:52Z] INFO  16:52:27,124 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-14T23:52Z] INFO  16:52:27,210 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:52Z] INFO  16:52:27,219 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:52Z] INFO  16:52:27,261 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.04
[2016-04-14T23:52Z] INFO  16:52:27,286 IntervalUtils - Processing 4463381 bp from intervals
[2016-04-14T23:52Z] INFO  16:52:27,367 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:52Z] INFO  16:52:27,427 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:52Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-7_0_15584548-prep.bam
[2016-04-14T23:52Z] INFO  16:52:27,596 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:52Z] INFO  16:52:27,597 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:52Z] INFO  16:52:27,597 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:52Z] INFO  16:52:27,597 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:52Z] INFO  16:52:27,621 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:52Z] INFO  16:52:27,725 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:52Z] INFO  16:52:28,452 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:52Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-8_79513976_95140568-prep-prealign.bam
[2016-04-14T23:52Z] GATK pre-alignment ('9', 0, 15510186) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-14T23:52Z] INFO  16:52:28,641 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@41fd9d8e
[2016-04-14T23:52Z] INFO  16:52:28,788 ProgressMeter -            done    149798.0    20.0 s       2.3 m      100.0%    20.0 s       0.0 s
[2016-04-14T23:52Z] INFO  16:52:28,788 ProgressMeter - Total runtime 20.32 secs, 0.34 min, 0.01 hours
[2016-04-14T23:52Z] INFO  16:52:28,789 MicroScheduler - 120 reads were filtered out during the traversal out of approximately 149918 total reads (0.08%)
[2016-04-14T23:52Z] INFO  16:52:28,789 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:52Z] INFO  16:52:28,789 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:52Z] INFO  16:52:28,790 MicroScheduler -   -> 120 reads (0.08% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:52Z] GATK RealignerTargetCreator: R14-18105_kapa-NGv3-PE100-NGv3-sort-8_79513976_95140568-prep-prealign.bam 8:79513977-95140568
[2016-04-14T23:52Z] GATK: RealignerTargetCreator
[2016-04-14T23:52Z] INFO  16:52:29,302 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@7172f77a
[2016-04-14T23:52Z] INFO  16:52:29,383 ProgressMeter -            done    324027.0    51.0 s       2.6 m      100.0%    51.0 s       0.0 s
[2016-04-14T23:52Z] INFO  16:52:29,384 ProgressMeter - Total runtime 51.34 secs, 0.86 min, 0.01 hours
[2016-04-14T23:52Z] INFO  16:52:29,385 MicroScheduler - 269 reads were filtered out during the traversal out of approximately 324296 total reads (0.08%)
[2016-04-14T23:52Z] INFO  16:52:29,386 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:52Z] INFO  16:52:29,386 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:52Z] INFO  16:52:29,387 MicroScheduler -   -> 269 reads (0.08% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:52Z] INFO  16:52:30,048 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@7172f77a
[2016-04-14T23:52Z] INFO  16:52:30,236 ProgressMeter -            done    730638.0    87.0 s     120.0 s      100.0%    87.0 s       0.0 s
[2016-04-14T23:52Z] INFO  16:52:30,236 ProgressMeter - Total runtime 87.83 secs, 1.46 min, 0.02 hours
[2016-04-14T23:52Z] INFO  16:52:30,237 MicroScheduler - 424 reads were filtered out during the traversal out of approximately 731062 total reads (0.06%)
[2016-04-14T23:52Z] INFO  16:52:30,237 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:52Z] INFO  16:52:30,238 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:52Z] INFO  16:52:30,246 MicroScheduler -   -> 424 reads (0.06% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:52Z] INFO  16:52:30,373 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:52Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-8_63775819_79510770-prep-prealign.bam
[2016-04-14T23:52Z] INFO  16:52:30,910 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:52Z] GATK RealignerTargetCreator: R14-18105_kapa-NGv3-PE100-NGv3-sort-8_63775819_79510770-prep-prealign.bam 8:63775820-79510770
[2016-04-14T23:52Z] GATK: RealignerTargetCreator
[2016-04-14T23:52Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-8_0_15517156-prep-prealign.bam
[2016-04-14T23:52Z] INFO  16:52:31,264 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:52Z] INFO  16:52:31,267 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:52Z] INFO  16:52:31,268 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:52Z] INFO  16:52:31,268 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:52Z] INFO  16:52:31,273 HelpFormatter - Program Args: -T PrintReads -L 9:1-15510186 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/9/tx/tmpMQ8imU/R14-18105_kapa-NGv3-PE100-NGv3-sort-9_0_15510186-prep-prealign.bam
[2016-04-14T23:52Z] INFO  16:52:31,286 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:52Z] INFO  16:52:31,286 HelpFormatter - Date/Time: 2016/04/14 16:52:31
[2016-04-14T23:52Z] INFO  16:52:31,286 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:52Z] INFO  16:52:31,286 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:52Z] INFO  16:52:31,434 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:52Z] INFO  16:52:31,673 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:52Z] INFO  16:52:31,749 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:52Z] INFO  16:52:31,752 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:52Z] INFO  16:52:31,753 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:52Z] INFO  16:52:31,753 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:52Z] INFO  16:52:31,758 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@7172f77a
[2016-04-14T23:52Z] INFO  16:52:31,758 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/8/R14-18105_kapa-NGv3-PE100-NGv3-sort-8_79513976_95140568-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/8/tx/tmpodb2QD/R14-18105_kapa-NGv3-PE100-NGv3-sort-8_79513976_95140568-prep-prealign-realign.intervals -l INFO -L 8:79513977-95140568 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-14T23:52Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-7_94750023_110303777-prep-prealign.bam
[2016-04-14T23:52Z] INFO  16:52:31,772 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:52Z] INFO  16:52:31,787 HelpFormatter - Date/Time: 2016/04/14 16:52:31
[2016-04-14T23:52Z] INFO  16:52:31,788 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:52Z] INFO  16:52:31,789 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:52Z] INFO  16:52:31,905 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:52Z] INFO  16:52:31,914 ProgressMeter -            done    142745.0    19.0 s       2.3 m      100.0%    19.0 s       0.0 s
[2016-04-14T23:52Z] INFO  16:52:31,915 ProgressMeter - Total runtime 19.87 secs, 0.33 min, 0.01 hours
[2016-04-14T23:52Z] INFO  16:52:31,915 MicroScheduler - 130 reads were filtered out during the traversal out of approximately 142875 total reads (0.09%)
[2016-04-14T23:52Z] INFO  16:52:31,916 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:52Z] INFO  16:52:31,916 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:52Z] INFO  16:52:31,916 MicroScheduler -   -> 130 reads (0.09% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:52Z] GATK RealignerTargetCreator: R14-18105_kapa-NGv3-PE100-NGv3-sort-8_0_15517156-prep-prealign.bam 8:1-15517156
[2016-04-14T23:52Z] GATK: RealignerTargetCreator
[2016-04-14T23:52Z] INFO  16:52:32,068 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-14T23:52Z] INFO  16:52:32,078 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:52Z] INFO  16:52:32,131 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-14T23:52Z] INFO  16:52:32,379 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-14T23:52Z] INFO  16:52:32,438 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:52Z] INFO  16:52:32,447 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:52Z] INFO  16:52:32,490 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.04
[2016-04-14T23:52Z] INFO  16:52:32,505 IntervalUtils - Processing 15510186 bp from intervals
[2016-04-14T23:52Z] INFO  16:52:32,506 IntervalUtils - Processing 15626592 bp from intervals
[2016-04-14T23:52Z] WARN  16:52:32,512 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:52Z] INFO  16:52:32,572 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:52Z] INFO  16:52:32,653 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:52Z] INFO  16:52:32,858 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:52Z] INFO  16:52:32,860 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:52Z] INFO  16:52:32,861 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:52Z] INFO  16:52:32,862 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:52Z] INFO  16:52:32,877 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:52Z] INFO  16:52:32,921 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:52Z] INFO  16:52:32,933 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:52Z] INFO  16:52:32,934 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:52Z] INFO  16:52:32,934 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-14T23:52Z] INFO  16:52:33,077 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:52Z] INFO  16:52:33,292 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:52Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-8_110656864_126194498-prep-prealign.bam
[2016-04-14T23:52Z] INFO  16:52:33,744 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:52Z] INFO  16:52:33,748 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:52Z] INFO  16:52:33,749 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:52Z] INFO  16:52:33,749 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:52Z] INFO  16:52:33,755 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/8/R14-18105_kapa-NGv3-PE100-NGv3-sort-8_63775819_79510770-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/8/tx/tmpNddRBK/R14-18105_kapa-NGv3-PE100-NGv3-sort-8_63775819_79510770-prep-prealign-realign.intervals -l INFO -L 8:63775820-79510770 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-14T23:52Z] GATK RealignerTargetCreator: R14-18105_kapa-NGv3-PE100-NGv3-sort-8_110656864_126194498-prep-prealign.bam 8:110656865-126194498
[2016-04-14T23:52Z] GATK: RealignerTargetCreator
[2016-04-14T23:52Z] INFO  16:52:33,792 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:52Z] INFO  16:52:33,793 HelpFormatter - Date/Time: 2016/04/14 16:52:33
[2016-04-14T23:52Z] INFO  16:52:33,793 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:52Z] INFO  16:52:33,793 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:52Z] INFO  16:52:33,939 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:52Z] GATK RealignerTargetCreator: R14-18105_kapa-NGv3-PE100-NGv3-sort-7_94750023_110303777-prep-prealign.bam 7:94750024-110303777
[2016-04-14T23:52Z] GATK: RealignerTargetCreator
[2016-04-14T23:52Z] INFO  16:52:34,252 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-14T23:52Z] INFO  16:52:34,264 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:52Z] INFO  16:52:34,337 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-14T23:52Z] INFO  16:52:34,738 IntervalUtils - Processing 15734951 bp from intervals
[2016-04-14T23:52Z] WARN  16:52:34,743 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:52Z] INFO  16:52:34,837 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:52Z] INFO  16:52:35,061 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:52Z] INFO  16:52:35,062 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:52Z] INFO  16:52:35,063 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:52Z] INFO  16:52:35,064 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-14T23:52Z] INFO  16:52:35,160 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:52Z] INFO  16:52:35,164 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:52Z] INFO  16:52:35,165 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:52Z] INFO  16:52:35,165 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:52Z] INFO  16:52:35,171 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/8/R14-18105_kapa-NGv3-PE100-NGv3-sort-8_0_15517156-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/8/tx/tmpitL591/R14-18105_kapa-NGv3-PE100-NGv3-sort-8_0_15517156-prep-prealign-realign.intervals -l INFO -L 8:1-15517156 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-14T23:52Z] INFO  16:52:35,203 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:52Z] INFO  16:52:35,214 HelpFormatter - Date/Time: 2016/04/14 16:52:35
[2016-04-14T23:52Z] INFO  16:52:35,215 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:52Z] INFO  16:52:35,216 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:52Z] INFO  16:52:35,344 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:52Z] INFO  16:52:35,626 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-14T23:52Z] INFO  16:52:35,646 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:52Z] INFO  16:52:35,773 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.13
[2016-04-14T23:52Z] INFO  16:52:36,018 IntervalUtils - Processing 15517156 bp from intervals
[2016-04-14T23:52Z] WARN  16:52:36,023 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:52Z] INFO  16:52:36,111 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:52Z] INFO  16:52:36,314 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:52Z] INFO  16:52:36,315 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:52Z] INFO  16:52:36,316 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:52Z] INFO  16:52:36,316 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-14T23:52Z] INFO  16:52:36,416 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@5fe152b7
[2016-04-14T23:52Z] INFO  16:52:36,524 ProgressMeter -      6:34508841    300006.0    30.0 s     100.0 s       22.1%     2.3 m     105.0 s
[2016-04-14T23:52Z] INFO  16:52:36,609 ProgressMeter -            done    124927.0    20.0 s       2.7 m      100.0%    20.0 s       0.0 s
[2016-04-14T23:52Z] INFO  16:52:36,610 ProgressMeter - Total runtime 20.11 secs, 0.34 min, 0.01 hours
[2016-04-14T23:52Z] INFO  16:52:36,610 MicroScheduler - 129 reads were filtered out during the traversal out of approximately 125056 total reads (0.10%)
[2016-04-14T23:52Z] INFO  16:52:36,611 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:52Z] INFO  16:52:36,611 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:52Z] INFO  16:52:36,611 MicroScheduler -   -> 129 reads (0.10% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:52Z] INFO  16:52:36,853 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:52Z] INFO  16:52:36,856 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:52Z] INFO  16:52:36,856 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:52Z] INFO  16:52:36,856 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:52Z] INFO  16:52:36,860 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/8/R14-18105_kapa-NGv3-PE100-NGv3-sort-8_110656864_126194498-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/8/tx/tmpkvRUli/R14-18105_kapa-NGv3-PE100-NGv3-sort-8_110656864_126194498-prep-prealign-realign.intervals -l INFO -L 8:110656865-126194498 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-14T23:52Z] INFO  16:52:36,872 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:52Z] INFO  16:52:36,872 HelpFormatter - Date/Time: 2016/04/14 16:52:36
[2016-04-14T23:52Z] INFO  16:52:36,872 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:52Z] INFO  16:52:36,872 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:52Z] INFO  16:52:37,041 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:52Z] INFO  16:52:37,289 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-14T23:52Z] INFO  16:52:37,299 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:52Z] INFO  16:52:37,341 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.04
[2016-04-14T23:52Z] INFO  16:52:37,401 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:52Z] INFO  16:52:37,404 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:52Z] INFO  16:52:37,404 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:52Z] INFO  16:52:37,404 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:52Z] INFO  16:52:37,411 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/7/R14-18105_kapa-NGv3-PE100-NGv3-sort-7_94750023_110303777-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/7/tx/tmp0DQRU3/R14-18105_kapa-NGv3-PE100-NGv3-sort-7_94750023_110303777-prep-prealign-realign.intervals -l INFO -L 7:94750024-110303777 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-14T23:52Z] INFO  16:52:37,425 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:52Z] INFO  16:52:37,426 HelpFormatter - Date/Time: 2016/04/14 16:52:37
[2016-04-14T23:52Z] INFO  16:52:37,426 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:52Z] INFO  16:52:37,438 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:52Z] INFO  16:52:37,573 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:52Z] INFO  16:52:37,736 IntervalUtils - Processing 15537634 bp from intervals
[2016-04-14T23:52Z] WARN  16:52:37,752 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:52Z] INFO  16:52:37,864 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-14T23:52Z] INFO  16:52:37,874 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:52Z] INFO  16:52:37,897 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:52Z] INFO  16:52:37,933 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-14T23:52Z] INFO  16:52:38,125 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:52Z] INFO  16:52:38,126 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:52Z] INFO  16:52:38,127 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:52Z] INFO  16:52:38,127 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-14T23:52Z] INFO  16:52:38,180 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:52Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-8_126369460_141889736-prep-prealign.bam
[2016-04-14T23:52Z] INFO  16:52:38,279 IntervalUtils - Processing 15553754 bp from intervals
[2016-04-14T23:52Z] WARN  16:52:38,285 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:52Z] INFO  16:52:38,451 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:52Z] GATK RealignerTargetCreator: R14-18105_kapa-NGv3-PE100-NGv3-sort-8_126369460_141889736-prep-prealign.bam 8:126369461-141889736
[2016-04-14T23:52Z] GATK: RealignerTargetCreator
[2016-04-14T23:52Z] INFO  16:52:38,708 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:52Z] INFO  16:52:38,720 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:52Z] INFO  16:52:38,721 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:52Z] INFO  16:52:38,722 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-14T23:52Z] INFO  16:52:39,709 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@7172f77a
[2016-04-14T23:52Z] INFO  16:52:39,817 ProgressMeter -            done    354408.0    54.0 s       2.6 m      100.0%    54.0 s       0.0 s
[2016-04-14T23:52Z] INFO  16:52:39,817 ProgressMeter - Total runtime 54.45 secs, 0.91 min, 0.02 hours
[2016-04-14T23:52Z] INFO  16:52:39,818 MicroScheduler - 177 reads were filtered out during the traversal out of approximately 354585 total reads (0.05%)
[2016-04-14T23:52Z] INFO  16:52:39,818 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:52Z] INFO  16:52:39,818 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:52Z] INFO  16:52:39,819 MicroScheduler -   -> 177 reads (0.05% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:52Z] INFO  16:52:40,079 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@41fd9d8e
[2016-04-14T23:52Z] INFO  16:52:40,217 ProgressMeter -            done    207488.0    28.0 s       2.3 m      100.0%    28.0 s       0.0 s
[2016-04-14T23:52Z] INFO  16:52:40,217 ProgressMeter - Total runtime 28.58 secs, 0.48 min, 0.01 hours
[2016-04-14T23:52Z] INFO  16:52:40,218 MicroScheduler - 134 reads were filtered out during the traversal out of approximately 207622 total reads (0.06%)
[2016-04-14T23:52Z] INFO  16:52:40,218 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:52Z] INFO  16:52:40,218 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:52Z] INFO  16:52:40,218 MicroScheduler -   -> 134 reads (0.06% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:52Z] INFO  16:52:41,389 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:52Z] INFO  16:52:41,393 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:52Z] INFO  16:52:41,393 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:52Z] INFO  16:52:41,394 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:52Z] INFO  16:52:41,398 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/8/R14-18105_kapa-NGv3-PE100-NGv3-sort-8_126369460_141889736-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/8/tx/tmp_gQyBN/R14-18105_kapa-NGv3-PE100-NGv3-sort-8_126369460_141889736-prep-prealign-realign.intervals -l INFO -L 8:126369461-141889736 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-14T23:52Z] INFO  16:52:41,413 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:52Z] INFO  16:52:41,416 HelpFormatter - Date/Time: 2016/04/14 16:52:41
[2016-04-14T23:52Z] INFO  16:52:41,418 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:52Z] INFO  16:52:41,418 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:52Z] INFO  16:52:41,425 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:52Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-8_15519664_31030618-prep-prealign.bam
[2016-04-14T23:52Z] INFO  16:52:41,516 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:52Z] INFO  16:52:41,671 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:52Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-8_95142853_110655419-prep-prealign.bam
[2016-04-14T23:52Z] INFO  16:52:41,760 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-14T23:52Z] INFO  16:52:41,779 ProgressMeter -            done   1.5656666E7    17.0 s       1.0 s      100.0%    17.0 s       0.0 s
[2016-04-14T23:52Z] INFO  16:52:41,780 ProgressMeter - Total runtime 17.04 secs, 0.28 min, 0.00 hours
[2016-04-14T23:52Z] INFO  16:52:41,784 MicroScheduler - 12477 reads were filtered out during the traversal out of approximately 142272 total reads (8.77%)
[2016-04-14T23:52Z] INFO  16:52:41,782 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:52Z] INFO  16:52:41,785 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:52Z] INFO  16:52:41,786 MicroScheduler -   -> 506 reads (0.36% of total) failing BadMateFilter
[2016-04-14T23:52Z] INFO  16:52:41,786 MicroScheduler -   -> 11114 reads (7.81% of total) failing DuplicateReadFilter
[2016-04-14T23:52Z] INFO  16:52:41,786 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-14T23:52Z] INFO  16:52:41,786 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:52Z] INFO  16:52:41,787 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-14T23:52Z] INFO  16:52:41,787 MicroScheduler -   -> 857 reads (0.60% of total) failing MappingQualityZeroFilter
[2016-04-14T23:52Z] INFO  16:52:41,787 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:52Z] INFO  16:52:41,787 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-14T23:52Z] INFO  16:52:41,788 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-14T23:52Z] INFO  16:52:41,856 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-14T23:52Z] INFO  16:52:42,114 IntervalUtils - Processing 15520276 bp from intervals
[2016-04-14T23:52Z] WARN  16:52:42,126 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:52Z] INFO  16:52:42,252 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:52Z] GATK RealignerTargetCreator: R14-18105_kapa-NGv3-PE100-NGv3-sort-8_95142853_110655419-prep-prealign.bam 8:95142854-110655419
[2016-04-14T23:52Z] GATK: RealignerTargetCreator
[2016-04-14T23:52Z] INFO  16:52:42,501 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:52Z] GATK RealignerTargetCreator: R14-18105_kapa-NGv3-PE100-NGv3-sort-8_15519664_31030618-prep-prealign.bam 8:15519665-31030618
[2016-04-14T23:52Z] INFO  16:52:42,502 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:52Z] INFO  16:52:42,503 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:52Z] GATK: RealignerTargetCreator
[2016-04-14T23:52Z] INFO  16:52:42,504 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-14T23:52Z] INFO  16:52:43,336 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:52Z] GATK: realign ('8', 48003022, 63659688) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-14T23:52Z] INFO  16:52:44,032 ProgressMeter -            done   1.6504519E7    18.0 s       1.0 s      100.0%    18.0 s       0.0 s
[2016-04-14T23:52Z] INFO  16:52:44,033 ProgressMeter - Total runtime 18.09 secs, 0.30 min, 0.01 hours
[2016-04-14T23:52Z] INFO  16:52:44,037 MicroScheduler - 16670 reads were filtered out during the traversal out of approximately 190340 total reads (8.76%)
[2016-04-14T23:52Z] INFO  16:52:44,038 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:52Z] INFO  16:52:44,038 MicroScheduler -   -> 560 reads (0.29% of total) failing BadMateFilter
[2016-04-14T23:52Z] INFO  16:52:44,039 MicroScheduler -   -> 15189 reads (7.98% of total) failing DuplicateReadFilter
[2016-04-14T23:52Z] INFO  16:52:44,039 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-14T23:52Z] INFO  16:52:44,040 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:52Z] INFO  16:52:44,041 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-14T23:52Z] INFO  16:52:44,041 MicroScheduler -   -> 921 reads (0.48% of total) failing MappingQualityZeroFilter
[2016-04-14T23:52Z] INFO  16:52:44,042 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:52Z] INFO  16:52:44,042 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-14T23:52Z] INFO  16:52:44,043 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-14T23:52Z] INFO  16:52:45,294 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:52Z] GATK: realign ('8', 31496910, 48001429) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-14T23:52Z] INFO  16:52:45,373 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:52Z] INFO  16:52:45,376 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:52Z] INFO  16:52:45,377 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:52Z] INFO  16:52:45,377 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:52Z] INFO  16:52:45,382 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/8/R14-18105_kapa-NGv3-PE100-NGv3-sort-8_95142853_110655419-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/8/tx/tmp8TAD0B/R14-18105_kapa-NGv3-PE100-NGv3-sort-8_95142853_110655419-prep-prealign-realign.intervals -l INFO -L 8:95142854-110655419 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-14T23:52Z] INFO  16:52:45,398 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:52Z] INFO  16:52:45,398 HelpFormatter - Date/Time: 2016/04/14 16:52:45
[2016-04-14T23:52Z] INFO  16:52:45,399 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:52Z] INFO  16:52:45,399 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:52Z] INFO  16:52:45,510 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:52Z] INFO  16:52:45,530 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:52Z] INFO  16:52:45,533 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:52Z] INFO  16:52:45,534 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:52Z] INFO  16:52:45,534 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:52Z] INFO  16:52:45,539 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/8/R14-18105_kapa-NGv3-PE100-NGv3-sort-8_15519664_31030618-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/8/tx/tmpzupgTx/R14-18105_kapa-NGv3-PE100-NGv3-sort-8_15519664_31030618-prep-prealign-realign.intervals -l INFO -L 8:15519665-31030618 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-14T23:52Z] INFO  16:52:45,564 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:52Z] INFO  16:52:45,565 HelpFormatter - Date/Time: 2016/04/14 16:52:45
[2016-04-14T23:52Z] INFO  16:52:45,566 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:52Z] INFO  16:52:45,566 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:52Z] INFO  16:52:45,675 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:52Z] INFO  16:52:45,748 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-14T23:52Z] INFO  16:52:45,770 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:52Z] INFO  16:52:45,848 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-14T23:52Z] INFO  16:52:45,928 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-14T23:52Z] INFO  16:52:45,939 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:52Z] INFO  16:52:46,025 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-14T23:52Z] INFO  16:52:46,201 IntervalUtils - Processing 15512566 bp from intervals
[2016-04-14T23:52Z] WARN  16:52:46,207 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:52Z] INFO  16:52:46,326 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:52Z] INFO  16:52:46,316 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:52Z] INFO  16:52:46,330 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:52Z] INFO  16:52:46,331 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:52Z] INFO  16:52:46,331 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:52Z] INFO  16:52:46,336 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/8/R14-18105_kapa-NGv3-PE100-NGv3-sort-8_48003022_63659688-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/8/R14-18105_kapa-NGv3-PE100-NGv3-sort-8_48003022_63659688-prep-prealign-realign.intervals -L 8:48003023-63659688 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/8/tx/tmpksbuh8/R14-18105_kapa-NGv3-PE100-NGv3-sort-8_48003022_63659688-prep.bam
[2016-04-14T23:52Z] INFO  16:52:46,367 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:52Z] INFO  16:52:46,368 HelpFormatter - Date/Time: 2016/04/14 16:52:46
[2016-04-14T23:52Z] INFO  16:52:46,368 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:52Z] INFO  16:52:46,368 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:52Z] INFO  16:52:46,426 IntervalUtils - Processing 15510954 bp from intervals
[2016-04-14T23:52Z] WARN  16:52:46,432 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:52Z] INFO  16:52:46,564 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:52Z] INFO  16:52:46,567 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:52Z] INFO  16:52:46,567 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:52Z] INFO  16:52:46,585 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:52Z] INFO  16:52:46,585 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-14T23:52Z] INFO  16:52:46,706 ProgressMeter -            done   1.5521428E7    24.0 s       1.0 s      100.0%    24.0 s       0.0 s
[2016-04-14T23:52Z] INFO  16:52:46,706 ProgressMeter - Total runtime 24.81 secs, 0.41 min, 0.01 hours
[2016-04-14T23:52Z] INFO  16:52:46,724 MicroScheduler - 108919 reads were filtered out during the traversal out of approximately 479627 total reads (22.71%)
[2016-04-14T23:52Z] INFO  16:52:46,724 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:52Z] INFO  16:52:46,724 MicroScheduler -   -> 876 reads (0.18% of total) failing BadMateFilter
[2016-04-14T23:52Z] INFO  16:52:46,725 MicroScheduler -   -> 32011 reads (6.67% of total) failing DuplicateReadFilter
[2016-04-14T23:52Z] INFO  16:52:46,725 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-14T23:52Z] INFO  16:52:46,725 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:52Z] INFO  16:52:46,726 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-14T23:52Z] INFO  16:52:46,726 MicroScheduler -   -> 76032 reads (15.85% of total) failing MappingQualityZeroFilter
[2016-04-14T23:52Z] INFO  16:52:46,726 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:52Z] INFO  16:52:46,727 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-14T23:52Z] INFO  16:52:46,727 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-14T23:52Z] INFO  16:52:46,750 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:52Z] INFO  16:52:46,886 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:52Z] INFO  16:52:46,887 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:52Z] INFO  16:52:46,888 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:52Z] INFO  16:52:46,888 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-14T23:52Z] INFO  16:52:46,912 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:52Z] INFO  16:52:46,922 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:52Z] INFO  16:52:46,975 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-14T23:52Z] INFO  16:52:47,475 IntervalUtils - Processing 15656666 bp from intervals
[2016-04-14T23:52Z] WARN  16:52:47,480 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:52Z] INFO  16:52:47,652 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:52Z] INFO  16:52:47,854 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:52Z] INFO  16:52:47,855 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:52Z] INFO  16:52:47,856 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:52Z] INFO  16:52:47,857 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:52Z] INFO  16:52:48,068 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:52Z] INFO  16:52:48,169 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:52Z] INFO  16:52:48,172 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:52Z] INFO  16:52:48,172 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:52Z] INFO  16:52:48,172 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:52Z] INFO  16:52:48,176 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/8/R14-18105_kapa-NGv3-PE100-NGv3-sort-8_31496910_48001429-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/8/R14-18105_kapa-NGv3-PE100-NGv3-sort-8_31496910_48001429-prep-prealign-realign.intervals -L 8:31496911-48001429 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/8/tx/tmpBXa53I/R14-18105_kapa-NGv3-PE100-NGv3-sort-8_31496910_48001429-prep.bam
[2016-04-14T23:52Z] INFO  16:52:48,180 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:52Z] INFO  16:52:48,200 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:52Z] INFO  16:52:48,205 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:52Z] INFO  16:52:48,206 HelpFormatter - Date/Time: 2016/04/14 16:52:48
[2016-04-14T23:52Z] INFO  16:52:48,206 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:52Z] INFO  16:52:48,206 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:52Z] GATK: realign ('7', 141629903, 157151331) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-14T23:52Z] INFO  16:52:48,305 ProgressMeter -            done    344751.0    22.0 s      66.0 s      100.0%    22.0 s       0.0 s
[2016-04-14T23:52Z] INFO  16:52:48,306 ProgressMeter - Total runtime 22.89 secs, 0.38 min, 0.01 hours
[2016-04-14T23:52Z] INFO  16:52:48,310 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 344751 total reads (0.00%)
[2016-04-14T23:52Z] INFO  16:52:48,311 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:52Z] INFO  16:52:48,311 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:52Z] INFO  16:52:48,312 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:52Z] INFO  16:52:48,414 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:52Z] INFO  16:52:48,584 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:52Z] INFO  16:52:48,594 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:52Z] INFO  16:52:48,659 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-14T23:52Z] INFO  16:52:49,038 IntervalUtils - Processing 16504519 bp from intervals
[2016-04-14T23:52Z] WARN  16:52:49,053 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:52Z] INFO  16:52:49,140 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:52Z] INFO  16:52:49,247 ProgressMeter -            done    396794.0    27.0 s      68.0 s      100.0%    27.0 s       0.0 s
[2016-04-14T23:52Z] INFO  16:52:49,247 ProgressMeter - Total runtime 27.25 secs, 0.45 min, 0.01 hours
[2016-04-14T23:52Z] INFO  16:52:49,250 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 396794 total reads (0.00%)
[2016-04-14T23:52Z] INFO  16:52:49,251 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:52Z] INFO  16:52:49,251 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:52Z] INFO  16:52:49,251 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:52Z] INFO  16:52:49,261 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:52Z] INFO  16:52:49,262 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:52Z] INFO  16:52:49,263 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:52Z] INFO  16:52:49,264 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:52Z] INFO  16:52:49,427 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:52Z] INFO  16:52:49,612 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:52Z] INFO  16:52:49,749 ProgressMeter -            done   1.5626592E7    16.0 s       1.0 s      100.0%    16.0 s       0.0 s
[2016-04-14T23:52Z] INFO  16:52:49,750 ProgressMeter - Total runtime 16.82 secs, 0.28 min, 0.00 hours
[2016-04-14T23:52Z] INFO  16:52:49,753 MicroScheduler - 8933 reads were filtered out during the traversal out of approximately 103323 total reads (8.65%)
[2016-04-14T23:52Z] INFO  16:52:49,754 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:52Z] INFO  16:52:49,754 MicroScheduler -   -> 433 reads (0.42% of total) failing BadMateFilter
[2016-04-14T23:52Z] INFO  16:52:49,754 MicroScheduler -   -> 7856 reads (7.60% of total) failing DuplicateReadFilter
[2016-04-14T23:52Z] INFO  16:52:49,755 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-14T23:52Z] INFO  16:52:49,755 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:52Z] INFO  16:52:49,755 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-14T23:52Z] INFO  16:52:49,755 MicroScheduler -   -> 644 reads (0.62% of total) failing MappingQualityZeroFilter
[2016-04-14T23:52Z] INFO  16:52:49,756 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:52Z] INFO  16:52:49,756 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-14T23:52Z] INFO  16:52:49,756 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-14T23:52Z] INFO  16:52:49,802 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:52Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-7_126086124_141619620-prep.bam
[2016-04-14T23:52Z] GATK pre-alignment ('9', 15564086, 32405601) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-14T23:52Z] INFO  16:52:50,840 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:52Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-7_63095909_78636522-prep.bam
[2016-04-14T23:52Z] INFO  16:52:50,952 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:52Z] INFO  16:52:50,956 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:52Z] INFO  16:52:50,956 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:52Z] INFO  16:52:50,957 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:52Z] INFO  16:52:50,962 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/7/R14-18105_kapa-NGv3-PE100-NGv3-sort-7_141629903_157151331-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/7/R14-18105_kapa-NGv3-PE100-NGv3-sort-7_141629903_157151331-prep-prealign-realign.intervals -L 7:141629904-157151331 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/7/tx/tmpWCt4Jo/R14-18105_kapa-NGv3-PE100-NGv3-sort-7_141629903_157151331-prep.bam
[2016-04-14T23:52Z] INFO  16:52:50,980 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:52Z] INFO  16:52:50,981 HelpFormatter - Date/Time: 2016/04/14 16:52:50
[2016-04-14T23:52Z] INFO  16:52:50,981 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:52Z] INFO  16:52:50,992 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:52Z] INFO  16:52:51,163 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:52Z] GATK: realign ('8', 79513976, 95140568) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-14T23:52Z] INFO  16:52:51,191 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:52Z] INFO  16:52:51,326 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:52Z] INFO  16:52:51,339 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:52Z] INFO  16:52:51,390 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-14T23:52Z] INFO  16:52:51,911 IntervalUtils - Processing 15521428 bp from intervals
[2016-04-14T23:52Z] WARN  16:52:51,927 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:52Z] INFO  16:52:52,019 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:52Z] INFO  16:52:52,128 ProgressMeter -            done   1.5734951E7    17.0 s       1.0 s      100.0%    17.0 s       0.0 s
[2016-04-14T23:52Z] INFO  16:52:52,129 ProgressMeter - Total runtime 17.07 secs, 0.28 min, 0.00 hours
[2016-04-14T23:52Z] INFO  16:52:52,155 MicroScheduler - 12727 reads were filtered out during the traversal out of approximately 150294 total reads (8.47%)
[2016-04-14T23:52Z] INFO  16:52:52,155 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:52Z] INFO  16:52:52,155 MicroScheduler -   -> 531 reads (0.35% of total) failing BadMateFilter
[2016-04-14T23:52Z] INFO  16:52:52,156 MicroScheduler -   -> 11807 reads (7.86% of total) failing DuplicateReadFilter
[2016-04-14T23:52Z] INFO  16:52:52,156 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-14T23:52Z] INFO  16:52:52,156 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:52Z] INFO  16:52:52,156 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-14T23:52Z] INFO  16:52:52,157 MicroScheduler -   -> 389 reads (0.26% of total) failing MappingQualityZeroFilter
[2016-04-14T23:52Z] INFO  16:52:52,157 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:52Z] INFO  16:52:52,157 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-14T23:52Z] INFO  16:52:52,157 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-14T23:52Z] INFO  16:52:52,164 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:52Z] INFO  16:52:52,165 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:52Z] INFO  16:52:52,166 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:52Z] INFO  16:52:52,166 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:52Z] GATK pre-alignment ('9', 32407258, 65506776) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-14T23:52Z] INFO  16:52:52,390 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:52Z] INFO  16:52:52,544 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:52Z] INFO  16:52:53,456 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:52Z] GATK: realign ('8', 63775819, 79510770) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-14T23:52Z] INFO  16:52:53,978 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:52Z] INFO  16:52:53,981 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:52Z] INFO  16:52:53,982 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:52Z] INFO  16:52:53,982 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:52Z] INFO  16:52:53,987 HelpFormatter - Program Args: -T PrintReads -L 9:15564087-32405601 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/9/tx/tmpVzp1UH/R14-18105_kapa-NGv3-PE100-NGv3-sort-9_15564086_32405601-prep-prealign.bam
[2016-04-14T23:52Z] INFO  16:52:53,996 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:52Z] INFO  16:52:53,996 HelpFormatter - Date/Time: 2016/04/14 16:52:53
[2016-04-14T23:52Z] INFO  16:52:53,997 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:52Z] INFO  16:52:53,997 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:52Z] INFO  16:52:54,203 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:52Z] INFO  16:52:54,207 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:52Z] INFO  16:52:54,207 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:52Z] INFO  16:52:54,208 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:52Z] INFO  16:52:54,213 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/8/R14-18105_kapa-NGv3-PE100-NGv3-sort-8_79513976_95140568-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/8/R14-18105_kapa-NGv3-PE100-NGv3-sort-8_79513976_95140568-prep-prealign-realign.intervals -L 8:79513977-95140568 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/8/tx/tmpOyXv0C/R14-18105_kapa-NGv3-PE100-NGv3-sort-8_79513976_95140568-prep.bam
[2016-04-14T23:52Z] INFO  16:52:54,228 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:52Z] INFO  16:52:54,229 HelpFormatter - Date/Time: 2016/04/14 16:52:54
[2016-04-14T23:52Z] INFO  16:52:54,230 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:52Z] INFO  16:52:54,230 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:52Z] INFO  16:52:54,235 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:52Z] INFO  16:52:54,493 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:52Z] INFO  16:52:54,611 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:52Z] INFO  16:52:54,635 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:52Z] INFO  16:52:54,678 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.04
[2016-04-14T23:52Z] INFO  16:52:55,067 IntervalUtils - Processing 15626592 bp from intervals
[2016-04-14T23:52Z] WARN  16:52:55,072 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:52Z] INFO  16:52:55,159 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:52Z] INFO  16:52:55,157 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:52Z] INFO  16:52:55,160 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:52Z] INFO  16:52:55,161 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:52Z] INFO  16:52:55,161 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:52Z] INFO  16:52:55,166 HelpFormatter - Program Args: -T PrintReads -L 9:32407259-65506776 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/9/tx/tmp8NnA_w/R14-18105_kapa-NGv3-PE100-NGv3-sort-9_32407258_65506776-prep-prealign.bam
[2016-04-14T23:52Z] INFO  16:52:55,176 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:52Z] INFO  16:52:55,176 HelpFormatter - Date/Time: 2016/04/14 16:52:55
[2016-04-14T23:52Z] INFO  16:52:55,177 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:52Z] INFO  16:52:55,177 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:52Z] INFO  16:52:55,328 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:52Z] INFO  16:52:55,344 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:52Z] INFO  16:52:55,355 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:52Z] INFO  16:52:55,356 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:52Z] INFO  16:52:55,356 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:52Z] INFO  16:52:55,399 ProgressMeter -            done   1.5537634E7    17.0 s       1.0 s      100.0%    17.0 s       0.0 s
[2016-04-14T23:52Z] INFO  16:52:55,400 ProgressMeter - Total runtime 17.27 secs, 0.29 min, 0.00 hours
[2016-04-14T23:52Z] INFO  16:52:55,415 MicroScheduler - 11701 reads were filtered out during the traversal out of approximately 143359 total reads (8.16%)
[2016-04-14T23:52Z] INFO  16:52:55,415 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:52Z] INFO  16:52:55,415 MicroScheduler -   -> 444 reads (0.31% of total) failing BadMateFilter
[2016-04-14T23:52Z] INFO  16:52:55,416 MicroScheduler -   -> 11053 reads (7.71% of total) failing DuplicateReadFilter
[2016-04-14T23:52Z] INFO  16:52:55,416 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-14T23:52Z] INFO  16:52:55,416 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:52Z] INFO  16:52:55,416 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-14T23:52Z] INFO  16:52:55,417 MicroScheduler -   -> 204 reads (0.14% of total) failing MappingQualityZeroFilter
[2016-04-14T23:52Z] INFO  16:52:55,417 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:52Z] INFO  16:52:55,429 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-14T23:52Z] INFO  16:52:55,429 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-14T23:52Z] INFO  16:52:55,459 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-14T23:52Z] INFO  16:52:55,525 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:52Z] INFO  16:52:55,529 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:52Z] INFO  16:52:55,537 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:52Z] INFO  16:52:55,574 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.04
[2016-04-14T23:52Z] INFO  16:52:55,588 IntervalUtils - Processing 16841515 bp from intervals
[2016-04-14T23:52Z] INFO  16:52:55,682 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:52Z] INFO  16:52:55,686 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:52Z] INFO  16:52:56,020 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:52Z] INFO  16:52:56,022 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:52Z] INFO  16:52:56,022 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:52Z] INFO  16:52:56,023 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:52Z] INFO  16:52:56,039 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:52Z] INFO  16:52:56,216 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:52Z] INFO  16:52:56,276 ProgressMeter -            done   1.5517156E7    19.0 s       1.0 s      100.0%    19.0 s       0.0 s
[2016-04-14T23:52Z] INFO  16:52:56,277 ProgressMeter - Total runtime 19.96 secs, 0.33 min, 0.01 hours
[2016-04-14T23:52Z] INFO  16:52:56,278 MicroScheduler - 116560 reads were filtered out during the traversal out of approximately 325759 total reads (35.78%)
[2016-04-14T23:52Z] INFO  16:52:56,279 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:52Z] INFO  16:52:56,280 MicroScheduler -   -> 578 reads (0.18% of total) failing BadMateFilter
[2016-04-14T23:52Z] INFO  16:52:56,280 MicroScheduler -   -> 18936 reads (5.81% of total) failing DuplicateReadFilter
[2016-04-14T23:52Z] INFO  16:52:56,281 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-14T23:52Z] INFO  16:52:56,281 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:52Z] INFO  16:52:56,282 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-14T23:52Z] INFO  16:52:56,283 MicroScheduler -   -> 97046 reads (29.79% of total) failing MappingQualityZeroFilter
[2016-04-14T23:52Z] INFO  16:52:56,283 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:52Z] INFO  16:52:56,284 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-14T23:52Z] INFO  16:52:56,297 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-14T23:52Z] INFO  16:52:56,431 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:52Z] INFO  16:52:56,434 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:52Z] INFO  16:52:56,435 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:52Z] INFO  16:52:56,435 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:52Z] INFO  16:52:56,440 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/8/R14-18105_kapa-NGv3-PE100-NGv3-sort-8_63775819_79510770-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/8/R14-18105_kapa-NGv3-PE100-NGv3-sort-8_63775819_79510770-prep-prealign-realign.intervals -L 8:63775820-79510770 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/8/tx/tmp3HBl3q/R14-18105_kapa-NGv3-PE100-NGv3-sort-8_63775819_79510770-prep.bam
[2016-04-14T23:52Z] INFO  16:52:56,473 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:52Z] INFO  16:52:56,474 HelpFormatter - Date/Time: 2016/04/14 16:52:56
[2016-04-14T23:52Z] INFO  16:52:56,474 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:52Z] INFO  16:52:56,474 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:52Z] INFO  16:52:56,689 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-14T23:52Z] INFO  16:52:56,738 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:52Z] INFO  16:52:56,747 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:52Z] INFO  16:52:56,753 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:52Z] INFO  16:52:56,803 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-14T23:52Z] INFO  16:52:56,818 IntervalUtils - Processing 33099518 bp from intervals
[2016-04-14T23:52Z] INFO  16:52:56,892 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:52Z] INFO  16:52:56,909 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:52Z] INFO  16:52:56,920 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:52Z] INFO  16:52:56,983 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:52Z] INFO  16:52:56,996 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-14T23:52Z] GATK: realign ('8', 110656864, 126194498) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-14T23:52Z] INFO  16:52:57,206 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:52Z] INFO  16:52:57,207 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:52Z] INFO  16:52:57,207 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:52Z] INFO  16:52:57,207 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:52Z] INFO  16:52:57,232 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:52Z] INFO  16:52:57,453 IntervalUtils - Processing 15734951 bp from intervals
[2016-04-14T23:52Z] WARN  16:52:57,469 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:52Z] INFO  16:52:57,492 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:52Z] INFO  16:52:57,560 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:52Z] INFO  16:52:57,669 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:52Z] GATK: realign ('8', 0, 15517156) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-14T23:52Z] INFO  16:52:57,772 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:52Z] INFO  16:52:57,773 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:52Z] INFO  16:52:57,773 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:52Z] INFO  16:52:57,773 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:52Z] INFO  16:52:57,807 ProgressMeter -     8:144993280    100002.0    30.0 s       5.0 m       69.3%    43.0 s      13.0 s
[2016-04-14T23:52Z] INFO  16:52:57,923 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:52Z] INFO  16:52:58,049 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:52Z] INFO  16:52:59,860 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:52Z] INFO  16:52:59,864 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:52Z] INFO  16:52:59,864 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:52Z] INFO  16:52:59,865 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:52Z] INFO  16:52:59,869 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/8/R14-18105_kapa-NGv3-PE100-NGv3-sort-8_110656864_126194498-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/8/R14-18105_kapa-NGv3-PE100-NGv3-sort-8_110656864_126194498-prep-prealign-realign.intervals -L 8:110656865-126194498 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/8/tx/tmpV4Z_mG/R14-18105_kapa-NGv3-PE100-NGv3-sort-8_110656864_126194498-prep.bam
[2016-04-14T23:52Z] INFO  16:52:59,893 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:52Z] INFO  16:52:59,901 HelpFormatter - Date/Time: 2016/04/14 16:52:59
[2016-04-14T23:52Z] INFO  16:52:59,902 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:52Z] INFO  16:52:59,903 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:53Z] INFO  16:53:00,078 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:53Z] INFO  16:53:00,166 ProgressMeter -            done    141838.0    12.0 s      86.0 s      100.0%    12.0 s       0.0 s
[2016-04-14T23:53Z] INFO  16:53:00,166 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:53Z] INFO  16:53:00,167 ProgressMeter - Total runtime 12.31 secs, 0.21 min, 0.00 hours
[2016-04-14T23:53Z] INFO  16:53:00,171 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 141838 total reads (0.00%)
[2016-04-14T23:53Z] INFO  16:53:00,171 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:53Z] INFO  16:53:00,172 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:53Z] INFO  16:53:00,172 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:53Z] INFO  16:53:00,175 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:53Z] INFO  16:53:00,212 ProgressMeter -            done   1.5520276E7    17.0 s       1.0 s      100.0%    17.0 s       0.0 s
[2016-04-14T23:53Z] INFO  16:53:00,213 ProgressMeter - Total runtime 17.71 secs, 0.30 min, 0.00 hours
[2016-04-14T23:53Z] INFO  16:53:00,217 MicroScheduler - 10655 reads were filtered out during the traversal out of approximately 125924 total reads (8.46%)
[2016-04-14T23:53Z] INFO  16:53:00,218 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:53Z] INFO  16:53:00,219 MicroScheduler -   -> 525 reads (0.42% of total) failing BadMateFilter
[2016-04-14T23:53Z] INFO  16:53:00,220 MicroScheduler -   -> 9862 reads (7.83% of total) failing DuplicateReadFilter
[2016-04-14T23:53Z] INFO  16:53:00,220 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-14T23:53Z] INFO  16:53:00,221 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:53Z] INFO  16:53:00,222 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-14T23:53Z] INFO  16:53:00,222 MicroScheduler -   -> 268 reads (0.21% of total) failing MappingQualityZeroFilter
[2016-04-14T23:53Z] INFO  16:53:00,223 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:53Z] INFO  16:53:00,223 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-14T23:53Z] INFO  16:53:00,224 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-14T23:53Z] INFO  16:53:00,226 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-14T23:53Z] INFO  16:53:00,465 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:53Z] INFO  16:53:00,468 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:53Z] INFO  16:53:00,469 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:53Z] INFO  16:53:00,469 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:53Z] INFO  16:53:00,474 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/8/R14-18105_kapa-NGv3-PE100-NGv3-sort-8_0_15517156-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/8/R14-18105_kapa-NGv3-PE100-NGv3-sort-8_0_15517156-prep-prealign-realign.intervals -L 8:1-15517156 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/8/tx/tmpVtAN8J/R14-18105_kapa-NGv3-PE100-NGv3-sort-8_0_15517156-prep.bam
[2016-04-14T23:53Z] INFO  16:53:00,501 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:53Z] INFO  16:53:00,512 HelpFormatter - Date/Time: 2016/04/14 16:53:00
[2016-04-14T23:53Z] INFO  16:53:00,513 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:53Z] INFO  16:53:00,514 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:53Z] INFO  16:53:00,566 IntervalUtils - Processing 15537634 bp from intervals
[2016-04-14T23:53Z] WARN  16:53:00,571 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:53Z] INFO  16:53:00,645 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:53Z] INFO  16:53:00,725 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:53Z] INFO  16:53:00,765 ProgressMeter -            done    886903.0    54.0 s      61.0 s      100.0%    54.0 s       0.0 s
[2016-04-14T23:53Z] INFO  16:53:00,765 ProgressMeter - Total runtime 54.26 secs, 0.90 min, 0.02 hours
[2016-04-14T23:53Z] INFO  16:53:00,769 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 886903 total reads (0.00%)
[2016-04-14T23:53Z] INFO  16:53:00,769 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:53Z] INFO  16:53:00,770 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:53Z] INFO  16:53:00,770 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:53Z] INFO  16:53:00,775 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:53Z] INFO  16:53:00,776 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:53Z] INFO  16:53:00,776 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:53Z] INFO  16:53:00,777 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:53Z] INFO  16:53:00,802 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:53Z] INFO  16:53:00,811 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:53Z] INFO  16:53:00,867 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-14T23:53Z] INFO  16:53:00,922 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:53Z] INFO  16:53:01,131 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:53Z] INFO  16:53:01,233 IntervalUtils - Processing 15517156 bp from intervals
[2016-04-14T23:53Z] WARN  16:53:01,248 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:53Z] INFO  16:53:01,327 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:53Z] INFO  16:53:01,441 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:53Z] INFO  16:53:01,442 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:53Z] INFO  16:53:01,443 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:53Z] INFO  16:53:01,443 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:53Z] INFO  16:53:01,501 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:53Z] GATK: realign ('8', 126369460, 141889736) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-14T23:53Z] INFO  16:53:01,527 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:53Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-8_48003022_63659688-prep.bam
[2016-04-14T23:53Z] INFO  16:53:01,580 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:53Z] INFO  16:53:01,744 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:53Z] GATK pre-alignment ('9', 65507205, 82187750) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-14T23:53Z] INFO  16:53:02,396 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:53Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-6_31083801_46593245-prep.bam
[2016-04-14T23:53Z] INFO  16:53:02,876 ProgressMeter -      9:15307481    100001.0    30.0 s       5.0 m       98.7%    30.0 s       0.0 s
[2016-04-14T23:53Z] INFO  16:53:03,292 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@7172f77a
[2016-04-14T23:53Z] INFO  16:53:03,318 ProgressMeter -            done    188813.0    14.0 s      74.0 s      100.0%    14.0 s       0.0 s
[2016-04-14T23:53Z] INFO  16:53:03,318 ProgressMeter - Total runtime 14.06 secs, 0.23 min, 0.00 hours
[2016-04-14T23:53Z] INFO  16:53:03,322 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 188813 total reads (0.00%)
[2016-04-14T23:53Z] INFO  16:53:03,323 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:53Z] INFO  16:53:03,323 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:53Z] INFO  16:53:03,323 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:53Z] INFO  16:53:03,362 ProgressMeter -            done    183840.0    30.0 s       2.8 m      100.0%    30.0 s       0.0 s
[2016-04-14T23:53Z] INFO  16:53:03,363 ProgressMeter - Total runtime 30.50 secs, 0.51 min, 0.01 hours
[2016-04-14T23:53Z] INFO  16:53:03,364 MicroScheduler - 142 reads were filtered out during the traversal out of approximately 183982 total reads (0.08%)
[2016-04-14T23:53Z] INFO  16:53:03,365 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:53Z] INFO  16:53:03,365 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:53Z] INFO  16:53:03,366 MicroScheduler -   -> 142 reads (0.08% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:53Z] INFO  16:53:04,492 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:53Z] INFO  16:53:04,494 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:53Z] INFO  16:53:04,495 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:53Z] INFO  16:53:04,495 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:53Z] INFO  16:53:04,499 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/8/R14-18105_kapa-NGv3-PE100-NGv3-sort-8_126369460_141889736-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/8/R14-18105_kapa-NGv3-PE100-NGv3-sort-8_126369460_141889736-prep-prealign-realign.intervals -L 8:126369461-141889736 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/8/tx/tmpBKVesu/R14-18105_kapa-NGv3-PE100-NGv3-sort-8_126369460_141889736-prep.bam
[2016-04-14T23:53Z] INFO  16:53:04,519 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:53Z] INFO  16:53:04,520 HelpFormatter - Date/Time: 2016/04/14 16:53:04
[2016-04-14T23:53Z] INFO  16:53:04,520 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:53Z] INFO  16:53:04,521 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:53Z] INFO  16:53:04,715 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:53Z] INFO  16:53:04,716 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:53Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-9_0_15510186-prep-prealign.bam
[2016-04-14T23:53Z] INFO  16:53:04,844 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:53Z] INFO  16:53:04,864 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:53Z] INFO  16:53:04,903 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:53Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-8_31496910_48001429-prep.bam
[2016-04-14T23:53Z] INFO  16:53:04,928 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-14T23:53Z] INFO  16:53:05,049 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:53Z] INFO  16:53:05,053 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:53Z] INFO  16:53:05,053 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:53Z] INFO  16:53:05,054 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:53Z] INFO  16:53:05,058 HelpFormatter - Program Args: -T PrintReads -L 9:65507206-82187750 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/9/tx/tmpZE5MyN/R14-18105_kapa-NGv3-PE100-NGv3-sort-9_65507205_82187750-prep-prealign.bam
[2016-04-14T23:53Z] INFO  16:53:05,068 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:53Z] INFO  16:53:05,073 HelpFormatter - Date/Time: 2016/04/14 16:53:05
[2016-04-14T23:53Z] INFO  16:53:05,073 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:53Z] INFO  16:53:05,074 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:53Z] INFO  16:53:05,227 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:53Z] INFO  16:53:05,374 IntervalUtils - Processing 15520276 bp from intervals
[2016-04-14T23:53Z] WARN  16:53:05,379 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:53Z] GATK pre-alignment ('9', 82188172, 97717561) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-14T23:53Z] INFO  16:53:05,443 ProgressMeter -            done   1.5512566E7    18.0 s       1.0 s      100.0%    18.0 s       0.0 s
[2016-04-14T23:53Z] INFO  16:53:05,443 ProgressMeter - Total runtime 18.88 secs, 0.31 min, 0.01 hours
[2016-04-14T23:53Z] INFO  16:53:05,447 MicroScheduler - 17231 reads were filtered out during the traversal out of approximately 209288 total reads (8.23%)
[2016-04-14T23:53Z] INFO  16:53:05,448 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:53Z] INFO  16:53:05,448 MicroScheduler -   -> 563 reads (0.27% of total) failing BadMateFilter
[2016-04-14T23:53Z] INFO  16:53:05,449 MicroScheduler -   -> 16232 reads (7.76% of total) failing DuplicateReadFilter
[2016-04-14T23:53Z] INFO  16:53:05,450 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-14T23:53Z] INFO  16:53:05,450 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:53Z] INFO  16:53:05,451 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-14T23:53Z] INFO  16:53:05,451 MicroScheduler -   -> 436 reads (0.21% of total) failing MappingQualityZeroFilter
[2016-04-14T23:53Z] INFO  16:53:05,451 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:53Z] INFO  16:53:05,451 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-14T23:53Z] INFO  16:53:05,452 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-14T23:53Z] INFO  16:53:05,455 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:53Z] GATK RealignerTargetCreator: R14-18105_kapa-NGv3-PE100-NGv3-sort-9_0_15510186-prep-prealign.bam 9:1-15510186
[2016-04-14T23:53Z] GATK: RealignerTargetCreator
[2016-04-14T23:53Z] GATK pre-alignment ('9', 97718189, 113228306) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-14T23:53Z] INFO  16:53:05,595 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:53Z] INFO  16:53:05,597 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:53Z] INFO  16:53:05,597 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:53Z] INFO  16:53:05,598 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:53Z] INFO  16:53:05,802 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:53Z] INFO  16:53:05,969 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:53Z] INFO  16:53:06,000 ProgressMeter -            done    102684.0    10.0 s     103.0 s      100.0%    10.0 s       0.0 s
[2016-04-14T23:53Z] INFO  16:53:06,000 ProgressMeter - Total runtime 10.65 secs, 0.18 min, 0.00 hours
[2016-04-14T23:53Z] INFO  16:53:06,004 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 102684 total reads (0.00%)
[2016-04-14T23:53Z] INFO  16:53:06,005 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:53Z] INFO  16:53:06,005 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:53Z] INFO  16:53:06,005 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:53Z] INFO  16:53:06,320 ProgressMeter -            done   1.5553754E7    27.0 s       1.0 s      100.0%    27.0 s       0.0 s
[2016-04-14T23:53Z] INFO  16:53:06,321 ProgressMeter - Total runtime 27.60 secs, 0.46 min, 0.01 hours
[2016-04-14T23:53Z] INFO  16:53:06,322 MicroScheduler - 181769 reads were filtered out during the traversal out of approximately 734623 total reads (24.74%)
[2016-04-14T23:53Z] INFO  16:53:06,323 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:53Z] INFO  16:53:06,324 MicroScheduler -   -> 1104 reads (0.15% of total) failing BadMateFilter
[2016-04-14T23:53Z] INFO  16:53:06,324 MicroScheduler -   -> 49543 reads (6.74% of total) failing DuplicateReadFilter
[2016-04-14T23:53Z] INFO  16:53:06,325 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-14T23:53Z] INFO  16:53:06,325 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:53Z] INFO  16:53:06,326 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-14T23:53Z] INFO  16:53:06,327 MicroScheduler -   -> 131122 reads (17.85% of total) failing MappingQualityZeroFilter
[2016-04-14T23:53Z] INFO  16:53:06,327 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:53Z] INFO  16:53:06,328 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-14T23:53Z] INFO  16:53:06,328 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-14T23:53Z] INFO  16:53:06,330 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-14T23:53Z] INFO  16:53:06,400 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:53Z] INFO  16:53:06,410 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:53Z] INFO  16:53:06,466 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-14T23:53Z] INFO  16:53:06,481 IntervalUtils - Processing 16680545 bp from intervals
[2016-04-14T23:53Z] INFO  16:53:06,585 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:53Z] INFO  16:53:06,835 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:53Z] GATK: realign ('8', 95142853, 110655419) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-14T23:53Z] INFO  16:53:06,871 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:53Z] INFO  16:53:06,873 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:53Z] INFO  16:53:06,873 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:53Z] INFO  16:53:06,874 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:53Z] INFO  16:53:06,908 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:53Z] INFO  16:53:07,136 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:53Z] INFO  16:53:07,631 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:53Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-8_79513976_95140568-prep.bam
[2016-04-14T23:53Z] INFO  16:53:07,747 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:53Z] GATK: realign ('7', 94750023, 110303777) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-14T23:53Z] GATK pre-alignment ('9', 113231219, 129089575) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-14T23:53Z] INFO  16:53:08,599 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:53Z] INFO  16:53:08,602 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:53Z] INFO  16:53:08,602 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:53Z] INFO  16:53:08,603 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:53Z] INFO  16:53:08,607 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/9/R14-18105_kapa-NGv3-PE100-NGv3-sort-9_0_15510186-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/9/tx/tmp6kLZhd/R14-18105_kapa-NGv3-PE100-NGv3-sort-9_0_15510186-prep-prealign-realign.intervals -l INFO -L 9:1-15510186 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-14T23:53Z] INFO  16:53:08,618 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:53Z] INFO  16:53:08,619 HelpFormatter - Date/Time: 2016/04/14 16:53:08
[2016-04-14T23:53Z] INFO  16:53:08,619 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:53Z] INFO  16:53:08,620 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:53Z] INFO  16:53:08,745 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:53Z] INFO  16:53:08,749 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:53Z] INFO  16:53:08,749 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:53Z] INFO  16:53:08,750 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:53Z] INFO  16:53:08,748 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:53Z] INFO  16:53:08,751 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:53Z] INFO  16:53:08,752 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:53Z] INFO  16:53:08,752 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:53Z] INFO  16:53:08,754 HelpFormatter - Program Args: -T PrintReads -L 9:82188173-97717561 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/9/tx/tmpgkDCRN/R14-18105_kapa-NGv3-PE100-NGv3-sort-9_82188172_97717561-prep-prealign.bam
[2016-04-14T23:53Z] INFO  16:53:08,757 HelpFormatter - Program Args: -T PrintReads -L 9:97718190-113228306 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/9/tx/tmpCs2gG6/R14-18105_kapa-NGv3-PE100-NGv3-sort-9_97718189_113228306-prep-prealign.bam
[2016-04-14T23:53Z] INFO  16:53:08,762 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:53Z] INFO  16:53:08,764 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:53Z] INFO  16:53:08,768 HelpFormatter - Date/Time: 2016/04/14 16:53:08
[2016-04-14T23:53Z] INFO  16:53:08,769 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:53Z] INFO  16:53:08,769 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:53Z] INFO  16:53:08,786 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:53Z] INFO  16:53:08,787 HelpFormatter - Date/Time: 2016/04/14 16:53:08
[2016-04-14T23:53Z] INFO  16:53:08,788 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:53Z] INFO  16:53:08,789 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:53Z] INFO  16:53:08,997 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:53Z] INFO  16:53:09,022 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-14T23:53Z] INFO  16:53:09,034 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:53Z] INFO  16:53:09,041 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:53Z] INFO  16:53:09,120 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-14T23:53Z] INFO  16:53:09,518 ProgressMeter -            done   1.5510954E7    22.0 s       1.0 s      100.0%    22.0 s       0.0 s
[2016-04-14T23:53Z] INFO  16:53:09,520 ProgressMeter - Total runtime 22.63 secs, 0.38 min, 0.01 hours
[2016-04-14T23:53Z] INFO  16:53:09,524 MicroScheduler - 30904 reads were filtered out during the traversal out of approximately 358308 total reads (8.62%)
[2016-04-14T23:53Z] INFO  16:53:09,525 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:53Z] INFO  16:53:09,526 MicroScheduler -   -> 847 reads (0.24% of total) failing BadMateFilter
[2016-04-14T23:53Z] INFO  16:53:09,526 MicroScheduler -   -> 28695 reads (8.01% of total) failing DuplicateReadFilter
[2016-04-14T23:53Z] INFO  16:53:09,527 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-14T23:53Z] INFO  16:53:09,528 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:53Z] INFO  16:53:09,528 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-14T23:53Z] INFO  16:53:09,529 MicroScheduler -   -> 1362 reads (0.38% of total) failing MappingQualityZeroFilter
[2016-04-14T23:53Z] INFO  16:53:09,529 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:53Z] INFO  16:53:09,530 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-14T23:53Z] INFO  16:53:09,531 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-14T23:53Z] INFO  16:53:09,561 IntervalUtils - Processing 15510186 bp from intervals
[2016-04-14T23:53Z] WARN  16:53:09,566 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:53Z] INFO  16:53:09,565 ProgressMeter -            done    149798.0    11.0 s      78.0 s      100.0%    11.0 s       0.0 s
[2016-04-14T23:53Z] INFO  16:53:09,566 ProgressMeter - Total runtime 11.79 secs, 0.20 min, 0.00 hours
[2016-04-14T23:53Z] INFO  16:53:09,569 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 149798 total reads (0.00%)
[2016-04-14T23:53Z] INFO  16:53:09,573 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:53Z] INFO  16:53:09,574 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:53Z] INFO  16:53:09,574 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:53Z] INFO  16:53:09,720 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:53Z] INFO  16:53:09,754 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:53Z] INFO  16:53:09,757 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:53Z] INFO  16:53:09,757 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:53Z] INFO  16:53:09,758 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:53Z] INFO  16:53:09,784 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/8/R14-18105_kapa-NGv3-PE100-NGv3-sort-8_95142853_110655419-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/8/R14-18105_kapa-NGv3-PE100-NGv3-sort-8_95142853_110655419-prep-prealign-realign.intervals -L 8:95142854-110655419 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/8/tx/tmpwnjyyX/R14-18105_kapa-NGv3-PE100-NGv3-sort-8_95142853_110655419-prep.bam
[2016-04-14T23:53Z] INFO  16:53:09,815 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:53Z] INFO  16:53:09,824 HelpFormatter - Date/Time: 2016/04/14 16:53:09
[2016-04-14T23:53Z] INFO  16:53:09,825 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:53Z] INFO  16:53:09,830 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:53Z] INFO  16:53:09,941 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:53Z] INFO  16:53:09,941 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:53Z] INFO  16:53:09,942 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:53Z] INFO  16:53:09,942 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-14T23:53Z] INFO  16:53:10,062 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:53Z] INFO  16:53:10,108 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-14T23:53Z] INFO  16:53:10,166 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:53Z] INFO  16:53:10,175 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:53Z] INFO  16:53:10,217 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:53Z] INFO  16:53:10,238 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:53Z] INFO  16:53:10,239 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-14T23:53Z] INFO  16:53:10,253 IntervalUtils - Processing 15510117 bp from intervals
[2016-04-14T23:53Z] INFO  16:53:10,310 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-14T23:53Z] INFO  16:53:10,314 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-14T23:53Z] INFO  16:53:10,327 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:53Z] INFO  16:53:10,394 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:53Z] INFO  16:53:10,409 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:53Z] INFO  16:53:10,474 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-14T23:53Z] INFO  16:53:10,506 IntervalUtils - Processing 15529389 bp from intervals
[2016-04-14T23:53Z] INFO  16:53:10,619 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:53Z] INFO  16:53:10,620 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:53Z] INFO  16:53:10,620 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:53Z] INFO  16:53:10,621 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:53Z] INFO  16:53:10,639 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:53Z] INFO  16:53:10,642 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:53Z] INFO  16:53:10,643 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:53Z] INFO  16:53:10,643 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:53Z] INFO  16:53:10,645 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:53Z] INFO  16:53:10,646 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:53Z] INFO  16:53:10,647 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/7/R14-18105_kapa-NGv3-PE100-NGv3-sort-7_94750023_110303777-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/7/R14-18105_kapa-NGv3-PE100-NGv3-sort-7_94750023_110303777-prep-prealign-realign.intervals -L 7:94750024-110303777 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/7/tx/tmpIrayaE/R14-18105_kapa-NGv3-PE100-NGv3-sort-7_94750023_110303777-prep.bam
[2016-04-14T23:53Z] INFO  16:53:10,670 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:53Z] INFO  16:53:10,681 HelpFormatter - Date/Time: 2016/04/14 16:53:10
[2016-04-14T23:53Z] INFO  16:53:10,682 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:53Z] INFO  16:53:10,683 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:53Z] INFO  16:53:10,804 IntervalUtils - Processing 15512566 bp from intervals
[2016-04-14T23:53Z] WARN  16:53:10,808 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:53Z] INFO  16:53:10,865 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:53Z] INFO  16:53:10,874 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:53Z] INFO  16:53:10,897 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:53Z] INFO  16:53:10,897 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:53Z] INFO  16:53:10,897 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:53Z] INFO  16:53:10,898 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:53Z] INFO  16:53:10,911 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:53Z] INFO  16:53:10,943 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:53Z] INFO  16:53:10,981 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:53Z] INFO  16:53:10,987 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:53Z] INFO  16:53:10,992 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:53Z] INFO  16:53:11,001 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:53Z] INFO  16:53:11,004 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:53Z] INFO  16:53:11,004 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:53Z] INFO  16:53:11,005 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:53Z] INFO  16:53:11,009 HelpFormatter - Program Args: -T PrintReads -L 9:113231220-129089575 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/9/tx/tmpILGKyK/R14-18105_kapa-NGv3-PE100-NGv3-sort-9_113231219_129089575-prep-prealign.bam
[2016-04-14T23:53Z] INFO  16:53:11,017 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:53Z] INFO  16:53:11,018 HelpFormatter - Date/Time: 2016/04/14 16:53:10
[2016-04-14T23:53Z] INFO  16:53:11,018 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:53Z] INFO  16:53:11,019 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:53Z] GATK: realign ('8', 15519664, 31030618) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-14T23:53Z] INFO  16:53:11,061 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:53Z] INFO  16:53:11,062 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:53Z] INFO  16:53:11,073 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:53Z] INFO  16:53:11,074 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:53Z] INFO  16:53:11,074 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:53Z] INFO  16:53:11,077 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:53Z] INFO  16:53:11,087 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.09
[2016-04-14T23:53Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-8_63775819_79510770-prep.bam
[2016-04-14T23:53Z] INFO  16:53:11,197 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:53Z] INFO  16:53:11,241 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:53Z] INFO  16:53:11,386 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:53Z] INFO  16:53:11,537 IntervalUtils - Processing 15553754 bp from intervals
[2016-04-14T23:53Z] WARN  16:53:11,551 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:53Z] GATK pre-alignment ('9', 129097484, 141213431) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-14T23:53Z] INFO  16:53:11,631 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:53Z] INFO  16:53:11,844 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:53Z] INFO  16:53:11,845 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:53Z] INFO  16:53:11,846 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:53Z] INFO  16:53:11,846 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:53Z] INFO  16:53:12,052 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:53Z] INFO  16:53:12,316 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:53Z] INFO  16:53:12,316 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-14T23:53Z] INFO  16:53:12,376 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:53Z] INFO  16:53:12,385 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:53Z] INFO  16:53:12,446 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-14T23:53Z] INFO  16:53:12,460 IntervalUtils - Processing 15858356 bp from intervals
[2016-04-14T23:53Z] INFO  16:53:12,539 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:53Z] INFO  16:53:12,897 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:53Z] INFO  16:53:12,898 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:53Z] INFO  16:53:12,899 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:53Z] INFO  16:53:12,900 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:53Z] INFO  16:53:12,913 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:53Z] INFO  16:53:13,123 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:53Z] INFO  16:53:14,174 ProgressMeter -            done    142745.0    13.0 s      93.0 s      100.0%    13.0 s       0.0 s
[2016-04-14T23:53Z] INFO  16:53:14,175 ProgressMeter - Total runtime 13.40 secs, 0.22 min, 0.00 hours
[2016-04-14T23:53Z] INFO  16:53:14,178 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 142745 total reads (0.00%)
[2016-04-14T23:53Z] INFO  16:53:14,178 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:53Z] INFO  16:53:14,178 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:53Z] INFO  16:53:14,179 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:53Z] INFO  16:53:14,253 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:53Z] INFO  16:53:14,256 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:53Z] INFO  16:53:14,256 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:53Z] INFO  16:53:14,256 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:53Z] INFO  16:53:14,260 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/8/R14-18105_kapa-NGv3-PE100-NGv3-sort-8_15519664_31030618-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/8/R14-18105_kapa-NGv3-PE100-NGv3-sort-8_15519664_31030618-prep-prealign-realign.intervals -L 8:15519665-31030618 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/8/tx/tmpVEyep9/R14-18105_kapa-NGv3-PE100-NGv3-sort-8_15519664_31030618-prep.bam
[2016-04-14T23:53Z] INFO  16:53:14,280 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:53Z] INFO  16:53:14,281 HelpFormatter - Date/Time: 2016/04/14 16:53:14
[2016-04-14T23:53Z] INFO  16:53:14,281 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:53Z] INFO  16:53:14,281 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:53Z] INFO  16:53:14,568 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:53Z] INFO  16:53:14,721 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@5fe152b7
[2016-04-14T23:53Z] INFO  16:53:14,726 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:53Z] INFO  16:53:14,739 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:53Z] INFO  16:53:14,832 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.09
[2016-04-14T23:53Z] INFO  16:53:14,846 ProgressMeter -            done    127949.0    18.0 s       2.5 m      100.0%    18.0 s       0.0 s
[2016-04-14T23:53Z] INFO  16:53:14,846 ProgressMeter - Total runtime 18.82 secs, 0.31 min, 0.01 hours
[2016-04-14T23:53Z] INFO  16:53:14,847 MicroScheduler - 131 reads were filtered out during the traversal out of approximately 128080 total reads (0.10%)
[2016-04-14T23:53Z] INFO  16:53:14,847 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:53Z] INFO  16:53:14,847 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:53Z] INFO  16:53:14,848 MicroScheduler -   -> 131 reads (0.10% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:53Z] INFO  16:53:15,151 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:53Z] INFO  16:53:15,154 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:53Z] INFO  16:53:15,155 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:53Z] INFO  16:53:15,155 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:53Z] INFO  16:53:15,160 HelpFormatter - Program Args: -T PrintReads -L 9:129097485-141213431 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/9/tx/tmpo4P4VX/R14-18105_kapa-NGv3-PE100-NGv3-sort-9_129097484_141213431-prep-prealign.bam
[2016-04-14T23:53Z] INFO  16:53:15,161 IntervalUtils - Processing 15510954 bp from intervals
[2016-04-14T23:53Z] WARN  16:53:15,167 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:53Z] INFO  16:53:15,169 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:53Z] INFO  16:53:15,174 HelpFormatter - Date/Time: 2016/04/14 16:53:15
[2016-04-14T23:53Z] INFO  16:53:15,175 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:53Z] INFO  16:53:15,176 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:53Z] INFO  16:53:15,299 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:53Z] INFO  16:53:15,410 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:53Z] INFO  16:53:15,523 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:53Z] INFO  16:53:15,539 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:53Z] INFO  16:53:15,541 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:53Z] INFO  16:53:15,542 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:53Z] INFO  16:53:15,670 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:53Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-8_110656864_126194498-prep.bam
[2016-04-14T23:53Z] INFO  16:53:15,737 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:53Z] INFO  16:53:15,932 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:53Z] GATK pre-alignment ('10', 0, 15559243) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-14T23:53Z] INFO  16:53:16,280 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-14T23:53Z] INFO  16:53:16,332 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:53Z] INFO  16:53:16,341 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:53Z] INFO  16:53:16,393 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-14T23:53Z] INFO  16:53:16,397 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:53Z] INFO  16:53:16,407 IntervalUtils - Processing 12115947 bp from intervals
[2016-04-14T23:53Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-9_15564086_32405601-prep-prealign.bam
[2016-04-14T23:53Z] INFO  16:53:16,516 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:53Z] INFO  16:53:16,598 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@5fe152b7
[2016-04-14T23:53Z] INFO  16:53:16,764 ProgressMeter -            done    390329.0    49.0 s       2.1 m       98.1%    49.0 s       0.0 s
[2016-04-14T23:53Z] INFO  16:53:16,764 ProgressMeter - Total runtime 49.17 secs, 0.82 min, 0.01 hours
[2016-04-14T23:53Z] INFO  16:53:16,765 MicroScheduler - 158 reads were filtered out during the traversal out of approximately 390487 total reads (0.04%)
[2016-04-14T23:53Z] INFO  16:53:16,765 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:53Z] INFO  16:53:16,765 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:53Z] INFO  16:53:16,766 MicroScheduler -   -> 158 reads (0.04% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:53Z] INFO  16:53:16,882 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:53Z] INFO  16:53:16,882 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:53Z] INFO  16:53:16,883 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:53Z] INFO  16:53:16,883 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:53Z] INFO  16:53:16,908 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:53Z] INFO  16:53:16,959 ProgressMeter -            done    124927.0    11.0 s      90.0 s      100.0%    11.0 s       0.0 s
[2016-04-14T23:53Z] INFO  16:53:16,960 ProgressMeter - Total runtime 11.36 secs, 0.19 min, 0.00 hours
[2016-04-14T23:53Z] INFO  16:53:16,972 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 124927 total reads (0.00%)
[2016-04-14T23:53Z] INFO  16:53:16,973 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:53Z] INFO  16:53:16,974 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:53Z] INFO  16:53:16,975 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:53Z] GATK RealignerTargetCreator: R14-18105_kapa-NGv3-PE100-NGv3-sort-9_15564086_32405601-prep-prealign.bam 9:15564087-32405601
[2016-04-14T23:53Z] GATK: RealignerTargetCreator
[2016-04-14T23:53Z] INFO  16:53:17,083 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:53Z] INFO  16:53:18,122 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:53Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-8_141900641_146364022-prep-prealign.bam
[2016-04-14T23:53Z] INFO  16:53:18,642 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:53Z] INFO  16:53:18,645 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:53Z] INFO  16:53:18,646 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:53Z] INFO  16:53:18,646 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:53Z] INFO  16:53:18,651 HelpFormatter - Program Args: -T PrintReads -L 10:1-15559243 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/10/tx/tmpiw468B/R14-18105_kapa-NGv3-PE100-NGv3-sort-10_0_15559243-prep-prealign.bam
[2016-04-14T23:53Z] INFO  16:53:18,680 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:53Z] INFO  16:53:18,681 HelpFormatter - Date/Time: 2016/04/14 16:53:18
[2016-04-14T23:53Z] INFO  16:53:18,682 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:53Z] INFO  16:53:18,686 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:53Z] INFO  16:53:18,769 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:53Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-8_126369460_141889736-prep.bam
[2016-04-14T23:53Z] INFO  16:53:18,876 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:53Z] GATK RealignerTargetCreator: R14-18105_kapa-NGv3-PE100-NGv3-sort-8_141900641_146364022-prep-prealign.bam 8:141900642-146364022
[2016-04-14T23:53Z] GATK: RealignerTargetCreator
[2016-04-14T23:53Z] GATK pre-alignment ('10', 15561288, 31134502) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-14T23:53Z] INFO  16:53:20,049 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:53Z] INFO  16:53:20,052 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:53Z] INFO  16:53:20,053 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:53Z] INFO  16:53:20,054 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:53Z] INFO  16:53:20,058 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/9/R14-18105_kapa-NGv3-PE100-NGv3-sort-9_15564086_32405601-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/9/tx/tmpE_rMCu/R14-18105_kapa-NGv3-PE100-NGv3-sort-9_15564086_32405601-prep-prealign-realign.intervals -l INFO -L 9:15564087-32405601 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-14T23:53Z] INFO  16:53:20,075 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:53Z] INFO  16:53:20,076 HelpFormatter - Date/Time: 2016/04/14 16:53:20
[2016-04-14T23:53Z] INFO  16:53:20,076 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:53Z] INFO  16:53:20,077 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:53Z] INFO  16:53:20,162 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-14T23:53Z] INFO  16:53:20,228 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:53Z] INFO  16:53:20,245 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:53Z] INFO  16:53:20,255 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:53Z] INFO  16:53:20,320 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-14T23:53Z] INFO  16:53:20,347 IntervalUtils - Processing 15559243 bp from intervals
[2016-04-14T23:53Z] INFO  16:53:20,450 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:53Z] INFO  16:53:20,487 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-14T23:53Z] INFO  16:53:20,499 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:53Z] INFO  16:53:20,582 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-14T23:53Z] INFO  16:53:20,803 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:53Z] INFO  16:53:20,804 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:53Z] INFO  16:53:20,805 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:53Z] INFO  16:53:20,805 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:53Z] INFO  16:53:20,831 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:53Z] INFO  16:53:20,995 IntervalUtils - Processing 16841515 bp from intervals
[2016-04-14T23:53Z] WARN  16:53:21,014 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:53Z] INFO  16:53:21,038 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:53Z] INFO  16:53:21,151 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:53Z] INFO  16:53:21,418 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:53Z] INFO  16:53:21,419 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:53Z] INFO  16:53:21,419 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:53Z] INFO  16:53:21,420 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-14T23:53Z] INFO  16:53:22,045 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:53Z] INFO  16:53:22,049 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:53Z] INFO  16:53:22,049 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:53Z] INFO  16:53:22,050 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:53Z] INFO  16:53:22,054 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/8/R14-18105_kapa-NGv3-PE100-NGv3-sort-8_141900641_146364022-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/8/tx/tmpJHQW4m/R14-18105_kapa-NGv3-PE100-NGv3-sort-8_141900641_146364022-prep-prealign-realign.intervals -l INFO -L 8:141900642-146364022 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-14T23:53Z] INFO  16:53:22,068 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:53Z] INFO  16:53:22,069 HelpFormatter - Date/Time: 2016/04/14 16:53:22
[2016-04-14T23:53Z] INFO  16:53:22,072 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:53Z] INFO  16:53:22,073 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:53Z] INFO  16:53:22,155 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:53Z] INFO  16:53:22,157 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:53Z] INFO  16:53:22,157 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:53Z] INFO  16:53:22,158 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:53Z] INFO  16:53:22,168 HelpFormatter - Program Args: -T PrintReads -L 10:15561289-31134502 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/10/tx/tmpTP9ALH/R14-18105_kapa-NGv3-PE100-NGv3-sort-10_15561288_31134502-prep-prealign.bam
[2016-04-14T23:53Z] INFO  16:53:22,182 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:53Z] INFO  16:53:22,191 ProgressMeter -     7:152102334    400007.0    30.0 s      75.0 s       67.5%    44.0 s      14.0 s
[2016-04-14T23:53Z] INFO  16:53:22,208 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:53Z] INFO  16:53:22,209 HelpFormatter - Date/Time: 2016/04/14 16:53:22
[2016-04-14T23:53Z] INFO  16:53:22,209 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:53Z] INFO  16:53:22,210 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:53Z] INFO  16:53:22,418 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:53Z] INFO  16:53:22,451 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-14T23:53Z] INFO  16:53:22,490 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:53Z] INFO  16:53:22,572 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-14T23:53Z] INFO  16:53:22,923 IntervalUtils - Processing 4463381 bp from intervals
[2016-04-14T23:53Z] WARN  16:53:22,928 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:53Z] INFO  16:53:22,997 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:53Z] INFO  16:53:23,158 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:53Z] INFO  16:53:23,173 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:53Z] INFO  16:53:23,174 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:53Z] INFO  16:53:23,175 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-14T23:53Z] INFO  16:53:23,631 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-14T23:53Z] INFO  16:53:23,709 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:53Z] INFO  16:53:23,718 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:53Z] INFO  16:53:23,776 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-14T23:53Z] INFO  16:53:23,790 IntervalUtils - Processing 15573214 bp from intervals
[2016-04-14T23:53Z] INFO  16:53:23,872 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:53Z] INFO  16:53:24,207 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:53Z] INFO  16:53:24,207 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:53Z] INFO  16:53:24,208 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:53Z] INFO  16:53:24,208 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:53Z] INFO  16:53:24,220 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:53Z] INFO  16:53:24,313 ProgressMeter -            done    475121.0    32.0 s      67.0 s      100.0%    32.0 s       0.0 s
[2016-04-14T23:53Z] INFO  16:53:24,313 ProgressMeter - Total runtime 32.15 secs, 0.54 min, 0.01 hours
[2016-04-14T23:53Z] INFO  16:53:24,317 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 475121 total reads (0.00%)
[2016-04-14T23:53Z] INFO  16:53:24,318 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:53Z] INFO  16:53:24,318 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:53Z] INFO  16:53:24,318 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:53Z] INFO  16:53:24,393 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:53Z] INFO  16:53:25,048 ProgressMeter -            done    324027.0    23.0 s      72.0 s      100.0%    23.0 s       0.0 s
[2016-04-14T23:53Z] INFO  16:53:25,049 ProgressMeter - Total runtime 23.61 secs, 0.39 min, 0.01 hours
[2016-04-14T23:53Z] INFO  16:53:25,052 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 324027 total reads (0.00%)
[2016-04-14T23:53Z] INFO  16:53:25,053 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:53Z] INFO  16:53:25,053 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:53Z] INFO  16:53:25,053 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:53Z] INFO  16:53:26,257 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:53Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-7_141629903_157151331-prep.bam
[2016-04-14T23:53Z] INFO  16:53:26,781 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:53Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-8_0_15517156-prep.bam
[2016-04-14T23:53Z] INFO  16:53:27,221 ProgressMeter -      9:35689797    100002.0    30.0 s       5.0 m        9.9%     5.0 m       4.5 m
[2016-04-14T23:53Z] INFO  16:53:27,325 ProgressMeter -            done    207488.0    16.0 s      78.0 s      100.0%    16.0 s       0.0 s
[2016-04-14T23:53Z] INFO  16:53:27,325 ProgressMeter - Total runtime 16.25 secs, 0.27 min, 0.00 hours
[2016-04-14T23:53Z] INFO  16:53:27,329 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 207488 total reads (0.00%)
[2016-04-14T23:53Z] INFO  16:53:27,329 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:53Z] INFO  16:53:27,329 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:53Z] INFO  16:53:27,330 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:53Z] GATK pre-alignment ('10', 31137459, 46960129) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-14T23:53Z] GATK pre-alignment ('10', 46960410, 62493077) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-14T23:53Z] INFO  16:53:28,288 ProgressMeter -            done   1.5510186E7    18.0 s       1.0 s      100.0%    18.0 s       0.0 s
[2016-04-14T23:53Z] INFO  16:53:28,289 ProgressMeter - Total runtime 18.35 secs, 0.31 min, 0.01 hours
[2016-04-14T23:53Z] INFO  16:53:28,293 MicroScheduler - 24927 reads were filtered out during the traversal out of approximately 184503 total reads (13.51%)
[2016-04-14T23:53Z] INFO  16:53:28,294 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:53Z] INFO  16:53:28,294 MicroScheduler -   -> 516 reads (0.28% of total) failing BadMateFilter
[2016-04-14T23:53Z] INFO  16:53:28,294 MicroScheduler -   -> 13919 reads (7.54% of total) failing DuplicateReadFilter
[2016-04-14T23:53Z] INFO  16:53:28,295 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-14T23:53Z] INFO  16:53:28,295 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:53Z] INFO  16:53:28,295 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-14T23:53Z] INFO  16:53:28,296 MicroScheduler -   -> 10492 reads (5.69% of total) failing MappingQualityZeroFilter
[2016-04-14T23:53Z] INFO  16:53:28,296 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:53Z] INFO  16:53:28,296 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-14T23:53Z] INFO  16:53:28,296 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-14T23:53Z] INFO  16:53:28,691 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:53Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-8_95142853_110655419-prep.bam
[2016-04-14T23:53Z] GATK pre-alignment ('10', 62539923, 78084243) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-14T23:53Z] INFO  16:53:29,631 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:53Z] GATK: realign ('9', 0, 15510186) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-14T23:53Z] INFO  16:53:30,647 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:53Z] INFO  16:53:30,651 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:53Z] INFO  16:53:30,651 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:53Z] INFO  16:53:30,652 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:53Z] INFO  16:53:30,657 HelpFormatter - Program Args: -T PrintReads -L 10:31137460-46960129 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/10/tx/tmpEW0War/R14-18105_kapa-NGv3-PE100-NGv3-sort-10_31137459_46960129-prep-prealign.bam
[2016-04-14T23:53Z] INFO  16:53:30,666 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:53Z] INFO  16:53:30,667 HelpFormatter - Date/Time: 2016/04/14 16:53:30
[2016-04-14T23:53Z] INFO  16:53:30,667 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:53Z] INFO  16:53:30,668 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:53Z] INFO  16:53:30,811 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:53Z] INFO  16:53:30,864 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:53Z] INFO  16:53:30,868 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:53Z] INFO  16:53:30,869 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:53Z] INFO  16:53:30,869 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:53Z] INFO  16:53:30,874 HelpFormatter - Program Args: -T PrintReads -L 10:46960411-62493077 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/10/tx/tmpd8ijuR/R14-18105_kapa-NGv3-PE100-NGv3-sort-10_46960410_62493077-prep-prealign.bam
[2016-04-14T23:53Z] INFO  16:53:30,900 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:53Z] INFO  16:53:30,901 HelpFormatter - Date/Time: 2016/04/14 16:53:30
[2016-04-14T23:53Z] INFO  16:53:30,901 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:53Z] INFO  16:53:30,902 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:53Z] INFO  16:53:31,152 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:53Z] INFO  16:53:31,769 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-14T23:53Z] INFO  16:53:31,818 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:53Z] INFO  16:53:31,827 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:53Z] INFO  16:53:31,868 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.04
[2016-04-14T23:53Z] INFO  16:53:31,885 IntervalUtils - Processing 15822670 bp from intervals
[2016-04-14T23:53Z] INFO  16:53:31,989 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:53Z] INFO  16:53:32,265 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:53Z] INFO  16:53:32,279 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:53Z] INFO  16:53:32,279 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:53Z] INFO  16:53:32,280 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:53Z] INFO  16:53:32,284 HelpFormatter - Program Args: -T PrintReads -L 10:62539924-78084243 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/10/tx/tmpTAgsgs/R14-18105_kapa-NGv3-PE100-NGv3-sort-10_62539923_78084243-prep-prealign.bam
[2016-04-14T23:53Z] INFO  16:53:32,290 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:53Z] INFO  16:53:32,291 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:53Z] INFO  16:53:32,292 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:53Z] INFO  16:53:32,293 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:53Z] INFO  16:53:32,293 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:53Z] INFO  16:53:32,293 HelpFormatter - Date/Time: 2016/04/14 16:53:32
[2016-04-14T23:53Z] INFO  16:53:32,293 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:53Z] INFO  16:53:32,293 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:53Z] INFO  16:53:32,307 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:53Z] INFO  16:53:32,375 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-14T23:53Z] INFO  16:53:32,435 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:53Z] INFO  16:53:32,433 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:53Z] INFO  16:53:32,436 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:53Z] INFO  16:53:32,436 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:53Z] INFO  16:53:32,436 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:53Z] INFO  16:53:32,440 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/9/R14-18105_kapa-NGv3-PE100-NGv3-sort-9_0_15510186-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/9/R14-18105_kapa-NGv3-PE100-NGv3-sort-9_0_15510186-prep-prealign-realign.intervals -L 9:1-15510186 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/9/tx/tmpolf8qZ/R14-18105_kapa-NGv3-PE100-NGv3-sort-9_0_15510186-prep.bam
[2016-04-14T23:53Z] INFO  16:53:32,445 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:53Z] INFO  16:53:32,450 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:53Z] INFO  16:53:32,456 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:53Z] INFO  16:53:32,457 HelpFormatter - Date/Time: 2016/04/14 16:53:32
[2016-04-14T23:53Z] INFO  16:53:32,458 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:53Z] INFO  16:53:32,458 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:53Z] INFO  16:53:32,467 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:53Z] INFO  16:53:32,485 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.04
[2016-04-14T23:53Z] INFO  16:53:32,507 IntervalUtils - Processing 15532667 bp from intervals
[2016-04-14T23:53Z] INFO  16:53:32,615 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:53Z] INFO  16:53:32,656 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:53Z] INFO  16:53:32,791 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:53Z] INFO  16:53:32,802 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:53Z] INFO  16:53:32,883 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-14T23:53Z] INFO  16:53:32,952 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:53Z] INFO  16:53:32,953 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:53Z] INFO  16:53:32,954 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:53Z] INFO  16:53:32,955 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:53Z] INFO  16:53:32,987 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:53Z] INFO  16:53:33,215 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:53Z] INFO  16:53:33,296 IntervalUtils - Processing 15510186 bp from intervals
[2016-04-14T23:53Z] WARN  16:53:33,302 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:53Z] INFO  16:53:33,446 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:53Z] INFO  16:53:33,585 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:53Z] INFO  16:53:33,586 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:53Z] INFO  16:53:33,587 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:53Z] INFO  16:53:33,588 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:53Z] INFO  16:53:33,704 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-14T23:53Z] INFO  16:53:33,747 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:53Z] INFO  16:53:33,782 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:53Z] INFO  16:53:33,813 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:53Z] INFO  16:53:33,859 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-14T23:53Z] INFO  16:53:33,873 IntervalUtils - Processing 15544320 bp from intervals
[2016-04-14T23:53Z] INFO  16:53:33,911 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:53Z] INFO  16:53:33,968 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:53Z] INFO  16:53:34,227 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:53Z] INFO  16:53:34,228 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:53Z] INFO  16:53:34,229 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:53Z] INFO  16:53:34,229 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:53Z] INFO  16:53:34,253 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:53Z] INFO  16:53:34,389 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:53Z] INFO  16:53:36,721 ProgressMeter -            done   4463381.0    13.0 s       3.0 s      100.0%    13.0 s       0.0 s
[2016-04-14T23:53Z] INFO  16:53:36,722 ProgressMeter - Total runtime 13.55 secs, 0.23 min, 0.00 hours
[2016-04-14T23:53Z] INFO  16:53:36,723 MicroScheduler - 40819 reads were filtered out during the traversal out of approximately 392388 total reads (10.40%)
[2016-04-14T23:53Z] INFO  16:53:36,724 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:53Z] INFO  16:53:36,725 MicroScheduler -   -> 665 reads (0.17% of total) failing BadMateFilter
[2016-04-14T23:53Z] INFO  16:53:36,725 MicroScheduler -   -> 31247 reads (7.96% of total) failing DuplicateReadFilter
[2016-04-14T23:53Z] INFO  16:53:36,726 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-14T23:53Z] INFO  16:53:36,727 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:53Z] INFO  16:53:36,727 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-14T23:53Z] INFO  16:53:36,728 MicroScheduler -   -> 8907 reads (2.27% of total) failing MappingQualityZeroFilter
[2016-04-14T23:53Z] INFO  16:53:36,728 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:53Z] INFO  16:53:36,729 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-14T23:53Z] INFO  16:53:36,730 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-14T23:53Z] INFO  16:53:36,893 ProgressMeter -      9:79954553    200011.0    30.0 s       2.5 m       86.6%    34.0 s       4.0 s
[2016-04-14T23:53Z] INFO  16:53:37,909 ProgressMeter -            done   1.6841515E7    16.0 s       0.0 s      100.0%    16.0 s       0.0 s
[2016-04-14T23:53Z] INFO  16:53:37,910 ProgressMeter - Total runtime 16.49 secs, 0.27 min, 0.00 hours
[2016-04-14T23:53Z] INFO  16:53:37,915 MicroScheduler - 12964 reads were filtered out during the traversal out of approximately 129084 total reads (10.04%)
[2016-04-14T23:53Z] INFO  16:53:37,916 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:53Z] INFO  16:53:37,917 MicroScheduler -   -> 496 reads (0.38% of total) failing BadMateFilter
[2016-04-14T23:53Z] INFO  16:53:37,918 MicroScheduler -   -> 9508 reads (7.37% of total) failing DuplicateReadFilter
[2016-04-14T23:53Z] INFO  16:53:37,919 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-14T23:53Z] INFO  16:53:37,919 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:53Z] INFO  16:53:37,920 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-14T23:53Z] INFO  16:53:37,921 MicroScheduler -   -> 2960 reads (2.29% of total) failing MappingQualityZeroFilter
[2016-04-14T23:53Z] INFO  16:53:37,922 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:53Z] INFO  16:53:37,922 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-14T23:53Z] INFO  16:53:37,923 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-14T23:53Z] INFO  16:53:37,966 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:53Z] GATK: realign ('8', 141900641, 146364022) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-14T23:53Z] INFO  16:53:38,104 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@41fd9d8e
[2016-04-14T23:53Z] INFO  16:53:38,264 ProgressMeter -            done    243980.0    31.0 s       2.1 m      100.0%    31.0 s       0.0 s
[2016-04-14T23:53Z] INFO  16:53:38,265 ProgressMeter - Total runtime 31.39 secs, 0.52 min, 0.01 hours
[2016-04-14T23:53Z] INFO  16:53:38,266 MicroScheduler - 166 reads were filtered out during the traversal out of approximately 244146 total reads (0.07%)
[2016-04-14T23:53Z] INFO  16:53:38,266 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:53Z] INFO  16:53:38,267 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:53Z] INFO  16:53:38,267 MicroScheduler -   -> 166 reads (0.07% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:53Z] INFO  16:53:39,083 ProgressMeter -            done    354408.0    23.0 s      66.0 s      100.0%    23.0 s       0.0 s
[2016-04-14T23:53Z] INFO  16:53:39,085 ProgressMeter - Total runtime 23.56 secs, 0.39 min, 0.01 hours
[2016-04-14T23:53Z] INFO  16:53:39,089 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 354408 total reads (0.00%)
[2016-04-14T23:53Z] INFO  16:53:39,104 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:53Z] INFO  16:53:39,105 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:53Z] INFO  16:53:39,106 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:53Z] INFO  16:53:39,457 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:53Z] GATK: realign ('9', 15564086, 32405601) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-14T23:53Z] INFO  16:53:39,988 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:53Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-9_65507205_82187750-prep-prealign.bam
[2016-04-14T23:53Z] INFO  16:53:40,632 ProgressMeter -     9:108200530    200005.0    30.0 s       2.5 m       67.6%    44.0 s      14.0 s
[2016-04-14T23:53Z] INFO  16:53:40,740 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:53Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-8_15519664_31030618-prep.bam
[2016-04-14T23:53Z] GATK RealignerTargetCreator: R14-18105_kapa-NGv3-PE100-NGv3-sort-9_65507205_82187750-prep-prealign.bam 9:65507206-82187750
[2016-04-14T23:53Z] GATK: RealignerTargetCreator
[2016-04-14T23:53Z] INFO  16:53:40,911 ProgressMeter -      9:94486420    200003.0    30.0 s       2.5 m       79.2%    37.0 s       7.0 s
[2016-04-14T23:53Z] INFO  16:53:41,081 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:53Z] INFO  16:53:41,084 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:53Z] INFO  16:53:41,085 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:53Z] INFO  16:53:41,085 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:53Z] INFO  16:53:41,090 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/8/R14-18105_kapa-NGv3-PE100-NGv3-sort-8_141900641_146364022-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/8/R14-18105_kapa-NGv3-PE100-NGv3-sort-8_141900641_146364022-prep-prealign-realign.intervals -L 8:141900642-146364022 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/8/tx/tmpBe1mhn/R14-18105_kapa-NGv3-PE100-NGv3-sort-8_141900641_146364022-prep.bam
[2016-04-14T23:53Z] INFO  16:53:41,103 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:53Z] INFO  16:53:41,104 HelpFormatter - Date/Time: 2016/04/14 16:53:41
[2016-04-14T23:53Z] INFO  16:53:41,104 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:53Z] INFO  16:53:41,105 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:53Z] INFO  16:53:41,368 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:53Z] INFO  16:53:41,493 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:53Z] INFO  16:53:41,504 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:53Z] INFO  16:53:41,565 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-14T23:53Z] GATK pre-alignment ('10', 78316966, 93841258) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-14T23:53Z] INFO  16:53:41,861 ProgressMeter -     7:100645837    300004.0    30.0 s     100.0 s       37.9%    79.0 s      49.0 s
[2016-04-14T23:53Z] INFO  16:53:41,986 IntervalUtils - Processing 4463381 bp from intervals
[2016-04-14T23:53Z] WARN  16:53:41,991 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:53Z] INFO  16:53:42,058 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:53Z] INFO  16:53:42,118 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:53Z] INFO  16:53:42,119 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:53Z] INFO  16:53:42,120 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:53Z] INFO  16:53:42,120 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:53Z] INFO  16:53:42,230 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:53Z] INFO  16:53:42,271 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:53Z] INFO  16:53:42,297 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:53Z] INFO  16:53:42,301 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:53Z] INFO  16:53:42,301 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:53Z] INFO  16:53:42,302 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:53Z] INFO  16:53:42,307 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/9/R14-18105_kapa-NGv3-PE100-NGv3-sort-9_15564086_32405601-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/9/R14-18105_kapa-NGv3-PE100-NGv3-sort-9_15564086_32405601-prep-prealign-realign.intervals -L 9:15564087-32405601 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/9/tx/tmpWZkQUn/R14-18105_kapa-NGv3-PE100-NGv3-sort-9_15564086_32405601-prep.bam
[2016-04-14T23:53Z] INFO  16:53:42,323 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:53Z] INFO  16:53:42,328 HelpFormatter - Date/Time: 2016/04/14 16:53:42
[2016-04-14T23:53Z] INFO  16:53:42,329 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:53Z] INFO  16:53:42,330 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:53Z] INFO  16:53:42,512 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:53Z] INFO  16:53:42,661 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:53Z] INFO  16:53:42,677 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:53Z] INFO  16:53:42,745 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-14T23:53Z] INFO  16:53:42,932 ProgressMeter -     9:123784052    200002.0    30.0 s       2.5 m       66.5%    45.0 s      15.0 s
[2016-04-14T23:53Z] INFO  16:53:43,048 IntervalUtils - Processing 16841515 bp from intervals
[2016-04-14T23:53Z] WARN  16:53:43,053 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:53Z] INFO  16:53:43,124 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:53Z] INFO  16:53:43,257 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:53Z] INFO  16:53:43,258 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:53Z] INFO  16:53:43,259 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:53Z] INFO  16:53:43,260 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:53Z] INFO  16:53:43,391 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:53Z] INFO  16:53:43,483 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:53Z] INFO  16:53:43,486 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:53Z] INFO  16:53:43,487 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:53Z] INFO  16:53:43,487 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:53Z] INFO  16:53:43,492 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/9/R14-18105_kapa-NGv3-PE100-NGv3-sort-9_65507205_82187750-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/9/tx/tmpEtaMLM/R14-18105_kapa-NGv3-PE100-NGv3-sort-9_65507205_82187750-prep-prealign-realign.intervals -l INFO -L 9:65507206-82187750 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-14T23:53Z] INFO  16:53:43,512 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:53Z] INFO  16:53:43,513 HelpFormatter - Date/Time: 2016/04/14 16:53:43
[2016-04-14T23:53Z] INFO  16:53:43,513 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:53Z] INFO  16:53:43,518 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:53Z] INFO  16:53:43,598 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:53Z] INFO  16:53:43,604 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:53Z] INFO  16:53:43,806 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-14T23:53Z] INFO  16:53:43,815 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:53Z] INFO  16:53:43,887 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-14T23:53Z] INFO  16:53:44,164 IntervalUtils - Processing 16680545 bp from intervals
[2016-04-14T23:53Z] WARN  16:53:44,170 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:53Z] INFO  16:53:44,254 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:53Z] INFO  16:53:44,451 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:53Z] INFO  16:53:44,452 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:53Z] INFO  16:53:44,452 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:53Z] INFO  16:53:44,453 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-14T23:53Z] INFO  16:53:44,487 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:53Z] INFO  16:53:44,490 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:53Z] INFO  16:53:44,491 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:53Z] INFO  16:53:44,492 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:53Z] INFO  16:53:44,496 HelpFormatter - Program Args: -T PrintReads -L 10:78316967-93841258 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/10/tx/tmpqUyCkD/R14-18105_kapa-NGv3-PE100-NGv3-sort-10_78316966_93841258-prep-prealign.bam
[2016-04-14T23:53Z] INFO  16:53:44,514 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:53Z] INFO  16:53:44,515 HelpFormatter - Date/Time: 2016/04/14 16:53:44
[2016-04-14T23:53Z] INFO  16:53:44,516 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:53Z] INFO  16:53:44,516 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:53Z] INFO  16:53:44,717 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:53Z] INFO  16:53:45,903 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-14T23:53Z] INFO  16:53:45,989 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:53Z] INFO  16:53:46,010 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:53Z] INFO  16:53:46,088 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-14T23:53Z] INFO  16:53:46,133 IntervalUtils - Processing 15524292 bp from intervals
[2016-04-14T23:53Z] INFO  16:53:46,227 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:53Z] INFO  16:53:46,453 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:53Z] INFO  16:53:46,454 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:53Z] INFO  16:53:46,455 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:53Z] INFO  16:53:46,456 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:53Z] INFO  16:53:46,469 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:53Z] INFO  16:53:46,607 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:53Z] INFO  16:53:47,162 ProgressMeter -            done    183840.0    13.0 s      73.0 s      100.0%    13.0 s       0.0 s
[2016-04-14T23:53Z] INFO  16:53:47,163 ProgressMeter - Total runtime 13.58 secs, 0.23 min, 0.00 hours
[2016-04-14T23:53Z] INFO  16:53:47,167 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 183840 total reads (0.00%)
[2016-04-14T23:53Z] INFO  16:53:47,168 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:53Z] INFO  16:53:47,168 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:53Z] INFO  16:53:47,169 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:53Z] INFO  16:53:47,731 ProgressMeter -     9:131671118    100002.0    30.0 s       5.1 m       21.2%     2.4 m     111.0 s
[2016-04-14T23:53Z] INFO  16:53:48,714 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:53Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-9_0_15510186-prep.bam
[2016-04-14T23:53Z] GATK pre-alignment ('10', 93851586, 111625070) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-14T23:53Z] INFO  16:53:49,729 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@7172f77a
[2016-04-14T23:53Z] INFO  16:53:49,883 ProgressMeter -            done    307361.0    39.0 s       2.1 m      100.0%    39.0 s       0.0 s
[2016-04-14T23:53Z] INFO  16:53:49,884 ProgressMeter - Total runtime 39.26 secs, 0.65 min, 0.01 hours
[2016-04-14T23:53Z] INFO  16:53:49,884 MicroScheduler - 166 reads were filtered out during the traversal out of approximately 307527 total reads (0.05%)
[2016-04-14T23:53Z] INFO  16:53:49,885 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:53Z] INFO  16:53:49,885 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:53Z] INFO  16:53:49,885 MicroScheduler -   -> 166 reads (0.05% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:53Z] INFO  16:53:50,140 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@7172f77a
[2016-04-14T23:53Z] INFO  16:53:50,214 ProgressMeter -            done    205498.0    26.0 s       2.1 m      100.0%    26.0 s       0.0 s
[2016-04-14T23:53Z] INFO  16:53:50,214 ProgressMeter - Total runtime 26.01 secs, 0.43 min, 0.01 hours
[2016-04-14T23:53Z] INFO  16:53:50,215 MicroScheduler - 157 reads were filtered out during the traversal out of approximately 205655 total reads (0.08%)
[2016-04-14T23:53Z] INFO  16:53:50,215 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:53Z] INFO  16:53:50,215 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:53Z] INFO  16:53:50,216 MicroScheduler -   -> 157 reads (0.08% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:53Z] INFO  16:53:51,183 ProgressMeter -     10:13481637    100002.0    30.0 s       5.1 m       86.6%    34.0 s       4.0 s
[2016-04-14T23:53Z] INFO  16:53:51,345 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:53Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-9_97718189_113228306-prep-prealign.bam
[2016-04-14T23:53Z] INFO  16:53:51,500 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:53Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-10_15561288_31134502-prep-prealign.bam
[2016-04-14T23:53Z] GATK RealignerTargetCreator: R14-18105_kapa-NGv3-PE100-NGv3-sort-10_15561288_31134502-prep-prealign.bam 10:15561289-31134502
[2016-04-14T23:53Z] GATK: RealignerTargetCreator
[2016-04-14T23:53Z] INFO  16:53:52,131 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:53Z] INFO  16:53:52,134 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:53Z] INFO  16:53:52,135 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:53Z] INFO  16:53:52,135 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:53Z] INFO  16:53:52,140 HelpFormatter - Program Args: -T PrintReads -L 10:93851587-111625070 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/10/tx/tmpEfRQl5/R14-18105_kapa-NGv3-PE100-NGv3-sort-10_93851586_111625070-prep-prealign.bam
[2016-04-14T23:53Z] INFO  16:53:52,157 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:53Z] INFO  16:53:52,158 HelpFormatter - Date/Time: 2016/04/14 16:53:52
[2016-04-14T23:53Z] INFO  16:53:52,159 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:53Z] INFO  16:53:52,159 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:53Z] INFO  16:53:52,298 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:53Z] GATK RealignerTargetCreator: R14-18105_kapa-NGv3-PE100-NGv3-sort-9_97718189_113228306-prep-prealign.bam 9:97718190-113228306
[2016-04-14T23:53Z] GATK: RealignerTargetCreator
[2016-04-14T23:53Z] INFO  16:53:53,180 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@7172f77a
[2016-04-14T23:53Z] INFO  16:53:53,348 ProgressMeter -            done    328621.0    42.0 s       2.2 m      100.0%    42.0 s       0.0 s
[2016-04-14T23:53Z] INFO  16:53:53,349 ProgressMeter - Total runtime 42.45 secs, 0.71 min, 0.01 hours
[2016-04-14T23:53Z] INFO  16:53:53,349 MicroScheduler - 173 reads were filtered out during the traversal out of approximately 328794 total reads (0.05%)
[2016-04-14T23:53Z] INFO  16:53:53,349 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:53Z] INFO  16:53:53,350 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:53Z] INFO  16:53:53,350 MicroScheduler -   -> 173 reads (0.05% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:53Z] INFO  16:53:53,612 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-14T23:53Z] INFO  16:53:53,729 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:53Z] INFO  16:53:53,748 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:53Z] INFO  16:53:53,803 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-14T23:53Z] INFO  16:53:53,826 IntervalUtils - Processing 17773484 bp from intervals
[2016-04-14T23:53Z] INFO  16:53:53,905 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:53Z] INFO  16:53:54,229 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:53Z] INFO  16:53:54,230 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:53Z] INFO  16:53:54,231 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:53Z] INFO  16:53:54,232 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:53Z] INFO  16:53:54,252 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:53Z] INFO  16:53:54,412 ProgressMeter -            done    127949.0    11.0 s      87.0 s      100.0%    11.0 s       0.0 s
[2016-04-14T23:53Z] INFO  16:53:54,413 ProgressMeter - Total runtime 11.16 secs, 0.19 min, 0.00 hours
[2016-04-14T23:53Z] INFO  16:53:54,417 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 127949 total reads (0.00%)
[2016-04-14T23:53Z] INFO  16:53:54,417 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:53Z] INFO  16:53:54,419 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:53Z] INFO  16:53:54,420 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:53Z] INFO  16:53:54,509 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:53Z] INFO  16:53:54,760 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:53Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-9_82188172_97717561-prep-prealign.bam
[2016-04-14T23:53Z] INFO  16:53:55,244 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:53Z] INFO  16:53:55,248 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:53Z] INFO  16:53:55,248 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:53Z] INFO  16:53:55,249 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:53Z] INFO  16:53:55,255 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/9/R14-18105_kapa-NGv3-PE100-NGv3-sort-9_97718189_113228306-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/9/tx/tmp3mPEj0/R14-18105_kapa-NGv3-PE100-NGv3-sort-9_97718189_113228306-prep-prealign-realign.intervals -l INFO -L 9:97718190-113228306 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-14T23:53Z] INFO  16:53:55,271 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:53Z] INFO  16:53:55,272 HelpFormatter - Date/Time: 2016/04/14 16:53:55
[2016-04-14T23:53Z] INFO  16:53:55,273 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:53Z] INFO  16:53:55,274 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:53Z] INFO  16:53:55,377 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:53Z] INFO  16:53:55,402 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:53Z] INFO  16:53:55,406 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:53Z] INFO  16:53:55,407 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:53Z] INFO  16:53:55,408 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:53Z] INFO  16:53:55,413 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/10/R14-18105_kapa-NGv3-PE100-NGv3-sort-10_15561288_31134502-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/10/tx/tmp5ZFMNh/R14-18105_kapa-NGv3-PE100-NGv3-sort-10_15561288_31134502-prep-prealign-realign.intervals -l INFO -L 10:15561289-31134502 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-14T23:53Z] INFO  16:53:55,423 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:53Z] INFO  16:53:55,423 HelpFormatter - Date/Time: 2016/04/14 16:53:55
[2016-04-14T23:53Z] INFO  16:53:55,423 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:53Z] INFO  16:53:55,424 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:53Z] INFO  16:53:55,565 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:53Z] INFO  16:53:55,566 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-14T23:53Z] INFO  16:53:55,578 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:53Z] INFO  16:53:55,652 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-14T23:53Z] GATK RealignerTargetCreator: R14-18105_kapa-NGv3-PE100-NGv3-sort-9_82188172_97717561-prep-prealign.bam 9:82188173-97717561
[2016-04-14T23:53Z] GATK: RealignerTargetCreator
[2016-04-14T23:53Z] INFO  16:53:55,774 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-14T23:53Z] INFO  16:53:55,784 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:53Z] INFO  16:53:55,844 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-14T23:53Z] INFO  16:53:56,012 IntervalUtils - Processing 15510117 bp from intervals
[2016-04-14T23:53Z] WARN  16:53:56,017 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:53Z] INFO  16:53:56,094 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:53Z] INFO  16:53:56,097 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:53Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-9_15564086_32405601-prep.bam
[2016-04-14T23:53Z] INFO  16:53:56,169 IntervalUtils - Processing 15573214 bp from intervals
[2016-04-14T23:53Z] WARN  16:53:56,174 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:53Z] INFO  16:53:56,332 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:53Z] INFO  16:53:56,333 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:53Z] INFO  16:53:56,333 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:53Z] INFO  16:53:56,334 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-14T23:53Z] INFO  16:53:56,347 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:53Z] INFO  16:53:56,515 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:53Z] INFO  16:53:56,515 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:53Z] INFO  16:53:56,516 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:53Z] INFO  16:53:56,516 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-14T23:53Z] GATK pre-alignment ('10', 111628371, 127265443) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-14T23:53Z] INFO  16:53:56,695 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@41fd9d8e
[2016-04-14T23:53Z] INFO  16:53:56,784 ProgressMeter -            done    229830.0    35.0 s       2.6 m      100.0%    35.0 s       0.0 s
[2016-04-14T23:53Z] INFO  16:53:56,792 ProgressMeter - Total runtime 35.99 secs, 0.60 min, 0.01 hours
[2016-04-14T23:53Z] INFO  16:53:56,793 MicroScheduler - 149 reads were filtered out during the traversal out of approximately 229979 total reads (0.06%)
[2016-04-14T23:53Z] INFO  16:53:56,794 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:53Z] INFO  16:53:56,795 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:53Z] INFO  16:53:56,796 MicroScheduler -   -> 149 reads (0.06% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:53Z] INFO  16:53:57,246 ProgressMeter -      9:65505006    400009.0    60.0 s       2.5 m      100.0%    60.0 s       0.0 s
[2016-04-14T23:53Z] INFO  16:53:57,253 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@32d5a4c6
[2016-04-14T23:53Z] INFO  16:53:57,389 ProgressMeter -            done    361709.0    44.0 s       2.1 m      100.0%    44.0 s       0.0 s
[2016-04-14T23:53Z] INFO  16:53:57,390 ProgressMeter - Total runtime 44.49 secs, 0.74 min, 0.01 hours
[2016-04-14T23:53Z] INFO  16:53:57,391 MicroScheduler - 183 reads were filtered out during the traversal out of approximately 361892 total reads (0.05%)
[2016-04-14T23:53Z] INFO  16:53:57,391 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:53Z] INFO  16:53:57,392 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:53Z] INFO  16:53:57,392 MicroScheduler -   -> 183 reads (0.05% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:53Z] INFO  16:53:57,883 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@7172f77a
[2016-04-14T23:53Z] INFO  16:53:58,006 ProgressMeter -            done    494702.0    60.0 s       2.0 m      100.0%    60.0 s       0.0 s
[2016-04-14T23:53Z] INFO  16:53:58,006 ProgressMeter - Total runtime 60.80 secs, 1.01 min, 0.02 hours
[2016-04-14T23:53Z] INFO  16:53:58,007 MicroScheduler - 225 reads were filtered out during the traversal out of approximately 494927 total reads (0.05%)
[2016-04-14T23:53Z] INFO  16:53:58,008 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:53Z] INFO  16:53:58,008 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:53Z] INFO  16:53:58,009 MicroScheduler -   -> 225 reads (0.05% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:53Z] INFO  16:53:58,083 ProgressMeter -            done    730638.0    46.0 s      63.0 s      100.0%    46.0 s       0.0 s
[2016-04-14T23:53Z] INFO  16:53:58,083 ProgressMeter - Total runtime 46.24 secs, 0.77 min, 0.01 hours
[2016-04-14T23:53Z] INFO  16:53:58,087 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 730638 total reads (0.00%)
[2016-04-14T23:53Z] INFO  16:53:58,087 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:53Z] INFO  16:53:58,088 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:53Z] INFO  16:53:58,088 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:53Z] INFO  16:53:58,355 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:53Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-10_0_15559243-prep-prealign.bam
[2016-04-14T23:53Z] INFO  16:53:58,602 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:53Z] INFO  16:53:58,605 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:53Z] INFO  16:53:58,606 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:53Z] INFO  16:53:58,606 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:53Z] INFO  16:53:58,611 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/9/R14-18105_kapa-NGv3-PE100-NGv3-sort-9_82188172_97717561-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/9/tx/tmpj_JvV6/R14-18105_kapa-NGv3-PE100-NGv3-sort-9_82188172_97717561-prep-prealign-realign.intervals -l INFO -L 9:82188173-97717561 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-14T23:53Z] INFO  16:53:58,631 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:53Z] INFO  16:53:58,632 HelpFormatter - Date/Time: 2016/04/14 16:53:58
[2016-04-14T23:53Z] INFO  16:53:58,633 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:53Z] INFO  16:53:58,633 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:53Z] INFO  16:53:58,721 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:53Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-9_113231219_129089575-prep-prealign.bam
[2016-04-14T23:53Z] INFO  16:53:58,794 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:53Z] INFO  16:53:59,048 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-14T23:53Z] INFO  16:53:59,058 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:53Z] INFO  16:53:59,125 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-14T23:53Z] GATK RealignerTargetCreator: R14-18105_kapa-NGv3-PE100-NGv3-sort-10_0_15559243-prep-prealign.bam 10:1-15559243
[2016-04-14T23:53Z] GATK: RealignerTargetCreator
[2016-04-14T23:53Z] INFO  16:53:59,462 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:53Z] INFO  16:53:59,466 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:53Z] INFO  16:53:59,466 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:53Z] INFO  16:53:59,467 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:53Z] INFO  16:53:59,473 HelpFormatter - Program Args: -T PrintReads -L 10:111628372-127265443 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/10/tx/tmpanqNXs/R14-18105_kapa-NGv3-PE100-NGv3-sort-10_111628371_127265443-prep-prealign.bam
[2016-04-14T23:53Z] INFO  16:53:59,480 IntervalUtils - Processing 15529389 bp from intervals
[2016-04-14T23:53Z] INFO  16:53:59,483 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:53Z] INFO  16:53:59,484 HelpFormatter - Date/Time: 2016/04/14 16:53:59
[2016-04-14T23:53Z] INFO  16:53:59,485 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:53Z] INFO  16:53:59,485 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:53Z] WARN  16:53:59,485 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:53Z] INFO  16:53:59,517 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:53Z] INFO  16:53:59,519 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:53Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-9_32407258_65506776-prep-prealign.bam
[2016-04-14T23:53Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-7_94750023_110303777-prep.bam
[2016-04-14T23:53Z] INFO  16:53:59,614 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:53Z] INFO  16:53:59,717 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:53Z] GATK RealignerTargetCreator: R14-18105_kapa-NGv3-PE100-NGv3-sort-9_113231219_129089575-prep-prealign.bam 9:113231220-129089575
[2016-04-14T23:53Z] GATK: RealignerTargetCreator
[2016-04-14T23:53Z] INFO  16:53:59,954 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:53Z] INFO  16:53:59,969 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:53Z] INFO  16:53:59,970 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:53Z] INFO  16:53:59,971 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-14T23:54Z] INFO  16:54:00,870 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-14T23:54Z] INFO  16:54:00,927 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:54Z] INFO  16:54:00,936 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:54Z] INFO  16:54:00,987 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-14T23:54Z] INFO  16:54:01,002 IntervalUtils - Processing 15637072 bp from intervals
[2016-04-14T23:54Z] INFO  16:54:01,098 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:54Z] GATK RealignerTargetCreator: R14-18105_kapa-NGv3-PE100-NGv3-sort-9_32407258_65506776-prep-prealign.bam 9:32407259-65506776
[2016-04-14T23:54Z] GATK: RealignerTargetCreator
[2016-04-14T23:54Z] INFO  16:54:01,367 ProgressMeter -            done   1.6680545E7    16.0 s       1.0 s      100.0%    16.0 s       0.0 s
[2016-04-14T23:54Z] INFO  16:54:01,368 ProgressMeter - Total runtime 16.92 secs, 0.28 min, 0.00 hours
[2016-04-14T23:54Z] INFO  16:54:01,371 MicroScheduler - 91505 reads were filtered out during the traversal out of approximately 245017 total reads (37.35%)
[2016-04-14T23:54Z] INFO  16:54:01,371 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:54Z] INFO  16:54:01,372 MicroScheduler -   -> 441 reads (0.18% of total) failing BadMateFilter
[2016-04-14T23:54Z] INFO  16:54:01,372 MicroScheduler -   -> 13273 reads (5.42% of total) failing DuplicateReadFilter
[2016-04-14T23:54Z] INFO  16:54:01,372 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-14T23:54Z] INFO  16:54:01,373 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:54Z] INFO  16:54:01,373 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-14T23:54Z] INFO  16:54:01,373 MicroScheduler -   -> 77791 reads (31.75% of total) failing MappingQualityZeroFilter
[2016-04-14T23:54Z] INFO  16:54:01,373 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:54Z] INFO  16:54:01,373 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-14T23:54Z] INFO  16:54:01,374 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-14T23:54Z] INFO  16:54:01,410 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:54Z] INFO  16:54:01,411 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:54Z] INFO  16:54:01,412 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:54Z] INFO  16:54:01,412 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:54Z] INFO  16:54:01,444 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:54Z] INFO  16:54:01,726 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:54Z] GATK pre-alignment ('10', 127328721, 135534747) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-14T23:54Z] INFO  16:54:02,305 ProgressMeter -     10:46274638    100003.0    30.0 s       5.0 m       95.7%    31.0 s       1.0 s
[2016-04-14T23:54Z] INFO  16:54:02,325 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:54Z] INFO  16:54:02,328 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:54Z] INFO  16:54:02,329 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:54Z] INFO  16:54:02,329 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:54Z] INFO  16:54:02,334 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/10/R14-18105_kapa-NGv3-PE100-NGv3-sort-10_0_15559243-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/10/tx/tmplDa2JG/R14-18105_kapa-NGv3-PE100-NGv3-sort-10_0_15559243-prep-prealign-realign.intervals -l INFO -L 10:1-15559243 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-14T23:54Z] INFO  16:54:02,367 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:54Z] INFO  16:54:02,368 HelpFormatter - Date/Time: 2016/04/14 16:54:02
[2016-04-14T23:54Z] INFO  16:54:02,369 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:54Z] INFO  16:54:02,373 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:54Z] INFO  16:54:02,476 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:54Z] INFO  16:54:02,660 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-14T23:54Z] INFO  16:54:02,670 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:54Z] INFO  16:54:02,714 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.04
[2016-04-14T23:54Z] INFO  16:54:02,793 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:54Z] INFO  16:54:02,796 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:54Z] INFO  16:54:02,797 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:54Z] INFO  16:54:02,798 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:54Z] INFO  16:54:02,803 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/9/R14-18105_kapa-NGv3-PE100-NGv3-sort-9_113231219_129089575-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/9/tx/tmpPhLijf/R14-18105_kapa-NGv3-PE100-NGv3-sort-9_113231219_129089575-prep-prealign-realign.intervals -l INFO -L 9:113231220-129089575 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-14T23:54Z] INFO  16:54:02,813 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:54Z] INFO  16:54:02,814 HelpFormatter - Date/Time: 2016/04/14 16:54:02
[2016-04-14T23:54Z] INFO  16:54:02,815 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:54Z] INFO  16:54:02,815 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:54Z] INFO  16:54:02,913 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:54Z] INFO  16:54:02,986 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:54Z] GATK: realign ('9', 65507205, 82187750) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-14T23:54Z] INFO  16:54:03,006 IntervalUtils - Processing 15559243 bp from intervals
[2016-04-14T23:54Z] WARN  16:54:03,012 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:54Z] INFO  16:54:03,015 ProgressMeter -     10:50081668    200007.0    30.0 s       2.5 m       20.1%     2.5 m     119.0 s
[2016-04-14T23:54Z] INFO  16:54:03,084 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:54Z] INFO  16:54:03,119 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-14T23:54Z] INFO  16:54:03,140 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:54Z] INFO  16:54:03,193 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-14T23:54Z] INFO  16:54:03,264 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:54Z] INFO  16:54:03,267 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:54Z] INFO  16:54:03,270 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:54Z] INFO  16:54:03,271 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-14T23:54Z] INFO  16:54:03,511 IntervalUtils - Processing 15858356 bp from intervals
[2016-04-14T23:54Z] WARN  16:54:03,516 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:54Z] INFO  16:54:03,597 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:54Z] INFO  16:54:03,798 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:54Z] INFO  16:54:03,800 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:54Z] INFO  16:54:03,801 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:54Z] INFO  16:54:03,802 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-14T23:54Z] INFO  16:54:04,251 ProgressMeter -     10:73594254    200004.0    30.0 s       2.5 m       71.1%    42.0 s      12.0 s
[2016-04-14T23:54Z] INFO  16:54:04,328 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:54Z] INFO  16:54:04,332 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:54Z] INFO  16:54:04,332 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:54Z] INFO  16:54:04,333 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:54Z] INFO  16:54:04,338 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/9/R14-18105_kapa-NGv3-PE100-NGv3-sort-9_32407258_65506776-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/9/tx/tmpnpUmlM/R14-18105_kapa-NGv3-PE100-NGv3-sort-9_32407258_65506776-prep-prealign-realign.intervals -l INFO -L 9:32407259-65506776 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-14T23:54Z] INFO  16:54:04,352 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:54Z] INFO  16:54:04,353 HelpFormatter - Date/Time: 2016/04/14 16:54:04
[2016-04-14T23:54Z] INFO  16:54:04,354 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:54Z] INFO  16:54:04,354 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:54Z] INFO  16:54:04,509 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:54Z] INFO  16:54:04,728 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-14T23:54Z] INFO  16:54:04,737 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:54Z] INFO  16:54:04,750 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:54Z] INFO  16:54:04,754 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:54Z] INFO  16:54:04,756 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:54Z] INFO  16:54:04,756 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:54Z] INFO  16:54:04,761 HelpFormatter - Program Args: -T PrintReads -L 10:127328722-135534747 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/10/tx/tmpGh2OYV/R14-18105_kapa-NGv3-PE100-NGv3-sort-10_127328721_135534747-prep-prealign.bam
[2016-04-14T23:54Z] INFO  16:54:04,770 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:54Z] INFO  16:54:04,771 HelpFormatter - Date/Time: 2016/04/14 16:54:04
[2016-04-14T23:54Z] INFO  16:54:04,772 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:54Z] INFO  16:54:04,772 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:54Z] INFO  16:54:04,813 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-14T23:54Z] INFO  16:54:04,936 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:54Z] INFO  16:54:05,092 IntervalUtils - Processing 33099518 bp from intervals
[2016-04-14T23:54Z] WARN  16:54:05,097 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:54Z] INFO  16:54:05,177 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:54Z] INFO  16:54:05,441 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:54Z] INFO  16:54:05,442 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:54Z] INFO  16:54:05,442 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:54Z] INFO  16:54:05,443 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-14T23:54Z] INFO  16:54:05,772 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@41fd9d8e
[2016-04-14T23:54Z] INFO  16:54:05,892 ProgressMeter -            done    218087.0    33.0 s       2.6 m      100.0%    33.0 s       0.0 s
[2016-04-14T23:54Z] INFO  16:54:05,893 ProgressMeter - Total runtime 33.60 secs, 0.56 min, 0.01 hours
[2016-04-14T23:54Z] INFO  16:54:05,893 MicroScheduler - 625 reads were filtered out during the traversal out of approximately 218712 total reads (0.29%)
[2016-04-14T23:54Z] INFO  16:54:05,894 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:54Z] INFO  16:54:05,894 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:54Z] INFO  16:54:05,894 MicroScheduler -   -> 625 reads (0.29% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:54Z] INFO  16:54:05,906 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:54Z] INFO  16:54:05,909 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:54Z] INFO  16:54:05,910 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:54Z] INFO  16:54:05,911 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:54Z] INFO  16:54:05,915 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/9/R14-18105_kapa-NGv3-PE100-NGv3-sort-9_65507205_82187750-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/9/R14-18105_kapa-NGv3-PE100-NGv3-sort-9_65507205_82187750-prep-prealign-realign.intervals -L 9:65507206-82187750 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/9/tx/tmpfu7j_H/R14-18105_kapa-NGv3-PE100-NGv3-sort-9_65507205_82187750-prep.bam
[2016-04-14T23:54Z] INFO  16:54:05,925 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:54Z] INFO  16:54:05,936 HelpFormatter - Date/Time: 2016/04/14 16:54:05
[2016-04-14T23:54Z] INFO  16:54:05,937 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:54Z] INFO  16:54:05,938 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:54Z] INFO  16:54:06,140 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-14T23:54Z] INFO  16:54:06,195 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:54Z] INFO  16:54:06,221 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:54Z] INFO  16:54:06,230 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:54Z] INFO  16:54:06,288 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-14T23:54Z] INFO  16:54:06,314 IntervalUtils - Processing 8206026 bp from intervals
[2016-04-14T23:54Z] INFO  16:54:06,367 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:54Z] INFO  16:54:06,380 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:54Z] INFO  16:54:06,446 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-14T23:54Z] INFO  16:54:06,461 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:54Z] INFO  16:54:06,803 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:54Z] INFO  16:54:06,815 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:54Z] INFO  16:54:06,816 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:54Z] INFO  16:54:06,816 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:54Z] INFO  16:54:06,836 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:54Z] INFO  16:54:06,912 IntervalUtils - Processing 16680545 bp from intervals
[2016-04-14T23:54Z] WARN  16:54:06,918 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:54Z] INFO  16:54:06,981 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:54Z] INFO  16:54:07,033 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:54Z] INFO  16:54:07,244 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:54Z] INFO  16:54:07,245 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:54Z] INFO  16:54:07,246 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:54Z] INFO  16:54:07,247 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:54Z] INFO  16:54:07,444 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:54Z] INFO  16:54:07,538 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:54Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-10_31137459_46960129-prep-prealign.bam
[2016-04-14T23:54Z] INFO  16:54:07,624 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:54Z] INFO  16:54:07,847 ProgressMeter -            done    390329.0    25.0 s      65.0 s       98.1%    25.0 s       0.0 s
[2016-04-14T23:54Z] INFO  16:54:07,847 ProgressMeter - Total runtime 25.73 secs, 0.43 min, 0.01 hours
[2016-04-14T23:54Z] INFO  16:54:07,851 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 390329 total reads (0.00%)
[2016-04-14T23:54Z] INFO  16:54:07,851 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:54Z] INFO  16:54:07,851 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:54Z] INFO  16:54:07,852 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:54Z] GATK RealignerTargetCreator: R14-18105_kapa-NGv3-PE100-NGv3-sort-10_31137459_46960129-prep-prealign.bam 10:31137460-46960129
[2016-04-14T23:54Z] GATK: RealignerTargetCreator
[2016-04-14T23:54Z] INFO  16:54:09,561 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:54Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-8_141900641_146364022-prep.bam
[2016-04-14T23:54Z] GATK pre-alignment ('11', 0, 15994658) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-14T23:54Z] INFO  16:54:10,918 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:54Z] INFO  16:54:10,922 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:54Z] INFO  16:54:10,923 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:54Z] INFO  16:54:10,923 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:54Z] INFO  16:54:10,928 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/10/R14-18105_kapa-NGv3-PE100-NGv3-sort-10_31137459_46960129-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/10/tx/tmpkHz9__/R14-18105_kapa-NGv3-PE100-NGv3-sort-10_31137459_46960129-prep-prealign-realign.intervals -l INFO -L 10:31137460-46960129 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-14T23:54Z] INFO  16:54:10,950 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:54Z] INFO  16:54:10,951 HelpFormatter - Date/Time: 2016/04/14 16:54:10
[2016-04-14T23:54Z] INFO  16:54:10,952 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:54Z] INFO  16:54:10,952 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:54Z] INFO  16:54:11,038 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:54Z] INFO  16:54:11,198 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-14T23:54Z] INFO  16:54:11,209 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:54Z] INFO  16:54:11,250 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.04
[2016-04-14T23:54Z] INFO  16:54:11,504 IntervalUtils - Processing 15822670 bp from intervals
[2016-04-14T23:54Z] WARN  16:54:11,509 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:54Z] INFO  16:54:11,575 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:54Z] INFO  16:54:11,724 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:54Z] INFO  16:54:11,725 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:54Z] INFO  16:54:11,726 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:54Z] INFO  16:54:11,727 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-14T23:54Z] INFO  16:54:13,784 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:54Z] INFO  16:54:13,788 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:54Z] INFO  16:54:13,788 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:54Z] INFO  16:54:13,789 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:54Z] INFO  16:54:13,793 HelpFormatter - Program Args: -T PrintReads -L 11:1-15994658 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/11/tx/tmpk0Kaeo/R14-18105_kapa-NGv3-PE100-NGv3-sort-11_0_15994658-prep-prealign.bam
[2016-04-14T23:54Z] INFO  16:54:13,803 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:54Z] INFO  16:54:13,803 HelpFormatter - Date/Time: 2016/04/14 16:54:13
[2016-04-14T23:54Z] INFO  16:54:13,803 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:54Z] INFO  16:54:13,804 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:54Z] INFO  16:54:13,972 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:54Z] INFO  16:54:14,612 ProgressMeter -            done   1.5573214E7    18.0 s       1.0 s      100.0%    18.0 s       0.0 s
[2016-04-14T23:54Z] INFO  16:54:14,613 ProgressMeter - Total runtime 18.10 secs, 0.30 min, 0.01 hours
[2016-04-14T23:54Z] INFO  16:54:14,617 MicroScheduler - 20087 reads were filtered out during the traversal out of approximately 206965 total reads (9.71%)
[2016-04-14T23:54Z] INFO  16:54:14,617 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:54Z] INFO  16:54:14,617 MicroScheduler -   -> 586 reads (0.28% of total) failing BadMateFilter
[2016-04-14T23:54Z] INFO  16:54:14,618 MicroScheduler -   -> 16118 reads (7.79% of total) failing DuplicateReadFilter
[2016-04-14T23:54Z] INFO  16:54:14,618 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-14T23:54Z] INFO  16:54:14,618 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:54Z] INFO  16:54:14,618 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-14T23:54Z] INFO  16:54:14,619 MicroScheduler -   -> 3383 reads (1.63% of total) failing MappingQualityZeroFilter
[2016-04-14T23:54Z] INFO  16:54:14,619 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:54Z] INFO  16:54:14,619 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-14T23:54Z] INFO  16:54:14,619 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-14T23:54Z] INFO  16:54:15,160 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-14T23:54Z] INFO  16:54:15,233 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:54Z] INFO  16:54:15,242 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:54Z] INFO  16:54:15,302 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-14T23:54Z] INFO  16:54:15,316 IntervalUtils - Processing 15994658 bp from intervals
[2016-04-14T23:54Z] INFO  16:54:15,393 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:54Z] INFO  16:54:15,689 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:54Z] INFO  16:54:15,690 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:54Z] INFO  16:54:15,691 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:54Z] INFO  16:54:15,692 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:54Z] INFO  16:54:15,717 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:54Z] INFO  16:54:15,868 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:54Z] INFO  16:54:16,082 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:54Z] GATK: realign ('10', 15561288, 31134502) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-14T23:54Z] INFO  16:54:16,319 ProgressMeter -            done   1.5510117E7    19.0 s       1.0 s      100.0%    19.0 s       0.0 s
[2016-04-14T23:54Z] INFO  16:54:16,320 ProgressMeter - Total runtime 19.99 secs, 0.33 min, 0.01 hours
[2016-04-14T23:54Z] INFO  16:54:16,324 MicroScheduler - 30581 reads were filtered out during the traversal out of approximately 309178 total reads (9.89%)
[2016-04-14T23:54Z] INFO  16:54:16,325 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:54Z] INFO  16:54:16,325 MicroScheduler -   -> 715 reads (0.23% of total) failing BadMateFilter
[2016-04-14T23:54Z] INFO  16:54:16,326 MicroScheduler -   -> 24190 reads (7.82% of total) failing DuplicateReadFilter
[2016-04-14T23:54Z] INFO  16:54:16,327 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-14T23:54Z] INFO  16:54:16,327 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:54Z] INFO  16:54:16,328 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-14T23:54Z] INFO  16:54:16,328 MicroScheduler -   -> 5676 reads (1.84% of total) failing MappingQualityZeroFilter
[2016-04-14T23:54Z] INFO  16:54:16,329 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:54Z] INFO  16:54:16,330 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-14T23:54Z] INFO  16:54:16,330 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-14T23:54Z] INFO  16:54:16,502 ProgressMeter -     10:89265241    100003.0    30.0 s       5.0 m       70.5%    42.0 s      12.0 s
[2016-04-14T23:54Z] INFO  16:54:17,732 ProgressMeter -     9:136535680    400005.0    60.0 s       2.5 m       61.4%    97.0 s      37.0 s
[2016-04-14T23:54Z] INFO  16:54:17,828 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:54Z] GATK: realign ('9', 97718189, 113228306) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-14T23:54Z] INFO  16:54:18,468 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@5fe152b7
[2016-04-14T23:54Z] INFO  16:54:18,569 ProgressMeter -            done    371701.0    44.0 s     119.0 s      100.0%    44.0 s       0.0 s
[2016-04-14T23:54Z] INFO  16:54:18,569 ProgressMeter - Total runtime 44.34 secs, 0.74 min, 0.01 hours
[2016-04-14T23:54Z] INFO  16:54:18,569 MicroScheduler - 164 reads were filtered out during the traversal out of approximately 371865 total reads (0.04%)
[2016-04-14T23:54Z] INFO  16:54:18,570 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:54Z] INFO  16:54:18,570 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:54Z] INFO  16:54:18,570 MicroScheduler -   -> 164 reads (0.04% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:54Z] INFO  16:54:18,972 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:54Z] INFO  16:54:18,976 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:54Z] INFO  16:54:18,977 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:54Z] INFO  16:54:18,977 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:54Z] INFO  16:54:18,983 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/10/R14-18105_kapa-NGv3-PE100-NGv3-sort-10_15561288_31134502-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/10/R14-18105_kapa-NGv3-PE100-NGv3-sort-10_15561288_31134502-prep-prealign-realign.intervals -L 10:15561289-31134502 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/10/tx/tmp7th1cS/R14-18105_kapa-NGv3-PE100-NGv3-sort-10_15561288_31134502-prep.bam
[2016-04-14T23:54Z] INFO  16:54:18,997 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:54Z] INFO  16:54:19,002 HelpFormatter - Date/Time: 2016/04/14 16:54:18
[2016-04-14T23:54Z] INFO  16:54:19,003 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:54Z] INFO  16:54:19,004 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:54Z] INFO  16:54:19,277 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:54Z] INFO  16:54:19,412 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:54Z] INFO  16:54:19,425 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:54Z] INFO  16:54:19,498 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-14T23:54Z] INFO  16:54:19,895 IntervalUtils - Processing 15573214 bp from intervals
[2016-04-14T23:54Z] WARN  16:54:19,900 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:54Z] INFO  16:54:19,994 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:54Z] INFO  16:54:20,061 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:54Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-10_62539923_78084243-prep-prealign.bam
[2016-04-14T23:54Z] INFO  16:54:20,151 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:54Z] INFO  16:54:20,152 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:54Z] INFO  16:54:20,153 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:54Z] INFO  16:54:20,154 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:54Z] INFO  16:54:20,342 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:54Z] INFO  16:54:20,518 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:54Z] INFO  16:54:20,596 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:54Z] INFO  16:54:20,599 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:54Z] INFO  16:54:20,599 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:54Z] INFO  16:54:20,599 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:54Z] INFO  16:54:20,602 ProgressMeter -            done   1.5529389E7    20.0 s       1.0 s      100.0%    20.0 s       0.0 s
[2016-04-14T23:54Z] INFO  16:54:20,603 ProgressMeter - Total runtime 20.63 secs, 0.34 min, 0.01 hours
[2016-04-14T23:54Z] INFO  16:54:20,608 MicroScheduler - 50269 reads were filtered out during the traversal out of approximately 330345 total reads (15.22%)
[2016-04-14T23:54Z] INFO  16:54:20,609 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:54Z] INFO  16:54:20,609 MicroScheduler -   -> 741 reads (0.22% of total) failing BadMateFilter
[2016-04-14T23:54Z] INFO  16:54:20,609 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/9/R14-18105_kapa-NGv3-PE100-NGv3-sort-9_97718189_113228306-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/9/R14-18105_kapa-NGv3-PE100-NGv3-sort-9_97718189_113228306-prep-prealign-realign.intervals -L 9:97718190-113228306 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/9/tx/tmpb4FDo6/R14-18105_kapa-NGv3-PE100-NGv3-sort-9_97718189_113228306-prep.bam
[2016-04-14T23:54Z] INFO  16:54:20,610 MicroScheduler -   -> 24863 reads (7.53% of total) failing DuplicateReadFilter
[2016-04-14T23:54Z] INFO  16:54:20,611 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-14T23:54Z] INFO  16:54:20,611 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:54Z] INFO  16:54:20,612 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-14T23:54Z] INFO  16:54:20,613 MicroScheduler -   -> 24665 reads (7.47% of total) failing MappingQualityZeroFilter
[2016-04-14T23:54Z] INFO  16:54:20,613 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:54Z] INFO  16:54:20,614 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-14T23:54Z] INFO  16:54:20,615 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-14T23:54Z] INFO  16:54:20,619 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:54Z] INFO  16:54:20,619 HelpFormatter - Date/Time: 2016/04/14 16:54:20
[2016-04-14T23:54Z] INFO  16:54:20,620 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:54Z] INFO  16:54:20,620 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:54Z] INFO  16:54:20,869 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:54Z] INFO  16:54:20,987 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:54Z] INFO  16:54:20,997 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:54Z] INFO  16:54:21,070 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-14T23:54Z] GATK RealignerTargetCreator: R14-18105_kapa-NGv3-PE100-NGv3-sort-10_62539923_78084243-prep-prealign.bam 10:62539924-78084243
[2016-04-14T23:54Z] GATK: RealignerTargetCreator
[2016-04-14T23:54Z] INFO  16:54:21,366 IntervalUtils - Processing 15510117 bp from intervals
[2016-04-14T23:54Z] WARN  16:54:21,371 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:54Z] INFO  16:54:21,466 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:54Z] INFO  16:54:21,589 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:54Z] INFO  16:54:21,591 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:54Z] INFO  16:54:21,591 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:54Z] INFO  16:54:21,603 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:54Z] INFO  16:54:21,867 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:54Z] INFO  16:54:22,029 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:54Z] INFO  16:54:22,069 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@41fd9d8e
[2016-04-14T23:54Z] INFO  16:54:22,162 ProgressMeter -            done    411647.0    49.0 s     119.0 s      100.0%    49.0 s       0.0 s
[2016-04-14T23:54Z] INFO  16:54:22,163 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:54Z] INFO  16:54:22,163 ProgressMeter - Total runtime 49.21 secs, 0.82 min, 0.01 hours
[2016-04-14T23:54Z] INFO  16:54:22,163 MicroScheduler - 187 reads were filtered out during the traversal out of approximately 411834 total reads (0.05%)
[2016-04-14T23:54Z] INFO  16:54:22,164 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:54Z] INFO  16:54:22,164 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:54Z] INFO  16:54:22,164 MicroScheduler -   -> 187 reads (0.05% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:54Z] GATK: realign ('9', 82188172, 97717561) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-14T23:54Z] INFO  16:54:22,587 ProgressMeter -            done   1.5559243E7    19.0 s       1.0 s      100.0%    19.0 s       0.0 s
[2016-04-14T23:54Z] INFO  16:54:22,588 ProgressMeter - Total runtime 19.32 secs, 0.32 min, 0.01 hours
[2016-04-14T23:54Z] INFO  16:54:22,593 MicroScheduler - 21783 reads were filtered out during the traversal out of approximately 231019 total reads (9.43%)
[2016-04-14T23:54Z] INFO  16:54:22,594 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:54Z] INFO  16:54:22,595 MicroScheduler -   -> 615 reads (0.27% of total) failing BadMateFilter
[2016-04-14T23:54Z] INFO  16:54:22,596 MicroScheduler -   -> 17895 reads (7.75% of total) failing DuplicateReadFilter
[2016-04-14T23:54Z] INFO  16:54:22,596 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-14T23:54Z] INFO  16:54:22,597 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:54Z] INFO  16:54:22,597 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-14T23:54Z] INFO  16:54:22,598 MicroScheduler -   -> 3273 reads (1.42% of total) failing MappingQualityZeroFilter
[2016-04-14T23:54Z] INFO  16:54:22,599 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:54Z] INFO  16:54:22,599 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-14T23:54Z] INFO  16:54:22,600 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-14T23:54Z] INFO  16:54:23,435 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:54Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-10_46960410_62493077-prep-prealign.bam
[2016-04-14T23:54Z] INFO  16:54:24,071 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:54Z] GATK: realign ('10', 0, 15559243) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-14T23:54Z] INFO  16:54:24,251 ProgressMeter -    10:100904201    200002.0    30.0 s       2.5 m       39.7%    75.0 s      45.0 s
[2016-04-14T23:54Z] INFO  16:54:24,268 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:54Z] INFO  16:54:24,272 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:54Z] INFO  16:54:24,273 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:54Z] INFO  16:54:24,273 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:54Z] INFO  16:54:24,278 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/10/R14-18105_kapa-NGv3-PE100-NGv3-sort-10_62539923_78084243-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/10/tx/tmpT3sl2S/R14-18105_kapa-NGv3-PE100-NGv3-sort-10_62539923_78084243-prep-prealign-realign.intervals -l INFO -L 10:62539924-78084243 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-14T23:54Z] INFO  16:54:24,310 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@41fd9d8e
[2016-04-14T23:54Z] INFO  16:54:24,314 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:54Z] INFO  16:54:24,315 HelpFormatter - Date/Time: 2016/04/14 16:54:24
[2016-04-14T23:54Z] INFO  16:54:24,316 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:54Z] INFO  16:54:24,317 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:54Z] INFO  16:54:24,432 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:54Z] INFO  16:54:24,515 ProgressMeter -            done    257369.0    38.0 s       2.5 m      100.0%    38.0 s       0.0 s
[2016-04-14T23:54Z] INFO  16:54:24,516 ProgressMeter - Total runtime 38.06 secs, 0.63 min, 0.01 hours
[2016-04-14T23:54Z] INFO  16:54:24,517 MicroScheduler - 155 reads were filtered out during the traversal out of approximately 257524 total reads (0.06%)
[2016-04-14T23:54Z] INFO  16:54:24,517 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:54Z] INFO  16:54:24,517 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:54Z] INFO  16:54:24,518 MicroScheduler -   -> 155 reads (0.06% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:54Z] INFO  16:54:24,631 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-14T23:54Z] INFO  16:54:24,663 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:54Z] INFO  16:54:24,733 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-14T23:54Z] GATK RealignerTargetCreator: R14-18105_kapa-NGv3-PE100-NGv3-sort-10_46960410_62493077-prep-prealign.bam 10:46960411-62493077
[2016-04-14T23:54Z] GATK: RealignerTargetCreator
[2016-04-14T23:54Z] INFO  16:54:24,975 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:54Z] INFO  16:54:24,978 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:54Z] INFO  16:54:24,979 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:54Z] INFO  16:54:24,979 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:54Z] INFO  16:54:24,984 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/9/R14-18105_kapa-NGv3-PE100-NGv3-sort-9_82188172_97717561-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/9/R14-18105_kapa-NGv3-PE100-NGv3-sort-9_82188172_97717561-prep-prealign-realign.intervals -L 9:82188173-97717561 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/9/tx/tmppUtzMO/R14-18105_kapa-NGv3-PE100-NGv3-sort-9_82188172_97717561-prep.bam
[2016-04-14T23:54Z] INFO  16:54:24,995 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:54Z] INFO  16:54:24,996 HelpFormatter - Date/Time: 2016/04/14 16:54:24
[2016-04-14T23:54Z] INFO  16:54:24,997 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:54Z] INFO  16:54:24,997 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:54Z] INFO  16:54:25,012 IntervalUtils - Processing 15544320 bp from intervals
[2016-04-14T23:54Z] WARN  16:54:25,017 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:54Z] INFO  16:54:25,089 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:54Z] INFO  16:54:25,219 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:54Z] INFO  16:54:25,279 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:54Z] INFO  16:54:25,280 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:54Z] INFO  16:54:25,291 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:54Z] INFO  16:54:25,291 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-14T23:54Z] INFO  16:54:25,307 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:54Z] INFO  16:54:25,316 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:54Z] INFO  16:54:25,382 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-14T23:54Z] INFO  16:54:25,397 ProgressMeter -            done   1.5858356E7    21.0 s       1.0 s      100.0%    21.0 s       0.0 s
[2016-04-14T23:54Z] INFO  16:54:25,397 ProgressMeter - Total runtime 21.60 secs, 0.36 min, 0.01 hours
[2016-04-14T23:54Z] INFO  16:54:25,401 MicroScheduler - 31241 reads were filtered out during the traversal out of approximately 363236 total reads (8.60%)
[2016-04-14T23:54Z] INFO  16:54:25,402 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:54Z] INFO  16:54:25,403 MicroScheduler -   -> 796 reads (0.22% of total) failing BadMateFilter
[2016-04-14T23:54Z] INFO  16:54:25,403 MicroScheduler -   -> 28393 reads (7.82% of total) failing DuplicateReadFilter
[2016-04-14T23:54Z] INFO  16:54:25,403 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-14T23:54Z] INFO  16:54:25,403 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:54Z] INFO  16:54:25,404 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-14T23:54Z] INFO  16:54:25,404 MicroScheduler -   -> 2052 reads (0.56% of total) failing MappingQualityZeroFilter
[2016-04-14T23:54Z] INFO  16:54:25,404 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:54Z] INFO  16:54:25,404 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-14T23:54Z] INFO  16:54:25,404 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-14T23:54Z] INFO  16:54:25,892 IntervalUtils - Processing 15529389 bp from intervals
[2016-04-14T23:54Z] WARN  16:54:25,899 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:54Z] INFO  16:54:25,906 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:54Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-10_78316966_93841258-prep-prealign.bam
[2016-04-14T23:54Z] INFO  16:54:26,066 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:54Z] INFO  16:54:26,089 ProgressMeter -            done    243980.0    18.0 s      77.0 s      100.0%    18.0 s       0.0 s
[2016-04-14T23:54Z] INFO  16:54:26,090 ProgressMeter - Total runtime 18.85 secs, 0.31 min, 0.01 hours
[2016-04-14T23:54Z] INFO  16:54:26,095 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 243980 total reads (0.00%)
[2016-04-14T23:54Z] INFO  16:54:26,096 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:54Z] INFO  16:54:26,096 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:54Z] INFO  16:54:26,098 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:54Z] INFO  16:54:26,229 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:54Z] INFO  16:54:26,229 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:54Z] INFO  16:54:26,230 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:54Z] INFO  16:54:26,230 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:54Z] INFO  16:54:26,398 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:54Z] INFO  16:54:26,559 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:54Z] GATK RealignerTargetCreator: R14-18105_kapa-NGv3-PE100-NGv3-sort-10_78316966_93841258-prep-prealign.bam 10:78316967-93841258
[2016-04-14T23:54Z] GATK: RealignerTargetCreator
[2016-04-14T23:54Z] INFO  16:54:26,909 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:54Z] GATK: realign ('9', 113231219, 129089575) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-14T23:54Z] INFO  16:54:27,053 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:54Z] INFO  16:54:27,056 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:54Z] INFO  16:54:27,057 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:54Z] INFO  16:54:27,057 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:54Z] INFO  16:54:27,062 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/10/R14-18105_kapa-NGv3-PE100-NGv3-sort-10_0_15559243-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/10/R14-18105_kapa-NGv3-PE100-NGv3-sort-10_0_15559243-prep-prealign-realign.intervals -L 10:1-15559243 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/10/tx/tmpGeHNYG/R14-18105_kapa-NGv3-PE100-NGv3-sort-10_0_15559243-prep.bam
[2016-04-14T23:54Z] INFO  16:54:27,079 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:54Z] INFO  16:54:27,080 HelpFormatter - Date/Time: 2016/04/14 16:54:27
[2016-04-14T23:54Z] INFO  16:54:27,080 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:54Z] INFO  16:54:27,081 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:54Z] INFO  16:54:27,353 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:54Z] INFO  16:54:27,519 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:54Z] INFO  16:54:27,534 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:54Z] INFO  16:54:27,598 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-14T23:54Z] INFO  16:54:27,657 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:54Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-9_65507205_82187750-prep.bam
[2016-04-14T23:54Z] INFO  16:54:27,915 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:54Z] INFO  16:54:27,923 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:54Z] INFO  16:54:27,924 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:54Z] INFO  16:54:27,925 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:54Z] INFO  16:54:27,929 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/10/R14-18105_kapa-NGv3-PE100-NGv3-sort-10_46960410_62493077-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/10/tx/tmp1vhlcx/R14-18105_kapa-NGv3-PE100-NGv3-sort-10_46960410_62493077-prep-prealign-realign.intervals -l INFO -L 10:46960411-62493077 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-14T23:54Z] INFO  16:54:27,950 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:54Z] INFO  16:54:27,950 HelpFormatter - Date/Time: 2016/04/14 16:54:27
[2016-04-14T23:54Z] INFO  16:54:27,951 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:54Z] INFO  16:54:27,952 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:54Z] INFO  16:54:28,035 IntervalUtils - Processing 15559243 bp from intervals
[2016-04-14T23:54Z] WARN  16:54:28,040 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:54Z] INFO  16:54:28,049 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:54Z] INFO  16:54:28,104 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:54Z] INFO  16:54:28,220 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:54Z] INFO  16:54:28,222 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:54Z] INFO  16:54:28,222 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:54Z] INFO  16:54:28,223 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:54Z] INFO  16:54:28,287 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-14T23:54Z] INFO  16:54:28,309 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:54Z] INFO  16:54:28,370 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:54Z] INFO  16:54:28,370 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-14T23:54Z] GATK pre-alignment ('11', 16007749, 31531554) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-14T23:54Z] INFO  16:54:28,617 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:54Z] INFO  16:54:28,715 ProgressMeter -            done   1.582267E7    16.0 s       1.0 s      100.0%    16.0 s       0.0 s
[2016-04-14T23:54Z] INFO  16:54:28,716 ProgressMeter - Total runtime 16.99 secs, 0.28 min, 0.00 hours
[2016-04-14T23:54Z] INFO  16:54:28,720 MicroScheduler - 57011 reads were filtered out during the traversal out of approximately 219644 total reads (25.96%)
[2016-04-14T23:54Z] INFO  16:54:28,721 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:54Z] INFO  16:54:28,722 MicroScheduler -   -> 930 reads (0.42% of total) failing BadMateFilter
[2016-04-14T23:54Z] INFO  16:54:28,723 MicroScheduler -   -> 14174 reads (6.45% of total) failing DuplicateReadFilter
[2016-04-14T23:54Z] INFO  16:54:28,723 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-14T23:54Z] INFO  16:54:28,724 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:54Z] INFO  16:54:28,724 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-14T23:54Z] INFO  16:54:28,725 MicroScheduler -   -> 41907 reads (19.08% of total) failing MappingQualityZeroFilter
[2016-04-14T23:54Z] INFO  16:54:28,726 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:54Z] INFO  16:54:28,726 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-14T23:54Z] INFO  16:54:28,727 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-14T23:54Z] INFO  16:54:28,793 IntervalUtils - Processing 15532667 bp from intervals
[2016-04-14T23:54Z] WARN  16:54:28,809 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:54Z] INFO  16:54:28,891 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:54Z] INFO  16:54:29,094 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:54Z] INFO  16:54:29,095 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:54Z] INFO  16:54:29,096 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:54Z] INFO  16:54:29,097 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-14T23:54Z] INFO  16:54:30,152 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:54Z] INFO  16:54:30,155 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:54Z] INFO  16:54:30,156 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:54Z] INFO  16:54:30,156 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:54Z] INFO  16:54:30,161 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/9/R14-18105_kapa-NGv3-PE100-NGv3-sort-9_113231219_129089575-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/9/R14-18105_kapa-NGv3-PE100-NGv3-sort-9_113231219_129089575-prep-prealign-realign.intervals -L 9:113231220-129089575 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/9/tx/tmpWrRBqQ/R14-18105_kapa-NGv3-PE100-NGv3-sort-9_113231219_129089575-prep.bam
[2016-04-14T23:54Z] INFO  16:54:30,170 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:54Z] INFO  16:54:30,171 HelpFormatter - Date/Time: 2016/04/14 16:54:30
[2016-04-14T23:54Z] INFO  16:54:30,172 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:54Z] INFO  16:54:30,173 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:54Z] INFO  16:54:30,241 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:54Z] INFO  16:54:30,244 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:54Z] INFO  16:54:30,245 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:54Z] INFO  16:54:30,245 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:54Z] INFO  16:54:30,250 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/10/R14-18105_kapa-NGv3-PE100-NGv3-sort-10_78316966_93841258-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/10/tx/tmpaxU5d9/R14-18105_kapa-NGv3-PE100-NGv3-sort-10_78316966_93841258-prep-prealign-realign.intervals -l INFO -L 10:78316967-93841258 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-14T23:54Z] INFO  16:54:30,259 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:54Z] INFO  16:54:30,260 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:54Z] INFO  16:54:30,261 HelpFormatter - Date/Time: 2016/04/14 16:54:30
[2016-04-14T23:54Z] INFO  16:54:30,262 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:54Z] INFO  16:54:30,262 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:54Z] GATK: realign ('10', 31137459, 46960129) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-14T23:54Z] INFO  16:54:30,347 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:54Z] INFO  16:54:30,364 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:54Z] INFO  16:54:30,504 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:54Z] INFO  16:54:30,513 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:54Z] INFO  16:54:30,559 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-14T23:54Z] INFO  16:54:30,568 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:54Z] INFO  16:54:30,598 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-14T23:54Z] INFO  16:54:30,608 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.04
[2016-04-14T23:54Z] INFO  16:54:30,847 IntervalUtils - Processing 15524292 bp from intervals
[2016-04-14T23:54Z] WARN  16:54:30,853 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:54Z] INFO  16:54:30,920 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:54Z] INFO  16:54:30,954 IntervalUtils - Processing 15858356 bp from intervals
[2016-04-14T23:54Z] WARN  16:54:30,960 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:54Z] INFO  16:54:30,969 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@7172f77a
[2016-04-14T23:54Z] INFO  16:54:31,031 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:54Z] INFO  16:54:31,171 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:54Z] INFO  16:54:31,172 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:54Z] INFO  16:54:31,173 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:54Z] INFO  16:54:31,174 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-14T23:54Z] INFO  16:54:31,189 ProgressMeter -            done    181282.0    24.0 s       2.2 m       99.4%    24.0 s       0.0 s
[2016-04-14T23:54Z] INFO  16:54:31,190 ProgressMeter - Total runtime 24.38 secs, 0.41 min, 0.01 hours
[2016-04-14T23:54Z] INFO  16:54:31,190 MicroScheduler - 167 reads were filtered out during the traversal out of approximately 181449 total reads (0.09%)
[2016-04-14T23:54Z] INFO  16:54:31,190 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:54Z] INFO  16:54:31,191 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:54Z] INFO  16:54:31,191 MicroScheduler -   -> 167 reads (0.09% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:54Z] INFO  16:54:31,222 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:54Z] INFO  16:54:31,222 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:54Z] INFO  16:54:31,223 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:54Z] INFO  16:54:31,223 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:54Z] INFO  16:54:31,388 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:54Z] INFO  16:54:31,433 ProgressMeter -    10:124034740    200002.0    30.0 s       2.5 m       79.3%    37.0 s       7.0 s
[2016-04-14T23:54Z] INFO  16:54:31,585 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:54Z] INFO  16:54:31,671 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:54Z] INFO  16:54:31,674 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:54Z] INFO  16:54:31,675 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:54Z] INFO  16:54:31,683 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:54Z] INFO  16:54:31,688 HelpFormatter - Program Args: -T PrintReads -L 11:16007750-31531554 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/11/tx/tmpR1kizE/R14-18105_kapa-NGv3-PE100-NGv3-sort-11_16007749_31531554-prep-prealign.bam
[2016-04-14T23:54Z] INFO  16:54:31,703 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:54Z] INFO  16:54:31,714 HelpFormatter - Date/Time: 2016/04/14 16:54:31
[2016-04-14T23:54Z] INFO  16:54:31,715 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:54Z] INFO  16:54:31,716 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:54Z] INFO  16:54:31,935 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:54Z] INFO  16:54:32,937 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:54Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-10_127328721_135534747-prep-prealign.bam
[2016-04-14T23:54Z] INFO  16:54:33,197 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-14T23:54Z] INFO  16:54:33,247 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:54Z] INFO  16:54:33,251 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:54Z] INFO  16:54:33,252 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:54Z] INFO  16:54:33,252 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:54Z] INFO  16:54:33,257 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/10/R14-18105_kapa-NGv3-PE100-NGv3-sort-10_31137459_46960129-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/10/R14-18105_kapa-NGv3-PE100-NGv3-sort-10_31137459_46960129-prep-prealign-realign.intervals -L 10:31137460-46960129 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/10/tx/tmpoAlO80/R14-18105_kapa-NGv3-PE100-NGv3-sort-10_31137459_46960129-prep.bam
[2016-04-14T23:54Z] INFO  16:54:33,267 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:54Z] INFO  16:54:33,273 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:54Z] INFO  16:54:33,274 HelpFormatter - Date/Time: 2016/04/14 16:54:33
[2016-04-14T23:54Z] INFO  16:54:33,275 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:54Z] INFO  16:54:33,275 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:54Z] INFO  16:54:33,286 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:54Z] INFO  16:54:33,337 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-14T23:54Z] INFO  16:54:33,356 IntervalUtils - Processing 15523805 bp from intervals
[2016-04-14T23:54Z] INFO  16:54:33,434 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:54Z] INFO  16:54:33,539 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:54Z] GATK RealignerTargetCreator: R14-18105_kapa-NGv3-PE100-NGv3-sort-10_127328721_135534747-prep-prealign.bam 10:127328722-135534747
[2016-04-14T23:54Z] GATK: RealignerTargetCreator
[2016-04-14T23:54Z] INFO  16:54:33,688 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:54Z] INFO  16:54:33,708 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:54Z] INFO  16:54:33,722 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:54Z] INFO  16:54:33,723 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:54Z] INFO  16:54:33,724 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:54Z] INFO  16:54:33,725 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:54Z] INFO  16:54:33,753 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:54Z] INFO  16:54:33,792 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-14T23:54Z] INFO  16:54:33,951 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:54Z] INFO  16:54:34,239 IntervalUtils - Processing 15822670 bp from intervals
[2016-04-14T23:54Z] WARN  16:54:34,246 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:54Z] INFO  16:54:34,315 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:54Z] INFO  16:54:34,461 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:54Z] INFO  16:54:34,462 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:54Z] INFO  16:54:34,463 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:54Z] INFO  16:54:34,464 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:54Z] INFO  16:54:34,618 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:54Z] INFO  16:54:34,788 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:54Z] INFO  16:54:35,463 ProgressMeter -      9:65505449   3.307959E7    30.0 s       0.0 s      100.0%    30.0 s       0.0 s
[2016-04-14T23:54Z] INFO  16:54:35,924 ProgressMeter -            done   3.3099518E7    30.0 s       0.0 s      100.0%    30.0 s       0.0 s
[2016-04-14T23:54Z] INFO  16:54:35,925 ProgressMeter - Total runtime 30.48 secs, 0.51 min, 0.01 hours
[2016-04-14T23:54Z] INFO  16:54:35,929 MicroScheduler - 164845 reads were filtered out during the traversal out of approximately 497065 total reads (33.16%)
[2016-04-14T23:54Z] INFO  16:54:35,930 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:54Z] INFO  16:54:35,931 MicroScheduler -   -> 632 reads (0.13% of total) failing BadMateFilter
[2016-04-14T23:54Z] INFO  16:54:35,942 MicroScheduler -   -> 28738 reads (5.78% of total) failing DuplicateReadFilter
[2016-04-14T23:54Z] INFO  16:54:35,943 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-14T23:54Z] INFO  16:54:35,943 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:54Z] INFO  16:54:35,943 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-14T23:54Z] INFO  16:54:35,944 MicroScheduler -   -> 135475 reads (27.25% of total) failing MappingQualityZeroFilter
[2016-04-14T23:54Z] INFO  16:54:35,944 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:54Z] INFO  16:54:35,944 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-14T23:54Z] INFO  16:54:35,944 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-14T23:54Z] INFO  16:54:36,587 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:54Z] INFO  16:54:36,597 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:54Z] INFO  16:54:36,598 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:54Z] INFO  16:54:36,598 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:54Z] INFO  16:54:36,603 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/10/R14-18105_kapa-NGv3-PE100-NGv3-sort-10_127328721_135534747-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/10/tx/tmp_1Qzkp/R14-18105_kapa-NGv3-PE100-NGv3-sort-10_127328721_135534747-prep-prealign-realign.intervals -l INFO -L 10:127328722-135534747 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-14T23:54Z] INFO  16:54:36,612 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:54Z] INFO  16:54:36,613 HelpFormatter - Date/Time: 2016/04/14 16:54:36
[2016-04-14T23:54Z] INFO  16:54:36,613 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:54Z] INFO  16:54:36,613 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:54Z] INFO  16:54:36,733 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:54Z] INFO  16:54:36,995 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-14T23:54Z] INFO  16:54:37,004 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:54Z] INFO  16:54:37,099 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.09
[2016-04-14T23:54Z] INFO  16:54:37,216 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:54Z] GATK: realign ('9', 32407258, 65506776) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-14T23:54Z] INFO  16:54:37,423 IntervalUtils - Processing 8206026 bp from intervals
[2016-04-14T23:54Z] WARN  16:54:37,428 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:54Z] INFO  16:54:37,530 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:54Z] INFO  16:54:37,739 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:54Z] INFO  16:54:37,740 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:54Z] INFO  16:54:37,740 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:54Z] INFO  16:54:37,741 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-14T23:54Z] INFO  16:54:37,784 ProgressMeter -            done    205498.0    17.0 s      85.0 s      100.0%    17.0 s       0.0 s
[2016-04-14T23:54Z] INFO  16:54:37,785 ProgressMeter - Total runtime 17.63 secs, 0.29 min, 0.00 hours
[2016-04-14T23:54Z] INFO  16:54:37,788 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 205498 total reads (0.00%)
[2016-04-14T23:54Z] INFO  16:54:37,789 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:54Z] INFO  16:54:37,789 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:54Z] INFO  16:54:37,789 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:54Z] INFO  16:54:39,319 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:54Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-10_15561288_31134502-prep.bam
[2016-04-14T23:54Z] GATK pre-alignment ('11', 31541602, 47074069) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-14T23:54Z] INFO  16:54:40,254 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@41fd9d8e
[2016-04-14T23:54Z] INFO  16:54:40,334 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:54Z] INFO  16:54:40,339 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:54Z] INFO  16:54:40,339 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:54Z] INFO  16:54:40,340 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:54Z] INFO  16:54:40,344 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/9/R14-18105_kapa-NGv3-PE100-NGv3-sort-9_32407258_65506776-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/9/R14-18105_kapa-NGv3-PE100-NGv3-sort-9_32407258_65506776-prep-prealign-realign.intervals -L 9:32407259-65506776 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/9/tx/tmpEMjt0R/R14-18105_kapa-NGv3-PE100-NGv3-sort-9_32407258_65506776-prep.bam
[2016-04-14T23:54Z] INFO  16:54:40,362 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:54Z] INFO  16:54:40,363 HelpFormatter - Date/Time: 2016/04/14 16:54:40
[2016-04-14T23:54Z] INFO  16:54:40,363 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:54Z] INFO  16:54:40,364 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:54Z] INFO  16:54:40,397 ProgressMeter -            done    310903.0    38.0 s       2.1 m      100.0%    38.0 s       0.0 s
[2016-04-14T23:54Z] INFO  16:54:40,413 ProgressMeter - Total runtime 39.00 secs, 0.65 min, 0.01 hours
[2016-04-14T23:54Z] INFO  16:54:40,414 MicroScheduler - 155 reads were filtered out during the traversal out of approximately 311058 total reads (0.05%)
[2016-04-14T23:54Z] INFO  16:54:40,415 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:54Z] INFO  16:54:40,416 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:54Z] INFO  16:54:40,417 MicroScheduler -   -> 155 reads (0.05% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:54Z] INFO  16:54:40,613 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:54Z] INFO  16:54:40,764 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:54Z] INFO  16:54:40,774 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:54Z] INFO  16:54:40,835 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-14T23:54Z] INFO  16:54:41,303 IntervalUtils - Processing 33099518 bp from intervals
[2016-04-14T23:54Z] WARN  16:54:41,307 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:54Z] INFO  16:54:41,418 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:54Z] INFO  16:54:41,658 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:54Z] INFO  16:54:41,663 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:54Z] INFO  16:54:41,670 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:54Z] INFO  16:54:41,671 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:54Z] INFO  16:54:41,848 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:54Z] INFO  16:54:41,854 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:54Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-10_111628371_127265443-prep-prealign.bam
[2016-04-14T23:54Z] INFO  16:54:42,092 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:54Z] INFO  16:54:42,761 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:54Z] INFO  16:54:42,763 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:54Z] INFO  16:54:42,764 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:54Z] INFO  16:54:42,764 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:54Z] INFO  16:54:42,768 HelpFormatter - Program Args: -T PrintReads -L 11:31541603-47074069 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/11/tx/tmpLtX9Nt/R14-18105_kapa-NGv3-PE100-NGv3-sort-11_31541602_47074069-prep-prealign.bam
[2016-04-14T23:54Z] INFO  16:54:42,783 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:54Z] INFO  16:54:42,784 HelpFormatter - Date/Time: 2016/04/14 16:54:42
[2016-04-14T23:54Z] INFO  16:54:42,784 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:54Z] INFO  16:54:42,784 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:54Z] INFO  16:54:42,939 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:54Z] GATK RealignerTargetCreator: R14-18105_kapa-NGv3-PE100-NGv3-sort-10_111628371_127265443-prep-prealign.bam 10:111628372-127265443
[2016-04-14T23:54Z] GATK: RealignerTargetCreator
[2016-04-14T23:54Z] INFO  16:54:44,001 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-14T23:54Z] INFO  16:54:44,064 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:54Z] INFO  16:54:44,073 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:54Z] INFO  16:54:44,119 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-14T23:54Z] INFO  16:54:44,164 IntervalUtils - Processing 15532467 bp from intervals
[2016-04-14T23:54Z] INFO  16:54:44,248 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:54Z] INFO  16:54:44,382 ProgressMeter -            done    307361.0    22.0 s      74.0 s      100.0%    22.0 s       0.0 s
[2016-04-14T23:54Z] INFO  16:54:44,383 ProgressMeter - Total runtime 22.79 secs, 0.38 min, 0.01 hours
[2016-04-14T23:54Z] INFO  16:54:44,386 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 307361 total reads (0.00%)
[2016-04-14T23:54Z] INFO  16:54:44,387 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:54Z] INFO  16:54:44,387 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:54Z] INFO  16:54:44,387 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:54Z] INFO  16:54:44,562 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:54Z] INFO  16:54:44,562 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:54Z] INFO  16:54:44,563 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:54Z] INFO  16:54:44,563 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:54Z] INFO  16:54:44,585 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:54Z] INFO  16:54:44,748 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:54Z] INFO  16:54:45,726 ProgressMeter -      11:1251812    200007.0    30.0 s       2.5 m        7.8%     6.4 m       5.9 m
[2016-04-14T23:54Z] INFO  16:54:45,761 ProgressMeter -            done    229830.0    17.0 s      76.0 s      100.0%    17.0 s       0.0 s
[2016-04-14T23:54Z] INFO  16:54:45,762 ProgressMeter - Total runtime 17.54 secs, 0.29 min, 0.00 hours
[2016-04-14T23:54Z] INFO  16:54:45,765 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 229830 total reads (0.00%)
[2016-04-14T23:54Z] INFO  16:54:45,766 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:54Z] INFO  16:54:45,766 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:54Z] INFO  16:54:45,766 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:54Z] INFO  16:54:45,866 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:54Z] INFO  16:54:45,870 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:54Z] INFO  16:54:45,870 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:54Z] INFO  16:54:45,871 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:54Z] INFO  16:54:45,876 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/10/R14-18105_kapa-NGv3-PE100-NGv3-sort-10_111628371_127265443-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/10/tx/tmpa0evMs/R14-18105_kapa-NGv3-PE100-NGv3-sort-10_111628371_127265443-prep-prealign-realign.intervals -l INFO -L 10:111628372-127265443 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-14T23:54Z] INFO  16:54:45,885 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:54Z] INFO  16:54:45,886 HelpFormatter - Date/Time: 2016/04/14 16:54:45
[2016-04-14T23:54Z] INFO  16:54:45,886 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:54Z] INFO  16:54:45,887 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:54Z] INFO  16:54:45,977 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:54Z] INFO  16:54:45,988 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:54Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-9_97718189_113228306-prep.bam
[2016-04-14T23:54Z] INFO  16:54:46,287 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-14T23:54Z] INFO  16:54:46,297 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:54Z] INFO  16:54:46,373 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-14T23:54Z] INFO  16:54:46,728 IntervalUtils - Processing 15637072 bp from intervals
[2016-04-14T23:54Z] WARN  16:54:46,732 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:54Z] INFO  16:54:46,803 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:54Z] GATK pre-alignment ('11', 47158866, 62678572) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-14T23:54Z] INFO  16:54:47,025 ProgressMeter -            done   1.554432E7    21.0 s       1.0 s      100.0%    21.0 s       0.0 s
[2016-04-14T23:54Z] INFO  16:54:47,026 ProgressMeter - Total runtime 21.75 secs, 0.36 min, 0.01 hours
[2016-04-14T23:54Z] INFO  16:54:47,030 MicroScheduler - 36993 reads were filtered out during the traversal out of approximately 373801 total reads (9.90%)
[2016-04-14T23:54Z] INFO  16:54:47,031 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:54Z] INFO  16:54:47,032 MicroScheduler -   -> 773 reads (0.21% of total) failing BadMateFilter
[2016-04-14T23:54Z] INFO  16:54:47,032 MicroScheduler -   -> 29052 reads (7.77% of total) failing DuplicateReadFilter
[2016-04-14T23:54Z] INFO  16:54:47,033 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-14T23:54Z] INFO  16:54:47,034 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:54Z] INFO  16:54:47,034 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-14T23:54Z] INFO  16:54:47,035 MicroScheduler -   -> 7168 reads (1.92% of total) failing MappingQualityZeroFilter
[2016-04-14T23:54Z] INFO  16:54:47,036 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:54Z] INFO  16:54:47,036 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-14T23:54Z] INFO  16:54:47,037 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-14T23:54Z] INFO  16:54:47,052 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:54Z] INFO  16:54:47,054 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:54Z] INFO  16:54:47,055 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:54Z] INFO  16:54:47,055 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-14T23:54Z] INFO  16:54:47,219 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:54Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-10_0_15559243-prep.bam
[2016-04-14T23:54Z] INFO  16:54:47,740 ProgressMeter -     9:140094316    700012.0    90.0 s       2.2 m       90.8%    99.0 s       9.0 s
[2016-04-14T23:54Z] GATK pre-alignment ('11', 62744265, 78270665) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-14T23:54Z] INFO  16:54:48,368 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:54Z] GATK: realign ('10', 62539923, 78084243) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-14T23:54Z] INFO  16:54:49,119 ProgressMeter -            done    328621.0    22.0 s      69.0 s      100.0%    22.0 s       0.0 s
[2016-04-14T23:54Z] INFO  16:54:49,119 ProgressMeter - Total runtime 22.89 secs, 0.38 min, 0.01 hours
[2016-04-14T23:54Z] INFO  16:54:49,123 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 328621 total reads (0.00%)
[2016-04-14T23:54Z] INFO  16:54:49,123 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:54Z] INFO  16:54:49,123 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:54Z] INFO  16:54:49,124 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:54Z] INFO  16:54:49,590 ProgressMeter -            done   1.5532667E7    20.0 s       1.0 s      100.0%    20.0 s       0.0 s
[2016-04-14T23:54Z] INFO  16:54:49,591 ProgressMeter - Total runtime 20.50 secs, 0.34 min, 0.01 hours
[2016-04-14T23:54Z] INFO  16:54:49,594 MicroScheduler - 155088 reads were filtered out during the traversal out of approximately 414426 total reads (37.42%)
[2016-04-14T23:54Z] INFO  16:54:49,595 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:54Z] INFO  16:54:49,595 MicroScheduler -   -> 605 reads (0.15% of total) failing BadMateFilter
[2016-04-14T23:54Z] INFO  16:54:49,595 MicroScheduler -   -> 24091 reads (5.81% of total) failing DuplicateReadFilter
[2016-04-14T23:54Z] INFO  16:54:49,596 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-14T23:54Z] INFO  16:54:49,596 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:54Z] INFO  16:54:49,596 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-14T23:54Z] INFO  16:54:49,596 MicroScheduler -   -> 130392 reads (31.46% of total) failing MappingQualityZeroFilter
[2016-04-14T23:54Z] INFO  16:54:49,596 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:54Z] INFO  16:54:49,597 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-14T23:54Z] INFO  16:54:49,597 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-14T23:54Z] INFO  16:54:49,663 ProgressMeter -            done   1.5524292E7    18.0 s       1.0 s      100.0%    18.0 s       0.0 s
[2016-04-14T23:54Z] INFO  16:54:49,664 ProgressMeter - Total runtime 18.49 secs, 0.31 min, 0.01 hours
[2016-04-14T23:54Z] INFO  16:54:49,668 MicroScheduler - 44754 reads were filtered out during the traversal out of approximately 258909 total reads (17.29%)
[2016-04-14T23:54Z] INFO  16:54:49,669 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:54Z] INFO  16:54:49,670 MicroScheduler -   -> 611 reads (0.24% of total) failing BadMateFilter
[2016-04-14T23:54Z] INFO  16:54:49,670 MicroScheduler -   -> 18493 reads (7.14% of total) failing DuplicateReadFilter
[2016-04-14T23:54Z] INFO  16:54:49,671 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-14T23:54Z] INFO  16:54:49,672 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:54Z] INFO  16:54:49,672 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-14T23:54Z] INFO  16:54:49,673 MicroScheduler -   -> 25650 reads (9.91% of total) failing MappingQualityZeroFilter
[2016-04-14T23:54Z] INFO  16:54:49,673 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:54Z] INFO  16:54:49,674 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-14T23:54Z] INFO  16:54:49,675 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-14T23:54Z] INFO  16:54:49,799 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:54Z] INFO  16:54:49,802 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:54Z] INFO  16:54:49,803 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:54Z] INFO  16:54:49,804 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:54Z] INFO  16:54:49,808 HelpFormatter - Program Args: -T PrintReads -L 11:47158867-62678572 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/11/tx/tmpfWmxyR/R14-18105_kapa-NGv3-PE100-NGv3-sort-11_47158866_62678572-prep-prealign.bam
[2016-04-14T23:54Z] INFO  16:54:49,824 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:54Z] INFO  16:54:49,825 HelpFormatter - Date/Time: 2016/04/14 16:54:49
[2016-04-14T23:54Z] INFO  16:54:49,826 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:54Z] INFO  16:54:49,826 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:54Z] INFO  16:54:49,987 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:54Z] INFO  16:54:50,500 ProgressMeter -            done   8206026.0    12.0 s       1.0 s      100.0%    12.0 s       0.0 s
[2016-04-14T23:54Z] INFO  16:54:50,501 ProgressMeter - Total runtime 12.76 secs, 0.21 min, 0.00 hours
[2016-04-14T23:54Z] INFO  16:54:50,505 MicroScheduler - 16299 reads were filtered out during the traversal out of approximately 182505 total reads (8.93%)
[2016-04-14T23:54Z] INFO  16:54:50,506 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:54Z] INFO  16:54:50,507 MicroScheduler -   -> 424 reads (0.23% of total) failing BadMateFilter
[2016-04-14T23:54Z] INFO  16:54:50,507 MicroScheduler -   -> 14200 reads (7.78% of total) failing DuplicateReadFilter
[2016-04-14T23:54Z] INFO  16:54:50,508 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-14T23:54Z] INFO  16:54:50,508 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:54Z] INFO  16:54:50,509 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-14T23:54Z] INFO  16:54:50,510 MicroScheduler -   -> 1675 reads (0.92% of total) failing MappingQualityZeroFilter
[2016-04-14T23:54Z] INFO  16:54:50,510 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:54Z] INFO  16:54:50,511 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-14T23:54Z] INFO  16:54:50,511 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-14T23:54Z] INFO  16:54:50,714 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:54Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-9_82188172_97717561-prep.bam
[2016-04-14T23:54Z] INFO  16:54:50,908 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:54Z] INFO  16:54:50,912 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:54Z] INFO  16:54:50,912 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:54Z] INFO  16:54:50,913 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:54Z] INFO  16:54:50,918 HelpFormatter - Program Args: -T PrintReads -L 11:62744266-78270665 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/11/tx/tmpii9PEr/R14-18105_kapa-NGv3-PE100-NGv3-sort-11_62744265_78270665-prep-prealign.bam
[2016-04-14T23:54Z] INFO  16:54:50,927 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:54Z] INFO  16:54:50,928 HelpFormatter - Date/Time: 2016/04/14 16:54:50
[2016-04-14T23:54Z] INFO  16:54:50,929 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:54Z] INFO  16:54:50,929 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:54Z] INFO  16:54:51,029 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:54Z] GATK: realign ('10', 46960410, 62493077) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-14T23:54Z] INFO  16:54:51,085 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:54Z] INFO  16:54:51,144 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-14T23:54Z] INFO  16:54:51,155 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:54Z] GATK: realign ('10', 78316966, 93841258) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-14T23:54Z] INFO  16:54:51,206 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:54Z] INFO  16:54:51,231 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:54Z] INFO  16:54:51,279 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-14T23:54Z] INFO  16:54:51,293 IntervalUtils - Processing 15519706 bp from intervals
[2016-04-14T23:54Z] INFO  16:54:51,400 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:54Z] INFO  16:54:51,538 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:54Z] INFO  16:54:51,551 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:54Z] INFO  16:54:51,552 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:54Z] INFO  16:54:51,552 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:54Z] INFO  16:54:51,556 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/10/R14-18105_kapa-NGv3-PE100-NGv3-sort-10_62539923_78084243-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/10/R14-18105_kapa-NGv3-PE100-NGv3-sort-10_62539923_78084243-prep-prealign-realign.intervals -L 10:62539924-78084243 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/10/tx/tmpbj8c59/R14-18105_kapa-NGv3-PE100-NGv3-sort-10_62539923_78084243-prep.bam
[2016-04-14T23:54Z] INFO  16:54:51,574 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:54Z] INFO  16:54:51,585 HelpFormatter - Date/Time: 2016/04/14 16:54:51
[2016-04-14T23:54Z] INFO  16:54:51,586 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:54Z] INFO  16:54:51,587 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:54Z] INFO  16:54:51,720 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:54Z] INFO  16:54:51,722 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:54Z] INFO  16:54:51,722 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:54Z] INFO  16:54:51,723 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:54Z] GATK pre-alignment ('11', 78277177, 93796886) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-14T23:54Z] INFO  16:54:51,751 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:54Z] INFO  16:54:51,834 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:54Z] INFO  16:54:51,881 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:54Z] INFO  16:54:51,921 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:54Z] GATK: realign ('10', 127328721, 135534747) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-14T23:54Z] INFO  16:54:51,965 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:54Z] INFO  16:54:51,975 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:54Z] INFO  16:54:52,048 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-14T23:54Z] INFO  16:54:52,119 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-14T23:54Z] INFO  16:54:52,200 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:54Z] INFO  16:54:52,209 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:54Z] INFO  16:54:52,265 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-14T23:54Z] INFO  16:54:52,280 IntervalUtils - Processing 15526400 bp from intervals
[2016-04-14T23:54Z] INFO  16:54:52,359 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:54Z] INFO  16:54:52,482 IntervalUtils - Processing 15544320 bp from intervals
[2016-04-14T23:54Z] WARN  16:54:52,487 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:54Z] INFO  16:54:52,565 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:54Z] INFO  16:54:52,700 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:54Z] INFO  16:54:52,701 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:54Z] INFO  16:54:52,702 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:54Z] INFO  16:54:52,703 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:54Z] INFO  16:54:52,809 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:54Z] INFO  16:54:52,810 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:54Z] INFO  16:54:52,810 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:54Z] INFO  16:54:52,811 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:54Z] INFO  16:54:52,860 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:54Z] INFO  16:54:52,945 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:54Z] INFO  16:54:53,086 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:54Z] INFO  16:54:53,109 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:54Z] INFO  16:54:53,968 ProgressMeter -            done    218087.0    19.0 s      89.0 s      100.0%    19.0 s       0.0 s
[2016-04-14T23:54Z] INFO  16:54:53,968 ProgressMeter - Total runtime 19.51 secs, 0.33 min, 0.01 hours
[2016-04-14T23:54Z] INFO  16:54:53,972 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 218087 total reads (0.00%)
[2016-04-14T23:54Z] INFO  16:54:53,973 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:54Z] INFO  16:54:53,973 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:54Z] INFO  16:54:53,974 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:54Z] INFO  16:54:54,281 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:54Z] INFO  16:54:54,284 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:54Z] INFO  16:54:54,285 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:54Z] INFO  16:54:54,286 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:54Z] INFO  16:54:54,291 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/10/R14-18105_kapa-NGv3-PE100-NGv3-sort-10_46960410_62493077-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/10/R14-18105_kapa-NGv3-PE100-NGv3-sort-10_46960410_62493077-prep-prealign-realign.intervals -L 10:46960411-62493077 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/10/tx/tmp8jr7L4/R14-18105_kapa-NGv3-PE100-NGv3-sort-10_46960410_62493077-prep.bam
[2016-04-14T23:54Z] INFO  16:54:54,316 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:54Z] INFO  16:54:54,317 HelpFormatter - Date/Time: 2016/04/14 16:54:54
[2016-04-14T23:54Z] INFO  16:54:54,318 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:54Z] INFO  16:54:54,318 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:54Z] INFO  16:54:54,319 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:54Z] INFO  16:54:54,321 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:54Z] INFO  16:54:54,322 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:54Z] INFO  16:54:54,322 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:54Z] INFO  16:54:54,333 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/10/R14-18105_kapa-NGv3-PE100-NGv3-sort-10_78316966_93841258-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/10/R14-18105_kapa-NGv3-PE100-NGv3-sort-10_78316966_93841258-prep-prealign-realign.intervals -L 10:78316967-93841258 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/10/tx/tmpTyvcM2/R14-18105_kapa-NGv3-PE100-NGv3-sort-10_78316966_93841258-prep.bam
[2016-04-14T23:54Z] INFO  16:54:54,357 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:54Z] INFO  16:54:54,358 HelpFormatter - Date/Time: 2016/04/14 16:54:54
[2016-04-14T23:54Z] INFO  16:54:54,359 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:54Z] INFO  16:54:54,360 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:54Z] INFO  16:54:54,620 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:54Z] INFO  16:54:54,626 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:54Z] INFO  16:54:54,746 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:54Z] INFO  16:54:54,751 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:54Z] INFO  16:54:54,756 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:54Z] INFO  16:54:54,761 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:54Z] INFO  16:54:54,805 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-14T23:54Z] INFO  16:54:54,824 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-14T23:54Z] INFO  16:54:55,108 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:54Z] INFO  16:54:55,111 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:54Z] INFO  16:54:55,112 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:54Z] INFO  16:54:55,113 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:54Z] INFO  16:54:55,117 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/10/R14-18105_kapa-NGv3-PE100-NGv3-sort-10_127328721_135534747-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/10/R14-18105_kapa-NGv3-PE100-NGv3-sort-10_127328721_135534747-prep-prealign-realign.intervals -L 10:127328722-135534747 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/10/tx/tmpPJNibe/R14-18105_kapa-NGv3-PE100-NGv3-sort-10_127328721_135534747-prep.bam
[2016-04-14T23:54Z] INFO  16:54:55,132 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:54Z] INFO  16:54:55,133 HelpFormatter - Date/Time: 2016/04/14 16:54:55
[2016-04-14T23:54Z] INFO  16:54:55,133 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:54Z] INFO  16:54:55,134 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:54Z] INFO  16:54:55,170 ProgressMeter -    10:106976731    500007.0    60.0 s       2.0 m       73.8%    81.0 s      21.0 s
[2016-04-14T23:54Z] INFO  16:54:55,193 IntervalUtils - Processing 15524292 bp from intervals
[2016-04-14T23:54Z] INFO  16:54:55,196 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:54Z] INFO  16:54:55,200 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:54Z] INFO  16:54:55,200 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:54Z] INFO  16:54:55,201 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:54Z] WARN  16:54:55,201 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:54Z] INFO  16:54:55,205 HelpFormatter - Program Args: -T PrintReads -L 11:78277178-93796886 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/11/tx/tmpZPWCHH/R14-18105_kapa-NGv3-PE100-NGv3-sort-11_78277177_93796886-prep-prealign.bam
[2016-04-14T23:54Z] INFO  16:54:55,218 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:54Z] INFO  16:54:55,219 HelpFormatter - Date/Time: 2016/04/14 16:54:55
[2016-04-14T23:54Z] INFO  16:54:55,220 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:54Z] INFO  16:54:55,220 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:54Z] INFO  16:54:55,247 IntervalUtils - Processing 15532667 bp from intervals
[2016-04-14T23:54Z] WARN  16:54:55,253 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:54Z] INFO  16:54:55,267 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:54Z] INFO  16:54:55,326 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:54Z] INFO  16:54:55,329 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:54Z] INFO  16:54:55,380 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:54Z] INFO  16:54:55,381 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:54Z] INFO  16:54:55,382 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:54Z] INFO  16:54:55,383 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:54Z] INFO  16:54:55,393 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:54Z] INFO  16:54:55,410 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:54Z] INFO  16:54:55,416 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:54Z] INFO  16:54:55,417 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:54Z] INFO  16:54:55,418 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:54Z] INFO  16:54:55,418 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:54Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-10_31137459_46960129-prep.bam
[2016-04-14T23:54Z] INFO  16:54:55,475 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:54Z] INFO  16:54:55,492 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:54Z] INFO  16:54:55,554 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:54Z] INFO  16:54:55,562 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-14T23:54Z] INFO  16:54:55,615 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:54Z] INFO  16:54:55,769 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:54Z] INFO  16:54:55,780 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:54Z] INFO  16:54:55,951 IntervalUtils - Processing 8206026 bp from intervals
[2016-04-14T23:54Z] WARN  16:54:55,956 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:54Z] INFO  16:54:56,072 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:54Z] GATK pre-alignment ('11', 93797496, 109964158) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-14T23:54Z] INFO  16:54:56,205 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:54Z] INFO  16:54:56,217 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:54Z] INFO  16:54:56,218 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:54Z] INFO  16:54:56,219 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:54Z] INFO  16:54:56,311 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@52f3b59
[2016-04-14T23:54Z] INFO  16:54:56,332 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-14T23:54Z] INFO  16:54:56,383 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:54Z] INFO  16:54:56,390 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:54Z] INFO  16:54:56,393 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:54Z] INFO  16:54:56,447 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-14T23:54Z] INFO  16:54:56,462 IntervalUtils - Processing 15519709 bp from intervals
[2016-04-14T23:54Z] INFO  16:54:56,468 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:54Z] INFO  16:54:56,480 ProgressMeter -            done    518970.0    62.0 s     119.0 s      100.0%    62.0 s       0.0 s
[2016-04-14T23:54Z] INFO  16:54:56,480 ProgressMeter - Total runtime 62.25 secs, 1.04 min, 0.02 hours
[2016-04-14T23:54Z] INFO  16:54:56,481 MicroScheduler - 204 reads were filtered out during the traversal out of approximately 519174 total reads (0.04%)
[2016-04-14T23:54Z] INFO  16:54:56,481 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:54Z] INFO  16:54:56,481 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:54Z] INFO  16:54:56,482 MicroScheduler -   -> 204 reads (0.04% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:54Z] INFO  16:54:56,560 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:54Z] INFO  16:54:56,864 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:54Z] INFO  16:54:56,865 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:54Z] INFO  16:54:56,865 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:54Z] INFO  16:54:56,866 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:54Z] INFO  16:54:56,902 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:54Z] INFO  16:54:57,171 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:54Z] INFO  16:54:57,357 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@7172f77a
[2016-04-14T23:54Z] INFO  16:54:57,519 ProgressMeter -            done    857787.0   100.0 s     117.0 s       99.3%   100.0 s       0.0 s
[2016-04-14T23:54Z] INFO  16:54:57,519 ProgressMeter - Total runtime 100.64 secs, 1.68 min, 0.03 hours
[2016-04-14T23:54Z] INFO  16:54:57,520 MicroScheduler - 404 reads were filtered out during the traversal out of approximately 858191 total reads (0.05%)
[2016-04-14T23:54Z] INFO  16:54:57,520 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:54Z] INFO  16:54:57,521 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:54Z] INFO  16:54:57,521 MicroScheduler -   -> 404 reads (0.05% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:54Z] INFO  16:54:57,654 ProgressMeter -            done    361709.0    26.0 s      73.0 s      100.0%    26.0 s       0.0 s
[2016-04-14T23:54Z] INFO  16:54:57,654 ProgressMeter - Total runtime 26.43 secs, 0.44 min, 0.01 hours
[2016-04-14T23:54Z] INFO  16:54:57,658 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 361709 total reads (0.00%)
[2016-04-14T23:54Z] INFO  16:54:57,658 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:54Z] INFO  16:54:57,658 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:54Z] INFO  16:54:57,659 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:54Z] INFO  16:54:57,797 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:54Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-10_93851586_111625070-prep-prealign.bam
[2016-04-14T23:54Z] INFO  16:54:58,983 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:54Z] INFO  16:54:58,987 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:54Z] INFO  16:54:58,988 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:54Z] INFO  16:54:58,988 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:54Z] INFO  16:54:58,994 HelpFormatter - Program Args: -T PrintReads -L 11:93797497-109964158 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/11/tx/tmp4KUkDw/R14-18105_kapa-NGv3-PE100-NGv3-sort-11_93797496_109964158-prep-prealign.bam
[2016-04-14T23:54Z] INFO  16:54:59,030 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:54Z] INFO  16:54:59,031 HelpFormatter - Date/Time: 2016/04/14 16:54:58
[2016-04-14T23:54Z] INFO  16:54:59,042 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:54Z] INFO  16:54:59,048 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:54Z] INFO  16:54:59,078 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:54Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-9_129097484_141213431-prep-prealign.bam
[2016-04-14T23:54Z] INFO  16:54:59,224 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:54Z] INFO  16:54:59,246 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:54Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-9_113231219_129089575-prep.bam
[2016-04-14T23:54Z] GATK RealignerTargetCreator: R14-18105_kapa-NGv3-PE100-NGv3-sort-10_93851586_111625070-prep-prealign.bam 10:93851587-111625070
[2016-04-14T23:54Z] GATK: RealignerTargetCreator
[2016-04-14T23:55Z] INFO  16:55:00,389 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-14T23:55Z] INFO  16:55:00,461 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:55Z] INFO  16:55:00,470 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:55Z] INFO  16:55:00,516 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-14T23:55Z] INFO  16:55:00,535 IntervalUtils - Processing 16166662 bp from intervals
[2016-04-14T23:55Z] GATK pre-alignment ('11', 110001730, 125514538) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-14T23:55Z] INFO  16:55:00,609 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:55Z] INFO  16:55:01,002 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:55Z] INFO  16:55:01,003 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:55Z] INFO  16:55:01,004 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:55Z] INFO  16:55:01,004 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:55Z] INFO  16:55:01,052 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:55Z] INFO  16:55:01,285 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:55Z] GATK RealignerTargetCreator: R14-18105_kapa-NGv3-PE100-NGv3-sort-9_129097484_141213431-prep-prealign.bam 9:129097485-141213431
[2016-04-14T23:55Z] GATK: RealignerTargetCreator
[2016-04-14T23:55Z] INFO  16:55:02,300 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@32d5a4c6
[2016-04-14T23:55Z] INFO  16:55:02,410 ProgressMeter -            done    209461.0    28.0 s       2.3 m      100.0%    28.0 s       0.0 s
[2016-04-14T23:55Z] INFO  16:55:02,411 ProgressMeter - Total runtime 28.69 secs, 0.48 min, 0.01 hours
[2016-04-14T23:55Z] INFO  16:55:02,411 MicroScheduler - 154 reads were filtered out during the traversal out of approximately 209615 total reads (0.07%)
[2016-04-14T23:55Z] INFO  16:55:02,411 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:55Z] INFO  16:55:02,412 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:55Z] INFO  16:55:02,412 MicroScheduler -   -> 154 reads (0.07% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:55Z] INFO  16:55:02,604 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:55Z] INFO  16:55:02,608 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:55Z] INFO  16:55:02,609 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:55Z] INFO  16:55:02,610 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:55Z] INFO  16:55:02,615 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/10/R14-18105_kapa-NGv3-PE100-NGv3-sort-10_93851586_111625070-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/10/tx/tmplfbYH4/R14-18105_kapa-NGv3-PE100-NGv3-sort-10_93851586_111625070-prep-prealign-realign.intervals -l INFO -L 10:93851587-111625070 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-14T23:55Z] INFO  16:55:02,637 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:55Z] INFO  16:55:02,637 HelpFormatter - Date/Time: 2016/04/14 16:55:02
[2016-04-14T23:55Z] INFO  16:55:02,637 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:55Z] INFO  16:55:02,638 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:55Z] INFO  16:55:02,758 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:55Z] INFO  16:55:03,037 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-14T23:55Z] INFO  16:55:03,047 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:55Z] INFO  16:55:03,152 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.10
[2016-04-14T23:55Z] INFO  16:55:03,555 IntervalUtils - Processing 17773484 bp from intervals
[2016-04-14T23:55Z] WARN  16:55:03,561 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:55Z] INFO  16:55:03,627 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:55Z] INFO  16:55:03,813 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:55Z] INFO  16:55:03,816 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:55Z] INFO  16:55:03,817 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:55Z] INFO  16:55:03,817 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:55Z] INFO  16:55:03,821 HelpFormatter - Program Args: -T PrintReads -L 11:110001731-125514538 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/11/tx/tmpX36dZn/R14-18105_kapa-NGv3-PE100-NGv3-sort-11_110001730_125514538-prep-prealign.bam
[2016-04-14T23:55Z] INFO  16:55:03,831 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:55Z] INFO  16:55:03,831 HelpFormatter - Date/Time: 2016/04/14 16:55:03
[2016-04-14T23:55Z] INFO  16:55:03,831 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:55Z] INFO  16:55:03,832 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:55Z] INFO  16:55:03,931 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:55Z] INFO  16:55:03,932 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:55Z] INFO  16:55:03,933 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:55Z] INFO  16:55:03,933 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-14T23:55Z] INFO  16:55:03,967 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:55Z] INFO  16:55:04,096 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:55Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-11_16007749_31531554-prep-prealign.bam
[2016-04-14T23:55Z] GATK RealignerTargetCreator: R14-18105_kapa-NGv3-PE100-NGv3-sort-11_16007749_31531554-prep-prealign.bam 11:16007750-31531554
[2016-04-14T23:55Z] GATK: RealignerTargetCreator
[2016-04-14T23:55Z] INFO  16:55:04,928 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:55Z] INFO  16:55:04,932 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:55Z] INFO  16:55:04,933 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:55Z] INFO  16:55:04,934 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:55Z] INFO  16:55:04,940 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/9/R14-18105_kapa-NGv3-PE100-NGv3-sort-9_129097484_141213431-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/9/tx/tmpE1oOHt/R14-18105_kapa-NGv3-PE100-NGv3-sort-9_129097484_141213431-prep-prealign-realign.intervals -l INFO -L 9:129097485-141213431 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-14T23:55Z] INFO  16:55:04,958 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:55Z] INFO  16:55:04,966 HelpFormatter - Date/Time: 2016/04/14 16:55:04
[2016-04-14T23:55Z] INFO  16:55:04,967 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:55Z] INFO  16:55:04,967 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:55Z] INFO  16:55:05,018 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-14T23:55Z] INFO  16:55:05,098 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:55Z] INFO  16:55:05,141 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:55Z] INFO  16:55:05,150 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:55Z] INFO  16:55:05,224 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-14T23:55Z] INFO  16:55:05,238 IntervalUtils - Processing 15512808 bp from intervals
[2016-04-14T23:55Z] INFO  16:55:05,308 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-14T23:55Z] INFO  16:55:05,326 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:55Z] INFO  16:55:05,357 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:55Z] INFO  16:55:05,381 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-14T23:55Z] INFO  16:55:05,629 IntervalUtils - Processing 12115947 bp from intervals
[2016-04-14T23:55Z] WARN  16:55:05,635 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:55Z] INFO  16:55:05,648 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:55Z] INFO  16:55:05,649 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:55Z] INFO  16:55:05,650 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:55Z] INFO  16:55:05,651 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:55Z] INFO  16:55:05,665 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:55Z] INFO  16:55:05,746 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:55Z] INFO  16:55:05,911 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:55Z] INFO  16:55:05,947 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:55Z] INFO  16:55:05,949 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:55Z] INFO  16:55:05,959 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:55Z] INFO  16:55:05,960 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-14T23:55Z] INFO  16:55:07,647 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:55Z] INFO  16:55:07,650 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:55Z] INFO  16:55:07,651 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:55Z] INFO  16:55:07,651 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:55Z] INFO  16:55:07,656 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/11/R14-18105_kapa-NGv3-PE100-NGv3-sort-11_16007749_31531554-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/11/tx/tmpJSLzq9/R14-18105_kapa-NGv3-PE100-NGv3-sort-11_16007749_31531554-prep-prealign-realign.intervals -l INFO -L 11:16007750-31531554 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-14T23:55Z] INFO  16:55:07,666 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:55Z] INFO  16:55:07,677 HelpFormatter - Date/Time: 2016/04/14 16:55:07
[2016-04-14T23:55Z] INFO  16:55:07,678 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:55Z] INFO  16:55:07,679 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:55Z] INFO  16:55:07,818 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:55Z] INFO  16:55:08,036 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-14T23:55Z] INFO  16:55:08,046 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:55Z] INFO  16:55:08,101 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-14T23:55Z] INFO  16:55:08,344 ProgressMeter -            done   1.5637072E7    21.0 s       1.0 s      100.0%    21.0 s       0.0 s
[2016-04-14T23:55Z] INFO  16:55:08,345 ProgressMeter - Total runtime 21.29 secs, 0.35 min, 0.01 hours
[2016-04-14T23:55Z] INFO  16:55:08,349 MicroScheduler - 35728 reads were filtered out during the traversal out of approximately 312895 total reads (11.42%)
[2016-04-14T23:55Z] INFO  16:55:08,350 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:55Z] INFO  16:55:08,351 MicroScheduler -   -> 731 reads (0.23% of total) failing BadMateFilter
[2016-04-14T23:55Z] INFO  16:55:08,351 MicroScheduler -   -> 24112 reads (7.71% of total) failing DuplicateReadFilter
[2016-04-14T23:55Z] INFO  16:55:08,352 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-14T23:55Z] INFO  16:55:08,353 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:55Z] INFO  16:55:08,353 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-14T23:55Z] INFO  16:55:08,354 MicroScheduler -   -> 10885 reads (3.48% of total) failing MappingQualityZeroFilter
[2016-04-14T23:55Z] INFO  16:55:08,354 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:55Z] INFO  16:55:08,355 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-14T23:55Z] INFO  16:55:08,356 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-14T23:55Z] INFO  16:55:08,410 IntervalUtils - Processing 15523805 bp from intervals
[2016-04-14T23:55Z] WARN  16:55:08,426 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:55Z] INFO  16:55:08,554 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:55Z] INFO  16:55:08,846 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:55Z] INFO  16:55:08,846 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:55Z] INFO  16:55:08,847 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:55Z] INFO  16:55:08,847 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-14T23:55Z] INFO  16:55:09,665 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:55Z] GATK: realign ('10', 111628371, 127265443) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-14T23:55Z] INFO  16:55:10,471 ProgressMeter -            done    181282.0    14.0 s      78.0 s       99.4%    14.0 s       0.0 s
[2016-04-14T23:55Z] INFO  16:55:10,472 ProgressMeter - Total runtime 14.26 secs, 0.24 min, 0.00 hours
[2016-04-14T23:55Z] INFO  16:55:10,476 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 181282 total reads (0.00%)
[2016-04-14T23:55Z] INFO  16:55:10,477 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:55Z] INFO  16:55:10,478 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:55Z] INFO  16:55:10,478 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:55Z] INFO  16:55:11,687 ProgressMeter -      9:65503688    400009.0    30.0 s      75.0 s      100.0%    30.0 s       0.0 s
[2016-04-14T23:55Z] INFO  16:55:11,859 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:55Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-10_127328721_135534747-prep.bam
[2016-04-14T23:55Z] INFO  16:55:12,146 ProgressMeter -            done    494702.0    30.0 s      61.0 s      100.0%    30.0 s       0.0 s
[2016-04-14T23:55Z] INFO  16:55:12,147 ProgressMeter - Total runtime 30.48 secs, 0.51 min, 0.01 hours
[2016-04-14T23:55Z] INFO  16:55:12,150 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 494702 total reads (0.00%)
[2016-04-14T23:55Z] INFO  16:55:12,151 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:55Z] INFO  16:55:12,151 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:55Z] INFO  16:55:12,152 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:55Z] INFO  16:55:12,223 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:55Z] INFO  16:55:12,226 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:55Z] INFO  16:55:12,227 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:55Z] INFO  16:55:12,227 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:55Z] INFO  16:55:12,232 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/10/R14-18105_kapa-NGv3-PE100-NGv3-sort-10_111628371_127265443-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/10/R14-18105_kapa-NGv3-PE100-NGv3-sort-10_111628371_127265443-prep-prealign-realign.intervals -L 10:111628372-127265443 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/10/tx/tmptFPhsA/R14-18105_kapa-NGv3-PE100-NGv3-sort-10_111628371_127265443-prep.bam
[2016-04-14T23:55Z] INFO  16:55:12,242 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:55Z] INFO  16:55:12,247 HelpFormatter - Date/Time: 2016/04/14 16:55:12
[2016-04-14T23:55Z] INFO  16:55:12,247 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:55Z] INFO  16:55:12,248 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:55Z] GATK pre-alignment ('11', 125523640, 135006516) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-14T23:55Z] INFO  16:55:12,451 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:55Z] INFO  16:55:12,527 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:55Z] INFO  16:55:12,536 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:55Z] INFO  16:55:12,585 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-14T23:55Z] INFO  16:55:12,902 IntervalUtils - Processing 15637072 bp from intervals
[2016-04-14T23:55Z] WARN  16:55:12,909 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:55Z] INFO  16:55:13,008 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:55Z] INFO  16:55:13,134 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:55Z] INFO  16:55:13,136 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:55Z] INFO  16:55:13,136 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:55Z] INFO  16:55:13,137 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:55Z] INFO  16:55:13,308 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:55Z] INFO  16:55:13,449 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:55Z] INFO  16:55:13,776 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:55Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-9_32407258_65506776-prep.bam
[2016-04-14T23:55Z] INFO  16:55:14,817 ProgressMeter -            done    257369.0    19.0 s      75.0 s      100.0%    19.0 s       0.0 s
[2016-04-14T23:55Z] INFO  16:55:14,818 ProgressMeter - Total runtime 19.44 secs, 0.32 min, 0.01 hours
[2016-04-14T23:55Z] INFO  16:55:14,823 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 257369 total reads (0.00%)
[2016-04-14T23:55Z] INFO  16:55:14,824 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:55Z] INFO  16:55:14,825 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:55Z] INFO  16:55:14,826 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:55Z] INFO  16:55:15,109 ProgressMeter -     11:46388914    100006.0    30.0 s       5.1 m       95.6%    31.0 s       1.0 s
[2016-04-14T23:55Z] GATK pre-alignment ('12', 0, 15637181) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-14T23:55Z] INFO  16:55:15,381 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:55Z] INFO  16:55:15,385 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:55Z] INFO  16:55:15,386 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:55Z] INFO  16:55:15,387 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:55Z] INFO  16:55:15,392 HelpFormatter - Program Args: -T PrintReads -L 11:125523641-135006516 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/11/tx/tmp26cHsE/R14-18105_kapa-NGv3-PE100-NGv3-sort-11_125523640_135006516-prep-prealign.bam
[2016-04-14T23:55Z] INFO  16:55:15,412 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:55Z] INFO  16:55:15,416 HelpFormatter - Date/Time: 2016/04/14 16:55:15
[2016-04-14T23:55Z] INFO  16:55:15,416 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:55Z] INFO  16:55:15,422 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:55Z] INFO  16:55:15,616 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:55Z] INFO  16:55:15,727 ProgressMeter -      11:5968793    500013.0    60.0 s     120.0 s       37.3%     2.7 m     100.0 s
[2016-04-14T23:55Z] INFO  16:55:16,318 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:55Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-10_78316966_93841258-prep.bam
[2016-04-14T23:55Z] INFO  16:55:16,626 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-14T23:55Z] INFO  16:55:16,707 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:55Z] INFO  16:55:16,716 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:55Z] INFO  16:55:16,778 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-14T23:55Z] INFO  16:55:16,799 IntervalUtils - Processing 9482876 bp from intervals
[2016-04-14T23:55Z] INFO  16:55:16,868 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:55Z] INFO  16:55:17,124 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:55Z] INFO  16:55:17,126 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:55Z] INFO  16:55:17,126 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:55Z] INFO  16:55:17,127 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:55Z] INFO  16:55:17,141 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:55Z] GATK pre-alignment ('12', 15650178, 31231471) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-14T23:55Z] INFO  16:55:17,241 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:55Z] INFO  16:55:17,977 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:55Z] INFO  16:55:17,980 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:55Z] INFO  16:55:17,980 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:55Z] INFO  16:55:17,981 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:55Z] INFO  16:55:17,985 HelpFormatter - Program Args: -T PrintReads -L 12:1-15637181 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/12/tx/tmpqoKfoa/R14-18105_kapa-NGv3-PE100-NGv3-sort-12_0_15637181-prep-prealign.bam
[2016-04-14T23:55Z] INFO  16:55:18,001 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:55Z] INFO  16:55:18,002 HelpFormatter - Date/Time: 2016/04/14 16:55:17
[2016-04-14T23:55Z] INFO  16:55:18,003 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:55Z] INFO  16:55:18,008 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:55Z] INFO  16:55:18,200 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:55Z] INFO  16:55:18,842 ProgressMeter -            done    371701.0    26.0 s      70.0 s      100.0%    26.0 s       0.0 s
[2016-04-14T23:55Z] INFO  16:55:18,842 ProgressMeter - Total runtime 26.14 secs, 0.44 min, 0.01 hours
[2016-04-14T23:55Z] INFO  16:55:18,846 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 371701 total reads (0.00%)
[2016-04-14T23:55Z] INFO  16:55:18,846 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:55Z] INFO  16:55:18,846 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:55Z] INFO  16:55:18,847 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:55Z] INFO  16:55:19,289 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-14T23:55Z] INFO  16:55:19,359 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:55Z] INFO  16:55:19,368 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:55Z] INFO  16:55:19,403 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.04
[2016-04-14T23:55Z] INFO  16:55:19,417 IntervalUtils - Processing 15637181 bp from intervals
[2016-04-14T23:55Z] INFO  16:55:19,486 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:55Z] INFO  16:55:19,805 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:55Z] INFO  16:55:19,806 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:55Z] INFO  16:55:19,807 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:55Z] INFO  16:55:19,807 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:55Z] INFO  16:55:19,821 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:55Z] INFO  16:55:19,989 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:55Z] INFO  16:55:20,137 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:55Z] INFO  16:55:20,140 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:55Z] INFO  16:55:20,141 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:55Z] INFO  16:55:20,141 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:55Z] INFO  16:55:20,146 HelpFormatter - Program Args: -T PrintReads -L 12:15650179-31231471 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/12/tx/tmpMe1c5Z/R14-18105_kapa-NGv3-PE100-NGv3-sort-12_15650178_31231471-prep-prealign.bam
[2016-04-14T23:55Z] INFO  16:55:20,156 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:55Z] INFO  16:55:20,156 HelpFormatter - Date/Time: 2016/04/14 16:55:20
[2016-04-14T23:55Z] INFO  16:55:20,156 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:55Z] INFO  16:55:20,157 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:55Z] INFO  16:55:20,335 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:55Z] INFO  16:55:20,433 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:55Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-10_62539923_78084243-prep.bam
[2016-04-14T23:55Z] INFO  16:55:21,642 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-14T23:55Z] INFO  16:55:21,691 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:55Z] INFO  16:55:21,701 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:55Z] GATK pre-alignment ('12', 31236746, 46754992) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-14T23:55Z] INFO  16:55:21,744 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.04
[2016-04-14T23:55Z] INFO  16:55:21,755 ProgressMeter -     11:57114673    200004.0    30.0 s       2.5 m       64.1%    46.0 s      16.0 s
[2016-04-14T23:55Z] INFO  16:55:21,759 IntervalUtils - Processing 15581293 bp from intervals
[2016-04-14T23:55Z] INFO  16:55:21,878 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:55Z] INFO  16:55:22,195 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:55Z] INFO  16:55:22,196 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:55Z] INFO  16:55:22,196 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:55Z] INFO  16:55:22,197 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:55Z] INFO  16:55:22,211 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:55Z] INFO  16:55:22,363 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@41fd9d8e
[2016-04-14T23:55Z] INFO  16:55:22,447 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:55Z] INFO  16:55:22,463 ProgressMeter -            done    241682.0    37.0 s       2.6 m      100.0%    37.0 s       0.0 s
[2016-04-14T23:55Z] INFO  16:55:22,463 ProgressMeter - Total runtime 37.90 secs, 0.63 min, 0.01 hours
[2016-04-14T23:55Z] INFO  16:55:22,464 MicroScheduler - 161 reads were filtered out during the traversal out of approximately 241843 total reads (0.07%)
[2016-04-14T23:55Z] INFO  16:55:22,464 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:55Z] INFO  16:55:22,464 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:55Z] INFO  16:55:22,465 MicroScheduler -   -> 161 reads (0.07% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:55Z] INFO  16:55:22,886 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@32d5a4c6
[2016-04-14T23:55Z] INFO  16:55:23,036 ProgressMeter -            done    194731.0    26.0 s       2.2 m      100.0%    26.0 s       0.0 s
[2016-04-14T23:55Z] INFO  16:55:23,036 ProgressMeter - Total runtime 26.17 secs, 0.44 min, 0.01 hours
[2016-04-14T23:55Z] INFO  16:55:23,037 MicroScheduler - 157 reads were filtered out during the traversal out of approximately 194888 total reads (0.08%)
[2016-04-14T23:55Z] INFO  16:55:23,037 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:55Z] INFO  16:55:23,038 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:55Z] INFO  16:55:23,038 MicroScheduler -   -> 157 reads (0.08% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:55Z] INFO  16:55:23,050 ProgressMeter -     11:64678335    100002.0    30.0 s       5.0 m       12.5%     4.0 m       3.5 m
[2016-04-14T23:55Z] INFO  16:55:23,700 ProgressMeter -            done    411647.0    28.0 s      68.0 s      100.0%    28.0 s       0.0 s
[2016-04-14T23:55Z] INFO  16:55:23,700 ProgressMeter - Total runtime 28.28 secs, 0.47 min, 0.01 hours
[2016-04-14T23:55Z] INFO  16:55:23,704 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 411647 total reads (0.00%)
[2016-04-14T23:55Z] INFO  16:55:23,704 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:55Z] INFO  16:55:23,705 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:55Z] INFO  16:55:23,705 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:55Z] INFO  16:55:23,900 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:55Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-11_31541602_47074069-prep-prealign.bam
[2016-04-14T23:55Z] INFO  16:55:24,413 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:55Z] INFO  16:55:24,416 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:55Z] INFO  16:55:24,417 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:55Z] INFO  16:55:24,417 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:55Z] INFO  16:55:24,422 HelpFormatter - Program Args: -T PrintReads -L 12:31236747-46754992 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/12/tx/tmpAB7Ua3/R14-18105_kapa-NGv3-PE100-NGv3-sort-12_31236746_46754992-prep-prealign.bam
[2016-04-14T23:55Z] INFO  16:55:24,431 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:55Z] INFO  16:55:24,443 HelpFormatter - Date/Time: 2016/04/14 16:55:24
[2016-04-14T23:55Z] INFO  16:55:24,444 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:55Z] INFO  16:55:24,445 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:55Z] INFO  16:55:24,515 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:55Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-11_78277177_93796886-prep-prealign.bam
[2016-04-14T23:55Z] INFO  16:55:24,605 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:55Z] GATK RealignerTargetCreator: R14-18105_kapa-NGv3-PE100-NGv3-sort-11_31541602_47074069-prep-prealign.bam 11:31541603-47074069
[2016-04-14T23:55Z] GATK: RealignerTargetCreator
[2016-04-14T23:55Z] GATK RealignerTargetCreator: R14-18105_kapa-NGv3-PE100-NGv3-sort-11_78277177_93796886-prep-prealign.bam 11:78277178-93796886
[2016-04-14T23:55Z] GATK: RealignerTargetCreator
[2016-04-14T23:55Z] INFO  16:55:25,187 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:55Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-10_46960410_62493077-prep.bam
[2016-04-14T23:55Z] INFO  16:55:25,759 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-14T23:55Z] INFO  16:55:25,815 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:55Z] INFO  16:55:25,838 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:55Z] INFO  16:55:25,885 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-14T23:55Z] INFO  16:55:25,913 IntervalUtils - Processing 15518246 bp from intervals
[2016-04-14T23:55Z] INFO  16:55:26,003 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@5fe152b7
[2016-04-14T23:55Z] INFO  16:55:26,026 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:55Z] INFO  16:55:26,182 ProgressMeter -            done    186390.0    25.0 s       2.3 m      100.0%    25.0 s       0.0 s
[2016-04-14T23:55Z] INFO  16:55:26,182 ProgressMeter - Total runtime 25.18 secs, 0.42 min, 0.01 hours
[2016-04-14T23:55Z] INFO  16:55:26,183 MicroScheduler - 123 reads were filtered out during the traversal out of approximately 186513 total reads (0.07%)
[2016-04-14T23:55Z] INFO  16:55:26,183 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:55Z] INFO  16:55:26,183 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:55Z] INFO  16:55:26,184 MicroScheduler -   -> 123 reads (0.07% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:55Z] INFO  16:55:26,241 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:55Z] INFO  16:55:26,242 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:55Z] INFO  16:55:26,242 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:55Z] INFO  16:55:26,242 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:55Z] INFO  16:55:26,275 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:55Z] INFO  16:55:26,462 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:55Z] GATK pre-alignment ('12', 46756066, 62654284) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-14T23:55Z] INFO  16:55:26,750 ProgressMeter -            done   1.5523805E7    17.0 s       1.0 s      100.0%    17.0 s       0.0 s
[2016-04-14T23:55Z] INFO  16:55:26,751 ProgressMeter - Total runtime 17.90 secs, 0.30 min, 0.00 hours
[2016-04-14T23:55Z] INFO  16:55:26,755 MicroScheduler - 17942 reads were filtered out during the traversal out of approximately 210933 total reads (8.51%)
[2016-04-14T23:55Z] INFO  16:55:26,756 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:55Z] INFO  16:55:26,756 MicroScheduler -   -> 571 reads (0.27% of total) failing BadMateFilter
[2016-04-14T23:55Z] INFO  16:55:26,756 MicroScheduler -   -> 16544 reads (7.84% of total) failing DuplicateReadFilter
[2016-04-14T23:55Z] INFO  16:55:26,756 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-14T23:55Z] INFO  16:55:26,757 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:55Z] INFO  16:55:26,757 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-14T23:55Z] INFO  16:55:26,757 MicroScheduler -   -> 827 reads (0.39% of total) failing MappingQualityZeroFilter
[2016-04-14T23:55Z] INFO  16:55:26,757 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:55Z] INFO  16:55:26,758 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-14T23:55Z] INFO  16:55:26,758 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-14T23:55Z] INFO  16:55:27,253 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:55Z] INFO  16:55:27,257 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:55Z] INFO  16:55:27,257 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:55Z] INFO  16:55:27,258 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:55Z] INFO  16:55:27,262 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/11/R14-18105_kapa-NGv3-PE100-NGv3-sort-11_31541602_47074069-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/11/tx/tmpgwPc3R/R14-18105_kapa-NGv3-PE100-NGv3-sort-11_31541602_47074069-prep-prealign-realign.intervals -l INFO -L 11:31541603-47074069 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-14T23:55Z] INFO  16:55:27,279 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:55Z] INFO  16:55:27,290 HelpFormatter - Date/Time: 2016/04/14 16:55:27
[2016-04-14T23:55Z] INFO  16:55:27,291 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:55Z] INFO  16:55:27,292 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:55Z] INFO  16:55:27,444 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:55Z] INFO  16:55:27,580 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:55Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-11_93797496_109964158-prep-prealign.bam
[2016-04-14T23:55Z] INFO  16:55:27,647 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-14T23:55Z] INFO  16:55:27,659 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:55Z] INFO  16:55:27,707 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-14T23:55Z] INFO  16:55:28,072 IntervalUtils - Processing 15532467 bp from intervals
[2016-04-14T23:55Z] WARN  16:55:28,077 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:55Z] INFO  16:55:28,158 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:55Z] INFO  16:55:28,246 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:55Z] GATK RealignerTargetCreator: R14-18105_kapa-NGv3-PE100-NGv3-sort-11_93797496_109964158-prep-prealign.bam 11:93797497-109964158
[2016-04-14T23:55Z] GATK: RealignerTargetCreator
[2016-04-14T23:55Z] INFO  16:55:28,249 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:55Z] INFO  16:55:28,255 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:55Z] INFO  16:55:28,256 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:55Z] INFO  16:55:28,257 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:55Z] INFO  16:55:28,261 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/11/R14-18105_kapa-NGv3-PE100-NGv3-sort-11_78277177_93796886-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/11/tx/tmpK5lLtx/R14-18105_kapa-NGv3-PE100-NGv3-sort-11_78277177_93796886-prep-prealign-realign.intervals -l INFO -L 11:78277178-93796886 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-14T23:55Z] GATK: realign ('11', 16007749, 31531554) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-14T23:55Z] INFO  16:55:28,279 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:55Z] INFO  16:55:28,291 HelpFormatter - Date/Time: 2016/04/14 16:55:28
[2016-04-14T23:55Z] INFO  16:55:28,292 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:55Z] INFO  16:55:28,293 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:55Z] INFO  16:55:28,339 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:55Z] INFO  16:55:28,340 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:55Z] INFO  16:55:28,341 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:55Z] INFO  16:55:28,342 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-14T23:55Z] INFO  16:55:28,410 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:55Z] INFO  16:55:28,595 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-14T23:55Z] INFO  16:55:28,604 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:55Z] INFO  16:55:28,687 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-14T23:55Z] INFO  16:55:29,192 IntervalUtils - Processing 15519709 bp from intervals
[2016-04-14T23:55Z] WARN  16:55:29,198 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:55Z] INFO  16:55:29,300 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:55Z] INFO  16:55:29,507 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:55Z] INFO  16:55:29,508 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:55Z] INFO  16:55:29,509 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:55Z] INFO  16:55:29,510 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-14T23:55Z] INFO  16:55:29,562 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:55Z] INFO  16:55:29,577 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:55Z] INFO  16:55:29,578 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:55Z] INFO  16:55:29,579 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:55Z] INFO  16:55:29,584 HelpFormatter - Program Args: -T PrintReads -L 12:46756067-62654284 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/12/tx/tmpBW_ZXD/R14-18105_kapa-NGv3-PE100-NGv3-sort-12_46756066_62654284-prep-prealign.bam
[2016-04-14T23:55Z] INFO  16:55:29,598 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:55Z] INFO  16:55:29,598 HelpFormatter - Date/Time: 2016/04/14 16:55:29
[2016-04-14T23:55Z] INFO  16:55:29,599 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:55Z] INFO  16:55:29,599 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:55Z] INFO  16:55:29,844 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:55Z] INFO  16:55:30,779 ProgressMeter -            done   1.7773484E7    26.0 s       1.0 s      100.0%    26.0 s       0.0 s
[2016-04-14T23:55Z] INFO  16:55:30,779 ProgressMeter - Total runtime 26.85 secs, 0.45 min, 0.01 hours
[2016-04-14T23:55Z] INFO  16:55:30,783 MicroScheduler - 43466 reads were filtered out during the traversal out of approximately 522689 total reads (8.32%)
[2016-04-14T23:55Z] INFO  16:55:30,783 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:55Z] INFO  16:55:30,784 MicroScheduler -   -> 1062 reads (0.20% of total) failing BadMateFilter
[2016-04-14T23:55Z] INFO  16:55:30,784 MicroScheduler -   -> 41123 reads (7.87% of total) failing DuplicateReadFilter
[2016-04-14T23:55Z] INFO  16:55:30,784 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-14T23:55Z] INFO  16:55:30,791 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:55Z] INFO  16:55:30,792 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-14T23:55Z] INFO  16:55:30,793 MicroScheduler -   -> 1281 reads (0.25% of total) failing MappingQualityZeroFilter
[2016-04-14T23:55Z] INFO  16:55:30,793 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:55Z] INFO  16:55:30,794 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-14T23:55Z] INFO  16:55:30,794 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-14T23:55Z] INFO  16:55:30,890 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-14T23:55Z] INFO  16:55:30,965 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:55Z] INFO  16:55:30,974 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:55Z] INFO  16:55:31,021 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-14T23:55Z] INFO  16:55:31,043 IntervalUtils - Processing 15898218 bp from intervals
[2016-04-14T23:55Z] INFO  16:55:31,185 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:55Z] INFO  16:55:31,299 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:55Z] INFO  16:55:31,302 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:55Z] INFO  16:55:31,302 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:55Z] INFO  16:55:31,303 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:55Z] INFO  16:55:31,307 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/11/R14-18105_kapa-NGv3-PE100-NGv3-sort-11_16007749_31531554-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/11/R14-18105_kapa-NGv3-PE100-NGv3-sort-11_16007749_31531554-prep-prealign-realign.intervals -L 11:16007750-31531554 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/11/tx/tmp_xtz3r/R14-18105_kapa-NGv3-PE100-NGv3-sort-11_16007749_31531554-prep.bam
[2016-04-14T23:55Z] INFO  16:55:31,330 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:55Z] INFO  16:55:31,330 HelpFormatter - Date/Time: 2016/04/14 16:55:31
[2016-04-14T23:55Z] INFO  16:55:31,330 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:55Z] INFO  16:55:31,331 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:55Z] INFO  16:55:31,489 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:55Z] INFO  16:55:31,493 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:55Z] INFO  16:55:31,494 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:55Z] INFO  16:55:31,494 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:55Z] INFO  16:55:31,499 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/11/R14-18105_kapa-NGv3-PE100-NGv3-sort-11_93797496_109964158-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/11/tx/tmpVQx941/R14-18105_kapa-NGv3-PE100-NGv3-sort-11_93797496_109964158-prep-prealign-realign.intervals -l INFO -L 11:93797497-109964158 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-14T23:55Z] INFO  16:55:31,508 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:55Z] INFO  16:55:31,508 HelpFormatter - Date/Time: 2016/04/14 16:55:31
[2016-04-14T23:55Z] INFO  16:55:31,509 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:55Z] INFO  16:55:31,509 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:55Z] INFO  16:55:31,574 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:55Z] INFO  16:55:31,575 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:55Z] INFO  16:55:31,578 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:55Z] INFO  16:55:31,576 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:55Z] INFO  16:55:31,577 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:55Z] INFO  16:55:31,591 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:55Z] INFO  16:55:31,677 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:55Z] INFO  16:55:31,688 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:55Z] INFO  16:55:31,698 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:55Z] INFO  16:55:31,743 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:55Z] INFO  16:55:31,787 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.09
[2016-04-14T23:55Z] INFO  16:55:31,882 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-14T23:55Z] INFO  16:55:31,902 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:55Z] INFO  16:55:31,978 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-14T23:55Z] INFO  16:55:32,217 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:55Z] GATK: realign ('10', 93851586, 111625070) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-14T23:55Z] INFO  16:55:32,265 IntervalUtils - Processing 15523805 bp from intervals
[2016-04-14T23:55Z] WARN  16:55:32,276 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:55Z] INFO  16:55:32,300 IntervalUtils - Processing 16166662 bp from intervals
[2016-04-14T23:55Z] WARN  16:55:32,305 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:55Z] INFO  16:55:32,386 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:55Z] INFO  16:55:32,388 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:55Z] INFO  16:55:32,511 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:55Z] INFO  16:55:32,513 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:55Z] INFO  16:55:32,513 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:55Z] INFO  16:55:32,514 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:55Z] INFO  16:55:32,692 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:55Z] INFO  16:55:32,704 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:55Z] INFO  16:55:32,705 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:55Z] INFO  16:55:32,706 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:55Z] INFO  16:55:32,707 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-14T23:55Z] INFO  16:55:32,839 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:55Z] INFO  16:55:33,943 ProgressMeter -            done    310903.0    20.0 s      66.0 s      100.0%    20.0 s       0.0 s
[2016-04-14T23:55Z] INFO  16:55:33,944 ProgressMeter - Total runtime 20.81 secs, 0.35 min, 0.01 hours
[2016-04-14T23:55Z] INFO  16:55:33,949 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 310903 total reads (0.00%)
[2016-04-14T23:55Z] INFO  16:55:33,950 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:55Z] INFO  16:55:33,950 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:55Z] INFO  16:55:33,951 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:55Z] INFO  16:55:34,734 ProgressMeter -            done   1.2115947E7    28.0 s       2.0 s      100.0%    28.0 s       0.0 s
[2016-04-14T23:55Z] INFO  16:55:34,735 ProgressMeter - Total runtime 28.79 secs, 0.48 min, 0.01 hours
[2016-04-14T23:55Z] INFO  16:55:34,739 MicroScheduler - 78036 reads were filtered out during the traversal out of approximately 863387 total reads (9.04%)
[2016-04-14T23:55Z] INFO  16:55:34,740 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:55Z] INFO  16:55:34,741 MicroScheduler -   -> 1420 reads (0.16% of total) failing BadMateFilter
[2016-04-14T23:55Z] INFO  16:55:34,741 MicroScheduler -   -> 67818 reads (7.85% of total) failing DuplicateReadFilter
[2016-04-14T23:55Z] INFO  16:55:34,742 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-14T23:55Z] INFO  16:55:34,743 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:55Z] INFO  16:55:34,743 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-14T23:55Z] INFO  16:55:34,744 MicroScheduler -   -> 8798 reads (1.02% of total) failing MappingQualityZeroFilter
[2016-04-14T23:55Z] INFO  16:55:34,744 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:55Z] INFO  16:55:34,745 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-14T23:55Z] INFO  16:55:34,746 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-14T23:55Z] INFO  16:55:35,287 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:55Z] INFO  16:55:35,290 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:55Z] INFO  16:55:35,291 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:55Z] INFO  16:55:35,292 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:55Z] INFO  16:55:35,296 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/10/R14-18105_kapa-NGv3-PE100-NGv3-sort-10_93851586_111625070-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/10/R14-18105_kapa-NGv3-PE100-NGv3-sort-10_93851586_111625070-prep-prealign-realign.intervals -L 10:93851587-111625070 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/10/tx/tmpY7SpCw/R14-18105_kapa-NGv3-PE100-NGv3-sort-10_93851586_111625070-prep.bam
[2016-04-14T23:55Z] INFO  16:55:35,316 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:55Z] INFO  16:55:35,323 HelpFormatter - Date/Time: 2016/04/14 16:55:35
[2016-04-14T23:55Z] INFO  16:55:35,324 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:55Z] INFO  16:55:35,329 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:55Z] INFO  16:55:35,471 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:55Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-10_111628371_127265443-prep.bam
[2016-04-14T23:55Z] INFO  16:55:35,532 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:55Z] INFO  16:55:35,683 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:55Z] INFO  16:55:35,692 ProgressMeter -    11:117985928    200002.0    30.0 s       2.5 m       51.5%    58.0 s      28.0 s
[2016-04-14T23:55Z] INFO  16:55:35,700 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:55Z] INFO  16:55:35,777 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-14T23:55Z] INFO  16:55:35,951 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:55Z] GATK: realign ('9', 129097484, 141213431) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-14T23:55Z] INFO  16:55:36,086 IntervalUtils - Processing 17773484 bp from intervals
[2016-04-14T23:55Z] WARN  16:55:36,091 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:55Z] INFO  16:55:36,240 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:55Z] INFO  16:55:36,447 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:55Z] INFO  16:55:36,447 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:55Z] INFO  16:55:36,447 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:55Z] INFO  16:55:36,448 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:55Z] GATK pre-alignment ('12', 62687959, 78225484) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-14T23:55Z] INFO  16:55:36,650 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:55Z] INFO  16:55:36,800 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:55Z] INFO  16:55:38,800 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:55Z] INFO  16:55:38,802 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:55Z] INFO  16:55:38,803 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:55Z] INFO  16:55:38,803 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:55Z] INFO  16:55:38,807 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/9/R14-18105_kapa-NGv3-PE100-NGv3-sort-9_129097484_141213431-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/9/R14-18105_kapa-NGv3-PE100-NGv3-sort-9_129097484_141213431-prep-prealign-realign.intervals -L 9:129097485-141213431 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/9/tx/tmpIzViGF/R14-18105_kapa-NGv3-PE100-NGv3-sort-9_129097484_141213431-prep.bam
[2016-04-14T23:55Z] INFO  16:55:38,827 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:55Z] INFO  16:55:38,827 HelpFormatter - Date/Time: 2016/04/14 16:55:38
[2016-04-14T23:55Z] INFO  16:55:38,827 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:55Z] INFO  16:55:38,827 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:55Z] INFO  16:55:39,113 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:55Z] INFO  16:55:39,219 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:55Z] INFO  16:55:39,229 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:55Z] INFO  16:55:39,288 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-14T23:55Z] INFO  16:55:39,458 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:55Z] INFO  16:55:39,462 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:55Z] INFO  16:55:39,462 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:55Z] INFO  16:55:39,463 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:55Z] INFO  16:55:39,468 HelpFormatter - Program Args: -T PrintReads -L 12:62687960-78225484 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/12/tx/tmp2qO9nu/R14-18105_kapa-NGv3-PE100-NGv3-sort-12_62687959_78225484-prep-prealign.bam
[2016-04-14T23:55Z] INFO  16:55:39,481 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:55Z] INFO  16:55:39,482 HelpFormatter - Date/Time: 2016/04/14 16:55:39
[2016-04-14T23:55Z] INFO  16:55:39,483 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:55Z] INFO  16:55:39,483 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:55Z] INFO  16:55:39,643 IntervalUtils - Processing 12115947 bp from intervals
[2016-04-14T23:55Z] WARN  16:55:39,649 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:55Z] INFO  16:55:39,700 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:55Z] INFO  16:55:39,728 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:55Z] INFO  16:55:39,897 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:55Z] INFO  16:55:39,898 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:55Z] INFO  16:55:39,899 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:55Z] INFO  16:55:39,900 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:55Z] INFO  16:55:40,157 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:55Z] INFO  16:55:40,315 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:55Z] INFO  16:55:40,866 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-14T23:55Z] INFO  16:55:40,923 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:55Z] INFO  16:55:40,933 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:55Z] INFO  16:55:40,984 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-14T23:55Z] INFO  16:55:40,998 IntervalUtils - Processing 15537525 bp from intervals
[2016-04-14T23:55Z] INFO  16:55:41,073 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:55Z] INFO  16:55:41,400 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:55Z] INFO  16:55:41,400 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:55Z] INFO  16:55:41,401 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:55Z] INFO  16:55:41,401 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:55Z] INFO  16:55:41,429 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:55Z] INFO  16:55:41,627 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:55Z] INFO  16:55:42,734 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@7172f77a
[2016-04-14T23:55Z] INFO  16:55:42,834 ProgressMeter -            done    163681.0    20.0 s       2.1 m      100.0%    20.0 s       0.0 s
[2016-04-14T23:55Z] INFO  16:55:42,835 ProgressMeter - Total runtime 20.64 secs, 0.34 min, 0.01 hours
[2016-04-14T23:55Z] INFO  16:55:42,835 MicroScheduler - 136 reads were filtered out during the traversal out of approximately 163817 total reads (0.08%)
[2016-04-14T23:55Z] INFO  16:55:42,836 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:55Z] INFO  16:55:42,836 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:55Z] INFO  16:55:42,836 MicroScheduler -   -> 136 reads (0.08% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:55Z] INFO  16:55:44,323 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:55Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-12_15650178_31231471-prep-prealign.bam
[2016-04-14T23:55Z] INFO  16:55:44,809 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@7172f77a
[2016-04-14T23:55Z] GATK RealignerTargetCreator: R14-18105_kapa-NGv3-PE100-NGv3-sort-12_15650178_31231471-prep-prealign.bam 12:15650179-31231471
[2016-04-14T23:55Z] GATK: RealignerTargetCreator
[2016-04-14T23:55Z] INFO  16:55:44,941 ProgressMeter -            done    177593.0    27.0 s       2.6 m       92.1%    29.0 s       2.0 s
[2016-04-14T23:55Z] INFO  16:55:44,942 ProgressMeter - Total runtime 27.82 secs, 0.46 min, 0.01 hours
[2016-04-14T23:55Z] INFO  16:55:44,943 MicroScheduler - 95 reads were filtered out during the traversal out of approximately 177688 total reads (0.05%)
[2016-04-14T23:55Z] INFO  16:55:44,944 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:55Z] INFO  16:55:44,944 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:55Z] INFO  16:55:44,945 MicroScheduler -   -> 95 reads (0.05% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:55Z] INFO  16:55:46,035 ProgressMeter -     11:14502684    800019.0    90.0 s     112.0 s       90.7%    99.0 s       9.0 s
[2016-04-14T23:55Z] INFO  16:55:46,089 ProgressMeter -            done   1.5519709E7    16.0 s       1.0 s      100.0%    16.0 s       0.0 s
[2016-04-14T23:55Z] INFO  16:55:46,089 ProgressMeter - Total runtime 16.58 secs, 0.28 min, 0.00 hours
[2016-04-14T23:55Z] INFO  16:55:46,094 MicroScheduler - 46099 reads were filtered out during the traversal out of approximately 195801 total reads (23.54%)
[2016-04-14T23:55Z] INFO  16:55:46,094 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:55Z] INFO  16:55:46,094 MicroScheduler -   -> 586 reads (0.30% of total) failing BadMateFilter
[2016-04-14T23:55Z] INFO  16:55:46,095 MicroScheduler -   -> 12841 reads (6.56% of total) failing DuplicateReadFilter
[2016-04-14T23:55Z] INFO  16:55:46,095 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-14T23:55Z] INFO  16:55:46,095 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:55Z] INFO  16:55:46,096 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-14T23:55Z] INFO  16:55:46,096 MicroScheduler -   -> 32672 reads (16.69% of total) failing MappingQualityZeroFilter
[2016-04-14T23:55Z] INFO  16:55:46,096 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:55Z] INFO  16:55:46,097 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-14T23:55Z] INFO  16:55:46,097 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-14T23:55Z] INFO  16:55:46,312 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:55Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-11_125523640_135006516-prep-prealign.bam
[2016-04-14T23:55Z] GATK RealignerTargetCreator: R14-18105_kapa-NGv3-PE100-NGv3-sort-11_125523640_135006516-prep-prealign.bam 11:125523641-135006516
[2016-04-14T23:55Z] GATK: RealignerTargetCreator
[2016-04-14T23:55Z] INFO  16:55:47,560 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@41fd9d8e
[2016-04-14T23:55Z] INFO  16:55:47,599 ProgressMeter -            done   1.5532467E7    19.0 s       1.0 s      100.0%    19.0 s       0.0 s
[2016-04-14T23:55Z] INFO  16:55:47,600 ProgressMeter - Total runtime 19.26 secs, 0.32 min, 0.01 hours
[2016-04-14T23:55Z] INFO  16:55:47,603 MicroScheduler - 20293 reads were filtered out during the traversal out of approximately 243610 total reads (8.33%)
[2016-04-14T23:55Z] INFO  16:55:47,604 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:55Z] INFO  16:55:47,604 MicroScheduler -   -> 601 reads (0.25% of total) failing BadMateFilter
[2016-04-14T23:55Z] INFO  16:55:47,604 MicroScheduler -   -> 19176 reads (7.87% of total) failing DuplicateReadFilter
[2016-04-14T23:55Z] INFO  16:55:47,604 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-14T23:55Z] INFO  16:55:47,605 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:55Z] INFO  16:55:47,605 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-14T23:55Z] INFO  16:55:47,605 MicroScheduler -   -> 516 reads (0.21% of total) failing MappingQualityZeroFilter
[2016-04-14T23:55Z] INFO  16:55:47,605 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:55Z] INFO  16:55:47,606 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-14T23:55Z] INFO  16:55:47,606 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-14T23:55Z] INFO  16:55:47,620 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:55Z] INFO  16:55:47,644 ProgressMeter -            done    821924.0    91.0 s     111.0 s      100.0%    91.0 s       0.0 s
[2016-04-14T23:55Z] INFO  16:55:47,645 ProgressMeter - Total runtime 91.95 secs, 1.53 min, 0.03 hours
[2016-04-14T23:55Z] INFO  16:55:47,645 MicroScheduler - 498 reads were filtered out during the traversal out of approximately 822422 total reads (0.06%)
[2016-04-14T23:55Z] INFO  16:55:47,646 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:55Z] INFO  16:55:47,647 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:55Z] INFO  16:55:47,647 MicroScheduler -   -> 498 reads (0.06% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:55Z] GATK: realign ('11', 78277177, 93796886) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-14T23:55Z] INFO  16:55:47,802 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:55Z] INFO  16:55:47,805 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:55Z] INFO  16:55:47,805 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:55Z] INFO  16:55:47,805 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:55Z] INFO  16:55:47,809 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/12/R14-18105_kapa-NGv3-PE100-NGv3-sort-12_15650178_31231471-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/12/tx/tmplPuAcM/R14-18105_kapa-NGv3-PE100-NGv3-sort-12_15650178_31231471-prep-prealign-realign.intervals -l INFO -L 12:15650179-31231471 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-14T23:55Z] INFO  16:55:47,821 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:55Z] INFO  16:55:47,822 HelpFormatter - Date/Time: 2016/04/14 16:55:47
[2016-04-14T23:55Z] INFO  16:55:47,822 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:55Z] INFO  16:55:47,822 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:55Z] INFO  16:55:47,951 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:55Z] INFO  16:55:48,257 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-14T23:55Z] INFO  16:55:48,294 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:55Z] INFO  16:55:48,379 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-14T23:55Z] INFO  16:55:48,390 ProgressMeter -            done    209461.0    15.0 s      75.0 s      100.0%    15.0 s       0.0 s
[2016-04-14T23:55Z] INFO  16:55:48,390 ProgressMeter - Total runtime 15.88 secs, 0.26 min, 0.00 hours
[2016-04-14T23:55Z] INFO  16:55:48,394 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 209461 total reads (0.00%)
[2016-04-14T23:55Z] INFO  16:55:48,394 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:55Z] INFO  16:55:48,395 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:55Z] INFO  16:55:48,395 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:55Z] INFO  16:55:48,779 IntervalUtils - Processing 15581293 bp from intervals
[2016-04-14T23:55Z] WARN  16:55:48,795 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:55Z] INFO  16:55:48,936 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:55Z] INFO  16:55:49,169 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:55Z] INFO  16:55:49,170 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:55Z] INFO  16:55:49,171 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:55Z] INFO  16:55:49,172 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-14T23:55Z] INFO  16:55:49,224 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:55Z] GATK: realign ('11', 31541602, 47074069) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-14T23:55Z] INFO  16:55:49,258 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:55Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-11_0_15994658-prep-prealign.bam
[2016-04-14T23:55Z] INFO  16:55:49,304 ProgressMeter -            done   1.6166662E7    16.0 s       1.0 s      100.0%    16.0 s       0.0 s
[2016-04-14T23:55Z] INFO  16:55:49,305 ProgressMeter - Total runtime 16.60 secs, 0.28 min, 0.00 hours
[2016-04-14T23:55Z] INFO  16:55:49,309 MicroScheduler - 15626 reads were filtered out during the traversal out of approximately 187351 total reads (8.34%)
[2016-04-14T23:55Z] INFO  16:55:49,310 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:55Z] INFO  16:55:49,311 MicroScheduler -   -> 534 reads (0.29% of total) failing BadMateFilter
[2016-04-14T23:55Z] INFO  16:55:49,311 MicroScheduler -   -> 14574 reads (7.78% of total) failing DuplicateReadFilter
[2016-04-14T23:55Z] INFO  16:55:49,312 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-14T23:55Z] INFO  16:55:49,313 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:55Z] INFO  16:55:49,313 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-14T23:55Z] INFO  16:55:49,314 MicroScheduler -   -> 518 reads (0.28% of total) failing MappingQualityZeroFilter
[2016-04-14T23:55Z] INFO  16:55:49,314 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:55Z] INFO  16:55:49,316 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-14T23:55Z] INFO  16:55:49,316 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-14T23:55Z] INFO  16:55:49,792 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:55Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-11_16007749_31531554-prep.bam
[2016-04-14T23:55Z] INFO  16:55:50,047 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:55Z] INFO  16:55:50,050 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:55Z] INFO  16:55:50,051 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:55Z] INFO  16:55:50,051 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:55Z] INFO  16:55:50,056 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/11/R14-18105_kapa-NGv3-PE100-NGv3-sort-11_125523640_135006516-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/11/tx/tmpGftymM/R14-18105_kapa-NGv3-PE100-NGv3-sort-11_125523640_135006516-prep-prealign-realign.intervals -l INFO -L 11:125523641-135006516 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-14T23:55Z] INFO  16:55:50,086 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:55Z] INFO  16:55:50,087 HelpFormatter - Date/Time: 2016/04/14 16:55:50
[2016-04-14T23:55Z] INFO  16:55:50,088 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:55Z] INFO  16:55:50,088 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:55Z] INFO  16:55:50,174 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:55Z] INFO  16:55:50,367 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-14T23:55Z] INFO  16:55:50,377 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:55Z] INFO  16:55:50,459 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-14T23:55Z] INFO  16:55:50,464 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:55Z] INFO  16:55:50,467 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:55Z] INFO  16:55:50,467 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:55Z] INFO  16:55:50,468 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:55Z] INFO  16:55:50,472 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/11/R14-18105_kapa-NGv3-PE100-NGv3-sort-11_78277177_93796886-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/11/R14-18105_kapa-NGv3-PE100-NGv3-sort-11_78277177_93796886-prep-prealign-realign.intervals -L 11:78277178-93796886 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/11/tx/tmp0Nl2mb/R14-18105_kapa-NGv3-PE100-NGv3-sort-11_78277177_93796886-prep.bam
[2016-04-14T23:55Z] INFO  16:55:50,492 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:55Z] INFO  16:55:50,493 HelpFormatter - Date/Time: 2016/04/14 16:55:50
[2016-04-14T23:55Z] INFO  16:55:50,493 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:55Z] INFO  16:55:50,494 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:55Z] GATK pre-alignment ('12', 78334098, 93863131) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-14T23:55Z] INFO  16:55:50,696 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:55Z] INFO  16:55:50,743 IntervalUtils - Processing 9482876 bp from intervals
[2016-04-14T23:55Z] WARN  16:55:50,748 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:55Z] INFO  16:55:50,757 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:55Z] GATK: realign ('11', 93797496, 109964158) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-14T23:55Z] INFO  16:55:50,816 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:55Z] INFO  16:55:50,854 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:55Z] INFO  16:55:50,867 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:55Z] INFO  16:55:50,929 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-14T23:55Z] INFO  16:55:50,966 ProgressMeter -      12:6166201    100002.0    31.0 s       5.2 m       39.4%    78.0 s      47.0 s
[2016-04-14T23:55Z] INFO  16:55:51,019 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:55Z] INFO  16:55:51,019 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:55Z] INFO  16:55:51,020 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:55Z] INFO  16:55:51,020 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-14T23:55Z] INFO  16:55:51,366 IntervalUtils - Processing 15519709 bp from intervals
[2016-04-14T23:55Z] WARN  16:55:51,371 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:55Z] INFO  16:55:51,453 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:55Z] INFO  16:55:51,599 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:55Z] INFO  16:55:51,611 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:55Z] INFO  16:55:51,612 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:55Z] INFO  16:55:51,613 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:55Z] GATK RealignerTargetCreator: R14-18105_kapa-NGv3-PE100-NGv3-sort-11_0_15994658-prep-prealign.bam 11:1-15994658
[2016-04-14T23:55Z] GATK: RealignerTargetCreator
[2016-04-14T23:55Z] INFO  16:55:51,799 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:55Z] INFO  16:55:51,955 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:55Z] INFO  16:55:52,348 ProgressMeter -     11:62362109    400007.0    60.0 s       2.5 m       98.0%    61.0 s       1.0 s
[2016-04-14T23:55Z] INFO  16:55:52,454 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:55Z] INFO  16:55:52,457 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:55Z] INFO  16:55:52,457 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:55Z] INFO  16:55:52,457 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:55Z] INFO  16:55:52,461 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/11/R14-18105_kapa-NGv3-PE100-NGv3-sort-11_31541602_47074069-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/11/R14-18105_kapa-NGv3-PE100-NGv3-sort-11_31541602_47074069-prep-prealign-realign.intervals -L 11:31541603-47074069 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/11/tx/tmpeLsS0B/R14-18105_kapa-NGv3-PE100-NGv3-sort-11_31541602_47074069-prep.bam
[2016-04-14T23:55Z] INFO  16:55:52,480 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:55Z] INFO  16:55:52,481 HelpFormatter - Date/Time: 2016/04/14 16:55:52
[2016-04-14T23:55Z] INFO  16:55:52,481 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:55Z] INFO  16:55:52,481 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:55Z] INFO  16:55:52,775 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:55Z] INFO  16:55:52,911 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:55Z] INFO  16:55:52,920 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:55Z] INFO  16:55:52,977 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-14T23:55Z] INFO  16:55:53,051 ProgressMeter -     11:66249869    300006.0    60.0 s       3.3 m       22.6%     4.4 m       3.4 m
[2016-04-14T23:55Z] INFO  16:55:53,382 IntervalUtils - Processing 15532467 bp from intervals
[2016-04-14T23:55Z] WARN  16:55:53,391 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:55Z] INFO  16:55:53,390 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:55Z] INFO  16:55:53,395 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:55Z] INFO  16:55:53,395 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:55Z] INFO  16:55:53,396 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:55Z] INFO  16:55:53,400 HelpFormatter - Program Args: -T PrintReads -L 12:78334099-93863131 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/12/tx/tmpsFkwnR/R14-18105_kapa-NGv3-PE100-NGv3-sort-12_78334098_93863131-prep-prealign.bam
[2016-04-14T23:55Z] INFO  16:55:53,409 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:55Z] INFO  16:55:53,410 HelpFormatter - Date/Time: 2016/04/14 16:55:53
[2016-04-14T23:55Z] INFO  16:55:53,410 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:55Z] INFO  16:55:53,421 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:55Z] INFO  16:55:53,501 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:55Z] INFO  16:55:53,549 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:55Z] INFO  16:55:53,552 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:55Z] INFO  16:55:53,553 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:55Z] INFO  16:55:53,553 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:55Z] INFO  16:55:53,558 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/11/R14-18105_kapa-NGv3-PE100-NGv3-sort-11_93797496_109964158-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/11/R14-18105_kapa-NGv3-PE100-NGv3-sort-11_93797496_109964158-prep-prealign-realign.intervals -L 11:93797497-109964158 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/11/tx/tmp4_0wvC/R14-18105_kapa-NGv3-PE100-NGv3-sort-11_93797496_109964158-prep.bam
[2016-04-14T23:55Z] INFO  16:55:53,588 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:55Z] INFO  16:55:53,598 HelpFormatter - Date/Time: 2016/04/14 16:55:53
[2016-04-14T23:55Z] INFO  16:55:53,599 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:55Z] INFO  16:55:53,600 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:55Z] INFO  16:55:53,613 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:55Z] INFO  16:55:53,615 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:55Z] INFO  16:55:53,615 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:55Z] INFO  16:55:53,616 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:55Z] INFO  16:55:53,660 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:55Z] INFO  16:55:53,839 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:55Z] INFO  16:55:53,878 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:55Z] INFO  16:55:54,064 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:55Z] INFO  16:55:54,073 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:55Z] INFO  16:55:54,113 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:55Z] INFO  16:55:54,133 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-14T23:55Z] INFO  16:55:54,452 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:55Z] INFO  16:55:54,455 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:55Z] INFO  16:55:54,456 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:55Z] INFO  16:55:54,456 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:55Z] INFO  16:55:54,461 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/11/R14-18105_kapa-NGv3-PE100-NGv3-sort-11_0_15994658-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/11/tx/tmpZ1uha6/R14-18105_kapa-NGv3-PE100-NGv3-sort-11_0_15994658-prep-prealign-realign.intervals -l INFO -L 11:1-15994658 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-14T23:55Z] INFO  16:55:54,472 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:55Z] INFO  16:55:54,483 HelpFormatter - Date/Time: 2016/04/14 16:55:54
[2016-04-14T23:55Z] INFO  16:55:54,484 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:55Z] INFO  16:55:54,485 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:55Z] INFO  16:55:54,537 IntervalUtils - Processing 16166662 bp from intervals
[2016-04-14T23:55Z] WARN  16:55:54,542 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:55Z] INFO  16:55:54,598 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:55Z] INFO  16:55:54,651 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:55Z] INFO  16:55:54,815 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:55Z] INFO  16:55:54,816 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:55Z] INFO  16:55:54,817 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:55Z] INFO  16:55:54,818 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:55Z] INFO  16:55:54,877 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-14T23:55Z] INFO  16:55:54,880 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-14T23:55Z] INFO  16:55:54,890 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:55Z] INFO  16:55:54,932 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:55Z] INFO  16:55:54,949 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:55Z] INFO  16:55:54,954 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-14T23:55Z] INFO  16:55:54,979 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:55Z] INFO  16:55:54,989 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.04
[2016-04-14T23:55Z] INFO  16:55:55,013 IntervalUtils - Processing 15529033 bp from intervals
[2016-04-14T23:55Z] INFO  16:55:55,113 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:55Z] INFO  16:55:55,131 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:55Z] INFO  16:55:55,276 IntervalUtils - Processing 15994658 bp from intervals
[2016-04-14T23:55Z] WARN  16:55:55,281 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:55Z] INFO  16:55:55,362 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:55Z] INFO  16:55:55,522 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:55Z] INFO  16:55:55,522 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:55Z] INFO  16:55:55,523 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:55Z] INFO  16:55:55,523 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:55Z] INFO  16:55:55,548 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:55Z] INFO  16:55:55,687 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:55Z] INFO  16:55:55,689 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:55Z] INFO  16:55:55,689 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:55Z] INFO  16:55:55,690 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-14T23:55Z] INFO  16:55:55,699 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:55Z] INFO  16:55:56,258 ProgressMeter -     12:46246023    100004.0    30.0 s       5.0 m       96.7%    31.0 s       1.0 s
[2016-04-14T23:55Z] INFO  16:55:57,234 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@41fd9d8e
[2016-04-14T23:55Z] INFO  16:55:57,317 ProgressMeter -            done    200500.0    31.0 s       2.6 m      100.0%    31.0 s       0.0 s
[2016-04-14T23:55Z] INFO  16:55:57,317 ProgressMeter - Total runtime 31.08 secs, 0.52 min, 0.01 hours
[2016-04-14T23:55Z] INFO  16:55:57,318 MicroScheduler - 211 reads were filtered out during the traversal out of approximately 200711 total reads (0.11%)
[2016-04-14T23:55Z] INFO  16:55:57,318 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:55Z] INFO  16:55:57,318 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:55Z] INFO  16:55:57,319 MicroScheduler -   -> 211 reads (0.11% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:55Z] INFO  16:55:58,634 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@41fd9d8e
[2016-04-14T23:55Z] INFO  16:55:58,696 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:55Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-12_31236746_46754992-prep-prealign.bam
[2016-04-14T23:55Z] INFO  16:55:58,758 ProgressMeter -            done    565617.0    67.0 s     118.0 s      100.0%    67.0 s       0.0 s
[2016-04-14T23:55Z] INFO  16:55:58,759 ProgressMeter - Total runtime 67.04 secs, 1.12 min, 0.02 hours
[2016-04-14T23:55Z] INFO  16:55:58,759 MicroScheduler - 385 reads were filtered out during the traversal out of approximately 566002 total reads (0.07%)
[2016-04-14T23:55Z] INFO  16:55:58,760 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:55Z] INFO  16:55:58,760 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:55Z] INFO  16:55:58,761 MicroScheduler -   -> 385 reads (0.07% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:55Z] GATK RealignerTargetCreator: R14-18105_kapa-NGv3-PE100-NGv3-sort-12_31236746_46754992-prep-prealign.bam 12:31236747-46754992
[2016-04-14T23:55Z] GATK: RealignerTargetCreator
[2016-04-14T23:56Z] INFO  16:56:00,304 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:56Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-11_47158866_62678572-prep-prealign.bam
[2016-04-14T23:56Z] INFO  16:56:01,694 ProgressMeter -     12:50348524    200003.0    30.0 s       2.5 m       22.6%     2.2 m     102.0 s
[2016-04-14T23:56Z] GATK RealignerTargetCreator: R14-18105_kapa-NGv3-PE100-NGv3-sort-11_47158866_62678572-prep-prealign.bam 11:47158867-62678572
[2016-04-14T23:56Z] GATK: RealignerTargetCreator
[2016-04-14T23:56Z] INFO  16:56:02,292 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:56Z] INFO  16:56:02,295 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:56Z] INFO  16:56:02,296 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:56Z] INFO  16:56:02,296 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:56Z] INFO  16:56:02,301 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/12/R14-18105_kapa-NGv3-PE100-NGv3-sort-12_31236746_46754992-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/12/tx/tmpD82zx8/R14-18105_kapa-NGv3-PE100-NGv3-sort-12_31236746_46754992-prep-prealign-realign.intervals -l INFO -L 12:31236747-46754992 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-14T23:56Z] INFO  16:56:02,321 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:56Z] INFO  16:56:02,322 HelpFormatter - Date/Time: 2016/04/14 16:56:02
[2016-04-14T23:56Z] INFO  16:56:02,322 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:56Z] INFO  16:56:02,323 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:56Z] INFO  16:56:02,425 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:56Z] INFO  16:56:02,604 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-14T23:56Z] INFO  16:56:02,635 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:56Z] INFO  16:56:02,698 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-14T23:56Z] INFO  16:56:02,999 IntervalUtils - Processing 15518246 bp from intervals
[2016-04-14T23:56Z] WARN  16:56:03,004 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:56Z] INFO  16:56:03,073 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:56Z] INFO  16:56:03,243 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:56Z] INFO  16:56:03,245 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:56Z] INFO  16:56:03,245 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:56Z] INFO  16:56:03,246 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-14T23:56Z] INFO  16:56:04,723 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:56Z] INFO  16:56:04,726 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:56Z] INFO  16:56:04,727 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:56Z] INFO  16:56:04,727 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:56Z] INFO  16:56:04,732 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/11/R14-18105_kapa-NGv3-PE100-NGv3-sort-11_47158866_62678572-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/11/tx/tmpno8wGh/R14-18105_kapa-NGv3-PE100-NGv3-sort-11_47158866_62678572-prep-prealign-realign.intervals -l INFO -L 11:47158867-62678572 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-14T23:56Z] INFO  16:56:04,743 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:56Z] INFO  16:56:04,749 HelpFormatter - Date/Time: 2016/04/14 16:56:04
[2016-04-14T23:56Z] INFO  16:56:04,750 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:56Z] INFO  16:56:04,750 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:56Z] INFO  16:56:04,873 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:56Z] INFO  16:56:05,050 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-14T23:56Z] INFO  16:56:05,060 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:56Z] INFO  16:56:05,103 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.04
[2016-04-14T23:56Z] INFO  16:56:05,343 IntervalUtils - Processing 15519706 bp from intervals
[2016-04-14T23:56Z] WARN  16:56:05,349 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:56Z] INFO  16:56:05,351 ProgressMeter -            done   9482876.0    14.0 s       1.0 s      100.0%    14.0 s       0.0 s
[2016-04-14T23:56Z] INFO  16:56:05,357 ProgressMeter - Total runtime 14.34 secs, 0.24 min, 0.00 hours
[2016-04-14T23:56Z] INFO  16:56:05,361 MicroScheduler - 15504 reads were filtered out during the traversal out of approximately 178218 total reads (8.70%)
[2016-04-14T23:56Z] INFO  16:56:05,362 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:56Z] INFO  16:56:05,362 MicroScheduler -   -> 433 reads (0.24% of total) failing BadMateFilter
[2016-04-14T23:56Z] INFO  16:56:05,363 MicroScheduler -   -> 14231 reads (7.99% of total) failing DuplicateReadFilter
[2016-04-14T23:56Z] INFO  16:56:05,364 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-14T23:56Z] INFO  16:56:05,364 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:56Z] INFO  16:56:05,365 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-14T23:56Z] INFO  16:56:05,366 MicroScheduler -   -> 840 reads (0.47% of total) failing MappingQualityZeroFilter
[2016-04-14T23:56Z] INFO  16:56:05,366 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:56Z] INFO  16:56:05,367 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-14T23:56Z] INFO  16:56:05,367 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-14T23:56Z] INFO  16:56:05,427 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:56Z] INFO  16:56:05,670 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:56Z] INFO  16:56:05,671 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:56Z] INFO  16:56:05,673 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:56Z] INFO  16:56:05,674 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-14T23:56Z] INFO  16:56:05,808 ProgressMeter -    11:124972239    500008.0    60.0 s     120.0 s       96.5%    62.0 s       2.0 s
[2016-04-14T23:56Z] INFO  16:56:05,858 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@41fd9d8e
[2016-04-14T23:56Z] INFO  16:56:06,003 ProgressMeter -            done    182081.0    24.0 s       2.3 m      100.0%    24.0 s       0.0 s
[2016-04-14T23:56Z] INFO  16:56:06,004 ProgressMeter - Total runtime 24.60 secs, 0.41 min, 0.01 hours
[2016-04-14T23:56Z] INFO  16:56:06,004 MicroScheduler - 142 reads were filtered out during the traversal out of approximately 182223 total reads (0.08%)
[2016-04-14T23:56Z] INFO  16:56:06,004 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:56Z] INFO  16:56:06,005 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:56Z] INFO  16:56:06,005 MicroScheduler -   -> 142 reads (0.08% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:56Z] INFO  16:56:06,342 ProgressMeter -            done    194731.0    14.0 s      75.0 s      100.0%    14.0 s       0.0 s
[2016-04-14T23:56Z] INFO  16:56:06,342 ProgressMeter - Total runtime 14.73 secs, 0.25 min, 0.00 hours
[2016-04-14T23:56Z] INFO  16:56:06,346 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 194731 total reads (0.00%)
[2016-04-14T23:56Z] INFO  16:56:06,346 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:56Z] INFO  16:56:06,645 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:56Z] INFO  16:56:06,645 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:56Z] INFO  16:56:06,705 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:56Z] GATK: realign ('11', 125523640, 135006516) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-14T23:56Z] INFO  16:56:06,869 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@41fd9d8e
[2016-04-14T23:56Z] INFO  16:56:07,024 ProgressMeter -            done   1.5581293E7    17.0 s       1.0 s      100.0%    17.0 s       0.0 s
[2016-04-14T23:56Z] INFO  16:56:07,025 ProgressMeter - Total runtime 17.85 secs, 0.30 min, 0.00 hours
[2016-04-14T23:56Z] INFO  16:56:07,033 MicroScheduler - 13962 reads were filtered out during the traversal out of approximately 164580 total reads (8.48%)
[2016-04-14T23:56Z] INFO  16:56:07,034 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:56Z] INFO  16:56:07,035 MicroScheduler -   -> 505 reads (0.31% of total) failing BadMateFilter
[2016-04-14T23:56Z] INFO  16:56:07,036 MicroScheduler -   -> 12970 reads (7.88% of total) failing DuplicateReadFilter
[2016-04-14T23:56Z] INFO  16:56:07,036 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-14T23:56Z] INFO  16:56:07,037 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:56Z] INFO  16:56:07,037 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-14T23:56Z] INFO  16:56:07,038 MicroScheduler -   -> 487 reads (0.30% of total) failing MappingQualityZeroFilter
[2016-04-14T23:56Z] INFO  16:56:07,039 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:56Z] INFO  16:56:07,039 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-14T23:56Z] INFO  16:56:07,040 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-14T23:56Z] INFO  16:56:07,088 ProgressMeter -            done    521028.0    61.0 s     117.0 s      100.0%    61.0 s       0.0 s
[2016-04-14T23:56Z] INFO  16:56:07,089 ProgressMeter - Total runtime 61.44 secs, 1.02 min, 0.02 hours
[2016-04-14T23:56Z] INFO  16:56:07,090 MicroScheduler - 245 reads were filtered out during the traversal out of approximately 521273 total reads (0.05%)
[2016-04-14T23:56Z] INFO  16:56:07,091 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:56Z] INFO  16:56:07,091 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:56Z] INFO  16:56:07,092 MicroScheduler -   -> 245 reads (0.05% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:56Z] INFO  16:56:07,228 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:56Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-12_62687959_78225484-prep-prealign.bam
[2016-04-14T23:56Z] INFO  16:56:07,450 ProgressMeter -    10:106130758    400005.0    31.0 s      77.0 s       69.1%    44.0 s      13.0 s
[2016-04-14T23:56Z] GATK RealignerTargetCreator: R14-18105_kapa-NGv3-PE100-NGv3-sort-12_62687959_78225484-prep-prealign.bam 12:62687960-78225484
[2016-04-14T23:56Z] GATK: RealignerTargetCreator
[2016-04-14T23:56Z] INFO  16:56:08,021 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:56Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-11_78277177_93796886-prep.bam
[2016-04-14T23:56Z] INFO  16:56:08,451 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:56Z] INFO  16:56:08,459 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:56Z] GATK: realign ('12', 15650178, 31231471) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-14T23:56Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-11_110001730_125514538-prep-prealign.bam
[2016-04-14T23:56Z] INFO  16:56:08,565 ProgressMeter -            done    518970.0    32.0 s      61.0 s      100.0%    32.0 s       0.0 s
[2016-04-14T23:56Z] INFO  16:56:08,565 ProgressMeter - Total runtime 32.12 secs, 0.54 min, 0.01 hours
[2016-04-14T23:56Z] INFO  16:56:08,570 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 518970 total reads (0.00%)
[2016-04-14T23:56Z] INFO  16:56:08,571 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:56Z] INFO  16:56:08,572 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:56Z] INFO  16:56:08,572 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:56Z] GATK pre-alignment ('12', 93870729, 109490566) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-14T23:56Z] INFO  16:56:08,842 ProgressMeter -            done    186390.0    14.0 s      75.0 s      100.0%    14.0 s       0.0 s
[2016-04-14T23:56Z] INFO  16:56:08,842 ProgressMeter - Total runtime 14.03 secs, 0.23 min, 0.00 hours
[2016-04-14T23:56Z] INFO  16:56:08,847 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 186390 total reads (0.00%)
[2016-04-14T23:56Z] INFO  16:56:08,847 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:56Z] INFO  16:56:08,848 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:56Z] INFO  16:56:08,848 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:56Z] INFO  16:56:09,347 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:56Z] INFO  16:56:09,350 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:56Z] INFO  16:56:09,351 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:56Z] INFO  16:56:09,351 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:56Z] INFO  16:56:09,356 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/11/R14-18105_kapa-NGv3-PE100-NGv3-sort-11_125523640_135006516-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/11/R14-18105_kapa-NGv3-PE100-NGv3-sort-11_125523640_135006516-prep-prealign-realign.intervals -L 11:125523641-135006516 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/11/tx/tmpiU_8Li/R14-18105_kapa-NGv3-PE100-NGv3-sort-11_125523640_135006516-prep.bam
[2016-04-14T23:56Z] INFO  16:56:09,382 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:56Z] INFO  16:56:09,383 HelpFormatter - Date/Time: 2016/04/14 16:56:09
[2016-04-14T23:56Z] INFO  16:56:09,384 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:56Z] INFO  16:56:09,384 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:56Z] INFO  16:56:09,643 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:56Z] INFO  16:56:09,758 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:56Z] INFO  16:56:09,767 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:56Z] INFO  16:56:09,790 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@7172f77a
[2016-04-14T23:56Z] INFO  16:56:09,826 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-14T23:56Z] INFO  16:56:09,915 ProgressMeter -            done     97815.0    14.0 s       2.5 m      100.0%    14.0 s       0.0 s
[2016-04-14T23:56Z] INFO  16:56:09,915 ProgressMeter - Total runtime 14.39 secs, 0.24 min, 0.00 hours
[2016-04-14T23:56Z] INFO  16:56:09,916 MicroScheduler - 116 reads were filtered out during the traversal out of approximately 97931 total reads (0.12%)
[2016-04-14T23:56Z] INFO  16:56:09,916 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:56Z] INFO  16:56:09,916 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:56Z] INFO  16:56:09,917 MicroScheduler -   -> 116 reads (0.12% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:56Z] GATK RealignerTargetCreator: R14-18105_kapa-NGv3-PE100-NGv3-sort-11_110001730_125514538-prep-prealign.bam 11:110001731-125514538
[2016-04-14T23:56Z] GATK: RealignerTargetCreator
[2016-04-14T23:56Z] INFO  16:56:10,314 IntervalUtils - Processing 9482876 bp from intervals
[2016-04-14T23:56Z] WARN  16:56:10,321 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:56Z] INFO  16:56:10,404 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:56Z] INFO  16:56:10,410 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:56Z] INFO  16:56:10,452 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:56Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-10_93851586_111625070-prep.bam
[2016-04-14T23:56Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-11_93797496_109964158-prep.bam
[2016-04-14T23:56Z] INFO  16:56:10,542 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:56Z] INFO  16:56:10,543 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:56Z] INFO  16:56:10,544 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:56Z] INFO  16:56:10,545 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:56Z] INFO  16:56:10,681 ProgressMeter -     9:136067123    400005.0    30.0 s      76.0 s       57.5%    52.0 s      22.0 s
[2016-04-14T23:56Z] INFO  16:56:10,691 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:56Z] INFO  16:56:10,794 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:56Z] INFO  16:56:10,901 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:56Z] INFO  16:56:10,905 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:56Z] INFO  16:56:10,906 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:56Z] INFO  16:56:10,906 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:56Z] INFO  16:56:10,910 ProgressMeter -            done    241682.0    17.0 s      71.0 s      100.0%    17.0 s       0.0 s
[2016-04-14T23:56Z] INFO  16:56:10,912 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/12/R14-18105_kapa-NGv3-PE100-NGv3-sort-12_62687959_78225484-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/12/tx/tmpyrPkM7/R14-18105_kapa-NGv3-PE100-NGv3-sort-12_62687959_78225484-prep-prealign-realign.intervals -l INFO -L 12:62687960-78225484 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-14T23:56Z] INFO  16:56:10,917 ProgressMeter - Total runtime 17.30 secs, 0.29 min, 0.00 hours
[2016-04-14T23:56Z] INFO  16:56:10,938 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 241682 total reads (0.00%)
[2016-04-14T23:56Z] INFO  16:56:10,939 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:56Z] INFO  16:56:10,939 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:56Z] INFO  16:56:10,939 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:56Z] INFO  16:56:10,939 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:56Z] INFO  16:56:10,940 HelpFormatter - Date/Time: 2016/04/14 16:56:10
[2016-04-14T23:56Z] INFO  16:56:10,942 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:56Z] INFO  16:56:10,943 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:56Z] INFO  16:56:11,065 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:56Z] GATK pre-alignment ('12', 109494486, 125263132) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-14T23:56Z] INFO  16:56:11,319 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:56Z] INFO  16:56:11,322 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:56Z] INFO  16:56:11,323 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:56Z] INFO  16:56:11,323 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:56Z] INFO  16:56:11,325 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-14T23:56Z] INFO  16:56:11,328 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/12/R14-18105_kapa-NGv3-PE100-NGv3-sort-12_15650178_31231471-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/12/R14-18105_kapa-NGv3-PE100-NGv3-sort-12_15650178_31231471-prep-prealign-realign.intervals -L 12:15650179-31231471 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/12/tx/tmpjTYjp8/R14-18105_kapa-NGv3-PE100-NGv3-sort-12_15650178_31231471-prep.bam
[2016-04-14T23:56Z] INFO  16:56:11,341 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:56Z] INFO  16:56:11,356 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:56Z] INFO  16:56:11,357 HelpFormatter - Date/Time: 2016/04/14 16:56:11
[2016-04-14T23:56Z] INFO  16:56:11,361 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:56Z] INFO  16:56:11,362 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:56Z] INFO  16:56:11,369 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:56Z] INFO  16:56:11,389 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-14T23:56Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-12_78334098_93863131-prep-prealign.bam
[2016-04-14T23:56Z] INFO  16:56:11,595 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:56Z] INFO  16:56:11,664 IntervalUtils - Processing 15537525 bp from intervals
[2016-04-14T23:56Z] WARN  16:56:11,670 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:56Z] INFO  16:56:11,713 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:56Z] INFO  16:56:11,717 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:56Z] INFO  16:56:11,718 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:56Z] INFO  16:56:11,718 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:56Z] INFO  16:56:11,723 HelpFormatter - Program Args: -T PrintReads -L 12:93870730-109490566 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/12/tx/tmpT3q6Px/R14-18105_kapa-NGv3-PE100-NGv3-sort-12_93870729_109490566-prep-prealign.bam
[2016-04-14T23:56Z] INFO  16:56:11,736 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:56Z] GATK RealignerTargetCreator: R14-18105_kapa-NGv3-PE100-NGv3-sort-12_78334098_93863131-prep-prealign.bam 12:78334099-93863131
[2016-04-14T23:56Z] GATK: RealignerTargetCreator
[2016-04-14T23:56Z] INFO  16:56:11,748 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:56Z] INFO  16:56:11,752 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:56Z] INFO  16:56:11,754 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:56Z] INFO  16:56:11,755 HelpFormatter - Date/Time: 2016/04/14 16:56:11
[2016-04-14T23:56Z] INFO  16:56:11,755 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:56Z] INFO  16:56:11,756 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:56Z] INFO  16:56:11,810 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-14T23:56Z] INFO  16:56:11,908 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:56Z] INFO  16:56:11,909 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:56Z] INFO  16:56:11,910 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:56Z] INFO  16:56:11,910 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-14T23:56Z] INFO  16:56:11,945 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:56Z] INFO  16:56:12,139 IntervalUtils - Processing 15581293 bp from intervals
[2016-04-14T23:56Z] WARN  16:56:12,154 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:56Z] GATK pre-alignment ('12', 125267228, 133851895) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-14T23:56Z] INFO  16:56:12,243 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:56Z] INFO  16:56:12,395 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:56Z] INFO  16:56:12,396 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:56Z] INFO  16:56:12,396 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:56Z] INFO  16:56:12,396 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:56Z] INFO  16:56:12,458 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:56Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-11_31541602_47074069-prep.bam
[2016-04-14T23:56Z] INFO  16:56:12,587 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:56Z] INFO  16:56:12,776 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:56Z] INFO  16:56:13,140 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:56Z] INFO  16:56:13,143 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:56Z] INFO  16:56:13,143 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:56Z] INFO  16:56:13,144 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:56Z] INFO  16:56:13,148 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/11/R14-18105_kapa-NGv3-PE100-NGv3-sort-11_110001730_125514538-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/11/tx/tmpOx2v4U/R14-18105_kapa-NGv3-PE100-NGv3-sort-11_110001730_125514538-prep-prealign-realign.intervals -l INFO -L 11:110001731-125514538 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-14T23:56Z] INFO  16:56:13,169 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:56Z] INFO  16:56:13,170 HelpFormatter - Date/Time: 2016/04/14 16:56:13
[2016-04-14T23:56Z] INFO  16:56:13,171 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:56Z] INFO  16:56:13,171 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:56Z] INFO  16:56:13,173 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-14T23:56Z] GATK pre-alignment ('13', 0, 19748299) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-14T23:56Z] INFO  16:56:13,267 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:56Z] INFO  16:56:13,269 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:56Z] INFO  16:56:13,289 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:56Z] INFO  16:56:13,357 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-14T23:56Z] INFO  16:56:13,382 IntervalUtils - Processing 15619837 bp from intervals
[2016-04-14T23:56Z] INFO  16:56:13,470 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-14T23:56Z] INFO  16:56:13,481 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:56Z] INFO  16:56:13,480 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:56Z] INFO  16:56:13,525 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-14T23:56Z] INFO  16:56:13,867 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:56Z] INFO  16:56:13,868 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:56Z] INFO  16:56:13,869 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:56Z] INFO  16:56:13,870 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:56Z] INFO  16:56:13,897 IntervalUtils - Processing 15512808 bp from intervals
[2016-04-14T23:56Z] WARN  16:56:13,904 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:56Z] INFO  16:56:13,907 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:56Z] INFO  16:56:13,940 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:56Z] INFO  16:56:13,943 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:56Z] INFO  16:56:13,944 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:56Z] INFO  16:56:13,945 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:56Z] INFO  16:56:13,949 HelpFormatter - Program Args: -T PrintReads -L 12:109494487-125263132 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/12/tx/tmp51UO3b/R14-18105_kapa-NGv3-PE100-NGv3-sort-12_109494486_125263132-prep-prealign.bam
[2016-04-14T23:56Z] INFO  16:56:13,969 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:56Z] INFO  16:56:13,970 HelpFormatter - Date/Time: 2016/04/14 16:56:13
[2016-04-14T23:56Z] INFO  16:56:13,970 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:56Z] INFO  16:56:13,971 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:56Z] INFO  16:56:13,999 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:56Z] INFO  16:56:14,138 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:56Z] INFO  16:56:14,143 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:56Z] INFO  16:56:14,402 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:56Z] INFO  16:56:14,404 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:56Z] INFO  16:56:14,404 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:56Z] INFO  16:56:14,405 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-14T23:56Z] INFO  16:56:14,869 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:56Z] INFO  16:56:14,872 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:56Z] INFO  16:56:14,872 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:56Z] INFO  16:56:14,873 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:56Z] INFO  16:56:14,878 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/12/R14-18105_kapa-NGv3-PE100-NGv3-sort-12_78334098_93863131-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/12/tx/tmpKlXQB1/R14-18105_kapa-NGv3-PE100-NGv3-sort-12_78334098_93863131-prep-prealign-realign.intervals -l INFO -L 12:78334099-93863131 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-14T23:56Z] INFO  16:56:14,918 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:56Z] INFO  16:56:14,933 HelpFormatter - Date/Time: 2016/04/14 16:56:14
[2016-04-14T23:56Z] INFO  16:56:14,934 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:56Z] INFO  16:56:14,935 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:56Z] INFO  16:56:15,016 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:56Z] INFO  16:56:15,019 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:56Z] INFO  16:56:15,020 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:56Z] INFO  16:56:15,020 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:56Z] INFO  16:56:15,025 HelpFormatter - Program Args: -T PrintReads -L 12:125267229-133851895 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/12/tx/tmpFac8L0/R14-18105_kapa-NGv3-PE100-NGv3-sort-12_125267228_133851895-prep-prealign.bam
[2016-04-14T23:56Z] INFO  16:56:15,034 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:56Z] INFO  16:56:15,034 HelpFormatter - Date/Time: 2016/04/14 16:56:15
[2016-04-14T23:56Z] INFO  16:56:15,034 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:56Z] INFO  16:56:15,034 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:56Z] INFO  16:56:15,055 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:56Z] INFO  16:56:15,266 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:56Z] INFO  16:56:15,308 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-14T23:56Z] INFO  16:56:15,319 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:56Z] INFO  16:56:15,396 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-14T23:56Z] INFO  16:56:15,407 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.09
[2016-04-14T23:56Z] INFO  16:56:15,454 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:56Z] INFO  16:56:15,463 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:56Z] INFO  16:56:15,510 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-14T23:56Z] INFO  16:56:15,524 IntervalUtils - Processing 15768646 bp from intervals
[2016-04-14T23:56Z] INFO  16:56:15,603 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:56Z] INFO  16:56:15,814 IntervalUtils - Processing 15529033 bp from intervals
[2016-04-14T23:56Z] WARN  16:56:15,819 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:56Z] INFO  16:56:15,919 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:56Z] INFO  16:56:15,948 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:56Z] INFO  16:56:15,949 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:56Z] INFO  16:56:15,949 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:56Z] INFO  16:56:15,949 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:56Z] INFO  16:56:15,981 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:56Z] INFO  16:56:16,146 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:56Z] INFO  16:56:16,147 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:56Z] INFO  16:56:16,148 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:56Z] INFO  16:56:16,148 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-14T23:56Z] INFO  16:56:16,153 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:56Z] INFO  16:56:16,480 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:56Z] INFO  16:56:16,484 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:56Z] INFO  16:56:16,485 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:56Z] INFO  16:56:16,485 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:56Z] INFO  16:56:16,490 HelpFormatter - Program Args: -T PrintReads -L 13:1-19748299 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/13/tx/tmpkcKziV/R14-18105_kapa-NGv3-PE100-NGv3-sort-13_0_19748299-prep-prealign.bam
[2016-04-14T23:56Z] INFO  16:56:16,499 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:56Z] INFO  16:56:16,510 HelpFormatter - Date/Time: 2016/04/14 16:56:16
[2016-04-14T23:56Z] INFO  16:56:16,511 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:56Z] INFO  16:56:16,512 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:56Z] INFO  16:56:16,522 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-14T23:56Z] INFO  16:56:16,596 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:56Z] INFO  16:56:16,605 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:56Z] INFO  16:56:16,655 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-14T23:56Z] INFO  16:56:16,677 IntervalUtils - Processing 8584667 bp from intervals
[2016-04-14T23:56Z] INFO  16:56:16,705 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:56Z] INFO  16:56:16,782 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:56Z] INFO  16:56:17,020 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:56Z] INFO  16:56:17,020 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:56Z] INFO  16:56:17,020 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:56Z] INFO  16:56:17,021 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:56Z] INFO  16:56:17,047 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:56Z] INFO  16:56:17,164 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:56Z] INFO  16:56:17,856 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-14T23:56Z] INFO  16:56:17,934 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:56Z] INFO  16:56:17,944 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:56Z] INFO  16:56:18,029 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.09
[2016-04-14T23:56Z] INFO  16:56:18,046 IntervalUtils - Processing 19748299 bp from intervals
[2016-04-14T23:56Z] INFO  16:56:18,132 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:56Z] INFO  16:56:18,538 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:56Z] INFO  16:56:18,539 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:56Z] INFO  16:56:18,539 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:56Z] INFO  16:56:18,540 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:56Z] INFO  16:56:18,582 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:56Z] INFO  16:56:18,590 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:56Z] INFO  16:56:20,620 ProgressMeter -            done   1.5518246E7    17.0 s       1.0 s      100.0%    17.0 s       0.0 s
[2016-04-14T23:56Z] INFO  16:56:20,621 ProgressMeter - Total runtime 17.38 secs, 0.29 min, 0.00 hours
[2016-04-14T23:56Z] INFO  16:56:20,626 MicroScheduler - 18478 reads were filtered out during the traversal out of approximately 202441 total reads (9.13%)
[2016-04-14T23:56Z] INFO  16:56:20,627 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:56Z] INFO  16:56:20,628 MicroScheduler -   -> 499 reads (0.25% of total) failing BadMateFilter
[2016-04-14T23:56Z] INFO  16:56:20,629 MicroScheduler -   -> 15543 reads (7.68% of total) failing DuplicateReadFilter
[2016-04-14T23:56Z] INFO  16:56:20,629 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-14T23:56Z] INFO  16:56:20,630 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:56Z] INFO  16:56:20,631 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-14T23:56Z] INFO  16:56:20,631 MicroScheduler -   -> 2436 reads (1.20% of total) failing MappingQualityZeroFilter
[2016-04-14T23:56Z] INFO  16:56:20,632 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:56Z] INFO  16:56:20,633 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-14T23:56Z] INFO  16:56:20,633 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-14T23:56Z] INFO  16:56:20,967 ProgressMeter -      12:9027611    300004.0    61.0 s       3.4 m       57.7%   105.0 s      44.0 s
[2016-04-14T23:56Z] INFO  16:56:21,494 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@7172f77a
[2016-04-14T23:56Z] INFO  16:56:21,560 ProgressMeter -            done      7285.0     3.0 s       6.9 m      100.0%     3.0 s       0.0 s
[2016-04-14T23:56Z] INFO  16:56:21,561 ProgressMeter - Total runtime 3.02 secs, 0.05 min, 0.00 hours
[2016-04-14T23:56Z] INFO  16:56:21,562 MicroScheduler - 5 reads were filtered out during the traversal out of approximately 7290 total reads (0.07%)
[2016-04-14T23:56Z] INFO  16:56:21,563 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:56Z] INFO  16:56:21,563 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:56Z] INFO  16:56:21,564 MicroScheduler -   -> 5 reads (0.07% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:56Z] INFO  16:56:22,065 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:56Z] GATK: realign ('12', 31236746, 46754992) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-14T23:56Z] INFO  16:56:22,992 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:56Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-13_0_19748299-prep-prealign.bam
[2016-04-14T23:56Z] GATK RealignerTargetCreator: R14-18105_kapa-NGv3-PE100-NGv3-sort-13_0_19748299-prep-prealign.bam 13:1-19748299
[2016-04-14T23:56Z] GATK: RealignerTargetCreator
[2016-04-14T23:56Z] INFO  16:56:23,387 ProgressMeter -     11:68571589    600014.0    90.0 s       2.5 m       37.5%     4.0 m       2.5 m
[2016-04-14T23:56Z] INFO  16:56:24,042 ProgressMeter -            done    177593.0    13.0 s      76.0 s       92.1%    14.0 s       1.0 s
[2016-04-14T23:56Z] INFO  16:56:24,042 ProgressMeter - Total runtime 13.50 secs, 0.22 min, 0.00 hours
[2016-04-14T23:56Z] INFO  16:56:24,047 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 177593 total reads (0.00%)
[2016-04-14T23:56Z] INFO  16:56:24,048 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:56Z] INFO  16:56:24,049 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:56Z] INFO  16:56:24,050 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:56Z] INFO  16:56:24,743 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:56Z] INFO  16:56:24,747 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:56Z] INFO  16:56:24,747 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:56Z] INFO  16:56:24,748 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:56Z] INFO  16:56:24,752 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/12/R14-18105_kapa-NGv3-PE100-NGv3-sort-12_31236746_46754992-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/12/R14-18105_kapa-NGv3-PE100-NGv3-sort-12_31236746_46754992-prep-prealign-realign.intervals -L 12:31236747-46754992 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/12/tx/tmpMSc1PU/R14-18105_kapa-NGv3-PE100-NGv3-sort-12_31236746_46754992-prep.bam
[2016-04-14T23:56Z] INFO  16:56:24,775 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:56Z] INFO  16:56:24,776 HelpFormatter - Date/Time: 2016/04/14 16:56:24
[2016-04-14T23:56Z] INFO  16:56:24,776 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:56Z] INFO  16:56:24,776 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:56Z] INFO  16:56:25,004 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:56Z] INFO  16:56:25,135 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:56Z] INFO  16:56:25,144 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:56Z] INFO  16:56:25,209 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-14T23:56Z] INFO  16:56:25,503 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:56Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-11_125523640_135006516-prep.bam
[2016-04-14T23:56Z] INFO  16:56:25,594 IntervalUtils - Processing 15518246 bp from intervals
[2016-04-14T23:56Z] WARN  16:56:25,599 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:56Z] INFO  16:56:25,674 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:56Z] INFO  16:56:25,704 ProgressMeter -     11:15994585   1.5990784E7    30.0 s       1.0 s      100.0%    30.0 s       0.0 s
[2016-04-14T23:56Z] INFO  16:56:25,716 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:56Z] INFO  16:56:25,720 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:56Z] INFO  16:56:25,721 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:56Z] INFO  16:56:25,721 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:56Z] INFO  16:56:25,726 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/13/R14-18105_kapa-NGv3-PE100-NGv3-sort-13_0_19748299-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/13/tx/tmpmwCY3Y/R14-18105_kapa-NGv3-PE100-NGv3-sort-13_0_19748299-prep-prealign-realign.intervals -l INFO -L 13:1-19748299 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-14T23:56Z] INFO  16:56:25,747 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:56Z] INFO  16:56:25,747 HelpFormatter - Date/Time: 2016/04/14 16:56:25
[2016-04-14T23:56Z] INFO  16:56:25,747 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:56Z] INFO  16:56:25,748 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:56Z] INFO  16:56:25,779 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:56Z] INFO  16:56:25,780 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:56Z] INFO  16:56:25,781 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:56Z] INFO  16:56:25,781 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:56Z] INFO  16:56:25,834 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:56Z] INFO  16:56:25,922 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:56Z] INFO  16:56:26,022 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-14T23:56Z] INFO  16:56:26,044 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:56Z] INFO  16:56:26,078 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:56Z] INFO  16:56:26,115 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-14T23:56Z] GATK pre-alignment ('13', 19751066, 35517251) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-14T23:56Z] INFO  16:56:26,281 ProgressMeter -            done   1.5994658E7    30.0 s       1.0 s      100.0%    30.0 s       0.0 s
[2016-04-14T23:56Z] INFO  16:56:26,282 ProgressMeter - Total runtime 30.59 secs, 0.51 min, 0.01 hours
[2016-04-14T23:56Z] INFO  16:56:26,283 MicroScheduler - 92576 reads were filtered out during the traversal out of approximately 826365 total reads (11.20%)
[2016-04-14T23:56Z] INFO  16:56:26,284 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:56Z] INFO  16:56:26,284 MicroScheduler -   -> 1491 reads (0.18% of total) failing BadMateFilter
[2016-04-14T23:56Z] INFO  16:56:26,285 MicroScheduler -   -> 68432 reads (8.28% of total) failing DuplicateReadFilter
[2016-04-14T23:56Z] INFO  16:56:26,286 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-14T23:56Z] INFO  16:56:26,286 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:56Z] INFO  16:56:26,287 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-14T23:56Z] INFO  16:56:26,287 MicroScheduler -   -> 22653 reads (2.74% of total) failing MappingQualityZeroFilter
[2016-04-14T23:56Z] INFO  16:56:26,288 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:56Z] INFO  16:56:26,289 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-14T23:56Z] INFO  16:56:26,290 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-14T23:56Z] INFO  16:56:26,398 IntervalUtils - Processing 19748299 bp from intervals
[2016-04-14T23:56Z] WARN  16:56:26,404 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:56Z] INFO  16:56:26,475 ProgressMeter -            done    163681.0    14.0 s      86.0 s      100.0%    14.0 s       0.0 s
[2016-04-14T23:56Z] INFO  16:56:26,476 ProgressMeter - Total runtime 14.08 secs, 0.23 min, 0.00 hours
[2016-04-14T23:56Z] INFO  16:56:26,479 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 163681 total reads (0.00%)
[2016-04-14T23:56Z] INFO  16:56:26,480 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:56Z] INFO  16:56:26,480 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:56Z] INFO  16:56:26,480 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:56Z] INFO  16:56:26,513 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:56Z] INFO  16:56:26,857 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:56Z] INFO  16:56:26,858 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:56Z] INFO  16:56:26,859 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:56Z] INFO  16:56:26,860 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-14T23:56Z] INFO  16:56:27,884 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:56Z] GATK: realign ('11', 0, 15994658) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-14T23:56Z] INFO  16:56:28,038 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:56Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-12_15650178_31231471-prep.bam
[2016-04-14T23:56Z] GATK pre-alignment ('13', 35615069, 51287376) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-14T23:56Z] INFO  16:56:29,046 ProgressMeter -            done   1.5537525E7    17.0 s       1.0 s      100.0%    17.0 s       0.0 s
[2016-04-14T23:56Z] INFO  16:56:29,048 ProgressMeter - Total runtime 17.14 secs, 0.29 min, 0.00 hours
[2016-04-14T23:56Z] INFO  16:56:29,053 MicroScheduler - 15607 reads were filtered out during the traversal out of approximately 182920 total reads (8.53%)
[2016-04-14T23:56Z] INFO  16:56:29,054 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:56Z] INFO  16:56:29,055 MicroScheduler -   -> 553 reads (0.30% of total) failing BadMateFilter
[2016-04-14T23:56Z] INFO  16:56:29,056 MicroScheduler -   -> 14327 reads (7.83% of total) failing DuplicateReadFilter
[2016-04-14T23:56Z] INFO  16:56:29,056 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-14T23:56Z] INFO  16:56:29,057 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:56Z] INFO  16:56:29,058 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-14T23:56Z] INFO  16:56:29,059 MicroScheduler -   -> 727 reads (0.40% of total) failing MappingQualityZeroFilter
[2016-04-14T23:56Z] INFO  16:56:29,059 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:56Z] INFO  16:56:29,060 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-14T23:56Z] INFO  16:56:29,061 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-14T23:56Z] INFO  16:56:29,439 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:56Z] INFO  16:56:29,445 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:56Z] INFO  16:56:29,446 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:56Z] INFO  16:56:29,446 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:56Z] INFO  16:56:29,452 HelpFormatter - Program Args: -T PrintReads -L 13:19751067-35517251 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/13/tx/tmp9vb_Fy/R14-18105_kapa-NGv3-PE100-NGv3-sort-13_19751066_35517251-prep-prealign.bam
[2016-04-14T23:56Z] INFO  16:56:29,462 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:56Z] INFO  16:56:29,462 HelpFormatter - Date/Time: 2016/04/14 16:56:29
[2016-04-14T23:56Z] INFO  16:56:29,463 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:56Z] INFO  16:56:29,463 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:56Z] INFO  16:56:29,640 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:56Z] INFO  16:56:30,575 ProgressMeter -            done   1.5519706E7    24.0 s       1.0 s      100.0%    24.0 s       0.0 s
[2016-04-14T23:56Z] INFO  16:56:30,577 ProgressMeter - Total runtime 24.91 secs, 0.42 min, 0.01 hours
[2016-04-14T23:56Z] INFO  16:56:30,581 MicroScheduler - 57706 reads were filtered out during the traversal out of approximately 569952 total reads (10.12%)
[2016-04-14T23:56Z] INFO  16:56:30,582 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:56Z] INFO  16:56:30,582 MicroScheduler -   -> 978 reads (0.17% of total) failing BadMateFilter
[2016-04-14T23:56Z] INFO  16:56:30,583 MicroScheduler -   -> 44451 reads (7.80% of total) failing DuplicateReadFilter
[2016-04-14T23:56Z] INFO  16:56:30,584 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-14T23:56Z] INFO  16:56:30,584 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:56Z] INFO  16:56:30,585 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-14T23:56Z] INFO  16:56:30,586 MicroScheduler -   -> 12277 reads (2.15% of total) failing MappingQualityZeroFilter
[2016-04-14T23:56Z] INFO  16:56:30,586 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:56Z] INFO  16:56:30,587 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-14T23:56Z] INFO  16:56:30,588 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-14T23:56Z] INFO  16:56:30,573 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:56Z] INFO  16:56:30,595 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:56Z] INFO  16:56:30,595 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:56Z] INFO  16:56:30,596 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:56Z] INFO  16:56:30,600 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/11/R14-18105_kapa-NGv3-PE100-NGv3-sort-11_0_15994658-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/11/R14-18105_kapa-NGv3-PE100-NGv3-sort-11_0_15994658-prep-prealign-realign.intervals -L 11:1-15994658 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/11/tx/tmp7O6Fzv/R14-18105_kapa-NGv3-PE100-NGv3-sort-11_0_15994658-prep.bam
[2016-04-14T23:56Z] INFO  16:56:30,611 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:56Z] INFO  16:56:30,622 HelpFormatter - Date/Time: 2016/04/14 16:56:30
[2016-04-14T23:56Z] INFO  16:56:30,623 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:56Z] INFO  16:56:30,623 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:56Z] INFO  16:56:30,728 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:56Z] GATK: realign ('12', 62687959, 78225484) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-14T23:56Z] INFO  16:56:30,759 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-14T23:56Z] INFO  16:56:30,836 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:56Z] INFO  16:56:30,842 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:56Z] INFO  16:56:30,844 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:56Z] INFO  16:56:30,890 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-14T23:56Z] INFO  16:56:30,904 IntervalUtils - Processing 15766185 bp from intervals
[2016-04-14T23:56Z] INFO  16:56:30,965 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:56Z] INFO  16:56:30,974 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:56Z] INFO  16:56:30,994 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:56Z] INFO  16:56:31,027 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-14T23:56Z] INFO  16:56:31,167 ProgressMeter -            done    857787.0    51.0 s      59.0 s       99.3%    51.0 s       0.0 s
[2016-04-14T23:56Z] INFO  16:56:31,168 ProgressMeter - Total runtime 51.27 secs, 0.85 min, 0.01 hours
[2016-04-14T23:56Z] INFO  16:56:31,171 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 857787 total reads (0.00%)
[2016-04-14T23:56Z] INFO  16:56:31,172 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:56Z] INFO  16:56:31,172 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:56Z] INFO  16:56:31,172 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:56Z] INFO  16:56:31,285 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:56Z] INFO  16:56:31,286 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:56Z] INFO  16:56:31,287 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:56Z] INFO  16:56:31,287 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:56Z] INFO  16:56:31,301 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:56Z] INFO  16:56:31,424 IntervalUtils - Processing 15994658 bp from intervals
[2016-04-14T23:56Z] WARN  16:56:31,429 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:56Z] INFO  16:56:31,503 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:56Z] INFO  16:56:31,512 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:56Z] INFO  16:56:31,515 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:56Z] INFO  16:56:31,516 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:56Z] INFO  16:56:31,516 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:56Z] INFO  16:56:31,521 HelpFormatter - Program Args: -T PrintReads -L 13:35615070-51287376 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/13/tx/tmpHcXHeE/R14-18105_kapa-NGv3-PE100-NGv3-sort-13_35615069_51287376-prep-prealign.bam
[2016-04-14T23:56Z] INFO  16:56:31,533 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:56Z] INFO  16:56:31,533 HelpFormatter - Date/Time: 2016/04/14 16:56:31
[2016-04-14T23:56Z] INFO  16:56:31,533 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:56Z] INFO  16:56:31,534 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:56Z] INFO  16:56:31,568 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:56Z] INFO  16:56:31,733 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:56Z] INFO  16:56:31,733 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:56Z] INFO  16:56:31,734 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:56Z] INFO  16:56:31,734 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:56Z] INFO  16:56:31,751 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:56Z] INFO  16:56:31,935 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:56Z] INFO  16:56:31,965 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:56Z] GATK: realign ('11', 47158866, 62678572) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-14T23:56Z] INFO  16:56:32,062 ProgressMeter -            done   1.5529033E7    15.0 s       1.0 s      100.0%    15.0 s       0.0 s
[2016-04-14T23:56Z] INFO  16:56:32,063 ProgressMeter - Total runtime 15.92 secs, 0.27 min, 0.00 hours
[2016-04-14T23:56Z] INFO  16:56:32,066 MicroScheduler - 8452 reads were filtered out during the traversal out of approximately 98139 total reads (8.61%)
[2016-04-14T23:56Z] INFO  16:56:32,067 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:56Z] INFO  16:56:32,067 MicroScheduler -   -> 412 reads (0.42% of total) failing BadMateFilter
[2016-04-14T23:56Z] INFO  16:56:32,067 MicroScheduler -   -> 7705 reads (7.85% of total) failing DuplicateReadFilter
[2016-04-14T23:56Z] INFO  16:56:32,068 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-14T23:56Z] INFO  16:56:32,068 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:56Z] INFO  16:56:32,068 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-14T23:56Z] INFO  16:56:32,068 MicroScheduler -   -> 335 reads (0.34% of total) failing MappingQualityZeroFilter
[2016-04-14T23:56Z] INFO  16:56:32,069 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:56Z] INFO  16:56:32,069 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-14T23:56Z] INFO  16:56:32,069 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-14T23:56Z] INFO  16:56:32,194 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:56Z] INFO  16:56:32,369 ProgressMeter -     12:53878100    400007.0    60.0 s       2.5 m       44.8%     2.2 m      73.0 s
[2016-04-14T23:56Z] INFO  16:56:32,620 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:56Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-9_129097484_141213431-prep.bam
[2016-04-14T23:56Z] INFO  16:56:32,998 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-14T23:56Z] INFO  16:56:33,065 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:56Z] INFO  16:56:33,075 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:56Z] INFO  16:56:33,131 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-14T23:56Z] INFO  16:56:33,146 IntervalUtils - Processing 15672307 bp from intervals
[2016-04-14T23:56Z] INFO  16:56:33,242 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:56Z] INFO  16:56:33,497 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:56Z] GATK: realign ('12', 78334098, 93863131) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-14T23:56Z] INFO  16:56:33,584 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:56Z] INFO  16:56:33,585 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:56Z] INFO  16:56:33,586 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:56Z] INFO  16:56:33,587 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:56Z] INFO  16:56:33,603 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:56Z] INFO  16:56:33,672 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:56Z] INFO  16:56:33,675 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:56Z] INFO  16:56:33,676 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:56Z] INFO  16:56:33,676 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:56Z] INFO  16:56:33,681 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/12/R14-18105_kapa-NGv3-PE100-NGv3-sort-12_62687959_78225484-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/12/R14-18105_kapa-NGv3-PE100-NGv3-sort-12_62687959_78225484-prep-prealign-realign.intervals -L 12:62687960-78225484 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/12/tx/tmpxbfi5P/R14-18105_kapa-NGv3-PE100-NGv3-sort-12_62687959_78225484-prep.bam
[2016-04-14T23:56Z] INFO  16:56:33,693 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:56Z] INFO  16:56:33,694 HelpFormatter - Date/Time: 2016/04/14 16:56:33
[2016-04-14T23:56Z] INFO  16:56:33,695 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:56Z] INFO  16:56:33,695 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:56Z] INFO  16:56:33,800 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:56Z] INFO  16:56:33,839 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:56Z] INFO  16:56:33,942 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:56Z] INFO  16:56:33,961 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:56Z] INFO  16:56:34,028 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-14T23:56Z] INFO  16:56:34,368 IntervalUtils - Processing 15537525 bp from intervals
[2016-04-14T23:56Z] WARN  16:56:34,373 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:56Z] INFO  16:56:34,475 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:56Z] INFO  16:56:34,596 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:56Z] INFO  16:56:34,597 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:56Z] INFO  16:56:34,598 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:56Z] INFO  16:56:34,598 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:56Z] INFO  16:56:34,643 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:56Z] INFO  16:56:34,647 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:56Z] INFO  16:56:34,647 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:56Z] INFO  16:56:34,648 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:56Z] INFO  16:56:34,652 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/11/R14-18105_kapa-NGv3-PE100-NGv3-sort-11_47158866_62678572-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/11/R14-18105_kapa-NGv3-PE100-NGv3-sort-11_47158866_62678572-prep-prealign-realign.intervals -L 11:47158867-62678572 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/11/tx/tmpVXjg01/R14-18105_kapa-NGv3-PE100-NGv3-sort-11_47158866_62678572-prep.bam
[2016-04-14T23:56Z] INFO  16:56:34,662 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:56Z] INFO  16:56:34,663 HelpFormatter - Date/Time: 2016/04/14 16:56:34
[2016-04-14T23:56Z] INFO  16:56:34,664 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:56Z] INFO  16:56:34,664 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:56Z] INFO  16:56:34,721 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:56Z] INFO  16:56:34,849 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:56Z] INFO  16:56:34,909 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:56Z] GATK pre-alignment ('13', 51396767, 67205543) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-14T23:56Z] INFO  16:56:35,061 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:56Z] INFO  16:56:35,078 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:56Z] INFO  16:56:35,150 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-14T23:56Z] INFO  16:56:35,767 IntervalUtils - Processing 15519706 bp from intervals
[2016-04-14T23:56Z] WARN  16:56:35,772 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:56Z] INFO  16:56:35,846 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:56Z] INFO  16:56:36,014 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:56Z] INFO  16:56:36,014 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:56Z] INFO  16:56:36,014 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:56Z] INFO  16:56:36,015 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:56Z] INFO  16:56:36,254 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:56Z] INFO  16:56:36,430 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:56Z] INFO  16:56:36,538 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:56Z] INFO  16:56:36,541 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:56Z] INFO  16:56:36,542 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:56Z] INFO  16:56:36,542 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:56Z] INFO  16:56:36,547 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/12/R14-18105_kapa-NGv3-PE100-NGv3-sort-12_78334098_93863131-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/12/R14-18105_kapa-NGv3-PE100-NGv3-sort-12_78334098_93863131-prep-prealign-realign.intervals -L 12:78334099-93863131 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/12/tx/tmpBD8O_A/R14-18105_kapa-NGv3-PE100-NGv3-sort-12_78334098_93863131-prep.bam
[2016-04-14T23:56Z] INFO  16:56:36,557 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:56Z] INFO  16:56:36,557 HelpFormatter - Date/Time: 2016/04/14 16:56:36
[2016-04-14T23:56Z] INFO  16:56:36,557 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:56Z] INFO  16:56:36,557 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:56Z] INFO  16:56:36,785 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:56Z] INFO  16:56:36,981 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:56Z] INFO  16:56:36,990 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:56Z] INFO  16:56:37,075 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-14T23:56Z] INFO  16:56:37,463 IntervalUtils - Processing 15529033 bp from intervals
[2016-04-14T23:56Z] WARN  16:56:37,468 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:56Z] INFO  16:56:37,580 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:56Z] INFO  16:56:37,695 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:56Z] INFO  16:56:37,696 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:56Z] INFO  16:56:37,697 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:56Z] INFO  16:56:37,697 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:56Z] INFO  16:56:37,847 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:56Z] INFO  16:56:37,850 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:56Z] INFO  16:56:37,851 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:56Z] INFO  16:56:37,851 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:56Z] INFO  16:56:37,856 HelpFormatter - Program Args: -T PrintReads -L 13:51396768-67205543 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/13/tx/tmptCXyF9/R14-18105_kapa-NGv3-PE100-NGv3-sort-13_51396767_67205543-prep-prealign.bam
[2016-04-14T23:56Z] INFO  16:56:37,890 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:56Z] INFO  16:56:37,891 HelpFormatter - Date/Time: 2016/04/14 16:56:37
[2016-04-14T23:56Z] INFO  16:56:37,891 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:56Z] INFO  16:56:37,891 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:56Z] INFO  16:56:37,892 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:56Z] INFO  16:56:38,056 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:56Z] INFO  16:56:38,082 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:56Z] INFO  16:56:38,772 ProgressMeter -            done   1.9748299E7    11.0 s       0.0 s      100.0%    11.0 s       0.0 s
[2016-04-14T23:56Z] INFO  16:56:38,773 ProgressMeter - Total runtime 11.92 secs, 0.20 min, 0.00 hours
[2016-04-14T23:56Z] INFO  16:56:38,777 MicroScheduler - 878 reads were filtered out during the traversal out of approximately 7345 total reads (11.95%)
[2016-04-14T23:56Z] INFO  16:56:38,789 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:56Z] INFO  16:56:38,790 MicroScheduler -   -> 34 reads (0.46% of total) failing BadMateFilter
[2016-04-14T23:56Z] INFO  16:56:38,790 MicroScheduler -   -> 562 reads (7.65% of total) failing DuplicateReadFilter
[2016-04-14T23:56Z] INFO  16:56:38,791 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-14T23:56Z] INFO  16:56:38,792 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:56Z] INFO  16:56:38,792 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-14T23:56Z] INFO  16:56:38,793 MicroScheduler -   -> 282 reads (3.84% of total) failing MappingQualityZeroFilter
[2016-04-14T23:56Z] INFO  16:56:38,794 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:56Z] INFO  16:56:38,794 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-14T23:56Z] INFO  16:56:38,795 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-14T23:56Z] INFO  16:56:38,921 ProgressMeter -            done   1.5512808E7    24.0 s       1.0 s      100.0%    24.0 s       0.0 s
[2016-04-14T23:56Z] INFO  16:56:38,922 ProgressMeter - Total runtime 24.52 secs, 0.41 min, 0.01 hours
[2016-04-14T23:56Z] INFO  16:56:38,926 MicroScheduler - 46711 reads were filtered out during the traversal out of approximately 524509 total reads (8.91%)
[2016-04-14T23:56Z] INFO  16:56:38,926 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:56Z] INFO  16:56:38,927 MicroScheduler -   -> 1068 reads (0.20% of total) failing BadMateFilter
[2016-04-14T23:56Z] INFO  16:56:38,927 MicroScheduler -   -> 41522 reads (7.92% of total) failing DuplicateReadFilter
[2016-04-14T23:56Z] INFO  16:56:38,927 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-14T23:56Z] INFO  16:56:38,927 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:56Z] INFO  16:56:38,928 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-14T23:56Z] INFO  16:56:38,928 MicroScheduler -   -> 4121 reads (0.79% of total) failing MappingQualityZeroFilter
[2016-04-14T23:56Z] INFO  16:56:38,928 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:56Z] INFO  16:56:38,928 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-14T23:56Z] INFO  16:56:38,929 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-14T23:56Z] INFO  16:56:39,240 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-14T23:56Z] INFO  16:56:39,304 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:56Z] INFO  16:56:39,313 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:56Z] INFO  16:56:39,370 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-14T23:56Z] INFO  16:56:39,406 IntervalUtils - Processing 15808776 bp from intervals
[2016-04-14T23:56Z] INFO  16:56:39,500 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:56Z] INFO  16:56:39,723 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:56Z] INFO  16:56:39,724 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:56Z] INFO  16:56:39,725 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:56Z] INFO  16:56:39,725 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:56Z] INFO  16:56:39,739 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:56Z] INFO  16:56:39,887 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:56Z] INFO  16:56:40,315 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:56Z] GATK: realign ('13', 0, 19748299) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-14T23:56Z] INFO  16:56:40,426 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:56Z] GATK: realign ('11', 110001730, 125514538) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-14T23:56Z] INFO  16:56:41,248 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@41fd9d8e
[2016-04-14T23:56Z] INFO  16:56:41,336 ProgressMeter -            done    558357.0    81.0 s       2.4 m      100.0%    81.0 s       0.0 s
[2016-04-14T23:56Z] INFO  16:56:41,337 ProgressMeter - Total runtime 81.53 secs, 1.36 min, 0.02 hours
[2016-04-14T23:56Z] INFO  16:56:41,337 MicroScheduler - 257 reads were filtered out during the traversal out of approximately 558614 total reads (0.05%)
[2016-04-14T23:56Z] INFO  16:56:41,338 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:56Z] INFO  16:56:41,338 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:56Z] INFO  16:56:41,338 MicroScheduler -   -> 257 reads (0.05% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:56Z] INFO  16:56:42,200 ProgressMeter -            done    200500.0    16.0 s      81.0 s      100.0%    16.0 s       0.0 s
[2016-04-14T23:56Z] INFO  16:56:42,201 ProgressMeter - Total runtime 16.42 secs, 0.27 min, 0.00 hours
[2016-04-14T23:56Z] INFO  16:56:42,204 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 200500 total reads (0.00%)
[2016-04-14T23:56Z] INFO  16:56:42,206 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:56Z] INFO  16:56:42,206 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:56Z] INFO  16:56:42,207 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:56Z] INFO  16:56:42,888 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:56Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-12_0_15637181-prep-prealign.bam
[2016-04-14T23:56Z] INFO  16:56:43,251 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:56Z] INFO  16:56:43,254 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:56Z] INFO  16:56:43,255 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:56Z] INFO  16:56:43,255 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:56Z] INFO  16:56:43,260 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/11/R14-18105_kapa-NGv3-PE100-NGv3-sort-11_110001730_125514538-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/11/R14-18105_kapa-NGv3-PE100-NGv3-sort-11_110001730_125514538-prep-prealign-realign.intervals -L 11:110001731-125514538 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/11/tx/tmpHvQPkR/R14-18105_kapa-NGv3-PE100-NGv3-sort-11_110001730_125514538-prep.bam
[2016-04-14T23:56Z] INFO  16:56:43,291 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:56Z] INFO  16:56:43,292 HelpFormatter - Date/Time: 2016/04/14 16:56:43
[2016-04-14T23:56Z] INFO  16:56:43,292 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:56Z] INFO  16:56:43,297 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:56Z] INFO  16:56:43,309 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:56Z] INFO  16:56:43,312 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:56Z] INFO  16:56:43,313 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:56Z] INFO  16:56:43,313 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:56Z] INFO  16:56:43,318 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/13/R14-18105_kapa-NGv3-PE100-NGv3-sort-13_0_19748299-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/13/R14-18105_kapa-NGv3-PE100-NGv3-sort-13_0_19748299-prep-prealign-realign.intervals -L 13:1-19748299 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/13/tx/tmpMB_HNp/R14-18105_kapa-NGv3-PE100-NGv3-sort-13_0_19748299-prep.bam
[2016-04-14T23:56Z] INFO  16:56:43,336 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:56Z] INFO  16:56:43,337 HelpFormatter - Date/Time: 2016/04/14 16:56:43
[2016-04-14T23:56Z] INFO  16:56:43,337 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:56Z] INFO  16:56:43,338 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:56Z] INFO  16:56:43,495 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:56Z] INFO  16:56:43,510 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:56Z] INFO  16:56:43,586 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:56Z] INFO  16:56:43,595 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:56Z] INFO  16:56:43,625 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:56Z] INFO  16:56:43,634 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:56Z] INFO  16:56:43,640 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.04
[2016-04-14T23:56Z] INFO  16:56:43,691 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:56Z] INFO  16:56:43,715 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-14T23:56Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-12_31236746_46754992-prep.bam
[2016-04-14T23:56Z] INFO  16:56:43,907 ProgressMeter -    12:107351015    200002.0    30.0 s       2.5 m       86.3%    34.0 s       4.0 s
[2016-04-14T23:56Z] INFO  16:56:44,107 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@5fe152b7
[2016-04-14T23:56Z] INFO  16:56:44,128 IntervalUtils - Processing 19748299 bp from intervals
[2016-04-14T23:56Z] WARN  16:56:44,141 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:56Z] INFO  16:56:44,190 IntervalUtils - Processing 15512808 bp from intervals
[2016-04-14T23:56Z] WARN  16:56:44,196 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:56Z] INFO  16:56:44,228 ProgressMeter -            done    209171.0    27.0 s       2.2 m       99.5%    27.0 s       0.0 s
[2016-04-14T23:56Z] INFO  16:56:44,229 ProgressMeter - Total runtime 27.21 secs, 0.45 min, 0.01 hours
[2016-04-14T23:56Z] INFO  16:56:44,230 MicroScheduler - 142 reads were filtered out during the traversal out of approximately 209313 total reads (0.07%)
[2016-04-14T23:56Z] INFO  16:56:44,230 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:56Z] INFO  16:56:44,231 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:56Z] INFO  16:56:44,232 MicroScheduler -   -> 142 reads (0.07% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:56Z] INFO  16:56:44,272 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:56Z] INFO  16:56:44,314 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:56Z] GATK pre-alignment ('13', 67477635, 84455642) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-14T23:56Z] INFO  16:56:44,470 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:56Z] INFO  16:56:44,471 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:56Z] INFO  16:56:44,472 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:56Z] INFO  16:56:44,473 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:56Z] INFO  16:56:44,556 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:56Z] INFO  16:56:44,558 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:56Z] INFO  16:56:44,559 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:56Z] INFO  16:56:44,560 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:56Z] INFO  16:56:44,594 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:56Z] INFO  16:56:44,614 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:56Z] INFO  16:56:44,661 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:56Z] INFO  16:56:44,828 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:56Z] GATK RealignerTargetCreator: R14-18105_kapa-NGv3-PE100-NGv3-sort-12_0_15637181-prep-prealign.bam 12:1-15637181
[2016-04-14T23:56Z] GATK: RealignerTargetCreator
[2016-04-14T23:56Z] INFO  16:56:45,770 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:56Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-12_125267228_133851895-prep-prealign.bam
[2016-04-14T23:56Z] INFO  16:56:46,347 ProgressMeter -    12:113328586    100001.0    30.0 s       5.1 m       24.3%     2.1 m      93.0 s
[2016-04-14T23:56Z] GATK RealignerTargetCreator: R14-18105_kapa-NGv3-PE100-NGv3-sort-12_125267228_133851895-prep-prealign.bam 12:125267229-133851895
[2016-04-14T23:56Z] GATK: RealignerTargetCreator
[2016-04-14T23:56Z] INFO  16:56:46,853 ProgressMeter -            done      7285.0     2.0 s       5.2 m      100.0%     2.0 s       0.0 s
[2016-04-14T23:56Z] INFO  16:56:46,854 ProgressMeter - Total runtime 2.30 secs, 0.04 min, 0.00 hours
[2016-04-14T23:56Z] INFO  16:56:46,857 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 7285 total reads (0.00%)
[2016-04-14T23:56Z] INFO  16:56:46,858 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:56Z] INFO  16:56:46,858 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:56Z] INFO  16:56:46,858 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:56Z] INFO  16:56:47,366 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:56Z] INFO  16:56:47,369 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:56Z] INFO  16:56:47,370 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:56Z] INFO  16:56:47,371 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:56Z] INFO  16:56:47,378 HelpFormatter - Program Args: -T PrintReads -L 13:67477636-84455642 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/13/tx/tmpvswSap/R14-18105_kapa-NGv3-PE100-NGv3-sort-13_67477635_84455642-prep-prealign.bam
[2016-04-14T23:56Z] INFO  16:56:47,381 ProgressMeter -            done     97815.0     9.0 s      99.0 s      100.0%     9.0 s       0.0 s
[2016-04-14T23:56Z] INFO  16:56:47,382 ProgressMeter - Total runtime 9.69 secs, 0.16 min, 0.00 hours
[2016-04-14T23:56Z] INFO  16:56:47,385 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 97815 total reads (0.00%)
[2016-04-14T23:56Z] INFO  16:56:47,386 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:56Z] INFO  16:56:47,386 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:56Z] INFO  16:56:47,386 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:56Z] INFO  16:56:47,425 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:56Z] INFO  16:56:47,425 HelpFormatter - Date/Time: 2016/04/14 16:56:47
[2016-04-14T23:56Z] INFO  16:56:47,425 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:56Z] INFO  16:56:47,426 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:56Z] INFO  16:56:47,596 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:56Z] INFO  16:56:47,854 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:56Z] INFO  16:56:47,857 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:56Z] INFO  16:56:47,857 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:56Z] INFO  16:56:47,857 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:56Z] INFO  16:56:47,872 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/12/R14-18105_kapa-NGv3-PE100-NGv3-sort-12_0_15637181-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/12/tx/tmptI5PEE/R14-18105_kapa-NGv3-PE100-NGv3-sort-12_0_15637181-prep-prealign-realign.intervals -l INFO -L 12:1-15637181 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-14T23:56Z] INFO  16:56:47,887 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:56Z] INFO  16:56:47,887 HelpFormatter - Date/Time: 2016/04/14 16:56:47
[2016-04-14T23:56Z] INFO  16:56:47,887 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:56Z] INFO  16:56:47,887 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:56Z] INFO  16:56:48,038 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:56Z] INFO  16:56:48,287 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:56Z] INFO  16:56:48,302 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-14T23:56Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-13_0_19748299-prep.bam
[2016-04-14T23:56Z] INFO  16:56:48,312 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:56Z] INFO  16:56:48,363 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-14T23:56Z] GATK pre-alignment ('13', 86368117, 101881935) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-14T23:56Z] INFO  16:56:48,403 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@7172f77a
[2016-04-14T23:56Z] INFO  16:56:48,479 ProgressMeter -            done    182081.0    13.0 s      76.0 s      100.0%    13.0 s       0.0 s
[2016-04-14T23:56Z] INFO  16:56:48,479 ProgressMeter - Total runtime 13.88 secs, 0.23 min, 0.00 hours
[2016-04-14T23:56Z] INFO  16:56:48,482 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 182081 total reads (0.00%)
[2016-04-14T23:56Z] INFO  16:56:48,482 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:56Z] INFO  16:56:48,483 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:56Z] INFO  16:56:48,483 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:56Z] INFO  16:56:48,550 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-14T23:56Z] INFO  16:56:48,573 ProgressMeter -            done    286037.0    34.0 s       2.0 m      100.0%    34.0 s       0.0 s
[2016-04-14T23:56Z] INFO  16:56:48,574 ProgressMeter - Total runtime 34.71 secs, 0.58 min, 0.01 hours
[2016-04-14T23:56Z] INFO  16:56:48,574 MicroScheduler - 169 reads were filtered out during the traversal out of approximately 286206 total reads (0.06%)
[2016-04-14T23:56Z] INFO  16:56:48,575 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:56Z] INFO  16:56:48,575 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:56Z] INFO  16:56:48,575 MicroScheduler -   -> 169 reads (0.06% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:56Z] INFO  16:56:48,624 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:56Z] INFO  16:56:48,625 IntervalUtils - Processing 15637181 bp from intervals
[2016-04-14T23:56Z] WARN  16:56:48,631 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:56Z] INFO  16:56:48,644 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:56Z] INFO  16:56:48,698 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-14T23:56Z] INFO  16:56:48,722 IntervalUtils - Processing 16978007 bp from intervals
[2016-04-14T23:56Z] INFO  16:56:48,742 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:56Z] INFO  16:56:48,833 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:56Z] INFO  16:56:48,878 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:56Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-12_78334098_93863131-prep.bam
[2016-04-14T23:56Z] INFO  16:56:48,956 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:56Z] INFO  16:56:48,968 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:56Z] INFO  16:56:48,969 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:56Z] INFO  16:56:48,969 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-14T23:56Z] INFO  16:56:49,076 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:56Z] INFO  16:56:49,077 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:56Z] INFO  16:56:49,078 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:56Z] INFO  16:56:49,079 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:56Z] INFO  16:56:49,122 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:56Z] GATK pre-alignment ('13', 101890105, 115169878) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-14T23:56Z] INFO  16:56:49,275 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:56Z] INFO  16:56:49,277 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:56Z] INFO  16:56:49,280 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:56Z] INFO  16:56:49,281 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:56Z] INFO  16:56:49,282 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:56Z] INFO  16:56:49,287 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/12/R14-18105_kapa-NGv3-PE100-NGv3-sort-12_125267228_133851895-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/12/tx/tmpsLBw4t/R14-18105_kapa-NGv3-PE100-NGv3-sort-12_125267228_133851895-prep-prealign-realign.intervals -l INFO -L 12:125267229-133851895 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-14T23:56Z] INFO  16:56:49,304 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:56Z] INFO  16:56:49,305 HelpFormatter - Date/Time: 2016/04/14 16:56:49
[2016-04-14T23:56Z] INFO  16:56:49,305 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:56Z] INFO  16:56:49,306 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:56Z] INFO  16:56:49,401 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:56Z] INFO  16:56:49,694 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-14T23:56Z] INFO  16:56:49,705 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:56Z] INFO  16:56:49,810 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.09
[2016-04-14T23:56Z] INFO  16:56:50,022 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:56Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-12_93870729_109490566-prep-prealign.bam
[2016-04-14T23:56Z] INFO  16:56:50,077 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:56Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-12_62687959_78225484-prep.bam
[2016-04-14T23:56Z] INFO  16:56:50,139 IntervalUtils - Processing 8584667 bp from intervals
[2016-04-14T23:56Z] WARN  16:56:50,145 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:56Z] INFO  16:56:50,255 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:56Z] INFO  16:56:50,494 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:56Z] INFO  16:56:50,495 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:56Z] INFO  16:56:50,496 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:56Z] INFO  16:56:50,497 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-14T23:56Z] GATK pre-alignment ('14', 0, 19378574) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-14T23:56Z] GATK RealignerTargetCreator: R14-18105_kapa-NGv3-PE100-NGv3-sort-12_93870729_109490566-prep-prealign.bam 12:93870730-109490566
[2016-04-14T23:56Z] GATK: RealignerTargetCreator
[2016-04-14T23:56Z] INFO  16:56:51,129 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:56Z] INFO  16:56:51,132 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:56Z] INFO  16:56:51,133 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:56Z] INFO  16:56:51,133 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:56Z] INFO  16:56:51,138 HelpFormatter - Program Args: -T PrintReads -L 13:86368118-101881935 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/13/tx/tmpVYo8En/R14-18105_kapa-NGv3-PE100-NGv3-sort-13_86368117_101881935-prep-prealign.bam
[2016-04-14T23:56Z] INFO  16:56:51,172 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:56Z] INFO  16:56:51,173 HelpFormatter - Date/Time: 2016/04/14 16:56:51
[2016-04-14T23:56Z] INFO  16:56:51,174 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:56Z] INFO  16:56:51,174 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:56Z] INFO  16:56:51,344 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:56Z] INFO  16:56:52,370 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:56Z] INFO  16:56:52,373 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:56Z] INFO  16:56:52,373 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:56Z] INFO  16:56:52,373 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:56Z] INFO  16:56:52,377 HelpFormatter - Program Args: -T PrintReads -L 13:101890106-115169878 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/13/tx/tmpbfxfGC/R14-18105_kapa-NGv3-PE100-NGv3-sort-13_101890105_115169878-prep-prealign.bam
[2016-04-14T23:56Z] INFO  16:56:52,386 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:56Z] INFO  16:56:52,387 HelpFormatter - Date/Time: 2016/04/14 16:56:52
[2016-04-14T23:56Z] INFO  16:56:52,388 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:56Z] INFO  16:56:52,388 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:56Z] INFO  16:56:52,547 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:56Z] INFO  16:56:52,550 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-14T23:56Z] INFO  16:56:52,608 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:56Z] INFO  16:56:52,618 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:56Z] INFO  16:56:52,666 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-14T23:56Z] INFO  16:56:52,680 IntervalUtils - Processing 15513818 bp from intervals
[2016-04-14T23:56Z] INFO  16:56:52,768 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:56Z] INFO  16:56:53,103 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:56Z] INFO  16:56:53,104 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:56Z] INFO  16:56:53,105 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:56Z] INFO  16:56:53,105 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:56Z] INFO  16:56:53,118 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:56Z] INFO  16:56:53,296 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:56Z] INFO  16:56:53,388 ProgressMeter -     11:74994435    800017.0   120.0 s       2.5 m       78.9%     2.5 m      32.0 s
[2016-04-14T23:56Z] INFO  16:56:53,601 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-14T23:56Z] INFO  16:56:53,679 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:56Z] INFO  16:56:53,708 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:56Z] INFO  16:56:53,772 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-14T23:56Z] INFO  16:56:53,801 IntervalUtils - Processing 13279773 bp from intervals
[2016-04-14T23:56Z] INFO  16:56:53,813 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:56Z] INFO  16:56:53,817 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:56Z] INFO  16:56:53,818 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:56Z] INFO  16:56:53,818 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:56Z] INFO  16:56:53,823 HelpFormatter - Program Args: -T PrintReads -L 14:1-19378574 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/14/tx/tmpXgAIr1/R14-18105_kapa-NGv3-PE100-NGv3-sort-14_0_19378574-prep-prealign.bam
[2016-04-14T23:56Z] INFO  16:56:53,831 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:56Z] INFO  16:56:53,832 HelpFormatter - Date/Time: 2016/04/14 16:56:53
[2016-04-14T23:56Z] INFO  16:56:53,832 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:56Z] INFO  16:56:53,832 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:56Z] INFO  16:56:53,832 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:56Z] INFO  16:56:53,835 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:56Z] INFO  16:56:53,836 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:56Z] INFO  16:56:53,836 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:56Z] INFO  16:56:53,841 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/12/R14-18105_kapa-NGv3-PE100-NGv3-sort-12_93870729_109490566-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/12/tx/tmpT1zUMZ/R14-18105_kapa-NGv3-PE100-NGv3-sort-12_93870729_109490566-prep-prealign-realign.intervals -l INFO -L 12:93870730-109490566 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-14T23:56Z] INFO  16:56:53,854 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:56Z] INFO  16:56:53,858 HelpFormatter - Date/Time: 2016/04/14 16:56:53
[2016-04-14T23:56Z] INFO  16:56:53,859 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:56Z] INFO  16:56:53,860 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:56Z] INFO  16:56:53,887 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:56Z] INFO  16:56:53,957 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:56Z] INFO  16:56:54,035 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:56Z] INFO  16:56:54,197 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-14T23:56Z] INFO  16:56:54,207 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:56Z] INFO  16:56:54,207 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:56Z] INFO  16:56:54,208 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:56Z] INFO  16:56:54,208 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:56Z] INFO  16:56:54,209 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:56Z] INFO  16:56:54,246 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:56Z] INFO  16:56:54,313 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.10
[2016-04-14T23:56Z] INFO  16:56:54,442 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:56Z] INFO  16:56:54,663 IntervalUtils - Processing 15619837 bp from intervals
[2016-04-14T23:56Z] WARN  16:56:54,669 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:56Z] INFO  16:56:54,745 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:56Z] INFO  16:56:54,944 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:56Z] INFO  16:56:54,945 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:56Z] INFO  16:56:54,946 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:56Z] INFO  16:56:54,947 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-14T23:56Z] INFO  16:56:55,192 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-14T23:56Z] INFO  16:56:55,258 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:56Z] INFO  16:56:55,268 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:56Z] INFO  16:56:55,322 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-14T23:56Z] INFO  16:56:55,337 IntervalUtils - Processing 19378574 bp from intervals
[2016-04-14T23:56Z] INFO  16:56:55,417 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:56Z] INFO  16:56:55,616 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@41fd9d8e
[2016-04-14T23:56Z] INFO  16:56:55,732 ProgressMeter -            done    108896.0    16.0 s       2.5 m      100.0%    16.0 s       0.0 s
[2016-04-14T23:56Z] INFO  16:56:55,734 ProgressMeter - Total runtime 16.01 secs, 0.27 min, 0.00 hours
[2016-04-14T23:56Z] INFO  16:56:55,734 MicroScheduler - 120 reads were filtered out during the traversal out of approximately 109016 total reads (0.11%)
[2016-04-14T23:56Z] INFO  16:56:55,734 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:56Z] INFO  16:56:55,735 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:56Z] INFO  16:56:55,736 MicroScheduler -   -> 120 reads (0.11% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:56Z] INFO  16:56:55,846 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:56Z] INFO  16:56:55,847 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:56Z] INFO  16:56:55,848 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:56Z] INFO  16:56:55,849 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:56Z] INFO  16:56:55,864 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:56Z] INFO  16:56:55,879 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:56Z] INFO  16:56:57,309 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:56Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-13_51396767_67205543-prep-prealign.bam
[2016-04-14T23:56Z] INFO  16:56:57,668 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@7172f77a
[2016-04-14T23:56Z] INFO  16:56:57,716 ProgressMeter -            done      3564.0     1.0 s       8.7 m      100.0%     1.0 s       0.0 s
[2016-04-14T23:56Z] INFO  16:56:57,717 ProgressMeter - Total runtime 1.87 secs, 0.03 min, 0.00 hours
[2016-04-14T23:56Z] INFO  16:56:57,717 MicroScheduler - 7 reads were filtered out during the traversal out of approximately 3571 total reads (0.20%)
[2016-04-14T23:56Z] INFO  16:56:57,718 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:56Z] INFO  16:56:57,718 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:56Z] INFO  16:56:57,718 MicroScheduler -   -> 7 reads (0.20% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:56Z] GATK RealignerTargetCreator: R14-18105_kapa-NGv3-PE100-NGv3-sort-13_51396767_67205543-prep-prealign.bam 13:51396768-67205543
[2016-04-14T23:56Z] GATK: RealignerTargetCreator
[2016-04-14T23:56Z] INFO  16:56:59,016 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:56Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-14_0_19378574-prep-prealign.bam
[2016-04-14T23:56Z] GATK RealignerTargetCreator: R14-18105_kapa-NGv3-PE100-NGv3-sort-14_0_19378574-prep-prealign.bam 14:1-19378574
[2016-04-14T23:56Z] GATK: RealignerTargetCreator
[2016-04-14T23:57Z] INFO  16:57:00,410 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:57Z] INFO  16:57:00,412 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:57Z] INFO  16:57:00,413 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:57Z] INFO  16:57:00,413 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:57Z] INFO  16:57:00,417 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/13/R14-18105_kapa-NGv3-PE100-NGv3-sort-13_51396767_67205543-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/13/tx/tmpJmHNct/R14-18105_kapa-NGv3-PE100-NGv3-sort-13_51396767_67205543-prep-prealign-realign.intervals -l INFO -L 13:51396768-67205543 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-14T23:57Z] INFO  16:57:00,443 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:57Z] INFO  16:57:00,444 HelpFormatter - Date/Time: 2016/04/14 16:57:00
[2016-04-14T23:57Z] INFO  16:57:00,444 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:57Z] INFO  16:57:00,444 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:57Z] INFO  16:57:00,561 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:57Z] INFO  16:57:00,764 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-14T23:57Z] INFO  16:57:00,773 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:57Z] INFO  16:57:00,825 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-14T23:57Z] INFO  16:57:01,086 IntervalUtils - Processing 15808776 bp from intervals
[2016-04-14T23:57Z] WARN  16:57:01,102 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:57Z] INFO  16:57:01,193 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:57Z] INFO  16:57:01,321 ProgressMeter -     13:33591000    200006.0    30.0 s       2.5 m       87.8%    34.0 s       4.0 s
[2016-04-14T23:57Z] INFO  16:57:01,352 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:57Z] INFO  16:57:01,353 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:57Z] INFO  16:57:01,354 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:57Z] INFO  16:57:01,354 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-14T23:57Z] INFO  16:57:01,681 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:57Z] INFO  16:57:01,685 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:57Z] INFO  16:57:01,685 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:57Z] INFO  16:57:01,686 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:57Z] INFO  16:57:01,690 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/14/R14-18105_kapa-NGv3-PE100-NGv3-sort-14_0_19378574-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/14/tx/tmpYP9oOa/R14-18105_kapa-NGv3-PE100-NGv3-sort-14_0_19378574-prep-prealign-realign.intervals -l INFO -L 14:1-19378574 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-14T23:57Z] INFO  16:57:01,711 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:57Z] INFO  16:57:01,712 HelpFormatter - Date/Time: 2016/04/14 16:57:01
[2016-04-14T23:57Z] INFO  16:57:01,712 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:57Z] INFO  16:57:01,713 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:57Z] INFO  16:57:01,748 ProgressMeter -      11:1769351    300008.0    30.0 s     100.0 s       11.1%     4.5 m       4.0 m
[2016-04-14T23:57Z] INFO  16:57:01,805 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:57Z] INFO  16:57:02,060 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-14T23:57Z] INFO  16:57:02,070 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:57Z] INFO  16:57:02,133 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-14T23:57Z] INFO  16:57:02,402 ProgressMeter -     12:57571056    700012.0    90.0 s       2.2 m       68.0%     2.2 m      42.0 s
[2016-04-14T23:57Z] INFO  16:57:02,422 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@41fd9d8e
[2016-04-14T23:57Z] INFO  16:57:02,449 IntervalUtils - Processing 19378574 bp from intervals
[2016-04-14T23:57Z] WARN  16:57:02,453 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:57Z] INFO  16:57:02,515 ProgressMeter -            done    264489.0    31.0 s     118.0 s      100.0%    31.0 s       0.0 s
[2016-04-14T23:57Z] INFO  16:57:02,516 ProgressMeter - Total runtime 31.23 secs, 0.52 min, 0.01 hours
[2016-04-14T23:57Z] INFO  16:57:02,516 MicroScheduler - 155 reads were filtered out during the traversal out of approximately 264644 total reads (0.06%)
[2016-04-14T23:57Z] INFO  16:57:02,516 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:57Z] INFO  16:57:02,517 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:57Z] INFO  16:57:02,517 MicroScheduler -   -> 155 reads (0.06% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:57Z] INFO  16:57:02,560 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:57Z] INFO  16:57:02,845 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:57Z] INFO  16:57:02,846 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:57Z] INFO  16:57:02,847 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:57Z] INFO  16:57:02,847 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-14T23:57Z] INFO  16:57:03,224 ProgressMeter -            done   8584667.0    12.0 s       1.0 s      100.0%    12.0 s       0.0 s
[2016-04-14T23:57Z] INFO  16:57:03,225 ProgressMeter - Total runtime 12.73 secs, 0.21 min, 0.00 hours
[2016-04-14T23:57Z] INFO  16:57:03,230 MicroScheduler - 27195 reads were filtered out during the traversal out of approximately 210358 total reads (12.93%)
[2016-04-14T23:57Z] INFO  16:57:03,231 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:57Z] INFO  16:57:03,232 MicroScheduler -   -> 497 reads (0.24% of total) failing BadMateFilter
[2016-04-14T23:57Z] INFO  16:57:03,233 MicroScheduler -   -> 16037 reads (7.62% of total) failing DuplicateReadFilter
[2016-04-14T23:57Z] INFO  16:57:03,233 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-14T23:57Z] INFO  16:57:03,234 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:57Z] INFO  16:57:03,235 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-14T23:57Z] INFO  16:57:03,235 MicroScheduler -   -> 10661 reads (5.07% of total) failing MappingQualityZeroFilter
[2016-04-14T23:57Z] INFO  16:57:03,236 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:57Z] INFO  16:57:03,236 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-14T23:57Z] INFO  16:57:03,236 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-14T23:57Z] INFO  16:57:03,607 ProgressMeter -     13:50594708    200002.0    30.0 s       2.5 m       95.6%    31.0 s       1.0 s
[2016-04-14T23:57Z] INFO  16:57:03,730 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@7172f77a
[2016-04-14T23:57Z] INFO  16:57:03,821 ProgressMeter -            done    235146.0    30.0 s       2.1 m      100.0%    30.0 s       0.0 s
[2016-04-14T23:57Z] INFO  16:57:03,821 ProgressMeter - Total runtime 30.24 secs, 0.50 min, 0.01 hours
[2016-04-14T23:57Z] INFO  16:57:03,822 MicroScheduler - 145 reads were filtered out during the traversal out of approximately 235291 total reads (0.06%)
[2016-04-14T23:57Z] INFO  16:57:03,822 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:57Z] INFO  16:57:03,822 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:57Z] INFO  16:57:03,823 MicroScheduler -   -> 145 reads (0.06% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:57Z] INFO  16:57:04,074 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:57Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-13_19751066_35517251-prep-prealign.bam
[2016-04-14T23:57Z] INFO  16:57:04,684 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:57Z] GATK: realign ('12', 125267228, 133851895) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-14T23:57Z] GATK RealignerTargetCreator: R14-18105_kapa-NGv3-PE100-NGv3-sort-13_19751066_35517251-prep-prealign.bam 13:19751067-35517251
[2016-04-14T23:57Z] GATK: RealignerTargetCreator
[2016-04-14T23:57Z] INFO  16:57:05,168 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:57Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-13_35615069_51287376-prep-prealign.bam
[2016-04-14T23:57Z] INFO  16:57:05,269 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@41fd9d8e
[2016-04-14T23:57Z] INFO  16:57:05,442 ProgressMeter -            done    932561.0     2.2 m       2.4 m      100.0%     2.2 m       0.0 s
[2016-04-14T23:57Z] INFO  16:57:05,442 ProgressMeter - Total runtime 132.63 secs, 2.21 min, 0.04 hours
[2016-04-14T23:57Z] INFO  16:57:05,443 MicroScheduler - 326 reads were filtered out during the traversal out of approximately 932887 total reads (0.03%)
[2016-04-14T23:57Z] INFO  16:57:05,443 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:57Z] INFO  16:57:05,443 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:57Z] INFO  16:57:05,444 MicroScheduler -   -> 326 reads (0.03% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:57Z] INFO  16:57:05,560 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@41fd9d8e
[2016-04-14T23:57Z] INFO  16:57:05,662 ProgressMeter -            done     93953.0    16.0 s       2.9 m      100.0%    16.0 s       0.0 s
[2016-04-14T23:57Z] INFO  16:57:05,663 ProgressMeter - Total runtime 16.59 secs, 0.28 min, 0.00 hours
[2016-04-14T23:57Z] INFO  16:57:05,663 MicroScheduler - 104 reads were filtered out during the traversal out of approximately 94057 total reads (0.11%)
[2016-04-14T23:57Z] INFO  16:57:05,663 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:57Z] INFO  16:57:05,664 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:57Z] INFO  16:57:05,664 MicroScheduler -   -> 104 reads (0.11% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:57Z] GATK RealignerTargetCreator: R14-18105_kapa-NGv3-PE100-NGv3-sort-13_35615069_51287376-prep-prealign.bam 13:35615070-51287376
[2016-04-14T23:57Z] GATK: RealignerTargetCreator
[2016-04-14T23:57Z] INFO  16:57:06,943 ProgressMeter -     11:62286390    400007.0    30.0 s      77.0 s       97.5%    30.0 s       0.0 s
[2016-04-14T23:57Z] INFO  16:57:07,125 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:57Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-13_67477635_84455642-prep-prealign.bam
[2016-04-14T23:57Z] INFO  16:57:07,215 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:57Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-11_62744265_78270665-prep-prealign.bam
[2016-04-14T23:57Z] INFO  16:57:07,342 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:57Z] INFO  16:57:07,346 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:57Z] INFO  16:57:07,346 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:57Z] INFO  16:57:07,347 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:57Z] INFO  16:57:07,362 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/12/R14-18105_kapa-NGv3-PE100-NGv3-sort-12_125267228_133851895-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/12/R14-18105_kapa-NGv3-PE100-NGv3-sort-12_125267228_133851895-prep-prealign-realign.intervals -L 12:125267229-133851895 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/12/tx/tmpxXqSJl/R14-18105_kapa-NGv3-PE100-NGv3-sort-12_125267228_133851895-prep.bam
[2016-04-14T23:57Z] INFO  16:57:07,371 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:57Z] INFO  16:57:07,372 HelpFormatter - Date/Time: 2016/04/14 16:57:07
[2016-04-14T23:57Z] INFO  16:57:07,373 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:57Z] INFO  16:57:07,373 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:57Z] GATK RealignerTargetCreator: R14-18105_kapa-NGv3-PE100-NGv3-sort-13_67477635_84455642-prep-prealign.bam 13:67477636-84455642
[2016-04-14T23:57Z] GATK: RealignerTargetCreator
[2016-04-14T23:57Z] INFO  16:57:07,556 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:57Z] INFO  16:57:07,638 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:57Z] INFO  16:57:07,649 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:57Z] INFO  16:57:07,697 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-14T23:57Z] INFO  16:57:07,911 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:57Z] INFO  16:57:07,915 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:57Z] INFO  16:57:07,915 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:57Z] INFO  16:57:07,916 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:57Z] INFO  16:57:07,923 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/13/R14-18105_kapa-NGv3-PE100-NGv3-sort-13_19751066_35517251-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/13/tx/tmp7JMW3M/R14-18105_kapa-NGv3-PE100-NGv3-sort-13_19751066_35517251-prep-prealign-realign.intervals -l INFO -L 13:19751067-35517251 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-14T23:57Z] INFO  16:57:07,936 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:57Z] INFO  16:57:07,937 HelpFormatter - Date/Time: 2016/04/14 16:57:07
[2016-04-14T23:57Z] INFO  16:57:07,937 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:57Z] INFO  16:57:07,937 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:57Z] INFO  16:57:08,054 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:57Z] INFO  16:57:08,192 IntervalUtils - Processing 8584667 bp from intervals
[2016-04-14T23:57Z] WARN  16:57:08,198 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:57Z] INFO  16:57:08,309 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:57Z] INFO  16:57:08,360 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-14T23:57Z] INFO  16:57:08,371 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:57Z] INFO  16:57:08,412 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:57Z] INFO  16:57:08,420 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:57Z] INFO  16:57:08,420 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:57Z] INFO  16:57:08,425 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:57Z] INFO  16:57:08,427 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-14T23:57Z] INFO  16:57:08,588 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:57Z] INFO  16:57:08,591 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:57Z] INFO  16:57:08,592 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:57Z] INFO  16:57:08,592 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:57Z] INFO  16:57:08,597 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/13/R14-18105_kapa-NGv3-PE100-NGv3-sort-13_35615069_51287376-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/13/tx/tmpHCdiYk/R14-18105_kapa-NGv3-PE100-NGv3-sort-13_35615069_51287376-prep-prealign-realign.intervals -l INFO -L 13:35615070-51287376 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-14T23:57Z] INFO  16:57:08,606 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:57Z] INFO  16:57:08,607 HelpFormatter - Date/Time: 2016/04/14 16:57:08
[2016-04-14T23:57Z] INFO  16:57:08,607 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:57Z] INFO  16:57:08,607 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:57Z] INFO  16:57:08,622 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:57Z] INFO  16:57:08,715 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:57Z] INFO  16:57:08,718 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:57Z] INFO  16:57:08,743 IntervalUtils - Processing 15766185 bp from intervals
[2016-04-14T23:57Z] WARN  16:57:08,748 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:57Z] INFO  16:57:08,852 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:57Z] INFO  16:57:08,975 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-14T23:57Z] INFO  16:57:08,986 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:57Z] INFO  16:57:09,036 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-14T23:57Z] INFO  16:57:09,148 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:57Z] INFO  16:57:09,149 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:57Z] INFO  16:57:09,157 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:57Z] INFO  16:57:09,158 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-14T23:57Z] INFO  16:57:09,316 IntervalUtils - Processing 15672307 bp from intervals
[2016-04-14T23:57Z] WARN  16:57:09,321 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:57Z] INFO  16:57:09,391 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:57Z] INFO  16:57:09,560 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:57Z] INFO  16:57:09,561 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:57Z] INFO  16:57:09,561 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:57Z] INFO  16:57:09,562 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-14T23:57Z] INFO  16:57:09,891 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@41fd9d8e
[2016-04-14T23:57Z] INFO  16:57:10,042 ProgressMeter -            done    117187.0    16.0 s       2.4 m      100.0%    16.0 s       0.0 s
[2016-04-14T23:57Z] INFO  16:57:10,043 ProgressMeter - Total runtime 16.94 secs, 0.28 min, 0.00 hours
[2016-04-14T23:57Z] INFO  16:57:10,043 MicroScheduler - 120 reads were filtered out during the traversal out of approximately 117307 total reads (0.10%)
[2016-04-14T23:57Z] INFO  16:57:10,044 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:57Z] INFO  16:57:10,045 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:57Z] INFO  16:57:10,045 MicroScheduler -   -> 120 reads (0.10% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:57Z] INFO  16:57:10,129 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:57Z] INFO  16:57:10,132 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:57Z] INFO  16:57:10,132 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:57Z] INFO  16:57:10,132 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:57Z] INFO  16:57:10,136 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/13/R14-18105_kapa-NGv3-PE100-NGv3-sort-13_67477635_84455642-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/13/tx/tmp_EyqZD/R14-18105_kapa-NGv3-PE100-NGv3-sort-13_67477635_84455642-prep-prealign-realign.intervals -l INFO -L 13:67477636-84455642 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-14T23:57Z] INFO  16:57:10,148 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:57Z] INFO  16:57:10,149 HelpFormatter - Date/Time: 2016/04/14 16:57:10
[2016-04-14T23:57Z] INFO  16:57:10,149 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:57Z] INFO  16:57:10,149 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:57Z] INFO  16:57:10,308 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:57Z] GATK RealignerTargetCreator: R14-18105_kapa-NGv3-PE100-NGv3-sort-11_62744265_78270665-prep-prealign.bam 11:62744266-78270665
[2016-04-14T23:57Z] GATK: RealignerTargetCreator
[2016-04-14T23:57Z] INFO  16:57:10,542 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-14T23:57Z] INFO  16:57:10,552 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:57Z] INFO  16:57:10,630 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-14T23:57Z] INFO  16:57:11,036 IntervalUtils - Processing 16978007 bp from intervals
[2016-04-14T23:57Z] WARN  16:57:11,041 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:57Z] INFO  16:57:11,138 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:57Z] INFO  16:57:11,383 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:57Z] INFO  16:57:11,383 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:57Z] INFO  16:57:11,384 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:57Z] INFO  16:57:11,384 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-14T23:57Z] INFO  16:57:11,839 ProgressMeter -            done    565617.0    35.0 s      63.0 s      100.0%    35.0 s       0.0 s
[2016-04-14T23:57Z] INFO  16:57:11,840 ProgressMeter - Total runtime 35.83 secs, 0.60 min, 0.01 hours
[2016-04-14T23:57Z] INFO  16:57:11,844 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 565617 total reads (0.00%)
[2016-04-14T23:57Z] INFO  16:57:11,844 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:57Z] INFO  16:57:11,844 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:57Z] INFO  16:57:11,845 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:57Z] INFO  16:57:11,985 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:57Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-13_86368117_101881935-prep-prealign.bam
[2016-04-14T23:57Z] INFO  16:57:12,258 ProgressMeter -            done   1.5619837E7    17.0 s       1.0 s      100.0%    17.0 s       0.0 s
[2016-04-14T23:57Z] INFO  16:57:12,259 ProgressMeter - Total runtime 17.31 secs, 0.29 min, 0.00 hours
[2016-04-14T23:57Z] INFO  16:57:12,275 MicroScheduler - 24865 reads were filtered out during the traversal out of approximately 288118 total reads (8.63%)
[2016-04-14T23:57Z] INFO  16:57:12,276 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:57Z] INFO  16:57:12,277 MicroScheduler -   -> 679 reads (0.24% of total) failing BadMateFilter
[2016-04-14T23:57Z] INFO  16:57:12,277 MicroScheduler -   -> 22408 reads (7.78% of total) failing DuplicateReadFilter
[2016-04-14T23:57Z] INFO  16:57:12,278 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-14T23:57Z] INFO  16:57:12,281 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:57Z] INFO  16:57:12,282 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-14T23:57Z] INFO  16:57:12,282 MicroScheduler -   -> 1778 reads (0.62% of total) failing MappingQualityZeroFilter
[2016-04-14T23:57Z] INFO  16:57:12,283 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:57Z] INFO  16:57:12,284 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-14T23:57Z] INFO  16:57:12,284 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-14T23:57Z] GATK RealignerTargetCreator: R14-18105_kapa-NGv3-PE100-NGv3-sort-13_86368117_101881935-prep-prealign.bam 13:86368118-101881935
[2016-04-14T23:57Z] GATK: RealignerTargetCreator
[2016-04-14T23:57Z] INFO  16:57:13,071 ProgressMeter -            done   1.9378574E7    10.0 s       0.0 s      100.0%    10.0 s       0.0 s
[2016-04-14T23:57Z] INFO  16:57:13,072 ProgressMeter - Total runtime 10.23 secs, 0.17 min, 0.00 hours
[2016-04-14T23:57Z] INFO  16:57:13,078 MicroScheduler - 1509 reads were filtered out during the traversal out of approximately 3564 total reads (42.34%)
[2016-04-14T23:57Z] INFO  16:57:13,088 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:57Z] INFO  16:57:13,089 MicroScheduler -   -> 11 reads (0.31% of total) failing BadMateFilter
[2016-04-14T23:57Z] INFO  16:57:13,089 MicroScheduler -   -> 226 reads (6.34% of total) failing DuplicateReadFilter
[2016-04-14T23:57Z] INFO  16:57:13,090 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-14T23:57Z] INFO  16:57:13,090 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:57Z] INFO  16:57:13,091 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-14T23:57Z] INFO  16:57:13,092 MicroScheduler -   -> 1272 reads (35.69% of total) failing MappingQualityZeroFilter
[2016-04-14T23:57Z] INFO  16:57:13,092 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:57Z] INFO  16:57:13,093 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-14T23:57Z] INFO  16:57:13,094 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-14T23:57Z] INFO  16:57:13,133 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:57Z] INFO  16:57:13,136 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:57Z] INFO  16:57:13,137 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:57Z] INFO  16:57:13,147 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:57Z] INFO  16:57:13,162 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/11/R14-18105_kapa-NGv3-PE100-NGv3-sort-11_62744265_78270665-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/11/tx/tmp6OsTkv/R14-18105_kapa-NGv3-PE100-NGv3-sort-11_62744265_78270665-prep-prealign-realign.intervals -l INFO -L 11:62744266-78270665 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-14T23:57Z] INFO  16:57:13,172 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:57Z] INFO  16:57:13,185 HelpFormatter - Date/Time: 2016/04/14 16:57:13
[2016-04-14T23:57Z] INFO  16:57:13,186 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:57Z] INFO  16:57:13,187 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:57Z] INFO  16:57:13,232 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:57Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-11_47158866_62678572-prep.bam
[2016-04-14T23:57Z] INFO  16:57:13,319 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:57Z] INFO  16:57:13,537 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-14T23:57Z] INFO  16:57:13,547 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:57Z] INFO  16:57:13,589 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:57Z] INFO  16:57:13,610 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-14T23:57Z] GATK: realign ('12', 93870729, 109490566) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-14T23:57Z] INFO  16:57:13,961 IntervalUtils - Processing 15526400 bp from intervals
[2016-04-14T23:57Z] WARN  16:57:13,966 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:57Z] INFO  16:57:14,116 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:57Z] INFO  16:57:14,193 ProgressMeter -            done   1.5637181E7    25.0 s       1.0 s      100.0%    25.0 s       0.0 s
[2016-04-14T23:57Z] INFO  16:57:14,194 ProgressMeter - Total runtime 25.23 secs, 0.42 min, 0.01 hours
[2016-04-14T23:57Z] INFO  16:57:14,198 MicroScheduler - 58481 reads were filtered out during the traversal out of approximately 561329 total reads (10.42%)
[2016-04-14T23:57Z] INFO  16:57:14,199 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:57Z] INFO  16:57:14,200 MicroScheduler -   -> 1025 reads (0.18% of total) failing BadMateFilter
[2016-04-14T23:57Z] INFO  16:57:14,200 MicroScheduler -   -> 43012 reads (7.66% of total) failing DuplicateReadFilter
[2016-04-14T23:57Z] INFO  16:57:14,201 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-14T23:57Z] INFO  16:57:14,201 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:57Z] INFO  16:57:14,201 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-14T23:57Z] INFO  16:57:14,202 MicroScheduler -   -> 14444 reads (2.57% of total) failing MappingQualityZeroFilter
[2016-04-14T23:57Z] INFO  16:57:14,202 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:57Z] INFO  16:57:14,203 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-14T23:57Z] INFO  16:57:14,203 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-14T23:57Z] INFO  16:57:14,336 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:57Z] INFO  16:57:14,336 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:57Z] INFO  16:57:14,337 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:57Z] INFO  16:57:14,338 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-14T23:57Z] INFO  16:57:14,404 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:57Z] GATK: realign ('14', 0, 19378574) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-14T23:57Z] INFO  16:57:14,486 ProgressMeter -    11:124757209    400006.0    30.0 s      75.0 s       95.1%    31.0 s       1.0 s
[2016-04-14T23:57Z] INFO  16:57:14,633 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@7172f77a
[2016-04-14T23:57Z] INFO  16:57:14,782 ProgressMeter -            done    893179.0   103.0 s     115.0 s      100.0%   103.0 s       0.0 s
[2016-04-14T23:57Z] INFO  16:57:14,782 ProgressMeter - Total runtime 103.21 secs, 1.72 min, 0.03 hours
[2016-04-14T23:57Z] INFO  16:57:14,783 MicroScheduler - 297 reads were filtered out during the traversal out of approximately 893476 total reads (0.03%)
[2016-04-14T23:57Z] INFO  16:57:14,783 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:57Z] INFO  16:57:14,784 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:57Z] INFO  16:57:14,784 MicroScheduler -   -> 297 reads (0.03% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:57Z] GATK pre-alignment ('14', 19553416, 35066851) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-14T23:57Z] INFO  16:57:15,265 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:57Z] INFO  16:57:15,268 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:57Z] INFO  16:57:15,269 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:57Z] INFO  16:57:15,269 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:57Z] INFO  16:57:15,275 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/13/R14-18105_kapa-NGv3-PE100-NGv3-sort-13_86368117_101881935-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/13/tx/tmpBzaWER/R14-18105_kapa-NGv3-PE100-NGv3-sort-13_86368117_101881935-prep-prealign-realign.intervals -l INFO -L 13:86368118-101881935 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-14T23:57Z] INFO  16:57:15,301 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:57Z] INFO  16:57:15,303 HelpFormatter - Date/Time: 2016/04/14 16:57:15
[2016-04-14T23:57Z] INFO  16:57:15,303 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:57Z] INFO  16:57:15,304 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:57Z] INFO  16:57:15,473 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:57Z] INFO  16:57:15,675 ProgressMeter -            done    521028.0    31.0 s      59.0 s      100.0%    31.0 s       0.0 s
[2016-04-14T23:57Z] INFO  16:57:15,675 ProgressMeter - Total runtime 31.20 secs, 0.52 min, 0.01 hours
[2016-04-14T23:57Z] INFO  16:57:15,679 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 521028 total reads (0.00%)
[2016-04-14T23:57Z] INFO  16:57:15,680 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:57Z] INFO  16:57:15,680 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:57Z] INFO  16:57:15,681 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:57Z] INFO  16:57:15,714 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:57Z] INFO  16:57:15,726 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-14T23:57Z] INFO  16:57:15,736 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:57Z] GATK: realign ('12', 0, 15637181) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-14T23:57Z] INFO  16:57:15,814 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-14T23:57Z] INFO  16:57:16,099 IntervalUtils - Processing 15513818 bp from intervals
[2016-04-14T23:57Z] WARN  16:57:16,104 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:57Z] INFO  16:57:16,199 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:57Z] INFO  16:57:16,253 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:57Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-12_46756066_62654284-prep-prealign.bam
[2016-04-14T23:57Z] INFO  16:57:16,371 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:57Z] INFO  16:57:16,372 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:57Z] INFO  16:57:16,373 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:57Z] INFO  16:57:16,373 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-14T23:57Z] INFO  16:57:16,565 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:57Z] INFO  16:57:16,569 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:57Z] INFO  16:57:16,569 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:57Z] INFO  16:57:16,569 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:57Z] INFO  16:57:16,573 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/12/R14-18105_kapa-NGv3-PE100-NGv3-sort-12_93870729_109490566-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/12/R14-18105_kapa-NGv3-PE100-NGv3-sort-12_93870729_109490566-prep-prealign-realign.intervals -L 12:93870730-109490566 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/12/tx/tmpDT7lRC/R14-18105_kapa-NGv3-PE100-NGv3-sort-12_93870729_109490566-prep.bam
[2016-04-14T23:57Z] INFO  16:57:16,583 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:57Z] INFO  16:57:16,583 HelpFormatter - Date/Time: 2016/04/14 16:57:16
[2016-04-14T23:57Z] INFO  16:57:16,584 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:57Z] INFO  16:57:16,584 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:57Z] INFO  16:57:16,678 ProgressMeter -    12:121442149    300003.0    60.0 s       3.4 m       75.8%    79.0 s      19.0 s
[2016-04-14T23:57Z] INFO  16:57:16,799 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:57Z] INFO  16:57:17,003 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:57Z] INFO  16:57:17,019 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:57Z] INFO  16:57:17,093 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-14T23:57Z] INFO  16:57:17,388 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:57Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-11_110001730_125514538-prep.bam
[2016-04-14T23:57Z] INFO  16:57:17,610 ProgressMeter -            done   1.5808776E7    16.0 s       1.0 s      100.0%    16.0 s       0.0 s
[2016-04-14T23:57Z] INFO  16:57:17,611 ProgressMeter - Total runtime 16.26 secs, 0.27 min, 0.00 hours
[2016-04-14T23:57Z] INFO  16:57:17,615 MicroScheduler - 32130 reads were filtered out during the traversal out of approximately 109876 total reads (29.24%)
[2016-04-14T23:57Z] INFO  16:57:17,616 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:57Z] INFO  16:57:17,617 MicroScheduler -   -> 399 reads (0.36% of total) failing BadMateFilter
[2016-04-14T23:57Z] INFO  16:57:17,617 MicroScheduler -   -> 6688 reads (6.09% of total) failing DuplicateReadFilter
[2016-04-14T23:57Z] INFO  16:57:17,618 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-14T23:57Z] INFO  16:57:17,619 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:57Z] INFO  16:57:17,619 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-14T23:57Z] INFO  16:57:17,620 MicroScheduler -   -> 25043 reads (22.79% of total) failing MappingQualityZeroFilter
[2016-04-14T23:57Z] INFO  16:57:17,621 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:57Z] INFO  16:57:17,621 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-14T23:57Z] INFO  16:57:17,622 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-14T23:57Z] INFO  16:57:17,624 IntervalUtils - Processing 15619837 bp from intervals
[2016-04-14T23:57Z] WARN  16:57:17,636 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:57Z] INFO  16:57:17,724 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:57Z] INFO  16:57:17,867 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:57Z] INFO  16:57:17,868 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:57Z] INFO  16:57:17,868 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:57Z] INFO  16:57:17,868 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:57Z] INFO  16:57:17,876 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:57Z] INFO  16:57:17,880 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:57Z] INFO  16:57:17,880 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:57Z] INFO  16:57:17,881 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:57Z] INFO  16:57:17,892 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/14/R14-18105_kapa-NGv3-PE100-NGv3-sort-14_0_19378574-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/14/R14-18105_kapa-NGv3-PE100-NGv3-sort-14_0_19378574-prep-prealign-realign.intervals -L 14:1-19378574 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/14/tx/tmp6asAup/R14-18105_kapa-NGv3-PE100-NGv3-sort-14_0_19378574-prep.bam
[2016-04-14T23:57Z] INFO  16:57:17,913 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:57Z] INFO  16:57:17,914 HelpFormatter - Date/Time: 2016/04/14 16:57:17
[2016-04-14T23:57Z] INFO  16:57:17,915 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:57Z] INFO  16:57:17,916 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:57Z] INFO  16:57:17,995 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:57Z] INFO  16:57:18,160 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:57Z] INFO  16:57:18,196 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:57Z] INFO  16:57:18,244 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:57Z] INFO  16:57:18,246 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:57Z] INFO  16:57:18,246 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:57Z] INFO  16:57:18,247 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:57Z] INFO  16:57:18,250 HelpFormatter - Program Args: -T PrintReads -L 14:19553417-35066851 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/14/tx/tmp00DAjc/R14-18105_kapa-NGv3-PE100-NGv3-sort-14_19553416_35066851-prep-prealign.bam
[2016-04-14T23:57Z] INFO  16:57:18,265 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:57Z] INFO  16:57:18,266 HelpFormatter - Date/Time: 2016/04/14 16:57:18
[2016-04-14T23:57Z] INFO  16:57:18,266 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:57Z] INFO  16:57:18,266 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:57Z] INFO  16:57:18,357 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:57Z] INFO  16:57:18,372 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:57Z] INFO  16:57:18,441 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-14T23:57Z] INFO  16:57:18,490 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:57Z] INFO  16:57:18,866 IntervalUtils - Processing 19378574 bp from intervals
[2016-04-14T23:57Z] WARN  16:57:18,882 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:57Z] INFO  16:57:18,958 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:57Z] INFO  16:57:18,974 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:57Z] INFO  16:57:18,976 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:57Z] INFO  16:57:18,976 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:57Z] INFO  16:57:18,976 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:57Z] INFO  16:57:18,980 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/12/R14-18105_kapa-NGv3-PE100-NGv3-sort-12_0_15637181-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/12/R14-18105_kapa-NGv3-PE100-NGv3-sort-12_0_15637181-prep-prealign-realign.intervals -L 12:1-15637181 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/12/tx/tmp_iNxT5/R14-18105_kapa-NGv3-PE100-NGv3-sort-12_0_15637181-prep.bam
[2016-04-14T23:57Z] INFO  16:57:18,990 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:57Z] INFO  16:57:18,991 HelpFormatter - Date/Time: 2016/04/14 16:57:18
[2016-04-14T23:57Z] INFO  16:57:18,991 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:57Z] INFO  16:57:19,001 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:57Z] INFO  16:57:19,060 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:57Z] GATK: realign ('13', 51396767, 67205543) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-14T23:57Z] GATK RealignerTargetCreator: R14-18105_kapa-NGv3-PE100-NGv3-sort-12_46756066_62654284-prep-prealign.bam 12:46756067-62654284
[2016-04-14T23:57Z] GATK: RealignerTargetCreator
[2016-04-14T23:57Z] INFO  16:57:19,201 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:57Z] INFO  16:57:19,203 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:57Z] INFO  16:57:19,204 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:57Z] INFO  16:57:19,204 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:57Z] INFO  16:57:19,246 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:57Z] INFO  16:57:19,262 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:57Z] GATK pre-alignment ('14', 35072553, 50583270) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-14T23:57Z] INFO  16:57:19,278 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:57Z] INFO  16:57:19,365 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:57Z] INFO  16:57:19,375 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:57Z] INFO  16:57:19,463 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.09
[2016-04-14T23:57Z] INFO  16:57:19,707 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-14T23:57Z] INFO  16:57:19,789 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:57Z] INFO  16:57:19,802 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:57Z] INFO  16:57:19,881 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-14T23:57Z] INFO  16:57:19,908 IntervalUtils - Processing 15513435 bp from intervals
[2016-04-14T23:57Z] INFO  16:57:19,915 IntervalUtils - Processing 15637181 bp from intervals
[2016-04-14T23:57Z] WARN  16:57:19,921 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:57Z] INFO  16:57:20,025 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:57Z] INFO  16:57:20,065 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:57Z] INFO  16:57:20,252 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:57Z] INFO  16:57:20,253 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:57Z] INFO  16:57:20,254 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:57Z] INFO  16:57:20,255 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:57Z] INFO  16:57:20,352 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:57Z] INFO  16:57:20,353 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:57Z] INFO  16:57:20,354 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:57Z] INFO  16:57:20,355 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:57Z] INFO  16:57:20,374 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:57Z] INFO  16:57:20,483 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:57Z] INFO  16:57:20,592 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:57Z] INFO  16:57:20,647 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:57Z] INFO  16:57:21,008 ProgressMeter -            done      3564.0     1.0 s       8.4 m      100.0%     1.0 s       0.0 s
[2016-04-14T23:57Z] INFO  16:57:21,008 ProgressMeter - Total runtime 1.81 secs, 0.03 min, 0.00 hours
[2016-04-14T23:57Z] INFO  16:57:21,012 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 3564 total reads (0.00%)
[2016-04-14T23:57Z] INFO  16:57:21,012 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:57Z] INFO  16:57:21,012 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:57Z] INFO  16:57:21,013 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:57Z] INFO  16:57:22,047 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:57Z] INFO  16:57:22,050 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:57Z] INFO  16:57:22,051 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:57Z] INFO  16:57:22,051 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:57Z] INFO  16:57:22,056 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/12/R14-18105_kapa-NGv3-PE100-NGv3-sort-12_46756066_62654284-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/12/tx/tmpyYgrcA/R14-18105_kapa-NGv3-PE100-NGv3-sort-12_46756066_62654284-prep-prealign-realign.intervals -l INFO -L 12:46756067-62654284 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-14T23:57Z] INFO  16:57:22,078 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:57Z] INFO  16:57:22,082 HelpFormatter - Date/Time: 2016/04/14 16:57:22
[2016-04-14T23:57Z] INFO  16:57:22,083 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:57Z] INFO  16:57:22,083 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:57Z] INFO  16:57:22,205 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:57Z] INFO  16:57:22,404 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:57Z] INFO  16:57:22,407 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:57Z] INFO  16:57:22,407 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:57Z] INFO  16:57:22,408 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:57Z] INFO  16:57:22,412 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/13/R14-18105_kapa-NGv3-PE100-NGv3-sort-13_51396767_67205543-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/13/R14-18105_kapa-NGv3-PE100-NGv3-sort-13_51396767_67205543-prep-prealign-realign.intervals -L 13:51396768-67205543 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/13/tx/tmpAB39lB/R14-18105_kapa-NGv3-PE100-NGv3-sort-13_51396767_67205543-prep.bam
[2016-04-14T23:57Z] INFO  16:57:22,423 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:57Z] INFO  16:57:22,419 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:57Z] INFO  16:57:22,422 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:57Z] INFO  16:57:22,423 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:57Z] INFO  16:57:22,423 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:57Z] INFO  16:57:22,428 HelpFormatter - Program Args: -T PrintReads -L 14:35072554-50583270 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/14/tx/tmpuG45WE/R14-18105_kapa-NGv3-PE100-NGv3-sort-14_35072553_50583270-prep-prealign.bam
[2016-04-14T23:57Z] INFO  16:57:22,432 HelpFormatter - Date/Time: 2016/04/14 16:57:22
[2016-04-14T23:57Z] INFO  16:57:22,433 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:57Z] INFO  16:57:22,433 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:57Z] INFO  16:57:22,433 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-14T23:57Z] INFO  16:57:22,437 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:57Z] INFO  16:57:22,439 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:57Z] INFO  16:57:22,440 HelpFormatter - Date/Time: 2016/04/14 16:57:22
[2016-04-14T23:57Z] INFO  16:57:22,440 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:57Z] INFO  16:57:22,442 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:57Z] INFO  16:57:22,442 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:57Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-14_0_19378574-prep.bam
[2016-04-14T23:57Z] INFO  16:57:22,503 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-14T23:57Z] GATK pre-alignment ('14', 50585061, 66096324) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-14T23:57Z] INFO  16:57:22,614 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@41fd9d8e
[2016-04-14T23:57Z] INFO  16:57:22,635 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:57Z] INFO  16:57:22,660 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:57Z] INFO  16:57:22,783 ProgressMeter -            done    215390.0    28.0 s       2.2 m       99.4%    28.0 s       0.0 s
[2016-04-14T23:57Z] INFO  16:57:22,783 ProgressMeter - Total runtime 28.58 secs, 0.48 min, 0.01 hours
[2016-04-14T23:57Z] INFO  16:57:22,784 MicroScheduler - 116 reads were filtered out during the traversal out of approximately 215506 total reads (0.05%)
[2016-04-14T23:57Z] INFO  16:57:22,784 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:57Z] INFO  16:57:22,784 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:57Z] INFO  16:57:22,784 MicroScheduler -   -> 116 reads (0.05% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:57Z] INFO  16:57:22,838 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:57Z] INFO  16:57:22,848 IntervalUtils - Processing 15898218 bp from intervals
[2016-04-14T23:57Z] INFO  16:57:22,850 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:57Z] WARN  16:57:22,855 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:57Z] INFO  16:57:22,922 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-14T23:57Z] INFO  16:57:22,937 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:57Z] INFO  16:57:23,267 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:57Z] INFO  16:57:23,267 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:57Z] INFO  16:57:23,268 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:57Z] INFO  16:57:23,268 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-14T23:57Z] INFO  16:57:23,542 IntervalUtils - Processing 15808776 bp from intervals
[2016-04-14T23:57Z] WARN  16:57:23,561 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:57Z] INFO  16:57:23,653 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:57Z] INFO  16:57:23,807 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:57Z] INFO  16:57:23,808 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:57Z] INFO  16:57:23,809 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:57Z] INFO  16:57:23,810 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:57Z] INFO  16:57:23,852 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-14T23:57Z] INFO  16:57:23,923 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:57Z] INFO  16:57:23,932 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:57Z] INFO  16:57:23,979 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:57Z] INFO  16:57:23,987 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-14T23:57Z] INFO  16:57:24,001 IntervalUtils - Processing 15510717 bp from intervals
[2016-04-14T23:57Z] INFO  16:57:24,085 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:57Z] INFO  16:57:24,112 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:57Z] INFO  16:57:24,317 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:57Z] INFO  16:57:24,318 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:57Z] INFO  16:57:24,319 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:57Z] INFO  16:57:24,320 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:57Z] INFO  16:57:24,333 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:57Z] INFO  16:57:24,409 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:57Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-13_101890105_115169878-prep-prealign.bam
[2016-04-14T23:57Z] INFO  16:57:24,477 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:57Z] GATK RealignerTargetCreator: R14-18105_kapa-NGv3-PE100-NGv3-sort-13_101890105_115169878-prep-prealign.bam 13:101890106-115169878
[2016-04-14T23:57Z] GATK: RealignerTargetCreator
[2016-04-14T23:57Z] INFO  16:57:25,303 ProgressMeter -            done    209171.0    16.0 s      80.0 s       99.5%    16.0 s       0.0 s
[2016-04-14T23:57Z] INFO  16:57:25,303 ProgressMeter - Total runtime 16.88 secs, 0.28 min, 0.00 hours
[2016-04-14T23:57Z] INFO  16:57:25,306 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 209171 total reads (0.00%)
[2016-04-14T23:57Z] INFO  16:57:25,307 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:57Z] INFO  16:57:25,307 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:57Z] INFO  16:57:25,308 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:57Z] INFO  16:57:25,401 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:57Z] INFO  16:57:25,404 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:57Z] INFO  16:57:25,405 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:57Z] INFO  16:57:25,406 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:57Z] INFO  16:57:25,410 HelpFormatter - Program Args: -T PrintReads -L 14:50585062-66096324 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/14/tx/tmpCc7kk7/R14-18105_kapa-NGv3-PE100-NGv3-sort-14_50585061_66096324-prep-prealign.bam
[2016-04-14T23:57Z] INFO  16:57:25,430 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:57Z] INFO  16:57:25,431 HelpFormatter - Date/Time: 2016/04/14 16:57:25
[2016-04-14T23:57Z] INFO  16:57:25,432 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:57Z] INFO  16:57:25,432 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:57Z] INFO  16:57:25,640 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:57Z] INFO  16:57:26,923 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:57Z] INFO  16:57:26,958 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-14T23:57Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-12_125267228_133851895-prep.bam
[2016-04-14T23:57Z] INFO  16:57:27,026 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:57Z] INFO  16:57:27,035 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:57Z] INFO  16:57:27,072 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.04
[2016-04-14T23:57Z] INFO  16:57:27,086 IntervalUtils - Processing 15511263 bp from intervals
[2016-04-14T23:57Z] INFO  16:57:27,164 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:57Z] INFO  16:57:27,597 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:57Z] INFO  16:57:27,599 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:57Z] INFO  16:57:27,600 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:57Z] INFO  16:57:27,600 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:57Z] INFO  16:57:27,618 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:57Z] INFO  16:57:27,785 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:57Z] GATK pre-alignment ('14', 66135960, 81646674) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-14T23:57Z] INFO  16:57:28,093 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:57Z] INFO  16:57:28,097 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:57Z] INFO  16:57:28,098 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:57Z] INFO  16:57:28,098 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:57Z] INFO  16:57:28,104 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/13/R14-18105_kapa-NGv3-PE100-NGv3-sort-13_101890105_115169878-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/13/tx/tmpQkqvE6/R14-18105_kapa-NGv3-PE100-NGv3-sort-13_101890105_115169878-prep-prealign-realign.intervals -l INFO -L 13:101890106-115169878 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-14T23:57Z] INFO  16:57:28,128 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:57Z] INFO  16:57:28,129 HelpFormatter - Date/Time: 2016/04/14 16:57:28
[2016-04-14T23:57Z] INFO  16:57:28,129 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:57Z] INFO  16:57:28,130 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:57Z] INFO  16:57:28,269 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:57Z] INFO  16:57:28,429 ProgressMeter -            done    821924.0    56.0 s      68.0 s      100.0%    56.0 s       0.0 s
[2016-04-14T23:57Z] INFO  16:57:28,430 ProgressMeter - Total runtime 56.70 secs, 0.94 min, 0.02 hours
[2016-04-14T23:57Z] INFO  16:57:28,433 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 821924 total reads (0.00%)
[2016-04-14T23:57Z] INFO  16:57:28,434 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:57Z] INFO  16:57:28,434 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:57Z] INFO  16:57:28,434 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:57Z] INFO  16:57:28,479 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-14T23:57Z] INFO  16:57:28,491 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:57Z] INFO  16:57:28,539 ProgressMeter -            done   1.6978007E7    17.0 s       1.0 s      100.0%    17.0 s       0.0 s
[2016-04-14T23:57Z] INFO  16:57:28,540 ProgressMeter - Total runtime 17.16 secs, 0.29 min, 0.00 hours
[2016-04-14T23:57Z] INFO  16:57:28,545 MicroScheduler - 8573 reads were filtered out during the traversal out of approximately 94605 total reads (9.06%)
[2016-04-14T23:57Z] INFO  16:57:28,545 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:57Z] INFO  16:57:28,546 MicroScheduler -   -> 480 reads (0.51% of total) failing BadMateFilter
[2016-04-14T23:57Z] INFO  16:57:28,546 MicroScheduler -   -> 7524 reads (7.95% of total) failing DuplicateReadFilter
[2016-04-14T23:57Z] INFO  16:57:28,546 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-14T23:57Z] INFO  16:57:28,547 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:57Z] INFO  16:57:28,547 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-14T23:57Z] INFO  16:57:28,555 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-14T23:57Z] INFO  16:57:28,547 MicroScheduler -   -> 569 reads (0.60% of total) failing MappingQualityZeroFilter
[2016-04-14T23:57Z] INFO  16:57:28,559 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:57Z] INFO  16:57:28,559 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-14T23:57Z] INFO  16:57:28,559 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-14T23:57Z] INFO  16:57:28,805 ProgressMeter -            done   1.5672307E7    19.0 s       1.0 s      100.0%    19.0 s       0.0 s
[2016-04-14T23:57Z] INFO  16:57:28,806 ProgressMeter - Total runtime 19.25 secs, 0.32 min, 0.01 hours
[2016-04-14T23:57Z] INFO  16:57:28,809 MicroScheduler - 20206 reads were filtered out during the traversal out of approximately 236881 total reads (8.53%)
[2016-04-14T23:57Z] INFO  16:57:28,810 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:57Z] INFO  16:57:28,811 MicroScheduler -   -> 669 reads (0.28% of total) failing BadMateFilter
[2016-04-14T23:57Z] INFO  16:57:28,812 MicroScheduler -   -> 18367 reads (7.75% of total) failing DuplicateReadFilter
[2016-04-14T23:57Z] INFO  16:57:28,812 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-14T23:57Z] INFO  16:57:28,813 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:57Z] INFO  16:57:28,813 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-14T23:57Z] INFO  16:57:28,814 MicroScheduler -   -> 1170 reads (0.49% of total) failing MappingQualityZeroFilter
[2016-04-14T23:57Z] INFO  16:57:28,815 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:57Z] INFO  16:57:28,815 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-14T23:57Z] INFO  16:57:28,816 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-14T23:57Z] INFO  16:57:28,918 IntervalUtils - Processing 13279773 bp from intervals
[2016-04-14T23:57Z] WARN  16:57:28,924 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:57Z] INFO  16:57:29,018 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:57Z] INFO  16:57:29,237 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:57Z] INFO  16:57:29,238 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:57Z] INFO  16:57:29,239 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:57Z] INFO  16:57:29,240 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-14T23:57Z] INFO  16:57:29,502 ProgressMeter -            done   1.5766185E7    20.0 s       1.0 s      100.0%    20.0 s       0.0 s
[2016-04-14T23:57Z] INFO  16:57:29,503 ProgressMeter - Total runtime 20.35 secs, 0.34 min, 0.01 hours
[2016-04-14T23:57Z] INFO  16:57:29,507 MicroScheduler - 23163 reads were filtered out during the traversal out of approximately 265623 total reads (8.72%)
[2016-04-14T23:57Z] INFO  16:57:29,508 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:57Z] INFO  16:57:29,509 MicroScheduler -   -> 675 reads (0.25% of total) failing BadMateFilter
[2016-04-14T23:57Z] INFO  16:57:29,509 MicroScheduler -   -> 20369 reads (7.67% of total) failing DuplicateReadFilter
[2016-04-14T23:57Z] INFO  16:57:29,510 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-14T23:57Z] INFO  16:57:29,511 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:57Z] INFO  16:57:29,512 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-14T23:57Z] INFO  16:57:29,512 MicroScheduler -   -> 2119 reads (0.80% of total) failing MappingQualityZeroFilter
[2016-04-14T23:57Z] INFO  16:57:29,513 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:57Z] INFO  16:57:29,514 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-14T23:57Z] INFO  16:57:29,514 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-14T23:57Z] INFO  16:57:30,087 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:57Z] INFO  16:57:30,128 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:57Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-11_0_15994658-prep.bam
[2016-04-14T23:57Z] GATK: realign ('13', 67477635, 84455642) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-14T23:57Z] INFO  16:57:30,227 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:57Z] GATK: realign ('13', 35615069, 51287376) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-14T23:57Z] INFO  16:57:30,741 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:57Z] INFO  16:57:30,744 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:57Z] INFO  16:57:30,744 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:57Z] INFO  16:57:30,745 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:57Z] INFO  16:57:30,750 HelpFormatter - Program Args: -T PrintReads -L 14:66135961-81646674 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/14/tx/tmpXOEFNc/R14-18105_kapa-NGv3-PE100-NGv3-sort-14_66135960_81646674-prep-prealign.bam
[2016-04-14T23:57Z] INFO  16:57:30,760 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:57Z] INFO  16:57:30,760 HelpFormatter - Date/Time: 2016/04/14 16:57:30
[2016-04-14T23:57Z] INFO  16:57:30,760 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:57Z] INFO  16:57:30,761 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:57Z] INFO  16:57:30,997 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:57Z] INFO  16:57:31,044 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:57Z] GATK: realign ('13', 19751066, 35517251) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-14T23:57Z] INFO  16:57:32,314 ProgressMeter -            done   1.5513818E7    15.0 s       1.0 s      100.0%    15.0 s       0.0 s
[2016-04-14T23:57Z] INFO  16:57:32,315 ProgressMeter - Total runtime 15.94 secs, 0.27 min, 0.00 hours
[2016-04-14T23:57Z] INFO  16:57:32,319 MicroScheduler - 10230 reads were filtered out during the traversal out of approximately 118174 total reads (8.66%)
[2016-04-14T23:57Z] INFO  16:57:32,320 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:57Z] INFO  16:57:32,321 MicroScheduler -   -> 494 reads (0.42% of total) failing BadMateFilter
[2016-04-14T23:57Z] INFO  16:57:32,322 MicroScheduler -   -> 9501 reads (8.04% of total) failing DuplicateReadFilter
[2016-04-14T23:57Z] INFO  16:57:32,323 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-14T23:57Z] INFO  16:57:32,323 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:57Z] INFO  16:57:32,324 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-14T23:57Z] INFO  16:57:32,325 MicroScheduler -   -> 235 reads (0.20% of total) failing MappingQualityZeroFilter
[2016-04-14T23:57Z] INFO  16:57:32,326 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:57Z] INFO  16:57:32,326 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-14T23:57Z] INFO  16:57:32,327 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-14T23:57Z] INFO  16:57:32,366 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-14T23:57Z] INFO  16:57:32,435 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:57Z] INFO  16:57:32,446 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:57Z] INFO  16:57:32,526 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-14T23:57Z] GATK pre-alignment ('14', 81651874, 97299968) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-14T23:57Z] INFO  16:57:32,554 IntervalUtils - Processing 15510714 bp from intervals
[2016-04-14T23:57Z] INFO  16:57:32,687 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:57Z] INFO  16:57:33,044 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:57Z] INFO  16:57:33,045 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:57Z] INFO  16:57:33,045 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:57Z] INFO  16:57:33,046 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:57Z] INFO  16:57:33,069 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:57Z] INFO  16:57:33,170 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:57Z] INFO  16:57:33,173 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:57Z] INFO  16:57:33,174 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:57Z] INFO  16:57:33,174 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:57Z] INFO  16:57:33,178 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/13/R14-18105_kapa-NGv3-PE100-NGv3-sort-13_67477635_84455642-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/13/R14-18105_kapa-NGv3-PE100-NGv3-sort-13_67477635_84455642-prep-prealign-realign.intervals -L 13:67477636-84455642 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/13/tx/tmpB3Huiu/R14-18105_kapa-NGv3-PE100-NGv3-sort-13_67477635_84455642-prep.bam
[2016-04-14T23:57Z] INFO  16:57:33,201 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:57Z] INFO  16:57:33,202 HelpFormatter - Date/Time: 2016/04/14 16:57:33
[2016-04-14T23:57Z] INFO  16:57:33,202 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:57Z] INFO  16:57:33,203 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:57Z] INFO  16:57:33,240 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:57Z] INFO  16:57:33,256 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:57Z] INFO  16:57:33,260 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:57Z] INFO  16:57:33,270 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:57Z] INFO  16:57:33,293 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:57Z] INFO  16:57:33,311 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/13/R14-18105_kapa-NGv3-PE100-NGv3-sort-13_35615069_51287376-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/13/R14-18105_kapa-NGv3-PE100-NGv3-sort-13_35615069_51287376-prep-prealign-realign.intervals -L 13:35615070-51287376 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/13/tx/tmpTQOz4K/R14-18105_kapa-NGv3-PE100-NGv3-sort-13_35615069_51287376-prep.bam
[2016-04-14T23:57Z] INFO  16:57:33,326 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:57Z] INFO  16:57:33,326 HelpFormatter - Date/Time: 2016/04/14 16:57:33
[2016-04-14T23:57Z] INFO  16:57:33,327 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:57Z] INFO  16:57:33,327 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:57Z] INFO  16:57:33,455 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:57Z] INFO  16:57:33,583 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:57Z] INFO  16:57:33,614 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:57Z] INFO  16:57:33,623 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:57Z] INFO  16:57:33,686 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-14T23:57Z] INFO  16:57:33,744 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:57Z] INFO  16:57:33,754 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:57Z] INFO  16:57:33,814 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-14T23:57Z] INFO  16:57:33,898 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:57Z] GATK: realign ('13', 86368117, 101881935) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-14T23:57Z] INFO  16:57:34,073 IntervalUtils - Processing 16978007 bp from intervals
[2016-04-14T23:57Z] WARN  16:57:34,077 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:57Z] INFO  16:57:34,173 IntervalUtils - Processing 15672307 bp from intervals
[2016-04-14T23:57Z] WARN  16:57:34,178 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:57Z] INFO  16:57:34,226 ProgressMeter -            done    108896.0    10.0 s      95.0 s      100.0%    10.0 s       0.0 s
[2016-04-14T23:57Z] INFO  16:57:34,226 ProgressMeter - Total runtime 10.42 secs, 0.17 min, 0.00 hours
[2016-04-14T23:57Z] INFO  16:57:34,230 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 108896 total reads (0.00%)
[2016-04-14T23:57Z] INFO  16:57:34,231 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:57Z] INFO  16:57:34,231 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:57Z] INFO  16:57:34,232 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:57Z] INFO  16:57:34,237 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:57Z] INFO  16:57:34,282 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:57Z] INFO  16:57:34,362 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:57Z] INFO  16:57:34,363 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:57Z] INFO  16:57:34,364 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:57Z] INFO  16:57:34,365 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:57Z] INFO  16:57:34,413 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:57Z] INFO  16:57:34,416 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:57Z] INFO  16:57:34,417 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:57Z] INFO  16:57:34,417 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:57Z] INFO  16:57:34,422 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/13/R14-18105_kapa-NGv3-PE100-NGv3-sort-13_19751066_35517251-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/13/R14-18105_kapa-NGv3-PE100-NGv3-sort-13_19751066_35517251-prep-prealign-realign.intervals -L 13:19751067-35517251 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/13/tx/tmp2ylDIf/R14-18105_kapa-NGv3-PE100-NGv3-sort-13_19751066_35517251-prep.bam
[2016-04-14T23:57Z] INFO  16:57:34,436 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:57Z] INFO  16:57:34,437 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:57Z] INFO  16:57:34,438 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:57Z] INFO  16:57:34,438 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:57Z] INFO  16:57:34,453 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:57Z] INFO  16:57:34,454 HelpFormatter - Date/Time: 2016/04/14 16:57:34
[2016-04-14T23:57Z] INFO  16:57:34,454 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:57Z] INFO  16:57:34,455 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:57Z] INFO  16:57:34,491 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:57Z] INFO  16:57:34,589 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:57Z] INFO  16:57:34,653 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:57Z] INFO  16:57:34,672 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:57Z] INFO  16:57:34,794 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:57Z] INFO  16:57:34,803 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:57Z] INFO  16:57:34,874 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-14T23:57Z] INFO  16:57:34,921 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:57Z] INFO  16:57:35,348 IntervalUtils - Processing 15766185 bp from intervals
[2016-04-14T23:57Z] WARN  16:57:35,370 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:57Z] INFO  16:57:35,442 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:57Z] INFO  16:57:35,597 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:57Z] INFO  16:57:35,607 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:57Z] INFO  16:57:35,608 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:57Z] INFO  16:57:35,609 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:57Z] INFO  16:57:35,610 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:57Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-13_51396767_67205543-prep.bam
[2016-04-14T23:57Z] INFO  16:57:35,665 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:57Z] INFO  16:57:35,669 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:57Z] INFO  16:57:35,669 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:57Z] INFO  16:57:35,670 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:57Z] INFO  16:57:35,674 HelpFormatter - Program Args: -T PrintReads -L 14:81651875-97299968 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/14/tx/tmpFMpSMO/R14-18105_kapa-NGv3-PE100-NGv3-sort-14_81651874_97299968-prep-prealign.bam
[2016-04-14T23:57Z] INFO  16:57:35,692 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:57Z] INFO  16:57:35,693 HelpFormatter - Date/Time: 2016/04/14 16:57:35
[2016-04-14T23:57Z] INFO  16:57:35,694 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:57Z] INFO  16:57:35,695 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:57Z] INFO  16:57:35,819 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:57Z] INFO  16:57:35,882 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:57Z] GATK pre-alignment ('14', 97304098, 107349540) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-14T23:57Z] INFO  16:57:36,006 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:57Z] INFO  16:57:36,957 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:57Z] INFO  16:57:36,960 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:57Z] INFO  16:57:36,960 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:57Z] INFO  16:57:36,960 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:57Z] INFO  16:57:36,979 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/13/R14-18105_kapa-NGv3-PE100-NGv3-sort-13_86368117_101881935-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/13/R14-18105_kapa-NGv3-PE100-NGv3-sort-13_86368117_101881935-prep-prealign-realign.intervals -L 13:86368118-101881935 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/13/tx/tmpiFj_8S/R14-18105_kapa-NGv3-PE100-NGv3-sort-13_86368117_101881935-prep.bam
[2016-04-14T23:57Z] INFO  16:57:36,997 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:57Z] INFO  16:57:36,998 HelpFormatter - Date/Time: 2016/04/14 16:57:36
[2016-04-14T23:57Z] INFO  16:57:36,998 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:57Z] INFO  16:57:36,998 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:57Z] INFO  16:57:37,204 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-14T23:57Z] INFO  16:57:37,262 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:57Z] INFO  16:57:37,283 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:57Z] INFO  16:57:37,292 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:57Z] INFO  16:57:37,346 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-14T23:57Z] INFO  16:57:37,361 IntervalUtils - Processing 15648094 bp from intervals
[2016-04-14T23:57Z] INFO  16:57:37,381 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:57Z] INFO  16:57:37,391 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:57Z] INFO  16:57:37,473 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:57Z] INFO  16:57:37,490 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.10
[2016-04-14T23:57Z] INFO  16:57:37,739 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:57Z] INFO  16:57:37,741 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:57Z] INFO  16:57:37,742 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:57Z] INFO  16:57:37,742 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:57Z] INFO  16:57:37,765 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:57Z] INFO  16:57:37,867 ProgressMeter -            done    286037.0    19.0 s      69.0 s      100.0%    19.0 s       0.0 s
[2016-04-14T23:57Z] INFO  16:57:37,868 ProgressMeter - Total runtime 20.00 secs, 0.33 min, 0.01 hours
[2016-04-14T23:57Z] INFO  16:57:37,872 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 286037 total reads (0.00%)
[2016-04-14T23:57Z] INFO  16:57:37,873 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:57Z] INFO  16:57:37,874 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:57Z] INFO  16:57:37,874 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:57Z] INFO  16:57:37,887 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:57Z] INFO  16:57:37,922 IntervalUtils - Processing 15513818 bp from intervals
[2016-04-14T23:57Z] WARN  16:57:37,927 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:57Z] INFO  16:57:38,009 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:57Z] INFO  16:57:38,154 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:57Z] INFO  16:57:38,155 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:57Z] INFO  16:57:38,155 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:57Z] INFO  16:57:38,156 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:57Z] INFO  16:57:38,334 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:57Z] INFO  16:57:38,541 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:57Z] INFO  16:57:38,817 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:57Z] INFO  16:57:38,820 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:57Z] INFO  16:57:38,821 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:57Z] INFO  16:57:38,821 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:57Z] INFO  16:57:38,826 HelpFormatter - Program Args: -T PrintReads -L 14:97304099-107349540 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/14/tx/tmpdL2YCL/R14-18105_kapa-NGv3-PE100-NGv3-sort-14_97304098_107349540-prep-prealign.bam
[2016-04-14T23:57Z] INFO  16:57:38,837 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:57Z] INFO  16:57:38,837 HelpFormatter - Date/Time: 2016/04/14 16:57:38
[2016-04-14T23:57Z] INFO  16:57:38,837 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:57Z] INFO  16:57:38,837 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:57Z] INFO  16:57:39,019 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:57Z] INFO  16:57:39,590 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:57Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-12_93870729_109490566-prep.bam
[2016-04-14T23:57Z] INFO  16:57:40,144 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-14T23:57Z] INFO  16:57:40,240 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:57Z] INFO  16:57:40,249 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:57Z] INFO  16:57:40,331 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-14T23:57Z] INFO  16:57:40,360 IntervalUtils - Processing 10045442 bp from intervals
[2016-04-14T23:57Z] INFO  16:57:40,483 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:57Z] GATK pre-alignment ('15', 0, 20740485) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-14T23:57Z] INFO  16:57:40,720 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:57Z] INFO  16:57:40,721 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:57Z] INFO  16:57:40,721 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:57Z] INFO  16:57:40,721 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:57Z] INFO  16:57:40,746 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:57Z] INFO  16:57:40,869 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:57Z] INFO  16:57:43,387 ProgressMeter -            done     93953.0     9.0 s      96.0 s      100.0%     9.0 s       0.0 s
[2016-04-14T23:57Z] INFO  16:57:43,388 ProgressMeter - Total runtime 9.02 secs, 0.15 min, 0.00 hours
[2016-04-14T23:57Z] INFO  16:57:43,393 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 93953 total reads (0.00%)
[2016-04-14T23:57Z] INFO  16:57:43,394 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:57Z] INFO  16:57:43,395 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:57Z] INFO  16:57:43,396 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:57Z] INFO  16:57:43,451 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@41fd9d8e
[2016-04-14T23:57Z] INFO  16:57:43,477 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:57Z] INFO  16:57:43,481 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:57Z] INFO  16:57:43,482 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:57Z] INFO  16:57:43,482 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:57Z] INFO  16:57:43,488 HelpFormatter - Program Args: -T PrintReads -L 15:1-20740485 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/15/tx/tmpqQvmGq/R14-18105_kapa-NGv3-PE100-NGv3-sort-15_0_20740485-prep-prealign.bam
[2016-04-14T23:57Z] INFO  16:57:43,498 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:57Z] INFO  16:57:43,507 HelpFormatter - Date/Time: 2016/04/14 16:57:43
[2016-04-14T23:57Z] INFO  16:57:43,508 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:57Z] INFO  16:57:43,508 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:57Z] INFO  16:57:43,552 ProgressMeter -            done    129459.0    19.0 s       2.5 m      100.0%    19.0 s       0.0 s
[2016-04-14T23:57Z] INFO  16:57:43,552 ProgressMeter - Total runtime 19.23 secs, 0.32 min, 0.01 hours
[2016-04-14T23:57Z] INFO  16:57:43,553 MicroScheduler - 126 reads were filtered out during the traversal out of approximately 129585 total reads (0.10%)
[2016-04-14T23:57Z] INFO  16:57:43,553 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:57Z] INFO  16:57:43,553 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:57Z] INFO  16:57:43,553 MicroScheduler -   -> 126 reads (0.10% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:57Z] INFO  16:57:43,691 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:57Z] INFO  16:57:44,343 ProgressMeter -     11:75303765   1.2556599E7    30.0 s       2.0 s       80.9%    37.0 s       7.0 s
[2016-04-14T23:57Z] INFO  16:57:44,631 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-14T23:57Z] INFO  16:57:44,723 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:57Z] INFO  16:57:44,732 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:57Z] INFO  16:57:44,777 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.04
[2016-04-14T23:57Z] INFO  16:57:44,791 IntervalUtils - Processing 20740485 bp from intervals
[2016-04-14T23:57Z] INFO  16:57:44,862 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:57Z] INFO  16:57:44,941 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:57Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-13_67477635_84455642-prep.bam
[2016-04-14T23:57Z] INFO  16:57:44,980 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:57Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-14_35072553_50583270-prep-prealign.bam
[2016-04-14T23:57Z] INFO  16:57:45,175 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:57Z] INFO  16:57:45,177 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:57Z] INFO  16:57:45,177 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:57Z] INFO  16:57:45,178 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:57Z] INFO  16:57:45,207 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:57Z] INFO  16:57:45,219 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:57Z] GATK pre-alignment ('15', 20741621, 36872162) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-14T23:57Z] GATK RealignerTargetCreator: R14-18105_kapa-NGv3-PE100-NGv3-sort-14_35072553_50583270-prep-prealign.bam 14:35072554-50583270
[2016-04-14T23:57Z] GATK: RealignerTargetCreator
[2016-04-14T23:57Z] INFO  16:57:45,476 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@7172f77a
[2016-04-14T23:57Z] INFO  16:57:45,610 ProgressMeter -            done    615091.0    89.0 s       2.4 m      100.0%    89.0 s       0.0 s
[2016-04-14T23:57Z] INFO  16:57:45,611 ProgressMeter - Total runtime 89.66 secs, 1.49 min, 0.02 hours
[2016-04-14T23:57Z] INFO  16:57:45,612 MicroScheduler - 240 reads were filtered out during the traversal out of approximately 615331 total reads (0.04%)
[2016-04-14T23:57Z] INFO  16:57:45,612 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:57Z] INFO  16:57:45,613 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:57Z] INFO  16:57:45,614 MicroScheduler -   -> 240 reads (0.04% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:57Z] INFO  16:57:46,348 ProgressMeter -            done   1.3279773E7    17.0 s       1.0 s      100.0%    17.0 s       0.0 s
[2016-04-14T23:57Z] INFO  16:57:46,349 ProgressMeter - Total runtime 17.11 secs, 0.29 min, 0.00 hours
[2016-04-14T23:57Z] INFO  16:57:46,353 MicroScheduler - 18097 reads were filtered out during the traversal out of approximately 216795 total reads (8.35%)
[2016-04-14T23:57Z] INFO  16:57:46,354 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:57Z] INFO  16:57:46,355 MicroScheduler -   -> 544 reads (0.25% of total) failing BadMateFilter
[2016-04-14T23:57Z] INFO  16:57:46,355 MicroScheduler -   -> 17008 reads (7.85% of total) failing DuplicateReadFilter
[2016-04-14T23:57Z] INFO  16:57:46,356 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-14T23:57Z] INFO  16:57:46,357 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:57Z] INFO  16:57:46,357 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-14T23:57Z] INFO  16:57:46,358 MicroScheduler -   -> 545 reads (0.25% of total) failing MappingQualityZeroFilter
[2016-04-14T23:57Z] INFO  16:57:46,358 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:57Z] INFO  16:57:46,359 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-14T23:57Z] INFO  16:57:46,360 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-14T23:57Z] INFO  16:57:46,996 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:57Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-12_109494486_125263132-prep-prealign.bam
[2016-04-14T23:57Z] INFO  16:57:47,799 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:57Z] GATK: realign ('13', 101890105, 115169878) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-14T23:57Z] INFO  16:57:47,889 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:57Z] INFO  16:57:47,893 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:57Z] INFO  16:57:47,894 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:57Z] INFO  16:57:47,895 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:57Z] INFO  16:57:47,901 HelpFormatter - Program Args: -T PrintReads -L 15:20741622-36872162 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/15/tx/tmppbyC2O/R14-18105_kapa-NGv3-PE100-NGv3-sort-15_20741621_36872162-prep-prealign.bam
[2016-04-14T23:57Z] INFO  16:57:47,911 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:57Z] INFO  16:57:47,911 HelpFormatter - Date/Time: 2016/04/14 16:57:47
[2016-04-14T23:57Z] INFO  16:57:47,911 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:57Z] INFO  16:57:47,911 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:57Z] INFO  16:57:48,071 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:57Z] INFO  16:57:48,074 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:57Z] INFO  16:57:48,075 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:57Z] INFO  16:57:48,075 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:57Z] INFO  16:57:48,081 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/14/R14-18105_kapa-NGv3-PE100-NGv3-sort-14_35072553_50583270-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/14/tx/tmpoaZrOA/R14-18105_kapa-NGv3-PE100-NGv3-sort-14_35072553_50583270-prep-prealign-realign.intervals -l INFO -L 14:35072554-50583270 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-14T23:57Z] INFO  16:57:48,107 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:57Z] INFO  16:57:48,108 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:57Z] INFO  16:57:48,108 HelpFormatter - Date/Time: 2016/04/14 16:57:48
[2016-04-14T23:57Z] INFO  16:57:48,108 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:57Z] INFO  16:57:48,113 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:57Z] INFO  16:57:48,231 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:57Z] INFO  16:57:48,430 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-14T23:57Z] INFO  16:57:48,439 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:57Z] INFO  16:57:48,511 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-14T23:57Z] INFO  16:57:48,595 ProgressMeter -            done   1.55264E7    34.0 s       2.0 s      100.0%    34.0 s       0.0 s
[2016-04-14T23:57Z] INFO  16:57:48,596 ProgressMeter - Total runtime 34.26 secs, 0.57 min, 0.01 hours
[2016-04-14T23:57Z] INFO  16:57:48,599 MicroScheduler - 81320 reads were filtered out during the traversal out of approximately 937808 total reads (8.67%)
[2016-04-14T23:57Z] INFO  16:57:48,601 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:57Z] INFO  16:57:48,602 MicroScheduler -   -> 1643 reads (0.18% of total) failing BadMateFilter
[2016-04-14T23:57Z] INFO  16:57:48,603 MicroScheduler -   -> 74739 reads (7.97% of total) failing DuplicateReadFilter
[2016-04-14T23:57Z] INFO  16:57:48,603 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-14T23:57Z] INFO  16:57:48,604 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:57Z] INFO  16:57:48,605 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-14T23:57Z] INFO  16:57:48,611 MicroScheduler -   -> 4938 reads (0.53% of total) failing MappingQualityZeroFilter
[2016-04-14T23:57Z] INFO  16:57:48,612 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:57Z] INFO  16:57:48,612 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-14T23:57Z] INFO  16:57:48,612 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-14T23:57Z] INFO  16:57:48,802 IntervalUtils - Processing 15510717 bp from intervals
[2016-04-14T23:57Z] WARN  16:57:48,807 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:57Z] INFO  16:57:48,870 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:57Z] INFO  16:57:49,049 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:57Z] INFO  16:57:49,050 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:57Z] INFO  16:57:49,051 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:57Z] INFO  16:57:49,051 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-14T23:57Z] GATK RealignerTargetCreator: R14-18105_kapa-NGv3-PE100-NGv3-sort-12_109494486_125263132-prep-prealign.bam 12:109494487-125263132
[2016-04-14T23:57Z] GATK: RealignerTargetCreator
[2016-04-14T23:57Z] INFO  16:57:49,455 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-14T23:57Z] INFO  16:57:49,502 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@41fd9d8e
[2016-04-14T23:57Z] INFO  16:57:49,544 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:57Z] INFO  16:57:49,556 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:57Z] INFO  16:57:49,561 ProgressMeter -            done     13946.0     4.0 s       5.2 m      100.0%     4.0 s       0.0 s
[2016-04-14T23:57Z] INFO  16:57:49,562 ProgressMeter - Total runtime 4.39 secs, 0.07 min, 0.00 hours
[2016-04-14T23:57Z] INFO  16:57:49,563 MicroScheduler - 21 reads were filtered out during the traversal out of approximately 13967 total reads (0.15%)
[2016-04-14T23:57Z] INFO  16:57:49,564 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:57Z] INFO  16:57:49,565 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:57Z] INFO  16:57:49,565 MicroScheduler -   -> 21 reads (0.15% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:57Z] INFO  16:57:49,652 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.10
[2016-04-14T23:57Z] INFO  16:57:49,671 ProgressMeter -            done    117187.0    11.0 s      98.0 s      100.0%    11.0 s       0.0 s
[2016-04-14T23:57Z] INFO  16:57:49,671 ProgressMeter - Total runtime 11.52 secs, 0.19 min, 0.00 hours
[2016-04-14T23:57Z] INFO  16:57:49,678 IntervalUtils - Processing 16130541 bp from intervals
[2016-04-14T23:57Z] INFO  16:57:49,682 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 117187 total reads (0.00%)
[2016-04-14T23:57Z] INFO  16:57:49,682 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:57Z] INFO  16:57:49,683 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:57Z] INFO  16:57:49,683 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:57Z] INFO  16:57:49,822 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:57Z] INFO  16:57:49,966 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:57Z] GATK: realign ('11', 62744265, 78270665) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-14T23:57Z] INFO  16:57:50,108 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:57Z] INFO  16:57:50,109 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:57Z] INFO  16:57:50,110 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:57Z] INFO  16:57:50,110 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:57Z] INFO  16:57:50,129 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:57Z] INFO  16:57:50,288 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:57Z] INFO  16:57:50,512 ProgressMeter -      12:9310439    400005.0    30.0 s      75.0 s       59.5%    50.0 s      20.0 s
[2016-04-14T23:57Z] INFO  16:57:50,810 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:57Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-15_0_20740485-prep-prealign.bam
[2016-04-14T23:57Z] GATK RealignerTargetCreator: R14-18105_kapa-NGv3-PE100-NGv3-sort-15_0_20740485-prep-prealign.bam 15:1-20740485
[2016-04-14T23:57Z] GATK: RealignerTargetCreator
[2016-04-14T23:57Z] INFO  16:57:50,948 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:57Z] INFO  16:57:50,954 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:57Z] INFO  16:57:50,955 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:57Z] INFO  16:57:50,955 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:57Z] INFO  16:57:50,960 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/13/R14-18105_kapa-NGv3-PE100-NGv3-sort-13_101890105_115169878-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/13/R14-18105_kapa-NGv3-PE100-NGv3-sort-13_101890105_115169878-prep-prealign-realign.intervals -L 13:101890106-115169878 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/13/tx/tmp6OxNsd/R14-18105_kapa-NGv3-PE100-NGv3-sort-13_101890105_115169878-prep.bam
[2016-04-14T23:57Z] INFO  16:57:50,984 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:57Z] INFO  16:57:50,985 HelpFormatter - Date/Time: 2016/04/14 16:57:50
[2016-04-14T23:57Z] INFO  16:57:50,985 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:57Z] INFO  16:57:50,986 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:57Z] INFO  16:57:51,138 ProgressMeter -     14:23240453    200003.0    30.0 s       2.6 m       23.8%     2.1 m      96.0 s
[2016-04-14T23:57Z] INFO  16:57:51,194 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:57Z] INFO  16:57:51,199 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:57Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-13_86368117_101881935-prep.bam
[2016-04-14T23:57Z] INFO  16:57:51,318 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:57Z] INFO  16:57:51,328 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:57Z] INFO  16:57:51,430 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.10
[2016-04-14T23:57Z] INFO  16:57:51,662 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:57Z] INFO  16:57:51,665 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:57Z] INFO  16:57:51,666 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:57Z] INFO  16:57:51,666 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:57Z] INFO  16:57:51,671 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/12/R14-18105_kapa-NGv3-PE100-NGv3-sort-12_109494486_125263132-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/12/tx/tmpfE39J4/R14-18105_kapa-NGv3-PE100-NGv3-sort-12_109494486_125263132-prep-prealign-realign.intervals -l INFO -L 12:109494487-125263132 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-14T23:57Z] INFO  16:57:51,691 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:57Z] INFO  16:57:51,692 HelpFormatter - Date/Time: 2016/04/14 16:57:51
[2016-04-14T23:57Z] INFO  16:57:51,693 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:57Z] INFO  16:57:51,702 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:57Z] GATK pre-alignment ('15', 36887086, 52402170) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-14T23:57Z] INFO  16:57:51,797 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:57Z] INFO  16:57:51,882 ProgressMeter -            done    235146.0    17.0 s      74.0 s      100.0%    17.0 s       0.0 s
[2016-04-14T23:57Z] INFO  16:57:51,883 ProgressMeter - Total runtime 17.45 secs, 0.29 min, 0.00 hours
[2016-04-14T23:57Z] INFO  16:57:51,886 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 235146 total reads (0.00%)
[2016-04-14T23:57Z] INFO  16:57:51,887 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:57Z] INFO  16:57:51,887 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:57Z] INFO  16:57:51,887 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:57Z] INFO  16:57:51,960 IntervalUtils - Processing 13279773 bp from intervals
[2016-04-14T23:57Z] WARN  16:57:51,976 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:57Z] INFO  16:57:51,991 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-14T23:57Z] INFO  16:57:52,000 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:57Z] INFO  16:57:52,070 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-14T23:57Z] INFO  16:57:52,109 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:57Z] INFO  16:57:52,222 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:57Z] INFO  16:57:52,223 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:57Z] INFO  16:57:52,224 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:57Z] INFO  16:57:52,224 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:57Z] INFO  16:57:52,330 IntervalUtils - Processing 15768646 bp from intervals
[2016-04-14T23:57Z] WARN  16:57:52,347 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:57Z] INFO  16:57:52,385 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:57Z] INFO  16:57:52,463 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:57Z] INFO  16:57:52,512 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:57Z] INFO  16:57:52,656 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:57Z] INFO  16:57:52,676 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:57Z] INFO  16:57:52,676 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:57Z] INFO  16:57:52,677 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-14T23:57Z] INFO  16:57:52,849 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:57Z] INFO  16:57:52,874 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:57Z] INFO  16:57:52,875 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:57Z] INFO  16:57:52,876 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:57Z] INFO  16:57:52,880 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/11/R14-18105_kapa-NGv3-PE100-NGv3-sort-11_62744265_78270665-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/11/R14-18105_kapa-NGv3-PE100-NGv3-sort-11_62744265_78270665-prep-prealign-realign.intervals -L 11:62744266-78270665 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/11/tx/tmpj4xCes/R14-18105_kapa-NGv3-PE100-NGv3-sort-11_62744265_78270665-prep.bam
[2016-04-14T23:57Z] INFO  16:57:52,890 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:57Z] INFO  16:57:52,890 HelpFormatter - Date/Time: 2016/04/14 16:57:52
[2016-04-14T23:57Z] INFO  16:57:52,890 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:57Z] INFO  16:57:52,891 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:57Z] INFO  16:57:53,186 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:57Z] INFO  16:57:53,291 ProgressMeter -     12:61754513   1.4978846E7    30.0 s       2.0 s       94.3%    31.0 s       1.0 s
[2016-04-14T23:57Z] INFO  16:57:53,306 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:57Z] INFO  16:57:53,322 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:57Z] INFO  16:57:53,394 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:57Z] INFO  16:57:53,399 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-14T23:57Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-13_35615069_51287376-prep.bam
[2016-04-14T23:57Z] INFO  16:57:53,911 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:57Z] INFO  16:57:53,914 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:57Z] INFO  16:57:53,914 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:57Z] INFO  16:57:53,914 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:57Z] INFO  16:57:53,918 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/15/R14-18105_kapa-NGv3-PE100-NGv3-sort-15_0_20740485-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/15/tx/tmpFxUW5h/R14-18105_kapa-NGv3-PE100-NGv3-sort-15_0_20740485-prep-prealign-realign.intervals -l INFO -L 15:1-20740485 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-14T23:57Z] INFO  16:57:53,942 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:57Z] INFO  16:57:53,942 HelpFormatter - Date/Time: 2016/04/14 16:57:53
[2016-04-14T23:57Z] INFO  16:57:53,942 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:57Z] INFO  16:57:53,942 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:57Z] INFO  16:57:53,977 IntervalUtils - Processing 15526400 bp from intervals
[2016-04-14T23:57Z] WARN  16:57:53,992 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:57Z] INFO  16:57:54,043 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:57Z] INFO  16:57:54,081 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:57Z] GATK pre-alignment ('15', 52404364, 67923265) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-14T23:57Z] INFO  16:57:54,290 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-14T23:57Z] INFO  16:57:54,306 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:57Z] INFO  16:57:54,312 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:57Z] INFO  16:57:54,313 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:57Z] INFO  16:57:54,313 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:57Z] INFO  16:57:54,314 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:57Z] INFO  16:57:54,369 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-14T23:57Z] INFO  16:57:54,429 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:57Z] INFO  16:57:54,432 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:57Z] INFO  16:57:54,433 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:57Z] INFO  16:57:54,434 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:57Z] INFO  16:57:54,438 HelpFormatter - Program Args: -T PrintReads -L 15:36887087-52402170 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/15/tx/tmptPHtbQ/R14-18105_kapa-NGv3-PE100-NGv3-sort-15_36887086_52402170-prep-prealign.bam
[2016-04-14T23:57Z] INFO  16:57:54,447 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:57Z] INFO  16:57:54,458 HelpFormatter - Date/Time: 2016/04/14 16:57:54
[2016-04-14T23:57Z] INFO  16:57:54,459 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:57Z] INFO  16:57:54,460 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:57Z] INFO  16:57:54,491 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:57Z] INFO  16:57:54,532 ProgressMeter -            done   1.5898218E7    31.0 s       1.0 s      100.0%    31.0 s       0.0 s
[2016-04-14T23:57Z] INFO  16:57:54,533 ProgressMeter - Total runtime 31.27 secs, 0.52 min, 0.01 hours
[2016-04-14T23:57Z] INFO  16:57:54,537 MicroScheduler - 82655 reads were filtered out during the traversal out of approximately 898077 total reads (9.20%)
[2016-04-14T23:57Z] INFO  16:57:54,538 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:57Z] INFO  16:57:54,539 MicroScheduler -   -> 1490 reads (0.17% of total) failing BadMateFilter
[2016-04-14T23:57Z] INFO  16:57:54,539 MicroScheduler -   -> 70214 reads (7.82% of total) failing DuplicateReadFilter
[2016-04-14T23:57Z] INFO  16:57:54,540 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-14T23:57Z] INFO  16:57:54,541 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:57Z] INFO  16:57:54,541 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-14T23:57Z] INFO  16:57:54,542 MicroScheduler -   -> 10951 reads (1.22% of total) failing MappingQualityZeroFilter
[2016-04-14T23:57Z] INFO  16:57:54,553 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:57Z] INFO  16:57:54,554 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-14T23:57Z] INFO  16:57:54,555 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-14T23:57Z] INFO  16:57:54,617 ProgressMeter -            done    264489.0    19.0 s      71.0 s      100.0%    19.0 s       0.0 s
[2016-04-14T23:57Z] INFO  16:57:54,618 ProgressMeter - Total runtime 19.01 secs, 0.32 min, 0.01 hours
[2016-04-14T23:57Z] INFO  16:57:54,619 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:57Z] INFO  16:57:54,621 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 264489 total reads (0.00%)
[2016-04-14T23:57Z] INFO  16:57:54,622 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:57Z] INFO  16:57:54,622 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:57Z] INFO  16:57:54,622 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:57Z] INFO  16:57:54,640 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:57Z] INFO  16:57:54,655 IntervalUtils - Processing 20740485 bp from intervals
[2016-04-14T23:57Z] WARN  16:57:54,660 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:57Z] INFO  16:57:54,751 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:57Z] INFO  16:57:55,057 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:57Z] INFO  16:57:55,058 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:57Z] INFO  16:57:55,059 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:57Z] INFO  16:57:55,060 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-14T23:57Z] INFO  16:57:55,704 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-14T23:57Z] INFO  16:57:55,795 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:57Z] INFO  16:57:55,805 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:57Z] INFO  16:57:55,868 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-14T23:57Z] INFO  16:57:55,883 IntervalUtils - Processing 15515084 bp from intervals
[2016-04-14T23:57Z] INFO  16:57:55,968 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:57Z] GATK: realign ('12', 46756066, 62654284) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-14T23:57Z] INFO  16:57:55,999 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:57Z] INFO  16:57:56,278 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:57Z] INFO  16:57:56,279 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:57Z] INFO  16:57:56,280 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:57Z] INFO  16:57:56,281 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:57Z] INFO  16:57:56,296 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:57Z] INFO  16:57:56,297 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:57Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-13_19751066_35517251-prep.bam
[2016-04-14T23:57Z] INFO  16:57:56,462 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:57Z] INFO  16:57:57,125 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:57Z] INFO  16:57:57,129 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:57Z] INFO  16:57:57,129 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:57Z] INFO  16:57:57,130 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:57Z] INFO  16:57:57,135 HelpFormatter - Program Args: -T PrintReads -L 15:52404365-67923265 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/15/tx/tmpeldsgb/R14-18105_kapa-NGv3-PE100-NGv3-sort-15_52404364_67923265-prep-prealign.bam
[2016-04-14T23:57Z] INFO  16:57:57,147 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:57Z] INFO  16:57:57,158 HelpFormatter - Date/Time: 2016/04/14 16:57:57
[2016-04-14T23:57Z] INFO  16:57:57,159 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:57Z] INFO  16:57:57,159 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:57Z] GATK pre-alignment ('15', 67932890, 83447639) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-14T23:57Z] INFO  16:57:57,226 ProgressMeter -            done    558357.0    36.0 s      66.0 s      100.0%    36.0 s       0.0 s
[2016-04-14T23:57Z] INFO  16:57:57,227 ProgressMeter - Total runtime 36.97 secs, 0.62 min, 0.01 hours
[2016-04-14T23:57Z] INFO  16:57:57,231 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 558357 total reads (0.00%)
[2016-04-14T23:57Z] INFO  16:57:57,232 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:57Z] INFO  16:57:57,233 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:57Z] INFO  16:57:57,233 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:57Z] INFO  16:57:57,339 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:57Z] INFO  16:57:57,631 ProgressMeter -     14:64681242    200005.0    30.0 s       2.5 m       90.9%    33.0 s       3.0 s
[2016-04-14T23:57Z] INFO  16:57:58,407 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-14T23:57Z] INFO  16:57:58,481 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:57Z] INFO  16:57:58,491 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:57Z] INFO  16:57:58,537 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-14T23:57Z] INFO  16:57:58,554 IntervalUtils - Processing 15518901 bp from intervals
[2016-04-14T23:57Z] INFO  16:57:58,645 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:57Z] INFO  16:57:58,665 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:57Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-12_0_15637181-prep.bam
[2016-04-14T23:57Z] INFO  16:57:58,954 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:57Z] INFO  16:57:58,955 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:57Z] INFO  16:57:58,956 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:57Z] INFO  16:57:58,957 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:57Z] INFO  16:57:58,970 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:57Z] INFO  16:57:59,046 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:57Z] INFO  16:57:59,049 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:57Z] INFO  16:57:59,050 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:57Z] INFO  16:57:59,051 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:57Z] INFO  16:57:59,055 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/12/R14-18105_kapa-NGv3-PE100-NGv3-sort-12_46756066_62654284-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/12/R14-18105_kapa-NGv3-PE100-NGv3-sort-12_46756066_62654284-prep-prealign-realign.intervals -L 12:46756067-62654284 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/12/tx/tmpJMi6BT/R14-18105_kapa-NGv3-PE100-NGv3-sort-12_46756066_62654284-prep.bam
[2016-04-14T23:57Z] INFO  16:57:59,092 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:57Z] INFO  16:57:59,092 HelpFormatter - Date/Time: 2016/04/14 16:57:59
[2016-04-14T23:57Z] INFO  16:57:59,094 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:57Z] INFO  16:57:59,092 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:57Z] INFO  16:57:59,092 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:57Z] INFO  16:57:59,292 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:57Z] INFO  16:57:59,400 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:57Z] INFO  16:57:59,409 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:57Z] INFO  16:57:59,453 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.04
[2016-04-14T23:57Z] INFO  16:57:59,836 IntervalUtils - Processing 15898218 bp from intervals
[2016-04-14T23:57Z] WARN  16:57:59,840 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:57Z] INFO  16:57:59,936 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:58Z] INFO  16:58:00,034 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:58Z] INFO  16:58:00,037 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:58Z] INFO  16:58:00,038 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:58Z] INFO  16:58:00,038 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:58Z] INFO  16:58:00,043 HelpFormatter - Program Args: -T PrintReads -L 15:67932891-83447639 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/15/tx/tmpaYT1w6/R14-18105_kapa-NGv3-PE100-NGv3-sort-15_67932890_83447639-prep-prealign.bam
[2016-04-14T23:58Z] INFO  16:58:00,052 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:58Z] INFO  16:58:00,053 HelpFormatter - Date/Time: 2016/04/14 16:58:00
[2016-04-14T23:58Z] INFO  16:58:00,053 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:58Z] INFO  16:58:00,053 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:58Z] INFO  16:58:00,102 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:58Z] INFO  16:58:00,104 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:58Z] INFO  16:58:00,105 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:58Z] INFO  16:58:00,106 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:58Z] INFO  16:58:00,265 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:58Z] INFO  16:58:00,309 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:58Z] GATK pre-alignment ('15', 83448996, 98982979) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-14T23:58Z] INFO  16:58:00,517 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:58Z] INFO  16:58:01,541 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-14T23:58Z] INFO  16:58:01,635 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:58Z] INFO  16:58:01,644 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:58Z] INFO  16:58:01,703 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-14T23:58Z] INFO  16:58:01,717 IntervalUtils - Processing 15514749 bp from intervals
[2016-04-14T23:58Z] INFO  16:58:01,801 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:58Z] INFO  16:58:02,200 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:58Z] INFO  16:58:02,200 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:58Z] INFO  16:58:02,200 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:58Z] INFO  16:58:02,201 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:58Z] INFO  16:58:02,226 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:58Z] INFO  16:58:02,437 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:58Z] INFO  16:58:03,204 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@7172f77a
[2016-04-14T23:58Z] INFO  16:58:03,314 ProgressMeter -            done    300526.0    35.0 s     118.0 s      100.0%    35.0 s       0.0 s
[2016-04-14T23:58Z] INFO  16:58:03,325 ProgressMeter - Total runtime 35.73 secs, 0.60 min, 0.01 hours
[2016-04-14T23:58Z] INFO  16:58:03,325 MicroScheduler - 159 reads were filtered out during the traversal out of approximately 300685 total reads (0.05%)
[2016-04-14T23:58Z] INFO  16:58:03,326 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:58Z] INFO  16:58:03,327 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:58Z] INFO  16:58:03,327 MicroScheduler -   -> 159 reads (0.05% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:58Z] INFO  16:58:03,450 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:58Z] INFO  16:58:03,454 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:58Z] INFO  16:58:03,454 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:58Z] INFO  16:58:03,455 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:58Z] INFO  16:58:03,460 HelpFormatter - Program Args: -T PrintReads -L 15:83448997-98982979 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/15/tx/tmpUK8Ac0/R14-18105_kapa-NGv3-PE100-NGv3-sort-15_83448996_98982979-prep-prealign.bam
[2016-04-14T23:58Z] INFO  16:58:03,470 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:58Z] INFO  16:58:03,471 HelpFormatter - Date/Time: 2016/04/14 16:58:03
[2016-04-14T23:58Z] INFO  16:58:03,472 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:58Z] INFO  16:58:03,483 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:58Z] INFO  16:58:03,638 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:58Z] INFO  16:58:03,694 ProgressMeter -     14:74388861    100001.0    30.0 s       5.1 m       53.2%    56.0 s      26.0 s
[2016-04-14T23:58Z] INFO  16:58:04,693 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:58Z] INFO  16:58:04,699 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-14T23:58Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-14_50585061_66096324-prep-prealign.bam
[2016-04-14T23:58Z] INFO  16:58:04,816 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:58Z] INFO  16:58:04,825 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:58Z] INFO  16:58:04,890 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-14T23:58Z] INFO  16:58:04,914 IntervalUtils - Processing 15533983 bp from intervals
[2016-04-14T23:58Z] INFO  16:58:05,058 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:58Z] INFO  16:58:05,225 ProgressMeter -            done   1.5510717E7    16.0 s       1.0 s      100.0%    16.0 s       0.0 s
[2016-04-14T23:58Z] INFO  16:58:05,227 ProgressMeter - Total runtime 16.18 secs, 0.27 min, 0.00 hours
[2016-04-14T23:58Z] INFO  16:58:05,230 MicroScheduler - 12838 reads were filtered out during the traversal out of approximately 130247 total reads (9.86%)
[2016-04-14T23:58Z] INFO  16:58:05,231 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:58Z] INFO  16:58:05,232 MicroScheduler -   -> 452 reads (0.35% of total) failing BadMateFilter
[2016-04-14T23:58Z] INFO  16:58:05,233 MicroScheduler -   -> 9911 reads (7.61% of total) failing DuplicateReadFilter
[2016-04-14T23:58Z] INFO  16:58:05,233 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-14T23:58Z] INFO  16:58:05,234 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:58Z] INFO  16:58:05,235 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-14T23:58Z] INFO  16:58:05,235 MicroScheduler -   -> 2475 reads (1.90% of total) failing MappingQualityZeroFilter
[2016-04-14T23:58Z] INFO  16:58:05,236 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:58Z] INFO  16:58:05,236 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-14T23:58Z] INFO  16:58:05,237 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-14T23:58Z] INFO  16:58:05,343 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:58Z] INFO  16:58:05,344 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:58Z] INFO  16:58:05,345 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:58Z] INFO  16:58:05,345 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:58Z] INFO  16:58:05,370 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:58Z] INFO  16:58:05,520 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:58Z] GATK RealignerTargetCreator: R14-18105_kapa-NGv3-PE100-NGv3-sort-14_50585061_66096324-prep-prealign.bam 14:50585062-66096324
[2016-04-14T23:58Z] GATK: RealignerTargetCreator
[2016-04-14T23:58Z] INFO  16:58:06,775 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:58Z] GATK: realign ('14', 35072553, 50583270) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-14T23:58Z] INFO  16:58:07,764 ProgressMeter -     14:95669477    200003.0    30.0 s       2.5 m       89.6%    33.0 s       3.0 s
[2016-04-14T23:58Z] INFO  16:58:08,251 ProgressMeter -            done   2.0740485E7    13.0 s       0.0 s      100.0%    13.0 s       0.0 s
[2016-04-14T23:58Z] INFO  16:58:08,252 ProgressMeter - Total runtime 13.19 secs, 0.22 min, 0.00 hours
[2016-04-14T23:58Z] INFO  16:58:08,256 MicroScheduler - 6732 reads were filtered out during the traversal out of approximately 14046 total reads (47.93%)
[2016-04-14T23:58Z] INFO  16:58:08,257 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:58Z] INFO  16:58:08,258 MicroScheduler -   -> 37 reads (0.26% of total) failing BadMateFilter
[2016-04-14T23:58Z] INFO  16:58:08,259 MicroScheduler -   -> 570 reads (4.06% of total) failing DuplicateReadFilter
[2016-04-14T23:58Z] INFO  16:58:08,259 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-14T23:58Z] INFO  16:58:08,260 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:58Z] INFO  16:58:08,261 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-14T23:58Z] INFO  16:58:08,262 MicroScheduler -   -> 6125 reads (43.61% of total) failing MappingQualityZeroFilter
[2016-04-14T23:58Z] INFO  16:58:08,262 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:58Z] INFO  16:58:08,263 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-14T23:58Z] INFO  16:58:08,264 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-14T23:58Z] INFO  16:58:08,593 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:58Z] INFO  16:58:08,597 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:58Z] INFO  16:58:08,597 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:58Z] INFO  16:58:08,598 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:58Z] INFO  16:58:08,602 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/14/R14-18105_kapa-NGv3-PE100-NGv3-sort-14_50585061_66096324-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/14/tx/tmpFQggPe/R14-18105_kapa-NGv3-PE100-NGv3-sort-14_50585061_66096324-prep-prealign-realign.intervals -l INFO -L 14:50585062-66096324 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-14T23:58Z] INFO  16:58:08,623 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:58Z] INFO  16:58:08,624 HelpFormatter - Date/Time: 2016/04/14 16:58:08
[2016-04-14T23:58Z] INFO  16:58:08,625 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:58Z] INFO  16:58:08,625 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:58Z] INFO  16:58:08,760 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:58Z] INFO  16:58:08,999 ProgressMeter -            done    215390.0    16.0 s      77.0 s       99.4%    16.0 s       0.0 s
[2016-04-14T23:58Z] INFO  16:58:08,999 ProgressMeter - Total runtime 16.78 secs, 0.28 min, 0.00 hours
[2016-04-14T23:58Z] INFO  16:58:09,000 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-14T23:58Z] INFO  16:58:09,002 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 215390 total reads (0.00%)
[2016-04-14T23:58Z] INFO  16:58:09,003 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:58Z] INFO  16:58:09,003 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:58Z] INFO  16:58:09,003 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:58Z] INFO  16:58:09,010 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:58Z] INFO  16:58:09,053 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.04
[2016-04-14T23:58Z] INFO  16:58:09,332 IntervalUtils - Processing 15511263 bp from intervals
[2016-04-14T23:58Z] WARN  16:58:09,337 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:58Z] INFO  16:58:09,429 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:58Z] INFO  16:58:09,483 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:58Z] INFO  16:58:09,486 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:58Z] INFO  16:58:09,486 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:58Z] INFO  16:58:09,486 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:58Z] INFO  16:58:09,490 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/14/R14-18105_kapa-NGv3-PE100-NGv3-sort-14_35072553_50583270-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/14/R14-18105_kapa-NGv3-PE100-NGv3-sort-14_35072553_50583270-prep-prealign-realign.intervals -L 14:35072554-50583270 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/14/tx/tmpRXUhFm/R14-18105_kapa-NGv3-PE100-NGv3-sort-14_35072553_50583270-prep.bam
[2016-04-14T23:58Z] INFO  16:58:09,521 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:58Z] INFO  16:58:09,531 HelpFormatter - Date/Time: 2016/04/14 16:58:09
[2016-04-14T23:58Z] INFO  16:58:09,532 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:58Z] INFO  16:58:09,533 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:58Z] INFO  16:58:09,610 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:58Z] GATK: realign ('15', 0, 20740485) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-14T23:58Z] INFO  16:58:09,658 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:58Z] INFO  16:58:09,659 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:58Z] INFO  16:58:09,660 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:58Z] INFO  16:58:09,660 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-14T23:58Z] INFO  16:58:09,763 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:58Z] INFO  16:58:09,888 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:58Z] INFO  16:58:09,898 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:58Z] INFO  16:58:09,969 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-14T23:58Z] INFO  16:58:10,415 IntervalUtils - Processing 15510717 bp from intervals
[2016-04-14T23:58Z] WARN  16:58:10,420 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:58Z] INFO  16:58:10,479 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:58Z] INFO  16:58:10,491 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:58Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-13_101890105_115169878-prep.bam
[2016-04-14T23:58Z] INFO  16:58:10,649 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:58Z] INFO  16:58:10,650 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:58Z] INFO  16:58:10,661 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:58Z] INFO  16:58:10,662 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:58Z] INFO  16:58:10,735 ProgressMeter -    14:104563934    100001.0    30.0 s       5.0 m       72.3%    41.0 s      11.0 s
[2016-04-14T23:58Z] INFO  16:58:10,834 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:58Z] INFO  16:58:11,003 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:58Z] GATK pre-alignment ('15', 98984299, 102531392) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-14T23:58Z] INFO  16:58:11,337 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@7172f77a
[2016-04-14T23:58Z] INFO  16:58:11,480 ProgressMeter -            done    255045.0    33.0 s       2.2 m      100.0%    33.0 s       0.0 s
[2016-04-14T23:58Z] INFO  16:58:11,481 ProgressMeter - Total runtime 33.74 secs, 0.56 min, 0.01 hours
[2016-04-14T23:58Z] INFO  16:58:11,481 MicroScheduler - 159 reads were filtered out during the traversal out of approximately 255204 total reads (0.06%)
[2016-04-14T23:58Z] INFO  16:58:11,482 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:58Z] INFO  16:58:11,482 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:58Z] INFO  16:58:11,482 MicroScheduler -   -> 159 reads (0.06% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:58Z] INFO  16:58:12,424 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:58Z] INFO  16:58:12,427 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:58Z] INFO  16:58:12,428 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:58Z] INFO  16:58:12,429 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:58Z] INFO  16:58:12,433 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/15/R14-18105_kapa-NGv3-PE100-NGv3-sort-15_0_20740485-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/15/R14-18105_kapa-NGv3-PE100-NGv3-sort-15_0_20740485-prep-prealign-realign.intervals -L 15:1-20740485 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/15/tx/tmpMkbk0U/R14-18105_kapa-NGv3-PE100-NGv3-sort-15_0_20740485-prep.bam
[2016-04-14T23:58Z] INFO  16:58:12,462 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:58Z] INFO  16:58:12,463 HelpFormatter - Date/Time: 2016/04/14 16:58:12
[2016-04-14T23:58Z] INFO  16:58:12,463 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:58Z] INFO  16:58:12,463 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:58Z] INFO  16:58:12,648 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:58Z] INFO  16:58:12,836 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:58Z] INFO  16:58:12,848 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:58Z] INFO  16:58:12,924 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-14T23:58Z] INFO  16:58:13,191 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:58Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-14_81651874_97299968-prep-prealign.bam
[2016-04-14T23:58Z] INFO  16:58:13,244 IntervalUtils - Processing 20740485 bp from intervals
[2016-04-14T23:58Z] WARN  16:58:13,250 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:58Z] INFO  16:58:13,379 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:58Z] INFO  16:58:13,587 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:58Z] INFO  16:58:13,589 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:58Z] INFO  16:58:13,589 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:58Z] INFO  16:58:13,590 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:58Z] INFO  16:58:13,657 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:58Z] INFO  16:58:13,685 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:58Z] GATK RealignerTargetCreator: R14-18105_kapa-NGv3-PE100-NGv3-sort-14_81651874_97299968-prep-prealign.bam 14:81651875-97299968
[2016-04-14T23:58Z] GATK: RealignerTargetCreator
[2016-04-14T23:58Z] INFO  16:58:14,112 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:58Z] INFO  16:58:14,116 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:58Z] INFO  16:58:14,117 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:58Z] INFO  16:58:14,117 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:58Z] INFO  16:58:14,122 HelpFormatter - Program Args: -T PrintReads -L 15:98984300-102531392 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/15/tx/tmpqxWCOD/R14-18105_kapa-NGv3-PE100-NGv3-sort-15_98984299_102531392-prep-prealign.bam
[2016-04-14T23:58Z] INFO  16:58:14,149 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:58Z] INFO  16:58:14,150 HelpFormatter - Date/Time: 2016/04/14 16:58:14
[2016-04-14T23:58Z] INFO  16:58:14,150 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:58Z] INFO  16:58:14,150 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:58Z] INFO  16:58:14,300 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:58Z] INFO  16:58:15,484 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-14T23:58Z] INFO  16:58:15,544 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:58Z] INFO  16:58:15,553 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:58Z] INFO  16:58:15,600 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-14T23:58Z] INFO  16:58:15,626 IntervalUtils - Processing 3547093 bp from intervals
[2016-04-14T23:58Z] INFO  16:58:15,714 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:58Z] INFO  16:58:15,964 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:58Z] INFO  16:58:15,964 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:58Z] INFO  16:58:15,965 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:58Z] INFO  16:58:15,965 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:58Z] INFO  16:58:15,993 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:58Z] INFO  16:58:16,029 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:58Z] INFO  16:58:16,728 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:58Z] INFO  16:58:16,730 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:58Z] INFO  16:58:16,730 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:58Z] INFO  16:58:16,731 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:58Z] INFO  16:58:16,736 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/14/R14-18105_kapa-NGv3-PE100-NGv3-sort-14_81651874_97299968-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/14/tx/tmpPf4wP5/R14-18105_kapa-NGv3-PE100-NGv3-sort-14_81651874_97299968-prep-prealign-realign.intervals -l INFO -L 14:81651875-97299968 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-14T23:58Z] INFO  16:58:16,754 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:58Z] INFO  16:58:16,755 HelpFormatter - Date/Time: 2016/04/14 16:58:16
[2016-04-14T23:58Z] INFO  16:58:16,756 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:58Z] INFO  16:58:16,767 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:58Z] INFO  16:58:16,907 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:58Z] INFO  16:58:17,076 ProgressMeter -            done     13946.0     3.0 s       4.2 m      100.0%     3.0 s       0.0 s
[2016-04-14T23:58Z] INFO  16:58:17,077 ProgressMeter - Total runtime 3.49 secs, 0.06 min, 0.00 hours
[2016-04-14T23:58Z] INFO  16:58:17,080 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 13946 total reads (0.00%)
[2016-04-14T23:58Z] INFO  16:58:17,081 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:58Z] INFO  16:58:17,081 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:58Z] INFO  16:58:17,081 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:58Z] INFO  16:58:17,121 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-14T23:58Z] INFO  16:58:17,131 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:58Z] INFO  16:58:17,193 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-14T23:58Z] INFO  16:58:17,480 IntervalUtils - Processing 15648094 bp from intervals
[2016-04-14T23:58Z] WARN  16:58:17,486 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:58Z] INFO  16:58:17,558 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:58Z] INFO  16:58:17,742 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:58Z] INFO  16:58:17,743 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:58Z] INFO  16:58:17,744 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:58Z] INFO  16:58:17,745 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-14T23:58Z] INFO  16:58:18,593 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:58Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-15_0_20740485-prep.bam
[2016-04-14T23:58Z] GATK pre-alignment ('16', 0, 15528616) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-14T23:58Z] INFO  16:58:19,588 ProgressMeter -            done   1.5768646E7    26.0 s       1.0 s      100.0%    26.0 s       0.0 s
[2016-04-14T23:58Z] INFO  16:58:19,589 ProgressMeter - Total runtime 26.91 secs, 0.45 min, 0.01 hours
[2016-04-14T23:58Z] INFO  16:58:19,593 MicroScheduler - 50719 reads were filtered out during the traversal out of approximately 618051 total reads (8.21%)
[2016-04-14T23:58Z] INFO  16:58:19,593 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:58Z] INFO  16:58:19,594 MicroScheduler -   -> 1138 reads (0.18% of total) failing BadMateFilter
[2016-04-14T23:58Z] INFO  16:58:19,594 MicroScheduler -   -> 48266 reads (7.81% of total) failing DuplicateReadFilter
[2016-04-14T23:58Z] INFO  16:58:19,594 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-14T23:58Z] INFO  16:58:19,594 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:58Z] INFO  16:58:19,595 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-14T23:58Z] INFO  16:58:19,595 MicroScheduler -   -> 1315 reads (0.21% of total) failing MappingQualityZeroFilter
[2016-04-14T23:58Z] INFO  16:58:19,595 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:58Z] INFO  16:58:19,595 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-14T23:58Z] INFO  16:58:19,596 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-14T23:58Z] INFO  16:58:20,570 ProgressMeter -     15:28798997    200005.0    30.0 s       2.5 m       50.0%    60.0 s      30.0 s
[2016-04-14T23:58Z] INFO  16:58:20,890 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:58Z] GATK: realign ('12', 109494486, 125263132) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-14T23:58Z] INFO  16:58:20,914 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@41fd9d8e
[2016-04-14T23:58Z] INFO  16:58:21,057 ProgressMeter -            done    392352.0    48.0 s       2.0 m       99.8%    48.0 s       0.0 s
[2016-04-14T23:58Z] INFO  16:58:21,058 ProgressMeter - Total runtime 48.01 secs, 0.80 min, 0.01 hours
[2016-04-14T23:58Z] INFO  16:58:21,058 MicroScheduler - 210 reads were filtered out during the traversal out of approximately 392562 total reads (0.05%)
[2016-04-14T23:58Z] INFO  16:58:21,058 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:58Z] INFO  16:58:21,059 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:58Z] INFO  16:58:21,059 MicroScheduler -   -> 210 reads (0.05% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:58Z] INFO  16:58:21,139 ProgressMeter -     14:31349775    400005.0    60.0 s       2.5 m       76.0%    78.0 s      18.0 s
[2016-04-14T23:58Z] INFO  16:58:21,486 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:58Z] INFO  16:58:21,489 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:58Z] INFO  16:58:21,490 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:58Z] INFO  16:58:21,490 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:58Z] INFO  16:58:21,495 HelpFormatter - Program Args: -T PrintReads -L 16:1-15528616 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/16/tx/tmpUi1VrM/R14-18105_kapa-NGv3-PE100-NGv3-sort-16_0_15528616-prep-prealign.bam
[2016-04-14T23:58Z] INFO  16:58:21,532 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:58Z] INFO  16:58:21,533 HelpFormatter - Date/Time: 2016/04/14 16:58:21
[2016-04-14T23:58Z] INFO  16:58:21,533 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:58Z] INFO  16:58:21,533 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:58Z] INFO  16:58:21,546 ProgressMeter -            done    129459.0    10.0 s      84.0 s      100.0%    10.0 s       0.0 s
[2016-04-14T23:58Z] INFO  16:58:21,546 ProgressMeter - Total runtime 10.90 secs, 0.18 min, 0.00 hours
[2016-04-14T23:58Z] INFO  16:58:21,550 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 129459 total reads (0.00%)
[2016-04-14T23:58Z] INFO  16:58:21,551 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:58Z] INFO  16:58:21,552 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:58Z] INFO  16:58:21,553 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:58Z] INFO  16:58:21,733 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:58Z] INFO  16:58:22,569 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:58Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-14_66135960_81646674-prep-prealign.bam
[2016-04-14T23:58Z] INFO  16:58:22,779 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-14T23:58Z] INFO  16:58:22,844 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:58Z] INFO  16:58:22,853 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:58Z] INFO  16:58:22,893 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.04
[2016-04-14T23:58Z] INFO  16:58:22,920 IntervalUtils - Processing 15528616 bp from intervals
[2016-04-14T23:58Z] INFO  16:58:22,992 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:58Z] INFO  16:58:23,079 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:58Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-14_35072553_50583270-prep.bam
[2016-04-14T23:58Z] INFO  16:58:23,281 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:58Z] INFO  16:58:23,282 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:58Z] INFO  16:58:23,283 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:58Z] INFO  16:58:23,284 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:58Z] INFO  16:58:23,316 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:58Z] INFO  16:58:23,509 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:58Z] GATK pre-alignment ('16', 15596122, 31106473) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-14T23:58Z] INFO  16:58:23,571 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:58Z] INFO  16:58:23,574 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:58Z] INFO  16:58:23,574 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:58Z] INFO  16:58:23,574 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:58Z] INFO  16:58:23,578 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/12/R14-18105_kapa-NGv3-PE100-NGv3-sort-12_109494486_125263132-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/12/R14-18105_kapa-NGv3-PE100-NGv3-sort-12_109494486_125263132-prep-prealign-realign.intervals -L 12:109494487-125263132 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/12/tx/tmporp633/R14-18105_kapa-NGv3-PE100-NGv3-sort-12_109494486_125263132-prep.bam
[2016-04-14T23:58Z] INFO  16:58:23,588 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:58Z] INFO  16:58:23,588 HelpFormatter - Date/Time: 2016/04/14 16:58:23
[2016-04-14T23:58Z] INFO  16:58:23,588 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:58Z] INFO  16:58:23,599 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:58Z] INFO  16:58:23,823 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:58Z] INFO  16:58:23,995 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:58Z] INFO  16:58:24,006 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:58Z] GATK RealignerTargetCreator: R14-18105_kapa-NGv3-PE100-NGv3-sort-14_66135960_81646674-prep-prealign.bam 14:66135961-81646674
[2016-04-14T23:58Z] GATK: RealignerTargetCreator
[2016-04-14T23:58Z] INFO  16:58:24,097 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.09
[2016-04-14T23:58Z] INFO  16:58:24,520 IntervalUtils - Processing 15768646 bp from intervals
[2016-04-14T23:58Z] WARN  16:58:24,526 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:58Z] INFO  16:58:24,616 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:58Z] INFO  16:58:24,782 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:58Z] INFO  16:58:24,782 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:58Z] INFO  16:58:24,783 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:58Z] INFO  16:58:24,783 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:58Z] INFO  16:58:25,036 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:58Z] INFO  16:58:25,222 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:58Z] INFO  16:58:25,332 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@41fd9d8e
[2016-04-14T23:58Z] INFO  16:58:25,424 ProgressMeter -            done    539322.0    65.0 s     120.0 s      100.0%    65.0 s       0.0 s
[2016-04-14T23:58Z] INFO  16:58:25,426 ProgressMeter - Total runtime 65.07 secs, 1.08 min, 0.02 hours
[2016-04-14T23:58Z] INFO  16:58:25,426 MicroScheduler - 233 reads were filtered out during the traversal out of approximately 539555 total reads (0.04%)
[2016-04-14T23:58Z] INFO  16:58:25,427 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:58Z] INFO  16:58:25,428 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:58Z] INFO  16:58:25,428 MicroScheduler -   -> 233 reads (0.04% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:58Z] INFO  16:58:26,056 ProgressMeter -     11:66478508    400009.0    31.0 s      79.0 s       24.1%     2.1 m      97.0 s
[2016-04-14T23:58Z] INFO  16:58:26,661 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@5fe152b7
[2016-04-14T23:58Z] INFO  16:58:26,726 ProgressMeter -     15:42132763    100001.0    30.0 s       5.1 m       33.8%    88.0 s      58.0 s
[2016-04-14T23:58Z] INFO  16:58:26,831 ProgressMeter -            done    340739.0    46.0 s       2.3 m       99.3%    46.0 s       0.0 s
[2016-04-14T23:58Z] INFO  16:58:26,833 ProgressMeter - Total runtime 46.11 secs, 0.77 min, 0.01 hours
[2016-04-14T23:58Z] INFO  16:58:26,834 MicroScheduler - 282 reads were filtered out during the traversal out of approximately 341021 total reads (0.08%)
[2016-04-14T23:58Z] INFO  16:58:26,835 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:58Z] INFO  16:58:26,836 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:58Z] INFO  16:58:26,836 MicroScheduler -   -> 282 reads (0.08% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:58Z] INFO  16:58:26,848 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:58Z] INFO  16:58:26,852 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:58Z] INFO  16:58:26,852 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:58Z] INFO  16:58:26,853 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:58Z] INFO  16:58:26,857 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/14/R14-18105_kapa-NGv3-PE100-NGv3-sort-14_66135960_81646674-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/14/tx/tmplfCCvt/R14-18105_kapa-NGv3-PE100-NGv3-sort-14_66135960_81646674-prep-prealign-realign.intervals -l INFO -L 14:66135961-81646674 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-14T23:58Z] INFO  16:58:26,869 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:58Z] INFO  16:58:26,869 HelpFormatter - Date/Time: 2016/04/14 16:58:26
[2016-04-14T23:58Z] INFO  16:58:26,869 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:58Z] INFO  16:58:26,870 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:58Z] INFO  16:58:26,886 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:58Z] INFO  16:58:26,890 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:58Z] INFO  16:58:26,890 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:58Z] INFO  16:58:26,891 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:58Z] INFO  16:58:26,896 HelpFormatter - Program Args: -T PrintReads -L 16:15596123-31106473 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/16/tx/tmpYno2lM/R14-18105_kapa-NGv3-PE100-NGv3-sort-16_15596122_31106473-prep-prealign.bam
[2016-04-14T23:58Z] INFO  16:58:26,905 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:58Z] INFO  16:58:26,914 HelpFormatter - Date/Time: 2016/04/14 16:58:26
[2016-04-14T23:58Z] INFO  16:58:26,915 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:58Z] INFO  16:58:26,915 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:58Z] INFO  16:58:26,969 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:58Z] INFO  16:58:27,025 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:58Z] INFO  16:58:27,066 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:58Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-14_19553416_35066851-prep-prealign.bam
[2016-04-14T23:58Z] INFO  16:58:27,162 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-14T23:58Z] INFO  16:58:27,172 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:58Z] INFO  16:58:27,221 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-14T23:58Z] INFO  16:58:27,486 IntervalUtils - Processing 15510714 bp from intervals
[2016-04-14T23:58Z] WARN  16:58:27,491 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:58Z] INFO  16:58:27,566 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:58Z] INFO  16:58:27,877 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:58Z] INFO  16:58:27,879 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:58Z] INFO  16:58:27,880 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:58Z] INFO  16:58:27,881 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-14T23:58Z] INFO  16:58:28,120 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:58Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-14_97304098_107349540-prep-prealign.bam
[2016-04-14T23:58Z] INFO  16:58:28,344 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-14T23:58Z] INFO  16:58:28,410 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:58Z] INFO  16:58:28,420 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:58Z] INFO  16:58:28,477 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-14T23:58Z] INFO  16:58:28,493 IntervalUtils - Processing 15510351 bp from intervals
[2016-04-14T23:58Z] INFO  16:58:28,581 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:58Z] GATK RealignerTargetCreator: R14-18105_kapa-NGv3-PE100-NGv3-sort-14_19553416_35066851-prep-prealign.bam 14:19553417-35066851
[2016-04-14T23:58Z] GATK: RealignerTargetCreator
[2016-04-14T23:58Z] INFO  16:58:28,780 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@5fe152b7
[2016-04-14T23:58Z] INFO  16:58:28,869 ProgressMeter -            done     91138.0    12.0 s       2.4 m       99.6%    12.0 s       0.0 s
[2016-04-14T23:58Z] INFO  16:58:28,870 ProgressMeter - Total runtime 12.91 secs, 0.22 min, 0.00 hours
[2016-04-14T23:58Z] INFO  16:58:28,871 MicroScheduler - 44 reads were filtered out during the traversal out of approximately 91182 total reads (0.05%)
[2016-04-14T23:58Z] INFO  16:58:28,872 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:58Z] INFO  16:58:28,873 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:58Z] INFO  16:58:28,873 MicroScheduler -   -> 44 reads (0.05% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:58Z] INFO  16:58:28,900 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:58Z] INFO  16:58:28,901 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:58Z] INFO  16:58:28,902 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:58Z] INFO  16:58:28,903 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:58Z] INFO  16:58:28,917 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:58Z] INFO  16:58:28,989 ProgressMeter -     15:64380957    200004.0    30.0 s       2.5 m       77.2%    38.0 s       8.0 s
[2016-04-14T23:58Z] INFO  16:58:29,052 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:58Z] GATK RealignerTargetCreator: R14-18105_kapa-NGv3-PE100-NGv3-sort-14_97304098_107349540-prep-prealign.bam 14:97304099-107349540
[2016-04-14T23:58Z] GATK: RealignerTargetCreator
[2016-04-14T23:58Z] INFO  16:58:29,519 ProgressMeter -            done   1.5511263E7    19.0 s       1.0 s      100.0%    19.0 s       0.0 s
[2016-04-14T23:58Z] INFO  16:58:29,520 ProgressMeter - Total runtime 19.86 secs, 0.33 min, 0.01 hours
[2016-04-14T23:58Z] INFO  16:58:29,525 MicroScheduler - 25009 reads were filtered out during the traversal out of approximately 302071 total reads (8.28%)
[2016-04-14T23:58Z] INFO  16:58:29,526 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:58Z] INFO  16:58:29,526 MicroScheduler -   -> 734 reads (0.24% of total) failing BadMateFilter
[2016-04-14T23:58Z] INFO  16:58:29,527 MicroScheduler -   -> 23774 reads (7.87% of total) failing DuplicateReadFilter
[2016-04-14T23:58Z] INFO  16:58:29,528 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-14T23:58Z] INFO  16:58:29,528 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:58Z] INFO  16:58:29,529 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-14T23:58Z] INFO  16:58:29,530 MicroScheduler -   -> 501 reads (0.17% of total) failing MappingQualityZeroFilter
[2016-04-14T23:58Z] INFO  16:58:29,530 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:58Z] INFO  16:58:29,531 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-14T23:58Z] INFO  16:58:29,531 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-14T23:58Z] INFO  16:58:30,531 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:58Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-15_98984299_102531392-prep-prealign.bam
[2016-04-14T23:58Z] GATK RealignerTargetCreator: R14-18105_kapa-NGv3-PE100-NGv3-sort-15_98984299_102531392-prep-prealign.bam 15:98984300-102531392
[2016-04-14T23:58Z] GATK: RealignerTargetCreator
[2016-04-14T23:58Z] INFO  16:58:31,122 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:58Z] GATK: realign ('14', 50585061, 66096324) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-14T23:58Z] INFO  16:58:31,527 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:58Z] INFO  16:58:31,530 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:58Z] INFO  16:58:31,531 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:58Z] INFO  16:58:31,531 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:58Z] INFO  16:58:31,536 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/14/R14-18105_kapa-NGv3-PE100-NGv3-sort-14_19553416_35066851-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/14/tx/tmpSbZWGA/R14-18105_kapa-NGv3-PE100-NGv3-sort-14_19553416_35066851-prep-prealign-realign.intervals -l INFO -L 14:19553417-35066851 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-14T23:58Z] INFO  16:58:31,556 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:58Z] INFO  16:58:31,557 HelpFormatter - Date/Time: 2016/04/14 16:58:31
[2016-04-14T23:58Z] INFO  16:58:31,557 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:58Z] INFO  16:58:31,558 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:58Z] INFO  16:58:31,678 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:58Z] INFO  16:58:31,921 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-14T23:58Z] INFO  16:58:31,931 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:58Z] INFO  16:58:32,003 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-14T23:58Z] INFO  16:58:32,071 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:58Z] INFO  16:58:32,075 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:58Z] INFO  16:58:32,075 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:58Z] INFO  16:58:32,076 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:58Z] INFO  16:58:32,080 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/14/R14-18105_kapa-NGv3-PE100-NGv3-sort-14_97304098_107349540-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/14/tx/tmpmVqVEY/R14-18105_kapa-NGv3-PE100-NGv3-sort-14_97304098_107349540-prep-prealign-realign.intervals -l INFO -L 14:97304099-107349540 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-14T23:58Z] INFO  16:58:32,116 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:58Z] INFO  16:58:32,117 HelpFormatter - Date/Time: 2016/04/14 16:58:32
[2016-04-14T23:58Z] INFO  16:58:32,118 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:58Z] INFO  16:58:32,118 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:58Z] INFO  16:58:32,216 ProgressMeter -     15:74742049    200004.0    30.0 s       2.5 m       43.9%    68.0 s      38.0 s
[2016-04-14T23:58Z] INFO  16:58:32,232 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:58Z] INFO  16:58:32,364 IntervalUtils - Processing 15513435 bp from intervals
[2016-04-14T23:58Z] WARN  16:58:32,369 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:58Z] INFO  16:58:32,446 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:58Z] INFO  16:58:32,466 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-14T23:58Z] INFO  16:58:32,476 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:58Z] INFO  16:58:32,480 ProgressMeter -     12:53819031    400007.0    32.0 s      80.0 s       44.4%    72.0 s      40.0 s
[2016-04-14T23:58Z] INFO  16:58:32,551 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-14T23:58Z] INFO  16:58:32,763 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:58Z] INFO  16:58:32,769 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:58Z] INFO  16:58:32,770 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:58Z] INFO  16:58:32,770 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-14T23:58Z] INFO  16:58:32,857 IntervalUtils - Processing 10045442 bp from intervals
[2016-04-14T23:58Z] WARN  16:58:32,862 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:58Z] INFO  16:58:32,928 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:58Z] INFO  16:58:33,132 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:58Z] INFO  16:58:33,133 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:58Z] INFO  16:58:33,134 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:58Z] INFO  16:58:33,135 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-14T23:58Z] INFO  16:58:33,778 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:58Z] INFO  16:58:33,780 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:58Z] INFO  16:58:33,780 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:58Z] INFO  16:58:33,781 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:58Z] INFO  16:58:33,785 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/15/R14-18105_kapa-NGv3-PE100-NGv3-sort-15_98984299_102531392-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/15/tx/tmpNEU7Uh/R14-18105_kapa-NGv3-PE100-NGv3-sort-15_98984299_102531392-prep-prealign-realign.intervals -l INFO -L 15:98984300-102531392 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-14T23:58Z] INFO  16:58:33,793 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:58Z] INFO  16:58:33,794 HelpFormatter - Date/Time: 2016/04/14 16:58:33
[2016-04-14T23:58Z] INFO  16:58:33,794 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:58Z] INFO  16:58:33,794 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:58Z] INFO  16:58:33,948 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:58Z] INFO  16:58:33,981 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:58Z] INFO  16:58:33,984 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:58Z] INFO  16:58:33,984 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:58Z] INFO  16:58:33,985 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:58Z] INFO  16:58:33,989 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/14/R14-18105_kapa-NGv3-PE100-NGv3-sort-14_50585061_66096324-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/14/R14-18105_kapa-NGv3-PE100-NGv3-sort-14_50585061_66096324-prep-prealign-realign.intervals -L 14:50585062-66096324 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/14/tx/tmpwMsAkY/R14-18105_kapa-NGv3-PE100-NGv3-sort-14_50585061_66096324-prep.bam
[2016-04-14T23:58Z] INFO  16:58:34,004 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:58Z] INFO  16:58:34,005 HelpFormatter - Date/Time: 2016/04/14 16:58:33
[2016-04-14T23:58Z] INFO  16:58:34,005 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:58Z] INFO  16:58:34,006 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:58Z] INFO  16:58:34,153 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-14T23:58Z] INFO  16:58:34,163 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:58Z] INFO  16:58:34,221 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:58Z] INFO  16:58:34,248 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-14T23:58Z] INFO  16:58:34,329 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:58Z] INFO  16:58:34,338 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:58Z] INFO  16:58:34,387 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-14T23:58Z] INFO  16:58:34,631 IntervalUtils - Processing 3547093 bp from intervals
[2016-04-14T23:58Z] WARN  16:58:34,636 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:58Z] INFO  16:58:34,705 IntervalUtils - Processing 15511263 bp from intervals
[2016-04-14T23:58Z] WARN  16:58:34,710 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:58Z] INFO  16:58:34,722 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:58Z] INFO  16:58:34,795 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:58Z] INFO  16:58:34,911 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:58Z] INFO  16:58:34,912 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:58Z] INFO  16:58:34,913 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:58Z] INFO  16:58:34,914 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-14T23:58Z] INFO  16:58:34,975 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:58Z] INFO  16:58:34,977 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:58Z] INFO  16:58:34,977 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:58Z] INFO  16:58:34,982 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:58Z] INFO  16:58:35,152 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:58Z] INFO  16:58:35,369 ProgressMeter -     15:90227368    200004.0    30.0 s       2.5 m       43.6%    68.0 s      38.0 s
[2016-04-14T23:58Z] INFO  16:58:35,372 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:58Z] INFO  16:58:37,424 ProgressMeter -            done   1.5648094E7    19.0 s       1.0 s      100.0%    19.0 s       0.0 s
[2016-04-14T23:58Z] INFO  16:58:37,425 ProgressMeter - Total runtime 19.68 secs, 0.33 min, 0.01 hours
[2016-04-14T23:58Z] INFO  16:58:37,436 MicroScheduler - 21385 reads were filtered out during the traversal out of approximately 256506 total reads (8.34%)
[2016-04-14T23:58Z] INFO  16:58:37,437 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:58Z] INFO  16:58:37,437 MicroScheduler -   -> 671 reads (0.26% of total) failing BadMateFilter
[2016-04-14T23:58Z] INFO  16:58:37,438 MicroScheduler -   -> 20150 reads (7.86% of total) failing DuplicateReadFilter
[2016-04-14T23:58Z] INFO  16:58:37,438 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-14T23:58Z] INFO  16:58:37,438 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:58Z] INFO  16:58:37,438 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-14T23:58Z] INFO  16:58:37,439 MicroScheduler -   -> 564 reads (0.22% of total) failing MappingQualityZeroFilter
[2016-04-14T23:58Z] INFO  16:58:37,439 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:58Z] INFO  16:58:37,439 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-14T23:58Z] INFO  16:58:37,439 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-14T23:58Z] INFO  16:58:38,801 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:58Z] GATK: realign ('14', 81651874, 97299968) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-14T23:58Z] INFO  16:58:41,530 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:58Z] INFO  16:58:41,533 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:58Z] INFO  16:58:41,534 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:58Z] INFO  16:58:41,534 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:58Z] INFO  16:58:41,539 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/14/R14-18105_kapa-NGv3-PE100-NGv3-sort-14_81651874_97299968-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/14/R14-18105_kapa-NGv3-PE100-NGv3-sort-14_81651874_97299968-prep-prealign-realign.intervals -L 14:81651875-97299968 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/14/tx/tmpg6b_3m/R14-18105_kapa-NGv3-PE100-NGv3-sort-14_81651874_97299968-prep.bam
[2016-04-14T23:58Z] INFO  16:58:41,552 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:58Z] INFO  16:58:41,560 HelpFormatter - Date/Time: 2016/04/14 16:58:41
[2016-04-14T23:58Z] INFO  16:58:41,561 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:58Z] INFO  16:58:41,561 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:58Z] INFO  16:58:41,605 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@41fd9d8e
[2016-04-14T23:58Z] INFO  16:58:41,724 ProgressMeter -            done    364790.0    42.0 s     117.0 s      100.0%    42.0 s       0.0 s
[2016-04-14T23:58Z] INFO  16:58:41,725 ProgressMeter - Total runtime 42.77 secs, 0.71 min, 0.01 hours
[2016-04-14T23:58Z] INFO  16:58:41,725 MicroScheduler - 164 reads were filtered out during the traversal out of approximately 364954 total reads (0.04%)
[2016-04-14T23:58Z] INFO  16:58:41,729 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:58Z] INFO  16:58:41,726 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:58Z] INFO  16:58:41,726 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:58Z] INFO  16:58:41,726 MicroScheduler -   -> 164 reads (0.04% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:58Z] INFO  16:58:41,809 ProgressMeter -            done   3547093.0     6.0 s       1.0 s      100.0%     6.0 s       0.0 s
[2016-04-14T23:58Z] INFO  16:58:41,811 ProgressMeter - Total runtime 6.90 secs, 0.11 min, 0.00 hours
[2016-04-14T23:58Z] INFO  16:58:41,815 MicroScheduler - 15071 reads were filtered out during the traversal out of approximately 92022 total reads (16.38%)
[2016-04-14T23:58Z] INFO  16:58:41,817 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:58Z] INFO  16:58:41,817 MicroScheduler -   -> 190 reads (0.21% of total) failing BadMateFilter
[2016-04-14T23:58Z] INFO  16:58:41,818 MicroScheduler -   -> 6877 reads (7.47% of total) failing DuplicateReadFilter
[2016-04-14T23:58Z] INFO  16:58:41,819 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-14T23:58Z] INFO  16:58:41,820 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:58Z] INFO  16:58:41,820 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-14T23:58Z] INFO  16:58:41,821 MicroScheduler -   -> 8004 reads (8.70% of total) failing MappingQualityZeroFilter
[2016-04-14T23:58Z] INFO  16:58:41,822 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:58Z] INFO  16:58:41,822 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-14T23:58Z] INFO  16:58:41,823 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-14T23:58Z] INFO  16:58:41,854 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:58Z] INFO  16:58:41,864 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:58Z] INFO  16:58:41,932 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-14T23:58Z] INFO  16:58:42,365 IntervalUtils - Processing 15648094 bp from intervals
[2016-04-14T23:58Z] WARN  16:58:42,380 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:58Z] INFO  16:58:42,451 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:58Z] INFO  16:58:42,561 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:58Z] INFO  16:58:42,562 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:58Z] INFO  16:58:42,563 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:58Z] INFO  16:58:42,563 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:58Z] INFO  16:58:42,707 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:58Z] INFO  16:58:42,851 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:58Z] INFO  16:58:43,034 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:58Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-15_52404364_67923265-prep-prealign.bam
[2016-04-14T23:58Z] INFO  16:58:43,317 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:58Z] GATK: realign ('15', 98984299, 102531392) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-14T23:58Z] GATK RealignerTargetCreator: R14-18105_kapa-NGv3-PE100-NGv3-sort-15_52404364_67923265-prep-prealign.bam 15:52404365-67923265
[2016-04-14T23:58Z] GATK: RealignerTargetCreator
[2016-04-14T23:58Z] INFO  16:58:46,251 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:58Z] INFO  16:58:46,254 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:58Z] INFO  16:58:46,255 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:58Z] INFO  16:58:46,255 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:58Z] INFO  16:58:46,260 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/15/R14-18105_kapa-NGv3-PE100-NGv3-sort-15_98984299_102531392-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/15/R14-18105_kapa-NGv3-PE100-NGv3-sort-15_98984299_102531392-prep-prealign-realign.intervals -L 15:98984300-102531392 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/15/tx/tmpejdDQx/R14-18105_kapa-NGv3-PE100-NGv3-sort-15_98984299_102531392-prep.bam
[2016-04-14T23:58Z] INFO  16:58:46,281 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:58Z] INFO  16:58:46,284 HelpFormatter - Date/Time: 2016/04/14 16:58:46
[2016-04-14T23:58Z] INFO  16:58:46,285 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:58Z] INFO  16:58:46,285 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:58Z] INFO  16:58:46,470 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:58Z] INFO  16:58:46,559 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:58Z] INFO  16:58:46,568 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:58Z] INFO  16:58:46,613 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.04
[2016-04-14T23:58Z] INFO  16:58:46,718 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:58Z] INFO  16:58:46,721 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:58Z] INFO  16:58:46,721 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:58Z] INFO  16:58:46,722 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:58Z] INFO  16:58:46,726 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/15/R14-18105_kapa-NGv3-PE100-NGv3-sort-15_52404364_67923265-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/15/tx/tmp42yRk9/R14-18105_kapa-NGv3-PE100-NGv3-sort-15_52404364_67923265-prep-prealign-realign.intervals -l INFO -L 15:52404365-67923265 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-14T23:58Z] INFO  16:58:46,753 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:58Z] INFO  16:58:46,754 HelpFormatter - Date/Time: 2016/04/14 16:58:46
[2016-04-14T23:58Z] INFO  16:58:46,754 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:58Z] INFO  16:58:46,759 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:58Z] INFO  16:58:46,883 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:58Z] INFO  16:58:47,075 IntervalUtils - Processing 3547093 bp from intervals
[2016-04-14T23:58Z] WARN  16:58:47,080 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:58Z] INFO  16:58:47,084 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-14T23:58Z] INFO  16:58:47,094 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:58Z] INFO  16:58:47,162 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-14T23:58Z] INFO  16:58:47,176 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:58Z] INFO  16:58:47,259 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:58Z] INFO  16:58:47,260 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:58Z] INFO  16:58:47,261 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:58Z] INFO  16:58:47,261 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:58Z] INFO  16:58:47,348 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:58Z] INFO  16:58:47,394 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:58Z] INFO  16:58:47,520 IntervalUtils - Processing 15518901 bp from intervals
[2016-04-14T23:58Z] WARN  16:58:47,526 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:58Z] INFO  16:58:47,635 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:58Z] INFO  16:58:47,884 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:58Z] INFO  16:58:47,885 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:58Z] INFO  16:58:47,886 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:58Z] INFO  16:58:47,887 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-14T23:58Z] INFO  16:58:48,189 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@41fd9d8e
[2016-04-14T23:58Z] INFO  16:58:48,320 ProgressMeter -            done    477814.0    58.0 s       2.0 m      100.0%    58.0 s       0.0 s
[2016-04-14T23:58Z] INFO  16:58:48,321 ProgressMeter - Total runtime 58.21 secs, 0.97 min, 0.02 hours
[2016-04-14T23:58Z] INFO  16:58:48,321 MicroScheduler - 250 reads were filtered out during the traversal out of approximately 478064 total reads (0.05%)
[2016-04-14T23:58Z] INFO  16:58:48,322 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:58Z] INFO  16:58:48,323 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:58Z] INFO  16:58:48,323 MicroScheduler -   -> 250 reads (0.05% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:58Z] INFO  16:58:48,728 ProgressMeter -            done    932561.0    54.0 s      58.0 s      100.0%    54.0 s       0.0 s
[2016-04-14T23:58Z] INFO  16:58:48,728 ProgressMeter - Total runtime 54.42 secs, 0.91 min, 0.02 hours
[2016-04-14T23:58Z] INFO  16:58:48,732 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 932561 total reads (0.00%)
[2016-04-14T23:58Z] INFO  16:58:48,732 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:58Z] INFO  16:58:48,733 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:58Z] INFO  16:58:48,733 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:58Z] INFO  16:58:49,064 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@41fd9d8e
[2016-04-14T23:58Z] INFO  16:58:49,227 ProgressMeter -            done    343500.0    43.0 s       2.1 m      100.0%    43.0 s       0.0 s
[2016-04-14T23:58Z] INFO  16:58:49,227 ProgressMeter - Total runtime 43.88 secs, 0.73 min, 0.01 hours
[2016-04-14T23:58Z] INFO  16:58:49,228 MicroScheduler - 142 reads were filtered out during the traversal out of approximately 343642 total reads (0.04%)
[2016-04-14T23:58Z] INFO  16:58:49,228 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:58Z] INFO  16:58:49,229 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:58Z] INFO  16:58:49,229 MicroScheduler -   -> 142 reads (0.04% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:58Z] INFO  16:58:49,739 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:58Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-15_20741621_36872162-prep-prealign.bam
[2016-04-14T23:58Z] INFO  16:58:49,880 ProgressMeter -            done   1.0045442E7    16.0 s       1.0 s      100.0%    16.0 s       0.0 s
[2016-04-14T23:58Z] INFO  16:58:49,881 ProgressMeter - Total runtime 16.75 secs, 0.28 min, 0.00 hours
[2016-04-14T23:58Z] INFO  16:58:49,885 MicroScheduler - 29691 reads were filtered out during the traversal out of approximately 342401 total reads (8.67%)
[2016-04-14T23:58Z] INFO  16:58:49,897 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:58Z] INFO  16:58:49,898 MicroScheduler -   -> 720 reads (0.21% of total) failing BadMateFilter
[2016-04-14T23:58Z] INFO  16:58:49,898 MicroScheduler -   -> 27695 reads (8.09% of total) failing DuplicateReadFilter
[2016-04-14T23:58Z] INFO  16:58:49,899 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-14T23:58Z] INFO  16:58:49,899 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:58Z] INFO  16:58:49,900 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-14T23:58Z] INFO  16:58:49,901 MicroScheduler -   -> 1276 reads (0.37% of total) failing MappingQualityZeroFilter
[2016-04-14T23:58Z] INFO  16:58:49,901 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:58Z] INFO  16:58:49,902 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-14T23:58Z] INFO  16:58:49,903 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-14T23:58Z] INFO  16:58:50,158 ProgressMeter -            done    893179.0    50.0 s      56.0 s      100.0%    50.0 s       0.0 s
[2016-04-14T23:58Z] INFO  16:58:50,159 ProgressMeter - Total runtime 50.06 secs, 0.83 min, 0.01 hours
[2016-04-14T23:58Z] INFO  16:58:50,163 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 893179 total reads (0.00%)
[2016-04-14T23:58Z] INFO  16:58:50,164 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:58Z] INFO  16:58:50,165 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:58Z] INFO  16:58:50,165 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:58Z] INFO  16:58:50,231 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:58Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-11_62744265_78270665-prep.bam
[2016-04-14T23:58Z] INFO  16:58:50,427 ProgressMeter -            done   1.5510714E7    22.0 s       1.0 s      100.0%    22.0 s       0.0 s
[2016-04-14T23:58Z] INFO  16:58:50,428 ProgressMeter - Total runtime 22.55 secs, 0.38 min, 0.01 hours
[2016-04-14T23:58Z] INFO  16:58:50,432 MicroScheduler - 34913 reads were filtered out during the traversal out of approximately 394960 total reads (8.84%)
[2016-04-14T23:58Z] INFO  16:58:50,438 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:58Z] INFO  16:58:50,438 MicroScheduler -   -> 829 reads (0.21% of total) failing BadMateFilter
[2016-04-14T23:58Z] INFO  16:58:50,439 MicroScheduler -   -> 31538 reads (7.99% of total) failing DuplicateReadFilter
[2016-04-14T23:58Z] INFO  16:58:50,440 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-14T23:58Z] INFO  16:58:50,440 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:58Z] INFO  16:58:50,441 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-14T23:58Z] INFO  16:58:50,441 MicroScheduler -   -> 2546 reads (0.64% of total) failing MappingQualityZeroFilter
[2016-04-14T23:58Z] INFO  16:58:50,453 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:58Z] INFO  16:58:50,454 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-14T23:58Z] INFO  16:58:50,454 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-14T23:58Z] INFO  16:58:50,903 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:58Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-15_83448996_98982979-prep-prealign.bam
[2016-04-14T23:58Z] GATK RealignerTargetCreator: R14-18105_kapa-NGv3-PE100-NGv3-sort-15_20741621_36872162-prep-prealign.bam 15:20741622-36872162
[2016-04-14T23:58Z] GATK: RealignerTargetCreator
[2016-04-14T23:58Z] INFO  16:58:51,626 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:58Z] GATK: realign ('14', 97304098, 107349540) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-14T23:58Z] INFO  16:58:51,795 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:58Z] INFO  16:58:51,814 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:58Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-12_46756066_62654284-prep.bam
[2016-04-14T23:58Z] GATK: realign ('14', 66135960, 81646674) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-14T23:58Z] GATK RealignerTargetCreator: R14-18105_kapa-NGv3-PE100-NGv3-sort-15_83448996_98982979-prep-prealign.bam 15:83448997-98982979
[2016-04-14T23:58Z] GATK: RealignerTargetCreator
[2016-04-14T23:58Z] GATK pre-alignment ('16', 31120544, 46629582) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-14T23:58Z] INFO  16:58:53,548 ProgressMeter -      16:1274578    100003.0    30.0 s       5.0 m        8.2%     6.1 m       5.6 m
[2016-04-14T23:58Z] INFO  16:58:54,365 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:58Z] INFO  16:58:54,369 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:58Z] INFO  16:58:54,370 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:58Z] INFO  16:58:54,370 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:58Z] INFO  16:58:54,376 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/15/R14-18105_kapa-NGv3-PE100-NGv3-sort-15_20741621_36872162-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/15/tx/tmpg4jINZ/R14-18105_kapa-NGv3-PE100-NGv3-sort-15_20741621_36872162-prep-prealign-realign.intervals -l INFO -L 15:20741622-36872162 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-14T23:58Z] INFO  16:58:54,419 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:58Z] INFO  16:58:54,422 HelpFormatter - Date/Time: 2016/04/14 16:58:54
[2016-04-14T23:58Z] INFO  16:58:54,422 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:58Z] INFO  16:58:54,423 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:58Z] INFO  16:58:54,532 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:58Z] INFO  16:58:54,567 ProgressMeter -            done    300526.0    19.0 s      65.0 s      100.0%    19.0 s       0.0 s
[2016-04-14T23:58Z] INFO  16:58:54,568 ProgressMeter - Total runtime 19.59 secs, 0.33 min, 0.01 hours
[2016-04-14T23:58Z] INFO  16:58:54,571 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 300526 total reads (0.00%)
[2016-04-14T23:58Z] INFO  16:58:54,572 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:58Z] INFO  16:58:54,572 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:58Z] INFO  16:58:54,572 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:58Z] INFO  16:58:54,708 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:58Z] INFO  16:58:54,713 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:58Z] INFO  16:58:54,714 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:58Z] INFO  16:58:54,715 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:58Z] INFO  16:58:54,720 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/14/R14-18105_kapa-NGv3-PE100-NGv3-sort-14_97304098_107349540-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/14/R14-18105_kapa-NGv3-PE100-NGv3-sort-14_97304098_107349540-prep-prealign-realign.intervals -L 14:97304099-107349540 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/14/tx/tmp4xZCpJ/R14-18105_kapa-NGv3-PE100-NGv3-sort-14_97304098_107349540-prep.bam
[2016-04-14T23:58Z] INFO  16:58:54,740 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:58Z] INFO  16:58:54,741 HelpFormatter - Date/Time: 2016/04/14 16:58:54
[2016-04-14T23:58Z] INFO  16:58:54,741 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:58Z] INFO  16:58:54,742 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:58Z] INFO  16:58:54,748 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-14T23:58Z] INFO  16:58:54,768 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:58Z] INFO  16:58:54,821 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-14T23:58Z] GATK pre-alignment ('16', 46633742, 64982002) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-14T23:58Z] INFO  16:58:54,981 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:58Z] INFO  16:58:55,020 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:58Z] INFO  16:58:55,023 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:58Z] INFO  16:58:55,024 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:58Z] INFO  16:58:55,025 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:58Z] INFO  16:58:55,022 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:58Z] INFO  16:58:55,025 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:58Z] INFO  16:58:55,025 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:58Z] INFO  16:58:55,025 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:58Z] INFO  16:58:55,029 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/14/R14-18105_kapa-NGv3-PE100-NGv3-sort-14_66135960_81646674-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/14/R14-18105_kapa-NGv3-PE100-NGv3-sort-14_66135960_81646674-prep-prealign-realign.intervals -L 14:66135961-81646674 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/14/tx/tmpfuNn8p/R14-18105_kapa-NGv3-PE100-NGv3-sort-14_66135960_81646674-prep.bam
[2016-04-14T23:58Z] INFO  16:58:55,029 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/15/R14-18105_kapa-NGv3-PE100-NGv3-sort-15_83448996_98982979-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/15/tx/tmpvMB0Pv/R14-18105_kapa-NGv3-PE100-NGv3-sort-15_83448996_98982979-prep-prealign-realign.intervals -l INFO -L 15:83448997-98982979 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-14T23:58Z] INFO  16:58:55,041 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:58Z] INFO  16:58:55,041 HelpFormatter - Date/Time: 2016/04/14 16:58:55
[2016-04-14T23:58Z] INFO  16:58:55,041 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:58Z] INFO  16:58:55,042 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:58Z] INFO  16:58:55,063 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:58Z] INFO  16:58:55,063 HelpFormatter - Date/Time: 2016/04/14 16:58:55
[2016-04-14T23:58Z] INFO  16:58:55,063 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:58Z] INFO  16:58:55,063 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:58Z] INFO  16:58:55,119 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:58Z] INFO  16:58:55,119 IntervalUtils - Processing 16130541 bp from intervals
[2016-04-14T23:58Z] WARN  16:58:55,124 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:58Z] INFO  16:58:55,129 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:58Z] INFO  16:58:55,160 ProgressMeter -            done     91138.0     7.0 s      86.0 s       99.6%     7.0 s       0.0 s
[2016-04-14T23:58Z] INFO  16:58:55,161 ProgressMeter - Total runtime 7.90 secs, 0.13 min, 0.00 hours
[2016-04-14T23:58Z] INFO  16:58:55,165 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 91138 total reads (0.00%)
[2016-04-14T23:58Z] INFO  16:58:55,166 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:58Z] INFO  16:58:55,166 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:58Z] INFO  16:58:55,167 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:58Z] INFO  16:58:55,181 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:58Z] INFO  16:58:55,207 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:58Z] INFO  16:58:55,218 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.09
[2016-04-14T23:58Z] INFO  16:58:55,310 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:58Z] INFO  16:58:55,447 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:58Z] INFO  16:58:55,447 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:58Z] INFO  16:58:55,448 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:58Z] INFO  16:58:55,448 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-14T23:58Z] INFO  16:58:55,458 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:58Z] INFO  16:58:55,469 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:58Z] INFO  16:58:55,492 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-14T23:58Z] INFO  16:58:55,503 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:58Z] INFO  16:58:55,515 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.04
[2016-04-14T23:58Z] INFO  16:58:55,582 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-14T23:58Z] INFO  16:58:55,630 IntervalUtils - Processing 10045442 bp from intervals
[2016-04-14T23:58Z] WARN  16:58:55,636 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:58Z] INFO  16:58:55,764 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:58Z] INFO  16:58:55,852 IntervalUtils - Processing 15533983 bp from intervals
[2016-04-14T23:58Z] WARN  16:58:55,858 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:58Z] INFO  16:58:55,910 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:58Z] INFO  16:58:55,911 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:58Z] INFO  16:58:55,912 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:58Z] INFO  16:58:55,913 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:58Z] INFO  16:58:55,945 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:58Z] INFO  16:58:55,971 IntervalUtils - Processing 15510714 bp from intervals
[2016-04-14T23:58Z] WARN  16:58:55,976 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:58Z] INFO  16:58:55,988 ProgressMeter -    12:121442149    300003.0    31.0 s     104.0 s       75.8%    40.0 s       9.0 s
[2016-04-14T23:58Z] INFO  16:58:56,056 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:58Z] INFO  16:58:56,093 ProgressMeter -            done   1.5513435E7    23.0 s       1.0 s      100.0%    23.0 s       0.0 s
[2016-04-14T23:58Z] INFO  16:58:56,094 ProgressMeter - Total runtime 23.33 secs, 0.39 min, 0.01 hours
[2016-04-14T23:58Z] INFO  16:58:56,095 MicroScheduler - 77426 reads were filtered out during the traversal out of approximately 542755 total reads (14.27%)
[2016-04-14T23:58Z] INFO  16:58:56,096 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:58Z] INFO  16:58:56,097 MicroScheduler -   -> 1027 reads (0.19% of total) failing BadMateFilter
[2016-04-14T23:58Z] INFO  16:58:56,097 MicroScheduler -   -> 40758 reads (7.51% of total) failing DuplicateReadFilter
[2016-04-14T23:58Z] INFO  16:58:56,097 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-14T23:58Z] INFO  16:58:56,097 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:58Z] INFO  16:58:56,098 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-14T23:58Z] INFO  16:58:56,098 MicroScheduler -   -> 35641 reads (6.57% of total) failing MappingQualityZeroFilter
[2016-04-14T23:58Z] INFO  16:58:56,098 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:58Z] INFO  16:58:56,098 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-14T23:58Z] INFO  16:58:56,099 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-14T23:58Z] INFO  16:58:56,102 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:58Z] INFO  16:58:56,140 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:58Z] INFO  16:58:56,141 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:58Z] INFO  16:58:56,142 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:58Z] INFO  16:58:56,142 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-14T23:58Z] INFO  16:58:56,166 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:58Z] INFO  16:58:56,235 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:58Z] INFO  16:58:56,239 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:58Z] INFO  16:58:56,239 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:58Z] INFO  16:58:56,240 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:58Z] INFO  16:58:56,240 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:58Z] INFO  16:58:56,242 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:58Z] INFO  16:58:56,246 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:58Z] INFO  16:58:56,247 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:58Z] INFO  16:58:56,248 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:58Z] INFO  16:58:56,253 HelpFormatter - Program Args: -T PrintReads -L 16:31120545-46629582 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/16/tx/tmpiyb5fa/R14-18105_kapa-NGv3-PE100-NGv3-sort-16_31120544_46629582-prep-prealign.bam
[2016-04-14T23:58Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-14_50585061_66096324-prep.bam
[2016-04-14T23:58Z] INFO  16:58:56,281 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:58Z] INFO  16:58:56,288 HelpFormatter - Date/Time: 2016/04/14 16:58:56
[2016-04-14T23:58Z] INFO  16:58:56,288 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:58Z] INFO  16:58:56,289 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:58Z] INFO  16:58:56,472 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:58Z] INFO  16:58:56,522 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:58Z] INFO  16:58:56,727 ProgressMeter -     15:44007867    300003.0    60.0 s       3.4 m       45.9%     2.2 m      70.0 s
[2016-04-14T23:58Z] INFO  16:58:56,758 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:58Z] INFO  16:58:56,762 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:58Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-15_98984299_102531392-prep.bam
[2016-04-14T23:58Z] GATK pre-alignment ('16', 64982511, 80574976) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-14T23:58Z] GATK pre-alignment ('16', 80575258, 90354753) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-14T23:58Z] INFO  16:58:57,545 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:58Z] GATK: realign ('14', 19553416, 35066851) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-14T23:58Z] INFO  16:58:57,779 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-14T23:58Z] INFO  16:58:57,851 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:58Z] INFO  16:58:57,867 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:58Z] INFO  16:58:57,932 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-14T23:58Z] INFO  16:58:57,946 IntervalUtils - Processing 15509038 bp from intervals
[2016-04-14T23:58Z] INFO  16:58:58,034 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:58Z] INFO  16:58:58,095 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:58Z] INFO  16:58:58,098 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:58Z] INFO  16:58:58,098 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:58Z] INFO  16:58:58,099 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:58Z] INFO  16:58:58,103 HelpFormatter - Program Args: -T PrintReads -L 16:46633743-64982002 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/16/tx/tmpZiybHK/R14-18105_kapa-NGv3-PE100-NGv3-sort-16_46633742_64982002-prep-prealign.bam
[2016-04-14T23:58Z] INFO  16:58:58,122 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:58Z] INFO  16:58:58,123 HelpFormatter - Date/Time: 2016/04/14 16:58:58
[2016-04-14T23:58Z] INFO  16:58:58,124 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:58Z] INFO  16:58:58,124 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:58Z] INFO  16:58:58,351 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:58Z] INFO  16:58:58,371 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:58Z] INFO  16:58:58,372 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:58Z] INFO  16:58:58,373 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:58Z] INFO  16:58:58,373 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:58Z] INFO  16:58:58,400 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:58Z] INFO  16:58:58,555 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:58Z] INFO  16:58:58,930 ProgressMeter -     16:19051844    200002.0    30.0 s       2.5 m       22.3%     2.2 m     104.0 s
[2016-04-14T23:58Z] INFO  16:58:59,718 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-14T23:58Z] INFO  16:58:59,786 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:58Z] INFO  16:58:59,795 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:58Z] INFO  16:58:59,846 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-14T23:58Z] INFO  16:58:59,872 IntervalUtils - Processing 18348260 bp from intervals
[2016-04-14T23:58Z] INFO  16:58:59,948 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:59Z] INFO  16:59:00,120 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:59Z] INFO  16:59:00,122 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:59Z] INFO  16:59:00,122 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:59Z] INFO  16:59:00,122 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:59Z] INFO  16:59:00,137 HelpFormatter - Program Args: -T PrintReads -L 16:64982512-80574976 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/16/tx/tmpcwMrA6/R14-18105_kapa-NGv3-PE100-NGv3-sort-16_64982511_80574976-prep-prealign.bam
[2016-04-14T23:59Z] INFO  16:59:00,145 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:59Z] INFO  16:59:00,145 HelpFormatter - Date/Time: 2016/04/14 16:59:00
[2016-04-14T23:59Z] INFO  16:59:00,146 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:59Z] INFO  16:59:00,146 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:59Z] INFO  16:59:00,317 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:59Z] INFO  16:59:00,317 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:59Z] INFO  16:59:00,318 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:59Z] INFO  16:59:00,318 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:59Z] INFO  16:59:00,350 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:59Z] INFO  16:59:00,355 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:59Z] INFO  16:59:00,407 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:59Z] INFO  16:59:00,411 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:59Z] INFO  16:59:00,411 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:59Z] INFO  16:59:00,412 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:59Z] INFO  16:59:00,416 HelpFormatter - Program Args: -T PrintReads -L 16:80575259-90354753 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/16/tx/tmpkcvOB7/R14-18105_kapa-NGv3-PE100-NGv3-sort-16_80575258_90354753-prep-prealign.bam
[2016-04-14T23:59Z] INFO  16:59:00,430 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:59Z] INFO  16:59:00,430 HelpFormatter - Date/Time: 2016/04/14 16:59:00
[2016-04-14T23:59Z] INFO  16:59:00,430 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:59Z] INFO  16:59:00,431 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:59Z] INFO  16:59:00,548 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:59Z] INFO  16:59:00,612 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:59Z] INFO  16:59:00,731 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:59Z] INFO  16:59:00,735 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:59Z] INFO  16:59:00,735 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:59Z] INFO  16:59:00,736 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:59Z] INFO  16:59:00,740 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/14/R14-18105_kapa-NGv3-PE100-NGv3-sort-14_19553416_35066851-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/14/R14-18105_kapa-NGv3-PE100-NGv3-sort-14_19553416_35066851-prep-prealign-realign.intervals -L 14:19553417-35066851 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/14/tx/tmpJ2S90V/R14-18105_kapa-NGv3-PE100-NGv3-sort-14_19553416_35066851-prep.bam
[2016-04-14T23:59Z] INFO  16:59:00,756 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:59Z] INFO  16:59:00,757 HelpFormatter - Date/Time: 2016/04/14 16:59:00
[2016-04-14T23:59Z] INFO  16:59:00,758 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:59Z] INFO  16:59:00,758 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:59Z] INFO  16:59:00,977 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:59Z] INFO  16:59:01,164 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:59Z] INFO  16:59:01,173 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:59Z] INFO  16:59:01,255 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-14T23:59Z] INFO  16:59:01,603 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-14T23:59Z] INFO  16:59:01,666 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:59Z] INFO  16:59:01,675 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:59Z] INFO  16:59:01,725 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-14T23:59Z] INFO  16:59:01,736 IntervalUtils - Processing 15513435 bp from intervals
[2016-04-14T23:59Z] INFO  16:59:01,743 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-14T23:59Z] WARN  16:59:01,750 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:59Z] INFO  16:59:01,753 IntervalUtils - Processing 15592465 bp from intervals
[2016-04-14T23:59Z] INFO  16:59:01,828 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:59Z] INFO  16:59:01,836 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:59Z] INFO  16:59:01,840 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:59Z] INFO  16:59:01,874 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:59Z] INFO  16:59:01,892 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-14T23:59Z] INFO  16:59:01,923 IntervalUtils - Processing 9779495 bp from intervals
[2016-04-14T23:59Z] INFO  16:59:02,007 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:59Z] INFO  16:59:02,008 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:59Z] INFO  16:59:02,008 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:59Z] INFO  16:59:02,009 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:59Z] INFO  16:59:02,100 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:59Z] INFO  16:59:02,155 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:59Z] INFO  16:59:02,170 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:59Z] INFO  16:59:02,171 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:59Z] INFO  16:59:02,172 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:59Z] INFO  16:59:02,172 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:59Z] INFO  16:59:02,191 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:59Z] INFO  16:59:02,217 ProgressMeter -     15:81648083    400007.0    60.0 s       2.5 m       88.4%    67.0 s       7.0 s
[2016-04-14T23:59Z] INFO  16:59:02,301 ProgressMeter -            done    255045.0    19.0 s      77.0 s      100.0%    19.0 s       0.0 s
[2016-04-14T23:59Z] INFO  16:59:02,301 ProgressMeter - Total runtime 19.74 secs, 0.33 min, 0.01 hours
[2016-04-14T23:59Z] INFO  16:59:02,304 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 255045 total reads (0.00%)
[2016-04-14T23:59Z] INFO  16:59:02,305 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:59Z] INFO  16:59:02,305 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:59Z] INFO  16:59:02,305 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:59Z] INFO  16:59:02,318 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:59Z] INFO  16:59:02,359 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:59Z] INFO  16:59:02,379 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:59Z] INFO  16:59:02,380 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:59Z] INFO  16:59:02,381 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:59Z] INFO  16:59:02,382 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:59Z] INFO  16:59:02,401 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:59Z] INFO  16:59:02,524 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:59Z] INFO  16:59:03,600 ProgressMeter -            done    615091.0    38.0 s      63.0 s      100.0%    38.0 s       0.0 s
[2016-04-14T23:59Z] INFO  16:59:03,601 ProgressMeter - Total runtime 38.82 secs, 0.65 min, 0.01 hours
[2016-04-14T23:59Z] INFO  16:59:03,604 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 615091 total reads (0.00%)
[2016-04-14T23:59Z] INFO  16:59:03,605 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:59Z] INFO  16:59:03,605 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:59Z] INFO  16:59:03,605 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:59Z] INFO  16:59:03,793 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:59Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-14_81651874_97299968-prep.bam
[2016-04-14T23:59Z] GATK pre-alignment ('17', 0, 15511002) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-14T23:59Z] INFO  16:59:05,081 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:59Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-12_109494486_125263132-prep.bam
[2016-04-14T23:59Z] GATK pre-alignment ('17', 15515955, 31039213) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-14T23:59Z] INFO  16:59:07,458 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:59Z] INFO  16:59:07,461 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:59Z] INFO  16:59:07,462 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:59Z] INFO  16:59:07,462 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:59Z] INFO  16:59:07,467 HelpFormatter - Program Args: -T PrintReads -L 17:1-15511002 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/17/tx/tmpY2XYra/R14-18105_kapa-NGv3-PE100-NGv3-sort-17_0_15511002-prep-prealign.bam
[2016-04-14T23:59Z] INFO  16:59:07,499 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:59Z] INFO  16:59:07,500 HelpFormatter - Date/Time: 2016/04/14 16:59:07
[2016-04-14T23:59Z] INFO  16:59:07,500 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:59Z] INFO  16:59:07,501 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:59Z] INFO  16:59:07,752 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:59Z] INFO  16:59:08,538 ProgressMeter -            done   1.5518901E7    20.0 s       1.0 s      100.0%    20.0 s       0.0 s
[2016-04-14T23:59Z] INFO  16:59:08,539 ProgressMeter - Total runtime 20.65 secs, 0.34 min, 0.01 hours
[2016-04-14T23:59Z] INFO  16:59:08,543 MicroScheduler - 29941 reads were filtered out during the traversal out of approximately 367178 total reads (8.15%)
[2016-04-14T23:59Z] INFO  16:59:08,543 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:59Z] INFO  16:59:08,543 MicroScheduler -   -> 770 reads (0.21% of total) failing BadMateFilter
[2016-04-14T23:59Z] INFO  16:59:08,544 MicroScheduler -   -> 28483 reads (7.76% of total) failing DuplicateReadFilter
[2016-04-14T23:59Z] INFO  16:59:08,544 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-14T23:59Z] INFO  16:59:08,544 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:59Z] INFO  16:59:08,544 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-14T23:59Z] INFO  16:59:08,545 MicroScheduler -   -> 688 reads (0.19% of total) failing MappingQualityZeroFilter
[2016-04-14T23:59Z] INFO  16:59:08,545 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:59Z] INFO  16:59:08,545 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-14T23:59Z] INFO  16:59:08,545 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-14T23:59Z] INFO  16:59:09,028 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-14T23:59Z] INFO  16:59:09,106 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:59Z] INFO  16:59:09,115 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:59Z] INFO  16:59:09,167 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-14T23:59Z] INFO  16:59:09,181 IntervalUtils - Processing 15511002 bp from intervals
[2016-04-14T23:59Z] INFO  16:59:09,290 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:59Z] INFO  16:59:09,698 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:59Z] INFO  16:59:09,699 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:59Z] INFO  16:59:09,700 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:59Z] INFO  16:59:09,701 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:59Z] INFO  16:59:09,714 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:59Z] INFO  16:59:09,853 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:59Z] INFO  16:59:09,860 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@7172f77a
[2016-04-14T23:59Z] INFO  16:59:09,919 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:59Z] INFO  16:59:09,922 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:59Z] INFO  16:59:09,922 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:59Z] INFO  16:59:09,923 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:59Z] INFO  16:59:09,927 HelpFormatter - Program Args: -T PrintReads -L 17:15515956-31039213 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/17/tx/tmpXOY5Fk/R14-18105_kapa-NGv3-PE100-NGv3-sort-17_15515955_31039213-prep-prealign.bam
[2016-04-14T23:59Z] INFO  16:59:09,957 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:59Z] INFO  16:59:09,962 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:59Z] INFO  16:59:09,963 HelpFormatter - Date/Time: 2016/04/14 16:59:09
[2016-04-14T23:59Z] INFO  16:59:09,963 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:59Z] INFO  16:59:09,964 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:59Z] GATK: realign ('15', 52404364, 67923265) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-14T23:59Z] INFO  16:59:10,023 ProgressMeter -            done    565258.0    67.0 s     119.0 s      100.0%    67.0 s       0.0 s
[2016-04-14T23:59Z] INFO  16:59:10,026 ProgressMeter - Total runtime 67.83 secs, 1.13 min, 0.02 hours
[2016-04-14T23:59Z] INFO  16:59:10,026 MicroScheduler - 257 reads were filtered out during the traversal out of approximately 565515 total reads (0.05%)
[2016-04-14T23:59Z] INFO  16:59:10,027 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:59Z] INFO  16:59:10,027 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:59Z] INFO  16:59:10,028 MicroScheduler -   -> 257 reads (0.05% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:59Z] INFO  16:59:10,137 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:59Z] INFO  16:59:11,202 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-14T23:59Z] INFO  16:59:11,256 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:59Z] INFO  16:59:11,265 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:59Z] INFO  16:59:11,309 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.04
[2016-04-14T23:59Z] INFO  16:59:11,323 IntervalUtils - Processing 15523258 bp from intervals
[2016-04-14T23:59Z] INFO  16:59:11,402 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:59Z] INFO  16:59:11,589 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:59Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-15_67932890_83447639-prep-prealign.bam
[2016-04-14T23:59Z] INFO  16:59:11,740 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:59Z] INFO  16:59:11,741 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:59Z] INFO  16:59:11,742 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:59Z] INFO  16:59:11,743 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:59Z] INFO  16:59:11,790 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:59Z] INFO  16:59:11,946 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:59Z] INFO  16:59:12,633 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:59Z] INFO  16:59:12,637 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:59Z] INFO  16:59:12,638 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:59Z] INFO  16:59:12,638 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:59Z] INFO  16:59:12,644 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/15/R14-18105_kapa-NGv3-PE100-NGv3-sort-15_52404364_67923265-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/15/R14-18105_kapa-NGv3-PE100-NGv3-sort-15_52404364_67923265-prep-prealign-realign.intervals -L 15:52404365-67923265 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/15/tx/tmpU0QiWc/R14-18105_kapa-NGv3-PE100-NGv3-sort-15_52404364_67923265-prep.bam
[2016-04-14T23:59Z] INFO  16:59:12,655 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:59Z] INFO  16:59:12,658 HelpFormatter - Date/Time: 2016/04/14 16:59:12
[2016-04-14T23:59Z] INFO  16:59:12,659 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:59Z] INFO  16:59:12,660 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:59Z] INFO  16:59:12,908 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:59Z] INFO  16:59:13,082 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:59Z] INFO  16:59:13,094 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:59Z] INFO  16:59:13,198 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.10
[2016-04-14T23:59Z] GATK RealignerTargetCreator: R14-18105_kapa-NGv3-PE100-NGv3-sort-15_67932890_83447639-prep-prealign.bam 15:67932891-83447639
[2016-04-14T23:59Z] GATK: RealignerTargetCreator
[2016-04-14T23:59Z] INFO  16:59:13,694 IntervalUtils - Processing 15518901 bp from intervals
[2016-04-14T23:59Z] WARN  16:59:13,700 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:59Z] INFO  16:59:13,792 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:59Z] INFO  16:59:13,905 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:59Z] INFO  16:59:13,906 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:59Z] INFO  16:59:13,907 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:59Z] INFO  16:59:13,908 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:59Z] INFO  16:59:14,083 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:59Z] INFO  16:59:14,326 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:59Z] INFO  16:59:15,852 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@41fd9d8e
[2016-04-14T23:59Z] INFO  16:59:15,974 ProgressMeter -            done    117605.0    17.0 s       2.5 m      100.0%    17.0 s       0.0 s
[2016-04-14T23:59Z] INFO  16:59:15,974 ProgressMeter - Total runtime 17.60 secs, 0.29 min, 0.00 hours
[2016-04-14T23:59Z] INFO  16:59:15,975 MicroScheduler - 184 reads were filtered out during the traversal out of approximately 117789 total reads (0.16%)
[2016-04-14T23:59Z] INFO  16:59:15,975 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:59Z] INFO  16:59:15,975 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:59Z] INFO  16:59:15,976 MicroScheduler -   -> 184 reads (0.16% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:59Z] INFO  16:59:16,190 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:59Z] INFO  16:59:16,194 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:59Z] INFO  16:59:16,194 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:59Z] INFO  16:59:16,195 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:59Z] INFO  16:59:16,200 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/15/R14-18105_kapa-NGv3-PE100-NGv3-sort-15_67932890_83447639-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/15/tx/tmplQWvWI/R14-18105_kapa-NGv3-PE100-NGv3-sort-15_67932890_83447639-prep-prealign-realign.intervals -l INFO -L 15:67932891-83447639 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-14T23:59Z] INFO  16:59:16,223 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:59Z] INFO  16:59:16,232 HelpFormatter - Date/Time: 2016/04/14 16:59:16
[2016-04-14T23:59Z] INFO  16:59:16,233 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:59Z] INFO  16:59:16,233 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:59Z] INFO  16:59:16,378 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:59Z] INFO  16:59:16,587 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-14T23:59Z] INFO  16:59:16,596 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:59Z] INFO  16:59:16,651 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-14T23:59Z] INFO  16:59:16,797 ProgressMeter -            done   1.5533983E7    20.0 s       1.0 s      100.0%    20.0 s       0.0 s
[2016-04-14T23:59Z] INFO  16:59:16,798 ProgressMeter - Total runtime 20.66 secs, 0.34 min, 0.01 hours
[2016-04-14T23:59Z] INFO  16:59:16,803 MicroScheduler - 54187 reads were filtered out during the traversal out of approximately 345875 total reads (15.67%)
[2016-04-14T23:59Z] INFO  16:59:16,804 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:59Z] INFO  16:59:16,804 MicroScheduler -   -> 707 reads (0.20% of total) failing BadMateFilter
[2016-04-14T23:59Z] INFO  16:59:16,805 MicroScheduler -   -> 25035 reads (7.24% of total) failing DuplicateReadFilter
[2016-04-14T23:59Z] INFO  16:59:16,806 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-14T23:59Z] INFO  16:59:16,806 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:59Z] INFO  16:59:16,807 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-14T23:59Z] INFO  16:59:16,807 MicroScheduler -   -> 28445 reads (8.22% of total) failing MappingQualityZeroFilter
[2016-04-14T23:59Z] INFO  16:59:16,808 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:59Z] INFO  16:59:16,809 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-14T23:59Z] INFO  16:59:16,809 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-14T23:59Z] INFO  16:59:16,969 IntervalUtils - Processing 15514749 bp from intervals
[2016-04-14T23:59Z] WARN  16:59:16,996 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:59Z] INFO  16:59:17,100 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:59Z] INFO  16:59:17,316 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:59Z] INFO  16:59:17,317 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:59Z] INFO  16:59:17,318 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:59Z] INFO  16:59:17,319 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-14T23:59Z] INFO  16:59:17,584 ProgressMeter -            done   1.6130541E7    22.0 s       1.0 s      100.0%    22.0 s       0.0 s
[2016-04-14T23:59Z] INFO  16:59:17,585 ProgressMeter - Total runtime 22.14 secs, 0.37 min, 0.01 hours
[2016-04-14T23:59Z] INFO  16:59:17,590 MicroScheduler - 199276 reads were filtered out during the traversal out of approximately 480818 total reads (41.45%)
[2016-04-14T23:59Z] INFO  16:59:17,591 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:59Z] INFO  16:59:17,591 MicroScheduler -   -> 662 reads (0.14% of total) failing BadMateFilter
[2016-04-14T23:59Z] INFO  16:59:17,592 MicroScheduler -   -> 24263 reads (5.05% of total) failing DuplicateReadFilter
[2016-04-14T23:59Z] INFO  16:59:17,593 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-14T23:59Z] INFO  16:59:17,593 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:59Z] INFO  16:59:17,594 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-14T23:59Z] INFO  16:59:17,594 MicroScheduler -   -> 174351 reads (36.26% of total) failing MappingQualityZeroFilter
[2016-04-14T23:59Z] INFO  16:59:17,595 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:59Z] INFO  16:59:17,596 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-14T23:59Z] INFO  16:59:17,596 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-14T23:59Z] INFO  16:59:17,727 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:59Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-16_31120544_46629582-prep-prealign.bam
[2016-04-14T23:59Z] GATK RealignerTargetCreator: R14-18105_kapa-NGv3-PE100-NGv3-sort-16_31120544_46629582-prep-prealign.bam 16:31120545-46629582
[2016-04-14T23:59Z] GATK: RealignerTargetCreator
[2016-04-14T23:59Z] INFO  16:59:18,183 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:59Z] GATK: realign ('15', 83448996, 98982979) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-14T23:59Z] INFO  16:59:18,902 ProgressMeter -            done    340739.0    22.0 s      67.0 s       99.3%    22.0 s       0.0 s
[2016-04-14T23:59Z] INFO  16:59:18,902 ProgressMeter - Total runtime 22.99 secs, 0.38 min, 0.01 hours
[2016-04-14T23:59Z] INFO  16:59:18,906 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 340739 total reads (0.00%)
[2016-04-14T23:59Z] INFO  16:59:18,907 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:59Z] INFO  16:59:18,908 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:59Z] INFO  16:59:18,909 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:59Z] INFO  16:59:19,031 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:59Z] GATK: realign ('15', 20741621, 36872162) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-14T23:59Z] INFO  16:59:20,681 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:59Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-14_97304098_107349540-prep.bam
[2016-04-14T23:59Z] INFO  16:59:20,988 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:59Z] INFO  16:59:20,996 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:59Z] INFO  16:59:20,997 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:59Z] INFO  16:59:20,997 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:59Z] INFO  16:59:21,009 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/15/R14-18105_kapa-NGv3-PE100-NGv3-sort-15_83448996_98982979-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/15/R14-18105_kapa-NGv3-PE100-NGv3-sort-15_83448996_98982979-prep-prealign-realign.intervals -L 15:83448997-98982979 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/15/tx/tmpHLJRNm/R14-18105_kapa-NGv3-PE100-NGv3-sort-15_83448996_98982979-prep.bam
[2016-04-14T23:59Z] INFO  16:59:21,019 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:59Z] INFO  16:59:21,020 HelpFormatter - Date/Time: 2016/04/14 16:59:20
[2016-04-14T23:59Z] INFO  16:59:21,021 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:59Z] INFO  16:59:21,021 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:59Z] INFO  16:59:21,228 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:59Z] INFO  16:59:21,232 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:59Z] INFO  16:59:21,232 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:59Z] INFO  16:59:21,233 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:59Z] INFO  16:59:21,237 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/16/R14-18105_kapa-NGv3-PE100-NGv3-sort-16_31120544_46629582-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/16/tx/tmpqnRDWp/R14-18105_kapa-NGv3-PE100-NGv3-sort-16_31120544_46629582-prep-prealign-realign.intervals -l INFO -L 16:31120545-46629582 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-14T23:59Z] INFO  16:59:21,246 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:59Z] INFO  16:59:21,246 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:59Z] INFO  16:59:21,247 HelpFormatter - Date/Time: 2016/04/14 16:59:21
[2016-04-14T23:59Z] INFO  16:59:21,247 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:59Z] INFO  16:59:21,248 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:59Z] INFO  16:59:21,348 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:59Z] INFO  16:59:21,358 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:59Z] INFO  16:59:21,382 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:59Z] INFO  16:59:21,434 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-14T23:59Z] INFO  16:59:21,567 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-14T23:59Z] INFO  16:59:21,576 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:59Z] INFO  16:59:21,627 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-14T23:59Z] GATK pre-alignment ('17', 31048040, 46607237) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-14T23:59Z] INFO  16:59:21,792 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:59Z] INFO  16:59:21,795 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:59Z] INFO  16:59:21,795 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:59Z] INFO  16:59:21,796 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:59Z] INFO  16:59:21,800 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/15/R14-18105_kapa-NGv3-PE100-NGv3-sort-15_20741621_36872162-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/15/R14-18105_kapa-NGv3-PE100-NGv3-sort-15_20741621_36872162-prep-prealign-realign.intervals -L 15:20741622-36872162 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/15/tx/tmpwaPLTI/R14-18105_kapa-NGv3-PE100-NGv3-sort-15_20741621_36872162-prep.bam
[2016-04-14T23:59Z] INFO  16:59:21,810 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:59Z] INFO  16:59:21,811 HelpFormatter - Date/Time: 2016/04/14 16:59:21
[2016-04-14T23:59Z] INFO  16:59:21,811 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:59Z] INFO  16:59:21,811 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:59Z] INFO  16:59:21,851 IntervalUtils - Processing 15533983 bp from intervals
[2016-04-14T23:59Z] WARN  16:59:21,856 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:59Z] INFO  16:59:21,922 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:59Z] INFO  16:59:21,944 IntervalUtils - Processing 15509038 bp from intervals
[2016-04-14T23:59Z] WARN  16:59:21,959 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:59Z] INFO  16:59:22,040 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:59Z] INFO  16:59:22,041 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:59Z] INFO  16:59:22,045 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:59Z] INFO  16:59:22,045 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:59Z] INFO  16:59:22,046 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:59Z] INFO  16:59:22,046 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:59Z] INFO  16:59:22,202 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:59Z] INFO  16:59:22,203 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:59Z] INFO  16:59:22,204 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:59Z] INFO  16:59:22,205 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-14T23:59Z] INFO  16:59:22,209 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:59Z] INFO  16:59:22,223 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:59Z] INFO  16:59:22,234 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:59Z] INFO  16:59:22,308 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-14T23:59Z] INFO  16:59:22,392 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:59Z] INFO  16:59:22,703 IntervalUtils - Processing 16130541 bp from intervals
[2016-04-14T23:59Z] WARN  16:59:22,713 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:59Z] INFO  16:59:22,769 ProgressMeter -            done    392352.0    26.0 s      67.0 s       99.8%    26.0 s       0.0 s
[2016-04-14T23:59Z] INFO  16:59:22,770 ProgressMeter - Total runtime 26.53 secs, 0.44 min, 0.01 hours
[2016-04-14T23:59Z] INFO  16:59:22,774 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 392352 total reads (0.00%)
[2016-04-14T23:59Z] INFO  16:59:22,775 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:59Z] INFO  16:59:22,786 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:59Z] INFO  16:59:22,786 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:59Z] INFO  16:59:22,787 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:59Z] INFO  16:59:22,914 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:59Z] INFO  16:59:22,915 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:59Z] INFO  16:59:22,916 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:59Z] INFO  16:59:22,917 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:59Z] INFO  16:59:23,113 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:59Z] INFO  16:59:23,284 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:59Z] INFO  16:59:23,294 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@7172f77a
[2016-04-14T23:59Z] INFO  16:59:23,414 ProgressMeter -            done    609200.0    87.0 s       2.4 m      100.0%    87.0 s       0.0 s
[2016-04-14T23:59Z] INFO  16:59:23,415 ProgressMeter - Total runtime 87.14 secs, 1.45 min, 0.02 hours
[2016-04-14T23:59Z] INFO  16:59:23,415 MicroScheduler - 361 reads were filtered out during the traversal out of approximately 609561 total reads (0.06%)
[2016-04-14T23:59Z] INFO  16:59:23,416 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:59Z] INFO  16:59:23,416 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:59Z] INFO  16:59:23,416 MicroScheduler -   -> 361 reads (0.06% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:59Z] INFO  16:59:23,549 ProgressMeter -      16:2303966    300008.0    60.0 s       3.3 m       14.8%     6.7 m       5.7 m
[2016-04-14T23:59Z] INFO  16:59:24,233 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:59Z] INFO  16:59:24,236 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:59Z] INFO  16:59:24,237 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:59Z] INFO  16:59:24,237 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:59Z] INFO  16:59:24,242 HelpFormatter - Program Args: -T PrintReads -L 17:31048041-46607237 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/17/tx/tmptc8fvS/R14-18105_kapa-NGv3-PE100-NGv3-sort-17_31048040_46607237-prep-prealign.bam
[2016-04-14T23:59Z] INFO  16:59:24,271 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:59Z] INFO  16:59:24,280 HelpFormatter - Date/Time: 2016/04/14 16:59:24
[2016-04-14T23:59Z] INFO  16:59:24,281 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:59Z] INFO  16:59:24,282 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:59Z] INFO  16:59:24,368 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:59Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-14_66135960_81646674-prep.bam
[2016-04-14T23:59Z] INFO  16:59:24,435 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:59Z] INFO  16:59:25,072 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:59Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-15_36887086_52402170-prep-prealign.bam
[2016-04-14T23:59Z] GATK pre-alignment ('17', 46607689, 62121560) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-14T23:59Z] INFO  16:59:25,688 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-14T23:59Z] INFO  16:59:25,753 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:59Z] INFO  16:59:25,763 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:59Z] INFO  16:59:25,814 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-14T23:59Z] INFO  16:59:25,828 IntervalUtils - Processing 15559197 bp from intervals
[2016-04-14T23:59Z] INFO  16:59:25,904 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:59Z] INFO  16:59:26,212 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:59Z] INFO  16:59:26,224 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:59Z] INFO  16:59:26,225 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:59Z] INFO  16:59:26,225 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:59Z] INFO  16:59:26,251 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:59Z] INFO  16:59:26,403 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:59Z] GATK RealignerTargetCreator: R14-18105_kapa-NGv3-PE100-NGv3-sort-15_36887086_52402170-prep-prealign.bam 15:36887087-52402170
[2016-04-14T23:59Z] GATK: RealignerTargetCreator
[2016-04-14T23:59Z] INFO  16:59:28,670 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:59Z] INFO  16:59:28,684 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:59Z] INFO  16:59:28,685 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:59Z] INFO  16:59:28,685 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:59Z] INFO  16:59:28,690 HelpFormatter - Program Args: -T PrintReads -L 17:46607690-62121560 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/17/tx/tmp1EgL6o/R14-18105_kapa-NGv3-PE100-NGv3-sort-17_46607689_62121560-prep-prealign.bam
[2016-04-14T23:59Z] INFO  16:59:28,699 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:59Z] INFO  16:59:28,699 HelpFormatter - Date/Time: 2016/04/14 16:59:28
[2016-04-14T23:59Z] INFO  16:59:28,699 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:59Z] INFO  16:59:28,721 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:59Z] INFO  16:59:28,874 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:59Z] INFO  16:59:29,633 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:59Z] INFO  16:59:29,637 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:59Z] INFO  16:59:29,638 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:59Z] INFO  16:59:29,638 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:59Z] INFO  16:59:29,643 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/15/R14-18105_kapa-NGv3-PE100-NGv3-sort-15_36887086_52402170-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/15/tx/tmprz1sP9/R14-18105_kapa-NGv3-PE100-NGv3-sort-15_36887086_52402170-prep-prealign-realign.intervals -l INFO -L 15:36887087-52402170 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-14T23:59Z] INFO  16:59:29,653 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:59Z] INFO  16:59:29,653 HelpFormatter - Date/Time: 2016/04/14 16:59:29
[2016-04-14T23:59Z] INFO  16:59:29,654 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:59Z] INFO  16:59:29,654 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:59Z] INFO  16:59:29,785 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:59Z] INFO  16:59:29,965 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-14T23:59Z] INFO  16:59:29,975 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:59Z] INFO  16:59:29,981 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-14T23:59Z] INFO  16:59:30,028 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-14T23:59Z] INFO  16:59:30,073 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:59Z] INFO  16:59:30,085 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:59Z] INFO  16:59:30,140 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-14T23:59Z] INFO  16:59:30,158 IntervalUtils - Processing 15513871 bp from intervals
[2016-04-14T23:59Z] INFO  16:59:30,248 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:59Z] INFO  16:59:30,310 IntervalUtils - Processing 15515084 bp from intervals
[2016-04-14T23:59Z] WARN  16:59:30,316 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:59Z] INFO  16:59:30,345 ProgressMeter -     16:57059872    200002.0    30.0 s       2.5 m       56.8%    52.0 s      22.0 s
[2016-04-14T23:59Z] INFO  16:59:30,410 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:59Z] INFO  16:59:30,541 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:59Z] INFO  16:59:30,543 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:59Z] INFO  16:59:30,544 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:59Z] INFO  16:59:30,545 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:59Z] INFO  16:59:30,559 ProgressMeter -     16:22545879    400011.0    61.0 s       2.6 m       44.8%     2.3 m      75.0 s
[2016-04-14T23:59Z] INFO  16:59:30,568 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:59Z] INFO  16:59:30,616 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:59Z] INFO  16:59:30,618 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:59Z] INFO  16:59:30,618 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:59Z] INFO  16:59:30,619 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-14T23:59Z] INFO  16:59:30,737 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:59Z] INFO  16:59:32,234 ProgressMeter -     16:68000757    200003.0    30.0 s       2.5 m       19.4%     2.6 m       2.1 m
[2016-04-14T23:59Z] INFO  16:59:32,402 ProgressMeter -     16:88748054    200004.0    30.0 s       2.5 m       83.6%    35.0 s       5.0 s
[2016-04-14T23:59Z] INFO  16:59:32,526 ProgressMeter -     14:24838402    400005.0    30.0 s      76.0 s       34.1%    88.0 s      58.0 s
[2016-04-14T23:59Z] INFO  16:59:35,645 ProgressMeter -            done    539322.0    33.0 s      62.0 s      100.0%    33.0 s       0.0 s
[2016-04-14T23:59Z] INFO  16:59:35,646 ProgressMeter - Total runtime 33.64 secs, 0.56 min, 0.01 hours
[2016-04-14T23:59Z] INFO  16:59:35,649 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 539322 total reads (0.00%)
[2016-04-14T23:59Z] INFO  16:59:35,650 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:59Z] INFO  16:59:35,651 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:59Z] INFO  16:59:35,652 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:59Z] INFO  16:59:36,884 ProgressMeter -            done   1.5509038E7    14.0 s       0.0 s      100.0%    14.0 s       0.0 s
[2016-04-14T23:59Z] INFO  16:59:36,884 ProgressMeter - Total runtime 14.68 secs, 0.24 min, 0.00 hours
[2016-04-14T23:59Z] INFO  16:59:36,888 MicroScheduler - 34358 reads were filtered out during the traversal out of approximately 118621 total reads (28.96%)
[2016-04-14T23:59Z] INFO  16:59:36,888 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:59Z] INFO  16:59:36,889 MicroScheduler -   -> 404 reads (0.34% of total) failing BadMateFilter
[2016-04-14T23:59Z] INFO  16:59:36,890 MicroScheduler -   -> 7071 reads (5.96% of total) failing DuplicateReadFilter
[2016-04-14T23:59Z] INFO  16:59:36,890 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-14T23:59Z] INFO  16:59:36,891 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:59Z] INFO  16:59:36,892 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-14T23:59Z] INFO  16:59:36,892 MicroScheduler -   -> 26883 reads (22.66% of total) failing MappingQualityZeroFilter
[2016-04-14T23:59Z] INFO  16:59:36,893 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:59Z] INFO  16:59:36,893 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-14T23:59Z] INFO  16:59:36,894 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-14T23:59Z] INFO  16:59:37,190 ProgressMeter -            done    364790.0    23.0 s      63.0 s      100.0%    23.0 s       0.0 s
[2016-04-14T23:59Z] INFO  16:59:37,190 ProgressMeter - Total runtime 23.28 secs, 0.39 min, 0.01 hours
[2016-04-14T23:59Z] INFO  16:59:37,194 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 364790 total reads (0.00%)
[2016-04-14T23:59Z] INFO  16:59:37,195 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:59Z] INFO  16:59:37,195 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:59Z] INFO  16:59:37,195 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:59Z] INFO  16:59:37,259 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:59Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-14_19553416_35066851-prep.bam
[2016-04-14T23:59Z] INFO  16:59:38,499 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:59Z] GATK: realign ('16', 31120544, 46629582) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-14T23:59Z] INFO  16:59:38,691 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:59Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-15_52404364_67923265-prep.bam
[2016-04-14T23:59Z] GATK pre-alignment ('17', 62122219, 77705154) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-14T23:59Z] INFO  16:59:39,727 ProgressMeter -      17:3618276    200007.0    30.0 s       2.5 m       23.3%     2.1 m      98.0 s
[2016-04-14T23:59Z] GATK pre-alignment ('17', 77707305, 81195210) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-14T23:59Z] INFO  16:59:41,098 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:59Z] INFO  16:59:41,101 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:59Z] INFO  16:59:41,101 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:59Z] INFO  16:59:41,101 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:59Z] INFO  16:59:41,105 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/16/R14-18105_kapa-NGv3-PE100-NGv3-sort-16_31120544_46629582-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/16/R14-18105_kapa-NGv3-PE100-NGv3-sort-16_31120544_46629582-prep-prealign-realign.intervals -L 16:31120545-46629582 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/16/tx/tmp_Rb9If/R14-18105_kapa-NGv3-PE100-NGv3-sort-16_31120544_46629582-prep.bam
[2016-04-14T23:59Z] INFO  16:59:41,131 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:59Z] INFO  16:59:41,132 HelpFormatter - Date/Time: 2016/04/14 16:59:41
[2016-04-14T23:59Z] INFO  16:59:41,132 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:59Z] INFO  16:59:41,132 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:59Z] INFO  16:59:41,349 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:59Z] INFO  16:59:41,504 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:59Z] INFO  16:59:41,521 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:59Z] INFO  16:59:41,583 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-14T23:59Z] INFO  16:59:41,770 ProgressMeter -     17:18509520    200004.0    30.0 s       2.5 m       19.3%     2.6 m       2.1 m
[2016-04-14T23:59Z] INFO  16:59:41,836 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:59Z] INFO  16:59:41,840 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:59Z] INFO  16:59:41,840 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:59Z] INFO  16:59:41,841 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:59Z] INFO  16:59:41,845 HelpFormatter - Program Args: -T PrintReads -L 17:62122220-77705154 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/17/tx/tmpuESE5_/R14-18105_kapa-NGv3-PE100-NGv3-sort-17_62122219_77705154-prep-prealign.bam
[2016-04-14T23:59Z] INFO  16:59:41,863 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:59Z] INFO  16:59:41,864 HelpFormatter - Date/Time: 2016/04/14 16:59:41
[2016-04-14T23:59Z] INFO  16:59:41,865 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:59Z] INFO  16:59:41,866 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:59Z] INFO  16:59:41,932 ProgressMeter -            done   1.5514749E7    24.0 s       1.0 s      100.0%    24.0 s       0.0 s
[2016-04-14T23:59Z] INFO  16:59:41,944 ProgressMeter - Total runtime 24.63 secs, 0.41 min, 0.01 hours
[2016-04-14T23:59Z] INFO  16:59:41,948 MicroScheduler - 121144 reads were filtered out during the traversal out of approximately 569696 total reads (21.26%)
[2016-04-14T23:59Z] INFO  16:59:41,949 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:59Z] INFO  16:59:41,950 MicroScheduler -   -> 945 reads (0.17% of total) failing BadMateFilter
[2016-04-14T23:59Z] INFO  16:59:41,951 MicroScheduler -   -> 38386 reads (6.74% of total) failing DuplicateReadFilter
[2016-04-14T23:59Z] INFO  16:59:41,962 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-14T23:59Z] INFO  16:59:41,963 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:59Z] INFO  16:59:41,964 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-14T23:59Z] INFO  16:59:41,965 MicroScheduler -   -> 81813 reads (14.36% of total) failing MappingQualityZeroFilter
[2016-04-14T23:59Z] INFO  16:59:41,965 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:59Z] INFO  16:59:41,966 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-14T23:59Z] INFO  16:59:41,967 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-14T23:59Z] INFO  16:59:41,974 IntervalUtils - Processing 15509038 bp from intervals
[2016-04-14T23:59Z] WARN  16:59:41,980 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:59Z] INFO  16:59:42,065 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:59Z] INFO  16:59:42,086 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:59Z] INFO  16:59:42,136 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:59Z] INFO  16:59:42,137 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:59Z] INFO  16:59:42,138 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:59Z] INFO  16:59:42,139 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:59Z] INFO  16:59:42,195 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:59Z] INFO  16:59:42,328 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:59Z] INFO  16:59:42,466 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:59Z] INFO  16:59:42,476 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:59Z] INFO  16:59:42,476 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:59Z] INFO  16:59:42,476 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:59Z] INFO  16:59:42,481 HelpFormatter - Program Args: -T PrintReads -L 17:77707306-81195210 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/17/tx/tmpWm5Eop/R14-18105_kapa-NGv3-PE100-NGv3-sort-17_77707305_81195210-prep-prealign.bam
[2016-04-14T23:59Z] INFO  16:59:42,507 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:59Z] INFO  16:59:42,507 HelpFormatter - Date/Time: 2016/04/14 16:59:42
[2016-04-14T23:59Z] INFO  16:59:42,507 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:59Z] INFO  16:59:42,508 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:59Z] INFO  16:59:42,700 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:59Z] INFO  16:59:43,062 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-14T23:59Z] INFO  16:59:43,159 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:59Z] INFO  16:59:43,168 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:59Z] INFO  16:59:43,214 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-14T23:59Z] INFO  16:59:43,232 IntervalUtils - Processing 15582935 bp from intervals
[2016-04-14T23:59Z] INFO  16:59:43,309 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:59Z] INFO  16:59:43,630 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:59Z] INFO  16:59:43,631 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:59Z] INFO  16:59:43,632 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:59Z] INFO  16:59:43,633 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:59Z] INFO  16:59:43,665 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:59Z] INFO  16:59:43,746 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-14T23:59Z] INFO  16:59:43,801 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:59Z] GATK: realign ('15', 67932890, 83447639) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-14T23:59Z] INFO  16:59:43,837 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:59Z] INFO  16:59:43,857 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:59Z] INFO  16:59:43,858 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:59Z] INFO  16:59:43,921 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-14T23:59Z] INFO  16:59:43,940 IntervalUtils - Processing 3487905 bp from intervals
[2016-04-14T23:59Z] INFO  16:59:44,014 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:59Z] INFO  16:59:44,315 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:59Z] INFO  16:59:44,317 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:59Z] INFO  16:59:44,318 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:59Z] INFO  16:59:44,318 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:59Z] INFO  16:59:44,331 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:59Z] INFO  16:59:44,373 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:59Z] INFO  16:59:44,553 ProgressMeter -            done    343500.0    22.0 s      65.0 s      100.0%    22.0 s       0.0 s
[2016-04-14T23:59Z] INFO  16:59:44,554 ProgressMeter - Total runtime 22.51 secs, 0.38 min, 0.01 hours
[2016-04-14T23:59Z] INFO  16:59:44,557 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 343500 total reads (0.00%)
[2016-04-14T23:59Z] INFO  16:59:44,558 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:59Z] INFO  16:59:44,558 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:59Z] INFO  16:59:44,558 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:59Z] INFO  16:59:44,709 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@5fe152b7
[2016-04-14T23:59Z] INFO  16:59:44,804 ProgressMeter -            done    370924.0    44.0 s     119.0 s      100.0%    44.0 s       0.0 s
[2016-04-14T23:59Z] INFO  16:59:44,805 ProgressMeter - Total runtime 44.49 secs, 0.74 min, 0.01 hours
[2016-04-14T23:59Z] INFO  16:59:44,805 MicroScheduler - 194 reads were filtered out during the traversal out of approximately 371118 total reads (0.05%)
[2016-04-14T23:59Z] INFO  16:59:44,806 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:59Z] INFO  16:59:44,806 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:59Z] INFO  16:59:44,806 MicroScheduler -   -> 194 reads (0.05% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:59Z] INFO  16:59:46,167 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:59Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-16_46633742_64982002-prep-prealign.bam
[2016-04-14T23:59Z] INFO  16:59:46,228 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:59Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-15_83448996_98982979-prep.bam
[2016-04-14T23:59Z] INFO  16:59:46,519 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:59Z] INFO  16:59:46,522 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:59Z] INFO  16:59:46,522 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:59Z] INFO  16:59:46,523 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:59Z] INFO  16:59:46,527 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/15/R14-18105_kapa-NGv3-PE100-NGv3-sort-15_67932890_83447639-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/15/R14-18105_kapa-NGv3-PE100-NGv3-sort-15_67932890_83447639-prep-prealign-realign.intervals -L 15:67932891-83447639 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/15/tx/tmpGtzSpL/R14-18105_kapa-NGv3-PE100-NGv3-sort-15_67932890_83447639-prep.bam
[2016-04-14T23:59Z] INFO  16:59:46,535 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:59Z] INFO  16:59:46,536 HelpFormatter - Date/Time: 2016/04/14 16:59:46
[2016-04-14T23:59Z] INFO  16:59:46,536 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:59Z] INFO  16:59:46,537 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:59Z] INFO  16:59:46,738 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:59Z] INFO  16:59:46,854 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:59Z] INFO  16:59:46,865 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:59Z] INFO  16:59:46,923 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-14T23:59Z] INFO  16:59:47,253 IntervalUtils - Processing 15514749 bp from intervals
[2016-04-14T23:59Z] WARN  16:59:47,258 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:59Z] GATK pre-alignment ('18', 0, 18531348) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-14T23:59Z] INFO  16:59:47,359 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:59Z] GATK RealignerTargetCreator: R14-18105_kapa-NGv3-PE100-NGv3-sort-16_46633742_64982002-prep-prealign.bam 16:46633743-64982002
[2016-04-14T23:59Z] GATK: RealignerTargetCreator
[2016-04-14T23:59Z] INFO  16:59:47,497 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:59Z] INFO  16:59:47,498 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:59Z] INFO  16:59:47,498 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:59Z] INFO  16:59:47,499 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:59Z] INFO  16:59:47,733 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:59Z] INFO  16:59:47,930 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:59Z] INFO  16:59:48,356 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@41fd9d8e
[2016-04-14T23:59Z] INFO  16:59:48,476 ProgressMeter -            done    376548.0    46.0 s       2.0 m       98.9%    46.0 s       0.0 s
[2016-04-14T23:59Z] INFO  16:59:48,476 ProgressMeter - Total runtime 46.10 secs, 0.77 min, 0.01 hours
[2016-04-14T23:59Z] INFO  16:59:48,477 MicroScheduler - 145 reads were filtered out during the traversal out of approximately 376693 total reads (0.04%)
[2016-04-14T23:59Z] INFO  16:59:48,477 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:59Z] INFO  16:59:48,478 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:59Z] INFO  16:59:48,478 MicroScheduler -   -> 145 reads (0.04% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:59Z] INFO  16:59:50,067 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:59Z] INFO  16:59:50,070 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:59Z] INFO  16:59:50,071 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:59Z] INFO  16:59:50,071 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:59Z] INFO  16:59:50,076 HelpFormatter - Program Args: -T PrintReads -L 18:1-18531348 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/18/tx/tmpSMstLP/R14-18105_kapa-NGv3-PE100-NGv3-sort-18_0_18531348-prep-prealign.bam
[2016-04-14T23:59Z] INFO  16:59:50,085 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:59Z] INFO  16:59:50,086 HelpFormatter - Date/Time: 2016/04/14 16:59:50
[2016-04-14T23:59Z] INFO  16:59:50,087 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:59Z] INFO  16:59:50,087 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:59Z] INFO  16:59:50,197 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:59Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-16_80575258_90354753-prep-prealign.bam
[2016-04-14T23:59Z] INFO  16:59:50,260 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:59Z] INFO  16:59:50,448 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:59Z] INFO  16:59:50,452 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:59Z] INFO  16:59:50,452 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:59Z] INFO  16:59:50,453 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:59Z] INFO  16:59:50,458 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/16/R14-18105_kapa-NGv3-PE100-NGv3-sort-16_46633742_64982002-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/16/tx/tmpuvzOin/R14-18105_kapa-NGv3-PE100-NGv3-sort-16_46633742_64982002-prep-prealign-realign.intervals -l INFO -L 16:46633743-64982002 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-14T23:59Z] INFO  16:59:50,467 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:59Z] INFO  16:59:50,475 HelpFormatter - Date/Time: 2016/04/14 16:59:50
[2016-04-14T23:59Z] INFO  16:59:50,476 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:59Z] INFO  16:59:50,476 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:59Z] INFO  16:59:50,561 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:59Z] INFO  16:59:50,744 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-14T23:59Z] INFO  16:59:50,753 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:59Z] INFO  16:59:50,817 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-14T23:59Z] INFO  16:59:51,123 IntervalUtils - Processing 18348260 bp from intervals
[2016-04-14T23:59Z] WARN  16:59:51,129 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:59Z] INFO  16:59:51,195 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:59Z] INFO  16:59:51,472 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:59Z] INFO  16:59:51,473 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:59Z] INFO  16:59:51,474 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:59Z] INFO  16:59:51,474 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-14T23:59Z] GATK RealignerTargetCreator: R14-18105_kapa-NGv3-PE100-NGv3-sort-16_80575258_90354753-prep-prealign.bam 16:80575259-90354753
[2016-04-14T23:59Z] GATK: RealignerTargetCreator
[2016-04-14T23:59Z] INFO  16:59:51,505 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-14T23:59Z] INFO  16:59:51,605 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:59Z] INFO  16:59:51,626 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:59Z] INFO  16:59:51,685 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-14T23:59Z] INFO  16:59:51,700 IntervalUtils - Processing 18531348 bp from intervals
[2016-04-14T23:59Z] INFO  16:59:51,784 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:59Z] INFO  16:59:52,050 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:59Z] INFO  16:59:52,052 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:59Z] INFO  16:59:52,052 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:59Z] INFO  16:59:52,053 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:59Z] INFO  16:59:52,067 ReadShardBalancer$1 - Loading BAM index data
[2016-04-14T23:59Z] INFO  16:59:52,284 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-14T23:59Z] INFO  16:59:52,602 ProgressMeter -            done    117605.0    10.0 s      88.0 s      100.0%    10.0 s       0.0 s
[2016-04-14T23:59Z] INFO  16:59:52,602 ProgressMeter - Total runtime 10.47 secs, 0.17 min, 0.00 hours
[2016-04-14T23:59Z] INFO  16:59:52,606 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 117605 total reads (0.00%)
[2016-04-14T23:59Z] INFO  16:59:52,607 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:59Z] INFO  16:59:52,607 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:59Z] INFO  16:59:52,607 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:59Z] INFO  16:59:52,972 ProgressMeter -            done    477814.0    30.0 s      62.0 s      100.0%    30.0 s       0.0 s
[2016-04-14T23:59Z] INFO  16:59:52,973 ProgressMeter - Total runtime 30.06 secs, 0.50 min, 0.01 hours
[2016-04-14T23:59Z] INFO  16:59:52,977 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 477814 total reads (0.00%)
[2016-04-14T23:59Z] INFO  16:59:52,979 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:59Z] INFO  16:59:52,980 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:59Z] INFO  16:59:52,980 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:59Z] INFO  16:59:54,290 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:59Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-16_31120544_46629582-prep.bam
[2016-04-14T23:59Z] INFO  16:59:54,671 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:59Z] INFO  16:59:54,674 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:59Z] INFO  16:59:54,674 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:59Z] INFO  16:59:54,674 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:59Z] INFO  16:59:54,678 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/16/R14-18105_kapa-NGv3-PE100-NGv3-sort-16_80575258_90354753-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/16/tx/tmpQdAZdv/R14-18105_kapa-NGv3-PE100-NGv3-sort-16_80575258_90354753-prep-prealign-realign.intervals -l INFO -L 16:80575259-90354753 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-14T23:59Z] INFO  16:59:54,705 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:59Z] INFO  16:59:54,705 HelpFormatter - Date/Time: 2016/04/14 16:59:54
[2016-04-14T23:59Z] INFO  16:59:54,705 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:59Z] INFO  16:59:54,705 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:59Z] INFO  16:59:54,797 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:59Z] INFO  16:59:54,819 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:59Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-15_20741621_36872162-prep.bam
[2016-04-14T23:59Z] GATK pre-alignment ('18', 18533538, 34081962) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-14T23:59Z] INFO  16:59:54,906 ProgressMeter -      16:4513737    500010.0    91.0 s       3.1 m       29.1%     5.2 m       3.7 m
[2016-04-14T23:59Z] INFO  16:59:55,055 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-14T23:59Z] INFO  16:59:55,074 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:59Z] INFO  16:59:55,138 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-14T23:59Z] INFO  16:59:55,450 IntervalUtils - Processing 9779495 bp from intervals
[2016-04-14T23:59Z] WARN  16:59:55,463 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-14T23:59Z] INFO  16:59:55,546 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:59Z] INFO  16:59:55,731 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:59Z] INFO  16:59:55,732 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:59Z] INFO  16:59:55,733 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:59Z] INFO  16:59:55,734 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-14T23:59Z] GATK pre-alignment ('18', 34092400, 49867248) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-14T23:59Z] INFO  16:59:56,240 ProgressMeter -     17:34803577    100002.0    30.0 s       5.0 m       24.1%     2.1 m      94.0 s
[2016-04-14T23:59Z] INFO  16:59:57,113 ProgressMeter -            done   1.5515084E7    26.0 s       1.0 s      100.0%    26.0 s       0.0 s
[2016-04-14T23:59Z] INFO  16:59:57,114 ProgressMeter - Total runtime 26.50 secs, 0.44 min, 0.01 hours
[2016-04-14T23:59Z] INFO  16:59:57,118 MicroScheduler - 81905 reads were filtered out during the traversal out of approximately 612799 total reads (13.37%)
[2016-04-14T23:59Z] INFO  16:59:57,119 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-14T23:59Z] INFO  16:59:57,120 MicroScheduler -   -> 1121 reads (0.18% of total) failing BadMateFilter
[2016-04-14T23:59Z] INFO  16:59:57,121 MicroScheduler -   -> 45169 reads (7.37% of total) failing DuplicateReadFilter
[2016-04-14T23:59Z] INFO  16:59:57,121 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-14T23:59Z] INFO  16:59:57,122 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-14T23:59Z] INFO  16:59:57,123 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-14T23:59Z] INFO  16:59:57,123 MicroScheduler -   -> 35615 reads (5.81% of total) failing MappingQualityZeroFilter
[2016-04-14T23:59Z] INFO  16:59:57,124 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-14T23:59Z] INFO  16:59:57,124 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-14T23:59Z] INFO  16:59:57,125 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-14T23:59Z] INFO  16:59:58,016 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:59Z] INFO  16:59:58,019 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:59Z] INFO  16:59:58,020 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:59Z] INFO  16:59:58,020 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:59Z] INFO  16:59:58,025 HelpFormatter - Program Args: -T PrintReads -L 18:18533539-34081962 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/18/tx/tmpyD9eo5/R14-18105_kapa-NGv3-PE100-NGv3-sort-18_18533538_34081962-prep-prealign.bam
[2016-04-14T23:59Z] INFO  16:59:58,042 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:59Z] INFO  16:59:58,042 HelpFormatter - Date/Time: 2016/04/14 16:59:58
[2016-04-14T23:59Z] INFO  16:59:58,042 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:59Z] INFO  16:59:58,043 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:59Z] INFO  16:59:58,231 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:59Z] INFO  16:59:58,482 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-14T23:59Z] GATK: realign ('15', 36887086, 52402170) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-14T23:59Z] INFO  16:59:59,031 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:59Z] INFO  16:59:59,034 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-14T23:59Z] INFO  16:59:59,034 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-14T23:59Z] INFO  16:59:59,035 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-14T23:59Z] INFO  16:59:59,040 HelpFormatter - Program Args: -T PrintReads -L 18:34092401-49867248 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/18/tx/tmpnF5mgb/R14-18105_kapa-NGv3-PE100-NGv3-sort-18_34092400_49867248-prep-prealign.bam
[2016-04-14T23:59Z] INFO  16:59:59,058 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-14T23:59Z] INFO  16:59:59,059 HelpFormatter - Date/Time: 2016/04/14 16:59:59
[2016-04-14T23:59Z] INFO  16:59:59,060 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:59Z] INFO  16:59:59,060 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-14T23:59Z] INFO  16:59:59,278 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-14T23:59Z] INFO  16:59:59,358 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-14T23:59Z] INFO  16:59:59,434 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-14T23:59Z] INFO  16:59:59,443 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-14T23:59Z] INFO  16:59:59,513 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-14T23:59Z] INFO  16:59:59,541 IntervalUtils - Processing 15548424 bp from intervals
[2016-04-14T23:59Z] INFO  16:59:59,618 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-14T23:59Z] INFO  16:59:59,909 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-14T23:59Z] INFO  16:59:59,911 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-14T23:59Z] INFO  16:59:59,911 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-14T23:59Z] INFO  16:59:59,912 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-14T23:59Z] INFO  16:59:59,927 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:00Z] INFO  17:00:00,069 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:00Z] INFO  17:00:00,488 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-15T00:00Z] INFO  17:00:00,539 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:00Z] INFO  17:00:00,548 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:00Z] INFO  17:00:00,573 ProgressMeter -     17:54939260    200003.0    30.0 s       2.5 m       53.7%    55.0 s      25.0 s
[2016-04-15T00:00Z] INFO  17:00:00,619 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-15T00:00Z] INFO  17:00:00,644 IntervalUtils - Processing 15774848 bp from intervals
[2016-04-15T00:00Z] INFO  17:00:00,804 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:00Z] INFO  17:00:01,090 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:00Z] INFO  17:00:01,091 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:00Z] INFO  17:00:01,092 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:00Z] INFO  17:00:01,092 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:00Z] INFO  17:00:01,106 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:00Z] INFO  17:00:01,245 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:00Z] INFO  17:00:01,370 ProgressMeter -     16:28875182    700032.0    92.0 s       2.2 m       85.6%   107.0 s      15.0 s
[2016-04-15T00:00Z] INFO  17:00:01,449 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:00Z] INFO  17:00:01,453 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:00Z] INFO  17:00:01,453 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:00Z] INFO  17:00:01,454 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:00Z] INFO  17:00:01,459 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/15/R14-18105_kapa-NGv3-PE100-NGv3-sort-15_36887086_52402170-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/15/R14-18105_kapa-NGv3-PE100-NGv3-sort-15_36887086_52402170-prep-prealign-realign.intervals -L 15:36887087-52402170 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/15/tx/tmp28pWe2/R14-18105_kapa-NGv3-PE100-NGv3-sort-15_36887086_52402170-prep.bam
[2016-04-15T00:00Z] INFO  17:00:01,467 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:00Z] INFO  17:00:01,468 HelpFormatter - Date/Time: 2016/04/14 17:00:01
[2016-04-15T00:00Z] INFO  17:00:01,468 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:00Z] INFO  17:00:01,469 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:00Z] INFO  17:00:01,683 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:00Z] INFO  17:00:01,780 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:00Z] INFO  17:00:01,790 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:00Z] INFO  17:00:01,862 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-15T00:00Z] INFO  17:00:02,271 IntervalUtils - Processing 15515084 bp from intervals
[2016-04-15T00:00Z] WARN  17:00:02,276 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:00Z] INFO  17:00:02,359 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:00Z] INFO  17:00:02,405 ProgressMeter -     16:72094617    400008.0    60.0 s       2.5 m       45.6%     2.2 m      71.0 s
[2016-04-15T00:00Z] INFO  17:00:02,481 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:00Z] INFO  17:00:02,482 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:00Z] INFO  17:00:02,482 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:00Z] INFO  17:00:02,483 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:00Z] INFO  17:00:02,673 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:00Z] INFO  17:00:02,904 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:00Z] INFO  17:00:10,601 ProgressMeter -      17:7213639    500012.0    60.0 s       2.0 m       46.5%     2.2 m      69.0 s
[2016-04-15T00:00Z] INFO  17:00:12,227 ProgressMeter -     17:27241148    400006.0    60.0 s       2.5 m       75.5%    79.0 s      19.0 s
[2016-04-15T00:00Z] INFO  17:00:13,448 ProgressMeter -            done   9779495.0    17.0 s       1.0 s      100.0%    17.0 s       0.0 s
[2016-04-15T00:00Z] INFO  17:00:13,449 ProgressMeter - Total runtime 17.72 secs, 0.30 min, 0.00 hours
[2016-04-15T00:00Z] INFO  17:00:13,450 MicroScheduler - 34995 reads were filtered out during the traversal out of approximately 378852 total reads (9.24%)
[2016-04-15T00:00Z] INFO  17:00:13,451 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:00Z] INFO  17:00:13,452 MicroScheduler -   -> 727 reads (0.19% of total) failing BadMateFilter
[2016-04-15T00:00Z] INFO  17:00:13,452 MicroScheduler -   -> 30539 reads (8.06% of total) failing DuplicateReadFilter
[2016-04-15T00:00Z] INFO  17:00:13,453 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:00Z] INFO  17:00:13,453 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:00Z] INFO  17:00:13,454 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:00Z] INFO  17:00:13,455 MicroScheduler -   -> 3729 reads (0.98% of total) failing MappingQualityZeroFilter
[2016-04-15T00:00Z] INFO  17:00:13,455 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:00Z] INFO  17:00:13,456 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-15T00:00Z] INFO  17:00:13,457 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:00Z] INFO  17:00:13,754 ProgressMeter -     17:71443773    100001.0    30.0 s       5.0 m       59.8%    50.0 s      20.0 s
[2016-04-15T00:00Z] INFO  17:00:14,898 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:00Z] GATK: realign ('16', 80575258, 90354753) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-15T00:00Z] INFO  17:00:15,419 ProgressMeter -     17:79873296    100004.0    31.0 s       5.2 m       62.1%    49.0 s      18.0 s
[2016-04-15T00:00Z] INFO  17:00:15,644 ProgressMeter -            done   1.834826E7    24.0 s       1.0 s      100.0%    24.0 s       0.0 s
[2016-04-15T00:00Z] INFO  17:00:15,645 ProgressMeter - Total runtime 24.17 secs, 0.40 min, 0.01 hours
[2016-04-15T00:00Z] INFO  17:00:15,671 MicroScheduler - 33068 reads were filtered out during the traversal out of approximately 373359 total reads (8.86%)
[2016-04-15T00:00Z] INFO  17:00:15,673 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:00Z] INFO  17:00:15,673 MicroScheduler -   -> 865 reads (0.23% of total) failing BadMateFilter
[2016-04-15T00:00Z] INFO  17:00:15,674 MicroScheduler -   -> 29504 reads (7.90% of total) failing DuplicateReadFilter
[2016-04-15T00:00Z] INFO  17:00:15,675 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:00Z] INFO  17:00:15,676 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:00Z] INFO  17:00:15,677 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:00Z] INFO  17:00:15,677 MicroScheduler -   -> 2699 reads (0.72% of total) failing MappingQualityZeroFilter
[2016-04-15T00:00Z] INFO  17:00:15,678 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:00Z] INFO  17:00:15,679 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-15T00:00Z] INFO  17:00:15,680 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:00Z] INFO  17:00:17,134 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:00Z] GATK: realign ('16', 46633742, 64982002) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-15T00:00Z] INFO  17:00:18,172 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:00Z] INFO  17:00:18,176 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:00Z] INFO  17:00:18,177 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:00Z] INFO  17:00:18,178 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:00Z] INFO  17:00:18,183 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/16/R14-18105_kapa-NGv3-PE100-NGv3-sort-16_80575258_90354753-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/16/R14-18105_kapa-NGv3-PE100-NGv3-sort-16_80575258_90354753-prep-prealign-realign.intervals -L 16:80575259-90354753 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/16/tx/tmpG77eR0/R14-18105_kapa-NGv3-PE100-NGv3-sort-16_80575258_90354753-prep.bam
[2016-04-15T00:00Z] INFO  17:00:18,212 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:00Z] INFO  17:00:18,213 HelpFormatter - Date/Time: 2016/04/14 17:00:18
[2016-04-15T00:00Z] INFO  17:00:18,213 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:00Z] INFO  17:00:18,214 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:00Z] INFO  17:00:18,298 ProgressMeter -     15:80253586    400007.0    30.0 s      76.0 s       79.4%    37.0 s       7.0 s
[2016-04-15T00:00Z] INFO  17:00:18,440 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:00Z] INFO  17:00:18,575 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:00Z] INFO  17:00:18,584 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:00Z] INFO  17:00:18,677 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.09
[2016-04-15T00:00Z] INFO  17:00:19,146 IntervalUtils - Processing 9779495 bp from intervals
[2016-04-15T00:00Z] WARN  17:00:19,151 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:00Z] INFO  17:00:19,286 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:00Z] INFO  17:00:19,435 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:00Z] INFO  17:00:19,436 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:00Z] INFO  17:00:19,437 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:00Z] INFO  17:00:19,438 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:00Z] INFO  17:00:19,592 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:00Z] INFO  17:00:19,755 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:00Z] INFO  17:00:19,994 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:00Z] INFO  17:00:19,998 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:00Z] INFO  17:00:19,998 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:00Z] INFO  17:00:19,999 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:00Z] INFO  17:00:20,003 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/16/R14-18105_kapa-NGv3-PE100-NGv3-sort-16_46633742_64982002-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/16/R14-18105_kapa-NGv3-PE100-NGv3-sort-16_46633742_64982002-prep-prealign-realign.intervals -L 16:46633743-64982002 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/16/tx/tmppQIDjd/R14-18105_kapa-NGv3-PE100-NGv3-sort-16_46633742_64982002-prep.bam
[2016-04-15T00:00Z] INFO  17:00:20,012 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:00Z] INFO  17:00:20,013 HelpFormatter - Date/Time: 2016/04/14 17:00:19
[2016-04-15T00:00Z] INFO  17:00:20,013 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:00Z] INFO  17:00:20,014 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:00Z] INFO  17:00:20,267 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:00Z] INFO  17:00:20,437 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:00Z] INFO  17:00:20,475 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:00Z] INFO  17:00:20,565 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.09
[2016-04-15T00:00Z] INFO  17:00:21,048 IntervalUtils - Processing 18348260 bp from intervals
[2016-04-15T00:00Z] WARN  17:00:21,064 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:00Z] INFO  17:00:21,190 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:00Z] INFO  17:00:21,379 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:00Z] INFO  17:00:21,381 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:00Z] INFO  17:00:21,381 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:00Z] INFO  17:00:21,382 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:00Z] INFO  17:00:21,520 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:00Z] INFO  17:00:21,736 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:00Z] INFO  17:00:22,086 ProgressMeter -     18:12999500    200006.0    30.0 s       2.5 m       70.1%    42.0 s      12.0 s
[2016-04-15T00:00Z] INFO  17:00:22,587 ProgressMeter -            done    565258.0    35.0 s      62.0 s      100.0%    35.0 s       0.0 s
[2016-04-15T00:00Z] INFO  17:00:22,588 ProgressMeter - Total runtime 35.09 secs, 0.58 min, 0.01 hours
[2016-04-15T00:00Z] INFO  17:00:22,592 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 565258 total reads (0.00%)
[2016-04-15T00:00Z] INFO  17:00:22,592 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:00Z] INFO  17:00:22,592 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:00Z] INFO  17:00:22,593 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:00Z] INFO  17:00:24,084 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:00Z] INFO  17:00:24,096 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@41fd9d8e
[2016-04-15T00:00Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-15_67932890_83447639-prep.bam
[2016-04-15T00:00Z] INFO  17:00:24,193 ProgressMeter -            done    699927.0    82.0 s     117.0 s      100.0%    82.0 s       0.0 s
[2016-04-15T00:00Z] INFO  17:00:24,194 ProgressMeter - Total runtime 82.02 secs, 1.37 min, 0.02 hours
[2016-04-15T00:00Z] INFO  17:00:24,194 MicroScheduler - 251 reads were filtered out during the traversal out of approximately 700178 total reads (0.04%)
[2016-04-15T00:00Z] INFO  17:00:24,194 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:00Z] INFO  17:00:24,195 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:00Z] INFO  17:00:24,195 MicroScheduler -   -> 251 reads (0.04% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:00Z] INFO  17:00:24,907 ProgressMeter -     16:14858674    800015.0     2.0 m       2.5 m       95.7%     2.1 m       5.0 s
[2016-04-15T00:00Z] INFO  17:00:25,448 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:00Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-16_64982511_80574976-prep-prealign.bam
[2016-04-15T00:00Z] INFO  17:00:25,669 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@7172f77a
[2016-04-15T00:00Z] INFO  17:00:25,741 ProgressMeter -            done    204821.0    25.0 s       2.1 m      100.0%    25.0 s       0.0 s
[2016-04-15T00:00Z] INFO  17:00:25,742 ProgressMeter - Total runtime 25.83 secs, 0.43 min, 0.01 hours
[2016-04-15T00:00Z] INFO  17:00:25,743 MicroScheduler - 136 reads were filtered out during the traversal out of approximately 204957 total reads (0.07%)
[2016-04-15T00:00Z] INFO  17:00:25,744 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:00Z] INFO  17:00:25,744 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:00Z] INFO  17:00:25,745 MicroScheduler -   -> 136 reads (0.07% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:00Z] GATK pre-alignment ('18', 50278423, 66344430) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-15T00:00Z] INFO  17:00:25,907 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@7172f77a
[2016-04-15T00:00Z] INFO  17:00:25,988 ProgressMeter -            done    267327.0    33.0 s       2.1 m      100.0%    33.0 s       0.0 s
[2016-04-15T00:00Z] INFO  17:00:25,988 ProgressMeter - Total runtime 33.94 secs, 0.57 min, 0.01 hours
[2016-04-15T00:00Z] INFO  17:00:25,989 MicroScheduler - 174 reads were filtered out during the traversal out of approximately 267501 total reads (0.07%)
[2016-04-15T00:00Z] INFO  17:00:25,989 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:00Z] INFO  17:00:25,990 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:00Z] INFO  17:00:25,990 MicroScheduler -   -> 174 reads (0.07% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:00Z] INFO  17:00:26,241 ProgressMeter -     17:37902187    300004.0    60.0 s       3.3 m       44.1%     2.3 m      76.0 s
[2016-04-15T00:00Z] INFO  17:00:26,501 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@7172f77a
[2016-04-15T00:00Z] INFO  17:00:26,616 ProgressMeter -            done    636094.0    74.0 s     117.0 s      100.0%    74.0 s       0.0 s
[2016-04-15T00:00Z] INFO  17:00:26,616 ProgressMeter - Total runtime 74.88 secs, 1.25 min, 0.02 hours
[2016-04-15T00:00Z] INFO  17:00:26,617 MicroScheduler - 262 reads were filtered out during the traversal out of approximately 636356 total reads (0.04%)
[2016-04-15T00:00Z] INFO  17:00:26,617 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:00Z] INFO  17:00:26,617 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:00Z] INFO  17:00:26,618 MicroScheduler -   -> 262 reads (0.04% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:00Z] INFO  17:00:27,017 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:00Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-18_18533538_34081962-prep-prealign.bam
[2016-04-15T00:00Z] INFO  17:00:27,382 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:00Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-18_0_18531348-prep-prealign.bam
[2016-04-15T00:00Z] GATK RealignerTargetCreator: R14-18105_kapa-NGv3-PE100-NGv3-sort-18_18533538_34081962-prep-prealign.bam 18:18533539-34081962
[2016-04-15T00:00Z] GATK: RealignerTargetCreator
[2016-04-15T00:00Z] GATK RealignerTargetCreator: R14-18105_kapa-NGv3-PE100-NGv3-sort-16_64982511_80574976-prep-prealign.bam 16:64982512-80574976
[2016-04-15T00:00Z] GATK: RealignerTargetCreator
[2016-04-15T00:00Z] INFO  17:00:28,138 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:00Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-17_15515955_31039213-prep-prealign.bam
[2016-04-15T00:00Z] GATK RealignerTargetCreator: R14-18105_kapa-NGv3-PE100-NGv3-sort-18_0_18531348-prep-prealign.bam 18:1-18531348
[2016-04-15T00:00Z] GATK: RealignerTargetCreator
[2016-04-15T00:00Z] INFO  17:00:28,589 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:00Z] INFO  17:00:28,593 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:00Z] INFO  17:00:28,594 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:00Z] INFO  17:00:28,594 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:00Z] INFO  17:00:28,600 HelpFormatter - Program Args: -T PrintReads -L 18:50278424-66344430 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/18/tx/tmpJhrDZ1/R14-18105_kapa-NGv3-PE100-NGv3-sort-18_50278423_66344430-prep-prealign.bam
[2016-04-15T00:00Z] INFO  17:00:28,611 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:00Z] INFO  17:00:28,622 HelpFormatter - Date/Time: 2016/04/14 17:00:28
[2016-04-15T00:00Z] INFO  17:00:28,623 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:00Z] INFO  17:00:28,624 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:00Z] INFO  17:00:28,880 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:00Z] INFO  17:00:29,360 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@41fd9d8e
[2016-04-15T00:00Z] INFO  17:00:29,476 ProgressMeter -            done    299528.0    45.0 s       2.5 m       95.9%    46.0 s       1.0 s
[2016-04-15T00:00Z] INFO  17:00:29,476 ProgressMeter - Total runtime 45.16 secs, 0.75 min, 0.01 hours
[2016-04-15T00:00Z] INFO  17:00:29,477 MicroScheduler - 102 reads were filtered out during the traversal out of approximately 299630 total reads (0.03%)
[2016-04-15T00:00Z] INFO  17:00:29,477 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:00Z] INFO  17:00:29,477 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:00Z] INFO  17:00:29,478 MicroScheduler -   -> 102 reads (0.03% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:00Z] INFO  17:00:29,894 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-15T00:00Z] INFO  17:00:29,955 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:00Z] INFO  17:00:29,965 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:00Z] INFO  17:00:30,020 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-15T00:00Z] INFO  17:00:30,053 IntervalUtils - Processing 16066007 bp from intervals
[2016-04-15T00:00Z] INFO  17:00:30,119 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@5fe152b7
[2016-04-15T00:00Z] INFO  17:00:30,139 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:00Z] INFO  17:00:30,199 ProgressMeter -            done    230183.0    29.0 s       2.1 m      100.0%    29.0 s       0.0 s
[2016-04-15T00:00Z] INFO  17:00:30,200 ProgressMeter - Total runtime 29.11 secs, 0.49 min, 0.01 hours
[2016-04-15T00:00Z] INFO  17:00:30,201 MicroScheduler - 185 reads were filtered out during the traversal out of approximately 230368 total reads (0.08%)
[2016-04-15T00:00Z] INFO  17:00:30,201 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:00Z] INFO  17:00:30,202 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:00Z] INFO  17:00:30,203 MicroScheduler -   -> 185 reads (0.08% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:00Z] INFO  17:00:30,383 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:00Z] INFO  17:00:30,384 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:00Z] INFO  17:00:30,384 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:00Z] INFO  17:00:30,385 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:00Z] INFO  17:00:30,398 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:00Z] GATK RealignerTargetCreator: R14-18105_kapa-NGv3-PE100-NGv3-sort-17_15515955_31039213-prep-prealign.bam 17:15515956-31039213
[2016-04-15T00:00Z] GATK: RealignerTargetCreator
[2016-04-15T00:00Z] INFO  17:00:30,618 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:00Z] INFO  17:00:30,689 ProgressMeter -     17:62007469    500008.0    60.0 s     120.0 s       99.3%    60.0 s       0.0 s
[2016-04-15T00:00Z] INFO  17:00:30,966 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:00Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-17_77707305_81195210-prep-prealign.bam
[2016-04-15T00:00Z] INFO  17:00:31,272 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:00Z] INFO  17:00:31,276 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:00Z] INFO  17:00:31,277 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:00Z] INFO  17:00:31,277 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:00Z] INFO  17:00:31,277 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:00Z] INFO  17:00:31,282 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:00Z] INFO  17:00:31,283 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:00Z] INFO  17:00:31,284 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:00Z] INFO  17:00:31,299 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/16/R14-18105_kapa-NGv3-PE100-NGv3-sort-16_64982511_80574976-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/16/tx/tmp2RvRFe/R14-18105_kapa-NGv3-PE100-NGv3-sort-16_64982511_80574976-prep-prealign-realign.intervals -l INFO -L 16:64982512-80574976 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:00Z] INFO  17:00:31,297 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/18/R14-18105_kapa-NGv3-PE100-NGv3-sort-18_0_18531348-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/18/tx/tmp6v7sBD/R14-18105_kapa-NGv3-PE100-NGv3-sort-18_0_18531348-prep-prealign-realign.intervals -l INFO -L 18:1-18531348 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:00Z] INFO  17:00:31,315 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:00Z] INFO  17:00:31,319 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:00Z] INFO  17:00:31,320 HelpFormatter - Date/Time: 2016/04/14 17:00:31
[2016-04-15T00:00Z] INFO  17:00:31,321 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:00Z] INFO  17:00:31,322 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:00Z] INFO  17:00:31,337 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:00Z] INFO  17:00:31,340 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:00Z] INFO  17:00:31,341 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:00Z] INFO  17:00:31,341 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:00Z] INFO  17:00:31,342 HelpFormatter - Date/Time: 2016/04/14 17:00:31
[2016-04-15T00:00Z] INFO  17:00:31,343 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:00Z] INFO  17:00:31,344 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:00Z] INFO  17:00:31,346 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/18/R14-18105_kapa-NGv3-PE100-NGv3-sort-18_18533538_34081962-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/18/tx/tmpNmh3nA/R14-18105_kapa-NGv3-PE100-NGv3-sort-18_18533538_34081962-prep-prealign-realign.intervals -l INFO -L 18:18533539-34081962 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:00Z] INFO  17:00:31,372 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:00Z] INFO  17:00:31,382 HelpFormatter - Date/Time: 2016/04/14 17:00:31
[2016-04-15T00:00Z] INFO  17:00:31,383 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:00Z] INFO  17:00:31,383 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:00Z] INFO  17:00:31,439 ProgressMeter -     16:30238369   1000045.0     2.0 m       2.0 m       94.4%     2.2 m       7.0 s
[2016-04-15T00:00Z] INFO  17:00:31,458 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:00Z] INFO  17:00:31,518 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:00Z] INFO  17:00:31,543 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:00Z] INFO  17:00:31,741 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T00:00Z] INFO  17:00:31,750 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T00:00Z] INFO  17:00:31,760 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:00Z] INFO  17:00:31,760 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:00Z] INFO  17:00:31,757 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:00Z] INFO  17:00:31,786 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T00:00Z] INFO  17:00:31,796 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:00Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-18_34092400_49867248-prep-prealign.bam
[2016-04-15T00:00Z] INFO  17:00:31,827 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-15T00:00Z] INFO  17:00:31,833 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-15T00:00Z] INFO  17:00:31,849 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-15T00:00Z] GATK RealignerTargetCreator: R14-18105_kapa-NGv3-PE100-NGv3-sort-17_77707305_81195210-prep-prealign.bam 17:77707306-81195210
[2016-04-15T00:00Z] GATK: RealignerTargetCreator
[2016-04-15T00:00Z] INFO  17:00:32,129 IntervalUtils - Processing 15548424 bp from intervals
[2016-04-15T00:00Z] WARN  17:00:32,134 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:00Z] INFO  17:00:32,186 IntervalUtils - Processing 15592465 bp from intervals
[2016-04-15T00:00Z] WARN  17:00:32,202 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:00Z] INFO  17:00:32,240 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:00Z] INFO  17:00:32,256 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@41fd9d8e
[2016-04-15T00:00Z] INFO  17:00:32,281 IntervalUtils - Processing 18531348 bp from intervals
[2016-04-15T00:00Z] WARN  17:00:32,286 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:00Z] INFO  17:00:32,341 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:00Z] INFO  17:00:32,368 ProgressMeter -            done    520757.0    61.0 s     118.0 s      100.0%    61.0 s       0.0 s
[2016-04-15T00:00Z] INFO  17:00:32,369 ProgressMeter - Total runtime 61.83 secs, 1.03 min, 0.02 hours
[2016-04-15T00:00Z] INFO  17:00:32,369 MicroScheduler - 249 reads were filtered out during the traversal out of approximately 521006 total reads (0.05%)
[2016-04-15T00:00Z] INFO  17:00:32,369 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:00Z] INFO  17:00:32,370 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:00Z] INFO  17:00:32,370 MicroScheduler -   -> 249 reads (0.05% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:00Z] INFO  17:00:32,376 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:00Z] INFO  17:00:32,470 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:00Z] INFO  17:00:32,472 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:00Z] INFO  17:00:32,472 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:00Z] INFO  17:00:32,473 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:00Z] INFO  17:00:32,530 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:00Z] INFO  17:00:32,531 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:00Z] INFO  17:00:32,532 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:00Z] INFO  17:00:32,533 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:00Z] GATK RealignerTargetCreator: R14-18105_kapa-NGv3-PE100-NGv3-sort-18_34092400_49867248-prep-prealign.bam 18:34092401-49867248
[2016-04-15T00:00Z] GATK: RealignerTargetCreator
[2016-04-15T00:00Z] INFO  17:00:32,605 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:00Z] INFO  17:00:32,606 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:00Z] INFO  17:00:32,607 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:00Z] INFO  17:00:32,608 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:00Z] INFO  17:00:33,473 ProgressMeter -     15:45387865    400005.0    30.0 s      77.0 s       54.8%    54.0 s      24.0 s
[2016-04-15T00:00Z] INFO  17:00:33,672 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:00Z] INFO  17:00:33,675 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:00Z] INFO  17:00:33,675 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:00Z] INFO  17:00:33,675 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:00Z] INFO  17:00:33,679 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/17/R14-18105_kapa-NGv3-PE100-NGv3-sort-17_15515955_31039213-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/17/tx/tmpOGsZit/R14-18105_kapa-NGv3-PE100-NGv3-sort-17_15515955_31039213-prep-prealign-realign.intervals -l INFO -L 17:15515956-31039213 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:00Z] INFO  17:00:33,717 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:00Z] INFO  17:00:33,718 HelpFormatter - Date/Time: 2016/04/14 17:00:33
[2016-04-15T00:00Z] INFO  17:00:33,718 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:00Z] INFO  17:00:33,718 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:00Z] INFO  17:00:33,861 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:00Z] INFO  17:00:34,114 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T00:00Z] INFO  17:00:34,138 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:00Z] INFO  17:00:34,197 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-15T00:00Z] INFO  17:00:34,514 IntervalUtils - Processing 15523258 bp from intervals
[2016-04-15T00:00Z] WARN  17:00:34,526 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:00Z] INFO  17:00:34,604 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:00Z] INFO  17:00:34,618 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:00Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-17_46607689_62121560-prep-prealign.bam
[2016-04-15T00:00Z] INFO  17:00:34,821 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:00Z] INFO  17:00:34,822 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:00Z] INFO  17:00:34,829 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:00Z] INFO  17:00:34,836 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:00Z] INFO  17:00:35,399 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:00Z] INFO  17:00:35,404 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:00Z] INFO  17:00:35,405 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:00Z] INFO  17:00:35,405 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:00Z] INFO  17:00:35,409 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/17/R14-18105_kapa-NGv3-PE100-NGv3-sort-17_77707305_81195210-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/17/tx/tmpqhIgbj/R14-18105_kapa-NGv3-PE100-NGv3-sort-17_77707305_81195210-prep-prealign-realign.intervals -l INFO -L 17:77707306-81195210 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:00Z] INFO  17:00:35,451 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:00Z] INFO  17:00:35,452 HelpFormatter - Date/Time: 2016/04/14 17:00:35
[2016-04-15T00:00Z] INFO  17:00:35,452 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:00Z] INFO  17:00:35,452 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:00Z] INFO  17:00:35,537 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:00Z] INFO  17:00:35,540 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:00Z] INFO  17:00:35,541 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:00Z] INFO  17:00:35,541 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:00Z] INFO  17:00:35,546 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/18/R14-18105_kapa-NGv3-PE100-NGv3-sort-18_34092400_49867248-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/18/tx/tmpLTxh7T/R14-18105_kapa-NGv3-PE100-NGv3-sort-18_34092400_49867248-prep-prealign-realign.intervals -l INFO -L 18:34092401-49867248 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:00Z] INFO  17:00:35,558 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:00Z] INFO  17:00:35,559 HelpFormatter - Date/Time: 2016/04/14 17:00:35
[2016-04-15T00:00Z] INFO  17:00:35,559 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:00Z] INFO  17:00:35,559 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:00Z] INFO  17:00:35,588 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:00Z] INFO  17:00:35,656 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:00Z] INFO  17:00:35,799 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T00:00Z] INFO  17:00:35,831 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:00Z] INFO  17:00:35,891 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-15T00:00Z] INFO  17:00:35,898 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T00:00Z] INFO  17:00:35,919 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:00Z] INFO  17:00:35,983 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-15T00:00Z] GATK RealignerTargetCreator: R14-18105_kapa-NGv3-PE100-NGv3-sort-17_46607689_62121560-prep-prealign.bam 17:46607690-62121560
[2016-04-15T00:00Z] GATK: RealignerTargetCreator
[2016-04-15T00:00Z] INFO  17:00:36,204 IntervalUtils - Processing 3487905 bp from intervals
[2016-04-15T00:00Z] WARN  17:00:36,209 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:00Z] INFO  17:00:36,335 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:00Z] INFO  17:00:36,383 IntervalUtils - Processing 15774848 bp from intervals
[2016-04-15T00:00Z] WARN  17:00:36,399 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:00Z] INFO  17:00:36,433 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:00Z] INFO  17:00:36,434 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:00Z] INFO  17:00:36,434 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:00Z] INFO  17:00:36,435 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:00Z] INFO  17:00:36,534 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:00Z] INFO  17:00:36,834 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:00Z] INFO  17:00:36,835 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:00Z] INFO  17:00:36,836 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:00Z] INFO  17:00:36,837 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:00Z] INFO  17:00:38,453 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@7172f77a
[2016-04-15T00:00Z] INFO  17:00:38,553 ProgressMeter -            done    943828.0     2.3 m       2.4 m      100.0%     2.3 m       0.0 s
[2016-04-15T00:00Z] INFO  17:00:38,554 ProgressMeter - Total runtime 135.27 secs, 2.25 min, 0.04 hours
[2016-04-15T00:00Z] INFO  17:00:38,555 MicroScheduler - 393 reads were filtered out during the traversal out of approximately 944221 total reads (0.04%)
[2016-04-15T00:00Z] INFO  17:00:38,555 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:00Z] INFO  17:00:38,556 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:00Z] INFO  17:00:38,557 MicroScheduler -   -> 393 reads (0.04% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:00Z] INFO  17:00:39,011 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:00Z] INFO  17:00:39,014 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:00Z] INFO  17:00:39,015 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:00Z] INFO  17:00:39,015 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:00Z] INFO  17:00:39,020 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/17/R14-18105_kapa-NGv3-PE100-NGv3-sort-17_46607689_62121560-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/17/tx/tmptcHRjK/R14-18105_kapa-NGv3-PE100-NGv3-sort-17_46607689_62121560-prep-prealign-realign.intervals -l INFO -L 17:46607690-62121560 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:00Z] INFO  17:00:39,049 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:00Z] INFO  17:00:39,050 HelpFormatter - Date/Time: 2016/04/14 17:00:39
[2016-04-15T00:00Z] INFO  17:00:39,050 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:00Z] INFO  17:00:39,051 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:00Z] INFO  17:00:39,190 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:00Z] INFO  17:00:39,397 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T00:00Z] INFO  17:00:39,406 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:00Z] INFO  17:00:39,492 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.09
[2016-04-15T00:00Z] INFO  17:00:39,839 IntervalUtils - Processing 15513871 bp from intervals
[2016-04-15T00:00Z] WARN  17:00:39,844 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:00Z] INFO  17:00:39,948 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:00Z] INFO  17:00:40,077 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:00Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-16_0_15528616-prep-prealign.bam
[2016-04-15T00:00Z] INFO  17:00:40,118 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:00Z] INFO  17:00:40,120 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:00Z] INFO  17:00:40,120 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:00Z] INFO  17:00:40,121 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:00Z] INFO  17:00:40,602 ProgressMeter -     17:10231326    700015.0    90.0 s       2.2 m       66.0%     2.3 m      46.0 s
[2016-04-15T00:00Z] INFO  17:00:42,125 ProgressMeter -            done    609200.0    39.0 s      65.0 s      100.0%    39.0 s       0.0 s
[2016-04-15T00:00Z] INFO  17:00:42,125 ProgressMeter - Total runtime 39.64 secs, 0.66 min, 0.01 hours
[2016-04-15T00:00Z] INFO  17:00:42,129 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 609200 total reads (0.00%)
[2016-04-15T00:00Z] INFO  17:00:42,129 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:00Z] INFO  17:00:42,129 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:00Z] INFO  17:00:42,130 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:00Z] GATK RealignerTargetCreator: R14-18105_kapa-NGv3-PE100-NGv3-sort-16_0_15528616-prep-prealign.bam 16:1-15528616
[2016-04-15T00:00Z] GATK: RealignerTargetCreator
[2016-04-15T00:00Z] INFO  17:00:43,638 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:00Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-15_36887086_52402170-prep.bam
[2016-04-15T00:00Z] INFO  17:00:43,755 ProgressMeter -     17:74003787    300003.0    60.0 s       3.3 m       76.2%    78.0 s      18.0 s
[2016-04-15T00:00Z] GATK pre-alignment ('18', 66346699, 78077248) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-15T00:00Z] INFO  17:00:45,800 ProgressMeter -            done    376548.0    26.0 s      70.0 s       98.9%    26.0 s       0.0 s
[2016-04-15T00:00Z] INFO  17:00:45,801 ProgressMeter - Total runtime 26.36 secs, 0.44 min, 0.01 hours
[2016-04-15T00:00Z] INFO  17:00:45,804 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 376548 total reads (0.00%)
[2016-04-15T00:00Z] INFO  17:00:45,804 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:00Z] INFO  17:00:45,805 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:00Z] INFO  17:00:45,805 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:00Z] INFO  17:00:45,930 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:00Z] INFO  17:00:45,934 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:00Z] INFO  17:00:45,934 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:00Z] INFO  17:00:45,935 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:00Z] INFO  17:00:45,941 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/16/R14-18105_kapa-NGv3-PE100-NGv3-sort-16_0_15528616-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/16/tx/tmpky9DNB/R14-18105_kapa-NGv3-PE100-NGv3-sort-16_0_15528616-prep-prealign-realign.intervals -l INFO -L 16:1-15528616 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:00Z] INFO  17:00:45,952 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:00Z] INFO  17:00:45,953 HelpFormatter - Date/Time: 2016/04/14 17:00:45
[2016-04-15T00:00Z] INFO  17:00:45,953 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:00Z] INFO  17:00:45,954 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:00Z] INFO  17:00:46,068 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:00Z] INFO  17:00:46,302 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T00:00Z] INFO  17:00:46,314 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:00Z] INFO  17:00:46,374 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-15T00:00Z] INFO  17:00:46,709 IntervalUtils - Processing 15528616 bp from intervals
[2016-04-15T00:00Z] WARN  17:00:46,714 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:00Z] INFO  17:00:46,796 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:00Z] INFO  17:00:47,002 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:00Z] INFO  17:00:47,004 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:00Z] INFO  17:00:47,004 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:00Z] INFO  17:00:47,005 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:00Z] INFO  17:00:47,011 ProgressMeter -            done    370924.0    25.0 s      69.0 s      100.0%    25.0 s       0.0 s
[2016-04-15T00:00Z] INFO  17:00:47,011 ProgressMeter - Total runtime 25.63 secs, 0.43 min, 0.01 hours
[2016-04-15T00:00Z] INFO  17:00:47,015 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 370924 total reads (0.00%)
[2016-04-15T00:00Z] INFO  17:00:47,016 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:00Z] INFO  17:00:47,016 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:00Z] INFO  17:00:47,016 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:00Z] INFO  17:00:47,467 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:00Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-16_80575258_90354753-prep.bam
[2016-04-15T00:00Z] INFO  17:00:47,583 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@41fd9d8e
[2016-04-15T00:00Z] INFO  17:00:47,719 ProgressMeter -            done   1227333.0     2.3 m     113.0 s      100.0%     2.3 m       0.0 s
[2016-04-15T00:00Z] INFO  17:00:47,720 ProgressMeter - Total runtime 138.82 secs, 2.31 min, 0.04 hours
[2016-04-15T00:00Z] INFO  17:00:47,720 MicroScheduler - 434 reads were filtered out during the traversal out of approximately 1227767 total reads (0.04%)
[2016-04-15T00:00Z] INFO  17:00:47,721 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:00Z] INFO  17:00:47,721 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:00Z] INFO  17:00:47,722 MicroScheduler -   -> 434 reads (0.04% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:00Z] INFO  17:00:48,375 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:00Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-16_46633742_64982002-prep.bam
[2016-04-15T00:00Z] INFO  17:00:48,707 ProgressMeter -            done   3487905.0    12.0 s       3.0 s      100.0%    12.0 s       0.0 s
[2016-04-15T00:00Z] INFO  17:00:48,707 ProgressMeter - Total runtime 12.27 secs, 0.20 min, 0.00 hours
[2016-04-15T00:00Z] INFO  17:00:48,711 MicroScheduler - 25320 reads were filtered out during the traversal out of approximately 301276 total reads (8.40%)
[2016-04-15T00:00Z] INFO  17:00:48,712 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:00Z] INFO  17:00:48,713 MicroScheduler -   -> 514 reads (0.17% of total) failing BadMateFilter
[2016-04-15T00:00Z] INFO  17:00:48,714 MicroScheduler -   -> 24303 reads (8.07% of total) failing DuplicateReadFilter
[2016-04-15T00:00Z] INFO  17:00:48,715 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:00Z] INFO  17:00:48,715 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:00Z] INFO  17:00:48,716 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:00Z] INFO  17:00:48,717 MicroScheduler -   -> 503 reads (0.17% of total) failing MappingQualityZeroFilter
[2016-04-15T00:00Z] INFO  17:00:48,718 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:00Z] INFO  17:00:48,718 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-15T00:00Z] INFO  17:00:48,719 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:00Z] GATK pre-alignment ('19', 0, 15509577) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-15T00:00Z] INFO  17:00:49,073 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:00Z] INFO  17:00:49,076 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:00Z] INFO  17:00:49,077 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:00Z] INFO  17:00:49,078 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:00Z] INFO  17:00:49,083 HelpFormatter - Program Args: -T PrintReads -L 18:66346700-78077248 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/18/tx/tmpm8UR9T/R14-18105_kapa-NGv3-PE100-NGv3-sort-18_66346699_78077248-prep-prealign.bam
[2016-04-15T00:00Z] INFO  17:00:49,103 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:00Z] INFO  17:00:49,104 HelpFormatter - Date/Time: 2016/04/14 17:00:49
[2016-04-15T00:00Z] INFO  17:00:49,104 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:00Z] INFO  17:00:49,105 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:00Z] INFO  17:00:49,239 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:00Z] INFO  17:00:49,290 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:00Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-16_15596122_31106473-prep-prealign.bam
[2016-04-15T00:00Z] GATK pre-alignment ('19', 15510112, 31025906) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-15T00:00Z] INFO  17:00:50,234 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:00Z] GATK: realign ('17', 77707305, 81195210) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-15T00:00Z] INFO  17:00:50,729 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-15T00:00Z] INFO  17:00:50,833 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:00Z] INFO  17:00:50,843 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:00Z] INFO  17:00:50,917 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-15T00:00Z] INFO  17:00:50,941 IntervalUtils - Processing 11730549 bp from intervals
[2016-04-15T00:00Z] INFO  17:00:51,078 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:00Z] INFO  17:00:51,344 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:00Z] INFO  17:00:51,345 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:00Z] INFO  17:00:51,346 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:00Z] INFO  17:00:51,347 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:00Z] INFO  17:00:51,360 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:00Z] INFO  17:00:51,491 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:00Z] INFO  17:00:51,945 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:00Z] INFO  17:00:51,949 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:00Z] INFO  17:00:51,950 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:00Z] INFO  17:00:51,951 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:00Z] INFO  17:00:51,956 HelpFormatter - Program Args: -T PrintReads -L 19:1-15509577 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/19/tx/tmpmUxXpH/R14-18105_kapa-NGv3-PE100-NGv3-sort-19_0_15509577-prep-prealign.bam
[2016-04-15T00:00Z] INFO  17:00:51,976 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:00Z] INFO  17:00:51,977 HelpFormatter - Date/Time: 2016/04/14 17:00:51
[2016-04-15T00:00Z] INFO  17:00:51,977 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:00Z] INFO  17:00:51,978 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:00Z] INFO  17:00:52,188 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:00Z] INFO  17:00:52,555 ProgressMeter -            done   1.5548424E7    20.0 s       1.0 s      100.0%    20.0 s       0.0 s
[2016-04-15T00:00Z] INFO  17:00:52,556 ProgressMeter - Total runtime 20.08 secs, 0.33 min, 0.01 hours
[2016-04-15T00:00Z] INFO  17:00:52,560 MicroScheduler - 17576 reads were filtered out during the traversal out of approximately 206434 total reads (8.51%)
[2016-04-15T00:00Z] INFO  17:00:52,562 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:00Z] INFO  17:00:52,562 MicroScheduler -   -> 587 reads (0.28% of total) failing BadMateFilter
[2016-04-15T00:00Z] INFO  17:00:52,563 MicroScheduler -   -> 16184 reads (7.84% of total) failing DuplicateReadFilter
[2016-04-15T00:00Z] INFO  17:00:52,564 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:00Z] INFO  17:00:52,564 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:00Z] INFO  17:00:52,565 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:00Z] INFO  17:00:52,566 MicroScheduler -   -> 805 reads (0.39% of total) failing MappingQualityZeroFilter
[2016-04-15T00:00Z] INFO  17:00:52,566 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:00Z] INFO  17:00:52,567 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-15T00:00Z] INFO  17:00:52,568 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:00Z] GATK RealignerTargetCreator: R14-18105_kapa-NGv3-PE100-NGv3-sort-16_15596122_31106473-prep-prealign.bam 16:15596123-31106473
[2016-04-15T00:00Z] GATK: RealignerTargetCreator
[2016-04-15T00:00Z] INFO  17:00:53,232 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:00Z] INFO  17:00:53,235 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:00Z] INFO  17:00:53,236 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:00Z] INFO  17:00:53,237 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:00Z] INFO  17:00:53,242 HelpFormatter - Program Args: -T PrintReads -L 19:15510113-31025906 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/19/tx/tmpD7OiPA/R14-18105_kapa-NGv3-PE100-NGv3-sort-19_15510112_31025906-prep-prealign.bam
[2016-04-15T00:00Z] INFO  17:00:53,259 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:00Z] INFO  17:00:53,259 HelpFormatter - Date/Time: 2016/04/14 17:00:53
[2016-04-15T00:00Z] INFO  17:00:53,260 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:00Z] INFO  17:00:53,260 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:00Z] INFO  17:00:53,327 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-15T00:00Z] INFO  17:00:53,417 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:00Z] INFO  17:00:53,428 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:00Z] INFO  17:00:53,462 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:00Z] INFO  17:00:53,465 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:00Z] INFO  17:00:53,466 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:00Z] INFO  17:00:53,467 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:00Z] INFO  17:00:53,467 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:00Z] INFO  17:00:53,473 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/17/R14-18105_kapa-NGv3-PE100-NGv3-sort-17_77707305_81195210-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/17/R14-18105_kapa-NGv3-PE100-NGv3-sort-17_77707305_81195210-prep-prealign-realign.intervals -L 17:77707306-81195210 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/17/tx/tmprQAXig/R14-18105_kapa-NGv3-PE100-NGv3-sort-17_77707305_81195210-prep.bam
[2016-04-15T00:00Z] INFO  17:00:53,475 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-15T00:00Z] INFO  17:00:53,492 IntervalUtils - Processing 15509577 bp from intervals
[2016-04-15T00:00Z] INFO  17:00:53,494 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:00Z] INFO  17:00:53,495 HelpFormatter - Date/Time: 2016/04/14 17:00:53
[2016-04-15T00:00Z] INFO  17:00:53,495 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:00Z] INFO  17:00:53,496 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:00Z] INFO  17:00:53,585 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:00Z] INFO  17:00:53,725 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@5fe152b7
[2016-04-15T00:00Z] INFO  17:00:53,724 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:00Z] INFO  17:00:53,810 ProgressMeter -            done   1.8531348E7    21.0 s       1.0 s      100.0%    21.0 s       0.0 s
[2016-04-15T00:00Z] INFO  17:00:53,812 ProgressMeter - Total runtime 21.21 secs, 0.35 min, 0.01 hours
[2016-04-15T00:00Z] INFO  17:00:53,816 MicroScheduler - 31740 reads were filtered out during the traversal out of approximately 268494 total reads (11.82%)
[2016-04-15T00:00Z] INFO  17:00:53,817 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:00Z] INFO  17:00:53,818 MicroScheduler -   -> 777 reads (0.29% of total) failing BadMateFilter
[2016-04-15T00:00Z] INFO  17:00:53,818 MicroScheduler -   -> 20227 reads (7.53% of total) failing DuplicateReadFilter
[2016-04-15T00:00Z] INFO  17:00:53,819 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:00Z] INFO  17:00:53,823 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:00Z] INFO  17:00:53,823 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:00Z] INFO  17:00:53,826 MicroScheduler -   -> 10736 reads (4.00% of total) failing MappingQualityZeroFilter
[2016-04-15T00:00Z] INFO  17:00:53,826 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:00Z] INFO  17:00:53,827 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-15T00:00Z] INFO  17:00:53,827 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:00Z] INFO  17:00:53,849 ProgressMeter -            done   1.5774848E7    17.0 s       1.0 s      100.0%    17.0 s       0.0 s
[2016-04-15T00:00Z] INFO  17:00:53,851 ProgressMeter - Total runtime 17.02 secs, 0.28 min, 0.00 hours
[2016-04-15T00:00Z] INFO  17:00:53,851 MicroScheduler - 70483 reads were filtered out during the traversal out of approximately 231478 total reads (30.45%)
[2016-04-15T00:00Z] INFO  17:00:53,852 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:00Z] INFO  17:00:53,853 MicroScheduler -   -> 598 reads (0.26% of total) failing BadMateFilter
[2016-04-15T00:00Z] INFO  17:00:53,853 MicroScheduler -   -> 14148 reads (6.11% of total) failing DuplicateReadFilter
[2016-04-15T00:00Z] INFO  17:00:53,854 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:00Z] INFO  17:00:53,855 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:00Z] INFO  17:00:53,855 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:00Z] INFO  17:00:53,856 MicroScheduler -   -> 55737 reads (24.08% of total) failing MappingQualityZeroFilter
[2016-04-15T00:00Z] INFO  17:00:53,857 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:00Z] INFO  17:00:53,857 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-15T00:00Z] INFO  17:00:53,858 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:00Z] INFO  17:00:53,859 ProgressMeter -            done    911042.0   104.0 s     114.0 s      100.0%   104.0 s       0.0 s
[2016-04-15T00:00Z] INFO  17:00:53,860 ProgressMeter - Total runtime 104.16 secs, 1.74 min, 0.03 hours
[2016-04-15T00:00Z] INFO  17:00:53,860 MicroScheduler - 359 reads were filtered out during the traversal out of approximately 911401 total reads (0.04%)
[2016-04-15T00:00Z] INFO  17:00:53,861 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:00Z] INFO  17:00:53,861 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:00Z] INFO  17:00:53,861 MicroScheduler -   -> 359 reads (0.04% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:00Z] INFO  17:00:53,908 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:00Z] INFO  17:00:53,919 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:00Z] INFO  17:00:54,006 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.09
[2016-04-15T00:00Z] INFO  17:00:54,023 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:00Z] INFO  17:00:54,024 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:00Z] INFO  17:00:54,025 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:00Z] INFO  17:00:54,026 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:00Z] INFO  17:00:54,052 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:00Z] INFO  17:00:54,122 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:00Z] GATK: realign ('18', 18533538, 34081962) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-15T00:00Z] INFO  17:00:54,230 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@5fe152b7
[2016-04-15T00:00Z] INFO  17:00:54,245 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:00Z] INFO  17:00:54,319 ProgressMeter -            done    152356.0    23.0 s       2.6 m      100.0%    23.0 s       0.0 s
[2016-04-15T00:00Z] INFO  17:00:54,320 ProgressMeter - Total runtime 23.94 secs, 0.40 min, 0.01 hours
[2016-04-15T00:00Z] INFO  17:00:54,320 MicroScheduler - 137 reads were filtered out during the traversal out of approximately 152493 total reads (0.09%)
[2016-04-15T00:00Z] INFO  17:00:54,321 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:00Z] INFO  17:00:54,322 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:00Z] INFO  17:00:54,322 MicroScheduler -   -> 137 reads (0.09% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:00Z] INFO  17:00:54,445 IntervalUtils - Processing 3487905 bp from intervals
[2016-04-15T00:00Z] WARN  17:00:54,461 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:00Z] INFO  17:00:54,575 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:00Z] INFO  17:00:54,673 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:00Z] INFO  17:00:54,674 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:00Z] INFO  17:00:54,675 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:00Z] INFO  17:00:54,676 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:00Z] INFO  17:00:54,696 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-15T00:00Z] INFO  17:00:54,790 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:00Z] INFO  17:00:54,799 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:00Z] INFO  17:00:54,823 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:00Z] INFO  17:00:54,868 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:00Z] INFO  17:00:54,881 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-15T00:00Z] INFO  17:00:54,895 IntervalUtils - Processing 15515794 bp from intervals
[2016-04-15T00:00Z] INFO  17:00:54,987 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:00Z] INFO  17:00:55,223 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:00Z] INFO  17:00:55,224 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:00Z] INFO  17:00:55,225 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:00Z] INFO  17:00:55,225 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:00Z] INFO  17:00:55,252 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:00Z] INFO  17:00:55,263 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:00Z] INFO  17:00:55,269 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:00Z] GATK: realign ('18', 34092400, 49867248) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-15T00:00Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-17_0_15511002-prep-prealign.bam
[2016-04-15T00:00Z] INFO  17:00:55,410 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:00Z] INFO  17:00:55,412 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:00Z] GATK: realign ('18', 0, 18531348) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-15T00:00Z] INFO  17:00:55,741 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:00Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-18_50278423_66344430-prep-prealign.bam
[2016-04-15T00:00Z] INFO  17:00:55,960 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:00Z] INFO  17:00:55,964 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:00Z] INFO  17:00:55,965 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:00Z] INFO  17:00:55,965 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:00Z] INFO  17:00:55,970 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/16/R14-18105_kapa-NGv3-PE100-NGv3-sort-16_15596122_31106473-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/16/tx/tmpjlpfMC/R14-18105_kapa-NGv3-PE100-NGv3-sort-16_15596122_31106473-prep-prealign-realign.intervals -l INFO -L 16:15596123-31106473 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:00Z] INFO  17:00:55,981 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:00Z] INFO  17:00:55,985 HelpFormatter - Date/Time: 2016/04/14 17:00:55
[2016-04-15T00:00Z] INFO  17:00:55,986 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:00Z] INFO  17:00:55,986 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:00Z] INFO  17:00:56,120 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:00Z] INFO  17:00:56,242 ProgressMeter -     17:39777921    500007.0    90.0 s       3.0 m       56.1%     2.7 m      70.0 s
[2016-04-15T00:00Z] GATK RealignerTargetCreator: R14-18105_kapa-NGv3-PE100-NGv3-sort-18_50278423_66344430-prep-prealign.bam 18:50278424-66344430
[2016-04-15T00:00Z] GATK: RealignerTargetCreator
[2016-04-15T00:00Z] INFO  17:00:56,380 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T00:00Z] INFO  17:00:56,400 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:00Z] INFO  17:00:56,513 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.11
[2016-04-15T00:00Z] INFO  17:00:56,971 IntervalUtils - Processing 15510351 bp from intervals
[2016-04-15T00:00Z] WARN  17:00:56,976 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:00Z] INFO  17:00:57,056 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:00Z] INFO  17:00:57,136 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:00Z] INFO  17:00:57,140 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:00Z] INFO  17:00:57,140 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:00Z] INFO  17:00:57,141 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:00Z] INFO  17:00:57,145 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/18/R14-18105_kapa-NGv3-PE100-NGv3-sort-18_18533538_34081962-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/18/R14-18105_kapa-NGv3-PE100-NGv3-sort-18_18533538_34081962-prep-prealign-realign.intervals -L 18:18533539-34081962 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/18/tx/tmpK7Nroa/R14-18105_kapa-NGv3-PE100-NGv3-sort-18_18533538_34081962-prep.bam
[2016-04-15T00:00Z] INFO  17:00:57,155 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:00Z] INFO  17:00:57,157 HelpFormatter - Date/Time: 2016/04/14 17:00:57
[2016-04-15T00:00Z] INFO  17:00:57,158 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:00Z] INFO  17:00:57,159 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:00Z] INFO  17:00:57,348 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:00Z] INFO  17:00:57,350 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:00Z] INFO  17:00:57,350 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:00Z] INFO  17:00:57,351 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:00Z] INFO  17:00:57,355 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:00Z] INFO  17:00:57,527 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:00Z] INFO  17:00:57,547 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:00Z] INFO  17:00:57,622 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-15T00:00Z] GATK RealignerTargetCreator: R14-18105_kapa-NGv3-PE100-NGv3-sort-17_0_15511002-prep-prealign.bam 17:1-15511002
[2016-04-15T00:00Z] GATK: RealignerTargetCreator
[2016-04-15T00:00Z] INFO  17:00:58,117 IntervalUtils - Processing 15548424 bp from intervals
[2016-04-15T00:00Z] WARN  17:00:58,132 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:00Z] INFO  17:00:58,215 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:00Z] INFO  17:00:58,334 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:00Z] INFO  17:00:58,337 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:00Z] INFO  17:00:58,338 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:00Z] INFO  17:00:58,338 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:00Z] INFO  17:00:58,343 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/18/R14-18105_kapa-NGv3-PE100-NGv3-sort-18_34092400_49867248-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/18/R14-18105_kapa-NGv3-PE100-NGv3-sort-18_34092400_49867248-prep-prealign-realign.intervals -L 18:34092401-49867248 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/18/tx/tmpgN_HEh/R14-18105_kapa-NGv3-PE100-NGv3-sort-18_34092400_49867248-prep.bam
[2016-04-15T00:00Z] INFO  17:00:58,364 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:00Z] INFO  17:00:58,364 HelpFormatter - Date/Time: 2016/04/14 17:00:58
[2016-04-15T00:00Z] INFO  17:00:58,365 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:00Z] INFO  17:00:58,365 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:00Z] INFO  17:00:58,385 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:00Z] INFO  17:00:58,386 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:00Z] INFO  17:00:58,387 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:00Z] INFO  17:00:58,387 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:00Z] INFO  17:00:58,500 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:00Z] INFO  17:00:58,504 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:00Z] INFO  17:00:58,504 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:00Z] INFO  17:00:58,505 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:00Z] INFO  17:00:58,509 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/18/R14-18105_kapa-NGv3-PE100-NGv3-sort-18_0_18531348-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/18/R14-18105_kapa-NGv3-PE100-NGv3-sort-18_0_18531348-prep-prealign-realign.intervals -L 18:1-18531348 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/18/tx/tmpry4SxD/R14-18105_kapa-NGv3-PE100-NGv3-sort-18_0_18531348-prep.bam
[2016-04-15T00:00Z] INFO  17:00:58,524 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:00Z] INFO  17:00:58,524 HelpFormatter - Date/Time: 2016/04/14 17:00:58
[2016-04-15T00:00Z] INFO  17:00:58,525 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:00Z] INFO  17:00:58,525 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:00Z] INFO  17:00:58,552 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:00Z] INFO  17:00:58,654 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:00Z] INFO  17:00:58,720 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:00Z] INFO  17:00:58,792 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:00Z] INFO  17:00:58,815 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:00Z] INFO  17:00:58,821 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:00Z] INFO  17:00:58,899 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-15T00:00Z] INFO  17:00:58,969 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:00Z] INFO  17:00:58,995 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:00Z] INFO  17:00:59,036 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.04
[2016-04-15T00:00Z] INFO  17:00:59,226 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:00Z] INFO  17:00:59,229 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:00Z] INFO  17:00:59,230 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:00Z] INFO  17:00:59,230 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:00Z] INFO  17:00:59,235 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/18/R14-18105_kapa-NGv3-PE100-NGv3-sort-18_50278423_66344430-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/18/tx/tmp4N4etJ/R14-18105_kapa-NGv3-PE100-NGv3-sort-18_50278423_66344430-prep-prealign-realign.intervals -l INFO -L 18:50278424-66344430 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:00Z] INFO  17:00:59,265 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:00Z] INFO  17:00:59,280 HelpFormatter - Date/Time: 2016/04/14 17:00:59
[2016-04-15T00:00Z] INFO  17:00:59,281 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:00Z] INFO  17:00:59,285 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:00Z] INFO  17:00:59,331 IntervalUtils - Processing 15774848 bp from intervals
[2016-04-15T00:00Z] WARN  17:00:59,336 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:00Z] INFO  17:00:59,410 IntervalUtils - Processing 18531348 bp from intervals
[2016-04-15T00:00Z] WARN  17:00:59,416 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:00Z] INFO  17:00:59,424 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:00Z] INFO  17:00:59,424 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:00Z] INFO  17:00:59,515 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:00Z] INFO  17:00:59,557 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:00Z] INFO  17:00:59,569 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:00Z] INFO  17:00:59,571 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:00Z] INFO  17:00:59,571 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:00Z] INFO  17:00:59,663 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T00:00Z] INFO  17:00:59,675 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:00Z] INFO  17:00:59,688 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:00Z] INFO  17:00:59,700 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:00Z] INFO  17:00:59,701 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:00Z] INFO  17:00:59,702 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:00Z] INFO  17:00:59,756 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:00Z] INFO  17:00:59,770 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.09
[2016-04-15T00:00Z] INFO  17:00:59,921 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:00Z] INFO  17:00:59,923 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:01Z] INFO  17:01:00,169 IntervalUtils - Processing 16066007 bp from intervals
[2016-04-15T00:01Z] WARN  17:01:00,186 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:01Z] INFO  17:01:00,205 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:01Z] INFO  17:01:00,282 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:01Z] INFO  17:01:00,551 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:01Z] INFO  17:01:00,552 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:01Z] INFO  17:01:00,553 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:01Z] INFO  17:01:00,554 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:01Z] INFO  17:01:00,858 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:01Z] INFO  17:01:00,861 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:01Z] INFO  17:01:00,862 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:01Z] INFO  17:01:00,863 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:01Z] INFO  17:01:00,867 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/17/R14-18105_kapa-NGv3-PE100-NGv3-sort-17_0_15511002-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/17/tx/tmpcFMWlz/R14-18105_kapa-NGv3-PE100-NGv3-sort-17_0_15511002-prep-prealign-realign.intervals -l INFO -L 17:1-15511002 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:01Z] INFO  17:01:00,883 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:01Z] INFO  17:01:00,891 HelpFormatter - Date/Time: 2016/04/14 17:01:00
[2016-04-15T00:01Z] INFO  17:01:00,892 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:01Z] INFO  17:01:00,892 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:01Z] INFO  17:01:01,040 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:01Z] INFO  17:01:01,263 ProgressMeter -            done   1.5592465E7    28.0 s       1.0 s      100.0%    28.0 s       0.0 s
[2016-04-15T00:01Z] INFO  17:01:01,282 ProgressMeter - Total runtime 28.75 secs, 0.48 min, 0.01 hours
[2016-04-15T00:01Z] INFO  17:01:01,283 MicroScheduler - 114845 reads were filtered out during the traversal out of approximately 703513 total reads (16.32%)
[2016-04-15T00:01Z] INFO  17:01:01,283 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:01Z] INFO  17:01:01,283 MicroScheduler -   -> 1081 reads (0.15% of total) failing BadMateFilter
[2016-04-15T00:01Z] INFO  17:01:01,284 MicroScheduler -   -> 52158 reads (7.41% of total) failing DuplicateReadFilter
[2016-04-15T00:01Z] INFO  17:01:01,284 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:01Z] INFO  17:01:01,284 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:01Z] INFO  17:01:01,284 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:01Z] INFO  17:01:01,285 MicroScheduler -   -> 61606 reads (8.76% of total) failing MappingQualityZeroFilter
[2016-04-15T00:01Z] INFO  17:01:01,285 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:01Z] INFO  17:01:01,285 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-15T00:01Z] INFO  17:01:01,285 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:01Z] INFO  17:01:01,315 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T00:01Z] INFO  17:01:01,335 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:01Z] INFO  17:01:01,412 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-15T00:01Z] INFO  17:01:01,716 IntervalUtils - Processing 15511002 bp from intervals
[2016-04-15T00:01Z] WARN  17:01:01,721 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:01Z] INFO  17:01:01,816 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:01Z] INFO  17:01:02,082 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:01Z] INFO  17:01:02,083 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:01Z] INFO  17:01:02,084 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:01Z] INFO  17:01:02,085 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:01Z] INFO  17:01:02,243 ProgressMeter -            done   1.5523258E7    27.0 s       1.0 s      100.0%    27.0 s       0.0 s
[2016-04-15T00:01Z] INFO  17:01:02,244 ProgressMeter - Total runtime 27.42 secs, 0.46 min, 0.01 hours
[2016-04-15T00:01Z] INFO  17:01:02,248 MicroScheduler - 83272 reads were filtered out during the traversal out of approximately 640560 total reads (13.00%)
[2016-04-15T00:01Z] INFO  17:01:02,249 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:01Z] INFO  17:01:02,250 MicroScheduler -   -> 1098 reads (0.17% of total) failing BadMateFilter
[2016-04-15T00:01Z] INFO  17:01:02,251 MicroScheduler -   -> 48282 reads (7.54% of total) failing DuplicateReadFilter
[2016-04-15T00:01Z] INFO  17:01:02,251 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:01Z] INFO  17:01:02,252 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:01Z] INFO  17:01:02,253 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:01Z] INFO  17:01:02,253 MicroScheduler -   -> 33892 reads (5.29% of total) failing MappingQualityZeroFilter
[2016-04-15T00:01Z] INFO  17:01:02,254 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:01Z] INFO  17:01:02,254 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-15T00:01Z] INFO  17:01:02,255 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:01Z] INFO  17:01:03,040 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:01Z] GATK: realign ('16', 64982511, 80574976) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-15T00:01Z] INFO  17:01:03,550 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:01Z] GATK: realign ('17', 15515955, 31039213) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-15T00:01Z] INFO  17:01:04,827 ProgressMeter -            done   1.5513871E7    24.0 s       1.0 s      100.0%    24.0 s       0.0 s
[2016-04-15T00:01Z] INFO  17:01:04,828 ProgressMeter - Total runtime 24.71 secs, 0.41 min, 0.01 hours
[2016-04-15T00:01Z] INFO  17:01:04,832 MicroScheduler - 57629 reads were filtered out during the traversal out of approximately 524043 total reads (11.00%)
[2016-04-15T00:01Z] INFO  17:01:04,833 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:01Z] INFO  17:01:04,834 MicroScheduler -   -> 1025 reads (0.20% of total) failing BadMateFilter
[2016-04-15T00:01Z] INFO  17:01:04,835 MicroScheduler -   -> 40043 reads (7.64% of total) failing DuplicateReadFilter
[2016-04-15T00:01Z] INFO  17:01:04,835 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:01Z] INFO  17:01:04,836 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:01Z] INFO  17:01:04,837 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:01Z] INFO  17:01:04,837 MicroScheduler -   -> 16561 reads (3.16% of total) failing MappingQualityZeroFilter
[2016-04-15T00:01Z] INFO  17:01:04,838 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:01Z] INFO  17:01:04,838 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-15T00:01Z] INFO  17:01:04,839 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:01Z] INFO  17:01:05,681 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:01Z] INFO  17:01:05,700 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:01Z] INFO  17:01:05,700 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:01Z] INFO  17:01:05,701 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:01Z] INFO  17:01:05,706 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/16/R14-18105_kapa-NGv3-PE100-NGv3-sort-16_64982511_80574976-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/16/R14-18105_kapa-NGv3-PE100-NGv3-sort-16_64982511_80574976-prep-prealign-realign.intervals -L 16:64982512-80574976 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/16/tx/tmp7523n7/R14-18105_kapa-NGv3-PE100-NGv3-sort-16_64982511_80574976-prep.bam
[2016-04-15T00:01Z] INFO  17:01:05,722 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:01Z] INFO  17:01:05,722 HelpFormatter - Date/Time: 2016/04/14 17:01:05
[2016-04-15T00:01Z] INFO  17:01:05,722 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:01Z] INFO  17:01:05,723 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:01Z] INFO  17:01:06,000 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:01Z] INFO  17:01:06,077 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:01Z] INFO  17:01:06,086 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:01Z] INFO  17:01:06,132 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.04
[2016-04-15T00:01Z] INFO  17:01:06,226 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:01Z] GATK: realign ('17', 46607689, 62121560) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-15T00:01Z] INFO  17:01:06,489 IntervalUtils - Processing 15592465 bp from intervals
[2016-04-15T00:01Z] WARN  17:01:06,494 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:01Z] INFO  17:01:06,548 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:01Z] INFO  17:01:06,551 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:01Z] INFO  17:01:06,552 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:01Z] INFO  17:01:06,552 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:01Z] INFO  17:01:06,557 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/17/R14-18105_kapa-NGv3-PE100-NGv3-sort-17_15515955_31039213-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/17/R14-18105_kapa-NGv3-PE100-NGv3-sort-17_15515955_31039213-prep-prealign-realign.intervals -L 17:15515956-31039213 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/17/tx/tmp_pDIr3/R14-18105_kapa-NGv3-PE100-NGv3-sort-17_15515955_31039213-prep.bam
[2016-04-15T00:01Z] INFO  17:01:06,566 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:01Z] INFO  17:01:06,567 HelpFormatter - Date/Time: 2016/04/14 17:01:06
[2016-04-15T00:01Z] INFO  17:01:06,568 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:01Z] INFO  17:01:06,568 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:01Z] INFO  17:01:06,581 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:01Z] INFO  17:01:06,729 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:01Z] INFO  17:01:06,730 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:01Z] INFO  17:01:06,731 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:01Z] INFO  17:01:06,732 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:01Z] INFO  17:01:06,792 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:01Z] INFO  17:01:06,918 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:01Z] INFO  17:01:06,922 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:01Z] INFO  17:01:06,927 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:01Z] INFO  17:01:07,002 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-15T00:01Z] INFO  17:01:07,147 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:01Z] INFO  17:01:07,438 IntervalUtils - Processing 15523258 bp from intervals
[2016-04-15T00:01Z] WARN  17:01:07,461 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:01Z] INFO  17:01:07,555 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:01Z] INFO  17:01:07,702 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:01Z] INFO  17:01:07,714 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:01Z] INFO  17:01:07,715 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:01Z] INFO  17:01:07,715 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:01Z] INFO  17:01:07,894 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:01Z] INFO  17:01:08,023 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:01Z] INFO  17:01:09,004 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:01Z] INFO  17:01:09,007 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:01Z] INFO  17:01:09,008 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:01Z] INFO  17:01:09,008 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:01Z] INFO  17:01:09,013 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/17/R14-18105_kapa-NGv3-PE100-NGv3-sort-17_46607689_62121560-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/17/R14-18105_kapa-NGv3-PE100-NGv3-sort-17_46607689_62121560-prep-prealign-realign.intervals -L 17:46607690-62121560 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/17/tx/tmp4q7nCH/R14-18105_kapa-NGv3-PE100-NGv3-sort-17_46607689_62121560-prep.bam
[2016-04-15T00:01Z] INFO  17:01:09,022 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:01Z] INFO  17:01:09,027 HelpFormatter - Date/Time: 2016/04/14 17:01:09
[2016-04-15T00:01Z] INFO  17:01:09,028 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:01Z] INFO  17:01:09,029 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:01Z] INFO  17:01:09,269 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:01Z] INFO  17:01:09,361 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:01Z] INFO  17:01:09,371 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:01Z] INFO  17:01:09,415 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.04
[2016-04-15T00:01Z] INFO  17:01:09,793 IntervalUtils - Processing 15513871 bp from intervals
[2016-04-15T00:01Z] WARN  17:01:09,798 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:01Z] INFO  17:01:09,879 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:01Z] INFO  17:01:10,004 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:01Z] INFO  17:01:10,004 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:01Z] INFO  17:01:10,004 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:01Z] INFO  17:01:10,005 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:01Z] INFO  17:01:10,168 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:01Z] INFO  17:01:10,318 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:01Z] INFO  17:01:10,483 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@41fd9d8e
[2016-04-15T00:01Z] INFO  17:01:10,593 ProgressMeter -            done    132491.0    19.0 s       2.4 m       99.4%    19.0 s       0.0 s
[2016-04-15T00:01Z] INFO  17:01:10,593 ProgressMeter - Total runtime 19.25 secs, 0.32 min, 0.01 hours
[2016-04-15T00:01Z] INFO  17:01:10,594 MicroScheduler - 95 reads were filtered out during the traversal out of approximately 132586 total reads (0.07%)
[2016-04-15T00:01Z] INFO  17:01:10,594 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:01Z] INFO  17:01:10,594 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:01Z] INFO  17:01:10,595 MicroScheduler -   -> 95 reads (0.07% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:01Z] INFO  17:01:11,954 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:01Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-18_66346699_78077248-prep-prealign.bam
[2016-04-15T00:01Z] INFO  17:01:12,106 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@7172f77a
[2016-04-15T00:01Z] INFO  17:01:12,192 ProgressMeter -            done    610087.0    88.0 s       2.4 m      100.0%    88.0 s       0.0 s
[2016-04-15T00:01Z] INFO  17:01:12,194 ProgressMeter - Total runtime 88.56 secs, 1.48 min, 0.02 hours
[2016-04-15T00:01Z] INFO  17:01:12,195 MicroScheduler - 281 reads were filtered out during the traversal out of approximately 610368 total reads (0.05%)
[2016-04-15T00:01Z] INFO  17:01:12,195 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:01Z] INFO  17:01:12,196 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:01Z] INFO  17:01:12,197 MicroScheduler -   -> 281 reads (0.05% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:01Z] GATK RealignerTargetCreator: R14-18105_kapa-NGv3-PE100-NGv3-sort-18_66346699_78077248-prep-prealign.bam 18:66346700-78077248
[2016-04-15T00:01Z] GATK: RealignerTargetCreator
[2016-04-15T00:01Z] INFO  17:01:13,554 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:01Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-17_62122219_77705154-prep-prealign.bam
[2016-04-15T00:01Z] INFO  17:01:14,632 ProgressMeter -            done    204821.0    16.0 s      79.0 s      100.0%    16.0 s       0.0 s
[2016-04-15T00:01Z] INFO  17:01:14,633 ProgressMeter - Total runtime 16.25 secs, 0.27 min, 0.00 hours
[2016-04-15T00:01Z] INFO  17:01:14,637 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 204821 total reads (0.00%)
[2016-04-15T00:01Z] INFO  17:01:14,637 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:01Z] INFO  17:01:14,637 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:01Z] INFO  17:01:14,638 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:01Z] INFO  17:01:14,842 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:01Z] INFO  17:01:14,848 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:01Z] INFO  17:01:14,848 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:01Z] INFO  17:01:14,849 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:01Z] INFO  17:01:14,854 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/18/R14-18105_kapa-NGv3-PE100-NGv3-sort-18_66346699_78077248-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/18/tx/tmprq23_8/R14-18105_kapa-NGv3-PE100-NGv3-sort-18_66346699_78077248-prep-prealign-realign.intervals -l INFO -L 18:66346700-78077248 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:01Z] INFO  17:01:14,862 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:01Z] INFO  17:01:14,863 HelpFormatter - Date/Time: 2016/04/14 17:01:14
[2016-04-15T00:01Z] INFO  17:01:14,864 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:01Z] INFO  17:01:14,864 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:01Z] INFO  17:01:14,936 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:01Z] INFO  17:01:15,165 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T00:01Z] INFO  17:01:15,166 ProgressMeter -            done    299528.0    20.0 s      68.0 s       95.9%    20.0 s       0.0 s
[2016-04-15T00:01Z] INFO  17:01:15,166 ProgressMeter - Total runtime 20.49 secs, 0.34 min, 0.01 hours
[2016-04-15T00:01Z] INFO  17:01:15,170 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 299528 total reads (0.00%)
[2016-04-15T00:01Z] INFO  17:01:15,170 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:01Z] INFO  17:01:15,170 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:01Z] INFO  17:01:15,171 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:01Z] INFO  17:01:15,185 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:01Z] GATK RealignerTargetCreator: R14-18105_kapa-NGv3-PE100-NGv3-sort-17_62122219_77705154-prep-prealign.bam 17:62122220-77705154
[2016-04-15T00:01Z] GATK: RealignerTargetCreator
[2016-04-15T00:01Z] INFO  17:01:15,266 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-15T00:01Z] INFO  17:01:15,513 IntervalUtils - Processing 11730549 bp from intervals
[2016-04-15T00:01Z] WARN  17:01:15,525 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:01Z] INFO  17:01:15,605 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:01Z] INFO  17:01:15,807 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:01Z] INFO  17:01:15,808 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:01Z] INFO  17:01:15,809 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:01Z] INFO  17:01:15,810 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:01Z] INFO  17:01:16,010 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:01Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-18_18533538_34081962-prep.bam
[2016-04-15T00:01Z] INFO  17:01:16,333 ProgressMeter -            done   1.6066007E7    15.0 s       0.0 s      100.0%    15.0 s       0.0 s
[2016-04-15T00:01Z] INFO  17:01:16,334 ProgressMeter - Total runtime 15.78 secs, 0.26 min, 0.00 hours
[2016-04-15T00:01Z] INFO  17:01:16,338 MicroScheduler - 12606 reads were filtered out during the traversal out of approximately 153627 total reads (8.21%)
[2016-04-15T00:01Z] INFO  17:01:16,338 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:01Z] INFO  17:01:16,339 MicroScheduler -   -> 540 reads (0.35% of total) failing BadMateFilter
[2016-04-15T00:01Z] INFO  17:01:16,339 MicroScheduler -   -> 11771 reads (7.66% of total) failing DuplicateReadFilter
[2016-04-15T00:01Z] INFO  17:01:16,339 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:01Z] INFO  17:01:16,340 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:01Z] INFO  17:01:16,340 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:01Z] INFO  17:01:16,340 MicroScheduler -   -> 295 reads (0.19% of total) failing MappingQualityZeroFilter
[2016-04-15T00:01Z] INFO  17:01:16,340 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:01Z] INFO  17:01:16,341 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-15T00:01Z] INFO  17:01:16,341 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:01Z] INFO  17:01:16,800 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:01Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-17_77707305_81195210-prep.bam
[2016-04-15T00:01Z] GATK pre-alignment ('19', 31038849, 46627578) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-15T00:01Z] INFO  17:01:17,008 ProgressMeter -     16:15083181   1.507328E7    30.0 s       1.0 s       97.1%    30.0 s       0.0 s
[2016-04-15T00:01Z] INFO  17:01:17,272 ProgressMeter -            done    230183.0    17.0 s      76.0 s      100.0%    17.0 s       0.0 s
[2016-04-15T00:01Z] INFO  17:01:17,273 ProgressMeter - Total runtime 17.70 secs, 0.30 min, 0.00 hours
[2016-04-15T00:01Z] INFO  17:01:17,299 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 230183 total reads (0.00%)
[2016-04-15T00:01Z] INFO  17:01:17,300 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:01Z] INFO  17:01:17,300 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:01Z] INFO  17:01:17,300 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:01Z] INFO  17:01:17,756 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:01Z] GATK: realign ('18', 50278423, 66344430) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-15T00:01Z] GATK pre-alignment ('19', 46627881, 59128983) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-15T00:01Z] INFO  17:01:18,147 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:01Z] INFO  17:01:18,150 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:01Z] INFO  17:01:18,151 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:01Z] INFO  17:01:18,151 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:01Z] INFO  17:01:18,156 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/17/R14-18105_kapa-NGv3-PE100-NGv3-sort-17_62122219_77705154-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/17/tx/tmpnA3LFH/R14-18105_kapa-NGv3-PE100-NGv3-sort-17_62122219_77705154-prep-prealign-realign.intervals -l INFO -L 17:62122220-77705154 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:01Z] INFO  17:01:18,185 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:01Z] INFO  17:01:18,186 HelpFormatter - Date/Time: 2016/04/14 17:01:18
[2016-04-15T00:01Z] INFO  17:01:18,186 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:01Z] INFO  17:01:18,187 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:01Z] INFO  17:01:18,335 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:01Z] INFO  17:01:18,491 ProgressMeter -            done   1.5528616E7    31.0 s       2.0 s      100.0%    31.0 s       0.0 s
[2016-04-15T00:01Z] INFO  17:01:18,492 ProgressMeter - Total runtime 31.49 secs, 0.52 min, 0.01 hours
[2016-04-15T00:01Z] INFO  17:01:18,496 MicroScheduler - 176526 reads were filtered out during the traversal out of approximately 948708 total reads (18.61%)
[2016-04-15T00:01Z] INFO  17:01:18,497 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:01Z] INFO  17:01:18,498 MicroScheduler -   -> 1576 reads (0.17% of total) failing BadMateFilter
[2016-04-15T00:01Z] INFO  17:01:18,499 MicroScheduler -   -> 67954 reads (7.16% of total) failing DuplicateReadFilter
[2016-04-15T00:01Z] INFO  17:01:18,499 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:01Z] INFO  17:01:18,500 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:01Z] INFO  17:01:18,500 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:01Z] INFO  17:01:18,501 MicroScheduler -   -> 106996 reads (11.28% of total) failing MappingQualityZeroFilter
[2016-04-15T00:01Z] INFO  17:01:18,502 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:01Z] INFO  17:01:18,502 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-15T00:01Z] INFO  17:01:18,503 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:01Z] INFO  17:01:18,570 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T00:01Z] INFO  17:01:18,590 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:01Z] INFO  17:01:18,674 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-15T00:01Z] INFO  17:01:18,741 ProgressMeter -            done    267327.0    19.0 s      71.0 s      100.0%    19.0 s       0.0 s
[2016-04-15T00:01Z] INFO  17:01:18,742 ProgressMeter - Total runtime 19.04 secs, 0.32 min, 0.01 hours
[2016-04-15T00:01Z] INFO  17:01:18,746 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 267327 total reads (0.00%)
[2016-04-15T00:01Z] INFO  17:01:18,747 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:01Z] INFO  17:01:18,748 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:01Z] INFO  17:01:18,748 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:01Z] INFO  17:01:18,932 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:01Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-18_34092400_49867248-prep.bam
[2016-04-15T00:01Z] INFO  17:01:19,006 IntervalUtils - Processing 15582935 bp from intervals
[2016-04-15T00:01Z] WARN  17:01:19,011 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:01Z] INFO  17:01:19,109 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:01Z] INFO  17:01:19,252 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:01Z] INFO  17:01:19,256 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:01Z] INFO  17:01:19,257 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:01Z] INFO  17:01:19,257 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:01Z] INFO  17:01:19,267 HelpFormatter - Program Args: -T PrintReads -L 19:31038850-46627578 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/19/tx/tmpox_gNP/R14-18105_kapa-NGv3-PE100-NGv3-sort-19_31038849_46627578-prep-prealign.bam
[2016-04-15T00:01Z] INFO  17:01:19,276 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:01Z] INFO  17:01:19,288 HelpFormatter - Date/Time: 2016/04/14 17:01:19
[2016-04-15T00:01Z] INFO  17:01:19,289 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:01Z] INFO  17:01:19,290 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:01Z] INFO  17:01:19,340 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:01Z] INFO  17:01:19,341 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:01Z] INFO  17:01:19,341 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:01Z] INFO  17:01:19,342 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:01Z] INFO  17:01:19,462 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:01Z] GATK pre-alignment ('20', 0, 15843471) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-15T00:01Z] INFO  17:01:20,100 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:01Z] GATK: realign ('16', 0, 15528616) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-15T00:01Z] INFO  17:01:20,347 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:01Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-18_0_18531348-prep.bam
[2016-04-15T00:01Z] INFO  17:01:20,596 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-15T00:01Z] INFO  17:01:20,669 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:01Z] INFO  17:01:20,678 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:01Z] INFO  17:01:20,732 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-15T00:01Z] INFO  17:01:20,746 IntervalUtils - Processing 15588729 bp from intervals
[2016-04-15T00:01Z] INFO  17:01:20,828 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:01Z] INFO  17:01:20,882 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:01Z] INFO  17:01:20,885 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:01Z] INFO  17:01:20,885 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:01Z] INFO  17:01:20,886 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:01Z] INFO  17:01:20,890 HelpFormatter - Program Args: -T PrintReads -L 19:46627882-59128983 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/19/tx/tmp9B3Fk3/R14-18105_kapa-NGv3-PE100-NGv3-sort-19_46627881_59128983-prep-prealign.bam
[2016-04-15T00:01Z] INFO  17:01:20,890 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:01Z] INFO  17:01:20,894 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:01Z] INFO  17:01:20,894 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:01Z] INFO  17:01:20,895 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:01Z] INFO  17:01:20,899 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/18/R14-18105_kapa-NGv3-PE100-NGv3-sort-18_50278423_66344430-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/18/R14-18105_kapa-NGv3-PE100-NGv3-sort-18_50278423_66344430-prep-prealign-realign.intervals -L 18:50278424-66344430 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/18/tx/tmpYsmUXx/R14-18105_kapa-NGv3-PE100-NGv3-sort-18_50278423_66344430-prep.bam
[2016-04-15T00:01Z] INFO  17:01:20,920 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:01Z] INFO  17:01:20,921 HelpFormatter - Date/Time: 2016/04/14 17:01:20
[2016-04-15T00:01Z] INFO  17:01:20,921 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:01Z] INFO  17:01:20,922 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:01Z] INFO  17:01:20,932 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:01Z] INFO  17:01:20,936 HelpFormatter - Date/Time: 2016/04/14 17:01:20
[2016-04-15T00:01Z] INFO  17:01:20,936 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:01Z] INFO  17:01:20,937 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:01Z] GATK pre-alignment ('20', 15866408, 31376818) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-15T00:01Z] INFO  17:01:21,128 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:01Z] INFO  17:01:21,138 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:01Z] INFO  17:01:21,139 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:01Z] INFO  17:01:21,140 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:01Z] INFO  17:01:21,141 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:01Z] INFO  17:01:21,154 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:01Z] INFO  17:01:21,158 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:01Z] INFO  17:01:21,305 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:01Z] INFO  17:01:21,318 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:01Z] INFO  17:01:21,326 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:01Z] INFO  17:01:21,380 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-15T00:01Z] INFO  17:01:21,753 IntervalUtils - Processing 16066007 bp from intervals
[2016-04-15T00:01Z] WARN  17:01:21,761 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:01Z] INFO  17:01:21,860 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:01Z] INFO  17:01:22,084 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:01Z] INFO  17:01:22,085 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:01Z] INFO  17:01:22,086 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:01Z] INFO  17:01:22,087 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:01Z] INFO  17:01:22,255 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:01Z] INFO  17:01:22,435 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:01Z] INFO  17:01:22,442 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-15T00:01Z] INFO  17:01:22,510 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:01Z] INFO  17:01:22,519 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:01Z] INFO  17:01:22,566 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-15T00:01Z] INFO  17:01:22,581 IntervalUtils - Processing 12501102 bp from intervals
[2016-04-15T00:01Z] INFO  17:01:22,675 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:01Z] INFO  17:01:22,682 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:01Z] INFO  17:01:22,685 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:01Z] INFO  17:01:22,686 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:01Z] INFO  17:01:22,686 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:01Z] INFO  17:01:22,691 HelpFormatter - Program Args: -T PrintReads -L 20:1-15843471 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/20/tx/tmpQJiV8f/R14-18105_kapa-NGv3-PE100-NGv3-sort-20_0_15843471-prep-prealign.bam
[2016-04-15T00:01Z] INFO  17:01:22,701 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:01Z] INFO  17:01:22,701 HelpFormatter - Date/Time: 2016/04/14 17:01:22
[2016-04-15T00:01Z] INFO  17:01:22,701 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:01Z] INFO  17:01:22,702 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:01Z] INFO  17:01:22,899 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:01Z] INFO  17:01:22,968 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:01Z] INFO  17:01:22,969 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:01Z] INFO  17:01:22,970 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:01Z] INFO  17:01:22,971 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:01Z] INFO  17:01:22,984 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:01Z] INFO  17:01:23,230 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:01Z] INFO  17:01:23,310 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:01Z] INFO  17:01:23,313 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:01Z] INFO  17:01:23,314 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:01Z] INFO  17:01:23,314 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:01Z] INFO  17:01:23,319 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/16/R14-18105_kapa-NGv3-PE100-NGv3-sort-16_0_15528616-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/16/R14-18105_kapa-NGv3-PE100-NGv3-sort-16_0_15528616-prep-prealign-realign.intervals -L 16:1-15528616 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/16/tx/tmpmaAv_a/R14-18105_kapa-NGv3-PE100-NGv3-sort-16_0_15528616-prep.bam
[2016-04-15T00:01Z] INFO  17:01:23,328 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:01Z] INFO  17:01:23,328 HelpFormatter - Date/Time: 2016/04/14 17:01:23
[2016-04-15T00:01Z] INFO  17:01:23,328 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:01Z] INFO  17:01:23,328 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:01Z] INFO  17:01:23,604 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:01Z] INFO  17:01:23,756 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:01Z] INFO  17:01:23,765 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:01Z] INFO  17:01:23,805 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.04
[2016-04-15T00:01Z] INFO  17:01:23,998 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:01Z] INFO  17:01:24,001 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:01Z] INFO  17:01:24,002 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:01Z] INFO  17:01:24,003 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:01Z] INFO  17:01:24,007 HelpFormatter - Program Args: -T PrintReads -L 20:15866409-31376818 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/20/tx/tmpyZNdeC/R14-18105_kapa-NGv3-PE100-NGv3-sort-20_15866408_31376818-prep-prealign.bam
[2016-04-15T00:01Z] INFO  17:01:24,016 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:01Z] INFO  17:01:24,017 HelpFormatter - Date/Time: 2016/04/14 17:01:23
[2016-04-15T00:01Z] INFO  17:01:24,017 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:01Z] INFO  17:01:24,018 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:01Z] INFO  17:01:24,112 ProgressMeter -      19:1754327    200004.0    30.0 s       2.5 m       11.3%     4.4 m       3.9 m
[2016-04-15T00:01Z] INFO  17:01:24,229 IntervalUtils - Processing 15528616 bp from intervals
[2016-04-15T00:01Z] WARN  17:01:24,234 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:01Z] INFO  17:01:24,262 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:01Z] INFO  17:01:24,263 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-15T00:01Z] INFO  17:01:24,334 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:01Z] INFO  17:01:24,344 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:01Z] INFO  17:01:24,367 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:01Z] INFO  17:01:24,412 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-15T00:01Z] INFO  17:01:24,443 IntervalUtils - Processing 15843471 bp from intervals
[2016-04-15T00:01Z] INFO  17:01:24,537 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:01Z] INFO  17:01:24,560 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:01Z] INFO  17:01:24,560 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:01Z] INFO  17:01:24,561 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:01Z] INFO  17:01:24,561 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:01Z] INFO  17:01:24,783 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:01Z] INFO  17:01:24,823 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:01Z] INFO  17:01:24,824 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:01Z] INFO  17:01:24,825 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:01Z] INFO  17:01:24,825 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:01Z] INFO  17:01:24,847 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:01Z] INFO  17:01:24,917 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:01Z] INFO  17:01:25,055 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:01Z] INFO  17:01:25,239 ProgressMeter -     19:17766714    200004.0    30.0 s       2.5 m       14.5%     3.4 m       2.9 m
[2016-04-15T00:01Z] INFO  17:01:25,326 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-15T00:01Z] INFO  17:01:25,394 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:01Z] INFO  17:01:25,403 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:01Z] INFO  17:01:25,456 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-15T00:01Z] INFO  17:01:25,470 IntervalUtils - Processing 15510410 bp from intervals
[2016-04-15T00:01Z] INFO  17:01:25,554 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:01Z] INFO  17:01:25,842 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:01Z] INFO  17:01:25,843 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:01Z] INFO  17:01:25,844 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:01Z] INFO  17:01:25,845 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:01Z] INFO  17:01:25,859 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:01Z] INFO  17:01:25,989 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:01Z] INFO  17:01:26,547 ProgressMeter -     17:41599534    800011.0   120.0 s       2.5 m       67.8%     2.9 m      56.0 s
[2016-04-15T00:01Z] INFO  17:01:27,384 ProgressMeter -     16:30992245   1.5386022E7    30.0 s       1.0 s       99.3%    30.0 s       0.0 s
[2016-04-15T00:01Z] INFO  17:01:28,884 ProgressMeter -            done   1.1730549E7    13.0 s       1.0 s      100.0%    13.0 s       0.0 s
[2016-04-15T00:01Z] INFO  17:01:28,886 ProgressMeter - Total runtime 13.08 secs, 0.22 min, 0.00 hours
[2016-04-15T00:01Z] INFO  17:01:28,890 MicroScheduler - 11397 reads were filtered out during the traversal out of approximately 133240 total reads (8.55%)
[2016-04-15T00:01Z] INFO  17:01:28,891 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:01Z] INFO  17:01:28,892 MicroScheduler -   -> 435 reads (0.33% of total) failing BadMateFilter
[2016-04-15T00:01Z] INFO  17:01:28,893 MicroScheduler -   -> 10638 reads (7.98% of total) failing DuplicateReadFilter
[2016-04-15T00:01Z] INFO  17:01:28,893 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:01Z] INFO  17:01:28,894 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:01Z] INFO  17:01:28,894 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:01Z] INFO  17:01:28,895 MicroScheduler -   -> 324 reads (0.24% of total) failing MappingQualityZeroFilter
[2016-04-15T00:01Z] INFO  17:01:28,896 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:01Z] INFO  17:01:28,896 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-15T00:01Z] INFO  17:01:28,897 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:01Z] INFO  17:01:28,947 ProgressMeter -            done   1.5510351E7    31.0 s       2.0 s      100.0%    31.0 s       0.0 s
[2016-04-15T00:01Z] INFO  17:01:28,948 ProgressMeter - Total runtime 31.60 secs, 0.53 min, 0.01 hours
[2016-04-15T00:01Z] INFO  17:01:28,949 MicroScheduler - 595505 reads were filtered out during the traversal out of approximately 1234269 total reads (48.25%)
[2016-04-15T00:01Z] INFO  17:01:28,950 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:01Z] INFO  17:01:28,951 MicroScheduler -   -> 1232 reads (0.10% of total) failing BadMateFilter
[2016-04-15T00:01Z] INFO  17:01:28,952 MicroScheduler -   -> 56640 reads (4.59% of total) failing DuplicateReadFilter
[2016-04-15T00:01Z] INFO  17:01:28,952 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:01Z] INFO  17:01:28,953 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:01Z] INFO  17:01:28,954 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:01Z] INFO  17:01:28,954 MicroScheduler -   -> 537633 reads (43.56% of total) failing MappingQualityZeroFilter
[2016-04-15T00:01Z] INFO  17:01:28,955 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:01Z] INFO  17:01:28,955 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-15T00:01Z] INFO  17:01:28,956 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:01Z] INFO  17:01:30,391 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:01Z] INFO  17:01:30,419 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:01Z] GATK: realign ('16', 15596122, 31106473) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-15T00:01Z] GATK: realign ('18', 66346699, 78077248) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-15T00:01Z] INFO  17:01:32,098 ProgressMeter -     17:14944309   1.4942208E7    30.0 s       2.0 s       96.3%    31.0 s       1.0 s
[2016-04-15T00:01Z] INFO  17:01:33,191 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:01Z] INFO  17:01:33,194 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:01Z] INFO  17:01:33,195 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:01Z] INFO  17:01:33,195 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:01Z] INFO  17:01:33,200 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/18/R14-18105_kapa-NGv3-PE100-NGv3-sort-18_66346699_78077248-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/18/R14-18105_kapa-NGv3-PE100-NGv3-sort-18_66346699_78077248-prep-prealign-realign.intervals -L 18:66346700-78077248 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/18/tx/tmpNQw0gY/R14-18105_kapa-NGv3-PE100-NGv3-sort-18_66346699_78077248-prep.bam
[2016-04-15T00:01Z] INFO  17:01:33,215 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:01Z] INFO  17:01:33,216 HelpFormatter - Date/Time: 2016/04/14 17:01:33
[2016-04-15T00:01Z] INFO  17:01:33,217 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:01Z] INFO  17:01:33,217 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:01Z] INFO  17:01:33,268 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:01Z] INFO  17:01:33,271 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:01Z] INFO  17:01:33,271 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:01Z] INFO  17:01:33,271 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:01Z] INFO  17:01:33,275 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/16/R14-18105_kapa-NGv3-PE100-NGv3-sort-16_15596122_31106473-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/16/R14-18105_kapa-NGv3-PE100-NGv3-sort-16_15596122_31106473-prep-prealign-realign.intervals -L 16:15596123-31106473 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/16/tx/tmpf0tCeM/R14-18105_kapa-NGv3-PE100-NGv3-sort-16_15596122_31106473-prep.bam
[2016-04-15T00:01Z] INFO  17:01:33,311 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:01Z] INFO  17:01:33,312 HelpFormatter - Date/Time: 2016/04/14 17:01:33
[2016-04-15T00:01Z] INFO  17:01:33,312 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:01Z] INFO  17:01:33,313 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:01Z] INFO  17:01:33,409 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:01Z] INFO  17:01:33,467 ProgressMeter -            done   1.5511002E7    31.0 s       2.0 s      100.0%    31.0 s       0.0 s
[2016-04-15T00:01Z] INFO  17:01:33,468 ProgressMeter - Total runtime 31.38 secs, 0.52 min, 0.01 hours
[2016-04-15T00:01Z] INFO  17:01:33,471 MicroScheduler - 83481 reads were filtered out during the traversal out of approximately 916214 total reads (9.11%)
[2016-04-15T00:01Z] INFO  17:01:33,472 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:01Z] INFO  17:01:33,472 MicroScheduler -   -> 1506 reads (0.16% of total) failing BadMateFilter
[2016-04-15T00:01Z] INFO  17:01:33,472 MicroScheduler -   -> 71830 reads (7.84% of total) failing DuplicateReadFilter
[2016-04-15T00:01Z] INFO  17:01:33,473 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:01Z] INFO  17:01:33,473 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:01Z] INFO  17:01:33,473 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:01Z] INFO  17:01:33,473 MicroScheduler -   -> 10145 reads (1.11% of total) failing MappingQualityZeroFilter
[2016-04-15T00:01Z] INFO  17:01:33,474 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:01Z] INFO  17:01:33,474 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-15T00:01Z] INFO  17:01:33,474 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:01Z] INFO  17:01:33,478 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:01Z] INFO  17:01:33,543 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:01Z] INFO  17:01:33,553 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:01Z] INFO  17:01:33,593 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.04
[2016-04-15T00:01Z] INFO  17:01:33,634 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:01Z] INFO  17:01:33,644 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:01Z] INFO  17:01:33,706 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-15T00:01Z] INFO  17:01:33,960 IntervalUtils - Processing 11730549 bp from intervals
[2016-04-15T00:01Z] WARN  17:01:33,965 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:01Z] INFO  17:01:34,052 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:01Z] INFO  17:01:34,152 IntervalUtils - Processing 15510351 bp from intervals
[2016-04-15T00:01Z] WARN  17:01:34,157 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:01Z] INFO  17:01:34,163 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:01Z] INFO  17:01:34,164 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:01Z] INFO  17:01:34,165 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:01Z] INFO  17:01:34,165 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:01Z] INFO  17:01:34,273 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:01Z] INFO  17:01:34,303 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:01Z] INFO  17:01:34,389 ProgressMeter -            done    152356.0    12.0 s      80.0 s      100.0%    12.0 s       0.0 s
[2016-04-15T00:01Z] INFO  17:01:34,390 ProgressMeter - Total runtime 12.30 secs, 0.21 min, 0.00 hours
[2016-04-15T00:01Z] INFO  17:01:34,393 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 152356 total reads (0.00%)
[2016-04-15T00:01Z] INFO  17:01:34,394 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:01Z] INFO  17:01:34,395 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:01Z] INFO  17:01:34,396 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:01Z] INFO  17:01:34,419 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:01Z] INFO  17:01:34,440 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:01Z] INFO  17:01:34,444 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:01Z] INFO  17:01:34,445 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:01Z] INFO  17:01:34,445 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:01Z] INFO  17:01:34,592 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:01Z] INFO  17:01:34,727 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:01Z] INFO  17:01:34,857 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:01Z] GATK: realign ('17', 0, 15511002) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-15T00:01Z] INFO  17:01:36,016 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:01Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-18_50278423_66344430-prep.bam
[2016-04-15T00:01Z] GATK pre-alignment ('20', 31379406, 47242465) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-15T00:01Z] INFO  17:01:36,745 ProgressMeter -     16:70883776    400008.0    30.0 s      75.0 s       37.8%    79.0 s      49.0 s
[2016-04-15T00:01Z] INFO  17:01:37,683 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:01Z] INFO  17:01:37,687 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:01Z] INFO  17:01:37,687 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:01Z] INFO  17:01:37,688 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:01Z] INFO  17:01:37,693 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/17/R14-18105_kapa-NGv3-PE100-NGv3-sort-17_0_15511002-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/17/R14-18105_kapa-NGv3-PE100-NGv3-sort-17_0_15511002-prep-prealign-realign.intervals -L 17:1-15511002 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/17/tx/tmpG0V6g9/R14-18105_kapa-NGv3-PE100-NGv3-sort-17_0_15511002-prep.bam
[2016-04-15T00:01Z] INFO  17:01:37,712 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:01Z] INFO  17:01:37,712 HelpFormatter - Date/Time: 2016/04/14 17:01:37
[2016-04-15T00:01Z] INFO  17:01:37,713 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:01Z] INFO  17:01:37,713 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:01Z] INFO  17:01:37,734 ProgressMeter -     17:26971969    400006.0    30.0 s      75.0 s       73.8%    40.0 s      10.0 s
[2016-04-15T00:01Z] INFO  17:01:37,954 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:01Z] INFO  17:01:38,092 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:01Z] INFO  17:01:38,102 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:01Z] INFO  17:01:38,148 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.04
[2016-04-15T00:01Z] INFO  17:01:38,540 IntervalUtils - Processing 15511002 bp from intervals
[2016-04-15T00:01Z] WARN  17:01:38,545 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:01Z] INFO  17:01:38,612 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:01Z] INFO  17:01:38,735 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:01Z] INFO  17:01:38,737 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:01Z] INFO  17:01:38,737 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:01Z] INFO  17:01:38,738 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:01Z] INFO  17:01:38,969 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:01Z] INFO  17:01:39,255 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:01Z] INFO  17:01:39,259 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:01Z] INFO  17:01:39,265 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:01Z] INFO  17:01:39,259 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:01Z] INFO  17:01:39,277 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:01Z] INFO  17:01:39,282 HelpFormatter - Program Args: -T PrintReads -L 20:31379407-47242465 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/20/tx/tmpJnD2aL/R14-18105_kapa-NGv3-PE100-NGv3-sort-20_31379406_47242465-prep-prealign.bam
[2016-04-15T00:01Z] INFO  17:01:39,299 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:01Z] INFO  17:01:39,300 HelpFormatter - Date/Time: 2016/04/14 17:01:39
[2016-04-15T00:01Z] INFO  17:01:39,301 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:01Z] INFO  17:01:39,301 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:01Z] INFO  17:01:39,497 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:01Z] INFO  17:01:40,739 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-15T00:01Z] INFO  17:01:40,805 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:01Z] INFO  17:01:40,816 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:01Z] INFO  17:01:40,864 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-15T00:01Z] INFO  17:01:40,879 IntervalUtils - Processing 15863059 bp from intervals
[2016-04-15T00:01Z] INFO  17:01:40,955 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:01Z] INFO  17:01:41,268 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:01Z] INFO  17:01:41,270 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:01Z] INFO  17:01:41,271 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:01Z] INFO  17:01:41,271 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:01Z] INFO  17:01:41,297 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:01Z] INFO  17:01:41,386 ProgressMeter -     17:61910406    400007.0    31.0 s      78.0 s       98.6%    31.0 s       0.0 s
[2016-04-15T00:01Z] INFO  17:01:41,476 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:01Z] INFO  17:01:42,283 ProgressMeter -            done    520757.0    32.0 s      61.0 s      100.0%    32.0 s       0.0 s
[2016-04-15T00:01Z] INFO  17:01:42,283 ProgressMeter - Total runtime 32.28 secs, 0.54 min, 0.01 hours
[2016-04-15T00:01Z] INFO  17:01:42,287 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 520757 total reads (0.00%)
[2016-04-15T00:01Z] INFO  17:01:42,288 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:01Z] INFO  17:01:42,288 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:01Z] INFO  17:01:42,288 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:01Z] INFO  17:01:43,879 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:01Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-17_46607689_62121560-prep.bam
[2016-04-15T00:01Z] INFO  17:01:44,357 ProgressMeter -            done    132491.0    10.0 s      76.0 s       99.4%    10.0 s       0.0 s
[2016-04-15T00:01Z] INFO  17:01:44,357 ProgressMeter - Total runtime 10.19 secs, 0.17 min, 0.00 hours
[2016-04-15T00:01Z] INFO  17:01:44,361 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 132491 total reads (0.00%)
[2016-04-15T00:01Z] INFO  17:01:44,361 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:01Z] INFO  17:01:44,362 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:01Z] INFO  17:01:44,362 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:01Z] INFO  17:01:45,382 ProgressMeter -            done   1.5582935E7    26.0 s       1.0 s      100.0%    26.0 s       0.0 s
[2016-04-15T00:01Z] INFO  17:01:45,383 ProgressMeter - Total runtime 26.04 secs, 0.43 min, 0.01 hours
[2016-04-15T00:01Z] INFO  17:01:45,388 MicroScheduler - 53803 reads were filtered out during the traversal out of approximately 613817 total reads (8.77%)
[2016-04-15T00:01Z] INFO  17:01:45,389 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:01Z] INFO  17:01:45,390 MicroScheduler -   -> 1139 reads (0.19% of total) failing BadMateFilter
[2016-04-15T00:01Z] INFO  17:01:45,391 MicroScheduler -   -> 48564 reads (7.91% of total) failing DuplicateReadFilter
[2016-04-15T00:01Z] INFO  17:01:45,391 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:01Z] INFO  17:01:45,392 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:01Z] INFO  17:01:45,393 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:01Z] INFO  17:01:45,394 MicroScheduler -   -> 4100 reads (0.67% of total) failing MappingQualityZeroFilter
[2016-04-15T00:01Z] INFO  17:01:45,394 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:01Z] INFO  17:01:45,395 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-15T00:01Z] INFO  17:01:45,396 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:01Z] GATK pre-alignment ('20', 47244085, 62830269) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-15T00:01Z] INFO  17:01:45,802 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:01Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-18_66346699_78077248-prep.bam
[2016-04-15T00:01Z] GATK pre-alignment ('20', 62831244, 63025520) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-15T00:01Z] INFO  17:01:46,371 ProgressMeter -            done    636094.0    38.0 s      60.0 s      100.0%    38.0 s       0.0 s
[2016-04-15T00:01Z] INFO  17:01:46,372 ProgressMeter - Total runtime 38.66 secs, 0.64 min, 0.01 hours
[2016-04-15T00:01Z] INFO  17:01:46,376 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 636094 total reads (0.00%)
[2016-04-15T00:01Z] INFO  17:01:46,376 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:01Z] INFO  17:01:46,377 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:01Z] INFO  17:01:46,377 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:01Z] INFO  17:01:46,631 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:01Z] GATK: realign ('17', 62122219, 77705154) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-15T00:01Z] INFO  17:01:47,931 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:01Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-17_15515955_31039213-prep.bam
[2016-04-15T00:01Z] INFO  17:01:48,662 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:01Z] INFO  17:01:48,665 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:01Z] INFO  17:01:48,665 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:01Z] INFO  17:01:48,666 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:01Z] INFO  17:01:48,670 HelpFormatter - Program Args: -T PrintReads -L 20:47244086-62830269 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/20/tx/tmpN4Bxlx/R14-18105_kapa-NGv3-PE100-NGv3-sort-20_47244085_62830269-prep-prealign.bam
[2016-04-15T00:01Z] INFO  17:01:48,685 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:01Z] INFO  17:01:48,699 HelpFormatter - Date/Time: 2016/04/14 17:01:48
[2016-04-15T00:01Z] INFO  17:01:48,700 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:01Z] INFO  17:01:48,700 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:01Z] INFO  17:01:48,795 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:01Z] INFO  17:01:48,798 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:01Z] INFO  17:01:48,799 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:01Z] INFO  17:01:48,799 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:01Z] INFO  17:01:48,804 HelpFormatter - Program Args: -T PrintReads -L 20:62831245-63025520 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/20/tx/tmppZf6It/R14-18105_kapa-NGv3-PE100-NGv3-sort-20_62831244_63025520-prep-prealign.bam
[2016-04-15T00:01Z] INFO  17:01:48,840 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:01Z] INFO  17:01:48,841 HelpFormatter - Date/Time: 2016/04/14 17:01:48
[2016-04-15T00:01Z] INFO  17:01:48,842 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:01Z] INFO  17:01:48,843 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:01Z] INFO  17:01:48,878 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:01Z] INFO  17:01:49,004 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:01Z] INFO  17:01:49,570 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:01Z] INFO  17:01:49,573 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:01Z] INFO  17:01:49,574 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:01Z] INFO  17:01:49,574 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:01Z] INFO  17:01:49,578 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/17/R14-18105_kapa-NGv3-PE100-NGv3-sort-17_62122219_77705154-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/17/R14-18105_kapa-NGv3-PE100-NGv3-sort-17_62122219_77705154-prep-prealign-realign.intervals -L 17:62122220-77705154 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/17/tx/tmpBeON7Z/R14-18105_kapa-NGv3-PE100-NGv3-sort-17_62122219_77705154-prep.bam
[2016-04-15T00:01Z] INFO  17:01:49,602 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:01Z] INFO  17:01:49,603 HelpFormatter - Date/Time: 2016/04/14 17:01:49
[2016-04-15T00:01Z] INFO  17:01:49,603 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:01Z] INFO  17:01:49,604 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:01Z] INFO  17:01:49,723 ProgressMeter -            done    699927.0    42.0 s      61.0 s      100.0%    42.0 s       0.0 s
[2016-04-15T00:01Z] INFO  17:01:49,724 ProgressMeter - Total runtime 42.99 secs, 0.72 min, 0.01 hours
[2016-04-15T00:01Z] INFO  17:01:49,728 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 699927 total reads (0.00%)
[2016-04-15T00:01Z] INFO  17:01:49,729 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:01Z] INFO  17:01:49,730 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:01Z] INFO  17:01:49,731 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:01Z] INFO  17:01:49,885 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:01Z] GATK pre-alignment ('21', 0, 15517120) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-15T00:01Z] INFO  17:01:50,042 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-15T00:01Z] INFO  17:01:50,048 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:01Z] INFO  17:01:50,059 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:01Z] INFO  17:01:50,106 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:01Z] INFO  17:01:50,115 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:01Z] INFO  17:01:50,135 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-15T00:01Z] INFO  17:01:50,141 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-15T00:01Z] INFO  17:01:50,161 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-15T00:01Z] INFO  17:01:50,175 IntervalUtils - Processing 194276 bp from intervals
[2016-04-15T00:01Z] INFO  17:01:50,216 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:01Z] INFO  17:01:50,227 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:01Z] INFO  17:01:50,256 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:01Z] INFO  17:01:50,285 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-15T00:01Z] INFO  17:01:50,311 IntervalUtils - Processing 15586184 bp from intervals
[2016-04-15T00:01Z] INFO  17:01:50,409 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:01Z] INFO  17:01:50,414 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:01Z] INFO  17:01:50,415 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:01Z] INFO  17:01:50,416 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:01Z] INFO  17:01:50,417 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:01Z] INFO  17:01:50,430 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:01Z] INFO  17:01:50,433 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:01Z] INFO  17:01:50,642 IntervalUtils - Processing 15582935 bp from intervals
[2016-04-15T00:01Z] WARN  17:01:50,663 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:01Z] INFO  17:01:50,692 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:01Z] INFO  17:01:50,693 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:01Z] INFO  17:01:50,694 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:01Z] INFO  17:01:50,695 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:01Z] INFO  17:01:50,745 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:01Z] INFO  17:01:50,750 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:01Z] INFO  17:01:50,879 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:01Z] INFO  17:01:50,880 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:01Z] INFO  17:01:50,881 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:01Z] INFO  17:01:50,882 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:01Z] INFO  17:01:50,990 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:01Z] INFO  17:01:51,079 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:01Z] INFO  17:01:51,266 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:01Z] INFO  17:01:51,401 ProgressMeter -     19:36038237    100001.0    30.0 s       5.0 m       32.1%    93.0 s      63.0 s
[2016-04-15T00:01Z] INFO  17:01:51,518 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:01Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-16_64982511_80574976-prep.bam
[2016-04-15T00:01Z] INFO  17:01:52,968 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:01Z] INFO  17:01:52,971 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:01Z] INFO  17:01:52,972 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:01Z] INFO  17:01:52,972 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:01Z] INFO  17:01:52,977 HelpFormatter - Program Args: -T PrintReads -L 21:1-15517120 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/21/tx/tmpKCfBcI/R14-18105_kapa-NGv3-PE100-NGv3-sort-21_0_15517120-prep-prealign.bam
[2016-04-15T00:01Z] INFO  17:01:52,987 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:01Z] INFO  17:01:52,987 HelpFormatter - Date/Time: 2016/04/14 17:01:52
[2016-04-15T00:01Z] INFO  17:01:52,987 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:01Z] INFO  17:01:52,988 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:01Z] INFO  17:01:52,996 ProgressMeter -     19:49232843    200002.0    30.0 s       2.5 m       20.8%     2.4 m     113.0 s
[2016-04-15T00:01Z] INFO  17:01:53,191 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:01Z] GATK pre-alignment ('21', 15524893, 31045484) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-15T00:01Z] INFO  17:01:53,953 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@32d5a4c6
[2016-04-15T00:01Z] INFO  17:01:54,017 ProgressMeter -            done      8517.0     3.0 s       7.0 m       65.9%     4.0 s       1.0 s
[2016-04-15T00:01Z] INFO  17:01:54,018 ProgressMeter - Total runtime 3.60 secs, 0.06 min, 0.00 hours
[2016-04-15T00:01Z] INFO  17:01:54,019 MicroScheduler - 4 reads were filtered out during the traversal out of approximately 8521 total reads (0.05%)
[2016-04-15T00:01Z] INFO  17:01:54,019 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:01Z] INFO  17:01:54,020 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:01Z] INFO  17:01:54,021 MicroScheduler -   -> 4 reads (0.05% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:01Z] INFO  17:01:54,385 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-15T00:01Z] INFO  17:01:54,468 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:01Z] INFO  17:01:54,480 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:01Z] INFO  17:01:54,527 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-15T00:01Z] INFO  17:01:54,566 IntervalUtils - Processing 15517120 bp from intervals
[2016-04-15T00:01Z] INFO  17:01:54,670 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:01Z] INFO  17:01:54,745 ProgressMeter -      19:4538462    400006.0    60.0 s       2.5 m       29.3%     3.4 m       2.4 m
[2016-04-15T00:01Z] INFO  17:01:54,843 ProgressMeter -      20:5904189    200002.0    30.0 s       2.5 m       37.3%    80.0 s      50.0 s
[2016-04-15T00:01Z] INFO  17:01:55,017 ProgressMeter -      16:2764126    400009.0    30.0 s      76.0 s       17.8%     2.8 m       2.3 m
[2016-04-15T00:01Z] INFO  17:01:55,020 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:01Z] INFO  17:01:55,020 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:01Z] INFO  17:01:55,021 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:01Z] INFO  17:01:55,021 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:01Z] INFO  17:01:55,051 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:01Z] INFO  17:01:55,161 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:01Z] INFO  17:01:55,342 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:01Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-20_62831244_63025520-prep-prealign.bam
[2016-04-15T00:01Z] GATK RealignerTargetCreator: R14-18105_kapa-NGv3-PE100-NGv3-sort-20_62831244_63025520-prep-prealign.bam 20:62831245-63025520
[2016-04-15T00:01Z] GATK: RealignerTargetCreator
[2016-04-15T00:01Z] INFO  17:01:55,826 ProgressMeter -     19:22156571    400007.0    60.0 s       2.5 m       42.8%     2.3 m      80.0 s
[2016-04-15T00:01Z] INFO  17:01:55,879 ProgressMeter -     20:30414483    100003.0    30.0 s       5.0 m       93.8%    31.0 s       1.0 s
[2016-04-15T00:01Z] INFO  17:01:56,500 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:01Z] INFO  17:01:56,503 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:01Z] INFO  17:01:56,504 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:01Z] INFO  17:01:56,504 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:01Z] INFO  17:01:56,509 HelpFormatter - Program Args: -T PrintReads -L 21:15524894-31045484 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/21/tx/tmpcj9Gqx/R14-18105_kapa-NGv3-PE100-NGv3-sort-21_15524893_31045484-prep-prealign.bam
[2016-04-15T00:01Z] INFO  17:01:56,537 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:01Z] INFO  17:01:56,544 HelpFormatter - Date/Time: 2016/04/14 17:01:56
[2016-04-15T00:01Z] INFO  17:01:56,545 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:01Z] INFO  17:01:56,546 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:01Z] INFO  17:01:56,548 ProgressMeter -     17:44895793   1000016.0     2.5 m       2.5 m       89.0%     2.8 m      18.0 s
[2016-04-15T00:01Z] INFO  17:01:56,763 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:01Z] INFO  17:01:57,954 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-15T00:01Z] INFO  17:01:58,035 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:01Z] INFO  17:01:58,048 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:01Z] INFO  17:01:58,085 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.04
[2016-04-15T00:01Z] INFO  17:01:58,098 IntervalUtils - Processing 15520591 bp from intervals
[2016-04-15T00:01Z] INFO  17:01:58,168 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:01Z] INFO  17:01:58,387 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:01Z] INFO  17:01:58,388 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:01Z] INFO  17:01:58,389 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:01Z] INFO  17:01:58,390 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:01Z] INFO  17:01:58,403 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:01Z] INFO  17:01:58,519 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:01Z] INFO  17:01:58,521 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:01Z] INFO  17:01:58,533 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:01Z] INFO  17:01:58,533 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:01Z] INFO  17:01:58,537 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/20/R14-18105_kapa-NGv3-PE100-NGv3-sort-20_62831244_63025520-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/20/tx/tmpmYUVs4/R14-18105_kapa-NGv3-PE100-NGv3-sort-20_62831244_63025520-prep-prealign-realign.intervals -l INFO -L 20:62831245-63025520 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:01Z] INFO  17:01:58,554 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:01Z] INFO  17:01:58,554 HelpFormatter - Date/Time: 2016/04/14 17:01:58
[2016-04-15T00:01Z] INFO  17:01:58,554 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:01Z] INFO  17:01:58,555 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:01Z] INFO  17:01:58,609 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:01Z] INFO  17:01:58,692 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:01Z] INFO  17:01:58,882 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T00:01Z] INFO  17:01:58,891 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:01Z] INFO  17:01:58,952 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-15T00:01Z] INFO  17:01:59,183 IntervalUtils - Processing 194276 bp from intervals
[2016-04-15T00:01Z] WARN  17:01:59,188 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:01Z] INFO  17:01:59,254 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:01Z] INFO  17:01:59,355 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:01Z] INFO  17:01:59,356 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:01Z] INFO  17:01:59,357 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:01Z] INFO  17:01:59,357 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:02Z] INFO  17:02:01,248 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@7172f77a
[2016-04-15T00:02Z] INFO  17:02:01,537 ProgressMeter -            done    194276.0     2.0 s      11.0 s      100.0%     2.0 s       0.0 s
[2016-04-15T00:02Z] INFO  17:02:01,538 ProgressMeter - Total runtime 2.18 secs, 0.04 min, 0.00 hours
[2016-04-15T00:02Z] INFO  17:02:01,541 MicroScheduler - 1037 reads were filtered out during the traversal out of approximately 8517 total reads (12.18%)
[2016-04-15T00:02Z] INFO  17:02:01,542 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:02Z] INFO  17:02:01,543 MicroScheduler -   -> 18 reads (0.21% of total) failing BadMateFilter
[2016-04-15T00:02Z] INFO  17:02:01,544 MicroScheduler -   -> 633 reads (7.43% of total) failing DuplicateReadFilter
[2016-04-15T00:02Z] INFO  17:02:01,544 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:02Z] INFO  17:02:01,545 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:02Z] INFO  17:02:01,545 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:02Z] INFO  17:02:01,546 MicroScheduler -   -> 386 reads (4.53% of total) failing MappingQualityZeroFilter
[2016-04-15T00:02Z] INFO  17:02:01,547 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:02Z] INFO  17:02:01,547 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-15T00:02Z] INFO  17:02:01,548 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:02Z] INFO  17:02:01,539 ProgressMeter -            done    303111.0    36.0 s       2.0 m      100.0%    36.0 s       0.0 s
[2016-04-15T00:02Z] INFO  17:02:01,550 ProgressMeter - Total runtime 36.73 secs, 0.61 min, 0.01 hours
[2016-04-15T00:02Z] INFO  17:02:01,550 MicroScheduler - 177 reads were filtered out during the traversal out of approximately 303288 total reads (0.06%)
[2016-04-15T00:02Z] INFO  17:02:01,551 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:02Z] INFO  17:02:01,551 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:02Z] INFO  17:02:01,551 MicroScheduler -   -> 177 reads (0.06% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:02Z] INFO  17:02:01,914 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@5fe152b7
[2016-04-15T00:02Z] INFO  17:02:01,948 ProgressMeter -            done     36429.0     6.0 s       3.2 m      100.0%     6.0 s       0.0 s
[2016-04-15T00:02Z] INFO  17:02:01,948 ProgressMeter - Total runtime 6.93 secs, 0.12 min, 0.00 hours
[2016-04-15T00:02Z] INFO  17:02:01,949 MicroScheduler - 143 reads were filtered out during the traversal out of approximately 36572 total reads (0.39%)
[2016-04-15T00:02Z] INFO  17:02:01,949 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:02Z] INFO  17:02:01,950 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:02Z] INFO  17:02:01,950 MicroScheduler -   -> 143 reads (0.39% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:02Z] INFO  17:02:02,591 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@41fd9d8e
[2016-04-15T00:02Z] INFO  17:02:02,668 ProgressMeter -            done    248642.0    36.0 s       2.5 m      100.0%    36.0 s       0.0 s
[2016-04-15T00:02Z] INFO  17:02:02,669 ProgressMeter - Total runtime 36.83 secs, 0.61 min, 0.01 hours
[2016-04-15T00:02Z] INFO  17:02:02,669 MicroScheduler - 174 reads were filtered out during the traversal out of approximately 248816 total reads (0.07%)
[2016-04-15T00:02Z] INFO  17:02:02,669 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:02Z] INFO  17:02:02,670 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:02Z] INFO  17:02:02,670 MicroScheduler -   -> 174 reads (0.07% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:02Z] INFO  17:02:03,103 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:02Z] INFO  17:02:03,110 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:02Z] GATK: realign ('20', 62831244, 63025520) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-15T00:02Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-20_0_15843471-prep-prealign.bam
[2016-04-15T00:02Z] INFO  17:02:03,241 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:02Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-21_0_15517120-prep-prealign.bam
[2016-04-15T00:02Z] INFO  17:02:03,417 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@7172f77a
[2016-04-15T00:02Z] GATK RealignerTargetCreator: R14-18105_kapa-NGv3-PE100-NGv3-sort-21_0_15517120-prep-prealign.bam 21:1-15517120
[2016-04-15T00:02Z] GATK: RealignerTargetCreator
[2016-04-15T00:02Z] INFO  17:02:03,515 ProgressMeter -            done    576393.0    68.0 s     118.0 s      100.0%    68.0 s       0.0 s
[2016-04-15T00:02Z] INFO  17:02:03,516 ProgressMeter - Total runtime 68.29 secs, 1.14 min, 0.02 hours
[2016-04-15T00:02Z] INFO  17:02:03,517 MicroScheduler - 320 reads were filtered out during the traversal out of approximately 576713 total reads (0.06%)
[2016-04-15T00:02Z] INFO  17:02:03,518 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:02Z] INFO  17:02:03,519 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:02Z] INFO  17:02:03,520 MicroScheduler -   -> 320 reads (0.06% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:02Z] INFO  17:02:04,140 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:02Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-20_15866408_31376818-prep-prealign.bam
[2016-04-15T00:02Z] GATK RealignerTargetCreator: R14-18105_kapa-NGv3-PE100-NGv3-sort-20_0_15843471-prep-prealign.bam 20:1-15843471
[2016-04-15T00:02Z] GATK: RealignerTargetCreator
[2016-04-15T00:02Z] GATK RealignerTargetCreator: R14-18105_kapa-NGv3-PE100-NGv3-sort-20_15866408_31376818-prep-prealign.bam 20:15866409-31376818
[2016-04-15T00:02Z] GATK: RealignerTargetCreator
[2016-04-15T00:02Z] INFO  17:02:05,221 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:02Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-19_15510112_31025906-prep-prealign.bam
[2016-04-15T00:02Z] INFO  17:02:06,221 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:02Z] INFO  17:02:06,225 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:02Z] INFO  17:02:06,225 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:02Z] INFO  17:02:06,226 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:02Z] INFO  17:02:06,231 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/20/R14-18105_kapa-NGv3-PE100-NGv3-sort-20_62831244_63025520-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/20/R14-18105_kapa-NGv3-PE100-NGv3-sort-20_62831244_63025520-prep-prealign-realign.intervals -L 20:62831245-63025520 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/20/tx/tmpGPjihT/R14-18105_kapa-NGv3-PE100-NGv3-sort-20_62831244_63025520-prep.bam
[2016-04-15T00:02Z] INFO  17:02:06,243 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:02Z] INFO  17:02:06,243 HelpFormatter - Date/Time: 2016/04/14 17:02:06
[2016-04-15T00:02Z] INFO  17:02:06,244 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:02Z] INFO  17:02:06,244 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:02Z] INFO  17:02:06,260 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:02Z] INFO  17:02:06,263 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:02Z] INFO  17:02:06,263 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:02Z] INFO  17:02:06,263 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:02Z] INFO  17:02:06,268 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/21/R14-18105_kapa-NGv3-PE100-NGv3-sort-21_0_15517120-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/21/tx/tmpNs8IUp/R14-18105_kapa-NGv3-PE100-NGv3-sort-21_0_15517120-prep-prealign-realign.intervals -l INFO -L 21:1-15517120 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:02Z] INFO  17:02:06,276 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:02Z] INFO  17:02:06,276 HelpFormatter - Date/Time: 2016/04/14 17:02:06
[2016-04-15T00:02Z] INFO  17:02:06,276 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:02Z] INFO  17:02:06,276 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:02Z] INFO  17:02:06,295 ProgressMeter -     16:22145842    400011.0    31.0 s      79.0 s       42.2%    73.0 s      42.0 s
[2016-04-15T00:02Z] INFO  17:02:06,353 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:02Z] INFO  17:02:06,493 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:02Z] INFO  17:02:06,566 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T00:02Z] INFO  17:02:06,575 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:02Z] INFO  17:02:06,647 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-15T00:02Z] INFO  17:02:06,658 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:02Z] INFO  17:02:06,667 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:02Z] GATK RealignerTargetCreator: R14-18105_kapa-NGv3-PE100-NGv3-sort-19_15510112_31025906-prep-prealign.bam 19:15510113-31025906
[2016-04-15T00:02Z] GATK: RealignerTargetCreator
[2016-04-15T00:02Z] INFO  17:02:06,712 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.04
[2016-04-15T00:02Z] INFO  17:02:07,020 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:02Z] INFO  17:02:07,023 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:02Z] INFO  17:02:07,024 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:02Z] INFO  17:02:07,024 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:02Z] INFO  17:02:07,029 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/20/R14-18105_kapa-NGv3-PE100-NGv3-sort-20_0_15843471-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/20/tx/tmpC2j05p/R14-18105_kapa-NGv3-PE100-NGv3-sort-20_0_15843471-prep-prealign-realign.intervals -l INFO -L 20:1-15843471 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:02Z] INFO  17:02:07,045 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:02Z] INFO  17:02:07,045 HelpFormatter - Date/Time: 2016/04/14 17:02:07
[2016-04-15T00:02Z] INFO  17:02:07,046 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:02Z] INFO  17:02:07,046 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:02Z] INFO  17:02:07,045 IntervalUtils - Processing 15517120 bp from intervals
[2016-04-15T00:02Z] WARN  17:02:07,049 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:02Z] INFO  17:02:07,082 IntervalUtils - Processing 194276 bp from intervals
[2016-04-15T00:02Z] WARN  17:02:07,087 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:02Z] INFO  17:02:07,140 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:02Z] INFO  17:02:07,152 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:02Z] INFO  17:02:07,180 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:02Z] INFO  17:02:07,186 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:02Z] INFO  17:02:07,187 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:02Z] INFO  17:02:07,187 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:02Z] INFO  17:02:07,188 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:02Z] INFO  17:02:07,215 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:02Z] INFO  17:02:07,218 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:02Z] INFO  17:02:07,359 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:02Z] INFO  17:02:07,360 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:02Z] INFO  17:02:07,360 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:02Z] INFO  17:02:07,361 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:02Z] INFO  17:02:07,429 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T00:02Z] INFO  17:02:07,439 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:02Z] INFO  17:02:07,475 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@7172f77a
[2016-04-15T00:02Z] INFO  17:02:07,504 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-15T00:02Z] INFO  17:02:07,620 ProgressMeter -            done   1119253.0     2.7 m       2.4 m      100.0%     2.7 m       0.0 s
[2016-04-15T00:02Z] INFO  17:02:07,620 ProgressMeter - Total runtime 161.40 secs, 2.69 min, 0.04 hours
[2016-04-15T00:02Z] INFO  17:02:07,620 MicroScheduler - 473 reads were filtered out during the traversal out of approximately 1119726 total reads (0.04%)
[2016-04-15T00:02Z] INFO  17:02:07,621 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:02Z] INFO  17:02:07,621 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:02Z] INFO  17:02:07,621 MicroScheduler -   -> 473 reads (0.04% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:02Z] INFO  17:02:07,787 IntervalUtils - Processing 15843471 bp from intervals
[2016-04-15T00:02Z] WARN  17:02:07,792 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:02Z] INFO  17:02:07,864 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:02Z] INFO  17:02:08,056 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:02Z] INFO  17:02:08,057 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:02Z] INFO  17:02:08,058 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:02Z] INFO  17:02:08,058 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:02Z] INFO  17:02:08,064 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:02Z] INFO  17:02:08,067 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:02Z] INFO  17:02:08,067 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:02Z] INFO  17:02:08,067 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:02Z] INFO  17:02:08,071 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/20/R14-18105_kapa-NGv3-PE100-NGv3-sort-20_15866408_31376818-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/20/tx/tmpu9od5F/R14-18105_kapa-NGv3-PE100-NGv3-sort-20_15866408_31376818-prep-prealign-realign.intervals -l INFO -L 20:15866409-31376818 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:02Z] INFO  17:02:08,092 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:02Z] INFO  17:02:08,092 HelpFormatter - Date/Time: 2016/04/14 17:02:08
[2016-04-15T00:02Z] INFO  17:02:08,092 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:02Z] INFO  17:02:08,093 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:02Z] INFO  17:02:08,184 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:02Z] INFO  17:02:08,444 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T00:02Z] INFO  17:02:08,455 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:02Z] INFO  17:02:08,501 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.04
[2016-04-15T00:02Z] INFO  17:02:08,873 IntervalUtils - Processing 15510410 bp from intervals
[2016-04-15T00:02Z] WARN  17:02:08,878 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:02Z] INFO  17:02:08,983 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:02Z] INFO  17:02:09,215 ProgressMeter -      17:6021475    400011.0    30.0 s      76.0 s       38.8%    77.0 s      47.0 s
[2016-04-15T00:02Z] INFO  17:02:09,220 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:02Z] INFO  17:02:09,228 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:02Z] INFO  17:02:09,228 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:02Z] INFO  17:02:09,229 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:02Z] INFO  17:02:09,229 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:02Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-17_31048040_46607237-prep-prealign.bam
[2016-04-15T00:02Z] INFO  17:02:09,343 ProgressMeter -            done      8517.0     2.0 s       4.2 m       65.9%     3.0 s       1.0 s
[2016-04-15T00:02Z] INFO  17:02:09,344 ProgressMeter - Total runtime 2.16 secs, 0.04 min, 0.00 hours
[2016-04-15T00:02Z] INFO  17:02:09,348 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 8517 total reads (0.00%)
[2016-04-15T00:02Z] INFO  17:02:09,349 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:02Z] INFO  17:02:09,350 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:02Z] INFO  17:02:09,351 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:02Z] INFO  17:02:09,564 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:02Z] INFO  17:02:09,567 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:02Z] INFO  17:02:09,568 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:02Z] INFO  17:02:09,568 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:02Z] INFO  17:02:09,573 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/19/R14-18105_kapa-NGv3-PE100-NGv3-sort-19_15510112_31025906-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/19/tx/tmpJzbXnN/R14-18105_kapa-NGv3-PE100-NGv3-sort-19_15510112_31025906-prep-prealign-realign.intervals -l INFO -L 19:15510113-31025906 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:02Z] INFO  17:02:09,591 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:02Z] INFO  17:02:09,603 HelpFormatter - Date/Time: 2016/04/14 17:02:09
[2016-04-15T00:02Z] INFO  17:02:09,604 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:02Z] INFO  17:02:09,605 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:02Z] INFO  17:02:09,687 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:02Z] INFO  17:02:09,787 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@5fe152b7
[2016-04-15T00:02Z] INFO  17:02:09,843 ProgressMeter -            done     73166.0    11.0 s       2.6 m      100.0%    11.0 s       0.0 s
[2016-04-15T00:02Z] INFO  17:02:09,844 ProgressMeter - Total runtime 11.46 secs, 0.19 min, 0.00 hours
[2016-04-15T00:02Z] INFO  17:02:09,844 MicroScheduler - 108 reads were filtered out during the traversal out of approximately 73274 total reads (0.15%)
[2016-04-15T00:02Z] INFO  17:02:09,844 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:02Z] INFO  17:02:09,846 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:02Z] INFO  17:02:09,847 MicroScheduler -   -> 108 reads (0.15% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:02Z] INFO  17:02:09,971 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T00:02Z] INFO  17:02:09,995 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:02Z] INFO  17:02:10,068 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-15T00:02Z] INFO  17:02:10,528 IntervalUtils - Processing 15515794 bp from intervals
[2016-04-15T00:02Z] WARN  17:02:10,533 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:02Z] INFO  17:02:10,698 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:02Z] INFO  17:02:10,709 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:02Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-20_62831244_63025520-prep.bam
[2016-04-15T00:02Z] INFO  17:02:10,807 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:02Z] INFO  17:02:10,808 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:02Z] INFO  17:02:10,809 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:02Z] INFO  17:02:10,810 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:02Z] GATK pre-alignment ('21', 31062047, 46591599) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-15T00:02Z] INFO  17:02:11,359 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:02Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-21_15524893_31045484-prep-prealign.bam
[2016-04-15T00:02Z] INFO  17:02:11,495 ProgressMeter -     20:35269744    200002.0    30.0 s       2.5 m       24.5%     2.0 m      92.0 s
[2016-04-15T00:02Z] GATK RealignerTargetCreator: R14-18105_kapa-NGv3-PE100-NGv3-sort-21_15524893_31045484-prep-prealign.bam 21:15524894-31045484
[2016-04-15T00:02Z] GATK: RealignerTargetCreator
[2016-04-15T00:02Z] GATK RealignerTargetCreator: R14-18105_kapa-NGv3-PE100-NGv3-sort-17_31048040_46607237-prep-prealign.bam 17:31048041-46607237
[2016-04-15T00:02Z] GATK: RealignerTargetCreator
[2016-04-15T00:02Z] INFO  17:02:13,764 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:02Z] INFO  17:02:13,768 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:02Z] INFO  17:02:13,768 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:02Z] INFO  17:02:13,769 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:02Z] INFO  17:02:13,773 HelpFormatter - Program Args: -T PrintReads -L 21:31062048-46591599 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/21/tx/tmpcWxUIm/R14-18105_kapa-NGv3-PE100-NGv3-sort-21_31062047_46591599-prep-prealign.bam
[2016-04-15T00:02Z] INFO  17:02:13,794 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:02Z] INFO  17:02:13,795 HelpFormatter - Date/Time: 2016/04/14 17:02:13
[2016-04-15T00:02Z] INFO  17:02:13,796 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:02Z] INFO  17:02:13,796 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:02Z] INFO  17:02:13,937 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:02Z] INFO  17:02:14,643 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:02Z] INFO  17:02:14,647 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:02Z] INFO  17:02:14,647 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:02Z] INFO  17:02:14,648 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:02Z] INFO  17:02:14,653 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/21/R14-18105_kapa-NGv3-PE100-NGv3-sort-21_15524893_31045484-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/21/tx/tmpoxcJhM/R14-18105_kapa-NGv3-PE100-NGv3-sort-21_15524893_31045484-prep-prealign-realign.intervals -l INFO -L 21:15524894-31045484 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:02Z] INFO  17:02:14,662 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:02Z] INFO  17:02:14,673 HelpFormatter - Date/Time: 2016/04/14 17:02:14
[2016-04-15T00:02Z] INFO  17:02:14,674 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:02Z] INFO  17:02:14,675 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:02Z] INFO  17:02:14,806 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:02Z] INFO  17:02:15,042 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T00:02Z] INFO  17:02:15,056 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:02Z] INFO  17:02:15,109 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-15T00:02Z] INFO  17:02:15,114 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-15T00:02Z] INFO  17:02:15,162 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:02Z] INFO  17:02:15,167 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:02Z] INFO  17:02:15,168 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:02Z] INFO  17:02:15,168 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:02Z] INFO  17:02:15,168 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:02Z] INFO  17:02:15,173 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/17/R14-18105_kapa-NGv3-PE100-NGv3-sort-17_31048040_46607237-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/17/tx/tmpKxk1Ac/R14-18105_kapa-NGv3-PE100-NGv3-sort-17_31048040_46607237-prep-prealign-realign.intervals -l INFO -L 17:31048041-46607237 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:02Z] INFO  17:02:15,177 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:02Z] INFO  17:02:15,207 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:02Z] INFO  17:02:15,230 HelpFormatter - Date/Time: 2016/04/14 17:02:15
[2016-04-15T00:02Z] INFO  17:02:15,230 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:02Z] INFO  17:02:15,231 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:02Z] INFO  17:02:15,232 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-15T00:02Z] INFO  17:02:15,259 IntervalUtils - Processing 15529552 bp from intervals
[2016-04-15T00:02Z] INFO  17:02:15,386 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:02Z] INFO  17:02:15,431 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:02Z] INFO  17:02:15,541 IntervalUtils - Processing 15520591 bp from intervals
[2016-04-15T00:02Z] WARN  17:02:15,546 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:02Z] INFO  17:02:15,654 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:02Z] INFO  17:02:15,670 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T00:02Z] INFO  17:02:15,705 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:02Z] INFO  17:02:15,763 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-15T00:02Z] INFO  17:02:15,770 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:02Z] INFO  17:02:15,770 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:02Z] INFO  17:02:15,771 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:02Z] INFO  17:02:15,771 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:02Z] INFO  17:02:15,795 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:02Z] INFO  17:02:15,923 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:02Z] INFO  17:02:15,924 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:02Z] INFO  17:02:15,925 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:02Z] INFO  17:02:15,925 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:02Z] INFO  17:02:15,951 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:02Z] INFO  17:02:16,048 IntervalUtils - Processing 15559197 bp from intervals
[2016-04-15T00:02Z] WARN  17:02:16,064 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:02Z] INFO  17:02:16,265 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:02Z] INFO  17:02:16,492 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:02Z] INFO  17:02:16,493 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:02Z] INFO  17:02:16,494 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:02Z] INFO  17:02:16,495 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:02Z] INFO  17:02:17,707 ProgressMeter -            done    943828.0    53.0 s      56.0 s      100.0%    53.0 s       0.0 s
[2016-04-15T00:02Z] INFO  17:02:17,708 ProgressMeter - Total runtime 53.15 secs, 0.89 min, 0.01 hours
[2016-04-15T00:02Z] INFO  17:02:17,712 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 943828 total reads (0.00%)
[2016-04-15T00:02Z] INFO  17:02:17,712 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:02Z] INFO  17:02:17,712 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:02Z] INFO  17:02:17,713 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:02Z] INFO  17:02:18,388 ProgressMeter -            done   1.551712E7    11.0 s       0.0 s      100.0%    11.0 s       0.0 s
[2016-04-15T00:02Z] INFO  17:02:18,389 ProgressMeter - Total runtime 11.03 secs, 0.18 min, 0.00 hours
[2016-04-15T00:02Z] INFO  17:02:18,400 MicroScheduler - 11065 reads were filtered out during the traversal out of approximately 36459 total reads (30.35%)
[2016-04-15T00:02Z] INFO  17:02:18,402 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:02Z] INFO  17:02:18,402 MicroScheduler -   -> 185 reads (0.51% of total) failing BadMateFilter
[2016-04-15T00:02Z] INFO  17:02:18,403 MicroScheduler -   -> 2303 reads (6.32% of total) failing DuplicateReadFilter
[2016-04-15T00:02Z] INFO  17:02:18,404 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:02Z] INFO  17:02:18,404 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:02Z] INFO  17:02:18,405 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:02Z] INFO  17:02:18,405 MicroScheduler -   -> 8577 reads (23.53% of total) failing MappingQualityZeroFilter
[2016-04-15T00:02Z] INFO  17:02:18,406 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:02Z] INFO  17:02:18,407 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-15T00:02Z] INFO  17:02:18,407 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:02Z] INFO  17:02:19,344 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:02Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-16_0_15528616-prep.bam
[2016-04-15T00:02Z] INFO  17:02:19,779 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:02Z] GATK: realign ('21', 0, 15517120) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-15T00:02Z] INFO  17:02:20,751 ProgressMeter -     20:57767104    200002.0    30.0 s       2.5 m       67.5%    44.0 s      14.0 s
[2016-04-15T00:02Z] INFO  17:02:21,402 ProgressMeter -     19:38696968    300004.0    60.0 s       3.3 m       49.1%     2.0 m      62.0 s
[2016-04-15T00:02Z] GATK pre-alignment ('21', 46595644, 48129895) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-15T00:02Z] INFO  17:02:22,414 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:02Z] INFO  17:02:22,418 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:02Z] INFO  17:02:22,418 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:02Z] INFO  17:02:22,419 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:02Z] INFO  17:02:22,424 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/21/R14-18105_kapa-NGv3-PE100-NGv3-sort-21_0_15517120-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/21/R14-18105_kapa-NGv3-PE100-NGv3-sort-21_0_15517120-prep-prealign-realign.intervals -L 21:1-15517120 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/21/tx/tmpigeGNp/R14-18105_kapa-NGv3-PE100-NGv3-sort-21_0_15517120-prep.bam
[2016-04-15T00:02Z] INFO  17:02:22,436 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:02Z] INFO  17:02:22,436 HelpFormatter - Date/Time: 2016/04/14 17:02:22
[2016-04-15T00:02Z] INFO  17:02:22,437 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:02Z] INFO  17:02:22,437 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:02Z] INFO  17:02:22,685 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:02Z] INFO  17:02:22,766 ProgressMeter -     17:74288050    400005.0    31.0 s      79.0 s       78.1%    39.0 s       8.0 s
[2016-04-15T00:02Z] INFO  17:02:22,818 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:02Z] INFO  17:02:22,829 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:02Z] INFO  17:02:22,898 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-15T00:02Z] INFO  17:02:23,313 IntervalUtils - Processing 15517120 bp from intervals
[2016-04-15T00:02Z] INFO  17:02:23,315 ProgressMeter -     19:51190089    400006.0    60.0 s       2.5 m       36.5%     2.7 m     104.0 s
[2016-04-15T00:02Z] WARN  17:02:23,318 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:02Z] INFO  17:02:23,408 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:02Z] INFO  17:02:23,543 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:02Z] INFO  17:02:23,545 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:02Z] INFO  17:02:23,545 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:02Z] INFO  17:02:23,546 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:02Z] INFO  17:02:23,580 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:02Z] INFO  17:02:23,631 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:02Z] INFO  17:02:24,755 ProgressMeter -      19:7916211    700010.0    90.0 s       2.2 m       51.0%     2.9 m      86.0 s
[2016-04-15T00:02Z] INFO  17:02:24,975 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:02Z] INFO  17:02:24,979 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:02Z] INFO  17:02:24,980 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:02Z] INFO  17:02:24,980 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:02Z] INFO  17:02:24,985 HelpFormatter - Program Args: -T PrintReads -L 21:46595645-48129895 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/21/tx/tmpaq8_Hu/R14-18105_kapa-NGv3-PE100-NGv3-sort-21_46595644_48129895-prep-prealign.bam
[2016-04-15T00:02Z] INFO  17:02:24,996 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:02Z] INFO  17:02:24,997 HelpFormatter - Date/Time: 2016/04/14 17:02:24
[2016-04-15T00:02Z] INFO  17:02:24,997 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:02Z] INFO  17:02:24,998 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:02Z] INFO  17:02:25,166 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:02Z] INFO  17:02:26,213 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-15T00:02Z] INFO  17:02:26,277 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:02Z] INFO  17:02:26,286 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:02Z] INFO  17:02:26,327 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.04
[2016-04-15T00:02Z] INFO  17:02:26,343 IntervalUtils - Processing 1534251 bp from intervals
[2016-04-15T00:02Z] INFO  17:02:26,433 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:02Z] INFO  17:02:26,603 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:02Z] INFO  17:02:26,604 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:02Z] INFO  17:02:26,605 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:02Z] INFO  17:02:26,605 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:02Z] INFO  17:02:26,637 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:02Z] INFO  17:02:26,657 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:02Z] INFO  17:02:28,186 ProgressMeter -            done     36429.0     4.0 s       2.1 m      100.0%     4.0 s       0.0 s
[2016-04-15T00:02Z] INFO  17:02:28,187 ProgressMeter - Total runtime 4.64 secs, 0.08 min, 0.00 hours
[2016-04-15T00:02Z] INFO  17:02:28,191 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 36429 total reads (0.00%)
[2016-04-15T00:02Z] INFO  17:02:28,192 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:02Z] INFO  17:02:28,192 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:02Z] INFO  17:02:28,192 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:02Z] INFO  17:02:28,237 ProgressMeter -            done    610087.0    37.0 s      61.0 s      100.0%    37.0 s       0.0 s
[2016-04-15T00:02Z] INFO  17:02:28,238 ProgressMeter - Total runtime 37.36 secs, 0.62 min, 0.01 hours
[2016-04-15T00:02Z] INFO  17:02:28,248 ProgressMeter -            done   1.5843471E7    20.0 s       1.0 s      100.0%    20.0 s       0.0 s
[2016-04-15T00:02Z] INFO  17:02:28,249 ProgressMeter - Total runtime 20.19 secs, 0.34 min, 0.01 hours
[2016-04-15T00:02Z] INFO  17:02:28,255 MicroScheduler - 26232 reads were filtered out during the traversal out of approximately 305665 total reads (8.58%)
[2016-04-15T00:02Z] INFO  17:02:28,256 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:02Z] INFO  17:02:28,257 MicroScheduler -   -> 724 reads (0.24% of total) failing BadMateFilter
[2016-04-15T00:02Z] INFO  17:02:28,258 MicroScheduler -   -> 24496 reads (8.01% of total) failing DuplicateReadFilter
[2016-04-15T00:02Z] INFO  17:02:28,258 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:02Z] INFO  17:02:28,259 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:02Z] INFO  17:02:28,260 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:02Z] INFO  17:02:28,261 MicroScheduler -   -> 1012 reads (0.33% of total) failing MappingQualityZeroFilter
[2016-04-15T00:02Z] INFO  17:02:28,261 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 610087 total reads (0.00%)
[2016-04-15T00:02Z] INFO  17:02:28,261 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:02Z] INFO  17:02:28,261 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:02Z] INFO  17:02:28,261 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:02Z] INFO  17:02:28,262 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:02Z] INFO  17:02:28,262 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-15T00:02Z] INFO  17:02:28,263 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:02Z] INFO  17:02:28,448 ProgressMeter -            done   1.551041E7    19.0 s       1.0 s      100.0%    19.0 s       0.0 s
[2016-04-15T00:02Z] INFO  17:02:28,449 ProgressMeter - Total runtime 19.22 secs, 0.32 min, 0.01 hours
[2016-04-15T00:02Z] INFO  17:02:28,453 MicroScheduler - 21370 reads were filtered out during the traversal out of approximately 250348 total reads (8.54%)
[2016-04-15T00:02Z] INFO  17:02:28,454 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:02Z] INFO  17:02:28,454 MicroScheduler -   -> 622 reads (0.25% of total) failing BadMateFilter
[2016-04-15T00:02Z] INFO  17:02:28,455 MicroScheduler -   -> 19593 reads (7.83% of total) failing DuplicateReadFilter
[2016-04-15T00:02Z] INFO  17:02:28,456 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:02Z] INFO  17:02:28,456 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:02Z] INFO  17:02:28,457 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:02Z] INFO  17:02:28,457 MicroScheduler -   -> 1155 reads (0.46% of total) failing MappingQualityZeroFilter
[2016-04-15T00:02Z] INFO  17:02:28,458 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:02Z] INFO  17:02:28,459 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-15T00:02Z] INFO  17:02:28,459 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:02Z] INFO  17:02:29,688 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:02Z] GATK: realign ('20', 0, 15843471) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-15T00:02Z] INFO  17:02:29,744 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:02Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-21_0_15517120-prep.bam
[2016-04-15T00:02Z] INFO  17:02:29,827 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:02Z] INFO  17:02:29,852 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:02Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-17_62122219_77705154-prep.bam
[2016-04-15T00:02Z] GATK: realign ('20', 15866408, 31376818) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-15T00:02Z] GATK pre-alignment ('22', 0, 16258303) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-15T00:02Z] INFO  17:02:30,985 ProgressMeter -            done    911042.0    52.0 s      57.0 s      100.0%    52.0 s       0.0 s
[2016-04-15T00:02Z] INFO  17:02:30,986 ProgressMeter - Total runtime 52.25 secs, 0.87 min, 0.01 hours
[2016-04-15T00:02Z] INFO  17:02:30,991 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 911042 total reads (0.00%)
[2016-04-15T00:02Z] INFO  17:02:30,992 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:02Z] INFO  17:02:30,993 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:02Z] INFO  17:02:30,993 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:02Z] INFO  17:02:31,296 ProgressMeter -            done   1.5520591E7    15.0 s       0.0 s      100.0%    15.0 s       0.0 s
[2016-04-15T00:02Z] INFO  17:02:31,297 ProgressMeter - Total runtime 15.37 secs, 0.26 min, 0.00 hours
[2016-04-15T00:02Z] INFO  17:02:31,301 MicroScheduler - 6343 reads were filtered out during the traversal out of approximately 73574 total reads (8.62%)
[2016-04-15T00:02Z] INFO  17:02:31,301 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:02Z] INFO  17:02:31,302 MicroScheduler -   -> 381 reads (0.52% of total) failing BadMateFilter
[2016-04-15T00:02Z] INFO  17:02:31,302 MicroScheduler -   -> 5658 reads (7.69% of total) failing DuplicateReadFilter
[2016-04-15T00:02Z] INFO  17:02:31,302 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:02Z] INFO  17:02:31,303 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:02Z] INFO  17:02:31,303 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:02Z] INFO  17:02:31,303 MicroScheduler -   -> 304 reads (0.41% of total) failing MappingQualityZeroFilter
[2016-04-15T00:02Z] INFO  17:02:31,303 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:02Z] INFO  17:02:31,304 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-15T00:02Z] INFO  17:02:31,304 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:02Z] GATK pre-alignment ('22', 16266928, 31795711) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-15T00:02Z] INFO  17:02:32,554 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:02Z] INFO  17:02:32,558 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:02Z] INFO  17:02:32,558 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:02Z] INFO  17:02:32,559 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:02Z] INFO  17:02:32,563 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/20/R14-18105_kapa-NGv3-PE100-NGv3-sort-20_0_15843471-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/20/R14-18105_kapa-NGv3-PE100-NGv3-sort-20_0_15843471-prep-prealign-realign.intervals -L 20:1-15843471 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/20/tx/tmp8EPs3z/R14-18105_kapa-NGv3-PE100-NGv3-sort-20_0_15843471-prep.bam
[2016-04-15T00:02Z] INFO  17:02:32,572 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:02Z] INFO  17:02:32,575 HelpFormatter - Date/Time: 2016/04/14 17:02:32
[2016-04-15T00:02Z] INFO  17:02:32,576 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:02Z] INFO  17:02:32,576 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:02Z] INFO  17:02:32,654 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:02Z] INFO  17:02:32,662 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:02Z] GATK: realign ('21', 15524893, 31045484) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-15T00:02Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-17_0_15511002-prep.bam
[2016-04-15T00:02Z] INFO  17:02:32,757 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:02Z] INFO  17:02:32,760 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:02Z] INFO  17:02:32,761 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:02Z] INFO  17:02:32,761 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:02Z] INFO  17:02:32,766 HelpFormatter - Program Args: -T PrintReads -L 22:1-16258303 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/22/tx/tmpaYqS__/R14-18105_kapa-NGv3-PE100-NGv3-sort-22_0_16258303-prep-prealign.bam
[2016-04-15T00:02Z] INFO  17:02:32,789 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:02Z] INFO  17:02:32,790 HelpFormatter - Date/Time: 2016/04/14 17:02:32
[2016-04-15T00:02Z] INFO  17:02:32,790 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:02Z] INFO  17:02:32,791 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:02Z] INFO  17:02:32,803 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:02Z] INFO  17:02:32,952 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:02Z] INFO  17:02:32,956 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:02Z] INFO  17:02:32,957 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:02Z] INFO  17:02:32,957 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:02Z] INFO  17:02:32,962 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/20/R14-18105_kapa-NGv3-PE100-NGv3-sort-20_15866408_31376818-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/20/R14-18105_kapa-NGv3-PE100-NGv3-sort-20_15866408_31376818-prep-prealign-realign.intervals -L 20:15866409-31376818 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/20/tx/tmpAPE_lW/R14-18105_kapa-NGv3-PE100-NGv3-sort-20_15866408_31376818-prep.bam
[2016-04-15T00:02Z] INFO  17:02:32,967 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:02Z] INFO  17:02:32,971 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:02Z] INFO  17:02:32,976 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:02Z] INFO  17:02:32,990 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:02Z] INFO  17:02:32,991 HelpFormatter - Date/Time: 2016/04/14 17:02:32
[2016-04-15T00:02Z] INFO  17:02:32,991 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:02Z] INFO  17:02:32,992 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:02Z] INFO  17:02:33,039 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-15T00:02Z] INFO  17:02:33,215 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:02Z] INFO  17:02:33,346 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:02Z] INFO  17:02:33,366 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:02Z] INFO  17:02:33,400 IntervalUtils - Processing 15843471 bp from intervals
[2016-04-15T00:02Z] WARN  17:02:33,428 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:02Z] INFO  17:02:33,443 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-15T00:02Z] INFO  17:02:33,522 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:02Z] INFO  17:02:33,651 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:02Z] INFO  17:02:33,664 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:02Z] INFO  17:02:33,665 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:02Z] INFO  17:02:33,665 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:02Z] INFO  17:02:33,840 IntervalUtils - Processing 15510410 bp from intervals
[2016-04-15T00:02Z] WARN  17:02:33,849 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:02Z] INFO  17:02:33,866 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:02Z] INFO  17:02:33,920 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:02Z] INFO  17:02:34,025 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:02Z] INFO  17:02:34,044 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:02Z] INFO  17:02:34,052 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:02Z] INFO  17:02:34,052 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:02Z] INFO  17:02:34,053 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:02Z] INFO  17:02:34,113 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-15T00:02Z] INFO  17:02:34,227 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:02Z] INFO  17:02:34,237 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:02Z] INFO  17:02:34,255 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:02Z] INFO  17:02:34,345 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.09
[2016-04-15T00:02Z] INFO  17:02:34,371 IntervalUtils - Processing 16258303 bp from intervals
[2016-04-15T00:02Z] INFO  17:02:34,386 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:02Z] INFO  17:02:34,463 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:02Z] INFO  17:02:34,739 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:02Z] INFO  17:02:34,743 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:02Z] INFO  17:02:34,743 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:02Z] INFO  17:02:34,744 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:02Z] INFO  17:02:34,749 HelpFormatter - Program Args: -T PrintReads -L 22:16266929-31795711 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/22/tx/tmpxoyons/R14-18105_kapa-NGv3-PE100-NGv3-sort-22_16266928_31795711-prep-prealign.bam
[2016-04-15T00:02Z] INFO  17:02:34,759 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:02Z] INFO  17:02:34,759 HelpFormatter - Date/Time: 2016/04/14 17:02:34
[2016-04-15T00:02Z] INFO  17:02:34,760 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:02Z] INFO  17:02:34,760 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:02Z] INFO  17:02:34,791 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:02Z] INFO  17:02:34,792 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:02Z] INFO  17:02:34,793 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:02Z] INFO  17:02:34,794 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:02Z] INFO  17:02:34,825 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:02Z] INFO  17:02:34,828 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:02Z] INFO  17:02:34,956 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:02Z] INFO  17:02:35,567 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:02Z] INFO  17:02:35,586 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:02Z] INFO  17:02:35,587 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:02Z] INFO  17:02:35,588 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:02Z] INFO  17:02:35,592 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/21/R14-18105_kapa-NGv3-PE100-NGv3-sort-21_15524893_31045484-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/21/R14-18105_kapa-NGv3-PE100-NGv3-sort-21_15524893_31045484-prep-prealign-realign.intervals -L 21:15524894-31045484 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/21/tx/tmpMqwi_u/R14-18105_kapa-NGv3-PE100-NGv3-sort-21_15524893_31045484-prep.bam
[2016-04-15T00:02Z] INFO  17:02:35,611 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:02Z] INFO  17:02:35,612 HelpFormatter - Date/Time: 2016/04/14 17:02:35
[2016-04-15T00:02Z] INFO  17:02:35,612 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:02Z] INFO  17:02:35,613 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:02Z] GATK pre-alignment ('22', 31796605, 47308085) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-15T00:02Z] INFO  17:02:35,905 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:02Z] INFO  17:02:35,932 ProgressMeter -            done   1.5515794E7    25.0 s       1.0 s      100.0%    25.0 s       0.0 s
[2016-04-15T00:02Z] INFO  17:02:35,933 ProgressMeter - Total runtime 25.13 secs, 0.42 min, 0.01 hours
[2016-04-15T00:02Z] INFO  17:02:35,938 MicroScheduler - 53867 reads were filtered out during the traversal out of approximately 579682 total reads (9.29%)
[2016-04-15T00:02Z] INFO  17:02:35,939 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:02Z] INFO  17:02:35,940 MicroScheduler -   -> 1285 reads (0.22% of total) failing BadMateFilter
[2016-04-15T00:02Z] INFO  17:02:35,941 MicroScheduler -   -> 46520 reads (8.03% of total) failing DuplicateReadFilter
[2016-04-15T00:02Z] INFO  17:02:35,942 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:02Z] INFO  17:02:35,942 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:02Z] INFO  17:02:35,943 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:02Z] INFO  17:02:35,944 MicroScheduler -   -> 6062 reads (1.05% of total) failing MappingQualityZeroFilter
[2016-04-15T00:02Z] INFO  17:02:35,944 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:02Z] INFO  17:02:35,945 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-15T00:02Z] INFO  17:02:35,946 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:02Z] INFO  17:02:36,052 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:02Z] INFO  17:02:36,066 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:02Z] INFO  17:02:36,127 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-15T00:02Z] INFO  17:02:36,257 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-15T00:02Z] INFO  17:02:36,366 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:02Z] INFO  17:02:36,377 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:02Z] INFO  17:02:36,447 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-15T00:02Z] INFO  17:02:36,486 IntervalUtils - Processing 15528783 bp from intervals
[2016-04-15T00:02Z] INFO  17:02:36,518 IntervalUtils - Processing 15520591 bp from intervals
[2016-04-15T00:02Z] WARN  17:02:36,524 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:02Z] INFO  17:02:36,574 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:02Z] INFO  17:02:36,646 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:02Z] INFO  17:02:36,738 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:02Z] INFO  17:02:36,739 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:02Z] INFO  17:02:36,740 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:02Z] INFO  17:02:36,741 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:02Z] INFO  17:02:36,880 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:02Z] INFO  17:02:36,881 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:02Z] INFO  17:02:36,882 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:02Z] INFO  17:02:36,883 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:02Z] INFO  17:02:36,911 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:02Z] INFO  17:02:36,927 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:02Z] INFO  17:02:37,073 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:02Z] INFO  17:02:37,079 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:02Z] INFO  17:02:37,450 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:02Z] GATK: realign ('19', 15510112, 31025906) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-15T00:02Z] INFO  17:02:38,250 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@41fd9d8e
[2016-04-15T00:02Z] INFO  17:02:38,304 ProgressMeter -            done      8409.0     3.0 s       7.0 m      100.0%     3.0 s       0.0 s
[2016-04-15T00:02Z] INFO  17:02:38,305 ProgressMeter - Total runtime 3.51 secs, 0.06 min, 0.00 hours
[2016-04-15T00:02Z] INFO  17:02:38,305 MicroScheduler - 16 reads were filtered out during the traversal out of approximately 8425 total reads (0.19%)
[2016-04-15T00:02Z] INFO  17:02:38,305 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:02Z] INFO  17:02:38,306 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:02Z] INFO  17:02:38,306 MicroScheduler -   -> 16 reads (0.19% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:02Z] INFO  17:02:38,575 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:02Z] INFO  17:02:38,579 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:02Z] INFO  17:02:38,579 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:02Z] INFO  17:02:38,580 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:02Z] INFO  17:02:38,585 HelpFormatter - Program Args: -T PrintReads -L 22:31796606-47308085 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/22/tx/tmpzac4Lj/R14-18105_kapa-NGv3-PE100-NGv3-sort-22_31796605_47308085-prep-prealign.bam
[2016-04-15T00:02Z] INFO  17:02:38,611 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:02Z] INFO  17:02:38,612 HelpFormatter - Date/Time: 2016/04/14 17:02:38
[2016-04-15T00:02Z] INFO  17:02:38,612 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:02Z] INFO  17:02:38,612 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:02Z] INFO  17:02:38,851 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:02Z] INFO  17:02:39,759 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:02Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-22_0_16258303-prep-prealign.bam
[2016-04-15T00:02Z] GATK RealignerTargetCreator: R14-18105_kapa-NGv3-PE100-NGv3-sort-22_0_16258303-prep-prealign.bam 22:1-16258303
[2016-04-15T00:02Z] GATK: RealignerTargetCreator
[2016-04-15T00:02Z] INFO  17:02:40,094 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-15T00:02Z] INFO  17:02:40,173 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:02Z] INFO  17:02:40,182 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:02Z] INFO  17:02:40,218 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:02Z] INFO  17:02:40,221 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.04
[2016-04-15T00:02Z] INFO  17:02:40,221 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:02Z] INFO  17:02:40,222 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:02Z] INFO  17:02:40,223 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:02Z] INFO  17:02:40,227 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/19/R14-18105_kapa-NGv3-PE100-NGv3-sort-19_15510112_31025906-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/19/R14-18105_kapa-NGv3-PE100-NGv3-sort-19_15510112_31025906-prep-prealign-realign.intervals -L 19:15510113-31025906 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/19/tx/tmptFZFA0/R14-18105_kapa-NGv3-PE100-NGv3-sort-19_15510112_31025906-prep.bam
[2016-04-15T00:02Z] INFO  17:02:40,238 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:02Z] INFO  17:02:40,238 HelpFormatter - Date/Time: 2016/04/14 17:02:40
[2016-04-15T00:02Z] INFO  17:02:40,239 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:02Z] INFO  17:02:40,249 IntervalUtils - Processing 15511480 bp from intervals
[2016-04-15T00:02Z] INFO  17:02:40,250 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:02Z] INFO  17:02:40,381 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:02Z] INFO  17:02:40,467 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:02Z] INFO  17:02:40,485 ProgressMeter -     16:30240473   1000045.0    66.0 s      66.0 s       94.4%    69.0 s       3.0 s
[2016-04-15T00:02Z] INFO  17:02:40,558 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:02Z] INFO  17:02:40,582 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:02Z] INFO  17:02:40,620 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:02Z] INFO  17:02:40,641 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:02Z] INFO  17:02:40,641 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:02Z] INFO  17:02:40,641 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:02Z] INFO  17:02:40,643 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-15T00:02Z] INFO  17:02:40,667 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:02Z] INFO  17:02:40,852 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:02Z] INFO  17:02:40,972 IntervalUtils - Processing 15515794 bp from intervals
[2016-04-15T00:02Z] WARN  17:02:40,977 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:02Z] INFO  17:02:41,109 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:02Z] INFO  17:02:41,237 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:02Z] INFO  17:02:41,238 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:02Z] INFO  17:02:41,239 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:02Z] INFO  17:02:41,240 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:02Z] INFO  17:02:41,449 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:02Z] INFO  17:02:41,645 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:02Z] INFO  17:02:41,662 ProgressMeter -     20:44536554    400006.0    60.0 s       2.5 m       82.9%    72.0 s      12.0 s
[2016-04-15T00:02Z] INFO  17:02:42,837 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:02Z] INFO  17:02:42,840 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:02Z] INFO  17:02:42,841 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:02Z] INFO  17:02:42,841 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:02Z] INFO  17:02:42,846 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/22/R14-18105_kapa-NGv3-PE100-NGv3-sort-22_0_16258303-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/22/tx/tmpv6Dkr_/R14-18105_kapa-NGv3-PE100-NGv3-sort-22_0_16258303-prep-prealign-realign.intervals -l INFO -L 22:1-16258303 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:02Z] INFO  17:02:42,867 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:02Z] INFO  17:02:42,868 HelpFormatter - Date/Time: 2016/04/14 17:02:42
[2016-04-15T00:02Z] INFO  17:02:42,869 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:02Z] INFO  17:02:42,873 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:02Z] INFO  17:02:42,959 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:02Z] INFO  17:02:43,163 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T00:02Z] INFO  17:02:43,173 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:02Z] INFO  17:02:43,244 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-15T00:02Z] INFO  17:02:43,498 IntervalUtils - Processing 16258303 bp from intervals
[2016-04-15T00:02Z] WARN  17:02:43,503 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:02Z] INFO  17:02:43,571 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:02Z] INFO  17:02:43,886 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:02Z] INFO  17:02:43,886 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:02Z] INFO  17:02:43,887 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:02Z] INFO  17:02:43,887 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:02Z] INFO  17:02:45,265 ProgressMeter -            done     73166.0     8.0 s     116.0 s      100.0%     8.0 s       0.0 s
[2016-04-15T00:02Z] INFO  17:02:45,266 ProgressMeter - Total runtime 8.53 secs, 0.14 min, 0.00 hours
[2016-04-15T00:02Z] INFO  17:02:45,269 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 73166 total reads (0.00%)
[2016-04-15T00:02Z] INFO  17:02:45,270 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:02Z] INFO  17:02:45,270 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:02Z] INFO  17:02:45,271 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:02Z] INFO  17:02:45,484 ProgressMeter -            done   1227333.0    71.0 s      57.0 s      100.0%    71.0 s       0.0 s
[2016-04-15T00:02Z] INFO  17:02:45,485 ProgressMeter - Total runtime 71.04 secs, 1.18 min, 0.02 hours
[2016-04-15T00:02Z] INFO  17:02:45,488 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 1227333 total reads (0.00%)
[2016-04-15T00:02Z] INFO  17:02:45,489 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:02Z] INFO  17:02:45,489 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:02Z] INFO  17:02:45,489 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:02Z] INFO  17:02:45,652 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@41fd9d8e
[2016-04-15T00:02Z] INFO  17:02:45,712 ProgressMeter -            done    113531.0    19.0 s       2.8 m       97.0%    19.0 s       0.0 s
[2016-04-15T00:02Z] INFO  17:02:45,713 ProgressMeter - Total runtime 19.11 secs, 0.32 min, 0.01 hours
[2016-04-15T00:02Z] INFO  17:02:45,713 MicroScheduler - 43 reads were filtered out during the traversal out of approximately 113574 total reads (0.04%)
[2016-04-15T00:02Z] INFO  17:02:45,713 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:02Z] INFO  17:02:45,714 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:02Z] INFO  17:02:45,714 MicroScheduler -   -> 43 reads (0.04% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:02Z] INFO  17:02:45,788 ProgressMeter -     21:40568479    200002.0    30.0 s       2.5 m       61.2%    49.0 s      19.0 s
[2016-04-15T00:02Z] INFO  17:02:46,511 ProgressMeter -     17:44040125   1.2959384E7    30.0 s       2.0 s       83.5%    35.0 s       5.0 s
[2016-04-15T00:02Z] INFO  17:02:46,751 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:02Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-21_15524893_31045484-prep.bam
[2016-04-15T00:02Z] INFO  17:02:46,853 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@41fd9d8e
[2016-04-15T00:02Z] INFO  17:02:46,897 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:02Z] INFO  17:02:46,916 ProgressMeter -            done    468237.0    56.0 s     120.0 s      100.0%    56.0 s       0.0 s
[2016-04-15T00:02Z] INFO  17:02:46,917 ProgressMeter - Total runtime 56.22 secs, 0.94 min, 0.02 hours
[2016-04-15T00:02Z] INFO  17:02:46,917 MicroScheduler - 206 reads were filtered out during the traversal out of approximately 468443 total reads (0.04%)
[2016-04-15T00:02Z] INFO  17:02:46,918 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:02Z] INFO  17:02:46,919 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:02Z] INFO  17:02:46,919 MicroScheduler -   -> 206 reads (0.04% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:02Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-16_15596122_31106473-prep.bam
[2016-04-15T00:02Z] GATK pre-alignment ('22', 47309229, 51304566) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-15T00:02Z] INFO  17:02:47,075 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:02Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-21_46595644_48129895-prep-prealign.bam
[2016-04-15T00:02Z] GATK RealignerTargetCreator: R14-18105_kapa-NGv3-PE100-NGv3-sort-21_46595644_48129895-prep-prealign.bam 21:46595645-48129895
[2016-04-15T00:02Z] GATK: RealignerTargetCreator
[2016-04-15T00:02Z] INFO  17:02:48,333 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:02Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-20_47244085_62830269-prep-prealign.bam
[2016-04-15T00:02Z] GATK RealignerTargetCreator: R14-18105_kapa-NGv3-PE100-NGv3-sort-20_47244085_62830269-prep-prealign.bam 20:47244086-62830269
[2016-04-15T00:02Z] GATK: RealignerTargetCreator
[2016-04-15T00:02Z] INFO  17:02:50,064 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:02Z] INFO  17:02:50,068 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:02Z] INFO  17:02:50,068 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:02Z] INFO  17:02:50,069 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:02Z] INFO  17:02:50,073 HelpFormatter - Program Args: -T PrintReads -L 22:47309230-51304566 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/22/tx/tmpNO518d/R14-18105_kapa-NGv3-PE100-NGv3-sort-22_47309229_51304566-prep-prealign.bam
[2016-04-15T00:02Z] INFO  17:02:50,096 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:02Z] INFO  17:02:50,096 HelpFormatter - Date/Time: 2016/04/14 17:02:50
[2016-04-15T00:02Z] INFO  17:02:50,096 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:02Z] INFO  17:02:50,097 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:02Z] INFO  17:02:50,328 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:02Z] INFO  17:02:50,353 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:02Z] INFO  17:02:50,357 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:02Z] INFO  17:02:50,357 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:02Z] INFO  17:02:50,358 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:02Z] INFO  17:02:50,363 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/21/R14-18105_kapa-NGv3-PE100-NGv3-sort-21_46595644_48129895-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/21/tx/tmpojN8wd/R14-18105_kapa-NGv3-PE100-NGv3-sort-21_46595644_48129895-prep-prealign-realign.intervals -l INFO -L 21:46595645-48129895 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:02Z] INFO  17:02:50,385 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:02Z] INFO  17:02:50,396 HelpFormatter - Date/Time: 2016/04/14 17:02:50
[2016-04-15T00:02Z] INFO  17:02:50,397 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:02Z] INFO  17:02:50,398 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:02Z] INFO  17:02:50,535 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:02Z] GATK pre-alignment ('X', 0, 15509380) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-15T00:02Z] INFO  17:02:50,789 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T00:02Z] INFO  17:02:50,800 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:02Z] INFO  17:02:50,884 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-15T00:02Z] INFO  17:02:50,976 ProgressMeter -            done   1.5559197E7    34.0 s       2.0 s      100.0%    34.0 s       0.0 s
[2016-04-15T00:02Z] INFO  17:02:50,977 ProgressMeter - Total runtime 34.48 secs, 0.57 min, 0.01 hours
[2016-04-15T00:02Z] INFO  17:02:50,981 MicroScheduler - 228647 reads were filtered out during the traversal out of approximately 1127611 total reads (20.28%)
[2016-04-15T00:02Z] INFO  17:02:50,981 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:02Z] INFO  17:02:50,981 MicroScheduler -   -> 1680 reads (0.15% of total) failing BadMateFilter
[2016-04-15T00:02Z] INFO  17:02:50,982 MicroScheduler -   -> 79521 reads (7.05% of total) failing DuplicateReadFilter
[2016-04-15T00:02Z] INFO  17:02:50,982 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:02Z] INFO  17:02:50,982 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:02Z] INFO  17:02:50,982 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:02Z] INFO  17:02:50,983 MicroScheduler -   -> 147446 reads (13.08% of total) failing MappingQualityZeroFilter
[2016-04-15T00:02Z] INFO  17:02:50,983 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:02Z] INFO  17:02:50,983 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-15T00:02Z] INFO  17:02:50,983 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:02Z] INFO  17:02:51,286 IntervalUtils - Processing 1534251 bp from intervals
[2016-04-15T00:02Z] WARN  17:02:51,290 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:02Z] INFO  17:02:51,382 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:02Z] INFO  17:02:51,403 ProgressMeter -     19:40392129    500006.0    90.0 s       3.0 m       60.0%     2.5 m      59.0 s
[2016-04-15T00:02Z] INFO  17:02:51,403 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@52f3b59
[2016-04-15T00:02Z] INFO  17:02:51,520 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:02Z] INFO  17:02:51,521 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:02Z] INFO  17:02:51,523 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:02Z] INFO  17:02:51,524 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:02Z] INFO  17:02:51,526 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-15T00:02Z] INFO  17:02:51,532 ProgressMeter -            done    575346.0    70.0 s       2.0 m      100.0%    70.0 s       0.0 s
[2016-04-15T00:02Z] INFO  17:02:51,533 ProgressMeter - Total runtime 70.26 secs, 1.17 min, 0.02 hours
[2016-04-15T00:02Z] INFO  17:02:51,533 MicroScheduler - 259 reads were filtered out during the traversal out of approximately 575605 total reads (0.04%)
[2016-04-15T00:02Z] INFO  17:02:51,534 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:02Z] INFO  17:02:51,534 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:02Z] INFO  17:02:51,536 MicroScheduler -   -> 259 reads (0.04% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:02Z] INFO  17:02:51,591 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:02Z] INFO  17:02:51,600 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:02Z] INFO  17:02:51,640 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.04
[2016-04-15T00:02Z] INFO  17:02:51,655 IntervalUtils - Processing 3995337 bp from intervals
[2016-04-15T00:02Z] INFO  17:02:51,726 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:02Z] INFO  17:02:51,913 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:02Z] INFO  17:02:51,914 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:02Z] INFO  17:02:51,933 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:02Z] INFO  17:02:51,934 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:02Z] INFO  17:02:51,959 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:02Z] INFO  17:02:52,030 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:02Z] INFO  17:02:52,510 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:02Z] GATK: realign ('17', 31048040, 46607237) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-15T00:02Z] INFO  17:02:52,978 ProgressMeter -            done    248642.0    18.0 s      76.0 s      100.0%    18.0 s       0.0 s
[2016-04-15T00:02Z] INFO  17:02:52,978 ProgressMeter - Total runtime 18.93 secs, 0.32 min, 0.01 hours
[2016-04-15T00:02Z] INFO  17:02:52,981 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 248642 total reads (0.00%)
[2016-04-15T00:02Z] INFO  17:02:52,982 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:02Z] INFO  17:02:52,982 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:02Z] INFO  17:02:52,983 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:02Z] INFO  17:02:53,003 ProgressMeter -            done   1.6258303E7     9.0 s       0.0 s      100.0%     9.0 s       0.0 s
[2016-04-15T00:02Z] INFO  17:02:53,004 ProgressMeter - Total runtime 9.12 secs, 0.15 min, 0.00 hours
[2016-04-15T00:02Z] INFO  17:02:53,007 MicroScheduler - 5778 reads were filtered out during the traversal out of approximately 8409 total reads (68.71%)
[2016-04-15T00:02Z] INFO  17:02:53,010 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:02Z] INFO  17:02:53,011 MicroScheduler -   -> 8 reads (0.10% of total) failing BadMateFilter
[2016-04-15T00:02Z] INFO  17:02:53,012 MicroScheduler -   -> 278 reads (3.31% of total) failing DuplicateReadFilter
[2016-04-15T00:02Z] INFO  17:02:53,012 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:02Z] INFO  17:02:53,013 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:02Z] INFO  17:02:53,014 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:02Z] INFO  17:02:53,014 MicroScheduler -   -> 5492 reads (65.31% of total) failing MappingQualityZeroFilter
[2016-04-15T00:02Z] INFO  17:02:53,015 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:02Z] INFO  17:02:53,016 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-15T00:02Z] INFO  17:02:53,016 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:02Z] INFO  17:02:53,072 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:02Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-20_31379406_47242465-prep-prealign.bam
[2016-04-15T00:02Z] INFO  17:02:53,156 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:02Z] INFO  17:02:53,159 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:02Z] INFO  17:02:53,160 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:02Z] INFO  17:02:53,160 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:02Z] INFO  17:02:53,165 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/20/R14-18105_kapa-NGv3-PE100-NGv3-sort-20_47244085_62830269-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/20/tx/tmpe_NSID/R14-18105_kapa-NGv3-PE100-NGv3-sort-20_47244085_62830269-prep-prealign-realign.intervals -l INFO -L 20:47244086-62830269 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:02Z] INFO  17:02:53,179 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:02Z] INFO  17:02:53,180 HelpFormatter - Date/Time: 2016/04/14 17:02:53
[2016-04-15T00:02Z] INFO  17:02:53,181 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:02Z] INFO  17:02:53,181 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:02Z] INFO  17:02:53,316 ProgressMeter -     19:54577335    700010.0    90.0 s       2.2 m       63.6%     2.4 m      51.0 s
[2016-04-15T00:02Z] INFO  17:02:53,333 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:02Z] INFO  17:02:53,580 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:02Z] INFO  17:02:53,583 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:02Z] INFO  17:02:53,584 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:02Z] INFO  17:02:53,585 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:02Z] INFO  17:02:53,589 HelpFormatter - Program Args: -T PrintReads -L X:1-15509380 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/X/tx/tmp7VBQDZ/R14-18105_kapa-NGv3-PE100-NGv3-sort-X_0_15509380-prep-prealign.bam
[2016-04-15T00:02Z] INFO  17:02:53,600 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T00:02Z] INFO  17:02:53,609 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:02Z] INFO  17:02:53,626 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:02Z] INFO  17:02:53,627 HelpFormatter - Date/Time: 2016/04/14 17:02:53
[2016-04-15T00:02Z] INFO  17:02:53,627 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:02Z] INFO  17:02:53,628 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:02Z] INFO  17:02:53,672 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-15T00:02Z] INFO  17:02:53,750 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:02Z] INFO  17:02:54,029 IntervalUtils - Processing 15586184 bp from intervals
[2016-04-15T00:02Z] WARN  17:02:54,033 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:02Z] INFO  17:02:54,204 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:02Z] INFO  17:02:54,479 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:02Z] INFO  17:02:54,480 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:02Z] INFO  17:02:54,480 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:02Z] INFO  17:02:54,481 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:02Z] INFO  17:02:54,484 ProgressMeter -            done    303111.0    20.0 s      68.0 s      100.0%    20.0 s       0.0 s
[2016-04-15T00:02Z] INFO  17:02:54,485 ProgressMeter - Total runtime 20.82 secs, 0.35 min, 0.01 hours
[2016-04-15T00:02Z] INFO  17:02:54,489 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 303111 total reads (0.00%)
[2016-04-15T00:02Z] INFO  17:02:54,489 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:02Z] INFO  17:02:54,489 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:02Z] INFO  17:02:54,490 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:02Z] INFO  17:02:54,524 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:02Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-20_15866408_31376818-prep.bam
[2016-04-15T00:02Z] INFO  17:02:54,687 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:02Z] GATK: realign ('22', 0, 16258303) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-15T00:02Z] INFO  17:02:54,788 ProgressMeter -     19:10449611   1000015.0   120.0 s     120.0 s       67.4%     3.0 m      58.0 s
[2016-04-15T00:02Z] GATK RealignerTargetCreator: R14-18105_kapa-NGv3-PE100-NGv3-sort-20_31379406_47242465-prep-prealign.bam 20:31379407-47242465
[2016-04-15T00:02Z] GATK: RealignerTargetCreator
[2016-04-15T00:02Z] INFO  17:02:55,003 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-15T00:02Z] INFO  17:02:55,075 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:02Z] INFO  17:02:55,090 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:02Z] INFO  17:02:55,142 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-15T00:02Z] INFO  17:02:55,156 IntervalUtils - Processing 15509380 bp from intervals
[2016-04-15T00:02Z] INFO  17:02:55,263 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:02Z] GATK pre-alignment ('X', 15518899, 31090070) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-15T00:02Z] INFO  17:02:55,299 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:02Z] INFO  17:02:55,303 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:02Z] INFO  17:02:55,304 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:02Z] INFO  17:02:55,304 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:02Z] INFO  17:02:55,311 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/17/R14-18105_kapa-NGv3-PE100-NGv3-sort-17_31048040_46607237-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/17/R14-18105_kapa-NGv3-PE100-NGv3-sort-17_31048040_46607237-prep-prealign-realign.intervals -L 17:31048041-46607237 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/17/tx/tmpfX1RUW/R14-18105_kapa-NGv3-PE100-NGv3-sort-17_31048040_46607237-prep.bam
[2016-04-15T00:02Z] INFO  17:02:55,321 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:02Z] INFO  17:02:55,326 HelpFormatter - Date/Time: 2016/04/14 17:02:55
[2016-04-15T00:02Z] INFO  17:02:55,327 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:02Z] INFO  17:02:55,327 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:02Z] INFO  17:02:55,588 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:02Z] INFO  17:02:55,627 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:02Z] INFO  17:02:55,627 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:02Z] INFO  17:02:55,628 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:02Z] INFO  17:02:55,628 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:02Z] INFO  17:02:55,652 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:02Z] INFO  17:02:55,803 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:02Z] INFO  17:02:55,812 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:02Z] INFO  17:02:55,813 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:02Z] INFO  17:02:55,893 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-15T00:02Z] INFO  17:02:56,022 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:02Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-20_0_15843471-prep.bam
[2016-04-15T00:02Z] INFO  17:02:56,294 IntervalUtils - Processing 15559197 bp from intervals
[2016-04-15T00:02Z] WARN  17:02:56,299 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:02Z] INFO  17:02:56,405 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:02Z] INFO  17:02:56,635 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:02Z] INFO  17:02:56,636 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:02Z] INFO  17:02:56,636 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:02Z] INFO  17:02:56,637 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:02Z] INFO  17:02:56,832 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:02Z] GATK pre-alignment ('X', 31139949, 46696637) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-15T00:02Z] INFO  17:02:57,132 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:02Z] INFO  17:02:57,559 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:02Z] INFO  17:02:57,562 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:02Z] INFO  17:02:57,562 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:02Z] INFO  17:02:57,563 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:02Z] INFO  17:02:57,567 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/22/R14-18105_kapa-NGv3-PE100-NGv3-sort-22_0_16258303-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/22/R14-18105_kapa-NGv3-PE100-NGv3-sort-22_0_16258303-prep-prealign-realign.intervals -L 22:1-16258303 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/22/tx/tmpmtzk6L/R14-18105_kapa-NGv3-PE100-NGv3-sort-22_0_16258303-prep.bam
[2016-04-15T00:02Z] INFO  17:02:57,584 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:02Z] INFO  17:02:57,591 HelpFormatter - Date/Time: 2016/04/14 17:02:57
[2016-04-15T00:02Z] INFO  17:02:57,592 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:02Z] INFO  17:02:57,592 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:02Z] INFO  17:02:57,798 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:02Z] INFO  17:02:57,815 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:02Z] INFO  17:02:57,818 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:02Z] INFO  17:02:57,818 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:02Z] INFO  17:02:57,819 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:02Z] INFO  17:02:57,823 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/20/R14-18105_kapa-NGv3-PE100-NGv3-sort-20_31379406_47242465-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/20/tx/tmpSp93nh/R14-18105_kapa-NGv3-PE100-NGv3-sort-20_31379406_47242465-prep-prealign-realign.intervals -l INFO -L 20:31379407-47242465 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:02Z] INFO  17:02:57,845 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:02Z] INFO  17:02:57,849 HelpFormatter - Date/Time: 2016/04/14 17:02:57
[2016-04-15T00:02Z] INFO  17:02:57,851 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:02Z] INFO  17:02:57,852 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:02Z] INFO  17:02:57,978 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:02Z] INFO  17:02:57,981 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:02Z] INFO  17:02:57,990 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:02Z] INFO  17:02:58,042 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-15T00:02Z] INFO  17:02:58,201 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T00:02Z] INFO  17:02:58,221 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:02Z] INFO  17:02:58,296 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:02Z] INFO  17:02:58,300 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:02Z] INFO  17:02:58,300 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:02Z] INFO  17:02:58,301 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:02Z] INFO  17:02:58,306 HelpFormatter - Program Args: -T PrintReads -L X:15518900-31090070 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/X/tx/tmp5msKbC/R14-18105_kapa-NGv3-PE100-NGv3-sort-X_15518899_31090070-prep-prealign.bam
[2016-04-15T00:02Z] INFO  17:02:58,307 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-15T00:02Z] INFO  17:02:58,316 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:02Z] INFO  17:02:58,330 HelpFormatter - Date/Time: 2016/04/14 17:02:58
[2016-04-15T00:02Z] INFO  17:02:58,331 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:02Z] INFO  17:02:58,332 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:02Z] INFO  17:02:58,397 IntervalUtils - Processing 16258303 bp from intervals
[2016-04-15T00:02Z] WARN  17:02:58,412 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:02Z] INFO  17:02:58,506 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:02Z] INFO  17:02:58,530 ProgressMeter -            done   1534251.0     7.0 s       4.0 s      100.0%     7.0 s       0.0 s
[2016-04-15T00:02Z] INFO  17:02:58,532 ProgressMeter - Total runtime 7.01 secs, 0.12 min, 0.00 hours
[2016-04-15T00:02Z] INFO  17:02:58,535 MicroScheduler - 9357 reads were filtered out during the traversal out of approximately 114029 total reads (8.21%)
[2016-04-15T00:02Z] INFO  17:02:58,536 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:02Z] INFO  17:02:58,537 MicroScheduler -   -> 210 reads (0.18% of total) failing BadMateFilter
[2016-04-15T00:02Z] INFO  17:02:58,538 MicroScheduler -   -> 9001 reads (7.89% of total) failing DuplicateReadFilter
[2016-04-15T00:02Z] INFO  17:02:58,538 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:02Z] INFO  17:02:58,539 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:02Z] INFO  17:02:58,539 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:02Z] INFO  17:02:58,540 MicroScheduler -   -> 146 reads (0.13% of total) failing MappingQualityZeroFilter
[2016-04-15T00:02Z] INFO  17:02:58,541 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:02Z] INFO  17:02:58,541 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-15T00:02Z] INFO  17:02:58,542 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:02Z] INFO  17:02:58,579 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:02Z] INFO  17:02:58,664 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:02Z] INFO  17:02:58,666 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:02Z] INFO  17:02:58,666 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:02Z] INFO  17:02:58,667 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:02Z] INFO  17:02:58,684 IntervalUtils - Processing 15863059 bp from intervals
[2016-04-15T00:02Z] WARN  17:02:58,689 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:02Z] INFO  17:02:58,730 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:02Z] INFO  17:02:58,740 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:02Z] INFO  17:02:58,800 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:02Z] INFO  17:02:58,993 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:02Z] INFO  17:02:58,994 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:02Z] INFO  17:02:58,995 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:02Z] INFO  17:02:58,995 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:02Z] INFO  17:02:59,738 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-15T00:02Z] INFO  17:02:59,817 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:02Z] INFO  17:02:59,834 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:02Z] INFO  17:02:59,883 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-15T00:02Z] INFO  17:02:59,897 IntervalUtils - Processing 15571171 bp from intervals
[2016-04-15T00:02Z] INFO  17:02:59,946 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:02Z] GATK: realign ('21', 46595644, 48129895) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-15T00:02Z] INFO  17:02:59,991 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:03Z] INFO  17:03:00,173 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:03Z] INFO  17:03:00,178 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:03Z] INFO  17:03:00,179 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:03Z] INFO  17:03:00,179 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:03Z] INFO  17:03:00,184 HelpFormatter - Program Args: -T PrintReads -L X:31139950-46696637 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/X/tx/tmpTizJWP/R14-18105_kapa-NGv3-PE100-NGv3-sort-X_31139949_46696637-prep-prealign.bam
[2016-04-15T00:03Z] INFO  17:03:00,197 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:03Z] INFO  17:03:00,220 HelpFormatter - Date/Time: 2016/04/14 17:03:00
[2016-04-15T00:03Z] INFO  17:03:00,221 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:03Z] INFO  17:03:00,222 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:03Z] INFO  17:03:00,281 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:03Z] INFO  17:03:00,282 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:03Z] INFO  17:03:00,283 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:03Z] INFO  17:03:00,301 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:03Z] INFO  17:03:00,319 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:03Z] INFO  17:03:00,419 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:03Z] INFO  17:03:00,473 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:03Z] INFO  17:03:00,739 ProgressMeter -            done      8409.0     2.0 s       4.1 m      100.0%     2.0 s       0.0 s
[2016-04-15T00:03Z] INFO  17:03:00,740 ProgressMeter - Total runtime 2.07 secs, 0.03 min, 0.00 hours
[2016-04-15T00:03Z] INFO  17:03:00,744 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 8409 total reads (0.00%)
[2016-04-15T00:03Z] INFO  17:03:00,744 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:03Z] INFO  17:03:00,746 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:03Z] INFO  17:03:00,747 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:03Z] INFO  17:03:01,656 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-15T00:03Z] INFO  17:03:01,715 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:03Z] INFO  17:03:01,724 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:03Z] INFO  17:03:01,757 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.03
[2016-04-15T00:03Z] INFO  17:03:01,771 IntervalUtils - Processing 15556688 bp from intervals
[2016-04-15T00:03Z] INFO  17:03:01,837 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:03Z] INFO  17:03:02,171 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:03Z] INFO  17:03:02,172 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:03Z] INFO  17:03:02,173 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:03Z] INFO  17:03:02,173 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:03Z] INFO  17:03:02,221 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:03Z] INFO  17:03:02,266 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:03Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-22_0_16258303-prep.bam
[2016-04-15T00:03Z] GATK pre-alignment ('X', 46712910, 62570698) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-15T00:03Z] INFO  17:03:02,455 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:03Z] INFO  17:03:02,783 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:03Z] INFO  17:03:02,786 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:03Z] INFO  17:03:02,787 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:03Z] INFO  17:03:02,787 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:03Z] INFO  17:03:02,799 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/21/R14-18105_kapa-NGv3-PE100-NGv3-sort-21_46595644_48129895-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/21/R14-18105_kapa-NGv3-PE100-NGv3-sort-21_46595644_48129895-prep-prealign-realign.intervals -L 21:46595645-48129895 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/21/tx/tmpRSq3MT/R14-18105_kapa-NGv3-PE100-NGv3-sort-21_46595644_48129895-prep.bam
[2016-04-15T00:03Z] INFO  17:03:02,809 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:03Z] INFO  17:03:02,810 HelpFormatter - Date/Time: 2016/04/14 17:03:02
[2016-04-15T00:03Z] INFO  17:03:02,810 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:03Z] INFO  17:03:02,811 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:03Z] INFO  17:03:03,044 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:03Z] INFO  17:03:03,263 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:03Z] INFO  17:03:03,290 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:03Z] INFO  17:03:03,364 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-15T00:03Z] INFO  17:03:03,783 IntervalUtils - Processing 1534251 bp from intervals
[2016-04-15T00:03Z] WARN  17:03:03,787 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:03Z] INFO  17:03:03,937 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:03Z] INFO  17:03:03,997 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:03Z] INFO  17:03:03,998 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:03Z] INFO  17:03:03,999 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:03Z] INFO  17:03:04,000 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:03Z] INFO  17:03:04,077 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:03Z] INFO  17:03:04,094 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:03Z] INFO  17:03:05,649 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:03Z] INFO  17:03:05,652 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:03Z] INFO  17:03:05,653 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:03Z] INFO  17:03:05,653 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:03Z] INFO  17:03:05,658 HelpFormatter - Program Args: -T PrintReads -L X:46712911-62570698 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/X/tx/tmphvxLeV/R14-18105_kapa-NGv3-PE100-NGv3-sort-X_46712910_62570698-prep-prealign.bam
[2016-04-15T00:03Z] INFO  17:03:05,669 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:03Z] INFO  17:03:05,670 HelpFormatter - Date/Time: 2016/04/14 17:03:05
[2016-04-15T00:03Z] INFO  17:03:05,670 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:03Z] INFO  17:03:05,671 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:03Z] INFO  17:03:05,837 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:03Z] INFO  17:03:07,137 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-15T00:03Z] INFO  17:03:07,202 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:03Z] INFO  17:03:07,211 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:03Z] INFO  17:03:07,258 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-15T00:03Z] INFO  17:03:07,282 IntervalUtils - Processing 15857788 bp from intervals
[2016-04-15T00:03Z] INFO  17:03:07,374 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:03Z] INFO  17:03:07,624 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:03Z] INFO  17:03:07,624 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:03Z] INFO  17:03:07,624 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:03Z] INFO  17:03:07,625 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:03Z] INFO  17:03:07,640 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:03Z] INFO  17:03:07,683 ProgressMeter -     22:20095060    100009.0    30.0 s       5.1 m       24.7%     2.0 m      91.0 s
[2016-04-15T00:03Z] INFO  17:03:07,798 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:03Z] INFO  17:03:10,656 ProgressMeter -     22:38119963    100001.0    30.0 s       5.0 m       40.8%    73.0 s      43.0 s
[2016-04-15T00:03Z] INFO  17:03:11,262 ProgressMeter -     19:19644215    300005.0    30.0 s     100.0 s       26.6%   112.0 s      82.0 s
[2016-04-15T00:03Z] INFO  17:03:11,814 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@41fd9d8e
[2016-04-15T00:03Z] INFO  17:03:11,925 ProgressMeter -            done    471995.0    56.0 s     118.0 s      100.0%    56.0 s       0.0 s
[2016-04-15T00:03Z] INFO  17:03:11,926 ProgressMeter - Total runtime 56.16 secs, 0.94 min, 0.02 hours
[2016-04-15T00:03Z] INFO  17:03:11,926 MicroScheduler - 209 reads were filtered out during the traversal out of approximately 472204 total reads (0.04%)
[2016-04-15T00:03Z] INFO  17:03:11,927 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:03Z] INFO  17:03:11,927 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:03Z] INFO  17:03:11,928 MicroScheduler -   -> 209 reads (0.04% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:03Z] INFO  17:03:12,505 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@32d5a4c6
[2016-04-15T00:03Z] INFO  17:03:12,602 ProgressMeter -            done    125405.0    16.0 s       2.3 m      100.0%    16.0 s       0.0 s
[2016-04-15T00:03Z] INFO  17:03:12,603 ProgressMeter - Total runtime 16.98 secs, 0.28 min, 0.00 hours
[2016-04-15T00:03Z] INFO  17:03:12,604 MicroScheduler - 130 reads were filtered out during the traversal out of approximately 125535 total reads (0.10%)
[2016-04-15T00:03Z] INFO  17:03:12,605 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:03Z] INFO  17:03:12,606 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:03Z] INFO  17:03:12,606 MicroScheduler -   -> 130 reads (0.10% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:03Z] INFO  17:03:13,060 ProgressMeter -            done    113531.0     9.0 s      79.0 s       97.0%     9.0 s       0.0 s
[2016-04-15T00:03Z] INFO  17:03:13,062 ProgressMeter - Total runtime 9.06 secs, 0.15 min, 0.00 hours
[2016-04-15T00:03Z] INFO  17:03:13,067 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 113531 total reads (0.00%)
[2016-04-15T00:03Z] INFO  17:03:13,068 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:03Z] INFO  17:03:13,069 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:03Z] INFO  17:03:13,070 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:03Z] INFO  17:03:13,298 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:03Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-21_31062047_46591599-prep-prealign.bam
[2016-04-15T00:03Z] INFO  17:03:14,064 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@41fd9d8e
[2016-04-15T00:03Z] INFO  17:03:14,099 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@7172f77a
[2016-04-15T00:03Z] INFO  17:03:14,117 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:03Z] INFO  17:03:14,142 ProgressMeter -            done     77691.0    11.0 s       2.6 m      100.0%    11.0 s       0.0 s
[2016-04-15T00:03Z] INFO  17:03:14,143 ProgressMeter - Total runtime 11.97 secs, 0.20 min, 0.00 hours
[2016-04-15T00:03Z] INFO  17:03:14,143 MicroScheduler - 90 reads were filtered out during the traversal out of approximately 77781 total reads (0.12%)
[2016-04-15T00:03Z] INFO  17:03:14,143 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:03Z] INFO  17:03:14,144 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:03Z] INFO  17:03:14,144 MicroScheduler -   -> 90 reads (0.12% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:03Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-X_0_15509380-prep-prealign.bam
[2016-04-15T00:03Z] INFO  17:03:14,198 ProgressMeter -            done    158346.0    22.0 s       2.3 m       97.9%    22.0 s       0.0 s
[2016-04-15T00:03Z] INFO  17:03:14,198 ProgressMeter - Total runtime 22.28 secs, 0.37 min, 0.01 hours
[2016-04-15T00:03Z] INFO  17:03:14,199 MicroScheduler - 84 reads were filtered out during the traversal out of approximately 158430 total reads (0.05%)
[2016-04-15T00:03Z] INFO  17:03:14,199 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:03Z] INFO  17:03:14,199 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:03Z] INFO  17:03:14,199 MicroScheduler -   -> 84 reads (0.05% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:03Z] INFO  17:03:14,434 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:03Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-21_46595644_48129895-prep.bam
[2016-04-15T00:03Z] GATK RealignerTargetCreator: R14-18105_kapa-NGv3-PE100-NGv3-sort-X_0_15509380-prep-prealign.bam X:1-15509380
[2016-04-15T00:03Z] GATK: RealignerTargetCreator
[2016-04-15T00:03Z] GATK RealignerTargetCreator: R14-18105_kapa-NGv3-PE100-NGv3-sort-21_31062047_46591599-prep-prealign.bam 21:31062048-46591599
[2016-04-15T00:03Z] GATK: RealignerTargetCreator
[2016-04-15T00:03Z] GATK pre-alignment ('X', 62857907, 78427545) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-15T00:03Z] INFO  17:03:15,487 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:03Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-X_31139949_46696637-prep-prealign.bam
[2016-04-15T00:03Z] INFO  17:03:15,664 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:03Z] INFO  17:03:15,699 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@5fe152b7
[2016-04-15T00:03Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-22_47309229_51304566-prep-prealign.bam
[2016-04-15T00:03Z] INFO  17:03:15,820 ProgressMeter -            done     99559.0    15.0 s       2.6 m      100.0%    15.0 s       0.0 s
[2016-04-15T00:03Z] INFO  17:03:15,822 ProgressMeter - Total runtime 15.54 secs, 0.26 min, 0.00 hours
[2016-04-15T00:03Z] INFO  17:03:15,823 MicroScheduler - 110 reads were filtered out during the traversal out of approximately 99669 total reads (0.11%)
[2016-04-15T00:03Z] INFO  17:03:15,823 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:03Z] INFO  17:03:15,824 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:03Z] INFO  17:03:15,825 MicroScheduler -   -> 110 reads (0.11% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:03Z] GATK RealignerTargetCreator: R14-18105_kapa-NGv3-PE100-NGv3-sort-X_31139949_46696637-prep-prealign.bam X:31139950-46696637
[2016-04-15T00:03Z] GATK: RealignerTargetCreator
[2016-04-15T00:03Z] GATK RealignerTargetCreator: R14-18105_kapa-NGv3-PE100-NGv3-sort-22_47309229_51304566-prep-prealign.bam 22:47309230-51304566
[2016-04-15T00:03Z] GATK: RealignerTargetCreator
[2016-04-15T00:03Z] INFO  17:03:17,484 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:03Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-X_15518899_31090070-prep-prealign.bam
[2016-04-15T00:03Z] INFO  17:03:17,627 ProgressMeter -            done   1.5586184E7    23.0 s       1.0 s      100.0%    23.0 s       0.0 s
[2016-04-15T00:03Z] INFO  17:03:17,628 ProgressMeter - Total runtime 23.15 secs, 0.39 min, 0.01 hours
[2016-04-15T00:03Z] INFO  17:03:17,631 MicroScheduler - 39661 reads were filtered out during the traversal out of approximately 470781 total reads (8.42%)
[2016-04-15T00:03Z] INFO  17:03:17,632 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:03Z] INFO  17:03:17,632 MicroScheduler -   -> 1055 reads (0.22% of total) failing BadMateFilter
[2016-04-15T00:03Z] INFO  17:03:17,633 MicroScheduler -   -> 37752 reads (8.02% of total) failing DuplicateReadFilter
[2016-04-15T00:03Z] INFO  17:03:17,633 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:03Z] INFO  17:03:17,633 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:03Z] INFO  17:03:17,633 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:03Z] INFO  17:03:17,633 MicroScheduler -   -> 854 reads (0.18% of total) failing MappingQualityZeroFilter
[2016-04-15T00:03Z] INFO  17:03:17,634 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:03Z] INFO  17:03:17,634 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-15T00:03Z] INFO  17:03:17,634 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:03Z] INFO  17:03:17,749 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:03Z] INFO  17:03:17,752 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:03Z] INFO  17:03:17,753 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:03Z] INFO  17:03:17,754 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:03Z] INFO  17:03:17,759 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/X/R14-18105_kapa-NGv3-PE100-NGv3-sort-X_0_15509380-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/X/tx/tmpSh9Clo/R14-18105_kapa-NGv3-PE100-NGv3-sort-X_0_15509380-prep-prealign-realign.intervals -l INFO -L X:1-15509380 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:03Z] INFO  17:03:17,784 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:03Z] INFO  17:03:17,802 HelpFormatter - Date/Time: 2016/04/14 17:03:17
[2016-04-15T00:03Z] INFO  17:03:17,803 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:03Z] INFO  17:03:17,804 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:03Z] INFO  17:03:17,830 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:03Z] INFO  17:03:17,843 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:03Z] INFO  17:03:17,844 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:03Z] INFO  17:03:17,844 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:03Z] INFO  17:03:17,849 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/21/R14-18105_kapa-NGv3-PE100-NGv3-sort-21_31062047_46591599-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/21/tx/tmpo1aidb/R14-18105_kapa-NGv3-PE100-NGv3-sort-21_31062047_46591599-prep-prealign-realign.intervals -l INFO -L 21:31062048-46591599 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:03Z] INFO  17:03:17,848 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:03Z] INFO  17:03:17,851 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:03Z] INFO  17:03:17,852 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:03Z] INFO  17:03:17,852 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:03Z] INFO  17:03:17,857 HelpFormatter - Program Args: -T PrintReads -L X:62857908-78427545 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/X/tx/tmpp2gL9s/R14-18105_kapa-NGv3-PE100-NGv3-sort-X_62857907_78427545-prep-prealign.bam
[2016-04-15T00:03Z] INFO  17:03:17,860 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:03Z] INFO  17:03:17,861 HelpFormatter - Date/Time: 2016/04/14 17:03:17
[2016-04-15T00:03Z] INFO  17:03:17,861 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:03Z] INFO  17:03:17,862 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:03Z] INFO  17:03:17,889 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:03Z] INFO  17:03:17,890 HelpFormatter - Date/Time: 2016/04/14 17:03:17
[2016-04-15T00:03Z] INFO  17:03:17,890 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:03Z] INFO  17:03:17,891 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:03Z] INFO  17:03:17,907 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:03Z] INFO  17:03:17,962 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:03Z] GATK RealignerTargetCreator: R14-18105_kapa-NGv3-PE100-NGv3-sort-X_15518899_31090070-prep-prealign.bam X:15518900-31090070
[2016-04-15T00:03Z] GATK: RealignerTargetCreator
[2016-04-15T00:03Z] INFO  17:03:18,046 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:03Z] INFO  17:03:18,192 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T00:03Z] INFO  17:03:18,218 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T00:03Z] INFO  17:03:18,227 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:03Z] INFO  17:03:18,229 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:03Z] INFO  17:03:18,296 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-15T00:03Z] INFO  17:03:18,329 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.10
[2016-04-15T00:03Z] INFO  17:03:18,568 IntervalUtils - Processing 15529552 bp from intervals
[2016-04-15T00:03Z] WARN  17:03:18,573 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:03Z] INFO  17:03:18,700 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:03Z] INFO  17:03:18,765 IntervalUtils - Processing 15509380 bp from intervals
[2016-04-15T00:03Z] WARN  17:03:18,781 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:03Z] INFO  17:03:18,794 ProgressMeter -            done    576393.0    37.0 s      65.0 s      100.0%    37.0 s       0.0 s
[2016-04-15T00:03Z] INFO  17:03:18,795 ProgressMeter - Total runtime 37.56 secs, 0.63 min, 0.01 hours
[2016-04-15T00:03Z] INFO  17:03:18,798 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 576393 total reads (0.00%)
[2016-04-15T00:03Z] INFO  17:03:18,799 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:03Z] INFO  17:03:18,799 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:03Z] INFO  17:03:18,799 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:03Z] INFO  17:03:18,906 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:03Z] INFO  17:03:18,908 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:03Z] INFO  17:03:18,908 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:03Z] INFO  17:03:18,909 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:03Z] INFO  17:03:18,920 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:03Z] INFO  17:03:18,924 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:03Z] INFO  17:03:18,924 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:03Z] INFO  17:03:18,925 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:03Z] INFO  17:03:18,928 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:03Z] INFO  17:03:18,930 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/X/R14-18105_kapa-NGv3-PE100-NGv3-sort-X_31139949_46696637-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/X/tx/tmpfaFY7X/R14-18105_kapa-NGv3-PE100-NGv3-sort-X_31139949_46696637-prep-prealign-realign.intervals -l INFO -L X:31139950-46696637 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:03Z] INFO  17:03:18,943 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:03Z] INFO  17:03:18,944 HelpFormatter - Date/Time: 2016/04/14 17:03:18
[2016-04-15T00:03Z] INFO  17:03:18,944 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:03Z] INFO  17:03:18,945 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:03Z] INFO  17:03:19,042 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:03Z] INFO  17:03:19,125 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:03Z] INFO  17:03:19,126 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:03Z] INFO  17:03:19,127 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:03Z] INFO  17:03:19,128 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:03Z] INFO  17:03:19,148 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:03Z] GATK: realign ('20', 47244085, 62830269) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-15T00:03Z] INFO  17:03:19,257 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-15T00:03Z] INFO  17:03:19,263 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T00:03Z] INFO  17:03:19,272 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:03Z] INFO  17:03:19,320 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:03Z] INFO  17:03:19,331 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:03Z] INFO  17:03:19,335 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-15T00:03Z] INFO  17:03:19,385 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-15T00:03Z] INFO  17:03:19,409 IntervalUtils - Processing 15569638 bp from intervals
[2016-04-15T00:03Z] INFO  17:03:19,513 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:03Z] INFO  17:03:19,551 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:03Z] INFO  17:03:19,554 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:03Z] INFO  17:03:19,555 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:03Z] INFO  17:03:19,555 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:03Z] INFO  17:03:19,560 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/22/R14-18105_kapa-NGv3-PE100-NGv3-sort-22_47309229_51304566-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/22/tx/tmpykVPm0/R14-18105_kapa-NGv3-PE100-NGv3-sort-22_47309229_51304566-prep-prealign-realign.intervals -l INFO -L 22:47309230-51304566 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:03Z] INFO  17:03:19,601 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:03Z] INFO  17:03:19,602 HelpFormatter - Date/Time: 2016/04/14 17:03:19
[2016-04-15T00:03Z] INFO  17:03:19,602 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:03Z] INFO  17:03:19,607 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:03Z] INFO  17:03:19,621 IntervalUtils - Processing 15556688 bp from intervals
[2016-04-15T00:03Z] WARN  17:03:19,626 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:03Z] INFO  17:03:19,709 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:03Z] INFO  17:03:19,715 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:03Z] INFO  17:03:19,837 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:03Z] INFO  17:03:19,838 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:03Z] INFO  17:03:19,849 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:03Z] INFO  17:03:19,850 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:03Z] INFO  17:03:19,875 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:03Z] INFO  17:03:19,880 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:03Z] INFO  17:03:19,882 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:03Z] INFO  17:03:19,883 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:03Z] INFO  17:03:19,883 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:03Z] INFO  17:03:19,989 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T00:03Z] INFO  17:03:20,005 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:03Z] INFO  17:03:20,073 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-15T00:03Z] INFO  17:03:20,099 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:03Z] INFO  17:03:20,171 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:03Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-19_15510112_31025906-prep.bam
[2016-04-15T00:03Z] INFO  17:03:20,373 IntervalUtils - Processing 3995337 bp from intervals
[2016-04-15T00:03Z] WARN  17:03:20,379 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:03Z] INFO  17:03:20,558 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:03Z] INFO  17:03:20,627 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:03Z] INFO  17:03:20,628 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:03Z] INFO  17:03:20,629 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:03Z] INFO  17:03:20,629 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:03Z] INFO  17:03:20,869 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:03Z] INFO  17:03:20,872 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:03Z] INFO  17:03:20,873 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:03Z] INFO  17:03:20,873 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:03Z] INFO  17:03:20,878 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/X/R14-18105_kapa-NGv3-PE100-NGv3-sort-X_15518899_31090070-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/X/tx/tmpm2q_Dh/R14-18105_kapa-NGv3-PE100-NGv3-sort-X_15518899_31090070-prep-prealign-realign.intervals -l INFO -L X:15518900-31090070 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:03Z] INFO  17:03:20,900 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:03Z] INFO  17:03:20,900 HelpFormatter - Date/Time: 2016/04/14 17:03:20
[2016-04-15T00:03Z] INFO  17:03:20,900 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:03Z] INFO  17:03:20,901 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:03Z] INFO  17:03:21,002 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:03Z] INFO  17:03:21,207 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T00:03Z] INFO  17:03:21,219 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:03Z] INFO  17:03:21,273 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-15T00:03Z] INFO  17:03:21,404 ProgressMeter -     19:42315298    700009.0   120.0 s       2.9 m       72.3%     2.8 m      45.0 s
[2016-04-15T00:03Z] INFO  17:03:21,720 IntervalUtils - Processing 15571171 bp from intervals
[2016-04-15T00:03Z] WARN  17:03:21,735 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:03Z] INFO  17:03:21,859 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:03Z] GATK pre-alignment ('X', 78616585, 95940189) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-15T00:03Z] INFO  17:03:22,072 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:03Z] INFO  17:03:22,073 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:03Z] INFO  17:03:22,075 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:03Z] INFO  17:03:22,076 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:03Z] INFO  17:03:22,123 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:03Z] INFO  17:03:22,126 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:03Z] INFO  17:03:22,127 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:03Z] INFO  17:03:22,128 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:03Z] INFO  17:03:22,131 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/20/R14-18105_kapa-NGv3-PE100-NGv3-sort-20_47244085_62830269-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/20/R14-18105_kapa-NGv3-PE100-NGv3-sort-20_47244085_62830269-prep-prealign-realign.intervals -L 20:47244086-62830269 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/20/tx/tmpJONonp/R14-18105_kapa-NGv3-PE100-NGv3-sort-20_47244085_62830269-prep.bam
[2016-04-15T00:03Z] INFO  17:03:22,140 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:03Z] INFO  17:03:22,141 HelpFormatter - Date/Time: 2016/04/14 17:03:22
[2016-04-15T00:03Z] INFO  17:03:22,142 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:03Z] INFO  17:03:22,142 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:03Z] INFO  17:03:22,304 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:03Z] INFO  17:03:22,436 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:03Z] INFO  17:03:22,445 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:03Z] INFO  17:03:22,535 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.09
[2016-04-15T00:03Z] INFO  17:03:22,928 IntervalUtils - Processing 15586184 bp from intervals
[2016-04-15T00:03Z] WARN  17:03:22,932 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:03Z] INFO  17:03:23,051 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:03Z] INFO  17:03:23,265 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:03Z] INFO  17:03:23,266 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:03Z] INFO  17:03:23,267 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:03Z] INFO  17:03:23,267 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:03Z] INFO  17:03:23,317 ProgressMeter -     19:56151680   1000024.0   120.0 s     120.0 s       76.2%     2.6 m      37.0 s
[2016-04-15T00:03Z] INFO  17:03:23,456 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:03Z] INFO  17:03:23,638 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:03Z] INFO  17:03:24,647 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:03Z] INFO  17:03:24,651 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:03Z] INFO  17:03:24,652 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:03Z] INFO  17:03:24,652 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:03Z] INFO  17:03:24,657 HelpFormatter - Program Args: -T PrintReads -L X:78616586-95940189 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/X/tx/tmpJNEK3U/R14-18105_kapa-NGv3-PE100-NGv3-sort-X_78616585_95940189-prep-prealign.bam
[2016-04-15T00:03Z] INFO  17:03:24,677 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:03Z] INFO  17:03:24,678 HelpFormatter - Date/Time: 2016/04/14 17:03:24
[2016-04-15T00:03Z] INFO  17:03:24,678 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:03Z] INFO  17:03:24,678 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:03Z] INFO  17:03:24,944 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:03Z] INFO  17:03:25,119 ProgressMeter -     19:12924009   1200018.0     2.5 m       2.1 m       83.3%     3.0 m      30.0 s
[2016-04-15T00:03Z] INFO  17:03:25,467 ProgressMeter -            done   1.5863059E7    26.0 s       1.0 s      100.0%    26.0 s       0.0 s
[2016-04-15T00:03Z] INFO  17:03:25,468 ProgressMeter - Total runtime 26.47 secs, 0.44 min, 0.01 hours
[2016-04-15T00:03Z] INFO  17:03:25,473 MicroScheduler - 47952 reads were filtered out during the traversal out of approximately 578842 total reads (8.28%)
[2016-04-15T00:03Z] INFO  17:03:25,475 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:03Z] INFO  17:03:25,475 MicroScheduler -   -> 1223 reads (0.21% of total) failing BadMateFilter
[2016-04-15T00:03Z] INFO  17:03:25,476 MicroScheduler -   -> 46062 reads (7.96% of total) failing DuplicateReadFilter
[2016-04-15T00:03Z] INFO  17:03:25,477 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:03Z] INFO  17:03:25,478 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:03Z] INFO  17:03:25,478 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:03Z] INFO  17:03:25,479 MicroScheduler -   -> 667 reads (0.12% of total) failing MappingQualityZeroFilter
[2016-04-15T00:03Z] INFO  17:03:25,480 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:03Z] INFO  17:03:25,481 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-15T00:03Z] INFO  17:03:25,481 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:03Z] INFO  17:03:26,188 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-15T00:03Z] INFO  17:03:26,242 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:03Z] INFO  17:03:26,252 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:03Z] INFO  17:03:26,293 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.04
[2016-04-15T00:03Z] INFO  17:03:26,308 IntervalUtils - Processing 17323604 bp from intervals
[2016-04-15T00:03Z] INFO  17:03:26,382 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:03Z] INFO  17:03:26,616 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:03Z] INFO  17:03:26,617 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:03Z] INFO  17:03:26,617 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:03Z] INFO  17:03:26,618 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:03Z] INFO  17:03:26,631 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:03Z] INFO  17:03:26,666 ProgressMeter -     17:38249567    400006.0    30.0 s      75.0 s       46.3%    64.0 s      34.0 s
[2016-04-15T00:03Z] INFO  17:03:26,775 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:03Z] INFO  17:03:26,954 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:03Z] GATK: realign ('20', 31379406, 47242465) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-15T00:03Z] INFO  17:03:29,499 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:03Z] INFO  17:03:29,503 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:03Z] INFO  17:03:29,504 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:03Z] INFO  17:03:29,505 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:03Z] INFO  17:03:29,510 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/20/R14-18105_kapa-NGv3-PE100-NGv3-sort-20_31379406_47242465-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/20/R14-18105_kapa-NGv3-PE100-NGv3-sort-20_31379406_47242465-prep-prealign-realign.intervals -L 20:31379407-47242465 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/20/tx/tmpdF6c1L/R14-18105_kapa-NGv3-PE100-NGv3-sort-20_31379406_47242465-prep.bam
[2016-04-15T00:03Z] INFO  17:03:29,522 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:03Z] INFO  17:03:29,523 HelpFormatter - Date/Time: 2016/04/14 17:03:29
[2016-04-15T00:03Z] INFO  17:03:29,523 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:03Z] INFO  17:03:29,523 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:03Z] INFO  17:03:29,584 ProgressMeter -            done   3995337.0     8.0 s       2.0 s      100.0%     8.0 s       0.0 s
[2016-04-15T00:03Z] INFO  17:03:29,585 ProgressMeter - Total runtime 8.96 secs, 0.15 min, 0.00 hours
[2016-04-15T00:03Z] INFO  17:03:29,607 MicroScheduler - 14400 reads were filtered out during the traversal out of approximately 159820 total reads (9.01%)
[2016-04-15T00:03Z] INFO  17:03:29,608 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:03Z] INFO  17:03:29,609 MicroScheduler -   -> 345 reads (0.22% of total) failing BadMateFilter
[2016-04-15T00:03Z] INFO  17:03:29,610 MicroScheduler -   -> 12699 reads (7.95% of total) failing DuplicateReadFilter
[2016-04-15T00:03Z] INFO  17:03:29,610 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:03Z] INFO  17:03:29,611 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:03Z] INFO  17:03:29,612 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:03Z] INFO  17:03:29,612 MicroScheduler -   -> 1356 reads (0.85% of total) failing MappingQualityZeroFilter
[2016-04-15T00:03Z] INFO  17:03:29,613 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:03Z] INFO  17:03:29,614 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-15T00:03Z] INFO  17:03:29,614 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:03Z] INFO  17:03:29,748 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:03Z] INFO  17:03:29,855 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:03Z] INFO  17:03:29,867 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:03Z] INFO  17:03:29,926 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-15T00:03Z] INFO  17:03:30,302 IntervalUtils - Processing 15863059 bp from intervals
[2016-04-15T00:03Z] WARN  17:03:30,306 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:03Z] INFO  17:03:30,396 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:03Z] INFO  17:03:30,493 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:03Z] INFO  17:03:30,495 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:03Z] INFO  17:03:30,496 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:03Z] INFO  17:03:30,496 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:03Z] INFO  17:03:30,697 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:03Z] INFO  17:03:30,864 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:03Z] INFO  17:03:31,363 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:03Z] GATK: realign ('22', 47309229, 51304566) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-15T00:03Z] INFO  17:03:33,661 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@7172f77a
[2016-04-15T00:03Z] INFO  17:03:33,792 ProgressMeter -            done     35131.0     7.0 s       3.4 m      100.0%     7.0 s       0.0 s
[2016-04-15T00:03Z] INFO  17:03:33,792 ProgressMeter - Total runtime 7.18 secs, 0.12 min, 0.00 hours
[2016-04-15T00:03Z] INFO  17:03:33,793 MicroScheduler - 66 reads were filtered out during the traversal out of approximately 35197 total reads (0.19%)
[2016-04-15T00:03Z] INFO  17:03:33,793 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:03Z] INFO  17:03:33,794 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:03Z] INFO  17:03:33,794 MicroScheduler -   -> 66 reads (0.19% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:03Z] INFO  17:03:34,111 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:03Z] INFO  17:03:34,114 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:03Z] INFO  17:03:34,115 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:03Z] INFO  17:03:34,115 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:03Z] INFO  17:03:34,119 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/22/R14-18105_kapa-NGv3-PE100-NGv3-sort-22_47309229_51304566-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/22/R14-18105_kapa-NGv3-PE100-NGv3-sort-22_47309229_51304566-prep-prealign-realign.intervals -L 22:47309230-51304566 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/22/tx/tmphUQqwt/R14-18105_kapa-NGv3-PE100-NGv3-sort-22_47309229_51304566-prep.bam
[2016-04-15T00:03Z] INFO  17:03:34,132 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:03Z] INFO  17:03:34,133 HelpFormatter - Date/Time: 2016/04/14 17:03:34
[2016-04-15T00:03Z] INFO  17:03:34,134 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:03Z] INFO  17:03:34,134 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:03Z] INFO  17:03:34,348 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:03Z] INFO  17:03:34,423 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:03Z] INFO  17:03:34,432 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:03Z] INFO  17:03:34,476 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.04
[2016-04-15T00:03Z] INFO  17:03:34,670 ProgressMeter -            done   1.5556688E7    14.0 s       0.0 s      100.0%    14.0 s       0.0 s
[2016-04-15T00:03Z] INFO  17:03:34,671 ProgressMeter - Total runtime 14.79 secs, 0.25 min, 0.00 hours
[2016-04-15T00:03Z] INFO  17:03:34,675 MicroScheduler - 6856 reads were filtered out during the traversal out of approximately 78049 total reads (8.78%)
[2016-04-15T00:03Z] INFO  17:03:34,676 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:03Z] INFO  17:03:34,677 MicroScheduler -   -> 278 reads (0.36% of total) failing BadMateFilter
[2016-04-15T00:03Z] INFO  17:03:34,678 MicroScheduler -   -> 6121 reads (7.84% of total) failing DuplicateReadFilter
[2016-04-15T00:03Z] INFO  17:03:34,679 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:03Z] INFO  17:03:34,679 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:03Z] INFO  17:03:34,680 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:03Z] INFO  17:03:34,681 MicroScheduler -   -> 457 reads (0.59% of total) failing MappingQualityZeroFilter
[2016-04-15T00:03Z] INFO  17:03:34,681 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:03Z] INFO  17:03:34,682 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-15T00:03Z] INFO  17:03:34,683 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:03Z] INFO  17:03:34,815 IntervalUtils - Processing 3995337 bp from intervals
[2016-04-15T00:03Z] WARN  17:03:34,821 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:03Z] INFO  17:03:34,906 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:03Z] INFO  17:03:34,983 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:03Z] INFO  17:03:34,984 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:03Z] INFO  17:03:34,985 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:03Z] INFO  17:03:34,990 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:03Z] INFO  17:03:35,112 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:03Z] INFO  17:03:35,158 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:03Z] INFO  17:03:35,204 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:03Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-X_78616585_95940189-prep-prealign.bam
[2016-04-15T00:03Z] GATK RealignerTargetCreator: R14-18105_kapa-NGv3-PE100-NGv3-sort-X_78616585_95940189-prep-prealign.bam X:78616586-95940189
[2016-04-15T00:03Z] GATK: RealignerTargetCreator
[2016-04-15T00:03Z] INFO  17:03:35,567 ProgressMeter -            done   1.550938E7    16.0 s       1.0 s      100.0%    16.0 s       0.0 s
[2016-04-15T00:03Z] INFO  17:03:35,568 ProgressMeter - Total runtime 16.44 secs, 0.27 min, 0.00 hours
[2016-04-15T00:03Z] INFO  17:03:35,573 MicroScheduler - 14607 reads were filtered out during the traversal out of approximately 126492 total reads (11.55%)
[2016-04-15T00:03Z] INFO  17:03:35,574 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:03Z] INFO  17:03:35,575 MicroScheduler -   -> 396 reads (0.31% of total) failing BadMateFilter
[2016-04-15T00:03Z] INFO  17:03:35,576 MicroScheduler -   -> 9707 reads (7.67% of total) failing DuplicateReadFilter
[2016-04-15T00:03Z] INFO  17:03:35,577 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:03Z] INFO  17:03:35,578 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:03Z] INFO  17:03:35,578 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:03Z] INFO  17:03:35,579 MicroScheduler -   -> 4504 reads (3.56% of total) failing MappingQualityZeroFilter
[2016-04-15T00:03Z] INFO  17:03:35,580 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:03Z] INFO  17:03:35,581 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-15T00:03Z] INFO  17:03:35,581 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:03Z] INFO  17:03:36,157 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:03Z] GATK: realign ('X', 31139949, 46696637) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-15T00:03Z] INFO  17:03:37,089 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:03Z] GATK: realign ('X', 0, 15509380) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-15T00:03Z] INFO  17:03:37,164 ProgressMeter -            done   1.5571171E7    15.0 s       0.0 s      100.0%    15.0 s       0.0 s
[2016-04-15T00:03Z] INFO  17:03:37,165 ProgressMeter - Total runtime 15.09 secs, 0.25 min, 0.00 hours
[2016-04-15T00:03Z] INFO  17:03:37,169 MicroScheduler - 9052 reads were filtered out during the traversal out of approximately 100232 total reads (9.03%)
[2016-04-15T00:03Z] INFO  17:03:37,170 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:03Z] INFO  17:03:37,171 MicroScheduler -   -> 311 reads (0.31% of total) failing BadMateFilter
[2016-04-15T00:03Z] INFO  17:03:37,172 MicroScheduler -   -> 7658 reads (7.64% of total) failing DuplicateReadFilter
[2016-04-15T00:03Z] INFO  17:03:37,172 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:03Z] INFO  17:03:37,173 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:03Z] INFO  17:03:37,174 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:03Z] INFO  17:03:37,174 MicroScheduler -   -> 1083 reads (1.08% of total) failing MappingQualityZeroFilter
[2016-04-15T00:03Z] INFO  17:03:37,175 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:03Z] INFO  17:03:37,175 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-15T00:03Z] INFO  17:03:37,176 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:03Z] INFO  17:03:37,650 ProgressMeter -      X:53409599    200003.0    30.0 s       2.5 m       42.2%    71.0 s      41.0 s
[2016-04-15T00:03Z] INFO  17:03:37,984 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:03Z] INFO  17:03:37,988 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:03Z] INFO  17:03:37,988 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:03Z] INFO  17:03:37,989 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:03Z] INFO  17:03:37,993 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/X/R14-18105_kapa-NGv3-PE100-NGv3-sort-X_78616585_95940189-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/X/tx/tmpDQdq9o/R14-18105_kapa-NGv3-PE100-NGv3-sort-X_78616585_95940189-prep-prealign-realign.intervals -l INFO -L X:78616586-95940189 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:03Z] INFO  17:03:38,007 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:03Z] INFO  17:03:38,008 HelpFormatter - Date/Time: 2016/04/14 17:03:37
[2016-04-15T00:03Z] INFO  17:03:38,008 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:03Z] INFO  17:03:38,009 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:03Z] INFO  17:03:38,085 ProgressMeter -     22:24178657    400013.0    61.0 s       2.6 m       50.9%   119.0 s      58.0 s
[2016-04-15T00:03Z] INFO  17:03:38,142 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:03Z] INFO  17:03:38,367 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T00:03Z] INFO  17:03:38,377 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:03Z] INFO  17:03:38,396 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:03Z] INFO  17:03:38,433 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-15T00:03Z] GATK: realign ('X', 15518899, 31090070) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-15T00:03Z] INFO  17:03:38,733 IntervalUtils - Processing 17323604 bp from intervals
[2016-04-15T00:03Z] WARN  17:03:38,738 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:03Z] INFO  17:03:38,766 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:03Z] INFO  17:03:38,770 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:03Z] INFO  17:03:38,771 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:03Z] INFO  17:03:38,772 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:03Z] INFO  17:03:38,777 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/X/R14-18105_kapa-NGv3-PE100-NGv3-sort-X_31139949_46696637-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/X/R14-18105_kapa-NGv3-PE100-NGv3-sort-X_31139949_46696637-prep-prealign-realign.intervals -L X:31139950-46696637 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/X/tx/tmp4GBkAp/R14-18105_kapa-NGv3-PE100-NGv3-sort-X_31139949_46696637-prep.bam
[2016-04-15T00:03Z] INFO  17:03:38,795 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:03Z] INFO  17:03:38,796 HelpFormatter - Date/Time: 2016/04/14 17:03:38
[2016-04-15T00:03Z] INFO  17:03:38,797 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:03Z] INFO  17:03:38,797 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:03Z] INFO  17:03:38,803 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:03Z] INFO  17:03:38,977 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:03Z] INFO  17:03:38,978 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:03Z] INFO  17:03:38,979 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:03Z] INFO  17:03:38,980 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:03Z] INFO  17:03:39,004 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:03Z] INFO  17:03:39,109 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:03Z] INFO  17:03:39,127 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:03Z] INFO  17:03:39,201 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-15T00:03Z] INFO  17:03:39,599 IntervalUtils - Processing 15556688 bp from intervals
[2016-04-15T00:03Z] WARN  17:03:39,608 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:03Z] INFO  17:03:39,739 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:03Z] INFO  17:03:39,882 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:03Z] INFO  17:03:39,883 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:03Z] INFO  17:03:39,884 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:03Z] INFO  17:03:39,884 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:03Z] INFO  17:03:39,992 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:03Z] INFO  17:03:40,036 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:03Z] INFO  17:03:40,039 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:03Z] INFO  17:03:40,040 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:03Z] INFO  17:03:40,040 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:03Z] INFO  17:03:40,045 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/X/R14-18105_kapa-NGv3-PE100-NGv3-sort-X_0_15509380-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/X/R14-18105_kapa-NGv3-PE100-NGv3-sort-X_0_15509380-prep-prealign-realign.intervals -L X:1-15509380 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/X/tx/tmpKJADsH/R14-18105_kapa-NGv3-PE100-NGv3-sort-X_0_15509380-prep.bam
[2016-04-15T00:03Z] INFO  17:03:40,060 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:03Z] INFO  17:03:40,061 HelpFormatter - Date/Time: 2016/04/14 17:03:40
[2016-04-15T00:03Z] INFO  17:03:40,061 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:03Z] INFO  17:03:40,062 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:03Z] INFO  17:03:40,165 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:03Z] INFO  17:03:40,362 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:03Z] INFO  17:03:40,537 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:03Z] INFO  17:03:40,557 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:03Z] INFO  17:03:40,632 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-15T00:03Z] INFO  17:03:40,664 ProgressMeter -     22:41998549    400007.0    60.0 s       2.5 m       65.8%    91.0 s      31.0 s
[2016-04-15T00:03Z] INFO  17:03:41,022 IntervalUtils - Processing 15509380 bp from intervals
[2016-04-15T00:03Z] WARN  17:03:41,028 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:03Z] INFO  17:03:41,093 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:03Z] INFO  17:03:41,166 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@7172f77a
[2016-04-15T00:03Z] INFO  17:03:41,209 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:03Z] INFO  17:03:41,210 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:03Z] INFO  17:03:41,211 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:03Z] INFO  17:03:41,212 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:03Z] INFO  17:03:41,282 ProgressMeter -            done    156686.0    21.0 s       2.3 m      100.0%    21.0 s       0.0 s
[2016-04-15T00:03Z] INFO  17:03:41,282 ProgressMeter - Total runtime 21.44 secs, 0.36 min, 0.01 hours
[2016-04-15T00:03Z] INFO  17:03:41,283 MicroScheduler - 121 reads were filtered out during the traversal out of approximately 156807 total reads (0.08%)
[2016-04-15T00:03Z] INFO  17:03:41,283 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:03Z] INFO  17:03:41,283 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:03Z] INFO  17:03:41,284 MicroScheduler -   -> 121 reads (0.08% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:03Z] INFO  17:03:41,321 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:03Z] INFO  17:03:41,411 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:03Z] INFO  17:03:41,418 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:03Z] INFO  17:03:41,419 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:03Z] INFO  17:03:41,419 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:03Z] INFO  17:03:41,423 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/X/R14-18105_kapa-NGv3-PE100-NGv3-sort-X_15518899_31090070-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/X/R14-18105_kapa-NGv3-PE100-NGv3-sort-X_15518899_31090070-prep-prealign-realign.intervals -L X:15518900-31090070 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/X/tx/tmpp0vjMs/R14-18105_kapa-NGv3-PE100-NGv3-sort-X_15518899_31090070-prep.bam
[2016-04-15T00:03Z] INFO  17:03:41,450 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:03Z] INFO  17:03:41,451 HelpFormatter - Date/Time: 2016/04/14 17:03:41
[2016-04-15T00:03Z] INFO  17:03:41,451 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:03Z] INFO  17:03:41,452 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:03Z] INFO  17:03:41,467 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:03Z] INFO  17:03:41,735 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:03Z] INFO  17:03:41,890 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:03Z] INFO  17:03:41,899 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:03Z] INFO  17:03:41,971 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-15T00:03Z] INFO  17:03:42,379 IntervalUtils - Processing 15571171 bp from intervals
[2016-04-15T00:03Z] WARN  17:03:42,384 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:03Z] INFO  17:03:42,471 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:03Z] INFO  17:03:42,648 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:03Z] INFO  17:03:42,649 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:03Z] INFO  17:03:42,650 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:03Z] INFO  17:03:42,651 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:03Z] INFO  17:03:42,796 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:03Z] INFO  17:03:42,958 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:03Z] INFO  17:03:43,019 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:03Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-X_62857907_78427545-prep-prealign.bam
[2016-04-15T00:03Z] INFO  17:03:43,288 ProgressMeter -            done   1.5529552E7    24.0 s       1.0 s      100.0%    24.0 s       0.0 s
[2016-04-15T00:03Z] INFO  17:03:43,289 ProgressMeter - Total runtime 24.38 secs, 0.41 min, 0.01 hours
[2016-04-15T00:03Z] INFO  17:03:43,293 MicroScheduler - 42933 reads were filtered out during the traversal out of approximately 474323 total reads (9.05%)
[2016-04-15T00:03Z] INFO  17:03:43,295 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:03Z] INFO  17:03:43,295 MicroScheduler -   -> 1030 reads (0.22% of total) failing BadMateFilter
[2016-04-15T00:03Z] INFO  17:03:43,296 MicroScheduler -   -> 38754 reads (8.17% of total) failing DuplicateReadFilter
[2016-04-15T00:03Z] INFO  17:03:43,297 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:03Z] INFO  17:03:43,297 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:03Z] INFO  17:03:43,300 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:03Z] INFO  17:03:43,301 MicroScheduler -   -> 3149 reads (0.66% of total) failing MappingQualityZeroFilter
[2016-04-15T00:03Z] INFO  17:03:43,302 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:03Z] INFO  17:03:43,303 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-15T00:03Z] INFO  17:03:43,304 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:03Z] GATK RealignerTargetCreator: R14-18105_kapa-NGv3-PE100-NGv3-sort-X_62857907_78427545-prep-prealign.bam X:62857908-78427545
[2016-04-15T00:03Z] GATK: RealignerTargetCreator
[2016-04-15T00:03Z] INFO  17:03:44,712 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:03Z] GATK: realign ('21', 31062047, 46591599) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-15T00:03Z] INFO  17:03:44,866 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@5fe152b7
[2016-04-15T00:03Z] INFO  17:03:44,973 ProgressMeter -            done    293576.0    37.0 s       2.1 m      100.0%    37.0 s       0.0 s
[2016-04-15T00:03Z] INFO  17:03:44,974 ProgressMeter - Total runtime 37.35 secs, 0.62 min, 0.01 hours
[2016-04-15T00:03Z] INFO  17:03:44,974 MicroScheduler - 145 reads were filtered out during the traversal out of approximately 293721 total reads (0.05%)
[2016-04-15T00:03Z] INFO  17:03:44,974 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:03Z] INFO  17:03:44,975 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:03Z] INFO  17:03:44,975 MicroScheduler -   -> 145 reads (0.05% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:03Z] INFO  17:03:45,568 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@41fd9d8e
[2016-04-15T00:03Z] INFO  17:03:45,653 ProgressMeter -            done   1515364.0     2.9 m     113.0 s      100.0%     2.9 m       0.0 s
[2016-04-15T00:03Z] INFO  17:03:45,654 ProgressMeter - Total runtime 171.63 secs, 2.86 min, 0.05 hours
[2016-04-15T00:03Z] INFO  17:03:45,655 MicroScheduler - 631 reads were filtered out during the traversal out of approximately 1515995 total reads (0.04%)
[2016-04-15T00:03Z] INFO  17:03:45,655 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:03Z] INFO  17:03:45,656 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:03Z] INFO  17:03:45,657 MicroScheduler -   -> 631 reads (0.04% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:03Z] INFO  17:03:46,315 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:03Z] INFO  17:03:46,319 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:03Z] INFO  17:03:46,320 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:03Z] INFO  17:03:46,321 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:03Z] INFO  17:03:46,326 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/X/R14-18105_kapa-NGv3-PE100-NGv3-sort-X_62857907_78427545-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/X/tx/tmp3lo4IO/R14-18105_kapa-NGv3-PE100-NGv3-sort-X_62857907_78427545-prep-prealign-realign.intervals -l INFO -L X:62857908-78427545 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:03Z] INFO  17:03:46,337 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:03Z] INFO  17:03:46,338 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:03Z] INFO  17:03:46,339 HelpFormatter - Date/Time: 2016/04/14 17:03:46
[2016-04-15T00:03Z] INFO  17:03:46,340 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:03Z] INFO  17:03:46,341 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:03Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-X_46712910_62570698-prep-prealign.bam
[2016-04-15T00:03Z] INFO  17:03:46,452 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:03Z] INFO  17:03:46,703 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T00:03Z] INFO  17:03:46,736 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:03Z] INFO  17:03:46,807 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-15T00:03Z] INFO  17:03:47,078 ProgressMeter -            done    158346.0    12.0 s      76.0 s       97.9%    12.0 s       0.0 s
[2016-04-15T00:03Z] INFO  17:03:47,079 ProgressMeter - Total runtime 12.10 secs, 0.20 min, 0.00 hours
[2016-04-15T00:03Z] INFO  17:03:47,089 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 158346 total reads (0.00%)
[2016-04-15T00:03Z] INFO  17:03:47,090 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:03Z] INFO  17:03:47,091 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:03Z] INFO  17:03:47,092 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:03Z] INFO  17:03:47,106 IntervalUtils - Processing 15569638 bp from intervals
[2016-04-15T00:03Z] WARN  17:03:47,111 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:03Z] INFO  17:03:47,185 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:03Z] INFO  17:03:47,388 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:03Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-19_0_15509577-prep-prealign.bam
[2016-04-15T00:03Z] GATK RealignerTargetCreator: R14-18105_kapa-NGv3-PE100-NGv3-sort-X_46712910_62570698-prep-prealign.bam X:46712911-62570698
[2016-04-15T00:03Z] GATK: RealignerTargetCreator
[2016-04-15T00:03Z] INFO  17:03:47,504 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:03Z] INFO  17:03:47,506 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:03Z] INFO  17:03:47,506 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:03Z] INFO  17:03:47,507 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:03Z] INFO  17:03:47,579 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:03Z] INFO  17:03:47,583 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:03Z] INFO  17:03:47,584 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:03Z] INFO  17:03:47,584 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:03Z] INFO  17:03:47,590 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/21/R14-18105_kapa-NGv3-PE100-NGv3-sort-21_31062047_46591599-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/21/R14-18105_kapa-NGv3-PE100-NGv3-sort-21_31062047_46591599-prep-prealign-realign.intervals -L 21:31062048-46591599 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/21/tx/tmpXXrawK/R14-18105_kapa-NGv3-PE100-NGv3-sort-21_31062047_46591599-prep.bam
[2016-04-15T00:03Z] INFO  17:03:47,617 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:03Z] INFO  17:03:47,618 HelpFormatter - Date/Time: 2016/04/14 17:03:47
[2016-04-15T00:03Z] INFO  17:03:47,619 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:03Z] INFO  17:03:47,620 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:03Z] INFO  17:03:47,795 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:03Z] INFO  17:03:47,868 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:03Z] INFO  17:03:47,877 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:03Z] INFO  17:03:47,919 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.04
[2016-04-15T00:03Z] INFO  17:03:48,217 IntervalUtils - Processing 15529552 bp from intervals
[2016-04-15T00:03Z] WARN  17:03:48,222 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:03Z] INFO  17:03:48,244 ProgressMeter -            done     77691.0     8.0 s     107.0 s      100.0%     8.0 s       0.0 s
[2016-04-15T00:03Z] INFO  17:03:48,244 ProgressMeter - Total runtime 8.36 secs, 0.14 min, 0.00 hours
[2016-04-15T00:03Z] INFO  17:03:48,247 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 77691 total reads (0.00%)
[2016-04-15T00:03Z] INFO  17:03:48,248 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:03Z] INFO  17:03:48,248 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:03Z] INFO  17:03:48,248 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:03Z] INFO  17:03:48,290 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:03Z] INFO  17:03:48,408 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:03Z] INFO  17:03:48,409 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:03Z] INFO  17:03:48,410 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:03Z] INFO  17:03:48,411 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:03Z] INFO  17:03:48,566 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:03Z] INFO  17:03:48,581 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:03Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-22_47309229_51304566-prep.bam
[2016-04-15T00:03Z] INFO  17:03:48,725 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:03Z] GATK pre-alignment ('X', 95990756, 111698889) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-15T00:03Z] INFO  17:03:49,801 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:03Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-X_31139949_46696637-prep.bam
[2016-04-15T00:03Z] GATK pre-alignment ('X', 111874647, 128581278) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-15T00:03Z] INFO  17:03:50,455 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:03Z] INFO  17:03:50,459 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:03Z] INFO  17:03:50,459 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:03Z] INFO  17:03:50,460 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:03Z] INFO  17:03:50,466 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/X/R14-18105_kapa-NGv3-PE100-NGv3-sort-X_46712910_62570698-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/X/tx/tmpKYoP6m/R14-18105_kapa-NGv3-PE100-NGv3-sort-X_46712910_62570698-prep-prealign-realign.intervals -l INFO -L X:46712911-62570698 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:03Z] INFO  17:03:50,481 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:03Z] INFO  17:03:50,482 HelpFormatter - Date/Time: 2016/04/14 17:03:50
[2016-04-15T00:03Z] INFO  17:03:50,483 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:03Z] INFO  17:03:50,483 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:03Z] INFO  17:03:50,579 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:03Z] INFO  17:03:50,837 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T00:03Z] INFO  17:03:50,849 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:03Z] INFO  17:03:50,909 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-15T00:03Z] INFO  17:03:51,269 IntervalUtils - Processing 15857788 bp from intervals
[2016-04-15T00:03Z] WARN  17:03:51,275 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:03Z] INFO  17:03:51,357 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:03Z] INFO  17:03:51,617 ProgressMeter -     19:44470469    900014.0     2.5 m       2.8 m       86.2%     2.9 m      24.0 s
[2016-04-15T00:03Z] INFO  17:03:51,657 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:03Z] INFO  17:03:51,658 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:03Z] INFO  17:03:51,658 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:03Z] INFO  17:03:51,659 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:03Z] INFO  17:03:51,835 ProgressMeter -            done     99559.0     9.0 s      92.0 s      100.0%     9.0 s       0.0 s
[2016-04-15T00:03Z] INFO  17:03:51,836 ProgressMeter - Total runtime 9.19 secs, 0.15 min, 0.00 hours
[2016-04-15T00:03Z] INFO  17:03:51,840 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 99559 total reads (0.00%)
[2016-04-15T00:03Z] INFO  17:03:51,846 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:03Z] INFO  17:03:51,847 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:03Z] INFO  17:03:51,847 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:03Z] INFO  17:03:52,282 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:03Z] INFO  17:03:52,285 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:03Z] INFO  17:03:52,286 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:03Z] INFO  17:03:52,287 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:03Z] INFO  17:03:52,292 HelpFormatter - Program Args: -T PrintReads -L X:95990757-111698889 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/X/tx/tmprturWf/R14-18105_kapa-NGv3-PE100-NGv3-sort-X_95990756_111698889-prep-prealign.bam
[2016-04-15T00:03Z] INFO  17:03:52,323 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:03Z] INFO  17:03:52,332 HelpFormatter - Date/Time: 2016/04/14 17:03:52
[2016-04-15T00:03Z] INFO  17:03:52,333 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:03Z] INFO  17:03:52,334 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:03Z] GATK RealignerTargetCreator: R14-18105_kapa-NGv3-PE100-NGv3-sort-19_0_15509577-prep-prealign.bam 19:1-15509577
[2016-04-15T00:03Z] GATK: RealignerTargetCreator
[2016-04-15T00:03Z] INFO  17:03:52,439 ProgressMeter -            done    125405.0    11.0 s      89.0 s      100.0%    11.0 s       0.0 s
[2016-04-15T00:03Z] INFO  17:03:52,439 ProgressMeter - Total runtime 11.23 secs, 0.19 min, 0.00 hours
[2016-04-15T00:03Z] INFO  17:03:52,445 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 125405 total reads (0.00%)
[2016-04-15T00:03Z] INFO  17:03:52,445 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:03Z] INFO  17:03:52,446 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:03Z] INFO  17:03:52,446 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:03Z] INFO  17:03:52,508 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:03Z] INFO  17:03:53,184 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:03Z] INFO  17:03:53,188 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:03Z] INFO  17:03:53,189 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:03Z] INFO  17:03:53,189 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:03Z] INFO  17:03:53,195 HelpFormatter - Program Args: -T PrintReads -L X:111874648-128581278 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/X/tx/tmputH1sd/R14-18105_kapa-NGv3-PE100-NGv3-sort-X_111874647_128581278-prep-prealign.bam
[2016-04-15T00:03Z] INFO  17:03:53,209 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:03Z] INFO  17:03:53,220 HelpFormatter - Date/Time: 2016/04/14 17:03:53
[2016-04-15T00:03Z] INFO  17:03:53,221 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:03Z] INFO  17:03:53,222 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:03Z] INFO  17:03:53,318 ProgressMeter -     19:58907859   1300030.0     2.5 m     115.0 s       98.2%     2.5 m       2.0 s
[2016-04-15T00:03Z] INFO  17:03:53,423 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:03Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-X_15518899_31090070-prep.bam
[2016-04-15T00:03Z] INFO  17:03:53,487 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:03Z] INFO  17:03:53,536 ProgressMeter -            done   1.7323604E7    14.0 s       0.0 s      100.0%    14.0 s       0.0 s
[2016-04-15T00:03Z] INFO  17:03:53,538 ProgressMeter - Total runtime 14.56 secs, 0.24 min, 0.00 hours
[2016-04-15T00:03Z] INFO  17:03:53,542 MicroScheduler - 4282 reads were filtered out during the traversal out of approximately 35258 total reads (12.14%)
[2016-04-15T00:03Z] INFO  17:03:53,543 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:03Z] INFO  17:03:53,544 MicroScheduler -   -> 219 reads (0.62% of total) failing BadMateFilter
[2016-04-15T00:03Z] INFO  17:03:53,545 MicroScheduler -   -> 2516 reads (7.14% of total) failing DuplicateReadFilter
[2016-04-15T00:03Z] INFO  17:03:53,546 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:03Z] INFO  17:03:53,546 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:03Z] INFO  17:03:53,547 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:03Z] INFO  17:03:53,548 MicroScheduler -   -> 1547 reads (4.39% of total) failing MappingQualityZeroFilter
[2016-04-15T00:03Z] INFO  17:03:53,549 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:03Z] INFO  17:03:53,549 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-15T00:03Z] INFO  17:03:53,550 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:03Z] INFO  17:03:53,658 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-15T00:03Z] INFO  17:03:53,740 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:03Z] INFO  17:03:53,749 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:03Z] INFO  17:03:53,789 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.04
[2016-04-15T00:03Z] INFO  17:03:53,803 IntervalUtils - Processing 15708133 bp from intervals
[2016-04-15T00:03Z] GATK pre-alignment ('X', 128582278, 144329181) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-15T00:03Z] INFO  17:03:53,859 ProgressMeter -     20:62715628    400005.0    30.0 s      76.0 s       99.3%    30.0 s       0.0 s
[2016-04-15T00:03Z] INFO  17:03:53,884 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:03Z] INFO  17:03:54,101 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:03Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-X_0_15509380-prep.bam
[2016-04-15T00:03Z] INFO  17:03:54,131 ProgressMeter -            done    468237.0    30.0 s      65.0 s      100.0%    30.0 s       0.0 s
[2016-04-15T00:03Z] INFO  17:03:54,132 ProgressMeter - Total runtime 30.87 secs, 0.51 min, 0.01 hours
[2016-04-15T00:03Z] INFO  17:03:54,135 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 468237 total reads (0.00%)
[2016-04-15T00:03Z] INFO  17:03:54,136 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:03Z] INFO  17:03:54,136 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:03Z] INFO  17:03:54,136 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:03Z] INFO  17:03:54,218 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:03Z] INFO  17:03:54,220 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:03Z] INFO  17:03:54,220 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:03Z] INFO  17:03:54,221 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:03Z] INFO  17:03:54,252 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:03Z] INFO  17:03:54,417 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:03Z] GATK pre-alignment ('X', 144337190, 155270560) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-15T00:03Z] INFO  17:03:54,728 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-15T00:03Z] INFO  17:03:54,779 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:03Z] INFO  17:03:54,789 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:03Z] INFO  17:03:54,824 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.04
[2016-04-15T00:03Z] INFO  17:03:54,838 IntervalUtils - Processing 16706631 bp from intervals
[2016-04-15T00:03Z] INFO  17:03:54,917 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:03Z] INFO  17:03:54,917 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:03Z] GATK: realign ('X', 78616585, 95940189) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-15T00:03Z] INFO  17:03:55,191 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:03Z] INFO  17:03:55,192 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:03Z] INFO  17:03:55,193 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:03Z] INFO  17:03:55,199 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:03Z] INFO  17:03:55,222 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:03Z] INFO  17:03:55,376 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:03Z] INFO  17:03:55,503 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:03Z] INFO  17:03:55,506 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:03Z] INFO  17:03:55,507 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:03Z] INFO  17:03:55,508 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:03Z] INFO  17:03:55,512 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/19/R14-18105_kapa-NGv3-PE100-NGv3-sort-19_0_15509577-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/19/tx/tmpahdc_y/R14-18105_kapa-NGv3-PE100-NGv3-sort-19_0_15509577-prep-prealign-realign.intervals -l INFO -L 19:1-15509577 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:03Z] INFO  17:03:55,522 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:03Z] INFO  17:03:55,533 HelpFormatter - Date/Time: 2016/04/14 17:03:55
[2016-04-15T00:03Z] INFO  17:03:55,534 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:03Z] INFO  17:03:55,534 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:03Z] INFO  17:03:55,673 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:03Z] INFO  17:03:55,845 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:03Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-20_47244085_62830269-prep.bam
[2016-04-15T00:03Z] INFO  17:03:55,932 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T00:03Z] INFO  17:03:55,952 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:03Z] INFO  17:03:56,048 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.10
[2016-04-15T00:03Z] INFO  17:03:56,440 IntervalUtils - Processing 15509577 bp from intervals
[2016-04-15T00:03Z] WARN  17:03:56,445 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:03Z] INFO  17:03:56,513 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:03Z] INFO  17:03:56,723 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:03Z] INFO  17:03:56,725 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:03Z] INFO  17:03:56,725 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:03Z] INFO  17:03:56,726 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:03Z] INFO  17:03:56,730 ProgressMeter -     17:42807448    800011.0    60.0 s      75.0 s       75.6%    79.0 s      19.0 s
[2016-04-15T00:03Z] INFO  17:03:56,750 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:03Z] INFO  17:03:56,753 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:03Z] INFO  17:03:56,754 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:03Z] INFO  17:03:56,754 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:03Z] INFO  17:03:56,758 HelpFormatter - Program Args: -T PrintReads -L X:128582279-144329181 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/X/tx/tmpvnl3ux/R14-18105_kapa-NGv3-PE100-NGv3-sort-X_128582278_144329181-prep-prealign.bam
[2016-04-15T00:03Z] INFO  17:03:56,768 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:03Z] INFO  17:03:56,769 HelpFormatter - Date/Time: 2016/04/14 17:03:56
[2016-04-15T00:03Z] INFO  17:03:56,770 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:03Z] INFO  17:03:56,770 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:03Z] INFO  17:03:56,925 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:03Z] INFO  17:03:57,147 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@7172f77a
[2016-04-15T00:03Z] INFO  17:03:57,256 ProgressMeter -            done   1351000.0     2.6 m     114.0 s       99.6%     2.6 m       0.0 s
[2016-04-15T00:03Z] INFO  17:03:57,256 ProgressMeter - Total runtime 154.29 secs, 2.57 min, 0.04 hours
[2016-04-15T00:03Z] INFO  17:03:57,257 MicroScheduler - 468 reads were filtered out during the traversal out of approximately 1351468 total reads (0.03%)
[2016-04-15T00:03Z] INFO  17:03:57,258 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:03Z] INFO  17:03:57,258 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:03Z] INFO  17:03:57,258 MicroScheduler -   -> 468 reads (0.03% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:03Z] INFO  17:03:57,287 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:03Z] INFO  17:03:57,290 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:03Z] INFO  17:03:57,291 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:03Z] INFO  17:03:57,291 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:03Z] INFO  17:03:57,296 HelpFormatter - Program Args: -T PrintReads -L X:144337191-155270560 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/X/tx/tmpbtMDuC/R14-18105_kapa-NGv3-PE100-NGv3-sort-X_144337190_155270560-prep-prealign.bam
[2016-04-15T00:03Z] INFO  17:03:57,306 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:03Z] INFO  17:03:57,306 HelpFormatter - Date/Time: 2016/04/14 17:03:57
[2016-04-15T00:03Z] INFO  17:03:57,306 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:03Z] GATK pre-alignment ('Y', 0, 15522993) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-15T00:03Z] INFO  17:03:57,307 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:03Z] INFO  17:03:57,500 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:03Z] INFO  17:03:57,830 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:03Z] INFO  17:03:57,833 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:03Z] INFO  17:03:57,834 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:03Z] INFO  17:03:57,834 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:03Z] INFO  17:03:57,839 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/X/R14-18105_kapa-NGv3-PE100-NGv3-sort-X_78616585_95940189-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/X/R14-18105_kapa-NGv3-PE100-NGv3-sort-X_78616585_95940189-prep-prealign-realign.intervals -L X:78616586-95940189 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/X/tx/tmpvRCDk0/R14-18105_kapa-NGv3-PE100-NGv3-sort-X_78616585_95940189-prep.bam
[2016-04-15T00:03Z] INFO  17:03:57,866 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:03Z] INFO  17:03:57,867 HelpFormatter - Date/Time: 2016/04/14 17:03:57
[2016-04-15T00:03Z] INFO  17:03:57,868 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:03Z] INFO  17:03:57,872 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:03Z] INFO  17:03:58,080 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-15T00:03Z] INFO  17:03:58,127 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:03Z] INFO  17:03:58,149 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:03Z] INFO  17:03:58,157 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:03Z] INFO  17:03:58,201 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:03Z] INFO  17:03:58,209 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-15T00:03Z] INFO  17:03:58,222 IntervalUtils - Processing 15746903 bp from intervals
[2016-04-15T00:03Z] INFO  17:03:58,231 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:03Z] INFO  17:03:58,301 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:03Z] INFO  17:03:58,311 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-15T00:03Z] INFO  17:03:58,654 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:03Z] INFO  17:03:58,656 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:03Z] INFO  17:03:58,656 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:03Z] INFO  17:03:58,657 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:03Z] INFO  17:03:58,670 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:03Z] INFO  17:03:58,671 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:03Z] INFO  17:03:58,682 IntervalUtils - Processing 17323604 bp from intervals
[2016-04-15T00:03Z] WARN  17:03:58,710 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:03Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-19_46627881_59128983-prep-prealign.bam
[2016-04-15T00:03Z] INFO  17:03:58,747 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-15T00:03Z] INFO  17:03:58,801 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:03Z] INFO  17:03:58,803 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:03Z] INFO  17:03:58,827 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:03Z] INFO  17:03:58,842 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:03Z] INFO  17:03:58,899 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:03Z] INFO  17:03:58,901 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:03Z] INFO  17:03:58,902 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:03Z] INFO  17:03:58,903 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:03Z] INFO  17:03:58,913 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-15T00:03Z] INFO  17:03:58,928 IntervalUtils - Processing 10933370 bp from intervals
[2016-04-15T00:03Z] INFO  17:03:59,009 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:03Z] INFO  17:03:59,054 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:03Z] INFO  17:03:59,212 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:03Z] INFO  17:03:59,344 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:03Z] INFO  17:03:59,345 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:03Z] INFO  17:03:59,346 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:03Z] INFO  17:03:59,347 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:03Z] INFO  17:03:59,360 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:03Z] INFO  17:03:59,487 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:04Z] INFO  17:04:00,378 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:04Z] INFO  17:04:00,382 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:04Z] INFO  17:04:00,383 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:04Z] INFO  17:04:00,384 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:04Z] INFO  17:04:00,389 HelpFormatter - Program Args: -T PrintReads -L Y:1-15522993 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/Y/tx/tmpxmpyPr/R14-18105_kapa-NGv3-PE100-NGv3-sort-Y_0_15522993-prep-prealign.bam
[2016-04-15T00:04Z] INFO  17:04:00,403 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:04Z] INFO  17:04:00,413 HelpFormatter - Date/Time: 2016/04/14 17:04:00
[2016-04-15T00:04Z] INFO  17:04:00,414 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:04Z] INFO  17:04:00,415 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:04Z] INFO  17:04:00,635 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:04Z] INFO  17:04:01,438 ProgressMeter -     20:44003905    400006.0    30.0 s      77.0 s       79.6%    37.0 s       7.0 s
[2016-04-15T00:04Z] INFO  17:04:02,055 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-15T00:04Z] INFO  17:04:02,128 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:04Z] INFO  17:04:02,148 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:04Z] INFO  17:04:02,196 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-15T00:04Z] INFO  17:04:02,211 IntervalUtils - Processing 15522993 bp from intervals
[2016-04-15T00:04Z] INFO  17:04:02,306 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:04Z] INFO  17:04:02,514 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:04Z] INFO  17:04:02,514 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:04Z] INFO  17:04:02,515 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:04Z] INFO  17:04:02,515 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:04Z] INFO  17:04:02,544 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:04Z] INFO  17:04:02,713 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:04Z] GATK RealignerTargetCreator: R14-18105_kapa-NGv3-PE100-NGv3-sort-19_46627881_59128983-prep-prealign.bam 19:46627882-59128983
[2016-04-15T00:04Z] GATK: RealignerTargetCreator
[2016-04-15T00:04Z] INFO  17:04:02,867 ProgressMeter -            done   1.5569638E7    15.0 s       0.0 s      100.0%    15.0 s       0.0 s
[2016-04-15T00:04Z] INFO  17:04:02,868 ProgressMeter - Total runtime 15.36 secs, 0.26 min, 0.00 hours
[2016-04-15T00:04Z] INFO  17:04:02,872 MicroScheduler - 23330 reads were filtered out during the traversal out of approximately 157751 total reads (14.79%)
[2016-04-15T00:04Z] INFO  17:04:02,873 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:04Z] INFO  17:04:02,882 MicroScheduler -   -> 363 reads (0.23% of total) failing BadMateFilter
[2016-04-15T00:04Z] INFO  17:04:02,883 MicroScheduler -   -> 11305 reads (7.17% of total) failing DuplicateReadFilter
[2016-04-15T00:04Z] INFO  17:04:02,883 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:04Z] INFO  17:04:02,884 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:04Z] INFO  17:04:02,885 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:04Z] INFO  17:04:02,885 MicroScheduler -   -> 11662 reads (7.39% of total) failing MappingQualityZeroFilter
[2016-04-15T00:04Z] INFO  17:04:02,886 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:04Z] INFO  17:04:02,886 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-15T00:04Z] INFO  17:04:02,887 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:04Z] INFO  17:04:03,544 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@41fd9d8e
[2016-04-15T00:04Z] INFO  17:04:03,615 ProgressMeter -            done    672527.0    82.0 s       2.1 m      100.0%    82.0 s       0.0 s
[2016-04-15T00:04Z] INFO  17:04:03,616 ProgressMeter - Total runtime 82.98 secs, 1.38 min, 0.02 hours
[2016-04-15T00:04Z] INFO  17:04:03,616 MicroScheduler - 292 reads were filtered out during the traversal out of approximately 672819 total reads (0.04%)
[2016-04-15T00:04Z] INFO  17:04:03,616 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:04Z] INFO  17:04:03,617 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:04Z] INFO  17:04:03,618 MicroScheduler -   -> 292 reads (0.04% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:04Z] INFO  17:04:04,446 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:04Z] GATK: realign ('X', 62857907, 78427545) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-15T00:04Z] INFO  17:04:04,557 ProgressMeter -            done     35131.0     5.0 s       2.7 m      100.0%     5.0 s       0.0 s
[2016-04-15T00:04Z] INFO  17:04:04,558 ProgressMeter - Total runtime 5.66 secs, 0.09 min, 0.00 hours
[2016-04-15T00:04Z] INFO  17:04:04,562 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 35131 total reads (0.00%)
[2016-04-15T00:04Z] INFO  17:04:04,562 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:04Z] INFO  17:04:04,563 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:04Z] INFO  17:04:04,563 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:04Z] INFO  17:04:04,841 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:04Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-22_31796605_47308085-prep-prealign.bam
[2016-04-15T00:04Z] INFO  17:04:05,335 ProgressMeter -            done   1119253.0    68.0 s      61.0 s      100.0%    68.0 s       0.0 s
[2016-04-15T00:04Z] INFO  17:04:05,336 ProgressMeter - Total runtime 68.70 secs, 1.15 min, 0.02 hours
[2016-04-15T00:04Z] INFO  17:04:05,340 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 1119253 total reads (0.00%)
[2016-04-15T00:04Z] INFO  17:04:05,341 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:04Z] INFO  17:04:05,342 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:04Z] INFO  17:04:05,343 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:04Z] INFO  17:04:05,348 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:04Z] INFO  17:04:05,352 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:04Z] INFO  17:04:05,352 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:04Z] INFO  17:04:05,353 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:04Z] INFO  17:04:05,358 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/19/R14-18105_kapa-NGv3-PE100-NGv3-sort-19_46627881_59128983-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/19/tx/tmp4GRJz2/R14-18105_kapa-NGv3-PE100-NGv3-sort-19_46627881_59128983-prep-prealign-realign.intervals -l INFO -L 19:46627882-59128983 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:04Z] INFO  17:04:05,370 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:04Z] INFO  17:04:05,371 HelpFormatter - Date/Time: 2016/04/14 17:04:05
[2016-04-15T00:04Z] INFO  17:04:05,371 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:04Z] INFO  17:04:05,372 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:04Z] INFO  17:04:05,496 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:04Z] INFO  17:04:05,733 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T00:04Z] INFO  17:04:05,756 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:04Z] INFO  17:04:05,814 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-15T00:04Z] INFO  17:04:06,086 IntervalUtils - Processing 12501102 bp from intervals
[2016-04-15T00:04Z] WARN  17:04:06,092 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:04Z] INFO  17:04:06,124 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:04Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-X_78616585_95940189-prep.bam
[2016-04-15T00:04Z] INFO  17:04:06,180 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:04Z] GATK pre-alignment ('Y', 15526614, 59222281) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-15T00:04Z] INFO  17:04:06,396 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:04Z] INFO  17:04:06,397 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:04Z] INFO  17:04:06,398 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:04Z] INFO  17:04:06,399 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:04Z] INFO  17:04:07,035 ProgressMeter -            done    575346.0    36.0 s      63.0 s      100.0%    36.0 s       0.0 s
[2016-04-15T00:04Z] INFO  17:04:07,036 ProgressMeter - Total runtime 36.54 secs, 0.61 min, 0.01 hours
[2016-04-15T00:04Z] INFO  17:04:07,040 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 575346 total reads (0.00%)
[2016-04-15T00:04Z] INFO  17:04:07,041 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:04Z] INFO  17:04:07,041 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:04Z] INFO  17:04:07,042 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:04Z] GATK RealignerTargetCreator: R14-18105_kapa-NGv3-PE100-NGv3-sort-22_31796605_47308085-prep-prealign.bam 22:31796606-47308085
[2016-04-15T00:04Z] GATK: RealignerTargetCreator
[2016-04-15T00:04Z] INFO  17:04:07,252 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:04Z] INFO  17:04:07,255 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:04Z] INFO  17:04:07,256 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:04Z] INFO  17:04:07,257 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:04Z] INFO  17:04:07,262 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/X/R14-18105_kapa-NGv3-PE100-NGv3-sort-X_62857907_78427545-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/X/R14-18105_kapa-NGv3-PE100-NGv3-sort-X_62857907_78427545-prep-prealign-realign.intervals -L X:62857908-78427545 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/X/tx/tmpzvRXoC/R14-18105_kapa-NGv3-PE100-NGv3-sort-X_62857907_78427545-prep.bam
[2016-04-15T00:04Z] INFO  17:04:07,277 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:04Z] INFO  17:04:07,278 HelpFormatter - Date/Time: 2016/04/14 17:04:07
[2016-04-15T00:04Z] INFO  17:04:07,278 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:04Z] INFO  17:04:07,278 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:04Z] INFO  17:04:07,534 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:04Z] INFO  17:04:07,660 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:04Z] INFO  17:04:07,680 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:04Z] INFO  17:04:07,770 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.09
[2016-04-15T00:04Z] INFO  17:04:08,114 IntervalUtils - Processing 15569638 bp from intervals
[2016-04-15T00:04Z] WARN  17:04:08,129 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:04Z] INFO  17:04:08,205 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:04Z] INFO  17:04:08,205 ProgressMeter -     22:30772548    700020.0    91.0 s       2.2 m       93.4%    97.0 s       6.0 s
[2016-04-15T00:04Z] INFO  17:04:08,213 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:04Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-17_31048040_46607237-prep.bam
[2016-04-15T00:04Z] INFO  17:04:08,294 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:04Z] INFO  17:04:08,294 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:04Z] INFO  17:04:08,294 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:04Z] INFO  17:04:08,295 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:04Z] INFO  17:04:08,354 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:04Z] INFO  17:04:08,536 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:04Z] INFO  17:04:08,863 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:04Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-20_31379406_47242465-prep.bam
[2016-04-15T00:04Z] INFO  17:04:09,365 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:04Z] INFO  17:04:09,368 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:04Z] INFO  17:04:09,369 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:04Z] INFO  17:04:09,369 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:04Z] INFO  17:04:09,374 HelpFormatter - Program Args: -T PrintReads -L Y:15526615-59222281 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/Y/tx/tmpWMXRFH/R14-18105_kapa-NGv3-PE100-NGv3-sort-Y_15526614_59222281-prep-prealign.bam
[2016-04-15T00:04Z] INFO  17:04:09,400 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:04Z] INFO  17:04:09,411 HelpFormatter - Date/Time: 2016/04/14 17:04:09
[2016-04-15T00:04Z] INFO  17:04:09,411 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:04Z] INFO  17:04:09,412 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:04Z] INFO  17:04:09,593 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:04Z] INFO  17:04:10,265 ProgressMeter -            done   1.5857788E7    18.0 s       1.0 s      100.0%    18.0 s       0.0 s
[2016-04-15T00:04Z] INFO  17:04:10,266 ProgressMeter - Total runtime 18.61 secs, 0.31 min, 0.01 hours
[2016-04-15T00:04Z] INFO  17:04:10,269 MicroScheduler - 106654 reads were filtered out during the traversal out of approximately 295451 total reads (36.10%)
[2016-04-15T00:04Z] INFO  17:04:10,269 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:04Z] INFO  17:04:10,270 MicroScheduler -   -> 384 reads (0.13% of total) failing BadMateFilter
[2016-04-15T00:04Z] INFO  17:04:10,270 MicroScheduler -   -> 16110 reads (5.45% of total) failing DuplicateReadFilter
[2016-04-15T00:04Z] INFO  17:04:10,270 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:04Z] INFO  17:04:10,270 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:04Z] INFO  17:04:10,271 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:04Z] INFO  17:04:10,271 MicroScheduler -   -> 90160 reads (30.52% of total) failing MappingQualityZeroFilter
[2016-04-15T00:04Z] INFO  17:04:10,271 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:04Z] INFO  17:04:10,271 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-15T00:04Z] INFO  17:04:10,272 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:04Z] INFO  17:04:10,320 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:04Z] INFO  17:04:10,323 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:04Z] INFO  17:04:10,324 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:04Z] INFO  17:04:10,324 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:04Z] INFO  17:04:10,329 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/22/R14-18105_kapa-NGv3-PE100-NGv3-sort-22_31796605_47308085-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/22/tx/tmpTa3jxU/R14-18105_kapa-NGv3-PE100-NGv3-sort-22_31796605_47308085-prep-prealign-realign.intervals -l INFO -L 22:31796606-47308085 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:04Z] INFO  17:04:10,357 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:04Z] INFO  17:04:10,358 HelpFormatter - Date/Time: 2016/04/14 17:04:10
[2016-04-15T00:04Z] INFO  17:04:10,359 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:04Z] INFO  17:04:10,359 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:04Z] INFO  17:04:10,482 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:04Z] INFO  17:04:10,552 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-15T00:04Z] GATK pre-alignment ('Y', 59228291, 59373566) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-15T00:04Z] INFO  17:04:10,627 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:04Z] INFO  17:04:10,643 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:04Z] INFO  17:04:10,702 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T00:04Z] INFO  17:04:10,707 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-15T00:04Z] INFO  17:04:10,711 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:04Z] INFO  17:04:10,735 IntervalUtils - Processing 43695667 bp from intervals
[2016-04-15T00:04Z] INFO  17:04:10,764 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-15T00:04Z] INFO  17:04:10,875 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:04Z] INFO  17:04:11,062 IntervalUtils - Processing 15511480 bp from intervals
[2016-04-15T00:04Z] WARN  17:04:11,067 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:04Z] INFO  17:04:11,136 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:04Z] INFO  17:04:11,197 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:04Z] INFO  17:04:11,199 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:04Z] INFO  17:04:11,200 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:04Z] INFO  17:04:11,201 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:04Z] INFO  17:04:11,220 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:04Z] Select unmapped reads
[2016-04-15T00:04Z] INFO  17:04:11,442 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:04Z] INFO  17:04:11,444 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:04Z] INFO  17:04:11,445 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:04Z] INFO  17:04:11,446 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:04Z] INFO  17:04:11,485 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@41fd9d8e
[2016-04-15T00:04Z] INFO  17:04:11,576 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:04Z] GATK: realign ('X', 46712910, 62570698) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-15T00:04Z] INFO  17:04:11,607 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:04Z] INFO  17:04:11,654 ProgressMeter -            done    104104.0    16.0 s       2.6 m       97.6%    16.0 s       0.0 s
[2016-04-15T00:04Z] INFO  17:04:11,654 ProgressMeter - Total runtime 16.46 secs, 0.27 min, 0.00 hours
[2016-04-15T00:04Z] INFO  17:04:11,655 MicroScheduler - 73 reads were filtered out during the traversal out of approximately 104177 total reads (0.07%)
[2016-04-15T00:04Z] INFO  17:04:11,655 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:04Z] INFO  17:04:11,655 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:04Z] INFO  17:04:11,656 MicroScheduler -   -> 73 reads (0.07% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:04Z] INFO  17:04:13,084 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:04Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-X_111874647_128581278-prep-prealign.bam
[2016-04-15T00:04Z] INFO  17:04:13,461 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:04Z] INFO  17:04:13,464 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:04Z] INFO  17:04:13,465 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:04Z] INFO  17:04:13,465 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:04Z] INFO  17:04:13,470 HelpFormatter - Program Args: -T PrintReads -L Y:59228292-59373566 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18105_kapa-NGv3-PE100-NGv3/R14-18105_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/Y/tx/tmpo15gQC/R14-18105_kapa-NGv3-PE100-NGv3-sort-Y_59228291_59373566-prep-prealign.bam
[2016-04-15T00:04Z] INFO  17:04:13,489 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:04Z] INFO  17:04:13,490 HelpFormatter - Date/Time: 2016/04/14 17:04:13
[2016-04-15T00:04Z] INFO  17:04:13,490 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:04Z] INFO  17:04:13,490 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:04Z] GATK RealignerTargetCreator: R14-18105_kapa-NGv3-PE100-NGv3-sort-X_111874647_128581278-prep-prealign.bam X:111874648-128581278
[2016-04-15T00:04Z] GATK: RealignerTargetCreator
[2016-04-15T00:04Z] INFO  17:04:13,692 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:04Z] INFO  17:04:14,662 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:04Z] INFO  17:04:14,665 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:04Z] INFO  17:04:14,665 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:04Z] INFO  17:04:14,666 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:04Z] INFO  17:04:14,670 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/X/R14-18105_kapa-NGv3-PE100-NGv3-sort-X_46712910_62570698-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/X/R14-18105_kapa-NGv3-PE100-NGv3-sort-X_46712910_62570698-prep-prealign-realign.intervals -L X:46712911-62570698 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/X/tx/tmpCmhzc7/R14-18105_kapa-NGv3-PE100-NGv3-sort-X_46712910_62570698-prep.bam
[2016-04-15T00:04Z] INFO  17:04:14,686 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:04Z] INFO  17:04:14,686 HelpFormatter - Date/Time: 2016/04/14 17:04:14
[2016-04-15T00:04Z] INFO  17:04:14,687 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:04Z] INFO  17:04:14,687 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:04Z] INFO  17:04:14,828 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-15T00:04Z] INFO  17:04:14,886 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:04Z] INFO  17:04:14,892 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:04Z] INFO  17:04:14,895 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:04Z] INFO  17:04:14,941 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-15T00:04Z] INFO  17:04:14,955 IntervalUtils - Processing 145275 bp from intervals
[2016-04-15T00:04Z] INFO  17:04:14,988 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@7172f77a
[2016-04-15T00:04Z] INFO  17:04:15,005 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:04Z] INFO  17:04:15,018 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:04Z] INFO  17:04:15,033 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:04Z] INFO  17:04:15,058 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.04
[2016-04-15T00:04Z] INFO  17:04:15,141 ProgressMeter -            done    152914.0    20.0 s       2.3 m      100.0%    20.0 s       0.0 s
[2016-04-15T00:04Z] INFO  17:04:15,142 ProgressMeter - Total runtime 20.92 secs, 0.35 min, 0.01 hours
[2016-04-15T00:04Z] INFO  17:04:15,142 MicroScheduler - 101 reads were filtered out during the traversal out of approximately 153015 total reads (0.07%)
[2016-04-15T00:04Z] INFO  17:04:15,143 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:04Z] INFO  17:04:15,143 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:04Z] INFO  17:04:15,143 MicroScheduler -   -> 101 reads (0.07% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:04Z] INFO  17:04:15,168 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@5fe152b7
[2016-04-15T00:04Z] INFO  17:04:15,193 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:04Z] INFO  17:04:15,194 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:04Z] INFO  17:04:15,195 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:04Z] INFO  17:04:15,196 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:04Z] INFO  17:04:15,213 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:04Z] INFO  17:04:15,215 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:04Z] INFO  17:04:15,229 ProgressMeter -            done    819395.0    98.0 s     120.0 s      100.0%    98.0 s       0.0 s
[2016-04-15T00:04Z] INFO  17:04:15,231 ProgressMeter - Total runtime 98.35 secs, 1.64 min, 0.03 hours
[2016-04-15T00:04Z] INFO  17:04:15,231 MicroScheduler - 283 reads were filtered out during the traversal out of approximately 819678 total reads (0.03%)
[2016-04-15T00:04Z] INFO  17:04:15,232 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:04Z] INFO  17:04:15,233 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:04Z] INFO  17:04:15,233 MicroScheduler -   -> 283 reads (0.03% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:04Z] INFO  17:04:15,246 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@5fe152b7
[2016-04-15T00:04Z] INFO  17:04:15,296 ProgressMeter -            done         0.0     0.0 s      28.0 h      100.0%     0.0 s       0.0 s
[2016-04-15T00:04Z] INFO  17:04:15,298 ProgressMeter - Total runtime 0.10 secs, 0.00 min, 0.00 hours
[2016-04-15T00:04Z] INFO  17:04:15,410 IntervalUtils - Processing 15857788 bp from intervals
[2016-04-15T00:04Z] WARN  17:04:15,415 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:04Z] INFO  17:04:15,508 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:04Z] INFO  17:04:15,613 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:04Z] INFO  17:04:15,614 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:04Z] INFO  17:04:15,625 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:04Z] INFO  17:04:15,630 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:04Z] INFO  17:04:15,700 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:04Z] INFO  17:04:15,851 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:04Z] INFO  17:04:16,475 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:04Z] INFO  17:04:16,477 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:04Z] INFO  17:04:16,478 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:04Z] INFO  17:04:16,478 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:04Z] INFO  17:04:16,482 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/X/R14-18105_kapa-NGv3-PE100-NGv3-sort-X_111874647_128581278-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/X/tx/tmpHQXXFj/R14-18105_kapa-NGv3-PE100-NGv3-sort-X_111874647_128581278-prep-prealign-realign.intervals -l INFO -L X:111874648-128581278 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:04Z] INFO  17:04:16,490 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:04Z] INFO  17:04:16,491 HelpFormatter - Date/Time: 2016/04/14 17:04:16
[2016-04-15T00:04Z] INFO  17:04:16,491 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:04Z] INFO  17:04:16,492 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:04Z] INFO  17:04:16,570 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:04Z] INFO  17:04:16,582 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:04Z] INFO  17:04:16,603 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:04Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-X_95990756_111698889-prep-prealign.bam
[2016-04-15T00:04Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-22_16266928_31795711-prep-prealign.bam
[2016-04-15T00:04Z] INFO  17:04:16,653 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:04Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-Y_59228291_59373566-prep-prealign.bam
[2016-04-15T00:04Z] GATK RealignerTargetCreator: R14-18105_kapa-NGv3-PE100-NGv3-sort-Y_59228291_59373566-prep-prealign.bam Y:59228292-59373566
[2016-04-15T00:04Z] GATK: RealignerTargetCreator
[2016-04-15T00:04Z] INFO  17:04:16,797 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T00:04Z] INFO  17:04:16,809 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:04Z] INFO  17:04:16,895 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.09
[2016-04-15T00:04Z] GATK RealignerTargetCreator: R14-18105_kapa-NGv3-PE100-NGv3-sort-X_95990756_111698889-prep-prealign.bam X:95990757-111698889
[2016-04-15T00:04Z] GATK: RealignerTargetCreator
[2016-04-15T00:04Z] INFO  17:04:17,238 IntervalUtils - Processing 16706631 bp from intervals
[2016-04-15T00:04Z] WARN  17:04:17,245 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:04Z] INFO  17:04:17,344 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:04Z] INFO  17:04:17,585 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:04Z] INFO  17:04:17,587 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:04Z] INFO  17:04:17,587 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:04Z] INFO  17:04:17,588 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:04Z] INFO  17:04:17,589 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@5fe152b7
[2016-04-15T00:04Z] INFO  17:04:17,752 ProgressMeter -            done    127890.0    19.0 s       2.5 m       99.6%    19.0 s       0.0 s
[2016-04-15T00:04Z] INFO  17:04:17,753 ProgressMeter - Total runtime 19.10 secs, 0.32 min, 0.01 hours
[2016-04-15T00:04Z] INFO  17:04:17,754 MicroScheduler - 84 reads were filtered out during the traversal out of approximately 127974 total reads (0.07%)
[2016-04-15T00:04Z] INFO  17:04:17,755 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:04Z] INFO  17:04:17,755 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:04Z] INFO  17:04:17,756 MicroScheduler -   -> 84 reads (0.07% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:04Z] INFO  17:04:18,437 ProgressMeter -     21:45978092    400005.0    30.0 s      75.0 s       96.0%    31.0 s       1.0 s
[2016-04-15T00:04Z] INFO  17:04:19,302 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:04Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-X_128582278_144329181-prep-prealign.bam
[2016-04-15T00:04Z] GATK RealignerTargetCreator: R14-18105_kapa-NGv3-PE100-NGv3-sort-22_16266928_31795711-prep-prealign.bam 22:16266929-31795711
[2016-04-15T00:04Z] GATK: RealignerTargetCreator
[2016-04-15T00:04Z] GATK RealignerTargetCreator: R14-18105_kapa-NGv3-PE100-NGv3-sort-X_128582278_144329181-prep-prealign.bam X:128582279-144329181
[2016-04-15T00:04Z] GATK: RealignerTargetCreator
[2016-04-15T00:04Z] INFO  17:04:19,796 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:04Z] INFO  17:04:19,799 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:04Z] INFO  17:04:19,800 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:04Z] INFO  17:04:19,800 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:04Z] INFO  17:04:19,805 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/Y/R14-18105_kapa-NGv3-PE100-NGv3-sort-Y_59228291_59373566-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/Y/tx/tmp7ORY3g/R14-18105_kapa-NGv3-PE100-NGv3-sort-Y_59228291_59373566-prep-prealign-realign.intervals -l INFO -L Y:59228292-59373566 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:04Z] INFO  17:04:19,813 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:04Z] INFO  17:04:19,814 HelpFormatter - Date/Time: 2016/04/14 17:04:19
[2016-04-15T00:04Z] INFO  17:04:19,814 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:04Z] INFO  17:04:19,815 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:04Z] INFO  17:04:19,907 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:04Z] INFO  17:04:20,100 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:04Z] INFO  17:04:20,103 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:04Z] INFO  17:04:20,104 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:04Z] INFO  17:04:20,104 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:04Z] INFO  17:04:20,109 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/X/R14-18105_kapa-NGv3-PE100-NGv3-sort-X_95990756_111698889-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/X/tx/tmp5D6sm3/R14-18105_kapa-NGv3-PE100-NGv3-sort-X_95990756_111698889-prep-prealign-realign.intervals -l INFO -L X:95990757-111698889 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:04Z] INFO  17:04:20,120 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:04Z] INFO  17:04:20,131 HelpFormatter - Date/Time: 2016/04/14 17:04:20
[2016-04-15T00:04Z] INFO  17:04:20,132 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:04Z] INFO  17:04:20,133 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:04Z] INFO  17:04:20,183 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T00:04Z] INFO  17:04:20,193 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:04Z] INFO  17:04:20,209 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@41fd9d8e
[2016-04-15T00:04Z] INFO  17:04:20,243 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-15T00:04Z] INFO  17:04:20,252 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:04Z] INFO  17:04:20,331 ProgressMeter -            done   1213624.0     3.0 m       2.5 m      100.0%     3.0 m       0.0 s
[2016-04-15T00:04Z] INFO  17:04:20,331 ProgressMeter - Total runtime 179.19 secs, 2.99 min, 0.05 hours
[2016-04-15T00:04Z] INFO  17:04:20,332 MicroScheduler - 436 reads were filtered out during the traversal out of approximately 1214060 total reads (0.04%)
[2016-04-15T00:04Z] INFO  17:04:20,332 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:04Z] INFO  17:04:20,332 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:04Z] INFO  17:04:20,332 MicroScheduler -   -> 436 reads (0.04% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:04Z] INFO  17:04:20,442 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T00:04Z] INFO  17:04:20,452 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:04Z] INFO  17:04:20,486 ProgressMeter -            done    156686.0    12.0 s      77.0 s      100.0%    12.0 s       0.0 s
[2016-04-15T00:04Z] INFO  17:04:20,486 ProgressMeter - Total runtime 12.19 secs, 0.20 min, 0.00 hours
[2016-04-15T00:04Z] INFO  17:04:20,490 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 156686 total reads (0.00%)
[2016-04-15T00:04Z] INFO  17:04:20,490 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:04Z] INFO  17:04:20,490 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:04Z] INFO  17:04:20,491 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:04Z] INFO  17:04:20,513 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-15T00:04Z] INFO  17:04:20,575 ProgressMeter -            done    471995.0    32.0 s      68.0 s      100.0%    32.0 s       0.0 s
[2016-04-15T00:04Z] INFO  17:04:20,576 ProgressMeter - Total runtime 32.17 secs, 0.54 min, 0.01 hours
[2016-04-15T00:04Z] INFO  17:04:20,580 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 471995 total reads (0.00%)
[2016-04-15T00:04Z] INFO  17:04:20,580 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:04Z] INFO  17:04:20,580 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:04Z] INFO  17:04:20,581 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:04Z] INFO  17:04:20,617 IntervalUtils - Processing 145275 bp from intervals
[2016-04-15T00:04Z] WARN  17:04:20,623 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:04Z] INFO  17:04:20,735 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:04Z] INFO  17:04:20,764 IntervalUtils - Processing 15708133 bp from intervals
[2016-04-15T00:04Z] WARN  17:04:20,769 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:04Z] INFO  17:04:20,837 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:04Z] INFO  17:04:20,852 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:04Z] INFO  17:04:20,853 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:04Z] INFO  17:04:20,854 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:04Z] INFO  17:04:20,854 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:04Z] INFO  17:04:21,050 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:04Z] INFO  17:04:21,051 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:04Z] INFO  17:04:21,052 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:04Z] INFO  17:04:21,053 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:04Z] INFO  17:04:21,430 ProgressMeter -            done    145275.0     0.0 s       3.0 s       99.9%     0.0 s       0.0 s
[2016-04-15T00:04Z] INFO  17:04:21,431 ProgressMeter - Total runtime 0.58 secs, 0.01 min, 0.00 hours
[2016-04-15T00:04Z] INFO  17:04:21,791 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:04Z] INFO  17:04:21,794 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@5fe152b7
[2016-04-15T00:04Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-19_31038849_46627578-prep-prealign.bam
[2016-04-15T00:04Z] INFO  17:04:21,850 ProgressMeter -            done    147134.0    19.0 s       2.2 m      100.0%    19.0 s       0.0 s
[2016-04-15T00:04Z] INFO  17:04:21,850 ProgressMeter - Total runtime 19.34 secs, 0.32 min, 0.01 hours
[2016-04-15T00:04Z] INFO  17:04:21,851 MicroScheduler - 229 reads were filtered out during the traversal out of approximately 147363 total reads (0.16%)
[2016-04-15T00:04Z] INFO  17:04:21,851 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:04Z] INFO  17:04:21,851 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:04Z] INFO  17:04:21,852 MicroScheduler -   -> 229 reads (0.16% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:04Z] INFO  17:04:21,920 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:04Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-X_62857907_78427545-prep.bam
[2016-04-15T00:04Z] INFO  17:04:22,082 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:04Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-21_31062047_46591599-prep.bam
[2016-04-15T00:04Z] INFO  17:04:22,277 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:04Z] INFO  17:04:22,281 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:04Z] INFO  17:04:22,282 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:04Z] INFO  17:04:22,283 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:04Z] INFO  17:04:22,288 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/22/R14-18105_kapa-NGv3-PE100-NGv3-sort-22_16266928_31795711-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/22/tx/tmpkh36FH/R14-18105_kapa-NGv3-PE100-NGv3-sort-22_16266928_31795711-prep-prealign-realign.intervals -l INFO -L 22:16266929-31795711 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:04Z] INFO  17:04:22,302 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:04Z] INFO  17:04:22,303 HelpFormatter - Date/Time: 2016/04/14 17:04:22
[2016-04-15T00:04Z] INFO  17:04:22,303 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:04Z] INFO  17:04:22,304 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:04Z] INFO  17:04:22,405 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:04Z] Select unanalyzed reads
[2016-04-15T00:04Z] INFO  17:04:22,636 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:04Z] INFO  17:04:22,639 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:04Z] INFO  17:04:22,639 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:04Z] INFO  17:04:22,640 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:04Z] INFO  17:04:22,645 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/X/R14-18105_kapa-NGv3-PE100-NGv3-sort-X_128582278_144329181-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/X/tx/tmpuiQlF7/R14-18105_kapa-NGv3-PE100-NGv3-sort-X_128582278_144329181-prep-prealign-realign.intervals -l INFO -L X:128582279-144329181 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:04Z] INFO  17:04:22,662 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:04Z] INFO  17:04:22,662 HelpFormatter - Date/Time: 2016/04/14 17:04:22
[2016-04-15T00:04Z] INFO  17:04:22,663 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:04Z] INFO  17:04:22,663 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:04Z] INFO  17:04:22,685 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T00:04Z] INFO  17:04:22,697 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:04Z] INFO  17:04:22,770 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-15T00:04Z] INFO  17:04:22,810 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:04Z] INFO  17:04:23,014 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:04Z] GATK: realign ('Y', 59228291, 59373566) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-15T00:04Z] INFO  17:04:23,050 IntervalUtils - Processing 15528783 bp from intervals
[2016-04-15T00:04Z] WARN  17:04:23,056 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:04Z] INFO  17:04:23,058 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T00:04Z] INFO  17:04:23,071 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:04Z] INFO  17:04:23,141 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-15T00:04Z] INFO  17:04:23,168 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:04Z] INFO  17:04:23,437 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:04Z] INFO  17:04:23,437 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:04Z] INFO  17:04:23,438 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:04Z] INFO  17:04:23,438 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:04Z] INFO  17:04:23,533 IntervalUtils - Processing 15746903 bp from intervals
[2016-04-15T00:04Z] WARN  17:04:23,539 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:04Z] INFO  17:04:23,552 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:04Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-Y_0_15522993-prep-prealign.bam
[2016-04-15T00:04Z] INFO  17:04:23,630 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:04Z] GATK pre-alignment ('1', 0, 15541927) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:04Z] INFO  17:04:23,856 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:04Z] INFO  17:04:23,857 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:04Z] INFO  17:04:23,858 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:04Z] INFO  17:04:23,859 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:04Z] GATK RealignerTargetCreator: R14-18105_kapa-NGv3-PE100-NGv3-sort-Y_0_15522993-prep-prealign.bam Y:1-15522993
[2016-04-15T00:04Z] GATK: RealignerTargetCreator
[2016-04-15T00:04Z] GATK RealignerTargetCreator: R14-18105_kapa-NGv3-PE100-NGv3-sort-19_31038849_46627578-prep-prealign.bam 19:31038850-46627578
[2016-04-15T00:04Z] GATK: RealignerTargetCreator
[2016-04-15T00:04Z] INFO  17:04:26,237 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:04Z] INFO  17:04:26,243 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:04Z] INFO  17:04:26,244 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:04Z] INFO  17:04:26,244 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:04Z] INFO  17:04:26,249 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/Y/R14-18105_kapa-NGv3-PE100-NGv3-sort-Y_59228291_59373566-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/Y/R14-18105_kapa-NGv3-PE100-NGv3-sort-Y_59228291_59373566-prep-prealign-realign.intervals -L Y:59228292-59373566 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/Y/tx/tmpLWQPSr/R14-18105_kapa-NGv3-PE100-NGv3-sort-Y_59228291_59373566-prep.bam
[2016-04-15T00:04Z] INFO  17:04:26,275 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:04Z] INFO  17:04:26,276 HelpFormatter - Date/Time: 2016/04/14 17:04:26
[2016-04-15T00:04Z] INFO  17:04:26,276 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:04Z] INFO  17:04:26,277 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:04Z] INFO  17:04:26,556 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:04Z] INFO  17:04:26,655 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@41fd9d8e
[2016-04-15T00:04Z] INFO  17:04:26,685 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:04Z] INFO  17:04:26,694 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:04Z] INFO  17:04:26,735 ProgressMeter -      19:9971173   9961472.0    30.0 s       3.0 s       64.3%    46.0 s      16.0 s
[2016-04-15T00:04Z] INFO  17:04:26,752 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-15T00:04Z] INFO  17:04:26,756 ProgressMeter -            done    104249.0    15.0 s       2.5 m       99.5%    15.0 s       0.0 s
[2016-04-15T00:04Z] INFO  17:04:26,756 ProgressMeter - Total runtime 15.56 secs, 0.26 min, 0.00 hours
[2016-04-15T00:04Z] INFO  17:04:26,757 MicroScheduler - 165 reads were filtered out during the traversal out of approximately 104414 total reads (0.16%)
[2016-04-15T00:04Z] INFO  17:04:26,757 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:04Z] INFO  17:04:26,758 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:04Z] INFO  17:04:26,758 MicroScheduler -   -> 165 reads (0.16% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:04Z] INFO  17:04:26,909 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:04Z] INFO  17:04:26,911 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:04Z] INFO  17:04:26,911 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:04Z] INFO  17:04:26,912 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:04Z] INFO  17:04:26,916 HelpFormatter - Program Args: -T PrintReads -L 1:1-15541927 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/1/tx/tmp0n4Odj/R14-18106_kapa-NGv3-PE100-NGv3-sort-1_0_15541927-prep-prealign.bam
[2016-04-15T00:04Z] INFO  17:04:26,945 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:04Z] INFO  17:04:26,946 HelpFormatter - Date/Time: 2016/04/14 17:04:26
[2016-04-15T00:04Z] INFO  17:04:26,947 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:04Z] INFO  17:04:26,947 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:04Z] INFO  17:04:27,158 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:04Z] INFO  17:04:27,177 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:04Z] INFO  17:04:27,180 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:04Z] INFO  17:04:27,180 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:04Z] INFO  17:04:27,181 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:04Z] INFO  17:04:27,186 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/Y/R14-18105_kapa-NGv3-PE100-NGv3-sort-Y_0_15522993-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/Y/tx/tmpx8x0S7/R14-18105_kapa-NGv3-PE100-NGv3-sort-Y_0_15522993-prep-prealign-realign.intervals -l INFO -L Y:1-15522993 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:04Z] INFO  17:04:27,188 IntervalUtils - Processing 145275 bp from intervals
[2016-04-15T00:04Z] WARN  17:04:27,193 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:04Z] INFO  17:04:27,198 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:04Z] INFO  17:04:27,209 HelpFormatter - Date/Time: 2016/04/14 17:04:27
[2016-04-15T00:04Z] INFO  17:04:27,210 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:04Z] INFO  17:04:27,210 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:04Z] INFO  17:04:27,259 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:04Z] INFO  17:04:27,286 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:04Z] INFO  17:04:27,287 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:04Z] INFO  17:04:27,288 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:04Z] INFO  17:04:27,289 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:04Z] INFO  17:04:27,338 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:04Z] INFO  17:04:27,339 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:04Z] INFO  17:04:27,340 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:04Z] INFO  17:04:27,398 ProgressMeter -            done         0.0     0.0 s      30.6 h      100.0%     0.0 s       0.0 s
[2016-04-15T00:04Z] INFO  17:04:27,401 ProgressMeter - Total runtime 0.11 secs, 0.00 min, 0.00 hours
[2016-04-15T00:04Z] INFO  17:04:27,590 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T00:04Z] INFO  17:04:27,616 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:04Z] INFO  17:04:27,660 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.04
[2016-04-15T00:04Z] INFO  17:04:28,007 IntervalUtils - Processing 15522993 bp from intervals
[2016-04-15T00:04Z] WARN  17:04:28,012 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:04Z] INFO  17:04:28,152 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:04Z] INFO  17:04:28,234 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-15T00:04Z] INFO  17:04:28,289 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:04Z] INFO  17:04:28,297 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:04Z] INFO  17:04:28,299 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:04Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-Y_15526614_59222281-prep-prealign.bam
[2016-04-15T00:04Z] INFO  17:04:28,340 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:04Z] INFO  17:04:28,341 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:04Z] INFO  17:04:28,342 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:04Z] INFO  17:04:28,342 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:04Z] INFO  17:04:28,396 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.10
[2016-04-15T00:04Z] INFO  17:04:28,424 IntervalUtils - Processing 15541927 bp from intervals
[2016-04-15T00:04Z] INFO  17:04:28,574 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:04Z] GATK RealignerTargetCreator: R14-18105_kapa-NGv3-PE100-NGv3-sort-Y_15526614_59222281-prep-prealign.bam Y:15526615-59222281
[2016-04-15T00:04Z] GATK: RealignerTargetCreator
[2016-04-15T00:04Z] INFO  17:04:28,836 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:04Z] INFO  17:04:28,846 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:04Z] INFO  17:04:28,848 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:04Z] INFO  17:04:28,848 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:04Z] INFO  17:04:28,849 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:04Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-Y_59228291_59373566-prep.bam
[2016-04-15T00:04Z] INFO  17:04:28,863 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:04Z] GATK pre-alignment ('1', 15545821, 31186478) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:04Z] INFO  17:04:29,018 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:04Z] INFO  17:04:29,120 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:04Z] INFO  17:04:29,123 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:04Z] INFO  17:04:29,123 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:04Z] INFO  17:04:29,124 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:04Z] INFO  17:04:29,128 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/19/R14-18105_kapa-NGv3-PE100-NGv3-sort-19_31038849_46627578-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/19/tx/tmp8ifdHK/R14-18105_kapa-NGv3-PE100-NGv3-sort-19_31038849_46627578-prep-prealign-realign.intervals -l INFO -L 19:31038850-46627578 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:04Z] INFO  17:04:29,136 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:04Z] INFO  17:04:29,137 HelpFormatter - Date/Time: 2016/04/14 17:04:29
[2016-04-15T00:04Z] INFO  17:04:29,138 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:04Z] INFO  17:04:29,138 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:04Z] INFO  17:04:29,278 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:04Z] INFO  17:04:29,370 ProgressMeter -     X:154687838    100001.0    30.0 s       5.0 m       94.7%    31.0 s       1.0 s
[2016-04-15T00:04Z] INFO  17:04:29,542 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T00:04Z] INFO  17:04:29,561 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:04Z] INFO  17:04:29,611 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-15T00:04Z] INFO  17:04:29,990 IntervalUtils - Processing 15588729 bp from intervals
[2016-04-15T00:04Z] WARN  17:04:29,996 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:04Z] INFO  17:04:30,108 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:04Z] INFO  17:04:30,450 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:04Z] INFO  17:04:30,452 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:04Z] INFO  17:04:30,452 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:04Z] INFO  17:04:30,453 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:04Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-noanalysis-prep.bam
[2016-04-15T00:04Z] GATK pre-alignment ('1', 31187093, 46714270) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:04Z] INFO  17:04:30,869 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@5fe152b7
[2016-04-15T00:04Z] INFO  17:04:30,980 ProgressMeter -            done    198839.0    31.0 s       2.7 m       99.9%    31.0 s       0.0 s
[2016-04-15T00:04Z] INFO  17:04:30,987 ProgressMeter - Total runtime 31.64 secs, 0.53 min, 0.01 hours
[2016-04-15T00:04Z] INFO  17:04:30,988 MicroScheduler - 92 reads were filtered out during the traversal out of approximately 198931 total reads (0.05%)
[2016-04-15T00:04Z] INFO  17:04:30,988 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:04Z] INFO  17:04:30,988 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:04Z] INFO  17:04:30,988 MicroScheduler -   -> 92 reads (0.05% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:04Z] INFO  17:04:31,497 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:04Z] INFO  17:04:31,500 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:04Z] INFO  17:04:31,500 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:04Z] INFO  17:04:31,500 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:04Z] INFO  17:04:31,504 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/Y/R14-18105_kapa-NGv3-PE100-NGv3-sort-Y_15526614_59222281-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/Y/tx/tmpvi4bz_/R14-18105_kapa-NGv3-PE100-NGv3-sort-Y_15526614_59222281-prep-prealign-realign.intervals -l INFO -L Y:15526615-59222281 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:04Z] INFO  17:04:31,550 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:04Z] INFO  17:04:31,551 HelpFormatter - Date/Time: 2016/04/14 17:04:31
[2016-04-15T00:04Z] INFO  17:04:31,552 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:04Z] INFO  17:04:31,552 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:04Z] INFO  17:04:31,665 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:04Z] INFO  17:04:31,834 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:04Z] INFO  17:04:31,838 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:04Z] INFO  17:04:31,838 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:04Z] INFO  17:04:31,839 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:04Z] INFO  17:04:31,843 HelpFormatter - Program Args: -T PrintReads -L 1:15545822-31186478 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/1/tx/tmpw46Bge/R14-18106_kapa-NGv3-PE100-NGv3-sort-1_15545821_31186478-prep-prealign.bam
[2016-04-15T00:04Z] INFO  17:04:31,851 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:04Z] INFO  17:04:31,852 HelpFormatter - Date/Time: 2016/04/14 17:04:31
[2016-04-15T00:04Z] INFO  17:04:31,853 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:04Z] INFO  17:04:31,853 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:04Z] INFO  17:04:31,869 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T00:04Z] INFO  17:04:31,888 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:04Z] INFO  17:04:31,953 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-15T00:04Z] INFO  17:04:32,081 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:04Z] INFO  17:04:32,257 IntervalUtils - Processing 43695667 bp from intervals
[2016-04-15T00:04Z] WARN  17:04:32,262 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:04Z] INFO  17:04:32,334 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:04Z] INFO  17:04:32,389 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:04Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-X_144337190_155270560-prep-prealign.bam
[2016-04-15T00:04Z] INFO  17:04:32,508 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:04Z] INFO  17:04:32,509 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:04Z] INFO  17:04:32,510 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:04Z] INFO  17:04:32,510 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:04Z] GATK RealignerTargetCreator: R14-18105_kapa-NGv3-PE100-NGv3-sort-X_144337190_155270560-prep-prealign.bam X:144337191-155270560
[2016-04-15T00:04Z] GATK: RealignerTargetCreator
[2016-04-15T00:04Z] INFO  17:04:33,171 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-15T00:04Z] INFO  17:04:33,240 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:04Z] INFO  17:04:33,249 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:04Z] INFO  17:04:33,306 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-15T00:04Z] INFO  17:04:33,363 IntervalUtils - Processing 15640657 bp from intervals
[2016-04-15T00:04Z] INFO  17:04:33,422 ProgressMeter -            done   1.6706631E7    15.0 s       0.0 s      100.0%    15.0 s       0.0 s
[2016-04-15T00:04Z] INFO  17:04:33,423 ProgressMeter - Total runtime 15.84 secs, 0.26 min, 0.00 hours
[2016-04-15T00:04Z] INFO  17:04:33,427 MicroScheduler - 28431 reads were filtered out during the traversal out of approximately 104911 total reads (27.10%)
[2016-04-15T00:04Z] INFO  17:04:33,427 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:04Z] INFO  17:04:33,427 MicroScheduler -   -> 268 reads (0.26% of total) failing BadMateFilter
[2016-04-15T00:04Z] INFO  17:04:33,428 MicroScheduler -   -> 6184 reads (5.89% of total) failing DuplicateReadFilter
[2016-04-15T00:04Z] INFO  17:04:33,428 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:04Z] INFO  17:04:33,428 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:04Z] INFO  17:04:33,428 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:04Z] INFO  17:04:33,429 MicroScheduler -   -> 21979 reads (20.95% of total) failing MappingQualityZeroFilter
[2016-04-15T00:04Z] INFO  17:04:33,429 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:04Z] INFO  17:04:33,429 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-15T00:04Z] INFO  17:04:33,429 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:04Z] INFO  17:04:33,489 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:04Z] INFO  17:04:33,721 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:04Z] INFO  17:04:33,721 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:04Z] INFO  17:04:33,722 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:04Z] INFO  17:04:33,722 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:04Z] INFO  17:04:33,744 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:04Z] INFO  17:04:33,791 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:04Z] INFO  17:04:33,794 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:04Z] INFO  17:04:33,795 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:04Z] INFO  17:04:33,795 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:04Z] INFO  17:04:33,800 HelpFormatter - Program Args: -T PrintReads -L 1:31187094-46714270 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/1/tx/tmpoi_TQO/R14-18106_kapa-NGv3-PE100-NGv3-sort-1_31187093_46714270-prep-prealign.bam
[2016-04-15T00:04Z] INFO  17:04:33,809 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:04Z] INFO  17:04:33,809 HelpFormatter - Date/Time: 2016/04/14 17:04:33
[2016-04-15T00:04Z] INFO  17:04:33,809 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:04Z] INFO  17:04:33,810 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:04Z] INFO  17:04:33,895 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:04Z] INFO  17:04:34,017 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:04Z] INFO  17:04:34,959 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:04Z] INFO  17:04:34,983 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-15T00:04Z] GATK: realign ('X', 111874647, 128581278) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-15T00:04Z] INFO  17:04:35,049 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:04Z] INFO  17:04:35,058 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:04Z] INFO  17:04:35,121 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-15T00:04Z] INFO  17:04:35,145 IntervalUtils - Processing 15527177 bp from intervals
[2016-04-15T00:04Z] INFO  17:04:35,242 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:04Z] INFO  17:04:35,602 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:04Z] INFO  17:04:35,603 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:04Z] INFO  17:04:35,603 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:04Z] INFO  17:04:35,604 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:04Z] INFO  17:04:35,642 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:04Z] INFO  17:04:35,777 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:04Z] INFO  17:04:35,801 ProgressMeter -            done    293576.0    20.0 s      68.0 s      100.0%    20.0 s       0.0 s
[2016-04-15T00:04Z] INFO  17:04:35,802 ProgressMeter - Total runtime 20.19 secs, 0.34 min, 0.01 hours
[2016-04-15T00:04Z] INFO  17:04:35,805 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 293576 total reads (0.00%)
[2016-04-15T00:04Z] INFO  17:04:35,806 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:04Z] INFO  17:04:35,807 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:04Z] INFO  17:04:35,817 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:04Z] INFO  17:04:35,808 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:04Z] INFO  17:04:35,820 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:04Z] INFO  17:04:35,821 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:04Z] INFO  17:04:35,821 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:04Z] INFO  17:04:35,826 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/X/R14-18105_kapa-NGv3-PE100-NGv3-sort-X_144337190_155270560-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/X/tx/tmpa0hAbw/R14-18105_kapa-NGv3-PE100-NGv3-sort-X_144337190_155270560-prep-prealign-realign.intervals -l INFO -L X:144337191-155270560 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:04Z] INFO  17:04:35,836 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:04Z] INFO  17:04:35,847 HelpFormatter - Date/Time: 2016/04/14 17:04:35
[2016-04-15T00:04Z] INFO  17:04:35,848 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:04Z] INFO  17:04:35,849 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:04Z] INFO  17:04:35,992 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:04Z] INFO  17:04:36,213 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T00:04Z] INFO  17:04:36,230 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:04Z] INFO  17:04:36,279 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-15T00:04Z] INFO  17:04:36,416 ProgressMeter -     19:55997829   9356247.0    30.0 s       3.0 s       75.0%    40.0 s      10.0 s
[2016-04-15T00:04Z] INFO  17:04:36,541 IntervalUtils - Processing 10933370 bp from intervals
[2016-04-15T00:04Z] WARN  17:04:36,549 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:04Z] INFO  17:04:36,630 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:04Z] INFO  17:04:36,795 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:04Z] INFO  17:04:36,796 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:04Z] INFO  17:04:36,797 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:04Z] INFO  17:04:36,798 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:04Z] INFO  17:04:37,318 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:04Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-X_46712910_62570698-prep.bam
[2016-04-15T00:04Z] INFO  17:04:37,676 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:04Z] INFO  17:04:37,679 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:04Z] INFO  17:04:37,680 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:04Z] INFO  17:04:37,681 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:04Z] INFO  17:04:37,695 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/X/R14-18105_kapa-NGv3-PE100-NGv3-sort-X_111874647_128581278-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/X/R14-18105_kapa-NGv3-PE100-NGv3-sort-X_111874647_128581278-prep-prealign-realign.intervals -L X:111874648-128581278 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/X/tx/tmpK4yIXy/R14-18105_kapa-NGv3-PE100-NGv3-sort-X_111874647_128581278-prep.bam
[2016-04-15T00:04Z] INFO  17:04:37,719 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:04Z] INFO  17:04:37,720 HelpFormatter - Date/Time: 2016/04/14 17:04:37
[2016-04-15T00:04Z] INFO  17:04:37,720 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:04Z] INFO  17:04:37,720 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:04Z] INFO  17:04:37,835 ProgressMeter -            done   1.5708133E7    16.0 s       1.0 s      100.0%    16.0 s       0.0 s
[2016-04-15T00:04Z] INFO  17:04:37,836 ProgressMeter - Total runtime 16.78 secs, 0.28 min, 0.00 hours
[2016-04-15T00:04Z] INFO  17:04:37,840 MicroScheduler - 25498 reads were filtered out during the traversal out of approximately 153799 total reads (16.58%)
[2016-04-15T00:04Z] INFO  17:04:37,840 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:04Z] INFO  17:04:37,840 MicroScheduler -   -> 361 reads (0.23% of total) failing BadMateFilter
[2016-04-15T00:04Z] INFO  17:04:37,841 MicroScheduler -   -> 10645 reads (6.92% of total) failing DuplicateReadFilter
[2016-04-15T00:04Z] INFO  17:04:37,841 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:04Z] INFO  17:04:37,841 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:04Z] INFO  17:04:37,841 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:04Z] INFO  17:04:37,842 MicroScheduler -   -> 14492 reads (9.42% of total) failing MappingQualityZeroFilter
[2016-04-15T00:04Z] INFO  17:04:37,843 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:04Z] INFO  17:04:37,843 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-15T00:04Z] INFO  17:04:37,844 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:04Z] INFO  17:04:37,948 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:04Z] INFO  17:04:38,081 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:04Z] INFO  17:04:38,090 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:04Z] INFO  17:04:38,133 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.04
[2016-04-15T00:04Z] GATK pre-alignment ('1', 46715671, 62228851) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:04Z] INFO  17:04:38,442 IntervalUtils - Processing 16706631 bp from intervals
[2016-04-15T00:04Z] WARN  17:04:38,448 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:04Z] INFO  17:04:38,529 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:04Z] INFO  17:04:38,598 ProgressMeter -            done   1.551148E7    27.0 s       1.0 s      100.0%    27.0 s       0.0 s
[2016-04-15T00:04Z] INFO  17:04:38,599 ProgressMeter - Total runtime 27.15 secs, 0.45 min, 0.01 hours
[2016-04-15T00:04Z] INFO  17:04:38,602 MicroScheduler - 60397 reads were filtered out during the traversal out of approximately 676106 total reads (8.93%)
[2016-04-15T00:04Z] INFO  17:04:38,603 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:04Z] INFO  17:04:38,603 MicroScheduler -   -> 1243 reads (0.18% of total) failing BadMateFilter
[2016-04-15T00:04Z] INFO  17:04:38,603 MicroScheduler -   -> 53101 reads (7.85% of total) failing DuplicateReadFilter
[2016-04-15T00:04Z] INFO  17:04:38,604 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:04Z] INFO  17:04:38,604 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:04Z] INFO  17:04:38,604 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:04Z] INFO  17:04:38,604 MicroScheduler -   -> 6053 reads (0.90% of total) failing MappingQualityZeroFilter
[2016-04-15T00:04Z] INFO  17:04:38,605 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:04Z] INFO  17:04:38,605 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-15T00:04Z] INFO  17:04:38,605 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:04Z] INFO  17:04:38,659 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:04Z] INFO  17:04:38,661 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:04Z] INFO  17:04:38,661 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:04Z] INFO  17:04:38,662 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:04Z] INFO  17:04:38,804 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:04Z] INFO  17:04:39,053 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:04Z] INFO  17:04:39,260 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:04Z] GATK: realign ('X', 95990756, 111698889) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-15T00:04Z] INFO  17:04:39,837 ProgressMeter -            done   1.5746903E7    15.0 s       1.0 s      100.0%    15.0 s       0.0 s
[2016-04-15T00:04Z] INFO  17:04:39,838 ProgressMeter - Total runtime 15.98 secs, 0.27 min, 0.00 hours
[2016-04-15T00:04Z] INFO  17:04:39,842 MicroScheduler - 33415 reads were filtered out during the traversal out of approximately 130367 total reads (25.63%)
[2016-04-15T00:04Z] INFO  17:04:39,843 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:04Z] INFO  17:04:39,844 MicroScheduler -   -> 275 reads (0.21% of total) failing BadMateFilter
[2016-04-15T00:04Z] INFO  17:04:39,844 MicroScheduler -   -> 8232 reads (6.31% of total) failing DuplicateReadFilter
[2016-04-15T00:04Z] INFO  17:04:39,844 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:04Z] INFO  17:04:39,845 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:04Z] INFO  17:04:39,845 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:04Z] INFO  17:04:39,845 MicroScheduler -   -> 24908 reads (19.11% of total) failing MappingQualityZeroFilter
[2016-04-15T00:04Z] INFO  17:04:39,845 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:04Z] INFO  17:04:39,846 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-15T00:04Z] INFO  17:04:39,846 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:04Z] INFO  17:04:40,037 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:04Z] GATK: realign ('22', 31796605, 47308085) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-15T00:04Z] INFO  17:04:41,156 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:04Z] INFO  17:04:41,159 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:04Z] INFO  17:04:41,160 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:04Z] INFO  17:04:41,161 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:04Z] INFO  17:04:41,165 HelpFormatter - Program Args: -T PrintReads -L 1:46715672-62228851 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/1/tx/tmprLcpqQ/R14-18106_kapa-NGv3-PE100-NGv3-sort-1_46715671_62228851-prep-prealign.bam
[2016-04-15T00:04Z] INFO  17:04:41,188 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:04Z] INFO  17:04:41,190 HelpFormatter - Date/Time: 2016/04/14 17:04:41
[2016-04-15T00:04Z] INFO  17:04:41,190 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:04Z] INFO  17:04:41,191 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:04Z] INFO  17:04:41,207 ProgressMeter -            done   1.5522993E7    12.0 s       0.0 s      100.0%    12.0 s       0.0 s
[2016-04-15T00:04Z] INFO  17:04:41,208 ProgressMeter - Total runtime 12.87 secs, 0.21 min, 0.00 hours
[2016-04-15T00:04Z] INFO  17:04:41,226 MicroScheduler - 108133 reads were filtered out during the traversal out of approximately 148500 total reads (72.82%)
[2016-04-15T00:04Z] INFO  17:04:41,227 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:04Z] INFO  17:04:41,228 MicroScheduler -   -> 319 reads (0.21% of total) failing BadMateFilter
[2016-04-15T00:04Z] INFO  17:04:41,228 MicroScheduler -   -> 3600 reads (2.42% of total) failing DuplicateReadFilter
[2016-04-15T00:04Z] INFO  17:04:41,228 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:04Z] INFO  17:04:41,229 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:04Z] INFO  17:04:41,229 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:04Z] INFO  17:04:41,229 MicroScheduler -   -> 104214 reads (70.18% of total) failing MappingQualityZeroFilter
[2016-04-15T00:04Z] INFO  17:04:41,229 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:04Z] INFO  17:04:41,230 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-15T00:04Z] INFO  17:04:41,230 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:04Z] INFO  17:04:41,323 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:04Z] GATK: realign ('X', 128582278, 144329181) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-15T00:04Z] INFO  17:04:41,391 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:04Z] INFO  17:04:42,319 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-15T00:04Z] INFO  17:04:42,359 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:04Z] INFO  17:04:42,362 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:04Z] INFO  17:04:42,363 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:04Z] INFO  17:04:42,364 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:04Z] INFO  17:04:42,368 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/X/R14-18105_kapa-NGv3-PE100-NGv3-sort-X_95990756_111698889-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/X/R14-18105_kapa-NGv3-PE100-NGv3-sort-X_95990756_111698889-prep-prealign-realign.intervals -L X:95990757-111698889 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/X/tx/tmpi6AAo3/R14-18105_kapa-NGv3-PE100-NGv3-sort-X_95990756_111698889-prep.bam
[2016-04-15T00:04Z] INFO  17:04:42,380 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:04Z] INFO  17:04:42,389 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:04Z] INFO  17:04:42,400 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:04Z] INFO  17:04:42,401 HelpFormatter - Date/Time: 2016/04/14 17:04:42
[2016-04-15T00:04Z] INFO  17:04:42,402 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:04Z] INFO  17:04:42,402 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:04Z] INFO  17:04:42,436 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-15T00:04Z] INFO  17:04:42,456 IntervalUtils - Processing 15513180 bp from intervals
[2016-04-15T00:04Z] INFO  17:04:42,577 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:04Z] INFO  17:04:42,591 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:04Z] INFO  17:04:42,679 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:04Z] GATK: realign ('Y', 0, 15522993) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-15T00:04Z] INFO  17:04:42,700 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:04Z] INFO  17:04:42,710 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:04Z] INFO  17:04:42,751 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.04
[2016-04-15T00:04Z] INFO  17:04:42,835 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:04Z] INFO  17:04:42,836 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:04Z] INFO  17:04:42,837 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:04Z] INFO  17:04:42,838 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:04Z] INFO  17:04:42,852 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:04Z] INFO  17:04:42,870 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:04Z] INFO  17:04:42,873 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:04Z] INFO  17:04:42,874 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:04Z] INFO  17:04:42,874 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:04Z] INFO  17:04:42,879 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/22/R14-18105_kapa-NGv3-PE100-NGv3-sort-22_31796605_47308085-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/22/R14-18105_kapa-NGv3-PE100-NGv3-sort-22_31796605_47308085-prep-prealign-realign.intervals -L 22:31796606-47308085 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/22/tx/tmp2hAnJP/R14-18105_kapa-NGv3-PE100-NGv3-sort-22_31796605_47308085-prep.bam
[2016-04-15T00:04Z] INFO  17:04:42,905 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:04Z] INFO  17:04:42,906 HelpFormatter - Date/Time: 2016/04/14 17:04:42
[2016-04-15T00:04Z] INFO  17:04:42,906 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:04Z] INFO  17:04:42,907 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:04Z] INFO  17:04:43,008 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:04Z] INFO  17:04:43,063 IntervalUtils - Processing 15708133 bp from intervals
[2016-04-15T00:04Z] WARN  17:04:43,068 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:04Z] INFO  17:04:43,079 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:04Z] INFO  17:04:43,133 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:04Z] INFO  17:04:43,248 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:04Z] INFO  17:04:43,266 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:04Z] INFO  17:04:43,267 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:04Z] INFO  17:04:43,268 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:04Z] INFO  17:04:43,268 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:04Z] INFO  17:04:43,272 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:04Z] INFO  17:04:43,354 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:04Z] INFO  17:04:43,357 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-15T00:04Z] INFO  17:04:43,417 ProgressMeter -            done   1.5509577E7    46.0 s       3.0 s      100.0%    46.0 s       0.0 s
[2016-04-15T00:04Z] INFO  17:04:43,418 ProgressMeter - Total runtime 46.69 secs, 0.78 min, 0.01 hours
[2016-04-15T00:04Z] INFO  17:04:43,421 MicroScheduler - 143132 reads were filtered out during the traversal out of approximately 1524115 total reads (9.39%)
[2016-04-15T00:04Z] INFO  17:04:43,422 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:04Z] INFO  17:04:43,422 MicroScheduler -   -> 2605 reads (0.17% of total) failing BadMateFilter
[2016-04-15T00:04Z] INFO  17:04:43,422 MicroScheduler -   -> 122017 reads (8.01% of total) failing DuplicateReadFilter
[2016-04-15T00:04Z] INFO  17:04:43,422 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:04Z] INFO  17:04:43,423 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:04Z] INFO  17:04:43,423 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:04Z] INFO  17:04:43,423 MicroScheduler -   -> 18510 reads (1.21% of total) failing MappingQualityZeroFilter
[2016-04-15T00:04Z] INFO  17:04:43,423 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:04Z] INFO  17:04:43,424 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-15T00:04Z] INFO  17:04:43,424 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:04Z] INFO  17:04:43,476 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:04Z] INFO  17:04:43,731 IntervalUtils - Processing 15511480 bp from intervals
[2016-04-15T00:04Z] WARN  17:04:43,736 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:04Z] INFO  17:04:43,861 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:04Z] INFO  17:04:44,115 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:04Z] INFO  17:04:44,118 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:04Z] INFO  17:04:44,124 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:04Z] INFO  17:04:44,125 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:04Z] INFO  17:04:44,233 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:04Z] INFO  17:04:44,237 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:04Z] INFO  17:04:44,237 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:04Z] INFO  17:04:44,238 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:04Z] INFO  17:04:44,242 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/X/R14-18105_kapa-NGv3-PE100-NGv3-sort-X_128582278_144329181-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/X/R14-18105_kapa-NGv3-PE100-NGv3-sort-X_128582278_144329181-prep-prealign-realign.intervals -L X:128582279-144329181 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/X/tx/tmpNX_3N5/R14-18105_kapa-NGv3-PE100-NGv3-sort-X_128582278_144329181-prep.bam
[2016-04-15T00:04Z] INFO  17:04:44,261 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:04Z] INFO  17:04:44,262 HelpFormatter - Date/Time: 2016/04/14 17:04:44
[2016-04-15T00:04Z] INFO  17:04:44,263 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:04Z] INFO  17:04:44,263 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:04Z] INFO  17:04:44,318 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:04Z] INFO  17:04:44,509 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:04Z] INFO  17:04:44,578 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:04Z] INFO  17:04:44,672 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:04Z] INFO  17:04:44,681 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:04Z] INFO  17:04:44,771 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.09
[2016-04-15T00:04Z] INFO  17:04:44,913 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:04Z] GATK: realign ('19', 0, 15509577) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-15T00:04Z] INFO  17:04:45,245 IntervalUtils - Processing 15746903 bp from intervals
[2016-04-15T00:04Z] WARN  17:04:45,251 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:04Z] INFO  17:04:45,329 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:04Z] INFO  17:04:45,504 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:04Z] INFO  17:04:45,505 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:04Z] INFO  17:04:45,506 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:04Z] INFO  17:04:45,512 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:04Z] INFO  17:04:45,613 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:04Z] INFO  17:04:45,648 ProgressMeter -            done   1.2501102E7    39.0 s       3.0 s      100.0%    39.0 s       0.0 s
[2016-04-15T00:04Z] INFO  17:04:45,649 ProgressMeter - Total runtime 39.25 secs, 0.65 min, 0.01 hours
[2016-04-15T00:04Z] INFO  17:04:45,653 MicroScheduler - 154285 reads were filtered out during the traversal out of approximately 1357923 total reads (11.36%)
[2016-04-15T00:04Z] INFO  17:04:45,653 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:04Z] INFO  17:04:45,653 MicroScheduler -   -> 2206 reads (0.16% of total) failing BadMateFilter
[2016-04-15T00:04Z] INFO  17:04:45,654 MicroScheduler -   -> 105426 reads (7.76% of total) failing DuplicateReadFilter
[2016-04-15T00:04Z] INFO  17:04:45,654 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:04Z] INFO  17:04:45,654 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:04Z] INFO  17:04:45,654 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:04Z] INFO  17:04:45,655 MicroScheduler -   -> 46653 reads (3.44% of total) failing MappingQualityZeroFilter
[2016-04-15T00:04Z] INFO  17:04:45,655 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:04Z] INFO  17:04:45,655 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-15T00:04Z] INFO  17:04:45,655 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:04Z] INFO  17:04:45,730 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:04Z] INFO  17:04:45,737 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:04Z] INFO  17:04:45,740 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:04Z] INFO  17:04:45,741 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:04Z] INFO  17:04:45,741 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:04Z] INFO  17:04:45,746 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/Y/R14-18105_kapa-NGv3-PE100-NGv3-sort-Y_0_15522993-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/Y/R14-18105_kapa-NGv3-PE100-NGv3-sort-Y_0_15522993-prep-prealign-realign.intervals -L Y:1-15522993 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/Y/tx/tmp2BMDce/R14-18105_kapa-NGv3-PE100-NGv3-sort-Y_0_15522993-prep.bam
[2016-04-15T00:04Z] INFO  17:04:45,765 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:04Z] INFO  17:04:45,766 HelpFormatter - Date/Time: 2016/04/14 17:04:45
[2016-04-15T00:04Z] INFO  17:04:45,767 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:04Z] INFO  17:04:45,767 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:04Z] INFO  17:04:45,981 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:04Z] INFO  17:04:46,110 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:04Z] INFO  17:04:46,123 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:04Z] INFO  17:04:46,176 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-15T00:04Z] INFO  17:04:46,649 IntervalUtils - Processing 15522993 bp from intervals
[2016-04-15T00:04Z] WARN  17:04:46,654 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:04Z] INFO  17:04:46,800 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:04Z] INFO  17:04:46,947 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:04Z] INFO  17:04:46,948 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:04Z] INFO  17:04:46,949 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:04Z] INFO  17:04:46,950 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:04Z] INFO  17:04:46,983 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:04Z] INFO  17:04:47,012 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:04Z] GATK: realign ('19', 46627881, 59128983) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-15T00:04Z] INFO  17:04:47,135 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:04Z] INFO  17:04:47,661 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:04Z] INFO  17:04:47,664 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:04Z] INFO  17:04:47,665 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:04Z] INFO  17:04:47,665 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:04Z] INFO  17:04:47,670 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/19/R14-18105_kapa-NGv3-PE100-NGv3-sort-19_0_15509577-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/19/R14-18105_kapa-NGv3-PE100-NGv3-sort-19_0_15509577-prep-prealign-realign.intervals -L 19:1-15509577 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/19/tx/tmp9LlucT/R14-18105_kapa-NGv3-PE100-NGv3-sort-19_0_15509577-prep.bam
[2016-04-15T00:04Z] INFO  17:04:47,703 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:04Z] INFO  17:04:47,704 HelpFormatter - Date/Time: 2016/04/14 17:04:47
[2016-04-15T00:04Z] INFO  17:04:47,705 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:04Z] INFO  17:04:47,706 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:04Z] INFO  17:04:47,952 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:04Z] INFO  17:04:48,043 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:04Z] INFO  17:04:48,052 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:04Z] INFO  17:04:48,117 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-15T00:04Z] INFO  17:04:48,471 IntervalUtils - Processing 15509577 bp from intervals
[2016-04-15T00:04Z] WARN  17:04:48,477 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:04Z] INFO  17:04:48,552 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:04Z] INFO  17:04:48,789 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:04Z] INFO  17:04:48,802 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:04Z] INFO  17:04:48,803 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:04Z] INFO  17:04:48,803 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:04Z] INFO  17:04:48,938 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:04Z] INFO  17:04:48,942 ProgressMeter -            done    104104.0    10.0 s      98.0 s       97.6%    10.0 s       0.0 s
[2016-04-15T00:04Z] INFO  17:04:48,942 ProgressMeter - Total runtime 10.28 secs, 0.17 min, 0.00 hours
[2016-04-15T00:04Z] INFO  17:04:48,946 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 104104 total reads (0.00%)
[2016-04-15T00:04Z] INFO  17:04:48,947 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:04Z] INFO  17:04:48,948 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:04Z] INFO  17:04:48,948 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:04Z] INFO  17:04:49,136 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:04Z] INFO  17:04:49,801 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:04Z] INFO  17:04:49,804 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:04Z] INFO  17:04:49,805 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:04Z] INFO  17:04:49,805 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:04Z] INFO  17:04:49,810 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/19/R14-18105_kapa-NGv3-PE100-NGv3-sort-19_46627881_59128983-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/19/R14-18105_kapa-NGv3-PE100-NGv3-sort-19_46627881_59128983-prep-prealign-realign.intervals -L 19:46627882-59128983 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/19/tx/tmp1GNO7W/R14-18105_kapa-NGv3-PE100-NGv3-sort-19_46627881_59128983-prep.bam
[2016-04-15T00:04Z] INFO  17:04:49,825 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:04Z] INFO  17:04:49,826 HelpFormatter - Date/Time: 2016/04/14 17:04:49
[2016-04-15T00:04Z] INFO  17:04:49,826 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:04Z] INFO  17:04:49,827 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:04Z] INFO  17:04:50,124 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:04Z] INFO  17:04:50,308 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:04Z] INFO  17:04:50,324 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:04Z] INFO  17:04:50,374 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:04Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-X_111874647_128581278-prep.bam
[2016-04-15T00:04Z] INFO  17:04:50,411 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-15T00:04Z] GATK pre-alignment ('1', 62231950, 77749296) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:04Z] INFO  17:04:50,827 IntervalUtils - Processing 12501102 bp from intervals
[2016-04-15T00:04Z] WARN  17:04:50,832 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:04Z] INFO  17:04:50,897 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:04Z] INFO  17:04:50,929 ProgressMeter -            done   1.093337E7    14.0 s       1.0 s      100.0%    14.0 s       0.0 s
[2016-04-15T00:04Z] INFO  17:04:50,930 ProgressMeter - Total runtime 14.13 secs, 0.24 min, 0.00 hours
[2016-04-15T00:04Z] INFO  17:04:50,933 MicroScheduler - 48557 reads were filtered out during the traversal out of approximately 199877 total reads (24.29%)
[2016-04-15T00:04Z] INFO  17:04:50,933 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:04Z] INFO  17:04:50,934 MicroScheduler -   -> 347 reads (0.17% of total) failing BadMateFilter
[2016-04-15T00:04Z] INFO  17:04:50,934 MicroScheduler -   -> 13053 reads (6.53% of total) failing DuplicateReadFilter
[2016-04-15T00:04Z] INFO  17:04:50,934 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:04Z] INFO  17:04:50,934 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:04Z] INFO  17:04:50,935 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:04Z] INFO  17:04:50,935 MicroScheduler -   -> 35157 reads (17.59% of total) failing MappingQualityZeroFilter
[2016-04-15T00:04Z] INFO  17:04:50,935 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:04Z] INFO  17:04:50,935 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-15T00:04Z] INFO  17:04:50,936 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:04Z] INFO  17:04:51,162 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:04Z] INFO  17:04:51,163 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:04Z] INFO  17:04:51,163 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:04Z] INFO  17:04:51,164 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:04Z] INFO  17:04:51,304 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:04Z] INFO  17:04:51,433 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:04Z] INFO  17:04:52,302 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:04Z] GATK: realign ('X', 144337190, 155270560) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-15T00:04Z] INFO  17:04:53,471 ProgressMeter -     22:31795661   1.5518032E7    30.0 s       1.0 s      100.0%    30.0 s       0.0 s
[2016-04-15T00:04Z] INFO  17:04:53,528 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:04Z] INFO  17:04:53,532 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:04Z] INFO  17:04:53,532 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:04Z] INFO  17:04:53,533 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:04Z] INFO  17:04:53,537 HelpFormatter - Program Args: -T PrintReads -L 1:62231951-77749296 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/1/tx/tmpzyZz_k/R14-18106_kapa-NGv3-PE100-NGv3-sort-1_62231950_77749296-prep-prealign.bam
[2016-04-15T00:04Z] INFO  17:04:53,546 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:04Z] INFO  17:04:53,547 HelpFormatter - Date/Time: 2016/04/14 17:04:53
[2016-04-15T00:04Z] INFO  17:04:53,547 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:04Z] INFO  17:04:53,548 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:04Z] INFO  17:04:53,731 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:04Z] INFO  17:04:54,218 ProgressMeter -            done   1.5528783E7    30.0 s       1.0 s      100.0%    30.0 s       0.0 s
[2016-04-15T00:04Z] INFO  17:04:54,218 ProgressMeter - Total runtime 30.78 secs, 0.51 min, 0.01 hours
[2016-04-15T00:04Z] INFO  17:04:54,219 MicroScheduler - 169766 reads were filtered out during the traversal out of approximately 823846 total reads (20.61%)
[2016-04-15T00:04Z] INFO  17:04:54,219 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:04Z] INFO  17:04:54,219 MicroScheduler -   -> 1196 reads (0.15% of total) failing BadMateFilter
[2016-04-15T00:04Z] INFO  17:04:54,220 MicroScheduler -   -> 58032 reads (7.04% of total) failing DuplicateReadFilter
[2016-04-15T00:04Z] INFO  17:04:54,220 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:04Z] INFO  17:04:54,220 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:04Z] INFO  17:04:54,220 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:04Z] INFO  17:04:54,221 MicroScheduler -   -> 110538 reads (13.42% of total) failing MappingQualityZeroFilter
[2016-04-15T00:04Z] INFO  17:04:54,221 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:04Z] INFO  17:04:54,221 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-15T00:04Z] INFO  17:04:54,221 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:04Z] INFO  17:04:54,897 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-15T00:04Z] INFO  17:04:54,973 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:04Z] INFO  17:04:54,983 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:04Z] INFO  17:04:55,018 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.03
[2016-04-15T00:04Z] INFO  17:04:55,032 IntervalUtils - Processing 15517346 bp from intervals
[2016-04-15T00:04Z] INFO  17:04:55,109 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:04Z] INFO  17:04:55,113 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:04Z] INFO  17:04:55,114 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:04Z] INFO  17:04:55,114 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:04Z] INFO  17:04:55,119 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/X/R14-18105_kapa-NGv3-PE100-NGv3-sort-X_144337190_155270560-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/X/R14-18105_kapa-NGv3-PE100-NGv3-sort-X_144337190_155270560-prep-prealign-realign.intervals -L X:144337191-155270560 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/X/tx/tmpr5xJqA/R14-18105_kapa-NGv3-PE100-NGv3-sort-X_144337190_155270560-prep.bam
[2016-04-15T00:04Z] INFO  17:04:55,130 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:04Z] INFO  17:04:55,130 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:04Z] INFO  17:04:55,131 HelpFormatter - Date/Time: 2016/04/14 17:04:55
[2016-04-15T00:04Z] INFO  17:04:55,131 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:04Z] INFO  17:04:55,132 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:04Z] INFO  17:04:55,266 ProgressMeter -            done    152914.0    11.0 s      78.0 s      100.0%    11.0 s       0.0 s
[2016-04-15T00:04Z] INFO  17:04:55,267 ProgressMeter - Total runtime 12.00 secs, 0.20 min, 0.00 hours
[2016-04-15T00:04Z] INFO  17:04:55,270 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 152914 total reads (0.00%)
[2016-04-15T00:04Z] INFO  17:04:55,271 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:04Z] INFO  17:04:55,271 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:04Z] INFO  17:04:55,272 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:04Z] INFO  17:04:55,339 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:04Z] INFO  17:04:55,393 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:04Z] INFO  17:04:55,394 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:04Z] INFO  17:04:55,394 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:04Z] INFO  17:04:55,394 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:04Z] INFO  17:04:55,425 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:04Z] INFO  17:04:55,503 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:04Z] INFO  17:04:55,517 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:04Z] INFO  17:04:55,594 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-15T00:04Z] INFO  17:04:55,602 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:04Z] INFO  17:04:55,674 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:04Z] GATK: realign ('22', 16266928, 31795711) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-15T00:04Z] INFO  17:04:56,007 IntervalUtils - Processing 10933370 bp from intervals
[2016-04-15T00:04Z] WARN  17:04:56,012 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:04Z] INFO  17:04:56,099 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:04Z] INFO  17:04:56,193 ProgressMeter -            done    127890.0    10.0 s      83.0 s       99.6%    10.0 s       0.0 s
[2016-04-15T00:04Z] INFO  17:04:56,193 ProgressMeter - Total runtime 10.69 secs, 0.18 min, 0.00 hours
[2016-04-15T00:04Z] INFO  17:04:56,208 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:04Z] INFO  17:04:56,209 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:04Z] INFO  17:04:56,210 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:04Z] INFO  17:04:56,210 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 127890 total reads (0.00%)
[2016-04-15T00:04Z] INFO  17:04:56,211 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:04Z] INFO  17:04:56,211 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:04Z] INFO  17:04:56,211 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:04Z] INFO  17:04:56,211 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:04Z] INFO  17:04:56,283 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:04Z] INFO  17:04:56,400 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:04Z] INFO  17:04:56,746 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:04Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-X_95990756_111698889-prep.bam
[2016-04-15T00:04Z] GATK pre-alignment ('1', 77752625, 93297674) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:04Z] INFO  17:04:57,849 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:04Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-X_128582278_144329181-prep.bam
[2016-04-15T00:04Z] INFO  17:04:58,063 ProgressMeter -            done    147134.0    11.0 s      75.0 s      100.0%    11.0 s       0.0 s
[2016-04-15T00:04Z] INFO  17:04:58,064 ProgressMeter - Total runtime 11.12 secs, 0.19 min, 0.00 hours
[2016-04-15T00:04Z] INFO  17:04:58,068 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 147134 total reads (0.00%)
[2016-04-15T00:04Z] INFO  17:04:58,068 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:04Z] INFO  17:04:58,068 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:04Z] INFO  17:04:58,069 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:04Z] GATK pre-alignment ('1', 93298945, 108993401) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:04Z] INFO  17:04:58,517 ProgressMeter -            done   4.3695667E7    26.0 s       0.0 s      100.0%    26.0 s       0.0 s
[2016-04-15T00:04Z] INFO  17:04:58,518 ProgressMeter - Total runtime 26.01 secs, 0.43 min, 0.01 hours
[2016-04-15T00:04Z] INFO  17:04:58,522 MicroScheduler - 89087 reads were filtered out during the traversal out of approximately 104657 total reads (85.12%)
[2016-04-15T00:04Z] INFO  17:04:58,523 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:04Z] INFO  17:04:58,524 MicroScheduler -   -> 119 reads (0.11% of total) failing BadMateFilter
[2016-04-15T00:04Z] INFO  17:04:58,525 MicroScheduler -   -> 1377 reads (1.32% of total) failing DuplicateReadFilter
[2016-04-15T00:04Z] INFO  17:04:58,525 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:04Z] INFO  17:04:58,526 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:04Z] INFO  17:04:58,526 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:04Z] INFO  17:04:58,527 MicroScheduler -   -> 87591 reads (83.69% of total) failing MappingQualityZeroFilter
[2016-04-15T00:04Z] INFO  17:04:58,528 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:04Z] INFO  17:04:58,528 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-15T00:04Z] INFO  17:04:58,529 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:04Z] INFO  17:04:58,584 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:04Z] INFO  17:04:58,597 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:04Z] INFO  17:04:58,598 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:04Z] INFO  17:04:58,599 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:04Z] INFO  17:04:58,613 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/22/R14-18105_kapa-NGv3-PE100-NGv3-sort-22_16266928_31795711-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/22/R14-18105_kapa-NGv3-PE100-NGv3-sort-22_16266928_31795711-prep-prealign-realign.intervals -L 22:16266929-31795711 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/22/tx/tmpr_p0Zn/R14-18105_kapa-NGv3-PE100-NGv3-sort-22_16266928_31795711-prep.bam
[2016-04-15T00:04Z] INFO  17:04:58,652 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:04Z] INFO  17:04:58,656 HelpFormatter - Date/Time: 2016/04/14 17:04:58
[2016-04-15T00:04Z] INFO  17:04:58,657 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:04Z] INFO  17:04:58,658 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:04Z] INFO  17:04:58,869 ProgressMeter -       1:2255153    200003.0    30.0 s       2.5 m       14.5%     3.4 m       2.9 m
[2016-04-15T00:04Z] INFO  17:04:58,877 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:04Z] INFO  17:04:59,003 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:04Z] INFO  17:04:59,012 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:04Z] INFO  17:04:59,072 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-15T00:04Z] INFO  17:04:59,366 IntervalUtils - Processing 15528783 bp from intervals
[2016-04-15T00:04Z] WARN  17:04:59,371 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:04Z] INFO  17:04:59,453 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:04Z] INFO  17:04:59,582 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:04Z] INFO  17:04:59,583 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:04Z] INFO  17:04:59,584 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:04Z] INFO  17:04:59,585 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:04Z] INFO  17:04:59,613 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:04Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-Y_0_15522993-prep.bam
[2016-04-15T00:04Z] INFO  17:04:59,802 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:04Z] INFO  17:04:59,903 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:04Z] INFO  17:04:59,947 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:04Z] GATK: realign ('Y', 15526614, 59222281) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-15T00:05Z] GATK pre-alignment ('1', 108994811, 143767848) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:05Z] INFO  17:05:00,299 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:05Z] INFO  17:05:00,303 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:05Z] INFO  17:05:00,303 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:05Z] INFO  17:05:00,304 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:05Z] INFO  17:05:00,308 HelpFormatter - Program Args: -T PrintReads -L 1:77752626-93297674 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/1/tx/tmp9VSg7O/R14-18106_kapa-NGv3-PE100-NGv3-sort-1_77752625_93297674-prep-prealign.bam
[2016-04-15T00:05Z] INFO  17:05:00,317 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:05Z] INFO  17:05:00,318 HelpFormatter - Date/Time: 2016/04/14 17:05:00
[2016-04-15T00:05Z] INFO  17:05:00,318 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:05Z] INFO  17:05:00,319 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:05Z] INFO  17:05:00,472 ProgressMeter -     19:42858261   1.1805311E7    30.0 s       2.0 s       75.8%    39.0 s       9.0 s
[2016-04-15T00:05Z] INFO  17:05:00,508 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:05Z] INFO  17:05:01,144 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:05Z] INFO  17:05:01,148 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:05Z] INFO  17:05:01,148 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:05Z] INFO  17:05:01,149 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:05Z] INFO  17:05:01,154 HelpFormatter - Program Args: -T PrintReads -L 1:93298946-108993401 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/1/tx/tmpeDEuiH/R14-18106_kapa-NGv3-PE100-NGv3-sort-1_93298945_108993401-prep-prealign.bam
[2016-04-15T00:05Z] INFO  17:05:01,177 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:05Z] INFO  17:05:01,185 HelpFormatter - Date/Time: 2016/04/14 17:05:01
[2016-04-15T00:05Z] INFO  17:05:01,186 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:05Z] INFO  17:05:01,187 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:05Z] INFO  17:05:01,435 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:05Z] INFO  17:05:02,026 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-15T00:05Z] INFO  17:05:02,093 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:05Z] INFO  17:05:02,103 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:05Z] INFO  17:05:02,162 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-15T00:05Z] INFO  17:05:02,178 IntervalUtils - Processing 15545049 bp from intervals
[2016-04-15T00:05Z] INFO  17:05:02,271 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:05Z] INFO  17:05:02,612 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:05Z] INFO  17:05:02,613 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:05Z] INFO  17:05:02,613 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:05Z] INFO  17:05:02,632 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:05Z] INFO  17:05:02,664 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:05Z] INFO  17:05:02,750 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-15T00:05Z] INFO  17:05:02,816 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:05Z] INFO  17:05:02,826 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:05Z] INFO  17:05:02,849 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:05Z] INFO  17:05:02,872 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-15T00:05Z] INFO  17:05:02,889 IntervalUtils - Processing 15694456 bp from intervals
[2016-04-15T00:05Z] INFO  17:05:02,971 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:05Z] INFO  17:05:03,244 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:05Z] INFO  17:05:03,245 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:05Z] INFO  17:05:03,246 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:05Z] INFO  17:05:03,246 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:05Z] INFO  17:05:03,261 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:05Z] INFO  17:05:03,310 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:05Z] INFO  17:05:03,313 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:05Z] INFO  17:05:03,314 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:05Z] INFO  17:05:03,315 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:05Z] INFO  17:05:03,319 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/Y/R14-18105_kapa-NGv3-PE100-NGv3-sort-Y_15526614_59222281-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/Y/R14-18105_kapa-NGv3-PE100-NGv3-sort-Y_15526614_59222281-prep-prealign-realign.intervals -L Y:15526615-59222281 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/Y/tx/tmp1welkz/R14-18105_kapa-NGv3-PE100-NGv3-sort-Y_15526614_59222281-prep.bam
[2016-04-15T00:05Z] INFO  17:05:03,337 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:05Z] INFO  17:05:03,338 HelpFormatter - Date/Time: 2016/04/14 17:05:03
[2016-04-15T00:05Z] INFO  17:05:03,338 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:05Z] INFO  17:05:03,339 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:05Z] INFO  17:05:03,416 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:05Z] INFO  17:05:03,510 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:05Z] INFO  17:05:03,513 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:05Z] INFO  17:05:03,514 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:05Z] INFO  17:05:03,514 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:05Z] INFO  17:05:03,519 HelpFormatter - Program Args: -T PrintReads -L 1:108994812-143767848 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/1/tx/tmpcvtis2/R14-18106_kapa-NGv3-PE100-NGv3-sort-1_108994811_143767848-prep-prealign.bam
[2016-04-15T00:05Z] INFO  17:05:03,523 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:05Z] INFO  17:05:03,527 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:05Z] INFO  17:05:03,528 HelpFormatter - Date/Time: 2016/04/14 17:05:03
[2016-04-15T00:05Z] INFO  17:05:03,529 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:05Z] INFO  17:05:03,529 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:05Z] INFO  17:05:03,689 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:05Z] INFO  17:05:03,711 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:05Z] INFO  17:05:03,727 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:05Z] INFO  17:05:03,761 ProgressMeter -      1:17312802    200002.0    30.0 s       2.5 m       11.3%     4.4 m       3.9 m
[2016-04-15T00:05Z] INFO  17:05:03,766 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-15T00:05Z] INFO  17:05:04,229 IntervalUtils - Processing 43695667 bp from intervals
[2016-04-15T00:05Z] WARN  17:05:04,245 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:05Z] INFO  17:05:04,373 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:05Z] INFO  17:05:04,546 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:05Z] INFO  17:05:04,547 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:05Z] INFO  17:05:04,548 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:05Z] INFO  17:05:04,548 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:05Z] INFO  17:05:04,620 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:05Z] INFO  17:05:04,943 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-15T00:05Z] INFO  17:05:04,988 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:05Z] INFO  17:05:05,042 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:05Z] INFO  17:05:05,051 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:05Z] INFO  17:05:05,097 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-15T00:05Z] INFO  17:05:05,110 IntervalUtils - Processing 34773037 bp from intervals
[2016-04-15T00:05Z] INFO  17:05:05,184 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:05Z] INFO  17:05:05,429 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:05Z] INFO  17:05:05,430 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:05Z] INFO  17:05:05,430 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:05Z] INFO  17:05:05,430 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:05Z] INFO  17:05:05,454 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:05Z] INFO  17:05:05,632 ProgressMeter -      1:35644370    100002.0    30.0 s       5.0 m       28.7%   104.0 s      74.0 s
[2016-04-15T00:05Z] INFO  17:05:05,706 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:05Z] INFO  17:05:09,915 ProgressMeter -            done   1.5588729E7    39.0 s       2.0 s      100.0%    39.0 s       0.0 s
[2016-04-15T00:05Z] INFO  17:05:09,916 ProgressMeter - Total runtime 39.46 secs, 0.66 min, 0.01 hours
[2016-04-15T00:05Z] INFO  17:05:09,919 MicroScheduler - 128310 reads were filtered out during the traversal out of approximately 1220493 total reads (10.51%)
[2016-04-15T00:05Z] INFO  17:05:09,920 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:05Z] INFO  17:05:09,920 MicroScheduler -   -> 1959 reads (0.16% of total) failing BadMateFilter
[2016-04-15T00:05Z] INFO  17:05:09,920 MicroScheduler -   -> 95213 reads (7.80% of total) failing DuplicateReadFilter
[2016-04-15T00:05Z] INFO  17:05:09,920 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:05Z] INFO  17:05:09,921 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:05Z] INFO  17:05:09,921 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:05Z] INFO  17:05:09,921 MicroScheduler -   -> 31138 reads (2.55% of total) failing MappingQualityZeroFilter
[2016-04-15T00:05Z] INFO  17:05:09,921 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:05Z] INFO  17:05:09,922 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-15T00:05Z] INFO  17:05:09,922 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:05Z] INFO  17:05:10,486 ProgressMeter -            done    198839.0    14.0 s      71.0 s       99.9%    14.0 s       0.0 s
[2016-04-15T00:05Z] INFO  17:05:10,487 ProgressMeter - Total runtime 14.28 secs, 0.24 min, 0.00 hours
[2016-04-15T00:05Z] INFO  17:05:10,490 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 198839 total reads (0.00%)
[2016-04-15T00:05Z] INFO  17:05:10,491 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:05Z] INFO  17:05:10,492 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:05Z] INFO  17:05:10,503 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:05Z] INFO  17:05:11,281 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:05Z] GATK: realign ('19', 31038849, 46627578) : R14-18105_kapa-NGv3-PE100-NGv3
[2016-04-15T00:05Z] INFO  17:05:12,056 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:05Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-X_144337190_155270560-prep.bam
[2016-04-15T00:05Z] GATK pre-alignment ('1', 143897546, 159410511) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:05Z] INFO  17:05:12,856 ProgressMeter -      1:54344377    100003.0    30.0 s       5.0 m       49.2%    61.0 s      31.0 s
[2016-04-15T00:05Z] INFO  17:05:13,672 ProgressMeter -            done    104249.0     9.0 s      87.0 s       99.5%     9.0 s       0.0 s
[2016-04-15T00:05Z] INFO  17:05:13,672 ProgressMeter - Total runtime 9.13 secs, 0.15 min, 0.00 hours
[2016-04-15T00:05Z] INFO  17:05:13,676 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 104249 total reads (0.00%)
[2016-04-15T00:05Z] INFO  17:05:13,676 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:05Z] INFO  17:05:13,676 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:05Z] INFO  17:05:13,677 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:05Z] INFO  17:05:13,924 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:05Z] INFO  17:05:13,927 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:05Z] INFO  17:05:13,927 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:05Z] INFO  17:05:13,928 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:05Z] INFO  17:05:13,932 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/19/R14-18105_kapa-NGv3-PE100-NGv3-sort-19_31038849_46627578-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/19/R14-18105_kapa-NGv3-PE100-NGv3-sort-19_31038849_46627578-prep-prealign-realign.intervals -L 19:31038850-46627578 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/19/tx/tmpZMUL7L/R14-18105_kapa-NGv3-PE100-NGv3-sort-19_31038849_46627578-prep.bam
[2016-04-15T00:05Z] INFO  17:05:13,950 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:05Z] INFO  17:05:13,950 HelpFormatter - Date/Time: 2016/04/14 17:05:13
[2016-04-15T00:05Z] INFO  17:05:13,950 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:05Z] INFO  17:05:13,951 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:05Z] INFO  17:05:14,177 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:05Z] INFO  17:05:14,308 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:05Z] INFO  17:05:14,317 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:05Z] INFO  17:05:14,375 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-15T00:05Z] INFO  17:05:14,680 IntervalUtils - Processing 15588729 bp from intervals
[2016-04-15T00:05Z] WARN  17:05:14,685 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:05Z] INFO  17:05:14,751 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:05Z] INFO  17:05:14,956 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:05Z] INFO  17:05:14,957 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:05Z] INFO  17:05:14,958 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:05Z] INFO  17:05:14,959 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:05Z] INFO  17:05:15,008 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:05Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-Y_15526614_59222281-prep.bam
[2016-04-15T00:05Z] INFO  17:05:15,139 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:05Z] INFO  17:05:15,325 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:05Z] GATK pre-alignment ('1', 159504867, 175046963) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:05Z] INFO  17:05:15,492 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:05Z] INFO  17:05:15,495 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:05Z] INFO  17:05:15,495 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:05Z] INFO  17:05:15,496 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:05Z] INFO  17:05:15,500 HelpFormatter - Program Args: -T PrintReads -L 1:143897547-159410511 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/1/tx/tmpv8kmwG/R14-18106_kapa-NGv3-PE100-NGv3-sort-1_143897546_159410511-prep-prealign.bam
[2016-04-15T00:05Z] INFO  17:05:15,509 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:05Z] INFO  17:05:15,510 HelpFormatter - Date/Time: 2016/04/14 17:05:15
[2016-04-15T00:05Z] INFO  17:05:15,510 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:05Z] INFO  17:05:15,511 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:05Z] INFO  17:05:15,660 ProgressMeter -     22:42095607    400007.0    31.0 s      78.0 s       66.4%    46.0 s      15.0 s
[2016-04-15T00:05Z] INFO  17:05:15,694 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:05Z] INFO  17:05:16,764 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-15T00:05Z] INFO  17:05:16,863 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:05Z] INFO  17:05:16,879 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:05Z] INFO  17:05:16,943 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-15T00:05Z] INFO  17:05:16,967 IntervalUtils - Processing 15512965 bp from intervals
[2016-04-15T00:05Z] INFO  17:05:17,074 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:05Z] INFO  17:05:17,331 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:05Z] INFO  17:05:17,331 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:05Z] INFO  17:05:17,332 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:05Z] INFO  17:05:17,332 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:05Z] INFO  17:05:17,357 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:05Z] INFO  17:05:17,494 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:05Z] INFO  17:05:18,168 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:05Z] INFO  17:05:18,171 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:05Z] INFO  17:05:18,172 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:05Z] INFO  17:05:18,172 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:05Z] INFO  17:05:18,177 HelpFormatter - Program Args: -T PrintReads -L 1:159504868-175046963 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/1/tx/tmpZUXuo5/R14-18106_kapa-NGv3-PE100-NGv3-sort-1_159504867_175046963-prep-prealign.bam
[2016-04-15T00:05Z] INFO  17:05:18,224 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:05Z] INFO  17:05:18,225 HelpFormatter - Date/Time: 2016/04/14 17:05:18
[2016-04-15T00:05Z] INFO  17:05:18,225 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:05Z] INFO  17:05:18,230 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:05Z] INFO  17:05:18,396 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:05Z] INFO  17:05:19,539 ProgressMeter -      19:4037403    400006.0    30.0 s      76.0 s       26.0%   115.0 s      85.0 s
[2016-04-15T00:05Z] INFO  17:05:19,642 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-15T00:05Z] INFO  17:05:19,695 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:05Z] INFO  17:05:19,704 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:05Z] INFO  17:05:19,753 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-15T00:05Z] INFO  17:05:19,767 IntervalUtils - Processing 15542096 bp from intervals
[2016-04-15T00:05Z] INFO  17:05:19,838 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:05Z] INFO  17:05:20,058 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:05Z] INFO  17:05:20,060 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:05Z] INFO  17:05:20,060 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:05Z] INFO  17:05:20,061 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:05Z] INFO  17:05:20,085 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:05Z] INFO  17:05:20,281 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:05Z] INFO  17:05:20,537 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@41fd9d8e
[2016-04-15T00:05Z] INFO  17:05:20,724 ProgressMeter -            done    176167.0    25.0 s       2.4 m      100.0%    25.0 s       0.0 s
[2016-04-15T00:05Z] INFO  17:05:20,725 ProgressMeter - Total runtime 25.33 secs, 0.42 min, 0.01 hours
[2016-04-15T00:05Z] INFO  17:05:20,726 MicroScheduler - 143 reads were filtered out during the traversal out of approximately 176310 total reads (0.08%)
[2016-04-15T00:05Z] INFO  17:05:20,727 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:05Z] INFO  17:05:20,728 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:05Z] INFO  17:05:20,728 MicroScheduler -   -> 143 reads (0.08% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:05Z] INFO  17:05:21,171 ProgressMeter -     19:50461827    400006.0    30.0 s      75.0 s       30.7%    97.0 s      67.0 s
[2016-04-15T00:05Z] INFO  17:05:22,210 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:05Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-1_62231950_77749296-prep-prealign.bam
[2016-04-15T00:05Z] GATK RealignerTargetCreator: R14-18106_kapa-NGv3-PE100-NGv3-sort-1_62231950_77749296-prep-prealign.bam 1:62231951-77749296
[2016-04-15T00:05Z] GATK: RealignerTargetCreator
[2016-04-15T00:05Z] INFO  17:05:23,031 ProgressMeter -            done    672527.0    38.0 s      57.0 s      100.0%    38.0 s       0.0 s
[2016-04-15T00:05Z] INFO  17:05:23,032 ProgressMeter - Total runtime 38.91 secs, 0.65 min, 0.01 hours
[2016-04-15T00:05Z] INFO  17:05:23,036 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 672527 total reads (0.00%)
[2016-04-15T00:05Z] INFO  17:05:23,037 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:05Z] INFO  17:05:23,038 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:05Z] INFO  17:05:23,038 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:05Z] INFO  17:05:24,491 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:05Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-22_31796605_47308085-prep.bam
[2016-04-15T00:05Z] INFO  17:05:24,631 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@5fe152b7
[2016-04-15T00:05Z] INFO  17:05:24,775 ProgressMeter -            done    168546.0    22.0 s       2.2 m      100.0%    22.0 s       0.0 s
[2016-04-15T00:05Z] INFO  17:05:24,775 ProgressMeter - Total runtime 22.16 secs, 0.37 min, 0.01 hours
[2016-04-15T00:05Z] INFO  17:05:24,776 MicroScheduler - 151 reads were filtered out during the traversal out of approximately 168697 total reads (0.09%)
[2016-04-15T00:05Z] INFO  17:05:24,776 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:05Z] INFO  17:05:24,776 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:05Z] INFO  17:05:24,777 MicroScheduler -   -> 151 reads (0.09% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:05Z] INFO  17:05:25,225 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:05Z] INFO  17:05:25,228 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:05Z] INFO  17:05:25,229 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:05Z] INFO  17:05:25,229 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:05Z] INFO  17:05:25,234 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/1/R14-18106_kapa-NGv3-PE100-NGv3-sort-1_62231950_77749296-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/1/tx/tmprvvQFe/R14-18106_kapa-NGv3-PE100-NGv3-sort-1_62231950_77749296-prep-prealign-realign.intervals -l INFO -L 1:62231951-77749296 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:05Z] INFO  17:05:25,252 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:05Z] INFO  17:05:25,254 HelpFormatter - Date/Time: 2016/04/14 17:05:25
[2016-04-15T00:05Z] INFO  17:05:25,255 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:05Z] INFO  17:05:25,255 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:05Z] INFO  17:05:25,336 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:05Z] INFO  17:05:25,408 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@41fd9d8e
[2016-04-15T00:05Z] INFO  17:05:25,531 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T00:05Z] INFO  17:05:25,541 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:05Z] INFO  17:05:25,583 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.04
[2016-04-15T00:05Z] INFO  17:05:25,623 ProgressMeter -            done    169200.0    22.0 s       2.2 m      100.0%    22.0 s       0.0 s
[2016-04-15T00:05Z] INFO  17:05:25,624 ProgressMeter - Total runtime 22.38 secs, 0.37 min, 0.01 hours
[2016-04-15T00:05Z] INFO  17:05:25,625 MicroScheduler - 138 reads were filtered out during the traversal out of approximately 169338 total reads (0.08%)
[2016-04-15T00:05Z] INFO  17:05:25,626 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:05Z] INFO  17:05:25,626 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:05Z] INFO  17:05:25,627 MicroScheduler -   -> 138 reads (0.08% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:05Z] INFO  17:05:25,643 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@7172f77a
[2016-04-15T00:05Z] INFO  17:05:25,770 ProgressMeter -            done    290918.0    42.0 s       2.5 m      100.0%    42.0 s       0.0 s
[2016-04-15T00:05Z] INFO  17:05:25,770 ProgressMeter - Total runtime 42.93 secs, 0.72 min, 0.01 hours
[2016-04-15T00:05Z] INFO  17:05:25,771 MicroScheduler - 181 reads were filtered out during the traversal out of approximately 291099 total reads (0.06%)
[2016-04-15T00:05Z] INFO  17:05:25,771 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:05Z] INFO  17:05:25,771 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:05Z] INFO  17:05:25,772 MicroScheduler -   -> 181 reads (0.06% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:05Z] INFO  17:05:25,878 IntervalUtils - Processing 15517346 bp from intervals
[2016-04-15T00:05Z] WARN  17:05:25,884 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:05Z] INFO  17:05:25,985 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:05Z] INFO  17:05:26,180 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:05Z] INFO  17:05:26,181 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:05Z] INFO  17:05:26,182 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:05Z] INFO  17:05:26,183 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:05Z] INFO  17:05:26,239 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:05Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-1_77752625_93297674-prep-prealign.bam
[2016-04-15T00:05Z] GATK pre-alignment ('1', 175048468, 192127886) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:05Z] GATK RealignerTargetCreator: R14-18106_kapa-NGv3-PE100-NGv3-sort-1_77752625_93297674-prep-prealign.bam 1:77752626-93297674
[2016-04-15T00:05Z] GATK: RealignerTargetCreator
[2016-04-15T00:05Z] INFO  17:05:27,033 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:05Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-1_93298945_108993401-prep-prealign.bam
[2016-04-15T00:05Z] INFO  17:05:27,181 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:05Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-1_46715671_62228851-prep-prealign.bam
[2016-04-15T00:05Z] GATK RealignerTargetCreator: R14-18106_kapa-NGv3-PE100-NGv3-sort-1_93298945_108993401-prep-prealign.bam 1:93298946-108993401
[2016-04-15T00:05Z] GATK: RealignerTargetCreator
[2016-04-15T00:05Z] GATK RealignerTargetCreator: R14-18106_kapa-NGv3-PE100-NGv3-sort-1_46715671_62228851-prep-prealign.bam 1:46715672-62228851
[2016-04-15T00:05Z] GATK: RealignerTargetCreator
[2016-04-15T00:05Z] INFO  17:05:28,870 ProgressMeter -      1:11190701    400007.0    60.0 s       2.5 m       72.0%    83.0 s      23.0 s
[2016-04-15T00:05Z] INFO  17:05:29,606 ProgressMeter -     22:21976033    400013.0    30.0 s      75.0 s       36.8%    81.0 s      51.0 s
[2016-04-15T00:05Z] INFO  17:05:30,119 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:05Z] INFO  17:05:30,123 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:05Z] INFO  17:05:30,123 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:05Z] INFO  17:05:30,124 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:05Z] INFO  17:05:30,128 HelpFormatter - Program Args: -T PrintReads -L 1:175048469-192127886 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/1/tx/tmp1ADWum/R14-18106_kapa-NGv3-PE100-NGv3-sort-1_175048468_192127886-prep-prealign.bam
[2016-04-15T00:05Z] INFO  17:05:30,136 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:05Z] INFO  17:05:30,136 HelpFormatter - Date/Time: 2016/04/14 17:05:30
[2016-04-15T00:05Z] INFO  17:05:30,136 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:05Z] INFO  17:05:30,137 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:05Z] INFO  17:05:30,155 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:05Z] INFO  17:05:30,158 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:05Z] INFO  17:05:30,159 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:05Z] INFO  17:05:30,160 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:05Z] INFO  17:05:30,181 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/1/R14-18106_kapa-NGv3-PE100-NGv3-sort-1_77752625_93297674-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/1/tx/tmpD9Ao0n/R14-18106_kapa-NGv3-PE100-NGv3-sort-1_77752625_93297674-prep-prealign-realign.intervals -l INFO -L 1:77752626-93297674 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:05Z] INFO  17:05:30,197 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:05Z] INFO  17:05:30,198 HelpFormatter - Date/Time: 2016/04/14 17:05:30
[2016-04-15T00:05Z] INFO  17:05:30,198 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:05Z] INFO  17:05:30,199 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:05Z] INFO  17:05:30,280 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:05Z] INFO  17:05:30,329 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:05Z] INFO  17:05:30,345 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:05Z] INFO  17:05:30,348 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:05Z] INFO  17:05:30,349 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:05Z] INFO  17:05:30,349 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:05Z] INFO  17:05:30,354 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/1/R14-18106_kapa-NGv3-PE100-NGv3-sort-1_93298945_108993401-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/1/tx/tmputfjWn/R14-18106_kapa-NGv3-PE100-NGv3-sort-1_93298945_108993401-prep-prealign-realign.intervals -l INFO -L 1:93298946-108993401 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:05Z] INFO  17:05:30,362 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:05Z] INFO  17:05:30,363 HelpFormatter - Date/Time: 2016/04/14 17:05:30
[2016-04-15T00:05Z] INFO  17:05:30,363 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:05Z] INFO  17:05:30,364 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:05Z] INFO  17:05:30,482 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:05Z] INFO  17:05:30,580 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T00:05Z] INFO  17:05:30,601 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:05Z] INFO  17:05:30,683 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-15T00:05Z] INFO  17:05:30,704 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T00:05Z] INFO  17:05:30,713 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:05Z] INFO  17:05:30,785 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-15T00:05Z] INFO  17:05:30,948 IntervalUtils - Processing 15545049 bp from intervals
[2016-04-15T00:05Z] WARN  17:05:30,964 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:05Z] INFO  17:05:31,136 IntervalUtils - Processing 15694456 bp from intervals
[2016-04-15T00:05Z] WARN  17:05:31,142 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:05Z] INFO  17:05:31,180 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:05Z] INFO  17:05:31,243 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:05Z] INFO  17:05:31,340 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-15T00:05Z] INFO  17:05:31,340 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:05Z] INFO  17:05:31,344 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:05Z] INFO  17:05:31,344 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:05Z] INFO  17:05:31,345 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:05Z] INFO  17:05:31,350 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/1/R14-18106_kapa-NGv3-PE100-NGv3-sort-1_46715671_62228851-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/1/tx/tmpURyGVA/R14-18106_kapa-NGv3-PE100-NGv3-sort-1_46715671_62228851-prep-prealign-realign.intervals -l INFO -L 1:46715672-62228851 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:05Z] INFO  17:05:31,359 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:05Z] INFO  17:05:31,360 HelpFormatter - Date/Time: 2016/04/14 17:05:31
[2016-04-15T00:05Z] INFO  17:05:31,361 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:05Z] INFO  17:05:31,361 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:05Z] INFO  17:05:31,363 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:05Z] INFO  17:05:31,364 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:05Z] INFO  17:05:31,364 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:05Z] INFO  17:05:31,376 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:05Z] INFO  17:05:31,403 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:05Z] INFO  17:05:31,410 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:05Z] INFO  17:05:31,411 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:05Z] INFO  17:05:31,412 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:05Z] INFO  17:05:31,412 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:05Z] INFO  17:05:31,413 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:05Z] INFO  17:05:31,455 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:05Z] INFO  17:05:31,457 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-15T00:05Z] INFO  17:05:31,480 IntervalUtils - Processing 17079418 bp from intervals
[2016-04-15T00:05Z] INFO  17:05:31,547 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:05Z] INFO  17:05:31,668 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T00:05Z] INFO  17:05:31,688 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:05Z] INFO  17:05:31,733 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.04
[2016-04-15T00:05Z] INFO  17:05:31,778 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:05Z] INFO  17:05:31,778 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:05Z] INFO  17:05:31,779 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:05Z] INFO  17:05:31,779 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:05Z] INFO  17:05:31,797 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:05Z] INFO  17:05:31,929 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:05Z] INFO  17:05:32,082 IntervalUtils - Processing 15513180 bp from intervals
[2016-04-15T00:05Z] WARN  17:05:32,086 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:05Z] INFO  17:05:32,168 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:05Z] INFO  17:05:32,406 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:05Z] INFO  17:05:32,407 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:05Z] INFO  17:05:32,408 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:05Z] INFO  17:05:32,409 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:05Z] INFO  17:05:33,788 ProgressMeter -      1:23847484    400004.0    60.0 s       2.5 m       53.1%   113.0 s      53.0 s
[2016-04-15T00:05Z] INFO  17:05:35,444 ProgressMeter -     1:114247244    200004.0    30.0 s       2.5 m       15.1%     3.3 m       2.8 m
[2016-04-15T00:05Z] INFO  17:05:36,445 ProgressMeter -      1:40318605    400006.0    60.0 s       2.5 m       58.8%   102.0 s      42.0 s
[2016-04-15T00:05Z] INFO  17:05:42,851 ProgressMeter -            done   1.5517346E7    16.0 s       1.0 s      100.0%    16.0 s       0.0 s
[2016-04-15T00:05Z] INFO  17:05:42,852 ProgressMeter - Total runtime 16.67 secs, 0.28 min, 0.00 hours
[2016-04-15T00:05Z] INFO  17:05:42,857 MicroScheduler - 14458 reads were filtered out during the traversal out of approximately 177481 total reads (8.15%)
[2016-04-15T00:05Z] INFO  17:05:42,859 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:05Z] INFO  17:05:42,860 MicroScheduler -   -> 591 reads (0.33% of total) failing BadMateFilter
[2016-04-15T00:05Z] INFO  17:05:42,860 MicroScheduler -   -> 13137 reads (7.40% of total) failing DuplicateReadFilter
[2016-04-15T00:05Z] INFO  17:05:42,861 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:05Z] INFO  17:05:42,862 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:05Z] INFO  17:05:42,863 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:05Z] INFO  17:05:42,863 MicroScheduler -   -> 730 reads (0.41% of total) failing MappingQualityZeroFilter
[2016-04-15T00:05Z] INFO  17:05:42,864 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:05Z] INFO  17:05:42,865 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-15T00:05Z] INFO  17:05:42,866 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:05Z] INFO  17:05:44,495 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:05Z] GATK: realign ('1', 62231950, 77749296) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:05Z] INFO  17:05:45,863 ProgressMeter -     19:38969291    400005.0    30.0 s      77.0 s       50.9%    58.0 s      28.0 s
[2016-04-15T00:05Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-nochrom-prep.bam
[2016-04-15T00:05Z] GATK pre-alignment ('1', 192128349, 207640257) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:05Z] INFO  17:05:47,160 ProgressMeter -            done   1.5694456E7    15.0 s       1.0 s      100.0%    15.0 s       0.0 s
[2016-04-15T00:05Z] INFO  17:05:47,161 ProgressMeter - Total runtime 15.75 secs, 0.26 min, 0.00 hours
[2016-04-15T00:05Z] INFO  17:05:47,165 MicroScheduler - 43253 reads were filtered out during the traversal out of approximately 170344 total reads (25.39%)
[2016-04-15T00:05Z] INFO  17:05:47,166 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:05Z] INFO  17:05:47,166 MicroScheduler -   -> 484 reads (0.28% of total) failing BadMateFilter
[2016-04-15T00:05Z] INFO  17:05:47,167 MicroScheduler -   -> 10299 reads (6.05% of total) failing DuplicateReadFilter
[2016-04-15T00:05Z] INFO  17:05:47,168 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:05Z] INFO  17:05:47,168 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:05Z] INFO  17:05:47,169 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:05Z] INFO  17:05:47,169 MicroScheduler -   -> 32470 reads (19.06% of total) failing MappingQualityZeroFilter
[2016-04-15T00:05Z] INFO  17:05:47,170 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:05Z] INFO  17:05:47,171 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-15T00:05Z] INFO  17:05:47,171 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:05Z] INFO  17:05:47,247 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:05Z] INFO  17:05:47,251 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:05Z] INFO  17:05:47,251 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:05Z] INFO  17:05:47,252 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:05Z] INFO  17:05:47,256 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/1/R14-18106_kapa-NGv3-PE100-NGv3-sort-1_62231950_77749296-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/1/R14-18106_kapa-NGv3-PE100-NGv3-sort-1_62231950_77749296-prep-prealign-realign.intervals -L 1:62231951-77749296 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/1/tx/tmp5EiNbN/R14-18106_kapa-NGv3-PE100-NGv3-sort-1_62231950_77749296-prep.bam
[2016-04-15T00:05Z] INFO  17:05:47,273 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:05Z] INFO  17:05:47,273 HelpFormatter - Date/Time: 2016/04/14 17:05:47
[2016-04-15T00:05Z] INFO  17:05:47,273 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:05Z] INFO  17:05:47,273 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:05Z] INFO  17:05:47,347 ProgressMeter -     1:145826458    100002.0    30.0 s       5.0 m       12.4%     4.0 m       3.5 m
[2016-04-15T00:05Z] INFO  17:05:47,451 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:05Z] INFO  17:05:47,641 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:05Z] INFO  17:05:47,670 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:05Z] INFO  17:05:47,725 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-15T00:05Z] INFO  17:05:47,893 ProgressMeter -            done   1.5545049E7    16.0 s       1.0 s      100.0%    16.0 s       0.0 s
[2016-04-15T00:05Z] INFO  17:05:47,894 ProgressMeter - Total runtime 16.53 secs, 0.28 min, 0.00 hours
[2016-04-15T00:05Z] INFO  17:05:47,898 MicroScheduler - 13453 reads were filtered out during the traversal out of approximately 169543 total reads (7.93%)
[2016-04-15T00:05Z] INFO  17:05:47,899 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:05Z] INFO  17:05:47,900 MicroScheduler -   -> 580 reads (0.34% of total) failing BadMateFilter
[2016-04-15T00:05Z] INFO  17:05:47,901 MicroScheduler -   -> 12341 reads (7.28% of total) failing DuplicateReadFilter
[2016-04-15T00:05Z] INFO  17:05:47,901 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:05Z] INFO  17:05:47,902 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:05Z] INFO  17:05:47,903 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:05Z] INFO  17:05:47,903 MicroScheduler -   -> 532 reads (0.31% of total) failing MappingQualityZeroFilter
[2016-04-15T00:05Z] INFO  17:05:47,904 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:05Z] INFO  17:05:47,904 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-15T00:05Z] INFO  17:05:47,905 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:05Z] INFO  17:05:48,107 IntervalUtils - Processing 15517346 bp from intervals
[2016-04-15T00:05Z] WARN  17:05:48,113 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:05Z] INFO  17:05:48,174 ProgressMeter -            done    819395.0    48.0 s      59.0 s      100.0%    48.0 s       0.0 s
[2016-04-15T00:05Z] INFO  17:05:48,175 ProgressMeter - Total runtime 48.59 secs, 0.81 min, 0.01 hours
[2016-04-15T00:05Z] INFO  17:05:48,178 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 819395 total reads (0.00%)
[2016-04-15T00:05Z] INFO  17:05:48,179 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:05Z] INFO  17:05:48,179 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:05Z] INFO  17:05:48,180 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:05Z] INFO  17:05:48,200 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:05Z] INFO  17:05:48,326 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:05Z] INFO  17:05:48,328 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:05Z] INFO  17:05:48,328 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:05Z] INFO  17:05:48,329 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:05Z] INFO  17:05:48,393 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:05Z] GATK: realign ('1', 93298945, 108993401) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:05Z] INFO  17:05:48,451 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:05Z] INFO  17:05:48,602 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:05Z] INFO  17:05:49,240 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:05Z] GATK: realign ('1', 77752625, 93297674) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:05Z] INFO  17:05:49,494 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:05Z] INFO  17:05:49,498 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:05Z] INFO  17:05:49,498 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:05Z] INFO  17:05:49,499 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:05Z] INFO  17:05:49,503 HelpFormatter - Program Args: -T PrintReads -L 1:192128350-207640257 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/1/tx/tmpz93o4J/R14-18106_kapa-NGv3-PE100-NGv3-sort-1_192128349_207640257-prep-prealign.bam
[2016-04-15T00:05Z] INFO  17:05:49,513 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:05Z] INFO  17:05:49,513 HelpFormatter - Date/Time: 2016/04/14 17:05:49
[2016-04-15T00:05Z] INFO  17:05:49,513 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:05Z] INFO  17:05:49,513 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:05Z] INFO  17:05:49,655 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:05Z] INFO  17:05:49,696 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:05Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-22_16266928_31795711-prep.bam
[2016-04-15T00:05Z] INFO  17:05:50,079 ProgressMeter -     1:166818893    200003.0    30.0 s       2.5 m       47.1%    63.0 s      33.0 s
[2016-04-15T00:05Z] INFO  17:05:50,401 ProgressMeter -     19:10421343   1000015.0    61.0 s      61.0 s       67.2%    90.0 s      29.0 s
[2016-04-15T00:05Z] INFO  17:05:50,824 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-15T00:05Z] INFO  17:05:50,881 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:05Z] INFO  17:05:50,891 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:05Z] INFO  17:05:50,968 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-15T00:05Z] INFO  17:05:50,982 IntervalUtils - Processing 15511908 bp from intervals
[2016-04-15T00:05Z] INFO  17:05:51,035 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:05Z] INFO  17:05:51,038 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:05Z] INFO  17:05:51,039 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:05Z] INFO  17:05:51,040 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:05Z] INFO  17:05:51,044 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/1/R14-18106_kapa-NGv3-PE100-NGv3-sort-1_93298945_108993401-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/1/R14-18106_kapa-NGv3-PE100-NGv3-sort-1_93298945_108993401-prep-prealign-realign.intervals -L 1:93298946-108993401 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/1/tx/tmpeiINpn/R14-18106_kapa-NGv3-PE100-NGv3-sort-1_93298945_108993401-prep.bam
[2016-04-15T00:05Z] INFO  17:05:51,065 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:05Z] INFO  17:05:51,066 HelpFormatter - Date/Time: 2016/04/14 17:05:51
[2016-04-15T00:05Z] INFO  17:05:51,067 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:05Z] INFO  17:05:51,067 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:05Z] INFO  17:05:51,073 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:05Z] INFO  17:05:51,133 ProgressMeter -            done   1.551318E7    18.0 s       1.0 s      100.0%    18.0 s       0.0 s
[2016-04-15T00:05Z] INFO  17:05:51,133 ProgressMeter - Total runtime 18.73 secs, 0.31 min, 0.01 hours
[2016-04-15T00:05Z] INFO  17:05:51,138 MicroScheduler - 24892 reads were filtered out during the traversal out of approximately 292842 total reads (8.50%)
[2016-04-15T00:05Z] INFO  17:05:51,138 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:05Z] INFO  17:05:51,139 MicroScheduler -   -> 734 reads (0.25% of total) failing BadMateFilter
[2016-04-15T00:05Z] INFO  17:05:51,139 MicroScheduler -   -> 21771 reads (7.43% of total) failing DuplicateReadFilter
[2016-04-15T00:05Z] INFO  17:05:51,139 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:05Z] INFO  17:05:51,140 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:05Z] INFO  17:05:51,140 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:05Z] INFO  17:05:51,140 MicroScheduler -   -> 2387 reads (0.82% of total) failing MappingQualityZeroFilter
[2016-04-15T00:05Z] INFO  17:05:51,140 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:05Z] INFO  17:05:51,141 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-15T00:05Z] INFO  17:05:51,142 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:05Z] INFO  17:05:51,313 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:05Z] INFO  17:05:51,328 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:05Z] INFO  17:05:51,330 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:05Z] INFO  17:05:51,331 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:05Z] INFO  17:05:51,331 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:05Z] INFO  17:05:51,369 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:05Z] INFO  17:05:51,444 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:05Z] INFO  17:05:51,454 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:05Z] INFO  17:05:51,532 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-15T00:05Z] INFO  17:05:51,594 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:05Z] INFO  17:05:51,778 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@41fd9d8e
[2016-04-15T00:05Z] INFO  17:05:51,867 ProgressMeter -            done    737705.0    83.0 s     112.0 s      100.0%    83.0 s       0.0 s
[2016-04-15T00:05Z] INFO  17:05:51,868 ProgressMeter - Total runtime 83.02 secs, 1.38 min, 0.02 hours
[2016-04-15T00:05Z] INFO  17:05:51,868 MicroScheduler - 333 reads were filtered out during the traversal out of approximately 738038 total reads (0.05%)
[2016-04-15T00:05Z] INFO  17:05:51,869 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:05Z] INFO  17:05:51,869 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:05Z] INFO  17:05:51,870 MicroScheduler -   -> 333 reads (0.05% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:05Z] INFO  17:05:51,962 IntervalUtils - Processing 15694456 bp from intervals
[2016-04-15T00:05Z] WARN  17:05:51,967 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:05Z] INFO  17:05:52,071 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:05Z] INFO  17:05:52,223 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:05Z] INFO  17:05:52,223 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:05Z] INFO  17:05:52,224 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:05Z] INFO  17:05:52,224 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:05Z] INFO  17:05:52,225 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:05Z] INFO  17:05:52,229 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:05Z] INFO  17:05:52,230 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:05Z] INFO  17:05:52,231 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:05Z] INFO  17:05:52,236 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/1/R14-18106_kapa-NGv3-PE100-NGv3-sort-1_77752625_93297674-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/1/R14-18106_kapa-NGv3-PE100-NGv3-sort-1_77752625_93297674-prep-prealign-realign.intervals -L 1:77752626-93297674 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/1/tx/tmpLA3AcR/R14-18106_kapa-NGv3-PE100-NGv3-sort-1_77752625_93297674-prep.bam
[2016-04-15T00:05Z] INFO  17:05:52,247 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:05Z] INFO  17:05:52,248 HelpFormatter - Date/Time: 2016/04/14 17:05:52
[2016-04-15T00:05Z] INFO  17:05:52,248 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:05Z] INFO  17:05:52,248 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:05Z] INFO  17:05:52,389 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:05Z] GATK pre-alignment ('1', 207641871, 223156451) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:05Z] INFO  17:05:52,484 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@41fd9d8e
[2016-04-15T00:05Z] INFO  17:05:52,510 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:05Z] INFO  17:05:52,552 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:05Z] INFO  17:05:52,604 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:05Z] INFO  17:05:52,634 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:05Z] INFO  17:05:52,645 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:05Z] GATK: realign ('1', 46715671, 62228851) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:05Z] INFO  17:05:52,698 ProgressMeter -            done    397516.0    47.0 s     118.0 s      100.0%    47.0 s       0.0 s
[2016-04-15T00:05Z] INFO  17:05:52,698 ProgressMeter - Total runtime 47.27 secs, 0.79 min, 0.01 hours
[2016-04-15T00:05Z] INFO  17:05:52,699 MicroScheduler - 202 reads were filtered out during the traversal out of approximately 397718 total reads (0.05%)
[2016-04-15T00:05Z] INFO  17:05:52,699 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:05Z] INFO  17:05:52,699 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:05Z] INFO  17:05:52,700 MicroScheduler -   -> 202 reads (0.05% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:05Z] INFO  17:05:52,712 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-15T00:05Z] INFO  17:05:53,172 IntervalUtils - Processing 15545049 bp from intervals
[2016-04-15T00:05Z] WARN  17:05:53,177 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:05Z] INFO  17:05:53,260 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:05Z] INFO  17:05:53,409 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:05Z] INFO  17:05:53,410 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:05Z] INFO  17:05:53,422 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:05Z] INFO  17:05:53,423 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:05Z] INFO  17:05:53,535 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:05Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-1_0_15541927-prep-prealign.bam
[2016-04-15T00:05Z] INFO  17:05:53,608 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:05Z] INFO  17:05:53,763 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:05Z] INFO  17:05:54,069 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:05Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-1_108994811_143767848-prep-prealign.bam
[2016-04-15T00:05Z] INFO  17:05:54,296 ProgressMeter -     19:56028800    900018.0    63.0 s      70.0 s       75.2%    83.0 s      20.0 s
[2016-04-15T00:05Z] INFO  17:05:55,191 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:05Z] INFO  17:05:55,194 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:05Z] INFO  17:05:55,194 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:05Z] INFO  17:05:55,194 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:05Z] INFO  17:05:55,209 HelpFormatter - Program Args: -T PrintReads -L 1:207641872-223156451 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/1/tx/tmpecFEJ1/R14-18106_kapa-NGv3-PE100-NGv3-sort-1_207641871_223156451-prep-prealign.bam
[2016-04-15T00:05Z] INFO  17:05:55,233 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:05Z] INFO  17:05:55,234 HelpFormatter - Date/Time: 2016/04/14 17:05:55
[2016-04-15T00:05Z] INFO  17:05:55,235 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:05Z] INFO  17:05:55,235 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:05Z] GATK RealignerTargetCreator: R14-18106_kapa-NGv3-PE100-NGv3-sort-1_108994811_143767848-prep-prealign.bam 1:108994812-143767848
[2016-04-15T00:05Z] GATK: RealignerTargetCreator
[2016-04-15T00:05Z] INFO  17:05:55,413 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:05Z] INFO  17:05:55,489 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:05Z] INFO  17:05:55,492 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:05Z] INFO  17:05:55,493 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:05Z] INFO  17:05:55,494 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:05Z] INFO  17:05:55,498 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/1/R14-18106_kapa-NGv3-PE100-NGv3-sort-1_46715671_62228851-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/1/R14-18106_kapa-NGv3-PE100-NGv3-sort-1_46715671_62228851-prep-prealign-realign.intervals -L 1:46715672-62228851 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/1/tx/tmp8CBux3/R14-18106_kapa-NGv3-PE100-NGv3-sort-1_46715671_62228851-prep.bam
[2016-04-15T00:05Z] GATK RealignerTargetCreator: R14-18106_kapa-NGv3-PE100-NGv3-sort-1_0_15541927-prep-prealign.bam 1:1-15541927
[2016-04-15T00:05Z] GATK: RealignerTargetCreator
[2016-04-15T00:05Z] INFO  17:05:55,528 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:05Z] INFO  17:05:55,529 HelpFormatter - Date/Time: 2016/04/14 17:05:55
[2016-04-15T00:05Z] INFO  17:05:55,529 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:05Z] INFO  17:05:55,530 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:05Z] INFO  17:05:55,745 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:05Z] INFO  17:05:55,889 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:05Z] INFO  17:05:55,898 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:05Z] INFO  17:05:55,964 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-15T00:05Z] INFO  17:05:56,482 IntervalUtils - Processing 15513180 bp from intervals
[2016-04-15T00:05Z] WARN  17:05:56,487 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:05Z] INFO  17:05:56,612 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:05Z] INFO  17:05:56,758 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-15T00:05Z] INFO  17:05:56,824 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:05Z] INFO  17:05:56,824 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:05Z] INFO  17:05:56,824 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:05Z] INFO  17:05:56,825 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:05Z] INFO  17:05:56,826 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:05Z] INFO  17:05:56,834 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:05Z] INFO  17:05:56,888 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-15T00:05Z] INFO  17:05:56,903 IntervalUtils - Processing 15514580 bp from intervals
[2016-04-15T00:05Z] INFO  17:05:56,982 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:05Z] INFO  17:05:56,998 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:05Z] INFO  17:05:57,164 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:05Z] INFO  17:05:57,250 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:05Z] INFO  17:05:57,251 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:05Z] INFO  17:05:57,254 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:05Z] INFO  17:05:57,254 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:05Z] INFO  17:05:57,282 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:05Z] INFO  17:05:57,495 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:05Z] INFO  17:05:58,209 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:05Z] INFO  17:05:58,222 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:05Z] INFO  17:05:58,223 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:05Z] INFO  17:05:58,224 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:05Z] INFO  17:05:58,239 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/1/R14-18106_kapa-NGv3-PE100-NGv3-sort-1_108994811_143767848-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/1/tx/tmpobVZUJ/R14-18106_kapa-NGv3-PE100-NGv3-sort-1_108994811_143767848-prep-prealign-realign.intervals -l INFO -L 1:108994812-143767848 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:05Z] INFO  17:05:58,248 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:05Z] INFO  17:05:58,249 HelpFormatter - Date/Time: 2016/04/14 17:05:58
[2016-04-15T00:05Z] INFO  17:05:58,249 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:05Z] INFO  17:05:58,250 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:05Z] INFO  17:05:58,358 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:05Z] INFO  17:05:58,621 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T00:05Z] INFO  17:05:58,630 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:05Z] INFO  17:05:58,701 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:05Z] INFO  17:05:58,704 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:05Z] INFO  17:05:58,704 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:05Z] INFO  17:05:58,704 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:05Z] INFO  17:05:58,715 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-15T00:05Z] INFO  17:05:58,717 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/1/R14-18106_kapa-NGv3-PE100-NGv3-sort-1_0_15541927-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/1/tx/tmpmDEUQz/R14-18106_kapa-NGv3-PE100-NGv3-sort-1_0_15541927-prep-prealign-realign.intervals -l INFO -L 1:1-15541927 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:05Z] INFO  17:05:58,726 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:05Z] INFO  17:05:58,732 HelpFormatter - Date/Time: 2016/04/14 17:05:58
[2016-04-15T00:05Z] INFO  17:05:58,732 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:05Z] INFO  17:05:58,733 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:05Z] INFO  17:05:58,825 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:05Z] INFO  17:05:59,015 IntervalUtils - Processing 34773037 bp from intervals
[2016-04-15T00:05Z] WARN  17:05:59,019 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:05Z] INFO  17:05:59,082 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T00:05Z] INFO  17:05:59,102 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:05Z] INFO  17:05:59,129 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:05Z] INFO  17:05:59,167 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-15T00:05Z] INFO  17:05:59,380 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:05Z] INFO  17:05:59,392 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:05Z] INFO  17:05:59,393 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:05Z] INFO  17:05:59,394 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:05Z] INFO  17:05:59,528 IntervalUtils - Processing 15541927 bp from intervals
[2016-04-15T00:05Z] WARN  17:05:59,534 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:05Z] INFO  17:05:59,627 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:05Z] INFO  17:05:59,832 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:05Z] INFO  17:05:59,833 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:05Z] INFO  17:05:59,834 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:05Z] INFO  17:05:59,835 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:06Z] INFO  17:06:01,796 ProgressMeter -     1:190067114    200003.0    30.0 s       2.5 m       87.9%    34.0 s       4.0 s
[2016-04-15T00:06Z] INFO  17:06:01,802 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@41fd9d8e
[2016-04-15T00:06Z] INFO  17:06:01,932 ProgressMeter -            done    764178.0    88.0 s     115.0 s      100.0%    88.0 s       0.0 s
[2016-04-15T00:06Z] INFO  17:06:01,933 ProgressMeter - Total runtime 88.21 secs, 1.47 min, 0.02 hours
[2016-04-15T00:06Z] INFO  17:06:01,933 MicroScheduler - 355 reads were filtered out during the traversal out of approximately 764533 total reads (0.05%)
[2016-04-15T00:06Z] INFO  17:06:01,933 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:06Z] INFO  17:06:01,934 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:06Z] INFO  17:06:01,934 MicroScheduler -   -> 355 reads (0.05% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:06Z] INFO  17:06:02,063 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@32d5a4c6
[2016-04-15T00:06Z] INFO  17:06:02,345 ProgressMeter -            done    251235.0    30.0 s       2.0 m      100.0%    30.0 s       0.0 s
[2016-04-15T00:06Z] INFO  17:06:02,346 ProgressMeter - Total runtime 30.57 secs, 0.51 min, 0.01 hours
[2016-04-15T00:06Z] INFO  17:06:02,346 MicroScheduler - 183 reads were filtered out during the traversal out of approximately 251418 total reads (0.07%)
[2016-04-15T00:06Z] INFO  17:06:02,347 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:06Z] INFO  17:06:02,347 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:06Z] INFO  17:06:02,347 MicroScheduler -   -> 183 reads (0.07% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:06Z] INFO  17:06:02,509 ProgressMeter -            done    176167.0    14.0 s      80.0 s      100.0%    14.0 s       0.0 s
[2016-04-15T00:06Z] INFO  17:06:02,509 ProgressMeter - Total runtime 14.18 secs, 0.24 min, 0.00 hours
[2016-04-15T00:06Z] INFO  17:06:02,513 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 176167 total reads (0.00%)
[2016-04-15T00:06Z] INFO  17:06:02,513 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:06Z] INFO  17:06:02,514 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:06Z] INFO  17:06:02,514 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:06Z] INFO  17:06:03,380 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:06Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-1_15545821_31186478-prep-prealign.bam
[2016-04-15T00:06Z] INFO  17:06:03,728 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:06Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-1_175048468_192127886-prep-prealign.bam
[2016-04-15T00:06Z] INFO  17:06:03,984 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:06Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-1_62231950_77749296-prep.bam
[2016-04-15T00:06Z] GATK RealignerTargetCreator: R14-18106_kapa-NGv3-PE100-NGv3-sort-1_175048468_192127886-prep-prealign.bam 1:175048469-192127886
[2016-04-15T00:06Z] GATK: RealignerTargetCreator
[2016-04-15T00:06Z] GATK pre-alignment ('1', 223162737, 240072524) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:06Z] INFO  17:06:05,862 ProgressMeter -            done    169200.0    13.0 s      80.0 s      100.0%    13.0 s       0.0 s
[2016-04-15T00:06Z] INFO  17:06:05,862 ProgressMeter - Total runtime 13.64 secs, 0.23 min, 0.00 hours
[2016-04-15T00:06Z] INFO  17:06:05,866 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 169200 total reads (0.00%)
[2016-04-15T00:06Z] INFO  17:06:05,866 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:06Z] INFO  17:06:05,866 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:06Z] INFO  17:06:05,867 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:06Z] GATK RealignerTargetCreator: R14-18106_kapa-NGv3-PE100-NGv3-sort-1_15545821_31186478-prep-prealign.bam 1:15545822-31186478
[2016-04-15T00:06Z] GATK: RealignerTargetCreator
[2016-04-15T00:06Z] INFO  17:06:06,446 ProgressMeter -      1:45508956    600013.0    90.0 s       2.5 m       92.2%    97.0 s       7.0 s
[2016-04-15T00:06Z] INFO  17:06:06,518 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@5fe152b7
[2016-04-15T00:06Z] INFO  17:06:06,643 ProgressMeter -            done    384925.0    46.0 s       2.0 m      100.0%    46.0 s       0.0 s
[2016-04-15T00:06Z] INFO  17:06:06,643 ProgressMeter - Total runtime 46.58 secs, 0.78 min, 0.01 hours
[2016-04-15T00:06Z] INFO  17:06:06,644 MicroScheduler - 186 reads were filtered out during the traversal out of approximately 385111 total reads (0.05%)
[2016-04-15T00:06Z] INFO  17:06:06,644 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:06Z] INFO  17:06:06,644 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:06Z] INFO  17:06:06,645 MicroScheduler -   -> 186 reads (0.05% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:06Z] INFO  17:06:07,365 ProgressMeter -            done    168546.0    13.0 s      82.0 s      100.0%    13.0 s       0.0 s
[2016-04-15T00:06Z] INFO  17:06:07,367 ProgressMeter - Total runtime 13.96 secs, 0.23 min, 0.00 hours
[2016-04-15T00:06Z] INFO  17:06:07,371 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 168546 total reads (0.00%)
[2016-04-15T00:06Z] INFO  17:06:07,372 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:06Z] INFO  17:06:07,372 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:06Z] INFO  17:06:07,373 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:06Z] INFO  17:06:07,481 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:06Z] INFO  17:06:07,491 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:06Z] INFO  17:06:07,494 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:06Z] INFO  17:06:07,494 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:06Z] INFO  17:06:07,494 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:06Z] INFO  17:06:07,500 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:06Z] INFO  17:06:07,501 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:06Z] INFO  17:06:07,502 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:06Z] INFO  17:06:07,506 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/1/R14-18106_kapa-NGv3-PE100-NGv3-sort-1_175048468_192127886-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/1/tx/tmph_1kRY/R14-18106_kapa-NGv3-PE100-NGv3-sort-1_175048468_192127886-prep-prealign-realign.intervals -l INFO -L 1:175048469-192127886 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:06Z] INFO  17:06:07,517 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:06Z] INFO  17:06:07,517 HelpFormatter - Date/Time: 2016/04/14 17:06:07
[2016-04-15T00:06Z] INFO  17:06:07,518 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:06Z] INFO  17:06:07,518 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:06Z] INFO  17:06:07,519 HelpFormatter - Program Args: -T PrintReads -L 1:223162738-240072524 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/1/tx/tmprGUBAC/R14-18106_kapa-NGv3-PE100-NGv3-sort-1_223162737_240072524-prep-prealign.bam
[2016-04-15T00:06Z] INFO  17:06:07,533 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:06Z] INFO  17:06:07,533 HelpFormatter - Date/Time: 2016/04/14 17:06:07
[2016-04-15T00:06Z] INFO  17:06:07,533 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:06Z] INFO  17:06:07,534 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:06Z] INFO  17:06:07,610 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:06Z] INFO  17:06:07,723 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:06Z] INFO  17:06:07,805 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:06Z] INFO  17:06:07,844 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T00:06Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-1_93298945_108993401-prep.bam
[2016-04-15T00:06Z] INFO  17:06:07,855 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:06Z] INFO  17:06:07,907 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:06Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-1_159504867_175046963-prep-prealign.bam
[2016-04-15T00:06Z] INFO  17:06:07,961 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.11
[2016-04-15T00:06Z] GATK pre-alignment ('1', 240255409, 249250621) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:06Z] INFO  17:06:08,550 IntervalUtils - Processing 17079418 bp from intervals
[2016-04-15T00:06Z] WARN  17:06:08,558 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:06Z] INFO  17:06:08,682 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:06Z] INFO  17:06:08,807 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:06Z] INFO  17:06:08,809 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:06Z] INFO  17:06:08,809 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:06Z] INFO  17:06:08,810 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:06Z] INFO  17:06:08,876 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:06Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-1_77752625_93297674-prep.bam
[2016-04-15T00:06Z] INFO  17:06:08,962 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:06Z] INFO  17:06:08,965 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:06Z] INFO  17:06:08,965 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:06Z] INFO  17:06:08,966 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:06Z] INFO  17:06:08,971 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/1/R14-18106_kapa-NGv3-PE100-NGv3-sort-1_15545821_31186478-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/1/tx/tmpfJliPW/R14-18106_kapa-NGv3-PE100-NGv3-sort-1_15545821_31186478-prep-prealign-realign.intervals -l INFO -L 1:15545822-31186478 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:06Z] INFO  17:06:08,978 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-15T00:06Z] INFO  17:06:08,994 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:06Z] INFO  17:06:08,995 HelpFormatter - Date/Time: 2016/04/14 17:06:08
[2016-04-15T00:06Z] INFO  17:06:08,995 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:06Z] INFO  17:06:09,000 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:06Z] INFO  17:06:09,065 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:06Z] INFO  17:06:09,072 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:06Z] INFO  17:06:09,081 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:06Z] INFO  17:06:09,139 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-15T00:06Z] INFO  17:06:09,155 IntervalUtils - Processing 16909787 bp from intervals
[2016-04-15T00:06Z] INFO  17:06:09,254 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:06Z] GATK RealignerTargetCreator: R14-18106_kapa-NGv3-PE100-NGv3-sort-1_159504867_175046963-prep-prealign.bam 1:159504868-175046963
[2016-04-15T00:06Z] GATK: RealignerTargetCreator
[2016-04-15T00:06Z] INFO  17:06:09,279 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T00:06Z] INFO  17:06:09,288 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:06Z] INFO  17:06:09,328 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.04
[2016-04-15T00:06Z] INFO  17:06:09,353 ProgressMeter -            done   1351000.0    78.0 s      57.0 s       99.6%    78.0 s       0.0 s
[2016-04-15T00:06Z] INFO  17:06:09,354 ProgressMeter - Total runtime 78.19 secs, 1.30 min, 0.02 hours
[2016-04-15T00:06Z] INFO  17:06:09,358 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 1351000 total reads (0.00%)
[2016-04-15T00:06Z] INFO  17:06:09,359 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:06Z] INFO  17:06:09,359 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:06Z] INFO  17:06:09,360 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:06Z] GATK pre-alignment ('2', 0, 15514844) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:06Z] INFO  17:06:09,626 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:06Z] INFO  17:06:09,628 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:06Z] INFO  17:06:09,628 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:06Z] INFO  17:06:09,629 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:06Z] INFO  17:06:09,645 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:06Z] INFO  17:06:09,663 IntervalUtils - Processing 15640657 bp from intervals
[2016-04-15T00:06Z] WARN  17:06:09,672 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:06Z] INFO  17:06:09,777 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:06Z] INFO  17:06:09,840 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:06Z] INFO  17:06:10,142 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:06Z] INFO  17:06:10,143 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:06Z] INFO  17:06:10,144 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:06Z] INFO  17:06:10,145 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:06Z] INFO  17:06:11,060 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:06Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-19_46627881_59128983-prep.bam
[2016-04-15T00:06Z] INFO  17:06:11,357 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:06Z] INFO  17:06:11,360 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:06Z] INFO  17:06:11,361 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:06Z] INFO  17:06:11,361 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:06Z] INFO  17:06:11,366 HelpFormatter - Program Args: -T PrintReads -L 1:240255410-249250621 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/1/tx/tmp9pmwqD/R14-18106_kapa-NGv3-PE100-NGv3-sort-1_240255409_249250621-prep-prealign.bam
[2016-04-15T00:06Z] INFO  17:06:11,400 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:06Z] INFO  17:06:11,408 HelpFormatter - Date/Time: 2016/04/14 17:06:11
[2016-04-15T00:06Z] INFO  17:06:11,409 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:06Z] INFO  17:06:11,413 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:06Z] INFO  17:06:11,562 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:06Z] INFO  17:06:12,469 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@7172f77a
[2016-04-15T00:06Z] INFO  17:06:12,600 ProgressMeter -            done    679619.0    96.0 s       2.4 m      100.0%    96.0 s       0.0 s
[2016-04-15T00:06Z] INFO  17:06:12,601 ProgressMeter - Total runtime 97.00 secs, 1.62 min, 0.03 hours
[2016-04-15T00:06Z] INFO  17:06:12,602 MicroScheduler - 305 reads were filtered out during the traversal out of approximately 679924 total reads (0.04%)
[2016-04-15T00:06Z] INFO  17:06:12,603 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:06Z] INFO  17:06:12,603 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:06Z] INFO  17:06:12,604 MicroScheduler -   -> 305 reads (0.04% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:06Z] INFO  17:06:12,613 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:06Z] INFO  17:06:12,616 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:06Z] INFO  17:06:12,617 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:06Z] INFO  17:06:12,618 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:06Z] INFO  17:06:12,622 HelpFormatter - Program Args: -T PrintReads -L 2:1-15514844 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/2/tx/tmpgjT74y/R14-18106_kapa-NGv3-PE100-NGv3-sort-2_0_15514844-prep-prealign.bam
[2016-04-15T00:06Z] INFO  17:06:12,626 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:06Z] INFO  17:06:12,628 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:06Z] INFO  17:06:12,628 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:06Z] INFO  17:06:12,628 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:06Z] INFO  17:06:12,632 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/1/R14-18106_kapa-NGv3-PE100-NGv3-sort-1_159504867_175046963-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/1/tx/tmpgH3lzM/R14-18106_kapa-NGv3-PE100-NGv3-sort-1_159504867_175046963-prep-prealign-realign.intervals -l INFO -L 1:159504868-175046963 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:06Z] INFO  17:06:12,633 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:06Z] INFO  17:06:12,634 HelpFormatter - Date/Time: 2016/04/14 17:06:12
[2016-04-15T00:06Z] INFO  17:06:12,634 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:06Z] INFO  17:06:12,635 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:06Z] INFO  17:06:12,656 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:06Z] INFO  17:06:12,656 HelpFormatter - Date/Time: 2016/04/14 17:06:12
[2016-04-15T00:06Z] INFO  17:06:12,657 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:06Z] INFO  17:06:12,658 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:06Z] INFO  17:06:12,677 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-15T00:06Z] INFO  17:06:12,744 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:06Z] INFO  17:06:12,746 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:06Z] INFO  17:06:12,755 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:06Z] INFO  17:06:12,781 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:06Z] INFO  17:06:12,832 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-15T00:06Z] INFO  17:06:12,847 IntervalUtils - Processing 8995212 bp from intervals
[2016-04-15T00:06Z] INFO  17:06:12,928 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:06Z] INFO  17:06:12,939 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T00:06Z] INFO  17:06:12,964 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:06Z] INFO  17:06:13,048 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-15T00:06Z] INFO  17:06:13,159 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:06Z] INFO  17:06:13,160 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:06Z] INFO  17:06:13,161 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:06Z] INFO  17:06:13,162 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:06Z] INFO  17:06:13,217 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:06Z] INFO  17:06:13,338 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:06Z] INFO  17:06:13,359 IntervalUtils - Processing 15542096 bp from intervals
[2016-04-15T00:06Z] WARN  17:06:13,364 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:06Z] INFO  17:06:13,477 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:06Z] INFO  17:06:13,632 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:06Z] INFO  17:06:13,633 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:06Z] INFO  17:06:13,634 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:06Z] INFO  17:06:13,635 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:06Z] INFO  17:06:13,915 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:06Z] INFO  17:06:13,923 ProgressMeter -            done   1515364.0    85.0 s      56.0 s      100.0%    85.0 s       0.0 s
[2016-04-15T00:06Z] INFO  17:06:13,923 ProgressMeter - Total runtime 85.12 secs, 1.42 min, 0.02 hours
[2016-04-15T00:06Z] INFO  17:06:13,926 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-15T00:06Z] INFO  17:06:13,927 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 1515364 total reads (0.00%)
[2016-04-15T00:06Z] INFO  17:06:13,928 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:06Z] INFO  17:06:13,928 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:06Z] INFO  17:06:13,929 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:06Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-1_31187093_46714270-prep-prealign.bam
[2016-04-15T00:06Z] INFO  17:06:14,005 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:06Z] INFO  17:06:14,026 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:06Z] INFO  17:06:14,077 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-15T00:06Z] INFO  17:06:14,094 IntervalUtils - Processing 15514844 bp from intervals
[2016-04-15T00:06Z] INFO  17:06:14,240 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:06Z] INFO  17:06:14,530 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:06Z] INFO  17:06:14,531 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:06Z] INFO  17:06:14,532 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:06Z] INFO  17:06:14,533 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:06Z] INFO  17:06:14,550 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:06Z] INFO  17:06:14,696 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:06Z] GATK pre-alignment ('2', 15519725, 31133925) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:06Z] INFO  17:06:15,517 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:06Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-19_0_15509577-prep.bam
[2016-04-15T00:06Z] GATK RealignerTargetCreator: R14-18106_kapa-NGv3-PE100-NGv3-sort-1_31187093_46714270-prep-prealign.bam 1:31187094-46714270
[2016-04-15T00:06Z] GATK: RealignerTargetCreator
[2016-04-15T00:06Z] INFO  17:06:17,464 ProgressMeter -     1:149377858    300008.0    60.0 s       3.3 m       35.3%     2.8 m     109.0 s
[2016-04-15T00:06Z] INFO  17:06:17,735 ProgressMeter -            done    290918.0    20.0 s      71.0 s      100.0%    20.0 s       0.0 s
[2016-04-15T00:06Z] INFO  17:06:17,735 ProgressMeter - Total runtime 20.91 secs, 0.35 min, 0.01 hours
[2016-04-15T00:06Z] INFO  17:06:17,743 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 290918 total reads (0.00%)
[2016-04-15T00:06Z] INFO  17:06:17,744 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:06Z] INFO  17:06:17,744 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:06Z] INFO  17:06:17,744 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:06Z] INFO  17:06:18,024 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:06Z] INFO  17:06:18,028 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:06Z] INFO  17:06:18,028 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:06Z] INFO  17:06:18,029 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:06Z] INFO  17:06:18,034 HelpFormatter - Program Args: -T PrintReads -L 2:15519726-31133925 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/2/tx/tmp5oRPTR/R14-18106_kapa-NGv3-PE100-NGv3-sort-2_15519725_31133925-prep-prealign.bam
[2016-04-15T00:06Z] INFO  17:06:18,052 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:06Z] INFO  17:06:18,053 HelpFormatter - Date/Time: 2016/04/14 17:06:18
[2016-04-15T00:06Z] INFO  17:06:18,053 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:06Z] INFO  17:06:18,054 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:06Z] INFO  17:06:18,254 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:06Z] INFO  17:06:19,164 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:06Z] INFO  17:06:19,167 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:06Z] INFO  17:06:19,168 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:06Z] INFO  17:06:19,168 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:06Z] INFO  17:06:19,173 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/1/R14-18106_kapa-NGv3-PE100-NGv3-sort-1_31187093_46714270-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/1/tx/tmpl4FIET/R14-18106_kapa-NGv3-PE100-NGv3-sort-1_31187093_46714270-prep-prealign-realign.intervals -l INFO -L 1:31187094-46714270 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:06Z] INFO  17:06:19,182 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:06Z] INFO  17:06:19,193 HelpFormatter - Date/Time: 2016/04/14 17:06:19
[2016-04-15T00:06Z] INFO  17:06:19,194 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:06Z] INFO  17:06:19,195 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:06Z] INFO  17:06:19,279 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:06Z] INFO  17:06:19,321 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:06Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-1_46715671_62228851-prep.bam
[2016-04-15T00:06Z] INFO  17:06:19,485 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T00:06Z] INFO  17:06:19,497 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:06Z] INFO  17:06:19,544 ProgressMeter -     19:44605008   1000016.0    64.0 s      64.0 s       87.0%    73.0 s       9.0 s
[2016-04-15T00:06Z] INFO  17:06:19,556 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-15T00:06Z] INFO  17:06:19,689 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-15T00:06Z] INFO  17:06:19,753 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:06Z] INFO  17:06:19,762 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:06Z] INFO  17:06:19,812 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-15T00:06Z] INFO  17:06:19,834 IntervalUtils - Processing 15614200 bp from intervals
[2016-04-15T00:06Z] INFO  17:06:19,874 IntervalUtils - Processing 15527177 bp from intervals
[2016-04-15T00:06Z] WARN  17:06:19,879 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:06Z] INFO  17:06:19,966 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:06Z] INFO  17:06:19,970 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:06Z] INFO  17:06:20,252 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:06Z] INFO  17:06:20,255 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:06Z] INFO  17:06:20,256 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:06Z] INFO  17:06:20,257 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:06Z] INFO  17:06:20,273 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:06Z] INFO  17:06:20,274 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:06Z] INFO  17:06:20,275 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:06Z] INFO  17:06:20,276 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:06Z] GATK pre-alignment ('2', 31135088, 46706841) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:06Z] INFO  17:06:20,301 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:06Z] GATK pre-alignment ('2', 46707543, 62228117) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:06Z] INFO  17:06:20,456 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:06Z] INFO  17:06:21,959 ProgressMeter -     1:202288250    100002.0    30.0 s       5.1 m       65.5%    45.0 s      15.0 s
[2016-04-15T00:06Z] INFO  17:06:23,186 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:06Z] INFO  17:06:23,189 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:06Z] INFO  17:06:23,190 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:06Z] INFO  17:06:23,191 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:06Z] INFO  17:06:23,196 HelpFormatter - Program Args: -T PrintReads -L 2:46707544-62228117 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/2/tx/tmpgODtiL/R14-18106_kapa-NGv3-PE100-NGv3-sort-2_46707543_62228117-prep-prealign.bam
[2016-04-15T00:06Z] INFO  17:06:23,205 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:06Z] INFO  17:06:23,206 HelpFormatter - Date/Time: 2016/04/14 17:06:23
[2016-04-15T00:06Z] INFO  17:06:23,206 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:06Z] INFO  17:06:23,207 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:06Z] INFO  17:06:23,378 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:06Z] INFO  17:06:23,535 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:06Z] INFO  17:06:23,538 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:06Z] INFO  17:06:23,539 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:06Z] INFO  17:06:23,539 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:06Z] INFO  17:06:23,544 HelpFormatter - Program Args: -T PrintReads -L 2:31135089-46706841 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/2/tx/tmpX7rxri/R14-18106_kapa-NGv3-PE100-NGv3-sort-2_31135088_46706841-prep-prealign.bam
[2016-04-15T00:06Z] INFO  17:06:23,572 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:06Z] INFO  17:06:23,579 HelpFormatter - Date/Time: 2016/04/14 17:06:23
[2016-04-15T00:06Z] INFO  17:06:23,580 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:06Z] INFO  17:06:23,580 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:06Z] INFO  17:06:23,764 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:06Z] INFO  17:06:24,647 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-15T00:06Z] INFO  17:06:24,718 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:06Z] INFO  17:06:24,727 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:06Z] INFO  17:06:24,802 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-15T00:06Z] INFO  17:06:24,817 IntervalUtils - Processing 15520574 bp from intervals
[2016-04-15T00:06Z] INFO  17:06:24,938 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:06Z] INFO  17:06:24,973 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-15T00:06Z] INFO  17:06:25,034 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:06Z] INFO  17:06:25,043 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:06Z] INFO  17:06:25,091 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-15T00:06Z] INFO  17:06:25,106 IntervalUtils - Processing 15571753 bp from intervals
[2016-04-15T00:06Z] INFO  17:06:25,188 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:06Z] INFO  17:06:25,267 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:06Z] INFO  17:06:25,268 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:06Z] INFO  17:06:25,268 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:06Z] INFO  17:06:25,269 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:06Z] INFO  17:06:25,284 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:06Z] INFO  17:06:25,476 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:06Z] INFO  17:06:25,477 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:06Z] INFO  17:06:25,478 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:06Z] INFO  17:06:25,478 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:06Z] INFO  17:06:25,494 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:06Z] INFO  17:06:25,499 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:06Z] INFO  17:06:25,623 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:06Z] INFO  17:06:26,091 ProgressMeter -            done   1213624.0    71.0 s      58.0 s      100.0%    71.0 s       0.0 s
[2016-04-15T00:06Z] INFO  17:06:26,092 ProgressMeter - Total runtime 71.13 secs, 1.19 min, 0.02 hours
[2016-04-15T00:06Z] INFO  17:06:26,096 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 1213624 total reads (0.00%)
[2016-04-15T00:06Z] INFO  17:06:26,097 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:06Z] INFO  17:06:26,097 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:06Z] INFO  17:06:26,097 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:06Z] INFO  17:06:27,287 ProgressMeter -     1:220864228    200004.0    30.0 s       2.5 m       85.2%    35.0 s       5.0 s
[2016-04-15T00:06Z] INFO  17:06:27,545 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:06Z] Index BAM file: R14-18105_kapa-NGv3-PE100-NGv3-sort-19_31038849_46627578-prep.bam
[2016-04-15T00:06Z] INFO  17:06:28,195 ProgressMeter -            done   1.5541927E7    28.0 s       1.0 s      100.0%    28.0 s       0.0 s
[2016-04-15T00:06Z] INFO  17:06:28,195 ProgressMeter - Total runtime 28.36 secs, 0.47 min, 0.01 hours
[2016-04-15T00:06Z] INFO  17:06:28,200 MicroScheduler - 164715 reads were filtered out during the traversal out of approximately 742002 total reads (22.20%)
[2016-04-15T00:06Z] INFO  17:06:28,200 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:06Z] INFO  17:06:28,200 MicroScheduler -   -> 1356 reads (0.18% of total) failing BadMateFilter
[2016-04-15T00:06Z] INFO  17:06:28,201 MicroScheduler -   -> 48481 reads (6.53% of total) failing DuplicateReadFilter
[2016-04-15T00:06Z] INFO  17:06:28,201 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:06Z] INFO  17:06:28,201 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:06Z] INFO  17:06:28,202 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:06Z] INFO  17:06:28,202 MicroScheduler -   -> 114878 reads (15.48% of total) failing MappingQualityZeroFilter
[2016-04-15T00:06Z] INFO  17:06:28,202 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:06Z] INFO  17:06:28,202 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-15T00:06Z] INFO  17:06:28,203 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:06Z] INFO  17:06:28,695 ProgressMeter -            done   1.7079418E7    19.0 s       1.0 s      100.0%    19.0 s       0.0 s
[2016-04-15T00:06Z] INFO  17:06:28,697 ProgressMeter - Total runtime 19.89 secs, 0.33 min, 0.01 hours
[2016-04-15T00:06Z] INFO  17:06:28,701 MicroScheduler - 20241 reads were filtered out during the traversal out of approximately 253366 total reads (7.99%)
[2016-04-15T00:06Z] INFO  17:06:28,703 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:06Z] INFO  17:06:28,703 MicroScheduler -   -> 798 reads (0.31% of total) failing BadMateFilter
[2016-04-15T00:06Z] INFO  17:06:28,705 MicroScheduler -   -> 19049 reads (7.52% of total) failing DuplicateReadFilter
[2016-04-15T00:06Z] INFO  17:06:28,706 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:06Z] INFO  17:06:28,707 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:06Z] INFO  17:06:28,707 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:06Z] INFO  17:06:28,708 MicroScheduler -   -> 394 reads (0.16% of total) failing MappingQualityZeroFilter
[2016-04-15T00:06Z] INFO  17:06:28,709 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:06Z] INFO  17:06:28,710 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-15T00:06Z] INFO  17:06:28,710 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:06Z] INFO  17:06:29,408 ProgressMeter -     1:143767817   3.4758405E7    30.0 s       0.0 s      100.0%    30.0 s       0.0 s
[2016-04-15T00:06Z] INFO  17:06:29,562 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:06Z] GATK: realign ('1', 0, 15541927) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:06Z] INFO  17:06:29,888 ProgressMeter -            done   3.4773037E7    30.0 s       0.0 s      100.0%    30.0 s       0.0 s
[2016-04-15T00:06Z] INFO  17:06:29,888 ProgressMeter - Total runtime 30.50 secs, 0.51 min, 0.01 hours
[2016-04-15T00:06Z] INFO  17:06:29,893 MicroScheduler - 44379 reads were filtered out during the traversal out of approximately 399827 total reads (11.10%)
[2016-04-15T00:06Z] INFO  17:06:29,896 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:06Z] INFO  17:06:29,897 MicroScheduler -   -> 1071 reads (0.27% of total) failing BadMateFilter
[2016-04-15T00:06Z] INFO  17:06:29,897 MicroScheduler -   -> 29301 reads (7.33% of total) failing DuplicateReadFilter
[2016-04-15T00:06Z] INFO  17:06:29,898 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:06Z] INFO  17:06:29,899 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:06Z] INFO  17:06:29,900 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:06Z] INFO  17:06:29,900 MicroScheduler -   -> 14007 reads (3.50% of total) failing MappingQualityZeroFilter
[2016-04-15T00:06Z] INFO  17:06:29,901 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:06Z] INFO  17:06:29,902 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-15T00:06Z] INFO  17:06:29,903 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:06Z] INFO  17:06:29,935 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@41fd9d8e
[2016-04-15T00:06Z] INFO  17:06:30,117 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:06Z] GATK: realign ('1', 175048468, 192127886) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:06Z] INFO  17:06:30,225 ProgressMeter -            done    246218.0    32.0 s       2.2 m      100.0%    32.0 s       0.0 s
[2016-04-15T00:06Z] INFO  17:06:30,236 ProgressMeter - Total runtime 32.99 secs, 0.55 min, 0.01 hours
[2016-04-15T00:06Z] INFO  17:06:30,236 MicroScheduler - 204 reads were filtered out during the traversal out of approximately 246422 total reads (0.08%)
[2016-04-15T00:06Z] INFO  17:06:30,237 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:06Z] INFO  17:06:30,237 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:06Z] INFO  17:06:30,237 MicroScheduler -   -> 204 reads (0.08% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:06Z] INFO  17:06:31,294 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:06Z] GATK: realign ('1', 108994811, 143767848) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:06Z] GATK pre-alignment ('2', 62362965, 79253295) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:06Z] INFO  17:06:31,589 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:06Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-1_207641871_223156451-prep-prealign.bam
[2016-04-15T00:06Z] GATK RealignerTargetCreator: R14-18106_kapa-NGv3-PE100-NGv3-sort-1_207641871_223156451-prep-prealign.bam 1:207641872-223156451
[2016-04-15T00:06Z] GATK: RealignerTargetCreator
[2016-04-15T00:06Z] INFO  17:06:32,725 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:06Z] INFO  17:06:32,728 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:06Z] INFO  17:06:32,728 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:06Z] INFO  17:06:32,728 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:06Z] INFO  17:06:32,733 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/1/R14-18106_kapa-NGv3-PE100-NGv3-sort-1_0_15541927-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/1/R14-18106_kapa-NGv3-PE100-NGv3-sort-1_0_15541927-prep-prealign-realign.intervals -L 1:1-15541927 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/1/tx/tmpDmq5Ye/R14-18106_kapa-NGv3-PE100-NGv3-sort-1_0_15541927-prep.bam
[2016-04-15T00:06Z] INFO  17:06:32,771 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:06Z] INFO  17:06:32,771 HelpFormatter - Date/Time: 2016/04/14 17:06:32
[2016-04-15T00:06Z] INFO  17:06:32,772 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:06Z] INFO  17:06:32,772 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:06Z] INFO  17:06:32,952 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:06Z] INFO  17:06:32,955 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:06Z] INFO  17:06:32,955 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:06Z] INFO  17:06:32,956 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:06Z] INFO  17:06:32,961 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/1/R14-18106_kapa-NGv3-PE100-NGv3-sort-1_175048468_192127886-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/1/R14-18106_kapa-NGv3-PE100-NGv3-sort-1_175048468_192127886-prep-prealign-realign.intervals -L 1:175048469-192127886 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/1/tx/tmpswc0RA/R14-18106_kapa-NGv3-PE100-NGv3-sort-1_175048468_192127886-prep.bam
[2016-04-15T00:06Z] INFO  17:06:32,994 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:06Z] INFO  17:06:32,994 HelpFormatter - Date/Time: 2016/04/14 17:06:32
[2016-04-15T00:06Z] INFO  17:06:32,994 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:06Z] INFO  17:06:32,995 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:06Z] INFO  17:06:33,014 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:06Z] INFO  17:06:33,115 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:06Z] INFO  17:06:33,124 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:06Z] INFO  17:06:33,177 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-15T00:06Z] INFO  17:06:33,219 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:06Z] INFO  17:06:33,347 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:06Z] INFO  17:06:33,356 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:06Z] INFO  17:06:33,399 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.04
[2016-04-15T00:06Z] INFO  17:06:33,482 IntervalUtils - Processing 15541927 bp from intervals
[2016-04-15T00:06Z] WARN  17:06:33,487 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:06Z] INFO  17:06:33,556 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:06Z] INFO  17:06:33,680 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:06Z] INFO  17:06:33,681 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:06Z] INFO  17:06:33,682 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:06Z] INFO  17:06:33,683 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:06Z] INFO  17:06:33,828 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:06Z] INFO  17:06:33,857 IntervalUtils - Processing 17079418 bp from intervals
[2016-04-15T00:06Z] WARN  17:06:33,878 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:06Z] INFO  17:06:33,961 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:06Z] INFO  17:06:34,023 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:06Z] INFO  17:06:34,166 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:06Z] INFO  17:06:34,169 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:06Z] INFO  17:06:34,169 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:06Z] INFO  17:06:34,170 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:06Z] INFO  17:06:34,171 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:06Z] INFO  17:06:34,174 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/1/R14-18106_kapa-NGv3-PE100-NGv3-sort-1_108994811_143767848-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/1/R14-18106_kapa-NGv3-PE100-NGv3-sort-1_108994811_143767848-prep-prealign-realign.intervals -L 1:108994812-143767848 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/1/tx/tmpQwgIFm/R14-18106_kapa-NGv3-PE100-NGv3-sort-1_108994811_143767848-prep.bam
[2016-04-15T00:06Z] INFO  17:06:34,178 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:06Z] INFO  17:06:34,179 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:06Z] INFO  17:06:34,179 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:06Z] INFO  17:06:34,227 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:06Z] INFO  17:06:34,228 HelpFormatter - Date/Time: 2016/04/14 17:06:34
[2016-04-15T00:06Z] INFO  17:06:34,228 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:06Z] INFO  17:06:34,229 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:06Z] INFO  17:06:34,382 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:06Z] INFO  17:06:34,425 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:06Z] INFO  17:06:34,584 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:06Z] INFO  17:06:34,593 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:06Z] INFO  17:06:34,594 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:06Z] INFO  17:06:34,665 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-15T00:06Z] INFO  17:06:34,670 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:06Z] INFO  17:06:34,673 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:06Z] INFO  17:06:34,674 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:06Z] INFO  17:06:34,674 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:06Z] INFO  17:06:34,679 HelpFormatter - Program Args: -T PrintReads -L 2:62362966-79253295 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/2/tx/tmpydTS8p/R14-18106_kapa-NGv3-PE100-NGv3-sort-2_62362965_79253295-prep-prealign.bam
[2016-04-15T00:06Z] INFO  17:06:34,694 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:06Z] INFO  17:06:34,695 HelpFormatter - Date/Time: 2016/04/14 17:06:34
[2016-04-15T00:06Z] INFO  17:06:34,695 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:06Z] INFO  17:06:34,696 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:06Z] INFO  17:06:34,910 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:06Z] INFO  17:06:34,980 IntervalUtils - Processing 34773037 bp from intervals
[2016-04-15T00:06Z] WARN  17:06:34,994 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:06Z] INFO  17:06:35,100 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:06Z] INFO  17:06:35,258 ProgressMeter -            done   1.5542096E7    21.0 s       1.0 s      100.0%    21.0 s       0.0 s
[2016-04-15T00:06Z] INFO  17:06:35,259 ProgressMeter - Total runtime 21.63 secs, 0.36 min, 0.01 hours
[2016-04-15T00:06Z] INFO  17:06:35,263 MicroScheduler - 34263 reads were filtered out during the traversal out of approximately 387321 total reads (8.85%)
[2016-04-15T00:06Z] INFO  17:06:35,264 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:06Z] INFO  17:06:35,264 MicroScheduler -   -> 922 reads (0.24% of total) failing BadMateFilter
[2016-04-15T00:06Z] INFO  17:06:35,265 MicroScheduler -   -> 28462 reads (7.35% of total) failing DuplicateReadFilter
[2016-04-15T00:06Z] INFO  17:06:35,266 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:06Z] INFO  17:06:35,266 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:06Z] INFO  17:06:35,267 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:06Z] INFO  17:06:35,267 MicroScheduler -   -> 4879 reads (1.26% of total) failing MappingQualityZeroFilter
[2016-04-15T00:06Z] INFO  17:06:35,268 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:06Z] INFO  17:06:35,268 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-15T00:06Z] INFO  17:06:35,269 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:06Z] INFO  17:06:35,322 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:06Z] INFO  17:06:35,323 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:06Z] INFO  17:06:35,324 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:06Z] INFO  17:06:35,325 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:06Z] INFO  17:06:35,484 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:06Z] INFO  17:06:35,757 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:06Z] INFO  17:06:35,759 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:06Z] INFO  17:06:35,760 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@5fe152b7
[2016-04-15T00:06Z] INFO  17:06:35,759 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:06Z] INFO  17:06:35,760 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:06Z] INFO  17:06:35,764 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/1/R14-18106_kapa-NGv3-PE100-NGv3-sort-1_207641871_223156451-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/1/tx/tmpr07avp/R14-18106_kapa-NGv3-PE100-NGv3-sort-1_207641871_223156451-prep-prealign-realign.intervals -l INFO -L 1:207641872-223156451 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:06Z] INFO  17:06:35,774 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:06Z] INFO  17:06:35,775 HelpFormatter - Date/Time: 2016/04/14 17:06:35
[2016-04-15T00:06Z] INFO  17:06:35,775 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:06Z] INFO  17:06:35,784 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:06Z] INFO  17:06:35,798 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:06Z] INFO  17:06:35,813 ProgressMeter -            done    150486.0    21.0 s       2.4 m       99.9%    21.0 s       0.0 s
[2016-04-15T00:06Z] INFO  17:06:35,814 ProgressMeter - Total runtime 21.28 secs, 0.35 min, 0.01 hours
[2016-04-15T00:06Z] INFO  17:06:35,814 MicroScheduler - 139 reads were filtered out during the traversal out of approximately 150625 total reads (0.09%)
[2016-04-15T00:06Z] INFO  17:06:35,815 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:06Z] INFO  17:06:35,815 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:06Z] INFO  17:06:35,815 MicroScheduler -   -> 139 reads (0.09% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:06Z] INFO  17:06:35,853 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:06Z] INFO  17:06:36,104 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T00:06Z] INFO  17:06:36,112 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-15T00:06Z] INFO  17:06:36,118 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:06Z] INFO  17:06:36,174 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-15T00:06Z] INFO  17:06:36,181 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:06Z] INFO  17:06:36,199 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:06Z] INFO  17:06:36,245 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-15T00:06Z] INFO  17:06:36,259 IntervalUtils - Processing 16890330 bp from intervals
[2016-04-15T00:06Z] INFO  17:06:36,361 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:06Z] INFO  17:06:36,480 IntervalUtils - Processing 15514580 bp from intervals
[2016-04-15T00:06Z] WARN  17:06:36,485 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:06Z] INFO  17:06:36,649 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:06Z] INFO  17:06:36,675 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:06Z] INFO  17:06:36,676 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:06Z] INFO  17:06:36,677 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:06Z] INFO  17:06:36,677 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:06Z] INFO  17:06:36,709 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:06Z] INFO  17:06:36,875 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:06Z] INFO  17:06:36,888 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:06Z] INFO  17:06:36,890 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:06Z] INFO  17:06:36,889 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:06Z] INFO  17:06:36,891 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:06Z] INFO  17:06:36,892 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:06Z] GATK: realign ('1', 159504867, 175046963) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:06Z] INFO  17:06:37,043 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:06Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-2_0_15514844-prep-prealign.bam
[2016-04-15T00:06Z] GATK RealignerTargetCreator: R14-18106_kapa-NGv3-PE100-NGv3-sort-2_0_15514844-prep-prealign.bam 2:1-15514844
[2016-04-15T00:06Z] GATK: RealignerTargetCreator
[2016-04-15T00:06Z] INFO  17:06:38,387 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@41fd9d8e
[2016-04-15T00:06Z] INFO  17:06:38,647 ProgressMeter -            done    190949.0    25.0 s       2.2 m       99.6%    25.0 s       0.0 s
[2016-04-15T00:06Z] INFO  17:06:38,648 ProgressMeter - Total runtime 25.49 secs, 0.42 min, 0.01 hours
[2016-04-15T00:06Z] INFO  17:06:38,649 MicroScheduler - 106 reads were filtered out during the traversal out of approximately 191055 total reads (0.06%)
[2016-04-15T00:06Z] INFO  17:06:38,650 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:06Z] INFO  17:06:38,651 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:06Z] INFO  17:06:38,652 MicroScheduler -   -> 106 reads (0.06% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:06Z] INFO  17:06:39,670 ProgressMeter -     1:228699401    200003.0    30.0 s       2.5 m       32.7%    91.0 s      61.0 s
[2016-04-15T00:06Z] INFO  17:06:40,144 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:06Z] INFO  17:06:40,151 ProgressMeter -      1:31186469   1.5616547E7    30.0 s       1.0 s      100.0%    30.0 s       0.0 s
[2016-04-15T00:06Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-1_240255409_249250621-prep-prealign.bam
[2016-04-15T00:06Z] INFO  17:06:40,300 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:06Z] INFO  17:06:40,303 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:06Z] INFO  17:06:40,303 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:06Z] INFO  17:06:40,304 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:06Z] INFO  17:06:40,308 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/1/R14-18106_kapa-NGv3-PE100-NGv3-sort-1_159504867_175046963-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/1/R14-18106_kapa-NGv3-PE100-NGv3-sort-1_159504867_175046963-prep-prealign-realign.intervals -L 1:159504868-175046963 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/1/tx/tmpsQH8dj/R14-18106_kapa-NGv3-PE100-NGv3-sort-1_159504867_175046963-prep.bam
[2016-04-15T00:06Z] INFO  17:06:40,330 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:06Z] INFO  17:06:40,331 HelpFormatter - Date/Time: 2016/04/14 17:06:40
[2016-04-15T00:06Z] INFO  17:06:40,332 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:06Z] INFO  17:06:40,332 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:06Z] INFO  17:06:40,486 ProgressMeter -            done   1.5640657E7    30.0 s       1.0 s      100.0%    30.0 s       0.0 s
[2016-04-15T00:06Z] INFO  17:06:40,487 ProgressMeter - Total runtime 30.34 secs, 0.51 min, 0.01 hours
[2016-04-15T00:06Z] INFO  17:06:40,488 MicroScheduler - 82424 reads were filtered out during the traversal out of approximately 768745 total reads (10.72%)
[2016-04-15T00:06Z] INFO  17:06:40,489 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:06Z] INFO  17:06:40,489 MicroScheduler -   -> 1512 reads (0.20% of total) failing BadMateFilter
[2016-04-15T00:06Z] INFO  17:06:40,490 MicroScheduler -   -> 57202 reads (7.44% of total) failing DuplicateReadFilter
[2016-04-15T00:06Z] INFO  17:06:40,491 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:06Z] INFO  17:06:40,491 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:06Z] INFO  17:06:40,492 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:06Z] INFO  17:06:40,492 MicroScheduler -   -> 23710 reads (3.08% of total) failing MappingQualityZeroFilter
[2016-04-15T00:06Z] INFO  17:06:40,493 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:06Z] INFO  17:06:40,494 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-15T00:06Z] INFO  17:06:40,494 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:06Z] INFO  17:06:40,649 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:06Z] INFO  17:06:40,649 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:06Z] INFO  17:06:40,653 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:06Z] INFO  17:06:40,653 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:06Z] INFO  17:06:40,654 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:06Z] INFO  17:06:40,658 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/2/R14-18106_kapa-NGv3-PE100-NGv3-sort-2_0_15514844-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/2/tx/tmpVv8NDX/R14-18106_kapa-NGv3-PE100-NGv3-sort-2_0_15514844-prep-prealign-realign.intervals -l INFO -L 2:1-15514844 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:06Z] INFO  17:06:40,685 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:06Z] INFO  17:06:40,686 HelpFormatter - Date/Time: 2016/04/14 17:06:40
[2016-04-15T00:06Z] INFO  17:06:40,686 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:06Z] INFO  17:06:40,687 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:06Z] GATK RealignerTargetCreator: R14-18106_kapa-NGv3-PE100-NGv3-sort-1_240255409_249250621-prep-prealign.bam 1:240255410-249250621
[2016-04-15T00:06Z] GATK: RealignerTargetCreator
[2016-04-15T00:06Z] INFO  17:06:40,776 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:06Z] INFO  17:06:40,799 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:06Z] INFO  17:06:40,813 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:06Z] INFO  17:06:40,882 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-15T00:06Z] INFO  17:06:41,004 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T00:06Z] INFO  17:06:41,041 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:06Z] INFO  17:06:41,103 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-15T00:06Z] INFO  17:06:41,351 IntervalUtils - Processing 15542096 bp from intervals
[2016-04-15T00:06Z] WARN  17:06:41,356 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:06Z] INFO  17:06:41,429 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:06Z] INFO  17:06:41,480 IntervalUtils - Processing 15514844 bp from intervals
[2016-04-15T00:06Z] WARN  17:06:41,485 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:06Z] INFO  17:06:41,586 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:06Z] INFO  17:06:41,587 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:06Z] INFO  17:06:41,588 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:06Z] INFO  17:06:41,589 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:06Z] INFO  17:06:41,593 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:06Z] INFO  17:06:41,787 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:06Z] INFO  17:06:41,798 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:06Z] INFO  17:06:41,799 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:06Z] INFO  17:06:41,800 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:06Z] INFO  17:06:41,801 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:06Z] INFO  17:06:41,933 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:06Z] INFO  17:06:42,020 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:06Z] GATK: realign ('1', 15545821, 31186478) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:06Z] INFO  17:06:43,804 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:06Z] INFO  17:06:43,807 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:06Z] INFO  17:06:43,808 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:06Z] INFO  17:06:43,809 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:06Z] INFO  17:06:43,813 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/1/R14-18106_kapa-NGv3-PE100-NGv3-sort-1_240255409_249250621-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/1/tx/tmpREjD3l/R14-18106_kapa-NGv3-PE100-NGv3-sort-1_240255409_249250621-prep-prealign-realign.intervals -l INFO -L 1:240255410-249250621 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:06Z] INFO  17:06:43,846 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:06Z] INFO  17:06:43,847 HelpFormatter - Date/Time: 2016/04/14 17:06:43
[2016-04-15T00:06Z] INFO  17:06:43,847 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:06Z] INFO  17:06:43,847 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:06Z] INFO  17:06:43,968 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:06Z] INFO  17:06:44,195 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T00:06Z] INFO  17:06:44,233 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:06Z] INFO  17:06:44,284 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-15T00:06Z] INFO  17:06:44,659 IntervalUtils - Processing 8995212 bp from intervals
[2016-04-15T00:06Z] WARN  17:06:44,664 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:06Z] INFO  17:06:44,782 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:06Z] INFO  17:06:44,884 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:06Z] INFO  17:06:44,888 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:06Z] INFO  17:06:44,889 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:06Z] INFO  17:06:44,889 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:06Z] INFO  17:06:44,895 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/1/R14-18106_kapa-NGv3-PE100-NGv3-sort-1_15545821_31186478-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/1/R14-18106_kapa-NGv3-PE100-NGv3-sort-1_15545821_31186478-prep-prealign-realign.intervals -L 1:15545822-31186478 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/1/tx/tmpr_zVDW/R14-18106_kapa-NGv3-PE100-NGv3-sort-1_15545821_31186478-prep.bam
[2016-04-15T00:06Z] INFO  17:06:44,912 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:06Z] INFO  17:06:44,913 HelpFormatter - Date/Time: 2016/04/14 17:06:44
[2016-04-15T00:06Z] INFO  17:06:44,914 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:06Z] INFO  17:06:44,915 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:06Z] INFO  17:06:45,071 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:06Z] INFO  17:06:45,073 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:06Z] INFO  17:06:45,074 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:06Z] INFO  17:06:45,074 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:06Z] INFO  17:06:45,164 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:06Z] INFO  17:06:45,293 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:06Z] INFO  17:06:45,303 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:06Z] INFO  17:06:45,371 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-15T00:06Z] INFO  17:06:45,770 IntervalUtils - Processing 15640657 bp from intervals
[2016-04-15T00:06Z] WARN  17:06:45,776 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:06Z] INFO  17:06:45,879 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:06Z] INFO  17:06:46,037 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:06Z] INFO  17:06:46,038 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:06Z] INFO  17:06:46,039 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:06Z] INFO  17:06:46,040 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:06Z] INFO  17:06:46,213 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:06Z] INFO  17:06:46,458 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:06Z] INFO  17:06:47,479 ProgressMeter -     1:152186774    600011.0    90.0 s       2.5 m       53.4%     2.8 m      78.0 s
[2016-04-15T00:06Z] INFO  17:06:47,604 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@41fd9d8e
[2016-04-15T00:06Z] INFO  17:06:47,698 ProgressMeter -            done    175689.0    22.0 s       2.1 m      100.0%    22.0 s       0.0 s
[2016-04-15T00:06Z] INFO  17:06:47,699 ProgressMeter - Total runtime 22.43 secs, 0.37 min, 0.01 hours
[2016-04-15T00:06Z] INFO  17:06:47,700 MicroScheduler - 161 reads were filtered out during the traversal out of approximately 175850 total reads (0.09%)
[2016-04-15T00:06Z] INFO  17:06:47,700 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:06Z] INFO  17:06:47,701 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:06Z] INFO  17:06:47,702 MicroScheduler -   -> 161 reads (0.09% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:06Z] INFO  17:06:49,168 ProgressMeter -            done   1.5527177E7    28.0 s       1.0 s      100.0%    28.0 s       0.0 s
[2016-04-15T00:06Z] INFO  17:06:49,169 ProgressMeter - Total runtime 28.91 secs, 0.48 min, 0.01 hours
[2016-04-15T00:06Z] INFO  17:06:49,174 MicroScheduler - 58297 reads were filtered out during the traversal out of approximately 683971 total reads (8.52%)
[2016-04-15T00:06Z] INFO  17:06:49,175 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:06Z] INFO  17:06:49,176 MicroScheduler -   -> 1393 reads (0.20% of total) failing BadMateFilter
[2016-04-15T00:06Z] INFO  17:06:49,177 MicroScheduler -   -> 50499 reads (7.38% of total) failing DuplicateReadFilter
[2016-04-15T00:06Z] INFO  17:06:49,178 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:06Z] INFO  17:06:49,178 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:06Z] INFO  17:06:49,179 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:06Z] INFO  17:06:49,180 MicroScheduler -   -> 6405 reads (0.94% of total) failing MappingQualityZeroFilter
[2016-04-15T00:06Z] INFO  17:06:49,181 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:06Z] INFO  17:06:49,181 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-15T00:06Z] INFO  17:06:49,182 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:06Z] INFO  17:06:49,347 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:06Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-2_46707543_62228117-prep-prealign.bam
[2016-04-15T00:06Z] GATK RealignerTargetCreator: R14-18106_kapa-NGv3-PE100-NGv3-sort-2_46707543_62228117-prep-prealign.bam 2:46707544-62228117
[2016-04-15T00:06Z] GATK: RealignerTargetCreator
[2016-04-15T00:06Z] INFO  17:06:50,290 ProgressMeter -      2:27306136    200004.0    30.0 s       2.5 m       75.5%    39.0 s       9.0 s
[2016-04-15T00:06Z] INFO  17:06:50,522 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:06Z] GATK: realign ('1', 31187093, 46714270) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:06Z] INFO  17:06:51,028 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@41fd9d8e
[2016-04-15T00:06Z] INFO  17:06:51,242 ProgressMeter -            done    395644.0    59.0 s       2.5 m      100.0%    59.0 s       0.0 s
[2016-04-15T00:06Z] INFO  17:06:51,244 ProgressMeter - Total runtime 59.91 secs, 1.00 min, 0.02 hours
[2016-04-15T00:06Z] INFO  17:06:51,245 MicroScheduler - 251 reads were filtered out during the traversal out of approximately 395895 total reads (0.06%)
[2016-04-15T00:06Z] INFO  17:06:51,246 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:06Z] INFO  17:06:51,246 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:06Z] INFO  17:06:51,247 MicroScheduler -   -> 251 reads (0.06% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:06Z] INFO  17:06:52,572 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:06Z] INFO  17:06:52,576 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:06Z] INFO  17:06:52,577 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:06Z] INFO  17:06:52,577 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:06Z] INFO  17:06:52,582 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/2/R14-18106_kapa-NGv3-PE100-NGv3-sort-2_46707543_62228117-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/2/tx/tmp86D2p7/R14-18106_kapa-NGv3-PE100-NGv3-sort-2_46707543_62228117-prep-prealign-realign.intervals -l INFO -L 2:46707544-62228117 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:06Z] INFO  17:06:52,612 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:06Z] INFO  17:06:52,613 HelpFormatter - Date/Time: 2016/04/14 17:06:52
[2016-04-15T00:06Z] INFO  17:06:52,613 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:06Z] INFO  17:06:52,614 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:06Z] INFO  17:06:52,716 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:06Z] INFO  17:06:52,806 ProgressMeter -            done    251235.0    18.0 s      74.0 s      100.0%    18.0 s       0.0 s
[2016-04-15T00:06Z] INFO  17:06:52,807 ProgressMeter - Total runtime 18.63 secs, 0.31 min, 0.01 hours
[2016-04-15T00:06Z] INFO  17:06:52,811 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 251235 total reads (0.00%)
[2016-04-15T00:06Z] INFO  17:06:52,812 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:06Z] INFO  17:06:52,812 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:06Z] INFO  17:06:52,812 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:06Z] INFO  17:06:52,857 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:06Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-1_192128349_207640257-prep-prealign.bam
[2016-04-15T00:06Z] INFO  17:06:52,980 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T00:06Z] INFO  17:06:52,991 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:06Z] INFO  17:06:53,066 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-15T00:06Z] INFO  17:06:53,251 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:06Z] INFO  17:06:53,255 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:06Z] INFO  17:06:53,255 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:06Z] INFO  17:06:53,256 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:06Z] INFO  17:06:53,261 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/1/R14-18106_kapa-NGv3-PE100-NGv3-sort-1_31187093_46714270-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/1/R14-18106_kapa-NGv3-PE100-NGv3-sort-1_31187093_46714270-prep-prealign-realign.intervals -L 1:31187094-46714270 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/1/tx/tmpRNrhlq/R14-18106_kapa-NGv3-PE100-NGv3-sort-1_31187093_46714270-prep.bam
[2016-04-15T00:06Z] INFO  17:06:53,277 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:06Z] INFO  17:06:53,278 HelpFormatter - Date/Time: 2016/04/14 17:06:53
[2016-04-15T00:06Z] INFO  17:06:53,278 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:06Z] INFO  17:06:53,279 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:06Z] INFO  17:06:53,452 IntervalUtils - Processing 15520574 bp from intervals
[2016-04-15T00:06Z] WARN  17:06:53,468 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:06Z] INFO  17:06:53,516 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:06Z] INFO  17:06:53,561 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:06Z] INFO  17:06:53,662 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:06Z] INFO  17:06:53,672 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:06Z] INFO  17:06:53,732 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-15T00:06Z] INFO  17:06:53,761 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:06Z] INFO  17:06:53,763 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:06Z] INFO  17:06:53,763 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:06Z] INFO  17:06:53,764 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:06Z] INFO  17:06:54,064 IntervalUtils - Processing 15527177 bp from intervals
[2016-04-15T00:06Z] WARN  17:06:54,069 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:06Z] GATK RealignerTargetCreator: R14-18106_kapa-NGv3-PE100-NGv3-sort-1_192128349_207640257-prep-prealign.bam 1:192128350-207640257
[2016-04-15T00:06Z] GATK: RealignerTargetCreator
[2016-04-15T00:06Z] INFO  17:06:54,174 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:06Z] INFO  17:06:54,295 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@6834dd3c
[2016-04-15T00:06Z] INFO  17:06:54,315 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:06Z] INFO  17:06:54,315 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:06Z] INFO  17:06:54,316 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:06Z] INFO  17:06:54,316 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:06Z] INFO  17:06:54,322 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:06Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-1_175048468_192127886-prep.bam
[2016-04-15T00:06Z] INFO  17:06:54,408 ProgressMeter -            done    222965.0    28.0 s       2.2 m      100.0%    28.0 s       0.0 s
[2016-04-15T00:06Z] INFO  17:06:54,409 ProgressMeter - Total runtime 28.93 secs, 0.48 min, 0.01 hours
[2016-04-15T00:06Z] INFO  17:06:54,409 MicroScheduler - 2229 reads were filtered out during the traversal out of approximately 225194 total reads (0.99%)
[2016-04-15T00:06Z] INFO  17:06:54,409 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:06Z] INFO  17:06:54,410 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:06Z] INFO  17:06:54,410 MicroScheduler -   -> 2229 reads (0.99% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:06Z] INFO  17:06:54,542 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:06Z] INFO  17:06:54,708 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:06Z] GATK pre-alignment ('2', 79253838, 95537822) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:06Z] INFO  17:06:55,543 ProgressMeter -            done   1.551458E7    18.0 s       1.0 s      100.0%    18.0 s       0.0 s
[2016-04-15T00:06Z] INFO  17:06:55,550 ProgressMeter - Total runtime 18.66 secs, 0.31 min, 0.01 hours
[2016-04-15T00:06Z] INFO  17:06:55,556 MicroScheduler - 32587 reads were filtered out during the traversal out of approximately 247261 total reads (13.18%)
[2016-04-15T00:06Z] INFO  17:06:55,557 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:06Z] INFO  17:06:55,558 MicroScheduler -   -> 711 reads (0.29% of total) failing BadMateFilter
[2016-04-15T00:06Z] INFO  17:06:55,559 MicroScheduler -   -> 17501 reads (7.08% of total) failing DuplicateReadFilter
[2016-04-15T00:06Z] INFO  17:06:55,559 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:06Z] INFO  17:06:55,560 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:06Z] INFO  17:06:55,560 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:06Z] INFO  17:06:55,561 MicroScheduler -   -> 14375 reads (5.81% of total) failing MappingQualityZeroFilter
[2016-04-15T00:06Z] INFO  17:06:55,562 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:06Z] INFO  17:06:55,562 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-15T00:06Z] INFO  17:06:55,563 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:06Z] INFO  17:06:55,803 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:06Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-2_31135088_46706841-prep-prealign.bam
[2016-04-15T00:06Z] GATK RealignerTargetCreator: R14-18106_kapa-NGv3-PE100-NGv3-sort-2_31135088_46706841-prep-prealign.bam 2:31135089-46706841
[2016-04-15T00:06Z] GATK: RealignerTargetCreator
[2016-04-15T00:06Z] INFO  17:06:56,923 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:06Z] INFO  17:06:56,948 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:06Z] INFO  17:06:56,952 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:06Z] INFO  17:06:56,953 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:06Z] INFO  17:06:56,953 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:06Z] INFO  17:06:56,959 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/1/R14-18106_kapa-NGv3-PE100-NGv3-sort-1_192128349_207640257-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/1/tx/tmpT5fLtN/R14-18106_kapa-NGv3-PE100-NGv3-sort-1_192128349_207640257-prep-prealign-realign.intervals -l INFO -L 1:192128350-207640257 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:06Z] GATK: realign ('1', 207641871, 223156451) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:06Z] INFO  17:06:56,988 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:06Z] INFO  17:06:56,988 HelpFormatter - Date/Time: 2016/04/14 17:06:56
[2016-04-15T00:06Z] INFO  17:06:56,988 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:06Z] INFO  17:06:56,988 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:06Z] INFO  17:06:57,138 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:06Z] INFO  17:06:57,389 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T00:06Z] INFO  17:06:57,406 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:06Z] INFO  17:06:57,511 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.10
[2016-04-15T00:06Z] INFO  17:06:57,783 IntervalUtils - Processing 15511908 bp from intervals
[2016-04-15T00:06Z] WARN  17:06:57,788 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:06Z] INFO  17:06:57,862 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:06Z] INFO  17:06:58,034 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:06Z] INFO  17:06:58,037 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:06Z] INFO  17:06:58,037 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:06Z] INFO  17:06:58,038 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:06Z] INFO  17:06:58,042 HelpFormatter - Program Args: -T PrintReads -L 2:79253839-95537822 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/2/tx/tmpYtY6mq/R14-18106_kapa-NGv3-PE100-NGv3-sort-2_79253838_95537822-prep-prealign.bam
[2016-04-15T00:06Z] INFO  17:06:58,051 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:06Z] INFO  17:06:58,052 HelpFormatter - Date/Time: 2016/04/14 17:06:58
[2016-04-15T00:06Z] INFO  17:06:58,052 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:06Z] INFO  17:06:58,053 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:06Z] INFO  17:06:58,078 ProgressMeter -            done   1.5514844E7    16.0 s       1.0 s      100.0%    16.0 s       0.0 s
[2016-04-15T00:06Z] INFO  17:06:58,079 ProgressMeter - Total runtime 16.28 secs, 0.27 min, 0.00 hours
[2016-04-15T00:06Z] INFO  17:06:58,083 MicroScheduler - 12277 reads were filtered out during the traversal out of approximately 151235 total reads (8.12%)
[2016-04-15T00:06Z] INFO  17:06:58,083 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:06Z] INFO  17:06:58,084 MicroScheduler -   -> 606 reads (0.40% of total) failing BadMateFilter
[2016-04-15T00:06Z] INFO  17:06:58,084 MicroScheduler -   -> 11339 reads (7.50% of total) failing DuplicateReadFilter
[2016-04-15T00:06Z] INFO  17:06:58,084 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:06Z] INFO  17:06:58,084 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:06Z] INFO  17:06:58,085 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:06Z] INFO  17:06:58,085 MicroScheduler -   -> 332 reads (0.22% of total) failing MappingQualityZeroFilter
[2016-04-15T00:06Z] INFO  17:06:58,085 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:06Z] INFO  17:06:58,085 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-15T00:06Z] INFO  17:06:58,086 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:06Z] INFO  17:06:58,098 ProgressMeter -            done   8995212.0    13.0 s       1.0 s      100.0%    13.0 s       0.0 s
[2016-04-15T00:06Z] INFO  17:06:58,099 ProgressMeter - Total runtime 13.03 secs, 0.22 min, 0.00 hours
[2016-04-15T00:06Z] INFO  17:06:58,103 MicroScheduler - 27524 reads were filtered out during the traversal out of approximately 192236 total reads (14.32%)
[2016-04-15T00:06Z] INFO  17:06:58,104 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:06Z] INFO  17:06:58,105 MicroScheduler -   -> 474 reads (0.25% of total) failing BadMateFilter
[2016-04-15T00:06Z] INFO  17:06:58,106 MicroScheduler -   -> 13878 reads (7.22% of total) failing DuplicateReadFilter
[2016-04-15T00:06Z] INFO  17:06:58,106 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:06Z] INFO  17:06:58,107 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:06Z] INFO  17:06:58,108 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:06Z] INFO  17:06:58,108 MicroScheduler -   -> 13172 reads (6.85% of total) failing MappingQualityZeroFilter
[2016-04-15T00:06Z] INFO  17:06:58,109 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:06Z] INFO  17:06:58,117 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:06Z] INFO  17:06:58,117 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:06Z] INFO  17:06:58,118 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:06Z] INFO  17:06:58,118 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:06Z] INFO  17:06:58,118 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-15T00:06Z] INFO  17:06:58,119 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:06Z] INFO  17:06:58,267 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:06Z] INFO  17:06:59,469 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-15T00:06Z] INFO  17:06:59,477 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:06Z] INFO  17:06:59,479 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:06Z] INFO  17:06:59,479 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:06Z] INFO  17:06:59,479 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:06Z] INFO  17:06:59,483 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/2/R14-18106_kapa-NGv3-PE100-NGv3-sort-2_31135088_46706841-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/2/tx/tmpm1PUtF/R14-18106_kapa-NGv3-PE100-NGv3-sort-2_31135088_46706841-prep-prealign-realign.intervals -l INFO -L 2:31135089-46706841 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:06Z] INFO  17:06:59,495 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:06Z] INFO  17:06:59,496 HelpFormatter - Date/Time: 2016/04/14 17:06:59
[2016-04-15T00:06Z] INFO  17:06:59,497 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:06Z] INFO  17:06:59,497 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:06Z] INFO  17:06:59,501 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:06Z] GATK: realign ('1', 240255409, 249250621) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:06Z] INFO  17:06:59,535 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:06Z] INFO  17:06:59,544 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:06Z] INFO  17:06:59,549 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:06Z] GATK: realign ('2', 0, 15514844) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:06Z] INFO  17:06:59,586 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:06Z] INFO  17:06:59,586 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.04
[2016-04-15T00:06Z] INFO  17:06:59,600 IntervalUtils - Processing 16283984 bp from intervals
[2016-04-15T00:06Z] INFO  17:06:59,704 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:06Z] INFO  17:06:59,707 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:06Z] INFO  17:06:59,708 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:06Z] INFO  17:06:59,708 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:06Z] INFO  17:06:59,713 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/1/R14-18106_kapa-NGv3-PE100-NGv3-sort-1_207641871_223156451-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/1/R14-18106_kapa-NGv3-PE100-NGv3-sort-1_207641871_223156451-prep-prealign-realign.intervals -L 1:207641872-223156451 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/1/tx/tmpzbLs4P/R14-18106_kapa-NGv3-PE100-NGv3-sort-1_207641871_223156451-prep.bam
[2016-04-15T00:06Z] INFO  17:06:59,734 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:06Z] INFO  17:06:59,734 HelpFormatter - Date/Time: 2016/04/14 17:06:59
[2016-04-15T00:06Z] INFO  17:06:59,735 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:06Z] INFO  17:06:59,735 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:06Z] INFO  17:06:59,752 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:06Z] INFO  17:06:59,752 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@41fd9d8e
[2016-04-15T00:06Z] INFO  17:06:59,822 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T00:06Z] INFO  17:06:59,832 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:06Z] INFO  17:06:59,885 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-15T00:06Z] INFO  17:06:59,965 ProgressMeter -            done    414783.0    50.0 s       2.0 m      100.0%    50.0 s       0.0 s
[2016-04-15T00:06Z] INFO  17:06:59,966 ProgressMeter - Total runtime 50.34 secs, 0.84 min, 0.01 hours
[2016-04-15T00:06Z] INFO  17:06:59,967 MicroScheduler - 237 reads were filtered out during the traversal out of approximately 415020 total reads (0.06%)
[2016-04-15T00:06Z] INFO  17:06:59,968 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:06Z] INFO  17:06:59,968 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:06Z] INFO  17:06:59,969 MicroScheduler -   -> 237 reads (0.06% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:07Z] INFO  17:07:00,020 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:07Z] INFO  17:07:00,140 IntervalUtils - Processing 15571753 bp from intervals
[2016-04-15T00:07Z] INFO  17:07:00,143 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:07Z] INFO  17:07:00,144 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:07Z] INFO  17:07:00,145 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:07Z] WARN  17:07:00,145 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:07Z] INFO  17:07:00,146 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:07Z] INFO  17:07:00,159 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:07Z] INFO  17:07:00,170 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:07Z] INFO  17:07:00,182 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:07Z] INFO  17:07:00,216 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:07Z] INFO  17:07:00,256 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-15T00:07Z] INFO  17:07:00,383 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:07Z] INFO  17:07:00,456 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:07Z] INFO  17:07:00,456 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:07Z] INFO  17:07:00,457 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:07Z] INFO  17:07:00,457 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:07Z] INFO  17:07:00,669 IntervalUtils - Processing 15514580 bp from intervals
[2016-04-15T00:07Z] WARN  17:07:00,684 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:07Z] INFO  17:07:00,756 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:07Z] INFO  17:07:00,887 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:07Z] INFO  17:07:00,888 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:07Z] INFO  17:07:00,889 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:07Z] INFO  17:07:00,890 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:07Z] INFO  17:07:01,022 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:07Z] INFO  17:07:01,166 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:07Z] INFO  17:07:01,481 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:07Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-1_223162737_240072524-prep-prealign.bam
[2016-04-15T00:07Z] INFO  17:07:02,668 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:07Z] INFO  17:07:02,672 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:07Z] INFO  17:07:02,672 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:07Z] INFO  17:07:02,673 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:07Z] INFO  17:07:02,678 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/1/R14-18106_kapa-NGv3-PE100-NGv3-sort-1_240255409_249250621-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/1/R14-18106_kapa-NGv3-PE100-NGv3-sort-1_240255409_249250621-prep-prealign-realign.intervals -L 1:240255410-249250621 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/1/tx/tmpg0rg0O/R14-18106_kapa-NGv3-PE100-NGv3-sort-1_240255409_249250621-prep.bam
[2016-04-15T00:07Z] INFO  17:07:02,701 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:07Z] INFO  17:07:02,702 HelpFormatter - Date/Time: 2016/04/14 17:07:02
[2016-04-15T00:07Z] INFO  17:07:02,703 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:07Z] INFO  17:07:02,707 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:07Z] GATK RealignerTargetCreator: R14-18106_kapa-NGv3-PE100-NGv3-sort-1_223162737_240072524-prep-prealign.bam 1:223162738-240072524
[2016-04-15T00:07Z] GATK: RealignerTargetCreator
[2016-04-15T00:07Z] INFO  17:07:02,904 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:07Z] INFO  17:07:02,986 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:07Z] INFO  17:07:02,989 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:07Z] INFO  17:07:02,990 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:07Z] INFO  17:07:02,990 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:07Z] INFO  17:07:02,995 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/2/R14-18106_kapa-NGv3-PE100-NGv3-sort-2_0_15514844-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/2/R14-18106_kapa-NGv3-PE100-NGv3-sort-2_0_15514844-prep-prealign-realign.intervals -L 2:1-15514844 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/2/tx/tmpHttDt0/R14-18106_kapa-NGv3-PE100-NGv3-sort-2_0_15514844-prep.bam
[2016-04-15T00:07Z] INFO  17:07:03,009 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:07Z] INFO  17:07:03,018 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:07Z] INFO  17:07:03,032 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:07Z] INFO  17:07:03,033 HelpFormatter - Date/Time: 2016/04/14 17:07:02
[2016-04-15T00:07Z] INFO  17:07:03,034 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:07Z] INFO  17:07:03,034 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:07Z] INFO  17:07:03,098 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-15T00:07Z] INFO  17:07:03,240 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:07Z] INFO  17:07:03,380 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:07Z] INFO  17:07:03,389 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:07Z] INFO  17:07:03,469 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-15T00:07Z] INFO  17:07:03,515 IntervalUtils - Processing 8995212 bp from intervals
[2016-04-15T00:07Z] WARN  17:07:03,531 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:07Z] INFO  17:07:03,622 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:07Z] INFO  17:07:03,770 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:07Z] INFO  17:07:03,772 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:07Z] INFO  17:07:03,772 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:07Z] INFO  17:07:03,773 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:07Z] INFO  17:07:03,869 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@41fd9d8e
[2016-04-15T00:07Z] INFO  17:07:03,976 IntervalUtils - Processing 15514844 bp from intervals
[2016-04-15T00:07Z] INFO  17:07:03,986 ProgressMeter -       1:9780376    400007.0    30.0 s      75.0 s       62.9%    47.0 s      17.0 s
[2016-04-15T00:07Z] WARN  17:07:03,992 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:07Z] INFO  17:07:03,992 ProgressMeter -            done    346609.0    43.0 s       2.1 m      100.0%    43.0 s       0.0 s
[2016-04-15T00:07Z] INFO  17:07:03,993 ProgressMeter - Total runtime 43.72 secs, 0.73 min, 0.01 hours
[2016-04-15T00:07Z] INFO  17:07:03,993 MicroScheduler - 198 reads were filtered out during the traversal out of approximately 346807 total reads (0.06%)
[2016-04-15T00:07Z] INFO  17:07:03,994 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:07Z] INFO  17:07:03,994 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:07Z] INFO  17:07:03,994 MicroScheduler -   -> 198 reads (0.06% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:07Z] INFO  17:07:04,006 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:07Z] INFO  17:07:04,072 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:07Z] INFO  17:07:04,110 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:07Z] INFO  17:07:04,180 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:07Z] INFO  17:07:04,181 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:07Z] INFO  17:07:04,182 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:07Z] INFO  17:07:04,182 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:07Z] INFO  17:07:04,347 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:07Z] INFO  17:07:04,512 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:07Z] INFO  17:07:05,226 ProgressMeter -            done    397516.0    29.0 s      75.0 s      100.0%    29.0 s       0.0 s
[2016-04-15T00:07Z] INFO  17:07:05,227 ProgressMeter - Total runtime 29.90 secs, 0.50 min, 0.01 hours
[2016-04-15T00:07Z] INFO  17:07:05,230 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 397516 total reads (0.00%)
[2016-04-15T00:07Z] INFO  17:07:05,231 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:07Z] INFO  17:07:05,231 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:07Z] INFO  17:07:05,231 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:07Z] INFO  17:07:05,781 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:07Z] INFO  17:07:05,785 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:07Z] INFO  17:07:05,785 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:07Z] INFO  17:07:05,786 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:07Z] INFO  17:07:05,791 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/1/R14-18106_kapa-NGv3-PE100-NGv3-sort-1_223162737_240072524-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/1/tx/tmpYev5sX/R14-18106_kapa-NGv3-PE100-NGv3-sort-1_223162737_240072524-prep-prealign-realign.intervals -l INFO -L 1:223162738-240072524 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:07Z] INFO  17:07:05,806 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:07Z] INFO  17:07:05,807 HelpFormatter - Date/Time: 2016/04/14 17:07:05
[2016-04-15T00:07Z] INFO  17:07:05,808 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:07Z] INFO  17:07:05,808 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:07Z] INFO  17:07:05,861 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:07Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-2_15519725_31133925-prep-prealign.bam
[2016-04-15T00:07Z] INFO  17:07:05,908 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:07Z] INFO  17:07:06,140 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T00:07Z] INFO  17:07:06,150 ProgressMeter -            done    384925.0    24.0 s      63.0 s      100.0%    24.0 s       0.0 s
[2016-04-15T00:07Z] INFO  17:07:06,150 ProgressMeter - Total runtime 24.56 secs, 0.41 min, 0.01 hours
[2016-04-15T00:07Z] INFO  17:07:06,152 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:07Z] INFO  17:07:06,153 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 384925 total reads (0.00%)
[2016-04-15T00:07Z] INFO  17:07:06,154 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:07Z] INFO  17:07:06,154 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:07Z] INFO  17:07:06,154 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:07Z] INFO  17:07:06,194 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.04
[2016-04-15T00:07Z] INFO  17:07:06,544 IntervalUtils - Processing 16909787 bp from intervals
[2016-04-15T00:07Z] WARN  17:07:06,550 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:07Z] INFO  17:07:06,632 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:07Z] INFO  17:07:06,696 ProgressMeter -      2:74141899    200002.0    30.0 s       2.5 m       69.7%    43.0 s      13.0 s
[2016-04-15T00:07Z] INFO  17:07:06,873 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:07Z] INFO  17:07:06,874 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:07Z] INFO  17:07:06,874 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:07Z] GATK RealignerTargetCreator: R14-18106_kapa-NGv3-PE100-NGv3-sort-2_15519725_31133925-prep-prealign.bam 2:15519726-31133925
[2016-04-15T00:07Z] INFO  17:07:06,875 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:07Z] GATK: RealignerTargetCreator
[2016-04-15T00:07Z] INFO  17:07:06,916 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:07Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-1_108994811_143767848-prep.bam
[2016-04-15T00:07Z] INFO  17:07:07,648 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:07Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-1_159504867_175046963-prep.bam
[2016-04-15T00:07Z] GATK pre-alignment ('2', 95538561, 111273222) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:07Z] GATK pre-alignment ('2', 111281072, 127413888) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:07Z] INFO  17:07:09,792 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:07Z] INFO  17:07:09,794 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:07Z] INFO  17:07:09,794 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:07Z] INFO  17:07:09,795 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:07Z] INFO  17:07:09,810 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/2/R14-18106_kapa-NGv3-PE100-NGv3-sort-2_15519725_31133925-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/2/tx/tmp8rrifn/R14-18106_kapa-NGv3-PE100-NGv3-sort-2_15519725_31133925-prep-prealign-realign.intervals -l INFO -L 2:15519726-31133925 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:07Z] INFO  17:07:09,823 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:07Z] INFO  17:07:09,823 HelpFormatter - Date/Time: 2016/04/14 17:07:09
[2016-04-15T00:07Z] INFO  17:07:09,823 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:07Z] INFO  17:07:09,824 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:07Z] INFO  17:07:09,971 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:07Z] INFO  17:07:10,229 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T00:07Z] INFO  17:07:10,238 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:07Z] INFO  17:07:10,306 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-15T00:07Z] INFO  17:07:10,343 ProgressMeter -            done   1.5520574E7    16.0 s       1.0 s      100.0%    16.0 s       0.0 s
[2016-04-15T00:07Z] INFO  17:07:10,344 ProgressMeter - Total runtime 16.58 secs, 0.28 min, 0.00 hours
[2016-04-15T00:07Z] INFO  17:07:10,348 MicroScheduler - 14044 reads were filtered out during the traversal out of approximately 176884 total reads (7.94%)
[2016-04-15T00:07Z] INFO  17:07:10,348 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:07Z] INFO  17:07:10,349 MicroScheduler -   -> 606 reads (0.34% of total) failing BadMateFilter
[2016-04-15T00:07Z] INFO  17:07:10,349 MicroScheduler -   -> 13111 reads (7.41% of total) failing DuplicateReadFilter
[2016-04-15T00:07Z] INFO  17:07:10,349 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:07Z] INFO  17:07:10,350 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:07Z] INFO  17:07:10,350 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:07Z] INFO  17:07:10,350 MicroScheduler -   -> 327 reads (0.18% of total) failing MappingQualityZeroFilter
[2016-04-15T00:07Z] INFO  17:07:10,350 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:07Z] INFO  17:07:10,351 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-15T00:07Z] INFO  17:07:10,351 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:07Z] INFO  17:07:10,578 IntervalUtils - Processing 15614200 bp from intervals
[2016-04-15T00:07Z] WARN  17:07:10,584 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:07Z] INFO  17:07:10,785 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:07Z] INFO  17:07:10,980 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:07Z] INFO  17:07:10,982 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:07Z] INFO  17:07:10,982 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:07Z] INFO  17:07:10,983 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:07Z] INFO  17:07:10,991 HelpFormatter - Program Args: -T PrintReads -L 2:95538562-111273222 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/2/tx/tmphP4HYW/R14-18106_kapa-NGv3-PE100-NGv3-sort-2_95538561_111273222-prep-prealign.bam
[2016-04-15T00:07Z] INFO  17:07:10,989 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:07Z] INFO  17:07:10,996 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:07Z] INFO  17:07:11,002 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:07Z] INFO  17:07:11,003 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:07Z] INFO  17:07:11,008 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:07Z] INFO  17:07:11,009 HelpFormatter - Date/Time: 2016/04/14 17:07:10
[2016-04-15T00:07Z] INFO  17:07:11,009 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:07Z] INFO  17:07:11,010 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:07Z] INFO  17:07:11,170 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:07Z] INFO  17:07:11,611 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:07Z] GATK: realign ('2', 46707543, 62228117) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:07Z] INFO  17:07:11,640 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:07Z] INFO  17:07:11,643 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:07Z] INFO  17:07:11,644 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:07Z] INFO  17:07:11,645 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:07Z] INFO  17:07:11,649 HelpFormatter - Program Args: -T PrintReads -L 2:111281073-127413888 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/2/tx/tmpPq_P0S/R14-18106_kapa-NGv3-PE100-NGv3-sort-2_111281072_127413888-prep-prealign.bam
[2016-04-15T00:07Z] INFO  17:07:11,666 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:07Z] INFO  17:07:11,667 HelpFormatter - Date/Time: 2016/04/14 17:07:11
[2016-04-15T00:07Z] INFO  17:07:11,667 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:07Z] INFO  17:07:11,668 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:07Z] INFO  17:07:11,883 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:07Z] INFO  17:07:12,292 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-15T00:07Z] INFO  17:07:12,352 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:07Z] INFO  17:07:12,362 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:07Z] INFO  17:07:12,408 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-15T00:07Z] INFO  17:07:12,422 IntervalUtils - Processing 15734661 bp from intervals
[2016-04-15T00:07Z] INFO  17:07:12,505 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:07Z] INFO  17:07:12,820 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:07Z] INFO  17:07:12,822 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:07Z] INFO  17:07:12,822 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:07Z] INFO  17:07:12,823 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:07Z] INFO  17:07:12,848 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:07Z] INFO  17:07:13,003 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:07Z] INFO  17:07:13,032 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-15T00:07Z] INFO  17:07:13,117 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:07Z] INFO  17:07:13,126 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:07Z] INFO  17:07:13,176 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-15T00:07Z] INFO  17:07:13,193 IntervalUtils - Processing 16132816 bp from intervals
[2016-04-15T00:07Z] INFO  17:07:13,272 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:07Z] INFO  17:07:13,588 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:07Z] INFO  17:07:13,589 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:07Z] INFO  17:07:13,601 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:07Z] INFO  17:07:13,602 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:07Z] INFO  17:07:13,634 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:07Z] INFO  17:07:13,766 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:07Z] INFO  17:07:14,111 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:07Z] INFO  17:07:14,114 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:07Z] INFO  17:07:14,115 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:07Z] INFO  17:07:14,115 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:07Z] INFO  17:07:14,120 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/2/R14-18106_kapa-NGv3-PE100-NGv3-sort-2_46707543_62228117-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/2/R14-18106_kapa-NGv3-PE100-NGv3-sort-2_46707543_62228117-prep-prealign-realign.intervals -L 2:46707544-62228117 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/2/tx/tmp5NHGfe/R14-18106_kapa-NGv3-PE100-NGv3-sort-2_46707543_62228117-prep.bam
[2016-04-15T00:07Z] INFO  17:07:14,130 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:07Z] INFO  17:07:14,136 HelpFormatter - Date/Time: 2016/04/14 17:07:14
[2016-04-15T00:07Z] INFO  17:07:14,137 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:07Z] INFO  17:07:14,137 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:07Z] INFO  17:07:14,423 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:07Z] INFO  17:07:14,577 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:07Z] INFO  17:07:14,602 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:07Z] INFO  17:07:14,702 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.10
[2016-04-15T00:07Z] INFO  17:07:15,077 IntervalUtils - Processing 15520574 bp from intervals
[2016-04-15T00:07Z] WARN  17:07:15,082 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:07Z] INFO  17:07:15,150 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:07Z] INFO  17:07:15,286 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:07Z] INFO  17:07:15,287 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:07Z] INFO  17:07:15,288 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:07Z] INFO  17:07:15,288 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:07Z] INFO  17:07:15,452 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:07Z] INFO  17:07:15,653 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:07Z] INFO  17:07:16,484 ProgressMeter -            done    150486.0    12.0 s      81.0 s       99.9%    12.0 s       0.0 s
[2016-04-15T00:07Z] INFO  17:07:16,484 ProgressMeter - Total runtime 12.30 secs, 0.21 min, 0.00 hours
[2016-04-15T00:07Z] INFO  17:07:16,488 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 150486 total reads (0.00%)
[2016-04-15T00:07Z] INFO  17:07:16,488 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:07Z] INFO  17:07:16,489 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:07Z] INFO  17:07:16,489 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:07Z] INFO  17:07:16,751 ProgressMeter -            done    737705.0    43.0 s      58.0 s      100.0%    43.0 s       0.0 s
[2016-04-15T00:07Z] INFO  17:07:16,751 ProgressMeter - Total runtime 43.07 secs, 0.72 min, 0.01 hours
[2016-04-15T00:07Z] INFO  17:07:16,756 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 737705 total reads (0.00%)
[2016-04-15T00:07Z] INFO  17:07:16,757 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:07Z] INFO  17:07:16,757 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:07Z] INFO  17:07:16,757 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:07Z] INFO  17:07:17,032 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@41fd9d8e
[2016-04-15T00:07Z] INFO  17:07:17,220 ProgressMeter -            done    320315.0    40.0 s       2.1 m      100.0%    40.0 s       0.0 s
[2016-04-15T00:07Z] INFO  17:07:17,221 ProgressMeter - Total runtime 40.54 secs, 0.68 min, 0.01 hours
[2016-04-15T00:07Z] INFO  17:07:17,221 MicroScheduler - 216 reads were filtered out during the traversal out of approximately 320531 total reads (0.07%)
[2016-04-15T00:07Z] INFO  17:07:17,221 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:07Z] INFO  17:07:17,222 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:07Z] INFO  17:07:17,222 MicroScheduler -   -> 216 reads (0.07% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:07Z] INFO  17:07:17,512 ProgressMeter -     1:154931871    800013.0   120.0 s       2.5 m       71.1%     2.8 m      48.0 s
[2016-04-15T00:07Z] INFO  17:07:17,550 ProgressMeter -            done    190949.0    13.0 s      72.0 s       99.6%    13.0 s       0.0 s
[2016-04-15T00:07Z] INFO  17:07:17,551 ProgressMeter - Total runtime 13.78 secs, 0.23 min, 0.00 hours
[2016-04-15T00:07Z] INFO  17:07:17,557 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 190949 total reads (0.00%)
[2016-04-15T00:07Z] INFO  17:07:17,558 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:07Z] INFO  17:07:17,559 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:07Z] INFO  17:07:17,560 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:07Z] INFO  17:07:18,217 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:07Z] INFO  17:07:18,251 ProgressMeter -      1:21936700    300003.0    32.0 s     107.0 s       40.9%    78.0 s      46.0 s
[2016-04-15T00:07Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-1_0_15541927-prep.bam
[2016-04-15T00:07Z] INFO  17:07:18,283 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:07Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-2_0_15514844-prep.bam
[2016-04-15T00:07Z] INFO  17:07:18,668 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:07Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-2_62362965_79253295-prep-prealign.bam
[2016-04-15T00:07Z] INFO  17:07:18,885 ProgressMeter -            done    246218.0    17.0 s      73.0 s      100.0%    17.0 s       0.0 s
[2016-04-15T00:07Z] INFO  17:07:18,885 ProgressMeter - Total runtime 18.00 secs, 0.30 min, 0.00 hours
[2016-04-15T00:07Z] INFO  17:07:18,889 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 246218 total reads (0.00%)
[2016-04-15T00:07Z] INFO  17:07:18,890 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:07Z] INFO  17:07:18,891 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:07Z] INFO  17:07:18,891 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:07Z] GATK pre-alignment ('2', 127433207, 143643105) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:07Z] INFO  17:07:19,153 ProgressMeter -            done   1.5571753E7    18.0 s       1.0 s      100.0%    18.0 s       0.0 s
[2016-04-15T00:07Z] INFO  17:07:19,153 ProgressMeter - Total runtime 18.70 secs, 0.31 min, 0.01 hours
[2016-04-15T00:07Z] INFO  17:07:19,157 MicroScheduler - 21293 reads were filtered out during the traversal out of approximately 224413 total reads (9.49%)
[2016-04-15T00:07Z] INFO  17:07:19,158 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:07Z] INFO  17:07:19,164 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:07Z] INFO  17:07:19,165 MicroScheduler -   -> 1767 reads (0.79% of total) failing BadMateFilter
[2016-04-15T00:07Z] INFO  17:07:19,166 MicroScheduler -   -> 16401 reads (7.31% of total) failing DuplicateReadFilter
[2016-04-15T00:07Z] INFO  17:07:19,166 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:07Z] INFO  17:07:19,167 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:07Z] INFO  17:07:19,167 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:07Z] INFO  17:07:19,167 MicroScheduler -   -> 3125 reads (1.39% of total) failing MappingQualityZeroFilter
[2016-04-15T00:07Z] INFO  17:07:19,168 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:07Z] INFO  17:07:19,168 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-15T00:07Z] INFO  17:07:19,169 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:07Z] INFO  17:07:19,178 ProgressMeter -            done   1.5511908E7    21.0 s       1.0 s      100.0%    21.0 s       0.0 s
[2016-04-15T00:07Z] INFO  17:07:19,179 ProgressMeter - Total runtime 21.06 secs, 0.35 min, 0.01 hours
[2016-04-15T00:07Z] INFO  17:07:19,184 MicroScheduler - 35125 reads were filtered out during the traversal out of approximately 398052 total reads (8.82%)
[2016-04-15T00:07Z] INFO  17:07:19,184 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:07Z] INFO  17:07:19,185 MicroScheduler -   -> 966 reads (0.24% of total) failing BadMateFilter
[2016-04-15T00:07Z] INFO  17:07:19,185 MicroScheduler -   -> 29210 reads (7.34% of total) failing DuplicateReadFilter
[2016-04-15T00:07Z] INFO  17:07:19,185 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:07Z] INFO  17:07:19,186 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:07Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-1_240255409_249250621-prep.bam
[2016-04-15T00:07Z] INFO  17:07:19,186 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:07Z] INFO  17:07:19,198 MicroScheduler -   -> 4949 reads (1.24% of total) failing MappingQualityZeroFilter
[2016-04-15T00:07Z] INFO  17:07:19,199 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:07Z] INFO  17:07:19,200 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-15T00:07Z] INFO  17:07:19,200 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:07Z] GATK RealignerTargetCreator: R14-18106_kapa-NGv3-PE100-NGv3-sort-2_62362965_79253295-prep-prealign.bam 2:62362966-79253295
[2016-04-15T00:07Z] GATK: RealignerTargetCreator
[2016-04-15T00:07Z] GATK pre-alignment ('2', 143676177, 159195597) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:07Z] INFO  17:07:20,521 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:07Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-1_207641871_223156451-prep.bam
[2016-04-15T00:07Z] INFO  17:07:20,664 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:07Z] GATK: realign ('2', 31135088, 46706841) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:07Z] INFO  17:07:20,773 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:07Z] GATK: realign ('1', 192128349, 207640257) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:07Z] GATK pre-alignment ('2', 159196753, 174774985) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:07Z] GATK pre-alignment ('2', 174777797, 190306304) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:07Z] INFO  17:07:22,059 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:07Z] INFO  17:07:22,063 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:07Z] INFO  17:07:22,063 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:07Z] INFO  17:07:22,063 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:07Z] INFO  17:07:22,068 HelpFormatter - Program Args: -T PrintReads -L 2:127433208-143643105 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/2/tx/tmpE_gslB/R14-18106_kapa-NGv3-PE100-NGv3-sort-2_127433207_143643105-prep-prealign.bam
[2016-04-15T00:07Z] INFO  17:07:22,078 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:07Z] INFO  17:07:22,078 HelpFormatter - Date/Time: 2016/04/14 17:07:22
[2016-04-15T00:07Z] INFO  17:07:22,078 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:07Z] INFO  17:07:22,079 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:07Z] INFO  17:07:22,260 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:07Z] INFO  17:07:22,668 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:07Z] INFO  17:07:22,671 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:07Z] INFO  17:07:22,671 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:07Z] INFO  17:07:22,672 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:07Z] INFO  17:07:22,676 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/2/R14-18106_kapa-NGv3-PE100-NGv3-sort-2_62362965_79253295-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/2/tx/tmpSDZjHD/R14-18106_kapa-NGv3-PE100-NGv3-sort-2_62362965_79253295-prep-prealign-realign.intervals -l INFO -L 2:62362966-79253295 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:07Z] INFO  17:07:22,693 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:07Z] INFO  17:07:22,693 HelpFormatter - Date/Time: 2016/04/14 17:07:22
[2016-04-15T00:07Z] INFO  17:07:22,693 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:07Z] INFO  17:07:22,693 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:07Z] INFO  17:07:22,779 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:07Z] INFO  17:07:23,007 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T00:07Z] INFO  17:07:23,020 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:07Z] INFO  17:07:23,082 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-15T00:07Z] INFO  17:07:23,237 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:07Z] INFO  17:07:23,240 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:07Z] INFO  17:07:23,241 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:07Z] INFO  17:07:23,241 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:07Z] INFO  17:07:23,246 HelpFormatter - Program Args: -T PrintReads -L 2:143676178-159195597 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/2/tx/tmp_Vm7eQ/R14-18106_kapa-NGv3-PE100-NGv3-sort-2_143676177_159195597-prep-prealign.bam
[2016-04-15T00:07Z] INFO  17:07:23,280 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:07Z] INFO  17:07:23,280 HelpFormatter - Date/Time: 2016/04/14 17:07:23
[2016-04-15T00:07Z] INFO  17:07:23,280 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:07Z] INFO  17:07:23,280 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:07Z] INFO  17:07:23,470 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-15T00:07Z] INFO  17:07:23,494 IntervalUtils - Processing 16890330 bp from intervals
[2016-04-15T00:07Z] WARN  17:07:23,499 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:07Z] INFO  17:07:23,525 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:07Z] INFO  17:07:23,534 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:07Z] INFO  17:07:23,565 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:07Z] INFO  17:07:23,566 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.03
[2016-04-15T00:07Z] INFO  17:07:23,580 IntervalUtils - Processing 16209898 bp from intervals
[2016-04-15T00:07Z] INFO  17:07:23,643 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:07Z] INFO  17:07:23,673 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:07Z] INFO  17:07:23,739 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:07Z] INFO  17:07:23,740 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:07Z] INFO  17:07:23,741 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:07Z] INFO  17:07:23,741 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:07Z] INFO  17:07:23,895 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:07Z] INFO  17:07:23,898 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:07Z] INFO  17:07:23,899 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:07Z] INFO  17:07:23,900 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:07Z] INFO  17:07:23,904 HelpFormatter - Program Args: -T PrintReads -L 2:159196754-174774985 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/2/tx/tmpvdxNkU/R14-18106_kapa-NGv3-PE100-NGv3-sort-2_159196753_174774985-prep-prealign.bam
[2016-04-15T00:07Z] INFO  17:07:23,915 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:07Z] INFO  17:07:23,916 HelpFormatter - Date/Time: 2016/04/14 17:07:23
[2016-04-15T00:07Z] INFO  17:07:23,917 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:07Z] INFO  17:07:23,917 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:07Z] INFO  17:07:23,917 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:07Z] INFO  17:07:23,921 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:07Z] INFO  17:07:23,921 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:07Z] INFO  17:07:23,922 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:07Z] INFO  17:07:23,926 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/2/R14-18106_kapa-NGv3-PE100-NGv3-sort-2_31135088_46706841-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/2/R14-18106_kapa-NGv3-PE100-NGv3-sort-2_31135088_46706841-prep-prealign-realign.intervals -L 2:31135089-46706841 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/2/tx/tmpcfcUdd/R14-18106_kapa-NGv3-PE100-NGv3-sort-2_31135088_46706841-prep.bam
[2016-04-15T00:07Z] INFO  17:07:23,936 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:07Z] INFO  17:07:23,937 HelpFormatter - Date/Time: 2016/04/14 17:07:23
[2016-04-15T00:07Z] INFO  17:07:23,937 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:07Z] INFO  17:07:23,937 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:07Z] INFO  17:07:23,986 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:07Z] INFO  17:07:23,987 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:07Z] INFO  17:07:23,988 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:07Z] INFO  17:07:23,989 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:07Z] INFO  17:07:23,992 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:07Z] INFO  17:07:24,003 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:07Z] INFO  17:07:23,996 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:07Z] INFO  17:07:24,004 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:07Z] INFO  17:07:24,005 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:07Z] INFO  17:07:24,017 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/1/R14-18106_kapa-NGv3-PE100-NGv3-sort-1_192128349_207640257-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/1/R14-18106_kapa-NGv3-PE100-NGv3-sort-1_192128349_207640257-prep-prealign-realign.intervals -L 1:192128350-207640257 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/1/tx/tmpSYsLjX/R14-18106_kapa-NGv3-PE100-NGv3-sort-1_192128349_207640257-prep.bam
[2016-04-15T00:07Z] INFO  17:07:24,042 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:07Z] INFO  17:07:24,043 HelpFormatter - Date/Time: 2016/04/14 17:07:23
[2016-04-15T00:07Z] INFO  17:07:24,043 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:07Z] INFO  17:07:24,048 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:07Z] INFO  17:07:24,078 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:07Z] INFO  17:07:24,144 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:07Z] INFO  17:07:24,151 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:07Z] INFO  17:07:24,257 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:07Z] INFO  17:07:24,256 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:07Z] INFO  17:07:24,259 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:07Z] INFO  17:07:24,260 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:07Z] INFO  17:07:24,260 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:07Z] INFO  17:07:24,265 HelpFormatter - Program Args: -T PrintReads -L 2:174777798-190306304 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/2/tx/tmpsT_AXe/R14-18106_kapa-NGv3-PE100-NGv3-sort-2_174777797_190306304-prep-prealign.bam
[2016-04-15T00:07Z] INFO  17:07:24,279 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:07Z] INFO  17:07:24,280 HelpFormatter - Date/Time: 2016/04/14 17:07:24
[2016-04-15T00:07Z] INFO  17:07:24,280 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:07Z] INFO  17:07:24,281 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:07Z] INFO  17:07:24,315 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:07Z] INFO  17:07:24,336 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:07Z] INFO  17:07:24,358 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:07Z] INFO  17:07:24,369 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:07Z] INFO  17:07:24,422 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-15T00:07Z] INFO  17:07:24,440 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-15T00:07Z] INFO  17:07:24,531 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:07Z] INFO  17:07:24,844 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-15T00:07Z] INFO  17:07:24,876 IntervalUtils - Processing 15571753 bp from intervals
[2016-04-15T00:07Z] WARN  17:07:24,883 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:07Z] INFO  17:07:24,918 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:07Z] INFO  17:07:24,927 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:07Z] INFO  17:07:24,974 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-15T00:07Z] INFO  17:07:24,988 IntervalUtils - Processing 15519420 bp from intervals
[2016-04-15T00:07Z] INFO  17:07:25,001 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:07Z] INFO  17:07:25,020 IntervalUtils - Processing 15511908 bp from intervals
[2016-04-15T00:07Z] WARN  17:07:25,025 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:07Z] INFO  17:07:25,088 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:07Z] INFO  17:07:25,109 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:07Z] INFO  17:07:25,137 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:07Z] INFO  17:07:25,138 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:07Z] INFO  17:07:25,139 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:07Z] INFO  17:07:25,140 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:07Z] INFO  17:07:25,325 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:07Z] INFO  17:07:25,326 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:07Z] INFO  17:07:25,327 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:07Z] INFO  17:07:25,327 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:07Z] INFO  17:07:25,327 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:07Z] INFO  17:07:25,361 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-15T00:07Z] INFO  17:07:25,464 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:07Z] INFO  17:07:25,469 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:07Z] INFO  17:07:25,471 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:07Z] INFO  17:07:25,471 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:07Z] INFO  17:07:25,472 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:07Z] INFO  17:07:25,473 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:07Z] INFO  17:07:25,494 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:07Z] INFO  17:07:25,494 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:07Z] INFO  17:07:25,546 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-15T00:07Z] INFO  17:07:25,581 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:07Z] INFO  17:07:25,581 IntervalUtils - Processing 15578232 bp from intervals
[2016-04-15T00:07Z] INFO  17:07:25,644 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:07Z] INFO  17:07:25,663 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:07Z] INFO  17:07:25,744 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-15T00:07Z] INFO  17:07:25,812 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:07Z] INFO  17:07:25,843 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:07Z] INFO  17:07:25,850 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:07Z] INFO  17:07:25,885 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.04
[2016-04-15T00:07Z] INFO  17:07:25,899 IntervalUtils - Processing 15528507 bp from intervals
[2016-04-15T00:07Z] INFO  17:07:25,976 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:07Z] INFO  17:07:25,977 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:07Z] INFO  17:07:25,977 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:07Z] INFO  17:07:25,978 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:07Z] INFO  17:07:25,979 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:07Z] INFO  17:07:25,992 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:07Z] INFO  17:07:26,147 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:07Z] INFO  17:07:26,310 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:07Z] INFO  17:07:26,311 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:07Z] INFO  17:07:26,312 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:07Z] INFO  17:07:26,313 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:07Z] INFO  17:07:26,329 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:07Z] INFO  17:07:26,360 ProgressMeter -      1:41006430    400006.0    32.0 s      80.0 s       63.2%    50.0 s      18.0 s
[2016-04-15T00:07Z] INFO  17:07:26,488 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:07Z] INFO  17:07:29,701 ProgressMeter -            done   1.6909787E7    22.0 s       1.0 s      100.0%    22.0 s       0.0 s
[2016-04-15T00:07Z] INFO  17:07:29,701 ProgressMeter - Total runtime 22.83 secs, 0.38 min, 0.01 hours
[2016-04-15T00:07Z] INFO  17:07:29,705 MicroScheduler - 34187 reads were filtered out during the traversal out of approximately 417037 total reads (8.20%)
[2016-04-15T00:07Z] INFO  17:07:29,706 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:07Z] INFO  17:07:29,706 MicroScheduler -   -> 1029 reads (0.25% of total) failing BadMateFilter
[2016-04-15T00:07Z] INFO  17:07:29,706 MicroScheduler -   -> 31163 reads (7.47% of total) failing DuplicateReadFilter
[2016-04-15T00:07Z] INFO  17:07:29,707 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:07Z] INFO  17:07:29,707 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:07Z] INFO  17:07:29,707 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:07Z] INFO  17:07:29,707 MicroScheduler -   -> 1995 reads (0.48% of total) failing MappingQualityZeroFilter
[2016-04-15T00:07Z] INFO  17:07:29,707 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:07Z] INFO  17:07:29,708 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-15T00:07Z] INFO  17:07:29,708 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:07Z] INFO  17:07:29,794 ProgressMeter -            done    175689.0    14.0 s      82.0 s      100.0%    14.0 s       0.0 s
[2016-04-15T00:07Z] INFO  17:07:29,794 ProgressMeter - Total runtime 14.51 secs, 0.24 min, 0.00 hours
[2016-04-15T00:07Z] INFO  17:07:29,798 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 175689 total reads (0.00%)
[2016-04-15T00:07Z] INFO  17:07:29,798 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:07Z] INFO  17:07:29,798 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:07Z] INFO  17:07:29,799 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:07Z] INFO  17:07:30,151 ProgressMeter -      2:95483263    200002.0    30.0 s       2.5 m       99.7%    30.0 s       0.0 s
[2016-04-15T00:07Z] INFO  17:07:30,697 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@41fd9d8e
[2016-04-15T00:07Z] INFO  17:07:30,841 ProgressMeter -            done    240579.0    30.0 s       2.1 m      100.0%    30.0 s       0.0 s
[2016-04-15T00:07Z] INFO  17:07:30,841 ProgressMeter - Total runtime 30.70 secs, 0.51 min, 0.01 hours
[2016-04-15T00:07Z] INFO  17:07:30,842 MicroScheduler - 358 reads were filtered out during the traversal out of approximately 240937 total reads (0.15%)
[2016-04-15T00:07Z] INFO  17:07:30,842 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:07Z] INFO  17:07:30,842 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:07Z] INFO  17:07:30,843 MicroScheduler -   -> 358 reads (0.15% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:07Z] INFO  17:07:31,041 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:07Z] GATK: realign ('1', 223162737, 240072524) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:07Z] INFO  17:07:31,316 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:07Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-2_46707543_62228117-prep.bam
[2016-04-15T00:07Z] GATK pre-alignment ('2', 190313104, 205830046) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:07Z] INFO  17:07:32,288 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:07Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-2_79253838_95537822-prep-prealign.bam
[2016-04-15T00:07Z] INFO  17:07:33,077 ProgressMeter -            done   1.56142E7    22.0 s       1.0 s      100.0%    22.0 s       0.0 s
[2016-04-15T00:07Z] INFO  17:07:33,078 ProgressMeter - Total runtime 22.08 secs, 0.37 min, 0.01 hours
[2016-04-15T00:07Z] INFO  17:07:33,081 MicroScheduler - 27649 reads were filtered out during the traversal out of approximately 348478 total reads (7.93%)
[2016-04-15T00:07Z] INFO  17:07:33,081 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:07Z] INFO  17:07:33,082 MicroScheduler -   -> 845 reads (0.24% of total) failing BadMateFilter
[2016-04-15T00:07Z] INFO  17:07:33,082 MicroScheduler -   -> 26391 reads (7.57% of total) failing DuplicateReadFilter
[2016-04-15T00:07Z] INFO  17:07:33,082 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:07Z] INFO  17:07:33,082 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:07Z] INFO  17:07:33,083 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:07Z] INFO  17:07:33,083 MicroScheduler -   -> 413 reads (0.12% of total) failing MappingQualityZeroFilter
[2016-04-15T00:07Z] INFO  17:07:33,083 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:07Z] INFO  17:07:33,083 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-15T00:07Z] INFO  17:07:33,084 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:07Z] GATK RealignerTargetCreator: R14-18106_kapa-NGv3-PE100-NGv3-sort-2_79253838_95537822-prep-prealign.bam 2:79253839-95537822
[2016-04-15T00:07Z] GATK: RealignerTargetCreator
[2016-04-15T00:07Z] INFO  17:07:34,360 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:07Z] INFO  17:07:34,363 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:07Z] INFO  17:07:34,364 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:07Z] INFO  17:07:34,365 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:07Z] INFO  17:07:34,370 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/1/R14-18106_kapa-NGv3-PE100-NGv3-sort-1_223162737_240072524-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/1/R14-18106_kapa-NGv3-PE100-NGv3-sort-1_223162737_240072524-prep-prealign-realign.intervals -L 1:223162738-240072524 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/1/tx/tmpbvIhYb/R14-18106_kapa-NGv3-PE100-NGv3-sort-1_223162737_240072524-prep.bam
[2016-04-15T00:07Z] INFO  17:07:34,384 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:07Z] INFO  17:07:34,388 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:07Z] INFO  17:07:34,385 HelpFormatter - Date/Time: 2016/04/14 17:07:34
[2016-04-15T00:07Z] INFO  17:07:34,390 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:07Z] INFO  17:07:34,390 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:07Z] GATK: realign ('2', 15519725, 31133925) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:07Z] INFO  17:07:34,566 ProgressMeter -            done    764178.0    48.0 s      63.0 s      100.0%    48.0 s       0.0 s
[2016-04-15T00:07Z] INFO  17:07:34,566 ProgressMeter - Total runtime 48.53 secs, 0.81 min, 0.01 hours
[2016-04-15T00:07Z] INFO  17:07:34,570 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 764178 total reads (0.00%)
[2016-04-15T00:07Z] INFO  17:07:34,570 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:07Z] INFO  17:07:34,571 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:07Z] INFO  17:07:34,571 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:07Z] INFO  17:07:34,599 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:07Z] INFO  17:07:34,699 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:07Z] INFO  17:07:34,716 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:07Z] INFO  17:07:34,791 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-15T00:07Z] INFO  17:07:34,831 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:07Z] INFO  17:07:34,834 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:07Z] INFO  17:07:34,835 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:07Z] INFO  17:07:34,835 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:07Z] INFO  17:07:34,840 HelpFormatter - Program Args: -T PrintReads -L 2:190313105-205830046 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/2/tx/tmp14jShB/R14-18106_kapa-NGv3-PE100-NGv3-sort-2_190313104_205830046-prep-prealign.bam
[2016-04-15T00:07Z] INFO  17:07:34,875 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:07Z] INFO  17:07:34,876 HelpFormatter - Date/Time: 2016/04/14 17:07:34
[2016-04-15T00:07Z] INFO  17:07:34,876 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:07Z] INFO  17:07:34,876 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:07Z] INFO  17:07:35,053 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:07Z] INFO  17:07:35,156 IntervalUtils - Processing 16909787 bp from intervals
[2016-04-15T00:07Z] WARN  17:07:35,161 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:07Z] INFO  17:07:35,241 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:07Z] INFO  17:07:35,429 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:07Z] INFO  17:07:35,430 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:07Z] INFO  17:07:35,431 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:07Z] INFO  17:07:35,431 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:07Z] INFO  17:07:35,437 ProgressMeter -            done    679619.0    41.0 s      60.0 s      100.0%    41.0 s       0.0 s
[2016-04-15T00:07Z] INFO  17:07:35,437 ProgressMeter - Total runtime 41.12 secs, 0.69 min, 0.01 hours
[2016-04-15T00:07Z] INFO  17:07:35,441 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 679619 total reads (0.00%)
[2016-04-15T00:07Z] INFO  17:07:35,441 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:07Z] INFO  17:07:35,442 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:07Z] INFO  17:07:35,442 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:07Z] INFO  17:07:35,651 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:07Z] INFO  17:07:35,867 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:07Z] INFO  17:07:36,068 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-15T00:07Z] INFO  17:07:36,122 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:07Z] INFO  17:07:36,125 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:07Z] INFO  17:07:36,126 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:07Z] INFO  17:07:36,126 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:07Z] INFO  17:07:36,131 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/2/R14-18106_kapa-NGv3-PE100-NGv3-sort-2_79253838_95537822-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/2/tx/tmpxw0eFE/R14-18106_kapa-NGv3-PE100-NGv3-sort-2_79253838_95537822-prep-prealign-realign.intervals -l INFO -L 2:79253839-95537822 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:07Z] INFO  17:07:36,134 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:07Z] INFO  17:07:36,143 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:07Z] INFO  17:07:36,154 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:07Z] INFO  17:07:36,155 HelpFormatter - Date/Time: 2016/04/14 17:07:36
[2016-04-15T00:07Z] INFO  17:07:36,155 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:07Z] INFO  17:07:36,156 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:07Z] INFO  17:07:36,194 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:07Z] INFO  17:07:36,196 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-15T00:07Z] INFO  17:07:36,210 IntervalUtils - Processing 15516942 bp from intervals
[2016-04-15T00:07Z] INFO  17:07:36,240 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:07Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-1_15545821_31186478-prep.bam
[2016-04-15T00:07Z] INFO  17:07:36,282 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:07Z] INFO  17:07:36,432 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T00:07Z] INFO  17:07:36,441 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:07Z] INFO  17:07:36,503 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-15T00:07Z] INFO  17:07:36,658 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:07Z] INFO  17:07:36,659 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:07Z] INFO  17:07:36,660 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:07Z] INFO  17:07:36,661 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:07Z] INFO  17:07:36,675 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:07Z] INFO  17:07:36,794 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:07Z] INFO  17:07:36,839 IntervalUtils - Processing 16283984 bp from intervals
[2016-04-15T00:07Z] WARN  17:07:36,844 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:07Z] INFO  17:07:36,908 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:07Z] INFO  17:07:36,990 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:07Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-1_31187093_46714270-prep.bam
[2016-04-15T00:07Z] INFO  17:07:37,086 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:07Z] INFO  17:07:37,087 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:07Z] INFO  17:07:37,087 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:07Z] INFO  17:07:37,088 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:07Z] INFO  17:07:37,128 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:07Z] INFO  17:07:37,131 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:07Z] INFO  17:07:37,132 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:07Z] INFO  17:07:37,132 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:07Z] INFO  17:07:37,137 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/2/R14-18106_kapa-NGv3-PE100-NGv3-sort-2_15519725_31133925-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/2/R14-18106_kapa-NGv3-PE100-NGv3-sort-2_15519725_31133925-prep-prealign-realign.intervals -L 2:15519726-31133925 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/2/tx/tmpRPHUvg/R14-18106_kapa-NGv3-PE100-NGv3-sort-2_15519725_31133925-prep.bam
[2016-04-15T00:07Z] INFO  17:07:37,146 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:07Z] INFO  17:07:37,156 HelpFormatter - Date/Time: 2016/04/14 17:07:37
[2016-04-15T00:07Z] INFO  17:07:37,156 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:07Z] INFO  17:07:37,157 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:07Z] INFO  17:07:37,400 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:07Z] INFO  17:07:37,599 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:07Z] INFO  17:07:37,608 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:07Z] INFO  17:07:37,680 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-15T00:07Z] INFO  17:07:38,036 IntervalUtils - Processing 15614200 bp from intervals
[2016-04-15T00:07Z] WARN  17:07:38,041 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:07Z] INFO  17:07:38,152 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:07Z] INFO  17:07:38,353 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:07Z] INFO  17:07:38,365 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:07Z] INFO  17:07:38,365 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:07Z] INFO  17:07:38,366 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:07Z] INFO  17:07:38,554 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:07Z] GATK pre-alignment ('2', 205912303, 222290862) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:07Z] INFO  17:07:38,721 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:07Z] GATK pre-alignment ('2', 222291154, 237994685) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:07Z] INFO  17:07:41,634 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:07Z] INFO  17:07:41,638 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:07Z] INFO  17:07:41,638 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:07Z] INFO  17:07:41,639 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:07Z] INFO  17:07:41,643 HelpFormatter - Program Args: -T PrintReads -L 2:205912304-222290862 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/2/tx/tmpc2KowT/R14-18106_kapa-NGv3-PE100-NGv3-sort-2_205912303_222290862-prep-prealign.bam
[2016-04-15T00:07Z] INFO  17:07:41,672 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:07Z] INFO  17:07:41,681 HelpFormatter - Date/Time: 2016/04/14 17:07:41
[2016-04-15T00:07Z] INFO  17:07:41,682 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:07Z] INFO  17:07:41,682 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:07Z] INFO  17:07:41,747 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:07Z] INFO  17:07:41,750 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:07Z] INFO  17:07:41,750 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:07Z] INFO  17:07:41,751 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:07Z] INFO  17:07:41,756 HelpFormatter - Program Args: -T PrintReads -L 2:222291155-237994685 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/2/tx/tmpiydSA6/R14-18106_kapa-NGv3-PE100-NGv3-sort-2_222291154_237994685-prep-prealign.bam
[2016-04-15T00:07Z] INFO  17:07:41,771 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:07Z] INFO  17:07:41,772 HelpFormatter - Date/Time: 2016/04/14 17:07:41
[2016-04-15T00:07Z] INFO  17:07:41,773 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:07Z] INFO  17:07:41,773 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:07Z] INFO  17:07:41,853 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:07Z] INFO  17:07:41,983 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:07Z] INFO  17:07:42,111 ProgressMeter -            done    222965.0    16.0 s      76.0 s      100.0%    16.0 s       0.0 s
[2016-04-15T00:07Z] INFO  17:07:42,111 ProgressMeter - Total runtime 16.97 secs, 0.28 min, 0.00 hours
[2016-04-15T00:07Z] INFO  17:07:42,116 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 222965 total reads (0.00%)
[2016-04-15T00:07Z] INFO  17:07:42,116 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:07Z] INFO  17:07:42,116 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:07Z] INFO  17:07:42,117 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:07Z] INFO  17:07:42,255 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@41fd9d8e
[2016-04-15T00:07Z] INFO  17:07:42,378 ProgressMeter -            done    223050.0    28.0 s       2.2 m      100.0%    28.0 s       0.0 s
[2016-04-15T00:07Z] INFO  17:07:42,378 ProgressMeter - Total runtime 28.79 secs, 0.48 min, 0.01 hours
[2016-04-15T00:07Z] INFO  17:07:42,379 MicroScheduler - 150 reads were filtered out during the traversal out of approximately 223200 total reads (0.07%)
[2016-04-15T00:07Z] INFO  17:07:42,379 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:07Z] INFO  17:07:42,380 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:07Z] INFO  17:07:42,380 MicroScheduler -   -> 150 reads (0.07% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:07Z] INFO  17:07:42,383 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@7172f77a
[2016-04-15T00:07Z] INFO  17:07:42,550 ProgressMeter -            done    118829.0    17.0 s       2.4 m      100.0%    17.0 s       0.0 s
[2016-04-15T00:07Z] INFO  17:07:42,551 ProgressMeter - Total runtime 17.08 secs, 0.28 min, 0.00 hours
[2016-04-15T00:07Z] INFO  17:07:42,551 MicroScheduler - 132 reads were filtered out during the traversal out of approximately 118961 total reads (0.11%)
[2016-04-15T00:07Z] INFO  17:07:42,551 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:07Z] INFO  17:07:42,552 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:07Z] INFO  17:07:42,552 MicroScheduler -   -> 132 reads (0.11% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:07Z] INFO  17:07:42,884 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-15T00:07Z] INFO  17:07:42,934 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:07Z] INFO  17:07:42,943 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:07Z] INFO  17:07:42,976 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.03
[2016-04-15T00:07Z] INFO  17:07:42,990 IntervalUtils - Processing 16378559 bp from intervals
[2016-04-15T00:07Z] INFO  17:07:43,008 ProgressMeter -      2:97916002    100001.0    30.0 s       5.0 m       15.1%     3.3 m       2.8 m
[2016-04-15T00:07Z] INFO  17:07:43,032 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-15T00:07Z] INFO  17:07:43,058 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:07Z] INFO  17:07:43,120 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:07Z] INFO  17:07:43,140 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:07Z] INFO  17:07:43,216 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-15T00:07Z] INFO  17:07:43,245 IntervalUtils - Processing 15703531 bp from intervals
[2016-04-15T00:07Z] INFO  17:07:43,345 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:07Z] INFO  17:07:43,346 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:07Z] INFO  17:07:43,347 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:07Z] INFO  17:07:43,347 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:07Z] INFO  17:07:43,361 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:07Z] INFO  17:07:43,391 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:07Z] INFO  17:07:43,518 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:07Z] INFO  17:07:43,615 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:07Z] INFO  17:07:43,616 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:07Z] INFO  17:07:43,617 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:07Z] INFO  17:07:43,617 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:07Z] INFO  17:07:43,617 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:07Z] INFO  17:07:43,631 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:07Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-2_111281072_127413888-prep-prealign.bam
[2016-04-15T00:07Z] INFO  17:07:43,682 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:07Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-2_31135088_46706841-prep.bam
[2016-04-15T00:07Z] INFO  17:07:43,808 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:07Z] INFO  17:07:43,981 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:07Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-2_143676177_159195597-prep-prealign.bam
[2016-04-15T00:07Z] GATK RealignerTargetCreator: R14-18106_kapa-NGv3-PE100-NGv3-sort-2_111281072_127413888-prep-prealign.bam 2:111281073-127413888
[2016-04-15T00:07Z] GATK: RealignerTargetCreator
[2016-04-15T00:07Z] GATK RealignerTargetCreator: R14-18106_kapa-NGv3-PE100-NGv3-sort-2_143676177_159195597-prep-prealign.bam 2:143676178-159195597
[2016-04-15T00:07Z] GATK: RealignerTargetCreator
[2016-04-15T00:07Z] GATK pre-alignment ('2', 237995374, 243199373) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:07Z] INFO  17:07:45,276 ProgressMeter -            done   1.689033E7    21.0 s       1.0 s      100.0%    21.0 s       0.0 s
[2016-04-15T00:07Z] INFO  17:07:45,277 ProgressMeter - Total runtime 21.54 secs, 0.36 min, 0.01 hours
[2016-04-15T00:07Z] INFO  17:07:45,281 MicroScheduler - 26976 reads were filtered out during the traversal out of approximately 322139 total reads (8.37%)
[2016-04-15T00:07Z] INFO  17:07:45,282 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:07Z] INFO  17:07:45,283 MicroScheduler -   -> 837 reads (0.26% of total) failing BadMateFilter
[2016-04-15T00:07Z] INFO  17:07:45,283 MicroScheduler -   -> 23770 reads (7.38% of total) failing DuplicateReadFilter
[2016-04-15T00:07Z] INFO  17:07:45,284 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:07Z] INFO  17:07:45,285 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:07Z] INFO  17:07:45,285 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:07Z] INFO  17:07:45,286 MicroScheduler -   -> 2369 reads (0.74% of total) failing MappingQualityZeroFilter
[2016-04-15T00:07Z] INFO  17:07:45,286 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:07Z] INFO  17:07:45,287 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-15T00:07Z] INFO  17:07:45,288 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:07Z] INFO  17:07:46,645 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:07Z] GATK: realign ('2', 62362965, 79253295) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:07Z] INFO  17:07:47,328 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:07Z] INFO  17:07:47,331 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:07Z] INFO  17:07:47,332 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:07Z] INFO  17:07:47,333 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:07Z] INFO  17:07:47,337 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/2/R14-18106_kapa-NGv3-PE100-NGv3-sort-2_111281072_127413888-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/2/tx/tmpTz3Akz/R14-18106_kapa-NGv3-PE100-NGv3-sort-2_111281072_127413888-prep-prealign-realign.intervals -l INFO -L 2:111281073-127413888 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:07Z] INFO  17:07:47,349 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:07Z] INFO  17:07:47,349 HelpFormatter - Date/Time: 2016/04/14 17:07:47
[2016-04-15T00:07Z] INFO  17:07:47,349 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:07Z] INFO  17:07:47,350 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:07Z] INFO  17:07:47,472 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:07Z] INFO  17:07:47,472 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:07Z] INFO  17:07:47,476 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:07Z] INFO  17:07:47,476 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:07Z] INFO  17:07:47,477 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:07Z] INFO  17:07:47,481 HelpFormatter - Program Args: -T PrintReads -L 2:237995375-243199373 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/2/tx/tmpBLdv6I/R14-18106_kapa-NGv3-PE100-NGv3-sort-2_237995374_243199373-prep-prealign.bam
[2016-04-15T00:07Z] INFO  17:07:47,489 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:07Z] INFO  17:07:47,490 HelpFormatter - Date/Time: 2016/04/14 17:07:47
[2016-04-15T00:07Z] INFO  17:07:47,491 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:07Z] INFO  17:07:47,491 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:07Z] INFO  17:07:47,589 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:07Z] INFO  17:07:47,593 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:07Z] INFO  17:07:47,594 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:07Z] INFO  17:07:47,595 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:07Z] INFO  17:07:47,600 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/2/R14-18106_kapa-NGv3-PE100-NGv3-sort-2_143676177_159195597-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/2/tx/tmpxwTc0g/R14-18106_kapa-NGv3-PE100-NGv3-sort-2_143676177_159195597-prep-prealign-realign.intervals -l INFO -L 2:143676178-159195597 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:07Z] INFO  17:07:47,611 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:07Z] INFO  17:07:47,611 HelpFormatter - Date/Time: 2016/04/14 17:07:47
[2016-04-15T00:07Z] INFO  17:07:47,612 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:07Z] INFO  17:07:47,612 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:07Z] INFO  17:07:47,648 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:07Z] INFO  17:07:47,733 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T00:07Z] INFO  17:07:47,736 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:07Z] INFO  17:07:47,751 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:07Z] INFO  17:07:47,808 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-15T00:07Z] INFO  17:07:47,941 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T00:07Z] INFO  17:07:47,973 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:07Z] INFO  17:07:48,031 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-15T00:07Z] INFO  17:07:48,136 IntervalUtils - Processing 16132816 bp from intervals
[2016-04-15T00:07Z] WARN  17:07:48,141 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:07Z] INFO  17:07:48,219 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:07Z] INFO  17:07:48,235 ProgressMeter -     1:156642565   1000015.0     2.5 m       2.5 m       82.2%     3.0 m      32.0 s
[2016-04-15T00:07Z] INFO  17:07:48,292 IntervalUtils - Processing 15519420 bp from intervals
[2016-04-15T00:07Z] WARN  17:07:48,297 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:07Z] INFO  17:07:48,366 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:07Z] INFO  17:07:48,521 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:07Z] INFO  17:07:48,523 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:07Z] INFO  17:07:48,523 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:07Z] INFO  17:07:48,524 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:07Z] INFO  17:07:48,573 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:07Z] INFO  17:07:48,575 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:07Z] INFO  17:07:48,575 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:07Z] INFO  17:07:48,576 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:07Z] INFO  17:07:48,724 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-15T00:07Z] INFO  17:07:48,781 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:07Z] INFO  17:07:48,790 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:07Z] INFO  17:07:48,852 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-15T00:07Z] INFO  17:07:48,894 IntervalUtils - Processing 5203999 bp from intervals
[2016-04-15T00:07Z] INFO  17:07:48,983 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:07Z] INFO  17:07:49,162 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:07Z] INFO  17:07:49,165 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:07Z] INFO  17:07:49,165 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:07Z] INFO  17:07:49,166 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:07Z] INFO  17:07:49,170 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/2/R14-18106_kapa-NGv3-PE100-NGv3-sort-2_62362965_79253295-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/2/R14-18106_kapa-NGv3-PE100-NGv3-sort-2_62362965_79253295-prep-prealign-realign.intervals -L 2:62362966-79253295 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/2/tx/tmpg07wto/R14-18106_kapa-NGv3-PE100-NGv3-sort-2_62362965_79253295-prep.bam
[2016-04-15T00:07Z] INFO  17:07:49,180 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:07Z] INFO  17:07:49,186 HelpFormatter - Date/Time: 2016/04/14 17:07:49
[2016-04-15T00:07Z] INFO  17:07:49,186 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:07Z] INFO  17:07:49,187 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:07Z] INFO  17:07:49,225 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:07Z] INFO  17:07:49,225 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:07Z] INFO  17:07:49,226 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:07Z] INFO  17:07:49,226 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:07Z] INFO  17:07:49,251 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:07Z] INFO  17:07:49,299 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:07Z] INFO  17:07:49,407 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:07Z] INFO  17:07:49,587 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:07Z] INFO  17:07:49,596 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:07Z] INFO  17:07:49,660 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-15T00:07Z] INFO  17:07:50,014 IntervalUtils - Processing 16890330 bp from intervals
[2016-04-15T00:07Z] WARN  17:07:50,028 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:07Z] INFO  17:07:50,107 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:07Z] INFO  17:07:50,260 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:07Z] INFO  17:07:50,261 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:07Z] INFO  17:07:50,262 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:07Z] INFO  17:07:50,262 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:07Z] INFO  17:07:50,467 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:07Z] INFO  17:07:50,716 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:07Z] INFO  17:07:51,440 ProgressMeter -            done    395644.0    26.0 s      66.0 s      100.0%    26.0 s       0.0 s
[2016-04-15T00:07Z] INFO  17:07:51,441 ProgressMeter - Total runtime 26.11 secs, 0.44 min, 0.01 hours
[2016-04-15T00:07Z] INFO  17:07:51,444 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 395644 total reads (0.00%)
[2016-04-15T00:07Z] INFO  17:07:51,456 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:07Z] INFO  17:07:51,457 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:07Z] INFO  17:07:51,457 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:07Z] INFO  17:07:53,149 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:07Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-1_192128349_207640257-prep.bam
[2016-04-15T00:07Z] GATK pre-alignment ('3', 0, 15512123) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:07Z] INFO  17:07:54,476 ProgressMeter -            done   1.6283984E7    17.0 s       1.0 s      100.0%    17.0 s       0.0 s
[2016-04-15T00:07Z] INFO  17:07:54,477 ProgressMeter - Total runtime 17.39 secs, 0.29 min, 0.00 hours
[2016-04-15T00:07Z] INFO  17:07:54,481 MicroScheduler - 82079 reads were filtered out during the traversal out of approximately 242093 total reads (33.90%)
[2016-04-15T00:07Z] INFO  17:07:54,482 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:07Z] INFO  17:07:54,483 MicroScheduler -   -> 726 reads (0.30% of total) failing BadMateFilter
[2016-04-15T00:07Z] INFO  17:07:54,483 MicroScheduler -   -> 13136 reads (5.43% of total) failing DuplicateReadFilter
[2016-04-15T00:07Z] INFO  17:07:54,484 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:07Z] INFO  17:07:54,485 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:07Z] INFO  17:07:54,485 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:07Z] INFO  17:07:54,486 MicroScheduler -   -> 68217 reads (28.18% of total) failing MappingQualityZeroFilter
[2016-04-15T00:07Z] INFO  17:07:54,486 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:07Z] INFO  17:07:54,487 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-15T00:07Z] INFO  17:07:54,488 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:07Z] INFO  17:07:54,499 ProgressMeter -     2:133636587    200002.0    30.0 s       2.5 m       38.3%    78.0 s      48.0 s
[2016-04-15T00:07Z] INFO  17:07:55,995 ProgressMeter -     2:170863534    200002.0    30.0 s       2.5 m       74.9%    40.0 s      10.0 s
[2016-04-15T00:07Z] INFO  17:07:56,069 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:07Z] GATK: realign ('2', 79253838, 95537822) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:07Z] INFO  17:07:56,350 ProgressMeter -     2:179639269    200002.0    30.0 s       2.5 m       31.3%    95.0 s      65.0 s
[2016-04-15T00:07Z] INFO  17:07:57,089 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:07Z] INFO  17:07:57,091 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:07Z] INFO  17:07:57,091 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:07Z] INFO  17:07:57,092 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:07Z] INFO  17:07:57,102 HelpFormatter - Program Args: -T PrintReads -L 3:1-15512123 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/3/tx/tmpnPsw6H/R14-18106_kapa-NGv3-PE100-NGv3-sort-3_0_15512123-prep-prealign.bam
[2016-04-15T00:07Z] INFO  17:07:57,117 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:07Z] INFO  17:07:57,117 HelpFormatter - Date/Time: 2016/04/14 17:07:57
[2016-04-15T00:07Z] INFO  17:07:57,118 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:07Z] INFO  17:07:57,118 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:07Z] INFO  17:07:57,325 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:07Z] INFO  17:07:58,350 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-15T00:07Z] INFO  17:07:58,432 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:07Z] INFO  17:07:58,441 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:07Z] INFO  17:07:58,491 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-15T00:07Z] INFO  17:07:58,506 IntervalUtils - Processing 15512123 bp from intervals
[2016-04-15T00:07Z] INFO  17:07:58,593 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:07Z] INFO  17:07:58,674 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:07Z] INFO  17:07:58,677 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:07Z] INFO  17:07:58,678 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:07Z] INFO  17:07:58,678 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:07Z] INFO  17:07:58,683 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/2/R14-18106_kapa-NGv3-PE100-NGv3-sort-2_79253838_95537822-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/2/R14-18106_kapa-NGv3-PE100-NGv3-sort-2_79253838_95537822-prep-prealign-realign.intervals -L 2:79253839-95537822 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/2/tx/tmpnqDLXI/R14-18106_kapa-NGv3-PE100-NGv3-sort-2_79253838_95537822-prep.bam
[2016-04-15T00:07Z] INFO  17:07:58,693 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:07Z] INFO  17:07:58,694 HelpFormatter - Date/Time: 2016/04/14 17:07:58
[2016-04-15T00:07Z] INFO  17:07:58,694 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:07Z] INFO  17:07:58,694 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:07Z] INFO  17:07:58,888 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:07Z] INFO  17:07:58,889 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:07Z] INFO  17:07:58,890 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:07Z] INFO  17:07:58,890 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:07Z] INFO  17:07:58,904 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:07Z] INFO  17:07:59,001 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:07Z] INFO  17:07:59,039 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:07Z] INFO  17:07:59,158 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:07Z] INFO  17:07:59,171 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:07Z] INFO  17:07:59,242 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-15T00:07Z] INFO  17:07:59,599 IntervalUtils - Processing 16283984 bp from intervals
[2016-04-15T00:07Z] WARN  17:07:59,605 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:07Z] INFO  17:07:59,728 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:07Z] INFO  17:07:59,929 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:07Z] INFO  17:07:59,930 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:07Z] INFO  17:07:59,931 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:07Z] INFO  17:07:59,932 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:08Z] INFO  17:08:00,048 ProgressMeter -            done    346609.0    21.0 s      62.0 s      100.0%    21.0 s       0.0 s
[2016-04-15T00:08Z] INFO  17:08:00,048 ProgressMeter - Total runtime 21.68 secs, 0.36 min, 0.01 hours
[2016-04-15T00:08Z] INFO  17:08:00,052 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 346609 total reads (0.00%)
[2016-04-15T00:08Z] INFO  17:08:00,052 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:08Z] INFO  17:08:00,053 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:08Z] INFO  17:08:00,053 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:08Z] INFO  17:08:00,054 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:08Z] INFO  17:08:00,196 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:08Z] INFO  17:08:01,525 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:08Z] INFO  17:08:01,791 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@32d5a4c6
[2016-04-15T00:08Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-2_15519725_31133925-prep.bam
[2016-04-15T00:08Z] INFO  17:08:02,002 ProgressMeter -            done    309235.0    38.0 s       2.0 m      100.0%    38.0 s       0.0 s
[2016-04-15T00:08Z] INFO  17:08:02,003 ProgressMeter - Total runtime 38.02 secs, 0.63 min, 0.01 hours
[2016-04-15T00:08Z] INFO  17:08:02,004 MicroScheduler - 191 reads were filtered out during the traversal out of approximately 309426 total reads (0.06%)
[2016-04-15T00:08Z] INFO  17:08:02,004 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:08Z] INFO  17:08:02,004 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:08Z] INFO  17:08:02,005 MicroScheduler -   -> 191 reads (0.06% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:08Z] INFO  17:08:02,181 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@5fe152b7
[2016-04-15T00:08Z] INFO  17:08:02,341 ProgressMeter -            done    285754.0    36.0 s       2.1 m      100.0%    36.0 s       0.0 s
[2016-04-15T00:08Z] INFO  17:08:02,342 ProgressMeter - Total runtime 36.36 secs, 0.61 min, 0.01 hours
[2016-04-15T00:08Z] INFO  17:08:02,342 MicroScheduler - 174 reads were filtered out during the traversal out of approximately 285928 total reads (0.06%)
[2016-04-15T00:08Z] INFO  17:08:02,343 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:08Z] INFO  17:08:02,343 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:08Z] INFO  17:08:02,344 MicroScheduler -   -> 174 reads (0.06% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:08Z] INFO  17:08:02,994 ProgressMeter -            done    414783.0    27.0 s      66.0 s      100.0%    27.0 s       0.0 s
[2016-04-15T00:08Z] INFO  17:08:02,995 ProgressMeter - Total runtime 27.57 secs, 0.46 min, 0.01 hours
[2016-04-15T00:08Z] INFO  17:08:02,999 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 414783 total reads (0.00%)
[2016-04-15T00:08Z] INFO  17:08:03,000 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:08Z] INFO  17:08:03,000 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:08Z] INFO  17:08:03,000 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:08Z] GATK pre-alignment ('3', 15515506, 31574805) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:08Z] INFO  17:08:03,399 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:08Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-2_127433207_143643105-prep-prealign.bam
[2016-04-15T00:08Z] INFO  17:08:03,814 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:08Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-2_159196753_174774985-prep-prealign.bam
[2016-04-15T00:08Z] INFO  17:08:04,441 ProgressMeter -            done   1.551942E7    15.0 s       1.0 s      100.0%    15.0 s       0.0 s
[2016-04-15T00:08Z] INFO  17:08:04,443 ProgressMeter - Total runtime 15.87 secs, 0.26 min, 0.00 hours
[2016-04-15T00:08Z] INFO  17:08:04,447 MicroScheduler - 18755 reads were filtered out during the traversal out of approximately 119592 total reads (15.68%)
[2016-04-15T00:08Z] INFO  17:08:04,448 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:08Z] INFO  17:08:04,449 MicroScheduler -   -> 494 reads (0.41% of total) failing BadMateFilter
[2016-04-15T00:08Z] INFO  17:08:04,450 MicroScheduler -   -> 8063 reads (6.74% of total) failing DuplicateReadFilter
[2016-04-15T00:08Z] INFO  17:08:04,451 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:08Z] INFO  17:08:04,451 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:08Z] INFO  17:08:04,452 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:08Z] INFO  17:08:04,453 MicroScheduler -   -> 10198 reads (8.53% of total) failing MappingQualityZeroFilter
[2016-04-15T00:08Z] INFO  17:08:04,453 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:08Z] INFO  17:08:04,454 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-15T00:08Z] INFO  17:08:04,455 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:08Z] GATK RealignerTargetCreator: R14-18106_kapa-NGv3-PE100-NGv3-sort-2_127433207_143643105-prep-prealign.bam 2:127433208-143643105
[2016-04-15T00:08Z] GATK: RealignerTargetCreator
[2016-04-15T00:08Z] INFO  17:08:04,536 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:08Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-1_223162737_240072524-prep.bam
[2016-04-15T00:08Z] GATK RealignerTargetCreator: R14-18106_kapa-NGv3-PE100-NGv3-sort-2_159196753_174774985-prep-prealign.bam 2:159196754-174774985
[2016-04-15T00:08Z] GATK: RealignerTargetCreator
[2016-04-15T00:08Z] INFO  17:08:05,808 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@41fd9d8e
[2016-04-15T00:08Z] INFO  17:08:05,981 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:08Z] GATK: realign ('2', 143676177, 159195597) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:08Z] INFO  17:08:06,036 ProgressMeter -            done   1189276.0     2.8 m       2.4 m      100.0%     2.8 m       0.0 s
[2016-04-15T00:08Z] INFO  17:08:06,036 ProgressMeter - Total runtime 168.71 secs, 2.81 min, 0.05 hours
[2016-04-15T00:08Z] INFO  17:08:06,037 MicroScheduler - 477 reads were filtered out during the traversal out of approximately 1189753 total reads (0.04%)
[2016-04-15T00:08Z] INFO  17:08:06,037 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:08Z] INFO  17:08:06,037 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:08Z] INFO  17:08:06,038 MicroScheduler -   -> 477 reads (0.04% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:08Z] INFO  17:08:06,046 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:08Z] INFO  17:08:06,049 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:08Z] INFO  17:08:06,050 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:08Z] INFO  17:08:06,050 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:08Z] INFO  17:08:06,074 HelpFormatter - Program Args: -T PrintReads -L 3:15515507-31574805 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/3/tx/tmp8_HYrV/R14-18106_kapa-NGv3-PE100-NGv3-sort-3_15515506_31574805-prep-prealign.bam
[2016-04-15T00:08Z] GATK pre-alignment ('3', 31617887, 47127804) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:08Z] INFO  17:08:06,089 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:08Z] INFO  17:08:06,090 HelpFormatter - Date/Time: 2016/04/14 17:08:06
[2016-04-15T00:08Z] INFO  17:08:06,091 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:08Z] INFO  17:08:06,091 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:08Z] INFO  17:08:06,331 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:08Z] INFO  17:08:06,442 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@7172f77a
[2016-04-15T00:08Z] INFO  17:08:06,678 ProgressMeter -            done    324384.0    40.0 s       2.1 m      100.0%    40.0 s       0.0 s
[2016-04-15T00:08Z] INFO  17:08:06,678 ProgressMeter - Total runtime 40.37 secs, 0.67 min, 0.01 hours
[2016-04-15T00:08Z] INFO  17:08:06,679 MicroScheduler - 265 reads were filtered out during the traversal out of approximately 324649 total reads (0.08%)
[2016-04-15T00:08Z] INFO  17:08:06,679 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:08Z] INFO  17:08:06,691 ProgressMeter -     2:202719660    100003.0    30.0 s       5.0 m       80.0%    37.0 s       7.0 s
[2016-04-15T00:08Z] INFO  17:08:06,679 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:08Z] INFO  17:08:06,680 MicroScheduler -   -> 265 reads (0.08% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:08Z] INFO  17:08:06,951 ProgressMeter -            done   1.6132816E7    18.0 s       1.0 s      100.0%    18.0 s       0.0 s
[2016-04-15T00:08Z] INFO  17:08:06,951 ProgressMeter - Total runtime 18.43 secs, 0.31 min, 0.01 hours
[2016-04-15T00:08Z] INFO  17:08:06,955 MicroScheduler - 72435 reads were filtered out during the traversal out of approximately 224637 total reads (32.25%)
[2016-04-15T00:08Z] INFO  17:08:06,955 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:08Z] INFO  17:08:06,955 MicroScheduler -   -> 553 reads (0.25% of total) failing BadMateFilter
[2016-04-15T00:08Z] INFO  17:08:06,956 MicroScheduler -   -> 12308 reads (5.48% of total) failing DuplicateReadFilter
[2016-04-15T00:08Z] INFO  17:08:06,956 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:08Z] INFO  17:08:06,956 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:08Z] INFO  17:08:06,956 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:08Z] INFO  17:08:06,957 MicroScheduler -   -> 59574 reads (26.52% of total) failing MappingQualityZeroFilter
[2016-04-15T00:08Z] INFO  17:08:06,957 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:08Z] INFO  17:08:06,957 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-15T00:08Z] INFO  17:08:06,957 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:08Z] INFO  17:08:07,463 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:08Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-1_143897546_159410511-prep-prealign.bam
[2016-04-15T00:08Z] INFO  17:08:07,648 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-15T00:08Z] INFO  17:08:07,722 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:08Z] INFO  17:08:07,731 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:08Z] INFO  17:08:07,804 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-15T00:08Z] INFO  17:08:07,836 IntervalUtils - Processing 16059299 bp from intervals
[2016-04-15T00:08Z] INFO  17:08:07,856 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:08Z] INFO  17:08:07,859 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:08Z] INFO  17:08:07,860 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:08Z] INFO  17:08:07,860 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:08Z] INFO  17:08:07,865 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/2/R14-18106_kapa-NGv3-PE100-NGv3-sort-2_127433207_143643105-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/2/tx/tmp_eT9Zs/R14-18106_kapa-NGv3-PE100-NGv3-sort-2_127433207_143643105-prep-prealign-realign.intervals -l INFO -L 2:127433208-143643105 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:08Z] INFO  17:08:07,895 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:08Z] INFO  17:08:07,896 HelpFormatter - Date/Time: 2016/04/14 17:08:07
[2016-04-15T00:08Z] INFO  17:08:07,897 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:08Z] INFO  17:08:07,897 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:08Z] INFO  17:08:07,920 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:08Z] INFO  17:08:07,933 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:08Z] INFO  17:08:07,935 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:08Z] INFO  17:08:07,936 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:08Z] INFO  17:08:07,936 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:08Z] INFO  17:08:07,940 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/2/R14-18106_kapa-NGv3-PE100-NGv3-sort-2_159196753_174774985-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/2/tx/tmpvrzdDm/R14-18106_kapa-NGv3-PE100-NGv3-sort-2_159196753_174774985-prep-prealign-realign.intervals -l INFO -L 2:159196754-174774985 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:08Z] INFO  17:08:07,963 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:08Z] INFO  17:08:07,964 HelpFormatter - Date/Time: 2016/04/14 17:08:07
[2016-04-15T00:08Z] INFO  17:08:07,964 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:08Z] INFO  17:08:07,964 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:08Z] INFO  17:08:07,988 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:08Z] INFO  17:08:08,125 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:08Z] INFO  17:08:08,147 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T00:08Z] INFO  17:08:08,158 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:08Z] INFO  17:08:08,185 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:08Z] INFO  17:08:08,187 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:08Z] INFO  17:08:08,187 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:08Z] INFO  17:08:08,188 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:08Z] INFO  17:08:08,201 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:08Z] INFO  17:08:08,212 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-15T00:08Z] INFO  17:08:08,300 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:08Z] GATK: realign ('2', 111281072, 127413888) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:08Z] INFO  17:08:08,321 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:08Z] INFO  17:08:08,322 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T00:08Z] INFO  17:08:08,327 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:08Z] INFO  17:08:08,331 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:08Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-2_174777797_190306304-prep-prealign.bam
[2016-04-15T00:08Z] INFO  17:08:08,406 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-15T00:08Z] INFO  17:08:08,457 IntervalUtils - Processing 16209898 bp from intervals
[2016-04-15T00:08Z] WARN  17:08:08,462 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:08Z] INFO  17:08:08,527 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:08Z] INFO  17:08:08,720 IntervalUtils - Processing 15578232 bp from intervals
[2016-04-15T00:08Z] WARN  17:08:08,726 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:08Z] INFO  17:08:08,802 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:08Z] INFO  17:08:08,803 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:08Z] INFO  17:08:08,804 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:08Z] INFO  17:08:08,805 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:08Z] INFO  17:08:08,818 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:08Z] INFO  17:08:09,126 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:08Z] INFO  17:08:09,127 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:08Z] INFO  17:08:09,128 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:08Z] INFO  17:08:09,129 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:08Z] INFO  17:08:09,229 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:08Z] INFO  17:08:09,233 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:08Z] INFO  17:08:09,234 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:08Z] INFO  17:08:09,234 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:08Z] INFO  17:08:09,240 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/2/R14-18106_kapa-NGv3-PE100-NGv3-sort-2_143676177_159195597-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/2/R14-18106_kapa-NGv3-PE100-NGv3-sort-2_143676177_159195597-prep-prealign-realign.intervals -L 2:143676178-159195597 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/2/tx/tmpSE7xVI/R14-18106_kapa-NGv3-PE100-NGv3-sort-2_143676177_159195597-prep.bam
[2016-04-15T00:08Z] INFO  17:08:09,262 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:08Z] INFO  17:08:09,265 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:08Z] INFO  17:08:09,265 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:08Z] INFO  17:08:09,265 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:08Z] INFO  17:08:09,270 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:08Z] INFO  17:08:09,271 HelpFormatter - Date/Time: 2016/04/14 17:08:09
[2016-04-15T00:08Z] INFO  17:08:09,271 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:08Z] INFO  17:08:09,271 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:08Z] INFO  17:08:09,270 HelpFormatter - Program Args: -T PrintReads -L 3:31617888-47127804 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/3/tx/tmpodsBnE/R14-18106_kapa-NGv3-PE100-NGv3-sort-3_31617887_47127804-prep-prealign.bam
[2016-04-15T00:08Z] INFO  17:08:09,294 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:08Z] INFO  17:08:09,305 HelpFormatter - Date/Time: 2016/04/14 17:08:09
[2016-04-15T00:08Z] INFO  17:08:09,306 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:08Z] INFO  17:08:09,307 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:08Z] GATK RealignerTargetCreator: R14-18106_kapa-NGv3-PE100-NGv3-sort-2_174777797_190306304-prep-prealign.bam 2:174777798-190306304
[2016-04-15T00:08Z] GATK: RealignerTargetCreator
[2016-04-15T00:08Z] INFO  17:08:09,516 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:08Z] INFO  17:08:09,575 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:08Z] INFO  17:08:09,693 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:08Z] INFO  17:08:09,703 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:08Z] INFO  17:08:09,783 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-15T00:08Z] INFO  17:08:10,248 IntervalUtils - Processing 15519420 bp from intervals
[2016-04-15T00:08Z] WARN  17:08:10,253 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:08Z] INFO  17:08:10,318 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:08Z] INFO  17:08:10,483 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:08Z] INFO  17:08:10,484 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:08Z] INFO  17:08:10,484 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:08Z] INFO  17:08:10,484 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:08Z] INFO  17:08:10,579 ProgressMeter -            done    320315.0    20.0 s      63.0 s      100.0%    20.0 s       0.0 s
[2016-04-15T00:08Z] INFO  17:08:10,579 ProgressMeter - Total runtime 20.32 secs, 0.34 min, 0.01 hours
[2016-04-15T00:08Z] INFO  17:08:10,583 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 320315 total reads (0.00%)
[2016-04-15T00:08Z] INFO  17:08:10,583 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:08Z] INFO  17:08:10,583 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:08Z] INFO  17:08:10,584 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:08Z] INFO  17:08:10,696 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:08Z] GATK RealignerTargetCreator: R14-18106_kapa-NGv3-PE100-NGv3-sort-1_143897546_159410511-prep-prealign.bam 1:143897547-159410511
[2016-04-15T00:08Z] GATK: RealignerTargetCreator
[2016-04-15T00:08Z] INFO  17:08:10,910 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:08Z] INFO  17:08:11,053 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-15T00:08Z] INFO  17:08:11,116 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:08Z] INFO  17:08:11,125 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:08Z] INFO  17:08:11,175 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-15T00:08Z] INFO  17:08:11,189 IntervalUtils - Processing 15509917 bp from intervals
[2016-04-15T00:08Z] INFO  17:08:11,259 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:08Z] INFO  17:08:11,539 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:08Z] INFO  17:08:11,543 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:08Z] INFO  17:08:11,543 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:08Z] INFO  17:08:11,544 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:08Z] INFO  17:08:11,555 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/2/R14-18106_kapa-NGv3-PE100-NGv3-sort-2_111281072_127413888-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/2/R14-18106_kapa-NGv3-PE100-NGv3-sort-2_111281072_127413888-prep-prealign-realign.intervals -L 2:111281073-127413888 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/2/tx/tmpQma14G/R14-18106_kapa-NGv3-PE100-NGv3-sort-2_111281072_127413888-prep.bam
[2016-04-15T00:08Z] INFO  17:08:11,561 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:08Z] INFO  17:08:11,561 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:08Z] INFO  17:08:11,562 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:08Z] INFO  17:08:11,563 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:08Z] INFO  17:08:11,577 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:08Z] INFO  17:08:11,609 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:08Z] INFO  17:08:11,610 HelpFormatter - Date/Time: 2016/04/14 17:08:11
[2016-04-15T00:08Z] INFO  17:08:11,611 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:08Z] INFO  17:08:11,616 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:08Z] INFO  17:08:11,788 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:08Z] INFO  17:08:11,842 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:08Z] INFO  17:08:11,999 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:08Z] INFO  17:08:12,009 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:08Z] INFO  17:08:12,052 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.04
[2016-04-15T00:08Z] INFO  17:08:12,103 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:08Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-2_62362965_79253295-prep.bam
[2016-04-15T00:08Z] INFO  17:08:12,405 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:08Z] INFO  17:08:12,408 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:08Z] INFO  17:08:12,409 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:08Z] INFO  17:08:12,409 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:08Z] INFO  17:08:12,414 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/2/R14-18106_kapa-NGv3-PE100-NGv3-sort-2_174777797_190306304-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/2/tx/tmpONbEaW/R14-18106_kapa-NGv3-PE100-NGv3-sort-2_174777797_190306304-prep-prealign-realign.intervals -l INFO -L 2:174777798-190306304 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:08Z] INFO  17:08:12,458 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:08Z] INFO  17:08:12,465 IntervalUtils - Processing 16132816 bp from intervals
[2016-04-15T00:08Z] INFO  17:08:12,468 HelpFormatter - Date/Time: 2016/04/14 17:08:12
[2016-04-15T00:08Z] WARN  17:08:12,470 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:08Z] INFO  17:08:12,469 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:08Z] INFO  17:08:12,474 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:08Z] INFO  17:08:12,541 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:08Z] INFO  17:08:12,591 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:08Z] INFO  17:08:12,683 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:08Z] INFO  17:08:12,685 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:08Z] INFO  17:08:12,685 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:08Z] INFO  17:08:12,686 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:08Z] INFO  17:08:12,839 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T00:08Z] INFO  17:08:12,849 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:08Z] INFO  17:08:12,894 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:08Z] INFO  17:08:12,914 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-15T00:08Z] INFO  17:08:13,009 ProgressMeter -     2:108475951    300008.0    60.0 s       3.3 m       82.2%    72.0 s      12.0 s
[2016-04-15T00:08Z] INFO  17:08:13,050 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:08Z] GATK pre-alignment ('3', 47129602, 62648069) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:08Z] INFO  17:08:13,239 IntervalUtils - Processing 15528507 bp from intervals
[2016-04-15T00:08Z] WARN  17:08:13,255 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:08Z] INFO  17:08:13,295 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@32d5a4c6
[2016-04-15T00:08Z] INFO  17:08:13,362 ProgressMeter -     2:219259336    200002.0    30.0 s       2.5 m       81.5%    36.0 s       6.0 s
[2016-04-15T00:08Z] INFO  17:08:13,424 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:08Z] INFO  17:08:13,563 ProgressMeter -            done    241537.0    36.0 s       2.5 m      100.0%    36.0 s       0.0 s
[2016-04-15T00:08Z] INFO  17:08:13,563 ProgressMeter - Total runtime 36.90 secs, 0.62 min, 0.01 hours
[2016-04-15T00:08Z] INFO  17:08:13,564 MicroScheduler - 186 reads were filtered out during the traversal out of approximately 241723 total reads (0.08%)
[2016-04-15T00:08Z] INFO  17:08:13,564 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:08Z] INFO  17:08:13,564 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:08Z] INFO  17:08:13,565 MicroScheduler -   -> 186 reads (0.08% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:08Z] INFO  17:08:13,715 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:08Z] INFO  17:08:13,716 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:08Z] INFO  17:08:13,722 ProgressMeter -     2:233348194    100001.0    30.0 s       5.0 m       70.4%    42.0 s      12.0 s
[2016-04-15T00:08Z] INFO  17:08:13,717 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:08Z] INFO  17:08:13,717 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:08Z] INFO  17:08:13,977 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:08Z] INFO  17:08:13,980 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:08Z] INFO  17:08:13,980 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:08Z] INFO  17:08:13,981 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:08Z] INFO  17:08:13,985 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/1/R14-18106_kapa-NGv3-PE100-NGv3-sort-1_143897546_159410511-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/1/tx/tmpk0t3vh/R14-18106_kapa-NGv3-PE100-NGv3-sort-1_143897546_159410511-prep-prealign-realign.intervals -l INFO -L 1:143897547-159410511 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:08Z] INFO  17:08:14,007 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:08Z] INFO  17:08:14,008 HelpFormatter - Date/Time: 2016/04/14 17:08:13
[2016-04-15T00:08Z] INFO  17:08:14,008 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:08Z] INFO  17:08:14,009 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:08Z] INFO  17:08:14,138 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:08Z] INFO  17:08:14,414 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T00:08Z] INFO  17:08:14,435 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:08Z] INFO  17:08:14,513 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-15T00:08Z] INFO  17:08:14,729 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:08Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-2_190313104_205830046-prep-prealign.bam
[2016-04-15T00:08Z] INFO  17:08:14,878 IntervalUtils - Processing 15512965 bp from intervals
[2016-04-15T00:08Z] WARN  17:08:14,883 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:08Z] INFO  17:08:14,949 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:08Z] INFO  17:08:15,186 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:08Z] INFO  17:08:15,187 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:08Z] INFO  17:08:15,188 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:08Z] INFO  17:08:15,188 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:08Z] GATK RealignerTargetCreator: R14-18106_kapa-NGv3-PE100-NGv3-sort-2_190313104_205830046-prep-prealign.bam 2:190313105-205830046
[2016-04-15T00:08Z] GATK: RealignerTargetCreator
[2016-04-15T00:08Z] INFO  17:08:16,151 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:08Z] INFO  17:08:16,155 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:08Z] INFO  17:08:16,155 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:08Z] INFO  17:08:16,156 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:08Z] INFO  17:08:16,160 HelpFormatter - Program Args: -T PrintReads -L 3:47129603-62648069 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/3/tx/tmpjXfy61/R14-18106_kapa-NGv3-PE100-NGv3-sort-3_47129602_62648069-prep-prealign.bam
[2016-04-15T00:08Z] INFO  17:08:16,178 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:08Z] INFO  17:08:16,179 HelpFormatter - Date/Time: 2016/04/14 17:08:16
[2016-04-15T00:08Z] INFO  17:08:16,179 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:08Z] INFO  17:08:16,179 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:08Z] INFO  17:08:16,397 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:08Z] INFO  17:08:16,625 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@32d5a4c6
[2016-04-15T00:08Z] INFO  17:08:16,812 ProgressMeter -            done    201177.0    27.0 s       2.3 m       97.4%    27.0 s       0.0 s
[2016-04-15T00:08Z] INFO  17:08:16,813 ProgressMeter - Total runtime 27.59 secs, 0.46 min, 0.01 hours
[2016-04-15T00:08Z] INFO  17:08:16,813 MicroScheduler - 105 reads were filtered out during the traversal out of approximately 201282 total reads (0.05%)
[2016-04-15T00:08Z] INFO  17:08:16,814 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:08Z] INFO  17:08:16,814 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:08Z] INFO  17:08:16,814 MicroScheduler -   -> 105 reads (0.05% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:08Z] INFO  17:08:17,623 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-15T00:08Z] INFO  17:08:17,725 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:08Z] INFO  17:08:17,734 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:08Z] INFO  17:08:17,793 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-15T00:08Z] INFO  17:08:17,817 IntervalUtils - Processing 15518467 bp from intervals
[2016-04-15T00:08Z] INFO  17:08:17,854 ProgressMeter -            done    240579.0    17.0 s      74.0 s      100.0%    17.0 s       0.0 s
[2016-04-15T00:08Z] INFO  17:08:17,854 ProgressMeter - Total runtime 17.92 secs, 0.30 min, 0.00 hours
[2016-04-15T00:08Z] INFO  17:08:17,857 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 240579 total reads (0.00%)
[2016-04-15T00:08Z] INFO  17:08:17,858 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:08Z] INFO  17:08:17,858 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:08Z] INFO  17:08:17,858 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:08Z] INFO  17:08:17,887 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:08Z] INFO  17:08:18,047 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:08Z] INFO  17:08:18,050 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:08Z] INFO  17:08:18,051 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:08Z] INFO  17:08:18,051 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:08Z] INFO  17:08:18,056 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/2/R14-18106_kapa-NGv3-PE100-NGv3-sort-2_190313104_205830046-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/2/tx/tmpUf3A5B/R14-18106_kapa-NGv3-PE100-NGv3-sort-2_190313104_205830046-prep-prealign-realign.intervals -l INFO -L 2:190313105-205830046 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:08Z] INFO  17:08:18,065 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:08Z] INFO  17:08:18,070 HelpFormatter - Date/Time: 2016/04/14 17:08:18
[2016-04-15T00:08Z] INFO  17:08:18,071 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:08Z] INFO  17:08:18,071 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:08Z] INFO  17:08:18,236 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:08Z] INFO  17:08:18,285 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:08Z] INFO  17:08:18,296 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:08Z] INFO  17:08:18,297 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:08Z] INFO  17:08:18,298 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:08Z] INFO  17:08:18,334 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:08Z] INFO  17:08:18,413 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:08Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-2_237995374_243199373-prep-prealign.bam
[2016-04-15T00:08Z] INFO  17:08:18,478 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T00:08Z] INFO  17:08:18,498 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:08Z] INFO  17:08:18,518 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:08Z] INFO  17:08:18,577 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-15T00:08Z] INFO  17:08:18,904 IntervalUtils - Processing 15516942 bp from intervals
[2016-04-15T00:08Z] WARN  17:08:18,910 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:08Z] INFO  17:08:19,038 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:08Z] GATK RealignerTargetCreator: R14-18106_kapa-NGv3-PE100-NGv3-sort-2_237995374_243199373-prep-prealign.bam 2:237995375-243199373
[2016-04-15T00:08Z] GATK: RealignerTargetCreator
[2016-04-15T00:08Z] INFO  17:08:19,298 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:08Z] INFO  17:08:19,299 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:08Z] INFO  17:08:19,300 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:08Z] INFO  17:08:19,301 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:08Z] INFO  17:08:19,536 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:08Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-2_79253838_95537822-prep.bam
[2016-04-15T00:08Z] GATK pre-alignment ('3', 62739115, 78648077) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:08Z] INFO  17:08:21,632 ProgressMeter -            done    118829.0    11.0 s      93.0 s      100.0%    11.0 s       0.0 s
[2016-04-15T00:08Z] INFO  17:08:21,634 ProgressMeter - Total runtime 11.15 secs, 0.19 min, 0.00 hours
[2016-04-15T00:08Z] INFO  17:08:21,638 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 118829 total reads (0.00%)
[2016-04-15T00:08Z] INFO  17:08:21,639 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:08Z] INFO  17:08:21,640 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:08Z] INFO  17:08:21,640 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:08Z] INFO  17:08:21,936 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:08Z] INFO  17:08:21,939 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:08Z] INFO  17:08:21,940 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:08Z] INFO  17:08:21,941 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:08Z] INFO  17:08:21,945 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/2/R14-18106_kapa-NGv3-PE100-NGv3-sort-2_237995374_243199373-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/2/tx/tmpgcUF_k/R14-18106_kapa-NGv3-PE100-NGv3-sort-2_237995374_243199373-prep-prealign-realign.intervals -l INFO -L 2:237995375-243199373 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:08Z] INFO  17:08:21,956 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:08Z] INFO  17:08:21,967 HelpFormatter - Date/Time: 2016/04/14 17:08:21
[2016-04-15T00:08Z] INFO  17:08:21,968 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:08Z] INFO  17:08:21,969 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:08Z] INFO  17:08:22,059 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:08Z] INFO  17:08:22,278 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T00:08Z] INFO  17:08:22,288 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:08Z] INFO  17:08:22,351 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-15T00:08Z] INFO  17:08:22,667 IntervalUtils - Processing 5203999 bp from intervals
[2016-04-15T00:08Z] WARN  17:08:22,673 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:08Z] INFO  17:08:22,871 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:08Z] INFO  17:08:22,970 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:08Z] INFO  17:08:22,971 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:08Z] INFO  17:08:22,972 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:08Z] INFO  17:08:22,973 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:08Z] INFO  17:08:23,150 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:08Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-2_143676177_159195597-prep.bam
[2016-04-15T00:08Z] INFO  17:08:23,284 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:08Z] INFO  17:08:23,287 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:08Z] INFO  17:08:23,288 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:08Z] INFO  17:08:23,288 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:08Z] INFO  17:08:23,293 HelpFormatter - Program Args: -T PrintReads -L 3:62739116-78648077 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/3/tx/tmptiqqxi/R14-18106_kapa-NGv3-PE100-NGv3-sort-3_62739115_78648077-prep-prealign.bam
[2016-04-15T00:08Z] INFO  17:08:23,302 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:08Z] INFO  17:08:23,303 HelpFormatter - Date/Time: 2016/04/14 17:08:23
[2016-04-15T00:08Z] INFO  17:08:23,303 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:08Z] INFO  17:08:23,304 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:08Z] INFO  17:08:23,525 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:08Z] GATK pre-alignment ('3', 78649262, 96533852) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:08Z] INFO  17:08:24,335 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@5fe152b7
[2016-04-15T00:08Z] INFO  17:08:24,446 ProgressMeter -            done    108987.0    16.0 s       2.5 m      100.0%    16.0 s       0.0 s
[2016-04-15T00:08Z] INFO  17:08:24,446 ProgressMeter - Total runtime 16.26 secs, 0.27 min, 0.00 hours
[2016-04-15T00:08Z] INFO  17:08:24,447 MicroScheduler - 117 reads were filtered out during the traversal out of approximately 109104 total reads (0.11%)
[2016-04-15T00:08Z] INFO  17:08:24,447 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:08Z] INFO  17:08:24,447 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:08Z] INFO  17:08:24,448 MicroScheduler -   -> 117 reads (0.11% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:08Z] INFO  17:08:24,624 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-15T00:08Z] INFO  17:08:24,713 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:08Z] INFO  17:08:24,722 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:08Z] INFO  17:08:24,770 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-15T00:08Z] INFO  17:08:24,794 IntervalUtils - Processing 15908962 bp from intervals
[2016-04-15T00:08Z] INFO  17:08:24,874 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:08Z] INFO  17:08:25,154 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:08Z] INFO  17:08:25,155 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:08Z] INFO  17:08:25,156 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:08Z] INFO  17:08:25,157 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:08Z] INFO  17:08:25,170 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:08Z] INFO  17:08:25,367 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:08Z] INFO  17:08:25,827 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:08Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-3_15515506_31574805-prep-prealign.bam
[2016-04-15T00:08Z] GATK RealignerTargetCreator: R14-18106_kapa-NGv3-PE100-NGv3-sort-3_15515506_31574805-prep-prealign.bam 3:15515507-31574805
[2016-04-15T00:08Z] GATK: RealignerTargetCreator
[2016-04-15T00:08Z] INFO  17:08:26,288 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:08Z] INFO  17:08:26,290 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:08Z] INFO  17:08:26,290 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:08Z] INFO  17:08:26,290 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:08Z] INFO  17:08:26,295 HelpFormatter - Program Args: -T PrintReads -L 3:78649263-96533852 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/3/tx/tmp6LGykh/R14-18106_kapa-NGv3-PE100-NGv3-sort-3_78649262_96533852-prep-prealign.bam
[2016-04-15T00:08Z] INFO  17:08:26,305 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:08Z] INFO  17:08:26,306 HelpFormatter - Date/Time: 2016/04/14 17:08:26
[2016-04-15T00:08Z] INFO  17:08:26,307 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:08Z] INFO  17:08:26,307 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:08Z] INFO  17:08:26,531 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:08Z] INFO  17:08:27,646 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@7172f77a
[2016-04-15T00:08Z] INFO  17:08:27,716 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-15T00:08Z] INFO  17:08:27,769 ProgressMeter -            done    504997.0    74.0 s       2.5 m      100.0%    74.0 s       0.0 s
[2016-04-15T00:08Z] INFO  17:08:27,770 ProgressMeter - Total runtime 74.95 secs, 1.25 min, 0.02 hours
[2016-04-15T00:08Z] INFO  17:08:27,770 MicroScheduler - 226 reads were filtered out during the traversal out of approximately 505223 total reads (0.04%)
[2016-04-15T00:08Z] INFO  17:08:27,770 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:08Z] INFO  17:08:27,771 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:08Z] INFO  17:08:27,771 MicroScheduler -   -> 226 reads (0.04% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:08Z] INFO  17:08:27,780 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:08Z] INFO  17:08:27,790 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:08Z] INFO  17:08:27,826 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.04
[2016-04-15T00:08Z] INFO  17:08:27,842 IntervalUtils - Processing 17884590 bp from intervals
[2016-04-15T00:08Z] INFO  17:08:27,917 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:08Z] INFO  17:08:28,259 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:08Z] INFO  17:08:28,260 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:08Z] INFO  17:08:28,260 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:08Z] INFO  17:08:28,260 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:08Z] INFO  17:08:28,296 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:08Z] INFO  17:08:28,508 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:08Z] INFO  17:08:28,969 ProgressMeter -            done   1.5578232E7    19.0 s       1.0 s      100.0%    19.0 s       0.0 s
[2016-04-15T00:08Z] INFO  17:08:28,970 ProgressMeter - Total runtime 19.84 secs, 0.33 min, 0.01 hours
[2016-04-15T00:08Z] INFO  17:08:28,974 MicroScheduler - 23262 reads were filtered out during the traversal out of approximately 287309 total reads (8.10%)
[2016-04-15T00:08Z] INFO  17:08:28,975 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:08Z] INFO  17:08:28,975 MicroScheduler -   -> 760 reads (0.26% of total) failing BadMateFilter
[2016-04-15T00:08Z] INFO  17:08:28,976 MicroScheduler -   -> 21140 reads (7.36% of total) failing DuplicateReadFilter
[2016-04-15T00:08Z] INFO  17:08:28,976 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:08Z] INFO  17:08:28,977 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:08Z] INFO  17:08:28,978 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:08Z] INFO  17:08:28,978 MicroScheduler -   -> 1362 reads (0.47% of total) failing MappingQualityZeroFilter
[2016-04-15T00:08Z] INFO  17:08:28,979 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:08Z] INFO  17:08:28,979 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-15T00:08Z] INFO  17:08:28,980 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:08Z] INFO  17:08:28,995 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@32d5a4c6
[2016-04-15T00:08Z] INFO  17:08:29,172 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:08Z] INFO  17:08:29,175 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:08Z] INFO  17:08:29,175 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:08Z] INFO  17:08:29,176 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:08Z] INFO  17:08:29,180 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/3/R14-18106_kapa-NGv3-PE100-NGv3-sort-3_15515506_31574805-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/3/tx/tmpTb8Kpu/R14-18106_kapa-NGv3-PE100-NGv3-sort-3_15515506_31574805-prep-prealign-realign.intervals -l INFO -L 3:15515507-31574805 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:08Z] INFO  17:08:29,189 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:08Z] INFO  17:08:29,189 HelpFormatter - Date/Time: 2016/04/14 17:08:29
[2016-04-15T00:08Z] INFO  17:08:29,190 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:08Z] INFO  17:08:29,190 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:08Z] INFO  17:08:29,192 ProgressMeter -            done    297739.0    45.0 s       2.6 m      100.0%    45.0 s       0.0 s
[2016-04-15T00:08Z] INFO  17:08:29,192 ProgressMeter - Total runtime 45.58 secs, 0.76 min, 0.01 hours
[2016-04-15T00:08Z] INFO  17:08:29,193 MicroScheduler - 230 reads were filtered out during the traversal out of approximately 297969 total reads (0.08%)
[2016-04-15T00:08Z] INFO  17:08:29,193 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:08Z] INFO  17:08:29,193 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:08Z] INFO  17:08:29,194 MicroScheduler -   -> 230 reads (0.08% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:08Z] INFO  17:08:29,219 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:08Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-2_95538561_111273222-prep-prealign.bam
[2016-04-15T00:08Z] INFO  17:08:29,285 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:08Z] INFO  17:08:29,473 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T00:08Z] INFO  17:08:29,482 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:08Z] INFO  17:08:29,532 ProgressMeter -            done   1.6209898E7    20.0 s       1.0 s      100.0%    20.0 s       0.0 s
[2016-04-15T00:08Z] INFO  17:08:29,533 ProgressMeter - Total runtime 20.73 secs, 0.35 min, 0.01 hours
[2016-04-15T00:08Z] INFO  17:08:29,532 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-15T00:08Z] INFO  17:08:29,537 MicroScheduler - 61997 reads were filtered out during the traversal out of approximately 310888 total reads (19.94%)
[2016-04-15T00:08Z] INFO  17:08:29,538 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:08Z] INFO  17:08:29,538 MicroScheduler -   -> 755 reads (0.24% of total) failing BadMateFilter
[2016-04-15T00:08Z] INFO  17:08:29,539 MicroScheduler -   -> 20758 reads (6.68% of total) failing DuplicateReadFilter
[2016-04-15T00:08Z] INFO  17:08:29,540 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:08Z] INFO  17:08:29,540 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:08Z] INFO  17:08:29,541 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:08Z] INFO  17:08:29,541 MicroScheduler -   -> 40484 reads (13.02% of total) failing MappingQualityZeroFilter
[2016-04-15T00:08Z] INFO  17:08:29,541 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:08Z] INFO  17:08:29,542 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-15T00:08Z] INFO  17:08:29,542 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:08Z] INFO  17:08:29,685 ProgressMeter -      3:12195174    100003.0    30.0 s       5.1 m       78.6%    38.0 s       8.0 s
[2016-04-15T00:08Z] INFO  17:08:29,867 IntervalUtils - Processing 16059299 bp from intervals
[2016-04-15T00:08Z] WARN  17:08:29,872 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:08Z] INFO  17:08:29,927 ProgressMeter -            done    223050.0    17.0 s      77.0 s      100.0%    17.0 s       0.0 s
[2016-04-15T00:08Z] INFO  17:08:29,927 ProgressMeter - Total runtime 17.24 secs, 0.29 min, 0.00 hours
[2016-04-15T00:08Z] INFO  17:08:29,931 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 223050 total reads (0.00%)
[2016-04-15T00:08Z] INFO  17:08:29,932 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:08Z] INFO  17:08:29,932 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:08Z] INFO  17:08:29,933 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:08Z] INFO  17:08:30,025 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:08Z] INFO  17:08:30,203 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:08Z] INFO  17:08:30,204 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:08Z] INFO  17:08:30,205 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:08Z] INFO  17:08:30,206 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:08Z] INFO  17:08:30,294 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:08Z] GATK: realign ('2', 159196753, 174774985) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:08Z] INFO  17:08:30,542 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@5fe152b7
[2016-04-15T00:08Z] INFO  17:08:30,569 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:08Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-2_222291154_237994685-prep-prealign.bam
[2016-04-15T00:08Z] INFO  17:08:30,807 ProgressMeter -            done    386691.0    47.0 s       2.0 m      100.0%    47.0 s       0.0 s
[2016-04-15T00:08Z] INFO  17:08:30,807 ProgressMeter - Total runtime 47.46 secs, 0.79 min, 0.01 hours
[2016-04-15T00:08Z] INFO  17:08:30,808 MicroScheduler - 210 reads were filtered out during the traversal out of approximately 386901 total reads (0.05%)
[2016-04-15T00:08Z] INFO  17:08:30,808 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:08Z] INFO  17:08:30,808 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:08Z] INFO  17:08:30,809 MicroScheduler -   -> 210 reads (0.05% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:08Z] GATK RealignerTargetCreator: R14-18106_kapa-NGv3-PE100-NGv3-sort-2_95538561_111273222-prep-prealign.bam 2:95538562-111273222
[2016-04-15T00:08Z] GATK: RealignerTargetCreator
[2016-04-15T00:08Z] INFO  17:08:31,131 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:08Z] GATK: realign ('2', 127433207, 143643105) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:08Z] INFO  17:08:31,377 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:08Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-2_111281072_127413888-prep.bam
[2016-04-15T00:08Z] GATK RealignerTargetCreator: R14-18106_kapa-NGv3-PE100-NGv3-sort-2_222291154_237994685-prep-prealign.bam 2:222291155-237994685
[2016-04-15T00:08Z] GATK: RealignerTargetCreator
[2016-04-15T00:08Z] GATK pre-alignment ('3', 96585668, 112185230) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:08Z] INFO  17:08:32,380 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:08Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-2_205912303_222290862-prep-prealign.bam
[2016-04-15T00:08Z] INFO  17:08:33,218 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:08Z] INFO  17:08:33,220 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:08Z] INFO  17:08:33,220 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:08Z] INFO  17:08:33,221 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:08Z] INFO  17:08:33,243 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/2/R14-18106_kapa-NGv3-PE100-NGv3-sort-2_159196753_174774985-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/2/R14-18106_kapa-NGv3-PE100-NGv3-sort-2_159196753_174774985-prep-prealign-realign.intervals -L 2:159196754-174774985 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/2/tx/tmpHAeHQ1/R14-18106_kapa-NGv3-PE100-NGv3-sort-2_159196753_174774985-prep.bam
[2016-04-15T00:08Z] INFO  17:08:33,259 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:08Z] INFO  17:08:33,259 HelpFormatter - Date/Time: 2016/04/14 17:08:33
[2016-04-15T00:08Z] INFO  17:08:33,259 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:08Z] INFO  17:08:33,260 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:08Z] INFO  17:08:33,523 ProgressMeter -            done   1.5528507E7    19.0 s       1.0 s      100.0%    19.0 s       0.0 s
[2016-04-15T00:08Z] INFO  17:08:33,524 ProgressMeter - Total runtime 19.81 secs, 0.33 min, 0.01 hours
[2016-04-15T00:08Z] INFO  17:08:33,528 MicroScheduler - 32151 reads were filtered out during the traversal out of approximately 326360 total reads (9.85%)
[2016-04-15T00:08Z] INFO  17:08:33,529 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:08Z] INFO  17:08:33,530 MicroScheduler -   -> 771 reads (0.24% of total) failing BadMateFilter
[2016-04-15T00:08Z] INFO  17:08:33,531 MicroScheduler -   -> 23913 reads (7.33% of total) failing DuplicateReadFilter
[2016-04-15T00:08Z] INFO  17:08:33,531 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:08Z] INFO  17:08:33,532 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:08Z] INFO  17:08:33,533 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:08Z] INFO  17:08:33,533 MicroScheduler -   -> 7467 reads (2.29% of total) failing MappingQualityZeroFilter
[2016-04-15T00:08Z] INFO  17:08:33,534 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:08Z] INFO  17:08:33,534 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-15T00:08Z] INFO  17:08:33,535 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:08Z] INFO  17:08:33,540 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:08Z] INFO  17:08:33,719 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:08Z] INFO  17:08:33,728 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:08Z] GATK RealignerTargetCreator: R14-18106_kapa-NGv3-PE100-NGv3-sort-2_205912303_222290862-prep-prealign.bam 2:205912304-222290862
[2016-04-15T00:08Z] GATK: RealignerTargetCreator
[2016-04-15T00:08Z] INFO  17:08:33,854 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.12
[2016-04-15T00:08Z] INFO  17:08:34,272 IntervalUtils - Processing 15578232 bp from intervals
[2016-04-15T00:08Z] WARN  17:08:34,277 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:08Z] INFO  17:08:34,321 ProgressMeter -            done   5203999.0    11.0 s       2.0 s      100.0%    11.0 s       0.0 s
[2016-04-15T00:08Z] INFO  17:08:34,322 ProgressMeter - Total runtime 11.35 secs, 0.19 min, 0.00 hours
[2016-04-15T00:08Z] INFO  17:08:34,326 MicroScheduler - 19175 reads were filtered out during the traversal out of approximately 202267 total reads (9.48%)
[2016-04-15T00:08Z] INFO  17:08:34,326 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:08Z] INFO  17:08:34,327 MicroScheduler -   -> 448 reads (0.22% of total) failing BadMateFilter
[2016-04-15T00:08Z] INFO  17:08:34,327 MicroScheduler -   -> 14966 reads (7.40% of total) failing DuplicateReadFilter
[2016-04-15T00:08Z] INFO  17:08:34,327 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:08Z] INFO  17:08:34,327 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:08Z] INFO  17:08:34,327 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:08Z] INFO  17:08:34,328 MicroScheduler -   -> 3761 reads (1.86% of total) failing MappingQualityZeroFilter
[2016-04-15T00:08Z] INFO  17:08:34,328 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:08Z] INFO  17:08:34,328 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-15T00:08Z] INFO  17:08:34,328 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:08Z] INFO  17:08:34,342 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:08Z] INFO  17:08:34,349 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:08Z] INFO  17:08:34,350 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:08Z] INFO  17:08:34,350 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:08Z] INFO  17:08:34,352 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:08Z] INFO  17:08:34,354 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/2/R14-18106_kapa-NGv3-PE100-NGv3-sort-2_127433207_143643105-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/2/R14-18106_kapa-NGv3-PE100-NGv3-sort-2_127433207_143643105-prep-prealign-realign.intervals -L 2:127433208-143643105 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/2/tx/tmpf1YWsQ/R14-18106_kapa-NGv3-PE100-NGv3-sort-2_127433207_143643105-prep.bam
[2016-04-15T00:08Z] INFO  17:08:34,354 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:08Z] INFO  17:08:34,358 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:08Z] INFO  17:08:34,358 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:08Z] INFO  17:08:34,359 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:08Z] INFO  17:08:34,363 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/2/R14-18106_kapa-NGv3-PE100-NGv3-sort-2_95538561_111273222-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/2/tx/tmpzMZy8Q/R14-18106_kapa-NGv3-PE100-NGv3-sort-2_95538561_111273222-prep-prealign-realign.intervals -l INFO -L 2:95538562-111273222 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:08Z] INFO  17:08:34,366 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:08Z] INFO  17:08:34,367 HelpFormatter - Date/Time: 2016/04/14 17:08:34
[2016-04-15T00:08Z] INFO  17:08:34,368 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:08Z] INFO  17:08:34,368 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:08Z] INFO  17:08:34,373 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:08Z] INFO  17:08:34,374 HelpFormatter - Date/Time: 2016/04/14 17:08:34
[2016-04-15T00:08Z] INFO  17:08:34,374 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:08Z] INFO  17:08:34,375 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:08Z] INFO  17:08:34,390 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:08Z] INFO  17:08:34,394 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:08Z] INFO  17:08:34,394 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:08Z] INFO  17:08:34,395 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:08Z] INFO  17:08:34,400 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/2/R14-18106_kapa-NGv3-PE100-NGv3-sort-2_222291154_237994685-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/2/tx/tmpeIg23u/R14-18106_kapa-NGv3-PE100-NGv3-sort-2_222291154_237994685-prep-prealign-realign.intervals -l INFO -L 2:222291155-237994685 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:08Z] INFO  17:08:34,411 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:08Z] INFO  17:08:34,412 HelpFormatter - Date/Time: 2016/04/14 17:08:34
[2016-04-15T00:08Z] INFO  17:08:34,413 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:08Z] INFO  17:08:34,413 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:08Z] INFO  17:08:34,483 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:08Z] INFO  17:08:34,500 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:08Z] INFO  17:08:34,516 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:08Z] INFO  17:08:34,517 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:08Z] INFO  17:08:34,517 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:08Z] INFO  17:08:34,560 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:08Z] INFO  17:08:34,578 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:08Z] INFO  17:08:34,639 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:08Z] INFO  17:08:34,764 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:08Z] INFO  17:08:34,771 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T00:08Z] INFO  17:08:34,777 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:08Z] INFO  17:08:34,781 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:08Z] INFO  17:08:34,827 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:08Z] INFO  17:08:34,837 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-15T00:08Z] INFO  17:08:34,828 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T00:08Z] INFO  17:08:34,840 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-15T00:08Z] INFO  17:08:34,857 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:08Z] INFO  17:08:34,912 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-15T00:08Z] INFO  17:08:34,998 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:08Z] INFO  17:08:35,002 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:08Z] INFO  17:08:35,002 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:08Z] INFO  17:08:35,003 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:08Z] INFO  17:08:35,007 HelpFormatter - Program Args: -T PrintReads -L 3:96585669-112185230 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/3/tx/tmpRwSPJ6/R14-18106_kapa-NGv3-PE100-NGv3-sort-3_96585668_112185230-prep-prealign.bam
[2016-04-15T00:08Z] INFO  17:08:35,017 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:08Z] INFO  17:08:35,022 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:08Z] INFO  17:08:35,027 HelpFormatter - Date/Time: 2016/04/14 17:08:34
[2016-04-15T00:08Z] INFO  17:08:35,028 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:08Z] INFO  17:08:35,029 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:08Z] GATK: realign ('2', 174777797, 190306304) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:08Z] INFO  17:08:35,159 IntervalUtils - Processing 15734661 bp from intervals
[2016-04-15T00:08Z] WARN  17:08:35,164 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:08Z] INFO  17:08:35,187 IntervalUtils - Processing 15703531 bp from intervals
[2016-04-15T00:08Z] WARN  17:08:35,192 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:08Z] INFO  17:08:35,228 IntervalUtils - Processing 16209898 bp from intervals
[2016-04-15T00:08Z] WARN  17:08:35,242 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:08Z] INFO  17:08:35,246 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:08Z] INFO  17:08:35,291 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:08Z] INFO  17:08:35,361 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:08Z] INFO  17:08:35,370 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:08Z] INFO  17:08:35,534 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:08Z] INFO  17:08:35,545 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:08Z] INFO  17:08:35,535 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:08Z] INFO  17:08:35,546 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:08Z] INFO  17:08:35,546 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:08Z] INFO  17:08:35,547 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:08Z] INFO  17:08:35,547 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:08Z] INFO  17:08:35,548 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:08Z] INFO  17:08:35,669 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:08Z] INFO  17:08:35,680 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:08Z] GATK: realign ('2', 237995374, 243199373) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:08Z] INFO  17:08:35,709 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:08Z] INFO  17:08:35,710 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:08Z] INFO  17:08:35,711 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:08Z] INFO  17:08:35,712 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:08Z] INFO  17:08:35,863 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:08Z] INFO  17:08:36,330 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-15T00:08Z] INFO  17:08:36,398 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:08Z] INFO  17:08:36,409 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:08Z] INFO  17:08:36,487 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-15T00:08Z] INFO  17:08:36,501 IntervalUtils - Processing 15599562 bp from intervals
[2016-04-15T00:08Z] INFO  17:08:36,534 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@5fe152b7
[2016-04-15T00:08Z] INFO  17:08:36,561 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:08Z] INFO  17:08:36,564 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:08Z] INFO  17:08:36,565 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:08Z] INFO  17:08:36,565 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:08Z] INFO  17:08:36,570 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/2/R14-18106_kapa-NGv3-PE100-NGv3-sort-2_205912303_222290862-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/2/tx/tmp97baFG/R14-18106_kapa-NGv3-PE100-NGv3-sort-2_205912303_222290862-prep-prealign-realign.intervals -l INFO -L 2:205912304-222290862 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:08Z] INFO  17:08:36,583 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:08Z] INFO  17:08:36,584 HelpFormatter - Date/Time: 2016/04/14 17:08:36
[2016-04-15T00:08Z] INFO  17:08:36,585 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:08Z] INFO  17:08:36,585 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:08Z] INFO  17:08:36,601 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:08Z] INFO  17:08:36,626 ProgressMeter -            done     44199.0     8.0 s       3.2 m      100.0%     8.0 s       0.0 s
[2016-04-15T00:08Z] INFO  17:08:36,627 ProgressMeter - Total runtime 8.37 secs, 0.14 min, 0.00 hours
[2016-04-15T00:08Z] INFO  17:08:36,627 MicroScheduler - 90 reads were filtered out during the traversal out of approximately 44289 total reads (0.20%)
[2016-04-15T00:08Z] INFO  17:08:36,627 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:08Z] INFO  17:08:36,628 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:08Z] INFO  17:08:36,628 MicroScheduler -   -> 90 reads (0.20% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:08Z] INFO  17:08:36,712 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:08Z] INFO  17:08:36,982 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:08Z] INFO  17:08:36,983 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:08Z] INFO  17:08:36,984 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:08Z] INFO  17:08:36,984 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:08Z] INFO  17:08:37,024 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:08Z] INFO  17:08:37,042 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T00:08Z] INFO  17:08:37,060 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:08Z] INFO  17:08:37,144 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-15T00:08Z] INFO  17:08:37,203 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:08Z] INFO  17:08:37,499 IntervalUtils - Processing 16378559 bp from intervals
[2016-04-15T00:08Z] WARN  17:08:37,504 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:08Z] INFO  17:08:37,631 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:08Z] INFO  17:08:37,846 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:08Z] INFO  17:08:37,848 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:08Z] INFO  17:08:37,848 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:08Z] INFO  17:08:37,849 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:08Z] INFO  17:08:38,101 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:08Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-3_78649262_96533852-prep-prealign.bam
[2016-04-15T00:08Z] INFO  17:08:38,273 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:08Z] INFO  17:08:38,276 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:08Z] INFO  17:08:38,277 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:08Z] INFO  17:08:38,277 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:08Z] INFO  17:08:38,282 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/2/R14-18106_kapa-NGv3-PE100-NGv3-sort-2_174777797_190306304-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/2/R14-18106_kapa-NGv3-PE100-NGv3-sort-2_174777797_190306304-prep-prealign-realign.intervals -L 2:174777798-190306304 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/2/tx/tmpHbVOH7/R14-18106_kapa-NGv3-PE100-NGv3-sort-2_174777797_190306304-prep.bam
[2016-04-15T00:08Z] INFO  17:08:38,292 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:08Z] INFO  17:08:38,303 HelpFormatter - Date/Time: 2016/04/14 17:08:38
[2016-04-15T00:08Z] INFO  17:08:38,304 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:08Z] INFO  17:08:38,305 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:08Z] GATK RealignerTargetCreator: R14-18106_kapa-NGv3-PE100-NGv3-sort-3_78649262_96533852-prep-prealign.bam 3:78649263-96533852
[2016-04-15T00:08Z] GATK: RealignerTargetCreator
[2016-04-15T00:08Z] INFO  17:08:38,403 ProgressMeter -            done   1.5516942E7    19.0 s       1.0 s      100.0%    19.0 s       0.0 s
[2016-04-15T00:08Z] INFO  17:08:38,404 ProgressMeter - Total runtime 19.10 secs, 0.32 min, 0.01 hours
[2016-04-15T00:08Z] INFO  17:08:38,408 MicroScheduler - 19092 reads were filtered out during the traversal out of approximately 243293 total reads (7.85%)
[2016-04-15T00:08Z] INFO  17:08:38,409 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:08Z] INFO  17:08:38,409 MicroScheduler -   -> 661 reads (0.27% of total) failing BadMateFilter
[2016-04-15T00:08Z] INFO  17:08:38,410 MicroScheduler -   -> 17837 reads (7.33% of total) failing DuplicateReadFilter
[2016-04-15T00:08Z] INFO  17:08:38,411 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:08Z] INFO  17:08:38,411 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:08Z] INFO  17:08:38,412 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:08Z] INFO  17:08:38,413 MicroScheduler -   -> 594 reads (0.24% of total) failing MappingQualityZeroFilter
[2016-04-15T00:08Z] INFO  17:08:38,413 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:08Z] INFO  17:08:38,414 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-15T00:08Z] INFO  17:08:38,414 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:08Z] INFO  17:08:38,533 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:08Z] INFO  17:08:38,727 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:08Z] INFO  17:08:38,737 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:08Z] INFO  17:08:38,795 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-15T00:08Z] INFO  17:08:39,123 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:08Z] INFO  17:08:39,126 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:08Z] INFO  17:08:39,126 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:08Z] INFO  17:08:39,126 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:08Z] INFO  17:08:39,130 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/2/R14-18106_kapa-NGv3-PE100-NGv3-sort-2_237995374_243199373-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/2/R14-18106_kapa-NGv3-PE100-NGv3-sort-2_237995374_243199373-prep-prealign-realign.intervals -L 2:237995375-243199373 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/2/tx/tmpLsCsZ_/R14-18106_kapa-NGv3-PE100-NGv3-sort-2_237995374_243199373-prep.bam
[2016-04-15T00:08Z] INFO  17:08:39,180 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:08Z] INFO  17:08:39,181 HelpFormatter - Date/Time: 2016/04/14 17:08:39
[2016-04-15T00:08Z] INFO  17:08:39,181 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:08Z] INFO  17:08:39,182 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:08Z] INFO  17:08:39,225 IntervalUtils - Processing 15528507 bp from intervals
[2016-04-15T00:08Z] WARN  17:08:39,231 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:08Z] INFO  17:08:39,313 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:08Z] INFO  17:08:39,402 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:08Z] INFO  17:08:39,471 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:08Z] INFO  17:08:39,482 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:08Z] INFO  17:08:39,484 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:08Z] INFO  17:08:39,484 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:08Z] INFO  17:08:39,493 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:08Z] INFO  17:08:39,503 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:08Z] INFO  17:08:39,577 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-15T00:08Z] INFO  17:08:39,659 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:08Z] INFO  17:08:39,776 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:08Z] GATK: realign ('2', 190313104, 205830046) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:08Z] INFO  17:08:39,827 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:08Z] INFO  17:08:40,074 IntervalUtils - Processing 5203999 bp from intervals
[2016-04-15T00:08Z] WARN  17:08:40,079 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:08Z] INFO  17:08:40,189 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:08Z] INFO  17:08:40,297 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:08Z] INFO  17:08:40,298 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:08Z] INFO  17:08:40,299 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:08Z] INFO  17:08:40,300 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:08Z] INFO  17:08:40,443 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:08Z] INFO  17:08:40,491 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:08Z] INFO  17:08:41,580 ProgressMeter -      3:39229714    200002.0    30.0 s       2.5 m       49.1%    61.0 s      31.0 s
[2016-04-15T00:08Z] INFO  17:08:41,611 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:08Z] INFO  17:08:41,625 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:08Z] INFO  17:08:41,626 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:08Z] INFO  17:08:41,627 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:08Z] INFO  17:08:41,631 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/3/R14-18106_kapa-NGv3-PE100-NGv3-sort-3_78649262_96533852-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/3/tx/tmpCQZwSP/R14-18106_kapa-NGv3-PE100-NGv3-sort-3_78649262_96533852-prep-prealign-realign.intervals -l INFO -L 3:78649263-96533852 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:08Z] INFO  17:08:41,649 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:08Z] INFO  17:08:41,650 HelpFormatter - Date/Time: 2016/04/14 17:08:41
[2016-04-15T00:08Z] INFO  17:08:41,650 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:08Z] INFO  17:08:41,651 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:08Z] INFO  17:08:41,775 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:08Z] INFO  17:08:41,985 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T00:08Z] INFO  17:08:41,995 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:08Z] INFO  17:08:42,047 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-15T00:08Z] INFO  17:08:42,331 IntervalUtils - Processing 17884590 bp from intervals
[2016-04-15T00:08Z] WARN  17:08:42,336 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:08Z] INFO  17:08:42,418 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:08Z] INFO  17:08:42,589 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:08Z] INFO  17:08:42,591 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:08Z] INFO  17:08:42,591 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:08Z] INFO  17:08:42,592 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:08Z] INFO  17:08:43,158 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:08Z] INFO  17:08:43,162 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:08Z] INFO  17:08:43,162 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:08Z] INFO  17:08:43,163 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:08Z] INFO  17:08:43,167 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/2/R14-18106_kapa-NGv3-PE100-NGv3-sort-2_190313104_205830046-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/2/R14-18106_kapa-NGv3-PE100-NGv3-sort-2_190313104_205830046-prep-prealign-realign.intervals -L 2:190313105-205830046 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/2/tx/tmpbq799H/R14-18106_kapa-NGv3-PE100-NGv3-sort-2_190313104_205830046-prep.bam
[2016-04-15T00:08Z] INFO  17:08:43,177 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:08Z] INFO  17:08:43,178 HelpFormatter - Date/Time: 2016/04/14 17:08:43
[2016-04-15T00:08Z] INFO  17:08:43,178 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:08Z] INFO  17:08:43,179 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:08Z] INFO  17:08:43,401 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:08Z] INFO  17:08:43,566 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:08Z] INFO  17:08:43,574 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:08Z] INFO  17:08:43,637 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-15T00:08Z] INFO  17:08:44,096 IntervalUtils - Processing 15516942 bp from intervals
[2016-04-15T00:08Z] WARN  17:08:44,101 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:08Z] INFO  17:08:44,177 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:08Z] INFO  17:08:44,295 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@41fd9d8e
[2016-04-15T00:08Z] INFO  17:08:44,311 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:08Z] INFO  17:08:44,312 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:08Z] INFO  17:08:44,313 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:08Z] INFO  17:08:44,313 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:08Z] INFO  17:08:44,442 ProgressMeter -            done    119686.0    19.0 s       2.7 m       97.9%    19.0 s       0.0 s
[2016-04-15T00:08Z] INFO  17:08:44,442 ProgressMeter - Total runtime 19.29 secs, 0.32 min, 0.01 hours
[2016-04-15T00:08Z] INFO  17:08:44,443 MicroScheduler - 141 reads were filtered out during the traversal out of approximately 119827 total reads (0.12%)
[2016-04-15T00:08Z] INFO  17:08:44,443 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:08Z] INFO  17:08:44,443 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:08Z] INFO  17:08:44,443 MicroScheduler -   -> 141 reads (0.12% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:08Z] INFO  17:08:44,491 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:08Z] INFO  17:08:44,665 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:08Z] INFO  17:08:45,133 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@7172f77a
[2016-04-15T00:08Z] INFO  17:08:45,201 ProgressMeter -     1:156557921   1.2651574E7    30.0 s       2.0 s       81.6%    36.0 s       6.0 s
[2016-04-15T00:08Z] INFO  17:08:45,248 ProgressMeter -            done    304671.0    46.0 s       2.5 m      100.0%    46.0 s       0.0 s
[2016-04-15T00:08Z] INFO  17:08:45,249 ProgressMeter - Total runtime 46.36 secs, 0.77 min, 0.01 hours
[2016-04-15T00:08Z] INFO  17:08:45,249 MicroScheduler - 188 reads were filtered out during the traversal out of approximately 304859 total reads (0.06%)
[2016-04-15T00:08Z] INFO  17:08:45,250 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:08Z] INFO  17:08:45,250 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:08Z] INFO  17:08:45,250 MicroScheduler -   -> 188 reads (0.06% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:08Z] INFO  17:08:45,941 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:08Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-3_62739115_78648077-prep-prealign.bam
[2016-04-15T00:08Z] INFO  17:08:46,150 ProgressMeter -            done   1.6059299E7    15.0 s       0.0 s      100.0%    15.0 s       0.0 s
[2016-04-15T00:08Z] INFO  17:08:46,151 ProgressMeter - Total runtime 15.95 secs, 0.27 min, 0.00 hours
[2016-04-15T00:08Z] INFO  17:08:46,155 MicroScheduler - 9046 reads were filtered out during the traversal out of approximately 109644 total reads (8.25%)
[2016-04-15T00:08Z] INFO  17:08:46,156 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:08Z] INFO  17:08:46,157 MicroScheduler -   -> 472 reads (0.43% of total) failing BadMateFilter
[2016-04-15T00:08Z] INFO  17:08:46,158 MicroScheduler -   -> 8041 reads (7.33% of total) failing DuplicateReadFilter
[2016-04-15T00:08Z] INFO  17:08:46,158 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:08Z] INFO  17:08:46,159 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:08Z] INFO  17:08:46,159 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:08Z] INFO  17:08:46,160 MicroScheduler -   -> 533 reads (0.49% of total) failing MappingQualityZeroFilter
[2016-04-15T00:08Z] INFO  17:08:46,160 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:08Z] INFO  17:08:46,161 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-15T00:08Z] INFO  17:08:46,162 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:08Z] GATK RealignerTargetCreator: R14-18106_kapa-NGv3-PE100-NGv3-sort-3_62739115_78648077-prep-prealign.bam 3:62739116-78648077
[2016-04-15T00:08Z] GATK: RealignerTargetCreator
[2016-04-15T00:08Z] INFO  17:08:46,669 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:08Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-3_0_15512123-prep-prealign.bam
[2016-04-15T00:08Z] GATK RealignerTargetCreator: R14-18106_kapa-NGv3-PE100-NGv3-sort-3_0_15512123-prep-prealign.bam 3:1-15512123
[2016-04-15T00:08Z] GATK: RealignerTargetCreator
[2016-04-15T00:08Z] INFO  17:08:48,323 ProgressMeter -      3:49160726    200003.0    30.0 s       2.5 m       13.1%     3.8 m       3.3 m
[2016-04-15T00:08Z] INFO  17:08:48,503 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:08Z] GATK: realign ('3', 15515506, 31574805) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:08Z] INFO  17:08:49,403 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:08Z] INFO  17:08:49,407 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:08Z] INFO  17:08:49,408 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:08Z] INFO  17:08:49,409 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:08Z] INFO  17:08:49,415 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/3/R14-18106_kapa-NGv3-PE100-NGv3-sort-3_62739115_78648077-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/3/tx/tmpYpNg2Z/R14-18106_kapa-NGv3-PE100-NGv3-sort-3_62739115_78648077-prep-prealign-realign.intervals -l INFO -L 3:62739116-78648077 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:08Z] INFO  17:08:49,437 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:08Z] INFO  17:08:49,438 HelpFormatter - Date/Time: 2016/04/14 17:08:49
[2016-04-15T00:08Z] INFO  17:08:49,439 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:08Z] INFO  17:08:49,440 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:08Z] INFO  17:08:49,555 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:08Z] INFO  17:08:49,809 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T00:08Z] INFO  17:08:49,829 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:08Z] INFO  17:08:49,916 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.09
[2016-04-15T00:08Z] INFO  17:08:50,200 IntervalUtils - Processing 15908962 bp from intervals
[2016-04-15T00:08Z] WARN  17:08:50,205 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:08Z] INFO  17:08:50,302 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:08Z] INFO  17:08:50,490 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:08Z] INFO  17:08:50,491 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:08Z] INFO  17:08:50,492 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:08Z] INFO  17:08:50,493 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:08Z] INFO  17:08:50,563 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:08Z] INFO  17:08:50,566 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:08Z] INFO  17:08:50,567 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:08Z] INFO  17:08:50,567 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:08Z] INFO  17:08:50,572 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/3/R14-18106_kapa-NGv3-PE100-NGv3-sort-3_0_15512123-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/3/tx/tmpB60uEo/R14-18106_kapa-NGv3-PE100-NGv3-sort-3_0_15512123-prep-prealign-realign.intervals -l INFO -L 3:1-15512123 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:08Z] INFO  17:08:50,584 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:08Z] INFO  17:08:50,584 HelpFormatter - Date/Time: 2016/04/14 17:08:50
[2016-04-15T00:08Z] INFO  17:08:50,584 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:08Z] INFO  17:08:50,584 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:08Z] INFO  17:08:50,670 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:08Z] INFO  17:08:50,833 ProgressMeter -            done   1.5512965E7    35.0 s       2.0 s      100.0%    35.0 s       0.0 s
[2016-04-15T00:08Z] INFO  17:08:50,834 ProgressMeter - Total runtime 35.65 secs, 0.59 min, 0.01 hours
[2016-04-15T00:08Z] INFO  17:08:50,834 MicroScheduler - 361941 reads were filtered out during the traversal out of approximately 1195194 total reads (30.28%)
[2016-04-15T00:08Z] INFO  17:08:50,835 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:08Z] INFO  17:08:50,835 MicroScheduler -   -> 1570 reads (0.13% of total) failing BadMateFilter
[2016-04-15T00:08Z] INFO  17:08:50,835 MicroScheduler -   -> 68945 reads (5.77% of total) failing DuplicateReadFilter
[2016-04-15T00:08Z] INFO  17:08:50,835 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:08Z] INFO  17:08:50,836 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:08Z] INFO  17:08:50,836 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:08Z] INFO  17:08:50,836 MicroScheduler -   -> 291426 reads (24.38% of total) failing MappingQualityZeroFilter
[2016-04-15T00:08Z] INFO  17:08:50,836 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:08Z] INFO  17:08:50,837 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-15T00:08Z] INFO  17:08:50,837 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:08Z] INFO  17:08:50,853 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T00:08Z] INFO  17:08:50,874 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:08Z] INFO  17:08:50,917 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.04
[2016-04-15T00:08Z] INFO  17:08:51,297 IntervalUtils - Processing 15512123 bp from intervals
[2016-04-15T00:08Z] WARN  17:08:51,302 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:08Z] INFO  17:08:51,392 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:08Z] INFO  17:08:51,555 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:08Z] INFO  17:08:51,558 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:08Z] INFO  17:08:51,559 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:08Z] INFO  17:08:51,559 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:08Z] INFO  17:08:51,564 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/3/R14-18106_kapa-NGv3-PE100-NGv3-sort-3_15515506_31574805-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/3/R14-18106_kapa-NGv3-PE100-NGv3-sort-3_15515506_31574805-prep-prealign-realign.intervals -L 3:15515507-31574805 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/3/tx/tmphXn22u/R14-18106_kapa-NGv3-PE100-NGv3-sort-3_15515506_31574805-prep.bam
[2016-04-15T00:08Z] INFO  17:08:51,581 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:08Z] INFO  17:08:51,582 HelpFormatter - Date/Time: 2016/04/14 17:08:51
[2016-04-15T00:08Z] INFO  17:08:51,582 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:08Z] INFO  17:08:51,583 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:08Z] INFO  17:08:51,616 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:08Z] INFO  17:08:51,617 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:08Z] INFO  17:08:51,618 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:08Z] INFO  17:08:51,618 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:08Z] INFO  17:08:51,841 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:08Z] INFO  17:08:51,998 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:08Z] INFO  17:08:52,007 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:08Z] INFO  17:08:52,092 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-15T00:08Z] INFO  17:08:52,176 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:08Z] GATK: realign ('1', 143897546, 159410511) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:08Z] INFO  17:08:52,570 IntervalUtils - Processing 16059299 bp from intervals
[2016-04-15T00:08Z] WARN  17:08:52,587 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:08Z] INFO  17:08:52,691 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:08Z] INFO  17:08:52,806 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:08Z] INFO  17:08:52,807 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:08Z] INFO  17:08:52,808 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:08Z] INFO  17:08:52,820 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:08Z] INFO  17:08:52,979 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:08Z] INFO  17:08:53,140 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:08Z] INFO  17:08:54,403 ProgressMeter -            done    201177.0    14.0 s      70.0 s       97.4%    14.0 s       0.0 s
[2016-04-15T00:08Z] INFO  17:08:54,415 ProgressMeter - Total runtime 14.12 secs, 0.24 min, 0.00 hours
[2016-04-15T00:08Z] INFO  17:08:54,419 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 201177 total reads (0.00%)
[2016-04-15T00:08Z] INFO  17:08:54,420 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:08Z] INFO  17:08:54,421 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:08Z] INFO  17:08:54,421 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:08Z] INFO  17:08:55,154 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:08Z] INFO  17:08:55,157 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:08Z] INFO  17:08:55,157 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:08Z] INFO  17:08:55,157 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:08Z] INFO  17:08:55,161 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/1/R14-18106_kapa-NGv3-PE100-NGv3-sort-1_143897546_159410511-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/1/R14-18106_kapa-NGv3-PE100-NGv3-sort-1_143897546_159410511-prep-prealign-realign.intervals -L 1:143897547-159410511 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/1/tx/tmpJxNIEu/R14-18106_kapa-NGv3-PE100-NGv3-sort-1_143897546_159410511-prep.bam
[2016-04-15T00:08Z] INFO  17:08:55,180 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:08Z] INFO  17:08:55,181 HelpFormatter - Date/Time: 2016/04/14 17:08:55
[2016-04-15T00:08Z] INFO  17:08:55,181 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:08Z] INFO  17:08:55,182 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:08Z] INFO  17:08:55,225 ProgressMeter -            done   1.5703531E7    19.0 s       1.0 s      100.0%    19.0 s       0.0 s
[2016-04-15T00:08Z] INFO  17:08:55,226 ProgressMeter - Total runtime 19.52 secs, 0.33 min, 0.01 hours
[2016-04-15T00:08Z] INFO  17:08:55,231 MicroScheduler - 26136 reads were filtered out during the traversal out of approximately 299848 total reads (8.72%)
[2016-04-15T00:08Z] INFO  17:08:55,232 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:08Z] INFO  17:08:55,233 MicroScheduler -   -> 818 reads (0.27% of total) failing BadMateFilter
[2016-04-15T00:08Z] INFO  17:08:55,234 MicroScheduler -   -> 22816 reads (7.61% of total) failing DuplicateReadFilter
[2016-04-15T00:08Z] INFO  17:08:55,235 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:08Z] INFO  17:08:55,235 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:08Z] INFO  17:08:55,236 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:08Z] INFO  17:08:55,237 MicroScheduler -   -> 2502 reads (0.83% of total) failing MappingQualityZeroFilter
[2016-04-15T00:08Z] INFO  17:08:55,237 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:08Z] INFO  17:08:55,238 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-15T00:08Z] INFO  17:08:55,238 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:08Z] INFO  17:08:55,349 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:08Z] INFO  17:08:55,438 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:08Z] INFO  17:08:55,458 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:08Z] INFO  17:08:55,521 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-15T00:08Z] INFO  17:08:55,776 ProgressMeter -            done    285754.0    21.0 s      74.0 s      100.0%    21.0 s       0.0 s
[2016-04-15T00:08Z] INFO  17:08:55,777 ProgressMeter - Total runtime 21.26 secs, 0.35 min, 0.01 hours
[2016-04-15T00:08Z] INFO  17:08:55,780 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 285754 total reads (0.00%)
[2016-04-15T00:08Z] INFO  17:08:55,781 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:08Z] INFO  17:08:55,781 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:08Z] INFO  17:08:55,781 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:08Z] INFO  17:08:55,920 IntervalUtils - Processing 15512965 bp from intervals
[2016-04-15T00:08Z] WARN  17:08:55,925 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:08Z] INFO  17:08:56,009 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:08Z] INFO  17:08:56,050 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:08Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-2_237995374_243199373-prep.bam
[2016-04-15T00:08Z] INFO  17:08:56,282 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:08Z] INFO  17:08:56,283 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:08Z] INFO  17:08:56,284 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:08Z] INFO  17:08:56,296 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:08Z] INFO  17:08:56,511 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:08Z] INFO  17:08:56,512 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:08Z] GATK: realign ('2', 222291154, 237994685) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:08Z] INFO  17:08:56,706 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:08Z] GATK pre-alignment ('3', 112188604, 127703121) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:08Z] INFO  17:08:57,049 ProgressMeter -            done   1.788459E7    14.0 s       0.0 s      100.0%    14.0 s       0.0 s
[2016-04-15T00:08Z] INFO  17:08:57,051 ProgressMeter - Total runtime 14.46 secs, 0.24 min, 0.00 hours
[2016-04-15T00:08Z] INFO  17:08:57,054 MicroScheduler - 3995 reads were filtered out during the traversal out of approximately 44461 total reads (8.99%)
[2016-04-15T00:08Z] INFO  17:08:57,067 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:08Z] INFO  17:08:57,067 MicroScheduler -   -> 368 reads (0.83% of total) failing BadMateFilter
[2016-04-15T00:08Z] INFO  17:08:57,067 MicroScheduler -   -> 3173 reads (7.14% of total) failing DuplicateReadFilter
[2016-04-15T00:08Z] INFO  17:08:57,068 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:08Z] INFO  17:08:57,068 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:08Z] INFO  17:08:57,068 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:08Z] INFO  17:08:57,068 MicroScheduler -   -> 454 reads (1.02% of total) failing MappingQualityZeroFilter
[2016-04-15T00:08Z] INFO  17:08:57,069 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:08Z] INFO  17:08:57,069 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-15T00:08Z] INFO  17:08:57,069 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:08Z] INFO  17:08:57,319 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:08Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-2_159196753_174774985-prep.bam
[2016-04-15T00:08Z] INFO  17:08:58,001 ProgressMeter -            done    309235.0    22.0 s      72.0 s      100.0%    22.0 s       0.0 s
[2016-04-15T00:08Z] INFO  17:08:58,002 ProgressMeter - Total runtime 22.46 secs, 0.37 min, 0.01 hours
[2016-04-15T00:08Z] INFO  17:08:58,005 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 309235 total reads (0.00%)
[2016-04-15T00:08Z] INFO  17:08:58,006 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:08Z] INFO  17:08:58,006 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:08Z] INFO  17:08:58,006 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:08Z] INFO  17:08:58,242 ProgressMeter -            done   1.5734661E7    22.0 s       1.0 s      100.0%    22.0 s       0.0 s
[2016-04-15T00:08Z] INFO  17:08:58,245 ProgressMeter - Total runtime 22.71 secs, 0.38 min, 0.01 hours
[2016-04-15T00:08Z] INFO  17:08:58,250 MicroScheduler - 128671 reads were filtered out during the traversal out of approximately 508517 total reads (25.30%)
[2016-04-15T00:08Z] INFO  17:08:58,251 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:08Z] INFO  17:08:58,252 MicroScheduler -   -> 897 reads (0.18% of total) failing BadMateFilter
[2016-04-15T00:08Z] INFO  17:08:58,253 MicroScheduler -   -> 31078 reads (6.11% of total) failing DuplicateReadFilter
[2016-04-15T00:08Z] INFO  17:08:58,253 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:08Z] INFO  17:08:58,254 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:08Z] INFO  17:08:58,255 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:08Z] INFO  17:08:58,255 MicroScheduler -   -> 96696 reads (19.02% of total) failing MappingQualityZeroFilter
[2016-04-15T00:08Z] INFO  17:08:58,256 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:08Z] INFO  17:08:58,257 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-15T00:08Z] INFO  17:08:58,257 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:08Z] INFO  17:08:58,330 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:08Z] GATK pre-alignment ('3', 127770401, 143293035) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:08Z] GATK: realign ('3', 78649262, 96533852) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:08Z] INFO  17:08:59,147 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:08Z] INFO  17:08:59,151 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:08Z] INFO  17:08:59,152 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:08Z] INFO  17:08:59,152 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:08Z] INFO  17:08:59,158 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/2/R14-18106_kapa-NGv3-PE100-NGv3-sort-2_222291154_237994685-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/2/R14-18106_kapa-NGv3-PE100-NGv3-sort-2_222291154_237994685-prep-prealign-realign.intervals -L 2:222291155-237994685 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/2/tx/tmpRqYjuX/R14-18106_kapa-NGv3-PE100-NGv3-sort-2_222291154_237994685-prep.bam
[2016-04-15T00:08Z] INFO  17:08:59,171 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:08Z] INFO  17:08:59,172 HelpFormatter - Date/Time: 2016/04/14 17:08:59
[2016-04-15T00:08Z] INFO  17:08:59,173 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:08Z] INFO  17:08:59,174 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:08Z] INFO  17:08:59,397 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:08Z] INFO  17:08:59,401 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:08Z] INFO  17:08:59,402 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:08Z] INFO  17:08:59,402 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:08Z] INFO  17:08:59,409 HelpFormatter - Program Args: -T PrintReads -L 3:112188605-127703121 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/3/tx/tmpwBdx6i/R14-18106_kapa-NGv3-PE100-NGv3-sort-3_112188604_127703121-prep-prealign.bam
[2016-04-15T00:08Z] INFO  17:08:59,427 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:08Z] INFO  17:08:59,428 HelpFormatter - Date/Time: 2016/04/14 17:08:59
[2016-04-15T00:08Z] INFO  17:08:59,428 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:08Z] INFO  17:08:59,428 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:08Z] INFO  17:08:59,438 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:08Z] INFO  17:08:59,555 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:08Z] INFO  17:08:59,569 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:08Z] INFO  17:08:59,581 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:08Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-2_127433207_143643105-prep.bam
[2016-04-15T00:08Z] INFO  17:08:59,638 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-15T00:08Z] INFO  17:08:59,656 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:08Z] INFO  17:08:59,671 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:08Z] GATK: realign ('2', 95538561, 111273222) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:08Z] INFO  17:08:59,913 ProgressMeter -            done   1.6378559E7    22.0 s       1.0 s      100.0%    22.0 s       0.0 s
[2016-04-15T00:08Z] INFO  17:08:59,914 ProgressMeter - Total runtime 22.07 secs, 0.37 min, 0.01 hours
[2016-04-15T00:08Z] INFO  17:08:59,917 MicroScheduler - 30633 reads were filtered out during the traversal out of approximately 388923 total reads (7.88%)
[2016-04-15T00:08Z] INFO  17:08:59,917 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:08Z] INFO  17:08:59,918 MicroScheduler -   -> 923 reads (0.24% of total) failing BadMateFilter
[2016-04-15T00:08Z] INFO  17:08:59,919 MicroScheduler -   -> 29178 reads (7.50% of total) failing DuplicateReadFilter
[2016-04-15T00:08Z] INFO  17:08:59,919 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:08Z] INFO  17:08:59,920 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:08Z] INFO  17:08:59,921 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:08Z] INFO  17:08:59,921 MicroScheduler -   -> 532 reads (0.14% of total) failing MappingQualityZeroFilter
[2016-04-15T00:08Z] INFO  17:08:59,921 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:08Z] INFO  17:08:59,922 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-15T00:08Z] INFO  17:08:59,922 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:08Z] INFO  17:08:59,997 IntervalUtils - Processing 15703531 bp from intervals
[2016-04-15T00:09Z] WARN  17:09:00,001 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:09Z] INFO  17:09:00,081 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:09Z] INFO  17:09:00,253 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:09Z] INFO  17:09:00,254 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:09Z] INFO  17:09:00,255 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:09Z] INFO  17:09:00,256 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:09Z] INFO  17:09:00,412 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:09Z] GATK pre-alignment ('3', 143297426, 158963696) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:09Z] INFO  17:09:00,621 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:09Z] INFO  17:09:00,833 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-15T00:09Z] INFO  17:09:00,977 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:09Z] INFO  17:09:00,988 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:09Z] INFO  17:09:01,043 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-15T00:09Z] INFO  17:09:01,061 IntervalUtils - Processing 15514517 bp from intervals
[2016-04-15T00:09Z] INFO  17:09:01,193 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:09Z] INFO  17:09:01,318 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:09Z] GATK: realign ('2', 205912303, 222290862) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:09Z] INFO  17:09:01,480 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:09Z] INFO  17:09:01,483 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:09Z] INFO  17:09:01,484 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:09Z] INFO  17:09:01,485 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:09Z] INFO  17:09:01,496 HelpFormatter - Program Args: -T PrintReads -L 3:127770402-143293035 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/3/tx/tmp8q0r_a/R14-18106_kapa-NGv3-PE100-NGv3-sort-3_127770401_143293035-prep-prealign.bam
[2016-04-15T00:09Z] INFO  17:09:01,509 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:09Z] INFO  17:09:01,509 HelpFormatter - Date/Time: 2016/04/14 17:09:01
[2016-04-15T00:09Z] INFO  17:09:01,509 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:09Z] INFO  17:09:01,509 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:09Z] INFO  17:09:01,557 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:09Z] INFO  17:09:01,562 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:09Z] INFO  17:09:01,562 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:09Z] INFO  17:09:01,563 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:09Z] INFO  17:09:01,569 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/3/R14-18106_kapa-NGv3-PE100-NGv3-sort-3_78649262_96533852-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/3/R14-18106_kapa-NGv3-PE100-NGv3-sort-3_78649262_96533852-prep-prealign-realign.intervals -L 3:78649263-96533852 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/3/tx/tmpGYLbd8/R14-18106_kapa-NGv3-PE100-NGv3-sort-3_78649262_96533852-prep.bam
[2016-04-15T00:09Z] INFO  17:09:01,593 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:09Z] INFO  17:09:01,593 HelpFormatter - Date/Time: 2016/04/14 17:09:01
[2016-04-15T00:09Z] INFO  17:09:01,593 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:09Z] INFO  17:09:01,594 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:09Z] INFO  17:09:01,671 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:09Z] INFO  17:09:01,683 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:09Z] INFO  17:09:01,683 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:09Z] INFO  17:09:01,684 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:09Z] INFO  17:09:01,700 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:09Z] INFO  17:09:01,715 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:09Z] INFO  17:09:01,880 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:09Z] INFO  17:09:01,930 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:09Z] INFO  17:09:02,014 ProgressMeter -            done    324384.0    22.0 s      69.0 s      100.0%    22.0 s       0.0 s
[2016-04-15T00:09Z] INFO  17:09:02,015 ProgressMeter - Total runtime 22.53 secs, 0.38 min, 0.01 hours
[2016-04-15T00:09Z] INFO  17:09:02,019 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 324384 total reads (0.00%)
[2016-04-15T00:09Z] INFO  17:09:02,020 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:09Z] INFO  17:09:02,021 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:09Z] INFO  17:09:02,021 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:09Z] INFO  17:09:02,043 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:09Z] INFO  17:09:02,053 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:09Z] INFO  17:09:02,035 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@32d5a4c6
[2016-04-15T00:09Z] INFO  17:09:02,123 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-15T00:09Z] INFO  17:09:02,239 ProgressMeter -            done    165058.0    25.0 s       2.6 m      100.0%    25.0 s       0.0 s
[2016-04-15T00:09Z] INFO  17:09:02,239 ProgressMeter - Total runtime 25.26 secs, 0.42 min, 0.01 hours
[2016-04-15T00:09Z] INFO  17:09:02,240 MicroScheduler - 143 reads were filtered out during the traversal out of approximately 165201 total reads (0.09%)
[2016-04-15T00:09Z] INFO  17:09:02,240 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:09Z] INFO  17:09:02,240 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:09Z] INFO  17:09:02,241 MicroScheduler -   -> 143 reads (0.09% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:09Z] INFO  17:09:02,587 IntervalUtils - Processing 17884590 bp from intervals
[2016-04-15T00:09Z] WARN  17:09:02,596 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:09Z] INFO  17:09:02,614 ProgressMeter -            done    241537.0    18.0 s      75.0 s      100.0%    18.0 s       0.0 s
[2016-04-15T00:09Z] INFO  17:09:02,614 ProgressMeter - Total runtime 18.30 secs, 0.31 min, 0.01 hours
[2016-04-15T00:09Z] INFO  17:09:02,618 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 241537 total reads (0.00%)
[2016-04-15T00:09Z] INFO  17:09:02,618 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:09Z] INFO  17:09:02,618 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:09Z] INFO  17:09:02,619 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:09Z] INFO  17:09:02,656 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:09Z] INFO  17:09:02,658 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:09Z] INFO  17:09:02,658 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:09Z] INFO  17:09:02,659 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:09Z] INFO  17:09:02,663 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/2/R14-18106_kapa-NGv3-PE100-NGv3-sort-2_95538561_111273222-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/2/R14-18106_kapa-NGv3-PE100-NGv3-sort-2_95538561_111273222-prep-prealign-realign.intervals -L 2:95538562-111273222 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/2/tx/tmprEfVtZ/R14-18106_kapa-NGv3-PE100-NGv3-sort-2_95538561_111273222-prep.bam
[2016-04-15T00:09Z] INFO  17:09:02,669 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:09Z] INFO  17:09:02,687 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:09Z] INFO  17:09:02,688 HelpFormatter - Date/Time: 2016/04/14 17:09:02
[2016-04-15T00:09Z] INFO  17:09:02,688 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:09Z] INFO  17:09:02,689 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:09Z] INFO  17:09:02,796 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:09Z] INFO  17:09:02,797 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:09Z] INFO  17:09:02,797 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:09Z] INFO  17:09:02,797 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:09Z] INFO  17:09:02,949 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:09Z] INFO  17:09:03,009 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:09Z] INFO  17:09:03,053 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-15T00:09Z] INFO  17:09:03,067 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:09Z] INFO  17:09:03,076 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:09Z] INFO  17:09:03,128 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:09Z] INFO  17:09:03,138 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-15T00:09Z] INFO  17:09:03,143 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:09Z] INFO  17:09:03,247 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.10
[2016-04-15T00:09Z] INFO  17:09:03,263 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:09Z] INFO  17:09:03,285 IntervalUtils - Processing 15522634 bp from intervals
[2016-04-15T00:09Z] INFO  17:09:03,436 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:09Z] INFO  17:09:03,445 IntervalUtils - Processing 15734661 bp from intervals
[2016-04-15T00:09Z] WARN  17:09:03,451 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:09Z] INFO  17:09:03,588 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:09Z] INFO  17:09:03,584 ProgressMeter -            done    108987.0    10.0 s      98.0 s      100.0%    10.0 s       0.0 s
[2016-04-15T00:09Z] INFO  17:09:03,585 ProgressMeter - Total runtime 10.78 secs, 0.18 min, 0.00 hours
[2016-04-15T00:09Z] INFO  17:09:03,588 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 108987 total reads (0.00%)
[2016-04-15T00:09Z] INFO  17:09:03,588 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:09Z] INFO  17:09:03,589 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:09Z] INFO  17:09:03,589 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:09Z] INFO  17:09:03,642 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:09Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-2_174777797_190306304-prep.bam
[2016-04-15T00:09Z] INFO  17:09:03,745 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:09Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-3_96585668_112185230-prep-prealign.bam
[2016-04-15T00:09Z] INFO  17:09:03,823 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:09Z] INFO  17:09:03,828 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:09Z] INFO  17:09:03,831 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:09Z] INFO  17:09:03,832 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:09Z] INFO  17:09:03,833 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:09Z] INFO  17:09:03,835 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:09Z] INFO  17:09:03,836 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:09Z] INFO  17:09:03,837 HelpFormatter - Program Args: -T PrintReads -L 3:143297427-158963696 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/3/tx/tmpxu_10v/R14-18106_kapa-NGv3-PE100-NGv3-sort-3_143297426_158963696-prep-prealign.bam
[2016-04-15T00:09Z] INFO  17:09:03,837 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:09Z] INFO  17:09:03,850 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:09Z] INFO  17:09:03,851 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:09Z] INFO  17:09:03,852 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:09Z] INFO  17:09:03,853 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:09Z] INFO  17:09:03,860 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:09Z] INFO  17:09:03,863 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:09Z] INFO  17:09:03,863 HelpFormatter - Date/Time: 2016/04/14 17:09:03
[2016-04-15T00:09Z] INFO  17:09:03,864 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:09Z] INFO  17:09:03,864 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:09Z] INFO  17:09:04,024 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:09Z] INFO  17:09:04,034 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:09Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-2_190313104_205830046-prep.bam
[2016-04-15T00:09Z] INFO  17:09:04,078 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:09Z] INFO  17:09:04,080 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:09Z] INFO  17:09:04,155 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:09Z] INFO  17:09:04,158 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:09Z] INFO  17:09:04,158 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:09Z] INFO  17:09:04,159 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:09Z] INFO  17:09:04,163 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/2/R14-18106_kapa-NGv3-PE100-NGv3-sort-2_205912303_222290862-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/2/R14-18106_kapa-NGv3-PE100-NGv3-sort-2_205912303_222290862-prep-prealign-realign.intervals -L 2:205912304-222290862 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/2/tx/tmpGqGfaX/R14-18106_kapa-NGv3-PE100-NGv3-sort-2_205912303_222290862-prep.bam
[2016-04-15T00:09Z] INFO  17:09:04,173 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:09Z] INFO  17:09:04,185 HelpFormatter - Date/Time: 2016/04/14 17:09:04
[2016-04-15T00:09Z] INFO  17:09:04,186 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:09Z] INFO  17:09:04,187 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:09Z] INFO  17:09:04,201 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:09Z] GATK RealignerTargetCreator: R14-18106_kapa-NGv3-PE100-NGv3-sort-3_96585668_112185230-prep-prealign.bam 3:96585669-112185230
[2016-04-15T00:09Z] GATK: RealignerTargetCreator
[2016-04-15T00:09Z] INFO  17:09:04,421 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:09Z] INFO  17:09:04,583 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:09Z] INFO  17:09:04,597 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:09Z] INFO  17:09:04,676 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-15T00:09Z] GATK pre-alignment ('3', 158970515, 174577240) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:09Z] GATK pre-alignment ('3', 174814579, 190326970) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:09Z] INFO  17:09:05,184 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:09Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-3_15515506_31574805-prep.bam
[2016-04-15T00:09Z] INFO  17:09:05,240 IntervalUtils - Processing 16378559 bp from intervals
[2016-04-15T00:09Z] WARN  17:09:05,266 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:09Z] INFO  17:09:05,292 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@41fd9d8e
[2016-04-15T00:09Z] INFO  17:09:05,355 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:09Z] INFO  17:09:05,372 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-15T00:09Z] INFO  17:09:05,384 ProgressMeter -            done    451475.0    53.0 s     119.0 s      100.0%    53.0 s       0.0 s
[2016-04-15T00:09Z] INFO  17:09:05,385 ProgressMeter - Total runtime 53.82 secs, 0.90 min, 0.01 hours
[2016-04-15T00:09Z] INFO  17:09:05,386 MicroScheduler - 204 reads were filtered out during the traversal out of approximately 451679 total reads (0.05%)
[2016-04-15T00:09Z] INFO  17:09:05,387 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:09Z] INFO  17:09:05,387 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:09Z] INFO  17:09:05,388 MicroScheduler -   -> 204 reads (0.05% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:09Z] INFO  17:09:05,475 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:09Z] INFO  17:09:05,484 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:09Z] INFO  17:09:05,513 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:09Z] INFO  17:09:05,514 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:09Z] INFO  17:09:05,514 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:09Z] INFO  17:09:05,515 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:09Z] INFO  17:09:05,540 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-15T00:09Z] GATK pre-alignment ('3', 190333063, 198022430) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:09Z] INFO  17:09:05,558 IntervalUtils - Processing 15666270 bp from intervals
[2016-04-15T00:09Z] INFO  17:09:05,639 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:09Z] INFO  17:09:05,690 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:09Z] INFO  17:09:05,883 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:09Z] INFO  17:09:05,971 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:09Z] INFO  17:09:05,973 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:09Z] INFO  17:09:05,973 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:09Z] INFO  17:09:05,974 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:09Z] INFO  17:09:05,997 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:09Z] INFO  17:09:06,146 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:09Z] INFO  17:09:06,996 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:09Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-3_31617887_47127804-prep-prealign.bam
[2016-04-15T00:09Z] INFO  17:09:07,740 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:09Z] INFO  17:09:07,743 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:09Z] INFO  17:09:07,744 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:09Z] INFO  17:09:07,744 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:09Z] INFO  17:09:07,749 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/3/R14-18106_kapa-NGv3-PE100-NGv3-sort-3_96585668_112185230-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/3/tx/tmpCEgu_a/R14-18106_kapa-NGv3-PE100-NGv3-sort-3_96585668_112185230-prep-prealign-realign.intervals -l INFO -L 3:96585669-112185230 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:09Z] INFO  17:09:07,774 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:09Z] INFO  17:09:07,785 HelpFormatter - Date/Time: 2016/04/14 17:09:07
[2016-04-15T00:09Z] INFO  17:09:07,786 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:09Z] INFO  17:09:07,787 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:09Z] INFO  17:09:07,904 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:09Z] INFO  17:09:07,906 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:09Z] INFO  17:09:07,906 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:09Z] INFO  17:09:07,907 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:09Z] INFO  17:09:07,911 HelpFormatter - Program Args: -T PrintReads -L 3:158970516-174577240 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/3/tx/tmpp4jPu8/R14-18106_kapa-NGv3-PE100-NGv3-sort-3_158970515_174577240-prep-prealign.bam
[2016-04-15T00:09Z] INFO  17:09:07,928 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:09Z] INFO  17:09:07,945 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:09Z] INFO  17:09:07,946 HelpFormatter - Date/Time: 2016/04/14 17:09:07
[2016-04-15T00:09Z] INFO  17:09:07,947 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:09Z] INFO  17:09:07,947 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:09Z] INFO  17:09:08,100 ProgressMeter -            done   1.5908962E7    17.0 s       1.0 s      100.0%    17.0 s       0.0 s
[2016-04-15T00:09Z] INFO  17:09:08,101 ProgressMeter - Total runtime 17.61 secs, 0.29 min, 0.00 hours
[2016-04-15T00:09Z] INFO  17:09:08,106 MicroScheduler - 13396 reads were filtered out during the traversal out of approximately 120169 total reads (11.15%)
[2016-04-15T00:09Z] INFO  17:09:08,109 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:09Z] INFO  17:09:08,110 MicroScheduler -   -> 515 reads (0.43% of total) failing BadMateFilter
[2016-04-15T00:09Z] INFO  17:09:08,110 MicroScheduler -   -> 8579 reads (7.14% of total) failing DuplicateReadFilter
[2016-04-15T00:09Z] INFO  17:09:08,120 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:09Z] INFO  17:09:08,121 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:09Z] INFO  17:09:08,122 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:09Z] INFO  17:09:08,123 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:09Z] INFO  17:09:08,124 MicroScheduler -   -> 4302 reads (3.58% of total) failing MappingQualityZeroFilter
[2016-04-15T00:09Z] INFO  17:09:08,124 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:09Z] INFO  17:09:08,125 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-15T00:09Z] INFO  17:09:08,125 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:09Z] INFO  17:09:08,142 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:09Z] INFO  17:09:08,145 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:09Z] INFO  17:09:08,146 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:09Z] INFO  17:09:08,146 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:09Z] INFO  17:09:08,151 HelpFormatter - Program Args: -T PrintReads -L 3:174814580-190326970 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/3/tx/tmpFfkavq/R14-18106_kapa-NGv3-PE100-NGv3-sort-3_174814579_190326970-prep-prealign.bam
[2016-04-15T00:09Z] INFO  17:09:08,172 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:09Z] INFO  17:09:08,173 HelpFormatter - Date/Time: 2016/04/14 17:09:08
[2016-04-15T00:09Z] INFO  17:09:08,173 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:09Z] INFO  17:09:08,174 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:09Z] INFO  17:09:08,205 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T00:09Z] INFO  17:09:08,225 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:09Z] INFO  17:09:08,318 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.09
[2016-04-15T00:09Z] INFO  17:09:08,338 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:09Z] GATK RealignerTargetCreator: R14-18106_kapa-NGv3-PE100-NGv3-sort-3_31617887_47127804-prep-prealign.bam 3:31617888-47127804
[2016-04-15T00:09Z] GATK: RealignerTargetCreator
[2016-04-15T00:09Z] INFO  17:09:08,613 IntervalUtils - Processing 15599562 bp from intervals
[2016-04-15T00:09Z] WARN  17:09:08,618 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:09Z] INFO  17:09:08,627 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:09Z] INFO  17:09:08,631 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:09Z] INFO  17:09:08,631 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:09Z] INFO  17:09:08,632 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:09Z] INFO  17:09:08,637 HelpFormatter - Program Args: -T PrintReads -L 3:190333064-198022430 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/3/tx/tmp6qeklW/R14-18106_kapa-NGv3-PE100-NGv3-sort-3_190333063_198022430-prep-prealign.bam
[2016-04-15T00:09Z] INFO  17:09:08,654 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:09Z] INFO  17:09:08,655 HelpFormatter - Date/Time: 2016/04/14 17:09:08
[2016-04-15T00:09Z] INFO  17:09:08,656 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:09Z] INFO  17:09:08,663 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:09Z] INFO  17:09:08,703 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:09Z] INFO  17:09:08,883 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:09Z] INFO  17:09:08,891 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:09Z] INFO  17:09:08,892 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:09Z] INFO  17:09:08,893 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:09Z] INFO  17:09:08,894 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:09Z] INFO  17:09:09,412 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-15T00:09Z] INFO  17:09:09,485 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:09Z] INFO  17:09:09,505 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:09Z] INFO  17:09:09,514 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-15T00:09Z] INFO  17:09:09,569 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-15T00:09Z] INFO  17:09:09,568 ProgressMeter -            done     44199.0     6.0 s       2.6 m      100.0%     6.0 s       0.0 s
[2016-04-15T00:09Z] INFO  17:09:09,569 ProgressMeter - Total runtime 6.77 secs, 0.11 min, 0.00 hours
[2016-04-15T00:09Z] INFO  17:09:09,572 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 44199 total reads (0.00%)
[2016-04-15T00:09Z] INFO  17:09:09,573 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:09Z] INFO  17:09:09,573 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:09Z] INFO  17:09:09,575 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:09Z] INFO  17:09:09,593 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:09Z] INFO  17:09:09,594 IntervalUtils - Processing 15606725 bp from intervals
[2016-04-15T00:09Z] INFO  17:09:09,604 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:09Z] INFO  17:09:09,666 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-15T00:09Z] INFO  17:09:09,698 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:09Z] INFO  17:09:09,713 IntervalUtils - Processing 15512391 bp from intervals
[2016-04-15T00:09Z] INFO  17:09:09,800 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:09Z] GATK: realign ('3', 62739115, 78648077) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:09Z] INFO  17:09:09,862 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:09Z] INFO  17:09:10,001 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-15T00:09Z] INFO  17:09:10,017 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:09Z] INFO  17:09:10,018 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:09Z] INFO  17:09:10,019 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:09Z] INFO  17:09:10,020 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:09Z] INFO  17:09:10,034 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:09Z] INFO  17:09:10,102 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:09Z] INFO  17:09:10,111 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:09Z] INFO  17:09:10,179 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-15T00:09Z] INFO  17:09:10,203 IntervalUtils - Processing 7689367 bp from intervals
[2016-04-15T00:09Z] INFO  17:09:10,247 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:09Z] INFO  17:09:10,248 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:09Z] INFO  17:09:10,249 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:09Z] INFO  17:09:10,250 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:09Z] INFO  17:09:10,263 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:09Z] INFO  17:09:10,277 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:09Z] INFO  17:09:10,285 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:09Z] INFO  17:09:10,425 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:09Z] INFO  17:09:10,604 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:09Z] INFO  17:09:10,605 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:09Z] INFO  17:09:10,606 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:09Z] INFO  17:09:10,607 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:09Z] INFO  17:09:10,644 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:09Z] INFO  17:09:10,789 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:09Z] INFO  17:09:11,136 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:09Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-3_78649262_96533852-prep.bam
[2016-04-15T00:09Z] GATK pre-alignment ('4', 0, 15511864) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:09Z] INFO  17:09:11,496 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:09Z] INFO  17:09:11,499 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:09Z] INFO  17:09:11,500 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:09Z] INFO  17:09:11,501 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:09Z] INFO  17:09:11,505 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/3/R14-18106_kapa-NGv3-PE100-NGv3-sort-3_31617887_47127804-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/3/tx/tmpSMhbCv/R14-18106_kapa-NGv3-PE100-NGv3-sort-3_31617887_47127804-prep-prealign-realign.intervals -l INFO -L 3:31617888-47127804 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:09Z] INFO  17:09:11,525 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:09Z] INFO  17:09:11,526 HelpFormatter - Date/Time: 2016/04/14 17:09:11
[2016-04-15T00:09Z] INFO  17:09:11,526 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:09Z] INFO  17:09:11,527 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:09Z] INFO  17:09:11,714 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:09Z] INFO  17:09:11,961 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T00:09Z] INFO  17:09:11,980 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:09Z] INFO  17:09:12,087 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.11
[2016-04-15T00:09Z] INFO  17:09:12,489 IntervalUtils - Processing 15509917 bp from intervals
[2016-04-15T00:09Z] WARN  17:09:12,494 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:09Z] INFO  17:09:12,602 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:09Z] INFO  17:09:12,814 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:09Z] INFO  17:09:12,814 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:09Z] INFO  17:09:12,815 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:09Z] INFO  17:09:12,815 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:09Z] INFO  17:09:12,836 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:09Z] INFO  17:09:12,840 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:09Z] INFO  17:09:12,841 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:09Z] INFO  17:09:12,841 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:09Z] INFO  17:09:12,846 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/3/R14-18106_kapa-NGv3-PE100-NGv3-sort-3_62739115_78648077-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/3/R14-18106_kapa-NGv3-PE100-NGv3-sort-3_62739115_78648077-prep-prealign-realign.intervals -L 3:62739116-78648077 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/3/tx/tmp5R95J9/R14-18106_kapa-NGv3-PE100-NGv3-sort-3_62739115_78648077-prep.bam
[2016-04-15T00:09Z] INFO  17:09:12,876 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:09Z] INFO  17:09:12,877 HelpFormatter - Date/Time: 2016/04/14 17:09:12
[2016-04-15T00:09Z] INFO  17:09:12,877 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:09Z] INFO  17:09:12,878 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:09Z] INFO  17:09:12,913 ProgressMeter -            done   1.5512123E7    21.0 s       1.0 s      100.0%    21.0 s       0.0 s
[2016-04-15T00:09Z] INFO  17:09:12,914 ProgressMeter - Total runtime 21.30 secs, 0.35 min, 0.01 hours
[2016-04-15T00:09Z] INFO  17:09:12,918 MicroScheduler - 24206 reads were filtered out during the traversal out of approximately 305980 total reads (7.91%)
[2016-04-15T00:09Z] INFO  17:09:12,919 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:09Z] INFO  17:09:12,920 MicroScheduler -   -> 829 reads (0.27% of total) failing BadMateFilter
[2016-04-15T00:09Z] INFO  17:09:12,921 MicroScheduler -   -> 22816 reads (7.46% of total) failing DuplicateReadFilter
[2016-04-15T00:09Z] INFO  17:09:12,921 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:09Z] INFO  17:09:12,922 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:09Z] INFO  17:09:12,923 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:09Z] INFO  17:09:12,923 MicroScheduler -   -> 561 reads (0.18% of total) failing MappingQualityZeroFilter
[2016-04-15T00:09Z] INFO  17:09:12,924 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:09Z] INFO  17:09:12,925 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-15T00:09Z] INFO  17:09:12,925 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:09Z] INFO  17:09:13,105 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:09Z] INFO  17:09:13,234 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:09Z] INFO  17:09:13,243 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:09Z] INFO  17:09:13,310 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-15T00:09Z] INFO  17:09:13,671 IntervalUtils - Processing 15908962 bp from intervals
[2016-04-15T00:09Z] WARN  17:09:13,687 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:09Z] INFO  17:09:13,837 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:09Z] INFO  17:09:13,999 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:09Z] INFO  17:09:14,001 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:09Z] INFO  17:09:14,002 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:09Z] INFO  17:09:14,003 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:09Z] INFO  17:09:14,260 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:09Z] INFO  17:09:14,429 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:09Z] INFO  17:09:14,493 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:09Z] GATK: realign ('3', 0, 15512123) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:09Z] INFO  17:09:14,706 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:09Z] INFO  17:09:14,709 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:09Z] INFO  17:09:14,710 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:09Z] INFO  17:09:14,710 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:09Z] INFO  17:09:14,715 HelpFormatter - Program Args: -T PrintReads -L 4:1-15511864 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/4/tx/tmp6MnHKX/R14-18106_kapa-NGv3-PE100-NGv3-sort-4_0_15511864-prep-prealign.bam
[2016-04-15T00:09Z] INFO  17:09:14,733 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:09Z] INFO  17:09:14,734 HelpFormatter - Date/Time: 2016/04/14 17:09:14
[2016-04-15T00:09Z] INFO  17:09:14,735 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:09Z] INFO  17:09:14,735 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:09Z] INFO  17:09:14,932 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:09Z] INFO  17:09:16,204 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-15T00:09Z] INFO  17:09:16,280 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:09Z] INFO  17:09:16,289 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:09Z] INFO  17:09:16,324 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.04
[2016-04-15T00:09Z] INFO  17:09:16,338 IntervalUtils - Processing 15511864 bp from intervals
[2016-04-15T00:09Z] INFO  17:09:16,415 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:09Z] INFO  17:09:16,661 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:09Z] INFO  17:09:16,663 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:09Z] INFO  17:09:16,663 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:09Z] INFO  17:09:16,664 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:09Z] INFO  17:09:16,679 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:09Z] INFO  17:09:16,833 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:09Z] INFO  17:09:17,435 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:09Z] INFO  17:09:17,439 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:09Z] INFO  17:09:17,440 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:09Z] INFO  17:09:17,440 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:09Z] INFO  17:09:17,445 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/3/R14-18106_kapa-NGv3-PE100-NGv3-sort-3_0_15512123-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/3/R14-18106_kapa-NGv3-PE100-NGv3-sort-3_0_15512123-prep-prealign-realign.intervals -L 3:1-15512123 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/3/tx/tmp7w9q3i/R14-18106_kapa-NGv3-PE100-NGv3-sort-3_0_15512123-prep.bam
[2016-04-15T00:09Z] INFO  17:09:17,456 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:09Z] INFO  17:09:17,462 HelpFormatter - Date/Time: 2016/04/14 17:09:17
[2016-04-15T00:09Z] INFO  17:09:17,463 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:09Z] INFO  17:09:17,464 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:09Z] INFO  17:09:17,657 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:09Z] INFO  17:09:17,792 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:09Z] INFO  17:09:17,806 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:09Z] INFO  17:09:17,852 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-15T00:09Z] INFO  17:09:18,320 IntervalUtils - Processing 15512123 bp from intervals
[2016-04-15T00:09Z] WARN  17:09:18,328 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:09Z] INFO  17:09:18,430 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:09Z] INFO  17:09:18,595 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:09Z] INFO  17:09:18,596 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:09Z] INFO  17:09:18,596 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:09Z] INFO  17:09:18,597 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:09Z] INFO  17:09:18,818 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:09Z] INFO  17:09:18,942 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:09Z] INFO  17:09:19,644 ProgressMeter -      3:52475189    400010.0    61.0 s       2.6 m       34.4%     3.0 m     116.0 s
[2016-04-15T00:09Z] INFO  17:09:22,741 ProgressMeter -            done    297739.0    22.0 s      75.0 s      100.0%    22.0 s       0.0 s
[2016-04-15T00:09Z] INFO  17:09:22,742 ProgressMeter - Total runtime 22.49 secs, 0.37 min, 0.01 hours
[2016-04-15T00:09Z] INFO  17:09:22,746 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 297739 total reads (0.00%)
[2016-04-15T00:09Z] INFO  17:09:22,746 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:09Z] INFO  17:09:22,751 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:09Z] INFO  17:09:22,751 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:09Z] INFO  17:09:24,301 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:09Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-2_222291154_237994685-prep.bam
[2016-04-15T00:09Z] INFO  17:09:24,695 ProgressMeter -            done    119686.0    10.0 s      89.0 s       97.9%    10.0 s       0.0 s
[2016-04-15T00:09Z] INFO  17:09:24,696 ProgressMeter - Total runtime 10.69 secs, 0.18 min, 0.00 hours
[2016-04-15T00:09Z] INFO  17:09:24,700 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 119686 total reads (0.00%)
[2016-04-15T00:09Z] INFO  17:09:24,700 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:09Z] INFO  17:09:24,700 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:09Z] INFO  17:09:24,701 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:09Z] GATK pre-alignment ('4', 15512869, 31144471) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:09Z] INFO  17:09:26,272 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:09Z] INFO  17:09:26,276 ProgressMeter -            done   1.5599562E7    17.0 s       1.0 s      100.0%    17.0 s       0.0 s
[2016-04-15T00:09Z] INFO  17:09:26,276 ProgressMeter - Total runtime 17.38 secs, 0.29 min, 0.00 hours
[2016-04-15T00:09Z] INFO  17:09:26,280 MicroScheduler - 13439 reads were filtered out during the traversal out of approximately 165948 total reads (8.10%)
[2016-04-15T00:09Z] INFO  17:09:26,281 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:09Z] INFO  17:09:26,281 MicroScheduler -   -> 563 reads (0.34% of total) failing BadMateFilter
[2016-04-15T00:09Z] INFO  17:09:26,281 MicroScheduler -   -> 12041 reads (7.26% of total) failing DuplicateReadFilter
[2016-04-15T00:09Z] INFO  17:09:26,281 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:09Z] INFO  17:09:26,282 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:09Z] INFO  17:09:26,282 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:09Z] INFO  17:09:26,282 MicroScheduler -   -> 835 reads (0.50% of total) failing MappingQualityZeroFilter
[2016-04-15T00:09Z] INFO  17:09:26,282 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:09Z] INFO  17:09:26,282 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-15T00:09Z] INFO  17:09:26,283 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:09Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-3_62739115_78648077-prep.bam
[2016-04-15T00:09Z] INFO  17:09:26,311 ProgressMeter -     1:149813886    400009.0    30.0 s      75.0 s       38.1%    78.0 s      48.0 s
[2016-04-15T00:09Z] GATK pre-alignment ('4', 36069528, 52709433) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:09Z] INFO  17:09:26,917 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@41fd9d8e
[2016-04-15T00:09Z] INFO  17:09:27,084 ProgressMeter -            done    124218.0    17.0 s       2.3 m      100.0%    17.0 s       0.0 s
[2016-04-15T00:09Z] INFO  17:09:27,084 ProgressMeter - Total runtime 17.07 secs, 0.28 min, 0.00 hours
[2016-04-15T00:09Z] INFO  17:09:27,085 MicroScheduler - 116 reads were filtered out during the traversal out of approximately 124334 total reads (0.09%)
[2016-04-15T00:09Z] INFO  17:09:27,085 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:09Z] INFO  17:09:27,086 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:09Z] INFO  17:09:27,086 MicroScheduler -   -> 116 reads (0.09% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:09Z] INFO  17:09:27,800 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:09Z] GATK: realign ('3', 96585668, 112185230) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:09Z] INFO  17:09:27,960 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:09Z] INFO  17:09:27,964 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:09Z] INFO  17:09:27,965 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:09Z] INFO  17:09:27,965 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:09Z] INFO  17:09:27,970 HelpFormatter - Program Args: -T PrintReads -L 4:15512870-31144471 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/4/tx/tmpwwDSE5/R14-18106_kapa-NGv3-PE100-NGv3-sort-4_15512869_31144471-prep-prealign.bam
[2016-04-15T00:09Z] INFO  17:09:27,997 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:09Z] INFO  17:09:27,998 HelpFormatter - Date/Time: 2016/04/14 17:09:27
[2016-04-15T00:09Z] INFO  17:09:27,999 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:09Z] INFO  17:09:27,999 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:09Z] INFO  17:09:28,152 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:09Z] INFO  17:09:28,618 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@32d5a4c6
[2016-04-15T00:09Z] INFO  17:09:28,808 ProgressMeter -            done    156957.0    22.0 s       2.4 m      100.0%    22.0 s       0.0 s
[2016-04-15T00:09Z] INFO  17:09:28,809 ProgressMeter - Total runtime 22.84 secs, 0.38 min, 0.01 hours
[2016-04-15T00:09Z] INFO  17:09:28,809 MicroScheduler - 136 reads were filtered out during the traversal out of approximately 157093 total reads (0.09%)
[2016-04-15T00:09Z] INFO  17:09:28,809 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:09Z] INFO  17:09:28,810 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:09Z] INFO  17:09:28,810 MicroScheduler -   -> 136 reads (0.09% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:09Z] INFO  17:09:28,842 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:09Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-3_158970515_174577240-prep-prealign.bam
[2016-04-15T00:09Z] INFO  17:09:29,188 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-15T00:09Z] INFO  17:09:29,282 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:09Z] INFO  17:09:29,303 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:09Z] GATK RealignerTargetCreator: R14-18106_kapa-NGv3-PE100-NGv3-sort-3_158970515_174577240-prep-prealign.bam 3:158970516-174577240
[2016-04-15T00:09Z] GATK: RealignerTargetCreator
[2016-04-15T00:09Z] INFO  17:09:29,370 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-15T00:09Z] INFO  17:09:29,387 IntervalUtils - Processing 15631602 bp from intervals
[2016-04-15T00:09Z] INFO  17:09:29,500 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:09Z] INFO  17:09:29,754 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:09Z] INFO  17:09:29,758 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:09Z] INFO  17:09:29,759 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:09Z] INFO  17:09:29,760 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:09Z] INFO  17:09:29,765 HelpFormatter - Program Args: -T PrintReads -L 4:36069529-52709433 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/4/tx/tmp42Cp_N/R14-18106_kapa-NGv3-PE100-NGv3-sort-4_36069528_52709433-prep-prealign.bam
[2016-04-15T00:09Z] INFO  17:09:29,786 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:09Z] INFO  17:09:29,787 HelpFormatter - Date/Time: 2016/04/14 17:09:29
[2016-04-15T00:09Z] INFO  17:09:29,787 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:09Z] INFO  17:09:29,788 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:09Z] INFO  17:09:29,819 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:09Z] INFO  17:09:29,820 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:09Z] INFO  17:09:29,821 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:09Z] INFO  17:09:29,822 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:09Z] INFO  17:09:29,840 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:09Z] INFO  17:09:30,007 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:09Z] INFO  17:09:30,059 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:09Z] INFO  17:09:30,104 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:09Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-3_143297426_158963696-prep-prealign.bam
[2016-04-15T00:09Z] INFO  17:09:30,577 ProgressMeter -            done    386691.0    25.0 s      64.0 s      100.0%    25.0 s       0.0 s
[2016-04-15T00:09Z] INFO  17:09:30,578 ProgressMeter - Total runtime 25.06 secs, 0.42 min, 0.01 hours
[2016-04-15T00:09Z] INFO  17:09:30,582 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 386691 total reads (0.00%)
[2016-04-15T00:09Z] INFO  17:09:30,588 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:09Z] INFO  17:09:30,592 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:09Z] INFO  17:09:30,593 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:09Z] INFO  17:09:30,593 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:09Z] INFO  17:09:30,588 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:09Z] INFO  17:09:30,589 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:09Z] INFO  17:09:30,589 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:09Z] INFO  17:09:30,599 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/3/R14-18106_kapa-NGv3-PE100-NGv3-sort-3_96585668_112185230-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/3/R14-18106_kapa-NGv3-PE100-NGv3-sort-3_96585668_112185230-prep-prealign-realign.intervals -L 3:96585669-112185230 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/3/tx/tmpeNUiFt/R14-18106_kapa-NGv3-PE100-NGv3-sort-3_96585668_112185230-prep.bam
[2016-04-15T00:09Z] INFO  17:09:30,610 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:09Z] GATK RealignerTargetCreator: R14-18106_kapa-NGv3-PE100-NGv3-sort-3_143297426_158963696-prep-prealign.bam 3:143297427-158963696
[2016-04-15T00:09Z] GATK: RealignerTargetCreator
[2016-04-15T00:09Z] INFO  17:09:30,621 HelpFormatter - Date/Time: 2016/04/14 17:09:30
[2016-04-15T00:09Z] INFO  17:09:30,629 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:09Z] INFO  17:09:30,630 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:09Z] INFO  17:09:30,918 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:09Z] INFO  17:09:31,023 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:09Z] INFO  17:09:31,032 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:09Z] INFO  17:09:31,084 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-15T00:09Z] INFO  17:09:31,169 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-15T00:09Z] INFO  17:09:31,236 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:09Z] INFO  17:09:31,245 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:09Z] INFO  17:09:31,309 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-15T00:09Z] INFO  17:09:31,324 IntervalUtils - Processing 16639905 bp from intervals
[2016-04-15T00:09Z] INFO  17:09:31,404 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:09Z] INFO  17:09:31,487 IntervalUtils - Processing 15599562 bp from intervals
[2016-04-15T00:09Z] WARN  17:09:31,492 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:09Z] INFO  17:09:31,582 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:09Z] INFO  17:09:31,674 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:09Z] INFO  17:09:31,676 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:09Z] INFO  17:09:31,676 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:09Z] INFO  17:09:31,677 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:09Z] INFO  17:09:31,716 ProgressMeter -     3:122631813    100001.0    30.0 s       5.0 m       67.3%    44.0 s      14.0 s
[2016-04-15T00:09Z] INFO  17:09:31,760 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:09Z] INFO  17:09:31,762 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:09Z] INFO  17:09:31,762 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:09Z] INFO  17:09:31,763 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:09Z] INFO  17:09:31,776 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:09Z] INFO  17:09:31,894 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:09Z] INFO  17:09:31,915 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:09Z] INFO  17:09:32,082 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:09Z] INFO  17:09:32,306 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:09Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-2_205912303_222290862-prep.bam
[2016-04-15T00:09Z] INFO  17:09:32,451 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:09Z] INFO  17:09:32,455 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:09Z] INFO  17:09:32,455 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:09Z] INFO  17:09:32,456 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:09Z] INFO  17:09:32,461 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/3/R14-18106_kapa-NGv3-PE100-NGv3-sort-3_158970515_174577240-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/3/tx/tmpvGJZr4/R14-18106_kapa-NGv3-PE100-NGv3-sort-3_158970515_174577240-prep-prealign-realign.intervals -l INFO -L 3:158970516-174577240 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:09Z] INFO  17:09:32,471 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:09Z] INFO  17:09:32,472 HelpFormatter - Date/Time: 2016/04/14 17:09:32
[2016-04-15T00:09Z] INFO  17:09:32,473 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:09Z] INFO  17:09:32,473 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:09Z] INFO  17:09:32,562 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:09Z] INFO  17:09:32,834 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T00:09Z] INFO  17:09:32,844 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:09Z] INFO  17:09:32,910 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-15T00:09Z] INFO  17:09:33,278 IntervalUtils - Processing 15606725 bp from intervals
[2016-04-15T00:09Z] WARN  17:09:33,282 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:09Z] INFO  17:09:33,435 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:09Z] INFO  17:09:33,438 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:09Z] INFO  17:09:33,438 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:09Z] INFO  17:09:33,438 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:09Z] INFO  17:09:33,442 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/3/R14-18106_kapa-NGv3-PE100-NGv3-sort-3_143297426_158963696-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/3/tx/tmpyvXicz/R14-18106_kapa-NGv3-PE100-NGv3-sort-3_143297426_158963696-prep-prealign-realign.intervals -l INFO -L 3:143297427-158963696 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:09Z] INFO  17:09:33,452 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:09Z] INFO  17:09:33,453 HelpFormatter - Date/Time: 2016/04/14 17:09:33
[2016-04-15T00:09Z] INFO  17:09:33,457 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:09Z] INFO  17:09:33,459 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:09Z] INFO  17:09:33,459 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:09Z] GATK pre-alignment ('4', 52709749, 68338393) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:09Z] INFO  17:09:33,562 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:09Z] INFO  17:09:33,725 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:09Z] INFO  17:09:33,737 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:09Z] INFO  17:09:33,738 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:09Z] INFO  17:09:33,738 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:09Z] INFO  17:09:33,791 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T00:09Z] INFO  17:09:33,815 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:09Z] INFO  17:09:33,856 ProgressMeter -     3:137787857    200002.0    30.0 s       2.5 m       64.5%    46.0 s      16.0 s
[2016-04-15T00:09Z] INFO  17:09:33,867 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-15T00:09Z] INFO  17:09:34,233 IntervalUtils - Processing 15666270 bp from intervals
[2016-04-15T00:09Z] WARN  17:09:34,249 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:09Z] INFO  17:09:34,344 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:09Z] INFO  17:09:34,549 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:09Z] INFO  17:09:34,550 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:09Z] INFO  17:09:34,551 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:09Z] INFO  17:09:34,551 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:09Z] INFO  17:09:34,579 ProgressMeter -     2:110565862    400009.0    30.0 s      76.0 s       95.5%    31.0 s       1.0 s
[2016-04-15T00:09Z] INFO  17:09:35,240 ProgressMeter -            done   1.5509917E7    22.0 s       1.0 s      100.0%    22.0 s       0.0 s
[2016-04-15T00:09Z] INFO  17:09:35,241 ProgressMeter - Total runtime 22.43 secs, 0.37 min, 0.01 hours
[2016-04-15T00:09Z] INFO  17:09:35,245 MicroScheduler - 36189 reads were filtered out during the traversal out of approximately 454100 total reads (7.97%)
[2016-04-15T00:09Z] INFO  17:09:35,257 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:09Z] INFO  17:09:35,258 MicroScheduler -   -> 1082 reads (0.24% of total) failing BadMateFilter
[2016-04-15T00:09Z] INFO  17:09:35,258 MicroScheduler -   -> 33806 reads (7.44% of total) failing DuplicateReadFilter
[2016-04-15T00:09Z] INFO  17:09:35,259 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:09Z] INFO  17:09:35,260 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:09Z] INFO  17:09:35,261 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:09Z] INFO  17:09:35,261 MicroScheduler -   -> 1301 reads (0.29% of total) failing MappingQualityZeroFilter
[2016-04-15T00:09Z] INFO  17:09:35,262 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:09Z] INFO  17:09:35,262 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-15T00:09Z] INFO  17:09:35,263 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:09Z] INFO  17:09:35,711 ProgressMeter -            done    504997.0    31.0 s      63.0 s      100.0%    31.0 s       0.0 s
[2016-04-15T00:09Z] INFO  17:09:35,712 ProgressMeter - Total runtime 31.86 secs, 0.53 min, 0.01 hours
[2016-04-15T00:09Z] INFO  17:09:35,715 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 504997 total reads (0.00%)
[2016-04-15T00:09Z] INFO  17:09:35,716 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:09Z] INFO  17:09:35,716 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:09Z] INFO  17:09:35,716 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:09Z] INFO  17:09:36,497 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:09Z] GATK: realign ('3', 31617887, 47127804) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:09Z] INFO  17:09:36,516 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:09Z] INFO  17:09:36,520 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:09Z] INFO  17:09:36,520 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:09Z] INFO  17:09:36,521 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:09Z] INFO  17:09:36,525 HelpFormatter - Program Args: -T PrintReads -L 4:52709750-68338393 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/4/tx/tmpAYoRiI/R14-18106_kapa-NGv3-PE100-NGv3-sort-4_52709749_68338393-prep-prealign.bam
[2016-04-15T00:09Z] INFO  17:09:36,534 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:09Z] INFO  17:09:36,535 HelpFormatter - Date/Time: 2016/04/14 17:09:36
[2016-04-15T00:09Z] INFO  17:09:36,536 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:09Z] INFO  17:09:36,536 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:09Z] INFO  17:09:36,727 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:09Z] INFO  17:09:37,224 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@41fd9d8e
[2016-04-15T00:09Z] INFO  17:09:37,378 ProgressMeter -            done    204628.0    26.0 s       2.2 m       99.1%    26.0 s       0.0 s
[2016-04-15T00:09Z] INFO  17:09:37,379 ProgressMeter - Total runtime 26.77 secs, 0.45 min, 0.01 hours
[2016-04-15T00:09Z] INFO  17:09:37,379 MicroScheduler - 127 reads were filtered out during the traversal out of approximately 204755 total reads (0.06%)
[2016-04-15T00:09Z] INFO  17:09:37,379 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:09Z] INFO  17:09:37,380 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:09Z] INFO  17:09:37,380 MicroScheduler -   -> 127 reads (0.06% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:09Z] INFO  17:09:37,456 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:09Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-2_95538561_111273222-prep.bam
[2016-04-15T00:09Z] INFO  17:09:37,868 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-15T00:09Z] INFO  17:09:37,954 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:09Z] INFO  17:09:37,973 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:09Z] INFO  17:09:38,027 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-15T00:09Z] INFO  17:09:38,042 IntervalUtils - Processing 15628644 bp from intervals
[2016-04-15T00:09Z] INFO  17:09:38,140 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:09Z] INFO  17:09:38,525 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:09Z] INFO  17:09:38,525 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:09Z] INFO  17:09:38,526 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:09Z] INFO  17:09:38,526 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:09Z] INFO  17:09:38,551 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:09Z] INFO  17:09:38,573 ProgressMeter -            done    304671.0    19.0 s      65.0 s      100.0%    19.0 s       0.0 s
[2016-04-15T00:09Z] INFO  17:09:38,573 ProgressMeter - Total runtime 19.98 secs, 0.33 min, 0.01 hours
[2016-04-15T00:09Z] INFO  17:09:38,577 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 304671 total reads (0.00%)
[2016-04-15T00:09Z] INFO  17:09:38,577 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:09Z] INFO  17:09:38,578 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:09Z] INFO  17:09:38,579 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:09Z] INFO  17:09:38,720 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:09Z] INFO  17:09:38,963 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:09Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-3_190333063_198022430-prep-prealign.bam
[2016-04-15T00:09Z] GATK pre-alignment ('4', 68340604, 83852298) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:09Z] INFO  17:09:39,576 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:09Z] INFO  17:09:39,580 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:09Z] INFO  17:09:39,580 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:09Z] INFO  17:09:39,581 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:09Z] INFO  17:09:39,585 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/3/R14-18106_kapa-NGv3-PE100-NGv3-sort-3_31617887_47127804-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/3/R14-18106_kapa-NGv3-PE100-NGv3-sort-3_31617887_47127804-prep-prealign-realign.intervals -L 3:31617888-47127804 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/3/tx/tmpss3oP5/R14-18106_kapa-NGv3-PE100-NGv3-sort-3_31617887_47127804-prep.bam
[2016-04-15T00:09Z] INFO  17:09:39,596 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:09Z] INFO  17:09:39,597 HelpFormatter - Date/Time: 2016/04/14 17:09:39
[2016-04-15T00:09Z] INFO  17:09:39,597 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:09Z] INFO  17:09:39,597 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:09Z] GATK RealignerTargetCreator: R14-18106_kapa-NGv3-PE100-NGv3-sort-3_190333063_198022430-prep-prealign.bam 3:190333064-198022430
[2016-04-15T00:09Z] GATK: RealignerTargetCreator
[2016-04-15T00:09Z] INFO  17:09:39,808 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:09Z] INFO  17:09:39,940 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:09Z] INFO  17:09:39,948 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:09Z] INFO  17:09:40,029 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-15T00:09Z] INFO  17:09:40,265 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:09Z] INFO  17:09:40,275 ProgressMeter -     3:186442898    200002.0    30.0 s       2.5 m       75.0%    40.0 s      10.0 s
[2016-04-15T00:09Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-3_0_15512123-prep.bam
[2016-04-15T00:09Z] INFO  17:09:40,330 IntervalUtils - Processing 15509917 bp from intervals
[2016-04-15T00:09Z] WARN  17:09:40,335 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:09Z] INFO  17:09:40,399 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:09Z] INFO  17:09:40,544 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:09Z] INFO  17:09:40,545 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:09Z] INFO  17:09:40,546 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:09Z] INFO  17:09:40,547 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:09Z] INFO  17:09:40,741 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:09Z] INFO  17:09:40,892 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:09Z] GATK pre-alignment ('4', 83857133, 99393738) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:09Z] INFO  17:09:41,975 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@41fd9d8e
[2016-04-15T00:09Z] INFO  17:09:42,059 ProgressMeter -            done    712839.0    83.0 s     117.0 s      100.0%    83.0 s       0.0 s
[2016-04-15T00:09Z] INFO  17:09:42,059 ProgressMeter - Total runtime 83.76 secs, 1.40 min, 0.02 hours
[2016-04-15T00:09Z] INFO  17:09:42,060 MicroScheduler - 276 reads were filtered out during the traversal out of approximately 713115 total reads (0.04%)
[2016-04-15T00:09Z] INFO  17:09:42,060 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:09Z] INFO  17:09:42,060 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:09Z] INFO  17:09:42,061 MicroScheduler -   -> 276 reads (0.04% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:09Z] INFO  17:09:42,241 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:09Z] INFO  17:09:42,245 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:09Z] INFO  17:09:42,245 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:09Z] INFO  17:09:42,246 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:09Z] INFO  17:09:42,250 HelpFormatter - Program Args: -T PrintReads -L 4:68340605-83852298 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/4/tx/tmpmQj_cq/R14-18106_kapa-NGv3-PE100-NGv3-sort-4_68340604_83852298-prep-prealign.bam
[2016-04-15T00:09Z] INFO  17:09:42,259 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:09Z] INFO  17:09:42,260 HelpFormatter - Date/Time: 2016/04/14 17:09:42
[2016-04-15T00:09Z] INFO  17:09:42,260 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:09Z] INFO  17:09:42,261 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:09Z] INFO  17:09:42,493 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:09Z] INFO  17:09:42,680 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:09Z] INFO  17:09:42,683 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:09Z] INFO  17:09:42,683 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:09Z] INFO  17:09:42,683 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:09Z] INFO  17:09:42,695 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/3/R14-18106_kapa-NGv3-PE100-NGv3-sort-3_190333063_198022430-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/3/tx/tmpduxOBS/R14-18106_kapa-NGv3-PE100-NGv3-sort-3_190333063_198022430-prep-prealign-realign.intervals -l INFO -L 3:190333064-198022430 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:09Z] INFO  17:09:42,713 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:09Z] INFO  17:09:42,721 HelpFormatter - Date/Time: 2016/04/14 17:09:42
[2016-04-15T00:09Z] INFO  17:09:42,722 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:09Z] INFO  17:09:42,722 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:09Z] INFO  17:09:42,814 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:09Z] INFO  17:09:43,057 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T00:09Z] INFO  17:09:43,067 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:09Z] INFO  17:09:43,129 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-15T00:09Z] INFO  17:09:43,432 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:09Z] INFO  17:09:43,472 IntervalUtils - Processing 7689367 bp from intervals
[2016-04-15T00:09Z] WARN  17:09:43,477 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:09Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-3_47129602_62648069-prep-prealign.bam
[2016-04-15T00:09Z] INFO  17:09:43,568 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:09Z] INFO  17:09:43,591 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-15T00:09Z] INFO  17:09:43,659 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:09Z] INFO  17:09:43,668 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:09Z] INFO  17:09:43,729 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-15T00:09Z] INFO  17:09:43,743 IntervalUtils - Processing 15511694 bp from intervals
[2016-04-15T00:09Z] INFO  17:09:43,767 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:09Z] INFO  17:09:43,768 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:09Z] INFO  17:09:43,769 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:09Z] INFO  17:09:43,770 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:09Z] INFO  17:09:43,846 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:09Z] INFO  17:09:43,892 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@41fd9d8e
[2016-04-15T00:09Z] INFO  17:09:44,118 ProgressMeter -            done    328146.0    40.0 s       2.0 m      100.0%    40.0 s       0.0 s
[2016-04-15T00:09Z] INFO  17:09:44,119 ProgressMeter - Total runtime 40.29 secs, 0.67 min, 0.01 hours
[2016-04-15T00:09Z] INFO  17:09:44,119 MicroScheduler - 205 reads were filtered out during the traversal out of approximately 328351 total reads (0.06%)
[2016-04-15T00:09Z] INFO  17:09:44,120 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:09Z] INFO  17:09:44,120 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:09Z] INFO  17:09:44,120 MicroScheduler -   -> 205 reads (0.06% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:09Z] INFO  17:09:44,158 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:09Z] INFO  17:09:44,159 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:09Z] INFO  17:09:44,160 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:09Z] INFO  17:09:44,160 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:09Z] INFO  17:09:44,173 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:09Z] INFO  17:09:44,190 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:09Z] INFO  17:09:44,194 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:09Z] INFO  17:09:44,195 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:09Z] INFO  17:09:44,195 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:09Z] INFO  17:09:44,200 HelpFormatter - Program Args: -T PrintReads -L 4:83857134-99393738 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/4/tx/tmpLjgJHA/R14-18106_kapa-NGv3-PE100-NGv3-sort-4_83857133_99393738-prep-prealign.bam
[2016-04-15T00:09Z] INFO  17:09:44,217 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:09Z] INFO  17:09:44,218 HelpFormatter - Date/Time: 2016/04/14 17:09:44
[2016-04-15T00:09Z] INFO  17:09:44,218 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:09Z] INFO  17:09:44,219 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:09Z] INFO  17:09:44,330 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:09Z] INFO  17:09:44,430 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:09Z] INFO  17:09:44,686 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@41fd9d8e
[2016-04-15T00:09Z] INFO  17:09:44,822 ProgressMeter -            done    274143.0    34.0 s       2.1 m      100.0%    34.0 s       0.0 s
[2016-04-15T00:09Z] INFO  17:09:44,823 ProgressMeter - Total runtime 34.57 secs, 0.58 min, 0.01 hours
[2016-04-15T00:09Z] INFO  17:09:44,823 MicroScheduler - 156 reads were filtered out during the traversal out of approximately 274299 total reads (0.06%)
[2016-04-15T00:09Z] INFO  17:09:44,823 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:09Z] INFO  17:09:44,824 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:09Z] INFO  17:09:44,824 MicroScheduler -   -> 156 reads (0.06% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:09Z] INFO  17:09:45,498 ProgressMeter -            done    165058.0    13.0 s      83.0 s      100.0%    13.0 s       0.0 s
[2016-04-15T00:09Z] INFO  17:09:45,498 ProgressMeter - Total runtime 13.82 secs, 0.23 min, 0.00 hours
[2016-04-15T00:09Z] INFO  17:09:45,502 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 165058 total reads (0.00%)
[2016-04-15T00:09Z] INFO  17:09:45,502 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:09Z] INFO  17:09:45,503 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:09Z] INFO  17:09:45,503 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:09Z] INFO  17:09:45,554 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:09Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-3_127770401_143293035-prep-prealign.bam
[2016-04-15T00:09Z] INFO  17:09:45,592 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-15T00:09Z] INFO  17:09:45,680 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:09Z] INFO  17:09:45,701 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:09Z] INFO  17:09:45,751 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-15T00:09Z] INFO  17:09:45,766 IntervalUtils - Processing 15536605 bp from intervals
[2016-04-15T00:09Z] INFO  17:09:45,878 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:09Z] GATK RealignerTargetCreator: R14-18106_kapa-NGv3-PE100-NGv3-sort-3_47129602_62648069-prep-prealign.bam 3:47129603-62648069
[2016-04-15T00:09Z] GATK: RealignerTargetCreator
[2016-04-15T00:09Z] INFO  17:09:46,171 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:09Z] INFO  17:09:46,172 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:09Z] INFO  17:09:46,173 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:09Z] INFO  17:09:46,174 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:09Z] INFO  17:09:46,219 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:09Z] INFO  17:09:46,329 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:09Z] INFO  17:09:46,358 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:09Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-3_174814579_190326970-prep-prealign.bam
[2016-04-15T00:09Z] GATK RealignerTargetCreator: R14-18106_kapa-NGv3-PE100-NGv3-sort-3_127770401_143293035-prep-prealign.bam 3:127770402-143293035
[2016-04-15T00:09Z] GATK: RealignerTargetCreator
[2016-04-15T00:09Z] INFO  17:09:46,705 ProgressMeter -       4:3415755    200003.0    30.0 s       2.5 m       22.0%     2.3 m     106.0 s
[2016-04-15T00:09Z] INFO  17:09:47,139 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:09Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-3_96585668_112185230-prep.bam
[2016-04-15T00:09Z] GATK RealignerTargetCreator: R14-18106_kapa-NGv3-PE100-NGv3-sort-3_174814579_190326970-prep-prealign.bam 3:174814580-190326970
[2016-04-15T00:09Z] GATK: RealignerTargetCreator
[2016-04-15T00:09Z] GATK pre-alignment ('4', 99397339, 115544957) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:09Z] INFO  17:09:48,977 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:09Z] INFO  17:09:48,980 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:09Z] INFO  17:09:48,981 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:09Z] INFO  17:09:48,981 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:09Z] INFO  17:09:48,985 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/3/R14-18106_kapa-NGv3-PE100-NGv3-sort-3_47129602_62648069-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/3/tx/tmpNUPodh/R14-18106_kapa-NGv3-PE100-NGv3-sort-3_47129602_62648069-prep-prealign-realign.intervals -l INFO -L 3:47129603-62648069 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:09Z] INFO  17:09:49,003 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:09Z] INFO  17:09:49,004 HelpFormatter - Date/Time: 2016/04/14 17:09:48
[2016-04-15T00:09Z] INFO  17:09:49,004 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:09Z] INFO  17:09:49,005 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:09Z] INFO  17:09:49,008 ProgressMeter -            done   1.5606725E7    15.0 s       0.0 s      100.0%    15.0 s       0.0 s
[2016-04-15T00:09Z] INFO  17:09:49,010 ProgressMeter - Total runtime 15.27 secs, 0.25 min, 0.00 hours
[2016-04-15T00:09Z] INFO  17:09:49,014 MicroScheduler - 10012 reads were filtered out during the traversal out of approximately 125198 total reads (8.00%)
[2016-04-15T00:09Z] INFO  17:09:49,015 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:09Z] INFO  17:09:49,015 MicroScheduler -   -> 556 reads (0.44% of total) failing BadMateFilter
[2016-04-15T00:09Z] INFO  17:09:49,016 MicroScheduler -   -> 9110 reads (7.28% of total) failing DuplicateReadFilter
[2016-04-15T00:09Z] INFO  17:09:49,017 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:09Z] INFO  17:09:49,017 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:09Z] INFO  17:09:49,018 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:09Z] INFO  17:09:49,018 MicroScheduler -   -> 346 reads (0.28% of total) failing MappingQualityZeroFilter
[2016-04-15T00:09Z] INFO  17:09:49,019 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:09Z] INFO  17:09:49,020 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-15T00:09Z] INFO  17:09:49,020 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:09Z] INFO  17:09:49,080 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@41fd9d8e
[2016-04-15T00:09Z] INFO  17:09:49,096 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:09Z] INFO  17:09:49,185 ProgressMeter -            done    111783.0    19.0 s       2.9 m      100.0%    19.0 s       0.0 s
[2016-04-15T00:09Z] INFO  17:09:49,185 ProgressMeter - Total runtime 19.37 secs, 0.32 min, 0.01 hours
[2016-04-15T00:09Z] INFO  17:09:49,186 MicroScheduler - 121 reads were filtered out during the traversal out of approximately 111904 total reads (0.11%)
[2016-04-15T00:09Z] INFO  17:09:49,186 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:09Z] INFO  17:09:49,187 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:09Z] INFO  17:09:49,187 MicroScheduler -   -> 121 reads (0.11% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:09Z] INFO  17:09:49,364 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T00:09Z] INFO  17:09:49,373 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:09Z] INFO  17:09:49,467 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.09
[2016-04-15T00:09Z] INFO  17:09:49,508 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:09Z] INFO  17:09:49,511 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:09Z] INFO  17:09:49,511 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:09Z] INFO  17:09:49,512 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:09Z] INFO  17:09:49,517 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/3/R14-18106_kapa-NGv3-PE100-NGv3-sort-3_127770401_143293035-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/3/tx/tmpiGk_ds/R14-18106_kapa-NGv3-PE100-NGv3-sort-3_127770401_143293035-prep-prealign-realign.intervals -l INFO -L 3:127770402-143293035 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:09Z] INFO  17:09:49,544 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:09Z] INFO  17:09:49,544 HelpFormatter - Date/Time: 2016/04/14 17:09:49
[2016-04-15T00:09Z] INFO  17:09:49,545 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:09Z] INFO  17:09:49,545 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:09Z] INFO  17:09:49,653 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:09Z] INFO  17:09:49,771 IntervalUtils - Processing 15518467 bp from intervals
[2016-04-15T00:09Z] WARN  17:09:49,786 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:09Z] INFO  17:09:49,873 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T00:09Z] INFO  17:09:49,890 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:09Z] INFO  17:09:49,937 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:09Z] INFO  17:09:49,940 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:09Z] INFO  17:09:49,941 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:09Z] INFO  17:09:49,941 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:09Z] INFO  17:09:49,942 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:09Z] INFO  17:09:49,946 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/3/R14-18106_kapa-NGv3-PE100-NGv3-sort-3_174814579_190326970-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/3/tx/tmpfOpYeA/R14-18106_kapa-NGv3-PE100-NGv3-sort-3_174814579_190326970-prep-prealign-realign.intervals -l INFO -L 3:174814580-190326970 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:09Z] INFO  17:09:49,956 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:09Z] INFO  17:09:49,963 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-15T00:09Z] INFO  17:09:49,967 HelpFormatter - Date/Time: 2016/04/14 17:09:49
[2016-04-15T00:09Z] INFO  17:09:49,968 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:09Z] INFO  17:09:49,969 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:09Z] INFO  17:09:50,087 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:09Z] INFO  17:09:50,187 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:09Z] INFO  17:09:50,199 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:09Z] INFO  17:09:50,200 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:09Z] INFO  17:09:50,200 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:09Z] INFO  17:09:50,248 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@41fd9d8e
[2016-04-15T00:09Z] INFO  17:09:50,294 IntervalUtils - Processing 15522634 bp from intervals
[2016-04-15T00:09Z] WARN  17:09:50,299 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:09Z] INFO  17:09:50,303 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:09Z] GATK: realign ('3', 158970515, 174577240) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:09Z] INFO  17:09:50,355 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T00:09Z] INFO  17:09:50,365 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:09Z] INFO  17:09:50,394 ProgressMeter -            done    349745.0    48.0 s       2.3 m      100.0%    48.0 s       0.0 s
[2016-04-15T00:09Z] INFO  17:09:50,394 ProgressMeter - Total runtime 48.71 secs, 0.81 min, 0.01 hours
[2016-04-15T00:09Z] INFO  17:09:50,395 MicroScheduler - 223 reads were filtered out during the traversal out of approximately 349968 total reads (0.06%)
[2016-04-15T00:09Z] INFO  17:09:50,395 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:09Z] INFO  17:09:50,395 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:09Z] INFO  17:09:50,396 MicroScheduler -   -> 223 reads (0.06% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:09Z] INFO  17:09:50,413 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-15T00:09Z] INFO  17:09:50,425 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:09Z] INFO  17:09:50,650 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:09Z] INFO  17:09:50,651 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:09Z] INFO  17:09:50,652 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:09Z] INFO  17:09:50,652 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:09Z] INFO  17:09:50,684 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:09Z] INFO  17:09:50,720 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:09Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-4_15512869_31144471-prep-prealign.bam
[2016-04-15T00:09Z] INFO  17:09:50,724 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:09Z] INFO  17:09:50,724 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:09Z] INFO  17:09:50,725 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:09Z] INFO  17:09:50,729 HelpFormatter - Program Args: -T PrintReads -L 4:99397340-115544957 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/4/tx/tmppiDxon/R14-18106_kapa-NGv3-PE100-NGv3-sort-4_99397339_115544957-prep-prealign.bam
[2016-04-15T00:09Z] INFO  17:09:50,738 IntervalUtils - Processing 15512391 bp from intervals
[2016-04-15T00:09Z] WARN  17:09:50,744 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:09Z] INFO  17:09:50,748 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:09Z] INFO  17:09:50,749 HelpFormatter - Date/Time: 2016/04/14 17:09:50
[2016-04-15T00:09Z] INFO  17:09:50,749 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:09Z] INFO  17:09:50,750 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:09Z] INFO  17:09:50,847 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:09Z] INFO  17:09:50,974 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:09Z] GATK RealignerTargetCreator: R14-18106_kapa-NGv3-PE100-NGv3-sort-4_15512869_31144471-prep-prealign.bam 4:15512870-31144471
[2016-04-15T00:09Z] GATK: RealignerTargetCreator
[2016-04-15T00:09Z] INFO  17:09:51,168 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:09Z] INFO  17:09:51,180 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:09Z] INFO  17:09:51,181 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:09Z] INFO  17:09:51,181 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:09Z] INFO  17:09:51,375 ProgressMeter -            done   1.566627E7    16.0 s       1.0 s      100.0%    16.0 s       0.0 s
[2016-04-15T00:09Z] INFO  17:09:51,376 ProgressMeter - Total runtime 16.83 secs, 0.28 min, 0.00 hours
[2016-04-15T00:09Z] INFO  17:09:51,379 MicroScheduler - 13173 reads were filtered out during the traversal out of approximately 158267 total reads (8.32%)
[2016-04-15T00:09Z] INFO  17:09:51,386 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:09Z] INFO  17:09:51,387 MicroScheduler -   -> 580 reads (0.37% of total) failing BadMateFilter
[2016-04-15T00:09Z] INFO  17:09:51,387 MicroScheduler -   -> 11427 reads (7.22% of total) failing DuplicateReadFilter
[2016-04-15T00:09Z] INFO  17:09:51,387 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:09Z] INFO  17:09:51,387 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:09Z] INFO  17:09:51,388 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:09Z] INFO  17:09:51,388 MicroScheduler -   -> 1166 reads (0.74% of total) failing MappingQualityZeroFilter
[2016-04-15T00:09Z] INFO  17:09:51,388 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:09Z] INFO  17:09:51,388 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-15T00:09Z] INFO  17:09:51,388 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:09Z] INFO  17:09:51,781 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:09Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-3_112188604_127703121-prep-prealign.bam
[2016-04-15T00:09Z] INFO  17:09:52,190 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-15T00:09Z] INFO  17:09:52,324 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:09Z] INFO  17:09:52,354 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:09Z] INFO  17:09:52,412 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-15T00:09Z] INFO  17:09:52,446 IntervalUtils - Processing 16147618 bp from intervals
[2016-04-15T00:09Z] INFO  17:09:52,535 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:09Z] INFO  17:09:52,639 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:09Z] GATK: realign ('3', 143297426, 158963696) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:09Z] GATK RealignerTargetCreator: R14-18106_kapa-NGv3-PE100-NGv3-sort-3_112188604_127703121-prep-prealign.bam 3:112188605-127703121
[2016-04-15T00:09Z] GATK: RealignerTargetCreator
[2016-04-15T00:09Z] INFO  17:09:52,862 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:09Z] INFO  17:09:52,864 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:09Z] INFO  17:09:52,864 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:09Z] INFO  17:09:52,865 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:09Z] INFO  17:09:52,882 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:09Z] INFO  17:09:53,077 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:09Z] INFO  17:09:53,091 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:09Z] INFO  17:09:53,091 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:09Z] INFO  17:09:53,092 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:09Z] INFO  17:09:53,096 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/3/R14-18106_kapa-NGv3-PE100-NGv3-sort-3_158970515_174577240-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/3/R14-18106_kapa-NGv3-PE100-NGv3-sort-3_158970515_174577240-prep-prealign-realign.intervals -L 3:158970516-174577240 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/3/tx/tmpPRjW7g/R14-18106_kapa-NGv3-PE100-NGv3-sort-3_158970515_174577240-prep.bam
[2016-04-15T00:09Z] INFO  17:09:53,118 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:09Z] INFO  17:09:53,119 HelpFormatter - Date/Time: 2016/04/14 17:09:53
[2016-04-15T00:09Z] INFO  17:09:53,119 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:09Z] INFO  17:09:53,120 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:09Z] INFO  17:09:53,136 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:09Z] INFO  17:09:53,309 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:09Z] INFO  17:09:53,493 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:09Z] INFO  17:09:53,519 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:09Z] INFO  17:09:53,576 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-15T00:09Z] INFO  17:09:54,018 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:09Z] INFO  17:09:54,020 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:09Z] INFO  17:09:54,020 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:09Z] INFO  17:09:54,021 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:09Z] INFO  17:09:54,036 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/4/R14-18106_kapa-NGv3-PE100-NGv3-sort-4_15512869_31144471-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/4/tx/tmp2vdwMB/R14-18106_kapa-NGv3-PE100-NGv3-sort-4_15512869_31144471-prep-prealign-realign.intervals -l INFO -L 4:15512870-31144471 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:09Z] INFO  17:09:54,055 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:09Z] INFO  17:09:54,055 HelpFormatter - Date/Time: 2016/04/14 17:09:54
[2016-04-15T00:09Z] INFO  17:09:54,056 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:09Z] INFO  17:09:54,056 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:09Z] INFO  17:09:54,114 IntervalUtils - Processing 15606725 bp from intervals
[2016-04-15T00:09Z] WARN  17:09:54,131 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:09Z] INFO  17:09:54,192 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:09Z] INFO  17:09:54,274 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:09Z] INFO  17:09:54,408 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T00:09Z] INFO  17:09:54,417 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:09Z] INFO  17:09:54,449 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:09Z] INFO  17:09:54,450 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:09Z] INFO  17:09:54,451 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:09Z] INFO  17:09:54,452 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:09Z] INFO  17:09:54,477 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-15T00:09Z] INFO  17:09:54,536 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@5fe152b7
[2016-04-15T00:09Z] INFO  17:09:54,609 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:09Z] INFO  17:09:54,684 ProgressMeter -            done    107517.0    16.0 s       2.5 m      100.0%    16.0 s       0.0 s
[2016-04-15T00:09Z] INFO  17:09:54,684 ProgressMeter - Total runtime 16.16 secs, 0.27 min, 0.00 hours
[2016-04-15T00:09Z] INFO  17:09:54,685 MicroScheduler - 127 reads were filtered out during the traversal out of approximately 107644 total reads (0.12%)
[2016-04-15T00:09Z] INFO  17:09:54,685 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:09Z] INFO  17:09:54,685 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:09Z] INFO  17:09:54,686 MicroScheduler -   -> 127 reads (0.12% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:09Z] INFO  17:09:54,874 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:09Z] INFO  17:09:54,901 IntervalUtils - Processing 15631602 bp from intervals
[2016-04-15T00:09Z] WARN  17:09:54,906 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:09Z] INFO  17:09:54,988 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:09Z] INFO  17:09:55,186 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:09Z] INFO  17:09:55,187 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:09Z] INFO  17:09:55,188 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:09Z] INFO  17:09:55,189 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:09Z] INFO  17:09:55,881 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:09Z] INFO  17:09:55,885 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:09Z] INFO  17:09:55,885 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:09Z] INFO  17:09:55,886 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:09Z] INFO  17:09:55,890 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/3/R14-18106_kapa-NGv3-PE100-NGv3-sort-3_112188604_127703121-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/3/tx/tmp2t78qN/R14-18106_kapa-NGv3-PE100-NGv3-sort-3_112188604_127703121-prep-prealign-realign.intervals -l INFO -L 3:112188605-127703121 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:09Z] INFO  17:09:55,919 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:09Z] INFO  17:09:55,919 HelpFormatter - Date/Time: 2016/04/14 17:09:55
[2016-04-15T00:09Z] INFO  17:09:55,920 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:09Z] INFO  17:09:55,920 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:09Z] INFO  17:09:55,944 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@41fd9d8e
[2016-04-15T00:09Z] INFO  17:09:56,017 ProgressMeter -            done    180252.0    24.0 s       2.2 m      100.0%    24.0 s       0.0 s
[2016-04-15T00:09Z] INFO  17:09:56,019 ProgressMeter - Total runtime 24.26 secs, 0.40 min, 0.01 hours
[2016-04-15T00:09Z] INFO  17:09:56,019 MicroScheduler - 450 reads were filtered out during the traversal out of approximately 180702 total reads (0.25%)
[2016-04-15T00:09Z] INFO  17:09:56,020 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:09Z] INFO  17:09:56,021 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:09Z] INFO  17:09:56,022 MicroScheduler -   -> 450 reads (0.25% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:09Z] INFO  17:09:56,055 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:09Z] INFO  17:09:56,058 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:09Z] INFO  17:09:56,059 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:09Z] INFO  17:09:56,060 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:09Z] INFO  17:09:56,064 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/3/R14-18106_kapa-NGv3-PE100-NGv3-sort-3_143297426_158963696-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/3/R14-18106_kapa-NGv3-PE100-NGv3-sort-3_143297426_158963696-prep-prealign-realign.intervals -L 3:143297427-158963696 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/3/tx/tmpUj5fxx/R14-18106_kapa-NGv3-PE100-NGv3-sort-3_143297426_158963696-prep.bam
[2016-04-15T00:09Z] INFO  17:09:56,068 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:09Z] INFO  17:09:56,075 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:09Z] INFO  17:09:56,086 HelpFormatter - Date/Time: 2016/04/14 17:09:56
[2016-04-15T00:09Z] INFO  17:09:56,087 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:09Z] INFO  17:09:56,088 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:09Z] INFO  17:09:56,266 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T00:09Z] INFO  17:09:56,287 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:09Z] INFO  17:09:56,312 ProgressMeter -     1:155247400    900014.0    60.0 s      66.0 s       73.2%    82.0 s      22.0 s
[2016-04-15T00:09Z] INFO  17:09:56,347 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:09Z] INFO  17:09:56,350 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-15T00:09Z] INFO  17:09:56,358 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:09Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-4_52709749_68338393-prep-prealign.bam
[2016-04-15T00:09Z] INFO  17:09:56,454 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:09Z] INFO  17:09:56,472 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:09Z] INFO  17:09:56,572 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.10
[2016-04-15T00:09Z] INFO  17:09:56,682 IntervalUtils - Processing 15514517 bp from intervals
[2016-04-15T00:09Z] WARN  17:09:56,687 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:09Z] INFO  17:09:56,758 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:09Z] GATK RealignerTargetCreator: R14-18106_kapa-NGv3-PE100-NGv3-sort-4_52709749_68338393-prep-prealign.bam 4:52709750-68338393
[2016-04-15T00:09Z] GATK: RealignerTargetCreator
[2016-04-15T00:09Z] INFO  17:09:56,995 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:09Z] INFO  17:09:56,996 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:09Z] INFO  17:09:56,996 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:09Z] INFO  17:09:57,000 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:09Z] INFO  17:09:57,019 IntervalUtils - Processing 15666270 bp from intervals
[2016-04-15T00:09Z] WARN  17:09:57,033 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:09Z] INFO  17:09:57,114 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:09Z] INFO  17:09:57,260 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:09Z] INFO  17:09:57,261 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:09Z] INFO  17:09:57,262 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:09Z] INFO  17:09:57,263 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:09Z] INFO  17:09:57,382 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:09Z] INFO  17:09:57,403 ProgressMeter -            done   7689367.0    13.0 s       1.0 s      100.0%    13.0 s       0.0 s
[2016-04-15T00:09Z] INFO  17:09:57,404 ProgressMeter - Total runtime 13.64 secs, 0.23 min, 0.00 hours
[2016-04-15T00:09Z] INFO  17:09:57,405 MicroScheduler - 31806 reads were filtered out during the traversal out of approximately 206142 total reads (15.43%)
[2016-04-15T00:09Z] INFO  17:09:57,406 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:09Z] INFO  17:09:57,407 MicroScheduler -   -> 486 reads (0.24% of total) failing BadMateFilter
[2016-04-15T00:09Z] INFO  17:09:57,407 MicroScheduler -   -> 14999 reads (7.28% of total) failing DuplicateReadFilter
[2016-04-15T00:09Z] INFO  17:09:57,408 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:09Z] INFO  17:09:57,408 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:09Z] INFO  17:09:57,409 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:09Z] INFO  17:09:57,410 MicroScheduler -   -> 16321 reads (7.92% of total) failing MappingQualityZeroFilter
[2016-04-15T00:09Z] INFO  17:09:57,410 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:09Z] INFO  17:09:57,411 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-15T00:09Z] INFO  17:09:57,411 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:09Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-4_36069528_52709433-prep-prealign.bam
[2016-04-15T00:09Z] INFO  17:09:57,439 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:09Z] INFO  17:09:57,651 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:09Z] GATK RealignerTargetCreator: R14-18106_kapa-NGv3-PE100-NGv3-sort-4_36069528_52709433-prep-prealign.bam 4:36069529-52709433
[2016-04-15T00:09Z] GATK: RealignerTargetCreator
[2016-04-15T00:09Z] INFO  17:09:58,717 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:09Z] GATK: realign ('3', 190333063, 198022430) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:09Z] INFO  17:09:59,734 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:09Z] INFO  17:09:59,738 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:09Z] INFO  17:09:59,738 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:09Z] INFO  17:09:59,738 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:09Z] INFO  17:09:59,743 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/4/R14-18106_kapa-NGv3-PE100-NGv3-sort-4_52709749_68338393-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/4/tx/tmpED44JZ/R14-18106_kapa-NGv3-PE100-NGv3-sort-4_52709749_68338393-prep-prealign-realign.intervals -l INFO -L 4:52709750-68338393 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:09Z] INFO  17:09:59,759 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:09Z] INFO  17:09:59,760 HelpFormatter - Date/Time: 2016/04/14 17:09:59
[2016-04-15T00:09Z] INFO  17:09:59,761 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:09Z] INFO  17:09:59,761 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:09Z] INFO  17:09:59,863 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:10Z] INFO  17:10:00,147 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T00:10Z] INFO  17:10:00,168 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:10Z] INFO  17:10:00,258 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.09
[2016-04-15T00:10Z] INFO  17:10:00,569 IntervalUtils - Processing 15628644 bp from intervals
[2016-04-15T00:10Z] WARN  17:10:00,574 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:10Z] INFO  17:10:00,670 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:10Z] INFO  17:10:00,909 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:10Z] INFO  17:10:00,919 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:10Z] INFO  17:10:00,919 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:10Z] INFO  17:10:00,925 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:10Z] INFO  17:10:01,034 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:10Z] INFO  17:10:01,038 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:10Z] INFO  17:10:01,039 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:10Z] INFO  17:10:01,039 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:10Z] INFO  17:10:01,044 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/4/R14-18106_kapa-NGv3-PE100-NGv3-sort-4_36069528_52709433-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/4/tx/tmpnBlaoE/R14-18106_kapa-NGv3-PE100-NGv3-sort-4_36069528_52709433-prep-prealign-realign.intervals -l INFO -L 4:36069529-52709433 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:10Z] INFO  17:10:01,069 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:10Z] INFO  17:10:01,070 HelpFormatter - Date/Time: 2016/04/14 17:10:01
[2016-04-15T00:10Z] INFO  17:10:01,071 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:10Z] INFO  17:10:01,071 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:10Z] INFO  17:10:01,160 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:10Z] INFO  17:10:01,424 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T00:10Z] INFO  17:10:01,434 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:10Z] INFO  17:10:01,504 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-15T00:10Z] INFO  17:10:01,642 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:10Z] INFO  17:10:01,645 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:10Z] INFO  17:10:01,646 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:10Z] INFO  17:10:01,646 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:10Z] INFO  17:10:01,651 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/3/R14-18106_kapa-NGv3-PE100-NGv3-sort-3_190333063_198022430-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/3/R14-18106_kapa-NGv3-PE100-NGv3-sort-3_190333063_198022430-prep-prealign-realign.intervals -L 3:190333064-198022430 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/3/tx/tmpQEAA_g/R14-18106_kapa-NGv3-PE100-NGv3-sort-3_190333063_198022430-prep.bam
[2016-04-15T00:10Z] INFO  17:10:01,671 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:10Z] INFO  17:10:01,672 HelpFormatter - Date/Time: 2016/04/14 17:10:01
[2016-04-15T00:10Z] INFO  17:10:01,672 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:10Z] INFO  17:10:01,673 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:10Z] INFO  17:10:01,831 IntervalUtils - Processing 16639905 bp from intervals
[2016-04-15T00:10Z] WARN  17:10:01,837 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:10Z] INFO  17:10:01,923 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:10Z] INFO  17:10:01,926 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:10Z] INFO  17:10:02,076 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:10Z] INFO  17:10:02,086 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:10Z] INFO  17:10:02,117 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:10Z] INFO  17:10:02,117 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:10Z] INFO  17:10:02,118 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:10Z] INFO  17:10:02,118 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:10Z] INFO  17:10:02,131 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.04
[2016-04-15T00:10Z] INFO  17:10:02,462 IntervalUtils - Processing 7689367 bp from intervals
[2016-04-15T00:10Z] WARN  17:10:02,467 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:10Z] INFO  17:10:02,539 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:10Z] INFO  17:10:02,665 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:10Z] INFO  17:10:02,666 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:10Z] INFO  17:10:02,666 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:10Z] INFO  17:10:02,667 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:10Z] INFO  17:10:02,786 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:10Z] INFO  17:10:02,860 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:10Z] INFO  17:10:06,412 ProgressMeter -            done    124218.0    11.0 s      96.0 s      100.0%    11.0 s       0.0 s
[2016-04-15T00:10Z] INFO  17:10:06,412 ProgressMeter - Total runtime 11.96 secs, 0.20 min, 0.00 hours
[2016-04-15T00:10Z] INFO  17:10:06,416 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 124218 total reads (0.00%)
[2016-04-15T00:10Z] INFO  17:10:06,416 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:10Z] INFO  17:10:06,416 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:10Z] INFO  17:10:06,417 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:10Z] INFO  17:10:07,187 ProgressMeter -            done   1189276.0    70.0 s      59.0 s      100.0%    70.0 s       0.0 s
[2016-04-15T00:10Z] INFO  17:10:07,188 ProgressMeter - Total runtime 70.90 secs, 1.18 min, 0.02 hours
[2016-04-15T00:10Z] INFO  17:10:07,192 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 1189276 total reads (0.00%)
[2016-04-15T00:10Z] INFO  17:10:07,193 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:10Z] INFO  17:10:07,193 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:10Z] INFO  17:10:07,194 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:10Z] INFO  17:10:07,642 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@41fd9d8e
[2016-04-15T00:10Z] INFO  17:10:07,740 ProgressMeter -            done    160802.0    21.0 s       2.2 m       99.9%    21.0 s       0.0 s
[2016-04-15T00:10Z] INFO  17:10:07,741 ProgressMeter - Total runtime 21.57 secs, 0.36 min, 0.01 hours
[2016-04-15T00:10Z] INFO  17:10:07,741 MicroScheduler - 144 reads were filtered out during the traversal out of approximately 160946 total reads (0.09%)
[2016-04-15T00:10Z] INFO  17:10:07,742 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:10Z] INFO  17:10:07,743 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:10Z] INFO  17:10:07,744 MicroScheduler -   -> 144 reads (0.09% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:10Z] INFO  17:10:07,821 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:10Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-3_158970515_174577240-prep.bam
[2016-04-15T00:10Z] GATK pre-alignment ('4', 115584857, 134074404) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:10Z] INFO  17:10:08,778 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:10Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-1_143897546_159410511-prep.bam
[2016-04-15T00:10Z] INFO  17:10:09,291 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:10Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-4_83857133_99393738-prep-prealign.bam
[2016-04-15T00:10Z] INFO  17:10:09,671 ProgressMeter -            done    451475.0    29.0 s      64.0 s      100.0%    29.0 s       0.0 s
[2016-04-15T00:10Z] INFO  17:10:09,671 ProgressMeter - Total runtime 29.13 secs, 0.49 min, 0.01 hours
[2016-04-15T00:10Z] INFO  17:10:09,675 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 451475 total reads (0.00%)
[2016-04-15T00:10Z] INFO  17:10:09,676 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:10Z] INFO  17:10:09,677 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:10Z] INFO  17:10:09,678 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:10Z] GATK RealignerTargetCreator: R14-18106_kapa-NGv3-PE100-NGv3-sort-4_83857133_99393738-prep-prealign.bam 4:83857134-99393738
[2016-04-15T00:10Z] GATK: RealignerTargetCreator
[2016-04-15T00:10Z] INFO  17:10:10,774 ProgressMeter -            done    156957.0    13.0 s      86.0 s      100.0%    13.0 s       0.0 s
[2016-04-15T00:10Z] INFO  17:10:10,774 ProgressMeter - Total runtime 13.51 secs, 0.23 min, 0.00 hours
[2016-04-15T00:10Z] INFO  17:10:10,778 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 156957 total reads (0.00%)
[2016-04-15T00:10Z] INFO  17:10:10,779 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:10Z] INFO  17:10:10,779 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:10Z] INFO  17:10:10,779 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:10Z] INFO  17:10:11,097 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:10Z] INFO  17:10:11,100 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:10Z] INFO  17:10:11,101 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:10Z] INFO  17:10:11,101 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:10Z] INFO  17:10:11,106 HelpFormatter - Program Args: -T PrintReads -L 4:115584858-134074404 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/4/tx/tmpba6Vc9/R14-18106_kapa-NGv3-PE100-NGv3-sort-4_115584857_134074404-prep-prealign.bam
[2016-04-15T00:10Z] INFO  17:10:11,116 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:10Z] INFO  17:10:11,117 HelpFormatter - Date/Time: 2016/04/14 17:10:11
[2016-04-15T00:10Z] INFO  17:10:11,117 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:10Z] INFO  17:10:11,117 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:10Z] INFO  17:10:11,168 ProgressMeter -            done   1.5631602E7    15.0 s       1.0 s      100.0%    15.0 s       0.0 s
[2016-04-15T00:10Z] INFO  17:10:11,169 ProgressMeter - Total runtime 15.98 secs, 0.27 min, 0.00 hours
[2016-04-15T00:10Z] INFO  17:10:11,173 MicroScheduler - 9016 reads were filtered out during the traversal out of approximately 112310 total reads (8.03%)
[2016-04-15T00:10Z] INFO  17:10:11,174 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:10Z] INFO  17:10:11,175 MicroScheduler -   -> 509 reads (0.45% of total) failing BadMateFilter
[2016-04-15T00:10Z] INFO  17:10:11,175 MicroScheduler -   -> 8301 reads (7.39% of total) failing DuplicateReadFilter
[2016-04-15T00:10Z] INFO  17:10:11,176 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:10Z] INFO  17:10:11,177 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:10Z] INFO  17:10:11,177 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:10Z] INFO  17:10:11,178 MicroScheduler -   -> 206 reads (0.18% of total) failing MappingQualityZeroFilter
[2016-04-15T00:10Z] INFO  17:10:11,179 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:10Z] INFO  17:10:11,179 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-15T00:10Z] INFO  17:10:11,180 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:10Z] INFO  17:10:11,290 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:10Z] INFO  17:10:11,323 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:10Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-3_31617887_47127804-prep.bam
[2016-04-15T00:10Z] INFO  17:10:11,617 ProgressMeter -            done   1.5512391E7    20.0 s       1.0 s      100.0%    20.0 s       0.0 s
[2016-04-15T00:10Z] INFO  17:10:11,618 ProgressMeter - Total runtime 20.44 secs, 0.34 min, 0.01 hours
[2016-04-15T00:10Z] INFO  17:10:11,636 MicroScheduler - 21761 reads were filtered out during the traversal out of approximately 276045 total reads (7.88%)
[2016-04-15T00:10Z] INFO  17:10:11,637 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:10Z] INFO  17:10:11,638 MicroScheduler -   -> 751 reads (0.27% of total) failing BadMateFilter
[2016-04-15T00:10Z] INFO  17:10:11,639 MicroScheduler -   -> 20232 reads (7.33% of total) failing DuplicateReadFilter
[2016-04-15T00:10Z] INFO  17:10:11,639 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:10Z] INFO  17:10:11,639 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:10Z] INFO  17:10:11,640 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:10Z] INFO  17:10:11,640 MicroScheduler -   -> 778 reads (0.28% of total) failing MappingQualityZeroFilter
[2016-04-15T00:10Z] INFO  17:10:11,640 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:10Z] INFO  17:10:11,641 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-15T00:10Z] INFO  17:10:11,641 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:10Z] INFO  17:10:12,249 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:10Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-3_143297426_158963696-prep.bam
[2016-04-15T00:10Z] INFO  17:10:12,438 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-15T00:10Z] INFO  17:10:12,528 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:10Z] INFO  17:10:12,538 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:10Z] INFO  17:10:12,572 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:10Z] INFO  17:10:12,594 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-15T00:10Z] GATK: realign ('4', 15512869, 31144471) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:10Z] INFO  17:10:12,609 IntervalUtils - Processing 18489547 bp from intervals
[2016-04-15T00:10Z] INFO  17:10:12,688 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:10Z] GATK pre-alignment ('4', 134075461, 150351181) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:10Z] INFO  17:10:12,796 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:10Z] INFO  17:10:12,800 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:10Z] INFO  17:10:12,801 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:10Z] INFO  17:10:12,801 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:10Z] GATK pre-alignment ('4', 150354547, 165878648) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:10Z] INFO  17:10:12,806 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/4/R14-18106_kapa-NGv3-PE100-NGv3-sort-4_83857133_99393738-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/4/tx/tmp3T2z11/R14-18106_kapa-NGv3-PE100-NGv3-sort-4_83857133_99393738-prep-prealign-realign.intervals -l INFO -L 4:83857134-99393738 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:10Z] INFO  17:10:12,825 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:10Z] INFO  17:10:12,826 HelpFormatter - Date/Time: 2016/04/14 17:10:12
[2016-04-15T00:10Z] INFO  17:10:12,826 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:10Z] INFO  17:10:12,826 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:10Z] GATK pre-alignment ('4', 165889318, 183245405) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:10Z] INFO  17:10:12,901 ProgressMeter -            done   1.5522634E7    22.0 s       1.0 s      100.0%    22.0 s       0.0 s
[2016-04-15T00:10Z] INFO  17:10:12,901 ProgressMeter - Total runtime 22.25 secs, 0.37 min, 0.01 hours
[2016-04-15T00:10Z] INFO  17:10:12,906 MicroScheduler - 26855 reads were filtered out during the traversal out of approximately 330337 total reads (8.13%)
[2016-04-15T00:10Z] INFO  17:10:12,907 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:10Z] INFO  17:10:12,908 MicroScheduler -   -> 922 reads (0.28% of total) failing BadMateFilter
[2016-04-15T00:10Z] INFO  17:10:12,909 MicroScheduler -   -> 24657 reads (7.46% of total) failing DuplicateReadFilter
[2016-04-15T00:10Z] INFO  17:10:12,909 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:10Z] INFO  17:10:12,910 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:10Z] INFO  17:10:12,911 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:10Z] INFO  17:10:12,911 MicroScheduler -   -> 1276 reads (0.39% of total) failing MappingQualityZeroFilter
[2016-04-15T00:10Z] INFO  17:10:12,912 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:10Z] INFO  17:10:12,912 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-15T00:10Z] INFO  17:10:12,912 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:10Z] INFO  17:10:12,956 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:10Z] INFO  17:10:12,968 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:10Z] INFO  17:10:12,981 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:10Z] INFO  17:10:12,983 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:10Z] INFO  17:10:12,984 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:10Z] INFO  17:10:12,985 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:10Z] GATK: realign ('3', 174814579, 190326970) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:10Z] INFO  17:10:13,001 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:10Z] INFO  17:10:13,156 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T00:10Z] INFO  17:10:13,179 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:10Z] INFO  17:10:13,242 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:10Z] INFO  17:10:13,253 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-15T00:10Z] INFO  17:10:13,637 IntervalUtils - Processing 15536605 bp from intervals
[2016-04-15T00:10Z] WARN  17:10:13,651 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:10Z] INFO  17:10:13,748 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:10Z] INFO  17:10:14,042 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:10Z] INFO  17:10:14,043 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:10Z] INFO  17:10:14,044 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:10Z] INFO  17:10:14,045 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:10Z] INFO  17:10:14,177 ProgressMeter -      4:81792535    200002.0    30.0 s       2.5 m       86.7%    34.0 s       4.0 s
[2016-04-15T00:10Z] INFO  17:10:14,617 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:10Z] GATK: realign ('3', 127770401, 143293035) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:10Z] INFO  17:10:15,731 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:10Z] INFO  17:10:15,734 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:10Z] INFO  17:10:15,735 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:10Z] INFO  17:10:15,735 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:10Z] INFO  17:10:15,740 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/4/R14-18106_kapa-NGv3-PE100-NGv3-sort-4_15512869_31144471-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/4/R14-18106_kapa-NGv3-PE100-NGv3-sort-4_15512869_31144471-prep-prealign-realign.intervals -L 4:15512870-31144471 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/4/tx/tmpvlHc16/R14-18106_kapa-NGv3-PE100-NGv3-sort-4_15512869_31144471-prep.bam
[2016-04-15T00:10Z] INFO  17:10:15,749 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:10Z] INFO  17:10:15,756 HelpFormatter - Date/Time: 2016/04/14 17:10:15
[2016-04-15T00:10Z] INFO  17:10:15,756 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:10Z] INFO  17:10:15,756 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:10Z] INFO  17:10:16,005 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:10Z] INFO  17:10:16,156 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:10Z] INFO  17:10:16,165 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:10Z] INFO  17:10:16,216 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-15T00:10Z] INFO  17:10:16,383 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:10Z] INFO  17:10:16,387 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:10Z] INFO  17:10:16,387 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:10Z] INFO  17:10:16,388 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:10Z] INFO  17:10:16,393 HelpFormatter - Program Args: -T PrintReads -L 4:134075462-150351181 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/4/tx/tmp8jpGU7/R14-18106_kapa-NGv3-PE100-NGv3-sort-4_134075461_150351181-prep-prealign.bam
[2016-04-15T00:10Z] INFO  17:10:16,402 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:10Z] INFO  17:10:16,403 HelpFormatter - Date/Time: 2016/04/14 17:10:16
[2016-04-15T00:10Z] INFO  17:10:16,403 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:10Z] INFO  17:10:16,404 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:10Z] INFO  17:10:16,442 ProgressMeter -            done   1.5628644E7    15.0 s       0.0 s      100.0%    15.0 s       0.0 s
[2016-04-15T00:10Z] INFO  17:10:16,443 ProgressMeter - Total runtime 15.52 secs, 0.26 min, 0.00 hours
[2016-04-15T00:10Z] INFO  17:10:16,447 MicroScheduler - 8453 reads were filtered out during the traversal out of approximately 107959 total reads (7.83%)
[2016-04-15T00:10Z] INFO  17:10:16,449 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:10Z] INFO  17:10:16,450 MicroScheduler -   -> 523 reads (0.48% of total) failing BadMateFilter
[2016-04-15T00:10Z] INFO  17:10:16,451 MicroScheduler -   -> 7653 reads (7.09% of total) failing DuplicateReadFilter
[2016-04-15T00:10Z] INFO  17:10:16,451 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:10Z] INFO  17:10:16,452 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:10Z] INFO  17:10:16,453 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:10Z] INFO  17:10:16,453 MicroScheduler -   -> 277 reads (0.26% of total) failing MappingQualityZeroFilter
[2016-04-15T00:10Z] INFO  17:10:16,466 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:10Z] INFO  17:10:16,467 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-15T00:10Z] INFO  17:10:16,467 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:10Z] INFO  17:10:16,609 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:10Z] INFO  17:10:16,623 IntervalUtils - Processing 15631602 bp from intervals
[2016-04-15T00:10Z] WARN  17:10:16,628 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:10Z] INFO  17:10:16,630 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@7172f77a
[2016-04-15T00:10Z] INFO  17:10:16,698 ProgressMeter -            done    264609.0    32.0 s       2.0 m      100.0%    32.0 s       0.0 s
[2016-04-15T00:10Z] INFO  17:10:16,700 ProgressMeter - Total runtime 32.54 secs, 0.54 min, 0.01 hours
[2016-04-15T00:10Z] INFO  17:10:16,701 MicroScheduler - 172 reads were filtered out during the traversal out of approximately 264781 total reads (0.06%)
[2016-04-15T00:10Z] INFO  17:10:16,701 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:10Z] INFO  17:10:16,704 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:10Z] INFO  17:10:16,705 MicroScheduler -   -> 172 reads (0.06% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:10Z] INFO  17:10:16,709 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:10Z] INFO  17:10:16,712 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:10Z] INFO  17:10:16,712 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:10Z] INFO  17:10:16,713 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:10Z] INFO  17:10:16,720 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/3/R14-18106_kapa-NGv3-PE100-NGv3-sort-3_174814579_190326970-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/3/R14-18106_kapa-NGv3-PE100-NGv3-sort-3_174814579_190326970-prep-prealign-realign.intervals -L 3:174814580-190326970 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/3/tx/tmpOmnK36/R14-18106_kapa-NGv3-PE100-NGv3-sort-3_174814579_190326970-prep.bam
[2016-04-15T00:10Z] INFO  17:10:16,731 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:10Z] INFO  17:10:16,732 HelpFormatter - Date/Time: 2016/04/14 17:10:16
[2016-04-15T00:10Z] INFO  17:10:16,732 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:10Z] INFO  17:10:16,733 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:10Z] INFO  17:10:16,740 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:10Z] INFO  17:10:16,787 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:10Z] INFO  17:10:16,802 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:10Z] INFO  17:10:16,803 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:10Z] INFO  17:10:16,803 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:10Z] INFO  17:10:16,807 HelpFormatter - Program Args: -T PrintReads -L 4:165889319-183245405 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/4/tx/tmpoUPPrZ/R14-18106_kapa-NGv3-PE100-NGv3-sort-4_165889318_183245405-prep-prealign.bam
[2016-04-15T00:10Z] INFO  17:10:16,809 ProgressMeter -       4:9241684    400020.0    60.0 s       2.5 m       59.6%   100.0 s      40.0 s
[2016-04-15T00:10Z] INFO  17:10:16,807 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:10Z] INFO  17:10:16,810 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:10Z] INFO  17:10:16,811 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:10Z] INFO  17:10:16,811 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:10Z] INFO  17:10:16,816 HelpFormatter - Program Args: -T PrintReads -L 4:150354548-165878648 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/4/tx/tmpGrEOh5/R14-18106_kapa-NGv3-PE100-NGv3-sort-4_150354547_165878648-prep-prealign.bam
[2016-04-15T00:10Z] INFO  17:10:16,831 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:10Z] INFO  17:10:16,831 HelpFormatter - Date/Time: 2016/04/14 17:10:16
[2016-04-15T00:10Z] INFO  17:10:16,831 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:10Z] INFO  17:10:16,831 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:10Z] INFO  17:10:16,842 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:10Z] INFO  17:10:16,843 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:10Z] INFO  17:10:16,844 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:10Z] INFO  17:10:16,845 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:10Z] INFO  17:10:16,847 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:10Z] INFO  17:10:16,857 HelpFormatter - Date/Time: 2016/04/14 17:10:16
[2016-04-15T00:10Z] INFO  17:10:16,858 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:10Z] INFO  17:10:16,859 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:10Z] INFO  17:10:16,926 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:10Z] INFO  17:10:17,033 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:10Z] INFO  17:10:17,041 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:10Z] INFO  17:10:17,044 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:10Z] INFO  17:10:17,063 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:10Z] INFO  17:10:17,073 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:10Z] INFO  17:10:17,154 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-15T00:10Z] INFO  17:10:17,205 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:10Z] INFO  17:10:17,547 IntervalUtils - Processing 15512391 bp from intervals
[2016-04-15T00:10Z] WARN  17:10:17,561 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:10Z] INFO  17:10:17,621 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:10Z] INFO  17:10:17,634 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:10Z] INFO  17:10:17,635 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:10Z] INFO  17:10:17,636 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:10Z] INFO  17:10:17,640 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/3/R14-18106_kapa-NGv3-PE100-NGv3-sort-3_127770401_143293035-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/3/R14-18106_kapa-NGv3-PE100-NGv3-sort-3_127770401_143293035-prep-prealign-realign.intervals -L 3:127770402-143293035 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/3/tx/tmpxHG1oQ/R14-18106_kapa-NGv3-PE100-NGv3-sort-3_127770401_143293035-prep.bam
[2016-04-15T00:10Z] INFO  17:10:17,666 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:10Z] INFO  17:10:17,667 HelpFormatter - Date/Time: 2016/04/14 17:10:17
[2016-04-15T00:10Z] INFO  17:10:17,668 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:10Z] INFO  17:10:17,668 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:10Z] INFO  17:10:17,693 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:10Z] INFO  17:10:17,839 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-15T00:10Z] INFO  17:10:17,846 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:10Z] INFO  17:10:17,901 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:10Z] INFO  17:10:17,910 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:10Z] INFO  17:10:17,941 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:10Z] INFO  17:10:17,944 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:10Z] INFO  17:10:17,953 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:10Z] INFO  17:10:17,957 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-15T00:10Z] GATK: realign ('4', 52709749, 68338393) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:10Z] INFO  17:10:17,978 IntervalUtils - Processing 16275720 bp from intervals
[2016-04-15T00:10Z] INFO  17:10:17,995 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:10Z] INFO  17:10:17,996 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:10Z] INFO  17:10:17,997 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:10Z] INFO  17:10:17,998 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:10Z] INFO  17:10:18,022 ProgressMeter -            done   1.5518467E7    27.0 s       1.0 s      100.0%    27.0 s       0.0 s
[2016-04-15T00:10Z] INFO  17:10:18,022 ProgressMeter - Total runtime 27.82 secs, 0.46 min, 0.01 hours
[2016-04-15T00:10Z] INFO  17:10:18,026 MicroScheduler - 57482 reads were filtered out during the traversal out of approximately 717216 total reads (8.01%)
[2016-04-15T00:10Z] INFO  17:10:18,027 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:10Z] INFO  17:10:18,027 MicroScheduler -   -> 1508 reads (0.21% of total) failing BadMateFilter
[2016-04-15T00:10Z] INFO  17:10:18,029 MicroScheduler -   -> 54498 reads (7.60% of total) failing DuplicateReadFilter
[2016-04-15T00:10Z] INFO  17:10:18,030 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:10Z] INFO  17:10:18,030 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:10Z] INFO  17:10:18,031 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:10Z] INFO  17:10:18,032 MicroScheduler -   -> 1476 reads (0.21% of total) failing MappingQualityZeroFilter
[2016-04-15T00:10Z] INFO  17:10:18,032 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-15T00:10Z] INFO  17:10:18,032 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:10Z] INFO  17:10:18,033 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-15T00:10Z] INFO  17:10:18,033 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:10Z] INFO  17:10:18,053 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:10Z] INFO  17:10:18,061 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@41fd9d8e
[2016-04-15T00:10Z] INFO  17:10:18,071 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:10Z] INFO  17:10:18,085 ProgressMeter -            done   1.5514517E7    21.0 s       1.0 s      100.0%    21.0 s       0.0 s
[2016-04-15T00:10Z] INFO  17:10:18,086 ProgressMeter - Total runtime 21.09 secs, 0.35 min, 0.01 hours
[2016-04-15T00:10Z] INFO  17:10:18,106 MicroScheduler - 29101 reads were filtered out during the traversal out of approximately 351351 total reads (8.28%)
[2016-04-15T00:10Z] INFO  17:10:18,107 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:10Z] INFO  17:10:18,107 MicroScheduler -   -> 910 reads (0.26% of total) failing BadMateFilter
[2016-04-15T00:10Z] INFO  17:10:18,108 MicroScheduler -   -> 26487 reads (7.54% of total) failing DuplicateReadFilter
[2016-04-15T00:10Z] INFO  17:10:18,108 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:10Z] INFO  17:10:18,108 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:10Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-4_68340604_83852298-prep-prealign.bam
[2016-04-15T00:10Z] INFO  17:10:18,108 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:10Z] INFO  17:10:18,109 MicroScheduler -   -> 1704 reads (0.48% of total) failing MappingQualityZeroFilter
[2016-04-15T00:10Z] INFO  17:10:18,109 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:10Z] INFO  17:10:18,109 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-15T00:10Z] INFO  17:10:18,109 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:10Z] INFO  17:10:18,172 ProgressMeter -            done    191911.0    25.0 s       2.2 m      100.0%    25.0 s       0.0 s
[2016-04-15T00:10Z] INFO  17:10:18,172 ProgressMeter - Total runtime 25.31 secs, 0.42 min, 0.01 hours
[2016-04-15T00:10Z] INFO  17:10:18,172 MicroScheduler - 136 reads were filtered out during the traversal out of approximately 192047 total reads (0.07%)
[2016-04-15T00:10Z] INFO  17:10:18,173 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:10Z] INFO  17:10:18,173 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:10Z] INFO  17:10:18,173 MicroScheduler -   -> 136 reads (0.07% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:10Z] INFO  17:10:18,201 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:10Z] INFO  17:10:18,233 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-15T00:10Z] INFO  17:10:18,262 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-15T00:10Z] INFO  17:10:18,327 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:10Z] INFO  17:10:18,336 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:10Z] INFO  17:10:18,379 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:10Z] INFO  17:10:18,382 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:10Z] INFO  17:10:18,386 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:10Z] INFO  17:10:18,387 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:10Z] INFO  17:10:18,387 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:10Z] INFO  17:10:18,387 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:10Z] INFO  17:10:18,396 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:10Z] INFO  17:10:18,414 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-15T00:10Z] INFO  17:10:18,435 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:10Z] INFO  17:10:18,442 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-15T00:10Z] INFO  17:10:18,442 IntervalUtils - Processing 17356087 bp from intervals
[2016-04-15T00:10Z] INFO  17:10:18,456 IntervalUtils - Processing 15524101 bp from intervals
[2016-04-15T00:10Z] INFO  17:10:18,525 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:10Z] INFO  17:10:18,591 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:10Z] INFO  17:10:18,614 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:10Z] INFO  17:10:18,656 IntervalUtils - Processing 15522634 bp from intervals
[2016-04-15T00:10Z] WARN  17:10:18,661 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:10Z] INFO  17:10:18,741 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:10Z] INFO  17:10:18,887 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:10Z] INFO  17:10:18,899 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:10Z] INFO  17:10:18,900 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:10Z] INFO  17:10:18,900 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:10Z] GATK RealignerTargetCreator: R14-18106_kapa-NGv3-PE100-NGv3-sort-4_68340604_83852298-prep-prealign.bam 4:68340605-83852298
[2016-04-15T00:10Z] GATK: RealignerTargetCreator
[2016-04-15T00:10Z] INFO  17:10:18,927 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:10Z] INFO  17:10:18,949 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:10Z] INFO  17:10:18,950 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:10Z] INFO  17:10:18,951 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:10Z] INFO  17:10:18,952 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:10Z] INFO  17:10:18,966 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:10Z] INFO  17:10:18,967 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:10Z] INFO  17:10:18,968 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:10Z] INFO  17:10:18,968 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:10Z] INFO  17:10:18,984 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:10Z] INFO  17:10:19,090 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:10Z] INFO  17:10:19,198 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:10Z] INFO  17:10:19,207 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:10Z] INFO  17:10:19,233 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:10Z] INFO  17:10:19,522 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:10Z] GATK: realign ('3', 47129602, 62648069) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:10Z] INFO  17:10:19,604 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:10Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-4_99397339_115544957-prep-prealign.bam
[2016-04-15T00:10Z] INFO  17:10:19,768 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:10Z] GATK: realign ('3', 112188604, 127703121) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:10Z] INFO  17:10:19,934 ProgressMeter -            done    204628.0    17.0 s      84.0 s       99.1%    17.0 s       0.0 s
[2016-04-15T00:10Z] INFO  17:10:19,935 ProgressMeter - Total runtime 17.27 secs, 0.29 min, 0.00 hours
[2016-04-15T00:10Z] INFO  17:10:19,938 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 204628 total reads (0.00%)
[2016-04-15T00:10Z] INFO  17:10:19,939 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:10Z] INFO  17:10:19,939 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:10Z] INFO  17:10:19,939 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:10Z] GATK RealignerTargetCreator: R14-18106_kapa-NGv3-PE100-NGv3-sort-4_99397339_115544957-prep-prealign.bam 4:99397340-115544957
[2016-04-15T00:10Z] GATK: RealignerTargetCreator
[2016-04-15T00:10Z] INFO  17:10:20,807 ProgressMeter -            done   1.6639905E7    18.0 s       1.0 s      100.0%    18.0 s       0.0 s
[2016-04-15T00:10Z] INFO  17:10:20,808 ProgressMeter - Total runtime 18.69 secs, 0.31 min, 0.01 hours
[2016-04-15T00:10Z] INFO  17:10:20,812 MicroScheduler - 17039 reads were filtered out during the traversal out of approximately 181305 total reads (9.40%)
[2016-04-15T00:10Z] INFO  17:10:20,813 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:10Z] INFO  17:10:20,813 MicroScheduler -   -> 799 reads (0.44% of total) failing BadMateFilter
[2016-04-15T00:10Z] INFO  17:10:20,814 MicroScheduler -   -> 12973 reads (7.16% of total) failing DuplicateReadFilter
[2016-04-15T00:10Z] INFO  17:10:20,825 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:10Z] INFO  17:10:20,826 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:10Z] INFO  17:10:20,827 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:10Z] INFO  17:10:20,828 MicroScheduler -   -> 3267 reads (1.80% of total) failing MappingQualityZeroFilter
[2016-04-15T00:10Z] INFO  17:10:20,829 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:10Z] INFO  17:10:20,829 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-15T00:10Z] INFO  17:10:20,830 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:10Z] INFO  17:10:20,967 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:10Z] INFO  17:10:20,971 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:10Z] INFO  17:10:20,972 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:10Z] INFO  17:10:20,972 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:10Z] INFO  17:10:20,977 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/4/R14-18106_kapa-NGv3-PE100-NGv3-sort-4_52709749_68338393-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/4/R14-18106_kapa-NGv3-PE100-NGv3-sort-4_52709749_68338393-prep-prealign-realign.intervals -L 4:52709750-68338393 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/4/tx/tmpHK_mqc/R14-18106_kapa-NGv3-PE100-NGv3-sort-4_52709749_68338393-prep.bam
[2016-04-15T00:10Z] INFO  17:10:21,013 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:10Z] INFO  17:10:21,014 HelpFormatter - Date/Time: 2016/04/14 17:10:20
[2016-04-15T00:10Z] INFO  17:10:21,014 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:10Z] INFO  17:10:21,014 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:10Z] INFO  17:10:21,278 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:10Z] INFO  17:10:21,430 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:10Z] INFO  17:10:21,440 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:10Z] INFO  17:10:21,509 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-15T00:10Z] INFO  17:10:21,612 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:10Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-3_190333063_198022430-prep.bam
[2016-04-15T00:10Z] INFO  17:10:21,800 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:10Z] INFO  17:10:21,804 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:10Z] INFO  17:10:21,804 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:10Z] INFO  17:10:21,805 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:10Z] INFO  17:10:21,809 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/4/R14-18106_kapa-NGv3-PE100-NGv3-sort-4_68340604_83852298-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/4/tx/tmpivleYb/R14-18106_kapa-NGv3-PE100-NGv3-sort-4_68340604_83852298-prep-prealign-realign.intervals -l INFO -L 4:68340605-83852298 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:10Z] INFO  17:10:21,821 IntervalUtils - Processing 15628644 bp from intervals
[2016-04-15T00:10Z] INFO  17:10:21,826 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:10Z] INFO  17:10:21,827 HelpFormatter - Date/Time: 2016/04/14 17:10:21
[2016-04-15T00:10Z] WARN  17:10:21,826 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:10Z] INFO  17:10:21,827 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:10Z] INFO  17:10:21,828 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:10Z] INFO  17:10:21,911 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:10Z] INFO  17:10:21,987 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:10Z] INFO  17:10:22,036 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:10Z] INFO  17:10:22,048 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:10Z] INFO  17:10:22,049 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:10Z] INFO  17:10:22,049 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:10Z] INFO  17:10:22,194 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:10Z] INFO  17:10:22,235 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T00:10Z] INFO  17:10:22,245 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:10Z] INFO  17:10:22,292 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-15T00:10Z] INFO  17:10:22,349 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:10Z] INFO  17:10:22,355 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:10Z] GATK: realign ('4', 36069528, 52709433) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:10Z] GATK pre-alignment ('4', 183267803, 191154276) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:10Z] INFO  17:10:22,518 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:10Z] INFO  17:10:22,521 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:10Z] INFO  17:10:22,521 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:10Z] INFO  17:10:22,522 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:10Z] INFO  17:10:22,526 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/3/R14-18106_kapa-NGv3-PE100-NGv3-sort-3_47129602_62648069-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/3/R14-18106_kapa-NGv3-PE100-NGv3-sort-3_47129602_62648069-prep-prealign-realign.intervals -L 3:47129603-62648069 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/3/tx/tmpcTSNJN/R14-18106_kapa-NGv3-PE100-NGv3-sort-3_47129602_62648069-prep.bam
[2016-04-15T00:10Z] INFO  17:10:22,546 IntervalUtils - Processing 15511694 bp from intervals
[2016-04-15T00:10Z] WARN  17:10:22,551 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:10Z] INFO  17:10:22,559 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:10Z] INFO  17:10:22,560 HelpFormatter - Date/Time: 2016/04/14 17:10:22
[2016-04-15T00:10Z] INFO  17:10:22,560 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:10Z] INFO  17:10:22,561 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:10Z] INFO  17:10:22,634 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:10Z] INFO  17:10:22,715 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:10Z] INFO  17:10:22,718 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:10Z] INFO  17:10:22,719 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:10Z] INFO  17:10:22,719 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:10Z] INFO  17:10:22,724 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/3/R14-18106_kapa-NGv3-PE100-NGv3-sort-3_112188604_127703121-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/3/R14-18106_kapa-NGv3-PE100-NGv3-sort-3_112188604_127703121-prep-prealign-realign.intervals -L 3:112188605-127703121 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/3/tx/tmpzZrdp5/R14-18106_kapa-NGv3-PE100-NGv3-sort-3_112188604_127703121-prep.bam
[2016-04-15T00:10Z] INFO  17:10:22,735 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:10Z] INFO  17:10:22,736 HelpFormatter - Date/Time: 2016/04/14 17:10:22
[2016-04-15T00:10Z] INFO  17:10:22,737 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:10Z] INFO  17:10:22,737 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:10Z] INFO  17:10:22,737 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:10Z] INFO  17:10:22,839 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:10Z] INFO  17:10:22,840 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:10Z] INFO  17:10:22,841 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:10Z] INFO  17:10:22,841 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:10Z] INFO  17:10:22,906 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:10Z] INFO  17:10:22,915 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:10Z] INFO  17:10:22,953 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:10Z] INFO  17:10:22,986 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-15T00:10Z] INFO  17:10:23,070 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:10Z] INFO  17:10:23,079 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:10Z] INFO  17:10:23,136 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-15T00:10Z] INFO  17:10:23,351 IntervalUtils - Processing 15518467 bp from intervals
[2016-04-15T00:10Z] WARN  17:10:23,365 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:10Z] INFO  17:10:23,436 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:10Z] INFO  17:10:23,472 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:10Z] INFO  17:10:23,475 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:10Z] INFO  17:10:23,476 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:10Z] INFO  17:10:23,477 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:10Z] INFO  17:10:23,481 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/4/R14-18106_kapa-NGv3-PE100-NGv3-sort-4_99397339_115544957-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/4/tx/tmpHKxNUX/R14-18106_kapa-NGv3-PE100-NGv3-sort-4_99397339_115544957-prep-prealign-realign.intervals -l INFO -L 4:99397340-115544957 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:10Z] INFO  17:10:23,491 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:10Z] INFO  17:10:23,498 HelpFormatter - Date/Time: 2016/04/14 17:10:23
[2016-04-15T00:10Z] INFO  17:10:23,499 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:10Z] INFO  17:10:23,500 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:10Z] INFO  17:10:23,625 IntervalUtils - Processing 15514517 bp from intervals
[2016-04-15T00:10Z] WARN  17:10:23,634 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:10Z] INFO  17:10:23,662 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:10Z] INFO  17:10:23,683 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:10Z] INFO  17:10:23,685 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:10Z] INFO  17:10:23,685 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:10Z] INFO  17:10:23,686 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:10Z] INFO  17:10:23,765 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:10Z] INFO  17:10:23,926 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:10Z] INFO  17:10:23,952 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:10Z] INFO  17:10:23,954 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:10Z] INFO  17:10:23,954 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:10Z] INFO  17:10:23,955 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:10Z] INFO  17:10:23,974 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T00:10Z] INFO  17:10:23,983 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:10Z] INFO  17:10:24,041 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-15T00:10Z] INFO  17:10:24,094 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:10Z] INFO  17:10:24,140 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:10Z] INFO  17:10:24,310 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:10Z] INFO  17:10:24,328 IntervalUtils - Processing 16147618 bp from intervals
[2016-04-15T00:10Z] WARN  17:10:24,333 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:10Z] INFO  17:10:24,414 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:10Z] INFO  17:10:24,623 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:10Z] INFO  17:10:24,624 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:10Z] INFO  17:10:24,625 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:10Z] INFO  17:10:24,625 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:10Z] INFO  17:10:25,464 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:10Z] INFO  17:10:25,470 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:10Z] INFO  17:10:25,471 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:10Z] INFO  17:10:25,472 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:10Z] INFO  17:10:25,478 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:10Z] INFO  17:10:25,485 HelpFormatter - Program Args: -T PrintReads -L 4:183267804-191154276 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/4/tx/tmpRleDfE/R14-18106_kapa-NGv3-PE100-NGv3-sort-4_183267803_191154276-prep-prealign.bam
[2016-04-15T00:10Z] INFO  17:10:25,486 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:10Z] INFO  17:10:25,487 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:10Z] INFO  17:10:25,487 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:10Z] INFO  17:10:25,491 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/4/R14-18106_kapa-NGv3-PE100-NGv3-sort-4_36069528_52709433-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/4/R14-18106_kapa-NGv3-PE100-NGv3-sort-4_36069528_52709433-prep-prealign-realign.intervals -L 4:36069529-52709433 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/4/tx/tmphdLDMl/R14-18106_kapa-NGv3-PE100-NGv3-sort-4_36069528_52709433-prep.bam
[2016-04-15T00:10Z] INFO  17:10:25,496 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:10Z] INFO  17:10:25,504 HelpFormatter - Date/Time: 2016/04/14 17:10:25
[2016-04-15T00:10Z] INFO  17:10:25,505 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:10Z] INFO  17:10:25,506 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:10Z] INFO  17:10:25,514 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:10Z] INFO  17:10:25,515 HelpFormatter - Date/Time: 2016/04/14 17:10:25
[2016-04-15T00:10Z] INFO  17:10:25,524 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:10Z] INFO  17:10:25,525 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:10Z] INFO  17:10:25,733 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:10Z] INFO  17:10:25,818 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:10Z] INFO  17:10:26,045 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:10Z] INFO  17:10:26,062 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:10Z] INFO  17:10:26,186 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.12
[2016-04-15T00:10Z] INFO  17:10:26,854 IntervalUtils - Processing 16639905 bp from intervals
[2016-04-15T00:10Z] WARN  17:10:26,859 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:10Z] INFO  17:10:27,025 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:10Z] INFO  17:10:27,147 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-15T00:10Z] INFO  17:10:27,201 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:10Z] INFO  17:10:27,202 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:10Z] INFO  17:10:27,202 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:10Z] INFO  17:10:27,203 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:10Z] INFO  17:10:27,206 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:10Z] INFO  17:10:27,222 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:10Z] INFO  17:10:27,260 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.04
[2016-04-15T00:10Z] INFO  17:10:27,275 IntervalUtils - Processing 7886473 bp from intervals
[2016-04-15T00:10Z] INFO  17:10:27,343 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:10Z] INFO  17:10:27,350 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:10Z] INFO  17:10:27,485 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:10Z] INFO  17:10:27,646 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:10Z] INFO  17:10:27,667 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:10Z] INFO  17:10:27,667 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:10Z] INFO  17:10:27,667 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:10Z] INFO  17:10:27,692 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:10Z] INFO  17:10:27,818 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:10Z] INFO  17:10:28,594 ProgressMeter -            done    111783.0    11.0 s     105.0 s      100.0%    11.0 s       0.0 s
[2016-04-15T00:10Z] INFO  17:10:28,594 ProgressMeter - Total runtime 11.75 secs, 0.20 min, 0.00 hours
[2016-04-15T00:10Z] INFO  17:10:28,598 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 111783 total reads (0.00%)
[2016-04-15T00:10Z] INFO  17:10:28,598 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:10Z] INFO  17:10:28,598 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:10Z] INFO  17:10:28,599 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:10Z] INFO  17:10:29,951 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:10Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-4_15512869_31144471-prep.bam
[2016-04-15T00:10Z] GATK pre-alignment ('5', 0, 15580921) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:10Z] INFO  17:10:32,254 ProgressMeter -            done   1.5536605E7    18.0 s       1.0 s      100.0%    18.0 s       0.0 s
[2016-04-15T00:10Z] INFO  17:10:32,255 ProgressMeter - Total runtime 18.21 secs, 0.30 min, 0.01 hours
[2016-04-15T00:10Z] INFO  17:10:32,259 MicroScheduler - 13332 reads were filtered out during the traversal out of approximately 161548 total reads (8.25%)
[2016-04-15T00:10Z] INFO  17:10:32,260 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:10Z] INFO  17:10:32,261 MicroScheduler -   -> 598 reads (0.37% of total) failing BadMateFilter
[2016-04-15T00:10Z] INFO  17:10:32,261 MicroScheduler -   -> 12244 reads (7.58% of total) failing DuplicateReadFilter
[2016-04-15T00:10Z] INFO  17:10:32,262 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:10Z] INFO  17:10:32,262 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:10Z] INFO  17:10:32,263 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:10Z] INFO  17:10:32,264 MicroScheduler -   -> 490 reads (0.30% of total) failing MappingQualityZeroFilter
[2016-04-15T00:10Z] INFO  17:10:32,264 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:10Z] INFO  17:10:32,265 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-15T00:10Z] INFO  17:10:32,265 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:10Z] INFO  17:10:32,518 ProgressMeter -            done    107517.0    10.0 s      97.0 s      100.0%    10.0 s       0.0 s
[2016-04-15T00:10Z] INFO  17:10:32,519 ProgressMeter - Total runtime 10.47 secs, 0.17 min, 0.00 hours
[2016-04-15T00:10Z] INFO  17:10:32,522 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 107517 total reads (0.00%)
[2016-04-15T00:10Z] INFO  17:10:32,524 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:10Z] INFO  17:10:32,524 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:10Z] INFO  17:10:32,525 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:10Z] INFO  17:10:33,200 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:10Z] INFO  17:10:33,204 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:10Z] INFO  17:10:33,204 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:10Z] INFO  17:10:33,205 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:10Z] INFO  17:10:33,211 HelpFormatter - Program Args: -T PrintReads -L 5:1-15580921 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/5/tx/tmpnuS5JA/R14-18106_kapa-NGv3-PE100-NGv3-sort-5_0_15580921-prep-prealign.bam
[2016-04-15T00:10Z] INFO  17:10:33,222 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:10Z] INFO  17:10:33,223 HelpFormatter - Date/Time: 2016/04/14 17:10:33
[2016-04-15T00:10Z] INFO  17:10:33,223 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:10Z] INFO  17:10:33,223 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:10Z] INFO  17:10:33,500 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:10Z] INFO  17:10:33,685 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:10Z] GATK: realign ('4', 83857133, 99393738) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:10Z] INFO  17:10:34,072 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:10Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-4_52709749_68338393-prep.bam
[2016-04-15T00:10Z] INFO  17:10:34,475 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@32d5a4c6
[2016-04-15T00:10Z] GATK pre-alignment ('5', 15616091, 31267808) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:10Z] INFO  17:10:34,632 ProgressMeter -            done     92554.0    15.0 s       2.8 m      100.0%    15.0 s       0.0 s
[2016-04-15T00:10Z] INFO  17:10:34,633 ProgressMeter - Total runtime 15.67 secs, 0.26 min, 0.00 hours
[2016-04-15T00:10Z] INFO  17:10:34,633 MicroScheduler - 136 reads were filtered out during the traversal out of approximately 92690 total reads (0.15%)
[2016-04-15T00:10Z] INFO  17:10:34,634 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:10Z] INFO  17:10:34,634 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:10Z] INFO  17:10:34,634 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-15T00:10Z] INFO  17:10:34,634 MicroScheduler -   -> 136 reads (0.15% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:10Z] INFO  17:10:34,720 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:10Z] INFO  17:10:34,740 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:10Z] INFO  17:10:34,809 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-15T00:10Z] INFO  17:10:34,838 IntervalUtils - Processing 15580921 bp from intervals
[2016-04-15T00:10Z] INFO  17:10:34,907 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:10Z] INFO  17:10:35,200 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:10Z] INFO  17:10:35,201 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:10Z] INFO  17:10:35,202 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:10Z] INFO  17:10:35,203 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:10Z] INFO  17:10:35,216 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:10Z] INFO  17:10:35,278 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@41fd9d8e
[2016-04-15T00:10Z] INFO  17:10:35,334 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:10Z] INFO  17:10:35,413 ProgressMeter -            done    116100.0    17.0 s       2.4 m       97.9%    17.0 s       0.0 s
[2016-04-15T00:10Z] INFO  17:10:35,414 ProgressMeter - Total runtime 17.03 secs, 0.28 min, 0.00 hours
[2016-04-15T00:10Z] INFO  17:10:35,414 MicroScheduler - 137 reads were filtered out during the traversal out of approximately 116237 total reads (0.12%)
[2016-04-15T00:10Z] INFO  17:10:35,415 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:10Z] INFO  17:10:35,415 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:10Z] INFO  17:10:35,415 MicroScheduler -   -> 137 reads (0.12% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:10Z] INFO  17:10:36,029 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:10Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-4_165889318_183245405-prep-prealign.bam
[2016-04-15T00:10Z] INFO  17:10:36,354 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:10Z] INFO  17:10:36,357 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:10Z] INFO  17:10:36,358 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:10Z] INFO  17:10:36,358 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:10Z] INFO  17:10:36,363 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/4/R14-18106_kapa-NGv3-PE100-NGv3-sort-4_83857133_99393738-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/4/R14-18106_kapa-NGv3-PE100-NGv3-sort-4_83857133_99393738-prep-prealign-realign.intervals -L 4:83857134-99393738 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/4/tx/tmpuuM2Yd/R14-18106_kapa-NGv3-PE100-NGv3-sort-4_83857133_99393738-prep.bam
[2016-04-15T00:10Z] INFO  17:10:36,378 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:10Z] INFO  17:10:36,392 HelpFormatter - Date/Time: 2016/04/14 17:10:36
[2016-04-15T00:10Z] INFO  17:10:36,393 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:10Z] INFO  17:10:36,394 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:10Z] GATK RealignerTargetCreator: R14-18106_kapa-NGv3-PE100-NGv3-sort-4_165889318_183245405-prep-prealign.bam 4:165889319-183245405
[2016-04-15T00:10Z] GATK: RealignerTargetCreator
[2016-04-15T00:10Z] INFO  17:10:36,634 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:10Z] INFO  17:10:36,759 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:10Z] INFO  17:10:36,770 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:10Z] INFO  17:10:36,840 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-15T00:10Z] INFO  17:10:36,878 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:10Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-4_134075461_150351181-prep-prealign.bam
[2016-04-15T00:10Z] INFO  17:10:37,267 IntervalUtils - Processing 15536605 bp from intervals
[2016-04-15T00:10Z] WARN  17:10:37,273 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:10Z] GATK RealignerTargetCreator: R14-18106_kapa-NGv3-PE100-NGv3-sort-4_134075461_150351181-prep-prealign.bam 4:134075462-150351181
[2016-04-15T00:10Z] GATK: RealignerTargetCreator
[2016-04-15T00:10Z] INFO  17:10:37,394 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:10Z] INFO  17:10:37,397 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:10Z] INFO  17:10:37,398 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:10Z] INFO  17:10:37,398 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:10Z] INFO  17:10:37,403 HelpFormatter - Program Args: -T PrintReads -L 5:15616092-31267808 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/5/tx/tmphEndVy/R14-18106_kapa-NGv3-PE100-NGv3-sort-5_15616091_31267808-prep-prealign.bam
[2016-04-15T00:10Z] INFO  17:10:37,405 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:10Z] INFO  17:10:37,412 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:10Z] INFO  17:10:37,412 HelpFormatter - Date/Time: 2016/04/14 17:10:37
[2016-04-15T00:10Z] INFO  17:10:37,412 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:10Z] INFO  17:10:37,413 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:10Z] INFO  17:10:37,567 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:10Z] INFO  17:10:37,579 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:10Z] INFO  17:10:37,580 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:10Z] INFO  17:10:37,581 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:10Z] INFO  17:10:37,666 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:10Z] INFO  17:10:37,781 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:10Z] INFO  17:10:37,787 ProgressMeter -            done    274143.0    19.0 s      72.0 s      100.0%    19.0 s       0.0 s
[2016-04-15T00:10Z] INFO  17:10:37,788 ProgressMeter - Total runtime 19.79 secs, 0.33 min, 0.01 hours
[2016-04-15T00:10Z] INFO  17:10:37,792 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 274143 total reads (0.00%)
[2016-04-15T00:10Z] INFO  17:10:37,792 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:10Z] INFO  17:10:37,793 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:10Z] INFO  17:10:37,793 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:10Z] INFO  17:10:37,928 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:10Z] INFO  17:10:38,710 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-15T00:10Z] INFO  17:10:38,767 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:10Z] INFO  17:10:38,776 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:10Z] INFO  17:10:38,820 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.04
[2016-04-15T00:10Z] INFO  17:10:38,845 IntervalUtils - Processing 15651717 bp from intervals
[2016-04-15T00:10Z] INFO  17:10:38,912 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:10Z] INFO  17:10:39,159 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:10Z] INFO  17:10:39,160 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:10Z] INFO  17:10:39,161 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:10Z] INFO  17:10:39,162 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:10Z] INFO  17:10:39,184 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:10Z] INFO  17:10:39,196 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:10Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-3_174814579_190326970-prep.bam
[2016-04-15T00:10Z] INFO  17:10:39,294 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:10Z] INFO  17:10:39,296 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:10Z] INFO  17:10:39,297 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:10Z] INFO  17:10:39,297 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:10Z] INFO  17:10:39,301 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/4/R14-18106_kapa-NGv3-PE100-NGv3-sort-4_165889318_183245405-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/4/tx/tmprkZXpb/R14-18106_kapa-NGv3-PE100-NGv3-sort-4_165889318_183245405-prep-prealign-realign.intervals -l INFO -L 4:165889319-183245405 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:10Z] INFO  17:10:39,311 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:10Z] INFO  17:10:39,311 HelpFormatter - Date/Time: 2016/04/14 17:10:39
[2016-04-15T00:10Z] INFO  17:10:39,311 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:10Z] INFO  17:10:39,311 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:10Z] INFO  17:10:39,329 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:10Z] INFO  17:10:39,416 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:10Z] INFO  17:10:39,449 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@32d5a4c6
[2016-04-15T00:10Z] INFO  17:10:39,621 ProgressMeter -            done    174214.0    26.0 s       2.5 m      100.0%    26.0 s       0.0 s
[2016-04-15T00:10Z] INFO  17:10:39,622 ProgressMeter - Total runtime 26.64 secs, 0.44 min, 0.01 hours
[2016-04-15T00:10Z] INFO  17:10:39,622 MicroScheduler - 158 reads were filtered out during the traversal out of approximately 174372 total reads (0.09%)
[2016-04-15T00:10Z] INFO  17:10:39,622 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:10Z] INFO  17:10:39,623 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:10Z] INFO  17:10:39,623 MicroScheduler -   -> 158 reads (0.09% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:10Z] INFO  17:10:39,623 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T00:10Z] INFO  17:10:39,648 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:10Z] INFO  17:10:39,712 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@7172f77a
[2016-04-15T00:10Z] INFO  17:10:39,722 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-15T00:10Z] INFO  17:10:39,976 ProgressMeter -            done    146590.0    21.0 s       2.4 m      100.0%    21.0 s       0.0 s
[2016-04-15T00:10Z] INFO  17:10:39,977 ProgressMeter - Total runtime 21.08 secs, 0.35 min, 0.01 hours
[2016-04-15T00:10Z] INFO  17:10:39,977 MicroScheduler - 136 reads were filtered out during the traversal out of approximately 146726 total reads (0.09%)
[2016-04-15T00:10Z] INFO  17:10:39,977 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:10Z] INFO  17:10:39,978 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:10Z] INFO  17:10:39,978 MicroScheduler -   -> 136 reads (0.09% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:10Z] INFO  17:10:39,998 IntervalUtils - Processing 17356087 bp from intervals
[2016-04-15T00:10Z] WARN  17:10:40,004 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:10Z] INFO  17:10:40,089 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:10Z] GATK pre-alignment ('5', 31294068, 49695124) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:10Z] INFO  17:10:40,271 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:10Z] INFO  17:10:40,272 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:10Z] INFO  17:10:40,272 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:10Z] INFO  17:10:40,273 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:10Z] INFO  17:10:40,506 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:10Z] INFO  17:10:40,524 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:10Z] INFO  17:10:40,524 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:10Z] INFO  17:10:40,524 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:10Z] INFO  17:10:40,528 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/4/R14-18106_kapa-NGv3-PE100-NGv3-sort-4_134075461_150351181-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/4/tx/tmpEntTfq/R14-18106_kapa-NGv3-PE100-NGv3-sort-4_134075461_150351181-prep-prealign-realign.intervals -l INFO -L 4:134075462-150351181 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:10Z] INFO  17:10:40,590 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:10Z] INFO  17:10:40,590 HelpFormatter - Date/Time: 2016/04/14 17:10:40
[2016-04-15T00:10Z] INFO  17:10:40,590 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:10Z] INFO  17:10:40,590 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:10Z] INFO  17:10:40,747 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:10Z] INFO  17:10:41,047 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T00:10Z] INFO  17:10:41,067 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:10Z] INFO  17:10:41,074 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:10Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-4_115584857_134074404-prep-prealign.bam
[2016-04-15T00:10Z] INFO  17:10:41,162 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.09
[2016-04-15T00:10Z] INFO  17:10:41,524 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:10Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-4_150354547_165878648-prep-prealign.bam
[2016-04-15T00:10Z] INFO  17:10:41,547 IntervalUtils - Processing 16275720 bp from intervals
[2016-04-15T00:10Z] WARN  17:10:41,568 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:10Z] GATK RealignerTargetCreator: R14-18106_kapa-NGv3-PE100-NGv3-sort-4_115584857_134074404-prep-prealign.bam 4:115584858-134074404
[2016-04-15T00:10Z] GATK: RealignerTargetCreator
[2016-04-15T00:10Z] INFO  17:10:41,703 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:10Z] INFO  17:10:41,982 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:10Z] INFO  17:10:41,983 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:10Z] INFO  17:10:41,983 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:10Z] INFO  17:10:41,983 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:10Z] GATK RealignerTargetCreator: R14-18106_kapa-NGv3-PE100-NGv3-sort-4_150354547_165878648-prep-prealign.bam 4:150354548-165878648
[2016-04-15T00:10Z] GATK: RealignerTargetCreator
[2016-04-15T00:10Z] INFO  17:10:42,144 ProgressMeter -            done    328146.0    23.0 s      70.0 s      100.0%    23.0 s       0.0 s
[2016-04-15T00:10Z] INFO  17:10:42,144 ProgressMeter - Total runtime 23.19 secs, 0.39 min, 0.01 hours
[2016-04-15T00:10Z] INFO  17:10:42,148 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 328146 total reads (0.00%)
[2016-04-15T00:10Z] INFO  17:10:42,148 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:10Z] INFO  17:10:42,149 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:10Z] INFO  17:10:42,149 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:10Z] INFO  17:10:42,658 ProgressMeter -            done    180252.0    15.0 s      85.0 s      100.0%    15.0 s       0.0 s
[2016-04-15T00:10Z] INFO  17:10:42,658 ProgressMeter - Total runtime 15.46 secs, 0.26 min, 0.00 hours
[2016-04-15T00:10Z] INFO  17:10:42,662 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 180252 total reads (0.00%)
[2016-04-15T00:10Z] INFO  17:10:42,662 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:10Z] INFO  17:10:42,662 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:10Z] INFO  17:10:42,663 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:10Z] INFO  17:10:42,819 ProgressMeter -            done   1.5511694E7    19.0 s       1.0 s      100.0%    19.0 s       0.0 s
[2016-04-15T00:10Z] INFO  17:10:42,820 ProgressMeter - Total runtime 19.98 secs, 0.33 min, 0.01 hours
[2016-04-15T00:10Z] INFO  17:10:42,824 MicroScheduler - 23390 reads were filtered out during the traversal out of approximately 266344 total reads (8.78%)
[2016-04-15T00:10Z] INFO  17:10:42,825 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:10Z] INFO  17:10:42,825 MicroScheduler -   -> 722 reads (0.27% of total) failing BadMateFilter
[2016-04-15T00:10Z] INFO  17:10:42,826 MicroScheduler -   -> 19295 reads (7.24% of total) failing DuplicateReadFilter
[2016-04-15T00:10Z] INFO  17:10:42,827 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:10Z] INFO  17:10:42,827 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:10Z] INFO  17:10:42,828 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:10Z] INFO  17:10:42,828 MicroScheduler -   -> 3373 reads (1.27% of total) failing MappingQualityZeroFilter
[2016-04-15T00:10Z] INFO  17:10:42,829 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:10Z] INFO  17:10:42,830 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-15T00:10Z] INFO  17:10:42,831 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:10Z] INFO  17:10:42,939 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:10Z] INFO  17:10:42,942 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:10Z] INFO  17:10:42,943 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:10Z] INFO  17:10:42,943 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:10Z] INFO  17:10:42,948 HelpFormatter - Program Args: -T PrintReads -L 5:31294069-49695124 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/5/tx/tmpUIIm6S/R14-18106_kapa-NGv3-PE100-NGv3-sort-5_31294068_49695124-prep-prealign.bam
[2016-04-15T00:10Z] INFO  17:10:42,957 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:10Z] INFO  17:10:42,958 HelpFormatter - Date/Time: 2016/04/14 17:10:42
[2016-04-15T00:10Z] INFO  17:10:42,959 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:10Z] INFO  17:10:42,959 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:10Z] INFO  17:10:43,170 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:10Z] INFO  17:10:43,177 ProgressMeter -            done   1.6147618E7    18.0 s       1.0 s      100.0%    18.0 s       0.0 s
[2016-04-15T00:10Z] INFO  17:10:43,178 ProgressMeter - Total runtime 18.55 secs, 0.31 min, 0.01 hours
[2016-04-15T00:10Z] INFO  17:10:43,181 MicroScheduler - 15414 reads were filtered out during the traversal out of approximately 192955 total reads (7.99%)
[2016-04-15T00:10Z] INFO  17:10:43,181 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:10Z] INFO  17:10:43,182 MicroScheduler -   -> 602 reads (0.31% of total) failing BadMateFilter
[2016-04-15T00:10Z] INFO  17:10:43,182 MicroScheduler -   -> 14044 reads (7.28% of total) failing DuplicateReadFilter
[2016-04-15T00:10Z] INFO  17:10:43,182 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:10Z] INFO  17:10:43,182 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:10Z] INFO  17:10:43,183 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:10Z] INFO  17:10:43,183 MicroScheduler -   -> 768 reads (0.40% of total) failing MappingQualityZeroFilter
[2016-04-15T00:10Z] INFO  17:10:43,183 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:10Z] INFO  17:10:43,183 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-15T00:10Z] INFO  17:10:43,183 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:10Z] INFO  17:10:43,679 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:10Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-3_127770401_143293035-prep.bam
[2016-04-15T00:10Z] INFO  17:10:44,306 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:10Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-4_36069528_52709433-prep.bam
[2016-04-15T00:10Z] INFO  17:10:44,363 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:10Z] INFO  17:10:44,374 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-15T00:10Z] GATK: realign ('4', 68340604, 83852298) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:10Z] INFO  17:10:44,439 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:10Z] INFO  17:10:44,463 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:10Z] INFO  17:10:44,516 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-15T00:10Z] INFO  17:10:44,540 IntervalUtils - Processing 18401056 bp from intervals
[2016-04-15T00:10Z] INFO  17:10:44,591 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:10Z] INFO  17:10:44,594 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:10Z] INFO  17:10:44,595 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:10Z] INFO  17:10:44,595 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:10Z] INFO  17:10:44,600 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/4/R14-18106_kapa-NGv3-PE100-NGv3-sort-4_115584857_134074404-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/4/tx/tmpqOwHIW/R14-18106_kapa-NGv3-PE100-NGv3-sort-4_115584857_134074404-prep-prealign-realign.intervals -l INFO -L 4:115584858-134074404 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:10Z] INFO  17:10:44,618 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:10Z] INFO  17:10:44,620 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:10Z] INFO  17:10:44,627 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:10Z] INFO  17:10:44,633 HelpFormatter - Date/Time: 2016/04/14 17:10:44
[2016-04-15T00:10Z] INFO  17:10:44,634 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:10Z] INFO  17:10:44,638 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:10Z] GATK: realign ('4', 99397339, 115544957) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:10Z] GATK pre-alignment ('5', 49695692, 65288736) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:10Z] INFO  17:10:44,751 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:10Z] INFO  17:10:44,753 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:10Z] INFO  17:10:44,757 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:10Z] INFO  17:10:44,758 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:10Z] INFO  17:10:44,758 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:10Z] INFO  17:10:44,763 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/4/R14-18106_kapa-NGv3-PE100-NGv3-sort-4_150354547_165878648-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/4/tx/tmpfydzSh/R14-18106_kapa-NGv3-PE100-NGv3-sort-4_150354547_165878648-prep-prealign-realign.intervals -l INFO -L 4:150354548-165878648 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:10Z] INFO  17:10:44,788 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:10Z] INFO  17:10:44,789 HelpFormatter - Date/Time: 2016/04/14 17:10:44
[2016-04-15T00:10Z] INFO  17:10:44,789 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:10Z] INFO  17:10:44,794 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:10Z] INFO  17:10:44,882 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:10Z] INFO  17:10:44,930 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:10Z] INFO  17:10:44,931 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:10Z] INFO  17:10:44,932 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:10Z] INFO  17:10:44,932 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:10Z] GATK pre-alignment ('5', 65290574, 80809536) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:10Z] INFO  17:10:44,962 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:10Z] INFO  17:10:44,967 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T00:10Z] INFO  17:10:44,977 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:10Z] INFO  17:10:45,030 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-15T00:10Z] INFO  17:10:45,098 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T00:10Z] INFO  17:10:45,107 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:10Z] INFO  17:10:45,115 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@5fe152b7
[2016-04-15T00:10Z] INFO  17:10:45,174 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:10Z] INFO  17:10:45,189 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-15T00:10Z] INFO  17:10:45,306 ProgressMeter -            done    136369.0    17.0 s       2.2 m       97.9%    17.0 s       0.0 s
[2016-04-15T00:10Z] INFO  17:10:45,307 ProgressMeter - Total runtime 17.64 secs, 0.29 min, 0.00 hours
[2016-04-15T00:10Z] INFO  17:10:45,307 MicroScheduler - 98 reads were filtered out during the traversal out of approximately 136467 total reads (0.07%)
[2016-04-15T00:10Z] INFO  17:10:45,307 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:10Z] INFO  17:10:45,308 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:10Z] INFO  17:10:45,308 MicroScheduler -   -> 98 reads (0.07% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:10Z] INFO  17:10:45,353 IntervalUtils - Processing 18489547 bp from intervals
[2016-04-15T00:10Z] WARN  17:10:45,358 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:10Z] INFO  17:10:45,426 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:10Z] INFO  17:10:45,472 ProgressMeter -            done    349745.0    21.0 s      61.0 s      100.0%    21.0 s       0.0 s
[2016-04-15T00:10Z] INFO  17:10:45,473 ProgressMeter - Total runtime 21.52 secs, 0.36 min, 0.01 hours
[2016-04-15T00:10Z] INFO  17:10:45,476 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 349745 total reads (0.00%)
[2016-04-15T00:10Z] INFO  17:10:45,477 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:10Z] INFO  17:10:45,477 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:10Z] INFO  17:10:45,478 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:10Z] INFO  17:10:45,596 IntervalUtils - Processing 15524101 bp from intervals
[2016-04-15T00:10Z] WARN  17:10:45,613 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:10Z] INFO  17:10:45,616 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:10Z] INFO  17:10:45,617 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:10Z] INFO  17:10:45,618 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:10Z] INFO  17:10:45,619 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:10Z] INFO  17:10:45,678 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:10Z] INFO  17:10:45,850 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:10Z] INFO  17:10:45,851 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:10Z] INFO  17:10:45,852 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:10Z] INFO  17:10:45,852 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:10Z] INFO  17:10:46,810 ProgressMeter -       4:9351739    700105.0    90.0 s       2.1 m       60.3%     2.5 m      59.0 s
[2016-04-15T00:10Z] INFO  17:10:46,845 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:10Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-4_183267803_191154276-prep-prealign.bam
[2016-04-15T00:10Z] INFO  17:10:46,992 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@32d5a4c6
[2016-04-15T00:10Z] INFO  17:10:47,061 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:10Z] INFO  17:10:47,099 ProgressMeter -            done     43210.0     7.0 s       3.1 m      100.0%     7.0 s       0.0 s
[2016-04-15T00:10Z] INFO  17:10:47,099 ProgressMeter - Total runtime 7.94 secs, 0.13 min, 0.00 hours
[2016-04-15T00:10Z] INFO  17:10:47,100 MicroScheduler - 115 reads were filtered out during the traversal out of approximately 43325 total reads (0.27%)
[2016-04-15T00:10Z] INFO  17:10:47,100 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:10Z] INFO  17:10:47,100 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:10Z] INFO  17:10:47,101 MicroScheduler -   -> 115 reads (0.27% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:10Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-3_112188604_127703121-prep.bam
[2016-04-15T00:10Z] INFO  17:10:47,385 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:10Z] INFO  17:10:47,388 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:10Z] INFO  17:10:47,389 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:10Z] INFO  17:10:47,390 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:10Z] INFO  17:10:47,394 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/4/R14-18106_kapa-NGv3-PE100-NGv3-sort-4_68340604_83852298-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/4/R14-18106_kapa-NGv3-PE100-NGv3-sort-4_68340604_83852298-prep-prealign-realign.intervals -L 4:68340605-83852298 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/4/tx/tmp9XVwUj/R14-18106_kapa-NGv3-PE100-NGv3-sort-4_68340604_83852298-prep.bam
[2016-04-15T00:10Z] INFO  17:10:47,435 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:10Z] INFO  17:10:47,444 HelpFormatter - Date/Time: 2016/04/14 17:10:47
[2016-04-15T00:10Z] INFO  17:10:47,444 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:10Z] INFO  17:10:47,445 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:10Z] GATK RealignerTargetCreator: R14-18106_kapa-NGv3-PE100-NGv3-sort-4_183267803_191154276-prep-prealign.bam 4:183267804-191154276
[2016-04-15T00:10Z] GATK: RealignerTargetCreator
[2016-04-15T00:10Z] INFO  17:10:47,651 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:10Z] INFO  17:10:47,791 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:10Z] INFO  17:10:47,819 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:10Z] INFO  17:10:47,821 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:10Z] INFO  17:10:47,824 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:10Z] INFO  17:10:47,825 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:10Z] INFO  17:10:47,825 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:10Z] INFO  17:10:47,830 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/4/R14-18106_kapa-NGv3-PE100-NGv3-sort-4_99397339_115544957-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/4/R14-18106_kapa-NGv3-PE100-NGv3-sort-4_99397339_115544957-prep-prealign-realign.intervals -L 4:99397340-115544957 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/4/tx/tmp0M0Y7f/R14-18106_kapa-NGv3-PE100-NGv3-sort-4_99397339_115544957-prep.bam
[2016-04-15T00:10Z] INFO  17:10:47,838 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:10Z] INFO  17:10:47,839 HelpFormatter - Date/Time: 2016/04/14 17:10:47
[2016-04-15T00:10Z] INFO  17:10:47,840 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:10Z] INFO  17:10:47,840 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:10Z] INFO  17:10:47,894 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-15T00:10Z] GATK pre-alignment ('5', 80911291, 96430739) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:10Z] INFO  17:10:48,061 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:10Z] INFO  17:10:48,076 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:10Z] INFO  17:10:48,078 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:10Z] INFO  17:10:48,078 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:10Z] INFO  17:10:48,079 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:10Z] INFO  17:10:48,083 HelpFormatter - Program Args: -T PrintReads -L 5:49695693-65288736 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/5/tx/tmpZwXWji/R14-18106_kapa-NGv3-PE100-NGv3-sort-5_49695692_65288736-prep-prealign.bam
[2016-04-15T00:10Z] INFO  17:10:48,107 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:10Z] INFO  17:10:48,108 HelpFormatter - Date/Time: 2016/04/14 17:10:48
[2016-04-15T00:10Z] INFO  17:10:48,108 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:10Z] INFO  17:10:48,123 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:10Z] INFO  17:10:48,183 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:10Z] INFO  17:10:48,186 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:10Z] INFO  17:10:48,186 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:10Z] INFO  17:10:48,187 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:10Z] INFO  17:10:48,191 HelpFormatter - Program Args: -T PrintReads -L 5:65290575-80809536 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/5/tx/tmpX_eqei/R14-18106_kapa-NGv3-PE100-NGv3-sort-5_65290574_80809536-prep-prealign.bam
[2016-04-15T00:10Z] INFO  17:10:48,212 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:10Z] INFO  17:10:48,212 HelpFormatter - Date/Time: 2016/04/14 17:10:48
[2016-04-15T00:10Z] INFO  17:10:48,212 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:10Z] INFO  17:10:48,212 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:10Z] INFO  17:10:48,219 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:10Z] INFO  17:10:48,238 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:10Z] INFO  17:10:48,309 IntervalUtils - Processing 15511694 bp from intervals
[2016-04-15T00:10Z] INFO  17:10:48,310 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-15T00:10Z] WARN  17:10:48,325 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:10Z] INFO  17:10:48,344 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:10Z] INFO  17:10:48,434 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:10Z] INFO  17:10:48,467 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:10Z] INFO  17:10:48,600 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:10Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-5_15616091_31267808-prep-prealign.bam
[2016-04-15T00:10Z] INFO  17:10:48,658 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:10Z] INFO  17:10:48,663 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:10Z] INFO  17:10:48,663 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:10Z] INFO  17:10:48,664 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:10Z] INFO  17:10:48,752 IntervalUtils - Processing 16147618 bp from intervals
[2016-04-15T00:10Z] WARN  17:10:48,756 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:10Z] GATK RealignerTargetCreator: R14-18106_kapa-NGv3-PE100-NGv3-sort-5_15616091_31267808-prep-prealign.bam 5:15616092-31267808
[2016-04-15T00:10Z] GATK: RealignerTargetCreator
[2016-04-15T00:10Z] INFO  17:10:48,873 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:10Z] INFO  17:10:48,880 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:10Z] INFO  17:10:49,016 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:10Z] INFO  17:10:49,018 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:10Z] INFO  17:10:49,018 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:10Z] INFO  17:10:49,019 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:10Z] INFO  17:10:49,041 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:10Z] INFO  17:10:49,215 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:10Z] INFO  17:10:49,380 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:10Z] INFO  17:10:49,655 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-15T00:10Z] INFO  17:10:49,742 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:10Z] INFO  17:10:49,758 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:10Z] INFO  17:10:49,810 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-15T00:10Z] INFO  17:10:49,820 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-15T00:10Z] INFO  17:10:49,834 IntervalUtils - Processing 15593044 bp from intervals
[2016-04-15T00:10Z] INFO  17:10:49,910 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:10Z] INFO  17:10:49,919 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:10Z] INFO  17:10:49,941 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:10Z] INFO  17:10:49,963 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.04
[2016-04-15T00:10Z] INFO  17:10:49,992 IntervalUtils - Processing 15518962 bp from intervals
[2016-04-15T00:10Z] INFO  17:10:50,140 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:10Z] INFO  17:10:50,179 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:10Z] INFO  17:10:50,179 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:10Z] INFO  17:10:50,180 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:10Z] INFO  17:10:50,180 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:10Z] INFO  17:10:50,207 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:10Z] INFO  17:10:50,379 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:10Z] INFO  17:10:50,382 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:10Z] INFO  17:10:50,382 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:10Z] INFO  17:10:50,383 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:10Z] INFO  17:10:50,383 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:10Z] INFO  17:10:50,387 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/4/R14-18106_kapa-NGv3-PE100-NGv3-sort-4_183267803_191154276-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/4/tx/tmpWMtKGC/R14-18106_kapa-NGv3-PE100-NGv3-sort-4_183267803_191154276-prep-prealign-realign.intervals -l INFO -L 4:183267804-191154276 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:10Z] INFO  17:10:50,402 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:10Z] INFO  17:10:50,403 HelpFormatter - Date/Time: 2016/04/14 17:10:50
[2016-04-15T00:10Z] INFO  17:10:50,403 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:10Z] INFO  17:10:50,404 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:10Z] INFO  17:10:50,523 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:10Z] INFO  17:10:50,524 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:10Z] INFO  17:10:50,525 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:10Z] INFO  17:10:50,525 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:10Z] INFO  17:10:50,530 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:10Z] INFO  17:10:50,541 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:10Z] INFO  17:10:50,681 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:10Z] INFO  17:10:50,787 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T00:10Z] INFO  17:10:50,796 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:10Z] INFO  17:10:50,878 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-15T00:10Z] INFO  17:10:51,238 IntervalUtils - Processing 7886473 bp from intervals
[2016-04-15T00:10Z] WARN  17:10:51,243 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:10Z] INFO  17:10:51,356 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:10Z] INFO  17:10:51,359 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:10Z] INFO  17:10:51,360 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:10Z] INFO  17:10:51,360 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:10Z] INFO  17:10:51,364 HelpFormatter - Program Args: -T PrintReads -L 5:80911292-96430739 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/5/tx/tmpIRI65J/R14-18106_kapa-NGv3-PE100-NGv3-sort-5_80911291_96430739-prep-prealign.bam
[2016-04-15T00:10Z] INFO  17:10:51,370 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:10Z] INFO  17:10:51,410 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:10Z] INFO  17:10:51,415 HelpFormatter - Date/Time: 2016/04/14 17:10:51
[2016-04-15T00:10Z] INFO  17:10:51,416 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:10Z] INFO  17:10:51,417 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:10Z] INFO  17:10:51,621 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:10Z] INFO  17:10:51,639 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:10Z] INFO  17:10:51,640 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:10Z] INFO  17:10:51,641 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:10Z] INFO  17:10:51,641 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:10Z] INFO  17:10:51,808 ProgressMeter -            done    160802.0    14.0 s      88.0 s       99.9%    14.0 s       0.0 s
[2016-04-15T00:10Z] INFO  17:10:51,809 ProgressMeter - Total runtime 14.23 secs, 0.24 min, 0.00 hours
[2016-04-15T00:10Z] INFO  17:10:51,812 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 160802 total reads (0.00%)
[2016-04-15T00:10Z] INFO  17:10:51,813 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:10Z] INFO  17:10:51,813 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:10Z] INFO  17:10:51,813 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:10Z] INFO  17:10:52,069 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:10Z] INFO  17:10:52,073 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:10Z] INFO  17:10:52,073 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:10Z] INFO  17:10:52,074 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:10Z] INFO  17:10:52,078 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/5/R14-18106_kapa-NGv3-PE100-NGv3-sort-5_15616091_31267808-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/5/tx/tmp2xnJmB/R14-18106_kapa-NGv3-PE100-NGv3-sort-5_15616091_31267808-prep-prealign-realign.intervals -l INFO -L 5:15616092-31267808 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:10Z] INFO  17:10:52,122 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:10Z] INFO  17:10:52,137 HelpFormatter - Date/Time: 2016/04/14 17:10:52
[2016-04-15T00:10Z] INFO  17:10:52,139 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:10Z] INFO  17:10:52,139 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:10Z] INFO  17:10:52,301 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:10Z] INFO  17:10:52,570 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T00:10Z] INFO  17:10:52,583 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:10Z] INFO  17:10:52,643 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-15T00:10Z] INFO  17:10:52,860 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-15T00:10Z] INFO  17:10:52,936 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:10Z] INFO  17:10:52,953 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:10Z] INFO  17:10:53,008 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-15T00:10Z] INFO  17:10:53,018 IntervalUtils - Processing 15651717 bp from intervals
[2016-04-15T00:10Z] INFO  17:10:53,022 IntervalUtils - Processing 15519448 bp from intervals
[2016-04-15T00:10Z] WARN  17:10:53,022 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:10Z] INFO  17:10:53,128 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:10Z] INFO  17:10:53,128 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:10Z] INFO  17:10:53,272 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:10Z] INFO  17:10:53,273 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:10Z] INFO  17:10:53,273 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:10Z] INFO  17:10:53,273 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:10Z] INFO  17:10:53,326 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:10Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-4_83857133_99393738-prep.bam
[2016-04-15T00:10Z] INFO  17:10:53,454 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:10Z] INFO  17:10:53,456 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:10Z] INFO  17:10:53,457 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:10Z] INFO  17:10:53,479 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:10Z] INFO  17:10:53,496 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:10Z] INFO  17:10:53,687 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:10Z] GATK pre-alignment ('5', 96432513, 112043579) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:10Z] INFO  17:10:56,752 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:10Z] INFO  17:10:56,765 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:10Z] INFO  17:10:56,766 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:10Z] INFO  17:10:56,767 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:10Z] INFO  17:10:56,772 HelpFormatter - Program Args: -T PrintReads -L 5:96432514-112043579 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/5/tx/tmp1t4nWQ/R14-18106_kapa-NGv3-PE100-NGv3-sort-5_96432513_112043579-prep-prealign.bam
[2016-04-15T00:10Z] INFO  17:10:56,783 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:10Z] INFO  17:10:56,783 HelpFormatter - Date/Time: 2016/04/14 17:10:56
[2016-04-15T00:10Z] INFO  17:10:56,783 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:10Z] INFO  17:10:56,783 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:10Z] INFO  17:10:56,952 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:10Z] INFO  17:10:56,979 ProgressMeter -      3:52281225    400010.0    33.0 s      83.0 s       33.2%    99.0 s      66.0 s
[2016-04-15T00:10Z] INFO  17:10:58,062 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-15T00:10Z] INFO  17:10:58,123 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:10Z] INFO  17:10:58,133 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:10Z] INFO  17:10:58,198 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-15T00:10Z] INFO  17:10:58,207 ProgressMeter -            done   1.7356087E7    17.0 s       1.0 s      100.0%    17.0 s       0.0 s
[2016-04-15T00:10Z] INFO  17:10:58,208 ProgressMeter - Total runtime 17.94 secs, 0.30 min, 0.00 hours
[2016-04-15T00:10Z] INFO  17:10:58,211 MicroScheduler - 7817 reads were filtered out during the traversal out of approximately 92871 total reads (8.42%)
[2016-04-15T00:10Z] INFO  17:10:58,213 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:10Z] INFO  17:10:58,213 MicroScheduler -   -> 500 reads (0.54% of total) failing BadMateFilter
[2016-04-15T00:10Z] INFO  17:10:58,214 MicroScheduler -   -> 6682 reads (7.19% of total) failing DuplicateReadFilter
[2016-04-15T00:10Z] INFO  17:10:58,215 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:10Z] INFO  17:10:58,215 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:10Z] INFO  17:10:58,216 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:10Z] INFO  17:10:58,216 MicroScheduler -   -> 635 reads (0.68% of total) failing MappingQualityZeroFilter
[2016-04-15T00:10Z] INFO  17:10:58,217 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:10Z] INFO  17:10:58,218 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-15T00:10Z] INFO  17:10:58,218 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:10Z] INFO  17:10:58,223 IntervalUtils - Processing 15611066 bp from intervals
[2016-04-15T00:10Z] INFO  17:10:58,322 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:10Z] INFO  17:10:58,614 ProgressMeter -            done   1.627572E7    16.0 s       1.0 s      100.0%    16.0 s       0.0 s
[2016-04-15T00:10Z] INFO  17:10:58,615 ProgressMeter - Total runtime 16.63 secs, 0.28 min, 0.00 hours
[2016-04-15T00:10Z] INFO  17:10:58,619 MicroScheduler - 9844 reads were filtered out during the traversal out of approximately 116810 total reads (8.43%)
[2016-04-15T00:10Z] INFO  17:10:58,619 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:10Z] INFO  17:10:58,620 MicroScheduler -   -> 521 reads (0.45% of total) failing BadMateFilter
[2016-04-15T00:10Z] INFO  17:10:58,620 MicroScheduler -   -> 8624 reads (7.38% of total) failing DuplicateReadFilter
[2016-04-15T00:10Z] INFO  17:10:58,620 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:10Z] INFO  17:10:58,620 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:10Z] INFO  17:10:58,621 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:10Z] INFO  17:10:58,621 MicroScheduler -   -> 699 reads (0.60% of total) failing MappingQualityZeroFilter
[2016-04-15T00:10Z] INFO  17:10:58,621 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:10Z] INFO  17:10:58,621 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-15T00:10Z] INFO  17:10:58,622 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:10Z] INFO  17:10:58,691 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:10Z] INFO  17:10:58,692 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:10Z] INFO  17:10:58,693 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:10Z] INFO  17:10:58,694 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:10Z] INFO  17:10:58,710 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:10Z] INFO  17:10:58,903 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:10Z] INFO  17:10:59,630 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:10Z] GATK: realign ('4', 165889318, 183245405) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:10Z] INFO  17:10:59,957 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:11Z] GATK: realign ('4', 134075461, 150351181) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:11Z] INFO  17:11:00,820 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@41fd9d8e
[2016-04-15T00:11Z] INFO  17:11:00,913 ProgressMeter -            done    907047.0   104.0 s     114.0 s      100.0%   104.0 s       0.0 s
[2016-04-15T00:11Z] INFO  17:11:00,914 ProgressMeter - Total runtime 104.25 secs, 1.74 min, 0.03 hours
[2016-04-15T00:11Z] INFO  17:11:00,914 MicroScheduler - 384 reads were filtered out during the traversal out of approximately 907431 total reads (0.04%)
[2016-04-15T00:11Z] INFO  17:11:00,914 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:11Z] INFO  17:11:00,915 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:11Z] INFO  17:11:00,915 MicroScheduler -   -> 384 reads (0.04% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:11Z] INFO  17:11:01,854 ProgressMeter -            done   7886473.0    10.0 s       1.0 s      100.0%    10.0 s       0.0 s
[2016-04-15T00:11Z] INFO  17:11:01,855 ProgressMeter - Total runtime 10.22 secs, 0.17 min, 0.00 hours
[2016-04-15T00:11Z] INFO  17:11:01,858 MicroScheduler - 13320 reads were filtered out during the traversal out of approximately 137199 total reads (9.71%)
[2016-04-15T00:11Z] INFO  17:11:01,859 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:11Z] INFO  17:11:01,859 MicroScheduler -   -> 401 reads (0.29% of total) failing BadMateFilter
[2016-04-15T00:11Z] INFO  17:11:01,859 MicroScheduler -   -> 10270 reads (7.49% of total) failing DuplicateReadFilter
[2016-04-15T00:11Z] INFO  17:11:01,867 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:11Z] INFO  17:11:01,867 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:11Z] INFO  17:11:01,867 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:11Z] INFO  17:11:01,867 MicroScheduler -   -> 2649 reads (1.93% of total) failing MappingQualityZeroFilter
[2016-04-15T00:11Z] INFO  17:11:01,868 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:11Z] INFO  17:11:01,868 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-15T00:11Z] INFO  17:11:01,868 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:11Z] INFO  17:11:02,509 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:11Z] INFO  17:11:02,513 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:11Z] INFO  17:11:02,513 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:11Z] INFO  17:11:02,514 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:11Z] INFO  17:11:02,518 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/4/R14-18106_kapa-NGv3-PE100-NGv3-sort-4_165889318_183245405-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/4/R14-18106_kapa-NGv3-PE100-NGv3-sort-4_165889318_183245405-prep-prealign-realign.intervals -L 4:165889319-183245405 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/4/tx/tmpeTwAod/R14-18106_kapa-NGv3-PE100-NGv3-sort-4_165889318_183245405-prep.bam
[2016-04-15T00:11Z] INFO  17:11:02,531 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:11Z] INFO  17:11:02,532 HelpFormatter - Date/Time: 2016/04/14 17:11:02
[2016-04-15T00:11Z] INFO  17:11:02,532 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:11Z] INFO  17:11:02,533 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:11Z] INFO  17:11:02,657 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:11Z] INFO  17:11:02,659 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:11Z] INFO  17:11:02,660 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:11Z] INFO  17:11:02,660 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:11Z] INFO  17:11:02,664 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/4/R14-18106_kapa-NGv3-PE100-NGv3-sort-4_134075461_150351181-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/4/R14-18106_kapa-NGv3-PE100-NGv3-sort-4_134075461_150351181-prep-prealign-realign.intervals -L 4:134075462-150351181 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/4/tx/tmp2Yrr17/R14-18106_kapa-NGv3-PE100-NGv3-sort-4_134075461_150351181-prep.bam
[2016-04-15T00:11Z] INFO  17:11:02,669 ProgressMeter -            done   1.5524101E7    16.0 s       1.0 s      100.0%    16.0 s       0.0 s
[2016-04-15T00:11Z] INFO  17:11:02,670 ProgressMeter - Total runtime 16.82 secs, 0.28 min, 0.00 hours
[2016-04-15T00:11Z] INFO  17:11:02,671 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:11Z] INFO  17:11:02,671 HelpFormatter - Date/Time: 2016/04/14 17:11:02
[2016-04-15T00:11Z] INFO  17:11:02,672 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:11Z] INFO  17:11:02,673 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:11Z] INFO  17:11:02,675 MicroScheduler - 12299 reads were filtered out during the traversal out of approximately 147306 total reads (8.35%)
[2016-04-15T00:11Z] INFO  17:11:02,676 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:11Z] INFO  17:11:02,677 MicroScheduler -   -> 535 reads (0.36% of total) failing BadMateFilter
[2016-04-15T00:11Z] INFO  17:11:02,678 MicroScheduler -   -> 11186 reads (7.59% of total) failing DuplicateReadFilter
[2016-04-15T00:11Z] INFO  17:11:02,679 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:11Z] INFO  17:11:02,679 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:11Z] INFO  17:11:02,680 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:11Z] INFO  17:11:02,681 MicroScheduler -   -> 578 reads (0.39% of total) failing MappingQualityZeroFilter
[2016-04-15T00:11Z] INFO  17:11:02,682 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:11Z] INFO  17:11:02,682 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-15T00:11Z] INFO  17:11:02,683 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:11Z] INFO  17:11:02,717 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:11Z] INFO  17:11:02,785 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@7172f77a
[2016-04-15T00:11Z] INFO  17:11:02,834 ProgressMeter -            done    207512.0    27.0 s       2.2 m      100.0%    27.0 s       0.0 s
[2016-04-15T00:11Z] INFO  17:11:02,835 ProgressMeter - Total runtime 27.63 secs, 0.46 min, 0.01 hours
[2016-04-15T00:11Z] INFO  17:11:02,836 MicroScheduler - 185 reads were filtered out during the traversal out of approximately 207697 total reads (0.09%)
[2016-04-15T00:11Z] INFO  17:11:02,837 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:11Z] INFO  17:11:02,837 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:11Z] INFO  17:11:02,838 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:11Z] INFO  17:11:02,838 MicroScheduler -   -> 185 reads (0.09% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:11Z] INFO  17:11:02,851 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:11Z] INFO  17:11:02,863 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:11Z] INFO  17:11:02,898 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:11Z] INFO  17:11:02,918 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-15T00:11Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-4_0_15511864-prep-prealign.bam
[2016-04-15T00:11Z] INFO  17:11:02,982 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:11Z] INFO  17:11:02,993 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:11Z] INFO  17:11:03,115 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.12
[2016-04-15T00:11Z] INFO  17:11:03,245 IntervalUtils - Processing 17356087 bp from intervals
[2016-04-15T00:11Z] WARN  17:11:03,250 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:11Z] INFO  17:11:03,328 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:11Z] INFO  17:11:03,493 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:11Z] INFO  17:11:03,494 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:11Z] INFO  17:11:03,495 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:11Z] INFO  17:11:03,496 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:11Z] INFO  17:11:03,583 IntervalUtils - Processing 16275720 bp from intervals
[2016-04-15T00:11Z] WARN  17:11:03,590 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:11Z] INFO  17:11:03,640 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:11Z] INFO  17:11:03,663 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:11Z] INFO  17:11:03,719 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:11Z] GATK: realign ('4', 183267803, 191154276) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:11Z] INFO  17:11:03,771 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:11Z] INFO  17:11:03,772 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:11Z] INFO  17:11:03,773 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:11Z] INFO  17:11:03,774 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:11Z] INFO  17:11:03,818 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:11Z] INFO  17:11:03,974 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:11Z] INFO  17:11:04,156 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:11Z] INFO  17:11:04,163 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:11Z] GATK: realign ('4', 150354547, 165878648) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:11Z] INFO  17:11:04,251 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:11Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-5_0_15580921-prep-prealign.bam
[2016-04-15T00:11Z] GATK RealignerTargetCreator: R14-18106_kapa-NGv3-PE100-NGv3-sort-5_0_15580921-prep-prealign.bam 5:1-15580921
[2016-04-15T00:11Z] INFO  17:11:05,168 ProgressMeter -            done    191911.0    16.0 s      84.0 s      100.0%    16.0 s       0.0 s
[2016-04-15T00:11Z] INFO  17:11:05,168 ProgressMeter - Total runtime 16.15 secs, 0.27 min, 0.00 hours
[2016-04-15T00:11Z] GATK: RealignerTargetCreator
[2016-04-15T00:11Z] INFO  17:11:05,172 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 191911 total reads (0.00%)
[2016-04-15T00:11Z] INFO  17:11:05,172 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:11Z] INFO  17:11:05,173 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:11Z] INFO  17:11:05,173 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:11Z] INFO  17:11:05,215 ProgressMeter -            done   1.8489547E7    19.0 s       1.0 s      100.0%    19.0 s       0.0 s
[2016-04-15T00:11Z] INFO  17:11:05,216 ProgressMeter - Total runtime 19.60 secs, 0.33 min, 0.01 hours
[2016-04-15T00:11Z] INFO  17:11:05,220 MicroScheduler - 15672 reads were filtered out during the traversal out of approximately 175437 total reads (8.93%)
[2016-04-15T00:11Z] INFO  17:11:05,220 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:11Z] INFO  17:11:05,221 MicroScheduler -   -> 601 reads (0.34% of total) failing BadMateFilter
[2016-04-15T00:11Z] INFO  17:11:05,221 MicroScheduler -   -> 12730 reads (7.26% of total) failing DuplicateReadFilter
[2016-04-15T00:11Z] INFO  17:11:05,221 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:11Z] INFO  17:11:05,222 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:11Z] INFO  17:11:05,222 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:11Z] INFO  17:11:05,222 MicroScheduler -   -> 2341 reads (1.33% of total) failing MappingQualityZeroFilter
[2016-04-15T00:11Z] INFO  17:11:05,223 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:11Z] INFO  17:11:05,223 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-15T00:11Z] INFO  17:11:05,223 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:11Z] GATK RealignerTargetCreator: R14-18106_kapa-NGv3-PE100-NGv3-sort-4_0_15511864-prep-prealign.bam 4:1-15511864
[2016-04-15T00:11Z] GATK: RealignerTargetCreator
[2016-04-15T00:11Z] INFO  17:11:06,859 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:11Z] INFO  17:11:06,863 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:11Z] INFO  17:11:06,863 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:11Z] INFO  17:11:06,864 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:11Z] INFO  17:11:06,868 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:11Z] INFO  17:11:06,868 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/4/R14-18106_kapa-NGv3-PE100-NGv3-sort-4_183267803_191154276-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/4/R14-18106_kapa-NGv3-PE100-NGv3-sort-4_183267803_191154276-prep-prealign-realign.intervals -L 4:183267804-191154276 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/4/tx/tmpQF5ykZ/R14-18106_kapa-NGv3-PE100-NGv3-sort-4_183267803_191154276-prep.bam
[2016-04-15T00:11Z] INFO  17:11:06,886 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:11Z] INFO  17:11:06,887 HelpFormatter - Date/Time: 2016/04/14 17:11:06
[2016-04-15T00:11Z] INFO  17:11:06,887 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:11Z] INFO  17:11:06,887 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:11Z] GATK: realign ('4', 115584857, 134074404) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:11Z] INFO  17:11:06,968 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:11Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-4_99397339_115544957-prep.bam
[2016-04-15T00:11Z] INFO  17:11:07,076 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:11Z] INFO  17:11:07,156 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:11Z] INFO  17:11:07,165 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:11Z] INFO  17:11:07,251 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-15T00:11Z] INFO  17:11:07,278 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:11Z] INFO  17:11:07,281 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:11Z] INFO  17:11:07,282 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:11Z] INFO  17:11:07,283 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:11Z] INFO  17:11:07,287 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/4/R14-18106_kapa-NGv3-PE100-NGv3-sort-4_150354547_165878648-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/4/R14-18106_kapa-NGv3-PE100-NGv3-sort-4_150354547_165878648-prep-prealign-realign.intervals -L 4:150354548-165878648 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/4/tx/tmpCL3x2u/R14-18106_kapa-NGv3-PE100-NGv3-sort-4_150354547_165878648-prep.bam
[2016-04-15T00:11Z] INFO  17:11:07,313 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:11Z] INFO  17:11:07,314 HelpFormatter - Date/Time: 2016/04/14 17:11:07
[2016-04-15T00:11Z] INFO  17:11:07,314 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:11Z] INFO  17:11:07,314 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:11Z] INFO  17:11:07,329 ProgressMeter -            done   1.5651717E7    14.0 s       0.0 s      100.0%    14.0 s       0.0 s
[2016-04-15T00:11Z] INFO  17:11:07,330 ProgressMeter - Total runtime 14.06 secs, 0.23 min, 0.00 hours
[2016-04-15T00:11Z] INFO  17:11:07,334 MicroScheduler - 4941 reads were filtered out during the traversal out of approximately 43759 total reads (11.29%)
[2016-04-15T00:11Z] INFO  17:11:07,335 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:11Z] INFO  17:11:07,336 MicroScheduler -   -> 349 reads (0.80% of total) failing BadMateFilter
[2016-04-15T00:11Z] INFO  17:11:07,337 MicroScheduler -   -> 3257 reads (7.44% of total) failing DuplicateReadFilter
[2016-04-15T00:11Z] INFO  17:11:07,337 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:11Z] INFO  17:11:07,338 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:11Z] INFO  17:11:07,338 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:11Z] INFO  17:11:07,339 MicroScheduler -   -> 1335 reads (3.05% of total) failing MappingQualityZeroFilter
[2016-04-15T00:11Z] INFO  17:11:07,340 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:11Z] INFO  17:11:07,340 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-15T00:11Z] INFO  17:11:07,341 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:11Z] INFO  17:11:07,496 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:11Z] INFO  17:11:07,654 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:11Z] INFO  17:11:07,663 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:11Z] INFO  17:11:07,674 IntervalUtils - Processing 7886473 bp from intervals
[2016-04-15T00:11Z] WARN  17:11:07,690 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:11Z] INFO  17:11:07,729 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-15T00:11Z] INFO  17:11:07,767 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:11Z] GATK pre-alignment ('5', 112073555, 127595521) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:11Z] INFO  17:11:07,798 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:11Z] INFO  17:11:07,801 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:11Z] INFO  17:11:07,802 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:11Z] INFO  17:11:07,802 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:11Z] INFO  17:11:07,806 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/5/R14-18106_kapa-NGv3-PE100-NGv3-sort-5_0_15580921-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/5/tx/tmp31rNyI/R14-18106_kapa-NGv3-PE100-NGv3-sort-5_0_15580921-prep-prealign-realign.intervals -l INFO -L 5:1-15580921 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:11Z] INFO  17:11:07,830 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:11Z] INFO  17:11:07,831 HelpFormatter - Date/Time: 2016/04/14 17:11:07
[2016-04-15T00:11Z] INFO  17:11:07,832 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:11Z] INFO  17:11:07,832 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:11Z] INFO  17:11:07,897 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:11Z] INFO  17:11:07,898 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:11Z] INFO  17:11:07,899 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:11Z] INFO  17:11:07,900 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:11Z] INFO  17:11:07,915 ProgressMeter -            done    712839.0    44.0 s      62.0 s      100.0%    44.0 s       0.0 s
[2016-04-15T00:11Z] INFO  17:11:07,916 ProgressMeter - Total runtime 44.23 secs, 0.74 min, 0.01 hours
[2016-04-15T00:11Z] INFO  17:11:07,920 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 712839 total reads (0.00%)
[2016-04-15T00:11Z] INFO  17:11:07,921 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:11Z] INFO  17:11:07,921 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:11Z] INFO  17:11:07,921 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:11Z] INFO  17:11:07,937 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:11Z] INFO  17:11:08,080 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:11Z] INFO  17:11:08,110 IntervalUtils - Processing 15524101 bp from intervals
[2016-04-15T00:11Z] WARN  17:11:08,115 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:11Z] INFO  17:11:08,164 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:11Z] INFO  17:11:08,184 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:11Z] INFO  17:11:08,275 ProgressMeter -            done    264609.0    19.0 s      74.0 s      100.0%    19.0 s       0.0 s
[2016-04-15T00:11Z] INFO  17:11:08,276 ProgressMeter - Total runtime 19.61 secs, 0.33 min, 0.01 hours
[2016-04-15T00:11Z] INFO  17:11:08,279 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 264609 total reads (0.00%)
[2016-04-15T00:11Z] INFO  17:11:08,279 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:11Z] INFO  17:11:08,280 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:11Z] INFO  17:11:08,280 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:11Z] INFO  17:11:08,287 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T00:11Z] INFO  17:11:08,303 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:11Z] INFO  17:11:08,306 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:11Z] INFO  17:11:08,307 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:11Z] INFO  17:11:08,307 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:11Z] INFO  17:11:08,308 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:11Z] INFO  17:11:08,385 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@7172f77a
[2016-04-15T00:11Z] INFO  17:11:08,391 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:11Z] INFO  17:11:08,394 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:11Z] INFO  17:11:08,395 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:11Z] INFO  17:11:08,396 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:11Z] INFO  17:11:08,400 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/4/R14-18106_kapa-NGv3-PE100-NGv3-sort-4_0_15511864-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/4/tx/tmpz6sp1f/R14-18106_kapa-NGv3-PE100-NGv3-sort-4_0_15511864-prep-prealign-realign.intervals -l INFO -L 4:1-15511864 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:11Z] INFO  17:11:08,418 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.11
[2016-04-15T00:11Z] INFO  17:11:08,431 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:11Z] INFO  17:11:08,432 HelpFormatter - Date/Time: 2016/04/14 17:11:08
[2016-04-15T00:11Z] INFO  17:11:08,432 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:11Z] INFO  17:11:08,433 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:11Z] INFO  17:11:08,481 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:11Z] INFO  17:11:08,493 ProgressMeter -            done    134519.0    18.0 s       2.3 m      100.0%    18.0 s       0.0 s
[2016-04-15T00:11Z] INFO  17:11:08,497 ProgressMeter - Total runtime 18.32 secs, 0.31 min, 0.01 hours
[2016-04-15T00:11Z] INFO  17:11:08,498 MicroScheduler - 116 reads were filtered out during the traversal out of approximately 134635 total reads (0.09%)
[2016-04-15T00:11Z] INFO  17:11:08,499 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:11Z] INFO  17:11:08,500 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:11Z] INFO  17:11:08,501 MicroScheduler -   -> 116 reads (0.09% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:11Z] INFO  17:11:08,537 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:11Z] INFO  17:11:08,619 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:11Z] INFO  17:11:08,774 IntervalUtils - Processing 15580921 bp from intervals
[2016-04-15T00:11Z] WARN  17:11:08,779 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:11Z] INFO  17:11:08,785 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:11Z] INFO  17:11:08,802 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T00:11Z] GATK: realign ('5', 15616091, 31267808) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:11Z] INFO  17:11:08,837 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:11Z] INFO  17:11:08,876 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:11Z] INFO  17:11:08,929 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.09
[2016-04-15T00:11Z] INFO  17:11:09,098 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:11Z] INFO  17:11:09,099 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:11Z] INFO  17:11:09,100 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:11Z] INFO  17:11:09,101 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:11Z] INFO  17:11:09,275 IntervalUtils - Processing 15511864 bp from intervals
[2016-04-15T00:11Z] WARN  17:11:09,280 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:11Z] INFO  17:11:09,359 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:11Z] INFO  17:11:09,619 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:11Z] INFO  17:11:09,633 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:11Z] INFO  17:11:09,635 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:11Z] INFO  17:11:09,636 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:11Z] INFO  17:11:09,637 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:11Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-3_47129602_62648069-prep.bam
[2016-04-15T00:11Z] INFO  17:11:09,774 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:11Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-4_68340604_83852298-prep.bam
[2016-04-15T00:11Z] INFO  17:11:09,881 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:11Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-5_49695692_65288736-prep-prealign.bam
[2016-04-15T00:11Z] INFO  17:11:10,095 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:11Z] INFO  17:11:10,098 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:11Z] INFO  17:11:10,099 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:11Z] INFO  17:11:10,099 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:11Z] INFO  17:11:10,104 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/4/R14-18106_kapa-NGv3-PE100-NGv3-sort-4_115584857_134074404-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/4/R14-18106_kapa-NGv3-PE100-NGv3-sort-4_115584857_134074404-prep-prealign-realign.intervals -L 4:115584858-134074404 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/4/tx/tmpuPd1VR/R14-18106_kapa-NGv3-PE100-NGv3-sort-4_115584857_134074404-prep.bam
[2016-04-15T00:11Z] INFO  17:11:10,144 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:11Z] INFO  17:11:10,145 HelpFormatter - Date/Time: 2016/04/14 17:11:10
[2016-04-15T00:11Z] INFO  17:11:10,146 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:11Z] INFO  17:11:10,147 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:11Z] INFO  17:11:10,352 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:11Z] GATK RealignerTargetCreator: R14-18106_kapa-NGv3-PE100-NGv3-sort-5_49695692_65288736-prep-prealign.bam 5:49695693-65288736
[2016-04-15T00:11Z] GATK: RealignerTargetCreator
[2016-04-15T00:11Z] INFO  17:11:10,510 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:11Z] INFO  17:11:10,531 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:11Z] INFO  17:11:10,609 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-15T00:11Z] GATK pre-alignment ('5', 127597427, 143191869) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:11Z] INFO  17:11:10,923 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:11Z] INFO  17:11:10,926 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:11Z] INFO  17:11:10,926 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:11Z] INFO  17:11:10,927 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:11Z] INFO  17:11:10,931 HelpFormatter - Program Args: -T PrintReads -L 5:112073556-127595521 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/5/tx/tmpKdJW9s/R14-18106_kapa-NGv3-PE100-NGv3-sort-5_112073555_127595521-prep-prealign.bam
[2016-04-15T00:11Z] INFO  17:11:10,959 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:11Z] INFO  17:11:10,960 HelpFormatter - Date/Time: 2016/04/14 17:11:10
[2016-04-15T00:11Z] INFO  17:11:10,960 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:11Z] INFO  17:11:10,961 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:11Z] INFO  17:11:10,969 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@5fe152b7
[2016-04-15T00:11Z] INFO  17:11:11,009 IntervalUtils - Processing 18489547 bp from intervals
[2016-04-15T00:11Z] WARN  17:11:11,014 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:11Z] INFO  17:11:11,104 ProgressMeter -            done     64595.0    12.0 s       3.2 m      100.0%    12.0 s       0.0 s
[2016-04-15T00:11Z] INFO  17:11:11,104 ProgressMeter - Total runtime 12.41 secs, 0.21 min, 0.00 hours
[2016-04-15T00:11Z] INFO  17:11:11,105 MicroScheduler - 95 reads were filtered out during the traversal out of approximately 64690 total reads (0.15%)
[2016-04-15T00:11Z] INFO  17:11:11,105 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:11Z] INFO  17:11:11,105 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:11Z] INFO  17:11:11,105 MicroScheduler -   -> 95 reads (0.15% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:11Z] INFO  17:11:11,116 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:11Z] INFO  17:11:11,170 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:11Z] INFO  17:11:11,270 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:11Z] INFO  17:11:11,271 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:11Z] INFO  17:11:11,272 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:11Z] INFO  17:11:11,273 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:11Z] INFO  17:11:11,512 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:11Z] INFO  17:11:11,713 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@7172f77a
[2016-04-15T00:11Z] INFO  17:11:11,738 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:11Z] INFO  17:11:11,828 ProgressMeter -            done    131238.0    18.0 s       2.3 m      100.0%    18.0 s       0.0 s
[2016-04-15T00:11Z] INFO  17:11:11,829 ProgressMeter - Total runtime 18.37 secs, 0.31 min, 0.01 hours
[2016-04-15T00:11Z] INFO  17:11:11,830 MicroScheduler - 184 reads were filtered out during the traversal out of approximately 131422 total reads (0.14%)
[2016-04-15T00:11Z] INFO  17:11:11,830 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:11Z] INFO  17:11:11,827 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:11Z] INFO  17:11:11,831 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:11Z] INFO  17:11:11,831 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:11Z] INFO  17:11:11,831 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:11Z] INFO  17:11:11,832 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:11Z] INFO  17:11:11,836 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/5/R14-18106_kapa-NGv3-PE100-NGv3-sort-5_15616091_31267808-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/5/R14-18106_kapa-NGv3-PE100-NGv3-sort-5_15616091_31267808-prep-prealign-realign.intervals -L 5:15616092-31267808 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/5/tx/tmpvYZCek/R14-18106_kapa-NGv3-PE100-NGv3-sort-5_15616091_31267808-prep.bam
[2016-04-15T00:11Z] GATK pre-alignment ('5', 143200044, 158710347) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:11Z] INFO  17:11:11,846 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:11Z] INFO  17:11:11,847 HelpFormatter - Date/Time: 2016/04/14 17:11:11
[2016-04-15T00:11Z] INFO  17:11:11,847 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:11Z] INFO  17:11:11,848 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:11Z] INFO  17:11:11,858 MicroScheduler -   -> 184 reads (0.14% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:11Z] INFO  17:11:12,109 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:11Z] INFO  17:11:12,317 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:11Z] INFO  17:11:12,337 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:11Z] INFO  17:11:12,410 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-15T00:11Z] INFO  17:11:12,546 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-15T00:11Z] INFO  17:11:12,650 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:11Z] INFO  17:11:12,659 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:11Z] INFO  17:11:12,705 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-15T00:11Z] INFO  17:11:12,720 IntervalUtils - Processing 15521966 bp from intervals
[2016-04-15T00:11Z] INFO  17:11:12,800 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:11Z] INFO  17:11:12,803 IntervalUtils - Processing 15651717 bp from intervals
[2016-04-15T00:11Z] WARN  17:11:12,808 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:11Z] INFO  17:11:12,940 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:11Z] INFO  17:11:13,103 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:11Z] INFO  17:11:13,104 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:11Z] INFO  17:11:13,105 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:11Z] INFO  17:11:13,105 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:11Z] INFO  17:11:13,122 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:11Z] INFO  17:11:13,133 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:11Z] INFO  17:11:13,134 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:11Z] INFO  17:11:13,135 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:11Z] INFO  17:11:13,148 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:11Z] INFO  17:11:13,249 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:11Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-5_96432513_112043579-prep-prealign.bam
[2016-04-15T00:11Z] INFO  17:11:13,277 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:11Z] INFO  17:11:13,295 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:11Z] INFO  17:11:13,346 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:11Z] INFO  17:11:13,353 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:11Z] INFO  17:11:13,356 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:11Z] INFO  17:11:13,357 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:11Z] INFO  17:11:13,358 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:11Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-5_80911291_96430739-prep-prealign.bam
[2016-04-15T00:11Z] INFO  17:11:13,362 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/5/R14-18106_kapa-NGv3-PE100-NGv3-sort-5_49695692_65288736-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/5/tx/tmpMaiM0_/R14-18106_kapa-NGv3-PE100-NGv3-sort-5_49695692_65288736-prep-prealign-realign.intervals -l INFO -L 5:49695693-65288736 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:11Z] INFO  17:11:13,371 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:11Z] INFO  17:11:13,371 HelpFormatter - Date/Time: 2016/04/14 17:11:13
[2016-04-15T00:11Z] INFO  17:11:13,371 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:11Z] INFO  17:11:13,372 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:11Z] INFO  17:11:13,465 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:11Z] GATK RealignerTargetCreator: R14-18106_kapa-NGv3-PE100-NGv3-sort-5_96432513_112043579-prep-prealign.bam 5:96432514-112043579
[2016-04-15T00:11Z] GATK: RealignerTargetCreator
[2016-04-15T00:11Z] INFO  17:11:13,520 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:11Z] INFO  17:11:13,754 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T00:11Z] INFO  17:11:13,774 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:11Z] INFO  17:11:13,825 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-15T00:11Z] INFO  17:11:13,825 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:11Z] INFO  17:11:13,828 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:11Z] INFO  17:11:13,829 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:11Z] INFO  17:11:13,829 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:11Z] INFO  17:11:13,834 HelpFormatter - Program Args: -T PrintReads -L 5:127597428-143191869 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/5/tx/tmpMO0jT8/R14-18106_kapa-NGv3-PE100-NGv3-sort-5_127597427_143191869-prep-prealign.bam
[2016-04-15T00:11Z] GATK RealignerTargetCreator: R14-18106_kapa-NGv3-PE100-NGv3-sort-5_80911291_96430739-prep-prealign.bam 5:80911292-96430739
[2016-04-15T00:11Z] GATK: RealignerTargetCreator
[2016-04-15T00:11Z] INFO  17:11:13,841 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:11Z] INFO  17:11:13,853 HelpFormatter - Date/Time: 2016/04/14 17:11:13
[2016-04-15T00:11Z] INFO  17:11:13,854 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:11Z] INFO  17:11:13,855 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:11Z] INFO  17:11:14,037 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:11Z] INFO  17:11:14,076 ProgressMeter -            done     92554.0    10.0 s     114.0 s      100.0%    10.0 s       0.0 s
[2016-04-15T00:11Z] INFO  17:11:14,077 ProgressMeter - Total runtime 10.58 secs, 0.18 min, 0.00 hours
[2016-04-15T00:11Z] INFO  17:11:14,080 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 92554 total reads (0.00%)
[2016-04-15T00:11Z] INFO  17:11:14,080 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:11Z] INFO  17:11:14,080 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:11Z] INFO  17:11:14,081 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:11Z] INFO  17:11:14,102 IntervalUtils - Processing 15593044 bp from intervals
[2016-04-15T00:11Z] WARN  17:11:14,107 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:11Z] INFO  17:11:14,204 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:11Z] INFO  17:11:14,434 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:11Z] INFO  17:11:14,435 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:11Z] INFO  17:11:14,436 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:11Z] INFO  17:11:14,437 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:11Z] INFO  17:11:14,524 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@41fd9d8e
[2016-04-15T00:11Z] INFO  17:11:14,624 ProgressMeter -            done    227440.0    29.0 s       2.2 m      100.0%    29.0 s       0.0 s
[2016-04-15T00:11Z] INFO  17:11:14,625 ProgressMeter - Total runtime 29.69 secs, 0.49 min, 0.01 hours
[2016-04-15T00:11Z] INFO  17:11:14,625 MicroScheduler - 159 reads were filtered out during the traversal out of approximately 227599 total reads (0.07%)
[2016-04-15T00:11Z] INFO  17:11:14,625 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:11Z] INFO  17:11:14,626 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:11Z] INFO  17:11:14,626 MicroScheduler -   -> 159 reads (0.07% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:11Z] INFO  17:11:14,878 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:11Z] INFO  17:11:14,891 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:11Z] INFO  17:11:14,892 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:11Z] INFO  17:11:14,893 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:11Z] INFO  17:11:14,897 HelpFormatter - Program Args: -T PrintReads -L 5:143200045-158710347 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/5/tx/tmpAbNS8K/R14-18106_kapa-NGv3-PE100-NGv3-sort-5_143200044_158710347-prep-prealign.bam
[2016-04-15T00:11Z] INFO  17:11:14,913 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:11Z] INFO  17:11:14,913 HelpFormatter - Date/Time: 2016/04/14 17:11:14
[2016-04-15T00:11Z] INFO  17:11:14,914 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:11Z] INFO  17:11:14,914 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:11Z] INFO  17:11:15,153 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:11Z] INFO  17:11:15,309 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-15T00:11Z] INFO  17:11:15,401 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:11Z] INFO  17:11:15,418 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:11Z] INFO  17:11:15,478 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-15T00:11Z] INFO  17:11:15,492 IntervalUtils - Processing 15594442 bp from intervals
[2016-04-15T00:11Z] INFO  17:11:15,571 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:11Z] INFO  17:11:15,834 ProgressMeter -            done    116100.0    12.0 s     103.0 s       97.9%    12.0 s       0.0 s
[2016-04-15T00:11Z] INFO  17:11:15,836 ProgressMeter - Total runtime 12.06 secs, 0.20 min, 0.00 hours
[2016-04-15T00:11Z] INFO  17:11:15,840 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 116100 total reads (0.00%)
[2016-04-15T00:11Z] INFO  17:11:15,852 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:11Z] INFO  17:11:15,853 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:11Z] INFO  17:11:15,853 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:11Z] INFO  17:11:15,859 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:11Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-4_165889318_183245405-prep.bam
[2016-04-15T00:11Z] INFO  17:11:15,973 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:11Z] INFO  17:11:15,985 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:11Z] INFO  17:11:15,986 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:11Z] INFO  17:11:15,986 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:11Z] INFO  17:11:16,032 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:11Z] INFO  17:11:16,164 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:11Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-5_31294068_49695124-prep-prealign.bam
[2016-04-15T00:11Z] INFO  17:11:16,223 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:11Z] GATK pre-alignment ('5', 158711911, 174870102) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:11Z] INFO  17:11:16,399 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-15T00:11Z] INFO  17:11:16,463 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:11Z] INFO  17:11:16,473 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:11Z] INFO  17:11:16,512 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:11Z] INFO  17:11:16,515 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:11Z] INFO  17:11:16,516 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:11Z] INFO  17:11:16,516 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:11Z] INFO  17:11:16,521 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/5/R14-18106_kapa-NGv3-PE100-NGv3-sort-5_96432513_112043579-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/5/tx/tmptd71HX/R14-18106_kapa-NGv3-PE100-NGv3-sort-5_96432513_112043579-prep-prealign-realign.intervals -l INFO -L 5:96432514-112043579 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:11Z] INFO  17:11:16,535 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:11Z] INFO  17:11:16,535 HelpFormatter - Date/Time: 2016/04/14 17:11:16
[2016-04-15T00:11Z] INFO  17:11:16,535 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:11Z] INFO  17:11:16,536 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:11Z] INFO  17:11:16,540 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-15T00:11Z] INFO  17:11:16,554 IntervalUtils - Processing 15510303 bp from intervals
[2016-04-15T00:11Z] INFO  17:11:16,660 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:11Z] INFO  17:11:16,664 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:11Z] INFO  17:11:16,883 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T00:11Z] INFO  17:11:16,893 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:11Z] INFO  17:11:16,952 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-15T00:11Z] GATK RealignerTargetCreator: R14-18106_kapa-NGv3-PE100-NGv3-sort-5_31294068_49695124-prep-prealign.bam 5:31294069-49695124
[2016-04-15T00:11Z] GATK: RealignerTargetCreator
[2016-04-15T00:11Z] INFO  17:11:16,966 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:11Z] INFO  17:11:16,967 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:11Z] INFO  17:11:16,967 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:11Z] INFO  17:11:16,967 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:11Z] INFO  17:11:17,000 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:11Z] INFO  17:11:17,160 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:11Z] INFO  17:11:17,236 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:11Z] INFO  17:11:17,240 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:11Z] INFO  17:11:17,241 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:11Z] INFO  17:11:17,241 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:11Z] INFO  17:11:17,246 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/5/R14-18106_kapa-NGv3-PE100-NGv3-sort-5_80911291_96430739-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/5/tx/tmpfqO5kc/R14-18106_kapa-NGv3-PE100-NGv3-sort-5_80911291_96430739-prep-prealign-realign.intervals -l INFO -L 5:80911292-96430739 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:11Z] INFO  17:11:17,255 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:11Z] INFO  17:11:17,266 HelpFormatter - Date/Time: 2016/04/14 17:11:17
[2016-04-15T00:11Z] INFO  17:11:17,266 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:11Z] INFO  17:11:17,267 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:11Z] INFO  17:11:17,274 IntervalUtils - Processing 15611066 bp from intervals
[2016-04-15T00:11Z] WARN  17:11:17,280 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:11Z] INFO  17:11:17,355 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:11Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-4_134075461_150351181-prep.bam
[2016-04-15T00:11Z] INFO  17:11:17,407 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:11Z] INFO  17:11:17,422 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:11Z] INFO  17:11:17,680 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T00:11Z] INFO  17:11:17,708 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:11Z] INFO  17:11:17,728 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:11Z] INFO  17:11:17,729 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:11Z] INFO  17:11:17,730 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:11Z] INFO  17:11:17,730 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:11Z] INFO  17:11:17,791 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-15T00:11Z] GATK pre-alignment ('5', 174919106, 180915260) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:11Z] INFO  17:11:18,034 IntervalUtils - Processing 15519448 bp from intervals
[2016-04-15T00:11Z] WARN  17:11:18,039 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:11Z] INFO  17:11:18,137 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:11Z] INFO  17:11:18,414 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:11Z] INFO  17:11:18,416 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:11Z] INFO  17:11:18,416 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:11Z] INFO  17:11:18,417 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:11Z] INFO  17:11:18,979 ProgressMeter -            done    136369.0    11.0 s      81.0 s       97.9%    11.0 s       0.0 s
[2016-04-15T00:11Z] INFO  17:11:18,980 ProgressMeter - Total runtime 11.08 secs, 0.18 min, 0.00 hours
[2016-04-15T00:11Z] INFO  17:11:18,983 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 136369 total reads (0.00%)
[2016-04-15T00:11Z] INFO  17:11:18,983 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:11Z] INFO  17:11:18,983 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:11Z] INFO  17:11:18,984 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:11Z] INFO  17:11:18,981 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:11Z] INFO  17:11:18,986 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:11Z] INFO  17:11:18,987 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:11Z] INFO  17:11:18,987 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:11Z] INFO  17:11:18,992 HelpFormatter - Program Args: -T PrintReads -L 5:158711912-174870102 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/5/tx/tmpbW_BgJ/R14-18106_kapa-NGv3-PE100-NGv3-sort-5_158711911_174870102-prep-prealign.bam
[2016-04-15T00:11Z] INFO  17:11:19,002 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:11Z] INFO  17:11:19,013 HelpFormatter - Date/Time: 2016/04/14 17:11:18
[2016-04-15T00:11Z] INFO  17:11:19,014 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:11Z] INFO  17:11:19,014 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:11Z] INFO  17:11:19,201 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:11Z] INFO  17:11:20,013 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:11Z] INFO  17:11:20,015 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:11Z] INFO  17:11:20,016 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:11Z] INFO  17:11:20,016 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:11Z] INFO  17:11:20,031 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/5/R14-18106_kapa-NGv3-PE100-NGv3-sort-5_31294068_49695124-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/5/tx/tmp_J1_5v/R14-18106_kapa-NGv3-PE100-NGv3-sort-5_31294068_49695124-prep-prealign-realign.intervals -l INFO -L 5:31294069-49695124 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:11Z] INFO  17:11:20,045 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:11Z] INFO  17:11:20,045 HelpFormatter - Date/Time: 2016/04/14 17:11:20
[2016-04-15T00:11Z] INFO  17:11:20,046 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:11Z] INFO  17:11:20,046 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:11Z] INFO  17:11:20,155 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:11Z] INFO  17:11:20,266 ProgressMeter -            done     43210.0     7.0 s       2.8 m      100.0%     7.0 s       0.0 s
[2016-04-15T00:11Z] INFO  17:11:20,267 ProgressMeter - Total runtime 7.16 secs, 0.12 min, 0.00 hours
[2016-04-15T00:11Z] INFO  17:11:20,271 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 43210 total reads (0.00%)
[2016-04-15T00:11Z] INFO  17:11:20,272 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:11Z] INFO  17:11:20,273 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:11Z] INFO  17:11:20,273 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:11Z] INFO  17:11:20,410 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T00:11Z] INFO  17:11:20,421 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:11Z] INFO  17:11:20,483 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-15T00:11Z] INFO  17:11:20,515 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-15T00:11Z] INFO  17:11:20,541 ProgressMeter -      5:79465394    200002.0    30.0 s       2.5 m       91.3%    32.0 s       2.0 s
[2016-04-15T00:11Z] INFO  17:11:20,589 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:11Z] INFO  17:11:20,599 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:11Z] INFO  17:11:20,649 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-15T00:11Z] INFO  17:11:20,664 IntervalUtils - Processing 16158191 bp from intervals
[2016-04-15T00:11Z] INFO  17:11:20,706 IntervalUtils - Processing 18401056 bp from intervals
[2016-04-15T00:11Z] WARN  17:11:20,711 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:11Z] INFO  17:11:20,730 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:11Z] INFO  17:11:20,736 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:11Z] INFO  17:11:20,737 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:11Z] INFO  17:11:20,737 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:11Z] INFO  17:11:20,741 HelpFormatter - Program Args: -T PrintReads -L 5:174919107-180915260 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/5/tx/tmpceoYDi/R14-18106_kapa-NGv3-PE100-NGv3-sort-5_174919106_180915260-prep-prealign.bam
[2016-04-15T00:11Z] INFO  17:11:20,742 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:11Z] INFO  17:11:20,750 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:11Z] INFO  17:11:20,754 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:11Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-4_183267803_191154276-prep.bam
[2016-04-15T00:11Z] INFO  17:11:20,761 HelpFormatter - Date/Time: 2016/04/14 17:11:20
[2016-04-15T00:11Z] INFO  17:11:20,762 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:11Z] INFO  17:11:20,763 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:11Z] INFO  17:11:20,790 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:11Z] INFO  17:11:20,934 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:11Z] INFO  17:11:20,972 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:11Z] INFO  17:11:20,973 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:11Z] INFO  17:11:20,973 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:11Z] INFO  17:11:20,974 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:11Z] INFO  17:11:21,098 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:11Z] INFO  17:11:21,099 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:11Z] INFO  17:11:21,100 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:11Z] INFO  17:11:21,101 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:11Z] INFO  17:11:21,123 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:11Z] INFO  17:11:21,280 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:11Z] GATK pre-alignment ('6', 0, 15509601) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:11Z] INFO  17:11:21,379 ProgressMeter -            done    146590.0    13.0 s      89.0 s      100.0%    13.0 s       0.0 s
[2016-04-15T00:11Z] INFO  17:11:21,379 ProgressMeter - Total runtime 13.07 secs, 0.22 min, 0.00 hours
[2016-04-15T00:11Z] INFO  17:11:21,383 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 146590 total reads (0.00%)
[2016-04-15T00:11Z] INFO  17:11:21,383 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:11Z] INFO  17:11:21,383 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:11Z] INFO  17:11:21,384 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:11Z] INFO  17:11:21,689 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:11Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-5_15616091_31267808-prep.bam
[2016-04-15T00:11Z] GATK pre-alignment ('6', 15511526, 31080332) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:11Z] INFO  17:11:22,044 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-15T00:11Z] INFO  17:11:22,175 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:11Z] INFO  17:11:22,186 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:11Z] INFO  17:11:22,260 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-15T00:11Z] INFO  17:11:22,276 IntervalUtils - Processing 5996154 bp from intervals
[2016-04-15T00:11Z] INFO  17:11:22,388 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:11Z] INFO  17:11:22,715 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:11Z] INFO  17:11:22,716 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:11Z] INFO  17:11:22,716 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:11Z] INFO  17:11:22,717 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:11Z] INFO  17:11:22,741 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:11Z] INFO  17:11:22,826 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:11Z] INFO  17:11:23,087 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@7172f77a
[2016-04-15T00:11Z] INFO  17:11:23,188 ProgressMeter -            done    255051.0    32.0 s       2.1 m      100.0%    32.0 s       0.0 s
[2016-04-15T00:11Z] INFO  17:11:23,189 ProgressMeter - Total runtime 32.67 secs, 0.54 min, 0.01 hours
[2016-04-15T00:11Z] INFO  17:11:23,189 MicroScheduler - 161 reads were filtered out during the traversal out of approximately 255212 total reads (0.06%)
[2016-04-15T00:11Z] INFO  17:11:23,190 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:11Z] INFO  17:11:23,190 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:11Z] INFO  17:11:23,190 MicroScheduler -   -> 161 reads (0.06% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:11Z] INFO  17:11:23,212 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:11Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-4_150354547_165878648-prep.bam
[2016-04-15T00:11Z] GATK pre-alignment ('6', 31083801, 46593245) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:11Z] INFO  17:11:24,657 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:11Z] INFO  17:11:24,661 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:11Z] INFO  17:11:24,661 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:11Z] INFO  17:11:24,662 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:11Z] INFO  17:11:24,666 HelpFormatter - Program Args: -T PrintReads -L 6:1-15509601 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/6/tx/tmpBP8uki/R14-18106_kapa-NGv3-PE100-NGv3-sort-6_0_15509601-prep-prealign.bam
[2016-04-15T00:11Z] INFO  17:11:24,694 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:11Z] INFO  17:11:24,700 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:11Z] INFO  17:11:24,702 HelpFormatter - Date/Time: 2016/04/14 17:11:24
[2016-04-15T00:11Z] INFO  17:11:24,702 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:11Z] INFO  17:11:24,703 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:11Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-5_65290574_80809536-prep-prealign.bam
[2016-04-15T00:11Z] INFO  17:11:24,894 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:11Z] INFO  17:11:25,123 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:11Z] INFO  17:11:25,126 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:11Z] INFO  17:11:25,126 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:11Z] INFO  17:11:25,126 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:11Z] INFO  17:11:25,130 HelpFormatter - Program Args: -T PrintReads -L 6:15511527-31080332 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/6/tx/tmpwqUJ2A/R14-18106_kapa-NGv3-PE100-NGv3-sort-6_15511526_31080332-prep-prealign.bam
[2016-04-15T00:11Z] INFO  17:11:25,142 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:11Z] INFO  17:11:25,153 HelpFormatter - Date/Time: 2016/04/14 17:11:25
[2016-04-15T00:11Z] INFO  17:11:25,154 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:11Z] INFO  17:11:25,154 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:11Z] INFO  17:11:25,337 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:11Z] GATK RealignerTargetCreator: R14-18106_kapa-NGv3-PE100-NGv3-sort-5_65290574_80809536-prep-prealign.bam 5:65290575-80809536
[2016-04-15T00:11Z] GATK: RealignerTargetCreator
[2016-04-15T00:11Z] INFO  17:11:25,996 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-15T00:11Z] INFO  17:11:26,073 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:11Z] INFO  17:11:26,084 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:11Z] INFO  17:11:26,146 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-15T00:11Z] INFO  17:11:26,171 IntervalUtils - Processing 15509601 bp from intervals
[2016-04-15T00:11Z] INFO  17:11:26,386 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:11Z] INFO  17:11:26,687 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-15T00:11Z] INFO  17:11:26,704 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:11Z] INFO  17:11:26,705 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:11Z] INFO  17:11:26,706 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:11Z] INFO  17:11:26,707 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:11Z] INFO  17:11:26,720 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:11Z] INFO  17:11:26,746 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:11Z] INFO  17:11:26,755 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:11Z] INFO  17:11:26,780 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:11Z] INFO  17:11:26,783 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:11Z] INFO  17:11:26,784 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:11Z] INFO  17:11:26,784 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:11Z] INFO  17:11:26,789 HelpFormatter - Program Args: -T PrintReads -L 6:31083802-46593245 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/6/tx/tmpf_U6nr/R14-18106_kapa-NGv3-PE100-NGv3-sort-6_31083801_46593245-prep-prealign.bam
[2016-04-15T00:11Z] INFO  17:11:26,803 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:11Z] INFO  17:11:26,804 HelpFormatter - Date/Time: 2016/04/14 17:11:26
[2016-04-15T00:11Z] INFO  17:11:26,805 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:11Z] INFO  17:11:26,805 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:11Z] INFO  17:11:26,822 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-15T00:11Z] INFO  17:11:26,839 IntervalUtils - Processing 15568806 bp from intervals
[2016-04-15T00:11Z] INFO  17:11:26,884 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:11Z] INFO  17:11:26,915 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:11Z] INFO  17:11:27,012 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:11Z] INFO  17:11:27,032 ProgressMeter -            done    174214.0    15.0 s      90.0 s      100.0%    15.0 s       0.0 s
[2016-04-15T00:11Z] INFO  17:11:27,034 ProgressMeter - Total runtime 15.76 secs, 0.26 min, 0.00 hours
[2016-04-15T00:11Z] INFO  17:11:27,038 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 174214 total reads (0.00%)
[2016-04-15T00:11Z] INFO  17:11:27,039 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:11Z] INFO  17:11:27,040 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:11Z] INFO  17:11:27,041 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:11Z] INFO  17:11:27,240 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:11Z] INFO  17:11:27,241 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:11Z] INFO  17:11:27,242 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:11Z] INFO  17:11:27,243 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:11Z] INFO  17:11:27,279 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:11Z] INFO  17:11:27,483 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:11Z] INFO  17:11:28,187 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-15T00:11Z] INFO  17:11:28,248 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:11Z] INFO  17:11:28,263 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:11Z] INFO  17:11:28,324 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-15T00:11Z] INFO  17:11:28,338 IntervalUtils - Processing 15509444 bp from intervals
[2016-04-15T00:11Z] INFO  17:11:28,358 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:11Z] INFO  17:11:28,361 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:11Z] INFO  17:11:28,362 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:11Z] INFO  17:11:28,362 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:11Z] INFO  17:11:28,367 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/5/R14-18106_kapa-NGv3-PE100-NGv3-sort-5_65290574_80809536-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/5/tx/tmpGDXSeV/R14-18106_kapa-NGv3-PE100-NGv3-sort-5_65290574_80809536-prep-prealign-realign.intervals -l INFO -L 5:65290575-80809536 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:11Z] INFO  17:11:28,379 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:11Z] INFO  17:11:28,380 HelpFormatter - Date/Time: 2016/04/14 17:11:28
[2016-04-15T00:11Z] INFO  17:11:28,380 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:11Z] INFO  17:11:28,381 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:11Z] INFO  17:11:28,440 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:11Z] INFO  17:11:28,513 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:11Z] INFO  17:11:28,520 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:11Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-4_115584857_134074404-prep.bam
[2016-04-15T00:11Z] INFO  17:11:28,741 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T00:11Z] INFO  17:11:28,751 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:11Z] INFO  17:11:28,799 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:11Z] INFO  17:11:28,800 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:11Z] INFO  17:11:28,800 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:11Z] INFO  17:11:28,801 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:11Z] INFO  17:11:28,823 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-15T00:11Z] INFO  17:11:28,829 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:11Z] INFO  17:11:28,980 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:11Z] INFO  17:11:29,119 IntervalUtils - Processing 15518962 bp from intervals
[2016-04-15T00:11Z] WARN  17:11:29,124 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:11Z] GATK pre-alignment ('6', 46598699, 62284307) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:11Z] INFO  17:11:29,197 ProgressMeter -            done   1.5580921E7    20.0 s       1.0 s      100.0%    20.0 s       0.0 s
[2016-04-15T00:11Z] INFO  17:11:29,198 ProgressMeter - Total runtime 20.10 secs, 0.33 min, 0.01 hours
[2016-04-15T00:11Z] INFO  17:11:29,202 MicroScheduler - 20810 reads were filtered out during the traversal out of approximately 208710 total reads (9.97%)
[2016-04-15T00:11Z] INFO  17:11:29,203 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:11Z] INFO  17:11:29,204 MicroScheduler -   -> 736 reads (0.35% of total) failing BadMateFilter
[2016-04-15T00:11Z] INFO  17:11:29,204 MicroScheduler -   -> 15695 reads (7.52% of total) failing DuplicateReadFilter
[2016-04-15T00:11Z] INFO  17:11:29,205 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:11Z] INFO  17:11:29,206 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:11Z] INFO  17:11:29,206 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:11Z] INFO  17:11:29,207 MicroScheduler -   -> 4379 reads (2.10% of total) failing MappingQualityZeroFilter
[2016-04-15T00:11Z] INFO  17:11:29,207 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:11Z] INFO  17:11:29,208 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:11Z] INFO  17:11:29,208 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-15T00:11Z] INFO  17:11:29,209 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:11Z] INFO  17:11:29,403 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:11Z] INFO  17:11:29,404 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:11Z] INFO  17:11:29,405 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:11Z] INFO  17:11:29,406 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:11Z] INFO  17:11:30,576 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:11Z] GATK: realign ('5', 0, 15580921) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:11Z] INFO  17:11:31,681 ProgressMeter -            done   1.5593044E7    17.0 s       1.0 s      100.0%    17.0 s       0.0 s
[2016-04-15T00:11Z] INFO  17:11:31,682 ProgressMeter - Total runtime 17.25 secs, 0.29 min, 0.00 hours
[2016-04-15T00:11Z] INFO  17:11:31,688 MicroScheduler - 10883 reads were filtered out during the traversal out of approximately 135176 total reads (8.05%)
[2016-04-15T00:11Z] INFO  17:11:31,689 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:11Z] INFO  17:11:31,690 MicroScheduler -   -> 501 reads (0.37% of total) failing BadMateFilter
[2016-04-15T00:11Z] INFO  17:11:31,691 MicroScheduler -   -> 9914 reads (7.33% of total) failing DuplicateReadFilter
[2016-04-15T00:11Z] INFO  17:11:31,691 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:11Z] INFO  17:11:31,692 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:11Z] INFO  17:11:31,693 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:11Z] INFO  17:11:31,693 MicroScheduler -   -> 468 reads (0.35% of total) failing MappingQualityZeroFilter
[2016-04-15T00:11Z] INFO  17:11:31,694 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:11Z] INFO  17:11:31,695 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-15T00:11Z] INFO  17:11:31,695 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:11Z] INFO  17:11:31,805 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:11Z] INFO  17:11:31,809 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:11Z] INFO  17:11:31,809 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:11Z] INFO  17:11:31,810 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:11Z] INFO  17:11:31,815 HelpFormatter - Program Args: -T PrintReads -L 6:46598700-62284307 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/6/tx/tmpZnUvZN/R14-18106_kapa-NGv3-PE100-NGv3-sort-6_46598699_62284307-prep-prealign.bam
[2016-04-15T00:11Z] INFO  17:11:31,827 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:11Z] INFO  17:11:31,828 HelpFormatter - Date/Time: 2016/04/14 17:11:31
[2016-04-15T00:11Z] INFO  17:11:31,828 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:11Z] INFO  17:11:31,829 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:11Z] INFO  17:11:32,038 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@41fd9d8e
[2016-04-15T00:11Z] INFO  17:11:32,085 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:11Z] INFO  17:11:32,221 ProgressMeter -            done    133162.0    19.0 s       2.4 m      100.0%    19.0 s       0.0 s
[2016-04-15T00:11Z] INFO  17:11:32,221 ProgressMeter - Total runtime 19.09 secs, 0.32 min, 0.01 hours
[2016-04-15T00:11Z] INFO  17:11:32,221 MicroScheduler - 137 reads were filtered out during the traversal out of approximately 133299 total reads (0.10%)
[2016-04-15T00:11Z] INFO  17:11:32,222 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:11Z] INFO  17:11:32,222 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:11Z] INFO  17:11:32,222 MicroScheduler -   -> 137 reads (0.10% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:11Z] INFO  17:11:32,589 ProgressMeter -            done   1.5611066E7    14.0 s       0.0 s      100.0%    14.0 s       0.0 s
[2016-04-15T00:11Z] INFO  17:11:32,595 ProgressMeter - Total runtime 14.87 secs, 0.25 min, 0.00 hours
[2016-04-15T00:11Z] INFO  17:11:32,599 MicroScheduler - 5756 reads were filtered out during the traversal out of approximately 65220 total reads (8.83%)
[2016-04-15T00:11Z] INFO  17:11:32,600 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:11Z] INFO  17:11:32,600 MicroScheduler -   -> 481 reads (0.74% of total) failing BadMateFilter
[2016-04-15T00:11Z] INFO  17:11:32,600 MicroScheduler -   -> 4677 reads (7.17% of total) failing DuplicateReadFilter
[2016-04-15T00:11Z] INFO  17:11:32,601 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:11Z] INFO  17:11:32,601 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:11Z] INFO  17:11:32,601 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:11Z] INFO  17:11:32,601 MicroScheduler -   -> 598 reads (0.92% of total) failing MappingQualityZeroFilter
[2016-04-15T00:11Z] INFO  17:11:32,602 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:11Z] INFO  17:11:32,602 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-15T00:11Z] INFO  17:11:32,602 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:11Z] INFO  17:11:33,083 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:11Z] GATK: realign ('5', 49695692, 65288736) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:11Z] INFO  17:11:33,418 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-15T00:11Z] INFO  17:11:33,502 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:11Z] INFO  17:11:33,513 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:11Z] INFO  17:11:33,538 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:11Z] INFO  17:11:33,542 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:11Z] INFO  17:11:33,543 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:11Z] INFO  17:11:33,543 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:11Z] INFO  17:11:33,549 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/5/R14-18106_kapa-NGv3-PE100-NGv3-sort-5_0_15580921-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/5/R14-18106_kapa-NGv3-PE100-NGv3-sort-5_0_15580921-prep-prealign-realign.intervals -L 5:1-15580921 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/5/tx/tmpElJ5B7/R14-18106_kapa-NGv3-PE100-NGv3-sort-5_0_15580921-prep.bam
[2016-04-15T00:11Z] INFO  17:11:33,563 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:11Z] INFO  17:11:33,564 HelpFormatter - Date/Time: 2016/04/14 17:11:33
[2016-04-15T00:11Z] INFO  17:11:33,565 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:11Z] INFO  17:11:33,565 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:11Z] INFO  17:11:33,591 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-15T00:11Z] INFO  17:11:33,608 IntervalUtils - Processing 15685608 bp from intervals
[2016-04-15T00:11Z] INFO  17:11:33,742 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:11Z] INFO  17:11:33,761 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:11Z] INFO  17:11:33,770 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:11Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-5_112073555_127595521-prep-prealign.bam
[2016-04-15T00:11Z] INFO  17:11:33,886 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:11Z] INFO  17:11:33,910 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:11Z] INFO  17:11:33,972 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-15T00:11Z] INFO  17:11:34,008 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:11Z] GATK: realign ('5', 96432513, 112043579) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:11Z] INFO  17:11:34,087 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:11Z] INFO  17:11:34,088 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:11Z] INFO  17:11:34,088 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:11Z] INFO  17:11:34,088 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:11Z] INFO  17:11:34,102 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:11Z] GATK RealignerTargetCreator: R14-18106_kapa-NGv3-PE100-NGv3-sort-5_112073555_127595521-prep-prealign.bam 5:112073556-127595521
[2016-04-15T00:11Z] GATK: RealignerTargetCreator
[2016-04-15T00:11Z] INFO  17:11:34,257 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:11Z] INFO  17:11:34,291 IntervalUtils - Processing 15580921 bp from intervals
[2016-04-15T00:11Z] WARN  17:11:34,296 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:11Z] INFO  17:11:34,386 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:11Z] INFO  17:11:34,559 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:11Z] INFO  17:11:34,560 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:11Z] INFO  17:11:34,561 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:11Z] INFO  17:11:34,561 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:11Z] INFO  17:11:34,710 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:11Z] INFO  17:11:34,877 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:11Z] INFO  17:11:36,081 ProgressMeter -            done   1.5511864E7    26.0 s       1.0 s      100.0%    26.0 s       0.0 s
[2016-04-15T00:11Z] INFO  17:11:36,082 ProgressMeter - Total runtime 26.45 secs, 0.44 min, 0.01 hours
[2016-04-15T00:11Z] INFO  17:11:36,083 MicroScheduler - 495560 reads were filtered out during the traversal out of approximately 909788 total reads (54.47%)
[2016-04-15T00:11Z] INFO  17:11:36,084 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:11Z] INFO  17:11:36,084 MicroScheduler -   -> 1058 reads (0.12% of total) failing BadMateFilter
[2016-04-15T00:11Z] INFO  17:11:36,085 MicroScheduler -   -> 40528 reads (4.45% of total) failing DuplicateReadFilter
[2016-04-15T00:11Z] INFO  17:11:36,086 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:11Z] INFO  17:11:36,086 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:11Z] INFO  17:11:36,087 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:11Z] INFO  17:11:36,087 MicroScheduler -   -> 453974 reads (49.90% of total) failing MappingQualityZeroFilter
[2016-04-15T00:11Z] INFO  17:11:36,088 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:11Z] INFO  17:11:36,089 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-15T00:11Z] INFO  17:11:36,089 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:11Z] INFO  17:11:36,159 ProgressMeter -            done   1.5519448E7    17.0 s       1.0 s      100.0%    17.0 s       0.0 s
[2016-04-15T00:11Z] INFO  17:11:36,160 ProgressMeter - Total runtime 17.74 secs, 0.30 min, 0.00 hours
[2016-04-15T00:11Z] INFO  17:11:36,163 MicroScheduler - 10220 reads were filtered out during the traversal out of approximately 132135 total reads (7.73%)
[2016-04-15T00:11Z] INFO  17:11:36,163 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:11Z] INFO  17:11:36,164 MicroScheduler -   -> 495 reads (0.37% of total) failing BadMateFilter
[2016-04-15T00:11Z] INFO  17:11:36,164 MicroScheduler -   -> 9422 reads (7.13% of total) failing DuplicateReadFilter
[2016-04-15T00:11Z] INFO  17:11:36,164 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:11Z] INFO  17:11:36,164 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:11Z] INFO  17:11:36,165 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:11Z] INFO  17:11:36,165 MicroScheduler -   -> 303 reads (0.23% of total) failing MappingQualityZeroFilter
[2016-04-15T00:11Z] INFO  17:11:36,165 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:11Z] INFO  17:11:36,165 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-15T00:11Z] INFO  17:11:36,165 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:11Z] INFO  17:11:36,242 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:11Z] INFO  17:11:36,246 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:11Z] INFO  17:11:36,246 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:11Z] INFO  17:11:36,247 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:11Z] INFO  17:11:36,254 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/5/R14-18106_kapa-NGv3-PE100-NGv3-sort-5_49695692_65288736-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/5/R14-18106_kapa-NGv3-PE100-NGv3-sort-5_49695692_65288736-prep-prealign-realign.intervals -L 5:49695693-65288736 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/5/tx/tmpSnNgCs/R14-18106_kapa-NGv3-PE100-NGv3-sort-5_49695692_65288736-prep.bam
[2016-04-15T00:11Z] INFO  17:11:36,279 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:11Z] INFO  17:11:36,280 HelpFormatter - Date/Time: 2016/04/14 17:11:36
[2016-04-15T00:11Z] INFO  17:11:36,281 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:11Z] INFO  17:11:36,281 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:11Z] INFO  17:11:36,512 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:11Z] INFO  17:11:36,642 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:11Z] INFO  17:11:36,663 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:11Z] INFO  17:11:36,739 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-15T00:11Z] INFO  17:11:37,149 IntervalUtils - Processing 15593044 bp from intervals
[2016-04-15T00:11Z] WARN  17:11:37,155 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:11Z] INFO  17:11:37,259 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:11Z] INFO  17:11:37,308 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:11Z] INFO  17:11:37,311 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:11Z] INFO  17:11:37,311 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:11Z] INFO  17:11:37,311 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:11Z] INFO  17:11:37,317 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:11Z] INFO  17:11:37,320 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:11Z] INFO  17:11:37,321 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:11Z] INFO  17:11:37,321 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:11Z] INFO  17:11:37,326 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/5/R14-18106_kapa-NGv3-PE100-NGv3-sort-5_112073555_127595521-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/5/tx/tmpXhZwAd/R14-18106_kapa-NGv3-PE100-NGv3-sort-5_112073555_127595521-prep-prealign-realign.intervals -l INFO -L 5:112073556-127595521 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:11Z] INFO  17:11:37,327 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/5/R14-18106_kapa-NGv3-PE100-NGv3-sort-5_96432513_112043579-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/5/R14-18106_kapa-NGv3-PE100-NGv3-sort-5_96432513_112043579-prep-prealign-realign.intervals -L 5:96432514-112043579 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/5/tx/tmpr5jx70/R14-18106_kapa-NGv3-PE100-NGv3-sort-5_96432513_112043579-prep.bam
[2016-04-15T00:11Z] INFO  17:11:37,362 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:11Z] INFO  17:11:37,363 HelpFormatter - Date/Time: 2016/04/14 17:11:37
[2016-04-15T00:11Z] INFO  17:11:37,364 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:11Z] INFO  17:11:37,364 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:11Z] INFO  17:11:37,364 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:11Z] INFO  17:11:37,364 HelpFormatter - Date/Time: 2016/04/14 17:11:37
[2016-04-15T00:11Z] INFO  17:11:37,365 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:11Z] INFO  17:11:37,365 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:11Z] INFO  17:11:37,438 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:11Z] INFO  17:11:37,439 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:11Z] INFO  17:11:37,439 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:11Z] INFO  17:11:37,441 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:11Z] INFO  17:11:37,451 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:11Z] INFO  17:11:37,579 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:11Z] INFO  17:11:37,614 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T00:11Z] INFO  17:11:37,624 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:11Z] INFO  17:11:37,626 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:11Z] INFO  17:11:37,647 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:11Z] GATK: realign ('4', 0, 15511864) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:11Z] INFO  17:11:37,673 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-15T00:11Z] INFO  17:11:37,705 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:11Z] INFO  17:11:37,723 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:11Z] INFO  17:11:37,729 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:11Z] INFO  17:11:37,738 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:11Z] GATK: realign ('5', 80911291, 96430739) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:11Z] INFO  17:11:37,793 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-15T00:11Z] INFO  17:11:37,975 IntervalUtils - Processing 15521966 bp from intervals
[2016-04-15T00:11Z] WARN  17:11:37,991 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:11Z] INFO  17:11:38,113 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:11Z] INFO  17:11:38,146 IntervalUtils - Processing 15611066 bp from intervals
[2016-04-15T00:11Z] WARN  17:11:38,151 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:11Z] INFO  17:11:38,245 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:11Z] INFO  17:11:38,375 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:11Z] INFO  17:11:38,379 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:11Z] INFO  17:11:38,380 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:11Z] INFO  17:11:38,381 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:11Z] INFO  17:11:38,383 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:11Z] INFO  17:11:38,384 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:11Z] INFO  17:11:38,385 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:11Z] INFO  17:11:38,385 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:11Z] INFO  17:11:38,566 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:11Z] INFO  17:11:38,789 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:11Z] INFO  17:11:40,174 ProgressMeter -            done   1.8401056E7    19.0 s       1.0 s      100.0%    19.0 s       0.0 s
[2016-04-15T00:11Z] INFO  17:11:40,187 ProgressMeter - Total runtime 19.21 secs, 0.32 min, 0.01 hours
[2016-04-15T00:11Z] INFO  17:11:40,192 MicroScheduler - 18351 reads were filtered out during the traversal out of approximately 228716 total reads (8.02%)
[2016-04-15T00:11Z] INFO  17:11:40,193 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:11Z] INFO  17:11:40,194 MicroScheduler -   -> 704 reads (0.31% of total) failing BadMateFilter
[2016-04-15T00:11Z] INFO  17:11:40,195 MicroScheduler -   -> 17120 reads (7.49% of total) failing DuplicateReadFilter
[2016-04-15T00:11Z] INFO  17:11:40,196 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:11Z] INFO  17:11:40,197 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:11Z] INFO  17:11:40,197 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:11Z] INFO  17:11:40,198 MicroScheduler -   -> 527 reads (0.23% of total) failing MappingQualityZeroFilter
[2016-04-15T00:11Z] INFO  17:11:40,199 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:11Z] INFO  17:11:40,200 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-15T00:11Z] INFO  17:11:40,200 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:11Z] INFO  17:11:40,576 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:11Z] INFO  17:11:40,579 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:11Z] INFO  17:11:40,580 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:11Z] INFO  17:11:40,581 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:11Z] INFO  17:11:40,585 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/4/R14-18106_kapa-NGv3-PE100-NGv3-sort-4_0_15511864-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/4/R14-18106_kapa-NGv3-PE100-NGv3-sort-4_0_15511864-prep-prealign-realign.intervals -L 4:1-15511864 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/4/tx/tmpgV8EoY/R14-18106_kapa-NGv3-PE100-NGv3-sort-4_0_15511864-prep.bam
[2016-04-15T00:11Z] INFO  17:11:40,615 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:11Z] INFO  17:11:40,616 HelpFormatter - Date/Time: 2016/04/14 17:11:40
[2016-04-15T00:11Z] INFO  17:11:40,616 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:11Z] INFO  17:11:40,616 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:11Z] INFO  17:11:40,865 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:11Z] INFO  17:11:40,873 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:11Z] INFO  17:11:40,876 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:11Z] INFO  17:11:40,877 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:11Z] INFO  17:11:40,877 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:11Z] INFO  17:11:40,882 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/5/R14-18106_kapa-NGv3-PE100-NGv3-sort-5_80911291_96430739-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/5/R14-18106_kapa-NGv3-PE100-NGv3-sort-5_80911291_96430739-prep-prealign-realign.intervals -L 5:80911292-96430739 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/5/tx/tmpFChO0I/R14-18106_kapa-NGv3-PE100-NGv3-sort-5_80911291_96430739-prep.bam
[2016-04-15T00:11Z] INFO  17:11:40,891 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:11Z] INFO  17:11:40,892 HelpFormatter - Date/Time: 2016/04/14 17:11:40
[2016-04-15T00:11Z] INFO  17:11:40,893 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:11Z] INFO  17:11:40,893 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:11Z] INFO  17:11:40,974 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:11Z] INFO  17:11:40,984 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:11Z] INFO  17:11:41,046 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-15T00:11Z] INFO  17:11:41,097 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:11Z] INFO  17:11:41,359 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:11Z] INFO  17:11:41,400 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:11Z] INFO  17:11:41,442 IntervalUtils - Processing 15511864 bp from intervals
[2016-04-15T00:11Z] WARN  17:11:41,448 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:11Z] INFO  17:11:41,481 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-15T00:11Z] INFO  17:11:41,528 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:11Z] INFO  17:11:41,639 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:11Z] INFO  17:11:41,640 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:11Z] INFO  17:11:41,641 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:11Z] INFO  17:11:41,642 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:11Z] INFO  17:11:41,795 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:11Z] INFO  17:11:41,802 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:11Z] GATK: realign ('5', 31294068, 49695124) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:11Z] INFO  17:11:41,908 IntervalUtils - Processing 15519448 bp from intervals
[2016-04-15T00:11Z] WARN  17:11:41,924 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:11Z] INFO  17:11:41,950 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:11Z] INFO  17:11:42,005 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:11Z] INFO  17:11:42,190 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:11Z] INFO  17:11:42,191 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:11Z] INFO  17:11:42,191 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:11Z] INFO  17:11:42,192 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:11Z] INFO  17:11:42,451 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:11Z] INFO  17:11:42,598 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:11Z] INFO  17:11:43,779 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@7172f77a
[2016-04-15T00:11Z] INFO  17:11:43,976 ProgressMeter -            done    160435.0    22.0 s       2.4 m      100.0%    22.0 s       0.0 s
[2016-04-15T00:11Z] INFO  17:11:43,976 ProgressMeter - Total runtime 22.88 secs, 0.38 min, 0.01 hours
[2016-04-15T00:11Z] INFO  17:11:43,976 MicroScheduler - 131 reads were filtered out during the traversal out of approximately 160566 total reads (0.08%)
[2016-04-15T00:11Z] INFO  17:11:43,977 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:11Z] INFO  17:11:43,977 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:11Z] INFO  17:11:43,977 MicroScheduler -   -> 131 reads (0.08% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:11Z] INFO  17:11:44,762 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:11Z] INFO  17:11:44,766 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:11Z] INFO  17:11:44,766 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:11Z] INFO  17:11:44,767 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:11Z] INFO  17:11:44,772 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/5/R14-18106_kapa-NGv3-PE100-NGv3-sort-5_31294068_49695124-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/5/R14-18106_kapa-NGv3-PE100-NGv3-sort-5_31294068_49695124-prep-prealign-realign.intervals -L 5:31294069-49695124 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/5/tx/tmpH0thQ6/R14-18106_kapa-NGv3-PE100-NGv3-sort-5_31294068_49695124-prep.bam
[2016-04-15T00:11Z] INFO  17:11:44,782 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:11Z] INFO  17:11:44,783 HelpFormatter - Date/Time: 2016/04/14 17:11:44
[2016-04-15T00:11Z] INFO  17:11:44,783 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:11Z] INFO  17:11:44,784 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:11Z] INFO  17:11:44,969 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:11Z] INFO  17:11:45,093 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:11Z] INFO  17:11:45,102 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:11Z] INFO  17:11:45,167 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-15T00:11Z] INFO  17:11:45,485 IntervalUtils - Processing 18401056 bp from intervals
[2016-04-15T00:11Z] WARN  17:11:45,490 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:11Z] INFO  17:11:45,569 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:11Z] INFO  17:11:45,656 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:11Z] INFO  17:11:45,657 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:11Z] INFO  17:11:45,657 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:11Z] INFO  17:11:45,658 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:11Z] INFO  17:11:45,740 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:11Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-5_158711911_174870102-prep-prealign.bam
[2016-04-15T00:11Z] INFO  17:11:45,818 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:11Z] INFO  17:11:45,996 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:11Z] GATK RealignerTargetCreator: R14-18106_kapa-NGv3-PE100-NGv3-sort-5_158711911_174870102-prep-prealign.bam 5:158711912-174870102
[2016-04-15T00:11Z] GATK: RealignerTargetCreator
[2016-04-15T00:11Z] INFO  17:11:46,251 ProgressMeter -     5:137802788    100003.0    30.0 s       5.0 m       65.4%    45.0 s      15.0 s
[2016-04-15T00:11Z] INFO  17:11:46,275 ProgressMeter -            done     64595.0     7.0 s       2.0 m      100.0%     7.0 s       0.0 s
[2016-04-15T00:11Z] INFO  17:11:46,276 ProgressMeter - Total runtime 7.89 secs, 0.13 min, 0.00 hours
[2016-04-15T00:11Z] INFO  17:11:46,279 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 64595 total reads (0.00%)
[2016-04-15T00:11Z] INFO  17:11:46,280 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:11Z] INFO  17:11:46,281 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:11Z] INFO  17:11:46,282 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:11Z] INFO  17:11:46,999 ProgressMeter -     5:151052773    200002.0    30.0 s       2.5 m       50.6%    59.0 s      29.0 s
[2016-04-15T00:11Z] INFO  17:11:47,853 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:11Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-5_96432513_112043579-prep.bam
[2016-04-15T00:11Z] GATK pre-alignment ('6', 62390867, 78173120) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:11Z] INFO  17:11:48,542 ProgressMeter -            done   1.5518962E7    19.0 s       1.0 s      100.0%    19.0 s       0.0 s
[2016-04-15T00:11Z] INFO  17:11:48,542 ProgressMeter - Total runtime 19.14 secs, 0.32 min, 0.01 hours
[2016-04-15T00:11Z] INFO  17:11:48,546 MicroScheduler - 41272 reads were filtered out during the traversal out of approximately 256219 total reads (16.11%)
[2016-04-15T00:11Z] INFO  17:11:48,547 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:11Z] INFO  17:11:48,547 MicroScheduler -   -> 669 reads (0.26% of total) failing BadMateFilter
[2016-04-15T00:11Z] INFO  17:11:48,548 MicroScheduler -   -> 17303 reads (6.75% of total) failing DuplicateReadFilter
[2016-04-15T00:11Z] INFO  17:11:48,549 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:11Z] INFO  17:11:48,549 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:11Z] INFO  17:11:48,550 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:11Z] INFO  17:11:48,550 MicroScheduler -   -> 23300 reads (9.09% of total) failing MappingQualityZeroFilter
[2016-04-15T00:11Z] INFO  17:11:48,551 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:11Z] INFO  17:11:48,552 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-15T00:11Z] INFO  17:11:48,552 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:11Z] INFO  17:11:49,013 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:11Z] INFO  17:11:49,016 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:11Z] INFO  17:11:49,017 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:11Z] INFO  17:11:49,017 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:11Z] INFO  17:11:49,022 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/5/R14-18106_kapa-NGv3-PE100-NGv3-sort-5_158711911_174870102-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/5/tx/tmp3C2iBD/R14-18106_kapa-NGv3-PE100-NGv3-sort-5_158711911_174870102-prep-prealign-realign.intervals -l INFO -L 5:158711912-174870102 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:11Z] INFO  17:11:49,031 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:11Z] INFO  17:11:49,031 HelpFormatter - Date/Time: 2016/04/14 17:11:49
[2016-04-15T00:11Z] INFO  17:11:49,032 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:11Z] INFO  17:11:49,033 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:11Z] INFO  17:11:49,128 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:11Z] INFO  17:11:49,334 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T00:11Z] INFO  17:11:49,343 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:11Z] INFO  17:11:49,403 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-15T00:11Z] INFO  17:11:49,710 IntervalUtils - Processing 16158191 bp from intervals
[2016-04-15T00:11Z] WARN  17:11:49,715 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:11Z] INFO  17:11:49,782 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:11Z] INFO  17:11:49,818 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:11Z] GATK: realign ('5', 65290574, 80809536) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:11Z] INFO  17:11:49,871 ProgressMeter -            done    134519.0    12.0 s      92.0 s      100.0%    12.0 s       0.0 s
[2016-04-15T00:11Z] INFO  17:11:49,871 ProgressMeter - Total runtime 12.43 secs, 0.21 min, 0.00 hours
[2016-04-15T00:11Z] INFO  17:11:49,875 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 134519 total reads (0.00%)
[2016-04-15T00:11Z] INFO  17:11:49,876 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:11Z] INFO  17:11:49,876 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:11Z] INFO  17:11:49,877 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:11Z] INFO  17:11:49,958 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:11Z] INFO  17:11:49,960 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:11Z] INFO  17:11:49,960 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:11Z] INFO  17:11:49,961 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:11Z] INFO  17:11:50,228 ProgressMeter -            done    207512.0    15.0 s      75.0 s      100.0%    15.0 s       0.0 s
[2016-04-15T00:11Z] INFO  17:11:50,229 ProgressMeter - Total runtime 15.67 secs, 0.26 min, 0.00 hours
[2016-04-15T00:11Z] INFO  17:11:50,233 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 207512 total reads (0.00%)
[2016-04-15T00:11Z] INFO  17:11:50,234 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:11Z] INFO  17:11:50,234 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:11Z] INFO  17:11:50,235 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:11Z] INFO  17:11:50,955 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:11Z] INFO  17:11:50,959 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:11Z] INFO  17:11:50,959 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:11Z] INFO  17:11:50,960 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:11Z] INFO  17:11:50,964 HelpFormatter - Program Args: -T PrintReads -L 6:62390868-78173120 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/6/tx/tmpJTKiQK/R14-18106_kapa-NGv3-PE100-NGv3-sort-6_62390867_78173120-prep-prealign.bam
[2016-04-15T00:11Z] INFO  17:11:50,982 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:11Z] INFO  17:11:50,984 HelpFormatter - Date/Time: 2016/04/14 17:11:50
[2016-04-15T00:11Z] INFO  17:11:50,985 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:11Z] INFO  17:11:50,985 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:11Z] INFO  17:11:51,127 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:11Z] INFO  17:11:51,348 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:11Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-5_49695692_65288736-prep.bam
[2016-04-15T00:11Z] INFO  17:11:51,584 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@7172f77a
[2016-04-15T00:11Z] INFO  17:11:51,643 ProgressMeter -            done    200588.0    24.0 s       2.1 m      100.0%    24.0 s       0.0 s
[2016-04-15T00:11Z] INFO  17:11:51,644 ProgressMeter - Total runtime 24.94 secs, 0.42 min, 0.01 hours
[2016-04-15T00:11Z] INFO  17:11:51,645 MicroScheduler - 161 reads were filtered out during the traversal out of approximately 200749 total reads (0.08%)
[2016-04-15T00:11Z] INFO  17:11:51,645 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:11Z] INFO  17:11:51,645 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:11Z] INFO  17:11:51,646 MicroScheduler -   -> 161 reads (0.08% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:11Z] GATK pre-alignment ('6', 78400388, 93953258) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:11Z] INFO  17:11:52,016 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:11Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-5_0_15580921-prep.bam
[2016-04-15T00:11Z] INFO  17:11:52,157 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-15T00:11Z] INFO  17:11:52,214 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:11Z] INFO  17:11:52,227 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:11Z] INFO  17:11:52,276 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-15T00:11Z] INFO  17:11:52,290 IntervalUtils - Processing 15782253 bp from intervals
[2016-04-15T00:11Z] INFO  17:11:52,363 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:11Z] INFO  17:11:52,445 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:11Z] INFO  17:11:52,448 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:11Z] INFO  17:11:52,448 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:11Z] INFO  17:11:52,449 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:11Z] INFO  17:11:52,453 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/5/R14-18106_kapa-NGv3-PE100-NGv3-sort-5_65290574_80809536-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/5/R14-18106_kapa-NGv3-PE100-NGv3-sort-5_65290574_80809536-prep-prealign-realign.intervals -L 5:65290575-80809536 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/5/tx/tmpGRxD93/R14-18106_kapa-NGv3-PE100-NGv3-sort-5_65290574_80809536-prep.bam
[2016-04-15T00:11Z] INFO  17:11:52,476 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:11Z] INFO  17:11:52,477 HelpFormatter - Date/Time: 2016/04/14 17:11:52
[2016-04-15T00:11Z] INFO  17:11:52,478 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:11Z] INFO  17:11:52,478 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:11Z] GATK pre-alignment ('6', 93955015, 109466584) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:11Z] INFO  17:11:52,681 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:11Z] INFO  17:11:52,687 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:11Z] INFO  17:11:52,688 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:11Z] INFO  17:11:52,689 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:11Z] INFO  17:11:52,689 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:11Z] INFO  17:11:52,702 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:11Z] INFO  17:11:52,741 ProgressMeter -     5:179538477    200005.0    30.0 s       2.5 m       77.0%    38.0 s       8.0 s
[2016-04-15T00:11Z] INFO  17:11:52,793 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:11Z] INFO  17:11:52,802 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:11Z] INFO  17:11:52,842 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.04
[2016-04-15T00:11Z] INFO  17:11:52,848 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:11Z] INFO  17:11:53,117 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:11Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-6_0_15509601-prep-prealign.bam
[2016-04-15T00:11Z] INFO  17:11:53,197 IntervalUtils - Processing 15518962 bp from intervals
[2016-04-15T00:11Z] WARN  17:11:53,202 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:11Z] INFO  17:11:53,277 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:11Z] INFO  17:11:53,397 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:11Z] INFO  17:11:53,397 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:11Z] INFO  17:11:53,398 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:11Z] INFO  17:11:53,398 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:11Z] INFO  17:11:53,478 ProgressMeter -            done    131238.0    11.0 s      85.0 s      100.0%    11.0 s       0.0 s
[2016-04-15T00:11Z] INFO  17:11:53,478 ProgressMeter - Total runtime 11.29 secs, 0.19 min, 0.00 hours
[2016-04-15T00:11Z] INFO  17:11:53,482 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 131238 total reads (0.00%)
[2016-04-15T00:11Z] INFO  17:11:53,483 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:11Z] INFO  17:11:53,483 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:11Z] INFO  17:11:53,484 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:11Z] INFO  17:11:53,585 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:11Z] INFO  17:11:53,790 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:11Z] GATK RealignerTargetCreator: R14-18106_kapa-NGv3-PE100-NGv3-sort-6_0_15509601-prep-prealign.bam 6:1-15509601
[2016-04-15T00:11Z] GATK: RealignerTargetCreator
[2016-04-15T00:11Z] INFO  17:11:54,741 ProgressMeter -            done   1.5521966E7    16.0 s       1.0 s      100.0%    16.0 s       0.0 s
[2016-04-15T00:11Z] INFO  17:11:54,742 ProgressMeter - Total runtime 16.37 secs, 0.27 min, 0.00 hours
[2016-04-15T00:11Z] INFO  17:11:54,745 MicroScheduler - 10786 reads were filtered out during the traversal out of approximately 133515 total reads (8.08%)
[2016-04-15T00:11Z] INFO  17:11:54,746 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:11Z] INFO  17:11:54,746 MicroScheduler -   -> 631 reads (0.47% of total) failing BadMateFilter
[2016-04-15T00:11Z] INFO  17:11:54,746 MicroScheduler -   -> 9936 reads (7.44% of total) failing DuplicateReadFilter
[2016-04-15T00:11Z] INFO  17:11:54,747 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:11Z] INFO  17:11:54,747 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:11Z] INFO  17:11:54,747 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:11Z] INFO  17:11:54,747 MicroScheduler -   -> 219 reads (0.16% of total) failing MappingQualityZeroFilter
[2016-04-15T00:11Z] INFO  17:11:54,748 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:11Z] INFO  17:11:54,748 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-15T00:11Z] INFO  17:11:54,748 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:11Z] INFO  17:11:54,855 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:11Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-5_80911291_96430739-prep.bam
[2016-04-15T00:11Z] INFO  17:11:55,031 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:11Z] INFO  17:11:55,035 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:11Z] INFO  17:11:55,036 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:11Z] INFO  17:11:55,036 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:11Z] INFO  17:11:55,042 HelpFormatter - Program Args: -T PrintReads -L 6:78400389-93953258 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/6/tx/tmplxTmDQ/R14-18106_kapa-NGv3-PE100-NGv3-sort-6_78400388_93953258-prep-prealign.bam
[2016-04-15T00:11Z] INFO  17:11:55,061 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:11Z] INFO  17:11:55,062 HelpFormatter - Date/Time: 2016/04/14 17:11:55
[2016-04-15T00:11Z] INFO  17:11:55,063 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:11Z] INFO  17:11:55,064 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:11Z] INFO  17:11:55,314 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:11Z] GATK pre-alignment ('6', 109467960, 124979532) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:11Z] INFO  17:11:55,608 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:11Z] INFO  17:11:55,611 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:11Z] INFO  17:11:55,612 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:11Z] INFO  17:11:55,612 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:11Z] INFO  17:11:55,617 HelpFormatter - Program Args: -T PrintReads -L 6:93955016-109466584 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/6/tx/tmp4ru1P4/R14-18106_kapa-NGv3-PE100-NGv3-sort-6_93955015_109466584-prep-prealign.bam
[2016-04-15T00:11Z] INFO  17:11:55,627 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:11Z] INFO  17:11:55,638 HelpFormatter - Date/Time: 2016/04/14 17:11:55
[2016-04-15T00:11Z] INFO  17:11:55,639 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:11Z] INFO  17:11:55,640 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:11Z] INFO  17:11:55,841 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:11Z] INFO  17:11:56,167 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:11Z] GATK: realign ('5', 112073555, 127595521) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:11Z] INFO  17:11:56,288 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@41fd9d8e
[2016-04-15T00:11Z] INFO  17:11:56,453 ProgressMeter -            done    311876.0    39.0 s       2.1 m      100.0%    39.0 s       0.0 s
[2016-04-15T00:11Z] INFO  17:11:56,454 ProgressMeter - Total runtime 39.49 secs, 0.66 min, 0.01 hours
[2016-04-15T00:11Z] INFO  17:11:56,455 MicroScheduler - 206 reads were filtered out during the traversal out of approximately 312082 total reads (0.07%)
[2016-04-15T00:11Z] INFO  17:11:56,456 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:11Z] INFO  17:11:56,457 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:11Z] INFO  17:11:56,457 MicroScheduler -   -> 206 reads (0.07% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:11Z] INFO  17:11:56,589 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-15T00:11Z] INFO  17:11:56,677 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:11Z] INFO  17:11:56,686 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:11Z] INFO  17:11:56,764 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-15T00:11Z] INFO  17:11:56,789 IntervalUtils - Processing 15552870 bp from intervals
[2016-04-15T00:11Z] INFO  17:11:56,892 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:11Z] INFO  17:11:56,987 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:11Z] INFO  17:11:56,991 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:11Z] INFO  17:11:56,991 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:11Z] INFO  17:11:56,992 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:11Z] INFO  17:11:56,996 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/6/R14-18106_kapa-NGv3-PE100-NGv3-sort-6_0_15509601-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/6/tx/tmpZ4kyPS/R14-18106_kapa-NGv3-PE100-NGv3-sort-6_0_15509601-prep-prealign-realign.intervals -l INFO -L 6:1-15509601 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:11Z] INFO  17:11:57,032 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:11Z] INFO  17:11:57,035 HelpFormatter - Date/Time: 2016/04/14 17:11:56
[2016-04-15T00:11Z] INFO  17:11:57,036 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:11Z] INFO  17:11:57,037 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:11Z] INFO  17:11:57,085 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-15T00:11Z] INFO  17:11:57,136 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:11Z] INFO  17:11:57,156 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:11Z] INFO  17:11:57,166 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:11Z] INFO  17:11:57,225 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-15T00:11Z] INFO  17:11:57,235 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:11Z] INFO  17:11:57,235 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:11Z] INFO  17:11:57,236 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:11Z] INFO  17:11:57,236 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:11Z] INFO  17:11:57,245 IntervalUtils - Processing 15511569 bp from intervals
[2016-04-15T00:11Z] INFO  17:11:57,267 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:11Z] INFO  17:11:57,355 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:11Z] INFO  17:11:57,384 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T00:11Z] INFO  17:11:57,393 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:11Z] INFO  17:11:57,411 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:11Z] INFO  17:11:57,458 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-15T00:11Z] INFO  17:11:57,719 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:11Z] INFO  17:11:57,731 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:11Z] INFO  17:11:57,732 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:11Z] INFO  17:11:57,733 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:11Z] INFO  17:11:57,764 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:11Z] INFO  17:11:57,791 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:11Z] INFO  17:11:57,798 IntervalUtils - Processing 15509601 bp from intervals
[2016-04-15T00:11Z] WARN  17:11:57,803 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:11Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-5_143200044_158710347-prep-prealign.bam
[2016-04-15T00:11Z] INFO  17:11:57,924 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:11Z] INFO  17:11:57,983 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:11Z] INFO  17:11:58,027 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:11Z] INFO  17:11:58,029 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:11Z] INFO  17:11:58,029 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:11Z] INFO  17:11:58,029 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:11Z] INFO  17:11:58,033 HelpFormatter - Program Args: -T PrintReads -L 6:109467961-124979532 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/6/tx/tmpXgix15/R14-18106_kapa-NGv3-PE100-NGv3-sort-6_109467960_124979532-prep-prealign.bam
[2016-04-15T00:11Z] INFO  17:11:58,061 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:11Z] INFO  17:11:58,062 HelpFormatter - Date/Time: 2016/04/14 17:11:58
[2016-04-15T00:11Z] INFO  17:11:58,062 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:11Z] INFO  17:11:58,062 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:11Z] INFO  17:11:58,090 ProgressMeter -      6:28297313    200004.0    30.0 s       2.6 m       82.1%    36.0 s       6.0 s
[2016-04-15T00:11Z] INFO  17:11:58,107 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:11Z] INFO  17:11:58,108 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:11Z] INFO  17:11:58,108 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:11Z] INFO  17:11:58,109 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:11Z] INFO  17:11:58,219 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:11Z] INFO  17:11:58,311 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@41fd9d8e
[2016-04-15T00:11Z] INFO  17:11:58,468 ProgressMeter -            done    285460.0    35.0 s       2.1 m       98.0%    35.0 s       0.0 s
[2016-04-15T00:11Z] INFO  17:11:58,469 ProgressMeter - Total runtime 35.75 secs, 0.60 min, 0.01 hours
[2016-04-15T00:11Z] INFO  17:11:58,470 MicroScheduler - 146 reads were filtered out during the traversal out of approximately 285606 total reads (0.05%)
[2016-04-15T00:11Z] INFO  17:11:58,471 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:11Z] INFO  17:11:58,472 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:11Z] INFO  17:11:58,472 MicroScheduler -   -> 146 reads (0.05% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:11Z] GATK RealignerTargetCreator: R14-18106_kapa-NGv3-PE100-NGv3-sort-5_143200044_158710347-prep-prealign.bam 5:143200045-158710347
[2016-04-15T00:11Z] GATK: RealignerTargetCreator
[2016-04-15T00:11Z] INFO  17:11:58,894 ProgressMeter -      6:32038115    200004.0    30.0 s       2.5 m        6.2%     8.1 m       7.6 m
[2016-04-15T00:11Z] INFO  17:11:58,919 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:11Z] INFO  17:11:58,922 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:11Z] INFO  17:11:58,922 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:11Z] INFO  17:11:58,923 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:11Z] INFO  17:11:58,927 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/5/R14-18106_kapa-NGv3-PE100-NGv3-sort-5_112073555_127595521-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/5/R14-18106_kapa-NGv3-PE100-NGv3-sort-5_112073555_127595521-prep-prealign-realign.intervals -L 5:112073556-127595521 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/5/tx/tmpqZ7dkt/R14-18106_kapa-NGv3-PE100-NGv3-sort-5_112073555_127595521-prep.bam
[2016-04-15T00:11Z] INFO  17:11:58,969 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:11Z] INFO  17:11:58,970 HelpFormatter - Date/Time: 2016/04/14 17:11:58
[2016-04-15T00:11Z] INFO  17:11:58,970 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:11Z] INFO  17:11:58,982 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:11Z] INFO  17:11:59,214 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:11Z] INFO  17:11:59,379 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:11Z] INFO  17:11:59,399 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:11Z] INFO  17:11:59,477 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-15T00:11Z] INFO  17:11:59,603 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-15T00:11Z] INFO  17:11:59,678 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:11Z] INFO  17:11:59,697 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:11Z] INFO  17:11:59,740 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.04
[2016-04-15T00:11Z] INFO  17:11:59,764 IntervalUtils - Processing 15511572 bp from intervals
[2016-04-15T00:11Z] INFO  17:11:59,817 IntervalUtils - Processing 15521966 bp from intervals
[2016-04-15T00:11Z] WARN  17:11:59,823 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:11Z] INFO  17:11:59,855 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:11Z] INFO  17:11:59,869 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:11Z] INFO  17:11:59,891 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:11Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-5_174919106_180915260-prep-prealign.bam
[2016-04-15T00:12Z] INFO  17:12:00,011 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:12Z] INFO  17:12:00,012 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:12Z] INFO  17:12:00,013 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:12Z] INFO  17:12:00,014 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:12Z] INFO  17:12:00,169 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@32d5a4c6
[2016-04-15T00:12Z] INFO  17:12:00,187 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:12Z] INFO  17:12:00,197 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:12Z] INFO  17:12:00,200 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:12Z] INFO  17:12:00,201 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:12Z] INFO  17:12:00,201 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:12Z] INFO  17:12:00,231 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:12Z] INFO  17:12:00,270 ProgressMeter -            done    190749.0    26.0 s       2.3 m      100.0%    26.0 s       0.0 s
[2016-04-15T00:12Z] INFO  17:12:00,271 ProgressMeter - Total runtime 26.18 secs, 0.44 min, 0.01 hours
[2016-04-15T00:12Z] INFO  17:12:00,277 MicroScheduler - 129 reads were filtered out during the traversal out of approximately 190878 total reads (0.07%)
[2016-04-15T00:12Z] INFO  17:12:00,278 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:12Z] INFO  17:12:00,278 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:12Z] INFO  17:12:00,279 MicroScheduler -   -> 129 reads (0.07% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:12Z] INFO  17:12:00,340 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:12Z] INFO  17:12:00,373 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:12Z] GATK RealignerTargetCreator: R14-18106_kapa-NGv3-PE100-NGv3-sort-5_174919106_180915260-prep-prealign.bam 5:174919107-180915260
[2016-04-15T00:12Z] GATK: RealignerTargetCreator
[2016-04-15T00:12Z] INFO  17:12:01,828 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:12Z] INFO  17:12:01,852 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:12Z] INFO  17:12:01,855 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:12Z] INFO  17:12:01,856 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:12Z] INFO  17:12:01,856 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:12Z] INFO  17:12:01,861 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/5/R14-18106_kapa-NGv3-PE100-NGv3-sort-5_143200044_158710347-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/5/tx/tmpUfFGim/R14-18106_kapa-NGv3-PE100-NGv3-sort-5_143200044_158710347-prep-prealign-realign.intervals -l INFO -L 5:143200045-158710347 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:12Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-6_46598699_62284307-prep-prealign.bam
[2016-04-15T00:12Z] INFO  17:12:01,910 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:12Z] INFO  17:12:01,911 HelpFormatter - Date/Time: 2016/04/14 17:12:01
[2016-04-15T00:12Z] INFO  17:12:01,912 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:12Z] INFO  17:12:01,912 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:12Z] INFO  17:12:01,925 ProgressMeter -            done    227440.0    16.0 s      71.0 s      100.0%    16.0 s       0.0 s
[2016-04-15T00:12Z] INFO  17:12:01,926 ProgressMeter - Total runtime 16.27 secs, 0.27 min, 0.00 hours
[2016-04-15T00:12Z] INFO  17:12:01,929 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 227440 total reads (0.00%)
[2016-04-15T00:12Z] INFO  17:12:01,930 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:12Z] INFO  17:12:01,930 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:12Z] INFO  17:12:01,932 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:12Z] INFO  17:12:02,019 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:12Z] INFO  17:12:02,232 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T00:12Z] INFO  17:12:02,242 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:12Z] INFO  17:12:02,287 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.04
[2016-04-15T00:12Z] GATK RealignerTargetCreator: R14-18106_kapa-NGv3-PE100-NGv3-sort-6_46598699_62284307-prep-prealign.bam 6:46598700-62284307
[2016-04-15T00:12Z] GATK: RealignerTargetCreator
[2016-04-15T00:12Z] INFO  17:12:02,673 IntervalUtils - Processing 15510303 bp from intervals
[2016-04-15T00:12Z] WARN  17:12:02,678 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:12Z] INFO  17:12:02,755 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:12Z] INFO  17:12:02,947 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:12Z] INFO  17:12:02,949 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:12Z] INFO  17:12:02,949 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:12Z] INFO  17:12:02,950 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:12Z] INFO  17:12:03,569 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:12Z] INFO  17:12:03,572 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:12Z] INFO  17:12:03,573 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:12Z] INFO  17:12:03,573 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:12Z] INFO  17:12:03,578 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/5/R14-18106_kapa-NGv3-PE100-NGv3-sort-5_174919106_180915260-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/5/tx/tmpm2H0LF/R14-18106_kapa-NGv3-PE100-NGv3-sort-5_174919106_180915260-prep-prealign-realign.intervals -l INFO -L 5:174919107-180915260 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:12Z] INFO  17:12:03,596 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:12Z] INFO  17:12:03,597 HelpFormatter - Date/Time: 2016/04/14 17:12:03
[2016-04-15T00:12Z] INFO  17:12:03,597 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:12Z] INFO  17:12:03,598 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:12Z] INFO  17:12:03,745 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:12Z] INFO  17:12:03,753 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:12Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-5_31294068_49695124-prep.bam
[2016-04-15T00:12Z] INFO  17:12:04,012 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T00:12Z] INFO  17:12:04,031 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:12Z] INFO  17:12:04,118 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.09
[2016-04-15T00:12Z] INFO  17:12:04,378 IntervalUtils - Processing 5996154 bp from intervals
[2016-04-15T00:12Z] WARN  17:12:04,383 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:12Z] GATK pre-alignment ('6', 125112484, 142397186) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:12Z] INFO  17:12:04,615 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:12Z] INFO  17:12:04,736 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:12Z] INFO  17:12:04,737 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:12Z] INFO  17:12:04,738 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:12Z] INFO  17:12:04,738 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:12Z] INFO  17:12:05,161 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:12Z] INFO  17:12:05,164 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:12Z] INFO  17:12:05,164 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:12Z] INFO  17:12:05,165 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:12Z] INFO  17:12:05,169 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/6/R14-18106_kapa-NGv3-PE100-NGv3-sort-6_46598699_62284307-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/6/tx/tmpsxUobW/R14-18106_kapa-NGv3-PE100-NGv3-sort-6_46598699_62284307-prep-prealign-realign.intervals -l INFO -L 6:46598700-62284307 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:12Z] INFO  17:12:05,207 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:12Z] INFO  17:12:05,208 HelpFormatter - Date/Time: 2016/04/14 17:12:05
[2016-04-15T00:12Z] INFO  17:12:05,209 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:12Z] INFO  17:12:05,210 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:12Z] INFO  17:12:05,327 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:12Z] INFO  17:12:05,535 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T00:12Z] INFO  17:12:05,560 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:12Z] INFO  17:12:05,629 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-15T00:12Z] INFO  17:12:06,054 IntervalUtils - Processing 15685608 bp from intervals
[2016-04-15T00:12Z] WARN  17:12:06,070 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:12Z] INFO  17:12:06,169 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:12Z] INFO  17:12:06,374 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:12Z] INFO  17:12:06,375 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:12Z] INFO  17:12:06,376 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:12Z] INFO  17:12:06,376 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:12Z] INFO  17:12:07,439 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:12Z] INFO  17:12:07,442 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:12Z] INFO  17:12:07,443 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:12Z] INFO  17:12:07,443 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:12Z] INFO  17:12:07,448 HelpFormatter - Program Args: -T PrintReads -L 6:125112485-142397186 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/6/tx/tmpgjDodx/R14-18106_kapa-NGv3-PE100-NGv3-sort-6_125112484_142397186-prep-prealign.bam
[2016-04-15T00:12Z] INFO  17:12:07,465 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:12Z] INFO  17:12:07,476 HelpFormatter - Date/Time: 2016/04/14 17:12:07
[2016-04-15T00:12Z] INFO  17:12:07,477 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:12Z] INFO  17:12:07,478 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:12Z] INFO  17:12:07,671 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:12Z] INFO  17:12:08,036 ProgressMeter -            done   1.6158191E7    18.0 s       1.0 s      100.0%    18.0 s       0.0 s
[2016-04-15T00:12Z] INFO  17:12:08,037 ProgressMeter - Total runtime 18.08 secs, 0.30 min, 0.01 hours
[2016-04-15T00:12Z] INFO  17:12:08,041 MicroScheduler - 13365 reads were filtered out during the traversal out of approximately 161649 total reads (8.27%)
[2016-04-15T00:12Z] INFO  17:12:08,042 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:12Z] INFO  17:12:08,042 MicroScheduler -   -> 624 reads (0.39% of total) failing BadMateFilter
[2016-04-15T00:12Z] INFO  17:12:08,043 MicroScheduler -   -> 12290 reads (7.60% of total) failing DuplicateReadFilter
[2016-04-15T00:12Z] INFO  17:12:08,043 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:12Z] INFO  17:12:08,043 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:12Z] INFO  17:12:08,043 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:12Z] INFO  17:12:08,044 MicroScheduler -   -> 451 reads (0.28% of total) failing MappingQualityZeroFilter
[2016-04-15T00:12Z] INFO  17:12:08,044 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:12Z] INFO  17:12:08,044 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-15T00:12Z] INFO  17:12:08,044 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:12Z] INFO  17:12:08,900 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-15T00:12Z] INFO  17:12:08,945 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:12Z] INFO  17:12:08,954 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:12Z] INFO  17:12:08,990 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.04
[2016-04-15T00:12Z] INFO  17:12:09,030 IntervalUtils - Processing 17284702 bp from intervals
[2016-04-15T00:12Z] INFO  17:12:09,110 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:12Z] INFO  17:12:09,374 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:12Z] INFO  17:12:09,375 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:12Z] INFO  17:12:09,376 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:12Z] INFO  17:12:09,376 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:12Z] INFO  17:12:09,420 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:12Z] INFO  17:12:09,451 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:12Z] GATK: realign ('5', 158711911, 174870102) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:12Z] INFO  17:12:09,611 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:12Z] INFO  17:12:11,503 ProgressMeter -            done    133162.0    11.0 s      86.0 s      100.0%    11.0 s       0.0 s
[2016-04-15T00:12Z] INFO  17:12:11,503 ProgressMeter - Total runtime 11.49 secs, 0.19 min, 0.00 hours
[2016-04-15T00:12Z] INFO  17:12:11,507 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 133162 total reads (0.00%)
[2016-04-15T00:12Z] INFO  17:12:11,507 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:12Z] INFO  17:12:11,507 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:12Z] INFO  17:12:11,508 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:12Z] INFO  17:12:11,981 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:12Z] INFO  17:12:11,984 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:12Z] INFO  17:12:11,985 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:12Z] INFO  17:12:11,985 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:12Z] INFO  17:12:11,990 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/5/R14-18106_kapa-NGv3-PE100-NGv3-sort-5_158711911_174870102-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/5/R14-18106_kapa-NGv3-PE100-NGv3-sort-5_158711911_174870102-prep-prealign-realign.intervals -L 5:158711912-174870102 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/5/tx/tmpqK5QM2/R14-18106_kapa-NGv3-PE100-NGv3-sort-5_158711911_174870102-prep.bam
[2016-04-15T00:12Z] INFO  17:12:12,004 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:12Z] INFO  17:12:12,009 HelpFormatter - Date/Time: 2016/04/14 17:12:11
[2016-04-15T00:12Z] INFO  17:12:12,010 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:12Z] INFO  17:12:12,010 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:12Z] INFO  17:12:12,236 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:12Z] INFO  17:12:12,322 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@7172f77a
[2016-04-15T00:12Z] INFO  17:12:12,385 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:12Z] INFO  17:12:12,397 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:12Z] INFO  17:12:12,455 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-15T00:12Z] INFO  17:12:12,517 ProgressMeter -            done    124316.0    19.0 s       2.7 m      100.0%    19.0 s       0.0 s
[2016-04-15T00:12Z] INFO  17:12:12,518 ProgressMeter - Total runtime 19.83 secs, 0.33 min, 0.01 hours
[2016-04-15T00:12Z] INFO  17:12:12,519 MicroScheduler - 135 reads were filtered out during the traversal out of approximately 124451 total reads (0.11%)
[2016-04-15T00:12Z] INFO  17:12:12,520 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:12Z] INFO  17:12:12,521 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:12Z] INFO  17:12:12,522 MicroScheduler -   -> 135 reads (0.11% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:12Z] INFO  17:12:12,836 ProgressMeter -       4:9218638    300004.0    31.0 s     103.0 s       59.4%    52.0 s      21.0 s
[2016-04-15T00:12Z] INFO  17:12:12,848 IntervalUtils - Processing 16158191 bp from intervals
[2016-04-15T00:12Z] WARN  17:12:12,853 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:12Z] INFO  17:12:12,891 ProgressMeter -            done    255051.0    19.0 s      76.0 s      100.0%    19.0 s       0.0 s
[2016-04-15T00:12Z] INFO  17:12:12,892 ProgressMeter - Total runtime 19.49 secs, 0.32 min, 0.01 hours
[2016-04-15T00:12Z] INFO  17:12:12,896 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 255051 total reads (0.00%)
[2016-04-15T00:12Z] INFO  17:12:12,898 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:12Z] INFO  17:12:12,898 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:12Z] INFO  17:12:12,899 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:12Z] INFO  17:12:12,951 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:12Z] INFO  17:12:13,058 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:12Z] INFO  17:12:13,059 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:12Z] INFO  17:12:13,060 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:12Z] INFO  17:12:13,065 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:12Z] INFO  17:12:13,094 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:12Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-5_112073555_127595521-prep.bam
[2016-04-15T00:12Z] INFO  17:12:13,219 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:12Z] INFO  17:12:13,264 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@41fd9d8e
[2016-04-15T00:12Z] INFO  17:12:13,354 ProgressMeter -            done    362608.0    46.0 s       2.1 m      100.0%    46.0 s       0.0 s
[2016-04-15T00:12Z] INFO  17:12:13,356 ProgressMeter - Total runtime 46.11 secs, 0.77 min, 0.01 hours
[2016-04-15T00:12Z] INFO  17:12:13,357 MicroScheduler - 203 reads were filtered out during the traversal out of approximately 362811 total reads (0.06%)
[2016-04-15T00:12Z] INFO  17:12:13,357 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:12Z] INFO  17:12:13,357 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:12Z] INFO  17:12:13,358 MicroScheduler -   -> 203 reads (0.06% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:12Z] INFO  17:12:13,360 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:12Z] GATK pre-alignment ('6', 142399691, 157963777) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:12Z] INFO  17:12:14,183 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@41fd9d8e
[2016-04-15T00:12Z] INFO  17:12:14,201 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:12Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-6_62390867_78173120-prep-prealign.bam
[2016-04-15T00:12Z] INFO  17:12:14,330 ProgressMeter -            done    111089.0    16.0 s       2.5 m      100.0%    16.0 s       0.0 s
[2016-04-15T00:12Z] INFO  17:12:14,331 ProgressMeter - Total runtime 16.60 secs, 0.28 min, 0.00 hours
[2016-04-15T00:12Z] INFO  17:12:14,332 MicroScheduler - 118 reads were filtered out during the traversal out of approximately 111207 total reads (0.11%)
[2016-04-15T00:12Z] INFO  17:12:14,332 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:12Z] INFO  17:12:14,333 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:12Z] INFO  17:12:14,333 MicroScheduler -   -> 118 reads (0.11% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:12Z] INFO  17:12:14,463 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:12Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-5_65290574_80809536-prep.bam
[2016-04-15T00:12Z] GATK RealignerTargetCreator: R14-18106_kapa-NGv3-PE100-NGv3-sort-6_62390867_78173120-prep-prealign.bam 6:62390868-78173120
[2016-04-15T00:12Z] GATK: RealignerTargetCreator
[2016-04-15T00:12Z] INFO  17:12:14,968 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:12Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-6_15511526_31080332-prep-prealign.bam
[2016-04-15T00:12Z] GATK pre-alignment ('6', 158013810, 171115067) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:12Z] INFO  17:12:15,854 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:12Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-6_93955015_109466584-prep-prealign.bam
[2016-04-15T00:12Z] GATK RealignerTargetCreator: R14-18106_kapa-NGv3-PE100-NGv3-sort-6_93955015_109466584-prep-prealign.bam 6:93955016-109466584
[2016-04-15T00:12Z] GATK: RealignerTargetCreator
[2016-04-15T00:12Z] GATK RealignerTargetCreator: R14-18106_kapa-NGv3-PE100-NGv3-sort-6_15511526_31080332-prep-prealign.bam 6:15511527-31080332
[2016-04-15T00:12Z] GATK: RealignerTargetCreator
[2016-04-15T00:12Z] INFO  17:12:16,503 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:12Z] INFO  17:12:16,506 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:12Z] INFO  17:12:16,506 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:12Z] INFO  17:12:16,507 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:12Z] INFO  17:12:16,512 HelpFormatter - Program Args: -T PrintReads -L 6:142399692-157963777 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/6/tx/tmpGr3PfO/R14-18106_kapa-NGv3-PE100-NGv3-sort-6_142399691_157963777-prep-prealign.bam
[2016-04-15T00:12Z] INFO  17:12:16,517 ProgressMeter -            done   1.5509601E7    18.0 s       1.0 s      100.0%    18.0 s       0.0 s
[2016-04-15T00:12Z] INFO  17:12:16,518 ProgressMeter - Total runtime 18.41 secs, 0.31 min, 0.01 hours
[2016-04-15T00:12Z] INFO  17:12:16,522 MicroScheduler - 23765 reads were filtered out during the traversal out of approximately 201884 total reads (11.77%)
[2016-04-15T00:12Z] INFO  17:12:16,523 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:12Z] INFO  17:12:16,523 MicroScheduler -   -> 682 reads (0.34% of total) failing BadMateFilter
[2016-04-15T00:12Z] INFO  17:12:16,524 MicroScheduler -   -> 14619 reads (7.24% of total) failing DuplicateReadFilter
[2016-04-15T00:12Z] INFO  17:12:16,525 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:12Z] INFO  17:12:16,525 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:12Z] INFO  17:12:16,526 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:12Z] INFO  17:12:16,526 MicroScheduler -   -> 8464 reads (4.19% of total) failing MappingQualityZeroFilter
[2016-04-15T00:12Z] INFO  17:12:16,527 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:12Z] INFO  17:12:16,528 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-15T00:12Z] INFO  17:12:16,528 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:12Z] INFO  17:12:16,539 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:12Z] INFO  17:12:16,541 HelpFormatter - Date/Time: 2016/04/14 17:12:16
[2016-04-15T00:12Z] INFO  17:12:16,541 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:12Z] INFO  17:12:16,542 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:12Z] INFO  17:12:16,609 ProgressMeter -     5:140590667    400018.0    60.0 s       2.5 m       83.3%    72.0 s      12.0 s
[2016-04-15T00:12Z] INFO  17:12:16,791 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:12Z] INFO  17:12:17,400 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:12Z] INFO  17:12:17,403 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:12Z] INFO  17:12:17,404 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:12Z] INFO  17:12:17,404 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:12Z] INFO  17:12:17,409 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/6/R14-18106_kapa-NGv3-PE100-NGv3-sort-6_62390867_78173120-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/6/tx/tmpP4VslJ/R14-18106_kapa-NGv3-PE100-NGv3-sort-6_62390867_78173120-prep-prealign-realign.intervals -l INFO -L 6:62390868-78173120 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:12Z] INFO  17:12:17,418 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:12Z] INFO  17:12:17,424 HelpFormatter - Date/Time: 2016/04/14 17:12:17
[2016-04-15T00:12Z] INFO  17:12:17,425 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:12Z] INFO  17:12:17,425 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:12Z] INFO  17:12:17,542 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:12Z] INFO  17:12:17,813 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T00:12Z] INFO  17:12:17,823 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:12Z] INFO  17:12:17,882 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-15T00:12Z] INFO  17:12:17,926 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:12Z] GATK: realign ('6', 0, 15509601) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:12Z] INFO  17:12:18,039 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-15T00:12Z] INFO  17:12:18,133 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:12Z] INFO  17:12:18,144 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:12Z] INFO  17:12:18,195 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-15T00:12Z] INFO  17:12:18,216 IntervalUtils - Processing 15564086 bp from intervals
[2016-04-15T00:12Z] INFO  17:12:18,298 ProgressMeter -            done   5996154.0    13.0 s       2.0 s      100.0%    13.0 s       0.0 s
[2016-04-15T00:12Z] INFO  17:12:18,299 ProgressMeter - Total runtime 13.56 secs, 0.23 min, 0.00 hours
[2016-04-15T00:12Z] INFO  17:12:18,301 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:12Z] INFO  17:12:18,303 MicroScheduler - 35935 reads were filtered out during the traversal out of approximately 287182 total reads (12.51%)
[2016-04-15T00:12Z] INFO  17:12:18,304 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:12Z] INFO  17:12:18,304 MicroScheduler -   -> 566 reads (0.20% of total) failing BadMateFilter
[2016-04-15T00:12Z] INFO  17:12:18,304 MicroScheduler -   -> 20496 reads (7.14% of total) failing DuplicateReadFilter
[2016-04-15T00:12Z] INFO  17:12:18,304 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:12Z] INFO  17:12:18,305 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:12Z] INFO  17:12:18,305 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:12Z] INFO  17:12:18,305 MicroScheduler -   -> 14873 reads (5.18% of total) failing MappingQualityZeroFilter
[2016-04-15T00:12Z] INFO  17:12:18,305 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:12Z] INFO  17:12:18,306 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-15T00:12Z] INFO  17:12:18,306 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:12Z] INFO  17:12:18,317 IntervalUtils - Processing 15782253 bp from intervals
[2016-04-15T00:12Z] WARN  17:12:18,322 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:12Z] INFO  17:12:18,414 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:12Z] INFO  17:12:18,466 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:12Z] INFO  17:12:18,470 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:12Z] INFO  17:12:18,470 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:12Z] INFO  17:12:18,471 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:12Z] INFO  17:12:18,475 HelpFormatter - Program Args: -T PrintReads -L 6:158013811-171115067 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/6/tx/tmpZy3YLf/R14-18106_kapa-NGv3-PE100-NGv3-sort-6_158013810_171115067-prep-prealign.bam
[2016-04-15T00:12Z] INFO  17:12:18,488 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:12Z] INFO  17:12:18,489 HelpFormatter - Date/Time: 2016/04/14 17:12:18
[2016-04-15T00:12Z] INFO  17:12:18,489 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:12Z] INFO  17:12:18,490 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:12Z] INFO  17:12:18,644 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:12Z] INFO  17:12:18,645 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:12Z] INFO  17:12:18,645 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:12Z] INFO  17:12:18,646 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:12Z] INFO  17:12:18,685 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:12Z] INFO  17:12:18,694 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:12Z] INFO  17:12:18,695 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:12Z] INFO  17:12:18,695 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:12Z] INFO  17:12:18,696 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:12Z] INFO  17:12:18,730 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:12Z] INFO  17:12:18,878 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:12Z] INFO  17:12:18,929 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@41fd9d8e
[2016-04-15T00:12Z] INFO  17:12:19,033 ProgressMeter -            done    153596.0    21.0 s       2.4 m      100.0%    21.0 s       0.0 s
[2016-04-15T00:12Z] INFO  17:12:19,033 ProgressMeter - Total runtime 21.80 secs, 0.36 min, 0.01 hours
[2016-04-15T00:12Z] INFO  17:12:19,034 MicroScheduler - 121 reads were filtered out during the traversal out of approximately 153717 total reads (0.08%)
[2016-04-15T00:12Z] INFO  17:12:19,034 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:12Z] INFO  17:12:19,034 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:12Z] INFO  17:12:19,035 MicroScheduler -   -> 121 reads (0.08% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:12Z] INFO  17:12:19,408 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:12Z] INFO  17:12:19,410 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:12Z] INFO  17:12:19,411 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:12Z] INFO  17:12:19,411 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:12Z] INFO  17:12:19,426 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/6/R14-18106_kapa-NGv3-PE100-NGv3-sort-6_93955015_109466584-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/6/tx/tmp7yUIf9/R14-18106_kapa-NGv3-PE100-NGv3-sort-6_93955015_109466584-prep-prealign-realign.intervals -l INFO -L 6:93955016-109466584 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:12Z] INFO  17:12:19,444 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:12Z] INFO  17:12:19,444 HelpFormatter - Date/Time: 2016/04/14 17:12:19
[2016-04-15T00:12Z] INFO  17:12:19,445 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:12Z] INFO  17:12:19,445 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:12Z] INFO  17:12:19,554 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:12Z] INFO  17:12:19,580 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:12Z] GATK: realign ('5', 174919106, 180915260) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:12Z] INFO  17:12:19,706 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:12Z] INFO  17:12:19,709 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:12Z] INFO  17:12:19,709 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:12Z] INFO  17:12:19,710 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:12Z] INFO  17:12:19,714 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/6/R14-18106_kapa-NGv3-PE100-NGv3-sort-6_15511526_31080332-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/6/tx/tmpI2Sq4j/R14-18106_kapa-NGv3-PE100-NGv3-sort-6_15511526_31080332-prep-prealign-realign.intervals -l INFO -L 6:15511527-31080332 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:12Z] INFO  17:12:19,723 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:12Z] INFO  17:12:19,724 HelpFormatter - Date/Time: 2016/04/14 17:12:19
[2016-04-15T00:12Z] INFO  17:12:19,725 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:12Z] INFO  17:12:19,725 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:12Z] INFO  17:12:19,813 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-15T00:12Z] INFO  17:12:19,829 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T00:12Z] INFO  17:12:19,848 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:12Z] INFO  17:12:19,871 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:12Z] INFO  17:12:19,876 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:12Z] INFO  17:12:19,885 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:12Z] INFO  17:12:19,924 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-15T00:12Z] INFO  17:12:19,944 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-15T00:12Z] INFO  17:12:19,977 IntervalUtils - Processing 13101257 bp from intervals
[2016-04-15T00:12Z] INFO  17:12:20,073 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:12Z] INFO  17:12:20,085 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T00:12Z] INFO  17:12:20,095 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:12Z] INFO  17:12:20,163 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-15T00:12Z] INFO  17:12:20,355 IntervalUtils - Processing 15511569 bp from intervals
[2016-04-15T00:12Z] WARN  17:12:20,376 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:12Z] INFO  17:12:20,492 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:12Z] INFO  17:12:20,493 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:12Z] INFO  17:12:20,494 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:12Z] INFO  17:12:20,495 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:12Z] INFO  17:12:20,495 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:12Z] INFO  17:12:20,515 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:12Z] INFO  17:12:20,553 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:12Z] INFO  17:12:20,555 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:12Z] INFO  17:12:20,555 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:12Z] INFO  17:12:20,555 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:12Z] INFO  17:12:20,559 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/6/R14-18106_kapa-NGv3-PE100-NGv3-sort-6_0_15509601-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/6/R14-18106_kapa-NGv3-PE100-NGv3-sort-6_0_15509601-prep-prealign-realign.intervals -L 6:1-15509601 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/6/tx/tmpdplIAE/R14-18106_kapa-NGv3-PE100-NGv3-sort-6_0_15509601-prep.bam
[2016-04-15T00:12Z] INFO  17:12:20,573 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:12Z] INFO  17:12:20,574 HelpFormatter - Date/Time: 2016/04/14 17:12:20
[2016-04-15T00:12Z] INFO  17:12:20,574 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:12Z] INFO  17:12:20,575 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:12Z] INFO  17:12:20,583 IntervalUtils - Processing 15568806 bp from intervals
[2016-04-15T00:12Z] WARN  17:12:20,587 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:12Z] INFO  17:12:20,646 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:12Z] INFO  17:12:20,663 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:12Z] INFO  17:12:20,670 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:12Z] INFO  17:12:20,688 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:12Z] INFO  17:12:20,689 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:12Z] INFO  17:12:20,690 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:12Z] INFO  17:12:20,691 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:12Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-6_78400388_93953258-prep-prealign.bam
[2016-04-15T00:12Z] INFO  17:12:20,792 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:12Z] INFO  17:12:20,891 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:12Z] INFO  17:12:20,901 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:12Z] INFO  17:12:20,915 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:12Z] INFO  17:12:20,916 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:12Z] INFO  17:12:20,917 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:12Z] INFO  17:12:20,917 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:12Z] INFO  17:12:20,957 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-15T00:12Z] GATK RealignerTargetCreator: R14-18106_kapa-NGv3-PE100-NGv3-sort-6_78400388_93953258-prep-prealign.bam 6:78400389-93953258
[2016-04-15T00:12Z] GATK: RealignerTargetCreator
[2016-04-15T00:12Z] INFO  17:12:21,432 IntervalUtils - Processing 15509601 bp from intervals
[2016-04-15T00:12Z] WARN  17:12:21,438 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:12Z] INFO  17:12:21,537 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:12Z] INFO  17:12:21,651 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:12Z] INFO  17:12:21,652 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:12Z] INFO  17:12:21,653 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:12Z] INFO  17:12:21,654 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:12Z] INFO  17:12:21,870 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:12Z] INFO  17:12:22,153 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:12Z] INFO  17:12:22,413 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:12Z] INFO  17:12:22,416 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:12Z] INFO  17:12:22,416 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:12Z] INFO  17:12:22,416 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:12Z] INFO  17:12:22,420 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/5/R14-18106_kapa-NGv3-PE100-NGv3-sort-5_174919106_180915260-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/5/R14-18106_kapa-NGv3-PE100-NGv3-sort-5_174919106_180915260-prep-prealign-realign.intervals -L 5:174919107-180915260 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/5/tx/tmpdmvsyq/R14-18106_kapa-NGv3-PE100-NGv3-sort-5_174919106_180915260-prep.bam
[2016-04-15T00:12Z] INFO  17:12:22,430 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:12Z] INFO  17:12:22,431 HelpFormatter - Date/Time: 2016/04/14 17:12:22
[2016-04-15T00:12Z] INFO  17:12:22,432 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:12Z] INFO  17:12:22,432 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:12Z] INFO  17:12:22,626 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:12Z] INFO  17:12:22,747 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:12Z] INFO  17:12:22,756 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:12Z] INFO  17:12:22,809 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-15T00:12Z] INFO  17:12:23,097 ProgressMeter -            done   1.5685608E7    16.0 s       1.0 s      100.0%    16.0 s       0.0 s
[2016-04-15T00:12Z] INFO  17:12:23,098 ProgressMeter - Total runtime 16.72 secs, 0.28 min, 0.00 hours
[2016-04-15T00:12Z] INFO  17:12:23,102 MicroScheduler - 15531 reads were filtered out during the traversal out of approximately 191880 total reads (8.09%)
[2016-04-15T00:12Z] INFO  17:12:23,103 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:12Z] INFO  17:12:23,103 MicroScheduler -   -> 635 reads (0.33% of total) failing BadMateFilter
[2016-04-15T00:12Z] INFO  17:12:23,103 MicroScheduler -   -> 13980 reads (7.29% of total) failing DuplicateReadFilter
[2016-04-15T00:12Z] INFO  17:12:23,104 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:12Z] INFO  17:12:23,104 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:12Z] INFO  17:12:23,104 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:12Z] INFO  17:12:23,104 MicroScheduler -   -> 916 reads (0.48% of total) failing MappingQualityZeroFilter
[2016-04-15T00:12Z] INFO  17:12:23,105 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:12Z] INFO  17:12:23,105 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-15T00:12Z] INFO  17:12:23,105 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:12Z] INFO  17:12:23,259 IntervalUtils - Processing 5996154 bp from intervals
[2016-04-15T00:12Z] WARN  17:12:23,283 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:12Z] INFO  17:12:23,381 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:12Z] INFO  17:12:23,499 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:12Z] INFO  17:12:23,500 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:12Z] INFO  17:12:23,500 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:12Z] INFO  17:12:23,501 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:12Z] INFO  17:12:23,650 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:12Z] INFO  17:12:23,684 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@7172f77a
[2016-04-15T00:12Z] INFO  17:12:23,767 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:12Z] INFO  17:12:23,900 ProgressMeter -            done    177620.0    23.0 s       2.2 m      100.0%    23.0 s       0.0 s
[2016-04-15T00:12Z] INFO  17:12:23,908 ProgressMeter - Total runtime 23.71 secs, 0.40 min, 0.01 hours
[2016-04-15T00:12Z] INFO  17:12:23,908 MicroScheduler - 125 reads were filtered out during the traversal out of approximately 177745 total reads (0.07%)
[2016-04-15T00:12Z] INFO  17:12:23,908 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:12Z] INFO  17:12:23,909 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:12Z] INFO  17:12:23,909 MicroScheduler -   -> 125 reads (0.07% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:12Z] INFO  17:12:24,245 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:12Z] INFO  17:12:24,247 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:12Z] INFO  17:12:24,247 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:12Z] INFO  17:12:24,247 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:12Z] INFO  17:12:24,256 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/6/R14-18106_kapa-NGv3-PE100-NGv3-sort-6_78400388_93953258-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/6/tx/tmpvpah0m/R14-18106_kapa-NGv3-PE100-NGv3-sort-6_78400388_93953258-prep-prealign-realign.intervals -l INFO -L 6:78400389-93953258 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:12Z] INFO  17:12:24,276 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:12Z] INFO  17:12:24,287 HelpFormatter - Date/Time: 2016/04/14 17:12:24
[2016-04-15T00:12Z] INFO  17:12:24,288 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:12Z] INFO  17:12:24,289 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:12Z] INFO  17:12:24,362 ProgressMeter -            done   1.5510303E7    21.0 s       1.0 s      100.0%    21.0 s       0.0 s
[2016-04-15T00:12Z] INFO  17:12:24,363 ProgressMeter - Total runtime 21.41 secs, 0.36 min, 0.01 hours
[2016-04-15T00:12Z] INFO  17:12:24,367 MicroScheduler - 25278 reads were filtered out during the traversal out of approximately 314342 total reads (8.04%)
[2016-04-15T00:12Z] INFO  17:12:24,368 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:12Z] INFO  17:12:24,369 MicroScheduler -   -> 862 reads (0.27% of total) failing BadMateFilter
[2016-04-15T00:12Z] INFO  17:12:24,370 MicroScheduler -   -> 23826 reads (7.58% of total) failing DuplicateReadFilter
[2016-04-15T00:12Z] INFO  17:12:24,370 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:12Z] INFO  17:12:24,371 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:12Z] INFO  17:12:24,372 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:12Z] INFO  17:12:24,372 MicroScheduler -   -> 590 reads (0.19% of total) failing MappingQualityZeroFilter
[2016-04-15T00:12Z] INFO  17:12:24,373 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:12Z] INFO  17:12:24,373 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-15T00:12Z] INFO  17:12:24,374 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:12Z] INFO  17:12:24,426 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:12Z] INFO  17:12:24,569 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:12Z] GATK: realign ('6', 46598699, 62284307) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:12Z] INFO  17:12:24,642 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T00:12Z] INFO  17:12:24,665 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:12Z] INFO  17:12:24,708 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.04
[2016-04-15T00:12Z] INFO  17:12:25,023 IntervalUtils - Processing 15552870 bp from intervals
[2016-04-15T00:12Z] WARN  17:12:25,032 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:12Z] INFO  17:12:25,184 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:12Z] INFO  17:12:25,307 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:12Z] INFO  17:12:25,307 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:12Z] INFO  17:12:25,308 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:12Z] INFO  17:12:25,308 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:12Z] INFO  17:12:25,465 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:12Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-6_109467960_124979532-prep-prealign.bam
[2016-04-15T00:12Z] INFO  17:12:25,612 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:12Z] GATK: realign ('5', 143200044, 158710347) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:12Z] GATK RealignerTargetCreator: R14-18106_kapa-NGv3-PE100-NGv3-sort-6_109467960_124979532-prep-prealign.bam 6:109467961-124979532
[2016-04-15T00:12Z] GATK: RealignerTargetCreator
[2016-04-15T00:12Z] INFO  17:12:26,478 ProgressMeter -            done    160435.0    13.0 s      83.0 s      100.0%    13.0 s       0.0 s
[2016-04-15T00:12Z] INFO  17:12:26,479 ProgressMeter - Total runtime 13.42 secs, 0.22 min, 0.00 hours
[2016-04-15T00:12Z] INFO  17:12:26,482 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 160435 total reads (0.00%)
[2016-04-15T00:12Z] INFO  17:12:26,483 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:12Z] INFO  17:12:26,483 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:12Z] INFO  17:12:26,483 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:12Z] INFO  17:12:27,639 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:12Z] INFO  17:12:27,642 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:12Z] INFO  17:12:27,643 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:12Z] INFO  17:12:27,643 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:12Z] INFO  17:12:27,648 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/6/R14-18106_kapa-NGv3-PE100-NGv3-sort-6_46598699_62284307-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/6/R14-18106_kapa-NGv3-PE100-NGv3-sort-6_46598699_62284307-prep-prealign-realign.intervals -L 6:46598700-62284307 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/6/tx/tmpYBIESd/R14-18106_kapa-NGv3-PE100-NGv3-sort-6_46598699_62284307-prep.bam
[2016-04-15T00:12Z] INFO  17:12:27,674 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:12Z] INFO  17:12:27,675 HelpFormatter - Date/Time: 2016/04/14 17:12:27
[2016-04-15T00:12Z] INFO  17:12:27,675 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:12Z] INFO  17:12:27,676 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:12Z] INFO  17:12:27,907 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:12Z] INFO  17:12:28,024 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:12Z] INFO  17:12:28,033 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:12Z] INFO  17:12:28,096 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-15T00:12Z] INFO  17:12:28,099 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:12Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-5_158711911_174870102-prep.bam
[2016-04-15T00:12Z] INFO  17:12:28,377 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:12Z] INFO  17:12:28,380 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:12Z] INFO  17:12:28,381 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:12Z] INFO  17:12:28,382 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:12Z] INFO  17:12:28,386 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/5/R14-18106_kapa-NGv3-PE100-NGv3-sort-5_143200044_158710347-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/5/R14-18106_kapa-NGv3-PE100-NGv3-sort-5_143200044_158710347-prep-prealign-realign.intervals -L 5:143200045-158710347 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/5/tx/tmpuI2nI7/R14-18106_kapa-NGv3-PE100-NGv3-sort-5_143200044_158710347-prep.bam
[2016-04-15T00:12Z] INFO  17:12:28,396 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:12Z] INFO  17:12:28,397 HelpFormatter - Date/Time: 2016/04/14 17:12:28
[2016-04-15T00:12Z] INFO  17:12:28,397 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:12Z] INFO  17:12:28,398 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:12Z] INFO  17:12:28,436 IntervalUtils - Processing 15685608 bp from intervals
[2016-04-15T00:12Z] WARN  17:12:28,442 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:12Z] INFO  17:12:28,531 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:12Z] GATK pre-alignment ('7', 0, 15584548) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:12Z] INFO  17:12:28,676 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:12Z] INFO  17:12:28,677 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:12Z] INFO  17:12:28,678 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:12Z] INFO  17:12:28,686 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:12Z] INFO  17:12:28,691 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:12Z] INFO  17:12:28,823 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:12Z] INFO  17:12:28,832 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:12Z] INFO  17:12:28,864 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:12Z] INFO  17:12:28,895 ProgressMeter -      6:36275533    400007.0    60.0 s       2.5 m       33.5%     3.0 m     119.0 s
[2016-04-15T00:12Z] INFO  17:12:28,897 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-15T00:12Z] INFO  17:12:28,999 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:12Z] INFO  17:12:29,087 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:12Z] INFO  17:12:29,090 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:12Z] INFO  17:12:29,091 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:12Z] INFO  17:12:29,091 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:12Z] INFO  17:12:29,096 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/6/R14-18106_kapa-NGv3-PE100-NGv3-sort-6_109467960_124979532-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/6/tx/tmpVQUK3R/R14-18106_kapa-NGv3-PE100-NGv3-sort-6_109467960_124979532-prep-prealign-realign.intervals -l INFO -L 6:109467961-124979532 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:12Z] INFO  17:12:29,126 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:12Z] INFO  17:12:29,127 HelpFormatter - Date/Time: 2016/04/14 17:12:29
[2016-04-15T00:12Z] INFO  17:12:29,128 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:12Z] INFO  17:12:29,128 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:12Z] INFO  17:12:29,230 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:12Z] INFO  17:12:29,353 IntervalUtils - Processing 15510303 bp from intervals
[2016-04-15T00:12Z] WARN  17:12:29,359 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:12Z] INFO  17:12:29,423 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:12Z] INFO  17:12:29,487 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T00:12Z] INFO  17:12:29,496 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:12Z] INFO  17:12:29,522 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:12Z] INFO  17:12:29,537 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.04
[2016-04-15T00:12Z] INFO  17:12:29,545 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:12Z] INFO  17:12:29,546 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:12Z] INFO  17:12:29,546 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:12Z] INFO  17:12:29,754 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:12Z] INFO  17:12:29,940 IntervalUtils - Processing 15511572 bp from intervals
[2016-04-15T00:12Z] WARN  17:12:29,948 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:12Z] INFO  17:12:29,949 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:12Z] INFO  17:12:30,102 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:12Z] INFO  17:12:30,283 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:12Z] INFO  17:12:30,284 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:12Z] INFO  17:12:30,284 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:12Z] INFO  17:12:30,284 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:12Z] INFO  17:12:31,876 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:12Z] INFO  17:12:31,879 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:12Z] INFO  17:12:31,880 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:12Z] INFO  17:12:31,880 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:12Z] INFO  17:12:31,885 HelpFormatter - Program Args: -T PrintReads -L 7:1-15584548 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/7/tx/tmpFb9c1L/R14-18106_kapa-NGv3-PE100-NGv3-sort-7_0_15584548-prep-prealign.bam
[2016-04-15T00:12Z] INFO  17:12:31,930 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:12Z] INFO  17:12:31,931 HelpFormatter - Date/Time: 2016/04/14 17:12:31
[2016-04-15T00:12Z] INFO  17:12:31,932 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:12Z] INFO  17:12:31,933 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:12Z] INFO  17:12:32,082 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:12Z] INFO  17:12:33,078 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-15T00:12Z] INFO  17:12:33,205 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:12Z] INFO  17:12:33,215 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:12Z] INFO  17:12:33,260 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-15T00:12Z] INFO  17:12:33,274 IntervalUtils - Processing 15584548 bp from intervals
[2016-04-15T00:12Z] INFO  17:12:33,370 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:12Z] INFO  17:12:33,727 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:12Z] INFO  17:12:33,727 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:12Z] INFO  17:12:33,739 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:12Z] INFO  17:12:33,739 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:12Z] INFO  17:12:33,770 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:12Z] INFO  17:12:33,836 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@41fd9d8e
[2016-04-15T00:12Z] INFO  17:12:33,954 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:12Z] INFO  17:12:34,036 ProgressMeter -            done    662374.0    78.0 s     117.0 s      100.0%    78.0 s       0.0 s
[2016-04-15T00:12Z] INFO  17:12:34,036 ProgressMeter - Total runtime 78.05 secs, 1.30 min, 0.02 hours
[2016-04-15T00:12Z] INFO  17:12:34,037 MicroScheduler - 302 reads were filtered out during the traversal out of approximately 662676 total reads (0.05%)
[2016-04-15T00:12Z] INFO  17:12:34,037 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:12Z] INFO  17:12:34,037 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:12Z] INFO  17:12:34,038 MicroScheduler -   -> 302 reads (0.05% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:12Z] INFO  17:12:34,111 ProgressMeter -            done    907047.0    52.0 s      57.0 s      100.0%    52.0 s       0.0 s
[2016-04-15T00:12Z] INFO  17:12:34,112 ProgressMeter - Total runtime 52.47 secs, 0.87 min, 0.01 hours
[2016-04-15T00:12Z] INFO  17:12:34,115 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 907047 total reads (0.00%)
[2016-04-15T00:12Z] INFO  17:12:34,116 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:12Z] INFO  17:12:34,116 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:12Z] INFO  17:12:34,116 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:12Z] INFO  17:12:35,317 ProgressMeter -            done   1.5782253E7    16.0 s       1.0 s      100.0%    16.0 s       0.0 s
[2016-04-15T00:12Z] INFO  17:12:35,317 ProgressMeter - Total runtime 16.67 secs, 0.28 min, 0.00 hours
[2016-04-15T00:12Z] INFO  17:12:35,322 MicroScheduler - 11428 reads were filtered out during the traversal out of approximately 125205 total reads (9.13%)
[2016-04-15T00:12Z] INFO  17:12:35,322 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:12Z] INFO  17:12:35,323 MicroScheduler -   -> 532 reads (0.42% of total) failing BadMateFilter
[2016-04-15T00:12Z] INFO  17:12:35,323 MicroScheduler -   -> 9147 reads (7.31% of total) failing DuplicateReadFilter
[2016-04-15T00:12Z] INFO  17:12:35,323 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:12Z] INFO  17:12:35,324 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:12Z] INFO  17:12:35,324 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:12Z] INFO  17:12:35,324 MicroScheduler -   -> 1749 reads (1.40% of total) failing MappingQualityZeroFilter
[2016-04-15T00:12Z] INFO  17:12:35,325 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:12Z] INFO  17:12:35,325 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-15T00:12Z] INFO  17:12:35,325 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:12Z] INFO  17:12:35,471 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:12Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-4_0_15511864-prep.bam
[2016-04-15T00:12Z] INFO  17:12:35,568 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:12Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-5_127597427_143191869-prep-prealign.bam
[2016-04-15T00:12Z] INFO  17:12:36,596 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:12Z] GATK: realign ('6', 62390867, 78173120) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:12Z] INFO  17:12:36,749 ProgressMeter -            done    200588.0    15.0 s      75.0 s      100.0%    15.0 s       0.0 s
[2016-04-15T00:12Z] INFO  17:12:36,749 ProgressMeter - Total runtime 15.10 secs, 0.25 min, 0.00 hours
[2016-04-15T00:12Z] INFO  17:12:36,772 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 200588 total reads (0.00%)
[2016-04-15T00:12Z] INFO  17:12:36,772 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:12Z] INFO  17:12:36,773 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:12Z] INFO  17:12:36,773 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:12Z] INFO  17:12:37,339 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@5fe152b7
[2016-04-15T00:12Z] INFO  17:12:37,342 ProgressMeter -            done   1.5511569E7    16.0 s       1.0 s      100.0%    16.0 s       0.0 s
[2016-04-15T00:12Z] INFO  17:12:37,343 ProgressMeter - Total runtime 16.65 secs, 0.28 min, 0.00 hours
[2016-04-15T00:12Z] INFO  17:12:37,347 MicroScheduler - 9438 reads were filtered out during the traversal out of approximately 111583 total reads (8.46%)
[2016-04-15T00:12Z] INFO  17:12:37,347 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:12Z] INFO  17:12:37,348 MicroScheduler -   -> 519 reads (0.47% of total) failing BadMateFilter
[2016-04-15T00:12Z] INFO  17:12:37,348 MicroScheduler -   -> 8023 reads (7.19% of total) failing DuplicateReadFilter
[2016-04-15T00:12Z] INFO  17:12:37,348 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:12Z] INFO  17:12:37,349 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:12Z] INFO  17:12:37,349 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:12Z] INFO  17:12:37,349 MicroScheduler -   -> 896 reads (0.80% of total) failing MappingQualityZeroFilter
[2016-04-15T00:12Z] INFO  17:12:37,350 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:12Z] INFO  17:12:37,350 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-15T00:12Z] INFO  17:12:37,350 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:12Z] INFO  17:12:37,615 ProgressMeter -            done    208566.0    28.0 s       2.3 m      100.0%    28.0 s       0.0 s
[2016-04-15T00:12Z] INFO  17:12:37,616 ProgressMeter - Total runtime 28.24 secs, 0.47 min, 0.01 hours
[2016-04-15T00:12Z] INFO  17:12:37,616 MicroScheduler - 196 reads were filtered out during the traversal out of approximately 208762 total reads (0.09%)
[2016-04-15T00:12Z] INFO  17:12:37,617 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:12Z] INFO  17:12:37,617 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:12Z] INFO  17:12:37,617 MicroScheduler -   -> 196 reads (0.09% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:12Z] GATK RealignerTargetCreator: R14-18106_kapa-NGv3-PE100-NGv3-sort-5_127597427_143191869-prep-prealign.bam 5:127597428-143191869
[2016-04-15T00:12Z] GATK: RealignerTargetCreator
[2016-04-15T00:12Z] INFO  17:12:38,270 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:12Z] GATK pre-alignment ('7', 15599765, 31117713) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:12Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-6_0_15509601-prep.bam
[2016-04-15T00:12Z] INFO  17:12:38,555 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:12Z] GATK: realign ('6', 93955015, 109466584) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:12Z] GATK pre-alignment ('7', 31120227, 47317818) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:12Z] INFO  17:12:39,055 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:12Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-6_125112484_142397186-prep-prealign.bam
[2016-04-15T00:12Z] INFO  17:12:39,843 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:12Z] INFO  17:12:39,846 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:12Z] INFO  17:12:39,847 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:12Z] INFO  17:12:39,848 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:12Z] INFO  17:12:39,852 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/6/R14-18106_kapa-NGv3-PE100-NGv3-sort-6_62390867_78173120-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/6/R14-18106_kapa-NGv3-PE100-NGv3-sort-6_62390867_78173120-prep-prealign-realign.intervals -L 6:62390868-78173120 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/6/tx/tmpYuTRxn/R14-18106_kapa-NGv3-PE100-NGv3-sort-6_62390867_78173120-prep.bam
[2016-04-15T00:12Z] GATK RealignerTargetCreator: R14-18106_kapa-NGv3-PE100-NGv3-sort-6_125112484_142397186-prep-prealign.bam 6:125112485-142397186
[2016-04-15T00:12Z] INFO  17:12:39,883 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:12Z] INFO  17:12:39,884 HelpFormatter - Date/Time: 2016/04/14 17:12:39
[2016-04-15T00:12Z] INFO  17:12:39,884 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:12Z] INFO  17:12:39,885 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:12Z] GATK: RealignerTargetCreator
[2016-04-15T00:12Z] INFO  17:12:40,060 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:12Z] INFO  17:12:40,135 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:12Z] INFO  17:12:40,144 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:12Z] INFO  17:12:40,189 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.04
[2016-04-15T00:12Z] INFO  17:12:40,547 IntervalUtils - Processing 15782253 bp from intervals
[2016-04-15T00:12Z] WARN  17:12:40,552 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:12Z] INFO  17:12:40,684 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:12Z] INFO  17:12:40,882 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:12Z] INFO  17:12:40,883 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:12Z] INFO  17:12:40,883 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:12Z] INFO  17:12:40,884 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:12Z] INFO  17:12:40,924 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:12Z] INFO  17:12:40,927 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:12Z] INFO  17:12:40,928 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:12Z] INFO  17:12:40,929 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:12Z] INFO  17:12:40,943 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/5/R14-18106_kapa-NGv3-PE100-NGv3-sort-5_127597427_143191869-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/5/tx/tmpm00jnb/R14-18106_kapa-NGv3-PE100-NGv3-sort-5_127597427_143191869-prep-prealign-realign.intervals -l INFO -L 5:127597428-143191869 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:12Z] INFO  17:12:40,966 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:12Z] INFO  17:12:40,967 HelpFormatter - Date/Time: 2016/04/14 17:12:40
[2016-04-15T00:12Z] INFO  17:12:40,967 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:12Z] INFO  17:12:40,967 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:12Z] INFO  17:12:41,077 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:12Z] INFO  17:12:41,094 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:12Z] INFO  17:12:41,169 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:12Z] INFO  17:12:41,172 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:12Z] INFO  17:12:41,173 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:12Z] INFO  17:12:41,173 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:12Z] INFO  17:12:41,178 HelpFormatter - Program Args: -T PrintReads -L 7:15599766-31117713 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/7/tx/tmpLEGQnE/R14-18106_kapa-NGv3-PE100-NGv3-sort-7_15599765_31117713-prep-prealign.bam
[2016-04-15T00:12Z] INFO  17:12:41,217 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:12Z] INFO  17:12:41,218 HelpFormatter - Date/Time: 2016/04/14 17:12:41
[2016-04-15T00:12Z] INFO  17:12:41,218 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:12Z] INFO  17:12:41,219 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:12Z] INFO  17:12:41,332 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:12Z] INFO  17:12:41,370 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T00:12Z] INFO  17:12:41,404 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:12Z] INFO  17:12:41,437 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:12Z] INFO  17:12:41,484 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-15T00:12Z] INFO  17:12:41,819 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:12Z] INFO  17:12:41,822 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:12Z] INFO  17:12:41,822 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:12Z] INFO  17:12:41,822 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:12Z] INFO  17:12:41,826 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/6/R14-18106_kapa-NGv3-PE100-NGv3-sort-6_93955015_109466584-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/6/R14-18106_kapa-NGv3-PE100-NGv3-sort-6_93955015_109466584-prep-prealign-realign.intervals -L 6:93955016-109466584 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/6/tx/tmpUU5u0g/R14-18106_kapa-NGv3-PE100-NGv3-sort-6_93955015_109466584-prep.bam
[2016-04-15T00:12Z] INFO  17:12:41,853 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:12Z] INFO  17:12:41,854 HelpFormatter - Date/Time: 2016/04/14 17:12:41
[2016-04-15T00:12Z] INFO  17:12:41,855 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:12Z] INFO  17:12:41,855 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:12Z] INFO  17:12:41,874 IntervalUtils - Processing 15594442 bp from intervals
[2016-04-15T00:12Z] WARN  17:12:41,879 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:12Z] INFO  17:12:41,938 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:12Z] INFO  17:12:41,941 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:12Z] INFO  17:12:41,942 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:12Z] INFO  17:12:41,943 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:12Z] INFO  17:12:41,952 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:12Z] INFO  17:12:41,960 HelpFormatter - Program Args: -T PrintReads -L 7:31120228-47317818 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/7/tx/tmpIF9Sru/R14-18106_kapa-NGv3-PE100-NGv3-sort-7_31120227_47317818-prep-prealign.bam
[2016-04-15T00:12Z] INFO  17:12:41,979 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:12Z] INFO  17:12:41,981 HelpFormatter - Date/Time: 2016/04/14 17:12:41
[2016-04-15T00:12Z] INFO  17:12:41,982 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:12Z] INFO  17:12:41,982 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:12Z] INFO  17:12:42,099 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:12Z] INFO  17:12:42,175 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:12Z] INFO  17:12:42,194 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:12Z] INFO  17:12:42,201 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:12Z] INFO  17:12:42,202 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:12Z] INFO  17:12:42,202 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:12Z] INFO  17:12:42,203 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:12Z] INFO  17:12:42,222 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:12Z] INFO  17:12:42,296 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-15T00:12Z] INFO  17:12:42,506 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:12Z] INFO  17:12:42,509 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:12Z] INFO  17:12:42,510 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:12Z] INFO  17:12:42,511 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:12Z] INFO  17:12:42,515 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/6/R14-18106_kapa-NGv3-PE100-NGv3-sort-6_125112484_142397186-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/6/tx/tmpiwBX6s/R14-18106_kapa-NGv3-PE100-NGv3-sort-6_125112484_142397186-prep-prealign-realign.intervals -l INFO -L 6:125112485-142397186 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:12Z] INFO  17:12:42,542 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:12Z] INFO  17:12:42,543 HelpFormatter - Date/Time: 2016/04/14 17:12:42
[2016-04-15T00:12Z] INFO  17:12:42,543 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:12Z] INFO  17:12:42,544 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:12Z] INFO  17:12:42,552 ProgressMeter -            done   1.5568806E7    21.0 s       1.0 s      100.0%    21.0 s       0.0 s
[2016-04-15T00:12Z] INFO  17:12:42,553 ProgressMeter - Total runtime 21.64 secs, 0.36 min, 0.01 hours
[2016-04-15T00:12Z] INFO  17:12:42,557 MicroScheduler - 32493 reads were filtered out during the traversal out of approximately 364732 total reads (8.91%)
[2016-04-15T00:12Z] INFO  17:12:42,558 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:12Z] INFO  17:12:42,559 MicroScheduler -   -> 829 reads (0.23% of total) failing BadMateFilter
[2016-04-15T00:12Z] INFO  17:12:42,560 MicroScheduler -   -> 26555 reads (7.28% of total) failing DuplicateReadFilter
[2016-04-15T00:12Z] INFO  17:12:42,560 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:12Z] INFO  17:12:42,561 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:12Z] INFO  17:12:42,561 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:12Z] INFO  17:12:42,562 MicroScheduler -   -> 5109 reads (1.40% of total) failing MappingQualityZeroFilter
[2016-04-15T00:12Z] INFO  17:12:42,563 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:12Z] INFO  17:12:42,563 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-15T00:12Z] INFO  17:12:42,564 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:12Z] INFO  17:12:42,568 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-15T00:12Z] INFO  17:12:42,674 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:12Z] INFO  17:12:42,683 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:12Z] INFO  17:12:42,687 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:12Z] INFO  17:12:42,713 IntervalUtils - Processing 15511569 bp from intervals
[2016-04-15T00:12Z] WARN  17:12:42,719 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:12Z] INFO  17:12:42,742 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-15T00:12Z] INFO  17:12:42,756 IntervalUtils - Processing 15517948 bp from intervals
[2016-04-15T00:12Z] INFO  17:12:42,829 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:12Z] INFO  17:12:42,836 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:12Z] INFO  17:12:42,923 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T00:12Z] INFO  17:12:42,932 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:12Z] INFO  17:12:42,977 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.04
[2016-04-15T00:12Z] INFO  17:12:42,977 ProgressMeter -            done    190749.0    14.0 s      74.0 s      100.0%    14.0 s       0.0 s
[2016-04-15T00:12Z] INFO  17:12:42,977 ProgressMeter - Total runtime 14.30 secs, 0.24 min, 0.00 hours
[2016-04-15T00:12Z] INFO  17:12:42,981 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 190749 total reads (0.00%)
[2016-04-15T00:12Z] INFO  17:12:42,981 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:12Z] INFO  17:12:42,981 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:12Z] INFO  17:12:42,982 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:12Z] INFO  17:12:43,016 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:12Z] INFO  17:12:43,017 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:12Z] INFO  17:12:43,018 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:12Z] INFO  17:12:43,022 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:12Z] INFO  17:12:43,181 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:12Z] INFO  17:12:43,182 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:12Z] INFO  17:12:43,183 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:12Z] INFO  17:12:43,184 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:12Z] INFO  17:12:43,196 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:12Z] INFO  17:12:43,206 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:12Z] INFO  17:12:43,285 IntervalUtils - Processing 17284702 bp from intervals
[2016-04-15T00:12Z] WARN  17:12:43,290 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:12Z] INFO  17:12:43,329 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:12Z] INFO  17:12:43,361 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:12Z] INFO  17:12:43,372 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:12Z] INFO  17:12:43,415 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-15T00:12Z] INFO  17:12:43,481 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:12Z] INFO  17:12:43,490 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:12Z] INFO  17:12:43,537 ProgressMeter -            done   1.555287E7    18.0 s       1.0 s      100.0%    18.0 s       0.0 s
[2016-04-15T00:12Z] INFO  17:12:43,538 ProgressMeter - Total runtime 18.23 secs, 0.30 min, 0.01 hours
[2016-04-15T00:12Z] INFO  17:12:43,541 MicroScheduler - 12112 reads were filtered out during the traversal out of approximately 154084 total reads (7.86%)
[2016-04-15T00:12Z] INFO  17:12:43,542 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:12Z] INFO  17:12:43,542 MicroScheduler -   -> 555 reads (0.36% of total) failing BadMateFilter
[2016-04-15T00:12Z] INFO  17:12:43,542 MicroScheduler -   -> 11070 reads (7.18% of total) failing DuplicateReadFilter
[2016-04-15T00:12Z] INFO  17:12:43,543 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:12Z] INFO  17:12:43,543 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:12Z] INFO  17:12:43,543 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:12Z] INFO  17:12:43,543 MicroScheduler -   -> 487 reads (0.32% of total) failing MappingQualityZeroFilter
[2016-04-15T00:12Z] INFO  17:12:43,544 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:12Z] INFO  17:12:43,544 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-15T00:12Z] INFO  17:12:43,544 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:12Z] INFO  17:12:43,561 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-15T00:12Z] INFO  17:12:43,587 IntervalUtils - Processing 16197591 bp from intervals
[2016-04-15T00:12Z] INFO  17:12:43,590 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:12Z] INFO  17:12:43,602 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:12Z] INFO  17:12:43,603 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:12Z] INFO  17:12:43,603 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:12Z] INFO  17:12:43,671 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:12Z] INFO  17:12:43,935 ProgressMeter -            done    285460.0    20.0 s      71.0 s       98.0%    20.0 s       0.0 s
[2016-04-15T00:12Z] INFO  17:12:43,936 ProgressMeter - Total runtime 20.44 secs, 0.34 min, 0.01 hours
[2016-04-15T00:12Z] INFO  17:12:43,939 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 285460 total reads (0.00%)
[2016-04-15T00:12Z] INFO  17:12:43,945 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:12Z] INFO  17:12:43,946 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:12Z] INFO  17:12:43,946 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:12Z] INFO  17:12:43,989 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:12Z] INFO  17:12:43,990 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:12Z] INFO  17:12:43,991 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:12Z] INFO  17:12:43,991 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:12Z] INFO  17:12:44,005 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:12Z] INFO  17:12:44,025 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:12Z] GATK: realign ('6', 15511526, 31080332) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:12Z] INFO  17:12:44,201 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:12Z] INFO  17:12:44,603 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:12Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-6_46598699_62284307-prep.bam
[2016-04-15T00:12Z] INFO  17:12:44,870 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:12Z] GATK: realign ('6', 78400388, 93953258) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:12Z] GATK pre-alignment ('7', 47319761, 63093154) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:12Z] INFO  17:12:45,536 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:12Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-5_174919106_180915260-prep.bam
[2016-04-15T00:12Z] GATK pre-alignment ('7', 63095909, 78636522) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:12Z] INFO  17:12:47,053 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:12Z] INFO  17:12:47,056 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:12Z] INFO  17:12:47,057 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:12Z] INFO  17:12:47,058 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:12Z] INFO  17:12:47,062 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/6/R14-18106_kapa-NGv3-PE100-NGv3-sort-6_15511526_31080332-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/6/R14-18106_kapa-NGv3-PE100-NGv3-sort-6_15511526_31080332-prep-prealign-realign.intervals -L 6:15511527-31080332 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/6/tx/tmpfkbRKx/R14-18106_kapa-NGv3-PE100-NGv3-sort-6_15511526_31080332-prep.bam
[2016-04-15T00:12Z] INFO  17:12:47,084 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:12Z] INFO  17:12:47,085 HelpFormatter - Date/Time: 2016/04/14 17:12:47
[2016-04-15T00:12Z] INFO  17:12:47,085 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:12Z] INFO  17:12:47,085 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:12Z] INFO  17:12:47,289 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:12Z] INFO  17:12:47,368 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:12Z] INFO  17:12:47,378 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:12Z] INFO  17:12:47,435 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-15T00:12Z] INFO  17:12:47,600 ProgressMeter -            done   1.5511572E7    17.0 s       1.0 s      100.0%    17.0 s       0.0 s
[2016-04-15T00:12Z] INFO  17:12:47,600 ProgressMeter - Total runtime 17.32 secs, 0.29 min, 0.00 hours
[2016-04-15T00:12Z] INFO  17:12:47,604 MicroScheduler - 14162 reads were filtered out during the traversal out of approximately 178311 total reads (7.94%)
[2016-04-15T00:12Z] INFO  17:12:47,604 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:12Z] INFO  17:12:47,604 MicroScheduler -   -> 634 reads (0.36% of total) failing BadMateFilter
[2016-04-15T00:12Z] INFO  17:12:47,605 MicroScheduler -   -> 13098 reads (7.35% of total) failing DuplicateReadFilter
[2016-04-15T00:12Z] INFO  17:12:47,605 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:12Z] INFO  17:12:47,605 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:12Z] INFO  17:12:47,605 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:12Z] INFO  17:12:47,606 MicroScheduler -   -> 430 reads (0.24% of total) failing MappingQualityZeroFilter
[2016-04-15T00:12Z] INFO  17:12:47,606 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:12Z] INFO  17:12:47,606 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-15T00:12Z] INFO  17:12:47,606 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:12Z] INFO  17:12:47,826 IntervalUtils - Processing 15568806 bp from intervals
[2016-04-15T00:12Z] WARN  17:12:47,839 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:12Z] INFO  17:12:47,934 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:12Z] INFO  17:12:47,937 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:12Z] INFO  17:12:47,937 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:12Z] INFO  17:12:47,938 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:12Z] INFO  17:12:47,942 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/6/R14-18106_kapa-NGv3-PE100-NGv3-sort-6_78400388_93953258-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/6/R14-18106_kapa-NGv3-PE100-NGv3-sort-6_78400388_93953258-prep-prealign-realign.intervals -L 6:78400389-93953258 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/6/tx/tmpcuiG3f/R14-18106_kapa-NGv3-PE100-NGv3-sort-6_78400388_93953258-prep.bam
[2016-04-15T00:12Z] INFO  17:12:47,951 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:12Z] INFO  17:12:47,956 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:12Z] INFO  17:12:47,956 HelpFormatter - Date/Time: 2016/04/14 17:12:47
[2016-04-15T00:12Z] INFO  17:12:47,957 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:12Z] INFO  17:12:47,958 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:12Z] INFO  17:12:48,088 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:12Z] INFO  17:12:48,107 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:12Z] INFO  17:12:48,108 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:12Z] INFO  17:12:48,108 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:12Z] INFO  17:12:48,163 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:12Z] INFO  17:12:48,279 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:12Z] INFO  17:12:48,289 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:12Z] INFO  17:12:48,289 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:12Z] INFO  17:12:48,310 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:12Z] INFO  17:12:48,314 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:12Z] INFO  17:12:48,314 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:12Z] INFO  17:12:48,315 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:12Z] INFO  17:12:48,319 HelpFormatter - Program Args: -T PrintReads -L 7:47319762-63093154 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/7/tx/tmp7QRrvb/R14-18106_kapa-NGv3-PE100-NGv3-sort-7_47319761_63093154-prep-prealign.bam
[2016-04-15T00:12Z] INFO  17:12:48,331 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:12Z] INFO  17:12:48,334 HelpFormatter - Date/Time: 2016/04/14 17:12:48
[2016-04-15T00:12Z] INFO  17:12:48,334 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:12Z] INFO  17:12:48,334 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:12Z] INFO  17:12:48,334 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.04
[2016-04-15T00:12Z] INFO  17:12:48,459 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:12Z] INFO  17:12:48,533 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:12Z] INFO  17:12:48,713 ProgressMeter -     6:154763242    200002.0    30.0 s       2.5 m       79.4%    37.0 s       7.0 s
[2016-04-15T00:12Z] INFO  17:12:48,741 IntervalUtils - Processing 15552870 bp from intervals
[2016-04-15T00:12Z] WARN  17:12:48,759 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:12Z] INFO  17:12:48,886 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:12Z] INFO  17:12:48,979 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:12Z] GATK: realign ('6', 109467960, 124979532) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:12Z] INFO  17:12:49,034 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:12Z] INFO  17:12:49,035 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:12Z] INFO  17:12:49,036 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:12Z] INFO  17:12:49,037 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:12Z] INFO  17:12:49,121 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@7172f77a
[2016-04-15T00:12Z] INFO  17:12:49,178 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:12Z] INFO  17:12:49,333 ProgressMeter -            done    231928.0    28.0 s       2.1 m       98.7%    28.0 s       0.0 s
[2016-04-15T00:12Z] INFO  17:12:49,334 ProgressMeter - Total runtime 28.84 secs, 0.48 min, 0.01 hours
[2016-04-15T00:12Z] INFO  17:12:49,334 MicroScheduler - 169 reads were filtered out during the traversal out of approximately 232097 total reads (0.07%)
[2016-04-15T00:12Z] INFO  17:12:49,334 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:12Z] INFO  17:12:49,335 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:12Z] INFO  17:12:49,335 MicroScheduler -   -> 169 reads (0.07% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:12Z] INFO  17:12:49,338 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:12Z] INFO  17:12:49,437 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:12Z] INFO  17:12:49,440 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:12Z] INFO  17:12:49,441 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:12Z] INFO  17:12:49,441 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:12Z] INFO  17:12:49,446 HelpFormatter - Program Args: -T PrintReads -L 7:63095910-78636522 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/7/tx/tmp4FOPvZ/R14-18106_kapa-NGv3-PE100-NGv3-sort-7_63095909_78636522-prep-prealign.bam
[2016-04-15T00:12Z] INFO  17:12:49,472 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:12Z] INFO  17:12:49,472 HelpFormatter - Date/Time: 2016/04/14 17:12:49
[2016-04-15T00:12Z] INFO  17:12:49,472 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:12Z] INFO  17:12:49,472 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:12Z] INFO  17:12:49,706 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:12Z] INFO  17:12:49,802 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-15T00:12Z] INFO  17:12:49,879 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:12Z] INFO  17:12:49,889 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:12Z] INFO  17:12:49,944 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-15T00:12Z] INFO  17:12:49,960 IntervalUtils - Processing 15773393 bp from intervals
[2016-04-15T00:12Z] INFO  17:12:50,069 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:12Z] INFO  17:12:50,362 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:12Z] INFO  17:12:50,364 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:12Z] INFO  17:12:50,365 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:12Z] INFO  17:12:50,365 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:12Z] INFO  17:12:50,386 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:12Z] INFO  17:12:50,546 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:12Z] INFO  17:12:50,802 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:12Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-6_158013810_171115067-prep-prealign.bam
[2016-04-15T00:12Z] INFO  17:12:50,973 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-15T00:12Z] INFO  17:12:51,038 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:12Z] INFO  17:12:51,055 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:12Z] INFO  17:12:51,113 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-15T00:12Z] INFO  17:12:51,145 IntervalUtils - Processing 15540613 bp from intervals
[2016-04-15T00:12Z] INFO  17:12:51,261 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:12Z] INFO  17:12:51,392 ProgressMeter -            done    311876.0    21.0 s      70.0 s      100.0%    21.0 s       0.0 s
[2016-04-15T00:12Z] INFO  17:12:51,392 ProgressMeter - Total runtime 21.85 secs, 0.36 min, 0.01 hours
[2016-04-15T00:12Z] INFO  17:12:51,396 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 311876 total reads (0.00%)
[2016-04-15T00:12Z] INFO  17:12:51,396 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:12Z] INFO  17:12:51,397 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:12Z] INFO  17:12:51,397 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:12Z] INFO  17:12:51,537 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:12Z] INFO  17:12:51,538 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:12Z] INFO  17:12:51,539 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:12Z] INFO  17:12:51,540 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:12Z] INFO  17:12:51,554 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:12Z] GATK RealignerTargetCreator: R14-18106_kapa-NGv3-PE100-NGv3-sort-6_158013810_171115067-prep-prealign.bam 6:158013811-171115067
[2016-04-15T00:12Z] GATK: RealignerTargetCreator
[2016-04-15T00:12Z] INFO  17:12:51,690 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:12Z] INFO  17:12:51,799 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@32d5a4c6
[2016-04-15T00:12Z] INFO  17:12:51,946 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:12Z] INFO  17:12:51,950 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:12Z] INFO  17:12:51,950 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:12Z] INFO  17:12:51,951 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:12Z] INFO  17:12:51,955 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/6/R14-18106_kapa-NGv3-PE100-NGv3-sort-6_109467960_124979532-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/6/R14-18106_kapa-NGv3-PE100-NGv3-sort-6_109467960_124979532-prep-prealign-realign.intervals -L 6:109467961-124979532 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/6/tx/tmp85pPoi/R14-18106_kapa-NGv3-PE100-NGv3-sort-6_109467960_124979532-prep.bam
[2016-04-15T00:12Z] INFO  17:12:51,965 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:12Z] INFO  17:12:51,971 HelpFormatter - Date/Time: 2016/04/14 17:12:51
[2016-04-15T00:12Z] INFO  17:12:51,972 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:12Z] INFO  17:12:51,972 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:12Z] INFO  17:12:52,054 ProgressMeter -            done    124316.0    11.0 s      89.0 s      100.0%    11.0 s       0.0 s
[2016-04-15T00:12Z] INFO  17:12:52,054 ProgressMeter - Total runtime 11.17 secs, 0.19 min, 0.00 hours
[2016-04-15T00:12Z] INFO  17:12:52,069 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 124316 total reads (0.00%)
[2016-04-15T00:12Z] INFO  17:12:52,069 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:12Z] INFO  17:12:52,070 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:12Z] INFO  17:12:52,070 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:12Z] INFO  17:12:52,153 ProgressMeter -            done    248048.0    33.0 s       2.2 m      100.0%    33.0 s       0.0 s
[2016-04-15T00:12Z] INFO  17:12:52,154 ProgressMeter - Total runtime 33.46 secs, 0.56 min, 0.01 hours
[2016-04-15T00:12Z] INFO  17:12:52,154 MicroScheduler - 149 reads were filtered out during the traversal out of approximately 248197 total reads (0.06%)
[2016-04-15T00:12Z] INFO  17:12:52,154 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:12Z] INFO  17:12:52,155 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:12Z] INFO  17:12:52,155 MicroScheduler -   -> 149 reads (0.06% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:12Z] INFO  17:12:52,212 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:12Z] INFO  17:12:52,318 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:12Z] INFO  17:12:52,327 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:12Z] INFO  17:12:52,384 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-15T00:12Z] INFO  17:12:52,801 IntervalUtils - Processing 15511572 bp from intervals
[2016-04-15T00:12Z] WARN  17:12:52,807 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:12Z] INFO  17:12:52,876 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:12Z] INFO  17:12:52,876 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:12Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-5_143200044_158710347-prep.bam
[2016-04-15T00:12Z] INFO  17:12:52,972 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:12Z] INFO  17:12:52,974 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:12Z] INFO  17:12:52,975 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:12Z] INFO  17:12:52,975 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:12Z] INFO  17:12:53,165 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:12Z] INFO  17:12:53,361 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:12Z] INFO  17:12:53,548 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:12Z] INFO  17:12:53,561 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:12Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-6_142399691_157963777-prep-prealign.bam
[2016-04-15T00:12Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-6_62390867_78173120-prep.bam
[2016-04-15T00:12Z] INFO  17:12:53,680 ProgressMeter -            done    111089.0    10.0 s      95.0 s      100.0%    10.0 s       0.0 s
[2016-04-15T00:12Z] INFO  17:12:53,681 ProgressMeter - Total runtime 10.66 secs, 0.18 min, 0.00 hours
[2016-04-15T00:12Z] INFO  17:12:53,685 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 111089 total reads (0.00%)
[2016-04-15T00:12Z] INFO  17:12:53,697 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:12Z] INFO  17:12:53,698 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:12Z] INFO  17:12:53,698 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:12Z] GATK pre-alignment ('7', 79082334, 94740703) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:12Z] GATK pre-alignment ('7', 94750023, 110303777) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:12Z] GATK RealignerTargetCreator: R14-18106_kapa-NGv3-PE100-NGv3-sort-6_142399691_157963777-prep-prealign.bam 6:142399692-157963777
[2016-04-15T00:12Z] GATK: RealignerTargetCreator
[2016-04-15T00:12Z] INFO  17:12:54,498 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:12Z] INFO  17:12:54,501 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:12Z] INFO  17:12:54,502 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:12Z] INFO  17:12:54,502 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:12Z] INFO  17:12:54,506 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/6/R14-18106_kapa-NGv3-PE100-NGv3-sort-6_158013810_171115067-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/6/tx/tmp89rYSh/R14-18106_kapa-NGv3-PE100-NGv3-sort-6_158013810_171115067-prep-prealign-realign.intervals -l INFO -L 6:158013811-171115067 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:12Z] INFO  17:12:54,527 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:12Z] INFO  17:12:54,529 HelpFormatter - Date/Time: 2016/04/14 17:12:54
[2016-04-15T00:12Z] INFO  17:12:54,532 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:12Z] INFO  17:12:54,532 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:12Z] INFO  17:12:54,710 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:12Z] INFO  17:12:55,104 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T00:12Z] INFO  17:12:55,126 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:12Z] INFO  17:12:55,223 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.10
[2016-04-15T00:12Z] INFO  17:12:55,263 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:12Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-6_93955015_109466584-prep.bam
[2016-04-15T00:12Z] GATK pre-alignment ('7', 110526648, 126079222) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:12Z] INFO  17:12:55,640 IntervalUtils - Processing 13101257 bp from intervals
[2016-04-15T00:12Z] WARN  17:12:55,648 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:12Z] INFO  17:12:55,734 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:12Z] INFO  17:12:55,949 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:12Z] INFO  17:12:55,949 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:12Z] INFO  17:12:55,950 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:12Z] INFO  17:12:55,950 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:12Z] INFO  17:12:57,366 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:12Z] INFO  17:12:57,370 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:12Z] INFO  17:12:57,370 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:12Z] INFO  17:12:57,371 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:12Z] INFO  17:12:57,375 HelpFormatter - Program Args: -T PrintReads -L 7:79082335-94740703 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/7/tx/tmp690mee/R14-18106_kapa-NGv3-PE100-NGv3-sort-7_79082334_94740703-prep-prealign.bam
[2016-04-15T00:12Z] INFO  17:12:57,409 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:12Z] INFO  17:12:57,410 HelpFormatter - Date/Time: 2016/04/14 17:12:57
[2016-04-15T00:12Z] INFO  17:12:57,410 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:12Z] INFO  17:12:57,415 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:12Z] INFO  17:12:57,427 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:12Z] INFO  17:12:57,431 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:12Z] INFO  17:12:57,432 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:12Z] INFO  17:12:57,432 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:12Z] INFO  17:12:57,437 HelpFormatter - Program Args: -T PrintReads -L 7:94750024-110303777 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/7/tx/tmp7y9uYy/R14-18106_kapa-NGv3-PE100-NGv3-sort-7_94750023_110303777-prep-prealign.bam
[2016-04-15T00:12Z] INFO  17:12:57,447 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:12Z] INFO  17:12:57,448 HelpFormatter - Date/Time: 2016/04/14 17:12:57
[2016-04-15T00:12Z] INFO  17:12:57,449 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:12Z] INFO  17:12:57,449 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:12Z] INFO  17:12:57,517 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:12Z] INFO  17:12:57,519 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:12Z] INFO  17:12:57,519 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:12Z] INFO  17:12:57,519 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:12Z] INFO  17:12:57,523 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/6/R14-18106_kapa-NGv3-PE100-NGv3-sort-6_142399691_157963777-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/6/tx/tmpcDC1EZ/R14-18106_kapa-NGv3-PE100-NGv3-sort-6_142399691_157963777-prep-prealign-realign.intervals -l INFO -L 6:142399692-157963777 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:12Z] INFO  17:12:57,551 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:12Z] INFO  17:12:57,551 HelpFormatter - Date/Time: 2016/04/14 17:12:57
[2016-04-15T00:12Z] INFO  17:12:57,551 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:12Z] INFO  17:12:57,551 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:12Z] INFO  17:12:57,563 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:12Z] INFO  17:12:57,586 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:12Z] INFO  17:12:57,703 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:12Z] INFO  17:12:57,915 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T00:12Z] INFO  17:12:57,924 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:12Z] INFO  17:12:57,985 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-15T00:12Z] INFO  17:12:58,362 IntervalUtils - Processing 15564086 bp from intervals
[2016-04-15T00:12Z] WARN  17:12:58,367 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:12Z] INFO  17:12:58,486 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:12Z] INFO  17:12:58,714 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:12Z] INFO  17:12:58,718 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:12Z] INFO  17:12:58,717 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:12Z] INFO  17:12:58,718 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:12Z] INFO  17:12:58,719 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:12Z] INFO  17:12:58,719 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:12Z] INFO  17:12:58,719 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:12Z] INFO  17:12:58,720 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:12Z] INFO  17:12:58,723 HelpFormatter - Program Args: -T PrintReads -L 7:110526649-126079222 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/7/tx/tmpKa2uEo/R14-18106_kapa-NGv3-PE100-NGv3-sort-7_110526648_126079222-prep-prealign.bam
[2016-04-15T00:12Z] INFO  17:12:58,735 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-15T00:12Z] INFO  17:12:58,740 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:12Z] INFO  17:12:58,741 HelpFormatter - Date/Time: 2016/04/14 17:12:58
[2016-04-15T00:12Z] INFO  17:12:58,741 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:12Z] INFO  17:12:58,742 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:12Z] INFO  17:12:58,826 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:12Z] INFO  17:12:58,835 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:12Z] INFO  17:12:58,884 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-15T00:12Z] INFO  17:12:58,896 ProgressMeter -      6:43223409    700012.0    90.0 s       2.1 m       78.3%   114.0 s      24.0 s
[2016-04-15T00:12Z] INFO  17:12:58,899 IntervalUtils - Processing 15658369 bp from intervals
[2016-04-15T00:12Z] INFO  17:12:58,900 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-15T00:12Z] INFO  17:12:58,944 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:12Z] INFO  17:12:58,968 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:12Z] INFO  17:12:58,977 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:12Z] INFO  17:12:58,992 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:12Z] INFO  17:12:59,033 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-15T00:12Z] INFO  17:12:59,051 IntervalUtils - Processing 15553754 bp from intervals
[2016-04-15T00:12Z] INFO  17:12:59,121 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:12Z] INFO  17:12:59,327 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:12Z] INFO  17:12:59,328 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:12Z] INFO  17:12:59,329 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:12Z] INFO  17:12:59,329 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:12Z] INFO  17:12:59,355 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:12Z] INFO  17:12:59,495 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:12Z] INFO  17:12:59,495 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:12Z] INFO  17:12:59,496 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:12Z] INFO  17:12:59,496 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:12Z] INFO  17:12:59,526 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:12Z] INFO  17:12:59,533 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:12Z] INFO  17:12:59,683 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:13Z] INFO  17:13:00,187 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-15T00:13Z] INFO  17:13:00,273 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:13Z] INFO  17:13:00,293 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:13Z] INFO  17:13:00,344 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-15T00:13Z] INFO  17:13:00,358 IntervalUtils - Processing 15552574 bp from intervals
[2016-04-15T00:13Z] INFO  17:13:00,464 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:13Z] INFO  17:13:00,698 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:13Z] INFO  17:13:00,699 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:13Z] INFO  17:13:00,700 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:13Z] INFO  17:13:00,701 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:13Z] INFO  17:13:00,743 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:13Z] INFO  17:13:00,893 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:13Z] INFO  17:13:01,798 ProgressMeter -            done    153596.0    12.0 s      83.0 s      100.0%    12.0 s       0.0 s
[2016-04-15T00:13Z] INFO  17:13:01,800 ProgressMeter - Total runtime 12.76 secs, 0.21 min, 0.00 hours
[2016-04-15T00:13Z] INFO  17:13:01,804 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 153596 total reads (0.00%)
[2016-04-15T00:13Z] INFO  17:13:01,805 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:13Z] INFO  17:13:01,806 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:13Z] INFO  17:13:01,806 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:13Z] INFO  17:13:02,460 ProgressMeter -            done   1.7284702E7    18.0 s       1.0 s      100.0%    18.0 s       0.0 s
[2016-04-15T00:13Z] INFO  17:13:02,461 ProgressMeter - Total runtime 18.86 secs, 0.31 min, 0.01 hours
[2016-04-15T00:13Z] INFO  17:13:02,465 MicroScheduler - 24100 reads were filtered out during the traversal out of approximately 210494 total reads (11.45%)
[2016-04-15T00:13Z] INFO  17:13:02,466 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:13Z] INFO  17:13:02,466 MicroScheduler -   -> 717 reads (0.34% of total) failing BadMateFilter
[2016-04-15T00:13Z] INFO  17:13:02,467 MicroScheduler -   -> 15286 reads (7.26% of total) failing DuplicateReadFilter
[2016-04-15T00:13Z] INFO  17:13:02,467 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:13Z] INFO  17:13:02,467 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:13Z] INFO  17:13:02,467 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:13Z] INFO  17:13:02,468 MicroScheduler -   -> 8097 reads (3.85% of total) failing MappingQualityZeroFilter
[2016-04-15T00:13Z] INFO  17:13:02,468 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:13Z] INFO  17:13:02,468 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-15T00:13Z] INFO  17:13:02,468 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:13Z] INFO  17:13:03,366 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:13Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-6_78400388_93953258-prep.bam
[2016-04-15T00:13Z] INFO  17:13:03,688 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:13Z] GATK: realign ('6', 125112484, 142397186) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:13Z] INFO  17:13:03,784 ProgressMeter -       7:6475912    200003.0    30.0 s       2.5 m       41.6%    72.0 s      42.0 s
[2016-04-15T00:13Z] GATK pre-alignment ('7', 126086124, 141619620) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:13Z] INFO  17:13:05,701 ProgressMeter -            done    177620.0    12.0 s      71.0 s      100.0%    12.0 s       0.0 s
[2016-04-15T00:13Z] INFO  17:13:05,702 ProgressMeter - Total runtime 12.73 secs, 0.21 min, 0.00 hours
[2016-04-15T00:13Z] INFO  17:13:05,706 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 177620 total reads (0.00%)
[2016-04-15T00:13Z] INFO  17:13:05,706 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:13Z] INFO  17:13:05,707 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:13Z] INFO  17:13:05,707 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:13Z] INFO  17:13:06,967 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:13Z] INFO  17:13:06,981 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:13Z] INFO  17:13:06,981 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:13Z] INFO  17:13:06,978 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:13Z] INFO  17:13:06,981 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:13Z] INFO  17:13:06,981 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:13Z] INFO  17:13:06,982 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:13Z] INFO  17:13:06,981 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:13Z] INFO  17:13:06,986 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/6/R14-18106_kapa-NGv3-PE100-NGv3-sort-6_125112484_142397186-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/6/R14-18106_kapa-NGv3-PE100-NGv3-sort-6_125112484_142397186-prep-prealign-realign.intervals -L 6:125112485-142397186 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/6/tx/tmpvoNhjc/R14-18106_kapa-NGv3-PE100-NGv3-sort-6_125112484_142397186-prep.bam
[2016-04-15T00:13Z] INFO  17:13:06,986 HelpFormatter - Program Args: -T PrintReads -L 7:126086125-141619620 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/7/tx/tmp8SCvQ9/R14-18106_kapa-NGv3-PE100-NGv3-sort-7_126086124_141619620-prep-prealign.bam
[2016-04-15T00:13Z] INFO  17:13:06,999 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:13Z] INFO  17:13:06,999 HelpFormatter - Date/Time: 2016/04/14 17:13:06
[2016-04-15T00:13Z] INFO  17:13:06,999 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:13Z] INFO  17:13:07,000 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:13Z] INFO  17:13:07,000 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:13Z] INFO  17:13:07,001 HelpFormatter - Date/Time: 2016/04/14 17:13:06
[2016-04-15T00:13Z] INFO  17:13:07,001 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:13Z] INFO  17:13:07,002 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:13Z] INFO  17:13:07,160 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:13Z] INFO  17:13:07,206 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:13Z] INFO  17:13:07,247 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:13Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-6_109467960_124979532-prep.bam
[2016-04-15T00:13Z] INFO  17:13:07,340 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:13Z] INFO  17:13:07,350 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:13Z] INFO  17:13:07,400 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-15T00:13Z] INFO  17:13:07,761 IntervalUtils - Processing 17284702 bp from intervals
[2016-04-15T00:13Z] WARN  17:13:07,767 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:13Z] INFO  17:13:07,890 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:13Z] GATK pre-alignment ('7', 141629903, 157151331) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:13Z] INFO  17:13:08,044 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:13Z] INFO  17:13:08,046 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:13Z] INFO  17:13:08,046 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:13Z] INFO  17:13:08,047 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:13Z] INFO  17:13:08,198 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:13Z] INFO  17:13:08,201 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-15T00:13Z] INFO  17:13:08,296 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:13Z] INFO  17:13:08,305 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:13Z] INFO  17:13:08,356 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-15T00:13Z] INFO  17:13:08,382 IntervalUtils - Processing 15533496 bp from intervals
[2016-04-15T00:13Z] INFO  17:13:08,393 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:13Z] INFO  17:13:08,543 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:13Z] INFO  17:13:08,935 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:13Z] INFO  17:13:08,936 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:13Z] INFO  17:13:08,937 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:13Z] INFO  17:13:08,938 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:13Z] INFO  17:13:08,976 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:13Z] INFO  17:13:09,179 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:13Z] INFO  17:13:09,572 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@41fd9d8e
[2016-04-15T00:13Z] INFO  17:13:09,688 ProgressMeter -            done    195606.0    26.0 s       2.3 m      100.0%    26.0 s       0.0 s
[2016-04-15T00:13Z] INFO  17:13:09,690 ProgressMeter - Total runtime 26.51 secs, 0.44 min, 0.01 hours
[2016-04-15T00:13Z] INFO  17:13:09,691 MicroScheduler - 193 reads were filtered out during the traversal out of approximately 195799 total reads (0.10%)
[2016-04-15T00:13Z] INFO  17:13:09,691 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:13Z] INFO  17:13:09,692 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:13Z] INFO  17:13:09,693 MicroScheduler -   -> 193 reads (0.10% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:13Z] INFO  17:13:09,998 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@7172f77a
[2016-04-15T00:13Z] INFO  17:13:10,038 ProgressMeter -            done   1.5594442E7    27.0 s       1.0 s      100.0%    27.0 s       0.0 s
[2016-04-15T00:13Z] INFO  17:13:10,039 ProgressMeter - Total runtime 27.84 secs, 0.46 min, 0.01 hours
[2016-04-15T00:13Z] INFO  17:13:10,044 MicroScheduler - 71952 reads were filtered out during the traversal out of approximately 666802 total reads (10.79%)
[2016-04-15T00:13Z] INFO  17:13:10,045 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:13Z] INFO  17:13:10,045 MicroScheduler -   -> 1343 reads (0.20% of total) failing BadMateFilter
[2016-04-15T00:13Z] INFO  17:13:10,045 MicroScheduler -   -> 53681 reads (8.05% of total) failing DuplicateReadFilter
[2016-04-15T00:13Z] INFO  17:13:10,046 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:13Z] INFO  17:13:10,046 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:13Z] INFO  17:13:10,046 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:13Z] INFO  17:13:10,047 MicroScheduler -   -> 16928 reads (2.54% of total) failing MappingQualityZeroFilter
[2016-04-15T00:13Z] INFO  17:13:10,047 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:13Z] INFO  17:13:10,047 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-15T00:13Z] INFO  17:13:10,047 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:13Z] INFO  17:13:10,106 ProgressMeter -            done    842714.0   101.0 s     120.0 s      100.0%   101.0 s       0.0 s
[2016-04-15T00:13Z] INFO  17:13:10,107 ProgressMeter - Total runtime 101.31 secs, 1.69 min, 0.03 hours
[2016-04-15T00:13Z] INFO  17:13:10,108 MicroScheduler - 332 reads were filtered out during the traversal out of approximately 843046 total reads (0.04%)
[2016-04-15T00:13Z] INFO  17:13:10,109 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:13Z] INFO  17:13:10,110 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:13Z] INFO  17:13:10,111 MicroScheduler -   -> 332 reads (0.04% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:13Z] INFO  17:13:11,016 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:13Z] INFO  17:13:11,020 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:13Z] INFO  17:13:11,020 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:13Z] INFO  17:13:11,021 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:13Z] INFO  17:13:11,025 HelpFormatter - Program Args: -T PrintReads -L 7:141629904-157151331 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/7/tx/tmpj7CrBL/R14-18106_kapa-NGv3-PE100-NGv3-sort-7_141629903_157151331-prep-prealign.bam
[2016-04-15T00:13Z] INFO  17:13:11,038 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:13Z] INFO  17:13:11,039 HelpFormatter - Date/Time: 2016/04/14 17:13:11
[2016-04-15T00:13Z] INFO  17:13:11,039 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:13Z] INFO  17:13:11,039 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:13Z] INFO  17:13:11,205 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:13Z] INFO  17:13:11,210 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@7172f77a
[2016-04-15T00:13Z] INFO  17:13:11,234 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:13Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-7_15599765_31117713-prep-prealign.bam
[2016-04-15T00:13Z] INFO  17:13:11,279 ProgressMeter -            done    155153.0    20.0 s       2.2 m      100.0%    20.0 s       0.0 s
[2016-04-15T00:13Z] INFO  17:13:11,280 ProgressMeter - Total runtime 20.92 secs, 0.35 min, 0.01 hours
[2016-04-15T00:13Z] INFO  17:13:11,280 MicroScheduler - 145 reads were filtered out during the traversal out of approximately 155298 total reads (0.09%)
[2016-04-15T00:13Z] INFO  17:13:11,281 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:13Z] INFO  17:13:11,282 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:13Z] INFO  17:13:11,283 MicroScheduler -   -> 145 reads (0.09% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:13Z] INFO  17:13:11,523 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:13Z] GATK: realign ('5', 127597427, 143191869) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:13Z] INFO  17:13:11,622 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:13Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-6_31083801_46593245-prep-prealign.bam
[2016-04-15T00:13Z] GATK RealignerTargetCreator: R14-18106_kapa-NGv3-PE100-NGv3-sort-7_15599765_31117713-prep-prealign.bam 7:15599766-31117713
[2016-04-15T00:13Z] GATK: RealignerTargetCreator
[2016-04-15T00:13Z] INFO  17:13:12,377 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-15T00:13Z] INFO  17:13:12,466 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:13Z] INFO  17:13:12,476 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:13Z] INFO  17:13:12,525 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-15T00:13Z] INFO  17:13:12,544 IntervalUtils - Processing 15521428 bp from intervals
[2016-04-15T00:13Z] INFO  17:13:12,554 ProgressMeter -            done    362608.0    24.0 s      67.0 s      100.0%    24.0 s       0.0 s
[2016-04-15T00:13Z] INFO  17:13:12,554 ProgressMeter - Total runtime 24.45 secs, 0.41 min, 0.01 hours
[2016-04-15T00:13Z] INFO  17:13:12,558 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 362608 total reads (0.00%)
[2016-04-15T00:13Z] INFO  17:13:12,558 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:13Z] INFO  17:13:12,558 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:13Z] INFO  17:13:12,559 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:13Z] INFO  17:13:12,595 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:13Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-7_47319761_63093154-prep-prealign.bam
[2016-04-15T00:13Z] INFO  17:13:12,666 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:13Z] INFO  17:13:13,007 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:13Z] INFO  17:13:13,007 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:13Z] INFO  17:13:13,008 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:13Z] INFO  17:13:13,008 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:13Z] INFO  17:13:13,034 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:13Z] INFO  17:13:13,190 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:13Z] GATK RealignerTargetCreator: R14-18106_kapa-NGv3-PE100-NGv3-sort-7_47319761_63093154-prep-prealign.bam 7:47319762-63093154
[2016-04-15T00:13Z] GATK: RealignerTargetCreator
[2016-04-15T00:13Z] INFO  17:13:13,639 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@5fe152b7
[2016-04-15T00:13Z] INFO  17:13:13,782 ProgressMeter -            done    307956.0    40.0 s       2.2 m      100.0%    40.0 s       0.0 s
[2016-04-15T00:13Z] INFO  17:13:13,782 ProgressMeter - Total runtime 40.06 secs, 0.67 min, 0.01 hours
[2016-04-15T00:13Z] INFO  17:13:13,783 MicroScheduler - 237 reads were filtered out during the traversal out of approximately 308193 total reads (0.08%)
[2016-04-15T00:13Z] INFO  17:13:13,783 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:13Z] INFO  17:13:13,783 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:13Z] INFO  17:13:13,784 MicroScheduler -   -> 237 reads (0.08% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:13Z] INFO  17:13:13,828 ProgressMeter -            done   1.3101257E7    17.0 s       1.0 s      100.0%    17.0 s       0.0 s
[2016-04-15T00:13Z] INFO  17:13:13,829 ProgressMeter - Total runtime 17.88 secs, 0.30 min, 0.00 hours
[2016-04-15T00:13Z] INFO  17:13:13,834 MicroScheduler - 29429 reads were filtered out during the traversal out of approximately 233849 total reads (12.58%)
[2016-04-15T00:13Z] INFO  17:13:13,835 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:13Z] INFO  17:13:13,836 MicroScheduler -   -> 659 reads (0.28% of total) failing BadMateFilter
[2016-04-15T00:13Z] INFO  17:13:13,836 MicroScheduler -   -> 16742 reads (7.16% of total) failing DuplicateReadFilter
[2016-04-15T00:13Z] INFO  17:13:13,836 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:13Z] INFO  17:13:13,836 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:13Z] INFO  17:13:13,837 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:13Z] INFO  17:13:13,837 MicroScheduler -   -> 12028 reads (5.14% of total) failing MappingQualityZeroFilter
[2016-04-15T00:13Z] INFO  17:13:13,837 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:13Z] INFO  17:13:13,838 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-15T00:13Z] INFO  17:13:13,838 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:13Z] INFO  17:13:13,985 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:13Z] INFO  17:13:14,008 ProgressMeter -      7:45128476    200002.0    30.0 s       2.5 m       86.5%    34.0 s       4.0 s
[2016-04-15T00:13Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-6_15511526_31080332-prep.bam
[2016-04-15T00:13Z] GATK RealignerTargetCreator: R14-18106_kapa-NGv3-PE100-NGv3-sort-6_31083801_46593245-prep-prealign.bam 6:31083802-46593245
[2016-04-15T00:13Z] GATK: RealignerTargetCreator
[2016-04-15T00:13Z] INFO  17:13:14,520 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:13Z] INFO  17:13:14,524 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:13Z] INFO  17:13:14,524 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:13Z] INFO  17:13:14,525 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:13Z] INFO  17:13:14,531 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/5/R14-18106_kapa-NGv3-PE100-NGv3-sort-5_127597427_143191869-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/5/R14-18106_kapa-NGv3-PE100-NGv3-sort-5_127597427_143191869-prep-prealign-realign.intervals -L 5:127597428-143191869 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/5/tx/tmpy7yzHY/R14-18106_kapa-NGv3-PE100-NGv3-sort-5_127597427_143191869-prep.bam
[2016-04-15T00:13Z] INFO  17:13:14,545 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:13Z] INFO  17:13:14,549 HelpFormatter - Date/Time: 2016/04/14 17:13:14
[2016-04-15T00:13Z] INFO  17:13:14,566 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:13Z] INFO  17:13:14,567 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:13Z] INFO  17:13:14,796 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:13Z] INFO  17:13:14,949 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:13Z] INFO  17:13:14,954 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:13Z] INFO  17:13:14,967 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:13Z] INFO  17:13:14,968 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:13Z] INFO  17:13:14,969 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:13Z] INFO  17:13:14,974 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/7/R14-18106_kapa-NGv3-PE100-NGv3-sort-7_15599765_31117713-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/7/tx/tmp7deoIg/R14-18106_kapa-NGv3-PE100-NGv3-sort-7_15599765_31117713-prep-prealign-realign.intervals -l INFO -L 7:15599766-31117713 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:13Z] INFO  17:13:14,988 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:13Z] INFO  17:13:15,008 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:13Z] INFO  17:13:15,009 HelpFormatter - Date/Time: 2016/04/14 17:13:14
[2016-04-15T00:13Z] INFO  17:13:15,009 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:13Z] INFO  17:13:15,010 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:13Z] INFO  17:13:15,044 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-15T00:13Z] INFO  17:13:15,135 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:13Z] INFO  17:13:15,201 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:13Z] GATK pre-alignment ('7', 157155854, 159138663) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:13Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-7_0_15584548-prep-prealign.bam
[2016-04-15T00:13Z] INFO  17:13:15,361 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T00:13Z] INFO  17:13:15,370 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:13Z] INFO  17:13:15,374 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:13Z] GATK: realign ('6', 158013810, 171115067) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:13Z] INFO  17:13:15,404 IntervalUtils - Processing 15594442 bp from intervals
[2016-04-15T00:13Z] WARN  17:13:15,421 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:13Z] INFO  17:13:15,440 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-15T00:13Z] INFO  17:13:15,500 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:13Z] INFO  17:13:15,692 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:13Z] INFO  17:13:15,693 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:13Z] INFO  17:13:15,694 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:13Z] INFO  17:13:15,695 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:13Z] INFO  17:13:15,734 IntervalUtils - Processing 15517948 bp from intervals
[2016-04-15T00:13Z] WARN  17:13:15,739 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:13Z] INFO  17:13:15,806 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@5fe152b7
[2016-04-15T00:13Z] INFO  17:13:15,813 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:13Z] INFO  17:13:15,871 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:13Z] INFO  17:13:15,954 ProgressMeter -            done    251259.0    31.0 s       2.1 m      100.0%    31.0 s       0.0 s
[2016-04-15T00:13Z] INFO  17:13:15,956 ProgressMeter - Total runtime 31.97 secs, 0.53 min, 0.01 hours
[2016-04-15T00:13Z] INFO  17:13:15,956 MicroScheduler - 192 reads were filtered out during the traversal out of approximately 251451 total reads (0.08%)
[2016-04-15T00:13Z] INFO  17:13:15,957 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:13Z] INFO  17:13:15,958 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:13Z] INFO  17:13:15,958 MicroScheduler -   -> 192 reads (0.08% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:13Z] INFO  17:13:16,019 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:13Z] INFO  17:13:16,060 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:13Z] INFO  17:13:16,061 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:13Z] INFO  17:13:16,062 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:13Z] INFO  17:13:16,063 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:13Z] INFO  17:13:16,095 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:13Z] INFO  17:13:16,098 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:13Z] INFO  17:13:16,099 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:13Z] INFO  17:13:16,099 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:13Z] INFO  17:13:16,104 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/7/R14-18106_kapa-NGv3-PE100-NGv3-sort-7_47319761_63093154-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/7/tx/tmpz03CPo/R14-18106_kapa-NGv3-PE100-NGv3-sort-7_47319761_63093154-prep-prealign-realign.intervals -l INFO -L 7:47319762-63093154 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:13Z] GATK RealignerTargetCreator: R14-18106_kapa-NGv3-PE100-NGv3-sort-7_0_15584548-prep-prealign.bam 7:1-15584548
[2016-04-15T00:13Z] GATK: RealignerTargetCreator
[2016-04-15T00:13Z] INFO  17:13:16,137 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:13Z] INFO  17:13:16,138 HelpFormatter - Date/Time: 2016/04/14 17:13:16
[2016-04-15T00:13Z] INFO  17:13:16,139 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:13Z] INFO  17:13:16,139 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:13Z] INFO  17:13:16,234 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:13Z] INFO  17:13:16,447 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T00:13Z] INFO  17:13:16,478 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:13Z] INFO  17:13:16,536 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-15T00:13Z] INFO  17:13:16,727 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@5fe152b7
[2016-04-15T00:13Z] INFO  17:13:16,874 ProgressMeter -            done    115410.0    16.0 s       2.3 m      100.0%    16.0 s       0.0 s
[2016-04-15T00:13Z] INFO  17:13:16,874 ProgressMeter - Total runtime 16.18 secs, 0.27 min, 0.00 hours
[2016-04-15T00:13Z] INFO  17:13:16,875 MicroScheduler - 108 reads were filtered out during the traversal out of approximately 115518 total reads (0.09%)
[2016-04-15T00:13Z] INFO  17:13:16,875 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:13Z] INFO  17:13:16,875 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:13Z] INFO  17:13:16,876 MicroScheduler -   -> 108 reads (0.09% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:13Z] INFO  17:13:16,880 IntervalUtils - Processing 15773393 bp from intervals
[2016-04-15T00:13Z] WARN  17:13:16,886 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:13Z] INFO  17:13:16,973 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:13Z] INFO  17:13:16,990 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:13Z] INFO  17:13:16,993 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:13Z] INFO  17:13:16,994 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:13Z] INFO  17:13:16,994 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:13Z] INFO  17:13:16,998 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/6/R14-18106_kapa-NGv3-PE100-NGv3-sort-6_31083801_46593245-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/6/tx/tmpML0XqX/R14-18106_kapa-NGv3-PE100-NGv3-sort-6_31083801_46593245-prep-prealign-realign.intervals -l INFO -L 6:31083802-46593245 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:13Z] INFO  17:13:17,029 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:13Z] INFO  17:13:17,038 HelpFormatter - Date/Time: 2016/04/14 17:13:16
[2016-04-15T00:13Z] INFO  17:13:17,039 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:13Z] INFO  17:13:17,039 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:13Z] INFO  17:13:17,186 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:13Z] INFO  17:13:17,314 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:13Z] INFO  17:13:17,345 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:13Z] INFO  17:13:17,347 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:13Z] INFO  17:13:17,348 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:13Z] INFO  17:13:17,392 ProgressMeter -            done   1.5564086E7    18.0 s       1.0 s      100.0%    18.0 s       0.0 s
[2016-04-15T00:13Z] INFO  17:13:17,392 ProgressMeter - Total runtime 18.67 secs, 0.31 min, 0.01 hours
[2016-04-15T00:13Z] INFO  17:13:17,397 MicroScheduler - 21887 reads were filtered out during the traversal out of approximately 249791 total reads (8.76%)
[2016-04-15T00:13Z] INFO  17:13:17,397 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:13Z] INFO  17:13:17,397 MicroScheduler -   -> 725 reads (0.29% of total) failing BadMateFilter
[2016-04-15T00:13Z] INFO  17:13:17,398 MicroScheduler -   -> 18434 reads (7.38% of total) failing DuplicateReadFilter
[2016-04-15T00:13Z] INFO  17:13:17,398 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:13Z] INFO  17:13:17,398 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:13Z] INFO  17:13:17,399 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:13Z] INFO  17:13:17,399 MicroScheduler -   -> 2728 reads (1.09% of total) failing MappingQualityZeroFilter
[2016-04-15T00:13Z] INFO  17:13:17,399 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:13Z] INFO  17:13:17,399 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-15T00:13Z] INFO  17:13:17,400 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:13Z] INFO  17:13:17,400 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:13Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-7_31120227_47317818-prep-prealign.bam
[2016-04-15T00:13Z] INFO  17:13:17,470 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T00:13Z] INFO  17:13:17,482 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:13Z] INFO  17:13:17,541 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-15T00:13Z] INFO  17:13:17,819 IntervalUtils - Processing 15509444 bp from intervals
[2016-04-15T00:13Z] WARN  17:13:17,825 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:13Z] INFO  17:13:17,900 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:13Z] INFO  17:13:18,188 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:13Z] INFO  17:13:18,189 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:13Z] INFO  17:13:18,190 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:13Z] INFO  17:13:18,190 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:13Z] GATK RealignerTargetCreator: R14-18106_kapa-NGv3-PE100-NGv3-sort-7_31120227_47317818-prep-prealign.bam 7:31120228-47317818
[2016-04-15T00:13Z] GATK: RealignerTargetCreator
[2016-04-15T00:13Z] INFO  17:13:18,602 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:13Z] INFO  17:13:18,606 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:13Z] INFO  17:13:18,606 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:13Z] INFO  17:13:18,607 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:13Z] INFO  17:13:18,612 HelpFormatter - Program Args: -T PrintReads -L 7:157155855-159138663 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/7/tx/tmptwzMMx/R14-18106_kapa-NGv3-PE100-NGv3-sort-7_157155854_159138663-prep-prealign.bam
[2016-04-15T00:13Z] INFO  17:13:18,646 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:13Z] INFO  17:13:18,656 HelpFormatter - Date/Time: 2016/04/14 17:13:18
[2016-04-15T00:13Z] INFO  17:13:18,657 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:13Z] INFO  17:13:18,658 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:13Z] INFO  17:13:18,658 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:13Z] INFO  17:13:18,661 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:13Z] INFO  17:13:18,664 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:13Z] INFO  17:13:18,665 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:13Z] INFO  17:13:18,665 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:13Z] INFO  17:13:18,670 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/6/R14-18106_kapa-NGv3-PE100-NGv3-sort-6_158013810_171115067-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/6/R14-18106_kapa-NGv3-PE100-NGv3-sort-6_158013810_171115067-prep-prealign-realign.intervals -L 6:158013811-171115067 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/6/tx/tmpfEcwe_/R14-18106_kapa-NGv3-PE100-NGv3-sort-6_158013810_171115067-prep.bam
[2016-04-15T00:13Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-7_110526648_126079222-prep-prealign.bam
[2016-04-15T00:13Z] INFO  17:13:18,701 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:13Z] INFO  17:13:18,707 HelpFormatter - Date/Time: 2016/04/14 17:13:18
[2016-04-15T00:13Z] INFO  17:13:18,708 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:13Z] INFO  17:13:18,709 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:13Z] INFO  17:13:18,837 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:13Z] INFO  17:13:18,919 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:13Z] INFO  17:13:19,063 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:13Z] INFO  17:13:19,067 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:13Z] INFO  17:13:19,071 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:13Z] GATK: realign ('6', 142399691, 157963777) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:13Z] INFO  17:13:19,143 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-15T00:13Z] GATK RealignerTargetCreator: R14-18106_kapa-NGv3-PE100-NGv3-sort-7_110526648_126079222-prep-prealign.bam 7:110526649-126079222
[2016-04-15T00:13Z] GATK: RealignerTargetCreator
[2016-04-15T00:13Z] INFO  17:13:19,352 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:13Z] INFO  17:13:19,355 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:13Z] INFO  17:13:19,356 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:13Z] INFO  17:13:19,356 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:13Z] INFO  17:13:19,361 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/7/R14-18106_kapa-NGv3-PE100-NGv3-sort-7_0_15584548-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/7/tx/tmpf3omyN/R14-18106_kapa-NGv3-PE100-NGv3-sort-7_0_15584548-prep-prealign-realign.intervals -l INFO -L 7:1-15584548 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:13Z] INFO  17:13:19,393 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:13Z] INFO  17:13:19,394 HelpFormatter - Date/Time: 2016/04/14 17:13:19
[2016-04-15T00:13Z] INFO  17:13:19,395 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:13Z] INFO  17:13:19,395 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:13Z] INFO  17:13:19,506 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:13Z] INFO  17:13:19,668 IntervalUtils - Processing 13101257 bp from intervals
[2016-04-15T00:13Z] WARN  17:13:19,674 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:13Z] INFO  17:13:19,748 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:13Z] INFO  17:13:19,811 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T00:13Z] INFO  17:13:19,820 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:13Z] INFO  17:13:19,888 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:13Z] INFO  17:13:19,889 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:13Z] INFO  17:13:19,889 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:13Z] INFO  17:13:19,890 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:13Z] INFO  17:13:19,890 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-15T00:13Z] INFO  17:13:20,044 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-15T00:13Z] INFO  17:13:20,080 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:13Z] INFO  17:13:20,109 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:13Z] INFO  17:13:20,118 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:13Z] INFO  17:13:20,172 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-15T00:13Z] INFO  17:13:20,185 IntervalUtils - Processing 1982809 bp from intervals
[2016-04-15T00:13Z] INFO  17:13:20,242 IntervalUtils - Processing 15584548 bp from intervals
[2016-04-15T00:13Z] WARN  17:13:20,247 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:13Z] INFO  17:13:20,256 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:13Z] INFO  17:13:20,258 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:13Z] INFO  17:13:20,340 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:13Z] INFO  17:13:20,591 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:13Z] INFO  17:13:20,592 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:13Z] INFO  17:13:20,593 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:13Z] INFO  17:13:20,593 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:13Z] INFO  17:13:20,625 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:13Z] INFO  17:13:20,637 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:13Z] INFO  17:13:20,638 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:13Z] INFO  17:13:20,639 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:13Z] INFO  17:13:20,639 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:13Z] INFO  17:13:20,647 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:13Z] INFO  17:13:20,816 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@32d5a4c6
[2016-04-15T00:13Z] INFO  17:13:20,928 ProgressMeter -            done    169165.0    21.0 s       2.1 m      100.0%    21.0 s       0.0 s
[2016-04-15T00:13Z] INFO  17:13:20,936 ProgressMeter - Total runtime 21.61 secs, 0.36 min, 0.01 hours
[2016-04-15T00:13Z] INFO  17:13:20,936 MicroScheduler - 126 reads were filtered out during the traversal out of approximately 169291 total reads (0.07%)
[2016-04-15T00:13Z] INFO  17:13:20,936 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:13Z] INFO  17:13:20,937 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:13Z] INFO  17:13:20,937 MicroScheduler -   -> 126 reads (0.07% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:13Z] INFO  17:13:20,994 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:13Z] INFO  17:13:20,996 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:13Z] INFO  17:13:20,997 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:13Z] INFO  17:13:20,997 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:13Z] INFO  17:13:21,012 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/7/R14-18106_kapa-NGv3-PE100-NGv3-sort-7_31120227_47317818-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/7/tx/tmpAtWqyc/R14-18106_kapa-NGv3-PE100-NGv3-sort-7_31120227_47317818-prep-prealign-realign.intervals -l INFO -L 7:31120228-47317818 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:13Z] INFO  17:13:21,027 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:13Z] INFO  17:13:21,027 HelpFormatter - Date/Time: 2016/04/14 17:13:20
[2016-04-15T00:13Z] INFO  17:13:21,028 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:13Z] INFO  17:13:21,028 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:13Z] INFO  17:13:21,146 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:13Z] INFO  17:13:21,384 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T00:13Z] INFO  17:13:21,393 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:13Z] INFO  17:13:21,486 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.09
[2016-04-15T00:13Z] INFO  17:13:21,909 IntervalUtils - Processing 16197591 bp from intervals
[2016-04-15T00:13Z] WARN  17:13:21,914 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:13Z] INFO  17:13:22,021 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:13Z] INFO  17:13:22,105 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:13Z] INFO  17:13:22,108 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:13Z] INFO  17:13:22,109 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:13Z] INFO  17:13:22,109 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:13Z] INFO  17:13:22,113 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/6/R14-18106_kapa-NGv3-PE100-NGv3-sort-6_142399691_157963777-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/6/R14-18106_kapa-NGv3-PE100-NGv3-sort-6_142399691_157963777-prep-prealign-realign.intervals -L 6:142399692-157963777 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/6/tx/tmpga0Hb1/R14-18106_kapa-NGv3-PE100-NGv3-sort-6_142399691_157963777-prep.bam
[2016-04-15T00:13Z] INFO  17:13:22,123 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:13Z] INFO  17:13:22,123 HelpFormatter - Date/Time: 2016/04/14 17:13:22
[2016-04-15T00:13Z] INFO  17:13:22,123 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:13Z] INFO  17:13:22,124 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:13Z] INFO  17:13:22,255 ProgressMeter -      7:73634614    200003.0    30.0 s       2.6 m       67.8%    44.0 s      14.0 s
[2016-04-15T00:13Z] INFO  17:13:22,333 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:13Z] INFO  17:13:22,333 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:13Z] INFO  17:13:22,334 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:13Z] INFO  17:13:22,334 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:13Z] INFO  17:13:22,391 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:13Z] INFO  17:13:22,482 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:13Z] INFO  17:13:22,491 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:13Z] INFO  17:13:22,535 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.04
[2016-04-15T00:13Z] INFO  17:13:22,593 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:13Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-7_79082334_94740703-prep-prealign.bam
[2016-04-15T00:13Z] INFO  17:13:22,628 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:13Z] INFO  17:13:22,641 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:13Z] INFO  17:13:22,642 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:13Z] INFO  17:13:22,642 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:13Z] INFO  17:13:22,646 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/7/R14-18106_kapa-NGv3-PE100-NGv3-sort-7_110526648_126079222-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/7/tx/tmpXR546g/R14-18106_kapa-NGv3-PE100-NGv3-sort-7_110526648_126079222-prep-prealign-realign.intervals -l INFO -L 7:110526649-126079222 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:13Z] INFO  17:13:22,660 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:13Z] INFO  17:13:22,663 HelpFormatter - Date/Time: 2016/04/14 17:13:22
[2016-04-15T00:13Z] INFO  17:13:22,664 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:13Z] INFO  17:13:22,664 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:13Z] INFO  17:13:22,772 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:13Z] INFO  17:13:22,923 IntervalUtils - Processing 15564086 bp from intervals
[2016-04-15T00:13Z] WARN  17:13:22,928 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:13Z] INFO  17:13:23,003 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:13Z] INFO  17:13:23,021 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T00:13Z] INFO  17:13:23,041 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:13Z] INFO  17:13:23,114 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:13Z] INFO  17:13:23,115 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:13Z] INFO  17:13:23,115 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:13Z] INFO  17:13:23,116 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:13Z] INFO  17:13:23,125 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-15T00:13Z] GATK RealignerTargetCreator: R14-18106_kapa-NGv3-PE100-NGv3-sort-7_79082334_94740703-prep-prealign.bam 7:79082335-94740703
[2016-04-15T00:13Z] GATK: RealignerTargetCreator
[2016-04-15T00:13Z] INFO  17:13:23,294 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:13Z] INFO  17:13:23,454 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:13Z] INFO  17:13:23,589 IntervalUtils - Processing 15552574 bp from intervals
[2016-04-15T00:13Z] WARN  17:13:23,601 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:13Z] INFO  17:13:23,688 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:13Z] INFO  17:13:23,863 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:13Z] INFO  17:13:23,864 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:13Z] INFO  17:13:23,865 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:13Z] INFO  17:13:23,865 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:13Z] INFO  17:13:26,068 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:13Z] INFO  17:13:26,071 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:13Z] INFO  17:13:26,071 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:13Z] INFO  17:13:26,071 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:13Z] INFO  17:13:26,085 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/7/R14-18106_kapa-NGv3-PE100-NGv3-sort-7_79082334_94740703-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/7/tx/tmpftrO4Z/R14-18106_kapa-NGv3-PE100-NGv3-sort-7_79082334_94740703-prep-prealign-realign.intervals -l INFO -L 7:79082335-94740703 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:13Z] INFO  17:13:26,099 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:13Z] INFO  17:13:26,100 HelpFormatter - Date/Time: 2016/04/14 17:13:26
[2016-04-15T00:13Z] INFO  17:13:26,101 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:13Z] INFO  17:13:26,101 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:13Z] INFO  17:13:26,198 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:13Z] INFO  17:13:26,456 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T00:13Z] INFO  17:13:26,467 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:13Z] INFO  17:13:26,470 ProgressMeter -            done    208566.0    18.0 s      88.0 s      100.0%    18.0 s       0.0 s
[2016-04-15T00:13Z] INFO  17:13:26,471 ProgressMeter - Total runtime 18.43 secs, 0.31 min, 0.01 hours
[2016-04-15T00:13Z] INFO  17:13:26,474 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 208566 total reads (0.00%)
[2016-04-15T00:13Z] INFO  17:13:26,475 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:13Z] INFO  17:13:26,476 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:13Z] INFO  17:13:26,476 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:13Z] INFO  17:13:26,518 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-15T00:13Z] INFO  17:13:26,619 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@32d5a4c6
[2016-04-15T00:13Z] INFO  17:13:26,757 ProgressMeter -            done     27833.0     6.0 s       3.7 m       94.3%     6.0 s       0.0 s
[2016-04-15T00:13Z] INFO  17:13:26,758 ProgressMeter - Total runtime 6.17 secs, 0.10 min, 0.00 hours
[2016-04-15T00:13Z] INFO  17:13:26,759 MicroScheduler - 25 reads were filtered out during the traversal out of approximately 27858 total reads (0.09%)
[2016-04-15T00:13Z] INFO  17:13:26,760 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:13Z] INFO  17:13:26,761 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:13Z] INFO  17:13:26,761 MicroScheduler -   -> 25 reads (0.09% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:13Z] INFO  17:13:26,796 IntervalUtils - Processing 15658369 bp from intervals
[2016-04-15T00:13Z] WARN  17:13:26,802 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:13Z] INFO  17:13:26,897 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:13Z] INFO  17:13:27,100 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:13Z] INFO  17:13:27,102 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:13Z] INFO  17:13:27,102 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:13Z] INFO  17:13:27,103 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:13Z] INFO  17:13:27,931 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:13Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-6_125112484_142397186-prep.bam
[2016-04-15T00:13Z] INFO  17:13:28,064 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:13Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-7_157155854_159138663-prep-prealign.bam
[2016-04-15T00:13Z] GATK RealignerTargetCreator: R14-18106_kapa-NGv3-PE100-NGv3-sort-7_157155854_159138663-prep-prealign.bam 7:157155855-159138663
[2016-04-15T00:13Z] GATK: RealignerTargetCreator
[2016-04-15T00:13Z] GATK pre-alignment ('8', 0, 15517156) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:13Z] INFO  17:13:29,552 ProgressMeter -      7:99972009    100003.0    30.0 s       5.0 m       33.6%    89.0 s      59.0 s
[2016-04-15T00:13Z] INFO  17:13:31,020 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:13Z] INFO  17:13:31,034 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:13Z] INFO  17:13:31,034 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:13Z] INFO  17:13:31,035 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:13Z] INFO  17:13:31,042 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/7/R14-18106_kapa-NGv3-PE100-NGv3-sort-7_157155854_159138663-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/7/tx/tmpwddSwT/R14-18106_kapa-NGv3-PE100-NGv3-sort-7_157155854_159138663-prep-prealign-realign.intervals -l INFO -L 7:157155855-159138663 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:13Z] INFO  17:13:31,051 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:13Z] INFO  17:13:31,051 HelpFormatter - Date/Time: 2016/04/14 17:13:31
[2016-04-15T00:13Z] INFO  17:13:31,051 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:13Z] INFO  17:13:31,052 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:13Z] INFO  17:13:31,193 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:13Z] INFO  17:13:31,413 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T00:13Z] INFO  17:13:31,423 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:13Z] INFO  17:13:31,485 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-15T00:13Z] INFO  17:13:31,574 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:13Z] INFO  17:13:31,577 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:13Z] INFO  17:13:31,578 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:13Z] INFO  17:13:31,579 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:13Z] INFO  17:13:31,583 HelpFormatter - Program Args: -T PrintReads -L 8:1-15517156 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/8/tx/tmpSAEbmW/R14-18106_kapa-NGv3-PE100-NGv3-sort-8_0_15517156-prep-prealign.bam
[2016-04-15T00:13Z] INFO  17:13:31,602 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:13Z] INFO  17:13:31,603 HelpFormatter - Date/Time: 2016/04/14 17:13:31
[2016-04-15T00:13Z] INFO  17:13:31,603 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:13Z] INFO  17:13:31,603 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:13Z] INFO  17:13:31,760 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:13Z] INFO  17:13:31,773 IntervalUtils - Processing 1982809 bp from intervals
[2016-04-15T00:13Z] WARN  17:13:31,779 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:13Z] INFO  17:13:31,861 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:13Z] INFO  17:13:31,994 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:13Z] INFO  17:13:31,995 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:13Z] INFO  17:13:31,995 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:13Z] INFO  17:13:31,996 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:13Z] INFO  17:13:32,807 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-15T00:13Z] INFO  17:13:32,884 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:13Z] INFO  17:13:32,903 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:13Z] INFO  17:13:32,962 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-15T00:13Z] INFO  17:13:32,977 IntervalUtils - Processing 15517156 bp from intervals
[2016-04-15T00:13Z] INFO  17:13:33,093 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:13Z] INFO  17:13:33,373 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:13Z] INFO  17:13:33,375 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:13Z] INFO  17:13:33,375 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:13Z] INFO  17:13:33,376 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:13Z] INFO  17:13:33,392 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:13Z] INFO  17:13:33,567 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:13Z] INFO  17:13:34,020 ProgressMeter -            done   1.5773393E7    16.0 s       1.0 s      100.0%    16.0 s       0.0 s
[2016-04-15T00:13Z] INFO  17:13:34,021 ProgressMeter - Total runtime 16.68 secs, 0.28 min, 0.00 hours
[2016-04-15T00:13Z] INFO  17:13:34,026 MicroScheduler - 27849 reads were filtered out during the traversal out of approximately 155747 total reads (17.88%)
[2016-04-15T00:13Z] INFO  17:13:34,028 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:13Z] INFO  17:13:34,028 MicroScheduler -   -> 557 reads (0.36% of total) failing BadMateFilter
[2016-04-15T00:13Z] INFO  17:13:34,028 MicroScheduler -   -> 10187 reads (6.54% of total) failing DuplicateReadFilter
[2016-04-15T00:13Z] INFO  17:13:34,029 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:13Z] INFO  17:13:34,029 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:13Z] INFO  17:13:34,029 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:13Z] INFO  17:13:34,030 MicroScheduler -   -> 17105 reads (10.98% of total) failing MappingQualityZeroFilter
[2016-04-15T00:13Z] INFO  17:13:34,030 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:13Z] INFO  17:13:34,030 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-15T00:13Z] INFO  17:13:34,030 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:13Z] INFO  17:13:35,169 ProgressMeter -            done   1.5517948E7    19.0 s       1.0 s      100.0%    19.0 s       0.0 s
[2016-04-15T00:13Z] INFO  17:13:35,170 ProgressMeter - Total runtime 19.11 secs, 0.32 min, 0.01 hours
[2016-04-15T00:13Z] INFO  17:13:35,173 MicroScheduler - 16187 reads were filtered out during the traversal out of approximately 196633 total reads (8.23%)
[2016-04-15T00:13Z] INFO  17:13:35,174 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:13Z] INFO  17:13:35,174 MicroScheduler -   -> 723 reads (0.37% of total) failing BadMateFilter
[2016-04-15T00:13Z] INFO  17:13:35,174 MicroScheduler -   -> 14195 reads (7.22% of total) failing DuplicateReadFilter
[2016-04-15T00:13Z] INFO  17:13:35,175 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:13Z] INFO  17:13:35,175 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:13Z] INFO  17:13:35,175 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:13Z] INFO  17:13:35,175 MicroScheduler -   -> 1269 reads (0.65% of total) failing MappingQualityZeroFilter
[2016-04-15T00:13Z] INFO  17:13:35,176 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:13Z] INFO  17:13:35,176 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-15T00:13Z] INFO  17:13:35,176 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:13Z] INFO  17:13:35,567 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:13Z] GATK: realign ('7', 47319761, 63093154) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:13Z] INFO  17:13:36,523 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:13Z] GATK: realign ('7', 15599765, 31117713) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:13Z] INFO  17:13:36,611 ProgressMeter -            done   1982809.0     4.0 s       2.0 s      100.0%     4.0 s       0.0 s
[2016-04-15T00:13Z] INFO  17:13:36,612 ProgressMeter - Total runtime 4.62 secs, 0.08 min, 0.00 hours
[2016-04-15T00:13Z] INFO  17:13:36,616 MicroScheduler - 2542 reads were filtered out during the traversal out of approximately 27981 total reads (9.08%)
[2016-04-15T00:13Z] INFO  17:13:36,618 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:13Z] INFO  17:13:36,618 MicroScheduler -   -> 120 reads (0.43% of total) failing BadMateFilter
[2016-04-15T00:13Z] INFO  17:13:36,619 MicroScheduler -   -> 2179 reads (7.79% of total) failing DuplicateReadFilter
[2016-04-15T00:13Z] INFO  17:13:36,620 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:13Z] INFO  17:13:36,621 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:13Z] INFO  17:13:36,621 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:13Z] INFO  17:13:36,622 MicroScheduler -   -> 243 reads (0.87% of total) failing MappingQualityZeroFilter
[2016-04-15T00:13Z] INFO  17:13:36,622 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:13Z] INFO  17:13:36,623 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-15T00:13Z] INFO  17:13:36,623 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:13Z] INFO  17:13:37,469 ProgressMeter -            done    231928.0    17.0 s      75.0 s       98.7%    17.0 s       0.0 s
[2016-04-15T00:13Z] INFO  17:13:37,469 ProgressMeter - Total runtime 17.58 secs, 0.29 min, 0.00 hours
[2016-04-15T00:13Z] INFO  17:13:37,473 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 231928 total reads (0.00%)
[2016-04-15T00:13Z] INFO  17:13:37,473 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:13Z] INFO  17:13:37,474 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:13Z] INFO  17:13:37,474 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:13Z] INFO  17:13:38,090 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:13Z] GATK: realign ('7', 157155854, 159138663) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:13Z] INFO  17:13:38,367 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:13Z] INFO  17:13:38,371 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:13Z] INFO  17:13:38,372 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:13Z] INFO  17:13:38,373 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:13Z] INFO  17:13:38,378 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/7/R14-18106_kapa-NGv3-PE100-NGv3-sort-7_47319761_63093154-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/7/R14-18106_kapa-NGv3-PE100-NGv3-sort-7_47319761_63093154-prep-prealign-realign.intervals -L 7:47319762-63093154 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/7/tx/tmpvhMViz/R14-18106_kapa-NGv3-PE100-NGv3-sort-7_47319761_63093154-prep.bam
[2016-04-15T00:13Z] INFO  17:13:38,389 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:13Z] INFO  17:13:38,389 HelpFormatter - Date/Time: 2016/04/14 17:13:38
[2016-04-15T00:13Z] INFO  17:13:38,389 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:13Z] INFO  17:13:38,390 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:13Z] INFO  17:13:38,622 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:13Z] INFO  17:13:38,720 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:13Z] INFO  17:13:38,729 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:13Z] INFO  17:13:38,775 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@7172f77a
[2016-04-15T00:13Z] INFO  17:13:38,792 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-15T00:13Z] INFO  17:13:38,931 ProgressMeter -            done   1.5584548E7    18.0 s       1.0 s      100.0%    18.0 s       0.0 s
[2016-04-15T00:13Z] INFO  17:13:38,931 ProgressMeter - Total runtime 18.29 secs, 0.30 min, 0.01 hours
[2016-04-15T00:13Z] INFO  17:13:38,935 MicroScheduler - 39704 reads were filtered out during the traversal out of approximately 309815 total reads (12.82%)
[2016-04-15T00:13Z] INFO  17:13:38,936 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:13Z] INFO  17:13:38,936 MicroScheduler -   -> 871 reads (0.28% of total) failing BadMateFilter
[2016-04-15T00:13Z] INFO  17:13:38,938 MicroScheduler -   -> 22125 reads (7.14% of total) failing DuplicateReadFilter
[2016-04-15T00:13Z] INFO  17:13:38,938 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:13Z] INFO  17:13:38,938 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:13Z] INFO  17:13:38,938 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:13Z] INFO  17:13:38,939 MicroScheduler -   -> 16708 reads (5.39% of total) failing MappingQualityZeroFilter
[2016-04-15T00:13Z] INFO  17:13:38,939 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:13Z] INFO  17:13:38,939 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-15T00:13Z] INFO  17:13:38,939 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:13Z] INFO  17:13:38,964 ProgressMeter -     7:135415053    100002.0    30.0 s       5.0 m       60.1%    49.0 s      19.0 s
[2016-04-15T00:13Z] INFO  17:13:39,000 ProgressMeter -            done    378291.0    47.0 s       2.1 m      100.0%    47.0 s       0.0 s
[2016-04-15T00:13Z] INFO  17:13:39,001 ProgressMeter - Total runtime 47.46 secs, 0.79 min, 0.01 hours
[2016-04-15T00:13Z] INFO  17:13:39,002 MicroScheduler - 235 reads were filtered out during the traversal out of approximately 378526 total reads (0.06%)
[2016-04-15T00:13Z] INFO  17:13:39,003 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:13Z] INFO  17:13:39,003 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:13Z] INFO  17:13:39,004 MicroScheduler -   -> 235 reads (0.06% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:13Z] INFO  17:13:39,122 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:13Z] INFO  17:13:39,135 IntervalUtils - Processing 15773393 bp from intervals
[2016-04-15T00:13Z] INFO  17:13:39,144 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:13Z] INFO  17:13:39,147 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:13Z] INFO  17:13:39,147 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:13Z] INFO  17:13:39,147 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:13Z] INFO  17:13:39,151 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/7/R14-18106_kapa-NGv3-PE100-NGv3-sort-7_15599765_31117713-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/7/R14-18106_kapa-NGv3-PE100-NGv3-sort-7_15599765_31117713-prep-prealign-realign.intervals -L 7:15599766-31117713 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/7/tx/tmpswoDq8/R14-18106_kapa-NGv3-PE100-NGv3-sort-7_15599765_31117713-prep.bam
[2016-04-15T00:13Z] WARN  17:13:39,154 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:13Z] INFO  17:13:39,168 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:13Z] INFO  17:13:39,169 HelpFormatter - Date/Time: 2016/04/14 17:13:39
[2016-04-15T00:13Z] INFO  17:13:39,169 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:13Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-6_158013810_171115067-prep.bam
[2016-04-15T00:13Z] INFO  17:13:39,170 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:13Z] INFO  17:13:39,241 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:13Z] INFO  17:13:39,348 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:13Z] INFO  17:13:39,348 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:13Z] INFO  17:13:39,349 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:13Z] INFO  17:13:39,350 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:13Z] INFO  17:13:39,350 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:13Z] INFO  17:13:39,422 ProgressMeter -            done   1.5552574E7    15.0 s       1.0 s      100.0%    15.0 s       0.0 s
[2016-04-15T00:13Z] INFO  17:13:39,422 ProgressMeter - Total runtime 15.56 secs, 0.26 min, 0.00 hours
[2016-04-15T00:13Z] INFO  17:13:39,426 MicroScheduler - 9220 reads were filtered out during the traversal out of approximately 116134 total reads (7.94%)
[2016-04-15T00:13Z] INFO  17:13:39,426 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:13Z] INFO  17:13:39,427 MicroScheduler -   -> 511 reads (0.44% of total) failing BadMateFilter
[2016-04-15T00:13Z] INFO  17:13:39,427 MicroScheduler -   -> 8478 reads (7.30% of total) failing DuplicateReadFilter
[2016-04-15T00:13Z] INFO  17:13:39,427 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:13Z] INFO  17:13:39,427 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:13Z] INFO  17:13:39,428 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:13Z] INFO  17:13:39,428 MicroScheduler -   -> 231 reads (0.20% of total) failing MappingQualityZeroFilter
[2016-04-15T00:13Z] INFO  17:13:39,428 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:13Z] INFO  17:13:39,428 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-15T00:13Z] INFO  17:13:39,428 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:13Z] INFO  17:13:39,478 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:13Z] INFO  17:13:39,510 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:13Z] INFO  17:13:39,519 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:13Z] INFO  17:13:39,575 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-15T00:13Z] INFO  17:13:39,658 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:13Z] INFO  17:13:39,902 ProgressMeter -            done    248048.0    16.0 s      67.0 s      100.0%    16.0 s       0.0 s
[2016-04-15T00:13Z] INFO  17:13:39,903 ProgressMeter - Total runtime 16.79 secs, 0.28 min, 0.00 hours
[2016-04-15T00:13Z] INFO  17:13:39,907 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 248048 total reads (0.00%)
[2016-04-15T00:13Z] INFO  17:13:39,908 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:13Z] INFO  17:13:39,908 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:13Z] INFO  17:13:39,908 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:13Z] GATK pre-alignment ('8', 15519664, 31030618) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:13Z] INFO  17:13:40,048 IntervalUtils - Processing 15517948 bp from intervals
[2016-04-15T00:13Z] WARN  17:13:40,065 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:13Z] INFO  17:13:40,211 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:13Z] INFO  17:13:40,411 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:13Z] INFO  17:13:40,413 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:13Z] INFO  17:13:40,414 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:13Z] INFO  17:13:40,415 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:13Z] INFO  17:13:40,422 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:13Z] INFO  17:13:40,441 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:13Z] GATK: realign ('7', 0, 15584548) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:13Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-7_63095909_78636522-prep-prealign.bam
[2016-04-15T00:13Z] INFO  17:13:40,598 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:13Z] INFO  17:13:40,896 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:13Z] INFO  17:13:40,926 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:13Z] GATK: realign ('7', 110526648, 126079222) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:13Z] INFO  17:13:41,206 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:13Z] INFO  17:13:41,210 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:13Z] INFO  17:13:41,211 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:13Z] INFO  17:13:41,212 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:13Z] INFO  17:13:41,217 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/7/R14-18106_kapa-NGv3-PE100-NGv3-sort-7_157155854_159138663-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/7/R14-18106_kapa-NGv3-PE100-NGv3-sort-7_157155854_159138663-prep-prealign-realign.intervals -L 7:157155855-159138663 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/7/tx/tmpI3sHoV/R14-18106_kapa-NGv3-PE100-NGv3-sort-7_157155854_159138663-prep.bam
[2016-04-15T00:13Z] INFO  17:13:41,242 ProgressMeter -            done   1.6197591E7    18.0 s       1.0 s      100.0%    18.0 s       0.0 s
[2016-04-15T00:13Z] INFO  17:13:41,243 ProgressMeter - Total runtime 18.91 secs, 0.32 min, 0.01 hours
[2016-04-15T00:13Z] INFO  17:13:41,247 MicroScheduler - 29872 reads were filtered out during the traversal out of approximately 252996 total reads (11.81%)
[2016-04-15T00:13Z] INFO  17:13:41,249 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:13Z] INFO  17:13:41,250 MicroScheduler -   -> 764 reads (0.30% of total) failing BadMateFilter
[2016-04-15T00:13Z] INFO  17:13:41,255 MicroScheduler -   -> 18204 reads (7.20% of total) failing DuplicateReadFilter
[2016-04-15T00:13Z] INFO  17:13:41,256 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:13Z] INFO  17:13:41,256 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:13Z] INFO  17:13:41,256 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:13Z] INFO  17:13:41,257 MicroScheduler -   -> 10904 reads (4.31% of total) failing MappingQualityZeroFilter
[2016-04-15T00:13Z] INFO  17:13:41,257 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:13Z] INFO  17:13:41,257 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-15T00:13Z] INFO  17:13:41,257 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:13Z] INFO  17:13:41,261 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:13Z] INFO  17:13:41,262 HelpFormatter - Date/Time: 2016/04/14 17:13:41
[2016-04-15T00:13Z] INFO  17:13:41,262 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:13Z] INFO  17:13:41,263 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:13Z] INFO  17:13:41,484 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:13Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-6_142399691_157963777-prep.bam
[2016-04-15T00:13Z] INFO  17:13:41,614 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:13Z] GATK RealignerTargetCreator: R14-18106_kapa-NGv3-PE100-NGv3-sort-7_63095909_78636522-prep-prealign.bam 7:63095910-78636522
[2016-04-15T00:13Z] GATK: RealignerTargetCreator
[2016-04-15T00:13Z] INFO  17:13:41,764 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:13Z] INFO  17:13:41,777 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:13Z] INFO  17:13:41,836 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-15T00:13Z] INFO  17:13:42,178 IntervalUtils - Processing 1982809 bp from intervals
[2016-04-15T00:13Z] WARN  17:13:42,193 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:13Z] INFO  17:13:42,271 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:13Z] GATK pre-alignment ('8', 31496910, 48001429) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:13Z] INFO  17:13:42,357 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:13Z] INFO  17:13:42,358 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:13Z] INFO  17:13:42,369 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:13Z] INFO  17:13:42,371 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:13Z] INFO  17:13:42,497 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:13Z] INFO  17:13:42,526 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:13Z] INFO  17:13:42,841 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:13Z] GATK: realign ('7', 31120227, 47317818) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:13Z] INFO  17:13:43,023 ProgressMeter -     7:148800750    200002.0    30.0 s       2.5 m       46.2%    64.0 s      34.0 s
[2016-04-15T00:13Z] INFO  17:13:43,307 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:13Z] INFO  17:13:43,310 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:13Z] INFO  17:13:43,310 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:13Z] INFO  17:13:43,310 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:13Z] INFO  17:13:43,325 HelpFormatter - Program Args: -T PrintReads -L 8:15519665-31030618 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/8/tx/tmpdIJJ7h/R14-18106_kapa-NGv3-PE100-NGv3-sort-8_15519664_31030618-prep-prealign.bam
[2016-04-15T00:13Z] INFO  17:13:43,335 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:13Z] INFO  17:13:43,335 HelpFormatter - Date/Time: 2016/04/14 17:13:43
[2016-04-15T00:13Z] INFO  17:13:43,336 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:13Z] INFO  17:13:43,336 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:13Z] INFO  17:13:43,560 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:13Z] INFO  17:13:43,702 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:13Z] INFO  17:13:43,704 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:13Z] INFO  17:13:43,704 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:13Z] INFO  17:13:43,705 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:13Z] INFO  17:13:43,709 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/7/R14-18106_kapa-NGv3-PE100-NGv3-sort-7_0_15584548-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/7/R14-18106_kapa-NGv3-PE100-NGv3-sort-7_0_15584548-prep-prealign-realign.intervals -L 7:1-15584548 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/7/tx/tmpLVBez0/R14-18106_kapa-NGv3-PE100-NGv3-sort-7_0_15584548-prep.bam
[2016-04-15T00:13Z] INFO  17:13:43,748 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:13Z] INFO  17:13:43,748 HelpFormatter - Date/Time: 2016/04/14 17:13:43
[2016-04-15T00:13Z] INFO  17:13:43,749 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:13Z] INFO  17:13:43,749 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:13Z] INFO  17:13:43,962 ProgressMeter -            done   1.5658369E7    16.0 s       1.0 s      100.0%    16.0 s       0.0 s
[2016-04-15T00:13Z] INFO  17:13:43,963 ProgressMeter - Total runtime 16.86 secs, 0.28 min, 0.00 hours
[2016-04-15T00:13Z] INFO  17:13:43,967 MicroScheduler - 13018 reads were filtered out during the traversal out of approximately 170222 total reads (7.65%)
[2016-04-15T00:13Z] INFO  17:13:43,978 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:13Z] INFO  17:13:43,982 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:13Z] INFO  17:13:43,982 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:13Z] INFO  17:13:43,983 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:13Z] INFO  17:13:43,987 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/7/R14-18106_kapa-NGv3-PE100-NGv3-sort-7_110526648_126079222-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/7/R14-18106_kapa-NGv3-PE100-NGv3-sort-7_110526648_126079222-prep-prealign-realign.intervals -L 7:110526649-126079222 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/7/tx/tmpQ9SsQ4/R14-18106_kapa-NGv3-PE100-NGv3-sort-7_110526648_126079222-prep.bam
[2016-04-15T00:13Z] INFO  17:13:43,989 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:13Z] INFO  17:13:43,990 MicroScheduler -   -> 562 reads (0.33% of total) failing BadMateFilter
[2016-04-15T00:13Z] INFO  17:13:43,991 MicroScheduler -   -> 12138 reads (7.13% of total) failing DuplicateReadFilter
[2016-04-15T00:13Z] INFO  17:13:43,992 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:13Z] INFO  17:13:43,992 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:13Z] INFO  17:13:43,993 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:13Z] INFO  17:13:43,994 MicroScheduler -   -> 318 reads (0.19% of total) failing MappingQualityZeroFilter
[2016-04-15T00:13Z] INFO  17:13:43,994 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:13Z] INFO  17:13:43,995 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-15T00:13Z] INFO  17:13:43,995 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:13Z] INFO  17:13:44,013 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:13Z] INFO  17:13:44,019 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:13Z] INFO  17:13:44,020 HelpFormatter - Date/Time: 2016/04/14 17:13:43
[2016-04-15T00:13Z] INFO  17:13:44,021 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:13Z] INFO  17:13:44,021 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:13Z] INFO  17:13:44,143 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:13Z] INFO  17:13:44,157 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:13Z] INFO  17:13:44,217 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:13Z] INFO  17:13:44,231 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-15T00:13Z] INFO  17:13:44,411 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:13Z] INFO  17:13:44,420 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:13Z] INFO  17:13:44,479 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-15T00:13Z] INFO  17:13:44,673 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:13Z] INFO  17:13:44,676 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:13Z] INFO  17:13:44,677 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:13Z] INFO  17:13:44,677 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:13Z] INFO  17:13:44,682 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/7/R14-18106_kapa-NGv3-PE100-NGv3-sort-7_63095909_78636522-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/7/tx/tmpr0BgK0/R14-18106_kapa-NGv3-PE100-NGv3-sort-7_63095909_78636522-prep-prealign-realign.intervals -l INFO -L 7:63095910-78636522 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:13Z] INFO  17:13:44,690 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:13Z] INFO  17:13:44,691 HelpFormatter - Date/Time: 2016/04/14 17:13:44
[2016-04-15T00:13Z] INFO  17:13:44,692 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:13Z] INFO  17:13:44,692 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:13Z] INFO  17:13:44,790 IntervalUtils - Processing 15584548 bp from intervals
[2016-04-15T00:13Z] WARN  17:13:44,795 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:13Z] INFO  17:13:44,798 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-15T00:13Z] INFO  17:13:44,816 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:13Z] INFO  17:13:44,871 IntervalUtils - Processing 15552574 bp from intervals
[2016-04-15T00:13Z] WARN  17:13:44,876 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:13Z] INFO  17:13:44,899 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:13Z] INFO  17:13:44,908 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:13Z] INFO  17:13:44,911 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:13Z] INFO  17:13:44,965 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-15T00:13Z] INFO  17:13:44,974 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:13Z] INFO  17:13:44,984 IntervalUtils - Processing 15510954 bp from intervals
[2016-04-15T00:13Z] INFO  17:13:45,066 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T00:13Z] INFO  17:13:45,073 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:13Z] INFO  17:13:45,074 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:13Z] INFO  17:13:45,075 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:13Z] INFO  17:13:45,075 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:13Z] INFO  17:13:45,076 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:13Z] INFO  17:13:45,096 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:13Z] INFO  17:13:45,168 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:13Z] INFO  17:13:45,168 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:13Z] INFO  17:13:45,168 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:13Z] INFO  17:13:45,169 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:13Z] INFO  17:13:45,174 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.10
[2016-04-15T00:13Z] INFO  17:13:45,231 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:13Z] INFO  17:13:45,292 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:13Z] INFO  17:13:45,295 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:13Z] INFO  17:13:45,295 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:13Z] INFO  17:13:45,296 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:13Z] INFO  17:13:45,300 HelpFormatter - Program Args: -T PrintReads -L 8:31496911-48001429 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/8/tx/tmplUrWRW/R14-18106_kapa-NGv3-PE100-NGv3-sort-8_31496910_48001429-prep-prealign.bam
[2016-04-15T00:13Z] INFO  17:13:45,305 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:13Z] INFO  17:13:45,308 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:13Z] INFO  17:13:45,309 HelpFormatter - Date/Time: 2016/04/14 17:13:45
[2016-04-15T00:13Z] INFO  17:13:45,310 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:13Z] INFO  17:13:45,310 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:13Z] INFO  17:13:45,414 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:13Z] INFO  17:13:45,418 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:13Z] INFO  17:13:45,420 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:13Z] INFO  17:13:45,432 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:13Z] INFO  17:13:45,432 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:13Z] INFO  17:13:45,432 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:13Z] GATK: realign ('7', 79082334, 94740703) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:13Z] INFO  17:13:45,450 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:13Z] INFO  17:13:45,457 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:13Z] INFO  17:13:45,461 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:13Z] INFO  17:13:45,477 IntervalUtils - Processing 15540613 bp from intervals
[2016-04-15T00:13Z] WARN  17:13:45,482 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:13Z] INFO  17:13:45,627 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:13Z] INFO  17:13:45,627 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:13Z] INFO  17:13:45,717 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:13Z] INFO  17:13:45,720 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:13Z] INFO  17:13:45,721 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:13Z] INFO  17:13:45,721 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:13Z] INFO  17:13:45,726 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/7/R14-18106_kapa-NGv3-PE100-NGv3-sort-7_31120227_47317818-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/7/R14-18106_kapa-NGv3-PE100-NGv3-sort-7_31120227_47317818-prep-prealign-realign.intervals -L 7:31120228-47317818 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/7/tx/tmp0cWrHp/R14-18106_kapa-NGv3-PE100-NGv3-sort-7_31120227_47317818-prep.bam
[2016-04-15T00:13Z] INFO  17:13:45,741 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:13Z] INFO  17:13:45,742 HelpFormatter - Date/Time: 2016/04/14 17:13:45
[2016-04-15T00:13Z] INFO  17:13:45,742 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:13Z] INFO  17:13:45,753 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:13Z] INFO  17:13:45,966 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:13Z] INFO  17:13:45,967 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:13Z] INFO  17:13:45,967 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:13Z] INFO  17:13:45,968 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:13Z] INFO  17:13:46,036 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:13Z] INFO  17:13:46,260 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:13Z] INFO  17:13:46,269 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:13Z] INFO  17:13:46,346 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-15T00:13Z] INFO  17:13:46,501 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-15T00:13Z] INFO  17:13:46,587 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:13Z] INFO  17:13:46,613 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:13Z] INFO  17:13:46,699 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.09
[2016-04-15T00:13Z] INFO  17:13:46,740 IntervalUtils - Processing 16504519 bp from intervals
[2016-04-15T00:13Z] INFO  17:13:46,842 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:13Z] INFO  17:13:46,853 IntervalUtils - Processing 16197591 bp from intervals
[2016-04-15T00:13Z] WARN  17:13:46,859 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:13Z] INFO  17:13:46,958 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:13Z] INFO  17:13:47,138 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:13Z] INFO  17:13:47,139 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:13Z] INFO  17:13:47,140 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:13Z] INFO  17:13:47,141 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:13Z] INFO  17:13:47,242 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:13Z] INFO  17:13:47,248 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:13Z] INFO  17:13:47,249 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:13Z] INFO  17:13:47,260 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:13Z] INFO  17:13:47,290 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:13Z] INFO  17:13:47,336 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:13Z] INFO  17:13:47,333 ProgressMeter -            done     27833.0     4.0 s       3.0 m       94.3%     4.0 s       0.0 s
[2016-04-15T00:13Z] INFO  17:13:47,334 ProgressMeter - Total runtime 4.98 secs, 0.08 min, 0.00 hours
[2016-04-15T00:13Z] INFO  17:13:47,338 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 27833 total reads (0.00%)
[2016-04-15T00:13Z] INFO  17:13:47,339 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:13Z] INFO  17:13:47,340 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:13Z] INFO  17:13:47,341 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:13Z] INFO  17:13:47,501 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:13Z] INFO  17:13:47,567 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:13Z] INFO  17:13:47,894 ProgressMeter -     5:140503724    400018.0    32.0 s      80.0 s       82.8%    38.0 s       6.0 s
[2016-04-15T00:13Z] INFO  17:13:48,204 ProgressMeter -      6:46421373   1.5332071E7    30.0 s       1.0 s       98.9%    30.0 s       0.0 s
[2016-04-15T00:13Z] INFO  17:13:48,673 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:13Z] INFO  17:13:48,677 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:13Z] INFO  17:13:48,677 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:13Z] INFO  17:13:48,678 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:13Z] INFO  17:13:48,704 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/7/R14-18106_kapa-NGv3-PE100-NGv3-sort-7_79082334_94740703-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/7/R14-18106_kapa-NGv3-PE100-NGv3-sort-7_79082334_94740703-prep-prealign-realign.intervals -L 7:79082335-94740703 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/7/tx/tmpzvwKo4/R14-18106_kapa-NGv3-PE100-NGv3-sort-7_79082334_94740703-prep.bam
[2016-04-15T00:13Z] INFO  17:13:48,721 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:13Z] INFO  17:13:48,729 HelpFormatter - Date/Time: 2016/04/14 17:13:48
[2016-04-15T00:13Z] INFO  17:13:48,730 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:13Z] INFO  17:13:48,730 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:13Z] INFO  17:13:48,782 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:13Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-7_157155854_159138663-prep.bam
[2016-04-15T00:13Z] INFO  17:13:48,966 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:13Z] GATK pre-alignment ('8', 48003022, 63659688) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:13Z] INFO  17:13:49,064 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:13Z] INFO  17:13:49,112 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:13Z] INFO  17:13:49,157 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.04
[2016-04-15T00:13Z] INFO  17:13:49,220 ProgressMeter -            done   1.5509444E7    31.0 s       2.0 s      100.0%    31.0 s       0.0 s
[2016-04-15T00:13Z] INFO  17:13:49,220 ProgressMeter - Total runtime 31.03 secs, 0.52 min, 0.01 hours
[2016-04-15T00:13Z] INFO  17:13:49,242 MicroScheduler - 107609 reads were filtered out during the traversal out of approximately 847886 total reads (12.69%)
[2016-04-15T00:13Z] INFO  17:13:49,243 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:13Z] INFO  17:13:49,243 MicroScheduler -   -> 1587 reads (0.19% of total) failing BadMateFilter
[2016-04-15T00:13Z] INFO  17:13:49,243 MicroScheduler -   -> 60727 reads (7.16% of total) failing DuplicateReadFilter
[2016-04-15T00:13Z] INFO  17:13:49,244 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:13Z] INFO  17:13:49,244 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:13Z] INFO  17:13:49,244 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:13Z] INFO  17:13:49,244 MicroScheduler -   -> 45295 reads (5.34% of total) failing MappingQualityZeroFilter
[2016-04-15T00:13Z] INFO  17:13:49,245 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:13Z] INFO  17:13:49,245 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-15T00:13Z] INFO  17:13:49,245 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:13Z] INFO  17:13:49,544 IntervalUtils - Processing 15658369 bp from intervals
[2016-04-15T00:13Z] WARN  17:13:49,550 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:13Z] INFO  17:13:49,624 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:13Z] INFO  17:13:49,734 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:13Z] INFO  17:13:49,735 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:13Z] INFO  17:13:49,736 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:13Z] INFO  17:13:49,737 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:13Z] INFO  17:13:49,924 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:13Z] INFO  17:13:50,054 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:13Z] INFO  17:13:50,510 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:13Z] GATK: realign ('6', 31083801, 46593245) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:13Z] INFO  17:13:51,833 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:13Z] INFO  17:13:51,836 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:13Z] INFO  17:13:51,836 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:13Z] INFO  17:13:51,837 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:13Z] INFO  17:13:51,841 HelpFormatter - Program Args: -T PrintReads -L 8:48003023-63659688 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/8/tx/tmpbbbuTl/R14-18106_kapa-NGv3-PE100-NGv3-sort-8_48003022_63659688-prep-prealign.bam
[2016-04-15T00:13Z] INFO  17:13:51,869 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:13Z] INFO  17:13:51,870 HelpFormatter - Date/Time: 2016/04/14 17:13:51
[2016-04-15T00:13Z] INFO  17:13:51,871 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:13Z] INFO  17:13:51,871 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:13Z] INFO  17:13:52,092 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:13Z] INFO  17:13:52,159 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@41fd9d8e
[2016-04-15T00:13Z] INFO  17:13:52,347 ProgressMeter -            done    324164.0    43.0 s       2.2 m      100.0%    43.0 s       0.0 s
[2016-04-15T00:13Z] INFO  17:13:52,348 ProgressMeter - Total runtime 43.41 secs, 0.72 min, 0.01 hours
[2016-04-15T00:13Z] INFO  17:13:52,348 MicroScheduler - 197 reads were filtered out during the traversal out of approximately 324361 total reads (0.06%)
[2016-04-15T00:13Z] INFO  17:13:52,349 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:13Z] INFO  17:13:52,349 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:13Z] INFO  17:13:52,349 MicroScheduler -   -> 197 reads (0.06% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:13Z] INFO  17:13:52,749 ProgressMeter -            done    155153.0    13.0 s      86.0 s      100.0%    13.0 s       0.0 s
[2016-04-15T00:13Z] INFO  17:13:52,749 ProgressMeter - Total runtime 13.40 secs, 0.22 min, 0.00 hours
[2016-04-15T00:13Z] INFO  17:13:52,753 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 155153 total reads (0.00%)
[2016-04-15T00:13Z] INFO  17:13:52,753 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:13Z] INFO  17:13:52,753 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:13Z] INFO  17:13:52,754 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:13Z] INFO  17:13:53,151 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:13Z] INFO  17:13:53,154 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:13Z] INFO  17:13:53,155 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:13Z] INFO  17:13:53,156 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:13Z] INFO  17:13:53,160 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/6/R14-18106_kapa-NGv3-PE100-NGv3-sort-6_31083801_46593245-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/6/R14-18106_kapa-NGv3-PE100-NGv3-sort-6_31083801_46593245-prep-prealign-realign.intervals -L 6:31083802-46593245 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/6/tx/tmpPHiHsj/R14-18106_kapa-NGv3-PE100-NGv3-sort-6_31083801_46593245-prep.bam
[2016-04-15T00:13Z] INFO  17:13:53,170 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:13Z] INFO  17:13:53,170 HelpFormatter - Date/Time: 2016/04/14 17:13:53
[2016-04-15T00:13Z] INFO  17:13:53,170 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:13Z] INFO  17:13:53,170 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:13Z] INFO  17:13:53,239 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-15T00:13Z] INFO  17:13:53,343 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:13Z] INFO  17:13:53,363 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:13Z] INFO  17:13:53,367 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:13Z] INFO  17:13:53,428 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-15T00:13Z] INFO  17:13:53,460 IntervalUtils - Processing 15656666 bp from intervals
[2016-04-15T00:13Z] INFO  17:13:53,524 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:13Z] INFO  17:13:53,534 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:13Z] INFO  17:13:53,579 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:13Z] INFO  17:13:53,630 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.10
[2016-04-15T00:13Z] INFO  17:13:53,875 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:13Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-7_126086124_141619620-prep-prealign.bam
[2016-04-15T00:13Z] INFO  17:13:53,948 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:13Z] INFO  17:13:53,949 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:13Z] INFO  17:13:53,950 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:13Z] INFO  17:13:53,950 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:13Z] INFO  17:13:53,966 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:13Z] INFO  17:13:54,053 IntervalUtils - Processing 15509444 bp from intervals
[2016-04-15T00:13Z] WARN  17:13:54,058 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:13Z] INFO  17:13:54,104 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:13Z] INFO  17:13:54,125 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:13Z] INFO  17:13:54,187 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:13Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-7_47319761_63093154-prep.bam
[2016-04-15T00:13Z] INFO  17:13:54,261 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:13Z] INFO  17:13:54,263 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:13Z] INFO  17:13:54,263 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:13Z] INFO  17:13:54,264 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:13Z] INFO  17:13:54,483 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:13Z] INFO  17:13:54,686 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:13Z] GATK pre-alignment ('8', 63775819, 79510770) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:13Z] GATK RealignerTargetCreator: R14-18106_kapa-NGv3-PE100-NGv3-sort-7_126086124_141619620-prep-prealign.bam 7:126086125-141619620
[2016-04-15T00:13Z] GATK: RealignerTargetCreator
[2016-04-15T00:13Z] INFO  17:13:55,536 ProgressMeter -            done    195606.0    15.0 s      77.0 s      100.0%    15.0 s       0.0 s
[2016-04-15T00:13Z] INFO  17:13:55,536 ProgressMeter - Total runtime 15.12 secs, 0.25 min, 0.00 hours
[2016-04-15T00:13Z] INFO  17:13:55,540 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 195606 total reads (0.00%)
[2016-04-15T00:13Z] INFO  17:13:55,541 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:13Z] INFO  17:13:55,541 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:13Z] INFO  17:13:55,541 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:13Z] INFO  17:13:56,155 ProgressMeter -            done    115410.0    10.0 s      95.0 s      100.0%    10.0 s       0.0 s
[2016-04-15T00:13Z] INFO  17:13:56,156 ProgressMeter - Total runtime 10.99 secs, 0.18 min, 0.00 hours
[2016-04-15T00:13Z] INFO  17:13:56,160 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 115410 total reads (0.00%)
[2016-04-15T00:13Z] INFO  17:13:56,160 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:13Z] INFO  17:13:56,162 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:13Z] INFO  17:13:56,163 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:13Z] INFO  17:13:57,063 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:13Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-7_15599765_31117713-prep.bam
[2016-04-15T00:13Z] INFO  17:13:57,508 ProgressMeter -            done    662374.0    41.0 s      63.0 s      100.0%    41.0 s       0.0 s
[2016-04-15T00:13Z] INFO  17:13:57,509 ProgressMeter - Total runtime 41.82 secs, 0.70 min, 0.01 hours
[2016-04-15T00:13Z] INFO  17:13:57,513 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 662374 total reads (0.00%)
[2016-04-15T00:13Z] INFO  17:13:57,514 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:13Z] INFO  17:13:57,515 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:13Z] INFO  17:13:57,516 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:13Z] INFO  17:13:57,548 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:13Z] INFO  17:13:57,551 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:13Z] INFO  17:13:57,551 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:13Z] INFO  17:13:57,551 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:13Z] INFO  17:13:57,556 HelpFormatter - Program Args: -T PrintReads -L 8:63775820-79510770 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/8/tx/tmplzRqb_/R14-18106_kapa-NGv3-PE100-NGv3-sort-8_63775819_79510770-prep-prealign.bam
[2016-04-15T00:13Z] INFO  17:13:57,566 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:13Z] INFO  17:13:57,577 HelpFormatter - Date/Time: 2016/04/14 17:13:57
[2016-04-15T00:13Z] INFO  17:13:57,578 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:13Z] INFO  17:13:57,579 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:13Z] INFO  17:13:57,640 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:13Z] INFO  17:13:57,669 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:13Z] INFO  17:13:57,672 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:13Z] INFO  17:13:57,673 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:13Z] INFO  17:13:57,673 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:13Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-7_110526648_126079222-prep.bam
[2016-04-15T00:13Z] INFO  17:13:57,678 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/7/R14-18106_kapa-NGv3-PE100-NGv3-sort-7_126086124_141619620-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/7/tx/tmpMEVTUI/R14-18106_kapa-NGv3-PE100-NGv3-sort-7_126086124_141619620-prep-prealign-realign.intervals -l INFO -L 7:126086125-141619620 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:13Z] INFO  17:13:57,694 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:13Z] INFO  17:13:57,695 HelpFormatter - Date/Time: 2016/04/14 17:13:57
[2016-04-15T00:13Z] INFO  17:13:57,695 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:13Z] INFO  17:13:57,696 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:13Z] INFO  17:13:57,745 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:13Z] GATK pre-alignment ('8', 79513976, 95140568) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:13Z] INFO  17:13:57,820 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:13Z] INFO  17:13:58,166 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T00:13Z] INFO  17:13:58,178 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:13Z] GATK pre-alignment ('8', 95142853, 110655419) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:13Z] INFO  17:13:58,228 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-15T00:13Z] INFO  17:13:58,665 IntervalUtils - Processing 15533496 bp from intervals
[2016-04-15T00:13Z] WARN  17:13:58,671 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:13Z] INFO  17:13:58,774 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:13Z] INFO  17:13:59,008 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-15T00:13Z] INFO  17:13:59,069 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:13Z] INFO  17:13:59,071 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:13Z] INFO  17:13:59,072 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:13Z] INFO  17:13:59,072 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:13Z] INFO  17:13:59,084 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:13Z] INFO  17:13:59,093 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:13Z] INFO  17:13:59,133 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.04
[2016-04-15T00:13Z] INFO  17:13:59,147 IntervalUtils - Processing 15734951 bp from intervals
[2016-04-15T00:13Z] INFO  17:13:59,153 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:13Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-5_127597427_143191869-prep.bam
[2016-04-15T00:13Z] INFO  17:13:59,220 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:13Z] INFO  17:13:59,502 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:13Z] INFO  17:13:59,503 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:13Z] INFO  17:13:59,503 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:13Z] INFO  17:13:59,504 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:13Z] INFO  17:13:59,517 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:13Z] INFO  17:13:59,710 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:14Z] INFO  17:14:00,610 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:14Z] INFO  17:14:00,613 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:14Z] INFO  17:14:00,614 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:14Z] INFO  17:14:00,614 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:14Z] INFO  17:14:00,619 HelpFormatter - Program Args: -T PrintReads -L 8:79513977-95140568 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/8/tx/tmpU1mMnq/R14-18106_kapa-NGv3-PE100-NGv3-sort-8_79513976_95140568-prep-prealign.bam
[2016-04-15T00:14Z] INFO  17:14:00,632 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:14Z] INFO  17:14:00,632 HelpFormatter - Date/Time: 2016/04/14 17:14:00
[2016-04-15T00:14Z] INFO  17:14:00,632 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:14Z] INFO  17:14:00,633 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:14Z] INFO  17:14:00,823 ProgressMeter -     7:101995631    400010.0    61.0 s       2.6 m       46.6%     2.2 m      69.0 s
[2016-04-15T00:14Z] INFO  17:14:00,827 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:14Z] GATK pre-alignment ('8', 110656864, 126194498) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:14Z] INFO  17:14:01,169 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:14Z] INFO  17:14:01,172 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:14Z] INFO  17:14:01,173 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:14Z] INFO  17:14:01,173 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:14Z] INFO  17:14:01,189 HelpFormatter - Program Args: -T PrintReads -L 8:95142854-110655419 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/8/tx/tmp8nd19d/R14-18106_kapa-NGv3-PE100-NGv3-sort-8_95142853_110655419-prep-prealign.bam
[2016-04-15T00:14Z] INFO  17:14:01,197 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:14Z] INFO  17:14:01,198 HelpFormatter - Date/Time: 2016/04/14 17:14:01
[2016-04-15T00:14Z] INFO  17:14:01,198 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:14Z] INFO  17:14:01,199 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:14Z] INFO  17:14:01,367 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:14Z] INFO  17:14:02,201 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-15T00:14Z] INFO  17:14:02,253 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:14Z] INFO  17:14:02,262 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:14Z] INFO  17:14:02,304 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.04
[2016-04-15T00:14Z] INFO  17:14:02,319 IntervalUtils - Processing 15626592 bp from intervals
[2016-04-15T00:14Z] INFO  17:14:02,418 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:14Z] INFO  17:14:02,589 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-15T00:14Z] INFO  17:14:02,695 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:14Z] INFO  17:14:02,704 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:14Z] INFO  17:14:02,746 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.04
[2016-04-15T00:14Z] INFO  17:14:02,765 IntervalUtils - Processing 15512566 bp from intervals
[2016-04-15T00:14Z] INFO  17:14:02,852 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:14Z] INFO  17:14:02,853 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:14Z] INFO  17:14:02,853 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:14Z] INFO  17:14:02,854 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:14Z] INFO  17:14:02,875 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:14Z] INFO  17:14:02,882 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:14Z] INFO  17:14:03,079 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:14Z] INFO  17:14:03,205 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:14Z] INFO  17:14:03,206 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:14Z] INFO  17:14:03,207 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:14Z] INFO  17:14:03,207 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:14Z] INFO  17:14:03,225 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:14Z] INFO  17:14:03,422 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:14Z] INFO  17:14:03,636 ProgressMeter -            done    169165.0    13.0 s      82.0 s      100.0%    13.0 s       0.0 s
[2016-04-15T00:14Z] INFO  17:14:03,637 ProgressMeter - Total runtime 13.90 secs, 0.23 min, 0.00 hours
[2016-04-15T00:14Z] INFO  17:14:03,641 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 169165 total reads (0.00%)
[2016-04-15T00:14Z] INFO  17:14:03,642 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:14Z] INFO  17:14:03,643 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:14Z] INFO  17:14:03,643 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:14Z] INFO  17:14:03,794 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:14Z] INFO  17:14:03,798 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:14Z] INFO  17:14:03,798 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:14Z] INFO  17:14:03,799 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:14Z] INFO  17:14:03,803 HelpFormatter - Program Args: -T PrintReads -L 8:110656865-126194498 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/8/tx/tmpBeNQr5/R14-18106_kapa-NGv3-PE100-NGv3-sort-8_110656864_126194498-prep-prealign.bam
[2016-04-15T00:14Z] INFO  17:14:03,823 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:14Z] INFO  17:14:03,824 HelpFormatter - Date/Time: 2016/04/14 17:14:03
[2016-04-15T00:14Z] INFO  17:14:03,824 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:14Z] INFO  17:14:03,829 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:14Z] INFO  17:14:03,888 ProgressMeter -       8:9567540    100001.0    30.0 s       5.1 m       61.7%    48.0 s      18.0 s
[2016-04-15T00:14Z] INFO  17:14:04,039 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:14Z] INFO  17:14:05,011 ProgressMeter -            done    251259.0    17.0 s      71.0 s      100.0%    17.0 s       0.0 s
[2016-04-15T00:14Z] INFO  17:14:05,011 ProgressMeter - Total runtime 17.87 secs, 0.30 min, 0.00 hours
[2016-04-15T00:14Z] INFO  17:14:05,014 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 251259 total reads (0.00%)
[2016-04-15T00:14Z] INFO  17:14:05,015 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:14Z] INFO  17:14:05,015 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:14Z] INFO  17:14:05,015 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:14Z] INFO  17:14:05,206 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-15T00:14Z] INFO  17:14:05,278 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:14Z] INFO  17:14:05,288 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:14Z] INFO  17:14:05,335 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-15T00:14Z] INFO  17:14:05,349 IntervalUtils - Processing 15537634 bp from intervals
[2016-04-15T00:14Z] INFO  17:14:05,433 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:14Z] INFO  17:14:05,440 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:14Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-7_79082334_94740703-prep.bam
[2016-04-15T00:14Z] INFO  17:14:05,700 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:14Z] INFO  17:14:05,701 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:14Z] INFO  17:14:05,702 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:14Z] INFO  17:14:05,702 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:14Z] INFO  17:14:05,722 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:14Z] INFO  17:14:05,875 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:14Z] GATK pre-alignment ('8', 126369460, 141889736) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:14Z] INFO  17:14:06,308 ProgressMeter -            done    307956.0    21.0 s      68.0 s      100.0%    21.0 s       0.0 s
[2016-04-15T00:14Z] INFO  17:14:06,308 ProgressMeter - Total runtime 21.23 secs, 0.35 min, 0.01 hours
[2016-04-15T00:14Z] INFO  17:14:06,312 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 307956 total reads (0.00%)
[2016-04-15T00:14Z] INFO  17:14:06,313 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:14Z] INFO  17:14:06,313 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:14Z] INFO  17:14:06,314 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:14Z] INFO  17:14:06,496 ProgressMeter -            done   1.5540613E7    20.0 s       1.0 s      100.0%    20.0 s       0.0 s
[2016-04-15T00:14Z] INFO  17:14:06,498 ProgressMeter - Total runtime 20.53 secs, 0.34 min, 0.01 hours
[2016-04-15T00:14Z] INFO  17:14:06,502 MicroScheduler - 119680 reads were filtered out during the traversal out of approximately 380575 total reads (31.45%)
[2016-04-15T00:14Z] INFO  17:14:06,503 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:14Z] INFO  17:14:06,503 MicroScheduler -   -> 793 reads (0.21% of total) failing BadMateFilter
[2016-04-15T00:14Z] INFO  17:14:06,503 MicroScheduler -   -> 21510 reads (5.65% of total) failing DuplicateReadFilter
[2016-04-15T00:14Z] INFO  17:14:06,503 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:14Z] INFO  17:14:06,504 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:14Z] INFO  17:14:06,504 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:14Z] INFO  17:14:06,504 MicroScheduler -   -> 97377 reads (25.59% of total) failing MappingQualityZeroFilter
[2016-04-15T00:14Z] INFO  17:14:06,504 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:14Z] INFO  17:14:06,505 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-15T00:14Z] INFO  17:14:06,505 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:14Z] INFO  17:14:06,520 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:14Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-7_31120227_47317818-prep.bam
[2016-04-15T00:14Z] GATK pre-alignment ('8', 141900641, 146364022) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:14Z] INFO  17:14:07,992 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:14Z] INFO  17:14:07,995 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:14Z] GATK: realign ('7', 63095909, 78636522) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:14Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-7_0_15584548-prep.bam
[2016-04-15T00:14Z] INFO  17:14:08,748 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:14Z] INFO  17:14:08,752 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:14Z] INFO  17:14:08,753 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:14Z] INFO  17:14:08,753 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:14Z] INFO  17:14:08,758 HelpFormatter - Program Args: -T PrintReads -L 8:126369461-141889736 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/8/tx/tmpYmBS5q/R14-18106_kapa-NGv3-PE100-NGv3-sort-8_126369460_141889736-prep-prealign.bam
[2016-04-15T00:14Z] INFO  17:14:08,768 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:14Z] INFO  17:14:08,769 HelpFormatter - Date/Time: 2016/04/14 17:14:08
[2016-04-15T00:14Z] INFO  17:14:08,770 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:14Z] INFO  17:14:08,770 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:14Z] INFO  17:14:08,979 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:14Z] GATK pre-alignment ('9', 0, 15510186) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:14Z] INFO  17:14:09,381 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@41fd9d8e
[2016-04-15T00:14Z] INFO  17:14:09,592 ProgressMeter -            done    450792.0    56.0 s       2.1 m      100.0%    56.0 s       0.0 s
[2016-04-15T00:14Z] INFO  17:14:09,592 ProgressMeter - Total runtime 56.58 secs, 0.94 min, 0.02 hours
[2016-04-15T00:14Z] INFO  17:14:09,592 MicroScheduler - 248 reads were filtered out during the traversal out of approximately 451040 total reads (0.05%)
[2016-04-15T00:14Z] INFO  17:14:09,593 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:14Z] INFO  17:14:09,593 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:14Z] INFO  17:14:09,593 MicroScheduler -   -> 248 reads (0.05% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:14Z] INFO  17:14:10,033 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-15T00:14Z] INFO  17:14:10,105 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:14Z] INFO  17:14:10,116 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:14Z] INFO  17:14:10,148 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:14Z] INFO  17:14:10,151 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:14Z] INFO  17:14:10,152 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:14Z] INFO  17:14:10,152 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:14Z] INFO  17:14:10,157 HelpFormatter - Program Args: -T PrintReads -L 8:141900642-146364022 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/8/tx/tmpwAUs9B/R14-18106_kapa-NGv3-PE100-NGv3-sort-8_141900641_146364022-prep-prealign.bam
[2016-04-15T00:14Z] INFO  17:14:10,169 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:14Z] INFO  17:14:10,170 HelpFormatter - Date/Time: 2016/04/14 17:14:10
[2016-04-15T00:14Z] INFO  17:14:10,170 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:14Z] INFO  17:14:10,171 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:14Z] INFO  17:14:10,176 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-15T00:14Z] INFO  17:14:10,191 IntervalUtils - Processing 15520276 bp from intervals
[2016-04-15T00:14Z] INFO  17:14:10,286 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:14Z] INFO  17:14:10,404 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:14Z] INFO  17:14:10,586 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:14Z] INFO  17:14:10,587 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:14Z] INFO  17:14:10,588 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:14Z] INFO  17:14:10,588 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:14Z] INFO  17:14:10,617 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:14Z] INFO  17:14:10,779 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:14Z] INFO  17:14:10,940 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:14Z] INFO  17:14:10,943 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:14Z] INFO  17:14:10,944 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:14Z] INFO  17:14:10,944 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:14Z] INFO  17:14:10,949 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/7/R14-18106_kapa-NGv3-PE100-NGv3-sort-7_63095909_78636522-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/7/R14-18106_kapa-NGv3-PE100-NGv3-sort-7_63095909_78636522-prep-prealign-realign.intervals -L 7:63095910-78636522 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/7/tx/tmpqbWjLx/R14-18106_kapa-NGv3-PE100-NGv3-sort-7_63095909_78636522-prep.bam
[2016-04-15T00:14Z] INFO  17:14:10,963 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:14Z] INFO  17:14:10,964 HelpFormatter - Date/Time: 2016/04/14 17:14:10
[2016-04-15T00:14Z] INFO  17:14:10,964 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:14Z] INFO  17:14:10,965 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:14Z] INFO  17:14:11,140 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:14Z] INFO  17:14:11,146 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:14Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-7_141629903_157151331-prep-prealign.bam
[2016-04-15T00:14Z] INFO  17:14:11,287 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:14Z] INFO  17:14:11,296 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:14Z] INFO  17:14:11,353 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-15T00:14Z] INFO  17:14:11,550 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-15T00:14Z] INFO  17:14:11,610 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:14Z] INFO  17:14:11,619 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:14Z] INFO  17:14:11,695 IntervalUtils - Processing 15540613 bp from intervals
[2016-04-15T00:14Z] WARN  17:14:11,700 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:14Z] INFO  17:14:11,707 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.09
[2016-04-15T00:14Z] INFO  17:14:11,739 IntervalUtils - Processing 4463381 bp from intervals
[2016-04-15T00:14Z] INFO  17:14:11,772 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:14Z] INFO  17:14:11,820 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:14Z] INFO  17:14:11,979 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:14Z] INFO  17:14:11,979 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:14Z] INFO  17:14:11,980 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:14Z] INFO  17:14:11,980 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:14Z] INFO  17:14:12,053 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:14Z] INFO  17:14:12,055 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:14Z] INFO  17:14:12,055 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:14Z] INFO  17:14:12,056 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:14Z] INFO  17:14:12,060 HelpFormatter - Program Args: -T PrintReads -L 9:1-15510186 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/9/tx/tmpjZgYs2/R14-18106_kapa-NGv3-PE100-NGv3-sort-9_0_15510186-prep-prealign.bam
[2016-04-15T00:14Z] INFO  17:14:12,073 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:14Z] INFO  17:14:12,074 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:14Z] INFO  17:14:12,075 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:14Z] INFO  17:14:12,075 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:14Z] INFO  17:14:12,084 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:14Z] INFO  17:14:12,084 HelpFormatter - Date/Time: 2016/04/14 17:14:12
[2016-04-15T00:14Z] INFO  17:14:12,084 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:14Z] INFO  17:14:12,085 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:14Z] INFO  17:14:12,118 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:14Z] INFO  17:14:12,213 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:14Z] INFO  17:14:12,251 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:14Z] INFO  17:14:12,303 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:14Z] INFO  17:14:12,423 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:14Z] INFO  17:14:12,457 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@41fd9d8e
[2016-04-15T00:14Z] GATK RealignerTargetCreator: R14-18106_kapa-NGv3-PE100-NGv3-sort-7_141629903_157151331-prep-prealign.bam 7:141629904-157151331
[2016-04-15T00:14Z] GATK: RealignerTargetCreator
[2016-04-15T00:14Z] INFO  17:14:12,549 ProgressMeter -            done    133058.0    18.0 s       2.3 m      100.0%    18.0 s       0.0 s
[2016-04-15T00:14Z] INFO  17:14:12,550 ProgressMeter - Total runtime 18.60 secs, 0.31 min, 0.01 hours
[2016-04-15T00:14Z] INFO  17:14:12,551 MicroScheduler - 132 reads were filtered out during the traversal out of approximately 133190 total reads (0.10%)
[2016-04-15T00:14Z] INFO  17:14:12,551 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:14Z] INFO  17:14:12,552 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:14Z] INFO  17:14:12,553 MicroScheduler -   -> 132 reads (0.10% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:14Z] INFO  17:14:13,574 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-15T00:14Z] INFO  17:14:13,670 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:14Z] INFO  17:14:13,719 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:14Z] INFO  17:14:13,792 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-15T00:14Z] INFO  17:14:13,818 IntervalUtils - Processing 15510186 bp from intervals
[2016-04-15T00:14Z] INFO  17:14:13,916 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:14Z] INFO  17:14:13,921 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:14Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-8_48003022_63659688-prep-prealign.bam
[2016-04-15T00:14Z] INFO  17:14:14,305 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:14Z] INFO  17:14:14,306 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:14Z] INFO  17:14:14,306 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:14Z] INFO  17:14:14,307 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:14Z] INFO  17:14:14,332 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:14Z] GATK RealignerTargetCreator: R14-18106_kapa-NGv3-PE100-NGv3-sort-8_48003022_63659688-prep-prealign.bam 8:48003023-63659688
[2016-04-15T00:14Z] GATK: RealignerTargetCreator
[2016-04-15T00:14Z] INFO  17:14:14,494 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:14Z] INFO  17:14:14,798 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@7172f77a
[2016-04-15T00:14Z] INFO  17:14:14,915 ProgressMeter -            done    176261.0    27.0 s       2.6 m      100.0%    27.0 s       0.0 s
[2016-04-15T00:14Z] INFO  17:14:14,916 ProgressMeter - Total runtime 27.67 secs, 0.46 min, 0.01 hours
[2016-04-15T00:14Z] INFO  17:14:14,916 MicroScheduler - 158 reads were filtered out during the traversal out of approximately 176419 total reads (0.09%)
[2016-04-15T00:14Z] INFO  17:14:14,917 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:14Z] INFO  17:14:14,917 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:14Z] INFO  17:14:14,917 MicroScheduler -   -> 158 reads (0.09% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:14Z] INFO  17:14:15,455 ProgressMeter -      8:26227847    200002.0    30.0 s       2.5 m       69.0%    43.0 s      13.0 s
[2016-04-15T00:14Z] INFO  17:14:15,499 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:14Z] INFO  17:14:15,502 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:14Z] INFO  17:14:15,503 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:14Z] INFO  17:14:15,503 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:14Z] INFO  17:14:15,508 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/7/R14-18106_kapa-NGv3-PE100-NGv3-sort-7_141629903_157151331-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/7/tx/tmpxn7poK/R14-18106_kapa-NGv3-PE100-NGv3-sort-7_141629903_157151331-prep-prealign-realign.intervals -l INFO -L 7:141629904-157151331 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:14Z] INFO  17:14:15,535 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:14Z] INFO  17:14:15,536 HelpFormatter - Date/Time: 2016/04/14 17:14:15
[2016-04-15T00:14Z] INFO  17:14:15,536 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:14Z] INFO  17:14:15,536 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:14Z] INFO  17:14:15,673 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:14Z] INFO  17:14:15,978 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T00:14Z] INFO  17:14:15,988 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:14Z] INFO  17:14:16,058 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-15T00:14Z] INFO  17:14:16,328 IntervalUtils - Processing 15521428 bp from intervals
[2016-04-15T00:14Z] WARN  17:14:16,334 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:14Z] INFO  17:14:16,401 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:14Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-8_31496910_48001429-prep-prealign.bam
[2016-04-15T00:14Z] INFO  17:14:16,442 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:14Z] INFO  17:14:16,658 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:14Z] INFO  17:14:16,659 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:14Z] INFO  17:14:16,660 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:14Z] INFO  17:14:16,661 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:14Z] GATK RealignerTargetCreator: R14-18106_kapa-NGv3-PE100-NGv3-sort-8_31496910_48001429-prep-prealign.bam 8:31496911-48001429
[2016-04-15T00:14Z] GATK: RealignerTargetCreator
[2016-04-15T00:14Z] INFO  17:14:17,025 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:14Z] INFO  17:14:17,028 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:14Z] INFO  17:14:17,029 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:14Z] INFO  17:14:17,030 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:14Z] INFO  17:14:17,034 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/8/R14-18106_kapa-NGv3-PE100-NGv3-sort-8_48003022_63659688-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/8/tx/tmpXamH3X/R14-18106_kapa-NGv3-PE100-NGv3-sort-8_48003022_63659688-prep-prealign-realign.intervals -l INFO -L 8:48003023-63659688 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:14Z] INFO  17:14:17,043 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:14Z] INFO  17:14:17,044 HelpFormatter - Date/Time: 2016/04/14 17:14:17
[2016-04-15T00:14Z] INFO  17:14:17,044 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:14Z] INFO  17:14:17,044 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:14Z] INFO  17:14:17,154 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:14Z] INFO  17:14:17,421 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T00:14Z] INFO  17:14:17,431 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:14Z] INFO  17:14:17,496 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-15T00:14Z] INFO  17:14:17,865 IntervalUtils - Processing 15656666 bp from intervals
[2016-04-15T00:14Z] WARN  17:14:17,882 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:14Z] INFO  17:14:18,033 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:14Z] INFO  17:14:18,241 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:14Z] INFO  17:14:18,242 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:14Z] INFO  17:14:18,243 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:14Z] INFO  17:14:18,243 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:14Z] INFO  17:14:18,387 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@7172f77a
[2016-04-15T00:14Z] INFO  17:14:18,513 ProgressMeter -            done     98032.0    15.0 s       2.7 m      100.0%    15.0 s       0.0 s
[2016-04-15T00:14Z] INFO  17:14:18,514 ProgressMeter - Total runtime 15.66 secs, 0.26 min, 0.00 hours
[2016-04-15T00:14Z] INFO  17:14:18,514 MicroScheduler - 120 reads were filtered out during the traversal out of approximately 98152 total reads (0.12%)
[2016-04-15T00:14Z] INFO  17:14:18,514 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:14Z] INFO  17:14:18,514 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:14Z] INFO  17:14:18,515 MicroScheduler -   -> 120 reads (0.12% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:14Z] INFO  17:14:18,565 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@41fd9d8e
[2016-04-15T00:14Z] INFO  17:14:18,631 ProgressMeter -            done    141799.0    19.0 s       2.2 m      100.0%    19.0 s       0.0 s
[2016-04-15T00:14Z] INFO  17:14:18,633 ProgressMeter - Total runtime 19.13 secs, 0.32 min, 0.01 hours
[2016-04-15T00:14Z] INFO  17:14:18,633 MicroScheduler - 133 reads were filtered out during the traversal out of approximately 141932 total reads (0.09%)
[2016-04-15T00:14Z] INFO  17:14:18,634 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:14Z] INFO  17:14:18,635 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:14Z] INFO  17:14:18,636 MicroScheduler -   -> 133 reads (0.09% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:14Z] INFO  17:14:19,529 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:14Z] INFO  17:14:19,532 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:14Z] INFO  17:14:19,533 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:14Z] INFO  17:14:19,533 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:14Z] INFO  17:14:19,538 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/8/R14-18106_kapa-NGv3-PE100-NGv3-sort-8_31496910_48001429-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/8/tx/tmpf73PBs/R14-18106_kapa-NGv3-PE100-NGv3-sort-8_31496910_48001429-prep-prealign-realign.intervals -l INFO -L 8:31496911-48001429 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:14Z] INFO  17:14:19,567 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:14Z] INFO  17:14:19,567 HelpFormatter - Date/Time: 2016/04/14 17:14:19
[2016-04-15T00:14Z] INFO  17:14:19,567 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:14Z] INFO  17:14:19,567 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:14Z] INFO  17:14:19,684 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:14Z] INFO  17:14:19,919 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T00:14Z] INFO  17:14:19,928 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:14Z] INFO  17:14:20,013 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@7172f77a
[2016-04-15T00:14Z] INFO  17:14:20,033 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.10
[2016-04-15T00:14Z] INFO  17:14:20,135 ProgressMeter -            done    304873.0    46.0 s       2.6 m      100.0%    46.0 s       0.0 s
[2016-04-15T00:14Z] INFO  17:14:20,135 ProgressMeter - Total runtime 46.76 secs, 0.78 min, 0.01 hours
[2016-04-15T00:14Z] INFO  17:14:20,136 MicroScheduler - 241 reads were filtered out during the traversal out of approximately 305114 total reads (0.08%)
[2016-04-15T00:14Z] INFO  17:14:20,136 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:14Z] INFO  17:14:20,136 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:14Z] INFO  17:14:20,137 MicroScheduler -   -> 241 reads (0.08% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:14Z] INFO  17:14:20,147 ProgressMeter -            done   1.5533496E7    21.0 s       1.0 s      100.0%    21.0 s       0.0 s
[2016-04-15T00:14Z] INFO  17:14:20,148 ProgressMeter - Total runtime 21.08 secs, 0.35 min, 0.01 hours
[2016-04-15T00:14Z] INFO  17:14:20,152 MicroScheduler - 26907 reads were filtered out during the traversal out of approximately 325756 total reads (8.26%)
[2016-04-15T00:14Z] INFO  17:14:20,153 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:14Z] INFO  17:14:20,154 MicroScheduler -   -> 881 reads (0.27% of total) failing BadMateFilter
[2016-04-15T00:14Z] INFO  17:14:20,154 MicroScheduler -   -> 24423 reads (7.50% of total) failing DuplicateReadFilter
[2016-04-15T00:14Z] INFO  17:14:20,155 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:14Z] INFO  17:14:20,155 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:14Z] INFO  17:14:20,156 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:14Z] INFO  17:14:20,157 MicroScheduler -   -> 1603 reads (0.49% of total) failing MappingQualityZeroFilter
[2016-04-15T00:14Z] INFO  17:14:20,157 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:14Z] INFO  17:14:20,158 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-15T00:14Z] INFO  17:14:20,158 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:14Z] INFO  17:14:20,189 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:14Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-8_79513976_95140568-prep-prealign.bam
[2016-04-15T00:14Z] INFO  17:14:20,282 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:14Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-8_63775819_79510770-prep-prealign.bam
[2016-04-15T00:14Z] INFO  17:14:20,381 IntervalUtils - Processing 16504519 bp from intervals
[2016-04-15T00:14Z] WARN  17:14:20,386 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:14Z] INFO  17:14:20,470 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:14Z] GATK RealignerTargetCreator: R14-18106_kapa-NGv3-PE100-NGv3-sort-8_79513976_95140568-prep-prealign.bam 8:79513977-95140568
[2016-04-15T00:14Z] GATK: RealignerTargetCreator
[2016-04-15T00:14Z] INFO  17:14:20,636 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:14Z] INFO  17:14:20,637 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:14Z] INFO  17:14:20,638 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:14Z] INFO  17:14:20,639 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:14Z] GATK RealignerTargetCreator: R14-18106_kapa-NGv3-PE100-NGv3-sort-8_63775819_79510770-prep-prealign.bam 8:63775820-79510770
[2016-04-15T00:14Z] GATK: RealignerTargetCreator
[2016-04-15T00:14Z] INFO  17:14:21,393 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:14Z] GATK: realign ('7', 126086124, 141619620) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:14Z] INFO  17:14:21,497 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:14Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-8_0_15517156-prep-prealign.bam
[2016-04-15T00:14Z] GATK RealignerTargetCreator: R14-18106_kapa-NGv3-PE100-NGv3-sort-8_0_15517156-prep-prealign.bam 8:1-15517156
[2016-04-15T00:14Z] GATK: RealignerTargetCreator
[2016-04-15T00:14Z] INFO  17:14:22,745 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@41fd9d8e
[2016-04-15T00:14Z] INFO  17:14:22,861 ProgressMeter -            done    699580.0    83.0 s     119.0 s      100.0%    83.0 s       0.0 s
[2016-04-15T00:14Z] INFO  17:14:22,862 ProgressMeter - Total runtime 83.37 secs, 1.39 min, 0.02 hours
[2016-04-15T00:14Z] INFO  17:14:22,862 MicroScheduler - 480 reads were filtered out during the traversal out of approximately 700060 total reads (0.07%)
[2016-04-15T00:14Z] INFO  17:14:22,863 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:14Z] INFO  17:14:22,863 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:14Z] INFO  17:14:22,865 MicroScheduler -   -> 480 reads (0.07% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:14Z] INFO  17:14:23,346 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:14Z] INFO  17:14:23,350 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:14Z] INFO  17:14:23,351 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:14Z] INFO  17:14:23,351 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:14Z] INFO  17:14:23,355 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/8/R14-18106_kapa-NGv3-PE100-NGv3-sort-8_79513976_95140568-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/8/tx/tmpVVB8oZ/R14-18106_kapa-NGv3-PE100-NGv3-sort-8_79513976_95140568-prep-prealign-realign.intervals -l INFO -L 8:79513977-95140568 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:14Z] INFO  17:14:23,364 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:14Z] INFO  17:14:23,375 HelpFormatter - Date/Time: 2016/04/14 17:14:23
[2016-04-15T00:14Z] INFO  17:14:23,376 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:14Z] INFO  17:14:23,377 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:14Z] INFO  17:14:23,519 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:14Z] INFO  17:14:23,768 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T00:14Z] INFO  17:14:23,788 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:14Z] INFO  17:14:23,781 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:14Z] INFO  17:14:23,794 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:14Z] INFO  17:14:23,794 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:14Z] INFO  17:14:23,795 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:14Z] INFO  17:14:23,799 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/8/R14-18106_kapa-NGv3-PE100-NGv3-sort-8_63775819_79510770-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/8/tx/tmpU4dzoc/R14-18106_kapa-NGv3-PE100-NGv3-sort-8_63775819_79510770-prep-prealign-realign.intervals -l INFO -L 8:63775820-79510770 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:14Z] INFO  17:14:23,836 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:14Z] INFO  17:14:23,837 HelpFormatter - Date/Time: 2016/04/14 17:14:23
[2016-04-15T00:14Z] INFO  17:14:23,838 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:14Z] INFO  17:14:23,838 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:14Z] INFO  17:14:23,843 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-15T00:14Z] INFO  17:14:23,858 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@41fd9d8e
[2016-04-15T00:14Z] INFO  17:14:23,962 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:14Z] INFO  17:14:23,973 ProgressMeter -            done    134745.0    18.0 s       2.3 m      100.0%    18.0 s       0.0 s
[2016-04-15T00:14Z] INFO  17:14:23,973 ProgressMeter - Total runtime 18.27 secs, 0.30 min, 0.01 hours
[2016-04-15T00:14Z] INFO  17:14:23,973 MicroScheduler - 110 reads were filtered out during the traversal out of approximately 134855 total reads (0.08%)
[2016-04-15T00:14Z] INFO  17:14:23,974 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:14Z] INFO  17:14:23,974 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:14Z] INFO  17:14:23,974 MicroScheduler -   -> 110 reads (0.08% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:14Z] INFO  17:14:24,075 IntervalUtils - Processing 15626592 bp from intervals
[2016-04-15T00:14Z] WARN  17:14:24,080 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:14Z] INFO  17:14:24,163 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:14Z] INFO  17:14:24,187 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T00:14Z] INFO  17:14:24,197 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:14Z] INFO  17:14:24,268 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-15T00:14Z] INFO  17:14:24,351 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:14Z] INFO  17:14:24,355 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:14Z] INFO  17:14:24,356 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:14Z] INFO  17:14:24,356 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:14Z] INFO  17:14:24,357 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:14Z] INFO  17:14:24,359 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:14Z] INFO  17:14:24,359 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:14Z] INFO  17:14:24,360 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:14Z] INFO  17:14:24,361 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/7/R14-18106_kapa-NGv3-PE100-NGv3-sort-7_126086124_141619620-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/7/R14-18106_kapa-NGv3-PE100-NGv3-sort-7_126086124_141619620-prep-prealign-realign.intervals -L 7:126086125-141619620 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/7/tx/tmpEki3sz/R14-18106_kapa-NGv3-PE100-NGv3-sort-7_126086124_141619620-prep.bam
[2016-04-15T00:14Z] INFO  17:14:24,371 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:14Z] INFO  17:14:24,382 HelpFormatter - Date/Time: 2016/04/14 17:14:24
[2016-04-15T00:14Z] INFO  17:14:24,382 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:14Z] INFO  17:14:24,383 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:14Z] INFO  17:14:24,597 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:14Z] INFO  17:14:24,617 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:14Z] INFO  17:14:24,625 IntervalUtils - Processing 15734951 bp from intervals
[2016-04-15T00:14Z] WARN  17:14:24,630 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:14Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-7_94750023_110303777-prep-prealign.bam
[2016-04-15T00:14Z] INFO  17:14:24,697 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:14Z] INFO  17:14:24,725 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:14Z] INFO  17:14:24,739 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:14Z] INFO  17:14:24,806 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-15T00:14Z] INFO  17:14:24,907 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:14Z] INFO  17:14:24,909 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:14Z] INFO  17:14:24,909 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:14Z] INFO  17:14:24,910 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:14Z] INFO  17:14:25,254 IntervalUtils - Processing 15533496 bp from intervals
[2016-04-15T00:14Z] WARN  17:14:25,259 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:14Z] INFO  17:14:25,357 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:14Z] INFO  17:14:25,368 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:14Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-8_110656864_126194498-prep-prealign.bam
[2016-04-15T00:14Z] INFO  17:14:25,541 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:14Z] INFO  17:14:25,545 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:14Z] INFO  17:14:25,545 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:14Z] INFO  17:14:25,546 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:14Z] INFO  17:14:25,550 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/8/R14-18106_kapa-NGv3-PE100-NGv3-sort-8_0_15517156-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/8/tx/tmpntR4mh/R14-18106_kapa-NGv3-PE100-NGv3-sort-8_0_15517156-prep-prealign-realign.intervals -l INFO -L 8:1-15517156 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:14Z] INFO  17:14:25,558 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:14Z] INFO  17:14:25,559 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:14Z] INFO  17:14:25,560 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:14Z] INFO  17:14:25,560 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:14Z] INFO  17:14:25,567 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:14Z] INFO  17:14:25,568 HelpFormatter - Date/Time: 2016/04/14 17:14:25
[2016-04-15T00:14Z] INFO  17:14:25,569 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:14Z] INFO  17:14:25,571 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:14Z] INFO  17:14:25,717 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:14Z] INFO  17:14:25,754 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:14Z] INFO  17:14:25,858 ProgressMeter -      6:35058840    400007.0    31.0 s      78.0 s       25.6%   120.0 s      89.0 s
[2016-04-15T00:14Z] GATK RealignerTargetCreator: R14-18106_kapa-NGv3-PE100-NGv3-sort-8_110656864_126194498-prep-prealign.bam 8:110656865-126194498
[2016-04-15T00:14Z] GATK: RealignerTargetCreator
[2016-04-15T00:14Z] INFO  17:14:25,930 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:14Z] INFO  17:14:25,964 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T00:14Z] INFO  17:14:25,992 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:14Z] INFO  17:14:26,036 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.04
[2016-04-15T00:14Z] INFO  17:14:26,153 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@7172f77a
[2016-04-15T00:14Z] INFO  17:14:26,267 ProgressMeter -            done    332750.0    40.0 s       2.0 m      100.0%    40.0 s       0.0 s
[2016-04-15T00:14Z] INFO  17:14:26,267 ProgressMeter - Total runtime 40.84 secs, 0.68 min, 0.01 hours
[2016-04-15T00:14Z] INFO  17:14:26,267 MicroScheduler - 179 reads were filtered out during the traversal out of approximately 332929 total reads (0.05%)
[2016-04-15T00:14Z] INFO  17:14:26,268 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:14Z] INFO  17:14:26,268 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:14Z] INFO  17:14:26,268 MicroScheduler -   -> 179 reads (0.05% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:14Z] INFO  17:14:26,368 IntervalUtils - Processing 15517156 bp from intervals
[2016-04-15T00:14Z] WARN  17:14:26,374 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:14Z] INFO  17:14:26,441 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:14Z] INFO  17:14:26,667 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:14Z] INFO  17:14:26,669 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:14Z] INFO  17:14:26,669 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:14Z] INFO  17:14:26,670 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:14Z] GATK RealignerTargetCreator: R14-18106_kapa-NGv3-PE100-NGv3-sort-7_94750023_110303777-prep-prealign.bam 7:94750024-110303777
[2016-04-15T00:14Z] GATK: RealignerTargetCreator
[2016-04-15T00:14Z] INFO  17:14:27,673 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:14Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-8_15519664_31030618-prep-prealign.bam
[2016-04-15T00:14Z] GATK RealignerTargetCreator: R14-18106_kapa-NGv3-PE100-NGv3-sort-8_15519664_31030618-prep-prealign.bam 8:15519665-31030618
[2016-04-15T00:14Z] GATK: RealignerTargetCreator
[2016-04-15T00:14Z] INFO  17:14:29,052 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:14Z] INFO  17:14:29,054 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:14Z] INFO  17:14:29,054 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:14Z] INFO  17:14:29,054 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:14Z] INFO  17:14:29,058 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/8/R14-18106_kapa-NGv3-PE100-NGv3-sort-8_110656864_126194498-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/8/tx/tmpF8BW31/R14-18106_kapa-NGv3-PE100-NGv3-sort-8_110656864_126194498-prep-prealign-realign.intervals -l INFO -L 8:110656865-126194498 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:14Z] INFO  17:14:29,077 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:14Z] INFO  17:14:29,078 HelpFormatter - Date/Time: 2016/04/14 17:14:29
[2016-04-15T00:14Z] INFO  17:14:29,079 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:14Z] INFO  17:14:29,079 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:14Z] INFO  17:14:29,191 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:14Z] INFO  17:14:29,343 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@6834dd3c
[2016-04-15T00:14Z] INFO  17:14:29,475 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T00:14Z] INFO  17:14:29,499 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:14Z] INFO  17:14:29,571 ProgressMeter -            done    116893.0    18.0 s       2.7 m      100.0%    18.0 s       0.0 s
[2016-04-15T00:14Z] INFO  17:14:29,572 ProgressMeter - Total runtime 18.99 secs, 0.32 min, 0.01 hours
[2016-04-15T00:14Z] INFO  17:14:29,572 MicroScheduler - 121 reads were filtered out during the traversal out of approximately 117014 total reads (0.10%)
[2016-04-15T00:14Z] INFO  17:14:29,573 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:14Z] INFO  17:14:29,573 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:14Z] INFO  17:14:29,573 MicroScheduler -   -> 121 reads (0.10% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:14Z] INFO  17:14:29,584 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-15T00:14Z] INFO  17:14:29,958 IntervalUtils - Processing 15537634 bp from intervals
[2016-04-15T00:14Z] WARN  17:14:29,964 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:14Z] INFO  17:14:30,054 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:14Z] INFO  17:14:30,245 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:14Z] INFO  17:14:30,248 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:14Z] INFO  17:14:30,248 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:14Z] INFO  17:14:30,248 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:14Z] INFO  17:14:30,254 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:14Z] INFO  17:14:30,255 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:14Z] INFO  17:14:30,256 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:14Z] INFO  17:14:30,256 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:14Z] INFO  17:14:30,264 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/7/R14-18106_kapa-NGv3-PE100-NGv3-sort-7_94750023_110303777-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/7/tx/tmpnvcTsq/R14-18106_kapa-NGv3-PE100-NGv3-sort-7_94750023_110303777-prep-prealign-realign.intervals -l INFO -L 7:94750024-110303777 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:14Z] INFO  17:14:30,273 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:14Z] INFO  17:14:30,274 HelpFormatter - Date/Time: 2016/04/14 17:14:30
[2016-04-15T00:14Z] INFO  17:14:30,274 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:14Z] INFO  17:14:30,274 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:14Z] INFO  17:14:30,384 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:14Z] INFO  17:14:30,597 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T00:14Z] INFO  17:14:30,608 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:14Z] INFO  17:14:30,669 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-15T00:14Z] INFO  17:14:30,941 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@7172f77a
[2016-04-15T00:14Z] INFO  17:14:31,040 IntervalUtils - Processing 15553754 bp from intervals
[2016-04-15T00:14Z] WARN  17:14:31,045 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:14Z] INFO  17:14:31,113 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:14Z] INFO  17:14:31,130 ProgressMeter -            done    198106.0    27.0 s       2.3 m      100.0%    27.0 s       0.0 s
[2016-04-15T00:14Z] INFO  17:14:31,131 ProgressMeter - Total runtime 27.93 secs, 0.47 min, 0.01 hours
[2016-04-15T00:14Z] INFO  17:14:31,131 MicroScheduler - 161 reads were filtered out during the traversal out of approximately 198267 total reads (0.08%)
[2016-04-15T00:14Z] INFO  17:14:31,131 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:14Z] INFO  17:14:31,132 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:14Z] INFO  17:14:31,132 MicroScheduler -   -> 161 reads (0.08% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:14Z] INFO  17:14:31,270 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:14Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-8_126369460_141889736-prep-prealign.bam
[2016-04-15T00:14Z] INFO  17:14:31,380 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:14Z] INFO  17:14:31,381 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:14Z] INFO  17:14:31,382 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:14Z] INFO  17:14:31,383 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:14Z] INFO  17:14:31,459 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:14Z] INFO  17:14:31,462 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:14Z] INFO  17:14:31,462 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:14Z] INFO  17:14:31,462 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:14Z] INFO  17:14:31,467 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/8/R14-18106_kapa-NGv3-PE100-NGv3-sort-8_15519664_31030618-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/8/tx/tmphmbYtu/R14-18106_kapa-NGv3-PE100-NGv3-sort-8_15519664_31030618-prep-prealign-realign.intervals -l INFO -L 8:15519665-31030618 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:14Z] INFO  17:14:31,512 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:14Z] INFO  17:14:31,513 HelpFormatter - Date/Time: 2016/04/14 17:14:31
[2016-04-15T00:14Z] INFO  17:14:31,513 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:14Z] INFO  17:14:31,513 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:14Z] INFO  17:14:31,683 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:14Z] GATK RealignerTargetCreator: R14-18106_kapa-NGv3-PE100-NGv3-sort-8_126369460_141889736-prep-prealign.bam 8:126369461-141889736
[2016-04-15T00:14Z] GATK: RealignerTargetCreator
[2016-04-15T00:14Z] INFO  17:14:31,868 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T00:14Z] INFO  17:14:31,877 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:14Z] INFO  17:14:31,929 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-15T00:14Z] INFO  17:14:32,260 IntervalUtils - Processing 15510954 bp from intervals
[2016-04-15T00:14Z] WARN  17:14:32,276 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:14Z] INFO  17:14:32,404 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:14Z] INFO  17:14:32,627 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:14Z] INFO  17:14:32,628 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:14Z] INFO  17:14:32,629 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:14Z] INFO  17:14:32,629 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:14Z] INFO  17:14:32,684 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:14Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-8_95142853_110655419-prep-prealign.bam
[2016-04-15T00:14Z] GATK RealignerTargetCreator: R14-18106_kapa-NGv3-PE100-NGv3-sort-8_95142853_110655419-prep-prealign.bam 8:95142854-110655419
[2016-04-15T00:14Z] GATK: RealignerTargetCreator
[2016-04-15T00:14Z] INFO  17:14:34,607 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:14Z] INFO  17:14:34,611 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:14Z] INFO  17:14:34,611 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:14Z] INFO  17:14:34,612 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:14Z] INFO  17:14:34,616 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/8/R14-18106_kapa-NGv3-PE100-NGv3-sort-8_126369460_141889736-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/8/tx/tmpzvQFRT/R14-18106_kapa-NGv3-PE100-NGv3-sort-8_126369460_141889736-prep-prealign-realign.intervals -l INFO -L 8:126369461-141889736 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:14Z] INFO  17:14:34,631 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:14Z] INFO  17:14:34,631 HelpFormatter - Date/Time: 2016/04/14 17:14:34
[2016-04-15T00:14Z] INFO  17:14:34,632 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:14Z] INFO  17:14:34,632 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:14Z] INFO  17:14:34,749 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:14Z] INFO  17:14:34,964 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T00:14Z] INFO  17:14:34,967 ProgressMeter -            done   1.5656666E7    16.0 s       1.0 s      100.0%    16.0 s       0.0 s
[2016-04-15T00:14Z] INFO  17:14:34,968 ProgressMeter - Total runtime 16.73 secs, 0.28 min, 0.00 hours
[2016-04-15T00:14Z] INFO  17:14:34,971 MicroScheduler - 11300 reads were filtered out during the traversal out of approximately 133428 total reads (8.47%)
[2016-04-15T00:14Z] INFO  17:14:34,972 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:14Z] INFO  17:14:34,973 MicroScheduler -   -> 592 reads (0.44% of total) failing BadMateFilter
[2016-04-15T00:14Z] INFO  17:14:34,974 MicroScheduler -   -> 9822 reads (7.36% of total) failing DuplicateReadFilter
[2016-04-15T00:14Z] INFO  17:14:34,974 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:14Z] INFO  17:14:34,974 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:14Z] INFO  17:14:34,975 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:14Z] INFO  17:14:34,976 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:14Z] INFO  17:14:34,977 MicroScheduler -   -> 886 reads (0.66% of total) failing MappingQualityZeroFilter
[2016-04-15T00:14Z] INFO  17:14:34,977 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:14Z] INFO  17:14:34,978 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-15T00:14Z] INFO  17:14:34,978 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:14Z] INFO  17:14:35,043 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-15T00:14Z] INFO  17:14:35,338 IntervalUtils - Processing 15520276 bp from intervals
[2016-04-15T00:14Z] WARN  17:14:35,343 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:14Z] INFO  17:14:35,451 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:14Z] INFO  17:14:35,718 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:14Z] INFO  17:14:35,718 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:14Z] INFO  17:14:35,719 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:14Z] INFO  17:14:35,719 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:14Z] INFO  17:14:36,377 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:14Z] INFO  17:14:36,381 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:14Z] INFO  17:14:36,381 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:14Z] INFO  17:14:36,382 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:14Z] INFO  17:14:36,386 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/8/R14-18106_kapa-NGv3-PE100-NGv3-sort-8_95142853_110655419-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/8/tx/tmpEkBG3a/R14-18106_kapa-NGv3-PE100-NGv3-sort-8_95142853_110655419-prep-prealign-realign.intervals -l INFO -L 8:95142854-110655419 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:14Z] INFO  17:14:36,399 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:14Z] INFO  17:14:36,399 HelpFormatter - Date/Time: 2016/04/14 17:14:36
[2016-04-15T00:14Z] INFO  17:14:36,400 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:14Z] INFO  17:14:36,400 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:14Z] INFO  17:14:36,510 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:14Z] INFO  17:14:36,570 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:14Z] GATK: realign ('8', 48003022, 63659688) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:14Z] INFO  17:14:36,713 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T00:14Z] INFO  17:14:36,739 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:14Z] INFO  17:14:36,828 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.09
[2016-04-15T00:14Z] INFO  17:14:37,237 IntervalUtils - Processing 15512566 bp from intervals
[2016-04-15T00:14Z] WARN  17:14:37,247 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:14Z] INFO  17:14:37,347 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:14Z] INFO  17:14:37,355 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@5fe152b7
[2016-04-15T00:14Z] INFO  17:14:37,427 ProgressMeter -            done    378291.0    25.0 s      67.0 s      100.0%    25.0 s       0.0 s
[2016-04-15T00:14Z] INFO  17:14:37,428 ProgressMeter - Total runtime 25.45 secs, 0.42 min, 0.01 hours
[2016-04-15T00:14Z] INFO  17:14:37,432 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 378291 total reads (0.00%)
[2016-04-15T00:14Z] INFO  17:14:37,433 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:14Z] INFO  17:14:37,433 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:14Z] INFO  17:14:37,433 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:14Z] INFO  17:14:37,453 ProgressMeter -            done    174453.0    23.0 s       2.2 m      100.0%    23.0 s       0.0 s
[2016-04-15T00:14Z] INFO  17:14:37,454 ProgressMeter - Total runtime 23.15 secs, 0.39 min, 0.01 hours
[2016-04-15T00:14Z] INFO  17:14:37,454 MicroScheduler - 161 reads were filtered out during the traversal out of approximately 174614 total reads (0.09%)
[2016-04-15T00:14Z] INFO  17:14:37,454 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:14Z] INFO  17:14:37,455 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:14Z] INFO  17:14:37,455 MicroScheduler -   -> 161 reads (0.09% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:14Z] INFO  17:14:37,564 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:14Z] INFO  17:14:37,565 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:14Z] INFO  17:14:37,566 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:14Z] INFO  17:14:37,567 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:14Z] INFO  17:14:38,511 ProgressMeter -            done   1.6504519E7    17.0 s       1.0 s      100.0%    17.0 s       0.0 s
[2016-04-15T00:14Z] INFO  17:14:38,511 ProgressMeter - Total runtime 17.87 secs, 0.30 min, 0.00 hours
[2016-04-15T00:14Z] INFO  17:14:38,526 MicroScheduler - 15039 reads were filtered out during the traversal out of approximately 177805 total reads (8.46%)
[2016-04-15T00:14Z] INFO  17:14:38,526 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:14Z] INFO  17:14:38,527 MicroScheduler -   -> 623 reads (0.35% of total) failing BadMateFilter
[2016-04-15T00:14Z] INFO  17:14:38,527 MicroScheduler -   -> 13163 reads (7.40% of total) failing DuplicateReadFilter
[2016-04-15T00:14Z] INFO  17:14:38,527 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:14Z] INFO  17:14:38,527 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:14Z] INFO  17:14:38,528 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:14Z] INFO  17:14:38,528 MicroScheduler -   -> 1253 reads (0.70% of total) failing MappingQualityZeroFilter
[2016-04-15T00:14Z] INFO  17:14:38,528 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:14Z] INFO  17:14:38,528 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-15T00:14Z] INFO  17:14:38,529 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:14Z] INFO  17:14:38,843 ProgressMeter -            done   1.5521428E7    22.0 s       1.0 s      100.0%    22.0 s       0.0 s
[2016-04-15T00:14Z] INFO  17:14:38,844 ProgressMeter - Total runtime 22.19 secs, 0.37 min, 0.01 hours
[2016-04-15T00:14Z] INFO  17:14:38,849 MicroScheduler - 107611 reads were filtered out during the traversal out of approximately 455119 total reads (23.64%)
[2016-04-15T00:14Z] INFO  17:14:38,850 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:14Z] INFO  17:14:38,851 MicroScheduler -   -> 979 reads (0.22% of total) failing BadMateFilter
[2016-04-15T00:14Z] INFO  17:14:38,852 MicroScheduler -   -> 28742 reads (6.32% of total) failing DuplicateReadFilter
[2016-04-15T00:14Z] INFO  17:14:38,852 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:14Z] INFO  17:14:38,853 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:14Z] INFO  17:14:38,854 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:14Z] INFO  17:14:38,855 MicroScheduler -   -> 77890 reads (17.11% of total) failing MappingQualityZeroFilter
[2016-04-15T00:14Z] INFO  17:14:38,855 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:14Z] INFO  17:14:38,856 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-15T00:14Z] INFO  17:14:38,857 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:14Z] INFO  17:14:38,894 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:14Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-7_63095909_78636522-prep.bam
[2016-04-15T00:14Z] INFO  17:14:39,050 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:14Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-9_0_15510186-prep-prealign.bam
[2016-04-15T00:14Z] INFO  17:14:39,344 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:14Z] INFO  17:14:39,348 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:14Z] INFO  17:14:39,348 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:14Z] INFO  17:14:39,349 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:14Z] INFO  17:14:39,354 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/8/R14-18106_kapa-NGv3-PE100-NGv3-sort-8_48003022_63659688-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/8/R14-18106_kapa-NGv3-PE100-NGv3-sort-8_48003022_63659688-prep-prealign-realign.intervals -L 8:48003023-63659688 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/8/tx/tmprLUd3S/R14-18106_kapa-NGv3-PE100-NGv3-sort-8_48003022_63659688-prep.bam
[2016-04-15T00:14Z] INFO  17:14:39,363 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:14Z] INFO  17:14:39,369 HelpFormatter - Date/Time: 2016/04/14 17:14:39
[2016-04-15T00:14Z] INFO  17:14:39,370 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:14Z] INFO  17:14:39,370 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:14Z] INFO  17:14:39,547 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:14Z] INFO  17:14:39,684 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:14Z] INFO  17:14:39,698 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:14Z] GATK RealignerTargetCreator: R14-18106_kapa-NGv3-PE100-NGv3-sort-9_0_15510186-prep-prealign.bam 9:1-15510186
[2016-04-15T00:14Z] GATK: RealignerTargetCreator
[2016-04-15T00:14Z] INFO  17:14:39,769 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-15T00:14Z] INFO  17:14:40,023 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:14Z] GATK: realign ('8', 31496910, 48001429) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:14Z] INFO  17:14:40,105 IntervalUtils - Processing 15656666 bp from intervals
[2016-04-15T00:14Z] WARN  17:14:40,111 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:14Z] GATK pre-alignment ('9', 15564086, 32405601) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:14Z] INFO  17:14:40,185 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:14Z] INFO  17:14:40,260 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:14Z] GATK: realign ('7', 141629903, 157151331) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:14Z] INFO  17:14:40,286 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:14Z] INFO  17:14:40,287 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:14Z] INFO  17:14:40,288 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:14Z] INFO  17:14:40,293 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:14Z] INFO  17:14:40,452 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:14Z] INFO  17:14:40,664 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:14Z] INFO  17:14:41,140 ProgressMeter -            done   1.5626592E7    16.0 s       1.0 s      100.0%    16.0 s       0.0 s
[2016-04-15T00:14Z] INFO  17:14:41,141 ProgressMeter - Total runtime 16.78 secs, 0.28 min, 0.00 hours
[2016-04-15T00:14Z] INFO  17:14:41,145 MicroScheduler - 7989 reads were filtered out during the traversal out of approximately 98632 total reads (8.10%)
[2016-04-15T00:14Z] INFO  17:14:41,146 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:14Z] INFO  17:14:41,147 MicroScheduler -   -> 448 reads (0.45% of total) failing BadMateFilter
[2016-04-15T00:14Z] INFO  17:14:41,148 MicroScheduler -   -> 6983 reads (7.08% of total) failing DuplicateReadFilter
[2016-04-15T00:14Z] INFO  17:14:41,148 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:14Z] INFO  17:14:41,149 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:14Z] INFO  17:14:41,149 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:14Z] INFO  17:14:41,150 MicroScheduler -   -> 558 reads (0.57% of total) failing MappingQualityZeroFilter
[2016-04-15T00:14Z] INFO  17:14:41,151 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:14Z] INFO  17:14:41,151 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-15T00:14Z] INFO  17:14:41,152 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:14Z] INFO  17:14:42,126 ProgressMeter -            done   1.5734951E7    17.0 s       1.0 s      100.0%    17.0 s       0.0 s
[2016-04-15T00:14Z] INFO  17:14:42,127 ProgressMeter - Total runtime 17.22 secs, 0.29 min, 0.00 hours
[2016-04-15T00:14Z] INFO  17:14:42,131 MicroScheduler - 11583 reads were filtered out during the traversal out of approximately 142275 total reads (8.14%)
[2016-04-15T00:14Z] INFO  17:14:42,132 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:14Z] INFO  17:14:42,133 MicroScheduler -   -> 566 reads (0.40% of total) failing BadMateFilter
[2016-04-15T00:14Z] INFO  17:14:42,133 MicroScheduler -   -> 10632 reads (7.47% of total) failing DuplicateReadFilter
[2016-04-15T00:14Z] INFO  17:14:42,134 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:14Z] INFO  17:14:42,135 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:14Z] INFO  17:14:42,135 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:14Z] INFO  17:14:42,136 MicroScheduler -   -> 385 reads (0.27% of total) failing MappingQualityZeroFilter
[2016-04-15T00:14Z] INFO  17:14:42,136 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:14Z] INFO  17:14:42,137 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-15T00:14Z] INFO  17:14:42,138 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:14Z] INFO  17:14:42,556 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:14Z] INFO  17:14:42,567 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:14Z] INFO  17:14:42,570 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:14Z] INFO  17:14:42,570 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:14Z] INFO  17:14:42,571 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:14Z] INFO  17:14:42,576 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/9/R14-18106_kapa-NGv3-PE100-NGv3-sort-9_0_15510186-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/9/tx/tmpHFHdJS/R14-18106_kapa-NGv3-PE100-NGv3-sort-9_0_15510186-prep-prealign-realign.intervals -l INFO -L 9:1-15510186 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:14Z] INFO  17:14:42,587 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:14Z] INFO  17:14:42,587 HelpFormatter - Date/Time: 2016/04/14 17:14:42
[2016-04-15T00:14Z] INFO  17:14:42,588 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:14Z] INFO  17:14:42,589 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:14Z] GATK: realign ('8', 79513976, 95140568) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:14Z] INFO  17:14:42,702 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:14Z] INFO  17:14:42,830 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:14Z] INFO  17:14:42,833 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:14Z] INFO  17:14:42,834 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:14Z] INFO  17:14:42,834 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:14Z] INFO  17:14:42,839 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/8/R14-18106_kapa-NGv3-PE100-NGv3-sort-8_31496910_48001429-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/8/R14-18106_kapa-NGv3-PE100-NGv3-sort-8_31496910_48001429-prep-prealign-realign.intervals -L 8:31496911-48001429 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/8/tx/tmpVyEcAv/R14-18106_kapa-NGv3-PE100-NGv3-sort-8_31496910_48001429-prep.bam
[2016-04-15T00:14Z] INFO  17:14:42,880 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:14Z] INFO  17:14:42,881 HelpFormatter - Date/Time: 2016/04/14 17:14:42
[2016-04-15T00:14Z] INFO  17:14:42,881 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:14Z] INFO  17:14:42,882 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:14Z] INFO  17:14:42,899 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T00:14Z] INFO  17:14:42,909 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:14Z] INFO  17:14:42,938 ProgressMeter -     8:144993076    100001.0    30.0 s       5.1 m       69.3%    43.0 s      13.0 s
[2016-04-15T00:14Z] INFO  17:14:42,962 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-15T00:14Z] INFO  17:14:42,981 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:14Z] INFO  17:14:42,985 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:14Z] INFO  17:14:42,985 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:14Z] INFO  17:14:42,986 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:14Z] INFO  17:14:42,990 HelpFormatter - Program Args: -T PrintReads -L 9:15564087-32405601 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/9/tx/tmp0Lmt8r/R14-18106_kapa-NGv3-PE100-NGv3-sort-9_15564086_32405601-prep-prealign.bam
[2016-04-15T00:14Z] INFO  17:14:43,001 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:14Z] INFO  17:14:43,002 HelpFormatter - Date/Time: 2016/04/14 17:14:42
[2016-04-15T00:14Z] INFO  17:14:43,002 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:14Z] INFO  17:14:43,002 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:14Z] INFO  17:14:43,062 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:14Z] INFO  17:14:43,178 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:14Z] INFO  17:14:43,180 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:14Z] INFO  17:14:43,181 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:14Z] INFO  17:14:43,181 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:14Z] INFO  17:14:43,191 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:14Z] INFO  17:14:43,194 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/7/R14-18106_kapa-NGv3-PE100-NGv3-sort-7_141629903_157151331-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/7/R14-18106_kapa-NGv3-PE100-NGv3-sort-7_141629903_157151331-prep-prealign-realign.intervals -L 7:141629904-157151331 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/7/tx/tmpCwGKxk/R14-18106_kapa-NGv3-PE100-NGv3-sort-7_141629903_157151331-prep.bam
[2016-04-15T00:14Z] INFO  17:14:43,208 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:14Z] INFO  17:14:43,208 HelpFormatter - Date/Time: 2016/04/14 17:14:43
[2016-04-15T00:14Z] INFO  17:14:43,208 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:14Z] INFO  17:14:43,220 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:14Z] INFO  17:14:43,208 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:14Z] INFO  17:14:43,238 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:14Z] INFO  17:14:43,289 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-15T00:14Z] INFO  17:14:43,379 IntervalUtils - Processing 15510186 bp from intervals
[2016-04-15T00:14Z] WARN  17:14:43,384 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:14Z] INFO  17:14:43,466 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:14Z] INFO  17:14:43,487 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:14Z] INFO  17:14:43,564 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:14Z] GATK: realign ('8', 63775819, 79510770) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:14Z] INFO  17:14:43,653 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:14Z] INFO  17:14:43,677 IntervalUtils - Processing 16504519 bp from intervals
[2016-04-15T00:14Z] WARN  17:14:43,682 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:14Z] INFO  17:14:43,686 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:14Z] INFO  17:14:43,737 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-15T00:14Z] INFO  17:14:43,740 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:14Z] INFO  17:14:43,741 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:14Z] INFO  17:14:43,741 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:14Z] INFO  17:14:43,741 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:14Z] INFO  17:14:43,793 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:14Z] INFO  17:14:43,935 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:14Z] INFO  17:14:43,936 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:14Z] INFO  17:14:43,937 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:14Z] INFO  17:14:43,937 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:14Z] INFO  17:14:44,090 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:14Z] INFO  17:14:44,187 IntervalUtils - Processing 15521428 bp from intervals
[2016-04-15T00:14Z] WARN  17:14:44,202 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:14Z] INFO  17:14:44,292 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:14Z] INFO  17:14:44,335 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:14Z] INFO  17:14:44,361 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-15T00:14Z] INFO  17:14:44,431 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:14Z] INFO  17:14:44,441 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:14Z] INFO  17:14:44,517 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-15T00:14Z] INFO  17:14:44,524 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:14Z] INFO  17:14:44,525 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:14Z] INFO  17:14:44,536 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:14Z] INFO  17:14:44,537 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:14Z] INFO  17:14:44,537 IntervalUtils - Processing 16841515 bp from intervals
[2016-04-15T00:14Z] INFO  17:14:44,683 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:14Z] INFO  17:14:44,742 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:14Z] INFO  17:14:44,962 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:14Z] INFO  17:14:44,988 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:14Z] INFO  17:14:44,989 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:14Z] INFO  17:14:44,990 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:14Z] INFO  17:14:44,991 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:14Z] INFO  17:14:45,004 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:14Z] INFO  17:14:45,169 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:14Z] INFO  17:14:45,511 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:14Z] INFO  17:14:45,514 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:14Z] INFO  17:14:45,515 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:14Z] INFO  17:14:45,515 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:14Z] INFO  17:14:45,520 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/8/R14-18106_kapa-NGv3-PE100-NGv3-sort-8_79513976_95140568-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/8/R14-18106_kapa-NGv3-PE100-NGv3-sort-8_79513976_95140568-prep-prealign-realign.intervals -L 8:79513977-95140568 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/8/tx/tmpNEHOiR/R14-18106_kapa-NGv3-PE100-NGv3-sort-8_79513976_95140568-prep.bam
[2016-04-15T00:14Z] INFO  17:14:45,551 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:14Z] INFO  17:14:45,552 HelpFormatter - Date/Time: 2016/04/14 17:14:45
[2016-04-15T00:14Z] INFO  17:14:45,553 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:14Z] INFO  17:14:45,553 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:14Z] INFO  17:14:45,651 ProgressMeter -            done    842714.0    51.0 s      60.0 s      100.0%    51.0 s       0.0 s
[2016-04-15T00:14Z] INFO  17:14:45,651 ProgressMeter - Total runtime 51.39 secs, 0.86 min, 0.01 hours
[2016-04-15T00:14Z] INFO  17:14:45,655 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 842714 total reads (0.00%)
[2016-04-15T00:14Z] INFO  17:14:45,655 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:14Z] INFO  17:14:45,656 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:14Z] INFO  17:14:45,656 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:14Z] INFO  17:14:45,808 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:14Z] INFO  17:14:45,959 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:14Z] INFO  17:14:45,974 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:14Z] INFO  17:14:46,063 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.09
[2016-04-15T00:14Z] INFO  17:14:46,432 ProgressMeter -            done   1.5517156E7    19.0 s       1.0 s      100.0%    19.0 s       0.0 s
[2016-04-15T00:14Z] INFO  17:14:46,438 ProgressMeter - Total runtime 19.77 secs, 0.33 min, 0.01 hours
[2016-04-15T00:14Z] INFO  17:14:46,442 MicroScheduler - 110117 reads were filtered out during the traversal out of approximately 306532 total reads (35.92%)
[2016-04-15T00:14Z] INFO  17:14:46,443 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:14Z] INFO  17:14:46,444 MicroScheduler -   -> 642 reads (0.21% of total) failing BadMateFilter
[2016-04-15T00:14Z] INFO  17:14:46,444 MicroScheduler -   -> 16845 reads (5.50% of total) failing DuplicateReadFilter
[2016-04-15T00:14Z] INFO  17:14:46,445 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:14Z] INFO  17:14:46,446 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:14Z] INFO  17:14:46,446 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:14Z] INFO  17:14:46,447 MicroScheduler -   -> 92630 reads (30.22% of total) failing MappingQualityZeroFilter
[2016-04-15T00:14Z] INFO  17:14:46,447 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:14Z] INFO  17:14:46,448 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-15T00:14Z] INFO  17:14:46,448 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:14Z] INFO  17:14:46,533 IntervalUtils - Processing 15626592 bp from intervals
[2016-04-15T00:14Z] WARN  17:14:46,537 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:14Z] INFO  17:14:46,607 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:14Z] INFO  17:14:46,718 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:14Z] INFO  17:14:46,719 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:14Z] INFO  17:14:46,720 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:14Z] INFO  17:14:46,720 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:14Z] INFO  17:14:46,816 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:14Z] INFO  17:14:46,818 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:14Z] INFO  17:14:46,819 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:14Z] INFO  17:14:46,819 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:14Z] INFO  17:14:46,823 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/8/R14-18106_kapa-NGv3-PE100-NGv3-sort-8_63775819_79510770-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/8/R14-18106_kapa-NGv3-PE100-NGv3-sort-8_63775819_79510770-prep-prealign-realign.intervals -L 8:63775820-79510770 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/8/tx/tmpM5YCFX/R14-18106_kapa-NGv3-PE100-NGv3-sort-8_63775819_79510770-prep.bam
[2016-04-15T00:14Z] INFO  17:14:46,844 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:14Z] INFO  17:14:46,845 HelpFormatter - Date/Time: 2016/04/14 17:14:46
[2016-04-15T00:14Z] INFO  17:14:46,846 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:14Z] INFO  17:14:46,846 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:14Z] INFO  17:14:46,880 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:14Z] INFO  17:14:47,046 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:14Z] INFO  17:14:47,077 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:14Z] INFO  17:14:47,217 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:14Z] INFO  17:14:47,232 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:14Z] INFO  17:14:47,256 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:14Z] INFO  17:14:47,297 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-15T00:14Z] INFO  17:14:47,302 ProgressMeter -            done   1.5537634E7    17.0 s       1.0 s      100.0%    17.0 s       0.0 s
[2016-04-15T00:14Z] INFO  17:14:47,303 ProgressMeter - Total runtime 17.05 secs, 0.28 min, 0.00 hours
[2016-04-15T00:14Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-6_31083801_46593245-prep.bam
[2016-04-15T00:14Z] INFO  17:14:47,307 MicroScheduler - 10524 reads were filtered out during the traversal out of approximately 135298 total reads (7.78%)
[2016-04-15T00:14Z] INFO  17:14:47,308 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:14Z] INFO  17:14:47,309 MicroScheduler -   -> 559 reads (0.41% of total) failing BadMateFilter
[2016-04-15T00:14Z] INFO  17:14:47,309 MicroScheduler -   -> 9750 reads (7.21% of total) failing DuplicateReadFilter
[2016-04-15T00:14Z] INFO  17:14:47,310 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:14Z] INFO  17:14:47,311 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:14Z] INFO  17:14:47,311 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:14Z] INFO  17:14:47,312 MicroScheduler -   -> 215 reads (0.16% of total) failing MappingQualityZeroFilter
[2016-04-15T00:14Z] INFO  17:14:47,312 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:14Z] INFO  17:14:47,312 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-15T00:14Z] INFO  17:14:47,313 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:14Z] INFO  17:14:47,673 IntervalUtils - Processing 15734951 bp from intervals
[2016-04-15T00:14Z] WARN  17:14:47,678 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:14Z] INFO  17:14:47,743 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:14Z] INFO  17:14:47,750 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:14Z] GATK: realign ('8', 0, 15517156) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:14Z] INFO  17:14:47,852 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:14Z] INFO  17:14:47,853 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:14Z] INFO  17:14:47,854 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:14Z] INFO  17:14:47,855 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:14Z] INFO  17:14:47,957 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:14Z] INFO  17:14:48,093 ProgressMeter -            done    324164.0    22.0 s      69.0 s      100.0%    22.0 s       0.0 s
[2016-04-15T00:14Z] INFO  17:14:48,093 ProgressMeter - Total runtime 22.53 secs, 0.38 min, 0.01 hours
[2016-04-15T00:14Z] INFO  17:14:48,096 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 324164 total reads (0.00%)
[2016-04-15T00:14Z] INFO  17:14:48,097 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:14Z] INFO  17:14:48,098 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:14Z] INFO  17:14:48,099 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:14Z] INFO  17:14:48,130 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:14Z] INFO  17:14:48,645 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:14Z] GATK: realign ('8', 110656864, 126194498) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:14Z] GATK pre-alignment ('9', 32407258, 65506776) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:14Z] INFO  17:14:49,914 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:14Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-7_126086124_141619620-prep.bam
[2016-04-15T00:14Z] INFO  17:14:50,690 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:14Z] INFO  17:14:50,693 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:14Z] INFO  17:14:50,694 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:14Z] INFO  17:14:50,694 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:14Z] INFO  17:14:50,699 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/8/R14-18106_kapa-NGv3-PE100-NGv3-sort-8_0_15517156-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/8/R14-18106_kapa-NGv3-PE100-NGv3-sort-8_0_15517156-prep-prealign-realign.intervals -L 8:1-15517156 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/8/tx/tmptUTcYW/R14-18106_kapa-NGv3-PE100-NGv3-sort-8_0_15517156-prep.bam
[2016-04-15T00:14Z] INFO  17:14:50,718 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:14Z] INFO  17:14:50,719 HelpFormatter - Date/Time: 2016/04/14 17:14:50
[2016-04-15T00:14Z] INFO  17:14:50,719 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:14Z] INFO  17:14:50,720 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:14Z] GATK pre-alignment ('9', 65507205, 82187750) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:14Z] INFO  17:14:50,963 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:14Z] INFO  17:14:51,106 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:14Z] INFO  17:14:51,115 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:14Z] INFO  17:14:51,187 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-15T00:14Z] INFO  17:14:51,636 IntervalUtils - Processing 15517156 bp from intervals
[2016-04-15T00:14Z] WARN  17:14:51,640 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:14Z] INFO  17:14:51,705 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:14Z] INFO  17:14:51,709 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:14Z] INFO  17:14:51,709 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:14Z] INFO  17:14:51,710 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:14Z] INFO  17:14:51,714 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/8/R14-18106_kapa-NGv3-PE100-NGv3-sort-8_110656864_126194498-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/8/R14-18106_kapa-NGv3-PE100-NGv3-sort-8_110656864_126194498-prep-prealign-realign.intervals -L 8:110656865-126194498 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/8/tx/tmp6_py9a/R14-18106_kapa-NGv3-PE100-NGv3-sort-8_110656864_126194498-prep.bam
[2016-04-15T00:14Z] INFO  17:14:51,738 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:14Z] INFO  17:14:51,739 HelpFormatter - Date/Time: 2016/04/14 17:14:51
[2016-04-15T00:14Z] INFO  17:14:51,739 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:14Z] INFO  17:14:51,739 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:14Z] INFO  17:14:51,744 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:14Z] INFO  17:14:51,865 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:14Z] INFO  17:14:51,866 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:14Z] INFO  17:14:51,866 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:14Z] INFO  17:14:51,867 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:14Z] INFO  17:14:52,023 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:14Z] INFO  17:14:52,056 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:14Z] INFO  17:14:52,189 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:14Z] INFO  17:14:52,198 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:14Z] INFO  17:14:52,218 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:14Z] INFO  17:14:52,286 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.09
[2016-04-15T00:14Z] INFO  17:14:52,673 ProgressMeter -            done   1.5520276E7    16.0 s       1.0 s      100.0%    16.0 s       0.0 s
[2016-04-15T00:14Z] INFO  17:14:52,674 ProgressMeter - Total runtime 16.96 secs, 0.28 min, 0.00 hours
[2016-04-15T00:14Z] INFO  17:14:52,678 MicroScheduler - 9468 reads were filtered out during the traversal out of approximately 117784 total reads (8.04%)
[2016-04-15T00:14Z] INFO  17:14:52,679 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:14Z] INFO  17:14:52,679 MicroScheduler -   -> 526 reads (0.45% of total) failing BadMateFilter
[2016-04-15T00:14Z] INFO  17:14:52,680 MicroScheduler -   -> 8714 reads (7.40% of total) failing DuplicateReadFilter
[2016-04-15T00:14Z] INFO  17:14:52,681 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:14Z] INFO  17:14:52,683 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:14Z] INFO  17:14:52,684 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:14Z] INFO  17:14:52,685 MicroScheduler -   -> 228 reads (0.19% of total) failing MappingQualityZeroFilter
[2016-04-15T00:14Z] INFO  17:14:52,685 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:14Z] INFO  17:14:52,686 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-15T00:14Z] INFO  17:14:52,686 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:14Z] INFO  17:14:52,715 IntervalUtils - Processing 15537634 bp from intervals
[2016-04-15T00:14Z] WARN  17:14:52,721 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:14Z] INFO  17:14:52,757 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:14Z] INFO  17:14:52,760 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:14Z] INFO  17:14:52,761 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:14Z] INFO  17:14:52,761 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:14Z] INFO  17:14:52,766 HelpFormatter - Program Args: -T PrintReads -L 9:32407259-65506776 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/9/tx/tmpBOoy7_/R14-18106_kapa-NGv3-PE100-NGv3-sort-9_32407258_65506776-prep-prealign.bam
[2016-04-15T00:14Z] INFO  17:14:52,782 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:14Z] INFO  17:14:52,783 HelpFormatter - Date/Time: 2016/04/14 17:14:52
[2016-04-15T00:14Z] INFO  17:14:52,784 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:14Z] INFO  17:14:52,784 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:14Z] INFO  17:14:52,795 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:14Z] INFO  17:14:52,887 ProgressMeter -            done    133058.0    12.0 s      94.0 s      100.0%    12.0 s       0.0 s
[2016-04-15T00:14Z] INFO  17:14:52,888 ProgressMeter - Total runtime 12.60 secs, 0.21 min, 0.00 hours
[2016-04-15T00:14Z] INFO  17:14:52,892 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 133058 total reads (0.00%)
[2016-04-15T00:14Z] INFO  17:14:52,893 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:14Z] INFO  17:14:52,894 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:14Z] INFO  17:14:52,894 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:14Z] INFO  17:14:52,927 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:14Z] INFO  17:14:52,927 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:14Z] INFO  17:14:52,928 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:14Z] INFO  17:14:52,928 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:14Z] INFO  17:14:52,969 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:14Z] INFO  17:14:52,982 ProgressMeter -            done   1.5510954E7    20.0 s       1.0 s      100.0%    20.0 s       0.0 s
[2016-04-15T00:14Z] INFO  17:14:52,982 ProgressMeter - Total runtime 20.35 secs, 0.34 min, 0.01 hours
[2016-04-15T00:14Z] INFO  17:14:52,986 MicroScheduler - 27581 reads were filtered out during the traversal out of approximately 336193 total reads (8.20%)
[2016-04-15T00:14Z] INFO  17:14:52,986 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:14Z] INFO  17:14:52,987 MicroScheduler -   -> 909 reads (0.27% of total) failing BadMateFilter
[2016-04-15T00:14Z] INFO  17:14:52,987 MicroScheduler -   -> 25307 reads (7.53% of total) failing DuplicateReadFilter
[2016-04-15T00:14Z] INFO  17:14:52,987 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:14Z] INFO  17:14:52,988 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:14Z] INFO  17:14:52,988 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:14Z] INFO  17:14:52,988 MicroScheduler -   -> 1365 reads (0.41% of total) failing MappingQualityZeroFilter
[2016-04-15T00:14Z] INFO  17:14:52,988 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:14Z] INFO  17:14:52,989 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-15T00:14Z] INFO  17:14:52,989 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:14Z] INFO  17:14:53,081 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:14Z] INFO  17:14:53,253 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:14Z] INFO  17:14:53,939 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:14Z] INFO  17:14:53,942 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:14Z] INFO  17:14:53,942 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:14Z] INFO  17:14:53,942 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:14Z] INFO  17:14:53,946 HelpFormatter - Program Args: -T PrintReads -L 9:65507206-82187750 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/9/tx/tmp5Db60b/R14-18106_kapa-NGv3-PE100-NGv3-sort-9_65507205_82187750-prep-prealign.bam
[2016-04-15T00:14Z] INFO  17:14:53,955 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:14Z] INFO  17:14:53,955 HelpFormatter - Date/Time: 2016/04/14 17:14:53
[2016-04-15T00:14Z] INFO  17:14:53,955 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:14Z] INFO  17:14:53,955 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:14Z] INFO  17:14:53,976 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-15T00:14Z] INFO  17:14:54,049 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:14Z] INFO  17:14:54,090 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:14Z] INFO  17:14:54,092 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:14Z] GATK: realign ('8', 126369460, 141889736) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:14Z] INFO  17:14:54,171 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:14Z] INFO  17:14:54,177 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.09
[2016-04-15T00:14Z] INFO  17:14:54,201 IntervalUtils - Processing 33099518 bp from intervals
[2016-04-15T00:14Z] INFO  17:14:54,345 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:14Z] INFO  17:14:54,579 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:14Z] INFO  17:14:54,580 ProgressMeter -            done   1.5512566E7    17.0 s       1.0 s      100.0%    17.0 s       0.0 s
[2016-04-15T00:14Z] INFO  17:14:54,581 ProgressMeter - Total runtime 17.02 secs, 0.28 min, 0.00 hours
[2016-04-15T00:14Z] INFO  17:14:54,584 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:14Z] INFO  17:14:54,585 MicroScheduler - 15956 reads were filtered out during the traversal out of approximately 199782 total reads (7.99%)
[2016-04-15T00:14Z] INFO  17:14:54,585 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:14Z] INFO  17:14:54,586 MicroScheduler -   -> 688 reads (0.34% of total) failing BadMateFilter
[2016-04-15T00:14Z] INFO  17:14:54,587 MicroScheduler -   -> 14852 reads (7.43% of total) failing DuplicateReadFilter
[2016-04-15T00:14Z] INFO  17:14:54,587 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:14Z] INFO  17:14:54,588 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:14Z] INFO  17:14:54,589 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:14Z] INFO  17:14:54,589 MicroScheduler -   -> 416 reads (0.21% of total) failing MappingQualityZeroFilter
[2016-04-15T00:14Z] INFO  17:14:54,590 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:14Z] INFO  17:14:54,590 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-15T00:14Z] INFO  17:14:54,591 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:14Z] GATK: realign ('8', 15519664, 31030618) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:14Z] INFO  17:14:54,627 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:14Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-8_48003022_63659688-prep.bam
[2016-04-15T00:14Z] INFO  17:14:54,634 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:14Z] INFO  17:14:54,635 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:14Z] INFO  17:14:54,636 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:14Z] INFO  17:14:54,650 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:14Z] INFO  17:14:54,963 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:14Z] GATK pre-alignment ('9', 82188172, 97717561) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:14Z] INFO  17:14:55,165 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-15T00:14Z] INFO  17:14:55,238 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:14Z] INFO  17:14:55,248 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:14Z] INFO  17:14:55,297 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-15T00:14Z] INFO  17:14:55,310 IntervalUtils - Processing 16680545 bp from intervals
[2016-04-15T00:14Z] INFO  17:14:55,386 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:14Z] INFO  17:14:55,710 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:14Z] INFO  17:14:55,713 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:14Z] INFO  17:14:55,713 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:14Z] INFO  17:14:55,714 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:14Z] INFO  17:14:55,728 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:14Z] INFO  17:14:55,891 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:14Z] INFO  17:14:55,983 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:14Z] GATK: realign ('8', 95142853, 110655419) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:14Z] INFO  17:14:56,683 ProgressMeter -            done     98032.0     9.0 s     101.0 s      100.0%     9.0 s       0.0 s
[2016-04-15T00:14Z] INFO  17:14:56,684 ProgressMeter - Total runtime 9.96 secs, 0.17 min, 0.00 hours
[2016-04-15T00:14Z] INFO  17:14:56,688 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 98032 total reads (0.00%)
[2016-04-15T00:14Z] INFO  17:14:56,688 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:14Z] INFO  17:14:56,688 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:14Z] INFO  17:14:56,689 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:14Z] INFO  17:14:56,912 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:14Z] INFO  17:14:56,916 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:14Z] INFO  17:14:56,917 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:14Z] INFO  17:14:56,917 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:14Z] INFO  17:14:56,922 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/8/R14-18106_kapa-NGv3-PE100-NGv3-sort-8_126369460_141889736-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/8/R14-18106_kapa-NGv3-PE100-NGv3-sort-8_126369460_141889736-prep-prealign-realign.intervals -L 8:126369461-141889736 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/8/tx/tmpp2Du9C/R14-18106_kapa-NGv3-PE100-NGv3-sort-8_126369460_141889736-prep.bam
[2016-04-15T00:14Z] INFO  17:14:56,941 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:14Z] INFO  17:14:56,943 HelpFormatter - Date/Time: 2016/04/14 17:14:56
[2016-04-15T00:14Z] INFO  17:14:56,943 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:14Z] INFO  17:14:56,944 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:14Z] INFO  17:14:57,143 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:14Z] INFO  17:14:57,241 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:14Z] INFO  17:14:57,251 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:14Z] INFO  17:14:57,304 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-15T00:14Z] INFO  17:14:57,811 IntervalUtils - Processing 15520276 bp from intervals
[2016-04-15T00:14Z] WARN  17:14:57,840 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:14Z] INFO  17:14:57,919 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:14Z] INFO  17:14:57,974 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:14Z] INFO  17:14:57,977 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:14Z] INFO  17:14:57,978 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:14Z] INFO  17:14:57,979 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:14Z] INFO  17:14:57,983 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/8/R14-18106_kapa-NGv3-PE100-NGv3-sort-8_15519664_31030618-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/8/R14-18106_kapa-NGv3-PE100-NGv3-sort-8_15519664_31030618-prep-prealign-realign.intervals -L 8:15519665-31030618 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/8/tx/tmp4JAvJe/R14-18106_kapa-NGv3-PE100-NGv3-sort-8_15519664_31030618-prep.bam
[2016-04-15T00:14Z] INFO  17:14:58,007 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:14Z] INFO  17:14:58,008 HelpFormatter - Date/Time: 2016/04/14 17:14:57
[2016-04-15T00:14Z] INFO  17:14:58,009 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:14Z] INFO  17:14:58,009 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:14Z] INFO  17:14:58,058 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:14Z] INFO  17:14:58,059 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:14Z] INFO  17:14:58,059 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:14Z] INFO  17:14:58,060 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:14Z] INFO  17:14:58,183 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:14Z] INFO  17:14:58,251 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:14Z] INFO  17:14:58,295 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:14Z] INFO  17:14:58,298 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:14Z] INFO  17:14:58,298 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:14Z] INFO  17:14:58,298 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:14Z] INFO  17:14:58,302 HelpFormatter - Program Args: -T PrintReads -L 9:82188173-97717561 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/9/tx/tmpcRGAoG/R14-18106_kapa-NGv3-PE100-NGv3-sort-9_82188172_97717561-prep-prealign.bam
[2016-04-15T00:14Z] INFO  17:14:58,324 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:14Z] INFO  17:14:58,324 HelpFormatter - Date/Time: 2016/04/14 17:14:58
[2016-04-15T00:14Z] INFO  17:14:58,324 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:14Z] INFO  17:14:58,325 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:14Z] INFO  17:14:58,336 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:14Z] INFO  17:14:58,342 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:14Z] INFO  17:14:58,351 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:14Z] INFO  17:14:58,403 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-15T00:14Z] INFO  17:14:58,440 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:14Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-8_79513976_95140568-prep.bam
[2016-04-15T00:14Z] INFO  17:14:58,477 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:14Z] INFO  17:14:58,729 ProgressMeter -            done    176261.0    14.0 s      83.0 s      100.0%    14.0 s       0.0 s
[2016-04-15T00:14Z] INFO  17:14:58,730 ProgressMeter - Total runtime 14.79 secs, 0.25 min, 0.00 hours
[2016-04-15T00:14Z] INFO  17:14:58,734 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 176261 total reads (0.00%)
[2016-04-15T00:14Z] INFO  17:14:58,734 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:14Z] INFO  17:14:58,734 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:14Z] INFO  17:14:58,735 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:14Z] INFO  17:14:58,762 ProgressMeter -            done   1.5553754E7    27.0 s       1.0 s      100.0%    27.0 s       0.0 s
[2016-04-15T00:14Z] INFO  17:14:58,763 ProgressMeter - Total runtime 27.38 secs, 0.46 min, 0.01 hours
[2016-04-15T00:14Z] INFO  17:14:58,764 MicroScheduler - 180498 reads were filtered out during the traversal out of approximately 703521 total reads (25.66%)
[2016-04-15T00:14Z] INFO  17:14:58,765 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:14Z] INFO  17:14:58,766 MicroScheduler -   -> 1260 reads (0.18% of total) failing BadMateFilter
[2016-04-15T00:14Z] INFO  17:14:58,767 MicroScheduler -   -> 44411 reads (6.31% of total) failing DuplicateReadFilter
[2016-04-15T00:14Z] INFO  17:14:58,768 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:14Z] INFO  17:14:58,768 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:14Z] INFO  17:14:58,769 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:14Z] INFO  17:14:58,770 MicroScheduler -   -> 134827 reads (19.16% of total) failing MappingQualityZeroFilter
[2016-04-15T00:14Z] INFO  17:14:58,770 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:14Z] INFO  17:14:58,771 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-15T00:14Z] INFO  17:14:58,772 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:14Z] GATK pre-alignment ('9', 97718189, 113228306) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:14Z] INFO  17:14:58,926 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:14Z] INFO  17:14:58,931 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:14Z] INFO  17:14:58,931 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:14Z] INFO  17:14:58,932 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:14Z] INFO  17:14:58,938 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/8/R14-18106_kapa-NGv3-PE100-NGv3-sort-8_95142853_110655419-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/8/R14-18106_kapa-NGv3-PE100-NGv3-sort-8_95142853_110655419-prep-prealign-realign.intervals -L 8:95142854-110655419 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/8/tx/tmp_r98HF/R14-18106_kapa-NGv3-PE100-NGv3-sort-8_95142853_110655419-prep.bam
[2016-04-15T00:14Z] INFO  17:14:58,965 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:14Z] INFO  17:14:58,966 HelpFormatter - Date/Time: 2016/04/14 17:14:58
[2016-04-15T00:14Z] INFO  17:14:58,967 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:14Z] INFO  17:14:58,971 IntervalUtils - Processing 15510954 bp from intervals
[2016-04-15T00:14Z] INFO  17:14:58,973 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:14Z] WARN  17:14:58,977 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:14Z] INFO  17:14:59,145 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:14Z] INFO  17:14:59,224 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:14Z] INFO  17:14:59,319 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:14Z] INFO  17:14:59,320 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:14Z] INFO  17:14:59,321 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:14Z] INFO  17:14:59,322 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:14Z] INFO  17:14:59,429 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:14Z] INFO  17:14:59,448 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:14Z] INFO  17:14:59,528 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-15T00:14Z] INFO  17:14:59,705 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:14Z] INFO  17:14:59,864 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-15T00:14Z] INFO  17:14:59,921 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:14Z] INFO  17:14:59,938 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:14Z] INFO  17:14:59,942 IntervalUtils - Processing 15512566 bp from intervals
[2016-04-15T00:14Z] INFO  17:14:59,947 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:14Z] WARN  17:14:59,947 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:14Z] INFO  17:14:59,982 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.03
[2016-04-15T00:14Z] INFO  17:14:59,994 IntervalUtils - Processing 15529389 bp from intervals
[2016-04-15T00:15Z] INFO  17:15:00,019 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:15Z] INFO  17:15:00,079 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:15Z] INFO  17:15:00,197 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:15Z] INFO  17:15:00,198 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:15Z] INFO  17:15:00,199 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:15Z] INFO  17:15:00,199 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:15Z] INFO  17:15:00,375 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:15Z] INFO  17:15:00,444 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:15Z] INFO  17:15:00,445 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:15Z] INFO  17:15:00,445 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:15Z] INFO  17:15:00,445 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:15Z] INFO  17:15:00,465 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:15Z] INFO  17:15:00,502 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:15Z] INFO  17:15:00,503 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:15Z] GATK: realign ('7', 94750023, 110303777) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:15Z] INFO  17:15:00,555 ProgressMeter -            done   1.5510186E7    16.0 s       1.0 s      100.0%    16.0 s       0.0 s
[2016-04-15T00:15Z] INFO  17:15:00,556 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:15Z] INFO  17:15:00,556 ProgressMeter - Total runtime 16.82 secs, 0.28 min, 0.00 hours
[2016-04-15T00:15Z] INFO  17:15:00,560 MicroScheduler - 22610 reads were filtered out during the traversal out of approximately 175066 total reads (12.92%)
[2016-04-15T00:15Z] INFO  17:15:00,561 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:15Z] INFO  17:15:00,562 MicroScheduler -   -> 630 reads (0.36% of total) failing BadMateFilter
[2016-04-15T00:15Z] INFO  17:15:00,562 MicroScheduler -   -> 12258 reads (7.00% of total) failing DuplicateReadFilter
[2016-04-15T00:15Z] INFO  17:15:00,563 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:15Z] INFO  17:15:00,564 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:15Z] INFO  17:15:00,564 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:15Z] INFO  17:15:00,565 MicroScheduler -   -> 9722 reads (5.55% of total) failing MappingQualityZeroFilter
[2016-04-15T00:15Z] INFO  17:15:00,565 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:15Z] INFO  17:15:00,566 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-15T00:15Z] INFO  17:15:00,567 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:15Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-8_31496910_48001429-prep.bam
[2016-04-15T00:15Z] INFO  17:15:00,597 ProgressMeter -            done    141799.0    12.0 s      89.0 s      100.0%    12.0 s       0.0 s
[2016-04-15T00:15Z] INFO  17:15:00,597 ProgressMeter - Total runtime 12.74 secs, 0.21 min, 0.00 hours
[2016-04-15T00:15Z] INFO  17:15:00,603 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 141799 total reads (0.00%)
[2016-04-15T00:15Z] INFO  17:15:00,605 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:15Z] INFO  17:15:00,605 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:15Z] INFO  17:15:00,606 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:15Z] INFO  17:15:00,645 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:15Z] GATK pre-alignment ('9', 113231219, 129089575) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:15Z] INFO  17:15:01,875 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:15Z] INFO  17:15:01,878 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:15Z] INFO  17:15:01,879 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:15Z] INFO  17:15:01,879 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:15Z] INFO  17:15:01,884 HelpFormatter - Program Args: -T PrintReads -L 9:97718190-113228306 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/9/tx/tmpdJ3L4d/R14-18106_kapa-NGv3-PE100-NGv3-sort-9_97718189_113228306-prep-prealign.bam
[2016-04-15T00:15Z] INFO  17:15:01,905 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:15Z] INFO  17:15:01,915 HelpFormatter - Date/Time: 2016/04/14 17:15:01
[2016-04-15T00:15Z] INFO  17:15:01,916 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:15Z] INFO  17:15:01,916 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:15Z] INFO  17:15:02,066 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:15Z] INFO  17:15:02,167 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:15Z] GATK: realign ('9', 0, 15510186) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:15Z] INFO  17:15:02,269 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:15Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-8_63775819_79510770-prep.bam
[2016-04-15T00:15Z] GATK pre-alignment ('9', 129097484, 141213431) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:15Z] INFO  17:15:03,365 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-15T00:15Z] INFO  17:15:03,430 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:15Z] INFO  17:15:03,438 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:15Z] INFO  17:15:03,506 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-15T00:15Z] INFO  17:15:03,521 IntervalUtils - Processing 15510117 bp from intervals
[2016-04-15T00:15Z] INFO  17:15:03,615 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:15Z] INFO  17:15:03,933 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:15Z] INFO  17:15:03,933 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:15Z] INFO  17:15:03,934 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:15Z] INFO  17:15:03,934 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:15Z] INFO  17:15:03,948 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:15Z] INFO  17:15:04,011 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:15Z] INFO  17:15:04,025 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:15Z] INFO  17:15:04,026 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:15Z] INFO  17:15:04,027 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:15Z] INFO  17:15:04,031 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/7/R14-18106_kapa-NGv3-PE100-NGv3-sort-7_94750023_110303777-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/7/R14-18106_kapa-NGv3-PE100-NGv3-sort-7_94750023_110303777-prep-prealign-realign.intervals -L 7:94750024-110303777 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/7/tx/tmpt3hGXK/R14-18106_kapa-NGv3-PE100-NGv3-sort-7_94750023_110303777-prep.bam
[2016-04-15T00:15Z] INFO  17:15:04,046 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:15Z] INFO  17:15:04,046 HelpFormatter - Date/Time: 2016/04/14 17:15:04
[2016-04-15T00:15Z] INFO  17:15:04,046 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:15Z] INFO  17:15:04,047 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:15Z] INFO  17:15:04,121 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:15Z] INFO  17:15:04,276 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:15Z] INFO  17:15:04,316 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:15Z] INFO  17:15:04,319 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:15Z] INFO  17:15:04,319 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:15Z] INFO  17:15:04,319 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:15Z] INFO  17:15:04,336 HelpFormatter - Program Args: -T PrintReads -L 9:113231220-129089575 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/9/tx/tmpZ24uM1/R14-18106_kapa-NGv3-PE100-NGv3-sort-9_113231219_129089575-prep-prealign.bam
[2016-04-15T00:15Z] INFO  17:15:04,352 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:15Z] INFO  17:15:04,352 HelpFormatter - Date/Time: 2016/04/14 17:15:04
[2016-04-15T00:15Z] INFO  17:15:04,353 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:15Z] INFO  17:15:04,353 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:15Z] INFO  17:15:04,397 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:15Z] INFO  17:15:04,407 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:15Z] INFO  17:15:04,479 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-15T00:15Z] INFO  17:15:04,558 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:15Z] INFO  17:15:04,821 IntervalUtils - Processing 15553754 bp from intervals
[2016-04-15T00:15Z] WARN  17:15:04,826 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:15Z] INFO  17:15:04,867 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:15Z] INFO  17:15:04,869 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:15Z] INFO  17:15:04,870 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:15Z] INFO  17:15:04,870 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:15Z] INFO  17:15:04,885 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/9/R14-18106_kapa-NGv3-PE100-NGv3-sort-9_0_15510186-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/9/R14-18106_kapa-NGv3-PE100-NGv3-sort-9_0_15510186-prep-prealign-realign.intervals -L 9:1-15510186 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/9/tx/tmpYoJUv0/R14-18106_kapa-NGv3-PE100-NGv3-sort-9_0_15510186-prep.bam
[2016-04-15T00:15Z] INFO  17:15:04,895 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:15Z] INFO  17:15:04,914 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:15Z] INFO  17:15:04,915 HelpFormatter - Date/Time: 2016/04/14 17:15:04
[2016-04-15T00:15Z] INFO  17:15:04,915 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:15Z] INFO  17:15:04,915 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:15Z] INFO  17:15:04,995 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@41fd9d8e
[2016-04-15T00:15Z] INFO  17:15:05,087 ProgressMeter -            done    120921.0    20.0 s       2.8 m      100.0%    20.0 s       0.0 s
[2016-04-15T00:15Z] INFO  17:15:05,088 ProgressMeter - Total runtime 20.10 secs, 0.33 min, 0.01 hours
[2016-04-15T00:15Z] INFO  17:15:05,089 MicroScheduler - 144 reads were filtered out during the traversal out of approximately 121065 total reads (0.12%)
[2016-04-15T00:15Z] INFO  17:15:05,090 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:15Z] INFO  17:15:05,090 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:15Z] INFO  17:15:05,091 MicroScheduler -   -> 144 reads (0.12% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:15Z] INFO  17:15:05,096 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:15Z] INFO  17:15:05,099 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:15Z] INFO  17:15:05,111 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:15Z] INFO  17:15:05,112 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:15Z] INFO  17:15:05,113 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:15Z] INFO  17:15:05,196 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:15Z] INFO  17:15:05,205 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:15Z] INFO  17:15:05,244 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.04
[2016-04-15T00:15Z] INFO  17:15:05,316 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:15Z] INFO  17:15:05,471 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:15Z] INFO  17:15:05,548 IntervalUtils - Processing 15510186 bp from intervals
[2016-04-15T00:15Z] WARN  17:15:05,553 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:15Z] INFO  17:15:05,618 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:15Z] INFO  17:15:05,618 ProgressMeter -            done    134745.0    12.0 s      94.0 s      100.0%    12.0 s       0.0 s
[2016-04-15T00:15Z] INFO  17:15:05,619 ProgressMeter - Total runtime 12.69 secs, 0.21 min, 0.00 hours
[2016-04-15T00:15Z] INFO  17:15:05,622 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 134745 total reads (0.00%)
[2016-04-15T00:15Z] INFO  17:15:05,623 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:15Z] INFO  17:15:05,623 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:15Z] INFO  17:15:05,623 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:15Z] INFO  17:15:05,693 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:15Z] INFO  17:15:05,702 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:15Z] INFO  17:15:05,702 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:15Z] INFO  17:15:05,703 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:15Z] INFO  17:15:05,704 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-15T00:15Z] INFO  17:15:05,707 HelpFormatter - Program Args: -T PrintReads -L 9:129097485-141213431 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/9/tx/tmpiz9Ka8/R14-18106_kapa-NGv3-PE100-NGv3-sort-9_129097484_141213431-prep-prealign.bam
[2016-04-15T00:15Z] INFO  17:15:05,732 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:15Z] INFO  17:15:05,733 HelpFormatter - Date/Time: 2016/04/14 17:15:05
[2016-04-15T00:15Z] INFO  17:15:05,734 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:15Z] INFO  17:15:05,734 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:15Z] INFO  17:15:05,782 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:15Z] INFO  17:15:05,791 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:15Z] INFO  17:15:05,800 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:15Z] INFO  17:15:05,821 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:15Z] INFO  17:15:05,822 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:15Z] INFO  17:15:05,822 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:15Z] INFO  17:15:05,840 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-15T00:15Z] INFO  17:15:05,865 IntervalUtils - Processing 15858356 bp from intervals
[2016-04-15T00:15Z] INFO  17:15:05,930 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:15Z] INFO  17:15:05,944 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:15Z] INFO  17:15:05,953 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:15Z] INFO  17:15:06,090 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:15Z] INFO  17:15:06,264 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:15Z] INFO  17:15:06,265 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:15Z] INFO  17:15:06,265 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:15Z] INFO  17:15:06,266 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:15Z] INFO  17:15:06,301 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:15Z] INFO  17:15:06,472 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:15Z] INFO  17:15:06,628 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:15Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-9_15564086_32405601-prep-prealign.bam
[2016-04-15T00:15Z] GATK RealignerTargetCreator: R14-18106_kapa-NGv3-PE100-NGv3-sort-9_15564086_32405601-prep-prealign.bam 9:15564087-32405601
[2016-04-15T00:15Z] GATK: RealignerTargetCreator
[2016-04-15T00:15Z] INFO  17:15:07,171 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-15T00:15Z] INFO  17:15:07,196 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:15Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-8_110656864_126194498-prep.bam
[2016-04-15T00:15Z] INFO  17:15:07,253 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:15Z] INFO  17:15:07,263 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:15Z] INFO  17:15:07,284 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@5fe152b7
[2016-04-15T00:15Z] INFO  17:15:07,309 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-15T00:15Z] INFO  17:15:07,322 IntervalUtils - Processing 12115947 bp from intervals
[2016-04-15T00:15Z] INFO  17:15:07,401 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:15Z] INFO  17:15:07,461 ProgressMeter -            done    354855.0    55.0 s       2.6 m       98.1%    56.0 s       1.0 s
[2016-04-15T00:15Z] INFO  17:15:07,461 ProgressMeter - Total runtime 55.39 secs, 0.92 min, 0.02 hours
[2016-04-15T00:15Z] INFO  17:15:07,462 MicroScheduler - 173 reads were filtered out during the traversal out of approximately 355028 total reads (0.05%)
[2016-04-15T00:15Z] INFO  17:15:07,462 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:15Z] INFO  17:15:07,462 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:15Z] INFO  17:15:07,463 MicroScheduler -   -> 173 reads (0.05% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:15Z] GATK pre-alignment ('10', 0, 15559243) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:15Z] INFO  17:15:07,807 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:15Z] INFO  17:15:07,808 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:15Z] INFO  17:15:07,808 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:15Z] INFO  17:15:07,809 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:15Z] INFO  17:15:07,841 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:15Z] INFO  17:15:08,033 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:15Z] INFO  17:15:09,030 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:15Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-8_141900641_146364022-prep-prealign.bam
[2016-04-15T00:15Z] INFO  17:15:09,478 ProgressMeter -            done    116893.0    11.0 s      97.0 s      100.0%    11.0 s       0.0 s
[2016-04-15T00:15Z] INFO  17:15:09,479 ProgressMeter - Total runtime 11.42 secs, 0.19 min, 0.00 hours
[2016-04-15T00:15Z] INFO  17:15:09,482 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 116893 total reads (0.00%)
[2016-04-15T00:15Z] INFO  17:15:09,483 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:15Z] INFO  17:15:09,483 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:15Z] INFO  17:15:09,483 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:15Z] INFO  17:15:09,872 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:15Z] INFO  17:15:09,876 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:15Z] INFO  17:15:09,876 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:15Z] INFO  17:15:09,877 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:15Z] INFO  17:15:09,881 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/9/R14-18106_kapa-NGv3-PE100-NGv3-sort-9_15564086_32405601-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/9/tx/tmpxaGwLQ/R14-18106_kapa-NGv3-PE100-NGv3-sort-9_15564086_32405601-prep-prealign-realign.intervals -l INFO -L 9:15564087-32405601 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:15Z] INFO  17:15:09,909 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:15Z] INFO  17:15:09,909 HelpFormatter - Date/Time: 2016/04/14 17:15:09
[2016-04-15T00:15Z] INFO  17:15:09,909 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:15Z] INFO  17:15:09,920 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:15Z] INFO  17:15:10,027 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:15Z] GATK RealignerTargetCreator: R14-18106_kapa-NGv3-PE100-NGv3-sort-8_141900641_146364022-prep-prealign.bam 8:141900642-146364022
[2016-04-15T00:15Z] GATK: RealignerTargetCreator
[2016-04-15T00:15Z] INFO  17:15:10,205 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T00:15Z] INFO  17:15:10,215 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:15Z] INFO  17:15:10,269 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-15T00:15Z] INFO  17:15:10,555 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:15Z] INFO  17:15:10,559 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:15Z] INFO  17:15:10,559 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:15Z] INFO  17:15:10,560 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:15Z] INFO  17:15:10,565 HelpFormatter - Program Args: -T PrintReads -L 10:1-15559243 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/10/tx/tmpiEX4XZ/R14-18106_kapa-NGv3-PE100-NGv3-sort-10_0_15559243-prep-prealign.bam
[2016-04-15T00:15Z] INFO  17:15:10,568 IntervalUtils - Processing 16841515 bp from intervals
[2016-04-15T00:15Z] WARN  17:15:10,573 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:15Z] INFO  17:15:10,578 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:15Z] INFO  17:15:10,589 HelpFormatter - Date/Time: 2016/04/14 17:15:10
[2016-04-15T00:15Z] INFO  17:15:10,590 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:15Z] INFO  17:15:10,591 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:15Z] INFO  17:15:10,647 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:15Z] INFO  17:15:10,827 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:15Z] INFO  17:15:10,941 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:15Z] INFO  17:15:10,942 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:15Z] INFO  17:15:10,943 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:15Z] INFO  17:15:10,944 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:15Z] INFO  17:15:11,279 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:15Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-8_126369460_141889736-prep.bam
[2016-04-15T00:15Z] GATK pre-alignment ('10', 15561288, 31134502) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:15Z] INFO  17:15:11,842 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-15T00:15Z] INFO  17:15:11,917 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:15Z] INFO  17:15:11,932 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:15Z] INFO  17:15:11,997 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-15T00:15Z] INFO  17:15:12,033 IntervalUtils - Processing 15559243 bp from intervals
[2016-04-15T00:15Z] INFO  17:15:12,169 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:15Z] INFO  17:15:12,534 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:15Z] INFO  17:15:12,535 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:15Z] INFO  17:15:12,536 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:15Z] INFO  17:15:12,536 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:15Z] INFO  17:15:12,552 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:15Z] INFO  17:15:12,775 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:15Z] INFO  17:15:12,778 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:15Z] INFO  17:15:12,778 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:15Z] INFO  17:15:12,779 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:15Z] INFO  17:15:12,783 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:15Z] INFO  17:15:12,783 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/8/R14-18106_kapa-NGv3-PE100-NGv3-sort-8_141900641_146364022-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/8/tx/tmp19KWfd/R14-18106_kapa-NGv3-PE100-NGv3-sort-8_141900641_146364022-prep-prealign-realign.intervals -l INFO -L 8:141900642-146364022 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:15Z] INFO  17:15:12,799 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:15Z] INFO  17:15:12,799 HelpFormatter - Date/Time: 2016/04/14 17:15:12
[2016-04-15T00:15Z] INFO  17:15:12,800 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:15Z] INFO  17:15:12,800 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:15Z] INFO  17:15:12,927 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:15Z] INFO  17:15:13,122 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T00:15Z] INFO  17:15:13,144 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:15Z] INFO  17:15:13,197 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-15T00:15Z] INFO  17:15:13,514 IntervalUtils - Processing 4463381 bp from intervals
[2016-04-15T00:15Z] WARN  17:15:13,530 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:15Z] INFO  17:15:13,534 ProgressMeter -            done    450792.0    29.0 s      64.0 s      100.0%    29.0 s       0.0 s
[2016-04-15T00:15Z] INFO  17:15:13,534 ProgressMeter - Total runtime 29.01 secs, 0.48 min, 0.01 hours
[2016-04-15T00:15Z] INFO  17:15:13,537 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 450792 total reads (0.00%)
[2016-04-15T00:15Z] INFO  17:15:13,545 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:15Z] INFO  17:15:13,546 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:15Z] INFO  17:15:13,547 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:15Z] INFO  17:15:13,674 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:15Z] INFO  17:15:13,842 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:15Z] INFO  17:15:13,843 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:15Z] INFO  17:15:13,844 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:15Z] INFO  17:15:13,845 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:15Z] INFO  17:15:14,731 ProgressMeter -            done    304873.0    22.0 s      74.0 s      100.0%    22.0 s       0.0 s
[2016-04-15T00:15Z] INFO  17:15:14,731 ProgressMeter - Total runtime 22.87 secs, 0.38 min, 0.01 hours
[2016-04-15T00:15Z] INFO  17:15:14,735 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 304873 total reads (0.00%)
[2016-04-15T00:15Z] INFO  17:15:14,735 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:15Z] INFO  17:15:14,735 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:15Z] INFO  17:15:14,735 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:15Z] INFO  17:15:14,890 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:15Z] INFO  17:15:14,894 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:15Z] INFO  17:15:14,895 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:15Z] INFO  17:15:14,895 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:15Z] INFO  17:15:14,933 HelpFormatter - Program Args: -T PrintReads -L 10:15561289-31134502 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/10/tx/tmp3G5SGe/R14-18106_kapa-NGv3-PE100-NGv3-sort-10_15561288_31134502-prep-prealign.bam
[2016-04-15T00:15Z] INFO  17:15:14,955 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:15Z] INFO  17:15:14,955 HelpFormatter - Date/Time: 2016/04/14 17:15:14
[2016-04-15T00:15Z] INFO  17:15:14,955 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:15Z] INFO  17:15:14,955 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:15Z] INFO  17:15:15,196 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:15Z] INFO  17:15:15,277 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:15Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-7_141629903_157151331-prep.bam
[2016-04-15T00:15Z] INFO  17:15:16,344 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:15Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-8_0_15517156-prep.bam
[2016-04-15T00:15Z] INFO  17:15:16,424 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-15T00:15Z] INFO  17:15:16,491 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:15Z] INFO  17:15:16,500 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:15Z] INFO  17:15:16,497 ProgressMeter -            done    198106.0    16.0 s      82.0 s      100.0%    16.0 s       0.0 s
[2016-04-15T00:15Z] INFO  17:15:16,497 ProgressMeter - Total runtime 16.30 secs, 0.27 min, 0.00 hours
[2016-04-15T00:15Z] INFO  17:15:16,501 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 198106 total reads (0.00%)
[2016-04-15T00:15Z] INFO  17:15:16,501 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:15Z] INFO  17:15:16,501 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:15Z] INFO  17:15:16,502 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:15Z] INFO  17:15:16,550 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-15T00:15Z] INFO  17:15:16,566 IntervalUtils - Processing 15573214 bp from intervals
[2016-04-15T00:15Z] INFO  17:15:16,656 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:15Z] GATK pre-alignment ('10', 31137459, 46960129) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:15Z] INFO  17:15:16,984 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:15Z] INFO  17:15:16,985 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:15Z] INFO  17:15:16,985 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:15Z] INFO  17:15:16,986 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:15Z] INFO  17:15:17,010 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:15Z] INFO  17:15:17,208 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:15Z] GATK pre-alignment ('10', 46960410, 62493077) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:15Z] INFO  17:15:18,051 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:15Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-8_95142853_110655419-prep.bam
[2016-04-15T00:15Z] GATK pre-alignment ('10', 62539923, 78084243) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:15Z] INFO  17:15:19,757 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:15Z] INFO  17:15:19,760 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:15Z] INFO  17:15:19,761 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:15Z] INFO  17:15:19,761 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:15Z] INFO  17:15:19,766 HelpFormatter - Program Args: -T PrintReads -L 10:31137460-46960129 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/10/tx/tmprFBTkL/R14-18106_kapa-NGv3-PE100-NGv3-sort-10_31137459_46960129-prep-prealign.bam
[2016-04-15T00:15Z] INFO  17:15:19,782 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:15Z] INFO  17:15:19,783 HelpFormatter - Date/Time: 2016/04/14 17:15:19
[2016-04-15T00:15Z] INFO  17:15:19,783 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:15Z] INFO  17:15:19,783 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:15Z] INFO  17:15:19,932 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:15Z] INFO  17:15:20,124 ProgressMeter -            done    174453.0    14.0 s      82.0 s      100.0%    14.0 s       0.0 s
[2016-04-15T00:15Z] INFO  17:15:20,124 ProgressMeter - Total runtime 14.31 secs, 0.24 min, 0.00 hours
[2016-04-15T00:15Z] INFO  17:15:20,128 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 174453 total reads (0.00%)
[2016-04-15T00:15Z] INFO  17:15:20,128 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:15Z] INFO  17:15:20,128 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:15Z] INFO  17:15:20,128 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:15Z] INFO  17:15:20,206 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:15Z] INFO  17:15:20,210 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:15Z] INFO  17:15:20,210 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:15Z] INFO  17:15:20,211 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:15Z] INFO  17:15:20,216 HelpFormatter - Program Args: -T PrintReads -L 10:46960411-62493077 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/10/tx/tmp6s9W4F/R14-18106_kapa-NGv3-PE100-NGv3-sort-10_46960410_62493077-prep-prealign.bam
[2016-04-15T00:15Z] INFO  17:15:20,225 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:15Z] INFO  17:15:20,236 HelpFormatter - Date/Time: 2016/04/14 17:15:20
[2016-04-15T00:15Z] INFO  17:15:20,237 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:15Z] INFO  17:15:20,238 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:15Z] INFO  17:15:20,388 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:15Z] INFO  17:15:20,995 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-15T00:15Z] INFO  17:15:21,061 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:15Z] INFO  17:15:21,070 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:15Z] INFO  17:15:21,119 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-15T00:15Z] INFO  17:15:21,134 IntervalUtils - Processing 15822670 bp from intervals
[2016-04-15T00:15Z] INFO  17:15:21,256 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:15Z] INFO  17:15:21,485 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-15T00:15Z] INFO  17:15:21,549 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:15Z] INFO  17:15:21,575 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:15Z] INFO  17:15:21,576 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:15Z] INFO  17:15:21,577 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:15Z] INFO  17:15:21,577 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:15Z] INFO  17:15:21,580 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:15Z] INFO  17:15:21,591 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:15Z] INFO  17:15:21,634 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-15T00:15Z] INFO  17:15:21,656 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:15Z] INFO  17:15:21,659 IntervalUtils - Processing 15532667 bp from intervals
[2016-04-15T00:15Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-9_0_15510186-prep.bam
[2016-04-15T00:15Z] INFO  17:15:21,743 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:15Z] INFO  17:15:21,776 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:15Z] INFO  17:15:22,004 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:15Z] INFO  17:15:22,018 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:15Z] INFO  17:15:22,019 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:15Z] INFO  17:15:22,019 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:15Z] INFO  17:15:22,024 HelpFormatter - Program Args: -T PrintReads -L 10:62539924-78084243 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/10/tx/tmpcJq3WG/R14-18106_kapa-NGv3-PE100-NGv3-sort-10_62539923_78084243-prep-prealign.bam
[2016-04-15T00:15Z] INFO  17:15:22,042 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:15Z] INFO  17:15:22,043 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:15Z] INFO  17:15:22,043 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:15Z] INFO  17:15:22,044 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:15Z] INFO  17:15:22,044 HelpFormatter - Date/Time: 2016/04/14 17:15:22
[2016-04-15T00:15Z] INFO  17:15:22,044 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:15Z] INFO  17:15:22,045 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:15Z] INFO  17:15:22,045 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:15Z] INFO  17:15:22,058 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:15Z] GATK pre-alignment ('10', 78316966, 93841258) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:15Z] INFO  17:15:22,239 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:15Z] INFO  17:15:22,262 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:15Z] INFO  17:15:23,034 ProgressMeter -            done    332750.0    23.0 s      71.0 s      100.0%    23.0 s       0.0 s
[2016-04-15T00:15Z] INFO  17:15:23,036 ProgressMeter - Total runtime 23.72 secs, 0.40 min, 0.01 hours
[2016-04-15T00:15Z] INFO  17:15:23,039 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 332750 total reads (0.00%)
[2016-04-15T00:15Z] INFO  17:15:23,041 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:15Z] INFO  17:15:23,041 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:15Z] INFO  17:15:23,042 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:15Z] INFO  17:15:23,385 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-15T00:15Z] INFO  17:15:23,464 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:15Z] INFO  17:15:23,474 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:15Z] INFO  17:15:23,531 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-15T00:15Z] INFO  17:15:23,545 IntervalUtils - Processing 15544320 bp from intervals
[2016-04-15T00:15Z] INFO  17:15:23,659 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:15Z] INFO  17:15:23,944 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:15Z] INFO  17:15:23,945 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:15Z] INFO  17:15:23,946 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:15Z] INFO  17:15:23,947 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:15Z] INFO  17:15:23,961 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:15Z] INFO  17:15:24,219 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:15Z] INFO  17:15:24,655 ProgressMeter -      9:35704564    100001.0    30.0 s       5.0 m       10.0%     5.0 m       4.5 m
[2016-04-15T00:15Z] INFO  17:15:24,744 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:15Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-8_15519664_31030618-prep.bam
[2016-04-15T00:15Z] INFO  17:15:24,827 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:15Z] INFO  17:15:24,830 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:15Z] INFO  17:15:24,831 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:15Z] INFO  17:15:24,832 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:15Z] INFO  17:15:24,836 HelpFormatter - Program Args: -T PrintReads -L 10:78316967-93841258 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/10/tx/tmpCUCqkY/R14-18106_kapa-NGv3-PE100-NGv3-sort-10_78316966_93841258-prep-prealign.bam
[2016-04-15T00:15Z] INFO  17:15:24,859 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:15Z] INFO  17:15:24,860 HelpFormatter - Date/Time: 2016/04/14 17:15:24
[2016-04-15T00:15Z] INFO  17:15:24,861 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:15Z] INFO  17:15:24,865 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:15Z] INFO  17:15:25,026 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:15Z] INFO  17:15:25,731 ProgressMeter -      9:79972720    200003.0    30.0 s       2.5 m       86.7%    34.0 s       4.0 s
[2016-04-15T00:15Z] GATK pre-alignment ('10', 93851586, 111625070) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:15Z] INFO  17:15:26,069 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-15T00:15Z] INFO  17:15:26,133 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:15Z] INFO  17:15:26,142 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:15Z] INFO  17:15:26,185 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.04
[2016-04-15T00:15Z] INFO  17:15:26,200 IntervalUtils - Processing 15524292 bp from intervals
[2016-04-15T00:15Z] INFO  17:15:26,280 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:15Z] INFO  17:15:26,566 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:15Z] INFO  17:15:26,567 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:15Z] INFO  17:15:26,568 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:15Z] INFO  17:15:26,568 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:15Z] INFO  17:15:26,582 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:15Z] INFO  17:15:26,742 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:15Z] INFO  17:15:26,846 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@5fe152b7
[2016-04-15T00:15Z] INFO  17:15:26,968 ProgressMeter -            done    228431.0    31.0 s       2.3 m      100.0%    31.0 s       0.0 s
[2016-04-15T00:15Z] INFO  17:15:26,974 ProgressMeter - Total runtime 31.26 secs, 0.52 min, 0.01 hours
[2016-04-15T00:15Z] INFO  17:15:26,974 MicroScheduler - 185 reads were filtered out during the traversal out of approximately 228616 total reads (0.08%)
[2016-04-15T00:15Z] INFO  17:15:26,974 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:15Z] INFO  17:15:26,975 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:15Z] INFO  17:15:26,975 MicroScheduler -   -> 185 reads (0.08% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:15Z] INFO  17:15:27,211 ProgressMeter -            done   4463381.0    13.0 s       2.0 s      100.0%    13.0 s       0.0 s
[2016-04-15T00:15Z] INFO  17:15:27,212 ProgressMeter - Total runtime 13.37 secs, 0.22 min, 0.00 hours
[2016-04-15T00:15Z] INFO  17:15:27,213 MicroScheduler - 36032 reads were filtered out during the traversal out of approximately 356661 total reads (10.10%)
[2016-04-15T00:15Z] INFO  17:15:27,214 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:15Z] INFO  17:15:27,215 MicroScheduler -   -> 787 reads (0.22% of total) failing BadMateFilter
[2016-04-15T00:15Z] INFO  17:15:27,215 MicroScheduler -   -> 27118 reads (7.60% of total) failing DuplicateReadFilter
[2016-04-15T00:15Z] INFO  17:15:27,216 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:15Z] INFO  17:15:27,216 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:15Z] INFO  17:15:27,217 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:15Z] INFO  17:15:27,218 MicroScheduler -   -> 8127 reads (2.28% of total) failing MappingQualityZeroFilter
[2016-04-15T00:15Z] INFO  17:15:27,218 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:15Z] INFO  17:15:27,219 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-15T00:15Z] INFO  17:15:27,219 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:15Z] INFO  17:15:27,594 ProgressMeter -            done   1.6841515E7    16.0 s       0.0 s      100.0%    16.0 s       0.0 s
[2016-04-15T00:15Z] INFO  17:15:27,595 ProgressMeter - Total runtime 16.65 secs, 0.28 min, 0.00 hours
[2016-04-15T00:15Z] INFO  17:15:27,599 MicroScheduler - 12065 reads were filtered out during the traversal out of approximately 122018 total reads (9.89%)
[2016-04-15T00:15Z] INFO  17:15:27,599 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:15Z] INFO  17:15:27,602 MicroScheduler -   -> 565 reads (0.46% of total) failing BadMateFilter
[2016-04-15T00:15Z] INFO  17:15:27,602 MicroScheduler -   -> 8814 reads (7.22% of total) failing DuplicateReadFilter
[2016-04-15T00:15Z] INFO  17:15:27,603 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:15Z] INFO  17:15:27,603 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:15Z] INFO  17:15:27,604 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:15Z] INFO  17:15:27,605 MicroScheduler -   -> 2686 reads (2.20% of total) failing MappingQualityZeroFilter
[2016-04-15T00:15Z] INFO  17:15:27,605 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:15Z] INFO  17:15:27,606 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-15T00:15Z] INFO  17:15:27,606 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:15Z] INFO  17:15:28,375 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:15Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-9_65507205_82187750-prep-prealign.bam
[2016-04-15T00:15Z] INFO  17:15:28,607 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:15Z] GATK: realign ('8', 141900641, 146364022) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:15Z] INFO  17:15:28,781 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:15Z] INFO  17:15:28,784 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:15Z] INFO  17:15:28,785 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:15Z] INFO  17:15:28,785 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:15Z] INFO  17:15:28,790 HelpFormatter - Program Args: -T PrintReads -L 10:93851587-111625070 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/10/tx/tmpamqFQY/R14-18106_kapa-NGv3-PE100-NGv3-sort-10_93851586_111625070-prep-prealign.bam
[2016-04-15T00:15Z] INFO  17:15:28,806 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:15Z] INFO  17:15:28,807 HelpFormatter - Date/Time: 2016/04/14 17:15:28
[2016-04-15T00:15Z] INFO  17:15:28,807 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:15Z] INFO  17:15:28,808 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:15Z] INFO  17:15:28,977 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:15Z] INFO  17:15:29,067 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:15Z] GATK RealignerTargetCreator: R14-18106_kapa-NGv3-PE100-NGv3-sort-9_65507205_82187750-prep-prealign.bam 9:65507206-82187750
[2016-04-15T00:15Z] GATK: RealignerTargetCreator
[2016-04-15T00:15Z] GATK: realign ('9', 15564086, 32405601) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:15Z] INFO  17:15:30,082 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-15T00:15Z] INFO  17:15:30,194 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:15Z] INFO  17:15:30,214 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:15Z] INFO  17:15:30,258 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.04
[2016-04-15T00:15Z] INFO  17:15:30,273 IntervalUtils - Processing 17773484 bp from intervals
[2016-04-15T00:15Z] INFO  17:15:30,345 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:15Z] INFO  17:15:30,455 ProgressMeter -      9:95400508    200002.0    30.0 s       2.5 m       85.1%    35.0 s       5.0 s
[2016-04-15T00:15Z] INFO  17:15:30,720 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:15Z] INFO  17:15:30,721 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:15Z] INFO  17:15:30,722 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:15Z] INFO  17:15:30,723 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:15Z] INFO  17:15:30,750 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:15Z] INFO  17:15:30,964 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:15Z] INFO  17:15:31,204 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:15Z] INFO  17:15:31,212 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:15Z] INFO  17:15:31,213 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:15Z] INFO  17:15:31,213 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:15Z] INFO  17:15:31,217 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/8/R14-18106_kapa-NGv3-PE100-NGv3-sort-8_141900641_146364022-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/8/R14-18106_kapa-NGv3-PE100-NGv3-sort-8_141900641_146364022-prep-prealign-realign.intervals -L 8:141900642-146364022 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/8/tx/tmpQ8Mxhe/R14-18106_kapa-NGv3-PE100-NGv3-sort-8_141900641_146364022-prep.bam
[2016-04-15T00:15Z] INFO  17:15:31,232 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:15Z] INFO  17:15:31,232 HelpFormatter - Date/Time: 2016/04/14 17:15:31
[2016-04-15T00:15Z] INFO  17:15:31,233 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:15Z] INFO  17:15:31,233 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:15Z] INFO  17:15:31,474 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:15Z] INFO  17:15:31,652 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:15Z] INFO  17:15:31,662 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:15Z] INFO  17:15:31,736 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-15T00:15Z] INFO  17:15:31,899 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:15Z] INFO  17:15:31,903 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:15Z] INFO  17:15:31,904 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:15Z] INFO  17:15:31,905 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:15Z] INFO  17:15:31,910 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/9/R14-18106_kapa-NGv3-PE100-NGv3-sort-9_15564086_32405601-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/9/R14-18106_kapa-NGv3-PE100-NGv3-sort-9_15564086_32405601-prep-prealign-realign.intervals -L 9:15564087-32405601 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/9/tx/tmpxk0Dbf/R14-18106_kapa-NGv3-PE100-NGv3-sort-9_15564086_32405601-prep.bam
[2016-04-15T00:15Z] INFO  17:15:31,921 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:15Z] INFO  17:15:31,922 HelpFormatter - Date/Time: 2016/04/14 17:15:31
[2016-04-15T00:15Z] INFO  17:15:31,923 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:15Z] INFO  17:15:31,924 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:15Z] INFO  17:15:32,061 IntervalUtils - Processing 4463381 bp from intervals
[2016-04-15T00:15Z] WARN  17:15:32,066 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:15Z] INFO  17:15:32,142 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:15Z] INFO  17:15:32,191 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:15Z] INFO  17:15:32,221 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:15Z] INFO  17:15:32,222 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:15Z] INFO  17:15:32,223 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:15Z] INFO  17:15:32,223 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:15Z] INFO  17:15:32,331 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:15Z] INFO  17:15:32,340 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:15Z] INFO  17:15:32,361 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:15Z] INFO  17:15:32,384 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.04
[2016-04-15T00:15Z] INFO  17:15:32,401 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:15Z] INFO  17:15:32,405 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:15Z] INFO  17:15:32,406 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:15Z] INFO  17:15:32,406 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:15Z] INFO  17:15:32,410 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:15Z] INFO  17:15:32,412 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/9/R14-18106_kapa-NGv3-PE100-NGv3-sort-9_65507205_82187750-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/9/tx/tmpfaBaTr/R14-18106_kapa-NGv3-PE100-NGv3-sort-9_65507205_82187750-prep-prealign-realign.intervals -l INFO -L 9:65507206-82187750 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:15Z] INFO  17:15:32,423 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:15Z] INFO  17:15:32,435 HelpFormatter - Date/Time: 2016/04/14 17:15:32
[2016-04-15T00:15Z] INFO  17:15:32,436 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:15Z] INFO  17:15:32,437 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:15Z] INFO  17:15:32,593 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:15Z] INFO  17:15:32,713 IntervalUtils - Processing 16841515 bp from intervals
[2016-04-15T00:15Z] WARN  17:15:32,719 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:15Z] INFO  17:15:32,797 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:15Z] INFO  17:15:32,860 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T00:15Z] INFO  17:15:32,881 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:15Z] INFO  17:15:32,896 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:15Z] INFO  17:15:32,898 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:15Z] INFO  17:15:32,898 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:15Z] INFO  17:15:32,899 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:15Z] INFO  17:15:32,936 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-15T00:15Z] INFO  17:15:33,029 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:15Z] INFO  17:15:33,226 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:15Z] INFO  17:15:33,320 IntervalUtils - Processing 16680545 bp from intervals
[2016-04-15T00:15Z] WARN  17:15:33,326 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:15Z] INFO  17:15:33,475 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:15Z] INFO  17:15:33,739 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:15Z] INFO  17:15:33,740 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:15Z] INFO  17:15:33,741 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:15Z] INFO  17:15:33,741 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:15Z] INFO  17:15:33,950 ProgressMeter -     9:110249854    200003.0    30.0 s       2.5 m       80.8%    37.0 s       7.0 s
[2016-04-15T00:15Z] INFO  17:15:35,653 ProgressMeter -     7:100656204    300007.0    30.0 s     101.0 s       38.0%    79.0 s      49.0 s
[2016-04-15T00:15Z] INFO  17:15:36,280 ProgressMeter -     9:124064269    200004.0    30.0 s       2.5 m       68.3%    43.0 s      13.0 s
[2016-04-15T00:15Z] INFO  17:15:37,827 ProgressMeter -     9:131821489    200005.0    30.0 s       2.5 m       22.5%     2.2 m     103.0 s
[2016-04-15T00:15Z] INFO  17:15:39,299 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@7172f77a
[2016-04-15T00:15Z] INFO  17:15:39,407 ProgressMeter -            done    286764.0    35.0 s       2.1 m      100.0%    35.0 s       0.0 s
[2016-04-15T00:15Z] INFO  17:15:39,408 ProgressMeter - Total runtime 35.47 secs, 0.59 min, 0.01 hours
[2016-04-15T00:15Z] INFO  17:15:39,408 MicroScheduler - 166 reads were filtered out during the traversal out of approximately 286930 total reads (0.06%)
[2016-04-15T00:15Z] INFO  17:15:39,409 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:15Z] INFO  17:15:39,409 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:15Z] INFO  17:15:39,409 MicroScheduler -   -> 166 reads (0.06% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:15Z] INFO  17:15:40,111 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@32d5a4c6
[2016-04-15T00:15Z] INFO  17:15:40,225 ProgressMeter -            done    309988.0    39.0 s       2.1 m      100.0%    39.0 s       0.0 s
[2016-04-15T00:15Z] INFO  17:15:40,225 ProgressMeter - Total runtime 39.78 secs, 0.66 min, 0.01 hours
[2016-04-15T00:15Z] INFO  17:15:40,226 MicroScheduler - 197 reads were filtered out during the traversal out of approximately 310185 total reads (0.06%)
[2016-04-15T00:15Z] INFO  17:15:40,227 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:15Z] INFO  17:15:40,228 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:15Z] INFO  17:15:40,228 MicroScheduler -   -> 197 reads (0.06% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:15Z] INFO  17:15:40,636 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:15Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-9_97718189_113228306-prep-prealign.bam
[2016-04-15T00:15Z] GATK RealignerTargetCreator: R14-18106_kapa-NGv3-PE100-NGv3-sort-9_97718189_113228306-prep-prealign.bam 9:97718190-113228306
[2016-04-15T00:15Z] GATK: RealignerTargetCreator
[2016-04-15T00:15Z] INFO  17:15:41,663 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:15Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-9_82188172_97717561-prep-prealign.bam
[2016-04-15T00:15Z] INFO  17:15:42,365 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@7172f77a
[2016-04-15T00:15Z] INFO  17:15:42,476 ProgressMeter -            done    194128.0    25.0 s       2.2 m      100.0%    25.0 s       0.0 s
[2016-04-15T00:15Z] INFO  17:15:42,477 ProgressMeter - Total runtime 25.49 secs, 0.42 min, 0.01 hours
[2016-04-15T00:15Z] INFO  17:15:42,477 MicroScheduler - 130 reads were filtered out during the traversal out of approximately 194258 total reads (0.07%)
[2016-04-15T00:15Z] INFO  17:15:42,478 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:15Z] INFO  17:15:42,478 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:15Z] INFO  17:15:42,478 MicroScheduler -   -> 130 reads (0.07% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:15Z] INFO  17:15:42,753 ProgressMeter -     10:13364968    100001.0    30.0 s       5.0 m       85.9%    34.0 s       4.0 s
[2016-04-15T00:15Z] GATK RealignerTargetCreator: R14-18106_kapa-NGv3-PE100-NGv3-sort-9_82188172_97717561-prep-prealign.bam 9:82188173-97717561
[2016-04-15T00:15Z] GATK: RealignerTargetCreator
[2016-04-15T00:15Z] INFO  17:15:44,051 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:15Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-10_15561288_31134502-prep-prealign.bam
[2016-04-15T00:15Z] INFO  17:15:44,508 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:15Z] INFO  17:15:44,512 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:15Z] INFO  17:15:44,512 ProgressMeter -            done    120921.0    11.0 s      96.0 s      100.0%    11.0 s       0.0 s
[2016-04-15T00:15Z] INFO  17:15:44,512 ProgressMeter - Total runtime 11.61 secs, 0.19 min, 0.00 hours
[2016-04-15T00:15Z] INFO  17:15:44,513 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:15Z] INFO  17:15:44,514 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:15Z] INFO  17:15:44,517 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 120921 total reads (0.00%)
[2016-04-15T00:15Z] INFO  17:15:44,517 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:15Z] INFO  17:15:44,517 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:15Z] INFO  17:15:44,518 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:15Z] INFO  17:15:44,519 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/9/R14-18106_kapa-NGv3-PE100-NGv3-sort-9_97718189_113228306-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/9/tx/tmpJBf09C/R14-18106_kapa-NGv3-PE100-NGv3-sort-9_97718189_113228306-prep-prealign-realign.intervals -l INFO -L 9:97718190-113228306 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:15Z] INFO  17:15:44,541 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:15Z] INFO  17:15:44,542 HelpFormatter - Date/Time: 2016/04/14 17:15:44
[2016-04-15T00:15Z] INFO  17:15:44,542 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:15Z] INFO  17:15:44,542 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:15Z] INFO  17:15:44,661 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:15Z] INFO  17:15:44,836 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T00:15Z] INFO  17:15:44,847 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:15Z] GATK RealignerTargetCreator: R14-18106_kapa-NGv3-PE100-NGv3-sort-10_15561288_31134502-prep-prealign.bam 10:15561289-31134502
[2016-04-15T00:15Z] GATK: RealignerTargetCreator
[2016-04-15T00:15Z] INFO  17:15:44,916 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-15T00:15Z] INFO  17:15:45,211 IntervalUtils - Processing 15510117 bp from intervals
[2016-04-15T00:15Z] WARN  17:15:45,231 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:15Z] INFO  17:15:45,339 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:15Z] INFO  17:15:45,551 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:15Z] INFO  17:15:45,553 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:15Z] INFO  17:15:45,554 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:15Z] INFO  17:15:45,554 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:15Z] INFO  17:15:45,831 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:15Z] INFO  17:15:45,834 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:15Z] INFO  17:15:45,835 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:15Z] INFO  17:15:45,836 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:15Z] INFO  17:15:45,840 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/9/R14-18106_kapa-NGv3-PE100-NGv3-sort-9_82188172_97717561-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/9/tx/tmpAGSeJq/R14-18106_kapa-NGv3-PE100-NGv3-sort-9_82188172_97717561-prep-prealign-realign.intervals -l INFO -L 9:82188173-97717561 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:15Z] INFO  17:15:45,850 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:15Z] INFO  17:15:45,861 HelpFormatter - Date/Time: 2016/04/14 17:15:45
[2016-04-15T00:15Z] INFO  17:15:45,861 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:15Z] INFO  17:15:45,866 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:15Z] INFO  17:15:45,967 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:15Z] INFO  17:15:46,041 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:15Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-9_15564086_32405601-prep.bam
[2016-04-15T00:15Z] INFO  17:15:46,200 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T00:15Z] INFO  17:15:46,209 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:15Z] INFO  17:15:46,297 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.09
[2016-04-15T00:15Z] GATK pre-alignment ('10', 111628371, 127265443) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:15Z] INFO  17:15:46,683 IntervalUtils - Processing 15529389 bp from intervals
[2016-04-15T00:15Z] WARN  17:15:46,689 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:15Z] INFO  17:15:46,785 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:15Z] INFO  17:15:47,019 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:15Z] INFO  17:15:47,021 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:15Z] INFO  17:15:47,021 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:15Z] INFO  17:15:47,022 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:15Z] INFO  17:15:47,811 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:15Z] INFO  17:15:47,814 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:15Z] INFO  17:15:47,815 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:15Z] INFO  17:15:47,816 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:15Z] INFO  17:15:47,820 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/10/R14-18106_kapa-NGv3-PE100-NGv3-sort-10_15561288_31134502-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/10/tx/tmpgWU6Ut/R14-18106_kapa-NGv3-PE100-NGv3-sort-10_15561288_31134502-prep-prealign-realign.intervals -l INFO -L 10:15561289-31134502 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:15Z] INFO  17:15:47,836 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:15Z] INFO  17:15:47,836 HelpFormatter - Date/Time: 2016/04/14 17:15:47
[2016-04-15T00:15Z] INFO  17:15:47,836 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:15Z] INFO  17:15:47,837 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:15Z] INFO  17:15:47,965 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:15Z] INFO  17:15:48,131 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@7172f77a
[2016-04-15T00:15Z] INFO  17:15:48,154 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T00:15Z] INFO  17:15:48,183 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:15Z] INFO  17:15:48,253 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-15T00:15Z] INFO  17:15:48,263 ProgressMeter -            done    216419.0    35.0 s       2.8 m      100.0%    35.0 s       0.0 s
[2016-04-15T00:15Z] INFO  17:15:48,264 ProgressMeter - Total runtime 35.73 secs, 0.60 min, 0.01 hours
[2016-04-15T00:15Z] INFO  17:15:48,264 MicroScheduler - 159 reads were filtered out during the traversal out of approximately 216578 total reads (0.07%)
[2016-04-15T00:15Z] INFO  17:15:48,265 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:15Z] INFO  17:15:48,265 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:15Z] INFO  17:15:48,265 MicroScheduler -   -> 159 reads (0.07% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:15Z] INFO  17:15:48,561 IntervalUtils - Processing 15573214 bp from intervals
[2016-04-15T00:15Z] WARN  17:15:48,577 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:15Z] INFO  17:15:48,659 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:15Z] INFO  17:15:48,869 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:15Z] INFO  17:15:48,870 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:15Z] INFO  17:15:48,871 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:15Z] INFO  17:15:48,871 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:15Z] INFO  17:15:49,040 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@7172f77a
[2016-04-15T00:15Z] INFO  17:15:49,163 ProgressMeter -            done    338932.0    42.0 s       2.1 m      100.0%    42.0 s       0.0 s
[2016-04-15T00:15Z] INFO  17:15:49,164 ProgressMeter - Total runtime 42.90 secs, 0.71 min, 0.01 hours
[2016-04-15T00:15Z] INFO  17:15:49,164 MicroScheduler - 190 reads were filtered out during the traversal out of approximately 339122 total reads (0.06%)
[2016-04-15T00:15Z] INFO  17:15:49,165 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:15Z] INFO  17:15:49,165 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:15Z] INFO  17:15:49,165 MicroScheduler -   -> 190 reads (0.06% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:15Z] INFO  17:15:49,542 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:15Z] INFO  17:15:49,545 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:15Z] INFO  17:15:49,546 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:15Z] INFO  17:15:49,546 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:15Z] INFO  17:15:49,551 HelpFormatter - Program Args: -T PrintReads -L 10:111628372-127265443 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/10/tx/tmpWYiImG/R14-18106_kapa-NGv3-PE100-NGv3-sort-10_111628371_127265443-prep-prealign.bam
[2016-04-15T00:15Z] INFO  17:15:49,566 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:15Z] INFO  17:15:49,567 HelpFormatter - Date/Time: 2016/04/14 17:15:49
[2016-04-15T00:15Z] INFO  17:15:49,568 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:15Z] INFO  17:15:49,568 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:15Z] INFO  17:15:49,758 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:15Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-10_0_15559243-prep-prealign.bam
[2016-04-15T00:15Z] INFO  17:15:49,803 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:15Z] INFO  17:15:50,383 ProgressMeter -            done    699580.0    45.0 s      64.0 s      100.0%    45.0 s       0.0 s
[2016-04-15T00:15Z] INFO  17:15:50,383 ProgressMeter - Total runtime 45.27 secs, 0.75 min, 0.01 hours
[2016-04-15T00:15Z] INFO  17:15:50,387 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 699580 total reads (0.00%)
[2016-04-15T00:15Z] INFO  17:15:50,387 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:15Z] INFO  17:15:50,388 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:15Z] INFO  17:15:50,388 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:15Z] GATK RealignerTargetCreator: R14-18106_kapa-NGv3-PE100-NGv3-sort-10_0_15559243-prep-prealign.bam 10:1-15559243
[2016-04-15T00:15Z] INFO  17:15:50,573 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:15Z] GATK: RealignerTargetCreator
[2016-04-15T00:15Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-9_113231219_129089575-prep-prealign.bam
[2016-04-15T00:15Z] INFO  17:15:50,992 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-15T00:15Z] INFO  17:15:51,105 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:15Z] INFO  17:15:51,116 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:15Z] INFO  17:15:51,179 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-15T00:15Z] INFO  17:15:51,185 ProgressMeter -            done   1.6680545E7    17.0 s       1.0 s      100.0%    17.0 s       0.0 s
[2016-04-15T00:15Z] INFO  17:15:51,186 ProgressMeter - Total runtime 17.45 secs, 0.29 min, 0.00 hours
[2016-04-15T00:15Z] INFO  17:15:51,191 MicroScheduler - 85246 reads were filtered out during the traversal out of approximately 229463 total reads (37.15%)
[2016-04-15T00:15Z] INFO  17:15:51,192 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:15Z] INFO  17:15:51,193 MicroScheduler -   -> 492 reads (0.21% of total) failing BadMateFilter
[2016-04-15T00:15Z] INFO  17:15:51,194 MicroScheduler -   -> 11799 reads (5.14% of total) failing DuplicateReadFilter
[2016-04-15T00:15Z] INFO  17:15:51,197 IntervalUtils - Processing 15637072 bp from intervals
[2016-04-15T00:15Z] INFO  17:15:51,198 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:15Z] INFO  17:15:51,199 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:15Z] INFO  17:15:51,199 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:15Z] INFO  17:15:51,200 MicroScheduler -   -> 72955 reads (31.79% of total) failing MappingQualityZeroFilter
[2016-04-15T00:15Z] INFO  17:15:51,201 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:15Z] INFO  17:15:51,202 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-15T00:15Z] INFO  17:15:51,202 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:15Z] INFO  17:15:51,284 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:15Z] INFO  17:15:51,594 ProgressMeter -     10:46322145    100001.0    30.0 s       5.0 m       96.0%    31.0 s       1.0 s
[2016-04-15T00:15Z] INFO  17:15:51,674 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:15Z] INFO  17:15:51,675 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:15Z] INFO  17:15:51,676 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:15Z] INFO  17:15:51,677 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:15Z] INFO  17:15:51,695 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:15Z] GATK RealignerTargetCreator: R14-18106_kapa-NGv3-PE100-NGv3-sort-9_113231219_129089575-prep-prealign.bam 9:113231220-129089575
[2016-04-15T00:15Z] GATK: RealignerTargetCreator
[2016-04-15T00:15Z] INFO  17:15:51,883 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:15Z] INFO  17:15:51,951 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:15Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-7_94750023_110303777-prep.bam
[2016-04-15T00:15Z] INFO  17:15:52,294 ProgressMeter -     10:50732434    100001.0    30.0 s       5.0 m       24.3%     2.1 m      93.0 s
[2016-04-15T00:15Z] INFO  17:15:52,562 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:15Z] GATK: realign ('9', 65507205, 82187750) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:15Z] INFO  17:15:53,503 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:15Z] INFO  17:15:53,506 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:15Z] INFO  17:15:53,507 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:15Z] INFO  17:15:53,508 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:15Z] INFO  17:15:53,512 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/10/R14-18106_kapa-NGv3-PE100-NGv3-sort-10_0_15559243-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/10/tx/tmpZYiun2/R14-18106_kapa-NGv3-PE100-NGv3-sort-10_0_15559243-prep-prealign-realign.intervals -l INFO -L 10:1-15559243 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:15Z] INFO  17:15:53,537 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:15Z] INFO  17:15:53,538 HelpFormatter - Date/Time: 2016/04/14 17:15:53
[2016-04-15T00:15Z] INFO  17:15:53,539 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:15Z] INFO  17:15:53,540 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:15Z] INFO  17:15:53,686 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:15Z] INFO  17:15:53,922 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T00:15Z] INFO  17:15:53,931 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:15Z] INFO  17:15:54,000 ProgressMeter -     10:74104939    200002.0    30.0 s       2.5 m       74.4%    40.0 s      10.0 s
[2016-04-15T00:15Z] INFO  17:15:54,026 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.09
[2016-04-15T00:15Z] INFO  17:15:54,072 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@7172f77a
[2016-04-15T00:15Z] INFO  17:15:54,201 ProgressMeter -            done    204545.0    32.0 s       2.7 m      100.0%    32.0 s       0.0 s
[2016-04-15T00:15Z] INFO  17:15:54,202 ProgressMeter - Total runtime 32.63 secs, 0.54 min, 0.01 hours
[2016-04-15T00:15Z] INFO  17:15:54,202 MicroScheduler - 666 reads were filtered out during the traversal out of approximately 205211 total reads (0.32%)
[2016-04-15T00:15Z] INFO  17:15:54,203 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:15Z] INFO  17:15:54,203 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:15Z] INFO  17:15:54,203 MicroScheduler -   -> 666 reads (0.32% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:15Z] GATK pre-alignment ('10', 127328721, 135534747) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:15Z] INFO  17:15:54,349 IntervalUtils - Processing 15559243 bp from intervals
[2016-04-15T00:15Z] WARN  17:15:54,355 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:15Z] INFO  17:15:54,436 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:15Z] INFO  17:15:54,607 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:15Z] INFO  17:15:54,608 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:15Z] INFO  17:15:54,609 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:15Z] INFO  17:15:54,609 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:15Z] INFO  17:15:54,679 ProgressMeter -      9:43685322    400010.0    60.0 s       2.5 m       34.1%     2.9 m     116.0 s
[2016-04-15T00:15Z] INFO  17:15:54,726 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:15Z] INFO  17:15:54,730 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:15Z] INFO  17:15:54,730 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:15Z] INFO  17:15:54,731 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:15Z] INFO  17:15:54,735 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/9/R14-18106_kapa-NGv3-PE100-NGv3-sort-9_113231219_129089575-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/9/tx/tmpCVrpyt/R14-18106_kapa-NGv3-PE100-NGv3-sort-9_113231219_129089575-prep-prealign-realign.intervals -l INFO -L 9:113231220-129089575 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:15Z] INFO  17:15:54,744 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:15Z] INFO  17:15:54,746 HelpFormatter - Date/Time: 2016/04/14 17:15:54
[2016-04-15T00:15Z] INFO  17:15:54,747 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:15Z] INFO  17:15:54,747 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:15Z] INFO  17:15:54,850 ProgressMeter -            done    354855.0    22.0 s      63.0 s       98.1%    22.0 s       0.0 s
[2016-04-15T00:15Z] INFO  17:15:54,851 ProgressMeter - Total runtime 22.63 secs, 0.38 min, 0.01 hours
[2016-04-15T00:15Z] INFO  17:15:54,855 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 354855 total reads (0.00%)
[2016-04-15T00:15Z] INFO  17:15:54,857 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:15Z] INFO  17:15:54,857 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:15Z] INFO  17:15:54,858 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:15Z] INFO  17:15:54,864 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:15Z] INFO  17:15:55,079 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T00:15Z] INFO  17:15:55,089 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:15Z] INFO  17:15:55,153 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-15T00:15Z] INFO  17:15:55,426 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:15Z] INFO  17:15:55,429 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:15Z] INFO  17:15:55,429 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:15Z] INFO  17:15:55,429 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:15Z] INFO  17:15:55,433 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/9/R14-18106_kapa-NGv3-PE100-NGv3-sort-9_65507205_82187750-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/9/R14-18106_kapa-NGv3-PE100-NGv3-sort-9_65507205_82187750-prep-prealign-realign.intervals -L 9:65507206-82187750 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/9/tx/tmpaXuVc5/R14-18106_kapa-NGv3-PE100-NGv3-sort-9_65507205_82187750-prep.bam
[2016-04-15T00:15Z] INFO  17:15:55,457 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:15Z] INFO  17:15:55,464 HelpFormatter - Date/Time: 2016/04/14 17:15:55
[2016-04-15T00:15Z] INFO  17:15:55,465 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:15Z] INFO  17:15:55,466 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:15Z] INFO  17:15:55,518 IntervalUtils - Processing 15858356 bp from intervals
[2016-04-15T00:15Z] WARN  17:15:55,523 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:15Z] INFO  17:15:55,559 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:15Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-10_31137459_46960129-prep-prealign.bam
[2016-04-15T00:15Z] INFO  17:15:55,649 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:15Z] INFO  17:15:55,667 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:15Z] INFO  17:15:55,742 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:15Z] INFO  17:15:55,751 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:15Z] INFO  17:15:55,795 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.04
[2016-04-15T00:15Z] INFO  17:15:55,891 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:15Z] INFO  17:15:55,892 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:15Z] INFO  17:15:55,893 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:15Z] INFO  17:15:55,893 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:15Z] INFO  17:15:56,114 IntervalUtils - Processing 16680545 bp from intervals
[2016-04-15T00:15Z] WARN  17:15:56,119 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:15Z] INFO  17:15:56,220 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:15Z] GATK RealignerTargetCreator: R14-18106_kapa-NGv3-PE100-NGv3-sort-10_31137459_46960129-prep-prealign.bam 10:31137460-46960129
[2016-04-15T00:15Z] GATK: RealignerTargetCreator
[2016-04-15T00:15Z] INFO  17:15:56,361 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:15Z] INFO  17:15:56,362 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:15Z] INFO  17:15:56,363 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:15Z] INFO  17:15:56,364 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:15Z] INFO  17:15:56,470 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:15Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-8_141900641_146364022-prep.bam
[2016-04-15T00:15Z] INFO  17:15:56,554 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:15Z] INFO  17:15:56,770 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:15Z] INFO  17:15:56,987 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:15Z] INFO  17:15:56,996 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:15Z] INFO  17:15:56,997 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:15Z] INFO  17:15:56,998 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:15Z] INFO  17:15:57,004 HelpFormatter - Program Args: -T PrintReads -L 10:127328722-135534747 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/10/tx/tmpLov31V/R14-18106_kapa-NGv3-PE100-NGv3-sort-10_127328721_135534747-prep-prealign.bam
[2016-04-15T00:15Z] INFO  17:15:57,051 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:15Z] INFO  17:15:57,052 HelpFormatter - Date/Time: 2016/04/14 17:15:56
[2016-04-15T00:15Z] INFO  17:15:57,053 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:15Z] INFO  17:15:57,053 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:15Z] INFO  17:15:57,265 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:15Z] INFO  17:15:57,273 ProgressMeter -     10:89690885    100001.0    30.0 s       5.1 m       73.3%    40.0 s      10.0 s
[2016-04-15T00:15Z] GATK pre-alignment ('11', 0, 15994658) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:15Z] INFO  17:15:58,453 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-15T00:15Z] INFO  17:15:58,522 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:15Z] INFO  17:15:58,531 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:15Z] INFO  17:15:58,587 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-15T00:15Z] INFO  17:15:58,590 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@41fd9d8e
[2016-04-15T00:15Z] INFO  17:15:58,601 IntervalUtils - Processing 8206026 bp from intervals
[2016-04-15T00:15Z] INFO  17:15:58,711 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:15Z] INFO  17:15:58,730 ProgressMeter -            done    467393.0    64.0 s       2.3 m      100.0%    64.0 s       0.0 s
[2016-04-15T00:15Z] INFO  17:15:58,731 ProgressMeter - Total runtime 64.10 secs, 1.07 min, 0.02 hours
[2016-04-15T00:15Z] INFO  17:15:58,732 MicroScheduler - 226 reads were filtered out during the traversal out of approximately 467619 total reads (0.05%)
[2016-04-15T00:15Z] INFO  17:15:58,732 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:15Z] INFO  17:15:58,732 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:15Z] INFO  17:15:58,732 MicroScheduler -   -> 226 reads (0.05% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:15Z] INFO  17:15:59,032 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:15Z] INFO  17:15:59,033 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:15Z] INFO  17:15:59,034 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:15Z] INFO  17:15:59,035 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:15Z] INFO  17:15:59,049 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:15Z] INFO  17:15:59,125 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:15Z] INFO  17:15:59,128 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:15Z] INFO  17:15:59,129 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:15Z] INFO  17:15:59,129 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:15Z] INFO  17:15:59,134 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/10/R14-18106_kapa-NGv3-PE100-NGv3-sort-10_31137459_46960129-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/10/tx/tmpaA9SFe/R14-18106_kapa-NGv3-PE100-NGv3-sort-10_31137459_46960129-prep-prealign-realign.intervals -l INFO -L 10:31137460-46960129 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:15Z] INFO  17:15:59,153 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:15Z] INFO  17:15:59,154 HelpFormatter - Date/Time: 2016/04/14 17:15:59
[2016-04-15T00:15Z] INFO  17:15:59,154 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:15Z] INFO  17:15:59,154 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:15Z] INFO  17:15:59,211 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:15Z] INFO  17:15:59,276 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:15Z] INFO  17:15:59,449 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T00:15Z] INFO  17:15:59,459 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:15Z] INFO  17:15:59,522 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-15T00:15Z] INFO  17:15:59,839 IntervalUtils - Processing 15822670 bp from intervals
[2016-04-15T00:15Z] WARN  17:15:59,844 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:15Z] INFO  17:15:59,926 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:16Z] INFO  17:16:00,096 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:16Z] INFO  17:16:00,111 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:16Z] INFO  17:16:00,112 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:16Z] INFO  17:16:00,113 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:16Z] INFO  17:16:00,113 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:16Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-9_32407258_65506776-prep-prealign.bam
[2016-04-15T00:16Z] INFO  17:16:00,533 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:16Z] INFO  17:16:00,536 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:16Z] INFO  17:16:00,537 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:16Z] INFO  17:16:00,538 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:16Z] INFO  17:16:00,542 HelpFormatter - Program Args: -T PrintReads -L 11:1-15994658 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/11/tx/tmpdItvtO/R14-18106_kapa-NGv3-PE100-NGv3-sort-11_0_15994658-prep-prealign.bam
[2016-04-15T00:16Z] INFO  17:16:00,563 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:16Z] INFO  17:16:00,564 HelpFormatter - Date/Time: 2016/04/14 17:16:00
[2016-04-15T00:16Z] INFO  17:16:00,564 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:16Z] INFO  17:16:00,565 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:16Z] INFO  17:16:00,715 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:16Z] INFO  17:16:00,752 ProgressMeter -    10:101090484    200002.0    30.0 s       2.5 m       40.7%    73.0 s      43.0 s
[2016-04-15T00:16Z] GATK RealignerTargetCreator: R14-18106_kapa-NGv3-PE100-NGv3-sort-9_32407258_65506776-prep-prealign.bam 9:32407259-65506776
[2016-04-15T00:16Z] GATK: RealignerTargetCreator
[2016-04-15T00:16Z] INFO  17:16:01,825 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-15T00:16Z] INFO  17:16:01,918 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:16Z] INFO  17:16:01,929 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:16Z] INFO  17:16:01,983 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-15T00:16Z] INFO  17:16:02,002 IntervalUtils - Processing 15994658 bp from intervals
[2016-04-15T00:16Z] INFO  17:16:02,119 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:16Z] INFO  17:16:02,483 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:16Z] INFO  17:16:02,484 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:16Z] INFO  17:16:02,485 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:16Z] INFO  17:16:02,486 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:16Z] INFO  17:16:02,526 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:16Z] INFO  17:16:02,761 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:16Z] INFO  17:16:04,424 ProgressMeter -            done   1.5510117E7    18.0 s       1.0 s      100.0%    18.0 s       0.0 s
[2016-04-15T00:16Z] INFO  17:16:04,425 ProgressMeter - Total runtime 18.87 secs, 0.31 min, 0.01 hours
[2016-04-15T00:16Z] INFO  17:16:04,429 MicroScheduler - 27467 reads were filtered out during the traversal out of approximately 288496 total reads (9.52%)
[2016-04-15T00:16Z] INFO  17:16:04,430 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:16Z] INFO  17:16:04,431 MicroScheduler -   -> 752 reads (0.26% of total) failing BadMateFilter
[2016-04-15T00:16Z] INFO  17:16:04,432 MicroScheduler -   -> 21468 reads (7.44% of total) failing DuplicateReadFilter
[2016-04-15T00:16Z] INFO  17:16:04,432 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:16Z] INFO  17:16:04,433 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:16Z] INFO  17:16:04,434 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:16Z] INFO  17:16:04,444 MicroScheduler -   -> 5247 reads (1.82% of total) failing MappingQualityZeroFilter
[2016-04-15T00:16Z] INFO  17:16:04,445 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:16Z] INFO  17:16:04,446 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-15T00:16Z] INFO  17:16:04,447 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:16Z] INFO  17:16:04,645 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:16Z] INFO  17:16:04,648 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:16Z] INFO  17:16:04,648 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:16Z] INFO  17:16:04,649 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:16Z] INFO  17:16:04,653 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/9/R14-18106_kapa-NGv3-PE100-NGv3-sort-9_32407258_65506776-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/9/tx/tmpNB0Vzz/R14-18106_kapa-NGv3-PE100-NGv3-sort-9_32407258_65506776-prep-prealign-realign.intervals -l INFO -L 9:32407259-65506776 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:16Z] INFO  17:16:04,662 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:16Z] INFO  17:16:04,662 HelpFormatter - Date/Time: 2016/04/14 17:16:04
[2016-04-15T00:16Z] INFO  17:16:04,662 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:16Z] INFO  17:16:04,662 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:16Z] INFO  17:16:04,787 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:16Z] INFO  17:16:04,993 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T00:16Z] INFO  17:16:05,013 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:16Z] INFO  17:16:05,049 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@7172f77a
[2016-04-15T00:16Z] INFO  17:16:05,065 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-15T00:16Z] INFO  17:16:05,118 ProgressMeter -            done    240702.0    38.0 s       2.7 m      100.0%    38.0 s       0.0 s
[2016-04-15T00:16Z] INFO  17:16:05,119 ProgressMeter - Total runtime 38.55 secs, 0.64 min, 0.01 hours
[2016-04-15T00:16Z] INFO  17:16:05,120 MicroScheduler - 163 reads were filtered out during the traversal out of approximately 240865 total reads (0.07%)
[2016-04-15T00:16Z] INFO  17:16:05,121 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:16Z] INFO  17:16:05,121 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:16Z] INFO  17:16:05,122 MicroScheduler -   -> 163 reads (0.07% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:16Z] INFO  17:16:05,345 IntervalUtils - Processing 33099518 bp from intervals
[2016-04-15T00:16Z] WARN  17:16:05,350 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:16Z] INFO  17:16:05,468 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:16Z] INFO  17:16:05,721 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:16Z] INFO  17:16:05,722 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:16Z] INFO  17:16:05,723 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:16Z] INFO  17:16:05,724 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:16Z] INFO  17:16:05,731 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:16Z] GATK: realign ('9', 97718189, 113228306) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:16Z] INFO  17:16:05,827 ProgressMeter -            done   1.5529389E7    18.0 s       1.0 s      100.0%    18.0 s       0.0 s
[2016-04-15T00:16Z] INFO  17:16:05,828 ProgressMeter - Total runtime 18.81 secs, 0.31 min, 0.01 hours
[2016-04-15T00:16Z] INFO  17:16:05,832 MicroScheduler - 46366 reads were filtered out during the traversal out of approximately 311646 total reads (14.88%)
[2016-04-15T00:16Z] INFO  17:16:05,835 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:16Z] INFO  17:16:05,835 MicroScheduler -   -> 842 reads (0.27% of total) failing BadMateFilter
[2016-04-15T00:16Z] INFO  17:16:05,836 MicroScheduler -   -> 22102 reads (7.09% of total) failing DuplicateReadFilter
[2016-04-15T00:16Z] INFO  17:16:05,837 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:16Z] INFO  17:16:05,837 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:16Z] INFO  17:16:05,838 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:16Z] INFO  17:16:05,838 MicroScheduler -   -> 23422 reads (7.52% of total) failing MappingQualityZeroFilter
[2016-04-15T00:16Z] INFO  17:16:05,839 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:16Z] INFO  17:16:05,840 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-15T00:16Z] INFO  17:16:05,840 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:16Z] INFO  17:16:06,362 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@5fe152b7
[2016-04-15T00:16Z] INFO  17:16:06,437 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:16Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-10_78316966_93841258-prep-prealign.bam
[2016-04-15T00:16Z] INFO  17:16:06,519 ProgressMeter -            done    347949.0    42.0 s       2.0 m      100.0%    42.0 s       0.0 s
[2016-04-15T00:16Z] INFO  17:16:06,520 ProgressMeter - Total runtime 42.58 secs, 0.71 min, 0.01 hours
[2016-04-15T00:16Z] INFO  17:16:06,521 MicroScheduler - 158 reads were filtered out during the traversal out of approximately 348107 total reads (0.05%)
[2016-04-15T00:16Z] INFO  17:16:06,521 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:16Z] INFO  17:16:06,521 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:16Z] INFO  17:16:06,522 MicroScheduler -   -> 158 reads (0.05% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:16Z] INFO  17:16:07,062 ProgressMeter -            done   1.5573214E7    18.0 s       1.0 s      100.0%    18.0 s       0.0 s
[2016-04-15T00:16Z] INFO  17:16:07,062 ProgressMeter - Total runtime 18.19 secs, 0.30 min, 0.01 hours
[2016-04-15T00:16Z] INFO  17:16:07,067 MicroScheduler - 18195 reads were filtered out during the traversal out of approximately 195654 total reads (9.30%)
[2016-04-15T00:16Z] INFO  17:16:07,069 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:16Z] INFO  17:16:07,070 MicroScheduler -   -> 640 reads (0.33% of total) failing BadMateFilter
[2016-04-15T00:16Z] INFO  17:16:07,070 MicroScheduler -   -> 14260 reads (7.29% of total) failing DuplicateReadFilter
[2016-04-15T00:16Z] INFO  17:16:07,071 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:16Z] INFO  17:16:07,072 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:16Z] INFO  17:16:07,073 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:16Z] INFO  17:16:07,074 MicroScheduler -   -> 3295 reads (1.68% of total) failing MappingQualityZeroFilter
[2016-04-15T00:16Z] INFO  17:16:07,074 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:16Z] INFO  17:16:07,075 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-15T00:16Z] INFO  17:16:07,076 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:16Z] INFO  17:16:07,302 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:16Z] GATK RealignerTargetCreator: R14-18106_kapa-NGv3-PE100-NGv3-sort-10_78316966_93841258-prep-prealign.bam 10:78316967-93841258
[2016-04-15T00:16Z] GATK: RealignerTargetCreator
[2016-04-15T00:16Z] GATK: realign ('9', 82188172, 97717561) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:16Z] INFO  17:16:08,037 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:16Z] INFO  17:16:08,056 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@41fd9d8e
[2016-04-15T00:16Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-10_62539923_78084243-prep-prealign.bam
[2016-04-15T00:16Z] INFO  17:16:08,222 ProgressMeter -            done    359902.0    46.0 s       2.1 m      100.0%    46.0 s       0.0 s
[2016-04-15T00:16Z] INFO  17:16:08,222 ProgressMeter - Total runtime 46.18 secs, 0.77 min, 0.01 hours
[2016-04-15T00:16Z] INFO  17:16:08,223 MicroScheduler - 170 reads were filtered out during the traversal out of approximately 360072 total reads (0.05%)
[2016-04-15T00:16Z] INFO  17:16:08,223 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:16Z] INFO  17:16:08,224 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:16Z] INFO  17:16:08,224 MicroScheduler -   -> 170 reads (0.05% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:16Z] INFO  17:16:08,479 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:16Z] GATK: realign ('10', 15561288, 31134502) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:16Z] INFO  17:16:08,573 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:16Z] INFO  17:16:08,577 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:16Z] INFO  17:16:08,577 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:16Z] INFO  17:16:08,578 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:16Z] INFO  17:16:08,582 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/9/R14-18106_kapa-NGv3-PE100-NGv3-sort-9_97718189_113228306-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/9/R14-18106_kapa-NGv3-PE100-NGv3-sort-9_97718189_113228306-prep-prealign-realign.intervals -L 9:97718190-113228306 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/9/tx/tmpUQMRHC/R14-18106_kapa-NGv3-PE100-NGv3-sort-9_97718189_113228306-prep.bam
[2016-04-15T00:16Z] INFO  17:16:08,595 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:16Z] INFO  17:16:08,598 HelpFormatter - Date/Time: 2016/04/14 17:16:08
[2016-04-15T00:16Z] INFO  17:16:08,599 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:16Z] INFO  17:16:08,600 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:16Z] INFO  17:16:08,798 ProgressMeter -     9:137715316    400008.0    60.0 s       2.5 m       71.1%    84.0 s      24.0 s
[2016-04-15T00:16Z] INFO  17:16:08,897 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:16Z] INFO  17:16:09,066 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:16Z] INFO  17:16:09,097 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:16Z] INFO  17:16:09,147 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-15T00:16Z] GATK RealignerTargetCreator: R14-18106_kapa-NGv3-PE100-NGv3-sort-10_62539923_78084243-prep-prealign.bam 10:62539924-78084243
[2016-04-15T00:16Z] GATK: RealignerTargetCreator
[2016-04-15T00:16Z] INFO  17:16:09,501 IntervalUtils - Processing 15510117 bp from intervals
[2016-04-15T00:16Z] WARN  17:16:09,507 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:16Z] INFO  17:16:09,634 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:16Z] INFO  17:16:09,675 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:16Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-10_46960410_62493077-prep-prealign.bam
[2016-04-15T00:16Z] INFO  17:16:09,828 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:16Z] INFO  17:16:09,829 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:16Z] INFO  17:16:09,830 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:16Z] INFO  17:16:09,831 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:16Z] INFO  17:16:10,016 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:16Z] INFO  17:16:10,181 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:16Z] INFO  17:16:10,277 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:16Z] INFO  17:16:10,281 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:16Z] INFO  17:16:10,281 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:16Z] INFO  17:16:10,282 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:16Z] INFO  17:16:10,290 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/9/R14-18106_kapa-NGv3-PE100-NGv3-sort-9_82188172_97717561-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/9/R14-18106_kapa-NGv3-PE100-NGv3-sort-9_82188172_97717561-prep-prealign-realign.intervals -L 9:82188173-97717561 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/9/tx/tmpQEnkL9/R14-18106_kapa-NGv3-PE100-NGv3-sort-9_82188172_97717561-prep.bam
[2016-04-15T00:16Z] INFO  17:16:10,299 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:16Z] INFO  17:16:10,299 HelpFormatter - Date/Time: 2016/04/14 17:16:10
[2016-04-15T00:16Z] INFO  17:16:10,300 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:16Z] INFO  17:16:10,301 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:16Z] INFO  17:16:10,475 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:16Z] INFO  17:16:10,562 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:16Z] INFO  17:16:10,575 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:16Z] INFO  17:16:10,576 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:16Z] INFO  17:16:10,576 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:16Z] INFO  17:16:10,580 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/10/R14-18106_kapa-NGv3-PE100-NGv3-sort-10_78316966_93841258-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/10/tx/tmpoA1Ypr/R14-18106_kapa-NGv3-PE100-NGv3-sort-10_78316966_93841258-prep-prealign-realign.intervals -l INFO -L 10:78316967-93841258 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:16Z] INFO  17:16:10,598 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:16Z] INFO  17:16:10,598 HelpFormatter - Date/Time: 2016/04/14 17:16:10
[2016-04-15T00:16Z] INFO  17:16:10,599 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:16Z] INFO  17:16:10,599 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:16Z] INFO  17:16:10,606 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:16Z] INFO  17:16:10,627 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:16Z] INFO  17:16:10,689 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-15T00:16Z] INFO  17:16:10,710 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:16Z] GATK RealignerTargetCreator: R14-18106_kapa-NGv3-PE100-NGv3-sort-10_46960410_62493077-prep-prealign.bam 10:46960411-62493077
[2016-04-15T00:16Z] GATK: RealignerTargetCreator
[2016-04-15T00:16Z] INFO  17:16:10,986 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T00:16Z] INFO  17:16:10,996 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:16Z] INFO  17:16:11,054 IntervalUtils - Processing 15529389 bp from intervals
[2016-04-15T00:16Z] WARN  17:16:11,059 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:16Z] INFO  17:16:11,066 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-15T00:16Z] INFO  17:16:11,140 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:16Z] INFO  17:16:11,328 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:16Z] INFO  17:16:11,329 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:16Z] INFO  17:16:11,329 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:16Z] INFO  17:16:11,329 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:16Z] INFO  17:16:11,470 IntervalUtils - Processing 15524292 bp from intervals
[2016-04-15T00:16Z] WARN  17:16:11,475 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:16Z] INFO  17:16:11,495 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:16Z] INFO  17:16:11,497 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:16Z] INFO  17:16:11,497 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:16Z] INFO  17:16:11,509 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:16Z] INFO  17:16:11,513 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/10/R14-18106_kapa-NGv3-PE100-NGv3-sort-10_15561288_31134502-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/10/R14-18106_kapa-NGv3-PE100-NGv3-sort-10_15561288_31134502-prep-prealign-realign.intervals -L 10:15561289-31134502 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/10/tx/tmp9QBMjO/R14-18106_kapa-NGv3-PE100-NGv3-sort-10_15561288_31134502-prep.bam
[2016-04-15T00:16Z] INFO  17:16:11,521 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:16Z] INFO  17:16:11,522 HelpFormatter - Date/Time: 2016/04/14 17:16:11
[2016-04-15T00:16Z] INFO  17:16:11,522 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:16Z] INFO  17:16:11,523 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:16Z] INFO  17:16:11,525 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:16Z] INFO  17:16:11,590 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:16Z] INFO  17:16:11,703 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:16Z] INFO  17:16:11,752 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:16Z] INFO  17:16:11,822 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:16Z] INFO  17:16:11,823 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:16Z] INFO  17:16:11,824 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:16Z] INFO  17:16:11,825 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:16Z] INFO  17:16:11,929 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:16Z] INFO  17:16:11,948 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:16Z] INFO  17:16:11,990 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.04
[2016-04-15T00:16Z] INFO  17:16:12,293 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:16Z] INFO  17:16:12,296 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:16Z] INFO  17:16:12,297 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:16Z] INFO  17:16:12,297 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:16Z] INFO  17:16:12,302 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/10/R14-18106_kapa-NGv3-PE100-NGv3-sort-10_62539923_78084243-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/10/tx/tmpRSf8YJ/R14-18106_kapa-NGv3-PE100-NGv3-sort-10_62539923_78084243-prep-prealign-realign.intervals -l INFO -L 10:62539924-78084243 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:16Z] INFO  17:16:12,322 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:16Z] INFO  17:16:12,323 HelpFormatter - Date/Time: 2016/04/14 17:16:12
[2016-04-15T00:16Z] INFO  17:16:12,323 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:16Z] INFO  17:16:12,323 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:16Z] INFO  17:16:12,439 IntervalUtils - Processing 15573214 bp from intervals
[2016-04-15T00:16Z] WARN  17:16:12,444 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:16Z] INFO  17:16:12,472 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:16Z] INFO  17:16:12,583 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:16Z] INFO  17:16:12,685 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T00:16Z] INFO  17:16:12,697 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:16Z] INFO  17:16:12,748 ProgressMeter -            done   1.5559243E7    18.0 s       1.0 s      100.0%    18.0 s       0.0 s
[2016-04-15T00:16Z] INFO  17:16:12,749 ProgressMeter - Total runtime 18.14 secs, 0.30 min, 0.01 hours
[2016-04-15T00:16Z] INFO  17:16:12,754 MicroScheduler - 19835 reads were filtered out during the traversal out of approximately 217555 total reads (9.12%)
[2016-04-15T00:16Z] INFO  17:16:12,756 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:16Z] INFO  17:16:12,757 MicroScheduler -   -> 697 reads (0.32% of total) failing BadMateFilter
[2016-04-15T00:16Z] INFO  17:16:12,758 MicroScheduler -   -> 16098 reads (7.40% of total) failing DuplicateReadFilter
[2016-04-15T00:16Z] INFO  17:16:12,777 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:16Z] INFO  17:16:12,758 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:16Z] INFO  17:16:12,779 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:16Z] INFO  17:16:12,780 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:16Z] INFO  17:16:12,780 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-15T00:16Z] INFO  17:16:12,779 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:16Z] INFO  17:16:12,781 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:16Z] INFO  17:16:12,780 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:16Z] INFO  17:16:12,780 MicroScheduler -   -> 3040 reads (1.40% of total) failing MappingQualityZeroFilter
[2016-04-15T00:16Z] INFO  17:16:12,780 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:16Z] INFO  17:16:12,781 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-15T00:16Z] INFO  17:16:12,782 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:16Z] INFO  17:16:12,993 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:16Z] INFO  17:16:13,179 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:16Z] INFO  17:16:13,294 IntervalUtils - Processing 15544320 bp from intervals
[2016-04-15T00:16Z] WARN  17:16:13,300 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:16Z] INFO  17:16:13,481 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:16Z] INFO  17:16:13,748 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:16Z] INFO  17:16:13,749 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:16Z] INFO  17:16:13,750 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:16Z] INFO  17:16:13,751 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:16Z] INFO  17:16:14,071 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:16Z] INFO  17:16:14,074 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:16Z] INFO  17:16:14,074 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:16Z] INFO  17:16:14,075 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:16Z] INFO  17:16:14,079 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/10/R14-18106_kapa-NGv3-PE100-NGv3-sort-10_46960410_62493077-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/10/tx/tmpzlEASN/R14-18106_kapa-NGv3-PE100-NGv3-sort-10_46960410_62493077-prep-prealign-realign.intervals -l INFO -L 10:46960411-62493077 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:16Z] INFO  17:16:14,098 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:16Z] INFO  17:16:14,099 HelpFormatter - Date/Time: 2016/04/14 17:16:14
[2016-04-15T00:16Z] INFO  17:16:14,099 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:16Z] INFO  17:16:14,100 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:16Z] INFO  17:16:14,217 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:16Z] INFO  17:16:14,387 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T00:16Z] INFO  17:16:14,396 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:16Z] INFO  17:16:14,420 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:16Z] INFO  17:16:14,442 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.04
[2016-04-15T00:16Z] GATK: realign ('10', 0, 15559243) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:16Z] INFO  17:16:14,817 IntervalUtils - Processing 15532667 bp from intervals
[2016-04-15T00:16Z] INFO  17:16:14,820 ProgressMeter -            done    228431.0    18.0 s      80.0 s      100.0%    18.0 s       0.0 s
[2016-04-15T00:16Z] INFO  17:16:14,824 ProgressMeter - Total runtime 18.46 secs, 0.31 min, 0.01 hours
[2016-04-15T00:16Z] INFO  17:16:14,828 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 228431 total reads (0.00%)
[2016-04-15T00:16Z] INFO  17:16:14,828 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:16Z] INFO  17:16:14,829 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:16Z] INFO  17:16:14,829 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:16Z] WARN  17:16:14,834 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:16Z] INFO  17:16:14,966 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:16Z] INFO  17:16:15,157 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:16Z] INFO  17:16:15,158 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:16Z] INFO  17:16:15,159 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:16Z] INFO  17:16:15,160 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:16Z] INFO  17:16:16,183 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:16Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-9_65507205_82187750-prep.bam
[2016-04-15T00:16Z] GATK pre-alignment ('11', 16007749, 31531554) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:16Z] INFO  17:16:17,337 ProgressMeter -            done   1.5858356E7    21.0 s       1.0 s      100.0%    21.0 s       0.0 s
[2016-04-15T00:16Z] INFO  17:16:17,338 ProgressMeter - Total runtime 21.45 secs, 0.36 min, 0.01 hours
[2016-04-15T00:16Z] INFO  17:16:17,342 MicroScheduler - 27944 reads were filtered out during the traversal out of approximately 340266 total reads (8.21%)
[2016-04-15T00:16Z] INFO  17:16:17,343 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:16Z] INFO  17:16:17,344 MicroScheduler -   -> 900 reads (0.26% of total) failing BadMateFilter
[2016-04-15T00:16Z] INFO  17:16:17,345 MicroScheduler -   -> 25153 reads (7.39% of total) failing DuplicateReadFilter
[2016-04-15T00:16Z] INFO  17:16:17,345 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:16Z] INFO  17:16:17,346 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:16Z] INFO  17:16:17,346 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:16Z] INFO  17:16:17,347 MicroScheduler -   -> 1891 reads (0.56% of total) failing MappingQualityZeroFilter
[2016-04-15T00:16Z] INFO  17:16:17,352 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:16Z] INFO  17:16:17,353 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-15T00:16Z] INFO  17:16:17,353 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:16Z] INFO  17:16:17,418 ProgressMeter -            done   1.582267E7    17.0 s       1.0 s      100.0%    17.0 s       0.0 s
[2016-04-15T00:16Z] INFO  17:16:17,420 ProgressMeter - Total runtime 17.31 secs, 0.29 min, 0.00 hours
[2016-04-15T00:16Z] INFO  17:16:17,424 MicroScheduler - 50730 reads were filtered out during the traversal out of approximately 205918 total reads (24.64%)
[2016-04-15T00:16Z] INFO  17:16:17,425 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:16Z] INFO  17:16:17,426 MicroScheduler -   -> 1080 reads (0.52% of total) failing BadMateFilter
[2016-04-15T00:16Z] INFO  17:16:17,426 MicroScheduler -   -> 12801 reads (6.22% of total) failing DuplicateReadFilter
[2016-04-15T00:16Z] INFO  17:16:17,427 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:16Z] INFO  17:16:17,428 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:16Z] INFO  17:16:17,428 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:16Z] INFO  17:16:17,429 MicroScheduler -   -> 36849 reads (17.89% of total) failing MappingQualityZeroFilter
[2016-04-15T00:16Z] INFO  17:16:17,429 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:16Z] INFO  17:16:17,429 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-15T00:16Z] INFO  17:16:17,430 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:16Z] INFO  17:16:17,437 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:16Z] INFO  17:16:17,440 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:16Z] INFO  17:16:17,441 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:16Z] INFO  17:16:17,441 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:16Z] INFO  17:16:17,446 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/10/R14-18106_kapa-NGv3-PE100-NGv3-sort-10_0_15559243-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/10/R14-18106_kapa-NGv3-PE100-NGv3-sort-10_0_15559243-prep-prealign-realign.intervals -L 10:1-15559243 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/10/tx/tmpBOtMWr/R14-18106_kapa-NGv3-PE100-NGv3-sort-10_0_15559243-prep.bam
[2016-04-15T00:16Z] INFO  17:16:17,456 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:16Z] INFO  17:16:17,467 HelpFormatter - Date/Time: 2016/04/14 17:16:17
[2016-04-15T00:16Z] INFO  17:16:17,468 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:16Z] INFO  17:16:17,469 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:16Z] INFO  17:16:17,707 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:16Z] INFO  17:16:17,878 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:16Z] INFO  17:16:17,887 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:16Z] INFO  17:16:17,947 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-15T00:16Z] INFO  17:16:18,285 IntervalUtils - Processing 15559243 bp from intervals
[2016-04-15T00:16Z] WARN  17:16:18,291 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:16Z] INFO  17:16:18,406 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:16Z] INFO  17:16:18,538 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:16Z] INFO  17:16:18,539 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:16Z] INFO  17:16:18,540 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:16Z] INFO  17:16:18,541 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:16Z] INFO  17:16:18,724 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:16Z] INFO  17:16:18,802 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:16Z] GATK: realign ('9', 113231219, 129089575) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:16Z] INFO  17:16:18,895 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:16Z] INFO  17:16:18,900 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:16Z] GATK: realign ('10', 31137459, 46960129) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:16Z] INFO  17:16:19,682 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:16Z] INFO  17:16:19,685 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:16Z] INFO  17:16:19,685 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:16Z] INFO  17:16:19,686 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:16Z] INFO  17:16:19,691 HelpFormatter - Program Args: -T PrintReads -L 11:16007750-31531554 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/11/tx/tmp8fK56I/R14-18106_kapa-NGv3-PE100-NGv3-sort-11_16007749_31531554-prep-prealign.bam
[2016-04-15T00:16Z] INFO  17:16:19,699 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:16Z] INFO  17:16:19,699 HelpFormatter - Date/Time: 2016/04/14 17:16:19
[2016-04-15T00:16Z] INFO  17:16:19,700 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:16Z] INFO  17:16:19,700 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:16Z] INFO  17:16:19,918 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:16Z] INFO  17:16:21,118 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-15T00:16Z] INFO  17:16:21,173 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:16Z] INFO  17:16:21,182 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:16Z] INFO  17:16:21,241 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-15T00:16Z] INFO  17:16:21,254 IntervalUtils - Processing 15523805 bp from intervals
[2016-04-15T00:16Z] INFO  17:16:21,336 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:16Z] INFO  17:16:21,504 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@41fd9d8e
[2016-04-15T00:16Z] INFO  17:16:21,625 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:16Z] INFO  17:16:21,626 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:16Z] INFO  17:16:21,626 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:16Z] INFO  17:16:21,627 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:16Z] INFO  17:16:21,643 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:16Z] INFO  17:16:21,656 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:16Z] INFO  17:16:21,659 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:16Z] INFO  17:16:21,659 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:16Z] INFO  17:16:21,660 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:16Z] INFO  17:16:21,664 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/9/R14-18106_kapa-NGv3-PE100-NGv3-sort-9_113231219_129089575-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/9/R14-18106_kapa-NGv3-PE100-NGv3-sort-9_113231219_129089575-prep-prealign-realign.intervals -L 9:113231220-129089575 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/9/tx/tmpwussdX/R14-18106_kapa-NGv3-PE100-NGv3-sort-9_113231219_129089575-prep.bam
[2016-04-15T00:16Z] INFO  17:16:21,674 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:16Z] INFO  17:16:21,675 HelpFormatter - Date/Time: 2016/04/14 17:16:21
[2016-04-15T00:16Z] INFO  17:16:21,675 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:16Z] INFO  17:16:21,676 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:16Z] INFO  17:16:21,680 ProgressMeter -            done    168780.0    22.0 s       2.2 m       99.0%    22.0 s       0.0 s
[2016-04-15T00:16Z] INFO  17:16:21,681 ProgressMeter - Total runtime 22.65 secs, 0.38 min, 0.01 hours
[2016-04-15T00:16Z] INFO  17:16:21,681 MicroScheduler - 188 reads were filtered out during the traversal out of approximately 168968 total reads (0.11%)
[2016-04-15T00:16Z] INFO  17:16:21,682 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:16Z] INFO  17:16:21,682 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:16Z] INFO  17:16:21,682 MicroScheduler -   -> 188 reads (0.11% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:16Z] INFO  17:16:21,714 ProgressMeter -    10:124337378    200004.0    30.0 s       2.5 m       81.3%    36.0 s       6.0 s
[2016-04-15T00:16Z] INFO  17:16:21,774 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:16Z] INFO  17:16:21,909 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:16Z] INFO  17:16:21,992 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:16Z] INFO  17:16:21,996 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:16Z] INFO  17:16:21,997 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:16Z] INFO  17:16:21,997 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:16Z] INFO  17:16:22,003 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/10/R14-18106_kapa-NGv3-PE100-NGv3-sort-10_31137459_46960129-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/10/R14-18106_kapa-NGv3-PE100-NGv3-sort-10_31137459_46960129-prep-prealign-realign.intervals -L 10:31137460-46960129 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/10/tx/tmpK0qitY/R14-18106_kapa-NGv3-PE100-NGv3-sort-10_31137459_46960129-prep.bam
[2016-04-15T00:16Z] INFO  17:16:22,017 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:16Z] INFO  17:16:22,018 HelpFormatter - Date/Time: 2016/04/14 17:16:21
[2016-04-15T00:16Z] INFO  17:16:22,018 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:16Z] INFO  17:16:22,019 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:16Z] INFO  17:16:22,056 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:16Z] INFO  17:16:22,071 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:16Z] INFO  17:16:22,131 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-15T00:16Z] INFO  17:16:22,280 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:16Z] INFO  17:16:22,487 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:16Z] INFO  17:16:22,499 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:16Z] INFO  17:16:22,551 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-15T00:16Z] INFO  17:16:22,639 IntervalUtils - Processing 15858356 bp from intervals
[2016-04-15T00:16Z] WARN  17:16:22,646 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:16Z] INFO  17:16:22,725 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:16Z] INFO  17:16:22,866 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:16Z] INFO  17:16:22,867 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:16Z] INFO  17:16:22,868 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:16Z] INFO  17:16:22,869 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:16Z] INFO  17:16:23,033 IntervalUtils - Processing 15822670 bp from intervals
[2016-04-15T00:16Z] WARN  17:16:23,052 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:16Z] INFO  17:16:23,066 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:16Z] INFO  17:16:23,141 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:16Z] INFO  17:16:23,194 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:16Z] INFO  17:16:23,214 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:16Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-10_127328721_135534747-prep-prealign.bam
[2016-04-15T00:16Z] INFO  17:16:23,299 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:16Z] INFO  17:16:23,300 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:16Z] INFO  17:16:23,300 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:16Z] INFO  17:16:23,300 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:16Z] INFO  17:16:23,451 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:16Z] INFO  17:16:23,643 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:16Z] GATK RealignerTargetCreator: R14-18106_kapa-NGv3-PE100-NGv3-sort-10_127328721_135534747-prep-prealign.bam 10:127328722-135534747
[2016-04-15T00:16Z] GATK: RealignerTargetCreator
[2016-04-15T00:16Z] INFO  17:16:26,589 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:16Z] INFO  17:16:26,591 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:16Z] INFO  17:16:26,591 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:16Z] INFO  17:16:26,592 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:16Z] INFO  17:16:26,596 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/10/R14-18106_kapa-NGv3-PE100-NGv3-sort-10_127328721_135534747-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/10/tx/tmpVYyJ2L/R14-18106_kapa-NGv3-PE100-NGv3-sort-10_127328721_135534747-prep-prealign-realign.intervals -l INFO -L 10:127328722-135534747 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:16Z] INFO  17:16:26,607 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:16Z] INFO  17:16:26,608 HelpFormatter - Date/Time: 2016/04/14 17:16:26
[2016-04-15T00:16Z] INFO  17:16:26,609 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:16Z] INFO  17:16:26,610 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:16Z] INFO  17:16:26,729 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:16Z] INFO  17:16:26,902 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T00:16Z] INFO  17:16:26,911 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:16Z] INFO  17:16:26,975 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-15T00:16Z] INFO  17:16:27,274 IntervalUtils - Processing 8206026 bp from intervals
[2016-04-15T00:16Z] WARN  17:16:27,279 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:16Z] INFO  17:16:27,391 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:16Z] INFO  17:16:27,548 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:16Z] INFO  17:16:27,549 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:16Z] INFO  17:16:27,550 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:16Z] INFO  17:16:27,550 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:16Z] INFO  17:16:27,832 ProgressMeter -            done    194128.0    15.0 s      77.0 s      100.0%    15.0 s       0.0 s
[2016-04-15T00:16Z] INFO  17:16:27,833 ProgressMeter - Total runtime 15.05 secs, 0.25 min, 0.00 hours
[2016-04-15T00:16Z] INFO  17:16:27,837 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 194128 total reads (0.00%)
[2016-04-15T00:16Z] INFO  17:16:27,838 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:16Z] INFO  17:16:27,838 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:16Z] INFO  17:16:27,838 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:16Z] INFO  17:16:29,156 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@5fe152b7
[2016-04-15T00:16Z] INFO  17:16:29,309 ProgressMeter -            done    486965.0    58.0 s     120.0 s      100.0%    58.0 s       0.0 s
[2016-04-15T00:16Z] INFO  17:16:29,310 ProgressMeter - Total runtime 58.59 secs, 0.98 min, 0.02 hours
[2016-04-15T00:16Z] INFO  17:16:29,311 MicroScheduler - 269 reads were filtered out during the traversal out of approximately 487234 total reads (0.06%)
[2016-04-15T00:16Z] INFO  17:16:29,312 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:16Z] INFO  17:16:29,312 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:16Z] INFO  17:16:29,313 MicroScheduler -   -> 269 reads (0.06% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:16Z] INFO  17:16:29,417 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:16Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-10_15561288_31134502-prep.bam
[2016-04-15T00:16Z] INFO  17:16:29,895 ProgressMeter -            done   1.5524292E7    18.0 s       1.0 s      100.0%    18.0 s       0.0 s
[2016-04-15T00:16Z] INFO  17:16:29,896 ProgressMeter - Total runtime 18.07 secs, 0.30 min, 0.01 hours
[2016-04-15T00:16Z] INFO  17:16:29,900 MicroScheduler - 39781 reads were filtered out during the traversal out of approximately 242151 total reads (16.43%)
[2016-04-15T00:16Z] INFO  17:16:29,901 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:16Z] INFO  17:16:29,902 MicroScheduler -   -> 652 reads (0.27% of total) failing BadMateFilter
[2016-04-15T00:16Z] INFO  17:16:29,903 MicroScheduler -   -> 16373 reads (6.76% of total) failing DuplicateReadFilter
[2016-04-15T00:16Z] INFO  17:16:29,903 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:16Z] INFO  17:16:29,904 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:16Z] INFO  17:16:29,905 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:16Z] INFO  17:16:29,906 MicroScheduler -   -> 22756 reads (9.40% of total) failing MappingQualityZeroFilter
[2016-04-15T00:16Z] INFO  17:16:29,907 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:16Z] INFO  17:16:29,907 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-15T00:16Z] INFO  17:16:29,908 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:16Z] GATK pre-alignment ('11', 31541602, 47074069) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:16Z] INFO  17:16:30,356 ProgressMeter -            done    286764.0    20.0 s      71.0 s      100.0%    20.0 s       0.0 s
[2016-04-15T00:16Z] INFO  17:16:30,357 ProgressMeter - Total runtime 20.53 secs, 0.34 min, 0.01 hours
[2016-04-15T00:16Z] INFO  17:16:30,360 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 286764 total reads (0.00%)
[2016-04-15T00:16Z] INFO  17:16:30,361 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:16Z] INFO  17:16:30,361 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:16Z] INFO  17:16:30,361 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:16Z] INFO  17:16:30,475 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@7172f77a
[2016-04-15T00:16Z] INFO  17:16:30,627 ProgressMeter -            done    297720.0    38.0 s       2.2 m      100.0%    38.0 s       0.0 s
[2016-04-15T00:16Z] INFO  17:16:30,627 ProgressMeter - Total runtime 38.95 secs, 0.65 min, 0.01 hours
[2016-04-15T00:16Z] INFO  17:16:30,627 MicroScheduler - 176 reads were filtered out during the traversal out of approximately 297896 total reads (0.06%)
[2016-04-15T00:16Z] INFO  17:16:30,628 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:16Z] INFO  17:16:30,628 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:16Z] INFO  17:16:30,628 MicroScheduler -   -> 176 reads (0.06% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:16Z] INFO  17:16:30,684 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:16Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-10_93851586_111625070-prep-prealign.bam
[2016-04-15T00:16Z] INFO  17:16:31,215 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:16Z] GATK: realign ('10', 78316966, 93841258) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:16Z] INFO  17:16:31,599 ProgressMeter -            done    309988.0    20.0 s      65.0 s      100.0%    20.0 s       0.0 s
[2016-04-15T00:16Z] INFO  17:16:31,601 ProgressMeter - Total runtime 20.27 secs, 0.34 min, 0.01 hours
[2016-04-15T00:16Z] INFO  17:16:31,608 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 309988 total reads (0.00%)
[2016-04-15T00:16Z] INFO  17:16:31,609 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:16Z] INFO  17:16:31,609 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:16Z] INFO  17:16:31,609 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:16Z] INFO  17:16:31,948 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:16Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-10_111628371_127265443-prep-prealign.bam
[2016-04-15T00:16Z] INFO  17:16:32,030 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:16Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-9_97718189_113228306-prep.bam
[2016-04-15T00:16Z] GATK RealignerTargetCreator: R14-18106_kapa-NGv3-PE100-NGv3-sort-10_93851586_111625070-prep-prealign.bam 10:93851587-111625070
[2016-04-15T00:16Z] GATK: RealignerTargetCreator
[2016-04-15T00:16Z] INFO  17:16:32,589 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:16Z] INFO  17:16:32,591 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:16Z] INFO  17:16:32,592 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:16Z] INFO  17:16:32,592 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:16Z] INFO  17:16:32,596 HelpFormatter - Program Args: -T PrintReads -L 11:31541603-47074069 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/11/tx/tmpv8hJnU/R14-18106_kapa-NGv3-PE100-NGv3-sort-11_31541602_47074069-prep-prealign.bam
[2016-04-15T00:16Z] INFO  17:16:32,609 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:16Z] INFO  17:16:32,610 HelpFormatter - Date/Time: 2016/04/14 17:16:32
[2016-04-15T00:16Z] INFO  17:16:32,615 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:16Z] INFO  17:16:32,616 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:16Z] INFO  17:16:32,824 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:16Z] GATK RealignerTargetCreator: R14-18106_kapa-NGv3-PE100-NGv3-sort-10_111628371_127265443-prep-prealign.bam 10:111628372-127265443
[2016-04-15T00:16Z] GATK: RealignerTargetCreator
[2016-04-15T00:16Z] INFO  17:16:32,832 ProgressMeter -      11:1093314    100002.0    30.0 s       5.1 m        6.8%     7.3 m       6.8 m
[2016-04-15T00:16Z] GATK pre-alignment ('11', 47158866, 62678572) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:16Z] INFO  17:16:33,074 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:16Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-9_82188172_97717561-prep.bam
[2016-04-15T00:16Z] INFO  17:16:34,068 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-15T00:16Z] INFO  17:16:34,109 ProgressMeter -            done   3.3099518E7    28.0 s       0.0 s      100.0%    28.0 s       0.0 s
[2016-04-15T00:16Z] INFO  17:16:34,110 ProgressMeter - Total runtime 28.39 secs, 0.47 min, 0.01 hours
[2016-04-15T00:16Z] INFO  17:16:34,114 MicroScheduler - 151931 reads were filtered out during the traversal out of approximately 469836 total reads (32.34%)
[2016-04-15T00:16Z] INFO  17:16:34,115 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:16Z] INFO  17:16:34,116 MicroScheduler -   -> 727 reads (0.15% of total) failing BadMateFilter
[2016-04-15T00:16Z] INFO  17:16:34,116 MicroScheduler -   -> 26267 reads (5.59% of total) failing DuplicateReadFilter
[2016-04-15T00:16Z] INFO  17:16:34,117 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:16Z] INFO  17:16:34,118 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:16Z] INFO  17:16:34,118 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:16Z] INFO  17:16:34,118 MicroScheduler -   -> 124937 reads (26.59% of total) failing MappingQualityZeroFilter
[2016-04-15T00:16Z] INFO  17:16:34,118 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:16Z] INFO  17:16:34,115 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:16Z] INFO  17:16:34,119 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-15T00:16Z] INFO  17:16:34,119 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:16Z] INFO  17:16:34,119 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:16Z] INFO  17:16:34,120 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:16Z] INFO  17:16:34,121 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:16Z] INFO  17:16:34,139 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/10/R14-18106_kapa-NGv3-PE100-NGv3-sort-10_78316966_93841258-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/10/R14-18106_kapa-NGv3-PE100-NGv3-sort-10_78316966_93841258-prep-prealign-realign.intervals -L 10:78316967-93841258 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/10/tx/tmpgaTN4I/R14-18106_kapa-NGv3-PE100-NGv3-sort-10_78316966_93841258-prep.bam
[2016-04-15T00:16Z] INFO  17:16:34,154 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:16Z] GATK pre-alignment ('11', 62744265, 78270665) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:16Z] INFO  17:16:34,163 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:16Z] INFO  17:16:34,183 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:16Z] INFO  17:16:34,183 HelpFormatter - Date/Time: 2016/04/14 17:16:34
[2016-04-15T00:16Z] INFO  17:16:34,184 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:16Z] INFO  17:16:34,184 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:16Z] INFO  17:16:34,216 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-15T00:16Z] INFO  17:16:34,243 IntervalUtils - Processing 15532467 bp from intervals
[2016-04-15T00:16Z] INFO  17:16:34,375 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:16Z] INFO  17:16:34,485 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:16Z] INFO  17:16:34,671 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:16Z] INFO  17:16:34,682 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:16Z] INFO  17:16:34,752 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-15T00:16Z] INFO  17:16:34,764 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:16Z] INFO  17:16:34,766 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:16Z] INFO  17:16:34,767 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:16Z] INFO  17:16:34,767 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:16Z] INFO  17:16:34,788 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:16Z] INFO  17:16:34,868 ProgressMeter -            done    216419.0    16.0 s      75.0 s      100.0%    16.0 s       0.0 s
[2016-04-15T00:16Z] INFO  17:16:34,870 ProgressMeter - Total runtime 16.33 secs, 0.27 min, 0.00 hours
[2016-04-15T00:16Z] INFO  17:16:34,874 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 216419 total reads (0.00%)
[2016-04-15T00:16Z] INFO  17:16:34,874 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:16Z] INFO  17:16:34,874 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:16Z] INFO  17:16:34,875 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:16Z] INFO  17:16:34,966 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:16Z] INFO  17:16:34,997 ProgressMeter -            done   1.554432E7    21.0 s       1.0 s      100.0%    21.0 s       0.0 s
[2016-04-15T00:16Z] INFO  17:16:35,002 ProgressMeter - Total runtime 21.25 secs, 0.35 min, 0.01 hours
[2016-04-15T00:16Z] INFO  17:16:35,007 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:16Z] INFO  17:16:35,011 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:16Z] INFO  17:16:35,011 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:16Z] INFO  17:16:35,012 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:16Z] INFO  17:16:35,016 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/10/R14-18106_kapa-NGv3-PE100-NGv3-sort-10_93851586_111625070-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/10/tx/tmpcnDz5t/R14-18106_kapa-NGv3-PE100-NGv3-sort-10_93851586_111625070-prep-prealign-realign.intervals -l INFO -L 10:93851587-111625070 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:16Z] INFO  17:16:35,018 MicroScheduler - 32849 reads were filtered out during the traversal out of approximately 349961 total reads (9.39%)
[2016-04-15T00:16Z] INFO  17:16:35,019 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:16Z] INFO  17:16:35,020 MicroScheduler -   -> 863 reads (0.25% of total) failing BadMateFilter
[2016-04-15T00:16Z] INFO  17:16:35,021 MicroScheduler -   -> 25892 reads (7.40% of total) failing DuplicateReadFilter
[2016-04-15T00:16Z] INFO  17:16:35,021 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:16Z] INFO  17:16:35,022 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:16Z] INFO  17:16:35,022 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:16Z] INFO  17:16:35,023 MicroScheduler -   -> 6094 reads (1.74% of total) failing MappingQualityZeroFilter
[2016-04-15T00:16Z] INFO  17:16:35,024 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:16Z] INFO  17:16:35,024 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-15T00:16Z] INFO  17:16:35,025 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:16Z] INFO  17:16:35,061 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:16Z] INFO  17:16:35,061 HelpFormatter - Date/Time: 2016/04/14 17:16:35
[2016-04-15T00:16Z] INFO  17:16:35,061 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:16Z] INFO  17:16:35,062 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:16Z] INFO  17:16:35,072 ProgressMeter -            done   1.5532667E7    19.0 s       1.0 s      100.0%    19.0 s       0.0 s
[2016-04-15T00:16Z] INFO  17:16:35,073 ProgressMeter - Total runtime 19.91 secs, 0.33 min, 0.01 hours
[2016-04-15T00:16Z] INFO  17:16:35,077 MicroScheduler - 130619 reads were filtered out during the traversal out of approximately 362206 total reads (36.06%)
[2016-04-15T00:16Z] INFO  17:16:35,078 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:16Z] INFO  17:16:35,078 MicroScheduler -   -> 649 reads (0.18% of total) failing BadMateFilter
[2016-04-15T00:16Z] INFO  17:16:35,079 MicroScheduler -   -> 19980 reads (5.52% of total) failing DuplicateReadFilter
[2016-04-15T00:16Z] INFO  17:16:35,080 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:16Z] INFO  17:16:35,080 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:16Z] INFO  17:16:35,081 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:16Z] INFO  17:16:35,082 MicroScheduler -   -> 109990 reads (30.37% of total) failing MappingQualityZeroFilter
[2016-04-15T00:16Z] INFO  17:16:35,082 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:16Z] INFO  17:16:35,083 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-15T00:16Z] INFO  17:16:35,083 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:16Z] INFO  17:16:35,191 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:16Z] INFO  17:16:35,258 IntervalUtils - Processing 15524292 bp from intervals
[2016-04-15T00:16Z] WARN  17:16:35,268 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:16Z] INFO  17:16:35,404 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:16Z] INFO  17:16:35,423 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T00:16Z] INFO  17:16:35,445 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:16Z] INFO  17:16:35,452 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:16Z] GATK: realign ('9', 32407258, 65506776) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:16Z] INFO  17:16:35,487 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.04
[2016-04-15T00:16Z] INFO  17:16:35,557 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:16Z] INFO  17:16:35,559 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:16Z] INFO  17:16:35,560 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:16Z] INFO  17:16:35,561 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:16Z] INFO  17:16:35,725 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:16Z] INFO  17:16:35,917 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:16Z] INFO  17:16:35,921 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:16Z] INFO  17:16:35,924 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:16Z] INFO  17:16:35,925 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:16Z] INFO  17:16:35,926 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:16Z] INFO  17:16:35,930 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/10/R14-18106_kapa-NGv3-PE100-NGv3-sort-10_111628371_127265443-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/10/tx/tmpYO11zD/R14-18106_kapa-NGv3-PE100-NGv3-sort-10_111628371_127265443-prep-prealign-realign.intervals -l INFO -L 10:111628372-127265443 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:16Z] INFO  17:16:35,938 IntervalUtils - Processing 17773484 bp from intervals
[2016-04-15T00:16Z] INFO  17:16:35,939 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:16Z] WARN  17:16:35,943 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:16Z] INFO  17:16:35,944 HelpFormatter - Date/Time: 2016/04/14 17:16:35
[2016-04-15T00:16Z] INFO  17:16:35,944 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:16Z] INFO  17:16:35,945 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:16Z] INFO  17:16:36,019 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:16Z] INFO  17:16:36,064 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:16Z] INFO  17:16:36,251 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:16Z] INFO  17:16:36,253 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:16Z] INFO  17:16:36,253 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:16Z] INFO  17:16:36,254 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:16Z] INFO  17:16:36,323 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:16Z] INFO  17:16:36,325 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:16Z] INFO  17:16:36,326 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:16Z] INFO  17:16:36,326 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:16Z] INFO  17:16:36,330 HelpFormatter - Program Args: -T PrintReads -L 11:47158867-62678572 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/11/tx/tmpqPadrZ/R14-18106_kapa-NGv3-PE100-NGv3-sort-11_47158866_62678572-prep-prealign.bam
[2016-04-15T00:16Z] INFO  17:16:36,356 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:16Z] INFO  17:16:36,357 HelpFormatter - Date/Time: 2016/04/14 17:16:36
[2016-04-15T00:16Z] INFO  17:16:36,357 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:16Z] INFO  17:16:36,357 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:16Z] INFO  17:16:36,388 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T00:16Z] INFO  17:16:36,398 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:16Z] INFO  17:16:36,442 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.04
[2016-04-15T00:16Z] INFO  17:16:36,563 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:16Z] INFO  17:16:36,564 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:16Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-10_0_15559243-prep.bam
[2016-04-15T00:16Z] INFO  17:16:36,628 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:16Z] INFO  17:16:36,643 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:16Z] GATK: realign ('10', 62539923, 78084243) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:16Z] GATK: realign ('10', 46960410, 62493077) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:16Z] INFO  17:16:36,757 IntervalUtils - Processing 15637072 bp from intervals
[2016-04-15T00:16Z] WARN  17:16:36,762 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:16Z] INFO  17:16:36,829 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:16Z] INFO  17:16:37,041 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:16Z] INFO  17:16:37,042 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:16Z] INFO  17:16:37,043 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:16Z] INFO  17:16:37,044 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:16Z] GATK pre-alignment ('11', 78277177, 93796886) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:16Z] INFO  17:16:37,416 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:16Z] INFO  17:16:37,420 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:16Z] INFO  17:16:37,421 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:16Z] INFO  17:16:37,421 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:16Z] INFO  17:16:37,426 HelpFormatter - Program Args: -T PrintReads -L 11:62744266-78270665 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/11/tx/tmpFQQ3Av/R14-18106_kapa-NGv3-PE100-NGv3-sort-11_62744265_78270665-prep-prealign.bam
[2016-04-15T00:16Z] INFO  17:16:37,436 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:16Z] INFO  17:16:37,437 HelpFormatter - Date/Time: 2016/04/14 17:16:37
[2016-04-15T00:16Z] INFO  17:16:37,438 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:16Z] INFO  17:16:37,439 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:16Z] INFO  17:16:37,633 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:16Z] INFO  17:16:37,700 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-15T00:16Z] INFO  17:16:37,780 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:16Z] INFO  17:16:37,790 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:16Z] INFO  17:16:37,850 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-15T00:16Z] INFO  17:16:37,876 IntervalUtils - Processing 15519706 bp from intervals
[2016-04-15T00:16Z] INFO  17:16:38,034 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:16Z] INFO  17:16:38,369 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:16Z] INFO  17:16:38,370 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:16Z] INFO  17:16:38,371 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:16Z] INFO  17:16:38,372 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:16Z] INFO  17:16:38,387 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:16Z] INFO  17:16:38,524 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:16Z] INFO  17:16:38,527 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:16Z] INFO  17:16:38,527 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:16Z] INFO  17:16:38,528 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:16Z] INFO  17:16:38,532 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/9/R14-18106_kapa-NGv3-PE100-NGv3-sort-9_32407258_65506776-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/9/R14-18106_kapa-NGv3-PE100-NGv3-sort-9_32407258_65506776-prep-prealign-realign.intervals -L 9:32407259-65506776 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/9/tx/tmpuBPAk7/R14-18106_kapa-NGv3-PE100-NGv3-sort-9_32407258_65506776-prep.bam
[2016-04-15T00:16Z] INFO  17:16:38,558 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:16Z] INFO  17:16:38,559 HelpFormatter - Date/Time: 2016/04/14 17:16:38
[2016-04-15T00:16Z] INFO  17:16:38,560 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:16Z] INFO  17:16:38,560 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:16Z] INFO  17:16:38,561 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:16Z] INFO  17:16:38,739 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:16Z] INFO  17:16:38,817 ProgressMeter -     9:140866095    700013.0    91.0 s       2.2 m       97.1%    93.0 s       2.0 s
[2016-04-15T00:16Z] INFO  17:16:38,828 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:16Z] INFO  17:16:38,829 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-15T00:16Z] INFO  17:16:38,837 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:16Z] INFO  17:16:38,896 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:16Z] INFO  17:16:38,907 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-15T00:16Z] INFO  17:16:38,909 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:16Z] INFO  17:16:38,967 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-15T00:16Z] INFO  17:16:38,981 IntervalUtils - Processing 15526400 bp from intervals
[2016-04-15T00:16Z] INFO  17:16:39,094 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:16Z] INFO  17:16:39,372 IntervalUtils - Processing 33099518 bp from intervals
[2016-04-15T00:16Z] WARN  17:16:39,388 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:16Z] INFO  17:16:39,511 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:16Z] INFO  17:16:39,545 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:16Z] INFO  17:16:39,545 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:16Z] INFO  17:16:39,546 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:16Z] INFO  17:16:39,546 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:16Z] INFO  17:16:39,576 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:16Z] INFO  17:16:39,719 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:16Z] INFO  17:16:39,721 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:16Z] INFO  17:16:39,721 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:16Z] INFO  17:16:39,722 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:16Z] INFO  17:16:39,727 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:16Z] INFO  17:16:39,861 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:16Z] INFO  17:16:39,904 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:16Z] INFO  17:16:39,907 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:16Z] INFO  17:16:39,908 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:16Z] INFO  17:16:39,908 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:16Z] INFO  17:16:39,913 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/10/R14-18106_kapa-NGv3-PE100-NGv3-sort-10_62539923_78084243-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/10/R14-18106_kapa-NGv3-PE100-NGv3-sort-10_62539923_78084243-prep-prealign-realign.intervals -L 10:62539924-78084243 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/10/tx/tmpBajP1G/R14-18106_kapa-NGv3-PE100-NGv3-sort-10_62539923_78084243-prep.bam
[2016-04-15T00:16Z] INFO  17:16:39,921 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:16Z] INFO  17:16:39,922 HelpFormatter - Date/Time: 2016/04/14 17:16:39
[2016-04-15T00:16Z] INFO  17:16:39,923 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:16Z] INFO  17:16:39,924 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:16Z] INFO  17:16:39,930 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:16Z] INFO  17:16:39,938 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@41fd9d8e
[2016-04-15T00:16Z] INFO  17:16:39,943 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:16Z] INFO  17:16:39,944 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:16Z] INFO  17:16:39,945 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:16Z] INFO  17:16:39,949 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/10/R14-18106_kapa-NGv3-PE100-NGv3-sort-10_46960410_62493077-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/10/R14-18106_kapa-NGv3-PE100-NGv3-sort-10_46960410_62493077-prep-prealign-realign.intervals -L 10:46960411-62493077 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/10/tx/tmpPVTamJ/R14-18106_kapa-NGv3-PE100-NGv3-sort-10_46960410_62493077-prep.bam
[2016-04-15T00:16Z] INFO  17:16:39,959 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:16Z] INFO  17:16:39,959 HelpFormatter - Date/Time: 2016/04/14 17:16:39
[2016-04-15T00:16Z] INFO  17:16:39,959 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:16Z] INFO  17:16:39,959 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:16Z] INFO  17:16:40,111 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:16Z] INFO  17:16:40,133 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:16Z] INFO  17:16:40,179 ProgressMeter -            done    789169.0    92.0 s     117.0 s       99.3%    92.0 s       0.0 s
[2016-04-15T00:16Z] INFO  17:16:40,179 ProgressMeter - Total runtime 92.37 secs, 1.54 min, 0.03 hours
[2016-04-15T00:16Z] INFO  17:16:40,180 MicroScheduler - 390 reads were filtered out during the traversal out of approximately 789559 total reads (0.05%)
[2016-04-15T00:16Z] INFO  17:16:40,180 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:16Z] INFO  17:16:40,181 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:16Z] INFO  17:16:40,181 MicroScheduler -   -> 390 reads (0.05% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:16Z] INFO  17:16:40,228 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:16Z] INFO  17:16:40,283 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:16Z] INFO  17:16:40,293 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:16Z] INFO  17:16:40,362 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-15T00:16Z] INFO  17:16:40,381 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:16Z] INFO  17:16:40,401 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:16Z] INFO  17:16:40,494 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.09
[2016-04-15T00:16Z] INFO  17:16:40,532 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:16Z] INFO  17:16:40,534 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:16Z] INFO  17:16:40,535 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:16Z] INFO  17:16:40,535 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:16Z] INFO  17:16:40,539 HelpFormatter - Program Args: -T PrintReads -L 11:78277178-93796886 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/11/tx/tmp_k7Hve/R14-18106_kapa-NGv3-PE100-NGv3-sort-11_78277177_93796886-prep-prealign.bam
[2016-04-15T00:16Z] INFO  17:16:40,566 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:16Z] INFO  17:16:40,566 HelpFormatter - Date/Time: 2016/04/14 17:16:40
[2016-04-15T00:16Z] INFO  17:16:40,567 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:16Z] INFO  17:16:40,567 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:16Z] INFO  17:16:40,608 ProgressMeter -            done   8206026.0    13.0 s       1.0 s      100.0%    13.0 s       0.0 s
[2016-04-15T00:16Z] INFO  17:16:40,609 ProgressMeter - Total runtime 13.06 secs, 0.22 min, 0.00 hours
[2016-04-15T00:16Z] INFO  17:16:40,612 MicroScheduler - 14603 reads were filtered out during the traversal out of approximately 169896 total reads (8.60%)
[2016-04-15T00:16Z] INFO  17:16:40,613 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:16Z] INFO  17:16:40,613 MicroScheduler -   -> 495 reads (0.29% of total) failing BadMateFilter
[2016-04-15T00:16Z] INFO  17:16:40,613 MicroScheduler -   -> 12707 reads (7.48% of total) failing DuplicateReadFilter
[2016-04-15T00:16Z] INFO  17:16:40,614 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:16Z] INFO  17:16:40,614 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:16Z] INFO  17:16:40,614 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:16Z] INFO  17:16:40,614 MicroScheduler -   -> 1401 reads (0.82% of total) failing MappingQualityZeroFilter
[2016-04-15T00:16Z] INFO  17:16:40,615 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:16Z] INFO  17:16:40,615 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-15T00:16Z] INFO  17:16:40,615 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:16Z] INFO  17:16:40,758 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:16Z] INFO  17:16:40,826 IntervalUtils - Processing 15532667 bp from intervals
[2016-04-15T00:16Z] WARN  17:16:40,841 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:16Z] INFO  17:16:40,859 IntervalUtils - Processing 15544320 bp from intervals
[2016-04-15T00:16Z] WARN  17:16:40,874 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:16Z] INFO  17:16:40,910 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:16Z] INFO  17:16:40,996 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:16Z] INFO  17:16:40,997 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:16Z] INFO  17:16:40,998 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:16Z] INFO  17:16:40,999 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:16Z] INFO  17:16:41,011 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:16Z] INFO  17:16:41,217 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:16Z] INFO  17:16:41,222 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:16Z] INFO  17:16:41,235 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:16Z] INFO  17:16:41,236 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:16Z] INFO  17:16:41,236 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:16Z] INFO  17:16:41,402 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:16Z] INFO  17:16:41,437 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:16Z] INFO  17:16:41,655 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:16Z] INFO  17:16:41,968 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:16Z] INFO  17:16:41,972 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-15T00:16Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-9_129097484_141213431-prep-prealign.bam
[2016-04-15T00:16Z] INFO  17:16:42,016 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:16Z] INFO  17:16:42,034 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:16Z] INFO  17:16:42,043 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:16Z] GATK: realign ('10', 127328721, 135534747) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:16Z] INFO  17:16:42,094 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-15T00:16Z] INFO  17:16:42,108 IntervalUtils - Processing 15519709 bp from intervals
[2016-04-15T00:16Z] INFO  17:16:42,191 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:16Z] INFO  17:16:42,329 ProgressMeter -            done    204545.0    19.0 s      93.0 s      100.0%    19.0 s       0.0 s
[2016-04-15T00:16Z] INFO  17:16:42,329 ProgressMeter - Total runtime 19.03 secs, 0.32 min, 0.01 hours
[2016-04-15T00:16Z] INFO  17:16:42,333 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 204545 total reads (0.00%)
[2016-04-15T00:16Z] INFO  17:16:42,334 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:16Z] INFO  17:16:42,335 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:16Z] INFO  17:16:42,335 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:16Z] INFO  17:16:42,479 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:16Z] INFO  17:16:42,480 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:16Z] INFO  17:16:42,480 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:16Z] INFO  17:16:42,481 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:16Z] INFO  17:16:42,514 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:16Z] INFO  17:16:42,752 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:16Z] INFO  17:16:44,044 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:16Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-10_31137459_46960129-prep.bam
[2016-04-15T00:16Z] GATK RealignerTargetCreator: R14-18106_kapa-NGv3-PE100-NGv3-sort-9_129097484_141213431-prep-prealign.bam 9:129097485-141213431
[2016-04-15T00:16Z] GATK: RealignerTargetCreator
[2016-04-15T00:16Z] GATK pre-alignment ('11', 93797496, 109964158) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:16Z] INFO  17:16:44,707 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:16Z] INFO  17:16:44,711 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:16Z] INFO  17:16:44,712 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:16Z] INFO  17:16:44,712 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:16Z] INFO  17:16:44,717 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/10/R14-18106_kapa-NGv3-PE100-NGv3-sort-10_127328721_135534747-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/10/R14-18106_kapa-NGv3-PE100-NGv3-sort-10_127328721_135534747-prep-prealign-realign.intervals -L 10:127328722-135534747 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/10/tx/tmprjgXm6/R14-18106_kapa-NGv3-PE100-NGv3-sort-10_127328721_135534747-prep.bam
[2016-04-15T00:16Z] INFO  17:16:44,730 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:16Z] INFO  17:16:44,742 HelpFormatter - Date/Time: 2016/04/14 17:16:44
[2016-04-15T00:16Z] INFO  17:16:44,743 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:16Z] INFO  17:16:44,743 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:16Z] INFO  17:16:44,939 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:16Z] INFO  17:16:45,067 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:16Z] INFO  17:16:45,077 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:16Z] INFO  17:16:45,121 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.04
[2016-04-15T00:16Z] INFO  17:16:45,554 IntervalUtils - Processing 8206026 bp from intervals
[2016-04-15T00:16Z] WARN  17:16:45,559 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:16Z] INFO  17:16:45,639 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:16Z] INFO  17:16:45,807 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:16Z] INFO  17:16:45,808 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:16Z] INFO  17:16:45,808 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:16Z] INFO  17:16:45,809 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:16Z] INFO  17:16:45,877 ProgressMeter -            done    338932.0    23.0 s      67.0 s      100.0%    23.0 s       0.0 s
[2016-04-15T00:16Z] INFO  17:16:45,878 ProgressMeter - Total runtime 23.01 secs, 0.38 min, 0.01 hours
[2016-04-15T00:16Z] INFO  17:16:45,881 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 338932 total reads (0.00%)
[2016-04-15T00:16Z] INFO  17:16:45,881 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:16Z] INFO  17:16:45,882 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:16Z] INFO  17:16:45,882 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:16Z] INFO  17:16:45,993 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:16Z] INFO  17:16:46,077 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:16Z] INFO  17:16:47,444 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:16Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-9_113231219_129089575-prep.bam
[2016-04-15T00:16Z] INFO  17:16:47,647 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:16Z] INFO  17:16:47,650 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:16Z] INFO  17:16:47,650 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:16Z] INFO  17:16:47,650 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:16Z] INFO  17:16:47,654 HelpFormatter - Program Args: -T PrintReads -L 11:93797497-109964158 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/11/tx/tmpe8WaHq/R14-18106_kapa-NGv3-PE100-NGv3-sort-11_93797496_109964158-prep-prealign.bam
[2016-04-15T00:16Z] INFO  17:16:47,678 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:16Z] INFO  17:16:47,679 HelpFormatter - Date/Time: 2016/04/14 17:16:47
[2016-04-15T00:16Z] INFO  17:16:47,679 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:16Z] INFO  17:16:47,680 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:16Z] INFO  17:16:47,724 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:16Z] INFO  17:16:47,739 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:16Z] INFO  17:16:47,739 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:16Z] INFO  17:16:47,740 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:16Z] INFO  17:16:47,745 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/9/R14-18106_kapa-NGv3-PE100-NGv3-sort-9_129097484_141213431-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/9/tx/tmpT22vRn/R14-18106_kapa-NGv3-PE100-NGv3-sort-9_129097484_141213431-prep-prealign-realign.intervals -l INFO -L 9:129097485-141213431 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:16Z] INFO  17:16:47,763 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:16Z] INFO  17:16:47,764 HelpFormatter - Date/Time: 2016/04/14 17:16:47
[2016-04-15T00:16Z] INFO  17:16:47,764 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:16Z] INFO  17:16:47,765 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:16Z] INFO  17:16:47,827 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:16Z] INFO  17:16:47,861 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:16Z] INFO  17:16:48,070 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T00:16Z] INFO  17:16:48,079 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:16Z] INFO  17:16:48,132 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-15T00:16Z] INFO  17:16:48,492 IntervalUtils - Processing 12115947 bp from intervals
[2016-04-15T00:16Z] WARN  17:16:48,497 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:16Z] GATK pre-alignment ('11', 110001730, 125514538) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:16Z] INFO  17:16:48,650 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:16Z] INFO  17:16:48,838 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-15T00:16Z] INFO  17:16:48,853 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:16Z] INFO  17:16:48,853 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:16Z] INFO  17:16:48,854 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:16Z] INFO  17:16:48,854 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:16Z] INFO  17:16:48,911 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:16Z] INFO  17:16:48,920 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:16Z] INFO  17:16:48,969 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-15T00:16Z] INFO  17:16:48,983 IntervalUtils - Processing 16166662 bp from intervals
[2016-04-15T00:16Z] INFO  17:16:49,054 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:16Z] INFO  17:16:49,308 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:16Z] INFO  17:16:49,310 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:16Z] INFO  17:16:49,310 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:16Z] INFO  17:16:49,311 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:16Z] INFO  17:16:49,326 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:16Z] INFO  17:16:49,524 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:16Z] INFO  17:16:51,418 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:16Z] INFO  17:16:51,422 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:16Z] INFO  17:16:51,422 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:16Z] INFO  17:16:51,423 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:16Z] INFO  17:16:51,428 HelpFormatter - Program Args: -T PrintReads -L 11:110001731-125514538 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/11/tx/tmpPtlCe1/R14-18106_kapa-NGv3-PE100-NGv3-sort-11_110001730_125514538-prep-prealign.bam
[2016-04-15T00:16Z] INFO  17:16:51,435 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@41fd9d8e
[2016-04-15T00:16Z] INFO  17:16:51,442 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:16Z] INFO  17:16:51,443 HelpFormatter - Date/Time: 2016/04/14 17:16:51
[2016-04-15T00:16Z] INFO  17:16:51,444 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:16Z] INFO  17:16:51,444 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:16Z] INFO  17:16:51,495 ProgressMeter -            done    196439.0    29.0 s       2.5 m      100.0%    29.0 s       0.0 s
[2016-04-15T00:16Z] INFO  17:16:51,496 ProgressMeter - Total runtime 29.87 secs, 0.50 min, 0.01 hours
[2016-04-15T00:16Z] INFO  17:16:51,497 MicroScheduler - 179 reads were filtered out during the traversal out of approximately 196618 total reads (0.09%)
[2016-04-15T00:16Z] INFO  17:16:51,498 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:16Z] INFO  17:16:51,499 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:16Z] INFO  17:16:51,499 MicroScheduler -   -> 179 reads (0.09% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:16Z] INFO  17:16:51,628 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:16Z] INFO  17:16:52,584 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-15T00:16Z] INFO  17:16:52,653 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:16Z] INFO  17:16:52,662 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:16Z] INFO  17:16:52,708 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-15T00:16Z] INFO  17:16:52,724 IntervalUtils - Processing 15512808 bp from intervals
[2016-04-15T00:16Z] INFO  17:16:52,734 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:16Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-11_16007749_31531554-prep-prealign.bam
[2016-04-15T00:16Z] INFO  17:16:52,801 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:16Z] INFO  17:16:53,058 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:16Z] INFO  17:16:53,059 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:16Z] INFO  17:16:53,060 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:16Z] INFO  17:16:53,061 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:16Z] INFO  17:16:53,081 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:16Z] INFO  17:16:53,256 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:16Z] INFO  17:16:53,318 ProgressMeter -            done    240702.0    17.0 s      73.0 s      100.0%    17.0 s       0.0 s
[2016-04-15T00:16Z] INFO  17:16:53,318 ProgressMeter - Total runtime 17.76 secs, 0.30 min, 0.00 hours
[2016-04-15T00:16Z] INFO  17:16:53,321 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 240702 total reads (0.00%)
[2016-04-15T00:16Z] INFO  17:16:53,322 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:16Z] INFO  17:16:53,322 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:16Z] INFO  17:16:53,322 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:16Z] GATK RealignerTargetCreator: R14-18106_kapa-NGv3-PE100-NGv3-sort-11_16007749_31531554-prep-prealign.bam 11:16007750-31531554
[2016-04-15T00:16Z] GATK: RealignerTargetCreator
[2016-04-15T00:16Z] INFO  17:16:54,866 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:16Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-10_78316966_93841258-prep.bam
[2016-04-15T00:16Z] GATK pre-alignment ('11', 125523640, 135006516) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:16Z] INFO  17:16:56,193 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:16Z] INFO  17:16:56,197 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:16Z] INFO  17:16:56,198 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:16Z] INFO  17:16:56,198 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:16Z] INFO  17:16:56,204 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/11/R14-18106_kapa-NGv3-PE100-NGv3-sort-11_16007749_31531554-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/11/tx/tmpv6wJC2/R14-18106_kapa-NGv3-PE100-NGv3-sort-11_16007749_31531554-prep-prealign-realign.intervals -l INFO -L 11:16007750-31531554 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:16Z] INFO  17:16:56,217 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:16Z] INFO  17:16:56,217 HelpFormatter - Date/Time: 2016/04/14 17:16:56
[2016-04-15T00:16Z] INFO  17:16:56,217 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:16Z] INFO  17:16:56,218 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:16Z] INFO  17:16:56,324 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:16Z] INFO  17:16:56,591 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T00:16Z] INFO  17:16:56,602 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:16Z] INFO  17:16:56,666 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-15T00:16Z] INFO  17:16:57,020 IntervalUtils - Processing 15523805 bp from intervals
[2016-04-15T00:16Z] WARN  17:16:57,024 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:16Z] INFO  17:16:57,117 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:16Z] INFO  17:16:57,305 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:16Z] INFO  17:16:57,307 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:16Z] INFO  17:16:57,307 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:16Z] INFO  17:16:57,308 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:16Z] INFO  17:16:57,450 ProgressMeter -            done   1.5637072E7    20.0 s       1.0 s      100.0%    20.0 s       0.0 s
[2016-04-15T00:16Z] INFO  17:16:57,451 ProgressMeter - Total runtime 20.41 secs, 0.34 min, 0.01 hours
[2016-04-15T00:16Z] INFO  17:16:57,455 MicroScheduler - 35982 reads were filtered out during the traversal out of approximately 299676 total reads (12.01%)
[2016-04-15T00:16Z] INFO  17:16:57,456 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:16Z] INFO  17:16:57,457 MicroScheduler -   -> 893 reads (0.30% of total) failing BadMateFilter
[2016-04-15T00:16Z] INFO  17:16:57,458 MicroScheduler -   -> 22029 reads (7.35% of total) failing DuplicateReadFilter
[2016-04-15T00:16Z] INFO  17:16:57,458 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:16Z] INFO  17:16:57,459 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:16Z] INFO  17:16:57,460 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:16Z] INFO  17:16:57,461 MicroScheduler -   -> 13060 reads (4.36% of total) failing MappingQualityZeroFilter
[2016-04-15T00:16Z] INFO  17:16:57,461 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:16Z] INFO  17:16:57,462 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-15T00:16Z] INFO  17:16:57,463 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:16Z] INFO  17:16:58,262 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:16Z] INFO  17:16:58,265 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:16Z] INFO  17:16:58,266 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:16Z] INFO  17:16:58,266 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:16Z] INFO  17:16:58,271 HelpFormatter - Program Args: -T PrintReads -L 11:125523641-135006516 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/11/tx/tmpcGu71t/R14-18106_kapa-NGv3-PE100-NGv3-sort-11_125523640_135006516-prep-prealign.bam
[2016-04-15T00:16Z] INFO  17:16:58,292 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:16Z] INFO  17:16:58,293 HelpFormatter - Date/Time: 2016/04/14 17:16:58
[2016-04-15T00:16Z] INFO  17:16:58,294 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:16Z] INFO  17:16:58,294 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:16Z] INFO  17:16:58,486 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:16Z] INFO  17:16:58,640 ProgressMeter -            done    168780.0    12.0 s      76.0 s       99.0%    12.0 s       0.0 s
[2016-04-15T00:16Z] INFO  17:16:58,640 ProgressMeter - Total runtime 12.83 secs, 0.21 min, 0.00 hours
[2016-04-15T00:16Z] INFO  17:16:58,643 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 168780 total reads (0.00%)
[2016-04-15T00:16Z] INFO  17:16:58,644 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:16Z] INFO  17:16:58,645 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:16Z] INFO  17:16:58,646 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:16Z] INFO  17:16:58,875 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:16Z] GATK: realign ('10', 111628371, 127265443) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:16Z] INFO  17:16:59,538 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-15T00:16Z] INFO  17:16:59,604 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:16Z] INFO  17:16:59,613 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:16Z] INFO  17:16:59,654 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.04
[2016-04-15T00:16Z] INFO  17:16:59,668 IntervalUtils - Processing 9482876 bp from intervals
[2016-04-15T00:16Z] INFO  17:16:59,743 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:17Z] INFO  17:17:00,045 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:17Z] INFO  17:17:00,046 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:17Z] INFO  17:17:00,047 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:17Z] INFO  17:17:00,047 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:17Z] INFO  17:17:00,074 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:17Z] INFO  17:17:00,117 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:17Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-10_127328721_135534747-prep.bam
[2016-04-15T00:17Z] INFO  17:17:00,173 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:17Z] GATK pre-alignment ('12', 0, 15637181) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:17Z] INFO  17:17:00,955 ProgressMeter -            done   1.7773484E7    24.0 s       1.0 s      100.0%    24.0 s       0.0 s
[2016-04-15T00:17Z] INFO  17:17:00,955 ProgressMeter - Total runtime 24.70 secs, 0.41 min, 0.01 hours
[2016-04-15T00:17Z] INFO  17:17:00,959 MicroScheduler - 39067 reads were filtered out during the traversal out of approximately 490316 total reads (7.97%)
[2016-04-15T00:17Z] INFO  17:17:00,959 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:17Z] INFO  17:17:00,960 MicroScheduler -   -> 1203 reads (0.25% of total) failing BadMateFilter
[2016-04-15T00:17Z] INFO  17:17:00,960 MicroScheduler -   -> 36629 reads (7.47% of total) failing DuplicateReadFilter
[2016-04-15T00:17Z] INFO  17:17:00,960 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:17Z] INFO  17:17:00,961 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:17Z] INFO  17:17:00,961 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:17Z] INFO  17:17:00,961 MicroScheduler -   -> 1235 reads (0.25% of total) failing MappingQualityZeroFilter
[2016-04-15T00:17Z] INFO  17:17:00,961 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:17Z] INFO  17:17:00,961 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-15T00:17Z] INFO  17:17:00,962 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:17Z] INFO  17:17:01,614 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:17Z] INFO  17:17:01,617 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:17Z] INFO  17:17:01,617 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:17Z] INFO  17:17:01,618 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:17Z] INFO  17:17:01,622 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/10/R14-18106_kapa-NGv3-PE100-NGv3-sort-10_111628371_127265443-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/10/R14-18106_kapa-NGv3-PE100-NGv3-sort-10_111628371_127265443-prep-prealign-realign.intervals -L 10:111628372-127265443 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/10/tx/tmp_X1Js5/R14-18106_kapa-NGv3-PE100-NGv3-sort-10_111628371_127265443-prep.bam
[2016-04-15T00:17Z] INFO  17:17:01,632 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:17Z] INFO  17:17:01,632 HelpFormatter - Date/Time: 2016/04/14 17:17:01
[2016-04-15T00:17Z] INFO  17:17:01,632 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:17Z] INFO  17:17:01,633 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:17Z] INFO  17:17:01,836 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:17Z] INFO  17:17:01,934 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:17Z] INFO  17:17:01,961 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:17Z] INFO  17:17:02,022 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-15T00:17Z] INFO  17:17:02,431 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:17Z] INFO  17:17:02,434 IntervalUtils - Processing 15637072 bp from intervals
[2016-04-15T00:17Z] WARN  17:17:02,440 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:17Z] GATK: realign ('10', 93851586, 111625070) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:17Z] INFO  17:17:02,522 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:17Z] INFO  17:17:02,681 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:17Z] INFO  17:17:02,683 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:17Z] INFO  17:17:02,683 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:17Z] INFO  17:17:02,684 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:17Z] INFO  17:17:02,858 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:17Z] INFO  17:17:03,059 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:17Z] INFO  17:17:03,384 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:17Z] INFO  17:17:03,387 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:17Z] INFO  17:17:03,388 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:17Z] INFO  17:17:03,388 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:17Z] INFO  17:17:03,393 HelpFormatter - Program Args: -T PrintReads -L 12:1-15637181 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/12/tx/tmp814mZt/R14-18106_kapa-NGv3-PE100-NGv3-sort-12_0_15637181-prep-prealign.bam
[2016-04-15T00:17Z] INFO  17:17:03,412 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:17Z] INFO  17:17:03,413 HelpFormatter - Date/Time: 2016/04/14 17:17:03
[2016-04-15T00:17Z] INFO  17:17:03,413 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:17Z] INFO  17:17:03,414 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:17Z] INFO  17:17:03,581 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:17Z] INFO  17:17:03,819 ProgressMeter -            done    347949.0    22.0 s      64.0 s      100.0%    22.0 s       0.0 s
[2016-04-15T00:17Z] INFO  17:17:03,820 ProgressMeter - Total runtime 22.59 secs, 0.38 min, 0.01 hours
[2016-04-15T00:17Z] INFO  17:17:03,823 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 347949 total reads (0.00%)
[2016-04-15T00:17Z] INFO  17:17:03,824 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:17Z] INFO  17:17:03,824 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:17Z] INFO  17:17:03,831 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:17Z] INFO  17:17:04,075 ProgressMeter -      11:4842704    300004.0    61.0 s       3.4 m       30.3%     3.4 m       2.3 m
[2016-04-15T00:17Z] INFO  17:17:04,607 ProgressMeter -            done    359902.0    23.0 s      65.0 s      100.0%    23.0 s       0.0 s
[2016-04-15T00:17Z] INFO  17:17:04,608 ProgressMeter - Total runtime 23.61 secs, 0.39 min, 0.01 hours
[2016-04-15T00:17Z] INFO  17:17:04,611 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 359902 total reads (0.00%)
[2016-04-15T00:17Z] INFO  17:17:04,611 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:17Z] INFO  17:17:04,611 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:17Z] INFO  17:17:04,612 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:17Z] INFO  17:17:04,843 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-15T00:17Z] INFO  17:17:04,894 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:17Z] INFO  17:17:04,903 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:17Z] INFO  17:17:04,956 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-15T00:17Z] INFO  17:17:04,985 IntervalUtils - Processing 15637181 bp from intervals
[2016-04-15T00:17Z] INFO  17:17:05,026 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:17Z] INFO  17:17:05,030 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:17Z] INFO  17:17:05,030 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:17Z] INFO  17:17:05,030 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:17Z] INFO  17:17:05,034 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/10/R14-18106_kapa-NGv3-PE100-NGv3-sort-10_93851586_111625070-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/10/R14-18106_kapa-NGv3-PE100-NGv3-sort-10_93851586_111625070-prep-prealign-realign.intervals -L 10:93851587-111625070 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/10/tx/tmpfJ9EMe/R14-18106_kapa-NGv3-PE100-NGv3-sort-10_93851586_111625070-prep.bam
[2016-04-15T00:17Z] INFO  17:17:05,054 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:17Z] INFO  17:17:05,054 HelpFormatter - Date/Time: 2016/04/14 17:17:05
[2016-04-15T00:17Z] INFO  17:17:05,055 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:17Z] INFO  17:17:05,055 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:17Z] INFO  17:17:05,145 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:17Z] INFO  17:17:05,277 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:17Z] INFO  17:17:05,387 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:17Z] INFO  17:17:05,397 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:17Z] INFO  17:17:05,439 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.04
[2016-04-15T00:17Z] INFO  17:17:05,478 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:17Z] INFO  17:17:05,479 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:17Z] INFO  17:17:05,480 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:17Z] INFO  17:17:05,481 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:17Z] INFO  17:17:05,494 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:17Z] INFO  17:17:05,505 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:17Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-10_62539923_78084243-prep.bam
[2016-04-15T00:17Z] INFO  17:17:05,582 ProgressMeter -     11:46408181    100002.0    30.0 s       5.1 m       95.7%    31.0 s       1.0 s
[2016-04-15T00:17Z] INFO  17:17:05,697 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:17Z] INFO  17:17:05,804 IntervalUtils - Processing 17773484 bp from intervals
[2016-04-15T00:17Z] WARN  17:17:05,818 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:17Z] INFO  17:17:05,948 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:17Z] INFO  17:17:06,070 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:17Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-10_46960410_62493077-prep.bam
[2016-04-15T00:17Z] INFO  17:17:06,151 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:17Z] INFO  17:17:06,152 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:17Z] INFO  17:17:06,153 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:17Z] INFO  17:17:06,153 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:17Z] INFO  17:17:06,426 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:17Z] GATK pre-alignment ('12', 15650178, 31231471) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:17Z] INFO  17:17:06,633 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:17Z] INFO  17:17:07,104 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@41fd9d8e
[2016-04-15T00:17Z] GATK pre-alignment ('12', 31236746, 46754992) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:17Z] INFO  17:17:07,231 ProgressMeter -            done    186346.0    24.0 s       2.2 m      100.0%    24.0 s       0.0 s
[2016-04-15T00:17Z] INFO  17:17:07,231 ProgressMeter - Total runtime 24.75 secs, 0.41 min, 0.01 hours
[2016-04-15T00:17Z] INFO  17:17:07,232 MicroScheduler - 130 reads were filtered out during the traversal out of approximately 186476 total reads (0.07%)
[2016-04-15T00:17Z] INFO  17:17:07,232 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:17Z] INFO  17:17:07,233 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:17Z] INFO  17:17:07,233 MicroScheduler -   -> 130 reads (0.07% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:17Z] INFO  17:17:08,151 ProgressMeter -            done    467393.0    28.0 s      60.0 s      100.0%    28.0 s       0.0 s
[2016-04-15T00:17Z] INFO  17:17:08,152 ProgressMeter - Total runtime 28.43 secs, 0.47 min, 0.01 hours
[2016-04-15T00:17Z] INFO  17:17:08,156 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 467393 total reads (0.00%)
[2016-04-15T00:17Z] INFO  17:17:08,156 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:17Z] INFO  17:17:08,156 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:17Z] INFO  17:17:08,157 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:17Z] INFO  17:17:08,390 ProgressMeter -     11:57317571    200005.0    30.0 s       2.5 m       65.5%    45.0 s      15.0 s
[2016-04-15T00:17Z] INFO  17:17:08,883 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:17Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-11_78277177_93796886-prep-prealign.bam
[2016-04-15T00:17Z] GATK RealignerTargetCreator: R14-18106_kapa-NGv3-PE100-NGv3-sort-11_78277177_93796886-prep-prealign.bam 11:78277178-93796886
[2016-04-15T00:17Z] GATK: RealignerTargetCreator
[2016-04-15T00:17Z] INFO  17:17:09,480 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:17Z] INFO  17:17:09,489 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:17Z] INFO  17:17:09,490 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:17Z] INFO  17:17:09,491 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:17Z] INFO  17:17:09,495 HelpFormatter - Program Args: -T PrintReads -L 12:15650179-31231471 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/12/tx/tmpT4fFwK/R14-18106_kapa-NGv3-PE100-NGv3-sort-12_15650178_31231471-prep-prealign.bam
[2016-04-15T00:17Z] INFO  17:17:09,520 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:17Z] INFO  17:17:09,520 HelpFormatter - Date/Time: 2016/04/14 17:17:09
[2016-04-15T00:17Z] INFO  17:17:09,521 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:17Z] INFO  17:17:09,522 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:17Z] INFO  17:17:09,560 ProgressMeter -     11:65057375    200002.0    30.0 s       2.5 m       14.9%     3.4 m       2.9 m
[2016-04-15T00:17Z] INFO  17:17:09,683 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:17Z] INFO  17:17:09,848 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:17Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-9_32407258_65506776-prep.bam
[2016-04-15T00:17Z] INFO  17:17:10,127 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:17Z] INFO  17:17:10,130 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:17Z] INFO  17:17:10,131 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:17Z] INFO  17:17:10,131 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:17Z] INFO  17:17:10,136 HelpFormatter - Program Args: -T PrintReads -L 12:31236747-46754992 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/12/tx/tmp2sUV1D/R14-18106_kapa-NGv3-PE100-NGv3-sort-12_31236746_46754992-prep-prealign.bam
[2016-04-15T00:17Z] INFO  17:17:10,146 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:17Z] INFO  17:17:10,157 HelpFormatter - Date/Time: 2016/04/14 17:17:10
[2016-04-15T00:17Z] INFO  17:17:10,158 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:17Z] INFO  17:17:10,159 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:17Z] INFO  17:17:10,316 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:17Z] INFO  17:17:10,764 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-15T00:17Z] INFO  17:17:10,825 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:17Z] INFO  17:17:10,833 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:17Z] INFO  17:17:10,873 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.04
[2016-04-15T00:17Z] INFO  17:17:10,898 IntervalUtils - Processing 15581293 bp from intervals
[2016-04-15T00:17Z] INFO  17:17:10,990 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:17Z] INFO  17:17:11,191 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@41fd9d8e
[2016-04-15T00:17Z] INFO  17:17:11,262 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:17Z] INFO  17:17:11,263 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:17Z] INFO  17:17:11,263 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:17Z] INFO  17:17:11,264 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:17Z] GATK pre-alignment ('12', 46756066, 62654284) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:17Z] INFO  17:17:11,277 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:17Z] INFO  17:17:11,288 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-15T00:17Z] INFO  17:17:11,340 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:17Z] INFO  17:17:11,349 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:17Z] INFO  17:17:11,408 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-15T00:17Z] INFO  17:17:11,409 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:17Z] INFO  17:17:11,414 ProgressMeter -            done    228516.0    36.0 s       2.7 m      100.0%    36.0 s       0.0 s
[2016-04-15T00:17Z] INFO  17:17:11,414 ProgressMeter - Total runtime 36.65 secs, 0.61 min, 0.01 hours
[2016-04-15T00:17Z] INFO  17:17:11,415 MicroScheduler - 169 reads were filtered out during the traversal out of approximately 228685 total reads (0.07%)
[2016-04-15T00:17Z] INFO  17:17:11,415 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:17Z] INFO  17:17:11,415 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:17Z] INFO  17:17:11,416 MicroScheduler -   -> 169 reads (0.07% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:17Z] INFO  17:17:11,424 IntervalUtils - Processing 15518246 bp from intervals
[2016-04-15T00:17Z] INFO  17:17:11,571 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:17Z] INFO  17:17:11,865 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:17Z] INFO  17:17:11,867 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:17Z] INFO  17:17:11,867 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:17Z] INFO  17:17:11,868 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:17Z] INFO  17:17:11,881 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:17Z] INFO  17:17:12,049 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:17Z] INFO  17:17:12,090 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:17Z] INFO  17:17:12,094 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:17Z] INFO  17:17:12,095 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:17Z] INFO  17:17:12,096 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:17Z] INFO  17:17:12,101 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/11/R14-18106_kapa-NGv3-PE100-NGv3-sort-11_78277177_93796886-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/11/tx/tmpHgmMFG/R14-18106_kapa-NGv3-PE100-NGv3-sort-11_78277177_93796886-prep-prealign-realign.intervals -l INFO -L 11:78277178-93796886 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:17Z] INFO  17:17:12,126 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:17Z] INFO  17:17:12,127 HelpFormatter - Date/Time: 2016/04/14 17:17:12
[2016-04-15T00:17Z] INFO  17:17:12,128 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:17Z] INFO  17:17:12,128 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:17Z] INFO  17:17:12,254 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:17Z] INFO  17:17:12,455 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T00:17Z] INFO  17:17:12,464 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:17Z] INFO  17:17:12,548 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-15T00:17Z] INFO  17:17:12,913 IntervalUtils - Processing 15519709 bp from intervals
[2016-04-15T00:17Z] INFO  17:17:12,923 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:17Z] WARN  17:17:12,929 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:17Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-11_31541602_47074069-prep-prealign.bam
[2016-04-15T00:17Z] INFO  17:17:13,070 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:17Z] INFO  17:17:13,414 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:17Z] INFO  17:17:13,426 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:17Z] INFO  17:17:13,427 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:17Z] INFO  17:17:13,427 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:17Z] GATK RealignerTargetCreator: R14-18106_kapa-NGv3-PE100-NGv3-sort-11_31541602_47074069-prep-prealign.bam 11:31541603-47074069
[2016-04-15T00:17Z] GATK: RealignerTargetCreator
[2016-04-15T00:17Z] INFO  17:17:13,945 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:17Z] INFO  17:17:13,949 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:17Z] INFO  17:17:13,950 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:17Z] INFO  17:17:13,950 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:17Z] INFO  17:17:13,955 HelpFormatter - Program Args: -T PrintReads -L 12:46756067-62654284 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/12/tx/tmpLr0x7c/R14-18106_kapa-NGv3-PE100-NGv3-sort-12_46756066_62654284-prep-prealign.bam
[2016-04-15T00:17Z] INFO  17:17:13,965 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:17Z] INFO  17:17:13,976 HelpFormatter - Date/Time: 2016/04/14 17:17:13
[2016-04-15T00:17Z] INFO  17:17:13,977 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:17Z] INFO  17:17:13,978 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:17Z] INFO  17:17:14,184 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:17Z] INFO  17:17:14,829 ProgressMeter -            done   1.5523805E7    17.0 s       1.0 s      100.0%    17.0 s       0.0 s
[2016-04-15T00:17Z] INFO  17:17:14,831 ProgressMeter - Total runtime 17.52 secs, 0.29 min, 0.00 hours
[2016-04-15T00:17Z] INFO  17:17:14,852 MicroScheduler - 16003 reads were filtered out during the traversal out of approximately 197838 total reads (8.09%)
[2016-04-15T00:17Z] INFO  17:17:14,853 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:17Z] INFO  17:17:14,854 MicroScheduler -   -> 662 reads (0.33% of total) failing BadMateFilter
[2016-04-15T00:17Z] INFO  17:17:14,855 MicroScheduler -   -> 14623 reads (7.39% of total) failing DuplicateReadFilter
[2016-04-15T00:17Z] INFO  17:17:14,855 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:17Z] INFO  17:17:14,856 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:17Z] INFO  17:17:14,857 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:17Z] INFO  17:17:14,857 MicroScheduler -   -> 718 reads (0.36% of total) failing MappingQualityZeroFilter
[2016-04-15T00:17Z] INFO  17:17:14,858 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:17Z] INFO  17:17:14,858 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-15T00:17Z] INFO  17:17:14,859 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:17Z] INFO  17:17:15,021 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@41fd9d8e
[2016-04-15T00:17Z] INFO  17:17:15,214 ProgressMeter -            done   1.2115947E7    26.0 s       2.0 s      100.0%    26.0 s       0.0 s
[2016-04-15T00:17Z] INFO  17:17:15,215 ProgressMeter - Total runtime 26.36 secs, 0.44 min, 0.01 hours
[2016-04-15T00:17Z] INFO  17:17:15,218 MicroScheduler - 70740 reads were filtered out during the traversal out of approximately 794081 total reads (8.91%)
[2016-04-15T00:17Z] INFO  17:17:15,219 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:17Z] INFO  17:17:15,219 MicroScheduler -   -> 1670 reads (0.21% of total) failing BadMateFilter
[2016-04-15T00:17Z] INFO  17:17:15,219 MicroScheduler -   -> 60789 reads (7.66% of total) failing DuplicateReadFilter
[2016-04-15T00:17Z] INFO  17:17:15,219 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:17Z] INFO  17:17:15,220 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:17Z] INFO  17:17:15,220 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:17Z] INFO  17:17:15,220 MicroScheduler -   -> 8281 reads (1.04% of total) failing MappingQualityZeroFilter
[2016-04-15T00:17Z] INFO  17:17:15,220 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:17Z] INFO  17:17:15,221 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-15T00:17Z] INFO  17:17:15,221 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:17Z] INFO  17:17:15,388 ProgressMeter -            done    177603.0    26.0 s       2.4 m      100.0%    26.0 s       0.0 s
[2016-04-15T00:17Z] INFO  17:17:15,389 ProgressMeter - Total runtime 26.08 secs, 0.43 min, 0.01 hours
[2016-04-15T00:17Z] INFO  17:17:15,389 MicroScheduler - 162 reads were filtered out during the traversal out of approximately 177765 total reads (0.09%)
[2016-04-15T00:17Z] INFO  17:17:15,389 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:17Z] INFO  17:17:15,390 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:17Z] INFO  17:17:15,390 MicroScheduler -   -> 162 reads (0.09% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:17Z] INFO  17:17:15,422 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-15T00:17Z] INFO  17:17:15,479 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:17Z] INFO  17:17:15,505 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:17Z] INFO  17:17:15,543 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.04
[2016-04-15T00:17Z] INFO  17:17:15,557 IntervalUtils - Processing 15898218 bp from intervals
[2016-04-15T00:17Z] INFO  17:17:15,637 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:17Z] INFO  17:17:15,995 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:17Z] INFO  17:17:15,996 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:17Z] INFO  17:17:15,997 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:17Z] INFO  17:17:15,998 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:17Z] INFO  17:17:16,011 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:17Z] INFO  17:17:16,173 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:17Z] INFO  17:17:16,222 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:17Z] GATK: realign ('11', 16007749, 31531554) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:17Z] INFO  17:17:16,366 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:17Z] INFO  17:17:16,370 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:17Z] INFO  17:17:16,370 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:17Z] INFO  17:17:16,371 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:17Z] INFO  17:17:16,375 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/11/R14-18106_kapa-NGv3-PE100-NGv3-sort-11_31541602_47074069-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/11/tx/tmpI974Q4/R14-18106_kapa-NGv3-PE100-NGv3-sort-11_31541602_47074069-prep-prealign-realign.intervals -l INFO -L 11:31541603-47074069 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:17Z] INFO  17:17:16,384 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:17Z] INFO  17:17:16,385 HelpFormatter - Date/Time: 2016/04/14 17:17:16
[2016-04-15T00:17Z] INFO  17:17:16,385 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:17Z] INFO  17:17:16,392 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:17Z] INFO  17:17:16,493 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:17Z] INFO  17:17:16,686 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:17Z] INFO  17:17:16,690 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T00:17Z] INFO  17:17:16,700 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:17Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-11_93797496_109964158-prep-prealign.bam
[2016-04-15T00:17Z] INFO  17:17:16,748 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:17Z] INFO  17:17:16,755 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-15T00:17Z] GATK: realign ('9', 129097484, 141213431) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:17Z] INFO  17:17:17,076 IntervalUtils - Processing 15532467 bp from intervals
[2016-04-15T00:17Z] WARN  17:17:17,082 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:17Z] INFO  17:17:17,337 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:17Z] GATK RealignerTargetCreator: R14-18106_kapa-NGv3-PE100-NGv3-sort-11_93797496_109964158-prep-prealign.bam 11:93797497-109964158
[2016-04-15T00:17Z] GATK: RealignerTargetCreator
[2016-04-15T00:17Z] INFO  17:17:17,502 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:17Z] INFO  17:17:17,504 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:17Z] INFO  17:17:17,505 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:17Z] INFO  17:17:17,505 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:17Z] INFO  17:17:19,223 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:17Z] INFO  17:17:19,227 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:17Z] INFO  17:17:19,227 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:17Z] INFO  17:17:19,228 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:17Z] INFO  17:17:19,233 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/11/R14-18106_kapa-NGv3-PE100-NGv3-sort-11_16007749_31531554-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/11/R14-18106_kapa-NGv3-PE100-NGv3-sort-11_16007749_31531554-prep-prealign-realign.intervals -L 11:16007750-31531554 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/11/tx/tmpLJjbiD/R14-18106_kapa-NGv3-PE100-NGv3-sort-11_16007749_31531554-prep.bam
[2016-04-15T00:17Z] INFO  17:17:19,243 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:17Z] INFO  17:17:19,254 HelpFormatter - Date/Time: 2016/04/14 17:17:19
[2016-04-15T00:17Z] INFO  17:17:19,255 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:17Z] INFO  17:17:19,256 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:17Z] INFO  17:17:19,528 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:17Z] INFO  17:17:19,534 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:17Z] INFO  17:17:19,537 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:17Z] INFO  17:17:19,538 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:17Z] INFO  17:17:19,538 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:17Z] INFO  17:17:19,543 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/9/R14-18106_kapa-NGv3-PE100-NGv3-sort-9_129097484_141213431-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/9/R14-18106_kapa-NGv3-PE100-NGv3-sort-9_129097484_141213431-prep-prealign-realign.intervals -L 9:129097485-141213431 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/9/tx/tmpP95EPC/R14-18106_kapa-NGv3-PE100-NGv3-sort-9_129097484_141213431-prep.bam
[2016-04-15T00:17Z] INFO  17:17:19,553 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:17Z] INFO  17:17:19,553 HelpFormatter - Date/Time: 2016/04/14 17:17:19
[2016-04-15T00:17Z] INFO  17:17:19,554 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:17Z] INFO  17:17:19,554 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:17Z] INFO  17:17:19,647 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:17Z] INFO  17:17:19,656 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:17Z] INFO  17:17:19,724 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-15T00:17Z] INFO  17:17:19,822 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:17Z] INFO  17:17:19,973 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:17Z] INFO  17:17:19,983 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:17Z] INFO  17:17:20,043 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-15T00:17Z] INFO  17:17:20,135 IntervalUtils - Processing 15523805 bp from intervals
[2016-04-15T00:17Z] WARN  17:17:20,150 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:17Z] INFO  17:17:20,256 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:17Z] INFO  17:17:20,340 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:17Z] INFO  17:17:20,341 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:17Z] INFO  17:17:20,342 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:17Z] INFO  17:17:20,343 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:17Z] INFO  17:17:20,396 IntervalUtils - Processing 12115947 bp from intervals
[2016-04-15T00:17Z] WARN  17:17:20,417 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:17Z] INFO  17:17:20,496 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:17Z] INFO  17:17:20,508 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:17Z] INFO  17:17:20,569 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:17Z] INFO  17:17:20,573 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:17Z] INFO  17:17:20,573 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:17Z] INFO  17:17:20,574 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:17Z] INFO  17:17:20,579 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/11/R14-18106_kapa-NGv3-PE100-NGv3-sort-11_93797496_109964158-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/11/tx/tmpZqL6OA/R14-18106_kapa-NGv3-PE100-NGv3-sort-11_93797496_109964158-prep-prealign-realign.intervals -l INFO -L 11:93797497-109964158 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:17Z] INFO  17:17:20,597 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:17Z] INFO  17:17:20,597 HelpFormatter - Date/Time: 2016/04/14 17:17:20
[2016-04-15T00:17Z] INFO  17:17:20,597 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:17Z] INFO  17:17:20,598 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:17Z] INFO  17:17:20,657 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:17Z] INFO  17:17:20,682 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:17Z] INFO  17:17:20,683 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:17Z] INFO  17:17:20,684 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:17Z] INFO  17:17:20,684 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:17Z] INFO  17:17:20,768 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:17Z] INFO  17:17:20,889 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:17Z] INFO  17:17:21,040 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:17Z] INFO  17:17:21,056 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T00:17Z] INFO  17:17:21,067 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:17Z] INFO  17:17:21,147 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-15T00:17Z] INFO  17:17:21,565 IntervalUtils - Processing 16166662 bp from intervals
[2016-04-15T00:17Z] WARN  17:17:21,571 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:17Z] INFO  17:17:21,671 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:17Z] INFO  17:17:21,891 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:17Z] INFO  17:17:21,900 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:17Z] INFO  17:17:21,901 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:17Z] INFO  17:17:21,902 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:17Z] INFO  17:17:23,395 ProgressMeter -            done    297720.0    20.0 s      69.0 s      100.0%    20.0 s       0.0 s
[2016-04-15T00:17Z] INFO  17:17:23,396 ProgressMeter - Total runtime 20.71 secs, 0.35 min, 0.01 hours
[2016-04-15T00:17Z] INFO  17:17:23,400 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 297720 total reads (0.00%)
[2016-04-15T00:17Z] INFO  17:17:23,402 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:17Z] INFO  17:17:23,402 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:17Z] INFO  17:17:23,403 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:17Z] INFO  17:17:23,478 ProgressMeter -    11:117651469    100001.0    30.0 s       5.1 m       49.3%    60.0 s      30.0 s
[2016-04-15T00:17Z] INFO  17:17:24,996 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:17Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-10_111628371_127265443-prep.bam
[2016-04-15T00:17Z] INFO  17:17:25,858 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@7172f77a
[2016-04-15T00:17Z] INFO  17:17:26,026 ProgressMeter -            done    164966.0    25.0 s       2.6 m       92.2%    27.0 s       2.0 s
[2016-04-15T00:17Z] INFO  17:17:26,028 ProgressMeter - Total runtime 25.98 secs, 0.43 min, 0.01 hours
[2016-04-15T00:17Z] INFO  17:17:26,029 MicroScheduler - 101 reads were filtered out during the traversal out of approximately 165067 total reads (0.06%)
[2016-04-15T00:17Z] INFO  17:17:26,029 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:17Z] INFO  17:17:26,030 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:17Z] INFO  17:17:26,031 MicroScheduler -   -> 101 reads (0.06% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:17Z] GATK pre-alignment ('12', 62687959, 78225484) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:17Z] INFO  17:17:27,601 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:17Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-11_125523640_135006516-prep-prealign.bam
[2016-04-15T00:17Z] GATK RealignerTargetCreator: R14-18106_kapa-NGv3-PE100-NGv3-sort-11_125523640_135006516-prep-prealign.bam 11:125523641-135006516
[2016-04-15T00:17Z] GATK: RealignerTargetCreator
[2016-04-15T00:17Z] INFO  17:17:29,300 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:17Z] INFO  17:17:29,304 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:17Z] INFO  17:17:29,304 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:17Z] INFO  17:17:29,305 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:17Z] INFO  17:17:29,310 HelpFormatter - Program Args: -T PrintReads -L 12:62687960-78225484 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/12/tx/tmpZguAew/R14-18106_kapa-NGv3-PE100-NGv3-sort-12_62687959_78225484-prep-prealign.bam
[2016-04-15T00:17Z] INFO  17:17:29,350 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:17Z] INFO  17:17:29,350 HelpFormatter - Date/Time: 2016/04/14 17:17:29
[2016-04-15T00:17Z] INFO  17:17:29,350 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:17Z] INFO  17:17:29,350 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:17Z] INFO  17:17:29,528 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:17Z] INFO  17:17:29,853 ProgressMeter -            done   1.5519709E7    16.0 s       1.0 s      100.0%    16.0 s       0.0 s
[2016-04-15T00:17Z] INFO  17:17:29,855 ProgressMeter - Total runtime 16.43 secs, 0.27 min, 0.00 hours
[2016-04-15T00:17Z] INFO  17:17:29,859 MicroScheduler - 44139 reads were filtered out during the traversal out of approximately 187334 total reads (23.56%)
[2016-04-15T00:17Z] INFO  17:17:29,860 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:17Z] INFO  17:17:29,861 MicroScheduler -   -> 612 reads (0.33% of total) failing BadMateFilter
[2016-04-15T00:17Z] INFO  17:17:29,862 MicroScheduler -   -> 11928 reads (6.37% of total) failing DuplicateReadFilter
[2016-04-15T00:17Z] INFO  17:17:29,862 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:17Z] INFO  17:17:29,863 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:17Z] INFO  17:17:29,864 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:17Z] INFO  17:17:29,864 MicroScheduler -   -> 31599 reads (16.87% of total) failing MappingQualityZeroFilter
[2016-04-15T00:17Z] INFO  17:17:29,865 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:17Z] INFO  17:17:29,865 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-15T00:17Z] INFO  17:17:29,866 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:17Z] INFO  17:17:30,591 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-15T00:17Z] INFO  17:17:30,665 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:17Z] INFO  17:17:30,674 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:17Z] INFO  17:17:30,735 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-15T00:17Z] INFO  17:17:30,753 IntervalUtils - Processing 15537525 bp from intervals
[2016-04-15T00:17Z] INFO  17:17:30,891 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:17Z] INFO  17:17:31,063 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:17Z] INFO  17:17:31,067 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:17Z] INFO  17:17:31,067 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:17Z] INFO  17:17:31,068 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:17Z] INFO  17:17:31,073 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/11/R14-18106_kapa-NGv3-PE100-NGv3-sort-11_125523640_135006516-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/11/tx/tmpjPHLQa/R14-18106_kapa-NGv3-PE100-NGv3-sort-11_125523640_135006516-prep-prealign-realign.intervals -l INFO -L 11:125523641-135006516 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:17Z] INFO  17:17:31,089 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:17Z] INFO  17:17:31,090 HelpFormatter - Date/Time: 2016/04/14 17:17:31
[2016-04-15T00:17Z] INFO  17:17:31,090 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:17Z] INFO  17:17:31,090 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:17Z] INFO  17:17:31,196 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:17Z] INFO  17:17:31,199 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:17Z] GATK: realign ('11', 78277177, 93796886) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:17Z] INFO  17:17:31,289 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:17Z] INFO  17:17:31,291 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:17Z] INFO  17:17:31,291 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:17Z] INFO  17:17:31,292 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:17Z] INFO  17:17:31,310 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:17Z] INFO  17:17:31,461 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T00:17Z] INFO  17:17:31,473 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:17Z] INFO  17:17:31,514 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:17Z] INFO  17:17:31,573 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-15T00:17Z] INFO  17:17:31,902 IntervalUtils - Processing 9482876 bp from intervals
[2016-04-15T00:17Z] WARN  17:17:31,908 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:17Z] INFO  17:17:32,020 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:17Z] INFO  17:17:32,209 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:17Z] INFO  17:17:32,210 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:17Z] INFO  17:17:32,211 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:17Z] INFO  17:17:32,212 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:17Z] INFO  17:17:33,654 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@41fd9d8e
[2016-04-15T00:17Z] INFO  17:17:33,736 ProgressMeter -            done    156928.0    22.0 s       2.4 m      100.0%    22.0 s       0.0 s
[2016-04-15T00:17Z] INFO  17:17:33,736 ProgressMeter - Total runtime 22.47 secs, 0.37 min, 0.01 hours
[2016-04-15T00:17Z] INFO  17:17:33,737 MicroScheduler - 147 reads were filtered out during the traversal out of approximately 157075 total reads (0.09%)
[2016-04-15T00:17Z] INFO  17:17:33,737 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:17Z] INFO  17:17:33,737 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:17Z] INFO  17:17:33,738 MicroScheduler -   -> 147 reads (0.09% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:17Z] INFO  17:17:33,814 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:17Z] INFO  17:17:33,818 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:17Z] INFO  17:17:33,818 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:17Z] INFO  17:17:33,819 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:17Z] INFO  17:17:33,823 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/11/R14-18106_kapa-NGv3-PE100-NGv3-sort-11_78277177_93796886-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/11/R14-18106_kapa-NGv3-PE100-NGv3-sort-11_78277177_93796886-prep-prealign-realign.intervals -L 11:78277178-93796886 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/11/tx/tmpE2t2lF/R14-18106_kapa-NGv3-PE100-NGv3-sort-11_78277177_93796886-prep.bam
[2016-04-15T00:17Z] INFO  17:17:33,836 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:17Z] INFO  17:17:33,837 HelpFormatter - Date/Time: 2016/04/14 17:17:33
[2016-04-15T00:17Z] INFO  17:17:33,837 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:17Z] INFO  17:17:33,838 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:17Z] INFO  17:17:34,029 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:17Z] INFO  17:17:34,076 ProgressMeter -      11:9161818    600010.0    91.0 s       2.5 m       57.3%     2.6 m      67.0 s
[2016-04-15T00:17Z] INFO  17:17:34,152 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:17Z] INFO  17:17:34,161 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:17Z] INFO  17:17:34,216 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-15T00:17Z] INFO  17:17:34,598 IntervalUtils - Processing 15519709 bp from intervals
[2016-04-15T00:17Z] WARN  17:17:34,603 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:17Z] INFO  17:17:34,732 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:17Z] INFO  17:17:34,916 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:17Z] INFO  17:17:34,916 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:17Z] INFO  17:17:34,917 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:17Z] INFO  17:17:34,917 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:17Z] INFO  17:17:34,931 ProgressMeter -            done    196439.0    14.0 s      74.0 s      100.0%    14.0 s       0.0 s
[2016-04-15T00:17Z] INFO  17:17:34,932 ProgressMeter - Total runtime 14.59 secs, 0.24 min, 0.00 hours
[2016-04-15T00:17Z] INFO  17:17:34,935 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 196439 total reads (0.00%)
[2016-04-15T00:17Z] INFO  17:17:34,936 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:17Z] INFO  17:17:34,936 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:17Z] INFO  17:17:34,936 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:17Z] INFO  17:17:35,078 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:17Z] INFO  17:17:35,223 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:17Z] INFO  17:17:35,256 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:17Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-12_15650178_31231471-prep-prealign.bam
[2016-04-15T00:17Z] INFO  17:17:35,486 ProgressMeter -      12:6568095    100002.0    30.0 s       5.0 m       42.0%    71.0 s      41.0 s
[2016-04-15T00:17Z] INFO  17:17:35,853 ProgressMeter -            done   1.5532467E7    18.0 s       1.0 s      100.0%    18.0 s       0.0 s
[2016-04-15T00:17Z] INFO  17:17:35,854 ProgressMeter - Total runtime 18.35 secs, 0.31 min, 0.01 hours
[2016-04-15T00:17Z] INFO  17:17:35,859 MicroScheduler - 18796 reads were filtered out during the traversal out of approximately 230336 total reads (8.16%)
[2016-04-15T00:17Z] INFO  17:17:35,860 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:17Z] INFO  17:17:35,861 MicroScheduler -   -> 691 reads (0.30% of total) failing BadMateFilter
[2016-04-15T00:17Z] INFO  17:17:35,862 MicroScheduler -   -> 17612 reads (7.65% of total) failing DuplicateReadFilter
[2016-04-15T00:17Z] INFO  17:17:35,863 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:17Z] INFO  17:17:35,863 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:17Z] INFO  17:17:35,864 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:17Z] INFO  17:17:35,865 MicroScheduler -   -> 493 reads (0.21% of total) failing MappingQualityZeroFilter
[2016-04-15T00:17Z] INFO  17:17:35,866 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:17Z] INFO  17:17:35,866 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-15T00:17Z] INFO  17:17:35,867 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:17Z] GATK RealignerTargetCreator: R14-18106_kapa-NGv3-PE100-NGv3-sort-12_15650178_31231471-prep-prealign.bam 12:15650179-31231471
[2016-04-15T00:17Z] GATK: RealignerTargetCreator
[2016-04-15T00:17Z] INFO  17:17:36,582 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:17Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-11_16007749_31531554-prep.bam
[2016-04-15T00:17Z] INFO  17:17:37,137 ProgressMeter -    10:106401768    400005.0    30.0 s      77.0 s       70.6%    42.0 s      12.0 s
[2016-04-15T00:17Z] GATK pre-alignment ('12', 78334098, 93863131) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:17Z] INFO  17:17:37,443 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:17Z] GATK: realign ('11', 31541602, 47074069) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:17Z] INFO  17:17:38,391 ProgressMeter -     11:62433458    400007.0    60.0 s       2.5 m       98.4%    60.0 s       0.0 s
[2016-04-15T00:17Z] INFO  17:17:38,555 ProgressMeter -            done    486965.0    32.0 s      66.0 s      100.0%    32.0 s       0.0 s
[2016-04-15T00:17Z] INFO  17:17:38,555 ProgressMeter - Total runtime 32.40 secs, 0.54 min, 0.01 hours
[2016-04-15T00:17Z] INFO  17:17:38,559 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 486965 total reads (0.00%)
[2016-04-15T00:17Z] INFO  17:17:38,560 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:17Z] INFO  17:17:38,560 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:17Z] INFO  17:17:38,560 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:17Z] INFO  17:17:38,833 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:17Z] INFO  17:17:38,836 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:17Z] INFO  17:17:38,837 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:17Z] INFO  17:17:38,837 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:17Z] INFO  17:17:38,842 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/12/R14-18106_kapa-NGv3-PE100-NGv3-sort-12_15650178_31231471-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/12/tx/tmpl4ogan/R14-18106_kapa-NGv3-PE100-NGv3-sort-12_15650178_31231471-prep-prealign-realign.intervals -l INFO -L 12:15650179-31231471 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:17Z] INFO  17:17:38,851 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:17Z] INFO  17:17:38,864 HelpFormatter - Date/Time: 2016/04/14 17:17:38
[2016-04-15T00:17Z] INFO  17:17:38,864 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:17Z] INFO  17:17:38,865 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:17Z] INFO  17:17:38,973 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:17Z] INFO  17:17:39,216 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T00:17Z] INFO  17:17:39,225 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:17Z] INFO  17:17:39,322 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.10
[2016-04-15T00:17Z] INFO  17:17:39,500 ProgressMeter -            done   1.6166662E7    17.0 s       1.0 s      100.0%    17.0 s       0.0 s
[2016-04-15T00:17Z] INFO  17:17:39,501 ProgressMeter - Total runtime 17.61 secs, 0.29 min, 0.00 hours
[2016-04-15T00:17Z] INFO  17:17:39,505 MicroScheduler - 14125 reads were filtered out during the traversal out of approximately 178526 total reads (7.91%)
[2016-04-15T00:17Z] INFO  17:17:39,505 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:17Z] INFO  17:17:39,505 MicroScheduler -   -> 628 reads (0.35% of total) failing BadMateFilter
[2016-04-15T00:17Z] INFO  17:17:39,506 MicroScheduler -   -> 13033 reads (7.30% of total) failing DuplicateReadFilter
[2016-04-15T00:17Z] INFO  17:17:39,506 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:17Z] INFO  17:17:39,506 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:17Z] INFO  17:17:39,506 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:17Z] INFO  17:17:39,507 MicroScheduler -   -> 464 reads (0.26% of total) failing MappingQualityZeroFilter
[2016-04-15T00:17Z] INFO  17:17:39,507 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:17Z] INFO  17:17:39,507 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-15T00:17Z] INFO  17:17:39,507 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:17Z] INFO  17:17:39,670 IntervalUtils - Processing 15581293 bp from intervals
[2016-04-15T00:17Z] WARN  17:17:39,675 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:17Z] INFO  17:17:39,753 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:17Z] INFO  17:17:39,934 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:17Z] INFO  17:17:39,936 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:17Z] INFO  17:17:39,936 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:17Z] INFO  17:17:39,937 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:17Z] INFO  17:17:40,227 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:17Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-10_93851586_111625070-prep.bam
[2016-04-15T00:17Z] INFO  17:17:40,290 ProgressMeter -     11:67395960    400006.0    60.0 s       2.5 m       30.0%     3.3 m       2.3 m
[2016-04-15T00:17Z] INFO  17:17:40,370 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:17Z] INFO  17:17:40,373 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:17Z] INFO  17:17:40,373 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:17Z] INFO  17:17:40,374 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:17Z] INFO  17:17:40,386 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/11/R14-18106_kapa-NGv3-PE100-NGv3-sort-11_31541602_47074069-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/11/R14-18106_kapa-NGv3-PE100-NGv3-sort-11_31541602_47074069-prep-prealign-realign.intervals -L 11:31541603-47074069 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/11/tx/tmppKkUTZ/R14-18106_kapa-NGv3-PE100-NGv3-sort-11_31541602_47074069-prep.bam
[2016-04-15T00:17Z] INFO  17:17:40,370 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:17Z] INFO  17:17:40,388 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:17Z] INFO  17:17:40,388 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:17Z] INFO  17:17:40,388 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:17Z] INFO  17:17:40,393 HelpFormatter - Program Args: -T PrintReads -L 12:78334099-93863131 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/12/tx/tmpOj8OqX/R14-18106_kapa-NGv3-PE100-NGv3-sort-12_78334098_93863131-prep-prealign.bam
[2016-04-15T00:17Z] INFO  17:17:40,402 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:17Z] INFO  17:17:40,402 HelpFormatter - Date/Time: 2016/04/14 17:17:40
[2016-04-15T00:17Z] INFO  17:17:40,402 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:17Z] INFO  17:17:40,403 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:17Z] INFO  17:17:40,422 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:17Z] INFO  17:17:40,423 HelpFormatter - Date/Time: 2016/04/14 17:17:40
[2016-04-15T00:17Z] INFO  17:17:40,423 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:17Z] INFO  17:17:40,424 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:17Z] INFO  17:17:40,606 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:17Z] INFO  17:17:40,618 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:17Z] INFO  17:17:40,771 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:17Z] INFO  17:17:40,782 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:17Z] INFO  17:17:40,832 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:17Z] INFO  17:17:40,859 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-15T00:17Z] GATK: realign ('11', 93797496, 109964158) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:17Z] INFO  17:17:41,391 IntervalUtils - Processing 15532467 bp from intervals
[2016-04-15T00:17Z] WARN  17:17:41,408 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:17Z] INFO  17:17:41,506 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:17Z] INFO  17:17:41,653 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:17Z] INFO  17:17:41,655 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:17Z] INFO  17:17:41,665 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:17Z] INFO  17:17:41,666 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:17Z] INFO  17:17:41,829 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:17Z] INFO  17:17:41,887 ProgressMeter -     12:45824684    100002.0    30.0 s       5.0 m       94.0%    31.0 s       1.0 s
[2016-04-15T00:17Z] GATK pre-alignment ('12', 93870729, 109490566) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:17Z] INFO  17:17:41,944 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-15T00:17Z] INFO  17:17:41,983 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:17Z] INFO  17:17:42,052 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:17Z] INFO  17:17:42,060 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:17Z] INFO  17:17:42,142 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-15T00:17Z] INFO  17:17:42,157 IntervalUtils - Processing 15529033 bp from intervals
[2016-04-15T00:17Z] INFO  17:17:42,167 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@5fe152b7
[2016-04-15T00:17Z] INFO  17:17:42,269 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:17Z] INFO  17:17:42,307 ProgressMeter -            done    535140.0    63.0 s     119.0 s      100.0%    63.0 s       0.0 s
[2016-04-15T00:17Z] INFO  17:17:42,310 ProgressMeter - Total runtime 63.94 secs, 1.07 min, 0.02 hours
[2016-04-15T00:17Z] INFO  17:17:42,310 MicroScheduler - 366 reads were filtered out during the traversal out of approximately 535506 total reads (0.07%)
[2016-04-15T00:17Z] INFO  17:17:42,311 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:17Z] INFO  17:17:42,311 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:17Z] INFO  17:17:42,311 MicroScheduler -   -> 366 reads (0.07% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:17Z] INFO  17:17:42,603 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:17Z] INFO  17:17:42,604 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:17Z] INFO  17:17:42,605 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:17Z] INFO  17:17:42,605 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:17Z] INFO  17:17:42,619 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:17Z] INFO  17:17:42,765 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:17Z] INFO  17:17:43,790 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:17Z] INFO  17:17:43,793 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:17Z] INFO  17:17:43,794 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:17Z] INFO  17:17:43,794 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:17Z] INFO  17:17:43,799 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/11/R14-18106_kapa-NGv3-PE100-NGv3-sort-11_93797496_109964158-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/11/R14-18106_kapa-NGv3-PE100-NGv3-sort-11_93797496_109964158-prep-prealign-realign.intervals -L 11:93797497-109964158 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/11/tx/tmpxbQzPU/R14-18106_kapa-NGv3-PE100-NGv3-sort-11_93797496_109964158-prep.bam
[2016-04-15T00:17Z] INFO  17:17:43,813 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:17Z] INFO  17:17:43,814 HelpFormatter - Date/Time: 2016/04/14 17:17:43
[2016-04-15T00:17Z] INFO  17:17:43,814 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:17Z] INFO  17:17:43,815 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:17Z] INFO  17:17:43,866 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@5fe152b7
[2016-04-15T00:17Z] INFO  17:17:43,934 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:17Z] INFO  17:17:43,954 ProgressMeter -            done    191582.0    32.0 s       2.8 m      100.0%    32.0 s       0.0 s
[2016-04-15T00:17Z] INFO  17:17:43,955 ProgressMeter - Total runtime 32.09 secs, 0.53 min, 0.01 hours
[2016-04-15T00:17Z] INFO  17:17:43,955 MicroScheduler - 186 reads were filtered out during the traversal out of approximately 191768 total reads (0.10%)
[2016-04-15T00:17Z] INFO  17:17:43,955 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:17Z] INFO  17:17:43,956 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:17Z] INFO  17:17:43,956 MicroScheduler -   -> 186 reads (0.10% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:17Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-11_47158866_62678572-prep-prealign.bam
[2016-04-15T00:17Z] INFO  17:17:44,007 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:17Z] INFO  17:17:44,151 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:17Z] INFO  17:17:44,160 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:17Z] INFO  17:17:44,222 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-15T00:17Z] INFO  17:17:44,483 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:17Z] INFO  17:17:44,486 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:17Z] INFO  17:17:44,487 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:17Z] INFO  17:17:44,487 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:17Z] INFO  17:17:44,492 HelpFormatter - Program Args: -T PrintReads -L 12:93870730-109490566 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/12/tx/tmp6BxNf4/R14-18106_kapa-NGv3-PE100-NGv3-sort-12_93870729_109490566-prep-prealign.bam
[2016-04-15T00:17Z] INFO  17:17:44,513 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:17Z] INFO  17:17:44,515 HelpFormatter - Date/Time: 2016/04/14 17:17:44
[2016-04-15T00:17Z] INFO  17:17:44,520 IntervalUtils - Processing 16166662 bp from intervals
[2016-04-15T00:17Z] WARN  17:17:44,525 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:17Z] INFO  17:17:44,526 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:17Z] INFO  17:17:44,527 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:17Z] INFO  17:17:44,594 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:17Z] INFO  17:17:44,684 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:17Z] INFO  17:17:44,738 ProgressMeter -            done   9482876.0    12.0 s       1.0 s      100.0%    12.0 s       0.0 s
[2016-04-15T00:17Z] INFO  17:17:44,739 ProgressMeter - Total runtime 12.53 secs, 0.21 min, 0.00 hours
[2016-04-15T00:17Z] INFO  17:17:44,754 MicroScheduler - 13690 reads were filtered out during the traversal out of approximately 165537 total reads (8.27%)
[2016-04-15T00:17Z] INFO  17:17:44,755 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:17Z] INFO  17:17:44,756 MicroScheduler -   -> 511 reads (0.31% of total) failing BadMateFilter
[2016-04-15T00:17Z] INFO  17:17:44,756 MicroScheduler -   -> 12368 reads (7.47% of total) failing DuplicateReadFilter
[2016-04-15T00:17Z] INFO  17:17:44,757 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:17Z] INFO  17:17:44,758 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:17Z] INFO  17:17:44,758 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:17Z] INFO  17:17:44,759 MicroScheduler -   -> 811 reads (0.49% of total) failing MappingQualityZeroFilter
[2016-04-15T00:17Z] INFO  17:17:44,759 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:17Z] INFO  17:17:44,760 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-15T00:17Z] INFO  17:17:44,761 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:17Z] INFO  17:17:44,803 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:17Z] INFO  17:17:44,804 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:17Z] INFO  17:17:44,805 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:17Z] INFO  17:17:44,806 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:17Z] INFO  17:17:44,993 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:17Z] INFO  17:17:45,160 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:17Z] INFO  17:17:45,398 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:17Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-12_31236746_46754992-prep-prealign.bam
[2016-04-15T00:17Z] GATK RealignerTargetCreator: R14-18106_kapa-NGv3-PE100-NGv3-sort-11_47158866_62678572-prep-prealign.bam 11:47158867-62678572
[2016-04-15T00:17Z] GATK: RealignerTargetCreator
[2016-04-15T00:17Z] INFO  17:17:45,799 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-15T00:17Z] INFO  17:17:45,870 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:17Z] INFO  17:17:45,882 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:17Z] INFO  17:17:45,929 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-15T00:17Z] INFO  17:17:45,947 IntervalUtils - Processing 15619837 bp from intervals
[2016-04-15T00:17Z] INFO  17:17:46,034 ProgressMeter -     12:50283483    100002.0    30.0 s       5.0 m       22.2%     2.3 m     105.0 s
[2016-04-15T00:17Z] INFO  17:17:46,067 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:17Z] GATK RealignerTargetCreator: R14-18106_kapa-NGv3-PE100-NGv3-sort-12_31236746_46754992-prep-prealign.bam 12:31236747-46754992
[2016-04-15T00:17Z] GATK: RealignerTargetCreator
[2016-04-15T00:17Z] INFO  17:17:46,222 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:17Z] GATK: realign ('11', 125523640, 135006516) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:17Z] INFO  17:17:46,453 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:17Z] INFO  17:17:46,453 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:17Z] INFO  17:17:46,454 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:17Z] INFO  17:17:46,454 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:17Z] INFO  17:17:46,482 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:17Z] INFO  17:17:46,654 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:17Z] INFO  17:17:49,017 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:17Z] INFO  17:17:49,021 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:17Z] INFO  17:17:49,022 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:17Z] INFO  17:17:49,022 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:17Z] INFO  17:17:49,027 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/12/R14-18106_kapa-NGv3-PE100-NGv3-sort-12_31236746_46754992-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/12/tx/tmp8dsO8J/R14-18106_kapa-NGv3-PE100-NGv3-sort-12_31236746_46754992-prep-prealign-realign.intervals -l INFO -L 12:31236747-46754992 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:17Z] INFO  17:17:49,033 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:17Z] INFO  17:17:49,037 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:17Z] INFO  17:17:49,037 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:17Z] INFO  17:17:49,038 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:17Z] INFO  17:17:49,040 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:17Z] INFO  17:17:49,041 HelpFormatter - Date/Time: 2016/04/14 17:17:49
[2016-04-15T00:17Z] INFO  17:17:49,042 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:17Z] INFO  17:17:49,042 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:17Z] INFO  17:17:49,043 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/11/R14-18106_kapa-NGv3-PE100-NGv3-sort-11_47158866_62678572-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/11/tx/tmpynMoa2/R14-18106_kapa-NGv3-PE100-NGv3-sort-11_47158866_62678572-prep-prealign-realign.intervals -l INFO -L 11:47158867-62678572 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:17Z] INFO  17:17:49,055 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:17Z] INFO  17:17:49,056 HelpFormatter - Date/Time: 2016/04/14 17:17:49
[2016-04-15T00:17Z] INFO  17:17:49,056 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:17Z] INFO  17:17:49,057 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:17Z] INFO  17:17:49,125 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:17Z] INFO  17:17:49,129 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:17Z] INFO  17:17:49,129 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:17Z] INFO  17:17:49,130 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:17Z] INFO  17:17:49,134 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/11/R14-18106_kapa-NGv3-PE100-NGv3-sort-11_125523640_135006516-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/11/R14-18106_kapa-NGv3-PE100-NGv3-sort-11_125523640_135006516-prep-prealign-realign.intervals -L 11:125523641-135006516 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/11/tx/tmpoLXUTU/R14-18106_kapa-NGv3-PE100-NGv3-sort-11_125523640_135006516-prep.bam
[2016-04-15T00:17Z] INFO  17:17:49,147 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:17Z] INFO  17:17:49,148 HelpFormatter - Date/Time: 2016/04/14 17:17:49
[2016-04-15T00:17Z] INFO  17:17:49,148 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:17Z] INFO  17:17:49,148 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:17Z] INFO  17:17:49,159 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:17Z] INFO  17:17:49,221 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:17Z] INFO  17:17:49,269 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@41fd9d8e
[2016-04-15T00:17Z] INFO  17:17:49,326 ProgressMeter -            done    760813.0   106.0 s       2.3 m      100.0%   106.0 s       0.0 s
[2016-04-15T00:17Z] INFO  17:17:49,327 ProgressMeter - Total runtime 106.84 secs, 1.78 min, 0.03 hours
[2016-04-15T00:17Z] INFO  17:17:49,327 MicroScheduler - 514 reads were filtered out during the traversal out of approximately 761327 total reads (0.07%)
[2016-04-15T00:17Z] INFO  17:17:49,327 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:17Z] INFO  17:17:49,328 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:17Z] INFO  17:17:49,329 MicroScheduler -   -> 514 reads (0.07% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:17Z] INFO  17:17:49,350 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:17Z] INFO  17:17:49,379 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T00:17Z] INFO  17:17:49,397 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:17Z] INFO  17:17:49,416 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T00:17Z] INFO  17:17:49,436 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:17Z] INFO  17:17:49,442 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:17Z] INFO  17:17:49,451 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:17Z] INFO  17:17:49,468 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-15T00:17Z] INFO  17:17:49,493 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-15T00:17Z] INFO  17:17:49,518 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-15T00:17Z] INFO  17:17:49,732 IntervalUtils - Processing 15518246 bp from intervals
[2016-04-15T00:17Z] WARN  17:17:49,737 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:17Z] INFO  17:17:49,805 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:17Z] INFO  17:17:49,896 IntervalUtils - Processing 15519706 bp from intervals
[2016-04-15T00:17Z] WARN  17:17:49,901 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:17Z] INFO  17:17:49,921 IntervalUtils - Processing 9482876 bp from intervals
[2016-04-15T00:17Z] WARN  17:17:49,927 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:17Z] INFO  17:17:49,987 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:17Z] INFO  17:17:50,025 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:17Z] INFO  17:17:50,026 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:17Z] INFO  17:17:50,027 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:17Z] INFO  17:17:50,028 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:17Z] INFO  17:17:50,046 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:17Z] INFO  17:17:50,132 ProgressMeter -            done    186346.0    15.0 s      81.0 s      100.0%    15.0 s       0.0 s
[2016-04-15T00:17Z] INFO  17:17:50,132 ProgressMeter - Total runtime 15.22 secs, 0.25 min, 0.00 hours
[2016-04-15T00:17Z] INFO  17:17:50,136 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 186346 total reads (0.00%)
[2016-04-15T00:17Z] INFO  17:17:50,137 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:17Z] INFO  17:17:50,137 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:17Z] INFO  17:17:50,137 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:17Z] INFO  17:17:50,139 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:17Z] INFO  17:17:50,140 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:17Z] INFO  17:17:50,141 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:17Z] INFO  17:17:50,142 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:17Z] INFO  17:17:50,197 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:17Z] INFO  17:17:50,198 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:17Z] INFO  17:17:50,199 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:17Z] INFO  17:17:50,200 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:17Z] INFO  17:17:50,255 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:17Z] INFO  17:17:50,336 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:17Z] INFO  17:17:50,592 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:17Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-11_0_15994658-prep-prealign.bam
[2016-04-15T00:17Z] INFO  17:17:51,654 ProgressMeter -     9:136262300    400008.0    30.0 s      77.0 s       59.1%    50.0 s      20.0 s
[2016-04-15T00:17Z] INFO  17:17:51,694 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:17Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-11_78277177_93796886-prep.bam
[2016-04-15T00:17Z] GATK pre-alignment ('12', 109494486, 125263132) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:17Z] GATK RealignerTargetCreator: R14-18106_kapa-NGv3-PE100-NGv3-sort-11_0_15994658-prep-prealign.bam 11:1-15994658
[2016-04-15T00:17Z] GATK: RealignerTargetCreator
[2016-04-15T00:17Z] INFO  17:17:53,537 ProgressMeter -    11:123601051    400005.0    60.0 s       2.5 m       87.7%    68.0 s       8.0 s
[2016-04-15T00:17Z] INFO  17:17:55,212 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:17Z] INFO  17:17:55,215 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:17Z] INFO  17:17:55,216 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:17Z] INFO  17:17:55,216 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:17Z] INFO  17:17:55,221 HelpFormatter - Program Args: -T PrintReads -L 12:109494487-125263132 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/12/tx/tmpRkMVsi/R14-18106_kapa-NGv3-PE100-NGv3-sort-12_109494486_125263132-prep-prealign.bam
[2016-04-15T00:17Z] INFO  17:17:55,249 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:17Z] INFO  17:17:55,251 HelpFormatter - Date/Time: 2016/04/14 17:17:55
[2016-04-15T00:17Z] INFO  17:17:55,260 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:17Z] INFO  17:17:55,261 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:17Z] INFO  17:17:55,445 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:17Z] INFO  17:17:55,498 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:17Z] INFO  17:17:55,502 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:17Z] INFO  17:17:55,503 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:17Z] INFO  17:17:55,503 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:17Z] INFO  17:17:55,508 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/11/R14-18106_kapa-NGv3-PE100-NGv3-sort-11_0_15994658-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/11/tx/tmpYvvUxe/R14-18106_kapa-NGv3-PE100-NGv3-sort-11_0_15994658-prep-prealign-realign.intervals -l INFO -L 11:1-15994658 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:17Z] INFO  17:17:55,519 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:17Z] INFO  17:17:55,519 HelpFormatter - Date/Time: 2016/04/14 17:17:55
[2016-04-15T00:17Z] INFO  17:17:55,519 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:17Z] INFO  17:17:55,519 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:17Z] INFO  17:17:55,646 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:17Z] INFO  17:17:55,887 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T00:17Z] INFO  17:17:55,920 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:17Z] INFO  17:17:56,005 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-15T00:17Z] INFO  17:17:56,343 IntervalUtils - Processing 15994658 bp from intervals
[2016-04-15T00:17Z] WARN  17:17:56,349 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:17Z] INFO  17:17:56,415 ProgressMeter -            done   1.5581293E7    16.0 s       1.0 s      100.0%    16.0 s       0.0 s
[2016-04-15T00:17Z] INFO  17:17:56,417 ProgressMeter - Total runtime 16.48 secs, 0.27 min, 0.00 hours
[2016-04-15T00:17Z] INFO  17:17:56,422 MicroScheduler - 12640 reads were filtered out during the traversal out of approximately 157774 total reads (8.01%)
[2016-04-15T00:17Z] INFO  17:17:56,423 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:17Z] INFO  17:17:56,424 MicroScheduler -   -> 559 reads (0.35% of total) failing BadMateFilter
[2016-04-15T00:17Z] INFO  17:17:56,425 MicroScheduler -   -> 11554 reads (7.32% of total) failing DuplicateReadFilter
[2016-04-15T00:17Z] INFO  17:17:56,426 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:17Z] INFO  17:17:56,427 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:17Z] INFO  17:17:56,428 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:17Z] INFO  17:17:56,430 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:17Z] INFO  17:17:56,439 MicroScheduler -   -> 527 reads (0.33% of total) failing MappingQualityZeroFilter
[2016-04-15T00:17Z] INFO  17:17:56,441 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:17Z] INFO  17:17:56,441 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-15T00:17Z] INFO  17:17:56,442 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:17Z] INFO  17:17:56,579 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-15T00:17Z] INFO  17:17:56,647 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:17Z] INFO  17:17:56,656 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:17Z] INFO  17:17:56,697 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:17Z] INFO  17:17:56,698 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:17Z] INFO  17:17:56,699 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:17Z] INFO  17:17:56,700 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:17Z] INFO  17:17:56,703 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-15T00:17Z] INFO  17:17:56,717 IntervalUtils - Processing 15768646 bp from intervals
[2016-04-15T00:17Z] INFO  17:17:56,800 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:17Z] INFO  17:17:57,132 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:17Z] INFO  17:17:57,133 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:17Z] INFO  17:17:57,134 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:17Z] INFO  17:17:57,134 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:17Z] INFO  17:17:57,149 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:17Z] INFO  17:17:57,283 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:17Z] INFO  17:17:57,700 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:17Z] GATK: realign ('12', 15650178, 31231471) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:17Z] INFO  17:17:57,876 ProgressMeter -            done    228516.0    16.0 s      70.0 s      100.0%    16.0 s       0.0 s
[2016-04-15T00:17Z] INFO  17:17:57,877 ProgressMeter - Total runtime 16.22 secs, 0.27 min, 0.00 hours
[2016-04-15T00:17Z] INFO  17:17:57,882 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 228516 total reads (0.00%)
[2016-04-15T00:17Z] INFO  17:17:57,894 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:17Z] INFO  17:17:57,895 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:17Z] INFO  17:17:57,895 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:17Z] INFO  17:17:57,935 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@7172f77a
[2016-04-15T00:17Z] INFO  17:17:58,067 ProgressMeter -            done     93582.0    15.0 s       2.8 m       99.8%    15.0 s       0.0 s
[2016-04-15T00:17Z] INFO  17:17:58,067 ProgressMeter - Total runtime 15.46 secs, 0.26 min, 0.00 hours
[2016-04-15T00:17Z] INFO  17:17:58,068 MicroScheduler - 103 reads were filtered out during the traversal out of approximately 93685 total reads (0.11%)
[2016-04-15T00:17Z] INFO  17:17:58,068 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:17Z] INFO  17:17:58,068 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:17Z] INFO  17:17:58,069 MicroScheduler -   -> 103 reads (0.11% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:17Z] INFO  17:17:58,274 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@7172f77a
[2016-04-15T00:17Z] INFO  17:17:58,406 ProgressMeter -            done    173037.0    27.0 s       2.6 m      100.0%    27.0 s       0.0 s
[2016-04-15T00:17Z] INFO  17:17:58,407 ProgressMeter - Total runtime 27.12 secs, 0.45 min, 0.01 hours
[2016-04-15T00:17Z] INFO  17:17:58,408 MicroScheduler - 155 reads were filtered out during the traversal out of approximately 173192 total reads (0.09%)
[2016-04-15T00:17Z] INFO  17:17:58,409 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:17Z] INFO  17:17:58,410 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:17Z] INFO  17:17:58,410 MicroScheduler -   -> 155 reads (0.09% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:17Z] INFO  17:17:59,340 ProgressMeter -            done    177603.0    14.0 s      81.0 s      100.0%    14.0 s       0.0 s
[2016-04-15T00:17Z] INFO  17:17:59,340 ProgressMeter - Total runtime 14.54 secs, 0.24 min, 0.00 hours
[2016-04-15T00:17Z] INFO  17:17:59,344 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 177603 total reads (0.00%)
[2016-04-15T00:17Z] INFO  17:17:59,345 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:17Z] INFO  17:17:59,345 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:17Z] INFO  17:17:59,345 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:17Z] INFO  17:17:59,555 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:17Z] INFO  17:17:59,558 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:17Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-11_31541602_47074069-prep.bam
[2016-04-15T00:17Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-12_78334098_93863131-prep-prealign.bam
[2016-04-15T00:17Z] INFO  17:17:59,938 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:17Z] GATK RealignerTargetCreator: R14-18106_kapa-NGv3-PE100-NGv3-sort-12_78334098_93863131-prep-prealign.bam 12:78334099-93863131
[2016-04-15T00:17Z] GATK: RealignerTargetCreator
[2016-04-15T00:17Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-12_62687959_78225484-prep-prealign.bam
[2016-04-15T00:18Z] GATK pre-alignment ('12', 125267228, 133851895) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:18Z] INFO  17:18:00,397 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:18Z] INFO  17:18:00,400 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:18Z] INFO  17:18:00,401 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:18Z] INFO  17:18:00,401 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:18Z] INFO  17:18:00,406 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/12/R14-18106_kapa-NGv3-PE100-NGv3-sort-12_15650178_31231471-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/12/R14-18106_kapa-NGv3-PE100-NGv3-sort-12_15650178_31231471-prep-prealign-realign.intervals -L 12:15650179-31231471 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/12/tx/tmpAMxAkF/R14-18106_kapa-NGv3-PE100-NGv3-sort-12_15650178_31231471-prep.bam
[2016-04-15T00:18Z] INFO  17:18:00,437 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:18Z] INFO  17:18:00,438 HelpFormatter - Date/Time: 2016/04/14 17:18:00
[2016-04-15T00:18Z] INFO  17:18:00,439 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:18Z] INFO  17:18:00,440 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:18Z] GATK RealignerTargetCreator: R14-18106_kapa-NGv3-PE100-NGv3-sort-12_62687959_78225484-prep-prealign.bam 12:62687960-78225484
[2016-04-15T00:18Z] GATK: RealignerTargetCreator
[2016-04-15T00:18Z] INFO  17:18:00,668 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:18Z] INFO  17:18:00,834 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:18Z] INFO  17:18:00,839 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:18Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-11_93797496_109964158-prep.bam
[2016-04-15T00:18Z] INFO  17:18:00,861 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:18Z] INFO  17:18:00,937 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-15T00:18Z] INFO  17:18:01,356 IntervalUtils - Processing 15581293 bp from intervals
[2016-04-15T00:18Z] WARN  17:18:01,363 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:18Z] INFO  17:18:01,447 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:18Z] GATK pre-alignment ('13', 0, 19748299) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:18Z] INFO  17:18:01,594 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:18Z] INFO  17:18:01,595 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:18Z] INFO  17:18:01,596 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:18Z] INFO  17:18:01,597 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:18Z] INFO  17:18:01,730 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:18Z] INFO  17:18:01,927 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:18Z] INFO  17:18:02,850 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:18Z] INFO  17:18:02,853 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:18Z] INFO  17:18:02,854 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:18Z] INFO  17:18:02,855 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:18Z] INFO  17:18:02,859 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/12/R14-18106_kapa-NGv3-PE100-NGv3-sort-12_78334098_93863131-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/12/tx/tmp_Hhnhn/R14-18106_kapa-NGv3-PE100-NGv3-sort-12_78334098_93863131-prep-prealign-realign.intervals -l INFO -L 12:78334099-93863131 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:18Z] INFO  17:18:02,867 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:18Z] INFO  17:18:02,868 HelpFormatter - Date/Time: 2016/04/14 17:18:02
[2016-04-15T00:18Z] INFO  17:18:02,869 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:18Z] INFO  17:18:02,869 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:18Z] INFO  17:18:02,906 ProgressMeter -            done    164966.0    12.0 s      77.0 s       92.2%    13.0 s       1.0 s
[2016-04-15T00:18Z] INFO  17:18:02,906 ProgressMeter - Total runtime 12.77 secs, 0.21 min, 0.00 hours
[2016-04-15T00:18Z] INFO  17:18:02,909 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 164966 total reads (0.00%)
[2016-04-15T00:18Z] INFO  17:18:02,910 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:18Z] INFO  17:18:02,910 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:18Z] INFO  17:18:02,910 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:18Z] INFO  17:18:02,997 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:18Z] INFO  17:18:03,024 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:18Z] INFO  17:18:03,027 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:18Z] INFO  17:18:03,028 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:18Z] INFO  17:18:03,028 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:18Z] INFO  17:18:03,033 HelpFormatter - Program Args: -T PrintReads -L 12:125267229-133851895 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/12/tx/tmpUbTyMU/R14-18106_kapa-NGv3-PE100-NGv3-sort-12_125267228_133851895-prep-prealign.bam
[2016-04-15T00:18Z] INFO  17:18:03,044 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:18Z] INFO  17:18:03,055 HelpFormatter - Date/Time: 2016/04/14 17:18:03
[2016-04-15T00:18Z] INFO  17:18:03,056 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:18Z] INFO  17:18:03,057 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:18Z] INFO  17:18:03,232 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:18Z] INFO  17:18:03,235 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T00:18Z] INFO  17:18:03,244 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:18Z] INFO  17:18:03,321 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-15T00:18Z] INFO  17:18:03,585 IntervalUtils - Processing 15529033 bp from intervals
[2016-04-15T00:18Z] WARN  17:18:03,590 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:18Z] INFO  17:18:03,654 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:18Z] INFO  17:18:03,657 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:18Z] INFO  17:18:03,657 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:18Z] INFO  17:18:03,657 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:18Z] INFO  17:18:03,664 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:18Z] INFO  17:18:03,672 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/12/R14-18106_kapa-NGv3-PE100-NGv3-sort-12_62687959_78225484-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/12/tx/tmpKx3Uxk/R14-18106_kapa-NGv3-PE100-NGv3-sort-12_62687959_78225484-prep-prealign-realign.intervals -l INFO -L 12:62687960-78225484 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:18Z] INFO  17:18:03,703 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:18Z] INFO  17:18:03,704 HelpFormatter - Date/Time: 2016/04/14 17:18:03
[2016-04-15T00:18Z] INFO  17:18:03,705 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:18Z] INFO  17:18:03,705 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:18Z] INFO  17:18:03,854 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:18Z] INFO  17:18:03,864 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@7172f77a
[2016-04-15T00:18Z] INFO  17:18:03,919 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:18Z] INFO  17:18:03,919 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:18Z] INFO  17:18:03,920 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:18Z] INFO  17:18:03,920 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:18Z] INFO  17:18:04,024 ProgressMeter -            done    489242.0    70.0 s       2.4 m      100.0%    70.0 s       0.0 s
[2016-04-15T00:18Z] INFO  17:18:04,025 ProgressMeter - Total runtime 70.97 secs, 1.18 min, 0.02 hours
[2016-04-15T00:18Z] INFO  17:18:04,025 MicroScheduler - 227 reads were filtered out during the traversal out of approximately 489469 total reads (0.05%)
[2016-04-15T00:18Z] INFO  17:18:04,025 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:18Z] INFO  17:18:04,026 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:18Z] INFO  17:18:04,026 MicroScheduler -   -> 227 reads (0.05% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:18Z] INFO  17:18:04,064 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T00:18Z] INFO  17:18:04,073 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:18Z] INFO  17:18:04,141 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-15T00:18Z] INFO  17:18:04,314 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-15T00:18Z] INFO  17:18:04,369 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:18Z] INFO  17:18:04,377 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:18Z] INFO  17:18:04,414 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.04
[2016-04-15T00:18Z] INFO  17:18:04,427 IntervalUtils - Processing 8584667 bp from intervals
[2016-04-15T00:18Z] INFO  17:18:04,428 IntervalUtils - Processing 15537525 bp from intervals
[2016-04-15T00:18Z] WARN  17:18:04,433 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:18Z] INFO  17:18:04,503 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:18Z] INFO  17:18:04,522 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:18Z] INFO  17:18:04,528 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:18Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-11_125523640_135006516-prep.bam
[2016-04-15T00:18Z] INFO  17:18:04,590 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:18Z] INFO  17:18:04,594 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:18Z] INFO  17:18:04,594 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:18Z] INFO  17:18:04,595 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:18Z] INFO  17:18:04,600 HelpFormatter - Program Args: -T PrintReads -L 13:1-19748299 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/13/tx/tmpH073Va/R14-18106_kapa-NGv3-PE100-NGv3-sort-13_0_19748299-prep-prealign.bam
[2016-04-15T00:18Z] INFO  17:18:04,615 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:18Z] INFO  17:18:04,616 HelpFormatter - Date/Time: 2016/04/14 17:18:04
[2016-04-15T00:18Z] INFO  17:18:04,616 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:18Z] INFO  17:18:04,616 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:18Z] INFO  17:18:04,739 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:18Z] INFO  17:18:04,740 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:18Z] INFO  17:18:04,741 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:18Z] INFO  17:18:04,741 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:18Z] INFO  17:18:04,814 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:18Z] INFO  17:18:04,815 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:18Z] INFO  17:18:04,816 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:18Z] INFO  17:18:04,817 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:18Z] INFO  17:18:04,818 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:18Z] INFO  17:18:04,843 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:18Z] INFO  17:18:05,000 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:18Z] GATK pre-alignment ('13', 19751066, 35517251) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:18Z] INFO  17:18:05,417 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:18Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-11_110001730_125514538-prep-prealign.bam
[2016-04-15T00:18Z] INFO  17:18:05,487 ProgressMeter -      12:9633227    400006.0    60.0 s       2.5 m       61.6%    97.0 s      37.0 s
[2016-04-15T00:18Z] INFO  17:18:06,354 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-15T00:18Z] INFO  17:18:06,426 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:18Z] INFO  17:18:06,436 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:18Z] INFO  17:18:06,493 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-15T00:18Z] INFO  17:18:06,508 IntervalUtils - Processing 19748299 bp from intervals
[2016-04-15T00:18Z] INFO  17:18:06,583 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:18Z] GATK RealignerTargetCreator: R14-18106_kapa-NGv3-PE100-NGv3-sort-11_110001730_125514538-prep-prealign.bam 11:110001731-125514538
[2016-04-15T00:18Z] GATK: RealignerTargetCreator
[2016-04-15T00:18Z] INFO  17:18:07,207 ProgressMeter -            done   1.5518246E7    17.0 s       1.0 s      100.0%    17.0 s       0.0 s
[2016-04-15T00:18Z] INFO  17:18:07,208 ProgressMeter - Total runtime 17.18 secs, 0.29 min, 0.00 hours
[2016-04-15T00:18Z] INFO  17:18:07,212 MicroScheduler - 17325 reads were filtered out during the traversal out of approximately 193537 total reads (8.95%)
[2016-04-15T00:18Z] INFO  17:18:07,212 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:18Z] INFO  17:18:07,213 MicroScheduler -   -> 555 reads (0.29% of total) failing BadMateFilter
[2016-04-15T00:18Z] INFO  17:18:07,213 MicroScheduler -   -> 14425 reads (7.45% of total) failing DuplicateReadFilter
[2016-04-15T00:18Z] INFO  17:18:07,213 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:18Z] INFO  17:18:07,213 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:18Z] INFO  17:18:07,214 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:18Z] INFO  17:18:07,214 MicroScheduler -   -> 2345 reads (1.21% of total) failing MappingQualityZeroFilter
[2016-04-15T00:18Z] INFO  17:18:07,214 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:18Z] INFO  17:18:07,214 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-15T00:18Z] INFO  17:18:07,214 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:18Z] INFO  17:18:07,232 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:18Z] INFO  17:18:07,233 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:18Z] INFO  17:18:07,234 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:18Z] INFO  17:18:07,234 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:18Z] INFO  17:18:07,259 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:18Z] INFO  17:18:07,266 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:18Z] INFO  17:18:08,041 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:18Z] INFO  17:18:08,044 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:18Z] INFO  17:18:08,045 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:18Z] INFO  17:18:08,046 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:18Z] INFO  17:18:08,050 HelpFormatter - Program Args: -T PrintReads -L 13:19751067-35517251 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/13/tx/tmpPwH0Nw/R14-18106_kapa-NGv3-PE100-NGv3-sort-13_19751066_35517251-prep-prealign.bam
[2016-04-15T00:18Z] INFO  17:18:08,064 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:18Z] INFO  17:18:08,065 HelpFormatter - Date/Time: 2016/04/14 17:18:08
[2016-04-15T00:18Z] INFO  17:18:08,066 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:18Z] INFO  17:18:08,066 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:18Z] INFO  17:18:08,158 ProgressMeter -            done    789169.0    47.0 s      60.0 s       99.3%    47.0 s       0.0 s
[2016-04-15T00:18Z] INFO  17:18:08,159 ProgressMeter - Total runtime 47.48 secs, 0.79 min, 0.01 hours
[2016-04-15T00:18Z] INFO  17:18:08,162 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 789169 total reads (0.00%)
[2016-04-15T00:18Z] INFO  17:18:08,163 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:18Z] INFO  17:18:08,163 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:18Z] INFO  17:18:08,163 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:18Z] INFO  17:18:08,240 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:18Z] INFO  17:18:08,629 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:18Z] GATK: realign ('12', 31236746, 46754992) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:18Z] INFO  17:18:09,302 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-15T00:18Z] INFO  17:18:09,420 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:18Z] INFO  17:18:09,441 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:18Z] INFO  17:18:09,507 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-15T00:18Z] INFO  17:18:09,524 IntervalUtils - Processing 15766185 bp from intervals
[2016-04-15T00:18Z] INFO  17:18:09,590 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:18Z] INFO  17:18:09,761 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:18Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-9_129097484_141213431-prep.bam
[2016-04-15T00:18Z] INFO  17:18:09,890 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:18Z] INFO  17:18:09,891 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:18Z] INFO  17:18:09,892 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:18Z] INFO  17:18:09,892 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:18Z] INFO  17:18:09,909 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:18Z] INFO  17:18:09,972 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:18Z] INFO  17:18:09,975 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:18Z] INFO  17:18:09,976 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:18Z] INFO  17:18:09,976 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:18Z] INFO  17:18:09,981 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/11/R14-18106_kapa-NGv3-PE100-NGv3-sort-11_110001730_125514538-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/11/tx/tmpKUEEOj/R14-18106_kapa-NGv3-PE100-NGv3-sort-11_110001730_125514538-prep-prealign-realign.intervals -l INFO -L 11:110001731-125514538 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:18Z] INFO  17:18:09,990 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:18Z] INFO  17:18:09,991 HelpFormatter - Date/Time: 2016/04/14 17:18:09
[2016-04-15T00:18Z] INFO  17:18:09,991 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:18Z] INFO  17:18:09,991 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:18Z] INFO  17:18:10,060 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:18Z] INFO  17:18:10,131 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@7172f77a
[2016-04-15T00:18Z] INFO  17:18:10,138 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:18Z] INFO  17:18:10,179 ProgressMeter -            done      6683.0     2.0 s       7.3 m      100.0%     2.0 s       0.0 s
[2016-04-15T00:18Z] INFO  17:18:10,181 ProgressMeter - Total runtime 2.95 secs, 0.05 min, 0.00 hours
[2016-04-15T00:18Z] INFO  17:18:10,181 MicroScheduler - 4 reads were filtered out during the traversal out of approximately 6687 total reads (0.06%)
[2016-04-15T00:18Z] INFO  17:18:10,182 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:18Z] INFO  17:18:10,183 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:18Z] INFO  17:18:10,183 MicroScheduler -   -> 4 reads (0.06% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:18Z] INFO  17:18:10,300 ProgressMeter -     11:74800390    700011.0    90.0 s       2.2 m       77.6%   115.0 s      25.0 s
[2016-04-15T00:18Z] INFO  17:18:10,360 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T00:18Z] INFO  17:18:10,368 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:18Z] INFO  17:18:10,440 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-15T00:18Z] INFO  17:18:10,705 IntervalUtils - Processing 15512808 bp from intervals
[2016-04-15T00:18Z] WARN  17:18:10,711 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:18Z] INFO  17:18:10,800 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:18Z] INFO  17:18:11,023 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:18Z] INFO  17:18:11,024 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:18Z] INFO  17:18:11,025 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:18Z] INFO  17:18:11,025 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:18Z] INFO  17:18:11,691 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:18Z] INFO  17:18:11,694 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:18Z] INFO  17:18:11,695 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:18Z] INFO  17:18:11,695 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:18Z] INFO  17:18:11,700 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/12/R14-18106_kapa-NGv3-PE100-NGv3-sort-12_31236746_46754992-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/12/R14-18106_kapa-NGv3-PE100-NGv3-sort-12_31236746_46754992-prep-prealign-realign.intervals -L 12:31236747-46754992 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/12/tx/tmp_mqcyZ/R14-18106_kapa-NGv3-PE100-NGv3-sort-12_31236746_46754992-prep.bam
[2016-04-15T00:18Z] INFO  17:18:11,710 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:18Z] INFO  17:18:11,710 HelpFormatter - Date/Time: 2016/04/14 17:18:11
[2016-04-15T00:18Z] INFO  17:18:11,710 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:18Z] INFO  17:18:11,711 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:18Z] INFO  17:18:11,718 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:18Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-13_0_19748299-prep-prealign.bam
[2016-04-15T00:18Z] GATK RealignerTargetCreator: R14-18106_kapa-NGv3-PE100-NGv3-sort-13_0_19748299-prep-prealign.bam 13:1-19748299
[2016-04-15T00:18Z] GATK: RealignerTargetCreator
[2016-04-15T00:18Z] INFO  17:18:11,921 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:18Z] INFO  17:18:12,027 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:18Z] INFO  17:18:12,037 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:18Z] INFO  17:18:12,114 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-15T00:18Z] GATK pre-alignment ('13', 35615069, 51287376) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:18Z] INFO  17:18:12,609 IntervalUtils - Processing 15518246 bp from intervals
[2016-04-15T00:18Z] WARN  17:18:12,614 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:18Z] INFO  17:18:12,755 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:18Z] INFO  17:18:12,912 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:18Z] INFO  17:18:12,912 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:18Z] INFO  17:18:12,913 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:18Z] INFO  17:18:12,913 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:18Z] INFO  17:18:13,111 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:18Z] INFO  17:18:13,301 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:18Z] INFO  17:18:14,607 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:18Z] INFO  17:18:14,610 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:18Z] INFO  17:18:14,610 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:18Z] INFO  17:18:14,610 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:18Z] INFO  17:18:14,614 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/13/R14-18106_kapa-NGv3-PE100-NGv3-sort-13_0_19748299-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/13/tx/tmphy4rIk/R14-18106_kapa-NGv3-PE100-NGv3-sort-13_0_19748299-prep-prealign-realign.intervals -l INFO -L 13:1-19748299 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:18Z] INFO  17:18:14,664 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:18Z] INFO  17:18:14,665 HelpFormatter - Date/Time: 2016/04/14 17:18:14
[2016-04-15T00:18Z] INFO  17:18:14,666 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:18Z] INFO  17:18:14,666 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:18Z] INFO  17:18:14,807 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:18Z] INFO  17:18:15,068 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T00:18Z] INFO  17:18:15,078 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:18Z] INFO  17:18:15,085 ProgressMeter -            done   1.5519706E7    24.0 s       1.0 s      100.0%    24.0 s       0.0 s
[2016-04-15T00:18Z] INFO  17:18:15,086 ProgressMeter - Total runtime 24.89 secs, 0.41 min, 0.01 hours
[2016-04-15T00:18Z] INFO  17:18:15,090 MicroScheduler - 56929 reads were filtered out during the traversal out of approximately 539409 total reads (10.55%)
[2016-04-15T00:18Z] INFO  17:18:15,091 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:18Z] INFO  17:18:15,101 MicroScheduler -   -> 1153 reads (0.21% of total) failing BadMateFilter
[2016-04-15T00:18Z] INFO  17:18:15,102 MicroScheduler -   -> 40123 reads (7.44% of total) failing DuplicateReadFilter
[2016-04-15T00:18Z] INFO  17:18:15,103 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:18Z] INFO  17:18:15,103 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:18Z] INFO  17:18:15,104 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:18Z] INFO  17:18:15,105 MicroScheduler -   -> 15653 reads (2.90% of total) failing MappingQualityZeroFilter
[2016-04-15T00:18Z] INFO  17:18:15,105 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:18Z] INFO  17:18:15,106 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-15T00:18Z] INFO  17:18:15,106 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:18Z] INFO  17:18:15,130 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:18Z] INFO  17:18:15,134 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:18Z] INFO  17:18:15,134 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:18Z] INFO  17:18:15,135 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:18Z] INFO  17:18:15,139 HelpFormatter - Program Args: -T PrintReads -L 13:35615070-51287376 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/13/tx/tmpbwQBU0/R14-18106_kapa-NGv3-PE100-NGv3-sort-13_35615069_51287376-prep-prealign.bam
[2016-04-15T00:18Z] INFO  17:18:15,155 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:18Z] INFO  17:18:15,156 HelpFormatter - Date/Time: 2016/04/14 17:18:15
[2016-04-15T00:18Z] INFO  17:18:15,157 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:18Z] INFO  17:18:15,157 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:18Z] INFO  17:18:15,160 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-15T00:18Z] INFO  17:18:15,304 ProgressMeter -            done    156928.0    13.0 s      87.0 s      100.0%    13.0 s       0.0 s
[2016-04-15T00:18Z] INFO  17:18:15,304 ProgressMeter - Total runtime 13.71 secs, 0.23 min, 0.00 hours
[2016-04-15T00:18Z] INFO  17:18:15,308 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 156928 total reads (0.00%)
[2016-04-15T00:18Z] INFO  17:18:15,308 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:18Z] INFO  17:18:15,308 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:18Z] INFO  17:18:15,309 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:18Z] INFO  17:18:15,365 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:18Z] INFO  17:18:15,443 IntervalUtils - Processing 19748299 bp from intervals
[2016-04-15T00:18Z] WARN  17:18:15,449 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:18Z] INFO  17:18:15,525 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:18Z] INFO  17:18:15,778 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:18Z] INFO  17:18:15,778 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:18Z] INFO  17:18:15,779 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:18Z] INFO  17:18:15,779 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:18Z] INFO  17:18:16,035 ProgressMeter -     12:53448123    300009.0    60.0 s       3.3 m       42.1%     2.4 m      82.0 s
[2016-04-15T00:18Z] INFO  17:18:16,433 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:18Z] GATK: realign ('11', 47158866, 62678572) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:18Z] INFO  17:18:16,554 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-15T00:18Z] INFO  17:18:16,605 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:18Z] INFO  17:18:16,614 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:18Z] INFO  17:18:16,655 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.04
[2016-04-15T00:18Z] INFO  17:18:16,672 IntervalUtils - Processing 15672307 bp from intervals
[2016-04-15T00:18Z] INFO  17:18:16,676 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:18Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-12_15650178_31231471-prep.bam
[2016-04-15T00:18Z] INFO  17:18:16,751 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:18Z] INFO  17:18:17,036 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:18Z] INFO  17:18:17,055 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:18Z] INFO  17:18:17,055 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:18Z] INFO  17:18:17,055 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:18Z] INFO  17:18:17,076 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:18Z] INFO  17:18:17,195 ProgressMeter -    12:104698514    100001.0    30.0 s       5.1 m       69.3%    43.0 s      13.0 s
[2016-04-15T00:18Z] INFO  17:18:17,238 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:18Z] GATK pre-alignment ('13', 51396767, 67205543) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:18Z] INFO  17:18:19,279 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:18Z] INFO  17:18:19,282 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:18Z] INFO  17:18:19,283 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:18Z] INFO  17:18:19,283 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:18Z] INFO  17:18:19,288 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/11/R14-18106_kapa-NGv3-PE100-NGv3-sort-11_47158866_62678572-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/11/R14-18106_kapa-NGv3-PE100-NGv3-sort-11_47158866_62678572-prep-prealign-realign.intervals -L 11:47158867-62678572 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/11/tx/tmp7Nonz_/R14-18106_kapa-NGv3-PE100-NGv3-sort-11_47158866_62678572-prep.bam
[2016-04-15T00:18Z] INFO  17:18:19,319 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:18Z] INFO  17:18:19,326 HelpFormatter - Date/Time: 2016/04/14 17:18:19
[2016-04-15T00:18Z] INFO  17:18:19,327 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:18Z] INFO  17:18:19,327 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:18Z] INFO  17:18:19,583 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:18Z] INFO  17:18:19,727 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:18Z] INFO  17:18:19,737 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:18Z] INFO  17:18:19,813 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-15T00:18Z] INFO  17:18:19,813 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@32d5a4c6
[2016-04-15T00:18Z] INFO  17:18:19,917 ProgressMeter -            done    535895.0    74.0 s       2.3 m      100.0%    74.0 s       0.0 s
[2016-04-15T00:18Z] INFO  17:18:19,917 ProgressMeter - Total runtime 74.44 secs, 1.24 min, 0.02 hours
[2016-04-15T00:18Z] INFO  17:18:19,918 MicroScheduler - 242 reads were filtered out during the traversal out of approximately 536137 total reads (0.05%)
[2016-04-15T00:18Z] INFO  17:18:19,918 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:18Z] INFO  17:18:19,918 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:18Z] INFO  17:18:19,919 MicroScheduler -   -> 242 reads (0.05% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:18Z] INFO  17:18:19,980 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:18Z] INFO  17:18:19,983 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:18Z] INFO  17:18:19,983 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:18Z] INFO  17:18:19,984 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:18Z] INFO  17:18:19,988 HelpFormatter - Program Args: -T PrintReads -L 13:51396768-67205543 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/13/tx/tmpME33E0/R14-18106_kapa-NGv3-PE100-NGv3-sort-13_51396767_67205543-prep-prealign.bam
[2016-04-15T00:18Z] INFO  17:18:20,001 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:18Z] INFO  17:18:20,002 HelpFormatter - Date/Time: 2016/04/14 17:18:19
[2016-04-15T00:18Z] INFO  17:18:20,002 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:18Z] INFO  17:18:20,002 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:18Z] INFO  17:18:20,031 ProgressMeter -            done   1.5529033E7    16.0 s       1.0 s      100.0%    16.0 s       0.0 s
[2016-04-15T00:18Z] INFO  17:18:20,032 ProgressMeter - Total runtime 16.11 secs, 0.27 min, 0.00 hours
[2016-04-15T00:18Z] INFO  17:18:20,037 MicroScheduler - 7766 reads were filtered out during the traversal out of approximately 93842 total reads (8.28%)
[2016-04-15T00:18Z] INFO  17:18:20,038 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:18Z] INFO  17:18:20,039 MicroScheduler -   -> 503 reads (0.54% of total) failing BadMateFilter
[2016-04-15T00:18Z] INFO  17:18:20,040 MicroScheduler -   -> 6913 reads (7.37% of total) failing DuplicateReadFilter
[2016-04-15T00:18Z] INFO  17:18:20,041 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:18Z] INFO  17:18:20,041 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:18Z] INFO  17:18:20,042 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:18Z] INFO  17:18:20,052 MicroScheduler -   -> 350 reads (0.37% of total) failing MappingQualityZeroFilter
[2016-04-15T00:18Z] INFO  17:18:20,052 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:18Z] INFO  17:18:20,053 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-15T00:18Z] INFO  17:18:20,053 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:18Z] INFO  17:18:20,122 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@5fe152b7
[2016-04-15T00:18Z] INFO  17:18:20,144 IntervalUtils - Processing 15519706 bp from intervals
[2016-04-15T00:18Z] INFO  17:18:20,149 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:18Z] WARN  17:18:20,149 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:18Z] INFO  17:18:20,219 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:18Z] INFO  17:18:20,258 ProgressMeter -            done    862476.0   100.0 s     116.0 s      100.0%   100.0 s       0.0 s
[2016-04-15T00:18Z] INFO  17:18:20,259 ProgressMeter - Total runtime 100.71 secs, 1.68 min, 0.03 hours
[2016-04-15T00:18Z] INFO  17:18:20,259 MicroScheduler - 387 reads were filtered out during the traversal out of approximately 862863 total reads (0.04%)
[2016-04-15T00:18Z] INFO  17:18:20,259 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:18Z] INFO  17:18:20,260 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:18Z] INFO  17:18:20,261 MicroScheduler -   -> 387 reads (0.04% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:18Z] INFO  17:18:20,340 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:18Z] INFO  17:18:20,341 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:18Z] INFO  17:18:20,342 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:18Z] INFO  17:18:20,343 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:18Z] INFO  17:18:20,482 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:18Z] INFO  17:18:20,660 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:18Z] INFO  17:18:21,181 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-15T00:18Z] INFO  17:18:21,267 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:18Z] INFO  17:18:21,276 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:18Z] INFO  17:18:21,320 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.04
[2016-04-15T00:18Z] INFO  17:18:21,335 IntervalUtils - Processing 15808776 bp from intervals
[2016-04-15T00:18Z] INFO  17:18:21,426 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:18Z] INFO  17:18:21,480 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:18Z] GATK: realign ('12', 78334098, 93863131) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:18Z] INFO  17:18:21,522 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:18Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-12_0_15637181-prep-prealign.bam
[2016-04-15T00:18Z] INFO  17:18:21,669 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:18Z] INFO  17:18:21,670 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:18Z] INFO  17:18:21,671 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:18Z] INFO  17:18:21,672 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:18Z] INFO  17:18:21,683 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:18Z] INFO  17:18:21,690 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:18Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-11_62744265_78270665-prep-prealign.bam
[2016-04-15T00:18Z] INFO  17:18:21,865 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:18Z] INFO  17:18:22,788 ProgressMeter -            done   1.5537525E7    18.0 s       1.0 s      100.0%    18.0 s       0.0 s
[2016-04-15T00:18Z] INFO  17:18:22,790 ProgressMeter - Total runtime 18.05 secs, 0.30 min, 0.01 hours
[2016-04-15T00:18Z] INFO  17:18:22,811 MicroScheduler - 14213 reads were filtered out during the traversal out of approximately 173839 total reads (8.18%)
[2016-04-15T00:18Z] INFO  17:18:22,812 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:18Z] INFO  17:18:22,813 MicroScheduler -   -> 671 reads (0.39% of total) failing BadMateFilter
[2016-04-15T00:18Z] INFO  17:18:22,814 MicroScheduler -   -> 12855 reads (7.39% of total) failing DuplicateReadFilter
[2016-04-15T00:18Z] INFO  17:18:22,826 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:18Z] INFO  17:18:22,827 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:18Z] INFO  17:18:22,827 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:18Z] INFO  17:18:22,828 MicroScheduler -   -> 687 reads (0.40% of total) failing MappingQualityZeroFilter
[2016-04-15T00:18Z] INFO  17:18:22,829 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:18Z] INFO  17:18:22,830 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-15T00:18Z] INFO  17:18:22,830 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:18Z] GATK RealignerTargetCreator: R14-18106_kapa-NGv3-PE100-NGv3-sort-12_0_15637181-prep-prealign.bam 12:1-15637181
[2016-04-15T00:18Z] GATK: RealignerTargetCreator
[2016-04-15T00:18Z] INFO  17:18:24,365 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:18Z] INFO  17:18:24,371 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:18Z] INFO  17:18:24,371 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:18Z] INFO  17:18:24,372 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:18Z] INFO  17:18:24,381 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/12/R14-18106_kapa-NGv3-PE100-NGv3-sort-12_78334098_93863131-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/12/R14-18106_kapa-NGv3-PE100-NGv3-sort-12_78334098_93863131-prep-prealign-realign.intervals -L 12:78334099-93863131 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/12/tx/tmpNgDy1F/R14-18106_kapa-NGv3-PE100-NGv3-sort-12_78334098_93863131-prep.bam
[2016-04-15T00:18Z] GATK RealignerTargetCreator: R14-18106_kapa-NGv3-PE100-NGv3-sort-11_62744265_78270665-prep-prealign.bam 11:62744266-78270665
[2016-04-15T00:18Z] GATK: RealignerTargetCreator
[2016-04-15T00:18Z] INFO  17:18:24,391 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:18Z] INFO  17:18:24,392 HelpFormatter - Date/Time: 2016/04/14 17:18:24
[2016-04-15T00:18Z] INFO  17:18:24,392 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:18Z] INFO  17:18:24,393 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:18Z] INFO  17:18:24,578 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:18Z] INFO  17:18:24,741 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:18Z] INFO  17:18:24,762 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:18Z] INFO  17:18:24,837 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-15T00:18Z] INFO  17:18:25,189 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:18Z] INFO  17:18:25,202 IntervalUtils - Processing 15529033 bp from intervals
[2016-04-15T00:18Z] GATK: realign ('12', 62687959, 78225484) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:18Z] WARN  17:18:25,210 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:18Z] INFO  17:18:25,306 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:18Z] INFO  17:18:25,392 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:18Z] INFO  17:18:25,393 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:18Z] INFO  17:18:25,394 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:18Z] INFO  17:18:25,395 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:18Z] INFO  17:18:25,632 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:18Z] INFO  17:18:25,639 ProgressMeter -            done   1.5994658E7    28.0 s       1.0 s      100.0%    28.0 s       0.0 s
[2016-04-15T00:18Z] INFO  17:18:25,640 ProgressMeter - Total runtime 28.94 secs, 0.48 min, 0.01 hours
[2016-04-15T00:18Z] INFO  17:18:25,641 MicroScheduler - 82677 reads were filtered out during the traversal out of approximately 764873 total reads (10.81%)
[2016-04-15T00:18Z] INFO  17:18:25,641 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:18Z] INFO  17:18:25,641 MicroScheduler -   -> 1601 reads (0.21% of total) failing BadMateFilter
[2016-04-15T00:18Z] INFO  17:18:25,642 MicroScheduler -   -> 60212 reads (7.87% of total) failing DuplicateReadFilter
[2016-04-15T00:18Z] INFO  17:18:25,642 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:18Z] INFO  17:18:25,642 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:18Z] INFO  17:18:25,643 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:18Z] INFO  17:18:25,643 MicroScheduler -   -> 20864 reads (2.73% of total) failing MappingQualityZeroFilter
[2016-04-15T00:18Z] INFO  17:18:25,643 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:18Z] INFO  17:18:25,643 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-15T00:18Z] INFO  17:18:25,644 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:18Z] INFO  17:18:25,833 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:18Z] INFO  17:18:26,141 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:18Z] INFO  17:18:26,144 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:18Z] INFO  17:18:26,145 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:18Z] INFO  17:18:26,145 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:18Z] INFO  17:18:26,150 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/12/R14-18106_kapa-NGv3-PE100-NGv3-sort-12_0_15637181-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/12/tx/tmpv3eZZX/R14-18106_kapa-NGv3-PE100-NGv3-sort-12_0_15637181-prep-prealign-realign.intervals -l INFO -L 12:1-15637181 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:18Z] INFO  17:18:26,171 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:18Z] INFO  17:18:26,172 HelpFormatter - Date/Time: 2016/04/14 17:18:26
[2016-04-15T00:18Z] INFO  17:18:26,173 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:18Z] INFO  17:18:26,173 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:18Z] INFO  17:18:26,311 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:18Z] INFO  17:18:26,513 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T00:18Z] INFO  17:18:26,530 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:18Z] INFO  17:18:26,630 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.10
[2016-04-15T00:18Z] INFO  17:18:27,023 IntervalUtils - Processing 15637181 bp from intervals
[2016-04-15T00:18Z] WARN  17:18:27,039 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:18Z] INFO  17:18:27,153 ProgressMeter -    12:113796717    200003.0    30.0 s       2.5 m       27.3%   109.0 s      79.0 s
[2016-04-15T00:18Z] INFO  17:18:27,155 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:18Z] INFO  17:18:27,182 ProgressMeter -            done    191582.0    14.0 s      74.0 s      100.0%    14.0 s       0.0 s
[2016-04-15T00:18Z] INFO  17:18:27,183 ProgressMeter - Total runtime 14.27 secs, 0.24 min, 0.00 hours
[2016-04-15T00:18Z] INFO  17:18:27,186 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:18Z] INFO  17:18:27,188 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 191582 total reads (0.00%)
[2016-04-15T00:18Z] INFO  17:18:27,188 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:18Z] INFO  17:18:27,188 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:18Z] INFO  17:18:27,189 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:18Z] GATK: realign ('11', 0, 15994658) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:18Z] INFO  17:18:27,426 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:18Z] INFO  17:18:27,427 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:18Z] INFO  17:18:27,427 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:18Z] INFO  17:18:27,428 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:18Z] INFO  17:18:27,438 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:18Z] INFO  17:18:27,441 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:18Z] INFO  17:18:27,442 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:18Z] INFO  17:18:27,442 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:18Z] INFO  17:18:27,447 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/11/R14-18106_kapa-NGv3-PE100-NGv3-sort-11_62744265_78270665-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/11/tx/tmpYIUd9K/R14-18106_kapa-NGv3-PE100-NGv3-sort-11_62744265_78270665-prep-prealign-realign.intervals -l INFO -L 11:62744266-78270665 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:18Z] INFO  17:18:27,465 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:18Z] INFO  17:18:27,466 HelpFormatter - Date/Time: 2016/04/14 17:18:27
[2016-04-15T00:18Z] INFO  17:18:27,466 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:18Z] INFO  17:18:27,467 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:18Z] INFO  17:18:27,610 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:18Z] INFO  17:18:27,688 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@41fd9d8e
[2016-04-15T00:18Z] INFO  17:18:27,855 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T00:18Z] INFO  17:18:27,857 ProgressMeter -            done    269872.0    41.0 s       2.6 m      100.0%    41.0 s       0.0 s
[2016-04-15T00:18Z] INFO  17:18:27,857 ProgressMeter - Total runtime 41.40 secs, 0.69 min, 0.01 hours
[2016-04-15T00:18Z] INFO  17:18:27,858 MicroScheduler - 185 reads were filtered out during the traversal out of approximately 270057 total reads (0.07%)
[2016-04-15T00:18Z] INFO  17:18:27,858 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:18Z] INFO  17:18:27,858 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:18Z] INFO  17:18:27,859 MicroScheduler -   -> 185 reads (0.07% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:18Z] INFO  17:18:27,874 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:18Z] INFO  17:18:27,947 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-15T00:18Z] INFO  17:18:28,243 IntervalUtils - Processing 15526400 bp from intervals
[2016-04-15T00:18Z] WARN  17:18:28,248 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:18Z] INFO  17:18:28,254 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:18Z] INFO  17:18:28,257 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:18Z] INFO  17:18:28,258 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:18Z] INFO  17:18:28,258 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:18Z] INFO  17:18:28,263 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/12/R14-18106_kapa-NGv3-PE100-NGv3-sort-12_62687959_78225484-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/12/R14-18106_kapa-NGv3-PE100-NGv3-sort-12_62687959_78225484-prep-prealign-realign.intervals -L 12:62687960-78225484 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/12/tx/tmpBnc3Zi/R14-18106_kapa-NGv3-PE100-NGv3-sort-12_62687959_78225484-prep.bam
[2016-04-15T00:18Z] INFO  17:18:28,295 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:18Z] INFO  17:18:28,296 HelpFormatter - Date/Time: 2016/04/14 17:18:28
[2016-04-15T00:18Z] INFO  17:18:28,296 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:18Z] INFO  17:18:28,297 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:18Z] INFO  17:18:28,461 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:18Z] INFO  17:18:28,515 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:18Z] INFO  17:18:28,649 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:18Z] INFO  17:18:28,650 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:18Z] INFO  17:18:28,651 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:18Z] INFO  17:18:28,652 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:18Z] INFO  17:18:28,654 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:18Z] INFO  17:18:28,664 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:18Z] INFO  17:18:28,767 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.10
[2016-04-15T00:18Z] INFO  17:18:28,774 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:18Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-12_31236746_46754992-prep.bam
[2016-04-15T00:18Z] INFO  17:18:28,840 ProgressMeter -            done   1.9748299E7    13.0 s       0.0 s      100.0%    13.0 s       0.0 s
[2016-04-15T00:18Z] INFO  17:18:28,843 ProgressMeter - Total runtime 13.06 secs, 0.22 min, 0.00 hours
[2016-04-15T00:18Z] INFO  17:18:28,847 MicroScheduler - 772 reads were filtered out during the traversal out of approximately 6744 total reads (11.45%)
[2016-04-15T00:18Z] INFO  17:18:28,848 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:18Z] INFO  17:18:28,849 MicroScheduler -   -> 43 reads (0.64% of total) failing BadMateFilter
[2016-04-15T00:18Z] INFO  17:18:28,850 MicroScheduler -   -> 471 reads (6.98% of total) failing DuplicateReadFilter
[2016-04-15T00:18Z] INFO  17:18:28,850 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:18Z] INFO  17:18:28,851 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:18Z] INFO  17:18:28,852 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:18Z] INFO  17:18:28,852 MicroScheduler -   -> 258 reads (3.83% of total) failing MappingQualityZeroFilter
[2016-04-15T00:18Z] INFO  17:18:28,853 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:18Z] INFO  17:18:28,854 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-15T00:18Z] INFO  17:18:28,855 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:18Z] INFO  17:18:29,286 IntervalUtils - Processing 15537525 bp from intervals
[2016-04-15T00:18Z] INFO  17:18:29,303 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:18Z] WARN  17:18:29,312 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:18Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-12_93870729_109490566-prep-prealign.bam
[2016-04-15T00:18Z] GATK pre-alignment ('13', 67477635, 84455642) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:18Z] INFO  17:18:29,429 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:18Z] INFO  17:18:29,534 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:18Z] INFO  17:18:29,535 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:18Z] INFO  17:18:29,546 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:18Z] INFO  17:18:29,558 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:18Z] INFO  17:18:29,757 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:18Z] INFO  17:18:30,015 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:18Z] INFO  17:18:30,018 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:18Z] INFO  17:18:30,019 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:18Z] INFO  17:18:30,020 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:18Z] INFO  17:18:30,021 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:18Z] INFO  17:18:30,024 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/11/R14-18106_kapa-NGv3-PE100-NGv3-sort-11_0_15994658-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/11/R14-18106_kapa-NGv3-PE100-NGv3-sort-11_0_15994658-prep-prealign-realign.intervals -L 11:1-15994658 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/11/tx/tmpH1zO36/R14-18106_kapa-NGv3-PE100-NGv3-sort-11_0_15994658-prep.bam
[2016-04-15T00:18Z] INFO  17:18:30,034 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:18Z] INFO  17:18:30,035 HelpFormatter - Date/Time: 2016/04/14 17:18:30
[2016-04-15T00:18Z] INFO  17:18:30,035 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:18Z] INFO  17:18:30,036 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:18Z] GATK RealignerTargetCreator: R14-18106_kapa-NGv3-PE100-NGv3-sort-12_93870729_109490566-prep-prealign.bam 12:93870730-109490566
[2016-04-15T00:18Z] GATK: RealignerTargetCreator
[2016-04-15T00:18Z] INFO  17:18:30,256 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:18Z] INFO  17:18:30,273 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:18Z] GATK: realign ('13', 0, 19748299) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:18Z] INFO  17:18:30,354 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:18Z] INFO  17:18:30,363 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:18Z] INFO  17:18:30,411 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-15T00:18Z] INFO  17:18:30,907 IntervalUtils - Processing 15994658 bp from intervals
[2016-04-15T00:18Z] WARN  17:18:30,916 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:18Z] INFO  17:18:31,037 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:18Z] INFO  17:18:31,264 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:18Z] INFO  17:18:31,265 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:18Z] INFO  17:18:31,265 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:18Z] INFO  17:18:31,279 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:18Z] INFO  17:18:31,550 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:18Z] INFO  17:18:31,725 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:18Z] INFO  17:18:32,304 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:18Z] INFO  17:18:32,307 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:18Z] INFO  17:18:32,308 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:18Z] INFO  17:18:32,308 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:18Z] INFO  17:18:32,313 HelpFormatter - Program Args: -T PrintReads -L 13:67477636-84455642 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/13/tx/tmpe8KZdL/R14-18106_kapa-NGv3-PE100-NGv3-sort-13_67477635_84455642-prep-prealign.bam
[2016-04-15T00:18Z] INFO  17:18:32,346 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:18Z] INFO  17:18:32,347 HelpFormatter - Date/Time: 2016/04/14 17:18:32
[2016-04-15T00:18Z] INFO  17:18:32,347 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:18Z] INFO  17:18:32,348 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:18Z] INFO  17:18:32,532 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:18Z] INFO  17:18:33,281 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:18Z] INFO  17:18:33,306 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:18Z] INFO  17:18:33,306 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:18Z] INFO  17:18:33,306 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:18Z] INFO  17:18:33,310 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/12/R14-18106_kapa-NGv3-PE100-NGv3-sort-12_93870729_109490566-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/12/tx/tmpX6IjJX/R14-18106_kapa-NGv3-PE100-NGv3-sort-12_93870729_109490566-prep-prealign-realign.intervals -l INFO -L 12:93870730-109490566 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:18Z] INFO  17:18:33,320 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:18Z] INFO  17:18:33,320 HelpFormatter - Date/Time: 2016/04/14 17:18:33
[2016-04-15T00:18Z] INFO  17:18:33,321 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:18Z] INFO  17:18:33,321 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:18Z] INFO  17:18:33,452 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:18Z] INFO  17:18:33,466 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:18Z] INFO  17:18:33,466 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:18Z] INFO  17:18:33,466 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:18Z] INFO  17:18:33,470 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/13/R14-18106_kapa-NGv3-PE100-NGv3-sort-13_0_19748299-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/13/R14-18106_kapa-NGv3-PE100-NGv3-sort-13_0_19748299-prep-prealign-realign.intervals -L 13:1-19748299 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/13/tx/tmpxKK9iS/R14-18106_kapa-NGv3-PE100-NGv3-sort-13_0_19748299-prep.bam
[2016-04-15T00:18Z] INFO  17:18:33,485 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:18Z] INFO  17:18:33,486 HelpFormatter - Date/Time: 2016/04/14 17:18:33
[2016-04-15T00:18Z] INFO  17:18:33,486 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:18Z] INFO  17:18:33,486 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:18Z] INFO  17:18:33,493 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:18Z] INFO  17:18:33,610 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-15T00:18Z] INFO  17:18:33,659 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:18Z] INFO  17:18:33,668 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:18Z] INFO  17:18:33,699 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T00:18Z] INFO  17:18:33,701 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.03
[2016-04-15T00:18Z] INFO  17:18:33,714 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:18Z] INFO  17:18:33,716 IntervalUtils - Processing 16978007 bp from intervals
[2016-04-15T00:18Z] INFO  17:18:33,716 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:18Z] INFO  17:18:33,777 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-15T00:18Z] INFO  17:18:33,791 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:18Z] INFO  17:18:33,839 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:18Z] INFO  17:18:33,849 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:18Z] INFO  17:18:33,922 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-15T00:18Z] INFO  17:18:34,017 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:18Z] INFO  17:18:34,017 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:18Z] INFO  17:18:34,017 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:18Z] INFO  17:18:34,018 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:18Z] INFO  17:18:34,068 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:18Z] INFO  17:18:34,159 IntervalUtils - Processing 15619837 bp from intervals
[2016-04-15T00:18Z] WARN  17:18:34,164 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:18Z] INFO  17:18:34,225 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:18Z] INFO  17:18:34,253 IntervalUtils - Processing 19748299 bp from intervals
[2016-04-15T00:18Z] WARN  17:18:34,258 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:18Z] INFO  17:18:34,276 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:18Z] INFO  17:18:34,382 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:18Z] INFO  17:18:34,555 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:18Z] INFO  17:18:34,556 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:18Z] INFO  17:18:34,556 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:18Z] INFO  17:18:34,557 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:18Z] INFO  17:18:34,605 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:18Z] INFO  17:18:34,606 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:18Z] INFO  17:18:34,607 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:18Z] INFO  17:18:34,608 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:18Z] INFO  17:18:34,640 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@41fd9d8e
[2016-04-15T00:18Z] INFO  17:18:34,669 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:18Z] INFO  17:18:34,706 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:18Z] INFO  17:18:34,821 ProgressMeter -    12:133811027    100002.0    30.0 s       5.0 m       99.5%    30.0 s       0.0 s
[2016-04-15T00:18Z] INFO  17:18:34,844 ProgressMeter -            done   1.5512808E7    23.0 s       1.0 s      100.0%    23.0 s       0.0 s
[2016-04-15T00:18Z] INFO  17:18:34,845 ProgressMeter - Total runtime 23.82 secs, 0.40 min, 0.01 hours
[2016-04-15T00:18Z] INFO  17:18:34,849 MicroScheduler - 41458 reads were filtered out during the traversal out of approximately 492421 total reads (8.42%)
[2016-04-15T00:18Z] INFO  17:18:34,850 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:18Z] INFO  17:18:34,850 MicroScheduler -   -> 1168 reads (0.24% of total) failing BadMateFilter
[2016-04-15T00:18Z] INFO  17:18:34,850 MicroScheduler -   -> 36561 reads (7.42% of total) failing DuplicateReadFilter
[2016-04-15T00:18Z] INFO  17:18:34,850 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:18Z] INFO  17:18:34,851 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:18Z] INFO  17:18:34,851 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:18Z] INFO  17:18:34,851 MicroScheduler -   -> 3729 reads (0.76% of total) failing MappingQualityZeroFilter
[2016-04-15T00:18Z] INFO  17:18:34,851 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:18Z] INFO  17:18:34,852 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-15T00:18Z] INFO  17:18:34,852 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:18Z] INFO  17:18:34,895 ProgressMeter -            done    194286.0    30.0 s       2.6 m       99.5%    30.0 s       0.0 s
[2016-04-15T00:18Z] INFO  17:18:34,896 ProgressMeter - Total runtime 30.08 secs, 0.50 min, 0.01 hours
[2016-04-15T00:18Z] INFO  17:18:34,897 MicroScheduler - 102 reads were filtered out during the traversal out of approximately 194388 total reads (0.05%)
[2016-04-15T00:18Z] INFO  17:18:34,897 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:18Z] INFO  17:18:34,897 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:18Z] INFO  17:18:34,898 MicroScheduler -   -> 102 reads (0.05% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:18Z] INFO  17:18:35,231 ProgressMeter -            done     93582.0     9.0 s     105.0 s       99.8%     9.0 s       0.0 s
[2016-04-15T00:18Z] INFO  17:18:35,232 ProgressMeter - Total runtime 9.84 secs, 0.16 min, 0.00 hours
[2016-04-15T00:18Z] INFO  17:18:35,236 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 93582 total reads (0.00%)
[2016-04-15T00:18Z] INFO  17:18:35,237 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:18Z] INFO  17:18:35,237 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:18Z] INFO  17:18:35,238 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:18Z] INFO  17:18:36,326 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:18Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-12_125267228_133851895-prep-prealign.bam
[2016-04-15T00:18Z] INFO  17:18:36,356 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:18Z] GATK: realign ('11', 110001730, 125514538) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:18Z] INFO  17:18:36,444 ProgressMeter -            done      6683.0     1.0 s       4.6 m      100.0%     1.0 s       0.0 s
[2016-04-15T00:18Z] INFO  17:18:36,444 ProgressMeter - Total runtime 1.84 secs, 0.03 min, 0.00 hours
[2016-04-15T00:18Z] INFO  17:18:36,448 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 6683 total reads (0.00%)
[2016-04-15T00:18Z] INFO  17:18:36,449 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:18Z] INFO  17:18:36,449 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:18Z] INFO  17:18:36,450 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:18Z] INFO  17:18:36,609 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:18Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-12_78334098_93863131-prep.bam
[2016-04-15T00:18Z] GATK RealignerTargetCreator: R14-18106_kapa-NGv3-PE100-NGv3-sort-12_125267228_133851895-prep-prealign.bam 12:125267229-133851895
[2016-04-15T00:18Z] GATK: RealignerTargetCreator
[2016-04-15T00:18Z] GATK pre-alignment ('13', 86368117, 101881935) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:18Z] INFO  17:18:37,970 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:18Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-13_0_19748299-prep.bam
[2016-04-15T00:18Z] GATK pre-alignment ('13', 101890105, 115169878) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:18Z] INFO  17:18:39,368 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:18Z] INFO  17:18:39,371 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:18Z] INFO  17:18:39,372 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:18Z] INFO  17:18:39,372 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:18Z] INFO  17:18:39,377 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/11/R14-18106_kapa-NGv3-PE100-NGv3-sort-11_110001730_125514538-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/11/R14-18106_kapa-NGv3-PE100-NGv3-sort-11_110001730_125514538-prep-prealign-realign.intervals -L 11:110001731-125514538 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/11/tx/tmpT4eMHQ/R14-18106_kapa-NGv3-PE100-NGv3-sort-11_110001730_125514538-prep.bam
[2016-04-15T00:18Z] INFO  17:18:39,387 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:18Z] INFO  17:18:39,398 HelpFormatter - Date/Time: 2016/04/14 17:18:39
[2016-04-15T00:18Z] INFO  17:18:39,399 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:18Z] INFO  17:18:39,400 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:18Z] INFO  17:18:39,665 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:18Z] INFO  17:18:39,860 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:18Z] INFO  17:18:39,883 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:18Z] INFO  17:18:39,913 ProgressMeter -     13:32365975    200002.0    30.0 s       2.5 m       80.0%    37.0 s       7.0 s
[2016-04-15T00:18Z] INFO  17:18:39,942 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:18Z] INFO  17:18:39,945 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-15T00:18Z] INFO  17:18:39,945 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:18Z] INFO  17:18:39,946 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:18Z] INFO  17:18:39,946 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:18Z] INFO  17:18:39,951 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/12/R14-18106_kapa-NGv3-PE100-NGv3-sort-12_125267228_133851895-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/12/tx/tmp23LhD_/R14-18106_kapa-NGv3-PE100-NGv3-sort-12_125267228_133851895-prep-prealign-realign.intervals -l INFO -L 12:125267229-133851895 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:18Z] INFO  17:18:39,960 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:18Z] INFO  17:18:39,961 HelpFormatter - Date/Time: 2016/04/14 17:18:39
[2016-04-15T00:18Z] INFO  17:18:39,962 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:18Z] INFO  17:18:39,962 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:18Z] INFO  17:18:40,065 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:18Z] INFO  17:18:40,299 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:18Z] INFO  17:18:40,303 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:18Z] INFO  17:18:40,303 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:18Z] INFO  17:18:40,303 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:18Z] INFO  17:18:40,308 HelpFormatter - Program Args: -T PrintReads -L 13:86368118-101881935 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/13/tx/tmp5J4OMu/R14-18106_kapa-NGv3-PE100-NGv3-sort-13_86368117_101881935-prep-prealign.bam
[2016-04-15T00:18Z] INFO  17:18:40,317 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:18Z] INFO  17:18:40,325 HelpFormatter - Date/Time: 2016/04/14 17:18:40
[2016-04-15T00:18Z] INFO  17:18:40,326 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:18Z] INFO  17:18:40,327 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:18Z] INFO  17:18:40,365 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T00:18Z] INFO  17:18:40,385 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:18Z] INFO  17:18:40,385 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@5fe152b7
[2016-04-15T00:18Z] INFO  17:18:40,386 IntervalUtils - Processing 15512808 bp from intervals
[2016-04-15T00:18Z] WARN  17:18:40,391 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:18Z] INFO  17:18:40,457 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:18Z] INFO  17:18:40,459 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-15T00:18Z] INFO  17:18:40,509 ProgressMeter -            done    101347.0    18.0 s       3.1 m      100.0%    18.0 s       0.0 s
[2016-04-15T00:18Z] INFO  17:18:40,510 ProgressMeter - Total runtime 18.84 secs, 0.31 min, 0.01 hours
[2016-04-15T00:18Z] INFO  17:18:40,510 MicroScheduler - 132 reads were filtered out during the traversal out of approximately 101479 total reads (0.13%)
[2016-04-15T00:18Z] INFO  17:18:40,511 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:18Z] INFO  17:18:40,511 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:18Z] INFO  17:18:40,511 MicroScheduler -   -> 132 reads (0.13% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:18Z] INFO  17:18:40,515 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:18Z] INFO  17:18:40,584 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:18Z] INFO  17:18:40,598 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:18Z] INFO  17:18:40,599 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:18Z] INFO  17:18:40,599 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:18Z] INFO  17:18:40,774 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:18Z] INFO  17:18:40,777 IntervalUtils - Processing 8584667 bp from intervals
[2016-04-15T00:18Z] WARN  17:18:40,782 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:18Z] INFO  17:18:40,906 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:18Z] INFO  17:18:40,968 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:18Z] INFO  17:18:40,972 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:18Z] INFO  17:18:40,972 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:18Z] INFO  17:18:40,973 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:18Z] INFO  17:18:40,977 HelpFormatter - Program Args: -T PrintReads -L 13:101890106-115169878 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/13/tx/tmphXd294/R14-18106_kapa-NGv3-PE100-NGv3-sort-13_101890105_115169878-prep-prealign.bam
[2016-04-15T00:18Z] INFO  17:18:40,987 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:18Z] INFO  17:18:40,998 HelpFormatter - Date/Time: 2016/04/14 17:18:40
[2016-04-15T00:18Z] INFO  17:18:40,999 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:18Z] INFO  17:18:41,000 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:18Z] INFO  17:18:41,001 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:18Z] INFO  17:18:41,109 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:18Z] INFO  17:18:41,109 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:18Z] INFO  17:18:41,110 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:18Z] INFO  17:18:41,110 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:18Z] INFO  17:18:41,189 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:18Z] INFO  17:18:41,640 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-15T00:18Z] INFO  17:18:41,710 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:18Z] INFO  17:18:41,720 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:18Z] INFO  17:18:41,760 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.04
[2016-04-15T00:18Z] INFO  17:18:41,774 IntervalUtils - Processing 15513818 bp from intervals
[2016-04-15T00:18Z] INFO  17:18:41,839 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:18Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-13_51396767_67205543-prep-prealign.bam
[2016-04-15T00:18Z] INFO  17:18:41,871 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:18Z] INFO  17:18:42,194 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:18Z] INFO  17:18:42,195 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:18Z] INFO  17:18:42,199 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:18Z] INFO  17:18:42,207 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:18Z] INFO  17:18:42,223 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:18Z] GATK RealignerTargetCreator: R14-18106_kapa-NGv3-PE100-NGv3-sort-13_51396767_67205543-prep-prealign.bam 13:51396768-67205543
[2016-04-15T00:18Z] GATK: RealignerTargetCreator
[2016-04-15T00:18Z] INFO  17:18:42,373 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:18Z] INFO  17:18:42,665 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-15T00:18Z] INFO  17:18:42,776 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:18Z] INFO  17:18:42,796 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:18Z] INFO  17:18:42,837 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.04
[2016-04-15T00:18Z] INFO  17:18:42,853 IntervalUtils - Processing 13279773 bp from intervals
[2016-04-15T00:18Z] INFO  17:18:42,959 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:18Z] INFO  17:18:43,250 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:18Z] INFO  17:18:43,251 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:18Z] INFO  17:18:43,252 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:18Z] INFO  17:18:43,252 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:18Z] INFO  17:18:43,266 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:18Z] INFO  17:18:43,420 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:18Z] INFO  17:18:44,327 ProgressMeter -            done    173037.0    14.0 s      85.0 s      100.0%    14.0 s       0.0 s
[2016-04-15T00:18Z] INFO  17:18:44,328 ProgressMeter - Total runtime 14.79 secs, 0.25 min, 0.00 hours
[2016-04-15T00:18Z] INFO  17:18:44,332 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 173037 total reads (0.00%)
[2016-04-15T00:18Z] INFO  17:18:44,333 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:18Z] INFO  17:18:44,334 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:18Z] INFO  17:18:44,334 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:18Z] INFO  17:18:45,055 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@7172f77a
[2016-04-15T00:18Z] INFO  17:18:45,164 ProgressMeter -            done    248882.0    35.0 s       2.4 m      100.0%    35.0 s       0.0 s
[2016-04-15T00:18Z] INFO  17:18:45,165 ProgressMeter - Total runtime 35.27 secs, 0.59 min, 0.01 hours
[2016-04-15T00:18Z] INFO  17:18:45,165 MicroScheduler - 171 reads were filtered out during the traversal out of approximately 249053 total reads (0.07%)
[2016-04-15T00:18Z] INFO  17:18:45,165 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:18Z] INFO  17:18:45,166 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:18Z] INFO  17:18:45,166 MicroScheduler -   -> 171 reads (0.07% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:18Z] INFO  17:18:45,287 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:18Z] INFO  17:18:45,291 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:18Z] INFO  17:18:45,291 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:18Z] INFO  17:18:45,292 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:18Z] INFO  17:18:45,297 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/13/R14-18106_kapa-NGv3-PE100-NGv3-sort-13_51396767_67205543-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/13/tx/tmpVtTiLa/R14-18106_kapa-NGv3-PE100-NGv3-sort-13_51396767_67205543-prep-prealign-realign.intervals -l INFO -L 13:51396768-67205543 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:18Z] INFO  17:18:45,317 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:18Z] INFO  17:18:45,318 HelpFormatter - Date/Time: 2016/04/14 17:18:45
[2016-04-15T00:18Z] INFO  17:18:45,319 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:18Z] INFO  17:18:45,320 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:18Z] INFO  17:18:45,428 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:18Z] INFO  17:18:45,645 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T00:18Z] INFO  17:18:45,661 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:18Z] INFO  17:18:45,723 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-15T00:18Z] INFO  17:18:45,724 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:18Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-12_62687959_78225484-prep.bam
[2016-04-15T00:18Z] INFO  17:18:46,036 ProgressMeter -     12:56713237    600015.0    90.0 s       2.5 m       62.6%     2.4 m      53.0 s
[2016-04-15T00:18Z] INFO  17:18:46,060 IntervalUtils - Processing 15808776 bp from intervals
[2016-04-15T00:18Z] WARN  17:18:46,066 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:18Z] INFO  17:18:46,228 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:18Z] GATK pre-alignment ('14', 0, 19378574) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:18Z] INFO  17:18:46,497 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:18Z] INFO  17:18:46,499 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:18Z] INFO  17:18:46,500 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:18Z] INFO  17:18:46,501 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:18Z] INFO  17:18:46,534 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:18Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-13_19751066_35517251-prep-prealign.bam
[2016-04-15T00:18Z] INFO  17:18:46,663 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@41fd9d8e
[2016-04-15T00:18Z] INFO  17:18:46,754 ProgressMeter -            done    225117.0    29.0 s       2.2 m      100.0%    29.0 s       0.0 s
[2016-04-15T00:18Z] INFO  17:18:46,755 ProgressMeter - Total runtime 29.70 secs, 0.50 min, 0.01 hours
[2016-04-15T00:18Z] INFO  17:18:46,755 MicroScheduler - 141 reads were filtered out during the traversal out of approximately 225258 total reads (0.06%)
[2016-04-15T00:18Z] INFO  17:18:46,755 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:18Z] INFO  17:18:46,755 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:18Z] INFO  17:18:46,756 MicroScheduler -   -> 141 reads (0.06% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:18Z] GATK RealignerTargetCreator: R14-18106_kapa-NGv3-PE100-NGv3-sort-13_19751066_35517251-prep-prealign.bam 13:19751067-35517251
[2016-04-15T00:18Z] GATK: RealignerTargetCreator
[2016-04-15T00:18Z] INFO  17:18:48,006 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@5fe152b7
[2016-04-15T00:18Z] INFO  17:18:48,140 ProgressMeter -            done     88937.0    14.0 s       2.6 m      100.0%    14.0 s       0.0 s
[2016-04-15T00:18Z] INFO  17:18:48,141 ProgressMeter - Total runtime 14.12 secs, 0.24 min, 0.00 hours
[2016-04-15T00:18Z] INFO  17:18:48,143 MicroScheduler - 93 reads were filtered out during the traversal out of approximately 89030 total reads (0.10%)
[2016-04-15T00:18Z] INFO  17:18:48,144 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:18Z] INFO  17:18:48,145 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:18Z] INFO  17:18:48,146 MicroScheduler -   -> 93 reads (0.10% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:18Z] INFO  17:18:48,147 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:18Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-13_35615069_51287376-prep-prealign.bam
[2016-04-15T00:18Z] GATK RealignerTargetCreator: R14-18106_kapa-NGv3-PE100-NGv3-sort-13_35615069_51287376-prep-prealign.bam 13:35615070-51287376
[2016-04-15T00:18Z] GATK: RealignerTargetCreator
[2016-04-15T00:18Z] INFO  17:18:49,523 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:18Z] INFO  17:18:49,527 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:18Z] INFO  17:18:49,527 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:18Z] INFO  17:18:49,528 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:18Z] INFO  17:18:49,533 HelpFormatter - Program Args: -T PrintReads -L 14:1-19378574 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/14/tx/tmpBrQKLK/R14-18106_kapa-NGv3-PE100-NGv3-sort-14_0_19378574-prep-prealign.bam
[2016-04-15T00:18Z] INFO  17:18:49,564 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:18Z] INFO  17:18:49,564 HelpFormatter - Date/Time: 2016/04/14 17:18:49
[2016-04-15T00:18Z] INFO  17:18:49,564 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:18Z] INFO  17:18:49,565 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:18Z] INFO  17:18:49,741 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:18Z] INFO  17:18:49,912 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:18Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-13_67477635_84455642-prep-prealign.bam
[2016-04-15T00:18Z] GATK RealignerTargetCreator: R14-18106_kapa-NGv3-PE100-NGv3-sort-13_67477635_84455642-prep-prealign.bam 13:67477636-84455642
[2016-04-15T00:18Z] GATK: RealignerTargetCreator
[2016-04-15T00:18Z] INFO  17:18:50,330 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:18Z] INFO  17:18:50,333 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:18Z] INFO  17:18:50,334 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:18Z] INFO  17:18:50,334 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:18Z] INFO  17:18:50,339 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/13/R14-18106_kapa-NGv3-PE100-NGv3-sort-13_19751066_35517251-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/13/tx/tmpl_BDXx/R14-18106_kapa-NGv3-PE100-NGv3-sort-13_19751066_35517251-prep-prealign-realign.intervals -l INFO -L 13:19751067-35517251 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:18Z] INFO  17:18:50,376 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:18Z] INFO  17:18:50,377 HelpFormatter - Date/Time: 2016/04/14 17:18:50
[2016-04-15T00:18Z] INFO  17:18:50,378 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:18Z] INFO  17:18:50,383 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:18Z] INFO  17:18:50,478 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:18Z] INFO  17:18:50,667 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T00:18Z] INFO  17:18:50,676 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:18Z] INFO  17:18:50,735 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-15T00:18Z] INFO  17:18:50,829 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-15T00:18Z] INFO  17:18:50,897 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:18Z] INFO  17:18:50,906 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:18Z] INFO  17:18:50,957 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-15T00:18Z] INFO  17:18:50,982 IntervalUtils - Processing 19378574 bp from intervals
[2016-04-15T00:18Z] INFO  17:18:51,064 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:18Z] INFO  17:18:51,096 IntervalUtils - Processing 15766185 bp from intervals
[2016-04-15T00:18Z] WARN  17:18:51,101 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:18Z] INFO  17:18:51,185 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:18Z] INFO  17:18:51,210 ProgressMeter -     11:62286783    400007.0    30.0 s      77.0 s       97.5%    30.0 s       0.0 s
[2016-04-15T00:18Z] INFO  17:18:51,335 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:18Z] INFO  17:18:51,337 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:18Z] INFO  17:18:51,337 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:18Z] INFO  17:18:51,338 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:18Z] INFO  17:18:51,476 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:18Z] INFO  17:18:51,477 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:18Z] INFO  17:18:51,478 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:18Z] INFO  17:18:51,478 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:18Z] INFO  17:18:51,510 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:18Z] INFO  17:18:51,513 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:18Z] INFO  17:18:51,750 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:18Z] INFO  17:18:51,753 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:18Z] INFO  17:18:51,754 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:18Z] INFO  17:18:51,754 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:18Z] INFO  17:18:51,759 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/13/R14-18106_kapa-NGv3-PE100-NGv3-sort-13_35615069_51287376-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/13/tx/tmpBWuvgS/R14-18106_kapa-NGv3-PE100-NGv3-sort-13_35615069_51287376-prep-prealign-realign.intervals -l INFO -L 13:35615070-51287376 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:18Z] INFO  17:18:51,806 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:18Z] INFO  17:18:51,807 HelpFormatter - Date/Time: 2016/04/14 17:18:51
[2016-04-15T00:18Z] INFO  17:18:51,807 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:18Z] INFO  17:18:51,808 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:18Z] INFO  17:18:51,913 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:18Z] INFO  17:18:52,108 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T00:18Z] INFO  17:18:52,128 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:18Z] INFO  17:18:52,217 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.09
[2016-04-15T00:18Z] INFO  17:18:52,406 ProgressMeter -            done   1.5637181E7    24.0 s       1.0 s      100.0%    24.0 s       0.0 s
[2016-04-15T00:18Z] INFO  17:18:52,407 ProgressMeter - Total runtime 24.98 secs, 0.42 min, 0.01 hours
[2016-04-15T00:18Z] INFO  17:18:52,411 MicroScheduler - 55725 reads were filtered out during the traversal out of approximately 538714 total reads (10.34%)
[2016-04-15T00:18Z] INFO  17:18:52,413 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:18Z] INFO  17:18:52,413 MicroScheduler -   -> 1146 reads (0.21% of total) failing BadMateFilter
[2016-04-15T00:18Z] INFO  17:18:52,414 MicroScheduler -   -> 39265 reads (7.29% of total) failing DuplicateReadFilter
[2016-04-15T00:18Z] INFO  17:18:52,415 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:18Z] INFO  17:18:52,415 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:18Z] INFO  17:18:52,416 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:18Z] INFO  17:18:52,416 MicroScheduler -   -> 15314 reads (2.84% of total) failing MappingQualityZeroFilter
[2016-04-15T00:18Z] INFO  17:18:52,417 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:18Z] INFO  17:18:52,418 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-15T00:18Z] INFO  17:18:52,418 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:18Z] INFO  17:18:52,591 IntervalUtils - Processing 15672307 bp from intervals
[2016-04-15T00:18Z] WARN  17:18:52,596 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:18Z] INFO  17:18:52,665 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:18Z] INFO  17:18:52,878 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:18Z] INFO  17:18:52,879 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:18Z] INFO  17:18:52,880 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:18Z] INFO  17:18:52,881 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:18Z] INFO  17:18:52,964 ProgressMeter -            done   1.5619837E7    18.0 s       1.0 s      100.0%    18.0 s       0.0 s
[2016-04-15T00:18Z] INFO  17:18:52,966 ProgressMeter - Total runtime 18.41 secs, 0.31 min, 0.01 hours
[2016-04-15T00:18Z] INFO  17:18:52,970 MicroScheduler - 22715 reads were filtered out during the traversal out of approximately 271736 total reads (8.36%)
[2016-04-15T00:18Z] INFO  17:18:52,971 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:18Z] INFO  17:18:52,972 MicroScheduler -   -> 781 reads (0.29% of total) failing BadMateFilter
[2016-04-15T00:18Z] INFO  17:18:52,972 MicroScheduler -   -> 20205 reads (7.44% of total) failing DuplicateReadFilter
[2016-04-15T00:18Z] INFO  17:18:52,973 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:18Z] INFO  17:18:52,973 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:18Z] INFO  17:18:52,974 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:18Z] INFO  17:18:52,975 MicroScheduler -   -> 1729 reads (0.64% of total) failing MappingQualityZeroFilter
[2016-04-15T00:18Z] INFO  17:18:52,975 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:18Z] INFO  17:18:52,976 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-15T00:18Z] INFO  17:18:52,977 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:18Z] INFO  17:18:53,029 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:18Z] INFO  17:18:53,032 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:18Z] INFO  17:18:53,033 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:18Z] INFO  17:18:53,033 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:18Z] INFO  17:18:53,038 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/13/R14-18106_kapa-NGv3-PE100-NGv3-sort-13_67477635_84455642-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/13/tx/tmpkeDMt1/R14-18106_kapa-NGv3-PE100-NGv3-sort-13_67477635_84455642-prep-prealign-realign.intervals -l INFO -L 13:67477636-84455642 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:18Z] INFO  17:18:53,047 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:18Z] INFO  17:18:53,047 HelpFormatter - Date/Time: 2016/04/14 17:18:53
[2016-04-15T00:18Z] INFO  17:18:53,047 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:18Z] INFO  17:18:53,047 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:18Z] INFO  17:18:53,210 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:18Z] INFO  17:18:53,478 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T00:18Z] INFO  17:18:53,487 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:18Z] INFO  17:18:53,571 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-15T00:18Z] INFO  17:18:53,586 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@41fd9d8e
[2016-04-15T00:18Z] INFO  17:18:53,653 ProgressMeter -            done      3731.0     2.0 s       9.7 m      100.0%     2.0 s       0.0 s
[2016-04-15T00:18Z] INFO  17:18:53,654 ProgressMeter - Total runtime 2.18 secs, 0.04 min, 0.00 hours
[2016-04-15T00:18Z] INFO  17:18:53,655 MicroScheduler - 5 reads were filtered out during the traversal out of approximately 3736 total reads (0.13%)
[2016-04-15T00:18Z] INFO  17:18:53,655 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:18Z] INFO  17:18:53,655 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:18Z] INFO  17:18:53,656 MicroScheduler -   -> 5 reads (0.13% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:18Z] INFO  17:18:53,829 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:18Z] INFO  17:18:53,851 ProgressMeter -            done   8584667.0    12.0 s       1.0 s      100.0%    12.0 s       0.0 s
[2016-04-15T00:18Z] INFO  17:18:53,852 ProgressMeter - Total runtime 12.74 secs, 0.21 min, 0.00 hours
[2016-04-15T00:18Z] INFO  17:18:53,855 MicroScheduler - 25261 reads were filtered out during the traversal out of approximately 195210 total reads (12.94%)
[2016-04-15T00:18Z] INFO  17:18:53,856 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:18Z] INFO  17:18:53,856 MicroScheduler -   -> 519 reads (0.27% of total) failing BadMateFilter
[2016-04-15T00:18Z] INFO  17:18:53,857 MicroScheduler -   -> 14277 reads (7.31% of total) failing DuplicateReadFilter
[2016-04-15T00:18Z] INFO  17:18:53,857 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:18Z] INFO  17:18:53,857 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:18Z] INFO  17:18:53,857 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:18Z] INFO  17:18:53,857 MicroScheduler -   -> 10465 reads (5.36% of total) failing MappingQualityZeroFilter
[2016-04-15T00:18Z] INFO  17:18:53,858 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:18Z] INFO  17:18:53,858 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-15T00:18Z] INFO  17:18:53,858 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:18Z] GATK: realign ('12', 0, 15637181) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:18Z] INFO  17:18:53,877 IntervalUtils - Processing 16978007 bp from intervals
[2016-04-15T00:18Z] WARN  17:18:53,882 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:18Z] INFO  17:18:53,965 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:18Z] INFO  17:18:54,196 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:18Z] INFO  17:18:54,197 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:18Z] INFO  17:18:54,198 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:18Z] INFO  17:18:54,199 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:18Z] INFO  17:18:54,252 ProgressMeter -            done    535140.0    33.0 s      63.0 s      100.0%    33.0 s       0.0 s
[2016-04-15T00:18Z] INFO  17:18:54,253 ProgressMeter - Total runtime 33.91 secs, 0.57 min, 0.01 hours
[2016-04-15T00:18Z] INFO  17:18:54,256 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 535140 total reads (0.00%)
[2016-04-15T00:18Z] INFO  17:18:54,257 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:18Z] INFO  17:18:54,257 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:18Z] INFO  17:18:54,257 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:18Z] INFO  17:18:54,342 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:18Z] GATK: realign ('12', 93870729, 109490566) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:18Z] INFO  17:18:54,925 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:18Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-14_0_19378574-prep-prealign.bam
[2016-04-15T00:18Z] GATK RealignerTargetCreator: R14-18106_kapa-NGv3-PE100-NGv3-sort-14_0_19378574-prep-prealign.bam 14:1-19378574
[2016-04-15T00:18Z] GATK: RealignerTargetCreator
[2016-04-15T00:18Z] INFO  17:18:55,282 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:18Z] GATK: realign ('12', 125267228, 133851895) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:18Z] INFO  17:18:56,008 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:18Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-11_47158866_62678572-prep.bam
[2016-04-15T00:18Z] INFO  17:18:56,753 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:18Z] INFO  17:18:56,757 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:18Z] INFO  17:18:56,757 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:18Z] INFO  17:18:56,758 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:18Z] INFO  17:18:56,762 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/12/R14-18106_kapa-NGv3-PE100-NGv3-sort-12_0_15637181-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/12/R14-18106_kapa-NGv3-PE100-NGv3-sort-12_0_15637181-prep-prealign-realign.intervals -L 12:1-15637181 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/12/tx/tmpPeKuST/R14-18106_kapa-NGv3-PE100-NGv3-sort-12_0_15637181-prep.bam
[2016-04-15T00:18Z] INFO  17:18:56,802 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:18Z] INFO  17:18:56,803 HelpFormatter - Date/Time: 2016/04/14 17:18:56
[2016-04-15T00:18Z] INFO  17:18:56,804 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:18Z] INFO  17:18:56,804 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:18Z] INFO  17:18:57,031 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:18Z] INFO  17:18:57,059 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:18Z] INFO  17:18:57,063 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:18Z] INFO  17:18:57,063 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:18Z] INFO  17:18:57,064 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:18Z] INFO  17:18:57,068 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/12/R14-18106_kapa-NGv3-PE100-NGv3-sort-12_93870729_109490566-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/12/R14-18106_kapa-NGv3-PE100-NGv3-sort-12_93870729_109490566-prep-prealign-realign.intervals -L 12:93870730-109490566 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/12/tx/tmp11zQJ9/R14-18106_kapa-NGv3-PE100-NGv3-sort-12_93870729_109490566-prep.bam
[2016-04-15T00:18Z] INFO  17:18:57,101 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:18Z] INFO  17:18:57,112 HelpFormatter - Date/Time: 2016/04/14 17:18:57
[2016-04-15T00:18Z] INFO  17:18:57,113 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:18Z] INFO  17:18:57,114 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:18Z] INFO  17:18:57,199 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:18Z] INFO  17:18:57,220 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:18Z] INFO  17:18:57,298 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-15T00:18Z] INFO  17:18:57,381 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:18Z] INFO  17:18:57,565 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:18Z] INFO  17:18:57,585 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:18Z] INFO  17:18:57,675 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.09
[2016-04-15T00:18Z] INFO  17:18:57,787 IntervalUtils - Processing 15637181 bp from intervals
[2016-04-15T00:18Z] WARN  17:18:57,792 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:18Z] GATK pre-alignment ('14', 19553416, 35066851) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:18Z] INFO  17:18:57,846 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:18Z] INFO  17:18:57,849 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:18Z] INFO  17:18:57,850 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:18Z] INFO  17:18:57,850 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:18Z] INFO  17:18:57,855 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/14/R14-18106_kapa-NGv3-PE100-NGv3-sort-14_0_19378574-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/14/tx/tmp9EXi8B/R14-18106_kapa-NGv3-PE100-NGv3-sort-14_0_19378574-prep-prealign-realign.intervals -l INFO -L 14:1-19378574 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:18Z] INFO  17:18:57,873 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:18Z] INFO  17:18:57,874 HelpFormatter - Date/Time: 2016/04/14 17:18:57
[2016-04-15T00:18Z] INFO  17:18:57,875 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:18Z] INFO  17:18:57,875 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:18Z] INFO  17:18:57,901 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:18Z] INFO  17:18:57,962 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:18Z] INFO  17:18:57,968 ProgressMeter -    12:123494435    400007.0    60.0 s       2.5 m       88.8%    67.0 s       7.0 s
[2016-04-15T00:18Z] INFO  17:18:58,063 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:18Z] INFO  17:18:58,069 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:18Z] INFO  17:18:58,071 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:18Z] INFO  17:18:58,071 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:18Z] INFO  17:18:58,117 IntervalUtils - Processing 15619837 bp from intervals
[2016-04-15T00:18Z] WARN  17:18:58,123 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:18Z] INFO  17:18:58,132 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T00:18Z] INFO  17:18:58,141 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:18Z] INFO  17:18:58,204 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-15T00:18Z] INFO  17:18:58,210 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:18Z] INFO  17:18:58,267 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:18Z] INFO  17:18:58,280 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:18Z] INFO  17:18:58,284 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:18Z] INFO  17:18:58,285 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:18Z] INFO  17:18:58,285 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:18Z] INFO  17:18:58,290 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/12/R14-18106_kapa-NGv3-PE100-NGv3-sort-12_125267228_133851895-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/12/R14-18106_kapa-NGv3-PE100-NGv3-sort-12_125267228_133851895-prep-prealign-realign.intervals -L 12:125267229-133851895 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/12/tx/tmpW2e5yq/R14-18106_kapa-NGv3-PE100-NGv3-sort-12_125267228_133851895-prep.bam
[2016-04-15T00:18Z] INFO  17:18:58,300 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:18Z] INFO  17:18:58,300 HelpFormatter - Date/Time: 2016/04/14 17:18:58
[2016-04-15T00:18Z] INFO  17:18:58,300 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:18Z] INFO  17:18:58,301 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:18Z] INFO  17:18:58,322 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@7172f77a
[2016-04-15T00:18Z] INFO  17:18:58,328 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:18Z] INFO  17:18:58,330 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:18Z] INFO  17:18:58,330 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:18Z] INFO  17:18:58,331 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:18Z] INFO  17:18:58,427 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:18Z] INFO  17:18:58,486 ProgressMeter -            done    109897.0    16.0 s       2.5 m      100.0%    16.0 s       0.0 s
[2016-04-15T00:18Z] INFO  17:18:58,487 ProgressMeter - Total runtime 16.29 secs, 0.27 min, 0.00 hours
[2016-04-15T00:18Z] INFO  17:18:58,487 MicroScheduler - 121 reads were filtered out during the traversal out of approximately 110018 total reads (0.11%)
[2016-04-15T00:18Z] INFO  17:18:58,487 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:18Z] INFO  17:18:58,488 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:18Z] INFO  17:18:58,488 MicroScheduler -   -> 121 reads (0.11% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:18Z] INFO  17:18:58,505 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:18Z] INFO  17:18:58,550 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:18Z] INFO  17:18:58,627 IntervalUtils - Processing 19378574 bp from intervals
[2016-04-15T00:18Z] WARN  17:18:58,633 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:18Z] INFO  17:18:58,654 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:18Z] INFO  17:18:58,668 ProgressMeter -     11:77638293   1.4883127E7    30.0 s       2.0 s       95.9%    31.0 s       1.0 s
[2016-04-15T00:18Z] INFO  17:18:58,713 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:18Z] INFO  17:18:58,723 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:18Z] INFO  17:18:58,733 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:18Z] INFO  17:18:58,771 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-15T00:18Z] INFO  17:18:59,101 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:18Z] INFO  17:18:59,102 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:18Z] INFO  17:18:59,102 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:18Z] INFO  17:18:59,102 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:18Z] INFO  17:18:59,176 IntervalUtils - Processing 8584667 bp from intervals
[2016-04-15T00:18Z] WARN  17:18:59,191 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:18Z] INFO  17:18:59,288 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:18Z] INFO  17:18:59,395 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:18Z] INFO  17:18:59,395 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:18Z] INFO  17:18:59,408 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:18Z] INFO  17:18:59,409 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:18Z] INFO  17:18:59,600 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:18Z] INFO  17:18:59,748 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:18Z] INFO  17:18:59,978 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:18Z] INFO  17:18:59,997 ProgressMeter -            done   1.55264E7    31.0 s       2.0 s      100.0%    31.0 s       0.0 s
[2016-04-15T00:18Z] INFO  17:18:59,998 ProgressMeter - Total runtime 31.35 secs, 0.52 min, 0.01 hours
[2016-04-15T00:19Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-13_86368117_101881935-prep-prealign.bam
[2016-04-15T00:19Z] INFO  17:19:00,012 MicroScheduler - 71545 reads were filtered out during the traversal out of approximately 867445 total reads (8.25%)
[2016-04-15T00:19Z] INFO  17:19:00,014 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:19Z] INFO  17:19:00,015 MicroScheduler -   -> 1813 reads (0.21% of total) failing BadMateFilter
[2016-04-15T00:19Z] INFO  17:19:00,016 MicroScheduler -   -> 64962 reads (7.49% of total) failing DuplicateReadFilter
[2016-04-15T00:19Z] INFO  17:19:00,016 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:19Z] INFO  17:19:00,017 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:19Z] INFO  17:19:00,030 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:19Z] INFO  17:19:00,031 MicroScheduler -   -> 4770 reads (0.55% of total) failing MappingQualityZeroFilter
[2016-04-15T00:19Z] INFO  17:19:00,032 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:19Z] INFO  17:19:00,032 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-15T00:19Z] INFO  17:19:00,032 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:19Z] GATK RealignerTargetCreator: R14-18106_kapa-NGv3-PE100-NGv3-sort-13_86368117_101881935-prep-prealign.bam 13:86368118-101881935
[2016-04-15T00:19Z] GATK: RealignerTargetCreator
[2016-04-15T00:19Z] INFO  17:19:00,452 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:19Z] INFO  17:19:00,456 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:19Z] INFO  17:19:00,457 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:19Z] INFO  17:19:00,457 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:19Z] INFO  17:19:00,462 HelpFormatter - Program Args: -T PrintReads -L 14:19553417-35066851 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/14/tx/tmpq1ELvp/R14-18106_kapa-NGv3-PE100-NGv3-sort-14_19553416_35066851-prep-prealign.bam
[2016-04-15T00:19Z] INFO  17:19:00,485 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:19Z] INFO  17:19:00,486 HelpFormatter - Date/Time: 2016/04/14 17:19:00
[2016-04-15T00:19Z] INFO  17:19:00,486 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:19Z] INFO  17:19:00,487 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:19Z] INFO  17:19:00,740 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:19Z] INFO  17:19:01,300 ProgressMeter -      11:2159740    300004.0    30.0 s     100.0 s       13.5%     3.7 m       3.2 m
[2016-04-15T00:19Z] INFO  17:19:01,444 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:19Z] GATK: realign ('11', 62744265, 78270665) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:19Z] INFO  17:19:01,968 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-15T00:19Z] INFO  17:19:02,032 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:19Z] INFO  17:19:02,042 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:19Z] INFO  17:19:02,085 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.04
[2016-04-15T00:19Z] INFO  17:19:02,105 IntervalUtils - Processing 15513435 bp from intervals
[2016-04-15T00:19Z] INFO  17:19:02,257 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:19Z] INFO  17:19:02,353 ProgressMeter -            done   1.5808776E7    15.0 s       1.0 s      100.0%    15.0 s       0.0 s
[2016-04-15T00:19Z] INFO  17:19:02,354 ProgressMeter - Total runtime 15.86 secs, 0.26 min, 0.00 hours
[2016-04-15T00:19Z] INFO  17:19:02,359 MicroScheduler - 28333 reads were filtered out during the traversal out of approximately 102411 total reads (27.67%)
[2016-04-15T00:19Z] INFO  17:19:02,360 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:19Z] INFO  17:19:02,360 MicroScheduler -   -> 485 reads (0.47% of total) failing BadMateFilter
[2016-04-15T00:19Z] INFO  17:19:02,361 MicroScheduler -   -> 6241 reads (6.09% of total) failing DuplicateReadFilter
[2016-04-15T00:19Z] INFO  17:19:02,362 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:19Z] INFO  17:19:02,362 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:19Z] INFO  17:19:02,363 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:19Z] INFO  17:19:02,364 MicroScheduler -   -> 21607 reads (21.10% of total) failing MappingQualityZeroFilter
[2016-04-15T00:19Z] INFO  17:19:02,365 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:19Z] INFO  17:19:02,365 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-15T00:19Z] INFO  17:19:02,366 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:19Z] INFO  17:19:02,529 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:19Z] INFO  17:19:02,530 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:19Z] INFO  17:19:02,531 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:19Z] INFO  17:19:02,531 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:19Z] INFO  17:19:02,553 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:19Z] INFO  17:19:02,676 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:19Z] INFO  17:19:03,224 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:19Z] INFO  17:19:03,228 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:19Z] INFO  17:19:03,228 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:19Z] INFO  17:19:03,229 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:19Z] INFO  17:19:03,234 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/13/R14-18106_kapa-NGv3-PE100-NGv3-sort-13_86368117_101881935-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/13/tx/tmpn1SXiI/R14-18106_kapa-NGv3-PE100-NGv3-sort-13_86368117_101881935-prep-prealign-realign.intervals -l INFO -L 13:86368118-101881935 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:19Z] INFO  17:19:03,243 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:19Z] INFO  17:19:03,254 HelpFormatter - Date/Time: 2016/04/14 17:19:03
[2016-04-15T00:19Z] INFO  17:19:03,255 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:19Z] INFO  17:19:03,256 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:19Z] INFO  17:19:03,399 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:19Z] INFO  17:19:03,611 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T00:19Z] INFO  17:19:03,621 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:19Z] INFO  17:19:03,703 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-15T00:19Z] INFO  17:19:03,732 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:19Z] GATK: realign ('13', 51396767, 67205543) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:19Z] INFO  17:19:04,078 IntervalUtils - Processing 15513818 bp from intervals
[2016-04-15T00:19Z] WARN  17:19:04,083 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:19Z] INFO  17:19:04,181 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:19Z] INFO  17:19:04,416 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:19Z] INFO  17:19:04,417 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:19Z] INFO  17:19:04,418 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:19Z] INFO  17:19:04,419 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:19Z] INFO  17:19:04,510 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:19Z] INFO  17:19:04,513 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:19Z] INFO  17:19:04,514 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:19Z] INFO  17:19:04,514 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:19Z] INFO  17:19:04,519 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/11/R14-18106_kapa-NGv3-PE100-NGv3-sort-11_62744265_78270665-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/11/R14-18106_kapa-NGv3-PE100-NGv3-sort-11_62744265_78270665-prep-prealign-realign.intervals -L 11:62744266-78270665 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/11/tx/tmptR1N8R/R14-18106_kapa-NGv3-PE100-NGv3-sort-11_62744265_78270665-prep.bam
[2016-04-15T00:19Z] INFO  17:19:04,568 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:19Z] INFO  17:19:04,569 HelpFormatter - Date/Time: 2016/04/14 17:19:04
[2016-04-15T00:19Z] INFO  17:19:04,569 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:19Z] INFO  17:19:04,570 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:19Z] INFO  17:19:04,842 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:19Z] INFO  17:19:04,994 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:19Z] INFO  17:19:05,016 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:19Z] INFO  17:19:05,088 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-15T00:19Z] INFO  17:19:05,549 IntervalUtils - Processing 15526400 bp from intervals
[2016-04-15T00:19Z] WARN  17:19:05,554 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:19Z] INFO  17:19:05,651 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:19Z] INFO  17:19:05,877 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@5fe152b7
[2016-04-15T00:19Z] INFO  17:19:05,887 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:19Z] INFO  17:19:05,888 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:19Z] INFO  17:19:05,889 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:19Z] INFO  17:19:05,890 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:19Z] INFO  17:19:06,047 ProgressMeter -            done    575948.0    68.0 s     119.0 s      100.0%    68.0 s       0.0 s
[2016-04-15T00:19Z] INFO  17:19:06,048 ProgressMeter - Total runtime 68.91 secs, 1.15 min, 0.02 hours
[2016-04-15T00:19Z] INFO  17:19:06,049 MicroScheduler - 262 reads were filtered out during the traversal out of approximately 576210 total reads (0.05%)
[2016-04-15T00:19Z] INFO  17:19:06,050 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:19Z] INFO  17:19:06,050 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:19Z] INFO  17:19:06,051 MicroScheduler -   -> 262 reads (0.05% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:19Z] INFO  17:19:06,102 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:19Z] INFO  17:19:06,362 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:19Z] INFO  17:19:06,919 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:19Z] INFO  17:19:06,922 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:19Z] INFO  17:19:06,923 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:19Z] INFO  17:19:06,923 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:19Z] INFO  17:19:06,928 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/13/R14-18106_kapa-NGv3-PE100-NGv3-sort-13_51396767_67205543-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/13/R14-18106_kapa-NGv3-PE100-NGv3-sort-13_51396767_67205543-prep-prealign-realign.intervals -L 13:51396768-67205543 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/13/tx/tmpPWtoPM/R14-18106_kapa-NGv3-PE100-NGv3-sort-13_51396767_67205543-prep.bam
[2016-04-15T00:19Z] INFO  17:19:06,945 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:19Z] INFO  17:19:06,946 HelpFormatter - Date/Time: 2016/04/14 17:19:06
[2016-04-15T00:19Z] INFO  17:19:06,946 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:19Z] INFO  17:19:06,946 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:19Z] INFO  17:19:07,152 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:19Z] INFO  17:19:07,265 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:19Z] INFO  17:19:07,274 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:19Z] INFO  17:19:07,334 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-15T00:19Z] INFO  17:19:07,517 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:19Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-12_109494486_125263132-prep-prealign.bam
[2016-04-15T00:19Z] INFO  17:19:07,748 IntervalUtils - Processing 15808776 bp from intervals
[2016-04-15T00:19Z] WARN  17:19:07,764 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:19Z] INFO  17:19:07,897 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:19Z] INFO  17:19:08,040 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:19Z] INFO  17:19:08,042 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:19Z] INFO  17:19:08,042 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:19Z] INFO  17:19:08,043 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:19Z] INFO  17:19:08,178 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:19Z] INFO  17:19:08,369 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:19Z] INFO  17:19:08,618 ProgressMeter -            done   1.9378574E7     9.0 s       0.0 s      100.0%     9.0 s       0.0 s
[2016-04-15T00:19Z] INFO  17:19:08,619 ProgressMeter - Total runtime 9.52 secs, 0.16 min, 0.00 hours
[2016-04-15T00:19Z] INFO  17:19:08,623 MicroScheduler - 1568 reads were filtered out during the traversal out of approximately 3731 total reads (42.03%)
[2016-04-15T00:19Z] INFO  17:19:08,624 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:19Z] INFO  17:19:08,625 MicroScheduler -   -> 11 reads (0.29% of total) failing BadMateFilter
[2016-04-15T00:19Z] INFO  17:19:08,626 MicroScheduler -   -> 168 reads (4.50% of total) failing DuplicateReadFilter
[2016-04-15T00:19Z] INFO  17:19:08,626 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:19Z] INFO  17:19:08,627 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:19Z] INFO  17:19:08,628 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:19Z] INFO  17:19:08,628 MicroScheduler -   -> 1389 reads (37.23% of total) failing MappingQualityZeroFilter
[2016-04-15T00:19Z] INFO  17:19:08,629 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:19Z] INFO  17:19:08,630 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-15T00:19Z] INFO  17:19:08,630 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:19Z] INFO  17:19:09,453 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@7172f77a
[2016-04-15T00:19Z] GATK RealignerTargetCreator: R14-18106_kapa-NGv3-PE100-NGv3-sort-12_109494486_125263132-prep-prealign.bam 12:109494487-125263132
[2016-04-15T00:19Z] GATK: RealignerTargetCreator
[2016-04-15T00:19Z] INFO  17:19:09,460 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@7172f77a
[2016-04-15T00:19Z] INFO  17:19:09,597 ProgressMeter -            done   1.5766185E7    18.0 s       1.0 s      100.0%    18.0 s       0.0 s
[2016-04-15T00:19Z] INFO  17:19:09,599 ProgressMeter - Total runtime 18.26 secs, 0.30 min, 0.01 hours
[2016-04-15T00:19Z] INFO  17:19:09,607 MicroScheduler - 21418 reads were filtered out during the traversal out of approximately 249967 total reads (8.57%)
[2016-04-15T00:19Z] INFO  17:19:09,608 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:19Z] INFO  17:19:09,609 MicroScheduler -   -> 734 reads (0.29% of total) failing BadMateFilter
[2016-04-15T00:19Z] INFO  17:19:09,610 MicroScheduler -   -> 18514 reads (7.41% of total) failing DuplicateReadFilter
[2016-04-15T00:19Z] INFO  17:19:09,611 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:19Z] INFO  17:19:09,612 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:19Z] INFO  17:19:09,612 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:19Z] INFO  17:19:09,613 MicroScheduler -   -> 2170 reads (0.87% of total) failing MappingQualityZeroFilter
[2016-04-15T00:19Z] INFO  17:19:09,614 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:19Z] INFO  17:19:09,615 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-15T00:19Z] INFO  17:19:09,615 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:19Z] INFO  17:19:09,683 ProgressMeter -            done    829889.0   113.0 s       2.3 m      100.0%   113.0 s       0.0 s
[2016-04-15T00:19Z] INFO  17:19:09,684 ProgressMeter - Total runtime 113.69 secs, 1.89 min, 0.03 hours
[2016-04-15T00:19Z] INFO  17:19:09,684 MicroScheduler - 344 reads were filtered out during the traversal out of approximately 830233 total reads (0.04%)
[2016-04-15T00:19Z] INFO  17:19:09,685 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:19Z] INFO  17:19:09,685 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:19Z] INFO  17:19:09,686 MicroScheduler -   -> 344 reads (0.04% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:19Z] INFO  17:19:09,763 ProgressMeter -            done    201708.0    26.0 s       2.2 m       99.4%    26.0 s       0.0 s
[2016-04-15T00:19Z] INFO  17:19:09,763 ProgressMeter - Total runtime 26.51 secs, 0.44 min, 0.01 hours
[2016-04-15T00:19Z] INFO  17:19:09,764 MicroScheduler - 146 reads were filtered out during the traversal out of approximately 201854 total reads (0.07%)
[2016-04-15T00:19Z] INFO  17:19:09,764 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:19Z] INFO  17:19:09,765 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:19Z] INFO  17:19:09,765 MicroScheduler -   -> 146 reads (0.07% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:19Z] INFO  17:19:09,991 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:19Z] GATK: realign ('14', 0, 19378574) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:19Z] INFO  17:19:10,424 ProgressMeter -            done   1.6978007E7    16.0 s       0.0 s      100.0%    16.0 s       0.0 s
[2016-04-15T00:19Z] INFO  17:19:10,425 ProgressMeter - Total runtime 16.23 secs, 0.27 min, 0.00 hours
[2016-04-15T00:19Z] INFO  17:19:10,428 MicroScheduler - 7485 reads were filtered out during the traversal out of approximately 89622 total reads (8.35%)
[2016-04-15T00:19Z] INFO  17:19:10,430 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:19Z] INFO  17:19:10,430 MicroScheduler -   -> 517 reads (0.58% of total) failing BadMateFilter
[2016-04-15T00:19Z] INFO  17:19:10,431 MicroScheduler -   -> 6285 reads (7.01% of total) failing DuplicateReadFilter
[2016-04-15T00:19Z] INFO  17:19:10,432 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:19Z] INFO  17:19:10,432 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:19Z] INFO  17:19:10,433 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:19Z] INFO  17:19:10,434 MicroScheduler -   -> 683 reads (0.76% of total) failing MappingQualityZeroFilter
[2016-04-15T00:19Z] INFO  17:19:10,434 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:19Z] INFO  17:19:10,435 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-15T00:19Z] INFO  17:19:10,435 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:19Z] INFO  17:19:11,046 ProgressMeter -            done    489242.0    30.0 s      62.0 s      100.0%    30.0 s       0.0 s
[2016-04-15T00:19Z] INFO  17:19:11,046 ProgressMeter - Total runtime 30.45 secs, 0.51 min, 0.01 hours
[2016-04-15T00:19Z] INFO  17:19:11,050 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 489242 total reads (0.00%)
[2016-04-15T00:19Z] INFO  17:19:11,051 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:19Z] INFO  17:19:11,051 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:19Z] INFO  17:19:11,051 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:19Z] INFO  17:19:11,142 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:19Z] GATK: realign ('13', 19751066, 35517251) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:19Z] INFO  17:19:11,296 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:19Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-12_46756066_62654284-prep-prealign.bam
[2016-04-15T00:19Z] INFO  17:19:11,457 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:19Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-13_101890105_115169878-prep-prealign.bam
[2016-04-15T00:19Z] INFO  17:19:11,555 ProgressMeter -            done   1.5672307E7    18.0 s       1.0 s      100.0%    18.0 s       0.0 s
[2016-04-15T00:19Z] INFO  17:19:11,556 ProgressMeter - Total runtime 18.68 secs, 0.31 min, 0.01 hours
[2016-04-15T00:19Z] INFO  17:19:11,559 MicroScheduler - 19133 reads were filtered out during the traversal out of approximately 226801 total reads (8.44%)
[2016-04-15T00:19Z] INFO  17:19:11,560 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:19Z] INFO  17:19:11,560 MicroScheduler -   -> 735 reads (0.32% of total) failing BadMateFilter
[2016-04-15T00:19Z] INFO  17:19:11,561 MicroScheduler -   -> 17265 reads (7.61% of total) failing DuplicateReadFilter
[2016-04-15T00:19Z] INFO  17:19:11,561 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:19Z] INFO  17:19:11,561 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:19Z] INFO  17:19:11,561 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:19Z] INFO  17:19:11,562 MicroScheduler -   -> 1133 reads (0.50% of total) failing MappingQualityZeroFilter
[2016-04-15T00:19Z] INFO  17:19:11,562 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:19Z] INFO  17:19:11,562 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-15T00:19Z] INFO  17:19:11,562 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:19Z] INFO  17:19:11,883 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:19Z] GATK: realign ('13', 67477635, 84455642) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:19Z] GATK RealignerTargetCreator: R14-18106_kapa-NGv3-PE100-NGv3-sort-13_101890105_115169878-prep-prealign.bam 13:101890106-115169878
[2016-04-15T00:19Z] GATK: RealignerTargetCreator
[2016-04-15T00:19Z] INFO  17:19:12,615 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:19Z] INFO  17:19:12,618 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:19Z] INFO  17:19:12,618 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:19Z] INFO  17:19:12,619 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:19Z] INFO  17:19:12,625 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/12/R14-18106_kapa-NGv3-PE100-NGv3-sort-12_109494486_125263132-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/12/tx/tmpSarHTd/R14-18106_kapa-NGv3-PE100-NGv3-sort-12_109494486_125263132-prep-prealign-realign.intervals -l INFO -L 12:109494487-125263132 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:19Z] INFO  17:19:12,649 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:19Z] INFO  17:19:12,665 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:19Z] INFO  17:19:12,666 HelpFormatter - Date/Time: 2016/04/14 17:19:12
[2016-04-15T00:19Z] INFO  17:19:12,666 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:19Z] INFO  17:19:12,666 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:19Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-11_110001730_125514538-prep.bam
[2016-04-15T00:19Z] INFO  17:19:12,815 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:19Z] INFO  17:19:12,858 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:19Z] GATK: realign ('13', 35615069, 51287376) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:19Z] INFO  17:19:12,951 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:19Z] INFO  17:19:12,953 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:19Z] INFO  17:19:12,954 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:19Z] INFO  17:19:12,954 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:19Z] INFO  17:19:12,958 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/14/R14-18106_kapa-NGv3-PE100-NGv3-sort-14_0_19378574-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/14/R14-18106_kapa-NGv3-PE100-NGv3-sort-14_0_19378574-prep-prealign-realign.intervals -L 14:1-19378574 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/14/tx/tmpw_B6zz/R14-18106_kapa-NGv3-PE100-NGv3-sort-14_0_19378574-prep.bam
[2016-04-15T00:19Z] INFO  17:19:12,966 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:19Z] INFO  17:19:12,967 HelpFormatter - Date/Time: 2016/04/14 17:19:12
[2016-04-15T00:19Z] INFO  17:19:12,967 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:19Z] INFO  17:19:12,968 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:19Z] INFO  17:19:13,029 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T00:19Z] INFO  17:19:13,058 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:19Z] INFO  17:19:13,142 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:19Z] INFO  17:19:13,149 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.09
[2016-04-15T00:19Z] INFO  17:19:13,279 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:19Z] INFO  17:19:13,294 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:19Z] INFO  17:19:13,399 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.10
[2016-04-15T00:19Z] INFO  17:19:13,529 IntervalUtils - Processing 15768646 bp from intervals
[2016-04-15T00:19Z] WARN  17:19:13,534 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:19Z] INFO  17:19:13,607 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:19Z] GATK RealignerTargetCreator: R14-18106_kapa-NGv3-PE100-NGv3-sort-12_46756066_62654284-prep-prealign.bam 12:46756067-62654284
[2016-04-15T00:19Z] GATK: RealignerTargetCreator
[2016-04-15T00:19Z] INFO  17:19:13,842 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:19Z] INFO  17:19:13,843 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:19Z] INFO  17:19:13,843 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:19Z] INFO  17:19:13,844 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:19Z] INFO  17:19:13,891 IntervalUtils - Processing 19378574 bp from intervals
[2016-04-15T00:19Z] WARN  17:19:13,896 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:19Z] INFO  17:19:13,992 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:19Z] INFO  17:19:14,041 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:19Z] INFO  17:19:14,044 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:19Z] INFO  17:19:14,044 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:19Z] INFO  17:19:14,044 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:19Z] INFO  17:19:14,049 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/13/R14-18106_kapa-NGv3-PE100-NGv3-sort-13_19751066_35517251-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/13/R14-18106_kapa-NGv3-PE100-NGv3-sort-13_19751066_35517251-prep-prealign-realign.intervals -L 13:19751067-35517251 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/13/tx/tmpqzvzIu/R14-18106_kapa-NGv3-PE100-NGv3-sort-13_19751066_35517251-prep.bam
[2016-04-15T00:19Z] INFO  17:19:14,063 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:19Z] INFO  17:19:14,063 HelpFormatter - Date/Time: 2016/04/14 17:19:14
[2016-04-15T00:19Z] INFO  17:19:14,064 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:19Z] INFO  17:19:14,064 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:19Z] INFO  17:19:14,245 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:19Z] INFO  17:19:14,246 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:19Z] INFO  17:19:14,247 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:19Z] INFO  17:19:14,248 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:19Z] INFO  17:19:14,309 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:19Z] INFO  17:19:14,313 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:19Z] INFO  17:19:14,376 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:19Z] GATK pre-alignment ('14', 35072553, 50583270) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:19Z] INFO  17:19:14,529 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:19Z] INFO  17:19:14,540 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:19Z] INFO  17:19:14,606 ProgressMeter -            done    194286.0    15.0 s      78.0 s       99.5%    15.0 s       0.0 s
[2016-04-15T00:19Z] INFO  17:19:14,606 ProgressMeter - Total runtime 15.21 secs, 0.25 min, 0.00 hours
[2016-04-15T00:19Z] INFO  17:19:14,610 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-15T00:19Z] INFO  17:19:14,610 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 194286 total reads (0.00%)
[2016-04-15T00:19Z] INFO  17:19:14,611 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:19Z] INFO  17:19:14,611 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:19Z] INFO  17:19:14,611 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:19Z] INFO  17:19:14,800 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:19Z] INFO  17:19:14,803 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:19Z] INFO  17:19:14,804 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:19Z] INFO  17:19:14,805 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:19Z] INFO  17:19:14,809 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/13/R14-18106_kapa-NGv3-PE100-NGv3-sort-13_67477635_84455642-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/13/R14-18106_kapa-NGv3-PE100-NGv3-sort-13_67477635_84455642-prep-prealign-realign.intervals -L 13:67477636-84455642 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/13/tx/tmpXjeEot/R14-18106_kapa-NGv3-PE100-NGv3-sort-13_67477635_84455642-prep.bam
[2016-04-15T00:19Z] INFO  17:19:14,830 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:19Z] INFO  17:19:14,831 HelpFormatter - Date/Time: 2016/04/14 17:19:14
[2016-04-15T00:19Z] INFO  17:19:14,832 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:19Z] INFO  17:19:14,833 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:19Z] INFO  17:19:15,103 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:19Z] INFO  17:19:15,156 IntervalUtils - Processing 15766185 bp from intervals
[2016-04-15T00:19Z] WARN  17:19:15,162 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:19Z] INFO  17:19:15,236 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:19Z] INFO  17:19:15,247 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:19Z] INFO  17:19:15,271 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:19Z] INFO  17:19:15,274 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:19Z] INFO  17:19:15,274 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:19Z] INFO  17:19:15,274 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:19Z] INFO  17:19:15,280 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:19Z] INFO  17:19:15,289 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/13/R14-18106_kapa-NGv3-PE100-NGv3-sort-13_101890105_115169878-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/13/tx/tmp23X_ai/R14-18106_kapa-NGv3-PE100-NGv3-sort-13_101890105_115169878-prep-prealign-realign.intervals -l INFO -L 13:101890106-115169878 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:19Z] INFO  17:19:15,306 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:19Z] INFO  17:19:15,307 HelpFormatter - Date/Time: 2016/04/14 17:19:15
[2016-04-15T00:19Z] INFO  17:19:15,307 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:19Z] INFO  17:19:15,308 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:19Z] INFO  17:19:15,325 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-15T00:19Z] INFO  17:19:15,447 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:19Z] INFO  17:19:15,448 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:19Z] INFO  17:19:15,449 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:19Z] INFO  17:19:15,450 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:19Z] INFO  17:19:15,477 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:19Z] INFO  17:19:15,686 IntervalUtils - Processing 16978007 bp from intervals
[2016-04-15T00:19Z] WARN  17:19:15,691 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:19Z] INFO  17:19:15,712 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:19Z] INFO  17:19:15,772 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T00:19Z] INFO  17:19:15,777 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:19Z] INFO  17:19:15,780 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:19Z] INFO  17:19:15,781 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:19Z] INFO  17:19:15,781 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:19Z] INFO  17:19:15,783 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:19Z] INFO  17:19:15,786 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/13/R14-18106_kapa-NGv3-PE100-NGv3-sort-13_35615069_51287376-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/13/R14-18106_kapa-NGv3-PE100-NGv3-sort-13_35615069_51287376-prep-prealign-realign.intervals -L 13:35615070-51287376 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/13/tx/tmpTXYaKb/R14-18106_kapa-NGv3-PE100-NGv3-sort-13_35615069_51287376-prep.bam
[2016-04-15T00:19Z] INFO  17:19:15,792 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:19Z] INFO  17:19:15,821 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:19Z] INFO  17:19:15,823 HelpFormatter - Date/Time: 2016/04/14 17:19:15
[2016-04-15T00:19Z] INFO  17:19:15,823 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:19Z] INFO  17:19:15,828 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:19Z] INFO  17:19:15,872 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-15T00:19Z] INFO  17:19:15,899 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:19Z] INFO  17:19:15,900 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:19Z] INFO  17:19:15,901 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:19Z] INFO  17:19:15,902 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:19Z] INFO  17:19:15,976 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:19Z] INFO  17:19:16,068 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:19Z] INFO  17:19:16,090 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:19Z] INFO  17:19:16,136 ProgressMeter -            done      3731.0     1.0 s       8.4 m      100.0%     1.0 s       0.0 s
[2016-04-15T00:19Z] INFO  17:19:16,137 ProgressMeter - Total runtime 1.89 secs, 0.03 min, 0.00 hours
[2016-04-15T00:19Z] INFO  17:19:16,141 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 3731 total reads (0.00%)
[2016-04-15T00:19Z] INFO  17:19:16,142 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:19Z] INFO  17:19:16,147 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:19Z] INFO  17:19:16,148 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:19Z] INFO  17:19:16,244 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:19Z] INFO  17:19:16,268 IntervalUtils - Processing 13279773 bp from intervals
[2016-04-15T00:19Z] WARN  17:19:16,273 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:19Z] INFO  17:19:16,277 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:19Z] INFO  17:19:16,285 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:19Z] INFO  17:19:16,351 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:19Z] INFO  17:19:16,365 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:19Z] INFO  17:19:16,371 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-15T00:19Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-12_125267228_133851895-prep.bam
[2016-04-15T00:19Z] INFO  17:19:16,542 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:19Z] INFO  17:19:16,544 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:19Z] INFO  17:19:16,541 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:19Z] INFO  17:19:16,544 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:19Z] INFO  17:19:16,545 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:19Z] INFO  17:19:16,545 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:19Z] INFO  17:19:16,545 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:19Z] INFO  17:19:16,546 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:19Z] INFO  17:19:16,550 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/12/R14-18106_kapa-NGv3-PE100-NGv3-sort-12_46756066_62654284-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/12/tx/tmpG82zfZ/R14-18106_kapa-NGv3-PE100-NGv3-sort-12_46756066_62654284-prep-prealign-realign.intervals -l INFO -L 12:46756067-62654284 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:19Z] INFO  17:19:16,575 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:19Z] INFO  17:19:16,576 HelpFormatter - Date/Time: 2016/04/14 17:19:16
[2016-04-15T00:19Z] INFO  17:19:16,576 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:19Z] INFO  17:19:16,577 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:19Z] INFO  17:19:16,674 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:19Z] INFO  17:19:16,760 IntervalUtils - Processing 15672307 bp from intervals
[2016-04-15T00:19Z] WARN  17:19:16,776 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:19Z] INFO  17:19:16,861 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T00:19Z] INFO  17:19:16,870 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:19Z] INFO  17:19:16,889 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:19Z] INFO  17:19:16,933 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-15T00:19Z] GATK pre-alignment ('14', 50585061, 66096324) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:19Z] INFO  17:19:17,073 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:19Z] INFO  17:19:17,074 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:19Z] INFO  17:19:17,074 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:19Z] INFO  17:19:17,074 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:19Z] INFO  17:19:17,329 IntervalUtils - Processing 15898218 bp from intervals
[2016-04-15T00:19Z] WARN  17:19:17,334 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:19Z] INFO  17:19:17,403 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:19Z] INFO  17:19:17,472 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:19Z] INFO  17:19:17,469 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:19Z] INFO  17:19:17,473 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:19Z] INFO  17:19:17,473 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:19Z] INFO  17:19:17,474 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:19Z] INFO  17:19:17,478 HelpFormatter - Program Args: -T PrintReads -L 14:35072554-50583270 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/14/tx/tmpZk4TVj/R14-18106_kapa-NGv3-PE100-NGv3-sort-14_35072553_50583270-prep-prealign.bam
[2016-04-15T00:19Z] INFO  17:19:17,497 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:19Z] INFO  17:19:17,498 HelpFormatter - Date/Time: 2016/04/14 17:19:17
[2016-04-15T00:19Z] INFO  17:19:17,498 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:19Z] INFO  17:19:17,499 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:19Z] INFO  17:19:17,597 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:19Z] INFO  17:19:17,643 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:19Z] INFO  17:19:17,749 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:19Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-14_0_19378574-prep.bam
[2016-04-15T00:19Z] INFO  17:19:17,844 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:19Z] INFO  17:19:17,845 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:19Z] INFO  17:19:17,846 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:19Z] INFO  17:19:17,846 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:19Z] GATK pre-alignment ('14', 66135960, 81646674) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:19Z] INFO  17:19:18,013 ProgressMeter -            done    101347.0     9.0 s      98.0 s      100.0%     9.0 s       0.0 s
[2016-04-15T00:19Z] INFO  17:19:18,013 ProgressMeter - Total runtime 9.97 secs, 0.17 min, 0.00 hours
[2016-04-15T00:19Z] INFO  17:19:18,017 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 101347 total reads (0.00%)
[2016-04-15T00:19Z] INFO  17:19:18,017 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:19Z] INFO  17:19:18,017 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:19Z] INFO  17:19:18,018 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:19Z] INFO  17:19:18,079 ProgressMeter -            done    269872.0    19.0 s      73.0 s      100.0%    19.0 s       0.0 s
[2016-04-15T00:19Z] INFO  17:19:18,079 ProgressMeter - Total runtime 19.75 secs, 0.33 min, 0.01 hours
[2016-04-15T00:19Z] INFO  17:19:18,084 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 269872 total reads (0.00%)
[2016-04-15T00:19Z] INFO  17:19:18,085 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:19Z] INFO  17:19:18,085 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:19Z] INFO  17:19:18,086 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:19Z] INFO  17:19:18,613 ProgressMeter -            done   1.5513818E7    14.0 s       0.0 s      100.0%    14.0 s       0.0 s
[2016-04-15T00:19Z] INFO  17:19:18,614 ProgressMeter - Total runtime 14.20 secs, 0.24 min, 0.00 hours
[2016-04-15T00:19Z] INFO  17:19:18,618 MicroScheduler - 9105 reads were filtered out during the traversal out of approximately 110830 total reads (8.22%)
[2016-04-15T00:19Z] INFO  17:19:18,618 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:19Z] INFO  17:19:18,619 MicroScheduler -   -> 509 reads (0.46% of total) failing BadMateFilter
[2016-04-15T00:19Z] INFO  17:19:18,619 MicroScheduler -   -> 8329 reads (7.52% of total) failing DuplicateReadFilter
[2016-04-15T00:19Z] INFO  17:19:18,619 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:19Z] INFO  17:19:18,619 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:19Z] INFO  17:19:18,620 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:19Z] INFO  17:19:18,620 MicroScheduler -   -> 267 reads (0.24% of total) failing MappingQualityZeroFilter
[2016-04-15T00:19Z] INFO  17:19:18,620 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:19Z] INFO  17:19:18,620 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-15T00:19Z] INFO  17:19:18,621 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:19Z] INFO  17:19:18,725 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-15T00:19Z] INFO  17:19:18,784 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:19Z] INFO  17:19:18,793 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:19Z] INFO  17:19:18,849 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-15T00:19Z] INFO  17:19:18,863 IntervalUtils - Processing 15510717 bp from intervals
[2016-04-15T00:19Z] INFO  17:19:18,941 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:19Z] INFO  17:19:19,298 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:19Z] INFO  17:19:19,299 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:19Z] INFO  17:19:19,300 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:19Z] INFO  17:19:19,300 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:19Z] INFO  17:19:19,325 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:19Z] INFO  17:19:19,479 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:19Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-13_51396767_67205543-prep.bam
[2016-04-15T00:19Z] INFO  17:19:19,550 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:19Z] INFO  17:19:19,678 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:19Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-12_93870729_109490566-prep.bam
[2016-04-15T00:19Z] GATK pre-alignment ('14', 81651874, 97299968) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:19Z] INFO  17:19:20,180 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:19Z] INFO  17:19:20,183 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:19Z] INFO  17:19:20,183 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:19Z] INFO  17:19:20,183 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:19Z] INFO  17:19:20,187 HelpFormatter - Program Args: -T PrintReads -L 14:50585062-66096324 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/14/tx/tmpQzw5mI/R14-18106_kapa-NGv3-PE100-NGv3-sort-14_50585061_66096324-prep-prealign.bam
[2016-04-15T00:19Z] INFO  17:19:20,210 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:19Z] INFO  17:19:20,211 HelpFormatter - Date/Time: 2016/04/14 17:19:20
[2016-04-15T00:19Z] INFO  17:19:20,212 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:19Z] INFO  17:19:20,212 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:19Z] INFO  17:19:20,278 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:19Z] GATK: realign ('13', 86368117, 101881935) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:19Z] INFO  17:19:20,415 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:19Z] GATK pre-alignment ('14', 97304098, 107349540) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:19Z] INFO  17:19:20,827 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:19Z] INFO  17:19:20,830 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:19Z] INFO  17:19:20,830 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:19Z] INFO  17:19:20,831 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:19Z] INFO  17:19:20,835 HelpFormatter - Program Args: -T PrintReads -L 14:66135961-81646674 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/14/tx/tmpFf5BdR/R14-18106_kapa-NGv3-PE100-NGv3-sort-14_66135960_81646674-prep-prealign.bam
[2016-04-15T00:19Z] INFO  17:19:20,877 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:19Z] INFO  17:19:20,878 HelpFormatter - Date/Time: 2016/04/14 17:19:20
[2016-04-15T00:19Z] INFO  17:19:20,879 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:19Z] INFO  17:19:20,879 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:19Z] INFO  17:19:21,048 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:19Z] INFO  17:19:21,630 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-15T00:19Z] INFO  17:19:21,691 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:19Z] INFO  17:19:21,701 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:19Z] INFO  17:19:21,767 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-15T00:19Z] INFO  17:19:21,780 IntervalUtils - Processing 15511263 bp from intervals
[2016-04-15T00:19Z] INFO  17:19:21,849 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:19Z] INFO  17:19:22,135 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-15T00:19Z] INFO  17:19:22,155 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:19Z] INFO  17:19:22,156 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:19Z] INFO  17:19:22,157 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:19Z] INFO  17:19:22,158 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:19Z] INFO  17:19:22,180 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:19Z] INFO  17:19:22,181 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:19Z] INFO  17:19:22,192 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:19Z] INFO  17:19:22,244 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-15T00:19Z] INFO  17:19:22,258 IntervalUtils - Processing 15510714 bp from intervals
[2016-04-15T00:19Z] INFO  17:19:22,324 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:19Z] INFO  17:19:22,328 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:19Z] INFO  17:19:22,601 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:19Z] INFO  17:19:22,603 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:19Z] INFO  17:19:22,603 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:19Z] INFO  17:19:22,604 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:19Z] INFO  17:19:22,625 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:19Z] INFO  17:19:22,807 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:19Z] INFO  17:19:23,114 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:19Z] INFO  17:19:23,117 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:19Z] INFO  17:19:23,117 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:19Z] INFO  17:19:23,117 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:19Z] INFO  17:19:23,121 HelpFormatter - Program Args: -T PrintReads -L 14:81651875-97299968 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/14/tx/tmpC1C61F/R14-18106_kapa-NGv3-PE100-NGv3-sort-14_81651874_97299968-prep-prealign.bam
[2016-04-15T00:19Z] INFO  17:19:23,131 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:19Z] INFO  17:19:23,137 HelpFormatter - Date/Time: 2016/04/14 17:19:23
[2016-04-15T00:19Z] INFO  17:19:23,138 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:19Z] INFO  17:19:23,138 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:19Z] INFO  17:19:23,299 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:19Z] INFO  17:19:23,301 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:19Z] INFO  17:19:23,302 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:19Z] INFO  17:19:23,302 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:19Z] INFO  17:19:23,306 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/13/R14-18106_kapa-NGv3-PE100-NGv3-sort-13_86368117_101881935-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/13/R14-18106_kapa-NGv3-PE100-NGv3-sort-13_86368117_101881935-prep-prealign-realign.intervals -L 13:86368118-101881935 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/13/tx/tmpD43VEY/R14-18106_kapa-NGv3-PE100-NGv3-sort-13_86368117_101881935-prep.bam
[2016-04-15T00:19Z] INFO  17:19:23,315 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:19Z] INFO  17:19:23,316 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:19Z] INFO  17:19:23,329 HelpFormatter - Date/Time: 2016/04/14 17:19:23
[2016-04-15T00:19Z] INFO  17:19:23,330 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:19Z] INFO  17:19:23,331 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:19Z] INFO  17:19:23,493 ProgressMeter -            done    760813.0    52.0 s      68.0 s      100.0%    52.0 s       0.0 s
[2016-04-15T00:19Z] INFO  17:19:23,493 ProgressMeter - Total runtime 52.23 secs, 0.87 min, 0.01 hours
[2016-04-15T00:19Z] INFO  17:19:23,497 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 760813 total reads (0.00%)
[2016-04-15T00:19Z] INFO  17:19:23,498 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:19Z] INFO  17:19:23,498 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:19Z] INFO  17:19:23,498 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:19Z] INFO  17:19:23,552 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:19Z] INFO  17:19:23,697 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:19Z] INFO  17:19:23,728 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:19Z] INFO  17:19:23,798 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-15T00:19Z] INFO  17:19:24,325 IntervalUtils - Processing 15513818 bp from intervals
[2016-04-15T00:19Z] WARN  17:19:24,329 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:19Z] INFO  17:19:24,368 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:19Z] INFO  17:19:24,378 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:19Z] INFO  17:19:24,379 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:19Z] INFO  17:19:24,379 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:19Z] INFO  17:19:24,384 HelpFormatter - Program Args: -T PrintReads -L 14:97304099-107349540 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/14/tx/tmpKJiAHE/R14-18106_kapa-NGv3-PE100-NGv3-sort-14_97304098_107349540-prep-prealign.bam
[2016-04-15T00:19Z] INFO  17:19:24,423 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:19Z] INFO  17:19:24,424 HelpFormatter - Date/Time: 2016/04/14 17:19:24
[2016-04-15T00:19Z] INFO  17:19:24,424 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:19Z] INFO  17:19:24,424 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:19Z] INFO  17:19:24,427 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:19Z] INFO  17:19:24,507 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-15T00:19Z] INFO  17:19:24,576 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:19Z] INFO  17:19:24,583 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:19Z] INFO  17:19:24,584 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:19Z] INFO  17:19:24,585 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:19Z] INFO  17:19:24,586 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:19Z] INFO  17:19:24,588 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:19Z] INFO  17:19:24,620 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:19Z] INFO  17:19:24,678 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-15T00:19Z] INFO  17:19:24,697 IntervalUtils - Processing 15648094 bp from intervals
[2016-04-15T00:19Z] INFO  17:19:24,733 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:19Z] INFO  17:19:24,799 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:19Z] INFO  17:19:24,873 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:19Z] INFO  17:19:25,157 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:19Z] INFO  17:19:25,158 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:19Z] INFO  17:19:25,158 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:19Z] INFO  17:19:25,159 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:19Z] INFO  17:19:25,211 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:19Z] INFO  17:19:25,298 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:19Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-11_0_15994658-prep.bam
[2016-04-15T00:19Z] INFO  17:19:25,424 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:19Z] INFO  17:19:25,659 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-15T00:19Z] INFO  17:19:25,718 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:19Z] INFO  17:19:25,726 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:19Z] INFO  17:19:25,773 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-15T00:19Z] INFO  17:19:25,787 IntervalUtils - Processing 10045442 bp from intervals
[2016-04-15T00:19Z] INFO  17:19:25,874 ProgressMeter -            done     88937.0     9.0 s     112.0 s      100.0%     9.0 s       0.0 s
[2016-04-15T00:19Z] INFO  17:19:25,874 ProgressMeter - Total runtime 9.97 secs, 0.17 min, 0.00 hours
[2016-04-15T00:19Z] INFO  17:19:25,878 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 88937 total reads (0.00%)
[2016-04-15T00:19Z] INFO  17:19:25,878 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:19Z] INFO  17:19:25,878 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:19Z] INFO  17:19:25,878 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:19Z] INFO  17:19:25,938 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:19Z] INFO  17:19:26,248 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:19Z] INFO  17:19:26,249 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:19Z] INFO  17:19:26,250 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:19Z] INFO  17:19:26,250 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:19Z] INFO  17:19:26,264 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:19Z] INFO  17:19:26,384 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:19Z] INFO  17:19:27,201 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:19Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-13_67477635_84455642-prep.bam
[2016-04-15T00:19Z] GATK pre-alignment ('15', 0, 20740485) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:19Z] GATK pre-alignment ('15', 20741621, 36872162) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:19Z] INFO  17:19:28,094 ProgressMeter -      12:9455431    300004.0    30.0 s     100.0 s       60.5%    49.0 s      19.0 s
[2016-04-15T00:19Z] INFO  17:19:30,443 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:19Z] INFO  17:19:30,446 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:19Z] INFO  17:19:30,447 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:19Z] INFO  17:19:30,448 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:19Z] INFO  17:19:30,452 HelpFormatter - Program Args: -T PrintReads -L 15:1-20740485 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/15/tx/tmpXIsSZo/R14-18106_kapa-NGv3-PE100-NGv3-sort-15_0_20740485-prep-prealign.bam
[2016-04-15T00:19Z] INFO  17:19:30,476 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:19Z] INFO  17:19:30,476 HelpFormatter - Date/Time: 2016/04/14 17:19:30
[2016-04-15T00:19Z] INFO  17:19:30,476 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:19Z] INFO  17:19:30,477 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:19Z] INFO  17:19:30,707 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:19Z] INFO  17:19:30,799 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:19Z] INFO  17:19:30,802 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:19Z] INFO  17:19:30,803 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:19Z] INFO  17:19:30,804 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:19Z] INFO  17:19:30,808 HelpFormatter - Program Args: -T PrintReads -L 15:20741622-36872162 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/15/tx/tmpun6WAO/R14-18106_kapa-NGv3-PE100-NGv3-sort-15_20741621_36872162-prep-prealign.bam
[2016-04-15T00:19Z] INFO  17:19:30,826 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:19Z] INFO  17:19:30,827 HelpFormatter - Date/Time: 2016/04/14 17:19:30
[2016-04-15T00:19Z] INFO  17:19:30,828 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:19Z] INFO  17:19:30,828 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:19Z] INFO  17:19:31,054 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:19Z] INFO  17:19:31,818 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-15T00:19Z] INFO  17:19:31,914 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:19Z] INFO  17:19:31,923 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:19Z] INFO  17:19:31,972 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-15T00:19Z] INFO  17:19:32,001 IntervalUtils - Processing 20740485 bp from intervals
[2016-04-15T00:19Z] INFO  17:19:32,081 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:19Z] INFO  17:19:32,142 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-15T00:19Z] INFO  17:19:32,205 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:19Z] INFO  17:19:32,215 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:19Z] INFO  17:19:32,267 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-15T00:19Z] INFO  17:19:32,281 IntervalUtils - Processing 16130541 bp from intervals
[2016-04-15T00:19Z] INFO  17:19:32,362 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:19Z] INFO  17:19:32,447 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:19Z] INFO  17:19:32,448 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:19Z] INFO  17:19:32,449 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:19Z] INFO  17:19:32,449 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:19Z] INFO  17:19:32,479 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:19Z] INFO  17:19:32,486 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:19Z] INFO  17:19:32,559 ProgressMeter -     14:23240526    100001.0    30.0 s       5.0 m       23.8%     2.1 m      96.0 s
[2016-04-15T00:19Z] INFO  17:19:32,673 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:19Z] INFO  17:19:32,674 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:19Z] INFO  17:19:32,675 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:19Z] INFO  17:19:32,675 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:19Z] INFO  17:19:32,711 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:19Z] INFO  17:19:32,978 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:19Z] INFO  17:19:33,537 ProgressMeter -            done   1.3279773E7    16.0 s       1.0 s      100.0%    16.0 s       0.0 s
[2016-04-15T00:19Z] INFO  17:19:33,538 ProgressMeter - Total runtime 16.99 secs, 0.28 min, 0.00 hours
[2016-04-15T00:19Z] INFO  17:19:33,542 MicroScheduler - 16233 reads were filtered out during the traversal out of approximately 203007 total reads (8.00%)
[2016-04-15T00:19Z] INFO  17:19:33,543 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:19Z] INFO  17:19:33,543 MicroScheduler -   -> 656 reads (0.32% of total) failing BadMateFilter
[2016-04-15T00:19Z] INFO  17:19:33,544 MicroScheduler -   -> 15187 reads (7.48% of total) failing DuplicateReadFilter
[2016-04-15T00:19Z] INFO  17:19:33,545 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:19Z] INFO  17:19:33,545 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:19Z] INFO  17:19:33,546 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:19Z] INFO  17:19:33,547 MicroScheduler -   -> 390 reads (0.19% of total) failing MappingQualityZeroFilter
[2016-04-15T00:19Z] INFO  17:19:33,547 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:19Z] INFO  17:19:33,548 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-15T00:19Z] INFO  17:19:33,549 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:19Z] INFO  17:19:33,916 ProgressMeter -            done    535895.0    35.0 s      66.0 s      100.0%    35.0 s       0.0 s
[2016-04-15T00:19Z] INFO  17:19:33,916 ProgressMeter - Total runtime 35.85 secs, 0.60 min, 0.01 hours
[2016-04-15T00:19Z] INFO  17:19:33,920 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 535895 total reads (0.00%)
[2016-04-15T00:19Z] INFO  17:19:33,921 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:19Z] INFO  17:19:33,921 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:19Z] INFO  17:19:33,921 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:19Z] INFO  17:19:34,204 ProgressMeter -            done    248882.0    18.0 s      75.0 s      100.0%    18.0 s       0.0 s
[2016-04-15T00:19Z] INFO  17:19:34,204 ProgressMeter - Total runtime 18.76 secs, 0.31 min, 0.01 hours
[2016-04-15T00:19Z] INFO  17:19:34,208 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 248882 total reads (0.00%)
[2016-04-15T00:19Z] INFO  17:19:34,209 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:19Z] INFO  17:19:34,209 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:19Z] INFO  17:19:34,209 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:19Z] INFO  17:19:35,022 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:19Z] GATK: realign ('13', 101890105, 115169878) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:19Z] INFO  17:19:35,489 ProgressMeter -            done    225117.0    18.0 s      81.0 s      100.0%    18.0 s       0.0 s
[2016-04-15T00:19Z] INFO  17:19:35,489 ProgressMeter - Total runtime 18.42 secs, 0.31 min, 0.01 hours
[2016-04-15T00:19Z] INFO  17:19:35,493 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 225117 total reads (0.00%)
[2016-04-15T00:19Z] INFO  17:19:35,494 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:19Z] INFO  17:19:35,495 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:19Z] INFO  17:19:35,496 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:19Z] INFO  17:19:35,599 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:19Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-12_0_15637181-prep.bam
[2016-04-15T00:19Z] INFO  17:19:35,765 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:19Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-13_19751066_35517251-prep.bam
[2016-04-15T00:19Z] INFO  17:19:35,907 ProgressMeter -            done    109897.0    11.0 s     103.0 s      100.0%    11.0 s       0.0 s
[2016-04-15T00:19Z] INFO  17:19:35,907 ProgressMeter - Total runtime 11.32 secs, 0.19 min, 0.00 hours
[2016-04-15T00:19Z] INFO  17:19:35,908 ProgressMeter -     11:66625663    400006.0    30.0 s      75.0 s       25.0%   120.0 s      90.0 s
[2016-04-15T00:19Z] INFO  17:19:35,923 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 109897 total reads (0.00%)
[2016-04-15T00:19Z] INFO  17:19:35,924 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:19Z] INFO  17:19:35,925 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:19Z] INFO  17:19:35,926 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:19Z] INFO  17:19:36,493 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@41fd9d8e
[2016-04-15T00:19Z] INFO  17:19:36,579 ProgressMeter -            done     12234.0     4.0 s       5.6 m      100.0%     4.0 s       0.0 s
[2016-04-15T00:19Z] INFO  17:19:36,581 ProgressMeter - Total runtime 4.13 secs, 0.07 min, 0.00 hours
[2016-04-15T00:19Z] INFO  17:19:36,582 MicroScheduler - 14 reads were filtered out during the traversal out of approximately 12248 total reads (0.11%)
[2016-04-15T00:19Z] INFO  17:19:36,582 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:19Z] INFO  17:19:36,582 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:19Z] INFO  17:19:36,583 MicroScheduler -   -> 14 reads (0.11% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:19Z] GATK pre-alignment ('15', 36887086, 52402170) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:19Z] INFO  17:19:36,900 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:19Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-13_35615069_51287376-prep.bam
[2016-04-15T00:19Z] INFO  17:19:37,244 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@41fd9d8e
[2016-04-15T00:19Z] INFO  17:19:37,312 ProgressMeter -            done    123885.0    18.0 s       2.4 m      100.0%    18.0 s       0.0 s
[2016-04-15T00:19Z] INFO  17:19:37,312 ProgressMeter - Total runtime 18.01 secs, 0.30 min, 0.01 hours
[2016-04-15T00:19Z] INFO  17:19:37,313 MicroScheduler - 115 reads were filtered out during the traversal out of approximately 124000 total reads (0.09%)
[2016-04-15T00:19Z] INFO  17:19:37,313 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:19Z] INFO  17:19:37,313 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:19Z] INFO  17:19:37,314 MicroScheduler -   -> 115 reads (0.09% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:19Z] INFO  17:19:37,378 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:19Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-13_86368117_101881935-prep.bam
[2016-04-15T00:19Z] GATK pre-alignment ('15', 52404364, 67923265) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:19Z] GATK pre-alignment ('15', 67932890, 83447639) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:19Z] GATK pre-alignment ('15', 83448996, 98982979) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:19Z] INFO  17:19:37,854 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:19Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-15_0_20740485-prep-prealign.bam
[2016-04-15T00:19Z] GATK RealignerTargetCreator: R14-18106_kapa-NGv3-PE100-NGv3-sort-15_0_20740485-prep-prealign.bam 15:1-20740485
[2016-04-15T00:19Z] GATK: RealignerTargetCreator
[2016-04-15T00:19Z] INFO  17:19:38,049 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:19Z] INFO  17:19:38,052 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:19Z] INFO  17:19:38,052 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:19Z] INFO  17:19:38,053 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:19Z] INFO  17:19:38,057 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/13/R14-18106_kapa-NGv3-PE100-NGv3-sort-13_101890105_115169878-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/13/R14-18106_kapa-NGv3-PE100-NGv3-sort-13_101890105_115169878-prep-prealign-realign.intervals -L 13:101890106-115169878 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/13/tx/tmpmb0q7u/R14-18106_kapa-NGv3-PE100-NGv3-sort-13_101890105_115169878-prep.bam
[2016-04-15T00:19Z] INFO  17:19:38,073 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:19Z] INFO  17:19:38,073 HelpFormatter - Date/Time: 2016/04/14 17:19:38
[2016-04-15T00:19Z] INFO  17:19:38,073 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:19Z] INFO  17:19:38,074 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:19Z] INFO  17:19:38,347 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:19Z] INFO  17:19:38,519 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:19Z] INFO  17:19:38,533 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:19Z] INFO  17:19:38,615 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-15T00:19Z] INFO  17:19:38,641 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:19Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-14_35072553_50583270-prep-prealign.bam
[2016-04-15T00:19Z] GATK RealignerTargetCreator: R14-18106_kapa-NGv3-PE100-NGv3-sort-14_35072553_50583270-prep-prealign.bam 14:35072554-50583270
[2016-04-15T00:19Z] GATK: RealignerTargetCreator
[2016-04-15T00:19Z] INFO  17:19:39,135 IntervalUtils - Processing 13279773 bp from intervals
[2016-04-15T00:19Z] WARN  17:19:39,148 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:19Z] INFO  17:19:39,242 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:19Z] INFO  17:19:39,332 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:19Z] INFO  17:19:39,333 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:19Z] INFO  17:19:39,334 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:19Z] INFO  17:19:39,335 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:19Z] INFO  17:19:39,495 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:19Z] INFO  17:19:39,618 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:19Z] INFO  17:19:39,758 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:19Z] INFO  17:19:39,761 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:19Z] INFO  17:19:39,762 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:19Z] INFO  17:19:39,771 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:19Z] INFO  17:19:39,776 HelpFormatter - Program Args: -T PrintReads -L 15:36887087-52402170 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/15/tx/tmpdeoz_e/R14-18106_kapa-NGv3-PE100-NGv3-sort-15_36887086_52402170-prep-prealign.bam
[2016-04-15T00:19Z] INFO  17:19:39,789 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:19Z] INFO  17:19:39,790 HelpFormatter - Date/Time: 2016/04/14 17:19:39
[2016-04-15T00:19Z] INFO  17:19:39,790 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:19Z] INFO  17:19:39,791 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:19Z] INFO  17:19:40,025 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:19Z] INFO  17:19:40,780 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:19Z] INFO  17:19:40,793 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:19Z] INFO  17:19:40,794 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:19Z] INFO  17:19:40,795 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:19Z] INFO  17:19:40,800 HelpFormatter - Program Args: -T PrintReads -L 15:52404365-67923265 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/15/tx/tmpcO76Tg/R14-18106_kapa-NGv3-PE100-NGv3-sort-15_52404364_67923265-prep-prealign.bam
[2016-04-15T00:19Z] INFO  17:19:40,834 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:19Z] INFO  17:19:40,835 HelpFormatter - Date/Time: 2016/04/14 17:19:40
[2016-04-15T00:19Z] INFO  17:19:40,835 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:19Z] INFO  17:19:40,840 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:19Z] INFO  17:19:40,922 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:19Z] INFO  17:19:40,925 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:19Z] INFO  17:19:40,926 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:19Z] INFO  17:19:40,926 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:19Z] INFO  17:19:40,931 HelpFormatter - Program Args: -T PrintReads -L 15:67932891-83447639 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/15/tx/tmp6ut3V7/R14-18106_kapa-NGv3-PE100-NGv3-sort-15_67932890_83447639-prep-prealign.bam
[2016-04-15T00:19Z] INFO  17:19:40,962 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:19Z] INFO  17:19:40,963 HelpFormatter - Date/Time: 2016/04/14 17:19:40
[2016-04-15T00:19Z] INFO  17:19:40,963 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:19Z] INFO  17:19:40,963 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:19Z] INFO  17:19:41,027 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:19Z] INFO  17:19:41,031 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:19Z] INFO  17:19:41,031 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:19Z] INFO  17:19:41,032 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:19Z] INFO  17:19:41,037 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/15/R14-18106_kapa-NGv3-PE100-NGv3-sort-15_0_20740485-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/15/tx/tmp8k087N/R14-18106_kapa-NGv3-PE100-NGv3-sort-15_0_20740485-prep-prealign-realign.intervals -l INFO -L 15:1-20740485 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:19Z] INFO  17:19:41,046 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:19Z] INFO  17:19:41,059 HelpFormatter - Date/Time: 2016/04/14 17:19:41
[2016-04-15T00:19Z] INFO  17:19:41,060 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:19Z] INFO  17:19:41,061 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:19Z] INFO  17:19:41,077 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:19Z] INFO  17:19:41,107 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-15T00:19Z] INFO  17:19:41,162 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:19Z] INFO  17:19:41,169 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:19Z] INFO  17:19:41,178 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:19Z] INFO  17:19:41,203 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:19Z] INFO  17:19:41,213 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:19Z] INFO  17:19:41,216 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:19Z] INFO  17:19:41,217 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:19Z] INFO  17:19:41,217 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:19Z] INFO  17:19:41,222 HelpFormatter - Program Args: -T PrintReads -L 15:83448997-98982979 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/15/tx/tmphK8zoC/R14-18106_kapa-NGv3-PE100-NGv3-sort-15_83448996_98982979-prep-prealign.bam
[2016-04-15T00:19Z] INFO  17:19:41,240 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:19Z] INFO  17:19:41,241 HelpFormatter - Date/Time: 2016/04/14 17:19:41
[2016-04-15T00:19Z] INFO  17:19:41,241 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:19Z] INFO  17:19:41,242 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:19Z] INFO  17:19:41,242 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-15T00:19Z] INFO  17:19:41,257 IntervalUtils - Processing 15515084 bp from intervals
[2016-04-15T00:19Z] INFO  17:19:41,301 ProgressMeter -            done   1.5768646E7    27.0 s       1.0 s      100.0%    27.0 s       0.0 s
[2016-04-15T00:19Z] INFO  17:19:41,302 ProgressMeter - Total runtime 27.46 secs, 0.46 min, 0.01 hours
[2016-04-15T00:19Z] INFO  17:19:41,307 MicroScheduler - 46339 reads were filtered out during the traversal out of approximately 578775 total reads (8.01%)
[2016-04-15T00:19Z] INFO  17:19:41,308 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:19Z] INFO  17:19:41,309 MicroScheduler -   -> 1283 reads (0.22% of total) failing BadMateFilter
[2016-04-15T00:19Z] INFO  17:19:41,309 MicroScheduler -   -> 43910 reads (7.59% of total) failing DuplicateReadFilter
[2016-04-15T00:19Z] INFO  17:19:41,310 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:19Z] INFO  17:19:41,311 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:19Z] INFO  17:19:41,311 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:19Z] INFO  17:19:41,312 MicroScheduler -   -> 1146 reads (0.20% of total) failing MappingQualityZeroFilter
[2016-04-15T00:19Z] INFO  17:19:41,312 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:19Z] INFO  17:19:41,313 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-15T00:19Z] INFO  17:19:41,314 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:19Z] INFO  17:19:41,341 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:19Z] INFO  17:19:41,434 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:19Z] INFO  17:19:41,468 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T00:19Z] INFO  17:19:41,499 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:19Z] INFO  17:19:41,576 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-15T00:19Z] INFO  17:19:41,701 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:19Z] INFO  17:19:41,702 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:19Z] INFO  17:19:41,703 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:19Z] INFO  17:19:41,704 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:19Z] INFO  17:19:41,717 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:19Z] INFO  17:19:41,873 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:19Z] INFO  17:19:41,976 IntervalUtils - Processing 20740485 bp from intervals
[2016-04-15T00:19Z] WARN  17:19:41,982 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:19Z] INFO  17:19:42,078 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:19Z] INFO  17:19:42,274 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:19Z] INFO  17:19:42,278 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:19Z] INFO  17:19:42,278 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:19Z] INFO  17:19:42,279 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:19Z] INFO  17:19:42,283 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/14/R14-18106_kapa-NGv3-PE100-NGv3-sort-14_35072553_50583270-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/14/tx/tmp6W3fSN/R14-18106_kapa-NGv3-PE100-NGv3-sort-14_35072553_50583270-prep-prealign-realign.intervals -l INFO -L 14:35072554-50583270 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:19Z] INFO  17:19:42,300 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:19Z] INFO  17:19:42,300 HelpFormatter - Date/Time: 2016/04/14 17:19:42
[2016-04-15T00:19Z] INFO  17:19:42,301 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:19Z] INFO  17:19:42,301 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:19Z] INFO  17:19:42,403 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-15T00:19Z] INFO  17:19:42,410 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:19Z] INFO  17:19:42,427 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:19Z] INFO  17:19:42,428 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:19Z] INFO  17:19:42,428 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:19Z] INFO  17:19:42,428 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:19Z] INFO  17:19:42,464 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:19Z] INFO  17:19:42,471 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-15T00:19Z] INFO  17:19:42,473 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:19Z] INFO  17:19:42,523 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-15T00:19Z] INFO  17:19:42,544 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:19Z] INFO  17:19:42,548 IntervalUtils - Processing 15514749 bp from intervals
[2016-04-15T00:19Z] INFO  17:19:42,554 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:19Z] INFO  17:19:42,601 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-15T00:19Z] INFO  17:19:42,609 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-15T00:19Z] INFO  17:19:42,622 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:19Z] INFO  17:19:42,630 IntervalUtils - Processing 15518901 bp from intervals
[2016-04-15T00:19Z] INFO  17:19:42,633 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:19Z] INFO  17:19:42,634 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T00:19Z] GATK: realign ('12', 109494486, 125263132) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:19Z] INFO  17:19:42,644 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:19Z] INFO  17:19:42,658 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:19Z] INFO  17:19:42,667 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:19Z] INFO  17:19:42,706 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:19Z] INFO  17:19:42,708 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-15T00:19Z] INFO  17:19:42,726 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-15T00:19Z] INFO  17:19:42,740 IntervalUtils - Processing 15533983 bp from intervals
[2016-04-15T00:19Z] INFO  17:19:42,843 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:19Z] INFO  17:19:42,927 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:19Z] INFO  17:19:42,927 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:19Z] INFO  17:19:42,939 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:19Z] INFO  17:19:42,939 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:19Z] INFO  17:19:42,959 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:19Z] INFO  17:19:42,960 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:19Z] INFO  17:19:42,961 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:19Z] INFO  17:19:42,961 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:19Z] INFO  17:19:42,974 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:19Z] INFO  17:19:42,991 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:19Z] INFO  17:19:43,019 IntervalUtils - Processing 15510717 bp from intervals
[2016-04-15T00:19Z] WARN  17:19:43,025 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:19Z] INFO  17:19:43,109 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:19Z] INFO  17:19:43,179 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:19Z] INFO  17:19:43,181 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:19Z] INFO  17:19:43,181 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:19Z] INFO  17:19:43,182 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:19Z] INFO  17:19:43,197 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:19Z] INFO  17:19:43,199 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:19Z] INFO  17:19:43,242 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:19Z] INFO  17:19:43,284 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:19Z] INFO  17:19:43,294 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:19Z] INFO  17:19:43,294 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:19Z] INFO  17:19:43,295 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:19Z] INFO  17:19:43,404 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:19Z] INFO  17:19:45,341 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:19Z] INFO  17:19:45,344 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:19Z] INFO  17:19:45,344 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:19Z] INFO  17:19:45,344 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:19Z] INFO  17:19:45,348 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/12/R14-18106_kapa-NGv3-PE100-NGv3-sort-12_109494486_125263132-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/12/R14-18106_kapa-NGv3-PE100-NGv3-sort-12_109494486_125263132-prep-prealign-realign.intervals -L 12:109494487-125263132 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/12/tx/tmpbZSBXE/R14-18106_kapa-NGv3-PE100-NGv3-sort-12_109494486_125263132-prep.bam
[2016-04-15T00:19Z] INFO  17:19:45,359 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:19Z] INFO  17:19:45,360 HelpFormatter - Date/Time: 2016/04/14 17:19:45
[2016-04-15T00:19Z] INFO  17:19:45,360 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:19Z] INFO  17:19:45,361 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:19Z] INFO  17:19:45,539 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:19Z] INFO  17:19:45,628 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:19Z] INFO  17:19:45,637 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:19Z] INFO  17:19:45,693 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-15T00:19Z] INFO  17:19:46,044 IntervalUtils - Processing 15768646 bp from intervals
[2016-04-15T00:19Z] WARN  17:19:46,049 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:19Z] INFO  17:19:46,155 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:19Z] INFO  17:19:46,342 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:19Z] INFO  17:19:46,342 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:19Z] INFO  17:19:46,343 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:19Z] INFO  17:19:46,343 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:19Z] INFO  17:19:46,630 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:19Z] INFO  17:19:46,844 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:19Z] INFO  17:19:47,864 ProgressMeter -     12:60925713   1.4159646E7    30.0 s       2.0 s       89.1%    33.0 s       3.0 s
[2016-04-15T00:19Z] INFO  17:19:49,475 ProgressMeter -            done   1.5898218E7    31.0 s       1.0 s      100.0%    31.0 s       0.0 s
[2016-04-15T00:19Z] INFO  17:19:49,476 ProgressMeter - Total runtime 31.63 secs, 0.53 min, 0.01 hours
[2016-04-15T00:19Z] INFO  17:19:49,480 MicroScheduler - 73663 reads were filtered out during the traversal out of approximately 834441 total reads (8.83%)
[2016-04-15T00:19Z] INFO  17:19:49,481 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:19Z] INFO  17:19:49,482 MicroScheduler -   -> 1663 reads (0.20% of total) failing BadMateFilter
[2016-04-15T00:19Z] INFO  17:19:49,483 MicroScheduler -   -> 62311 reads (7.47% of total) failing DuplicateReadFilter
[2016-04-15T00:19Z] INFO  17:19:49,483 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:19Z] INFO  17:19:49,484 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:19Z] INFO  17:19:49,484 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:19Z] INFO  17:19:49,485 MicroScheduler -   -> 9689 reads (1.16% of total) failing MappingQualityZeroFilter
[2016-04-15T00:19Z] INFO  17:19:49,486 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:19Z] INFO  17:19:49,486 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-15T00:19Z] INFO  17:19:49,487 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:19Z] INFO  17:19:51,061 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:19Z] GATK: realign ('12', 46756066, 62654284) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:19Z] INFO  17:19:52,181 ProgressMeter -     14:64630334    200003.0    30.0 s       2.5 m       90.5%    33.0 s       3.0 s
[2016-04-15T00:19Z] INFO  17:19:52,928 ProgressMeter -            done   2.0740485E7    10.0 s       0.0 s      100.0%    10.0 s       0.0 s
[2016-04-15T00:19Z] INFO  17:19:52,930 ProgressMeter - Total runtime 10.50 secs, 0.18 min, 0.00 hours
[2016-04-15T00:19Z] INFO  17:19:52,934 MicroScheduler - 6162 reads were filtered out during the traversal out of approximately 12294 total reads (50.12%)
[2016-04-15T00:19Z] INFO  17:19:52,935 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:19Z] INFO  17:19:52,936 MicroScheduler -   -> 33 reads (0.27% of total) failing BadMateFilter
[2016-04-15T00:19Z] INFO  17:19:52,936 MicroScheduler -   -> 474 reads (3.86% of total) failing DuplicateReadFilter
[2016-04-15T00:19Z] INFO  17:19:52,937 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:19Z] INFO  17:19:52,938 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:19Z] INFO  17:19:52,938 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:19Z] INFO  17:19:52,939 MicroScheduler -   -> 5655 reads (46.00% of total) failing MappingQualityZeroFilter
[2016-04-15T00:19Z] INFO  17:19:52,940 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:19Z] INFO  17:19:52,944 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-15T00:19Z] INFO  17:19:52,945 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:19Z] INFO  17:19:52,955 ProgressMeter -     14:74363300    100003.0    30.0 s       5.1 m       53.0%    56.0 s      26.0 s
[2016-04-15T00:19Z] INFO  17:19:53,743 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:19Z] INFO  17:19:53,747 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:19Z] INFO  17:19:53,747 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:19Z] INFO  17:19:53,748 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:19Z] INFO  17:19:53,752 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/12/R14-18106_kapa-NGv3-PE100-NGv3-sort-12_46756066_62654284-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/12/R14-18106_kapa-NGv3-PE100-NGv3-sort-12_46756066_62654284-prep-prealign-realign.intervals -L 12:46756067-62654284 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/12/tx/tmpaAyPA7/R14-18106_kapa-NGv3-PE100-NGv3-sort-12_46756066_62654284-prep.bam
[2016-04-15T00:19Z] INFO  17:19:53,766 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:19Z] INFO  17:19:53,768 HelpFormatter - Date/Time: 2016/04/14 17:19:53
[2016-04-15T00:19Z] INFO  17:19:53,769 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:19Z] INFO  17:19:53,770 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:19Z] INFO  17:19:53,944 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:19Z] INFO  17:19:54,033 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:19Z] INFO  17:19:54,042 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:19Z] INFO  17:19:54,090 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-15T00:19Z] INFO  17:19:54,226 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:19Z] GATK: realign ('15', 0, 20740485) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:19Z] INFO  17:19:54,386 IntervalUtils - Processing 15898218 bp from intervals
[2016-04-15T00:19Z] WARN  17:19:54,391 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:19Z] INFO  17:19:54,458 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:19Z] INFO  17:19:54,583 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:19Z] INFO  17:19:54,595 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:19Z] INFO  17:19:54,596 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:19Z] INFO  17:19:54,596 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:19Z] INFO  17:19:54,786 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:19Z] INFO  17:19:54,992 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:19Z] INFO  17:19:55,018 ProgressMeter -            done    201708.0    15.0 s      77.0 s       99.4%    15.0 s       0.0 s
[2016-04-15T00:19Z] INFO  17:19:55,019 ProgressMeter - Total runtime 15.69 secs, 0.26 min, 0.00 hours
[2016-04-15T00:19Z] INFO  17:19:55,022 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 201708 total reads (0.00%)
[2016-04-15T00:19Z] INFO  17:19:55,025 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:19Z] INFO  17:19:55,025 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:19Z] INFO  17:19:55,026 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:19Z] INFO  17:19:55,115 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@5fe152b7
[2016-04-15T00:19Z] INFO  17:19:55,192 ProgressMeter -     14:97300013    200002.0    30.0 s       2.5 m      100.0%    30.0 s       0.0 s
[2016-04-15T00:19Z] INFO  17:19:55,277 ProgressMeter -            done    237937.0    30.0 s       2.1 m      100.0%    30.0 s       0.0 s
[2016-04-15T00:19Z] INFO  17:19:55,278 ProgressMeter - Total runtime 30.12 secs, 0.50 min, 0.01 hours
[2016-04-15T00:19Z] INFO  17:19:55,278 MicroScheduler - 156 reads were filtered out during the traversal out of approximately 238093 total reads (0.07%)
[2016-04-15T00:19Z] INFO  17:19:55,279 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:19Z] INFO  17:19:55,279 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:19Z] INFO  17:19:55,279 MicroScheduler -   -> 156 reads (0.07% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:19Z] INFO  17:19:56,268 ProgressMeter -    14:105342736    200003.0    30.0 s       2.5 m       80.0%    37.0 s       7.0 s
[2016-04-15T00:19Z] INFO  17:19:56,420 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:19Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-13_101890105_115169878-prep.bam
[2016-04-15T00:19Z] INFO  17:19:56,570 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:19Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-14_81651874_97299968-prep-prealign.bam
[2016-04-15T00:19Z] INFO  17:19:56,842 ProgressMeter -            done    862476.0    50.0 s      59.0 s      100.0%    50.0 s       0.0 s
[2016-04-15T00:19Z] INFO  17:19:56,840 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:19Z] INFO  17:19:56,843 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:19Z] INFO  17:19:56,844 ProgressMeter - Total runtime 50.96 secs, 0.85 min, 0.01 hours
[2016-04-15T00:19Z] INFO  17:19:56,844 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:19Z] INFO  17:19:56,844 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:19Z] INFO  17:19:56,848 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 862476 total reads (0.00%)
[2016-04-15T00:19Z] INFO  17:19:56,849 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:19Z] INFO  17:19:56,849 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/15/R14-18106_kapa-NGv3-PE100-NGv3-sort-15_0_20740485-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/15/R14-18106_kapa-NGv3-PE100-NGv3-sort-15_0_20740485-prep-prealign-realign.intervals -L 15:1-20740485 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/15/tx/tmpWSTprQ/R14-18106_kapa-NGv3-PE100-NGv3-sort-15_0_20740485-prep.bam
[2016-04-15T00:19Z] INFO  17:19:56,849 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:19Z] INFO  17:19:56,850 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:19Z] INFO  17:19:56,882 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:19Z] INFO  17:19:56,883 HelpFormatter - Date/Time: 2016/04/14 17:19:56
[2016-04-15T00:19Z] INFO  17:19:56,883 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:19Z] INFO  17:19:56,883 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:19Z] GATK pre-alignment ('15', 98984299, 102531392) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:19Z] INFO  17:19:57,130 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:19Z] INFO  17:19:57,244 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:19Z] INFO  17:19:57,254 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:19Z] GATK RealignerTargetCreator: R14-18106_kapa-NGv3-PE100-NGv3-sort-14_81651874_97299968-prep-prealign.bam 14:81651875-97299968
[2016-04-15T00:19Z] GATK: RealignerTargetCreator
[2016-04-15T00:19Z] INFO  17:19:57,332 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-15T00:19Z] INFO  17:19:57,746 IntervalUtils - Processing 20740485 bp from intervals
[2016-04-15T00:19Z] WARN  17:19:57,763 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:19Z] INFO  17:19:57,876 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:19Z] INFO  17:19:58,085 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:19Z] INFO  17:19:58,086 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:19Z] INFO  17:19:58,087 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:19Z] INFO  17:19:58,088 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:19Z] INFO  17:19:58,136 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:19Z] INFO  17:19:58,148 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:19Z] INFO  17:19:58,638 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:19Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-11_62744265_78270665-prep.bam
[2016-04-15T00:19Z] INFO  17:19:58,861 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@52f3b59
[2016-04-15T00:19Z] INFO  17:19:59,038 ProgressMeter -            done    284613.0    36.0 s       2.2 m      100.0%    36.0 s       0.0 s
[2016-04-15T00:19Z] INFO  17:19:59,039 ProgressMeter - Total runtime 36.88 secs, 0.61 min, 0.01 hours
[2016-04-15T00:19Z] INFO  17:19:59,039 MicroScheduler - 192 reads were filtered out during the traversal out of approximately 284805 total reads (0.07%)
[2016-04-15T00:19Z] INFO  17:19:59,040 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:19Z] INFO  17:19:59,040 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:19Z] INFO  17:19:59,040 MicroScheduler -   -> 192 reads (0.07% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:19Z] INFO  17:19:59,230 ProgressMeter -            done   1.5510717E7    15.0 s       1.0 s      100.0%    15.0 s       0.0 s
[2016-04-15T00:19Z] INFO  17:19:59,232 ProgressMeter - Total runtime 15.94 secs, 0.27 min, 0.00 hours
[2016-04-15T00:19Z] INFO  17:19:59,236 MicroScheduler - 11943 reads were filtered out during the traversal out of approximately 124639 total reads (9.58%)
[2016-04-15T00:19Z] INFO  17:19:59,237 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:19Z] INFO  17:19:59,237 MicroScheduler -   -> 495 reads (0.40% of total) failing BadMateFilter
[2016-04-15T00:19Z] INFO  17:19:59,238 MicroScheduler -   -> 9070 reads (7.28% of total) failing DuplicateReadFilter
[2016-04-15T00:19Z] INFO  17:19:59,239 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:19Z] INFO  17:19:59,239 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:19Z] INFO  17:19:59,240 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:19Z] INFO  17:19:59,240 MicroScheduler -   -> 2378 reads (1.91% of total) failing MappingQualityZeroFilter
[2016-04-15T00:19Z] INFO  17:19:59,241 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:19Z] INFO  17:19:59,242 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-15T00:19Z] INFO  17:19:59,243 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:19Z] INFO  17:19:59,826 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:19Z] INFO  17:19:59,830 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:19Z] INFO  17:19:59,830 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:19Z] INFO  17:19:59,831 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:19Z] INFO  17:19:59,835 HelpFormatter - Program Args: -T PrintReads -L 15:98984300-102531392 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/15/tx/tmpTjI5yc/R14-18106_kapa-NGv3-PE100-NGv3-sort-15_98984299_102531392-prep-prealign.bam
[2016-04-15T00:19Z] INFO  17:19:59,844 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:19Z] INFO  17:19:59,844 HelpFormatter - Date/Time: 2016/04/14 17:19:59
[2016-04-15T00:19Z] INFO  17:19:59,845 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:19Z] INFO  17:19:59,845 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:19Z] INFO  17:19:59,973 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:19Z] INFO  17:19:59,977 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:19Z] INFO  17:19:59,977 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:19Z] INFO  17:19:59,978 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:19Z] INFO  17:19:59,982 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/14/R14-18106_kapa-NGv3-PE100-NGv3-sort-14_81651874_97299968-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/14/tx/tmpo1pgmV/R14-18106_kapa-NGv3-PE100-NGv3-sort-14_81651874_97299968-prep-prealign-realign.intervals -l INFO -L 14:81651875-97299968 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:20Z] INFO  17:20:00,001 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:20Z] INFO  17:20:00,002 HelpFormatter - Date/Time: 2016/04/14 17:19:59
[2016-04-15T00:20Z] INFO  17:20:00,002 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:20Z] INFO  17:20:00,003 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:20Z] INFO  17:20:00,024 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:20Z] INFO  17:20:00,104 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:20Z] INFO  17:20:00,292 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T00:20Z] INFO  17:20:00,313 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:20Z] INFO  17:20:00,372 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-15T00:20Z] INFO  17:20:00,685 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:20Z] INFO  17:20:00,698 IntervalUtils - Processing 15648094 bp from intervals
[2016-04-15T00:20Z] WARN  17:20:00,704 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:20Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-14_50585061_66096324-prep-prealign.bam
[2016-04-15T00:20Z] INFO  17:20:00,755 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:20Z] GATK: realign ('14', 35072553, 50583270) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:20Z] INFO  17:20:00,815 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:20Z] INFO  17:20:01,056 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:20Z] INFO  17:20:01,058 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:20Z] INFO  17:20:01,058 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:20Z] INFO  17:20:01,059 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:20Z] INFO  17:20:01,085 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-15T00:20Z] GATK pre-alignment ('16', 0, 15528616) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:20Z] INFO  17:20:01,157 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:20Z] INFO  17:20:01,179 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:20Z] INFO  17:20:01,244 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-15T00:20Z] INFO  17:20:01,265 IntervalUtils - Processing 3547093 bp from intervals
[2016-04-15T00:20Z] INFO  17:20:01,337 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:20Z] INFO  17:20:01,339 ProgressMeter -            done     12234.0     3.0 s       4.4 m      100.0%     3.0 s       0.0 s
[2016-04-15T00:20Z] INFO  17:20:01,340 ProgressMeter - Total runtime 3.25 secs, 0.05 min, 0.00 hours
[2016-04-15T00:20Z] INFO  17:20:01,343 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 12234 total reads (0.00%)
[2016-04-15T00:20Z] INFO  17:20:01,344 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:20Z] INFO  17:20:01,344 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:20Z] INFO  17:20:01,353 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:20Z] GATK RealignerTargetCreator: R14-18106_kapa-NGv3-PE100-NGv3-sort-14_50585061_66096324-prep-prealign.bam 14:50585062-66096324
[2016-04-15T00:20Z] GATK: RealignerTargetCreator
[2016-04-15T00:20Z] INFO  17:20:01,610 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:20Z] INFO  17:20:01,611 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:20Z] INFO  17:20:01,612 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:20Z] INFO  17:20:01,613 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:20Z] INFO  17:20:01,626 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:20Z] INFO  17:20:01,666 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:20Z] INFO  17:20:02,598 ProgressMeter -     14:24976846    400005.0    60.0 s       2.5 m       35.0%     2.9 m     111.0 s
[2016-04-15T00:20Z] INFO  17:20:02,710 ProgressMeter -     15:28901329    100002.0    30.0 s       5.0 m       50.6%    59.0 s      29.0 s
[2016-04-15T00:20Z] INFO  17:20:02,721 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:20Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-15_0_20740485-prep.bam
[2016-04-15T00:20Z] GATK pre-alignment ('16', 15596122, 31106473) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:20Z] INFO  17:20:03,954 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:20Z] INFO  17:20:03,958 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:20Z] INFO  17:20:03,958 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:20Z] INFO  17:20:03,959 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:20Z] INFO  17:20:03,963 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/14/R14-18106_kapa-NGv3-PE100-NGv3-sort-14_35072553_50583270-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/14/R14-18106_kapa-NGv3-PE100-NGv3-sort-14_35072553_50583270-prep-prealign-realign.intervals -L 14:35072554-50583270 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/14/tx/tmp3721Th/R14-18106_kapa-NGv3-PE100-NGv3-sort-14_35072553_50583270-prep.bam
[2016-04-15T00:20Z] INFO  17:20:03,986 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:20Z] INFO  17:20:03,987 HelpFormatter - Date/Time: 2016/04/14 17:20:03
[2016-04-15T00:20Z] INFO  17:20:03,987 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:20Z] INFO  17:20:03,988 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:20Z] INFO  17:20:03,993 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:20Z] INFO  17:20:03,996 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:20Z] INFO  17:20:03,997 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:20Z] INFO  17:20:03,997 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:20Z] INFO  17:20:04,002 HelpFormatter - Program Args: -T PrintReads -L 16:1-15528616 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/16/tx/tmpIlX0YC/R14-18106_kapa-NGv3-PE100-NGv3-sort-16_0_15528616-prep-prealign.bam
[2016-04-15T00:20Z] INFO  17:20:04,041 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:20Z] INFO  17:20:04,042 HelpFormatter - Date/Time: 2016/04/14 17:20:03
[2016-04-15T00:20Z] INFO  17:20:04,043 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:20Z] INFO  17:20:04,043 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:20Z] INFO  17:20:04,275 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:20Z] INFO  17:20:04,295 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:20Z] INFO  17:20:04,360 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:20Z] INFO  17:20:04,363 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:20Z] INFO  17:20:04,364 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:20Z] INFO  17:20:04,364 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:20Z] INFO  17:20:04,369 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/14/R14-18106_kapa-NGv3-PE100-NGv3-sort-14_50585061_66096324-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/14/tx/tmpFqItNz/R14-18106_kapa-NGv3-PE100-NGv3-sort-14_50585061_66096324-prep-prealign-realign.intervals -l INFO -L 14:50585062-66096324 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:20Z] INFO  17:20:04,387 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:20Z] INFO  17:20:04,388 HelpFormatter - Date/Time: 2016/04/14 17:20:04
[2016-04-15T00:20Z] INFO  17:20:04,389 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:20Z] INFO  17:20:04,389 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:20Z] INFO  17:20:04,446 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:20Z] INFO  17:20:04,455 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:20Z] INFO  17:20:04,519 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:20Z] INFO  17:20:04,546 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.09
[2016-04-15T00:20Z] INFO  17:20:04,732 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T00:20Z] INFO  17:20:04,742 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:20Z] INFO  17:20:04,826 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-15T00:20Z] INFO  17:20:05,004 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@7172f77a
[2016-04-15T00:20Z] INFO  17:20:05,008 IntervalUtils - Processing 15510717 bp from intervals
[2016-04-15T00:20Z] WARN  17:20:05,022 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:20Z] INFO  17:20:05,117 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:20Z] INFO  17:20:05,137 IntervalUtils - Processing 15511263 bp from intervals
[2016-04-15T00:20Z] WARN  17:20:05,142 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:20Z] INFO  17:20:05,161 ProgressMeter -            done    313880.0    38.0 s       2.1 m       98.1%    38.0 s       0.0 s
[2016-04-15T00:20Z] INFO  17:20:05,161 ProgressMeter - Total runtime 38.91 secs, 0.65 min, 0.01 hours
[2016-04-15T00:20Z] INFO  17:20:05,162 MicroScheduler - 290 reads were filtered out during the traversal out of approximately 314170 total reads (0.09%)
[2016-04-15T00:20Z] INFO  17:20:05,162 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:20Z] INFO  17:20:05,162 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:20Z] INFO  17:20:05,162 MicroScheduler -   -> 290 reads (0.09% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:20Z] INFO  17:20:05,227 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:20Z] INFO  17:20:05,262 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:20Z] INFO  17:20:05,274 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:20Z] INFO  17:20:05,274 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:20Z] INFO  17:20:05,274 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:20Z] INFO  17:20:05,323 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-15T00:20Z] INFO  17:20:05,409 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:20Z] INFO  17:20:05,410 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:20Z] INFO  17:20:05,411 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:20Z] INFO  17:20:05,412 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:20Z] INFO  17:20:05,413 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:20Z] INFO  17:20:05,417 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:20Z] INFO  17:20:05,445 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:20Z] INFO  17:20:05,477 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-15T00:20Z] INFO  17:20:05,502 IntervalUtils - Processing 15528616 bp from intervals
[2016-04-15T00:20Z] INFO  17:20:05,565 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:20Z] INFO  17:20:05,568 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:20Z] INFO  17:20:05,569 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:20Z] INFO  17:20:05,569 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:20Z] INFO  17:20:05,574 HelpFormatter - Program Args: -T PrintReads -L 16:15596123-31106473 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/16/tx/tmpm0Th7h/R14-18106_kapa-NGv3-PE100-NGv3-sort-16_15596122_31106473-prep-prealign.bam
[2016-04-15T00:20Z] INFO  17:20:05,586 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:20Z] INFO  17:20:05,586 HelpFormatter - Date/Time: 2016/04/14 17:20:05
[2016-04-15T00:20Z] INFO  17:20:05,587 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:20Z] INFO  17:20:05,587 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:20Z] INFO  17:20:05,600 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:20Z] INFO  17:20:05,612 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:20Z] INFO  17:20:05,750 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:20Z] INFO  17:20:05,955 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:20Z] INFO  17:20:05,956 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:20Z] INFO  17:20:05,957 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:20Z] INFO  17:20:05,957 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:20Z] INFO  17:20:05,971 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:20Z] INFO  17:20:06,124 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:20Z] INFO  17:20:06,585 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:20Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-14_97304098_107349540-prep-prealign.bam
[2016-04-15T00:20Z] INFO  17:20:07,052 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-15T00:20Z] INFO  17:20:07,161 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:20Z] INFO  17:20:07,171 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:20Z] INFO  17:20:07,225 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-15T00:20Z] INFO  17:20:07,250 IntervalUtils - Processing 15510351 bp from intervals
[2016-04-15T00:20Z] INFO  17:20:07,343 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:20Z] GATK RealignerTargetCreator: R14-18106_kapa-NGv3-PE100-NGv3-sort-14_97304098_107349540-prep-prealign.bam 14:97304099-107349540
[2016-04-15T00:20Z] GATK: RealignerTargetCreator
[2016-04-15T00:20Z] INFO  17:20:07,716 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:20Z] INFO  17:20:07,717 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:20Z] INFO  17:20:07,718 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:20Z] INFO  17:20:07,719 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:20Z] INFO  17:20:07,735 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:20Z] INFO  17:20:07,894 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:20Z] INFO  17:20:09,232 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@41fd9d8e
[2016-04-15T00:20Z] INFO  17:20:09,340 ProgressMeter -            done    512962.0    66.0 s       2.2 m      100.0%    66.0 s       0.0 s
[2016-04-15T00:20Z] INFO  17:20:09,341 ProgressMeter - Total runtime 66.81 secs, 1.11 min, 0.02 hours
[2016-04-15T00:20Z] INFO  17:20:09,341 MicroScheduler - 221 reads were filtered out during the traversal out of approximately 513183 total reads (0.04%)
[2016-04-15T00:20Z] INFO  17:20:09,342 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:20Z] INFO  17:20:09,342 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:20Z] INFO  17:20:09,342 MicroScheduler -   -> 221 reads (0.04% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:20Z] INFO  17:20:10,244 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:20Z] INFO  17:20:10,247 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:20Z] INFO  17:20:10,248 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:20Z] INFO  17:20:10,248 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:20Z] INFO  17:20:10,253 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/14/R14-18106_kapa-NGv3-PE100-NGv3-sort-14_97304098_107349540-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/14/tx/tmpsTkHby/R14-18106_kapa-NGv3-PE100-NGv3-sort-14_97304098_107349540-prep-prealign-realign.intervals -l INFO -L 14:97304099-107349540 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:20Z] INFO  17:20:10,287 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:20Z] INFO  17:20:10,288 HelpFormatter - Date/Time: 2016/04/14 17:20:10
[2016-04-15T00:20Z] INFO  17:20:10,289 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:20Z] INFO  17:20:10,289 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:20Z] INFO  17:20:10,428 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:20Z] INFO  17:20:10,687 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T00:20Z] INFO  17:20:10,697 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:20Z] INFO  17:20:10,749 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-15T00:20Z] INFO  17:20:10,845 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:20Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-14_19553416_35066851-prep-prealign.bam
[2016-04-15T00:20Z] INFO  17:20:11,046 IntervalUtils - Processing 10045442 bp from intervals
[2016-04-15T00:20Z] WARN  17:20:11,052 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:20Z] INFO  17:20:11,122 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:20Z] INFO  17:20:11,264 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:20Z] INFO  17:20:11,265 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:20Z] INFO  17:20:11,266 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:20Z] INFO  17:20:11,267 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:20Z] INFO  17:20:11,720 ProgressMeter -     15:42363364    200002.0    30.0 s       2.5 m       35.3%    84.0 s      54.0 s
[2016-04-15T00:20Z] GATK RealignerTargetCreator: R14-18106_kapa-NGv3-PE100-NGv3-sort-14_19553416_35066851-prep-prealign.bam 14:19553417-35066851
[2016-04-15T00:20Z] GATK: RealignerTargetCreator
[2016-04-15T00:20Z] INFO  17:20:12,986 ProgressMeter -     15:64039947    200004.0    30.0 s       2.5 m       75.0%    40.0 s      10.0 s
[2016-04-15T00:20Z] INFO  17:20:13,200 ProgressMeter -     15:90808029    200005.0    30.0 s       2.5 m       47.4%    63.0 s      33.0 s
[2016-04-15T00:20Z] INFO  17:20:13,385 ProgressMeter -     15:74704110    100001.0    30.0 s       5.1 m       43.6%    68.0 s      38.0 s
[2016-04-15T00:20Z] INFO  17:20:14,930 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:20Z] INFO  17:20:14,934 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:20Z] INFO  17:20:14,935 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:20Z] INFO  17:20:14,935 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:20Z] INFO  17:20:14,940 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/14/R14-18106_kapa-NGv3-PE100-NGv3-sort-14_19553416_35066851-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/14/tx/tmp848Q_p/R14-18106_kapa-NGv3-PE100-NGv3-sort-14_19553416_35066851-prep-prealign-realign.intervals -l INFO -L 14:19553417-35066851 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:20Z] INFO  17:20:14,953 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:20Z] INFO  17:20:14,964 HelpFormatter - Date/Time: 2016/04/14 17:20:14
[2016-04-15T00:20Z] INFO  17:20:14,965 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:20Z] INFO  17:20:14,966 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:20Z] INFO  17:20:15,111 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:20Z] INFO  17:20:15,392 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T00:20Z] INFO  17:20:15,414 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:20Z] INFO  17:20:15,498 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-15T00:20Z] INFO  17:20:15,604 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@5fe152b7
[2016-04-15T00:20Z] INFO  17:20:15,720 ProgressMeter -            done    368868.0    53.0 s       2.4 m       99.8%    53.0 s       0.0 s
[2016-04-15T00:20Z] INFO  17:20:15,721 ProgressMeter - Total runtime 53.12 secs, 0.89 min, 0.01 hours
[2016-04-15T00:20Z] INFO  17:20:15,721 MicroScheduler - 264 reads were filtered out during the traversal out of approximately 369132 total reads (0.07%)
[2016-04-15T00:20Z] INFO  17:20:15,722 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:20Z] INFO  17:20:15,722 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:20Z] INFO  17:20:15,722 MicroScheduler -   -> 264 reads (0.07% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:20Z] INFO  17:20:15,857 IntervalUtils - Processing 15513435 bp from intervals
[2016-04-15T00:20Z] WARN  17:20:15,862 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:20Z] INFO  17:20:15,955 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:20Z] INFO  17:20:16,123 ProgressMeter -            done    123885.0    10.0 s      87.0 s      100.0%    10.0 s       0.0 s
[2016-04-15T00:20Z] INFO  17:20:16,124 ProgressMeter - Total runtime 10.85 secs, 0.18 min, 0.00 hours
[2016-04-15T00:20Z] INFO  17:20:16,127 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 123885 total reads (0.00%)
[2016-04-15T00:20Z] INFO  17:20:16,128 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:20Z] INFO  17:20:16,128 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:20Z] INFO  17:20:16,128 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:20Z] INFO  17:20:16,172 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:20Z] INFO  17:20:16,174 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:20Z] INFO  17:20:16,174 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:20Z] INFO  17:20:16,175 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:20Z] INFO  17:20:16,627 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@41fd9d8e
[2016-04-15T00:20Z] INFO  17:20:16,734 ProgressMeter -            done     84112.0    15.0 s       3.0 m       99.6%    15.0 s       0.0 s
[2016-04-15T00:20Z] INFO  17:20:16,734 ProgressMeter - Total runtime 15.12 secs, 0.25 min, 0.00 hours
[2016-04-15T00:20Z] INFO  17:20:16,735 MicroScheduler - 37 reads were filtered out during the traversal out of approximately 84149 total reads (0.04%)
[2016-04-15T00:20Z] INFO  17:20:16,735 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:20Z] INFO  17:20:16,735 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:20Z] INFO  17:20:16,736 MicroScheduler -   -> 37 reads (0.04% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:20Z] INFO  17:20:17,121 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:20Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-14_66135960_81646674-prep-prealign.bam
[2016-04-15T00:20Z] INFO  17:20:17,539 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:20Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-14_35072553_50583270-prep.bam
[2016-04-15T00:20Z] GATK pre-alignment ('16', 31120544, 46629582) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:20Z] INFO  17:20:18,149 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:20Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-15_98984299_102531392-prep-prealign.bam
[2016-04-15T00:20Z] GATK RealignerTargetCreator: R14-18106_kapa-NGv3-PE100-NGv3-sort-14_66135960_81646674-prep-prealign.bam 14:66135961-81646674
[2016-04-15T00:20Z] GATK: RealignerTargetCreator
[2016-04-15T00:20Z] GATK RealignerTargetCreator: R14-18106_kapa-NGv3-PE100-NGv3-sort-15_98984299_102531392-prep-prealign.bam 15:98984300-102531392
[2016-04-15T00:20Z] GATK: RealignerTargetCreator
[2016-04-15T00:20Z] INFO  17:20:18,613 ProgressMeter -    12:124071487    500009.0    32.0 s      64.0 s       92.4%    34.0 s       2.0 s
[2016-04-15T00:20Z] INFO  17:20:19,521 ProgressMeter -            done   1.5648094E7    18.0 s       1.0 s      100.0%    18.0 s       0.0 s
[2016-04-15T00:20Z] INFO  17:20:19,522 ProgressMeter - Total runtime 18.46 secs, 0.31 min, 0.01 hours
[2016-04-15T00:20Z] INFO  17:20:19,527 MicroScheduler - 19121 reads were filtered out during the traversal out of approximately 239272 total reads (7.99%)
[2016-04-15T00:20Z] INFO  17:20:19,528 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:20Z] INFO  17:20:19,529 MicroScheduler -   -> 763 reads (0.32% of total) failing BadMateFilter
[2016-04-15T00:20Z] INFO  17:20:19,530 MicroScheduler -   -> 17863 reads (7.47% of total) failing DuplicateReadFilter
[2016-04-15T00:20Z] INFO  17:20:19,531 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:20Z] INFO  17:20:19,531 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:20Z] INFO  17:20:19,532 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:20Z] INFO  17:20:19,533 MicroScheduler -   -> 495 reads (0.21% of total) failing MappingQualityZeroFilter
[2016-04-15T00:20Z] INFO  17:20:19,534 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:20Z] INFO  17:20:19,535 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-15T00:20Z] INFO  17:20:19,536 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:20Z] INFO  17:20:20,844 ProgressMeter -            done    575948.0    34.0 s      59.0 s      100.0%    34.0 s       0.0 s
[2016-04-15T00:20Z] INFO  17:20:20,845 ProgressMeter - Total runtime 34.50 secs, 0.58 min, 0.01 hours
[2016-04-15T00:20Z] INFO  17:20:20,848 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 575948 total reads (0.00%)
[2016-04-15T00:20Z] INFO  17:20:20,849 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:20Z] INFO  17:20:20,849 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:20Z] INFO  17:20:20,849 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:20Z] INFO  17:20:21,100 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:20Z] GATK: realign ('14', 81651874, 97299968) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:20Z] INFO  17:20:21,133 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:20Z] INFO  17:20:21,137 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:20Z] INFO  17:20:21,137 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:20Z] INFO  17:20:21,138 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:20Z] INFO  17:20:21,143 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/14/R14-18106_kapa-NGv3-PE100-NGv3-sort-14_66135960_81646674-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/14/tx/tmpxzpxru/R14-18106_kapa-NGv3-PE100-NGv3-sort-14_66135960_81646674-prep-prealign-realign.intervals -l INFO -L 14:66135961-81646674 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:20Z] INFO  17:20:21,141 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:20Z] INFO  17:20:21,143 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:20Z] INFO  17:20:21,144 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:20Z] INFO  17:20:21,144 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:20Z] INFO  17:20:21,148 HelpFormatter - Program Args: -T PrintReads -L 16:31120545-46629582 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/16/tx/tmpc5Ly6S/R14-18106_kapa-NGv3-PE100-NGv3-sort-16_31120544_46629582-prep-prealign.bam
[2016-04-15T00:20Z] INFO  17:20:21,152 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:20Z] INFO  17:20:21,152 HelpFormatter - Date/Time: 2016/04/14 17:20:21
[2016-04-15T00:20Z] INFO  17:20:21,153 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:20Z] INFO  17:20:21,153 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:20Z] INFO  17:20:21,171 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:20Z] INFO  17:20:21,172 HelpFormatter - Date/Time: 2016/04/14 17:20:21
[2016-04-15T00:20Z] INFO  17:20:21,173 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:20Z] INFO  17:20:21,177 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:20Z] INFO  17:20:21,267 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:20Z] INFO  17:20:21,270 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:20Z] INFO  17:20:21,274 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:20Z] INFO  17:20:21,275 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:20Z] INFO  17:20:21,275 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:20Z] INFO  17:20:21,294 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/15/R14-18106_kapa-NGv3-PE100-NGv3-sort-15_98984299_102531392-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/15/tx/tmpW_7oa9/R14-18106_kapa-NGv3-PE100-NGv3-sort-15_98984299_102531392-prep-prealign-realign.intervals -l INFO -L 15:98984300-102531392 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:20Z] INFO  17:20:21,304 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:20Z] INFO  17:20:21,315 HelpFormatter - Date/Time: 2016/04/14 17:20:21
[2016-04-15T00:20Z] INFO  17:20:21,316 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:20Z] INFO  17:20:21,317 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:20Z] INFO  17:20:21,323 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:20Z] INFO  17:20:21,425 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:20Z] INFO  17:20:21,466 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T00:20Z] INFO  17:20:21,486 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:20Z] INFO  17:20:21,541 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-15T00:20Z] INFO  17:20:21,694 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T00:20Z] INFO  17:20:21,709 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:20Z] INFO  17:20:21,761 IntervalUtils - Processing 15510714 bp from intervals
[2016-04-15T00:20Z] WARN  17:20:21,767 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:20Z] INFO  17:20:21,783 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-15T00:20Z] INFO  17:20:21,850 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:20Z] INFO  17:20:21,951 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@7172f77a
[2016-04-15T00:20Z] INFO  17:20:22,059 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:20Z] INFO  17:20:22,063 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:20Z] INFO  17:20:22,063 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:20Z] INFO  17:20:22,064 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:20Z] INFO  17:20:22,120 ProgressMeter -            done    325167.0    38.0 s     119.0 s      100.0%    38.0 s       0.0 s
[2016-04-15T00:20Z] INFO  17:20:22,121 ProgressMeter - Total runtime 38.94 secs, 0.65 min, 0.01 hours
[2016-04-15T00:20Z] INFO  17:20:22,122 MicroScheduler - 200 reads were filtered out during the traversal out of approximately 325367 total reads (0.06%)
[2016-04-15T00:20Z] INFO  17:20:22,122 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:20Z] INFO  17:20:22,122 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:20Z] INFO  17:20:22,123 MicroScheduler -   -> 200 reads (0.06% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:20Z] INFO  17:20:22,207 IntervalUtils - Processing 3547093 bp from intervals
[2016-04-15T00:20Z] WARN  17:20:22,213 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:20Z] INFO  17:20:22,369 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:20Z] INFO  17:20:22,381 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:20Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-12_109494486_125263132-prep.bam
[2016-04-15T00:20Z] INFO  17:20:22,475 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:20Z] INFO  17:20:22,476 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:20Z] INFO  17:20:22,477 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:20Z] INFO  17:20:22,478 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:20Z] INFO  17:20:22,740 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-15T00:20Z] INFO  17:20:22,864 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:20Z] INFO  17:20:22,882 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:20Z] INFO  17:20:22,936 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-15T00:20Z] INFO  17:20:22,950 IntervalUtils - Processing 15509038 bp from intervals
[2016-04-15T00:20Z] INFO  17:20:23,024 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:20Z] INFO  17:20:23,363 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:20Z] INFO  17:20:23,364 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:20Z] INFO  17:20:23,365 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:20Z] INFO  17:20:23,366 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:20Z] INFO  17:20:23,402 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:20Z] INFO  17:20:23,606 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:20Z] INFO  17:20:23,633 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:20Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-15_83448996_98982979-prep-prealign.bam
[2016-04-15T00:20Z] INFO  17:20:23,921 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:20Z] INFO  17:20:23,924 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:20Z] INFO  17:20:23,925 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:20Z] INFO  17:20:23,925 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:20Z] INFO  17:20:23,930 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/14/R14-18106_kapa-NGv3-PE100-NGv3-sort-14_81651874_97299968-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/14/R14-18106_kapa-NGv3-PE100-NGv3-sort-14_81651874_97299968-prep-prealign-realign.intervals -L 14:81651875-97299968 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/14/tx/tmpMtyfRa/R14-18106_kapa-NGv3-PE100-NGv3-sort-14_81651874_97299968-prep.bam
[2016-04-15T00:20Z] INFO  17:20:23,939 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:20Z] INFO  17:20:23,940 HelpFormatter - Date/Time: 2016/04/14 17:20:23
[2016-04-15T00:20Z] INFO  17:20:23,940 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:20Z] INFO  17:20:23,940 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:20Z] GATK pre-alignment ('16', 46633742, 64982002) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:20Z] INFO  17:20:24,136 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:20Z] INFO  17:20:24,285 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:20Z] INFO  17:20:24,312 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:20Z] INFO  17:20:24,366 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-15T00:20Z] GATK RealignerTargetCreator: R14-18106_kapa-NGv3-PE100-NGv3-sort-15_83448996_98982979-prep-prealign.bam 15:83448997-98982979
[2016-04-15T00:20Z] GATK: RealignerTargetCreator
[2016-04-15T00:20Z] INFO  17:20:24,752 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@5fe152b7
[2016-04-15T00:20Z] INFO  17:20:24,783 IntervalUtils - Processing 15648094 bp from intervals
[2016-04-15T00:20Z] WARN  17:20:24,788 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:20Z] INFO  17:20:24,854 ProgressMeter -            done    344068.0    41.0 s       2.0 m      100.0%    41.0 s       0.0 s
[2016-04-15T00:20Z] INFO  17:20:24,855 ProgressMeter - Total runtime 41.90 secs, 0.70 min, 0.01 hours
[2016-04-15T00:20Z] INFO  17:20:24,856 MicroScheduler - 183 reads were filtered out during the traversal out of approximately 344251 total reads (0.05%)
[2016-04-15T00:20Z] INFO  17:20:24,857 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:20Z] INFO  17:20:24,858 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:20Z] INFO  17:20:24,858 MicroScheduler -   -> 183 reads (0.05% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:20Z] INFO  17:20:24,874 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:20Z] INFO  17:20:24,967 ProgressMeter -            done   1.5511263E7    19.0 s       1.0 s      100.0%    19.0 s       0.0 s
[2016-04-15T00:20Z] INFO  17:20:24,968 ProgressMeter - Total runtime 19.56 secs, 0.33 min, 0.01 hours
[2016-04-15T00:20Z] INFO  17:20:24,973 MicroScheduler - 22256 reads were filtered out during the traversal out of approximately 286015 total reads (7.78%)
[2016-04-15T00:20Z] INFO  17:20:24,974 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:20Z] INFO  17:20:24,974 MicroScheduler -   -> 847 reads (0.30% of total) failing BadMateFilter
[2016-04-15T00:20Z] INFO  17:20:24,974 MicroScheduler -   -> 20911 reads (7.31% of total) failing DuplicateReadFilter
[2016-04-15T00:20Z] INFO  17:20:24,974 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:20Z] INFO  17:20:24,975 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:20Z] INFO  17:20:24,975 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:20Z] INFO  17:20:24,975 MicroScheduler -   -> 498 reads (0.17% of total) failing MappingQualityZeroFilter
[2016-04-15T00:20Z] INFO  17:20:24,975 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:20Z] INFO  17:20:24,976 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-15T00:20Z] INFO  17:20:24,976 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:20Z] INFO  17:20:25,014 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:20Z] INFO  17:20:25,015 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:20Z] INFO  17:20:25,016 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:20Z] INFO  17:20:25,017 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:20Z] INFO  17:20:25,227 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:20Z] INFO  17:20:25,374 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:20Z] INFO  17:20:26,139 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:20Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-15_52404364_67923265-prep-prealign.bam
[2016-04-15T00:20Z] INFO  17:20:26,585 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:20Z] GATK: realign ('14', 50585061, 66096324) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:20Z] INFO  17:20:26,974 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:20Z] INFO  17:20:26,977 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:20Z] INFO  17:20:26,978 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:20Z] INFO  17:20:26,978 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:20Z] INFO  17:20:26,983 HelpFormatter - Program Args: -T PrintReads -L 16:46633743-64982002 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/16/tx/tmp28UICi/R14-18106_kapa-NGv3-PE100-NGv3-sort-16_46633742_64982002-prep-prealign.bam
[2016-04-15T00:20Z] INFO  17:20:26,992 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:20Z] INFO  17:20:27,001 HelpFormatter - Date/Time: 2016/04/14 17:20:26
[2016-04-15T00:20Z] INFO  17:20:27,002 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:20Z] INFO  17:20:27,002 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:20Z] INFO  17:20:27,188 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:20Z] GATK RealignerTargetCreator: R14-18106_kapa-NGv3-PE100-NGv3-sort-15_52404364_67923265-prep-prealign.bam 15:52404365-67923265
[2016-04-15T00:20Z] GATK: RealignerTargetCreator
[2016-04-15T00:20Z] INFO  17:20:27,295 ProgressMeter -            done   1.0045442E7    16.0 s       1.0 s      100.0%    16.0 s       0.0 s
[2016-04-15T00:20Z] INFO  17:20:27,296 ProgressMeter - Total runtime 16.03 secs, 0.27 min, 0.00 hours
[2016-04-15T00:20Z] INFO  17:20:27,312 MicroScheduler - 25922 reads were filtered out during the traversal out of approximately 315464 total reads (8.22%)
[2016-04-15T00:20Z] INFO  17:20:27,313 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:20Z] INFO  17:20:27,314 MicroScheduler -   -> 817 reads (0.26% of total) failing BadMateFilter
[2016-04-15T00:20Z] INFO  17:20:27,315 MicroScheduler -   -> 23948 reads (7.59% of total) failing DuplicateReadFilter
[2016-04-15T00:20Z] INFO  17:20:27,316 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:20Z] INFO  17:20:27,316 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:20Z] INFO  17:20:27,317 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:20Z] INFO  17:20:27,317 MicroScheduler -   -> 1157 reads (0.37% of total) failing MappingQualityZeroFilter
[2016-04-15T00:20Z] INFO  17:20:27,318 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:20Z] INFO  17:20:27,319 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-15T00:20Z] INFO  17:20:27,319 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:20Z] INFO  17:20:27,447 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:20Z] INFO  17:20:27,451 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:20Z] INFO  17:20:27,451 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:20Z] INFO  17:20:27,452 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:20Z] INFO  17:20:27,457 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/15/R14-18106_kapa-NGv3-PE100-NGv3-sort-15_83448996_98982979-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/15/tx/tmpImYs2e/R14-18106_kapa-NGv3-PE100-NGv3-sort-15_83448996_98982979-prep-prealign-realign.intervals -l INFO -L 15:83448997-98982979 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:20Z] INFO  17:20:27,474 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:20Z] INFO  17:20:27,474 HelpFormatter - Date/Time: 2016/04/14 17:20:27
[2016-04-15T00:20Z] INFO  17:20:27,475 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:20Z] INFO  17:20:27,475 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:20Z] INFO  17:20:27,566 ProgressMeter -     12:53895967    400010.0    32.0 s      82.0 s       44.9%    71.0 s      39.0 s
[2016-04-15T00:20Z] INFO  17:20:27,643 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:20Z] INFO  17:20:27,852 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T00:20Z] INFO  17:20:27,862 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:20Z] INFO  17:20:27,938 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-15T00:20Z] INFO  17:20:28,295 IntervalUtils - Processing 15533983 bp from intervals
[2016-04-15T00:20Z] WARN  17:20:28,300 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:20Z] INFO  17:20:28,301 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-15T00:20Z] INFO  17:20:28,388 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:20Z] INFO  17:20:28,397 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:20Z] INFO  17:20:28,425 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:20Z] INFO  17:20:28,437 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.04
[2016-04-15T00:20Z] INFO  17:20:28,452 IntervalUtils - Processing 18348260 bp from intervals
[2016-04-15T00:20Z] INFO  17:20:28,519 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:20Z] INFO  17:20:28,654 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:20Z] INFO  17:20:28,655 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:20Z] INFO  17:20:28,656 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:20Z] INFO  17:20:28,657 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:20Z] INFO  17:20:28,801 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:20Z] INFO  17:20:28,802 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:20Z] INFO  17:20:28,803 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:20Z] INFO  17:20:28,804 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:20Z] INFO  17:20:28,819 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:20Z] INFO  17:20:28,821 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:20Z] GATK: realign ('14', 97304098, 107349540) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:20Z] INFO  17:20:29,068 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:20Z] INFO  17:20:29,511 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:20Z] INFO  17:20:29,514 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:20Z] INFO  17:20:29,514 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:20Z] INFO  17:20:29,515 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:20Z] INFO  17:20:29,520 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/14/R14-18106_kapa-NGv3-PE100-NGv3-sort-14_50585061_66096324-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/14/R14-18106_kapa-NGv3-PE100-NGv3-sort-14_50585061_66096324-prep-prealign-realign.intervals -L 14:50585062-66096324 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/14/tx/tmp9LSvLj/R14-18106_kapa-NGv3-PE100-NGv3-sort-14_50585061_66096324-prep.bam
[2016-04-15T00:20Z] INFO  17:20:29,544 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:20Z] INFO  17:20:29,545 HelpFormatter - Date/Time: 2016/04/14 17:20:29
[2016-04-15T00:20Z] INFO  17:20:29,545 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:20Z] INFO  17:20:29,546 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:20Z] INFO  17:20:29,713 ProgressMeter -            done   3547093.0     7.0 s       2.0 s      100.0%     7.0 s       0.0 s
[2016-04-15T00:20Z] INFO  17:20:29,714 ProgressMeter - Total runtime 7.24 secs, 0.12 min, 0.00 hours
[2016-04-15T00:20Z] INFO  17:20:29,718 MicroScheduler - 12755 reads were filtered out during the traversal out of approximately 84958 total reads (15.01%)
[2016-04-15T00:20Z] INFO  17:20:29,719 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:20Z] INFO  17:20:29,720 MicroScheduler -   -> 195 reads (0.23% of total) failing BadMateFilter
[2016-04-15T00:20Z] INFO  17:20:29,721 MicroScheduler -   -> 5988 reads (7.05% of total) failing DuplicateReadFilter
[2016-04-15T00:20Z] INFO  17:20:29,721 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:20Z] INFO  17:20:29,722 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:20Z] INFO  17:20:29,722 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:20Z] INFO  17:20:29,723 MicroScheduler -   -> 6572 reads (7.74% of total) failing MappingQualityZeroFilter
[2016-04-15T00:20Z] INFO  17:20:29,724 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:20Z] INFO  17:20:29,724 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-15T00:20Z] INFO  17:20:29,735 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:20Z] INFO  17:20:29,808 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:20Z] INFO  17:20:29,962 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:20Z] INFO  17:20:29,966 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:20Z] INFO  17:20:29,966 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:20Z] INFO  17:20:29,967 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:20Z] INFO  17:20:29,972 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/15/R14-18106_kapa-NGv3-PE100-NGv3-sort-15_52404364_67923265-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/15/tx/tmpMMmos3/R14-18106_kapa-NGv3-PE100-NGv3-sort-15_52404364_67923265-prep-prealign-realign.intervals -l INFO -L 15:52404365-67923265 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:20Z] INFO  17:20:29,982 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:20Z] INFO  17:20:29,991 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:20Z] INFO  17:20:29,992 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:20Z] INFO  17:20:29,993 HelpFormatter - Date/Time: 2016/04/14 17:20:29
[2016-04-15T00:20Z] INFO  17:20:29,994 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:20Z] INFO  17:20:29,994 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:20Z] INFO  17:20:30,065 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-15T00:20Z] INFO  17:20:30,101 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:20Z] INFO  17:20:30,389 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T00:20Z] INFO  17:20:30,405 IntervalUtils - Processing 15511263 bp from intervals
[2016-04-15T00:20Z] WARN  17:20:30,410 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:20Z] INFO  17:20:30,413 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:20Z] INFO  17:20:30,472 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-15T00:20Z] INFO  17:20:30,493 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:20Z] INFO  17:20:30,597 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:20Z] INFO  17:20:30,598 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:20Z] INFO  17:20:30,599 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:20Z] INFO  17:20:30,600 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:20Z] INFO  17:20:30,781 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:20Z] INFO  17:20:30,862 IntervalUtils - Processing 15518901 bp from intervals
[2016-04-15T00:20Z] WARN  17:20:30,868 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:20Z] INFO  17:20:30,957 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:20Z] INFO  17:20:30,983 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:20Z] INFO  17:20:31,114 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:20Z] GATK: realign ('15', 98984299, 102531392) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:20Z] INFO  17:20:31,188 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:20Z] INFO  17:20:31,189 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:20Z] INFO  17:20:31,190 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:20Z] INFO  17:20:31,190 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:20Z] INFO  17:20:31,897 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:20Z] INFO  17:20:31,915 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:20Z] INFO  17:20:31,920 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:20Z] INFO  17:20:31,921 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:20Z] INFO  17:20:31,926 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/14/R14-18106_kapa-NGv3-PE100-NGv3-sort-14_97304098_107349540-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/14/R14-18106_kapa-NGv3-PE100-NGv3-sort-14_97304098_107349540-prep-prealign-realign.intervals -L 14:97304099-107349540 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/14/tx/tmpSQzSAK/R14-18106_kapa-NGv3-PE100-NGv3-sort-14_97304098_107349540-prep.bam
[2016-04-15T00:20Z] INFO  17:20:31,945 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:20Z] INFO  17:20:31,946 HelpFormatter - Date/Time: 2016/04/14 17:20:31
[2016-04-15T00:20Z] INFO  17:20:31,946 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:20Z] INFO  17:20:31,947 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:20Z] INFO  17:20:32,196 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:20Z] INFO  17:20:32,309 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:20Z] INFO  17:20:32,319 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:20Z] INFO  17:20:32,371 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-15T00:20Z] INFO  17:20:32,715 ProgressMeter -     15:35274991    400007.0    60.0 s       2.5 m       90.1%    66.0 s       6.0 s
[2016-04-15T00:20Z] INFO  17:20:32,724 IntervalUtils - Processing 10045442 bp from intervals
[2016-04-15T00:20Z] WARN  17:20:32,729 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:20Z] INFO  17:20:32,799 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:20Z] INFO  17:20:32,901 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:20Z] INFO  17:20:32,902 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:20Z] INFO  17:20:32,903 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:20Z] INFO  17:20:32,904 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:20Z] INFO  17:20:33,063 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:20Z] INFO  17:20:33,149 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:20Z] INFO  17:20:33,462 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@41fd9d8e
[2016-04-15T00:20Z] INFO  17:20:33,580 ProgressMeter -            done    444588.0    60.0 s       2.3 m      100.0%    60.0 s       0.0 s
[2016-04-15T00:20Z] INFO  17:20:33,580 ProgressMeter - Total runtime 60.91 secs, 1.02 min, 0.02 hours
[2016-04-15T00:20Z] INFO  17:20:33,581 MicroScheduler - 292 reads were filtered out during the traversal out of approximately 444880 total reads (0.07%)
[2016-04-15T00:20Z] INFO  17:20:33,581 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:20Z] INFO  17:20:33,581 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:20Z] INFO  17:20:33,582 MicroScheduler -   -> 292 reads (0.07% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:20Z] INFO  17:20:33,883 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:20Z] INFO  17:20:33,886 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:20Z] INFO  17:20:33,887 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:20Z] INFO  17:20:33,887 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:20Z] INFO  17:20:33,892 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/15/R14-18106_kapa-NGv3-PE100-NGv3-sort-15_98984299_102531392-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/15/R14-18106_kapa-NGv3-PE100-NGv3-sort-15_98984299_102531392-prep-prealign-realign.intervals -L 15:98984300-102531392 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/15/tx/tmpImrvtR/R14-18106_kapa-NGv3-PE100-NGv3-sort-15_98984299_102531392-prep.bam
[2016-04-15T00:20Z] INFO  17:20:33,902 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:20Z] INFO  17:20:33,902 HelpFormatter - Date/Time: 2016/04/14 17:20:33
[2016-04-15T00:20Z] INFO  17:20:33,903 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:20Z] INFO  17:20:33,903 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:20Z] INFO  17:20:34,185 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:20Z] INFO  17:20:34,330 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:20Z] INFO  17:20:34,338 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:20Z] INFO  17:20:34,397 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-15T00:20Z] INFO  17:20:34,781 IntervalUtils - Processing 3547093 bp from intervals
[2016-04-15T00:20Z] WARN  17:20:34,786 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:20Z] INFO  17:20:34,867 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:20Z] INFO  17:20:34,931 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:20Z] INFO  17:20:34,932 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:20Z] INFO  17:20:34,933 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:20Z] INFO  17:20:34,934 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:20Z] INFO  17:20:35,002 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:20Z] INFO  17:20:35,035 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:20Z] INFO  17:20:35,297 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:20Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-15_20741621_36872162-prep-prealign.bam
[2016-04-15T00:20Z] INFO  17:20:35,984 ProgressMeter -      16:1603406    200003.0    30.0 s       2.5 m       10.3%     4.8 m       4.3 m
[2016-04-15T00:20Z] GATK RealignerTargetCreator: R14-18106_kapa-NGv3-PE100-NGv3-sort-15_20741621_36872162-prep-prealign.bam 15:20741622-36872162
[2016-04-15T00:20Z] GATK: RealignerTargetCreator
[2016-04-15T00:20Z] INFO  17:20:37,747 ProgressMeter -     16:19451704    200002.0    30.0 s       2.5 m       24.9%   120.0 s      90.0 s
[2016-04-15T00:20Z] INFO  17:20:38,446 ProgressMeter -            done   1.5513435E7    22.0 s       1.0 s      100.0%    22.0 s       0.0 s
[2016-04-15T00:20Z] INFO  17:20:38,447 ProgressMeter - Total runtime 22.27 secs, 0.37 min, 0.01 hours
[2016-04-15T00:20Z] INFO  17:20:38,448 MicroScheduler - 74202 reads were filtered out during the traversal out of approximately 516283 total reads (14.37%)
[2016-04-15T00:20Z] INFO  17:20:38,449 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:20Z] INFO  17:20:38,450 MicroScheduler -   -> 1113 reads (0.22% of total) failing BadMateFilter
[2016-04-15T00:20Z] INFO  17:20:38,450 MicroScheduler -   -> 36956 reads (7.16% of total) failing DuplicateReadFilter
[2016-04-15T00:20Z] INFO  17:20:38,451 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:20Z] INFO  17:20:38,451 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:20Z] INFO  17:20:38,452 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:20Z] INFO  17:20:38,453 MicroScheduler -   -> 36133 reads (7.00% of total) failing MappingQualityZeroFilter
[2016-04-15T00:20Z] INFO  17:20:38,453 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:20Z] INFO  17:20:38,454 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-15T00:20Z] INFO  17:20:38,455 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:20Z] INFO  17:20:39,387 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:20Z] INFO  17:20:39,391 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:20Z] INFO  17:20:39,392 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:20Z] INFO  17:20:39,392 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:20Z] INFO  17:20:39,398 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/15/R14-18106_kapa-NGv3-PE100-NGv3-sort-15_20741621_36872162-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/15/tx/tmpCLakqr/R14-18106_kapa-NGv3-PE100-NGv3-sort-15_20741621_36872162-prep-prealign-realign.intervals -l INFO -L 15:20741622-36872162 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:20Z] INFO  17:20:39,421 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:20Z] INFO  17:20:39,422 HelpFormatter - Date/Time: 2016/04/14 17:20:39
[2016-04-15T00:20Z] INFO  17:20:39,423 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:20Z] INFO  17:20:39,424 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:20Z] INFO  17:20:39,545 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:20Z] INFO  17:20:39,700 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@41fd9d8e
[2016-04-15T00:20Z] INFO  17:20:39,753 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T00:20Z] INFO  17:20:39,762 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:20Z] INFO  17:20:39,786 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:20Z] INFO  17:20:39,789 ProgressMeter -            done    110598.0    16.0 s       2.5 m      100.0%    16.0 s       0.0 s
[2016-04-15T00:20Z] INFO  17:20:39,789 ProgressMeter - Total runtime 16.43 secs, 0.27 min, 0.00 hours
[2016-04-15T00:20Z] INFO  17:20:39,790 MicroScheduler - 170 reads were filtered out during the traversal out of approximately 110768 total reads (0.15%)
[2016-04-15T00:20Z] INFO  17:20:39,790 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:20Z] INFO  17:20:39,790 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:20Z] INFO  17:20:39,791 MicroScheduler -   -> 170 reads (0.15% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:20Z] INFO  17:20:39,810 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-15T00:20Z] GATK: realign ('14', 19553416, 35066851) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:20Z] INFO  17:20:40,069 IntervalUtils - Processing 16130541 bp from intervals
[2016-04-15T00:20Z] WARN  17:20:40,076 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:20Z] INFO  17:20:40,193 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:20Z] INFO  17:20:40,364 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:20Z] INFO  17:20:40,366 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:20Z] INFO  17:20:40,367 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:20Z] INFO  17:20:40,368 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:20Z] INFO  17:20:41,165 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:20Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-16_31120544_46629582-prep-prealign.bam
[2016-04-15T00:20Z] GATK RealignerTargetCreator: R14-18106_kapa-NGv3-PE100-NGv3-sort-16_31120544_46629582-prep-prealign.bam 16:31120545-46629582
[2016-04-15T00:20Z] GATK: RealignerTargetCreator
[2016-04-15T00:20Z] INFO  17:20:42,065 ProgressMeter -     15:49620866    500007.0    60.0 s     120.0 s       82.1%    73.0 s      13.0 s
[2016-04-15T00:20Z] INFO  17:20:42,448 ProgressMeter -            done     84112.0     7.0 s      89.0 s       99.6%     7.0 s       0.0 s
[2016-04-15T00:20Z] INFO  17:20:42,449 ProgressMeter - Total runtime 7.52 secs, 0.13 min, 0.00 hours
[2016-04-15T00:20Z] INFO  17:20:42,452 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 84112 total reads (0.00%)
[2016-04-15T00:20Z] INFO  17:20:42,453 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:20Z] INFO  17:20:42,454 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:20Z] INFO  17:20:42,454 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:20Z] INFO  17:20:42,525 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:20Z] INFO  17:20:42,528 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:20Z] INFO  17:20:42,528 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:20Z] INFO  17:20:42,528 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:20Z] INFO  17:20:42,532 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/14/R14-18106_kapa-NGv3-PE100-NGv3-sort-14_19553416_35066851-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/14/R14-18106_kapa-NGv3-PE100-NGv3-sort-14_19553416_35066851-prep-prealign-realign.intervals -L 14:19553417-35066851 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/14/tx/tmpOXjUhi/R14-18106_kapa-NGv3-PE100-NGv3-sort-14_19553416_35066851-prep.bam
[2016-04-15T00:20Z] INFO  17:20:42,555 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:20Z] INFO  17:20:42,555 HelpFormatter - Date/Time: 2016/04/14 17:20:42
[2016-04-15T00:20Z] INFO  17:20:42,555 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:20Z] INFO  17:20:42,555 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:20Z] INFO  17:20:42,834 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:20Z] INFO  17:20:42,862 ProgressMeter -            done    237937.0    17.0 s      75.0 s      100.0%    17.0 s       0.0 s
[2016-04-15T00:20Z] INFO  17:20:42,863 ProgressMeter - Total runtime 17.85 secs, 0.30 min, 0.00 hours
[2016-04-15T00:20Z] INFO  17:20:42,867 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 237937 total reads (0.00%)
[2016-04-15T00:20Z] INFO  17:20:42,867 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:20Z] INFO  17:20:42,867 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:20Z] INFO  17:20:42,868 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:20Z] INFO  17:20:42,954 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:20Z] INFO  17:20:42,967 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:20Z] INFO  17:20:43,022 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-15T00:20Z] INFO  17:20:43,217 ProgressMeter -            done   1.5510714E7    21.0 s       1.0 s      100.0%    21.0 s       0.0 s
[2016-04-15T00:20Z] INFO  17:20:43,217 ProgressMeter - Total runtime 21.15 secs, 0.35 min, 0.01 hours
[2016-04-15T00:20Z] INFO  17:20:43,221 MicroScheduler - 31475 reads were filtered out during the traversal out of approximately 371180 total reads (8.48%)
[2016-04-15T00:20Z] INFO  17:20:43,221 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:20Z] INFO  17:20:43,222 MicroScheduler -   -> 1036 reads (0.28% of total) failing BadMateFilter
[2016-04-15T00:20Z] INFO  17:20:43,222 MicroScheduler -   -> 27551 reads (7.42% of total) failing DuplicateReadFilter
[2016-04-15T00:20Z] INFO  17:20:43,222 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:20Z] INFO  17:20:43,222 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:20Z] INFO  17:20:43,222 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:20Z] INFO  17:20:43,223 MicroScheduler -   -> 2888 reads (0.78% of total) failing MappingQualityZeroFilter
[2016-04-15T00:20Z] INFO  17:20:43,223 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:20Z] INFO  17:20:43,223 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-15T00:20Z] INFO  17:20:43,223 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:20Z] INFO  17:20:43,395 IntervalUtils - Processing 15513435 bp from intervals
[2016-04-15T00:20Z] WARN  17:20:43,410 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:20Z] INFO  17:20:43,485 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:20Z] INFO  17:20:43,569 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:20Z] INFO  17:20:43,571 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:20Z] INFO  17:20:43,571 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:20Z] INFO  17:20:43,572 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:20Z] INFO  17:20:43,603 ProgressMeter -     15:82808654    400006.0    60.0 s       2.5 m       95.9%    62.0 s       2.0 s
[2016-04-15T00:20Z] INFO  17:20:43,718 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:20Z] INFO  17:20:43,843 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:20Z] INFO  17:20:43,958 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:20Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-15_98984299_102531392-prep.bam
[2016-04-15T00:20Z] INFO  17:20:44,237 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:20Z] GATK pre-alignment ('16', 64982511, 80574976) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:20Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-14_81651874_97299968-prep.bam
[2016-04-15T00:20Z] INFO  17:20:44,288 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:20Z] INFO  17:20:44,291 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:20Z] INFO  17:20:44,292 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:20Z] INFO  17:20:44,292 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:20Z] INFO  17:20:44,297 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/16/R14-18106_kapa-NGv3-PE100-NGv3-sort-16_31120544_46629582-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/16/tx/tmpWMPXRj/R14-18106_kapa-NGv3-PE100-NGv3-sort-16_31120544_46629582-prep-prealign-realign.intervals -l INFO -L 16:31120545-46629582 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:20Z] INFO  17:20:44,306 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:20Z] INFO  17:20:44,319 HelpFormatter - Date/Time: 2016/04/14 17:20:44
[2016-04-15T00:20Z] INFO  17:20:44,320 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:20Z] INFO  17:20:44,320 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:20Z] INFO  17:20:44,435 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:20Z] INFO  17:20:44,433 ProgressMeter -            done    829889.0    49.0 s      60.0 s      100.0%    49.0 s       0.0 s
[2016-04-15T00:20Z] INFO  17:20:44,433 ProgressMeter - Total runtime 49.84 secs, 0.83 min, 0.01 hours
[2016-04-15T00:20Z] INFO  17:20:44,437 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 829889 total reads (0.00%)
[2016-04-15T00:20Z] INFO  17:20:44,437 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:20Z] INFO  17:20:44,437 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:20Z] INFO  17:20:44,438 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:20Z] INFO  17:20:44,532 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:20Z] GATK: realign ('14', 66135960, 81646674) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:20Z] INFO  17:20:44,595 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T00:20Z] INFO  17:20:44,606 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:20Z] INFO  17:20:44,651 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.04
[2016-04-15T00:20Z] GATK pre-alignment ('16', 80575258, 90354753) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:20Z] INFO  17:20:45,128 IntervalUtils - Processing 15509038 bp from intervals
[2016-04-15T00:20Z] WARN  17:20:45,134 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:20Z] INFO  17:20:45,268 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:20Z] INFO  17:20:45,424 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:20Z] INFO  17:20:45,425 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:20Z] INFO  17:20:45,426 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:20Z] INFO  17:20:45,427 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:20Z] INFO  17:20:45,921 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:20Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-12_46756066_62654284-prep.bam
[2016-04-15T00:20Z] INFO  17:20:47,038 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:20Z] INFO  17:20:47,041 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:20Z] INFO  17:20:47,041 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:20Z] INFO  17:20:47,041 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:20Z] INFO  17:20:47,045 HelpFormatter - Program Args: -T PrintReads -L 16:64982512-80574976 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/16/tx/tmpAJM6UV/R14-18106_kapa-NGv3-PE100-NGv3-sort-16_64982511_80574976-prep-prealign.bam
[2016-04-15T00:20Z] INFO  17:20:47,053 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:20Z] INFO  17:20:47,054 HelpFormatter - Date/Time: 2016/04/14 17:20:47
[2016-04-15T00:20Z] INFO  17:20:47,055 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:20Z] INFO  17:20:47,055 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:20Z] INFO  17:20:47,254 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:20Z] INFO  17:20:47,571 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@52f3b59
[2016-04-15T00:20Z] INFO  17:20:47,665 ProgressMeter -            done    570486.0    65.0 s     115.0 s      100.0%    65.0 s       0.0 s
[2016-04-15T00:20Z] INFO  17:20:47,666 ProgressMeter - Total runtime 65.96 secs, 1.10 min, 0.02 hours
[2016-04-15T00:20Z] INFO  17:20:47,666 MicroScheduler - 392 reads were filtered out during the traversal out of approximately 570878 total reads (0.07%)
[2016-04-15T00:20Z] INFO  17:20:47,667 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:20Z] INFO  17:20:47,667 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:20Z] INFO  17:20:47,667 MicroScheduler -   -> 392 reads (0.07% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:20Z] INFO  17:20:47,716 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:20Z] INFO  17:20:47,720 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:20Z] INFO  17:20:47,721 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:20Z] INFO  17:20:47,721 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:20Z] INFO  17:20:47,727 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/14/R14-18106_kapa-NGv3-PE100-NGv3-sort-14_66135960_81646674-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/14/R14-18106_kapa-NGv3-PE100-NGv3-sort-14_66135960_81646674-prep-prealign-realign.intervals -L 14:66135961-81646674 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/14/tx/tmp167G1W/R14-18106_kapa-NGv3-PE100-NGv3-sort-14_66135960_81646674-prep.bam
[2016-04-15T00:20Z] INFO  17:20:47,758 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:20Z] INFO  17:20:47,759 HelpFormatter - Date/Time: 2016/04/14 17:20:47
[2016-04-15T00:20Z] INFO  17:20:47,760 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:20Z] INFO  17:20:47,760 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:20Z] INFO  17:20:48,011 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:20Z] INFO  17:20:48,071 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@41fd9d8e
[2016-04-15T00:20Z] INFO  17:20:48,213 ProgressMeter -            done    540450.0    65.0 s     120.0 s      100.0%    65.0 s       0.0 s
[2016-04-15T00:20Z] INFO  17:20:48,214 ProgressMeter - Total runtime 65.29 secs, 1.09 min, 0.02 hours
[2016-04-15T00:20Z] INFO  17:20:48,214 MicroScheduler - 239 reads were filtered out during the traversal out of approximately 540689 total reads (0.04%)
[2016-04-15T00:20Z] INFO  17:20:48,214 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:20Z] INFO  17:20:48,215 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:20Z] INFO  17:20:48,216 MicroScheduler -   -> 239 reads (0.04% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:20Z] INFO  17:20:48,234 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:20Z] INFO  17:20:48,255 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:20Z] INFO  17:20:48,284 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:20Z] INFO  17:20:48,287 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:20Z] INFO  17:20:48,288 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:20Z] INFO  17:20:48,289 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:20Z] INFO  17:20:48,294 HelpFormatter - Program Args: -T PrintReads -L 16:80575259-90354753 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/16/tx/tmpREZQ0M/R14-18106_kapa-NGv3-PE100-NGv3-sort-16_80575258_90354753-prep-prealign.bam
[2016-04-15T00:20Z] INFO  17:20:48,310 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:20Z] INFO  17:20:48,311 HelpFormatter - Date/Time: 2016/04/14 17:20:48
[2016-04-15T00:20Z] INFO  17:20:48,311 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:20Z] INFO  17:20:48,312 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:20Z] INFO  17:20:48,326 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-15T00:20Z] INFO  17:20:48,347 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.09
[2016-04-15T00:20Z] INFO  17:20:48,426 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:20Z] INFO  17:20:48,435 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:20Z] INFO  17:20:48,471 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.04
[2016-04-15T00:20Z] INFO  17:20:48,485 IntervalUtils - Processing 15592465 bp from intervals
[2016-04-15T00:20Z] INFO  17:20:48,592 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:20Z] GATK pre-alignment ('17', 0, 15511002) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:20Z] INFO  17:20:48,623 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:20Z] INFO  17:20:48,870 IntervalUtils - Processing 15510714 bp from intervals
[2016-04-15T00:20Z] INFO  17:20:48,905 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:20Z] WARN  17:20:48,909 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:20Z] INFO  17:20:48,909 ProgressMeter -            done   1.5533983E7    20.0 s       1.0 s      100.0%    20.0 s       0.0 s
[2016-04-15T00:20Z] INFO  17:20:48,917 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:20Z] INFO  17:20:48,918 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:20Z] INFO  17:20:48,918 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:20Z] INFO  17:20:48,924 ProgressMeter - Total runtime 20.27 secs, 0.34 min, 0.01 hours
[2016-04-15T00:20Z] INFO  17:20:48,925 MicroScheduler - 53664 reads were filtered out during the traversal out of approximately 327295 total reads (16.40%)
[2016-04-15T00:20Z] INFO  17:20:48,926 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:20Z] INFO  17:20:48,926 MicroScheduler -   -> 808 reads (0.25% of total) failing BadMateFilter
[2016-04-15T00:20Z] INFO  17:20:48,927 MicroScheduler -   -> 21971 reads (6.71% of total) failing DuplicateReadFilter
[2016-04-15T00:20Z] INFO  17:20:48,928 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:20Z] INFO  17:20:48,928 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:20Z] INFO  17:20:48,929 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:20Z] INFO  17:20:48,929 MicroScheduler -   -> 30885 reads (9.44% of total) failing MappingQualityZeroFilter
[2016-04-15T00:20Z] INFO  17:20:48,930 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:20Z] INFO  17:20:48,931 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-15T00:20Z] INFO  17:20:48,931 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:20Z] INFO  17:20:48,954 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:20Z] INFO  17:20:49,000 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:20Z] INFO  17:20:49,101 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:20Z] INFO  17:20:49,160 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:20Z] INFO  17:20:49,166 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:20Z] INFO  17:20:49,167 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:20Z] INFO  17:20:49,167 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:20Z] INFO  17:20:49,334 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:20Z] INFO  17:20:49,341 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:20Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-15_36887086_52402170-prep-prealign.bam
[2016-04-15T00:20Z] INFO  17:20:49,535 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:20Z] INFO  17:20:49,671 ProgressMeter -            done    284613.0    19.0 s      67.0 s      100.0%    19.0 s       0.0 s
[2016-04-15T00:20Z] INFO  17:20:49,672 ProgressMeter - Total runtime 19.07 secs, 0.32 min, 0.01 hours
[2016-04-15T00:20Z] INFO  17:20:49,675 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 284613 total reads (0.00%)
[2016-04-15T00:20Z] INFO  17:20:49,675 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:20Z] INFO  17:20:49,676 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:20Z] INFO  17:20:49,676 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:20Z] INFO  17:20:49,733 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:20Z] INFO  17:20:49,766 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-15T00:20Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-15_67932890_83447639-prep-prealign.bam
[2016-04-15T00:20Z] INFO  17:20:49,826 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:20Z] INFO  17:20:49,835 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:20Z] INFO  17:20:49,889 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-15T00:20Z] INFO  17:20:49,903 IntervalUtils - Processing 9779495 bp from intervals
[2016-04-15T00:20Z] INFO  17:20:49,986 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:20Z] INFO  17:20:50,242 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:20Z] INFO  17:20:50,242 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:20Z] INFO  17:20:50,242 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:20Z] INFO  17:20:50,243 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:20Z] INFO  17:20:50,257 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:20Z] INFO  17:20:50,290 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:20Z] GATK: realign ('15', 83448996, 98982979) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:20Z] INFO  17:20:50,367 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:20Z] GATK RealignerTargetCreator: R14-18106_kapa-NGv3-PE100-NGv3-sort-15_36887086_52402170-prep-prealign.bam 15:36887087-52402170
[2016-04-15T00:20Z] GATK: RealignerTargetCreator
[2016-04-15T00:20Z] INFO  17:20:51,288 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:20Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-14_50585061_66096324-prep.bam
[2016-04-15T00:20Z] GATK RealignerTargetCreator: R14-18106_kapa-NGv3-PE100-NGv3-sort-15_67932890_83447639-prep-prealign.bam 15:67932891-83447639
[2016-04-15T00:20Z] GATK: RealignerTargetCreator
[2016-04-15T00:20Z] INFO  17:20:51,551 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:20Z] INFO  17:20:51,554 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:20Z] INFO  17:20:51,555 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:20Z] INFO  17:20:51,556 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:20Z] INFO  17:20:51,560 HelpFormatter - Program Args: -T PrintReads -L 17:1-15511002 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/17/tx/tmp7fj_pL/R14-18106_kapa-NGv3-PE100-NGv3-sort-17_0_15511002-prep-prealign.bam
[2016-04-15T00:20Z] INFO  17:20:51,568 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:20Z] INFO  17:20:51,569 HelpFormatter - Date/Time: 2016/04/14 17:20:51
[2016-04-15T00:20Z] INFO  17:20:51,570 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:20Z] INFO  17:20:51,570 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:20Z] INFO  17:20:51,741 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:20Z] GATK pre-alignment ('17', 15515955, 31039213) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:20Z] INFO  17:20:52,953 ProgressMeter -            done   1.5518901E7    21.0 s       1.0 s      100.0%    21.0 s       0.0 s
[2016-04-15T00:20Z] INFO  17:20:52,954 ProgressMeter - Total runtime 21.77 secs, 0.36 min, 0.01 hours
[2016-04-15T00:20Z] INFO  17:20:52,958 MicroScheduler - 27357 reads were filtered out during the traversal out of approximately 346328 total reads (7.90%)
[2016-04-15T00:20Z] INFO  17:20:52,959 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:20Z] INFO  17:20:52,960 MicroScheduler -   -> 929 reads (0.27% of total) failing BadMateFilter
[2016-04-15T00:20Z] INFO  17:20:52,960 MicroScheduler -   -> 25784 reads (7.44% of total) failing DuplicateReadFilter
[2016-04-15T00:20Z] INFO  17:20:52,961 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:20Z] INFO  17:20:52,961 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:20Z] INFO  17:20:52,962 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:20Z] INFO  17:20:52,963 MicroScheduler -   -> 644 reads (0.19% of total) failing MappingQualityZeroFilter
[2016-04-15T00:20Z] INFO  17:20:52,963 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:20Z] INFO  17:20:52,964 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-15T00:20Z] INFO  17:20:52,965 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:20Z] INFO  17:20:53,024 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-15T00:20Z] INFO  17:20:53,110 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:20Z] INFO  17:20:53,118 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:20Z] INFO  17:20:53,151 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:20Z] INFO  17:20:53,155 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:20Z] INFO  17:20:53,155 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:20Z] INFO  17:20:53,156 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:20Z] INFO  17:20:53,160 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/15/R14-18106_kapa-NGv3-PE100-NGv3-sort-15_83448996_98982979-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/15/R14-18106_kapa-NGv3-PE100-NGv3-sort-15_83448996_98982979-prep-prealign-realign.intervals -L 15:83448997-98982979 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/15/tx/tmpT5xquj/R14-18106_kapa-NGv3-PE100-NGv3-sort-15_83448996_98982979-prep.bam
[2016-04-15T00:20Z] INFO  17:20:53,185 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:20Z] INFO  17:20:53,193 HelpFormatter - Date/Time: 2016/04/14 17:20:53
[2016-04-15T00:20Z] INFO  17:20:53,193 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:20Z] INFO  17:20:53,194 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:20Z] INFO  17:20:53,194 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-15T00:20Z] INFO  17:20:53,230 IntervalUtils - Processing 15511002 bp from intervals
[2016-04-15T00:20Z] INFO  17:20:53,332 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:20Z] INFO  17:20:53,391 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:20Z] INFO  17:20:53,503 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:20Z] INFO  17:20:53,512 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:20Z] INFO  17:20:53,575 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-15T00:20Z] INFO  17:20:53,651 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:20Z] INFO  17:20:53,655 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:20Z] INFO  17:20:53,655 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:20Z] INFO  17:20:53,656 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:20Z] INFO  17:20:53,660 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/15/R14-18106_kapa-NGv3-PE100-NGv3-sort-15_36887086_52402170-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/15/tx/tmpqYO8pw/R14-18106_kapa-NGv3-PE100-NGv3-sort-15_36887086_52402170-prep-prealign-realign.intervals -l INFO -L 15:36887087-52402170 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:20Z] INFO  17:20:53,670 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:20Z] INFO  17:20:53,670 HelpFormatter - Date/Time: 2016/04/14 17:20:53
[2016-04-15T00:20Z] INFO  17:20:53,670 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:20Z] INFO  17:20:53,670 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:20Z] INFO  17:20:53,698 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:20Z] INFO  17:20:53,698 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:20Z] INFO  17:20:53,699 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:20Z] INFO  17:20:53,699 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:20Z] INFO  17:20:53,728 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:20Z] INFO  17:20:53,815 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:20Z] INFO  17:20:53,872 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:20Z] INFO  17:20:53,979 IntervalUtils - Processing 15533983 bp from intervals
[2016-04-15T00:20Z] WARN  17:20:53,984 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:20Z] INFO  17:20:54,046 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:20Z] INFO  17:20:54,046 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T00:20Z] INFO  17:20:54,057 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:20Z] INFO  17:20:54,125 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-15T00:20Z] INFO  17:20:54,197 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:20Z] INFO  17:20:54,198 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:20Z] INFO  17:20:54,199 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:20Z] INFO  17:20:54,200 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:20Z] INFO  17:20:54,240 ProgressMeter -            done    313880.0    21.0 s      67.0 s       98.1%    21.0 s       0.0 s
[2016-04-15T00:20Z] INFO  17:20:54,241 ProgressMeter - Total runtime 21.34 secs, 0.36 min, 0.01 hours
[2016-04-15T00:20Z] INFO  17:20:54,245 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 313880 total reads (0.00%)
[2016-04-15T00:20Z] INFO  17:20:54,257 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:20Z] INFO  17:20:54,258 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:20Z] INFO  17:20:54,258 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:20Z] INFO  17:20:54,364 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:20Z] INFO  17:20:54,417 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:20Z] GATK: realign ('15', 52404364, 67923265) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:20Z] INFO  17:20:54,442 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:20Z] INFO  17:20:54,446 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:20Z] INFO  17:20:54,446 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:20Z] INFO  17:20:54,447 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:20Z] INFO  17:20:54,452 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/15/R14-18106_kapa-NGv3-PE100-NGv3-sort-15_67932890_83447639-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/15/tx/tmpvB8FGU/R14-18106_kapa-NGv3-PE100-NGv3-sort-15_67932890_83447639-prep-prealign-realign.intervals -l INFO -L 15:67932891-83447639 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:20Z] INFO  17:20:54,469 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:20Z] INFO  17:20:54,470 HelpFormatter - Date/Time: 2016/04/14 17:20:54
[2016-04-15T00:20Z] INFO  17:20:54,470 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:20Z] INFO  17:20:54,470 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:20Z] INFO  17:20:54,476 IntervalUtils - Processing 15515084 bp from intervals
[2016-04-15T00:20Z] WARN  17:20:54,481 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:20Z] INFO  17:20:54,573 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:20Z] INFO  17:20:54,577 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:20Z] INFO  17:20:54,583 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:20Z] INFO  17:20:54,790 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T00:20Z] INFO  17:20:54,796 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:20Z] INFO  17:20:54,808 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:20Z] INFO  17:20:54,809 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:20Z] INFO  17:20:54,810 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:20Z] INFO  17:20:54,809 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:20Z] INFO  17:20:54,898 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.09
[2016-04-15T00:20Z] INFO  17:20:55,270 IntervalUtils - Processing 15514749 bp from intervals
[2016-04-15T00:20Z] WARN  17:20:55,276 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:20Z] INFO  17:20:55,352 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:20Z] INFO  17:20:55,354 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:20Z] INFO  17:20:55,355 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:20Z] INFO  17:20:55,355 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:20Z] INFO  17:20:55,359 HelpFormatter - Program Args: -T PrintReads -L 17:15515956-31039213 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/17/tx/tmpzoRvvQ/R14-18106_kapa-NGv3-PE100-NGv3-sort-17_15515955_31039213-prep-prealign.bam
[2016-04-15T00:20Z] INFO  17:20:55,361 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:20Z] INFO  17:20:55,378 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:20Z] INFO  17:20:55,378 HelpFormatter - Date/Time: 2016/04/14 17:20:55
[2016-04-15T00:20Z] INFO  17:20:55,422 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:20Z] INFO  17:20:55,423 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:20Z] INFO  17:20:55,626 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:20Z] INFO  17:20:55,627 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:20Z] INFO  17:20:55,628 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:20Z] INFO  17:20:55,628 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:20Z] INFO  17:20:55,699 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:20Z] INFO  17:20:55,942 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:20Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-14_97304098_107349540-prep.bam
[2016-04-15T00:20Z] INFO  17:20:56,936 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-15T00:20Z] GATK pre-alignment ('17', 31048040, 46607237) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:20Z] INFO  17:20:57,015 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:20Z] INFO  17:20:57,025 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:20Z] INFO  17:20:57,066 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.04
[2016-04-15T00:20Z] INFO  17:20:57,081 IntervalUtils - Processing 15523258 bp from intervals
[2016-04-15T00:20Z] INFO  17:20:57,204 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:20Z] INFO  17:20:57,538 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:20Z] INFO  17:20:57,539 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:20Z] INFO  17:20:57,540 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:20Z] INFO  17:20:57,541 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:20Z] INFO  17:20:57,578 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:20Z] INFO  17:20:57,576 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:20Z] INFO  17:20:57,580 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:20Z] INFO  17:20:57,581 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:20Z] INFO  17:20:57,581 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:20Z] INFO  17:20:57,586 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/15/R14-18106_kapa-NGv3-PE100-NGv3-sort-15_52404364_67923265-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/15/R14-18106_kapa-NGv3-PE100-NGv3-sort-15_52404364_67923265-prep-prealign-realign.intervals -L 15:52404365-67923265 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/15/tx/tmpkR7WZf/R14-18106_kapa-NGv3-PE100-NGv3-sort-15_52404364_67923265-prep.bam
[2016-04-15T00:20Z] INFO  17:20:57,598 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:20Z] INFO  17:20:57,598 HelpFormatter - Date/Time: 2016/04/14 17:20:57
[2016-04-15T00:20Z] INFO  17:20:57,598 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:20Z] INFO  17:20:57,610 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:20Z] INFO  17:20:57,818 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:20Z] INFO  17:20:57,856 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:20Z] INFO  17:20:57,998 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:20Z] INFO  17:20:58,023 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:20Z] INFO  17:20:58,087 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-15T00:20Z] INFO  17:20:58,409 IntervalUtils - Processing 15518901 bp from intervals
[2016-04-15T00:20Z] WARN  17:20:58,415 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:20Z] INFO  17:20:58,529 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:20Z] INFO  17:20:58,641 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:20Z] INFO  17:20:58,643 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:20Z] INFO  17:20:58,643 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:20Z] INFO  17:20:58,644 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:20Z] INFO  17:20:58,828 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:20Z] INFO  17:20:58,831 ProgressMeter -     16:57157378    200002.0    30.0 s       2.5 m       57.4%    52.0 s      22.0 s
[2016-04-15T00:20Z] INFO  17:20:59,036 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:20Z] INFO  17:20:59,511 ProgressMeter -            done   1.5509038E7    14.0 s       0.0 s      100.0%    14.0 s       0.0 s
[2016-04-15T00:20Z] INFO  17:20:59,512 ProgressMeter - Total runtime 14.09 secs, 0.23 min, 0.00 hours
[2016-04-15T00:20Z] INFO  17:20:59,516 MicroScheduler - 30739 reads were filtered out during the traversal out of approximately 111550 total reads (27.56%)
[2016-04-15T00:20Z] INFO  17:20:59,517 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:20Z] INFO  17:20:59,518 MicroScheduler -   -> 383 reads (0.34% of total) failing BadMateFilter
[2016-04-15T00:20Z] INFO  17:20:59,518 MicroScheduler -   -> 6385 reads (5.72% of total) failing DuplicateReadFilter
[2016-04-15T00:20Z] INFO  17:20:59,519 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:20Z] INFO  17:20:59,520 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:20Z] INFO  17:20:59,520 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:20Z] INFO  17:20:59,521 MicroScheduler -   -> 23971 reads (21.49% of total) failing MappingQualityZeroFilter
[2016-04-15T00:20Z] INFO  17:20:59,522 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:20Z] INFO  17:20:59,522 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-15T00:20Z] INFO  17:20:59,523 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:21Z] INFO  17:21:00,065 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:21Z] INFO  17:21:00,069 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:21Z] INFO  17:21:00,069 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:21Z] INFO  17:21:00,070 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:21Z] INFO  17:21:00,074 HelpFormatter - Program Args: -T PrintReads -L 17:31048041-46607237 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/17/tx/tmpHTWeV_/R14-18106_kapa-NGv3-PE100-NGv3-sort-17_31048040_46607237-prep-prealign.bam
[2016-04-15T00:21Z] INFO  17:21:00,109 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:21Z] INFO  17:21:00,118 HelpFormatter - Date/Time: 2016/04/14 17:21:00
[2016-04-15T00:21Z] INFO  17:21:00,119 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:21Z] INFO  17:21:00,119 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:21Z] INFO  17:21:00,308 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:21Z] INFO  17:21:00,866 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:21Z] GATK: realign ('16', 31120544, 46629582) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:21Z] INFO  17:21:01,413 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-15T00:21Z] INFO  17:21:01,480 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:21Z] INFO  17:21:01,489 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:21Z] INFO  17:21:01,523 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.03
[2016-04-15T00:21Z] INFO  17:21:01,538 IntervalUtils - Processing 15559197 bp from intervals
[2016-04-15T00:21Z] INFO  17:21:01,640 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:21Z] INFO  17:21:01,935 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:21Z] INFO  17:21:01,936 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:21Z] INFO  17:21:01,936 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:21Z] INFO  17:21:01,937 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:21Z] INFO  17:21:01,959 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:21Z] INFO  17:21:02,101 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:21Z] INFO  17:21:02,555 ProgressMeter -            done   1.6130541E7    22.0 s       1.0 s      100.0%    22.0 s       0.0 s
[2016-04-15T00:21Z] INFO  17:21:02,556 ProgressMeter - Total runtime 22.19 secs, 0.37 min, 0.01 hours
[2016-04-15T00:21Z] INFO  17:21:02,559 MicroScheduler - 182452 reads were filtered out during the traversal out of approximately 447394 total reads (40.78%)
[2016-04-15T00:21Z] INFO  17:21:02,559 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:21Z] INFO  17:21:02,560 MicroScheduler -   -> 787 reads (0.18% of total) failing BadMateFilter
[2016-04-15T00:21Z] INFO  17:21:02,560 MicroScheduler -   -> 21091 reads (4.71% of total) failing DuplicateReadFilter
[2016-04-15T00:21Z] INFO  17:21:02,560 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:21Z] INFO  17:21:02,560 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:21Z] INFO  17:21:02,561 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:21Z] INFO  17:21:02,561 MicroScheduler -   -> 160574 reads (35.89% of total) failing MappingQualityZeroFilter
[2016-04-15T00:21Z] INFO  17:21:02,561 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:21Z] INFO  17:21:02,561 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-15T00:21Z] INFO  17:21:02,562 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:21Z] INFO  17:21:03,845 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:21Z] INFO  17:21:03,848 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:21Z] INFO  17:21:03,849 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:21Z] INFO  17:21:03,850 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:21Z] INFO  17:21:03,854 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/16/R14-18106_kapa-NGv3-PE100-NGv3-sort-16_31120544_46629582-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/16/R14-18106_kapa-NGv3-PE100-NGv3-sort-16_31120544_46629582-prep-prealign-realign.intervals -L 16:31120545-46629582 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/16/tx/tmp7FhDR7/R14-18106_kapa-NGv3-PE100-NGv3-sort-16_31120544_46629582-prep.bam
[2016-04-15T00:21Z] INFO  17:21:03,875 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:21Z] INFO  17:21:03,875 HelpFormatter - Date/Time: 2016/04/14 17:21:03
[2016-04-15T00:21Z] INFO  17:21:03,875 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:21Z] INFO  17:21:03,875 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:21Z] INFO  17:21:03,930 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:21Z] GATK: realign ('15', 20741621, 36872162) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:21Z] INFO  17:21:04,096 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:21Z] INFO  17:21:04,255 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:21Z] INFO  17:21:04,275 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:21Z] INFO  17:21:04,367 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.09
[2016-04-15T00:21Z] INFO  17:21:04,854 IntervalUtils - Processing 15509038 bp from intervals
[2016-04-15T00:21Z] WARN  17:21:04,863 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:21Z] INFO  17:21:04,955 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:21Z] INFO  17:21:05,018 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:21Z] INFO  17:21:05,019 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:21Z] INFO  17:21:05,020 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:21Z] INFO  17:21:05,021 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:21Z] INFO  17:21:05,087 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:21Z] INFO  17:21:05,202 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:21Z] INFO  17:21:06,227 ProgressMeter -      16:3651060    400009.0    60.0 s       2.5 m       23.5%     4.3 m       3.3 m
[2016-04-15T00:21Z] INFO  17:21:07,037 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:21Z] INFO  17:21:07,041 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:21Z] INFO  17:21:07,042 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:21Z] INFO  17:21:07,042 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:21Z] INFO  17:21:07,048 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/15/R14-18106_kapa-NGv3-PE100-NGv3-sort-15_20741621_36872162-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/15/R14-18106_kapa-NGv3-PE100-NGv3-sort-15_20741621_36872162-prep-prealign-realign.intervals -L 15:20741622-36872162 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/15/tx/tmp3Ya8Mu/R14-18106_kapa-NGv3-PE100-NGv3-sort-15_20741621_36872162-prep.bam
[2016-04-15T00:21Z] INFO  17:21:07,060 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:21Z] INFO  17:21:07,060 HelpFormatter - Date/Time: 2016/04/14 17:21:07
[2016-04-15T00:21Z] INFO  17:21:07,060 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:21Z] INFO  17:21:07,060 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:21Z] INFO  17:21:07,290 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:21Z] INFO  17:21:07,393 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:21Z] INFO  17:21:07,404 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:21Z] INFO  17:21:07,474 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-15T00:21Z] INFO  17:21:07,769 ProgressMeter -     16:22547417    400011.0    60.0 s       2.5 m       44.8%     2.2 m      73.0 s
[2016-04-15T00:21Z] INFO  17:21:07,927 IntervalUtils - Processing 16130541 bp from intervals
[2016-04-15T00:21Z] WARN  17:21:07,932 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:21Z] INFO  17:21:08,001 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:21Z] INFO  17:21:08,102 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:21Z] INFO  17:21:08,103 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:21Z] INFO  17:21:08,104 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:21Z] INFO  17:21:08,105 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:21Z] INFO  17:21:08,265 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:21Z] INFO  17:21:08,419 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:21Z] INFO  17:21:12,008 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@5fe152b7
[2016-04-15T00:21Z] INFO  17:21:12,184 ProgressMeter -            done    345430.0    43.0 s       2.1 m      100.0%    43.0 s       0.0 s
[2016-04-15T00:21Z] INFO  17:21:12,185 ProgressMeter - Total runtime 43.38 secs, 0.72 min, 0.01 hours
[2016-04-15T00:21Z] INFO  17:21:12,185 MicroScheduler - 197 reads were filtered out during the traversal out of approximately 345627 total reads (0.06%)
[2016-04-15T00:21Z] INFO  17:21:12,186 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:21Z] INFO  17:21:12,186 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:21Z] INFO  17:21:12,186 MicroScheduler -   -> 197 reads (0.06% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:21Z] INFO  17:21:13,586 ProgressMeter -     14:31778405    400005.0    30.0 s      75.0 s       78.8%    38.0 s       8.0 s
[2016-04-15T00:21Z] INFO  17:21:13,593 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:21Z] INFO  17:21:13,607 ProgressMeter -            done    368868.0    24.0 s      66.0 s       99.8%    24.0 s       0.0 s
[2016-04-15T00:21Z] INFO  17:21:13,607 ProgressMeter - Total runtime 24.44 secs, 0.41 min, 0.01 hours
[2016-04-15T00:21Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-16_46633742_64982002-prep-prealign.bam
[2016-04-15T00:21Z] INFO  17:21:13,611 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 368868 total reads (0.00%)
[2016-04-15T00:21Z] INFO  17:21:13,612 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:21Z] INFO  17:21:13,612 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:21Z] INFO  17:21:13,613 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:21Z] INFO  17:21:14,291 ProgressMeter -            done    110598.0     9.0 s      83.0 s      100.0%     9.0 s       0.0 s
[2016-04-15T00:21Z] INFO  17:21:14,291 ProgressMeter - Total runtime 9.27 secs, 0.15 min, 0.00 hours
[2016-04-15T00:21Z] INFO  17:21:14,296 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 110598 total reads (0.00%)
[2016-04-15T00:21Z] INFO  17:21:14,296 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:21Z] INFO  17:21:14,297 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:21Z] INFO  17:21:14,297 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:21Z] INFO  17:21:14,647 ProgressMeter -            done    512962.0    31.0 s      60.0 s      100.0%    31.0 s       0.0 s
[2016-04-15T00:21Z] INFO  17:21:14,648 ProgressMeter - Total runtime 31.08 secs, 0.52 min, 0.01 hours
[2016-04-15T00:21Z] INFO  17:21:14,659 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 512962 total reads (0.00%)
[2016-04-15T00:21Z] INFO  17:21:14,660 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:21Z] INFO  17:21:14,660 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:21Z] INFO  17:21:14,660 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:21Z] GATK RealignerTargetCreator: R14-18106_kapa-NGv3-PE100-NGv3-sort-16_46633742_64982002-prep-prealign.bam 16:46633743-64982002
[2016-04-15T00:21Z] GATK: RealignerTargetCreator
[2016-04-15T00:21Z] INFO  17:21:15,164 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:21Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-14_66135960_81646674-prep.bam
[2016-04-15T00:21Z] INFO  17:21:15,850 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:21Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-16_31120544_46629582-prep.bam
[2016-04-15T00:21Z] INFO  17:21:16,084 ProgressMeter -            done    325167.0    21.0 s      67.0 s      100.0%    21.0 s       0.0 s
[2016-04-15T00:21Z] INFO  17:21:16,085 ProgressMeter - Total runtime 21.89 secs, 0.36 min, 0.01 hours
[2016-04-15T00:21Z] INFO  17:21:16,089 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 325167 total reads (0.00%)
[2016-04-15T00:21Z] INFO  17:21:16,089 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:21Z] INFO  17:21:16,089 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:21Z] INFO  17:21:16,090 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:21Z] GATK pre-alignment ('17', 46607689, 62121560) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:21Z] GATK pre-alignment ('17', 62122219, 77705154) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:21Z] INFO  17:21:16,427 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:21Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-14_19553416_35066851-prep.bam
[2016-04-15T00:21Z] INFO  17:21:17,604 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:21Z] INFO  17:21:17,608 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:21Z] INFO  17:21:17,609 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:21Z] INFO  17:21:17,610 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:21Z] INFO  17:21:17,615 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/16/R14-18106_kapa-NGv3-PE100-NGv3-sort-16_46633742_64982002-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/16/tx/tmpFX_8Vn/R14-18106_kapa-NGv3-PE100-NGv3-sort-16_46633742_64982002-prep-prealign-realign.intervals -l INFO -L 16:46633743-64982002 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:21Z] INFO  17:21:17,627 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:21Z] INFO  17:21:17,627 HelpFormatter - Date/Time: 2016/04/14 17:21:17
[2016-04-15T00:21Z] INFO  17:21:17,628 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:21Z] INFO  17:21:17,628 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:21Z] INFO  17:21:17,658 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:21Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-15_83448996_98982979-prep.bam
[2016-04-15T00:21Z] INFO  17:21:17,755 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:21Z] INFO  17:21:18,033 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T00:21Z] INFO  17:21:18,057 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:21Z] INFO  17:21:18,148 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.09
[2016-04-15T00:21Z] GATK pre-alignment ('17', 77707305, 81195210) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:21Z] INFO  17:21:18,509 IntervalUtils - Processing 18348260 bp from intervals
[2016-04-15T00:21Z] WARN  17:21:18,514 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:21Z] INFO  17:21:18,655 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:21Z] INFO  17:21:18,797 ProgressMeter -            done   1.5514749E7    23.0 s       1.0 s      100.0%    23.0 s       0.0 s
[2016-04-15T00:21Z] INFO  17:21:18,798 ProgressMeter - Total runtime 23.17 secs, 0.39 min, 0.01 hours
[2016-04-15T00:21Z] INFO  17:21:18,803 MicroScheduler - 123619 reads were filtered out during the traversal out of approximately 544750 total reads (22.69%)
[2016-04-15T00:21Z] INFO  17:21:18,804 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:21Z] INFO  17:21:18,805 MicroScheduler -   -> 1030 reads (0.19% of total) failing BadMateFilter
[2016-04-15T00:21Z] INFO  17:21:18,806 MicroScheduler -   -> 34417 reads (6.32% of total) failing DuplicateReadFilter
[2016-04-15T00:21Z] INFO  17:21:18,806 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:21Z] INFO  17:21:18,807 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:21Z] INFO  17:21:18,808 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:21Z] INFO  17:21:18,809 MicroScheduler -   -> 88172 reads (16.19% of total) failing MappingQualityZeroFilter
[2016-04-15T00:21Z] INFO  17:21:18,809 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:21Z] INFO  17:21:18,810 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-15T00:21Z] INFO  17:21:18,811 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:21Z] GATK pre-alignment ('18', 0, 18531348) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:21Z] INFO  17:21:18,946 ProgressMeter -     16:68024949    100005.0    30.0 s       5.0 m       19.5%     2.6 m       2.1 m
[2016-04-15T00:21Z] INFO  17:21:18,949 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:21Z] INFO  17:21:18,949 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:21Z] INFO  17:21:18,950 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:21Z] INFO  17:21:18,950 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:21Z] INFO  17:21:19,252 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:21Z] INFO  17:21:19,256 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:21Z] INFO  17:21:19,257 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:21Z] INFO  17:21:19,257 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:21Z] INFO  17:21:19,263 HelpFormatter - Program Args: -T PrintReads -L 17:46607690-62121560 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/17/tx/tmpB5NSLB/R14-18106_kapa-NGv3-PE100-NGv3-sort-17_46607689_62121560-prep-prealign.bam
[2016-04-15T00:21Z] INFO  17:21:19,273 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:21Z] INFO  17:21:19,284 HelpFormatter - Date/Time: 2016/04/14 17:21:19
[2016-04-15T00:21Z] INFO  17:21:19,285 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:21Z] INFO  17:21:19,286 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:21Z] INFO  17:21:19,299 ProgressMeter -            done   1.5515084E7    24.0 s       1.0 s      100.0%    24.0 s       0.0 s
[2016-04-15T00:21Z] INFO  17:21:19,301 ProgressMeter - Total runtime 24.49 secs, 0.41 min, 0.01 hours
[2016-04-15T00:21Z] INFO  17:21:19,305 MicroScheduler - 74981 reads were filtered out during the traversal out of approximately 573825 total reads (13.07%)
[2016-04-15T00:21Z] INFO  17:21:19,306 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:21Z] INFO  17:21:19,308 MicroScheduler -   -> 1255 reads (0.22% of total) failing BadMateFilter
[2016-04-15T00:21Z] INFO  17:21:19,309 MicroScheduler -   -> 41020 reads (7.15% of total) failing DuplicateReadFilter
[2016-04-15T00:21Z] INFO  17:21:19,310 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:21Z] INFO  17:21:19,310 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:21Z] INFO  17:21:19,311 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:21Z] INFO  17:21:19,312 MicroScheduler -   -> 32706 reads (5.70% of total) failing MappingQualityZeroFilter
[2016-04-15T00:21Z] INFO  17:21:19,313 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:21Z] INFO  17:21:19,313 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-15T00:21Z] INFO  17:21:19,314 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:21Z] INFO  17:21:19,464 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:21Z] INFO  17:21:19,501 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:21Z] INFO  17:21:19,505 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:21Z] INFO  17:21:19,506 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:21Z] INFO  17:21:19,507 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:21Z] INFO  17:21:19,527 HelpFormatter - Program Args: -T PrintReads -L 17:62122220-77705154 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/17/tx/tmpe1ohg7/R14-18106_kapa-NGv3-PE100-NGv3-sort-17_62122219_77705154-prep-prealign.bam
[2016-04-15T00:21Z] INFO  17:21:19,552 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:21Z] INFO  17:21:19,559 HelpFormatter - Date/Time: 2016/04/14 17:21:19
[2016-04-15T00:21Z] INFO  17:21:19,560 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:21Z] INFO  17:21:19,560 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:21Z] INFO  17:21:19,763 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:21Z] INFO  17:21:20,247 ProgressMeter -     16:88872520    200002.0    30.0 s       2.5 m       84.8%    35.0 s       5.0 s
[2016-04-15T00:21Z] INFO  17:21:20,356 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:21Z] GATK: realign ('15', 67932890, 83447639) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:21Z] INFO  17:21:20,668 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-15T00:21Z] INFO  17:21:20,731 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:21Z] INFO  17:21:20,740 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:21Z] INFO  17:21:20,774 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.03
[2016-04-15T00:21Z] INFO  17:21:20,788 IntervalUtils - Processing 15513871 bp from intervals
[2016-04-15T00:21Z] INFO  17:21:20,866 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:21Z] INFO  17:21:20,873 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:21Z] GATK: realign ('15', 36887086, 52402170) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:21Z] INFO  17:21:21,024 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-15T00:21Z] INFO  17:21:21,094 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:21Z] INFO  17:21:21,114 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:21Z] INFO  17:21:21,124 ProgressMeter -            done    344068.0    22.0 s      65.0 s      100.0%    22.0 s       0.0 s
[2016-04-15T00:21Z] INFO  17:21:21,125 ProgressMeter - Total runtime 22.48 secs, 0.37 min, 0.01 hours
[2016-04-15T00:21Z] INFO  17:21:21,128 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 344068 total reads (0.00%)
[2016-04-15T00:21Z] INFO  17:21:21,128 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:21Z] INFO  17:21:21,129 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:21Z] INFO  17:21:21,129 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:21Z] INFO  17:21:21,129 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:21Z] INFO  17:21:21,129 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:21Z] INFO  17:21:21,130 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:21Z] INFO  17:21:21,131 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:21Z] INFO  17:21:21,160 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-15T00:21Z] INFO  17:21:21,160 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:21Z] INFO  17:21:21,174 IntervalUtils - Processing 15582935 bp from intervals
[2016-04-15T00:21Z] INFO  17:21:21,264 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:21Z] INFO  17:21:21,293 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:21Z] INFO  17:21:21,494 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:21Z] INFO  17:21:21,497 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:21Z] INFO  17:21:21,498 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:21Z] INFO  17:21:21,498 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:21Z] INFO  17:21:21,503 HelpFormatter - Program Args: -T PrintReads -L 17:77707306-81195210 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/17/tx/tmpCP1aVd/R14-18106_kapa-NGv3-PE100-NGv3-sort-17_77707305_81195210-prep-prealign.bam
[2016-04-15T00:21Z] INFO  17:21:21,535 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:21Z] INFO  17:21:21,536 HelpFormatter - Date/Time: 2016/04/14 17:21:21
[2016-04-15T00:21Z] INFO  17:21:21,536 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:21Z] INFO  17:21:21,537 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:21Z] INFO  17:21:21,651 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:21Z] INFO  17:21:21,652 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:21Z] INFO  17:21:21,652 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:21Z] INFO  17:21:21,653 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:21Z] INFO  17:21:21,667 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:21Z] INFO  17:21:21,673 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:21Z] INFO  17:21:21,846 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:21Z] INFO  17:21:21,899 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:21Z] INFO  17:21:21,912 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:21Z] INFO  17:21:21,913 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:21Z] INFO  17:21:21,914 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:21Z] INFO  17:21:21,918 HelpFormatter - Program Args: -T PrintReads -L 18:1-18531348 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/18/tx/tmp3bwIIX/R14-18106_kapa-NGv3-PE100-NGv3-sort-18_0_18531348-prep-prealign.bam
[2016-04-15T00:21Z] INFO  17:21:21,933 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:21Z] INFO  17:21:21,934 HelpFormatter - Date/Time: 2016/04/14 17:21:21
[2016-04-15T00:21Z] INFO  17:21:21,934 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:21Z] INFO  17:21:21,934 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:21Z] INFO  17:21:22,195 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:21Z] INFO  17:21:22,746 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:21Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-15_52404364_67923265-prep.bam
[2016-04-15T00:21Z] INFO  17:21:22,830 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-15T00:21Z] INFO  17:21:22,915 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:21Z] INFO  17:21:22,924 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:21Z] INFO  17:21:22,976 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-15T00:21Z] INFO  17:21:22,989 IntervalUtils - Processing 3487905 bp from intervals
[2016-04-15T00:21Z] INFO  17:21:23,071 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:21Z] INFO  17:21:23,338 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:21Z] INFO  17:21:23,339 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:21Z] INFO  17:21:23,340 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:21Z] INFO  17:21:23,350 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:21Z] INFO  17:21:23,377 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:21Z] INFO  17:21:23,437 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:21Z] INFO  17:21:23,440 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:21Z] INFO  17:21:23,440 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:21Z] INFO  17:21:23,441 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:21Z] INFO  17:21:23,445 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/15/R14-18106_kapa-NGv3-PE100-NGv3-sort-15_67932890_83447639-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/15/R14-18106_kapa-NGv3-PE100-NGv3-sort-15_67932890_83447639-prep-prealign-realign.intervals -L 15:67932891-83447639 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/15/tx/tmpstYlTx/R14-18106_kapa-NGv3-PE100-NGv3-sort-15_67932890_83447639-prep.bam
[2016-04-15T00:21Z] INFO  17:21:23,451 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:21Z] INFO  17:21:23,475 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:21Z] INFO  17:21:23,476 HelpFormatter - Date/Time: 2016/04/14 17:21:23
[2016-04-15T00:21Z] INFO  17:21:23,477 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:21Z] INFO  17:21:23,477 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:21Z] INFO  17:21:23,589 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-15T00:21Z] INFO  17:21:23,645 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:21Z] INFO  17:21:23,654 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:21Z] INFO  17:21:23,659 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:21Z] INFO  17:21:23,715 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-15T00:21Z] INFO  17:21:23,719 ProgressMeter -      17:3649141    200002.0    30.0 s       2.5 m       23.5%     2.1 m      97.0 s
[2016-04-15T00:21Z] INFO  17:21:23,744 IntervalUtils - Processing 18531348 bp from intervals
[2016-04-15T00:21Z] INFO  17:21:23,784 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:21Z] INFO  17:21:23,795 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:21Z] INFO  17:21:23,841 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.04
[2016-04-15T00:21Z] GATK pre-alignment ('18', 18533538, 34081962) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:21Z] INFO  17:21:23,847 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:21Z] INFO  17:21:23,915 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:21Z] INFO  17:21:23,918 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:21Z] INFO  17:21:23,919 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:21Z] INFO  17:21:23,919 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:21Z] INFO  17:21:23,924 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/15/R14-18106_kapa-NGv3-PE100-NGv3-sort-15_36887086_52402170-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/15/R14-18106_kapa-NGv3-PE100-NGv3-sort-15_36887086_52402170-prep-prealign-realign.intervals -L 15:36887087-52402170 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/15/tx/tmpa2RaCs/R14-18106_kapa-NGv3-PE100-NGv3-sort-15_36887086_52402170-prep.bam
[2016-04-15T00:21Z] INFO  17:21:23,934 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:21Z] INFO  17:21:23,934 HelpFormatter - Date/Time: 2016/04/14 17:21:23
[2016-04-15T00:21Z] INFO  17:21:23,934 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:21Z] INFO  17:21:23,935 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:21Z] INFO  17:21:24,140 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:21Z] INFO  17:21:24,160 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:21Z] INFO  17:21:24,172 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:21Z] INFO  17:21:24,173 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:21Z] INFO  17:21:24,173 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:21Z] INFO  17:21:24,198 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:21Z] INFO  17:21:24,252 IntervalUtils - Processing 15514749 bp from intervals
[2016-04-15T00:21Z] WARN  17:21:24,269 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:21Z] INFO  17:21:24,294 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:21Z] INFO  17:21:24,307 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:21Z] INFO  17:21:24,368 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-15T00:21Z] INFO  17:21:24,398 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:21Z] INFO  17:21:24,424 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:21Z] INFO  17:21:24,553 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:21Z] INFO  17:21:24,554 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:21Z] INFO  17:21:24,555 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:21Z] INFO  17:21:24,560 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:21Z] INFO  17:21:24,725 IntervalUtils - Processing 15515084 bp from intervals
[2016-04-15T00:21Z] WARN  17:21:24,729 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:21Z] INFO  17:21:24,765 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:21Z] INFO  17:21:24,834 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:21Z] INFO  17:21:24,899 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:21Z] INFO  17:21:25,014 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:21Z] INFO  17:21:25,027 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:21Z] INFO  17:21:25,028 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:21Z] INFO  17:21:25,028 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:21Z] INFO  17:21:25,205 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:21Z] INFO  17:21:25,355 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:21Z] INFO  17:21:26,771 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:21Z] INFO  17:21:26,774 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:21Z] INFO  17:21:26,775 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:21Z] INFO  17:21:26,776 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:21Z] INFO  17:21:26,780 HelpFormatter - Program Args: -T PrintReads -L 18:18533539-34081962 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/18/tx/tmp5faYtX/R14-18106_kapa-NGv3-PE100-NGv3-sort-18_18533538_34081962-prep-prealign.bam
[2016-04-15T00:21Z] INFO  17:21:26,804 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:21Z] INFO  17:21:26,805 HelpFormatter - Date/Time: 2016/04/14 17:21:26
[2016-04-15T00:21Z] INFO  17:21:26,805 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:21Z] INFO  17:21:26,806 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:21Z] INFO  17:21:26,975 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:21Z] INFO  17:21:27,566 ProgressMeter -     17:18661641    200002.0    30.0 s       2.5 m       20.3%     2.5 m     118.0 s
[2016-04-15T00:21Z] INFO  17:21:28,121 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-15T00:21Z] INFO  17:21:28,193 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:21Z] INFO  17:21:28,202 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:21Z] INFO  17:21:28,243 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.04
[2016-04-15T00:21Z] INFO  17:21:28,258 IntervalUtils - Processing 15548424 bp from intervals
[2016-04-15T00:21Z] INFO  17:21:28,335 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:21Z] INFO  17:21:28,636 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:21Z] INFO  17:21:28,637 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:21Z] INFO  17:21:28,638 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:21Z] INFO  17:21:28,639 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:21Z] INFO  17:21:28,653 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:21Z] INFO  17:21:28,834 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:21Z] INFO  17:21:31,958 ProgressMeter -     17:35921680    200011.0    30.0 s       2.5 m       31.3%    95.0 s      65.0 s
[2016-04-15T00:21Z] INFO  17:21:33,202 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@7172f77a
[2016-04-15T00:21Z] INFO  17:21:33,324 ProgressMeter -            done    345706.0    43.0 s       2.1 m       99.1%    43.0 s       0.0 s
[2016-04-15T00:21Z] INFO  17:21:33,324 ProgressMeter - Total runtime 43.08 secs, 0.72 min, 0.01 hours
[2016-04-15T00:21Z] INFO  17:21:33,325 MicroScheduler - 178 reads were filtered out during the traversal out of approximately 345884 total reads (0.05%)
[2016-04-15T00:21Z] INFO  17:21:33,325 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:21Z] INFO  17:21:33,325 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:21Z] INFO  17:21:33,326 MicroScheduler -   -> 178 reads (0.05% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:21Z] INFO  17:21:35,045 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:21Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-16_80575258_90354753-prep-prealign.bam
[2016-04-15T00:21Z] GATK RealignerTargetCreator: R14-18106_kapa-NGv3-PE100-NGv3-sort-16_80575258_90354753-prep-prealign.bam 16:80575259-90354753
[2016-04-15T00:21Z] GATK: RealignerTargetCreator
[2016-04-15T00:21Z] INFO  17:21:36,228 ProgressMeter -     16:14958543    700016.0    90.0 s       2.1 m       96.3%    93.0 s       3.0 s
[2016-04-15T00:21Z] INFO  17:21:36,787 ProgressMeter -            done    444588.0    28.0 s      64.0 s      100.0%    28.0 s       0.0 s
[2016-04-15T00:21Z] INFO  17:21:36,788 ProgressMeter - Total runtime 28.68 secs, 0.48 min, 0.01 hours
[2016-04-15T00:21Z] INFO  17:21:36,792 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 444588 total reads (0.00%)
[2016-04-15T00:21Z] INFO  17:21:36,792 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:21Z] INFO  17:21:36,792 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:21Z] INFO  17:21:36,793 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:21Z] INFO  17:21:37,830 ProgressMeter -     16:28877566    700018.0    90.0 s       2.1 m       85.6%   105.0 s      15.0 s
[2016-04-15T00:21Z] INFO  17:21:38,420 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:21Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-15_20741621_36872162-prep.bam
[2016-04-15T00:21Z] INFO  17:21:38,897 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:21Z] INFO  17:21:38,900 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:21Z] INFO  17:21:38,900 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:21Z] INFO  17:21:38,900 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:21Z] INFO  17:21:38,904 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/16/R14-18106_kapa-NGv3-PE100-NGv3-sort-16_80575258_90354753-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/16/tx/tmpUacztU/R14-18106_kapa-NGv3-PE100-NGv3-sort-16_80575258_90354753-prep-prealign-realign.intervals -l INFO -L 16:80575259-90354753 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:21Z] INFO  17:21:38,912 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:21Z] INFO  17:21:38,916 HelpFormatter - Date/Time: 2016/04/14 17:21:38
[2016-04-15T00:21Z] INFO  17:21:38,922 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:21Z] INFO  17:21:38,922 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:21Z] INFO  17:21:39,007 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:21Z] INFO  17:21:39,213 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T00:21Z] INFO  17:21:39,224 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:21Z] INFO  17:21:39,294 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-15T00:21Z] INFO  17:21:39,622 IntervalUtils - Processing 9779495 bp from intervals
[2016-04-15T00:21Z] WARN  17:21:39,626 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:21Z] INFO  17:21:39,694 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:21Z] GATK pre-alignment ('18', 34092400, 49867248) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:21Z] INFO  17:21:39,864 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:21Z] INFO  17:21:39,865 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:21Z] INFO  17:21:39,866 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:21Z] INFO  17:21:39,867 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:21Z] INFO  17:21:42,776 ProgressMeter -            done   1.834826E7    23.0 s       1.0 s      100.0%    23.0 s       0.0 s
[2016-04-15T00:21Z] INFO  17:21:42,776 ProgressMeter - Total runtime 23.83 secs, 0.40 min, 0.01 hours
[2016-04-15T00:21Z] INFO  17:21:42,780 MicroScheduler - 29431 reads were filtered out during the traversal out of approximately 347586 total reads (8.47%)
[2016-04-15T00:21Z] INFO  17:21:42,781 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:21Z] INFO  17:21:42,781 MicroScheduler -   -> 989 reads (0.28% of total) failing BadMateFilter
[2016-04-15T00:21Z] INFO  17:21:42,782 MicroScheduler -   -> 25956 reads (7.47% of total) failing DuplicateReadFilter
[2016-04-15T00:21Z] INFO  17:21:42,782 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:21Z] INFO  17:21:42,782 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:21Z] INFO  17:21:42,783 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:21Z] INFO  17:21:42,783 MicroScheduler -   -> 2486 reads (0.72% of total) failing MappingQualityZeroFilter
[2016-04-15T00:21Z] INFO  17:21:42,783 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:21Z] INFO  17:21:42,784 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-15T00:21Z] INFO  17:21:42,784 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:21Z] INFO  17:21:42,899 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:21Z] INFO  17:21:42,901 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:21Z] INFO  17:21:42,901 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:21Z] INFO  17:21:42,902 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:21Z] INFO  17:21:42,906 HelpFormatter - Program Args: -T PrintReads -L 18:34092401-49867248 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/18/tx/tmpzJXjML/R14-18106_kapa-NGv3-PE100-NGv3-sort-18_34092400_49867248-prep-prealign.bam
[2016-04-15T00:21Z] INFO  17:21:42,931 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:21Z] INFO  17:21:42,932 HelpFormatter - Date/Time: 2016/04/14 17:21:42
[2016-04-15T00:21Z] INFO  17:21:42,932 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:21Z] INFO  17:21:42,933 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:21Z] INFO  17:21:43,091 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:21Z] INFO  17:21:44,070 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:21Z] GATK: realign ('16', 46633742, 64982002) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:21Z] INFO  17:21:44,297 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-15T00:21Z] INFO  17:21:44,371 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:21Z] INFO  17:21:44,383 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:21Z] INFO  17:21:44,466 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-15T00:21Z] INFO  17:21:44,494 IntervalUtils - Processing 15774848 bp from intervals
[2016-04-15T00:21Z] INFO  17:21:44,585 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:21Z] INFO  17:21:44,829 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:21Z] INFO  17:21:44,830 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:21Z] INFO  17:21:44,831 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:21Z] INFO  17:21:44,831 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:21Z] INFO  17:21:44,854 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:21Z] INFO  17:21:45,005 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:21Z] INFO  17:21:45,185 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@7172f77a
[2016-04-15T00:21Z] INFO  17:21:45,249 ProgressMeter -            done    864399.0    99.0 s     114.0 s      100.0%    99.0 s       0.0 s
[2016-04-15T00:21Z] INFO  17:21:45,249 ProgressMeter - Total runtime 99.29 secs, 1.65 min, 0.03 hours
[2016-04-15T00:21Z] INFO  17:21:45,250 MicroScheduler - 456 reads were filtered out during the traversal out of approximately 864855 total reads (0.05%)
[2016-04-15T00:21Z] INFO  17:21:45,250 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:21Z] INFO  17:21:45,250 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:21Z] INFO  17:21:45,251 MicroScheduler -   -> 456 reads (0.05% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:21Z] INFO  17:21:46,746 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:21Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-16_0_15528616-prep-prealign.bam
[2016-04-15T00:21Z] INFO  17:21:46,794 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:21Z] INFO  17:21:46,798 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:21Z] INFO  17:21:46,798 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:21Z] INFO  17:21:46,799 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:21Z] INFO  17:21:46,804 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/16/R14-18106_kapa-NGv3-PE100-NGv3-sort-16_46633742_64982002-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/16/R14-18106_kapa-NGv3-PE100-NGv3-sort-16_46633742_64982002-prep-prealign-realign.intervals -L 16:46633743-64982002 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/16/tx/tmpMwWsfw/R14-18106_kapa-NGv3-PE100-NGv3-sort-16_46633742_64982002-prep.bam
[2016-04-15T00:21Z] INFO  17:21:46,823 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:21Z] INFO  17:21:46,823 HelpFormatter - Date/Time: 2016/04/14 17:21:46
[2016-04-15T00:21Z] INFO  17:21:46,823 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:21Z] INFO  17:21:46,824 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:21Z] INFO  17:21:47,041 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:21Z] INFO  17:21:47,192 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:21Z] INFO  17:21:47,212 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:21Z] INFO  17:21:47,264 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-15T00:21Z] INFO  17:21:47,610 IntervalUtils - Processing 18348260 bp from intervals
[2016-04-15T00:21Z] WARN  17:21:47,615 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:21Z] INFO  17:21:47,698 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:21Z] INFO  17:21:47,899 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:21Z] INFO  17:21:47,911 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:21Z] INFO  17:21:47,912 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:21Z] INFO  17:21:47,913 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:21Z] INFO  17:21:48,114 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:21Z] INFO  17:21:48,427 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:21Z] GATK RealignerTargetCreator: R14-18106_kapa-NGv3-PE100-NGv3-sort-16_0_15528616-prep-prealign.bam 16:1-15528616
[2016-04-15T00:21Z] GATK: RealignerTargetCreator
[2016-04-15T00:21Z] INFO  17:21:49,930 ProgressMeter -     16:71416682    400014.0    61.0 s       2.5 m       41.3%     2.5 m      86.0 s
[2016-04-15T00:21Z] INFO  17:21:51,148 ProgressMeter -     17:56058186    200002.0    30.0 s       2.5 m       60.9%    49.0 s      19.0 s
[2016-04-15T00:21Z] INFO  17:21:51,805 ProgressMeter -     17:72559031    200004.0    30.0 s       2.5 m       67.0%    44.0 s      14.0 s
[2016-04-15T00:21Z] INFO  17:21:52,412 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@41fd9d8e
[2016-04-15T00:21Z] INFO  17:21:52,415 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:21Z] INFO  17:21:52,417 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:21Z] INFO  17:21:52,417 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:21Z] INFO  17:21:52,417 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:21Z] INFO  17:21:52,430 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/16/R14-18106_kapa-NGv3-PE100-NGv3-sort-16_0_15528616-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/16/tx/tmp3pA29m/R14-18106_kapa-NGv3-PE100-NGv3-sort-16_0_15528616-prep-prealign-realign.intervals -l INFO -L 16:1-15528616 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:21Z] INFO  17:21:52,457 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:21Z] INFO  17:21:52,457 HelpFormatter - Date/Time: 2016/04/14 17:21:52
[2016-04-15T00:21Z] INFO  17:21:52,457 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:21Z] INFO  17:21:52,457 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:21Z] INFO  17:21:52,481 ProgressMeter -            done    194654.0    23.0 s       2.0 m       99.2%    23.0 s       0.0 s
[2016-04-15T00:21Z] INFO  17:21:52,481 ProgressMeter - Total runtime 23.84 secs, 0.40 min, 0.01 hours
[2016-04-15T00:21Z] INFO  17:21:52,482 MicroScheduler - 132 reads were filtered out during the traversal out of approximately 194786 total reads (0.07%)
[2016-04-15T00:21Z] INFO  17:21:52,482 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:21Z] INFO  17:21:52,482 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:21Z] INFO  17:21:52,483 MicroScheduler -   -> 132 reads (0.07% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:21Z] INFO  17:21:52,550 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:21Z] INFO  17:21:52,742 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T00:21Z] INFO  17:21:52,755 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:21Z] INFO  17:21:52,821 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-15T00:21Z] INFO  17:21:53,147 IntervalUtils - Processing 15528616 bp from intervals
[2016-04-15T00:21Z] WARN  17:21:53,151 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:21Z] INFO  17:21:53,334 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:21Z] INFO  17:21:53,368 ProgressMeter -     17:80274772    200002.0    30.0 s       2.5 m       73.6%    40.0 s      10.0 s
[2016-04-15T00:21Z] INFO  17:21:53,544 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:21Z] INFO  17:21:53,544 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:21Z] INFO  17:21:53,545 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:21Z] INFO  17:21:53,545 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:21Z] INFO  17:21:53,752 ProgressMeter -      17:7286442    400004.0    60.0 s       2.5 m       47.0%     2.1 m      67.0 s
[2016-04-15T00:21Z] INFO  17:21:53,962 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:21Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-18_18533538_34081962-prep-prealign.bam
[2016-04-15T00:21Z] INFO  17:21:54,188 ProgressMeter -     18:13741551    200004.0    30.0 s       2.5 m       74.2%    40.0 s      10.0 s
[2016-04-15T00:21Z] INFO  17:21:54,593 ProgressMeter -     15:82638893    400006.0    30.0 s      75.0 s       94.8%    31.0 s       1.0 s
[2016-04-15T00:21Z] GATK RealignerTargetCreator: R14-18106_kapa-NGv3-PE100-NGv3-sort-18_18533538_34081962-prep-prealign.bam 18:18533539-34081962
[2016-04-15T00:21Z] GATK: RealignerTargetCreator
[2016-04-15T00:21Z] INFO  17:21:55,042 ProgressMeter -     15:49081188    400004.0    30.0 s      75.0 s       78.6%    38.0 s       8.0 s
[2016-04-15T00:21Z] INFO  17:21:56,426 ProgressMeter -            done   9779495.0    16.0 s       1.0 s      100.0%    16.0 s       0.0 s
[2016-04-15T00:21Z] INFO  17:21:56,427 ProgressMeter - Total runtime 16.56 secs, 0.28 min, 0.00 hours
[2016-04-15T00:21Z] INFO  17:21:56,428 MicroScheduler - 30684 reads were filtered out during the traversal out of approximately 347841 total reads (8.82%)
[2016-04-15T00:21Z] INFO  17:21:56,429 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:21Z] INFO  17:21:56,429 MicroScheduler -   -> 831 reads (0.24% of total) failing BadMateFilter
[2016-04-15T00:21Z] INFO  17:21:56,430 MicroScheduler -   -> 26631 reads (7.66% of total) failing DuplicateReadFilter
[2016-04-15T00:21Z] INFO  17:21:56,431 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:21Z] INFO  17:21:56,431 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:21Z] INFO  17:21:56,432 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:21Z] INFO  17:21:56,432 MicroScheduler -   -> 3222 reads (0.93% of total) failing MappingQualityZeroFilter
[2016-04-15T00:21Z] INFO  17:21:56,433 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:21Z] INFO  17:21:56,434 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-15T00:21Z] INFO  17:21:56,434 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:21Z] INFO  17:21:56,555 ProgressMeter -            done    540450.0    32.0 s      59.0 s      100.0%    32.0 s       0.0 s
[2016-04-15T00:21Z] INFO  17:21:56,556 ProgressMeter - Total runtime 32.00 secs, 0.53 min, 0.01 hours
[2016-04-15T00:21Z] INFO  17:21:56,560 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 540450 total reads (0.00%)
[2016-04-15T00:21Z] INFO  17:21:56,560 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:21Z] INFO  17:21:56,560 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:21Z] INFO  17:21:56,561 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:21Z] INFO  17:21:56,766 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@41fd9d8e
[2016-04-15T00:21Z] INFO  17:21:56,852 ProgressMeter -            done    250945.0    32.0 s       2.2 m      100.0%    32.0 s       0.0 s
[2016-04-15T00:21Z] INFO  17:21:56,852 ProgressMeter - Total runtime 32.68 secs, 0.54 min, 0.01 hours
[2016-04-15T00:21Z] INFO  17:21:56,852 MicroScheduler - 172 reads were filtered out during the traversal out of approximately 251117 total reads (0.07%)
[2016-04-15T00:21Z] INFO  17:21:56,853 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:21Z] INFO  17:21:56,853 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:21Z] INFO  17:21:56,853 MicroScheduler -   -> 172 reads (0.07% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:21Z] INFO  17:21:57,533 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:21Z] INFO  17:21:57,536 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:21Z] INFO  17:21:57,537 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:21Z] INFO  17:21:57,537 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:21Z] INFO  17:21:57,542 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/18/R14-18106_kapa-NGv3-PE100-NGv3-sort-18_18533538_34081962-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/18/tx/tmpQOgvf2/R14-18106_kapa-NGv3-PE100-NGv3-sort-18_18533538_34081962-prep-prealign-realign.intervals -l INFO -L 18:18533539-34081962 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:21Z] INFO  17:21:57,551 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:21Z] INFO  17:21:57,552 HelpFormatter - Date/Time: 2016/04/14 17:21:57
[2016-04-15T00:21Z] INFO  17:21:57,553 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:21Z] INFO  17:21:57,553 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:21Z] INFO  17:21:57,633 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:21Z] INFO  17:21:57,648 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:21Z] GATK: realign ('16', 80575258, 90354753) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:21Z] INFO  17:21:57,768 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@5fe152b7
[2016-04-15T00:21Z] INFO  17:21:57,833 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T00:21Z] INFO  17:21:57,844 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:21Z] INFO  17:21:57,926 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-15T00:21Z] INFO  17:21:57,986 ProgressMeter -            done    272808.0    34.0 s       2.1 m       99.8%    34.0 s       0.0 s
[2016-04-15T00:21Z] INFO  17:21:57,986 ProgressMeter - Total runtime 34.65 secs, 0.58 min, 0.01 hours
[2016-04-15T00:21Z] INFO  17:21:57,987 MicroScheduler - 113 reads were filtered out during the traversal out of approximately 272921 total reads (0.04%)
[2016-04-15T00:21Z] INFO  17:21:57,987 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:21Z] INFO  17:21:57,988 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:21Z] INFO  17:21:57,988 MicroScheduler -   -> 113 reads (0.04% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:21Z] INFO  17:21:58,136 ProgressMeter -     17:27943787    400004.0    60.0 s       2.5 m       80.1%    74.0 s      14.0 s
[2016-04-15T00:21Z] INFO  17:21:58,233 IntervalUtils - Processing 15548424 bp from intervals
[2016-04-15T00:21Z] WARN  17:21:58,240 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:21Z] INFO  17:21:58,292 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:21Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-15_67932890_83447639-prep.bam
[2016-04-15T00:21Z] INFO  17:21:58,339 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:21Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-18_0_18531348-prep-prealign.bam
[2016-04-15T00:21Z] INFO  17:21:58,430 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:21Z] INFO  17:21:58,572 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:21Z] INFO  17:21:58,573 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:21Z] INFO  17:21:58,574 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:21Z] INFO  17:21:58,575 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:21Z] INFO  17:21:58,940 ProgressMeter -            done    570486.0    33.0 s      59.0 s      100.0%    33.0 s       0.0 s
[2016-04-15T00:21Z] INFO  17:21:58,941 ProgressMeter - Total runtime 33.91 secs, 0.57 min, 0.01 hours
[2016-04-15T00:21Z] INFO  17:21:58,945 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 570486 total reads (0.00%)
[2016-04-15T00:21Z] INFO  17:21:58,946 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:21Z] INFO  17:21:58,947 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:21Z] INFO  17:21:58,947 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:21Z] GATK RealignerTargetCreator: R14-18106_kapa-NGv3-PE100-NGv3-sort-18_0_18531348-prep-prealign.bam 18:1-18531348
[2016-04-15T00:21Z] GATK: RealignerTargetCreator
[2016-04-15T00:21Z] INFO  17:21:59,494 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:21Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-17_77707305_81195210-prep-prealign.bam
[2016-04-15T00:21Z] GATK pre-alignment ('18', 50278423, 66344430) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:22Z] INFO  17:22:00,475 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:22Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-15_36887086_52402170-prep.bam
[2016-04-15T00:22Z] GATK RealignerTargetCreator: R14-18106_kapa-NGv3-PE100-NGv3-sort-17_77707305_81195210-prep-prealign.bam 17:77707306-81195210
[2016-04-15T00:22Z] GATK: RealignerTargetCreator
[2016-04-15T00:22Z] INFO  17:22:00,803 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:22Z] INFO  17:22:00,815 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:22Z] INFO  17:22:00,816 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:22Z] INFO  17:22:00,816 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:22Z] INFO  17:22:00,822 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/16/R14-18106_kapa-NGv3-PE100-NGv3-sort-16_80575258_90354753-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/16/R14-18106_kapa-NGv3-PE100-NGv3-sort-16_80575258_90354753-prep-prealign-realign.intervals -L 16:80575259-90354753 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/16/tx/tmp9_WLt1/R14-18106_kapa-NGv3-PE100-NGv3-sort-16_80575258_90354753-prep.bam
[2016-04-15T00:22Z] INFO  17:22:00,843 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:22Z] INFO  17:22:00,844 HelpFormatter - Date/Time: 2016/04/14 17:22:00
[2016-04-15T00:22Z] INFO  17:22:00,845 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:22Z] INFO  17:22:00,845 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:22Z] INFO  17:22:01,132 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:22Z] INFO  17:22:01,339 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:22Z] INFO  17:22:01,350 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:22Z] INFO  17:22:01,442 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.09
[2016-04-15T00:22Z] INFO  17:22:01,922 IntervalUtils - Processing 9779495 bp from intervals
[2016-04-15T00:22Z] WARN  17:22:01,931 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:22Z] INFO  17:22:02,007 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:22Z] GATK pre-alignment ('18', 66346699, 78077248) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:22Z] INFO  17:22:02,111 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:22Z] INFO  17:22:02,112 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:22Z] INFO  17:22:02,112 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:22Z] INFO  17:22:02,113 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:22Z] INFO  17:22:02,302 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:22Z] INFO  17:22:02,315 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:22Z] INFO  17:22:02,318 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:22Z] INFO  17:22:02,319 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:22Z] INFO  17:22:02,319 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:22Z] INFO  17:22:02,324 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/18/R14-18106_kapa-NGv3-PE100-NGv3-sort-18_0_18531348-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/18/tx/tmpMUItPS/R14-18106_kapa-NGv3-PE100-NGv3-sort-18_0_18531348-prep-prealign-realign.intervals -l INFO -L 18:1-18531348 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:22Z] INFO  17:22:02,362 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:22Z] INFO  17:22:02,363 HelpFormatter - Date/Time: 2016/04/14 17:22:02
[2016-04-15T00:22Z] INFO  17:22:02,363 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:22Z] INFO  17:22:02,364 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:22Z] INFO  17:22:02,468 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:22Z] INFO  17:22:02,489 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:22Z] INFO  17:22:02,503 ProgressMeter -     17:39388823    400013.0    60.0 s       2.5 m       53.6%   111.0 s      51.0 s
[2016-04-15T00:22Z] INFO  17:22:02,763 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T00:22Z] INFO  17:22:02,772 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:22Z] INFO  17:22:02,834 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-15T00:22Z] INFO  17:22:03,000 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:22Z] INFO  17:22:03,003 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:22Z] INFO  17:22:03,003 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:22Z] INFO  17:22:03,003 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:22Z] INFO  17:22:03,014 HelpFormatter - Program Args: -T PrintReads -L 18:50278424-66344430 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/18/tx/tmpaBxyrE/R14-18106_kapa-NGv3-PE100-NGv3-sort-18_50278423_66344430-prep-prealign.bam
[2016-04-15T00:22Z] INFO  17:22:03,024 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:22Z] INFO  17:22:03,024 HelpFormatter - Date/Time: 2016/04/14 17:22:02
[2016-04-15T00:22Z] INFO  17:22:03,025 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:22Z] INFO  17:22:03,025 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:22Z] INFO  17:22:03,134 IntervalUtils - Processing 18531348 bp from intervals
[2016-04-15T00:22Z] WARN  17:22:03,139 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:22Z] INFO  17:22:03,226 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:22Z] INFO  17:22:03,249 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:22Z] INFO  17:22:03,437 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:22Z] INFO  17:22:03,438 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:22Z] INFO  17:22:03,439 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:22Z] INFO  17:22:03,440 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:22Z] INFO  17:22:03,646 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:22Z] INFO  17:22:03,649 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:22Z] INFO  17:22:03,650 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:22Z] INFO  17:22:03,650 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:22Z] INFO  17:22:03,655 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/17/R14-18106_kapa-NGv3-PE100-NGv3-sort-17_77707305_81195210-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/17/tx/tmpJCmbmH/R14-18106_kapa-NGv3-PE100-NGv3-sort-17_77707305_81195210-prep-prealign-realign.intervals -l INFO -L 17:77707306-81195210 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:22Z] INFO  17:22:03,671 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:22Z] INFO  17:22:03,672 HelpFormatter - Date/Time: 2016/04/14 17:22:03
[2016-04-15T00:22Z] INFO  17:22:03,673 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:22Z] INFO  17:22:03,673 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:22Z] INFO  17:22:03,826 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:22Z] INFO  17:22:04,048 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T00:22Z] INFO  17:22:04,058 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:22Z] INFO  17:22:04,128 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-15T00:22Z] INFO  17:22:04,399 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-15T00:22Z] INFO  17:22:04,418 IntervalUtils - Processing 3487905 bp from intervals
[2016-04-15T00:22Z] WARN  17:22:04,430 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:22Z] INFO  17:22:04,476 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:22Z] INFO  17:22:04,484 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:22Z] INFO  17:22:04,530 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-15T00:22Z] INFO  17:22:04,554 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:22Z] INFO  17:22:04,575 IntervalUtils - Processing 16066007 bp from intervals
[2016-04-15T00:22Z] INFO  17:22:04,673 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:22Z] INFO  17:22:04,688 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:22Z] INFO  17:22:04,688 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:22Z] INFO  17:22:04,689 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:22Z] INFO  17:22:04,689 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:22Z] INFO  17:22:04,763 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:22Z] INFO  17:22:04,776 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:22Z] INFO  17:22:04,776 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:22Z] INFO  17:22:04,776 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:22Z] INFO  17:22:04,780 HelpFormatter - Program Args: -T PrintReads -L 18:66346700-78077248 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/18/tx/tmpro8kI9/R14-18106_kapa-NGv3-PE100-NGv3-sort-18_66346699_78077248-prep-prealign.bam
[2016-04-15T00:22Z] INFO  17:22:04,788 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:22Z] INFO  17:22:04,797 HelpFormatter - Date/Time: 2016/04/14 17:22:04
[2016-04-15T00:22Z] INFO  17:22:04,798 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:22Z] INFO  17:22:04,798 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:22Z] INFO  17:22:04,923 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:22Z] INFO  17:22:04,924 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:22Z] INFO  17:22:04,925 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:22Z] INFO  17:22:04,926 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:22Z] INFO  17:22:04,940 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:22Z] INFO  17:22:05,004 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:22Z] INFO  17:22:05,070 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:22Z] INFO  17:22:06,469 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-15T00:22Z] INFO  17:22:06,562 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:22Z] INFO  17:22:06,571 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:22Z] INFO  17:22:06,623 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-15T00:22Z] INFO  17:22:06,639 IntervalUtils - Processing 11730549 bp from intervals
[2016-04-15T00:22Z] INFO  17:22:06,751 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:22Z] INFO  17:22:07,039 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:22Z] INFO  17:22:07,040 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:22Z] INFO  17:22:07,041 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:22Z] INFO  17:22:07,042 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:22Z] INFO  17:22:07,056 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:22Z] INFO  17:22:07,200 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:22Z] INFO  17:22:07,755 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@41fd9d8e
[2016-04-15T00:22Z] INFO  17:22:07,852 ProgressMeter -            done    594389.0    70.0 s     118.0 s      100.0%    70.0 s       0.0 s
[2016-04-15T00:22Z] INFO  17:22:07,853 ProgressMeter - Total runtime 70.31 secs, 1.17 min, 0.02 hours
[2016-04-15T00:22Z] INFO  17:22:07,853 MicroScheduler - 277 reads were filtered out during the traversal out of approximately 594666 total reads (0.05%)
[2016-04-15T00:22Z] INFO  17:22:07,854 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:22Z] INFO  17:22:07,855 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:22Z] INFO  17:22:07,855 MicroScheduler -   -> 277 reads (0.05% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:22Z] INFO  17:22:08,243 ProgressMeter -     16:30435614   1000021.0   120.0 s     120.0 s       95.7%     2.1 m       5.0 s
[2016-04-15T00:22Z] INFO  17:22:09,356 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:22Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-17_15515955_31039213-prep-prealign.bam
[2016-04-15T00:22Z] INFO  17:22:10,950 ProgressMeter -            done    345430.0    23.0 s      66.0 s      100.0%    23.0 s       0.0 s
[2016-04-15T00:22Z] INFO  17:22:10,950 ProgressMeter - Total runtime 23.04 secs, 0.38 min, 0.01 hours
[2016-04-15T00:22Z] INFO  17:22:10,954 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 345430 total reads (0.00%)
[2016-04-15T00:22Z] INFO  17:22:10,955 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:22Z] INFO  17:22:10,955 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:22Z] INFO  17:22:10,955 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:22Z] GATK RealignerTargetCreator: R14-18106_kapa-NGv3-PE100-NGv3-sort-17_15515955_31039213-prep-prealign.bam 17:15515956-31039213
[2016-04-15T00:22Z] GATK: RealignerTargetCreator
[2016-04-15T00:22Z] INFO  17:22:12,604 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:22Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-16_46633742_64982002-prep.bam
[2016-04-15T00:22Z] INFO  17:22:14,150 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@7172f77a
[2016-04-15T00:22Z] INFO  17:22:14,167 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:22Z] INFO  17:22:14,176 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:22Z] INFO  17:22:14,181 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:22Z] INFO  17:22:14,182 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:22Z] INFO  17:22:14,188 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/17/R14-18106_kapa-NGv3-PE100-NGv3-sort-17_15515955_31039213-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/17/tx/tmpTIfavS/R14-18106_kapa-NGv3-PE100-NGv3-sort-17_15515955_31039213-prep-prealign-realign.intervals -l INFO -L 17:15515956-31039213 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:22Z] INFO  17:22:14,200 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:22Z] INFO  17:22:14,211 HelpFormatter - Date/Time: 2016/04/14 17:22:14
[2016-04-15T00:22Z] INFO  17:22:14,212 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:22Z] INFO  17:22:14,213 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:22Z] INFO  17:22:14,246 ProgressMeter -            done    610691.0    85.0 s       2.3 m      100.0%    85.0 s       0.0 s
[2016-04-15T00:22Z] INFO  17:22:14,249 ProgressMeter - Total runtime 85.33 secs, 1.42 min, 0.02 hours
[2016-04-15T00:22Z] INFO  17:22:14,250 MicroScheduler - 273 reads were filtered out during the traversal out of approximately 610964 total reads (0.04%)
[2016-04-15T00:22Z] INFO  17:22:14,250 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:22Z] INFO  17:22:14,250 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:22Z] INFO  17:22:14,251 MicroScheduler -   -> 273 reads (0.04% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:22Z] GATK pre-alignment ('19', 0, 15509577) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:22Z] INFO  17:22:14,354 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:22Z] INFO  17:22:14,552 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T00:22Z] INFO  17:22:14,565 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:22Z] INFO  17:22:14,624 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-15T00:22Z] INFO  17:22:14,628 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@32d5a4c6
[2016-04-15T00:22Z] INFO  17:22:14,702 ProgressMeter -            done    230877.0    29.0 s       2.2 m      100.0%    29.0 s       0.0 s
[2016-04-15T00:22Z] INFO  17:22:14,702 ProgressMeter - Total runtime 29.87 secs, 0.50 min, 0.01 hours
[2016-04-15T00:22Z] INFO  17:22:14,703 MicroScheduler - 169 reads were filtered out during the traversal out of approximately 231046 total reads (0.07%)
[2016-04-15T00:22Z] INFO  17:22:14,703 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:22Z] INFO  17:22:14,703 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:22Z] INFO  17:22:14,703 MicroScheduler -   -> 169 reads (0.07% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:22Z] INFO  17:22:14,923 IntervalUtils - Processing 15523258 bp from intervals
[2016-04-15T00:22Z] WARN  17:22:14,928 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:22Z] INFO  17:22:15,004 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:22Z] INFO  17:22:15,293 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:22Z] INFO  17:22:15,294 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:22Z] INFO  17:22:15,295 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:22Z] INFO  17:22:15,296 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:22Z] INFO  17:22:15,722 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:22Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-16_64982511_80574976-prep-prealign.bam
[2016-04-15T00:22Z] INFO  17:22:15,838 ProgressMeter -            done   3487905.0    11.0 s       3.0 s      100.0%    11.0 s       0.0 s
[2016-04-15T00:22Z] INFO  17:22:15,851 ProgressMeter - Total runtime 11.16 secs, 0.19 min, 0.00 hours
[2016-04-15T00:22Z] INFO  17:22:15,856 MicroScheduler - 21879 reads were filtered out during the traversal out of approximately 274337 total reads (7.98%)
[2016-04-15T00:22Z] INFO  17:22:15,857 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:22Z] INFO  17:22:15,858 MicroScheduler -   -> 524 reads (0.19% of total) failing BadMateFilter
[2016-04-15T00:22Z] INFO  17:22:15,859 MicroScheduler -   -> 20925 reads (7.63% of total) failing DuplicateReadFilter
[2016-04-15T00:22Z] INFO  17:22:15,859 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:22Z] INFO  17:22:15,860 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:22Z] INFO  17:22:15,861 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:22Z] INFO  17:22:15,862 MicroScheduler -   -> 430 reads (0.16% of total) failing MappingQualityZeroFilter
[2016-04-15T00:22Z] INFO  17:22:15,863 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:22Z] INFO  17:22:15,863 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-15T00:22Z] INFO  17:22:15,864 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:22Z] INFO  17:22:16,190 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:22Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-18_34092400_49867248-prep-prealign.bam
[2016-04-15T00:22Z] INFO  17:22:16,767 ProgressMeter -            done   1.5548424E7    18.0 s       1.0 s      100.0%    18.0 s       0.0 s
[2016-04-15T00:22Z] INFO  17:22:16,768 ProgressMeter - Total runtime 18.20 secs, 0.30 min, 0.01 hours
[2016-04-15T00:22Z] INFO  17:22:16,773 MicroScheduler - 15987 reads were filtered out during the traversal out of approximately 196266 total reads (8.15%)
[2016-04-15T00:22Z] INFO  17:22:16,774 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:22Z] INFO  17:22:16,775 MicroScheduler -   -> 641 reads (0.33% of total) failing BadMateFilter
[2016-04-15T00:22Z] INFO  17:22:16,776 MicroScheduler -   -> 14546 reads (7.41% of total) failing DuplicateReadFilter
[2016-04-15T00:22Z] INFO  17:22:16,776 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:22Z] INFO  17:22:16,777 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:22Z] INFO  17:22:16,778 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:22Z] INFO  17:22:16,779 MicroScheduler -   -> 800 reads (0.41% of total) failing MappingQualityZeroFilter
[2016-04-15T00:22Z] INFO  17:22:16,779 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:22Z] INFO  17:22:16,780 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-15T00:22Z] INFO  17:22:16,781 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:22Z] INFO  17:22:16,818 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:22Z] INFO  17:22:16,822 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:22Z] INFO  17:22:16,823 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:22Z] INFO  17:22:16,823 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:22Z] INFO  17:22:16,828 HelpFormatter - Program Args: -T PrintReads -L 19:1-15509577 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/19/tx/tmpsyEttq/R14-18106_kapa-NGv3-PE100-NGv3-sort-19_0_15509577-prep-prealign.bam
[2016-04-15T00:22Z] INFO  17:22:16,839 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:22Z] INFO  17:22:16,850 HelpFormatter - Date/Time: 2016/04/14 17:22:16
[2016-04-15T00:22Z] INFO  17:22:16,851 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:22Z] INFO  17:22:16,852 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:22Z] INFO  17:22:17,044 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:22Z] GATK RealignerTargetCreator: R14-18106_kapa-NGv3-PE100-NGv3-sort-18_34092400_49867248-prep-prealign.bam 18:34092401-49867248
[2016-04-15T00:22Z] GATK: RealignerTargetCreator
[2016-04-15T00:22Z] INFO  17:22:17,173 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:22Z] GATK: realign ('17', 77707305, 81195210) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:22Z] GATK RealignerTargetCreator: R14-18106_kapa-NGv3-PE100-NGv3-sort-16_64982511_80574976-prep-prealign.bam 16:64982512-80574976
[2016-04-15T00:22Z] GATK: RealignerTargetCreator
[2016-04-15T00:22Z] INFO  17:22:18,329 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-15T00:22Z] INFO  17:22:18,392 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:22Z] INFO  17:22:18,404 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@41fd9d8e
[2016-04-15T00:22Z] INFO  17:22:18,416 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:22Z] GATK: realign ('18', 18533538, 34081962) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:22Z] INFO  17:22:18,427 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:22Z] INFO  17:22:18,470 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.04
[2016-04-15T00:22Z] INFO  17:22:18,486 IntervalUtils - Processing 15509577 bp from intervals
[2016-04-15T00:22Z] INFO  17:22:18,583 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:22Z] INFO  17:22:18,600 ProgressMeter -            done    482260.0    57.0 s     119.0 s      100.0%    57.0 s       0.0 s
[2016-04-15T00:22Z] INFO  17:22:18,601 ProgressMeter - Total runtime 57.47 secs, 0.96 min, 0.02 hours
[2016-04-15T00:22Z] INFO  17:22:18,601 MicroScheduler - 220 reads were filtered out during the traversal out of approximately 482480 total reads (0.05%)
[2016-04-15T00:22Z] INFO  17:22:18,602 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:22Z] INFO  17:22:18,602 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:22Z] INFO  17:22:18,602 MicroScheduler -   -> 220 reads (0.05% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:22Z] INFO  17:22:18,910 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:22Z] INFO  17:22:18,911 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:22Z] INFO  17:22:18,911 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:22Z] INFO  17:22:18,912 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:22Z] INFO  17:22:18,938 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:22Z] INFO  17:22:19,102 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:22Z] INFO  17:22:19,582 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@41fd9d8e
[2016-04-15T00:22Z] INFO  17:22:19,697 ProgressMeter -            done   1115743.0     2.2 m     118.0 s      100.0%     2.2 m       0.0 s
[2016-04-15T00:22Z] INFO  17:22:19,697 ProgressMeter - Total runtime 131.98 secs, 2.20 min, 0.04 hours
[2016-04-15T00:22Z] INFO  17:22:19,698 MicroScheduler - 429 reads were filtered out during the traversal out of approximately 1116172 total reads (0.04%)
[2016-04-15T00:22Z] INFO  17:22:19,699 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:22Z] INFO  17:22:19,699 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:22Z] INFO  17:22:19,699 MicroScheduler -   -> 429 reads (0.04% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:22Z] INFO  17:22:20,404 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:22Z] INFO  17:22:20,407 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:22Z] INFO  17:22:20,408 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:22Z] INFO  17:22:20,408 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:22Z] INFO  17:22:20,413 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/17/R14-18106_kapa-NGv3-PE100-NGv3-sort-17_77707305_81195210-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/17/R14-18106_kapa-NGv3-PE100-NGv3-sort-17_77707305_81195210-prep-prealign-realign.intervals -L 17:77707306-81195210 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/17/tx/tmpLA0EOe/R14-18106_kapa-NGv3-PE100-NGv3-sort-17_77707305_81195210-prep.bam
[2016-04-15T00:22Z] INFO  17:22:20,412 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:22Z] INFO  17:22:20,416 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:22Z] INFO  17:22:20,416 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:22Z] INFO  17:22:20,417 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:22Z] INFO  17:22:20,421 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/16/R14-18106_kapa-NGv3-PE100-NGv3-sort-16_64982511_80574976-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/16/tx/tmpIdWQLo/R14-18106_kapa-NGv3-PE100-NGv3-sort-16_64982511_80574976-prep-prealign-realign.intervals -l INFO -L 16:64982512-80574976 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:22Z] INFO  17:22:20,426 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:22Z] INFO  17:22:20,427 HelpFormatter - Date/Time: 2016/04/14 17:22:20
[2016-04-15T00:22Z] INFO  17:22:20,428 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:22Z] INFO  17:22:20,428 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:22Z] INFO  17:22:20,431 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:22Z] INFO  17:22:20,434 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:22Z] INFO  17:22:20,435 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:22Z] INFO  17:22:20,435 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:22Z] INFO  17:22:20,436 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:22Z] INFO  17:22:20,436 HelpFormatter - Date/Time: 2016/04/14 17:22:20
[2016-04-15T00:22Z] INFO  17:22:20,436 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:22Z] INFO  17:22:20,436 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:22Z] INFO  17:22:20,440 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/18/R14-18106_kapa-NGv3-PE100-NGv3-sort-18_34092400_49867248-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/18/tx/tmpKZ_2gV/R14-18106_kapa-NGv3-PE100-NGv3-sort-18_34092400_49867248-prep-prealign-realign.intervals -l INFO -L 18:34092401-49867248 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:22Z] INFO  17:22:20,448 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:22Z] INFO  17:22:20,449 HelpFormatter - Date/Time: 2016/04/14 17:22:20
[2016-04-15T00:22Z] INFO  17:22:20,450 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:22Z] INFO  17:22:20,450 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:22Z] INFO  17:22:20,537 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:22Z] INFO  17:22:20,550 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:22Z] INFO  17:22:20,592 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:22Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-17_46607689_62121560-prep-prealign.bam
[2016-04-15T00:22Z] INFO  17:22:20,642 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:22Z] INFO  17:22:20,743 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T00:22Z] INFO  17:22:20,753 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:22Z] INFO  17:22:20,778 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T00:22Z] INFO  17:22:20,791 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:22Z] INFO  17:22:20,806 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:22Z] INFO  17:22:20,816 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:22Z] INFO  17:22:20,836 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-15T00:22Z] INFO  17:22:20,846 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-15T00:22Z] INFO  17:22:20,894 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-15T00:22Z] INFO  17:22:21,128 IntervalUtils - Processing 15592465 bp from intervals
[2016-04-15T00:22Z] WARN  17:22:21,133 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:22Z] INFO  17:22:21,165 IntervalUtils - Processing 15774848 bp from intervals
[2016-04-15T00:22Z] WARN  17:22:21,170 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:22Z] INFO  17:22:21,232 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:22Z] INFO  17:22:21,257 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:22Z] INFO  17:22:21,285 IntervalUtils - Processing 3487905 bp from intervals
[2016-04-15T00:22Z] WARN  17:22:21,290 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:22Z] INFO  17:22:21,301 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:22Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-16_15596122_31106473-prep-prealign.bam
[2016-04-15T00:22Z] INFO  17:22:21,337 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:22Z] INFO  17:22:21,341 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:22Z] INFO  17:22:21,341 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:22Z] INFO  17:22:21,342 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:22Z] INFO  17:22:21,346 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/18/R14-18106_kapa-NGv3-PE100-NGv3-sort-18_18533538_34081962-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/18/R14-18106_kapa-NGv3-PE100-NGv3-sort-18_18533538_34081962-prep-prealign-realign.intervals -L 18:18533539-34081962 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/18/tx/tmpWf8xoo/R14-18106_kapa-NGv3-PE100-NGv3-sort-18_18533538_34081962-prep.bam
[2016-04-15T00:22Z] INFO  17:22:21,355 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:22Z] INFO  17:22:21,356 HelpFormatter - Date/Time: 2016/04/14 17:22:21
[2016-04-15T00:22Z] INFO  17:22:21,357 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:22Z] INFO  17:22:21,358 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:22Z] INFO  17:22:21,389 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:22Z] INFO  17:22:21,461 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:22Z] INFO  17:22:21,462 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:22Z] INFO  17:22:21,463 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:22Z] INFO  17:22:21,463 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:22Z] INFO  17:22:21,471 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:22Z] INFO  17:22:21,472 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:22Z] INFO  17:22:21,473 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:22Z] INFO  17:22:21,474 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:22Z] INFO  17:22:21,473 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:22Z] INFO  17:22:21,475 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:22Z] INFO  17:22:21,475 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:22Z] INFO  17:22:21,476 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:22Z] INFO  17:22:21,544 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:22Z] INFO  17:22:21,585 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:22Z] INFO  17:22:21,588 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:22Z] INFO  17:22:21,688 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:22Z] INFO  17:22:21,700 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:22Z] INFO  17:22:21,743 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.04
[2016-04-15T00:22Z] INFO  17:22:21,806 ProgressMeter -     17:76128628    400007.0    60.0 s       2.5 m       89.9%    66.0 s       6.0 s
[2016-04-15T00:22Z] INFO  17:22:22,085 IntervalUtils - Processing 15548424 bp from intervals
[2016-04-15T00:22Z] WARN  17:22:22,090 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:22Z] GATK RealignerTargetCreator: R14-18106_kapa-NGv3-PE100-NGv3-sort-17_46607689_62121560-prep-prealign.bam 17:46607690-62121560
[2016-04-15T00:22Z] GATK: RealignerTargetCreator
[2016-04-15T00:22Z] INFO  17:22:22,222 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:22Z] INFO  17:22:22,345 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:22Z] INFO  17:22:22,346 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:22Z] INFO  17:22:22,347 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:22Z] INFO  17:22:22,348 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:22Z] INFO  17:22:22,535 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:22Z] INFO  17:22:22,735 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:22Z] INFO  17:22:23,563 ProgressMeter -     16:14920357   1.4893056E7    30.0 s       2.0 s       96.1%    31.0 s       1.0 s
[2016-04-15T00:22Z] INFO  17:22:23,753 ProgressMeter -     17:10322042    700014.0    90.0 s       2.1 m       66.5%     2.3 m      45.0 s
[2016-04-15T00:22Z] INFO  17:22:24,482 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@41fd9d8e
[2016-04-15T00:22Z] INFO  17:22:24,605 ProgressMeter -            done    143833.0    19.0 s       2.3 m      100.0%    19.0 s       0.0 s
[2016-04-15T00:22Z] INFO  17:22:24,606 ProgressMeter - Total runtime 19.68 secs, 0.33 min, 0.01 hours
[2016-04-15T00:22Z] INFO  17:22:24,607 MicroScheduler - 132 reads were filtered out during the traversal out of approximately 143965 total reads (0.09%)
[2016-04-15T00:22Z] INFO  17:22:24,608 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:22Z] INFO  17:22:24,609 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:22Z] INFO  17:22:24,610 MicroScheduler -   -> 132 reads (0.09% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:22Z] GATK RealignerTargetCreator: R14-18106_kapa-NGv3-PE100-NGv3-sort-16_15596122_31106473-prep-prealign.bam 16:15596123-31106473
[2016-04-15T00:22Z] GATK: RealignerTargetCreator
[2016-04-15T00:22Z] INFO  17:22:24,974 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:22Z] INFO  17:22:24,976 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:22Z] INFO  17:22:24,976 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:22Z] INFO  17:22:24,977 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:22Z] INFO  17:22:24,981 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/17/R14-18106_kapa-NGv3-PE100-NGv3-sort-17_46607689_62121560-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/17/tx/tmpTfecdl/R14-18106_kapa-NGv3-PE100-NGv3-sort-17_46607689_62121560-prep-prealign-realign.intervals -l INFO -L 17:46607690-62121560 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:22Z] INFO  17:22:24,989 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:22Z] INFO  17:22:24,990 HelpFormatter - Date/Time: 2016/04/14 17:22:24
[2016-04-15T00:22Z] INFO  17:22:24,991 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:22Z] INFO  17:22:24,992 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:22Z] INFO  17:22:25,115 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:22Z] INFO  17:22:25,219 ProgressMeter -            done   1.8531348E7    21.0 s       1.0 s      100.0%    21.0 s       0.0 s
[2016-04-15T00:22Z] INFO  17:22:25,220 ProgressMeter - Total runtime 21.78 secs, 0.36 min, 0.01 hours
[2016-04-15T00:22Z] INFO  17:22:25,224 MicroScheduler - 28746 reads were filtered out during the traversal out of approximately 251977 total reads (11.41%)
[2016-04-15T00:22Z] INFO  17:22:25,225 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:22Z] INFO  17:22:25,226 MicroScheduler -   -> 854 reads (0.34% of total) failing BadMateFilter
[2016-04-15T00:22Z] INFO  17:22:25,226 MicroScheduler -   -> 18325 reads (7.27% of total) failing DuplicateReadFilter
[2016-04-15T00:22Z] INFO  17:22:25,227 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:22Z] INFO  17:22:25,228 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:22Z] INFO  17:22:25,228 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:22Z] INFO  17:22:25,229 MicroScheduler -   -> 9567 reads (3.80% of total) failing MappingQualityZeroFilter
[2016-04-15T00:22Z] INFO  17:22:25,229 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:22Z] INFO  17:22:25,230 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-15T00:22Z] INFO  17:22:25,231 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:22Z] INFO  17:22:25,266 ProgressMeter -            done    345706.0    23.0 s      66.0 s       99.1%    23.0 s       0.0 s
[2016-04-15T00:22Z] INFO  17:22:25,266 ProgressMeter - Total runtime 23.15 secs, 0.39 min, 0.01 hours
[2016-04-15T00:22Z] INFO  17:22:25,270 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 345706 total reads (0.00%)
[2016-04-15T00:22Z] INFO  17:22:25,270 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:22Z] INFO  17:22:25,270 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:22Z] INFO  17:22:25,271 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:22Z] INFO  17:22:25,377 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T00:22Z] INFO  17:22:25,379 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@5fe152b7
[2016-04-15T00:22Z] INFO  17:22:25,389 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:22Z] INFO  17:22:25,428 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.04
[2016-04-15T00:22Z] INFO  17:22:25,475 ProgressMeter -            done    123740.0    18.0 s       2.5 m       99.4%    18.0 s       0.0 s
[2016-04-15T00:22Z] INFO  17:22:25,475 ProgressMeter - Total runtime 18.44 secs, 0.31 min, 0.01 hours
[2016-04-15T00:22Z] INFO  17:22:25,475 MicroScheduler - 102 reads were filtered out during the traversal out of approximately 123842 total reads (0.08%)
[2016-04-15T00:22Z] INFO  17:22:25,476 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:22Z] INFO  17:22:25,476 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:22Z] INFO  17:22:25,476 MicroScheduler -   -> 102 reads (0.08% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:22Z] INFO  17:22:25,728 IntervalUtils - Processing 15513871 bp from intervals
[2016-04-15T00:22Z] WARN  17:22:25,741 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:22Z] INFO  17:22:25,809 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:22Z] INFO  17:22:25,928 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:22Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-18_50278423_66344430-prep-prealign.bam
[2016-04-15T00:22Z] INFO  17:22:25,976 ProgressMeter -            done   1.5528616E7    32.0 s       2.0 s      100.0%    32.0 s       0.0 s
[2016-04-15T00:22Z] INFO  17:22:25,977 ProgressMeter - Total runtime 32.43 secs, 0.54 min, 0.01 hours
[2016-04-15T00:22Z] INFO  17:22:25,982 MicroScheduler - 158127 reads were filtered out during the traversal out of approximately 869019 total reads (18.20%)
[2016-04-15T00:22Z] INFO  17:22:25,983 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:22Z] INFO  17:22:25,983 MicroScheduler -   -> 1718 reads (0.20% of total) failing BadMateFilter
[2016-04-15T00:22Z] INFO  17:22:25,984 MicroScheduler -   -> 59805 reads (6.88% of total) failing DuplicateReadFilter
[2016-04-15T00:22Z] INFO  17:22:25,985 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:22Z] INFO  17:22:25,985 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:22Z] INFO  17:22:25,986 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:22Z] INFO  17:22:25,986 MicroScheduler -   -> 96604 reads (11.12% of total) failing MappingQualityZeroFilter
[2016-04-15T00:22Z] INFO  17:22:25,987 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:22Z] INFO  17:22:25,988 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-15T00:22Z] INFO  17:22:25,988 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:22Z] INFO  17:22:26,032 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:22Z] INFO  17:22:26,032 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:22Z] INFO  17:22:26,033 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:22Z] INFO  17:22:26,033 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:22Z] GATK RealignerTargetCreator: R14-18106_kapa-NGv3-PE100-NGv3-sort-18_50278423_66344430-prep-prealign.bam 18:50278424-66344430
[2016-04-15T00:22Z] GATK: RealignerTargetCreator
[2016-04-15T00:22Z] INFO  17:22:26,548 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:22Z] GATK: realign ('18', 0, 18531348) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:22Z] INFO  17:22:26,782 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:22Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-16_80575258_90354753-prep.bam
[2016-04-15T00:22Z] INFO  17:22:26,954 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:22Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-18_66346699_78077248-prep-prealign.bam
[2016-04-15T00:22Z] INFO  17:22:27,330 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:22Z] GATK: realign ('16', 0, 15528616) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:22Z] GATK RealignerTargetCreator: R14-18106_kapa-NGv3-PE100-NGv3-sort-18_66346699_78077248-prep-prealign.bam 18:66346700-78077248
[2016-04-15T00:22Z] GATK: RealignerTargetCreator
[2016-04-15T00:22Z] INFO  17:22:27,721 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:22Z] INFO  17:22:27,724 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:22Z] INFO  17:22:27,725 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:22Z] INFO  17:22:27,726 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:22Z] INFO  17:22:27,730 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/16/R14-18106_kapa-NGv3-PE100-NGv3-sort-16_15596122_31106473-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/16/tx/tmpJsHEsW/R14-18106_kapa-NGv3-PE100-NGv3-sort-16_15596122_31106473-prep-prealign-realign.intervals -l INFO -L 16:15596123-31106473 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:22Z] INFO  17:22:27,758 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:22Z] INFO  17:22:27,759 HelpFormatter - Date/Time: 2016/04/14 17:22:27
[2016-04-15T00:22Z] INFO  17:22:27,760 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:22Z] INFO  17:22:27,765 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:22Z] GATK pre-alignment ('19', 15510112, 31025906) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:22Z] INFO  17:22:27,884 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:22Z] INFO  17:22:28,095 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T00:22Z] INFO  17:22:28,104 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:22Z] INFO  17:22:28,189 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-15T00:22Z] INFO  17:22:28,535 IntervalUtils - Processing 15510351 bp from intervals
[2016-04-15T00:22Z] WARN  17:22:28,540 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:22Z] INFO  17:22:28,627 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:22Z] INFO  17:22:28,863 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:22Z] INFO  17:22:28,864 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:22Z] INFO  17:22:28,865 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:22Z] INFO  17:22:28,866 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:22Z] INFO  17:22:29,658 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:22Z] INFO  17:22:29,662 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:22Z] INFO  17:22:29,662 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:22Z] INFO  17:22:29,663 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:22Z] INFO  17:22:29,668 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/18/R14-18106_kapa-NGv3-PE100-NGv3-sort-18_0_18531348-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/18/R14-18106_kapa-NGv3-PE100-NGv3-sort-18_0_18531348-prep-prealign-realign.intervals -L 18:1-18531348 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/18/tx/tmpl092gY/R14-18106_kapa-NGv3-PE100-NGv3-sort-18_0_18531348-prep.bam
[2016-04-15T00:22Z] INFO  17:22:29,679 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@7172f77a
[2016-04-15T00:22Z] INFO  17:22:29,693 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:22Z] INFO  17:22:29,701 HelpFormatter - Date/Time: 2016/04/14 17:22:29
[2016-04-15T00:22Z] INFO  17:22:29,702 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:22Z] INFO  17:22:29,702 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:22Z] INFO  17:22:29,792 ProgressMeter -            done    567045.0    68.0 s     120.0 s      100.0%    68.0 s       0.0 s
[2016-04-15T00:22Z] INFO  17:22:29,793 ProgressMeter - Total runtime 68.14 secs, 1.14 min, 0.02 hours
[2016-04-15T00:22Z] INFO  17:22:29,794 MicroScheduler - 273 reads were filtered out during the traversal out of approximately 567318 total reads (0.05%)
[2016-04-15T00:22Z] INFO  17:22:29,795 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:22Z] INFO  17:22:29,796 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:22Z] INFO  17:22:29,796 MicroScheduler -   -> 273 reads (0.05% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:22Z] INFO  17:22:29,870 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:22Z] INFO  17:22:29,874 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:22Z] INFO  17:22:29,874 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:22Z] INFO  17:22:29,875 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:22Z] INFO  17:22:29,879 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/18/R14-18106_kapa-NGv3-PE100-NGv3-sort-18_50278423_66344430-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/18/tx/tmpqIWKiP/R14-18106_kapa-NGv3-PE100-NGv3-sort-18_50278423_66344430-prep-prealign-realign.intervals -l INFO -L 18:50278424-66344430 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:22Z] INFO  17:22:29,891 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:22Z] INFO  17:22:29,892 HelpFormatter - Date/Time: 2016/04/14 17:22:29
[2016-04-15T00:22Z] INFO  17:22:29,892 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:22Z] INFO  17:22:29,892 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:22Z] INFO  17:22:29,903 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:22Z] INFO  17:22:30,007 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:22Z] INFO  17:22:30,017 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:22Z] INFO  17:22:30,035 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:22Z] INFO  17:22:30,083 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-15T00:22Z] INFO  17:22:30,232 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T00:22Z] INFO  17:22:30,253 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:22Z] INFO  17:22:30,311 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-15T00:22Z] INFO  17:22:30,386 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:22Z] INFO  17:22:30,399 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:22Z] INFO  17:22:30,400 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:22Z] INFO  17:22:30,401 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:22Z] INFO  17:22:30,420 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/16/R14-18106_kapa-NGv3-PE100-NGv3-sort-16_0_15528616-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/16/R14-18106_kapa-NGv3-PE100-NGv3-sort-16_0_15528616-prep-prealign-realign.intervals -L 16:1-15528616 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/16/tx/tmpKhTwfO/R14-18106_kapa-NGv3-PE100-NGv3-sort-16_0_15528616-prep.bam
[2016-04-15T00:22Z] INFO  17:22:30,440 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:22Z] INFO  17:22:30,441 HelpFormatter - Date/Time: 2016/04/14 17:22:30
[2016-04-15T00:22Z] INFO  17:22:30,441 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:22Z] INFO  17:22:30,442 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:22Z] INFO  17:22:30,463 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:22Z] INFO  17:22:30,476 IntervalUtils - Processing 18531348 bp from intervals
[2016-04-15T00:22Z] INFO  17:22:30,477 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:22Z] INFO  17:22:30,478 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:22Z] INFO  17:22:30,479 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:22Z] WARN  17:22:30,481 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:22Z] INFO  17:22:30,483 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/18/R14-18106_kapa-NGv3-PE100-NGv3-sort-18_66346699_78077248-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/18/tx/tmpplOrgZ/R14-18106_kapa-NGv3-PE100-NGv3-sort-18_66346699_78077248-prep-prealign-realign.intervals -l INFO -L 18:66346700-78077248 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:22Z] INFO  17:22:30,497 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:22Z] INFO  17:22:30,498 HelpFormatter - Date/Time: 2016/04/14 17:22:30
[2016-04-15T00:22Z] INFO  17:22:30,498 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:22Z] INFO  17:22:30,499 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:22Z] INFO  17:22:30,567 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:22Z] INFO  17:22:30,594 IntervalUtils - Processing 16066007 bp from intervals
[2016-04-15T00:22Z] WARN  17:22:30,599 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:22Z] INFO  17:22:30,616 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:22Z] INFO  17:22:30,653 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:22Z] INFO  17:22:30,678 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:22Z] INFO  17:22:30,694 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:22Z] INFO  17:22:30,695 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:22Z] INFO  17:22:30,696 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:22Z] INFO  17:22:30,697 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:22Z] INFO  17:22:30,758 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:22Z] INFO  17:22:30,767 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:22Z] INFO  17:22:30,817 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T00:22Z] INFO  17:22:30,823 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:22Z] INFO  17:22:30,826 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:22Z] INFO  17:22:30,826 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:22Z] INFO  17:22:30,826 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:22Z] INFO  17:22:30,827 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:22Z] INFO  17:22:30,831 HelpFormatter - Program Args: -T PrintReads -L 19:15510113-31025906 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/19/tx/tmpIzH5Kd/R14-18106_kapa-NGv3-PE100-NGv3-sort-19_15510112_31025906-prep-prealign.bam
[2016-04-15T00:22Z] INFO  17:22:30,835 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-15T00:22Z] INFO  17:22:30,840 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:22Z] INFO  17:22:30,840 HelpFormatter - Date/Time: 2016/04/14 17:22:30
[2016-04-15T00:22Z] INFO  17:22:30,841 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:22Z] INFO  17:22:30,841 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:22Z] INFO  17:22:30,883 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-15T00:22Z] INFO  17:22:30,898 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:22Z] INFO  17:22:30,912 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:22Z] INFO  17:22:30,913 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:22Z] INFO  17:22:30,913 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:22Z] INFO  17:22:30,914 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:22Z] INFO  17:22:31,039 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:22Z] INFO  17:22:31,141 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:22Z] INFO  17:22:31,186 IntervalUtils - Processing 11730549 bp from intervals
[2016-04-15T00:22Z] WARN  17:22:31,191 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:22Z] INFO  17:22:31,195 IntervalUtils - Processing 15528616 bp from intervals
[2016-04-15T00:22Z] WARN  17:22:31,200 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:22Z] INFO  17:22:31,276 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:22Z] INFO  17:22:31,297 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:22Z] INFO  17:22:31,309 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:22Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-17_62122219_77705154-prep-prealign.bam
[2016-04-15T00:22Z] INFO  17:22:31,509 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:22Z] INFO  17:22:31,510 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:22Z] INFO  17:22:31,511 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:22Z] INFO  17:22:31,512 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:22Z] INFO  17:22:31,552 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:22Z] INFO  17:22:31,553 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:22Z] INFO  17:22:31,553 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:22Z] INFO  17:22:31,553 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:22Z] INFO  17:22:31,693 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:22Z] INFO  17:22:31,861 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:22Z] INFO  17:22:32,183 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-15T00:22Z] INFO  17:22:32,275 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:22Z] INFO  17:22:32,284 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:22Z] INFO  17:22:32,326 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.04
[2016-04-15T00:22Z] INFO  17:22:32,340 IntervalUtils - Processing 15515794 bp from intervals
[2016-04-15T00:22Z] INFO  17:22:32,467 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:22Z] INFO  17:22:32,504 ProgressMeter -     17:41610468    700026.0    90.0 s       2.2 m       67.9%     2.2 m      42.0 s
[2016-04-15T00:22Z] INFO  17:22:32,743 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:22Z] INFO  17:22:32,744 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:22Z] INFO  17:22:32,753 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:22Z] INFO  17:22:32,754 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:22Z] INFO  17:22:32,780 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:22Z] GATK RealignerTargetCreator: R14-18106_kapa-NGv3-PE100-NGv3-sort-17_62122219_77705154-prep-prealign.bam 17:62122220-77705154
[2016-04-15T00:22Z] GATK: RealignerTargetCreator
[2016-04-15T00:22Z] INFO  17:22:32,950 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:22Z] INFO  17:22:34,923 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@41fd9d8e
[2016-04-15T00:22Z] INFO  17:22:35,014 ProgressMeter -            done    846661.0   101.0 s     119.0 s      100.0%   101.0 s       0.0 s
[2016-04-15T00:22Z] INFO  17:22:35,015 ProgressMeter - Total runtime 101.32 secs, 1.69 min, 0.03 hours
[2016-04-15T00:22Z] INFO  17:22:35,015 MicroScheduler - 440 reads were filtered out during the traversal out of approximately 847101 total reads (0.05%)
[2016-04-15T00:22Z] INFO  17:22:35,016 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:22Z] INFO  17:22:35,017 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:22Z] INFO  17:22:35,017 MicroScheduler -   -> 440 reads (0.05% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:22Z] INFO  17:22:35,658 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:22Z] INFO  17:22:35,662 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:22Z] INFO  17:22:35,662 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:22Z] INFO  17:22:35,663 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:22Z] INFO  17:22:35,667 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/17/R14-18106_kapa-NGv3-PE100-NGv3-sort-17_62122219_77705154-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/17/tx/tmp0kzWMa/R14-18106_kapa-NGv3-PE100-NGv3-sort-17_62122219_77705154-prep-prealign-realign.intervals -l INFO -L 17:62122220-77705154 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:22Z] INFO  17:22:35,679 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:22Z] INFO  17:22:35,680 HelpFormatter - Date/Time: 2016/04/14 17:22:35
[2016-04-15T00:22Z] INFO  17:22:35,681 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:22Z] INFO  17:22:35,692 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:22Z] INFO  17:22:35,808 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:22Z] INFO  17:22:36,005 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T00:22Z] INFO  17:22:36,015 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:22Z] INFO  17:22:36,077 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-15T00:22Z] INFO  17:22:36,378 IntervalUtils - Processing 15582935 bp from intervals
[2016-04-15T00:22Z] WARN  17:22:36,383 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:22Z] INFO  17:22:36,460 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:22Z] INFO  17:22:36,480 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:22Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-17_0_15511002-prep-prealign.bam
[2016-04-15T00:22Z] INFO  17:22:36,658 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:22Z] INFO  17:22:36,658 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:22Z] INFO  17:22:36,658 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:22Z] INFO  17:22:36,659 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:22Z] INFO  17:22:37,408 ProgressMeter -            done    194654.0    15.0 s      77.0 s       99.2%    15.0 s       0.0 s
[2016-04-15T00:22Z] INFO  17:22:37,409 ProgressMeter - Total runtime 15.06 secs, 0.25 min, 0.00 hours
[2016-04-15T00:22Z] INFO  17:22:37,413 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 194654 total reads (0.00%)
[2016-04-15T00:22Z] INFO  17:22:37,416 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:22Z] INFO  17:22:37,417 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:22Z] INFO  17:22:37,418 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:22Z] INFO  17:22:39,112 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:22Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-18_18533538_34081962-prep.bam
[2016-04-15T00:22Z] GATK RealignerTargetCreator: R14-18106_kapa-NGv3-PE100-NGv3-sort-17_0_15511002-prep-prealign.bam 17:1-15511002
[2016-04-15T00:22Z] GATK: RealignerTargetCreator
[2016-04-15T00:22Z] INFO  17:22:39,735 ProgressMeter -            done   1.5774848E7    18.0 s       1.0 s      100.0%    18.0 s       0.0 s
[2016-04-15T00:22Z] INFO  17:22:39,736 ProgressMeter - Total runtime 18.26 secs, 0.30 min, 0.01 hours
[2016-04-15T00:22Z] INFO  17:22:39,736 MicroScheduler - 76027 reads were filtered out during the traversal out of approximately 232074 total reads (32.76%)
[2016-04-15T00:22Z] INFO  17:22:39,737 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:22Z] INFO  17:22:39,737 MicroScheduler -   -> 661 reads (0.28% of total) failing BadMateFilter
[2016-04-15T00:22Z] INFO  17:22:39,737 MicroScheduler -   -> 13306 reads (5.73% of total) failing DuplicateReadFilter
[2016-04-15T00:22Z] INFO  17:22:39,737 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:22Z] INFO  17:22:39,738 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:22Z] INFO  17:22:39,738 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:22Z] INFO  17:22:39,738 MicroScheduler -   -> 62060 reads (26.74% of total) failing MappingQualityZeroFilter
[2016-04-15T00:22Z] INFO  17:22:39,738 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:22Z] INFO  17:22:39,739 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-15T00:22Z] INFO  17:22:39,739 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:22Z] GATK pre-alignment ('19', 31038849, 46627578) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:22Z] INFO  17:22:41,287 ProgressMeter -            done    272808.0    19.0 s      72.0 s       99.8%    19.0 s       0.0 s
[2016-04-15T00:22Z] INFO  17:22:41,289 ProgressMeter - Total runtime 19.83 secs, 0.33 min, 0.01 hours
[2016-04-15T00:22Z] INFO  17:22:41,294 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 272808 total reads (0.00%)
[2016-04-15T00:22Z] INFO  17:22:41,295 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:22Z] INFO  17:22:41,296 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:22Z] INFO  17:22:41,297 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:22Z] INFO  17:22:41,939 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:22Z] GATK: realign ('18', 34092400, 49867248) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:22Z] INFO  17:22:42,052 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:22Z] INFO  17:22:42,056 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:22Z] INFO  17:22:42,057 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:22Z] INFO  17:22:42,058 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:22Z] INFO  17:22:42,063 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/17/R14-18106_kapa-NGv3-PE100-NGv3-sort-17_0_15511002-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/17/tx/tmpBMEkAY/R14-18106_kapa-NGv3-PE100-NGv3-sort-17_0_15511002-prep-prealign-realign.intervals -l INFO -L 17:1-15511002 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:22Z] INFO  17:22:42,074 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:22Z] INFO  17:22:42,075 HelpFormatter - Date/Time: 2016/04/14 17:22:42
[2016-04-15T00:22Z] INFO  17:22:42,076 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:22Z] INFO  17:22:42,076 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:22Z] INFO  17:22:42,222 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:22Z] INFO  17:22:42,499 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T00:22Z] INFO  17:22:42,517 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:22Z] INFO  17:22:42,521 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:22Z] INFO  17:22:42,521 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:22Z] INFO  17:22:42,521 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:22Z] INFO  17:22:42,526 HelpFormatter - Program Args: -T PrintReads -L 19:31038850-46627578 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/19/tx/tmpTkOXIZ/R14-18106_kapa-NGv3-PE100-NGv3-sort-19_31038849_46627578-prep-prealign.bam
[2016-04-15T00:22Z] INFO  17:22:42,528 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:22Z] INFO  17:22:42,538 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:22Z] INFO  17:22:42,539 HelpFormatter - Date/Time: 2016/04/14 17:22:42
[2016-04-15T00:22Z] INFO  17:22:42,540 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:22Z] INFO  17:22:42,540 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:22Z] INFO  17:22:42,593 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-15T00:22Z] INFO  17:22:42,622 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:22Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-17_77707305_81195210-prep.bam
[2016-04-15T00:22Z] INFO  17:22:42,739 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:22Z] INFO  17:22:42,997 IntervalUtils - Processing 15511002 bp from intervals
[2016-04-15T00:22Z] WARN  17:22:43,003 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:22Z] INFO  17:22:43,137 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:22Z] INFO  17:22:43,415 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:22Z] INFO  17:22:43,417 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:22Z] INFO  17:22:43,417 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:22Z] INFO  17:22:43,418 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:22Z] GATK pre-alignment ('19', 46627881, 59128983) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:22Z] INFO  17:22:43,846 ProgressMeter -            done   1.5523258E7    28.0 s       1.0 s      100.0%    28.0 s       0.0 s
[2016-04-15T00:22Z] INFO  17:22:43,847 ProgressMeter - Total runtime 28.55 secs, 0.48 min, 0.01 hours
[2016-04-15T00:22Z] INFO  17:22:43,851 MicroScheduler - 74948 reads were filtered out during the traversal out of approximately 598607 total reads (12.52%)
[2016-04-15T00:22Z] INFO  17:22:43,851 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:22Z] INFO  17:22:43,852 MicroScheduler -   -> 1221 reads (0.20% of total) failing BadMateFilter
[2016-04-15T00:22Z] INFO  17:22:43,852 MicroScheduler -   -> 42834 reads (7.16% of total) failing DuplicateReadFilter
[2016-04-15T00:22Z] INFO  17:22:43,852 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:22Z] INFO  17:22:43,852 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:22Z] INFO  17:22:43,853 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:22Z] INFO  17:22:43,853 MicroScheduler -   -> 30893 reads (5.16% of total) failing MappingQualityZeroFilter
[2016-04-15T00:22Z] INFO  17:22:43,853 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:22Z] INFO  17:22:43,854 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-15T00:22Z] INFO  17:22:43,854 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:22Z] INFO  17:22:44,091 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-15T00:22Z] INFO  17:22:44,141 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:22Z] INFO  17:22:44,150 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:22Z] INFO  17:22:44,184 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.03
[2016-04-15T00:22Z] INFO  17:22:44,198 IntervalUtils - Processing 15588729 bp from intervals
[2016-04-15T00:22Z] INFO  17:22:44,268 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:22Z] INFO  17:22:44,618 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:22Z] INFO  17:22:44,619 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:22Z] INFO  17:22:44,619 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:22Z] INFO  17:22:44,620 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:22Z] INFO  17:22:44,633 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:22Z] INFO  17:22:44,770 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:22Z] INFO  17:22:44,943 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:22Z] INFO  17:22:44,947 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:22Z] INFO  17:22:44,947 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:22Z] INFO  17:22:44,948 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:22Z] INFO  17:22:44,952 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/18/R14-18106_kapa-NGv3-PE100-NGv3-sort-18_34092400_49867248-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/18/R14-18106_kapa-NGv3-PE100-NGv3-sort-18_34092400_49867248-prep-prealign-realign.intervals -L 18:34092401-49867248 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/18/tx/tmph49Xa0/R14-18106_kapa-NGv3-PE100-NGv3-sort-18_34092400_49867248-prep.bam
[2016-04-15T00:22Z] INFO  17:22:44,969 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:22Z] INFO  17:22:44,970 HelpFormatter - Date/Time: 2016/04/14 17:22:44
[2016-04-15T00:22Z] INFO  17:22:44,971 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:22Z] INFO  17:22:44,971 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:22Z] INFO  17:22:45,150 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:22Z] INFO  17:22:45,224 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:22Z] GATK: realign ('17', 15515955, 31039213) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:22Z] INFO  17:22:45,272 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:22Z] INFO  17:22:45,291 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:22Z] INFO  17:22:45,361 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-15T00:22Z] INFO  17:22:45,473 ProgressMeter -            done   1.1730549E7    13.0 s       1.0 s      100.0%    13.0 s       0.0 s
[2016-04-15T00:22Z] INFO  17:22:45,474 ProgressMeter - Total runtime 13.96 secs, 0.23 min, 0.00 hours
[2016-04-15T00:22Z] INFO  17:22:45,478 MicroScheduler - 10235 reads were filtered out during the traversal out of approximately 124461 total reads (8.22%)
[2016-04-15T00:22Z] INFO  17:22:45,479 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:22Z] INFO  17:22:45,480 MicroScheduler -   -> 473 reads (0.38% of total) failing BadMateFilter
[2016-04-15T00:22Z] INFO  17:22:45,480 MicroScheduler -   -> 9440 reads (7.58% of total) failing DuplicateReadFilter
[2016-04-15T00:22Z] INFO  17:22:45,481 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:22Z] INFO  17:22:45,482 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:22Z] INFO  17:22:45,482 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:22Z] INFO  17:22:45,483 MicroScheduler -   -> 322 reads (0.26% of total) failing MappingQualityZeroFilter
[2016-04-15T00:22Z] INFO  17:22:45,483 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:22Z] INFO  17:22:45,484 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-15T00:22Z] INFO  17:22:45,485 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:22Z] INFO  17:22:45,737 IntervalUtils - Processing 15774848 bp from intervals
[2016-04-15T00:22Z] WARN  17:22:45,742 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:22Z] INFO  17:22:45,815 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:22Z] INFO  17:22:45,996 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:22Z] INFO  17:22:45,997 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:22Z] INFO  17:22:45,998 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:22Z] INFO  17:22:45,998 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:22Z] INFO  17:22:46,199 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:22Z] INFO  17:22:46,357 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:22Z] INFO  17:22:46,469 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:22Z] INFO  17:22:46,472 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:22Z] INFO  17:22:46,473 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:22Z] INFO  17:22:46,473 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:22Z] INFO  17:22:46,478 HelpFormatter - Program Args: -T PrintReads -L 19:46627882-59128983 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/19/tx/tmp6_x2yE/R14-18106_kapa-NGv3-PE100-NGv3-sort-19_46627881_59128983-prep-prealign.bam
[2016-04-15T00:22Z] INFO  17:22:46,486 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:22Z] INFO  17:22:46,487 HelpFormatter - Date/Time: 2016/04/14 17:22:46
[2016-04-15T00:22Z] INFO  17:22:46,487 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:22Z] INFO  17:22:46,487 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:22Z] INFO  17:22:46,696 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:22Z] INFO  17:22:46,804 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:22Z] GATK: realign ('18', 66346699, 78077248) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:22Z] INFO  17:22:47,750 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-15T00:22Z] INFO  17:22:47,833 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:22Z] INFO  17:22:47,842 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:22Z] INFO  17:22:47,883 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.04
[2016-04-15T00:22Z] INFO  17:22:47,898 IntervalUtils - Processing 12501102 bp from intervals
[2016-04-15T00:22Z] INFO  17:22:47,992 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:22Z] INFO  17:22:48,094 ProgressMeter -            done   1.5592465E7    26.0 s       1.0 s      100.0%    26.0 s       0.0 s
[2016-04-15T00:22Z] INFO  17:22:48,095 ProgressMeter - Total runtime 26.62 secs, 0.44 min, 0.01 hours
[2016-04-15T00:22Z] INFO  17:22:48,099 MicroScheduler - 88070 reads were filtered out during the traversal out of approximately 614164 total reads (14.34%)
[2016-04-15T00:22Z] INFO  17:22:48,100 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:22Z] INFO  17:22:48,100 MicroScheduler -   -> 1245 reads (0.20% of total) failing BadMateFilter
[2016-04-15T00:22Z] INFO  17:22:48,100 MicroScheduler -   -> 43689 reads (7.11% of total) failing DuplicateReadFilter
[2016-04-15T00:22Z] INFO  17:22:48,101 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:22Z] INFO  17:22:48,101 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:22Z] INFO  17:22:48,101 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:22Z] INFO  17:22:48,102 MicroScheduler -   -> 43136 reads (7.02% of total) failing MappingQualityZeroFilter
[2016-04-15T00:22Z] INFO  17:22:48,102 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:22Z] INFO  17:22:48,102 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-15T00:22Z] INFO  17:22:48,103 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:22Z] INFO  17:22:48,205 ProgressMeter -            done   1.6066007E7    17.0 s       1.0 s      100.0%    17.0 s       0.0 s
[2016-04-15T00:22Z] INFO  17:22:48,207 ProgressMeter - Total runtime 17.29 secs, 0.29 min, 0.00 hours
[2016-04-15T00:22Z] INFO  17:22:48,212 MicroScheduler - 11779 reads were filtered out during the traversal out of approximately 145095 total reads (8.12%)
[2016-04-15T00:22Z] INFO  17:22:48,213 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:22Z] INFO  17:22:48,214 MicroScheduler -   -> 583 reads (0.40% of total) failing BadMateFilter
[2016-04-15T00:22Z] INFO  17:22:48,215 MicroScheduler -   -> 10878 reads (7.50% of total) failing DuplicateReadFilter
[2016-04-15T00:22Z] INFO  17:22:48,215 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:22Z] INFO  17:22:48,216 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:22Z] INFO  17:22:48,217 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:22Z] INFO  17:22:48,218 MicroScheduler -   -> 318 reads (0.22% of total) failing MappingQualityZeroFilter
[2016-04-15T00:22Z] INFO  17:22:48,219 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:22Z] INFO  17:22:48,219 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-15T00:22Z] INFO  17:22:48,220 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:22Z] INFO  17:22:48,244 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:22Z] INFO  17:22:48,245 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:22Z] INFO  17:22:48,246 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:22Z] INFO  17:22:48,247 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:22Z] INFO  17:22:48,277 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:22Z] INFO  17:22:48,425 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:22Z] INFO  17:22:48,573 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:22Z] INFO  17:22:48,577 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:22Z] INFO  17:22:48,577 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:22Z] INFO  17:22:48,578 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:22Z] INFO  17:22:48,583 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/17/R14-18106_kapa-NGv3-PE100-NGv3-sort-17_15515955_31039213-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/17/R14-18106_kapa-NGv3-PE100-NGv3-sort-17_15515955_31039213-prep-prealign-realign.intervals -L 17:15515956-31039213 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/17/tx/tmpP2IA4l/R14-18106_kapa-NGv3-PE100-NGv3-sort-17_15515955_31039213-prep.bam
[2016-04-15T00:22Z] INFO  17:22:48,620 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:22Z] INFO  17:22:48,621 HelpFormatter - Date/Time: 2016/04/14 17:22:48
[2016-04-15T00:22Z] INFO  17:22:48,622 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:22Z] INFO  17:22:48,622 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:22Z] INFO  17:22:48,834 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:22Z] INFO  17:22:48,944 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:22Z] INFO  17:22:48,954 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:22Z] INFO  17:22:49,020 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-15T00:22Z] INFO  17:22:49,367 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:22Z] GATK: realign ('16', 64982511, 80574976) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:22Z] INFO  17:22:49,459 IntervalUtils - Processing 15523258 bp from intervals
[2016-04-15T00:22Z] WARN  17:22:49,474 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:22Z] INFO  17:22:49,475 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:22Z] INFO  17:22:49,479 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:22Z] INFO  17:22:49,479 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:22Z] INFO  17:22:49,480 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:22Z] INFO  17:22:49,484 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/18/R14-18106_kapa-NGv3-PE100-NGv3-sort-18_66346699_78077248-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/18/R14-18106_kapa-NGv3-PE100-NGv3-sort-18_66346699_78077248-prep-prealign-realign.intervals -L 18:66346700-78077248 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/18/tx/tmpKT5FPR/R14-18106_kapa-NGv3-PE100-NGv3-sort-18_66346699_78077248-prep.bam
[2016-04-15T00:22Z] INFO  17:22:49,494 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:22Z] INFO  17:22:49,495 HelpFormatter - Date/Time: 2016/04/14 17:22:49
[2016-04-15T00:22Z] INFO  17:22:49,495 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:22Z] INFO  17:22:49,496 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:22Z] INFO  17:22:49,565 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:22Z] INFO  17:22:49,575 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:22Z] GATK: realign ('18', 50278423, 66344430) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:22Z] INFO  17:22:49,591 ProgressMeter -      19:1627503    100001.0    30.0 s       5.1 m       10.5%     4.8 m       4.3 m
[2016-04-15T00:22Z] INFO  17:22:49,713 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:22Z] INFO  17:22:49,727 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:22Z] INFO  17:22:49,728 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:22Z] INFO  17:22:49,729 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:22Z] INFO  17:22:49,730 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:22Z] INFO  17:22:49,897 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:22Z] INFO  17:22:49,903 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:22Z] INFO  17:22:49,917 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:22Z] INFO  17:22:50,003 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-15T00:22Z] INFO  17:22:50,148 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:22Z] INFO  17:22:50,305 IntervalUtils - Processing 11730549 bp from intervals
[2016-04-15T00:22Z] WARN  17:22:50,310 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:22Z] INFO  17:22:50,340 ProgressMeter -            done    250945.0    19.0 s      78.0 s      100.0%    19.0 s       0.0 s
[2016-04-15T00:22Z] INFO  17:22:50,340 ProgressMeter - Total runtime 19.65 secs, 0.33 min, 0.01 hours
[2016-04-15T00:22Z] INFO  17:22:50,344 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 250945 total reads (0.00%)
[2016-04-15T00:22Z] INFO  17:22:50,344 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:22Z] INFO  17:22:50,345 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:22Z] INFO  17:22:50,345 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:22Z] INFO  17:22:50,379 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:22Z] INFO  17:22:50,524 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:22Z] INFO  17:22:50,526 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:22Z] INFO  17:22:50,527 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:22Z] INFO  17:22:50,528 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:22Z] INFO  17:22:50,645 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:22Z] INFO  17:22:50,765 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:22Z] INFO  17:22:50,968 ProgressMeter -            done   1.5513871E7    24.0 s       1.0 s      100.0%    24.0 s       0.0 s
[2016-04-15T00:22Z] INFO  17:22:50,969 ProgressMeter - Total runtime 24.94 secs, 0.42 min, 0.01 hours
[2016-04-15T00:22Z] INFO  17:22:50,974 MicroScheduler - 51396 reads were filtered out during the traversal out of approximately 485178 total reads (10.59%)
[2016-04-15T00:22Z] INFO  17:22:50,975 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:22Z] INFO  17:22:50,976 MicroScheduler -   -> 1077 reads (0.22% of total) failing BadMateFilter
[2016-04-15T00:22Z] INFO  17:22:50,976 MicroScheduler -   -> 35631 reads (7.34% of total) failing DuplicateReadFilter
[2016-04-15T00:22Z] INFO  17:22:50,977 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:22Z] INFO  17:22:50,978 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:22Z] INFO  17:22:50,978 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:22Z] INFO  17:22:50,979 MicroScheduler -   -> 14688 reads (3.03% of total) failing MappingQualityZeroFilter
[2016-04-15T00:22Z] INFO  17:22:50,979 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:22Z] INFO  17:22:50,980 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-15T00:22Z] INFO  17:22:50,980 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:22Z] INFO  17:22:51,887 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:22Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-18_0_18531348-prep.bam
[2016-04-15T00:22Z] INFO  17:22:52,190 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:22Z] INFO  17:22:52,193 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:22Z] INFO  17:22:52,194 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:22Z] INFO  17:22:52,194 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:22Z] INFO  17:22:52,199 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/16/R14-18106_kapa-NGv3-PE100-NGv3-sort-16_64982511_80574976-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/16/R14-18106_kapa-NGv3-PE100-NGv3-sort-16_64982511_80574976-prep-prealign-realign.intervals -L 16:64982512-80574976 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/16/tx/tmpbF1hHf/R14-18106_kapa-NGv3-PE100-NGv3-sort-16_64982511_80574976-prep.bam
[2016-04-15T00:22Z] INFO  17:22:52,209 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:22Z] INFO  17:22:52,210 HelpFormatter - Date/Time: 2016/04/14 17:22:52
[2016-04-15T00:22Z] INFO  17:22:52,210 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:22Z] INFO  17:22:52,211 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:22Z] INFO  17:22:52,363 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:22Z] INFO  17:22:52,367 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:22Z] INFO  17:22:52,368 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:22Z] INFO  17:22:52,368 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:22Z] INFO  17:22:52,373 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/18/R14-18106_kapa-NGv3-PE100-NGv3-sort-18_50278423_66344430-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/18/R14-18106_kapa-NGv3-PE100-NGv3-sort-18_50278423_66344430-prep-prealign-realign.intervals -L 18:50278424-66344430 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/18/tx/tmpmJWktN/R14-18106_kapa-NGv3-PE100-NGv3-sort-18_50278423_66344430-prep.bam
[2016-04-15T00:22Z] INFO  17:22:52,383 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:22Z] INFO  17:22:52,386 HelpFormatter - Date/Time: 2016/04/14 17:22:52
[2016-04-15T00:22Z] INFO  17:22:52,395 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:22Z] INFO  17:22:52,396 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:22Z] INFO  17:22:52,420 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:22Z] INFO  17:22:52,429 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:22Z] GATK: realign ('17', 46607689, 62121560) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:22Z] INFO  17:22:52,588 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:22Z] INFO  17:22:52,597 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:22Z] INFO  17:22:52,613 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:22Z] GATK pre-alignment ('20', 0, 15843471) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:22Z] INFO  17:22:52,661 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-15T00:22Z] INFO  17:22:52,731 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:22Z] INFO  17:22:52,741 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:22Z] INFO  17:22:52,809 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-15T00:22Z] INFO  17:22:52,978 IntervalUtils - Processing 15592465 bp from intervals
[2016-04-15T00:22Z] WARN  17:22:52,983 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:22Z] INFO  17:22:53,050 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:22Z] INFO  17:22:53,246 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:22Z] INFO  17:22:53,247 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:22Z] INFO  17:22:53,248 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:22Z] INFO  17:22:53,249 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:22Z] INFO  17:22:53,421 IntervalUtils - Processing 16066007 bp from intervals
[2016-04-15T00:22Z] WARN  17:22:53,437 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:22Z] INFO  17:22:53,452 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:22Z] INFO  17:22:53,559 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:22Z] INFO  17:22:53,613 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:22Z] INFO  17:22:53,687 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:22Z] INFO  17:22:53,688 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:22Z] INFO  17:22:53,688 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:22Z] INFO  17:22:53,689 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:22Z] INFO  17:22:53,867 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:22Z] INFO  17:22:54,066 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:22Z] INFO  17:22:55,267 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:22Z] INFO  17:22:55,270 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:22Z] INFO  17:22:55,271 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:22Z] INFO  17:22:55,271 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:22Z] INFO  17:22:55,276 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/17/R14-18106_kapa-NGv3-PE100-NGv3-sort-17_46607689_62121560-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/17/R14-18106_kapa-NGv3-PE100-NGv3-sort-17_46607689_62121560-prep-prealign-realign.intervals -L 17:46607690-62121560 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/17/tx/tmpMt4Ou5/R14-18106_kapa-NGv3-PE100-NGv3-sort-17_46607689_62121560-prep.bam
[2016-04-15T00:22Z] INFO  17:22:55,286 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:22Z] INFO  17:22:55,297 HelpFormatter - Date/Time: 2016/04/14 17:22:55
[2016-04-15T00:22Z] INFO  17:22:55,298 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:22Z] INFO  17:22:55,299 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:22Z] INFO  17:22:55,526 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:22Z] INFO  17:22:55,674 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:22Z] INFO  17:22:55,683 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:22Z] INFO  17:22:55,722 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:22Z] INFO  17:22:55,725 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.04
[2016-04-15T00:22Z] INFO  17:22:55,725 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:22Z] INFO  17:22:55,726 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:22Z] INFO  17:22:55,727 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:22Z] INFO  17:22:55,731 HelpFormatter - Program Args: -T PrintReads -L 20:1-15843471 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/20/tx/tmpNntE_0/R14-18106_kapa-NGv3-PE100-NGv3-sort-20_0_15843471-prep-prealign.bam
[2016-04-15T00:22Z] INFO  17:22:55,761 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:22Z] INFO  17:22:55,762 HelpFormatter - Date/Time: 2016/04/14 17:22:55
[2016-04-15T00:22Z] INFO  17:22:55,763 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:22Z] INFO  17:22:55,764 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:22Z] INFO  17:22:55,942 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:22Z] INFO  17:22:56,071 IntervalUtils - Processing 15513871 bp from intervals
[2016-04-15T00:22Z] WARN  17:22:56,077 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:22Z] INFO  17:22:56,155 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:22Z] INFO  17:22:56,352 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:22Z] INFO  17:22:56,353 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:22Z] INFO  17:22:56,354 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:22Z] INFO  17:22:56,355 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:22Z] INFO  17:22:56,554 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:22Z] INFO  17:22:56,772 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:22Z] INFO  17:22:57,105 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-15T00:22Z] INFO  17:22:57,159 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:22Z] INFO  17:22:57,168 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:22Z] INFO  17:22:57,210 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.04
[2016-04-15T00:22Z] INFO  17:22:57,224 IntervalUtils - Processing 15843471 bp from intervals
[2016-04-15T00:22Z] INFO  17:22:57,295 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:22Z] INFO  17:22:57,598 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:22Z] INFO  17:22:57,599 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:22Z] INFO  17:22:57,600 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:22Z] INFO  17:22:57,601 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:22Z] INFO  17:22:57,614 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:22Z] INFO  17:22:57,736 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:22Z] INFO  17:22:58,895 ProgressMeter -     16:30780753   1.517303E7    30.0 s       1.0 s       97.9%    30.0 s       0.0 s
[2016-04-15T00:23Z] INFO  17:23:00,682 ProgressMeter -            done   1.5510351E7    31.0 s       2.0 s      100.0%    31.0 s       0.0 s
[2016-04-15T00:23Z] INFO  17:23:00,684 ProgressMeter - Total runtime 31.82 secs, 0.53 min, 0.01 hours
[2016-04-15T00:23Z] INFO  17:23:00,685 MicroScheduler - 530096 reads were filtered out during the traversal out of approximately 1122307 total reads (47.23%)
[2016-04-15T00:23Z] INFO  17:23:00,686 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:23Z] INFO  17:23:00,687 MicroScheduler -   -> 1280 reads (0.11% of total) failing BadMateFilter
[2016-04-15T00:23Z] INFO  17:23:00,687 MicroScheduler -   -> 50046 reads (4.46% of total) failing DuplicateReadFilter
[2016-04-15T00:23Z] INFO  17:23:00,688 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:23Z] INFO  17:23:00,689 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:23Z] INFO  17:23:00,689 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:23Z] INFO  17:23:00,690 MicroScheduler -   -> 478770 reads (42.66% of total) failing MappingQualityZeroFilter
[2016-04-15T00:23Z] INFO  17:23:00,691 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:23Z] INFO  17:23:00,691 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-15T00:23Z] INFO  17:23:00,692 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:23Z] INFO  17:23:01,513 ProgressMeter -            done    123740.0    10.0 s      88.0 s       99.4%    10.0 s       0.0 s
[2016-04-15T00:23Z] INFO  17:23:01,514 ProgressMeter - Total runtime 10.99 secs, 0.18 min, 0.00 hours
[2016-04-15T00:23Z] INFO  17:23:01,519 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 123740 total reads (0.00%)
[2016-04-15T00:23Z] INFO  17:23:01,531 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:23Z] INFO  17:23:01,532 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:23Z] INFO  17:23:01,532 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:23Z] INFO  17:23:02,088 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:23Z] GATK: realign ('16', 15596122, 31106473) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:23Z] INFO  17:23:02,505 ProgressMeter -     17:46051375   1000031.0   120.0 s     120.0 s       96.4%     2.1 m       4.0 s
[2016-04-15T00:23Z] INFO  17:23:02,769 ProgressMeter -     19:17897436    200004.0    30.0 s       2.5 m       15.4%     3.2 m       2.7 m
[2016-04-15T00:23Z] INFO  17:23:03,070 ProgressMeter -            done    230877.0    17.0 s      73.0 s      100.0%    17.0 s       0.0 s
[2016-04-15T00:23Z] INFO  17:23:03,071 ProgressMeter - Total runtime 17.07 secs, 0.28 min, 0.00 hours
[2016-04-15T00:23Z] INFO  17:23:03,076 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 230877 total reads (0.00%)
[2016-04-15T00:23Z] INFO  17:23:03,078 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:23Z] INFO  17:23:03,078 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:23Z] INFO  17:23:03,079 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:23Z] INFO  17:23:03,172 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:23Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-18_66346699_78077248-prep.bam
[2016-04-15T00:23Z] INFO  17:23:03,272 ProgressMeter -            done   1.5582935E7    26.0 s       1.0 s      100.0%    26.0 s       0.0 s
[2016-04-15T00:23Z] INFO  17:23:03,283 ProgressMeter - Total runtime 26.63 secs, 0.44 min, 0.01 hours
[2016-04-15T00:23Z] INFO  17:23:03,288 MicroScheduler - 48429 reads were filtered out during the traversal out of approximately 570389 total reads (8.49%)
[2016-04-15T00:23Z] INFO  17:23:03,289 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:23Z] INFO  17:23:03,289 MicroScheduler -   -> 1279 reads (0.22% of total) failing BadMateFilter
[2016-04-15T00:23Z] INFO  17:23:03,289 MicroScheduler -   -> 43354 reads (7.60% of total) failing DuplicateReadFilter
[2016-04-15T00:23Z] INFO  17:23:03,290 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:23Z] INFO  17:23:03,290 ProgressMeter -      16:3107405    400009.0    31.0 s      79.0 s       20.0%     2.6 m       2.1 m
[2016-04-15T00:23Z] INFO  17:23:03,290 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:23Z] INFO  17:23:03,290 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:23Z] INFO  17:23:03,290 MicroScheduler -   -> 3796 reads (0.67% of total) failing MappingQualityZeroFilter
[2016-04-15T00:23Z] INFO  17:23:03,293 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:23Z] INFO  17:23:03,293 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-15T00:23Z] INFO  17:23:03,293 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:23Z] GATK pre-alignment ('20', 15866408, 31376818) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:23Z] INFO  17:23:03,932 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@41fd9d8e
[2016-04-15T00:23Z] INFO  17:23:04,029 ProgressMeter -            done   1043083.0     2.0 m     117.0 s      100.0%     2.0 m       0.0 s
[2016-04-15T00:23Z] INFO  17:23:04,031 ProgressMeter - Total runtime 122.10 secs, 2.03 min, 0.03 hours
[2016-04-15T00:23Z] INFO  17:23:04,032 MicroScheduler - 437 reads were filtered out during the traversal out of approximately 1043520 total reads (0.04%)
[2016-04-15T00:23Z] INFO  17:23:04,033 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:23Z] INFO  17:23:04,033 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:23Z] INFO  17:23:04,034 MicroScheduler -   -> 437 reads (0.04% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:23Z] INFO  17:23:04,778 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:23Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-18_34092400_49867248-prep.bam
[2016-04-15T00:23Z] INFO  17:23:05,362 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:23Z] INFO  17:23:05,365 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:23Z] INFO  17:23:05,366 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:23Z] INFO  17:23:05,366 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:23Z] INFO  17:23:05,374 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/16/R14-18106_kapa-NGv3-PE100-NGv3-sort-16_15596122_31106473-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/16/R14-18106_kapa-NGv3-PE100-NGv3-sort-16_15596122_31106473-prep-prealign-realign.intervals -L 16:15596123-31106473 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/16/tx/tmpWu8ZpS/R14-18106_kapa-NGv3-PE100-NGv3-sort-16_15596122_31106473-prep.bam
[2016-04-15T00:23Z] INFO  17:23:05,393 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:23Z] INFO  17:23:05,394 HelpFormatter - Date/Time: 2016/04/14 17:23:05
[2016-04-15T00:23Z] INFO  17:23:05,395 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:23Z] INFO  17:23:05,395 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:23Z] INFO  17:23:05,559 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:23Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-17_31048040_46607237-prep-prealign.bam
[2016-04-15T00:23Z] INFO  17:23:05,617 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:23Z] GATK pre-alignment ('20', 31379406, 47242465) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:23Z] INFO  17:23:05,705 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:23Z] INFO  17:23:05,707 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:23Z] INFO  17:23:05,717 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:23Z] GATK: realign ('17', 62122219, 77705154) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:23Z] INFO  17:23:05,780 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-15T00:23Z] INFO  17:23:06,257 ProgressMeter -            done    143833.0    12.0 s      87.0 s      100.0%    12.0 s       0.0 s
[2016-04-15T00:23Z] INFO  17:23:06,259 ProgressMeter - Total runtime 12.57 secs, 0.21 min, 0.00 hours
[2016-04-15T00:23Z] INFO  17:23:06,269 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 143833 total reads (0.00%)
[2016-04-15T00:23Z] INFO  17:23:06,270 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:23Z] INFO  17:23:06,271 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:23Z] INFO  17:23:06,272 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:23Z] INFO  17:23:06,294 IntervalUtils - Processing 15510351 bp from intervals
[2016-04-15T00:23Z] WARN  17:23:06,301 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:23Z] INFO  17:23:06,437 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:23Z] INFO  17:23:06,662 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:23Z] INFO  17:23:06,664 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:23Z] INFO  17:23:06,665 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:23Z] INFO  17:23:06,666 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:23Z] INFO  17:23:06,817 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:23Z] INFO  17:23:06,809 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:23Z] INFO  17:23:06,819 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:23Z] INFO  17:23:06,819 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:23Z] INFO  17:23:06,820 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:23Z] INFO  17:23:06,825 HelpFormatter - Program Args: -T PrintReads -L 20:15866409-31376818 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/20/tx/tmphlO3mq/R14-18106_kapa-NGv3-PE100-NGv3-sort-20_15866408_31376818-prep-prealign.bam
[2016-04-15T00:23Z] INFO  17:23:06,838 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:23Z] INFO  17:23:06,839 HelpFormatter - Date/Time: 2016/04/14 17:23:06
[2016-04-15T00:23Z] INFO  17:23:06,839 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:23Z] INFO  17:23:06,839 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:23Z] INFO  17:23:06,979 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:23Z] INFO  17:23:06,998 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:23Z] INFO  17:23:07,977 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:23Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-18_50278423_66344430-prep.bam
[2016-04-15T00:23Z] INFO  17:23:08,298 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-15T00:23Z] INFO  17:23:08,381 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:23Z] INFO  17:23:08,402 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:23Z] INFO  17:23:08,484 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-15T00:23Z] INFO  17:23:08,501 IntervalUtils - Processing 15510410 bp from intervals
[2016-04-15T00:23Z] GATK pre-alignment ('20', 47244085, 62830269) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:23Z] INFO  17:23:08,541 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:23Z] INFO  17:23:08,545 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:23Z] INFO  17:23:08,545 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:23Z] INFO  17:23:08,546 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:23Z] INFO  17:23:08,551 HelpFormatter - Program Args: -T PrintReads -L 20:31379407-47242465 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/20/tx/tmpeTNAAG/R14-18106_kapa-NGv3-PE100-NGv3-sort-20_31379406_47242465-prep-prealign.bam
[2016-04-15T00:23Z] INFO  17:23:08,560 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:23Z] INFO  17:23:08,562 HelpFormatter - Date/Time: 2016/04/14 17:23:08
[2016-04-15T00:23Z] INFO  17:23:08,562 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:23Z] INFO  17:23:08,563 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:23Z] INFO  17:23:08,594 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:23Z] INFO  17:23:08,622 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:23Z] INFO  17:23:08,626 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:23Z] INFO  17:23:08,627 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:23Z] INFO  17:23:08,627 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:23Z] INFO  17:23:08,632 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/17/R14-18106_kapa-NGv3-PE100-NGv3-sort-17_62122219_77705154-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/17/R14-18106_kapa-NGv3-PE100-NGv3-sort-17_62122219_77705154-prep-prealign-realign.intervals -L 17:62122220-77705154 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/17/tx/tmpqsXOAN/R14-18106_kapa-NGv3-PE100-NGv3-sort-17_62122219_77705154-prep.bam
[2016-04-15T00:23Z] INFO  17:23:08,644 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:23Z] INFO  17:23:08,651 HelpFormatter - Date/Time: 2016/04/14 17:23:08
[2016-04-15T00:23Z] INFO  17:23:08,652 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:23Z] INFO  17:23:08,652 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:23Z] INFO  17:23:08,736 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:23Z] GATK RealignerTargetCreator: R14-18106_kapa-NGv3-PE100-NGv3-sort-17_31048040_46607237-prep-prealign.bam 17:31048041-46607237
[2016-04-15T00:23Z] GATK: RealignerTargetCreator
[2016-04-15T00:23Z] INFO  17:23:08,870 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:23Z] INFO  17:23:08,871 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:23Z] INFO  17:23:08,872 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:23Z] INFO  17:23:08,873 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:23Z] INFO  17:23:08,899 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:23Z] INFO  17:23:08,934 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:23Z] INFO  17:23:09,085 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:23Z] INFO  17:23:09,088 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:23Z] INFO  17:23:09,109 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:23Z] INFO  17:23:09,225 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.12
[2016-04-15T00:23Z] INFO  17:23:09,713 IntervalUtils - Processing 15582935 bp from intervals
[2016-04-15T00:23Z] WARN  17:23:09,719 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:23Z] INFO  17:23:09,794 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:23Z] INFO  17:23:09,944 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:23Z] INFO  17:23:09,945 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:23Z] INFO  17:23:09,946 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:23Z] INFO  17:23:09,947 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:23Z] INFO  17:23:10,135 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:23Z] INFO  17:23:10,153 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-15T00:23Z] INFO  17:23:10,256 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:23Z] INFO  17:23:10,270 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:23Z] INFO  17:23:10,273 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:23Z] INFO  17:23:10,378 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.10
[2016-04-15T00:23Z] INFO  17:23:10,403 IntervalUtils - Processing 15863059 bp from intervals
[2016-04-15T00:23Z] INFO  17:23:10,556 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:23Z] INFO  17:23:10,858 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:23Z] INFO  17:23:10,859 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:23Z] INFO  17:23:10,860 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:23Z] INFO  17:23:10,861 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:23Z] INFO  17:23:10,876 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:23Z] INFO  17:23:11,043 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:23Z] INFO  17:23:11,803 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:23Z] INFO  17:23:11,806 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:23Z] INFO  17:23:11,807 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:23Z] INFO  17:23:11,807 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:23Z] INFO  17:23:11,812 HelpFormatter - Program Args: -T PrintReads -L 20:47244086-62830269 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/20/tx/tmpJRDiji/R14-18106_kapa-NGv3-PE100-NGv3-sort-20_47244085_62830269-prep-prealign.bam
[2016-04-15T00:23Z] INFO  17:23:11,820 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:23Z] INFO  17:23:11,820 HelpFormatter - Date/Time: 2016/04/14 17:23:11
[2016-04-15T00:23Z] INFO  17:23:11,820 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:23Z] INFO  17:23:11,820 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:23Z] INFO  17:23:11,896 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:23Z] INFO  17:23:11,899 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:23Z] INFO  17:23:11,900 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:23Z] INFO  17:23:11,901 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:23Z] INFO  17:23:11,905 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/17/R14-18106_kapa-NGv3-PE100-NGv3-sort-17_31048040_46607237-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/17/tx/tmpzREEb3/R14-18106_kapa-NGv3-PE100-NGv3-sort-17_31048040_46607237-prep-prealign-realign.intervals -l INFO -L 17:31048041-46607237 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:23Z] INFO  17:23:11,915 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:23Z] INFO  17:23:11,926 HelpFormatter - Date/Time: 2016/04/14 17:23:11
[2016-04-15T00:23Z] INFO  17:23:11,927 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:23Z] INFO  17:23:11,928 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:23Z] INFO  17:23:12,015 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:23Z] INFO  17:23:12,053 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:23Z] INFO  17:23:12,284 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T00:23Z] INFO  17:23:12,293 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:23Z] INFO  17:23:12,368 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-15T00:23Z] INFO  17:23:12,837 IntervalUtils - Processing 15559197 bp from intervals
[2016-04-15T00:23Z] WARN  17:23:12,842 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:23Z] INFO  17:23:12,959 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:23Z] INFO  17:23:13,191 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:23Z] INFO  17:23:13,192 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:23Z] INFO  17:23:13,193 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:23Z] INFO  17:23:13,194 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:23Z] INFO  17:23:13,246 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-15T00:23Z] INFO  17:23:13,324 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:23Z] INFO  17:23:13,337 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:23Z] INFO  17:23:13,383 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-15T00:23Z] INFO  17:23:13,411 IntervalUtils - Processing 15586184 bp from intervals
[2016-04-15T00:23Z] INFO  17:23:13,439 ProgressMeter -     17:15011045   1.5007744E7    30.0 s       2.0 s       96.8%    30.0 s       0.0 s
[2016-04-15T00:23Z] INFO  17:23:13,529 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:23Z] INFO  17:23:13,803 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:23Z] INFO  17:23:13,804 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:23Z] INFO  17:23:13,805 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:23Z] INFO  17:23:13,806 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:23Z] INFO  17:23:13,821 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:23Z] INFO  17:23:13,966 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:23Z] INFO  17:23:14,653 ProgressMeter -     19:36293897    200007.0    30.0 s       2.5 m       33.7%    88.0 s      58.0 s
[2016-04-15T00:23Z] INFO  17:23:14,706 ProgressMeter -            done   1.5511002E7    31.0 s       2.0 s      100.0%    31.0 s       0.0 s
[2016-04-15T00:23Z] INFO  17:23:14,707 ProgressMeter - Total runtime 31.29 secs, 0.52 min, 0.01 hours
[2016-04-15T00:23Z] INFO  17:23:14,711 MicroScheduler - 74965 reads were filtered out during the traversal out of approximately 851490 total reads (8.80%)
[2016-04-15T00:23Z] INFO  17:23:14,713 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:23Z] INFO  17:23:14,713 MicroScheduler -   -> 1885 reads (0.22% of total) failing BadMateFilter
[2016-04-15T00:23Z] INFO  17:23:14,719 MicroScheduler -   -> 63336 reads (7.44% of total) failing DuplicateReadFilter
[2016-04-15T00:23Z] INFO  17:23:14,720 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:23Z] INFO  17:23:14,720 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:23Z] INFO  17:23:14,721 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:23Z] INFO  17:23:14,721 MicroScheduler -   -> 9744 reads (1.14% of total) failing MappingQualityZeroFilter
[2016-04-15T00:23Z] INFO  17:23:14,722 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:23Z] INFO  17:23:14,723 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-15T00:23Z] INFO  17:23:14,723 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:23Z] INFO  17:23:16,207 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:23Z] GATK: realign ('17', 0, 15511002) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:23Z] INFO  17:23:18,882 ProgressMeter -     19:49131972    100001.0    30.0 s       5.1 m       20.0%     2.5 m     119.0 s
[2016-04-15T00:23Z] INFO  17:23:19,019 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:23Z] INFO  17:23:19,022 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:23Z] INFO  17:23:19,022 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:23Z] INFO  17:23:19,023 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:23Z] INFO  17:23:19,027 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/17/R14-18106_kapa-NGv3-PE100-NGv3-sort-17_0_15511002-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/17/R14-18106_kapa-NGv3-PE100-NGv3-sort-17_0_15511002-prep-prealign-realign.intervals -L 17:1-15511002 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/17/tx/tmph8TuLr/R14-18106_kapa-NGv3-PE100-NGv3-sort-17_0_15511002-prep.bam
[2016-04-15T00:23Z] INFO  17:23:19,041 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:23Z] INFO  17:23:19,041 HelpFormatter - Date/Time: 2016/04/14 17:23:19
[2016-04-15T00:23Z] INFO  17:23:19,041 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:23Z] INFO  17:23:19,042 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:23Z] INFO  17:23:19,255 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:23Z] INFO  17:23:19,378 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:23Z] INFO  17:23:19,388 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:23Z] INFO  17:23:19,444 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-15T00:23Z] INFO  17:23:19,592 ProgressMeter -      19:4117565    300004.0    60.0 s       3.4 m       26.5%     3.8 m       2.8 m
[2016-04-15T00:23Z] INFO  17:23:19,766 ProgressMeter -     17:27061059    400004.0    30.0 s      75.0 s       74.4%    40.0 s      10.0 s
[2016-04-15T00:23Z] INFO  17:23:19,792 IntervalUtils - Processing 15511002 bp from intervals
[2016-04-15T00:23Z] WARN  17:23:19,799 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:23Z] INFO  17:23:19,932 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:23Z] INFO  17:23:20,100 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:23Z] INFO  17:23:20,100 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:23Z] INFO  17:23:20,101 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:23Z] INFO  17:23:20,101 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:23Z] INFO  17:23:20,366 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:23Z] INFO  17:23:20,571 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:23Z] INFO  17:23:23,384 ProgressMeter -            done    864399.0    51.0 s      59.0 s      100.0%    51.0 s       0.0 s
[2016-04-15T00:23Z] INFO  17:23:23,384 ProgressMeter - Total runtime 51.83 secs, 0.86 min, 0.01 hours
[2016-04-15T00:23Z] INFO  17:23:23,408 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 864399 total reads (0.00%)
[2016-04-15T00:23Z] INFO  17:23:23,410 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:23Z] INFO  17:23:23,410 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:23Z] INFO  17:23:23,411 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:23Z] INFO  17:23:24,645 ProgressMeter -     16:72042662    400014.0    31.0 s      78.0 s       45.3%    68.0 s      37.0 s
[2016-04-15T00:23Z] INFO  17:23:25,068 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:23Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-16_0_15528616-prep.bam
[2016-04-15T00:23Z] INFO  17:23:25,851 ProgressMeter -            done    482260.0    29.0 s      61.0 s      100.0%    29.0 s       0.0 s
[2016-04-15T00:23Z] INFO  17:23:25,853 ProgressMeter - Total runtime 29.50 secs, 0.49 min, 0.01 hours
[2016-04-15T00:23Z] INFO  17:23:25,857 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 482260 total reads (0.00%)
[2016-04-15T00:23Z] INFO  17:23:25,862 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:23Z] INFO  17:23:25,864 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:23Z] INFO  17:23:25,864 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:23Z] INFO  17:23:26,618 ProgressMeter -            done    594389.0    36.0 s      62.0 s      100.0%    36.0 s       0.0 s
[2016-04-15T00:23Z] INFO  17:23:26,620 ProgressMeter - Total runtime 36.89 secs, 0.61 min, 0.01 hours
[2016-04-15T00:23Z] INFO  17:23:26,624 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 594389 total reads (0.00%)
[2016-04-15T00:23Z] INFO  17:23:26,625 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:23Z] INFO  17:23:26,626 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:23Z] INFO  17:23:26,626 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:23Z] INFO  17:23:27,609 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:23Z] INFO  17:23:27,620 ProgressMeter -      20:6012768    200006.0    30.0 s       2.5 m       38.0%    79.0 s      49.0 s
[2016-04-15T00:23Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-17_46607689_62121560-prep.bam
[2016-04-15T00:23Z] GATK pre-alignment ('20', 62831244, 63025520) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:23Z] INFO  17:23:28,245 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:23Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-17_15515955_31039213-prep.bam
[2016-04-15T00:23Z] GATK pre-alignment ('21', 0, 15517120) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:23Z] GATK pre-alignment ('21', 15524893, 31045484) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:23Z] INFO  17:23:30,824 ProgressMeter -            done    610691.0    37.0 s      61.0 s      100.0%    37.0 s       0.0 s
[2016-04-15T00:23Z] INFO  17:23:30,824 ProgressMeter - Total runtime 37.58 secs, 0.63 min, 0.01 hours
[2016-04-15T00:23Z] INFO  17:23:30,828 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 610691 total reads (0.00%)
[2016-04-15T00:23Z] INFO  17:23:30,829 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:23Z] INFO  17:23:30,829 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:23Z] INFO  17:23:30,829 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:23Z] INFO  17:23:30,845 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:23Z] INFO  17:23:30,856 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:23Z] INFO  17:23:30,857 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:23Z] INFO  17:23:30,858 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:23Z] INFO  17:23:30,868 HelpFormatter - Program Args: -T PrintReads -L 20:62831245-63025520 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/20/tx/tmpR4QAr2/R14-18106_kapa-NGv3-PE100-NGv3-sort-20_62831244_63025520-prep-prealign.bam
[2016-04-15T00:23Z] INFO  17:23:30,878 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:23Z] INFO  17:23:30,879 HelpFormatter - Date/Time: 2016/04/14 17:23:30
[2016-04-15T00:23Z] INFO  17:23:30,879 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:23Z] INFO  17:23:30,879 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:23Z] INFO  17:23:31,051 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:23Z] INFO  17:23:32,249 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-15T00:23Z] INFO  17:23:32,327 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:23Z] INFO  17:23:32,336 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:23Z] INFO  17:23:32,369 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:23Z] INFO  17:23:32,372 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:23Z] INFO  17:23:32,373 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:23Z] INFO  17:23:32,373 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:23Z] INFO  17:23:32,378 HelpFormatter - Program Args: -T PrintReads -L 21:1-15517120 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/21/tx/tmpfsrgdz/R14-18106_kapa-NGv3-PE100-NGv3-sort-21_0_15517120-prep-prealign.bam
[2016-04-15T00:23Z] INFO  17:23:32,387 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:23Z] INFO  17:23:32,394 HelpFormatter - Date/Time: 2016/04/14 17:23:32
[2016-04-15T00:23Z] INFO  17:23:32,395 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:23Z] INFO  17:23:32,396 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:23Z] INFO  17:23:32,408 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-15T00:23Z] INFO  17:23:32,434 IntervalUtils - Processing 194276 bp from intervals
[2016-04-15T00:23Z] INFO  17:23:32,517 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:23Z] INFO  17:23:32,547 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:23Z] INFO  17:23:32,584 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:23Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-16_64982511_80574976-prep.bam
[2016-04-15T00:23Z] INFO  17:23:32,709 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:23Z] INFO  17:23:32,717 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:23Z] INFO  17:23:32,718 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:23Z] INFO  17:23:32,718 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:23Z] INFO  17:23:32,747 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:23Z] INFO  17:23:32,749 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:23Z] INFO  17:23:32,770 ProgressMeter -     19:22940570    400006.0    60.0 s       2.5 m       47.9%     2.1 m      65.0 s
[2016-04-15T00:23Z] INFO  17:23:32,817 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:23Z] INFO  17:23:32,828 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:23Z] INFO  17:23:32,828 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:23Z] INFO  17:23:32,829 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:23Z] INFO  17:23:32,834 HelpFormatter - Program Args: -T PrintReads -L 21:15524894-31045484 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/21/tx/tmpZyYBeQ/R14-18106_kapa-NGv3-PE100-NGv3-sort-21_15524893_31045484-prep-prealign.bam
[2016-04-15T00:23Z] INFO  17:23:32,842 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:23Z] INFO  17:23:32,842 HelpFormatter - Date/Time: 2016/04/14 17:23:32
[2016-04-15T00:23Z] INFO  17:23:32,842 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:23Z] INFO  17:23:32,843 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:23Z] INFO  17:23:33,066 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:23Z] INFO  17:23:33,259 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@41fd9d8e
[2016-04-15T00:23Z] INFO  17:23:33,341 ProgressMeter -            done    282389.0    35.0 s       2.1 m       99.6%    35.0 s       0.0 s
[2016-04-15T00:23Z] INFO  17:23:33,341 ProgressMeter - Total runtime 35.74 secs, 0.60 min, 0.01 hours
[2016-04-15T00:23Z] INFO  17:23:33,342 MicroScheduler - 180 reads were filtered out during the traversal out of approximately 282569 total reads (0.06%)
[2016-04-15T00:23Z] INFO  17:23:33,342 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:23Z] INFO  17:23:33,342 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:23Z] INFO  17:23:33,343 MicroScheduler -   -> 180 reads (0.06% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:23Z] INFO  17:23:33,720 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-15T00:23Z] INFO  17:23:33,797 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:23Z] INFO  17:23:33,806 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:23Z] INFO  17:23:33,870 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-15T00:23Z] INFO  17:23:33,884 IntervalUtils - Processing 15517120 bp from intervals
[2016-04-15T00:23Z] INFO  17:23:33,986 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:23Z] GATK pre-alignment ('21', 31062047, 46591599) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:23Z] INFO  17:23:34,268 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:23Z] INFO  17:23:34,269 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:23Z] INFO  17:23:34,269 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:23Z] INFO  17:23:34,270 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:23Z] INFO  17:23:34,284 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:23Z] INFO  17:23:34,355 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:23Z] INFO  17:23:34,363 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-15T00:23Z] INFO  17:23:34,449 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:23Z] INFO  17:23:34,458 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:23Z] INFO  17:23:34,514 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-15T00:23Z] INFO  17:23:34,540 IntervalUtils - Processing 15520591 bp from intervals
[2016-04-15T00:23Z] INFO  17:23:34,624 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:23Z] INFO  17:23:34,814 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:23Z] INFO  17:23:34,825 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:23Z] INFO  17:23:34,845 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:23Z] INFO  17:23:34,846 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:23Z] INFO  17:23:34,846 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:23Z] INFO  17:23:34,872 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:23Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-20_0_15843471-prep-prealign.bam
[2016-04-15T00:23Z] INFO  17:23:35,109 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:23Z] INFO  17:23:35,785 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@41fd9d8e
[2016-04-15T00:23Z] GATK RealignerTargetCreator: R14-18106_kapa-NGv3-PE100-NGv3-sort-20_0_15843471-prep-prealign.bam 20:1-15843471
[2016-04-15T00:23Z] GATK: RealignerTargetCreator
[2016-04-15T00:23Z] INFO  17:23:35,905 ProgressMeter -            done      8341.0     3.0 s       6.4 m       66.0%     4.0 s       1.0 s
[2016-04-15T00:23Z] INFO  17:23:35,905 ProgressMeter - Total runtime 3.19 secs, 0.05 min, 0.00 hours
[2016-04-15T00:23Z] INFO  17:23:35,906 MicroScheduler - 5 reads were filtered out during the traversal out of approximately 8346 total reads (0.06%)
[2016-04-15T00:23Z] INFO  17:23:35,906 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:23Z] INFO  17:23:35,907 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:23Z] INFO  17:23:35,907 MicroScheduler -   -> 5 reads (0.06% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:23Z] INFO  17:23:36,681 ProgressMeter -     16:22535301    400011.0    30.0 s      75.0 s       44.7%    67.0 s      37.0 s
[2016-04-15T00:23Z] INFO  17:23:37,142 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:23Z] INFO  17:23:37,145 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:23Z] INFO  17:23:37,146 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:23Z] INFO  17:23:37,146 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:23Z] INFO  17:23:37,151 HelpFormatter - Program Args: -T PrintReads -L 21:31062048-46591599 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/21/tx/tmpv7k_We/R14-18106_kapa-NGv3-PE100-NGv3-sort-21_31062047_46591599-prep-prealign.bam
[2016-04-15T00:23Z] INFO  17:23:37,157 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@7172f77a
[2016-04-15T00:23Z] INFO  17:23:37,166 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:23Z] INFO  17:23:37,166 HelpFormatter - Date/Time: 2016/04/14 17:23:37
[2016-04-15T00:23Z] INFO  17:23:37,166 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:23Z] INFO  17:23:37,167 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:23Z] INFO  17:23:37,239 ProgressMeter -            done    535626.0    64.0 s     120.0 s      100.0%    64.0 s       0.0 s
[2016-04-15T00:23Z] INFO  17:23:37,240 ProgressMeter - Total runtime 64.50 secs, 1.07 min, 0.02 hours
[2016-04-15T00:23Z] INFO  17:23:37,240 MicroScheduler - 333 reads were filtered out during the traversal out of approximately 535959 total reads (0.06%)
[2016-04-15T00:23Z] INFO  17:23:37,241 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:23Z] INFO  17:23:37,241 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:23Z] INFO  17:23:37,241 MicroScheduler -   -> 333 reads (0.06% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:23Z] INFO  17:23:37,282 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:23Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-20_62831244_63025520-prep-prealign.bam
[2016-04-15T00:23Z] INFO  17:23:37,405 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:23Z] GATK RealignerTargetCreator: R14-18106_kapa-NGv3-PE100-NGv3-sort-20_62831244_63025520-prep-prealign.bam 20:62831245-63025520
[2016-04-15T00:23Z] GATK: RealignerTargetCreator
[2016-04-15T00:23Z] INFO  17:23:37,776 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@6834dd3c
[2016-04-15T00:23Z] INFO  17:23:37,830 ProgressMeter -            done    230574.0    28.0 s       2.1 m      100.0%    28.0 s       0.0 s
[2016-04-15T00:23Z] INFO  17:23:37,830 ProgressMeter - Total runtime 28.96 secs, 0.48 min, 0.01 hours
[2016-04-15T00:23Z] INFO  17:23:37,831 MicroScheduler - 155 reads were filtered out during the traversal out of approximately 230729 total reads (0.07%)
[2016-04-15T00:23Z] INFO  17:23:37,831 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:23Z] INFO  17:23:37,831 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:23Z] INFO  17:23:37,832 MicroScheduler -   -> 155 reads (0.07% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:23Z] INFO  17:23:38,328 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-15T00:23Z] INFO  17:23:38,384 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:23Z] INFO  17:23:38,408 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:23Z] INFO  17:23:38,467 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-15T00:23Z] INFO  17:23:38,482 IntervalUtils - Processing 15529552 bp from intervals
[2016-04-15T00:23Z] INFO  17:23:38,564 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:23Z] INFO  17:23:38,670 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:23Z] INFO  17:23:38,673 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:23Z] INFO  17:23:38,674 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:23Z] INFO  17:23:38,674 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:23Z] INFO  17:23:38,679 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/20/R14-18106_kapa-NGv3-PE100-NGv3-sort-20_0_15843471-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/20/tx/tmpTstjRD/R14-18106_kapa-NGv3-PE100-NGv3-sort-20_0_15843471-prep-prealign-realign.intervals -l INFO -L 20:1-15843471 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:23Z] INFO  17:23:38,688 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:23Z] INFO  17:23:38,698 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:23Z] INFO  17:23:38,698 HelpFormatter - Date/Time: 2016/04/14 17:23:38
[2016-04-15T00:23Z] INFO  17:23:38,698 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:23Z] INFO  17:23:38,699 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:23Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-19_15510112_31025906-prep-prealign.bam
[2016-04-15T00:23Z] INFO  17:23:38,764 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:23Z] INFO  17:23:38,765 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:23Z] INFO  17:23:38,766 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:23Z] INFO  17:23:38,767 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:23Z] INFO  17:23:38,804 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:23Z] INFO  17:23:38,821 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:23Z] INFO  17:23:38,982 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:23Z] INFO  17:23:39,108 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T00:23Z] INFO  17:23:39,120 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:23Z] INFO  17:23:39,187 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-15T00:23Z] INFO  17:23:39,296 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:23Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-20_15866408_31376818-prep-prealign.bam
[2016-04-15T00:23Z] INFO  17:23:39,431 IntervalUtils - Processing 15843471 bp from intervals
[2016-04-15T00:23Z] WARN  17:23:39,436 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:23Z] INFO  17:23:39,587 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:23Z] INFO  17:23:39,695 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:23Z] INFO  17:23:39,696 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:23Z] INFO  17:23:39,696 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:23Z] INFO  17:23:39,697 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:23Z] GATK RealignerTargetCreator: R14-18106_kapa-NGv3-PE100-NGv3-sort-20_15866408_31376818-prep-prealign.bam 20:15866409-31376818
[2016-04-15T00:23Z] GATK: RealignerTargetCreator
[2016-04-15T00:23Z] INFO  17:23:40,243 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:23Z] INFO  17:23:40,247 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:23Z] INFO  17:23:40,247 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:23Z] INFO  17:23:40,248 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:23Z] INFO  17:23:40,253 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/20/R14-18106_kapa-NGv3-PE100-NGv3-sort-20_62831244_63025520-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/20/tx/tmpTPrnvL/R14-18106_kapa-NGv3-PE100-NGv3-sort-20_62831244_63025520-prep-prealign-realign.intervals -l INFO -L 20:62831245-63025520 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:23Z] INFO  17:23:40,264 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:23Z] INFO  17:23:40,275 HelpFormatter - Date/Time: 2016/04/14 17:23:40
[2016-04-15T00:23Z] INFO  17:23:40,276 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:23Z] INFO  17:23:40,277 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:23Z] GATK RealignerTargetCreator: R14-18106_kapa-NGv3-PE100-NGv3-sort-19_15510112_31025906-prep-prealign.bam 19:15510113-31025906
[2016-04-15T00:23Z] GATK: RealignerTargetCreator
[2016-04-15T00:23Z] INFO  17:23:40,451 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:23Z] INFO  17:23:40,700 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T00:23Z] INFO  17:23:40,715 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:23Z] INFO  17:23:40,782 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-15T00:23Z] INFO  17:23:40,857 ProgressMeter -     17:75212188    400007.0    30.0 s      77.0 s       84.0%    35.0 s       5.0 s
[2016-04-15T00:23Z] INFO  17:23:40,887 ProgressMeter -     20:35467736    200005.0    30.0 s       2.5 m       25.8%   116.0 s      86.0 s
[2016-04-15T00:23Z] INFO  17:23:41,146 IntervalUtils - Processing 194276 bp from intervals
[2016-04-15T00:23Z] WARN  17:23:41,152 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:23Z] INFO  17:23:41,346 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:23Z] INFO  17:23:41,403 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:23Z] INFO  17:23:41,405 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:23Z] INFO  17:23:41,406 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:23Z] INFO  17:23:41,406 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:23Z] INFO  17:23:41,807 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@7172f77a
[2016-04-15T00:23Z] INFO  17:23:41,883 ProgressMeter -            done     37030.0     7.0 s       3.4 m      100.0%     7.0 s       0.0 s
[2016-04-15T00:23Z] INFO  17:23:41,884 ProgressMeter - Total runtime 7.62 secs, 0.13 min, 0.00 hours
[2016-04-15T00:23Z] INFO  17:23:41,884 MicroScheduler - 126 reads were filtered out during the traversal out of approximately 37156 total reads (0.34%)
[2016-04-15T00:23Z] INFO  17:23:41,885 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:23Z] INFO  17:23:41,885 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:23Z] INFO  17:23:41,885 MicroScheduler -   -> 126 reads (0.34% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:23Z] INFO  17:23:43,108 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:23Z] INFO  17:23:43,111 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:23Z] INFO  17:23:43,112 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:23Z] INFO  17:23:43,113 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:23Z] INFO  17:23:43,117 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/20/R14-18106_kapa-NGv3-PE100-NGv3-sort-20_15866408_31376818-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/20/tx/tmp1OnEP2/R14-18106_kapa-NGv3-PE100-NGv3-sort-20_15866408_31376818-prep-prealign-realign.intervals -l INFO -L 20:15866409-31376818 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:23Z] INFO  17:23:43,134 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:23Z] INFO  17:23:43,135 HelpFormatter - Date/Time: 2016/04/14 17:23:43
[2016-04-15T00:23Z] INFO  17:23:43,135 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:23Z] INFO  17:23:43,135 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:23Z] INFO  17:23:43,207 ProgressMeter -     17:44851009   1.3794968E7    30.0 s       2.0 s       88.7%    33.0 s       3.0 s
[2016-04-15T00:23Z] INFO  17:23:43,218 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:23Z] INFO  17:23:43,242 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:23Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-21_0_15517120-prep-prealign.bam
[2016-04-15T00:23Z] INFO  17:23:43,245 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:23Z] INFO  17:23:43,246 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:23Z] INFO  17:23:43,246 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:23Z] INFO  17:23:43,251 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/19/R14-18106_kapa-NGv3-PE100-NGv3-sort-19_15510112_31025906-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/19/tx/tmpEeo1rr/R14-18106_kapa-NGv3-PE100-NGv3-sort-19_15510112_31025906-prep-prealign-realign.intervals -l INFO -L 19:15510113-31025906 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:23Z] INFO  17:23:43,257 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:23Z] INFO  17:23:43,268 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:23Z] INFO  17:23:43,269 HelpFormatter - Date/Time: 2016/04/14 17:23:43
[2016-04-15T00:23Z] INFO  17:23:43,269 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:23Z] INFO  17:23:43,270 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:23Z] INFO  17:23:43,379 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:23Z] GATK RealignerTargetCreator: R14-18106_kapa-NGv3-PE100-NGv3-sort-21_0_15517120-prep-prealign.bam 21:1-15517120
[2016-04-15T00:23Z] GATK: RealignerTargetCreator
[2016-04-15T00:23Z] INFO  17:23:43,468 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T00:23Z] INFO  17:23:43,482 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:23Z] INFO  17:23:43,552 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-15T00:23Z] INFO  17:23:43,642 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T00:23Z] INFO  17:23:43,651 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:23Z] INFO  17:23:43,713 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-15T00:23Z] INFO  17:23:43,977 IntervalUtils - Processing 15515794 bp from intervals
[2016-04-15T00:23Z] WARN  17:23:43,982 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:23Z] INFO  17:23:44,070 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:23Z] INFO  17:23:44,077 ProgressMeter -            done    194276.0     2.0 s      13.0 s      100.0%     2.0 s       0.0 s
[2016-04-15T00:23Z] INFO  17:23:44,077 IntervalUtils - Processing 15510410 bp from intervals
[2016-04-15T00:23Z] INFO  17:23:44,078 ProgressMeter - Total runtime 2.67 secs, 0.04 min, 0.00 hours
[2016-04-15T00:23Z] WARN  17:23:44,094 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:23Z] INFO  17:23:44,093 MicroScheduler - 985 reads were filtered out during the traversal out of approximately 8341 total reads (11.81%)
[2016-04-15T00:23Z] INFO  17:23:44,093 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:23Z] INFO  17:23:44,094 MicroScheduler -   -> 18 reads (0.22% of total) failing BadMateFilter
[2016-04-15T00:23Z] INFO  17:23:44,094 MicroScheduler -   -> 510 reads (6.11% of total) failing DuplicateReadFilter
[2016-04-15T00:23Z] INFO  17:23:44,094 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:23Z] INFO  17:23:44,094 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:23Z] INFO  17:23:44,095 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:23Z] INFO  17:23:44,095 MicroScheduler -   -> 457 reads (5.48% of total) failing MappingQualityZeroFilter
[2016-04-15T00:23Z] INFO  17:23:44,095 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:23Z] INFO  17:23:44,096 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-15T00:23Z] INFO  17:23:44,096 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:23Z] INFO  17:23:44,243 ProgressMeter -     20:58330433    200003.0    30.0 s       2.5 m       71.1%    42.0 s      12.0 s
[2016-04-15T00:23Z] INFO  17:23:44,281 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:23Z] INFO  17:23:44,381 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:23Z] INFO  17:23:44,382 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:23Z] INFO  17:23:44,382 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:23Z] INFO  17:23:44,382 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:23Z] INFO  17:23:44,462 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:23Z] INFO  17:23:44,463 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:23Z] INFO  17:23:44,464 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:23Z] INFO  17:23:44,465 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:23Z] INFO  17:23:44,677 ProgressMeter -     19:39868662    400009.0    60.0 s       2.5 m       56.6%   105.0 s      45.0 s
[2016-04-15T00:23Z] INFO  17:23:45,995 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:23Z] GATK: realign ('20', 62831244, 63025520) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:23Z] INFO  17:23:46,251 ProgressMeter -            done    567045.0    36.0 s      64.0 s      100.0%    36.0 s       0.0 s
[2016-04-15T00:23Z] INFO  17:23:46,251 ProgressMeter - Total runtime 36.31 secs, 0.61 min, 0.01 hours
[2016-04-15T00:23Z] INFO  17:23:46,261 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 567045 total reads (0.00%)
[2016-04-15T00:23Z] INFO  17:23:46,267 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:23Z] INFO  17:23:46,267 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:23Z] INFO  17:23:46,268 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:23Z] INFO  17:23:46,389 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:23Z] INFO  17:23:46,393 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:23Z] INFO  17:23:46,393 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:23Z] INFO  17:23:46,394 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:23Z] INFO  17:23:46,398 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/21/R14-18106_kapa-NGv3-PE100-NGv3-sort-21_0_15517120-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/21/tx/tmpc8574p/R14-18106_kapa-NGv3-PE100-NGv3-sort-21_0_15517120-prep-prealign-realign.intervals -l INFO -L 21:1-15517120 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:23Z] INFO  17:23:46,413 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:23Z] INFO  17:23:46,414 HelpFormatter - Date/Time: 2016/04/14 17:23:46
[2016-04-15T00:23Z] INFO  17:23:46,415 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:23Z] INFO  17:23:46,415 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:23Z] INFO  17:23:46,458 ProgressMeter -            done   1.5559197E7    33.0 s       2.0 s      100.0%    33.0 s       0.0 s
[2016-04-15T00:23Z] INFO  17:23:46,458 ProgressMeter - Total runtime 33.27 secs, 0.55 min, 0.01 hours
[2016-04-15T00:23Z] INFO  17:23:46,462 MicroScheduler - 211786 reads were filtered out during the traversal out of approximately 1050987 total reads (20.15%)
[2016-04-15T00:23Z] INFO  17:23:46,462 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:23Z] INFO  17:23:46,473 MicroScheduler -   -> 1792 reads (0.17% of total) failing BadMateFilter
[2016-04-15T00:23Z] INFO  17:23:46,474 MicroScheduler -   -> 70557 reads (6.71% of total) failing DuplicateReadFilter
[2016-04-15T00:23Z] INFO  17:23:46,474 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:23Z] INFO  17:23:46,475 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:23Z] INFO  17:23:46,475 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:23Z] INFO  17:23:46,475 MicroScheduler -   -> 139437 reads (13.27% of total) failing MappingQualityZeroFilter
[2016-04-15T00:23Z] INFO  17:23:46,475 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:23Z] INFO  17:23:46,476 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-15T00:23Z] INFO  17:23:46,476 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:23Z] INFO  17:23:46,510 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:23Z] INFO  17:23:46,755 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T00:23Z] INFO  17:23:46,764 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:23Z] INFO  17:23:46,856 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.09
[2016-04-15T00:23Z] INFO  17:23:46,957 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@5fe152b7
[2016-04-15T00:23Z] INFO  17:23:47,070 ProgressMeter -            done     70387.0    12.0 s       2.9 m      100.0%    12.0 s       0.0 s
[2016-04-15T00:23Z] INFO  17:23:47,071 ProgressMeter - Total runtime 12.23 secs, 0.20 min, 0.00 hours
[2016-04-15T00:23Z] INFO  17:23:47,071 MicroScheduler - 98 reads were filtered out during the traversal out of approximately 70485 total reads (0.14%)
[2016-04-15T00:23Z] INFO  17:23:47,072 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:23Z] INFO  17:23:47,072 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:23Z] INFO  17:23:47,072 MicroScheduler -   -> 98 reads (0.14% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:23Z] INFO  17:23:47,326 IntervalUtils - Processing 15517120 bp from intervals
[2016-04-15T00:23Z] WARN  17:23:47,331 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:23Z] INFO  17:23:47,429 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:23Z] INFO  17:23:47,611 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:23Z] INFO  17:23:47,612 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:23Z] INFO  17:23:47,613 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:23Z] INFO  17:23:47,613 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:23Z] INFO  17:23:47,663 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:23Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-17_62122219_77705154-prep.bam
[2016-04-15T00:23Z] INFO  17:23:48,004 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:23Z] GATK: realign ('17', 31048040, 46607237) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:23Z] INFO  17:23:48,555 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:23Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-21_15524893_31045484-prep-prealign.bam
[2016-04-15T00:23Z] GATK RealignerTargetCreator: R14-18106_kapa-NGv3-PE100-NGv3-sort-21_15524893_31045484-prep-prealign.bam 21:15524894-31045484
[2016-04-15T00:23Z] GATK: RealignerTargetCreator
[2016-04-15T00:23Z] INFO  17:23:48,883 ProgressMeter -     19:50548652    300004.0    60.0 s       3.4 m       31.4%     3.2 m       2.2 m
[2016-04-15T00:23Z] INFO  17:23:48,888 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:23Z] INFO  17:23:48,892 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:23Z] INFO  17:23:48,893 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:23Z] INFO  17:23:48,893 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:23Z] INFO  17:23:48,899 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/20/R14-18106_kapa-NGv3-PE100-NGv3-sort-20_62831244_63025520-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/20/R14-18106_kapa-NGv3-PE100-NGv3-sort-20_62831244_63025520-prep-prealign-realign.intervals -L 20:62831245-63025520 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/20/tx/tmpjIvNZ3/R14-18106_kapa-NGv3-PE100-NGv3-sort-20_62831244_63025520-prep.bam
[2016-04-15T00:23Z] INFO  17:23:48,918 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:23Z] INFO  17:23:48,929 HelpFormatter - Date/Time: 2016/04/14 17:23:48
[2016-04-15T00:23Z] INFO  17:23:48,930 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:23Z] INFO  17:23:48,931 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:23Z] INFO  17:23:49,225 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:23Z] GATK pre-alignment ('21', 46595644, 48129895) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:23Z] INFO  17:23:49,357 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:23Z] INFO  17:23:49,369 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:23Z] INFO  17:23:49,464 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.09
[2016-04-15T00:23Z] INFO  17:23:49,751 ProgressMeter -      19:6736671    500008.0    90.0 s       3.0 m       43.4%     3.5 m     117.0 s
[2016-04-15T00:23Z] INFO  17:23:49,876 IntervalUtils - Processing 194276 bp from intervals
[2016-04-15T00:23Z] WARN  17:23:49,887 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:23Z] INFO  17:23:49,994 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:23Z] INFO  17:23:50,032 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:23Z] INFO  17:23:50,034 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:23Z] INFO  17:23:50,034 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:23Z] INFO  17:23:50,035 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:23Z] INFO  17:23:50,080 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:23Z] INFO  17:23:50,083 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:23Z] INFO  17:23:50,129 ProgressMeter -      17:6683264    400004.0    30.0 s      75.0 s       43.1%    69.0 s      39.0 s
[2016-04-15T00:23Z] INFO  17:23:51,146 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:23Z] INFO  17:23:51,150 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:23Z] INFO  17:23:51,150 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:23Z] INFO  17:23:51,151 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:23Z] INFO  17:23:51,155 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/17/R14-18106_kapa-NGv3-PE100-NGv3-sort-17_31048040_46607237-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/17/R14-18106_kapa-NGv3-PE100-NGv3-sort-17_31048040_46607237-prep-prealign-realign.intervals -L 17:31048041-46607237 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/17/tx/tmp19XOgP/R14-18106_kapa-NGv3-PE100-NGv3-sort-17_31048040_46607237-prep.bam
[2016-04-15T00:23Z] INFO  17:23:51,174 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:23Z] INFO  17:23:51,175 HelpFormatter - Date/Time: 2016/04/14 17:23:51
[2016-04-15T00:23Z] INFO  17:23:51,175 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:23Z] INFO  17:23:51,176 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:23Z] INFO  17:23:51,396 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:23Z] INFO  17:23:51,522 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:23Z] INFO  17:23:51,531 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:23Z] INFO  17:23:51,589 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-15T00:23Z] INFO  17:23:51,921 IntervalUtils - Processing 15559197 bp from intervals
[2016-04-15T00:23Z] WARN  17:23:51,927 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:23Z] INFO  17:23:51,979 ProgressMeter -            done      8341.0     1.0 s       3.9 m       66.0%     1.0 s       0.0 s
[2016-04-15T00:23Z] INFO  17:23:51,980 ProgressMeter - Total runtime 1.95 secs, 0.03 min, 0.00 hours
[2016-04-15T00:23Z] INFO  17:23:51,984 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 8341 total reads (0.00%)
[2016-04-15T00:23Z] INFO  17:23:51,993 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:23Z] INFO  17:23:51,997 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:23Z] INFO  17:23:51,998 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:23Z] INFO  17:23:51,998 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:23Z] INFO  17:23:52,146 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:23Z] INFO  17:23:52,147 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:23Z] INFO  17:23:52,148 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:23Z] INFO  17:23:52,149 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:23Z] INFO  17:23:52,336 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:23Z] INFO  17:23:52,386 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:23Z] INFO  17:23:52,390 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:23Z] INFO  17:23:52,390 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:23Z] INFO  17:23:52,391 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:23Z] INFO  17:23:52,396 HelpFormatter - Program Args: -T PrintReads -L 21:46595645-48129895 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/21/tx/tmp4gFW_k/R14-18106_kapa-NGv3-PE100-NGv3-sort-21_46595644_48129895-prep-prealign.bam
[2016-04-15T00:23Z] INFO  17:23:52,404 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:23Z] INFO  17:23:52,415 HelpFormatter - Date/Time: 2016/04/14 17:23:52
[2016-04-15T00:23Z] INFO  17:23:52,416 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:23Z] INFO  17:23:52,417 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:23Z] INFO  17:23:52,472 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:23Z] INFO  17:23:52,475 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:23Z] INFO  17:23:52,476 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:23Z] INFO  17:23:52,476 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:23Z] INFO  17:23:52,481 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/21/R14-18106_kapa-NGv3-PE100-NGv3-sort-21_15524893_31045484-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/21/tx/tmpVkOdTz/R14-18106_kapa-NGv3-PE100-NGv3-sort-21_15524893_31045484-prep-prealign-realign.intervals -l INFO -L 21:15524894-31045484 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:23Z] INFO  17:23:52,491 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:23Z] INFO  17:23:52,503 HelpFormatter - Date/Time: 2016/04/14 17:23:52
[2016-04-15T00:23Z] INFO  17:23:52,504 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:23Z] INFO  17:23:52,505 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:23Z] INFO  17:23:52,510 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:23Z] INFO  17:23:52,607 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:23Z] INFO  17:23:52,610 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:23Z] INFO  17:23:52,814 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T00:23Z] INFO  17:23:52,836 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:23Z] INFO  17:23:52,882 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-15T00:23Z] INFO  17:23:53,116 IntervalUtils - Processing 15520591 bp from intervals
[2016-04-15T00:23Z] WARN  17:23:53,122 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:23Z] INFO  17:23:53,279 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:23Z] INFO  17:23:53,412 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:23Z] INFO  17:23:53,413 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:23Z] INFO  17:23:53,414 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:23Z] INFO  17:23:53,415 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:23Z] INFO  17:23:53,477 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:23Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-20_62831244_63025520-prep.bam
[2016-04-15T00:23Z] GATK pre-alignment ('22', 0, 16258303) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:23Z] INFO  17:23:53,738 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-15T00:23Z] INFO  17:23:53,844 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:23Z] INFO  17:23:53,863 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:23Z] INFO  17:23:53,932 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-15T00:23Z] INFO  17:23:53,950 IntervalUtils - Processing 1534251 bp from intervals
[2016-04-15T00:23Z] INFO  17:23:54,104 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:23Z] INFO  17:23:54,255 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:23Z] INFO  17:23:54,257 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:23Z] INFO  17:23:54,257 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:23Z] INFO  17:23:54,258 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:23Z] INFO  17:23:54,273 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:23Z] INFO  17:23:54,306 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:23Z] INFO  17:23:56,500 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:23Z] INFO  17:23:56,503 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:23Z] INFO  17:23:56,504 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:23Z] INFO  17:23:56,504 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:23Z] INFO  17:23:56,508 HelpFormatter - Program Args: -T PrintReads -L 22:1-16258303 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/22/tx/tmpYG4iAz/R14-18106_kapa-NGv3-PE100-NGv3-sort-22_0_16258303-prep-prealign.bam
[2016-04-15T00:23Z] INFO  17:23:56,517 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:23Z] INFO  17:23:56,528 HelpFormatter - Date/Time: 2016/04/14 17:23:56
[2016-04-15T00:23Z] INFO  17:23:56,529 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:23Z] INFO  17:23:56,530 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:23Z] INFO  17:23:56,737 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:23Z] INFO  17:23:57,702 ProgressMeter -            done   1.551712E7    10.0 s       0.0 s      100.0%    10.0 s       0.0 s
[2016-04-15T00:23Z] INFO  17:23:57,702 ProgressMeter - Total runtime 10.09 secs, 0.17 min, 0.00 hours
[2016-04-15T00:23Z] INFO  17:23:57,706 MicroScheduler - 10735 reads were filtered out during the traversal out of approximately 37052 total reads (28.97%)
[2016-04-15T00:23Z] INFO  17:23:57,706 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:23Z] INFO  17:23:57,706 MicroScheduler -   -> 234 reads (0.63% of total) failing BadMateFilter
[2016-04-15T00:23Z] INFO  17:23:57,707 MicroScheduler -   -> 2085 reads (5.63% of total) failing DuplicateReadFilter
[2016-04-15T00:23Z] INFO  17:23:57,707 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:23Z] INFO  17:23:57,707 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:23Z] INFO  17:23:57,707 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:23Z] INFO  17:23:57,708 MicroScheduler -   -> 8416 reads (22.71% of total) failing MappingQualityZeroFilter
[2016-04-15T00:23Z] INFO  17:23:57,708 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:23Z] INFO  17:23:57,708 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-15T00:23Z] INFO  17:23:57,708 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:23Z] INFO  17:23:57,817 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-15T00:23Z] INFO  17:23:57,915 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:23Z] INFO  17:23:57,935 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:23Z] INFO  17:23:58,000 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-15T00:23Z] INFO  17:23:58,026 IntervalUtils - Processing 16258303 bp from intervals
[2016-04-15T00:23Z] INFO  17:23:58,116 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:23Z] INFO  17:23:58,552 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:23Z] INFO  17:23:58,554 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:23Z] INFO  17:23:58,554 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:23Z] INFO  17:23:58,555 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:23Z] INFO  17:23:58,573 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:23Z] INFO  17:23:58,583 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:23Z] INFO  17:23:59,021 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:23Z] GATK: realign ('21', 0, 15517120) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:24Z] INFO  17:24:00,244 ProgressMeter -            done   1.5843471E7    20.0 s       1.0 s      100.0%    20.0 s       0.0 s
[2016-04-15T00:24Z] INFO  17:24:00,244 ProgressMeter - Total runtime 20.55 secs, 0.34 min, 0.01 hours
[2016-04-15T00:24Z] INFO  17:24:00,248 MicroScheduler - 23642 reads were filtered out during the traversal out of approximately 285030 total reads (8.29%)
[2016-04-15T00:24Z] INFO  17:24:00,249 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:24Z] INFO  17:24:00,249 MicroScheduler -   -> 825 reads (0.29% of total) failing BadMateFilter
[2016-04-15T00:24Z] INFO  17:24:00,249 MicroScheduler -   -> 21758 reads (7.63% of total) failing DuplicateReadFilter
[2016-04-15T00:24Z] INFO  17:24:00,249 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:24Z] INFO  17:24:00,250 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:24Z] INFO  17:24:00,250 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:24Z] INFO  17:24:00,250 MicroScheduler -   -> 1059 reads (0.37% of total) failing MappingQualityZeroFilter
[2016-04-15T00:24Z] INFO  17:24:00,250 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:24Z] INFO  17:24:00,251 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-15T00:24Z] INFO  17:24:00,251 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:24Z] INFO  17:24:01,444 ProgressMeter -            done   1.551041E7    16.0 s       1.0 s      100.0%    16.0 s       0.0 s
[2016-04-15T00:24Z] INFO  17:24:01,444 ProgressMeter - Total runtime 16.98 secs, 0.28 min, 0.00 hours
[2016-04-15T00:24Z] INFO  17:24:01,448 MicroScheduler - 19260 reads were filtered out during the traversal out of approximately 232163 total reads (8.30%)
[2016-04-15T00:24Z] INFO  17:24:01,448 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:24Z] INFO  17:24:01,449 MicroScheduler -   -> 754 reads (0.32% of total) failing BadMateFilter
[2016-04-15T00:24Z] INFO  17:24:01,449 MicroScheduler -   -> 17304 reads (7.45% of total) failing DuplicateReadFilter
[2016-04-15T00:24Z] INFO  17:24:01,449 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:24Z] INFO  17:24:01,449 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:24Z] INFO  17:24:01,450 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:24Z] INFO  17:24:01,450 MicroScheduler -   -> 1202 reads (0.52% of total) failing MappingQualityZeroFilter
[2016-04-15T00:24Z] INFO  17:24:01,450 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:24Z] INFO  17:24:01,450 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-15T00:24Z] INFO  17:24:01,451 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:24Z] INFO  17:24:01,473 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:24Z] GATK: realign ('20', 0, 15843471) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:24Z] INFO  17:24:01,565 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@5fe152b7
[2016-04-15T00:24Z] INFO  17:24:01,616 ProgressMeter -            done      8898.0     3.0 s       5.7 m      100.0%     3.0 s       0.0 s
[2016-04-15T00:24Z] INFO  17:24:01,617 ProgressMeter - Total runtime 3.06 secs, 0.05 min, 0.00 hours
[2016-04-15T00:24Z] INFO  17:24:01,617 MicroScheduler - 3 reads were filtered out during the traversal out of approximately 8901 total reads (0.03%)
[2016-04-15T00:24Z] INFO  17:24:01,617 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:24Z] INFO  17:24:01,618 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:24Z] INFO  17:24:01,618 MicroScheduler -   -> 3 reads (0.03% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:24Z] INFO  17:24:01,963 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:24Z] INFO  17:24:01,966 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:24Z] INFO  17:24:01,967 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:24Z] INFO  17:24:01,967 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:24Z] INFO  17:24:01,972 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/21/R14-18106_kapa-NGv3-PE100-NGv3-sort-21_0_15517120-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/21/R14-18106_kapa-NGv3-PE100-NGv3-sort-21_0_15517120-prep-prealign-realign.intervals -L 21:1-15517120 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/21/tx/tmpX4iXxc/R14-18106_kapa-NGv3-PE100-NGv3-sort-21_0_15517120-prep.bam
[2016-04-15T00:24Z] INFO  17:24:02,021 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:24Z] INFO  17:24:02,022 HelpFormatter - Date/Time: 2016/04/14 17:24:01
[2016-04-15T00:24Z] INFO  17:24:02,023 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:24Z] INFO  17:24:02,023 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:24Z] INFO  17:24:02,255 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:24Z] INFO  17:24:02,360 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:24Z] INFO  17:24:02,372 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:24Z] INFO  17:24:02,421 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-15T00:24Z] INFO  17:24:02,863 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:24Z] INFO  17:24:02,873 IntervalUtils - Processing 15517120 bp from intervals
[2016-04-15T00:24Z] GATK: realign ('20', 15866408, 31376818) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:24Z] WARN  17:24:02,879 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:24Z] INFO  17:24:02,916 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:24Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-22_0_16258303-prep-prealign.bam
[2016-04-15T00:24Z] INFO  17:24:02,996 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:24Z] GATK RealignerTargetCreator: R14-18106_kapa-NGv3-PE100-NGv3-sort-22_0_16258303-prep-prealign.bam 22:1-16258303
[2016-04-15T00:24Z] GATK: RealignerTargetCreator
[2016-04-15T00:24Z] INFO  17:24:03,128 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:24Z] INFO  17:24:03,129 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:24Z] INFO  17:24:03,130 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:24Z] INFO  17:24:03,131 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:24Z] INFO  17:24:03,185 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:24Z] INFO  17:24:03,232 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:24Z] INFO  17:24:04,143 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:24Z] INFO  17:24:04,145 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:24Z] INFO  17:24:04,146 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:24Z] INFO  17:24:04,146 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:24Z] INFO  17:24:04,150 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/20/R14-18106_kapa-NGv3-PE100-NGv3-sort-20_0_15843471-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/20/R14-18106_kapa-NGv3-PE100-NGv3-sort-20_0_15843471-prep-prealign-realign.intervals -L 20:1-15843471 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/20/tx/tmpgOChdf/R14-18106_kapa-NGv3-PE100-NGv3-sort-20_0_15843471-prep.bam
[2016-04-15T00:24Z] INFO  17:24:04,168 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:24Z] INFO  17:24:04,169 HelpFormatter - Date/Time: 2016/04/14 17:24:04
[2016-04-15T00:24Z] INFO  17:24:04,169 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:24Z] INFO  17:24:04,169 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:24Z] INFO  17:24:04,401 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:24Z] INFO  17:24:04,511 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:24Z] INFO  17:24:04,520 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:24Z] INFO  17:24:04,575 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-15T00:24Z] INFO  17:24:04,919 IntervalUtils - Processing 15843471 bp from intervals
[2016-04-15T00:24Z] WARN  17:24:04,924 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:24Z] INFO  17:24:05,000 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:24Z] INFO  17:24:05,187 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:24Z] INFO  17:24:05,188 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:24Z] INFO  17:24:05,189 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:24Z] INFO  17:24:05,193 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:24Z] INFO  17:24:05,360 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:24Z] INFO  17:24:05,479 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:24Z] INFO  17:24:05,482 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:24Z] INFO  17:24:05,483 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:24Z] INFO  17:24:05,483 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:24Z] INFO  17:24:05,487 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/20/R14-18106_kapa-NGv3-PE100-NGv3-sort-20_15866408_31376818-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/20/R14-18106_kapa-NGv3-PE100-NGv3-sort-20_15866408_31376818-prep-prealign-realign.intervals -L 20:15866409-31376818 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/20/tx/tmpTaCRpx/R14-18106_kapa-NGv3-PE100-NGv3-sort-20_15866408_31376818-prep.bam
[2016-04-15T00:24Z] INFO  17:24:05,500 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:24Z] INFO  17:24:05,501 HelpFormatter - Date/Time: 2016/04/14 17:24:05
[2016-04-15T00:24Z] INFO  17:24:05,501 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:24Z] INFO  17:24:05,502 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:24Z] INFO  17:24:05,505 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:24Z] INFO  17:24:05,727 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:24Z] INFO  17:24:05,732 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@32d5a4c6
[2016-04-15T00:24Z] INFO  17:24:05,809 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:24Z] INFO  17:24:05,813 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:24Z] INFO  17:24:05,824 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:24Z] INFO  17:24:05,825 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:24Z] INFO  17:24:05,830 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/22/R14-18106_kapa-NGv3-PE100-NGv3-sort-22_0_16258303-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/22/tx/tmppZwjoC/R14-18106_kapa-NGv3-PE100-NGv3-sort-22_0_16258303-prep-prealign-realign.intervals -l INFO -L 22:1-16258303 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:24Z] INFO  17:24:05,838 ProgressMeter -            done    431215.0    52.0 s     120.0 s      100.0%    52.0 s       0.0 s
[2016-04-15T00:24Z] INFO  17:24:05,838 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:24Z] INFO  17:24:05,839 ProgressMeter - Total runtime 52.03 secs, 0.87 min, 0.01 hours
[2016-04-15T00:24Z] INFO  17:24:05,839 MicroScheduler - 246 reads were filtered out during the traversal out of approximately 431461 total reads (0.06%)
[2016-04-15T00:24Z] INFO  17:24:05,839 HelpFormatter - Date/Time: 2016/04/14 17:24:05
[2016-04-15T00:24Z] INFO  17:24:05,839 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:24Z] INFO  17:24:05,840 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:24Z] INFO  17:24:05,840 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:24Z] INFO  17:24:05,840 MicroScheduler -   -> 246 reads (0.06% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:24Z] INFO  17:24:05,841 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:24Z] INFO  17:24:05,852 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:24Z] INFO  17:24:05,880 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:24Z] INFO  17:24:05,923 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:24Z] INFO  17:24:05,964 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-15T00:24Z] INFO  17:24:06,162 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T00:24Z] INFO  17:24:06,182 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:24Z] INFO  17:24:06,238 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-15T00:24Z] INFO  17:24:06,276 IntervalUtils - Processing 15510410 bp from intervals
[2016-04-15T00:24Z] WARN  17:24:06,281 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:24Z] INFO  17:24:06,351 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:24Z] INFO  17:24:06,437 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:24Z] INFO  17:24:06,438 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:24Z] INFO  17:24:06,439 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:24Z] INFO  17:24:06,440 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:24Z] INFO  17:24:06,600 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:24Z] INFO  17:24:06,605 IntervalUtils - Processing 16258303 bp from intervals
[2016-04-15T00:24Z] WARN  17:24:06,611 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:24Z] INFO  17:24:06,729 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:24Z] INFO  17:24:06,775 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:24Z] INFO  17:24:06,942 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:24Z] INFO  17:24:06,943 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:24Z] INFO  17:24:06,944 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:24Z] INFO  17:24:06,945 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:24Z] INFO  17:24:07,078 ProgressMeter -     16:31073046   1000021.0    60.0 s      60.0 s       99.8%    60.0 s       0.0 s
[2016-04-15T00:24Z] INFO  17:24:07,365 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:24Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-20_47244085_62830269-prep-prealign.bam
[2016-04-15T00:24Z] INFO  17:24:07,841 ProgressMeter -            done   1115743.0    61.0 s      54.0 s      100.0%    61.0 s       0.0 s
[2016-04-15T00:24Z] INFO  17:24:07,842 ProgressMeter - Total runtime 61.18 secs, 1.02 min, 0.02 hours
[2016-04-15T00:24Z] INFO  17:24:07,845 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 1115743 total reads (0.00%)
[2016-04-15T00:24Z] INFO  17:24:07,846 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:24Z] INFO  17:24:07,846 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:24Z] INFO  17:24:07,846 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:24Z] INFO  17:24:07,986 ProgressMeter -            done     37030.0     4.0 s       2.2 m      100.0%     4.0 s       0.0 s
[2016-04-15T00:24Z] INFO  17:24:07,987 ProgressMeter - Total runtime 4.86 secs, 0.08 min, 0.00 hours
[2016-04-15T00:24Z] INFO  17:24:08,002 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 37030 total reads (0.00%)
[2016-04-15T00:24Z] INFO  17:24:08,002 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:24Z] INFO  17:24:08,003 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:24Z] INFO  17:24:08,003 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:24Z] INFO  17:24:08,530 ProgressMeter -            done   1.5520591E7    15.0 s       0.0 s      100.0%    15.0 s       0.0 s
[2016-04-15T00:24Z] INFO  17:24:08,531 ProgressMeter - Total runtime 15.12 secs, 0.25 min, 0.00 hours
[2016-04-15T00:24Z] INFO  17:24:08,535 MicroScheduler - 5836 reads were filtered out during the traversal out of approximately 70814 total reads (8.24%)
[2016-04-15T00:24Z] INFO  17:24:08,536 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:24Z] INFO  17:24:08,536 MicroScheduler -   -> 448 reads (0.63% of total) failing BadMateFilter
[2016-04-15T00:24Z] INFO  17:24:08,537 MicroScheduler -   -> 5096 reads (7.20% of total) failing DuplicateReadFilter
[2016-04-15T00:24Z] INFO  17:24:08,538 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:24Z] INFO  17:24:08,538 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:24Z] INFO  17:24:08,539 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:24Z] INFO  17:24:08,539 MicroScheduler -   -> 292 reads (0.41% of total) failing MappingQualityZeroFilter
[2016-04-15T00:24Z] INFO  17:24:08,539 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:24Z] INFO  17:24:08,539 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-15T00:24Z] INFO  17:24:08,539 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:24Z] INFO  17:24:08,725 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@41fd9d8e
[2016-04-15T00:24Z] INFO  17:24:08,804 ProgressMeter -            done    103853.0    14.0 s       2.3 m       97.0%    14.0 s       0.0 s
[2016-04-15T00:24Z] INFO  17:24:08,805 ProgressMeter - Total runtime 14.55 secs, 0.24 min, 0.00 hours
[2016-04-15T00:24Z] INFO  17:24:08,805 MicroScheduler - 54 reads were filtered out during the traversal out of approximately 103907 total reads (0.05%)
[2016-04-15T00:24Z] INFO  17:24:08,806 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:24Z] INFO  17:24:08,806 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:24Z] INFO  17:24:08,806 MicroScheduler -   -> 54 reads (0.05% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:24Z] INFO  17:24:08,811 ProgressMeter -            done   1.5515794E7    24.0 s       1.0 s      100.0%    24.0 s       0.0 s
[2016-04-15T00:24Z] INFO  17:24:08,812 ProgressMeter - Total runtime 24.43 secs, 0.41 min, 0.01 hours
[2016-04-15T00:24Z] INFO  17:24:08,816 MicroScheduler - 48082 reads were filtered out during the traversal out of approximately 538725 total reads (8.93%)
[2016-04-15T00:24Z] INFO  17:24:08,817 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:24Z] INFO  17:24:08,818 MicroScheduler -   -> 1312 reads (0.24% of total) failing BadMateFilter
[2016-04-15T00:24Z] INFO  17:24:08,819 MicroScheduler -   -> 40839 reads (7.58% of total) failing DuplicateReadFilter
[2016-04-15T00:24Z] INFO  17:24:08,820 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:24Z] INFO  17:24:08,821 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:24Z] INFO  17:24:08,821 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:24Z] INFO  17:24:08,822 MicroScheduler -   -> 5931 reads (1.10% of total) failing MappingQualityZeroFilter
[2016-04-15T00:24Z] INFO  17:24:08,823 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:24Z] INFO  17:24:08,824 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-15T00:24Z] INFO  17:24:08,824 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:24Z] GATK RealignerTargetCreator: R14-18106_kapa-NGv3-PE100-NGv3-sort-20_47244085_62830269-prep-prealign.bam 20:47244086-62830269
[2016-04-15T00:24Z] GATK: RealignerTargetCreator
[2016-04-15T00:24Z] INFO  17:24:09,383 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:24Z] INFO  17:24:09,396 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:24Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-16_15596122_31106473-prep.bam
[2016-04-15T00:24Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-21_0_15517120-prep.bam
[2016-04-15T00:24Z] INFO  17:24:09,490 ProgressMeter -     21:38997640    100002.0    30.0 s       5.1 m       51.1%    58.0 s      28.0 s
[2016-04-15T00:24Z] GATK pre-alignment ('22', 16266928, 31795711) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:24Z] INFO  17:24:09,964 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:24Z] GATK: realign ('21', 15524893, 31045484) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:24Z] INFO  17:24:10,257 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:24Z] GATK: realign ('19', 15510112, 31025906) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:24Z] INFO  17:24:10,348 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:24Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-21_46595644_48129895-prep-prealign.bam
[2016-04-15T00:24Z] GATK RealignerTargetCreator: R14-18106_kapa-NGv3-PE100-NGv3-sort-21_46595644_48129895-prep-prealign.bam 21:46595645-48129895
[2016-04-15T00:24Z] GATK: RealignerTargetCreator
[2016-04-15T00:24Z] INFO  17:24:10,888 ProgressMeter -     20:45355727    500008.0    60.0 s     120.0 s       88.1%    68.0 s       8.0 s
[2016-04-15T00:24Z] INFO  17:24:11,628 ProgressMeter -            done    846661.0    51.0 s      60.0 s      100.0%    51.0 s       0.0 s
[2016-04-15T00:24Z] INFO  17:24:11,630 ProgressMeter - Total runtime 51.53 secs, 0.86 min, 0.01 hours
[2016-04-15T00:24Z] INFO  17:24:11,634 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 846661 total reads (0.00%)
[2016-04-15T00:24Z] INFO  17:24:11,646 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:24Z] INFO  17:24:11,647 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:24Z] INFO  17:24:11,647 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:24Z] INFO  17:24:12,238 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:24Z] INFO  17:24:12,241 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:24Z] INFO  17:24:12,242 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:24Z] INFO  17:24:12,242 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:24Z] INFO  17:24:12,247 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/20/R14-18106_kapa-NGv3-PE100-NGv3-sort-20_47244085_62830269-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/20/tx/tmp43Lu0e/R14-18106_kapa-NGv3-PE100-NGv3-sort-20_47244085_62830269-prep-prealign-realign.intervals -l INFO -L 20:47244086-62830269 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:24Z] INFO  17:24:12,271 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:24Z] INFO  17:24:12,272 HelpFormatter - Date/Time: 2016/04/14 17:24:12
[2016-04-15T00:24Z] INFO  17:24:12,273 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:24Z] INFO  17:24:12,273 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:24Z] INFO  17:24:12,368 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:24Z] INFO  17:24:12,568 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T00:24Z] INFO  17:24:12,579 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:24Z] INFO  17:24:12,675 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.10
[2016-04-15T00:24Z] INFO  17:24:12,978 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:24Z] INFO  17:24:12,982 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:24Z] INFO  17:24:12,982 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:24Z] INFO  17:24:12,983 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:24Z] INFO  17:24:12,987 HelpFormatter - Program Args: -T PrintReads -L 22:16266929-31795711 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/22/tx/tmpXlQpYA/R14-18106_kapa-NGv3-PE100-NGv3-sort-22_16266928_31795711-prep-prealign.bam
[2016-04-15T00:24Z] INFO  17:24:13,009 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:24Z] INFO  17:24:13,010 HelpFormatter - Date/Time: 2016/04/14 17:24:12
[2016-04-15T00:24Z] INFO  17:24:13,010 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:24Z] INFO  17:24:13,010 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:24Z] INFO  17:24:13,035 IntervalUtils - Processing 15586184 bp from intervals
[2016-04-15T00:24Z] WARN  17:24:13,048 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:24Z] GATK pre-alignment ('22', 31796605, 47308085) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:24Z] INFO  17:24:13,096 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:24Z] INFO  17:24:13,099 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:24Z] INFO  17:24:13,099 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:24Z] INFO  17:24:13,099 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:24Z] INFO  17:24:13,103 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/21/R14-18106_kapa-NGv3-PE100-NGv3-sort-21_15524893_31045484-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/21/R14-18106_kapa-NGv3-PE100-NGv3-sort-21_15524893_31045484-prep-prealign-realign.intervals -L 21:15524894-31045484 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/21/tx/tmpjZtwMf/R14-18106_kapa-NGv3-PE100-NGv3-sort-21_15524893_31045484-prep.bam
[2016-04-15T00:24Z] INFO  17:24:13,114 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:24Z] INFO  17:24:13,115 HelpFormatter - Date/Time: 2016/04/14 17:24:13
[2016-04-15T00:24Z] INFO  17:24:13,115 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:24Z] INFO  17:24:13,116 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:24Z] INFO  17:24:13,155 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:24Z] INFO  17:24:13,181 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@7172f77a
[2016-04-15T00:24Z] INFO  17:24:13,217 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:24Z] INFO  17:24:13,220 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:24Z] INFO  17:24:13,221 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:24Z] INFO  17:24:13,221 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:24Z] INFO  17:24:13,225 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/19/R14-18106_kapa-NGv3-PE100-NGv3-sort-19_15510112_31025906-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/19/R14-18106_kapa-NGv3-PE100-NGv3-sort-19_15510112_31025906-prep-prealign-realign.intervals -L 19:15510113-31025906 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/19/tx/tmpTjgLEV/R14-18106_kapa-NGv3-PE100-NGv3-sort-19_15510112_31025906-prep.bam
[2016-04-15T00:24Z] INFO  17:24:13,232 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:24Z] INFO  17:24:13,233 HelpFormatter - Date/Time: 2016/04/14 17:24:13
[2016-04-15T00:24Z] INFO  17:24:13,234 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:24Z] INFO  17:24:13,234 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:24Z] INFO  17:24:13,262 ProgressMeter -            done    535250.0    62.0 s     116.0 s      100.0%    62.0 s       0.0 s
[2016-04-15T00:24Z] INFO  17:24:13,263 ProgressMeter - Total runtime 62.40 secs, 1.04 min, 0.02 hours
[2016-04-15T00:24Z] INFO  17:24:13,263 MicroScheduler - 268 reads were filtered out during the traversal out of approximately 535518 total reads (0.05%)
[2016-04-15T00:24Z] INFO  17:24:13,263 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:24Z] INFO  17:24:13,264 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:24Z] INFO  17:24:13,265 MicroScheduler -   -> 268 reads (0.05% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:24Z] INFO  17:24:13,281 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:24Z] INFO  17:24:13,403 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:24Z] INFO  17:24:13,404 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:24Z] INFO  17:24:13,405 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:24Z] INFO  17:24:13,406 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:24Z] INFO  17:24:13,427 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:24Z] INFO  17:24:13,485 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:24Z] INFO  17:24:13,587 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:24Z] INFO  17:24:13,600 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:24Z] INFO  17:24:13,651 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:24Z] INFO  17:24:13,659 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:24Z] INFO  17:24:13,664 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-15T00:24Z] INFO  17:24:13,687 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:24Z] INFO  17:24:13,677 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:24Z] INFO  17:24:13,698 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:24Z] INFO  17:24:13,699 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:24Z] INFO  17:24:13,700 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:24Z] INFO  17:24:13,704 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/21/R14-18106_kapa-NGv3-PE100-NGv3-sort-21_46595644_48129895-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/21/tx/tmpBW4F0I/R14-18106_kapa-NGv3-PE100-NGv3-sort-21_46595644_48129895-prep-prealign-realign.intervals -l INFO -L 21:46595645-48129895 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:24Z] INFO  17:24:13,716 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:24Z] INFO  17:24:13,717 HelpFormatter - Date/Time: 2016/04/14 17:24:13
[2016-04-15T00:24Z] INFO  17:24:13,723 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:24Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-17_0_15511002-prep.bam
[2016-04-15T00:24Z] INFO  17:24:13,727 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:24Z] INFO  17:24:13,729 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-15T00:24Z] INFO  17:24:13,833 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:24Z] INFO  17:24:14,145 IntervalUtils - Processing 15520591 bp from intervals
[2016-04-15T00:24Z] INFO  17:24:14,168 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T00:24Z] WARN  17:24:14,178 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:24Z] INFO  17:24:14,179 IntervalUtils - Processing 15515794 bp from intervals
[2016-04-15T00:24Z] WARN  17:24:14,184 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:24Z] INFO  17:24:14,194 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:24Z] INFO  17:24:14,247 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:24Z] INFO  17:24:14,265 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-15T00:24Z] INFO  17:24:14,270 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:24Z] INFO  17:24:14,355 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:24Z] INFO  17:24:14,356 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:24Z] INFO  17:24:14,356 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:24Z] INFO  17:24:14,357 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:24Z] INFO  17:24:14,473 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:24Z] INFO  17:24:14,486 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:24Z] INFO  17:24:14,487 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:24Z] INFO  17:24:14,488 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:24Z] INFO  17:24:14,509 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:24Z] INFO  17:24:14,541 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-15T00:24Z] INFO  17:24:14,631 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:24Z] INFO  17:24:14,656 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:24Z] INFO  17:24:14,662 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:24Z] INFO  17:24:14,674 IntervalUtils - Processing 1534251 bp from intervals
[2016-04-15T00:24Z] WARN  17:24:14,679 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:24Z] INFO  17:24:14,718 ProgressMeter -     19:42402157    700013.0    90.0 s       2.1 m       72.9%     2.1 m      33.0 s
[2016-04-15T00:24Z] INFO  17:24:14,721 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-15T00:24Z] INFO  17:24:14,727 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:24Z] INFO  17:24:14,735 IntervalUtils - Processing 15528783 bp from intervals
[2016-04-15T00:24Z] INFO  17:24:14,749 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:24Z] INFO  17:24:14,794 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:24Z] INFO  17:24:14,795 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:24Z] INFO  17:24:14,796 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:24Z] INFO  17:24:14,797 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:24Z] INFO  17:24:14,812 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:24Z] INFO  17:24:14,860 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:24Z] INFO  17:24:14,979 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:24Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-20_31379406_47242465-prep-prealign.bam
[2016-04-15T00:24Z] INFO  17:24:15,166 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:24Z] INFO  17:24:15,166 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:24Z] INFO  17:24:15,167 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:24Z] INFO  17:24:15,167 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:24Z] INFO  17:24:15,200 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:24Z] INFO  17:24:15,374 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:24Z] INFO  17:24:15,693 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:24Z] INFO  17:24:15,696 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:24Z] INFO  17:24:15,697 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:24Z] INFO  17:24:15,697 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:24Z] INFO  17:24:15,702 HelpFormatter - Program Args: -T PrintReads -L 22:31796606-47308085 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/22/tx/tmpNB0Z_C/R14-18106_kapa-NGv3-PE100-NGv3-sort-22_31796605_47308085-prep-prealign.bam
[2016-04-15T00:24Z] INFO  17:24:15,720 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:24Z] INFO  17:24:15,721 HelpFormatter - Date/Time: 2016/04/14 17:24:15
[2016-04-15T00:24Z] INFO  17:24:15,721 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:24Z] INFO  17:24:15,722 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:24Z] INFO  17:24:15,854 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:24Z] GATK pre-alignment ('22', 47309229, 51304566) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:24Z] GATK RealignerTargetCreator: R14-18106_kapa-NGv3-PE100-NGv3-sort-20_31379406_47242465-prep-prealign.bam 20:31379407-47242465
[2016-04-15T00:24Z] GATK: RealignerTargetCreator
[2016-04-15T00:24Z] INFO  17:24:17,216 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-15T00:24Z] INFO  17:24:17,277 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:24Z] INFO  17:24:17,286 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:24Z] INFO  17:24:17,352 ProgressMeter -            done   1.6258303E7    10.0 s       0.0 s      100.0%    10.0 s       0.0 s
[2016-04-15T00:24Z] INFO  17:24:17,353 ProgressMeter - Total runtime 10.41 secs, 0.17 min, 0.00 hours
[2016-04-15T00:24Z] INFO  17:24:17,357 MicroScheduler - 6090 reads were filtered out during the traversal out of approximately 8898 total reads (68.44%)
[2016-04-15T00:24Z] INFO  17:24:17,358 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:24Z] INFO  17:24:17,359 MicroScheduler -   -> 9 reads (0.10% of total) failing BadMateFilter
[2016-04-15T00:24Z] INFO  17:24:17,359 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-15T00:24Z] INFO  17:24:17,359 MicroScheduler -   -> 278 reads (3.12% of total) failing DuplicateReadFilter
[2016-04-15T00:24Z] INFO  17:24:17,360 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:24Z] INFO  17:24:17,361 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:24Z] INFO  17:24:17,361 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:24Z] INFO  17:24:17,362 MicroScheduler -   -> 5803 reads (65.22% of total) failing MappingQualityZeroFilter
[2016-04-15T00:24Z] INFO  17:24:17,363 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:24Z] INFO  17:24:17,363 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-15T00:24Z] INFO  17:24:17,364 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:24Z] INFO  17:24:17,380 IntervalUtils - Processing 15511480 bp from intervals
[2016-04-15T00:24Z] INFO  17:24:17,503 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:24Z] INFO  17:24:17,806 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:24Z] INFO  17:24:17,808 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:24Z] INFO  17:24:17,808 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:24Z] INFO  17:24:17,809 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:24Z] INFO  17:24:17,823 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:24Z] INFO  17:24:17,985 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:24Z] INFO  17:24:18,739 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:24Z] GATK: realign ('22', 0, 16258303) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:24Z] INFO  17:24:18,890 ProgressMeter -     19:53086228    600008.0    90.0 s       2.5 m       51.7%     2.9 m      84.0 s
[2016-04-15T00:24Z] INFO  17:24:19,371 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:24Z] INFO  17:24:19,374 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:24Z] INFO  17:24:19,375 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:24Z] INFO  17:24:19,375 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:24Z] INFO  17:24:19,380 HelpFormatter - Program Args: -T PrintReads -L 22:47309230-51304566 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/22/tx/tmpzEAiW4/R14-18106_kapa-NGv3-PE100-NGv3-sort-22_47309229_51304566-prep-prealign.bam
[2016-04-15T00:24Z] INFO  17:24:19,395 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:24Z] INFO  17:24:19,407 HelpFormatter - Date/Time: 2016/04/14 17:24:19
[2016-04-15T00:24Z] INFO  17:24:19,407 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:24Z] INFO  17:24:19,408 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:24Z] INFO  17:24:19,597 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:24Z] INFO  17:24:19,752 ProgressMeter -      19:9071478    800013.0   120.0 s       2.5 m       58.5%     3.4 m      85.0 s
[2016-04-15T00:24Z] INFO  17:24:19,839 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:24Z] INFO  17:24:19,842 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:24Z] INFO  17:24:19,842 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:24Z] INFO  17:24:19,842 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:24Z] INFO  17:24:19,848 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/20/R14-18106_kapa-NGv3-PE100-NGv3-sort-20_31379406_47242465-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/20/tx/tmpZK1RUr/R14-18106_kapa-NGv3-PE100-NGv3-sort-20_31379406_47242465-prep-prealign-realign.intervals -l INFO -L 20:31379407-47242465 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:24Z] INFO  17:24:19,865 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:24Z] INFO  17:24:19,867 HelpFormatter - Date/Time: 2016/04/14 17:24:19
[2016-04-15T00:24Z] INFO  17:24:19,867 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:24Z] INFO  17:24:19,867 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:24Z] INFO  17:24:20,020 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:24Z] INFO  17:24:20,273 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T00:24Z] INFO  17:24:20,289 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:24Z] INFO  17:24:20,374 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-15T00:24Z] INFO  17:24:20,737 IntervalUtils - Processing 15863059 bp from intervals
[2016-04-15T00:24Z] WARN  17:24:20,742 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:24Z] INFO  17:24:20,844 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-15T00:24Z] INFO  17:24:20,853 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:24Z] INFO  17:24:20,913 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:24Z] INFO  17:24:20,923 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:24Z] INFO  17:24:20,972 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-15T00:24Z] INFO  17:24:20,995 IntervalUtils - Processing 3995337 bp from intervals
[2016-04-15T00:24Z] INFO  17:24:21,105 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:24Z] INFO  17:24:21,124 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:24Z] INFO  17:24:21,128 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:24Z] INFO  17:24:21,129 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:24Z] INFO  17:24:21,130 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:24Z] INFO  17:24:21,136 ProgressMeter -            done   1534251.0     6.0 s       4.0 s      100.0%     6.0 s       0.0 s
[2016-04-15T00:24Z] INFO  17:24:21,137 ProgressMeter - Total runtime 6.34 secs, 0.11 min, 0.00 hours
[2016-04-15T00:24Z] INFO  17:24:21,141 MicroScheduler - 8224 reads were filtered out during the traversal out of approximately 104349 total reads (7.88%)
[2016-04-15T00:24Z] INFO  17:24:21,142 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:24Z] INFO  17:24:21,144 MicroScheduler -   -> 203 reads (0.19% of total) failing BadMateFilter
[2016-04-15T00:24Z] INFO  17:24:21,144 MicroScheduler -   -> 7879 reads (7.55% of total) failing DuplicateReadFilter
[2016-04-15T00:24Z] INFO  17:24:21,144 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:24Z] INFO  17:24:21,144 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:24Z] INFO  17:24:21,145 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:24Z] INFO  17:24:21,145 MicroScheduler -   -> 142 reads (0.14% of total) failing MappingQualityZeroFilter
[2016-04-15T00:24Z] INFO  17:24:21,145 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:24Z] INFO  17:24:21,145 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-15T00:24Z] INFO  17:24:21,146 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:24Z] INFO  17:24:21,299 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:24Z] INFO  17:24:21,300 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:24Z] INFO  17:24:21,300 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:24Z] INFO  17:24:21,300 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:24Z] INFO  17:24:21,333 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:24Z] INFO  17:24:21,408 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:24Z] INFO  17:24:21,490 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:24Z] INFO  17:24:21,493 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:24Z] INFO  17:24:21,494 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:24Z] INFO  17:24:21,495 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:24Z] INFO  17:24:21,499 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/22/R14-18106_kapa-NGv3-PE100-NGv3-sort-22_0_16258303-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/22/R14-18106_kapa-NGv3-PE100-NGv3-sort-22_0_16258303-prep-prealign-realign.intervals -L 22:1-16258303 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/22/tx/tmpdGvYtU/R14-18106_kapa-NGv3-PE100-NGv3-sort-22_0_16258303-prep.bam
[2016-04-15T00:24Z] INFO  17:24:21,509 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:24Z] INFO  17:24:21,520 HelpFormatter - Date/Time: 2016/04/14 17:24:21
[2016-04-15T00:24Z] INFO  17:24:21,521 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:24Z] INFO  17:24:21,522 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:24Z] INFO  17:24:21,769 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:24Z] INFO  17:24:21,904 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:24Z] INFO  17:24:21,913 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:24Z] INFO  17:24:21,984 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-15T00:24Z] INFO  17:24:22,158 ProgressMeter -     17:39156089    400013.0    30.0 s      75.0 s       52.1%    57.0 s      27.0 s
[2016-04-15T00:24Z] INFO  17:24:22,407 IntervalUtils - Processing 16258303 bp from intervals
[2016-04-15T00:24Z] WARN  17:24:22,412 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:24Z] INFO  17:24:22,557 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:24Z] INFO  17:24:22,732 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:24Z] GATK: realign ('21', 46595644, 48129895) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:24Z] INFO  17:24:22,771 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:24Z] INFO  17:24:22,772 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:24Z] INFO  17:24:22,773 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:24Z] INFO  17:24:22,774 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:24Z] INFO  17:24:22,836 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:24Z] INFO  17:24:22,839 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:24Z] INFO  17:24:22,930 ProgressMeter -            done     70387.0     8.0 s     119.0 s      100.0%     8.0 s       0.0 s
[2016-04-15T00:24Z] INFO  17:24:22,931 ProgressMeter - Total runtime 8.45 secs, 0.14 min, 0.00 hours
[2016-04-15T00:24Z] INFO  17:24:22,934 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 70387 total reads (0.00%)
[2016-04-15T00:24Z] INFO  17:24:22,934 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:24Z] INFO  17:24:22,935 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:24Z] INFO  17:24:22,935 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:24Z] INFO  17:24:24,357 ProgressMeter -            done    282389.0    19.0 s      67.0 s       99.6%    19.0 s       0.0 s
[2016-04-15T00:24Z] INFO  17:24:24,358 ProgressMeter - Total runtime 19.17 secs, 0.32 min, 0.01 hours
[2016-04-15T00:24Z] INFO  17:24:24,361 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 282389 total reads (0.00%)
[2016-04-15T00:24Z] INFO  17:24:24,362 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:24Z] INFO  17:24:24,362 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:24Z] INFO  17:24:24,362 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:24Z] INFO  17:24:24,446 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:24Z] INFO  17:24:24,605 ProgressMeter -            done      8898.0     1.0 s       3.4 m      100.0%     1.0 s       0.0 s
[2016-04-15T00:24Z] INFO  17:24:24,606 ProgressMeter - Total runtime 1.83 secs, 0.03 min, 0.00 hours
[2016-04-15T00:24Z] INFO  17:24:24,609 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 8898 total reads (0.00%)
[2016-04-15T00:24Z] INFO  17:24:24,610 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:24Z] INFO  17:24:24,610 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:24Z] INFO  17:24:24,610 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:24Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-21_15524893_31045484-prep.bam
[2016-04-15T00:24Z] INFO  17:24:24,683 ProgressMeter -            done    230574.0    18.0 s      79.0 s      100.0%    18.0 s       0.0 s
[2016-04-15T00:24Z] INFO  17:24:24,685 ProgressMeter - Total runtime 18.25 secs, 0.30 min, 0.01 hours
[2016-04-15T00:24Z] INFO  17:24:24,689 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 230574 total reads (0.00%)
[2016-04-15T00:24Z] INFO  17:24:24,690 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:24Z] INFO  17:24:24,690 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:24Z] INFO  17:24:24,690 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:24Z] GATK pre-alignment ('X', 0, 15509380) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:24Z] INFO  17:24:25,675 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:24Z] INFO  17:24:25,679 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:24Z] INFO  17:24:25,680 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:24Z] INFO  17:24:25,680 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:24Z] INFO  17:24:25,686 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/21/R14-18106_kapa-NGv3-PE100-NGv3-sort-21_46595644_48129895-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/21/R14-18106_kapa-NGv3-PE100-NGv3-sort-21_46595644_48129895-prep-prealign-realign.intervals -L 21:46595645-48129895 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/21/tx/tmpx14Pij/R14-18106_kapa-NGv3-PE100-NGv3-sort-21_46595644_48129895-prep.bam
[2016-04-15T00:24Z] INFO  17:24:25,707 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:24Z] INFO  17:24:25,708 HelpFormatter - Date/Time: 2016/04/14 17:24:25
[2016-04-15T00:24Z] INFO  17:24:25,709 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:24Z] INFO  17:24:25,709 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:24Z] INFO  17:24:25,894 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:24Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-20_0_15843471-prep.bam
[2016-04-15T00:24Z] INFO  17:24:25,955 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:24Z] INFO  17:24:26,064 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:24Z] INFO  17:24:26,076 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:24Z] INFO  17:24:26,085 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:24Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-20_15866408_31376818-prep.bam
[2016-04-15T00:24Z] INFO  17:24:26,141 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-15T00:24Z] INFO  17:24:26,169 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:24Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-22_0_16258303-prep.bam
[2016-04-15T00:24Z] GATK pre-alignment ('X', 15518899, 31090070) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:24Z] INFO  17:24:26,632 IntervalUtils - Processing 1534251 bp from intervals
[2016-04-15T00:24Z] WARN  17:24:26,639 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:24Z] INFO  17:24:26,718 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:24Z] INFO  17:24:26,769 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:24Z] INFO  17:24:26,771 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:24Z] INFO  17:24:26,773 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:24Z] INFO  17:24:26,773 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:24Z] GATK pre-alignment ('X', 31139949, 46696637) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:24Z] GATK pre-alignment ('X', 46712910, 62570698) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:24Z] INFO  17:24:26,871 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:24Z] INFO  17:24:26,908 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:24Z] INFO  17:24:27,595 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:24Z] INFO  17:24:27,599 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:24Z] INFO  17:24:27,600 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:24Z] INFO  17:24:27,601 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:24Z] INFO  17:24:27,607 HelpFormatter - Program Args: -T PrintReads -L X:1-15509380 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/X/tx/tmpvWZUj2/R14-18106_kapa-NGv3-PE100-NGv3-sort-X_0_15509380-prep-prealign.bam
[2016-04-15T00:24Z] INFO  17:24:27,618 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:24Z] INFO  17:24:27,619 HelpFormatter - Date/Time: 2016/04/14 17:24:27
[2016-04-15T00:24Z] INFO  17:24:27,619 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:24Z] INFO  17:24:27,619 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:24Z] INFO  17:24:27,853 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:24Z] INFO  17:24:28,849 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-15T00:24Z] INFO  17:24:28,929 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:24Z] INFO  17:24:28,946 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:24Z] INFO  17:24:29,001 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-15T00:24Z] INFO  17:24:29,015 IntervalUtils - Processing 15509380 bp from intervals
[2016-04-15T00:24Z] INFO  17:24:29,112 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:24Z] INFO  17:24:29,319 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:24Z] INFO  17:24:29,323 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:24Z] INFO  17:24:29,323 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:24Z] INFO  17:24:29,324 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:24Z] INFO  17:24:29,329 HelpFormatter - Program Args: -T PrintReads -L X:15518900-31090070 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/X/tx/tmpe4_DaL/R14-18106_kapa-NGv3-PE100-NGv3-sort-X_15518899_31090070-prep-prealign.bam
[2016-04-15T00:24Z] INFO  17:24:29,345 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:24Z] INFO  17:24:29,346 HelpFormatter - Date/Time: 2016/04/14 17:24:29
[2016-04-15T00:24Z] INFO  17:24:29,348 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:24Z] INFO  17:24:29,349 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:24Z] INFO  17:24:29,419 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:24Z] INFO  17:24:29,420 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:24Z] INFO  17:24:29,421 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:24Z] INFO  17:24:29,422 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:24Z] INFO  17:24:29,439 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:24Z] INFO  17:24:29,527 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:24Z] INFO  17:24:29,597 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:24Z] INFO  17:24:29,689 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:24Z] INFO  17:24:29,692 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:24Z] INFO  17:24:29,693 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:24Z] INFO  17:24:29,694 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:24Z] INFO  17:24:29,698 HelpFormatter - Program Args: -T PrintReads -L X:31139950-46696637 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/X/tx/tmpynr7EJ/R14-18106_kapa-NGv3-PE100-NGv3-sort-X_31139949_46696637-prep-prealign.bam
[2016-04-15T00:24Z] INFO  17:24:29,747 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:24Z] INFO  17:24:29,747 HelpFormatter - Date/Time: 2016/04/14 17:24:29
[2016-04-15T00:24Z] INFO  17:24:29,747 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:24Z] INFO  17:24:29,748 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:24Z] INFO  17:24:29,758 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:24Z] INFO  17:24:29,762 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:24Z] INFO  17:24:29,762 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:24Z] INFO  17:24:29,763 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:24Z] INFO  17:24:29,768 HelpFormatter - Program Args: -T PrintReads -L X:46712911-62570698 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/X/tx/tmpjn3nWy/R14-18106_kapa-NGv3-PE100-NGv3-sort-X_46712910_62570698-prep-prealign.bam
[2016-04-15T00:24Z] INFO  17:24:29,786 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:24Z] INFO  17:24:29,787 HelpFormatter - Date/Time: 2016/04/14 17:24:29
[2016-04-15T00:24Z] INFO  17:24:29,787 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:24Z] INFO  17:24:29,788 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:24Z] INFO  17:24:29,945 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:24Z] INFO  17:24:29,959 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:24Z] INFO  17:24:30,525 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-15T00:24Z] INFO  17:24:30,596 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:24Z] INFO  17:24:30,605 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:24Z] INFO  17:24:30,644 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.04
[2016-04-15T00:24Z] INFO  17:24:30,658 IntervalUtils - Processing 15571171 bp from intervals
[2016-04-15T00:24Z] INFO  17:24:30,751 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:24Z] INFO  17:24:31,040 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:24Z] INFO  17:24:31,041 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:24Z] INFO  17:24:31,042 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:24Z] INFO  17:24:31,043 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:24Z] INFO  17:24:31,057 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:24Z] INFO  17:24:31,245 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:24Z] INFO  17:24:31,323 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-15T00:24Z] INFO  17:24:31,382 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:24Z] INFO  17:24:31,390 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:24Z] INFO  17:24:31,392 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-15T00:24Z] INFO  17:24:31,438 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-15T00:24Z] INFO  17:24:31,462 IntervalUtils - Processing 15556688 bp from intervals
[2016-04-15T00:24Z] INFO  17:24:31,463 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:24Z] INFO  17:24:31,472 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:24Z] INFO  17:24:31,545 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-15T00:24Z] INFO  17:24:31,556 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:24Z] INFO  17:24:31,560 IntervalUtils - Processing 15857788 bp from intervals
[2016-04-15T00:24Z] INFO  17:24:31,662 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:24Z] INFO  17:24:31,843 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:24Z] INFO  17:24:31,844 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:24Z] INFO  17:24:31,844 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:24Z] INFO  17:24:31,845 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:24Z] INFO  17:24:31,863 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:24Z] INFO  17:24:31,896 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:24Z] INFO  17:24:31,897 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:24Z] INFO  17:24:31,897 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:24Z] INFO  17:24:31,898 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:24Z] INFO  17:24:31,912 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:24Z] INFO  17:24:32,003 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:24Z] INFO  17:24:32,065 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:24Z] INFO  17:24:35,151 ProgressMeter -            done    103853.0     8.0 s      80.0 s       97.0%     8.0 s       0.0 s
[2016-04-15T00:24Z] INFO  17:24:35,151 ProgressMeter - Total runtime 8.38 secs, 0.14 min, 0.00 hours
[2016-04-15T00:24Z] INFO  17:24:35,155 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 103853 total reads (0.00%)
[2016-04-15T00:24Z] INFO  17:24:35,155 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:24Z] INFO  17:24:35,156 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:24Z] INFO  17:24:35,156 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:24Z] INFO  17:24:36,195 ProgressMeter -            done   1.5586184E7    22.0 s       1.0 s      100.0%    22.0 s       0.0 s
[2016-04-15T00:24Z] INFO  17:24:36,197 ProgressMeter - Total runtime 22.79 secs, 0.38 min, 0.01 hours
[2016-04-15T00:24Z] INFO  17:24:36,201 MicroScheduler - 34851 reads were filtered out during the traversal out of approximately 433734 total reads (8.04%)
[2016-04-15T00:24Z] INFO  17:24:36,202 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:24Z] INFO  17:24:36,202 MicroScheduler -   -> 1152 reads (0.27% of total) failing BadMateFilter
[2016-04-15T00:24Z] INFO  17:24:36,203 MicroScheduler -   -> 32996 reads (7.61% of total) failing DuplicateReadFilter
[2016-04-15T00:24Z] INFO  17:24:36,204 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:24Z] INFO  17:24:36,204 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:24Z] INFO  17:24:36,205 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:24Z] INFO  17:24:36,205 MicroScheduler -   -> 703 reads (0.16% of total) failing MappingQualityZeroFilter
[2016-04-15T00:24Z] INFO  17:24:36,206 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:24Z] INFO  17:24:36,207 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-15T00:24Z] INFO  17:24:36,207 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:24Z] INFO  17:24:36,553 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:24Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-21_46595644_48129895-prep.bam
[2016-04-15T00:24Z] GATK pre-alignment ('X', 62857907, 78427545) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:24Z] INFO  17:24:37,552 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:24Z] GATK: realign ('20', 47244085, 62830269) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:24Z] INFO  17:24:39,491 ProgressMeter -     21:45999972    300006.0    60.0 s       3.4 m       96.2%    62.0 s       2.0 s
[2016-04-15T00:24Z] INFO  17:24:39,675 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:24Z] INFO  17:24:39,679 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:24Z] INFO  17:24:39,679 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:24Z] INFO  17:24:39,680 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:24Z] INFO  17:24:39,684 HelpFormatter - Program Args: -T PrintReads -L X:62857908-78427545 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/X/tx/tmpIYcEl6/R14-18106_kapa-NGv3-PE100-NGv3-sort-X_62857907_78427545-prep-prealign.bam
[2016-04-15T00:24Z] INFO  17:24:39,695 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:24Z] INFO  17:24:39,699 HelpFormatter - Date/Time: 2016/04/14 17:24:39
[2016-04-15T00:24Z] INFO  17:24:39,699 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:24Z] INFO  17:24:39,705 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:24Z] INFO  17:24:39,895 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:24Z] INFO  17:24:40,025 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:24Z] INFO  17:24:40,028 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:24Z] INFO  17:24:40,029 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:24Z] INFO  17:24:40,029 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:24Z] INFO  17:24:40,034 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/20/R14-18106_kapa-NGv3-PE100-NGv3-sort-20_47244085_62830269-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/20/R14-18106_kapa-NGv3-PE100-NGv3-sort-20_47244085_62830269-prep-prealign-realign.intervals -L 20:47244086-62830269 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/20/tx/tmpfcWL6X/R14-18106_kapa-NGv3-PE100-NGv3-sort-20_47244085_62830269-prep.bam
[2016-04-15T00:24Z] INFO  17:24:40,043 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:24Z] INFO  17:24:40,044 HelpFormatter - Date/Time: 2016/04/14 17:24:40
[2016-04-15T00:24Z] INFO  17:24:40,044 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:24Z] INFO  17:24:40,047 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:24Z] INFO  17:24:40,275 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:24Z] INFO  17:24:40,377 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@5fe152b7
[2016-04-15T00:24Z] INFO  17:24:40,386 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:24Z] INFO  17:24:40,403 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:24Z] INFO  17:24:40,449 ProgressMeter -            done    142471.0    19.0 s       2.2 m       97.9%    19.0 s       0.0 s
[2016-04-15T00:24Z] INFO  17:24:40,450 ProgressMeter - Total runtime 19.15 secs, 0.32 min, 0.01 hours
[2016-04-15T00:24Z] INFO  17:24:40,451 MicroScheduler - 75 reads were filtered out during the traversal out of approximately 142546 total reads (0.05%)
[2016-04-15T00:24Z] INFO  17:24:40,452 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:24Z] INFO  17:24:40,452 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:24Z] INFO  17:24:40,453 MicroScheduler -   -> 75 reads (0.05% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:24Z] INFO  17:24:40,461 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-15T00:24Z] INFO  17:24:40,798 IntervalUtils - Processing 15586184 bp from intervals
[2016-04-15T00:24Z] WARN  17:24:40,814 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:24Z] INFO  17:24:40,913 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:24Z] INFO  17:24:41,032 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-15T00:24Z] INFO  17:24:41,084 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:24Z] INFO  17:24:41,093 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:24Z] INFO  17:24:41,130 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:24Z] INFO  17:24:41,131 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:24Z] INFO  17:24:41,132 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:24Z] INFO  17:24:41,133 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:24Z] INFO  17:24:41,146 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-15T00:24Z] INFO  17:24:41,161 IntervalUtils - Processing 15569638 bp from intervals
[2016-04-15T00:24Z] INFO  17:24:41,244 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:24Z] INFO  17:24:41,293 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:24Z] INFO  17:24:41,488 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:24Z] INFO  17:24:41,493 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:24Z] INFO  17:24:41,494 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:24Z] INFO  17:24:41,495 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:24Z] INFO  17:24:41,495 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:24Z] INFO  17:24:41,511 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:24Z] INFO  17:24:41,655 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:24Z] INFO  17:24:42,070 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:24Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-22_47309229_51304566-prep-prealign.bam
[2016-04-15T00:24Z] GATK RealignerTargetCreator: R14-18106_kapa-NGv3-PE100-NGv3-sort-22_47309229_51304566-prep-prealign.bam 22:47309230-51304566
[2016-04-15T00:24Z] GATK: RealignerTargetCreator
[2016-04-15T00:24Z] INFO  17:24:42,815 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@41fd9d8e
[2016-04-15T00:24Z] INFO  17:24:42,885 ProgressMeter -            done     73798.0    11.0 s       2.5 m       99.5%    11.0 s       0.0 s
[2016-04-15T00:24Z] INFO  17:24:42,885 ProgressMeter - Total runtime 11.04 secs, 0.18 min, 0.00 hours
[2016-04-15T00:24Z] INFO  17:24:42,886 MicroScheduler - 84 reads were filtered out during the traversal out of approximately 73882 total reads (0.11%)
[2016-04-15T00:24Z] INFO  17:24:42,886 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:24Z] INFO  17:24:42,886 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:24Z] INFO  17:24:42,887 MicroScheduler -   -> 84 reads (0.11% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:24Z] INFO  17:24:44,216 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:24Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-X_31139949_46696637-prep-prealign.bam
[2016-04-15T00:24Z] INFO  17:24:44,345 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@32d5a4c6
[2016-04-15T00:24Z] INFO  17:24:44,478 ProgressMeter -            done    438789.0    65.0 s       2.5 m      100.0%    65.0 s       0.0 s
[2016-04-15T00:24Z] INFO  17:24:44,479 ProgressMeter - Total runtime 65.71 secs, 1.10 min, 0.02 hours
[2016-04-15T00:24Z] INFO  17:24:44,480 MicroScheduler - 225 reads were filtered out during the traversal out of approximately 439014 total reads (0.05%)
[2016-04-15T00:24Z] INFO  17:24:44,480 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:24Z] INFO  17:24:44,480 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:24Z] INFO  17:24:44,481 MicroScheduler -   -> 225 reads (0.05% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:24Z] GATK RealignerTargetCreator: R14-18106_kapa-NGv3-PE100-NGv3-sort-X_31139949_46696637-prep-prealign.bam X:31139950-46696637
[2016-04-15T00:24Z] GATK: RealignerTargetCreator
[2016-04-15T00:24Z] INFO  17:24:44,719 ProgressMeter -     19:45783981   1000017.0   120.0 s     120.0 s       94.6%     2.1 m       6.0 s
[2016-04-15T00:24Z] INFO  17:24:45,179 ProgressMeter -     22:20137066    200005.0    30.0 s       2.5 m       24.9%   120.0 s      90.0 s
[2016-04-15T00:24Z] INFO  17:24:45,200 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:24Z] INFO  17:24:45,204 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:24Z] INFO  17:24:45,205 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:24Z] INFO  17:24:45,206 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:24Z] INFO  17:24:45,211 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/22/R14-18106_kapa-NGv3-PE100-NGv3-sort-22_47309229_51304566-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/22/tx/tmpkiT6NZ/R14-18106_kapa-NGv3-PE100-NGv3-sort-22_47309229_51304566-prep-prealign-realign.intervals -l INFO -L 22:47309230-51304566 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:24Z] INFO  17:24:45,232 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:24Z] INFO  17:24:45,233 HelpFormatter - Date/Time: 2016/04/14 17:24:45
[2016-04-15T00:24Z] INFO  17:24:45,234 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:24Z] INFO  17:24:45,234 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:24Z] INFO  17:24:45,350 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:24Z] INFO  17:24:45,570 ProgressMeter -     19:22363721    400006.0    31.0 s      78.0 s       44.2%    70.0 s      39.0 s
[2016-04-15T00:24Z] INFO  17:24:45,587 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T00:24Z] INFO  17:24:45,599 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:24Z] INFO  17:24:45,689 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.09
[2016-04-15T00:24Z] INFO  17:24:45,832 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:24Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-21_31062047_46591599-prep-prealign.bam
[2016-04-15T00:24Z] INFO  17:24:45,965 IntervalUtils - Processing 3995337 bp from intervals
[2016-04-15T00:24Z] WARN  17:24:45,970 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:24Z] INFO  17:24:46,050 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:24Z] INFO  17:24:46,198 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:24Z] INFO  17:24:46,199 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:24Z] INFO  17:24:46,200 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:24Z] INFO  17:24:46,200 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:24Z] INFO  17:24:47,086 ProgressMeter -            done   1.5863059E7    25.0 s       1.0 s      100.0%    25.0 s       0.0 s
[2016-04-15T00:24Z] INFO  17:24:47,088 ProgressMeter - Total runtime 25.96 secs, 0.43 min, 0.01 hours
[2016-04-15T00:24Z] INFO  17:24:47,092 MicroScheduler - 42753 reads were filtered out during the traversal out of approximately 538483 total reads (7.94%)
[2016-04-15T00:24Z] INFO  17:24:47,094 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:24Z] INFO  17:24:47,095 MicroScheduler -   -> 1313 reads (0.24% of total) failing BadMateFilter
[2016-04-15T00:24Z] INFO  17:24:47,095 MicroScheduler -   -> 40821 reads (7.58% of total) failing DuplicateReadFilter
[2016-04-15T00:24Z] INFO  17:24:47,096 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:24Z] INFO  17:24:47,096 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:24Z] INFO  17:24:47,097 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:24Z] INFO  17:24:47,098 MicroScheduler -   -> 619 reads (0.11% of total) failing MappingQualityZeroFilter
[2016-04-15T00:24Z] INFO  17:24:47,098 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:24Z] INFO  17:24:47,099 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-15T00:24Z] INFO  17:24:47,099 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:24Z] GATK RealignerTargetCreator: R14-18106_kapa-NGv3-PE100-NGv3-sort-21_31062047_46591599-prep-prealign.bam 21:31062048-46591599
[2016-04-15T00:24Z] GATK: RealignerTargetCreator
[2016-04-15T00:24Z] INFO  17:24:47,167 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:24Z] INFO  17:24:47,171 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:24Z] INFO  17:24:47,172 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:24Z] INFO  17:24:47,173 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:24Z] INFO  17:24:47,178 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/X/R14-18106_kapa-NGv3-PE100-NGv3-sort-X_31139949_46696637-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/X/tx/tmpKTs5PS/R14-18106_kapa-NGv3-PE100-NGv3-sort-X_31139949_46696637-prep-prealign-realign.intervals -l INFO -L X:31139950-46696637 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:24Z] INFO  17:24:47,189 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:24Z] INFO  17:24:47,198 HelpFormatter - Date/Time: 2016/04/14 17:24:47
[2016-04-15T00:24Z] INFO  17:24:47,199 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:24Z] INFO  17:24:47,200 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:24Z] INFO  17:24:47,298 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@41fd9d8e
[2016-04-15T00:24Z] INFO  17:24:47,337 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:24Z] INFO  17:24:47,368 ProgressMeter -            done     94427.0    16.0 s       2.9 m      100.0%    16.0 s       0.0 s
[2016-04-15T00:24Z] INFO  17:24:47,370 ProgressMeter - Total runtime 16.33 secs, 0.27 min, 0.00 hours
[2016-04-15T00:24Z] INFO  17:24:47,370 MicroScheduler - 120 reads were filtered out during the traversal out of approximately 94547 total reads (0.13%)
[2016-04-15T00:24Z] INFO  17:24:47,371 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:24Z] INFO  17:24:47,372 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:24Z] INFO  17:24:47,373 MicroScheduler -   -> 120 reads (0.13% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:24Z] INFO  17:24:47,616 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T00:24Z] INFO  17:24:47,662 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:24Z] INFO  17:24:47,722 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-15T00:24Z] INFO  17:24:47,823 ProgressMeter -     22:38121332    100001.0    30.0 s       5.0 m       40.8%    73.0 s      43.0 s
[2016-04-15T00:24Z] INFO  17:24:48,115 IntervalUtils - Processing 15556688 bp from intervals
[2016-04-15T00:24Z] WARN  17:24:48,120 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:24Z] INFO  17:24:48,250 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:24Z] INFO  17:24:48,328 ProgressMeter -            done    535626.0    33.0 s      63.0 s      100.0%    33.0 s       0.0 s
[2016-04-15T00:24Z] INFO  17:24:48,329 ProgressMeter - Total runtime 33.97 secs, 0.57 min, 0.01 hours
[2016-04-15T00:24Z] INFO  17:24:48,333 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 535626 total reads (0.00%)
[2016-04-15T00:24Z] INFO  17:24:48,333 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:24Z] INFO  17:24:48,334 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:24Z] INFO  17:24:48,334 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:24Z] INFO  17:24:48,381 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:24Z] INFO  17:24:48,382 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:24Z] INFO  17:24:48,383 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:24Z] INFO  17:24:48,384 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:24Z] INFO  17:24:48,527 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:24Z] GATK: realign ('20', 31379406, 47242465) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:24Z] INFO  17:24:48,821 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:24Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-X_15518899_31090070-prep-prealign.bam
[2016-04-15T00:24Z] INFO  17:24:48,891 ProgressMeter -     19:55539178    800012.0   120.0 s       2.5 m       71.3%     2.8 m      48.0 s
[2016-04-15T00:24Z] GATK RealignerTargetCreator: R14-18106_kapa-NGv3-PE100-NGv3-sort-X_15518899_31090070-prep-prealign.bam X:15518900-31090070
[2016-04-15T00:24Z] GATK: RealignerTargetCreator
[2016-04-15T00:24Z] INFO  17:24:49,730 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@41fd9d8e
[2016-04-15T00:24Z] INFO  17:24:49,753 ProgressMeter -     19:11350361   1000019.0     2.5 m       2.5 m       73.2%     3.4 m      54.0 s
[2016-04-15T00:24Z] INFO  17:24:49,790 ProgressMeter -            done    119454.0    20.0 s       2.8 m      100.0%    20.0 s       0.0 s
[2016-04-15T00:24Z] INFO  17:24:49,791 ProgressMeter - Total runtime 20.37 secs, 0.34 min, 0.01 hours
[2016-04-15T00:24Z] INFO  17:24:49,792 MicroScheduler - 125 reads were filtered out during the traversal out of approximately 119579 total reads (0.10%)
[2016-04-15T00:24Z] INFO  17:24:49,793 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:24Z] INFO  17:24:49,793 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:24Z] INFO  17:24:49,794 MicroScheduler -   -> 125 reads (0.10% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:24Z] INFO  17:24:50,054 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:24Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-19_15510112_31025906-prep.bam
[2016-04-15T00:24Z] INFO  17:24:50,166 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:24Z] INFO  17:24:50,204 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:24Z] INFO  17:24:50,205 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:24Z] INFO  17:24:50,205 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:24Z] INFO  17:24:50,210 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/21/R14-18106_kapa-NGv3-PE100-NGv3-sort-21_31062047_46591599-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/21/tx/tmpTcn6Qi/R14-18106_kapa-NGv3-PE100-NGv3-sort-21_31062047_46591599-prep-prealign-realign.intervals -l INFO -L 21:31062048-46591599 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:24Z] INFO  17:24:50,222 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:24Z] INFO  17:24:50,223 HelpFormatter - Date/Time: 2016/04/14 17:24:50
[2016-04-15T00:24Z] INFO  17:24:50,223 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:24Z] INFO  17:24:50,224 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:24Z] INFO  17:24:50,313 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:24Z] INFO  17:24:50,536 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T00:24Z] INFO  17:24:50,554 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:24Z] INFO  17:24:50,615 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-15T00:24Z] INFO  17:24:50,911 ProgressMeter -            done   1043083.0    58.0 s      56.0 s      100.0%    58.0 s       0.0 s
[2016-04-15T00:24Z] INFO  17:24:50,911 ProgressMeter - Total runtime 58.76 secs, 0.98 min, 0.02 hours
[2016-04-15T00:24Z] INFO  17:24:50,915 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 1043083 total reads (0.00%)
[2016-04-15T00:24Z] INFO  17:24:50,916 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:24Z] INFO  17:24:50,916 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:24Z] INFO  17:24:50,917 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:24Z] INFO  17:24:50,917 IntervalUtils - Processing 15529552 bp from intervals
[2016-04-15T00:24Z] WARN  17:24:50,933 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:24Z] INFO  17:24:51,093 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:24Z] INFO  17:24:51,210 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:24Z] INFO  17:24:51,213 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:24Z] INFO  17:24:51,214 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:24Z] INFO  17:24:51,214 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:24Z] INFO  17:24:51,219 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/20/R14-18106_kapa-NGv3-PE100-NGv3-sort-20_31379406_47242465-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/20/R14-18106_kapa-NGv3-PE100-NGv3-sort-20_31379406_47242465-prep-prealign-realign.intervals -L 20:31379407-47242465 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/20/tx/tmpo0n0kL/R14-18106_kapa-NGv3-PE100-NGv3-sort-20_31379406_47242465-prep.bam
[2016-04-15T00:24Z] INFO  17:24:51,231 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:24Z] INFO  17:24:51,237 HelpFormatter - Date/Time: 2016/04/14 17:24:51
[2016-04-15T00:24Z] INFO  17:24:51,238 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:24Z] INFO  17:24:51,239 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:24Z] INFO  17:24:51,241 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:24Z] INFO  17:24:51,244 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:24Z] INFO  17:24:51,245 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:24Z] INFO  17:24:51,246 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:24Z] INFO  17:24:51,247 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:24Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-X_0_15509380-prep-prealign.bam
[2016-04-15T00:24Z] INFO  17:24:51,469 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:24Z] INFO  17:24:51,550 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:24Z] INFO  17:24:51,559 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:24Z] INFO  17:24:51,617 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-15T00:24Z] GATK RealignerTargetCreator: R14-18106_kapa-NGv3-PE100-NGv3-sort-X_0_15509380-prep-prealign.bam X:1-15509380
[2016-04-15T00:24Z] GATK: RealignerTargetCreator
[2016-04-15T00:24Z] GATK pre-alignment ('X', 78616585, 95940189) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:24Z] INFO  17:24:52,110 IntervalUtils - Processing 15863059 bp from intervals
[2016-04-15T00:24Z] WARN  17:24:52,124 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:24Z] INFO  17:24:52,222 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@5fe152b7
[2016-04-15T00:24Z] INFO  17:24:52,230 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:24Z] INFO  17:24:52,342 ProgressMeter -            done   1124002.0     2.1 m     113.0 s      100.0%     2.1 m       0.0 s
[2016-04-15T00:24Z] INFO  17:24:52,348 ProgressMeter - Total runtime 127.73 secs, 2.13 min, 0.04 hours
[2016-04-15T00:24Z] INFO  17:24:52,348 MicroScheduler - 496 reads were filtered out during the traversal out of approximately 1124498 total reads (0.04%)
[2016-04-15T00:24Z] INFO  17:24:52,349 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:24Z] INFO  17:24:52,349 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:24Z] INFO  17:24:52,349 MicroScheduler -   -> 496 reads (0.04% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:24Z] INFO  17:24:52,352 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:24Z] INFO  17:24:52,354 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:24Z] INFO  17:24:52,354 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:24Z] INFO  17:24:52,355 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:24Z] INFO  17:24:52,498 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:24Z] INFO  17:24:52,502 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:24Z] INFO  17:24:52,502 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:24Z] INFO  17:24:52,503 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:24Z] INFO  17:24:52,510 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:24Z] INFO  17:24:52,513 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/X/R14-18106_kapa-NGv3-PE100-NGv3-sort-X_15518899_31090070-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/X/tx/tmp8vpZIj/R14-18106_kapa-NGv3-PE100-NGv3-sort-X_15518899_31090070-prep-prealign-realign.intervals -l INFO -L X:15518900-31090070 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:24Z] INFO  17:24:52,534 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:24Z] INFO  17:24:52,541 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:24Z] INFO  17:24:52,543 HelpFormatter - Date/Time: 2016/04/14 17:24:52
[2016-04-15T00:24Z] INFO  17:24:52,543 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:24Z] INFO  17:24:52,544 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:24Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-17_31048040_46607237-prep.bam
[2016-04-15T00:24Z] INFO  17:24:52,640 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:24Z] INFO  17:24:52,698 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:24Z] INFO  17:24:52,878 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T00:24Z] INFO  17:24:52,887 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:24Z] INFO  17:24:52,927 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.04
[2016-04-15T00:24Z] INFO  17:24:53,177 IntervalUtils - Processing 15571171 bp from intervals
[2016-04-15T00:24Z] WARN  17:24:53,182 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:24Z] INFO  17:24:53,278 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:24Z] INFO  17:24:53,531 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:24Z] INFO  17:24:53,532 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:24Z] INFO  17:24:53,532 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:24Z] INFO  17:24:53,532 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:24Z] INFO  17:24:54,099 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:24Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-19_31038849_46627578-prep-prealign.bam
[2016-04-15T00:24Z] INFO  17:24:54,805 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:24Z] INFO  17:24:54,809 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:24Z] INFO  17:24:54,809 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:24Z] INFO  17:24:54,810 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:24Z] INFO  17:24:54,814 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/X/R14-18106_kapa-NGv3-PE100-NGv3-sort-X_0_15509380-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/X/tx/tmp8e65lt/R14-18106_kapa-NGv3-PE100-NGv3-sort-X_0_15509380-prep-prealign-realign.intervals -l INFO -L X:1-15509380 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:24Z] INFO  17:24:54,834 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:24Z] INFO  17:24:54,835 HelpFormatter - Date/Time: 2016/04/14 17:24:54
[2016-04-15T00:24Z] INFO  17:24:54,835 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:24Z] INFO  17:24:54,836 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:24Z] INFO  17:24:54,938 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:24Z] INFO  17:24:55,052 ProgressMeter -            done   3995337.0     8.0 s       2.0 s      100.0%     8.0 s       0.0 s
[2016-04-15T00:24Z] INFO  17:24:55,053 ProgressMeter - Total runtime 8.85 secs, 0.15 min, 0.00 hours
[2016-04-15T00:24Z] INFO  17:24:55,057 MicroScheduler - 12325 reads were filtered out during the traversal out of approximately 143834 total reads (8.57%)
[2016-04-15T00:24Z] INFO  17:24:55,057 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:24Z] INFO  17:24:55,057 MicroScheduler -   -> 360 reads (0.25% of total) failing BadMateFilter
[2016-04-15T00:24Z] INFO  17:24:55,058 MicroScheduler -   -> 10757 reads (7.48% of total) failing DuplicateReadFilter
[2016-04-15T00:24Z] INFO  17:24:55,058 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:24Z] INFO  17:24:55,058 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:24Z] INFO  17:24:55,059 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:24Z] INFO  17:24:55,059 MicroScheduler -   -> 1208 reads (0.84% of total) failing MappingQualityZeroFilter
[2016-04-15T00:24Z] INFO  17:24:55,059 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:24Z] INFO  17:24:55,060 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-15T00:24Z] INFO  17:24:55,060 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:24Z] INFO  17:24:55,184 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T00:24Z] INFO  17:24:55,205 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:24Z] INFO  17:24:55,287 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-15T00:24Z] INFO  17:24:55,363 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:24Z] INFO  17:24:55,370 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:24Z] INFO  17:24:55,370 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:24Z] INFO  17:24:55,370 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:24Z] INFO  17:24:55,379 HelpFormatter - Program Args: -T PrintReads -L X:78616586-95940189 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/X/tx/tmpjxkKxo/R14-18106_kapa-NGv3-PE100-NGv3-sort-X_78616585_95940189-prep-prealign.bam
[2016-04-15T00:24Z] INFO  17:24:55,394 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:24Z] INFO  17:24:55,394 HelpFormatter - Date/Time: 2016/04/14 17:24:55
[2016-04-15T00:24Z] INFO  17:24:55,394 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:24Z] INFO  17:24:55,395 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:24Z] GATK pre-alignment ('X', 95990756, 111698889) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:24Z] INFO  17:24:55,604 IntervalUtils - Processing 15509380 bp from intervals
[2016-04-15T00:24Z] WARN  17:24:55,612 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:24Z] INFO  17:24:55,627 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:24Z] INFO  17:24:55,691 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:24Z] INFO  17:24:55,934 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:24Z] INFO  17:24:55,935 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:24Z] INFO  17:24:55,936 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:24Z] INFO  17:24:55,937 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:24Z] INFO  17:24:56,613 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:24Z] GATK: realign ('22', 47309229, 51304566) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:24Z] INFO  17:24:56,819 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-15T00:24Z] INFO  17:24:56,871 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:24Z] INFO  17:24:56,880 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:24Z] INFO  17:24:56,914 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.03
[2016-04-15T00:24Z] INFO  17:24:56,929 IntervalUtils - Processing 17323604 bp from intervals
[2016-04-15T00:24Z] INFO  17:24:56,999 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:24Z] INFO  17:24:57,369 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:24Z] INFO  17:24:57,370 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:24Z] INFO  17:24:57,373 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:24Z] INFO  17:24:57,373 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:24Z] INFO  17:24:57,388 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:24Z] GATK RealignerTargetCreator: R14-18106_kapa-NGv3-PE100-NGv3-sort-19_31038849_46627578-prep-prealign.bam 19:31038850-46627578
[2016-04-15T00:24Z] GATK: RealignerTargetCreator
[2016-04-15T00:24Z] INFO  17:24:57,602 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:24Z] INFO  17:24:58,306 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:24Z] INFO  17:24:58,310 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:24Z] INFO  17:24:58,310 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:24Z] INFO  17:24:58,311 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:24Z] INFO  17:24:58,315 HelpFormatter - Program Args: -T PrintReads -L X:95990757-111698889 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/X/tx/tmpcM0puI/R14-18106_kapa-NGv3-PE100-NGv3-sort-X_95990756_111698889-prep-prealign.bam
[2016-04-15T00:24Z] INFO  17:24:58,328 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:24Z] INFO  17:24:58,332 HelpFormatter - Date/Time: 2016/04/14 17:24:58
[2016-04-15T00:24Z] INFO  17:24:58,333 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:24Z] INFO  17:24:58,344 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:24Z] INFO  17:24:58,571 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:24Z] INFO  17:24:59,580 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:24Z] INFO  17:24:59,584 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:24Z] INFO  17:24:59,585 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:24Z] INFO  17:24:59,585 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:24Z] INFO  17:24:59,590 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/22/R14-18106_kapa-NGv3-PE100-NGv3-sort-22_47309229_51304566-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/22/R14-18106_kapa-NGv3-PE100-NGv3-sort-22_47309229_51304566-prep-prealign-realign.intervals -L 22:47309230-51304566 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/22/tx/tmp3s7H2s/R14-18106_kapa-NGv3-PE100-NGv3-sort-22_47309229_51304566-prep.bam
[2016-04-15T00:24Z] INFO  17:24:59,620 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:24Z] INFO  17:24:59,620 HelpFormatter - Date/Time: 2016/04/14 17:24:59
[2016-04-15T00:24Z] INFO  17:24:59,620 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:24Z] INFO  17:24:59,620 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:24Z] INFO  17:24:59,902 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-15T00:24Z] INFO  17:24:59,909 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:24Z] INFO  17:24:59,977 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:24Z] INFO  17:24:59,986 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:25Z] INFO  17:25:00,039 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-15T00:25Z] INFO  17:25:00,054 IntervalUtils - Processing 15708133 bp from intervals
[2016-04-15T00:25Z] INFO  17:25:00,058 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:25Z] INFO  17:25:00,067 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:25Z] INFO  17:25:00,113 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-15T00:25Z] INFO  17:25:00,139 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:25Z] INFO  17:25:00,293 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:25Z] INFO  17:25:00,297 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:25Z] INFO  17:25:00,297 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:25Z] INFO  17:25:00,298 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:25Z] INFO  17:25:00,302 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/19/R14-18106_kapa-NGv3-PE100-NGv3-sort-19_31038849_46627578-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/19/tx/tmpKekkx8/R14-18106_kapa-NGv3-PE100-NGv3-sort-19_31038849_46627578-prep-prealign-realign.intervals -l INFO -L 19:31038850-46627578 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:25Z] INFO  17:25:00,313 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:25Z] INFO  17:25:00,314 HelpFormatter - Date/Time: 2016/04/14 17:25:00
[2016-04-15T00:25Z] INFO  17:25:00,315 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:25Z] INFO  17:25:00,316 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:25Z] INFO  17:25:00,419 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:25Z] INFO  17:25:00,427 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:25Z] INFO  17:25:00,428 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:25Z] INFO  17:25:00,429 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:25Z] INFO  17:25:00,430 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:25Z] INFO  17:25:00,445 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:25Z] INFO  17:25:00,511 IntervalUtils - Processing 3995337 bp from intervals
[2016-04-15T00:25Z] WARN  17:25:00,516 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:25Z] INFO  17:25:00,569 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:25Z] INFO  17:25:00,593 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:25Z] INFO  17:25:00,629 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T00:25Z] INFO  17:25:00,640 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:25Z] INFO  17:25:00,660 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:25Z] INFO  17:25:00,660 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:25Z] INFO  17:25:00,661 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:25Z] INFO  17:25:00,664 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:25Z] INFO  17:25:00,723 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-15T00:25Z] INFO  17:25:00,778 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:25Z] INFO  17:25:00,818 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:25Z] INFO  17:25:00,992 IntervalUtils - Processing 15588729 bp from intervals
[2016-04-15T00:25Z] WARN  17:25:00,997 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:25Z] INFO  17:25:01,077 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:25Z] INFO  17:25:01,308 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:25Z] INFO  17:25:01,310 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:25Z] INFO  17:25:01,310 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:25Z] INFO  17:25:01,311 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:25Z] INFO  17:25:01,916 ProgressMeter -      X:53222444    200006.0    30.0 s       2.5 m       41.0%    73.0 s      43.0 s
[2016-04-15T00:25Z] INFO  17:25:03,226 ProgressMeter -            done   1.5556688E7    14.0 s       0.0 s      100.0%    14.0 s       0.0 s
[2016-04-15T00:25Z] INFO  17:25:03,227 ProgressMeter - Total runtime 14.84 secs, 0.25 min, 0.00 hours
[2016-04-15T00:25Z] INFO  17:25:03,230 MicroScheduler - 6363 reads were filtered out during the traversal out of approximately 74196 total reads (8.58%)
[2016-04-15T00:25Z] INFO  17:25:03,231 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:25Z] INFO  17:25:03,232 MicroScheduler -   -> 286 reads (0.39% of total) failing BadMateFilter
[2016-04-15T00:25Z] INFO  17:25:03,232 MicroScheduler -   -> 5640 reads (7.60% of total) failing DuplicateReadFilter
[2016-04-15T00:25Z] INFO  17:25:03,233 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:25Z] INFO  17:25:03,233 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:25Z] INFO  17:25:03,234 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:25Z] INFO  17:25:03,235 MicroScheduler -   -> 437 reads (0.59% of total) failing MappingQualityZeroFilter
[2016-04-15T00:25Z] INFO  17:25:03,235 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:25Z] INFO  17:25:03,236 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-15T00:25Z] INFO  17:25:03,237 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:25Z] INFO  17:25:04,201 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@7172f77a
[2016-04-15T00:25Z] INFO  17:25:04,361 ProgressMeter -            done     33491.0     6.0 s       3.5 m      100.0%     6.0 s       0.0 s
[2016-04-15T00:25Z] INFO  17:25:04,361 ProgressMeter - Total runtime 6.99 secs, 0.12 min, 0.00 hours
[2016-04-15T00:25Z] INFO  17:25:04,362 MicroScheduler - 69 reads were filtered out during the traversal out of approximately 33560 total reads (0.21%)
[2016-04-15T00:25Z] INFO  17:25:04,362 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:25Z] INFO  17:25:04,363 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:25Z] INFO  17:25:04,364 MicroScheduler -   -> 69 reads (0.21% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:25Z] INFO  17:25:04,644 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:25Z] GATK: realign ('X', 31139949, 46696637) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:25Z] INFO  17:25:05,678 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:25Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-X_78616585_95940189-prep-prealign.bam
[2016-04-15T00:25Z] GATK RealignerTargetCreator: R14-18106_kapa-NGv3-PE100-NGv3-sort-X_78616585_95940189-prep-prealign.bam X:78616586-95940189
[2016-04-15T00:25Z] GATK: RealignerTargetCreator
[2016-04-15T00:25Z] INFO  17:25:06,450 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@5fe152b7
[2016-04-15T00:25Z] INFO  17:25:06,524 ProgressMeter -            done    148927.0    25.0 s       2.8 m      100.0%    25.0 s       0.0 s
[2016-04-15T00:25Z] INFO  17:25:06,525 ProgressMeter - Total runtime 25.03 secs, 0.42 min, 0.01 hours
[2016-04-15T00:25Z] INFO  17:25:06,525 MicroScheduler - 121 reads were filtered out during the traversal out of approximately 149048 total reads (0.08%)
[2016-04-15T00:25Z] INFO  17:25:06,526 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:25Z] INFO  17:25:06,526 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:25Z] INFO  17:25:06,526 MicroScheduler -   -> 121 reads (0.08% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:25Z] INFO  17:25:07,491 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:25Z] INFO  17:25:07,515 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:25Z] INFO  17:25:07,516 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:25Z] INFO  17:25:07,516 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:25Z] INFO  17:25:07,520 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/X/R14-18106_kapa-NGv3-PE100-NGv3-sort-X_31139949_46696637-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/X/R14-18106_kapa-NGv3-PE100-NGv3-sort-X_31139949_46696637-prep-prealign-realign.intervals -L X:31139950-46696637 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/X/tx/tmpclzhOS/R14-18106_kapa-NGv3-PE100-NGv3-sort-X_31139949_46696637-prep.bam
[2016-04-15T00:25Z] INFO  17:25:07,534 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:25Z] INFO  17:25:07,535 HelpFormatter - Date/Time: 2016/04/14 17:25:07
[2016-04-15T00:25Z] INFO  17:25:07,535 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:25Z] INFO  17:25:07,535 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:25Z] INFO  17:25:07,793 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:25Z] INFO  17:25:07,910 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:25Z] INFO  17:25:07,919 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:25Z] INFO  17:25:07,981 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-15T00:25Z] INFO  17:25:07,989 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:25Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-X_62857907_78427545-prep-prealign.bam
[2016-04-15T00:25Z] INFO  17:25:08,425 IntervalUtils - Processing 15556688 bp from intervals
[2016-04-15T00:25Z] WARN  17:25:08,430 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:25Z] GATK RealignerTargetCreator: R14-18106_kapa-NGv3-PE100-NGv3-sort-X_62857907_78427545-prep-prealign.bam X:62857908-78427545
[2016-04-15T00:25Z] GATK: RealignerTargetCreator
[2016-04-15T00:25Z] INFO  17:25:08,548 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:25Z] INFO  17:25:08,648 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:25Z] INFO  17:25:08,649 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:25Z] INFO  17:25:08,650 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:25Z] INFO  17:25:08,651 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:25Z] INFO  17:25:08,721 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:25Z] INFO  17:25:08,859 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:25Z] INFO  17:25:08,862 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:25Z] INFO  17:25:08,863 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:25Z] INFO  17:25:08,863 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:25Z] INFO  17:25:08,881 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/X/R14-18106_kapa-NGv3-PE100-NGv3-sort-X_78616585_95940189-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/X/tx/tmpcp9GFm/R14-18106_kapa-NGv3-PE100-NGv3-sort-X_78616585_95940189-prep-prealign-realign.intervals -l INFO -L X:78616586-95940189 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:25Z] INFO  17:25:08,892 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:25Z] INFO  17:25:08,926 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:25Z] INFO  17:25:08,931 HelpFormatter - Date/Time: 2016/04/14 17:25:08
[2016-04-15T00:25Z] INFO  17:25:08,931 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:25Z] INFO  17:25:08,932 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:25Z] INFO  17:25:09,000 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@41fd9d8e
[2016-04-15T00:25Z] INFO  17:25:09,101 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:25Z] INFO  17:25:09,209 ProgressMeter -            done    297529.0    37.0 s       2.1 m      100.0%    37.0 s       0.0 s
[2016-04-15T00:25Z] INFO  17:25:09,210 ProgressMeter - Total runtime 37.31 secs, 0.62 min, 0.01 hours
[2016-04-15T00:25Z] INFO  17:25:09,210 MicroScheduler - 191 reads were filtered out during the traversal out of approximately 297720 total reads (0.06%)
[2016-04-15T00:25Z] INFO  17:25:09,211 ProgressMeter -            done    431215.0    28.0 s      65.0 s      100.0%    28.0 s       0.0 s
[2016-04-15T00:25Z] INFO  17:25:09,210 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:25Z] INFO  17:25:09,211 ProgressMeter - Total runtime 28.08 secs, 0.47 min, 0.01 hours
[2016-04-15T00:25Z] INFO  17:25:09,211 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:25Z] INFO  17:25:09,211 MicroScheduler -   -> 191 reads (0.06% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:25Z] INFO  17:25:09,215 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 431215 total reads (0.00%)
[2016-04-15T00:25Z] INFO  17:25:09,216 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:25Z] INFO  17:25:09,216 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:25Z] INFO  17:25:09,216 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:25Z] INFO  17:25:09,238 ProgressMeter -            done   1.5571171E7    15.0 s       1.0 s      100.0%    15.0 s       0.0 s
[2016-04-15T00:25Z] INFO  17:25:09,239 ProgressMeter - Total runtime 15.71 secs, 0.26 min, 0.00 hours
[2016-04-15T00:25Z] INFO  17:25:09,243 MicroScheduler - 8462 reads were filtered out during the traversal out of approximately 95017 total reads (8.91%)
[2016-04-15T00:25Z] INFO  17:25:09,243 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:25Z] INFO  17:25:09,244 MicroScheduler -   -> 334 reads (0.35% of total) failing BadMateFilter
[2016-04-15T00:25Z] INFO  17:25:09,244 MicroScheduler -   -> 7009 reads (7.38% of total) failing DuplicateReadFilter
[2016-04-15T00:25Z] INFO  17:25:09,244 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:25Z] INFO  17:25:09,244 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:25Z] INFO  17:25:09,245 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:25Z] INFO  17:25:09,245 MicroScheduler -   -> 1119 reads (1.18% of total) failing MappingQualityZeroFilter
[2016-04-15T00:25Z] INFO  17:25:09,245 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:25Z] INFO  17:25:09,245 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-15T00:25Z] INFO  17:25:09,246 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:25Z] INFO  17:25:09,391 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T00:25Z] INFO  17:25:09,403 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:25Z] INFO  17:25:09,488 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-15T00:25Z] INFO  17:25:09,835 IntervalUtils - Processing 17323604 bp from intervals
[2016-04-15T00:25Z] WARN  17:25:09,840 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:25Z] INFO  17:25:09,942 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:25Z] INFO  17:25:10,198 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:25Z] INFO  17:25:10,200 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:25Z] INFO  17:25:10,201 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:25Z] INFO  17:25:10,201 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:25Z] INFO  17:25:10,611 ProgressMeter -            done   1.550938E7    14.0 s       0.0 s      100.0%    14.0 s       0.0 s
[2016-04-15T00:25Z] INFO  17:25:10,612 ProgressMeter - Total runtime 14.68 secs, 0.24 min, 0.00 hours
[2016-04-15T00:25Z] INFO  17:25:10,616 MicroScheduler - 13552 reads were filtered out during the traversal out of approximately 120383 total reads (11.26%)
[2016-04-15T00:25Z] INFO  17:25:10,616 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:25Z] INFO  17:25:10,617 MicroScheduler -   -> 444 reads (0.37% of total) failing BadMateFilter
[2016-04-15T00:25Z] INFO  17:25:10,617 MicroScheduler -   -> 8743 reads (7.26% of total) failing DuplicateReadFilter
[2016-04-15T00:25Z] INFO  17:25:10,617 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:25Z] INFO  17:25:10,618 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:25Z] INFO  17:25:10,618 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:25Z] INFO  17:25:10,618 MicroScheduler -   -> 4365 reads (3.63% of total) failing MappingQualityZeroFilter
[2016-04-15T00:25Z] INFO  17:25:10,619 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:25Z] INFO  17:25:10,619 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-15T00:25Z] INFO  17:25:10,619 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:25Z] INFO  17:25:10,817 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:25Z] INFO  17:25:10,830 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:25Z] GATK: realign ('X', 15518899, 31090070) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:25Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-X_46712910_62570698-prep-prealign.bam
[2016-04-15T00:25Z] INFO  17:25:10,890 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:25Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-20_47244085_62830269-prep.bam
[2016-04-15T00:25Z] INFO  17:25:11,429 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:25Z] INFO  17:25:11,433 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:25Z] INFO  17:25:11,433 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:25Z] INFO  17:25:11,434 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:25Z] INFO  17:25:11,440 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/X/R14-18106_kapa-NGv3-PE100-NGv3-sort-X_62857907_78427545-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/X/tx/tmpag52Ma/R14-18106_kapa-NGv3-PE100-NGv3-sort-X_62857907_78427545-prep-prealign-realign.intervals -l INFO -L X:62857908-78427545 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:25Z] INFO  17:25:11,451 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:25Z] INFO  17:25:11,451 HelpFormatter - Date/Time: 2016/04/14 17:25:11
[2016-04-15T00:25Z] INFO  17:25:11,452 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:25Z] INFO  17:25:11,452 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:25Z] INFO  17:25:11,628 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:25Z] GATK RealignerTargetCreator: R14-18106_kapa-NGv3-PE100-NGv3-sort-X_46712910_62570698-prep-prealign.bam X:46712911-62570698
[2016-04-15T00:25Z] GATK: RealignerTargetCreator
[2016-04-15T00:25Z] INFO  17:25:11,886 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T00:25Z] INFO  17:25:11,898 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:25Z] INFO  17:25:11,945 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:25Z] INFO  17:25:11,945 ProgressMeter -            done    142471.0    11.0 s      79.0 s       97.9%    11.0 s       0.0 s
[2016-04-15T00:25Z] INFO  17:25:11,946 ProgressMeter - Total runtime 11.29 secs, 0.19 min, 0.00 hours
[2016-04-15T00:25Z] INFO  17:25:11,951 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 142471 total reads (0.00%)
[2016-04-15T00:25Z] INFO  17:25:11,951 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:25Z] INFO  17:25:11,952 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:25Z] INFO  17:25:11,952 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:25Z] GATK: realign ('X', 0, 15509380) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:25Z] INFO  17:25:11,978 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-15T00:25Z] GATK pre-alignment ('X', 111874647, 128581278) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:25Z] INFO  17:25:12,416 IntervalUtils - Processing 15569638 bp from intervals
[2016-04-15T00:25Z] WARN  17:25:12,423 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:25Z] INFO  17:25:12,602 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:25Z] INFO  17:25:12,797 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:25Z] INFO  17:25:12,798 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:25Z] INFO  17:25:12,798 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:25Z] INFO  17:25:12,798 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:25Z] INFO  17:25:13,566 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:25Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-22_47309229_51304566-prep.bam
[2016-04-15T00:25Z] INFO  17:25:13,672 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:25Z] INFO  17:25:13,675 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:25Z] INFO  17:25:13,675 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:25Z] INFO  17:25:13,676 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:25Z] INFO  17:25:13,680 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/X/R14-18106_kapa-NGv3-PE100-NGv3-sort-X_15518899_31090070-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/X/R14-18106_kapa-NGv3-PE100-NGv3-sort-X_15518899_31090070-prep-prealign-realign.intervals -L X:15518900-31090070 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/X/tx/tmpY0rQKS/R14-18106_kapa-NGv3-PE100-NGv3-sort-X_15518899_31090070-prep.bam
[2016-04-15T00:25Z] INFO  17:25:13,714 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:25Z] INFO  17:25:13,715 HelpFormatter - Date/Time: 2016/04/14 17:25:13
[2016-04-15T00:25Z] INFO  17:25:13,716 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:25Z] INFO  17:25:13,716 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:25Z] INFO  17:25:13,989 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:25Z] GATK pre-alignment ('X', 128582278, 144329181) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:25Z] INFO  17:25:14,093 ProgressMeter -            done   1.5529552E7    22.0 s       1.0 s      100.0%    22.0 s       0.0 s
[2016-04-15T00:25Z] INFO  17:25:14,095 ProgressMeter - Total runtime 22.85 secs, 0.38 min, 0.01 hours
[2016-04-15T00:25Z] INFO  17:25:14,098 MicroScheduler - 38249 reads were filtered out during the traversal out of approximately 440937 total reads (8.67%)
[2016-04-15T00:25Z] INFO  17:25:14,099 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:25Z] INFO  17:25:14,100 MicroScheduler -   -> 1097 reads (0.25% of total) failing BadMateFilter
[2016-04-15T00:25Z] INFO  17:25:14,101 MicroScheduler -   -> 34063 reads (7.73% of total) failing DuplicateReadFilter
[2016-04-15T00:25Z] INFO  17:25:14,101 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:25Z] INFO  17:25:14,102 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:25Z] INFO  17:25:14,103 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:25Z] INFO  17:25:14,103 MicroScheduler -   -> 3089 reads (0.70% of total) failing MappingQualityZeroFilter
[2016-04-15T00:25Z] INFO  17:25:14,109 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:25Z] INFO  17:25:14,110 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-15T00:25Z] INFO  17:25:14,111 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:25Z] INFO  17:25:14,116 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:25Z] INFO  17:25:14,128 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:25Z] INFO  17:25:14,184 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-15T00:25Z] INFO  17:25:14,591 IntervalUtils - Processing 15571171 bp from intervals
[2016-04-15T00:25Z] WARN  17:25:14,613 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:25Z] INFO  17:25:14,733 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:25Z] INFO  17:25:14,804 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:25Z] INFO  17:25:14,807 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:25Z] INFO  17:25:14,808 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:25Z] INFO  17:25:14,808 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:25Z] INFO  17:25:14,813 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/X/R14-18106_kapa-NGv3-PE100-NGv3-sort-X_46712910_62570698-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/X/tx/tmpewo6ff/R14-18106_kapa-NGv3-PE100-NGv3-sort-X_46712910_62570698-prep-prealign-realign.intervals -l INFO -L X:46712911-62570698 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:25Z] INFO  17:25:14,822 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:25Z] INFO  17:25:14,823 HelpFormatter - Date/Time: 2016/04/14 17:25:14
[2016-04-15T00:25Z] INFO  17:25:14,824 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:25Z] INFO  17:25:14,824 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:25Z] INFO  17:25:14,865 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:25Z] INFO  17:25:14,866 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:25Z] INFO  17:25:14,867 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:25Z] INFO  17:25:14,867 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:25Z] INFO  17:25:14,955 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:25Z] INFO  17:25:14,962 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:25Z] INFO  17:25:15,132 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:25Z] INFO  17:25:15,145 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:25Z] INFO  17:25:15,148 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:25Z] INFO  17:25:15,148 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:25Z] INFO  17:25:15,149 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:25Z] INFO  17:25:15,153 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/X/R14-18106_kapa-NGv3-PE100-NGv3-sort-X_0_15509380-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/X/R14-18106_kapa-NGv3-PE100-NGv3-sort-X_0_15509380-prep-prealign-realign.intervals -L X:1-15509380 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/X/tx/tmpcQ9rC5/R14-18106_kapa-NGv3-PE100-NGv3-sort-X_0_15509380-prep.bam
[2016-04-15T00:25Z] INFO  17:25:15,163 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:25Z] INFO  17:25:15,164 HelpFormatter - Date/Time: 2016/04/14 17:25:15
[2016-04-15T00:25Z] INFO  17:25:15,164 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:25Z] INFO  17:25:15,165 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:25Z] INFO  17:25:15,175 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T00:25Z] INFO  17:25:15,180 ProgressMeter -     22:25024251    400007.0    60.0 s       2.5 m       56.4%   106.0 s      46.0 s
[2016-04-15T00:25Z] INFO  17:25:15,188 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:25Z] INFO  17:25:15,239 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-15T00:25Z] INFO  17:25:15,362 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:25Z] INFO  17:25:15,374 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:25Z] INFO  17:25:15,378 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:25Z] INFO  17:25:15,378 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:25Z] INFO  17:25:15,379 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:25Z] INFO  17:25:15,383 HelpFormatter - Program Args: -T PrintReads -L X:111874648-128581278 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/X/tx/tmp6kxX1Y/R14-18106_kapa-NGv3-PE100-NGv3-sort-X_111874647_128581278-prep-prealign.bam
[2016-04-15T00:25Z] INFO  17:25:15,395 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:25Z] INFO  17:25:15,396 HelpFormatter - Date/Time: 2016/04/14 17:25:15
[2016-04-15T00:25Z] INFO  17:25:15,396 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:25Z] INFO  17:25:15,397 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:25Z] INFO  17:25:15,441 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:25Z] GATK: realign ('21', 31062047, 46591599) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:25Z] INFO  17:25:15,491 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:25Z] INFO  17:25:15,500 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:25Z] INFO  17:25:15,509 IntervalUtils - Processing 15857788 bp from intervals
[2016-04-15T00:25Z] WARN  17:25:15,515 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:25Z] INFO  17:25:15,555 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-15T00:25Z] INFO  17:25:15,578 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:25Z] INFO  17:25:15,592 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:25Z] INFO  17:25:15,832 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:25Z] INFO  17:25:15,834 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:25Z] INFO  17:25:15,834 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:25Z] INFO  17:25:15,835 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:25Z] INFO  17:25:15,934 IntervalUtils - Processing 15509380 bp from intervals
[2016-04-15T00:25Z] WARN  17:25:15,946 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:25Z] INFO  17:25:16,077 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:25Z] INFO  17:25:16,196 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:25Z] INFO  17:25:16,198 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:25Z] INFO  17:25:16,198 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:25Z] INFO  17:25:16,199 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:25Z] INFO  17:25:16,337 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:25Z] INFO  17:25:16,510 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:25Z] INFO  17:25:16,625 ProgressMeter -            done     73798.0     7.0 s     108.0 s       99.5%     7.0 s       0.0 s
[2016-04-15T00:25Z] INFO  17:25:16,626 ProgressMeter - Total runtime 7.98 secs, 0.13 min, 0.00 hours
[2016-04-15T00:25Z] INFO  17:25:16,631 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 73798 total reads (0.00%)
[2016-04-15T00:25Z] INFO  17:25:16,632 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:25Z] INFO  17:25:16,633 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:25Z] INFO  17:25:16,633 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:25Z] INFO  17:25:17,025 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-15T00:25Z] INFO  17:25:17,124 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:25Z] INFO  17:25:17,132 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:25Z] INFO  17:25:17,198 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:25Z] INFO  17:25:17,205 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:25Z] INFO  17:25:17,206 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:25Z] INFO  17:25:17,206 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:25Z] INFO  17:25:17,211 HelpFormatter - Program Args: -T PrintReads -L X:128582279-144329181 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/X/tx/tmpxSWq0e/R14-18106_kapa-NGv3-PE100-NGv3-sort-X_128582278_144329181-prep-prealign.bam
[2016-04-15T00:25Z] INFO  17:25:17,225 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.09
[2016-04-15T00:25Z] INFO  17:25:17,235 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:25Z] INFO  17:25:17,236 HelpFormatter - Date/Time: 2016/04/14 17:25:17
[2016-04-15T00:25Z] INFO  17:25:17,237 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:25Z] INFO  17:25:17,237 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:25Z] INFO  17:25:17,281 IntervalUtils - Processing 16706631 bp from intervals
[2016-04-15T00:25Z] INFO  17:25:17,409 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:25Z] INFO  17:25:17,419 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:25Z] INFO  17:25:17,787 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:25Z] INFO  17:25:17,788 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:25Z] INFO  17:25:17,788 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:25Z] INFO  17:25:17,789 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:25Z] INFO  17:25:17,818 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:25Z] INFO  17:25:17,824 ProgressMeter -     22:41923339    400005.0    60.0 s       2.5 m       65.3%    91.0 s      31.0 s
[2016-04-15T00:25Z] INFO  17:25:18,063 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:25Z] INFO  17:25:18,175 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:25Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-X_31139949_46696637-prep.bam
[2016-04-15T00:25Z] INFO  17:25:18,485 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-15T00:25Z] INFO  17:25:18,548 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:25Z] INFO  17:25:18,551 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:25Z] INFO  17:25:18,552 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:25Z] INFO  17:25:18,553 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:25Z] INFO  17:25:18,557 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/21/R14-18106_kapa-NGv3-PE100-NGv3-sort-21_31062047_46591599-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/21/R14-18106_kapa-NGv3-PE100-NGv3-sort-21_31062047_46591599-prep-prealign-realign.intervals -L 21:31062048-46591599 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/21/tx/tmpEcqCWp/R14-18106_kapa-NGv3-PE100-NGv3-sort-21_31062047_46591599-prep.bam
[2016-04-15T00:25Z] INFO  17:25:18,569 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:25Z] INFO  17:25:18,577 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:25Z] INFO  17:25:18,577 HelpFormatter - Date/Time: 2016/04/14 17:25:18
[2016-04-15T00:25Z] INFO  17:25:18,577 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:25Z] INFO  17:25:18,578 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:25Z] INFO  17:25:18,577 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:25Z] GATK pre-alignment ('X', 144337190, 155270560) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:25Z] INFO  17:25:18,634 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-15T00:25Z] INFO  17:25:18,651 IntervalUtils - Processing 15746903 bp from intervals
[2016-04-15T00:25Z] INFO  17:25:18,766 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:25Z] INFO  17:25:18,818 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:25Z] INFO  17:25:18,892 ProgressMeter -     19:57839137   1000018.0     2.5 m       2.5 m       89.7%     2.8 m      17.0 s
[2016-04-15T00:25Z] INFO  17:25:19,019 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:25Z] INFO  17:25:19,029 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:25Z] INFO  17:25:19,050 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:25Z] INFO  17:25:19,052 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:25Z] INFO  17:25:19,052 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:25Z] INFO  17:25:19,053 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:25Z] INFO  17:25:19,078 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:25Z] INFO  17:25:19,103 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-15T00:25Z] INFO  17:25:19,234 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:25Z] INFO  17:25:19,534 IntervalUtils - Processing 15529552 bp from intervals
[2016-04-15T00:25Z] WARN  17:25:19,539 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:25Z] INFO  17:25:19,611 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:25Z] INFO  17:25:19,730 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:25Z] INFO  17:25:19,731 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:25Z] INFO  17:25:19,732 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:25Z] INFO  17:25:19,733 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:25Z] INFO  17:25:19,754 ProgressMeter -     19:13397671   1200025.0     3.0 m       2.5 m       86.4%     3.5 m      28.0 s
[2016-04-15T00:25Z] INFO  17:25:19,891 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:25Z] INFO  17:25:20,124 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:25Z] INFO  17:25:20,520 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@41fd9d8e
[2016-04-15T00:25Z] INFO  17:25:20,659 ProgressMeter -            done    145099.0    20.0 s       2.3 m      100.0%    20.0 s       0.0 s
[2016-04-15T00:25Z] INFO  17:25:20,660 ProgressMeter - Total runtime 20.23 secs, 0.34 min, 0.01 hours
[2016-04-15T00:25Z] INFO  17:25:20,660 MicroScheduler - 87 reads were filtered out during the traversal out of approximately 145186 total reads (0.06%)
[2016-04-15T00:25Z] INFO  17:25:20,660 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:25Z] INFO  17:25:20,661 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:25Z] INFO  17:25:20,661 MicroScheduler -   -> 87 reads (0.06% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:25Z] INFO  17:25:21,370 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:25Z] INFO  17:25:21,373 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:25Z] INFO  17:25:21,374 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:25Z] INFO  17:25:21,374 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:25Z] INFO  17:25:21,379 HelpFormatter - Program Args: -T PrintReads -L X:144337191-155270560 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/X/tx/tmp8f1YVt/R14-18106_kapa-NGv3-PE100-NGv3-sort-X_144337190_155270560-prep-prealign.bam
[2016-04-15T00:25Z] INFO  17:25:21,388 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:25Z] INFO  17:25:21,392 HelpFormatter - Date/Time: 2016/04/14 17:25:21
[2016-04-15T00:25Z] INFO  17:25:21,393 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:25Z] INFO  17:25:21,393 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:25Z] INFO  17:25:21,577 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:25Z] INFO  17:25:22,299 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:25Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-X_95990756_111698889-prep-prealign.bam
[2016-04-15T00:25Z] INFO  17:25:22,700 ProgressMeter -     20:44520330    400007.0    30.0 s      75.0 s       82.8%    36.0 s       6.0 s
[2016-04-15T00:25Z] INFO  17:25:22,748 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-15T00:25Z] INFO  17:25:22,798 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:25Z] GATK RealignerTargetCreator: R14-18106_kapa-NGv3-PE100-NGv3-sort-X_95990756_111698889-prep-prealign.bam X:95990757-111698889
[2016-04-15T00:25Z] GATK: RealignerTargetCreator
[2016-04-15T00:25Z] INFO  17:25:22,807 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:25Z] INFO  17:25:22,850 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.04
[2016-04-15T00:25Z] INFO  17:25:22,864 IntervalUtils - Processing 10933370 bp from intervals
[2016-04-15T00:25Z] INFO  17:25:22,934 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:25Z] INFO  17:25:23,238 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:25Z] INFO  17:25:23,239 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:25Z] INFO  17:25:23,240 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:25Z] INFO  17:25:23,241 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:25Z] INFO  17:25:23,289 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:25Z] INFO  17:25:23,334 ProgressMeter -            done     94427.0     8.0 s      89.0 s      100.0%     8.0 s       0.0 s
[2016-04-15T00:25Z] INFO  17:25:23,334 ProgressMeter - Total runtime 8.47 secs, 0.14 min, 0.00 hours
[2016-04-15T00:25Z] INFO  17:25:23,338 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 94427 total reads (0.00%)
[2016-04-15T00:25Z] INFO  17:25:23,339 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:25Z] INFO  17:25:23,340 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:25Z] INFO  17:25:23,341 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:25Z] INFO  17:25:23,402 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:25Z] INFO  17:25:24,494 ProgressMeter -            done   1.7323604E7    14.0 s       0.0 s      100.0%    14.0 s       0.0 s
[2016-04-15T00:25Z] INFO  17:25:24,495 ProgressMeter - Total runtime 14.30 secs, 0.24 min, 0.00 hours
[2016-04-15T00:25Z] INFO  17:25:24,500 MicroScheduler - 4108 reads were filtered out during the traversal out of approximately 33627 total reads (12.22%)
[2016-04-15T00:25Z] INFO  17:25:24,501 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:25Z] INFO  17:25:24,502 MicroScheduler -   -> 223 reads (0.66% of total) failing BadMateFilter
[2016-04-15T00:25Z] INFO  17:25:24,503 MicroScheduler -   -> 2393 reads (7.12% of total) failing DuplicateReadFilter
[2016-04-15T00:25Z] INFO  17:25:24,504 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:25Z] INFO  17:25:24,504 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:25Z] INFO  17:25:24,505 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:25Z] INFO  17:25:24,506 MicroScheduler -   -> 1492 reads (4.44% of total) failing MappingQualityZeroFilter
[2016-04-15T00:25Z] INFO  17:25:24,507 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:25Z] INFO  17:25:24,508 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-15T00:25Z] INFO  17:25:24,508 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:25Z] INFO  17:25:24,739 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:25Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-X_15518899_31090070-prep.bam
[2016-04-15T00:25Z] GATK pre-alignment ('Y', 0, 15522993) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:25Z] INFO  17:25:25,470 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:25Z] INFO  17:25:25,473 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:25Z] INFO  17:25:25,474 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:25Z] INFO  17:25:25,474 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:25Z] INFO  17:25:25,479 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/X/R14-18106_kapa-NGv3-PE100-NGv3-sort-X_95990756_111698889-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/X/tx/tmpgwDxSJ/R14-18106_kapa-NGv3-PE100-NGv3-sort-X_95990756_111698889-prep-prealign-realign.intervals -l INFO -L X:95990757-111698889 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:25Z] INFO  17:25:25,494 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:25Z] INFO  17:25:25,494 HelpFormatter - Date/Time: 2016/04/14 17:25:25
[2016-04-15T00:25Z] INFO  17:25:25,495 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:25Z] INFO  17:25:25,495 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:25Z] INFO  17:25:25,542 ProgressMeter -            done    535250.0    33.0 s      62.0 s      100.0%    33.0 s       0.0 s
[2016-04-15T00:25Z] INFO  17:25:25,543 ProgressMeter - Total runtime 33.19 secs, 0.55 min, 0.01 hours
[2016-04-15T00:25Z] INFO  17:25:25,546 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 535250 total reads (0.00%)
[2016-04-15T00:25Z] INFO  17:25:25,546 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:25Z] INFO  17:25:25,547 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:25Z] INFO  17:25:25,547 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:25Z] INFO  17:25:25,633 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:25Z] INFO  17:25:25,897 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T00:25Z] INFO  17:25:25,910 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:25Z] INFO  17:25:25,971 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-15T00:25Z] INFO  17:25:26,013 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:25Z] GATK: realign ('X', 78616585, 95940189) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:25Z] INFO  17:25:26,223 IntervalUtils - Processing 15708133 bp from intervals
[2016-04-15T00:25Z] WARN  17:25:26,228 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:25Z] INFO  17:25:26,331 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:25Z] INFO  17:25:26,497 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:25Z] INFO  17:25:26,498 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:25Z] INFO  17:25:26,499 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:25Z] INFO  17:25:26,500 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:25Z] INFO  17:25:26,989 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:25Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-20_31379406_47242465-prep.bam
[2016-04-15T00:25Z] INFO  17:25:27,367 ProgressMeter -            done    119454.0    11.0 s      93.0 s      100.0%    11.0 s       0.0 s
[2016-04-15T00:25Z] INFO  17:25:27,367 ProgressMeter - Total runtime 11.17 secs, 0.19 min, 0.00 hours
[2016-04-15T00:25Z] INFO  17:25:27,371 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 119454 total reads (0.00%)
[2016-04-15T00:25Z] INFO  17:25:27,372 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:25Z] INFO  17:25:27,372 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:25Z] INFO  17:25:27,372 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:25Z] INFO  17:25:27,656 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:25Z] INFO  17:25:27,659 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:25Z] INFO  17:25:27,660 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:25Z] INFO  17:25:27,660 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:25Z] INFO  17:25:27,665 HelpFormatter - Program Args: -T PrintReads -L Y:1-15522993 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/Y/tx/tmpYWSiJk/R14-18106_kapa-NGv3-PE100-NGv3-sort-Y_0_15522993-prep-prealign.bam
[2016-04-15T00:25Z] INFO  17:25:27,678 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:25Z] INFO  17:25:27,679 HelpFormatter - Date/Time: 2016/04/14 17:25:27
[2016-04-15T00:25Z] INFO  17:25:27,679 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:25Z] INFO  17:25:27,680 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:25Z] INFO  17:25:27,819 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:25Z] INFO  17:25:28,834 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:25Z] INFO  17:25:28,837 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:25Z] INFO  17:25:28,838 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:25Z] INFO  17:25:28,838 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:25Z] INFO  17:25:28,843 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/X/R14-18106_kapa-NGv3-PE100-NGv3-sort-X_78616585_95940189-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/X/R14-18106_kapa-NGv3-PE100-NGv3-sort-X_78616585_95940189-prep-prealign-realign.intervals -L X:78616586-95940189 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/X/tx/tmpqZU0ny/R14-18106_kapa-NGv3-PE100-NGv3-sort-X_78616585_95940189-prep.bam
[2016-04-15T00:25Z] INFO  17:25:28,853 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:25Z] INFO  17:25:28,854 HelpFormatter - Date/Time: 2016/04/14 17:25:28
[2016-04-15T00:25Z] INFO  17:25:28,854 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:25Z] INFO  17:25:28,855 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:25Z] INFO  17:25:28,871 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:25Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-X_0_15509380-prep.bam
[2016-04-15T00:25Z] GATK pre-alignment ('Y', 15526614, 59222281) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:25Z] INFO  17:25:29,036 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-15T00:25Z] INFO  17:25:29,079 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:25Z] INFO  17:25:29,088 ProgressMeter -            done   1.5569638E7    16.0 s       1.0 s      100.0%    16.0 s       0.0 s
[2016-04-15T00:25Z] INFO  17:25:29,089 ProgressMeter - Total runtime 16.29 secs, 0.27 min, 0.00 hours
[2016-04-15T00:25Z] INFO  17:25:29,097 MicroScheduler - 21925 reads were filtered out during the traversal out of approximately 149954 total reads (14.62%)
[2016-04-15T00:25Z] INFO  17:25:29,097 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:25Z] INFO  17:25:29,097 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:25Z] INFO  17:25:29,097 MicroScheduler -   -> 422 reads (0.28% of total) failing BadMateFilter
[2016-04-15T00:25Z] INFO  17:25:29,098 MicroScheduler -   -> 10693 reads (7.13% of total) failing DuplicateReadFilter
[2016-04-15T00:25Z] INFO  17:25:29,098 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:25Z] INFO  17:25:29,098 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:25Z] INFO  17:25:29,099 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:25Z] INFO  17:25:29,099 MicroScheduler -   -> 10810 reads (7.21% of total) failing MappingQualityZeroFilter
[2016-04-15T00:25Z] INFO  17:25:29,099 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:25Z] INFO  17:25:29,100 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-15T00:25Z] INFO  17:25:29,100 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:25Z] INFO  17:25:29,106 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:25Z] INFO  17:25:29,168 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-15T00:25Z] INFO  17:25:29,181 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:25Z] INFO  17:25:29,182 IntervalUtils - Processing 15522993 bp from intervals
[2016-04-15T00:25Z] INFO  17:25:29,190 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:25Z] INFO  17:25:29,243 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-15T00:25Z] INFO  17:25:29,296 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:25Z] GATK pre-alignment ('Y', 59228291, 59373566) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:25Z] INFO  17:25:29,470 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:25Z] INFO  17:25:29,471 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:25Z] INFO  17:25:29,471 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:25Z] INFO  17:25:29,472 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:25Z] INFO  17:25:29,508 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:25Z] INFO  17:25:29,620 IntervalUtils - Processing 17323604 bp from intervals
[2016-04-15T00:25Z] WARN  17:25:29,625 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:25Z] INFO  17:25:29,707 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:25Z] INFO  17:25:29,741 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:25Z] INFO  17:25:29,837 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:25Z] INFO  17:25:29,838 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:25Z] INFO  17:25:29,839 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:25Z] INFO  17:25:29,840 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:25Z] INFO  17:25:29,986 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:25Z] INFO  17:25:30,156 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:25Z] INFO  17:25:30,524 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:25Z] GATK: realign ('X', 62857907, 78427545) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:25Z] INFO  17:25:31,327 ProgressMeter -     19:44422925   1.3378175E7    30.0 s       2.0 s       85.9%    34.0 s       4.0 s
[2016-04-15T00:25Z] INFO  17:25:32,020 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:25Z] INFO  17:25:32,023 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:25Z] INFO  17:25:32,024 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:25Z] INFO  17:25:32,024 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:25Z] INFO  17:25:32,028 HelpFormatter - Program Args: -T PrintReads -L Y:15526615-59222281 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/Y/tx/tmpN9ZSqe/R14-18106_kapa-NGv3-PE100-NGv3-sort-Y_15526614_59222281-prep-prealign.bam
[2016-04-15T00:25Z] INFO  17:25:32,045 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:25Z] INFO  17:25:32,046 HelpFormatter - Date/Time: 2016/04/14 17:25:32
[2016-04-15T00:25Z] INFO  17:25:32,047 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:25Z] INFO  17:25:32,047 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:25Z] INFO  17:25:32,265 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:25Z] INFO  17:25:32,407 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:25Z] INFO  17:25:32,411 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:25Z] INFO  17:25:32,411 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:25Z] INFO  17:25:32,412 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:25Z] INFO  17:25:32,416 HelpFormatter - Program Args: -T PrintReads -L Y:59228292-59373566 -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.bam -BQSR /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/align/R14-18106_kapa-NGv3-PE100-NGv3/R14-18106_kapa-NGv3-PE100-NGv3-sort.grp -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/Y/tx/tmpbiCr8a/R14-18106_kapa-NGv3-PE100-NGv3-sort-Y_59228291_59373566-prep-prealign.bam
[2016-04-15T00:25Z] INFO  17:25:32,450 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:25Z] INFO  17:25:32,451 HelpFormatter - Date/Time: 2016/04/14 17:25:32
[2016-04-15T00:25Z] INFO  17:25:32,451 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:25Z] INFO  17:25:32,452 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:25Z] INFO  17:25:32,645 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:25Z] INFO  17:25:32,768 ProgressMeter -            done   1.5857788E7    16.0 s       1.0 s      100.0%    16.0 s       0.0 s
[2016-04-15T00:25Z] INFO  17:25:32,769 ProgressMeter - Total runtime 16.94 secs, 0.28 min, 0.00 hours
[2016-04-15T00:25Z] INFO  17:25:32,773 MicroScheduler - 121234 reads were filtered out during the traversal out of approximately 299411 total reads (40.49%)
[2016-04-15T00:25Z] INFO  17:25:32,774 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:25Z] INFO  17:25:32,775 MicroScheduler -   -> 472 reads (0.16% of total) failing BadMateFilter
[2016-04-15T00:25Z] INFO  17:25:32,775 MicroScheduler -   -> 14292 reads (4.77% of total) failing DuplicateReadFilter
[2016-04-15T00:25Z] INFO  17:25:32,776 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:25Z] INFO  17:25:32,777 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:25Z] INFO  17:25:32,777 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:25Z] INFO  17:25:32,778 MicroScheduler -   -> 106470 reads (35.56% of total) failing MappingQualityZeroFilter
[2016-04-15T00:25Z] INFO  17:25:32,779 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:25Z] INFO  17:25:32,779 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-15T00:25Z] INFO  17:25:32,780 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:25Z] INFO  17:25:33,284 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-15T00:25Z] INFO  17:25:33,294 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@41fd9d8e
[2016-04-15T00:25Z] INFO  17:25:33,367 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:25Z] INFO  17:25:33,375 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:25Z] INFO  17:25:33,405 ProgressMeter -            done    101409.0    15.0 s       2.6 m      100.0%    15.0 s       0.0 s
[2016-04-15T00:25Z] INFO  17:25:33,406 ProgressMeter - Total runtime 15.62 secs, 0.26 min, 0.00 hours
[2016-04-15T00:25Z] INFO  17:25:33,407 MicroScheduler - 111 reads were filtered out during the traversal out of approximately 101520 total reads (0.11%)
[2016-04-15T00:25Z] INFO  17:25:33,407 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:25Z] INFO  17:25:33,408 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:25Z] INFO  17:25:33,409 MicroScheduler -   -> 111 reads (0.11% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:25Z] INFO  17:25:33,421 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-15T00:25Z] INFO  17:25:33,447 IntervalUtils - Processing 43695667 bp from intervals
[2016-04-15T00:25Z] INFO  17:25:33,477 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:25Z] INFO  17:25:33,481 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:25Z] INFO  17:25:33,481 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:25Z] INFO  17:25:33,482 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:25Z] INFO  17:25:33,487 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/X/R14-18106_kapa-NGv3-PE100-NGv3-sort-X_62857907_78427545-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/X/R14-18106_kapa-NGv3-PE100-NGv3-sort-X_62857907_78427545-prep-prealign-realign.intervals -L X:62857908-78427545 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/X/tx/tmpZZggwF/R14-18106_kapa-NGv3-PE100-NGv3-sort-X_62857907_78427545-prep.bam
[2016-04-15T00:25Z] INFO  17:25:33,499 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:25Z] INFO  17:25:33,502 HelpFormatter - Date/Time: 2016/04/14 17:25:33
[2016-04-15T00:25Z] INFO  17:25:33,505 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:25Z] INFO  17:25:33,506 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:25Z] INFO  17:25:33,540 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:25Z] INFO  17:25:33,738 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:25Z] INFO  17:25:33,802 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:25Z] INFO  17:25:33,814 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:25Z] INFO  17:25:33,815 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:25Z] INFO  17:25:33,815 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:25Z] INFO  17:25:33,852 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:25Z] INFO  17:25:33,872 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:25Z] INFO  17:25:33,884 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:25Z] INFO  17:25:33,919 ContextCovariate - 		Context sizes: base substitution model 2, indel substitution model 3
[2016-04-15T00:25Z] INFO  17:25:33,965 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-15T00:25Z] INFO  17:25:33,989 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:25Z] INFO  17:25:33,997 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:25Z] INFO  17:25:34,048 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-15T00:25Z] INFO  17:25:34,063 IntervalUtils - Processing 145275 bp from intervals
[2016-04-15T00:25Z] INFO  17:25:34,077 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:25Z] GATK: realign ('X', 46712910, 62570698) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:25Z] INFO  17:25:34,133 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:25Z] INFO  17:25:34,234 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:25Z] INFO  17:25:34,273 IntervalUtils - Processing 15569638 bp from intervals
[2016-04-15T00:25Z] INFO  17:25:34,273 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:25Z] INFO  17:25:34,274 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:25Z] INFO  17:25:34,275 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:25Z] INFO  17:25:34,275 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:25Z] WARN  17:25:34,278 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:25Z] INFO  17:25:34,302 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:25Z] INFO  17:25:34,303 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:25Z] INFO  17:25:34,350 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@7172f77a
[2016-04-15T00:25Z] INFO  17:25:34,388 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:25Z] INFO  17:25:34,413 ProgressMeter -            done         0.0     0.0 s      38.5 h      100.0%     0.0 s       0.0 s
[2016-04-15T00:25Z] INFO  17:25:34,414 ProgressMeter - Total runtime 0.14 secs, 0.00 min, 0.00 hours
[2016-04-15T00:25Z] INFO  17:25:34,547 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:25Z] INFO  17:25:34,548 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:25Z] INFO  17:25:34,548 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:25Z] INFO  17:25:34,549 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:25Z] INFO  17:25:34,614 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:25Z] INFO  17:25:34,749 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:25Z] INFO  17:25:34,811 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:25Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-X_111874647_128581278-prep-prealign.bam
[2016-04-15T00:25Z] GATK RealignerTargetCreator: R14-18106_kapa-NGv3-PE100-NGv3-sort-X_111874647_128581278-prep-prealign.bam X:111874648-128581278
[2016-04-15T00:25Z] GATK: RealignerTargetCreator
[2016-04-15T00:25Z] INFO  17:25:35,229 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@41fd9d8e
[2016-04-15T00:25Z] INFO  17:25:35,344 ProgressMeter -            done    110572.0    16.0 s       2.5 m       98.5%    16.0 s       0.0 s
[2016-04-15T00:25Z] INFO  17:25:35,345 ProgressMeter - Total runtime 16.29 secs, 0.27 min, 0.00 hours
[2016-04-15T00:25Z] INFO  17:25:35,345 MicroScheduler - 97 reads were filtered out during the traversal out of approximately 110669 total reads (0.09%)
[2016-04-15T00:25Z] INFO  17:25:35,345 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:25Z] INFO  17:25:35,346 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:25Z] INFO  17:25:35,346 MicroScheduler -   -> 97 reads (0.09% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:25Z] INFO  17:25:35,848 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:25Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-Y_59228291_59373566-prep-prealign.bam
[2016-04-15T00:25Z] GATK RealignerTargetCreator: R14-18106_kapa-NGv3-PE100-NGv3-sort-Y_59228291_59373566-prep-prealign.bam Y:59228292-59373566
[2016-04-15T00:25Z] GATK: RealignerTargetCreator
[2016-04-15T00:25Z] INFO  17:25:36,109 ProgressMeter -            done     33491.0     6.0 s       3.1 m      100.0%     6.0 s       0.0 s
[2016-04-15T00:25Z] INFO  17:25:36,110 ProgressMeter - Total runtime 6.27 secs, 0.10 min, 0.00 hours
[2016-04-15T00:25Z] INFO  17:25:36,114 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 33491 total reads (0.00%)
[2016-04-15T00:25Z] INFO  17:25:36,115 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:25Z] INFO  17:25:36,115 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:25Z] INFO  17:25:36,116 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:25Z] INFO  17:25:36,832 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:25Z] INFO  17:25:36,845 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:25Z] INFO  17:25:36,846 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:25Z] INFO  17:25:36,847 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:25Z] INFO  17:25:36,852 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/X/R14-18106_kapa-NGv3-PE100-NGv3-sort-X_46712910_62570698-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/X/R14-18106_kapa-NGv3-PE100-NGv3-sort-X_46712910_62570698-prep-prealign-realign.intervals -L X:46712911-62570698 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/X/tx/tmpO0UrmJ/R14-18106_kapa-NGv3-PE100-NGv3-sort-X_46712910_62570698-prep.bam
[2016-04-15T00:25Z] INFO  17:25:36,862 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:25Z] INFO  17:25:36,872 HelpFormatter - Date/Time: 2016/04/14 17:25:36
[2016-04-15T00:25Z] INFO  17:25:36,873 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:25Z] INFO  17:25:36,874 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:25Z] INFO  17:25:36,935 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:25Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-X_128582278_144329181-prep-prealign.bam
[2016-04-15T00:25Z] INFO  17:25:37,139 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:25Z] INFO  17:25:37,326 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:25Z] INFO  17:25:37,337 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:25Z] INFO  17:25:37,362 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@7172f77a
[2016-04-15T00:25Z] GATK RealignerTargetCreator: R14-18106_kapa-NGv3-PE100-NGv3-sort-X_128582278_144329181-prep-prealign.bam X:128582279-144329181
[2016-04-15T00:25Z] INFO  17:25:37,426 ProgressMeter -            done   1.5588729E7    36.0 s       2.0 s      100.0%    36.0 s       0.0 s
[2016-04-15T00:25Z] INFO  17:25:37,426 ProgressMeter - Total runtime 36.12 secs, 0.60 min, 0.01 hours
[2016-04-15T00:25Z] GATK: RealignerTargetCreator
[2016-04-15T00:25Z] INFO  17:25:37,430 MicroScheduler - 115635 reads were filtered out during the traversal out of approximately 1130316 total reads (10.23%)
[2016-04-15T00:25Z] INFO  17:25:37,431 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:25Z] INFO  17:25:37,431 MicroScheduler -   -> 2217 reads (0.20% of total) failing BadMateFilter
[2016-04-15T00:25Z] INFO  17:25:37,431 MicroScheduler -   -> 84628 reads (7.49% of total) failing DuplicateReadFilter
[2016-04-15T00:25Z] INFO  17:25:37,431 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:25Z] INFO  17:25:37,432 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:25Z] INFO  17:25:37,432 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:25Z] INFO  17:25:37,432 MicroScheduler -   -> 28790 reads (2.55% of total) failing MappingQualityZeroFilter
[2016-04-15T00:25Z] INFO  17:25:37,432 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:25Z] INFO  17:25:37,433 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-15T00:25Z] INFO  17:25:37,433 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:25Z] INFO  17:25:37,442 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.10
[2016-04-15T00:25Z] INFO  17:25:37,510 ProgressMeter -            done   1394338.0     3.3 m       2.4 m      100.0%     3.3 m       0.0 s
[2016-04-15T00:25Z] INFO  17:25:37,510 ProgressMeter - Total runtime 198.60 secs, 3.31 min, 0.06 hours
[2016-04-15T00:25Z] INFO  17:25:37,511 MicroScheduler - 657 reads were filtered out during the traversal out of approximately 1394995 total reads (0.05%)
[2016-04-15T00:25Z] INFO  17:25:37,511 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:25Z] INFO  17:25:37,512 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:25Z] INFO  17:25:37,512 MicroScheduler -   -> 657 reads (0.05% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:25Z] INFO  17:25:37,724 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:25Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-X_78616585_95940189-prep.bam
[2016-04-15T00:25Z] INFO  17:25:37,877 IntervalUtils - Processing 15857788 bp from intervals
[2016-04-15T00:25Z] WARN  17:25:37,882 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:25Z] Select unmapped reads
[2016-04-15T00:25Z] INFO  17:25:37,971 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:25Z] INFO  17:25:38,019 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:25Z] INFO  17:25:38,023 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:25Z] INFO  17:25:38,023 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:25Z] INFO  17:25:38,024 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:25Z] INFO  17:25:38,028 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/X/R14-18106_kapa-NGv3-PE100-NGv3-sort-X_111874647_128581278-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/X/tx/tmpLr_65O/R14-18106_kapa-NGv3-PE100-NGv3-sort-X_111874647_128581278-prep-prealign-realign.intervals -l INFO -L X:111874648-128581278 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:25Z] INFO  17:25:38,057 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:25Z] INFO  17:25:38,058 HelpFormatter - Date/Time: 2016/04/14 17:25:38
[2016-04-15T00:25Z] INFO  17:25:38,058 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:25Z] INFO  17:25:38,059 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:25Z] INFO  17:25:38,130 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:25Z] INFO  17:25:38,131 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:25Z] INFO  17:25:38,132 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:25Z] INFO  17:25:38,133 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:25Z] INFO  17:25:38,188 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:25Z] INFO  17:25:38,193 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:25Z] INFO  17:25:38,348 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:25Z] INFO  17:25:38,402 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T00:25Z] INFO  17:25:38,422 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:25Z] INFO  17:25:38,482 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-15T00:25Z] INFO  17:25:38,559 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:25Z] INFO  17:25:38,563 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:25Z] INFO  17:25:38,563 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:25Z] INFO  17:25:38,564 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:25Z] INFO  17:25:38,568 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/Y/R14-18106_kapa-NGv3-PE100-NGv3-sort-Y_59228291_59373566-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/Y/tx/tmpRYFiZd/R14-18106_kapa-NGv3-PE100-NGv3-sort-Y_59228291_59373566-prep-prealign-realign.intervals -l INFO -L Y:59228292-59373566 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:25Z] INFO  17:25:38,576 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:25Z] INFO  17:25:38,583 HelpFormatter - Date/Time: 2016/04/14 17:25:38
[2016-04-15T00:25Z] INFO  17:25:38,583 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:25Z] INFO  17:25:38,584 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:25Z] INFO  17:25:38,706 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:25Z] INFO  17:25:38,734 IntervalUtils - Processing 16706631 bp from intervals
[2016-04-15T00:25Z] WARN  17:25:38,739 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:25Z] INFO  17:25:38,825 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:25Z] INFO  17:25:38,849 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:25Z] GATK: realign ('19', 31038849, 46627578) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:25Z] INFO  17:25:38,894 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T00:25Z] INFO  17:25:38,905 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:25Z] INFO  17:25:38,958 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-15T00:25Z] INFO  17:25:39,007 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:25Z] INFO  17:25:39,028 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:25Z] INFO  17:25:39,029 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:25Z] INFO  17:25:39,030 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:25Z] INFO  17:25:39,030 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:25Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-19_0_15509577-prep-prealign.bam
[2016-04-15T00:25Z] INFO  17:25:39,251 IntervalUtils - Processing 145275 bp from intervals
[2016-04-15T00:25Z] WARN  17:25:39,256 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:25Z] INFO  17:25:39,325 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:25Z] INFO  17:25:39,363 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:25Z] INFO  17:25:39,369 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:25Z] INFO  17:25:39,370 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:25Z] INFO  17:25:39,371 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:25Z] INFO  17:25:40,107 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:25Z] INFO  17:25:40,111 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:25Z] INFO  17:25:40,111 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:25Z] INFO  17:25:40,112 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:25Z] INFO  17:25:40,116 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/X/R14-18106_kapa-NGv3-PE100-NGv3-sort-X_128582278_144329181-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/X/tx/tmpwrlzZm/R14-18106_kapa-NGv3-PE100-NGv3-sort-X_128582278_144329181-prep-prealign-realign.intervals -l INFO -L X:128582279-144329181 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:25Z] INFO  17:25:40,125 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:25Z] INFO  17:25:40,126 HelpFormatter - Date/Time: 2016/04/14 17:25:40
[2016-04-15T00:25Z] INFO  17:25:40,126 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:25Z] INFO  17:25:40,132 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:25Z] INFO  17:25:40,258 ProgressMeter -            done    145275.0     0.0 s       6.0 s       99.9%     0.0 s       0.0 s
[2016-04-15T00:25Z] INFO  17:25:40,259 ProgressMeter - Total runtime 0.89 secs, 0.01 min, 0.00 hours
[2016-04-15T00:25Z] INFO  17:25:40,296 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:25Z] INFO  17:25:40,365 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@41fd9d8e
[2016-04-15T00:25Z] INFO  17:25:40,425 ProgressMeter -            done    741668.0    85.0 s     114.0 s      100.0%    85.0 s       0.0 s
[2016-04-15T00:25Z] INFO  17:25:40,425 ProgressMeter - Total runtime 85.26 secs, 1.42 min, 0.02 hours
[2016-04-15T00:25Z] INFO  17:25:40,426 MicroScheduler - 334 reads were filtered out during the traversal out of approximately 742002 total reads (0.05%)
[2016-04-15T00:25Z] INFO  17:25:40,426 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:25Z] INFO  17:25:40,426 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:25Z] INFO  17:25:40,430 MicroScheduler -   -> 334 reads (0.05% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:25Z] INFO  17:25:40,517 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T00:25Z] INFO  17:25:40,528 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:25Z] INFO  17:25:40,569 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.04
[2016-04-15T00:25Z] INFO  17:25:40,865 IntervalUtils - Processing 15746903 bp from intervals
[2016-04-15T00:25Z] WARN  17:25:40,870 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:25Z] INFO  17:25:40,954 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:25Z] INFO  17:25:41,134 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:25Z] INFO  17:25:41,135 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:25Z] INFO  17:25:41,136 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:25Z] INFO  17:25:41,136 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:25Z] INFO  17:25:41,488 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:25Z] GATK: realign ('Y', 59228291, 59373566) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:25Z] INFO  17:25:41,823 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@41fd9d8e
[2016-04-15T00:25Z] INFO  17:25:41,904 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:25Z] INFO  17:25:41,924 ProgressMeter -            done   1242372.0     2.9 m       2.3 m       99.6%     2.9 m       0.0 s
[2016-04-15T00:25Z] INFO  17:25:41,925 ProgressMeter - Total runtime 173.68 secs, 2.89 min, 0.05 hours
[2016-04-15T00:25Z] INFO  17:25:41,925 MicroScheduler - 512 reads were filtered out during the traversal out of approximately 1242884 total reads (0.04%)
[2016-04-15T00:25Z] INFO  17:25:41,926 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:25Z] INFO  17:25:41,926 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:25Z] INFO  17:25:41,927 MicroScheduler -   -> 512 reads (0.04% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:25Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-22_16266928_31795711-prep-prealign.bam
[2016-04-15T00:25Z] INFO  17:25:41,940 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:25Z] INFO  17:25:41,944 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:25Z] INFO  17:25:41,945 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:25Z] INFO  17:25:41,945 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:25Z] INFO  17:25:41,950 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/19/R14-18106_kapa-NGv3-PE100-NGv3-sort-19_31038849_46627578-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/19/R14-18106_kapa-NGv3-PE100-NGv3-sort-19_31038849_46627578-prep-prealign-realign.intervals -L 19:31038850-46627578 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/19/tx/tmp1YIpA0/R14-18106_kapa-NGv3-PE100-NGv3-sort-19_31038849_46627578-prep.bam
[2016-04-15T00:25Z] INFO  17:25:41,960 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:25Z] INFO  17:25:41,961 HelpFormatter - Date/Time: 2016/04/14 17:25:41
[2016-04-15T00:25Z] INFO  17:25:41,961 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:25Z] INFO  17:25:41,961 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:25Z] INFO  17:25:42,292 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:25Z] INFO  17:25:42,409 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:25Z] INFO  17:25:42,420 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:25Z] INFO  17:25:42,486 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-15T00:25Z] INFO  17:25:42,793 ProgressMeter -            done   1.5708133E7    16.0 s       1.0 s      100.0%    16.0 s       0.0 s
[2016-04-15T00:25Z] INFO  17:25:42,794 ProgressMeter - Total runtime 16.30 secs, 0.27 min, 0.00 hours
[2016-04-15T00:25Z] INFO  17:25:42,798 MicroScheduler - 23281 reads were filtered out during the traversal out of approximately 145912 total reads (15.96%)
[2016-04-15T00:25Z] INFO  17:25:42,810 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:25Z] INFO  17:25:42,811 MicroScheduler -   -> 356 reads (0.24% of total) failing BadMateFilter
[2016-04-15T00:25Z] INFO  17:25:42,811 MicroScheduler -   -> 9599 reads (6.58% of total) failing DuplicateReadFilter
[2016-04-15T00:25Z] INFO  17:25:42,812 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:25Z] INFO  17:25:42,813 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:25Z] INFO  17:25:42,814 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:25Z] INFO  17:25:42,814 MicroScheduler -   -> 13326 reads (9.13% of total) failing MappingQualityZeroFilter
[2016-04-15T00:25Z] INFO  17:25:42,815 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:25Z] INFO  17:25:42,816 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-15T00:25Z] INFO  17:25:42,817 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:25Z] GATK RealignerTargetCreator: R14-18106_kapa-NGv3-PE100-NGv3-sort-19_0_15509577-prep-prealign.bam 19:1-15509577
[2016-04-15T00:25Z] GATK: RealignerTargetCreator
[2016-04-15T00:25Z] INFO  17:25:42,873 IntervalUtils - Processing 15588729 bp from intervals
[2016-04-15T00:25Z] WARN  17:25:42,879 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:25Z] INFO  17:25:43,022 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:25Z] INFO  17:25:43,196 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:25Z] INFO  17:25:43,198 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:25Z] INFO  17:25:43,199 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:25Z] INFO  17:25:43,200 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:25Z] INFO  17:25:43,432 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:25Z] INFO  17:25:43,561 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:25Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-19_46627881_59128983-prep-prealign.bam
[2016-04-15T00:25Z] INFO  17:25:43,691 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:25Z] GATK RealignerTargetCreator: R14-18106_kapa-NGv3-PE100-NGv3-sort-22_16266928_31795711-prep-prealign.bam 22:16266929-31795711
[2016-04-15T00:25Z] GATK: RealignerTargetCreator
[2016-04-15T00:25Z] INFO  17:25:44,438 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:25Z] INFO  17:25:44,440 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:25Z] INFO  17:25:44,441 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:25Z] INFO  17:25:44,441 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:25Z] INFO  17:25:44,445 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/Y/R14-18106_kapa-NGv3-PE100-NGv3-sort-Y_59228291_59373566-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/Y/R14-18106_kapa-NGv3-PE100-NGv3-sort-Y_59228291_59373566-prep-prealign-realign.intervals -L Y:59228292-59373566 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/Y/tx/tmpvLDG3w/R14-18106_kapa-NGv3-PE100-NGv3-sort-Y_59228291_59373566-prep.bam
[2016-04-15T00:25Z] INFO  17:25:44,454 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:25Z] INFO  17:25:44,454 HelpFormatter - Date/Time: 2016/04/14 17:25:44
[2016-04-15T00:25Z] INFO  17:25:44,454 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:25Z] INFO  17:25:44,454 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:25Z] INFO  17:25:44,689 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:25Z] INFO  17:25:44,816 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:25Z] INFO  17:25:44,843 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:25Z] INFO  17:25:44,852 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:25Z] GATK: realign ('X', 95990756, 111698889) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:25Z] INFO  17:25:44,890 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@7172f77a
[2016-04-15T00:25Z] INFO  17:25:44,916 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-15T00:25Z] INFO  17:25:45,001 ProgressMeter -            done    627612.0    87.0 s       2.3 m      100.0%    87.0 s       0.0 s
[2016-04-15T00:25Z] INFO  17:25:45,002 ProgressMeter - Total runtime 87.19 secs, 1.45 min, 0.02 hours
[2016-04-15T00:25Z] INFO  17:25:45,002 MicroScheduler - 301 reads were filtered out during the traversal out of approximately 627913 total reads (0.05%)
[2016-04-15T00:25Z] INFO  17:25:45,003 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:25Z] INFO  17:25:45,003 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:25Z] INFO  17:25:45,003 MicroScheduler -   -> 301 reads (0.05% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:25Z] INFO  17:25:45,319 IntervalUtils - Processing 145275 bp from intervals
[2016-04-15T00:25Z] WARN  17:25:45,324 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:25Z] INFO  17:25:45,435 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:25Z] INFO  17:25:45,456 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:25Z] INFO  17:25:45,457 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:25Z] INFO  17:25:45,458 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:25Z] INFO  17:25:45,459 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:25Z] INFO  17:25:45,501 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:25Z] INFO  17:25:45,502 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:25Z] INFO  17:25:45,581 ProgressMeter -            done         0.0     0.0 s      34.2 h      100.0%     0.0 s       0.0 s
[2016-04-15T00:25Z] INFO  17:25:45,582 ProgressMeter - Total runtime 0.12 secs, 0.00 min, 0.00 hours
[2016-04-15T00:25Z] INFO  17:25:45,848 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:25Z] INFO  17:25:45,851 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:25Z] INFO  17:25:45,851 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:25Z] INFO  17:25:45,852 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:25Z] INFO  17:25:45,857 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/19/R14-18106_kapa-NGv3-PE100-NGv3-sort-19_0_15509577-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/19/tx/tmppB_7Xc/R14-18106_kapa-NGv3-PE100-NGv3-sort-19_0_15509577-prep-prealign-realign.intervals -l INFO -L 19:1-15509577 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:25Z] INFO  17:25:45,873 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:25Z] INFO  17:25:45,874 HelpFormatter - Date/Time: 2016/04/14 17:25:45
[2016-04-15T00:25Z] INFO  17:25:45,875 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:25Z] INFO  17:25:45,875 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:25Z] INFO  17:25:46,018 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:25Z] INFO  17:25:46,286 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T00:25Z] INFO  17:25:46,329 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:25Z] INFO  17:25:46,373 ProgressMeter -            done    148927.0    11.0 s      79.0 s      100.0%    11.0 s       0.0 s
[2016-04-15T00:25Z] INFO  17:25:46,374 ProgressMeter - Total runtime 11.83 secs, 0.20 min, 0.00 hours
[2016-04-15T00:25Z] INFO  17:25:46,379 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 148927 total reads (0.00%)
[2016-04-15T00:25Z] INFO  17:25:46,382 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-15T00:25Z] INFO  17:25:46,390 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:25Z] INFO  17:25:46,392 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:25Z] INFO  17:25:46,392 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:25Z] INFO  17:25:46,545 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:25Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-22_31796605_47308085-prep-prealign.bam
[2016-04-15T00:25Z] INFO  17:25:46,759 IntervalUtils - Processing 15509577 bp from intervals
[2016-04-15T00:25Z] WARN  17:25:46,769 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:25Z] INFO  17:25:46,947 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:25Z] INFO  17:25:46,949 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:25Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-Y_59228291_59373566-prep.bam
[2016-04-15T00:25Z] Select unanalyzed reads
[2016-04-15T00:25Z] INFO  17:25:47,082 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:25Z] INFO  17:25:47,083 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:25Z] INFO  17:25:47,084 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:25Z] INFO  17:25:47,085 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:25Z] INFO  17:25:47,098 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:25Z] INFO  17:25:47,101 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:25Z] INFO  17:25:47,101 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:25Z] INFO  17:25:47,101 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:25Z] INFO  17:25:47,105 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/22/R14-18106_kapa-NGv3-PE100-NGv3-sort-22_16266928_31795711-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/22/tx/tmpHwq3We/R14-18106_kapa-NGv3-PE100-NGv3-sort-22_16266928_31795711-prep-prealign-realign.intervals -l INFO -L 22:16266929-31795711 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:25Z] INFO  17:25:47,114 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:25Z] INFO  17:25:47,115 HelpFormatter - Date/Time: 2016/04/14 17:25:47
[2016-04-15T00:25Z] INFO  17:25:47,121 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:25Z] INFO  17:25:47,122 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:25Z] GATK RealignerTargetCreator: R14-18106_kapa-NGv3-PE100-NGv3-sort-19_46627881_59128983-prep-prealign.bam 19:46627882-59128983
[2016-04-15T00:25Z] GATK: RealignerTargetCreator
[2016-04-15T00:25Z] INFO  17:25:47,232 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:25Z] INFO  17:25:47,436 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T00:25Z] INFO  17:25:47,445 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:25Z] INFO  17:25:47,512 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-15T00:25Z] INFO  17:25:47,601 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:25Z] INFO  17:25:47,605 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:25Z] INFO  17:25:47,605 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:25Z] INFO  17:25:47,606 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:25Z] INFO  17:25:47,610 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/X/R14-18106_kapa-NGv3-PE100-NGv3-sort-X_95990756_111698889-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/X/R14-18106_kapa-NGv3-PE100-NGv3-sort-X_95990756_111698889-prep-prealign-realign.intervals -L X:95990757-111698889 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/X/tx/tmp2xz6ss/R14-18106_kapa-NGv3-PE100-NGv3-sort-X_95990756_111698889-prep.bam
[2016-04-15T00:25Z] INFO  17:25:47,626 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:25Z] INFO  17:25:47,642 HelpFormatter - Date/Time: 2016/04/14 17:25:47
[2016-04-15T00:25Z] INFO  17:25:47,642 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:25Z] INFO  17:25:47,643 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:25Z] INFO  17:25:47,794 IntervalUtils - Processing 15528783 bp from intervals
[2016-04-15T00:25Z] WARN  17:25:47,800 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:25Z] INFO  17:25:47,896 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:25Z] INFO  17:25:47,931 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:25Z] INFO  17:25:47,987 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:25Z] INFO  17:25:47,998 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:25Z] INFO  17:25:48,047 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-15T00:25Z] INFO  17:25:48,104 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:25Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-X_62857907_78427545-prep.bam
[2016-04-15T00:25Z] INFO  17:25:48,263 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:25Z] INFO  17:25:48,263 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:25Z] INFO  17:25:48,264 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:25Z] INFO  17:25:48,264 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:25Z] INFO  17:25:48,419 IntervalUtils - Processing 15708133 bp from intervals
[2016-04-15T00:25Z] WARN  17:25:48,433 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:25Z] INFO  17:25:48,561 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:25Z] INFO  17:25:48,671 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:25Z] INFO  17:25:48,678 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:25Z] INFO  17:25:48,679 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:25Z] INFO  17:25:48,680 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:25Z] GATK RealignerTargetCreator: R14-18106_kapa-NGv3-PE100-NGv3-sort-22_31796605_47308085-prep-prealign.bam 22:31796606-47308085
[2016-04-15T00:25Z] GATK: RealignerTargetCreator
[2016-04-15T00:25Z] INFO  17:25:48,783 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:25Z] INFO  17:25:48,986 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@7172f77a
[2016-04-15T00:25Z] INFO  17:25:48,989 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:25Z] INFO  17:25:49,069 ProgressMeter -            done    438789.0    29.0 s      66.0 s      100.0%    29.0 s       0.0 s
[2016-04-15T00:25Z] INFO  17:25:49,070 ProgressMeter - Total runtime 29.34 secs, 0.49 min, 0.01 hours
[2016-04-15T00:25Z] INFO  17:25:49,075 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 438789 total reads (0.00%)
[2016-04-15T00:25Z] INFO  17:25:49,076 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:25Z] INFO  17:25:49,076 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:25Z] INFO  17:25:49,077 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:25Z] INFO  17:25:49,116 ProgressMeter -            done     99060.0    15.0 s       2.6 m       99.5%    15.0 s       0.0 s
[2016-04-15T00:25Z] INFO  17:25:49,118 ProgressMeter - Total runtime 15.30 secs, 0.26 min, 0.00 hours
[2016-04-15T00:25Z] INFO  17:25:49,125 MicroScheduler - 189 reads were filtered out during the traversal out of approximately 99249 total reads (0.19%)
[2016-04-15T00:25Z] INFO  17:25:49,126 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:25Z] INFO  17:25:49,127 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:25Z] INFO  17:25:49,128 MicroScheduler -   -> 189 reads (0.19% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:25Z] INFO  17:25:50,143 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:25Z] INFO  17:25:50,147 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:25Z] INFO  17:25:50,147 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:25Z] INFO  17:25:50,148 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:25Z] INFO  17:25:50,173 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/19/R14-18106_kapa-NGv3-PE100-NGv3-sort-19_46627881_59128983-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/19/tx/tmpiLqsbz/R14-18106_kapa-NGv3-PE100-NGv3-sort-19_46627881_59128983-prep-prealign-realign.intervals -l INFO -L 19:46627882-59128983 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:25Z] INFO  17:25:50,193 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:25Z] INFO  17:25:50,194 HelpFormatter - Date/Time: 2016/04/14 17:25:50
[2016-04-15T00:25Z] INFO  17:25:50,194 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:25Z] INFO  17:25:50,194 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:25Z] INFO  17:25:50,312 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:25Z] INFO  17:25:50,503 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:25Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-Y_15526614_59222281-prep-prealign.bam
[2016-04-15T00:25Z] INFO  17:25:50,539 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T00:25Z] INFO  17:25:50,566 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:25Z] INFO  17:25:50,619 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-15T00:25Z] GATK RealignerTargetCreator: R14-18106_kapa-NGv3-PE100-NGv3-sort-Y_15526614_59222281-prep-prealign.bam Y:15526615-59222281
[2016-04-15T00:25Z] GATK: RealignerTargetCreator
[2016-04-15T00:25Z] INFO  17:25:50,915 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:25Z] INFO  17:25:50,922 IntervalUtils - Processing 12501102 bp from intervals
[2016-04-15T00:25Z] WARN  17:25:50,927 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:25Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-21_31062047_46591599-prep.bam
[2016-04-15T00:25Z] INFO  17:25:50,998 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:25Z] INFO  17:25:51,200 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:25Z] INFO  17:25:51,201 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:25Z] INFO  17:25:51,202 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:25Z] INFO  17:25:51,202 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:25Z] INFO  17:25:51,671 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:25Z] INFO  17:25:51,675 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:25Z] INFO  17:25:51,675 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:25Z] INFO  17:25:51,676 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:25Z] INFO  17:25:51,682 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/22/R14-18106_kapa-NGv3-PE100-NGv3-sort-22_31796605_47308085-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/22/tx/tmpl2UhJ7/R14-18106_kapa-NGv3-PE100-NGv3-sort-22_31796605_47308085-prep-prealign-realign.intervals -l INFO -L 22:31796606-47308085 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:25Z] INFO  17:25:51,696 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:25Z] INFO  17:25:51,707 HelpFormatter - Date/Time: 2016/04/14 17:25:51
[2016-04-15T00:25Z] INFO  17:25:51,708 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:25Z] INFO  17:25:51,709 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:25Z] INFO  17:25:51,837 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:25Z] INFO  17:25:52,144 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T00:25Z] INFO  17:25:52,167 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:25Z] INFO  17:25:52,269 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.10
[2016-04-15T00:25Z] INFO  17:25:52,617 IntervalUtils - Processing 15511480 bp from intervals
[2016-04-15T00:25Z] WARN  17:25:52,623 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:25Z] INFO  17:25:52,705 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:25Z] INFO  17:25:52,930 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:25Z] INFO  17:25:52,931 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:25Z] INFO  17:25:52,931 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:25Z] INFO  17:25:52,931 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:25Z] INFO  17:25:52,944 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@41fd9d8e
[2016-04-15T00:25Z] INFO  17:25:53,009 ProgressMeter -            done    138037.0    23.0 s       2.8 m      100.0%    23.0 s       0.0 s
[2016-04-15T00:25Z] INFO  17:25:53,010 ProgressMeter - Total runtime 23.54 secs, 0.39 min, 0.01 hours
[2016-04-15T00:25Z] INFO  17:25:53,010 MicroScheduler - 237 reads were filtered out during the traversal out of approximately 138274 total reads (0.17%)
[2016-04-15T00:25Z] INFO  17:25:53,011 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:25Z] INFO  17:25:53,011 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:25Z] INFO  17:25:53,011 MicroScheduler -   -> 237 reads (0.17% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:25Z] INFO  17:25:53,272 ProgressMeter -     X:155252728    100001.0    30.0 s       5.0 m       99.8%    30.0 s       0.0 s
[2016-04-15T00:25Z] INFO  17:25:53,383 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:25Z] INFO  17:25:53,386 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:25Z] INFO  17:25:53,387 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:25Z] INFO  17:25:53,387 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:25Z] INFO  17:25:53,392 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/Y/R14-18106_kapa-NGv3-PE100-NGv3-sort-Y_15526614_59222281-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/Y/tx/tmp26egJ8/R14-18106_kapa-NGv3-PE100-NGv3-sort-Y_15526614_59222281-prep-prealign-realign.intervals -l INFO -L Y:15526615-59222281 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:25Z] INFO  17:25:53,401 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:25Z] INFO  17:25:53,402 HelpFormatter - Date/Time: 2016/04/14 17:25:53
[2016-04-15T00:25Z] INFO  17:25:53,402 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:25Z] INFO  17:25:53,403 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:25Z] INFO  17:25:53,489 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:25Z] INFO  17:25:53,566 Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.gatk.engine.io.stubs.SAMFileWriterStub@7172f77a
[2016-04-15T00:25Z] INFO  17:25:53,748 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T00:25Z] INFO  17:25:53,749 ProgressMeter -            done    186116.0    30.0 s       2.7 m       99.9%    30.0 s       0.0 s
[2016-04-15T00:25Z] INFO  17:25:53,750 ProgressMeter - Total runtime 30.51 secs, 0.51 min, 0.01 hours
[2016-04-15T00:25Z] INFO  17:25:53,751 MicroScheduler - 144 reads were filtered out during the traversal out of approximately 186260 total reads (0.08%)
[2016-04-15T00:25Z] INFO  17:25:53,752 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:25Z] INFO  17:25:53,753 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:25Z] INFO  17:25:53,753 MicroScheduler -   -> 144 reads (0.08% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:25Z] INFO  17:25:53,759 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:25Z] INFO  17:25:53,836 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-15T00:25Z] INFO  17:25:54,268 IntervalUtils - Processing 43695667 bp from intervals
[2016-04-15T00:25Z] WARN  17:25:54,274 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:25Z] INFO  17:25:54,414 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:25Z] INFO  17:25:54,422 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:25Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-Y_0_15522993-prep-prealign.bam
[2016-04-15T00:25Z] INFO  17:25:54,644 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:25Z] INFO  17:25:54,645 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:25Z] INFO  17:25:54,645 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:25Z] INFO  17:25:54,645 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:25Z] INFO  17:25:54,757 ProgressMeter -            done   1.6706631E7    15.0 s       0.0 s      100.0%    15.0 s       0.0 s
[2016-04-15T00:25Z] INFO  17:25:54,758 ProgressMeter - Total runtime 15.73 secs, 0.26 min, 0.00 hours
[2016-04-15T00:25Z] INFO  17:25:54,762 MicroScheduler - 29977 reads were filtered out during the traversal out of approximately 102171 total reads (29.34%)
[2016-04-15T00:25Z] INFO  17:25:54,762 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:25Z] INFO  17:25:54,763 MicroScheduler -   -> 329 reads (0.32% of total) failing BadMateFilter
[2016-04-15T00:25Z] INFO  17:25:54,763 MicroScheduler -   -> 5796 reads (5.67% of total) failing DuplicateReadFilter
[2016-04-15T00:25Z] INFO  17:25:54,763 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:25Z] INFO  17:25:54,764 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:25Z] INFO  17:25:54,764 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:25Z] INFO  17:25:54,766 MicroScheduler -   -> 23852 reads (23.35% of total) failing MappingQualityZeroFilter
[2016-04-15T00:25Z] INFO  17:25:54,766 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:25Z] INFO  17:25:54,766 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-15T00:25Z] INFO  17:25:54,767 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:25Z] GATK RealignerTargetCreator: R14-18106_kapa-NGv3-PE100-NGv3-sort-Y_0_15522993-prep-prealign.bam Y:1-15522993
[2016-04-15T00:25Z] GATK: RealignerTargetCreator
[2016-04-15T00:25Z] INFO  17:25:55,096 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:25Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-X_144337190_155270560-prep-prealign.bam
[2016-04-15T00:25Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-noanalysis-prep.bam
[2016-04-15T00:25Z] GATK RealignerTargetCreator: R14-18106_kapa-NGv3-PE100-NGv3-sort-X_144337190_155270560-prep-prealign.bam X:144337191-155270560
[2016-04-15T00:25Z] GATK: RealignerTargetCreator
[2016-04-15T00:25Z] INFO  17:25:56,198 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:25Z] GATK: realign ('X', 111874647, 128581278) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:25Z] INFO  17:25:56,553 ProgressMeter -            done   1.5746903E7    15.0 s       0.0 s      100.0%    15.0 s       0.0 s
[2016-04-15T00:25Z] INFO  17:25:56,554 ProgressMeter - Total runtime 15.42 secs, 0.26 min, 0.00 hours
[2016-04-15T00:25Z] INFO  17:25:56,558 MicroScheduler - 21480 reads were filtered out during the traversal out of approximately 112345 total reads (19.12%)
[2016-04-15T00:25Z] INFO  17:25:56,559 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:25Z] INFO  17:25:56,560 MicroScheduler -   -> 366 reads (0.33% of total) failing BadMateFilter
[2016-04-15T00:25Z] INFO  17:25:56,560 MicroScheduler -   -> 7395 reads (6.58% of total) failing DuplicateReadFilter
[2016-04-15T00:25Z] INFO  17:25:56,560 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:25Z] INFO  17:25:56,561 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:25Z] INFO  17:25:56,561 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:25Z] INFO  17:25:56,561 MicroScheduler -   -> 13719 reads (12.21% of total) failing MappingQualityZeroFilter
[2016-04-15T00:25Z] INFO  17:25:56,561 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:25Z] INFO  17:25:56,562 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-15T00:25Z] INFO  17:25:56,562 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:25Z] INFO  17:25:57,505 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:25Z] INFO  17:25:57,530 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:25Z] INFO  17:25:57,531 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:25Z] INFO  17:25:57,532 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:25Z] INFO  17:25:57,537 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/Y/R14-18106_kapa-NGv3-PE100-NGv3-sort-Y_0_15522993-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/Y/tx/tmpYXMvkl/R14-18106_kapa-NGv3-PE100-NGv3-sort-Y_0_15522993-prep-prealign-realign.intervals -l INFO -L Y:1-15522993 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:25Z] INFO  17:25:57,548 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:25Z] INFO  17:25:57,549 HelpFormatter - Date/Time: 2016/04/14 17:25:57
[2016-04-15T00:25Z] INFO  17:25:57,550 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:25Z] INFO  17:25:57,551 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:25Z] INFO  17:25:57,669 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:25Z] INFO  17:25:57,845 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T00:25Z] INFO  17:25:57,856 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:25Z] INFO  17:25:57,904 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-15T00:25Z] INFO  17:25:57,907 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:25Z] GATK: realign ('X', 128582278, 144329181) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:25Z] INFO  17:25:58,218 ProgressMeter -            done    297529.0    20.0 s      67.0 s      100.0%    20.0 s       0.0 s
[2016-04-15T00:25Z] INFO  17:25:58,219 ProgressMeter - Total runtime 20.09 secs, 0.33 min, 0.01 hours
[2016-04-15T00:25Z] INFO  17:25:58,223 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 297529 total reads (0.00%)
[2016-04-15T00:25Z] INFO  17:25:58,223 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:25Z] INFO  17:25:58,224 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:25Z] INFO  17:25:58,225 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:25Z] INFO  17:25:58,245 IntervalUtils - Processing 15522993 bp from intervals
[2016-04-15T00:25Z] WARN  17:25:58,251 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:25Z] INFO  17:25:58,432 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:25Z] INFO  17:25:58,482 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:25Z] INFO  17:25:58,485 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:25Z] INFO  17:25:58,486 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:25Z] INFO  17:25:58,487 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:25Z] INFO  17:25:58,492 HelpFormatter - Program Args: -T RealignerTargetCreator -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/X/R14-18106_kapa-NGv3-PE100-NGv3-sort-X_144337190_155270560-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/X/tx/tmpSj1DpH/R14-18106_kapa-NGv3-PE100-NGv3-sort-X_144337190_155270560-prep-prealign-realign.intervals -l INFO -L X:144337191-155270560 --interval_set_rule INTERSECTION --known /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:25Z] INFO  17:25:58,504 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:25Z] INFO  17:25:58,505 HelpFormatter - Date/Time: 2016/04/14 17:25:58
[2016-04-15T00:25Z] INFO  17:25:58,506 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:25Z] INFO  17:25:58,506 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:25Z] INFO  17:25:58,551 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:25Z] INFO  17:25:58,552 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:25Z] INFO  17:25:58,553 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:25Z] INFO  17:25:58,554 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:25Z] INFO  17:25:58,603 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:25Z] INFO  17:25:58,811 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T00:25Z] INFO  17:25:58,822 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:25Z] INFO  17:25:58,833 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:25Z] INFO  17:25:58,846 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:25Z] INFO  17:25:58,846 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:25Z] INFO  17:25:58,846 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:25Z] INFO  17:25:58,852 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/X/R14-18106_kapa-NGv3-PE100-NGv3-sort-X_111874647_128581278-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/X/R14-18106_kapa-NGv3-PE100-NGv3-sort-X_111874647_128581278-prep-prealign-realign.intervals -L X:111874648-128581278 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/X/tx/tmppJWy6_/R14-18106_kapa-NGv3-PE100-NGv3-sort-X_111874647_128581278-prep.bam
[2016-04-15T00:25Z] INFO  17:25:58,862 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:25Z] INFO  17:25:58,862 HelpFormatter - Date/Time: 2016/04/14 17:25:58
[2016-04-15T00:25Z] INFO  17:25:58,862 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:25Z] INFO  17:25:58,863 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:25Z] INFO  17:25:58,870 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-15T00:25Z] INFO  17:25:59,051 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:25Z] INFO  17:25:59,156 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:25Z] INFO  17:25:59,167 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:25Z] INFO  17:25:59,199 IntervalUtils - Processing 10933370 bp from intervals
[2016-04-15T00:25Z] WARN  17:25:59,205 IndexDictionaryUtils - Track known doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:25Z] INFO  17:25:59,238 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-15T00:25Z] INFO  17:25:59,286 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:25Z] INFO  17:25:59,481 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:25Z] INFO  17:25:59,482 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:25Z] INFO  17:25:59,483 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:25Z] INFO  17:25:59,484 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:25Z] INFO  17:25:59,671 IntervalUtils - Processing 16706631 bp from intervals
[2016-04-15T00:25Z] WARN  17:25:59,677 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:25Z] INFO  17:25:59,757 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:25Z] INFO  17:25:59,760 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:25Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-X_46712910_62570698-prep.bam
[2016-04-15T00:25Z] INFO  17:25:59,846 ProgressMeter -            done    145099.0    11.0 s      76.0 s      100.0%    11.0 s       0.0 s
[2016-04-15T00:25Z] INFO  17:25:59,847 ProgressMeter - Total runtime 11.17 secs, 0.19 min, 0.00 hours
[2016-04-15T00:25Z] INFO  17:25:59,852 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 145099 total reads (0.00%)
[2016-04-15T00:25Z] INFO  17:25:59,853 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:25Z] INFO  17:25:59,854 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:25Z] INFO  17:25:59,855 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:25Z] INFO  17:25:59,883 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:25Z] INFO  17:25:59,884 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:25Z] INFO  17:25:59,885 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:25Z] INFO  17:25:59,890 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:25Z] INFO  17:25:59,963 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:26Z] INFO  17:26:00,119 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:26Z] INFO  17:26:00,571 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:26Z] INFO  17:26:00,574 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:26Z] INFO  17:26:00,575 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:26Z] INFO  17:26:00,575 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:26Z] INFO  17:26:00,580 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/X/R14-18106_kapa-NGv3-PE100-NGv3-sort-X_128582278_144329181-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/X/R14-18106_kapa-NGv3-PE100-NGv3-sort-X_128582278_144329181-prep-prealign-realign.intervals -L X:128582279-144329181 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/X/tx/tmpUCZ3oK/R14-18106_kapa-NGv3-PE100-NGv3-sort-X_128582278_144329181-prep.bam
[2016-04-15T00:26Z] INFO  17:26:00,603 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:26Z] INFO  17:26:00,604 HelpFormatter - Date/Time: 2016/04/14 17:26:00
[2016-04-15T00:26Z] INFO  17:26:00,604 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:26Z] INFO  17:26:00,604 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:26Z] INFO  17:26:00,837 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:26Z] INFO  17:26:00,947 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:26Z] INFO  17:26:00,958 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:26Z] INFO  17:26:01,005 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-15T00:26Z] INFO  17:26:01,406 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:26Z] INFO  17:26:01,413 IntervalUtils - Processing 15746903 bp from intervals
[2016-04-15T00:26Z] WARN  17:26:01,419 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:26Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-X_95990756_111698889-prep.bam
[2016-04-15T00:26Z] INFO  17:26:01,506 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:26Z] INFO  17:26:01,614 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:26Z] INFO  17:26:01,615 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:26Z] INFO  17:26:01,616 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:26Z] INFO  17:26:01,616 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:26Z] INFO  17:26:01,684 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:26Z] INFO  17:26:01,829 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:26Z] INFO  17:26:07,753 ProgressMeter -            done    101409.0     7.0 s      77.0 s      100.0%     7.0 s       0.0 s
[2016-04-15T00:26Z] INFO  17:26:07,754 ProgressMeter - Total runtime 7.87 secs, 0.13 min, 0.00 hours
[2016-04-15T00:26Z] INFO  17:26:07,757 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 101409 total reads (0.00%)
[2016-04-15T00:26Z] INFO  17:26:07,758 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:26Z] INFO  17:26:07,758 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:26Z] INFO  17:26:07,758 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:26Z] INFO  17:26:08,604 ProgressMeter -            done   1.5522993E7    10.0 s       0.0 s      100.0%    10.0 s       0.0 s
[2016-04-15T00:26Z] INFO  17:26:08,604 ProgressMeter - Total runtime 10.05 secs, 0.17 min, 0.00 hours
[2016-04-15T00:26Z] INFO  17:26:08,608 MicroScheduler - 100699 reads were filtered out during the traversal out of approximately 139319 total reads (72.28%)
[2016-04-15T00:26Z] INFO  17:26:08,609 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:26Z] INFO  17:26:08,609 MicroScheduler -   -> 351 reads (0.25% of total) failing BadMateFilter
[2016-04-15T00:26Z] INFO  17:26:08,610 MicroScheduler -   -> 3244 reads (2.33% of total) failing DuplicateReadFilter
[2016-04-15T00:26Z] INFO  17:26:08,610 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:26Z] INFO  17:26:08,610 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:26Z] INFO  17:26:08,610 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:26Z] INFO  17:26:08,611 MicroScheduler -   -> 97104 reads (69.70% of total) failing MappingQualityZeroFilter
[2016-04-15T00:26Z] INFO  17:26:08,611 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:26Z] INFO  17:26:08,611 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-15T00:26Z] INFO  17:26:08,612 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:26Z] INFO  17:26:09,024 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:26Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-X_111874647_128581278-prep.bam
[2016-04-15T00:26Z] INFO  17:26:09,836 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:26Z] GATK: realign ('Y', 0, 15522993) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:26Z] INFO  17:26:10,029 ProgressMeter -            done    110572.0     8.0 s      76.0 s       98.5%     8.0 s       0.0 s
[2016-04-15T00:26Z] INFO  17:26:10,030 ProgressMeter - Total runtime 8.41 secs, 0.14 min, 0.00 hours
[2016-04-15T00:26Z] INFO  17:26:10,034 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 110572 total reads (0.00%)
[2016-04-15T00:26Z] INFO  17:26:10,034 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:26Z] INFO  17:26:10,035 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:26Z] INFO  17:26:10,035 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:26Z] INFO  17:26:11,078 ProgressMeter -            done   1.093337E7    11.0 s       1.0 s      100.0%    11.0 s       0.0 s
[2016-04-15T00:26Z] INFO  17:26:11,078 ProgressMeter - Total runtime 11.60 secs, 0.19 min, 0.00 hours
[2016-04-15T00:26Z] INFO  17:26:11,083 MicroScheduler - 44505 reads were filtered out during the traversal out of approximately 187039 total reads (23.79%)
[2016-04-15T00:26Z] INFO  17:26:11,083 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:26Z] INFO  17:26:11,083 MicroScheduler -   -> 381 reads (0.20% of total) failing BadMateFilter
[2016-04-15T00:26Z] INFO  17:26:11,084 MicroScheduler -   -> 11951 reads (6.39% of total) failing DuplicateReadFilter
[2016-04-15T00:26Z] INFO  17:26:11,084 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:26Z] INFO  17:26:11,084 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:26Z] INFO  17:26:11,085 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:26Z] INFO  17:26:11,085 MicroScheduler -   -> 32173 reads (17.20% of total) failing MappingQualityZeroFilter
[2016-04-15T00:26Z] INFO  17:26:11,085 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:26Z] INFO  17:26:11,086 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-15T00:26Z] INFO  17:26:11,086 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:26Z] INFO  17:26:11,347 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:26Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-X_128582278_144329181-prep.bam
[2016-04-15T00:26Z] INFO  17:26:11,849 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:26Z] INFO  17:26:11,852 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:26Z] INFO  17:26:11,853 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:26Z] INFO  17:26:11,854 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:26Z] INFO  17:26:11,858 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/Y/R14-18106_kapa-NGv3-PE100-NGv3-sort-Y_0_15522993-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/Y/R14-18106_kapa-NGv3-PE100-NGv3-sort-Y_0_15522993-prep-prealign-realign.intervals -L Y:1-15522993 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/Y/tx/tmpMyIur0/R14-18106_kapa-NGv3-PE100-NGv3-sort-Y_0_15522993-prep.bam
[2016-04-15T00:26Z] INFO  17:26:11,868 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:26Z] INFO  17:26:11,869 HelpFormatter - Date/Time: 2016/04/14 17:26:11
[2016-04-15T00:26Z] INFO  17:26:11,870 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:26Z] INFO  17:26:11,871 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:26Z] INFO  17:26:12,046 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:26Z] INFO  17:26:12,138 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:26Z] INFO  17:26:12,143 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:26Z] INFO  17:26:12,148 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:26Z] GATK: realign ('X', 144337190, 155270560) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:26Z] INFO  17:26:12,195 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-15T00:26Z] INFO  17:26:12,508 IntervalUtils - Processing 15522993 bp from intervals
[2016-04-15T00:26Z] WARN  17:26:12,512 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:26Z] INFO  17:26:12,576 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:26Z] INFO  17:26:12,646 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:26Z] INFO  17:26:12,647 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:26Z] INFO  17:26:12,647 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:26Z] INFO  17:26:12,647 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:26Z] INFO  17:26:12,674 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:26Z] INFO  17:26:12,767 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:26Z] INFO  17:26:13,218 ProgressMeter -     19:39401410    400009.0    30.0 s      75.0 s       53.6%    55.0 s      25.0 s
[2016-04-15T00:26Z] INFO  17:26:13,965 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:26Z] INFO  17:26:13,968 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:26Z] INFO  17:26:13,968 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:26Z] INFO  17:26:13,968 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:26Z] INFO  17:26:13,973 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/X/R14-18106_kapa-NGv3-PE100-NGv3-sort-X_144337190_155270560-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/X/R14-18106_kapa-NGv3-PE100-NGv3-sort-X_144337190_155270560-prep-prealign-realign.intervals -L X:144337191-155270560 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/X/tx/tmpdXGIW2/R14-18106_kapa-NGv3-PE100-NGv3-sort-X_144337190_155270560-prep.bam
[2016-04-15T00:26Z] INFO  17:26:13,982 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:26Z] INFO  17:26:13,983 HelpFormatter - Date/Time: 2016/04/14 17:26:13
[2016-04-15T00:26Z] INFO  17:26:13,984 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:26Z] INFO  17:26:13,985 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:26Z] INFO  17:26:14,144 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:26Z] INFO  17:26:14,223 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:26Z] INFO  17:26:14,231 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:26Z] INFO  17:26:14,270 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.04
[2016-04-15T00:26Z] INFO  17:26:14,355 ProgressMeter -            done   1.5528783E7    26.0 s       1.0 s      100.0%    26.0 s       0.0 s
[2016-04-15T00:26Z] INFO  17:26:14,356 ProgressMeter - Total runtime 26.09 secs, 0.43 min, 0.01 hours
[2016-04-15T00:26Z] INFO  17:26:14,359 MicroScheduler - 146945 reads were filtered out during the traversal out of approximately 745892 total reads (19.70%)
[2016-04-15T00:26Z] INFO  17:26:14,360 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:26Z] INFO  17:26:14,360 MicroScheduler -   -> 1466 reads (0.20% of total) failing BadMateFilter
[2016-04-15T00:26Z] INFO  17:26:14,360 MicroScheduler -   -> 50272 reads (6.74% of total) failing DuplicateReadFilter
[2016-04-15T00:26Z] INFO  17:26:14,360 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:26Z] INFO  17:26:14,361 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:26Z] INFO  17:26:14,361 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:26Z] INFO  17:26:14,361 MicroScheduler -   -> 95207 reads (12.76% of total) failing MappingQualityZeroFilter
[2016-04-15T00:26Z] INFO  17:26:14,361 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:26Z] INFO  17:26:14,362 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-15T00:26Z] INFO  17:26:14,362 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:26Z] INFO  17:26:14,567 IntervalUtils - Processing 10933370 bp from intervals
[2016-04-15T00:26Z] WARN  17:26:14,572 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:26Z] INFO  17:26:14,647 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:26Z] INFO  17:26:14,730 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:26Z] INFO  17:26:14,731 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:26Z] INFO  17:26:14,731 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:26Z] INFO  17:26:14,732 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:26Z] INFO  17:26:14,785 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:26Z] INFO  17:26:14,894 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:26Z] INFO  17:26:15,403 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:26Z] GATK: realign ('22', 16266928, 31795711) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:26Z] INFO  17:26:16,712 ProgressMeter -            done   1.551148E7    23.0 s       1.0 s      100.0%    23.0 s       0.0 s
[2016-04-15T00:26Z] INFO  17:26:16,712 ProgressMeter - Total runtime 23.78 secs, 0.40 min, 0.01 hours
[2016-04-15T00:26Z] INFO  17:26:16,717 MicroScheduler - 54954 reads were filtered out during the traversal out of approximately 630913 total reads (8.71%)
[2016-04-15T00:26Z] INFO  17:26:16,717 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:26Z] INFO  17:26:16,717 MicroScheduler -   -> 1376 reads (0.22% of total) failing BadMateFilter
[2016-04-15T00:26Z] INFO  17:26:16,718 MicroScheduler -   -> 47870 reads (7.59% of total) failing DuplicateReadFilter
[2016-04-15T00:26Z] INFO  17:26:16,718 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:26Z] INFO  17:26:16,718 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:26Z] INFO  17:26:16,719 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:26Z] INFO  17:26:16,719 MicroScheduler -   -> 5708 reads (0.90% of total) failing MappingQualityZeroFilter
[2016-04-15T00:26Z] INFO  17:26:16,719 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:26Z] INFO  17:26:16,719 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-15T00:26Z] INFO  17:26:16,720 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:26Z] INFO  17:26:17,091 ProgressMeter -     19:11475201   1.14688E7    30.0 s       2.0 s       74.0%    40.0 s      10.0 s
[2016-04-15T00:26Z] INFO  17:26:17,368 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:26Z] INFO  17:26:17,371 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:26Z] INFO  17:26:17,371 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:26Z] INFO  17:26:17,371 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:26Z] INFO  17:26:17,376 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/22/R14-18106_kapa-NGv3-PE100-NGv3-sort-22_16266928_31795711-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/22/R14-18106_kapa-NGv3-PE100-NGv3-sort-22_16266928_31795711-prep-prealign-realign.intervals -L 22:16266929-31795711 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/22/tx/tmplQlC70/R14-18106_kapa-NGv3-PE100-NGv3-sort-22_16266928_31795711-prep.bam
[2016-04-15T00:26Z] INFO  17:26:17,385 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:26Z] INFO  17:26:17,386 HelpFormatter - Date/Time: 2016/04/14 17:26:17
[2016-04-15T00:26Z] INFO  17:26:17,386 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:26Z] INFO  17:26:17,386 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:26Z] INFO  17:26:17,564 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:26Z] INFO  17:26:17,654 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:26Z] INFO  17:26:17,664 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:26Z] INFO  17:26:17,710 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.04
[2016-04-15T00:26Z] INFO  17:26:17,894 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:26Z] GATK: realign ('22', 31796605, 47308085) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:26Z] INFO  17:26:18,027 IntervalUtils - Processing 15528783 bp from intervals
[2016-04-15T00:26Z] WARN  17:26:18,032 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:26Z] INFO  17:26:18,108 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:26Z] INFO  17:26:18,225 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:26Z] INFO  17:26:18,226 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:26Z] INFO  17:26:18,226 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:26Z] INFO  17:26:18,226 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:26Z] INFO  17:26:18,379 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:26Z] INFO  17:26:18,388 ProgressMeter -            done   4.3695667E7    23.0 s       0.0 s      100.0%    23.0 s       0.0 s
[2016-04-15T00:26Z] INFO  17:26:18,388 ProgressMeter - Total runtime 23.74 secs, 0.40 min, 0.01 hours
[2016-04-15T00:26Z] INFO  17:26:18,391 MicroScheduler - 84432 reads were filtered out during the traversal out of approximately 99435 total reads (84.91%)
[2016-04-15T00:26Z] INFO  17:26:18,392 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:26Z] INFO  17:26:18,392 MicroScheduler -   -> 150 reads (0.15% of total) failing BadMateFilter
[2016-04-15T00:26Z] INFO  17:26:18,392 MicroScheduler -   -> 1285 reads (1.29% of total) failing DuplicateReadFilter
[2016-04-15T00:26Z] INFO  17:26:18,393 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:26Z] INFO  17:26:18,393 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:26Z] INFO  17:26:18,393 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:26Z] INFO  17:26:18,393 MicroScheduler -   -> 82997 reads (83.47% of total) failing MappingQualityZeroFilter
[2016-04-15T00:26Z] INFO  17:26:18,394 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:26Z] INFO  17:26:18,394 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-15T00:26Z] INFO  17:26:18,394 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:26Z] INFO  17:26:18,507 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:26Z] INFO  17:26:19,417 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:26Z] GATK: realign ('Y', 15526614, 59222281) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:26Z] INFO  17:26:19,837 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:26Z] INFO  17:26:19,840 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:26Z] INFO  17:26:19,840 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:26Z] INFO  17:26:19,840 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:26Z] INFO  17:26:19,845 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/22/R14-18106_kapa-NGv3-PE100-NGv3-sort-22_31796605_47308085-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/22/R14-18106_kapa-NGv3-PE100-NGv3-sort-22_31796605_47308085-prep-prealign-realign.intervals -L 22:31796606-47308085 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/22/tx/tmp5dS1rq/R14-18106_kapa-NGv3-PE100-NGv3-sort-22_31796605_47308085-prep.bam
[2016-04-15T00:26Z] INFO  17:26:19,854 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:26Z] INFO  17:26:19,855 HelpFormatter - Date/Time: 2016/04/14 17:26:19
[2016-04-15T00:26Z] INFO  17:26:19,856 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:26Z] INFO  17:26:19,856 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:26Z] INFO  17:26:20,031 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:26Z] INFO  17:26:20,121 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:26Z] INFO  17:26:20,131 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:26Z] INFO  17:26:20,179 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-15T00:26Z] INFO  17:26:20,523 IntervalUtils - Processing 15511480 bp from intervals
[2016-04-15T00:26Z] WARN  17:26:20,529 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:26Z] INFO  17:26:20,615 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:26Z] INFO  17:26:20,763 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:26Z] INFO  17:26:20,764 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:26Z] INFO  17:26:20,765 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:26Z] INFO  17:26:20,766 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:26Z] INFO  17:26:20,938 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:26Z] INFO  17:26:21,113 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:26Z] INFO  17:26:21,222 ProgressMeter -     19:58002561   1.1371479E7    30.0 s       2.0 s       91.0%    32.0 s       2.0 s
[2016-04-15T00:26Z] INFO  17:26:21,632 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:26Z] INFO  17:26:21,635 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:26Z] INFO  17:26:21,636 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:26Z] INFO  17:26:21,636 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:26Z] INFO  17:26:21,641 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/Y/R14-18106_kapa-NGv3-PE100-NGv3-sort-Y_15526614_59222281-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/Y/R14-18106_kapa-NGv3-PE100-NGv3-sort-Y_15526614_59222281-prep-prealign-realign.intervals -L Y:15526615-59222281 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/Y/tx/tmplPo9tc/R14-18106_kapa-NGv3-PE100-NGv3-sort-Y_15526614_59222281-prep.bam
[2016-04-15T00:26Z] INFO  17:26:21,651 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:26Z] INFO  17:26:21,652 HelpFormatter - Date/Time: 2016/04/14 17:26:21
[2016-04-15T00:26Z] INFO  17:26:21,653 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:26Z] INFO  17:26:21,653 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:26Z] INFO  17:26:21,743 ProgressMeter -            done    138037.0     9.0 s      65.0 s      100.0%     9.0 s       0.0 s
[2016-04-15T00:26Z] INFO  17:26:21,743 ProgressMeter - Total runtime 9.10 secs, 0.15 min, 0.00 hours
[2016-04-15T00:26Z] INFO  17:26:21,748 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 138037 total reads (0.00%)
[2016-04-15T00:26Z] INFO  17:26:21,748 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:26Z] INFO  17:26:21,749 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:26Z] INFO  17:26:21,749 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:26Z] INFO  17:26:21,822 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:26Z] INFO  17:26:21,915 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:26Z] INFO  17:26:21,925 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:26Z] INFO  17:26:21,970 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.04
[2016-04-15T00:26Z] INFO  17:26:22,308 IntervalUtils - Processing 43695667 bp from intervals
[2016-04-15T00:26Z] WARN  17:26:22,313 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:26Z] INFO  17:26:22,390 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:26Z] INFO  17:26:22,487 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:26Z] INFO  17:26:22,488 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:26Z] INFO  17:26:22,488 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:26Z] INFO  17:26:22,489 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:26Z] INFO  17:26:22,527 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:26Z] INFO  17:26:22,801 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:26Z] INFO  17:26:22,961 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:26Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-Y_0_15522993-prep.bam
[2016-04-15T00:26Z] INFO  17:26:25,027 ProgressMeter -            done   1.2501102E7    33.0 s       2.0 s      100.0%    33.0 s       0.0 s
[2016-04-15T00:26Z] INFO  17:26:25,028 ProgressMeter - Total runtime 33.83 secs, 0.56 min, 0.01 hours
[2016-04-15T00:26Z] INFO  17:26:25,031 MicroScheduler - 136142 reads were filtered out during the traversal out of approximately 1248774 total reads (10.90%)
[2016-04-15T00:26Z] INFO  17:26:25,032 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:26Z] INFO  17:26:25,033 MicroScheduler -   -> 2388 reads (0.19% of total) failing BadMateFilter
[2016-04-15T00:26Z] INFO  17:26:25,034 MicroScheduler -   -> 92294 reads (7.39% of total) failing DuplicateReadFilter
[2016-04-15T00:26Z] INFO  17:26:25,034 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:26Z] INFO  17:26:25,035 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:26Z] INFO  17:26:25,036 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:26Z] INFO  17:26:25,036 MicroScheduler -   -> 41460 reads (3.32% of total) failing MappingQualityZeroFilter
[2016-04-15T00:26Z] INFO  17:26:25,037 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:26Z] INFO  17:26:25,037 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-15T00:26Z] INFO  17:26:25,038 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:26Z] INFO  17:26:25,751 ProgressMeter -            done   1.5509577E7    38.0 s       2.0 s      100.0%    38.0 s       0.0 s
[2016-04-15T00:26Z] INFO  17:26:25,752 ProgressMeter - Total runtime 38.67 secs, 0.64 min, 0.01 hours
[2016-04-15T00:26Z] INFO  17:26:25,755 MicroScheduler - 124898 reads were filtered out during the traversal out of approximately 1402111 total reads (8.91%)
[2016-04-15T00:26Z] INFO  17:26:25,755 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:26Z] INFO  17:26:25,756 MicroScheduler -   -> 2997 reads (0.21% of total) failing BadMateFilter
[2016-04-15T00:26Z] INFO  17:26:25,756 MicroScheduler -   -> 105340 reads (7.51% of total) failing DuplicateReadFilter
[2016-04-15T00:26Z] INFO  17:26:25,756 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:26Z] INFO  17:26:25,757 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:26Z] INFO  17:26:25,757 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:26Z] INFO  17:26:25,757 MicroScheduler -   -> 16561 reads (1.18% of total) failing MappingQualityZeroFilter
[2016-04-15T00:26Z] INFO  17:26:25,757 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:26Z] INFO  17:26:25,758 MicroScheduler -   -> 0 reads (0.00% of total) failing Platform454Filter
[2016-04-15T00:26Z] INFO  17:26:25,758 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:26Z] INFO  17:26:25,990 ProgressMeter -            done    186116.0    11.0 s      60.0 s       99.9%    11.0 s       0.0 s
[2016-04-15T00:26Z] INFO  17:26:25,990 ProgressMeter - Total runtime 11.26 secs, 0.19 min, 0.00 hours
[2016-04-15T00:26Z] INFO  17:26:25,994 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 186116 total reads (0.00%)
[2016-04-15T00:26Z] INFO  17:26:25,995 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:26Z] INFO  17:26:25,995 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:26Z] INFO  17:26:25,995 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:26Z] INFO  17:26:26,034 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:26Z] GATK: realign ('19', 46627881, 59128983) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:26Z] INFO  17:26:27,011 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:26Z] GATK: realign ('19', 0, 15509577) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T00:26Z] INFO  17:26:27,173 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:26Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-X_144337190_155270560-prep.bam
[2016-04-15T00:26Z] INFO  17:26:28,100 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:26Z] INFO  17:26:28,102 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:26Z] INFO  17:26:28,102 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:26Z] INFO  17:26:28,102 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:26Z] INFO  17:26:28,106 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/19/R14-18106_kapa-NGv3-PE100-NGv3-sort-19_46627881_59128983-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/19/R14-18106_kapa-NGv3-PE100-NGv3-sort-19_46627881_59128983-prep-prealign-realign.intervals -L 19:46627882-59128983 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/19/tx/tmpU3qT77/R14-18106_kapa-NGv3-PE100-NGv3-sort-19_46627881_59128983-prep.bam
[2016-04-15T00:26Z] INFO  17:26:28,115 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:26Z] INFO  17:26:28,115 HelpFormatter - Date/Time: 2016/04/14 17:26:28
[2016-04-15T00:26Z] INFO  17:26:28,115 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:26Z] INFO  17:26:28,115 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:26Z] INFO  17:26:28,256 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:26Z] INFO  17:26:28,329 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:26Z] INFO  17:26:28,337 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:26Z] INFO  17:26:28,387 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-15T00:26Z] INFO  17:26:28,655 IntervalUtils - Processing 12501102 bp from intervals
[2016-04-15T00:26Z] WARN  17:26:28,659 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:26Z] INFO  17:26:28,717 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:26Z] INFO  17:26:28,814 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:26Z] INFO  17:26:28,814 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:26Z] INFO  17:26:28,815 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:26Z] INFO  17:26:28,815 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:26Z] INFO  17:26:28,851 ProgressMeter -            done     99060.0     6.0 s      64.0 s       99.5%     6.0 s       0.0 s
[2016-04-15T00:26Z] INFO  17:26:28,852 ProgressMeter - Total runtime 6.36 secs, 0.11 min, 0.00 hours
[2016-04-15T00:26Z] INFO  17:26:28,855 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 99060 total reads (0.00%)
[2016-04-15T00:26Z] INFO  17:26:28,856 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:26Z] INFO  17:26:28,856 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:26Z] INFO  17:26:28,856 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:26Z] INFO  17:26:28,926 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:26Z] INFO  17:26:28,928 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:26Z] INFO  17:26:28,928 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:26Z] INFO  17:26:28,928 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:26Z] INFO  17:26:28,932 HelpFormatter - Program Args: -T IndelRealigner -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/19/R14-18106_kapa-NGv3-PE100-NGv3-sort-19_0_15509577-prep-prealign.bam -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -targetIntervals /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/19/R14-18106_kapa-NGv3-PE100-NGv3-sort-19_0_15509577-prep-prealign-realign.intervals -L 19:1-15509577 --knownAlleles /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/Mills_and_1000G_gold_standard.indels.vcf.gz -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/19/tx/tmpGbO8_U/R14-18106_kapa-NGv3-PE100-NGv3-sort-19_0_15509577-prep.bam
[2016-04-15T00:26Z] INFO  17:26:28,940 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:26Z] INFO  17:26:28,940 HelpFormatter - Date/Time: 2016/04/14 17:26:28
[2016-04-15T00:26Z] INFO  17:26:28,941 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:26Z] INFO  17:26:28,941 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:26Z] INFO  17:26:28,942 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:26Z] INFO  17:26:29,077 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:26Z] INFO  17:26:29,077 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:26Z] INFO  17:26:29,145 GenomeAnalysisEngine - Downsampling Settings: No downsampling
[2016-04-15T00:26Z] INFO  17:26:29,153 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:26Z] INFO  17:26:29,190 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.04
[2016-04-15T00:26Z] INFO  17:26:29,461 IntervalUtils - Processing 15509577 bp from intervals
[2016-04-15T00:26Z] WARN  17:26:29,465 IndexDictionaryUtils - Track knownAlleles doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:26Z] INFO  17:26:29,527 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:26Z] INFO  17:26:29,627 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:26Z] INFO  17:26:29,628 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:26Z] INFO  17:26:29,629 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:26Z] INFO  17:26:29,629 ProgressMeter -        Location |     reads | elapsed |     reads | completed | runtime |   runtime
[2016-04-15T00:26Z] INFO  17:26:29,751 ReadShardBalancer$1 - Loading BAM index data
[2016-04-15T00:26Z] INFO  17:26:29,876 ReadShardBalancer$1 - Done loading BAM index data
[2016-04-15T00:26Z] INFO  17:26:30,021 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:26Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-Y_15526614_59222281-prep.bam
[2016-04-15T00:26Z] INFO  17:26:40,547 ProgressMeter -            done   1124002.0    57.0 s      51.0 s      100.0%    57.0 s       0.0 s
[2016-04-15T00:26Z] INFO  17:26:40,547 ProgressMeter - Total runtime 57.35 secs, 0.96 min, 0.02 hours
[2016-04-15T00:26Z] INFO  17:26:40,550 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 1124002 total reads (0.00%)
[2016-04-15T00:26Z] INFO  17:26:40,551 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:26Z] INFO  17:26:40,551 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:26Z] INFO  17:26:40,551 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:26Z] INFO  17:26:41,777 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:26Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-19_31038849_46627578-prep.bam
[2016-04-15T00:26Z] INFO  17:26:48,240 ProgressMeter -     22:29540906    500008.0    30.0 s      60.0 s       85.5%    35.0 s       5.0 s
[2016-04-15T00:26Z] INFO  17:26:49,379 ProgressMeter -            done    627612.0    28.0 s      45.0 s      100.0%    28.0 s       0.0 s
[2016-04-15T00:26Z] INFO  17:26:49,380 ProgressMeter - Total runtime 28.62 secs, 0.48 min, 0.01 hours
[2016-04-15T00:26Z] INFO  17:26:49,383 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 627612 total reads (0.00%)
[2016-04-15T00:26Z] INFO  17:26:49,384 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:26Z] INFO  17:26:49,384 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:26Z] INFO  17:26:49,384 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:26Z] INFO  17:26:50,487 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:26Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-22_31796605_47308085-prep.bam
[2016-04-15T00:26Z] INFO  17:26:52,339 ProgressMeter -            done    741668.0    34.0 s      45.0 s      100.0%    34.0 s       0.0 s
[2016-04-15T00:26Z] INFO  17:26:52,340 ProgressMeter - Total runtime 34.11 secs, 0.57 min, 0.01 hours
[2016-04-15T00:26Z] INFO  17:26:52,343 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 741668 total reads (0.00%)
[2016-04-15T00:26Z] INFO  17:26:52,344 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:26Z] INFO  17:26:52,344 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:26Z] INFO  17:26:52,344 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:26Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-nochrom-prep.bam
[2016-04-15T00:26Z] INFO  17:26:53,508 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:26Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-22_16266928_31795711-prep.bam
[2016-04-15T00:26Z] INFO  17:26:59,998 ProgressMeter -     19:53057247    500007.0    31.0 s      62.0 s       51.4%    60.0 s      29.0 s
[2016-04-15T00:27Z] INFO  17:27:00,283 ProgressMeter -      19:7532173    600010.0    30.0 s      51.0 s       48.6%    61.0 s      31.0 s
[2016-04-15T00:27Z] INFO  17:27:22,586 ProgressMeter -            done   1242372.0    53.0 s      43.0 s       99.6%    53.0 s       0.0 s
[2016-04-15T00:27Z] INFO  17:27:22,587 ProgressMeter - Total runtime 53.77 secs, 0.90 min, 0.01 hours
[2016-04-15T00:27Z] INFO  17:27:22,590 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 1242372 total reads (0.00%)
[2016-04-15T00:27Z] INFO  17:27:22,590 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:27Z] INFO  17:27:22,590 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:27Z] INFO  17:27:22,591 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:27Z] INFO  17:27:23,771 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:27Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-19_46627881_59128983-prep.bam
[2016-04-15T00:27Z] INFO  17:27:26,737 ProgressMeter -            done   1394338.0    57.0 s      40.0 s      100.0%    57.0 s       0.0 s
[2016-04-15T00:27Z] INFO  17:27:26,737 ProgressMeter - Total runtime 57.11 secs, 0.95 min, 0.02 hours
[2016-04-15T00:27Z] INFO  17:27:26,740 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 1394338 total reads (0.00%)
[2016-04-15T00:27Z] INFO  17:27:26,740 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:27Z] INFO  17:27:26,741 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:27Z] INFO  17:27:26,741 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:27Z] INFO  17:27:28,419 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:27Z] Index BAM file: R14-18106_kapa-NGv3-PE100-NGv3-sort-19_0_15509577-prep.bam
[2016-04-15T00:27Z] Timing: variant calling
[2016-04-15T00:27Z] multiprocessing: variantcall_sample
[2016-04-15T00:27Z] GATK: UnifiedGenotyper
[2016-04-15T00:27Z] GATK: UnifiedGenotyper
[2016-04-15T00:27Z] GATK: UnifiedGenotyper
[2016-04-15T00:27Z] GATK: UnifiedGenotyper
[2016-04-15T00:27Z] GATK: UnifiedGenotyper
[2016-04-15T00:27Z] GATK: UnifiedGenotyper
[2016-04-15T00:27Z] GATK: UnifiedGenotyper
[2016-04-15T00:27Z] GATK: UnifiedGenotyper
[2016-04-15T00:27Z] GATK: UnifiedGenotyper
[2016-04-15T00:27Z] GATK: UnifiedGenotyper
[2016-04-15T00:27Z] GATK: UnifiedGenotyper
[2016-04-15T00:27Z] GATK: UnifiedGenotyper
[2016-04-15T00:27Z] GATK: UnifiedGenotyper
[2016-04-15T00:27Z] GATK: UnifiedGenotyper
[2016-04-15T00:27Z] GATK: UnifiedGenotyper
[2016-04-15T00:27Z] GATK: UnifiedGenotyper
[2016-04-15T00:27Z] INFO  17:27:39,824 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:27Z] INFO  17:27:39,830 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:27Z] INFO  17:27:39,831 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:27Z] INFO  17:27:39,832 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:27Z] INFO  17:27:39,841 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/1/R14-18106_kapa-NGv3-PE100-NGv3-sort-1_46715671_62228851-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/1/R14-18106_kapa-NGv3-PE100-NGv3-1_46715671_62228851-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/1/tx/tmpehDJYB/R14-18106_kapa-NGv3-PE100-NGv3-1_46715671_62228851.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:27Z] INFO  17:27:39,867 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:27Z] INFO  17:27:39,869 HelpFormatter - Date/Time: 2016/04/14 17:27:39
[2016-04-15T00:27Z] INFO  17:27:39,870 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:27Z] INFO  17:27:39,871 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:27Z] INFO  17:27:40,110 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:27Z] INFO  17:27:40,352 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:27Z] INFO  17:27:40,378 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:27Z] INFO  17:27:40,477 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.10
[2016-04-15T00:27Z] INFO  17:27:40,993 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:27Z] INFO  17:27:40,997 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:27Z] INFO  17:27:40,998 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:27Z] INFO  17:27:40,998 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:27Z] INFO  17:27:41,004 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/1/R14-18106_kapa-NGv3-PE100-NGv3-sort-1_0_15541927-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/1/R14-18106_kapa-NGv3-PE100-NGv3-1_0_15541927-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/1/tx/tmpJgH4w6/R14-18106_kapa-NGv3-PE100-NGv3-1_0_15541927.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:27Z] INFO  17:27:41,023 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:27Z] INFO  17:27:41,024 HelpFormatter - Date/Time: 2016/04/14 17:27:40
[2016-04-15T00:27Z] INFO  17:27:41,024 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:27Z] INFO  17:27:41,024 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:27Z] INFO  17:27:41,041 IntervalUtils - Processing 180557 bp from intervals
[2016-04-15T00:27Z] WARN  17:27:41,047 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:27Z] INFO  17:27:41,146 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:27Z] INFO  17:27:41,183 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:27Z] INFO  17:27:41,252 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:27Z] INFO  17:27:41,253 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:27Z] INFO  17:27:41,253 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:27Z] INFO  17:27:41,253 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:27Z] INFO  17:27:41,305 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:27Z] INFO  17:27:41,305 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:27Z] INFO  17:27:41,415 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:27Z] INFO  17:27:41,436 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:27Z] INFO  17:27:41,510 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-15T00:27Z] INFO  17:27:42,006 IntervalUtils - Processing 390138 bp from intervals
[2016-04-15T00:27Z] WARN  17:27:42,014 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:27Z] INFO  17:27:42,039 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:27Z] INFO  17:27:42,043 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:27Z] INFO  17:27:42,043 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:27Z] INFO  17:27:42,044 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:27Z] INFO  17:27:42,055 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:27Z] INFO  17:27:42,059 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:27Z] INFO  17:27:42,060 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:27Z] INFO  17:27:42,060 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:27Z] INFO  17:27:42,060 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/1/R14-18106_kapa-NGv3-PE100-NGv3-sort-1_93298945_108993401-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/1/R14-18106_kapa-NGv3-PE100-NGv3-1_93298945_108993401-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/1/tx/tmpfJJXIW/R14-18106_kapa-NGv3-PE100-NGv3-1_93298945_108993401.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:27Z] INFO  17:27:42,066 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/1/R14-18106_kapa-NGv3-PE100-NGv3-sort-1_15545821_31186478-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/1/R14-18106_kapa-NGv3-PE100-NGv3-1_15545821_31186478-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/1/tx/tmp_7EDBI/R14-18106_kapa-NGv3-PE100-NGv3-1_15545821_31186478.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:27Z] INFO  17:27:42,072 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:27Z] INFO  17:27:42,072 HelpFormatter - Date/Time: 2016/04/14 17:27:42
[2016-04-15T00:27Z] INFO  17:27:42,073 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:27Z] INFO  17:27:42,073 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:27Z] INFO  17:27:42,082 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:27Z] INFO  17:27:42,085 HelpFormatter - Date/Time: 2016/04/14 17:27:42
[2016-04-15T00:27Z] INFO  17:27:42,092 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:27Z] INFO  17:27:42,106 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:27Z] INFO  17:27:42,120 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:27Z] INFO  17:27:42,170 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:27Z] INFO  17:27:42,184 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:27Z] INFO  17:27:42,184 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:27Z] INFO  17:27:42,184 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:27Z] INFO  17:27:42,189 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/1/R14-18106_kapa-NGv3-PE100-NGv3-sort-1_77752625_93297674-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/1/R14-18106_kapa-NGv3-PE100-NGv3-1_77752625_93297674-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/1/tx/tmpX7O9Lf/R14-18106_kapa-NGv3-PE100-NGv3-1_77752625_93297674.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:27Z] INFO  17:27:42,201 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:27Z] INFO  17:27:42,202 HelpFormatter - Date/Time: 2016/04/14 17:27:42
[2016-04-15T00:27Z] INFO  17:27:42,202 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:27Z] INFO  17:27:42,203 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:27Z] INFO  17:27:42,220 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:27Z] INFO  17:27:42,221 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:27Z] INFO  17:27:42,222 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:27Z] INFO  17:27:42,223 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:27Z] INFO  17:27:42,226 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:27Z] INFO  17:27:42,284 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:27Z] INFO  17:27:42,285 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:27Z] INFO  17:27:42,296 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:27Z] INFO  17:27:42,415 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:27Z] INFO  17:27:42,529 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:27Z] INFO  17:27:42,540 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:27Z] INFO  17:27:42,555 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:27Z] INFO  17:27:42,566 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:27Z] INFO  17:27:42,666 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:27Z] INFO  17:27:42,670 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:27Z] INFO  17:27:42,671 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:27Z] INFO  17:27:42,672 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:27Z] INFO  17:27:42,671 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:27Z] INFO  17:27:42,674 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:27Z] INFO  17:27:42,675 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:27Z] INFO  17:27:42,676 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:27Z] INFO  17:27:42,678 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/1/R14-18106_kapa-NGv3-PE100-NGv3-sort-1_143897546_159410511-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/1/R14-18106_kapa-NGv3-PE100-NGv3-1_143897546_159410511-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/1/tx/tmp4XrjrL/R14-18106_kapa-NGv3-PE100-NGv3-1_143897546_159410511.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:27Z] INFO  17:27:42,681 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/1/R14-18106_kapa-NGv3-PE100-NGv3-sort-1_31187093_46714270-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/1/R14-18106_kapa-NGv3-PE100-NGv3-1_31187093_46714270-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/1/tx/tmpaPeGdb/R14-18106_kapa-NGv3-PE100-NGv3-1_31187093_46714270.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:27Z] INFO  17:27:42,680 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:27Z] INFO  17:27:42,684 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:27Z] INFO  17:27:42,685 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:27Z] INFO  17:27:42,685 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:27Z] INFO  17:27:42,688 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:27Z] INFO  17:27:42,689 HelpFormatter - Date/Time: 2016/04/14 17:27:42
[2016-04-15T00:27Z] INFO  17:27:42,690 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:27Z] INFO  17:27:42,690 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:27Z] INFO  17:27:42,690 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/1/R14-18106_kapa-NGv3-PE100-NGv3-sort-1_62231950_77749296-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/1/R14-18106_kapa-NGv3-PE100-NGv3-1_62231950_77749296-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/1/tx/tmpGR8gi9/R14-18106_kapa-NGv3-PE100-NGv3-1_62231950_77749296.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:27Z] INFO  17:27:42,696 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.16
[2016-04-15T00:27Z] INFO  17:27:42,714 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:27Z] INFO  17:27:42,719 HelpFormatter - Date/Time: 2016/04/14 17:27:42
[2016-04-15T00:27Z] INFO  17:27:42,720 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:27Z] INFO  17:27:42,731 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:27Z] INFO  17:27:42,744 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.17
[2016-04-15T00:27Z] INFO  17:27:42,754 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:27Z] INFO  17:27:42,755 HelpFormatter - Date/Time: 2016/04/14 17:27:42
[2016-04-15T00:27Z] INFO  17:27:42,756 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:27Z] INFO  17:27:42,757 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:27Z] INFO  17:27:42,771 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:27Z] INFO  17:27:42,790 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:27Z] INFO  17:27:42,865 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-15T00:27Z] INFO  17:27:42,902 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:27Z] INFO  17:27:42,901 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:27Z] INFO  17:27:42,922 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:27Z] INFO  17:27:43,163 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:27Z] INFO  17:27:43,175 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:27Z] INFO  17:27:43,179 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:27Z] INFO  17:27:43,190 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:27Z] INFO  17:27:43,210 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:27Z] INFO  17:27:43,212 IntervalUtils - Processing 113118 bp from intervals
[2016-04-15T00:27Z] WARN  17:27:43,218 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:27Z] INFO  17:27:43,221 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:27Z] INFO  17:27:43,264 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.09
[2016-04-15T00:27Z] INFO  17:27:43,280 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.09
[2016-04-15T00:27Z] INFO  17:27:43,319 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.10
[2016-04-15T00:27Z] INFO  17:27:43,323 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:27Z] INFO  17:27:43,332 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:27Z] INFO  17:27:43,335 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:27Z] INFO  17:27:43,336 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:27Z] INFO  17:27:43,336 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:27Z] INFO  17:27:43,341 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/1/R14-18106_kapa-NGv3-PE100-NGv3-sort-1_240255409_249250621-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/1/R14-18106_kapa-NGv3-PE100-NGv3-1_240255409_249250621-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/1/tx/tmpIqpzNb/R14-18106_kapa-NGv3-PE100-NGv3-1_240255409_249250621.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:27Z] INFO  17:27:43,350 IntervalUtils - Processing 386393 bp from intervals
[2016-04-15T00:27Z] INFO  17:27:43,354 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:27Z] WARN  17:27:43,357 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:27Z] INFO  17:27:43,360 IntervalUtils - Processing 145368 bp from intervals
[2016-04-15T00:27Z] INFO  17:27:43,364 HelpFormatter - Date/Time: 2016/04/14 17:27:43
[2016-04-15T00:27Z] INFO  17:27:43,365 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:27Z] INFO  17:27:43,366 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:27Z] WARN  17:27:43,377 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:27Z] INFO  17:27:43,407 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:27Z] INFO  17:27:43,419 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:27Z] INFO  17:27:43,420 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:27Z] INFO  17:27:43,421 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:27Z] INFO  17:27:43,445 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:27Z] INFO  17:27:43,499 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:27Z] INFO  17:27:43,521 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:27Z] INFO  17:27:43,522 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:27Z] INFO  17:27:43,526 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:27Z] INFO  17:27:43,636 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:27Z] INFO  17:27:43,637 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:27Z] INFO  17:27:43,641 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:27Z] INFO  17:27:43,642 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:27Z] INFO  17:27:43,643 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:27Z] INFO  17:27:43,644 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:27Z] INFO  17:27:43,644 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:27Z] INFO  17:27:43,645 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:27Z] INFO  17:27:43,709 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:27Z] INFO  17:27:43,710 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:27Z] INFO  17:27:43,714 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:27Z] INFO  17:27:43,716 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:27Z] INFO  17:27:43,906 IntervalUtils - Processing 431182 bp from intervals
[2016-04-15T00:27Z] INFO  17:27:43,908 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:27Z] WARN  17:27:43,921 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:27Z] INFO  17:27:43,947 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:27Z] INFO  17:27:43,960 IntervalUtils - Processing 150085 bp from intervals
[2016-04-15T00:27Z] WARN  17:27:43,966 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:27Z] INFO  17:27:43,975 IntervalUtils - Processing 517409 bp from intervals
[2016-04-15T00:27Z] WARN  17:27:43,984 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:27Z] INFO  17:27:44,000 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:27Z] INFO  17:27:44,062 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.11
[2016-04-15T00:27Z] INFO  17:27:44,070 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:27Z] INFO  17:27:44,078 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:27Z] INFO  17:27:44,089 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:27Z] INFO  17:27:44,090 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:27Z] INFO  17:27:44,091 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:27Z] INFO  17:27:44,092 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:27Z] INFO  17:27:44,145 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:27Z] INFO  17:27:44,146 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:27Z] INFO  17:27:44,168 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:27Z] INFO  17:27:44,169 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:27Z] INFO  17:27:44,170 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:27Z] INFO  17:27:44,170 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:27Z] INFO  17:27:44,201 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:27Z] INFO  17:27:44,205 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:27Z] INFO  17:27:44,205 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:27Z] INFO  17:27:44,206 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:27Z] INFO  17:27:44,210 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/1/R14-18106_kapa-NGv3-PE100-NGv3-sort-1_159504867_175046963-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/1/R14-18106_kapa-NGv3-PE100-NGv3-1_159504867_175046963-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/1/tx/tmpuwGGNV/R14-18106_kapa-NGv3-PE100-NGv3-1_159504867_175046963.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:27Z] INFO  17:27:44,226 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:27Z] INFO  17:27:44,227 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:27Z] INFO  17:27:44,228 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:27Z] INFO  17:27:44,229 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:27Z] INFO  17:27:44,233 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:27Z] INFO  17:27:44,234 HelpFormatter - Date/Time: 2016/04/14 17:27:44
[2016-04-15T00:27Z] INFO  17:27:44,235 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:27Z] INFO  17:27:44,235 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:27Z] INFO  17:27:44,250 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:27Z] INFO  17:27:44,256 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:27Z] INFO  17:27:44,307 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:27Z] INFO  17:27:44,313 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:27Z] INFO  17:27:44,425 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:27Z] INFO  17:27:44,502 IntervalUtils - Processing 129443 bp from intervals
[2016-04-15T00:27Z] WARN  17:27:44,518 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:27Z] INFO  17:27:44,559 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:27Z] INFO  17:27:44,563 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:27Z] INFO  17:27:44,564 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:27Z] INFO  17:27:44,565 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:27Z] INFO  17:27:44,570 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/1/R14-18106_kapa-NGv3-PE100-NGv3-sort-1_223162737_240072524-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/1/R14-18106_kapa-NGv3-PE100-NGv3-1_223162737_240072524-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/1/tx/tmpjJoFsP/R14-18106_kapa-NGv3-PE100-NGv3-1_223162737_240072524.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:27Z] INFO  17:27:44,589 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:27Z] INFO  17:27:44,591 HelpFormatter - Date/Time: 2016/04/14 17:27:44
[2016-04-15T00:27Z] INFO  17:27:44,591 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:27Z] INFO  17:27:44,592 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:27Z] INFO  17:27:44,613 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:27Z] INFO  17:27:44,692 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:27Z] INFO  17:27:44,725 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:27Z] INFO  17:27:44,775 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:27Z] INFO  17:27:44,776 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:27Z] INFO  17:27:44,776 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:27Z] INFO  17:27:44,777 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:27Z] INFO  17:27:44,782 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:27Z] INFO  17:27:44,785 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:27Z] INFO  17:27:44,785 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:27Z] INFO  17:27:44,785 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:27Z] INFO  17:27:44,789 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/1/R14-18106_kapa-NGv3-PE100-NGv3-sort-1_192128349_207640257-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/1/R14-18106_kapa-NGv3-PE100-NGv3-1_192128349_207640257-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/1/tx/tmpDyeWCZ/R14-18106_kapa-NGv3-PE100-NGv3-1_192128349_207640257.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:27Z] INFO  17:27:44,833 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:27Z] INFO  17:27:44,833 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:27Z] INFO  17:27:44,834 HelpFormatter - Date/Time: 2016/04/14 17:27:44
[2016-04-15T00:27Z] INFO  17:27:44,834 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:27Z] INFO  17:27:44,835 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:27Z] INFO  17:27:44,867 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:27Z] INFO  17:27:44,867 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:27Z] INFO  17:27:44,858 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.13
[2016-04-15T00:27Z] INFO  17:27:44,881 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:27Z] INFO  17:27:44,885 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:27Z] INFO  17:27:44,883 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:27Z] INFO  17:27:44,885 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:27Z] INFO  17:27:44,886 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:27Z] INFO  17:27:44,886 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:27Z] INFO  17:27:44,886 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:27Z] INFO  17:27:44,887 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:27Z] INFO  17:27:44,891 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/1/R14-18106_kapa-NGv3-PE100-NGv3-sort-1_108994811_143767848-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/1/R14-18106_kapa-NGv3-PE100-NGv3-1_108994811_143767848-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/1/tx/tmpDztUgc/R14-18106_kapa-NGv3-PE100-NGv3-1_108994811_143767848.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:27Z] INFO  17:27:44,891 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/2/R14-18106_kapa-NGv3-PE100-NGv3-sort-2_0_15514844-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/2/R14-18106_kapa-NGv3-PE100-NGv3-2_0_15514844-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/2/tx/tmpQRI9On/R14-18106_kapa-NGv3-PE100-NGv3-2_0_15514844.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:27Z] INFO  17:27:44,906 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:27Z] INFO  17:27:44,907 HelpFormatter - Date/Time: 2016/04/14 17:27:44
[2016-04-15T00:27Z] INFO  17:27:44,907 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:27Z] INFO  17:27:44,905 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:27Z] INFO  17:27:44,908 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:27Z] INFO  17:27:44,908 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:27Z] INFO  17:27:44,909 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:27Z] INFO  17:27:44,909 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:27Z] INFO  17:27:44,909 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:27Z] INFO  17:27:44,910 HelpFormatter - Date/Time: 2016/04/14 17:27:44
[2016-04-15T00:27Z] INFO  17:27:44,911 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:27Z] INFO  17:27:44,911 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:27Z] INFO  17:27:44,914 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/1/R14-18106_kapa-NGv3-PE100-NGv3-sort-1_207641871_223156451-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/1/R14-18106_kapa-NGv3-PE100-NGv3-1_207641871_223156451-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/1/tx/tmp419spt/R14-18106_kapa-NGv3-PE100-NGv3-1_207641871_223156451.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:27Z] INFO  17:27:44,933 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:27Z] INFO  17:27:44,936 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:27Z] INFO  17:27:44,937 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:27Z] INFO  17:27:44,938 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:27Z] INFO  17:27:44,937 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:27Z] INFO  17:27:44,937 HelpFormatter - Date/Time: 2016/04/14 17:27:44
[2016-04-15T00:27Z] INFO  17:27:44,937 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:27Z] INFO  17:27:44,938 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:27Z] INFO  17:27:44,942 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/1/R14-18106_kapa-NGv3-PE100-NGv3-sort-1_175048468_192127886-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/1/R14-18106_kapa-NGv3-PE100-NGv3-1_175048468_192127886-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/1/tx/tmpb_LtIz/R14-18106_kapa-NGv3-PE100-NGv3-1_175048468_192127886.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:27Z] INFO  17:27:44,966 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:27Z] INFO  17:27:44,967 HelpFormatter - Date/Time: 2016/04/14 17:27:44
[2016-04-15T00:27Z] INFO  17:27:44,973 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:27Z] INFO  17:27:44,974 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:27Z] INFO  17:27:45,073 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:27Z] INFO  17:27:45,092 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:27Z] INFO  17:27:45,110 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:27Z] INFO  17:27:45,145 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:27Z] INFO  17:27:45,152 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:27Z] INFO  17:27:45,161 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:27Z] INFO  17:27:45,164 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:27Z] INFO  17:27:45,251 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.09
[2016-04-15T00:27Z] INFO  17:27:45,345 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:27Z] INFO  17:27:45,354 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:27Z] INFO  17:27:45,414 IntervalUtils - Processing 261574 bp from intervals
[2016-04-15T00:27Z] WARN  17:27:45,420 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:27Z] INFO  17:27:45,422 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:27Z] INFO  17:27:45,433 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:27Z] INFO  17:27:45,441 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.09
[2016-04-15T00:27Z] INFO  17:27:45,445 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:27Z] INFO  17:27:45,453 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:27Z] INFO  17:27:45,472 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:27Z] INFO  17:27:45,485 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:27Z] INFO  17:27:45,492 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:27Z] INFO  17:27:45,483 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:27Z] INFO  17:27:45,501 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:27Z] INFO  17:27:45,539 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.09
[2016-04-15T00:27Z] INFO  17:27:45,548 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.10
[2016-04-15T00:27Z] INFO  17:27:45,579 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.09
[2016-04-15T00:27Z] INFO  17:27:45,588 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.09
[2016-04-15T00:27Z] INFO  17:27:45,657 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:27Z] INFO  17:27:45,658 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:27Z] INFO  17:27:45,658 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:27Z] INFO  17:27:45,659 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:27Z] INFO  17:27:45,755 IntervalUtils - Processing 294039 bp from intervals
[2016-04-15T00:27Z] WARN  17:27:45,760 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:27Z] INFO  17:27:45,784 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:27Z] INFO  17:27:45,790 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:27Z] INFO  17:27:45,897 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:27Z] INFO  17:27:46,078 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:27Z] INFO  17:27:46,079 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:27Z] INFO  17:27:46,079 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:27Z] INFO  17:27:46,085 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:27Z] INFO  17:27:46,158 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:27Z] INFO  17:27:46,159 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:27Z] INFO  17:27:46,183 IntervalUtils - Processing 282740 bp from intervals
[2016-04-15T00:27Z] WARN  17:27:46,194 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:27Z] INFO  17:27:46,199 IntervalUtils - Processing 258252 bp from intervals
[2016-04-15T00:27Z] WARN  17:27:46,215 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:27Z] INFO  17:27:46,216 IntervalUtils - Processing 191568 bp from intervals
[2016-04-15T00:27Z] WARN  17:27:46,221 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:27Z] INFO  17:27:46,309 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:27Z] INFO  17:27:46,317 IntervalUtils - Processing 105700 bp from intervals
[2016-04-15T00:27Z] WARN  17:27:46,341 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:27Z] INFO  17:27:46,358 IntervalUtils - Processing 175773 bp from intervals
[2016-04-15T00:27Z] INFO  17:27:46,360 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:27Z] WARN  17:27:46,363 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:27Z] INFO  17:27:46,373 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:27Z] INFO  17:27:46,431 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:27Z] INFO  17:27:46,432 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:27Z] INFO  17:27:46,432 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:27Z] INFO  17:27:46,434 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:27Z] INFO  17:27:46,435 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:27Z] INFO  17:27:46,467 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:27Z] INFO  17:27:46,490 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:27Z] INFO  17:27:46,490 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:27Z] INFO  17:27:46,491 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:27Z] INFO  17:27:46,491 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:27Z] INFO  17:27:46,499 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:27Z] INFO  17:27:46,502 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:27Z] INFO  17:27:46,503 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:27Z] INFO  17:27:46,504 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:27Z] INFO  17:27:46,505 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:27Z] INFO  17:27:46,511 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:27Z] INFO  17:27:46,512 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:27Z] INFO  17:27:46,513 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:27Z] INFO  17:27:46,516 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:27Z] INFO  17:27:46,517 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:27Z] INFO  17:27:46,553 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:27Z] INFO  17:27:46,554 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:27Z] INFO  17:27:46,588 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:27Z] INFO  17:27:46,589 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:27Z] INFO  17:27:46,603 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:27Z] INFO  17:27:46,617 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:27Z] INFO  17:27:46,618 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:27Z] INFO  17:27:46,618 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:27Z] INFO  17:27:46,624 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:27Z] INFO  17:27:46,635 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:27Z] INFO  17:27:46,726 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:27Z] INFO  17:27:46,727 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:28Z] INFO  17:28:00,489 ProgressMeter -            done    343044.0    17.0 s      49.0 s      100.0%    17.0 s       0.0 s
[2016-04-15T00:28Z] INFO  17:28:00,489 ProgressMeter - Total runtime 17.07 secs, 0.28 min, 0.00 hours
[2016-04-15T00:28Z] INFO  17:28:00,490 MicroScheduler - 10120 reads were filtered out during the traversal out of approximately 139533 total reads (7.25%)
[2016-04-15T00:28Z] INFO  17:28:00,491 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:28Z] INFO  17:28:00,491 MicroScheduler -   -> 222 reads (0.16% of total) failing BadMateFilter
[2016-04-15T00:28Z] INFO  17:28:00,491 MicroScheduler -   -> 9820 reads (7.04% of total) failing DuplicateReadFilter
[2016-04-15T00:28Z] INFO  17:28:00,492 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:28Z] INFO  17:28:00,492 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:28Z] INFO  17:28:00,492 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:28Z] INFO  17:28:00,492 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:28Z] INFO  17:28:00,492 MicroScheduler -   -> 78 reads (0.06% of total) failing UnmappedReadFilter
[2016-04-15T00:28Z] INFO  17:28:01,473 ProgressMeter -            done    285546.0    14.0 s      52.0 s      100.0%    14.0 s       0.0 s
[2016-04-15T00:28Z] INFO  17:28:01,473 ProgressMeter - Total runtime 14.96 secs, 0.25 min, 0.00 hours
[2016-04-15T00:28Z] INFO  17:28:01,474 MicroScheduler - 10280 reads were filtered out during the traversal out of approximately 129346 total reads (7.95%)
[2016-04-15T00:28Z] INFO  17:28:01,474 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:28Z] INFO  17:28:01,475 MicroScheduler -   -> 227 reads (0.18% of total) failing BadMateFilter
[2016-04-15T00:28Z] INFO  17:28:01,475 MicroScheduler -   -> 9962 reads (7.70% of total) failing DuplicateReadFilter
[2016-04-15T00:28Z] INFO  17:28:01,475 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:28Z] INFO  17:28:01,475 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:28Z] INFO  17:28:01,476 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:28Z] INFO  17:28:01,476 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:28Z] INFO  17:28:01,476 MicroScheduler -   -> 91 reads (0.07% of total) failing UnmappedReadFilter
[2016-04-15T00:28Z] INFO  17:28:01,729 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:28Z] INFO  17:28:02,046 ProgressMeter -            done    406382.0    18.0 s      45.0 s      100.0%    18.0 s       0.0 s
[2016-04-15T00:28Z] INFO  17:28:02,046 ProgressMeter - Total runtime 18.40 secs, 0.31 min, 0.01 hours
[2016-04-15T00:28Z] INFO  17:28:02,047 MicroScheduler - 11191 reads were filtered out during the traversal out of approximately 144516 total reads (7.74%)
[2016-04-15T00:28Z] INFO  17:28:02,047 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:28Z] INFO  17:28:02,047 MicroScheduler -   -> 268 reads (0.19% of total) failing BadMateFilter
[2016-04-15T00:28Z] INFO  17:28:02,048 MicroScheduler -   -> 10834 reads (7.50% of total) failing DuplicateReadFilter
[2016-04-15T00:28Z] INFO  17:28:02,048 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:28Z] INFO  17:28:02,048 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:28Z] INFO  17:28:02,048 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:28Z] INFO  17:28:02,049 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:28Z] INFO  17:28:02,049 MicroScheduler -   -> 89 reads (0.06% of total) failing UnmappedReadFilter
[2016-04-15T00:28Z] GATK: UnifiedGenotyper
[2016-04-15T00:28Z] INFO  17:28:02,471 ProgressMeter -            done    356392.0    18.0 s      51.0 s      100.0%    18.0 s       0.0 s
[2016-04-15T00:28Z] INFO  17:28:02,472 ProgressMeter - Total runtime 18.30 secs, 0.31 min, 0.01 hours
[2016-04-15T00:28Z] INFO  17:28:02,472 MicroScheduler - 12160 reads were filtered out during the traversal out of approximately 154831 total reads (7.85%)
[2016-04-15T00:28Z] INFO  17:28:02,472 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:28Z] INFO  17:28:02,473 MicroScheduler -   -> 257 reads (0.17% of total) failing BadMateFilter
[2016-04-15T00:28Z] INFO  17:28:02,473 MicroScheduler -   -> 11801 reads (7.62% of total) failing DuplicateReadFilter
[2016-04-15T00:28Z] INFO  17:28:02,473 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:28Z] INFO  17:28:02,473 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:28Z] INFO  17:28:02,474 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:28Z] INFO  17:28:02,474 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:28Z] INFO  17:28:02,474 MicroScheduler -   -> 102 reads (0.07% of total) failing UnmappedReadFilter
[2016-04-15T00:28Z] INFO  17:28:02,898 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:28Z] GATK: UnifiedGenotyper
[2016-04-15T00:28Z] INFO  17:28:03,379 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:28Z] INFO  17:28:03,404 ProgressMeter -            done    264653.0    18.0 s      70.0 s      100.0%    18.0 s       0.0 s
[2016-04-15T00:28Z] INFO  17:28:03,404 ProgressMeter - Total runtime 18.63 secs, 0.31 min, 0.01 hours
[2016-04-15T00:28Z] INFO  17:28:03,405 MicroScheduler - 13156 reads were filtered out during the traversal out of approximately 166769 total reads (7.89%)
[2016-04-15T00:28Z] INFO  17:28:03,405 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:28Z] INFO  17:28:03,405 MicroScheduler -   -> 279 reads (0.17% of total) failing BadMateFilter
[2016-04-15T00:28Z] INFO  17:28:03,405 MicroScheduler -   -> 12752 reads (7.65% of total) failing DuplicateReadFilter
[2016-04-15T00:28Z] INFO  17:28:03,406 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:28Z] INFO  17:28:03,406 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:28Z] INFO  17:28:03,406 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:28Z] INFO  17:28:03,407 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:28Z] INFO  17:28:03,407 MicroScheduler -   -> 125 reads (0.07% of total) failing UnmappedReadFilter
[2016-04-15T00:28Z] GATK: UnifiedGenotyper
[2016-04-15T00:28Z] INFO  17:28:03,982 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:28Z] INFO  17:28:04,182 ProgressMeter -            done    578834.0    22.0 s      39.0 s      100.0%    22.0 s       0.0 s
[2016-04-15T00:28Z] INFO  17:28:04,183 ProgressMeter - Total runtime 22.93 secs, 0.38 min, 0.01 hours
[2016-04-15T00:28Z] INFO  17:28:04,184 MicroScheduler - 19203 reads were filtered out during the traversal out of approximately 242505 total reads (7.92%)
[2016-04-15T00:28Z] INFO  17:28:04,184 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:28Z] INFO  17:28:04,184 MicroScheduler -   -> 383 reads (0.16% of total) failing BadMateFilter
[2016-04-15T00:28Z] INFO  17:28:04,185 MicroScheduler -   -> 18667 reads (7.70% of total) failing DuplicateReadFilter
[2016-04-15T00:28Z] INFO  17:28:04,185 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:28Z] INFO  17:28:04,185 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:28Z] INFO  17:28:04,187 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:28Z] INFO  17:28:04,187 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:28Z] INFO  17:28:04,188 MicroScheduler -   -> 153 reads (0.06% of total) failing UnmappedReadFilter
[2016-04-15T00:28Z] GATK: UnifiedGenotyper
[2016-04-15T00:28Z] INFO  17:28:04,920 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:28Z] INFO  17:28:04,951 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:28Z] INFO  17:28:04,955 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:28Z] INFO  17:28:04,955 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:28Z] INFO  17:28:04,956 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:28Z] INFO  17:28:04,961 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/2/R14-18106_kapa-NGv3-PE100-NGv3-sort-2_15519725_31133925-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/2/R14-18106_kapa-NGv3-PE100-NGv3-2_15519725_31133925-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/2/tx/tmp4KFuHJ/R14-18106_kapa-NGv3-PE100-NGv3-2_15519725_31133925.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:28Z] INFO  17:28:04,971 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:28Z] INFO  17:28:04,971 HelpFormatter - Date/Time: 2016/04/14 17:28:04
[2016-04-15T00:28Z] INFO  17:28:04,971 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:28Z] INFO  17:28:04,972 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:28Z] GATK: UnifiedGenotyper
[2016-04-15T00:28Z] INFO  17:28:05,151 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:28Z] INFO  17:28:05,367 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:28Z] INFO  17:28:05,376 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:28Z] INFO  17:28:05,449 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-15T00:28Z] INFO  17:28:05,512 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:28Z] GATK: UnifiedGenotyper
[2016-04-15T00:28Z] INFO  17:28:05,968 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:28Z] INFO  17:28:05,971 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:28Z] INFO  17:28:05,972 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:28Z] INFO  17:28:05,972 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:28Z] INFO  17:28:05,984 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/2/R14-18106_kapa-NGv3-PE100-NGv3-sort-2_31135088_46706841-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/2/R14-18106_kapa-NGv3-PE100-NGv3-2_31135088_46706841-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/2/tx/tmpmxv15U/R14-18106_kapa-NGv3-PE100-NGv3-2_31135088_46706841.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:28Z] INFO  17:28:05,985 IntervalUtils - Processing 231513 bp from intervals
[2016-04-15T00:28Z] WARN  17:28:05,991 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:28Z] INFO  17:28:05,997 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:28Z] INFO  17:28:05,997 HelpFormatter - Date/Time: 2016/04/14 17:28:05
[2016-04-15T00:28Z] INFO  17:28:05,997 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:28Z] INFO  17:28:05,998 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:28Z] INFO  17:28:06,174 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:28Z] INFO  17:28:06,235 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:28Z] INFO  17:28:06,299 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:28Z] INFO  17:28:06,300 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:28Z] INFO  17:28:06,301 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:28Z] INFO  17:28:06,302 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:28Z] INFO  17:28:06,367 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:28Z] INFO  17:28:06,368 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:28Z] INFO  17:28:06,508 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:28Z] INFO  17:28:06,518 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:28Z] INFO  17:28:06,547 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:28Z] INFO  17:28:06,551 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:28Z] INFO  17:28:06,551 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:28Z] INFO  17:28:06,552 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:28Z] INFO  17:28:06,556 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/2/R14-18106_kapa-NGv3-PE100-NGv3-sort-2_46707543_62228117-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/2/R14-18106_kapa-NGv3-PE100-NGv3-2_46707543_62228117-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/2/tx/tmpbkUU6E/R14-18106_kapa-NGv3-PE100-NGv3-2_46707543_62228117.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:28Z] INFO  17:28:06,580 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:28Z] INFO  17:28:06,580 HelpFormatter - Date/Time: 2016/04/14 17:28:06
[2016-04-15T00:28Z] INFO  17:28:06,580 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:28Z] INFO  17:28:06,580 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:28Z] INFO  17:28:06,601 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-15T00:28Z] INFO  17:28:06,746 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:28Z] INFO  17:28:06,931 IntervalUtils - Processing 167641 bp from intervals
[2016-04-15T00:28Z] WARN  17:28:06,936 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:28Z] INFO  17:28:06,987 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:28Z] INFO  17:28:06,998 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:28Z] INFO  17:28:07,030 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:28Z] INFO  17:28:07,086 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.09
[2016-04-15T00:28Z] INFO  17:28:07,120 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:28Z] INFO  17:28:07,121 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:28Z] INFO  17:28:07,122 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:28Z] INFO  17:28:07,123 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:28Z] INFO  17:28:07,185 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:28Z] INFO  17:28:07,186 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:28Z] INFO  17:28:07,253 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:28Z] INFO  17:28:07,256 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:28Z] INFO  17:28:07,257 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:28Z] INFO  17:28:07,257 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:28Z] INFO  17:28:07,262 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/2/R14-18106_kapa-NGv3-PE100-NGv3-sort-2_62362965_79253295-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/2/R14-18106_kapa-NGv3-PE100-NGv3-2_62362965_79253295-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/2/tx/tmpUNCnFH/R14-18106_kapa-NGv3-PE100-NGv3-2_62362965_79253295.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:28Z] INFO  17:28:07,293 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:28Z] INFO  17:28:07,294 HelpFormatter - Date/Time: 2016/04/14 17:28:07
[2016-04-15T00:28Z] INFO  17:28:07,294 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:28Z] INFO  17:28:07,295 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:28Z] INFO  17:28:07,348 ProgressMeter -            done    638757.0    20.0 s      32.0 s      100.0%    20.0 s       0.0 s
[2016-04-15T00:28Z] INFO  17:28:07,349 ProgressMeter - Total runtime 20.86 secs, 0.35 min, 0.01 hours
[2016-04-15T00:28Z] INFO  17:28:07,350 MicroScheduler - 17786 reads were filtered out during the traversal out of approximately 222571 total reads (7.99%)
[2016-04-15T00:28Z] INFO  17:28:07,351 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:28Z] INFO  17:28:07,352 MicroScheduler -   -> 385 reads (0.17% of total) failing BadMateFilter
[2016-04-15T00:28Z] INFO  17:28:07,353 MicroScheduler -   -> 17257 reads (7.75% of total) failing DuplicateReadFilter
[2016-04-15T00:28Z] INFO  17:28:07,353 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:28Z] INFO  17:28:07,354 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:28Z] INFO  17:28:07,355 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:28Z] INFO  17:28:07,356 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:28Z] INFO  17:28:07,356 MicroScheduler -   -> 144 reads (0.06% of total) failing UnmappedReadFilter
[2016-04-15T00:28Z] INFO  17:28:07,516 IntervalUtils - Processing 139959 bp from intervals
[2016-04-15T00:28Z] WARN  17:28:07,521 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:28Z] INFO  17:28:07,555 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:28Z] INFO  17:28:07,593 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:28Z] INFO  17:28:07,662 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:28Z] INFO  17:28:07,669 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:28Z] INFO  17:28:07,670 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:28Z] INFO  17:28:07,670 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:28Z] INFO  17:28:07,742 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:28Z] INFO  17:28:07,750 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:28Z] INFO  17:28:07,772 ProgressMeter -            done    540256.0    21.0 s      39.0 s      100.0%    21.0 s       0.0 s
[2016-04-15T00:28Z] INFO  17:28:07,773 ProgressMeter - Total runtime 21.16 secs, 0.35 min, 0.01 hours
[2016-04-15T00:28Z] INFO  17:28:07,773 MicroScheduler - 16321 reads were filtered out during the traversal out of approximately 210844 total reads (7.74%)
[2016-04-15T00:28Z] INFO  17:28:07,774 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:28Z] INFO  17:28:07,774 MicroScheduler -   -> 338 reads (0.16% of total) failing BadMateFilter
[2016-04-15T00:28Z] INFO  17:28:07,774 MicroScheduler -   -> 15859 reads (7.52% of total) failing DuplicateReadFilter
[2016-04-15T00:28Z] INFO  17:28:07,774 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:28Z] INFO  17:28:07,775 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:28Z] INFO  17:28:07,775 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:28Z] INFO  17:28:07,775 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:28Z] INFO  17:28:07,775 MicroScheduler -   -> 124 reads (0.06% of total) failing UnmappedReadFilter
[2016-04-15T00:28Z] INFO  17:28:07,838 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:28Z] INFO  17:28:07,847 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:28Z] INFO  17:28:07,945 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.10
[2016-04-15T00:28Z] INFO  17:28:08,139 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:28Z] INFO  17:28:08,141 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:28Z] INFO  17:28:08,142 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:28Z] INFO  17:28:08,142 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:28Z] INFO  17:28:08,146 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/2/R14-18106_kapa-NGv3-PE100-NGv3-sort-2_79253838_95537822-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/2/R14-18106_kapa-NGv3-PE100-NGv3-2_79253838_95537822-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/2/tx/tmphNdE2o/R14-18106_kapa-NGv3-PE100-NGv3-2_79253838_95537822.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:28Z] INFO  17:28:08,178 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:28Z] INFO  17:28:08,179 HelpFormatter - Date/Time: 2016/04/14 17:28:08
[2016-04-15T00:28Z] INFO  17:28:08,179 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:28Z] INFO  17:28:08,179 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:28Z] INFO  17:28:08,334 IntervalUtils - Processing 224219 bp from intervals
[2016-04-15T00:28Z] WARN  17:28:08,351 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:28Z] INFO  17:28:08,447 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:28Z] INFO  17:28:08,470 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:28Z] INFO  17:28:08,577 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:28Z] INFO  17:28:08,580 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:28Z] INFO  17:28:08,581 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:28Z] INFO  17:28:08,581 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:28Z] INFO  17:28:08,586 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/2/R14-18106_kapa-NGv3-PE100-NGv3-sort-2_95538561_111273222-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/2/R14-18106_kapa-NGv3-PE100-NGv3-2_95538561_111273222-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/2/tx/tmpgGBEQl/R14-18106_kapa-NGv3-PE100-NGv3-2_95538561_111273222.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:28Z] INFO  17:28:08,593 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:28Z] INFO  17:28:08,594 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:28Z] INFO  17:28:08,594 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:28Z] INFO  17:28:08,595 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:28Z] INFO  17:28:08,595 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:28Z] INFO  17:28:08,596 HelpFormatter - Date/Time: 2016/04/14 17:28:08
[2016-04-15T00:28Z] INFO  17:28:08,596 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:28Z] INFO  17:28:08,596 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:28Z] INFO  17:28:08,641 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:28Z] INFO  17:28:08,642 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:28Z] INFO  17:28:08,713 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:28Z] INFO  17:28:08,722 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:28Z] INFO  17:28:08,768 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:28Z] INFO  17:28:08,793 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:28Z] INFO  17:28:08,818 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.10
[2016-04-15T00:28Z] GATK: UnifiedGenotyper
[2016-04-15T00:28Z] INFO  17:28:09,024 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:28Z] INFO  17:28:09,033 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:28Z] INFO  17:28:09,104 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-15T00:28Z] INFO  17:28:09,135 IntervalUtils - Processing 101744 bp from intervals
[2016-04-15T00:28Z] WARN  17:28:09,140 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:28Z] INFO  17:28:09,224 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:28Z] INFO  17:28:09,273 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:28Z] INFO  17:28:09,308 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:28Z] INFO  17:28:09,309 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:28Z] INFO  17:28:09,310 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:28Z] INFO  17:28:09,310 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:28Z] INFO  17:28:09,353 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:28Z] INFO  17:28:09,354 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:28Z] INFO  17:28:09,568 IntervalUtils - Processing 250759 bp from intervals
[2016-04-15T00:28Z] WARN  17:28:09,574 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:28Z] GATK: UnifiedGenotyper
[2016-04-15T00:28Z] INFO  17:28:09,656 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:28Z] INFO  17:28:09,790 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:28Z] INFO  17:28:09,791 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:28Z] INFO  17:28:09,791 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:28Z] INFO  17:28:09,792 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:28Z] INFO  17:28:09,838 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:28Z] INFO  17:28:09,839 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:28Z] INFO  17:28:12,021 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:28Z] INFO  17:28:12,026 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:28Z] INFO  17:28:12,027 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:28Z] INFO  17:28:12,028 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:28Z] INFO  17:28:12,032 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/2/R14-18106_kapa-NGv3-PE100-NGv3-sort-2_111281072_127413888-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/2/R14-18106_kapa-NGv3-PE100-NGv3-2_111281072_127413888-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/2/tx/tmpwRBqma/R14-18106_kapa-NGv3-PE100-NGv3-2_111281072_127413888.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:28Z] INFO  17:28:12,063 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:28Z] INFO  17:28:12,072 HelpFormatter - Date/Time: 2016/04/14 17:28:12
[2016-04-15T00:28Z] INFO  17:28:12,073 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:28Z] INFO  17:28:12,074 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:28Z] INFO  17:28:12,240 ProgressMeter -       1:9801251   1320276.0    30.0 s      22.0 s       60.7%    49.0 s      19.0 s
[2016-04-15T00:28Z] INFO  17:28:12,258 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:28Z] INFO  17:28:12,448 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:28Z] INFO  17:28:12,458 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:28Z] INFO  17:28:12,510 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:28Z] INFO  17:28:12,512 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:28Z] INFO  17:28:12,513 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:28Z] INFO  17:28:12,513 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:28Z] INFO  17:28:12,517 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/2/R14-18106_kapa-NGv3-PE100-NGv3-sort-2_127433207_143643105-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/2/R14-18106_kapa-NGv3-PE100-NGv3-2_127433207_143643105-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/2/tx/tmpEQtStr/R14-18106_kapa-NGv3-PE100-NGv3-2_127433207_143643105.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:28Z] INFO  17:28:12,536 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:28Z] INFO  17:28:12,537 HelpFormatter - Date/Time: 2016/04/14 17:28:12
[2016-04-15T00:28Z] INFO  17:28:12,537 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:28Z] INFO  17:28:12,538 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:28Z] INFO  17:28:12,538 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-15T00:28Z] INFO  17:28:12,729 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:28Z] INFO  17:28:13,043 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:28Z] INFO  17:28:13,047 IntervalUtils - Processing 123675 bp from intervals
[2016-04-15T00:28Z] WARN  17:28:13,052 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:28Z] INFO  17:28:13,055 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:28Z] INFO  17:28:13,123 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:28Z] INFO  17:28:13,154 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.10
[2016-04-15T00:28Z] INFO  17:28:13,203 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:28Z] INFO  17:28:13,204 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:28Z] INFO  17:28:13,205 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:28Z] INFO  17:28:13,205 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:28Z] INFO  17:28:13,253 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:28Z] INFO  17:28:13,254 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:28Z] INFO  17:28:13,598 IntervalUtils - Processing 171560 bp from intervals
[2016-04-15T00:28Z] WARN  17:28:13,603 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:28Z] INFO  17:28:13,660 ProgressMeter -      1:24387550   1112336.0    30.0 s      26.0 s       61.3%    48.0 s      18.0 s
[2016-04-15T00:28Z] INFO  17:28:13,689 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:28Z] INFO  17:28:13,827 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:28Z] INFO  17:28:13,828 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:28Z] INFO  17:28:13,828 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:28Z] INFO  17:28:13,833 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:28Z] INFO  17:28:13,915 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:28Z] INFO  17:28:13,916 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:28Z] INFO  17:28:14,031 ProgressMeter -            done    911237.0    28.0 s      31.0 s      100.0%    28.0 s       0.0 s
[2016-04-15T00:28Z] INFO  17:28:14,032 ProgressMeter - Total runtime 28.37 secs, 0.47 min, 0.01 hours
[2016-04-15T00:28Z] INFO  17:28:14,032 MicroScheduler - 26065 reads were filtered out during the traversal out of approximately 331895 total reads (7.85%)
[2016-04-15T00:28Z] INFO  17:28:14,032 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:28Z] INFO  17:28:14,033 MicroScheduler -   -> 544 reads (0.16% of total) failing BadMateFilter
[2016-04-15T00:28Z] INFO  17:28:14,033 MicroScheduler -   -> 25320 reads (7.63% of total) failing DuplicateReadFilter
[2016-04-15T00:28Z] INFO  17:28:14,033 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:28Z] INFO  17:28:14,033 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:28Z] INFO  17:28:14,034 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:28Z] INFO  17:28:14,034 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:28Z] INFO  17:28:14,034 MicroScheduler -   -> 201 reads (0.06% of total) failing UnmappedReadFilter
[2016-04-15T00:28Z] INFO  17:28:14,116 ProgressMeter -      1:40882752   1149163.0    30.0 s      26.0 s       64.0%    46.0 s      16.0 s
[2016-04-15T00:28Z] INFO  17:28:14,260 ProgressMeter -     1:153012704    949722.0    30.0 s      31.0 s       44.7%    67.0 s      37.0 s
[2016-04-15T00:28Z] INFO  17:28:15,327 ProgressMeter -            done    970614.0    28.0 s      29.0 s      100.0%    28.0 s       0.0 s
[2016-04-15T00:28Z] INFO  17:28:15,329 ProgressMeter - Total runtime 28.90 secs, 0.48 min, 0.01 hours
[2016-04-15T00:28Z] INFO  17:28:15,330 MicroScheduler - 26953 reads were filtered out during the traversal out of approximately 338299 total reads (7.97%)
[2016-04-15T00:28Z] INFO  17:28:15,331 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:28Z] INFO  17:28:15,332 MicroScheduler -   -> 507 reads (0.15% of total) failing BadMateFilter
[2016-04-15T00:28Z] INFO  17:28:15,332 MicroScheduler -   -> 26225 reads (7.75% of total) failing DuplicateReadFilter
[2016-04-15T00:28Z] INFO  17:28:15,333 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:28Z] INFO  17:28:15,334 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:28Z] INFO  17:28:15,334 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:28Z] INFO  17:28:15,335 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:28Z] INFO  17:28:15,336 MicroScheduler -   -> 221 reads (0.07% of total) failing UnmappedReadFilter
[2016-04-15T00:28Z] INFO  17:28:15,472 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:28Z] GATK: UnifiedGenotyper
[2016-04-15T00:28Z] INFO  17:28:16,123 ProgressMeter -     1:238053861    967744.0    30.0 s      31.0 s       99.4%    30.0 s       0.0 s
[2016-04-15T00:28Z] INFO  17:28:16,375 ProgressMeter -            done    971140.0    30.0 s      31.0 s      100.0%    30.0 s       0.0 s
[2016-04-15T00:28Z] INFO  17:28:16,376 ProgressMeter - Total runtime 30.30 secs, 0.50 min, 0.01 hours
[2016-04-15T00:28Z] INFO  17:28:16,376 MicroScheduler - 28845 reads were filtered out during the traversal out of approximately 364560 total reads (7.91%)
[2016-04-15T00:28Z] INFO  17:28:16,377 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:28Z] INFO  17:28:16,377 MicroScheduler -   -> 611 reads (0.17% of total) failing BadMateFilter
[2016-04-15T00:28Z] INFO  17:28:16,377 MicroScheduler -   -> 28015 reads (7.68% of total) failing DuplicateReadFilter
[2016-04-15T00:28Z] INFO  17:28:16,378 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:28Z] INFO  17:28:16,378 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:28Z] INFO  17:28:16,378 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:28Z] INFO  17:28:16,379 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:28Z] INFO  17:28:16,379 MicroScheduler -   -> 219 reads (0.06% of total) failing UnmappedReadFilter
[2016-04-15T00:28Z] INFO  17:28:16,550 ProgressMeter -     1:207498967    987420.0    30.0 s      30.0 s       99.5%    30.0 s       0.0 s
[2016-04-15T00:28Z] INFO  17:28:16,795 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:28Z] INFO  17:28:16,915 ProgressMeter -            done    991088.0    30.0 s      30.0 s      100.0%    30.0 s       0.0 s
[2016-04-15T00:28Z] INFO  17:28:16,915 ProgressMeter - Total runtime 30.41 secs, 0.51 min, 0.01 hours
[2016-04-15T00:28Z] INFO  17:28:16,916 MicroScheduler - 27054 reads were filtered out during the traversal out of approximately 345054 total reads (7.84%)
[2016-04-15T00:28Z] INFO  17:28:16,916 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:28Z] INFO  17:28:16,916 MicroScheduler -   -> 595 reads (0.17% of total) failing BadMateFilter
[2016-04-15T00:28Z] INFO  17:28:16,917 MicroScheduler -   -> 26209 reads (7.60% of total) failing DuplicateReadFilter
[2016-04-15T00:28Z] INFO  17:28:16,917 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:28Z] INFO  17:28:16,917 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:28Z] INFO  17:28:16,918 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:28Z] INFO  17:28:16,918 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:28Z] INFO  17:28:16,918 MicroScheduler -   -> 250 reads (0.07% of total) failing UnmappedReadFilter
[2016-04-15T00:28Z] GATK: UnifiedGenotyper
[2016-04-15T00:28Z] INFO  17:28:18,061 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:28Z] INFO  17:28:18,414 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:28Z] GATK: UnifiedGenotyper
[2016-04-15T00:28Z] GATK: UnifiedGenotyper
[2016-04-15T00:28Z] INFO  17:28:18,769 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:28Z] INFO  17:28:18,782 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:28Z] INFO  17:28:18,782 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:28Z] INFO  17:28:18,783 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:28Z] INFO  17:28:18,787 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/2/R14-18106_kapa-NGv3-PE100-NGv3-sort-2_143676177_159195597-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/2/R14-18106_kapa-NGv3-PE100-NGv3-2_143676177_159195597-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/2/tx/tmpC0E6YT/R14-18106_kapa-NGv3-PE100-NGv3-2_143676177_159195597.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:28Z] INFO  17:28:18,804 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:28Z] INFO  17:28:18,805 HelpFormatter - Date/Time: 2016/04/14 17:28:18
[2016-04-15T00:28Z] INFO  17:28:18,805 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:28Z] INFO  17:28:18,806 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:28Z] INFO  17:28:18,964 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:28Z] INFO  17:28:19,221 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:28Z] INFO  17:28:19,234 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:28Z] INFO  17:28:19,325 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.09
[2016-04-15T00:28Z] INFO  17:28:19,649 IntervalUtils - Processing 92555 bp from intervals
[2016-04-15T00:28Z] WARN  17:28:19,654 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:28Z] INFO  17:28:19,721 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:28Z] INFO  17:28:19,798 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:28Z] INFO  17:28:19,798 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:28Z] INFO  17:28:19,799 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:28Z] INFO  17:28:19,799 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:28Z] INFO  17:28:19,848 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:28Z] INFO  17:28:19,849 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:28Z] INFO  17:28:20,120 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:28Z] INFO  17:28:20,123 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:28Z] INFO  17:28:20,124 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:28Z] INFO  17:28:20,124 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:28Z] INFO  17:28:20,129 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/2/R14-18106_kapa-NGv3-PE100-NGv3-sort-2_159196753_174774985-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/2/R14-18106_kapa-NGv3-PE100-NGv3-2_159196753_174774985-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/2/tx/tmpHo0pQr/R14-18106_kapa-NGv3-PE100-NGv3-2_159196753_174774985.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:28Z] INFO  17:28:20,157 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:28Z] INFO  17:28:20,157 HelpFormatter - Date/Time: 2016/04/14 17:28:20
[2016-04-15T00:28Z] INFO  17:28:20,157 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:28Z] INFO  17:28:20,157 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:28Z] INFO  17:28:20,348 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:28Z] INFO  17:28:20,590 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:28Z] INFO  17:28:20,611 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:28Z] INFO  17:28:20,699 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.09
[2016-04-15T00:28Z] INFO  17:28:21,146 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:28Z] INFO  17:28:21,149 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:28Z] INFO  17:28:21,150 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:28Z] INFO  17:28:21,150 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:28Z] INFO  17:28:21,155 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/2/R14-18106_kapa-NGv3-PE100-NGv3-sort-2_174777797_190306304-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/2/R14-18106_kapa-NGv3-PE100-NGv3-2_174777797_190306304-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/2/tx/tmpgUbf_g/R14-18106_kapa-NGv3-PE100-NGv3-2_174777797_190306304.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:28Z] INFO  17:28:21,160 IntervalUtils - Processing 216485 bp from intervals
[2016-04-15T00:28Z] INFO  17:28:21,165 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:28Z] INFO  17:28:21,165 HelpFormatter - Date/Time: 2016/04/14 17:28:21
[2016-04-15T00:28Z] INFO  17:28:21,166 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:28Z] INFO  17:28:21,167 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:28Z] WARN  17:28:21,176 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:28Z] INFO  17:28:21,286 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:28Z] INFO  17:28:21,336 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:28Z] INFO  17:28:21,366 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:28Z] INFO  17:28:21,367 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:28Z] INFO  17:28:21,368 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:28Z] INFO  17:28:21,369 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:28Z] INFO  17:28:21,416 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:28Z] INFO  17:28:21,417 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:28Z] INFO  17:28:21,514 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:28Z] INFO  17:28:21,524 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:28Z] INFO  17:28:21,524 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:28Z] INFO  17:28:21,525 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:28Z] INFO  17:28:21,530 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/2/R14-18106_kapa-NGv3-PE100-NGv3-sort-2_190313104_205830046-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/2/R14-18106_kapa-NGv3-PE100-NGv3-2_190313104_205830046-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/2/tx/tmpQA9Dvv/R14-18106_kapa-NGv3-PE100-NGv3-2_190313104_205830046.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:28Z] INFO  17:28:21,548 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:28Z] INFO  17:28:21,549 HelpFormatter - Date/Time: 2016/04/14 17:28:21
[2016-04-15T00:28Z] INFO  17:28:21,549 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:28Z] INFO  17:28:21,550 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:28Z] INFO  17:28:21,590 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:28Z] INFO  17:28:21,605 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:28Z] INFO  17:28:21,667 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:28Z] INFO  17:28:21,704 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.10
[2016-04-15T00:28Z] INFO  17:28:21,857 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:28Z] INFO  17:28:21,866 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:28Z] INFO  17:28:21,951 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-15T00:28Z] INFO  17:28:22,130 IntervalUtils - Processing 253764 bp from intervals
[2016-04-15T00:28Z] WARN  17:28:22,136 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:28Z] INFO  17:28:22,237 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:28Z] INFO  17:28:22,373 IntervalUtils - Processing 204460 bp from intervals
[2016-04-15T00:28Z] WARN  17:28:22,378 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:28Z] INFO  17:28:22,393 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:28Z] INFO  17:28:22,394 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:28Z] INFO  17:28:22,395 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:28Z] INFO  17:28:22,397 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:28Z] INFO  17:28:22,444 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:28Z] INFO  17:28:22,466 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:28Z] INFO  17:28:22,467 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:28Z] INFO  17:28:22,524 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:28Z] INFO  17:28:22,526 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:28Z] INFO  17:28:22,526 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:28Z] INFO  17:28:22,527 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:28Z] INFO  17:28:22,569 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:28Z] INFO  17:28:22,570 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:28Z] INFO  17:28:23,117 ProgressMeter -            done    451799.0    15.0 s      34.0 s       99.9%    15.0 s       0.0 s
[2016-04-15T00:28Z] INFO  17:28:23,118 ProgressMeter - Total runtime 15.45 secs, 0.26 min, 0.00 hours
[2016-04-15T00:28Z] INFO  17:28:23,118 MicroScheduler - 12122 reads were filtered out during the traversal out of approximately 154845 total reads (7.83%)
[2016-04-15T00:28Z] INFO  17:28:23,119 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:28Z] INFO  17:28:23,119 MicroScheduler -   -> 235 reads (0.15% of total) failing BadMateFilter
[2016-04-15T00:28Z] INFO  17:28:23,119 MicroScheduler -   -> 11783 reads (7.61% of total) failing DuplicateReadFilter
[2016-04-15T00:28Z] INFO  17:28:23,120 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:28Z] INFO  17:28:23,120 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:28Z] INFO  17:28:23,120 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:28Z] INFO  17:28:23,121 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:28Z] INFO  17:28:23,121 MicroScheduler -   -> 104 reads (0.07% of total) failing UnmappedReadFilter
[2016-04-15T00:28Z] INFO  17:28:24,456 ProgressMeter -            done    366382.0    15.0 s      41.0 s       99.9%    15.0 s       0.0 s
[2016-04-15T00:28Z] INFO  17:28:24,456 ProgressMeter - Total runtime 15.15 secs, 0.25 min, 0.00 hours
[2016-04-15T00:28Z] INFO  17:28:24,457 MicroScheduler - 11391 reads were filtered out during the traversal out of approximately 161076 total reads (7.07%)
[2016-04-15T00:28Z] INFO  17:28:24,457 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:28Z] INFO  17:28:24,457 MicroScheduler -   -> 283 reads (0.18% of total) failing BadMateFilter
[2016-04-15T00:28Z] INFO  17:28:24,457 MicroScheduler -   -> 11013 reads (6.84% of total) failing DuplicateReadFilter
[2016-04-15T00:28Z] INFO  17:28:24,458 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:28Z] INFO  17:28:24,458 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:28Z] INFO  17:28:24,458 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:28Z] INFO  17:28:24,458 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:28Z] INFO  17:28:24,459 MicroScheduler -   -> 95 reads (0.06% of total) failing UnmappedReadFilter
[2016-04-15T00:28Z] INFO  17:28:24,486 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:28Z] GATK: UnifiedGenotyper
[2016-04-15T00:28Z] INFO  17:28:25,719 ProgressMeter -            done    491998.0    18.0 s      37.0 s      100.0%    18.0 s       0.0 s
[2016-04-15T00:28Z] INFO  17:28:25,720 ProgressMeter - Total runtime 18.60 secs, 0.31 min, 0.01 hours
[2016-04-15T00:28Z] INFO  17:28:25,720 MicroScheduler - 15052 reads were filtered out during the traversal out of approximately 191369 total reads (7.87%)
[2016-04-15T00:28Z] INFO  17:28:25,721 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:28Z] INFO  17:28:25,721 MicroScheduler -   -> 268 reads (0.14% of total) failing BadMateFilter
[2016-04-15T00:28Z] INFO  17:28:25,721 MicroScheduler -   -> 14682 reads (7.67% of total) failing DuplicateReadFilter
[2016-04-15T00:28Z] INFO  17:28:25,722 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:28Z] INFO  17:28:25,722 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:28Z] INFO  17:28:25,722 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:28Z] INFO  17:28:25,723 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:28Z] INFO  17:28:25,723 MicroScheduler -   -> 102 reads (0.05% of total) failing UnmappedReadFilter
[2016-04-15T00:28Z] INFO  17:28:25,967 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:28Z] GATK: UnifiedGenotyper
[2016-04-15T00:28Z] INFO  17:28:27,184 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:28Z] INFO  17:28:27,188 ProgressMeter -            done   1670041.0    43.0 s      26.0 s      100.0%    43.0 s       0.0 s
[2016-04-15T00:28Z] INFO  17:28:27,189 ProgressMeter - Total runtime 43.55 secs, 0.73 min, 0.01 hours
[2016-04-15T00:28Z] INFO  17:28:27,189 MicroScheduler - 46918 reads were filtered out during the traversal out of approximately 584642 total reads (8.03%)
[2016-04-15T00:28Z] INFO  17:28:27,190 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:28Z] INFO  17:28:27,190 MicroScheduler -   -> 992 reads (0.17% of total) failing BadMateFilter
[2016-04-15T00:28Z] INFO  17:28:27,190 MicroScheduler -   -> 45551 reads (7.79% of total) failing DuplicateReadFilter
[2016-04-15T00:28Z] INFO  17:28:27,190 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:28Z] INFO  17:28:27,191 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:28Z] INFO  17:28:27,191 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:28Z] INFO  17:28:27,191 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:28Z] INFO  17:28:27,191 MicroScheduler -   -> 375 reads (0.06% of total) failing UnmappedReadFilter
[2016-04-15T00:28Z] GATK: UnifiedGenotyper
[2016-04-15T00:28Z] INFO  17:28:27,458 ProgressMeter -            done   2049259.0    43.0 s      21.0 s      100.0%    43.0 s       0.0 s
[2016-04-15T00:28Z] INFO  17:28:27,458 ProgressMeter - Total runtime 43.37 secs, 0.72 min, 0.01 hours
[2016-04-15T00:28Z] INFO  17:28:27,459 MicroScheduler - 46343 reads were filtered out during the traversal out of approximately 592825 total reads (7.82%)
[2016-04-15T00:28Z] INFO  17:28:27,459 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:28Z] INFO  17:28:27,460 MicroScheduler -   -> 949 reads (0.16% of total) failing BadMateFilter
[2016-04-15T00:28Z] INFO  17:28:27,460 MicroScheduler -   -> 45007 reads (7.59% of total) failing DuplicateReadFilter
[2016-04-15T00:28Z] INFO  17:28:27,460 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:28Z] INFO  17:28:27,460 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:28Z] INFO  17:28:27,461 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:28Z] INFO  17:28:27,461 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:28Z] INFO  17:28:27,461 MicroScheduler -   -> 387 reads (0.07% of total) failing UnmappedReadFilter
[2016-04-15T00:28Z] INFO  17:28:28,059 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:28Z] INFO  17:28:28,062 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:28Z] INFO  17:28:28,062 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:28Z] INFO  17:28:28,063 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:28Z] INFO  17:28:28,069 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/2/R14-18106_kapa-NGv3-PE100-NGv3-sort-2_205912303_222290862-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/2/R14-18106_kapa-NGv3-PE100-NGv3-2_205912303_222290862-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/2/tx/tmpADEcOo/R14-18106_kapa-NGv3-PE100-NGv3-2_205912303_222290862.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:28Z] INFO  17:28:28,088 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:28Z] INFO  17:28:28,089 HelpFormatter - Date/Time: 2016/04/14 17:28:28
[2016-04-15T00:28Z] INFO  17:28:28,089 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:28Z] INFO  17:28:28,089 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:28Z] INFO  17:28:28,232 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:28Z] INFO  17:28:28,448 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:28Z] INFO  17:28:28,458 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:28Z] INFO  17:28:28,559 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.10
[2016-04-15T00:28Z] INFO  17:28:28,580 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:28Z] INFO  17:28:28,837 ProgressMeter -            done   1809594.0    46.0 s      25.0 s      100.0%    46.0 s       0.0 s
[2016-04-15T00:28Z] INFO  17:28:28,838 ProgressMeter - Total runtime 46.62 secs, 0.78 min, 0.01 hours
[2016-04-15T00:28Z] INFO  17:28:28,838 MicroScheduler - 46154 reads were filtered out during the traversal out of approximately 602833 total reads (7.66%)
[2016-04-15T00:28Z] INFO  17:28:28,838 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:28Z] INFO  17:28:28,839 MicroScheduler -   -> 1075 reads (0.18% of total) failing BadMateFilter
[2016-04-15T00:28Z] INFO  17:28:28,839 MicroScheduler -   -> 44642 reads (7.41% of total) failing DuplicateReadFilter
[2016-04-15T00:28Z] INFO  17:28:28,839 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:28Z] INFO  17:28:28,839 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:28Z] INFO  17:28:28,840 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:28Z] INFO  17:28:28,840 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:28Z] INFO  17:28:28,840 MicroScheduler -   -> 437 reads (0.07% of total) failing UnmappedReadFilter
[2016-04-15T00:28Z] GATK: UnifiedGenotyper
[2016-04-15T00:28Z] INFO  17:28:29,025 IntervalUtils - Processing 247026 bp from intervals
[2016-04-15T00:28Z] WARN  17:28:29,031 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:28Z] INFO  17:28:29,140 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:28Z] INFO  17:28:29,262 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:28Z] INFO  17:28:29,296 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:28Z] INFO  17:28:29,298 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:28Z] INFO  17:28:29,299 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:28Z] INFO  17:28:29,299 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:28Z] INFO  17:28:29,319 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:28Z] INFO  17:28:29,322 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:28Z] INFO  17:28:29,323 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:28Z] INFO  17:28:29,323 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:28Z] INFO  17:28:29,328 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/2/R14-18106_kapa-NGv3-PE100-NGv3-sort-2_222291154_237994685-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/2/R14-18106_kapa-NGv3-PE100-NGv3-2_222291154_237994685-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/2/tx/tmpCAv9jv/R14-18106_kapa-NGv3-PE100-NGv3-2_222291154_237994685.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:28Z] INFO  17:28:29,343 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:28Z] INFO  17:28:29,344 HelpFormatter - Date/Time: 2016/04/14 17:28:29
[2016-04-15T00:28Z] INFO  17:28:29,344 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:28Z] INFO  17:28:29,345 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:28Z] INFO  17:28:29,393 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:28Z] INFO  17:28:29,394 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:28Z] INFO  17:28:29,511 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:28Z] GATK: UnifiedGenotyper
[2016-04-15T00:28Z] INFO  17:28:29,738 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:28Z] INFO  17:28:29,747 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:28Z] INFO  17:28:29,816 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-15T00:28Z] INFO  17:28:30,072 ProgressMeter -            done    353576.0    16.0 s      47.0 s       99.9%    16.0 s       0.0 s
[2016-04-15T00:28Z] INFO  17:28:30,074 ProgressMeter - Total runtime 16.87 secs, 0.28 min, 0.00 hours
[2016-04-15T00:28Z] INFO  17:28:30,074 MicroScheduler - 12889 reads were filtered out during the traversal out of approximately 189528 total reads (6.80%)
[2016-04-15T00:28Z] INFO  17:28:30,075 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:28Z] INFO  17:28:30,076 MicroScheduler -   -> 310 reads (0.16% of total) failing BadMateFilter
[2016-04-15T00:28Z] INFO  17:28:30,076 MicroScheduler -   -> 12460 reads (6.57% of total) failing DuplicateReadFilter
[2016-04-15T00:28Z] INFO  17:28:30,077 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:28Z] INFO  17:28:30,077 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:28Z] INFO  17:28:30,078 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:28Z] INFO  17:28:30,079 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:28Z] INFO  17:28:30,079 MicroScheduler -   -> 119 reads (0.06% of total) failing UnmappedReadFilter
[2016-04-15T00:28Z] INFO  17:28:30,196 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:28Z] INFO  17:28:30,202 IntervalUtils - Processing 186854 bp from intervals
[2016-04-15T00:28Z] WARN  17:28:30,207 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:28Z] INFO  17:28:30,285 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:28Z] INFO  17:28:30,365 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:28Z] INFO  17:28:30,368 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:28Z] INFO  17:28:30,369 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:28Z] INFO  17:28:30,370 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:28Z] INFO  17:28:30,374 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/2/R14-18106_kapa-NGv3-PE100-NGv3-sort-2_237995374_243199373-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/2/R14-18106_kapa-NGv3-PE100-NGv3-2_237995374_243199373-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/2/tx/tmp6U2oH0/R14-18106_kapa-NGv3-PE100-NGv3-2_237995374_243199373.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:28Z] INFO  17:28:30,388 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:28Z] INFO  17:28:30,394 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:28Z] INFO  17:28:30,395 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:28Z] INFO  17:28:30,395 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:28Z] INFO  17:28:30,409 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:28Z] INFO  17:28:30,410 HelpFormatter - Date/Time: 2016/04/14 17:28:30
[2016-04-15T00:28Z] INFO  17:28:30,411 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:28Z] INFO  17:28:30,411 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:28Z] INFO  17:28:30,452 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:28Z] INFO  17:28:30,452 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:28Z] GATK: UnifiedGenotyper
[2016-04-15T00:28Z] INFO  17:28:30,550 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:28Z] INFO  17:28:30,621 ProgressMeter -            done   1055597.0    24.0 s      23.0 s      100.0%    24.0 s       0.0 s
[2016-04-15T00:28Z] INFO  17:28:30,621 ProgressMeter - Total runtime 24.32 secs, 0.41 min, 0.01 hours
[2016-04-15T00:28Z] INFO  17:28:30,622 MicroScheduler - 24103 reads were filtered out during the traversal out of approximately 301505 total reads (7.99%)
[2016-04-15T00:28Z] INFO  17:28:30,622 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:28Z] INFO  17:28:30,622 MicroScheduler -   -> 467 reads (0.15% of total) failing BadMateFilter
[2016-04-15T00:28Z] INFO  17:28:30,622 MicroScheduler -   -> 23469 reads (7.78% of total) failing DuplicateReadFilter
[2016-04-15T00:28Z] INFO  17:28:30,623 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:28Z] INFO  17:28:30,623 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:28Z] INFO  17:28:30,623 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:28Z] INFO  17:28:30,623 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:28Z] INFO  17:28:30,624 MicroScheduler -   -> 167 reads (0.06% of total) failing UnmappedReadFilter
[2016-04-15T00:28Z] INFO  17:28:30,798 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:28Z] INFO  17:28:30,810 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:28Z] INFO  17:28:30,907 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.10
[2016-04-15T00:28Z] INFO  17:28:31,425 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:28Z] INFO  17:28:31,438 ProgressMeter -            done    341277.0    11.0 s      34.0 s       99.9%    11.0 s       0.0 s
[2016-04-15T00:28Z] INFO  17:28:31,438 ProgressMeter - Total runtime 11.64 secs, 0.19 min, 0.00 hours
[2016-04-15T00:28Z] INFO  17:28:31,439 MicroScheduler - 7864 reads were filtered out during the traversal out of approximately 105111 total reads (7.48%)
[2016-04-15T00:28Z] INFO  17:28:31,439 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:28Z] INFO  17:28:31,439 MicroScheduler -   -> 172 reads (0.16% of total) failing BadMateFilter
[2016-04-15T00:28Z] INFO  17:28:31,440 MicroScheduler -   -> 7637 reads (7.27% of total) failing DuplicateReadFilter
[2016-04-15T00:28Z] INFO  17:28:31,440 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:28Z] INFO  17:28:31,440 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:28Z] INFO  17:28:31,441 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:28Z] INFO  17:28:31,441 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:28Z] INFO  17:28:31,441 MicroScheduler -   -> 55 reads (0.05% of total) failing UnmappedReadFilter
[2016-04-15T00:28Z] INFO  17:28:31,443 IntervalUtils - Processing 128077 bp from intervals
[2016-04-15T00:28Z] WARN  17:28:31,450 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:28Z] INFO  17:28:31,600 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:28Z] INFO  17:28:31,633 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:28Z] INFO  17:28:31,637 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:28Z] INFO  17:28:31,638 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:28Z] INFO  17:28:31,639 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:28Z] INFO  17:28:31,644 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/3/R14-18106_kapa-NGv3-PE100-NGv3-sort-3_0_15512123-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/3/R14-18106_kapa-NGv3-PE100-NGv3-3_0_15512123-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/3/tx/tmposa6HR/R14-18106_kapa-NGv3-PE100-NGv3-3_0_15512123.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:28Z] INFO  17:28:31,665 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:28Z] INFO  17:28:31,666 HelpFormatter - Date/Time: 2016/04/14 17:28:31
[2016-04-15T00:28Z] INFO  17:28:31,666 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:28Z] INFO  17:28:31,667 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:28Z] INFO  17:28:31,717 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:28Z] INFO  17:28:31,718 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:28Z] INFO  17:28:31,718 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:28Z] INFO  17:28:31,718 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:28Z] INFO  17:28:31,778 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:28Z] INFO  17:28:31,779 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:28Z] GATK: UnifiedGenotyper
[2016-04-15T00:28Z] INFO  17:28:31,874 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:28Z] INFO  17:28:32,040 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:28Z] INFO  17:28:32,049 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:28Z] INFO  17:28:32,052 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:28Z] GATK: UnifiedGenotyper
[2016-04-15T00:28Z] INFO  17:28:32,310 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.26
[2016-04-15T00:28Z] INFO  17:28:32,641 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:28Z] INFO  17:28:32,655 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:28Z] INFO  17:28:32,656 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:28Z] INFO  17:28:32,657 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:28Z] INFO  17:28:32,662 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/3/R14-18106_kapa-NGv3-PE100-NGv3-sort-3_15515506_31574805-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/3/R14-18106_kapa-NGv3-PE100-NGv3-3_15515506_31574805-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/3/tx/tmpzUD1qs/R14-18106_kapa-NGv3-PE100-NGv3-3_15515506_31574805.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:28Z] INFO  17:28:32,672 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:28Z] INFO  17:28:32,682 HelpFormatter - Date/Time: 2016/04/14 17:28:32
[2016-04-15T00:28Z] INFO  17:28:32,683 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:28Z] INFO  17:28:32,683 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:28Z] INFO  17:28:32,749 IntervalUtils - Processing 188511 bp from intervals
[2016-04-15T00:28Z] WARN  17:28:32,754 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:28Z] INFO  17:28:32,833 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:28Z] INFO  17:28:32,907 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:28Z] INFO  17:28:32,940 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:28Z] INFO  17:28:32,941 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:28Z] INFO  17:28:32,941 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:28Z] INFO  17:28:32,942 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:28Z] INFO  17:28:33,011 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:28Z] INFO  17:28:33,031 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:28Z] INFO  17:28:33,032 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:28Z] INFO  17:28:33,096 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:28Z] INFO  17:28:33,113 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:28Z] INFO  17:28:33,172 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-15T00:28Z] INFO  17:28:33,219 ProgressMeter -            done    769087.0    24.0 s      32.0 s      100.0%    24.0 s       0.0 s
[2016-04-15T00:28Z] INFO  17:28:33,220 ProgressMeter - Total runtime 24.63 secs, 0.41 min, 0.01 hours
[2016-04-15T00:28Z] INFO  17:28:33,221 MicroScheduler - 22012 reads were filtered out during the traversal out of approximately 280097 total reads (7.86%)
[2016-04-15T00:28Z] INFO  17:28:33,222 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:28Z] INFO  17:28:33,222 MicroScheduler -   -> 455 reads (0.16% of total) failing BadMateFilter
[2016-04-15T00:28Z] INFO  17:28:33,223 MicroScheduler -   -> 21366 reads (7.63% of total) failing DuplicateReadFilter
[2016-04-15T00:28Z] INFO  17:28:33,224 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:28Z] INFO  17:28:33,224 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:28Z] INFO  17:28:33,225 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:28Z] INFO  17:28:33,225 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:28Z] INFO  17:28:33,226 MicroScheduler -   -> 191 reads (0.07% of total) failing UnmappedReadFilter
[2016-04-15T00:28Z] GATK: UnifiedGenotyper
[2016-04-15T00:28Z] INFO  17:28:33,555 IntervalUtils - Processing 86168 bp from intervals
[2016-04-15T00:28Z] WARN  17:28:33,559 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:28Z] INFO  17:28:33,626 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:28Z] INFO  17:28:33,685 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:28Z] INFO  17:28:33,687 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:28Z] INFO  17:28:33,685 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:28Z] INFO  17:28:33,687 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:28Z] INFO  17:28:33,688 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:28Z] INFO  17:28:33,688 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:28Z] INFO  17:28:33,688 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:28Z] INFO  17:28:33,688 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:28Z] INFO  17:28:33,692 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/3/R14-18106_kapa-NGv3-PE100-NGv3-sort-3_31617887_47127804-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/3/R14-18106_kapa-NGv3-PE100-NGv3-3_31617887_47127804-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/3/tx/tmpZZaajZ/R14-18106_kapa-NGv3-PE100-NGv3-3_31617887_47127804.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:28Z] INFO  17:28:33,713 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:28Z] INFO  17:28:33,713 HelpFormatter - Date/Time: 2016/04/14 17:28:33
[2016-04-15T00:28Z] INFO  17:28:33,714 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:28Z] INFO  17:28:33,719 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:28Z] INFO  17:28:33,733 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:28Z] INFO  17:28:33,734 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:28Z] INFO  17:28:33,934 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:28Z] INFO  17:28:34,177 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:28Z] INFO  17:28:34,192 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:28Z] INFO  17:28:34,286 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.09
[2016-04-15T00:28Z] INFO  17:28:34,714 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:28Z] INFO  17:28:34,749 IntervalUtils - Processing 307437 bp from intervals
[2016-04-15T00:28Z] INFO  17:28:34,751 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:28Z] INFO  17:28:34,754 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:28Z] INFO  17:28:34,754 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:28Z] INFO  17:28:34,755 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:28Z] INFO  17:28:34,759 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/3/R14-18106_kapa-NGv3-PE100-NGv3-sort-3_47129602_62648069-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/3/R14-18106_kapa-NGv3-PE100-NGv3-3_47129602_62648069-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/3/tx/tmp4i49Kl/R14-18106_kapa-NGv3-PE100-NGv3-3_47129602_62648069.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:28Z] WARN  17:28:34,766 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:28Z] INFO  17:28:34,802 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:28Z] INFO  17:28:34,808 HelpFormatter - Date/Time: 2016/04/14 17:28:34
[2016-04-15T00:28Z] INFO  17:28:34,809 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:28Z] INFO  17:28:34,809 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:28Z] INFO  17:28:34,906 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:28Z] GATK: UnifiedGenotyper
[2016-04-15T00:28Z] INFO  17:28:35,072 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:28Z] INFO  17:28:35,079 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:28Z] INFO  17:28:35,080 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:28Z] INFO  17:28:35,080 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:28Z] INFO  17:28:35,081 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:28Z] INFO  17:28:35,164 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:28Z] INFO  17:28:35,165 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:28Z] INFO  17:28:35,386 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:28Z] INFO  17:28:35,396 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:28Z] INFO  17:28:35,508 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.11
[2016-04-15T00:28Z] INFO  17:28:35,562 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:28Z] INFO  17:28:35,565 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:28Z] INFO  17:28:35,566 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:28Z] INFO  17:28:35,566 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:28Z] INFO  17:28:35,570 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/3/R14-18106_kapa-NGv3-PE100-NGv3-sort-3_62739115_78648077-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/3/R14-18106_kapa-NGv3-PE100-NGv3-3_62739115_78648077-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/3/tx/tmpk2tySJ/R14-18106_kapa-NGv3-PE100-NGv3-3_62739115_78648077.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:28Z] INFO  17:28:35,610 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:28Z] INFO  17:28:35,626 HelpFormatter - Date/Time: 2016/04/14 17:28:35
[2016-04-15T00:28Z] INFO  17:28:35,626 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:28Z] INFO  17:28:35,627 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:28Z] INFO  17:28:35,776 ProgressMeter -            done    525700.0    21.0 s      41.0 s      100.0%    21.0 s       0.0 s
[2016-04-15T00:28Z] INFO  17:28:35,776 ProgressMeter - Total runtime 21.95 secs, 0.37 min, 0.01 hours
[2016-04-15T00:28Z] INFO  17:28:35,777 MicroScheduler - 19619 reads were filtered out during the traversal out of approximately 255431 total reads (7.68%)
[2016-04-15T00:28Z] INFO  17:28:35,777 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:28Z] INFO  17:28:35,777 MicroScheduler -   -> 417 reads (0.16% of total) failing BadMateFilter
[2016-04-15T00:28Z] INFO  17:28:35,778 MicroScheduler -   -> 19014 reads (7.44% of total) failing DuplicateReadFilter
[2016-04-15T00:28Z] INFO  17:28:35,778 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:28Z] INFO  17:28:35,778 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:28Z] INFO  17:28:35,778 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:28Z] INFO  17:28:35,779 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:28Z] INFO  17:28:35,779 MicroScheduler -   -> 188 reads (0.07% of total) failing UnmappedReadFilter
[2016-04-15T00:28Z] INFO  17:28:35,910 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:28Z] INFO  17:28:36,105 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:28Z] INFO  17:28:36,126 IntervalUtils - Processing 430308 bp from intervals
[2016-04-15T00:28Z] WARN  17:28:36,131 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:28Z] INFO  17:28:36,147 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:28Z] INFO  17:28:36,208 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:28Z] INFO  17:28:36,242 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.10
[2016-04-15T00:28Z] INFO  17:28:36,311 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:28Z] INFO  17:28:36,312 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:28Z] INFO  17:28:36,313 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:28Z] INFO  17:28:36,313 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:28Z] INFO  17:28:36,377 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:28Z] INFO  17:28:36,388 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:28Z] INFO  17:28:36,719 IntervalUtils - Processing 82160 bp from intervals
[2016-04-15T00:28Z] WARN  17:28:36,724 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:28Z] INFO  17:28:36,818 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:28Z] INFO  17:28:36,861 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:28Z] INFO  17:28:36,864 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:28Z] INFO  17:28:36,865 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:28Z] INFO  17:28:36,865 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:28Z] INFO  17:28:36,870 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/3/R14-18106_kapa-NGv3-PE100-NGv3-sort-3_78649262_96533852-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/3/R14-18106_kapa-NGv3-PE100-NGv3-3_78649262_96533852-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/3/tx/tmpHoKBO8/R14-18106_kapa-NGv3-PE100-NGv3-3_78649262_96533852.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:28Z] INFO  17:28:36,907 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:28Z] INFO  17:28:36,909 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:28Z] INFO  17:28:36,910 HelpFormatter - Date/Time: 2016/04/14 17:28:36
[2016-04-15T00:28Z] INFO  17:28:36,910 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:28Z] INFO  17:28:36,911 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:28Z] INFO  17:28:36,921 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:28Z] INFO  17:28:36,921 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:28Z] INFO  17:28:36,932 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:28Z] INFO  17:28:36,988 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:28Z] INFO  17:28:36,988 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:28Z] INFO  17:28:37,066 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:28Z] INFO  17:28:37,212 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:28Z] INFO  17:28:37,239 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:28Z] INFO  17:28:37,249 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:28Z] INFO  17:28:37,322 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-15T00:28Z] GATK: UnifiedGenotyper
[2016-04-15T00:28Z] INFO  17:28:37,699 IntervalUtils - Processing 30411 bp from intervals
[2016-04-15T00:28Z] WARN  17:28:37,704 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:28Z] INFO  17:28:37,776 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:28Z] INFO  17:28:37,851 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:28Z] INFO  17:28:37,854 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:28Z] INFO  17:28:37,855 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:28Z] INFO  17:28:37,856 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:28Z] INFO  17:28:37,860 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/3/R14-18106_kapa-NGv3-PE100-NGv3-sort-3_96585668_112185230-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/3/R14-18106_kapa-NGv3-PE100-NGv3-3_96585668_112185230-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/3/tx/tmpKsITAi/R14-18106_kapa-NGv3-PE100-NGv3-3_96585668_112185230.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:28Z] INFO  17:28:37,866 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:28Z] INFO  17:28:37,867 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:28Z] INFO  17:28:37,879 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:28Z] INFO  17:28:37,880 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:28Z] INFO  17:28:37,900 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:28Z] INFO  17:28:37,901 HelpFormatter - Date/Time: 2016/04/14 17:28:37
[2016-04-15T00:28Z] INFO  17:28:37,901 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:28Z] INFO  17:28:37,902 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:28Z] INFO  17:28:37,938 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:28Z] INFO  17:28:37,939 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:28Z] INFO  17:28:38,149 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:28Z] INFO  17:28:38,358 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:28Z] INFO  17:28:38,371 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:28Z] INFO  17:28:38,466 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.09
[2016-04-15T00:28Z] INFO  17:28:38,929 IntervalUtils - Processing 140565 bp from intervals
[2016-04-15T00:28Z] WARN  17:28:38,948 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:28Z] INFO  17:28:39,030 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:28Z] INFO  17:28:39,158 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:28Z] INFO  17:28:39,159 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:28Z] INFO  17:28:39,160 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:28Z] INFO  17:28:39,161 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:28Z] INFO  17:28:39,252 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:28Z] INFO  17:28:39,263 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:28Z] INFO  17:28:39,488 ProgressMeter -            done   2535127.0    55.0 s      21.0 s      100.0%    55.0 s       0.0 s
[2016-04-15T00:28Z] INFO  17:28:39,488 ProgressMeter - Total runtime 55.26 secs, 0.92 min, 0.02 hours
[2016-04-15T00:28Z] INFO  17:28:39,488 MicroScheduler - 64236 reads were filtered out during the traversal out of approximately 819662 total reads (7.84%)
[2016-04-15T00:28Z] INFO  17:28:39,489 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:28Z] INFO  17:28:39,489 MicroScheduler -   -> 1308 reads (0.16% of total) failing BadMateFilter
[2016-04-15T00:28Z] INFO  17:28:39,489 MicroScheduler -   -> 62361 reads (7.61% of total) failing DuplicateReadFilter
[2016-04-15T00:28Z] INFO  17:28:39,489 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:28Z] INFO  17:28:39,490 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:28Z] INFO  17:28:39,490 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:28Z] INFO  17:28:39,490 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:28Z] INFO  17:28:39,490 MicroScheduler -   -> 567 reads (0.07% of total) failing UnmappedReadFilter
[2016-04-15T00:28Z] INFO  17:28:39,806 ProgressMeter -     2:110583978    987718.0    30.0 s      30.0 s       97.1%    30.0 s       0.0 s
[2016-04-15T00:28Z] INFO  17:28:40,637 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:28Z] INFO  17:28:40,639 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:28Z] INFO  17:28:40,640 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:28Z] INFO  17:28:40,640 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:28Z] INFO  17:28:40,645 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/3/R14-18106_kapa-NGv3-PE100-NGv3-sort-3_112188604_127703121-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/3/R14-18106_kapa-NGv3-PE100-NGv3-3_112188604_127703121-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/3/tx/tmpQZXscs/R14-18106_kapa-NGv3-PE100-NGv3-3_112188604_127703121.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:28Z] INFO  17:28:40,657 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:28Z] INFO  17:28:40,673 HelpFormatter - Date/Time: 2016/04/14 17:28:40
[2016-04-15T00:28Z] INFO  17:28:40,680 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:28Z] INFO  17:28:40,681 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:28Z] INFO  17:28:40,830 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:28Z] INFO  17:28:40,834 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:28Z] INFO  17:28:40,844 ProgressMeter -            done   1019400.0    31.0 s      30.0 s      100.0%    31.0 s       0.0 s
[2016-04-15T00:28Z] INFO  17:28:40,844 ProgressMeter - Total runtime 31.05 secs, 0.52 min, 0.01 hours
[2016-04-15T00:28Z] INFO  17:28:40,844 MicroScheduler - 30047 reads were filtered out during the traversal out of approximately 411800 total reads (7.30%)
[2016-04-15T00:28Z] INFO  17:28:40,845 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:28Z] INFO  17:28:40,845 MicroScheduler -   -> 656 reads (0.16% of total) failing BadMateFilter
[2016-04-15T00:28Z] INFO  17:28:40,845 MicroScheduler -   -> 29147 reads (7.08% of total) failing DuplicateReadFilter
[2016-04-15T00:28Z] INFO  17:28:40,846 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:28Z] INFO  17:28:40,846 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:28Z] INFO  17:28:40,846 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:28Z] INFO  17:28:40,846 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:28Z] INFO  17:28:40,847 MicroScheduler -   -> 244 reads (0.06% of total) failing UnmappedReadFilter
[2016-04-15T00:28Z] INFO  17:28:41,029 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:28Z] INFO  17:28:41,055 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:28Z] INFO  17:28:41,151 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.10
[2016-04-15T00:28Z] GATK: UnifiedGenotyper
[2016-04-15T00:28Z] INFO  17:28:41,587 IntervalUtils - Processing 249953 bp from intervals
[2016-04-15T00:28Z] WARN  17:28:41,592 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:28Z] INFO  17:28:41,706 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:28Z] INFO  17:28:41,815 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:28Z] INFO  17:28:41,817 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:28Z] INFO  17:28:41,817 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:28Z] INFO  17:28:41,818 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:28Z] INFO  17:28:41,862 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:28Z] INFO  17:28:41,863 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:28Z] INFO  17:28:42,226 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:28Z] GATK: UnifiedGenotyper
[2016-04-15T00:28Z] INFO  17:28:42,670 ProgressMeter -            done    606340.0    20.0 s      33.0 s      100.0%    20.0 s       0.0 s
[2016-04-15T00:28Z] INFO  17:28:42,671 ProgressMeter - Total runtime 20.15 secs, 0.34 min, 0.01 hours
[2016-04-15T00:28Z] INFO  17:28:42,672 MicroScheduler - 16447 reads were filtered out during the traversal out of approximately 212154 total reads (7.75%)
[2016-04-15T00:28Z] INFO  17:28:42,673 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:28Z] INFO  17:28:42,674 MicroScheduler -   -> 332 reads (0.16% of total) failing BadMateFilter
[2016-04-15T00:28Z] INFO  17:28:42,674 MicroScheduler -   -> 15989 reads (7.54% of total) failing DuplicateReadFilter
[2016-04-15T00:28Z] INFO  17:28:42,675 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:28Z] INFO  17:28:42,676 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:28Z] INFO  17:28:42,677 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:28Z] INFO  17:28:42,677 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:28Z] INFO  17:28:42,678 MicroScheduler -   -> 126 reads (0.06% of total) failing UnmappedReadFilter
[2016-04-15T00:28Z] INFO  17:28:43,831 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:28Z] INFO  17:28:43,834 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:28Z] INFO  17:28:43,834 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:28Z] INFO  17:28:43,835 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:28Z] INFO  17:28:43,839 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/3/R14-18106_kapa-NGv3-PE100-NGv3-sort-3_127770401_143293035-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/3/R14-18106_kapa-NGv3-PE100-NGv3-3_127770401_143293035-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/3/tx/tmpnSU6GS/R14-18106_kapa-NGv3-PE100-NGv3-3_127770401_143293035.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:28Z] INFO  17:28:43,853 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:28Z] INFO  17:28:43,854 HelpFormatter - Date/Time: 2016/04/14 17:28:43
[2016-04-15T00:28Z] INFO  17:28:43,854 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:28Z] INFO  17:28:43,855 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:28Z] INFO  17:28:44,025 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:28Z] INFO  17:28:44,217 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:28Z] INFO  17:28:44,234 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:28Z] INFO  17:28:44,243 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:28Z] INFO  17:28:44,306 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-15T00:28Z] GATK: UnifiedGenotyper
[2016-04-15T00:28Z] INFO  17:28:44,595 ProgressMeter -            done    626517.0    23.0 s      37.0 s      100.0%    23.0 s       0.0 s
[2016-04-15T00:28Z] INFO  17:28:44,596 ProgressMeter - Total runtime 23.23 secs, 0.39 min, 0.01 hours
[2016-04-15T00:28Z] INFO  17:28:44,596 MicroScheduler - 19193 reads were filtered out during the traversal out of approximately 245716 total reads (7.81%)
[2016-04-15T00:28Z] INFO  17:28:44,596 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:28Z] INFO  17:28:44,597 MicroScheduler -   -> 387 reads (0.16% of total) failing BadMateFilter
[2016-04-15T00:28Z] INFO  17:28:44,597 MicroScheduler -   -> 18643 reads (7.59% of total) failing DuplicateReadFilter
[2016-04-15T00:28Z] INFO  17:28:44,597 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:28Z] INFO  17:28:44,597 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:28Z] INFO  17:28:44,598 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:28Z] INFO  17:28:44,598 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:28Z] INFO  17:28:44,598 MicroScheduler -   -> 163 reads (0.07% of total) failing UnmappedReadFilter
[2016-04-15T00:28Z] INFO  17:28:44,735 IntervalUtils - Processing 238450 bp from intervals
[2016-04-15T00:28Z] WARN  17:28:44,747 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:28Z] INFO  17:28:44,811 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:28Z] INFO  17:28:44,914 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:28Z] INFO  17:28:44,915 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:28Z] INFO  17:28:44,916 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:28Z] INFO  17:28:44,916 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:28Z] INFO  17:28:44,969 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:28Z] INFO  17:28:44,969 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:28Z] INFO  17:28:45,735 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:28Z] INFO  17:28:45,738 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:28Z] INFO  17:28:45,739 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:28Z] INFO  17:28:45,739 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:28Z] INFO  17:28:45,744 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/3/R14-18106_kapa-NGv3-PE100-NGv3-sort-3_143297426_158963696-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/3/R14-18106_kapa-NGv3-PE100-NGv3-3_143297426_158963696-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/3/tx/tmp_ihVi3/R14-18106_kapa-NGv3-PE100-NGv3-3_143297426_158963696.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:28Z] INFO  17:28:45,771 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:28Z] INFO  17:28:45,772 HelpFormatter - Date/Time: 2016/04/14 17:28:45
[2016-04-15T00:28Z] INFO  17:28:45,772 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:28Z] INFO  17:28:45,773 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:28Z] INFO  17:28:45,834 ProgressMeter -            done     56098.0     7.0 s       2.4 m       99.7%     7.0 s       0.0 s
[2016-04-15T00:28Z] INFO  17:28:45,835 ProgressMeter - Total runtime 7.97 secs, 0.13 min, 0.00 hours
[2016-04-15T00:28Z] INFO  17:28:45,836 MicroScheduler - 2678 reads were filtered out during the traversal out of approximately 34946 total reads (7.66%)
[2016-04-15T00:28Z] INFO  17:28:45,837 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:28Z] INFO  17:28:45,837 MicroScheduler -   -> 61 reads (0.17% of total) failing BadMateFilter
[2016-04-15T00:28Z] INFO  17:28:45,838 MicroScheduler -   -> 2593 reads (7.42% of total) failing DuplicateReadFilter
[2016-04-15T00:28Z] INFO  17:28:45,839 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:28Z] INFO  17:28:45,839 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:28Z] INFO  17:28:45,840 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:28Z] INFO  17:28:45,841 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:28Z] INFO  17:28:45,841 MicroScheduler -   -> 24 reads (0.07% of total) failing UnmappedReadFilter
[2016-04-15T00:28Z] INFO  17:28:45,976 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:28Z] INFO  17:28:46,074 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:28Z] INFO  17:28:46,187 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:28Z] INFO  17:28:46,197 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:28Z] INFO  17:28:46,273 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-15T00:28Z] GATK: UnifiedGenotyper
[2016-04-15T00:28Z] INFO  17:28:46,710 IntervalUtils - Processing 125161 bp from intervals
[2016-04-15T00:28Z] WARN  17:28:46,715 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:28Z] INFO  17:28:46,783 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:28Z] INFO  17:28:46,918 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:28Z] INFO  17:28:46,919 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:28Z] INFO  17:28:46,919 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:28Z] INFO  17:28:46,920 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:28Z] INFO  17:28:47,030 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:28Z] INFO  17:28:47,030 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:28Z] INFO  17:28:47,089 ProgressMeter -            done    206627.0    13.0 s      64.0 s      100.0%    13.0 s       0.0 s
[2016-04-15T00:28Z] INFO  17:28:47,090 ProgressMeter - Total runtime 13.40 secs, 0.22 min, 0.00 hours
[2016-04-15T00:28Z] INFO  17:28:47,090 MicroScheduler - 7339 reads were filtered out during the traversal out of approximately 93696 total reads (7.83%)
[2016-04-15T00:28Z] INFO  17:28:47,091 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:28Z] INFO  17:28:47,091 MicroScheduler -   -> 149 reads (0.16% of total) failing BadMateFilter
[2016-04-15T00:28Z] INFO  17:28:47,091 MicroScheduler -   -> 7141 reads (7.62% of total) failing DuplicateReadFilter
[2016-04-15T00:28Z] INFO  17:28:47,091 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:28Z] INFO  17:28:47,092 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:28Z] INFO  17:28:47,092 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:28Z] INFO  17:28:47,092 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:28Z] INFO  17:28:47,092 MicroScheduler -   -> 49 reads (0.05% of total) failing UnmappedReadFilter
[2016-04-15T00:28Z] INFO  17:28:47,295 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:28Z] INFO  17:28:47,298 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:28Z] INFO  17:28:47,299 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:28Z] INFO  17:28:47,300 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:28Z] INFO  17:28:47,304 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/3/R14-18106_kapa-NGv3-PE100-NGv3-sort-3_158970515_174577240-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/3/R14-18106_kapa-NGv3-PE100-NGv3-3_158970515_174577240-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/3/tx/tmpwFZ4xl/R14-18106_kapa-NGv3-PE100-NGv3-3_158970515_174577240.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:28Z] INFO  17:28:47,315 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:28Z] INFO  17:28:47,328 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:28Z] INFO  17:28:47,330 HelpFormatter - Date/Time: 2016/04/14 17:28:47
[2016-04-15T00:28Z] INFO  17:28:47,331 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:28Z] INFO  17:28:47,332 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:28Z] INFO  17:28:47,477 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:28Z] GATK: UnifiedGenotyper
[2016-04-15T00:28Z] INFO  17:28:47,674 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:28Z] INFO  17:28:47,690 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:28Z] INFO  17:28:47,765 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-15T00:28Z] INFO  17:28:48,229 IntervalUtils - Processing 102254 bp from intervals
[2016-04-15T00:28Z] WARN  17:28:48,234 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:28Z] INFO  17:28:48,360 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:28Z] INFO  17:28:48,443 ProgressMeter -            done   1634209.0    26.0 s      15.0 s      100.0%    26.0 s       0.0 s
[2016-04-15T00:28Z] INFO  17:28:48,444 ProgressMeter - Total runtime 26.05 secs, 0.43 min, 0.01 hours
[2016-04-15T00:28Z] INFO  17:28:48,445 MicroScheduler - 23135 reads were filtered out during the traversal out of approximately 300020 total reads (7.71%)
[2016-04-15T00:28Z] INFO  17:28:48,445 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:28Z] INFO  17:28:48,445 MicroScheduler -   -> 436 reads (0.15% of total) failing BadMateFilter
[2016-04-15T00:28Z] INFO  17:28:48,445 MicroScheduler -   -> 22501 reads (7.50% of total) failing DuplicateReadFilter
[2016-04-15T00:28Z] INFO  17:28:48,446 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:28Z] INFO  17:28:48,446 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:28Z] INFO  17:28:48,446 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:28Z] INFO  17:28:48,446 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:28Z] INFO  17:28:48,447 MicroScheduler -   -> 198 reads (0.07% of total) failing UnmappedReadFilter
[2016-04-15T00:28Z] INFO  17:28:48,474 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:28Z] INFO  17:28:48,475 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:28Z] INFO  17:28:48,476 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:28Z] INFO  17:28:48,476 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:28Z] INFO  17:28:48,524 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:28Z] INFO  17:28:48,525 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:28Z] INFO  17:28:48,628 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:28Z] INFO  17:28:48,631 ProgressMeter -            done    469618.0    16.0 s      36.0 s      100.0%    16.0 s       0.0 s
[2016-04-15T00:28Z] INFO  17:28:48,632 ProgressMeter - Total runtime 16.91 secs, 0.28 min, 0.00 hours
[2016-04-15T00:28Z] INFO  17:28:48,632 MicroScheduler - 13674 reads were filtered out during the traversal out of approximately 172343 total reads (7.93%)
[2016-04-15T00:28Z] INFO  17:28:48,632 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:28Z] INFO  17:28:48,632 MicroScheduler -   -> 296 reads (0.17% of total) failing BadMateFilter
[2016-04-15T00:28Z] INFO  17:28:48,633 MicroScheduler -   -> 13272 reads (7.70% of total) failing DuplicateReadFilter
[2016-04-15T00:28Z] INFO  17:28:48,633 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:28Z] INFO  17:28:48,633 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:28Z] INFO  17:28:48,633 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:28Z] INFO  17:28:48,634 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:28Z] INFO  17:28:48,634 MicroScheduler -   -> 106 reads (0.06% of total) failing UnmappedReadFilter
[2016-04-15T00:28Z] GATK: UnifiedGenotyper
[2016-04-15T00:28Z] INFO  17:28:49,137 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:28Z] INFO  17:28:49,140 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:28Z] INFO  17:28:49,141 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:28Z] INFO  17:28:49,141 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:28Z] INFO  17:28:49,160 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/3/R14-18106_kapa-NGv3-PE100-NGv3-sort-3_174814579_190326970-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/3/R14-18106_kapa-NGv3-PE100-NGv3-3_174814579_190326970-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/3/tx/tmpnKiGwE/R14-18106_kapa-NGv3-PE100-NGv3-3_174814579_190326970.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:28Z] INFO  17:28:49,169 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:28Z] INFO  17:28:49,169 HelpFormatter - Date/Time: 2016/04/14 17:28:49
[2016-04-15T00:28Z] INFO  17:28:49,169 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:28Z] INFO  17:28:49,169 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:28Z] INFO  17:28:49,342 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:28Z] INFO  17:28:49,621 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:28Z] INFO  17:28:49,633 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:28Z] INFO  17:28:49,726 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.09
[2016-04-15T00:28Z] INFO  17:28:50,034 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:28Z] INFO  17:28:50,108 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:28Z] INFO  17:28:50,115 IntervalUtils - Processing 184739 bp from intervals
[2016-04-15T00:28Z] WARN  17:28:50,135 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:28Z] INFO  17:28:50,234 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:28Z] INFO  17:28:50,328 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:28Z] INFO  17:28:50,329 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:28Z] INFO  17:28:50,330 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:28Z] GATK: UnifiedGenotyper
[2016-04-15T00:28Z] INFO  17:28:50,330 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:28Z] GATK: UnifiedGenotyper
[2016-04-15T00:28Z] INFO  17:28:50,383 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:28Z] INFO  17:28:50,384 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:28Z] INFO  17:28:50,612 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:28Z] INFO  17:28:50,615 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:28Z] INFO  17:28:50,616 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:28Z] INFO  17:28:50,617 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:28Z] INFO  17:28:50,621 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/3/R14-18106_kapa-NGv3-PE100-NGv3-sort-3_190333063_198022430-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/3/R14-18106_kapa-NGv3-PE100-NGv3-3_190333063_198022430-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/3/tx/tmpUPN6nw/R14-18106_kapa-NGv3-PE100-NGv3-3_190333063_198022430.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:28Z] INFO  17:28:50,653 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:28Z] INFO  17:28:50,654 HelpFormatter - Date/Time: 2016/04/14 17:28:50
[2016-04-15T00:28Z] INFO  17:28:50,654 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:28Z] INFO  17:28:50,659 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:28Z] INFO  17:28:50,732 ProgressMeter -            done    217382.0    13.0 s      63.0 s      100.0%    13.0 s       0.0 s
[2016-04-15T00:28Z] INFO  17:28:50,737 ProgressMeter - Total runtime 13.82 secs, 0.23 min, 0.00 hours
[2016-04-15T00:28Z] INFO  17:28:50,738 MicroScheduler - 7410 reads were filtered out during the traversal out of approximately 95338 total reads (7.77%)
[2016-04-15T00:28Z] INFO  17:28:50,738 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:28Z] INFO  17:28:50,738 MicroScheduler -   -> 160 reads (0.17% of total) failing BadMateFilter
[2016-04-15T00:28Z] INFO  17:28:50,738 MicroScheduler -   -> 7200 reads (7.55% of total) failing DuplicateReadFilter
[2016-04-15T00:28Z] INFO  17:28:50,739 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:28Z] INFO  17:28:50,739 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:28Z] INFO  17:28:50,739 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:28Z] INFO  17:28:50,739 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:28Z] INFO  17:28:50,740 MicroScheduler -   -> 50 reads (0.05% of total) failing UnmappedReadFilter
[2016-04-15T00:28Z] INFO  17:28:50,848 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:28Z] INFO  17:28:51,071 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:28Z] INFO  17:28:51,085 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:28Z] INFO  17:28:51,179 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.09
[2016-04-15T00:28Z] INFO  17:28:51,643 IntervalUtils - Processing 118955 bp from intervals
[2016-04-15T00:28Z] WARN  17:28:51,647 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:28Z] INFO  17:28:51,712 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:28Z] INFO  17:28:51,784 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:28Z] INFO  17:28:51,785 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:28Z] INFO  17:28:51,786 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:28Z] INFO  17:28:51,786 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:28Z] INFO  17:28:51,852 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:28Z] INFO  17:28:51,854 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:28Z] INFO  17:28:51,855 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:28Z] INFO  17:28:51,855 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:28Z] INFO  17:28:51,859 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/4/R14-18106_kapa-NGv3-PE100-NGv3-sort-4_0_15511864-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/4/R14-18106_kapa-NGv3-PE100-NGv3-4_0_15511864-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/4/tx/tmpsR6oGC/R14-18106_kapa-NGv3-PE100-NGv3-4_0_15511864.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:28Z] INFO  17:28:51,866 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:28Z] INFO  17:28:51,867 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:28Z] INFO  17:28:51,901 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:28Z] INFO  17:28:51,902 HelpFormatter - Date/Time: 2016/04/14 17:28:51
[2016-04-15T00:28Z] INFO  17:28:51,902 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:28Z] INFO  17:28:51,903 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:28Z] INFO  17:28:52,040 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:28Z] INFO  17:28:52,161 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:28Z] INFO  17:28:52,233 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:28Z] INFO  17:28:52,242 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:28Z] INFO  17:28:52,298 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-15T00:28Z] GATK: UnifiedGenotyper
[2016-04-15T00:28Z] INFO  17:28:52,818 IntervalUtils - Processing 255565 bp from intervals
[2016-04-15T00:28Z] WARN  17:28:52,824 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:28Z] INFO  17:28:52,937 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:28Z] INFO  17:28:53,069 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:28Z] INFO  17:28:53,070 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:28Z] INFO  17:28:53,071 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:28Z] INFO  17:28:53,072 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:28Z] INFO  17:28:53,132 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:28Z] INFO  17:28:53,134 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:28Z] INFO  17:28:53,441 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:28Z] INFO  17:28:53,444 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:28Z] INFO  17:28:53,444 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:28Z] INFO  17:28:53,445 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:28Z] INFO  17:28:53,449 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/4/R14-18106_kapa-NGv3-PE100-NGv3-sort-4_36069528_52709433-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/4/R14-18106_kapa-NGv3-PE100-NGv3-4_36069528_52709433-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/4/tx/tmpI3icfx/R14-18106_kapa-NGv3-PE100-NGv3-4_36069528_52709433.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:28Z] INFO  17:28:53,463 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:28Z] INFO  17:28:53,462 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:28Z] INFO  17:28:53,465 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:28Z] INFO  17:28:53,466 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:28Z] INFO  17:28:53,466 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:28Z] INFO  17:28:53,464 HelpFormatter - Date/Time: 2016/04/14 17:28:53
[2016-04-15T00:28Z] INFO  17:28:53,465 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:28Z] INFO  17:28:53,465 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:28Z] INFO  17:28:53,471 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/4/R14-18106_kapa-NGv3-PE100-NGv3-sort-4_15512869_31144471-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/4/R14-18106_kapa-NGv3-PE100-NGv3-4_15512869_31144471-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/4/tx/tmp0djRYc/R14-18106_kapa-NGv3-PE100-NGv3-4_15512869_31144471.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:28Z] INFO  17:28:53,487 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:28Z] INFO  17:28:53,488 HelpFormatter - Date/Time: 2016/04/14 17:28:53
[2016-04-15T00:28Z] INFO  17:28:53,488 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:28Z] INFO  17:28:53,489 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:28Z] INFO  17:28:53,610 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:28Z] INFO  17:28:53,682 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:28Z] INFO  17:28:53,803 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:28Z] INFO  17:28:53,817 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:28Z] INFO  17:28:53,898 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-15T00:28Z] INFO  17:28:53,900 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:28Z] INFO  17:28:53,909 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:28Z] INFO  17:28:53,969 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-15T00:28Z] INFO  17:28:54,369 IntervalUtils - Processing 142047 bp from intervals
[2016-04-15T00:28Z] WARN  17:28:54,374 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:28Z] INFO  17:28:54,445 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:28Z] INFO  17:28:54,472 IntervalUtils - Processing 90668 bp from intervals
[2016-04-15T00:28Z] WARN  17:28:54,490 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:28Z] INFO  17:28:54,562 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:28Z] INFO  17:28:54,563 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:28Z] INFO  17:28:54,564 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:28Z] INFO  17:28:54,564 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:28Z] INFO  17:28:54,612 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:28Z] INFO  17:28:54,661 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:28Z] INFO  17:28:54,662 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:28Z] INFO  17:28:54,663 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:28Z] INFO  17:28:54,663 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:28Z] INFO  17:28:54,663 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:28Z] INFO  17:28:54,664 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:28Z] INFO  17:28:54,668 ProgressMeter -            done    587434.0    24.0 s      41.0 s      100.0%    24.0 s       0.0 s
[2016-04-15T00:28Z] INFO  17:28:54,669 ProgressMeter - Total runtime 24.28 secs, 0.40 min, 0.01 hours
[2016-04-15T00:28Z] INFO  17:28:54,669 MicroScheduler - 20895 reads were filtered out during the traversal out of approximately 257686 total reads (8.11%)
[2016-04-15T00:28Z] INFO  17:28:54,670 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:28Z] INFO  17:28:54,670 MicroScheduler -   -> 401 reads (0.16% of total) failing BadMateFilter
[2016-04-15T00:28Z] INFO  17:28:54,670 MicroScheduler -   -> 20329 reads (7.89% of total) failing DuplicateReadFilter
[2016-04-15T00:28Z] INFO  17:28:54,670 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:28Z] INFO  17:28:54,671 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:28Z] INFO  17:28:54,671 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:28Z] INFO  17:28:54,671 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:28Z] INFO  17:28:54,672 MicroScheduler -   -> 165 reads (0.06% of total) failing UnmappedReadFilter
[2016-04-15T00:28Z] INFO  17:28:54,718 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:28Z] INFO  17:28:54,719 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:28Z] INFO  17:28:54,978 ProgressMeter -            done    356274.0    15.0 s      44.0 s       99.9%    15.0 s       0.0 s
[2016-04-15T00:28Z] INFO  17:28:54,979 ProgressMeter - Total runtime 15.82 secs, 0.26 min, 0.00 hours
[2016-04-15T00:28Z] INFO  17:28:54,979 MicroScheduler - 11000 reads were filtered out during the traversal out of approximately 143220 total reads (7.68%)
[2016-04-15T00:28Z] INFO  17:28:54,979 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:28Z] INFO  17:28:54,980 MicroScheduler -   -> 208 reads (0.15% of total) failing BadMateFilter
[2016-04-15T00:28Z] INFO  17:28:54,980 MicroScheduler -   -> 10712 reads (7.48% of total) failing DuplicateReadFilter
[2016-04-15T00:28Z] INFO  17:28:54,980 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:28Z] INFO  17:28:54,980 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:28Z] INFO  17:28:54,981 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:28Z] INFO  17:28:54,981 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:28Z] INFO  17:28:54,981 MicroScheduler -   -> 80 reads (0.06% of total) failing UnmappedReadFilter
[2016-04-15T00:28Z] INFO  17:28:55,444 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:28Z] INFO  17:28:55,447 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:28Z] INFO  17:28:55,448 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:28Z] INFO  17:28:55,449 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:28Z] INFO  17:28:55,454 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/4/R14-18106_kapa-NGv3-PE100-NGv3-sort-4_52709749_68338393-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/4/R14-18106_kapa-NGv3-PE100-NGv3-4_52709749_68338393-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/4/tx/tmpc_bG7i/R14-18106_kapa-NGv3-PE100-NGv3-4_52709749_68338393.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:28Z] INFO  17:28:55,466 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:28Z] INFO  17:28:55,467 HelpFormatter - Date/Time: 2016/04/14 17:28:55
[2016-04-15T00:28Z] INFO  17:28:55,467 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:28Z] INFO  17:28:55,467 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:28Z] INFO  17:28:55,665 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:28Z] INFO  17:28:55,885 ProgressMeter -            done    666709.0    22.0 s      34.0 s      100.0%    22.0 s       0.0 s
[2016-04-15T00:28Z] INFO  17:28:55,886 ProgressMeter - Total runtime 22.95 secs, 0.38 min, 0.01 hours
[2016-04-15T00:28Z] INFO  17:28:55,886 MicroScheduler - 20570 reads were filtered out during the traversal out of approximately 259730 total reads (7.92%)
[2016-04-15T00:28Z] INFO  17:28:55,887 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:28Z] INFO  17:28:55,887 MicroScheduler -   -> 436 reads (0.17% of total) failing BadMateFilter
[2016-04-15T00:28Z] INFO  17:28:55,887 MicroScheduler -   -> 19988 reads (7.70% of total) failing DuplicateReadFilter
[2016-04-15T00:28Z] INFO  17:28:55,887 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:28Z] INFO  17:28:55,888 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:28Z] INFO  17:28:55,888 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:28Z] INFO  17:28:55,888 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:28Z] INFO  17:28:55,888 MicroScheduler -   -> 146 reads (0.06% of total) failing UnmappedReadFilter
[2016-04-15T00:28Z] INFO  17:28:55,925 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:28Z] INFO  17:28:55,934 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:28Z] INFO  17:28:56,082 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.15
[2016-04-15T00:28Z] INFO  17:28:56,246 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:28Z] INFO  17:28:56,292 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:28Z] INFO  17:28:56,504 ProgressMeter -            done   1181875.0    27.0 s      23.0 s      100.0%    27.0 s       0.0 s
[2016-04-15T00:28Z] INFO  17:28:56,504 ProgressMeter - Total runtime 27.21 secs, 0.45 min, 0.01 hours
[2016-04-15T00:28Z] INFO  17:28:56,505 MicroScheduler - 26606 reads were filtered out during the traversal out of approximately 336232 total reads (7.91%)
[2016-04-15T00:28Z] INFO  17:28:56,505 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:28Z] INFO  17:28:56,505 MicroScheduler -   -> 524 reads (0.16% of total) failing BadMateFilter
[2016-04-15T00:28Z] INFO  17:28:56,506 MicroScheduler -   -> 25859 reads (7.69% of total) failing DuplicateReadFilter
[2016-04-15T00:28Z] INFO  17:28:56,506 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:28Z] INFO  17:28:56,506 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:28Z] INFO  17:28:56,506 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:28Z] INFO  17:28:56,506 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:28Z] INFO  17:28:56,507 MicroScheduler -   -> 223 reads (0.07% of total) failing UnmappedReadFilter
[2016-04-15T00:28Z] GATK: UnifiedGenotyper
[2016-04-15T00:28Z] INFO  17:28:56,579 IntervalUtils - Processing 83782 bp from intervals
[2016-04-15T00:28Z] WARN  17:28:56,583 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:28Z] GATK: UnifiedGenotyper
[2016-04-15T00:28Z] INFO  17:28:56,675 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:28Z] INFO  17:28:56,745 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:28Z] INFO  17:28:56,749 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:28Z] INFO  17:28:56,760 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:28Z] INFO  17:28:56,761 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:28Z] INFO  17:28:56,850 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:28Z] INFO  17:28:56,851 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:28Z] INFO  17:28:57,192 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:28Z] GATK: UnifiedGenotyper
[2016-04-15T00:28Z] INFO  17:28:57,949 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:28Z] GATK: UnifiedGenotyper
[2016-04-15T00:28Z] INFO  17:28:59,374 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:28Z] INFO  17:28:59,377 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:28Z] INFO  17:28:59,377 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:28Z] INFO  17:28:59,378 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:28Z] INFO  17:28:59,382 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/4/R14-18106_kapa-NGv3-PE100-NGv3-sort-4_68340604_83852298-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/4/R14-18106_kapa-NGv3-PE100-NGv3-4_68340604_83852298-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/4/tx/tmpvXTkiu/R14-18106_kapa-NGv3-PE100-NGv3-4_68340604_83852298.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:28Z] INFO  17:28:59,392 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:28Z] INFO  17:28:59,392 HelpFormatter - Date/Time: 2016/04/14 17:28:59
[2016-04-15T00:28Z] INFO  17:28:59,392 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:28Z] INFO  17:28:59,392 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:28Z] INFO  17:28:59,620 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:28Z] INFO  17:28:59,783 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:28Z] INFO  17:28:59,798 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:28Z] INFO  17:28:59,798 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:28Z] INFO  17:28:59,798 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:28Z] INFO  17:28:59,819 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/4/R14-18106_kapa-NGv3-PE100-NGv3-sort-4_83857133_99393738-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/4/R14-18106_kapa-NGv3-PE100-NGv3-4_83857133_99393738-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/4/tx/tmpmkLyhg/R14-18106_kapa-NGv3-PE100-NGv3-4_83857133_99393738.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:28Z] INFO  17:28:59,830 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:28Z] INFO  17:28:59,839 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:28Z] INFO  17:28:59,846 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:28Z] INFO  17:28:59,857 HelpFormatter - Date/Time: 2016/04/14 17:28:59
[2016-04-15T00:28Z] INFO  17:28:59,858 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:28Z] INFO  17:28:59,859 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:28Z] INFO  17:28:59,942 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.10
[2016-04-15T00:29Z] INFO  17:29:00,062 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:29Z] INFO  17:29:00,297 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:29Z] INFO  17:29:00,316 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:29Z] INFO  17:29:00,360 IntervalUtils - Processing 197466 bp from intervals
[2016-04-15T00:29Z] WARN  17:29:00,366 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:29Z] INFO  17:29:00,405 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.09
[2016-04-15T00:29Z] INFO  17:29:00,448 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:29Z] INFO  17:29:00,510 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:29Z] INFO  17:29:00,511 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:29Z] INFO  17:29:00,512 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:29Z] INFO  17:29:00,513 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:29Z] INFO  17:29:00,554 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:29Z] INFO  17:29:00,555 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:29Z] INFO  17:29:00,664 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:29Z] INFO  17:29:00,667 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:29Z] INFO  17:29:00,667 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:29Z] INFO  17:29:00,667 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:29Z] INFO  17:29:00,672 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/4/R14-18106_kapa-NGv3-PE100-NGv3-sort-4_99397339_115544957-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/4/R14-18106_kapa-NGv3-PE100-NGv3-4_99397339_115544957-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/4/tx/tmp0BKRiE/R14-18106_kapa-NGv3-PE100-NGv3-4_99397339_115544957.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:29Z] INFO  17:29:00,687 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:29Z] INFO  17:29:00,687 HelpFormatter - Date/Time: 2016/04/14 17:29:00
[2016-04-15T00:29Z] INFO  17:29:00,687 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:29Z] INFO  17:29:00,688 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:29Z] INFO  17:29:00,832 IntervalUtils - Processing 124091 bp from intervals
[2016-04-15T00:29Z] WARN  17:29:00,843 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:29Z] INFO  17:29:00,968 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:29Z] INFO  17:29:00,968 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:29Z] INFO  17:29:01,059 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:29Z] INFO  17:29:01,062 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:29Z] INFO  17:29:01,095 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:29Z] INFO  17:29:01,096 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:29Z] INFO  17:29:01,172 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:29Z] INFO  17:29:01,180 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:29Z] INFO  17:29:01,180 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:29Z] INFO  17:29:01,183 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:29Z] INFO  17:29:01,207 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:29Z] INFO  17:29:01,212 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:29Z] INFO  17:29:01,213 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:29Z] INFO  17:29:01,214 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:29Z] INFO  17:29:01,218 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/4/R14-18106_kapa-NGv3-PE100-NGv3-sort-4_115584857_134074404-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/4/R14-18106_kapa-NGv3-PE100-NGv3-4_115584857_134074404-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/4/tx/tmphKPWgv/R14-18106_kapa-NGv3-PE100-NGv3-4_115584857_134074404.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:29Z] INFO  17:29:01,239 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:29Z] INFO  17:29:01,240 HelpFormatter - Date/Time: 2016/04/14 17:29:01
[2016-04-15T00:29Z] INFO  17:29:01,240 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:29Z] INFO  17:29:01,243 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:29Z] INFO  17:29:01,301 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.11
[2016-04-15T00:29Z] INFO  17:29:01,409 ProgressMeter -            done    258232.0    12.0 s      50.0 s      100.0%    12.0 s       0.0 s
[2016-04-15T00:29Z] INFO  17:29:01,410 ProgressMeter - Total runtime 12.94 secs, 0.22 min, 0.00 hours
[2016-04-15T00:29Z] INFO  17:29:01,411 MicroScheduler - 8394 reads were filtered out during the traversal out of approximately 108167 total reads (7.76%)
[2016-04-15T00:29Z] INFO  17:29:01,411 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:29Z] INFO  17:29:01,411 MicroScheduler -   -> 204 reads (0.19% of total) failing BadMateFilter
[2016-04-15T00:29Z] INFO  17:29:01,412 MicroScheduler -   -> 8117 reads (7.50% of total) failing DuplicateReadFilter
[2016-04-15T00:29Z] INFO  17:29:01,412 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:29Z] INFO  17:29:01,412 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:29Z] INFO  17:29:01,413 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:29Z] INFO  17:29:01,413 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:29Z] INFO  17:29:01,413 MicroScheduler -   -> 73 reads (0.07% of total) failing UnmappedReadFilter
[2016-04-15T00:29Z] INFO  17:29:01,430 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:29Z] INFO  17:29:01,814 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:29Z] INFO  17:29:01,865 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:29Z] INFO  17:29:01,962 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.10
[2016-04-15T00:29Z] INFO  17:29:01,975 IntervalUtils - Processing 153852 bp from intervals
[2016-04-15T00:29Z] WARN  17:29:01,981 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:29Z] INFO  17:29:02,083 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:29Z] INFO  17:29:02,179 ProgressMeter -            done    309734.0    15.0 s      49.0 s       99.9%    15.0 s       0.0 s
[2016-04-15T00:29Z] INFO  17:29:02,180 ProgressMeter - Total runtime 15.26 secs, 0.25 min, 0.00 hours
[2016-04-15T00:29Z] INFO  17:29:02,180 MicroScheduler - 10371 reads were filtered out during the traversal out of approximately 134882 total reads (7.69%)
[2016-04-15T00:29Z] INFO  17:29:02,180 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:29Z] INFO  17:29:02,181 MicroScheduler -   -> 219 reads (0.16% of total) failing BadMateFilter
[2016-04-15T00:29Z] INFO  17:29:02,181 MicroScheduler -   -> 10060 reads (7.46% of total) failing DuplicateReadFilter
[2016-04-15T00:29Z] INFO  17:29:02,181 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:29Z] INFO  17:29:02,181 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:29Z] INFO  17:29:02,182 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:29Z] INFO  17:29:02,182 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:29Z] INFO  17:29:02,182 MicroScheduler -   -> 92 reads (0.07% of total) failing UnmappedReadFilter
[2016-04-15T00:29Z] INFO  17:29:02,191 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:29Z] INFO  17:29:02,192 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:29Z] INFO  17:29:02,192 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:29Z] INFO  17:29:02,193 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:29Z] INFO  17:29:02,289 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:29Z] INFO  17:29:02,290 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:29Z] INFO  17:29:02,484 IntervalUtils - Processing 157938 bp from intervals
[2016-04-15T00:29Z] WARN  17:29:02,499 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:29Z] INFO  17:29:02,626 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:29Z] INFO  17:29:02,699 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:29Z] INFO  17:29:02,699 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:29Z] INFO  17:29:02,700 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:29Z] INFO  17:29:02,700 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:29Z] INFO  17:29:02,748 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:29Z] INFO  17:29:02,749 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:29Z] INFO  17:29:02,868 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:29Z] GATK: UnifiedGenotyper
[2016-04-15T00:29Z] INFO  17:29:03,545 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:29Z] GATK: UnifiedGenotyper
[2016-04-15T00:29Z] INFO  17:29:05,108 ProgressMeter -      3:47018227    938681.0    30.0 s      31.0 s       96.4%    31.0 s       1.0 s
[2016-04-15T00:29Z] INFO  17:29:06,328 ProgressMeter -            done   1082933.0    31.0 s      28.0 s      100.0%    31.0 s       0.0 s
[2016-04-15T00:29Z] INFO  17:29:06,329 ProgressMeter - Total runtime 31.25 secs, 0.52 min, 0.01 hours
[2016-04-15T00:29Z] INFO  17:29:06,329 MicroScheduler - 31416 reads were filtered out during the traversal out of approximately 398617 total reads (7.88%)
[2016-04-15T00:29Z] INFO  17:29:06,330 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:29Z] INFO  17:29:06,330 MicroScheduler -   -> 672 reads (0.17% of total) failing BadMateFilter
[2016-04-15T00:29Z] INFO  17:29:06,330 MicroScheduler -   -> 30493 reads (7.65% of total) failing DuplicateReadFilter
[2016-04-15T00:29Z] INFO  17:29:06,330 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:29Z] INFO  17:29:06,331 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:29Z] INFO  17:29:06,331 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:29Z] INFO  17:29:06,331 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:29Z] INFO  17:29:06,332 MicroScheduler -   -> 251 reads (0.06% of total) failing UnmappedReadFilter
[2016-04-15T00:29Z] INFO  17:29:06,334 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:29Z] INFO  17:29:06,338 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:29Z] INFO  17:29:06,338 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:29Z] INFO  17:29:06,339 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:29Z] INFO  17:29:06,341 ProgressMeter -      3:52428581   2054739.0    30.0 s      14.0 s       64.4%    46.0 s      16.0 s
[2016-04-15T00:29Z] INFO  17:29:06,343 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/4/R14-18106_kapa-NGv3-PE100-NGv3-sort-4_134075461_150351181-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/4/R14-18106_kapa-NGv3-PE100-NGv3-4_134075461_150351181-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/4/tx/tmpVBSmqI/R14-18106_kapa-NGv3-PE100-NGv3-4_134075461_150351181.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:29Z] INFO  17:29:06,354 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:29Z] INFO  17:29:06,361 HelpFormatter - Date/Time: 2016/04/14 17:29:06
[2016-04-15T00:29Z] INFO  17:29:06,362 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:29Z] INFO  17:29:06,363 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:29Z] INFO  17:29:06,542 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:29Z] INFO  17:29:06,765 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:29Z] INFO  17:29:06,769 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:29Z] INFO  17:29:06,769 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:29Z] INFO  17:29:06,770 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:29Z] INFO  17:29:06,774 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/4/R14-18106_kapa-NGv3-PE100-NGv3-sort-4_150354547_165878648-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/4/R14-18106_kapa-NGv3-PE100-NGv3-4_150354547_165878648-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/4/tx/tmptYekhI/R14-18106_kapa-NGv3-PE100-NGv3-4_150354547_165878648.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:29Z] INFO  17:29:06,787 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:29Z] INFO  17:29:06,787 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:29Z] INFO  17:29:06,787 HelpFormatter - Date/Time: 2016/04/14 17:29:06
[2016-04-15T00:29Z] INFO  17:29:06,787 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:29Z] INFO  17:29:06,788 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:29Z] INFO  17:29:06,812 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:29Z] INFO  17:29:06,901 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-15T00:29Z] INFO  17:29:06,952 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:29Z] INFO  17:29:07,206 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:29Z] INFO  17:29:07,209 ProgressMeter -            done    230295.0    12.0 s      54.0 s       99.9%    12.0 s       0.0 s
[2016-04-15T00:29Z] INFO  17:29:07,210 ProgressMeter - Total runtime 12.55 secs, 0.21 min, 0.00 hours
[2016-04-15T00:29Z] INFO  17:29:07,210 MicroScheduler - 7674 reads were filtered out during the traversal out of approximately 97091 total reads (7.90%)
[2016-04-15T00:29Z] INFO  17:29:07,210 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:29Z] INFO  17:29:07,211 MicroScheduler -   -> 160 reads (0.16% of total) failing BadMateFilter
[2016-04-15T00:29Z] INFO  17:29:07,211 MicroScheduler -   -> 7458 reads (7.68% of total) failing DuplicateReadFilter
[2016-04-15T00:29Z] INFO  17:29:07,211 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:29Z] INFO  17:29:07,211 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:29Z] INFO  17:29:07,212 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:29Z] INFO  17:29:07,212 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:29Z] INFO  17:29:07,212 MicroScheduler -   -> 56 reads (0.06% of total) failing UnmappedReadFilter
[2016-04-15T00:29Z] INFO  17:29:07,215 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:29Z] INFO  17:29:07,277 IntervalUtils - Processing 86890 bp from intervals
[2016-04-15T00:29Z] WARN  17:29:07,282 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:29Z] INFO  17:29:07,303 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.09
[2016-04-15T00:29Z] INFO  17:29:07,370 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:29Z] INFO  17:29:07,481 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:29Z] INFO  17:29:07,482 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:29Z] INFO  17:29:07,483 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:29Z] INFO  17:29:07,484 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:29Z] INFO  17:29:07,529 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:29Z] INFO  17:29:07,530 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:29Z] INFO  17:29:07,627 IntervalUtils - Processing 119752 bp from intervals
[2016-04-15T00:29Z] WARN  17:29:07,633 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:29Z] INFO  17:29:07,732 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:29Z] INFO  17:29:07,819 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:29Z] INFO  17:29:07,820 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:29Z] INFO  17:29:07,821 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:29Z] INFO  17:29:07,822 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:29Z] INFO  17:29:07,859 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:29Z] INFO  17:29:07,883 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:29Z] INFO  17:29:07,883 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:29Z] GATK: UnifiedGenotyper
[2016-04-15T00:29Z] INFO  17:29:08,463 ProgressMeter -            done    680726.0    26.0 s      39.0 s      100.0%    26.0 s       0.0 s
[2016-04-15T00:29Z] INFO  17:29:08,464 ProgressMeter - Total runtime 26.65 secs, 0.44 min, 0.01 hours
[2016-04-15T00:29Z] INFO  17:29:08,464 MicroScheduler - 24163 reads were filtered out during the traversal out of approximately 303175 total reads (7.97%)
[2016-04-15T00:29Z] INFO  17:29:08,464 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:29Z] INFO  17:29:08,465 MicroScheduler -   -> 469 reads (0.15% of total) failing BadMateFilter
[2016-04-15T00:29Z] INFO  17:29:08,465 MicroScheduler -   -> 23485 reads (7.75% of total) failing DuplicateReadFilter
[2016-04-15T00:29Z] INFO  17:29:08,465 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:29Z] INFO  17:29:08,466 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:29Z] INFO  17:29:08,466 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:29Z] INFO  17:29:08,466 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:29Z] INFO  17:29:08,467 MicroScheduler -   -> 209 reads (0.07% of total) failing UnmappedReadFilter
[2016-04-15T00:29Z] INFO  17:29:08,506 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:29Z] GATK: UnifiedGenotyper
[2016-04-15T00:29Z] INFO  17:29:08,958 ProgressMeter -            done    720572.0    24.0 s      33.0 s      100.0%    24.0 s       0.0 s
[2016-04-15T00:29Z] INFO  17:29:08,958 ProgressMeter - Total runtime 24.04 secs, 0.40 min, 0.01 hours
[2016-04-15T00:29Z] INFO  17:29:08,959 MicroScheduler - 22358 reads were filtered out during the traversal out of approximately 282632 total reads (7.91%)
[2016-04-15T00:29Z] INFO  17:29:08,959 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:29Z] INFO  17:29:08,960 MicroScheduler -   -> 514 reads (0.18% of total) failing BadMateFilter
[2016-04-15T00:29Z] INFO  17:29:08,960 MicroScheduler -   -> 21674 reads (7.67% of total) failing DuplicateReadFilter
[2016-04-15T00:29Z] INFO  17:29:08,960 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:29Z] INFO  17:29:08,960 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:29Z] INFO  17:29:08,961 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:29Z] INFO  17:29:08,961 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:29Z] INFO  17:29:08,961 MicroScheduler -   -> 170 reads (0.06% of total) failing UnmappedReadFilter
[2016-04-15T00:29Z] INFO  17:29:09,545 ProgressMeter -            done    351075.0    17.0 s      50.0 s       99.9%    17.0 s       0.0 s
[2016-04-15T00:29Z] INFO  17:29:09,546 ProgressMeter - Total runtime 17.76 secs, 0.30 min, 0.00 hours
[2016-04-15T00:29Z] INFO  17:29:09,546 MicroScheduler - 13712 reads were filtered out during the traversal out of approximately 166324 total reads (8.24%)
[2016-04-15T00:29Z] INFO  17:29:09,547 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:29Z] INFO  17:29:09,547 MicroScheduler -   -> 289 reads (0.17% of total) failing BadMateFilter
[2016-04-15T00:29Z] INFO  17:29:09,547 MicroScheduler -   -> 13307 reads (8.00% of total) failing DuplicateReadFilter
[2016-04-15T00:29Z] INFO  17:29:09,548 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:29Z] INFO  17:29:09,548 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:29Z] INFO  17:29:09,548 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:29Z] INFO  17:29:09,549 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:29Z] INFO  17:29:09,549 MicroScheduler -   -> 116 reads (0.07% of total) failing UnmappedReadFilter
[2016-04-15T00:29Z] INFO  17:29:09,661 ProgressMeter -            done    255123.0    12.0 s      50.0 s       99.9%    12.0 s       0.0 s
[2016-04-15T00:29Z] INFO  17:29:09,662 ProgressMeter - Total runtime 12.91 secs, 0.22 min, 0.00 hours
[2016-04-15T00:29Z] INFO  17:29:09,662 MicroScheduler - 6889 reads were filtered out during the traversal out of approximately 91502 total reads (7.53%)
[2016-04-15T00:29Z] INFO  17:29:09,663 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:29Z] INFO  17:29:09,663 MicroScheduler -   -> 184 reads (0.20% of total) failing BadMateFilter
[2016-04-15T00:29Z] INFO  17:29:09,663 MicroScheduler -   -> 6642 reads (7.26% of total) failing DuplicateReadFilter
[2016-04-15T00:29Z] INFO  17:29:09,664 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:29Z] INFO  17:29:09,664 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:29Z] INFO  17:29:09,664 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:29Z] INFO  17:29:09,665 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:29Z] INFO  17:29:09,665 MicroScheduler -   -> 63 reads (0.07% of total) failing UnmappedReadFilter
[2016-04-15T00:29Z] INFO  17:29:09,891 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:29Z] GATK: UnifiedGenotyper
[2016-04-15T00:29Z] INFO  17:29:10,385 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:29Z] GATK: UnifiedGenotyper
[2016-04-15T00:29Z] INFO  17:29:10,873 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:29Z] INFO  17:29:10,886 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:29Z] INFO  17:29:10,887 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:29Z] INFO  17:29:10,888 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:29Z] INFO  17:29:10,892 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/4/R14-18106_kapa-NGv3-PE100-NGv3-sort-4_165889318_183245405-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/4/R14-18106_kapa-NGv3-PE100-NGv3-4_165889318_183245405-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/4/tx/tmpllVjbd/R14-18106_kapa-NGv3-PE100-NGv3-4_165889318_183245405.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:29Z] INFO  17:29:10,917 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:29Z] INFO  17:29:10,917 HelpFormatter - Date/Time: 2016/04/14 17:29:10
[2016-04-15T00:29Z] INFO  17:29:10,917 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:29Z] INFO  17:29:10,918 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:29Z] INFO  17:29:11,003 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:29Z] INFO  17:29:11,058 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:29Z] INFO  17:29:11,164 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:29Z] GATK: UnifiedGenotyper
[2016-04-15T00:29Z] GATK: UnifiedGenotyper
[2016-04-15T00:29Z] INFO  17:29:11,474 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:29Z] INFO  17:29:11,501 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:29Z] INFO  17:29:11,610 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.09
[2016-04-15T00:29Z] INFO  17:29:11,922 ProgressMeter -            done    359128.0    17.0 s      48.0 s      100.0%    17.0 s       0.0 s
[2016-04-15T00:29Z] INFO  17:29:11,923 ProgressMeter - Total runtime 17.36 secs, 0.29 min, 0.00 hours
[2016-04-15T00:29Z] INFO  17:29:11,924 MicroScheduler - 11794 reads were filtered out during the traversal out of approximately 152805 total reads (7.72%)
[2016-04-15T00:29Z] INFO  17:29:11,924 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:29Z] INFO  17:29:11,925 MicroScheduler -   -> 232 reads (0.15% of total) failing BadMateFilter
[2016-04-15T00:29Z] INFO  17:29:11,925 MicroScheduler -   -> 11447 reads (7.49% of total) failing DuplicateReadFilter
[2016-04-15T00:29Z] INFO  17:29:11,926 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:29Z] INFO  17:29:11,926 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:29Z] INFO  17:29:11,927 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:29Z] INFO  17:29:11,927 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:29Z] INFO  17:29:11,927 MicroScheduler -   -> 115 reads (0.08% of total) failing UnmappedReadFilter
[2016-04-15T00:29Z] INFO  17:29:12,095 IntervalUtils - Processing 78538 bp from intervals
[2016-04-15T00:29Z] WARN  17:29:12,107 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:29Z] INFO  17:29:12,183 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:29Z] INFO  17:29:12,217 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:29Z] INFO  17:29:12,222 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:29Z] INFO  17:29:12,223 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:29Z] INFO  17:29:12,223 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:29Z] INFO  17:29:12,228 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/4/R14-18106_kapa-NGv3-PE100-NGv3-sort-4_183267803_191154276-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/4/R14-18106_kapa-NGv3-PE100-NGv3-4_183267803_191154276-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/4/tx/tmpjDcky8/R14-18106_kapa-NGv3-PE100-NGv3-4_183267803_191154276.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:29Z] INFO  17:29:12,273 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:29Z] INFO  17:29:12,273 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:29Z] INFO  17:29:12,274 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:29Z] INFO  17:29:12,275 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:29Z] INFO  17:29:12,276 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:29Z] INFO  17:29:12,273 HelpFormatter - Date/Time: 2016/04/14 17:29:12
[2016-04-15T00:29Z] INFO  17:29:12,274 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:29Z] INFO  17:29:12,274 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:29Z] INFO  17:29:12,396 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:29Z] INFO  17:29:12,401 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:29Z] INFO  17:29:12,539 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:29Z] INFO  17:29:12,819 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:29Z] INFO  17:29:12,828 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:29Z] INFO  17:29:12,905 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-15T00:29Z] INFO  17:29:13,167 ProgressMeter -            done    782811.0    22.0 s      29.0 s      100.0%    22.0 s       0.0 s
[2016-04-15T00:29Z] INFO  17:29:13,167 ProgressMeter - Total runtime 22.84 secs, 0.38 min, 0.01 hours
[2016-04-15T00:29Z] INFO  17:29:13,168 MicroScheduler - 18569 reads were filtered out during the traversal out of approximately 238146 total reads (7.80%)
[2016-04-15T00:29Z] INFO  17:29:13,168 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:29Z] INFO  17:29:13,168 MicroScheduler -   -> 370 reads (0.16% of total) failing BadMateFilter
[2016-04-15T00:29Z] INFO  17:29:13,169 MicroScheduler -   -> 18042 reads (7.58% of total) failing DuplicateReadFilter
[2016-04-15T00:29Z] INFO  17:29:13,169 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:29Z] INFO  17:29:13,169 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:29Z] INFO  17:29:13,169 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:29Z] INFO  17:29:13,170 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:29Z] INFO  17:29:13,170 MicroScheduler -   -> 157 reads (0.07% of total) failing UnmappedReadFilter
[2016-04-15T00:29Z] INFO  17:29:13,339 IntervalUtils - Processing 99602 bp from intervals
[2016-04-15T00:29Z] WARN  17:29:13,344 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:29Z] INFO  17:29:13,409 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:29Z] INFO  17:29:13,421 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:29Z] INFO  17:29:13,474 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:29Z] INFO  17:29:13,475 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:29Z] INFO  17:29:13,475 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:29Z] INFO  17:29:13,478 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:29Z] INFO  17:29:13,521 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:29Z] INFO  17:29:13,522 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:29Z] INFO  17:29:13,528 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:29Z] INFO  17:29:13,531 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:29Z] INFO  17:29:13,532 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:29Z] INFO  17:29:13,532 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:29Z] INFO  17:29:13,537 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/5/R14-18106_kapa-NGv3-PE100-NGv3-sort-5_0_15580921-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/5/R14-18106_kapa-NGv3-PE100-NGv3-5_0_15580921-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/5/tx/tmpFZ6wMF/R14-18106_kapa-NGv3-PE100-NGv3-5_0_15580921.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:29Z] INFO  17:29:13,575 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:29Z] INFO  17:29:13,579 HelpFormatter - Date/Time: 2016/04/14 17:29:13
[2016-04-15T00:29Z] INFO  17:29:13,580 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:29Z] INFO  17:29:13,580 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:29Z] GATK: UnifiedGenotyper
[2016-04-15T00:29Z] INFO  17:29:13,786 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:29Z] INFO  17:29:13,898 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:29Z] INFO  17:29:13,901 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:29Z] INFO  17:29:13,902 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:29Z] INFO  17:29:13,902 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:29Z] INFO  17:29:13,907 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/5/R14-18106_kapa-NGv3-PE100-NGv3-sort-5_15616091_31267808-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/5/R14-18106_kapa-NGv3-PE100-NGv3-5_15616091_31267808-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/5/tx/tmpZmF3YV/R14-18106_kapa-NGv3-PE100-NGv3-5_15616091_31267808.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:29Z] INFO  17:29:13,938 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:29Z] INFO  17:29:13,939 HelpFormatter - Date/Time: 2016/04/14 17:29:13
[2016-04-15T00:29Z] INFO  17:29:13,939 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:29Z] INFO  17:29:13,939 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:29Z] INFO  17:29:14,056 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:29Z] INFO  17:29:14,070 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:29Z] INFO  17:29:14,070 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:29Z] INFO  17:29:14,071 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:29Z] INFO  17:29:14,076 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/5/R14-18106_kapa-NGv3-PE100-NGv3-sort-5_31294068_49695124-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/5/R14-18106_kapa-NGv3-PE100-NGv3-5_31294068_49695124-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/5/tx/tmpngf2LB/R14-18106_kapa-NGv3-PE100-NGv3-5_31294068_49695124.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:29Z] INFO  17:29:14,077 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:29Z] INFO  17:29:14,087 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:29Z] INFO  17:29:14,095 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:29Z] INFO  17:29:14,096 HelpFormatter - Date/Time: 2016/04/14 17:29:14
[2016-04-15T00:29Z] INFO  17:29:14,097 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:29Z] INFO  17:29:14,097 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:29Z] INFO  17:29:14,195 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:29Z] INFO  17:29:14,207 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.12
[2016-04-15T00:29Z] INFO  17:29:14,346 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:29Z] INFO  17:29:14,543 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:29Z] INFO  17:29:14,554 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:29Z] INFO  17:29:14,596 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:29Z] INFO  17:29:14,600 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:29Z] INFO  17:29:14,601 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:29Z] INFO  17:29:14,602 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:29Z] INFO  17:29:14,607 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/5/R14-18106_kapa-NGv3-PE100-NGv3-sort-5_49695692_65288736-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/5/R14-18106_kapa-NGv3-PE100-NGv3-5_49695692_65288736-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/5/tx/tmpqRa4q4/R14-18106_kapa-NGv3-PE100-NGv3-5_49695692_65288736.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:29Z] INFO  17:29:14,620 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:29Z] INFO  17:29:14,621 HelpFormatter - Date/Time: 2016/04/14 17:29:14
[2016-04-15T00:29Z] INFO  17:29:14,622 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:29Z] INFO  17:29:14,623 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:29Z] INFO  17:29:14,640 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-15T00:29Z] INFO  17:29:14,641 IntervalUtils - Processing 125185 bp from intervals
[2016-04-15T00:29Z] INFO  17:29:14,639 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:29Z] WARN  17:29:14,646 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:29Z] INFO  17:29:14,654 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:29Z] INFO  17:29:14,709 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:29Z] INFO  17:29:14,728 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-15T00:29Z] INFO  17:29:14,774 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:29Z] INFO  17:29:14,821 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:29Z] INFO  17:29:14,863 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:29Z] INFO  17:29:14,865 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:29Z] INFO  17:29:14,865 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:29Z] INFO  17:29:14,866 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:29Z] INFO  17:29:14,924 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:29Z] INFO  17:29:14,925 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:29Z] GATK: UnifiedGenotyper
[2016-04-15T00:29Z] INFO  17:29:15,034 IntervalUtils - Processing 26887 bp from intervals
[2016-04-15T00:29Z] WARN  17:29:15,050 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:29Z] INFO  17:29:15,118 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:29Z] INFO  17:29:15,138 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:29Z] INFO  17:29:15,147 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:29Z] INFO  17:29:15,192 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-15T00:29Z] INFO  17:29:15,202 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:29Z] INFO  17:29:15,202 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:29Z] INFO  17:29:15,203 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:29Z] INFO  17:29:15,203 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:29Z] INFO  17:29:15,260 IntervalUtils - Processing 183626 bp from intervals
[2016-04-15T00:29Z] WARN  17:29:15,265 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:29Z] INFO  17:29:15,275 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:29Z] INFO  17:29:15,276 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:29Z] INFO  17:29:15,372 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:29Z] INFO  17:29:15,485 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:29Z] INFO  17:29:15,486 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:29Z] INFO  17:29:15,486 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:29Z] INFO  17:29:15,486 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:29Z] INFO  17:29:15,535 IntervalUtils - Processing 108713 bp from intervals
[2016-04-15T00:29Z] WARN  17:29:15,540 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:29Z] INFO  17:29:15,548 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:29Z] INFO  17:29:15,549 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:29Z] INFO  17:29:15,645 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:29Z] INFO  17:29:15,709 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:29Z] INFO  17:29:15,710 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:29Z] INFO  17:29:15,711 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:29Z] INFO  17:29:15,712 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:29Z] INFO  17:29:15,780 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:29Z] INFO  17:29:15,781 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:29Z] INFO  17:29:16,464 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:29Z] INFO  17:29:16,467 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:29Z] INFO  17:29:16,468 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:29Z] INFO  17:29:16,468 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:29Z] INFO  17:29:16,473 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/5/R14-18106_kapa-NGv3-PE100-NGv3-sort-5_65290574_80809536-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/5/R14-18106_kapa-NGv3-PE100-NGv3-5_65290574_80809536-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/5/tx/tmpZx4G8E/R14-18106_kapa-NGv3-PE100-NGv3-5_65290574_80809536.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:29Z] INFO  17:29:16,483 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:29Z] INFO  17:29:16,484 HelpFormatter - Date/Time: 2016/04/14 17:29:16
[2016-04-15T00:29Z] INFO  17:29:16,484 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:29Z] INFO  17:29:16,485 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:29Z] INFO  17:29:16,717 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:29Z] INFO  17:29:16,983 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:29Z] INFO  17:29:16,992 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:29Z] INFO  17:29:17,084 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.09
[2016-04-15T00:29Z] INFO  17:29:17,565 IntervalUtils - Processing 203113 bp from intervals
[2016-04-15T00:29Z] WARN  17:29:17,582 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:29Z] INFO  17:29:17,709 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:29Z] INFO  17:29:17,834 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:29Z] INFO  17:29:17,835 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:29Z] INFO  17:29:17,836 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:29Z] INFO  17:29:17,836 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:29Z] INFO  17:29:17,888 ProgressMeter -            done    303616.0    16.0 s      55.0 s       99.9%    16.0 s       0.0 s
[2016-04-15T00:29Z] INFO  17:29:17,889 ProgressMeter - Total runtime 16.83 secs, 0.28 min, 0.00 hours
[2016-04-15T00:29Z] INFO  17:29:17,889 MicroScheduler - 11520 reads were filtered out during the traversal out of approximately 142494 total reads (8.08%)
[2016-04-15T00:29Z] INFO  17:29:17,890 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:29Z] INFO  17:29:17,890 MicroScheduler -   -> 265 reads (0.19% of total) failing BadMateFilter
[2016-04-15T00:29Z] INFO  17:29:17,890 MicroScheduler -   -> 11164 reads (7.83% of total) failing DuplicateReadFilter
[2016-04-15T00:29Z] INFO  17:29:17,890 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:29Z] INFO  17:29:17,890 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:29Z] INFO  17:29:17,891 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:29Z] INFO  17:29:17,891 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:29Z] INFO  17:29:17,891 MicroScheduler -   -> 91 reads (0.06% of total) failing UnmappedReadFilter
[2016-04-15T00:29Z] INFO  17:29:17,914 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:29Z] INFO  17:29:17,917 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:29Z] INFO  17:29:17,918 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:29Z] INFO  17:29:17,918 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:29Z] INFO  17:29:17,923 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/5/R14-18106_kapa-NGv3-PE100-NGv3-sort-5_80911291_96430739-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/5/R14-18106_kapa-NGv3-PE100-NGv3-5_80911291_96430739-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/5/tx/tmpXoddFe/R14-18106_kapa-NGv3-PE100-NGv3-5_80911291_96430739.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:29Z] INFO  17:29:17,923 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:29Z] INFO  17:29:17,934 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:29Z] INFO  17:29:17,939 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:29Z] INFO  17:29:17,940 HelpFormatter - Date/Time: 2016/04/14 17:29:17
[2016-04-15T00:29Z] INFO  17:29:17,940 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:29Z] INFO  17:29:17,941 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:29Z] INFO  17:29:18,169 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:29Z] INFO  17:29:18,427 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:29Z] INFO  17:29:18,436 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:29Z] INFO  17:29:18,518 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-15T00:29Z] INFO  17:29:18,548 ProgressMeter -            done    675755.0    15.0 s      23.0 s      100.0%    15.0 s       0.0 s
[2016-04-15T00:29Z] INFO  17:29:18,549 ProgressMeter - Total runtime 15.85 secs, 0.26 min, 0.00 hours
[2016-04-15T00:29Z] INFO  17:29:18,550 MicroScheduler - 11466 reads were filtered out during the traversal out of approximately 148540 total reads (7.72%)
[2016-04-15T00:29Z] INFO  17:29:18,551 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:29Z] INFO  17:29:18,552 MicroScheduler -   -> 209 reads (0.14% of total) failing BadMateFilter
[2016-04-15T00:29Z] INFO  17:29:18,552 MicroScheduler -   -> 11175 reads (7.52% of total) failing DuplicateReadFilter
[2016-04-15T00:29Z] INFO  17:29:18,553 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:29Z] INFO  17:29:18,553 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:29Z] INFO  17:29:18,554 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:29Z] INFO  17:29:18,555 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:29Z] INFO  17:29:18,555 MicroScheduler -   -> 82 reads (0.06% of total) failing UnmappedReadFilter
[2016-04-15T00:29Z] INFO  17:29:18,819 ProgressMeter -            done    430817.0    16.0 s      38.0 s      100.0%    16.0 s       0.0 s
[2016-04-15T00:29Z] INFO  17:29:18,820 ProgressMeter - Total runtime 16.63 secs, 0.28 min, 0.00 hours
[2016-04-15T00:29Z] INFO  17:29:18,821 MicroScheduler - 12884 reads were filtered out during the traversal out of approximately 166350 total reads (7.75%)
[2016-04-15T00:29Z] INFO  17:29:18,822 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:29Z] INFO  17:29:18,822 MicroScheduler -   -> 244 reads (0.15% of total) failing BadMateFilter
[2016-04-15T00:29Z] INFO  17:29:18,823 MicroScheduler -   -> 12531 reads (7.53% of total) failing DuplicateReadFilter
[2016-04-15T00:29Z] INFO  17:29:18,824 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:29Z] INFO  17:29:18,824 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:29Z] INFO  17:29:18,825 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:29Z] INFO  17:29:18,825 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:29Z] INFO  17:29:18,826 MicroScheduler -   -> 109 reads (0.07% of total) failing UnmappedReadFilter
[2016-04-15T00:29Z] INFO  17:29:18,855 ProgressMeter -            done   2880332.0    42.0 s      14.0 s      100.0%    42.0 s       0.0 s
[2016-04-15T00:29Z] INFO  17:29:18,855 ProgressMeter - Total runtime 42.54 secs, 0.71 min, 0.01 hours
[2016-04-15T00:29Z] INFO  17:29:18,855 MicroScheduler - 50577 reads were filtered out during the traversal out of approximately 631031 total reads (8.01%)
[2016-04-15T00:29Z] INFO  17:29:18,856 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:29Z] INFO  17:29:18,856 MicroScheduler -   -> 1069 reads (0.17% of total) failing BadMateFilter
[2016-04-15T00:29Z] INFO  17:29:18,856 MicroScheduler -   -> 49139 reads (7.79% of total) failing DuplicateReadFilter
[2016-04-15T00:29Z] INFO  17:29:18,856 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:29Z] INFO  17:29:18,857 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:29Z] INFO  17:29:18,857 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:29Z] INFO  17:29:18,857 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:29Z] INFO  17:29:18,857 MicroScheduler -   -> 369 reads (0.06% of total) failing UnmappedReadFilter
[2016-04-15T00:29Z] INFO  17:29:19,005 IntervalUtils - Processing 113632 bp from intervals
[2016-04-15T00:29Z] WARN  17:29:19,011 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:29Z] INFO  17:29:19,113 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:29Z] INFO  17:29:19,189 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:29Z] INFO  17:29:19,190 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:29Z] INFO  17:29:19,191 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:29Z] INFO  17:29:19,192 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:29Z] INFO  17:29:19,236 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:29Z] INFO  17:29:19,237 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:29Z] INFO  17:29:19,545 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:29Z] GATK: UnifiedGenotyper
[2016-04-15T00:29Z] INFO  17:29:19,919 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:29Z] INFO  17:29:20,077 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:29Z] GATK: UnifiedGenotyper
[2016-04-15T00:29Z] INFO  17:29:20,351 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:29Z] GATK: UnifiedGenotyper
[2016-04-15T00:29Z] GATK: UnifiedGenotyper
[2016-04-15T00:29Z] INFO  17:29:21,440 ProgressMeter -            done    205509.0    13.0 s      67.0 s       99.9%    13.0 s       0.0 s
[2016-04-15T00:29Z] INFO  17:29:21,441 ProgressMeter - Total runtime 13.96 secs, 0.23 min, 0.00 hours
[2016-04-15T00:29Z] INFO  17:29:21,441 MicroScheduler - 7919 reads were filtered out during the traversal out of approximately 100223 total reads (7.90%)
[2016-04-15T00:29Z] INFO  17:29:21,441 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:29Z] INFO  17:29:21,442 MicroScheduler -   -> 183 reads (0.18% of total) failing BadMateFilter
[2016-04-15T00:29Z] INFO  17:29:21,442 MicroScheduler -   -> 7667 reads (7.65% of total) failing DuplicateReadFilter
[2016-04-15T00:29Z] INFO  17:29:21,442 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:29Z] INFO  17:29:21,443 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:29Z] INFO  17:29:21,443 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:29Z] INFO  17:29:21,443 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:29Z] INFO  17:29:21,444 MicroScheduler -   -> 69 reads (0.07% of total) failing UnmappedReadFilter
[2016-04-15T00:29Z] INFO  17:29:22,020 ProgressMeter -            done    538645.0    21.0 s      39.0 s      100.0%    21.0 s       0.0 s
[2016-04-15T00:29Z] INFO  17:29:22,020 ProgressMeter - Total runtime 21.51 secs, 0.36 min, 0.01 hours
[2016-04-15T00:29Z] INFO  17:29:22,021 MicroScheduler - 17340 reads were filtered out during the traversal out of approximately 224220 total reads (7.73%)
[2016-04-15T00:29Z] INFO  17:29:22,021 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:29Z] INFO  17:29:22,021 MicroScheduler -   -> 366 reads (0.16% of total) failing BadMateFilter
[2016-04-15T00:29Z] INFO  17:29:22,022 MicroScheduler -   -> 16832 reads (7.51% of total) failing DuplicateReadFilter
[2016-04-15T00:29Z] INFO  17:29:22,022 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:29Z] INFO  17:29:22,022 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:29Z] INFO  17:29:22,022 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:29Z] INFO  17:29:22,023 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:29Z] INFO  17:29:22,023 MicroScheduler -   -> 142 reads (0.06% of total) failing UnmappedReadFilter
[2016-04-15T00:29Z] INFO  17:29:22,097 ProgressMeter -            done     60320.0     6.0 s     114.0 s       99.9%     6.0 s       0.0 s
[2016-04-15T00:29Z] INFO  17:29:22,097 ProgressMeter - Total runtime 6.89 secs, 0.11 min, 0.00 hours
[2016-04-15T00:29Z] INFO  17:29:22,098 MicroScheduler - 2776 reads were filtered out during the traversal out of approximately 33340 total reads (8.33%)
[2016-04-15T00:29Z] INFO  17:29:22,098 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:29Z] INFO  17:29:22,098 MicroScheduler -   -> 49 reads (0.15% of total) failing BadMateFilter
[2016-04-15T00:29Z] INFO  17:29:22,098 MicroScheduler -   -> 2696 reads (8.09% of total) failing DuplicateReadFilter
[2016-04-15T00:29Z] INFO  17:29:22,099 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:29Z] INFO  17:29:22,099 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:29Z] INFO  17:29:22,099 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:29Z] INFO  17:29:22,100 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:29Z] INFO  17:29:22,100 MicroScheduler -   -> 31 reads (0.09% of total) failing UnmappedReadFilter
[2016-04-15T00:29Z] INFO  17:29:22,689 ProgressMeter -            done    310683.0    14.0 s      47.0 s       99.9%    14.0 s       0.0 s
[2016-04-15T00:29Z] INFO  17:29:22,689 ProgressMeter - Total runtime 14.87 secs, 0.25 min, 0.00 hours
[2016-04-15T00:29Z] INFO  17:29:22,690 MicroScheduler - 10385 reads were filtered out during the traversal out of approximately 129891 total reads (8.00%)
[2016-04-15T00:29Z] INFO  17:29:22,690 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:29Z] INFO  17:29:22,690 MicroScheduler -   -> 217 reads (0.17% of total) failing BadMateFilter
[2016-04-15T00:29Z] INFO  17:29:22,691 MicroScheduler -   -> 10085 reads (7.76% of total) failing DuplicateReadFilter
[2016-04-15T00:29Z] INFO  17:29:22,691 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:29Z] INFO  17:29:22,691 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:29Z] INFO  17:29:22,692 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:29Z] INFO  17:29:22,692 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:29Z] INFO  17:29:22,692 MicroScheduler -   -> 83 reads (0.06% of total) failing UnmappedReadFilter
[2016-04-15T00:29Z] INFO  17:29:22,793 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:29Z] INFO  17:29:22,797 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:29Z] INFO  17:29:22,798 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:29Z] INFO  17:29:22,798 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:29Z] INFO  17:29:22,804 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/5/R14-18106_kapa-NGv3-PE100-NGv3-sort-5_96432513_112043579-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/5/R14-18106_kapa-NGv3-PE100-NGv3-5_96432513_112043579-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/5/tx/tmpm6fGnc/R14-18106_kapa-NGv3-PE100-NGv3-5_96432513_112043579.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:29Z] INFO  17:29:22,817 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:29Z] INFO  17:29:22,818 HelpFormatter - Date/Time: 2016/04/14 17:29:22
[2016-04-15T00:29Z] INFO  17:29:22,819 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:29Z] INFO  17:29:22,820 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:29Z] INFO  17:29:22,881 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:29Z] INFO  17:29:23,004 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:29Z] INFO  17:29:23,091 ProgressMeter -      4:13603570    784375.0    30.0 s      38.0 s       96.0%    31.0 s       1.0 s
[2016-04-15T00:29Z] GATK: UnifiedGenotyper
[2016-04-15T00:29Z] INFO  17:29:23,171 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:29Z] INFO  17:29:23,190 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:29Z] INFO  17:29:23,190 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:29Z] INFO  17:29:23,191 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:29Z] INFO  17:29:23,197 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/5/R14-18106_kapa-NGv3-PE100-NGv3-sort-5_112073555_127595521-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/5/R14-18106_kapa-NGv3-PE100-NGv3-5_112073555_127595521-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/5/tx/tmpE64E4q/R14-18106_kapa-NGv3-PE100-NGv3-5_112073555_127595521.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:29Z] INFO  17:29:23,230 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:29Z] INFO  17:29:23,231 HelpFormatter - Date/Time: 2016/04/14 17:29:23
[2016-04-15T00:29Z] INFO  17:29:23,231 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:29Z] INFO  17:29:23,232 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:29Z] INFO  17:29:23,287 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:29Z] INFO  17:29:23,297 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:29Z] INFO  17:29:23,366 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-15T00:29Z] INFO  17:29:23,405 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:29Z] INFO  17:29:23,456 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:29Z] INFO  17:29:23,538 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:29Z] INFO  17:29:23,686 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:29Z] INFO  17:29:23,708 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:29Z] INFO  17:29:23,778 ProgressMeter -            done    829685.0    30.0 s      37.0 s      100.0%    30.0 s       0.0 s
[2016-04-15T00:29Z] INFO  17:29:23,778 ProgressMeter - Total runtime 30.71 secs, 0.51 min, 0.01 hours
[2016-04-15T00:29Z] INFO  17:29:23,779 MicroScheduler - 29137 reads were filtered out during the traversal out of approximately 381642 total reads (7.63%)
[2016-04-15T00:29Z] INFO  17:29:23,779 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:29Z] INFO  17:29:23,779 MicroScheduler -   -> 707 reads (0.19% of total) failing BadMateFilter
[2016-04-15T00:29Z] INFO  17:29:23,780 MicroScheduler -   -> 28147 reads (7.38% of total) failing DuplicateReadFilter
[2016-04-15T00:29Z] INFO  17:29:23,780 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:29Z] INFO  17:29:23,780 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:29Z] INFO  17:29:23,780 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:29Z] INFO  17:29:23,781 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:29Z] INFO  17:29:23,781 MicroScheduler -   -> 283 reads (0.07% of total) failing UnmappedReadFilter
[2016-04-15T00:29Z] INFO  17:29:23,780 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:29Z] INFO  17:29:23,798 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:29Z] INFO  17:29:23,799 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:29Z] INFO  17:29:23,799 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:29Z] GATK: UnifiedGenotyper
[2016-04-15T00:29Z] INFO  17:29:23,805 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/5/R14-18106_kapa-NGv3-PE100-NGv3-sort-5_143200044_158710347-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/5/R14-18106_kapa-NGv3-PE100-NGv3-5_143200044_158710347-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/5/tx/tmpKDNYHC/R14-18106_kapa-NGv3-PE100-NGv3-5_143200044_158710347.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:29Z] INFO  17:29:23,814 IntervalUtils - Processing 57322 bp from intervals
[2016-04-15T00:29Z] INFO  17:29:23,817 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.11
[2016-04-15T00:29Z] INFO  17:29:23,813 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:29Z] INFO  17:29:23,819 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:29Z] INFO  17:29:23,820 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:29Z] INFO  17:29:23,827 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:29Z] WARN  17:29:23,830 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:29Z] INFO  17:29:23,846 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/5/R14-18106_kapa-NGv3-PE100-NGv3-sort-5_127597427_143191869-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/5/R14-18106_kapa-NGv3-PE100-NGv3-5_127597427_143191869-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/5/tx/tmpAReR__/R14-18106_kapa-NGv3-PE100-NGv3-5_127597427_143191869.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:29Z] INFO  17:29:23,846 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:29Z] INFO  17:29:23,846 HelpFormatter - Date/Time: 2016/04/14 17:29:23
[2016-04-15T00:29Z] INFO  17:29:23,846 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:29Z] INFO  17:29:23,847 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:29Z] INFO  17:29:23,872 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:29Z] INFO  17:29:23,873 HelpFormatter - Date/Time: 2016/04/14 17:29:23
[2016-04-15T00:29Z] INFO  17:29:23,873 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:29Z] INFO  17:29:23,873 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:29Z] GATK: UnifiedGenotyper
[2016-04-15T00:29Z] INFO  17:29:23,927 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:29Z] INFO  17:29:24,011 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:29Z] INFO  17:29:24,015 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:29Z] INFO  17:29:24,016 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:29Z] INFO  17:29:24,027 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:29Z] INFO  17:29:24,074 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:29Z] INFO  17:29:24,080 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:29Z] INFO  17:29:24,081 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:29Z] INFO  17:29:24,085 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:29Z] INFO  17:29:24,126 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:29Z] INFO  17:29:24,319 IntervalUtils - Processing 103986 bp from intervals
[2016-04-15T00:29Z] WARN  17:29:24,335 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:29Z] INFO  17:29:24,391 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:29Z] INFO  17:29:24,392 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:29Z] INFO  17:29:24,400 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:29Z] INFO  17:29:24,401 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:29Z] INFO  17:29:24,453 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:29Z] INFO  17:29:24,495 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.09
[2016-04-15T00:29Z] INFO  17:29:24,500 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.10
[2016-04-15T00:29Z] GATK: UnifiedGenotyper
[2016-04-15T00:29Z] INFO  17:29:24,549 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:29Z] INFO  17:29:24,550 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:29Z] INFO  17:29:24,550 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:29Z] INFO  17:29:24,551 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:29Z] INFO  17:29:24,617 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:29Z] INFO  17:29:24,628 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:29Z] INFO  17:29:24,973 IntervalUtils - Processing 393653 bp from intervals
[2016-04-15T00:29Z] WARN  17:29:24,994 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:29Z] INFO  17:29:25,052 IntervalUtils - Processing 205172 bp from intervals
[2016-04-15T00:29Z] WARN  17:29:25,068 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:29Z] INFO  17:29:25,101 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:29Z] INFO  17:29:25,154 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:29Z] INFO  17:29:25,155 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:29Z] INFO  17:29:25,167 ProgressMeter -            done    172946.0    12.0 s      74.0 s      100.0%    12.0 s       0.0 s
[2016-04-15T00:29Z] INFO  17:29:25,168 ProgressMeter - Total runtime 12.89 secs, 0.21 min, 0.00 hours
[2016-04-15T00:29Z] INFO  17:29:25,169 MicroScheduler - 6193 reads were filtered out during the traversal out of approximately 80190 total reads (7.72%)
[2016-04-15T00:29Z] INFO  17:29:25,170 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:29Z] INFO  17:29:25,171 MicroScheduler -   -> 136 reads (0.17% of total) failing BadMateFilter
[2016-04-15T00:29Z] INFO  17:29:25,171 MicroScheduler -   -> 6004 reads (7.49% of total) failing DuplicateReadFilter
[2016-04-15T00:29Z] INFO  17:29:25,172 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:29Z] INFO  17:29:25,172 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:29Z] INFO  17:29:25,173 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:29Z] INFO  17:29:25,174 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:29Z] INFO  17:29:25,174 MicroScheduler -   -> 53 reads (0.07% of total) failing UnmappedReadFilter
[2016-04-15T00:29Z] INFO  17:29:25,238 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:29Z] INFO  17:29:25,239 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:29Z] INFO  17:29:25,240 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:29Z] INFO  17:29:25,241 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:29Z] INFO  17:29:25,290 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:29Z] INFO  17:29:25,291 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:29Z] INFO  17:29:25,296 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:29Z] INFO  17:29:25,297 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:29Z] INFO  17:29:25,298 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:29Z] INFO  17:29:25,299 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:29Z] INFO  17:29:25,359 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:29Z] INFO  17:29:25,360 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:29Z] GATK: UnifiedGenotyper
[2016-04-15T00:29Z] INFO  17:29:26,364 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:29Z] INFO  17:29:26,367 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:29Z] INFO  17:29:26,368 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:29Z] INFO  17:29:26,368 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:29Z] INFO  17:29:26,373 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/5/R14-18106_kapa-NGv3-PE100-NGv3-sort-5_158711911_174870102-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/5/R14-18106_kapa-NGv3-PE100-NGv3-5_158711911_174870102-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/5/tx/tmpchUiow/R14-18106_kapa-NGv3-PE100-NGv3-5_158711911_174870102.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:29Z] INFO  17:29:26,407 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:29Z] INFO  17:29:26,413 HelpFormatter - Date/Time: 2016/04/14 17:29:26
[2016-04-15T00:29Z] INFO  17:29:26,414 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:29Z] INFO  17:29:26,414 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:29Z] INFO  17:29:26,564 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:29Z] INFO  17:29:26,577 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:29Z] INFO  17:29:26,843 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:29Z] INFO  17:29:26,852 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:29Z] GATK: UnifiedGenotyper
[2016-04-15T00:29Z] INFO  17:29:26,903 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:29Z] INFO  17:29:26,906 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:29Z] INFO  17:29:26,906 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:29Z] INFO  17:29:26,907 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:29Z] INFO  17:29:26,911 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/6/R14-18106_kapa-NGv3-PE100-NGv3-sort-6_0_15509601-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/6/R14-18106_kapa-NGv3-PE100-NGv3-6_0_15509601-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/6/tx/tmp0gCdAL/R14-18106_kapa-NGv3-PE100-NGv3-6_0_15509601.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:29Z] INFO  17:29:26,920 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:29Z] INFO  17:29:26,928 HelpFormatter - Date/Time: 2016/04/14 17:29:26
[2016-04-15T00:29Z] INFO  17:29:26,929 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:29Z] INFO  17:29:26,929 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:29Z] INFO  17:29:26,930 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-15T00:29Z] INFO  17:29:27,067 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:29Z] INFO  17:29:27,070 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:29Z] INFO  17:29:27,071 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:29Z] INFO  17:29:27,072 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:29Z] INFO  17:29:27,076 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/5/R14-18106_kapa-NGv3-PE100-NGv3-sort-5_174919106_180915260-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/5/R14-18106_kapa-NGv3-PE100-NGv3-5_174919106_180915260-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/5/tx/tmpmDGgsA/R14-18106_kapa-NGv3-PE100-NGv3-5_174919106_180915260.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:29Z] INFO  17:29:27,105 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:29Z] INFO  17:29:27,108 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:29Z] INFO  17:29:27,116 HelpFormatter - Date/Time: 2016/04/14 17:29:27
[2016-04-15T00:29Z] INFO  17:29:27,117 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:29Z] INFO  17:29:27,118 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:29Z] INFO  17:29:27,304 IntervalUtils - Processing 104189 bp from intervals
[2016-04-15T00:29Z] WARN  17:29:27,309 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:29Z] INFO  17:29:27,312 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:29Z] INFO  17:29:27,374 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:29Z] INFO  17:29:27,385 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:29Z] INFO  17:29:27,393 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:29Z] INFO  17:29:27,432 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:29Z] INFO  17:29:27,433 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:29Z] INFO  17:29:27,434 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:29Z] INFO  17:29:27,435 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:29Z] INFO  17:29:27,449 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:29Z] INFO  17:29:27,452 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:29Z] INFO  17:29:27,453 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:29Z] INFO  17:29:27,453 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:29Z] INFO  17:29:27,457 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/6/R14-18106_kapa-NGv3-PE100-NGv3-sort-6_15511526_31080332-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/6/R14-18106_kapa-NGv3-PE100-NGv3-6_15511526_31080332-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/6/tx/tmpH7mg8S/R14-18106_kapa-NGv3-PE100-NGv3-6_15511526_31080332.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:29Z] INFO  17:29:27,478 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:29Z] INFO  17:29:27,479 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:29Z] INFO  17:29:27,480 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:29Z] INFO  17:29:27,481 HelpFormatter - Date/Time: 2016/04/14 17:29:27
[2016-04-15T00:29Z] INFO  17:29:27,481 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:29Z] INFO  17:29:27,482 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:29Z] INFO  17:29:27,489 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.09
[2016-04-15T00:29Z] INFO  17:29:27,624 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:29Z] INFO  17:29:27,633 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:29Z] INFO  17:29:27,660 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:29Z] INFO  17:29:27,697 ProgressMeter -            done    326544.0    14.0 s      43.0 s       99.9%    14.0 s       0.0 s
[2016-04-15T00:29Z] INFO  17:29:27,697 ProgressMeter - Total runtime 14.22 secs, 0.24 min, 0.00 hours
[2016-04-15T00:29Z] INFO  17:29:27,698 MicroScheduler - 9701 reads were filtered out during the traversal out of approximately 121509 total reads (7.98%)
[2016-04-15T00:29Z] INFO  17:29:27,698 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:29Z] INFO  17:29:27,698 MicroScheduler -   -> 204 reads (0.17% of total) failing BadMateFilter
[2016-04-15T00:29Z] INFO  17:29:27,699 MicroScheduler -   -> 9418 reads (7.75% of total) failing DuplicateReadFilter
[2016-04-15T00:29Z] INFO  17:29:27,699 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:29Z] INFO  17:29:27,699 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:29Z] INFO  17:29:27,699 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:29Z] INFO  17:29:27,700 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:29Z] INFO  17:29:27,700 MicroScheduler -   -> 79 reads (0.07% of total) failing UnmappedReadFilter
[2016-04-15T00:29Z] INFO  17:29:27,771 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.11
[2016-04-15T00:29Z] INFO  17:29:27,902 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:29Z] INFO  17:29:27,912 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:29Z] INFO  17:29:27,993 IntervalUtils - Processing 139546 bp from intervals
[2016-04-15T00:29Z] WARN  17:29:27,998 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:29Z] INFO  17:29:28,017 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.10
[2016-04-15T00:29Z] INFO  17:29:28,110 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:29Z] INFO  17:29:28,204 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:29Z] INFO  17:29:28,205 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:29Z] INFO  17:29:28,206 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:29Z] INFO  17:29:28,207 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:29Z] INFO  17:29:28,253 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:29Z] INFO  17:29:28,258 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:29Z] INFO  17:29:28,395 IntervalUtils - Processing 163171 bp from intervals
[2016-04-15T00:29Z] WARN  17:29:28,430 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:29Z] INFO  17:29:28,570 IntervalUtils - Processing 239663 bp from intervals
[2016-04-15T00:29Z] WARN  17:29:28,576 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:29Z] INFO  17:29:28,589 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:29Z] INFO  17:29:28,655 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:29Z] INFO  17:29:28,704 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:29Z] INFO  17:29:28,705 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:29Z] INFO  17:29:28,706 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:29Z] INFO  17:29:28,706 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:29Z] INFO  17:29:28,786 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:29Z] INFO  17:29:28,787 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:29Z] INFO  17:29:28,789 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:29Z] INFO  17:29:28,789 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:29Z] INFO  17:29:28,790 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:29Z] INFO  17:29:28,793 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:29Z] INFO  17:29:28,826 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:29Z] INFO  17:29:28,829 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:29Z] INFO  17:29:28,830 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:29Z] INFO  17:29:28,830 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:29Z] INFO  17:29:28,835 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/6/R14-18106_kapa-NGv3-PE100-NGv3-sort-6_31083801_46593245-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/6/R14-18106_kapa-NGv3-PE100-NGv3-6_31083801_46593245-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/6/tx/tmp5YGez1/R14-18106_kapa-NGv3-PE100-NGv3-6_31083801_46593245.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:29Z] INFO  17:29:28,849 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:29Z] INFO  17:29:28,850 HelpFormatter - Date/Time: 2016/04/14 17:29:28
[2016-04-15T00:29Z] INFO  17:29:28,851 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:29Z] INFO  17:29:28,851 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:29Z] INFO  17:29:28,856 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:29Z] INFO  17:29:28,857 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:29Z] INFO  17:29:29,062 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:29Z] INFO  17:29:29,316 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:29Z] INFO  17:29:29,328 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:29Z] INFO  17:29:29,334 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:29Z] INFO  17:29:29,425 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.10
[2016-04-15T00:29Z] GATK: UnifiedGenotyper
[2016-04-15T00:29Z] INFO  17:29:29,944 IntervalUtils - Processing 501134 bp from intervals
[2016-04-15T00:29Z] WARN  17:29:29,949 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:29Z] INFO  17:29:30,069 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:29Z] INFO  17:29:30,235 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:29Z] INFO  17:29:30,236 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:29Z] INFO  17:29:30,237 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:29Z] INFO  17:29:30,238 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:29Z] INFO  17:29:30,269 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:29Z] INFO  17:29:30,272 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:29Z] INFO  17:29:30,273 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:29Z] INFO  17:29:30,273 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:29Z] INFO  17:29:30,278 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/6/R14-18106_kapa-NGv3-PE100-NGv3-sort-6_46598699_62284307-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/6/R14-18106_kapa-NGv3-PE100-NGv3-6_46598699_62284307-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/6/tx/tmplabv1_/R14-18106_kapa-NGv3-PE100-NGv3-6_46598699_62284307.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:29Z] INFO  17:29:30,297 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:29Z] INFO  17:29:30,298 HelpFormatter - Date/Time: 2016/04/14 17:29:30
[2016-04-15T00:29Z] INFO  17:29:30,298 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:29Z] INFO  17:29:30,299 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:29Z] INFO  17:29:30,314 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:29Z] INFO  17:29:30,315 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:29Z] INFO  17:29:30,504 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:29Z] INFO  17:29:30,734 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:29Z] INFO  17:29:30,743 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:29Z] INFO  17:29:30,854 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.10
[2016-04-15T00:29Z] INFO  17:29:30,882 ProgressMeter -            done    292827.0    15.0 s      51.0 s       99.9%    15.0 s       0.0 s
[2016-04-15T00:29Z] INFO  17:29:30,882 ProgressMeter - Total runtime 15.17 secs, 0.25 min, 0.00 hours
[2016-04-15T00:29Z] INFO  17:29:30,883 MicroScheduler - 8911 reads were filtered out during the traversal out of approximately 114436 total reads (7.79%)
[2016-04-15T00:29Z] INFO  17:29:30,883 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:29Z] INFO  17:29:30,883 MicroScheduler -   -> 174 reads (0.15% of total) failing BadMateFilter
[2016-04-15T00:29Z] INFO  17:29:30,884 MicroScheduler -   -> 8655 reads (7.56% of total) failing DuplicateReadFilter
[2016-04-15T00:29Z] INFO  17:29:30,884 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:29Z] INFO  17:29:30,884 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:29Z] INFO  17:29:30,884 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:29Z] INFO  17:29:30,884 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:29Z] INFO  17:29:30,885 MicroScheduler -   -> 82 reads (0.07% of total) failing UnmappedReadFilter
[2016-04-15T00:29Z] INFO  17:29:31,325 IntervalUtils - Processing 157522 bp from intervals
[2016-04-15T00:29Z] WARN  17:29:31,330 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:29Z] INFO  17:29:31,457 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:29Z] INFO  17:29:31,570 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:29Z] INFO  17:29:31,582 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:29Z] INFO  17:29:31,583 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:29Z] INFO  17:29:31,584 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:29Z] INFO  17:29:31,660 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:29Z] INFO  17:29:31,661 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:29Z] INFO  17:29:31,888 ProgressMeter -            done    392693.0    17.0 s      43.0 s       99.9%    17.0 s       0.0 s
[2016-04-15T00:29Z] INFO  17:29:31,889 ProgressMeter - Total runtime 17.02 secs, 0.28 min, 0.00 hours
[2016-04-15T00:29Z] INFO  17:29:31,890 MicroScheduler - 13931 reads were filtered out during the traversal out of approximately 170448 total reads (8.17%)
[2016-04-15T00:29Z] INFO  17:29:31,890 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:29Z] INFO  17:29:31,891 MicroScheduler -   -> 321 reads (0.19% of total) failing BadMateFilter
[2016-04-15T00:29Z] INFO  17:29:31,895 MicroScheduler -   -> 13486 reads (7.91% of total) failing DuplicateReadFilter
[2016-04-15T00:29Z] INFO  17:29:31,896 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:29Z] INFO  17:29:31,897 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:29Z] INFO  17:29:31,898 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:29Z] INFO  17:29:31,898 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:29Z] INFO  17:29:31,899 MicroScheduler -   -> 124 reads (0.07% of total) failing UnmappedReadFilter
[2016-04-15T00:29Z] INFO  17:29:32,496 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:29Z] GATK: UnifiedGenotyper
[2016-04-15T00:29Z] INFO  17:29:32,856 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:29Z] INFO  17:29:32,859 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:29Z] INFO  17:29:32,860 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:29Z] INFO  17:29:32,861 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:29Z] INFO  17:29:32,865 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/6/R14-18106_kapa-NGv3-PE100-NGv3-sort-6_62390867_78173120-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/6/R14-18106_kapa-NGv3-PE100-NGv3-6_62390867_78173120-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/6/tx/tmpVZL4uC/R14-18106_kapa-NGv3-PE100-NGv3-6_62390867_78173120.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:29Z] INFO  17:29:32,874 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:29Z] INFO  17:29:32,886 HelpFormatter - Date/Time: 2016/04/14 17:29:32
[2016-04-15T00:29Z] INFO  17:29:32,887 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:29Z] INFO  17:29:32,888 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:29Z] INFO  17:29:33,104 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:29Z] INFO  17:29:33,373 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:29Z] INFO  17:29:33,391 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:29Z] INFO  17:29:33,391 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:29Z] INFO  17:29:33,485 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.09
[2016-04-15T00:29Z] GATK: UnifiedGenotyper
[2016-04-15T00:29Z] INFO  17:29:33,929 IntervalUtils - Processing 103397 bp from intervals
[2016-04-15T00:29Z] WARN  17:29:33,934 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:29Z] INFO  17:29:33,934 ProgressMeter -            done    152663.0     9.0 s      64.0 s       99.9%     9.0 s       0.0 s
[2016-04-15T00:29Z] INFO  17:29:33,935 ProgressMeter - Total runtime 9.92 secs, 0.17 min, 0.00 hours
[2016-04-15T00:29Z] INFO  17:29:33,936 MicroScheduler - 4070 reads were filtered out during the traversal out of approximately 52717 total reads (7.72%)
[2016-04-15T00:29Z] INFO  17:29:33,936 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:29Z] INFO  17:29:33,937 MicroScheduler -   -> 98 reads (0.19% of total) failing BadMateFilter
[2016-04-15T00:29Z] INFO  17:29:33,938 MicroScheduler -   -> 3923 reads (7.44% of total) failing DuplicateReadFilter
[2016-04-15T00:29Z] INFO  17:29:33,938 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:29Z] INFO  17:29:33,939 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:29Z] INFO  17:29:33,940 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:29Z] INFO  17:29:33,940 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:29Z] INFO  17:29:33,941 MicroScheduler -   -> 49 reads (0.09% of total) failing UnmappedReadFilter
[2016-04-15T00:29Z] INFO  17:29:34,074 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:29Z] INFO  17:29:34,173 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:29Z] INFO  17:29:34,174 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:29Z] INFO  17:29:34,175 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:29Z] INFO  17:29:34,175 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:29Z] INFO  17:29:34,245 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:29Z] INFO  17:29:34,256 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:29Z] INFO  17:29:34,463 ProgressMeter -            done    373968.0    15.0 s      40.0 s       99.9%    15.0 s       0.0 s
[2016-04-15T00:29Z] INFO  17:29:34,463 ProgressMeter - Total runtime 15.27 secs, 0.25 min, 0.00 hours
[2016-04-15T00:29Z] INFO  17:29:34,464 MicroScheduler - 8689 reads were filtered out during the traversal out of approximately 114848 total reads (7.57%)
[2016-04-15T00:29Z] INFO  17:29:34,464 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:29Z] INFO  17:29:34,464 MicroScheduler -   -> 192 reads (0.17% of total) failing BadMateFilter
[2016-04-15T00:29Z] INFO  17:29:34,464 MicroScheduler -   -> 8426 reads (7.34% of total) failing DuplicateReadFilter
[2016-04-15T00:29Z] INFO  17:29:34,465 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:29Z] INFO  17:29:34,465 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:29Z] INFO  17:29:34,465 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:29Z] INFO  17:29:34,465 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:29Z] INFO  17:29:34,466 MicroScheduler -   -> 71 reads (0.06% of total) failing UnmappedReadFilter
[2016-04-15T00:29Z] INFO  17:29:35,639 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:29Z] INFO  17:29:35,735 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:29Z] INFO  17:29:35,941 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:29Z] INFO  17:29:35,944 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:29Z] INFO  17:29:35,945 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:29Z] INFO  17:29:35,945 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:29Z] INFO  17:29:35,950 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/6/R14-18106_kapa-NGv3-PE100-NGv3-sort-6_78400388_93953258-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/6/R14-18106_kapa-NGv3-PE100-NGv3-6_78400388_93953258-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/6/tx/tmp4zA9ez/R14-18106_kapa-NGv3-PE100-NGv3-6_78400388_93953258.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:29Z] GATK: UnifiedGenotyper
[2016-04-15T00:29Z] INFO  17:29:35,960 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:29Z] GATK: UnifiedGenotyper
[2016-04-15T00:29Z] INFO  17:29:35,971 HelpFormatter - Date/Time: 2016/04/14 17:29:35
[2016-04-15T00:29Z] INFO  17:29:35,972 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:29Z] INFO  17:29:35,972 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:29Z] INFO  17:29:36,039 ProgressMeter -            done    536506.0    20.0 s      38.0 s      100.0%    20.0 s       0.0 s
[2016-04-15T00:29Z] INFO  17:29:36,039 ProgressMeter - Total runtime 20.55 secs, 0.34 min, 0.01 hours
[2016-04-15T00:29Z] INFO  17:29:36,039 MicroScheduler - 15677 reads were filtered out during the traversal out of approximately 197186 total reads (7.95%)
[2016-04-15T00:29Z] INFO  17:29:36,040 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:29Z] INFO  17:29:36,040 MicroScheduler -   -> 324 reads (0.16% of total) failing BadMateFilter
[2016-04-15T00:29Z] INFO  17:29:36,040 MicroScheduler -   -> 15217 reads (7.72% of total) failing DuplicateReadFilter
[2016-04-15T00:29Z] INFO  17:29:36,040 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:29Z] INFO  17:29:36,041 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:29Z] INFO  17:29:36,041 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:29Z] INFO  17:29:36,041 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:29Z] INFO  17:29:36,041 MicroScheduler -   -> 136 reads (0.07% of total) failing UnmappedReadFilter
[2016-04-15T00:29Z] INFO  17:29:36,137 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:29Z] INFO  17:29:36,386 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:29Z] INFO  17:29:36,398 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:29Z] INFO  17:29:36,531 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.13
[2016-04-15T00:29Z] INFO  17:29:36,678 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:29Z] INFO  17:29:36,681 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:29Z] INFO  17:29:36,681 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:29Z] INFO  17:29:36,682 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:29Z] INFO  17:29:36,686 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/6/R14-18106_kapa-NGv3-PE100-NGv3-sort-6_93955015_109466584-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/6/R14-18106_kapa-NGv3-PE100-NGv3-6_93955015_109466584-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/6/tx/tmp7Dz6Ai/R14-18106_kapa-NGv3-PE100-NGv3-6_93955015_109466584.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:29Z] INFO  17:29:36,703 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:29Z] INFO  17:29:36,704 HelpFormatter - Date/Time: 2016/04/14 17:29:36
[2016-04-15T00:29Z] INFO  17:29:36,704 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:29Z] INFO  17:29:36,705 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:29Z] INFO  17:29:36,919 IntervalUtils - Processing 131721 bp from intervals
[2016-04-15T00:29Z] WARN  17:29:36,924 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:29Z] INFO  17:29:36,993 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:29Z] INFO  17:29:37,057 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:29Z] INFO  17:29:37,134 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:29Z] INFO  17:29:37,135 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:29Z] INFO  17:29:37,136 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:29Z] INFO  17:29:37,137 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:29Z] INFO  17:29:37,226 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:29Z] INFO  17:29:37,227 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:29Z] INFO  17:29:37,286 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:29Z] INFO  17:29:37,297 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:29Z] INFO  17:29:37,366 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-15T00:29Z] INFO  17:29:37,538 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:29Z] INFO  17:29:37,854 IntervalUtils - Processing 95525 bp from intervals
[2016-04-15T00:29Z] WARN  17:29:37,860 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:29Z] GATK: UnifiedGenotyper
[2016-04-15T00:29Z] INFO  17:29:37,935 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:29Z] INFO  17:29:38,019 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:29Z] INFO  17:29:38,020 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:29Z] INFO  17:29:38,020 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:29Z] INFO  17:29:38,020 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:29Z] INFO  17:29:38,100 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:29Z] INFO  17:29:38,101 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:29Z] INFO  17:29:38,735 ProgressMeter -            done    235248.0    14.0 s      60.0 s       99.9%    14.0 s       0.0 s
[2016-04-15T00:29Z] INFO  17:29:38,735 ProgressMeter - Total runtime 14.19 secs, 0.24 min, 0.00 hours
[2016-04-15T00:29Z] INFO  17:29:38,736 MicroScheduler - 9244 reads were filtered out during the traversal out of approximately 116145 total reads (7.96%)
[2016-04-15T00:29Z] INFO  17:29:38,736 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:29Z] INFO  17:29:38,736 MicroScheduler -   -> 265 reads (0.23% of total) failing BadMateFilter
[2016-04-15T00:29Z] INFO  17:29:38,737 MicroScheduler -   -> 8901 reads (7.66% of total) failing DuplicateReadFilter
[2016-04-15T00:29Z] INFO  17:29:38,737 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:29Z] INFO  17:29:38,737 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:29Z] INFO  17:29:38,738 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:29Z] INFO  17:29:38,738 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:29Z] INFO  17:29:38,738 MicroScheduler -   -> 78 reads (0.07% of total) failing UnmappedReadFilter
[2016-04-15T00:29Z] INFO  17:29:39,105 ProgressMeter -            done    554557.0    21.0 s      38.0 s      100.0%    21.0 s       0.0 s
[2016-04-15T00:29Z] INFO  17:29:39,106 ProgressMeter - Total runtime 21.27 secs, 0.35 min, 0.01 hours
[2016-04-15T00:29Z] INFO  17:29:39,106 MicroScheduler - 16213 reads were filtered out during the traversal out of approximately 211733 total reads (7.66%)
[2016-04-15T00:29Z] INFO  17:29:39,107 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:29Z] INFO  17:29:39,109 MicroScheduler -   -> 336 reads (0.16% of total) failing BadMateFilter
[2016-04-15T00:29Z] INFO  17:29:39,109 MicroScheduler -   -> 15759 reads (7.44% of total) failing DuplicateReadFilter
[2016-04-15T00:29Z] INFO  17:29:39,110 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:29Z] INFO  17:29:39,110 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:29Z] INFO  17:29:39,110 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:29Z] INFO  17:29:39,110 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:29Z] INFO  17:29:39,110 MicroScheduler -   -> 118 reads (0.06% of total) failing UnmappedReadFilter
[2016-04-15T00:29Z] INFO  17:29:39,243 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:29Z] INFO  17:29:39,246 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:29Z] INFO  17:29:39,246 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:29Z] INFO  17:29:39,247 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:29Z] INFO  17:29:39,251 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/6/R14-18106_kapa-NGv3-PE100-NGv3-sort-6_109467960_124979532-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/6/R14-18106_kapa-NGv3-PE100-NGv3-6_109467960_124979532-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/6/tx/tmpeqHger/R14-18106_kapa-NGv3-PE100-NGv3-6_109467960_124979532.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:29Z] INFO  17:29:39,261 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:29Z] INFO  17:29:39,261 HelpFormatter - Date/Time: 2016/04/14 17:29:39
[2016-04-15T00:29Z] INFO  17:29:39,261 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:29Z] INFO  17:29:39,262 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:29Z] INFO  17:29:39,371 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:29Z] INFO  17:29:39,374 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:29Z] INFO  17:29:39,375 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:29Z] INFO  17:29:39,375 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:29Z] INFO  17:29:39,380 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/6/R14-18106_kapa-NGv3-PE100-NGv3-sort-6_125112484_142397186-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/6/R14-18106_kapa-NGv3-PE100-NGv3-6_125112484_142397186-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/6/tx/tmpxvhg6P/R14-18106_kapa-NGv3-PE100-NGv3-6_125112484_142397186.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:29Z] INFO  17:29:39,394 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:29Z] INFO  17:29:39,402 HelpFormatter - Date/Time: 2016/04/14 17:29:39
[2016-04-15T00:29Z] INFO  17:29:39,403 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:29Z] INFO  17:29:39,404 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:29Z] INFO  17:29:39,432 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:29Z] INFO  17:29:39,686 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:29Z] INFO  17:29:39,692 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:29Z] INFO  17:29:39,700 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:29Z] INFO  17:29:39,844 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.14
[2016-04-15T00:29Z] INFO  17:29:39,925 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:29Z] INFO  17:29:39,933 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:29Z] INFO  17:29:40,034 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.10
[2016-04-15T00:29Z] INFO  17:29:40,145 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:29Z] INFO  17:29:40,393 IntervalUtils - Processing 147815 bp from intervals
[2016-04-15T00:29Z] WARN  17:29:40,409 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:29Z] INFO  17:29:40,479 IntervalUtils - Processing 156964 bp from intervals
[2016-04-15T00:29Z] WARN  17:29:40,483 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:29Z] GATK: UnifiedGenotyper
[2016-04-15T00:29Z] INFO  17:29:40,545 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:29Z] INFO  17:29:40,566 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:29Z] INFO  17:29:40,578 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:29Z] INFO  17:29:40,643 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:29Z] INFO  17:29:40,644 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:29Z] INFO  17:29:40,644 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:29Z] INFO  17:29:40,644 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:29Z] INFO  17:29:40,684 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:29Z] INFO  17:29:40,685 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:29Z] INFO  17:29:40,685 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:29Z] INFO  17:29:40,685 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:29Z] INFO  17:29:40,707 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:29Z] INFO  17:29:40,708 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:29Z] INFO  17:29:40,770 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:29Z] INFO  17:29:40,776 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:29Z] GATK: UnifiedGenotyper
[2016-04-15T00:29Z] INFO  17:29:40,956 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:29Z] INFO  17:29:40,959 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:29Z] INFO  17:29:40,960 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:29Z] INFO  17:29:40,961 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:29Z] INFO  17:29:40,967 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/6/R14-18106_kapa-NGv3-PE100-NGv3-sort-6_142399691_157963777-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/6/R14-18106_kapa-NGv3-PE100-NGv3-6_142399691_157963777-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/6/tx/tmpia2PBm/R14-18106_kapa-NGv3-PE100-NGv3-6_142399691_157963777.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:29Z] INFO  17:29:40,981 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:29Z] INFO  17:29:40,981 HelpFormatter - Date/Time: 2016/04/14 17:29:40
[2016-04-15T00:29Z] INFO  17:29:40,981 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:29Z] INFO  17:29:40,982 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:29Z] INFO  17:29:41,141 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:29Z] INFO  17:29:41,397 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:29Z] INFO  17:29:41,405 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:29Z] INFO  17:29:41,475 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-15T00:29Z] INFO  17:29:42,160 IntervalUtils - Processing 183871 bp from intervals
[2016-04-15T00:29Z] WARN  17:29:42,174 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:29Z] INFO  17:29:42,282 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:29Z] INFO  17:29:42,434 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:29Z] INFO  17:29:42,435 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:29Z] INFO  17:29:42,436 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:29Z] INFO  17:29:42,437 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:29Z] INFO  17:29:42,533 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:29Z] INFO  17:29:42,534 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:29Z] INFO  17:29:43,059 ProgressMeter -            done    237846.0    15.0 s      65.0 s      100.0%    15.0 s       0.0 s
[2016-04-15T00:29Z] INFO  17:29:43,060 ProgressMeter - Total runtime 15.63 secs, 0.26 min, 0.00 hours
[2016-04-15T00:29Z] INFO  17:29:43,060 MicroScheduler - 11015 reads were filtered out during the traversal out of approximately 135912 total reads (8.10%)
[2016-04-15T00:29Z] INFO  17:29:43,061 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:29Z] INFO  17:29:43,061 MicroScheduler -   -> 231 reads (0.17% of total) failing BadMateFilter
[2016-04-15T00:29Z] INFO  17:29:43,061 MicroScheduler -   -> 10692 reads (7.87% of total) failing DuplicateReadFilter
[2016-04-15T00:29Z] INFO  17:29:43,061 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:29Z] INFO  17:29:43,062 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:29Z] INFO  17:29:43,062 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:29Z] INFO  17:29:43,062 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:29Z] INFO  17:29:43,062 MicroScheduler -   -> 92 reads (0.07% of total) failing UnmappedReadFilter
[2016-04-15T00:29Z] INFO  17:29:43,542 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:29Z] INFO  17:29:43,545 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:29Z] INFO  17:29:43,546 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:29Z] INFO  17:29:43,546 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:29Z] INFO  17:29:43,551 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/7/R14-18106_kapa-NGv3-PE100-NGv3-sort-7_0_15584548-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/7/R14-18106_kapa-NGv3-PE100-NGv3-7_0_15584548-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/7/tx/tmpIMSo8k/R14-18106_kapa-NGv3-PE100-NGv3-7_0_15584548.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:29Z] INFO  17:29:43,563 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:29Z] INFO  17:29:43,565 HelpFormatter - Date/Time: 2016/04/14 17:29:43
[2016-04-15T00:29Z] INFO  17:29:43,566 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:29Z] INFO  17:29:43,566 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:29Z] INFO  17:29:43,638 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:29Z] INFO  17:29:43,642 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:29Z] INFO  17:29:43,642 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:29Z] INFO  17:29:43,643 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:29Z] INFO  17:29:43,648 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/6/R14-18106_kapa-NGv3-PE100-NGv3-sort-6_158013810_171115067-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/6/R14-18106_kapa-NGv3-PE100-NGv3-6_158013810_171115067-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/6/tx/tmpB93pzD/R14-18106_kapa-NGv3-PE100-NGv3-6_158013810_171115067.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:29Z] INFO  17:29:43,665 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:29Z] INFO  17:29:43,666 HelpFormatter - Date/Time: 2016/04/14 17:29:43
[2016-04-15T00:29Z] INFO  17:29:43,666 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:29Z] INFO  17:29:43,667 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:29Z] INFO  17:29:43,805 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:29Z] INFO  17:29:43,843 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:29Z] INFO  17:29:44,068 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:29Z] INFO  17:29:44,077 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:29Z] INFO  17:29:44,094 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:29Z] INFO  17:29:44,103 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:29Z] INFO  17:29:44,196 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.09
[2016-04-15T00:29Z] INFO  17:29:44,197 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.12
[2016-04-15T00:29Z] INFO  17:29:44,413 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:29Z] INFO  17:29:44,573 IntervalUtils - Processing 143202 bp from intervals
[2016-04-15T00:29Z] WARN  17:29:44,578 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:29Z] INFO  17:29:44,661 IntervalUtils - Processing 187602 bp from intervals
[2016-04-15T00:29Z] WARN  17:29:44,665 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:29Z] INFO  17:29:44,722 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:29Z] GATK: UnifiedGenotyper
[2016-04-15T00:29Z] INFO  17:29:44,786 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:29Z] INFO  17:29:44,825 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:29Z] INFO  17:29:44,825 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:29Z] INFO  17:29:44,828 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:29Z] INFO  17:29:44,829 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:29Z] INFO  17:29:44,871 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:29Z] INFO  17:29:44,872 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:29Z] INFO  17:29:44,873 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:29Z] INFO  17:29:44,874 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:29Z] INFO  17:29:44,878 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:29Z] INFO  17:29:44,878 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:29Z] INFO  17:29:44,921 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:29Z] INFO  17:29:44,922 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:29Z] INFO  17:29:48,018 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:29Z] INFO  17:29:48,022 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:29Z] INFO  17:29:48,022 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:29Z] INFO  17:29:48,023 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:29Z] INFO  17:29:48,028 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/7/R14-18106_kapa-NGv3-PE100-NGv3-sort-7_15599765_31117713-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/7/R14-18106_kapa-NGv3-PE100-NGv3-7_15599765_31117713-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/7/tx/tmpxIOAJK/R14-18106_kapa-NGv3-PE100-NGv3-7_15599765_31117713.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:29Z] INFO  17:29:48,046 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:29Z] INFO  17:29:48,047 HelpFormatter - Date/Time: 2016/04/14 17:29:48
[2016-04-15T00:29Z] INFO  17:29:48,047 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:29Z] INFO  17:29:48,048 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:29Z] INFO  17:29:48,203 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:29Z] INFO  17:29:48,542 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:29Z] INFO  17:29:48,552 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:29Z] INFO  17:29:48,650 ProgressMeter -            done    269142.0    14.0 s      53.0 s       99.9%    14.0 s       0.0 s
[2016-04-15T00:29Z] INFO  17:29:48,650 ProgressMeter - Total runtime 14.48 secs, 0.24 min, 0.00 hours
[2016-04-15T00:29Z] INFO  17:29:48,650 MicroScheduler - 8314 reads were filtered out during the traversal out of approximately 106971 total reads (7.77%)
[2016-04-15T00:29Z] INFO  17:29:48,651 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:29Z] INFO  17:29:48,651 MicroScheduler -   -> 192 reads (0.18% of total) failing BadMateFilter
[2016-04-15T00:29Z] INFO  17:29:48,651 MicroScheduler -   -> 8056 reads (7.53% of total) failing DuplicateReadFilter
[2016-04-15T00:29Z] INFO  17:29:48,652 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:29Z] INFO  17:29:48,652 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:29Z] INFO  17:29:48,652 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:29Z] INFO  17:29:48,652 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:29Z] INFO  17:29:48,652 MicroScheduler -   -> 66 reads (0.06% of total) failing UnmappedReadFilter
[2016-04-15T00:29Z] INFO  17:29:48,662 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.11
[2016-04-15T00:29Z] INFO  17:29:48,920 ProgressMeter -            done    472667.0    17.0 s      36.0 s      100.0%    17.0 s       0.0 s
[2016-04-15T00:29Z] INFO  17:29:48,921 ProgressMeter - Total runtime 17.34 secs, 0.29 min, 0.00 hours
[2016-04-15T00:29Z] INFO  17:29:48,921 MicroScheduler - 13058 reads were filtered out during the traversal out of approximately 168607 total reads (7.74%)
[2016-04-15T00:29Z] INFO  17:29:48,922 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:29Z] INFO  17:29:48,922 MicroScheduler -   -> 275 reads (0.16% of total) failing BadMateFilter
[2016-04-15T00:29Z] INFO  17:29:48,922 MicroScheduler -   -> 12655 reads (7.51% of total) failing DuplicateReadFilter
[2016-04-15T00:29Z] INFO  17:29:48,922 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:29Z] INFO  17:29:48,923 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:29Z] INFO  17:29:48,923 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:29Z] INFO  17:29:48,923 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:29Z] INFO  17:29:48,923 MicroScheduler -   -> 128 reads (0.08% of total) failing UnmappedReadFilter
[2016-04-15T00:29Z] INFO  17:29:49,037 ProgressMeter -            done    349428.0    20.0 s      59.0 s      100.0%    20.0 s       0.0 s
[2016-04-15T00:29Z] INFO  17:29:49,037 ProgressMeter - Total runtime 20.83 secs, 0.35 min, 0.01 hours
[2016-04-15T00:29Z] INFO  17:29:49,038 MicroScheduler - 13711 reads were filtered out during the traversal out of approximately 173150 total reads (7.92%)
[2016-04-15T00:29Z] INFO  17:29:49,038 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:29Z] INFO  17:29:49,038 MicroScheduler -   -> 285 reads (0.16% of total) failing BadMateFilter
[2016-04-15T00:29Z] INFO  17:29:49,039 MicroScheduler -   -> 13327 reads (7.70% of total) failing DuplicateReadFilter
[2016-04-15T00:29Z] INFO  17:29:49,039 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:29Z] INFO  17:29:49,040 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:29Z] INFO  17:29:49,040 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:29Z] INFO  17:29:49,040 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:29Z] INFO  17:29:49,041 MicroScheduler -   -> 99 reads (0.06% of total) failing UnmappedReadFilter
[2016-04-15T00:29Z] INFO  17:29:49,098 IntervalUtils - Processing 149727 bp from intervals
[2016-04-15T00:29Z] WARN  17:29:49,103 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:29Z] INFO  17:29:49,178 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:29Z] INFO  17:29:49,254 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:29Z] INFO  17:29:49,255 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:29Z] INFO  17:29:49,255 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:29Z] INFO  17:29:49,256 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:29Z] INFO  17:29:49,302 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:29Z] INFO  17:29:49,303 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:29Z] INFO  17:29:49,323 ProgressMeter -            done    712768.0    20.0 s      28.0 s      100.0%    20.0 s       0.0 s
[2016-04-15T00:29Z] INFO  17:29:49,324 ProgressMeter - Total runtime 20.62 secs, 0.34 min, 0.01 hours
[2016-04-15T00:29Z] INFO  17:29:49,328 MicroScheduler - 18812 reads were filtered out during the traversal out of approximately 241252 total reads (7.80%)
[2016-04-15T00:29Z] INFO  17:29:49,328 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:29Z] INFO  17:29:49,339 MicroScheduler -   -> 402 reads (0.17% of total) failing BadMateFilter
[2016-04-15T00:29Z] INFO  17:29:49,340 MicroScheduler -   -> 18254 reads (7.57% of total) failing DuplicateReadFilter
[2016-04-15T00:29Z] INFO  17:29:49,341 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:29Z] INFO  17:29:49,341 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:29Z] INFO  17:29:49,342 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:29Z] INFO  17:29:49,343 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:29Z] INFO  17:29:49,343 MicroScheduler -   -> 156 reads (0.06% of total) failing UnmappedReadFilter
[2016-04-15T00:29Z] INFO  17:29:49,671 ProgressMeter -            done    639654.0    24.0 s      38.0 s      100.0%    24.0 s       0.0 s
[2016-04-15T00:29Z] INFO  17:29:49,671 ProgressMeter - Total runtime 24.37 secs, 0.41 min, 0.01 hours
[2016-04-15T00:29Z] INFO  17:29:49,672 MicroScheduler - 21730 reads were filtered out during the traversal out of approximately 271316 total reads (8.01%)
[2016-04-15T00:29Z] INFO  17:29:49,672 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:29Z] INFO  17:29:49,672 MicroScheduler -   -> 466 reads (0.17% of total) failing BadMateFilter
[2016-04-15T00:29Z] INFO  17:29:49,673 MicroScheduler -   -> 21121 reads (7.78% of total) failing DuplicateReadFilter
[2016-04-15T00:29Z] INFO  17:29:49,673 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:29Z] INFO  17:29:49,673 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:29Z] INFO  17:29:49,673 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:29Z] INFO  17:29:49,674 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:29Z] INFO  17:29:49,674 MicroScheduler -   -> 143 reads (0.05% of total) failing UnmappedReadFilter
[2016-04-15T00:29Z] INFO  17:29:50,179 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:29Z] GATK: UnifiedGenotyper
[2016-04-15T00:29Z] INFO  17:29:50,614 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:29Z] INFO  17:29:50,638 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:29Z] INFO  17:29:50,842 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:29Z] GATK: UnifiedGenotyper
[2016-04-15T00:29Z] GATK: UnifiedGenotyper
[2016-04-15T00:29Z] INFO  17:29:51,036 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:29Z] GATK: UnifiedGenotyper
[2016-04-15T00:29Z] INFO  17:29:51,221 ProgressMeter -            done    213234.0    13.0 s      61.0 s       99.9%    13.0 s       0.0 s
[2016-04-15T00:29Z] INFO  17:29:51,221 ProgressMeter - Total runtime 13.20 secs, 0.22 min, 0.00 hours
[2016-04-15T00:29Z] INFO  17:29:51,222 MicroScheduler - 7481 reads were filtered out during the traversal out of approximately 97405 total reads (7.68%)
[2016-04-15T00:29Z] INFO  17:29:51,222 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:29Z] INFO  17:29:51,223 MicroScheduler -   -> 143 reads (0.15% of total) failing BadMateFilter
[2016-04-15T00:29Z] INFO  17:29:51,224 MicroScheduler -   -> 7264 reads (7.46% of total) failing DuplicateReadFilter
[2016-04-15T00:29Z] INFO  17:29:51,224 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:29Z] INFO  17:29:51,224 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:29Z] INFO  17:29:51,225 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:29Z] INFO  17:29:51,225 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:29Z] INFO  17:29:51,225 MicroScheduler -   -> 74 reads (0.08% of total) failing UnmappedReadFilter
[2016-04-15T00:29Z] GATK: UnifiedGenotyper
[2016-04-15T00:29Z] INFO  17:29:51,441 ProgressMeter -            done    399770.0    14.0 s      35.0 s      100.0%    14.0 s       0.0 s
[2016-04-15T00:29Z] INFO  17:29:51,442 ProgressMeter - Total runtime 14.31 secs, 0.24 min, 0.00 hours
[2016-04-15T00:29Z] INFO  17:29:51,442 MicroScheduler - 10172 reads were filtered out during the traversal out of approximately 133709 total reads (7.61%)
[2016-04-15T00:29Z] INFO  17:29:51,442 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:29Z] INFO  17:29:51,443 MicroScheduler -   -> 205 reads (0.15% of total) failing BadMateFilter
[2016-04-15T00:29Z] INFO  17:29:51,443 MicroScheduler -   -> 9883 reads (7.39% of total) failing DuplicateReadFilter
[2016-04-15T00:29Z] INFO  17:29:51,443 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:29Z] INFO  17:29:51,444 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:29Z] INFO  17:29:51,444 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:29Z] INFO  17:29:51,444 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:29Z] INFO  17:29:51,445 MicroScheduler -   -> 84 reads (0.06% of total) failing UnmappedReadFilter
[2016-04-15T00:29Z] INFO  17:29:52,907 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:29Z] INFO  17:29:53,060 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:29Z] GATK: UnifiedGenotyper
[2016-04-15T00:29Z] GATK: UnifiedGenotyper
[2016-04-15T00:29Z] INFO  17:29:53,618 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:29Z] INFO  17:29:53,621 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:29Z] INFO  17:29:53,622 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:29Z] INFO  17:29:53,622 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:29Z] INFO  17:29:53,627 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/7/R14-18106_kapa-NGv3-PE100-NGv3-sort-7_31120227_47317818-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/7/R14-18106_kapa-NGv3-PE100-NGv3-7_31120227_47317818-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/7/tx/tmpSjyrif/R14-18106_kapa-NGv3-PE100-NGv3-7_31120227_47317818.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:29Z] INFO  17:29:53,666 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:29Z] INFO  17:29:53,667 HelpFormatter - Date/Time: 2016/04/14 17:29:53
[2016-04-15T00:29Z] INFO  17:29:53,667 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:29Z] INFO  17:29:53,667 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:29Z] INFO  17:29:53,905 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:29Z] INFO  17:29:53,937 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:29Z] INFO  17:29:53,939 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:29Z] INFO  17:29:53,939 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:29Z] INFO  17:29:53,940 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:29Z] INFO  17:29:53,944 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/7/R14-18106_kapa-NGv3-PE100-NGv3-sort-7_47319761_63093154-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/7/R14-18106_kapa-NGv3-PE100-NGv3-7_47319761_63093154-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/7/tx/tmphDlPV_/R14-18106_kapa-NGv3-PE100-NGv3-7_47319761_63093154.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:29Z] INFO  17:29:53,987 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:29Z] INFO  17:29:53,988 HelpFormatter - Date/Time: 2016/04/14 17:29:53
[2016-04-15T00:29Z] INFO  17:29:53,988 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:29Z] INFO  17:29:53,988 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:29Z] INFO  17:29:54,156 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:29Z] INFO  17:29:54,179 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:29Z] INFO  17:29:54,218 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:29Z] INFO  17:29:54,291 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-15T00:29Z] INFO  17:29:54,391 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:29Z] INFO  17:29:54,401 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:29Z] INFO  17:29:54,394 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:29Z] INFO  17:29:54,405 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:29Z] INFO  17:29:54,406 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:29Z] INFO  17:29:54,410 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:29Z] INFO  17:29:54,410 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/7/R14-18106_kapa-NGv3-PE100-NGv3-sort-7_79082334_94740703-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/7/R14-18106_kapa-NGv3-PE100-NGv3-7_79082334_94740703-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/7/tx/tmpoebaJl/R14-18106_kapa-NGv3-PE100-NGv3-7_79082334_94740703.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:29Z] INFO  17:29:54,430 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:29Z] INFO  17:29:54,431 HelpFormatter - Date/Time: 2016/04/14 17:29:54
[2016-04-15T00:29Z] INFO  17:29:54,431 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:29Z] INFO  17:29:54,431 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:29Z] INFO  17:29:54,494 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-15T00:29Z] INFO  17:29:54,624 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:29Z] INFO  17:29:54,628 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:29Z] INFO  17:29:54,628 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:29Z] INFO  17:29:54,629 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:29Z] INFO  17:29:54,633 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/7/R14-18106_kapa-NGv3-PE100-NGv3-sort-7_63095909_78636522-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/7/R14-18106_kapa-NGv3-PE100-NGv3-7_63095909_78636522-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/7/tx/tmpnm1b2o/R14-18106_kapa-NGv3-PE100-NGv3-7_63095909_78636522.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:29Z] INFO  17:29:54,659 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:29Z] INFO  17:29:54,660 HelpFormatter - Date/Time: 2016/04/14 17:29:54
[2016-04-15T00:29Z] INFO  17:29:54,661 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:29Z] INFO  17:29:54,663 IntervalUtils - Processing 138106 bp from intervals
[2016-04-15T00:29Z] INFO  17:29:54,665 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:29Z] WARN  17:29:54,667 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:29Z] INFO  17:29:54,678 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:29Z] INFO  17:29:54,682 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:29Z] INFO  17:29:54,683 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:29Z] INFO  17:29:54,683 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:29Z] INFO  17:29:54,687 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:29Z] INFO  17:29:54,688 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/7/R14-18106_kapa-NGv3-PE100-NGv3-sort-7_94750023_110303777-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/7/R14-18106_kapa-NGv3-PE100-NGv3-7_94750023_110303777-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/7/tx/tmpLAxgzr/R14-18106_kapa-NGv3-PE100-NGv3-7_94750023_110303777.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:29Z] INFO  17:29:54,708 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:29Z] INFO  17:29:54,709 HelpFormatter - Date/Time: 2016/04/14 17:29:54
[2016-04-15T00:29Z] INFO  17:29:54,710 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:29Z] INFO  17:29:54,710 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:29Z] INFO  17:29:54,795 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:29Z] INFO  17:29:54,840 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:29Z] INFO  17:29:54,863 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:29Z] INFO  17:29:54,865 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:29Z] INFO  17:29:54,865 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:29Z] INFO  17:29:54,866 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:29Z] INFO  17:29:54,880 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:29Z] INFO  17:29:54,904 IntervalUtils - Processing 74873 bp from intervals
[2016-04-15T00:29Z] WARN  17:29:54,908 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:29Z] INFO  17:29:54,910 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:29Z] INFO  17:29:54,919 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:29Z] INFO  17:29:54,933 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:29Z] INFO  17:29:54,934 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:29Z] INFO  17:29:55,006 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.09
[2016-04-15T00:29Z] INFO  17:29:55,044 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:29Z] INFO  17:29:55,092 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:29Z] INFO  17:29:55,093 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:29Z] INFO  17:29:55,094 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:29Z] INFO  17:29:55,095 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:29Z] INFO  17:29:55,106 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:29Z] INFO  17:29:55,127 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:29Z] INFO  17:29:55,127 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:29Z] INFO  17:29:55,139 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:29Z] INFO  17:29:55,143 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:29Z] INFO  17:29:55,144 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:29Z] INFO  17:29:55,207 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-15T00:29Z] INFO  17:29:55,239 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.11
[2016-04-15T00:29Z] INFO  17:29:55,267 ProgressMeter -     5:140558837    963223.0    30.0 s      31.0 s       69.3%    43.0 s      13.0 s
[2016-04-15T00:29Z] INFO  17:29:55,403 IntervalUtils - Processing 163786 bp from intervals
[2016-04-15T00:29Z] WARN  17:29:55,427 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:29Z] INFO  17:29:55,523 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:29Z] INFO  17:29:55,563 IntervalUtils - Processing 352548 bp from intervals
[2016-04-15T00:29Z] WARN  17:29:55,568 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:29Z] INFO  17:29:55,624 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:29Z] INFO  17:29:55,625 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:29Z] INFO  17:29:55,626 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:29Z] INFO  17:29:55,626 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:29Z] INFO  17:29:55,644 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:29Z] INFO  17:29:55,648 IntervalUtils - Processing 152751 bp from intervals
[2016-04-15T00:29Z] WARN  17:29:55,653 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:29Z] INFO  17:29:55,682 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:29Z] INFO  17:29:55,683 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:29Z] INFO  17:29:55,720 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:29Z] INFO  17:29:55,757 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:29Z] INFO  17:29:55,758 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:29Z] INFO  17:29:55,759 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:29Z] INFO  17:29:55,760 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:29Z] INFO  17:29:55,808 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:29Z] INFO  17:29:55,808 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:29Z] INFO  17:29:55,809 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:29Z] INFO  17:29:55,809 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:29Z] INFO  17:29:55,810 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:29Z] INFO  17:29:55,810 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:29Z] INFO  17:29:55,858 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:29Z] INFO  17:29:55,861 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:29Z] INFO  17:29:55,861 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:29Z] INFO  17:29:55,862 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:29Z] INFO  17:29:55,866 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/7/R14-18106_kapa-NGv3-PE100-NGv3-sort-7_110526648_126079222-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/7/R14-18106_kapa-NGv3-PE100-NGv3-7_110526648_126079222-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/7/tx/tmpKzXttq/R14-18106_kapa-NGv3-PE100-NGv3-7_110526648_126079222.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:29Z] INFO  17:29:55,876 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:29Z] INFO  17:29:55,877 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:29Z] INFO  17:29:55,877 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:29Z] INFO  17:29:55,888 HelpFormatter - Date/Time: 2016/04/14 17:29:55
[2016-04-15T00:29Z] INFO  17:29:55,889 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:29Z] INFO  17:29:55,890 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:29Z] INFO  17:29:55,983 ProgressMeter -            done    821918.0    27.0 s      33.0 s      100.0%    27.0 s       0.0 s
[2016-04-15T00:29Z] INFO  17:29:55,983 ProgressMeter - Total runtime 27.19 secs, 0.45 min, 0.01 hours
[2016-04-15T00:29Z] INFO  17:29:55,984 MicroScheduler - 24779 reads were filtered out during the traversal out of approximately 320254 total reads (7.74%)
[2016-04-15T00:29Z] INFO  17:29:55,984 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:29Z] INFO  17:29:55,984 MicroScheduler -   -> 489 reads (0.15% of total) failing BadMateFilter
[2016-04-15T00:29Z] INFO  17:29:55,984 MicroScheduler -   -> 24091 reads (7.52% of total) failing DuplicateReadFilter
[2016-04-15T00:29Z] INFO  17:29:55,985 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:29Z] INFO  17:29:55,985 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:29Z] INFO  17:29:55,985 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:29Z] INFO  17:29:55,985 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:29Z] INFO  17:29:55,986 MicroScheduler -   -> 199 reads (0.06% of total) failing UnmappedReadFilter
[2016-04-15T00:29Z] INFO  17:29:56,054 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:29Z] INFO  17:29:56,267 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:29Z] INFO  17:29:56,270 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:29Z] INFO  17:29:56,270 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:29Z] INFO  17:29:56,270 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:29Z] INFO  17:29:56,271 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:29Z] INFO  17:29:56,274 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/7/R14-18106_kapa-NGv3-PE100-NGv3-sort-7_126086124_141619620-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/7/R14-18106_kapa-NGv3-PE100-NGv3-7_126086124_141619620-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/7/tx/tmp8R5ARH/R14-18106_kapa-NGv3-PE100-NGv3-7_126086124_141619620.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:29Z] INFO  17:29:56,279 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:29Z] INFO  17:29:56,293 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:29Z] INFO  17:29:56,293 HelpFormatter - Date/Time: 2016/04/14 17:29:56
[2016-04-15T00:29Z] INFO  17:29:56,293 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:29Z] INFO  17:29:56,293 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:29Z] INFO  17:29:56,368 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.09
[2016-04-15T00:29Z] INFO  17:29:56,467 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:29Z] INFO  17:29:56,706 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:29Z] INFO  17:29:56,716 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:29Z] INFO  17:29:56,751 IntervalUtils - Processing 97998 bp from intervals
[2016-04-15T00:29Z] WARN  17:29:56,757 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:29Z] INFO  17:29:56,808 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.09
[2016-04-15T00:29Z] INFO  17:29:56,889 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:29Z] INFO  17:29:57,007 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:29Z] INFO  17:29:57,008 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:29Z] INFO  17:29:57,010 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:29Z] INFO  17:29:57,011 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:29Z] INFO  17:29:57,067 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:29Z] INFO  17:29:57,068 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:29Z] INFO  17:29:57,327 IntervalUtils - Processing 219678 bp from intervals
[2016-04-15T00:29Z] WARN  17:29:57,332 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:29Z] INFO  17:29:57,415 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:29Z] INFO  17:29:57,430 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:29Z] INFO  17:29:57,484 ProgressMeter -            done    414458.0    16.0 s      40.0 s      100.0%    16.0 s       0.0 s
[2016-04-15T00:29Z] INFO  17:29:57,485 ProgressMeter - Total runtime 16.84 secs, 0.28 min, 0.00 hours
[2016-04-15T00:29Z] INFO  17:29:57,485 MicroScheduler - 12165 reads were filtered out during the traversal out of approximately 156412 total reads (7.78%)
[2016-04-15T00:29Z] INFO  17:29:57,486 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:29Z] INFO  17:29:57,486 MicroScheduler -   -> 265 reads (0.17% of total) failing BadMateFilter
[2016-04-15T00:29Z] INFO  17:29:57,486 MicroScheduler -   -> 11802 reads (7.55% of total) failing DuplicateReadFilter
[2016-04-15T00:29Z] INFO  17:29:57,487 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:29Z] INFO  17:29:57,487 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:29Z] INFO  17:29:57,487 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:29Z] INFO  17:29:57,487 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:29Z] INFO  17:29:57,488 MicroScheduler -   -> 98 reads (0.06% of total) failing UnmappedReadFilter
[2016-04-15T00:29Z] INFO  17:29:57,526 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:29Z] INFO  17:29:57,528 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:29Z] INFO  17:29:57,528 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:29Z] INFO  17:29:57,529 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:29Z] INFO  17:29:57,584 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:29Z] INFO  17:29:57,590 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:29Z] GATK: UnifiedGenotyper
[2016-04-15T00:29Z] INFO  17:29:58,813 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:29Z] GATK: UnifiedGenotyper
[2016-04-15T00:30Z] INFO  17:30:00,253 ProgressMeter -            done    394136.0    19.0 s      49.0 s      100.0%    19.0 s       0.0 s
[2016-04-15T00:30Z] INFO  17:30:00,253 ProgressMeter - Total runtime 19.57 secs, 0.33 min, 0.01 hours
[2016-04-15T00:30Z] INFO  17:30:00,254 MicroScheduler - 14421 reads were filtered out during the traversal out of approximately 184082 total reads (7.83%)
[2016-04-15T00:30Z] INFO  17:30:00,254 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:30Z] INFO  17:30:00,254 MicroScheduler -   -> 338 reads (0.18% of total) failing BadMateFilter
[2016-04-15T00:30Z] INFO  17:30:00,254 MicroScheduler -   -> 13960 reads (7.58% of total) failing DuplicateReadFilter
[2016-04-15T00:30Z] INFO  17:30:00,255 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:30Z] INFO  17:30:00,255 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:30Z] INFO  17:30:00,255 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:30Z] INFO  17:30:00,255 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:30Z] INFO  17:30:00,256 MicroScheduler -   -> 123 reads (0.07% of total) failing UnmappedReadFilter
[2016-04-15T00:30Z] INFO  17:30:00,260 ProgressMeter -      6:35393145   1952966.0    30.0 s      15.0 s       47.8%    62.0 s      32.0 s
[2016-04-15T00:30Z] INFO  17:30:01,028 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:30Z] INFO  17:30:01,047 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:30Z] INFO  17:30:01,047 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:30Z] INFO  17:30:01,047 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:30Z] INFO  17:30:01,056 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/7/R14-18106_kapa-NGv3-PE100-NGv3-sort-7_141629903_157151331-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/7/R14-18106_kapa-NGv3-PE100-NGv3-7_141629903_157151331-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/7/tx/tmp7_BlSO/R14-18106_kapa-NGv3-PE100-NGv3-7_141629903_157151331.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:30Z] INFO  17:30:01,086 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:30Z] INFO  17:30:01,086 HelpFormatter - Date/Time: 2016/04/14 17:30:01
[2016-04-15T00:30Z] INFO  17:30:01,086 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:30Z] INFO  17:30:01,087 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:30Z] INFO  17:30:01,336 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:30Z] INFO  17:30:01,628 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:30Z] INFO  17:30:01,647 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:30Z] INFO  17:30:01,721 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-15T00:30Z] INFO  17:30:01,873 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:30Z] INFO  17:30:02,022 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:30Z] INFO  17:30:02,024 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:30Z] INFO  17:30:02,024 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:30Z] INFO  17:30:02,024 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:30Z] INFO  17:30:02,028 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/7/R14-18106_kapa-NGv3-PE100-NGv3-sort-7_157155854_159138663-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/7/R14-18106_kapa-NGv3-PE100-NGv3-7_157155854_159138663-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/7/tx/tmp8dMZJr/R14-18106_kapa-NGv3-PE100-NGv3-7_157155854_159138663.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:30Z] INFO  17:30:02,037 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:30Z] INFO  17:30:02,037 HelpFormatter - Date/Time: 2016/04/14 17:30:02
[2016-04-15T00:30Z] INFO  17:30:02,037 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:30Z] INFO  17:30:02,037 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:30Z] GATK: UnifiedGenotyper
[2016-04-15T00:30Z] INFO  17:30:02,235 IntervalUtils - Processing 248696 bp from intervals
[2016-04-15T00:30Z] WARN  17:30:02,241 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:30Z] INFO  17:30:02,280 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:30Z] INFO  17:30:02,338 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:30Z] INFO  17:30:02,455 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:30Z] INFO  17:30:02,464 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:30Z] INFO  17:30:02,534 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:30Z] INFO  17:30:02,536 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:30Z] INFO  17:30:02,532 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-15T00:30Z] INFO  17:30:02,537 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:30Z] INFO  17:30:02,537 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:30Z] INFO  17:30:02,624 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:30Z] INFO  17:30:02,625 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:30Z] INFO  17:30:03,069 IntervalUtils - Processing 17619 bp from intervals
[2016-04-15T00:30Z] WARN  17:30:03,075 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:30Z] INFO  17:30:03,192 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:30Z] INFO  17:30:03,246 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:30Z] INFO  17:30:03,248 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:30Z] INFO  17:30:03,249 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:30Z] INFO  17:30:03,250 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:30Z] INFO  17:30:03,299 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:30Z] INFO  17:30:03,300 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:30Z] INFO  17:30:03,463 ProgressMeter -            done    448393.0    21.0 s      46.0 s      100.0%    21.0 s       0.0 s
[2016-04-15T00:30Z] INFO  17:30:03,463 ProgressMeter - Total runtime 21.03 secs, 0.35 min, 0.01 hours
[2016-04-15T00:30Z] INFO  17:30:03,464 MicroScheduler - 17145 reads were filtered out during the traversal out of approximately 219662 total reads (7.81%)
[2016-04-15T00:30Z] INFO  17:30:03,464 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:30Z] INFO  17:30:03,464 MicroScheduler -   -> 366 reads (0.17% of total) failing BadMateFilter
[2016-04-15T00:30Z] INFO  17:30:03,465 MicroScheduler -   -> 16617 reads (7.56% of total) failing DuplicateReadFilter
[2016-04-15T00:30Z] INFO  17:30:03,465 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:30Z] INFO  17:30:03,465 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:30Z] INFO  17:30:03,466 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:30Z] INFO  17:30:03,466 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:30Z] INFO  17:30:03,466 MicroScheduler -   -> 162 reads (0.07% of total) failing UnmappedReadFilter
[2016-04-15T00:30Z] INFO  17:30:03,693 ProgressMeter -            done    442893.0    18.0 s      42.0 s       99.9%    18.0 s       0.0 s
[2016-04-15T00:30Z] INFO  17:30:03,693 ProgressMeter - Total runtime 18.87 secs, 0.31 min, 0.01 hours
[2016-04-15T00:30Z] INFO  17:30:03,694 MicroScheduler - 15328 reads were filtered out during the traversal out of approximately 192068 total reads (7.98%)
[2016-04-15T00:30Z] INFO  17:30:03,694 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:30Z] INFO  17:30:03,694 MicroScheduler -   -> 342 reads (0.18% of total) failing BadMateFilter
[2016-04-15T00:30Z] INFO  17:30:03,694 MicroScheduler -   -> 14878 reads (7.75% of total) failing DuplicateReadFilter
[2016-04-15T00:30Z] INFO  17:30:03,695 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:30Z] INFO  17:30:03,695 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:30Z] INFO  17:30:03,695 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:30Z] INFO  17:30:03,695 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:30Z] INFO  17:30:03,696 MicroScheduler -   -> 108 reads (0.06% of total) failing UnmappedReadFilter
[2016-04-15T00:30Z] INFO  17:30:04,792 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:30Z] INFO  17:30:04,984 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:30Z] INFO  17:30:04,988 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:30Z] INFO  17:30:04,988 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:30Z] INFO  17:30:04,989 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:30Z] INFO  17:30:04,994 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/8/R14-18106_kapa-NGv3-PE100-NGv3-sort-8_0_15517156-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/8/R14-18106_kapa-NGv3-PE100-NGv3-8_0_15517156-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/8/tx/tmp6qD8Mj/R14-18106_kapa-NGv3-PE100-NGv3-8_0_15517156.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:30Z] INFO  17:30:05,012 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:30Z] INFO  17:30:05,013 HelpFormatter - Date/Time: 2016/04/14 17:30:04
[2016-04-15T00:30Z] INFO  17:30:05,014 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:30Z] INFO  17:30:05,015 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:30Z] GATK: UnifiedGenotyper
[2016-04-15T00:30Z] INFO  17:30:05,174 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:30Z] INFO  17:30:05,219 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:30Z] INFO  17:30:05,425 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:30Z] INFO  17:30:05,436 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:30Z] GATK: UnifiedGenotyper
[2016-04-15T00:30Z] INFO  17:30:05,506 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-15T00:30Z] INFO  17:30:05,901 IntervalUtils - Processing 115548 bp from intervals
[2016-04-15T00:30Z] WARN  17:30:05,922 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:30Z] INFO  17:30:06,014 ProgressMeter -            done   1341967.0    40.0 s      30.0 s      100.0%    40.0 s       0.0 s
[2016-04-15T00:30Z] INFO  17:30:06,014 ProgressMeter - Total runtime 40.77 secs, 0.68 min, 0.01 hours
[2016-04-15T00:30Z] INFO  17:30:06,014 MicroScheduler - 51780 reads were filtered out during the traversal out of approximately 606819 total reads (8.53%)
[2016-04-15T00:30Z] INFO  17:30:06,015 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:30Z] INFO  17:30:06,015 MicroScheduler -   -> 983 reads (0.16% of total) failing BadMateFilter
[2016-04-15T00:30Z] INFO  17:30:06,016 MicroScheduler -   -> 50388 reads (8.30% of total) failing DuplicateReadFilter
[2016-04-15T00:30Z] INFO  17:30:06,016 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:30Z] INFO  17:30:06,016 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:30Z] INFO  17:30:06,016 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:30Z] INFO  17:30:06,017 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:30Z] INFO  17:30:06,020 MicroScheduler -   -> 409 reads (0.07% of total) failing UnmappedReadFilter
[2016-04-15T00:30Z] INFO  17:30:06,055 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:30Z] INFO  17:30:06,204 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:30Z] INFO  17:30:06,216 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:30Z] INFO  17:30:06,217 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:30Z] INFO  17:30:06,218 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:30Z] INFO  17:30:06,281 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:30Z] INFO  17:30:06,282 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:30Z] INFO  17:30:06,885 ProgressMeter -            done    637397.0    22.0 s      34.0 s      100.0%    22.0 s       0.0 s
[2016-04-15T00:30Z] INFO  17:30:06,885 ProgressMeter - Total runtime 22.01 secs, 0.37 min, 0.01 hours
[2016-04-15T00:30Z] INFO  17:30:06,886 MicroScheduler - 20056 reads were filtered out during the traversal out of approximately 255735 total reads (7.84%)
[2016-04-15T00:30Z] INFO  17:30:06,886 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:30Z] INFO  17:30:06,886 MicroScheduler -   -> 513 reads (0.20% of total) failing BadMateFilter
[2016-04-15T00:30Z] INFO  17:30:06,886 MicroScheduler -   -> 19357 reads (7.57% of total) failing DuplicateReadFilter
[2016-04-15T00:30Z] INFO  17:30:06,887 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:30Z] INFO  17:30:06,887 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:30Z] INFO  17:30:06,887 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:30Z] INFO  17:30:06,887 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:30Z] INFO  17:30:06,888 MicroScheduler -   -> 186 reads (0.07% of total) failing UnmappedReadFilter
[2016-04-15T00:30Z] INFO  17:30:07,431 ProgressMeter -            done    357849.0    18.0 s      50.0 s      100.0%    18.0 s       0.0 s
[2016-04-15T00:30Z] INFO  17:30:07,431 ProgressMeter - Total runtime 18.18 secs, 0.30 min, 0.01 hours
[2016-04-15T00:30Z] INFO  17:30:07,432 MicroScheduler - 12854 reads were filtered out during the traversal out of approximately 166305 total reads (7.73%)
[2016-04-15T00:30Z] INFO  17:30:07,432 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:30Z] INFO  17:30:07,432 MicroScheduler -   -> 321 reads (0.19% of total) failing BadMateFilter
[2016-04-15T00:30Z] INFO  17:30:07,433 MicroScheduler -   -> 12428 reads (7.47% of total) failing DuplicateReadFilter
[2016-04-15T00:30Z] INFO  17:30:07,433 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:30Z] INFO  17:30:07,433 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:30Z] INFO  17:30:07,433 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:30Z] INFO  17:30:07,434 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:30Z] INFO  17:30:07,434 MicroScheduler -   -> 105 reads (0.06% of total) failing UnmappedReadFilter
[2016-04-15T00:30Z] INFO  17:30:07,587 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:30Z] GATK: UnifiedGenotyper
[2016-04-15T00:30Z] INFO  17:30:08,160 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:30Z] INFO  17:30:08,163 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:30Z] INFO  17:30:08,164 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:30Z] INFO  17:30:08,165 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:30Z] INFO  17:30:08,169 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/8/R14-18106_kapa-NGv3-PE100-NGv3-sort-8_15519664_31030618-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/8/R14-18106_kapa-NGv3-PE100-NGv3-8_15519664_31030618-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/8/tx/tmp8LBIq2/R14-18106_kapa-NGv3-PE100-NGv3-8_15519664_31030618.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:30Z] INFO  17:30:08,178 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:30Z] INFO  17:30:08,179 HelpFormatter - Date/Time: 2016/04/14 17:30:08
[2016-04-15T00:30Z] INFO  17:30:08,179 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:30Z] INFO  17:30:08,180 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:30Z] INFO  17:30:08,364 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:30Z] INFO  17:30:08,441 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:30Z] INFO  17:30:08,475 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:30Z] INFO  17:30:08,478 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:30Z] INFO  17:30:08,479 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:30Z] INFO  17:30:08,479 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:30Z] INFO  17:30:08,484 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/8/R14-18106_kapa-NGv3-PE100-NGv3-sort-8_31496910_48001429-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/8/R14-18106_kapa-NGv3-PE100-NGv3-8_31496910_48001429-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/8/tx/tmpAIUykH/R14-18106_kapa-NGv3-PE100-NGv3-8_31496910_48001429.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:30Z] INFO  17:30:08,512 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:30Z] INFO  17:30:08,513 HelpFormatter - Date/Time: 2016/04/14 17:30:08
[2016-04-15T00:30Z] INFO  17:30:08,514 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:30Z] INFO  17:30:08,514 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:30Z] INFO  17:30:08,562 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:30Z] INFO  17:30:08,571 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:30Z] INFO  17:30:08,623 ProgressMeter -            done     46373.0     5.0 s     115.0 s       99.7%     5.0 s       0.0 s
[2016-04-15T00:30Z] INFO  17:30:08,625 ProgressMeter - Total runtime 5.38 secs, 0.09 min, 0.00 hours
[2016-04-15T00:30Z] INFO  17:30:08,625 MicroScheduler - 1902 reads were filtered out during the traversal out of approximately 22806 total reads (8.34%)
[2016-04-15T00:30Z] INFO  17:30:08,626 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:30Z] INFO  17:30:08,627 MicroScheduler -   -> 51 reads (0.22% of total) failing BadMateFilter
[2016-04-15T00:30Z] INFO  17:30:08,627 MicroScheduler -   -> 1841 reads (8.07% of total) failing DuplicateReadFilter
[2016-04-15T00:30Z] INFO  17:30:08,627 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:30Z] INFO  17:30:08,627 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:30Z] INFO  17:30:08,628 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:30Z] INFO  17:30:08,628 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:30Z] INFO  17:30:08,628 MicroScheduler -   -> 10 reads (0.04% of total) failing UnmappedReadFilter
[2016-04-15T00:30Z] INFO  17:30:08,660 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.09
[2016-04-15T00:30Z] INFO  17:30:08,667 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:30Z] GATK: UnifiedGenotyper
[2016-04-15T00:30Z] INFO  17:30:08,868 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:30Z] INFO  17:30:08,877 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:30Z] INFO  17:30:08,936 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:30Z] INFO  17:30:08,957 ProgressMeter -            done    186536.0    13.0 s      74.0 s       99.9%    13.0 s       0.0 s
[2016-04-15T00:30Z] INFO  17:30:08,959 ProgressMeter - Total runtime 13.87 secs, 0.23 min, 0.00 hours
[2016-04-15T00:30Z] INFO  17:30:08,959 MicroScheduler - 7635 reads were filtered out during the traversal out of approximately 97718 total reads (7.81%)
[2016-04-15T00:30Z] INFO  17:30:08,960 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:30Z] INFO  17:30:08,960 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-15T00:30Z] INFO  17:30:08,961 MicroScheduler -   -> 167 reads (0.17% of total) failing BadMateFilter
[2016-04-15T00:30Z] INFO  17:30:08,961 MicroScheduler -   -> 7408 reads (7.58% of total) failing DuplicateReadFilter
[2016-04-15T00:30Z] INFO  17:30:08,961 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:30Z] INFO  17:30:08,961 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:30Z] INFO  17:30:08,962 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:30Z] INFO  17:30:08,963 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:30Z] INFO  17:30:08,963 MicroScheduler -   -> 60 reads (0.06% of total) failing UnmappedReadFilter
[2016-04-15T00:30Z] INFO  17:30:09,036 IntervalUtils - Processing 233081 bp from intervals
[2016-04-15T00:30Z] WARN  17:30:09,042 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:30Z] INFO  17:30:09,110 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:30Z] INFO  17:30:09,218 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:30Z] INFO  17:30:09,218 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:30Z] INFO  17:30:09,219 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:30Z] INFO  17:30:09,219 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:30Z] GATK: UnifiedGenotyper
[2016-04-15T00:30Z] INFO  17:30:09,293 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:30Z] INFO  17:30:09,293 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:30Z] INFO  17:30:09,321 IntervalUtils - Processing 125262 bp from intervals
[2016-04-15T00:30Z] WARN  17:30:09,326 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:30Z] INFO  17:30:09,408 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:30Z] INFO  17:30:09,484 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:30Z] INFO  17:30:09,485 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:30Z] INFO  17:30:09,486 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:30Z] INFO  17:30:09,489 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:30Z] INFO  17:30:09,560 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:30Z] INFO  17:30:09,560 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:30Z] INFO  17:30:10,043 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:30Z] INFO  17:30:10,195 ProgressMeter -            done    214671.0    13.0 s      61.0 s       99.9%    13.0 s       0.0 s
[2016-04-15T00:30Z] INFO  17:30:10,196 ProgressMeter - Total runtime 13.19 secs, 0.22 min, 0.00 hours
[2016-04-15T00:30Z] INFO  17:30:10,196 MicroScheduler - 7946 reads were filtered out during the traversal out of approximately 102967 total reads (7.72%)
[2016-04-15T00:30Z] INFO  17:30:10,197 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:30Z] INFO  17:30:10,197 MicroScheduler -   -> 174 reads (0.17% of total) failing BadMateFilter
[2016-04-15T00:30Z] INFO  17:30:10,197 MicroScheduler -   -> 7709 reads (7.49% of total) failing DuplicateReadFilter
[2016-04-15T00:30Z] INFO  17:30:10,197 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:30Z] INFO  17:30:10,198 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:30Z] INFO  17:30:10,198 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:30Z] INFO  17:30:10,198 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:30Z] INFO  17:30:10,198 MicroScheduler -   -> 63 reads (0.06% of total) failing UnmappedReadFilter
[2016-04-15T00:30Z] GATK: UnifiedGenotyper
[2016-04-15T00:30Z] INFO  17:30:10,486 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:30Z] INFO  17:30:10,670 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:30Z] INFO  17:30:10,674 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:30Z] INFO  17:30:10,674 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:30Z] INFO  17:30:10,675 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:30Z] INFO  17:30:10,682 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/8/R14-18106_kapa-NGv3-PE100-NGv3-sort-8_48003022_63659688-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/8/R14-18106_kapa-NGv3-PE100-NGv3-8_48003022_63659688-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/8/tx/tmp2CdOF3/R14-18106_kapa-NGv3-PE100-NGv3-8_48003022_63659688.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:30Z] INFO  17:30:10,715 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:30Z] INFO  17:30:10,716 HelpFormatter - Date/Time: 2016/04/14 17:30:10
[2016-04-15T00:30Z] INFO  17:30:10,716 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:30Z] INFO  17:30:10,717 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:30Z] GATK: UnifiedGenotyper
[2016-04-15T00:30Z] INFO  17:30:10,914 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:30Z] INFO  17:30:11,227 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:30Z] INFO  17:30:11,238 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:30Z] INFO  17:30:11,322 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-15T00:30Z] INFO  17:30:11,480 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:30Z] INFO  17:30:11,781 IntervalUtils - Processing 104159 bp from intervals
[2016-04-15T00:30Z] WARN  17:30:11,786 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:30Z] GATK: UnifiedGenotyper
[2016-04-15T00:30Z] INFO  17:30:11,882 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:30Z] INFO  17:30:11,965 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:30Z] INFO  17:30:11,966 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:30Z] INFO  17:30:11,967 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:30Z] INFO  17:30:11,967 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:30Z] INFO  17:30:11,972 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:30Z] INFO  17:30:11,974 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:30Z] INFO  17:30:11,974 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:30Z] INFO  17:30:11,975 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:30Z] INFO  17:30:11,980 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/8/R14-18106_kapa-NGv3-PE100-NGv3-sort-8_63775819_79510770-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/8/R14-18106_kapa-NGv3-PE100-NGv3-8_63775819_79510770-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/8/tx/tmpDE7yRs/R14-18106_kapa-NGv3-PE100-NGv3-8_63775819_79510770.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:30Z] INFO  17:30:11,990 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:30Z] INFO  17:30:11,991 HelpFormatter - Date/Time: 2016/04/14 17:30:11
[2016-04-15T00:30Z] INFO  17:30:11,991 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:30Z] INFO  17:30:11,991 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:30Z] INFO  17:30:12,014 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:30Z] INFO  17:30:12,015 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:30Z] INFO  17:30:12,104 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:30Z] INFO  17:30:12,107 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:30Z] INFO  17:30:12,107 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:30Z] INFO  17:30:12,108 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:30Z] INFO  17:30:12,113 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/8/R14-18106_kapa-NGv3-PE100-NGv3-sort-8_79513976_95140568-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/8/R14-18106_kapa-NGv3-PE100-NGv3-8_79513976_95140568-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/8/tx/tmpEhiD0H/R14-18106_kapa-NGv3-PE100-NGv3-8_79513976_95140568.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:30Z] INFO  17:30:12,126 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:30Z] INFO  17:30:12,127 HelpFormatter - Date/Time: 2016/04/14 17:30:12
[2016-04-15T00:30Z] INFO  17:30:12,131 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:30Z] INFO  17:30:12,132 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:30Z] INFO  17:30:12,133 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:30Z] INFO  17:30:12,409 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:30Z] INFO  17:30:12,413 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:30Z] INFO  17:30:12,431 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:30Z] INFO  17:30:12,535 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.10
[2016-04-15T00:30Z] INFO  17:30:12,686 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:30Z] INFO  17:30:12,695 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:30Z] INFO  17:30:12,786 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.09
[2016-04-15T00:30Z] INFO  17:30:13,025 ProgressMeter -            done    434204.0    17.0 s      40.0 s      100.0%    17.0 s       0.0 s
[2016-04-15T00:30Z] INFO  17:30:13,025 ProgressMeter - Total runtime 17.40 secs, 0.29 min, 0.00 hours
[2016-04-15T00:30Z] INFO  17:30:13,025 MicroScheduler - 11439 reads were filtered out during the traversal out of approximately 152301 total reads (7.51%)
[2016-04-15T00:30Z] INFO  17:30:13,026 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:30Z] INFO  17:30:13,026 MicroScheduler -   -> 243 reads (0.16% of total) failing BadMateFilter
[2016-04-15T00:30Z] INFO  17:30:13,026 MicroScheduler -   -> 11117 reads (7.30% of total) failing DuplicateReadFilter
[2016-04-15T00:30Z] INFO  17:30:13,026 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:30Z] INFO  17:30:13,027 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:30Z] INFO  17:30:13,027 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:30Z] INFO  17:30:13,027 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:30Z] INFO  17:30:13,027 MicroScheduler -   -> 79 reads (0.05% of total) failing UnmappedReadFilter
[2016-04-15T00:30Z] INFO  17:30:13,123 IntervalUtils - Processing 117209 bp from intervals
[2016-04-15T00:30Z] WARN  17:30:13,128 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:30Z] INFO  17:30:13,149 IntervalUtils - Processing 78340 bp from intervals
[2016-04-15T00:30Z] WARN  17:30:13,154 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:30Z] INFO  17:30:13,293 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:30Z] INFO  17:30:13,292 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:30Z] INFO  17:30:13,404 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:30Z] INFO  17:30:13,405 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:30Z] INFO  17:30:13,406 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:30Z] INFO  17:30:13,407 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:30Z] INFO  17:30:13,409 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:30Z] INFO  17:30:13,410 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:30Z] INFO  17:30:13,411 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:30Z] INFO  17:30:13,411 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:30Z] INFO  17:30:13,439 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:30Z] INFO  17:30:13,442 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:30Z] INFO  17:30:13,443 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:30Z] INFO  17:30:13,443 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:30Z] INFO  17:30:13,448 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/8/R14-18106_kapa-NGv3-PE100-NGv3-sort-8_95142853_110655419-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/8/R14-18106_kapa-NGv3-PE100-NGv3-8_95142853_110655419-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/8/tx/tmp6QMcwS/R14-18106_kapa-NGv3-PE100-NGv3-8_95142853_110655419.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:30Z] INFO  17:30:13,451 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:30Z] INFO  17:30:13,452 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:30Z] INFO  17:30:13,453 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:30Z] INFO  17:30:13,454 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:30Z] INFO  17:30:13,456 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:30Z] INFO  17:30:13,457 HelpFormatter - Date/Time: 2016/04/14 17:30:13
[2016-04-15T00:30Z] INFO  17:30:13,457 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:30Z] INFO  17:30:13,457 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:30Z] INFO  17:30:13,606 ProgressMeter -            done    438420.0    18.0 s      42.0 s      100.0%    18.0 s       0.0 s
[2016-04-15T00:30Z] INFO  17:30:13,606 ProgressMeter - Total runtime 18.74 secs, 0.31 min, 0.01 hours
[2016-04-15T00:30Z] INFO  17:30:13,607 MicroScheduler - 15423 reads were filtered out during the traversal out of approximately 193930 total reads (7.95%)
[2016-04-15T00:30Z] INFO  17:30:13,607 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:30Z] INFO  17:30:13,607 MicroScheduler -   -> 349 reads (0.18% of total) failing BadMateFilter
[2016-04-15T00:30Z] INFO  17:30:13,608 MicroScheduler -   -> 14973 reads (7.72% of total) failing DuplicateReadFilter
[2016-04-15T00:30Z] INFO  17:30:13,608 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:30Z] INFO  17:30:13,608 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:30Z] INFO  17:30:13,608 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:30Z] INFO  17:30:13,609 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:30Z] INFO  17:30:13,609 MicroScheduler -   -> 101 reads (0.05% of total) failing UnmappedReadFilter
[2016-04-15T00:30Z] INFO  17:30:13,619 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:30Z] INFO  17:30:13,820 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:30Z] INFO  17:30:13,829 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:30Z] INFO  17:30:13,833 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:30Z] INFO  17:30:13,836 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:30Z] INFO  17:30:13,837 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:30Z] INFO  17:30:13,837 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:30Z] INFO  17:30:13,841 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/8/R14-18106_kapa-NGv3-PE100-NGv3-sort-8_110656864_126194498-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/8/R14-18106_kapa-NGv3-PE100-NGv3-8_110656864_126194498-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/8/tx/tmpCRPvm7/R14-18106_kapa-NGv3-PE100-NGv3-8_110656864_126194498.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:30Z] INFO  17:30:13,850 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:30Z] INFO  17:30:13,851 HelpFormatter - Date/Time: 2016/04/14 17:30:13
[2016-04-15T00:30Z] INFO  17:30:13,852 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:30Z] INFO  17:30:13,852 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:30Z] INFO  17:30:13,913 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-15T00:30Z] INFO  17:30:14,018 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:30Z] INFO  17:30:14,287 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:30Z] INFO  17:30:14,307 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:30Z] INFO  17:30:14,319 IntervalUtils - Processing 161638 bp from intervals
[2016-04-15T00:30Z] WARN  17:30:14,324 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:30Z] INFO  17:30:14,388 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-15T00:30Z] INFO  17:30:14,407 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:30Z] INFO  17:30:14,472 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:30Z] INFO  17:30:14,473 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:30Z] INFO  17:30:14,474 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:30Z] INFO  17:30:14,474 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:30Z] INFO  17:30:14,520 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:30Z] INFO  17:30:14,521 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:30Z] INFO  17:30:14,588 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:30Z] INFO  17:30:14,792 IntervalUtils - Processing 102393 bp from intervals
[2016-04-15T00:30Z] WARN  17:30:14,797 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:30Z] INFO  17:30:14,811 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:30Z] INFO  17:30:14,825 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:30Z] INFO  17:30:14,826 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:30Z] INFO  17:30:14,826 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:30Z] INFO  17:30:14,831 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/8/R14-18106_kapa-NGv3-PE100-NGv3-sort-8_126369460_141889736-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/8/R14-18106_kapa-NGv3-PE100-NGv3-8_126369460_141889736-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/8/tx/tmpAsNyNT/R14-18106_kapa-NGv3-PE100-NGv3-8_126369460_141889736.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:30Z] INFO  17:30:14,859 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:30Z] INFO  17:30:14,861 HelpFormatter - Date/Time: 2016/04/14 17:30:14
[2016-04-15T00:30Z] INFO  17:30:14,861 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:30Z] INFO  17:30:14,861 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:30Z] INFO  17:30:14,880 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:30Z] GATK: UnifiedGenotyper
[2016-04-15T00:30Z] INFO  17:30:15,006 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:30Z] INFO  17:30:15,007 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:30Z] INFO  17:30:15,023 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:30Z] INFO  17:30:15,024 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:30Z] INFO  17:30:15,069 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:30Z] INFO  17:30:15,110 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:30Z] INFO  17:30:15,114 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:30Z] INFO  17:30:15,118 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:30Z] INFO  17:30:15,301 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:30Z] INFO  17:30:15,315 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:30Z] GATK: UnifiedGenotyper
[2016-04-15T00:30Z] INFO  17:30:15,631 ProgressMeter -            done    457571.0    19.0 s      43.0 s      100.0%    19.0 s       0.0 s
[2016-04-15T00:30Z] INFO  17:30:15,631 ProgressMeter - Total runtime 19.82 secs, 0.33 min, 0.01 hours
[2016-04-15T00:30Z] INFO  17:30:15,631 MicroScheduler - 17025 reads were filtered out during the traversal out of approximately 226461 total reads (7.52%)
[2016-04-15T00:30Z] INFO  17:30:15,632 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:30Z] INFO  17:30:15,632 MicroScheduler -   -> 432 reads (0.19% of total) failing BadMateFilter
[2016-04-15T00:30Z] INFO  17:30:15,632 MicroScheduler -   -> 16458 reads (7.27% of total) failing DuplicateReadFilter
[2016-04-15T00:30Z] INFO  17:30:15,632 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:30Z] INFO  17:30:15,633 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:30Z] INFO  17:30:15,633 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:30Z] INFO  17:30:15,633 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:30Z] INFO  17:30:15,633 MicroScheduler -   -> 135 reads (0.06% of total) failing UnmappedReadFilter
[2016-04-15T00:30Z] INFO  17:30:15,681 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.36
[2016-04-15T00:30Z] INFO  17:30:16,111 IntervalUtils - Processing 72911 bp from intervals
[2016-04-15T00:30Z] WARN  17:30:16,115 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:30Z] INFO  17:30:16,234 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:30Z] INFO  17:30:16,318 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:30Z] INFO  17:30:16,319 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:30Z] INFO  17:30:16,320 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:30Z] INFO  17:30:16,321 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:30Z] INFO  17:30:16,372 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:30Z] INFO  17:30:16,372 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:30Z] INFO  17:30:17,048 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:30Z] GATK: UnifiedGenotyper
[2016-04-15T00:30Z] INFO  17:30:17,599 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:30Z] INFO  17:30:17,602 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:30Z] INFO  17:30:17,603 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:30Z] INFO  17:30:17,603 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:30Z] INFO  17:30:17,608 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/8/R14-18106_kapa-NGv3-PE100-NGv3-sort-8_141900641_146364022-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/8/R14-18106_kapa-NGv3-PE100-NGv3-8_141900641_146364022-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/8/tx/tmpfpZrOk/R14-18106_kapa-NGv3-PE100-NGv3-8_141900641_146364022.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:30Z] INFO  17:30:17,624 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:30Z] INFO  17:30:17,625 HelpFormatter - Date/Time: 2016/04/14 17:30:17
[2016-04-15T00:30Z] INFO  17:30:17,625 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:30Z] INFO  17:30:17,626 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:30Z] INFO  17:30:17,805 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:30Z] INFO  17:30:18,029 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:30Z] INFO  17:30:18,049 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:30Z] INFO  17:30:18,145 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-15T00:30Z] INFO  17:30:18,646 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:30Z] INFO  17:30:18,648 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:30Z] INFO  17:30:18,648 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:30Z] INFO  17:30:18,649 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:30Z] INFO  17:30:18,653 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/9/R14-18106_kapa-NGv3-PE100-NGv3-sort-9_0_15510186-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/9/R14-18106_kapa-NGv3-PE100-NGv3-9_0_15510186-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/9/tx/tmp3CcPgL/R14-18106_kapa-NGv3-PE100-NGv3-9_0_15510186.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:30Z] INFO  17:30:18,668 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:30Z] INFO  17:30:18,669 HelpFormatter - Date/Time: 2016/04/14 17:30:18
[2016-04-15T00:30Z] INFO  17:30:18,669 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:30Z] INFO  17:30:18,669 IntervalUtils - Processing 204618 bp from intervals
[2016-04-15T00:30Z] INFO  17:30:18,670 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:30Z] WARN  17:30:18,675 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:30Z] INFO  17:30:18,773 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:30Z] INFO  17:30:18,878 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:30Z] INFO  17:30:18,879 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:30Z] INFO  17:30:18,880 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:30Z] INFO  17:30:18,881 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:30Z] INFO  17:30:18,893 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:30Z] INFO  17:30:18,927 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:30Z] INFO  17:30:18,928 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:30Z] INFO  17:30:19,195 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:30Z] INFO  17:30:19,204 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:30Z] INFO  17:30:19,297 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.09
[2016-04-15T00:30Z] INFO  17:30:19,858 IntervalUtils - Processing 123193 bp from intervals
[2016-04-15T00:30Z] WARN  17:30:19,863 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:30Z] INFO  17:30:19,963 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:30Z] INFO  17:30:20,061 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:30Z] INFO  17:30:20,062 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:30Z] INFO  17:30:20,063 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:30Z] INFO  17:30:20,063 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:30Z] INFO  17:30:20,115 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:30Z] INFO  17:30:20,116 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:30Z] INFO  17:30:20,904 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:30Z] INFO  17:30:20,908 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:30Z] INFO  17:30:20,908 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:30Z] INFO  17:30:20,909 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:30Z] INFO  17:30:20,915 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/9/R14-18106_kapa-NGv3-PE100-NGv3-sort-9_15564086_32405601-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/9/R14-18106_kapa-NGv3-PE100-NGv3-9_15564086_32405601-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/9/tx/tmpvFaJVA/R14-18106_kapa-NGv3-PE100-NGv3-9_15564086_32405601.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:30Z] INFO  17:30:20,955 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:30Z] INFO  17:30:20,956 HelpFormatter - Date/Time: 2016/04/14 17:30:20
[2016-04-15T00:30Z] INFO  17:30:20,956 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:30Z] INFO  17:30:20,957 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:30Z] INFO  17:30:21,161 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:30Z] INFO  17:30:21,436 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:30Z] INFO  17:30:21,447 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:30Z] INFO  17:30:21,528 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-15T00:30Z] INFO  17:30:21,873 IntervalUtils - Processing 89361 bp from intervals
[2016-04-15T00:30Z] WARN  17:30:21,878 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:30Z] INFO  17:30:21,985 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:30Z] INFO  17:30:22,070 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:30Z] INFO  17:30:22,071 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:30Z] INFO  17:30:22,072 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:30Z] INFO  17:30:22,073 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:30Z] INFO  17:30:22,117 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:30Z] INFO  17:30:22,118 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:30Z] INFO  17:30:22,330 ProgressMeter -            done    735970.0    24.0 s      33.0 s      100.0%    24.0 s       0.0 s
[2016-04-15T00:30Z] INFO  17:30:22,331 ProgressMeter - Total runtime 24.80 secs, 0.41 min, 0.01 hours
[2016-04-15T00:30Z] INFO  17:30:22,331 MicroScheduler - 22201 reads were filtered out during the traversal out of approximately 276937 total reads (8.02%)
[2016-04-15T00:30Z] INFO  17:30:22,331 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:30Z] INFO  17:30:22,332 MicroScheduler -   -> 481 reads (0.17% of total) failing BadMateFilter
[2016-04-15T00:30Z] INFO  17:30:22,332 MicroScheduler -   -> 21585 reads (7.79% of total) failing DuplicateReadFilter
[2016-04-15T00:30Z] INFO  17:30:22,332 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:30Z] INFO  17:30:22,332 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:30Z] INFO  17:30:22,333 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:30Z] INFO  17:30:22,333 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:30Z] INFO  17:30:22,333 MicroScheduler -   -> 135 reads (0.05% of total) failing UnmappedReadFilter
[2016-04-15T00:30Z] INFO  17:30:22,476 ProgressMeter -            done   3191514.0    52.0 s      16.0 s      100.0%    52.0 s       0.0 s
[2016-04-15T00:30Z] INFO  17:30:22,477 ProgressMeter - Total runtime 52.24 secs, 0.87 min, 0.01 hours
[2016-04-15T00:30Z] INFO  17:30:22,477 MicroScheduler - 57281 reads were filtered out during the traversal out of approximately 734341 total reads (7.80%)
[2016-04-15T00:30Z] INFO  17:30:22,477 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:30Z] INFO  17:30:22,478 MicroScheduler -   -> 1200 reads (0.16% of total) failing BadMateFilter
[2016-04-15T00:30Z] INFO  17:30:22,478 MicroScheduler -   -> 55611 reads (7.57% of total) failing DuplicateReadFilter
[2016-04-15T00:30Z] INFO  17:30:22,478 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:30Z] INFO  17:30:22,478 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:30Z] INFO  17:30:22,479 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:30Z] INFO  17:30:22,479 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:30Z] INFO  17:30:22,479 MicroScheduler -   -> 470 reads (0.06% of total) failing UnmappedReadFilter
[2016-04-15T00:30Z] INFO  17:30:23,981 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:30Z] INFO  17:30:24,093 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:30Z] GATK: UnifiedGenotyper
[2016-04-15T00:30Z] GATK: UnifiedGenotyper
[2016-04-15T00:30Z] INFO  17:30:25,140 ProgressMeter -            done    239009.0    18.0 s      79.0 s      100.0%    18.0 s       0.0 s
[2016-04-15T00:30Z] INFO  17:30:25,140 ProgressMeter - Total runtime 18.92 secs, 0.32 min, 0.01 hours
[2016-04-15T00:30Z] INFO  17:30:25,141 MicroScheduler - 13772 reads were filtered out during the traversal out of approximately 182672 total reads (7.54%)
[2016-04-15T00:30Z] INFO  17:30:25,141 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:30Z] INFO  17:30:25,141 MicroScheduler -   -> 287 reads (0.16% of total) failing BadMateFilter
[2016-04-15T00:30Z] INFO  17:30:25,142 MicroScheduler -   -> 13364 reads (7.32% of total) failing DuplicateReadFilter
[2016-04-15T00:30Z] INFO  17:30:25,142 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:30Z] INFO  17:30:25,142 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:30Z] INFO  17:30:25,143 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:30Z] INFO  17:30:25,143 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:30Z] INFO  17:30:25,143 MicroScheduler -   -> 121 reads (0.07% of total) failing UnmappedReadFilter
[2016-04-15T00:30Z] INFO  17:30:25,750 ProgressMeter -            done    184917.0    12.0 s      66.0 s      100.0%    12.0 s       0.0 s
[2016-04-15T00:30Z] INFO  17:30:25,751 ProgressMeter - Total runtime 12.35 secs, 0.21 min, 0.00 hours
[2016-04-15T00:30Z] INFO  17:30:25,751 MicroScheduler - 6167 reads were filtered out during the traversal out of approximately 81342 total reads (7.58%)
[2016-04-15T00:30Z] INFO  17:30:25,751 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:30Z] INFO  17:30:25,752 MicroScheduler -   -> 130 reads (0.16% of total) failing BadMateFilter
[2016-04-15T00:30Z] INFO  17:30:25,752 MicroScheduler -   -> 5995 reads (7.37% of total) failing DuplicateReadFilter
[2016-04-15T00:30Z] INFO  17:30:25,752 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:30Z] INFO  17:30:25,752 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:30Z] INFO  17:30:25,753 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:30Z] INFO  17:30:25,753 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:30Z] INFO  17:30:25,753 MicroScheduler -   -> 42 reads (0.05% of total) failing UnmappedReadFilter
[2016-04-15T00:30Z] INFO  17:30:25,794 ProgressMeter -            done    284373.0    13.0 s      48.0 s       99.9%    13.0 s       0.0 s
[2016-04-15T00:30Z] INFO  17:30:25,795 ProgressMeter - Total runtime 13.83 secs, 0.23 min, 0.00 hours
[2016-04-15T00:30Z] INFO  17:30:25,795 MicroScheduler - 8945 reads were filtered out during the traversal out of approximately 114004 total reads (7.85%)
[2016-04-15T00:30Z] INFO  17:30:25,795 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:30Z] INFO  17:30:25,796 MicroScheduler -   -> 214 reads (0.19% of total) failing BadMateFilter
[2016-04-15T00:30Z] INFO  17:30:25,796 MicroScheduler -   -> 8671 reads (7.61% of total) failing DuplicateReadFilter
[2016-04-15T00:30Z] INFO  17:30:25,796 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:30Z] INFO  17:30:25,796 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:30Z] INFO  17:30:25,797 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:30Z] INFO  17:30:25,797 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:30Z] INFO  17:30:25,797 MicroScheduler -   -> 60 reads (0.05% of total) failing UnmappedReadFilter
[2016-04-15T00:30Z] INFO  17:30:25,794 ProgressMeter -     7:101897697   1035159.0    30.0 s      29.0 s       64.0%    46.0 s      16.0 s
[2016-04-15T00:30Z] INFO  17:30:26,054 ProgressMeter -            done    405639.0    16.0 s      40.0 s      100.0%    16.0 s       0.0 s
[2016-04-15T00:30Z] INFO  17:30:26,054 ProgressMeter - Total runtime 16.57 secs, 0.28 min, 0.00 hours
[2016-04-15T00:30Z] INFO  17:30:26,055 MicroScheduler - 11939 reads were filtered out during the traversal out of approximately 150477 total reads (7.93%)
[2016-04-15T00:30Z] INFO  17:30:26,055 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:30Z] INFO  17:30:26,055 MicroScheduler -   -> 261 reads (0.17% of total) failing BadMateFilter
[2016-04-15T00:30Z] INFO  17:30:26,056 MicroScheduler -   -> 11573 reads (7.69% of total) failing DuplicateReadFilter
[2016-04-15T00:30Z] INFO  17:30:26,056 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:30Z] INFO  17:30:26,056 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:30Z] INFO  17:30:26,057 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:30Z] INFO  17:30:26,057 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:30Z] INFO  17:30:26,057 MicroScheduler -   -> 105 reads (0.07% of total) failing UnmappedReadFilter
[2016-04-15T00:30Z] INFO  17:30:26,786 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:30Z] GATK: UnifiedGenotyper
[2016-04-15T00:30Z] INFO  17:30:27,293 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:30Z] INFO  17:30:27,335 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:30Z] INFO  17:30:27,416 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:30Z] INFO  17:30:27,419 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:30Z] INFO  17:30:27,423 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:30Z] INFO  17:30:27,424 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:30Z] INFO  17:30:27,424 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:30Z] INFO  17:30:27,430 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/9/R14-18106_kapa-NGv3-PE100-NGv3-sort-9_32407258_65506776-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/9/R14-18106_kapa-NGv3-PE100-NGv3-9_32407258_65506776-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/9/tx/tmpmq_bk8/R14-18106_kapa-NGv3-PE100-NGv3-9_32407258_65506776.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:30Z] INFO  17:30:27,452 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:30Z] INFO  17:30:27,454 HelpFormatter - Date/Time: 2016/04/14 17:30:27
[2016-04-15T00:30Z] INFO  17:30:27,454 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:30Z] INFO  17:30:27,455 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:30Z] GATK: UnifiedGenotyper
[2016-04-15T00:30Z] INFO  17:30:27,655 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:30Z] INFO  17:30:27,680 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:30Z] INFO  17:30:27,684 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:30Z] INFO  17:30:27,685 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:30Z] INFO  17:30:27,685 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:30Z] INFO  17:30:27,691 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/9/R14-18106_kapa-NGv3-PE100-NGv3-sort-9_65507205_82187750-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/9/R14-18106_kapa-NGv3-PE100-NGv3-9_65507205_82187750-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/9/tx/tmpVQbdaE/R14-18106_kapa-NGv3-PE100-NGv3-9_65507205_82187750.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:30Z] GATK: UnifiedGenotyper
[2016-04-15T00:30Z] INFO  17:30:27,703 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:30Z] INFO  17:30:27,708 HelpFormatter - Date/Time: 2016/04/14 17:30:27
[2016-04-15T00:30Z] INFO  17:30:27,709 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:30Z] INFO  17:30:27,709 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:30Z] INFO  17:30:27,896 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:30Z] INFO  17:30:27,907 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:30Z] GATK: UnifiedGenotyper
[2016-04-15T00:30Z] INFO  17:30:27,947 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:30Z] INFO  17:30:27,975 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-15T00:30Z] INFO  17:30:28,250 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:30Z] INFO  17:30:28,261 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:30Z] INFO  17:30:28,393 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.12
[2016-04-15T00:30Z] INFO  17:30:28,467 IntervalUtils - Processing 223679 bp from intervals
[2016-04-15T00:30Z] WARN  17:30:28,485 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:30Z] INFO  17:30:28,613 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:30Z] INFO  17:30:28,624 ProgressMeter -            done    271335.0    15.0 s      56.0 s      100.0%    15.0 s       0.0 s
[2016-04-15T00:30Z] INFO  17:30:28,624 ProgressMeter - Total runtime 15.21 secs, 0.25 min, 0.00 hours
[2016-04-15T00:30Z] INFO  17:30:28,625 MicroScheduler - 9794 reads were filtered out during the traversal out of approximately 124580 total reads (7.86%)
[2016-04-15T00:30Z] INFO  17:30:28,625 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:30Z] INFO  17:30:28,625 MicroScheduler -   -> 197 reads (0.16% of total) failing BadMateFilter
[2016-04-15T00:30Z] INFO  17:30:28,625 MicroScheduler -   -> 9521 reads (7.64% of total) failing DuplicateReadFilter
[2016-04-15T00:30Z] INFO  17:30:28,626 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:30Z] INFO  17:30:28,626 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:30Z] INFO  17:30:28,626 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:30Z] INFO  17:30:28,627 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:30Z] INFO  17:30:28,627 MicroScheduler -   -> 76 reads (0.06% of total) failing UnmappedReadFilter
[2016-04-15T00:30Z] INFO  17:30:28,730 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:30Z] INFO  17:30:28,731 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:30Z] INFO  17:30:28,732 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:30Z] INFO  17:30:28,733 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:30Z] INFO  17:30:28,774 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:30Z] INFO  17:30:28,775 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:30Z] INFO  17:30:28,867 IntervalUtils - Processing 119378 bp from intervals
[2016-04-15T00:30Z] WARN  17:30:28,872 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:30Z] INFO  17:30:28,998 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:30Z] INFO  17:30:29,074 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:30Z] INFO  17:30:29,075 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:30Z] INFO  17:30:29,076 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:30Z] INFO  17:30:29,076 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:30Z] INFO  17:30:29,133 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:30Z] INFO  17:30:29,134 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:30Z] INFO  17:30:29,246 ProgressMeter -            done    175776.0    12.0 s      73.0 s       99.9%    12.0 s       0.0 s
[2016-04-15T00:30Z] INFO  17:30:29,247 ProgressMeter - Total runtime 12.93 secs, 0.22 min, 0.00 hours
[2016-04-15T00:30Z] INFO  17:30:29,248 MicroScheduler - 7707 reads were filtered out during the traversal out of approximately 97650 total reads (7.89%)
[2016-04-15T00:30Z] INFO  17:30:29,248 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:30Z] INFO  17:30:29,249 MicroScheduler -   -> 151 reads (0.15% of total) failing BadMateFilter
[2016-04-15T00:30Z] INFO  17:30:29,249 MicroScheduler -   -> 7514 reads (7.69% of total) failing DuplicateReadFilter
[2016-04-15T00:30Z] INFO  17:30:29,249 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:30Z] INFO  17:30:29,249 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:30Z] INFO  17:30:29,250 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:30Z] INFO  17:30:29,250 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:30Z] INFO  17:30:29,250 MicroScheduler -   -> 42 reads (0.04% of total) failing UnmappedReadFilter
[2016-04-15T00:30Z] INFO  17:30:29,964 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:30Z] INFO  17:30:30,111 ProgressMeter -            done    255372.0    15.0 s      59.0 s       99.9%    15.0 s       0.0 s
[2016-04-15T00:30Z] INFO  17:30:30,112 ProgressMeter - Total runtime 15.10 secs, 0.25 min, 0.00 hours
[2016-04-15T00:30Z] INFO  17:30:30,112 MicroScheduler - 8960 reads were filtered out during the traversal out of approximately 117730 total reads (7.61%)
[2016-04-15T00:30Z] INFO  17:30:30,112 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:30Z] INFO  17:30:30,113 MicroScheduler -   -> 187 reads (0.16% of total) failing BadMateFilter
[2016-04-15T00:30Z] INFO  17:30:30,113 MicroScheduler -   -> 8697 reads (7.39% of total) failing DuplicateReadFilter
[2016-04-15T00:30Z] INFO  17:30:30,113 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:30Z] INFO  17:30:30,114 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:30Z] INFO  17:30:30,114 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:30Z] INFO  17:30:30,114 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:30Z] INFO  17:30:30,115 MicroScheduler -   -> 76 reads (0.06% of total) failing UnmappedReadFilter
[2016-04-15T00:30Z] INFO  17:30:30,122 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:30Z] INFO  17:30:30,125 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:30Z] INFO  17:30:30,126 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:30Z] INFO  17:30:30,127 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:30Z] INFO  17:30:30,131 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/9/R14-18106_kapa-NGv3-PE100-NGv3-sort-9_82188172_97717561-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/9/R14-18106_kapa-NGv3-PE100-NGv3-9_82188172_97717561-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/9/tx/tmpCOSe9y/R14-18106_kapa-NGv3-PE100-NGv3-9_82188172_97717561.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:30Z] INFO  17:30:30,145 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:30Z] INFO  17:30:30,146 HelpFormatter - Date/Time: 2016/04/14 17:30:30
[2016-04-15T00:30Z] INFO  17:30:30,146 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:30Z] INFO  17:30:30,147 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:30Z] INFO  17:30:30,326 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:30Z] GATK: UnifiedGenotyper
[2016-04-15T00:30Z] INFO  17:30:30,501 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:30Z] INFO  17:30:30,510 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:30Z] INFO  17:30:30,574 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-15T00:30Z] INFO  17:30:30,625 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:30Z] INFO  17:30:30,719 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:30Z] INFO  17:30:30,722 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:30Z] INFO  17:30:30,723 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:30Z] INFO  17:30:30,723 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:30Z] INFO  17:30:30,728 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/9/R14-18106_kapa-NGv3-PE100-NGv3-sort-9_97718189_113228306-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/9/R14-18106_kapa-NGv3-PE100-NGv3-9_97718189_113228306-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/9/tx/tmpjXosgF/R14-18106_kapa-NGv3-PE100-NGv3-9_97718189_113228306.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:30Z] INFO  17:30:30,771 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:30Z] INFO  17:30:30,774 HelpFormatter - Date/Time: 2016/04/14 17:30:30
[2016-04-15T00:30Z] INFO  17:30:30,774 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:30Z] INFO  17:30:30,775 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:30Z] INFO  17:30:30,900 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:30Z] INFO  17:30:30,905 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:30Z] INFO  17:30:30,909 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:30Z] INFO  17:30:30,910 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:30Z] INFO  17:30:30,915 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/9/R14-18106_kapa-NGv3-PE100-NGv3-sort-9_113231219_129089575-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/9/R14-18106_kapa-NGv3-PE100-NGv3-9_113231219_129089575-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/9/tx/tmpe9W0py/R14-18106_kapa-NGv3-PE100-NGv3-9_113231219_129089575.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:30Z] INFO  17:30:30,928 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:30Z] GATK: UnifiedGenotyper
[2016-04-15T00:30Z] INFO  17:30:30,933 HelpFormatter - Date/Time: 2016/04/14 17:30:30
[2016-04-15T00:30Z] INFO  17:30:30,934 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:30Z] INFO  17:30:30,935 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:30Z] INFO  17:30:30,944 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:30Z] INFO  17:30:30,947 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:30Z] INFO  17:30:30,948 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:30Z] INFO  17:30:30,949 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:30Z] INFO  17:30:30,954 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/9/R14-18106_kapa-NGv3-PE100-NGv3-sort-9_129097484_141213431-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/9/R14-18106_kapa-NGv3-PE100-NGv3-9_129097484_141213431-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/9/tx/tmpdVmJNk/R14-18106_kapa-NGv3-PE100-NGv3-9_129097484_141213431.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:30Z] INFO  17:30:30,956 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:30Z] INFO  17:30:30,973 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:30Z] INFO  17:30:30,974 HelpFormatter - Date/Time: 2016/04/14 17:30:30
[2016-04-15T00:30Z] INFO  17:30:30,974 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:30Z] INFO  17:30:30,975 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:30Z] INFO  17:30:31,044 IntervalUtils - Processing 181286 bp from intervals
[2016-04-15T00:30Z] WARN  17:30:31,060 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:30Z] INFO  17:30:31,147 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:30Z] INFO  17:30:31,165 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:30Z] INFO  17:30:31,194 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:30Z] INFO  17:30:31,220 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:30Z] INFO  17:30:31,238 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:30Z] INFO  17:30:31,312 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:30Z] INFO  17:30:31,317 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:30Z] INFO  17:30:31,317 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:30Z] INFO  17:30:31,318 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:30Z] INFO  17:30:31,321 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-15T00:30Z] INFO  17:30:31,408 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:30Z] INFO  17:30:31,409 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:30Z] INFO  17:30:31,463 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:30Z] INFO  17:30:31,467 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:30Z] INFO  17:30:31,474 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:30Z] INFO  17:30:31,477 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:30Z] INFO  17:30:31,542 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-15T00:30Z] INFO  17:30:31,568 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.09
[2016-04-15T00:30Z] INFO  17:30:31,750 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:30Z] INFO  17:30:31,925 IntervalUtils - Processing 199321 bp from intervals
[2016-04-15T00:30Z] WARN  17:30:31,930 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:30Z] GATK: UnifiedGenotyper
[2016-04-15T00:30Z] INFO  17:30:32,022 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:30Z] INFO  17:30:32,055 IntervalUtils - Processing 455246 bp from intervals
[2016-04-15T00:30Z] WARN  17:30:32,064 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:30Z] INFO  17:30:32,065 IntervalUtils - Processing 228449 bp from intervals
[2016-04-15T00:30Z] WARN  17:30:32,081 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:30Z] INFO  17:30:32,141 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:30Z] INFO  17:30:32,147 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:30Z] INFO  17:30:32,148 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:30Z] INFO  17:30:32,149 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:30Z] INFO  17:30:32,185 ProgressMeter -            done   1158758.0    29.0 s      25.0 s      100.0%    29.0 s       0.0 s
[2016-04-15T00:30Z] INFO  17:30:32,185 ProgressMeter - Total runtime 29.65 secs, 0.49 min, 0.01 hours
[2016-04-15T00:30Z] INFO  17:30:32,186 MicroScheduler - 28274 reads were filtered out during the traversal out of approximately 379805 total reads (7.44%)
[2016-04-15T00:30Z] INFO  17:30:32,186 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:30Z] INFO  17:30:32,186 MicroScheduler -   -> 673 reads (0.18% of total) failing BadMateFilter
[2016-04-15T00:30Z] INFO  17:30:32,187 MicroScheduler -   -> 27344 reads (7.20% of total) failing DuplicateReadFilter
[2016-04-15T00:30Z] INFO  17:30:32,187 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:30Z] INFO  17:30:32,187 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:30Z] INFO  17:30:32,187 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:30Z] INFO  17:30:32,187 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:30Z] INFO  17:30:32,188 MicroScheduler -   -> 257 reads (0.07% of total) failing UnmappedReadFilter
[2016-04-15T00:30Z] INFO  17:30:32,211 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:30Z] INFO  17:30:32,216 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:30Z] INFO  17:30:32,231 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:30Z] INFO  17:30:32,231 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:30Z] INFO  17:30:32,331 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:30Z] INFO  17:30:32,335 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:30Z] INFO  17:30:32,336 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:30Z] INFO  17:30:32,340 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:30Z] INFO  17:30:32,372 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:30Z] INFO  17:30:32,373 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:30Z] INFO  17:30:32,373 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:30Z] INFO  17:30:32,374 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:30Z] INFO  17:30:32,385 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:30Z] INFO  17:30:32,385 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:30Z] INFO  17:30:32,422 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:30Z] INFO  17:30:32,423 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:30Z] INFO  17:30:33,336 ProgressMeter -            done    445208.0    18.0 s      42.0 s      100.0%    18.0 s       0.0 s
[2016-04-15T00:30Z] INFO  17:30:33,337 ProgressMeter - Total runtime 18.86 secs, 0.31 min, 0.01 hours
[2016-04-15T00:30Z] INFO  17:30:33,337 MicroScheduler - 13759 reads were filtered out during the traversal out of approximately 175677 total reads (7.83%)
[2016-04-15T00:30Z] INFO  17:30:33,337 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:30Z] INFO  17:30:33,337 MicroScheduler -   -> 325 reads (0.18% of total) failing BadMateFilter
[2016-04-15T00:30Z] INFO  17:30:33,338 MicroScheduler -   -> 13306 reads (7.57% of total) failing DuplicateReadFilter
[2016-04-15T00:30Z] INFO  17:30:33,338 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:30Z] INFO  17:30:33,338 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:30Z] INFO  17:30:33,338 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:30Z] INFO  17:30:33,339 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:30Z] INFO  17:30:33,339 MicroScheduler -   -> 128 reads (0.07% of total) failing UnmappedReadFilter
[2016-04-15T00:30Z] INFO  17:30:33,579 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:30Z] INFO  17:30:33,582 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:30Z] INFO  17:30:33,583 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:30Z] INFO  17:30:33,584 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:30Z] INFO  17:30:33,588 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/10/R14-18106_kapa-NGv3-PE100-NGv3-sort-10_0_15559243-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/10/R14-18106_kapa-NGv3-PE100-NGv3-10_0_15559243-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/10/tx/tmppmnWZg/R14-18106_kapa-NGv3-PE100-NGv3-10_0_15559243.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:30Z] INFO  17:30:33,628 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:30Z] INFO  17:30:33,634 HelpFormatter - Date/Time: 2016/04/14 17:30:33
[2016-04-15T00:30Z] INFO  17:30:33,635 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:30Z] INFO  17:30:33,636 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:30Z] INFO  17:30:33,899 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:30Z] INFO  17:30:33,909 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:30Z] INFO  17:30:33,913 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:30Z] INFO  17:30:33,915 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:30Z] INFO  17:30:33,915 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:30Z] INFO  17:30:33,915 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:30Z] INFO  17:30:33,919 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/10/R14-18106_kapa-NGv3-PE100-NGv3-sort-10_15561288_31134502-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/10/R14-18106_kapa-NGv3-PE100-NGv3-10_15561288_31134502-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/10/tx/tmprC_BkI/R14-18106_kapa-NGv3-PE100-NGv3-10_15561288_31134502.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:30Z] INFO  17:30:33,947 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:30Z] INFO  17:30:33,948 HelpFormatter - Date/Time: 2016/04/14 17:30:33
[2016-04-15T00:30Z] INFO  17:30:33,949 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:30Z] INFO  17:30:33,949 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:30Z] INFO  17:30:34,141 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:30Z] INFO  17:30:34,147 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:30Z] INFO  17:30:34,178 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:30Z] GATK: UnifiedGenotyper
[2016-04-15T00:30Z] INFO  17:30:34,255 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-15T00:30Z] INFO  17:30:34,384 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:30Z] INFO  17:30:34,410 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:30Z] INFO  17:30:34,491 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-15T00:30Z] INFO  17:30:34,704 IntervalUtils - Processing 145147 bp from intervals
[2016-04-15T00:30Z] WARN  17:30:34,715 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:30Z] INFO  17:30:34,791 ProgressMeter -            done    771215.0    25.0 s      33.0 s      100.0%    25.0 s       0.0 s
[2016-04-15T00:30Z] INFO  17:30:34,792 ProgressMeter - Total runtime 25.57 secs, 0.43 min, 0.01 hours
[2016-04-15T00:30Z] INFO  17:30:34,793 MicroScheduler - 23191 reads were filtered out during the traversal out of approximately 289907 total reads (8.00%)
[2016-04-15T00:30Z] INFO  17:30:34,794 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:30Z] INFO  17:30:34,794 MicroScheduler -   -> 483 reads (0.17% of total) failing BadMateFilter
[2016-04-15T00:30Z] INFO  17:30:34,795 MicroScheduler -   -> 22505 reads (7.76% of total) failing DuplicateReadFilter
[2016-04-15T00:30Z] INFO  17:30:34,796 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:30Z] INFO  17:30:34,796 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:30Z] INFO  17:30:34,796 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:30Z] INFO  17:30:34,795 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:30Z] INFO  17:30:34,798 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:30Z] INFO  17:30:34,798 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:30Z] INFO  17:30:34,798 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:30Z] INFO  17:30:34,798 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:30Z] INFO  17:30:34,799 MicroScheduler -   -> 203 reads (0.07% of total) failing UnmappedReadFilter
[2016-04-15T00:30Z] INFO  17:30:34,799 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:30Z] INFO  17:30:34,804 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/10/R14-18106_kapa-NGv3-PE100-NGv3-sort-10_31137459_46960129-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/10/R14-18106_kapa-NGv3-PE100-NGv3-10_31137459_46960129-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/10/tx/tmp1KDCZv/R14-18106_kapa-NGv3-PE100-NGv3-10_31137459_46960129.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:30Z] INFO  17:30:34,812 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:30Z] INFO  17:30:34,812 HelpFormatter - Date/Time: 2016/04/14 17:30:34
[2016-04-15T00:30Z] INFO  17:30:34,812 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:30Z] INFO  17:30:34,812 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:30Z] INFO  17:30:34,812 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:30Z] INFO  17:30:34,884 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:30Z] INFO  17:30:34,886 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:30Z] INFO  17:30:34,886 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:30Z] INFO  17:30:34,897 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:30Z] INFO  17:30:34,980 IntervalUtils - Processing 156629 bp from intervals
[2016-04-15T00:30Z] INFO  17:30:34,980 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:30Z] INFO  17:30:34,981 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:30Z] WARN  17:30:35,025 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:30Z] INFO  17:30:35,053 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:30Z] GATK: UnifiedGenotyper
[2016-04-15T00:30Z] INFO  17:30:35,153 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:30Z] INFO  17:30:35,258 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:30Z] INFO  17:30:35,286 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:30Z] INFO  17:30:35,287 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:30Z] INFO  17:30:35,287 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:30Z] INFO  17:30:35,303 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:30Z] INFO  17:30:35,322 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:30Z] INFO  17:30:35,352 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:30Z] INFO  17:30:35,353 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:30Z] INFO  17:30:35,407 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-15T00:30Z] INFO  17:30:35,822 IntervalUtils - Processing 103621 bp from intervals
[2016-04-15T00:30Z] WARN  17:30:35,827 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:30Z] INFO  17:30:35,959 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:30Z] INFO  17:30:36,045 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:30Z] INFO  17:30:36,046 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:30Z] INFO  17:30:36,047 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:30Z] INFO  17:30:36,047 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:30Z] INFO  17:30:36,066 ProgressMeter -            done   1463815.0    40.0 s      27.0 s      100.0%    40.0 s       0.0 s
[2016-04-15T00:30Z] INFO  17:30:36,066 ProgressMeter - Total runtime 40.31 secs, 0.67 min, 0.01 hours
[2016-04-15T00:30Z] INFO  17:30:36,067 MicroScheduler - 46887 reads were filtered out during the traversal out of approximately 611974 total reads (7.66%)
[2016-04-15T00:30Z] INFO  17:30:36,067 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:30Z] INFO  17:30:36,067 MicroScheduler -   -> 1103 reads (0.18% of total) failing BadMateFilter
[2016-04-15T00:30Z] INFO  17:30:36,068 MicroScheduler -   -> 45339 reads (7.41% of total) failing DuplicateReadFilter
[2016-04-15T00:30Z] INFO  17:30:36,068 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:30Z] INFO  17:30:36,068 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:30Z] INFO  17:30:36,068 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:30Z] INFO  17:30:36,068 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:30Z] INFO  17:30:36,069 MicroScheduler -   -> 445 reads (0.07% of total) failing UnmappedReadFilter
[2016-04-15T00:30Z] INFO  17:30:36,113 ProgressMeter -            done    186579.0    14.0 s      75.0 s       99.9%    14.0 s       0.0 s
[2016-04-15T00:30Z] INFO  17:30:36,114 ProgressMeter - Total runtime 14.04 secs, 0.23 min, 0.00 hours
[2016-04-15T00:30Z] INFO  17:30:36,114 MicroScheduler - 8107 reads were filtered out during the traversal out of approximately 105062 total reads (7.72%)
[2016-04-15T00:30Z] INFO  17:30:36,115 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:30Z] INFO  17:30:36,115 MicroScheduler -   -> 171 reads (0.16% of total) failing BadMateFilter
[2016-04-15T00:30Z] INFO  17:30:36,115 MicroScheduler -   -> 7880 reads (7.50% of total) failing DuplicateReadFilter
[2016-04-15T00:30Z] INFO  17:30:36,115 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:30Z] INFO  17:30:36,116 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:30Z] INFO  17:30:36,116 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:30Z] INFO  17:30:36,116 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:30Z] INFO  17:30:36,116 MicroScheduler -   -> 56 reads (0.05% of total) failing UnmappedReadFilter
[2016-04-15T00:30Z] INFO  17:30:36,125 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:30Z] INFO  17:30:36,136 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:30Z] INFO  17:30:36,240 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:30Z] GATK: UnifiedGenotyper
[2016-04-15T00:30Z] INFO  17:30:37,152 ProgressMeter -            done    316474.0    17.0 s      54.0 s       99.9%    17.0 s       0.0 s
[2016-04-15T00:30Z] INFO  17:30:37,153 ProgressMeter - Total runtime 17.09 secs, 0.28 min, 0.00 hours
[2016-04-15T00:30Z] INFO  17:30:37,153 MicroScheduler - 11576 reads were filtered out during the traversal out of approximately 151221 total reads (7.66%)
[2016-04-15T00:30Z] INFO  17:30:37,154 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:30Z] INFO  17:30:37,154 MicroScheduler -   -> 274 reads (0.18% of total) failing BadMateFilter
[2016-04-15T00:30Z] INFO  17:30:37,156 MicroScheduler -   -> 11220 reads (7.42% of total) failing DuplicateReadFilter
[2016-04-15T00:30Z] INFO  17:30:37,157 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:30Z] INFO  17:30:37,157 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:30Z] INFO  17:30:37,157 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:30Z] INFO  17:30:37,158 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:30Z] INFO  17:30:37,158 MicroScheduler -   -> 82 reads (0.05% of total) failing UnmappedReadFilter
[2016-04-15T00:30Z] INFO  17:30:37,311 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:30Z] INFO  17:30:37,313 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:30Z] INFO  17:30:37,313 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:30Z] INFO  17:30:37,313 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:30Z] INFO  17:30:37,329 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/10/R14-18106_kapa-NGv3-PE100-NGv3-sort-10_46960410_62493077-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/10/R14-18106_kapa-NGv3-PE100-NGv3-10_46960410_62493077-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/10/tx/tmpAveWrB/R14-18106_kapa-NGv3-PE100-NGv3-10_46960410_62493077.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:30Z] INFO  17:30:37,347 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:30Z] INFO  17:30:37,348 HelpFormatter - Date/Time: 2016/04/14 17:30:37
[2016-04-15T00:30Z] INFO  17:30:37,348 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:30Z] INFO  17:30:37,349 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:30Z] INFO  17:30:37,570 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:30Z] INFO  17:30:37,736 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:30Z] INFO  17:30:37,746 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:30Z] INFO  17:30:37,752 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:30Z] INFO  17:30:37,848 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.10
[2016-04-15T00:30Z] INFO  17:30:38,138 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:30Z] GATK: UnifiedGenotyper
[2016-04-15T00:30Z] INFO  17:30:38,292 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:30Z] INFO  17:30:38,295 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:30Z] INFO  17:30:38,296 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:30Z] INFO  17:30:38,297 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:30Z] INFO  17:30:38,301 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/10/R14-18106_kapa-NGv3-PE100-NGv3-sort-10_62539923_78084243-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/10/R14-18106_kapa-NGv3-PE100-NGv3-10_62539923_78084243-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/10/tx/tmpyzcq8M/R14-18106_kapa-NGv3-PE100-NGv3-10_62539923_78084243.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:30Z] INFO  17:30:38,311 IntervalUtils - Processing 143638 bp from intervals
[2016-04-15T00:30Z] WARN  17:30:38,316 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:30Z] INFO  17:30:38,323 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:30Z] INFO  17:30:38,324 HelpFormatter - Date/Time: 2016/04/14 17:30:38
[2016-04-15T00:30Z] INFO  17:30:38,324 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:30Z] INFO  17:30:38,324 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:30Z] INFO  17:30:38,448 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:30Z] GATK: UnifiedGenotyper
[2016-04-15T00:30Z] INFO  17:30:38,537 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:30Z] INFO  17:30:38,564 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:30Z] INFO  17:30:38,565 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:30Z] INFO  17:30:38,569 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:30Z] INFO  17:30:38,570 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:30Z] INFO  17:30:38,649 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:30Z] INFO  17:30:38,660 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:30Z] INFO  17:30:38,727 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:30Z] INFO  17:30:38,737 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:30Z] INFO  17:30:38,746 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:30Z] INFO  17:30:38,812 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-15T00:30Z] GATK: UnifiedGenotyper
[2016-04-15T00:30Z] INFO  17:30:39,270 IntervalUtils - Processing 230109 bp from intervals
[2016-04-15T00:30Z] WARN  17:30:39,276 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:30Z] INFO  17:30:39,346 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:30Z] INFO  17:30:39,506 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:30Z] INFO  17:30:39,507 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:30Z] INFO  17:30:39,507 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:30Z] INFO  17:30:39,507 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:30Z] INFO  17:30:39,592 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:30Z] INFO  17:30:39,592 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:30Z] INFO  17:30:39,923 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:30Z] INFO  17:30:39,927 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:30Z] INFO  17:30:39,927 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:30Z] INFO  17:30:39,928 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:30Z] INFO  17:30:39,932 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/10/R14-18106_kapa-NGv3-PE100-NGv3-sort-10_78316966_93841258-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/10/R14-18106_kapa-NGv3-PE100-NGv3-10_78316966_93841258-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/10/tx/tmpUEsG5Z/R14-18106_kapa-NGv3-PE100-NGv3-10_78316966_93841258.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:30Z] INFO  17:30:39,942 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:30Z] INFO  17:30:39,946 HelpFormatter - Date/Time: 2016/04/14 17:30:39
[2016-04-15T00:30Z] INFO  17:30:39,946 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:30Z] INFO  17:30:39,958 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:30Z] INFO  17:30:40,187 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:30Z] INFO  17:30:40,469 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:30Z] INFO  17:30:40,490 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:30Z] INFO  17:30:40,595 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.10
[2016-04-15T00:30Z] INFO  17:30:41,072 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:30Z] INFO  17:30:41,084 IntervalUtils - Processing 148808 bp from intervals
[2016-04-15T00:30Z] WARN  17:30:41,089 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:30Z] INFO  17:30:41,090 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:30Z] INFO  17:30:41,091 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:30Z] INFO  17:30:41,092 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:30Z] INFO  17:30:41,096 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/10/R14-18106_kapa-NGv3-PE100-NGv3-sort-10_93851586_111625070-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/10/R14-18106_kapa-NGv3-PE100-NGv3-10_93851586_111625070-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/10/tx/tmp9xVXgG/R14-18106_kapa-NGv3-PE100-NGv3-10_93851586_111625070.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:30Z] INFO  17:30:41,105 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:30Z] INFO  17:30:41,106 HelpFormatter - Date/Time: 2016/04/14 17:30:41
[2016-04-15T00:30Z] INFO  17:30:41,107 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:30Z] INFO  17:30:41,108 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:30Z] INFO  17:30:41,230 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:30Z] INFO  17:30:41,327 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:30Z] INFO  17:30:41,329 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:30Z] INFO  17:30:41,329 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:30Z] INFO  17:30:41,330 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:30Z] INFO  17:30:41,336 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:30Z] INFO  17:30:41,445 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:30Z] INFO  17:30:41,452 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:30Z] INFO  17:30:41,543 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:30Z] INFO  17:30:41,545 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:30Z] INFO  17:30:41,545 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:30Z] INFO  17:30:41,545 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:30Z] INFO  17:30:41,566 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/10/R14-18106_kapa-NGv3-PE100-NGv3-sort-10_111628371_127265443-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/10/R14-18106_kapa-NGv3-PE100-NGv3-10_111628371_127265443-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/10/tx/tmpmXRd7n/R14-18106_kapa-NGv3-PE100-NGv3-10_111628371_127265443.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:30Z] INFO  17:30:41,575 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:30Z] INFO  17:30:41,576 HelpFormatter - Date/Time: 2016/04/14 17:30:41
[2016-04-15T00:30Z] INFO  17:30:41,576 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:30Z] INFO  17:30:41,577 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:30Z] INFO  17:30:41,604 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:30Z] INFO  17:30:41,624 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:30Z] INFO  17:30:41,697 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-15T00:30Z] INFO  17:30:41,827 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:30Z] INFO  17:30:41,830 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:30Z] INFO  17:30:41,830 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:30Z] INFO  17:30:41,831 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:30Z] INFO  17:30:41,841 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/10/R14-18106_kapa-NGv3-PE100-NGv3-sort-10_127328721_135534747-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/10/R14-18106_kapa-NGv3-PE100-NGv3-10_127328721_135534747-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/10/tx/tmp_Ry8R7/R14-18106_kapa-NGv3-PE100-NGv3-10_127328721_135534747.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:30Z] INFO  17:30:41,853 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:30Z] INFO  17:30:41,854 HelpFormatter - Date/Time: 2016/04/14 17:30:41
[2016-04-15T00:30Z] INFO  17:30:41,854 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:30Z] INFO  17:30:41,855 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:30Z] INFO  17:30:41,862 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:30Z] INFO  17:30:42,029 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:30Z] INFO  17:30:42,102 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:30Z] INFO  17:30:42,119 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:30Z] INFO  17:30:42,191 IntervalUtils - Processing 335852 bp from intervals
[2016-04-15T00:30Z] WARN  17:30:42,207 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:30Z] INFO  17:30:42,250 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.13
[2016-04-15T00:30Z] INFO  17:30:42,273 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:30Z] INFO  17:30:42,355 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:30Z] INFO  17:30:42,368 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:30Z] INFO  17:30:42,405 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:30Z] INFO  17:30:42,406 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:30Z] INFO  17:30:42,407 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:30Z] INFO  17:30:42,408 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:30Z] INFO  17:30:42,457 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:30Z] INFO  17:30:42,458 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:30Z] INFO  17:30:42,485 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.12
[2016-04-15T00:30Z] INFO  17:30:42,728 IntervalUtils - Processing 210787 bp from intervals
[2016-04-15T00:30Z] WARN  17:30:42,748 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:30Z] INFO  17:30:42,900 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:30Z] INFO  17:30:42,925 IntervalUtils - Processing 102137 bp from intervals
[2016-04-15T00:30Z] WARN  17:30:42,930 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:30Z] INFO  17:30:43,024 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:30Z] INFO  17:30:43,025 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:30Z] INFO  17:30:43,026 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:30Z] INFO  17:30:43,026 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:30Z] INFO  17:30:43,033 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:30Z] INFO  17:30:43,074 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:30Z] INFO  17:30:43,075 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:30Z] INFO  17:30:43,110 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:30Z] INFO  17:30:43,122 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:30Z] INFO  17:30:43,123 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:30Z] INFO  17:30:43,123 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:30Z] INFO  17:30:43,207 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:30Z] INFO  17:30:43,216 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:30Z] INFO  17:30:43,581 ProgressMeter -            done   1313389.0    24.0 s      18.0 s      100.0%    24.0 s       0.0 s
[2016-04-15T00:30Z] INFO  17:30:43,582 ProgressMeter - Total runtime 24.70 secs, 0.41 min, 0.01 hours
[2016-04-15T00:30Z] INFO  17:30:43,582 MicroScheduler - 26270 reads were filtered out during the traversal out of approximately 322525 total reads (8.15%)
[2016-04-15T00:30Z] INFO  17:30:43,582 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:30Z] INFO  17:30:43,583 MicroScheduler -   -> 666 reads (0.21% of total) failing BadMateFilter
[2016-04-15T00:30Z] INFO  17:30:43,583 MicroScheduler -   -> 25227 reads (7.82% of total) failing DuplicateReadFilter
[2016-04-15T00:30Z] INFO  17:30:43,583 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:30Z] INFO  17:30:43,583 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:30Z] INFO  17:30:43,584 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:30Z] INFO  17:30:43,584 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:30Z] INFO  17:30:43,584 MicroScheduler -   -> 377 reads (0.12% of total) failing UnmappedReadFilter
[2016-04-15T00:30Z] INFO  17:30:44,954 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:30Z] GATK: UnifiedGenotyper
[2016-04-15T00:30Z] INFO  17:30:45,980 ProgressMeter -            done    294057.0    16.0 s      57.0 s      100.0%    16.0 s       0.0 s
[2016-04-15T00:30Z] INFO  17:30:45,981 ProgressMeter - Total runtime 16.91 secs, 0.28 min, 0.00 hours
[2016-04-15T00:30Z] INFO  17:30:45,981 MicroScheduler - 11851 reads were filtered out during the traversal out of approximately 168735 total reads (7.02%)
[2016-04-15T00:30Z] INFO  17:30:45,981 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:30Z] INFO  17:30:45,982 MicroScheduler -   -> 265 reads (0.16% of total) failing BadMateFilter
[2016-04-15T00:30Z] INFO  17:30:45,982 MicroScheduler -   -> 11485 reads (6.81% of total) failing DuplicateReadFilter
[2016-04-15T00:30Z] INFO  17:30:45,982 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:30Z] INFO  17:30:45,982 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:30Z] INFO  17:30:45,983 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:30Z] INFO  17:30:45,983 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:30Z] INFO  17:30:45,983 MicroScheduler -   -> 101 reads (0.06% of total) failing UnmappedReadFilter
[2016-04-15T00:30Z] INFO  17:30:47,448 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:30Z] GATK: UnifiedGenotyper
[2016-04-15T00:30Z] INFO  17:30:48,376 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:30Z] INFO  17:30:48,380 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:30Z] INFO  17:30:48,381 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:30Z] INFO  17:30:48,381 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:30Z] INFO  17:30:48,387 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/11/R14-18106_kapa-NGv3-PE100-NGv3-sort-11_0_15994658-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/11/R14-18106_kapa-NGv3-PE100-NGv3-11_0_15994658-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/11/tx/tmpI8PIpi/R14-18106_kapa-NGv3-PE100-NGv3-11_0_15994658.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:30Z] INFO  17:30:48,410 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:30Z] INFO  17:30:48,420 HelpFormatter - Date/Time: 2016/04/14 17:30:48
[2016-04-15T00:30Z] INFO  17:30:48,421 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:30Z] INFO  17:30:48,421 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:30Z] INFO  17:30:48,587 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:30Z] INFO  17:30:48,780 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:30Z] INFO  17:30:48,790 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:30Z] INFO  17:30:48,847 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-15T00:30Z] INFO  17:30:49,238 IntervalUtils - Processing 438345 bp from intervals
[2016-04-15T00:30Z] WARN  17:30:49,243 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:30Z] INFO  17:30:49,346 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:30Z] INFO  17:30:49,475 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:30Z] INFO  17:30:49,476 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:30Z] INFO  17:30:49,477 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:30Z] INFO  17:30:49,477 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:30Z] INFO  17:30:49,536 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:30Z] INFO  17:30:49,537 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:30Z] INFO  17:30:50,363 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:30Z] INFO  17:30:50,367 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:30Z] INFO  17:30:50,368 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:30Z] INFO  17:30:50,368 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:30Z] INFO  17:30:50,374 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/11/R14-18106_kapa-NGv3-PE100-NGv3-sort-11_16007749_31531554-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/11/R14-18106_kapa-NGv3-PE100-NGv3-11_16007749_31531554-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/11/tx/tmpL3nCRR/R14-18106_kapa-NGv3-PE100-NGv3-11_16007749_31531554.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:30Z] INFO  17:30:50,386 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:30Z] INFO  17:30:50,388 HelpFormatter - Date/Time: 2016/04/14 17:30:50
[2016-04-15T00:30Z] INFO  17:30:50,389 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:30Z] INFO  17:30:50,389 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:30Z] INFO  17:30:50,607 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:30Z] INFO  17:30:50,868 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:30Z] INFO  17:30:50,879 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:30Z] INFO  17:30:50,948 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-15T00:30Z] INFO  17:30:51,121 ProgressMeter -            done    272797.0    15.0 s      55.0 s       99.9%    15.0 s       0.0 s
[2016-04-15T00:30Z] INFO  17:30:51,122 ProgressMeter - Total runtime 15.08 secs, 0.25 min, 0.00 hours
[2016-04-15T00:30Z] INFO  17:30:51,123 MicroScheduler - 10408 reads were filtered out during the traversal out of approximately 137879 total reads (7.55%)
[2016-04-15T00:30Z] INFO  17:30:51,124 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:30Z] INFO  17:30:51,125 MicroScheduler -   -> 265 reads (0.19% of total) failing BadMateFilter
[2016-04-15T00:30Z] INFO  17:30:51,126 MicroScheduler -   -> 10050 reads (7.29% of total) failing DuplicateReadFilter
[2016-04-15T00:30Z] INFO  17:30:51,126 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:30Z] INFO  17:30:51,127 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:30Z] INFO  17:30:51,128 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:30Z] INFO  17:30:51,129 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:30Z] INFO  17:30:51,129 MicroScheduler -   -> 93 reads (0.07% of total) failing UnmappedReadFilter
[2016-04-15T00:30Z] INFO  17:30:51,574 IntervalUtils - Processing 144906 bp from intervals
[2016-04-15T00:30Z] WARN  17:30:51,581 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:30Z] INFO  17:30:51,691 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:30Z] INFO  17:30:51,773 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:30Z] INFO  17:30:51,774 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:30Z] INFO  17:30:51,775 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:30Z] INFO  17:30:51,776 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:30Z] INFO  17:30:51,819 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:30Z] INFO  17:30:51,820 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:30Z] INFO  17:30:52,472 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:30Z] GATK: UnifiedGenotyper
[2016-04-15T00:30Z] INFO  17:30:53,817 ProgressMeter -            done    477875.0    22.0 s      47.0 s      100.0%    22.0 s       0.0 s
[2016-04-15T00:30Z] INFO  17:30:53,817 ProgressMeter - Total runtime 22.50 secs, 0.38 min, 0.01 hours
[2016-04-15T00:30Z] INFO  17:30:53,818 MicroScheduler - 19709 reads were filtered out during the traversal out of approximately 251475 total reads (7.84%)
[2016-04-15T00:30Z] INFO  17:30:53,818 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:30Z] INFO  17:30:53,818 MicroScheduler -   -> 456 reads (0.18% of total) failing BadMateFilter
[2016-04-15T00:30Z] INFO  17:30:53,818 MicroScheduler -   -> 19076 reads (7.59% of total) failing DuplicateReadFilter
[2016-04-15T00:30Z] INFO  17:30:53,819 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:30Z] INFO  17:30:53,819 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:30Z] INFO  17:30:53,819 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:30Z] INFO  17:30:53,819 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:30Z] INFO  17:30:53,820 MicroScheduler -   -> 177 reads (0.07% of total) failing UnmappedReadFilter
[2016-04-15T00:30Z] INFO  17:30:54,207 ProgressMeter -            done    465734.0    19.0 s      41.0 s       99.9%    19.0 s       0.0 s
[2016-04-15T00:30Z] INFO  17:30:54,207 ProgressMeter - Total runtime 19.32 secs, 0.32 min, 0.01 hours
[2016-04-15T00:30Z] INFO  17:30:54,208 MicroScheduler - 14543 reads were filtered out during the traversal out of approximately 185109 total reads (7.86%)
[2016-04-15T00:30Z] INFO  17:30:54,208 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:30Z] INFO  17:30:54,208 MicroScheduler -   -> 307 reads (0.17% of total) failing BadMateFilter
[2016-04-15T00:30Z] INFO  17:30:54,208 MicroScheduler -   -> 14135 reads (7.64% of total) failing DuplicateReadFilter
[2016-04-15T00:30Z] INFO  17:30:54,209 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:30Z] INFO  17:30:54,209 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:30Z] INFO  17:30:54,209 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:30Z] INFO  17:30:54,209 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:30Z] INFO  17:30:54,210 MicroScheduler -   -> 101 reads (0.05% of total) failing UnmappedReadFilter
[2016-04-15T00:30Z] INFO  17:30:54,324 ProgressMeter -            done    421173.0    19.0 s      45.0 s      100.0%    19.0 s       0.0 s
[2016-04-15T00:30Z] INFO  17:30:54,325 ProgressMeter - Total runtime 19.07 secs, 0.32 min, 0.01 hours
[2016-04-15T00:30Z] INFO  17:30:54,326 MicroScheduler - 13059 reads were filtered out during the traversal out of approximately 167029 total reads (7.82%)
[2016-04-15T00:30Z] INFO  17:30:54,327 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:30Z] INFO  17:30:54,327 MicroScheduler -   -> 271 reads (0.16% of total) failing BadMateFilter
[2016-04-15T00:30Z] INFO  17:30:54,328 MicroScheduler -   -> 12666 reads (7.58% of total) failing DuplicateReadFilter
[2016-04-15T00:30Z] INFO  17:30:54,329 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:30Z] INFO  17:30:54,329 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:30Z] INFO  17:30:54,330 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:30Z] INFO  17:30:54,330 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:30Z] INFO  17:30:54,331 MicroScheduler -   -> 122 reads (0.07% of total) failing UnmappedReadFilter
[2016-04-15T00:30Z] INFO  17:30:55,148 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:30Z] INFO  17:30:55,234 ProgressMeter -            done    539922.0    23.0 s      42.0 s      100.0%    23.0 s       0.0 s
[2016-04-15T00:30Z] INFO  17:30:55,235 ProgressMeter - Total runtime 23.09 secs, 0.38 min, 0.01 hours
[2016-04-15T00:30Z] INFO  17:30:55,235 MicroScheduler - 19466 reads were filtered out during the traversal out of approximately 244084 total reads (7.98%)
[2016-04-15T00:30Z] INFO  17:30:55,235 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:30Z] INFO  17:30:55,236 MicroScheduler -   -> 381 reads (0.16% of total) failing BadMateFilter
[2016-04-15T00:30Z] INFO  17:30:55,236 MicroScheduler -   -> 18926 reads (7.75% of total) failing DuplicateReadFilter
[2016-04-15T00:30Z] INFO  17:30:55,236 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:30Z] INFO  17:30:55,236 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:30Z] INFO  17:30:55,237 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:30Z] INFO  17:30:55,237 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:30Z] INFO  17:30:55,237 MicroScheduler -   -> 159 reads (0.07% of total) failing UnmappedReadFilter
[2016-04-15T00:30Z] INFO  17:30:55,353 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:30Z] INFO  17:30:55,355 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:30Z] INFO  17:30:55,355 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:30Z] INFO  17:30:55,355 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:30Z] INFO  17:30:55,359 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/11/R14-18106_kapa-NGv3-PE100-NGv3-sort-11_31541602_47074069-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/11/R14-18106_kapa-NGv3-PE100-NGv3-11_31541602_47074069-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/11/tx/tmpN8Mjtn/R14-18106_kapa-NGv3-PE100-NGv3-11_31541602_47074069.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:30Z] INFO  17:30:55,382 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:30Z] INFO  17:30:55,383 HelpFormatter - Date/Time: 2016/04/14 17:30:55
[2016-04-15T00:30Z] INFO  17:30:55,383 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:30Z] INFO  17:30:55,383 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:30Z] GATK: UnifiedGenotyper
[2016-04-15T00:30Z] INFO  17:30:55,601 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:30Z] INFO  17:30:55,663 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:30Z] INFO  17:30:55,837 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:30Z] INFO  17:30:55,858 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:30Z] INFO  17:30:55,862 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:30Z] INFO  17:30:55,920 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-15T00:30Z] GATK: UnifiedGenotyper
[2016-04-15T00:30Z] GATK: UnifiedGenotyper
[2016-04-15T00:30Z] INFO  17:30:56,252 IntervalUtils - Processing 150047 bp from intervals
[2016-04-15T00:30Z] WARN  17:30:56,268 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:30Z] INFO  17:30:56,359 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:30Z] INFO  17:30:56,447 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:30Z] INFO  17:30:56,447 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:30Z] INFO  17:30:56,448 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:30Z] INFO  17:30:56,448 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:30Z] INFO  17:30:56,510 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:30Z] INFO  17:30:56,510 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:30Z] INFO  17:30:56,511 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:30Z] GATK: UnifiedGenotyper
[2016-04-15T00:30Z] INFO  17:30:56,875 ProgressMeter -            done    360383.0    13.0 s      38.0 s       99.9%    13.0 s       0.0 s
[2016-04-15T00:30Z] INFO  17:30:56,875 ProgressMeter - Total runtime 13.75 secs, 0.23 min, 0.00 hours
[2016-04-15T00:30Z] INFO  17:30:56,875 MicroScheduler - 11449 reads were filtered out during the traversal out of approximately 143562 total reads (7.97%)
[2016-04-15T00:30Z] INFO  17:30:56,876 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:30Z] INFO  17:30:56,876 MicroScheduler -   -> 251 reads (0.17% of total) failing BadMateFilter
[2016-04-15T00:30Z] INFO  17:30:56,876 MicroScheduler -   -> 11115 reads (7.74% of total) failing DuplicateReadFilter
[2016-04-15T00:30Z] INFO  17:30:56,877 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:30Z] INFO  17:30:56,877 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:30Z] INFO  17:30:56,877 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:30Z] INFO  17:30:56,878 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:30Z] INFO  17:30:56,878 MicroScheduler -   -> 83 reads (0.06% of total) failing UnmappedReadFilter
[2016-04-15T00:30Z] INFO  17:30:56,971 ProgressMeter -            done    946777.0    28.0 s      29.0 s      100.0%    28.0 s       0.0 s
[2016-04-15T00:30Z] INFO  17:30:56,972 ProgressMeter - Total runtime 28.24 secs, 0.47 min, 0.01 hours
[2016-04-15T00:30Z] INFO  17:30:56,972 MicroScheduler - 26370 reads were filtered out during the traversal out of approximately 382614 total reads (6.89%)
[2016-04-15T00:30Z] INFO  17:30:56,973 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:30Z] INFO  17:30:56,973 MicroScheduler -   -> 633 reads (0.17% of total) failing BadMateFilter
[2016-04-15T00:30Z] INFO  17:30:56,973 MicroScheduler -   -> 25518 reads (6.67% of total) failing DuplicateReadFilter
[2016-04-15T00:30Z] INFO  17:30:56,974 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:30Z] INFO  17:30:56,974 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:30Z] INFO  17:30:56,974 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:30Z] INFO  17:30:56,975 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:30Z] INFO  17:30:56,975 MicroScheduler -   -> 219 reads (0.06% of total) failing UnmappedReadFilter
[2016-04-15T00:30Z] INFO  17:30:57,886 ProgressMeter -            done    678904.0    25.0 s      37.0 s      100.0%    25.0 s       0.0 s
[2016-04-15T00:30Z] INFO  17:30:57,886 ProgressMeter - Total runtime 25.55 secs, 0.43 min, 0.01 hours
[2016-04-15T00:30Z] INFO  17:30:57,887 MicroScheduler - 23253 reads were filtered out during the traversal out of approximately 295252 total reads (7.88%)
[2016-04-15T00:30Z] INFO  17:30:57,887 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:30Z] INFO  17:30:57,887 MicroScheduler -   -> 506 reads (0.17% of total) failing BadMateFilter
[2016-04-15T00:30Z] INFO  17:30:57,888 MicroScheduler -   -> 22565 reads (7.64% of total) failing DuplicateReadFilter
[2016-04-15T00:30Z] INFO  17:30:57,888 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:30Z] INFO  17:30:57,891 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:30Z] INFO  17:30:57,892 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:30Z] INFO  17:30:57,892 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:30Z] INFO  17:30:57,893 MicroScheduler -   -> 182 reads (0.06% of total) failing UnmappedReadFilter
[2016-04-15T00:30Z] INFO  17:30:58,217 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:30Z] INFO  17:30:58,221 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:30Z] INFO  17:30:58,221 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:30Z] INFO  17:30:58,222 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:30Z] INFO  17:30:58,226 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/11/R14-18106_kapa-NGv3-PE100-NGv3-sort-11_47158866_62678572-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/11/R14-18106_kapa-NGv3-PE100-NGv3-11_47158866_62678572-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/11/tx/tmpK2U3hW/R14-18106_kapa-NGv3-PE100-NGv3-11_47158866_62678572.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:30Z] INFO  17:30:58,257 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:30Z] INFO  17:30:58,267 HelpFormatter - Date/Time: 2016/04/14 17:30:58
[2016-04-15T00:30Z] INFO  17:30:58,268 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:30Z] INFO  17:30:58,269 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:30Z] INFO  17:30:58,422 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:30Z] INFO  17:30:58,550 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:30Z] INFO  17:30:58,569 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:30Z] INFO  17:30:58,646 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:30Z] INFO  17:30:58,656 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:30Z] INFO  17:30:58,737 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-15T00:30Z] GATK: UnifiedGenotyper
[2016-04-15T00:30Z] GATK: UnifiedGenotyper
[2016-04-15T00:30Z] INFO  17:30:59,162 ProgressMeter -            done    405882.0    20.0 s      50.0 s      100.0%    20.0 s       0.0 s
[2016-04-15T00:30Z] INFO  17:30:59,162 ProgressMeter - Total runtime 20.60 secs, 0.34 min, 0.01 hours
[2016-04-15T00:30Z] INFO  17:30:59,163 MicroScheduler - 17581 reads were filtered out during the traversal out of approximately 244556 total reads (7.19%)
[2016-04-15T00:30Z] INFO  17:30:59,163 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:30Z] INFO  17:30:59,164 MicroScheduler -   -> 382 reads (0.16% of total) failing BadMateFilter
[2016-04-15T00:30Z] INFO  17:30:59,164 MicroScheduler -   -> 17049 reads (6.97% of total) failing DuplicateReadFilter
[2016-04-15T00:30Z] INFO  17:30:59,164 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:30Z] INFO  17:30:59,164 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:30Z] INFO  17:30:59,165 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:30Z] INFO  17:30:59,165 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:30Z] INFO  17:30:59,165 MicroScheduler -   -> 150 reads (0.06% of total) failing UnmappedReadFilter
[2016-04-15T00:30Z] INFO  17:30:59,189 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:30Z] INFO  17:30:59,191 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:30Z] INFO  17:30:59,191 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:30Z] INFO  17:30:59,192 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:30Z] INFO  17:30:59,195 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/11/R14-18106_kapa-NGv3-PE100-NGv3-sort-11_62744265_78270665-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/11/R14-18106_kapa-NGv3-PE100-NGv3-11_62744265_78270665-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/11/tx/tmpBL2hkX/R14-18106_kapa-NGv3-PE100-NGv3-11_62744265_78270665.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:30Z] INFO  17:30:59,206 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:30Z] INFO  17:30:59,206 HelpFormatter - Date/Time: 2016/04/14 17:30:59
[2016-04-15T00:30Z] INFO  17:30:59,206 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:30Z] INFO  17:30:59,207 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:30Z] INFO  17:30:59,239 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:30Z] INFO  17:30:59,263 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:30Z] INFO  17:30:59,266 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:30Z] INFO  17:30:59,267 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:30Z] INFO  17:30:59,267 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:30Z] INFO  17:30:59,272 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/11/R14-18106_kapa-NGv3-PE100-NGv3-sort-11_78277177_93796886-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/11/R14-18106_kapa-NGv3-PE100-NGv3-11_78277177_93796886-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/11/tx/tmpcKNqdL/R14-18106_kapa-NGv3-PE100-NGv3-11_78277177_93796886.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:30Z] INFO  17:30:59,282 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:30Z] INFO  17:30:59,286 IntervalUtils - Processing 330540 bp from intervals
[2016-04-15T00:30Z] WARN  17:30:59,293 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:30Z] INFO  17:30:59,293 HelpFormatter - Date/Time: 2016/04/14 17:30:59
[2016-04-15T00:30Z] INFO  17:30:59,294 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:30Z] INFO  17:30:59,295 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:30Z] INFO  17:30:59,376 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:30Z] INFO  17:30:59,439 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:30Z] INFO  17:30:59,452 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:30Z] INFO  17:30:59,453 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:30Z] INFO  17:30:59,454 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:30Z] INFO  17:30:59,455 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:30Z] INFO  17:30:59,487 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:30Z] INFO  17:30:59,507 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:30Z] INFO  17:30:59,508 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:30Z] INFO  17:30:59,585 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:30Z] INFO  17:30:59,588 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:30Z] INFO  17:30:59,589 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:30Z] INFO  17:30:59,589 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:30Z] INFO  17:30:59,601 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/11/R14-18106_kapa-NGv3-PE100-NGv3-sort-11_93797496_109964158-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/11/R14-18106_kapa-NGv3-PE100-NGv3-11_93797496_109964158-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/11/tx/tmpVnyfnk/R14-18106_kapa-NGv3-PE100-NGv3-11_93797496_109964158.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:30Z] GATK: UnifiedGenotyper
[2016-04-15T00:30Z] INFO  17:30:59,635 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:30Z] INFO  17:30:59,643 HelpFormatter - Date/Time: 2016/04/14 17:30:59
[2016-04-15T00:30Z] INFO  17:30:59,644 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:30Z] INFO  17:30:59,644 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:30Z] INFO  17:30:59,692 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:30Z] INFO  17:30:59,695 ProgressMeter -            done    459685.0    18.0 s      39.0 s       99.9%    18.0 s       0.0 s
[2016-04-15T00:30Z] INFO  17:30:59,695 ProgressMeter - Total runtime 18.37 secs, 0.31 min, 0.01 hours
[2016-04-15T00:30Z] INFO  17:30:59,696 MicroScheduler - 14581 reads were filtered out during the traversal out of approximately 190099 total reads (7.67%)
[2016-04-15T00:30Z] INFO  17:30:59,696 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:30Z] INFO  17:30:59,696 MicroScheduler -   -> 323 reads (0.17% of total) failing BadMateFilter
[2016-04-15T00:30Z] INFO  17:30:59,697 MicroScheduler -   -> 14152 reads (7.44% of total) failing DuplicateReadFilter
[2016-04-15T00:30Z] INFO  17:30:59,697 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:30Z] INFO  17:30:59,697 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:30Z] INFO  17:30:59,697 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:30Z] INFO  17:30:59,698 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:30Z] INFO  17:30:59,698 MicroScheduler -   -> 106 reads (0.06% of total) failing UnmappedReadFilter
[2016-04-15T00:30Z] INFO  17:30:59,702 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:30Z] INFO  17:30:59,709 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:30Z] INFO  17:30:59,718 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:30Z] INFO  17:30:59,783 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-15T00:30Z] INFO  17:30:59,797 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.10
[2016-04-15T00:30Z] INFO  17:30:59,838 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:31Z] INFO  17:31:00,070 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:31Z] INFO  17:31:00,089 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:31Z] INFO  17:31:00,176 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.09
[2016-04-15T00:31Z] INFO  17:31:00,192 IntervalUtils - Processing 119993 bp from intervals
[2016-04-15T00:31Z] WARN  17:31:00,197 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:31Z] INFO  17:31:00,295 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:31Z] INFO  17:31:00,345 IntervalUtils - Processing 515206 bp from intervals
[2016-04-15T00:31Z] WARN  17:31:00,354 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:31Z] INFO  17:31:00,381 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:31Z] INFO  17:31:00,381 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:31Z] INFO  17:31:00,382 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:31Z] INFO  17:31:00,382 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:31Z] INFO  17:31:00,432 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:31Z] INFO  17:31:00,469 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:31Z] INFO  17:31:00,469 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:31Z] INFO  17:31:00,521 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:31Z] INFO  17:31:00,523 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:31Z] INFO  17:31:00,524 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:31Z] INFO  17:31:00,525 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:31Z] INFO  17:31:00,525 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:31Z] INFO  17:31:00,629 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:31Z] INFO  17:31:00,630 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:31Z] INFO  17:31:00,641 IntervalUtils - Processing 148585 bp from intervals
[2016-04-15T00:31Z] WARN  17:31:00,650 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:31Z] INFO  17:31:00,733 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:31Z] GATK: UnifiedGenotyper
[2016-04-15T00:31Z] INFO  17:31:00,841 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:31Z] INFO  17:31:00,853 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:31Z] INFO  17:31:00,854 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:31Z] INFO  17:31:00,854 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:31Z] INFO  17:31:00,941 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:31Z] INFO  17:31:00,942 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:31Z] INFO  17:31:01,215 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:31Z] GATK: UnifiedGenotyper
[2016-04-15T00:31Z] INFO  17:31:01,923 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:31Z] INFO  17:31:01,933 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:31Z] INFO  17:31:01,934 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:31Z] INFO  17:31:01,934 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:31Z] INFO  17:31:01,939 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/11/R14-18106_kapa-NGv3-PE100-NGv3-sort-11_110001730_125514538-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/11/R14-18106_kapa-NGv3-PE100-NGv3-11_110001730_125514538-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/11/tx/tmpnXo6dn/R14-18106_kapa-NGv3-PE100-NGv3-11_110001730_125514538.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:31Z] INFO  17:31:01,958 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:31Z] INFO  17:31:01,959 HelpFormatter - Date/Time: 2016/04/14 17:31:01
[2016-04-15T00:31Z] INFO  17:31:01,959 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:31Z] INFO  17:31:01,960 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:31Z] INFO  17:31:01,992 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:31Z] INFO  17:31:01,995 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:31Z] INFO  17:31:01,996 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:31Z] INFO  17:31:01,996 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:31Z] INFO  17:31:02,001 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/11/R14-18106_kapa-NGv3-PE100-NGv3-sort-11_125523640_135006516-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/11/R14-18106_kapa-NGv3-PE100-NGv3-11_125523640_135006516-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/11/tx/tmpcF6myI/R14-18106_kapa-NGv3-PE100-NGv3-11_125523640_135006516.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:31Z] INFO  17:31:02,040 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:31Z] INFO  17:31:02,043 HelpFormatter - Date/Time: 2016/04/14 17:31:01
[2016-04-15T00:31Z] INFO  17:31:02,044 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:31Z] INFO  17:31:02,044 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:31Z] INFO  17:31:02,166 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:31Z] INFO  17:31:02,321 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:31Z] INFO  17:31:02,355 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:31Z] INFO  17:31:02,384 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:31Z] INFO  17:31:02,382 ProgressMeter -     9:136383996   1284437.0    30.0 s      23.0 s       56.0%    53.0 s      23.0 s
[2016-04-15T00:31Z] INFO  17:31:02,485 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.10
[2016-04-15T00:31Z] INFO  17:31:02,572 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:31Z] INFO  17:31:02,593 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:31Z] INFO  17:31:02,655 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-15T00:31Z] INFO  17:31:02,719 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:31Z] INFO  17:31:02,723 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:31Z] INFO  17:31:02,724 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:31Z] INFO  17:31:02,724 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:31Z] INFO  17:31:02,729 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/12/R14-18106_kapa-NGv3-PE100-NGv3-sort-12_0_15637181-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/12/R14-18106_kapa-NGv3-PE100-NGv3-12_0_15637181-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/12/tx/tmp36Gty0/R14-18106_kapa-NGv3-PE100-NGv3-12_0_15637181.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:31Z] INFO  17:31:02,745 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:31Z] INFO  17:31:02,746 HelpFormatter - Date/Time: 2016/04/14 17:31:02
[2016-04-15T00:31Z] INFO  17:31:02,746 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:31Z] INFO  17:31:02,747 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:31Z] INFO  17:31:02,981 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:31Z] INFO  17:31:03,036 IntervalUtils - Processing 318135 bp from intervals
[2016-04-15T00:31Z] WARN  17:31:03,041 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:31Z] INFO  17:31:03,181 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:31Z] INFO  17:31:03,237 IntervalUtils - Processing 106404 bp from intervals
[2016-04-15T00:31Z] WARN  17:31:03,244 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:31Z] INFO  17:31:03,245 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:31Z] INFO  17:31:03,254 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:31Z] INFO  17:31:03,344 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:31Z] INFO  17:31:03,345 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:31Z] INFO  17:31:03,346 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:31Z] INFO  17:31:03,347 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:31Z] INFO  17:31:03,350 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.09
[2016-04-15T00:31Z] INFO  17:31:03,386 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:31Z] INFO  17:31:03,391 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:31Z] INFO  17:31:03,392 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:31Z] INFO  17:31:03,451 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:31Z] INFO  17:31:03,455 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:31Z] INFO  17:31:03,455 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:31Z] INFO  17:31:03,456 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:31Z] INFO  17:31:03,460 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/12/R14-18106_kapa-NGv3-PE100-NGv3-sort-12_15650178_31231471-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/12/R14-18106_kapa-NGv3-PE100-NGv3-12_15650178_31231471-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/12/tx/tmpvzUUnb/R14-18106_kapa-NGv3-PE100-NGv3-12_15650178_31231471.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:31Z] INFO  17:31:03,473 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:31Z] INFO  17:31:03,474 HelpFormatter - Date/Time: 2016/04/14 17:31:03
[2016-04-15T00:31Z] INFO  17:31:03,474 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:31Z] INFO  17:31:03,475 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:31Z] INFO  17:31:03,503 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:31Z] INFO  17:31:03,504 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:31Z] INFO  17:31:03,505 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:31Z] INFO  17:31:03,505 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:31Z] INFO  17:31:03,589 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:31Z] INFO  17:31:03,590 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:31Z] INFO  17:31:03,639 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:31Z] INFO  17:31:03,787 IntervalUtils - Processing 329920 bp from intervals
[2016-04-15T00:31Z] WARN  17:31:03,796 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:31Z] INFO  17:31:03,839 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:31Z] INFO  17:31:03,848 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:31Z] INFO  17:31:03,915 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:31Z] INFO  17:31:03,924 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-15T00:31Z] INFO  17:31:04,076 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:31Z] INFO  17:31:04,076 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:31Z] INFO  17:31:04,077 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:31Z] INFO  17:31:04,077 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:31Z] INFO  17:31:04,141 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:31Z] INFO  17:31:04,142 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:31Z] INFO  17:31:04,313 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:31Z] INFO  17:31:04,316 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:31Z] INFO  17:31:04,317 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:31Z] INFO  17:31:04,317 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:31Z] INFO  17:31:04,322 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/12/R14-18106_kapa-NGv3-PE100-NGv3-sort-12_31236746_46754992-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/12/R14-18106_kapa-NGv3-PE100-NGv3-12_31236746_46754992-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/12/tx/tmpNQGtCI/R14-18106_kapa-NGv3-PE100-NGv3-12_31236746_46754992.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:31Z] INFO  17:31:04,360 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:31Z] INFO  17:31:04,360 HelpFormatter - Date/Time: 2016/04/14 17:31:04
[2016-04-15T00:31Z] INFO  17:31:04,361 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:31Z] INFO  17:31:04,361 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:31Z] INFO  17:31:04,456 IntervalUtils - Processing 134686 bp from intervals
[2016-04-15T00:31Z] WARN  17:31:04,472 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:31Z] INFO  17:31:04,566 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:31Z] INFO  17:31:04,615 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:31Z] INFO  17:31:04,649 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:31Z] INFO  17:31:04,650 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:31Z] INFO  17:31:04,651 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:31Z] INFO  17:31:04,651 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:31Z] INFO  17:31:04,744 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:31Z] INFO  17:31:04,745 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:31Z] INFO  17:31:04,813 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:31Z] INFO  17:31:04,822 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:31Z] INFO  17:31:04,913 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.09
[2016-04-15T00:31Z] INFO  17:31:05,274 IntervalUtils - Processing 136917 bp from intervals
[2016-04-15T00:31Z] WARN  17:31:05,279 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:31Z] INFO  17:31:05,384 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:31Z] INFO  17:31:05,463 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:31Z] INFO  17:31:05,464 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:31Z] INFO  17:31:05,464 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:31Z] INFO  17:31:05,465 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:31Z] INFO  17:31:05,528 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:31Z] INFO  17:31:05,529 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:31Z] INFO  17:31:06,866 ProgressMeter -            done    818570.0    27.0 s      33.0 s      100.0%    27.0 s       0.0 s
[2016-04-15T00:31Z] INFO  17:31:06,867 ProgressMeter - Total runtime 27.36 secs, 0.46 min, 0.01 hours
[2016-04-15T00:31Z] INFO  17:31:06,867 MicroScheduler - 23853 reads were filtered out during the traversal out of approximately 301396 total reads (7.91%)
[2016-04-15T00:31Z] INFO  17:31:06,868 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:31Z] INFO  17:31:06,868 MicroScheduler -   -> 469 reads (0.16% of total) failing BadMateFilter
[2016-04-15T00:31Z] INFO  17:31:06,868 MicroScheduler -   -> 23185 reads (7.69% of total) failing DuplicateReadFilter
[2016-04-15T00:31Z] INFO  17:31:06,868 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:31Z] INFO  17:31:06,869 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:31Z] INFO  17:31:06,869 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:31Z] INFO  17:31:06,869 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:31Z] INFO  17:31:06,869 MicroScheduler -   -> 199 reads (0.07% of total) failing UnmappedReadFilter
[2016-04-15T00:31Z] INFO  17:31:07,018 ProgressMeter -            done    665309.0    23.0 s      36.0 s      100.0%    23.0 s       0.0 s
[2016-04-15T00:31Z] INFO  17:31:07,019 ProgressMeter - Total runtime 23.99 secs, 0.40 min, 0.01 hours
[2016-04-15T00:31Z] INFO  17:31:07,019 MicroScheduler - 20796 reads were filtered out during the traversal out of approximately 258907 total reads (8.03%)
[2016-04-15T00:31Z] INFO  17:31:07,019 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:31Z] INFO  17:31:07,020 MicroScheduler -   -> 468 reads (0.18% of total) failing BadMateFilter
[2016-04-15T00:31Z] INFO  17:31:07,020 MicroScheduler -   -> 20156 reads (7.79% of total) failing DuplicateReadFilter
[2016-04-15T00:31Z] INFO  17:31:07,020 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:31Z] INFO  17:31:07,020 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:31Z] INFO  17:31:07,021 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:31Z] INFO  17:31:07,021 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:31Z] INFO  17:31:07,021 MicroScheduler -   -> 172 reads (0.07% of total) failing UnmappedReadFilter
[2016-04-15T00:31Z] INFO  17:31:08,175 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:31Z] INFO  17:31:08,394 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:31Z] GATK: UnifiedGenotyper
[2016-04-15T00:31Z] GATK: UnifiedGenotyper
[2016-04-15T00:31Z] INFO  17:31:08,875 ProgressMeter -            done    449347.0    17.0 s      38.0 s      100.0%    17.0 s       0.0 s
[2016-04-15T00:31Z] INFO  17:31:08,876 ProgressMeter - Total runtime 17.10 secs, 0.29 min, 0.00 hours
[2016-04-15T00:31Z] INFO  17:31:08,876 MicroScheduler - 13277 reads were filtered out during the traversal out of approximately 169045 total reads (7.85%)
[2016-04-15T00:31Z] INFO  17:31:08,876 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:31Z] INFO  17:31:08,877 MicroScheduler -   -> 306 reads (0.18% of total) failing BadMateFilter
[2016-04-15T00:31Z] INFO  17:31:08,877 MicroScheduler -   -> 12867 reads (7.61% of total) failing DuplicateReadFilter
[2016-04-15T00:31Z] INFO  17:31:08,877 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:31Z] INFO  17:31:08,877 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:31Z] INFO  17:31:08,878 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:31Z] INFO  17:31:08,878 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:31Z] INFO  17:31:08,878 MicroScheduler -   -> 104 reads (0.06% of total) failing UnmappedReadFilter
[2016-04-15T00:31Z] INFO  17:31:10,329 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:31Z] GATK: UnifiedGenotyper
[2016-04-15T00:31Z] INFO  17:31:11,708 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:31Z] INFO  17:31:11,711 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:31Z] INFO  17:31:11,712 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:31Z] INFO  17:31:11,712 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:31Z] INFO  17:31:11,717 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/12/R14-18106_kapa-NGv3-PE100-NGv3-sort-12_46756066_62654284-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/12/R14-18106_kapa-NGv3-PE100-NGv3-12_46756066_62654284-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/12/tx/tmpgASOJS/R14-18106_kapa-NGv3-PE100-NGv3-12_46756066_62654284.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:31Z] INFO  17:31:11,738 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:31Z] INFO  17:31:11,738 HelpFormatter - Date/Time: 2016/04/14 17:31:11
[2016-04-15T00:31Z] INFO  17:31:11,738 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:31Z] INFO  17:31:11,738 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:31Z] INFO  17:31:11,769 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:31Z] INFO  17:31:11,772 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:31Z] INFO  17:31:11,772 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:31Z] INFO  17:31:11,773 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:31Z] INFO  17:31:11,778 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/12/R14-18106_kapa-NGv3-PE100-NGv3-sort-12_62687959_78225484-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/12/R14-18106_kapa-NGv3-PE100-NGv3-12_62687959_78225484-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/12/tx/tmpq_oP0L/R14-18106_kapa-NGv3-PE100-NGv3-12_62687959_78225484.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:31Z] INFO  17:31:11,789 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:31Z] INFO  17:31:11,794 HelpFormatter - Date/Time: 2016/04/14 17:31:11
[2016-04-15T00:31Z] INFO  17:31:11,795 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:31Z] INFO  17:31:11,796 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:31Z] INFO  17:31:11,946 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:31Z] INFO  17:31:11,998 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:31Z] INFO  17:31:12,141 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:31Z] INFO  17:31:12,153 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:31Z] INFO  17:31:12,211 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:31Z] INFO  17:31:12,233 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:31Z] INFO  17:31:12,257 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.10
[2016-04-15T00:31Z] INFO  17:31:12,332 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.10
[2016-04-15T00:31Z] INFO  17:31:12,429 ProgressMeter -    10:105145183   1140017.0    30.0 s      26.0 s       85.8%    34.0 s       4.0 s
[2016-04-15T00:31Z] INFO  17:31:12,767 IntervalUtils - Processing 146919 bp from intervals
[2016-04-15T00:31Z] WARN  17:31:12,771 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:31Z] INFO  17:31:12,887 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:31Z] INFO  17:31:12,899 IntervalUtils - Processing 504306 bp from intervals
[2016-04-15T00:31Z] WARN  17:31:12,916 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:31Z] INFO  17:31:12,977 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:31Z] INFO  17:31:12,978 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:31Z] INFO  17:31:12,979 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:31Z] INFO  17:31:12,980 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:31Z] INFO  17:31:13,024 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:31Z] INFO  17:31:13,044 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:31Z] INFO  17:31:13,045 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:31Z] INFO  17:31:13,127 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:31Z] INFO  17:31:13,128 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:31Z] INFO  17:31:13,129 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:31Z] INFO  17:31:13,129 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:31Z] INFO  17:31:13,175 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:31Z] INFO  17:31:13,176 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:31Z] INFO  17:31:13,573 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:31Z] INFO  17:31:13,576 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:31Z] INFO  17:31:13,577 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:31Z] INFO  17:31:13,578 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:31Z] INFO  17:31:13,582 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/12/R14-18106_kapa-NGv3-PE100-NGv3-sort-12_78334098_93863131-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/12/R14-18106_kapa-NGv3-PE100-NGv3-12_78334098_93863131-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/12/tx/tmpWvZBbQ/R14-18106_kapa-NGv3-PE100-NGv3-12_78334098_93863131.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:31Z] INFO  17:31:13,618 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:31Z] INFO  17:31:13,618 HelpFormatter - Date/Time: 2016/04/14 17:31:13
[2016-04-15T00:31Z] INFO  17:31:13,618 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:31Z] INFO  17:31:13,618 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:31Z] INFO  17:31:13,899 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:31Z] INFO  17:31:14,188 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:31Z] INFO  17:31:14,210 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:31Z] INFO  17:31:14,295 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-15T00:31Z] INFO  17:31:14,746 IntervalUtils - Processing 88957 bp from intervals
[2016-04-15T00:31Z] WARN  17:31:14,762 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:31Z] INFO  17:31:14,769 ProgressMeter -            done    576314.0    18.0 s      31.0 s      100.0%    18.0 s       0.0 s
[2016-04-15T00:31Z] INFO  17:31:14,770 ProgressMeter - Total runtime 18.32 secs, 0.31 min, 0.01 hours
[2016-04-15T00:31Z] INFO  17:31:14,770 MicroScheduler - 16061 reads were filtered out during the traversal out of approximately 198824 total reads (8.08%)
[2016-04-15T00:31Z] INFO  17:31:14,770 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:31Z] INFO  17:31:14,771 MicroScheduler -   -> 307 reads (0.15% of total) failing BadMateFilter
[2016-04-15T00:31Z] INFO  17:31:14,771 MicroScheduler -   -> 15628 reads (7.86% of total) failing DuplicateReadFilter
[2016-04-15T00:31Z] INFO  17:31:14,771 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:31Z] INFO  17:31:14,771 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:31Z] INFO  17:31:14,772 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:31Z] INFO  17:31:14,772 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:31Z] INFO  17:31:14,772 MicroScheduler -   -> 126 reads (0.06% of total) failing UnmappedReadFilter
[2016-04-15T00:31Z] INFO  17:31:14,857 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:31Z] INFO  17:31:14,938 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:31Z] INFO  17:31:14,939 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:31Z] INFO  17:31:14,939 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:31Z] INFO  17:31:14,940 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:31Z] INFO  17:31:15,032 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:31Z] INFO  17:31:15,033 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:31Z] INFO  17:31:15,941 ProgressMeter -            done    278160.0    15.0 s      55.0 s      100.0%    15.0 s       0.0 s
[2016-04-15T00:31Z] INFO  17:31:15,943 ProgressMeter - Total runtime 15.56 secs, 0.26 min, 0.00 hours
[2016-04-15T00:31Z] INFO  17:31:15,943 MicroScheduler - 11531 reads were filtered out during the traversal out of approximately 150384 total reads (7.67%)
[2016-04-15T00:31Z] INFO  17:31:15,944 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:31Z] INFO  17:31:15,945 MicroScheduler -   -> 256 reads (0.17% of total) failing BadMateFilter
[2016-04-15T00:31Z] INFO  17:31:15,946 MicroScheduler -   -> 11187 reads (7.44% of total) failing DuplicateReadFilter
[2016-04-15T00:31Z] INFO  17:31:15,946 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:31Z] INFO  17:31:15,947 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:31Z] INFO  17:31:15,948 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:31Z] INFO  17:31:15,949 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:31Z] INFO  17:31:15,950 MicroScheduler -   -> 88 reads (0.06% of total) failing UnmappedReadFilter
[2016-04-15T00:31Z] INFO  17:31:16,059 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:31Z] INFO  17:31:16,185 ProgressMeter -            done   1324132.0    33.0 s      25.0 s      100.0%    33.0 s       0.0 s
[2016-04-15T00:31Z] INFO  17:31:16,185 ProgressMeter - Total runtime 33.78 secs, 0.56 min, 0.01 hours
[2016-04-15T00:31Z] INFO  17:31:16,186 MicroScheduler - 33579 reads were filtered out during the traversal out of approximately 423790 total reads (7.92%)
[2016-04-15T00:31Z] INFO  17:31:16,186 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:31Z] INFO  17:31:16,187 MicroScheduler -   -> 730 reads (0.17% of total) failing BadMateFilter
[2016-04-15T00:31Z] INFO  17:31:16,187 MicroScheduler -   -> 32593 reads (7.69% of total) failing DuplicateReadFilter
[2016-04-15T00:31Z] INFO  17:31:16,187 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:31Z] INFO  17:31:16,188 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:31Z] INFO  17:31:16,188 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:31Z] INFO  17:31:16,188 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:31Z] INFO  17:31:16,189 MicroScheduler -   -> 256 reads (0.06% of total) failing UnmappedReadFilter
[2016-04-15T00:31Z] GATK: UnifiedGenotyper
[2016-04-15T00:31Z] INFO  17:31:17,520 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:31Z] GATK: UnifiedGenotyper
[2016-04-15T00:31Z] INFO  17:31:17,842 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:31Z] INFO  17:31:17,935 ProgressMeter -            done    400167.0    17.0 s      42.0 s      100.0%    17.0 s       0.0 s
[2016-04-15T00:31Z] INFO  17:31:17,936 ProgressMeter - Total runtime 17.08 secs, 0.28 min, 0.00 hours
[2016-04-15T00:31Z] INFO  17:31:17,936 MicroScheduler - 12160 reads were filtered out during the traversal out of approximately 156921 total reads (7.75%)
[2016-04-15T00:31Z] INFO  17:31:17,936 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:31Z] INFO  17:31:17,936 MicroScheduler -   -> 251 reads (0.16% of total) failing BadMateFilter
[2016-04-15T00:31Z] INFO  17:31:17,937 MicroScheduler -   -> 11807 reads (7.52% of total) failing DuplicateReadFilter
[2016-04-15T00:31Z] INFO  17:31:17,937 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:31Z] INFO  17:31:17,937 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:31Z] INFO  17:31:17,937 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:31Z] INFO  17:31:17,938 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:31Z] INFO  17:31:17,938 MicroScheduler -   -> 102 reads (0.07% of total) failing UnmappedReadFilter
[2016-04-15T00:31Z] GATK: UnifiedGenotyper
[2016-04-15T00:31Z] INFO  17:31:18,797 ProgressMeter -            done    387169.0    15.0 s      39.0 s       99.9%    15.0 s       0.0 s
[2016-04-15T00:31Z] INFO  17:31:18,798 ProgressMeter - Total runtime 15.29 secs, 0.25 min, 0.00 hours
[2016-04-15T00:31Z] INFO  17:31:18,798 MicroScheduler - 11376 reads were filtered out during the traversal out of approximately 142868 total reads (7.96%)
[2016-04-15T00:31Z] INFO  17:31:18,798 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:31Z] INFO  17:31:18,798 MicroScheduler -   -> 258 reads (0.18% of total) failing BadMateFilter
[2016-04-15T00:31Z] INFO  17:31:18,799 MicroScheduler -   -> 11020 reads (7.71% of total) failing DuplicateReadFilter
[2016-04-15T00:31Z] INFO  17:31:18,799 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:31Z] INFO  17:31:18,799 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:31Z] INFO  17:31:18,799 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:31Z] INFO  17:31:18,800 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:31Z] INFO  17:31:18,800 MicroScheduler -   -> 98 reads (0.07% of total) failing UnmappedReadFilter
[2016-04-15T00:31Z] INFO  17:31:19,124 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:31Z] INFO  17:31:19,127 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:31Z] INFO  17:31:19,127 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:31Z] INFO  17:31:19,127 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:31Z] INFO  17:31:19,131 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/12/R14-18106_kapa-NGv3-PE100-NGv3-sort-12_93870729_109490566-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/12/R14-18106_kapa-NGv3-PE100-NGv3-12_93870729_109490566-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/12/tx/tmp6fVquW/R14-18106_kapa-NGv3-PE100-NGv3-12_93870729_109490566.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:31Z] INFO  17:31:19,140 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:31Z] INFO  17:31:19,141 HelpFormatter - Date/Time: 2016/04/14 17:31:19
[2016-04-15T00:31Z] INFO  17:31:19,142 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:31Z] INFO  17:31:19,142 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:31Z] INFO  17:31:19,283 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:31Z] INFO  17:31:19,346 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:31Z] INFO  17:31:19,492 ProgressMeter -      11:6231480   1346638.0    30.0 s      22.0 s       55.3%    54.0 s      24.0 s
[2016-04-15T00:31Z] INFO  17:31:19,517 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:31Z] INFO  17:31:19,526 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:31Z] INFO  17:31:19,608 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-15T00:31Z] GATK: UnifiedGenotyper
[2016-04-15T00:31Z] INFO  17:31:19,972 IntervalUtils - Processing 201796 bp from intervals
[2016-04-15T00:31Z] WARN  17:31:19,980 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:31Z] INFO  17:31:20,064 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:31Z] INFO  17:31:20,143 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:31Z] INFO  17:31:20,144 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:31Z] INFO  17:31:20,145 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:31Z] INFO  17:31:20,146 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:31Z] INFO  17:31:20,186 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:31Z] INFO  17:31:20,187 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:31Z] INFO  17:31:20,291 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:31Z] INFO  17:31:20,388 ProgressMeter -            done    352890.0    15.0 s      44.0 s      100.0%    15.0 s       0.0 s
[2016-04-15T00:31Z] INFO  17:31:20,388 ProgressMeter - Total runtime 15.74 secs, 0.26 min, 0.00 hours
[2016-04-15T00:31Z] INFO  17:31:20,389 MicroScheduler - 10313 reads were filtered out during the traversal out of approximately 132005 total reads (7.81%)
[2016-04-15T00:31Z] INFO  17:31:20,389 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:31Z] INFO  17:31:20,389 MicroScheduler -   -> 223 reads (0.17% of total) failing BadMateFilter
[2016-04-15T00:31Z] INFO  17:31:20,389 MicroScheduler -   -> 10002 reads (7.58% of total) failing DuplicateReadFilter
[2016-04-15T00:31Z] INFO  17:31:20,390 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:31Z] INFO  17:31:20,390 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:31Z] INFO  17:31:20,390 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:31Z] INFO  17:31:20,390 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:31Z] INFO  17:31:20,391 MicroScheduler -   -> 88 reads (0.07% of total) failing UnmappedReadFilter
[2016-04-15T00:31Z] GATK: UnifiedGenotyper
[2016-04-15T00:31Z] INFO  17:31:20,824 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:31Z] INFO  17:31:20,827 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:31Z] INFO  17:31:20,828 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:31Z] INFO  17:31:20,829 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:31Z] INFO  17:31:20,834 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/12/R14-18106_kapa-NGv3-PE100-NGv3-sort-12_109494486_125263132-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/12/R14-18106_kapa-NGv3-PE100-NGv3-12_109494486_125263132-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/12/tx/tmppNN_39/R14-18106_kapa-NGv3-PE100-NGv3-12_109494486_125263132.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:31Z] INFO  17:31:20,863 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:31Z] INFO  17:31:20,863 HelpFormatter - Date/Time: 2016/04/14 17:31:20
[2016-04-15T00:31Z] INFO  17:31:20,863 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:31Z] INFO  17:31:20,864 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:31Z] INFO  17:31:21,004 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:31Z] INFO  17:31:21,008 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:31Z] INFO  17:31:21,008 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:31Z] INFO  17:31:21,009 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:31Z] INFO  17:31:21,015 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/12/R14-18106_kapa-NGv3-PE100-NGv3-sort-12_125267228_133851895-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/12/R14-18106_kapa-NGv3-PE100-NGv3-12_125267228_133851895-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/12/tx/tmpnztLF7/R14-18106_kapa-NGv3-PE100-NGv3-12_125267228_133851895.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:31Z] INFO  17:31:21,025 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:31Z] INFO  17:31:21,037 HelpFormatter - Date/Time: 2016/04/14 17:31:21
[2016-04-15T00:31Z] INFO  17:31:21,038 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:31Z] INFO  17:31:21,039 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:31Z] INFO  17:31:21,121 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:31Z] INFO  17:31:21,209 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:31Z] INFO  17:31:21,427 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:31Z] INFO  17:31:21,438 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:31Z] INFO  17:31:21,518 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:31Z] INFO  17:31:21,523 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-15T00:31Z] INFO  17:31:21,529 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:31Z] INFO  17:31:21,608 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-15T00:31Z] INFO  17:31:21,635 ProgressMeter -            done   2509744.0    49.0 s      19.0 s      100.0%    49.0 s       0.0 s
[2016-04-15T00:31Z] INFO  17:31:21,636 ProgressMeter - Total runtime 49.26 secs, 0.82 min, 0.01 hours
[2016-04-15T00:31Z] INFO  17:31:21,636 MicroScheduler - 54966 reads were filtered out during the traversal out of approximately 674417 total reads (8.15%)
[2016-04-15T00:31Z] INFO  17:31:21,636 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:31Z] INFO  17:31:21,637 MicroScheduler -   -> 1227 reads (0.18% of total) failing BadMateFilter
[2016-04-15T00:31Z] INFO  17:31:21,637 MicroScheduler -   -> 53316 reads (7.91% of total) failing DuplicateReadFilter
[2016-04-15T00:31Z] INFO  17:31:21,637 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:31Z] INFO  17:31:21,638 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:31Z] INFO  17:31:21,638 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:31Z] INFO  17:31:21,638 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:31Z] INFO  17:31:21,638 MicroScheduler -   -> 423 reads (0.06% of total) failing UnmappedReadFilter
[2016-04-15T00:31Z] INFO  17:31:21,766 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:31Z] INFO  17:31:21,950 IntervalUtils - Processing 364987 bp from intervals
[2016-04-15T00:31Z] WARN  17:31:21,956 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:31Z] INFO  17:31:22,020 IntervalUtils - Processing 106872 bp from intervals
[2016-04-15T00:31Z] INFO  17:31:22,023 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:31Z] WARN  17:31:22,025 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:31Z] GATK: UnifiedGenotyper
[2016-04-15T00:31Z] INFO  17:31:22,117 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:31Z] INFO  17:31:22,138 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:31Z] INFO  17:31:22,140 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:31Z] INFO  17:31:22,140 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:31Z] INFO  17:31:22,141 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:31Z] INFO  17:31:22,166 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:31Z] INFO  17:31:22,167 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:31Z] INFO  17:31:22,168 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:31Z] INFO  17:31:22,169 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:31Z] INFO  17:31:22,218 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:31Z] INFO  17:31:22,219 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:31Z] INFO  17:31:22,277 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:31Z] INFO  17:31:22,277 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:31Z] INFO  17:31:22,408 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:31Z] INFO  17:31:22,411 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:31Z] INFO  17:31:22,412 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:31Z] INFO  17:31:22,412 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:31Z] INFO  17:31:22,417 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/13/R14-18106_kapa-NGv3-PE100-NGv3-sort-13_0_19748299-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/13/R14-18106_kapa-NGv3-PE100-NGv3-13_0_19748299-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/13/tx/tmpBXAElQ/R14-18106_kapa-NGv3-PE100-NGv3-13_0_19748299.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:31Z] INFO  17:31:22,463 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:31Z] INFO  17:31:22,471 HelpFormatter - Date/Time: 2016/04/14 17:31:22
[2016-04-15T00:31Z] INFO  17:31:22,471 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:31Z] INFO  17:31:22,472 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:31Z] INFO  17:31:22,669 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:31Z] INFO  17:31:22,808 ProgressMeter -            done    441963.0    17.0 s      39.0 s       99.9%    17.0 s       0.0 s
[2016-04-15T00:31Z] INFO  17:31:22,820 ProgressMeter - Total runtime 17.36 secs, 0.29 min, 0.00 hours
[2016-04-15T00:31Z] INFO  17:31:22,822 MicroScheduler - 13550 reads were filtered out during the traversal out of approximately 170602 total reads (7.94%)
[2016-04-15T00:31Z] INFO  17:31:22,823 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:31Z] INFO  17:31:22,823 MicroScheduler -   -> 280 reads (0.16% of total) failing BadMateFilter
[2016-04-15T00:31Z] INFO  17:31:22,824 MicroScheduler -   -> 13148 reads (7.71% of total) failing DuplicateReadFilter
[2016-04-15T00:31Z] INFO  17:31:22,825 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:31Z] INFO  17:31:22,826 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:31Z] INFO  17:31:22,826 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:31Z] INFO  17:31:22,827 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:31Z] INFO  17:31:22,828 MicroScheduler -   -> 122 reads (0.07% of total) failing UnmappedReadFilter
[2016-04-15T00:31Z] INFO  17:31:22,904 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:31Z] INFO  17:31:22,918 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:31Z] INFO  17:31:22,996 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-15T00:31Z] INFO  17:31:23,216 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:31Z] INFO  17:31:23,440 IntervalUtils - Processing 297 bp from intervals
[2016-04-15T00:31Z] WARN  17:31:23,457 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:31Z] GATK: UnifiedGenotyper
[2016-04-15T00:31Z] INFO  17:31:23,592 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:31Z] INFO  17:31:23,597 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:31Z] INFO  17:31:23,598 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:31Z] INFO  17:31:23,599 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:31Z] INFO  17:31:23,599 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:31Z] INFO  17:31:23,605 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/13/R14-18106_kapa-NGv3-PE100-NGv3-sort-13_19751066_35517251-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/13/R14-18106_kapa-NGv3-PE100-NGv3-13_19751066_35517251-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/13/tx/tmp9BlUmK/R14-18106_kapa-NGv3-PE100-NGv3-13_19751066_35517251.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:31Z] INFO  17:31:23,615 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:31Z] INFO  17:31:23,626 HelpFormatter - Date/Time: 2016/04/14 17:31:23
[2016-04-15T00:31Z] INFO  17:31:23,627 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:31Z] INFO  17:31:23,628 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:31Z] INFO  17:31:23,630 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:31Z] INFO  17:31:23,631 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:31Z] INFO  17:31:23,643 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:31Z] INFO  17:31:23,644 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:31Z] INFO  17:31:23,732 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:31Z] INFO  17:31:23,733 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:31Z] INFO  17:31:23,837 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:31Z] INFO  17:31:24,128 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:31Z] INFO  17:31:24,137 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:31Z] INFO  17:31:24,227 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.09
[2016-04-15T00:31Z] INFO  17:31:24,348 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:31Z] GATK: UnifiedGenotyper
[2016-04-15T00:31Z] INFO  17:31:24,759 IntervalUtils - Processing 201552 bp from intervals
[2016-04-15T00:31Z] WARN  17:31:24,781 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:31Z] INFO  17:31:24,917 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:31Z] INFO  17:31:25,020 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:31Z] INFO  17:31:25,020 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:31Z] INFO  17:31:25,021 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:31Z] INFO  17:31:25,021 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:31Z] INFO  17:31:25,043 ProgressMeter -            done       297.0     1.0 s      79.1 m       67.3%     1.0 s       0.0 s
[2016-04-15T00:31Z] INFO  17:31:25,043 ProgressMeter - Total runtime 1.41 secs, 0.02 min, 0.00 hours
[2016-04-15T00:31Z] INFO  17:31:25,044 MicroScheduler - 60 reads were filtered out during the traversal out of approximately 851 total reads (7.05%)
[2016-04-15T00:31Z] INFO  17:31:25,044 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:31Z] INFO  17:31:25,044 MicroScheduler -   -> 0 reads (0.00% of total) failing BadMateFilter
[2016-04-15T00:31Z] INFO  17:31:25,044 MicroScheduler -   -> 59 reads (6.93% of total) failing DuplicateReadFilter
[2016-04-15T00:31Z] INFO  17:31:25,045 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:31Z] INFO  17:31:25,045 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:31Z] INFO  17:31:25,045 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:31Z] INFO  17:31:25,046 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:31Z] INFO  17:31:25,046 MicroScheduler -   -> 1 reads (0.12% of total) failing UnmappedReadFilter
[2016-04-15T00:31Z] INFO  17:31:25,083 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:31Z] INFO  17:31:25,084 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:31Z] INFO  17:31:25,213 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:31Z] INFO  17:31:25,217 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:31Z] INFO  17:31:25,217 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:31Z] INFO  17:31:25,218 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:31Z] INFO  17:31:25,223 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/13/R14-18106_kapa-NGv3-PE100-NGv3-sort-13_35615069_51287376-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/13/R14-18106_kapa-NGv3-PE100-NGv3-13_35615069_51287376-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/13/tx/tmpi0yS44/R14-18106_kapa-NGv3-PE100-NGv3-13_35615069_51287376.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:31Z] INFO  17:31:25,239 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:31Z] INFO  17:31:25,239 HelpFormatter - Date/Time: 2016/04/14 17:31:25
[2016-04-15T00:31Z] INFO  17:31:25,239 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:31Z] INFO  17:31:25,240 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:31Z] INFO  17:31:25,441 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:31Z] INFO  17:31:25,721 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:31Z] INFO  17:31:25,730 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:31Z] INFO  17:31:25,821 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.09
[2016-04-15T00:31Z] INFO  17:31:25,847 ProgressMeter -            done    243833.0    10.0 s      44.0 s       99.9%    10.0 s       0.0 s
[2016-04-15T00:31Z] INFO  17:31:25,847 ProgressMeter - Total runtime 10.91 secs, 0.18 min, 0.00 hours
[2016-04-15T00:31Z] INFO  17:31:25,848 MicroScheduler - 6465 reads were filtered out during the traversal out of approximately 82201 total reads (7.86%)
[2016-04-15T00:31Z] INFO  17:31:25,848 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:31Z] INFO  17:31:25,848 MicroScheduler -   -> 141 reads (0.17% of total) failing BadMateFilter
[2016-04-15T00:31Z] INFO  17:31:25,849 MicroScheduler -   -> 6274 reads (7.63% of total) failing DuplicateReadFilter
[2016-04-15T00:31Z] INFO  17:31:25,849 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:31Z] INFO  17:31:25,849 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:31Z] INFO  17:31:25,849 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:31Z] INFO  17:31:25,850 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:31Z] INFO  17:31:25,850 MicroScheduler -   -> 50 reads (0.06% of total) failing UnmappedReadFilter
[2016-04-15T00:31Z] INFO  17:31:26,382 IntervalUtils - Processing 179232 bp from intervals
[2016-04-15T00:31Z] WARN  17:31:26,387 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:31Z] INFO  17:31:26,400 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:31Z] INFO  17:31:26,403 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:31Z] INFO  17:31:26,404 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:31Z] INFO  17:31:26,404 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:31Z] INFO  17:31:26,409 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/13/R14-18106_kapa-NGv3-PE100-NGv3-sort-13_51396767_67205543-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/13/R14-18106_kapa-NGv3-PE100-NGv3-13_51396767_67205543-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/13/tx/tmpMpjZ6l/R14-18106_kapa-NGv3-PE100-NGv3-13_51396767_67205543.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:31Z] INFO  17:31:26,434 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:31Z] INFO  17:31:26,442 HelpFormatter - Date/Time: 2016/04/14 17:31:26
[2016-04-15T00:31Z] INFO  17:31:26,445 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:31Z] INFO  17:31:26,446 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:31Z] INFO  17:31:26,551 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:31Z] INFO  17:31:26,611 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:31Z] INFO  17:31:26,642 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:31Z] INFO  17:31:26,651 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:31Z] INFO  17:31:26,652 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:31Z] INFO  17:31:26,653 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:31Z] INFO  17:31:26,654 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:31Z] INFO  17:31:26,702 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:31Z] INFO  17:31:26,703 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:31Z] GATK: UnifiedGenotyper
[2016-04-15T00:31Z] INFO  17:31:26,847 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:31Z] INFO  17:31:26,867 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:31Z] INFO  17:31:26,949 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-15T00:31Z] INFO  17:31:27,278 IntervalUtils - Processing 59966 bp from intervals
[2016-04-15T00:31Z] WARN  17:31:27,282 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:31Z] INFO  17:31:27,340 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:31Z] INFO  17:31:27,385 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:31Z] INFO  17:31:27,471 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:31Z] INFO  17:31:27,472 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:31Z] INFO  17:31:27,473 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:31Z] INFO  17:31:27,471 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:31Z] INFO  17:31:27,474 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:31Z] INFO  17:31:27,483 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:31Z] INFO  17:31:27,483 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:31Z] INFO  17:31:27,483 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:31Z] INFO  17:31:27,487 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/13/R14-18106_kapa-NGv3-PE100-NGv3-sort-13_67477635_84455642-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/13/R14-18106_kapa-NGv3-PE100-NGv3-13_67477635_84455642-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/13/tx/tmp0kHeAw/R14-18106_kapa-NGv3-PE100-NGv3-13_67477635_84455642.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:31Z] INFO  17:31:27,509 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:31Z] INFO  17:31:27,509 HelpFormatter - Date/Time: 2016/04/14 17:31:27
[2016-04-15T00:31Z] INFO  17:31:27,509 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:31Z] INFO  17:31:27,510 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:31Z] GATK: UnifiedGenotyper
[2016-04-15T00:31Z] INFO  17:31:27,550 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:31Z] INFO  17:31:27,561 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:31Z] INFO  17:31:27,681 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:31Z] INFO  17:31:27,942 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:31Z] INFO  17:31:27,961 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:31Z] INFO  17:31:28,067 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.11
[2016-04-15T00:31Z] INFO  17:31:28,576 IntervalUtils - Processing 69582 bp from intervals
[2016-04-15T00:31Z] WARN  17:31:28,582 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:31Z] INFO  17:31:28,706 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:31Z] INFO  17:31:28,773 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:31Z] INFO  17:31:28,774 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:31Z] INFO  17:31:28,775 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:31Z] INFO  17:31:28,776 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:31Z] INFO  17:31:28,834 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:31Z] INFO  17:31:28,834 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:31Z] INFO  17:31:28,951 ProgressMeter -            done    406794.0    15.0 s      39.0 s      100.0%    15.0 s       0.0 s
[2016-04-15T00:31Z] INFO  17:31:28,951 ProgressMeter - Total runtime 15.97 secs, 0.27 min, 0.00 hours
[2016-04-15T00:31Z] INFO  17:31:28,951 MicroScheduler - 11793 reads were filtered out during the traversal out of approximately 150015 total reads (7.86%)
[2016-04-15T00:31Z] INFO  17:31:28,952 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:31Z] INFO  17:31:28,952 MicroScheduler -   -> 274 reads (0.18% of total) failing BadMateFilter
[2016-04-15T00:31Z] INFO  17:31:28,952 MicroScheduler -   -> 11411 reads (7.61% of total) failing DuplicateReadFilter
[2016-04-15T00:31Z] INFO  17:31:28,952 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:31Z] INFO  17:31:28,953 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:31Z] INFO  17:31:28,953 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:31Z] INFO  17:31:28,953 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:31Z] INFO  17:31:28,954 MicroScheduler -   -> 108 reads (0.07% of total) failing UnmappedReadFilter
[2016-04-15T00:31Z] INFO  17:31:29,477 ProgressMeter -     11:61906185    945071.0    30.0 s      31.0 s       80.2%    37.0 s       7.0 s
[2016-04-15T00:31Z] INFO  17:31:29,842 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:31Z] INFO  17:31:29,845 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:31Z] INFO  17:31:29,846 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:31Z] INFO  17:31:29,846 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:31Z] INFO  17:31:29,851 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/13/R14-18106_kapa-NGv3-PE100-NGv3-sort-13_86368117_101881935-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/13/R14-18106_kapa-NGv3-PE100-NGv3-13_86368117_101881935-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/13/tx/tmp3OsJSc/R14-18106_kapa-NGv3-PE100-NGv3-13_86368117_101881935.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:31Z] INFO  17:31:29,870 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:31Z] INFO  17:31:29,878 HelpFormatter - Date/Time: 2016/04/14 17:31:29
[2016-04-15T00:31Z] INFO  17:31:29,879 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:31Z] INFO  17:31:29,879 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:31Z] INFO  17:31:30,075 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:31Z] INFO  17:31:30,280 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:31Z] INFO  17:31:30,289 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:31Z] INFO  17:31:30,322 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:31Z] INFO  17:31:30,369 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-15T00:31Z] INFO  17:31:30,372 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:31Z] INFO  17:31:30,375 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:31Z] INFO  17:31:30,375 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:31Z] INFO  17:31:30,376 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:31Z] INFO  17:31:30,381 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/13/R14-18106_kapa-NGv3-PE100-NGv3-sort-13_101890105_115169878-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/13/R14-18106_kapa-NGv3-PE100-NGv3-13_101890105_115169878-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/13/tx/tmpyDUvBO/R14-18106_kapa-NGv3-PE100-NGv3-13_101890105_115169878.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:31Z] INFO  17:31:30,393 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:31Z] INFO  17:31:30,394 HelpFormatter - Date/Time: 2016/04/14 17:31:30
[2016-04-15T00:31Z] INFO  17:31:30,394 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:31Z] INFO  17:31:30,395 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:31Z] INFO  17:31:30,550 ProgressMeter -     11:67173066   1797861.0    30.0 s      16.0 s       52.3%    57.0 s      27.0 s
[2016-04-15T00:31Z] INFO  17:31:30,605 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:31Z] GATK: UnifiedGenotyper
[2016-04-15T00:31Z] INFO  17:31:30,744 IntervalUtils - Processing 75123 bp from intervals
[2016-04-15T00:31Z] WARN  17:31:30,767 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:31Z] INFO  17:31:30,900 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:31Z] INFO  17:31:30,915 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:31Z] INFO  17:31:30,925 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:31Z] INFO  17:31:30,971 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:31Z] INFO  17:31:30,972 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:31Z] INFO  17:31:30,973 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:31Z] INFO  17:31:30,974 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:31Z] INFO  17:31:31,012 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.09
[2016-04-15T00:31Z] INFO  17:31:31,037 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:31Z] INFO  17:31:31,038 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:31Z] INFO  17:31:31,624 IntervalUtils - Processing 144481 bp from intervals
[2016-04-15T00:31Z] WARN  17:31:31,628 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:31Z] INFO  17:31:31,724 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:31Z] INFO  17:31:31,809 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:31Z] INFO  17:31:31,834 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:31Z] INFO  17:31:31,834 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:31Z] INFO  17:31:31,835 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:31Z] INFO  17:31:31,919 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:31Z] INFO  17:31:31,920 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:31Z] INFO  17:31:33,370 ProgressMeter -    11:123886882   1131977.0    30.0 s      26.0 s       84.6%    35.0 s       5.0 s
[2016-04-15T00:31Z] INFO  17:31:33,628 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:31Z] INFO  17:31:33,631 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:31Z] INFO  17:31:33,631 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:31Z] INFO  17:31:33,631 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:31Z] INFO  17:31:33,635 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/14/R14-18106_kapa-NGv3-PE100-NGv3-sort-14_0_19378574-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/14/R14-18106_kapa-NGv3-PE100-NGv3-14_0_19378574-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/14/tx/tmpj4dqMe/R14-18106_kapa-NGv3-PE100-NGv3-14_0_19378574.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:31Z] INFO  17:31:33,664 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:31Z] INFO  17:31:33,665 HelpFormatter - Date/Time: 2016/04/14 17:31:33
[2016-04-15T00:31Z] INFO  17:31:33,666 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:31Z] INFO  17:31:33,667 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:31Z] INFO  17:31:33,929 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:31Z] INFO  17:31:34,110 ProgressMeter -     12:10373239   1143348.0    30.0 s      26.0 s       77.6%    38.0 s       8.0 s
[2016-04-15T00:31Z] INFO  17:31:34,140 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:31Z] INFO  17:31:34,152 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:31Z] INFO  17:31:34,204 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-15T00:31Z] INFO  17:31:34,519 IntervalUtils - Processing 981 bp from intervals
[2016-04-15T00:31Z] WARN  17:31:34,536 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:31Z] INFO  17:31:34,657 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:31Z] INFO  17:31:34,693 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:31Z] INFO  17:31:34,693 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:31Z] INFO  17:31:34,694 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:31Z] INFO  17:31:34,694 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:31Z] INFO  17:31:34,779 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:31Z] INFO  17:31:34,779 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:31Z] INFO  17:31:35,191 ProgressMeter -            done   1302582.0    35.0 s      27.0 s      100.0%    35.0 s       0.0 s
[2016-04-15T00:31Z] INFO  17:31:35,192 ProgressMeter - Total runtime 35.74 secs, 0.60 min, 0.01 hours
[2016-04-15T00:31Z] INFO  17:31:35,192 MicroScheduler - 36614 reads were filtered out during the traversal out of approximately 459054 total reads (7.98%)
[2016-04-15T00:31Z] INFO  17:31:35,193 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:31Z] INFO  17:31:35,193 MicroScheduler -   -> 804 reads (0.18% of total) failing BadMateFilter
[2016-04-15T00:31Z] INFO  17:31:35,193 MicroScheduler -   -> 35507 reads (7.73% of total) failing DuplicateReadFilter
[2016-04-15T00:31Z] INFO  17:31:35,193 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:31Z] INFO  17:31:35,194 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:31Z] INFO  17:31:35,194 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:31Z] INFO  17:31:35,194 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:31Z] INFO  17:31:35,195 MicroScheduler -   -> 303 reads (0.07% of total) failing UnmappedReadFilter
[2016-04-15T00:31Z] INFO  17:31:36,346 ProgressMeter -            done   2117017.0    46.0 s      22.0 s      100.0%    46.0 s       0.0 s
[2016-04-15T00:31Z] INFO  17:31:36,348 ProgressMeter - Total runtime 46.87 secs, 0.78 min, 0.01 hours
[2016-04-15T00:31Z] INFO  17:31:36,348 MicroScheduler - 58067 reads were filtered out during the traversal out of approximately 678207 total reads (8.56%)
[2016-04-15T00:31Z] INFO  17:31:36,348 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:31Z] INFO  17:31:36,349 MicroScheduler -   -> 1229 reads (0.18% of total) failing BadMateFilter
[2016-04-15T00:31Z] INFO  17:31:36,349 MicroScheduler -   -> 56284 reads (8.30% of total) failing DuplicateReadFilter
[2016-04-15T00:31Z] INFO  17:31:36,349 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:31Z] INFO  17:31:36,350 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:31Z] INFO  17:31:36,350 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:31Z] INFO  17:31:36,350 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:31Z] INFO  17:31:36,350 MicroScheduler -   -> 554 reads (0.08% of total) failing UnmappedReadFilter
[2016-04-15T00:31Z] INFO  17:31:36,730 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:31Z] GATK: UnifiedGenotyper
[2016-04-15T00:31Z] INFO  17:31:37,420 ProgressMeter -            done       981.0     2.0 s      46.3 m       91.7%     2.0 s       0.0 s
[2016-04-15T00:31Z] INFO  17:31:37,421 ProgressMeter - Total runtime 2.73 secs, 0.05 min, 0.00 hours
[2016-04-15T00:31Z] INFO  17:31:37,422 MicroScheduler - 223 reads were filtered out during the traversal out of approximately 3386 total reads (6.59%)
[2016-04-15T00:31Z] INFO  17:31:37,422 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:31Z] INFO  17:31:37,422 MicroScheduler -   -> 6 reads (0.18% of total) failing BadMateFilter
[2016-04-15T00:31Z] INFO  17:31:37,423 MicroScheduler -   -> 215 reads (6.35% of total) failing DuplicateReadFilter
[2016-04-15T00:31Z] INFO  17:31:37,423 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:31Z] INFO  17:31:37,423 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:31Z] INFO  17:31:37,424 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:31Z] INFO  17:31:37,424 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:31Z] INFO  17:31:37,425 MicroScheduler -   -> 2 reads (0.06% of total) failing UnmappedReadFilter
[2016-04-15T00:31Z] INFO  17:31:37,559 ProgressMeter -            done    370183.0    15.0 s      41.0 s      100.0%    15.0 s       0.0 s
[2016-04-15T00:31Z] INFO  17:31:37,560 ProgressMeter - Total runtime 15.39 secs, 0.26 min, 0.00 hours
[2016-04-15T00:31Z] INFO  17:31:37,560 MicroScheduler - 13267 reads were filtered out during the traversal out of approximately 166659 total reads (7.96%)
[2016-04-15T00:31Z] INFO  17:31:37,560 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:31Z] INFO  17:31:37,561 MicroScheduler -   -> 291 reads (0.17% of total) failing BadMateFilter
[2016-04-15T00:31Z] INFO  17:31:37,561 MicroScheduler -   -> 12859 reads (7.72% of total) failing DuplicateReadFilter
[2016-04-15T00:31Z] INFO  17:31:37,561 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:31Z] INFO  17:31:37,561 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:31Z] INFO  17:31:37,562 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:31Z] INFO  17:31:37,562 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:31Z] INFO  17:31:37,562 MicroScheduler -   -> 117 reads (0.07% of total) failing UnmappedReadFilter
[2016-04-15T00:31Z] INFO  17:31:37,629 ProgressMeter -            done    144034.0    10.0 s      70.0 s      100.0%    10.0 s       0.0 s
[2016-04-15T00:31Z] INFO  17:31:37,630 ProgressMeter - Total runtime 10.16 secs, 0.17 min, 0.00 hours
[2016-04-15T00:31Z] INFO  17:31:37,631 MicroScheduler - 5974 reads were filtered out during the traversal out of approximately 82923 total reads (7.20%)
[2016-04-15T00:31Z] INFO  17:31:37,632 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:31Z] INFO  17:31:37,632 MicroScheduler -   -> 152 reads (0.18% of total) failing BadMateFilter
[2016-04-15T00:31Z] INFO  17:31:37,633 MicroScheduler -   -> 5772 reads (6.96% of total) failing DuplicateReadFilter
[2016-04-15T00:31Z] INFO  17:31:37,633 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:31Z] INFO  17:31:37,634 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:31Z] INFO  17:31:37,634 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:31Z] INFO  17:31:37,634 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:31Z] INFO  17:31:37,634 MicroScheduler -   -> 50 reads (0.06% of total) failing UnmappedReadFilter
[2016-04-15T00:31Z] INFO  17:31:37,797 ProgressMeter -            done   1335468.0    34.0 s      25.0 s      100.0%    34.0 s       0.0 s
[2016-04-15T00:31Z] INFO  17:31:37,798 ProgressMeter - Total runtime 34.45 secs, 0.57 min, 0.01 hours
[2016-04-15T00:31Z] INFO  17:31:37,798 MicroScheduler - 33817 reads were filtered out during the traversal out of approximately 427988 total reads (7.90%)
[2016-04-15T00:31Z] INFO  17:31:37,799 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:31Z] INFO  17:31:37,799 MicroScheduler -   -> 731 reads (0.17% of total) failing BadMateFilter
[2016-04-15T00:31Z] INFO  17:31:37,799 MicroScheduler -   -> 32841 reads (7.67% of total) failing DuplicateReadFilter
[2016-04-15T00:31Z] INFO  17:31:37,800 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:31Z] INFO  17:31:37,800 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:31Z] INFO  17:31:37,800 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:31Z] INFO  17:31:37,800 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:31Z] INFO  17:31:37,801 MicroScheduler -   -> 245 reads (0.06% of total) failing UnmappedReadFilter
[2016-04-15T00:31Z] INFO  17:31:37,955 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:31Z] GATK: UnifiedGenotyper
[2016-04-15T00:31Z] INFO  17:31:38,624 ProgressMeter -            done    188528.0     9.0 s      52.0 s       99.9%     9.0 s       0.0 s
[2016-04-15T00:31Z] INFO  17:31:38,624 ProgressMeter - Total runtime 9.85 secs, 0.16 min, 0.00 hours
[2016-04-15T00:31Z] INFO  17:31:38,624 MicroScheduler - 5558 reads were filtered out during the traversal out of approximately 73392 total reads (7.57%)
[2016-04-15T00:31Z] INFO  17:31:38,625 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:31Z] INFO  17:31:38,625 MicroScheduler -   -> 123 reads (0.17% of total) failing BadMateFilter
[2016-04-15T00:31Z] INFO  17:31:38,626 MicroScheduler -   -> 5394 reads (7.35% of total) failing DuplicateReadFilter
[2016-04-15T00:31Z] INFO  17:31:38,626 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:31Z] INFO  17:31:38,626 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:31Z] INFO  17:31:38,626 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:31Z] INFO  17:31:38,627 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:31Z] INFO  17:31:38,627 MicroScheduler -   -> 41 reads (0.06% of total) failing UnmappedReadFilter
[2016-04-15T00:31Z] INFO  17:31:38,862 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:31Z] INFO  17:31:39,030 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:31Z] INFO  17:31:39,038 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:31Z] INFO  17:31:39,132 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:31Z] GATK: UnifiedGenotyper
[2016-04-15T00:31Z] GATK: UnifiedGenotyper
[2016-04-15T00:31Z] GATK: UnifiedGenotyper
[2016-04-15T00:31Z] GATK: UnifiedGenotyper
[2016-04-15T00:31Z] INFO  17:31:40,135 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:31Z] INFO  17:31:40,139 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:31Z] INFO  17:31:40,140 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:31Z] INFO  17:31:40,140 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:31Z] INFO  17:31:40,146 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/14/R14-18106_kapa-NGv3-PE100-NGv3-sort-14_19553416_35066851-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/14/R14-18106_kapa-NGv3-PE100-NGv3-14_19553416_35066851-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/14/tx/tmpYK3SiH/R14-18106_kapa-NGv3-PE100-NGv3-14_19553416_35066851.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:31Z] INFO  17:31:40,157 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:31Z] INFO  17:31:40,159 HelpFormatter - Date/Time: 2016/04/14 17:31:40
[2016-04-15T00:31Z] INFO  17:31:40,159 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:31Z] INFO  17:31:40,160 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:31Z] INFO  17:31:40,201 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:31Z] INFO  17:31:40,401 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:31Z] GATK: UnifiedGenotyper
[2016-04-15T00:31Z] INFO  17:31:40,610 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:31Z] INFO  17:31:40,619 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:31Z] INFO  17:31:40,690 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-15T00:31Z] INFO  17:31:41,218 ProgressMeter -            done   1314044.0    37.0 s      28.0 s      100.0%    37.0 s       0.0 s
[2016-04-15T00:31Z] INFO  17:31:41,218 ProgressMeter - Total runtime 37.14 secs, 0.62 min, 0.01 hours
[2016-04-15T00:31Z] INFO  17:31:41,219 MicroScheduler - 35074 reads were filtered out during the traversal out of approximately 443778 total reads (7.90%)
[2016-04-15T00:31Z] INFO  17:31:41,219 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:31Z] INFO  17:31:41,219 MicroScheduler -   -> 742 reads (0.17% of total) failing BadMateFilter
[2016-04-15T00:31Z] INFO  17:31:41,219 MicroScheduler -   -> 34047 reads (7.67% of total) failing DuplicateReadFilter
[2016-04-15T00:31Z] INFO  17:31:41,220 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:31Z] INFO  17:31:41,220 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:31Z] INFO  17:31:41,220 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:31Z] INFO  17:31:41,220 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:31Z] INFO  17:31:41,221 MicroScheduler -   -> 285 reads (0.06% of total) failing UnmappedReadFilter
[2016-04-15T00:31Z] INFO  17:31:41,238 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:31Z] INFO  17:31:41,241 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:31Z] INFO  17:31:41,242 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:31Z] INFO  17:31:41,243 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:31Z] INFO  17:31:41,248 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/14/R14-18106_kapa-NGv3-PE100-NGv3-sort-14_35072553_50583270-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/14/R14-18106_kapa-NGv3-PE100-NGv3-14_35072553_50583270-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/14/tx/tmpaj14t7/R14-18106_kapa-NGv3-PE100-NGv3-14_35072553_50583270.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:31Z] INFO  17:31:41,262 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:31Z] INFO  17:31:41,273 HelpFormatter - Date/Time: 2016/04/14 17:31:41
[2016-04-15T00:31Z] INFO  17:31:41,274 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:31Z] INFO  17:31:41,275 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:31Z] INFO  17:31:41,291 IntervalUtils - Processing 291951 bp from intervals
[2016-04-15T00:31Z] WARN  17:31:41,297 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:31Z] INFO  17:31:41,431 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:31Z] INFO  17:31:41,479 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:31Z] INFO  17:31:41,554 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:31Z] INFO  17:31:41,555 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:31Z] INFO  17:31:41,556 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:31Z] INFO  17:31:41,557 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:31Z] INFO  17:31:41,629 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:31Z] INFO  17:31:41,631 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:31Z] INFO  17:31:41,703 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:31Z] INFO  17:31:41,712 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:31Z] INFO  17:31:41,771 ProgressMeter -            done    596495.0    21.0 s      36.0 s      100.0%    21.0 s       0.0 s
[2016-04-15T00:31Z] INFO  17:31:41,771 ProgressMeter - Total runtime 21.63 secs, 0.36 min, 0.01 hours
[2016-04-15T00:31Z] INFO  17:31:41,772 MicroScheduler - 18208 reads were filtered out during the traversal out of approximately 230478 total reads (7.90%)
[2016-04-15T00:31Z] INFO  17:31:41,772 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:31Z] INFO  17:31:41,772 MicroScheduler -   -> 377 reads (0.16% of total) failing BadMateFilter
[2016-04-15T00:31Z] INFO  17:31:41,773 MicroScheduler -   -> 17715 reads (7.69% of total) failing DuplicateReadFilter
[2016-04-15T00:31Z] INFO  17:31:41,773 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:31Z] INFO  17:31:41,773 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:31Z] INFO  17:31:41,773 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:31Z] INFO  17:31:41,774 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:31Z] INFO  17:31:41,774 MicroScheduler -   -> 116 reads (0.05% of total) failing UnmappedReadFilter
[2016-04-15T00:31Z] INFO  17:31:41,777 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-15T00:31Z] INFO  17:31:42,176 IntervalUtils - Processing 108903 bp from intervals
[2016-04-15T00:31Z] WARN  17:31:42,182 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:31Z] INFO  17:31:42,256 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:31Z] INFO  17:31:42,288 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:31Z] INFO  17:31:42,291 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:31Z] INFO  17:31:42,291 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:31Z] INFO  17:31:42,292 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:31Z] INFO  17:31:42,296 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/14/R14-18106_kapa-NGv3-PE100-NGv3-sort-14_50585061_66096324-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/14/R14-18106_kapa-NGv3-PE100-NGv3-14_50585061_66096324-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/14/tx/tmp2aRkXJ/R14-18106_kapa-NGv3-PE100-NGv3-14_50585061_66096324.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:31Z] INFO  17:31:42,318 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:31Z] INFO  17:31:42,318 HelpFormatter - Date/Time: 2016/04/14 17:31:42
[2016-04-15T00:31Z] INFO  17:31:42,321 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:31Z] INFO  17:31:42,321 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:31Z] INFO  17:31:42,358 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:31Z] INFO  17:31:42,359 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:31Z] INFO  17:31:42,359 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:31Z] INFO  17:31:42,360 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:31Z] INFO  17:31:42,407 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:31Z] INFO  17:31:42,408 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:31Z] INFO  17:31:42,453 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:31Z] INFO  17:31:42,472 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:31Z] INFO  17:31:42,475 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:31Z] INFO  17:31:42,476 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:31Z] INFO  17:31:42,476 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:31Z] INFO  17:31:42,481 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/14/R14-18106_kapa-NGv3-PE100-NGv3-sort-14_97304098_107349540-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/14/R14-18106_kapa-NGv3-PE100-NGv3-14_97304098_107349540-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/14/tx/tmpxl4kWm/R14-18106_kapa-NGv3-PE100-NGv3-14_97304098_107349540.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:31Z] INFO  17:31:42,491 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:31Z] INFO  17:31:42,502 HelpFormatter - Date/Time: 2016/04/14 17:31:42
[2016-04-15T00:31Z] INFO  17:31:42,503 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:31Z] INFO  17:31:42,504 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:31Z] INFO  17:31:42,661 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:31Z] INFO  17:31:42,665 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:31Z] INFO  17:31:42,665 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:31Z] INFO  17:31:42,666 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:31Z] INFO  17:31:42,671 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/14/R14-18106_kapa-NGv3-PE100-NGv3-sort-14_66135960_81646674-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/14/R14-18106_kapa-NGv3-PE100-NGv3-14_66135960_81646674-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/14/tx/tmpWhdJD4/R14-18106_kapa-NGv3-PE100-NGv3-14_66135960_81646674.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:31Z] INFO  17:31:42,674 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:31Z] INFO  17:31:42,682 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:31Z] INFO  17:31:42,685 HelpFormatter - Date/Time: 2016/04/14 17:31:42
[2016-04-15T00:31Z] INFO  17:31:42,685 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:31Z] INFO  17:31:42,686 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:31Z] INFO  17:31:42,700 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:31Z] INFO  17:31:42,708 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:31Z] INFO  17:31:42,734 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:31Z] INFO  17:31:42,755 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:31Z] INFO  17:31:42,759 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:31Z] INFO  17:31:42,760 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:31Z] INFO  17:31:42,760 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:31Z] INFO  17:31:42,766 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/14/R14-18106_kapa-NGv3-PE100-NGv3-sort-14_81651874_97299968-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/14/R14-18106_kapa-NGv3-PE100-NGv3-14_81651874_97299968-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/14/tx/tmpuaa5_K/R14-18106_kapa-NGv3-PE100-NGv3-14_81651874_97299968.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:31Z] INFO  17:31:42,780 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:31Z] INFO  17:31:42,781 HelpFormatter - Date/Time: 2016/04/14 17:31:42
[2016-04-15T00:31Z] INFO  17:31:42,782 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:31Z] INFO  17:31:42,783 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:31Z] INFO  17:31:42,793 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-15T00:31Z] INFO  17:31:42,841 ProgressMeter -            done    183411.0    11.0 s      64.0 s       99.9%    11.0 s       0.0 s
[2016-04-15T00:31Z] INFO  17:31:42,841 ProgressMeter - Total runtime 11.87 secs, 0.20 min, 0.00 hours
[2016-04-15T00:31Z] INFO  17:31:42,842 MicroScheduler - 7648 reads were filtered out during the traversal out of approximately 94697 total reads (8.08%)
[2016-04-15T00:31Z] INFO  17:31:42,842 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:31Z] INFO  17:31:42,842 MicroScheduler -   -> 191 reads (0.20% of total) failing BadMateFilter
[2016-04-15T00:31Z] INFO  17:31:42,843 MicroScheduler -   -> 7398 reads (7.81% of total) failing DuplicateReadFilter
[2016-04-15T00:31Z] INFO  17:31:42,843 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:31Z] INFO  17:31:42,843 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:31Z] INFO  17:31:42,843 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:31Z] INFO  17:31:42,844 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:31Z] INFO  17:31:42,844 MicroScheduler -   -> 59 reads (0.06% of total) failing UnmappedReadFilter
[2016-04-15T00:31Z] GATK: UnifiedGenotyper
[2016-04-15T00:31Z] INFO  17:31:42,967 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:31Z] INFO  17:31:42,969 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:31Z] INFO  17:31:43,011 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:31Z] INFO  17:31:43,021 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:31Z] INFO  17:31:43,064 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:31Z] INFO  17:31:43,109 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.09
[2016-04-15T00:31Z] INFO  17:31:43,154 ProgressMeter -     12:53875925   1501416.0    30.0 s      19.0 s       54.8%    54.0 s      24.0 s
[2016-04-15T00:31Z] INFO  17:31:43,166 IntervalUtils - Processing 226771 bp from intervals
[2016-04-15T00:31Z] WARN  17:31:43,171 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:31Z] INFO  17:31:43,244 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:31Z] INFO  17:31:43,255 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:31Z] INFO  17:31:43,256 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:31Z] INFO  17:31:43,265 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:31Z] INFO  17:31:43,298 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:31Z] INFO  17:31:43,364 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.11
[2016-04-15T00:31Z] INFO  17:31:43,370 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-15T00:31Z] INFO  17:31:43,375 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:31Z] INFO  17:31:43,387 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:31Z] INFO  17:31:43,388 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:31Z] INFO  17:31:43,389 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:31Z] INFO  17:31:43,467 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:31Z] INFO  17:31:43,478 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:31Z] GATK: UnifiedGenotyper
[2016-04-15T00:31Z] INFO  17:31:43,492 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:31Z] INFO  17:31:43,495 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:31Z] INFO  17:31:43,496 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:31Z] INFO  17:31:43,496 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:31Z] INFO  17:31:43,501 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/15/R14-18106_kapa-NGv3-PE100-NGv3-sort-15_0_20740485-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/15/R14-18106_kapa-NGv3-PE100-NGv3-15_0_20740485-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/15/tx/tmpFrgv6W/R14-18106_kapa-NGv3-PE100-NGv3-15_0_20740485.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:31Z] INFO  17:31:43,523 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:31Z] INFO  17:31:43,524 HelpFormatter - Date/Time: 2016/04/14 17:31:43
[2016-04-15T00:31Z] INFO  17:31:43,525 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:31Z] INFO  17:31:43,525 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:31Z] INFO  17:31:43,554 IntervalUtils - Processing 188545 bp from intervals
[2016-04-15T00:31Z] WARN  17:31:43,559 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:31Z] INFO  17:31:43,629 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:31Z] INFO  17:31:43,719 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:31Z] INFO  17:31:43,722 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:31Z] INFO  17:31:43,723 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:31Z] INFO  17:31:43,724 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:31Z] INFO  17:31:43,725 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:31Z] INFO  17:31:43,815 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:31Z] INFO  17:31:43,816 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:31Z] INFO  17:31:43,926 IntervalUtils - Processing 176504 bp from intervals
[2016-04-15T00:31Z] WARN  17:31:43,932 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:31Z] INFO  17:31:43,946 IntervalUtils - Processing 245410 bp from intervals
[2016-04-15T00:31Z] WARN  17:31:43,950 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:31Z] INFO  17:31:43,954 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:31Z] INFO  17:31:43,963 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:31Z] INFO  17:31:44,030 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:31Z] INFO  17:31:44,044 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-15T00:31Z] INFO  17:31:44,102 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:31Z] INFO  17:31:44,172 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:31Z] INFO  17:31:44,173 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:31Z] INFO  17:31:44,173 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:31Z] INFO  17:31:44,174 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:31Z] INFO  17:31:44,215 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:31Z] INFO  17:31:44,230 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:31Z] INFO  17:31:44,231 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:31Z] INFO  17:31:44,277 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:31Z] INFO  17:31:44,284 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:31Z] INFO  17:31:44,285 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:31Z] INFO  17:31:44,286 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:31Z] INFO  17:31:44,331 IntervalUtils - Processing 989 bp from intervals
[2016-04-15T00:31Z] WARN  17:31:44,336 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:31Z] INFO  17:31:44,375 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:31Z] INFO  17:31:44,375 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:31Z] INFO  17:31:44,409 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:31Z] INFO  17:31:44,451 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:31Z] INFO  17:31:44,451 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:31Z] INFO  17:31:44,452 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:31Z] INFO  17:31:44,452 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:31Z] GATK: UnifiedGenotyper
[2016-04-15T00:31Z] INFO  17:31:44,528 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:31Z] INFO  17:31:44,529 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:31Z] INFO  17:31:45,999 ProgressMeter -            done    469270.0    19.0 s      41.0 s      100.0%    19.0 s       0.0 s
[2016-04-15T00:31Z] INFO  17:31:46,000 ProgressMeter - Total runtime 19.35 secs, 0.32 min, 0.01 hours
[2016-04-15T00:31Z] INFO  17:31:46,000 MicroScheduler - 15790 reads were filtered out during the traversal out of approximately 195914 total reads (8.06%)
[2016-04-15T00:31Z] INFO  17:31:46,001 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:31Z] INFO  17:31:46,001 MicroScheduler -   -> 342 reads (0.17% of total) failing BadMateFilter
[2016-04-15T00:31Z] INFO  17:31:46,001 MicroScheduler -   -> 15345 reads (7.83% of total) failing DuplicateReadFilter
[2016-04-15T00:31Z] INFO  17:31:46,001 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:31Z] INFO  17:31:46,002 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:31Z] INFO  17:31:46,002 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:31Z] INFO  17:31:46,002 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:31Z] INFO  17:31:46,002 MicroScheduler -   -> 103 reads (0.05% of total) failing UnmappedReadFilter
[2016-04-15T00:31Z] INFO  17:31:46,260 ProgressMeter -            done    504383.0    21.0 s      42.0 s      100.0%    21.0 s       0.0 s
[2016-04-15T00:31Z] INFO  17:31:46,261 ProgressMeter - Total runtime 21.24 secs, 0.35 min, 0.01 hours
[2016-04-15T00:31Z] INFO  17:31:46,261 MicroScheduler - 16792 reads were filtered out during the traversal out of approximately 212963 total reads (7.88%)
[2016-04-15T00:31Z] INFO  17:31:46,261 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:31Z] INFO  17:31:46,262 MicroScheduler -   -> 381 reads (0.18% of total) failing BadMateFilter
[2016-04-15T00:31Z] INFO  17:31:46,262 MicroScheduler -   -> 16275 reads (7.64% of total) failing DuplicateReadFilter
[2016-04-15T00:31Z] INFO  17:31:46,262 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:31Z] INFO  17:31:46,262 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:31Z] INFO  17:31:46,263 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:31Z] INFO  17:31:46,263 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:31Z] INFO  17:31:46,263 MicroScheduler -   -> 136 reads (0.06% of total) failing UnmappedReadFilter
[2016-04-15T00:31Z] INFO  17:31:46,512 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:31Z] INFO  17:31:46,516 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:31Z] INFO  17:31:46,516 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:31Z] INFO  17:31:46,517 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:31Z] INFO  17:31:46,521 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/15/R14-18106_kapa-NGv3-PE100-NGv3-sort-15_36887086_52402170-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/15/R14-18106_kapa-NGv3-PE100-NGv3-15_36887086_52402170-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/15/tx/tmpPMfxEJ/R14-18106_kapa-NGv3-PE100-NGv3-15_36887086_52402170.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:31Z] INFO  17:31:46,527 ProgressMeter -            done       989.0     2.0 s      35.0 m       91.0%     2.0 s       0.0 s
[2016-04-15T00:31Z] INFO  17:31:46,527 ProgressMeter - Total runtime 2.08 secs, 0.03 min, 0.00 hours
[2016-04-15T00:31Z] INFO  17:31:46,528 MicroScheduler - 65 reads were filtered out during the traversal out of approximately 1623 total reads (4.00%)
[2016-04-15T00:31Z] INFO  17:31:46,528 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:31Z] INFO  17:31:46,528 MicroScheduler -   -> 7 reads (0.43% of total) failing BadMateFilter
[2016-04-15T00:31Z] INFO  17:31:46,529 MicroScheduler -   -> 56 reads (3.45% of total) failing DuplicateReadFilter
[2016-04-15T00:31Z] INFO  17:31:46,529 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:31Z] INFO  17:31:46,529 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:31Z] INFO  17:31:46,530 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:31Z] INFO  17:31:46,530 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:31Z] INFO  17:31:46,530 MicroScheduler -   -> 2 reads (0.12% of total) failing UnmappedReadFilter
[2016-04-15T00:31Z] INFO  17:31:46,550 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:31Z] INFO  17:31:46,556 HelpFormatter - Date/Time: 2016/04/14 17:31:46
[2016-04-15T00:31Z] INFO  17:31:46,557 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:31Z] INFO  17:31:46,558 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:31Z] INFO  17:31:46,563 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:31Z] INFO  17:31:46,566 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:31Z] INFO  17:31:46,567 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:31Z] INFO  17:31:46,567 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:31Z] INFO  17:31:46,572 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/15/R14-18106_kapa-NGv3-PE100-NGv3-sort-15_20741621_36872162-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/15/R14-18106_kapa-NGv3-PE100-NGv3-15_20741621_36872162-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/15/tx/tmpB0ZxL0/R14-18106_kapa-NGv3-PE100-NGv3-15_20741621_36872162.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:31Z] INFO  17:31:46,581 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:31Z] INFO  17:31:46,581 HelpFormatter - Date/Time: 2016/04/14 17:31:46
[2016-04-15T00:31Z] INFO  17:31:46,582 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:31Z] INFO  17:31:46,582 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:31Z] INFO  17:31:46,731 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:31Z] INFO  17:31:46,763 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:31Z] INFO  17:31:46,961 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:31Z] INFO  17:31:46,983 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:31Z] INFO  17:31:47,022 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:31Z] INFO  17:31:47,046 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:31Z] INFO  17:31:47,095 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.11
[2016-04-15T00:31Z] INFO  17:31:47,154 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.11
[2016-04-15T00:31Z] INFO  17:31:47,615 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:31Z] INFO  17:31:47,618 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:31Z] INFO  17:31:47,619 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:31Z] INFO  17:31:47,620 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:31Z] INFO  17:31:47,624 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/15/R14-18106_kapa-NGv3-PE100-NGv3-sort-15_52404364_67923265-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/15/R14-18106_kapa-NGv3-PE100-NGv3-15_52404364_67923265-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/15/tx/tmp4gO670/R14-18106_kapa-NGv3-PE100-NGv3-15_52404364_67923265.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:31Z] INFO  17:31:47,646 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:31Z] INFO  17:31:47,647 IntervalUtils - Processing 374190 bp from intervals
[2016-04-15T00:31Z] INFO  17:31:47,653 HelpFormatter - Date/Time: 2016/04/14 17:31:47
[2016-04-15T00:31Z] INFO  17:31:47,654 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:31Z] WARN  17:31:47,652 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:31Z] INFO  17:31:47,654 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:31Z] INFO  17:31:47,660 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:31Z] INFO  17:31:47,739 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:31Z] INFO  17:31:47,775 IntervalUtils - Processing 177979 bp from intervals
[2016-04-15T00:31Z] WARN  17:31:47,791 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:31Z] INFO  17:31:47,848 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:31Z] INFO  17:31:47,849 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:31Z] INFO  17:31:47,850 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:31Z] INFO  17:31:47,850 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:31Z] INFO  17:31:47,878 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:31Z] INFO  17:31:47,890 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:31Z] INFO  17:31:47,925 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:31Z] INFO  17:31:47,926 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:31Z] INFO  17:31:47,949 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:31Z] INFO  17:31:47,974 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:31Z] INFO  17:31:47,976 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:31Z] INFO  17:31:47,977 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:31Z] INFO  17:31:47,978 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:31Z] INFO  17:31:48,033 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:31Z] INFO  17:31:48,034 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:31Z] GATK: UnifiedGenotyper
[2016-04-15T00:31Z] INFO  17:31:48,086 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:31Z] INFO  17:31:48,125 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:31Z] INFO  17:31:48,146 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:31Z] INFO  17:31:48,207 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-15T00:31Z] GATK: UnifiedGenotyper
[2016-04-15T00:31Z] GATK: UnifiedGenotyper
[2016-04-15T00:31Z] INFO  17:31:48,719 IntervalUtils - Processing 254619 bp from intervals
[2016-04-15T00:31Z] WARN  17:31:48,725 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:31Z] INFO  17:31:48,823 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:31Z] INFO  17:31:48,909 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:31Z] INFO  17:31:48,911 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:31Z] INFO  17:31:48,911 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:31Z] INFO  17:31:48,912 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:31Z] INFO  17:31:48,958 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:31Z] INFO  17:31:48,959 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:31Z] INFO  17:31:50,288 ProgressMeter -            done    399815.0    18.0 s      46.0 s      100.0%    18.0 s       0.0 s
[2016-04-15T00:31Z] INFO  17:31:50,288 ProgressMeter - Total runtime 18.48 secs, 0.31 min, 0.01 hours
[2016-04-15T00:31Z] INFO  17:31:50,288 MicroScheduler - 14085 reads were filtered out during the traversal out of approximately 177881 total reads (7.92%)
[2016-04-15T00:31Z] INFO  17:31:50,289 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:31Z] INFO  17:31:50,289 MicroScheduler -   -> 322 reads (0.18% of total) failing BadMateFilter
[2016-04-15T00:31Z] INFO  17:31:50,289 MicroScheduler -   -> 13647 reads (7.67% of total) failing DuplicateReadFilter
[2016-04-15T00:31Z] INFO  17:31:50,289 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:31Z] INFO  17:31:50,290 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:31Z] INFO  17:31:50,290 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:31Z] INFO  17:31:50,290 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:31Z] INFO  17:31:50,290 MicroScheduler -   -> 116 reads (0.07% of total) failing UnmappedReadFilter
[2016-04-15T00:31Z] INFO  17:31:51,101 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:31Z] INFO  17:31:51,105 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:31Z] INFO  17:31:51,105 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:31Z] INFO  17:31:51,106 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:31Z] INFO  17:31:51,110 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/15/R14-18106_kapa-NGv3-PE100-NGv3-sort-15_67932890_83447639-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/15/R14-18106_kapa-NGv3-PE100-NGv3-15_67932890_83447639-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/15/tx/tmpV2uRSy/R14-18106_kapa-NGv3-PE100-NGv3-15_67932890_83447639.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:31Z] INFO  17:31:51,156 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:31Z] INFO  17:31:51,157 HelpFormatter - Date/Time: 2016/04/14 17:31:51
[2016-04-15T00:31Z] INFO  17:31:51,157 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:31Z] INFO  17:31:51,158 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:31Z] INFO  17:31:51,347 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:31Z] INFO  17:31:51,417 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:31Z] INFO  17:31:51,420 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:31Z] INFO  17:31:51,421 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:31Z] INFO  17:31:51,421 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:31Z] INFO  17:31:51,426 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/15/R14-18106_kapa-NGv3-PE100-NGv3-sort-15_98984299_102531392-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/15/R14-18106_kapa-NGv3-PE100-NGv3-15_98984299_102531392-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/15/tx/tmpfYEMM_/R14-18106_kapa-NGv3-PE100-NGv3-15_98984299_102531392.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:31Z] INFO  17:31:51,439 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:31Z] INFO  17:31:51,448 HelpFormatter - Date/Time: 2016/04/14 17:31:51
[2016-04-15T00:31Z] INFO  17:31:51,449 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:31Z] INFO  17:31:51,449 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:31Z] INFO  17:31:51,469 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:31Z] INFO  17:31:51,489 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:31Z] INFO  17:31:51,490 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:31Z] INFO  17:31:51,491 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:31Z] INFO  17:31:51,495 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/15/R14-18106_kapa-NGv3-PE100-NGv3-sort-15_83448996_98982979-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/15/R14-18106_kapa-NGv3-PE100-NGv3-15_83448996_98982979-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/15/tx/tmpozcVea/R14-18106_kapa-NGv3-PE100-NGv3-15_83448996_98982979.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:31Z] INFO  17:31:51,522 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:31Z] INFO  17:31:51,523 HelpFormatter - Date/Time: 2016/04/14 17:31:51
[2016-04-15T00:31Z] INFO  17:31:51,524 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:31Z] INFO  17:31:51,524 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:31Z] INFO  17:31:51,586 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:31Z] INFO  17:31:51,599 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:31Z] INFO  17:31:51,653 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:31Z] INFO  17:31:51,651 ProgressMeter -            done   2754858.0    51.0 s      18.0 s      100.0%    51.0 s       0.0 s
[2016-04-15T00:31Z] INFO  17:31:51,651 ProgressMeter - Total runtime 51.13 secs, 0.85 min, 0.01 hours
[2016-04-15T00:31Z] INFO  17:31:51,652 MicroScheduler - 59182 reads were filtered out during the traversal out of approximately 744410 total reads (7.95%)
[2016-04-15T00:31Z] INFO  17:31:51,652 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:31Z] INFO  17:31:51,652 MicroScheduler -   -> 1353 reads (0.18% of total) failing BadMateFilter
[2016-04-15T00:31Z] INFO  17:31:51,652 MicroScheduler -   -> 57333 reads (7.70% of total) failing DuplicateReadFilter
[2016-04-15T00:31Z] INFO  17:31:51,653 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:31Z] INFO  17:31:51,653 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:31Z] INFO  17:31:51,653 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:31Z] INFO  17:31:51,653 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:31Z] INFO  17:31:51,655 MicroScheduler -   -> 496 reads (0.07% of total) failing UnmappedReadFilter
[2016-04-15T00:31Z] INFO  17:31:51,681 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:31Z] INFO  17:31:51,728 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.13
[2016-04-15T00:31Z] INFO  17:31:51,743 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:31Z] INFO  17:31:51,910 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:31Z] INFO  17:31:51,919 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:31Z] INFO  17:31:51,936 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:31Z] INFO  17:31:51,945 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:31Z] INFO  17:31:52,011 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-15T00:31Z] INFO  17:31:52,016 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.10
[2016-04-15T00:31Z] GATK: UnifiedGenotyper
[2016-04-15T00:31Z] INFO  17:31:52,161 ProgressMeter -    12:123214746   1054171.0    30.0 s      28.0 s       81.2%    36.0 s       6.0 s
[2016-04-15T00:31Z] INFO  17:31:52,251 IntervalUtils - Processing 293221 bp from intervals
[2016-04-15T00:31Z] WARN  17:31:52,267 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:31Z] INFO  17:31:52,388 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:31Z] INFO  17:31:52,485 IntervalUtils - Processing 184993 bp from intervals
[2016-04-15T00:31Z] WARN  17:31:52,491 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:31Z] INFO  17:31:52,494 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:31Z] INFO  17:31:52,495 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:31Z] INFO  17:31:52,496 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:31Z] INFO  17:31:52,497 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:31Z] INFO  17:31:52,540 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:31Z] INFO  17:31:52,540 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:31Z] INFO  17:31:52,578 IntervalUtils - Processing 49123 bp from intervals
[2016-04-15T00:31Z] INFO  17:31:52,579 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:31Z] WARN  17:31:52,583 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:31Z] INFO  17:31:52,662 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:31Z] INFO  17:31:52,663 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:31Z] INFO  17:31:52,664 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:31Z] INFO  17:31:52,665 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:31Z] INFO  17:31:52,685 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:31Z] INFO  17:31:52,732 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:31Z] INFO  17:31:52,733 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:31Z] INFO  17:31:52,761 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:31Z] INFO  17:31:52,762 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:31Z] INFO  17:31:52,763 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:31Z] INFO  17:31:52,764 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:31Z] INFO  17:31:52,873 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:31Z] INFO  17:31:52,874 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:31Z] INFO  17:31:53,006 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:31Z] GATK: UnifiedGenotyper
[2016-04-15T00:31Z] INFO  17:31:55,215 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:31Z] INFO  17:31:55,218 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:31Z] INFO  17:31:55,219 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:31Z] INFO  17:31:55,220 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:31Z] INFO  17:31:55,224 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/16/R14-18106_kapa-NGv3-PE100-NGv3-sort-16_0_15528616-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/16/R14-18106_kapa-NGv3-PE100-NGv3-16_0_15528616-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/16/tx/tmpo_jfXf/R14-18106_kapa-NGv3-PE100-NGv3-16_0_15528616.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:31Z] INFO  17:31:55,238 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:31Z] INFO  17:31:55,239 HelpFormatter - Date/Time: 2016/04/14 17:31:55
[2016-04-15T00:31Z] INFO  17:31:55,240 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:31Z] INFO  17:31:55,240 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:31Z] INFO  17:31:55,385 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:31Z] INFO  17:31:55,616 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:31Z] INFO  17:31:55,629 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:31Z] INFO  17:31:55,720 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.09
[2016-04-15T00:31Z] INFO  17:31:56,145 IntervalUtils - Processing 436708 bp from intervals
[2016-04-15T00:31Z] WARN  17:31:56,150 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:31Z] INFO  17:31:56,214 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:31Z] INFO  17:31:56,217 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:31Z] INFO  17:31:56,218 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:31Z] INFO  17:31:56,218 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:31Z] INFO  17:31:56,223 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/16/R14-18106_kapa-NGv3-PE100-NGv3-sort-16_15596122_31106473-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/16/R14-18106_kapa-NGv3-PE100-NGv3-16_15596122_31106473-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/16/tx/tmpvOe1Bw/R14-18106_kapa-NGv3-PE100-NGv3-16_15596122_31106473.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:31Z] INFO  17:31:56,227 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:31Z] INFO  17:31:56,233 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:31Z] INFO  17:31:56,244 HelpFormatter - Date/Time: 2016/04/14 17:31:56
[2016-04-15T00:31Z] INFO  17:31:56,245 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:31Z] INFO  17:31:56,246 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:31Z] INFO  17:31:56,367 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:31Z] INFO  17:31:56,369 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:31Z] INFO  17:31:56,370 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:31Z] INFO  17:31:56,370 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:31Z] INFO  17:31:56,447 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:31Z] INFO  17:31:56,448 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:31Z] INFO  17:31:56,457 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:31Z] INFO  17:31:56,676 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:31Z] INFO  17:31:56,696 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:31Z] INFO  17:31:56,771 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-15T00:31Z] INFO  17:31:57,140 ProgressMeter -            done    291019.0    14.0 s      50.0 s       99.9%    14.0 s       0.0 s
[2016-04-15T00:31Z] INFO  17:31:57,141 ProgressMeter - Total runtime 14.78 secs, 0.25 min, 0.00 hours
[2016-04-15T00:31Z] INFO  17:31:57,141 MicroScheduler - 8218 reads were filtered out during the traversal out of approximately 105571 total reads (7.78%)
[2016-04-15T00:31Z] INFO  17:31:57,141 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:31Z] INFO  17:31:57,142 MicroScheduler -   -> 168 reads (0.16% of total) failing BadMateFilter
[2016-04-15T00:31Z] INFO  17:31:57,142 MicroScheduler -   -> 7983 reads (7.56% of total) failing DuplicateReadFilter
[2016-04-15T00:31Z] INFO  17:31:57,142 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:31Z] INFO  17:31:57,142 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:31Z] INFO  17:31:57,143 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:31Z] INFO  17:31:57,143 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:31Z] INFO  17:31:57,143 MicroScheduler -   -> 67 reads (0.06% of total) failing UnmappedReadFilter
[2016-04-15T00:31Z] INFO  17:31:57,229 IntervalUtils - Processing 400248 bp from intervals
[2016-04-15T00:31Z] WARN  17:31:57,234 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:31Z] INFO  17:31:57,363 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:31Z] INFO  17:31:57,479 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:31Z] INFO  17:31:57,480 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:31Z] INFO  17:31:57,481 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:31Z] INFO  17:31:57,482 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:31Z] INFO  17:31:57,525 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:31Z] INFO  17:31:57,526 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:31Z] INFO  17:31:58,463 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:31Z] INFO  17:31:58,603 ProgressMeter -            done   1353894.0    36.0 s      26.0 s      100.0%    36.0 s       0.0 s
[2016-04-15T00:31Z] INFO  17:31:58,603 ProgressMeter - Total runtime 36.46 secs, 0.61 min, 0.01 hours
[2016-04-15T00:31Z] INFO  17:31:58,604 MicroScheduler - 40009 reads were filtered out during the traversal out of approximately 496670 total reads (8.06%)
[2016-04-15T00:31Z] INFO  17:31:58,604 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:31Z] INFO  17:31:58,604 MicroScheduler -   -> 829 reads (0.17% of total) failing BadMateFilter
[2016-04-15T00:31Z] INFO  17:31:58,605 MicroScheduler -   -> 38864 reads (7.82% of total) failing DuplicateReadFilter
[2016-04-15T00:31Z] INFO  17:31:58,605 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:31Z] INFO  17:31:58,605 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:31Z] INFO  17:31:58,606 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:31Z] INFO  17:31:58,606 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:31Z] INFO  17:31:58,607 MicroScheduler -   -> 316 reads (0.06% of total) failing UnmappedReadFilter
[2016-04-15T00:31Z] GATK: UnifiedGenotyper
[2016-04-15T00:32Z] INFO  17:32:00,117 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:32Z] GATK: UnifiedGenotyper
[2016-04-15T00:32Z] INFO  17:32:01,352 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:32Z] INFO  17:32:01,355 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:32Z] INFO  17:32:01,356 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:32Z] INFO  17:32:01,356 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:32Z] INFO  17:32:01,362 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/16/R14-18106_kapa-NGv3-PE100-NGv3-sort-16_31120544_46629582-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/16/R14-18106_kapa-NGv3-PE100-NGv3-16_31120544_46629582-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/16/tx/tmpjvuVU7/R14-18106_kapa-NGv3-PE100-NGv3-16_31120544_46629582.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:32Z] INFO  17:32:01,371 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:32Z] INFO  17:32:01,372 HelpFormatter - Date/Time: 2016/04/14 17:32:01
[2016-04-15T00:32Z] INFO  17:32:01,373 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:32Z] INFO  17:32:01,373 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:32Z] INFO  17:32:01,570 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:32Z] INFO  17:32:01,801 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:32Z] INFO  17:32:01,810 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:32Z] INFO  17:32:01,879 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-15T00:32Z] INFO  17:32:02,268 IntervalUtils - Processing 40143 bp from intervals
[2016-04-15T00:32Z] WARN  17:32:02,277 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:32Z] INFO  17:32:02,363 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:32Z] INFO  17:32:02,386 ProgressMeter -            done    131383.0     9.0 s      73.0 s      100.0%     9.0 s       0.0 s
[2016-04-15T00:32Z] INFO  17:32:02,386 ProgressMeter - Total runtime 9.62 secs, 0.16 min, 0.00 hours
[2016-04-15T00:32Z] INFO  17:32:02,387 MicroScheduler - 5127 reads were filtered out during the traversal out of approximately 65659 total reads (7.81%)
[2016-04-15T00:32Z] INFO  17:32:02,387 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:32Z] INFO  17:32:02,387 MicroScheduler -   -> 104 reads (0.16% of total) failing BadMateFilter
[2016-04-15T00:32Z] INFO  17:32:02,387 MicroScheduler -   -> 4988 reads (7.60% of total) failing DuplicateReadFilter
[2016-04-15T00:32Z] INFO  17:32:02,388 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:32Z] INFO  17:32:02,388 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:32Z] INFO  17:32:02,388 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:32Z] INFO  17:32:02,388 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:32Z] INFO  17:32:02,389 MicroScheduler -   -> 35 reads (0.05% of total) failing UnmappedReadFilter
[2016-04-15T00:32Z] INFO  17:32:02,410 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:32Z] INFO  17:32:02,411 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:32Z] INFO  17:32:02,412 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:32Z] INFO  17:32:02,413 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:32Z] INFO  17:32:02,468 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:32Z] INFO  17:32:02,469 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:32Z] INFO  17:32:02,719 ProgressMeter -            done   3065212.0    49.0 s      16.0 s      100.0%    49.0 s       0.0 s
[2016-04-15T00:32Z] INFO  17:32:02,719 ProgressMeter - Total runtime 49.59 secs, 0.83 min, 0.01 hours
[2016-04-15T00:32Z] INFO  17:32:02,720 MicroScheduler - 57371 reads were filtered out during the traversal out of approximately 723007 total reads (7.94%)
[2016-04-15T00:32Z] INFO  17:32:02,720 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:32Z] INFO  17:32:02,720 MicroScheduler -   -> 1233 reads (0.17% of total) failing BadMateFilter
[2016-04-15T00:32Z] INFO  17:32:02,720 MicroScheduler -   -> 55649 reads (7.70% of total) failing DuplicateReadFilter
[2016-04-15T00:32Z] INFO  17:32:02,721 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:32Z] INFO  17:32:02,721 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:32Z] INFO  17:32:02,721 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:32Z] INFO  17:32:02,721 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:32Z] INFO  17:32:02,722 MicroScheduler -   -> 489 reads (0.07% of total) failing UnmappedReadFilter
[2016-04-15T00:32Z] INFO  17:32:03,259 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:32Z] INFO  17:32:03,262 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:32Z] INFO  17:32:03,263 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:32Z] INFO  17:32:03,263 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:32Z] INFO  17:32:03,267 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/16/R14-18106_kapa-NGv3-PE100-NGv3-sort-16_46633742_64982002-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/16/R14-18106_kapa-NGv3-PE100-NGv3-16_46633742_64982002-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/16/tx/tmpzW6TwQ/R14-18106_kapa-NGv3-PE100-NGv3-16_46633742_64982002.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:32Z] INFO  17:32:03,275 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:32Z] INFO  17:32:03,276 HelpFormatter - Date/Time: 2016/04/14 17:32:03
[2016-04-15T00:32Z] INFO  17:32:03,276 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:32Z] INFO  17:32:03,277 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:32Z] INFO  17:32:03,431 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:32Z] INFO  17:32:03,633 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:32Z] INFO  17:32:03,640 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:32Z] INFO  17:32:03,654 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:32Z] INFO  17:32:03,744 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.09
[2016-04-15T00:32Z] GATK: UnifiedGenotyper
[2016-04-15T00:32Z] INFO  17:32:04,112 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:32Z] INFO  17:32:04,157 IntervalUtils - Processing 224129 bp from intervals
[2016-04-15T00:32Z] WARN  17:32:04,163 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:32Z] INFO  17:32:04,281 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:32Z] INFO  17:32:04,376 ProgressMeter -            done    545455.0    20.0 s      37.0 s      100.0%    20.0 s       0.0 s
[2016-04-15T00:32Z] INFO  17:32:04,377 ProgressMeter - Total runtime 20.20 secs, 0.34 min, 0.01 hours
[2016-04-15T00:32Z] INFO  17:32:04,377 MicroScheduler - 16308 reads were filtered out during the traversal out of approximately 206131 total reads (7.91%)
[2016-04-15T00:32Z] GATK: UnifiedGenotyper
[2016-04-15T00:32Z] INFO  17:32:04,378 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:32Z] INFO  17:32:04,378 MicroScheduler -   -> 387 reads (0.19% of total) failing BadMateFilter
[2016-04-15T00:32Z] INFO  17:32:04,378 MicroScheduler -   -> 15802 reads (7.67% of total) failing DuplicateReadFilter
[2016-04-15T00:32Z] INFO  17:32:04,378 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:32Z] INFO  17:32:04,379 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:32Z] INFO  17:32:04,379 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:32Z] INFO  17:32:04,379 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:32Z] INFO  17:32:04,379 MicroScheduler -   -> 119 reads (0.06% of total) failing UnmappedReadFilter
[2016-04-15T00:32Z] INFO  17:32:04,414 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:32Z] INFO  17:32:04,415 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:32Z] INFO  17:32:04,416 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:32Z] INFO  17:32:04,417 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:32Z] INFO  17:32:04,476 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:32Z] INFO  17:32:04,477 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:32Z] INFO  17:32:04,941 ProgressMeter -            done    695639.0    21.0 s      30.0 s      100.0%    21.0 s       0.0 s
[2016-04-15T00:32Z] INFO  17:32:04,941 ProgressMeter - Total runtime 21.55 secs, 0.36 min, 0.01 hours
[2016-04-15T00:32Z] INFO  17:32:04,942 MicroScheduler - 19341 reads were filtered out during the traversal out of approximately 249860 total reads (7.74%)
[2016-04-15T00:32Z] INFO  17:32:04,942 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:32Z] INFO  17:32:04,942 MicroScheduler -   -> 457 reads (0.18% of total) failing BadMateFilter
[2016-04-15T00:32Z] INFO  17:32:04,943 MicroScheduler -   -> 18718 reads (7.49% of total) failing DuplicateReadFilter
[2016-04-15T00:32Z] INFO  17:32:04,943 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:32Z] INFO  17:32:04,943 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:32Z] INFO  17:32:04,943 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:32Z] INFO  17:32:04,944 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:32Z] INFO  17:32:04,944 MicroScheduler -   -> 166 reads (0.07% of total) failing UnmappedReadFilter
[2016-04-15T00:32Z] INFO  17:32:05,639 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:32Z] GATK: UnifiedGenotyper
[2016-04-15T00:32Z] INFO  17:32:06,300 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:32Z] GATK: UnifiedGenotyper
[2016-04-15T00:32Z] INFO  17:32:06,709 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:32Z] INFO  17:32:06,712 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:32Z] INFO  17:32:06,713 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:32Z] INFO  17:32:06,714 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:32Z] INFO  17:32:06,718 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/16/R14-18106_kapa-NGv3-PE100-NGv3-sort-16_64982511_80574976-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/16/R14-18106_kapa-NGv3-PE100-NGv3-16_64982511_80574976-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/16/tx/tmpZ1x5YL/R14-18106_kapa-NGv3-PE100-NGv3-16_64982511_80574976.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:32Z] INFO  17:32:06,751 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:32Z] INFO  17:32:06,752 HelpFormatter - Date/Time: 2016/04/14 17:32:06
[2016-04-15T00:32Z] INFO  17:32:06,753 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:32Z] INFO  17:32:06,753 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:32Z] INFO  17:32:06,942 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:32Z] INFO  17:32:06,946 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:32Z] INFO  17:32:06,945 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:32Z] INFO  17:32:06,946 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:32Z] INFO  17:32:06,946 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:32Z] INFO  17:32:06,950 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/16/R14-18106_kapa-NGv3-PE100-NGv3-sort-16_80575258_90354753-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/16/R14-18106_kapa-NGv3-PE100-NGv3-16_80575258_90354753-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/16/tx/tmp3T_hKD/R14-18106_kapa-NGv3-PE100-NGv3-16_80575258_90354753.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:32Z] INFO  17:32:06,960 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:32Z] INFO  17:32:06,960 HelpFormatter - Date/Time: 2016/04/14 17:32:06
[2016-04-15T00:32Z] INFO  17:32:06,961 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:32Z] INFO  17:32:06,961 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:32Z] INFO  17:32:07,135 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:32Z] INFO  17:32:07,145 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:32Z] INFO  17:32:07,160 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:32Z] INFO  17:32:07,220 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-15T00:32Z] INFO  17:32:07,366 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:32Z] INFO  17:32:07,374 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:32Z] INFO  17:32:07,491 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.12
[2016-04-15T00:32Z] INFO  17:32:07,798 IntervalUtils - Processing 344918 bp from intervals
[2016-04-15T00:32Z] WARN  17:32:07,817 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:32Z] INFO  17:32:07,956 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:32Z] INFO  17:32:08,031 IntervalUtils - Processing 203451 bp from intervals
[2016-04-15T00:32Z] WARN  17:32:08,036 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:32Z] INFO  17:32:08,075 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:32Z] INFO  17:32:08,076 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:32Z] INFO  17:32:08,077 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:32Z] INFO  17:32:08,077 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:32Z] INFO  17:32:08,115 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:32Z] INFO  17:32:08,136 ProgressMeter -            done    817418.0    24.0 s      29.0 s      100.0%    24.0 s       0.0 s
[2016-04-15T00:32Z] INFO  17:32:08,136 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:32Z] INFO  17:32:08,136 ProgressMeter - Total runtime 24.41 secs, 0.41 min, 0.01 hours
[2016-04-15T00:32Z] INFO  17:32:08,137 MicroScheduler - 22075 reads were filtered out during the traversal out of approximately 275368 total reads (8.02%)
[2016-04-15T00:32Z] INFO  17:32:08,137 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:32Z] INFO  17:32:08,137 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:32Z] INFO  17:32:08,137 MicroScheduler -   -> 505 reads (0.18% of total) failing BadMateFilter
[2016-04-15T00:32Z] INFO  17:32:08,138 MicroScheduler -   -> 21389 reads (7.77% of total) failing DuplicateReadFilter
[2016-04-15T00:32Z] INFO  17:32:08,138 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:32Z] INFO  17:32:08,138 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:32Z] INFO  17:32:08,138 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:32Z] INFO  17:32:08,139 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:32Z] INFO  17:32:08,139 MicroScheduler -   -> 181 reads (0.07% of total) failing UnmappedReadFilter
[2016-04-15T00:32Z] INFO  17:32:08,228 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:32Z] INFO  17:32:08,229 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:32Z] INFO  17:32:08,230 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:32Z] INFO  17:32:08,231 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:32Z] INFO  17:32:08,284 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:32Z] INFO  17:32:08,285 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:32Z] INFO  17:32:08,483 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:32Z] INFO  17:32:08,485 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:32Z] INFO  17:32:08,485 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:32Z] INFO  17:32:08,485 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:32Z] INFO  17:32:08,489 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/17/R14-18106_kapa-NGv3-PE100-NGv3-sort-17_0_15511002-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/17/R14-18106_kapa-NGv3-PE100-NGv3-17_0_15511002-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/17/tx/tmpmnoueO/R14-18106_kapa-NGv3-PE100-NGv3-17_0_15511002.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:32Z] INFO  17:32:08,498 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:32Z] INFO  17:32:08,510 HelpFormatter - Date/Time: 2016/04/14 17:32:08
[2016-04-15T00:32Z] INFO  17:32:08,511 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:32Z] INFO  17:32:08,512 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:32Z] INFO  17:32:08,644 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:32Z] INFO  17:32:08,848 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:32Z] INFO  17:32:08,864 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:32Z] INFO  17:32:08,948 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-15T00:32Z] INFO  17:32:08,965 ProgressMeter -            done    633510.0    20.0 s      33.0 s      100.0%    20.0 s       0.0 s
[2016-04-15T00:32Z] INFO  17:32:08,966 ProgressMeter - Total runtime 20.99 secs, 0.35 min, 0.01 hours
[2016-04-15T00:32Z] INFO  17:32:08,966 MicroScheduler - 17878 reads were filtered out during the traversal out of approximately 259076 total reads (6.90%)
[2016-04-15T00:32Z] INFO  17:32:08,967 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:32Z] INFO  17:32:08,967 MicroScheduler -   -> 531 reads (0.20% of total) failing BadMateFilter
[2016-04-15T00:32Z] INFO  17:32:08,967 MicroScheduler -   -> 17174 reads (6.63% of total) failing DuplicateReadFilter
[2016-04-15T00:32Z] INFO  17:32:08,967 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:32Z] INFO  17:32:08,968 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:32Z] INFO  17:32:08,968 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:32Z] INFO  17:32:08,968 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:32Z] INFO  17:32:08,968 MicroScheduler -   -> 173 reads (0.07% of total) failing UnmappedReadFilter
[2016-04-15T00:32Z] INFO  17:32:09,505 IntervalUtils - Processing 497719 bp from intervals
[2016-04-15T00:32Z] WARN  17:32:09,511 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:32Z] INFO  17:32:09,584 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:32Z] INFO  17:32:09,587 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:32Z] INFO  17:32:09,588 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:32Z] INFO  17:32:09,588 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:32Z] INFO  17:32:09,593 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/17/R14-18106_kapa-NGv3-PE100-NGv3-sort-17_15515955_31039213-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/17/R14-18106_kapa-NGv3-PE100-NGv3-17_15515955_31039213-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/17/tx/tmpMo5oGR/R14-18106_kapa-NGv3-PE100-NGv3-17_15515955_31039213.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:32Z] INFO  17:32:09,602 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:32Z] INFO  17:32:09,602 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:32Z] INFO  17:32:09,613 HelpFormatter - Date/Time: 2016/04/14 17:32:09
[2016-04-15T00:32Z] INFO  17:32:09,614 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:32Z] INFO  17:32:09,614 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:32Z] INFO  17:32:09,739 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:32Z] INFO  17:32:09,739 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:32Z] INFO  17:32:09,740 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:32Z] INFO  17:32:09,740 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:32Z] INFO  17:32:09,757 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:32Z] INFO  17:32:09,783 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:32Z] INFO  17:32:09,783 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:32Z] INFO  17:32:09,967 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:32Z] INFO  17:32:09,976 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:32Z] INFO  17:32:10,052 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-15T00:32Z] INFO  17:32:10,213 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:32Z] INFO  17:32:10,351 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:32Z] INFO  17:32:10,497 IntervalUtils - Processing 320055 bp from intervals
[2016-04-15T00:32Z] WARN  17:32:10,503 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:32Z] GATK: UnifiedGenotyper
[2016-04-15T00:32Z] INFO  17:32:10,572 ProgressMeter -            done    727916.0    26.0 s      36.0 s      100.0%    26.0 s       0.0 s
[2016-04-15T00:32Z] INFO  17:32:10,573 ProgressMeter - Total runtime 26.29 secs, 0.44 min, 0.01 hours
[2016-04-15T00:32Z] INFO  17:32:10,573 MicroScheduler - 25176 reads were filtered out during the traversal out of approximately 318672 total reads (7.90%)
[2016-04-15T00:32Z] INFO  17:32:10,573 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:32Z] INFO  17:32:10,573 MicroScheduler -   -> 593 reads (0.19% of total) failing BadMateFilter
[2016-04-15T00:32Z] INFO  17:32:10,574 MicroScheduler -   -> 24364 reads (7.65% of total) failing DuplicateReadFilter
[2016-04-15T00:32Z] INFO  17:32:10,574 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:32Z] INFO  17:32:10,574 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:32Z] INFO  17:32:10,574 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:32Z] INFO  17:32:10,575 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:32Z] INFO  17:32:10,575 MicroScheduler -   -> 219 reads (0.07% of total) failing UnmappedReadFilter
[2016-04-15T00:32Z] INFO  17:32:10,586 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:32Z] INFO  17:32:10,689 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:32Z] INFO  17:32:10,698 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:32Z] INFO  17:32:10,699 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:32Z] GATK: UnifiedGenotyper
[2016-04-15T00:32Z] INFO  17:32:10,700 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:32Z] INFO  17:32:10,765 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:32Z] INFO  17:32:10,766 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:32Z] INFO  17:32:10,828 ProgressMeter -            done    240450.0     8.0 s      35.0 s      100.0%     8.0 s       0.0 s
[2016-04-15T00:32Z] INFO  17:32:10,829 ProgressMeter - Total runtime 8.42 secs, 0.14 min, 0.00 hours
[2016-04-15T00:32Z] INFO  17:32:10,830 MicroScheduler - 4678 reads were filtered out during the traversal out of approximately 65761 total reads (7.11%)
[2016-04-15T00:32Z] INFO  17:32:10,831 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:32Z] INFO  17:32:10,832 MicroScheduler -   -> 129 reads (0.20% of total) failing BadMateFilter
[2016-04-15T00:32Z] INFO  17:32:10,832 MicroScheduler -   -> 4494 reads (6.83% of total) failing DuplicateReadFilter
[2016-04-15T00:32Z] INFO  17:32:10,833 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:32Z] INFO  17:32:10,834 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:32Z] INFO  17:32:10,834 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:32Z] INFO  17:32:10,835 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:32Z] INFO  17:32:10,836 MicroScheduler -   -> 55 reads (0.08% of total) failing UnmappedReadFilter
[2016-04-15T00:32Z] INFO  17:32:11,582 ProgressMeter -     14:31535503   1593499.0    30.0 s      18.0 s       88.0%    34.0 s       4.0 s
[2016-04-15T00:32Z] INFO  17:32:12,009 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:32Z] INFO  17:32:12,338 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:32Z] GATK: UnifiedGenotyper
[2016-04-15T00:32Z] GATK: UnifiedGenotyper
[2016-04-15T00:32Z] INFO  17:32:13,657 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:32Z] INFO  17:32:13,661 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:32Z] INFO  17:32:13,661 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:32Z] INFO  17:32:13,662 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:32Z] INFO  17:32:13,667 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/17/R14-18106_kapa-NGv3-PE100-NGv3-sort-17_31048040_46607237-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/17/R14-18106_kapa-NGv3-PE100-NGv3-17_31048040_46607237-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/17/tx/tmpATid6C/R14-18106_kapa-NGv3-PE100-NGv3-17_31048040_46607237.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:32Z] INFO  17:32:13,683 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:32Z] INFO  17:32:13,684 HelpFormatter - Date/Time: 2016/04/14 17:32:13
[2016-04-15T00:32Z] INFO  17:32:13,684 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:32Z] INFO  17:32:13,685 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:32Z] INFO  17:32:13,683 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:32Z] INFO  17:32:13,687 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:32Z] INFO  17:32:13,687 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:32Z] INFO  17:32:13,688 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:32Z] INFO  17:32:13,692 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/17/R14-18106_kapa-NGv3-PE100-NGv3-sort-17_46607689_62121560-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/17/R14-18106_kapa-NGv3-PE100-NGv3-17_46607689_62121560-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/17/tx/tmpth1kyU/R14-18106_kapa-NGv3-PE100-NGv3-17_46607689_62121560.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:32Z] INFO  17:32:13,711 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:32Z] INFO  17:32:13,712 HelpFormatter - Date/Time: 2016/04/14 17:32:13
[2016-04-15T00:32Z] INFO  17:32:13,713 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:32Z] INFO  17:32:13,713 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:32Z] INFO  17:32:13,860 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:32Z] INFO  17:32:13,924 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:32Z] INFO  17:32:13,975 ProgressMeter -            done    711142.0    21.0 s      29.0 s      100.0%    21.0 s       0.0 s
[2016-04-15T00:32Z] INFO  17:32:13,975 ProgressMeter - Total runtime 21.31 secs, 0.36 min, 0.01 hours
[2016-04-15T00:32Z] INFO  17:32:13,976 MicroScheduler - 19765 reads were filtered out during the traversal out of approximately 260645 total reads (7.58%)
[2016-04-15T00:32Z] INFO  17:32:13,976 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:32Z] INFO  17:32:13,976 MicroScheduler -   -> 445 reads (0.17% of total) failing BadMateFilter
[2016-04-15T00:32Z] INFO  17:32:13,977 MicroScheduler -   -> 19160 reads (7.35% of total) failing DuplicateReadFilter
[2016-04-15T00:32Z] INFO  17:32:13,977 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:32Z] INFO  17:32:13,977 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:32Z] INFO  17:32:13,977 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:32Z] INFO  17:32:13,978 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:32Z] INFO  17:32:13,978 MicroScheduler -   -> 160 reads (0.06% of total) failing UnmappedReadFilter
[2016-04-15T00:32Z] INFO  17:32:13,980 ProgressMeter -            done   1676712.0    32.0 s      19.0 s      100.0%    32.0 s       0.0 s
[2016-04-15T00:32Z] INFO  17:32:13,981 ProgressMeter - Total runtime 32.43 secs, 0.54 min, 0.01 hours
[2016-04-15T00:32Z] INFO  17:32:13,982 MicroScheduler - 34301 reads were filtered out during the traversal out of approximately 429272 total reads (7.99%)
[2016-04-15T00:32Z] INFO  17:32:13,982 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:32Z] INFO  17:32:13,982 MicroScheduler -   -> 752 reads (0.18% of total) failing BadMateFilter
[2016-04-15T00:32Z] INFO  17:32:13,983 MicroScheduler -   -> 33252 reads (7.75% of total) failing DuplicateReadFilter
[2016-04-15T00:32Z] INFO  17:32:13,983 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:32Z] INFO  17:32:13,983 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:32Z] INFO  17:32:13,983 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:32Z] INFO  17:32:13,983 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:32Z] INFO  17:32:13,994 MicroScheduler -   -> 297 reads (0.07% of total) failing UnmappedReadFilter
[2016-04-15T00:32Z] INFO  17:32:14,131 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:32Z] INFO  17:32:14,140 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:32Z] INFO  17:32:14,190 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:32Z] INFO  17:32:14,211 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:32Z] INFO  17:32:14,231 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.09
[2016-04-15T00:32Z] INFO  17:32:14,334 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.12
[2016-04-15T00:32Z] INFO  17:32:14,741 IntervalUtils - Processing 543518 bp from intervals
[2016-04-15T00:32Z] WARN  17:32:14,747 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:32Z] INFO  17:32:14,819 IntervalUtils - Processing 295968 bp from intervals
[2016-04-15T00:32Z] WARN  17:32:14,825 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:32Z] INFO  17:32:14,862 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:32Z] INFO  17:32:14,958 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:32Z] INFO  17:32:14,991 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:32Z] INFO  17:32:14,992 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:32Z] INFO  17:32:14,993 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:32Z] INFO  17:32:14,994 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:32Z] INFO  17:32:15,034 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:32Z] INFO  17:32:15,035 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:32Z] INFO  17:32:15,037 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:32Z] INFO  17:32:15,038 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:32Z] INFO  17:32:15,039 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:32Z] INFO  17:32:15,040 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:32Z] INFO  17:32:15,087 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:32Z] INFO  17:32:15,088 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:32Z] INFO  17:32:15,456 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:32Z] INFO  17:32:15,458 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:32Z] INFO  17:32:15,459 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:32Z] INFO  17:32:15,459 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:32Z] INFO  17:32:15,463 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/17/R14-18106_kapa-NGv3-PE100-NGv3-sort-17_62122219_77705154-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/17/R14-18106_kapa-NGv3-PE100-NGv3-17_62122219_77705154-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/17/tx/tmpB7zCpK/R14-18106_kapa-NGv3-PE100-NGv3-17_62122219_77705154.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:32Z] INFO  17:32:15,470 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:32Z] INFO  17:32:15,473 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:32Z] INFO  17:32:15,474 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:32Z] INFO  17:32:15,474 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:32Z] INFO  17:32:15,471 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:32Z] INFO  17:32:15,472 HelpFormatter - Date/Time: 2016/04/14 17:32:15
[2016-04-15T00:32Z] INFO  17:32:15,473 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:32Z] INFO  17:32:15,474 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:32Z] INFO  17:32:15,479 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/17/R14-18106_kapa-NGv3-PE100-NGv3-sort-17_77707305_81195210-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/17/R14-18106_kapa-NGv3-PE100-NGv3-17_77707305_81195210-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/17/tx/tmpsGq6RZ/R14-18106_kapa-NGv3-PE100-NGv3-17_77707305_81195210.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:32Z] INFO  17:32:15,499 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:32Z] INFO  17:32:15,500 HelpFormatter - Date/Time: 2016/04/14 17:32:15
[2016-04-15T00:32Z] INFO  17:32:15,501 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:32Z] INFO  17:32:15,506 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:32Z] INFO  17:32:15,537 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:32Z] INFO  17:32:15,610 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:32Z] INFO  17:32:15,647 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:32Z] INFO  17:32:15,646 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:32Z] GATK: UnifiedGenotyper
[2016-04-15T00:32Z] INFO  17:32:15,905 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:32Z] GATK: UnifiedGenotyper
[2016-04-15T00:32Z] INFO  17:32:15,916 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:32Z] INFO  17:32:15,920 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:32Z] INFO  17:32:15,939 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:32Z] INFO  17:32:16,027 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.09
[2016-04-15T00:32Z] INFO  17:32:16,038 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.12
[2016-04-15T00:32Z] INFO  17:32:16,374 ProgressMeter -            done    802075.0    27.0 s      34.0 s      100.0%    27.0 s       0.0 s
[2016-04-15T00:32Z] INFO  17:32:16,374 ProgressMeter - Total runtime 27.46 secs, 0.46 min, 0.01 hours
[2016-04-15T00:32Z] INFO  17:32:16,375 MicroScheduler - 23720 reads were filtered out during the traversal out of approximately 300265 total reads (7.90%)
[2016-04-15T00:32Z] INFO  17:32:16,375 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:32Z] INFO  17:32:16,376 MicroScheduler -   -> 515 reads (0.17% of total) failing BadMateFilter
[2016-04-15T00:32Z] INFO  17:32:16,376 MicroScheduler -   -> 23005 reads (7.66% of total) failing DuplicateReadFilter
[2016-04-15T00:32Z] INFO  17:32:16,376 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:32Z] INFO  17:32:16,377 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:32Z] INFO  17:32:16,377 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:32Z] INFO  17:32:16,377 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:32Z] INFO  17:32:16,377 MicroScheduler -   -> 200 reads (0.07% of total) failing UnmappedReadFilter
[2016-04-15T00:32Z] INFO  17:32:16,486 IntervalUtils - Processing 160149 bp from intervals
[2016-04-15T00:32Z] WARN  17:32:16,499 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:32Z] INFO  17:32:16,610 IntervalUtils - Processing 345298 bp from intervals
[2016-04-15T00:32Z] WARN  17:32:16,617 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:32Z] INFO  17:32:16,651 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:32Z] INFO  17:32:16,736 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:32Z] INFO  17:32:16,777 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:32Z] INFO  17:32:16,778 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:32Z] INFO  17:32:16,779 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:32Z] INFO  17:32:16,779 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:32Z] INFO  17:32:16,874 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:32Z] INFO  17:32:16,879 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:32Z] INFO  17:32:16,885 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:32Z] INFO  17:32:16,892 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:32Z] INFO  17:32:16,893 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:32Z] INFO  17:32:16,893 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:32Z] INFO  17:32:16,963 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:32Z] INFO  17:32:16,964 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:32Z] INFO  17:32:17,806 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:32Z] INFO  17:32:17,869 ProgressMeter -     15:48936803   1617300.0    30.0 s      18.0 s       82.6%    36.0 s       6.0 s
[2016-04-15T00:32Z] GATK: UnifiedGenotyper
[2016-04-15T00:32Z] INFO  17:32:18,955 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:32Z] INFO  17:32:18,958 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:32Z] INFO  17:32:18,959 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:32Z] INFO  17:32:18,959 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:32Z] INFO  17:32:18,964 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/18/R14-18106_kapa-NGv3-PE100-NGv3-sort-18_0_18531348-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/18/R14-18106_kapa-NGv3-PE100-NGv3-18_0_18531348-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/18/tx/tmp5hlKkj/R14-18106_kapa-NGv3-PE100-NGv3-18_0_18531348.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:32Z] INFO  17:32:18,980 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:32Z] INFO  17:32:18,984 HelpFormatter - Date/Time: 2016/04/14 17:32:18
[2016-04-15T00:32Z] INFO  17:32:18,985 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:32Z] INFO  17:32:18,986 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:32Z] INFO  17:32:19,097 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:32Z] INFO  17:32:19,101 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:32Z] INFO  17:32:19,102 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:32Z] INFO  17:32:19,102 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:32Z] INFO  17:32:19,107 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/18/R14-18106_kapa-NGv3-PE100-NGv3-sort-18_18533538_34081962-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/18/R14-18106_kapa-NGv3-PE100-NGv3-18_18533538_34081962-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/18/tx/tmpyC4mZr/R14-18106_kapa-NGv3-PE100-NGv3-18_18533538_34081962.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:32Z] INFO  17:32:19,121 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:32Z] INFO  17:32:19,122 HelpFormatter - Date/Time: 2016/04/14 17:32:19
[2016-04-15T00:32Z] INFO  17:32:19,122 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:32Z] INFO  17:32:19,123 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:32Z] INFO  17:32:19,232 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:32Z] INFO  17:32:19,362 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:32Z] INFO  17:32:19,469 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:32Z] INFO  17:32:19,478 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:32Z] INFO  17:32:19,564 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-15T00:32Z] INFO  17:32:19,567 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:32Z] INFO  17:32:19,576 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:32Z] INFO  17:32:19,644 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-15T00:32Z] INFO  17:32:19,964 IntervalUtils - Processing 162632 bp from intervals
[2016-04-15T00:32Z] WARN  17:32:19,969 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:32Z] INFO  17:32:20,085 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:32Z] INFO  17:32:20,171 IntervalUtils - Processing 148606 bp from intervals
[2016-04-15T00:32Z] WARN  17:32:20,177 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:32Z] INFO  17:32:20,197 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:32Z] INFO  17:32:20,198 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:32Z] INFO  17:32:20,198 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:32Z] INFO  17:32:20,199 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:32Z] INFO  17:32:20,252 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:32Z] INFO  17:32:20,281 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:32Z] INFO  17:32:20,282 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:32Z] INFO  17:32:20,363 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:32Z] INFO  17:32:20,364 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:32Z] INFO  17:32:20,365 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:32Z] INFO  17:32:20,365 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:32Z] INFO  17:32:20,463 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:32Z] INFO  17:32:20,464 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:32Z] INFO  17:32:20,936 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:32Z] INFO  17:32:20,939 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:32Z] INFO  17:32:20,940 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:32Z] INFO  17:32:20,940 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:32Z] INFO  17:32:20,949 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/18/R14-18106_kapa-NGv3-PE100-NGv3-sort-18_34092400_49867248-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/18/R14-18106_kapa-NGv3-PE100-NGv3-18_34092400_49867248-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/18/tx/tmpoelC_L/R14-18106_kapa-NGv3-PE100-NGv3-18_34092400_49867248.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:32Z] INFO  17:32:20,959 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:32Z] INFO  17:32:20,970 HelpFormatter - Date/Time: 2016/04/14 17:32:20
[2016-04-15T00:32Z] INFO  17:32:20,971 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:32Z] INFO  17:32:20,972 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:32Z] INFO  17:32:21,163 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:32Z] INFO  17:32:21,408 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:32Z] INFO  17:32:21,428 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:32Z] INFO  17:32:21,519 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.09
[2016-04-15T00:32Z] INFO  17:32:21,992 IntervalUtils - Processing 116317 bp from intervals
[2016-04-15T00:32Z] WARN  17:32:21,997 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:32Z] INFO  17:32:22,113 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:32Z] INFO  17:32:22,198 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:32Z] INFO  17:32:22,199 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:32Z] INFO  17:32:22,200 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:32Z] INFO  17:32:22,202 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:32Z] INFO  17:32:22,216 ProgressMeter -            done   1805916.0    34.0 s      19.0 s      100.0%    34.0 s       0.0 s
[2016-04-15T00:32Z] INFO  17:32:22,217 ProgressMeter - Total runtime 34.37 secs, 0.57 min, 0.01 hours
[2016-04-15T00:32Z] INFO  17:32:22,218 MicroScheduler - 38284 reads were filtered out during the traversal out of approximately 484972 total reads (7.89%)
[2016-04-15T00:32Z] INFO  17:32:22,218 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:32Z] INFO  17:32:22,218 MicroScheduler -   -> 853 reads (0.18% of total) failing BadMateFilter
[2016-04-15T00:32Z] INFO  17:32:22,218 MicroScheduler -   -> 37145 reads (7.66% of total) failing DuplicateReadFilter
[2016-04-15T00:32Z] INFO  17:32:22,221 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:32Z] INFO  17:32:22,222 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:32Z] INFO  17:32:22,222 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:32Z] INFO  17:32:22,223 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:32Z] INFO  17:32:22,225 MicroScheduler -   -> 286 reads (0.06% of total) failing UnmappedReadFilter
[2016-04-15T00:32Z] INFO  17:32:22,276 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:32Z] INFO  17:32:22,277 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:32Z] INFO  17:32:22,524 ProgressMeter -     15:83205552   1019287.0    30.0 s      29.0 s       97.2%    30.0 s       0.0 s
[2016-04-15T00:32Z] INFO  17:32:23,136 ProgressMeter -            done   1052407.0    30.0 s      29.0 s      100.0%    30.0 s       0.0 s
[2016-04-15T00:32Z] INFO  17:32:23,136 ProgressMeter - Total runtime 30.64 secs, 0.51 min, 0.01 hours
[2016-04-15T00:32Z] INFO  17:32:23,137 MicroScheduler - 31190 reads were filtered out during the traversal out of approximately 415168 total reads (7.51%)
[2016-04-15T00:32Z] INFO  17:32:23,137 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:32Z] INFO  17:32:23,137 MicroScheduler -   -> 674 reads (0.16% of total) failing BadMateFilter
[2016-04-15T00:32Z] INFO  17:32:23,138 MicroScheduler -   -> 30281 reads (7.29% of total) failing DuplicateReadFilter
[2016-04-15T00:32Z] INFO  17:32:23,138 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:32Z] INFO  17:32:23,138 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:32Z] INFO  17:32:23,138 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:32Z] INFO  17:32:23,139 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:32Z] INFO  17:32:23,149 MicroScheduler -   -> 235 reads (0.06% of total) failing UnmappedReadFilter
[2016-04-15T00:32Z] INFO  17:32:23,735 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:32Z] GATK: UnifiedGenotyper
[2016-04-15T00:32Z] INFO  17:32:24,716 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:32Z] GATK: UnifiedGenotyper
[2016-04-15T00:32Z] INFO  17:32:26,393 ProgressMeter -      16:3652119   2010312.0    30.0 s      14.0 s       64.3%    46.0 s      16.0 s
[2016-04-15T00:32Z] INFO  17:32:26,955 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:32Z] INFO  17:32:26,957 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:32Z] INFO  17:32:26,957 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:32Z] INFO  17:32:26,958 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:32Z] INFO  17:32:26,962 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/18/R14-18106_kapa-NGv3-PE100-NGv3-sort-18_50278423_66344430-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/18/R14-18106_kapa-NGv3-PE100-NGv3-18_50278423_66344430-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/18/tx/tmpGufGUE/R14-18106_kapa-NGv3-PE100-NGv3-18_50278423_66344430.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:32Z] INFO  17:32:26,978 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:32Z] INFO  17:32:26,978 HelpFormatter - Date/Time: 2016/04/14 17:32:26
[2016-04-15T00:32Z] INFO  17:32:26,978 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:32Z] INFO  17:32:26,979 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:32Z] INFO  17:32:27,152 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:32Z] INFO  17:32:27,366 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:32Z] INFO  17:32:27,379 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:32Z] INFO  17:32:27,459 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-15T00:32Z] INFO  17:32:27,485 ProgressMeter -     16:28668165    929260.0    30.0 s      32.0 s       63.4%    47.0 s      17.0 s
[2016-04-15T00:32Z] INFO  17:32:27,883 IntervalUtils - Processing 111880 bp from intervals
[2016-04-15T00:32Z] WARN  17:32:27,889 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:32Z] INFO  17:32:27,966 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:32Z] INFO  17:32:28,016 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:32Z] INFO  17:32:28,017 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:32Z] INFO  17:32:28,018 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:32Z] INFO  17:32:28,019 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:32Z] INFO  17:32:28,060 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:32Z] INFO  17:32:28,061 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:32Z] INFO  17:32:28,245 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:32Z] INFO  17:32:28,250 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:32Z] INFO  17:32:28,250 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:32Z] INFO  17:32:28,251 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:32Z] INFO  17:32:28,257 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/18/R14-18106_kapa-NGv3-PE100-NGv3-sort-18_66346699_78077248-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/18/R14-18106_kapa-NGv3-PE100-NGv3-18_66346699_78077248-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/18/tx/tmp_ysBkL/R14-18106_kapa-NGv3-PE100-NGv3-18_66346699_78077248.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:32Z] INFO  17:32:28,293 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:32Z] INFO  17:32:28,294 HelpFormatter - Date/Time: 2016/04/14 17:32:28
[2016-04-15T00:32Z] INFO  17:32:28,295 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:32Z] INFO  17:32:28,303 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:32Z] INFO  17:32:28,451 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:32Z] INFO  17:32:28,656 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:32Z] INFO  17:32:28,666 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:32Z] INFO  17:32:28,775 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.11
[2016-04-15T00:32Z] INFO  17:32:29,125 ProgressMeter -            done    892419.0    24.0 s      27.0 s      100.0%    24.0 s       0.0 s
[2016-04-15T00:32Z] INFO  17:32:29,126 ProgressMeter - Total runtime 24.71 secs, 0.41 min, 0.01 hours
[2016-04-15T00:32Z] INFO  17:32:29,126 MicroScheduler - 23369 reads were filtered out during the traversal out of approximately 293360 total reads (7.97%)
[2016-04-15T00:32Z] INFO  17:32:29,127 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:32Z] INFO  17:32:29,127 MicroScheduler -   -> 539 reads (0.18% of total) failing BadMateFilter
[2016-04-15T00:32Z] INFO  17:32:29,127 MicroScheduler -   -> 22641 reads (7.72% of total) failing DuplicateReadFilter
[2016-04-15T00:32Z] INFO  17:32:29,128 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:32Z] INFO  17:32:29,128 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:32Z] INFO  17:32:29,128 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:32Z] INFO  17:32:29,129 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:32Z] INFO  17:32:29,129 MicroScheduler -   -> 189 reads (0.06% of total) failing UnmappedReadFilter
[2016-04-15T00:32Z] INFO  17:32:29,153 IntervalUtils - Processing 87308 bp from intervals
[2016-04-15T00:32Z] WARN  17:32:29,159 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:32Z] INFO  17:32:29,296 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:32Z] INFO  17:32:29,408 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:32Z] INFO  17:32:29,409 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:32Z] INFO  17:32:29,409 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:32Z] INFO  17:32:29,410 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:32Z] INFO  17:32:29,461 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:32Z] INFO  17:32:29,462 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:32Z] INFO  17:32:30,593 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:32Z] GATK: UnifiedGenotyper
[2016-04-15T00:32Z] INFO  17:32:32,490 ProgressMeter -            done    861644.0    24.0 s      28.0 s      100.0%    24.0 s       0.0 s
[2016-04-15T00:32Z] INFO  17:32:32,490 ProgressMeter - Total runtime 24.26 secs, 0.40 min, 0.01 hours
[2016-04-15T00:32Z] INFO  17:32:32,491 MicroScheduler - 24281 reads were filtered out during the traversal out of approximately 297794 total reads (8.15%)
[2016-04-15T00:32Z] INFO  17:32:32,491 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:32Z] INFO  17:32:32,492 MicroScheduler -   -> 532 reads (0.18% of total) failing BadMateFilter
[2016-04-15T00:32Z] INFO  17:32:32,492 MicroScheduler -   -> 23559 reads (7.91% of total) failing DuplicateReadFilter
[2016-04-15T00:32Z] INFO  17:32:32,492 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:32Z] INFO  17:32:32,493 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:32Z] INFO  17:32:32,493 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:32Z] INFO  17:32:32,493 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:32Z] INFO  17:32:32,493 MicroScheduler -   -> 190 reads (0.06% of total) failing UnmappedReadFilter
[2016-04-15T00:32Z] INFO  17:32:33,629 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:32Z] INFO  17:32:33,632 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:32Z] INFO  17:32:33,633 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:32Z] INFO  17:32:33,633 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:32Z] INFO  17:32:33,638 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/19/R14-18106_kapa-NGv3-PE100-NGv3-sort-19_0_15509577-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/19/R14-18106_kapa-NGv3-PE100-NGv3-19_0_15509577-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/19/tx/tmpIP37L8/R14-18106_kapa-NGv3-PE100-NGv3-19_0_15509577.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:32Z] INFO  17:32:33,653 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:32Z] INFO  17:32:33,653 HelpFormatter - Date/Time: 2016/04/14 17:32:33
[2016-04-15T00:32Z] INFO  17:32:33,654 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:32Z] INFO  17:32:33,654 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:32Z] INFO  17:32:33,837 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:32Z] INFO  17:32:33,841 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:32Z] INFO  17:32:34,143 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:32Z] INFO  17:32:34,164 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:32Z] GATK: UnifiedGenotyper
[2016-04-15T00:32Z] INFO  17:32:34,244 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-15T00:32Z] INFO  17:32:34,888 IntervalUtils - Processing 793280 bp from intervals
[2016-04-15T00:32Z] WARN  17:32:34,894 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:32Z] INFO  17:32:35,039 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:32Z] INFO  17:32:35,227 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:32Z] INFO  17:32:35,233 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:32Z] INFO  17:32:35,233 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:32Z] INFO  17:32:35,233 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:32Z] INFO  17:32:35,286 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:32Z] INFO  17:32:35,287 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:32Z] INFO  17:32:37,138 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:32Z] INFO  17:32:37,141 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:32Z] INFO  17:32:37,141 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:32Z] INFO  17:32:37,141 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:32Z] INFO  17:32:37,146 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/19/R14-18106_kapa-NGv3-PE100-NGv3-sort-19_15510112_31025906-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/19/R14-18106_kapa-NGv3-PE100-NGv3-19_15510112_31025906-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/19/tx/tmp_1U3yB/R14-18106_kapa-NGv3-PE100-NGv3-19_15510112_31025906.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:32Z] INFO  17:32:37,181 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:32Z] INFO  17:32:37,182 HelpFormatter - Date/Time: 2016/04/14 17:32:37
[2016-04-15T00:32Z] INFO  17:32:37,182 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:32Z] INFO  17:32:37,183 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:32Z] INFO  17:32:37,270 ProgressMeter -            done    934025.0    20.0 s      21.0 s      100.0%    20.0 s       0.0 s
[2016-04-15T00:32Z] INFO  17:32:37,270 ProgressMeter - Total runtime 20.49 secs, 0.34 min, 0.01 hours
[2016-04-15T00:32Z] INFO  17:32:37,271 MicroScheduler - 19227 reads were filtered out during the traversal out of approximately 238347 total reads (8.07%)
[2016-04-15T00:32Z] INFO  17:32:37,271 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:32Z] INFO  17:32:37,271 MicroScheduler -   -> 404 reads (0.17% of total) failing BadMateFilter
[2016-04-15T00:32Z] INFO  17:32:37,272 MicroScheduler -   -> 18696 reads (7.84% of total) failing DuplicateReadFilter
[2016-04-15T00:32Z] INFO  17:32:37,272 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:32Z] INFO  17:32:37,272 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:32Z] INFO  17:32:37,273 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:32Z] INFO  17:32:37,273 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:32Z] INFO  17:32:37,273 MicroScheduler -   -> 127 reads (0.05% of total) failing UnmappedReadFilter
[2016-04-15T00:32Z] INFO  17:32:37,358 ProgressMeter -            done    391274.0    16.0 s      43.0 s      100.0%    16.0 s       0.0 s
[2016-04-15T00:32Z] INFO  17:32:37,359 ProgressMeter - Total runtime 17.00 secs, 0.28 min, 0.00 hours
[2016-04-15T00:32Z] INFO  17:32:37,360 MicroScheduler - 13546 reads were filtered out during the traversal out of approximately 171993 total reads (7.88%)
[2016-04-15T00:32Z] INFO  17:32:37,361 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:32Z] INFO  17:32:37,362 MicroScheduler -   -> 290 reads (0.17% of total) failing BadMateFilter
[2016-04-15T00:32Z] INFO  17:32:37,362 MicroScheduler -   -> 13130 reads (7.63% of total) failing DuplicateReadFilter
[2016-04-15T00:32Z] INFO  17:32:37,363 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:32Z] INFO  17:32:37,364 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:32Z] INFO  17:32:37,364 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:32Z] INFO  17:32:37,365 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:32Z] INFO  17:32:37,366 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:32Z] INFO  17:32:37,366 MicroScheduler -   -> 126 reads (0.07% of total) failing UnmappedReadFilter
[2016-04-15T00:32Z] INFO  17:32:37,639 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:32Z] INFO  17:32:37,650 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:32Z] INFO  17:32:37,721 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-15T00:32Z] INFO  17:32:38,095 ProgressMeter -     16:74424393   1468128.0    30.0 s      20.0 s       82.6%    36.0 s       6.0 s
[2016-04-15T00:32Z] INFO  17:32:38,129 IntervalUtils - Processing 296880 bp from intervals
[2016-04-15T00:32Z] WARN  17:32:38,136 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:32Z] INFO  17:32:38,217 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:32Z] INFO  17:32:38,329 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:32Z] INFO  17:32:38,330 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:32Z] INFO  17:32:38,330 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:32Z] INFO  17:32:38,330 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:32Z] INFO  17:32:38,399 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:32Z] INFO  17:32:38,400 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:32Z] INFO  17:32:38,661 ProgressMeter -            done    322965.0    16.0 s      50.0 s       99.9%    16.0 s       0.0 s
[2016-04-15T00:32Z] INFO  17:32:38,662 ProgressMeter - Total runtime 16.46 secs, 0.27 min, 0.00 hours
[2016-04-15T00:32Z] INFO  17:32:38,662 MicroScheduler - 16037 reads were filtered out during the traversal out of approximately 208940 total reads (7.68%)
[2016-04-15T00:32Z] INFO  17:32:38,662 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:32Z] INFO  17:32:38,663 MicroScheduler -   -> 351 reads (0.17% of total) failing BadMateFilter
[2016-04-15T00:32Z] INFO  17:32:38,663 MicroScheduler -   -> 15549 reads (7.44% of total) failing DuplicateReadFilter
[2016-04-15T00:32Z] INFO  17:32:38,663 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:32Z] INFO  17:32:38,663 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:32Z] INFO  17:32:38,664 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:32Z] INFO  17:32:38,664 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:32Z] INFO  17:32:38,664 MicroScheduler -   -> 137 reads (0.07% of total) failing UnmappedReadFilter
[2016-04-15T00:32Z] INFO  17:32:38,669 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:32Z] INFO  17:32:38,796 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:32Z] GATK: UnifiedGenotyper
[2016-04-15T00:32Z] GATK: UnifiedGenotyper
[2016-04-15T00:32Z] INFO  17:32:39,206 ProgressMeter -            done    443441.0    19.0 s      42.0 s      100.0%    19.0 s       0.0 s
[2016-04-15T00:32Z] INFO  17:32:39,206 ProgressMeter - Total runtime 19.01 secs, 0.32 min, 0.01 hours
[2016-04-15T00:32Z] INFO  17:32:39,207 MicroScheduler - 15442 reads were filtered out during the traversal out of approximately 193562 total reads (7.98%)
[2016-04-15T00:32Z] INFO  17:32:39,207 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:32Z] INFO  17:32:39,208 MicroScheduler -   -> 336 reads (0.17% of total) failing BadMateFilter
[2016-04-15T00:32Z] INFO  17:32:39,208 MicroScheduler -   -> 14981 reads (7.74% of total) failing DuplicateReadFilter
[2016-04-15T00:32Z] INFO  17:32:39,208 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:32Z] INFO  17:32:39,208 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:32Z] INFO  17:32:39,209 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:32Z] INFO  17:32:39,209 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:32Z] INFO  17:32:39,209 MicroScheduler -   -> 125 reads (0.06% of total) failing UnmappedReadFilter
[2016-04-15T00:32Z] INFO  17:32:39,744 ProgressMeter -      17:7120837   1331045.0    30.0 s      22.0 s       51.8%    57.0 s      27.0 s
[2016-04-15T00:32Z] INFO  17:32:40,196 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:32Z] GATK: UnifiedGenotyper
[2016-04-15T00:32Z] INFO  17:32:40,714 ProgressMeter -     17:28783480   1337181.0    30.0 s      22.0 s       85.3%    35.0 s       5.0 s
[2016-04-15T00:32Z] INFO  17:32:41,181 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:32Z] GATK: UnifiedGenotyper
[2016-04-15T00:32Z] INFO  17:32:41,620 ProgressMeter -            done    175642.0    12.0 s      69.0 s       99.9%    12.0 s       0.0 s
[2016-04-15T00:32Z] INFO  17:32:41,620 ProgressMeter - Total runtime 12.21 secs, 0.20 min, 0.00 hours
[2016-04-15T00:32Z] INFO  17:32:41,621 MicroScheduler - 8861 reads were filtered out during the traversal out of approximately 110309 total reads (8.03%)
[2016-04-15T00:32Z] INFO  17:32:41,621 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:32Z] INFO  17:32:41,621 MicroScheduler -   -> 203 reads (0.18% of total) failing BadMateFilter
[2016-04-15T00:32Z] INFO  17:32:41,622 MicroScheduler -   -> 8560 reads (7.76% of total) failing DuplicateReadFilter
[2016-04-15T00:32Z] INFO  17:32:41,622 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:32Z] INFO  17:32:41,622 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:32Z] INFO  17:32:41,622 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:32Z] INFO  17:32:41,623 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:32Z] INFO  17:32:41,623 MicroScheduler -   -> 98 reads (0.09% of total) failing UnmappedReadFilter
[2016-04-15T00:32Z] INFO  17:32:41,876 ProgressMeter -            done   1795980.0    44.0 s      24.0 s      100.0%    44.0 s       0.0 s
[2016-04-15T00:32Z] INFO  17:32:41,876 ProgressMeter - Total runtime 44.40 secs, 0.74 min, 0.01 hours
[2016-04-15T00:32Z] INFO  17:32:41,877 MicroScheduler - 52359 reads were filtered out during the traversal out of approximately 743169 total reads (7.05%)
[2016-04-15T00:32Z] INFO  17:32:41,877 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:32Z] INFO  17:32:41,877 MicroScheduler -   -> 1271 reads (0.17% of total) failing BadMateFilter
[2016-04-15T00:32Z] INFO  17:32:41,877 MicroScheduler -   -> 50601 reads (6.81% of total) failing DuplicateReadFilter
[2016-04-15T00:32Z] INFO  17:32:41,878 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:32Z] INFO  17:32:41,878 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:32Z] INFO  17:32:41,878 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:32Z] INFO  17:32:41,878 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:32Z] INFO  17:32:41,879 MicroScheduler -   -> 487 reads (0.07% of total) failing UnmappedReadFilter
[2016-04-15T00:32Z] INFO  17:32:41,920 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:32Z] INFO  17:32:41,923 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:32Z] INFO  17:32:41,924 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:32Z] INFO  17:32:41,925 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:32Z] INFO  17:32:41,929 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/19/R14-18106_kapa-NGv3-PE100-NGv3-sort-19_31038849_46627578-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/19/R14-18106_kapa-NGv3-PE100-NGv3-19_31038849_46627578-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/19/tx/tmpSFLaZ5/R14-18106_kapa-NGv3-PE100-NGv3-19_31038849_46627578.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:32Z] INFO  17:32:41,939 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:32Z] INFO  17:32:41,939 HelpFormatter - Date/Time: 2016/04/14 17:32:41
[2016-04-15T00:32Z] INFO  17:32:41,940 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:32Z] INFO  17:32:41,940 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:32Z] INFO  17:32:42,061 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:32Z] INFO  17:32:42,064 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:32Z] INFO  17:32:42,065 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:32Z] INFO  17:32:42,065 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:32Z] INFO  17:32:42,070 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/19/R14-18106_kapa-NGv3-PE100-NGv3-sort-19_46627881_59128983-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/19/R14-18106_kapa-NGv3-PE100-NGv3-19_46627881_59128983-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/19/tx/tmpua6Azw/R14-18106_kapa-NGv3-PE100-NGv3-19_46627881_59128983.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:32Z] INFO  17:32:42,080 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:32Z] INFO  17:32:42,081 HelpFormatter - Date/Time: 2016/04/14 17:32:42
[2016-04-15T00:32Z] INFO  17:32:42,082 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:32Z] INFO  17:32:42,082 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:32Z] INFO  17:32:42,143 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:32Z] INFO  17:32:42,270 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:32Z] INFO  17:32:42,421 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:32Z] INFO  17:32:42,433 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:32Z] INFO  17:32:42,456 ProgressMeter -            done    242253.0    14.0 s      59.0 s       99.9%    14.0 s       0.0 s
[2016-04-15T00:32Z] INFO  17:32:42,457 ProgressMeter - Total runtime 14.44 secs, 0.24 min, 0.00 hours
[2016-04-15T00:32Z] INFO  17:32:42,457 MicroScheduler - 10054 reads were filtered out during the traversal out of approximately 126572 total reads (7.94%)
[2016-04-15T00:32Z] INFO  17:32:42,457 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:32Z] INFO  17:32:42,458 MicroScheduler -   -> 223 reads (0.18% of total) failing BadMateFilter
[2016-04-15T00:32Z] INFO  17:32:42,458 MicroScheduler -   -> 9735 reads (7.69% of total) failing DuplicateReadFilter
[2016-04-15T00:32Z] INFO  17:32:42,458 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:32Z] INFO  17:32:42,458 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:32Z] INFO  17:32:42,459 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:32Z] INFO  17:32:42,459 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:32Z] INFO  17:32:42,459 MicroScheduler -   -> 96 reads (0.08% of total) failing UnmappedReadFilter
[2016-04-15T00:32Z] INFO  17:32:42,512 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:32Z] INFO  17:32:42,514 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-15T00:32Z] INFO  17:32:42,521 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:32Z] INFO  17:32:42,613 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.09
[2016-04-15T00:32Z] INFO  17:32:42,851 ProgressMeter -            done   2608342.0    46.0 s      17.0 s      100.0%    46.0 s       0.0 s
[2016-04-15T00:32Z] INFO  17:32:42,851 ProgressMeter - Total runtime 46.48 secs, 0.77 min, 0.01 hours
[2016-04-15T00:32Z] INFO  17:32:42,851 MicroScheduler - 54218 reads were filtered out during the traversal out of approximately 692312 total reads (7.83%)
[2016-04-15T00:32Z] INFO  17:32:42,852 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:32Z] INFO  17:32:42,852 MicroScheduler -   -> 1290 reads (0.19% of total) failing BadMateFilter
[2016-04-15T00:32Z] INFO  17:32:42,852 MicroScheduler -   -> 52479 reads (7.58% of total) failing DuplicateReadFilter
[2016-04-15T00:32Z] INFO  17:32:42,852 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:32Z] INFO  17:32:42,853 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:32Z] INFO  17:32:42,853 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:32Z] INFO  17:32:42,853 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:32Z] INFO  17:32:42,853 MicroScheduler -   -> 449 reads (0.06% of total) failing UnmappedReadFilter
[2016-04-15T00:32Z] INFO  17:32:43,007 IntervalUtils - Processing 631764 bp from intervals
[2016-04-15T00:32Z] WARN  17:32:43,013 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:32Z] INFO  17:32:43,019 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:32Z] INFO  17:32:43,072 IntervalUtils - Processing 711484 bp from intervals
[2016-04-15T00:32Z] WARN  17:32:43,078 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:32Z] INFO  17:32:43,087 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:32Z] INFO  17:32:43,160 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:32Z] INFO  17:32:43,241 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:32Z] INFO  17:32:43,245 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:32Z] INFO  17:32:43,245 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:32Z] INFO  17:32:43,246 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:32Z] INFO  17:32:43,250 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/20/R14-18106_kapa-NGv3-PE100-NGv3-sort-20_0_15843471-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/20/R14-18106_kapa-NGv3-PE100-NGv3-20_0_15843471-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/20/tx/tmpqQjpGj/R14-18106_kapa-NGv3-PE100-NGv3-20_0_15843471.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:32Z] INFO  17:32:43,261 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:32Z] INFO  17:32:43,262 HelpFormatter - Date/Time: 2016/04/14 17:32:43
[2016-04-15T00:32Z] INFO  17:32:43,263 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:32Z] INFO  17:32:43,263 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:32Z] INFO  17:32:43,271 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:32Z] INFO  17:32:43,272 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:32Z] INFO  17:32:43,273 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:32Z] INFO  17:32:43,274 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:32Z] GATK: UnifiedGenotyper
[2016-04-15T00:32Z] INFO  17:32:43,303 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:32Z] INFO  17:32:43,304 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:32Z] INFO  17:32:43,305 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:32Z] INFO  17:32:43,305 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:32Z] INFO  17:32:43,315 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:32Z] INFO  17:32:43,316 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:32Z] INFO  17:32:43,345 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:32Z] INFO  17:32:43,345 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:32Z] INFO  17:32:43,378 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:32Z] INFO  17:32:43,446 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:32Z] INFO  17:32:43,645 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:32Z] INFO  17:32:43,654 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:32Z] GATK: UnifiedGenotyper
[2016-04-15T00:32Z] INFO  17:32:43,731 ProgressMeter -            done   1653515.0    35.0 s      21.0 s      100.0%    35.0 s       0.0 s
[2016-04-15T00:32Z] INFO  17:32:43,732 ProgressMeter - Total runtime 35.66 secs, 0.59 min, 0.01 hours
[2016-04-15T00:32Z] INFO  17:32:43,733 MicroScheduler - 40365 reads were filtered out during the traversal out of approximately 516263 total reads (7.82%)
[2016-04-15T00:32Z] INFO  17:32:43,734 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:32Z] INFO  17:32:43,734 MicroScheduler -   -> 900 reads (0.17% of total) failing BadMateFilter
[2016-04-15T00:32Z] INFO  17:32:43,735 MicroScheduler -   -> 39136 reads (7.58% of total) failing DuplicateReadFilter
[2016-04-15T00:32Z] INFO  17:32:43,735 ProgressMeter -            done   1490193.0    33.0 s      22.0 s      100.0%    33.0 s       0.0 s
[2016-04-15T00:32Z] INFO  17:32:43,735 ProgressMeter - Total runtime 33.04 secs, 0.55 min, 0.01 hours
[2016-04-15T00:32Z] INFO  17:32:43,736 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:32Z] INFO  17:32:43,736 MicroScheduler - 36907 reads were filtered out during the traversal out of approximately 465396 total reads (7.93%)
[2016-04-15T00:32Z] INFO  17:32:43,736 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:32Z] INFO  17:32:43,736 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:32Z] INFO  17:32:43,736 MicroScheduler -   -> 793 reads (0.17% of total) failing BadMateFilter
[2016-04-15T00:32Z] INFO  17:32:43,737 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:32Z] INFO  17:32:43,736 MicroScheduler -   -> 35784 reads (7.69% of total) failing DuplicateReadFilter
[2016-04-15T00:32Z] INFO  17:32:43,737 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:32Z] INFO  17:32:43,737 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:32Z] INFO  17:32:43,737 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:32Z] INFO  17:32:43,738 MicroScheduler -   -> 329 reads (0.06% of total) failing UnmappedReadFilter
[2016-04-15T00:32Z] INFO  17:32:43,737 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:32Z] INFO  17:32:43,737 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:32Z] INFO  17:32:43,738 MicroScheduler -   -> 330 reads (0.07% of total) failing UnmappedReadFilter
[2016-04-15T00:32Z] INFO  17:32:43,761 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.11
[2016-04-15T00:32Z] INFO  17:32:44,102 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:32Z] INFO  17:32:44,224 IntervalUtils - Processing 179899 bp from intervals
[2016-04-15T00:32Z] WARN  17:32:44,230 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:32Z] INFO  17:32:44,379 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:32Z] INFO  17:32:44,382 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:32Z] INFO  17:32:44,383 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:32Z] INFO  17:32:44,383 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:32Z] INFO  17:32:44,386 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:32Z] INFO  17:32:44,388 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/20/R14-18106_kapa-NGv3-PE100-NGv3-sort-20_15866408_31376818-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/20/R14-18106_kapa-NGv3-PE100-NGv3-20_15866408_31376818-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/20/tx/tmpCqdd92/R14-18106_kapa-NGv3-PE100-NGv3-20_15866408_31376818.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:32Z] INFO  17:32:44,415 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:32Z] INFO  17:32:44,417 HelpFormatter - Date/Time: 2016/04/14 17:32:44
[2016-04-15T00:32Z] INFO  17:32:44,417 ProgressMeter -            done   1302364.0    29.0 s      22.0 s      100.0%    29.0 s       0.0 s
[2016-04-15T00:32Z] INFO  17:32:44,417 ProgressMeter - Total runtime 29.38 secs, 0.49 min, 0.01 hours
[2016-04-15T00:32Z] INFO  17:32:44,417 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:32Z] INFO  17:32:44,418 MicroScheduler - 31198 reads were filtered out during the traversal out of approximately 393480 total reads (7.93%)
[2016-04-15T00:32Z] INFO  17:32:44,418 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:32Z] INFO  17:32:44,418 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:32Z] INFO  17:32:44,418 MicroScheduler -   -> 655 reads (0.17% of total) failing BadMateFilter
[2016-04-15T00:32Z] INFO  17:32:44,418 MicroScheduler -   -> 30295 reads (7.70% of total) failing DuplicateReadFilter
[2016-04-15T00:32Z] INFO  17:32:44,419 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:32Z] INFO  17:32:44,419 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:32Z] INFO  17:32:44,419 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:32Z] INFO  17:32:44,420 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:32Z] INFO  17:32:44,420 MicroScheduler -   -> 248 reads (0.06% of total) failing UnmappedReadFilter
[2016-04-15T00:32Z] GATK: UnifiedGenotyper
[2016-04-15T00:32Z] INFO  17:32:44,448 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:32Z] INFO  17:32:44,485 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:32Z] INFO  17:32:44,486 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:32Z] INFO  17:32:44,487 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:32Z] INFO  17:32:44,488 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:32Z] INFO  17:32:44,558 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:32Z] INFO  17:32:44,559 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:32Z] INFO  17:32:44,670 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:32Z] GATK: UnifiedGenotyper
[2016-04-15T00:32Z] INFO  17:32:44,940 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:32Z] INFO  17:32:44,950 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:32Z] INFO  17:32:45,008 ProgressMeter -     17:39681095    992719.0    30.0 s      30.0 s       48.1%    62.0 s      32.0 s
[2016-04-15T00:32Z] INFO  17:32:45,034 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-15T00:32Z] INFO  17:32:45,167 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:32Z] INFO  17:32:45,268 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:32Z] INFO  17:32:45,420 IntervalUtils - Processing 150913 bp from intervals
[2016-04-15T00:32Z] GATK: UnifiedGenotyper
[2016-04-15T00:32Z] WARN  17:32:45,426 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:32Z] INFO  17:32:45,544 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:32Z] INFO  17:32:45,635 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:32Z] INFO  17:32:45,635 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:32Z] INFO  17:32:45,636 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:32Z] INFO  17:32:45,636 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:32Z] GATK: UnifiedGenotyper
[2016-04-15T00:32Z] INFO  17:32:45,688 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:32Z] INFO  17:32:45,689 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:32Z] INFO  17:32:46,011 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:32Z] INFO  17:32:46,117 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:32Z] INFO  17:32:46,120 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:32Z] INFO  17:32:46,120 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:32Z] INFO  17:32:46,120 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:32Z] INFO  17:32:46,124 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/20/R14-18106_kapa-NGv3-PE100-NGv3-sort-20_31379406_47242465-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/20/R14-18106_kapa-NGv3-PE100-NGv3-20_31379406_47242465-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/20/tx/tmp68fUwp/R14-18106_kapa-NGv3-PE100-NGv3-20_31379406_47242465.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:32Z] INFO  17:32:46,162 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:32Z] INFO  17:32:46,163 HelpFormatter - Date/Time: 2016/04/14 17:32:46
[2016-04-15T00:32Z] INFO  17:32:46,163 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:32Z] INFO  17:32:46,163 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:32Z] INFO  17:32:46,268 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:32Z] INFO  17:32:46,271 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:32Z] INFO  17:32:46,276 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:32Z] INFO  17:32:46,278 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:32Z] GATK: UnifiedGenotyper
[2016-04-15T00:32Z] INFO  17:32:46,283 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/20/R14-18106_kapa-NGv3-PE100-NGv3-sort-20_47244085_62830269-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/20/R14-18106_kapa-NGv3-PE100-NGv3-20_47244085_62830269-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/20/tx/tmpULvS6L/R14-18106_kapa-NGv3-PE100-NGv3-20_47244085_62830269.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:32Z] INFO  17:32:46,309 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:32Z] INFO  17:32:46,310 HelpFormatter - Date/Time: 2016/04/14 17:32:46
[2016-04-15T00:32Z] INFO  17:32:46,311 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:32Z] INFO  17:32:46,311 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:32Z] INFO  17:32:46,357 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:32Z] INFO  17:32:46,540 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:32Z] INFO  17:32:46,639 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:32Z] INFO  17:32:46,654 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:32Z] INFO  17:32:46,774 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.12
[2016-04-15T00:32Z] INFO  17:32:46,803 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:32Z] INFO  17:32:46,814 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:32Z] INFO  17:32:46,901 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.09
[2016-04-15T00:32Z] INFO  17:32:46,908 ProgressMeter -     17:75471825   1439666.0    30.0 s      20.0 s       85.2%    35.0 s       5.0 s
[2016-04-15T00:32Z] INFO  17:32:47,347 IntervalUtils - Processing 269605 bp from intervals
[2016-04-15T00:32Z] WARN  17:32:47,352 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:32Z] INFO  17:32:47,434 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:32Z] INFO  17:32:47,443 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:32Z] INFO  17:32:47,446 IntervalUtils - Processing 321885 bp from intervals
[2016-04-15T00:32Z] WARN  17:32:47,452 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:32Z] INFO  17:32:47,456 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:32Z] INFO  17:32:47,457 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:32Z] INFO  17:32:47,457 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:32Z] INFO  17:32:47,461 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/20/R14-18106_kapa-NGv3-PE100-NGv3-sort-20_62831244_63025520-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/20/R14-18106_kapa-NGv3-PE100-NGv3-20_62831244_63025520-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/20/tx/tmpXax1Yk/R14-18106_kapa-NGv3-PE100-NGv3-20_62831244_63025520.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:32Z] INFO  17:32:47,487 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:32Z] INFO  17:32:47,487 HelpFormatter - Date/Time: 2016/04/14 17:32:47
[2016-04-15T00:32Z] INFO  17:32:47,487 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:32Z] INFO  17:32:47,488 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:32Z] INFO  17:32:47,534 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:32Z] INFO  17:32:47,535 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:32Z] INFO  17:32:47,536 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:32Z] INFO  17:32:47,537 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:32Z] INFO  17:32:47,547 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:32Z] INFO  17:32:47,603 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:32Z] INFO  17:32:47,604 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:32Z] INFO  17:32:47,659 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:32Z] INFO  17:32:47,678 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:32Z] INFO  17:32:47,679 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:32Z] INFO  17:32:47,685 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:32Z] INFO  17:32:47,686 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:32Z] INFO  17:32:47,777 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:32Z] INFO  17:32:47,778 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:32Z] INFO  17:32:47,838 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:32Z] INFO  17:32:47,841 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:32Z] INFO  17:32:47,842 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:32Z] INFO  17:32:47,842 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:32Z] INFO  17:32:47,847 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/21/R14-18106_kapa-NGv3-PE100-NGv3-sort-21_0_15517120-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/21/R14-18106_kapa-NGv3-PE100-NGv3-21_0_15517120-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/21/tx/tmp1_rk4w/R14-18106_kapa-NGv3-PE100-NGv3-21_0_15517120.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:32Z] INFO  17:32:47,859 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:32Z] INFO  17:32:47,871 HelpFormatter - Date/Time: 2016/04/14 17:32:47
[2016-04-15T00:32Z] INFO  17:32:47,872 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:32Z] INFO  17:32:47,873 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:32Z] INFO  17:32:47,943 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:32Z] INFO  17:32:47,952 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:32Z] INFO  17:32:48,003 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-15T00:32Z] INFO  17:32:48,081 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:32Z] INFO  17:32:48,314 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:32Z] INFO  17:32:48,324 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:32Z] INFO  17:32:48,413 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.09
[2016-04-15T00:32Z] INFO  17:32:48,442 IntervalUtils - Processing 4397 bp from intervals
[2016-04-15T00:32Z] WARN  17:32:48,447 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:32Z] INFO  17:32:48,485 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:32Z] INFO  17:32:48,488 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:32Z] INFO  17:32:48,489 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:32Z] INFO  17:32:48,489 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:32Z] INFO  17:32:48,493 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/21/R14-18106_kapa-NGv3-PE100-NGv3-sort-21_15524893_31045484-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/21/R14-18106_kapa-NGv3-PE100-NGv3-21_15524893_31045484-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/21/tx/tmpg24_Lu/R14-18106_kapa-NGv3-PE100-NGv3-21_15524893_31045484.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:32Z] INFO  17:32:48,512 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:32Z] INFO  17:32:48,513 HelpFormatter - Date/Time: 2016/04/14 17:32:48
[2016-04-15T00:32Z] INFO  17:32:48,513 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:32Z] INFO  17:32:48,514 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:32Z] INFO  17:32:48,561 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:32Z] INFO  17:32:48,605 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:32Z] INFO  17:32:48,607 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:32Z] INFO  17:32:48,607 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:32Z] INFO  17:32:48,608 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:32Z] INFO  17:32:48,655 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:32Z] INFO  17:32:48,656 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:32Z] INFO  17:32:48,680 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:32Z] INFO  17:32:48,683 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:32Z] INFO  17:32:48,684 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:32Z] INFO  17:32:48,684 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:32Z] INFO  17:32:48,689 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/21/R14-18106_kapa-NGv3-PE100-NGv3-sort-21_31062047_46591599-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/21/R14-18106_kapa-NGv3-PE100-NGv3-21_31062047_46591599-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/21/tx/tmpvnDK2T/R14-18106_kapa-NGv3-PE100-NGv3-21_31062047_46591599.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:32Z] INFO  17:32:48,708 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:32Z] INFO  17:32:48,716 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:32Z] INFO  17:32:48,717 HelpFormatter - Date/Time: 2016/04/14 17:32:48
[2016-04-15T00:32Z] INFO  17:32:48,717 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:32Z] INFO  17:32:48,718 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:32Z] INFO  17:32:48,733 IntervalUtils - Processing 4504 bp from intervals
[2016-04-15T00:32Z] WARN  17:32:48,746 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:32Z] INFO  17:32:48,870 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:32Z] INFO  17:32:48,892 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:32Z] INFO  17:32:48,893 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:32Z] INFO  17:32:48,894 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:32Z] INFO  17:32:48,895 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:32Z] INFO  17:32:48,941 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:32Z] INFO  17:32:48,942 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:32Z] INFO  17:32:48,986 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:32Z] INFO  17:32:49,017 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:32Z] INFO  17:32:49,028 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:32Z] INFO  17:32:49,148 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.12
[2016-04-15T00:32Z] INFO  17:32:49,221 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:32Z] INFO  17:32:49,240 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:32Z] INFO  17:32:49,331 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.09
[2016-04-15T00:32Z] INFO  17:32:49,484 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:32Z] INFO  17:32:49,486 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:32Z] INFO  17:32:49,486 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:32Z] INFO  17:32:49,486 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:32Z] INFO  17:32:49,490 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/21/R14-18106_kapa-NGv3-PE100-NGv3-sort-21_46595644_48129895-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/21/R14-18106_kapa-NGv3-PE100-NGv3-21_46595644_48129895-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/21/tx/tmplgav16/R14-18106_kapa-NGv3-PE100-NGv3-21_46595644_48129895.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:32Z] INFO  17:32:49,517 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:32Z] INFO  17:32:49,517 HelpFormatter - Date/Time: 2016/04/14 17:32:49
[2016-04-15T00:32Z] INFO  17:32:49,517 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:32Z] INFO  17:32:49,518 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:32Z] INFO  17:32:49,582 IntervalUtils - Processing 58639 bp from intervals
[2016-04-15T00:32Z] WARN  17:32:49,587 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:32Z] INFO  17:32:49,713 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:32Z] INFO  17:32:49,735 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:32Z] INFO  17:32:49,816 IntervalUtils - Processing 282111 bp from intervals
[2016-04-15T00:32Z] INFO  17:32:49,818 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:32Z] WARN  17:32:49,822 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:32Z] INFO  17:32:49,827 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:32Z] INFO  17:32:49,828 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:32Z] INFO  17:32:49,829 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:32Z] INFO  17:32:49,897 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:32Z] INFO  17:32:49,938 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:32Z] INFO  17:32:49,939 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:32Z] INFO  17:32:50,006 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:32Z] INFO  17:32:50,013 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:32Z] INFO  17:32:50,014 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:32Z] INFO  17:32:50,014 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:32Z] INFO  17:32:50,015 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:32Z] INFO  17:32:50,018 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:32Z] INFO  17:32:50,083 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-15T00:32Z] INFO  17:32:50,092 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:32Z] INFO  17:32:50,100 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:32Z] INFO  17:32:50,436 IntervalUtils - Processing 63011 bp from intervals
[2016-04-15T00:32Z] WARN  17:32:50,441 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:32Z] INFO  17:32:50,558 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:32Z] INFO  17:32:50,612 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:32Z] INFO  17:32:50,613 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:32Z] INFO  17:32:50,614 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:32Z] INFO  17:32:50,614 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:32Z] INFO  17:32:50,673 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:32Z] INFO  17:32:50,674 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:32Z] INFO  17:32:51,892 ProgressMeter -            done     15700.0     3.0 s       3.5 m       98.2%     3.0 s       0.0 s
[2016-04-15T00:32Z] INFO  17:32:51,893 ProgressMeter - Total runtime 3.29 secs, 0.05 min, 0.00 hours
[2016-04-15T00:32Z] INFO  17:32:51,894 MicroScheduler - 418 reads were filtered out during the traversal out of approximately 5917 total reads (7.06%)
[2016-04-15T00:32Z] INFO  17:32:51,895 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:32Z] INFO  17:32:51,895 MicroScheduler -   -> 11 reads (0.19% of total) failing BadMateFilter
[2016-04-15T00:32Z] INFO  17:32:51,896 MicroScheduler -   -> 404 reads (6.83% of total) failing DuplicateReadFilter
[2016-04-15T00:32Z] INFO  17:32:51,896 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:32Z] INFO  17:32:51,896 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:32Z] INFO  17:32:51,897 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:32Z] INFO  17:32:51,897 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:32Z] INFO  17:32:51,897 MicroScheduler -   -> 3 reads (0.05% of total) failing UnmappedReadFilter
[2016-04-15T00:32Z] INFO  17:32:52,010 ProgressMeter -            done   1664309.0    35.0 s      21.0 s      100.0%    35.0 s       0.0 s
[2016-04-15T00:32Z] INFO  17:32:52,010 ProgressMeter - Total runtime 35.12 secs, 0.59 min, 0.01 hours
[2016-04-15T00:32Z] INFO  17:32:52,010 MicroScheduler - 39287 reads were filtered out during the traversal out of approximately 486066 total reads (8.08%)
[2016-04-15T00:32Z] INFO  17:32:52,011 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:32Z] INFO  17:32:52,011 MicroScheduler -   -> 812 reads (0.17% of total) failing BadMateFilter
[2016-04-15T00:32Z] INFO  17:32:52,011 MicroScheduler -   -> 38145 reads (7.85% of total) failing DuplicateReadFilter
[2016-04-15T00:32Z] INFO  17:32:52,012 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:32Z] INFO  17:32:52,012 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:32Z] INFO  17:32:52,012 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:32Z] INFO  17:32:52,012 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:32Z] INFO  17:32:52,016 MicroScheduler -   -> 330 reads (0.07% of total) failing UnmappedReadFilter
[2016-04-15T00:32Z] INFO  17:32:53,343 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:32Z] INFO  17:32:53,549 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:32Z] GATK: UnifiedGenotyper
[2016-04-15T00:32Z] GATK: UnifiedGenotyper
[2016-04-15T00:32Z] INFO  17:32:53,957 ProgressMeter -            done     11154.0     5.0 s       7.6 m       98.3%     5.0 s       0.0 s
[2016-04-15T00:32Z] INFO  17:32:53,958 ProgressMeter - Total runtime 5.06 secs, 0.08 min, 0.00 hours
[2016-04-15T00:32Z] INFO  17:32:53,958 MicroScheduler - 1240 reads were filtered out during the traversal out of approximately 16217 total reads (7.65%)
[2016-04-15T00:32Z] INFO  17:32:53,959 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:32Z] INFO  17:32:53,959 MicroScheduler -   -> 50 reads (0.31% of total) failing BadMateFilter
[2016-04-15T00:32Z] INFO  17:32:53,959 MicroScheduler -   -> 1181 reads (7.28% of total) failing DuplicateReadFilter
[2016-04-15T00:32Z] INFO  17:32:53,960 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:32Z] INFO  17:32:53,960 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:32Z] INFO  17:32:53,960 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:32Z] INFO  17:32:53,960 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:32Z] INFO  17:32:53,961 MicroScheduler -   -> 9 reads (0.06% of total) failing UnmappedReadFilter
[2016-04-15T00:32Z] INFO  17:32:55,441 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:32Z] GATK: UnifiedGenotyper
[2016-04-15T00:32Z] INFO  17:32:56,449 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:32Z] INFO  17:32:56,452 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:32Z] INFO  17:32:56,452 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:32Z] INFO  17:32:56,453 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:32Z] INFO  17:32:56,457 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/22/R14-18106_kapa-NGv3-PE100-NGv3-sort-22_0_16258303-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/22/R14-18106_kapa-NGv3-PE100-NGv3-22_0_16258303-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/22/tx/tmpwXU5ST/R14-18106_kapa-NGv3-PE100-NGv3-22_0_16258303.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:32Z] INFO  17:32:56,467 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:32Z] INFO  17:32:56,467 HelpFormatter - Date/Time: 2016/04/14 17:32:56
[2016-04-15T00:32Z] INFO  17:32:56,467 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:32Z] INFO  17:32:56,468 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:32Z] INFO  17:32:56,694 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:32Z] INFO  17:32:56,842 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:32Z] INFO  17:32:56,845 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:32Z] INFO  17:32:56,846 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:32Z] INFO  17:32:56,847 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:32Z] INFO  17:32:56,851 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/22/R14-18106_kapa-NGv3-PE100-NGv3-sort-22_16266928_31795711-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/22/R14-18106_kapa-NGv3-PE100-NGv3-22_16266928_31795711-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/22/tx/tmpgQdWYP/R14-18106_kapa-NGv3-PE100-NGv3-22_16266928_31795711.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:32Z] INFO  17:32:56,890 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:32Z] INFO  17:32:56,891 HelpFormatter - Date/Time: 2016/04/14 17:32:56
[2016-04-15T00:32Z] INFO  17:32:56,891 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:32Z] INFO  17:32:56,896 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:32Z] INFO  17:32:56,908 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:32Z] INFO  17:32:56,917 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:32Z] INFO  17:32:57,015 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.10
[2016-04-15T00:32Z] INFO  17:32:57,061 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:32Z] INFO  17:32:57,266 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:32Z] INFO  17:32:57,275 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:32Z] INFO  17:32:57,306 IntervalUtils - Processing 118 bp from intervals
[2016-04-15T00:32Z] WARN  17:32:57,311 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:32Z] INFO  17:32:57,364 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.09
[2016-04-15T00:32Z] INFO  17:32:57,382 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:32Z] INFO  17:32:57,410 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:32Z] INFO  17:32:57,410 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:32Z] INFO  17:32:57,411 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:32Z] INFO  17:32:57,411 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:32Z] INFO  17:32:57,459 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:32Z] INFO  17:32:57,460 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:32Z] INFO  17:32:57,852 IntervalUtils - Processing 372769 bp from intervals
[2016-04-15T00:32Z] WARN  17:32:57,861 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:32Z] INFO  17:32:58,027 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:32Z] INFO  17:32:58,176 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:32Z] INFO  17:32:58,177 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:32Z] INFO  17:32:58,177 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:32Z] INFO  17:32:58,178 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:32Z] INFO  17:32:58,278 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:32Z] INFO  17:32:58,288 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:32Z] INFO  17:32:58,482 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:32Z] INFO  17:32:58,486 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:32Z] INFO  17:32:58,487 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:32Z] INFO  17:32:58,488 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:32Z] INFO  17:32:58,493 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/22/R14-18106_kapa-NGv3-PE100-NGv3-sort-22_31796605_47308085-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/22/R14-18106_kapa-NGv3-PE100-NGv3-22_31796605_47308085-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/22/tx/tmpcdg8TB/R14-18106_kapa-NGv3-PE100-NGv3-22_31796605_47308085.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:32Z] INFO  17:32:58,513 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:32Z] INFO  17:32:58,514 HelpFormatter - Date/Time: 2016/04/14 17:32:58
[2016-04-15T00:32Z] INFO  17:32:58,515 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:32Z] INFO  17:32:58,515 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:32Z] INFO  17:32:58,734 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:32Z] INFO  17:32:58,745 ProgressMeter -            done       118.0     1.0 s       3.1 h       84.7%     1.0 s       0.0 s
[2016-04-15T00:32Z] INFO  17:32:58,745 ProgressMeter - Total runtime 1.33 secs, 0.02 min, 0.00 hours
[2016-04-15T00:32Z] INFO  17:32:58,749 MicroScheduler - 19 reads were filtered out during the traversal out of approximately 290 total reads (6.55%)
[2016-04-15T00:32Z] INFO  17:32:58,749 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:32Z] INFO  17:32:58,750 MicroScheduler -   -> 1 reads (0.34% of total) failing BadMateFilter
[2016-04-15T00:32Z] INFO  17:32:58,750 MicroScheduler -   -> 18 reads (6.21% of total) failing DuplicateReadFilter
[2016-04-15T00:32Z] INFO  17:32:58,750 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:32Z] INFO  17:32:58,753 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:32Z] INFO  17:32:58,754 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:32Z] INFO  17:32:58,755 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:32Z] INFO  17:32:58,755 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:32Z] INFO  17:32:58,866 ProgressMeter -            done    144598.0     9.0 s      62.0 s       99.9%     9.0 s       0.0 s
[2016-04-15T00:32Z] INFO  17:32:58,866 ProgressMeter - Total runtime 9.04 secs, 0.15 min, 0.00 hours
[2016-04-15T00:32Z] INFO  17:32:58,867 MicroScheduler - 4665 reads were filtered out during the traversal out of approximately 60611 total reads (7.70%)
[2016-04-15T00:32Z] INFO  17:32:58,867 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:32Z] INFO  17:32:58,867 MicroScheduler -   -> 113 reads (0.19% of total) failing BadMateFilter
[2016-04-15T00:32Z] INFO  17:32:58,868 MicroScheduler -   -> 4510 reads (7.44% of total) failing DuplicateReadFilter
[2016-04-15T00:32Z] INFO  17:32:58,868 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:32Z] INFO  17:32:58,868 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:32Z] INFO  17:32:58,868 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:32Z] INFO  17:32:58,869 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:32Z] INFO  17:32:58,869 MicroScheduler -   -> 42 reads (0.07% of total) failing UnmappedReadFilter
[2016-04-15T00:32Z] INFO  17:32:58,985 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:32Z] INFO  17:32:58,994 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:32Z] INFO  17:32:59,066 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-15T00:32Z] INFO  17:32:59,520 IntervalUtils - Processing 366557 bp from intervals
[2016-04-15T00:32Z] WARN  17:32:59,526 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:32Z] INFO  17:32:59,608 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:32Z] INFO  17:32:59,730 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:32Z] INFO  17:32:59,732 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:32Z] INFO  17:32:59,732 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:32Z] INFO  17:32:59,733 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:32Z] INFO  17:32:59,776 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:32Z] INFO  17:32:59,777 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:33Z] INFO  17:33:00,132 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:33Z] GATK: UnifiedGenotyper
[2016-04-15T00:33Z] INFO  17:33:00,360 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:33Z] GATK: UnifiedGenotyper
[2016-04-15T00:33Z] INFO  17:33:02,860 ProgressMeter -            done    282818.0    12.0 s      43.0 s       99.9%    12.0 s       0.0 s
[2016-04-15T00:33Z] INFO  17:33:02,860 ProgressMeter - Total runtime 12.25 secs, 0.20 min, 0.00 hours
[2016-04-15T00:33Z] INFO  17:33:02,860 MicroScheduler - 7199 reads were filtered out during the traversal out of approximately 89580 total reads (8.04%)
[2016-04-15T00:33Z] INFO  17:33:02,861 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:33Z] INFO  17:33:02,861 MicroScheduler -   -> 163 reads (0.18% of total) failing BadMateFilter
[2016-04-15T00:33Z] INFO  17:33:02,861 MicroScheduler -   -> 6966 reads (7.78% of total) failing DuplicateReadFilter
[2016-04-15T00:33Z] INFO  17:33:02,862 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:33Z] INFO  17:33:02,862 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:33Z] INFO  17:33:02,862 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:33Z] INFO  17:33:02,862 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:33Z] INFO  17:33:02,863 MicroScheduler -   -> 70 reads (0.08% of total) failing UnmappedReadFilter
[2016-04-15T00:33Z] INFO  17:33:02,940 ProgressMeter -            done   2975101.0    53.0 s      17.0 s      100.0%    53.0 s       0.0 s
[2016-04-15T00:33Z] INFO  17:33:02,940 ProgressMeter - Total runtime 53.20 secs, 0.89 min, 0.01 hours
[2016-04-15T00:33Z] INFO  17:33:02,941 MicroScheduler - 58766 reads were filtered out during the traversal out of approximately 740926 total reads (7.93%)
[2016-04-15T00:33Z] INFO  17:33:02,941 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:33Z] INFO  17:33:02,941 MicroScheduler -   -> 1396 reads (0.19% of total) failing BadMateFilter
[2016-04-15T00:33Z] INFO  17:33:02,942 MicroScheduler -   -> 56876 reads (7.68% of total) failing DuplicateReadFilter
[2016-04-15T00:33Z] INFO  17:33:02,942 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:33Z] INFO  17:33:02,942 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:33Z] INFO  17:33:02,942 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:33Z] INFO  17:33:02,943 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:33Z] INFO  17:33:02,943 MicroScheduler -   -> 494 reads (0.07% of total) failing UnmappedReadFilter
[2016-04-15T00:33Z] INFO  17:33:03,105 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:33Z] INFO  17:33:03,108 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:33Z] INFO  17:33:03,109 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:33Z] INFO  17:33:03,110 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:33Z] INFO  17:33:03,114 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/22/R14-18106_kapa-NGv3-PE100-NGv3-sort-22_47309229_51304566-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/22/R14-18106_kapa-NGv3-PE100-NGv3-22_47309229_51304566-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/22/tx/tmpWpfShY/R14-18106_kapa-NGv3-PE100-NGv3-22_47309229_51304566.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:33Z] INFO  17:33:03,131 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:33Z] INFO  17:33:03,132 HelpFormatter - Date/Time: 2016/04/14 17:33:03
[2016-04-15T00:33Z] INFO  17:33:03,132 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:33Z] INFO  17:33:03,133 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:33Z] INFO  17:33:03,280 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:33Z] INFO  17:33:03,357 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:33Z] INFO  17:33:03,361 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:33Z] INFO  17:33:03,361 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:33Z] INFO  17:33:03,362 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:33Z] INFO  17:33:03,366 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/X/R14-18106_kapa-NGv3-PE100-NGv3-sort-X_0_15509380-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/X/R14-18106_kapa-NGv3-PE100-NGv3-X_0_15509380-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/X/tx/tmptV5VrP/R14-18106_kapa-NGv3-PE100-NGv3-X_0_15509380.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:33Z] INFO  17:33:03,374 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:33Z] INFO  17:33:03,375 HelpFormatter - Date/Time: 2016/04/14 17:33:03
[2016-04-15T00:33Z] INFO  17:33:03,376 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:33Z] INFO  17:33:03,376 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:33Z] INFO  17:33:03,433 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:33Z] INFO  17:33:03,443 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:33Z] INFO  17:33:03,525 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-15T00:33Z] INFO  17:33:03,534 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:33Z] INFO  17:33:03,735 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:33Z] INFO  17:33:03,745 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:33Z] INFO  17:33:03,799 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-15T00:33Z] INFO  17:33:03,917 IntervalUtils - Processing 81362 bp from intervals
[2016-04-15T00:33Z] WARN  17:33:03,944 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:33Z] INFO  17:33:04,058 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:33Z] INFO  17:33:04,113 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:33Z] INFO  17:33:04,115 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:33Z] INFO  17:33:04,116 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:33Z] INFO  17:33:04,116 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:33Z] INFO  17:33:04,159 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:33Z] INFO  17:33:04,160 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:33Z] INFO  17:33:04,163 IntervalUtils - Processing 114122 bp from intervals
[2016-04-15T00:33Z] WARN  17:33:04,168 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:33Z] INFO  17:33:04,223 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:33Z] INFO  17:33:04,245 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:33Z] INFO  17:33:04,295 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:33Z] INFO  17:33:04,296 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:33Z] INFO  17:33:04,297 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:33Z] INFO  17:33:04,298 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:33Z] INFO  17:33:04,327 ProgressMeter -            done    403180.0    18.0 s      46.0 s      100.0%    18.0 s       0.0 s
[2016-04-15T00:33Z] INFO  17:33:04,327 ProgressMeter - Total runtime 18.69 secs, 0.31 min, 0.01 hours
[2016-04-15T00:33Z] INFO  17:33:04,327 MicroScheduler - 15566 reads were filtered out during the traversal out of approximately 196216 total reads (7.93%)
[2016-04-15T00:33Z] INFO  17:33:04,328 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:33Z] INFO  17:33:04,328 MicroScheduler -   -> 348 reads (0.18% of total) failing BadMateFilter
[2016-04-15T00:33Z] INFO  17:33:04,328 MicroScheduler -   -> 15093 reads (7.69% of total) failing DuplicateReadFilter
[2016-04-15T00:33Z] INFO  17:33:04,328 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:33Z] INFO  17:33:04,329 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:33Z] INFO  17:33:04,329 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:33Z] INFO  17:33:04,329 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:33Z] INFO  17:33:04,329 MicroScheduler -   -> 125 reads (0.06% of total) failing UnmappedReadFilter
[2016-04-15T00:33Z] INFO  17:33:04,351 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:33Z] INFO  17:33:04,352 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:33Z] INFO  17:33:04,441 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:33Z] GATK: UnifiedGenotyper
[2016-04-15T00:33Z] GATK: UnifiedGenotyper
[2016-04-15T00:33Z] INFO  17:33:05,258 ProgressMeter -      19:4658017   1389517.0    30.0 s      21.0 s       32.8%    91.0 s      61.0 s
[2016-04-15T00:33Z] INFO  17:33:05,769 ProgressMeter -            done    626854.0    21.0 s      33.0 s      100.0%    21.0 s       0.0 s
[2016-04-15T00:33Z] INFO  17:33:05,769 ProgressMeter - Total runtime 21.28 secs, 0.35 min, 0.01 hours
[2016-04-15T00:33Z] INFO  17:33:05,769 MicroScheduler - 19894 reads were filtered out during the traversal out of approximately 246609 total reads (8.07%)
[2016-04-15T00:33Z] INFO  17:33:05,770 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:33Z] INFO  17:33:05,770 MicroScheduler -   -> 418 reads (0.17% of total) failing BadMateFilter
[2016-04-15T00:33Z] INFO  17:33:05,770 MicroScheduler -   -> 19327 reads (7.84% of total) failing DuplicateReadFilter
[2016-04-15T00:33Z] INFO  17:33:05,770 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:33Z] INFO  17:33:05,771 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:33Z] INFO  17:33:05,771 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:33Z] INFO  17:33:05,771 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:33Z] INFO  17:33:05,771 MicroScheduler -   -> 149 reads (0.06% of total) failing UnmappedReadFilter
[2016-04-15T00:33Z] INFO  17:33:05,885 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:33Z] GATK: UnifiedGenotyper
[2016-04-15T00:33Z] INFO  17:33:07,153 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:33Z] INFO  17:33:07,171 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:33Z] INFO  17:33:07,176 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:33Z] INFO  17:33:07,176 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:33Z] INFO  17:33:07,177 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:33Z] INFO  17:33:07,183 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/X/R14-18106_kapa-NGv3-PE100-NGv3-sort-X_15518899_31090070-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/X/R14-18106_kapa-NGv3-PE100-NGv3-X_15518899_31090070-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/X/tx/tmpmHyinT/R14-18106_kapa-NGv3-PE100-NGv3-X_15518899_31090070.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:33Z] INFO  17:33:07,195 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:33Z] INFO  17:33:07,196 HelpFormatter - Date/Time: 2016/04/14 17:33:07
[2016-04-15T00:33Z] INFO  17:33:07,196 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:33Z] INFO  17:33:07,197 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:33Z] INFO  17:33:07,446 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:33Z] GATK: UnifiedGenotyper
[2016-04-15T00:33Z] INFO  17:33:07,693 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:33Z] INFO  17:33:07,702 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:33Z] INFO  17:33:07,780 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-15T00:33Z] INFO  17:33:07,863 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:33Z] INFO  17:33:07,866 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:33Z] INFO  17:33:07,867 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:33Z] INFO  17:33:07,867 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:33Z] INFO  17:33:07,872 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/X/R14-18106_kapa-NGv3-PE100-NGv3-sort-X_31139949_46696637-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/X/R14-18106_kapa-NGv3-PE100-NGv3-X_31139949_46696637-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/X/tx/tmpDXX6lY/R14-18106_kapa-NGv3-PE100-NGv3-X_31139949_46696637.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:33Z] INFO  17:33:07,886 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:33Z] INFO  17:33:07,894 HelpFormatter - Date/Time: 2016/04/14 17:33:07
[2016-04-15T00:33Z] INFO  17:33:07,895 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:33Z] INFO  17:33:07,896 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:33Z] INFO  17:33:08,083 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:33Z] INFO  17:33:08,283 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:33Z] INFO  17:33:08,292 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:33Z] INFO  17:33:08,328 IntervalUtils - Processing 133046 bp from intervals
[2016-04-15T00:33Z] INFO  17:33:08,347 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-15T00:33Z] INFO  17:33:08,347 ProgressMeter -     19:22486660   1100304.0    30.0 s      27.0 s       88.3%    33.0 s       3.0 s
[2016-04-15T00:33Z] WARN  17:33:08,352 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:33Z] INFO  17:33:08,483 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:33Z] INFO  17:33:08,607 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:33Z] INFO  17:33:08,608 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:33Z] INFO  17:33:08,609 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:33Z] INFO  17:33:08,609 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:33Z] INFO  17:33:08,678 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:33Z] INFO  17:33:08,678 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:33Z] INFO  17:33:08,692 IntervalUtils - Processing 99894 bp from intervals
[2016-04-15T00:33Z] WARN  17:33:08,697 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:33Z] INFO  17:33:08,797 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:33Z] INFO  17:33:08,891 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:33Z] INFO  17:33:08,892 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:33Z] INFO  17:33:08,892 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:33Z] INFO  17:33:08,893 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:33Z] INFO  17:33:08,959 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:33Z] INFO  17:33:08,959 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:33Z] INFO  17:33:09,165 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:33Z] INFO  17:33:09,169 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:33Z] INFO  17:33:09,169 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:33Z] INFO  17:33:09,170 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:33Z] INFO  17:33:09,174 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/X/R14-18106_kapa-NGv3-PE100-NGv3-sort-X_46712910_62570698-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/X/R14-18106_kapa-NGv3-PE100-NGv3-X_46712910_62570698-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/X/tx/tmphV0_Ex/R14-18106_kapa-NGv3-PE100-NGv3-X_46712910_62570698.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:33Z] INFO  17:33:09,193 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:33Z] INFO  17:33:09,194 HelpFormatter - Date/Time: 2016/04/14 17:33:09
[2016-04-15T00:33Z] INFO  17:33:09,194 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:33Z] INFO  17:33:09,195 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:33Z] INFO  17:33:09,274 ProgressMeter -            done   2489748.0    54.0 s      21.0 s      100.0%    54.0 s       0.0 s
[2016-04-15T00:33Z] INFO  17:33:09,274 ProgressMeter - Total runtime 54.28 secs, 0.90 min, 0.02 hours
[2016-04-15T00:33Z] INFO  17:33:09,275 MicroScheduler - 67072 reads were filtered out during the traversal out of approximately 871955 total reads (7.69%)
[2016-04-15T00:33Z] INFO  17:33:09,275 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:33Z] INFO  17:33:09,275 MicroScheduler -   -> 1474 reads (0.17% of total) failing BadMateFilter
[2016-04-15T00:33Z] INFO  17:33:09,276 MicroScheduler -   -> 65060 reads (7.46% of total) failing DuplicateReadFilter
[2016-04-15T00:33Z] INFO  17:33:09,276 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:33Z] INFO  17:33:09,276 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:33Z] INFO  17:33:09,276 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:33Z] INFO  17:33:09,276 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:33Z] INFO  17:33:09,277 MicroScheduler -   -> 538 reads (0.06% of total) failing UnmappedReadFilter
[2016-04-15T00:33Z] INFO  17:33:09,408 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:33Z] INFO  17:33:09,644 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:33Z] INFO  17:33:09,658 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:33Z] INFO  17:33:09,759 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.10
[2016-04-15T00:33Z] INFO  17:33:10,194 IntervalUtils - Processing 228299 bp from intervals
[2016-04-15T00:33Z] WARN  17:33:10,200 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:33Z] INFO  17:33:10,227 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:33Z] INFO  17:33:10,231 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:33Z] INFO  17:33:10,232 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:33Z] INFO  17:33:10,233 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:33Z] INFO  17:33:10,238 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/X/R14-18106_kapa-NGv3-PE100-NGv3-sort-X_62857907_78427545-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/X/R14-18106_kapa-NGv3-PE100-NGv3-X_62857907_78427545-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/X/tx/tmpjofJsd/R14-18106_kapa-NGv3-PE100-NGv3-X_62857907_78427545.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:33Z] INFO  17:33:10,248 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:33Z] INFO  17:33:10,250 HelpFormatter - Date/Time: 2016/04/14 17:33:10
[2016-04-15T00:33Z] INFO  17:33:10,250 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:33Z] INFO  17:33:10,251 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:33Z] INFO  17:33:10,293 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:33Z] INFO  17:33:10,368 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:33Z] INFO  17:33:10,370 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:33Z] INFO  17:33:10,371 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:33Z] INFO  17:33:10,372 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:33Z] INFO  17:33:10,435 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:33Z] INFO  17:33:10,436 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:33Z] INFO  17:33:10,563 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:33Z] INFO  17:33:10,801 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:33Z] INFO  17:33:10,813 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:33Z] INFO  17:33:10,896 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-15T00:33Z] INFO  17:33:10,910 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:33Z] GATK: UnifiedGenotyper
[2016-04-15T00:33Z] INFO  17:33:11,306 IntervalUtils - Processing 175038 bp from intervals
[2016-04-15T00:33Z] WARN  17:33:11,322 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:33Z] INFO  17:33:11,456 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:33Z] INFO  17:33:11,564 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:33Z] INFO  17:33:11,576 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:33Z] INFO  17:33:11,577 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:33Z] INFO  17:33:11,578 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:33Z] INFO  17:33:11,627 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:33Z] INFO  17:33:11,628 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:33Z] INFO  17:33:11,801 ProgressMeter -            done   1154046.0    33.0 s      29.0 s      100.0%    33.0 s       0.0 s
[2016-04-15T00:33Z] INFO  17:33:11,801 ProgressMeter - Total runtime 33.47 secs, 0.56 min, 0.01 hours
[2016-04-15T00:33Z] INFO  17:33:11,802 MicroScheduler - 37095 reads were filtered out during the traversal out of approximately 459515 total reads (8.07%)
[2016-04-15T00:33Z] INFO  17:33:11,802 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:33Z] INFO  17:33:11,802 MicroScheduler -   -> 790 reads (0.17% of total) failing BadMateFilter
[2016-04-15T00:33Z] INFO  17:33:11,802 MicroScheduler -   -> 35986 reads (7.83% of total) failing DuplicateReadFilter
[2016-04-15T00:33Z] INFO  17:33:11,803 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:33Z] INFO  17:33:11,803 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:33Z] INFO  17:33:11,803 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:33Z] INFO  17:33:11,803 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:33Z] INFO  17:33:11,804 MicroScheduler -   -> 319 reads (0.07% of total) failing UnmappedReadFilter
[2016-04-15T00:33Z] INFO  17:33:13,285 ProgressMeter -     19:39669164   1311466.0    30.0 s      22.0 s       44.7%    67.0 s      37.0 s
[2016-04-15T00:33Z] INFO  17:33:13,305 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:33Z] INFO  17:33:13,321 ProgressMeter -     19:51381760   1259596.0    30.0 s      23.0 s       38.9%    77.0 s      47.0 s
[2016-04-15T00:33Z] GATK: UnifiedGenotyper
[2016-04-15T00:33Z] INFO  17:33:14,279 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:33Z] INFO  17:33:14,282 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:33Z] INFO  17:33:14,282 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:33Z] INFO  17:33:14,282 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:33Z] INFO  17:33:14,286 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/X/R14-18106_kapa-NGv3-PE100-NGv3-sort-X_78616585_95940189-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/X/R14-18106_kapa-NGv3-PE100-NGv3-X_78616585_95940189-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/X/tx/tmpp3OvUf/R14-18106_kapa-NGv3-PE100-NGv3-X_78616585_95940189.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:33Z] INFO  17:33:14,318 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:33Z] INFO  17:33:14,318 HelpFormatter - Date/Time: 2016/04/14 17:33:14
[2016-04-15T00:33Z] INFO  17:33:14,319 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:33Z] INFO  17:33:14,319 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:33Z] INFO  17:33:14,574 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:33Z] INFO  17:33:14,799 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:33Z] INFO  17:33:14,819 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:33Z] INFO  17:33:14,882 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-15T00:33Z] INFO  17:33:15,235 IntervalUtils - Processing 45787 bp from intervals
[2016-04-15T00:33Z] WARN  17:33:15,240 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:33Z] INFO  17:33:15,338 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:33Z] INFO  17:33:15,435 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:33Z] INFO  17:33:15,436 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:33Z] INFO  17:33:15,436 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:33Z] INFO  17:33:15,436 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:33Z] INFO  17:33:15,480 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:33Z] INFO  17:33:15,481 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:33Z] INFO  17:33:16,351 ProgressMeter -            done    281156.0    12.0 s      42.0 s       99.9%    12.0 s       0.0 s
[2016-04-15T00:33Z] INFO  17:33:16,352 ProgressMeter - Total runtime 12.06 secs, 0.20 min, 0.00 hours
[2016-04-15T00:33Z] INFO  17:33:16,353 MicroScheduler - 6989 reads were filtered out during the traversal out of approximately 88515 total reads (7.90%)
[2016-04-15T00:33Z] INFO  17:33:16,354 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:33Z] INFO  17:33:16,354 MicroScheduler -   -> 192 reads (0.22% of total) failing BadMateFilter
[2016-04-15T00:33Z] INFO  17:33:16,354 MicroScheduler -   -> 6737 reads (7.61% of total) failing DuplicateReadFilter
[2016-04-15T00:33Z] INFO  17:33:16,354 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:33Z] INFO  17:33:16,355 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:33Z] INFO  17:33:16,355 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:33Z] INFO  17:33:16,355 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:33Z] INFO  17:33:16,356 MicroScheduler -   -> 60 reads (0.07% of total) failing UnmappedReadFilter
[2016-04-15T00:33Z] INFO  17:33:16,391 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:33Z] INFO  17:33:16,395 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:33Z] INFO  17:33:16,396 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:33Z] INFO  17:33:16,397 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:33Z] INFO  17:33:16,402 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/X/R14-18106_kapa-NGv3-PE100-NGv3-sort-X_95990756_111698889-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/X/R14-18106_kapa-NGv3-PE100-NGv3-X_95990756_111698889-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/X/tx/tmpr4MmS1/R14-18106_kapa-NGv3-PE100-NGv3-X_95990756_111698889.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:33Z] INFO  17:33:16,428 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:33Z] INFO  17:33:16,429 HelpFormatter - Date/Time: 2016/04/14 17:33:16
[2016-04-15T00:33Z] INFO  17:33:16,430 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:33Z] INFO  17:33:16,431 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:33Z] INFO  17:33:16,681 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:33Z] INFO  17:33:16,932 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:33Z] INFO  17:33:16,943 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:33Z] INFO  17:33:17,177 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.23
[2016-04-15T00:33Z] INFO  17:33:17,547 ProgressMeter -     20:62598734   1182920.0    30.0 s      25.0 s       96.3%    31.0 s       1.0 s
[2016-04-15T00:33Z] INFO  17:33:17,682 IntervalUtils - Processing 181656 bp from intervals
[2016-04-15T00:33Z] WARN  17:33:17,688 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:33Z] INFO  17:33:17,701 ProgressMeter -     20:44828162   1107531.0    30.0 s      27.0 s       91.0%    32.0 s       2.0 s
[2016-04-15T00:33Z] INFO  17:33:17,709 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:33Z] INFO  17:33:17,794 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:33Z] INFO  17:33:17,804 ProgressMeter -            done    613276.0    13.0 s      22.0 s      100.0%    13.0 s       0.0 s
[2016-04-15T00:33Z] INFO  17:33:17,805 ProgressMeter - Total runtime 13.69 secs, 0.23 min, 0.00 hours
[2016-04-15T00:33Z] INFO  17:33:17,805 MicroScheduler - 9959 reads were filtered out during the traversal out of approximately 125658 total reads (7.93%)
[2016-04-15T00:33Z] INFO  17:33:17,806 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:33Z] INFO  17:33:17,806 MicroScheduler -   -> 255 reads (0.20% of total) failing BadMateFilter
[2016-04-15T00:33Z] INFO  17:33:17,807 MicroScheduler -   -> 9632 reads (7.67% of total) failing DuplicateReadFilter
[2016-04-15T00:33Z] INFO  17:33:17,807 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:33Z] INFO  17:33:17,807 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:33Z] INFO  17:33:17,807 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:33Z] INFO  17:33:17,808 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:33Z] INFO  17:33:17,808 MicroScheduler -   -> 72 reads (0.06% of total) failing UnmappedReadFilter
[2016-04-15T00:33Z] INFO  17:33:17,872 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:33Z] INFO  17:33:17,873 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:33Z] INFO  17:33:17,874 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:33Z] INFO  17:33:17,882 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:33Z] INFO  17:33:17,939 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:33Z] INFO  17:33:17,940 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:33Z] GATK: UnifiedGenotyper
[2016-04-15T00:33Z] INFO  17:33:18,468 ProgressMeter -            done   1223679.0    30.0 s      25.0 s      100.0%    30.0 s       0.0 s
[2016-04-15T00:33Z] INFO  17:33:18,468 ProgressMeter - Total runtime 30.93 secs, 0.52 min, 0.01 hours
[2016-04-15T00:33Z] INFO  17:33:18,469 MicroScheduler - 30601 reads were filtered out during the traversal out of approximately 379479 total reads (8.06%)
[2016-04-15T00:33Z] INFO  17:33:18,469 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:33Z] INFO  17:33:18,470 MicroScheduler -   -> 713 reads (0.19% of total) failing BadMateFilter
[2016-04-15T00:33Z] INFO  17:33:18,470 MicroScheduler -   -> 29640 reads (7.81% of total) failing DuplicateReadFilter
[2016-04-15T00:33Z] INFO  17:33:18,470 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:33Z] INFO  17:33:18,470 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:33Z] INFO  17:33:18,471 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:33Z] INFO  17:33:18,471 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:33Z] INFO  17:33:18,471 MicroScheduler -   -> 248 reads (0.07% of total) failing UnmappedReadFilter
[2016-04-15T00:33Z] INFO  17:33:18,979 ProgressMeter -            done    248425.0    10.0 s      40.0 s      100.0%    10.0 s       0.0 s
[2016-04-15T00:33Z] INFO  17:33:18,979 ProgressMeter - Total runtime 10.09 secs, 0.17 min, 0.00 hours
[2016-04-15T00:33Z] INFO  17:33:18,980 MicroScheduler - 4961 reads were filtered out during the traversal out of approximately 61790 total reads (8.03%)
[2016-04-15T00:33Z] INFO  17:33:18,980 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:33Z] INFO  17:33:18,980 MicroScheduler -   -> 101 reads (0.16% of total) failing BadMateFilter
[2016-04-15T00:33Z] INFO  17:33:18,981 MicroScheduler -   -> 4818 reads (7.80% of total) failing DuplicateReadFilter
[2016-04-15T00:33Z] INFO  17:33:18,981 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:33Z] INFO  17:33:18,981 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:33Z] INFO  17:33:18,981 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:33Z] INFO  17:33:18,982 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:33Z] INFO  17:33:18,982 MicroScheduler -   -> 42 reads (0.07% of total) failing UnmappedReadFilter
[2016-04-15T00:33Z] INFO  17:33:19,145 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:33Z] GATK: UnifiedGenotyper
[2016-04-15T00:33Z] INFO  17:33:19,848 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:33Z] INFO  17:33:20,042 ProgressMeter -     21:46311824    852347.0    30.0 s      35.0 s       99.2%    30.0 s       0.0 s
[2016-04-15T00:33Z] GATK: UnifiedGenotyper
[2016-04-15T00:33Z] INFO  17:33:20,257 ProgressMeter -            done    861650.0    30.0 s      35.0 s      100.0%    30.0 s       0.0 s
[2016-04-15T00:33Z] INFO  17:33:20,257 ProgressMeter - Total runtime 30.24 secs, 0.50 min, 0.01 hours
[2016-04-15T00:33Z] INFO  17:33:20,258 MicroScheduler - 31462 reads were filtered out during the traversal out of approximately 382849 total reads (8.22%)
[2016-04-15T00:33Z] INFO  17:33:20,258 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:33Z] INFO  17:33:20,258 MicroScheduler -   -> 640 reads (0.17% of total) failing BadMateFilter
[2016-04-15T00:33Z] INFO  17:33:20,258 MicroScheduler -   -> 30579 reads (7.99% of total) failing DuplicateReadFilter
[2016-04-15T00:33Z] INFO  17:33:20,259 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:33Z] INFO  17:33:20,259 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:33Z] INFO  17:33:20,259 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:33Z] INFO  17:33:20,259 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:33Z] INFO  17:33:20,260 MicroScheduler -   -> 243 reads (0.06% of total) failing UnmappedReadFilter
[2016-04-15T00:33Z] INFO  17:33:20,328 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:33Z] INFO  17:33:20,488 ProgressMeter -            done   1208060.0    32.0 s      27.0 s      100.0%    32.0 s       0.0 s
[2016-04-15T00:33Z] INFO  17:33:20,488 ProgressMeter - Total runtime 32.81 secs, 0.55 min, 0.01 hours
[2016-04-15T00:33Z] INFO  17:33:20,488 MicroScheduler - 37176 reads were filtered out during the traversal out of approximately 461863 total reads (8.05%)
[2016-04-15T00:33Z] INFO  17:33:20,489 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:33Z] INFO  17:33:20,489 MicroScheduler -   -> 825 reads (0.18% of total) failing BadMateFilter
[2016-04-15T00:33Z] INFO  17:33:20,489 MicroScheduler -   -> 36070 reads (7.81% of total) failing DuplicateReadFilter
[2016-04-15T00:33Z] INFO  17:33:20,489 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:33Z] INFO  17:33:20,490 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:33Z] INFO  17:33:20,490 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:33Z] INFO  17:33:20,490 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:33Z] INFO  17:33:20,491 MicroScheduler -   -> 281 reads (0.06% of total) failing UnmappedReadFilter
[2016-04-15T00:33Z] GATK: UnifiedGenotyper
[2016-04-15T00:33Z] INFO  17:33:21,107 ProgressMeter -            done    312881.0    12.0 s      39.0 s      100.0%    12.0 s       0.0 s
[2016-04-15T00:33Z] INFO  17:33:21,107 ProgressMeter - Total runtime 12.50 secs, 0.21 min, 0.00 hours
[2016-04-15T00:33Z] INFO  17:33:21,108 MicroScheduler - 6368 reads were filtered out during the traversal out of approximately 80835 total reads (7.88%)
[2016-04-15T00:33Z] INFO  17:33:21,108 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:33Z] INFO  17:33:21,108 MicroScheduler -   -> 129 reads (0.16% of total) failing BadMateFilter
[2016-04-15T00:33Z] INFO  17:33:21,109 MicroScheduler -   -> 6189 reads (7.66% of total) failing DuplicateReadFilter
[2016-04-15T00:33Z] INFO  17:33:21,109 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:33Z] INFO  17:33:21,109 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:33Z] INFO  17:33:21,110 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:33Z] INFO  17:33:21,110 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:33Z] INFO  17:33:21,110 MicroScheduler -   -> 50 reads (0.06% of total) failing UnmappedReadFilter
[2016-04-15T00:33Z] INFO  17:33:21,125 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:33Z] INFO  17:33:21,128 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:33Z] INFO  17:33:21,129 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:33Z] INFO  17:33:21,129 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:33Z] INFO  17:33:21,134 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/X/R14-18106_kapa-NGv3-PE100-NGv3-sort-X_111874647_128581278-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/X/R14-18106_kapa-NGv3-PE100-NGv3-X_111874647_128581278-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/X/tx/tmpAfvYXm/R14-18106_kapa-NGv3-PE100-NGv3-X_111874647_128581278.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:33Z] INFO  17:33:21,149 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:33Z] INFO  17:33:21,150 HelpFormatter - Date/Time: 2016/04/14 17:33:21
[2016-04-15T00:33Z] INFO  17:33:21,150 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:33Z] INFO  17:33:21,154 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:33Z] INFO  17:33:21,323 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:33Z] INFO  17:33:21,642 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:33Z] INFO  17:33:21,658 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:33Z] INFO  17:33:21,739 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-15T00:33Z] INFO  17:33:21,754 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:33Z] INFO  17:33:21,878 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:33Z] INFO  17:33:22,013 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:33Z] INFO  17:33:22,016 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:33Z] INFO  17:33:22,016 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:33Z] INFO  17:33:22,017 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:33Z] INFO  17:33:22,021 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/X/R14-18106_kapa-NGv3-PE100-NGv3-sort-X_128582278_144329181-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/X/R14-18106_kapa-NGv3-PE100-NGv3-X_128582278_144329181-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/X/tx/tmpWyTtc8/R14-18106_kapa-NGv3-PE100-NGv3-X_128582278_144329181.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:33Z] GATK: UnifiedGenotyper
[2016-04-15T00:33Z] INFO  17:33:22,039 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:33Z] INFO  17:33:22,052 HelpFormatter - Date/Time: 2016/04/14 17:33:22
[2016-04-15T00:33Z] INFO  17:33:22,053 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:33Z] INFO  17:33:22,053 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:33Z] INFO  17:33:22,069 IntervalUtils - Processing 115535 bp from intervals
[2016-04-15T00:33Z] WARN  17:33:22,076 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:33Z] GATK: UnifiedGenotyper
[2016-04-15T00:33Z] INFO  17:33:22,175 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:33Z] INFO  17:33:22,211 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:33Z] INFO  17:33:22,255 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:33Z] INFO  17:33:22,256 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:33Z] INFO  17:33:22,257 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:33Z] INFO  17:33:22,257 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:33Z] INFO  17:33:22,308 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:33Z] INFO  17:33:22,309 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:33Z] INFO  17:33:22,398 ProgressMeter -            done    104106.0     6.0 s      66.0 s       99.9%     6.0 s       0.0 s
[2016-04-15T00:33Z] INFO  17:33:22,400 ProgressMeter - Total runtime 6.96 secs, 0.12 min, 0.00 hours
[2016-04-15T00:33Z] INFO  17:33:22,400 MicroScheduler - 1983 reads were filtered out during the traversal out of approximately 25755 total reads (7.70%)
[2016-04-15T00:33Z] INFO  17:33:22,401 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:33Z] INFO  17:33:22,402 MicroScheduler -   -> 56 reads (0.22% of total) failing BadMateFilter
[2016-04-15T00:33Z] INFO  17:33:22,402 MicroScheduler -   -> 1917 reads (7.44% of total) failing DuplicateReadFilter
[2016-04-15T00:33Z] INFO  17:33:22,403 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:33Z] INFO  17:33:22,403 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:33Z] INFO  17:33:22,404 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:33Z] INFO  17:33:22,405 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:33Z] INFO  17:33:22,405 MicroScheduler -   -> 10 reads (0.04% of total) failing UnmappedReadFilter
[2016-04-15T00:33Z] INFO  17:33:22,410 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:33Z] INFO  17:33:22,421 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:33Z] INFO  17:33:22,494 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-15T00:33Z] INFO  17:33:22,531 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:33Z] GATK: HaplotypeCaller
[2016-04-15T00:33Z] INFO  17:33:22,871 IntervalUtils - Processing 143302 bp from intervals
[2016-04-15T00:33Z] WARN  17:33:22,877 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:33Z] INFO  17:33:22,966 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:33Z] INFO  17:33:22,969 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:33Z] INFO  17:33:22,969 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:33Z] INFO  17:33:22,970 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:33Z] INFO  17:33:22,974 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/X/R14-18106_kapa-NGv3-PE100-NGv3-sort-X_144337190_155270560-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/X/R14-18106_kapa-NGv3-PE100-NGv3-X_144337190_155270560-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/X/tx/tmpmqXjWO/R14-18106_kapa-NGv3-PE100-NGv3-X_144337190_155270560.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:33Z] INFO  17:33:23,007 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:33Z] INFO  17:33:23,014 HelpFormatter - Date/Time: 2016/04/14 17:33:22
[2016-04-15T00:33Z] INFO  17:33:23,015 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:33Z] INFO  17:33:23,016 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:33Z] INFO  17:33:23,019 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:33Z] INFO  17:33:23,113 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:33Z] INFO  17:33:23,114 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:33Z] INFO  17:33:23,114 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:33Z] INFO  17:33:23,115 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:33Z] INFO  17:33:23,159 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:33Z] INFO  17:33:23,166 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:33Z] INFO  17:33:23,165 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:33Z] INFO  17:33:23,390 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:33Z] INFO  17:33:23,395 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:33Z] INFO  17:33:23,399 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:33Z] INFO  17:33:23,401 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:33Z] INFO  17:33:23,412 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:33Z] INFO  17:33:23,413 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:33Z] INFO  17:33:23,418 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/Y/R14-18106_kapa-NGv3-PE100-NGv3-sort-Y_0_15522993-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/Y/R14-18106_kapa-NGv3-PE100-NGv3-Y_0_15522993-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/Y/tx/tmpfBnylQ/R14-18106_kapa-NGv3-PE100-NGv3-Y_0_15522993.vcf.gz -ploidy 1 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:33Z] INFO  17:33:23,437 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:33Z] INFO  17:33:23,438 HelpFormatter - Date/Time: 2016/04/14 17:33:23
[2016-04-15T00:33Z] INFO  17:33:23,439 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:33Z] INFO  17:33:23,439 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:33Z] INFO  17:33:23,473 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-15T00:33Z] INFO  17:33:23,614 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:33Z] INFO  17:33:23,723 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:33Z] INFO  17:33:23,831 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:33Z] INFO  17:33:23,842 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:33Z] INFO  17:33:23,936 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.09
[2016-04-15T00:33Z] INFO  17:33:23,959 IntervalUtils - Processing 184337 bp from intervals
[2016-04-15T00:33Z] WARN  17:33:23,966 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:33Z] GATK: HaplotypeCaller
[2016-04-15T00:33Z] INFO  17:33:24,077 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:33Z] INFO  17:33:24,276 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:33Z] INFO  17:33:24,277 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:33Z] INFO  17:33:24,278 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:33Z] INFO  17:33:24,279 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:33Z] INFO  17:33:24,379 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:33Z] INFO  17:33:24,379 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:33Z] INFO  17:33:24,417 IntervalUtils - Processing 52192 bp from intervals
[2016-04-15T00:33Z] WARN  17:33:24,423 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:33Z] INFO  17:33:24,588 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:33Z] INFO  17:33:24,688 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:33Z] INFO  17:33:24,689 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:33Z] INFO  17:33:24,690 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:33Z] INFO  17:33:24,691 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:33Z] INFO  17:33:24,760 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:33Z] INFO  17:33:24,779 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:33Z] INFO  17:33:25,067 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:33Z] INFO  17:33:25,086 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:33Z] INFO  17:33:25,086 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:33Z] INFO  17:33:25,086 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:33Z] INFO  17:33:25,090 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/Y/R14-18106_kapa-NGv3-PE100-NGv3-sort-Y_15526614_59222281-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/Y/R14-18106_kapa-NGv3-PE100-NGv3-Y_15526614_59222281-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/Y/tx/tmp4Twk_3/R14-18106_kapa-NGv3-PE100-NGv3-Y_15526614_59222281.vcf.gz -ploidy 1 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:33Z] INFO  17:33:25,121 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:33Z] INFO  17:33:25,121 HelpFormatter - Date/Time: 2016/04/14 17:33:25
[2016-04-15T00:33Z] INFO  17:33:25,122 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:33Z] INFO  17:33:25,122 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:33Z] INFO  17:33:25,346 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:33Z] INFO  17:33:25,360 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:33Z] INFO  17:33:25,363 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:33Z] INFO  17:33:25,363 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:33Z] INFO  17:33:25,364 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:33Z] INFO  17:33:25,369 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/Y/R14-18106_kapa-NGv3-PE100-NGv3-sort-Y_59228291_59373566-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/Y/R14-18106_kapa-NGv3-PE100-NGv3-Y_59228291_59373566-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/Y/tx/tmpBgjNwC/R14-18106_kapa-NGv3-PE100-NGv3-Y_59228291_59373566.vcf.gz -ploidy 1 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:33Z] INFO  17:33:25,379 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:33Z] INFO  17:33:25,386 HelpFormatter - Date/Time: 2016/04/14 17:33:25
[2016-04-15T00:33Z] INFO  17:33:25,392 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:33Z] INFO  17:33:25,393 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:33Z] INFO  17:33:25,598 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:33Z] INFO  17:33:25,613 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:33Z] INFO  17:33:25,623 ProgressMeter -            done    626722.0    14.0 s      22.0 s      100.0%    14.0 s       0.0 s
[2016-04-15T00:33Z] INFO  17:33:25,623 ProgressMeter - Total runtime 14.05 secs, 0.23 min, 0.00 hours
[2016-04-15T00:33Z] INFO  17:33:25,624 MicroScheduler - 9927 reads were filtered out during the traversal out of approximately 125755 total reads (7.89%)
[2016-04-15T00:33Z] INFO  17:33:25,624 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:33Z] INFO  17:33:25,624 MicroScheduler -   -> 245 reads (0.19% of total) failing BadMateFilter
[2016-04-15T00:33Z] INFO  17:33:25,625 MicroScheduler -   -> 9583 reads (7.62% of total) failing DuplicateReadFilter
[2016-04-15T00:33Z] INFO  17:33:25,625 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:33Z] INFO  17:33:25,625 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:33Z] INFO  17:33:25,625 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:33Z] INFO  17:33:25,626 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:33Z] INFO  17:33:25,626 MicroScheduler -   -> 99 reads (0.08% of total) failing UnmappedReadFilter
[2016-04-15T00:33Z] INFO  17:33:25,673 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:33Z] INFO  17:33:25,679 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-15T00:33Z] INFO  17:33:25,757 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:33Z] INFO  17:33:25,761 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:33Z] INFO  17:33:25,761 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:33Z] INFO  17:33:25,762 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:33Z] INFO  17:33:25,766 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/1/R14-18106_kapa-NGv3-PE100-NGv3-sort-1_0_15541927-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/1/R14-18106_kapa-NGv3-PE100-NGv3-1_0_15541927-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/1/tx/tmpTpgnZg/R14-18106_kapa-NGv3-PE100-NGv3-1_0_15541927.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:33Z] INFO  17:33:25,799 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:33Z] INFO  17:33:25,809 HelpFormatter - Date/Time: 2016/04/14 17:33:25
[2016-04-15T00:33Z] INFO  17:33:25,810 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:33Z] INFO  17:33:25,814 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:33Z] WARN  17:33:25,855 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T00:33Z] WARN  17:33:25,858 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/1/tx/tmpTpgnZg/R14-18106_kapa-NGv3-PE100-NGv3-1_0_15541927.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T00:33Z] INFO  17:33:25,890 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:33Z] INFO  17:33:25,899 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:33Z] INFO  17:33:25,971 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-15T00:33Z] INFO  17:33:26,088 IntervalUtils - Processing 44713 bp from intervals
[2016-04-15T00:33Z] INFO  17:33:26,089 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:33Z] WARN  17:33:26,093 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:33Z] INFO  17:33:26,162 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:33Z] INFO  17:33:26,241 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:33Z] INFO  17:33:26,242 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:33Z] INFO  17:33:26,242 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:33Z] INFO  17:33:26,243 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:33Z] INFO  17:33:26,281 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T00:33Z] INFO  17:33:26,290 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:33Z] INFO  17:33:26,306 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:33Z] INFO  17:33:26,307 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:33Z] INFO  17:33:26,314 IntervalUtils - Processing 2412 bp from intervals
[2016-04-15T00:33Z] WARN  17:33:26,319 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:33Z] INFO  17:33:26,384 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.09
[2016-04-15T00:33Z] INFO  17:33:26,409 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T00:33Z] INFO  17:33:26,466 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:33Z] INFO  17:33:26,489 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:33Z] INFO  17:33:26,489 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:33Z] INFO  17:33:26,490 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:33Z] INFO  17:33:26,491 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:33Z] INFO  17:33:26,564 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:33Z] INFO  17:33:26,565 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:33Z] INFO  17:33:26,844 IntervalUtils - Processing 390138 bp from intervals
[2016-04-15T00:33Z] WARN  17:33:26,860 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:33Z] INFO  17:33:26,947 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:33Z] INFO  17:33:27,027 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:33Z] INFO  17:33:27,075 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:33Z] INFO  17:33:27,075 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:33Z] INFO  17:33:27,075 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T00:33Z] INFO  17:33:27,076 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T00:33Z] INFO  17:33:27,086 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T00:33Z] INFO  17:33:27,087 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T00:33Z] INFO  17:33:27,143 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:33Z] INFO  17:33:27,147 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:33Z] INFO  17:33:27,147 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:33Z] INFO  17:33:27,148 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:33Z] INFO  17:33:27,152 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/1/R14-18106_kapa-NGv3-PE100-NGv3-sort-1_15545821_31186478-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/1/R14-18106_kapa-NGv3-PE100-NGv3-1_15545821_31186478-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/1/tx/tmp6lQaOR/R14-18106_kapa-NGv3-PE100-NGv3-1_15545821_31186478.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:33Z] INFO  17:33:27,179 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:33Z] INFO  17:33:27,180 HelpFormatter - Date/Time: 2016/04/14 17:33:27
[2016-04-15T00:33Z] INFO  17:33:27,181 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:33Z] INFO  17:33:27,181 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:33Z] WARN  17:33:27,229 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T00:33Z] WARN  17:33:27,238 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/1/tx/tmp6lQaOR/R14-18106_kapa-NGv3-PE100-NGv3-1_15545821_31186478.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T00:33Z] INFO  17:33:27,259 ProgressMeter -            done     16030.0     0.0 s      47.0 s       96.1%     0.0 s       0.0 s
[2016-04-15T00:33Z] INFO  17:33:27,259 ProgressMeter - Total runtime 0.77 secs, 0.01 min, 0.00 hours
[2016-04-15T00:33Z] INFO  17:33:27,336 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T00:33Z] INFO  17:33:27,458 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:33Z] GATK: HaplotypeCaller
[2016-04-15T00:33Z] INFO  17:33:27,627 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T00:33Z] INFO  17:33:27,637 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:33Z] INFO  17:33:27,722 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-15T00:33Z] INFO  17:33:27,748 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T00:33Z] INFO  17:33:28,167 IntervalUtils - Processing 386393 bp from intervals
[2016-04-15T00:33Z] WARN  17:33:28,172 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:33Z] INFO  17:33:28,199 ProgressMeter -     22:28194551    915175.0    30.0 s      32.0 s       71.5%    41.0 s      11.0 s
[2016-04-15T00:33Z] INFO  17:33:28,313 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:33Z] INFO  17:33:28,436 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:33Z] INFO  17:33:28,437 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:33Z] INFO  17:33:28,438 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T00:33Z] INFO  17:33:28,439 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T00:33Z] INFO  17:33:28,440 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T00:33Z] INFO  17:33:28,440 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T00:33Z] INFO  17:33:28,597 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:33Z] INFO  17:33:28,653 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T00:33Z] GATK: HaplotypeCaller
[2016-04-15T00:33Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T00:33Z] INFO  17:33:29,246 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T00:33Z] INFO  17:33:29,247 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T00:33Z] INFO  17:33:29,255 ProgressMeter -            done   1090417.0    18.0 s      17.0 s      100.0%    18.0 s       0.0 s
[2016-04-15T00:33Z] INFO  17:33:29,256 ProgressMeter - Total runtime 18.89 secs, 0.31 min, 0.01 hours
[2016-04-15T00:33Z] INFO  17:33:29,256 MicroScheduler - 16109 reads were filtered out during the traversal out of approximately 225802 total reads (7.13%)
[2016-04-15T00:33Z] INFO  17:33:29,257 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:33Z] INFO  17:33:29,257 MicroScheduler -   -> 378 reads (0.17% of total) failing BadMateFilter
[2016-04-15T00:33Z] INFO  17:33:29,257 MicroScheduler -   -> 15595 reads (6.91% of total) failing DuplicateReadFilter
[2016-04-15T00:33Z] INFO  17:33:29,257 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:33Z] INFO  17:33:29,258 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:33Z] INFO  17:33:29,258 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:33Z] INFO  17:33:29,258 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:33Z] INFO  17:33:29,258 MicroScheduler -   -> 136 reads (0.06% of total) failing UnmappedReadFilter
[2016-04-15T00:33Z] WARN  17:33:29,403 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T00:33Z] WARN  17:33:29,404 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T00:33Z] INFO  17:33:29,739 ProgressMeter -     22:42262835    909321.0    30.0 s      32.0 s       68.5%    43.0 s      13.0 s
[2016-04-15T00:33Z] INFO  17:33:30,529 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:33Z] INFO  17:33:30,532 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:33Z] INFO  17:33:30,533 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:33Z] INFO  17:33:30,533 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:33Z] INFO  17:33:30,538 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/1/R14-18106_kapa-NGv3-PE100-NGv3-sort-1_31187093_46714270-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/1/R14-18106_kapa-NGv3-PE100-NGv3-1_31187093_46714270-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/1/tx/tmpLPesxZ/R14-18106_kapa-NGv3-PE100-NGv3-1_31187093_46714270.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:33Z] INFO  17:33:30,546 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:33Z] INFO  17:33:30,547 HelpFormatter - Date/Time: 2016/04/14 17:33:30
[2016-04-15T00:33Z] INFO  17:33:30,547 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:33Z] INFO  17:33:30,548 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:33Z] WARN  17:33:30,570 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T00:33Z] WARN  17:33:30,573 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/1/tx/tmpLPesxZ/R14-18106_kapa-NGv3-PE100-NGv3-1_31187093_46714270.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T00:33Z] INFO  17:33:30,696 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:33Z] INFO  17:33:30,705 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:33Z] INFO  17:33:30,873 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T00:33Z] INFO  17:33:30,894 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:33Z] INFO  17:33:30,968 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-15T00:33Z] INFO  17:33:31,011 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T00:33Z] GATK: HaplotypeCaller
[2016-04-15T00:33Z] INFO  17:33:31,453 IntervalUtils - Processing 431182 bp from intervals
[2016-04-15T00:33Z] WARN  17:33:31,468 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:33Z] INFO  17:33:31,573 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:33Z] INFO  17:33:31,762 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:33Z] INFO  17:33:31,763 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:33Z] INFO  17:33:31,765 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T00:33Z] INFO  17:33:31,766 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T00:33Z] INFO  17:33:31,781 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T00:33Z] INFO  17:33:31,781 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T00:33Z] INFO  17:33:31,975 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T00:33Z] INFO  17:33:32,305 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:33Z] INFO  17:33:32,308 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:33Z] INFO  17:33:32,309 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:33Z] INFO  17:33:32,309 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:33Z] INFO  17:33:32,314 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/1/R14-18106_kapa-NGv3-PE100-NGv3-sort-1_46715671_62228851-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/1/R14-18106_kapa-NGv3-PE100-NGv3-1_46715671_62228851-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/1/tx/tmpqduDnj/R14-18106_kapa-NGv3-PE100-NGv3-1_46715671_62228851.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:33Z] INFO  17:33:32,322 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:33Z] INFO  17:33:32,323 HelpFormatter - Date/Time: 2016/04/14 17:33:32
[2016-04-15T00:33Z] INFO  17:33:32,324 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:33Z] INFO  17:33:32,324 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:33Z] WARN  17:33:32,347 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T00:33Z] WARN  17:33:32,350 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/1/tx/tmpqduDnj/R14-18106_kapa-NGv3-PE100-NGv3-1_46715671_62228851.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T00:33Z] INFO  17:33:32,563 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:33Z] INFO  17:33:32,692 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T00:33Z] INFO  17:33:32,701 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:33Z] INFO  17:33:32,760 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-15T00:33Z] INFO  17:33:32,781 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T00:33Z] INFO  17:33:33,126 ProgressMeter -            done    518040.0    15.0 s      29.0 s      100.0%    15.0 s       0.0 s
[2016-04-15T00:33Z] INFO  17:33:33,126 ProgressMeter - Total runtime 15.25 secs, 0.25 min, 0.00 hours
[2016-04-15T00:33Z] INFO  17:33:33,127 MicroScheduler - 9073 reads were filtered out during the traversal out of approximately 123607 total reads (7.34%)
[2016-04-15T00:33Z] INFO  17:33:33,127 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:33Z] INFO  17:33:33,127 MicroScheduler -   -> 187 reads (0.15% of total) failing BadMateFilter
[2016-04-15T00:33Z] INFO  17:33:33,127 MicroScheduler -   -> 8807 reads (7.13% of total) failing DuplicateReadFilter
[2016-04-15T00:33Z] INFO  17:33:33,128 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:33Z] INFO  17:33:33,128 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:33Z] INFO  17:33:33,128 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:33Z] INFO  17:33:33,128 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:33Z] INFO  17:33:33,129 MicroScheduler -   -> 79 reads (0.06% of total) failing UnmappedReadFilter
[2016-04-15T00:33Z] INFO  17:33:33,365 IntervalUtils - Processing 180557 bp from intervals
[2016-04-15T00:33Z] WARN  17:33:33,380 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:33Z] INFO  17:33:33,500 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:33Z] INFO  17:33:33,594 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:33Z] INFO  17:33:33,594 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:33Z] INFO  17:33:33,595 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T00:33Z] INFO  17:33:33,595 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T00:33Z] INFO  17:33:33,602 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T00:33Z] INFO  17:33:33,603 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T00:33Z] INFO  17:33:33,844 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T00:33Z] INFO  17:33:33,846 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:33Z] INFO  17:33:33,849 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:33Z] INFO  17:33:33,850 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:33Z] INFO  17:33:33,850 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:33Z] INFO  17:33:33,854 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/1/R14-18106_kapa-NGv3-PE100-NGv3-sort-1_62231950_77749296-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/1/R14-18106_kapa-NGv3-PE100-NGv3-1_62231950_77749296-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/1/tx/tmp7SZl1u/R14-18106_kapa-NGv3-PE100-NGv3-1_62231950_77749296.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:33Z] INFO  17:33:33,869 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:33Z] INFO  17:33:33,870 HelpFormatter - Date/Time: 2016/04/14 17:33:33
[2016-04-15T00:33Z] INFO  17:33:33,871 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:33Z] INFO  17:33:33,871 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:33Z] WARN  17:33:33,894 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T00:33Z] WARN  17:33:33,913 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/1/tx/tmp7SZl1u/R14-18106_kapa-NGv3-PE100-NGv3-1_62231950_77749296.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T00:33Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T00:33Z] INFO  17:33:34,047 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T00:33Z] INFO  17:33:34,047 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T00:33Z] INFO  17:33:34,100 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:33Z] INFO  17:33:34,275 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T00:33Z] INFO  17:33:34,289 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:33Z] INFO  17:33:34,362 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-15T00:33Z] INFO  17:33:34,378 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T00:33Z] WARN  17:33:34,379 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T00:33Z] WARN  17:33:34,380 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T00:33Z] INFO  17:33:34,479 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:33Z] INFO  17:33:34,568 ProgressMeter -            done   1149428.0     9.0 s       8.0 s      100.0%     9.0 s       0.0 s
[2016-04-15T00:33Z] INFO  17:33:34,568 ProgressMeter - Total runtime 9.88 secs, 0.16 min, 0.00 hours
[2016-04-15T00:33Z] INFO  17:33:34,569 MicroScheduler - 3788 reads were filtered out during the traversal out of approximately 77496 total reads (4.89%)
[2016-04-15T00:33Z] INFO  17:33:34,569 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:33Z] INFO  17:33:34,570 MicroScheduler -   -> 138 reads (0.18% of total) failing BadMateFilter
[2016-04-15T00:33Z] INFO  17:33:34,570 MicroScheduler -   -> 3610 reads (4.66% of total) failing DuplicateReadFilter
[2016-04-15T00:33Z] INFO  17:33:34,571 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:33Z] INFO  17:33:34,571 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:33Z] INFO  17:33:34,571 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:33Z] INFO  17:33:34,571 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:33Z] INFO  17:33:34,572 MicroScheduler -   -> 40 reads (0.05% of total) failing UnmappedReadFilter
[2016-04-15T00:33Z] INFO  17:33:34,832 IntervalUtils - Processing 150085 bp from intervals
[2016-04-15T00:33Z] WARN  17:33:34,839 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:33Z] GATK: HaplotypeCaller
[2016-04-15T00:33Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T00:33Z] INFO  17:33:34,934 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T00:33Z] INFO  17:33:34,934 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T00:33Z] INFO  17:33:34,958 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:33Z] INFO  17:33:35,091 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:33Z] INFO  17:33:35,092 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:33Z] INFO  17:33:35,093 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T00:33Z] INFO  17:33:35,094 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T00:33Z] INFO  17:33:35,121 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T00:33Z] INFO  17:33:35,121 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T00:33Z] WARN  17:33:35,216 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T00:33Z] WARN  17:33:35,218 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T00:33Z] INFO  17:33:35,260 ProgressMeter -     19:11130267   2985113.0    60.0 s      20.0 s       73.0%    82.0 s      22.0 s
[2016-04-15T00:33Z] INFO  17:33:35,403 ProgressMeter -            done    306895.0    13.0 s      42.0 s      100.0%    13.0 s       0.0 s
[2016-04-15T00:33Z] INFO  17:33:35,403 ProgressMeter - Total runtime 13.15 secs, 0.22 min, 0.00 hours
[2016-04-15T00:33Z] INFO  17:33:35,404 MicroScheduler - 5511 reads were filtered out during the traversal out of approximately 81867 total reads (6.73%)
[2016-04-15T00:33Z] INFO  17:33:35,404 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:33Z] INFO  17:33:35,404 MicroScheduler -   -> 153 reads (0.19% of total) failing BadMateFilter
[2016-04-15T00:33Z] INFO  17:33:35,405 MicroScheduler -   -> 5311 reads (6.49% of total) failing DuplicateReadFilter
[2016-04-15T00:33Z] INFO  17:33:35,405 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:33Z] INFO  17:33:35,405 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:33Z] INFO  17:33:35,405 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:33Z] INFO  17:33:35,405 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:33Z] INFO  17:33:35,406 MicroScheduler -   -> 47 reads (0.06% of total) failing UnmappedReadFilter
[2016-04-15T00:33Z] INFO  17:33:35,406 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T00:33Z] INFO  17:33:35,692 ProgressMeter -            done    145748.0     9.0 s      64.0 s       99.9%     9.0 s       0.0 s
[2016-04-15T00:33Z] INFO  17:33:35,693 ProgressMeter - Total runtime 9.45 secs, 0.16 min, 0.00 hours
[2016-04-15T00:33Z] INFO  17:33:35,693 MicroScheduler - 2599 reads were filtered out during the traversal out of approximately 70483 total reads (3.69%)
[2016-04-15T00:33Z] INFO  17:33:35,694 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:33Z] INFO  17:33:35,694 MicroScheduler -   -> 136 reads (0.19% of total) failing BadMateFilter
[2016-04-15T00:33Z] INFO  17:33:35,694 MicroScheduler -   -> 2396 reads (3.40% of total) failing DuplicateReadFilter
[2016-04-15T00:33Z] INFO  17:33:35,694 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:33Z] INFO  17:33:35,695 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:33Z] INFO  17:33:35,695 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:33Z] INFO  17:33:35,695 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:33Z] INFO  17:33:35,696 MicroScheduler -   -> 67 reads (0.10% of total) failing UnmappedReadFilter
[2016-04-15T00:33Z] INFO  17:33:36,069 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:33Z] GATK: HaplotypeCaller
[2016-04-15T00:33Z] INFO  17:33:36,885 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:33Z] GATK: HaplotypeCaller
[2016-04-15T00:33Z] INFO  17:33:37,261 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:33Z] INFO  17:33:37,359 ProgressMeter -            done    405872.0    14.0 s      35.0 s       99.9%    14.0 s       0.0 s
[2016-04-15T00:33Z] INFO  17:33:37,359 ProgressMeter - Total runtime 14.25 secs, 0.24 min, 0.00 hours
[2016-04-15T00:33Z] INFO  17:33:37,360 MicroScheduler - 7082 reads were filtered out during the traversal out of approximately 94749 total reads (7.47%)
[2016-04-15T00:33Z] INFO  17:33:37,360 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:33Z] INFO  17:33:37,360 MicroScheduler -   -> 192 reads (0.20% of total) failing BadMateFilter
[2016-04-15T00:33Z] INFO  17:33:37,360 MicroScheduler -   -> 6823 reads (7.20% of total) failing DuplicateReadFilter
[2016-04-15T00:33Z] INFO  17:33:37,361 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:33Z] INFO  17:33:37,361 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:33Z] INFO  17:33:37,361 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:33Z] INFO  17:33:37,361 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:33Z] INFO  17:33:37,362 MicroScheduler -   -> 67 reads (0.07% of total) failing UnmappedReadFilter
[2016-04-15T00:33Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T00:33Z] INFO  17:33:37,548 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T00:33Z] INFO  17:33:37,549 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T00:33Z] GATK: HaplotypeCaller
[2016-04-15T00:33Z] INFO  17:33:37,640 ProgressMeter -            done   1359315.0    39.0 s      29.0 s      100.0%    39.0 s       0.0 s
[2016-04-15T00:33Z] INFO  17:33:37,640 ProgressMeter - Total runtime 39.46 secs, 0.66 min, 0.01 hours
[2016-04-15T00:33Z] INFO  17:33:37,641 MicroScheduler - 44614 reads were filtered out during the traversal out of approximately 568644 total reads (7.85%)
[2016-04-15T00:33Z] INFO  17:33:37,641 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:33Z] INFO  17:33:37,641 MicroScheduler -   -> 1041 reads (0.18% of total) failing BadMateFilter
[2016-04-15T00:33Z] INFO  17:33:37,642 MicroScheduler -   -> 43211 reads (7.60% of total) failing DuplicateReadFilter
[2016-04-15T00:33Z] INFO  17:33:37,642 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:33Z] INFO  17:33:37,642 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:33Z] INFO  17:33:37,642 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:33Z] INFO  17:33:37,642 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:33Z] INFO  17:33:37,643 MicroScheduler -   -> 362 reads (0.06% of total) failing UnmappedReadFilter
[2016-04-15T00:33Z] WARN  17:33:37,800 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T00:33Z] WARN  17:33:37,802 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T00:33Z] INFO  17:33:37,958 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:33Z] INFO  17:33:37,968 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:33Z] INFO  17:33:37,969 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:33Z] INFO  17:33:37,969 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:33Z] INFO  17:33:37,974 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/1/R14-18106_kapa-NGv3-PE100-NGv3-sort-1_77752625_93297674-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/1/R14-18106_kapa-NGv3-PE100-NGv3-1_77752625_93297674-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/1/tx/tmpKQB4Yw/R14-18106_kapa-NGv3-PE100-NGv3-1_77752625_93297674.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:33Z] INFO  17:33:37,992 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:33Z] INFO  17:33:37,993 HelpFormatter - Date/Time: 2016/04/14 17:33:37
[2016-04-15T00:33Z] INFO  17:33:37,993 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:33Z] INFO  17:33:37,994 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:33Z] WARN  17:33:38,030 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T00:33Z] WARN  17:33:38,033 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/1/tx/tmpKQB4Yw/R14-18106_kapa-NGv3-PE100-NGv3-1_77752625_93297674.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T00:33Z] INFO  17:33:38,248 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:33Z] INFO  17:33:38,518 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T00:33Z] INFO  17:33:38,526 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:33Z] INFO  17:33:38,644 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.12
[2016-04-15T00:33Z] INFO  17:33:38,676 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T00:33Z] INFO  17:33:38,777 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:33Z] GATK: HaplotypeCaller
[2016-04-15T00:33Z] INFO  17:33:39,194 IntervalUtils - Processing 145368 bp from intervals
[2016-04-15T00:33Z] WARN  17:33:39,213 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:33Z] INFO  17:33:39,225 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:33Z] INFO  17:33:39,344 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:33Z] INFO  17:33:39,499 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:33Z] INFO  17:33:39,500 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:33Z] INFO  17:33:39,501 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T00:33Z] INFO  17:33:39,502 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T00:33Z] GATK: HaplotypeCaller
[2016-04-15T00:33Z] INFO  17:33:39,514 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T00:33Z] INFO  17:33:39,515 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T00:33Z] INFO  17:33:39,567 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:33Z] INFO  17:33:39,570 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:33Z] INFO  17:33:39,571 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:33Z] INFO  17:33:39,572 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:33Z] INFO  17:33:39,577 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/1/R14-18106_kapa-NGv3-PE100-NGv3-sort-1_93298945_108993401-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/1/R14-18106_kapa-NGv3-PE100-NGv3-1_93298945_108993401-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/1/tx/tmp1S2W8p/R14-18106_kapa-NGv3-PE100-NGv3-1_93298945_108993401.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:33Z] INFO  17:33:39,586 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:33Z] INFO  17:33:39,594 HelpFormatter - Date/Time: 2016/04/14 17:33:39
[2016-04-15T00:33Z] INFO  17:33:39,595 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:33Z] INFO  17:33:39,595 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:33Z] WARN  17:33:39,629 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T00:33Z] WARN  17:33:39,632 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/1/tx/tmp1S2W8p/R14-18106_kapa-NGv3-PE100-NGv3-1_93298945_108993401.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T00:33Z] INFO  17:33:39,760 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T00:33Z] INFO  17:33:39,828 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:33Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T00:33Z] INFO  17:33:40,010 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T00:33Z] INFO  17:33:40,011 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T00:33Z] INFO  17:33:40,032 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T00:33Z] INFO  17:33:40,049 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:33Z] INFO  17:33:40,126 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:33Z] INFO  17:33:40,129 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:33Z] INFO  17:33:40,130 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:33Z] INFO  17:33:40,130 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:33Z] INFO  17:33:40,130 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-15T00:33Z] INFO  17:33:40,134 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/1/R14-18106_kapa-NGv3-PE100-NGv3-sort-1_108994811_143767848-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/1/R14-18106_kapa-NGv3-PE100-NGv3-1_108994811_143767848-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/1/tx/tmpu0WD_C/R14-18106_kapa-NGv3-PE100-NGv3-1_108994811_143767848.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:33Z] INFO  17:33:40,155 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T00:33Z] INFO  17:33:40,161 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:33Z] INFO  17:33:40,162 HelpFormatter - Date/Time: 2016/04/14 17:33:40
[2016-04-15T00:33Z] INFO  17:33:40,162 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:33Z] INFO  17:33:40,163 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:33Z] WARN  17:33:40,184 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T00:33Z] WARN  17:33:40,187 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/1/tx/tmpu0WD_C/R14-18106_kapa-NGv3-PE100-NGv3-1_108994811_143767848.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T00:33Z] WARN  17:33:40,278 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T00:33Z] WARN  17:33:40,279 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T00:33Z] INFO  17:33:40,332 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:33Z] INFO  17:33:40,512 IntervalUtils - Processing 113118 bp from intervals
[2016-04-15T00:33Z] WARN  17:33:40,528 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:33Z] INFO  17:33:40,535 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T00:33Z] INFO  17:33:40,564 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:33Z] INFO  17:33:40,580 ProgressMeter -            done   1247079.0    40.0 s      32.0 s      100.0%    40.0 s       0.0 s
[2016-04-15T00:33Z] INFO  17:33:40,581 ProgressMeter - Total runtime 40.85 secs, 0.68 min, 0.01 hours
[2016-04-15T00:33Z] INFO  17:33:40,581 MicroScheduler - 42890 reads were filtered out during the traversal out of approximately 531090 total reads (8.08%)
[2016-04-15T00:33Z] INFO  17:33:40,582 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:33Z] INFO  17:33:40,582 MicroScheduler -   -> 908 reads (0.17% of total) failing BadMateFilter
[2016-04-15T00:33Z] INFO  17:33:40,582 MicroScheduler -   -> 41652 reads (7.84% of total) failing DuplicateReadFilter
[2016-04-15T00:33Z] INFO  17:33:40,582 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:33Z] INFO  17:33:40,583 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:33Z] INFO  17:33:40,583 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:33Z] INFO  17:33:40,583 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:33Z] INFO  17:33:40,583 MicroScheduler -   -> 330 reads (0.06% of total) failing UnmappedReadFilter
[2016-04-15T00:33Z] INFO  17:33:40,649 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-15T00:33Z] INFO  17:33:40,667 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T00:33Z] INFO  17:33:40,682 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:33Z] INFO  17:33:40,727 ProgressMeter -            done   1012323.0    16.0 s      16.0 s      100.0%    16.0 s       0.0 s
[2016-04-15T00:33Z] INFO  17:33:40,728 ProgressMeter - Total runtime 16.45 secs, 0.27 min, 0.00 hours
[2016-04-15T00:33Z] INFO  17:33:40,728 MicroScheduler - 11069 reads were filtered out during the traversal out of approximately 145956 total reads (7.58%)
[2016-04-15T00:33Z] INFO  17:33:40,728 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:33Z] INFO  17:33:40,729 MicroScheduler -   -> 261 reads (0.18% of total) failing BadMateFilter
[2016-04-15T00:33Z] INFO  17:33:40,729 MicroScheduler -   -> 10710 reads (7.34% of total) failing DuplicateReadFilter
[2016-04-15T00:33Z] INFO  17:33:40,729 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:33Z] INFO  17:33:40,729 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:33Z] INFO  17:33:40,730 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:33Z] INFO  17:33:40,730 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:33Z] INFO  17:33:40,730 MicroScheduler -   -> 98 reads (0.07% of total) failing UnmappedReadFilter
[2016-04-15T00:33Z] INFO  17:33:40,791 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:33Z] INFO  17:33:40,792 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:33Z] INFO  17:33:40,793 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T00:33Z] INFO  17:33:40,794 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T00:33Z] INFO  17:33:40,794 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T00:33Z] INFO  17:33:40,794 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T00:33Z] INFO  17:33:40,973 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T00:33Z] INFO  17:33:41,219 IntervalUtils - Processing 258252 bp from intervals
[2016-04-15T00:33Z] WARN  17:33:41,224 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:33Z] INFO  17:33:41,292 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:33Z] INFO  17:33:41,380 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:33Z] INFO  17:33:41,383 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:33Z] INFO  17:33:41,384 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:33Z] INFO  17:33:41,384 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:33Z] INFO  17:33:41,389 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/1/R14-18106_kapa-NGv3-PE100-NGv3-sort-1_143897546_159410511-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/1/R14-18106_kapa-NGv3-PE100-NGv3-1_143897546_159410511-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/1/tx/tmpGNEOIG/R14-18106_kapa-NGv3-PE100-NGv3-1_143897546_159410511.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:33Z] INFO  17:33:41,411 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:33Z] INFO  17:33:41,413 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:33Z] INFO  17:33:41,413 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T00:33Z] INFO  17:33:41,414 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T00:33Z] INFO  17:33:41,415 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T00:33Z] INFO  17:33:41,415 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T00:33Z] INFO  17:33:41,418 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:33Z] INFO  17:33:41,419 HelpFormatter - Date/Time: 2016/04/14 17:33:41
[2016-04-15T00:33Z] INFO  17:33:41,419 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:33Z] INFO  17:33:41,420 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:33Z] WARN  17:33:41,466 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T00:33Z] WARN  17:33:41,469 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/1/tx/tmpGNEOIG/R14-18106_kapa-NGv3-PE100-NGv3-1_143897546_159410511.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T00:33Z] INFO  17:33:41,585 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T00:33Z] INFO  17:33:41,763 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:33Z] INFO  17:33:41,961 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T00:33Z] INFO  17:33:41,976 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:33Z] INFO  17:33:42,061 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-15T00:33Z] INFO  17:33:42,086 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T00:33Z] INFO  17:33:42,217 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:33Z] INFO  17:33:42,221 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:33Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T00:33Z] INFO  17:33:42,325 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T00:33Z] INFO  17:33:42,336 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T00:33Z] GATK: HaplotypeCaller
[2016-04-15T00:33Z] WARN  17:33:42,604 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T00:33Z] WARN  17:33:42,605 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T00:33Z] GATK: HaplotypeCaller
[2016-04-15T00:33Z] INFO  17:33:42,689 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:33Z] INFO  17:33:42,692 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:33Z] INFO  17:33:42,693 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:33Z] INFO  17:33:42,693 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:33Z] INFO  17:33:42,698 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/1/R14-18106_kapa-NGv3-PE100-NGv3-sort-1_159504867_175046963-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/1/R14-18106_kapa-NGv3-PE100-NGv3-1_159504867_175046963-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/1/tx/tmpK3E88B/R14-18106_kapa-NGv3-PE100-NGv3-1_159504867_175046963.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:33Z] INFO  17:33:42,716 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:33Z] INFO  17:33:42,717 HelpFormatter - Date/Time: 2016/04/14 17:33:42
[2016-04-15T00:33Z] INFO  17:33:42,717 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:33Z] INFO  17:33:42,718 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:33Z] INFO  17:33:42,769 IntervalUtils - Processing 517409 bp from intervals
[2016-04-15T00:33Z] WARN  17:33:42,780 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T00:33Z] WARN  17:33:42,786 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:33Z] WARN  17:33:42,794 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/1/tx/tmpK3E88B/R14-18106_kapa-NGv3-PE100-NGv3-1_159504867_175046963.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T00:33Z] INFO  17:33:42,868 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:33Z] INFO  17:33:43,014 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:33Z] INFO  17:33:43,045 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:33Z] INFO  17:33:43,057 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:33Z] INFO  17:33:43,071 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T00:33Z] INFO  17:33:43,073 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T00:33Z] INFO  17:33:43,080 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T00:33Z] INFO  17:33:43,081 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T00:33Z] INFO  17:33:43,277 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T00:33Z] INFO  17:33:43,286 ProgressMeter -     19:45852078   2508628.0    60.0 s      23.0 s       92.0%    65.0 s       5.0 s
[2016-04-15T00:33Z] INFO  17:33:43,313 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T00:33Z] INFO  17:33:43,322 ProgressMeter -     19:57133236   2406060.0    60.0 s      24.0 s       82.4%    72.0 s      12.0 s
[2016-04-15T00:33Z] INFO  17:33:43,330 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:33Z] INFO  17:33:43,440 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.10
[2016-04-15T00:33Z] INFO  17:33:43,457 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T00:33Z] INFO  17:33:43,509 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:33Z] INFO  17:33:43,513 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:33Z] INFO  17:33:43,514 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:33Z] INFO  17:33:43,514 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:33Z] INFO  17:33:43,519 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/1/R14-18106_kapa-NGv3-PE100-NGv3-sort-1_175048468_192127886-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/1/R14-18106_kapa-NGv3-PE100-NGv3-1_175048468_192127886-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/1/tx/tmpYDd77V/R14-18106_kapa-NGv3-PE100-NGv3-1_175048468_192127886.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:33Z] INFO  17:33:43,554 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:33Z] INFO  17:33:43,555 HelpFormatter - Date/Time: 2016/04/14 17:33:43
[2016-04-15T00:33Z] INFO  17:33:43,556 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:33Z] INFO  17:33:43,556 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:33Z] WARN  17:33:43,593 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T00:33Z] WARN  17:33:43,596 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/1/tx/tmpYDd77V/R14-18106_kapa-NGv3-PE100-NGv3-1_175048468_192127886.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T00:33Z] INFO  17:33:43,930 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:33Z] INFO  17:33:44,040 IntervalUtils - Processing 261574 bp from intervals
[2016-04-15T00:33Z] WARN  17:33:44,046 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:33Z] INFO  17:33:44,104 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T00:33Z] INFO  17:33:44,125 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:33Z] INFO  17:33:44,169 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:33Z] INFO  17:33:44,231 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.10
[2016-04-15T00:33Z] INFO  17:33:44,259 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T00:33Z] INFO  17:33:44,363 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:33Z] INFO  17:33:44,373 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:33Z] INFO  17:33:44,374 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T00:33Z] INFO  17:33:44,374 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T00:33Z] INFO  17:33:44,386 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T00:33Z] INFO  17:33:44,387 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T00:33Z] INFO  17:33:44,718 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T00:33Z] INFO  17:33:44,824 IntervalUtils - Processing 191568 bp from intervals
[2016-04-15T00:33Z] WARN  17:33:44,837 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:33Z] INFO  17:33:44,999 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:33Z] INFO  17:33:45,157 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:33Z] INFO  17:33:45,158 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:33Z] INFO  17:33:45,159 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T00:33Z] INFO  17:33:45,160 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T00:33Z] INFO  17:33:45,161 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T00:33Z] INFO  17:33:45,161 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T00:33Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T00:33Z] INFO  17:33:45,246 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T00:33Z] INFO  17:33:45,257 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T00:33Z] INFO  17:33:45,462 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T00:33Z] WARN  17:33:45,583 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T00:33Z] WARN  17:33:45,584 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T00:33Z] INFO  17:33:46,255 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:33Z] INFO  17:33:46,258 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:33Z] INFO  17:33:46,259 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:33Z] INFO  17:33:46,260 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:33Z] INFO  17:33:46,264 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/1/R14-18106_kapa-NGv3-PE100-NGv3-sort-1_192128349_207640257-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/1/R14-18106_kapa-NGv3-PE100-NGv3-1_192128349_207640257-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/1/tx/tmpOCivYT/R14-18106_kapa-NGv3-PE100-NGv3-1_192128349_207640257.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:33Z] INFO  17:33:46,273 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:33Z] INFO  17:33:46,274 HelpFormatter - Date/Time: 2016/04/14 17:33:46
[2016-04-15T00:33Z] INFO  17:33:46,275 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:33Z] INFO  17:33:46,275 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:33Z] WARN  17:33:46,320 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T00:33Z] WARN  17:33:46,323 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/1/tx/tmpOCivYT/R14-18106_kapa-NGv3-PE100-NGv3-1_192128349_207640257.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T00:33Z] INFO  17:33:46,621 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:33Z] INFO  17:33:46,793 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:33Z] INFO  17:33:46,804 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:33Z] INFO  17:33:46,805 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:33Z] INFO  17:33:46,805 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:33Z] INFO  17:33:46,809 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/1/R14-18106_kapa-NGv3-PE100-NGv3-sort-1_207641871_223156451-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/1/R14-18106_kapa-NGv3-PE100-NGv3-1_207641871_223156451-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/1/tx/tmphdnE0j/R14-18106_kapa-NGv3-PE100-NGv3-1_207641871_223156451.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:33Z] INFO  17:33:46,839 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:33Z] INFO  17:33:46,840 HelpFormatter - Date/Time: 2016/04/14 17:33:46
[2016-04-15T00:33Z] INFO  17:33:46,840 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:33Z] INFO  17:33:46,841 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:33Z] WARN  17:33:46,885 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T00:33Z] WARN  17:33:46,888 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/1/tx/tmphdnE0j/R14-18106_kapa-NGv3-PE100-NGv3-1_207641871_223156451.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T00:33Z] INFO  17:33:46,928 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T00:33Z] INFO  17:33:46,938 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:33Z] INFO  17:33:47,028 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.09
[2016-04-15T00:33Z] INFO  17:33:47,057 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T00:33Z] INFO  17:33:47,257 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:33Z] INFO  17:33:47,554 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T00:33Z] INFO  17:33:47,591 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:33Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T00:33Z] INFO  17:33:47,628 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T00:33Z] INFO  17:33:47,629 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T00:33Z] INFO  17:33:47,672 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-15T00:33Z] INFO  17:33:47,712 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T00:33Z] INFO  17:33:47,774 IntervalUtils - Processing 282740 bp from intervals
[2016-04-15T00:33Z] WARN  17:33:47,779 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:33Z] INFO  17:33:47,934 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:33Z] INFO  17:33:48,152 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:33Z] INFO  17:33:48,153 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:33Z] INFO  17:33:48,154 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T00:33Z] INFO  17:33:48,155 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T00:33Z] WARN  17:33:48,163 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T00:33Z] WARN  17:33:48,164 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T00:33Z] INFO  17:33:48,164 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T00:33Z] INFO  17:33:48,165 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T00:33Z] INFO  17:33:48,354 IntervalUtils - Processing 175773 bp from intervals
[2016-04-15T00:33Z] WARN  17:33:48,364 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:33Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T00:33Z] INFO  17:33:48,460 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T00:33Z] INFO  17:33:48,461 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T00:33Z] INFO  17:33:48,486 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:33Z] INFO  17:33:48,501 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T00:33Z] INFO  17:33:48,637 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:33Z] INFO  17:33:48,638 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:33Z] INFO  17:33:48,638 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T00:33Z] INFO  17:33:48,639 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T00:33Z] INFO  17:33:48,648 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T00:33Z] INFO  17:33:48,648 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T00:33Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T00:33Z] INFO  17:33:48,745 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T00:33Z] INFO  17:33:48,746 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T00:33Z] WARN  17:33:48,816 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T00:33Z] WARN  17:33:48,818 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T00:33Z] INFO  17:33:48,818 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T00:33Z] INFO  17:33:49,041 ProgressMeter -            done   2766033.0    65.0 s      23.0 s      100.0%    65.0 s       0.0 s
[2016-04-15T00:33Z] INFO  17:33:49,041 ProgressMeter - Total runtime 65.77 secs, 1.10 min, 0.02 hours
[2016-04-15T00:33Z] INFO  17:33:49,042 MicroScheduler - 78932 reads were filtered out during the traversal out of approximately 982474 total reads (8.03%)
[2016-04-15T00:33Z] INFO  17:33:49,042 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:33Z] INFO  17:33:49,042 MicroScheduler -   -> 1777 reads (0.18% of total) failing BadMateFilter
[2016-04-15T00:33Z] INFO  17:33:49,042 MicroScheduler -   -> 76511 reads (7.79% of total) failing DuplicateReadFilter
[2016-04-15T00:33Z] INFO  17:33:49,043 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:33Z] INFO  17:33:49,043 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:33Z] INFO  17:33:49,043 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:33Z] INFO  17:33:49,043 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:33Z] INFO  17:33:49,044 MicroScheduler -   -> 644 reads (0.07% of total) failing UnmappedReadFilter
[2016-04-15T00:33Z] WARN  17:33:49,115 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T00:33Z] WARN  17:33:49,116 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T00:33Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T00:33Z] INFO  17:33:49,284 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T00:33Z] INFO  17:33:49,285 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T00:33Z] WARN  17:33:49,496 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T00:33Z] WARN  17:33:49,497 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T00:33Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T00:33Z] INFO  17:33:50,723 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T00:33Z] INFO  17:33:50,732 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T00:33Z] INFO  17:33:50,734 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:33Z] WARN  17:33:51,013 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T00:33Z] WARN  17:33:51,014 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T00:33Z] GATK: HaplotypeCaller
[2016-04-15T00:33Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T00:33Z] INFO  17:33:53,969 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T00:33Z] INFO  17:33:53,979 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T00:33Z] WARN  17:33:54,280 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T00:33Z] WARN  17:33:54,282 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T00:33Z] INFO  17:33:55,577 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:33Z] INFO  17:33:55,598 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:33Z] INFO  17:33:55,598 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:33Z] INFO  17:33:55,598 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:33Z] INFO  17:33:55,602 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/1/R14-18106_kapa-NGv3-PE100-NGv3-sort-1_223162737_240072524-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/1/R14-18106_kapa-NGv3-PE100-NGv3-1_223162737_240072524-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/1/tx/tmplI7ZrH/R14-18106_kapa-NGv3-PE100-NGv3-1_223162737_240072524.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:33Z] INFO  17:33:55,636 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:33Z] INFO  17:33:55,637 HelpFormatter - Date/Time: 2016/04/14 17:33:55
[2016-04-15T00:33Z] INFO  17:33:55,637 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:33Z] INFO  17:33:55,637 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:33Z] WARN  17:33:55,678 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T00:33Z] WARN  17:33:55,681 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/1/tx/tmplI7ZrH/R14-18106_kapa-NGv3-PE100-NGv3-1_223162737_240072524.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T00:33Z] INFO  17:33:55,908 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:33Z] INFO  17:33:56,137 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T00:33Z] INFO  17:33:56,164 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:33Z] INFO  17:33:56,250 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.09
[2016-04-15T00:33Z] INFO  17:33:56,291 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T00:33Z] INFO  17:33:56,310 ProgressMeter -            done   4005652.0    81.0 s      20.0 s      100.0%    81.0 s       0.0 s
[2016-04-15T00:33Z] INFO  17:33:56,310 ProgressMeter - Total runtime 81.08 secs, 1.35 min, 0.02 hours
[2016-04-15T00:33Z] INFO  17:33:56,310 MicroScheduler - 97586 reads were filtered out during the traversal out of approximately 1216426 total reads (8.02%)
[2016-04-15T00:33Z] INFO  17:33:56,311 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:33Z] INFO  17:33:56,311 MicroScheduler -   -> 2384 reads (0.20% of total) failing BadMateFilter
[2016-04-15T00:33Z] INFO  17:33:56,311 MicroScheduler -   -> 94356 reads (7.76% of total) failing DuplicateReadFilter
[2016-04-15T00:33Z] INFO  17:33:56,311 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:33Z] INFO  17:33:56,312 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:33Z] INFO  17:33:56,312 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:33Z] INFO  17:33:56,312 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:33Z] INFO  17:33:56,312 MicroScheduler -   -> 846 reads (0.07% of total) failing UnmappedReadFilter
[2016-04-15T00:33Z] INFO  17:33:56,846 IntervalUtils - Processing 294039 bp from intervals
[2016-04-15T00:33Z] WARN  17:33:56,859 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:33Z] INFO  17:33:56,962 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:33Z] INFO  17:33:57,090 ProgressMeter -       1:1749276      1.3636221E7    30.0 s            2.0 s       21.8%     2.3 m     107.0 s
[2016-04-15T00:33Z] INFO  17:33:57,121 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:33Z] INFO  17:33:57,123 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:33Z] INFO  17:33:57,124 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T00:33Z] INFO  17:33:57,124 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T00:33Z] INFO  17:33:57,135 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T00:33Z] INFO  17:33:57,143 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T00:33Z] INFO  17:33:57,358 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T00:33Z] INFO  17:33:57,964 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:33Z] INFO  17:33:58,237 ProgressMeter -            done   2732198.0    74.0 s      27.0 s      100.0%    74.0 s       0.0 s
[2016-04-15T00:33Z] INFO  17:33:58,238 ProgressMeter - Total runtime 74.93 secs, 1.25 min, 0.02 hours
[2016-04-15T00:33Z] INFO  17:33:58,238 MicroScheduler - 86498 reads were filtered out during the traversal out of approximately 1087209 total reads (7.96%)
[2016-04-15T00:33Z] INFO  17:33:58,239 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:33Z] INFO  17:33:58,240 MicroScheduler -   -> 2028 reads (0.19% of total) failing BadMateFilter
[2016-04-15T00:33Z] INFO  17:33:58,240 MicroScheduler -   -> 83715 reads (7.70% of total) failing DuplicateReadFilter
[2016-04-15T00:33Z] INFO  17:33:58,240 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:33Z] INFO  17:33:58,240 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:33Z] INFO  17:33:58,241 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:33Z] INFO  17:33:58,241 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:33Z] INFO  17:33:58,241 MicroScheduler -   -> 755 reads (0.07% of total) failing UnmappedReadFilter
[2016-04-15T00:33Z] GATK: HaplotypeCaller
[2016-04-15T00:33Z] INFO  17:33:58,459 ProgressMeter -      1:17084013        6978609.0    30.0 s            4.0 s       15.0%     3.3 m       2.8 m
[2016-04-15T00:33Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T00:33Z] INFO  17:33:59,611 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T00:33Z] INFO  17:33:59,622 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T00:33Z] INFO  17:33:59,977 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:33Z] WARN  17:33:59,982 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T00:33Z] WARN  17:33:59,982 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T00:34Z] GATK: HaplotypeCaller
[2016-04-15T00:34Z] INFO  17:34:01,784 ProgressMeter -      1:33747188      1.3814129E7    30.0 s            2.0 s       18.4%     2.7 m       2.2 m
[2016-04-15T00:34Z] INFO  17:34:02,226 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:34Z] INFO  17:34:02,229 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:34Z] INFO  17:34:02,230 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:34Z] INFO  17:34:02,230 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:34Z] INFO  17:34:02,235 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/1/R14-18106_kapa-NGv3-PE100-NGv3-sort-1_240255409_249250621-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/1/R14-18106_kapa-NGv3-PE100-NGv3-1_240255409_249250621-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/1/tx/tmplSZy6V/R14-18106_kapa-NGv3-PE100-NGv3-1_240255409_249250621.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:34Z] INFO  17:34:02,257 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:34Z] INFO  17:34:02,266 HelpFormatter - Date/Time: 2016/04/14 17:34:02
[2016-04-15T00:34Z] INFO  17:34:02,266 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:34Z] INFO  17:34:02,267 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:34Z] WARN  17:34:02,311 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T00:34Z] WARN  17:34:02,314 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/1/tx/tmplSZy6V/R14-18106_kapa-NGv3-PE100-NGv3-1_240255409_249250621.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T00:34Z] WARN  17:34:02,414 ExactAFCalculator - this tool is currently set to genotype at most 6 alternate alleles in a given context, but the context at 1:98185720 has 8 alternate alleles so only the top alleles will be used; see the --max_alternate_alleles argument
[2016-04-15T00:34Z] INFO  17:34:02,532 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:34Z] INFO  17:34:02,732 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T00:34Z] INFO  17:34:02,741 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:34Z] INFO  17:34:02,804 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-15T00:34Z] INFO  17:34:02,831 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T00:34Z] INFO  17:34:03,328 IntervalUtils - Processing 129443 bp from intervals
[2016-04-15T00:34Z] WARN  17:34:03,344 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:34Z] INFO  17:34:03,443 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:34Z] INFO  17:34:03,447 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:34Z] INFO  17:34:03,447 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:34Z] INFO  17:34:03,448 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:34Z] INFO  17:34:03,452 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/2/R14-18106_kapa-NGv3-PE100-NGv3-sort-2_0_15514844-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/2/R14-18106_kapa-NGv3-PE100-NGv3-2_0_15514844-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/2/tx/tmpxM_lTM/R14-18106_kapa-NGv3-PE100-NGv3-2_0_15514844.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:34Z] INFO  17:34:03,457 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:34Z] INFO  17:34:03,472 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:34Z] INFO  17:34:03,473 HelpFormatter - Date/Time: 2016/04/14 17:34:03
[2016-04-15T00:34Z] INFO  17:34:03,473 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:34Z] INFO  17:34:03,474 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:34Z] WARN  17:34:03,501 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T00:34Z] WARN  17:34:03,509 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/2/tx/tmpxM_lTM/R14-18106_kapa-NGv3-PE100-NGv3-2_0_15514844.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T00:34Z] INFO  17:34:03,577 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:34Z] INFO  17:34:03,578 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:34Z] INFO  17:34:03,579 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T00:34Z] INFO  17:34:03,579 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T00:34Z] INFO  17:34:03,580 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T00:34Z] INFO  17:34:03,580 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T00:34Z] INFO  17:34:03,622 ProgressMeter -      1:52704818       1.462706E7    30.0 s            2.0 s       39.5%    75.0 s      45.0 s
[2016-04-15T00:34Z] INFO  17:34:03,706 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:34Z] INFO  17:34:03,816 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T00:34Z] INFO  17:34:03,870 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T00:34Z] INFO  17:34:03,891 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:34Z] INFO  17:34:03,982 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.09
[2016-04-15T00:34Z] INFO  17:34:03,999 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T00:34Z] INFO  17:34:04,379 IntervalUtils - Processing 105700 bp from intervals
[2016-04-15T00:34Z] WARN  17:34:04,385 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:34Z] INFO  17:34:04,524 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:34Z] INFO  17:34:04,614 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:34Z] INFO  17:34:04,615 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:34Z] INFO  17:34:04,615 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T00:34Z] INFO  17:34:04,627 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T00:34Z] INFO  17:34:04,641 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T00:34Z] INFO  17:34:04,642 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T00:34Z] INFO  17:34:04,886 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T00:34Z] INFO  17:34:05,123 ProgressMeter -      1:68906536      2.0907745E7    30.0 s            1.0 s       59.6%    50.0 s      20.0 s
[2016-04-15T00:34Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T00:34Z] INFO  17:34:06,090 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T00:34Z] INFO  17:34:06,095 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T00:34Z] WARN  17:34:06,724 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T00:34Z] WARN  17:34:06,725 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T00:34Z] INFO  17:34:09,516 ProgressMeter -      1:89453935      2.2852399E7    30.0 s            1.0 s       61.3%    48.0 s      18.0 s
[2016-04-15T00:34Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T00:34Z] INFO  17:34:09,841 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T00:34Z] INFO  17:34:09,843 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T00:34Z] WARN  17:34:10,118 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T00:34Z] WARN  17:34:10,120 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T00:34Z] INFO  17:34:10,808 ProgressMeter -     1:103352363      2.1458613E7    30.0 s            1.0 s       77.0%    38.0 s       8.0 s
[2016-04-15T00:34Z] INFO  17:34:11,438 ProgressMeter -     1:110993839      1.4838851E7    30.0 s            2.0 s       31.0%    96.0 s      66.0 s
[2016-04-15T00:34Z] INFO  17:34:13,097 ProgressMeter -     1:145096525         442092.0    30.0 s           67.0 s        3.0%    16.5 m      16.0 m
[2016-04-15T00:34Z] INFO  17:34:14,398 ProgressMeter -     1:161334755      1.6114186E7    30.0 s            1.0 s       31.2%    96.0 s      66.0 s
[2016-04-15T00:34Z] INFO  17:34:15,208 ProgressMeter -     1:181024361      1.6923672E7    30.0 s            1.0 s       44.5%    67.0 s      37.0 s
[2016-04-15T00:34Z] INFO  17:34:16,614 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.006170107
[2016-04-15T00:34Z] INFO  17:34:16,615 PairHMM - Total compute time in PairHMM computeLikelihoods() : 0.48050762300000005
[2016-04-15T00:34Z] INFO  17:34:16,616 HaplotypeCaller - Ran local assembly on 875 active regions
[2016-04-15T00:34Z] INFO  17:34:16,680 ProgressMeter -            done       3.770404E7    35.0 s            0.0 s      100.0%    35.0 s       0.0 s
[2016-04-15T00:34Z] INFO  17:34:16,680 ProgressMeter - Total runtime 35.89 secs, 0.60 min, 0.01 hours
[2016-04-15T00:34Z] INFO  17:34:16,680 MicroScheduler - 36079 reads were filtered out during the traversal out of approximately 154962 total reads (23.28%)
[2016-04-15T00:34Z] INFO  17:34:16,681 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:34Z] INFO  17:34:16,681 MicroScheduler -   -> 9648 reads (6.23% of total) failing DuplicateReadFilter
[2016-04-15T00:34Z] INFO  17:34:16,681 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:34Z] INFO  17:34:16,682 MicroScheduler -   -> 26431 reads (17.06% of total) failing HCMappingQualityFilter
[2016-04-15T00:34Z] INFO  17:34:16,682 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:34Z] INFO  17:34:16,682 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:34Z] INFO  17:34:16,682 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:34Z] INFO  17:34:16,683 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:34Z] INFO  17:34:17,387 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.007678662
[2016-04-15T00:34Z] INFO  17:34:17,388 PairHMM - Total compute time in PairHMM computeLikelihoods() : 0.315664257
[2016-04-15T00:34Z] INFO  17:34:17,389 HaplotypeCaller - Ran local assembly on 1093 active regions
[2016-04-15T00:34Z] INFO  17:34:17,433 ProgressMeter -            done      5.6255126E7    42.0 s            0.0 s      100.0%    42.0 s       0.0 s
[2016-04-15T00:34Z] INFO  17:34:17,434 ProgressMeter - Total runtime 42.34 secs, 0.71 min, 0.01 hours
[2016-04-15T00:34Z] INFO  17:34:17,434 MicroScheduler - 13000 reads were filtered out during the traversal out of approximately 169750 total reads (7.66%)
[2016-04-15T00:34Z] INFO  17:34:17,434 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:34Z] INFO  17:34:17,434 MicroScheduler -   -> 12710 reads (7.49% of total) failing DuplicateReadFilter
[2016-04-15T00:34Z] INFO  17:34:17,435 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:34Z] INFO  17:34:17,435 MicroScheduler -   -> 290 reads (0.17% of total) failing HCMappingQualityFilter
[2016-04-15T00:34Z] INFO  17:34:17,435 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:34Z] INFO  17:34:17,435 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:34Z] INFO  17:34:17,436 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:34Z] INFO  17:34:17,436 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:34Z] INFO  17:34:18,029 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:34Z] INFO  17:34:18,174 ProgressMeter -     1:201163401      2.1125762E7    30.0 s            1.0 s       33.6%    89.0 s      59.0 s
[2016-04-15T00:34Z] GATK: HaplotypeCaller
[2016-04-15T00:34Z] INFO  17:34:18,674 ProgressMeter -     1:213186435      1.5503178E7    30.0 s            1.0 s       48.5%    61.0 s      31.0 s
[2016-04-15T00:34Z] INFO  17:34:18,965 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:34Z] GATK: HaplotypeCaller
[2016-04-15T00:34Z] INFO  17:34:19,340 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.00650723
[2016-04-15T00:34Z] INFO  17:34:19,341 PairHMM - Total compute time in PairHMM computeLikelihoods() : 0.588524222
[2016-04-15T00:34Z] INFO  17:34:19,342 HaplotypeCaller - Ran local assembly on 1099 active regions
[2016-04-15T00:34Z] INFO  17:34:19,373 ProgressMeter -            done      5.3650037E7    39.0 s            0.0 s      100.0%    39.0 s       0.0 s
[2016-04-15T00:34Z] INFO  17:34:19,374 ProgressMeter - Total runtime 39.87 secs, 0.66 min, 0.01 hours
[2016-04-15T00:34Z] INFO  17:34:19,375 MicroScheduler - 11788 reads were filtered out during the traversal out of approximately 157257 total reads (7.50%)
[2016-04-15T00:34Z] INFO  17:34:19,375 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:34Z] INFO  17:34:19,375 MicroScheduler -   -> 11532 reads (7.33% of total) failing DuplicateReadFilter
[2016-04-15T00:34Z] INFO  17:34:19,375 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:34Z] INFO  17:34:19,376 MicroScheduler -   -> 256 reads (0.16% of total) failing HCMappingQualityFilter
[2016-04-15T00:34Z] INFO  17:34:19,376 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:34Z] INFO  17:34:19,376 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:34Z] INFO  17:34:19,376 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:34Z] INFO  17:34:19,377 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:34Z] INFO  17:34:20,563 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:34Z] INFO  17:34:20,836 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:34Z] INFO  17:34:20,839 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:34Z] INFO  17:34:20,839 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:34Z] INFO  17:34:20,839 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:34Z] INFO  17:34:20,843 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/2/R14-18106_kapa-NGv3-PE100-NGv3-sort-2_15519725_31133925-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/2/R14-18106_kapa-NGv3-PE100-NGv3-2_15519725_31133925-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/2/tx/tmpfvmCSg/R14-18106_kapa-NGv3-PE100-NGv3-2_15519725_31133925.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:34Z] INFO  17:34:20,858 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:34Z] INFO  17:34:20,859 HelpFormatter - Date/Time: 2016/04/14 17:34:20
[2016-04-15T00:34Z] INFO  17:34:20,860 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:34Z] INFO  17:34:20,860 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:34Z] WARN  17:34:20,907 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T00:34Z] WARN  17:34:20,909 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/2/tx/tmpfvmCSg/R14-18106_kapa-NGv3-PE100-NGv3-2_15519725_31133925.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T00:34Z] GATK: HaplotypeCaller
[2016-04-15T00:34Z] INFO  17:34:21,077 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:34Z] INFO  17:34:21,323 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T00:34Z] INFO  17:34:21,333 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:34Z] INFO  17:34:21,415 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-15T00:34Z] INFO  17:34:21,433 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T00:34Z] INFO  17:34:21,794 IntervalUtils - Processing 231513 bp from intervals
[2016-04-15T00:34Z] WARN  17:34:21,799 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:34Z] INFO  17:34:21,868 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:34Z] INFO  17:34:21,983 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:34Z] INFO  17:34:21,985 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:34Z] INFO  17:34:21,985 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T00:34Z] INFO  17:34:22,004 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T00:34Z] INFO  17:34:22,008 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T00:34Z] INFO  17:34:22,009 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T00:34Z] INFO  17:34:22,054 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:34Z] INFO  17:34:22,057 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:34Z] INFO  17:34:22,058 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:34Z] INFO  17:34:22,058 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:34Z] INFO  17:34:22,064 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/2/R14-18106_kapa-NGv3-PE100-NGv3-sort-2_31135088_46706841-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/2/R14-18106_kapa-NGv3-PE100-NGv3-2_31135088_46706841-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/2/tx/tmpMFMqyO/R14-18106_kapa-NGv3-PE100-NGv3-2_31135088_46706841.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:34Z] INFO  17:34:22,076 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:34Z] INFO  17:34:22,076 HelpFormatter - Date/Time: 2016/04/14 17:34:22
[2016-04-15T00:34Z] INFO  17:34:22,077 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:34Z] INFO  17:34:22,077 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:34Z] WARN  17:34:22,106 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T00:34Z] WARN  17:34:22,111 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/2/tx/tmpMFMqyO/R14-18106_kapa-NGv3-PE100-NGv3-2_31135088_46706841.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T00:34Z] INFO  17:34:22,155 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T00:34Z] INFO  17:34:22,296 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:34Z] INFO  17:34:22,469 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T00:34Z] INFO  17:34:22,479 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:34Z] INFO  17:34:22,548 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-15T00:34Z] INFO  17:34:22,573 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T00:34Z] INFO  17:34:22,903 IntervalUtils - Processing 167641 bp from intervals
[2016-04-15T00:34Z] WARN  17:34:22,909 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:34Z] INFO  17:34:23,067 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:34Z] INFO  17:34:23,171 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:34Z] INFO  17:34:23,172 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:34Z] INFO  17:34:23,173 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T00:34Z] INFO  17:34:23,173 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T00:34Z] INFO  17:34:23,174 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T00:34Z] INFO  17:34:23,174 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T00:34Z] INFO  17:34:23,384 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T00:34Z] INFO  17:34:23,656 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:34Z] INFO  17:34:23,659 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:34Z] INFO  17:34:23,659 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:34Z] INFO  17:34:23,659 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:34Z] INFO  17:34:23,664 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/2/R14-18106_kapa-NGv3-PE100-NGv3-sort-2_46707543_62228117-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/2/R14-18106_kapa-NGv3-PE100-NGv3-2_46707543_62228117-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/2/tx/tmpikGNiN/R14-18106_kapa-NGv3-PE100-NGv3-2_46707543_62228117.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:34Z] INFO  17:34:23,678 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:34Z] INFO  17:34:23,679 HelpFormatter - Date/Time: 2016/04/14 17:34:23
[2016-04-15T00:34Z] INFO  17:34:23,679 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:34Z] INFO  17:34:23,690 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:34Z] WARN  17:34:23,727 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T00:34Z] WARN  17:34:23,730 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/2/tx/tmpikGNiN/R14-18106_kapa-NGv3-PE100-NGv3-2_46707543_62228117.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T00:34Z] INFO  17:34:24,022 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:34Z] INFO  17:34:24,266 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T00:34Z] INFO  17:34:24,276 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:34Z] INFO  17:34:24,359 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-15T00:34Z] INFO  17:34:24,391 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T00:34Z] INFO  17:34:24,838 IntervalUtils - Processing 139959 bp from intervals
[2016-04-15T00:34Z] WARN  17:34:24,844 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:34Z] INFO  17:34:24,913 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:34Z] INFO  17:34:24,970 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:34Z] INFO  17:34:24,971 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:34Z] INFO  17:34:24,972 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T00:34Z] INFO  17:34:24,973 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T00:34Z] INFO  17:34:24,985 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T00:34Z] INFO  17:34:24,985 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T00:34Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T00:34Z] INFO  17:34:25,110 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T00:34Z] INFO  17:34:25,111 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T00:34Z] INFO  17:34:25,195 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T00:34Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T00:34Z] INFO  17:34:25,291 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T00:34Z] INFO  17:34:25,292 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T00:34Z] WARN  17:34:25,352 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T00:34Z] WARN  17:34:25,353 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T00:34Z] WARN  17:34:25,555 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T00:34Z] WARN  17:34:25,556 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T00:34Z] INFO  17:34:26,349 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.012048920000000001
[2016-04-15T00:34Z] INFO  17:34:26,349 PairHMM - Total compute time in PairHMM computeLikelihoods() : 0.836116693
[2016-04-15T00:34Z] INFO  17:34:26,350 HaplotypeCaller - Ran local assembly on 1437 active regions
[2016-04-15T00:34Z] INFO  17:34:26,426 ProgressMeter -            done      9.8875698E7    52.0 s            0.0 s      100.0%    52.0 s       0.0 s
[2016-04-15T00:34Z] INFO  17:34:26,426 ProgressMeter - Total runtime 52.83 secs, 0.88 min, 0.01 hours
[2016-04-15T00:34Z] INFO  17:34:26,427 MicroScheduler - 22542 reads were filtered out during the traversal out of approximately 275475 total reads (8.18%)
[2016-04-15T00:34Z] INFO  17:34:26,428 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:34Z] INFO  17:34:26,428 MicroScheduler -   -> 20727 reads (7.52% of total) failing DuplicateReadFilter
[2016-04-15T00:34Z] INFO  17:34:26,428 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:34Z] INFO  17:34:26,429 MicroScheduler -   -> 1815 reads (0.66% of total) failing HCMappingQualityFilter
[2016-04-15T00:34Z] INFO  17:34:26,429 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:34Z] INFO  17:34:26,429 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:34Z] INFO  17:34:26,430 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:34Z] INFO  17:34:26,430 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:34Z] INFO  17:34:27,091 ProgressMeter -       1:8931950     1.13031155E8    60.0 s            0.0 s       55.5%   108.0 s      48.0 s
[2016-04-15T00:34Z] INFO  17:34:27,155 ProgressMeter -     1:228430884      2.3200357E7    30.0 s            1.0 s       34.0%    88.0 s      58.0 s
[2016-04-15T00:34Z] INFO  17:34:27,935 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:34Z] GATK: HaplotypeCaller
[2016-04-15T00:34Z] INFO  17:34:28,460 ProgressMeter -      1:19414310      2.6348441E7    60.0 s            2.0 s       26.3%     3.8 m       2.8 m
[2016-04-15T00:34Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T00:34Z] INFO  17:34:29,412 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T00:34Z] INFO  17:34:29,413 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T00:34Z] WARN  17:34:29,731 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T00:34Z] WARN  17:34:29,732 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T00:34Z] INFO  17:34:31,293 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:34Z] INFO  17:34:31,297 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:34Z] INFO  17:34:31,297 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:34Z] INFO  17:34:31,298 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:34Z] INFO  17:34:31,302 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/2/R14-18106_kapa-NGv3-PE100-NGv3-sort-2_62362965_79253295-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/2/R14-18106_kapa-NGv3-PE100-NGv3-2_62362965_79253295-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/2/tx/tmpLQphNj/R14-18106_kapa-NGv3-PE100-NGv3-2_62362965_79253295.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:34Z] INFO  17:34:31,320 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:34Z] INFO  17:34:31,321 HelpFormatter - Date/Time: 2016/04/14 17:34:31
[2016-04-15T00:34Z] INFO  17:34:31,321 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:34Z] INFO  17:34:31,322 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:34Z] WARN  17:34:31,344 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T00:34Z] WARN  17:34:31,347 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/2/tx/tmpLQphNj/R14-18106_kapa-NGv3-PE100-NGv3-2_62362965_79253295.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T00:34Z] INFO  17:34:31,589 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:34Z] INFO  17:34:31,785 ProgressMeter -      1:40028033     1.23109099E8    60.0 s            0.0 s       56.5%   106.0 s      46.0 s
[2016-04-15T00:34Z] INFO  17:34:31,824 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T00:34Z] INFO  17:34:31,856 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:34Z] INFO  17:34:31,935 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-15T00:34Z] INFO  17:34:31,949 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T00:34Z] INFO  17:34:32,285 IntervalUtils - Processing 224219 bp from intervals
[2016-04-15T00:34Z] WARN  17:34:32,291 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:34Z] INFO  17:34:32,373 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:34Z] INFO  17:34:32,485 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:34Z] INFO  17:34:32,486 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:34Z] INFO  17:34:32,487 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T00:34Z] INFO  17:34:32,488 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T00:34Z] INFO  17:34:32,503 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T00:34Z] INFO  17:34:32,504 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T00:34Z] INFO  17:34:32,747 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T00:34Z] INFO  17:34:33,617 ProgressMeter -     1:248059780       1.676651E7    30.0 s            1.0 s       73.3%    40.0 s      10.0 s
[2016-04-15T00:34Z] INFO  17:34:34,644 ProgressMeter -      2:15327004        2.99725E7    30.0 s            1.0 s       97.2%    30.0 s       0.0 s
[2016-04-15T00:34Z] INFO  17:34:35,100 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.009081936
[2016-04-15T00:34Z] INFO  17:34:35,101 PairHMM - Total compute time in PairHMM computeLikelihoods() : 0.45499146500000004
[2016-04-15T00:34Z] INFO  17:34:35,101 HaplotypeCaller - Ran local assembly on 825 active regions
[2016-04-15T00:34Z] INFO  17:34:35,158 ProgressMeter -            done      3.2059538E7    30.0 s            0.0 s      100.0%    30.0 s       0.0 s
[2016-04-15T00:34Z] INFO  17:34:35,158 ProgressMeter - Total runtime 30.54 secs, 0.51 min, 0.01 hours
[2016-04-15T00:34Z] INFO  17:34:35,159 MicroScheduler - 11216 reads were filtered out during the traversal out of approximately 145273 total reads (7.72%)
[2016-04-15T00:34Z] INFO  17:34:35,159 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:34Z] INFO  17:34:35,159 MicroScheduler -   -> 11006 reads (7.58% of total) failing DuplicateReadFilter
[2016-04-15T00:34Z] INFO  17:34:35,160 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:34Z] INFO  17:34:35,160 MicroScheduler -   -> 210 reads (0.14% of total) failing HCMappingQualityFilter
[2016-04-15T00:34Z] INFO  17:34:35,160 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:34Z] INFO  17:34:35,161 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:34Z] INFO  17:34:35,161 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:34Z] INFO  17:34:35,161 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:34Z] INFO  17:34:36,032 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.00947068
[2016-04-15T00:34Z] INFO  17:34:36,033 PairHMM - Total compute time in PairHMM computeLikelihoods() : 0.723146595
[2016-04-15T00:34Z] INFO  17:34:36,034 HaplotypeCaller - Ran local assembly on 1219 active regions
[2016-04-15T00:34Z] INFO  17:34:36,110 ProgressMeter -            done      7.1291223E7    47.0 s            0.0 s      100.0%    47.0 s       0.0 s
[2016-04-15T00:34Z] INFO  17:34:36,110 ProgressMeter - Total runtime 47.47 secs, 0.79 min, 0.01 hours
[2016-04-15T00:34Z] INFO  17:34:36,111 MicroScheduler - 29535 reads were filtered out during the traversal out of approximately 230943 total reads (12.79%)
[2016-04-15T00:34Z] INFO  17:34:36,111 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:34Z] INFO  17:34:36,111 MicroScheduler -   -> 16530 reads (7.16% of total) failing DuplicateReadFilter
[2016-04-15T00:34Z] INFO  17:34:36,112 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:34Z] INFO  17:34:36,112 MicroScheduler -   -> 13005 reads (5.63% of total) failing HCMappingQualityFilter
[2016-04-15T00:34Z] INFO  17:34:36,112 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:34Z] INFO  17:34:36,112 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:34Z] INFO  17:34:36,113 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:34Z] INFO  17:34:36,113 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:34Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T00:34Z] INFO  17:34:36,309 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T00:34Z] INFO  17:34:36,310 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T00:34Z] INFO  17:34:36,455 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:34Z] WARN  17:34:36,525 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T00:34Z] WARN  17:34:36,526 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T00:34Z] GATK: HaplotypeCaller
[2016-04-15T00:34Z] INFO  17:34:37,387 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:34Z] INFO  17:34:37,756 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.020656258
[2016-04-15T00:34Z] INFO  17:34:37,757 PairHMM - Total compute time in PairHMM computeLikelihoods() : 0.541727535
[2016-04-15T00:34Z] INFO  17:34:37,758 HaplotypeCaller - Ran local assembly on 1359 active regions
[2016-04-15T00:34Z] GATK: HaplotypeCaller
[2016-04-15T00:34Z] INFO  17:34:37,787 ProgressMeter -            done      9.8539022E7    52.0 s            0.0 s      100.0%    52.0 s       0.0 s
[2016-04-15T00:34Z] INFO  17:34:37,788 ProgressMeter - Total runtime 52.63 secs, 0.88 min, 0.01 hours
[2016-04-15T00:34Z] INFO  17:34:37,789 MicroScheduler - 18876 reads were filtered out during the traversal out of approximately 245054 total reads (7.70%)
[2016-04-15T00:34Z] INFO  17:34:37,790 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:34Z] INFO  17:34:37,790 MicroScheduler -   -> 18607 reads (7.59% of total) failing DuplicateReadFilter
[2016-04-15T00:34Z] INFO  17:34:37,791 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:34Z] INFO  17:34:37,792 MicroScheduler -   -> 269 reads (0.11% of total) failing HCMappingQualityFilter
[2016-04-15T00:34Z] INFO  17:34:37,792 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:34Z] INFO  17:34:37,793 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:34Z] INFO  17:34:37,793 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:34Z] INFO  17:34:37,794 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:34Z] INFO  17:34:39,274 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:34Z] GATK: HaplotypeCaller
[2016-04-15T00:34Z] INFO  17:34:39,927 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:34Z] INFO  17:34:39,931 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:34Z] INFO  17:34:39,931 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:34Z] INFO  17:34:39,932 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:34Z] INFO  17:34:39,940 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/2/R14-18106_kapa-NGv3-PE100-NGv3-sort-2_79253838_95537822-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/2/R14-18106_kapa-NGv3-PE100-NGv3-2_79253838_95537822-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/2/tx/tmpZnjwdC/R14-18106_kapa-NGv3-PE100-NGv3-2_79253838_95537822.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:34Z] INFO  17:34:39,960 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:34Z] INFO  17:34:39,960 HelpFormatter - Date/Time: 2016/04/14 17:34:39
[2016-04-15T00:34Z] INFO  17:34:39,961 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:34Z] INFO  17:34:39,961 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:34Z] WARN  17:34:40,033 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T00:34Z] WARN  17:34:40,051 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/2/tx/tmpZnjwdC/R14-18106_kapa-NGv3-PE100-NGv3-2_79253838_95537822.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T00:34Z] INFO  17:34:40,304 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:34Z] INFO  17:34:40,457 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T00:34Z] INFO  17:34:40,470 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:34Z] INFO  17:34:40,541 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-15T00:34Z] INFO  17:34:40,568 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T00:34Z] INFO  17:34:40,784 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:34Z] INFO  17:34:40,788 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:34Z] INFO  17:34:40,788 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:34Z] INFO  17:34:40,789 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:34Z] INFO  17:34:40,793 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/2/R14-18106_kapa-NGv3-PE100-NGv3-sort-2_95538561_111273222-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/2/R14-18106_kapa-NGv3-PE100-NGv3-2_95538561_111273222-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/2/tx/tmpjWcEP1/R14-18106_kapa-NGv3-PE100-NGv3-2_95538561_111273222.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:34Z] INFO  17:34:40,813 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:34Z] INFO  17:34:40,814 HelpFormatter - Date/Time: 2016/04/14 17:34:40
[2016-04-15T00:34Z] INFO  17:34:40,815 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:34Z] INFO  17:34:40,816 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:34Z] WARN  17:34:40,838 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T00:34Z] WARN  17:34:40,841 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/2/tx/tmpjWcEP1/R14-18106_kapa-NGv3-PE100-NGv3-2_95538561_111273222.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T00:34Z] INFO  17:34:41,068 IntervalUtils - Processing 101744 bp from intervals
[2016-04-15T00:34Z] INFO  17:34:41,072 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:34Z] WARN  17:34:41,075 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:34Z] INFO  17:34:41,168 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:34Z] INFO  17:34:41,249 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:34Z] INFO  17:34:41,250 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:34Z] INFO  17:34:41,251 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T00:34Z] INFO  17:34:41,252 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T00:34Z] INFO  17:34:41,254 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T00:34Z] INFO  17:34:41,253 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T00:34Z] INFO  17:34:41,253 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T00:34Z] INFO  17:34:41,263 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:34Z] INFO  17:34:41,364 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.10
[2016-04-15T00:34Z] INFO  17:34:41,408 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T00:34Z] INFO  17:34:41,439 ProgressMeter -     1:119474455     1.28887268E8    60.0 s            0.0 s       89.3%    67.0 s       7.0 s
[2016-04-15T00:34Z] INFO  17:34:41,445 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T00:34Z] INFO  17:34:41,797 IntervalUtils - Processing 250759 bp from intervals
[2016-04-15T00:34Z] WARN  17:34:41,803 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:34Z] INFO  17:34:41,934 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:34Z] INFO  17:34:42,070 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:34Z] INFO  17:34:42,071 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:34Z] INFO  17:34:42,077 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T00:34Z] INFO  17:34:42,078 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T00:34Z] INFO  17:34:42,084 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T00:34Z] INFO  17:34:42,084 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T00:34Z] INFO  17:34:42,234 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T00:34Z] INFO  17:34:42,760 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:34Z] INFO  17:34:42,763 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:34Z] INFO  17:34:42,763 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:34Z] INFO  17:34:42,764 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:34Z] INFO  17:34:42,768 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/2/R14-18106_kapa-NGv3-PE100-NGv3-sort-2_111281072_127413888-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/2/R14-18106_kapa-NGv3-PE100-NGv3-2_111281072_127413888-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/2/tx/tmp6j93i_/R14-18106_kapa-NGv3-PE100-NGv3-2_111281072_127413888.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:34Z] INFO  17:34:42,783 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:34Z] INFO  17:34:42,794 HelpFormatter - Date/Time: 2016/04/14 17:34:42
[2016-04-15T00:34Z] INFO  17:34:42,795 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:34Z] INFO  17:34:42,796 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:34Z] WARN  17:34:42,835 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T00:34Z] WARN  17:34:42,838 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/2/tx/tmp6j93i_/R14-18106_kapa-NGv3-PE100-NGv3-2_111281072_127413888.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T00:34Z] INFO  17:34:43,099 ProgressMeter -     1:151079698       3.976359E7    60.0 s            1.0 s       25.2%     4.0 m       3.0 m
[2016-04-15T00:34Z] INFO  17:34:43,123 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:34Z] INFO  17:34:43,309 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T00:34Z] INFO  17:34:43,319 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:34Z] INFO  17:34:43,378 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-15T00:34Z] INFO  17:34:43,413 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T00:34Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T00:34Z] INFO  17:34:43,510 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T00:34Z] INFO  17:34:43,511 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T00:34Z] INFO  17:34:43,802 IntervalUtils - Processing 123675 bp from intervals
[2016-04-15T00:34Z] WARN  17:34:43,808 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:34Z] WARN  17:34:43,813 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T00:34Z] WARN  17:34:43,813 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T00:34Z] INFO  17:34:43,886 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:34Z] INFO  17:34:43,990 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:34Z] INFO  17:34:43,992 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:34Z] INFO  17:34:43,992 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T00:34Z] INFO  17:34:43,993 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T00:34Z] INFO  17:34:43,994 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T00:34Z] INFO  17:34:43,994 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T00:34Z] INFO  17:34:44,240 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T00:34Z] INFO  17:34:44,404 ProgressMeter -     1:172381539     1.24963134E8    60.0 s            0.0 s       85.1%    70.0 s      10.0 s
[2016-04-15T00:34Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T00:34Z] INFO  17:34:46,976 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T00:34Z] INFO  17:34:46,987 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T00:34Z] INFO  17:34:47,239 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.014289102000000001
[2016-04-15T00:34Z] INFO  17:34:47,240 PairHMM - Total compute time in PairHMM computeLikelihoods() : 2.5128118500000003
[2016-04-15T00:34Z] INFO  17:34:47,241 HaplotypeCaller - Ran local assembly on 887 active regions
[2016-04-15T00:34Z] WARN  17:34:47,290 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T00:34Z] WARN  17:34:47,290 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T00:34Z] INFO  17:34:47,331 ProgressMeter -            done      2.1915914E7    43.0 s            1.0 s      100.0%    43.0 s       0.0 s
[2016-04-15T00:34Z] INFO  17:34:47,332 ProgressMeter - Total runtime 43.75 secs, 0.73 min, 0.01 hours
[2016-04-15T00:34Z] INFO  17:34:47,332 MicroScheduler - 25741 reads were filtered out during the traversal out of approximately 176718 total reads (14.57%)
[2016-04-15T00:34Z] INFO  17:34:47,332 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:34Z] INFO  17:34:47,333 MicroScheduler -   -> 12773 reads (7.23% of total) failing DuplicateReadFilter
[2016-04-15T00:34Z] INFO  17:34:47,333 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:34Z] INFO  17:34:47,333 MicroScheduler -   -> 12968 reads (7.34% of total) failing HCMappingQualityFilter
[2016-04-15T00:34Z] INFO  17:34:47,333 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:34Z] INFO  17:34:47,336 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:34Z] INFO  17:34:47,336 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:34Z] INFO  17:34:47,336 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:34Z] INFO  17:34:48,176 ProgressMeter -     1:206325238      1.5023787E8    60.0 s            0.0 s       87.4%    68.0 s       8.0 s
[2016-04-15T00:34Z] INFO  17:34:48,669 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:34Z] GATK: HaplotypeCaller
[2016-04-15T00:34Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T00:34Z] INFO  17:34:51,156 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T00:34Z] INFO  17:34:51,157 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T00:34Z] WARN  17:34:51,421 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T00:34Z] WARN  17:34:51,422 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T00:34Z] INFO  17:34:52,017 ProgressMeter -      2:26410276      2.8258411E7    30.0 s            1.0 s       46.1%    65.0 s      35.0 s
[2016-04-15T00:34Z] INFO  17:34:52,065 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.017511306
[2016-04-15T00:34Z] INFO  17:34:52,066 PairHMM - Total compute time in PairHMM computeLikelihoods() : 0.796074108
[2016-04-15T00:34Z] INFO  17:34:52,067 HaplotypeCaller - Ran local assembly on 1894 active regions
[2016-04-15T00:34Z] INFO  17:34:52,124 ProgressMeter -            done     1.74572625E8    67.0 s            0.0 s      100.0%    67.0 s       0.0 s
[2016-04-15T00:34Z] INFO  17:34:52,124 ProgressMeter - Total runtime 67.75 secs, 1.13 min, 0.02 hours
[2016-04-15T00:34Z] INFO  17:34:52,125 MicroScheduler - 31911 reads were filtered out during the traversal out of approximately 370608 total reads (8.61%)
[2016-04-15T00:34Z] INFO  17:34:52,125 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:34Z] INFO  17:34:52,125 MicroScheduler -   -> 27514 reads (7.42% of total) failing DuplicateReadFilter
[2016-04-15T00:34Z] INFO  17:34:52,125 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:34Z] INFO  17:34:52,126 MicroScheduler -   -> 4397 reads (1.19% of total) failing HCMappingQualityFilter
[2016-04-15T00:34Z] INFO  17:34:52,126 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:34Z] INFO  17:34:52,126 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:34Z] INFO  17:34:52,126 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:34Z] INFO  17:34:52,126 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:34Z] INFO  17:34:52,462 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:34Z] INFO  17:34:52,464 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:34Z] INFO  17:34:52,465 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:34Z] INFO  17:34:52,465 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:34Z] INFO  17:34:52,480 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/2/R14-18106_kapa-NGv3-PE100-NGv3-sort-2_127433207_143643105-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/2/R14-18106_kapa-NGv3-PE100-NGv3-2_127433207_143643105-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/2/tx/tmpDbReZt/R14-18106_kapa-NGv3-PE100-NGv3-2_127433207_143643105.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:34Z] INFO  17:34:52,496 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:34Z] INFO  17:34:52,497 HelpFormatter - Date/Time: 2016/04/14 17:34:52
[2016-04-15T00:34Z] INFO  17:34:52,498 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:34Z] INFO  17:34:52,498 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:34Z] WARN  17:34:52,544 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T00:34Z] WARN  17:34:52,550 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/2/tx/tmpDbReZt/R14-18106_kapa-NGv3-PE100-NGv3-2_127433207_143643105.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T00:34Z] INFO  17:34:52,812 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:34Z] INFO  17:34:53,075 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T00:34Z] INFO  17:34:53,084 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:34Z] INFO  17:34:53,175 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.09
[2016-04-15T00:34Z] INFO  17:34:53,195 ProgressMeter -      2:42981923      3.9472235E7    30.0 s            0.0 s       70.5%    42.0 s      12.0 s
[2016-04-15T00:34Z] INFO  17:34:53,202 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T00:34Z] INFO  17:34:53,629 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:34Z] INFO  17:34:53,635 IntervalUtils - Processing 171560 bp from intervals
[2016-04-15T00:34Z] WARN  17:34:53,641 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:34Z] INFO  17:34:53,804 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:34Z] GATK: HaplotypeCaller
[2016-04-15T00:34Z] INFO  17:34:53,941 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.02904696
[2016-04-15T00:34Z] INFO  17:34:53,948 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:34Z] INFO  17:34:53,949 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:34Z] INFO  17:34:53,950 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T00:34Z] INFO  17:34:53,951 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T00:34Z] INFO  17:34:53,952 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T00:34Z] INFO  17:34:53,956 PairHMM - Total compute time in PairHMM computeLikelihoods() : 3.7195764760000003
[2016-04-15T00:34Z] INFO  17:34:53,957 HaplotypeCaller - Ran local assembly on 1814 active regions
[2016-04-15T00:34Z] INFO  17:34:53,952 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T00:34Z] INFO  17:34:54,020 ProgressMeter -            done     1.55311872E8    72.0 s            0.0 s      100.0%    72.0 s       0.0 s
[2016-04-15T00:34Z] INFO  17:34:54,020 ProgressMeter - Total runtime 72.61 secs, 1.21 min, 0.02 hours
[2016-04-15T00:34Z] INFO  17:34:54,021 MicroScheduler - 36828 reads were filtered out during the traversal out of approximately 373026 total reads (9.87%)
[2016-04-15T00:34Z] INFO  17:34:54,021 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:34Z] INFO  17:34:54,022 MicroScheduler -   -> 27925 reads (7.49% of total) failing DuplicateReadFilter
[2016-04-15T00:34Z] INFO  17:34:54,022 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:34Z] INFO  17:34:54,022 MicroScheduler -   -> 8903 reads (2.39% of total) failing HCMappingQualityFilter
[2016-04-15T00:34Z] INFO  17:34:54,023 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:34Z] INFO  17:34:54,023 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:34Z] INFO  17:34:54,023 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:34Z] INFO  17:34:54,024 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:34Z] INFO  17:34:54,189 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T00:34Z] INFO  17:34:54,847 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.018558228
[2016-04-15T00:34Z] INFO  17:34:54,848 PairHMM - Total compute time in PairHMM computeLikelihoods() : 0.986058136
[2016-04-15T00:34Z] INFO  17:34:54,848 HaplotypeCaller - Ran local assembly on 2020 active regions
[2016-04-15T00:34Z] INFO  17:34:54,910 ProgressMeter -            done     1.89229853E8    66.0 s            0.0 s      100.0%    66.0 s       0.0 s
[2016-04-15T00:34Z] INFO  17:34:54,910 ProgressMeter - Total runtime 66.76 secs, 1.11 min, 0.02 hours
[2016-04-15T00:34Z] INFO  17:34:54,911 MicroScheduler - 33123 reads were filtered out during the traversal out of approximately 384763 total reads (8.61%)
[2016-04-15T00:34Z] INFO  17:34:54,911 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:34Z] INFO  17:34:54,911 MicroScheduler -   -> 28503 reads (7.41% of total) failing DuplicateReadFilter
[2016-04-15T00:34Z] INFO  17:34:54,911 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:34Z] INFO  17:34:54,912 MicroScheduler -   -> 4620 reads (1.20% of total) failing HCMappingQualityFilter
[2016-04-15T00:34Z] INFO  17:34:54,912 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:34Z] INFO  17:34:54,912 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:34Z] INFO  17:34:54,912 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:34Z] INFO  17:34:54,912 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:34Z] INFO  17:34:54,998 ProgressMeter -      2:56411760       2.363844E7    30.0 s            1.0 s       68.0%    44.0 s      14.0 s
[2016-04-15T00:34Z] INFO  17:34:55,427 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:34Z] GATK: HaplotypeCaller
[2016-04-15T00:34Z] INFO  17:34:56,106 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:34Z] GATK: HaplotypeCaller
[2016-04-15T00:34Z] INFO  17:34:56,761 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:34Z] INFO  17:34:56,765 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:34Z] INFO  17:34:56,765 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:34Z] INFO  17:34:56,766 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:34Z] INFO  17:34:56,770 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/2/R14-18106_kapa-NGv3-PE100-NGv3-sort-2_143676177_159195597-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/2/R14-18106_kapa-NGv3-PE100-NGv3-2_143676177_159195597-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/2/tx/tmpppMMuu/R14-18106_kapa-NGv3-PE100-NGv3-2_143676177_159195597.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:34Z] INFO  17:34:56,788 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:34Z] INFO  17:34:56,789 HelpFormatter - Date/Time: 2016/04/14 17:34:56
[2016-04-15T00:34Z] INFO  17:34:56,790 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:34Z] INFO  17:34:56,790 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:34Z] WARN  17:34:56,814 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T00:34Z] WARN  17:34:56,819 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/2/tx/tmpppMMuu/R14-18106_kapa-NGv3-PE100-NGv3-2_143676177_159195597.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T00:34Z] INFO  17:34:57,063 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:34Z] INFO  17:34:57,092 ProgressMeter -      1:12854840     2.85356246E8    90.0 s            0.0 s       87.2%   103.0 s      13.0 s
[2016-04-15T00:34Z] INFO  17:34:57,157 ProgressMeter -     1:235901371     1.24395852E8    60.0 s            0.0 s       82.4%    72.0 s      12.0 s
[2016-04-15T00:34Z] INFO  17:34:57,300 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T00:34Z] INFO  17:34:57,309 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:34Z] INFO  17:34:57,394 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-15T00:34Z] INFO  17:34:57,420 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T00:34Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T00:34Z] INFO  17:34:57,502 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T00:34Z] INFO  17:34:57,503 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T00:34Z] WARN  17:34:57,925 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T00:34Z] INFO  17:34:57,927 IntervalUtils - Processing 92555 bp from intervals
[2016-04-15T00:34Z] WARN  17:34:57,926 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T00:34Z] WARN  17:34:57,942 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:34Z] INFO  17:34:58,086 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:34Z] INFO  17:34:58,174 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:34Z] INFO  17:34:58,175 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:34Z] INFO  17:34:58,176 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T00:34Z] INFO  17:34:58,183 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T00:34Z] INFO  17:34:58,195 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T00:34Z] INFO  17:34:58,196 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T00:34Z] INFO  17:34:58,395 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T00:34Z] INFO  17:34:58,461 ProgressMeter -      1:24416028     1.47208693E8    90.0 s            0.0 s       61.9%     2.4 m      55.0 s
[2016-04-15T00:34Z] INFO  17:34:58,464 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:34Z] INFO  17:34:58,467 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:34Z] INFO  17:34:58,468 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:34Z] INFO  17:34:58,469 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:34Z] INFO  17:34:58,473 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/2/R14-18106_kapa-NGv3-PE100-NGv3-sort-2_159196753_174774985-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/2/R14-18106_kapa-NGv3-PE100-NGv3-2_159196753_174774985-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/2/tx/tmpo1dtQ1/R14-18106_kapa-NGv3-PE100-NGv3-2_159196753_174774985.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:34Z] INFO  17:34:58,482 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:34Z] INFO  17:34:58,493 HelpFormatter - Date/Time: 2016/04/14 17:34:58
[2016-04-15T00:34Z] INFO  17:34:58,494 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:34Z] INFO  17:34:58,495 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:34Z] WARN  17:34:58,517 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T00:34Z] WARN  17:34:58,520 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/2/tx/tmpo1dtQ1/R14-18106_kapa-NGv3-PE100-NGv3-2_159196753_174774985.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T00:34Z] INFO  17:34:58,757 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:34Z] INFO  17:34:58,891 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T00:34Z] INFO  17:34:58,900 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:34Z] INFO  17:34:58,976 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-15T00:34Z] INFO  17:34:58,997 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T00:34Z] INFO  17:34:59,405 IntervalUtils - Processing 216485 bp from intervals
[2016-04-15T00:34Z] WARN  17:34:59,410 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:34Z] INFO  17:34:59,424 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:34Z] INFO  17:34:59,428 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:34Z] INFO  17:34:59,428 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:34Z] INFO  17:34:59,429 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:34Z] INFO  17:34:59,433 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/2/R14-18106_kapa-NGv3-PE100-NGv3-sort-2_174777797_190306304-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/2/R14-18106_kapa-NGv3-PE100-NGv3-2_174777797_190306304-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/2/tx/tmp4JnEMI/R14-18106_kapa-NGv3-PE100-NGv3-2_174777797_190306304.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:34Z] INFO  17:34:59,443 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:34Z] INFO  17:34:59,454 HelpFormatter - Date/Time: 2016/04/14 17:34:59
[2016-04-15T00:34Z] INFO  17:34:59,455 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:34Z] INFO  17:34:59,456 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:34Z] WARN  17:34:59,501 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T00:34Z] WARN  17:34:59,504 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/2/tx/tmp4JnEMI/R14-18106_kapa-NGv3-PE100-NGv3-2_174777797_190306304.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T00:34Z] INFO  17:34:59,527 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:34Z] INFO  17:34:59,718 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:34Z] INFO  17:34:59,719 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:34Z] INFO  17:34:59,720 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T00:34Z] INFO  17:34:59,721 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T00:34Z] INFO  17:34:59,738 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:34Z] INFO  17:34:59,741 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T00:34Z] INFO  17:34:59,742 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T00:34Z] INFO  17:34:59,923 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T00:34Z] INFO  17:34:59,944 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:34Z] INFO  17:34:59,975 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T00:35Z] INFO  17:35:00,036 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.09
[2016-04-15T00:35Z] INFO  17:35:00,071 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T00:35Z] INFO  17:35:00,491 IntervalUtils - Processing 253764 bp from intervals
[2016-04-15T00:35Z] WARN  17:35:00,507 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:35Z] INFO  17:35:00,653 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:35Z] INFO  17:35:00,823 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:35Z] INFO  17:35:00,836 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:35Z] INFO  17:35:00,837 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T00:35Z] INFO  17:35:00,838 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T00:35Z] INFO  17:35:00,839 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T00:35Z] INFO  17:35:00,839 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T00:35Z] INFO  17:35:01,126 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T00:35Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T00:35Z] INFO  17:35:01,732 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T00:35Z] INFO  17:35:01,733 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T00:35Z] INFO  17:35:01,790 ProgressMeter -      1:45480612      3.3765884E8    90.0 s            0.0 s       91.6%    98.0 s       8.0 s
[2016-04-15T00:35Z] WARN  17:35:02,021 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T00:35Z] WARN  17:35:02,022 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T00:35Z] INFO  17:35:02,505 ProgressMeter -      2:71503794      2.5443187E7    30.0 s            1.0 s       46.6%    64.0 s      34.0 s
[2016-04-15T00:35Z] INFO  17:35:02,708 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.0069083190000000004
[2016-04-15T00:35Z] INFO  17:35:02,709 PairHMM - Total compute time in PairHMM computeLikelihoods() : 0.20672846900000003
[2016-04-15T00:35Z] INFO  17:35:02,709 HaplotypeCaller - Ran local assembly on 1258 active regions
[2016-04-15T00:35Z] INFO  17:35:02,756 ProgressMeter -            done       7.519483E7    39.0 s            0.0 s      100.0%    39.0 s       0.0 s
[2016-04-15T00:35Z] INFO  17:35:02,756 ProgressMeter - Total runtime 39.58 secs, 0.66 min, 0.01 hours
[2016-04-15T00:35Z] INFO  17:35:02,757 MicroScheduler - 16222 reads were filtered out during the traversal out of approximately 212160 total reads (7.65%)
[2016-04-15T00:35Z] INFO  17:35:02,757 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:35Z] INFO  17:35:02,757 MicroScheduler -   -> 15934 reads (7.51% of total) failing DuplicateReadFilter
[2016-04-15T00:35Z] INFO  17:35:02,757 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:35Z] INFO  17:35:02,758 MicroScheduler -   -> 288 reads (0.14% of total) failing HCMappingQualityFilter
[2016-04-15T00:35Z] INFO  17:35:02,758 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:35Z] INFO  17:35:02,758 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:35Z] INFO  17:35:02,758 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:35Z] INFO  17:35:02,759 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:35Z] INFO  17:35:03,952 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.007902958
[2016-04-15T00:35Z] INFO  17:35:03,952 PairHMM - Total compute time in PairHMM computeLikelihoods() : 0.329407145
[2016-04-15T00:35Z] INFO  17:35:03,953 HaplotypeCaller - Ran local assembly on 1029 active regions
[2016-04-15T00:35Z] INFO  17:35:04,008 ProgressMeter -            done       4.967453E7    39.0 s            0.0 s      100.0%    39.0 s       0.0 s
[2016-04-15T00:35Z] INFO  17:35:04,008 ProgressMeter - Total runtime 39.04 secs, 0.65 min, 0.01 hours
[2016-04-15T00:35Z] INFO  17:35:04,009 MicroScheduler - 12806 reads were filtered out during the traversal out of approximately 169330 total reads (7.56%)
[2016-04-15T00:35Z] INFO  17:35:04,009 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:35Z] INFO  17:35:04,009 MicroScheduler -   -> 12645 reads (7.47% of total) failing DuplicateReadFilter
[2016-04-15T00:35Z] INFO  17:35:04,009 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:35Z] INFO  17:35:04,010 MicroScheduler -   -> 161 reads (0.10% of total) failing HCMappingQualityFilter
[2016-04-15T00:35Z] INFO  17:35:04,010 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:35Z] INFO  17:35:04,010 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:35Z] INFO  17:35:04,010 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:35Z] INFO  17:35:04,011 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:35Z] INFO  17:35:04,143 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:35Z] GATK: HaplotypeCaller
[2016-04-15T00:35Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T00:35Z] INFO  17:35:04,831 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T00:35Z] INFO  17:35:04,832 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T00:35Z] WARN  17:35:05,056 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T00:35Z] WARN  17:35:05,068 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T00:35Z] INFO  17:35:05,428 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:35Z] GATK: HaplotypeCaller
[2016-04-15T00:35Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T00:35Z] INFO  17:35:07,101 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T00:35Z] INFO  17:35:07,102 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T00:35Z] WARN  17:35:07,429 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T00:35Z] WARN  17:35:07,430 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T00:35Z] INFO  17:35:07,467 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:35Z] INFO  17:35:07,470 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:35Z] INFO  17:35:07,471 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:35Z] INFO  17:35:07,472 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:35Z] INFO  17:35:07,479 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/2/R14-18106_kapa-NGv3-PE100-NGv3-sort-2_190313104_205830046-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/2/R14-18106_kapa-NGv3-PE100-NGv3-2_190313104_205830046-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/2/tx/tmpOKaB9U/R14-18106_kapa-NGv3-PE100-NGv3-2_190313104_205830046.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:35Z] INFO  17:35:07,492 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:35Z] INFO  17:35:07,493 HelpFormatter - Date/Time: 2016/04/14 17:35:07
[2016-04-15T00:35Z] INFO  17:35:07,493 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:35Z] INFO  17:35:07,494 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:35Z] WARN  17:35:07,552 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T00:35Z] WARN  17:35:07,554 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/2/tx/tmpOKaB9U/R14-18106_kapa-NGv3-PE100-NGv3-2_190313104_205830046.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T00:35Z] INFO  17:35:07,613 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.016200689
[2016-04-15T00:35Z] INFO  17:35:07,614 PairHMM - Total compute time in PairHMM computeLikelihoods() : 0.830237525
[2016-04-15T00:35Z] INFO  17:35:07,614 HaplotypeCaller - Ran local assembly on 2103 active regions
[2016-04-15T00:35Z] INFO  17:35:07,690 ProgressMeter -            done     2.06201078E8    70.0 s            0.0 s      100.0%    70.0 s       0.0 s
[2016-04-15T00:35Z] INFO  17:35:07,691 ProgressMeter - Total runtime 70.57 secs, 1.18 min, 0.02 hours
[2016-04-15T00:35Z] INFO  17:35:07,691 MicroScheduler - 31807 reads were filtered out during the traversal out of approximately 402760 total reads (7.90%)
[2016-04-15T00:35Z] INFO  17:35:07,691 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:35Z] INFO  17:35:07,692 MicroScheduler -   -> 30398 reads (7.55% of total) failing DuplicateReadFilter
[2016-04-15T00:35Z] INFO  17:35:07,692 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:35Z] INFO  17:35:07,692 MicroScheduler -   -> 1409 reads (0.35% of total) failing HCMappingQualityFilter
[2016-04-15T00:35Z] INFO  17:35:07,692 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:35Z] INFO  17:35:07,693 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:35Z] INFO  17:35:07,693 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:35Z] INFO  17:35:07,693 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:35Z] INFO  17:35:07,723 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:35Z] INFO  17:35:07,921 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T00:35Z] INFO  17:35:07,933 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:35Z] INFO  17:35:08,029 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.10
[2016-04-15T00:35Z] INFO  17:35:08,057 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T00:35Z] INFO  17:35:08,533 IntervalUtils - Processing 204460 bp from intervals
[2016-04-15T00:35Z] INFO  17:35:08,536 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.017522316
[2016-04-15T00:35Z] INFO  17:35:08,537 PairHMM - Total compute time in PairHMM computeLikelihoods() : 1.2975250870000001
[2016-04-15T00:35Z] WARN  17:35:08,538 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:35Z] INFO  17:35:08,538 HaplotypeCaller - Ran local assembly on 3091 active regions
[2016-04-15T00:35Z] INFO  17:35:08,589 ProgressMeter -            done     3.97207864E8    96.0 s            0.0 s      100.0%    96.0 s       0.0 s
[2016-04-15T00:35Z] INFO  17:35:08,590 ProgressMeter - Total runtime 96.83 secs, 1.61 min, 0.03 hours
[2016-04-15T00:35Z] INFO  17:35:08,590 MicroScheduler - 54544 reads were filtered out during the traversal out of approximately 662487 total reads (8.23%)
[2016-04-15T00:35Z] INFO  17:35:08,590 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:35Z] INFO  17:35:08,591 MicroScheduler -   -> 49323 reads (7.45% of total) failing DuplicateReadFilter
[2016-04-15T00:35Z] INFO  17:35:08,591 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:35Z] INFO  17:35:08,591 MicroScheduler -   -> 5221 reads (0.79% of total) failing HCMappingQualityFilter
[2016-04-15T00:35Z] INFO  17:35:08,592 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:35Z] INFO  17:35:08,592 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:35Z] INFO  17:35:08,592 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:35Z] INFO  17:35:08,592 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:35Z] INFO  17:35:08,670 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:35Z] INFO  17:35:08,779 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:35Z] INFO  17:35:08,792 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:35Z] INFO  17:35:08,793 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:35Z] INFO  17:35:08,793 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:35Z] INFO  17:35:08,798 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:35Z] INFO  17:35:08,799 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:35Z] INFO  17:35:08,798 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/2/R14-18106_kapa-NGv3-PE100-NGv3-sort-2_205912303_222290862-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/2/R14-18106_kapa-NGv3-PE100-NGv3-2_205912303_222290862-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/2/tx/tmpsCyRWF/R14-18106_kapa-NGv3-PE100-NGv3-2_205912303_222290862.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:35Z] INFO  17:35:08,800 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T00:35Z] INFO  17:35:08,800 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T00:35Z] INFO  17:35:08,801 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T00:35Z] INFO  17:35:08,801 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T00:35Z] INFO  17:35:08,820 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:35Z] INFO  17:35:08,821 HelpFormatter - Date/Time: 2016/04/14 17:35:08
[2016-04-15T00:35Z] INFO  17:35:08,821 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:35Z] INFO  17:35:08,822 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:35Z] WARN  17:35:08,848 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T00:35Z] WARN  17:35:08,850 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/2/tx/tmpsCyRWF/R14-18106_kapa-NGv3-PE100-NGv3-2_205912303_222290862.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T00:35Z] INFO  17:35:09,016 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T00:35Z] INFO  17:35:09,059 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:35Z] INFO  17:35:09,178 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:35Z] INFO  17:35:09,225 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T00:35Z] INFO  17:35:09,235 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:35Z] INFO  17:35:09,332 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.10
[2016-04-15T00:35Z] INFO  17:35:09,363 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T00:35Z] GATK: HaplotypeCaller
[2016-04-15T00:35Z] INFO  17:35:09,864 IntervalUtils - Processing 247026 bp from intervals
[2016-04-15T00:35Z] WARN  17:35:09,880 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:35Z] INFO  17:35:10,011 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:35Z] INFO  17:35:10,015 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:35Z] INFO  17:35:10,145 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:35Z] INFO  17:35:10,146 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:35Z] INFO  17:35:10,147 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T00:35Z] INFO  17:35:10,148 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T00:35Z] INFO  17:35:10,160 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T00:35Z] INFO  17:35:10,161 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T00:35Z] INFO  17:35:10,187 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.006587802
[2016-04-15T00:35Z] INFO  17:35:10,188 PairHMM - Total compute time in PairHMM computeLikelihoods() : 0.23365528900000002
[2016-04-15T00:35Z] INFO  17:35:10,189 HaplotypeCaller - Ran local assembly on 758 active regions
[2016-04-15T00:35Z] GATK: HaplotypeCaller
[2016-04-15T00:35Z] INFO  17:35:10,366 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T00:35Z] INFO  17:35:10,960 ProgressMeter -            done      2.4918497E7    29.0 s            1.0 s      100.0%    29.0 s       0.0 s
[2016-04-15T00:35Z] INFO  17:35:10,960 ProgressMeter - Total runtime 29.71 secs, 0.50 min, 0.01 hours
[2016-04-15T00:35Z] INFO  17:35:10,960 MicroScheduler - 58579 reads were filtered out during the traversal out of approximately 178522 total reads (32.81%)
[2016-04-15T00:35Z] INFO  17:35:10,961 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:35Z] INFO  17:35:10,961 MicroScheduler -   -> 10006 reads (5.60% of total) failing DuplicateReadFilter
[2016-04-15T00:35Z] INFO  17:35:10,961 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:35Z] INFO  17:35:10,962 MicroScheduler -   -> 48573 reads (27.21% of total) failing HCMappingQualityFilter
[2016-04-15T00:35Z] INFO  17:35:10,962 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:35Z] INFO  17:35:10,962 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:35Z] INFO  17:35:10,962 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:35Z] INFO  17:35:10,962 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:35Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T00:35Z] INFO  17:35:11,970 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T00:35Z] INFO  17:35:11,971 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T00:35Z] INFO  17:35:12,100 ProgressMeter -      2:97530718        9671732.0    30.0 s            3.0 s       26.4%   113.0 s      83.0 s
[2016-04-15T00:35Z] WARN  17:35:12,169 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T00:35Z] WARN  17:35:12,170 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T00:35Z] INFO  17:35:12,297 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:35Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T00:35Z] INFO  17:35:12,499 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T00:35Z] INFO  17:35:12,501 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T00:35Z] GATK: HaplotypeCaller
[2016-04-15T00:35Z] INFO  17:35:12,704 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:35Z] INFO  17:35:12,707 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:35Z] INFO  17:35:12,708 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:35Z] INFO  17:35:12,708 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:35Z] INFO  17:35:12,713 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/2/R14-18106_kapa-NGv3-PE100-NGv3-sort-2_222291154_237994685-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/2/R14-18106_kapa-NGv3-PE100-NGv3-2_222291154_237994685-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/2/tx/tmpn3TyzQ/R14-18106_kapa-NGv3-PE100-NGv3-2_222291154_237994685.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:35Z] INFO  17:35:12,745 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:35Z] INFO  17:35:12,746 HelpFormatter - Date/Time: 2016/04/14 17:35:12
[2016-04-15T00:35Z] INFO  17:35:12,747 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:35Z] INFO  17:35:12,747 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:35Z] WARN  17:35:12,782 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T00:35Z] WARN  17:35:12,785 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/2/tx/tmpn3TyzQ/R14-18106_kapa-NGv3-PE100-NGv3-2_222291154_237994685.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T00:35Z] WARN  17:35:12,851 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T00:35Z] WARN  17:35:12,852 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T00:35Z] INFO  17:35:12,964 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:35Z] INFO  17:35:13,100 ProgressMeter -     1:152281037      7.5033226E7    90.0 s            1.0 s       39.5%     3.8 m       2.3 m
[2016-04-15T00:35Z] INFO  17:35:13,172 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T00:35Z] INFO  17:35:13,192 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:35Z] INFO  17:35:13,275 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-15T00:35Z] INFO  17:35:13,304 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T00:35Z] INFO  17:35:13,734 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:35Z] INFO  17:35:13,738 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:35Z] INFO  17:35:13,738 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:35Z] INFO  17:35:13,739 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:35Z] INFO  17:35:13,744 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/2/R14-18106_kapa-NGv3-PE100-NGv3-sort-2_237995374_243199373-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/2/R14-18106_kapa-NGv3-PE100-NGv3-2_237995374_243199373-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/2/tx/tmp37PLC_/R14-18106_kapa-NGv3-PE100-NGv3-2_237995374_243199373.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:35Z] INFO  17:35:13,787 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:35Z] INFO  17:35:13,788 HelpFormatter - Date/Time: 2016/04/14 17:35:13
[2016-04-15T00:35Z] INFO  17:35:13,789 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:35Z] INFO  17:35:13,789 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:35Z] WARN  17:35:13,830 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T00:35Z] WARN  17:35:13,840 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/2/tx/tmp37PLC_/R14-18106_kapa-NGv3-PE100-NGv3-2_237995374_243199373.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T00:35Z] INFO  17:35:13,853 IntervalUtils - Processing 186854 bp from intervals
[2016-04-15T00:35Z] WARN  17:35:13,858 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:35Z] INFO  17:35:14,011 ProgressMeter -     2:120709705       2.564517E7    30.0 s            1.0 s       78.1%    38.0 s       8.0 s
[2016-04-15T00:35Z] INFO  17:35:14,019 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:35Z] INFO  17:35:14,120 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:35Z] INFO  17:35:14,168 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:35Z] INFO  17:35:14,173 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:35Z] INFO  17:35:14,173 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T00:35Z] INFO  17:35:14,173 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T00:35Z] INFO  17:35:14,181 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T00:35Z] INFO  17:35:14,182 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T00:35Z] INFO  17:35:14,329 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T00:35Z] INFO  17:35:14,338 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:35Z] INFO  17:35:14,444 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.11
[2016-04-15T00:35Z] INFO  17:35:14,461 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T00:35Z] INFO  17:35:14,486 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T00:35Z] INFO  17:35:14,938 IntervalUtils - Processing 128077 bp from intervals
[2016-04-15T00:35Z] WARN  17:35:14,942 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:35Z] INFO  17:35:15,101 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:35Z] INFO  17:35:15,168 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:35Z] INFO  17:35:15,170 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:35Z] INFO  17:35:15,170 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T00:35Z] INFO  17:35:15,171 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T00:35Z] INFO  17:35:15,172 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T00:35Z] INFO  17:35:15,172 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T00:35Z] INFO  17:35:15,420 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T00:35Z] INFO  17:35:16,246 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:35Z] INFO  17:35:16,248 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:35Z] INFO  17:35:16,248 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:35Z] INFO  17:35:16,249 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:35Z] INFO  17:35:16,264 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/3/R14-18106_kapa-NGv3-PE100-NGv3-sort-3_0_15512123-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/3/R14-18106_kapa-NGv3-PE100-NGv3-3_0_15512123-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/3/tx/tmpq0HKhI/R14-18106_kapa-NGv3-PE100-NGv3-3_0_15512123.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:35Z] INFO  17:35:16,290 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:35Z] INFO  17:35:16,291 HelpFormatter - Date/Time: 2016/04/14 17:35:16
[2016-04-15T00:35Z] INFO  17:35:16,291 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:35Z] INFO  17:35:16,291 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:35Z] WARN  17:35:16,325 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T00:35Z] WARN  17:35:16,328 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/3/tx/tmpq0HKhI/R14-18106_kapa-NGv3-PE100-NGv3-3_0_15512123.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T00:35Z] INFO  17:35:16,595 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:35Z] INFO  17:35:16,773 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T00:35Z] INFO  17:35:16,796 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:35Z] INFO  17:35:16,890 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.09
[2016-04-15T00:35Z] INFO  17:35:16,922 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T00:35Z] INFO  17:35:17,430 IntervalUtils - Processing 188511 bp from intervals
[2016-04-15T00:35Z] WARN  17:35:17,434 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:35Z] INFO  17:35:17,511 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:35Z] INFO  17:35:17,632 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:35Z] INFO  17:35:17,632 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:35Z] INFO  17:35:17,633 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T00:35Z] INFO  17:35:17,633 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T00:35Z] INFO  17:35:17,650 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T00:35Z] INFO  17:35:17,651 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T00:35Z] INFO  17:35:17,876 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T00:35Z] INFO  17:35:17,995 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.011706763
[2016-04-15T00:35Z] INFO  17:35:17,997 PairHMM - Total compute time in PairHMM computeLikelihoods() : 0.560150429
[2016-04-15T00:35Z] INFO  17:35:17,998 HaplotypeCaller - Ran local assembly on 1770 active regions
[2016-04-15T00:35Z] INFO  17:35:18,054 ProgressMeter -            done      1.3985948E8    56.0 s            0.0 s      100.0%    56.0 s       0.0 s
[2016-04-15T00:35Z] INFO  17:35:18,054 ProgressMeter - Total runtime 56.07 secs, 0.93 min, 0.02 hours
[2016-04-15T00:35Z] INFO  17:35:18,055 MicroScheduler - 26149 reads were filtered out during the traversal out of approximately 338602 total reads (7.72%)
[2016-04-15T00:35Z] INFO  17:35:18,055 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:35Z] INFO  17:35:18,055 MicroScheduler -   -> 25819 reads (7.63% of total) failing DuplicateReadFilter
[2016-04-15T00:35Z] INFO  17:35:18,055 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:35Z] INFO  17:35:18,056 MicroScheduler -   -> 330 reads (0.10% of total) failing HCMappingQualityFilter
[2016-04-15T00:35Z] INFO  17:35:18,056 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:35Z] INFO  17:35:18,056 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:35Z] INFO  17:35:18,056 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:35Z] INFO  17:35:18,057 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:35Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T00:35Z] INFO  17:35:19,392 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T00:35Z] INFO  17:35:19,393 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T00:35Z] INFO  17:35:19,537 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:35Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T00:35Z] INFO  17:35:19,572 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T00:35Z] INFO  17:35:19,573 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T00:35Z] WARN  17:35:19,617 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T00:35Z] WARN  17:35:19,618 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T00:35Z] GATK: HaplotypeCaller
[2016-04-15T00:35Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T00:35Z] INFO  17:35:19,827 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T00:35Z] INFO  17:35:19,828 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T00:35Z] INFO  17:35:19,855 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.039773905000000005
[2016-04-15T00:35Z] INFO  17:35:19,856 PairHMM - Total compute time in PairHMM computeLikelihoods() : 9.558195333
[2016-04-15T00:35Z] INFO  17:35:19,857 HaplotypeCaller - Ran local assembly on 2792 active regions
[2016-04-15T00:35Z] WARN  17:35:19,867 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T00:35Z] WARN  17:35:19,868 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T00:35Z] INFO  17:35:19,901 ProgressMeter -            done     3.27575124E8   112.0 s            0.0 s      100.0%   112.0 s       0.0 s
[2016-04-15T00:35Z] INFO  17:35:19,902 ProgressMeter - Total runtime 112.83 secs, 1.88 min, 0.03 hours
[2016-04-15T00:35Z] INFO  17:35:19,903 MicroScheduler - 131918 reads were filtered out during the traversal out of approximately 674805 total reads (19.55%)
[2016-04-15T00:35Z] INFO  17:35:19,903 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:35Z] INFO  17:35:19,904 MicroScheduler -   -> 45866 reads (6.80% of total) failing DuplicateReadFilter
[2016-04-15T00:35Z] INFO  17:35:19,904 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:35Z] INFO  17:35:19,904 MicroScheduler -   -> 86052 reads (12.75% of total) failing HCMappingQualityFilter
[2016-04-15T00:35Z] INFO  17:35:19,904 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:35Z] INFO  17:35:19,905 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:35Z] INFO  17:35:19,905 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:35Z] INFO  17:35:19,905 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:35Z] WARN  17:35:20,295 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T00:35Z] WARN  17:35:20,296 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T00:35Z] INFO  17:35:21,162 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.007935371
[2016-04-15T00:35Z] INFO  17:35:21,163 PairHMM - Total compute time in PairHMM computeLikelihoods() : 0.448564055
[2016-04-15T00:35Z] INFO  17:35:21,163 HaplotypeCaller - Ran local assembly on 970 active regions
[2016-04-15T00:35Z] INFO  17:35:21,205 ProgressMeter -            done      4.1916896E7    37.0 s            0.0 s      100.0%    37.0 s       0.0 s
[2016-04-15T00:35Z] INFO  17:35:21,206 ProgressMeter - Total runtime 37.21 secs, 0.62 min, 0.01 hours
[2016-04-15T00:35Z] INFO  17:35:21,207 MicroScheduler - 67515 reads were filtered out during the traversal out of approximately 208538 total reads (32.38%)
[2016-04-15T00:35Z] INFO  17:35:21,208 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:35Z] INFO  17:35:21,208 MicroScheduler -   -> 11510 reads (5.52% of total) failing DuplicateReadFilter
[2016-04-15T00:35Z] INFO  17:35:21,209 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:35Z] INFO  17:35:21,210 MicroScheduler -   -> 56005 reads (26.86% of total) failing HCMappingQualityFilter
[2016-04-15T00:35Z] INFO  17:35:21,210 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:35Z] INFO  17:35:21,211 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:35Z] INFO  17:35:21,211 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:35Z] INFO  17:35:21,212 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:35Z] INFO  17:35:21,495 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:35Z] GATK: HaplotypeCaller
[2016-04-15T00:35Z] INFO  17:35:22,624 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:35Z] INFO  17:35:22,806 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:35Z] INFO  17:35:22,810 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:35Z] INFO  17:35:22,810 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:35Z] INFO  17:35:22,811 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:35Z] INFO  17:35:22,816 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/3/R14-18106_kapa-NGv3-PE100-NGv3-sort-3_15515506_31574805-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/3/R14-18106_kapa-NGv3-PE100-NGv3-3_15515506_31574805-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/3/tx/tmpy9faTp/R14-18106_kapa-NGv3-PE100-NGv3-3_15515506_31574805.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:35Z] INFO  17:35:22,853 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:35Z] INFO  17:35:22,854 HelpFormatter - Date/Time: 2016/04/14 17:35:22
[2016-04-15T00:35Z] INFO  17:35:22,855 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:35Z] INFO  17:35:22,856 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:35Z] WARN  17:35:22,924 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T00:35Z] WARN  17:35:22,934 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/3/tx/tmpy9faTp/R14-18106_kapa-NGv3-PE100-NGv3-3_15515506_31574805.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T00:35Z] GATK: HaplotypeCaller
[2016-04-15T00:35Z] INFO  17:35:23,237 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:35Z] INFO  17:35:23,536 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T00:35Z] INFO  17:35:23,556 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:35Z] INFO  17:35:23,639 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-15T00:35Z] INFO  17:35:23,675 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T00:35Z] INFO  17:35:23,971 ProgressMeter -     2:131674065      1.1258981E7    30.0 s            2.0 s       44.2%    67.0 s      37.0 s
[2016-04-15T00:35Z] INFO  17:35:24,183 IntervalUtils - Processing 86168 bp from intervals
[2016-04-15T00:35Z] WARN  17:35:24,188 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:35Z] INFO  17:35:24,316 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:35Z] INFO  17:35:24,385 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:35Z] INFO  17:35:24,387 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:35Z] INFO  17:35:24,387 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T00:35Z] INFO  17:35:24,388 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T00:35Z] INFO  17:35:24,389 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T00:35Z] INFO  17:35:24,389 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T00:35Z] INFO  17:35:24,576 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T00:35Z] INFO  17:35:24,917 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:35Z] INFO  17:35:24,920 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:35Z] INFO  17:35:24,921 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:35Z] INFO  17:35:24,921 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:35Z] INFO  17:35:24,926 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/3/R14-18106_kapa-NGv3-PE100-NGv3-sort-3_31617887_47127804-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/3/R14-18106_kapa-NGv3-PE100-NGv3-3_31617887_47127804-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/3/tx/tmpg0PkLT/R14-18106_kapa-NGv3-PE100-NGv3-3_31617887_47127804.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:35Z] INFO  17:35:24,956 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:35Z] INFO  17:35:24,957 HelpFormatter - Date/Time: 2016/04/14 17:35:24
[2016-04-15T00:35Z] INFO  17:35:24,958 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:35Z] INFO  17:35:24,958 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:35Z] WARN  17:35:24,988 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T00:35Z] WARN  17:35:24,991 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/3/tx/tmpg0PkLT/R14-18106_kapa-NGv3-PE100-NGv3-3_31617887_47127804.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T00:35Z] INFO  17:35:25,188 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:35Z] INFO  17:35:25,380 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T00:35Z] INFO  17:35:25,409 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:35Z] INFO  17:35:25,491 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-15T00:35Z] INFO  17:35:25,514 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T00:35Z] INFO  17:35:25,906 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.0050077260000000005
[2016-04-15T00:35Z] INFO  17:35:25,907 PairHMM - Total compute time in PairHMM computeLikelihoods() : 0.18079482400000002
[2016-04-15T00:35Z] INFO  17:35:25,907 HaplotypeCaller - Ran local assembly on 697 active regions
[2016-04-15T00:35Z] INFO  17:35:25,971 IntervalUtils - Processing 307437 bp from intervals
[2016-04-15T00:35Z] INFO  17:35:25,968 ProgressMeter -            done      2.4452471E7    27.0 s            1.0 s      100.0%    27.0 s       0.0 s
[2016-04-15T00:35Z] INFO  17:35:25,968 ProgressMeter - Total runtime 27.79 secs, 0.46 min, 0.01 hours
[2016-04-15T00:35Z] INFO  17:35:25,968 MicroScheduler - 17917 reads were filtered out during the traversal out of approximately 115130 total reads (15.56%)
[2016-04-15T00:35Z] INFO  17:35:25,969 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:35Z] INFO  17:35:25,969 MicroScheduler -   -> 7844 reads (6.81% of total) failing DuplicateReadFilter
[2016-04-15T00:35Z] INFO  17:35:25,969 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:35Z] INFO  17:35:25,971 MicroScheduler -   -> 10073 reads (8.75% of total) failing HCMappingQualityFilter
[2016-04-15T00:35Z] INFO  17:35:25,972 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:35Z] INFO  17:35:25,972 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:35Z] INFO  17:35:25,972 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:35Z] INFO  17:35:25,972 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:35Z] WARN  17:35:25,976 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:35Z] INFO  17:35:26,052 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:35Z] INFO  17:35:26,162 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:35Z] INFO  17:35:26,163 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:35Z] INFO  17:35:26,164 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T00:35Z] INFO  17:35:26,165 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T00:35Z] INFO  17:35:26,184 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T00:35Z] INFO  17:35:26,184 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T00:35Z] INFO  17:35:26,425 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:35Z] INFO  17:35:26,428 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:35Z] INFO  17:35:26,429 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:35Z] INFO  17:35:26,429 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:35Z] INFO  17:35:26,434 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/3/R14-18106_kapa-NGv3-PE100-NGv3-sort-3_47129602_62648069-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/3/R14-18106_kapa-NGv3-PE100-NGv3-3_47129602_62648069-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/3/tx/tmpTvu2Zy/R14-18106_kapa-NGv3-PE100-NGv3-3_47129602_62648069.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:35Z] INFO  17:35:26,454 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:35Z] INFO  17:35:26,455 HelpFormatter - Date/Time: 2016/04/14 17:35:26
[2016-04-15T00:35Z] INFO  17:35:26,456 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:35Z] INFO  17:35:26,456 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:35Z] INFO  17:35:26,461 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T00:35Z] WARN  17:35:26,507 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T00:35Z] WARN  17:35:26,510 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/3/tx/tmpTvu2Zy/R14-18106_kapa-NGv3-PE100-NGv3-3_47129602_62648069.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T00:35Z] INFO  17:35:26,757 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:35Z] INFO  17:35:26,998 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.010870603000000001
[2016-04-15T00:35Z] INFO  17:35:26,999 PairHMM - Total compute time in PairHMM computeLikelihoods() : 0.8715225830000001
[2016-04-15T00:35Z] INFO  17:35:26,999 HaplotypeCaller - Ran local assembly on 1559 active regions
[2016-04-15T00:35Z] INFO  17:35:27,013 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T00:35Z] INFO  17:35:27,048 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:35Z] INFO  17:35:27,057 ProgressMeter -            done     1.00598827E8    54.0 s            0.0 s      100.0%    54.0 s       0.0 s
[2016-04-15T00:35Z] INFO  17:35:27,057 ProgressMeter - Total runtime 54.57 secs, 0.91 min, 0.02 hours
[2016-04-15T00:35Z] INFO  17:35:27,058 MicroScheduler - 23875 reads were filtered out during the traversal out of approximately 308959 total reads (7.73%)
[2016-04-15T00:35Z] INFO  17:35:27,058 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:35Z] INFO  17:35:27,058 MicroScheduler -   -> 23086 reads (7.47% of total) failing DuplicateReadFilter
[2016-04-15T00:35Z] INFO  17:35:27,062 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:35Z] INFO  17:35:27,062 MicroScheduler -   -> 789 reads (0.26% of total) failing HCMappingQualityFilter
[2016-04-15T00:35Z] INFO  17:35:27,063 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:35Z] INFO  17:35:27,063 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:35Z] INFO  17:35:27,063 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:35Z] INFO  17:35:27,063 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:35Z] INFO  17:35:27,150 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.10
[2016-04-15T00:35Z] INFO  17:35:27,179 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T00:35Z] INFO  17:35:27,379 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:35Z] INFO  17:35:27,677 IntervalUtils - Processing 430308 bp from intervals
[2016-04-15T00:35Z] WARN  17:35:27,683 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:35Z] GATK: HaplotypeCaller
[2016-04-15T00:35Z] INFO  17:35:27,771 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:35Z] INFO  17:35:27,946 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:35Z] INFO  17:35:27,948 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:35Z] INFO  17:35:27,948 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T00:35Z] INFO  17:35:27,949 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T00:35Z] INFO  17:35:27,950 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T00:35Z] INFO  17:35:27,950 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T00:35Z] INFO  17:35:28,121 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T00:35Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T00:35Z] INFO  17:35:28,401 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T00:35Z] INFO  17:35:28,401 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T00:35Z] INFO  17:35:28,462 ProgressMeter -      1:28661344     3.20677274E8   120.0 s            0.0 s       93.7%     2.1 m       8.0 s
[2016-04-15T00:35Z] WARN  17:35:28,572 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T00:35Z] WARN  17:35:28,573 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T00:35Z] INFO  17:35:28,865 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:35Z] GATK: HaplotypeCaller
[2016-04-15T00:35Z] INFO  17:35:29,744 ProgressMeter -     2:167760393      3.1374726E7    30.0 s            0.0 s       52.0%    57.0 s      27.0 s
[2016-04-15T00:35Z] INFO  17:35:30,865 ProgressMeter -     2:179473059        9900601.0    30.0 s            3.0 s       44.1%    68.0 s      38.0 s
[2016-04-15T00:35Z] INFO  17:35:30,942 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:35Z] INFO  17:35:30,945 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:35Z] INFO  17:35:30,945 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:35Z] INFO  17:35:30,946 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:35Z] INFO  17:35:30,950 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/3/R14-18106_kapa-NGv3-PE100-NGv3-sort-3_62739115_78648077-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/3/R14-18106_kapa-NGv3-PE100-NGv3-3_62739115_78648077-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/3/tx/tmpOposdv/R14-18106_kapa-NGv3-PE100-NGv3-3_62739115_78648077.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:35Z] INFO  17:35:30,969 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:35Z] INFO  17:35:30,970 HelpFormatter - Date/Time: 2016/04/14 17:35:30
[2016-04-15T00:35Z] INFO  17:35:30,970 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:35Z] INFO  17:35:30,971 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:35Z] WARN  17:35:30,994 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T00:35Z] WARN  17:35:30,997 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/3/tx/tmpOposdv/R14-18106_kapa-NGv3-PE100-NGv3-3_62739115_78648077.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T00:35Z] INFO  17:35:31,176 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:35Z] INFO  17:35:31,361 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T00:35Z] INFO  17:35:31,371 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:35Z] INFO  17:35:31,448 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-15T00:35Z] INFO  17:35:31,467 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T00:35Z] INFO  17:35:31,771 IntervalUtils - Processing 82160 bp from intervals
[2016-04-15T00:35Z] WARN  17:35:31,798 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:35Z] INFO  17:35:31,934 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:35Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T00:35Z] INFO  17:35:31,985 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T00:35Z] INFO  17:35:31,985 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T00:35Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T00:35Z] INFO  17:35:32,007 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:35Z] INFO  17:35:32,013 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:35Z] INFO  17:35:32,014 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T00:35Z] INFO  17:35:32,015 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T00:35Z] INFO  17:35:32,022 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T00:35Z] INFO  17:35:32,022 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T00:35Z] INFO  17:35:32,026 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T00:35Z] INFO  17:35:32,027 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T00:35Z] INFO  17:35:32,214 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T00:35Z] WARN  17:35:32,264 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T00:35Z] WARN  17:35:32,264 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T00:35Z] WARN  17:35:32,311 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T00:35Z] WARN  17:35:32,312 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T00:35Z] INFO  17:35:32,796 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:35Z] INFO  17:35:32,799 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:35Z] INFO  17:35:32,800 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:35Z] INFO  17:35:32,801 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:35Z] INFO  17:35:32,805 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/3/R14-18106_kapa-NGv3-PE100-NGv3-sort-3_78649262_96533852-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/3/R14-18106_kapa-NGv3-PE100-NGv3-3_78649262_96533852-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/3/tx/tmp6usxhC/R14-18106_kapa-NGv3-PE100-NGv3-3_78649262_96533852.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:35Z] INFO  17:35:32,816 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:35Z] INFO  17:35:32,817 HelpFormatter - Date/Time: 2016/04/14 17:35:32
[2016-04-15T00:35Z] INFO  17:35:32,818 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:35Z] INFO  17:35:32,818 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:35Z] WARN  17:35:32,876 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T00:35Z] WARN  17:35:32,878 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/3/tx/tmp6usxhC/R14-18106_kapa-NGv3-PE100-NGv3-3_78649262_96533852.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T00:35Z] INFO  17:35:33,163 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:35Z] INFO  17:35:33,446 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T00:35Z] INFO  17:35:33,456 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:35Z] INFO  17:35:33,570 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.11
[2016-04-15T00:35Z] INFO  17:35:33,611 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T00:35Z] INFO  17:35:34,116 IntervalUtils - Processing 30411 bp from intervals
[2016-04-15T00:35Z] WARN  17:35:34,122 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:35Z] INFO  17:35:34,172 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.08153577000000001
[2016-04-15T00:35Z] INFO  17:35:34,173 PairHMM - Total compute time in PairHMM computeLikelihoods() : 15.917363025
[2016-04-15T00:35Z] INFO  17:35:34,173 HaplotypeCaller - Ran local assembly on 2994 active regions
[2016-04-15T00:35Z] INFO  17:35:34,225 ProgressMeter -            done     3.72740812E8     2.1 m            0.0 s      100.0%     2.1 m       0.0 s
[2016-04-15T00:35Z] INFO  17:35:34,226 ProgressMeter - Total runtime 125.79 secs, 2.10 min, 0.03 hours
[2016-04-15T00:35Z] INFO  17:35:34,226 MicroScheduler - 59787 reads were filtered out during the traversal out of approximately 663905 total reads (9.01%)
[2016-04-15T00:35Z] INFO  17:35:34,226 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:35Z] INFO  17:35:34,227 MicroScheduler -   -> 50296 reads (7.58% of total) failing DuplicateReadFilter
[2016-04-15T00:35Z] INFO  17:35:34,227 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:35Z] INFO  17:35:34,227 MicroScheduler -   -> 9491 reads (1.43% of total) failing HCMappingQualityFilter
[2016-04-15T00:35Z] INFO  17:35:34,228 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:35Z] INFO  17:35:34,228 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:35Z] INFO  17:35:34,228 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:35Z] INFO  17:35:34,228 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:35Z] INFO  17:35:34,247 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:35Z] INFO  17:35:34,318 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:35Z] INFO  17:35:34,319 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:35Z] INFO  17:35:34,320 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T00:35Z] INFO  17:35:34,321 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T00:35Z] INFO  17:35:34,331 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T00:35Z] INFO  17:35:34,332 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T00:35Z] INFO  17:35:34,549 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T00:35Z] INFO  17:35:35,605 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:35Z] GATK: HaplotypeCaller
[2016-04-15T00:35Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T00:35Z] INFO  17:35:37,493 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T00:35Z] INFO  17:35:37,504 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T00:35Z] WARN  17:35:37,852 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T00:35Z] WARN  17:35:37,853 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T00:35Z] INFO  17:35:38,814 ProgressMeter -     2:200820889      3.0450905E7    30.0 s            0.0 s       52.9%    56.0 s      26.0 s
[2016-04-15T00:35Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T00:35Z] INFO  17:35:38,897 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T00:35Z] INFO  17:35:38,898 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T00:35Z] WARN  17:35:39,169 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T00:35Z] WARN  17:35:39,170 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T00:35Z] INFO  17:35:39,228 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:35Z] INFO  17:35:39,231 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:35Z] INFO  17:35:39,232 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:35Z] INFO  17:35:39,232 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:35Z] INFO  17:35:39,237 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/3/R14-18106_kapa-NGv3-PE100-NGv3-sort-3_96585668_112185230-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/3/R14-18106_kapa-NGv3-PE100-NGv3-3_96585668_112185230-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/3/tx/tmpCS0Hxn/R14-18106_kapa-NGv3-PE100-NGv3-3_96585668_112185230.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:35Z] INFO  17:35:39,251 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:35Z] INFO  17:35:39,252 HelpFormatter - Date/Time: 2016/04/14 17:35:39
[2016-04-15T00:35Z] INFO  17:35:39,253 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:35Z] INFO  17:35:39,253 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:35Z] WARN  17:35:39,276 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T00:35Z] WARN  17:35:39,279 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/3/tx/tmpCS0Hxn/R14-18106_kapa-NGv3-PE100-NGv3-3_96585668_112185230.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T00:35Z] INFO  17:35:39,505 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:35Z] INFO  17:35:39,701 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T00:35Z] INFO  17:35:39,710 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:35Z] INFO  17:35:39,796 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.09
[2016-04-15T00:35Z] INFO  17:35:39,825 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T00:35Z] INFO  17:35:40,163 ProgressMeter -     2:214794684      2.4146157E7    30.0 s            1.0 s       36.9%    81.0 s      51.0 s
[2016-04-15T00:35Z] INFO  17:35:40,322 IntervalUtils - Processing 140565 bp from intervals
[2016-04-15T00:35Z] WARN  17:35:40,328 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:35Z] INFO  17:35:40,501 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:35Z] INFO  17:35:40,651 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:35Z] INFO  17:35:40,651 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:35Z] INFO  17:35:40,652 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T00:35Z] INFO  17:35:40,652 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T00:35Z] INFO  17:35:40,659 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T00:35Z] INFO  17:35:40,660 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T00:35Z] INFO  17:35:40,946 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T00:35Z] INFO  17:35:42,101 ProgressMeter -     2:103450875       8.326965E7    60.0 s            0.0 s       72.5%    82.0 s      22.0 s
[2016-04-15T00:35Z] INFO  17:35:43,101 ProgressMeter -     1:153909224     1.19246822E8   120.0 s            1.0 s       49.7%     4.0 m       2.0 m
[2016-04-15T00:35Z] INFO  17:35:44,188 ProgressMeter -     2:231407661      2.4918415E7    30.0 s            1.0 s       47.5%    63.0 s      33.0 s
[2016-04-15T00:35Z] INFO  17:35:45,193 ProgressMeter -     2:242053971      1.9260192E7    30.0 s            1.0 s       67.4%    44.0 s      14.0 s
[2016-04-15T00:35Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T00:35Z] INFO  17:35:47,491 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T00:35Z] INFO  17:35:47,492 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T00:35Z] INFO  17:35:47,653 ProgressMeter -       3:9952677      1.4216821E7    30.0 s            2.0 s       40.3%    74.0 s      44.0 s
[2016-04-15T00:35Z] WARN  17:35:47,745 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T00:35Z] WARN  17:35:47,745 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T00:35Z] INFO  17:35:50,192 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.007989326
[2016-04-15T00:35Z] INFO  17:35:50,193 PairHMM - Total compute time in PairHMM computeLikelihoods() : 0.383512793
[2016-04-15T00:35Z] INFO  17:35:50,194 HaplotypeCaller - Ran local assembly on 1566 active regions
[2016-04-15T00:35Z] INFO  17:35:50,252 ProgressMeter -            done     1.25465506E8    50.0 s            0.0 s      100.0%    50.0 s       0.0 s
[2016-04-15T00:35Z] INFO  17:35:50,252 ProgressMeter - Total runtime 50.53 secs, 0.84 min, 0.01 hours
[2016-04-15T00:35Z] INFO  17:35:50,252 MicroScheduler - 20708 reads were filtered out during the traversal out of approximately 269930 total reads (7.67%)
[2016-04-15T00:35Z] INFO  17:35:50,253 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:35Z] INFO  17:35:50,253 MicroScheduler -   -> 20055 reads (7.43% of total) failing DuplicateReadFilter
[2016-04-15T00:35Z] INFO  17:35:50,253 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:35Z] INFO  17:35:50,253 MicroScheduler -   -> 653 reads (0.24% of total) failing HCMappingQualityFilter
[2016-04-15T00:35Z] INFO  17:35:50,253 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:35Z] INFO  17:35:50,254 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:35Z] INFO  17:35:50,254 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:35Z] INFO  17:35:50,254 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:35Z] INFO  17:35:51,594 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:35Z] GATK: HaplotypeCaller
[2016-04-15T00:35Z] INFO  17:35:52,177 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.002247743
[2016-04-15T00:35Z] INFO  17:35:52,178 PairHMM - Total compute time in PairHMM computeLikelihoods() : 0.035403874
[2016-04-15T00:35Z] INFO  17:35:52,179 HaplotypeCaller - Ran local assembly on 199 active regions
[2016-04-15T00:35Z] INFO  17:35:52,223 ProgressMeter -            done        2089463.0    17.0 s            8.0 s      100.0%    17.0 s       0.0 s
[2016-04-15T00:35Z] INFO  17:35:52,224 ProgressMeter - Total runtime 17.90 secs, 0.30 min, 0.00 hours
[2016-04-15T00:35Z] INFO  17:35:52,224 MicroScheduler - 2830 reads were filtered out during the traversal out of approximately 37972 total reads (7.45%)
[2016-04-15T00:35Z] INFO  17:35:52,224 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:35Z] INFO  17:35:52,225 MicroScheduler -   -> 2789 reads (7.34% of total) failing DuplicateReadFilter
[2016-04-15T00:35Z] INFO  17:35:52,225 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:35Z] INFO  17:35:52,225 MicroScheduler -   -> 41 reads (0.11% of total) failing HCMappingQualityFilter
[2016-04-15T00:35Z] INFO  17:35:52,225 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:35Z] INFO  17:35:52,226 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:35Z] INFO  17:35:52,226 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:35Z] INFO  17:35:52,226 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:35Z] INFO  17:35:53,578 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:35Z] GATK: HaplotypeCaller
[2016-04-15T00:35Z] INFO  17:35:53,981 ProgressMeter -     2:141232861      5.7477368E7    60.0 s            1.0 s       94.4%    63.0 s       3.0 s
[2016-04-15T00:35Z] INFO  17:35:54,150 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.010593705
[2016-04-15T00:35Z] INFO  17:35:54,160 PairHMM - Total compute time in PairHMM computeLikelihoods() : 0.18078264700000002
[2016-04-15T00:35Z] INFO  17:35:54,161 HaplotypeCaller - Ran local assembly on 634 active regions
[2016-04-15T00:35Z] INFO  17:35:54,205 ProgressMeter -            done      2.0117694E7    29.0 s            1.0 s      100.0%    29.0 s       0.0 s
[2016-04-15T00:35Z] INFO  17:35:54,205 ProgressMeter - Total runtime 29.82 secs, 0.50 min, 0.01 hours
[2016-04-15T00:35Z] INFO  17:35:54,205 MicroScheduler - 7918 reads were filtered out during the traversal out of approximately 103312 total reads (7.66%)
[2016-04-15T00:35Z] INFO  17:35:54,206 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:35Z] INFO  17:35:54,206 MicroScheduler -   -> 7731 reads (7.48% of total) failing DuplicateReadFilter
[2016-04-15T00:35Z] INFO  17:35:54,206 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:35Z] INFO  17:35:54,207 MicroScheduler -   -> 187 reads (0.18% of total) failing HCMappingQualityFilter
[2016-04-15T00:35Z] INFO  17:35:54,207 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:35Z] INFO  17:35:54,207 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:35Z] INFO  17:35:54,207 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:35Z] INFO  17:35:54,208 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:35Z] INFO  17:35:54,545 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.012648209
[2016-04-15T00:35Z] INFO  17:35:54,546 PairHMM - Total compute time in PairHMM computeLikelihoods() : 0.8695502070000001
[2016-04-15T00:35Z] INFO  17:35:54,547 HaplotypeCaller - Ran local assembly on 978 active regions
[2016-04-15T00:35Z] INFO  17:35:54,625 ProgressMeter -            done      3.8908959E7    39.0 s            1.0 s      100.0%    39.0 s       0.0 s
[2016-04-15T00:35Z] INFO  17:35:54,626 ProgressMeter - Total runtime 39.46 secs, 0.66 min, 0.01 hours
[2016-04-15T00:35Z] INFO  17:35:54,626 MicroScheduler - 18316 reads were filtered out during the traversal out of approximately 194875 total reads (9.40%)
[2016-04-15T00:35Z] INFO  17:35:54,627 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:35Z] INFO  17:35:54,627 MicroScheduler -   -> 14534 reads (7.46% of total) failing DuplicateReadFilter
[2016-04-15T00:35Z] INFO  17:35:54,627 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:35Z] INFO  17:35:54,627 MicroScheduler -   -> 3782 reads (1.94% of total) failing HCMappingQualityFilter
[2016-04-15T00:35Z] INFO  17:35:54,628 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:35Z] INFO  17:35:54,628 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:35Z] INFO  17:35:54,628 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:35Z] INFO  17:35:54,628 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:35Z] INFO  17:35:54,750 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:35Z] INFO  17:35:54,754 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:35Z] INFO  17:35:54,754 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:35Z] INFO  17:35:54,755 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:35Z] INFO  17:35:54,759 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/3/R14-18106_kapa-NGv3-PE100-NGv3-sort-3_112188604_127703121-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/3/R14-18106_kapa-NGv3-PE100-NGv3-3_112188604_127703121-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/3/tx/tmp_jyKAT/R14-18106_kapa-NGv3-PE100-NGv3-3_112188604_127703121.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:35Z] INFO  17:35:54,771 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:35Z] INFO  17:35:54,773 HelpFormatter - Date/Time: 2016/04/14 17:35:54
[2016-04-15T00:35Z] INFO  17:35:54,774 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:35Z] INFO  17:35:54,774 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:35Z] WARN  17:35:54,800 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T00:35Z] WARN  17:35:54,803 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/3/tx/tmp_jyKAT/R14-18106_kapa-NGv3-PE100-NGv3-3_112188604_127703121.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T00:35Z] INFO  17:35:54,936 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:35Z] INFO  17:35:55,140 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T00:35Z] INFO  17:35:55,150 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:35Z] INFO  17:35:55,253 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.10
[2016-04-15T00:35Z] INFO  17:35:55,280 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T00:35Z] INFO  17:35:55,579 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:35Z] INFO  17:35:55,593 IntervalUtils - Processing 249953 bp from intervals
[2016-04-15T00:35Z] WARN  17:35:55,599 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:35Z] INFO  17:35:55,709 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:35Z] INFO  17:35:55,848 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:35Z] INFO  17:35:55,849 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:35Z] INFO  17:35:55,850 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T00:35Z] INFO  17:35:55,851 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T00:35Z] INFO  17:35:55,860 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T00:35Z] INFO  17:35:55,860 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T00:35Z] GATK: HaplotypeCaller
[2016-04-15T00:35Z] INFO  17:35:56,013 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:35Z] INFO  17:35:56,033 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.01838713
[2016-04-15T00:35Z] INFO  17:35:56,034 PairHMM - Total compute time in PairHMM computeLikelihoods() : 4.387774263
[2016-04-15T00:35Z] INFO  17:35:56,035 HaplotypeCaller - Ran local assembly on 1897 active regions
[2016-04-15T00:35Z] INFO  17:35:56,041 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.019165843000000002
[2016-04-15T00:35Z] INFO  17:35:56,042 PairHMM - Total compute time in PairHMM computeLikelihoods() : 0.404893361
[2016-04-15T00:35Z] INFO  17:35:56,043 HaplotypeCaller - Ran local assembly on 1499 active regions
[2016-04-15T00:35Z] INFO  17:35:56,079 ProgressMeter -            done     1.46584651E8    74.0 s            0.0 s      100.0%    74.0 s       0.0 s
[2016-04-15T00:35Z] INFO  17:35:56,080 ProgressMeter - Total runtime 74.01 secs, 1.23 min, 0.02 hours
[2016-04-15T00:35Z] INFO  17:35:56,080 MicroScheduler - 111584 reads were filtered out during the traversal out of approximately 456144 total reads (24.46%)
[2016-04-15T00:35Z] INFO  17:35:56,081 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:35Z] INFO  17:35:56,083 MicroScheduler -   -> 28342 reads (6.21% of total) failing DuplicateReadFilter
[2016-04-15T00:35Z] INFO  17:35:56,083 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:35Z] INFO  17:35:56,083 MicroScheduler -   -> 83242 reads (18.25% of total) failing HCMappingQualityFilter
[2016-04-15T00:35Z] INFO  17:35:56,083 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:35Z] INFO  17:35:56,084 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:35Z] INFO  17:35:56,084 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:35Z] INFO  17:35:56,084 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:35Z] INFO  17:35:56,118 ProgressMeter -            done     1.12411448E8    47.0 s            0.0 s      100.0%    47.0 s       0.0 s
[2016-04-15T00:35Z] INFO  17:35:56,119 ProgressMeter - Total runtime 47.32 secs, 0.79 min, 0.01 hours
[2016-04-15T00:35Z] INFO  17:35:56,120 MicroScheduler - 17512 reads were filtered out during the traversal out of approximately 232015 total reads (7.55%)
[2016-04-15T00:35Z] INFO  17:35:56,121 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:35Z] INFO  17:35:56,122 MicroScheduler -   -> 17130 reads (7.38% of total) failing DuplicateReadFilter
[2016-04-15T00:35Z] INFO  17:35:56,123 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:35Z] INFO  17:35:56,123 MicroScheduler -   -> 382 reads (0.16% of total) failing HCMappingQualityFilter
[2016-04-15T00:35Z] INFO  17:35:56,124 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:35Z] INFO  17:35:56,125 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:35Z] INFO  17:35:56,126 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:35Z] INFO  17:35:56,127 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:35Z] INFO  17:35:56,166 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T00:35Z] INFO  17:35:56,192 ProgressMeter -      3:38401899      2.4528907E7    30.0 s            1.0 s       31.5%    95.0 s      65.0 s
[2016-04-15T00:35Z] GATK: HaplotypeCaller
[2016-04-15T00:35Z] INFO  17:35:56,356 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.01852117
[2016-04-15T00:35Z] INFO  17:35:56,357 PairHMM - Total compute time in PairHMM computeLikelihoods() : 6.207122436000001
[2016-04-15T00:35Z] INFO  17:35:56,358 HaplotypeCaller - Ran local assembly on 1244 active regions
[2016-04-15T00:35Z] INFO  17:35:56,432 ProgressMeter -            done      6.7478645E7    62.0 s            0.0 s      100.0%    62.0 s       0.0 s
[2016-04-15T00:35Z] INFO  17:35:56,439 ProgressMeter - Total runtime 62.49 secs, 1.04 min, 0.02 hours
[2016-04-15T00:35Z] INFO  17:35:56,439 MicroScheduler - 59460 reads were filtered out during the traversal out of approximately 280637 total reads (21.19%)
[2016-04-15T00:35Z] INFO  17:35:56,440 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:35Z] INFO  17:35:56,440 MicroScheduler -   -> 18571 reads (6.62% of total) failing DuplicateReadFilter
[2016-04-15T00:35Z] INFO  17:35:56,440 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:35Z] INFO  17:35:56,441 MicroScheduler -   -> 40889 reads (14.57% of total) failing HCMappingQualityFilter
[2016-04-15T00:35Z] INFO  17:35:56,441 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:35Z] INFO  17:35:56,441 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:35Z] INFO  17:35:56,442 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:35Z] INFO  17:35:56,442 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:35Z] INFO  17:35:56,914 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:35Z] INFO  17:35:56,918 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:35Z] INFO  17:35:56,918 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:35Z] INFO  17:35:56,919 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:35Z] INFO  17:35:56,925 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/3/R14-18106_kapa-NGv3-PE100-NGv3-sort-3_127770401_143293035-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/3/R14-18106_kapa-NGv3-PE100-NGv3-3_127770401_143293035-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/3/tx/tmposiv11/R14-18106_kapa-NGv3-PE100-NGv3-3_127770401_143293035.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:35Z] INFO  17:35:56,960 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:35Z] INFO  17:35:56,961 HelpFormatter - Date/Time: 2016/04/14 17:35:56
[2016-04-15T00:35Z] INFO  17:35:56,962 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:35Z] INFO  17:35:56,962 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:35Z] WARN  17:35:56,990 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T00:35Z] WARN  17:35:56,994 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/3/tx/tmposiv11/R14-18106_kapa-NGv3-PE100-NGv3-3_127770401_143293035.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T00:35Z] INFO  17:35:57,280 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:35Z] INFO  17:35:57,495 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T00:35Z] INFO  17:35:57,509 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:35Z] INFO  17:35:57,604 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.09
[2016-04-15T00:35Z] INFO  17:35:57,618 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T00:35Z] INFO  17:35:57,674 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:35Z] INFO  17:35:57,716 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:35Z] INFO  17:35:57,915 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:35Z] GATK: HaplotypeCaller
[2016-04-15T00:35Z] GATK: HaplotypeCaller
[2016-04-15T00:35Z] INFO  17:35:57,975 ProgressMeter -      3:49148699      2.3522069E7    30.0 s            1.0 s       27.4%   109.0 s      79.0 s
[2016-04-15T00:35Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T00:35Z] INFO  17:35:58,048 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T00:35Z] INFO  17:35:58,049 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T00:35Z] INFO  17:35:58,106 IntervalUtils - Processing 238450 bp from intervals
[2016-04-15T00:35Z] WARN  17:35:58,118 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:35Z] INFO  17:35:58,254 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:35Z] GATK: HaplotypeCaller
[2016-04-15T00:35Z] WARN  17:35:58,352 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T00:35Z] WARN  17:35:58,353 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T00:35Z] INFO  17:35:58,383 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:35Z] INFO  17:35:58,384 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:35Z] INFO  17:35:58,385 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T00:35Z] INFO  17:35:58,386 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T00:35Z] INFO  17:35:58,386 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T00:35Z] INFO  17:35:58,387 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T00:35Z] INFO  17:35:58,667 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T00:35Z] INFO  17:35:59,043 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.010761929
[2016-04-15T00:35Z] INFO  17:35:59,044 PairHMM - Total compute time in PairHMM computeLikelihoods() : 0.6478265040000001
[2016-04-15T00:35Z] INFO  17:35:59,044 HaplotypeCaller - Ran local assembly on 1672 active regions
[2016-04-15T00:35Z] INFO  17:35:59,104 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:35Z] INFO  17:35:59,112 ProgressMeter -            done     1.20474354E8    58.0 s            0.0 s      100.0%    58.0 s       0.0 s
[2016-04-15T00:35Z] INFO  17:35:59,112 ProgressMeter - Total runtime 58.28 secs, 0.97 min, 0.02 hours
[2016-04-15T00:35Z] INFO  17:35:59,118 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:35Z] INFO  17:35:59,119 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:35Z] INFO  17:35:59,113 MicroScheduler - 30436 reads were filtered out during the traversal out of approximately 317350 total reads (9.59%)
[2016-04-15T00:35Z] INFO  17:35:59,113 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:35Z] INFO  17:35:59,114 MicroScheduler -   -> 23296 reads (7.34% of total) failing DuplicateReadFilter
[2016-04-15T00:35Z] INFO  17:35:59,114 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:35Z] INFO  17:35:59,114 MicroScheduler -   -> 7140 reads (2.25% of total) failing HCMappingQualityFilter
[2016-04-15T00:35Z] INFO  17:35:59,115 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:35Z] INFO  17:35:59,115 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:35Z] INFO  17:35:59,115 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:35Z] INFO  17:35:59,115 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:35Z] INFO  17:35:59,120 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:35Z] INFO  17:35:59,124 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/3/R14-18106_kapa-NGv3-PE100-NGv3-sort-3_143297426_158963696-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/3/R14-18106_kapa-NGv3-PE100-NGv3-3_143297426_158963696-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/3/tx/tmptIWtMb/R14-18106_kapa-NGv3-PE100-NGv3-3_143297426_158963696.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:35Z] INFO  17:35:59,144 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:35Z] INFO  17:35:59,144 HelpFormatter - Date/Time: 2016/04/14 17:35:59
[2016-04-15T00:35Z] INFO  17:35:59,144 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:35Z] INFO  17:35:59,145 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:35Z] WARN  17:35:59,175 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T00:35Z] WARN  17:35:59,178 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/3/tx/tmptIWtMb/R14-18106_kapa-NGv3-PE100-NGv3-3_143297426_158963696.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T00:35Z] INFO  17:35:59,391 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:35Z] INFO  17:35:59,542 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:35Z] INFO  17:35:59,546 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:35Z] INFO  17:35:59,547 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:35Z] INFO  17:35:59,547 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:35Z] INFO  17:35:59,552 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/3/R14-18106_kapa-NGv3-PE100-NGv3-sort-3_158970515_174577240-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/3/R14-18106_kapa-NGv3-PE100-NGv3-3_158970515_174577240-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/3/tx/tmpF32mfh/R14-18106_kapa-NGv3-PE100-NGv3-3_158970515_174577240.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:35Z] INFO  17:35:59,562 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:35Z] INFO  17:35:59,574 HelpFormatter - Date/Time: 2016/04/14 17:35:59
[2016-04-15T00:35Z] INFO  17:35:59,575 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:35Z] INFO  17:35:59,576 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:35Z] WARN  17:35:59,610 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T00:35Z] WARN  17:35:59,622 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/3/tx/tmpF32mfh/R14-18106_kapa-NGv3-PE100-NGv3-3_158970515_174577240.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T00:35Z] INFO  17:35:59,677 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T00:35Z] INFO  17:35:59,690 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:35Z] INFO  17:35:59,801 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.11
[2016-04-15T00:35Z] INFO  17:35:59,845 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T00:35Z] INFO  17:35:59,913 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:36Z] INFO  17:36:00,168 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T00:36Z] INFO  17:36:00,189 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:36Z] INFO  17:36:00,286 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.10
[2016-04-15T00:36Z] INFO  17:36:00,308 IntervalUtils - Processing 125161 bp from intervals
[2016-04-15T00:36Z] WARN  17:36:00,313 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:36Z] INFO  17:36:00,318 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T00:36Z] INFO  17:36:00,486 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:36Z] INFO  17:36:00,581 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:36Z] INFO  17:36:00,588 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:36Z] INFO  17:36:00,589 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:36Z] INFO  17:36:00,590 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T00:36Z] INFO  17:36:00,590 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T00:36Z] INFO  17:36:00,591 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T00:36Z] INFO  17:36:00,591 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T00:36Z] INFO  17:36:00,790 IntervalUtils - Processing 102254 bp from intervals
[2016-04-15T00:36Z] WARN  17:36:00,796 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:36Z] INFO  17:36:00,811 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T00:36Z] INFO  17:36:00,883 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:36Z] INFO  17:36:00,952 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:36Z] INFO  17:36:00,953 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:36Z] INFO  17:36:00,954 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T00:36Z] INFO  17:36:00,955 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T00:36Z] INFO  17:36:00,955 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T00:36Z] INFO  17:36:00,955 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T00:36Z] GATK: HaplotypeCaller
[2016-04-15T00:36Z] INFO  17:36:01,183 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:36Z] INFO  17:36:01,186 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:36Z] INFO  17:36:01,186 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:36Z] INFO  17:36:01,187 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:36Z] INFO  17:36:01,188 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T00:36Z] INFO  17:36:01,192 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/4/R14-18106_kapa-NGv3-PE100-NGv3-sort-4_0_15511864-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/4/R14-18106_kapa-NGv3-PE100-NGv3-4_0_15511864-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/4/tx/tmpZid3MY/R14-18106_kapa-NGv3-PE100-NGv3-4_0_15511864.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:36Z] INFO  17:36:01,209 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:36Z] INFO  17:36:01,210 HelpFormatter - Date/Time: 2016/04/14 17:36:01
[2016-04-15T00:36Z] INFO  17:36:01,210 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:36Z] INFO  17:36:01,211 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:36Z] WARN  17:36:01,257 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T00:36Z] WARN  17:36:01,260 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/4/tx/tmpZid3MY/R14-18106_kapa-NGv3-PE100-NGv3-4_0_15511864.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T00:36Z] INFO  17:36:01,277 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:36Z] INFO  17:36:01,280 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:36Z] INFO  17:36:01,280 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:36Z] INFO  17:36:01,281 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:36Z] INFO  17:36:01,286 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/3/R14-18106_kapa-NGv3-PE100-NGv3-sort-3_174814579_190326970-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/3/R14-18106_kapa-NGv3-PE100-NGv3-3_174814579_190326970-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/3/tx/tmpNDHlyA/R14-18106_kapa-NGv3-PE100-NGv3-3_174814579_190326970.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:36Z] INFO  17:36:01,296 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:36Z] INFO  17:36:01,299 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:36Z] INFO  17:36:01,300 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:36Z] INFO  17:36:01,300 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:36Z] INFO  17:36:01,305 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/3/R14-18106_kapa-NGv3-PE100-NGv3-sort-3_190333063_198022430-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/3/R14-18106_kapa-NGv3-PE100-NGv3-3_190333063_198022430-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/3/tx/tmpAKELfz/R14-18106_kapa-NGv3-PE100-NGv3-3_190333063_198022430.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:36Z] INFO  17:36:01,313 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:36Z] INFO  17:36:01,314 HelpFormatter - Date/Time: 2016/04/14 17:36:01
[2016-04-15T00:36Z] INFO  17:36:01,315 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:36Z] INFO  17:36:01,315 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:36Z] INFO  17:36:01,320 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:36Z] INFO  17:36:01,321 HelpFormatter - Date/Time: 2016/04/14 17:36:01
[2016-04-15T00:36Z] INFO  17:36:01,322 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:36Z] INFO  17:36:01,322 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:36Z] WARN  17:36:01,345 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T00:36Z] WARN  17:36:01,348 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/3/tx/tmpNDHlyA/R14-18106_kapa-NGv3-PE100-NGv3-3_174814579_190326970.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T00:36Z] WARN  17:36:01,348 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T00:36Z] WARN  17:36:01,351 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/3/tx/tmpAKELfz/R14-18106_kapa-NGv3-PE100-NGv3-3_190333063_198022430.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T00:36Z] INFO  17:36:01,446 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:36Z] INFO  17:36:01,544 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:36Z] INFO  17:36:01,601 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:36Z] INFO  17:36:01,744 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T00:36Z] INFO  17:36:01,746 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T00:36Z] INFO  17:36:01,756 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:36Z] INFO  17:36:01,766 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:36Z] INFO  17:36:01,799 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T00:36Z] INFO  17:36:01,808 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:36Z] INFO  17:36:01,837 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-15T00:36Z] INFO  17:36:01,857 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.09
[2016-04-15T00:36Z] INFO  17:36:01,861 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T00:36Z] INFO  17:36:01,886 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-15T00:36Z] INFO  17:36:01,888 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T00:36Z] INFO  17:36:01,923 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T00:36Z] INFO  17:36:02,024 ProgressMeter -      3:77089246      1.4142952E7    30.0 s            2.0 s       93.9%    31.0 s       1.0 s
[2016-04-15T00:36Z] INFO  17:36:02,286 IntervalUtils - Processing 184739 bp from intervals
[2016-04-15T00:36Z] WARN  17:36:02,302 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:36Z] INFO  17:36:02,380 IntervalUtils - Processing 255565 bp from intervals
[2016-04-15T00:36Z] WARN  17:36:02,385 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:36Z] INFO  17:36:02,442 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:36Z] INFO  17:36:02,455 IntervalUtils - Processing 118955 bp from intervals
[2016-04-15T00:36Z] WARN  17:36:02,461 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:36Z] INFO  17:36:02,497 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:36Z] INFO  17:36:02,583 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:36Z] INFO  17:36:02,584 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:36Z] INFO  17:36:02,585 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T00:36Z] INFO  17:36:02,585 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T00:36Z] INFO  17:36:02,586 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T00:36Z] INFO  17:36:02,586 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T00:36Z] INFO  17:36:02,603 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:36Z] INFO  17:36:02,635 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:36Z] INFO  17:36:02,636 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:36Z] INFO  17:36:02,637 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T00:36Z] INFO  17:36:02,638 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T00:36Z] INFO  17:36:02,647 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T00:36Z] INFO  17:36:02,648 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T00:36Z] INFO  17:36:02,705 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:36Z] INFO  17:36:02,706 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:36Z] INFO  17:36:02,707 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T00:36Z] INFO  17:36:02,707 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T00:36Z] INFO  17:36:02,733 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T00:36Z] INFO  17:36:02,734 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T00:36Z] INFO  17:36:02,835 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T00:36Z] INFO  17:36:02,965 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T00:36Z] INFO  17:36:03,035 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T00:36Z] INFO  17:36:03,367 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.008472949
[2016-04-15T00:36Z] INFO  17:36:03,368 PairHMM - Total compute time in PairHMM computeLikelihoods() : 0.738197553
[2016-04-15T00:36Z] INFO  17:36:03,379 HaplotypeCaller - Ran local assembly on 593 active regions
[2016-04-15T00:36Z] INFO  17:36:03,438 ProgressMeter -            done      1.6464959E7    31.0 s            1.0 s      100.0%    31.0 s       0.0 s
[2016-04-15T00:36Z] INFO  17:36:03,439 ProgressMeter - Total runtime 31.43 secs, 0.52 min, 0.01 hours
[2016-04-15T00:36Z] INFO  17:36:03,439 MicroScheduler - 11187 reads were filtered out during the traversal out of approximately 105375 total reads (10.62%)
[2016-04-15T00:36Z] INFO  17:36:03,439 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:36Z] INFO  17:36:03,440 MicroScheduler -   -> 7669 reads (7.28% of total) failing DuplicateReadFilter
[2016-04-15T00:36Z] INFO  17:36:03,440 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:36Z] INFO  17:36:03,440 MicroScheduler -   -> 3518 reads (3.34% of total) failing HCMappingQualityFilter
[2016-04-15T00:36Z] INFO  17:36:03,440 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:36Z] INFO  17:36:03,441 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:36Z] INFO  17:36:03,441 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:36Z] INFO  17:36:03,441 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:36Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T00:36Z] INFO  17:36:03,882 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T00:36Z] INFO  17:36:03,883 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T00:36Z] WARN  17:36:04,194 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T00:36Z] WARN  17:36:04,216 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T00:36Z] INFO  17:36:04,370 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:36Z] INFO  17:36:04,373 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:36Z] INFO  17:36:04,374 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:36Z] INFO  17:36:04,374 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:36Z] INFO  17:36:04,379 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/4/R14-18106_kapa-NGv3-PE100-NGv3-sort-4_15512869_31144471-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/4/R14-18106_kapa-NGv3-PE100-NGv3-4_15512869_31144471-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/4/tx/tmpaMzSY7/R14-18106_kapa-NGv3-PE100-NGv3-4_15512869_31144471.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:36Z] INFO  17:36:04,411 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:36Z] INFO  17:36:04,421 HelpFormatter - Date/Time: 2016/04/14 17:36:04
[2016-04-15T00:36Z] INFO  17:36:04,422 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:36Z] INFO  17:36:04,422 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:36Z] WARN  17:36:04,461 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T00:36Z] WARN  17:36:04,466 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/4/tx/tmpaMzSY7/R14-18106_kapa-NGv3-PE100-NGv3-4_15512869_31144471.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T00:36Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T00:36Z] INFO  17:36:04,493 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T00:36Z] INFO  17:36:04,494 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T00:36Z] INFO  17:36:04,747 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:36Z] WARN  17:36:04,816 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T00:36Z] WARN  17:36:04,843 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T00:36Z] INFO  17:36:04,968 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T00:36Z] INFO  17:36:04,978 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:36Z] INFO  17:36:05,051 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-15T00:36Z] INFO  17:36:05,081 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T00:36Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T00:36Z] INFO  17:36:05,160 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T00:36Z] INFO  17:36:05,174 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T00:36Z] INFO  17:36:05,241 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:36Z] WARN  17:36:05,514 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T00:36Z] WARN  17:36:05,525 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T00:36Z] GATK: HaplotypeCaller
[2016-04-15T00:36Z] INFO  17:36:05,653 IntervalUtils - Processing 90668 bp from intervals
[2016-04-15T00:36Z] WARN  17:36:05,659 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:36Z] INFO  17:36:05,811 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:36Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T00:36Z] INFO  17:36:05,891 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T00:36Z] INFO  17:36:05,903 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T00:36Z] INFO  17:36:05,928 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:36Z] INFO  17:36:05,940 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:36Z] INFO  17:36:05,941 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T00:36Z] INFO  17:36:05,942 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T00:36Z] INFO  17:36:05,943 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T00:36Z] INFO  17:36:05,943 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T00:36Z] INFO  17:36:06,185 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T00:36Z] WARN  17:36:06,222 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T00:36Z] WARN  17:36:06,223 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T00:36Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T00:36Z] INFO  17:36:06,642 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T00:36Z] INFO  17:36:06,650 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T00:36Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T00:36Z] INFO  17:36:06,896 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T00:36Z] INFO  17:36:06,897 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T00:36Z] WARN  17:36:07,240 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T00:36Z] WARN  17:36:07,241 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T00:36Z] WARN  17:36:07,728 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T00:36Z] WARN  17:36:07,729 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T00:36Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T00:36Z] INFO  17:36:08,329 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T00:36Z] INFO  17:36:08,341 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T00:36Z] WARN  17:36:08,781 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T00:36Z] WARN  17:36:08,783 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T00:36Z] INFO  17:36:09,259 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:36Z] INFO  17:36:09,273 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:36Z] INFO  17:36:09,274 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:36Z] INFO  17:36:09,275 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:36Z] INFO  17:36:09,280 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/4/R14-18106_kapa-NGv3-PE100-NGv3-sort-4_36069528_52709433-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/4/R14-18106_kapa-NGv3-PE100-NGv3-4_36069528_52709433-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/4/tx/tmpE86X3n/R14-18106_kapa-NGv3-PE100-NGv3-4_36069528_52709433.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:36Z] INFO  17:36:09,313 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:36Z] INFO  17:36:09,314 HelpFormatter - Date/Time: 2016/04/14 17:36:09
[2016-04-15T00:36Z] INFO  17:36:09,315 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:36Z] INFO  17:36:09,315 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:36Z] WARN  17:36:09,361 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T00:36Z] WARN  17:36:09,364 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/4/tx/tmpE86X3n/R14-18106_kapa-NGv3-PE100-NGv3-4_36069528_52709433.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T00:36Z] INFO  17:36:09,693 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:36Z] INFO  17:36:09,867 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T00:36Z] INFO  17:36:09,888 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:36Z] INFO  17:36:09,962 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-15T00:36Z] INFO  17:36:09,987 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T00:36Z] INFO  17:36:10,185 ProgressMeter -     2:220362566     1.21593008E8    60.0 s            0.0 s       90.9%    66.0 s       6.0 s
[2016-04-15T00:36Z] INFO  17:36:10,313 IntervalUtils - Processing 142047 bp from intervals
[2016-04-15T00:36Z] WARN  17:36:10,318 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:36Z] INFO  17:36:10,401 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:36Z] INFO  17:36:10,491 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:36Z] INFO  17:36:10,492 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:36Z] INFO  17:36:10,493 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T00:36Z] INFO  17:36:10,514 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T00:36Z] INFO  17:36:10,526 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T00:36Z] INFO  17:36:10,527 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T00:36Z] INFO  17:36:10,688 ProgressMeter -     3:108159994      2.7011906E7    30.0 s            1.0 s       70.8%    42.0 s      12.0 s
[2016-04-15T00:36Z] INFO  17:36:10,768 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T00:36Z] INFO  17:36:11,408 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.014473487
[2016-04-15T00:36Z] INFO  17:36:11,417 PairHMM - Total compute time in PairHMM computeLikelihoods() : 2.255949574
[2016-04-15T00:36Z] INFO  17:36:11,418 HaplotypeCaller - Ran local assembly on 1461 active regions
[2016-04-15T00:36Z] INFO  17:36:11,468 ProgressMeter -            done      9.2172487E7    57.0 s            0.0 s      100.0%    57.0 s       0.0 s
[2016-04-15T00:36Z] INFO  17:36:11,469 ProgressMeter - Total runtime 57.30 secs, 0.95 min, 0.02 hours
[2016-04-15T00:36Z] INFO  17:36:11,470 MicroScheduler - 24532 reads were filtered out during the traversal out of approximately 286388 total reads (8.57%)
[2016-04-15T00:36Z] INFO  17:36:11,471 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:36Z] INFO  17:36:11,471 MicroScheduler -   -> 21963 reads (7.67% of total) failing DuplicateReadFilter
[2016-04-15T00:36Z] INFO  17:36:11,472 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:36Z] INFO  17:36:11,472 MicroScheduler -   -> 2569 reads (0.90% of total) failing HCMappingQualityFilter
[2016-04-15T00:36Z] INFO  17:36:11,473 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:36Z] INFO  17:36:11,474 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:36Z] INFO  17:36:11,474 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:36Z] INFO  17:36:11,475 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:36Z] INFO  17:36:13,102 ProgressMeter -     1:156438050     3.35934946E8     2.5 m            0.0 s       80.1%     3.1 m      37.0 s
[2016-04-15T00:36Z] INFO  17:36:13,143 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:36Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T00:36Z] INFO  17:36:13,290 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T00:36Z] INFO  17:36:13,291 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T00:36Z] GATK: HaplotypeCaller
[2016-04-15T00:36Z] WARN  17:36:13,582 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T00:36Z] WARN  17:36:13,582 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T00:36Z] INFO  17:36:15,438 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.015959048
[2016-04-15T00:36Z] INFO  17:36:15,439 PairHMM - Total compute time in PairHMM computeLikelihoods() : 0.832432452
[2016-04-15T00:36Z] INFO  17:36:15,439 HaplotypeCaller - Ran local assembly on 1401 active regions
[2016-04-15T00:36Z] INFO  17:36:15,495 ProgressMeter -            done      9.3035935E7    57.0 s            0.0 s      100.0%    57.0 s       0.0 s
[2016-04-15T00:36Z] INFO  17:36:15,495 ProgressMeter - Total runtime 57.86 secs, 0.96 min, 0.02 hours
[2016-04-15T00:36Z] INFO  17:36:15,496 MicroScheduler - 22725 reads were filtered out during the traversal out of approximately 294583 total reads (7.71%)
[2016-04-15T00:36Z] INFO  17:36:15,496 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:36Z] INFO  17:36:15,496 MicroScheduler -   -> 22208 reads (7.54% of total) failing DuplicateReadFilter
[2016-04-15T00:36Z] INFO  17:36:15,496 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:36Z] INFO  17:36:15,497 MicroScheduler -   -> 517 reads (0.18% of total) failing HCMappingQualityFilter
[2016-04-15T00:36Z] INFO  17:36:15,497 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:36Z] INFO  17:36:15,497 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:36Z] INFO  17:36:15,497 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:36Z] INFO  17:36:15,498 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:36Z] INFO  17:36:17,032 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:36Z] INFO  17:36:17,036 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:36Z] INFO  17:36:17,036 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:36Z] INFO  17:36:17,037 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:36Z] INFO  17:36:17,042 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/4/R14-18106_kapa-NGv3-PE100-NGv3-sort-4_52709749_68338393-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/4/R14-18106_kapa-NGv3-PE100-NGv3-4_52709749_68338393-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/4/tx/tmpxkQ7cm/R14-18106_kapa-NGv3-PE100-NGv3-4_52709749_68338393.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:36Z] INFO  17:36:17,062 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:36Z] INFO  17:36:17,063 HelpFormatter - Date/Time: 2016/04/14 17:36:17
[2016-04-15T00:36Z] INFO  17:36:17,063 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:36Z] INFO  17:36:17,064 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:36Z] WARN  17:36:17,109 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T00:36Z] WARN  17:36:17,112 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/4/tx/tmpxkQ7cm/R14-18106_kapa-NGv3-PE100-NGv3-4_52709749_68338393.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T00:36Z] INFO  17:36:17,135 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:36Z] INFO  17:36:17,354 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:36Z] GATK: HaplotypeCaller
[2016-04-15T00:36Z] INFO  17:36:17,512 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T00:36Z] INFO  17:36:17,538 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:36Z] INFO  17:36:17,886 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.35
[2016-04-15T00:36Z] INFO  17:36:17,900 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T00:36Z] INFO  17:36:18,045 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.014998226000000002
[2016-04-15T00:36Z] INFO  17:36:18,046 PairHMM - Total compute time in PairHMM computeLikelihoods() : 0.8709801620000001
[2016-04-15T00:36Z] INFO  17:36:18,046 HaplotypeCaller - Ran local assembly on 1849 active regions
[2016-04-15T00:36Z] INFO  17:36:18,122 ProgressMeter -            done     1.39336955E8    67.0 s            0.0 s      100.0%    67.0 s       0.0 s
[2016-04-15T00:36Z] INFO  17:36:18,123 ProgressMeter - Total runtime 67.98 secs, 1.13 min, 0.02 hours
[2016-04-15T00:36Z] INFO  17:36:18,126 MicroScheduler - 28764 reads were filtered out during the traversal out of approximately 376043 total reads (7.65%)
[2016-04-15T00:36Z] INFO  17:36:18,133 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:36Z] INFO  17:36:18,134 MicroScheduler -   -> 28347 reads (7.54% of total) failing DuplicateReadFilter
[2016-04-15T00:36Z] INFO  17:36:18,134 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:36Z] INFO  17:36:18,134 MicroScheduler -   -> 417 reads (0.11% of total) failing HCMappingQualityFilter
[2016-04-15T00:36Z] INFO  17:36:18,134 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:36Z] INFO  17:36:18,134 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:36Z] INFO  17:36:18,135 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:36Z] INFO  17:36:18,135 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:36Z] INFO  17:36:18,340 IntervalUtils - Processing 83782 bp from intervals
[2016-04-15T00:36Z] WARN  17:36:18,346 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:36Z] INFO  17:36:18,503 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:36Z] INFO  17:36:18,602 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:36Z] INFO  17:36:18,603 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:36Z] INFO  17:36:18,614 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T00:36Z] INFO  17:36:18,615 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T00:36Z] INFO  17:36:18,626 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T00:36Z] INFO  17:36:18,627 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T00:36Z] INFO  17:36:18,852 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T00:36Z] INFO  17:36:19,463 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:36Z] GATK: HaplotypeCaller
[2016-04-15T00:36Z] INFO  17:36:19,977 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.010214029000000001
[2016-04-15T00:36Z] INFO  17:36:19,978 PairHMM - Total compute time in PairHMM computeLikelihoods() : 0.437274351
[2016-04-15T00:36Z] INFO  17:36:19,979 HaplotypeCaller - Ran local assembly on 1062 active regions
[2016-04-15T00:36Z] INFO  17:36:20,037 ProgressMeter -            done      5.7451533E7    39.0 s            0.0 s      100.0%    39.0 s       0.0 s
[2016-04-15T00:36Z] INFO  17:36:20,037 ProgressMeter - Total runtime 39.39 secs, 0.66 min, 0.01 hours
[2016-04-15T00:36Z] INFO  17:36:20,038 MicroScheduler - 12308 reads were filtered out during the traversal out of approximately 157259 total reads (7.83%)
[2016-04-15T00:36Z] INFO  17:36:20,038 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:36Z] INFO  17:36:20,038 MicroScheduler -   -> 11475 reads (7.30% of total) failing DuplicateReadFilter
[2016-04-15T00:36Z] INFO  17:36:20,038 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:36Z] INFO  17:36:20,039 MicroScheduler -   -> 833 reads (0.53% of total) failing HCMappingQualityFilter
[2016-04-15T00:36Z] INFO  17:36:20,039 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:36Z] INFO  17:36:20,039 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:36Z] INFO  17:36:20,039 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:36Z] INFO  17:36:20,040 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:36Z] INFO  17:36:20,265 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:36Z] INFO  17:36:20,267 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:36Z] INFO  17:36:20,268 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:36Z] INFO  17:36:20,268 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:36Z] INFO  17:36:20,272 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/4/R14-18106_kapa-NGv3-PE100-NGv3-sort-4_68340604_83852298-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/4/R14-18106_kapa-NGv3-PE100-NGv3-4_68340604_83852298-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/4/tx/tmphsMJ_i/R14-18106_kapa-NGv3-PE100-NGv3-4_68340604_83852298.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:36Z] INFO  17:36:20,299 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:36Z] INFO  17:36:20,299 HelpFormatter - Date/Time: 2016/04/14 17:36:20
[2016-04-15T00:36Z] INFO  17:36:20,299 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:36Z] INFO  17:36:20,300 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:36Z] WARN  17:36:20,386 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T00:36Z] WARN  17:36:20,388 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/4/tx/tmphsMJ_i/R14-18106_kapa-NGv3-PE100-NGv3-4_68340604_83852298.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T00:36Z] INFO  17:36:20,607 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:36Z] INFO  17:36:20,867 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T00:36Z] INFO  17:36:20,877 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:36Z] INFO  17:36:20,968 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.09
[2016-04-15T00:36Z] INFO  17:36:20,995 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T00:36Z] INFO  17:36:21,542 IntervalUtils - Processing 197466 bp from intervals
[2016-04-15T00:36Z] WARN  17:36:21,548 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:36Z] INFO  17:36:21,619 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:36Z] INFO  17:36:21,644 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:36Z] INFO  17:36:21,729 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:36Z] INFO  17:36:21,729 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:36Z] INFO  17:36:21,730 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T00:36Z] INFO  17:36:21,730 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T00:36Z] INFO  17:36:21,738 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T00:36Z] INFO  17:36:21,739 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T00:36Z] GATK: HaplotypeCaller
[2016-04-15T00:36Z] INFO  17:36:21,997 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T00:36Z] INFO  17:36:22,684 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:36Z] INFO  17:36:22,688 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:36Z] INFO  17:36:22,688 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:36Z] INFO  17:36:22,689 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:36Z] INFO  17:36:22,693 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/4/R14-18106_kapa-NGv3-PE100-NGv3-sort-4_83857133_99393738-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/4/R14-18106_kapa-NGv3-PE100-NGv3-4_83857133_99393738-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/4/tx/tmpLvFilq/R14-18106_kapa-NGv3-PE100-NGv3-4_83857133_99393738.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:36Z] INFO  17:36:22,725 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:36Z] INFO  17:36:22,726 HelpFormatter - Date/Time: 2016/04/14 17:36:22
[2016-04-15T00:36Z] INFO  17:36:22,726 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:36Z] INFO  17:36:22,727 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:36Z] WARN  17:36:22,785 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T00:36Z] WARN  17:36:22,788 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/4/tx/tmpLvFilq/R14-18106_kapa-NGv3-PE100-NGv3-4_83857133_99393738.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T00:36Z] INFO  17:36:23,054 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:36Z] INFO  17:36:23,290 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T00:36Z] INFO  17:36:23,299 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:36Z] INFO  17:36:23,385 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-15T00:36Z] INFO  17:36:23,423 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T00:36Z] INFO  17:36:23,838 IntervalUtils - Processing 124091 bp from intervals
[2016-04-15T00:36Z] WARN  17:36:23,843 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:36Z] INFO  17:36:23,931 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:36Z] INFO  17:36:24,050 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:36Z] INFO  17:36:24,051 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:36Z] INFO  17:36:24,052 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T00:36Z] INFO  17:36:24,053 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T00:36Z] INFO  17:36:24,065 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T00:36Z] INFO  17:36:24,066 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T00:36Z] INFO  17:36:24,334 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T00:36Z] INFO  17:36:24,975 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:36Z] INFO  17:36:24,978 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:36Z] INFO  17:36:24,979 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:36Z] INFO  17:36:24,979 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:36Z] INFO  17:36:24,988 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/4/R14-18106_kapa-NGv3-PE100-NGv3-sort-4_99397339_115544957-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/4/R14-18106_kapa-NGv3-PE100-NGv3-4_99397339_115544957-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/4/tx/tmpbz4O16/R14-18106_kapa-NGv3-PE100-NGv3-4_99397339_115544957.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:36Z] INFO  17:36:24,997 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:36Z] INFO  17:36:24,998 HelpFormatter - Date/Time: 2016/04/14 17:36:24
[2016-04-15T00:36Z] INFO  17:36:24,999 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:36Z] INFO  17:36:24,999 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:36Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T00:36Z] INFO  17:36:25,021 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T00:36Z] WARN  17:36:25,022 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T00:36Z] WARN  17:36:25,025 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/4/tx/tmpbz4O16/R14-18106_kapa-NGv3-PE100-NGv3-4_99397339_115544957.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T00:36Z] INFO  17:36:25,032 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T00:36Z] INFO  17:36:25,238 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:36Z] WARN  17:36:25,318 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T00:36Z] WARN  17:36:25,319 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T00:36Z] INFO  17:36:25,500 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T00:36Z] INFO  17:36:25,521 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:36Z] INFO  17:36:25,588 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-15T00:36Z] INFO  17:36:25,609 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T00:36Z] INFO  17:36:25,862 ProgressMeter -     3:120489575       1.993094E7    30.0 s            1.0 s       35.9%    83.0 s      53.0 s
[2016-04-15T00:36Z] INFO  17:36:26,046 IntervalUtils - Processing 153852 bp from intervals
[2016-04-15T00:36Z] WARN  17:36:26,051 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:36Z] INFO  17:36:26,189 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:36Z] INFO  17:36:26,193 ProgressMeter -      3:44952450     1.11263041E8    60.0 s            0.0 s       78.7%    76.0 s      16.0 s
[2016-04-15T00:36Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T00:36Z] INFO  17:36:26,270 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T00:36Z] INFO  17:36:26,273 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T00:36Z] INFO  17:36:26,290 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:36Z] INFO  17:36:26,291 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:36Z] INFO  17:36:26,292 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T00:36Z] INFO  17:36:26,293 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T00:36Z] INFO  17:36:26,305 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T00:36Z] INFO  17:36:26,306 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T00:36Z] INFO  17:36:26,485 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T00:36Z] WARN  17:36:26,529 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T00:36Z] WARN  17:36:26,531 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T00:36Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T00:36Z] INFO  17:36:27,471 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T00:36Z] INFO  17:36:27,471 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T00:36Z] WARN  17:36:27,688 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T00:36Z] WARN  17:36:27,689 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T00:36Z] INFO  17:36:27,980 ProgressMeter -      3:52257435     1.25896784E8    60.0 s            0.0 s       60.5%    99.0 s      39.0 s
[2016-04-15T00:36Z] INFO  17:36:28,407 ProgressMeter -     3:132440832      2.6357917E7    30.0 s            1.0 s       40.7%    73.0 s      43.0 s
[2016-04-15T00:36Z] INFO  17:36:30,612 ProgressMeter -     3:154859898      1.4603014E7    30.0 s            2.0 s       67.4%    44.0 s      14.0 s
[2016-04-15T00:36Z] INFO  17:36:30,969 ProgressMeter -     3:172365904      2.3816702E7    30.0 s            1.0 s       92.2%    32.0 s       2.0 s
[2016-04-15T00:36Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T00:36Z] INFO  17:36:31,503 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T00:36Z] INFO  17:36:31,504 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T00:36Z] WARN  17:36:32,033 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T00:36Z] WARN  17:36:32,034 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T00:36Z] INFO  17:36:32,609 ProgressMeter -     3:183994680      2.0055298E7    30.0 s            1.0 s       50.5%    59.0 s      29.0 s
[2016-04-15T00:36Z] INFO  17:36:32,660 ProgressMeter -       4:1659135        5604554.0    30.0 s            5.0 s       22.5%     2.2 m     103.0 s
[2016-04-15T00:36Z] INFO  17:36:32,736 ProgressMeter -     3:195506102        7445396.0    30.0 s            4.0 s       45.9%    65.0 s      35.0 s
[2016-04-15T00:36Z] INFO  17:36:33,434 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.005388734
[2016-04-15T00:36Z] INFO  17:36:33,435 PairHMM - Total compute time in PairHMM computeLikelihoods() : 0.14083668800000002
[2016-04-15T00:36Z] INFO  17:36:33,435 HaplotypeCaller - Ran local assembly on 735 active regions
[2016-04-15T00:36Z] INFO  17:36:33,488 ProgressMeter -            done      2.7921091E7    32.0 s            1.0 s      100.0%    32.0 s       0.0 s
[2016-04-15T00:36Z] INFO  17:36:33,488 ProgressMeter - Total runtime 32.53 secs, 0.54 min, 0.01 hours
[2016-04-15T00:36Z] INFO  17:36:33,488 MicroScheduler - 8770 reads were filtered out during the traversal out of approximately 117799 total reads (7.44%)
[2016-04-15T00:36Z] INFO  17:36:33,489 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:36Z] INFO  17:36:33,489 MicroScheduler -   -> 8659 reads (7.35% of total) failing DuplicateReadFilter
[2016-04-15T00:36Z] INFO  17:36:33,489 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:36Z] INFO  17:36:33,489 MicroScheduler -   -> 111 reads (0.09% of total) failing HCMappingQualityFilter
[2016-04-15T00:36Z] INFO  17:36:33,490 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:36Z] INFO  17:36:33,490 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:36Z] INFO  17:36:33,490 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:36Z] INFO  17:36:33,490 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:36Z] INFO  17:36:34,469 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.064199215
[2016-04-15T00:36Z] INFO  17:36:34,470 PairHMM - Total compute time in PairHMM computeLikelihoods() : 27.410127723000002
[2016-04-15T00:36Z] INFO  17:36:34,470 HaplotypeCaller - Ran local assembly on 3738 active regions
[2016-04-15T00:36Z] INFO  17:36:34,524 ProgressMeter -            done     5.34487573E8     2.9 m            0.0 s      100.0%     2.9 m       0.0 s
[2016-04-15T00:36Z] INFO  17:36:34,524 ProgressMeter - Total runtime 171.47 secs, 2.86 min, 0.05 hours
[2016-04-15T00:36Z] INFO  17:36:34,524 MicroScheduler - 146609 reads were filtered out during the traversal out of approximately 903848 total reads (16.22%)
[2016-04-15T00:36Z] INFO  17:36:34,525 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:36Z] INFO  17:36:34,525 MicroScheduler -   -> 63204 reads (6.99% of total) failing DuplicateReadFilter
[2016-04-15T00:36Z] INFO  17:36:34,525 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:36Z] INFO  17:36:34,526 MicroScheduler -   -> 83405 reads (9.23% of total) failing HCMappingQualityFilter
[2016-04-15T00:36Z] INFO  17:36:34,526 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:36Z] INFO  17:36:34,526 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:36Z] INFO  17:36:34,526 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:36Z] INFO  17:36:34,527 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:36Z] INFO  17:36:34,940 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:36Z] GATK: HaplotypeCaller
[2016-04-15T00:36Z] INFO  17:36:35,970 ProgressMeter -      4:27024618      2.0305729E7    30.0 s            1.0 s       94.4%    31.0 s       1.0 s
[2016-04-15T00:36Z] INFO  17:36:36,071 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:36Z] GATK: HaplotypeCaller
[2016-04-15T00:36Z] INFO  17:36:36,671 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.0059096190000000005
[2016-04-15T00:36Z] INFO  17:36:36,672 PairHMM - Total compute time in PairHMM computeLikelihoods() : 0.292127884
[2016-04-15T00:36Z] INFO  17:36:36,673 HaplotypeCaller - Ran local assembly on 679 active regions
[2016-04-15T00:36Z] INFO  17:36:36,727 ProgressMeter -            done      2.0932049E7    30.0 s            1.0 s      100.0%    30.0 s       0.0 s
[2016-04-15T00:36Z] INFO  17:36:36,727 ProgressMeter - Total runtime 30.79 secs, 0.51 min, 0.01 hours
[2016-04-15T00:36Z] INFO  17:36:36,729 MicroScheduler - 8176 reads were filtered out during the traversal out of approximately 107518 total reads (7.60%)
[2016-04-15T00:36Z] INFO  17:36:36,729 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:36Z] INFO  17:36:36,729 MicroScheduler -   -> 8053 reads (7.49% of total) failing DuplicateReadFilter
[2016-04-15T00:36Z] INFO  17:36:36,729 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:36Z] INFO  17:36:36,730 MicroScheduler -   -> 123 reads (0.11% of total) failing HCMappingQualityFilter
[2016-04-15T00:36Z] INFO  17:36:36,730 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:36Z] INFO  17:36:36,730 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:36Z] INFO  17:36:36,730 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:36Z] INFO  17:36:36,731 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:36Z] INFO  17:36:38,167 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:36Z] INFO  17:36:38,268 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:36Z] INFO  17:36:38,270 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:36Z] INFO  17:36:38,270 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:36Z] INFO  17:36:38,270 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:36Z] INFO  17:36:38,285 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/4/R14-18106_kapa-NGv3-PE100-NGv3-sort-4_115584857_134074404-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/4/R14-18106_kapa-NGv3-PE100-NGv3-4_115584857_134074404-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/4/tx/tmpNr6fnH/R14-18106_kapa-NGv3-PE100-NGv3-4_115584857_134074404.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:36Z] INFO  17:36:38,303 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:36Z] INFO  17:36:38,303 HelpFormatter - Date/Time: 2016/04/14 17:36:38
[2016-04-15T00:36Z] INFO  17:36:38,303 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:36Z] INFO  17:36:38,304 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:36Z] WARN  17:36:38,348 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T00:36Z] WARN  17:36:38,350 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/4/tx/tmpNr6fnH/R14-18106_kapa-NGv3-PE100-NGv3-4_115584857_134074404.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T00:36Z] GATK: HaplotypeCaller
[2016-04-15T00:36Z] INFO  17:36:38,554 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:36Z] INFO  17:36:38,764 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T00:36Z] INFO  17:36:38,773 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:36Z] INFO  17:36:38,856 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-15T00:36Z] INFO  17:36:38,882 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T00:36Z] INFO  17:36:39,053 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.019434474
[2016-04-15T00:36Z] INFO  17:36:39,043 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.022682459000000002
[2016-04-15T00:36Z] INFO  17:36:39,054 PairHMM - Total compute time in PairHMM computeLikelihoods() : 0.40776982500000003
[2016-04-15T00:36Z] INFO  17:36:39,054 HaplotypeCaller - Ran local assembly on 892 active regions
[2016-04-15T00:36Z] INFO  17:36:39,066 PairHMM - Total compute time in PairHMM computeLikelihoods() : 1.542715673
[2016-04-15T00:36Z] INFO  17:36:39,068 HaplotypeCaller - Ran local assembly on 2114 active regions
[2016-04-15T00:36Z] INFO  17:36:39,108 ProgressMeter -            done     1.83827552E8    72.0 s            0.0 s      100.0%    72.0 s       0.0 s
[2016-04-15T00:36Z] INFO  17:36:39,108 ProgressMeter - Total runtime 72.95 secs, 1.22 min, 0.02 hours
[2016-04-15T00:36Z] INFO  17:36:39,109 MicroScheduler - 34045 reads were filtered out during the traversal out of approximately 438274 total reads (7.77%)
[2016-04-15T00:36Z] INFO  17:36:39,110 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:36Z] INFO  17:36:39,110 MicroScheduler -   -> 32911 reads (7.51% of total) failing DuplicateReadFilter
[2016-04-15T00:36Z] INFO  17:36:39,110 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:36Z] INFO  17:36:39,110 MicroScheduler -   -> 1134 reads (0.26% of total) failing HCMappingQualityFilter
[2016-04-15T00:36Z] INFO  17:36:39,111 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:36Z] INFO  17:36:39,111 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:36Z] INFO  17:36:39,111 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:36Z] INFO  17:36:39,111 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:36Z] INFO  17:36:39,138 ProgressMeter -            done      3.5894583E7    38.0 s            1.0 s      100.0%    38.0 s       0.0 s
[2016-04-15T00:36Z] INFO  17:36:39,139 ProgressMeter - Total runtime 38.55 secs, 0.64 min, 0.01 hours
[2016-04-15T00:36Z] INFO  17:36:39,139 MicroScheduler - 11409 reads were filtered out during the traversal out of approximately 146082 total reads (7.81%)
[2016-04-15T00:36Z] INFO  17:36:39,139 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:36Z] INFO  17:36:39,140 MicroScheduler -   -> 10709 reads (7.33% of total) failing DuplicateReadFilter
[2016-04-15T00:36Z] INFO  17:36:39,140 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:36Z] INFO  17:36:39,140 MicroScheduler -   -> 700 reads (0.48% of total) failing HCMappingQualityFilter
[2016-04-15T00:36Z] INFO  17:36:39,140 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:36Z] INFO  17:36:39,141 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:36Z] INFO  17:36:39,141 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:36Z] INFO  17:36:39,141 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:36Z] INFO  17:36:39,275 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:36Z] INFO  17:36:39,278 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:36Z] INFO  17:36:39,279 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:36Z] INFO  17:36:39,279 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:36Z] INFO  17:36:39,284 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/4/R14-18106_kapa-NGv3-PE100-NGv3-sort-4_134075461_150351181-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/4/R14-18106_kapa-NGv3-PE100-NGv3-4_134075461_150351181-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/4/tx/tmplTrWVz/R14-18106_kapa-NGv3-PE100-NGv3-4_134075461_150351181.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:36Z] INFO  17:36:39,301 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:36Z] INFO  17:36:39,312 HelpFormatter - Date/Time: 2016/04/14 17:36:39
[2016-04-15T00:36Z] INFO  17:36:39,313 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:36Z] INFO  17:36:39,314 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:36Z] INFO  17:36:39,326 IntervalUtils - Processing 157938 bp from intervals
[2016-04-15T00:36Z] WARN  17:36:39,331 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:36Z] WARN  17:36:39,343 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T00:36Z] WARN  17:36:39,352 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/4/tx/tmplTrWVz/R14-18106_kapa-NGv3-PE100-NGv3-4_134075461_150351181.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T00:36Z] INFO  17:36:39,473 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:36Z] INFO  17:36:39,577 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:36Z] INFO  17:36:39,578 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:36Z] INFO  17:36:39,578 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T00:36Z] INFO  17:36:39,578 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T00:36Z] INFO  17:36:39,584 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T00:36Z] INFO  17:36:39,584 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T00:36Z] INFO  17:36:39,607 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:36Z] INFO  17:36:39,766 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T00:36Z] INFO  17:36:39,838 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T00:36Z] INFO  17:36:39,848 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:36Z] INFO  17:36:39,943 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-15T00:36Z] INFO  17:36:39,966 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T00:36Z] INFO  17:36:40,249 IntervalUtils - Processing 86890 bp from intervals
[2016-04-15T00:36Z] WARN  17:36:40,255 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:36Z] INFO  17:36:40,363 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:36Z] INFO  17:36:40,446 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:36Z] INFO  17:36:40,485 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:36Z] INFO  17:36:40,486 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:36Z] INFO  17:36:40,487 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T00:36Z] INFO  17:36:40,487 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T00:36Z] INFO  17:36:40,488 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T00:36Z] INFO  17:36:40,488 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T00:36Z] INFO  17:36:40,536 ProgressMeter -      4:44450540      2.1882364E7    30.0 s            1.0 s       64.1%    46.0 s      16.0 s
[2016-04-15T00:36Z] INFO  17:36:40,666 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:36Z] INFO  17:36:40,726 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T00:36Z] GATK: HaplotypeCaller
[2016-04-15T00:36Z] GATK: HaplotypeCaller
[2016-04-15T00:36Z] INFO  17:36:41,362 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:36Z] INFO  17:36:41,365 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:36Z] INFO  17:36:41,365 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:36Z] INFO  17:36:41,365 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:36Z] INFO  17:36:41,386 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/4/R14-18106_kapa-NGv3-PE100-NGv3-sort-4_150354547_165878648-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/4/R14-18106_kapa-NGv3-PE100-NGv3-4_150354547_165878648-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/4/tx/tmpwI5B9B/R14-18106_kapa-NGv3-PE100-NGv3-4_150354547_165878648.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:36Z] INFO  17:36:41,402 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:36Z] INFO  17:36:41,402 HelpFormatter - Date/Time: 2016/04/14 17:36:41
[2016-04-15T00:36Z] INFO  17:36:41,403 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:36Z] INFO  17:36:41,403 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:36Z] WARN  17:36:41,452 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T00:36Z] WARN  17:36:41,469 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/4/tx/tmpwI5B9B/R14-18106_kapa-NGv3-PE100-NGv3-4_150354547_165878648.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T00:36Z] INFO  17:36:41,730 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:36Z] INFO  17:36:41,944 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T00:36Z] INFO  17:36:41,954 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:36Z] INFO  17:36:42,024 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-15T00:36Z] INFO  17:36:42,060 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T00:36Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T00:36Z] INFO  17:36:42,141 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T00:36Z] INFO  17:36:42,142 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T00:36Z] WARN  17:36:42,389 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T00:36Z] WARN  17:36:42,391 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T00:36Z] INFO  17:36:42,393 IntervalUtils - Processing 119752 bp from intervals
[2016-04-15T00:36Z] WARN  17:36:42,398 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:36Z] INFO  17:36:42,553 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:36Z] INFO  17:36:42,674 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:36Z] INFO  17:36:42,675 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:36Z] INFO  17:36:42,676 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T00:36Z] INFO  17:36:42,682 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T00:36Z] INFO  17:36:42,691 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T00:36Z] INFO  17:36:42,692 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T00:36Z] INFO  17:36:42,928 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T00:36Z] INFO  17:36:44,019 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:36Z] INFO  17:36:44,021 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:36Z] INFO  17:36:44,021 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:36Z] INFO  17:36:44,022 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:36Z] INFO  17:36:44,026 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/4/R14-18106_kapa-NGv3-PE100-NGv3-sort-4_165889318_183245405-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/4/R14-18106_kapa-NGv3-PE100-NGv3-4_165889318_183245405-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/4/tx/tmpe1L6wj/R14-18106_kapa-NGv3-PE100-NGv3-4_165889318_183245405.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:36Z] INFO  17:36:44,064 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:36Z] INFO  17:36:44,072 HelpFormatter - Date/Time: 2016/04/14 17:36:44
[2016-04-15T00:36Z] INFO  17:36:44,078 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:36Z] INFO  17:36:44,079 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:36Z] INFO  17:36:44,103 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:36Z] INFO  17:36:44,106 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:36Z] INFO  17:36:44,107 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:36Z] INFO  17:36:44,107 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:36Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T00:36Z] INFO  17:36:44,117 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/4/R14-18106_kapa-NGv3-PE100-NGv3-sort-4_183267803_191154276-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/4/R14-18106_kapa-NGv3-PE100-NGv3-4_183267803_191154276-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/4/tx/tmpXSukzr/R14-18106_kapa-NGv3-PE100-NGv3-4_183267803_191154276.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:36Z] INFO  17:36:44,120 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T00:36Z] INFO  17:36:44,121 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T00:36Z] WARN  17:36:44,123 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T00:36Z] WARN  17:36:44,126 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/4/tx/tmpe1L6wj/R14-18106_kapa-NGv3-PE100-NGv3-4_165889318_183245405.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T00:36Z] INFO  17:36:44,129 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:36Z] INFO  17:36:44,141 HelpFormatter - Date/Time: 2016/04/14 17:36:44
[2016-04-15T00:36Z] INFO  17:36:44,142 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:36Z] INFO  17:36:44,143 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:36Z] WARN  17:36:44,183 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T00:36Z] WARN  17:36:44,186 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/4/tx/tmpXSukzr/R14-18106_kapa-NGv3-PE100-NGv3-4_183267803_191154276.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T00:36Z] INFO  17:36:44,403 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:36Z] WARN  17:36:44,438 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T00:36Z] WARN  17:36:44,439 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T00:36Z] INFO  17:36:44,459 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:36Z] INFO  17:36:44,633 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T00:36Z] INFO  17:36:44,658 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:36Z] INFO  17:36:44,694 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T00:36Z] INFO  17:36:44,703 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:36Z] INFO  17:36:44,737 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-15T00:36Z] INFO  17:36:44,766 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T00:36Z] INFO  17:36:44,808 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.10
[2016-04-15T00:36Z] INFO  17:36:44,823 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T00:36Z] INFO  17:36:45,103 IntervalUtils - Processing 78538 bp from intervals
[2016-04-15T00:36Z] WARN  17:36:45,107 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:36Z] INFO  17:36:45,231 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:36Z] INFO  17:36:45,305 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:36Z] INFO  17:36:45,306 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:36Z] INFO  17:36:45,307 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T00:36Z] INFO  17:36:45,308 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T00:36Z] INFO  17:36:45,308 IntervalUtils - Processing 99602 bp from intervals
[2016-04-15T00:36Z] INFO  17:36:45,308 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T00:36Z] INFO  17:36:45,309 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T00:36Z] WARN  17:36:45,324 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:36Z] INFO  17:36:45,433 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:36Z] INFO  17:36:45,476 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T00:36Z] INFO  17:36:45,536 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:36Z] INFO  17:36:45,537 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:36Z] INFO  17:36:45,546 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T00:36Z] INFO  17:36:45,548 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T00:36Z] INFO  17:36:45,561 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T00:36Z] INFO  17:36:45,562 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T00:36Z] INFO  17:36:45,708 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T00:36Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T00:36Z] INFO  17:36:46,283 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T00:36Z] INFO  17:36:46,283 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T00:36Z] WARN  17:36:46,605 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T00:36Z] WARN  17:36:46,606 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T00:36Z] INFO  17:36:48,640 ProgressMeter -      4:66217107      1.6859409E7    30.0 s            1.0 s       96.9%    30.0 s       0.0 s
[2016-04-15T00:36Z] INFO  17:36:49,816 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.0060434320000000005
[2016-04-15T00:36Z] INFO  17:36:49,816 PairHMM - Total compute time in PairHMM computeLikelihoods() : 0.6637569480000001
[2016-04-15T00:36Z] INFO  17:36:49,817 HaplotypeCaller - Ran local assembly on 639 active regions
[2016-04-15T00:36Z] INFO  17:36:49,882 ProgressMeter -            done      1.8095278E7    31.0 s            1.0 s      100.0%    31.0 s       0.0 s
[2016-04-15T00:36Z] INFO  17:36:49,882 ProgressMeter - Total runtime 31.28 secs, 0.52 min, 0.01 hours
[2016-04-15T00:36Z] INFO  17:36:49,882 MicroScheduler - 7336 reads were filtered out during the traversal out of approximately 100716 total reads (7.28%)
[2016-04-15T00:36Z] INFO  17:36:49,883 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:36Z] INFO  17:36:49,883 MicroScheduler -   -> 7201 reads (7.15% of total) failing DuplicateReadFilter
[2016-04-15T00:36Z] INFO  17:36:49,883 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:36Z] INFO  17:36:49,883 MicroScheduler -   -> 135 reads (0.13% of total) failing HCMappingQualityFilter
[2016-04-15T00:36Z] INFO  17:36:49,884 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:36Z] INFO  17:36:49,884 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:36Z] INFO  17:36:49,884 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:36Z] INFO  17:36:49,884 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:36Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T00:36Z] INFO  17:36:49,954 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T00:36Z] INFO  17:36:49,966 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T00:36Z] INFO  17:36:50,033 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.008241121
[2016-04-15T00:36Z] INFO  17:36:50,034 PairHMM - Total compute time in PairHMM computeLikelihoods() : 0.304620488
[2016-04-15T00:36Z] INFO  17:36:50,045 HaplotypeCaller - Ran local assembly on 1044 active regions
[2016-04-15T00:36Z] INFO  17:36:50,087 ProgressMeter -            done      5.6156843E7    39.0 s            0.0 s      100.0%    39.0 s       0.0 s
[2016-04-15T00:36Z] INFO  17:36:50,087 ProgressMeter - Total runtime 39.60 secs, 0.66 min, 0.01 hours
[2016-04-15T00:36Z] INFO  17:36:50,088 MicroScheduler - 12692 reads were filtered out during the traversal out of approximately 167125 total reads (7.59%)
[2016-04-15T00:36Z] INFO  17:36:50,088 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:36Z] INFO  17:36:50,088 MicroScheduler -   -> 12261 reads (7.34% of total) failing DuplicateReadFilter
[2016-04-15T00:36Z] INFO  17:36:50,088 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:36Z] INFO  17:36:50,089 MicroScheduler -   -> 431 reads (0.26% of total) failing HCMappingQualityFilter
[2016-04-15T00:36Z] INFO  17:36:50,089 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:36Z] INFO  17:36:50,089 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:36Z] INFO  17:36:50,089 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:36Z] INFO  17:36:50,090 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:36Z] WARN  17:36:50,290 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T00:36Z] WARN  17:36:50,291 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T00:36Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T00:36Z] INFO  17:36:50,780 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T00:36Z] INFO  17:36:50,781 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T00:36Z] WARN  17:36:51,080 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T00:36Z] WARN  17:36:51,081 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T00:36Z] INFO  17:36:51,556 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:36Z] INFO  17:36:51,581 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:36Z] INFO  17:36:51,746 ProgressMeter -      4:76587233      3.0867007E7    30.0 s            0.0 s       53.5%    56.0 s      26.0 s
[2016-04-15T00:36Z] GATK: HaplotypeCaller
[2016-04-15T00:36Z] GATK: HaplotypeCaller
[2016-04-15T00:36Z] INFO  17:36:54,080 ProgressMeter -      4:88536815        8706540.0    30.0 s            3.0 s       46.6%    64.0 s      34.0 s
[2016-04-15T00:36Z] INFO  17:36:55,026 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:36Z] INFO  17:36:55,040 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:36Z] INFO  17:36:55,041 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:36Z] INFO  17:36:55,042 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:36Z] INFO  17:36:55,046 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/5/R14-18106_kapa-NGv3-PE100-NGv3-sort-5_0_15580921-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/5/R14-18106_kapa-NGv3-PE100-NGv3-5_0_15580921-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/5/tx/tmphywA9x/R14-18106_kapa-NGv3-PE100-NGv3-5_0_15580921.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:36Z] INFO  17:36:55,062 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:36Z] INFO  17:36:55,062 HelpFormatter - Date/Time: 2016/04/14 17:36:55
[2016-04-15T00:36Z] INFO  17:36:55,062 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:36Z] INFO  17:36:55,063 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:36Z] WARN  17:36:55,100 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T00:36Z] WARN  17:36:55,103 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/5/tx/tmphywA9x/R14-18106_kapa-NGv3-PE100-NGv3-5_0_15580921.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T00:36Z] INFO  17:36:55,322 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:36Z] INFO  17:36:55,352 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:36Z] INFO  17:36:55,356 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:36Z] INFO  17:36:55,357 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:36Z] INFO  17:36:55,358 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:36Z] INFO  17:36:55,362 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/5/R14-18106_kapa-NGv3-PE100-NGv3-sort-5_15616091_31267808-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/5/R14-18106_kapa-NGv3-PE100-NGv3-5_15616091_31267808-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/5/tx/tmpzYUEnJ/R14-18106_kapa-NGv3-PE100-NGv3-5_15616091_31267808.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:36Z] INFO  17:36:55,375 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:36Z] INFO  17:36:55,375 HelpFormatter - Date/Time: 2016/04/14 17:36:55
[2016-04-15T00:36Z] INFO  17:36:55,375 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:36Z] INFO  17:36:55,375 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:36Z] WARN  17:36:55,397 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T00:36Z] WARN  17:36:55,400 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/5/tx/tmpzYUEnJ/R14-18106_kapa-NGv3-PE100-NGv3-5_15616091_31267808.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T00:36Z] INFO  17:36:55,503 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T00:36Z] INFO  17:36:55,513 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:36Z] INFO  17:36:55,568 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:36Z] INFO  17:36:55,600 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.09
[2016-04-15T00:36Z] INFO  17:36:55,625 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T00:36Z] INFO  17:36:55,754 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T00:36Z] INFO  17:36:55,781 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:36Z] INFO  17:36:55,850 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-15T00:36Z] INFO  17:36:55,866 ProgressMeter -     3:126222838     1.16838832E8    60.0 s            0.0 s       90.6%    66.0 s       6.0 s
[2016-04-15T00:36Z] INFO  17:36:55,890 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T00:36Z] INFO  17:36:55,948 IntervalUtils - Processing 125185 bp from intervals
[2016-04-15T00:36Z] WARN  17:36:55,954 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:36Z] INFO  17:36:56,067 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:36Z] INFO  17:36:56,074 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.012515973000000001
[2016-04-15T00:36Z] INFO  17:36:56,075 PairHMM - Total compute time in PairHMM computeLikelihoods() : 0.6972684290000001
[2016-04-15T00:36Z] INFO  17:36:56,076 HaplotypeCaller - Ran local assembly on 1410 active regions
[2016-04-15T00:36Z] INFO  17:36:56,160 ProgressMeter -            done      8.1782422E7    53.0 s            0.0 s      100.0%    53.0 s       0.0 s
[2016-04-15T00:36Z] INFO  17:36:56,161 ProgressMeter - Total runtime 53.58 secs, 0.89 min, 0.01 hours
[2016-04-15T00:36Z] INFO  17:36:56,162 MicroScheduler - 20285 reads were filtered out during the traversal out of approximately 264433 total reads (7.67%)
[2016-04-15T00:36Z] INFO  17:36:56,162 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:36Z] INFO  17:36:56,163 MicroScheduler -   -> 19594 reads (7.41% of total) failing DuplicateReadFilter
[2016-04-15T00:36Z] INFO  17:36:56,163 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:36Z] INFO  17:36:56,164 MicroScheduler -   -> 691 reads (0.26% of total) failing HCMappingQualityFilter
[2016-04-15T00:36Z] INFO  17:36:56,165 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:36Z] INFO  17:36:56,165 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:36Z] INFO  17:36:56,166 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:36Z] INFO  17:36:56,166 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:36Z] INFO  17:36:56,220 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:36Z] INFO  17:36:56,221 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:36Z] INFO  17:36:56,222 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T00:36Z] INFO  17:36:56,223 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T00:36Z] INFO  17:36:56,235 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T00:36Z] INFO  17:36:56,236 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T00:36Z] INFO  17:36:56,246 IntervalUtils - Processing 26887 bp from intervals
[2016-04-15T00:36Z] WARN  17:36:56,253 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:36Z] INFO  17:36:56,308 ProgressMeter -     4:109805378      2.5849936E7    30.0 s            1.0 s       62.7%    47.0 s      17.0 s
[2016-04-15T00:36Z] INFO  17:36:56,337 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:36Z] INFO  17:36:56,427 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:36Z] INFO  17:36:56,439 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:36Z] INFO  17:36:56,440 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T00:36Z] INFO  17:36:56,441 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T00:36Z] INFO  17:36:56,453 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T00:36Z] INFO  17:36:56,453 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T00:36Z] INFO  17:36:56,525 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T00:36Z] INFO  17:36:56,626 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T00:36Z] INFO  17:36:57,152 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.010657512000000001
[2016-04-15T00:36Z] INFO  17:36:57,153 PairHMM - Total compute time in PairHMM computeLikelihoods() : 0.7168317630000001
[2016-04-15T00:36Z] INFO  17:36:57,153 HaplotypeCaller - Ran local assembly on 1736 active regions
[2016-04-15T00:36Z] INFO  17:36:57,209 ProgressMeter -            done      1.4553848E8    58.0 s            0.0 s      100.0%    58.0 s       0.0 s
[2016-04-15T00:36Z] INFO  17:36:57,210 ProgressMeter - Total runtime 58.83 secs, 0.98 min, 0.02 hours
[2016-04-15T00:36Z] INFO  17:36:57,211 MicroScheduler - 24495 reads were filtered out during the traversal out of approximately 312769 total reads (7.83%)
[2016-04-15T00:36Z] INFO  17:36:57,211 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:36Z] INFO  17:36:57,211 MicroScheduler -   -> 23505 reads (7.52% of total) failing DuplicateReadFilter
[2016-04-15T00:36Z] INFO  17:36:57,212 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:36Z] INFO  17:36:57,212 MicroScheduler -   -> 990 reads (0.32% of total) failing HCMappingQualityFilter
[2016-04-15T00:36Z] INFO  17:36:57,212 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:36Z] INFO  17:36:57,212 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:36Z] INFO  17:36:57,213 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:36Z] INFO  17:36:57,213 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:36Z] INFO  17:36:57,601 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:36Z] INFO  17:36:57,981 ProgressMeter -      3:58407296     4.00323509E8    90.0 s            0.0 s       94.5%    95.0 s       5.0 s
[2016-04-15T00:36Z] GATK: HaplotypeCaller
[2016-04-15T00:36Z] INFO  17:36:58,833 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:36Z] GATK: HaplotypeCaller
[2016-04-15T00:37Z] INFO  17:37:01,222 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:37Z] INFO  17:37:01,226 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:37Z] INFO  17:37:01,226 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:37Z] INFO  17:37:01,227 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:37Z] INFO  17:37:01,231 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/5/R14-18106_kapa-NGv3-PE100-NGv3-sort-5_31294068_49695124-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/5/R14-18106_kapa-NGv3-PE100-NGv3-5_31294068_49695124-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/5/tx/tmp8gT0UR/R14-18106_kapa-NGv3-PE100-NGv3-5_31294068_49695124.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:37Z] INFO  17:37:01,267 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:37Z] INFO  17:37:01,268 HelpFormatter - Date/Time: 2016/04/14 17:37:01
[2016-04-15T00:37Z] INFO  17:37:01,269 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:37Z] INFO  17:37:01,269 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:37Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T00:37Z] WARN  17:37:01,297 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T00:37Z] WARN  17:37:01,300 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/5/tx/tmp8gT0UR/R14-18106_kapa-NGv3-PE100-NGv3-5_31294068_49695124.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T00:37Z] INFO  17:37:01,305 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T00:37Z] INFO  17:37:01,307 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T00:37Z] INFO  17:37:01,520 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:37Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T00:37Z] INFO  17:37:01,569 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T00:37Z] INFO  17:37:01,580 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T00:37Z] INFO  17:37:01,602 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.015198330000000001
[2016-04-15T00:37Z] INFO  17:37:01,602 PairHMM - Total compute time in PairHMM computeLikelihoods() : 0.904466918
[2016-04-15T00:37Z] INFO  17:37:01,602 HaplotypeCaller - Ran local assembly on 1780 active regions
[2016-04-15T00:37Z] INFO  17:37:01,660 ProgressMeter -            done     1.43172621E8    65.0 s            0.0 s      100.0%    65.0 s       0.0 s
[2016-04-15T00:37Z] INFO  17:37:01,660 ProgressMeter - Total runtime 65.81 secs, 1.10 min, 0.02 hours
[2016-04-15T00:37Z] INFO  17:37:01,660 MicroScheduler - 27008 reads were filtered out during the traversal out of approximately 335908 total reads (8.04%)
[2016-04-15T00:37Z] INFO  17:37:01,661 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:37Z] INFO  17:37:01,661 MicroScheduler -   -> 25489 reads (7.59% of total) failing DuplicateReadFilter
[2016-04-15T00:37Z] INFO  17:37:01,661 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:37Z] INFO  17:37:01,661 MicroScheduler -   -> 1519 reads (0.45% of total) failing HCMappingQualityFilter
[2016-04-15T00:37Z] INFO  17:37:01,662 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:37Z] INFO  17:37:01,662 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:37Z] INFO  17:37:01,662 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:37Z] INFO  17:37:01,663 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:37Z] WARN  17:37:01,755 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T00:37Z] WARN  17:37:01,756 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T00:37Z] INFO  17:37:01,750 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T00:37Z] INFO  17:37:01,776 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:37Z] WARN  17:37:01,861 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T00:37Z] WARN  17:37:01,862 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T00:37Z] INFO  17:37:01,877 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.10
[2016-04-15T00:37Z] INFO  17:37:01,893 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T00:37Z] INFO  17:37:02,247 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:37Z] INFO  17:37:02,249 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:37Z] INFO  17:37:02,249 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:37Z] INFO  17:37:02,250 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:37Z] INFO  17:37:02,254 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/5/R14-18106_kapa-NGv3-PE100-NGv3-sort-5_49695692_65288736-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/5/R14-18106_kapa-NGv3-PE100-NGv3-5_49695692_65288736-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/5/tx/tmpJ8VVmY/R14-18106_kapa-NGv3-PE100-NGv3-5_49695692_65288736.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:37Z] INFO  17:37:02,265 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:37Z] INFO  17:37:02,265 HelpFormatter - Date/Time: 2016/04/14 17:37:02
[2016-04-15T00:37Z] INFO  17:37:02,265 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:37Z] INFO  17:37:02,265 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:37Z] WARN  17:37:02,318 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T00:37Z] WARN  17:37:02,321 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/5/tx/tmpJ8VVmY/R14-18106_kapa-NGv3-PE100-NGv3-5_49695692_65288736.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T00:37Z] INFO  17:37:02,449 IntervalUtils - Processing 183626 bp from intervals
[2016-04-15T00:37Z] WARN  17:37:02,465 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:37Z] INFO  17:37:02,553 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:37Z] INFO  17:37:02,586 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:37Z] INFO  17:37:02,661 ProgressMeter -       4:6826411      7.2661068E7    60.0 s            0.0 s       70.7%    84.0 s      24.0 s
[2016-04-15T00:37Z] INFO  17:37:02,728 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:37Z] INFO  17:37:02,729 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:37Z] INFO  17:37:02,729 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T00:37Z] INFO  17:37:02,729 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T00:37Z] INFO  17:37:02,738 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T00:37Z] INFO  17:37:02,739 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T00:37Z] INFO  17:37:02,745 ProgressMeter -     3:195509332        7445396.0    60.0 s            8.0 s       48.6%     2.1 m      63.0 s
[2016-04-15T00:37Z] INFO  17:37:02,881 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T00:37Z] INFO  17:37:02,891 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:37Z] INFO  17:37:02,979 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:37Z] INFO  17:37:02,983 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.09
[2016-04-15T00:37Z] INFO  17:37:02,994 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T00:37Z] INFO  17:37:03,017 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T00:37Z] GATK: HaplotypeCaller
[2016-04-15T00:37Z] INFO  17:37:03,482 IntervalUtils - Processing 108713 bp from intervals
[2016-04-15T00:37Z] WARN  17:37:03,487 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:37Z] INFO  17:37:03,625 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:37Z] INFO  17:37:03,705 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:37Z] INFO  17:37:03,706 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:37Z] INFO  17:37:03,707 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T00:37Z] INFO  17:37:03,708 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T00:37Z] INFO  17:37:03,708 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T00:37Z] INFO  17:37:03,709 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T00:37Z] INFO  17:37:03,880 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T00:37Z] INFO  17:37:04,073 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.031460225
[2016-04-15T00:37Z] INFO  17:37:04,073 PairHMM - Total compute time in PairHMM computeLikelihoods() : 0.832492781
[2016-04-15T00:37Z] INFO  17:37:04,073 HaplotypeCaller - Ran local assembly on 3231 active regions
[2016-04-15T00:37Z] INFO  17:37:04,145 ProgressMeter -            done     4.57477008E8    96.0 s            0.0 s      100.0%    96.0 s       0.0 s
[2016-04-15T00:37Z] INFO  17:37:04,146 ProgressMeter - Total runtime 96.20 secs, 1.60 min, 0.03 hours
[2016-04-15T00:37Z] INFO  17:37:04,146 MicroScheduler - 55255 reads were filtered out during the traversal out of approximately 700993 total reads (7.88%)
[2016-04-15T00:37Z] INFO  17:37:04,147 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:37Z] INFO  17:37:04,147 MicroScheduler -   -> 53541 reads (7.64% of total) failing DuplicateReadFilter
[2016-04-15T00:37Z] INFO  17:37:04,147 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:37Z] INFO  17:37:04,147 MicroScheduler -   -> 1714 reads (0.24% of total) failing HCMappingQualityFilter
[2016-04-15T00:37Z] INFO  17:37:04,148 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:37Z] INFO  17:37:04,148 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:37Z] INFO  17:37:04,148 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:37Z] INFO  17:37:04,148 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:37Z] INFO  17:37:05,556 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:37Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T00:37Z] INFO  17:37:05,802 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T00:37Z] INFO  17:37:05,803 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T00:37Z] GATK: HaplotypeCaller
[2016-04-15T00:37Z] WARN  17:37:06,212 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T00:37Z] WARN  17:37:06,213 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T00:37Z] INFO  17:37:06,316 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:37Z] INFO  17:37:06,319 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:37Z] INFO  17:37:06,320 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:37Z] INFO  17:37:06,320 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:37Z] INFO  17:37:06,341 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/5/R14-18106_kapa-NGv3-PE100-NGv3-sort-5_65290574_80809536-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/5/R14-18106_kapa-NGv3-PE100-NGv3-5_65290574_80809536-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/5/tx/tmp_JYOf1/R14-18106_kapa-NGv3-PE100-NGv3-5_65290574_80809536.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:37Z] INFO  17:37:06,359 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:37Z] INFO  17:37:06,372 HelpFormatter - Date/Time: 2016/04/14 17:37:06
[2016-04-15T00:37Z] INFO  17:37:06,373 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:37Z] INFO  17:37:06,374 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:37Z] WARN  17:37:06,407 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T00:37Z] WARN  17:37:06,410 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/5/tx/tmp_JYOf1/R14-18106_kapa-NGv3-PE100-NGv3-5_65290574_80809536.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T00:37Z] INFO  17:37:06,590 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:37Z] INFO  17:37:06,822 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T00:37Z] INFO  17:37:06,832 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:37Z] INFO  17:37:06,907 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-15T00:37Z] INFO  17:37:06,920 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T00:37Z] INFO  17:37:07,512 IntervalUtils - Processing 203113 bp from intervals
[2016-04-15T00:37Z] WARN  17:37:07,545 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:37Z] INFO  17:37:07,610 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.018126729
[2016-04-15T00:37Z] INFO  17:37:07,611 PairHMM - Total compute time in PairHMM computeLikelihoods() : 0.942111173
[2016-04-15T00:37Z] INFO  17:37:07,611 HaplotypeCaller - Ran local assembly on 1126 active regions
[2016-04-15T00:37Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T00:37Z] INFO  17:37:07,628 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T00:37Z] INFO  17:37:07,641 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:37Z] INFO  17:37:07,643 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T00:37Z] INFO  17:37:07,662 ProgressMeter -            done      5.9405179E7    41.0 s            0.0 s      100.0%    41.0 s       0.0 s
[2016-04-15T00:37Z] INFO  17:37:07,662 ProgressMeter - Total runtime 41.37 secs, 0.69 min, 0.01 hours
[2016-04-15T00:37Z] INFO  17:37:07,663 MicroScheduler - 14122 reads were filtered out during the traversal out of approximately 183013 total reads (7.72%)
[2016-04-15T00:37Z] INFO  17:37:07,663 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:37Z] INFO  17:37:07,664 MicroScheduler -   -> 13457 reads (7.35% of total) failing DuplicateReadFilter
[2016-04-15T00:37Z] INFO  17:37:07,664 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:37Z] INFO  17:37:07,664 MicroScheduler -   -> 665 reads (0.36% of total) failing HCMappingQualityFilter
[2016-04-15T00:37Z] INFO  17:37:07,664 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:37Z] INFO  17:37:07,665 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:37Z] INFO  17:37:07,665 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:37Z] INFO  17:37:07,665 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:37Z] INFO  17:37:07,743 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:37Z] INFO  17:37:07,744 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:37Z] INFO  17:37:07,745 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T00:37Z] INFO  17:37:07,746 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T00:37Z] INFO  17:37:07,746 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T00:37Z] INFO  17:37:07,746 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T00:37Z] INFO  17:37:07,953 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T00:37Z] WARN  17:37:08,018 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T00:37Z] WARN  17:37:08,019 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T00:37Z] INFO  17:37:08,691 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:37Z] INFO  17:37:08,695 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:37Z] INFO  17:37:08,695 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:37Z] INFO  17:37:08,696 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:37Z] INFO  17:37:08,700 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/5/R14-18106_kapa-NGv3-PE100-NGv3-sort-5_80911291_96430739-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/5/R14-18106_kapa-NGv3-PE100-NGv3-5_80911291_96430739-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/5/tx/tmp7i3Pkf/R14-18106_kapa-NGv3-PE100-NGv3-5_80911291_96430739.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:37Z] INFO  17:37:08,715 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:37Z] INFO  17:37:08,715 HelpFormatter - Date/Time: 2016/04/14 17:37:08
[2016-04-15T00:37Z] INFO  17:37:08,715 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:37Z] INFO  17:37:08,715 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:37Z] WARN  17:37:08,745 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T00:37Z] WARN  17:37:08,748 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/5/tx/tmp7i3Pkf/R14-18106_kapa-NGv3-PE100-NGv3-5_80911291_96430739.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T00:37Z] INFO  17:37:08,957 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:37Z] INFO  17:37:08,965 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:37Z] INFO  17:37:09,156 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T00:37Z] INFO  17:37:09,174 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:37Z] GATK: HaplotypeCaller
[2016-04-15T00:37Z] INFO  17:37:09,259 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-15T00:37Z] INFO  17:37:09,281 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T00:37Z] INFO  17:37:09,579 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.00570746
[2016-04-15T00:37Z] INFO  17:37:09,591 PairHMM - Total compute time in PairHMM computeLikelihoods() : 0.291570555
[2016-04-15T00:37Z] INFO  17:37:09,592 HaplotypeCaller - Ran local assembly on 601 active regions
[2016-04-15T00:37Z] INFO  17:37:09,612 ProgressMeter -     4:125593242      2.2243201E7    30.0 s            1.0 s       69.0%    43.0 s      13.0 s
[2016-04-15T00:37Z] INFO  17:37:09,648 ProgressMeter -            done      1.9501835E7    29.0 s            1.0 s      100.0%    29.0 s       0.0 s
[2016-04-15T00:37Z] INFO  17:37:09,649 ProgressMeter - Total runtime 29.16 secs, 0.49 min, 0.01 hours
[2016-04-15T00:37Z] INFO  17:37:09,649 MicroScheduler - 8573 reads were filtered out during the traversal out of approximately 109019 total reads (7.86%)
[2016-04-15T00:37Z] INFO  17:37:09,650 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:37Z] INFO  17:37:09,650 MicroScheduler -   -> 8177 reads (7.50% of total) failing DuplicateReadFilter
[2016-04-15T00:37Z] INFO  17:37:09,650 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:37Z] INFO  17:37:09,650 MicroScheduler -   -> 396 reads (0.36% of total) failing HCMappingQualityFilter
[2016-04-15T00:37Z] INFO  17:37:09,651 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:37Z] INFO  17:37:09,651 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:37Z] INFO  17:37:09,651 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:37Z] INFO  17:37:09,651 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:37Z] INFO  17:37:09,825 IntervalUtils - Processing 113632 bp from intervals
[2016-04-15T00:37Z] WARN  17:37:09,830 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:37Z] INFO  17:37:09,973 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:37Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T00:37Z] INFO  17:37:10,075 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:37Z] INFO  17:37:10,083 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T00:37Z] INFO  17:37:10,087 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:37Z] INFO  17:37:10,088 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T00:37Z] INFO  17:37:10,088 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T00:37Z] INFO  17:37:10,094 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T00:37Z] INFO  17:37:10,097 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T00:37Z] INFO  17:37:10,097 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T00:37Z] WARN  17:37:10,351 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T00:37Z] WARN  17:37:10,353 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T00:37Z] INFO  17:37:10,369 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T00:37Z] INFO  17:37:11,495 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:37Z] GATK: HaplotypeCaller
[2016-04-15T00:37Z] INFO  17:37:12,095 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.017169877
[2016-04-15T00:37Z] INFO  17:37:12,096 PairHMM - Total compute time in PairHMM computeLikelihoods() : 0.830612083
[2016-04-15T00:37Z] INFO  17:37:12,097 HaplotypeCaller - Ran local assembly on 1474 active regions
[2016-04-15T00:37Z] INFO  17:37:12,132 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:37Z] INFO  17:37:12,146 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:37Z] INFO  17:37:12,147 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:37Z] INFO  17:37:12,148 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:37Z] INFO  17:37:12,148 ProgressMeter -            done      9.7624838E7    50.0 s            0.0 s      100.0%    50.0 s       0.0 s
[2016-04-15T00:37Z] INFO  17:37:12,149 ProgressMeter - Total runtime 50.42 secs, 0.84 min, 0.01 hours
[2016-04-15T00:37Z] INFO  17:37:12,150 MicroScheduler - 20728 reads were filtered out during the traversal out of approximately 246145 total reads (8.42%)
[2016-04-15T00:37Z] INFO  17:37:12,151 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:37Z] INFO  17:37:12,151 MicroScheduler -   -> 18017 reads (7.32% of total) failing DuplicateReadFilter
[2016-04-15T00:37Z] INFO  17:37:12,152 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:37Z] INFO  17:37:12,153 MicroScheduler -   -> 2711 reads (1.10% of total) failing HCMappingQualityFilter
[2016-04-15T00:37Z] INFO  17:37:12,153 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:37Z] INFO  17:37:12,153 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/5/R14-18106_kapa-NGv3-PE100-NGv3-sort-5_96432513_112043579-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/5/R14-18106_kapa-NGv3-PE100-NGv3-5_96432513_112043579-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/5/tx/tmpexN9qD/R14-18106_kapa-NGv3-PE100-NGv3-5_96432513_112043579.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:37Z] INFO  17:37:12,154 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:37Z] INFO  17:37:12,154 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:37Z] INFO  17:37:12,155 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:37Z] INFO  17:37:12,172 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:37Z] INFO  17:37:12,173 HelpFormatter - Date/Time: 2016/04/14 17:37:12
[2016-04-15T00:37Z] INFO  17:37:12,174 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:37Z] INFO  17:37:12,174 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:37Z] WARN  17:37:12,198 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T00:37Z] WARN  17:37:12,201 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/5/tx/tmpexN9qD/R14-18106_kapa-NGv3-PE100-NGv3-5_96432513_112043579.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T00:37Z] INFO  17:37:12,443 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:37Z] INFO  17:37:12,671 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T00:37Z] INFO  17:37:12,692 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:37Z] INFO  17:37:12,697 ProgressMeter -     4:159956185      2.4246415E7    30.0 s            1.0 s       84.3%    35.0 s       5.0 s
[2016-04-15T00:37Z] INFO  17:37:12,777 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-15T00:37Z] INFO  17:37:12,794 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T00:37Z] INFO  17:37:13,180 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.002613718
[2016-04-15T00:37Z] INFO  17:37:13,181 PairHMM - Total compute time in PairHMM computeLikelihoods() : 0.08116100100000001
[2016-04-15T00:37Z] INFO  17:37:13,182 HaplotypeCaller - Ran local assembly on 170 active regions
[2016-04-15T00:37Z] INFO  17:37:13,221 IntervalUtils - Processing 57322 bp from intervals
[2016-04-15T00:37Z] WARN  17:37:13,226 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:37Z] INFO  17:37:13,229 ProgressMeter -            done        1678889.0    16.0 s           10.0 s      100.0%    16.0 s       0.0 s
[2016-04-15T00:37Z] INFO  17:37:13,229 ProgressMeter - Total runtime 16.79 secs, 0.28 min, 0.00 hours
[2016-04-15T00:37Z] INFO  17:37:13,229 MicroScheduler - 4621 reads were filtered out during the traversal out of approximately 35715 total reads (12.94%)
[2016-04-15T00:37Z] INFO  17:37:13,231 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:37Z] INFO  17:37:13,231 MicroScheduler -   -> 2701 reads (7.56% of total) failing DuplicateReadFilter
[2016-04-15T00:37Z] INFO  17:37:13,232 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:37Z] INFO  17:37:13,232 MicroScheduler -   -> 1920 reads (5.38% of total) failing HCMappingQualityFilter
[2016-04-15T00:37Z] INFO  17:37:13,232 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:37Z] INFO  17:37:13,232 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:37Z] INFO  17:37:13,233 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:37Z] INFO  17:37:13,233 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:37Z] INFO  17:37:13,366 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:37Z] INFO  17:37:13,479 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:37Z] INFO  17:37:13,480 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:37Z] INFO  17:37:13,480 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T00:37Z] INFO  17:37:13,481 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T00:37Z] INFO  17:37:13,500 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T00:37Z] INFO  17:37:13,501 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T00:37Z] INFO  17:37:13,658 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T00:37Z] INFO  17:37:13,796 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:37Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T00:37Z] INFO  17:37:14,065 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T00:37Z] INFO  17:37:14,065 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T00:37Z] GATK: HaplotypeCaller
[2016-04-15T00:37Z] WARN  17:37:14,347 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T00:37Z] WARN  17:37:14,359 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T00:37Z] INFO  17:37:14,509 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.004782183000000001
[2016-04-15T00:37Z] INFO  17:37:14,510 PairHMM - Total compute time in PairHMM computeLikelihoods() : 0.48288038400000005
[2016-04-15T00:37Z] INFO  17:37:14,511 HaplotypeCaller - Ran local assembly on 592 active regions
[2016-04-15T00:37Z] INFO  17:37:14,517 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:37Z] INFO  17:37:14,568 ProgressMeter -            done      1.6341003E7    29.0 s            1.0 s      100.0%    29.0 s       0.0 s
[2016-04-15T00:37Z] INFO  17:37:14,569 ProgressMeter - Total runtime 29.26 secs, 0.49 min, 0.01 hours
[2016-04-15T00:37Z] INFO  17:37:14,569 MicroScheduler - 6929 reads were filtered out during the traversal out of approximately 88220 total reads (7.85%)
[2016-04-15T00:37Z] INFO  17:37:14,570 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:37Z] INFO  17:37:14,570 MicroScheduler -   -> 6428 reads (7.29% of total) failing DuplicateReadFilter
[2016-04-15T00:37Z] INFO  17:37:14,570 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:37Z] INFO  17:37:14,570 MicroScheduler -   -> 501 reads (0.57% of total) failing HCMappingQualityFilter
[2016-04-15T00:37Z] INFO  17:37:14,571 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:37Z] INFO  17:37:14,571 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:37Z] INFO  17:37:14,571 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:37Z] INFO  17:37:14,571 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:37Z] GATK: HaplotypeCaller
[2016-04-15T00:37Z] INFO  17:37:15,297 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:37Z] INFO  17:37:15,300 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:37Z] INFO  17:37:15,300 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:37Z] INFO  17:37:15,301 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:37Z] INFO  17:37:15,305 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/5/R14-18106_kapa-NGv3-PE100-NGv3-sort-5_112073555_127595521-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/5/R14-18106_kapa-NGv3-PE100-NGv3-5_112073555_127595521-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/5/tx/tmplFpIMW/R14-18106_kapa-NGv3-PE100-NGv3-5_112073555_127595521.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:37Z] INFO  17:37:15,315 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:37Z] INFO  17:37:15,326 HelpFormatter - Date/Time: 2016/04/14 17:37:15
[2016-04-15T00:37Z] INFO  17:37:15,327 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:37Z] INFO  17:37:15,328 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:37Z] WARN  17:37:15,361 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T00:37Z] WARN  17:37:15,372 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/5/tx/tmplFpIMW/R14-18106_kapa-NGv3-PE100-NGv3-5_112073555_127595521.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T00:37Z] INFO  17:37:15,567 ProgressMeter -     4:187630139      1.5547155E7    30.0 s            1.0 s       93.8%    31.0 s       1.0 s
[2016-04-15T00:37Z] INFO  17:37:15,625 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:37Z] INFO  17:37:15,817 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T00:37Z] INFO  17:37:15,838 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:37Z] INFO  17:37:15,881 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:37Z] INFO  17:37:15,887 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-15T00:37Z] INFO  17:37:15,911 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T00:37Z] GATK: HaplotypeCaller
[2016-04-15T00:37Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T00:37Z] INFO  17:37:16,259 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T00:37Z] INFO  17:37:16,260 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T00:37Z] INFO  17:37:16,314 IntervalUtils - Processing 103986 bp from intervals
[2016-04-15T00:37Z] WARN  17:37:16,320 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:37Z] INFO  17:37:16,405 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:37Z] INFO  17:37:16,507 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:37Z] INFO  17:37:16,514 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:37Z] INFO  17:37:16,515 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T00:37Z] INFO  17:37:16,516 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T00:37Z] INFO  17:37:16,516 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T00:37Z] INFO  17:37:16,517 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T00:37Z] WARN  17:37:16,554 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T00:37Z] WARN  17:37:16,555 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T00:37Z] INFO  17:37:16,739 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T00:37Z] INFO  17:37:17,346 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:37Z] INFO  17:37:17,350 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:37Z] INFO  17:37:17,350 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:37Z] INFO  17:37:17,351 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:37Z] INFO  17:37:17,355 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/5/R14-18106_kapa-NGv3-PE100-NGv3-sort-5_127597427_143191869-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/5/R14-18106_kapa-NGv3-PE100-NGv3-5_127597427_143191869-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/5/tx/tmpmMX_OX/R14-18106_kapa-NGv3-PE100-NGv3-5_127597427_143191869.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:37Z] INFO  17:37:17,364 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:37Z] INFO  17:37:17,372 HelpFormatter - Date/Time: 2016/04/14 17:37:17
[2016-04-15T00:37Z] INFO  17:37:17,375 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:37Z] INFO  17:37:17,376 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:37Z] WARN  17:37:17,402 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T00:37Z] WARN  17:37:17,405 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/5/tx/tmpmMX_OX/R14-18106_kapa-NGv3-PE100-NGv3-5_127597427_143191869.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T00:37Z] INFO  17:37:17,649 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:37Z] INFO  17:37:17,810 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T00:37Z] INFO  17:37:17,820 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:37Z] INFO  17:37:17,908 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.09
[2016-04-15T00:37Z] INFO  17:37:17,936 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T00:37Z] INFO  17:37:18,072 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:37Z] INFO  17:37:18,076 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:37Z] INFO  17:37:18,076 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:37Z] INFO  17:37:18,077 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:37Z] INFO  17:37:18,082 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/5/R14-18106_kapa-NGv3-PE100-NGv3-sort-5_143200044_158710347-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/5/R14-18106_kapa-NGv3-PE100-NGv3-5_143200044_158710347-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/5/tx/tmpzgVtF1/R14-18106_kapa-NGv3-PE100-NGv3-5_143200044_158710347.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:37Z] INFO  17:37:18,102 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:37Z] INFO  17:37:18,103 HelpFormatter - Date/Time: 2016/04/14 17:37:18
[2016-04-15T00:37Z] INFO  17:37:18,103 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:37Z] INFO  17:37:18,103 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:37Z] WARN  17:37:18,148 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T00:37Z] WARN  17:37:18,166 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/5/tx/tmpzgVtF1/R14-18106_kapa-NGv3-PE100-NGv3-5_143200044_158710347.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T00:37Z] INFO  17:37:18,414 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:37Z] INFO  17:37:18,494 IntervalUtils - Processing 393653 bp from intervals
[2016-04-15T00:37Z] WARN  17:37:18,510 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:37Z] INFO  17:37:18,612 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.006523755
[2016-04-15T00:37Z] INFO  17:37:18,616 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:37Z] INFO  17:37:18,621 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T00:37Z] INFO  17:37:18,623 PairHMM - Total compute time in PairHMM computeLikelihoods() : 0.44373054900000003
[2016-04-15T00:37Z] INFO  17:37:18,624 HaplotypeCaller - Ran local assembly on 832 active regions
[2016-04-15T00:37Z] INFO  17:37:18,635 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:37Z] INFO  17:37:18,688 ProgressMeter -            done      3.2744349E7    36.0 s            1.0 s      100.0%    36.0 s       0.0 s
[2016-04-15T00:37Z] INFO  17:37:18,689 ProgressMeter - Total runtime 36.01 secs, 0.60 min, 0.01 hours
[2016-04-15T00:37Z] INFO  17:37:18,689 MicroScheduler - 10967 reads were filtered out during the traversal out of approximately 141186 total reads (7.77%)
[2016-04-15T00:37Z] INFO  17:37:18,689 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:37Z] INFO  17:37:18,690 MicroScheduler -   -> 10805 reads (7.65% of total) failing DuplicateReadFilter
[2016-04-15T00:37Z] INFO  17:37:18,691 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:37Z] INFO  17:37:18,691 MicroScheduler -   -> 162 reads (0.11% of total) failing HCMappingQualityFilter
[2016-04-15T00:37Z] INFO  17:37:18,691 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:37Z] INFO  17:37:18,691 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:37Z] INFO  17:37:18,692 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:37Z] INFO  17:37:18,692 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:37Z] INFO  17:37:18,735 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.10
[2016-04-15T00:37Z] INFO  17:37:18,774 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T00:37Z] INFO  17:37:18,777 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:37Z] INFO  17:37:18,778 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:37Z] INFO  17:37:18,778 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T00:37Z] INFO  17:37:18,779 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T00:37Z] INFO  17:37:18,779 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T00:37Z] INFO  17:37:18,780 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T00:37Z] INFO  17:37:19,049 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T00:37Z] INFO  17:37:19,244 IntervalUtils - Processing 205172 bp from intervals
[2016-04-15T00:37Z] WARN  17:37:19,250 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:37Z] INFO  17:37:19,378 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:37Z] INFO  17:37:19,527 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:37Z] INFO  17:37:19,528 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:37Z] INFO  17:37:19,529 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T00:37Z] INFO  17:37:19,530 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T00:37Z] INFO  17:37:19,549 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T00:37Z] INFO  17:37:19,550 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T00:37Z] INFO  17:37:19,748 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T00:37Z] INFO  17:37:19,786 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:37Z] INFO  17:37:19,800 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:37Z] INFO  17:37:19,801 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:37Z] INFO  17:37:19,802 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:37Z] INFO  17:37:19,807 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/5/R14-18106_kapa-NGv3-PE100-NGv3-sort-5_158711911_174870102-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/5/R14-18106_kapa-NGv3-PE100-NGv3-5_158711911_174870102-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/5/tx/tmpPMDstC/R14-18106_kapa-NGv3-PE100-NGv3-5_158711911_174870102.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:37Z] INFO  17:37:19,840 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:37Z] INFO  17:37:19,841 HelpFormatter - Date/Time: 2016/04/14 17:37:19
[2016-04-15T00:37Z] INFO  17:37:19,842 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:37Z] INFO  17:37:19,842 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:37Z] INFO  17:37:19,865 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.010702822
[2016-04-15T00:37Z] INFO  17:37:19,866 PairHMM - Total compute time in PairHMM computeLikelihoods() : 1.035855804
[2016-04-15T00:37Z] INFO  17:37:19,866 HaplotypeCaller - Ran local assembly on 715 active regions
[2016-04-15T00:37Z] WARN  17:37:19,903 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T00:37Z] WARN  17:37:19,913 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/5/tx/tmpPMDstC/R14-18106_kapa-NGv3-PE100-NGv3-5_158711911_174870102.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T00:37Z] INFO  17:37:19,966 ProgressMeter -            done      1.8181148E7    34.0 s            1.0 s      100.0%    34.0 s       0.0 s
[2016-04-15T00:37Z] INFO  17:37:19,967 ProgressMeter - Total runtime 34.43 secs, 0.57 min, 0.01 hours
[2016-04-15T00:37Z] INFO  17:37:19,968 MicroScheduler - 12500 reads were filtered out during the traversal out of approximately 131326 total reads (9.52%)
[2016-04-15T00:37Z] INFO  17:37:19,968 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:37Z] INFO  17:37:19,968 MicroScheduler -   -> 9890 reads (7.53% of total) failing DuplicateReadFilter
[2016-04-15T00:37Z] INFO  17:37:19,968 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:37Z] INFO  17:37:19,969 MicroScheduler -   -> 2610 reads (1.99% of total) failing HCMappingQualityFilter
[2016-04-15T00:37Z] INFO  17:37:19,969 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:37Z] INFO  17:37:19,969 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:37Z] INFO  17:37:19,969 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:37Z] INFO  17:37:19,970 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:37Z] INFO  17:37:20,231 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:37Z] INFO  17:37:20,276 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:37Z] INFO  17:37:20,320 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.0077441030000000004
[2016-04-15T00:37Z] INFO  17:37:20,321 PairHMM - Total compute time in PairHMM computeLikelihoods() : 0.5690723320000001
[2016-04-15T00:37Z] INFO  17:37:20,322 HaplotypeCaller - Ran local assembly on 1031 active regions
[2016-04-15T00:37Z] INFO  17:37:20,378 ProgressMeter -            done      4.4117255E7    40.0 s            0.0 s      100.0%    40.0 s       0.0 s
[2016-04-15T00:37Z] INFO  17:37:20,378 ProgressMeter - Total runtime 40.80 secs, 0.68 min, 0.01 hours
[2016-04-15T00:37Z] INFO  17:37:20,379 MicroScheduler - 11838 reads were filtered out during the traversal out of approximately 157942 total reads (7.50%)
[2016-04-15T00:37Z] INFO  17:37:20,379 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:37Z] INFO  17:37:20,379 MicroScheduler -   -> 11706 reads (7.41% of total) failing DuplicateReadFilter
[2016-04-15T00:37Z] INFO  17:37:20,380 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:37Z] INFO  17:37:20,380 MicroScheduler -   -> 132 reads (0.08% of total) failing HCMappingQualityFilter
[2016-04-15T00:37Z] INFO  17:37:20,380 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:37Z] INFO  17:37:20,380 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:37Z] INFO  17:37:20,381 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:37Z] INFO  17:37:20,381 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:37Z] INFO  17:37:20,453 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T00:37Z] INFO  17:37:20,481 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:37Z] INFO  17:37:20,569 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.09
[2016-04-15T00:37Z] INFO  17:37:20,612 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T00:37Z] GATK: HaplotypeCaller
[2016-04-15T00:37Z] INFO  17:37:20,946 IntervalUtils - Processing 104189 bp from intervals
[2016-04-15T00:37Z] WARN  17:37:20,951 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:37Z] INFO  17:37:21,194 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:37Z] INFO  17:37:21,321 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:37Z] INFO  17:37:21,333 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:37Z] INFO  17:37:21,334 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T00:37Z] INFO  17:37:21,334 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T00:37Z] INFO  17:37:21,355 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T00:37Z] INFO  17:37:21,356 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T00:37Z] INFO  17:37:21,615 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T00:37Z] INFO  17:37:21,623 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:37Z] GATK: HaplotypeCaller
[2016-04-15T00:37Z] INFO  17:37:22,103 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:37Z] GATK: HaplotypeCaller
[2016-04-15T00:37Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T00:37Z] INFO  17:37:22,741 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T00:37Z] INFO  17:37:22,742 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T00:37Z] INFO  17:37:22,930 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.037106841
[2016-04-15T00:37Z] INFO  17:37:22,932 PairHMM - Total compute time in PairHMM computeLikelihoods() : 3.8006165910000003
[2016-04-15T00:37Z] INFO  17:37:22,932 HaplotypeCaller - Ran local assembly on 1862 active regions
[2016-04-15T00:37Z] INFO  17:37:22,971 ProgressMeter -            done     1.38636459E8    80.0 s            0.0 s      100.0%    80.0 s       0.0 s
[2016-04-15T00:37Z] INFO  17:37:22,972 ProgressMeter - Total runtime 80.34 secs, 1.34 min, 0.02 hours
[2016-04-15T00:37Z] INFO  17:37:22,972 MicroScheduler - 67740 reads were filtered out during the traversal out of approximately 421542 total reads (16.07%)
[2016-04-15T00:37Z] INFO  17:37:22,973 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:37Z] INFO  17:37:22,974 MicroScheduler -   -> 29361 reads (6.97% of total) failing DuplicateReadFilter
[2016-04-15T00:37Z] INFO  17:37:22,975 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:37Z] INFO  17:37:22,975 MicroScheduler -   -> 38379 reads (9.10% of total) failing HCMappingQualityFilter
[2016-04-15T00:37Z] INFO  17:37:22,976 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:37Z] INFO  17:37:22,976 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:37Z] INFO  17:37:22,977 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:37Z] INFO  17:37:22,978 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:37Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T00:37Z] INFO  17:37:23,002 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T00:37Z] INFO  17:37:23,014 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T00:37Z] WARN  17:37:23,155 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T00:37Z] WARN  17:37:23,156 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T00:37Z] WARN  17:37:23,329 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T00:37Z] WARN  17:37:23,330 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T00:37Z] INFO  17:37:24,081 ProgressMeter -      4:89053765      1.1752835E7    60.0 s            5.0 s       55.6%   107.0 s      47.0 s
[2016-04-15T00:37Z] INFO  17:37:24,118 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:37Z] INFO  17:37:24,132 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:37Z] INFO  17:37:24,133 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:37Z] INFO  17:37:24,134 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:37Z] INFO  17:37:24,139 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/5/R14-18106_kapa-NGv3-PE100-NGv3-sort-5_174919106_180915260-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/5/R14-18106_kapa-NGv3-PE100-NGv3-5_174919106_180915260-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/5/tx/tmpRQb0Cv/R14-18106_kapa-NGv3-PE100-NGv3-5_174919106_180915260.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:37Z] INFO  17:37:24,171 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:37Z] INFO  17:37:24,172 HelpFormatter - Date/Time: 2016/04/14 17:37:24
[2016-04-15T00:37Z] INFO  17:37:24,172 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:37Z] INFO  17:37:24,173 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:37Z] WARN  17:37:24,251 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T00:37Z] WARN  17:37:24,261 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/5/tx/tmpRQb0Cv/R14-18106_kapa-NGv3-PE100-NGv3-5_174919106_180915260.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T00:37Z] INFO  17:37:24,552 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:37Z] INFO  17:37:24,563 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:37Z] INFO  17:37:24,841 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T00:37Z] INFO  17:37:24,851 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:37Z] INFO  17:37:24,952 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.10
[2016-04-15T00:37Z] INFO  17:37:24,978 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T00:37Z] GATK: HaplotypeCaller
[2016-04-15T00:37Z] INFO  17:37:25,374 IntervalUtils - Processing 163171 bp from intervals
[2016-04-15T00:37Z] WARN  17:37:25,389 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:37Z] INFO  17:37:25,428 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:37Z] INFO  17:37:25,431 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:37Z] INFO  17:37:25,431 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:37Z] INFO  17:37:25,431 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:37Z] INFO  17:37:25,446 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/6/R14-18106_kapa-NGv3-PE100-NGv3-sort-6_0_15509601-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/6/R14-18106_kapa-NGv3-PE100-NGv3-6_0_15509601-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/6/tx/tmpn15PDD/R14-18106_kapa-NGv3-PE100-NGv3-6_0_15509601.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:37Z] INFO  17:37:25,489 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:37Z] INFO  17:37:25,492 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:37Z] INFO  17:37:25,492 HelpFormatter - Date/Time: 2016/04/14 17:37:25
[2016-04-15T00:37Z] INFO  17:37:25,493 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:37Z] INFO  17:37:25,494 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:37Z] WARN  17:37:25,521 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T00:37Z] WARN  17:37:25,524 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/6/tx/tmpn15PDD/R14-18106_kapa-NGv3-PE100-NGv3-6_0_15509601.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T00:37Z] INFO  17:37:25,575 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:37Z] INFO  17:37:25,576 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:37Z] INFO  17:37:25,577 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T00:37Z] INFO  17:37:25,578 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T00:37Z] INFO  17:37:25,578 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T00:37Z] INFO  17:37:25,579 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T00:37Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T00:37Z] INFO  17:37:25,730 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T00:37Z] INFO  17:37:25,740 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T00:37Z] INFO  17:37:25,755 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T00:37Z] INFO  17:37:25,839 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:37Z] INFO  17:37:26,036 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T00:37Z] INFO  17:37:26,056 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:37Z] WARN  17:37:26,096 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T00:37Z] WARN  17:37:26,107 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T00:37Z] INFO  17:37:26,179 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.12
[2016-04-15T00:37Z] INFO  17:37:26,201 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T00:37Z] INFO  17:37:26,238 ProgressMeter -       5:6616840      1.1663999E7    30.0 s            2.0 s       53.7%    55.0 s      25.0 s
[2016-04-15T00:37Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T00:37Z] INFO  17:37:26,379 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T00:37Z] INFO  17:37:26,380 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T00:37Z] INFO  17:37:26,410 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:37Z] INFO  17:37:26,414 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:37Z] INFO  17:37:26,414 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:37Z] INFO  17:37:26,415 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:37Z] INFO  17:37:26,419 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/6/R14-18106_kapa-NGv3-PE100-NGv3-sort-6_15511526_31080332-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/6/R14-18106_kapa-NGv3-PE100-NGv3-6_15511526_31080332-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/6/tx/tmpzM8j4b/R14-18106_kapa-NGv3-PE100-NGv3-6_15511526_31080332.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:37Z] INFO  17:37:26,430 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:37Z] INFO  17:37:26,434 HelpFormatter - Date/Time: 2016/04/14 17:37:26
[2016-04-15T00:37Z] INFO  17:37:26,435 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:37Z] INFO  17:37:26,435 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:37Z] WARN  17:37:26,460 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T00:37Z] WARN  17:37:26,463 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/6/tx/tmpzM8j4b/R14-18106_kapa-NGv3-PE100-NGv3-6_15511526_31080332.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T00:37Z] INFO  17:37:26,601 IntervalUtils - Processing 139546 bp from intervals
[2016-04-15T00:37Z] WARN  17:37:26,606 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:37Z] INFO  17:37:26,697 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:37Z] WARN  17:37:26,801 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T00:37Z] WARN  17:37:26,802 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T00:37Z] INFO  17:37:26,807 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:37Z] INFO  17:37:26,808 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:37Z] INFO  17:37:26,809 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T00:37Z] INFO  17:37:26,809 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T00:37Z] INFO  17:37:26,820 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T00:37Z] INFO  17:37:26,820 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T00:37Z] INFO  17:37:26,873 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:37Z] INFO  17:37:27,031 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T00:37Z] INFO  17:37:27,089 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T00:37Z] INFO  17:37:27,099 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:37Z] INFO  17:37:27,164 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-15T00:37Z] INFO  17:37:27,181 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T00:37Z] INFO  17:37:27,666 IntervalUtils - Processing 239663 bp from intervals
[2016-04-15T00:37Z] WARN  17:37:27,700 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:37Z] INFO  17:37:27,837 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:37Z] INFO  17:37:27,967 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:37Z] INFO  17:37:27,968 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:37Z] INFO  17:37:27,980 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T00:37Z] INFO  17:37:27,981 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T00:37Z] INFO  17:37:27,990 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T00:37Z] INFO  17:37:27,990 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T00:37Z] INFO  17:37:28,247 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T00:37Z] INFO  17:37:28,944 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:37Z] INFO  17:37:28,950 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:37Z] INFO  17:37:28,958 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:37Z] INFO  17:37:28,958 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:37Z] INFO  17:37:28,963 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/6/R14-18106_kapa-NGv3-PE100-NGv3-sort-6_31083801_46593245-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/6/R14-18106_kapa-NGv3-PE100-NGv3-6_31083801_46593245-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/6/tx/tmprO4M_H/R14-18106_kapa-NGv3-PE100-NGv3-6_31083801_46593245.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:37Z] INFO  17:37:28,984 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:37Z] INFO  17:37:28,990 HelpFormatter - Date/Time: 2016/04/14 17:37:28
[2016-04-15T00:37Z] INFO  17:37:28,991 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:37Z] INFO  17:37:28,992 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:37Z] WARN  17:37:29,034 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T00:37Z] WARN  17:37:29,056 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/6/tx/tmprO4M_H/R14-18106_kapa-NGv3-PE100-NGv3-6_31083801_46593245.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T00:37Z] INFO  17:37:29,488 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:37Z] INFO  17:37:29,735 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T00:37Z] INFO  17:37:29,756 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:37Z] INFO  17:37:29,840 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-15T00:37Z] INFO  17:37:29,870 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T00:37Z] INFO  17:37:30,660 IntervalUtils - Processing 501134 bp from intervals
[2016-04-15T00:37Z] WARN  17:37:30,680 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:37Z] INFO  17:37:30,789 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:37Z] INFO  17:37:31,029 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:37Z] INFO  17:37:31,037 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:37Z] INFO  17:37:31,039 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T00:37Z] INFO  17:37:31,039 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T00:37Z] INFO  17:37:31,051 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T00:37Z] INFO  17:37:31,053 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T00:37Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T00:37Z] INFO  17:37:31,143 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T00:37Z] INFO  17:37:31,155 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T00:37Z] INFO  17:37:31,401 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T00:37Z] WARN  17:37:31,490 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T00:37Z] WARN  17:37:31,491 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T00:37Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T00:37Z] INFO  17:37:31,823 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T00:37Z] INFO  17:37:31,825 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T00:37Z] WARN  17:37:32,531 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T00:37Z] WARN  17:37:32,532 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T00:37Z] INFO  17:37:32,746 ProgressMeter -     3:195515618        7445396.0    90.0 s           12.0 s       53.9%     2.8 m      77.0 s
[2016-04-15T00:37Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T00:37Z] INFO  17:37:32,751 ProgressMeter -      5:37205416      2.2853967E7    30.0 s            1.0 s       53.5%    56.0 s      26.0 s
[2016-04-15T00:37Z] INFO  17:37:32,763 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T00:37Z] INFO  17:37:32,775 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T00:37Z] WARN  17:37:33,086 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T00:37Z] WARN  17:37:33,097 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T00:37Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T00:37Z] INFO  17:37:33,627 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T00:37Z] INFO  17:37:33,647 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T00:37Z] INFO  17:37:33,726 ProgressMeter -      5:63986641      2.2184714E7    30.0 s            1.0 s       82.5%    36.0 s       6.0 s
[2016-04-15T00:37Z] WARN  17:37:34,030 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T00:37Z] WARN  17:37:34,031 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T00:37Z] INFO  17:37:37,020 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.005680939
[2016-04-15T00:37Z] INFO  17:37:37,021 PairHMM - Total compute time in PairHMM computeLikelihoods() : 0.261904529
[2016-04-15T00:37Z] INFO  17:37:37,021 HaplotypeCaller - Ran local assembly on 842 active regions
[2016-04-15T00:37Z] INFO  17:37:37,064 ProgressMeter -            done      3.3641126E7    33.0 s            0.0 s      100.0%    33.0 s       0.0 s
[2016-04-15T00:37Z] INFO  17:37:37,065 ProgressMeter - Total runtime 33.36 secs, 0.56 min, 0.01 hours
[2016-04-15T00:37Z] INFO  17:37:37,073 MicroScheduler - 9496 reads were filtered out during the traversal out of approximately 126528 total reads (7.51%)
[2016-04-15T00:37Z] INFO  17:37:37,073 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:37Z] INFO  17:37:37,074 MicroScheduler -   -> 9337 reads (7.38% of total) failing DuplicateReadFilter
[2016-04-15T00:37Z] INFO  17:37:37,074 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:37Z] INFO  17:37:37,074 MicroScheduler -   -> 159 reads (0.13% of total) failing HCMappingQualityFilter
[2016-04-15T00:37Z] INFO  17:37:37,074 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:37Z] INFO  17:37:37,075 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:37Z] INFO  17:37:37,075 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:37Z] INFO  17:37:37,075 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:37Z] INFO  17:37:37,171 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.004463036
[2016-04-15T00:37Z] INFO  17:37:37,172 PairHMM - Total compute time in PairHMM computeLikelihoods() : 0.12759567600000002
[2016-04-15T00:37Z] INFO  17:37:37,173 HaplotypeCaller - Ran local assembly on 429 active regions
[2016-04-15T00:37Z] INFO  17:37:37,241 ProgressMeter -            done        9535184.0    23.0 s            2.0 s      100.0%    23.0 s       0.0 s
[2016-04-15T00:37Z] INFO  17:37:37,241 ProgressMeter - Total runtime 23.76 secs, 0.40 min, 0.01 hours
[2016-04-15T00:37Z] INFO  17:37:37,242 MicroScheduler - 4314 reads were filtered out during the traversal out of approximately 57603 total reads (7.49%)
[2016-04-15T00:37Z] INFO  17:37:37,242 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:37Z] INFO  17:37:37,242 MicroScheduler -   -> 4219 reads (7.32% of total) failing DuplicateReadFilter
[2016-04-15T00:37Z] INFO  17:37:37,243 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:37Z] INFO  17:37:37,250 MicroScheduler -   -> 95 reads (0.16% of total) failing HCMappingQualityFilter
[2016-04-15T00:37Z] INFO  17:37:37,250 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:37Z] INFO  17:37:37,250 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:37Z] INFO  17:37:37,250 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:37Z] INFO  17:37:37,251 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:37Z] INFO  17:37:37,770 ProgressMeter -      5:74077685      2.3945709E7    30.0 s            1.0 s       46.7%    64.0 s      34.0 s
[2016-04-15T00:37Z] INFO  17:37:38,576 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:37Z] INFO  17:37:38,803 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:37Z] GATK: HaplotypeCaller
[2016-04-15T00:37Z] INFO  17:37:39,023 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.037454342
[2016-04-15T00:37Z] INFO  17:37:39,024 PairHMM - Total compute time in PairHMM computeLikelihoods() : 30.147722306000002
[2016-04-15T00:37Z] INFO  17:37:39,025 HaplotypeCaller - Ran local assembly on 880 active regions
[2016-04-15T00:37Z] INFO  17:37:39,081 ProgressMeter -            done      3.7254023E7    75.0 s            2.0 s      100.0%    75.0 s       0.0 s
[2016-04-15T00:37Z] INFO  17:37:39,082 ProgressMeter - Total runtime 75.03 secs, 1.25 min, 0.02 hours
[2016-04-15T00:37Z] INFO  17:37:39,082 MicroScheduler - 12438 reads were filtered out during the traversal out of approximately 154545 total reads (8.05%)
[2016-04-15T00:37Z] INFO  17:37:39,084 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:37Z] INFO  17:37:39,084 MicroScheduler -   -> 11802 reads (7.64% of total) failing DuplicateReadFilter
[2016-04-15T00:37Z] INFO  17:37:39,084 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:37Z] INFO  17:37:39,085 MicroScheduler -   -> 636 reads (0.41% of total) failing HCMappingQualityFilter
[2016-04-15T00:37Z] INFO  17:37:39,085 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:37Z] INFO  17:37:39,085 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:37Z] INFO  17:37:39,086 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:37Z] INFO  17:37:39,086 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:37Z] GATK: HaplotypeCaller
[2016-04-15T00:37Z] INFO  17:37:40,111 ProgressMeter -      5:93856000      1.0733977E7    30.0 s            2.0 s       64.5%    46.0 s      16.0 s
[2016-04-15T00:37Z] INFO  17:37:40,813 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:37Z] GATK: HaplotypeCaller
[2016-04-15T00:37Z] INFO  17:37:42,532 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:37Z] INFO  17:37:42,536 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:37Z] INFO  17:37:42,536 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:37Z] INFO  17:37:42,537 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:37Z] INFO  17:37:42,541 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/6/R14-18106_kapa-NGv3-PE100-NGv3-sort-6_62390867_78173120-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/6/R14-18106_kapa-NGv3-PE100-NGv3-6_62390867_78173120-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/6/tx/tmpkB9C1S/R14-18106_kapa-NGv3-PE100-NGv3-6_62390867_78173120.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:37Z] INFO  17:37:42,561 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:37Z] INFO  17:37:42,562 HelpFormatter - Date/Time: 2016/04/14 17:37:42
[2016-04-15T00:37Z] INFO  17:37:42,563 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:37Z] INFO  17:37:42,563 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:37Z] WARN  17:37:42,597 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T00:37Z] INFO  17:37:42,606 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:37Z] INFO  17:37:42,609 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:37Z] INFO  17:37:42,610 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:37Z] INFO  17:37:42,610 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:37Z] WARN  17:37:42,611 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/6/tx/tmpkB9C1S/R14-18106_kapa-NGv3-PE100-NGv3-6_62390867_78173120.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T00:37Z] INFO  17:37:42,615 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/6/R14-18106_kapa-NGv3-PE100-NGv3-sort-6_46598699_62284307-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/6/R14-18106_kapa-NGv3-PE100-NGv3-6_46598699_62284307-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/6/tx/tmpCuyEhA/R14-18106_kapa-NGv3-PE100-NGv3-6_46598699_62284307.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:37Z] INFO  17:37:42,624 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:37Z] INFO  17:37:42,625 HelpFormatter - Date/Time: 2016/04/14 17:37:42
[2016-04-15T00:37Z] INFO  17:37:42,625 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:37Z] INFO  17:37:42,626 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:37Z] WARN  17:37:42,648 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T00:37Z] WARN  17:37:42,655 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/6/tx/tmpCuyEhA/R14-18106_kapa-NGv3-PE100-NGv3-6_46598699_62284307.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T00:37Z] INFO  17:37:42,899 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:37Z] INFO  17:37:42,971 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:37Z] INFO  17:37:43,098 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T00:37Z] INFO  17:37:43,108 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:37Z] INFO  17:37:43,114 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.010014476000000001
[2016-04-15T00:37Z] INFO  17:37:43,115 PairHMM - Total compute time in PairHMM computeLikelihoods() : 1.120263542
[2016-04-15T00:37Z] INFO  17:37:43,116 HaplotypeCaller - Ran local assembly on 959 active regions
[2016-04-15T00:37Z] INFO  17:37:43,154 ProgressMeter -            done      4.4963609E7    46.0 s            1.0 s      100.0%    46.0 s       0.0 s
[2016-04-15T00:37Z] INFO  17:37:43,155 ProgressMeter - Total runtime 46.93 secs, 0.78 min, 0.01 hours
[2016-04-15T00:37Z] INFO  17:37:43,156 MicroScheduler - 18750 reads were filtered out during the traversal out of approximately 193557 total reads (9.69%)
[2016-04-15T00:37Z] INFO  17:37:43,156 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:37Z] INFO  17:37:43,157 MicroScheduler -   -> 14758 reads (7.62% of total) failing DuplicateReadFilter
[2016-04-15T00:37Z] INFO  17:37:43,167 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:37Z] INFO  17:37:43,168 MicroScheduler -   -> 3992 reads (2.06% of total) failing HCMappingQualityFilter
[2016-04-15T00:37Z] INFO  17:37:43,168 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:37Z] INFO  17:37:43,169 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:37Z] INFO  17:37:43,170 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:37Z] INFO  17:37:43,170 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:37Z] INFO  17:37:43,183 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T00:37Z] INFO  17:37:43,193 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:37Z] INFO  17:37:43,193 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-15T00:37Z] INFO  17:37:43,228 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T00:37Z] INFO  17:37:43,293 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.10
[2016-04-15T00:37Z] INFO  17:37:43,320 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T00:37Z] INFO  17:37:43,577 IntervalUtils - Processing 103397 bp from intervals
[2016-04-15T00:37Z] WARN  17:37:43,582 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:37Z] INFO  17:37:43,682 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:37Z] INFO  17:37:43,682 IntervalUtils - Processing 157522 bp from intervals
[2016-04-15T00:37Z] WARN  17:37:43,687 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:37Z] INFO  17:37:43,766 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:37Z] INFO  17:37:43,767 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:37Z] INFO  17:37:43,767 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:37Z] INFO  17:37:43,768 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T00:37Z] INFO  17:37:43,769 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T00:37Z] INFO  17:37:43,770 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T00:37Z] INFO  17:37:43,770 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T00:37Z] INFO  17:37:43,846 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:37Z] INFO  17:37:43,847 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:37Z] INFO  17:37:43,848 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T00:37Z] INFO  17:37:43,849 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T00:37Z] INFO  17:37:43,850 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T00:37Z] INFO  17:37:43,850 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T00:37Z] INFO  17:37:43,994 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T00:37Z] INFO  17:37:44,029 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T00:37Z] INFO  17:37:44,493 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:37Z] INFO  17:37:44,496 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:37Z] INFO  17:37:44,497 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:37Z] INFO  17:37:44,498 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:37Z] INFO  17:37:44,502 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/6/R14-18106_kapa-NGv3-PE100-NGv3-sort-6_78400388_93953258-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/6/R14-18106_kapa-NGv3-PE100-NGv3-6_78400388_93953258-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/6/tx/tmpsDAd85/R14-18106_kapa-NGv3-PE100-NGv3-6_78400388_93953258.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:37Z] INFO  17:37:44,512 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:37Z] INFO  17:37:44,512 HelpFormatter - Date/Time: 2016/04/14 17:37:44
[2016-04-15T00:37Z] INFO  17:37:44,512 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:37Z] INFO  17:37:44,512 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:37Z] WARN  17:37:44,543 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T00:37Z] WARN  17:37:44,546 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/6/tx/tmpsDAd85/R14-18106_kapa-NGv3-PE100-NGv3-6_78400388_93953258.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T00:37Z] INFO  17:37:44,656 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:37Z] INFO  17:37:44,767 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:37Z] INFO  17:37:45,034 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T00:37Z] INFO  17:37:45,057 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:37Z] GATK: HaplotypeCaller
[2016-04-15T00:37Z] INFO  17:37:45,211 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.15
[2016-04-15T00:37Z] INFO  17:37:45,239 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T00:37Z] INFO  17:37:45,760 IntervalUtils - Processing 131721 bp from intervals
[2016-04-15T00:37Z] WARN  17:37:45,769 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:37Z] INFO  17:37:45,933 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:37Z] INFO  17:37:46,061 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:37Z] INFO  17:37:46,062 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:37Z] INFO  17:37:46,063 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T00:37Z] INFO  17:37:46,064 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T00:37Z] INFO  17:37:46,065 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T00:37Z] INFO  17:37:46,065 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T00:37Z] INFO  17:37:46,303 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T00:37Z] INFO  17:37:46,532 ProgressMeter -     5:123983973      1.6654533E7    30.0 s            1.0 s       77.3%    38.0 s       8.0 s
[2016-04-15T00:37Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T00:37Z] INFO  17:37:46,618 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T00:37Z] INFO  17:37:46,619 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T00:37Z] WARN  17:37:46,831 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T00:37Z] WARN  17:37:46,832 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T00:37Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T00:37Z] INFO  17:37:46,902 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T00:37Z] INFO  17:37:46,903 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T00:37Z] WARN  17:37:47,204 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T00:37Z] WARN  17:37:47,205 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T00:37Z] INFO  17:37:48,012 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.007530683000000001
[2016-04-15T00:37Z] INFO  17:37:48,012 PairHMM - Total compute time in PairHMM computeLikelihoods() : 0.40855154600000004
[2016-04-15T00:37Z] INFO  17:37:48,013 HaplotypeCaller - Ran local assembly on 787 active regions
[2016-04-15T00:37Z] INFO  17:37:48,080 ProgressMeter -            done      3.2848972E7    37.0 s            1.0 s      100.0%    37.0 s       0.0 s
[2016-04-15T00:37Z] INFO  17:37:48,081 ProgressMeter - Total runtime 37.99 secs, 0.63 min, 0.01 hours
[2016-04-15T00:37Z] INFO  17:37:48,081 MicroScheduler - 9126 reads were filtered out during the traversal out of approximately 124700 total reads (7.32%)
[2016-04-15T00:37Z] INFO  17:37:48,081 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:37Z] INFO  17:37:48,082 MicroScheduler -   -> 8992 reads (7.21% of total) failing DuplicateReadFilter
[2016-04-15T00:37Z] INFO  17:37:48,082 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:37Z] INFO  17:37:48,082 MicroScheduler -   -> 134 reads (0.11% of total) failing HCMappingQualityFilter
[2016-04-15T00:37Z] INFO  17:37:48,082 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:37Z] INFO  17:37:48,083 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:37Z] INFO  17:37:48,083 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:37Z] INFO  17:37:48,083 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:37Z] INFO  17:37:48,093 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:37Z] INFO  17:37:48,097 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:37Z] INFO  17:37:48,097 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:37Z] INFO  17:37:48,098 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:37Z] INFO  17:37:48,105 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/6/R14-18106_kapa-NGv3-PE100-NGv3-sort-6_93955015_109466584-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/6/R14-18106_kapa-NGv3-PE100-NGv3-6_93955015_109466584-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/6/tx/tmpHOMZYe/R14-18106_kapa-NGv3-PE100-NGv3-6_93955015_109466584.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:37Z] INFO  17:37:48,115 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:37Z] INFO  17:37:48,116 HelpFormatter - Date/Time: 2016/04/14 17:37:48
[2016-04-15T00:37Z] INFO  17:37:48,117 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:37Z] INFO  17:37:48,117 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:37Z] WARN  17:37:48,193 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T00:37Z] WARN  17:37:48,205 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/6/tx/tmpHOMZYe/R14-18106_kapa-NGv3-PE100-NGv3-6_93955015_109466584.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T00:37Z] INFO  17:37:48,404 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:37Z] INFO  17:37:48,567 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T00:37Z] INFO  17:37:48,577 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:37Z] INFO  17:37:48,671 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.09
[2016-04-15T00:37Z] INFO  17:37:48,696 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T00:37Z] INFO  17:37:48,800 ProgressMeter -     5:134686603      2.6111834E7    30.0 s            1.0 s       25.6%   116.0 s      86.0 s
[2016-04-15T00:37Z] INFO  17:37:49,028 IntervalUtils - Processing 95525 bp from intervals
[2016-04-15T00:37Z] WARN  17:37:49,033 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:37Z] INFO  17:37:49,119 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:37Z] INFO  17:37:49,195 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:37Z] INFO  17:37:49,196 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:37Z] INFO  17:37:49,197 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T00:37Z] INFO  17:37:49,197 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T00:37Z] INFO  17:37:49,198 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T00:37Z] INFO  17:37:49,198 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T00:37Z] INFO  17:37:49,402 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T00:37Z] INFO  17:37:49,406 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:37Z] INFO  17:37:49,552 ProgressMeter -     5:149460561      1.6500519E7    30.0 s            1.0 s       40.7%    73.0 s      43.0 s
[2016-04-15T00:37Z] GATK: HaplotypeCaller
[2016-04-15T00:37Z] INFO  17:37:49,896 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.046029301
[2016-04-15T00:37Z] INFO  17:37:49,897 PairHMM - Total compute time in PairHMM computeLikelihoods() : 48.048118627
[2016-04-15T00:37Z] INFO  17:37:49,898 HaplotypeCaller - Ran local assembly on 904 active regions
[2016-04-15T00:37Z] INFO  17:37:49,962 ProgressMeter -            done      3.3552483E7   107.0 s            3.0 s      100.0%   107.0 s       0.0 s
[2016-04-15T00:37Z] INFO  17:37:49,962 ProgressMeter - Total runtime 107.26 secs, 1.79 min, 0.03 hours
[2016-04-15T00:37Z] INFO  17:37:49,962 MicroScheduler - 27175 reads were filtered out during the traversal out of approximately 179965 total reads (15.10%)
[2016-04-15T00:37Z] INFO  17:37:49,963 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:37Z] INFO  17:37:49,963 MicroScheduler -   -> 13255 reads (7.37% of total) failing DuplicateReadFilter
[2016-04-15T00:37Z] INFO  17:37:49,963 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:37Z] INFO  17:37:49,964 MicroScheduler -   -> 13920 reads (7.73% of total) failing HCMappingQualityFilter
[2016-04-15T00:37Z] INFO  17:37:49,964 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:37Z] INFO  17:37:49,964 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:37Z] INFO  17:37:49,964 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:37Z] INFO  17:37:49,965 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:37Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T00:37Z] INFO  17:37:50,759 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T00:37Z] INFO  17:37:50,760 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T00:37Z] INFO  17:37:50,779 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.007344827000000001
[2016-04-15T00:37Z] INFO  17:37:50,780 PairHMM - Total compute time in PairHMM computeLikelihoods() : 0.499516919
[2016-04-15T00:37Z] INFO  17:37:50,780 HaplotypeCaller - Ran local assembly on 1306 active regions
[2016-04-15T00:37Z] INFO  17:37:50,799 ProgressMeter -            done      8.6588753E7    48.0 s            0.0 s      100.0%    48.0 s       0.0 s
[2016-04-15T00:37Z] INFO  17:37:50,800 ProgressMeter - Total runtime 48.07 secs, 0.80 min, 0.01 hours
[2016-04-15T00:37Z] INFO  17:37:50,800 MicroScheduler - 16628 reads were filtered out during the traversal out of approximately 216766 total reads (7.67%)
[2016-04-15T00:37Z] INFO  17:37:50,808 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:37Z] INFO  17:37:50,809 MicroScheduler -   -> 16390 reads (7.56% of total) failing DuplicateReadFilter
[2016-04-15T00:37Z] INFO  17:37:50,810 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:37Z] INFO  17:37:50,811 MicroScheduler -   -> 238 reads (0.11% of total) failing HCMappingQualityFilter
[2016-04-15T00:37Z] INFO  17:37:50,811 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:37Z] INFO  17:37:50,812 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:37Z] INFO  17:37:50,812 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:37Z] INFO  17:37:50,813 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:37Z] WARN  17:37:51,030 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T00:37Z] WARN  17:37:51,031 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T00:37Z] INFO  17:37:51,372 ProgressMeter -     5:171479933      1.8685026E7    30.0 s            1.0 s       72.6%    41.0 s      11.0 s
[2016-04-15T00:37Z] INFO  17:37:51,546 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:37Z] GATK: HaplotypeCaller
[2016-04-15T00:37Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T00:37Z] INFO  17:37:52,069 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T00:37Z] INFO  17:37:52,070 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T00:37Z] INFO  17:37:52,223 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.007736115000000001
[2016-04-15T00:37Z] INFO  17:37:52,224 PairHMM - Total compute time in PairHMM computeLikelihoods() : 0.35581522400000004
[2016-04-15T00:37Z] INFO  17:37:52,225 HaplotypeCaller - Ran local assembly on 759 active regions
[2016-04-15T00:37Z] INFO  17:37:52,317 ProgressMeter -            done      2.8586597E7    35.0 s            1.0 s      100.0%    35.0 s       0.0 s
[2016-04-15T00:37Z] INFO  17:37:52,318 ProgressMeter - Total runtime 35.81 secs, 0.60 min, 0.01 hours
[2016-04-15T00:37Z] INFO  17:37:52,319 MicroScheduler - 9700 reads were filtered out during the traversal out of approximately 127010 total reads (7.64%)
[2016-04-15T00:37Z] INFO  17:37:52,319 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:37Z] INFO  17:37:52,319 MicroScheduler -   -> 9573 reads (7.54% of total) failing DuplicateReadFilter
[2016-04-15T00:37Z] INFO  17:37:52,319 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:37Z] INFO  17:37:52,320 MicroScheduler -   -> 127 reads (0.10% of total) failing HCMappingQualityFilter
[2016-04-15T00:37Z] INFO  17:37:52,320 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:37Z] INFO  17:37:52,320 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:37Z] INFO  17:37:52,319 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:37Z] INFO  17:37:52,320 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:37Z] INFO  17:37:52,320 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:37Z] WARN  17:37:52,347 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T00:37Z] WARN  17:37:52,348 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T00:37Z] GATK: HaplotypeCaller
[2016-04-15T00:37Z] INFO  17:37:52,687 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:37Z] INFO  17:37:52,690 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:37Z] INFO  17:37:52,691 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:37Z] INFO  17:37:52,691 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:37Z] INFO  17:37:52,696 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/6/R14-18106_kapa-NGv3-PE100-NGv3-sort-6_109467960_124979532-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/6/R14-18106_kapa-NGv3-PE100-NGv3-6_109467960_124979532-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/6/tx/tmpFLlurf/R14-18106_kapa-NGv3-PE100-NGv3-6_109467960_124979532.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:37Z] INFO  17:37:52,719 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:37Z] INFO  17:37:52,720 HelpFormatter - Date/Time: 2016/04/14 17:37:52
[2016-04-15T00:37Z] INFO  17:37:52,720 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:37Z] INFO  17:37:52,721 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:37Z] WARN  17:37:52,745 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T00:37Z] WARN  17:37:52,748 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/6/tx/tmpFLlurf/R14-18106_kapa-NGv3-PE100-NGv3-6_109467960_124979532.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T00:37Z] INFO  17:37:52,993 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:37Z] INFO  17:37:53,175 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T00:37Z] INFO  17:37:53,191 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:37Z] INFO  17:37:53,289 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.10
[2016-04-15T00:37Z] INFO  17:37:53,325 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T00:37Z] INFO  17:37:53,784 IntervalUtils - Processing 147815 bp from intervals
[2016-04-15T00:37Z] WARN  17:37:53,789 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:37Z] INFO  17:37:53,827 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:37Z] INFO  17:37:53,935 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:37Z] INFO  17:37:54,058 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:37Z] INFO  17:37:54,059 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:37Z] INFO  17:37:54,059 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T00:37Z] INFO  17:37:54,060 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T00:37Z] INFO  17:37:54,068 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T00:37Z] INFO  17:37:54,069 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T00:37Z] GATK: HaplotypeCaller
[2016-04-15T00:37Z] INFO  17:37:54,314 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T00:37Z] INFO  17:37:55,196 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:37Z] INFO  17:37:55,200 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:37Z] INFO  17:37:55,200 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:37Z] INFO  17:37:55,201 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:37Z] INFO  17:37:55,207 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/6/R14-18106_kapa-NGv3-PE100-NGv3-sort-6_125112484_142397186-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/6/R14-18106_kapa-NGv3-PE100-NGv3-6_125112484_142397186-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/6/tx/tmpDUmHnN/R14-18106_kapa-NGv3-PE100-NGv3-6_125112484_142397186.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:37Z] INFO  17:37:55,240 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:37Z] INFO  17:37:55,241 HelpFormatter - Date/Time: 2016/04/14 17:37:55
[2016-04-15T00:37Z] INFO  17:37:55,241 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:37Z] INFO  17:37:55,242 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:37Z] WARN  17:37:55,269 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T00:37Z] WARN  17:37:55,277 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/6/tx/tmpDUmHnN/R14-18106_kapa-NGv3-PE100-NGv3-6_125112484_142397186.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T00:37Z] INFO  17:37:55,468 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:37Z] INFO  17:37:55,598 ProgressMeter -     5:178043949      1.6287276E7    30.0 s            1.0 s       51.0%    58.0 s      28.0 s
[2016-04-15T00:37Z] INFO  17:37:55,804 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T00:37Z] INFO  17:37:55,814 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:37Z] INFO  17:37:55,910 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.10
[2016-04-15T00:37Z] INFO  17:37:55,955 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T00:37Z] INFO  17:37:55,987 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:37Z] INFO  17:37:55,989 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:37Z] INFO  17:37:55,990 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:37Z] INFO  17:37:55,990 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:37Z] INFO  17:37:56,004 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/6/R14-18106_kapa-NGv3-PE100-NGv3-sort-6_142399691_157963777-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/6/R14-18106_kapa-NGv3-PE100-NGv3-6_142399691_157963777-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/6/tx/tmph18yh6/R14-18106_kapa-NGv3-PE100-NGv3-6_142399691_157963777.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:37Z] INFO  17:37:56,017 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:37Z] INFO  17:37:56,018 HelpFormatter - Date/Time: 2016/04/14 17:37:55
[2016-04-15T00:37Z] INFO  17:37:56,018 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:37Z] INFO  17:37:56,018 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:37Z] WARN  17:37:56,064 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T00:37Z] WARN  17:37:56,078 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/6/tx/tmph18yh6/R14-18106_kapa-NGv3-PE100-NGv3-6_142399691_157963777.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T00:37Z] INFO  17:37:56,292 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:37Z] INFO  17:37:56,563 IntervalUtils - Processing 156964 bp from intervals
[2016-04-15T00:37Z] WARN  17:37:56,572 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:37Z] INFO  17:37:56,650 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T00:37Z] INFO  17:37:56,670 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:37Z] INFO  17:37:56,737 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:37Z] INFO  17:37:56,755 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-15T00:37Z] INFO  17:37:56,774 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T00:37Z] INFO  17:37:56,827 ProgressMeter -       6:7290164        8384645.0    30.0 s            3.0 s       45.2%    66.0 s      36.0 s
[2016-04-15T00:37Z] INFO  17:37:56,892 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:37Z] INFO  17:37:56,899 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:37Z] INFO  17:37:56,900 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T00:37Z] INFO  17:37:56,901 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T00:37Z] INFO  17:37:56,918 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T00:37Z] INFO  17:37:56,919 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T00:37Z] INFO  17:37:57,197 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T00:37Z] INFO  17:37:57,237 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:37Z] INFO  17:37:57,240 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:37Z] INFO  17:37:57,241 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:37Z] INFO  17:37:57,241 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:37Z] INFO  17:37:57,245 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/6/R14-18106_kapa-NGv3-PE100-NGv3-sort-6_158013810_171115067-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/6/R14-18106_kapa-NGv3-PE100-NGv3-6_158013810_171115067-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/6/tx/tmphC7C69/R14-18106_kapa-NGv3-PE100-NGv3-6_158013810_171115067.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:37Z] INFO  17:37:57,264 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:37Z] INFO  17:37:57,265 HelpFormatter - Date/Time: 2016/04/14 17:37:57
[2016-04-15T00:37Z] INFO  17:37:57,266 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:37Z] INFO  17:37:57,266 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:37Z] INFO  17:37:57,304 IntervalUtils - Processing 183871 bp from intervals
[2016-04-15T00:37Z] WARN  17:37:57,300 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T00:37Z] WARN  17:37:57,307 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/6/tx/tmphC7C69/R14-18106_kapa-NGv3-PE100-NGv3-6_158013810_171115067.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T00:37Z] WARN  17:37:57,309 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:37Z] INFO  17:37:57,450 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:37Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T00:37Z] INFO  17:37:57,511 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T00:37Z] INFO  17:37:57,528 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T00:37Z] INFO  17:37:57,577 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:37Z] INFO  17:37:57,593 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:37Z] INFO  17:37:57,595 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:37Z] INFO  17:37:57,596 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T00:37Z] INFO  17:37:57,596 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T00:37Z] INFO  17:37:57,609 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T00:37Z] INFO  17:37:57,610 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T00:37Z] INFO  17:37:57,772 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T00:37Z] INFO  17:37:57,783 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:37Z] WARN  17:37:57,862 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T00:37Z] WARN  17:37:57,863 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T00:37Z] INFO  17:37:57,863 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-15T00:37Z] INFO  17:37:57,888 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T00:37Z] INFO  17:37:57,893 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T00:37Z] INFO  17:37:58,019 ProgressMeter -      6:25850987      1.6416186E7    30.0 s            1.0 s       31.5%    95.0 s      65.0 s
[2016-04-15T00:37Z] INFO  17:37:58,371 IntervalUtils - Processing 143202 bp from intervals
[2016-04-15T00:37Z] WARN  17:37:58,390 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:37Z] INFO  17:37:58,534 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:37Z] INFO  17:37:58,638 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:37Z] INFO  17:37:58,638 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:37Z] INFO  17:37:58,639 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T00:37Z] INFO  17:37:58,639 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T00:37Z] INFO  17:37:58,655 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T00:37Z] INFO  17:37:58,656 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T00:37Z] INFO  17:37:58,814 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T00:37Z] INFO  17:37:59,370 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.008941351
[2016-04-15T00:37Z] INFO  17:37:59,370 PairHMM - Total compute time in PairHMM computeLikelihoods() : 0.5702170430000001
[2016-04-15T00:37Z] INFO  17:37:59,370 HaplotypeCaller - Ran local assembly on 1483 active regions
[2016-04-15T00:37Z] INFO  17:37:59,430 ProgressMeter -            done     1.03497862E8    51.0 s            0.0 s      100.0%    51.0 s       0.0 s
[2016-04-15T00:37Z] INFO  17:37:59,430 ProgressMeter - Total runtime 51.69 secs, 0.86 min, 0.01 hours
[2016-04-15T00:37Z] INFO  17:37:59,431 MicroScheduler - 28854 reads were filtered out during the traversal out of approximately 231759 total reads (12.45%)
[2016-04-15T00:37Z] INFO  17:37:59,431 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:37Z] INFO  17:37:59,432 MicroScheduler -   -> 16420 reads (7.08% of total) failing DuplicateReadFilter
[2016-04-15T00:37Z] INFO  17:37:59,432 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:37Z] INFO  17:37:59,432 MicroScheduler -   -> 12434 reads (5.37% of total) failing HCMappingQualityFilter
[2016-04-15T00:37Z] INFO  17:37:59,432 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:37Z] INFO  17:37:59,433 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:37Z] INFO  17:37:59,433 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:37Z] INFO  17:37:59,433 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:38Z] INFO  17:38:00,682 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:38Z] INFO  17:38:00,948 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.018945470000000002
[2016-04-15T00:38Z] INFO  17:38:00,950 PairHMM - Total compute time in PairHMM computeLikelihoods() : 0.687431321
[2016-04-15T00:38Z] INFO  17:38:00,950 HaplotypeCaller - Ran local assembly on 770 active regions
[2016-04-15T00:38Z] GATK: HaplotypeCaller
[2016-04-15T00:38Z] INFO  17:38:01,049 ProgressMeter -            done      2.8976366E7    39.0 s            1.0 s      100.0%    39.0 s       0.0 s
[2016-04-15T00:38Z] INFO  17:38:01,050 ProgressMeter - Total runtime 39.72 secs, 0.66 min, 0.01 hours
[2016-04-15T00:38Z] INFO  17:38:01,051 MicroScheduler - 11972 reads were filtered out during the traversal out of approximately 152926 total reads (7.83%)
[2016-04-15T00:38Z] INFO  17:38:01,051 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:38Z] INFO  17:38:01,052 MicroScheduler -   -> 11795 reads (7.71% of total) failing DuplicateReadFilter
[2016-04-15T00:38Z] INFO  17:38:01,054 ProgressMeter -      6:31516061         558998.0    30.0 s           53.0 s        3.3%    15.2 m      14.7 m
[2016-04-15T00:38Z] INFO  17:38:01,053 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:38Z] INFO  17:38:01,053 MicroScheduler -   -> 177 reads (0.12% of total) failing HCMappingQualityFilter
[2016-04-15T00:38Z] INFO  17:38:01,053 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:38Z] INFO  17:38:01,053 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:38Z] INFO  17:38:01,054 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:38Z] INFO  17:38:01,054 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:38Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T00:38Z] INFO  17:38:01,331 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T00:38Z] INFO  17:38:01,343 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T00:38Z] WARN  17:38:01,808 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T00:38Z] WARN  17:38:01,808 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T00:38Z] INFO  17:38:02,535 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:38Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T00:38Z] GATK: HaplotypeCaller
[2016-04-15T00:38Z] INFO  17:38:02,815 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T00:38Z] INFO  17:38:02,824 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T00:38Z] WARN  17:38:03,156 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T00:38Z] WARN  17:38:03,167 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T00:38Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T00:38Z] INFO  17:38:03,501 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T00:38Z] INFO  17:38:03,502 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T00:38Z] WARN  17:38:03,814 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T00:38Z] WARN  17:38:03,815 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T00:38Z] INFO  17:38:04,553 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:38Z] INFO  17:38:04,566 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:38Z] INFO  17:38:04,567 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:38Z] INFO  17:38:04,568 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:38Z] INFO  17:38:04,572 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/7/R14-18106_kapa-NGv3-PE100-NGv3-sort-7_0_15584548-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/7/R14-18106_kapa-NGv3-PE100-NGv3-7_0_15584548-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/7/tx/tmpUwSd2y/R14-18106_kapa-NGv3-PE100-NGv3-7_0_15584548.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:38Z] INFO  17:38:04,593 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:38Z] INFO  17:38:04,594 HelpFormatter - Date/Time: 2016/04/14 17:38:04
[2016-04-15T00:38Z] INFO  17:38:04,595 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:38Z] INFO  17:38:04,595 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:38Z] WARN  17:38:04,632 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T00:38Z] WARN  17:38:04,645 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/7/tx/tmpUwSd2y/R14-18106_kapa-NGv3-PE100-NGv3-7_0_15584548.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T00:38Z] INFO  17:38:04,970 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:38Z] INFO  17:38:05,214 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T00:38Z] INFO  17:38:05,224 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:38Z] INFO  17:38:05,339 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.11
[2016-04-15T00:38Z] INFO  17:38:05,354 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T00:38Z] INFO  17:38:05,824 IntervalUtils - Processing 187602 bp from intervals
[2016-04-15T00:38Z] WARN  17:38:05,830 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:38Z] INFO  17:38:05,956 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:38Z] INFO  17:38:06,061 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:38Z] INFO  17:38:06,063 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:38Z] INFO  17:38:06,063 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T00:38Z] INFO  17:38:06,064 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T00:38Z] INFO  17:38:06,074 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T00:38Z] INFO  17:38:06,074 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T00:38Z] INFO  17:38:06,341 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T00:38Z] INFO  17:38:06,486 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:38Z] INFO  17:38:06,489 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:38Z] INFO  17:38:06,490 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:38Z] INFO  17:38:06,491 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:38Z] INFO  17:38:06,495 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/7/R14-18106_kapa-NGv3-PE100-NGv3-sort-7_15599765_31117713-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/7/R14-18106_kapa-NGv3-PE100-NGv3-7_15599765_31117713-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/7/tx/tmpjcX7kC/R14-18106_kapa-NGv3-PE100-NGv3-7_15599765_31117713.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:38Z] INFO  17:38:06,509 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:38Z] INFO  17:38:06,510 HelpFormatter - Date/Time: 2016/04/14 17:38:06
[2016-04-15T00:38Z] INFO  17:38:06,510 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:38Z] INFO  17:38:06,511 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:38Z] WARN  17:38:06,549 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T00:38Z] WARN  17:38:06,552 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/7/tx/tmpjcX7kC/R14-18106_kapa-NGv3-PE100-NGv3-7_15599765_31117713.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T00:38Z] INFO  17:38:06,755 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:38Z] INFO  17:38:06,903 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T00:38Z] INFO  17:38:06,913 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:38Z] INFO  17:38:06,999 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-15T00:38Z] INFO  17:38:07,025 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T00:38Z] INFO  17:38:07,533 IntervalUtils - Processing 149727 bp from intervals
[2016-04-15T00:38Z] WARN  17:38:07,538 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:38Z] INFO  17:38:07,679 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:38Z] INFO  17:38:07,822 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:38Z] INFO  17:38:07,824 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:38Z] INFO  17:38:07,824 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T00:38Z] INFO  17:38:07,825 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T00:38Z] INFO  17:38:07,837 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T00:38Z] INFO  17:38:07,838 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T00:38Z] INFO  17:38:08,037 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T00:38Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T00:38Z] INFO  17:38:10,169 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T00:38Z] INFO  17:38:10,169 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T00:38Z] WARN  17:38:10,466 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T00:38Z] WARN  17:38:10,467 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T00:38Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T00:38Z] INFO  17:38:11,972 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T00:38Z] INFO  17:38:11,973 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T00:38Z] WARN  17:38:12,427 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T00:38Z] WARN  17:38:12,439 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T00:38Z] INFO  17:38:13,793 ProgressMeter -      6:76024826      2.1788991E7    30.0 s            1.0 s       88.7%    33.0 s       3.0 s
[2016-04-15T00:38Z] INFO  17:38:13,868 ProgressMeter -      6:54095669      2.2693957E7    30.0 s            1.0 s       59.1%    50.0 s      20.0 s
[2016-04-15T00:38Z] INFO  17:38:15,182 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.011096987
[2016-04-15T00:38Z] INFO  17:38:15,183 PairHMM - Total compute time in PairHMM computeLikelihoods() : 0.8250126590000001
[2016-04-15T00:38Z] INFO  17:38:15,184 HaplotypeCaller - Ran local assembly on 1201 active regions
[2016-04-15T00:38Z] INFO  17:38:15,244 ProgressMeter -            done      5.3274727E7    49.0 s            0.0 s      100.0%    49.0 s       0.0 s
[2016-04-15T00:38Z] INFO  17:38:15,244 ProgressMeter - Total runtime 49.67 secs, 0.83 min, 0.01 hours
[2016-04-15T00:38Z] INFO  17:38:15,245 MicroScheduler - 30415 reads were filtered out during the traversal out of approximately 268946 total reads (11.31%)
[2016-04-15T00:38Z] INFO  17:38:15,245 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:38Z] INFO  17:38:15,245 MicroScheduler -   -> 19539 reads (7.27% of total) failing DuplicateReadFilter
[2016-04-15T00:38Z] INFO  17:38:15,245 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:38Z] INFO  17:38:15,246 MicroScheduler -   -> 10876 reads (4.04% of total) failing HCMappingQualityFilter
[2016-04-15T00:38Z] INFO  17:38:15,246 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:38Z] INFO  17:38:15,246 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:38Z] INFO  17:38:15,246 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:38Z] INFO  17:38:15,247 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:38Z] INFO  17:38:15,737 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.006350856
[2016-04-15T00:38Z] INFO  17:38:15,737 PairHMM - Total compute time in PairHMM computeLikelihoods() : 0.38120595100000004
[2016-04-15T00:38Z] INFO  17:38:15,737 HaplotypeCaller - Ran local assembly on 777 active regions
[2016-04-15T00:38Z] INFO  17:38:15,806 ProgressMeter -            done      2.9471788E7    32.0 s            1.0 s      100.0%    32.0 s       0.0 s
[2016-04-15T00:38Z] INFO  17:38:15,806 ProgressMeter - Total runtime 32.04 secs, 0.53 min, 0.01 hours
[2016-04-15T00:38Z] INFO  17:38:15,808 MicroScheduler - 10333 reads were filtered out during the traversal out of approximately 116742 total reads (8.85%)
[2016-04-15T00:38Z] INFO  17:38:15,808 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:38Z] INFO  17:38:15,809 MicroScheduler -   -> 8593 reads (7.36% of total) failing DuplicateReadFilter
[2016-04-15T00:38Z] INFO  17:38:15,809 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:38Z] INFO  17:38:15,809 MicroScheduler -   -> 1740 reads (1.49% of total) failing HCMappingQualityFilter
[2016-04-15T00:38Z] INFO  17:38:15,809 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:38Z] INFO  17:38:15,810 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:38Z] INFO  17:38:15,810 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:38Z] INFO  17:38:15,810 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:38Z] INFO  17:38:16,084 ProgressMeter -      6:88331731      1.7235615E7    30.0 s            1.0 s       64.9%    46.0 s      16.0 s
[2016-04-15T00:38Z] INFO  17:38:16,567 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:38Z] GATK: HaplotypeCaller
[2016-04-15T00:38Z] INFO  17:38:17,221 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:38Z] INFO  17:38:17,525 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.013754081000000001
[2016-04-15T00:38Z] INFO  17:38:17,526 PairHMM - Total compute time in PairHMM computeLikelihoods() : 1.107253877
[2016-04-15T00:38Z] INFO  17:38:17,527 HaplotypeCaller - Ran local assembly on 987 active regions
[2016-04-15T00:38Z] GATK: HaplotypeCaller
[2016-04-15T00:38Z] INFO  17:38:17,589 ProgressMeter -            done      4.2296058E7    50.0 s            1.0 s      100.0%    50.0 s       0.0 s
[2016-04-15T00:38Z] INFO  17:38:17,589 ProgressMeter - Total runtime 50.78 secs, 0.85 min, 0.01 hours
[2016-04-15T00:38Z] INFO  17:38:17,589 MicroScheduler - 20472 reads were filtered out during the traversal out of approximately 189394 total reads (10.81%)
[2016-04-15T00:38Z] INFO  17:38:17,590 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:38Z] INFO  17:38:17,590 MicroScheduler -   -> 13940 reads (7.36% of total) failing DuplicateReadFilter
[2016-04-15T00:38Z] INFO  17:38:17,590 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:38Z] INFO  17:38:17,590 MicroScheduler -   -> 6532 reads (3.45% of total) failing HCMappingQualityFilter
[2016-04-15T00:38Z] INFO  17:38:17,590 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:38Z] INFO  17:38:17,591 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:38Z] INFO  17:38:17,591 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:38Z] INFO  17:38:17,591 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:38Z] INFO  17:38:18,802 ProgressMeter -     5:140187300     1.08321246E8    60.0 s            0.0 s       56.4%   106.0 s      46.0 s
[2016-04-15T00:38Z] INFO  17:38:19,174 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:38Z] INFO  17:38:19,208 ProgressMeter -     6:108986058       1.964312E7    30.0 s            1.0 s       94.4%    31.0 s       1.0 s
[2016-04-15T00:38Z] INFO  17:38:19,337 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.029959172000000003
[2016-04-15T00:38Z] INFO  17:38:19,338 PairHMM - Total compute time in PairHMM computeLikelihoods() : 1.652516506
[2016-04-15T00:38Z] INFO  17:38:19,338 HaplotypeCaller - Ran local assembly on 1526 active regions
[2016-04-15T00:38Z] INFO  17:38:19,393 ProgressMeter -            done     1.03846414E8    59.0 s            0.0 s      100.0%    59.0 s       0.0 s
[2016-04-15T00:38Z] INFO  17:38:19,394 ProgressMeter - Total runtime 59.87 secs, 1.00 min, 0.02 hours
[2016-04-15T00:38Z] INFO  17:38:19,395 MicroScheduler - 23401 reads were filtered out during the traversal out of approximately 302878 total reads (7.73%)
[2016-04-15T00:38Z] INFO  17:38:19,395 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:38Z] INFO  17:38:19,395 MicroScheduler -   -> 23164 reads (7.65% of total) failing DuplicateReadFilter
[2016-04-15T00:38Z] INFO  17:38:19,395 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:38Z] INFO  17:38:19,396 MicroScheduler -   -> 237 reads (0.08% of total) failing HCMappingQualityFilter
[2016-04-15T00:38Z] INFO  17:38:19,396 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:38Z] INFO  17:38:19,396 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:38Z] INFO  17:38:19,396 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:38Z] INFO  17:38:19,397 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:38Z] GATK: HaplotypeCaller
[2016-04-15T00:38Z] INFO  17:38:19,859 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:38Z] INFO  17:38:19,863 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:38Z] INFO  17:38:19,864 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:38Z] INFO  17:38:19,864 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:38Z] INFO  17:38:19,876 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/7/R14-18106_kapa-NGv3-PE100-NGv3-sort-7_31120227_47317818-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/7/R14-18106_kapa-NGv3-PE100-NGv3-7_31120227_47317818-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/7/tx/tmpEfhVAM/R14-18106_kapa-NGv3-PE100-NGv3-7_31120227_47317818.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:38Z] INFO  17:38:19,891 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:38Z] INFO  17:38:19,892 HelpFormatter - Date/Time: 2016/04/14 17:38:19
[2016-04-15T00:38Z] INFO  17:38:19,892 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:38Z] INFO  17:38:19,892 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:38Z] WARN  17:38:19,919 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T00:38Z] WARN  17:38:19,923 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/7/tx/tmpEfhVAM/R14-18106_kapa-NGv3-PE100-NGv3-7_31120227_47317818.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T00:38Z] INFO  17:38:20,122 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.006534392
[2016-04-15T00:38Z] INFO  17:38:20,124 PairHMM - Total compute time in PairHMM computeLikelihoods() : 0.20993250100000002
[2016-04-15T00:38Z] INFO  17:38:20,124 HaplotypeCaller - Ran local assembly on 683 active regions
[2016-04-15T00:38Z] INFO  17:38:20,190 ProgressMeter -            done      2.2700296E7    30.0 s            1.0 s      100.0%    30.0 s       0.0 s
[2016-04-15T00:38Z] INFO  17:38:20,191 ProgressMeter - Total runtime 31.00 secs, 0.52 min, 0.01 hours
[2016-04-15T00:38Z] INFO  17:38:20,191 MicroScheduler - 8598 reads were filtered out during the traversal out of approximately 106159 total reads (8.10%)
[2016-04-15T00:38Z] INFO  17:38:20,192 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:38Z] INFO  17:38:20,192 MicroScheduler -   -> 7738 reads (7.29% of total) failing DuplicateReadFilter
[2016-04-15T00:38Z] INFO  17:38:20,192 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:38Z] INFO  17:38:20,192 MicroScheduler -   -> 860 reads (0.81% of total) failing HCMappingQualityFilter
[2016-04-15T00:38Z] INFO  17:38:20,193 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:38Z] INFO  17:38:20,193 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:38Z] INFO  17:38:20,193 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:38Z] INFO  17:38:20,194 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:38Z] INFO  17:38:20,189 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:38Z] INFO  17:38:20,437 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T00:38Z] INFO  17:38:20,448 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:38Z] INFO  17:38:20,540 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.09
[2016-04-15T00:38Z] INFO  17:38:20,554 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:38Z] INFO  17:38:20,558 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:38Z] INFO  17:38:20,559 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:38Z] INFO  17:38:20,559 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:38Z] INFO  17:38:20,565 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/7/R14-18106_kapa-NGv3-PE100-NGv3-sort-7_47319761_63093154-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/7/R14-18106_kapa-NGv3-PE100-NGv3-7_47319761_63093154-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/7/tx/tmpzJrAq2/R14-18106_kapa-NGv3-PE100-NGv3-7_47319761_63093154.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:38Z] INFO  17:38:20,575 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:38Z] INFO  17:38:20,576 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T00:38Z] INFO  17:38:20,586 HelpFormatter - Date/Time: 2016/04/14 17:38:20
[2016-04-15T00:38Z] INFO  17:38:20,587 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:38Z] INFO  17:38:20,588 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:38Z] WARN  17:38:20,628 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T00:38Z] WARN  17:38:20,632 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/7/tx/tmpzJrAq2/R14-18106_kapa-NGv3-PE100-NGv3-7_47319761_63093154.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T00:38Z] INFO  17:38:20,762 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:38Z] INFO  17:38:20,822 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:38Z] INFO  17:38:20,972 IntervalUtils - Processing 138106 bp from intervals
[2016-04-15T00:38Z] WARN  17:38:20,977 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:38Z] INFO  17:38:21,059 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T00:38Z] INFO  17:38:21,080 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:38Z] INFO  17:38:21,088 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:38Z] GATK: HaplotypeCaller
[2016-04-15T00:38Z] INFO  17:38:21,153 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-15T00:38Z] INFO  17:38:21,181 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T00:38Z] INFO  17:38:21,192 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:38Z] INFO  17:38:21,200 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:38Z] INFO  17:38:21,201 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T00:38Z] INFO  17:38:21,201 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T00:38Z] INFO  17:38:21,212 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T00:38Z] INFO  17:38:21,213 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T00:38Z] INFO  17:38:21,488 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T00:38Z] INFO  17:38:21,646 IntervalUtils - Processing 74873 bp from intervals
[2016-04-15T00:38Z] WARN  17:38:21,666 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:38Z] INFO  17:38:21,748 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:38Z] INFO  17:38:21,793 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:38Z] INFO  17:38:21,926 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:38Z] INFO  17:38:21,928 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:38Z] INFO  17:38:21,928 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T00:38Z] INFO  17:38:21,929 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T00:38Z] INFO  17:38:21,941 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T00:38Z] INFO  17:38:21,942 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T00:38Z] GATK: HaplotypeCaller
[2016-04-15T00:38Z] INFO  17:38:22,263 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T00:38Z] INFO  17:38:22,495 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:38Z] INFO  17:38:22,498 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:38Z] INFO  17:38:22,499 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:38Z] INFO  17:38:22,499 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:38Z] INFO  17:38:22,504 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/7/R14-18106_kapa-NGv3-PE100-NGv3-sort-7_63095909_78636522-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/7/R14-18106_kapa-NGv3-PE100-NGv3-7_63095909_78636522-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/7/tx/tmp9uHXTo/R14-18106_kapa-NGv3-PE100-NGv3-7_63095909_78636522.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:38Z] INFO  17:38:22,515 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:38Z] INFO  17:38:22,515 HelpFormatter - Date/Time: 2016/04/14 17:38:22
[2016-04-15T00:38Z] INFO  17:38:22,515 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:38Z] INFO  17:38:22,515 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:38Z] WARN  17:38:22,571 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T00:38Z] WARN  17:38:22,575 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/7/tx/tmp9uHXTo/R14-18106_kapa-NGv3-PE100-NGv3-7_63095909_78636522.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T00:38Z] INFO  17:38:22,769 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:38Z] INFO  17:38:22,982 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T00:38Z] INFO  17:38:23,015 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:38Z] INFO  17:38:23,108 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.09
[2016-04-15T00:38Z] INFO  17:38:23,139 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T00:38Z] INFO  17:38:23,645 IntervalUtils - Processing 152751 bp from intervals
[2016-04-15T00:38Z] WARN  17:38:23,669 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:38Z] INFO  17:38:23,817 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:38Z] INFO  17:38:23,970 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:38Z] INFO  17:38:23,971 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:38Z] INFO  17:38:23,971 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T00:38Z] INFO  17:38:23,972 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T00:38Z] INFO  17:38:23,981 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T00:38Z] INFO  17:38:23,981 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T00:38Z] INFO  17:38:24,062 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:38Z] INFO  17:38:24,078 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:38Z] INFO  17:38:24,078 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:38Z] INFO  17:38:24,079 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:38Z] INFO  17:38:24,083 ProgressMeter -     6:118596622      2.8802602E7    30.0 s            1.0 s       73.9%    40.0 s      10.0 s
[2016-04-15T00:38Z] INFO  17:38:24,083 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/7/R14-18106_kapa-NGv3-PE100-NGv3-sort-7_79082334_94740703-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/7/R14-18106_kapa-NGv3-PE100-NGv3-7_79082334_94740703-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/7/tx/tmps2Lef0/R14-18106_kapa-NGv3-PE100-NGv3-7_79082334_94740703.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:38Z] INFO  17:38:24,094 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:38Z] INFO  17:38:24,094 HelpFormatter - Date/Time: 2016/04/14 17:38:24
[2016-04-15T00:38Z] INFO  17:38:24,094 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:38Z] INFO  17:38:24,095 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:38Z] WARN  17:38:24,139 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T00:38Z] WARN  17:38:24,141 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/7/tx/tmps2Lef0/R14-18106_kapa-NGv3-PE100-NGv3-7_79082334_94740703.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T00:38Z] INFO  17:38:24,213 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T00:38Z] INFO  17:38:24,419 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:38Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T00:38Z] INFO  17:38:24,500 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T00:38Z] INFO  17:38:24,500 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T00:38Z] INFO  17:38:24,641 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T00:38Z] INFO  17:38:24,651 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:38Z] INFO  17:38:24,718 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-15T00:38Z] INFO  17:38:24,744 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T00:38Z] WARN  17:38:24,833 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T00:38Z] WARN  17:38:24,843 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T00:38Z] INFO  17:38:25,058 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:38Z] INFO  17:38:25,062 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:38Z] INFO  17:38:25,062 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:38Z] INFO  17:38:25,063 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:38Z] INFO  17:38:25,068 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/7/R14-18106_kapa-NGv3-PE100-NGv3-sort-7_94750023_110303777-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/7/R14-18106_kapa-NGv3-PE100-NGv3-7_94750023_110303777-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/7/tx/tmpaiVQuQ/R14-18106_kapa-NGv3-PE100-NGv3-7_94750023_110303777.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:38Z] INFO  17:38:25,097 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:38Z] INFO  17:38:25,107 IntervalUtils - Processing 163786 bp from intervals
[2016-04-15T00:38Z] INFO  17:38:25,108 HelpFormatter - Date/Time: 2016/04/14 17:38:25
[2016-04-15T00:38Z] INFO  17:38:25,108 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:38Z] WARN  17:38:25,112 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:38Z] INFO  17:38:25,109 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:38Z] WARN  17:38:25,148 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T00:38Z] WARN  17:38:25,161 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/7/tx/tmpaiVQuQ/R14-18106_kapa-NGv3-PE100-NGv3-7_94750023_110303777.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T00:38Z] INFO  17:38:25,184 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:38Z] INFO  17:38:25,301 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:38Z] INFO  17:38:25,302 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:38Z] INFO  17:38:25,303 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T00:38Z] INFO  17:38:25,304 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T00:38Z] INFO  17:38:25,305 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T00:38Z] INFO  17:38:25,305 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T00:38Z] INFO  17:38:25,317 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.006257119
[2016-04-15T00:38Z] INFO  17:38:25,318 PairHMM - Total compute time in PairHMM computeLikelihoods() : 0.326770381
[2016-04-15T00:38Z] INFO  17:38:25,319 HaplotypeCaller - Ran local assembly on 922 active regions
[2016-04-15T00:38Z] INFO  17:38:25,385 ProgressMeter -            done      4.2012935E7    39.0 s            0.0 s      100.0%    39.0 s       0.0 s
[2016-04-15T00:38Z] INFO  17:38:25,385 ProgressMeter - Total runtime 39.32 secs, 0.66 min, 0.01 hours
[2016-04-15T00:38Z] INFO  17:38:25,386 MicroScheduler - 10753 reads were filtered out during the traversal out of approximately 145746 total reads (7.38%)
[2016-04-15T00:38Z] INFO  17:38:25,386 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:38Z] INFO  17:38:25,386 MicroScheduler -   -> 10587 reads (7.26% of total) failing DuplicateReadFilter
[2016-04-15T00:38Z] INFO  17:38:25,387 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:38Z] INFO  17:38:25,387 MicroScheduler -   -> 166 reads (0.11% of total) failing HCMappingQualityFilter
[2016-04-15T00:38Z] INFO  17:38:25,387 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:38Z] INFO  17:38:25,387 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:38Z] INFO  17:38:25,388 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:38Z] INFO  17:38:25,388 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:38Z] INFO  17:38:25,414 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:38Z] INFO  17:38:25,510 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T00:38Z] INFO  17:38:25,642 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T00:38Z] INFO  17:38:25,651 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:38Z] INFO  17:38:25,746 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.09
[2016-04-15T00:38Z] INFO  17:38:25,773 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T00:38Z] INFO  17:38:26,206 IntervalUtils - Processing 352548 bp from intervals
[2016-04-15T00:38Z] WARN  17:38:26,212 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:38Z] INFO  17:38:26,289 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:38Z] INFO  17:38:26,409 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:38Z] INFO  17:38:26,410 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:38Z] INFO  17:38:26,411 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T00:38Z] INFO  17:38:26,412 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T00:38Z] INFO  17:38:26,412 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T00:38Z] INFO  17:38:26,413 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T00:38Z] INFO  17:38:26,626 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T00:38Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T00:38Z] INFO  17:38:26,681 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T00:38Z] INFO  17:38:26,682 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T00:38Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T00:38Z] INFO  17:38:26,788 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T00:38Z] INFO  17:38:26,788 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T00:38Z] INFO  17:38:26,928 ProgressMeter -     6:135357964      2.3434807E7    30.0 s            1.0 s       61.2%    49.0 s      19.0 s
[2016-04-15T00:38Z] INFO  17:38:26,942 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:38Z] WARN  17:38:26,996 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T00:38Z] WARN  17:38:26,997 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T00:38Z] WARN  17:38:27,007 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T00:38Z] WARN  17:38:27,008 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T00:38Z] GATK: HaplotypeCaller
[2016-04-15T00:38Z] INFO  17:38:27,612 ProgressMeter -     6:150240952      1.9143339E7    30.0 s            1.0 s       50.9%    58.0 s      28.0 s
[2016-04-15T00:38Z] INFO  17:38:28,025 ProgressMeter -      6:29911899      5.1372452E7    60.0 s            1.0 s       74.0%    81.0 s      21.0 s
[2016-04-15T00:38Z] INFO  17:38:28,658 ProgressMeter -     6:166721212      1.8992716E7    30.0 s            1.0 s       60.2%    49.0 s      19.0 s
[2016-04-15T00:38Z] INFO  17:38:30,284 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:38Z] INFO  17:38:30,286 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:38Z] INFO  17:38:30,286 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:38Z] INFO  17:38:30,287 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:38Z] INFO  17:38:30,302 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/7/R14-18106_kapa-NGv3-PE100-NGv3-sort-7_110526648_126079222-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/7/R14-18106_kapa-NGv3-PE100-NGv3-7_110526648_126079222-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/7/tx/tmp1sn745/R14-18106_kapa-NGv3-PE100-NGv3-7_110526648_126079222.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:38Z] INFO  17:38:30,319 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:38Z] INFO  17:38:30,320 HelpFormatter - Date/Time: 2016/04/14 17:38:30
[2016-04-15T00:38Z] INFO  17:38:30,320 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:38Z] INFO  17:38:30,321 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:38Z] WARN  17:38:30,366 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T00:38Z] WARN  17:38:30,370 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/7/tx/tmp1sn745/R14-18106_kapa-NGv3-PE100-NGv3-7_110526648_126079222.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T00:38Z] INFO  17:38:30,638 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:38Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T00:38Z] INFO  17:38:30,847 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T00:38Z] INFO  17:38:30,847 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T00:38Z] INFO  17:38:30,963 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T00:38Z] INFO  17:38:30,981 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:38Z] INFO  17:38:31,055 ProgressMeter -      6:32551886      2.8415957E7    60.0 s            2.0 s       26.3%     3.8 m       2.8 m
[2016-04-15T00:38Z] WARN  17:38:31,069 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T00:38Z] WARN  17:38:31,070 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T00:38Z] INFO  17:38:31,075 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.09
[2016-04-15T00:38Z] INFO  17:38:31,103 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T00:38Z] INFO  17:38:31,259 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.009076657
[2016-04-15T00:38Z] INFO  17:38:31,260 PairHMM - Total compute time in PairHMM computeLikelihoods() : 2.782710877
[2016-04-15T00:38Z] INFO  17:38:31,261 HaplotypeCaller - Ran local assembly on 1063 active regions
[2016-04-15T00:38Z] INFO  17:38:31,310 ProgressMeter -            done      4.9918554E7    47.0 s            0.0 s      100.0%    47.0 s       0.0 s
[2016-04-15T00:38Z] INFO  17:38:31,311 ProgressMeter - Total runtime 47.46 secs, 0.79 min, 0.01 hours
[2016-04-15T00:38Z] INFO  17:38:31,311 MicroScheduler - 14141 reads were filtered out during the traversal out of approximately 183090 total reads (7.72%)
[2016-04-15T00:38Z] INFO  17:38:31,311 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:38Z] INFO  17:38:31,311 MicroScheduler -   -> 13453 reads (7.35% of total) failing DuplicateReadFilter
[2016-04-15T00:38Z] INFO  17:38:31,312 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:38Z] INFO  17:38:31,312 MicroScheduler -   -> 688 reads (0.38% of total) failing HCMappingQualityFilter
[2016-04-15T00:38Z] INFO  17:38:31,312 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:38Z] INFO  17:38:31,312 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:38Z] INFO  17:38:31,313 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:38Z] INFO  17:38:31,313 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:38Z] INFO  17:38:31,575 IntervalUtils - Processing 97998 bp from intervals
[2016-04-15T00:38Z] WARN  17:38:31,580 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:38Z] INFO  17:38:31,711 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:38Z] INFO  17:38:31,840 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:38Z] INFO  17:38:31,841 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:38Z] INFO  17:38:31,841 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T00:38Z] INFO  17:38:31,841 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T00:38Z] INFO  17:38:31,844 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T00:38Z] INFO  17:38:31,845 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T00:38Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T00:38Z] INFO  17:38:31,963 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T00:38Z] INFO  17:38:31,964 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T00:38Z] INFO  17:38:32,060 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T00:38Z] WARN  17:38:32,317 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T00:38Z] WARN  17:38:32,318 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T00:38Z] INFO  17:38:32,681 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.023213425000000003
[2016-04-15T00:38Z] INFO  17:38:32,682 PairHMM - Total compute time in PairHMM computeLikelihoods() : 0.420273469
[2016-04-15T00:38Z] INFO  17:38:32,683 HaplotypeCaller - Ran local assembly on 1053 active regions
[2016-04-15T00:38Z] INFO  17:38:32,736 ProgressMeter -            done      5.3468356E7    38.0 s            0.0 s      100.0%    38.0 s       0.0 s
[2016-04-15T00:38Z] INFO  17:38:32,737 ProgressMeter - Total runtime 38.68 secs, 0.64 min, 0.01 hours
[2016-04-15T00:38Z] INFO  17:38:32,737 MicroScheduler - 12999 reads were filtered out during the traversal out of approximately 171343 total reads (7.59%)
[2016-04-15T00:38Z] INFO  17:38:32,738 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:38Z] INFO  17:38:32,738 MicroScheduler -   -> 12659 reads (7.39% of total) failing DuplicateReadFilter
[2016-04-15T00:38Z] INFO  17:38:32,738 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:38Z] INFO  17:38:32,739 MicroScheduler -   -> 340 reads (0.20% of total) failing HCMappingQualityFilter
[2016-04-15T00:38Z] INFO  17:38:32,739 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:38Z] INFO  17:38:32,739 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:38Z] INFO  17:38:32,739 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:38Z] INFO  17:38:32,740 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:38Z] INFO  17:38:32,985 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:38Z] GATK: HaplotypeCaller
[2016-04-15T00:38Z] INFO  17:38:34,272 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:38Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T00:38Z] GATK: HaplotypeCaller
[2016-04-15T00:38Z] INFO  17:38:34,710 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T00:38Z] INFO  17:38:34,711 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T00:38Z] WARN  17:38:34,996 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T00:38Z] WARN  17:38:34,998 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T00:38Z] INFO  17:38:36,096 ProgressMeter -       7:4900691      1.5871479E7    30.0 s            1.0 s       44.2%    67.0 s      37.0 s
[2016-04-15T00:38Z] INFO  17:38:36,355 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:38Z] INFO  17:38:36,359 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:38Z] INFO  17:38:36,359 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:38Z] INFO  17:38:36,360 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:38Z] INFO  17:38:36,364 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/7/R14-18106_kapa-NGv3-PE100-NGv3-sort-7_126086124_141619620-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/7/R14-18106_kapa-NGv3-PE100-NGv3-7_126086124_141619620-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/7/tx/tmp15cY5a/R14-18106_kapa-NGv3-PE100-NGv3-7_126086124_141619620.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:38Z] INFO  17:38:36,397 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:38Z] INFO  17:38:36,398 HelpFormatter - Date/Time: 2016/04/14 17:38:36
[2016-04-15T00:38Z] INFO  17:38:36,398 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:38Z] INFO  17:38:36,399 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:38Z] WARN  17:38:36,447 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T00:38Z] WARN  17:38:36,453 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/7/tx/tmp15cY5a/R14-18106_kapa-NGv3-PE100-NGv3-7_126086124_141619620.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T00:38Z] INFO  17:38:36,720 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:38Z] INFO  17:38:36,935 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T00:38Z] INFO  17:38:36,956 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:38Z] INFO  17:38:37,015 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-15T00:38Z] INFO  17:38:37,031 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T00:38Z] INFO  17:38:37,461 IntervalUtils - Processing 219678 bp from intervals
[2016-04-15T00:38Z] WARN  17:38:37,466 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:38Z] INFO  17:38:37,601 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:38Z] INFO  17:38:37,737 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:38Z] INFO  17:38:37,740 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:38Z] INFO  17:38:37,741 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:38Z] INFO  17:38:37,742 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:38Z] INFO  17:38:37,746 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/7/R14-18106_kapa-NGv3-PE100-NGv3-sort-7_141629903_157151331-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/7/R14-18106_kapa-NGv3-PE100-NGv3-7_141629903_157151331-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/7/tx/tmppDhd_5/R14-18106_kapa-NGv3-PE100-NGv3-7_141629903_157151331.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:38Z] INFO  17:38:37,757 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:38Z] INFO  17:38:37,758 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:38Z] INFO  17:38:37,759 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T00:38Z] INFO  17:38:37,760 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T00:38Z] INFO  17:38:37,767 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T00:38Z] INFO  17:38:37,768 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T00:38Z] INFO  17:38:37,778 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:38Z] INFO  17:38:37,779 HelpFormatter - Date/Time: 2016/04/14 17:38:37
[2016-04-15T00:38Z] INFO  17:38:37,780 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:38Z] INFO  17:38:37,780 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:38Z] WARN  17:38:37,822 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T00:38Z] WARN  17:38:37,825 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/7/tx/tmppDhd_5/R14-18106_kapa-NGv3-PE100-NGv3-7_141629903_157151331.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T00:38Z] INFO  17:38:37,840 ProgressMeter -      7:27134884      2.6858685E7    30.0 s            1.0 s       64.8%    46.0 s      16.0 s
[2016-04-15T00:38Z] INFO  17:38:37,984 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:38Z] INFO  17:38:38,014 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T00:38Z] INFO  17:38:38,213 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T00:38Z] INFO  17:38:38,223 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:38Z] INFO  17:38:38,325 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.10
[2016-04-15T00:38Z] INFO  17:38:38,348 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T00:38Z] INFO  17:38:38,708 IntervalUtils - Processing 248696 bp from intervals
[2016-04-15T00:38Z] WARN  17:38:38,714 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:38Z] INFO  17:38:38,846 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:38Z] INFO  17:38:38,986 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:38Z] INFO  17:38:38,987 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:38Z] INFO  17:38:38,988 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T00:38Z] INFO  17:38:38,988 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T00:38Z] INFO  17:38:38,989 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T00:38Z] INFO  17:38:38,989 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T00:38Z] INFO  17:38:39,200 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T00:38Z] INFO  17:38:40,303 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.009649013000000001
[2016-04-15T00:38Z] INFO  17:38:40,304 PairHMM - Total compute time in PairHMM computeLikelihoods() : 0.631547324
[2016-04-15T00:38Z] INFO  17:38:40,305 HaplotypeCaller - Ran local assembly on 1102 active regions
[2016-04-15T00:38Z] INFO  17:38:40,369 ProgressMeter -            done      5.9409326E7    43.0 s            0.0 s      100.0%    43.0 s       0.0 s
[2016-04-15T00:38Z] INFO  17:38:40,369 ProgressMeter - Total runtime 43.47 secs, 0.72 min, 0.01 hours
[2016-04-15T00:38Z] INFO  17:38:40,370 MicroScheduler - 22106 reads were filtered out during the traversal out of approximately 200273 total reads (11.04%)
[2016-04-15T00:38Z] INFO  17:38:40,371 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:38Z] INFO  17:38:40,371 MicroScheduler -   -> 14682 reads (7.33% of total) failing DuplicateReadFilter
[2016-04-15T00:38Z] INFO  17:38:40,371 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:38Z] INFO  17:38:40,371 MicroScheduler -   -> 7424 reads (3.71% of total) failing HCMappingQualityFilter
[2016-04-15T00:38Z] INFO  17:38:40,372 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:38Z] INFO  17:38:40,372 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:38Z] INFO  17:38:40,372 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:38Z] INFO  17:38:40,372 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:38Z] INFO  17:38:41,847 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:38Z] GATK: HaplotypeCaller
[2016-04-15T00:38Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T00:38Z] INFO  17:38:42,483 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T00:38Z] INFO  17:38:42,484 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T00:38Z] WARN  17:38:42,713 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T00:38Z] WARN  17:38:42,714 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T00:38Z] INFO  17:38:43,881 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.028083820000000002
[2016-04-15T00:38Z] INFO  17:38:43,882 PairHMM - Total compute time in PairHMM computeLikelihoods() : 1.6701083410000002
[2016-04-15T00:38Z] INFO  17:38:43,882 HaplotypeCaller - Ran local assembly on 1092 active regions
[2016-04-15T00:38Z] INFO  17:38:43,928 ProgressMeter -            done      5.0541583E7    45.0 s            0.0 s      100.0%    45.0 s       0.0 s
[2016-04-15T00:38Z] INFO  17:38:43,929 ProgressMeter - Total runtime 45.29 secs, 0.75 min, 0.01 hours
[2016-04-15T00:38Z] INFO  17:38:43,930 MicroScheduler - 19498 reads were filtered out during the traversal out of approximately 214394 total reads (9.09%)
[2016-04-15T00:38Z] INFO  17:38:43,931 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:38Z] INFO  17:38:43,932 MicroScheduler -   -> 16091 reads (7.51% of total) failing DuplicateReadFilter
[2016-04-15T00:38Z] INFO  17:38:43,932 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:38Z] INFO  17:38:43,933 MicroScheduler -   -> 3407 reads (1.59% of total) failing HCMappingQualityFilter
[2016-04-15T00:38Z] INFO  17:38:43,933 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:38Z] INFO  17:38:43,934 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:38Z] INFO  17:38:43,934 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:38Z] INFO  17:38:43,935 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:38Z] INFO  17:38:45,248 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:38Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T00:38Z] INFO  17:38:45,416 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T00:38Z] INFO  17:38:45,427 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T00:38Z] INFO  17:38:45,560 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:38Z] INFO  17:38:45,563 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:38Z] INFO  17:38:45,564 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:38Z] INFO  17:38:45,564 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:38Z] INFO  17:38:45,569 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/7/R14-18106_kapa-NGv3-PE100-NGv3-sort-7_157155854_159138663-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/7/R14-18106_kapa-NGv3-PE100-NGv3-7_157155854_159138663-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/7/tx/tmpup1J3M/R14-18106_kapa-NGv3-PE100-NGv3-7_157155854_159138663.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:38Z] INFO  17:38:45,580 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:38Z] INFO  17:38:45,583 HelpFormatter - Date/Time: 2016/04/14 17:38:45
[2016-04-15T00:38Z] INFO  17:38:45,583 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:38Z] INFO  17:38:45,585 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:38Z] WARN  17:38:45,619 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T00:38Z] WARN  17:38:45,621 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/7/tx/tmpup1J3M/R14-18106_kapa-NGv3-PE100-NGv3-7_157155854_159138663.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T00:38Z] GATK: HaplotypeCaller
[2016-04-15T00:38Z] WARN  17:38:45,759 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T00:38Z] WARN  17:38:45,760 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T00:38Z] INFO  17:38:45,829 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:38Z] INFO  17:38:46,000 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T00:38Z] INFO  17:38:46,010 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:38Z] INFO  17:38:46,079 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-15T00:38Z] INFO  17:38:46,099 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T00:38Z] INFO  17:38:46,454 IntervalUtils - Processing 17619 bp from intervals
[2016-04-15T00:38Z] WARN  17:38:46,459 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:38Z] INFO  17:38:46,617 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:38Z] INFO  17:38:46,690 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:38Z] INFO  17:38:46,691 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:38Z] INFO  17:38:46,691 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T00:38Z] INFO  17:38:46,692 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T00:38Z] INFO  17:38:46,703 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T00:38Z] INFO  17:38:46,704 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T00:38Z] INFO  17:38:46,963 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T00:38Z] INFO  17:38:46,987 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.040507158
[2016-04-15T00:38Z] INFO  17:38:46,988 PairHMM - Total compute time in PairHMM computeLikelihoods() : 8.587207961
[2016-04-15T00:38Z] INFO  17:38:46,988 HaplotypeCaller - Ran local assembly on 1668 active regions
[2016-04-15T00:38Z] INFO  17:38:47,050 ProgressMeter -            done      9.0413204E7    79.0 s            0.0 s      100.0%    79.0 s       0.0 s
[2016-04-15T00:38Z] INFO  17:38:47,050 ProgressMeter - Total runtime 79.08 secs, 1.32 min, 0.02 hours
[2016-04-15T00:38Z] INFO  17:38:47,050 MicroScheduler - 30746 reads were filtered out during the traversal out of approximately 347200 total reads (8.86%)
[2016-04-15T00:38Z] INFO  17:38:47,051 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:38Z] INFO  17:38:47,051 MicroScheduler -   -> 25343 reads (7.30% of total) failing DuplicateReadFilter
[2016-04-15T00:38Z] INFO  17:38:47,051 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:38Z] INFO  17:38:47,051 MicroScheduler -   -> 5403 reads (1.56% of total) failing HCMappingQualityFilter
[2016-04-15T00:38Z] INFO  17:38:47,052 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:38Z] INFO  17:38:47,052 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:38Z] INFO  17:38:47,052 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:38Z] INFO  17:38:47,052 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:38Z] INFO  17:38:48,454 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.010003304000000001
[2016-04-15T00:38Z] INFO  17:38:48,455 PairHMM - Total compute time in PairHMM computeLikelihoods() : 0.412448493
[2016-04-15T00:38Z] INFO  17:38:48,455 HaplotypeCaller - Ran local assembly on 1254 active regions
[2016-04-15T00:38Z] INFO  17:38:48,515 ProgressMeter -            done      7.7025077E7    50.0 s            0.0 s      100.0%    50.0 s       0.0 s
[2016-04-15T00:38Z] INFO  17:38:48,515 ProgressMeter - Total runtime 50.92 secs, 0.85 min, 0.01 hours
[2016-04-15T00:38Z] INFO  17:38:48,516 MicroScheduler - 20621 reads were filtered out during the traversal out of approximately 239753 total reads (8.60%)
[2016-04-15T00:38Z] INFO  17:38:48,516 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:38Z] INFO  17:38:48,517 MicroScheduler -   -> 17786 reads (7.42% of total) failing DuplicateReadFilter
[2016-04-15T00:38Z] INFO  17:38:48,517 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:38Z] INFO  17:38:48,517 MicroScheduler -   -> 2835 reads (1.18% of total) failing HCMappingQualityFilter
[2016-04-15T00:38Z] INFO  17:38:48,517 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:38Z] INFO  17:38:48,517 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:38Z] INFO  17:38:48,518 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:38Z] INFO  17:38:48,518 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:38Z] INFO  17:38:48,549 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:38Z] INFO  17:38:48,722 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:38Z] INFO  17:38:48,725 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:38Z] INFO  17:38:48,726 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:38Z] INFO  17:38:48,726 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:38Z] INFO  17:38:48,731 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/8/R14-18106_kapa-NGv3-PE100-NGv3-sort-8_0_15517156-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/8/R14-18106_kapa-NGv3-PE100-NGv3-8_0_15517156-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/8/tx/tmpKHB9nf/R14-18106_kapa-NGv3-PE100-NGv3-8_0_15517156.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:38Z] INFO  17:38:48,754 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:38Z] INFO  17:38:48,755 HelpFormatter - Date/Time: 2016/04/14 17:38:48
[2016-04-15T00:38Z] INFO  17:38:48,755 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:38Z] INFO  17:38:48,756 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:38Z] WARN  17:38:48,801 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T00:38Z] WARN  17:38:48,804 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/8/tx/tmpKHB9nf/R14-18106_kapa-NGv3-PE100-NGv3-8_0_15517156.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T00:38Z] INFO  17:38:48,807 ProgressMeter -     5:140593696      1.1700426E8    90.0 s            0.0 s       72.9%     2.1 m      33.0 s
[2016-04-15T00:38Z] GATK: HaplotypeCaller
[2016-04-15T00:38Z] INFO  17:38:49,024 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:38Z] INFO  17:38:49,228 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T00:38Z] INFO  17:38:49,238 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:38Z] INFO  17:38:49,339 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.10
[2016-04-15T00:38Z] INFO  17:38:49,379 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T00:38Z] INFO  17:38:49,848 IntervalUtils - Processing 115548 bp from intervals
[2016-04-15T00:38Z] WARN  17:38:49,854 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:38Z] INFO  17:38:49,971 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:38Z] INFO  17:38:50,026 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:38Z] INFO  17:38:50,111 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:38Z] INFO  17:38:50,112 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:38Z] INFO  17:38:50,124 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T00:38Z] INFO  17:38:50,125 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T00:38Z] INFO  17:38:50,143 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T00:38Z] INFO  17:38:50,143 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T00:38Z] GATK: HaplotypeCaller
[2016-04-15T00:38Z] INFO  17:38:50,363 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T00:38Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T00:38Z] INFO  17:38:50,531 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T00:38Z] INFO  17:38:50,531 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T00:38Z] INFO  17:38:50,636 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.009668477
[2016-04-15T00:38Z] INFO  17:38:50,637 PairHMM - Total compute time in PairHMM computeLikelihoods() : 0.513965
[2016-04-15T00:38Z] INFO  17:38:50,637 HaplotypeCaller - Ran local assembly on 1114 active regions
[2016-04-15T00:38Z] INFO  17:38:50,682 ProgressMeter -            done       5.703208E7    42.0 s            0.0 s      100.0%    42.0 s       0.0 s
[2016-04-15T00:38Z] INFO  17:38:50,682 ProgressMeter - Total runtime 42.86 secs, 0.71 min, 0.01 hours
[2016-04-15T00:38Z] INFO  17:38:50,683 MicroScheduler - 13879 reads were filtered out during the traversal out of approximately 184895 total reads (7.51%)
[2016-04-15T00:38Z] INFO  17:38:50,683 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:38Z] INFO  17:38:50,683 MicroScheduler -   -> 13560 reads (7.33% of total) failing DuplicateReadFilter
[2016-04-15T00:38Z] INFO  17:38:50,683 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:38Z] INFO  17:38:50,684 MicroScheduler -   -> 319 reads (0.17% of total) failing HCMappingQualityFilter
[2016-04-15T00:38Z] INFO  17:38:50,684 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:38Z] INFO  17:38:50,684 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:38Z] INFO  17:38:50,684 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:38Z] INFO  17:38:50,685 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:38Z] WARN  17:38:50,804 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T00:38Z] WARN  17:38:50,806 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T00:38Z] INFO  17:38:51,215 ProgressMeter -      7:43447211      1.6838511E7    30.0 s            1.0 s       55.6%    53.0 s      23.0 s
[2016-04-15T00:38Z] INFO  17:38:51,859 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.008119535
[2016-04-15T00:38Z] INFO  17:38:51,860 PairHMM - Total compute time in PairHMM computeLikelihoods() : 0.340247739
[2016-04-15T00:38Z] INFO  17:38:51,861 HaplotypeCaller - Ran local assembly on 591 active regions
[2016-04-15T00:38Z] INFO  17:38:51,909 ProgressMeter -            done      1.4657262E7    29.0 s            2.0 s      100.0%    29.0 s       0.0 s
[2016-04-15T00:38Z] INFO  17:38:51,910 ProgressMeter - Total runtime 29.98 secs, 0.50 min, 0.01 hours
[2016-04-15T00:38Z] INFO  17:38:51,911 MicroScheduler - 11822 reads were filtered out during the traversal out of approximately 109995 total reads (10.75%)
[2016-04-15T00:38Z] INFO  17:38:51,911 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:38Z] INFO  17:38:51,912 MicroScheduler -   -> 8055 reads (7.32% of total) failing DuplicateReadFilter
[2016-04-15T00:38Z] INFO  17:38:51,913 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:38Z] INFO  17:38:51,913 MicroScheduler -   -> 3767 reads (3.42% of total) failing HCMappingQualityFilter
[2016-04-15T00:38Z] INFO  17:38:51,914 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:38Z] INFO  17:38:51,914 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:38Z] INFO  17:38:51,915 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:38Z] INFO  17:38:51,916 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:38Z] INFO  17:38:52,219 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:38Z] INFO  17:38:52,222 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:38Z] INFO  17:38:52,223 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:38Z] INFO  17:38:52,223 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:38Z] INFO  17:38:52,228 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/8/R14-18106_kapa-NGv3-PE100-NGv3-sort-8_15519664_31030618-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/8/R14-18106_kapa-NGv3-PE100-NGv3-8_15519664_31030618-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/8/tx/tmpGC3t3H/R14-18106_kapa-NGv3-PE100-NGv3-8_15519664_31030618.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:38Z] INFO  17:38:52,247 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:38Z] INFO  17:38:52,257 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:38Z] INFO  17:38:52,258 HelpFormatter - Date/Time: 2016/04/14 17:38:52
[2016-04-15T00:38Z] INFO  17:38:52,259 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:38Z] INFO  17:38:52,259 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:38Z] WARN  17:38:52,300 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T00:38Z] WARN  17:38:52,303 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/8/tx/tmpGC3t3H/R14-18106_kapa-NGv3-PE100-NGv3-8_15519664_31030618.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T00:38Z] GATK: HaplotypeCaller
[2016-04-15T00:38Z] INFO  17:38:52,529 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:38Z] INFO  17:38:52,771 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T00:38Z] INFO  17:38:52,781 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:38Z] INFO  17:38:52,889 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.11
[2016-04-15T00:38Z] INFO  17:38:52,904 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T00:38Z] INFO  17:38:53,372 IntervalUtils - Processing 233081 bp from intervals
[2016-04-15T00:38Z] WARN  17:38:53,378 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:38Z] INFO  17:38:53,480 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:38Z] INFO  17:38:53,487 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:38Z] INFO  17:38:53,508 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:38Z] INFO  17:38:53,512 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:38Z] INFO  17:38:53,512 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:38Z] INFO  17:38:53,513 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:38Z] INFO  17:38:53,517 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/8/R14-18106_kapa-NGv3-PE100-NGv3-sort-8_31496910_48001429-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/8/R14-18106_kapa-NGv3-PE100-NGv3-8_31496910_48001429-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/8/tx/tmpb14sEy/R14-18106_kapa-NGv3-PE100-NGv3-8_31496910_48001429.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:38Z] INFO  17:38:53,544 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:38Z] INFO  17:38:53,545 HelpFormatter - Date/Time: 2016/04/14 17:38:53
[2016-04-15T00:38Z] INFO  17:38:53,545 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:38Z] INFO  17:38:53,546 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:38Z] WARN  17:38:53,594 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T00:38Z] WARN  17:38:53,597 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/8/tx/tmpb14sEy/R14-18106_kapa-NGv3-PE100-NGv3-8_31496910_48001429.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T00:38Z] INFO  17:38:53,642 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:38Z] INFO  17:38:53,643 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:38Z] INFO  17:38:53,644 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T00:38Z] INFO  17:38:53,644 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T00:38Z] INFO  17:38:53,645 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T00:38Z] INFO  17:38:53,645 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T00:38Z] INFO  17:38:53,778 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:38Z] GATK: HaplotypeCaller
[2016-04-15T00:38Z] INFO  17:38:53,846 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T00:38Z] INFO  17:38:53,991 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T00:38Z] INFO  17:38:53,988 ProgressMeter -      7:73960139      1.9900082E7    30.0 s            1.0 s       57.9%    51.0 s      21.0 s
[2016-04-15T00:38Z] INFO  17:38:54,019 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:38Z] INFO  17:38:54,122 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.10
[2016-04-15T00:38Z] INFO  17:38:54,140 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T00:38Z] INFO  17:38:54,618 IntervalUtils - Processing 125262 bp from intervals
[2016-04-15T00:38Z] WARN  17:38:54,637 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:38Z] INFO  17:38:54,759 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:38Z] INFO  17:38:54,860 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:38Z] INFO  17:38:54,894 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:38Z] INFO  17:38:54,895 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T00:38Z] INFO  17:38:54,896 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T00:38Z] INFO  17:38:54,908 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T00:38Z] INFO  17:38:54,911 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T00:38Z] INFO  17:38:55,121 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T00:38Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T00:38Z] INFO  17:38:55,270 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T00:38Z] INFO  17:38:55,271 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T00:38Z] INFO  17:38:55,314 ProgressMeter -      7:90894596      2.1177247E7    30.0 s            1.0 s       58.5%    51.0 s      21.0 s
[2016-04-15T00:38Z] WARN  17:38:55,457 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T00:38Z] WARN  17:38:55,459 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T00:38Z] INFO  17:38:55,458 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:38Z] INFO  17:38:55,462 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:38Z] INFO  17:38:55,462 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:38Z] INFO  17:38:55,463 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:38Z] INFO  17:38:55,467 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/8/R14-18106_kapa-NGv3-PE100-NGv3-sort-8_48003022_63659688-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/8/R14-18106_kapa-NGv3-PE100-NGv3-8_48003022_63659688-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/8/tx/tmpVHkD3E/R14-18106_kapa-NGv3-PE100-NGv3-8_48003022_63659688.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:38Z] INFO  17:38:55,477 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:38Z] INFO  17:38:55,477 HelpFormatter - Date/Time: 2016/04/14 17:38:55
[2016-04-15T00:38Z] INFO  17:38:55,478 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:38Z] INFO  17:38:55,478 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:38Z] WARN  17:38:55,525 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T00:38Z] WARN  17:38:55,527 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/8/tx/tmpVHkD3E/R14-18106_kapa-NGv3-PE100-NGv3-8_48003022_63659688.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T00:38Z] INFO  17:38:55,806 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:38Z] INFO  17:38:56,095 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T00:38Z] INFO  17:38:56,105 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:38Z] INFO  17:38:56,177 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-15T00:38Z] INFO  17:38:56,191 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T00:38Z] INFO  17:38:56,431 ProgressMeter -      7:99695764      1.9128281E7    30.0 s            1.0 s       27.4%   109.0 s      79.0 s
[2016-04-15T00:38Z] INFO  17:38:56,696 IntervalUtils - Processing 104159 bp from intervals
[2016-04-15T00:38Z] WARN  17:38:56,701 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:38Z] INFO  17:38:56,823 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:38Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T00:38Z] INFO  17:38:56,928 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T00:38Z] INFO  17:38:56,939 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T00:38Z] INFO  17:38:56,941 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:38Z] INFO  17:38:56,942 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:38Z] INFO  17:38:56,942 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T00:38Z] INFO  17:38:56,943 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T00:38Z] INFO  17:38:56,946 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T00:38Z] INFO  17:38:56,947 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T00:38Z] INFO  17:38:56,967 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:38Z] INFO  17:38:56,970 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:38Z] INFO  17:38:56,971 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:38Z] INFO  17:38:56,971 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:38Z] INFO  17:38:56,976 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/8/R14-18106_kapa-NGv3-PE100-NGv3-sort-8_63775819_79510770-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/8/R14-18106_kapa-NGv3-PE100-NGv3-8_63775819_79510770-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/8/tx/tmpbgClYq/R14-18106_kapa-NGv3-PE100-NGv3-8_63775819_79510770.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:38Z] INFO  17:38:56,985 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:38Z] INFO  17:38:56,996 HelpFormatter - Date/Time: 2016/04/14 17:38:56
[2016-04-15T00:38Z] INFO  17:38:56,997 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:38Z] INFO  17:38:56,998 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:38Z] WARN  17:38:57,043 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T00:38Z] WARN  17:38:57,046 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/8/tx/tmpbgClYq/R14-18106_kapa-NGv3-PE100-NGv3-8_63775819_79510770.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T00:38Z] INFO  17:38:57,180 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T00:38Z] WARN  17:38:57,204 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T00:38Z] WARN  17:38:57,205 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T00:38Z] INFO  17:38:57,280 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:38Z] INFO  17:38:57,589 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T00:38Z] INFO  17:38:57,612 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:38Z] INFO  17:38:57,698 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.10
[2016-04-15T00:38Z] INFO  17:38:57,728 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T00:38Z] INFO  17:38:58,040 IntervalUtils - Processing 117209 bp from intervals
[2016-04-15T00:38Z] WARN  17:38:58,045 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:38Z] INFO  17:38:58,118 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:38Z] INFO  17:38:58,250 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:38Z] INFO  17:38:58,252 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:38Z] INFO  17:38:58,264 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T00:38Z] INFO  17:38:58,265 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T00:38Z] INFO  17:38:58,274 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T00:38Z] INFO  17:38:58,275 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T00:38Z] INFO  17:38:58,505 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T00:38Z] INFO  17:38:58,524 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.002145544
[2016-04-15T00:38Z] INFO  17:38:58,524 PairHMM - Total compute time in PairHMM computeLikelihoods() : 0.03157032
[2016-04-15T00:38Z] INFO  17:38:58,525 HaplotypeCaller - Ran local assembly on 152 active regions
[2016-04-15T00:38Z] INFO  17:38:58,607 ProgressMeter -            done        1060833.0    11.0 s           11.0 s      100.0%    11.0 s       0.0 s
[2016-04-15T00:38Z] INFO  17:38:58,607 ProgressMeter - Total runtime 11.92 secs, 0.20 min, 0.00 hours
[2016-04-15T00:38Z] INFO  17:38:58,608 MicroScheduler - 2305 reads were filtered out during the traversal out of approximately 26399 total reads (8.73%)
[2016-04-15T00:38Z] INFO  17:38:58,609 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:38Z] INFO  17:38:58,609 MicroScheduler -   -> 2105 reads (7.97% of total) failing DuplicateReadFilter
[2016-04-15T00:38Z] INFO  17:38:58,610 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:38Z] INFO  17:38:58,610 MicroScheduler -   -> 200 reads (0.76% of total) failing HCMappingQualityFilter
[2016-04-15T00:38Z] INFO  17:38:58,610 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:38Z] INFO  17:38:58,610 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:38Z] INFO  17:38:58,611 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:38Z] INFO  17:38:58,611 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:38Z] INFO  17:38:59,133 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.021918490000000002
[2016-04-15T00:38Z] INFO  17:38:59,145 PairHMM - Total compute time in PairHMM computeLikelihoods() : 0.8361374570000001
[2016-04-15T00:38Z] INFO  17:38:59,146 HaplotypeCaller - Ran local assembly on 1385 active regions
[2016-04-15T00:38Z] INFO  17:38:59,184 ProgressMeter -            done      8.7090457E7    53.0 s            0.0 s      100.0%    53.0 s       0.0 s
[2016-04-15T00:38Z] INFO  17:38:59,184 ProgressMeter - Total runtime 53.12 secs, 0.89 min, 0.01 hours
[2016-04-15T00:38Z] INFO  17:38:59,185 MicroScheduler - 35929 reads were filtered out during the traversal out of approximately 287763 total reads (12.49%)
[2016-04-15T00:38Z] INFO  17:38:59,185 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:38Z] INFO  17:38:59,185 MicroScheduler -   -> 20718 reads (7.20% of total) failing DuplicateReadFilter
[2016-04-15T00:38Z] INFO  17:38:59,186 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:38Z] INFO  17:38:59,186 MicroScheduler -   -> 15211 reads (5.29% of total) failing HCMappingQualityFilter
[2016-04-15T00:38Z] INFO  17:38:59,186 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:38Z] INFO  17:38:59,186 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:38Z] INFO  17:38:59,186 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:38Z] INFO  17:38:59,187 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:38Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T00:38Z] INFO  17:38:59,491 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T00:38Z] INFO  17:38:59,491 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T00:38Z] WARN  17:38:59,808 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T00:38Z] WARN  17:38:59,810 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T00:39Z] INFO  17:39:00,055 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:39Z] GATK: HaplotypeCaller
[2016-04-15T00:39Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T00:39Z] INFO  17:39:00,442 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T00:39Z] INFO  17:39:00,443 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T00:39Z] INFO  17:39:00,734 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:39Z] WARN  17:39:00,768 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T00:39Z] WARN  17:39:00,769 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T00:39Z] GATK: HaplotypeCaller
[2016-04-15T00:39Z] INFO  17:39:01,056 ProgressMeter -      6:33633612      6.3369708E7    90.0 s            1.0 s       38.6%     3.9 m       2.4 m
[2016-04-15T00:39Z] INFO  17:39:01,857 ProgressMeter -     7:123673057      2.1394386E7    30.0 s            1.0 s       95.9%    31.0 s       1.0 s
[2016-04-15T00:39Z] INFO  17:39:03,485 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.016455513
[2016-04-15T00:39Z] INFO  17:39:03,485 PairHMM - Total compute time in PairHMM computeLikelihoods() : 0.732607345
[2016-04-15T00:39Z] INFO  17:39:03,492 HaplotypeCaller - Ran local assembly on 701 active regions
[2016-04-15T00:39Z] INFO  17:39:03,554 ProgressMeter -            done      2.3520612E7    31.0 s            1.0 s      100.0%    31.0 s       0.0 s
[2016-04-15T00:39Z] INFO  17:39:03,555 ProgressMeter - Total runtime 31.71 secs, 0.53 min, 0.01 hours
[2016-04-15T00:39Z] INFO  17:39:03,555 MicroScheduler - 8461 reads were filtered out during the traversal out of approximately 112786 total reads (7.50%)
[2016-04-15T00:39Z] INFO  17:39:03,556 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:39Z] INFO  17:39:03,556 MicroScheduler -   -> 8318 reads (7.38% of total) failing DuplicateReadFilter
[2016-04-15T00:39Z] INFO  17:39:03,556 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:39Z] INFO  17:39:03,556 MicroScheduler -   -> 143 reads (0.13% of total) failing HCMappingQualityFilter
[2016-04-15T00:39Z] INFO  17:39:03,557 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:39Z] INFO  17:39:03,557 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:39Z] INFO  17:39:03,557 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:39Z] INFO  17:39:03,557 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:39Z] INFO  17:39:03,665 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:39Z] INFO  17:39:03,687 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:39Z] INFO  17:39:03,687 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:39Z] INFO  17:39:03,688 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:39Z] INFO  17:39:03,693 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/8/R14-18106_kapa-NGv3-PE100-NGv3-sort-8_79513976_95140568-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/8/R14-18106_kapa-NGv3-PE100-NGv3-8_79513976_95140568-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/8/tx/tmp8ZBM7D/R14-18106_kapa-NGv3-PE100-NGv3-8_79513976_95140568.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:39Z] INFO  17:39:03,703 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:39Z] INFO  17:39:03,712 HelpFormatter - Date/Time: 2016/04/14 17:39:03
[2016-04-15T00:39Z] INFO  17:39:03,713 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:39Z] INFO  17:39:03,714 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:39Z] WARN  17:39:03,738 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T00:39Z] WARN  17:39:03,741 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/8/tx/tmp8ZBM7D/R14-18106_kapa-NGv3-PE100-NGv3-8_79513976_95140568.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T00:39Z] INFO  17:39:04,042 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:39Z] INFO  17:39:04,250 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T00:39Z] INFO  17:39:04,260 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:39Z] INFO  17:39:04,322 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-15T00:39Z] INFO  17:39:04,367 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T00:39Z] INFO  17:39:04,490 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:39Z] INFO  17:39:04,493 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:39Z] INFO  17:39:04,494 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:39Z] INFO  17:39:04,494 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:39Z] INFO  17:39:04,498 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/8/R14-18106_kapa-NGv3-PE100-NGv3-sort-8_95142853_110655419-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/8/R14-18106_kapa-NGv3-PE100-NGv3-8_95142853_110655419-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/8/tx/tmphyVkYu/R14-18106_kapa-NGv3-PE100-NGv3-8_95142853_110655419.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:39Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T00:39Z] INFO  17:39:04,508 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:39Z] INFO  17:39:04,512 HelpFormatter - Date/Time: 2016/04/14 17:39:04
[2016-04-15T00:39Z] INFO  17:39:04,513 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:39Z] INFO  17:39:04,513 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:39Z] INFO  17:39:04,513 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T00:39Z] INFO  17:39:04,514 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T00:39Z] WARN  17:39:04,537 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T00:39Z] WARN  17:39:04,540 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/8/tx/tmphyVkYu/R14-18106_kapa-NGv3-PE100-NGv3-8_95142853_110655419.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T00:39Z] INFO  17:39:04,759 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:39Z] WARN  17:39:04,803 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T00:39Z] WARN  17:39:04,803 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T00:39Z] INFO  17:39:04,859 IntervalUtils - Processing 78340 bp from intervals
[2016-04-15T00:39Z] WARN  17:39:04,865 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:39Z] INFO  17:39:04,961 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T00:39Z] INFO  17:39:04,971 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:39Z] INFO  17:39:05,017 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:39Z] INFO  17:39:05,061 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.09
[2016-04-15T00:39Z] INFO  17:39:05,100 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T00:39Z] INFO  17:39:05,118 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:39Z] INFO  17:39:05,119 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:39Z] INFO  17:39:05,119 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T00:39Z] INFO  17:39:05,120 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T00:39Z] INFO  17:39:05,131 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T00:39Z] INFO  17:39:05,131 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T00:39Z] INFO  17:39:05,154 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:39Z] INFO  17:39:05,330 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T00:39Z] GATK: HaplotypeCaller
[2016-04-15T00:39Z] INFO  17:39:05,565 IntervalUtils - Processing 161638 bp from intervals
[2016-04-15T00:39Z] WARN  17:39:05,577 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:39Z] INFO  17:39:05,687 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:39Z] INFO  17:39:05,817 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:39Z] INFO  17:39:05,819 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:39Z] INFO  17:39:05,819 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T00:39Z] INFO  17:39:05,820 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T00:39Z] INFO  17:39:05,821 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T00:39Z] INFO  17:39:05,821 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T00:39Z] INFO  17:39:06,113 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T00:39Z] INFO  17:39:06,790 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.007077263
[2016-04-15T00:39Z] INFO  17:39:06,791 PairHMM - Total compute time in PairHMM computeLikelihoods() : 0.374121233
[2016-04-15T00:39Z] INFO  17:39:06,792 HaplotypeCaller - Ran local assembly on 1145 active regions
[2016-04-15T00:39Z] INFO  17:39:06,845 ProgressMeter -            done      6.0270329E7    41.0 s            0.0 s      100.0%    41.0 s       0.0 s
[2016-04-15T00:39Z] INFO  17:39:06,845 ProgressMeter - Total runtime 41.54 secs, 0.69 min, 0.01 hours
[2016-04-15T00:39Z] INFO  17:39:06,846 MicroScheduler - 12125 reads were filtered out during the traversal out of approximately 164816 total reads (7.36%)
[2016-04-15T00:39Z] INFO  17:39:06,846 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:39Z] INFO  17:39:06,846 MicroScheduler -   -> 11858 reads (7.19% of total) failing DuplicateReadFilter
[2016-04-15T00:39Z] INFO  17:39:06,848 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:39Z] INFO  17:39:06,848 MicroScheduler -   -> 267 reads (0.16% of total) failing HCMappingQualityFilter
[2016-04-15T00:39Z] INFO  17:39:06,849 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:39Z] INFO  17:39:06,849 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:39Z] INFO  17:39:06,849 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:39Z] INFO  17:39:06,849 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:39Z] INFO  17:39:07,780 ProgressMeter -     7:131241019       2.300277E7    30.0 s            1.0 s       40.1%    74.0 s      44.0 s
[2016-04-15T00:39Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T00:39Z] INFO  17:39:08,345 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T00:39Z] INFO  17:39:08,346 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T00:39Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T00:39Z] INFO  17:39:08,459 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T00:39Z] INFO  17:39:08,459 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T00:39Z] INFO  17:39:08,569 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:39Z] INFO  17:39:08,632 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.011286357
[2016-04-15T00:39Z] INFO  17:39:08,633 PairHMM - Total compute time in PairHMM computeLikelihoods() : 1.156323006
[2016-04-15T00:39Z] INFO  17:39:08,633 HaplotypeCaller - Ran local assembly on 1176 active regions
[2016-04-15T00:39Z] INFO  17:39:08,687 ProgressMeter -            done      6.3591551E7    44.0 s            0.0 s      100.0%    44.0 s       0.0 s
[2016-04-15T00:39Z] INFO  17:39:08,688 ProgressMeter - Total runtime 44.72 secs, 0.75 min, 0.01 hours
[2016-04-15T00:39Z] INFO  17:39:08,699 MicroScheduler - 53676 reads were filtered out during the traversal out of approximately 255843 total reads (20.98%)
[2016-04-15T00:39Z] INFO  17:39:08,700 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:39Z] INFO  17:39:08,701 MicroScheduler -   -> 16729 reads (6.54% of total) failing DuplicateReadFilter
[2016-04-15T00:39Z] INFO  17:39:08,701 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:39Z] INFO  17:39:08,702 MicroScheduler -   -> 36947 reads (14.44% of total) failing HCMappingQualityFilter
[2016-04-15T00:39Z] INFO  17:39:08,703 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:39Z] INFO  17:39:08,703 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:39Z] INFO  17:39:08,704 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:39Z] INFO  17:39:08,704 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:39Z] WARN  17:39:08,708 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T00:39Z] WARN  17:39:08,709 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T00:39Z] WARN  17:39:08,736 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T00:39Z] WARN  17:39:08,737 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T00:39Z] INFO  17:39:08,762 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.049970652000000004
[2016-04-15T00:39Z] INFO  17:39:08,763 PairHMM - Total compute time in PairHMM computeLikelihoods() : 1.492718954
[2016-04-15T00:39Z] INFO  17:39:08,764 HaplotypeCaller - Ran local assembly on 1121 active regions
[2016-04-15T00:39Z] INFO  17:39:08,807 ProgressMeter -            done      4.9480485E7    47.0 s            0.0 s      100.0%    47.0 s       0.0 s
[2016-04-15T00:39Z] INFO  17:39:08,808 ProgressMeter - Total runtime 47.61 secs, 0.79 min, 0.01 hours
[2016-04-15T00:39Z] INFO  17:39:08,808 MicroScheduler - 23529 reads were filtered out during the traversal out of approximately 218638 total reads (10.76%)
[2016-04-15T00:39Z] INFO  17:39:08,809 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:39Z] INFO  17:39:08,807 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:39Z] INFO  17:39:08,812 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:39Z] INFO  17:39:08,812 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:39Z] INFO  17:39:08,813 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:39Z] INFO  17:39:08,809 MicroScheduler -   -> 15958 reads (7.30% of total) failing DuplicateReadFilter
[2016-04-15T00:39Z] INFO  17:39:08,811 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:39Z] INFO  17:39:08,811 MicroScheduler -   -> 7571 reads (3.46% of total) failing HCMappingQualityFilter
[2016-04-15T00:39Z] INFO  17:39:08,811 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:39Z] INFO  17:39:08,812 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:39Z] INFO  17:39:08,812 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:39Z] INFO  17:39:08,812 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:39Z] INFO  17:39:08,819 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/8/R14-18106_kapa-NGv3-PE100-NGv3-sort-8_110656864_126194498-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/8/R14-18106_kapa-NGv3-PE100-NGv3-8_110656864_126194498-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/8/tx/tmpzif5s2/R14-18106_kapa-NGv3-PE100-NGv3-8_110656864_126194498.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:39Z] GATK: HaplotypeCaller
[2016-04-15T00:39Z] INFO  17:39:08,853 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:39Z] INFO  17:39:08,864 HelpFormatter - Date/Time: 2016/04/14 17:39:08
[2016-04-15T00:39Z] INFO  17:39:08,865 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:39Z] INFO  17:39:08,866 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:39Z] WARN  17:39:08,894 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T00:39Z] WARN  17:39:08,898 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/8/tx/tmpzif5s2/R14-18106_kapa-NGv3-PE100-NGv3-8_110656864_126194498.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T00:39Z] INFO  17:39:09,010 ProgressMeter -     7:148456396      1.0640028E7    30.0 s            2.0 s       32.8%    91.0 s      61.0 s
[2016-04-15T00:39Z] INFO  17:39:09,126 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:39Z] INFO  17:39:09,408 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T00:39Z] INFO  17:39:09,419 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:39Z] INFO  17:39:09,502 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-15T00:39Z] INFO  17:39:09,532 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T00:39Z] INFO  17:39:09,944 IntervalUtils - Processing 102393 bp from intervals
[2016-04-15T00:39Z] WARN  17:39:09,950 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:39Z] INFO  17:39:10,071 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:39Z] INFO  17:39:10,190 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:39Z] INFO  17:39:10,191 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:39Z] INFO  17:39:10,192 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T00:39Z] INFO  17:39:10,193 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T00:39Z] INFO  17:39:10,215 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T00:39Z] INFO  17:39:10,216 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T00:39Z] INFO  17:39:10,446 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:39Z] INFO  17:39:10,450 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T00:39Z] INFO  17:39:10,484 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:39Z] GATK: HaplotypeCaller
[2016-04-15T00:39Z] GATK: HaplotypeCaller
[2016-04-15T00:39Z] INFO  17:39:11,731 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:39Z] INFO  17:39:11,734 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:39Z] INFO  17:39:11,734 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:39Z] INFO  17:39:11,734 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:39Z] INFO  17:39:11,739 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/8/R14-18106_kapa-NGv3-PE100-NGv3-sort-8_126369460_141889736-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/8/R14-18106_kapa-NGv3-PE100-NGv3-8_126369460_141889736-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/8/tx/tmpNNkDtz/R14-18106_kapa-NGv3-PE100-NGv3-8_126369460_141889736.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:39Z] INFO  17:39:11,751 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:39Z] INFO  17:39:11,752 HelpFormatter - Date/Time: 2016/04/14 17:39:11
[2016-04-15T00:39Z] INFO  17:39:11,753 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:39Z] INFO  17:39:11,753 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:39Z] WARN  17:39:11,781 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T00:39Z] WARN  17:39:11,784 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/8/tx/tmpNNkDtz/R14-18106_kapa-NGv3-PE100-NGv3-8_126369460_141889736.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T00:39Z] INFO  17:39:12,067 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:39Z] INFO  17:39:12,365 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T00:39Z] INFO  17:39:12,375 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:39Z] INFO  17:39:12,654 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.28
[2016-04-15T00:39Z] INFO  17:39:12,684 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T00:39Z] INFO  17:39:12,957 IntervalUtils - Processing 72911 bp from intervals
[2016-04-15T00:39Z] WARN  17:39:12,963 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:39Z] INFO  17:39:13,085 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:39Z] INFO  17:39:13,190 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:39Z] INFO  17:39:13,191 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:39Z] INFO  17:39:13,194 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T00:39Z] INFO  17:39:13,195 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T00:39Z] INFO  17:39:13,196 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T00:39Z] INFO  17:39:13,196 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T00:39Z] INFO  17:39:13,504 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T00:39Z] INFO  17:39:13,734 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:39Z] INFO  17:39:13,736 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:39Z] INFO  17:39:13,736 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:39Z] INFO  17:39:13,737 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:39Z] INFO  17:39:13,742 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/9/R14-18106_kapa-NGv3-PE100-NGv3-sort-9_0_15510186-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/9/R14-18106_kapa-NGv3-PE100-NGv3-9_0_15510186-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/9/tx/tmpJhmfJO/R14-18106_kapa-NGv3-PE100-NGv3-9_0_15510186.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:39Z] INFO  17:39:13,777 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:39Z] INFO  17:39:13,778 HelpFormatter - Date/Time: 2016/04/14 17:39:13
[2016-04-15T00:39Z] INFO  17:39:13,779 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:39Z] INFO  17:39:13,779 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:39Z] WARN  17:39:13,861 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T00:39Z] WARN  17:39:13,864 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/9/tx/tmpJhmfJO/R14-18106_kapa-NGv3-PE100-NGv3-9_0_15510186.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T00:39Z] INFO  17:39:14,132 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:39Z] INFO  17:39:14,144 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:39Z] INFO  17:39:14,146 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:39Z] INFO  17:39:14,146 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:39Z] INFO  17:39:14,147 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:39Z] INFO  17:39:14,158 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/8/R14-18106_kapa-NGv3-PE100-NGv3-sort-8_141900641_146364022-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/8/R14-18106_kapa-NGv3-PE100-NGv3-8_141900641_146364022-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/8/tx/tmp878U57/R14-18106_kapa-NGv3-PE100-NGv3-8_141900641_146364022.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:39Z] INFO  17:39:14,178 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:39Z] INFO  17:39:14,179 HelpFormatter - Date/Time: 2016/04/14 17:39:14
[2016-04-15T00:39Z] INFO  17:39:14,179 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:39Z] INFO  17:39:14,180 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:39Z] WARN  17:39:14,225 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T00:39Z] WARN  17:39:14,251 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/8/tx/tmp878U57/R14-18106_kapa-NGv3-PE100-NGv3-8_141900641_146364022.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T00:39Z] INFO  17:39:14,466 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T00:39Z] INFO  17:39:14,476 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:39Z] INFO  17:39:14,556 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:39Z] INFO  17:39:14,557 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-15T00:39Z] INFO  17:39:14,592 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T00:39Z] INFO  17:39:14,748 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T00:39Z] INFO  17:39:14,766 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:39Z] INFO  17:39:14,851 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-15T00:39Z] INFO  17:39:14,879 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T00:39Z] INFO  17:39:15,079 IntervalUtils - Processing 123193 bp from intervals
[2016-04-15T00:39Z] WARN  17:39:15,085 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:39Z] INFO  17:39:15,193 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:39Z] INFO  17:39:15,257 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:39Z] INFO  17:39:15,259 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:39Z] INFO  17:39:15,259 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T00:39Z] INFO  17:39:15,260 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T00:39Z] INFO  17:39:15,261 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T00:39Z] INFO  17:39:15,261 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T00:39Z] INFO  17:39:15,431 IntervalUtils - Processing 204618 bp from intervals
[2016-04-15T00:39Z] WARN  17:39:15,436 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:39Z] INFO  17:39:15,513 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:39Z] INFO  17:39:15,515 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T00:39Z] INFO  17:39:15,595 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:39Z] INFO  17:39:15,596 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:39Z] INFO  17:39:15,597 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T00:39Z] INFO  17:39:15,598 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T00:39Z] INFO  17:39:15,599 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T00:39Z] INFO  17:39:15,600 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T00:39Z] INFO  17:39:15,822 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.051469084000000005
[2016-04-15T00:39Z] INFO  17:39:15,822 PairHMM - Total compute time in PairHMM computeLikelihoods() : 7.139663463000001
[2016-04-15T00:39Z] INFO  17:39:15,822 HaplotypeCaller - Ran local assembly on 2494 active regions
[2016-04-15T00:39Z] INFO  17:39:15,876 ProgressMeter -            done     1.86500366E8   117.0 s            0.0 s      100.0%   117.0 s       0.0 s
[2016-04-15T00:39Z] INFO  17:39:15,877 ProgressMeter - Total runtime 117.10 secs, 1.95 min, 0.03 hours
[2016-04-15T00:39Z] INFO  17:39:15,877 MicroScheduler - 69702 reads were filtered out during the traversal out of approximately 642819 total reads (10.84%)
[2016-04-15T00:39Z] INFO  17:39:15,877 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:39Z] INFO  17:39:15,878 MicroScheduler -   -> 51503 reads (8.01% of total) failing DuplicateReadFilter
[2016-04-15T00:39Z] INFO  17:39:15,878 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:39Z] INFO  17:39:15,878 MicroScheduler -   -> 18199 reads (2.83% of total) failing HCMappingQualityFilter
[2016-04-15T00:39Z] INFO  17:39:15,878 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:39Z] INFO  17:39:15,879 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:39Z] INFO  17:39:15,879 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:39Z] INFO  17:39:15,879 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:39Z] INFO  17:39:15,888 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T00:39Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T00:39Z] INFO  17:39:16,044 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T00:39Z] INFO  17:39:16,045 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T00:39Z] WARN  17:39:16,316 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T00:39Z] WARN  17:39:16,317 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T00:39Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T00:39Z] INFO  17:39:16,591 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T00:39Z] INFO  17:39:16,592 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T00:39Z] WARN  17:39:16,960 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T00:39Z] WARN  17:39:16,967 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T00:39Z] INFO  17:39:17,594 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:39Z] GATK: HaplotypeCaller
[2016-04-15T00:39Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T00:39Z] INFO  17:39:18,307 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T00:39Z] INFO  17:39:18,307 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T00:39Z] WARN  17:39:18,592 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T00:39Z] WARN  17:39:18,603 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T00:39Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T00:39Z] INFO  17:39:19,481 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T00:39Z] INFO  17:39:19,494 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T00:39Z] WARN  17:39:19,889 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T00:39Z] WARN  17:39:19,900 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T00:39Z] INFO  17:39:20,145 ProgressMeter -       8:8999161        9250732.0    30.0 s            3.0 s       55.9%    53.0 s      23.0 s
[2016-04-15T00:39Z] INFO  17:39:21,505 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:39Z] INFO  17:39:21,507 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:39Z] INFO  17:39:21,508 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:39Z] INFO  17:39:21,508 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:39Z] INFO  17:39:21,523 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/9/R14-18106_kapa-NGv3-PE100-NGv3-sort-9_15564086_32405601-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/9/R14-18106_kapa-NGv3-PE100-NGv3-9_15564086_32405601-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/9/tx/tmp3q91IN/R14-18106_kapa-NGv3-PE100-NGv3-9_15564086_32405601.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:39Z] INFO  17:39:21,540 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:39Z] INFO  17:39:21,540 HelpFormatter - Date/Time: 2016/04/14 17:39:21
[2016-04-15T00:39Z] INFO  17:39:21,540 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:39Z] INFO  17:39:21,540 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:39Z] WARN  17:39:21,597 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T00:39Z] WARN  17:39:21,608 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/9/tx/tmp3q91IN/R14-18106_kapa-NGv3-PE100-NGv3-9_15564086_32405601.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T00:39Z] INFO  17:39:21,822 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:39Z] INFO  17:39:22,030 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T00:39Z] INFO  17:39:22,039 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:39Z] INFO  17:39:22,134 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.09
[2016-04-15T00:39Z] INFO  17:39:22,165 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T00:39Z] INFO  17:39:22,494 IntervalUtils - Processing 89361 bp from intervals
[2016-04-15T00:39Z] WARN  17:39:22,500 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:39Z] INFO  17:39:22,600 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:39Z] INFO  17:39:22,670 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:39Z] INFO  17:39:22,672 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:39Z] INFO  17:39:22,672 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T00:39Z] INFO  17:39:22,673 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T00:39Z] INFO  17:39:22,674 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T00:39Z] INFO  17:39:22,674 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T00:39Z] INFO  17:39:22,871 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T00:39Z] INFO  17:39:23,673 ProgressMeter -      8:22437040      2.0674651E7    30.0 s            1.0 s       38.5%    78.0 s      48.0 s
[2016-04-15T00:39Z] INFO  17:39:24,912 ProgressMeter -      8:41363430      1.9159463E7    30.0 s            1.0 s       64.4%    46.0 s      16.0 s
[2016-04-15T00:39Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T00:39Z] INFO  17:39:25,245 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T00:39Z] INFO  17:39:25,245 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T00:39Z] WARN  17:39:25,521 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T00:39Z] WARN  17:39:25,522 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T00:39Z] INFO  17:39:26,432 ProgressMeter -     7:100551998      5.4804197E7    60.0 s            1.0 s       48.0%     2.1 m      64.0 s
[2016-04-15T00:39Z] INFO  17:39:26,957 ProgressMeter -      8:59572188      1.6158098E7    30.0 s            1.0 s       78.8%    38.0 s       8.0 s
[2016-04-15T00:39Z] INFO  17:39:28,288 ProgressMeter -      8:75227498      2.3194526E7    30.0 s            1.0 s       84.7%    35.0 s       5.0 s
[2016-04-15T00:39Z] INFO  17:39:30,898 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.0040321670000000006
[2016-04-15T00:39Z] INFO  17:39:30,899 PairHMM - Total compute time in PairHMM computeLikelihoods() : 1.329516863
[2016-04-15T00:39Z] INFO  17:39:30,900 HaplotypeCaller - Ran local assembly on 711 active regions
[2016-04-15T00:39Z] INFO  17:39:30,942 ProgressMeter -            done      2.5170077E7    34.0 s            1.0 s      100.0%    34.0 s       0.0 s
[2016-04-15T00:39Z] INFO  17:39:30,943 ProgressMeter - Total runtime 34.00 secs, 0.57 min, 0.01 hours
[2016-04-15T00:39Z] INFO  17:39:30,944 MicroScheduler - 10066 reads were filtered out during the traversal out of approximately 125198 total reads (8.04%)
[2016-04-15T00:39Z] INFO  17:39:30,945 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:39Z] INFO  17:39:30,946 MicroScheduler -   -> 9300 reads (7.43% of total) failing DuplicateReadFilter
[2016-04-15T00:39Z] INFO  17:39:30,946 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:39Z] INFO  17:39:30,947 MicroScheduler -   -> 766 reads (0.61% of total) failing HCMappingQualityFilter
[2016-04-15T00:39Z] INFO  17:39:30,948 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:39Z] INFO  17:39:30,948 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:39Z] INFO  17:39:30,949 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:39Z] INFO  17:39:30,949 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:39Z] INFO  17:39:31,057 ProgressMeter -      6:39271765     2.42519515E8   120.0 s            0.0 s       65.2%     3.1 m      64.0 s
[2016-04-15T00:39Z] INFO  17:39:32,150 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.004283096
[2016-04-15T00:39Z] INFO  17:39:32,150 PairHMM - Total compute time in PairHMM computeLikelihoods() : 0.071338444
[2016-04-15T00:39Z] INFO  17:39:32,151 HaplotypeCaller - Ran local assembly on 606 active regions
[2016-04-15T00:39Z] INFO  17:39:32,209 ProgressMeter -            done      1.7516305E7    27.0 s            1.0 s      100.0%    27.0 s       0.0 s
[2016-04-15T00:39Z] INFO  17:39:32,210 ProgressMeter - Total runtime 27.09 secs, 0.45 min, 0.01 hours
[2016-04-15T00:39Z] INFO  17:39:32,210 MicroScheduler - 6582 reads were filtered out during the traversal out of approximately 89787 total reads (7.33%)
[2016-04-15T00:39Z] INFO  17:39:32,211 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:39Z] INFO  17:39:32,211 MicroScheduler -   -> 6473 reads (7.21% of total) failing DuplicateReadFilter
[2016-04-15T00:39Z] INFO  17:39:32,212 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:39Z] INFO  17:39:32,212 MicroScheduler -   -> 109 reads (0.12% of total) failing HCMappingQualityFilter
[2016-04-15T00:39Z] INFO  17:39:32,212 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:39Z] INFO  17:39:32,212 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:39Z] INFO  17:39:32,213 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:39Z] INFO  17:39:32,213 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:39Z] INFO  17:39:32,356 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:39Z] GATK: HaplotypeCaller
[2016-04-15T00:39Z] INFO  17:39:32,984 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.005425333
[2016-04-15T00:39Z] INFO  17:39:32,987 PairHMM - Total compute time in PairHMM computeLikelihoods() : 0.13376757
[2016-04-15T00:39Z] INFO  17:39:32,988 HaplotypeCaller - Ran local assembly on 780 active regions
[2016-04-15T00:39Z] INFO  17:39:33,036 ProgressMeter -            done      2.8015737E7    34.0 s            1.0 s      100.0%    34.0 s       0.0 s
[2016-04-15T00:39Z] INFO  17:39:33,037 ProgressMeter - Total runtime 34.79 secs, 0.58 min, 0.01 hours
[2016-04-15T00:39Z] INFO  17:39:33,038 MicroScheduler - 10421 reads were filtered out during the traversal out of approximately 135002 total reads (7.72%)
[2016-04-15T00:39Z] INFO  17:39:33,039 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:39Z] INFO  17:39:33,040 MicroScheduler -   -> 10176 reads (7.54% of total) failing DuplicateReadFilter
[2016-04-15T00:39Z] INFO  17:39:33,040 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:39Z] INFO  17:39:33,041 MicroScheduler -   -> 245 reads (0.18% of total) failing HCMappingQualityFilter
[2016-04-15T00:39Z] INFO  17:39:33,042 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:39Z] INFO  17:39:33,042 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:39Z] INFO  17:39:33,043 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:39Z] INFO  17:39:33,044 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:39Z] INFO  17:39:33,226 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.019155455000000002
[2016-04-15T00:39Z] INFO  17:39:33,226 PairHMM - Total compute time in PairHMM computeLikelihoods() : 0.302030689
[2016-04-15T00:39Z] INFO  17:39:33,226 HaplotypeCaller - Ran local assembly on 916 active regions
[2016-04-15T00:39Z] INFO  17:39:33,280 ProgressMeter -            done      4.4752116E7    38.0 s            0.0 s      100.0%    38.0 s       0.0 s
[2016-04-15T00:39Z] INFO  17:39:33,280 ProgressMeter - Total runtime 38.39 secs, 0.64 min, 0.01 hours
[2016-04-15T00:39Z] INFO  17:39:33,281 MicroScheduler - 12784 reads were filtered out during the traversal out of approximately 167076 total reads (7.65%)
[2016-04-15T00:39Z] INFO  17:39:33,281 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:39Z] INFO  17:39:33,281 MicroScheduler -   -> 12606 reads (7.55% of total) failing DuplicateReadFilter
[2016-04-15T00:39Z] INFO  17:39:33,281 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:39Z] INFO  17:39:33,282 MicroScheduler -   -> 178 reads (0.11% of total) failing HCMappingQualityFilter
[2016-04-15T00:39Z] INFO  17:39:33,282 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:39Z] INFO  17:39:33,282 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:39Z] INFO  17:39:33,282 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:39Z] INFO  17:39:33,283 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:39Z] INFO  17:39:33,604 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:39Z] GATK: HaplotypeCaller
[2016-04-15T00:39Z] INFO  17:39:34,371 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:39Z] GATK: HaplotypeCaller
[2016-04-15T00:39Z] INFO  17:39:34,734 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:39Z] GATK: HaplotypeCaller
[2016-04-15T00:39Z] INFO  17:39:35,199 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:39Z] INFO  17:39:35,203 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:39Z] INFO  17:39:35,203 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:39Z] INFO  17:39:35,204 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:39Z] INFO  17:39:35,209 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/9/R14-18106_kapa-NGv3-PE100-NGv3-sort-9_32407258_65506776-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/9/R14-18106_kapa-NGv3-PE100-NGv3-9_32407258_65506776-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/9/tx/tmpFm3DtB/R14-18106_kapa-NGv3-PE100-NGv3-9_32407258_65506776.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:39Z] INFO  17:39:35,216 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:39Z] INFO  17:39:35,217 HelpFormatter - Date/Time: 2016/04/14 17:39:35
[2016-04-15T00:39Z] INFO  17:39:35,217 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:39Z] INFO  17:39:35,218 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:39Z] WARN  17:39:35,241 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T00:39Z] WARN  17:39:35,244 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/9/tx/tmpFm3DtB/R14-18106_kapa-NGv3-PE100-NGv3-9_32407258_65506776.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T00:39Z] INFO  17:39:35,401 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:39Z] INFO  17:39:35,609 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T00:39Z] INFO  17:39:35,620 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:39Z] INFO  17:39:35,700 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-15T00:39Z] INFO  17:39:35,724 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T00:39Z] INFO  17:39:35,865 ProgressMeter -     8:101724590      1.8770485E7    30.0 s            1.0 s       53.0%    56.0 s      26.0 s
[2016-04-15T00:39Z] INFO  17:39:36,317 IntervalUtils - Processing 223679 bp from intervals
[2016-04-15T00:39Z] WARN  17:39:36,334 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:39Z] INFO  17:39:36,454 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:39Z] INFO  17:39:36,554 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:39Z] INFO  17:39:36,556 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:39Z] INFO  17:39:36,557 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T00:39Z] INFO  17:39:36,557 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T00:39Z] INFO  17:39:36,562 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T00:39Z] INFO  17:39:36,563 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T00:39Z] INFO  17:39:36,576 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.028592248
[2016-04-15T00:39Z] INFO  17:39:36,577 PairHMM - Total compute time in PairHMM computeLikelihoods() : 1.881582241
[2016-04-15T00:39Z] INFO  17:39:36,578 HaplotypeCaller - Ran local assembly on 849 active regions
[2016-04-15T00:39Z] INFO  17:39:36,623 ProgressMeter -            done      2.7109958E7    46.0 s            1.0 s      100.0%    46.0 s       0.0 s
[2016-04-15T00:39Z] INFO  17:39:36,623 ProgressMeter - Total runtime 46.51 secs, 0.78 min, 0.01 hours
[2016-04-15T00:39Z] INFO  17:39:36,623 MicroScheduler - 53929 reads were filtered out during the traversal out of approximately 203154 total reads (26.55%)
[2016-04-15T00:39Z] INFO  17:39:36,624 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:39Z] INFO  17:39:36,624 MicroScheduler -   -> 12699 reads (6.25% of total) failing DuplicateReadFilter
[2016-04-15T00:39Z] INFO  17:39:36,624 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:39Z] INFO  17:39:36,624 MicroScheduler -   -> 41230 reads (20.29% of total) failing HCMappingQualityFilter
[2016-04-15T00:39Z] INFO  17:39:36,625 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:39Z] INFO  17:39:36,625 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:39Z] INFO  17:39:36,625 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:39Z] INFO  17:39:36,626 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:39Z] INFO  17:39:36,823 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T00:39Z] INFO  17:39:37,056 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:39Z] INFO  17:39:37,059 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:39Z] INFO  17:39:37,060 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:39Z] INFO  17:39:37,060 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:39Z] INFO  17:39:37,065 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/9/R14-18106_kapa-NGv3-PE100-NGv3-sort-9_65507205_82187750-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/9/R14-18106_kapa-NGv3-PE100-NGv3-9_65507205_82187750-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/9/tx/tmp9gswLw/R14-18106_kapa-NGv3-PE100-NGv3-9_65507205_82187750.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:39Z] INFO  17:39:37,080 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:39Z] INFO  17:39:37,080 HelpFormatter - Date/Time: 2016/04/14 17:39:37
[2016-04-15T00:39Z] INFO  17:39:37,080 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:39Z] INFO  17:39:37,081 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:39Z] WARN  17:39:37,122 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T00:39Z] WARN  17:39:37,125 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/9/tx/tmp9gswLw/R14-18106_kapa-NGv3-PE100-NGv3-9_65507205_82187750.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T00:39Z] INFO  17:39:37,323 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:39Z] INFO  17:39:37,588 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T00:39Z] INFO  17:39:37,598 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:39Z] INFO  17:39:37,681 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-15T00:39Z] INFO  17:39:37,721 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T00:39Z] INFO  17:39:37,781 ProgressMeter -     7:141539138     1.21400411E8    60.0 s            0.0 s       99.4%    60.0 s       0.0 s
[2016-04-15T00:39Z] INFO  17:39:38,007 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:39Z] INFO  17:39:38,066 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:39Z] INFO  17:39:38,070 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:39Z] INFO  17:39:38,071 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:39Z] INFO  17:39:38,072 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:39Z] INFO  17:39:38,077 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/9/R14-18106_kapa-NGv3-PE100-NGv3-sort-9_97718189_113228306-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/9/R14-18106_kapa-NGv3-PE100-NGv3-9_97718189_113228306-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/9/tx/tmps2guMa/R14-18106_kapa-NGv3-PE100-NGv3-9_97718189_113228306.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:39Z] INFO  17:39:38,087 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:39Z] INFO  17:39:38,098 HelpFormatter - Date/Time: 2016/04/14 17:39:38
[2016-04-15T00:39Z] INFO  17:39:38,099 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:39Z] INFO  17:39:38,100 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:39Z] INFO  17:39:38,115 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:39Z] INFO  17:39:38,119 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:39Z] INFO  17:39:38,119 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:39Z] INFO  17:39:38,120 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:39Z] INFO  17:39:38,125 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/9/R14-18106_kapa-NGv3-PE100-NGv3-sort-9_82188172_97717561-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/9/R14-18106_kapa-NGv3-PE100-NGv3-9_82188172_97717561-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/9/tx/tmp1m7wFN/R14-18106_kapa-NGv3-PE100-NGv3-9_82188172_97717561.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:39Z] WARN  17:39:38,140 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T00:39Z] WARN  17:39:38,143 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/9/tx/tmps2guMa/R14-18106_kapa-NGv3-PE100-NGv3-9_97718189_113228306.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T00:39Z] INFO  17:39:38,147 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:39Z] INFO  17:39:38,148 HelpFormatter - Date/Time: 2016/04/14 17:39:38
[2016-04-15T00:39Z] INFO  17:39:38,148 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:39Z] INFO  17:39:38,148 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:39Z] INFO  17:39:38,166 IntervalUtils - Processing 119378 bp from intervals
[2016-04-15T00:39Z] WARN  17:39:38,171 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:39Z] INFO  17:39:38,175 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.01272405
[2016-04-15T00:39Z] INFO  17:39:38,176 PairHMM - Total compute time in PairHMM computeLikelihoods() : 1.1092387590000001
[2016-04-15T00:39Z] INFO  17:39:38,176 HaplotypeCaller - Ran local assembly on 1623 active regions
[2016-04-15T00:39Z] WARN  17:39:38,211 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T00:39Z] WARN  17:39:38,214 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/9/tx/tmp1m7wFN/R14-18106_kapa-NGv3-PE100-NGv3-9_82188172_97717561.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T00:39Z] INFO  17:39:38,219 ProgressMeter -            done      1.2205741E8    60.0 s            0.0 s      100.0%    60.0 s       0.0 s
[2016-04-15T00:39Z] INFO  17:39:38,220 ProgressMeter - Total runtime 60.46 secs, 1.01 min, 0.02 hours
[2016-04-15T00:39Z] INFO  17:39:38,221 MicroScheduler - 24529 reads were filtered out during the traversal out of approximately 309989 total reads (7.91%)
[2016-04-15T00:39Z] INFO  17:39:38,222 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:39Z] INFO  17:39:38,222 MicroScheduler -   -> 23555 reads (7.60% of total) failing DuplicateReadFilter
[2016-04-15T00:39Z] INFO  17:39:38,223 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:39Z] INFO  17:39:38,224 MicroScheduler -   -> 974 reads (0.31% of total) failing HCMappingQualityFilter
[2016-04-15T00:39Z] INFO  17:39:38,224 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:39Z] INFO  17:39:38,225 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:39Z] INFO  17:39:38,226 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:39Z] INFO  17:39:38,226 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:39Z] GATK: HaplotypeCaller
[2016-04-15T00:39Z] INFO  17:39:38,340 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:39Z] INFO  17:39:38,425 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:39Z] INFO  17:39:38,474 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:39Z] INFO  17:39:38,474 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:39Z] INFO  17:39:38,475 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T00:39Z] INFO  17:39:38,475 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T00:39Z] INFO  17:39:38,478 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:39Z] INFO  17:39:38,494 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T00:39Z] INFO  17:39:38,494 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T00:39Z] INFO  17:39:38,711 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T00:39Z] INFO  17:39:38,731 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:39Z] INFO  17:39:38,746 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T00:39Z] INFO  17:39:38,746 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T00:39Z] INFO  17:39:38,756 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:39Z] INFO  17:39:38,805 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-15T00:39Z] INFO  17:39:38,835 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-15T00:39Z] INFO  17:39:38,843 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T00:39Z] INFO  17:39:38,853 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T00:39Z] INFO  17:39:39,011 ProgressMeter -     7:151884800      7.7177372E7    60.0 s            0.0 s       87.1%    68.0 s       8.0 s
[2016-04-15T00:39Z] INFO  17:39:39,246 IntervalUtils - Processing 181286 bp from intervals
[2016-04-15T00:39Z] WARN  17:39:39,252 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:39Z] INFO  17:39:39,298 IntervalUtils - Processing 199321 bp from intervals
[2016-04-15T00:39Z] WARN  17:39:39,305 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:39Z] INFO  17:39:39,349 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:39Z] INFO  17:39:39,430 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:39Z] INFO  17:39:39,435 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:39Z] INFO  17:39:39,437 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:39Z] INFO  17:39:39,437 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T00:39Z] INFO  17:39:39,438 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T00:39Z] INFO  17:39:39,450 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T00:39Z] INFO  17:39:39,451 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T00:39Z] INFO  17:39:39,560 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:39Z] INFO  17:39:39,560 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:39Z] INFO  17:39:39,561 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T00:39Z] INFO  17:39:39,561 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T00:39Z] INFO  17:39:39,570 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T00:39Z] INFO  17:39:39,574 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T00:39Z] INFO  17:39:39,735 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T00:39Z] INFO  17:39:39,792 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T00:39Z] INFO  17:39:39,869 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:39Z] GATK: HaplotypeCaller
[2016-04-15T00:39Z] INFO  17:39:40,218 ProgressMeter -     8:124982275      1.8429517E7    30.0 s            1.0 s       79.2%    37.0 s       7.0 s
[2016-04-15T00:39Z] INFO  17:39:41,459 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:39Z] INFO  17:39:41,461 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:39Z] INFO  17:39:41,461 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:39Z] INFO  17:39:41,461 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:39Z] INFO  17:39:41,480 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/9/R14-18106_kapa-NGv3-PE100-NGv3-sort-9_113231219_129089575-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/9/R14-18106_kapa-NGv3-PE100-NGv3-9_113231219_129089575-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/9/tx/tmpp78r8s/R14-18106_kapa-NGv3-PE100-NGv3-9_113231219_129089575.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:39Z] INFO  17:39:41,489 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:39Z] INFO  17:39:41,489 HelpFormatter - Date/Time: 2016/04/14 17:39:41
[2016-04-15T00:39Z] INFO  17:39:41,489 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:39Z] INFO  17:39:41,489 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:39Z] WARN  17:39:41,534 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T00:39Z] WARN  17:39:41,545 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/9/tx/tmpp78r8s/R14-18106_kapa-NGv3-PE100-NGv3-9_113231219_129089575.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T00:39Z] INFO  17:39:41,761 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:39Z] INFO  17:39:42,020 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T00:39Z] INFO  17:39:42,030 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:39Z] INFO  17:39:42,129 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.10
[2016-04-15T00:39Z] INFO  17:39:42,154 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T00:39Z] INFO  17:39:42,258 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.006516264000000001
[2016-04-15T00:39Z] INFO  17:39:42,259 PairHMM - Total compute time in PairHMM computeLikelihoods() : 0.23755979100000002
[2016-04-15T00:39Z] INFO  17:39:42,259 HaplotypeCaller - Ran local assembly on 605 active regions
[2016-04-15T00:39Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T00:39Z] INFO  17:39:42,318 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T00:39Z] INFO  17:39:42,316 ProgressMeter -            done      1.8346896E7    29.0 s            1.0 s      100.0%    29.0 s       0.0 s
[2016-04-15T00:39Z] INFO  17:39:42,316 ProgressMeter - Total runtime 29.13 secs, 0.49 min, 0.01 hours
[2016-04-15T00:39Z] INFO  17:39:42,317 MicroScheduler - 8499 reads were filtered out during the traversal out of approximately 111754 total reads (7.61%)
[2016-04-15T00:39Z] INFO  17:39:42,317 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:39Z] INFO  17:39:42,317 MicroScheduler -   -> 8391 reads (7.51% of total) failing DuplicateReadFilter
[2016-04-15T00:39Z] INFO  17:39:42,317 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:39Z] INFO  17:39:42,318 MicroScheduler -   -> 108 reads (0.10% of total) failing HCMappingQualityFilter
[2016-04-15T00:39Z] INFO  17:39:42,318 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:39Z] INFO  17:39:42,318 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:39Z] INFO  17:39:42,318 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:39Z] INFO  17:39:42,319 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:39Z] INFO  17:39:42,320 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T00:39Z] WARN  17:39:42,579 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T00:39Z] WARN  17:39:42,580 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T00:39Z] INFO  17:39:42,740 IntervalUtils - Processing 228449 bp from intervals
[2016-04-15T00:39Z] WARN  17:39:42,745 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:39Z] INFO  17:39:42,856 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:39Z] INFO  17:39:42,998 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:39Z] INFO  17:39:42,999 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:39Z] INFO  17:39:43,000 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T00:39Z] INFO  17:39:43,000 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T00:39Z] INFO  17:39:43,009 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T00:39Z] INFO  17:39:43,009 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T00:39Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T00:39Z] INFO  17:39:43,040 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T00:39Z] INFO  17:39:43,041 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T00:39Z] INFO  17:39:43,080 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:39Z] INFO  17:39:43,083 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:39Z] INFO  17:39:43,083 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:39Z] INFO  17:39:43,084 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:39Z] INFO  17:39:43,088 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/9/R14-18106_kapa-NGv3-PE100-NGv3-sort-9_129097484_141213431-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/9/R14-18106_kapa-NGv3-PE100-NGv3-9_129097484_141213431-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/9/tx/tmpOpM3F_/R14-18106_kapa-NGv3-PE100-NGv3-9_129097484_141213431.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:39Z] INFO  17:39:43,118 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:39Z] INFO  17:39:43,128 HelpFormatter - Date/Time: 2016/04/14 17:39:43
[2016-04-15T00:39Z] INFO  17:39:43,129 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:39Z] INFO  17:39:43,130 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:39Z] WARN  17:39:43,173 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T00:39Z] WARN  17:39:43,176 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/9/tx/tmpOpM3F_/R14-18106_kapa-NGv3-PE100-NGv3-9_129097484_141213431.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T00:39Z] INFO  17:39:43,305 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T00:39Z] INFO  17:39:43,365 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:39Z] WARN  17:39:43,365 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T00:39Z] WARN  17:39:43,366 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T00:39Z] INFO  17:39:43,584 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T00:39Z] INFO  17:39:43,593 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:39Z] INFO  17:39:43,678 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-15T00:39Z] INFO  17:39:43,702 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T00:39Z] INFO  17:39:43,919 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:39Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T00:39Z] INFO  17:39:44,223 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T00:39Z] INFO  17:39:44,224 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T00:39Z] INFO  17:39:44,303 IntervalUtils - Processing 455246 bp from intervals
[2016-04-15T00:39Z] WARN  17:39:44,333 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:39Z] GATK: HaplotypeCaller
[2016-04-15T00:39Z] INFO  17:39:44,469 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:39Z] INFO  17:39:44,639 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:39Z] INFO  17:39:44,641 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:39Z] INFO  17:39:44,641 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T00:39Z] WARN  17:39:44,641 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T00:39Z] WARN  17:39:44,642 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T00:39Z] INFO  17:39:44,652 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T00:39Z] INFO  17:39:44,664 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T00:39Z] INFO  17:39:44,665 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T00:39Z] INFO  17:39:44,754 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.007226023000000001
[2016-04-15T00:39Z] INFO  17:39:44,755 PairHMM - Total compute time in PairHMM computeLikelihoods() : 0.412511063
[2016-04-15T00:39Z] INFO  17:39:44,755 HaplotypeCaller - Ran local assembly on 765 active regions
[2016-04-15T00:39Z] INFO  17:39:44,811 ProgressMeter -            done       2.937439E7    34.0 s            1.0 s      100.0%    34.0 s       0.0 s
[2016-04-15T00:39Z] INFO  17:39:44,812 ProgressMeter - Total runtime 34.62 secs, 0.58 min, 0.01 hours
[2016-04-15T00:39Z] INFO  17:39:44,813 MicroScheduler - 9567 reads were filtered out during the traversal out of approximately 130062 total reads (7.36%)
[2016-04-15T00:39Z] INFO  17:39:44,814 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:39Z] INFO  17:39:44,814 MicroScheduler -   -> 9442 reads (7.26% of total) failing DuplicateReadFilter
[2016-04-15T00:39Z] INFO  17:39:44,815 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:39Z] INFO  17:39:44,816 MicroScheduler -   -> 125 reads (0.10% of total) failing HCMappingQualityFilter
[2016-04-15T00:39Z] INFO  17:39:44,816 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:39Z] INFO  17:39:44,817 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:39Z] INFO  17:39:44,817 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:39Z] INFO  17:39:44,818 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:39Z] INFO  17:39:44,922 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T00:39Z] INFO  17:39:45,282 ProgressMeter -      9:12777608      2.2680917E7    30.0 s            1.0 s       79.9%    37.0 s       7.0 s
[2016-04-15T00:39Z] INFO  17:39:45,627 ProgressMeter -     8:144644684        7303293.0    30.0 s            4.0 s       32.9%    91.0 s      61.0 s
[2016-04-15T00:39Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T00:39Z] INFO  17:39:45,977 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T00:39Z] INFO  17:39:45,977 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T00:39Z] INFO  17:39:46,387 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:39Z] WARN  17:39:46,470 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T00:39Z] WARN  17:39:46,471 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T00:39Z] GATK: HaplotypeCaller
[2016-04-15T00:39Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T00:39Z] INFO  17:39:47,350 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T00:39Z] INFO  17:39:47,350 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T00:39Z] INFO  17:39:47,857 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:39Z] INFO  17:39:47,860 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:39Z] INFO  17:39:47,861 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:39Z] INFO  17:39:47,861 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:39Z] INFO  17:39:47,866 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/10/R14-18106_kapa-NGv3-PE100-NGv3-sort-10_0_15559243-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/10/R14-18106_kapa-NGv3-PE100-NGv3-10_0_15559243-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/10/tx/tmp5cKyCj/R14-18106_kapa-NGv3-PE100-NGv3-10_0_15559243.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:39Z] WARN  17:39:47,866 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T00:39Z] WARN  17:39:47,870 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T00:39Z] INFO  17:39:47,874 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:39Z] INFO  17:39:47,875 HelpFormatter - Date/Time: 2016/04/14 17:39:47
[2016-04-15T00:39Z] INFO  17:39:47,876 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:39Z] INFO  17:39:47,887 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:39Z] WARN  17:39:47,919 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T00:39Z] WARN  17:39:47,933 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/10/tx/tmp5cKyCj/R14-18106_kapa-NGv3-PE100-NGv3-10_0_15559243.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T00:39Z] INFO  17:39:48,180 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:39Z] INFO  17:39:48,461 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T00:39Z] INFO  17:39:48,470 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:39Z] INFO  17:39:48,605 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.13
[2016-04-15T00:39Z] INFO  17:39:48,641 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T00:39Z] INFO  17:39:49,149 IntervalUtils - Processing 145147 bp from intervals
[2016-04-15T00:39Z] WARN  17:39:49,155 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:39Z] INFO  17:39:49,404 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:39Z] INFO  17:39:49,541 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:39Z] INFO  17:39:49,542 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:39Z] INFO  17:39:49,543 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T00:39Z] INFO  17:39:49,543 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T00:39Z] INFO  17:39:49,557 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T00:39Z] INFO  17:39:49,562 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T00:39Z] INFO  17:39:49,873 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T00:39Z] INFO  17:39:50,305 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:39Z] INFO  17:39:50,308 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:39Z] INFO  17:39:50,308 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:39Z] INFO  17:39:50,309 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:39Z] INFO  17:39:50,313 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/10/R14-18106_kapa-NGv3-PE100-NGv3-sort-10_15561288_31134502-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/10/R14-18106_kapa-NGv3-PE100-NGv3-10_15561288_31134502-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/10/tx/tmpRIBxlJ/R14-18106_kapa-NGv3-PE100-NGv3-10_15561288_31134502.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:39Z] INFO  17:39:50,340 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:39Z] INFO  17:39:50,341 HelpFormatter - Date/Time: 2016/04/14 17:39:50
[2016-04-15T00:39Z] INFO  17:39:50,342 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:39Z] INFO  17:39:50,342 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:39Z] WARN  17:39:50,380 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T00:39Z] WARN  17:39:50,383 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/10/tx/tmpRIBxlJ/R14-18106_kapa-NGv3-PE100-NGv3-10_15561288_31134502.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T00:39Z] INFO  17:39:50,424 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.007259444
[2016-04-15T00:39Z] INFO  17:39:50,425 PairHMM - Total compute time in PairHMM computeLikelihoods() : 0.32361512200000003
[2016-04-15T00:39Z] INFO  17:39:50,426 HaplotypeCaller - Ran local assembly on 893 active regions
[2016-04-15T00:39Z] INFO  17:39:50,491 ProgressMeter -            done      3.9438501E7    35.0 s            0.0 s      100.0%    35.0 s       0.0 s
[2016-04-15T00:39Z] INFO  17:39:50,492 ProgressMeter - Total runtime 35.23 secs, 0.59 min, 0.01 hours
[2016-04-15T00:39Z] INFO  17:39:50,493 MicroScheduler - 21831 reads were filtered out during the traversal out of approximately 167301 total reads (13.05%)
[2016-04-15T00:39Z] INFO  17:39:50,493 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:39Z] INFO  17:39:50,494 MicroScheduler -   -> 11754 reads (7.03% of total) failing DuplicateReadFilter
[2016-04-15T00:39Z] INFO  17:39:50,494 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:39Z] INFO  17:39:50,494 MicroScheduler -   -> 10077 reads (6.02% of total) failing HCMappingQualityFilter
[2016-04-15T00:39Z] INFO  17:39:50,494 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:39Z] INFO  17:39:50,494 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:39Z] INFO  17:39:50,495 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:39Z] INFO  17:39:50,495 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:39Z] INFO  17:39:50,579 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:39Z] INFO  17:39:50,778 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T00:39Z] INFO  17:39:50,799 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:39Z] INFO  17:39:50,894 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.09
[2016-04-15T00:39Z] INFO  17:39:50,926 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T00:39Z] INFO  17:39:51,349 IntervalUtils - Processing 156629 bp from intervals
[2016-04-15T00:39Z] WARN  17:39:51,355 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:39Z] INFO  17:39:51,527 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:39Z] INFO  17:39:51,653 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:39Z] INFO  17:39:51,659 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:39Z] INFO  17:39:51,660 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T00:39Z] INFO  17:39:51,661 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T00:39Z] INFO  17:39:51,672 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T00:39Z] INFO  17:39:51,672 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T00:39Z] INFO  17:39:51,961 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T00:39Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T00:39Z] INFO  17:39:52,446 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T00:39Z] INFO  17:39:52,446 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T00:39Z] INFO  17:39:52,688 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:39Z] INFO  17:39:52,699 ProgressMeter -      9:27950669      1.7240228E7    30.0 s            1.0 s       99.9%    30.0 s       0.0 s
[2016-04-15T00:39Z] WARN  17:39:52,830 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T00:39Z] WARN  17:39:52,831 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T00:39Z] WARN  17:39:52,956 ExactAFCalculator - this tool is currently set to genotype at most 6 alternate alleles in a given context, but the context at 9:85861584 has 9 alternate alleles so only the top alleles will be used; see the --max_alternate_alleles argument
[2016-04-15T00:39Z] GATK: HaplotypeCaller
[2016-04-15T00:39Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T00:39Z] INFO  17:39:53,314 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T00:39Z] INFO  17:39:53,314 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T00:39Z] INFO  17:39:53,674 ProgressMeter -      8:30946481     1.30502624E8    60.0 s            0.0 s       98.9%    60.0 s       0.0 s
[2016-04-15T00:39Z] INFO  17:39:53,751 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.020758256000000003
[2016-04-15T00:39Z] INFO  17:39:53,763 PairHMM - Total compute time in PairHMM computeLikelihoods() : 3.2740036270000004
[2016-04-15T00:39Z] INFO  17:39:53,764 HaplotypeCaller - Ran local assembly on 1144 active regions
[2016-04-15T00:39Z] INFO  17:39:53,783 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.00748618
[2016-04-15T00:39Z] INFO  17:39:53,784 PairHMM - Total compute time in PairHMM computeLikelihoods() : 0.34383320500000003
[2016-04-15T00:39Z] WARN  17:39:53,784 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T00:39Z] INFO  17:39:53,785 HaplotypeCaller - Ran local assembly on 626 active regions
[2016-04-15T00:39Z] WARN  17:39:53,784 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T00:39Z] INFO  17:39:53,802 ProgressMeter -            done      6.7177744E7    47.0 s            0.0 s      100.0%    47.0 s       0.0 s
[2016-04-15T00:39Z] INFO  17:39:53,802 ProgressMeter - Total runtime 47.98 secs, 0.80 min, 0.01 hours
[2016-04-15T00:39Z] INFO  17:39:53,803 MicroScheduler - 14601 reads were filtered out during the traversal out of approximately 191774 total reads (7.61%)
[2016-04-15T00:39Z] INFO  17:39:53,803 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:39Z] INFO  17:39:53,803 MicroScheduler -   -> 14306 reads (7.46% of total) failing DuplicateReadFilter
[2016-04-15T00:39Z] INFO  17:39:53,803 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:39Z] INFO  17:39:53,804 MicroScheduler -   -> 295 reads (0.15% of total) failing HCMappingQualityFilter
[2016-04-15T00:39Z] INFO  17:39:53,804 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:39Z] INFO  17:39:53,804 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:39Z] INFO  17:39:53,804 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:39Z] INFO  17:39:53,805 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:39Z] INFO  17:39:53,843 ProgressMeter -            done      1.7418853E7    31.0 s            1.0 s      100.0%    31.0 s       0.0 s
[2016-04-15T00:39Z] INFO  17:39:53,843 ProgressMeter - Total runtime 31.17 secs, 0.52 min, 0.01 hours
[2016-04-15T00:39Z] INFO  17:39:53,845 MicroScheduler - 11012 reads were filtered out during the traversal out of approximately 113839 total reads (9.67%)
[2016-04-15T00:39Z] INFO  17:39:53,845 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:39Z] INFO  17:39:53,845 MicroScheduler -   -> 8251 reads (7.25% of total) failing DuplicateReadFilter
[2016-04-15T00:39Z] INFO  17:39:53,846 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:39Z] INFO  17:39:53,846 MicroScheduler -   -> 2761 reads (2.43% of total) failing HCMappingQualityFilter
[2016-04-15T00:39Z] INFO  17:39:53,846 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:39Z] INFO  17:39:53,846 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:39Z] INFO  17:39:53,847 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:39Z] INFO  17:39:53,847 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:39Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T00:39Z] INFO  17:39:53,898 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T00:39Z] INFO  17:39:53,898 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T00:39Z] WARN  17:39:54,133 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T00:39Z] WARN  17:39:54,133 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T00:39Z] INFO  17:39:54,232 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.014771144000000002
[2016-04-15T00:39Z] INFO  17:39:54,233 PairHMM - Total compute time in PairHMM computeLikelihoods() : 1.582497821
[2016-04-15T00:39Z] INFO  17:39:54,233 HaplotypeCaller - Ran local assembly on 1799 active regions
[2016-04-15T00:39Z] INFO  17:39:54,284 ProgressMeter -            done     1.35599805E8    60.0 s            0.0 s      100.0%    60.0 s       0.0 s
[2016-04-15T00:39Z] INFO  17:39:54,284 ProgressMeter - Total runtime 60.64 secs, 1.01 min, 0.02 hours
[2016-04-15T00:39Z] INFO  17:39:54,285 MicroScheduler - 26013 reads were filtered out during the traversal out of approximately 323544 total reads (8.04%)
[2016-04-15T00:39Z] INFO  17:39:54,285 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:39Z] INFO  17:39:54,285 MicroScheduler -   -> 24547 reads (7.59% of total) failing DuplicateReadFilter
[2016-04-15T00:39Z] INFO  17:39:54,286 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:39Z] INFO  17:39:54,286 MicroScheduler -   -> 1466 reads (0.45% of total) failing HCMappingQualityFilter
[2016-04-15T00:39Z] INFO  17:39:54,286 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:39Z] INFO  17:39:54,286 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:39Z] INFO  17:39:54,286 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:39Z] INFO  17:39:54,287 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:39Z] INFO  17:39:55,282 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:39Z] INFO  17:39:55,496 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:39Z] GATK: HaplotypeCaller
[2016-04-15T00:39Z] GATK: HaplotypeCaller
[2016-04-15T00:39Z] INFO  17:39:55,999 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:39Z] INFO  17:39:56,096 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:39Z] INFO  17:39:56,098 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:39Z] INFO  17:39:56,098 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:39Z] INFO  17:39:56,098 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:39Z] INFO  17:39:56,114 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/10/R14-18106_kapa-NGv3-PE100-NGv3-sort-10_31137459_46960129-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/10/R14-18106_kapa-NGv3-PE100-NGv3-10_31137459_46960129-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/10/tx/tmp9eSqWW/R14-18106_kapa-NGv3-PE100-NGv3-10_31137459_46960129.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:39Z] INFO  17:39:56,128 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:39Z] INFO  17:39:56,143 HelpFormatter - Date/Time: 2016/04/14 17:39:56
[2016-04-15T00:39Z] INFO  17:39:56,144 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:39Z] INFO  17:39:56,145 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:39Z] WARN  17:39:56,210 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T00:39Z] WARN  17:39:56,222 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/10/tx/tmp9eSqWW/R14-18106_kapa-NGv3-PE100-NGv3-10_31137459_46960129.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T00:39Z] INFO  17:39:56,283 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.033265982
[2016-04-15T00:39Z] INFO  17:39:56,284 PairHMM - Total compute time in PairHMM computeLikelihoods() : 9.355029598
[2016-04-15T00:39Z] INFO  17:39:56,285 HaplotypeCaller - Ran local assembly on 1714 active regions
[2016-04-15T00:39Z] INFO  17:39:56,330 ProgressMeter -            done     1.17619154E8    77.0 s            0.0 s      100.0%    77.0 s       0.0 s
[2016-04-15T00:39Z] INFO  17:39:56,331 ProgressMeter - Total runtime 77.34 secs, 1.29 min, 0.02 hours
[2016-04-15T00:39Z] INFO  17:39:56,331 MicroScheduler - 86131 reads were filtered out during the traversal out of approximately 413782 total reads (20.82%)
[2016-04-15T00:39Z] INFO  17:39:56,331 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:39Z] INFO  17:39:56,333 MicroScheduler -   -> 27242 reads (6.58% of total) failing DuplicateReadFilter
[2016-04-15T00:39Z] INFO  17:39:56,333 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:39Z] INFO  17:39:56,333 MicroScheduler -   -> 58889 reads (14.23% of total) failing HCMappingQualityFilter
[2016-04-15T00:39Z] INFO  17:39:56,333 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:39Z] INFO  17:39:56,334 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:39Z] INFO  17:39:56,334 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:39Z] INFO  17:39:56,334 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:39Z] INFO  17:39:56,433 ProgressMeter -     7:100646810      5.6169526E7    90.0 s            1.0 s       52.2%     2.9 m      82.0 s
[2016-04-15T00:39Z] INFO  17:39:56,446 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:39Z] GATK: HaplotypeCaller
[2016-04-15T00:39Z] INFO  17:39:56,653 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T00:39Z] INFO  17:39:56,673 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:39Z] INFO  17:39:56,762 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.09
[2016-04-15T00:39Z] INFO  17:39:56,783 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T00:39Z] INFO  17:39:57,313 IntervalUtils - Processing 103621 bp from intervals
[2016-04-15T00:39Z] WARN  17:39:57,329 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:39Z] INFO  17:39:57,473 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:39Z] INFO  17:39:57,575 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:39Z] INFO  17:39:57,579 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:39Z] INFO  17:39:57,580 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T00:39Z] INFO  17:39:57,581 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T00:39Z] INFO  17:39:57,593 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T00:39Z] INFO  17:39:57,593 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T00:39Z] INFO  17:39:57,869 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T00:39Z] INFO  17:39:58,011 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:39Z] GATK: HaplotypeCaller
[2016-04-15T00:39Z] INFO  17:39:58,720 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:39Z] INFO  17:39:58,723 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:39Z] INFO  17:39:58,724 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:39Z] INFO  17:39:58,724 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:39Z] INFO  17:39:58,729 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/10/R14-18106_kapa-NGv3-PE100-NGv3-sort-10_46960410_62493077-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/10/R14-18106_kapa-NGv3-PE100-NGv3-10_46960410_62493077-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/10/tx/tmpFE8PBG/R14-18106_kapa-NGv3-PE100-NGv3-10_46960410_62493077.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:39Z] INFO  17:39:58,739 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:39Z] INFO  17:39:58,750 HelpFormatter - Date/Time: 2016/04/14 17:39:58
[2016-04-15T00:39Z] INFO  17:39:58,751 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:39Z] INFO  17:39:58,752 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:39Z] WARN  17:39:58,797 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T00:39Z] WARN  17:39:58,800 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/10/tx/tmpFE8PBG/R14-18106_kapa-NGv3-PE100-NGv3-10_46960410_62493077.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T00:39Z] INFO  17:39:59,058 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:39Z] INFO  17:39:59,066 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:39Z] INFO  17:39:59,070 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:39Z] INFO  17:39:59,070 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:39Z] INFO  17:39:59,071 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:39Z] INFO  17:39:59,076 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/10/R14-18106_kapa-NGv3-PE100-NGv3-sort-10_62539923_78084243-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/10/R14-18106_kapa-NGv3-PE100-NGv3-10_62539923_78084243-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/10/tx/tmpeGeyZZ/R14-18106_kapa-NGv3-PE100-NGv3-10_62539923_78084243.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:39Z] INFO  17:39:59,104 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:39Z] INFO  17:39:59,105 HelpFormatter - Date/Time: 2016/04/14 17:39:59
[2016-04-15T00:39Z] INFO  17:39:59,105 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:39Z] INFO  17:39:59,106 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:39Z] WARN  17:39:59,128 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T00:39Z] WARN  17:39:59,131 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/10/tx/tmpeGeyZZ/R14-18106_kapa-NGv3-PE100-NGv3-10_62539923_78084243.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T00:39Z] INFO  17:39:59,314 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T00:39Z] INFO  17:39:59,324 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:39Z] INFO  17:39:59,403 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:39Z] INFO  17:39:59,416 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.09
[2016-04-15T00:39Z] INFO  17:39:59,446 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T00:39Z] INFO  17:39:59,574 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T00:39Z] INFO  17:39:59,584 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:39Z] INFO  17:39:59,679 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.09
[2016-04-15T00:39Z] INFO  17:39:59,710 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T00:39Z] INFO  17:39:59,752 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:39Z] INFO  17:39:59,755 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:39Z] INFO  17:39:59,756 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:39Z] INFO  17:39:59,757 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:39Z] INFO  17:39:59,761 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/10/R14-18106_kapa-NGv3-PE100-NGv3-sort-10_78316966_93841258-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/10/R14-18106_kapa-NGv3-PE100-NGv3-10_78316966_93841258-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/10/tx/tmpWFBpWO/R14-18106_kapa-NGv3-PE100-NGv3-10_78316966_93841258.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:39Z] INFO  17:39:59,770 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:39Z] INFO  17:39:59,771 HelpFormatter - Date/Time: 2016/04/14 17:39:59
[2016-04-15T00:39Z] INFO  17:39:59,772 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:39Z] INFO  17:39:59,772 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:39Z] WARN  17:39:59,817 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T00:39Z] WARN  17:39:59,820 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/10/tx/tmpWFBpWO/R14-18106_kapa-NGv3-PE100-NGv3-10_78316966_93841258.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T00:39Z] INFO  17:39:59,924 IntervalUtils - Processing 143638 bp from intervals
[2016-04-15T00:39Z] WARN  17:39:59,929 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:40Z] INFO  17:40:00,079 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:40Z] INFO  17:40:00,124 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:40Z] INFO  17:40:00,240 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:40Z] INFO  17:40:00,241 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:40Z] INFO  17:40:00,241 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T00:40Z] INFO  17:40:00,241 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T00:40Z] INFO  17:40:00,255 IntervalUtils - Processing 230109 bp from intervals
[2016-04-15T00:40Z] WARN  17:40:00,261 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:40Z] INFO  17:40:00,261 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T00:40Z] INFO  17:40:00,262 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T00:40Z] INFO  17:40:00,326 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T00:40Z] INFO  17:40:00,336 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:40Z] INFO  17:40:00,410 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:40Z] INFO  17:40:00,429 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.09
[2016-04-15T00:40Z] INFO  17:40:00,455 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T00:40Z] INFO  17:40:00,517 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T00:40Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T00:40Z] INFO  17:40:00,538 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T00:40Z] INFO  17:40:00,539 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T00:40Z] INFO  17:40:00,561 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:40Z] INFO  17:40:00,562 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:40Z] INFO  17:40:00,563 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T00:40Z] INFO  17:40:00,564 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T00:40Z] INFO  17:40:00,576 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T00:40Z] INFO  17:40:00,576 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T00:40Z] INFO  17:40:00,847 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T00:40Z] INFO  17:40:00,953 IntervalUtils - Processing 148808 bp from intervals
[2016-04-15T00:40Z] WARN  17:40:00,958 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:40Z] WARN  17:40:00,973 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T00:40Z] WARN  17:40:00,973 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T00:40Z] INFO  17:40:01,059 ProgressMeter -      6:44229363     5.05545099E8     2.5 m            0.0 s       95.5%     2.6 m       7.0 s
[2016-04-15T00:40Z] INFO  17:40:01,108 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:40Z] INFO  17:40:01,278 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:40Z] INFO  17:40:01,279 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:40Z] INFO  17:40:01,280 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T00:40Z] INFO  17:40:01,281 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T00:40Z] INFO  17:40:01,293 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T00:40Z] INFO  17:40:01,294 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T00:40Z] INFO  17:40:01,604 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T00:40Z] INFO  17:40:01,802 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:40Z] INFO  17:40:01,805 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:40Z] INFO  17:40:01,806 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:40Z] INFO  17:40:01,806 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:40Z] INFO  17:40:01,811 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/10/R14-18106_kapa-NGv3-PE100-NGv3-sort-10_93851586_111625070-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/10/R14-18106_kapa-NGv3-PE100-NGv3-10_93851586_111625070-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/10/tx/tmpNOlPPj/R14-18106_kapa-NGv3-PE100-NGv3-10_93851586_111625070.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:40Z] INFO  17:40:01,841 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:40Z] INFO  17:40:01,841 HelpFormatter - Date/Time: 2016/04/14 17:40:01
[2016-04-15T00:40Z] INFO  17:40:01,841 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:40Z] INFO  17:40:01,841 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:40Z] WARN  17:40:01,889 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T00:40Z] WARN  17:40:01,900 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/10/tx/tmpNOlPPj/R14-18106_kapa-NGv3-PE100-NGv3-10_93851586_111625070.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T00:40Z] INFO  17:40:02,183 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:40Z] INFO  17:40:02,388 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T00:40Z] INFO  17:40:02,398 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:40Z] INFO  17:40:02,509 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.11
[2016-04-15T00:40Z] INFO  17:40:02,562 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T00:40Z] INFO  17:40:02,996 IntervalUtils - Processing 335852 bp from intervals
[2016-04-15T00:40Z] WARN  17:40:03,008 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:40Z] INFO  17:40:03,103 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:40Z] INFO  17:40:03,261 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:40Z] INFO  17:40:03,262 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:40Z] INFO  17:40:03,263 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T00:40Z] INFO  17:40:03,263 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T00:40Z] INFO  17:40:03,264 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T00:40Z] INFO  17:40:03,264 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T00:40Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T00:40Z] INFO  17:40:03,295 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T00:40Z] INFO  17:40:03,296 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T00:40Z] INFO  17:40:03,559 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T00:40Z] WARN  17:40:03,560 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T00:40Z] WARN  17:40:03,567 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T00:40Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T00:40Z] INFO  17:40:05,056 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T00:40Z] INFO  17:40:05,068 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T00:40Z] WARN  17:40:05,220 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T00:40Z] WARN  17:40:05,221 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T00:40Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T00:40Z] INFO  17:40:05,828 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T00:40Z] INFO  17:40:05,834 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T00:40Z] WARN  17:40:06,308 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T00:40Z] WARN  17:40:06,309 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T00:40Z] INFO  17:40:06,576 ProgressMeter -      9:34635811        8710922.0    30.0 s            3.0 s       26.4%   113.0 s      83.0 s
[2016-04-15T00:40Z] INFO  17:40:07,006 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.037949389
[2016-04-15T00:40Z] INFO  17:40:07,007 PairHMM - Total compute time in PairHMM computeLikelihoods() : 19.825281474
[2016-04-15T00:40Z] INFO  17:40:07,008 HaplotypeCaller - Ran local assembly on 3721 active regions
[2016-04-15T00:40Z] INFO  17:40:07,036 ProgressMeter -            done     5.57488561E8     2.6 m            0.0 s      100.0%     2.6 m       0.0 s
[2016-04-15T00:40Z] INFO  17:40:07,037 ProgressMeter - Total runtime 156.00 secs, 2.60 min, 0.04 hours
[2016-04-15T00:40Z] INFO  17:40:07,038 MicroScheduler - 97605 reads were filtered out during the traversal out of approximately 816177 total reads (11.96%)
[2016-04-15T00:40Z] INFO  17:40:07,039 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:40Z] INFO  17:40:07,039 MicroScheduler -   -> 59223 reads (7.26% of total) failing DuplicateReadFilter
[2016-04-15T00:40Z] INFO  17:40:07,040 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:40Z] INFO  17:40:07,040 MicroScheduler -   -> 38382 reads (4.70% of total) failing HCMappingQualityFilter
[2016-04-15T00:40Z] INFO  17:40:07,041 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:40Z] INFO  17:40:07,042 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:40Z] INFO  17:40:07,042 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:40Z] INFO  17:40:07,043 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:40Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T00:40Z] INFO  17:40:07,400 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T00:40Z] INFO  17:40:07,401 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T00:40Z] WARN  17:40:07,797 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T00:40Z] WARN  17:40:07,797 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T00:40Z] INFO  17:40:08,429 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:40Z] INFO  17:40:08,497 ProgressMeter -      9:78942925      2.2594487E7    30.0 s            1.0 s       74.5%    40.0 s      10.0 s
[2016-04-15T00:40Z] GATK: HaplotypeCaller
[2016-04-15T00:40Z] INFO  17:40:09,476 ProgressMeter -      9:91660661      1.5796785E7    30.0 s            1.0 s       52.6%    57.0 s      27.0 s
[2016-04-15T00:40Z] INFO  17:40:09,579 ProgressMeter -     9:103212839      2.0791452E7    30.0 s            1.0 s       45.9%    65.0 s      35.0 s
[2016-04-15T00:40Z] INFO  17:40:11,932 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:40Z] INFO  17:40:11,935 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:40Z] INFO  17:40:11,936 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:40Z] INFO  17:40:11,936 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:40Z] INFO  17:40:11,941 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/10/R14-18106_kapa-NGv3-PE100-NGv3-sort-10_111628371_127265443-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/10/R14-18106_kapa-NGv3-PE100-NGv3-10_111628371_127265443-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/10/tx/tmpqlAVbY/R14-18106_kapa-NGv3-PE100-NGv3-10_111628371_127265443.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:40Z] INFO  17:40:11,960 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:40Z] INFO  17:40:11,961 HelpFormatter - Date/Time: 2016/04/14 17:40:11
[2016-04-15T00:40Z] INFO  17:40:11,961 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:40Z] INFO  17:40:11,962 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:40Z] WARN  17:40:11,984 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T00:40Z] WARN  17:40:11,987 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/10/tx/tmpqlAVbY/R14-18106_kapa-NGv3-PE100-NGv3-10_111628371_127265443.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T00:40Z] INFO  17:40:12,273 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:40Z] INFO  17:40:12,477 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T00:40Z] INFO  17:40:12,486 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:40Z] INFO  17:40:12,571 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-15T00:40Z] INFO  17:40:12,598 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T00:40Z] INFO  17:40:13,002 IntervalUtils - Processing 210787 bp from intervals
[2016-04-15T00:40Z] WARN  17:40:13,007 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:40Z] INFO  17:40:13,018 ProgressMeter -     9:117793832      2.2890654E7    30.0 s            1.0 s       39.6%    75.0 s      45.0 s
[2016-04-15T00:40Z] INFO  17:40:13,104 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:40Z] INFO  17:40:13,218 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:40Z] INFO  17:40:13,219 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:40Z] INFO  17:40:13,220 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T00:40Z] INFO  17:40:13,221 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T00:40Z] INFO  17:40:13,222 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T00:40Z] INFO  17:40:13,222 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T00:40Z] INFO  17:40:13,436 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T00:40Z] INFO  17:40:14,676 ProgressMeter -     9:131370328      1.9275924E7    30.0 s            1.0 s       18.9%     2.6 m       2.1 m
[2016-04-15T00:40Z] INFO  17:40:15,185 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.008895175
[2016-04-15T00:40Z] INFO  17:40:15,186 PairHMM - Total compute time in PairHMM computeLikelihoods() : 0.9183482610000001
[2016-04-15T00:40Z] INFO  17:40:15,187 HaplotypeCaller - Ran local assembly on 913 active regions
[2016-04-15T00:40Z] INFO  17:40:15,238 ProgressMeter -            done      3.7646403E7    36.0 s            0.0 s      100.0%    36.0 s       0.0 s
[2016-04-15T00:40Z] INFO  17:40:15,239 ProgressMeter - Total runtime 36.76 secs, 0.61 min, 0.01 hours
[2016-04-15T00:40Z] INFO  17:40:15,240 MicroScheduler - 61627 reads were filtered out during the traversal out of approximately 186103 total reads (33.11%)
[2016-04-15T00:40Z] INFO  17:40:15,240 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:40Z] INFO  17:40:15,240 MicroScheduler -   -> 10293 reads (5.53% of total) failing DuplicateReadFilter
[2016-04-15T00:40Z] INFO  17:40:15,240 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:40Z] INFO  17:40:15,241 MicroScheduler -   -> 51334 reads (27.58% of total) failing HCMappingQualityFilter
[2016-04-15T00:40Z] INFO  17:40:15,241 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:40Z] INFO  17:40:15,241 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:40Z] INFO  17:40:15,241 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:40Z] INFO  17:40:15,242 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:40Z] INFO  17:40:15,628 ProgressMeter -     8:145667634      3.1140137E7    60.0 s            1.0 s       81.7%    73.0 s      13.0 s
[2016-04-15T00:40Z] INFO  17:40:16,732 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:40Z] GATK: HaplotypeCaller
[2016-04-15T00:40Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T00:40Z] INFO  17:40:19,143 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T00:40Z] INFO  17:40:19,145 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T00:40Z] WARN  17:40:19,409 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T00:40Z] WARN  17:40:19,410 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T00:40Z] INFO  17:40:19,564 ProgressMeter -      10:7776885       1.670368E7    30.0 s            1.0 s       53.1%    56.0 s      26.0 s
[2016-04-15T00:40Z] INFO  17:40:19,889 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:40Z] INFO  17:40:19,902 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:40Z] INFO  17:40:19,903 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:40Z] INFO  17:40:19,904 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:40Z] INFO  17:40:19,908 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/10/R14-18106_kapa-NGv3-PE100-NGv3-sort-10_127328721_135534747-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/10/R14-18106_kapa-NGv3-PE100-NGv3-10_127328721_135534747-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/10/tx/tmpZ3xOQ5/R14-18106_kapa-NGv3-PE100-NGv3-10_127328721_135534747.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:40Z] INFO  17:40:19,940 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:40Z] INFO  17:40:19,941 HelpFormatter - Date/Time: 2016/04/14 17:40:19
[2016-04-15T00:40Z] INFO  17:40:19,942 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:40Z] INFO  17:40:19,942 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:40Z] WARN  17:40:19,999 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T00:40Z] WARN  17:40:20,005 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/10/tx/tmpZ3xOQ5/R14-18106_kapa-NGv3-PE100-NGv3-10_127328721_135534747.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T00:40Z] INFO  17:40:20,239 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:40Z] INFO  17:40:20,529 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T00:40Z] INFO  17:40:20,538 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:40Z] INFO  17:40:20,636 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.10
[2016-04-15T00:40Z] INFO  17:40:20,664 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T00:40Z] INFO  17:40:21,049 IntervalUtils - Processing 102137 bp from intervals
[2016-04-15T00:40Z] WARN  17:40:21,076 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:40Z] INFO  17:40:21,149 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:40Z] INFO  17:40:21,203 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:40Z] INFO  17:40:21,204 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:40Z] INFO  17:40:21,204 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T00:40Z] INFO  17:40:21,205 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T00:40Z] INFO  17:40:21,206 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T00:40Z] INFO  17:40:21,206 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T00:40Z] INFO  17:40:21,420 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T00:40Z] INFO  17:40:21,685 ProgressMeter -     10:25510086      2.2204385E7    30.0 s            1.0 s       62.4%    48.0 s      18.0 s
[2016-04-15T00:40Z] INFO  17:40:24,041 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.036650309
[2016-04-15T00:40Z] INFO  17:40:24,042 PairHMM - Total compute time in PairHMM computeLikelihoods() : 4.293257735
[2016-04-15T00:40Z] INFO  17:40:24,053 HaplotypeCaller - Ran local assembly on 1456 active regions
[2016-04-15T00:40Z] INFO  17:40:24,087 ProgressMeter -            done      4.6020795E7    68.0 s            1.0 s      100.0%    68.0 s       0.0 s
[2016-04-15T00:40Z] INFO  17:40:24,088 ProgressMeter - Total runtime 68.49 secs, 1.14 min, 0.02 hours
[2016-04-15T00:40Z] INFO  17:40:24,088 MicroScheduler - 33144 reads were filtered out during the traversal out of approximately 348302 total reads (9.52%)
[2016-04-15T00:40Z] INFO  17:40:24,089 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:40Z] INFO  17:40:24,090 MicroScheduler -   -> 26750 reads (7.68% of total) failing DuplicateReadFilter
[2016-04-15T00:40Z] INFO  17:40:24,091 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:40Z] INFO  17:40:24,091 MicroScheduler -   -> 6394 reads (1.84% of total) failing HCMappingQualityFilter
[2016-04-15T00:40Z] INFO  17:40:24,092 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:40Z] INFO  17:40:24,093 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:40Z] INFO  17:40:24,093 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:40Z] INFO  17:40:24,094 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:40Z] INFO  17:40:25,512 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:40Z] GATK: HaplotypeCaller
[2016-04-15T00:40Z] INFO  17:40:26,434 ProgressMeter -     7:106820324     1.99740189E8   120.0 s            0.0 s       89.1%     2.2 m      14.0 s
[2016-04-15T00:40Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T00:40Z] INFO  17:40:27,286 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T00:40Z] INFO  17:40:27,286 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T00:40Z] INFO  17:40:27,602 ProgressMeter -     10:45799038       1.454754E7    30.0 s            2.0 s       84.3%    35.0 s       5.0 s
[2016-04-15T00:40Z] WARN  17:40:27,605 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T00:40Z] WARN  17:40:27,606 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T00:40Z] INFO  17:40:28,088 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.008534926
[2016-04-15T00:40Z] INFO  17:40:28,089 PairHMM - Total compute time in PairHMM computeLikelihoods() : 0.6417578420000001
[2016-04-15T00:40Z] INFO  17:40:28,089 HaplotypeCaller - Ran local assembly on 1173 active regions
[2016-04-15T00:40Z] INFO  17:40:28,146 ProgressMeter -            done      6.7952989E7    48.0 s            0.0 s      100.0%    48.0 s       0.0 s
[2016-04-15T00:40Z] INFO  17:40:28,146 ProgressMeter - Total runtime 48.71 secs, 0.81 min, 0.01 hours
[2016-04-15T00:40Z] INFO  17:40:28,147 MicroScheduler - 40728 reads were filtered out during the traversal out of approximately 273507 total reads (14.89%)
[2016-04-15T00:40Z] INFO  17:40:28,147 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:40Z] INFO  17:40:28,147 MicroScheduler -   -> 19439 reads (7.11% of total) failing DuplicateReadFilter
[2016-04-15T00:40Z] INFO  17:40:28,147 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:40Z] INFO  17:40:28,148 MicroScheduler -   -> 21289 reads (7.78% of total) failing HCMappingQualityFilter
[2016-04-15T00:40Z] INFO  17:40:28,148 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:40Z] INFO  17:40:28,148 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:40Z] INFO  17:40:28,148 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:40Z] INFO  17:40:28,149 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:40Z] INFO  17:40:28,641 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:40Z] INFO  17:40:28,661 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:40Z] INFO  17:40:28,662 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:40Z] INFO  17:40:28,663 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:40Z] INFO  17:40:28,667 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/11/R14-18106_kapa-NGv3-PE100-NGv3-sort-11_0_15994658-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/11/R14-18106_kapa-NGv3-PE100-NGv3-11_0_15994658-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/11/tx/tmpTpS2jI/R14-18106_kapa-NGv3-PE100-NGv3-11_0_15994658.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:40Z] INFO  17:40:28,675 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:40Z] INFO  17:40:28,676 HelpFormatter - Date/Time: 2016/04/14 17:40:28
[2016-04-15T00:40Z] INFO  17:40:28,677 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:40Z] INFO  17:40:28,677 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:40Z] WARN  17:40:28,702 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T00:40Z] WARN  17:40:28,709 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/11/tx/tmpTpS2jI/R14-18106_kapa-NGv3-PE100-NGv3-11_0_15994658.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T00:40Z] INFO  17:40:28,929 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:40Z] INFO  17:40:29,101 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T00:40Z] INFO  17:40:29,118 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:40Z] INFO  17:40:29,182 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-15T00:40Z] INFO  17:40:29,207 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T00:40Z] INFO  17:40:29,589 IntervalUtils - Processing 438345 bp from intervals
[2016-04-15T00:40Z] WARN  17:40:29,595 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:40Z] INFO  17:40:29,670 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:40Z] INFO  17:40:29,813 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:40Z] INFO  17:40:29,814 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:40Z] INFO  17:40:29,815 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T00:40Z] INFO  17:40:29,816 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T00:40Z] INFO  17:40:29,834 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T00:40Z] INFO  17:40:29,834 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T00:40Z] INFO  17:40:29,918 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:40Z] INFO  17:40:30,023 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T00:40Z] GATK: HaplotypeCaller
[2016-04-15T00:40Z] INFO  17:40:30,264 ProgressMeter -     10:50184842        6277681.0    30.0 s            4.0 s       33.4%    89.0 s      59.0 s
[2016-04-15T00:40Z] INFO  17:40:30,330 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.007228501
[2016-04-15T00:40Z] INFO  17:40:30,331 PairHMM - Total compute time in PairHMM computeLikelihoods() : 0.32122743600000003
[2016-04-15T00:40Z] INFO  17:40:30,332 HaplotypeCaller - Ran local assembly on 731 active regions
[2016-04-15T00:40Z] INFO  17:40:30,396 ProgressMeter -            done      2.2800337E7    32.0 s            1.0 s      100.0%    32.0 s       0.0 s
[2016-04-15T00:40Z] INFO  17:40:30,397 ProgressMeter - Total runtime 32.82 secs, 0.55 min, 0.01 hours
[2016-04-15T00:40Z] INFO  17:40:30,397 MicroScheduler - 29304 reads were filtered out during the traversal out of approximately 150542 total reads (19.47%)
[2016-04-15T00:40Z] INFO  17:40:30,398 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:40Z] INFO  17:40:30,398 MicroScheduler -   -> 10006 reads (6.65% of total) failing DuplicateReadFilter
[2016-04-15T00:40Z] INFO  17:40:30,398 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:40Z] INFO  17:40:30,399 MicroScheduler -   -> 19298 reads (12.82% of total) failing HCMappingQualityFilter
[2016-04-15T00:40Z] INFO  17:40:30,399 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:40Z] INFO  17:40:30,399 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:40Z] INFO  17:40:30,399 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:40Z] INFO  17:40:30,399 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:40Z] INFO  17:40:30,578 ProgressMeter -     10:71655332      2.4630816E7    30.0 s            1.0 s       44.3%    67.0 s      37.0 s
[2016-04-15T00:40Z] INFO  17:40:31,307 ProgressMeter -     10:88992425      1.7320566E7    30.0 s            1.0 s       58.7%    51.0 s      21.0 s
[2016-04-15T00:40Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T00:40Z] INFO  17:40:32,078 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:40Z] INFO  17:40:32,095 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T00:40Z] INFO  17:40:32,101 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T00:40Z] GATK: HaplotypeCaller
[2016-04-15T00:40Z] WARN  17:40:32,407 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T00:40Z] WARN  17:40:32,408 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T00:40Z] INFO  17:40:33,159 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.051319302000000004
[2016-04-15T00:40Z] INFO  17:40:33,159 PairHMM - Total compute time in PairHMM computeLikelihoods() : 21.279826788
[2016-04-15T00:40Z] INFO  17:40:33,160 HaplotypeCaller - Ran local assembly on 2499 active regions
[2016-04-15T00:40Z] INFO  17:40:33,172 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.02163063
[2016-04-15T00:40Z] INFO  17:40:33,173 PairHMM - Total compute time in PairHMM computeLikelihoods() : 1.4409314530000001
[2016-04-15T00:40Z] INFO  17:40:33,174 HaplotypeCaller - Ran local assembly on 1371 active regions
[2016-04-15T00:40Z] INFO  17:40:33,216 ProgressMeter -            done      2.7011063E8     2.1 m            0.0 s      100.0%     2.1 m       0.0 s
[2016-04-15T00:40Z] INFO  17:40:33,217 ProgressMeter - Total runtime 126.81 secs, 2.11 min, 0.04 hours
[2016-04-15T00:40Z] INFO  17:40:33,218 MicroScheduler - 171930 reads were filtered out during the traversal out of approximately 669319 total reads (25.69%)
[2016-04-15T00:40Z] INFO  17:40:33,218 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:40Z] INFO  17:40:33,219 MicroScheduler -   -> 42438 reads (6.34% of total) failing DuplicateReadFilter
[2016-04-15T00:40Z] INFO  17:40:33,219 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:40Z] INFO  17:40:33,219 MicroScheduler -   -> 129492 reads (19.35% of total) failing HCMappingQualityFilter
[2016-04-15T00:40Z] INFO  17:40:33,219 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:40Z] INFO  17:40:33,220 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:40Z] INFO  17:40:33,220 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:40Z] INFO  17:40:33,220 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:40Z] INFO  17:40:33,239 ProgressMeter -            done      8.2992301E7    53.0 s            0.0 s      100.0%    53.0 s       0.0 s
[2016-04-15T00:40Z] INFO  17:40:33,240 ProgressMeter - Total runtime 53.68 secs, 0.89 min, 0.01 hours
[2016-04-15T00:40Z] INFO  17:40:33,240 MicroScheduler - 24000 reads were filtered out during the traversal out of approximately 268180 total reads (8.95%)
[2016-04-15T00:40Z] INFO  17:40:33,241 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:40Z] INFO  17:40:33,242 MicroScheduler -   -> 20265 reads (7.56% of total) failing DuplicateReadFilter
[2016-04-15T00:40Z] INFO  17:40:33,242 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:40Z] INFO  17:40:33,243 MicroScheduler -   -> 3735 reads (1.39% of total) failing HCMappingQualityFilter
[2016-04-15T00:40Z] INFO  17:40:33,244 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:40Z] INFO  17:40:33,244 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:40Z] INFO  17:40:33,245 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:40Z] INFO  17:40:33,245 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:40Z] INFO  17:40:33,290 ProgressMeter -     10:99186065      3.3948401E7    30.0 s            0.0 s       34.6%    86.0 s      56.0 s
[2016-04-15T00:40Z] INFO  17:40:33,345 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:40Z] INFO  17:40:33,348 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:40Z] INFO  17:40:33,348 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:40Z] INFO  17:40:33,348 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:40Z] INFO  17:40:33,352 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/11/R14-18106_kapa-NGv3-PE100-NGv3-sort-11_16007749_31531554-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/11/R14-18106_kapa-NGv3-PE100-NGv3-11_16007749_31531554-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/11/tx/tmpHDJHZc/R14-18106_kapa-NGv3-PE100-NGv3-11_16007749_31531554.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:40Z] INFO  17:40:33,373 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:40Z] INFO  17:40:33,374 HelpFormatter - Date/Time: 2016/04/14 17:40:33
[2016-04-15T00:40Z] INFO  17:40:33,374 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:40Z] INFO  17:40:33,374 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:40Z] WARN  17:40:33,406 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T00:40Z] WARN  17:40:33,413 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/11/tx/tmpHDJHZc/R14-18106_kapa-NGv3-PE100-NGv3-11_16007749_31531554.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T00:40Z] INFO  17:40:33,638 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:40Z] INFO  17:40:33,850 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T00:40Z] INFO  17:40:33,871 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:40Z] INFO  17:40:33,956 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-15T00:40Z] INFO  17:40:33,980 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T00:40Z] INFO  17:40:34,359 IntervalUtils - Processing 144906 bp from intervals
[2016-04-15T00:40Z] WARN  17:40:34,365 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:40Z] INFO  17:40:34,521 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:40Z] INFO  17:40:34,633 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:40Z] INFO  17:40:34,634 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:40Z] INFO  17:40:34,641 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T00:40Z] INFO  17:40:34,642 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T00:40Z] INFO  17:40:34,647 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:40Z] INFO  17:40:34,650 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T00:40Z] INFO  17:40:34,651 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T00:40Z] INFO  17:40:34,686 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:40Z] INFO  17:40:34,879 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T00:40Z] GATK: HaplotypeCaller
[2016-04-15T00:40Z] GATK: HaplotypeCaller
[2016-04-15T00:40Z] INFO  17:40:35,168 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.009565901
[2016-04-15T00:40Z] INFO  17:40:35,169 PairHMM - Total compute time in PairHMM computeLikelihoods() : 0.768344766
[2016-04-15T00:40Z] INFO  17:40:35,170 HaplotypeCaller - Ran local assembly on 1179 active regions
[2016-04-15T00:40Z] INFO  17:40:35,203 ProgressMeter -            done      6.1102753E7    43.0 s            0.0 s      100.0%    43.0 s       0.0 s
[2016-04-15T00:40Z] INFO  17:40:35,225 ProgressMeter - Total runtime 43.57 secs, 0.73 min, 0.01 hours
[2016-04-15T00:40Z] INFO  17:40:35,225 MicroScheduler - 15038 reads were filtered out during the traversal out of approximately 182763 total reads (8.23%)
[2016-04-15T00:40Z] INFO  17:40:35,225 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:40Z] INFO  17:40:35,226 MicroScheduler -   -> 13499 reads (7.39% of total) failing DuplicateReadFilter
[2016-04-15T00:40Z] INFO  17:40:35,226 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:40Z] INFO  17:40:35,226 MicroScheduler -   -> 1539 reads (0.84% of total) failing HCMappingQualityFilter
[2016-04-15T00:40Z] INFO  17:40:35,226 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:40Z] INFO  17:40:35,227 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:40Z] INFO  17:40:35,227 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:40Z] INFO  17:40:35,227 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:40Z] INFO  17:40:35,340 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:40Z] INFO  17:40:35,344 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:40Z] INFO  17:40:35,345 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:40Z] INFO  17:40:35,345 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:40Z] INFO  17:40:35,351 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/11/R14-18106_kapa-NGv3-PE100-NGv3-sort-11_31541602_47074069-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/11/R14-18106_kapa-NGv3-PE100-NGv3-11_31541602_47074069-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/11/tx/tmpKNsltd/R14-18106_kapa-NGv3-PE100-NGv3-11_31541602_47074069.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:40Z] INFO  17:40:35,364 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:40Z] INFO  17:40:35,377 HelpFormatter - Date/Time: 2016/04/14 17:40:35
[2016-04-15T00:40Z] INFO  17:40:35,378 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:40Z] INFO  17:40:35,379 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:40Z] WARN  17:40:35,431 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T00:40Z] WARN  17:40:35,435 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/11/tx/tmpKNsltd/R14-18106_kapa-NGv3-PE100-NGv3-11_31541602_47074069.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T00:40Z] INFO  17:40:35,459 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.011210897000000001
[2016-04-15T00:40Z] INFO  17:40:35,460 PairHMM - Total compute time in PairHMM computeLikelihoods() : 0.610366564
[2016-04-15T00:40Z] INFO  17:40:35,461 HaplotypeCaller - Ran local assembly on 1168 active regions
[2016-04-15T00:40Z] INFO  17:40:35,498 ProgressMeter -            done      5.6897824E7    45.0 s            0.0 s      100.0%    45.0 s       0.0 s
[2016-04-15T00:40Z] INFO  17:40:35,510 ProgressMeter - Total runtime 45.97 secs, 0.77 min, 0.01 hours
[2016-04-15T00:40Z] INFO  17:40:35,511 MicroScheduler - 19018 reads were filtered out during the traversal out of approximately 209233 total reads (9.09%)
[2016-04-15T00:40Z] INFO  17:40:35,512 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:40Z] INFO  17:40:35,512 MicroScheduler -   -> 15551 reads (7.43% of total) failing DuplicateReadFilter
[2016-04-15T00:40Z] INFO  17:40:35,513 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:40Z] INFO  17:40:35,514 MicroScheduler -   -> 3467 reads (1.66% of total) failing HCMappingQualityFilter
[2016-04-15T00:40Z] INFO  17:40:35,514 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:40Z] INFO  17:40:35,515 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:40Z] INFO  17:40:35,515 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:40Z] INFO  17:40:35,516 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:40Z] INFO  17:40:35,716 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:40Z] INFO  17:40:35,983 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T00:40Z] INFO  17:40:36,013 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:40Z] INFO  17:40:36,076 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-15T00:40Z] INFO  17:40:36,097 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T00:40Z] INFO  17:40:36,577 ProgressMeter -      9:43133413      7.8874582E7    60.0 s            0.0 s       94.9%    63.0 s       3.0 s
[2016-04-15T00:40Z] INFO  17:40:36,665 IntervalUtils - Processing 150047 bp from intervals
[2016-04-15T00:40Z] WARN  17:40:36,672 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:40Z] INFO  17:40:36,781 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:40Z] INFO  17:40:36,845 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:40Z] INFO  17:40:36,859 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:40Z] INFO  17:40:36,860 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:40Z] INFO  17:40:36,861 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T00:40Z] INFO  17:40:36,862 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T00:40Z] INFO  17:40:36,862 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T00:40Z] INFO  17:40:36,863 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T00:40Z] INFO  17:40:36,901 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:40Z] INFO  17:40:37,031 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T00:40Z] GATK: HaplotypeCaller
[2016-04-15T00:40Z] GATK: HaplotypeCaller
[2016-04-15T00:40Z] INFO  17:40:37,963 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:40Z] INFO  17:40:37,977 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:40Z] INFO  17:40:37,978 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:40Z] INFO  17:40:37,979 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:40Z] INFO  17:40:37,995 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/11/R14-18106_kapa-NGv3-PE100-NGv3-sort-11_62744265_78270665-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/11/R14-18106_kapa-NGv3-PE100-NGv3-11_62744265_78270665-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/11/tx/tmpBB971q/R14-18106_kapa-NGv3-PE100-NGv3-11_62744265_78270665.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:40Z] INFO  17:40:38,005 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:40Z] INFO  17:40:38,006 HelpFormatter - Date/Time: 2016/04/14 17:40:37
[2016-04-15T00:40Z] INFO  17:40:38,006 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:40Z] INFO  17:40:38,007 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:40Z] INFO  17:40:38,041 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:40Z] INFO  17:40:38,044 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:40Z] INFO  17:40:38,045 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:40Z] INFO  17:40:38,045 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:40Z] INFO  17:40:38,049 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/11/R14-18106_kapa-NGv3-PE100-NGv3-sort-11_47158866_62678572-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/11/R14-18106_kapa-NGv3-PE100-NGv3-11_47158866_62678572-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/11/tx/tmp6XCeJC/R14-18106_kapa-NGv3-PE100-NGv3-11_47158866_62678572.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:40Z] WARN  17:40:38,054 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T00:40Z] WARN  17:40:38,056 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/11/tx/tmpBB971q/R14-18106_kapa-NGv3-PE100-NGv3-11_62744265_78270665.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T00:40Z] INFO  17:40:38,065 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:40Z] INFO  17:40:38,066 HelpFormatter - Date/Time: 2016/04/14 17:40:38
[2016-04-15T00:40Z] INFO  17:40:38,067 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:40Z] INFO  17:40:38,067 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:40Z] WARN  17:40:38,115 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T00:40Z] WARN  17:40:38,117 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/11/tx/tmp6XCeJC/R14-18106_kapa-NGv3-PE100-NGv3-11_47158866_62678572.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T00:40Z] INFO  17:40:38,292 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:40Z] INFO  17:40:38,321 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:40Z] INFO  17:40:38,536 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T00:40Z] INFO  17:40:38,551 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T00:40Z] INFO  17:40:38,560 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:40Z] INFO  17:40:38,577 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:40Z] INFO  17:40:38,660 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.10
[2016-04-15T00:40Z] INFO  17:40:38,688 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.11
[2016-04-15T00:40Z] INFO  17:40:38,687 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T00:40Z] INFO  17:40:38,712 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T00:40Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T00:40Z] INFO  17:40:38,875 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T00:40Z] INFO  17:40:38,876 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T00:40Z] WARN  17:40:39,207 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T00:40Z] WARN  17:40:39,208 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T00:40Z] INFO  17:40:39,249 IntervalUtils - Processing 330540 bp from intervals
[2016-04-15T00:40Z] WARN  17:40:39,254 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:40Z] INFO  17:40:39,312 IntervalUtils - Processing 515206 bp from intervals
[2016-04-15T00:40Z] WARN  17:40:39,335 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:40Z] INFO  17:40:39,338 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:40Z] INFO  17:40:39,408 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:40Z] INFO  17:40:39,443 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:40Z] INFO  17:40:39,443 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:40Z] INFO  17:40:39,444 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T00:40Z] INFO  17:40:39,444 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T00:40Z] INFO  17:40:39,452 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T00:40Z] INFO  17:40:39,453 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T00:40Z] INFO  17:40:39,571 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:40Z] INFO  17:40:39,572 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:40Z] INFO  17:40:39,573 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T00:40Z] INFO  17:40:39,573 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T00:40Z] INFO  17:40:39,574 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T00:40Z] INFO  17:40:39,574 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T00:40Z] INFO  17:40:39,779 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T00:40Z] INFO  17:40:39,786 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T00:40Z] INFO  17:40:40,239 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:40Z] INFO  17:40:40,242 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:40Z] INFO  17:40:40,242 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:40Z] INFO  17:40:40,243 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:40Z] INFO  17:40:40,248 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/11/R14-18106_kapa-NGv3-PE100-NGv3-sort-11_93797496_109964158-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/11/R14-18106_kapa-NGv3-PE100-NGv3-11_93797496_109964158-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/11/tx/tmpwX8siB/R14-18106_kapa-NGv3-PE100-NGv3-11_93797496_109964158.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:40Z] INFO  17:40:40,260 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:40Z] INFO  17:40:40,261 HelpFormatter - Date/Time: 2016/04/14 17:40:40
[2016-04-15T00:40Z] INFO  17:40:40,261 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:40Z] INFO  17:40:40,262 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:40Z] INFO  17:40:40,292 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:40Z] INFO  17:40:40,296 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:40Z] INFO  17:40:40,296 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:40Z] INFO  17:40:40,297 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:40Z] INFO  17:40:40,301 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/11/R14-18106_kapa-NGv3-PE100-NGv3-sort-11_78277177_93796886-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/11/R14-18106_kapa-NGv3-PE100-NGv3-11_78277177_93796886-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/11/tx/tmp5ndwKj/R14-18106_kapa-NGv3-PE100-NGv3-11_78277177_93796886.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:40Z] WARN  17:40:40,305 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T00:40Z] WARN  17:40:40,308 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/11/tx/tmpwX8siB/R14-18106_kapa-NGv3-PE100-NGv3-11_93797496_109964158.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T00:40Z] INFO  17:40:40,312 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:40Z] INFO  17:40:40,319 HelpFormatter - Date/Time: 2016/04/14 17:40:40
[2016-04-15T00:40Z] INFO  17:40:40,320 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:40Z] INFO  17:40:40,321 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:40Z] INFO  17:40:40,336 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.014031765000000002
[2016-04-15T00:40Z] INFO  17:40:40,337 PairHMM - Total compute time in PairHMM computeLikelihoods() : 4.950440221
[2016-04-15T00:40Z] INFO  17:40:40,338 HaplotypeCaller - Ran local assembly on 1494 active regions
[2016-04-15T00:40Z] WARN  17:40:40,354 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T00:40Z] WARN  17:40:40,357 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/11/tx/tmp5ndwKj/R14-18106_kapa-NGv3-PE100-NGv3-11_78277177_93796886.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T00:40Z] INFO  17:40:40,379 ProgressMeter -            done      8.5421311E7    63.0 s            0.0 s      100.0%    63.0 s       0.0 s
[2016-04-15T00:40Z] INFO  17:40:40,380 ProgressMeter - Total runtime 63.82 secs, 1.06 min, 0.02 hours
[2016-04-15T00:40Z] INFO  17:40:40,380 MicroScheduler - 126533 reads were filtered out during the traversal out of approximately 416046 total reads (30.41%)
[2016-04-15T00:40Z] INFO  17:40:40,381 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:40Z] INFO  17:40:40,382 MicroScheduler -   -> 24093 reads (5.79% of total) failing DuplicateReadFilter
[2016-04-15T00:40Z] INFO  17:40:40,382 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:40Z] INFO  17:40:40,383 MicroScheduler -   -> 102440 reads (24.62% of total) failing HCMappingQualityFilter
[2016-04-15T00:40Z] INFO  17:40:40,384 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:40Z] INFO  17:40:40,384 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:40Z] INFO  17:40:40,385 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:40Z] INFO  17:40:40,395 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:40Z] INFO  17:40:40,529 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:40Z] INFO  17:40:40,598 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:40Z] INFO  17:40:40,841 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T00:40Z] INFO  17:40:40,854 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T00:40Z] INFO  17:40:40,858 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:40Z] INFO  17:40:40,869 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:40Z] INFO  17:40:40,955 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-15T00:40Z] INFO  17:40:40,983 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T00:40Z] INFO  17:40:40,988 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.13
[2016-04-15T00:40Z] INFO  17:40:41,012 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T00:40Z] INFO  17:40:41,311 IntervalUtils - Processing 119993 bp from intervals
[2016-04-15T00:40Z] WARN  17:40:41,339 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:40Z] INFO  17:40:41,435 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:40Z] INFO  17:40:41,463 IntervalUtils - Processing 148585 bp from intervals
[2016-04-15T00:40Z] WARN  17:40:41,469 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:40Z] INFO  17:40:41,534 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:40Z] INFO  17:40:41,535 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:40Z] INFO  17:40:41,535 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T00:40Z] INFO  17:40:41,536 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T00:40Z] INFO  17:40:41,558 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T00:40Z] INFO  17:40:41,559 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T00:40Z] INFO  17:40:41,594 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:40Z] INFO  17:40:41,689 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:40Z] INFO  17:40:41,690 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:40Z] INFO  17:40:41,691 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T00:40Z] INFO  17:40:41,691 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T00:40Z] INFO  17:40:41,703 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T00:40Z] INFO  17:40:41,704 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T00:40Z] INFO  17:40:41,781 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T00:40Z] INFO  17:40:41,815 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.013296986
[2016-04-15T00:40Z] INFO  17:40:41,822 PairHMM - Total compute time in PairHMM computeLikelihoods() : 1.009739765
[2016-04-15T00:40Z] INFO  17:40:41,823 HaplotypeCaller - Ran local assembly on 1672 active regions
[2016-04-15T00:40Z] INFO  17:40:41,847 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T00:40Z] INFO  17:40:41,887 ProgressMeter -            done     1.27765104E8    58.0 s            0.0 s      100.0%    58.0 s       0.0 s
[2016-04-15T00:40Z] INFO  17:40:41,888 ProgressMeter - Total runtime 58.89 secs, 0.98 min, 0.02 hours
[2016-04-15T00:40Z] INFO  17:40:41,889 MicroScheduler - 26124 reads were filtered out during the traversal out of approximately 329884 total reads (7.92%)
[2016-04-15T00:40Z] INFO  17:40:41,889 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:40Z] INFO  17:40:41,889 MicroScheduler -   -> 24599 reads (7.46% of total) failing DuplicateReadFilter
[2016-04-15T00:40Z] INFO  17:40:41,889 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:40Z] INFO  17:40:41,890 MicroScheduler -   -> 1525 reads (0.46% of total) failing HCMappingQualityFilter
[2016-04-15T00:40Z] INFO  17:40:41,890 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:40Z] INFO  17:40:41,890 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:40Z] INFO  17:40:41,890 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:40Z] INFO  17:40:41,891 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:40Z] INFO  17:40:41,917 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:40Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T00:40Z] INFO  17:40:42,053 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T00:40Z] INFO  17:40:42,064 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T00:40Z] GATK: HaplotypeCaller
[2016-04-15T00:40Z] WARN  17:40:42,334 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T00:40Z] WARN  17:40:42,335 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T00:40Z] INFO  17:40:42,615 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.008334612
[2016-04-15T00:40Z] INFO  17:40:42,616 PairHMM - Total compute time in PairHMM computeLikelihoods() : 0.294229575
[2016-04-15T00:40Z] INFO  17:40:42,617 HaplotypeCaller - Ran local assembly on 1097 active regions
[2016-04-15T00:40Z] INFO  17:40:42,662 ProgressMeter -            done      5.4493851E7    41.0 s            0.0 s      100.0%    41.0 s       0.0 s
[2016-04-15T00:40Z] INFO  17:40:42,662 ProgressMeter - Total runtime 41.38 secs, 0.69 min, 0.01 hours
[2016-04-15T00:40Z] INFO  17:40:42,663 MicroScheduler - 27420 reads were filtered out during the traversal out of approximately 211718 total reads (12.95%)
[2016-04-15T00:40Z] INFO  17:40:42,664 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:40Z] INFO  17:40:42,664 MicroScheduler -   -> 15006 reads (7.09% of total) failing DuplicateReadFilter
[2016-04-15T00:40Z] INFO  17:40:42,664 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:40Z] INFO  17:40:42,664 MicroScheduler -   -> 12414 reads (5.86% of total) failing HCMappingQualityFilter
[2016-04-15T00:40Z] INFO  17:40:42,665 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:40Z] INFO  17:40:42,665 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:40Z] INFO  17:40:42,665 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:40Z] INFO  17:40:42,665 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:40Z] INFO  17:40:43,246 ProgressMeter -    10:119768539      3.0661009E7    30.0 s            0.0 s       50.6%    59.0 s      29.0 s
[2016-04-15T00:40Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T00:40Z] INFO  17:40:43,291 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T00:40Z] INFO  17:40:43,303 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T00:40Z] INFO  17:40:43,411 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:40Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T00:40Z] INFO  17:40:43,612 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T00:40Z] INFO  17:40:43,613 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T00:40Z] WARN  17:40:43,667 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T00:40Z] WARN  17:40:43,678 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T00:40Z] GATK: HaplotypeCaller
[2016-04-15T00:40Z] WARN  17:40:43,888 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T00:40Z] WARN  17:40:43,889 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T00:40Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T00:40Z] INFO  17:40:43,916 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T00:40Z] INFO  17:40:43,917 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T00:40Z] WARN  17:40:44,191 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T00:40Z] WARN  17:40:44,192 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T00:40Z] INFO  17:40:44,247 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:40Z] GATK: HaplotypeCaller
[2016-04-15T00:40Z] INFO  17:40:44,677 ProgressMeter -     9:136037799     1.36940478E8    60.0 s            0.0 s       51.0%   117.0 s      57.0 s
[2016-04-15T00:40Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T00:40Z] INFO  17:40:45,242 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T00:40Z] INFO  17:40:45,243 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T00:40Z] INFO  17:40:45,510 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:40Z] INFO  17:40:45,524 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:40Z] INFO  17:40:45,525 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:40Z] INFO  17:40:45,526 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:40Z] INFO  17:40:45,530 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/11/R14-18106_kapa-NGv3-PE100-NGv3-sort-11_110001730_125514538-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/11/R14-18106_kapa-NGv3-PE100-NGv3-11_110001730_125514538-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/11/tx/tmpX1oJ0L/R14-18106_kapa-NGv3-PE100-NGv3-11_110001730_125514538.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:40Z] WARN  17:40:45,521 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T00:40Z] WARN  17:40:45,533 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T00:40Z] INFO  17:40:45,550 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:40Z] INFO  17:40:45,551 HelpFormatter - Date/Time: 2016/04/14 17:40:45
[2016-04-15T00:40Z] INFO  17:40:45,552 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:40Z] INFO  17:40:45,552 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:40Z] WARN  17:40:45,627 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T00:40Z] WARN  17:40:45,638 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/11/tx/tmpX1oJ0L/R14-18106_kapa-NGv3-PE100-NGv3-11_110001730_125514538.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T00:40Z] INFO  17:40:46,006 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:40Z] INFO  17:40:46,228 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T00:40Z] INFO  17:40:46,237 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:40Z] INFO  17:40:46,329 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.09
[2016-04-15T00:40Z] INFO  17:40:46,359 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T00:40Z] INFO  17:40:46,921 IntervalUtils - Processing 318135 bp from intervals
[2016-04-15T00:40Z] WARN  17:40:46,928 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:40Z] INFO  17:40:47,078 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:40Z] INFO  17:40:47,175 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:40Z] INFO  17:40:47,178 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:40Z] INFO  17:40:47,179 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:40Z] INFO  17:40:47,180 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:40Z] INFO  17:40:47,184 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/11/R14-18106_kapa-NGv3-PE100-NGv3-sort-11_125523640_135006516-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/11/R14-18106_kapa-NGv3-PE100-NGv3-11_125523640_135006516-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/11/tx/tmp_uhtf2/R14-18106_kapa-NGv3-PE100-NGv3-11_125523640_135006516.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:40Z] INFO  17:40:47,193 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:40Z] INFO  17:40:47,201 HelpFormatter - Date/Time: 2016/04/14 17:40:47
[2016-04-15T00:40Z] INFO  17:40:47,202 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:40Z] INFO  17:40:47,203 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:40Z] INFO  17:40:47,214 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:40Z] INFO  17:40:47,215 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:40Z] INFO  17:40:47,216 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T00:40Z] INFO  17:40:47,217 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T00:40Z] INFO  17:40:47,218 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T00:40Z] INFO  17:40:47,218 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T00:40Z] WARN  17:40:47,257 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T00:40Z] WARN  17:40:47,270 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/11/tx/tmp_uhtf2/R14-18106_kapa-NGv3-PE100-NGv3-11_125523640_135006516.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T00:40Z] INFO  17:40:47,516 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T00:40Z] INFO  17:40:47,645 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:40Z] INFO  17:40:47,870 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T00:40Z] INFO  17:40:47,879 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:40Z] INFO  17:40:47,977 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.10
[2016-04-15T00:40Z] INFO  17:40:48,006 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T00:40Z] INFO  17:40:48,455 IntervalUtils - Processing 106404 bp from intervals
[2016-04-15T00:40Z] WARN  17:40:48,470 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:40Z] INFO  17:40:48,609 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:40Z] INFO  17:40:48,613 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:40Z] INFO  17:40:48,613 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:40Z] INFO  17:40:48,614 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:40Z] INFO  17:40:48,617 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:40Z] INFO  17:40:48,618 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/12/R14-18106_kapa-NGv3-PE100-NGv3-sort-12_0_15637181-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/12/R14-18106_kapa-NGv3-PE100-NGv3-12_0_15637181-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/12/tx/tmpFBfSzD/R14-18106_kapa-NGv3-PE100-NGv3-12_0_15637181.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:40Z] INFO  17:40:48,655 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:40Z] INFO  17:40:48,665 HelpFormatter - Date/Time: 2016/04/14 17:40:48
[2016-04-15T00:40Z] INFO  17:40:48,666 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:40Z] INFO  17:40:48,666 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:40Z] WARN  17:40:48,715 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T00:40Z] INFO  17:40:48,718 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:40Z] WARN  17:40:48,718 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/12/tx/tmpFBfSzD/R14-18106_kapa-NGv3-PE100-NGv3-12_0_15637181.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T00:40Z] INFO  17:40:48,719 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:40Z] INFO  17:40:48,720 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T00:40Z] INFO  17:40:48,720 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T00:40Z] INFO  17:40:48,721 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T00:40Z] INFO  17:40:48,721 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T00:40Z] INFO  17:40:48,909 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:40Z] INFO  17:40:48,966 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T00:40Z] INFO  17:40:49,190 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T00:40Z] INFO  17:40:49,200 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:40Z] INFO  17:40:49,312 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.11
[2016-04-15T00:40Z] INFO  17:40:49,349 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T00:40Z] INFO  17:40:49,881 IntervalUtils - Processing 329920 bp from intervals
[2016-04-15T00:40Z] WARN  17:40:49,886 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:40Z] INFO  17:40:50,018 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:40Z] INFO  17:40:50,185 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:40Z] INFO  17:40:50,187 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:40Z] INFO  17:40:50,187 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T00:40Z] INFO  17:40:50,188 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T00:40Z] INFO  17:40:50,189 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T00:40Z] INFO  17:40:50,189 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T00:40Z] INFO  17:40:50,481 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T00:40Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T00:40Z] INFO  17:40:50,597 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T00:40Z] INFO  17:40:50,597 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T00:40Z] WARN  17:40:50,885 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T00:40Z] WARN  17:40:50,886 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T00:40Z] INFO  17:40:51,212 ProgressMeter -    10:135076737      1.8083954E7    30.0 s            1.0 s       83.4%    35.0 s       5.0 s
[2016-04-15T00:40Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T00:40Z] INFO  17:40:51,861 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T00:40Z] INFO  17:40:51,861 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T00:40Z] WARN  17:40:52,248 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T00:40Z] WARN  17:40:52,255 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T00:40Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T00:40Z] INFO  17:40:52,580 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T00:40Z] INFO  17:40:52,580 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T00:40Z] WARN  17:40:52,870 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T00:40Z] WARN  17:40:52,872 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T00:40Z] INFO  17:40:55,998 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.019113855000000003
[2016-04-15T00:40Z] INFO  17:40:55,998 PairHMM - Total compute time in PairHMM computeLikelihoods() : 4.286642041
[2016-04-15T00:40Z] INFO  17:40:55,999 HaplotypeCaller - Ran local assembly on 1085 active regions
[2016-04-15T00:40Z] INFO  17:40:56,059 ProgressMeter -            done      4.8765504E7    55.0 s            1.0 s      100.0%    55.0 s       0.0 s
[2016-04-15T00:40Z] INFO  17:40:56,060 ProgressMeter - Total runtime 55.82 secs, 0.93 min, 0.02 hours
[2016-04-15T00:40Z] INFO  17:40:56,061 MicroScheduler - 85525 reads were filtered out during the traversal out of approximately 270454 total reads (31.62%)
[2016-04-15T00:40Z] INFO  17:40:56,061 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:40Z] INFO  17:40:56,061 MicroScheduler -   -> 15708 reads (5.81% of total) failing DuplicateReadFilter
[2016-04-15T00:40Z] INFO  17:40:56,061 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:40Z] INFO  17:40:56,062 MicroScheduler -   -> 69817 reads (25.81% of total) failing HCMappingQualityFilter
[2016-04-15T00:40Z] INFO  17:40:56,062 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:40Z] INFO  17:40:56,062 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:40Z] INFO  17:40:56,062 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:40Z] INFO  17:40:56,063 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:40Z] INFO  17:40:57,651 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:40Z] GATK: HaplotypeCaller
[2016-04-15T00:40Z] INFO  17:40:59,854 ProgressMeter -      11:1016891        9985430.0    30.0 s            3.0 s       16.4%     3.0 m       2.5 m
[2016-04-15T00:41Z] INFO  17:41:00,579 ProgressMeter -     10:76871506     1.20656421E8    60.0 s            0.0 s       97.0%    61.0 s       1.0 s
[2016-04-15T00:41Z] INFO  17:41:00,725 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.029936849
[2016-04-15T00:41Z] INFO  17:41:00,725 PairHMM - Total compute time in PairHMM computeLikelihoods() : 3.98335015
[2016-04-15T00:41Z] INFO  17:41:00,725 HaplotypeCaller - Ran local assembly on 820 active regions
[2016-04-15T00:41Z] INFO  17:41:00,783 ProgressMeter -            done      2.7883461E7    39.0 s            1.0 s      100.0%    39.0 s       0.0 s
[2016-04-15T00:41Z] INFO  17:41:00,784 ProgressMeter - Total runtime 39.58 secs, 0.66 min, 0.01 hours
[2016-04-15T00:41Z] INFO  17:41:00,784 MicroScheduler - 13782 reads were filtered out during the traversal out of approximately 163917 total reads (8.41%)
[2016-04-15T00:41Z] INFO  17:41:00,784 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:41Z] INFO  17:41:00,785 MicroScheduler -   -> 12380 reads (7.55% of total) failing DuplicateReadFilter
[2016-04-15T00:41Z] INFO  17:41:00,785 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:41Z] INFO  17:41:00,785 MicroScheduler -   -> 1402 reads (0.86% of total) failing HCMappingQualityFilter
[2016-04-15T00:41Z] INFO  17:41:00,785 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:41Z] INFO  17:41:00,786 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:41Z] INFO  17:41:00,786 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:41Z] INFO  17:41:00,786 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:41Z] INFO  17:41:01,131 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:41Z] INFO  17:41:01,135 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:41Z] INFO  17:41:01,135 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:41Z] INFO  17:41:01,136 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:41Z] INFO  17:41:01,141 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/12/R14-18106_kapa-NGv3-PE100-NGv3-sort-12_15650178_31231471-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/12/R14-18106_kapa-NGv3-PE100-NGv3-12_15650178_31231471-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/12/tx/tmpUkcS40/R14-18106_kapa-NGv3-PE100-NGv3-12_15650178_31231471.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:41Z] INFO  17:41:01,160 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:41Z] INFO  17:41:01,160 HelpFormatter - Date/Time: 2016/04/14 17:41:01
[2016-04-15T00:41Z] INFO  17:41:01,160 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:41Z] INFO  17:41:01,161 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:41Z] WARN  17:41:01,196 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T00:41Z] WARN  17:41:01,198 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/12/tx/tmpUkcS40/R14-18106_kapa-NGv3-PE100-NGv3-12_15650178_31231471.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T00:41Z] INFO  17:41:01,402 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:41Z] INFO  17:41:01,601 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T00:41Z] INFO  17:41:01,610 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:41Z] INFO  17:41:01,690 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-15T00:41Z] INFO  17:41:01,712 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T00:41Z] INFO  17:41:02,174 IntervalUtils - Processing 134686 bp from intervals
[2016-04-15T00:41Z] WARN  17:41:02,180 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:41Z] INFO  17:41:02,248 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:41Z] INFO  17:41:02,254 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:41Z] INFO  17:41:02,357 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:41Z] INFO  17:41:02,357 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:41Z] INFO  17:41:02,358 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T00:41Z] INFO  17:41:02,358 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T00:41Z] INFO  17:41:02,368 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T00:41Z] INFO  17:41:02,369 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T00:41Z] INFO  17:41:02,387 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.013272135000000001
[2016-04-15T00:41Z] INFO  17:41:02,388 PairHMM - Total compute time in PairHMM computeLikelihoods() : 1.39145216
[2016-04-15T00:41Z] INFO  17:41:02,389 HaplotypeCaller - Ran local assembly on 1620 active regions
[2016-04-15T00:41Z] INFO  17:41:02,431 ProgressMeter -            done     1.26783317E8    61.0 s            0.0 s      100.0%    61.0 s       0.0 s
[2016-04-15T00:41Z] INFO  17:41:02,431 ProgressMeter - Total runtime 61.87 secs, 1.03 min, 0.02 hours
[2016-04-15T00:41Z] INFO  17:41:02,432 MicroScheduler - 31069 reads were filtered out during the traversal out of approximately 333840 total reads (9.31%)
[2016-04-15T00:41Z] INFO  17:41:02,432 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:41Z] INFO  17:41:02,432 MicroScheduler -   -> 24870 reads (7.45% of total) failing DuplicateReadFilter
[2016-04-15T00:41Z] INFO  17:41:02,432 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:41Z] INFO  17:41:02,433 MicroScheduler -   -> 6199 reads (1.86% of total) failing HCMappingQualityFilter
[2016-04-15T00:41Z] INFO  17:41:02,433 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:41Z] INFO  17:41:02,433 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:41Z] INFO  17:41:02,433 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:41Z] INFO  17:41:02,434 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:41Z] INFO  17:41:02,596 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T00:41Z] GATK: HaplotypeCaller
[2016-04-15T00:41Z] INFO  17:41:03,291 ProgressMeter -    10:104155718     1.50780845E8    60.0 s            0.0 s       75.5%    79.0 s      19.0 s
[2016-04-15T00:41Z] INFO  17:41:03,919 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:41Z] GATK: HaplotypeCaller
[2016-04-15T00:41Z] INFO  17:41:04,659 ProgressMeter -     11:20483582      2.1089523E7    30.0 s            1.0 s       63.3%    47.0 s      17.0 s
[2016-04-15T00:41Z] INFO  17:41:05,571 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:41Z] INFO  17:41:05,578 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:41Z] INFO  17:41:05,589 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:41Z] INFO  17:41:05,590 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:41Z] INFO  17:41:05,595 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/12/R14-18106_kapa-NGv3-PE100-NGv3-sort-12_31236746_46754992-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/12/R14-18106_kapa-NGv3-PE100-NGv3-12_31236746_46754992-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/12/tx/tmpjTbJDk/R14-18106_kapa-NGv3-PE100-NGv3-12_31236746_46754992.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:41Z] INFO  17:41:05,610 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:41Z] INFO  17:41:05,610 HelpFormatter - Date/Time: 2016/04/14 17:41:05
[2016-04-15T00:41Z] INFO  17:41:05,610 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:41Z] INFO  17:41:05,610 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:41Z] WARN  17:41:05,645 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T00:41Z] WARN  17:41:05,647 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/12/tx/tmpjTbJDk/R14-18106_kapa-NGv3-PE100-NGv3-12_31236746_46754992.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T00:41Z] INFO  17:41:05,816 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:41Z] INFO  17:41:05,990 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T00:41Z] INFO  17:41:06,005 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:41Z] INFO  17:41:06,085 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-15T00:41Z] INFO  17:41:06,100 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T00:41Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T00:41Z] INFO  17:41:06,285 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T00:41Z] INFO  17:41:06,286 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T00:41Z] INFO  17:41:06,443 IntervalUtils - Processing 136917 bp from intervals
[2016-04-15T00:41Z] WARN  17:41:06,449 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:41Z] INFO  17:41:06,556 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:41Z] WARN  17:41:06,557 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T00:41Z] WARN  17:41:06,558 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T00:41Z] INFO  17:41:06,638 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:41Z] INFO  17:41:06,640 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:41Z] INFO  17:41:06,640 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T00:41Z] INFO  17:41:06,641 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T00:41Z] INFO  17:41:06,656 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T00:41Z] INFO  17:41:06,656 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T00:41Z] INFO  17:41:06,857 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T00:41Z] INFO  17:41:06,874 ProgressMeter -     11:43941522      1.7933889E7    30.0 s            1.0 s       55.5%    54.0 s      24.0 s
[2016-04-15T00:41Z] INFO  17:41:07,250 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:41Z] INFO  17:41:07,264 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:41Z] INFO  17:41:07,265 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:41Z] INFO  17:41:07,265 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:41Z] INFO  17:41:07,270 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/12/R14-18106_kapa-NGv3-PE100-NGv3-sort-12_46756066_62654284-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/12/R14-18106_kapa-NGv3-PE100-NGv3-12_46756066_62654284-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/12/tx/tmpO_LAM5/R14-18106_kapa-NGv3-PE100-NGv3-12_46756066_62654284.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:41Z] INFO  17:41:07,298 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:41Z] INFO  17:41:07,299 HelpFormatter - Date/Time: 2016/04/14 17:41:07
[2016-04-15T00:41Z] INFO  17:41:07,299 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:41Z] INFO  17:41:07,300 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:41Z] WARN  17:41:07,345 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T00:41Z] WARN  17:41:07,356 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/12/tx/tmpO_LAM5/R14-18106_kapa-NGv3-PE100-NGv3-12_46756066_62654284.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T00:41Z] INFO  17:41:07,561 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:41Z] INFO  17:41:07,768 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T00:41Z] INFO  17:41:07,789 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:41Z] INFO  17:41:07,879 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.09
[2016-04-15T00:41Z] INFO  17:41:07,897 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T00:41Z] INFO  17:41:08,351 IntervalUtils - Processing 504306 bp from intervals
[2016-04-15T00:41Z] WARN  17:41:08,365 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:41Z] INFO  17:41:08,501 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:41Z] INFO  17:41:08,672 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:41Z] INFO  17:41:08,672 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:41Z] INFO  17:41:08,673 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T00:41Z] INFO  17:41:08,673 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T00:41Z] INFO  17:41:08,684 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T00:41Z] INFO  17:41:08,684 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T00:41Z] INFO  17:41:08,884 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T00:41Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T00:41Z] INFO  17:41:09,462 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T00:41Z] INFO  17:41:09,463 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T00:41Z] INFO  17:41:09,471 ProgressMeter -     11:48373671        6934557.0    30.0 s            4.0 s       16.8%     3.0 m       2.5 m
[2016-04-15T00:41Z] INFO  17:41:09,494 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.023739821
[2016-04-15T00:41Z] INFO  17:41:09,495 PairHMM - Total compute time in PairHMM computeLikelihoods() : 1.7702088180000002
[2016-04-15T00:41Z] INFO  17:41:09,495 HaplotypeCaller - Ran local assembly on 1607 active regions
[2016-04-15T00:41Z] INFO  17:41:09,552 ProgressMeter -            done     1.10097324E8    56.0 s            0.0 s      100.0%    56.0 s       0.0 s
[2016-04-15T00:41Z] INFO  17:41:09,553 ProgressMeter - Total runtime 56.33 secs, 0.94 min, 0.02 hours
[2016-04-15T00:41Z] INFO  17:41:09,554 MicroScheduler - 32238 reads were filtered out during the traversal out of approximately 288190 total reads (11.19%)
[2016-04-15T00:41Z] INFO  17:41:09,554 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:41Z] INFO  17:41:09,554 MicroScheduler -   -> 21508 reads (7.46% of total) failing DuplicateReadFilter
[2016-04-15T00:41Z] INFO  17:41:09,554 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:41Z] INFO  17:41:09,555 MicroScheduler -   -> 10730 reads (3.72% of total) failing HCMappingQualityFilter
[2016-04-15T00:41Z] INFO  17:41:09,555 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:41Z] INFO  17:41:09,555 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:41Z] INFO  17:41:09,555 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:41Z] INFO  17:41:09,555 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:41Z] INFO  17:41:09,595 ProgressMeter -     11:64567155      1.3460528E7    30.0 s            2.0 s       16.2%     3.1 m       2.6 m
[2016-04-15T00:41Z] WARN  17:41:09,729 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T00:41Z] WARN  17:41:09,730 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T00:41Z] INFO  17:41:10,969 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:41Z] GATK: HaplotypeCaller
[2016-04-15T00:41Z] INFO  17:41:11,580 ProgressMeter -     11:92086619      1.8211813E7    30.0 s            1.0 s       72.4%    41.0 s      11.0 s
[2016-04-15T00:41Z] INFO  17:41:11,706 ProgressMeter -    11:104972135      2.5639934E7    30.0 s            1.0 s       65.3%    45.0 s      15.0 s
[2016-04-15T00:41Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T00:41Z] INFO  17:41:13,134 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T00:41Z] INFO  17:41:13,135 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T00:41Z] WARN  17:41:13,401 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T00:41Z] WARN  17:41:13,402 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T00:41Z] INFO  17:41:14,331 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:41Z] INFO  17:41:14,335 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:41Z] INFO  17:41:14,335 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:41Z] INFO  17:41:14,336 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:41Z] INFO  17:41:14,341 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/12/R14-18106_kapa-NGv3-PE100-NGv3-sort-12_62687959_78225484-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/12/R14-18106_kapa-NGv3-PE100-NGv3-12_62687959_78225484-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/12/tx/tmpQmKbN1/R14-18106_kapa-NGv3-PE100-NGv3-12_62687959_78225484.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:41Z] INFO  17:41:14,350 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:41Z] INFO  17:41:14,351 HelpFormatter - Date/Time: 2016/04/14 17:41:14
[2016-04-15T00:41Z] INFO  17:41:14,352 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:41Z] INFO  17:41:14,360 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:41Z] WARN  17:41:14,398 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T00:41Z] WARN  17:41:14,413 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/12/tx/tmpQmKbN1/R14-18106_kapa-NGv3-PE100-NGv3-12_62687959_78225484.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T00:41Z] INFO  17:41:14,668 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:41Z] INFO  17:41:14,678 ProgressMeter -     9:139399125     2.96171082E8    90.0 s            0.0 s       76.0%   118.0 s      28.0 s
[2016-04-15T00:41Z] INFO  17:41:14,890 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T00:41Z] INFO  17:41:14,900 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:41Z] INFO  17:41:14,984 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-15T00:41Z] INFO  17:41:15,016 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T00:41Z] INFO  17:41:15,429 IntervalUtils - Processing 146919 bp from intervals
[2016-04-15T00:41Z] WARN  17:41:15,445 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:41Z] INFO  17:41:15,566 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:41Z] INFO  17:41:15,682 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:41Z] INFO  17:41:15,683 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:41Z] INFO  17:41:15,684 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T00:41Z] INFO  17:41:15,684 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T00:41Z] INFO  17:41:15,693 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T00:41Z] INFO  17:41:15,693 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T00:41Z] INFO  17:41:16,001 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T00:41Z] INFO  17:41:17,237 ProgressMeter -    11:116691983      1.9058692E7    30.0 s            1.0 s       27.7%   108.0 s      78.0 s
[2016-04-15T00:41Z] INFO  17:41:17,768 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.010652778
[2016-04-15T00:41Z] INFO  17:41:17,769 PairHMM - Total compute time in PairHMM computeLikelihoods() : 0.6809782080000001
[2016-04-15T00:41Z] INFO  17:41:17,770 HaplotypeCaller - Ran local assembly on 1089 active regions
[2016-04-15T00:41Z] INFO  17:41:17,827 ProgressMeter -            done      5.2775059E7    43.0 s            0.0 s      100.0%    43.0 s       0.0 s
[2016-04-15T00:41Z] INFO  17:41:17,828 ProgressMeter - Total runtime 43.19 secs, 0.72 min, 0.01 hours
[2016-04-15T00:41Z] INFO  17:41:17,828 MicroScheduler - 14713 reads were filtered out during the traversal out of approximately 187832 total reads (7.83%)
[2016-04-15T00:41Z] INFO  17:41:17,828 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:41Z] INFO  17:41:17,829 MicroScheduler -   -> 14019 reads (7.46% of total) failing DuplicateReadFilter
[2016-04-15T00:41Z] INFO  17:41:17,829 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:41Z] INFO  17:41:17,830 MicroScheduler -   -> 694 reads (0.37% of total) failing HCMappingQualityFilter
[2016-04-15T00:41Z] INFO  17:41:17,830 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:41Z] INFO  17:41:17,830 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:41Z] INFO  17:41:17,830 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:41Z] INFO  17:41:17,831 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:41Z] INFO  17:41:18,184 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.007217862
[2016-04-15T00:41Z] INFO  17:41:18,184 PairHMM - Total compute time in PairHMM computeLikelihoods() : 0.445887297
[2016-04-15T00:41Z] INFO  17:41:18,185 HaplotypeCaller - Ran local assembly on 783 active regions
[2016-04-15T00:41Z] INFO  17:41:18,238 ProgressMeter -            done      2.9891248E7    36.0 s            1.0 s      100.0%    36.0 s       0.0 s
[2016-04-15T00:41Z] INFO  17:41:18,239 ProgressMeter - Total runtime 36.70 secs, 0.61 min, 0.01 hours
[2016-04-15T00:41Z] INFO  17:41:18,239 MicroScheduler - 31440 reads were filtered out during the traversal out of approximately 161806 total reads (19.43%)
[2016-04-15T00:41Z] INFO  17:41:18,239 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:41Z] INFO  17:41:18,240 MicroScheduler -   -> 10854 reads (6.71% of total) failing DuplicateReadFilter
[2016-04-15T00:41Z] INFO  17:41:18,241 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:41Z] INFO  17:41:18,241 MicroScheduler -   -> 20586 reads (12.72% of total) failing HCMappingQualityFilter
[2016-04-15T00:41Z] INFO  17:41:18,241 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:41Z] INFO  17:41:18,241 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:41Z] INFO  17:41:18,241 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:41Z] INFO  17:41:18,242 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:41Z] INFO  17:41:18,758 ProgressMeter -    11:133402204      1.3476038E7    30.0 s            2.0 s       80.8%    37.0 s       7.0 s
[2016-04-15T00:41Z] INFO  17:41:19,018 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.01457447
[2016-04-15T00:41Z] INFO  17:41:19,019 PairHMM - Total compute time in PairHMM computeLikelihoods() : 0.7085883890000001
[2016-04-15T00:41Z] INFO  17:41:19,019 HaplotypeCaller - Ran local assembly on 2479 active regions
[2016-04-15T00:41Z] INFO  17:41:19,068 ProgressMeter -            done     2.79147334E8    75.0 s            0.0 s      100.0%    75.0 s       0.0 s
[2016-04-15T00:41Z] INFO  17:41:19,069 ProgressMeter - Total runtime 75.81 secs, 1.26 min, 0.02 hours
[2016-04-15T00:41Z] INFO  17:41:19,069 MicroScheduler - 36675 reads were filtered out during the traversal out of approximately 474397 total reads (7.73%)
[2016-04-15T00:41Z] INFO  17:41:19,069 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:41Z] INFO  17:41:19,069 MicroScheduler -   -> 35743 reads (7.53% of total) failing DuplicateReadFilter
[2016-04-15T00:41Z] INFO  17:41:19,070 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:41Z] INFO  17:41:19,070 MicroScheduler -   -> 932 reads (0.20% of total) failing HCMappingQualityFilter
[2016-04-15T00:41Z] INFO  17:41:19,070 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:41Z] INFO  17:41:19,070 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:41Z] INFO  17:41:19,071 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:41Z] INFO  17:41:19,071 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:41Z] INFO  17:41:19,681 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:41Z] INFO  17:41:19,802 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:41Z] GATK: HaplotypeCaller
[2016-04-15T00:41Z] GATK: HaplotypeCaller
[2016-04-15T00:41Z] INFO  17:41:20,209 ProgressMeter -      12:5541440      2.1041869E7    30.0 s            1.0 s       28.1%   106.0 s      76.0 s
[2016-04-15T00:41Z] INFO  17:41:20,267 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:41Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T00:41Z] INFO  17:41:20,477 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T00:41Z] INFO  17:41:20,478 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T00:41Z] INFO  17:41:20,567 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.008813559
[2016-04-15T00:41Z] INFO  17:41:20,567 PairHMM - Total compute time in PairHMM computeLikelihoods() : 0.567585749
[2016-04-15T00:41Z] INFO  17:41:20,567 HaplotypeCaller - Ran local assembly on 1092 active regions
[2016-04-15T00:41Z] GATK: HaplotypeCaller
[2016-04-15T00:41Z] INFO  17:41:20,639 ProgressMeter -            done      5.3488435E7    43.0 s            0.0 s      100.0%    43.0 s       0.0 s
[2016-04-15T00:41Z] INFO  17:41:20,639 ProgressMeter - Total runtime 43.78 secs, 0.73 min, 0.01 hours
[2016-04-15T00:41Z] INFO  17:41:20,641 MicroScheduler - 17509 reads were filtered out during the traversal out of approximately 221795 total reads (7.89%)
[2016-04-15T00:41Z] INFO  17:41:20,641 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:41Z] INFO  17:41:20,641 MicroScheduler -   -> 17093 reads (7.71% of total) failing DuplicateReadFilter
[2016-04-15T00:41Z] INFO  17:41:20,641 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:41Z] INFO  17:41:20,642 MicroScheduler -   -> 416 reads (0.19% of total) failing HCMappingQualityFilter
[2016-04-15T00:41Z] INFO  17:41:20,642 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:41Z] INFO  17:41:20,642 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:41Z] INFO  17:41:20,642 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:41Z] INFO  17:41:20,643 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:41Z] WARN  17:41:20,768 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T00:41Z] WARN  17:41:20,773 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T00:41Z] INFO  17:41:21,050 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.007300038000000001
[2016-04-15T00:41Z] INFO  17:41:21,051 PairHMM - Total compute time in PairHMM computeLikelihoods() : 0.24688432400000002
[2016-04-15T00:41Z] INFO  17:41:21,052 HaplotypeCaller - Ran local assembly on 1058 active regions
[2016-04-15T00:41Z] INFO  17:41:21,102 ProgressMeter -            done      5.5507672E7    39.0 s            0.0 s      100.0%    39.0 s       0.0 s
[2016-04-15T00:41Z] INFO  17:41:21,104 ProgressMeter - Total runtime 39.41 secs, 0.66 min, 0.01 hours
[2016-04-15T00:41Z] INFO  17:41:21,104 MicroScheduler - 12938 reads were filtered out during the traversal out of approximately 171349 total reads (7.55%)
[2016-04-15T00:41Z] INFO  17:41:21,105 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:41Z] INFO  17:41:21,105 MicroScheduler -   -> 12639 reads (7.38% of total) failing DuplicateReadFilter
[2016-04-15T00:41Z] INFO  17:41:21,105 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:41Z] INFO  17:41:21,106 MicroScheduler -   -> 299 reads (0.17% of total) failing HCMappingQualityFilter
[2016-04-15T00:41Z] INFO  17:41:21,106 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:41Z] INFO  17:41:21,106 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:41Z] INFO  17:41:21,106 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:41Z] INFO  17:41:21,107 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:41Z] INFO  17:41:22,276 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:41Z] GATK: HaplotypeCaller
[2016-04-15T00:41Z] INFO  17:41:22,635 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.009125933000000001
[2016-04-15T00:41Z] INFO  17:41:22,636 PairHMM - Total compute time in PairHMM computeLikelihoods() : 0.5540049330000001
[2016-04-15T00:41Z] INFO  17:41:22,636 HaplotypeCaller - Ran local assembly on 767 active regions
[2016-04-15T00:41Z] INFO  17:41:22,681 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:41Z] INFO  17:41:22,691 ProgressMeter -            done      2.5784333E7    33.0 s            1.0 s      100.0%    33.0 s       0.0 s
[2016-04-15T00:41Z] INFO  17:41:22,691 ProgressMeter - Total runtime 33.97 secs, 0.57 min, 0.01 hours
[2016-04-15T00:41Z] INFO  17:41:22,691 MicroScheduler - 12799 reads were filtered out during the traversal out of approximately 159988 total reads (8.00%)
[2016-04-15T00:41Z] INFO  17:41:22,692 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:41Z] INFO  17:41:22,692 MicroScheduler -   -> 12090 reads (7.56% of total) failing DuplicateReadFilter
[2016-04-15T00:41Z] INFO  17:41:22,692 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:41Z] INFO  17:41:22,692 MicroScheduler -   -> 709 reads (0.44% of total) failing HCMappingQualityFilter
[2016-04-15T00:41Z] INFO  17:41:22,692 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:41Z] INFO  17:41:22,693 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:41Z] INFO  17:41:22,693 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:41Z] INFO  17:41:22,693 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:41Z] GATK: HaplotypeCaller
[2016-04-15T00:41Z] INFO  17:41:23,146 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:41Z] INFO  17:41:23,150 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:41Z] INFO  17:41:23,150 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:41Z] INFO  17:41:23,151 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:41Z] INFO  17:41:23,155 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/12/R14-18106_kapa-NGv3-PE100-NGv3-sort-12_78334098_93863131-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/12/R14-18106_kapa-NGv3-PE100-NGv3-12_78334098_93863131-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/12/tx/tmpVC0i2z/R14-18106_kapa-NGv3-PE100-NGv3-12_78334098_93863131.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:41Z] INFO  17:41:23,187 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:41Z] INFO  17:41:23,198 HelpFormatter - Date/Time: 2016/04/14 17:41:23
[2016-04-15T00:41Z] INFO  17:41:23,198 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:41Z] INFO  17:41:23,199 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:41Z] WARN  17:41:23,249 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T00:41Z] WARN  17:41:23,252 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/12/tx/tmpVC0i2z/R14-18106_kapa-NGv3-PE100-NGv3-12_78334098_93863131.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T00:41Z] INFO  17:41:23,280 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:41Z] INFO  17:41:23,283 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:41Z] INFO  17:41:23,284 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:41Z] INFO  17:41:23,284 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:41Z] INFO  17:41:23,289 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/12/R14-18106_kapa-NGv3-PE100-NGv3-sort-12_93870729_109490566-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/12/R14-18106_kapa-NGv3-PE100-NGv3-12_93870729_109490566-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/12/tx/tmp_vCCw6/R14-18106_kapa-NGv3-PE100-NGv3-12_93870729_109490566.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:41Z] INFO  17:41:23,318 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:41Z] INFO  17:41:23,319 HelpFormatter - Date/Time: 2016/04/14 17:41:23
[2016-04-15T00:41Z] INFO  17:41:23,320 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:41Z] INFO  17:41:23,320 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:41Z] WARN  17:41:23,360 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T00:41Z] WARN  17:41:23,363 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/12/tx/tmp_vCCw6/R14-18106_kapa-NGv3-PE100-NGv3-12_93870729_109490566.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T00:41Z] INFO  17:41:23,496 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:41Z] INFO  17:41:23,549 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:41Z] INFO  17:41:23,612 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:41Z] INFO  17:41:23,616 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:41Z] INFO  17:41:23,616 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:41Z] INFO  17:41:23,617 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:41Z] INFO  17:41:23,621 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/12/R14-18106_kapa-NGv3-PE100-NGv3-sort-12_109494486_125263132-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/12/R14-18106_kapa-NGv3-PE100-NGv3-12_109494486_125263132-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/12/tx/tmpn4adk1/R14-18106_kapa-NGv3-PE100-NGv3-12_109494486_125263132.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:41Z] INFO  17:41:23,663 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:41Z] INFO  17:41:23,668 HelpFormatter - Date/Time: 2016/04/14 17:41:23
[2016-04-15T00:41Z] INFO  17:41:23,669 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:41Z] INFO  17:41:23,674 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:41Z] INFO  17:41:23,717 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T00:41Z] WARN  17:41:23,715 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T00:41Z] INFO  17:41:23,727 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:41Z] WARN  17:41:23,729 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/12/tx/tmpn4adk1/R14-18106_kapa-NGv3-PE100-NGv3-12_109494486_125263132.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T00:41Z] INFO  17:41:23,814 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T00:41Z] INFO  17:41:23,834 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.10
[2016-04-15T00:41Z] INFO  17:41:23,847 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T00:41Z] INFO  17:41:23,849 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:41Z] INFO  17:41:23,912 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:41Z] INFO  17:41:23,934 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.09
[2016-04-15T00:41Z] INFO  17:41:23,953 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T00:41Z] INFO  17:41:23,993 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:41Z] INFO  17:41:24,057 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T00:41Z] INFO  17:41:24,066 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:41Z] INFO  17:41:24,126 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-15T00:41Z] INFO  17:41:24,147 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T00:41Z] INFO  17:41:24,308 IntervalUtils - Processing 88957 bp from intervals
[2016-04-15T00:41Z] WARN  17:41:24,313 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:41Z] GATK: HaplotypeCaller
[2016-04-15T00:41Z] INFO  17:41:24,416 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:41Z] INFO  17:41:24,463 IntervalUtils - Processing 201796 bp from intervals
[2016-04-15T00:41Z] WARN  17:41:24,468 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:41Z] INFO  17:41:24,521 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:41Z] INFO  17:41:24,521 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:41Z] INFO  17:41:24,522 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T00:41Z] INFO  17:41:24,522 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T00:41Z] INFO  17:41:24,533 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T00:41Z] INFO  17:41:24,534 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T00:41Z] INFO  17:41:24,572 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:41Z] INFO  17:41:24,604 IntervalUtils - Processing 364987 bp from intervals
[2016-04-15T00:41Z] WARN  17:41:24,620 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:41Z] INFO  17:41:24,688 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:41Z] INFO  17:41:24,689 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:41Z] INFO  17:41:24,690 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T00:41Z] INFO  17:41:24,690 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:41Z] INFO  17:41:24,691 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T00:41Z] INFO  17:41:24,703 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T00:41Z] INFO  17:41:24,704 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T00:41Z] INFO  17:41:24,784 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T00:41Z] INFO  17:41:24,812 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:41Z] INFO  17:41:24,813 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:41Z] INFO  17:41:24,813 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T00:41Z] INFO  17:41:24,814 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T00:41Z] INFO  17:41:24,815 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T00:41Z] INFO  17:41:24,815 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T00:41Z] INFO  17:41:24,891 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T00:41Z] INFO  17:41:25,021 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T00:41Z] INFO  17:41:25,608 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:41Z] INFO  17:41:25,611 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:41Z] INFO  17:41:25,612 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:41Z] INFO  17:41:25,612 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:41Z] INFO  17:41:25,617 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/12/R14-18106_kapa-NGv3-PE100-NGv3-sort-12_125267228_133851895-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/12/R14-18106_kapa-NGv3-PE100-NGv3-12_125267228_133851895-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/12/tx/tmpHVLaDt/R14-18106_kapa-NGv3-PE100-NGv3-12_125267228_133851895.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:41Z] INFO  17:41:25,640 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:41Z] INFO  17:41:25,646 HelpFormatter - Date/Time: 2016/04/14 17:41:25
[2016-04-15T00:41Z] INFO  17:41:25,647 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:41Z] INFO  17:41:25,648 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:41Z] WARN  17:41:25,678 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T00:41Z] WARN  17:41:25,681 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/12/tx/tmpHVLaDt/R14-18106_kapa-NGv3-PE100-NGv3-12_125267228_133851895.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T00:41Z] INFO  17:41:25,921 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:41Z] INFO  17:41:26,023 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:41Z] INFO  17:41:26,026 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:41Z] INFO  17:41:26,027 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:41Z] INFO  17:41:26,028 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:41Z] INFO  17:41:26,032 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/13/R14-18106_kapa-NGv3-PE100-NGv3-sort-13_0_19748299-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/13/R14-18106_kapa-NGv3-PE100-NGv3-13_0_19748299-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/13/tx/tmpIpwJ91/R14-18106_kapa-NGv3-PE100-NGv3-13_0_19748299.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:41Z] INFO  17:41:26,075 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:41Z] INFO  17:41:26,075 HelpFormatter - Date/Time: 2016/04/14 17:41:26
[2016-04-15T00:41Z] INFO  17:41:26,076 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:41Z] INFO  17:41:26,076 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:41Z] WARN  17:41:26,128 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T00:41Z] WARN  17:41:26,131 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/13/tx/tmpIpwJ91/R14-18106_kapa-NGv3-PE100-NGv3-13_0_19748299.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T00:41Z] INFO  17:41:26,182 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T00:41Z] INFO  17:41:26,201 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:41Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T00:41Z] INFO  17:41:26,261 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T00:41Z] INFO  17:41:26,262 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T00:41Z] INFO  17:41:26,290 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.09
[2016-04-15T00:41Z] INFO  17:41:26,320 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:41Z] INFO  17:41:26,329 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T00:41Z] WARN  17:41:26,537 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T00:41Z] WARN  17:41:26,538 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T00:41Z] INFO  17:41:26,561 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T00:41Z] INFO  17:41:26,571 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:41Z] INFO  17:41:26,689 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.12
[2016-04-15T00:41Z] INFO  17:41:26,710 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T00:41Z] INFO  17:41:26,795 IntervalUtils - Processing 106872 bp from intervals
[2016-04-15T00:41Z] WARN  17:41:26,801 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:41Z] INFO  17:41:26,894 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:41Z] INFO  17:41:26,976 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:41Z] INFO  17:41:26,977 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:41Z] INFO  17:41:26,978 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T00:41Z] INFO  17:41:26,979 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T00:41Z] INFO  17:41:26,979 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T00:41Z] INFO  17:41:26,980 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T00:41Z] INFO  17:41:27,075 IntervalUtils - Processing 297 bp from intervals
[2016-04-15T00:41Z] WARN  17:41:27,085 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:41Z] INFO  17:41:27,233 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:41Z] INFO  17:41:27,241 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T00:41Z] INFO  17:41:27,277 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:41Z] INFO  17:41:27,284 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:41Z] INFO  17:41:27,285 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T00:41Z] INFO  17:41:27,286 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T00:41Z] INFO  17:41:27,293 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T00:41Z] INFO  17:41:27,293 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T00:41Z] INFO  17:41:27,488 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T00:41Z] INFO  17:41:27,566 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:41Z] INFO  17:41:27,569 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:41Z] INFO  17:41:27,569 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:41Z] INFO  17:41:27,570 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:41Z] INFO  17:41:27,574 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/13/R14-18106_kapa-NGv3-PE100-NGv3-sort-13_19751066_35517251-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/13/R14-18106_kapa-NGv3-PE100-NGv3-13_19751066_35517251-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/13/tx/tmp0hsuVE/R14-18106_kapa-NGv3-PE100-NGv3-13_19751066_35517251.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:41Z] INFO  17:41:27,642 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:41Z] INFO  17:41:27,642 HelpFormatter - Date/Time: 2016/04/14 17:41:27
[2016-04-15T00:41Z] INFO  17:41:27,642 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:41Z] INFO  17:41:27,643 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:41Z] WARN  17:41:27,665 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T00:41Z] WARN  17:41:27,668 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/13/tx/tmp0hsuVE/R14-18106_kapa-NGv3-PE100-NGv3-13_19751066_35517251.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T00:41Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T00:41Z] INFO  17:41:27,730 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T00:41Z] INFO  17:41:27,730 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T00:41Z] INFO  17:41:27,892 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:41Z] WARN  17:41:28,075 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T00:41Z] WARN  17:41:28,075 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T00:41Z] INFO  17:41:28,124 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T00:41Z] INFO  17:41:28,133 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:41Z] INFO  17:41:28,248 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.11
[2016-04-15T00:41Z] INFO  17:41:28,295 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T00:41Z] INFO  17:41:28,816 IntervalUtils - Processing 201552 bp from intervals
[2016-04-15T00:41Z] WARN  17:41:28,822 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:41Z] INFO  17:41:28,944 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:41Z] INFO  17:41:29,070 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:41Z] INFO  17:41:29,070 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:41Z] INFO  17:41:29,071 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T00:41Z] INFO  17:41:29,071 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T00:41Z] INFO  17:41:29,085 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T00:41Z] INFO  17:41:29,086 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T00:41Z] INFO  17:41:29,379 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T00:41Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T00:41Z] INFO  17:41:29,609 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T00:41Z] INFO  17:41:29,610 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T00:41Z] INFO  17:41:29,622 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.0
[2016-04-15T00:41Z] INFO  17:41:29,623 PairHMM - Total compute time in PairHMM computeLikelihoods() : 0.0
[2016-04-15T00:41Z] INFO  17:41:29,624 HaplotypeCaller - Ran local assembly on 1 active regions
[2016-04-15T00:41Z] INFO  17:41:29,657 ProgressMeter -            done            297.0     2.0 s            2.2 h       99.7%     2.0 s       0.0 s
[2016-04-15T00:41Z] INFO  17:41:29,658 ProgressMeter - Total runtime 2.37 secs, 0.04 min, 0.00 hours
[2016-04-15T00:41Z] INFO  17:41:29,659 MicroScheduler - 63 reads were filtered out during the traversal out of approximately 893 total reads (7.05%)
[2016-04-15T00:41Z] INFO  17:41:29,660 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:41Z] INFO  17:41:29,661 MicroScheduler -   -> 62 reads (6.94% of total) failing DuplicateReadFilter
[2016-04-15T00:41Z] INFO  17:41:29,661 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:41Z] INFO  17:41:29,665 MicroScheduler -   -> 1 reads (0.11% of total) failing HCMappingQualityFilter
[2016-04-15T00:41Z] INFO  17:41:29,669 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:41Z] INFO  17:41:29,669 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:41Z] INFO  17:41:29,677 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:41Z] INFO  17:41:29,677 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:41Z] INFO  17:41:29,855 ProgressMeter -      11:1017155        9985430.0    60.0 s            6.0 s       16.5%     6.1 m       5.1 m
[2016-04-15T00:41Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T00:41Z] INFO  17:41:30,411 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T00:41Z] INFO  17:41:30,426 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T00:41Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T00:41Z] INFO  17:41:30,564 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T00:41Z] INFO  17:41:30,565 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T00:41Z] WARN  17:41:30,815 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T00:41Z] WARN  17:41:30,816 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T00:41Z] WARN  17:41:30,961 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T00:41Z] WARN  17:41:30,962 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T00:41Z] INFO  17:41:31,151 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:41Z] GATK: HaplotypeCaller
[2016-04-15T00:41Z] INFO  17:41:32,381 ProgressMeter -     12:27800662      3.4189828E7    30.0 s            0.0 s       80.2%    37.0 s       7.0 s
[2016-04-15T00:41Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T00:41Z] INFO  17:41:33,187 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T00:41Z] INFO  17:41:33,188 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T00:41Z] WARN  17:41:34,003 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T00:41Z] WARN  17:41:34,004 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T00:41Z] WARN  17:41:34,110 ExactAFCalculator - this tool is currently set to genotype at most 6 alternate alleles in a given context, but the context at 12:27953282 has 8 alternate alleles so only the top alleles will be used; see the --max_alternate_alleles argument
[2016-04-15T00:41Z] WARN  17:41:34,124 ExactAFCalculator - this tool is currently set to genotype at most 6 alternate alleles in a given context, but the context at 12:27953284 has 9 alternate alleles so only the top alleles will be used; see the --max_alternate_alleles argument
[2016-04-15T00:41Z] INFO  17:41:34,625 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:41Z] INFO  17:41:34,628 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:41Z] INFO  17:41:34,629 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:41Z] INFO  17:41:34,629 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:41Z] INFO  17:41:34,634 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/13/R14-18106_kapa-NGv3-PE100-NGv3-sort-13_35615069_51287376-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/13/R14-18106_kapa-NGv3-PE100-NGv3-13_35615069_51287376-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/13/tx/tmpZfuVPF/R14-18106_kapa-NGv3-PE100-NGv3-13_35615069_51287376.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:41Z] INFO  17:41:34,675 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:41Z] INFO  17:41:34,691 HelpFormatter - Date/Time: 2016/04/14 17:41:34
[2016-04-15T00:41Z] INFO  17:41:34,692 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:41Z] INFO  17:41:34,692 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:41Z] WARN  17:41:34,753 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T00:41Z] WARN  17:41:34,756 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/13/tx/tmpZfuVPF/R14-18106_kapa-NGv3-PE100-NGv3-13_35615069_51287376.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T00:41Z] INFO  17:41:34,916 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:41Z] INFO  17:41:35,260 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T00:41Z] INFO  17:41:35,289 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:41Z] INFO  17:41:35,355 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-15T00:41Z] INFO  17:41:35,396 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T00:41Z] INFO  17:41:35,908 IntervalUtils - Processing 179232 bp from intervals
[2016-04-15T00:41Z] WARN  17:41:35,913 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:41Z] INFO  17:41:35,993 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:41Z] INFO  17:41:36,161 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:41Z] INFO  17:41:36,162 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:41Z] INFO  17:41:36,163 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T00:41Z] INFO  17:41:36,164 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T00:41Z] INFO  17:41:36,186 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T00:41Z] INFO  17:41:36,187 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T00:41Z] INFO  17:41:36,459 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T00:41Z] INFO  17:41:36,657 ProgressMeter -     12:40877055      1.2902841E7    30.0 s            2.0 s       52.1%    57.0 s      27.0 s
[2016-04-15T00:41Z] INFO  17:41:38,201 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.006356406
[2016-04-15T00:41Z] INFO  17:41:38,202 PairHMM - Total compute time in PairHMM computeLikelihoods() : 0.612281115
[2016-04-15T00:41Z] INFO  17:41:38,202 HaplotypeCaller - Ran local assembly on 1075 active regions
[2016-04-15T00:41Z] INFO  17:41:38,233 ProgressMeter -            done      5.5983758E7    35.0 s            0.0 s      100.0%    35.0 s       0.0 s
[2016-04-15T00:41Z] INFO  17:41:38,234 ProgressMeter - Total runtime 35.88 secs, 0.60 min, 0.01 hours
[2016-04-15T00:41Z] INFO  17:41:38,234 MicroScheduler - 11177 reads were filtered out during the traversal out of approximately 146487 total reads (7.63%)
[2016-04-15T00:41Z] INFO  17:41:38,234 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:41Z] INFO  17:41:38,235 MicroScheduler -   -> 10867 reads (7.42% of total) failing DuplicateReadFilter
[2016-04-15T00:41Z] INFO  17:41:38,235 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:41Z] INFO  17:41:38,235 MicroScheduler -   -> 310 reads (0.21% of total) failing HCMappingQualityFilter
[2016-04-15T00:41Z] INFO  17:41:38,235 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:41Z] INFO  17:41:38,236 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:41Z] INFO  17:41:38,236 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:41Z] INFO  17:41:38,236 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:41Z] INFO  17:41:38,688 ProgressMeter -     12:49993772      1.7519673E7    30.0 s            1.0 s       19.9%     2.5 m     120.0 s
[2016-04-15T00:41Z] INFO  17:41:39,475 ProgressMeter -     11:56468647      1.3735118E7    60.0 s            4.0 s       32.9%     3.0 m       2.0 m
[2016-04-15T00:41Z] INFO  17:41:39,505 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.040791154
[2016-04-15T00:41Z] INFO  17:41:39,506 PairHMM - Total compute time in PairHMM computeLikelihoods() : 3.4214560840000003
[2016-04-15T00:41Z] INFO  17:41:39,506 HaplotypeCaller - Ran local assembly on 3594 active regions
[2016-04-15T00:41Z] INFO  17:41:39,541 ProgressMeter -            done     4.74191826E8   114.0 s            0.0 s      100.0%   114.0 s       0.0 s
[2016-04-15T00:41Z] INFO  17:41:39,542 ProgressMeter - Total runtime 114.90 secs, 1.92 min, 0.03 hours
[2016-04-15T00:41Z] INFO  17:41:39,542 MicroScheduler - 65918 reads were filtered out during the traversal out of approximately 766572 total reads (8.60%)
[2016-04-15T00:41Z] INFO  17:41:39,542 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:41Z] INFO  17:41:39,542 MicroScheduler -   -> 59237 reads (7.73% of total) failing DuplicateReadFilter
[2016-04-15T00:41Z] INFO  17:41:39,543 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:41Z] INFO  17:41:39,543 MicroScheduler -   -> 6681 reads (0.87% of total) failing HCMappingQualityFilter
[2016-04-15T00:41Z] INFO  17:41:39,543 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:41Z] INFO  17:41:39,543 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:41Z] INFO  17:41:39,544 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:41Z] INFO  17:41:39,544 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:41Z] INFO  17:41:39,610 ProgressMeter -     11:66392085      9.6057259E7    60.0 s            0.0 s       44.3%     2.3 m      75.0 s
[2016-04-15T00:41Z] INFO  17:41:39,794 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:41Z] GATK: HaplotypeCaller
[2016-04-15T00:41Z] INFO  17:41:41,162 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:41Z] GATK: HaplotypeCaller
[2016-04-15T00:41Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T00:41Z] INFO  17:41:43,026 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T00:41Z] INFO  17:41:43,026 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T00:41Z] INFO  17:41:43,291 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:41Z] INFO  17:41:43,294 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:41Z] INFO  17:41:43,295 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:41Z] INFO  17:41:43,295 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:41Z] INFO  17:41:43,300 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/13/R14-18106_kapa-NGv3-PE100-NGv3-sort-13_51396767_67205543-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/13/R14-18106_kapa-NGv3-PE100-NGv3-13_51396767_67205543-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/13/tx/tmpuIYU5S/R14-18106_kapa-NGv3-PE100-NGv3-13_51396767_67205543.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:41Z] WARN  17:41:43,328 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T00:41Z] WARN  17:41:43,329 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T00:41Z] INFO  17:41:43,330 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:41Z] INFO  17:41:43,340 HelpFormatter - Date/Time: 2016/04/14 17:41:43
[2016-04-15T00:41Z] INFO  17:41:43,341 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:41Z] INFO  17:41:43,341 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:41Z] WARN  17:41:43,376 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T00:41Z] WARN  17:41:43,379 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/13/tx/tmpuIYU5S/R14-18106_kapa-NGv3-PE100-NGv3-13_51396767_67205543.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T00:41Z] INFO  17:41:43,563 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:41Z] INFO  17:41:43,785 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T00:41Z] INFO  17:41:43,795 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:41Z] INFO  17:41:43,846 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-15T00:41Z] INFO  17:41:43,863 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T00:41Z] INFO  17:41:44,173 IntervalUtils - Processing 59966 bp from intervals
[2016-04-15T00:41Z] WARN  17:41:44,187 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:41Z] INFO  17:41:44,275 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:41Z] INFO  17:41:44,352 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:41Z] INFO  17:41:44,357 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:41Z] INFO  17:41:44,358 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T00:41Z] INFO  17:41:44,363 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T00:41Z] INFO  17:41:44,381 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T00:41Z] INFO  17:41:44,382 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T00:41Z] INFO  17:41:44,511 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:41Z] INFO  17:41:44,514 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:41Z] INFO  17:41:44,514 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:41Z] INFO  17:41:44,515 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:41Z] INFO  17:41:44,519 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/13/R14-18106_kapa-NGv3-PE100-NGv3-sort-13_67477635_84455642-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/13/R14-18106_kapa-NGv3-PE100-NGv3-13_67477635_84455642-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/13/tx/tmpm1BZLX/R14-18106_kapa-NGv3-PE100-NGv3-13_67477635_84455642.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:41Z] INFO  17:41:44,535 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:41Z] INFO  17:41:44,546 HelpFormatter - Date/Time: 2016/04/14 17:41:44
[2016-04-15T00:41Z] INFO  17:41:44,547 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:41Z] INFO  17:41:44,548 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:41Z] WARN  17:41:44,587 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T00:41Z] WARN  17:41:44,600 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/13/tx/tmpm1BZLX/R14-18106_kapa-NGv3-PE100-NGv3-13_67477635_84455642.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T00:41Z] INFO  17:41:44,664 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T00:41Z] INFO  17:41:44,809 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:41Z] INFO  17:41:44,964 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T00:41Z] INFO  17:41:44,973 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:41Z] INFO  17:41:45,045 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-15T00:41Z] INFO  17:41:45,065 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T00:41Z] INFO  17:41:45,600 IntervalUtils - Processing 69582 bp from intervals
[2016-04-15T00:41Z] WARN  17:41:45,615 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:41Z] INFO  17:41:45,713 ProgressMeter -     12:71551458      2.6799714E7    30.0 s            1.0 s       67.7%    44.0 s      14.0 s
[2016-04-15T00:41Z] INFO  17:41:45,753 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:41Z] INFO  17:41:45,862 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:41Z] INFO  17:41:45,863 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:41Z] INFO  17:41:45,864 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T00:41Z] INFO  17:41:45,864 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T00:41Z] INFO  17:41:45,872 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T00:41Z] INFO  17:41:45,873 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T00:41Z] INFO  17:41:46,065 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T00:41Z] INFO  17:41:47,238 ProgressMeter -    11:120200926     1.06025758E8    60.0 s            0.0 s       69.7%    86.0 s      26.0 s
[2016-04-15T00:41Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T00:41Z] INFO  17:41:47,298 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T00:41Z] INFO  17:41:47,299 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T00:41Z] WARN  17:41:47,652 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T00:41Z] WARN  17:41:47,653 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T00:41Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T00:41Z] INFO  17:41:48,254 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T00:41Z] INFO  17:41:48,265 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T00:41Z] WARN  17:41:48,493 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T00:41Z] WARN  17:41:48,494 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T00:41Z] INFO  17:41:49,667 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.00461911
[2016-04-15T00:41Z] INFO  17:41:49,668 PairHMM - Total compute time in PairHMM computeLikelihoods() : 0.11629784900000001
[2016-04-15T00:41Z] INFO  17:41:49,669 HaplotypeCaller - Ran local assembly on 653 active regions
[2016-04-15T00:41Z] INFO  17:41:49,731 ProgressMeter -            done        2.16241E7    25.0 s            1.0 s      100.0%    25.0 s       0.0 s
[2016-04-15T00:41Z] INFO  17:41:49,731 ProgressMeter - Total runtime 25.21 secs, 0.42 min, 0.01 hours
[2016-04-15T00:41Z] INFO  17:41:49,731 MicroScheduler - 6856 reads were filtered out during the traversal out of approximately 89589 total reads (7.65%)
[2016-04-15T00:41Z] INFO  17:41:49,732 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:41Z] INFO  17:41:49,732 MicroScheduler -   -> 6699 reads (7.48% of total) failing DuplicateReadFilter
[2016-04-15T00:41Z] INFO  17:41:49,732 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:41Z] INFO  17:41:49,733 MicroScheduler -   -> 157 reads (0.18% of total) failing HCMappingQualityFilter
[2016-04-15T00:41Z] INFO  17:41:49,733 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:41Z] INFO  17:41:49,733 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:41Z] INFO  17:41:49,733 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:41Z] INFO  17:41:49,733 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:41Z] INFO  17:41:50,219 ProgressMeter -      12:8384224     1.02121057E8    60.0 s            0.0 s       64.2%    93.0 s      33.0 s
[2016-04-15T00:41Z] INFO  17:41:51,253 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:41Z] GATK: HaplotypeCaller
[2016-04-15T00:41Z] INFO  17:41:53,799 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.006204541
[2016-04-15T00:41Z] INFO  17:41:53,800 PairHMM - Total compute time in PairHMM computeLikelihoods() : 0.298486405
[2016-04-15T00:41Z] INFO  17:41:53,800 HaplotypeCaller - Ran local assembly on 1082 active regions
[2016-04-15T00:41Z] INFO  17:41:53,851 ProgressMeter -            done       5.533073E7    38.0 s            0.0 s      100.0%    38.0 s       0.0 s
[2016-04-15T00:41Z] INFO  17:41:53,852 ProgressMeter - Total runtime 38.17 secs, 0.64 min, 0.01 hours
[2016-04-15T00:41Z] INFO  17:41:53,853 MicroScheduler - 12725 reads were filtered out during the traversal out of approximately 164594 total reads (7.73%)
[2016-04-15T00:41Z] INFO  17:41:53,853 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:41Z] INFO  17:41:53,853 MicroScheduler -   -> 12238 reads (7.44% of total) failing DuplicateReadFilter
[2016-04-15T00:41Z] INFO  17:41:53,853 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:41Z] INFO  17:41:53,854 MicroScheduler -   -> 487 reads (0.30% of total) failing HCMappingQualityFilter
[2016-04-15T00:41Z] INFO  17:41:53,854 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:41Z] INFO  17:41:53,854 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:41Z] INFO  17:41:53,854 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:41Z] INFO  17:41:53,855 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:41Z] INFO  17:41:54,318 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:41Z] INFO  17:41:54,321 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:41Z] INFO  17:41:54,322 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:41Z] INFO  17:41:54,323 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:41Z] INFO  17:41:54,328 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/13/R14-18106_kapa-NGv3-PE100-NGv3-sort-13_86368117_101881935-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/13/R14-18106_kapa-NGv3-PE100-NGv3-13_86368117_101881935-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/13/tx/tmpO5r_o8/R14-18106_kapa-NGv3-PE100-NGv3-13_86368117_101881935.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:41Z] INFO  17:41:54,338 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:41Z] INFO  17:41:54,343 HelpFormatter - Date/Time: 2016/04/14 17:41:54
[2016-04-15T00:41Z] INFO  17:41:54,344 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:41Z] INFO  17:41:54,345 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:41Z] WARN  17:41:54,370 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T00:41Z] WARN  17:41:54,384 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/13/tx/tmpO5r_o8/R14-18106_kapa-NGv3-PE100-NGv3-13_86368117_101881935.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T00:41Z] INFO  17:41:54,558 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:41Z] INFO  17:41:54,720 ProgressMeter -    12:102813287      4.0459172E7    30.0 s            0.0 s       56.9%    52.0 s      22.0 s
[2016-04-15T00:41Z] INFO  17:41:54,795 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T00:41Z] INFO  17:41:54,835 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:41Z] INFO  17:41:54,835 ProgressMeter -    12:113388498      3.6069035E7    30.0 s            0.0 s       30.6%    98.0 s      68.0 s
[2016-04-15T00:41Z] INFO  17:41:54,910 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-15T00:41Z] INFO  17:41:54,948 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T00:41Z] INFO  17:41:55,100 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:41Z] INFO  17:41:55,373 IntervalUtils - Processing 75123 bp from intervals
[2016-04-15T00:41Z] WARN  17:41:55,378 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:41Z] GATK: HaplotypeCaller
[2016-04-15T00:41Z] INFO  17:41:55,486 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:41Z] INFO  17:41:55,601 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:41Z] INFO  17:41:55,601 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:41Z] INFO  17:41:55,602 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T00:41Z] INFO  17:41:55,603 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T00:41Z] INFO  17:41:55,604 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T00:41Z] INFO  17:41:55,604 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T00:41Z] INFO  17:41:55,816 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T00:41Z] INFO  17:41:56,999 ProgressMeter -    12:133067157        9524618.0    30.0 s            3.0 s       57.8%    51.0 s      21.0 s
[2016-04-15T00:41Z] INFO  17:41:58,675 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:41Z] INFO  17:41:58,678 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:41Z] INFO  17:41:58,679 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:41Z] INFO  17:41:58,679 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:41Z] INFO  17:41:58,684 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/13/R14-18106_kapa-NGv3-PE100-NGv3-sort-13_101890105_115169878-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/13/R14-18106_kapa-NGv3-PE100-NGv3-13_101890105_115169878-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/13/tx/tmpCsrQTi/R14-18106_kapa-NGv3-PE100-NGv3-13_101890105_115169878.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:41Z] INFO  17:41:58,693 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:41Z] INFO  17:41:58,693 HelpFormatter - Date/Time: 2016/04/14 17:41:58
[2016-04-15T00:41Z] INFO  17:41:58,693 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:41Z] INFO  17:41:58,694 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:41Z] WARN  17:41:58,738 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T00:41Z] WARN  17:41:58,744 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/13/tx/tmpCsrQTi/R14-18106_kapa-NGv3-PE100-NGv3-13_101890105_115169878.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T00:41Z] INFO  17:41:58,958 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:41Z] INFO  17:41:59,088 ProgressMeter -     13:25424581      1.3882298E7    30.0 s            2.0 s       39.7%    75.0 s      45.0 s
[2016-04-15T00:41Z] INFO  17:41:59,183 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T00:41Z] INFO  17:41:59,194 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:41Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T00:41Z] INFO  17:41:59,227 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T00:41Z] INFO  17:41:59,228 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T00:41Z] INFO  17:41:59,295 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.10
[2016-04-15T00:41Z] INFO  17:41:59,322 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T00:41Z] WARN  17:41:59,539 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T00:41Z] WARN  17:41:59,540 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T00:41Z] INFO  17:41:59,677 IntervalUtils - Processing 144481 bp from intervals
[2016-04-15T00:41Z] WARN  17:41:59,694 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:41Z] INFO  17:41:59,780 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:41Z] INFO  17:41:59,848 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:41Z] INFO  17:41:59,849 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:41Z] INFO  17:41:59,850 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T00:41Z] INFO  17:41:59,850 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T00:41Z] INFO  17:41:59,851 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T00:41Z] INFO  17:41:59,851 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T00:41Z] INFO  17:41:59,856 ProgressMeter -      11:1018241        9985430.0    90.0 s            9.0 s       16.7%     9.0 m       7.5 m
[2016-04-15T00:42Z] INFO  17:42:00,133 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T00:42Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T00:42Z] INFO  17:42:04,623 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T00:42Z] INFO  17:42:04,625 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T00:42Z] WARN  17:42:04,894 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T00:42Z] WARN  17:42:04,906 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T00:42Z] INFO  17:42:05,089 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.0033872280000000004
[2016-04-15T00:42Z] INFO  17:42:05,090 PairHMM - Total compute time in PairHMM computeLikelihoods() : 0.061204479000000006
[2016-04-15T00:42Z] INFO  17:42:05,090 HaplotypeCaller - Ran local assembly on 383 active regions
[2016-04-15T00:42Z] INFO  17:42:05,147 ProgressMeter -            done        7043015.0    20.0 s            2.0 s      100.0%    20.0 s       0.0 s
[2016-04-15T00:42Z] INFO  17:42:05,148 ProgressMeter - Total runtime 20.79 secs, 0.35 min, 0.01 hours
[2016-04-15T00:42Z] INFO  17:42:05,148 MicroScheduler - 22206 reads were filtered out during the traversal out of approximately 89399 total reads (24.84%)
[2016-04-15T00:42Z] INFO  17:42:05,148 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:42Z] INFO  17:42:05,148 MicroScheduler -   -> 5695 reads (6.37% of total) failing DuplicateReadFilter
[2016-04-15T00:42Z] INFO  17:42:05,149 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:42Z] INFO  17:42:05,149 MicroScheduler -   -> 16511 reads (18.47% of total) failing HCMappingQualityFilter
[2016-04-15T00:42Z] INFO  17:42:05,149 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:42Z] INFO  17:42:05,150 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:42Z] INFO  17:42:05,150 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:42Z] INFO  17:42:05,150 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:42Z] INFO  17:42:05,561 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.034855872
[2016-04-15T00:42Z] INFO  17:42:05,562 PairHMM - Total compute time in PairHMM computeLikelihoods() : 3.3007853660000004
[2016-04-15T00:42Z] INFO  17:42:05,563 HaplotypeCaller - Ran local assembly on 778 active regions
[2016-04-15T00:42Z] INFO  17:42:05,600 ProgressMeter -            done      2.2806798E7    38.0 s            1.0 s      100.0%    38.0 s       0.0 s
[2016-04-15T00:42Z] INFO  17:42:05,601 ProgressMeter - Total runtime 38.62 secs, 0.64 min, 0.01 hours
[2016-04-15T00:42Z] INFO  17:42:05,602 MicroScheduler - 24392 reads were filtered out during the traversal out of approximately 186512 total reads (13.08%)
[2016-04-15T00:42Z] INFO  17:42:05,602 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:42Z] INFO  17:42:05,602 MicroScheduler -   -> 13693 reads (7.34% of total) failing DuplicateReadFilter
[2016-04-15T00:42Z] INFO  17:42:05,603 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:42Z] INFO  17:42:05,603 MicroScheduler -   -> 10699 reads (5.74% of total) failing HCMappingQualityFilter
[2016-04-15T00:42Z] INFO  17:42:05,603 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:42Z] INFO  17:42:05,604 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:42Z] INFO  17:42:05,604 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:42Z] INFO  17:42:05,604 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:42Z] INFO  17:42:06,189 ProgressMeter -     13:45841493      2.8826108E7    30.0 s            1.0 s       62.2%    48.0 s      18.0 s
[2016-04-15T00:42Z] INFO  17:42:06,431 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:42Z] GATK: HaplotypeCaller
[2016-04-15T00:42Z] INFO  17:42:06,658 ProgressMeter -     12:41967467      2.0646586E7    60.0 s            2.0 s       66.3%    90.0 s      30.0 s
[2016-04-15T00:42Z] INFO  17:42:07,101 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:42Z] GATK: HaplotypeCaller
[2016-04-15T00:42Z] INFO  17:42:07,969 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.004549762000000001
[2016-04-15T00:42Z] INFO  17:42:07,981 PairHMM - Total compute time in PairHMM computeLikelihoods() : 0.056034899000000006
[2016-04-15T00:42Z] INFO  17:42:07,983 HaplotypeCaller - Ran local assembly on 475 active regions
[2016-04-15T00:42Z] INFO  17:42:08,027 ProgressMeter -            done      1.1587684E7    22.0 s            1.0 s      100.0%    22.0 s       0.0 s
[2016-04-15T00:42Z] INFO  17:42:08,028 ProgressMeter - Total runtime 22.16 secs, 0.37 min, 0.01 hours
[2016-04-15T00:42Z] INFO  17:42:08,028 MicroScheduler - 5770 reads were filtered out during the traversal out of approximately 79471 total reads (7.26%)
[2016-04-15T00:42Z] INFO  17:42:08,028 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:42Z] INFO  17:42:08,029 MicroScheduler -   -> 5709 reads (7.18% of total) failing DuplicateReadFilter
[2016-04-15T00:42Z] INFO  17:42:08,030 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:42Z] INFO  17:42:08,030 MicroScheduler -   -> 61 reads (0.08% of total) failing HCMappingQualityFilter
[2016-04-15T00:42Z] INFO  17:42:08,030 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:42Z] INFO  17:42:08,030 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:42Z] INFO  17:42:08,031 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:42Z] INFO  17:42:08,031 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:42Z] INFO  17:42:08,180 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.028368514
[2016-04-15T00:42Z] INFO  17:42:08,181 PairHMM - Total compute time in PairHMM computeLikelihoods() : 3.315167996
[2016-04-15T00:42Z] INFO  17:42:08,181 HaplotypeCaller - Ran local assembly on 2326 active regions
[2016-04-15T00:42Z] INFO  17:42:08,250 ProgressMeter -            done     2.23715124E8    81.0 s            0.0 s      100.0%    81.0 s       0.0 s
[2016-04-15T00:42Z] INFO  17:42:08,251 ProgressMeter - Total runtime 81.04 secs, 1.35 min, 0.02 hours
[2016-04-15T00:42Z] INFO  17:42:08,251 MicroScheduler - 38852 reads were filtered out during the traversal out of approximately 476648 total reads (8.15%)
[2016-04-15T00:42Z] INFO  17:42:08,252 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:42Z] INFO  17:42:08,252 MicroScheduler -   -> 35746 reads (7.50% of total) failing DuplicateReadFilter
[2016-04-15T00:42Z] INFO  17:42:08,252 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:42Z] INFO  17:42:08,252 MicroScheduler -   -> 3106 reads (0.65% of total) failing HCMappingQualityFilter
[2016-04-15T00:42Z] INFO  17:42:08,253 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:42Z] INFO  17:42:08,253 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:42Z] INFO  17:42:08,253 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:42Z] INFO  17:42:08,253 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:42Z] INFO  17:42:08,689 ProgressMeter -     12:53242772     1.23634014E8    60.0 s            0.0 s       46.9%     2.1 m      68.0 s
[2016-04-15T00:42Z] INFO  17:42:09,476 ProgressMeter -     11:61136181     1.07305853E8    90.0 s            0.0 s       71.6%     2.1 m      35.0 s
[2016-04-15T00:42Z] INFO  17:42:09,611 ProgressMeter -     11:71807563     2.87264229E8    90.0 s            0.0 s       72.1%     2.1 m      34.0 s
[2016-04-15T00:42Z] INFO  17:42:09,644 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:42Z] INFO  17:42:09,650 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:42Z] INFO  17:42:09,653 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:42Z] INFO  17:42:09,653 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:42Z] INFO  17:42:09,654 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:42Z] INFO  17:42:09,659 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/14/R14-18106_kapa-NGv3-PE100-NGv3-sort-14_0_19378574-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/14/R14-18106_kapa-NGv3-PE100-NGv3-14_0_19378574-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/14/tx/tmphwo4wW/R14-18106_kapa-NGv3-PE100-NGv3-14_0_19378574.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:42Z] INFO  17:42:09,678 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:42Z] INFO  17:42:09,679 HelpFormatter - Date/Time: 2016/04/14 17:42:09
[2016-04-15T00:42Z] INFO  17:42:09,679 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:42Z] INFO  17:42:09,680 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:42Z] WARN  17:42:09,714 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T00:42Z] WARN  17:42:09,718 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/14/tx/tmphwo4wW/R14-18106_kapa-NGv3-PE100-NGv3-14_0_19378574.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T00:42Z] INFO  17:42:09,722 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:42Z] INFO  17:42:09,888 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:42Z] GATK: HaplotypeCaller
[2016-04-15T00:42Z] GATK: HaplotypeCaller
[2016-04-15T00:42Z] INFO  17:42:10,146 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T00:42Z] INFO  17:42:10,167 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:42Z] INFO  17:42:10,232 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-15T00:42Z] INFO  17:42:10,250 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T00:42Z] INFO  17:42:10,637 IntervalUtils - Processing 981 bp from intervals
[2016-04-15T00:42Z] WARN  17:42:10,659 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:42Z] INFO  17:42:10,700 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:42Z] INFO  17:42:10,703 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:42Z] INFO  17:42:10,704 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:42Z] INFO  17:42:10,704 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:42Z] INFO  17:42:10,709 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/14/R14-18106_kapa-NGv3-PE100-NGv3-sort-14_19553416_35066851-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/14/R14-18106_kapa-NGv3-PE100-NGv3-14_19553416_35066851-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/14/tx/tmpTa_Z2p/R14-18106_kapa-NGv3-PE100-NGv3-14_19553416_35066851.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:42Z] INFO  17:42:10,717 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:42Z] INFO  17:42:10,718 HelpFormatter - Date/Time: 2016/04/14 17:42:10
[2016-04-15T00:42Z] INFO  17:42:10,718 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:42Z] INFO  17:42:10,719 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:42Z] INFO  17:42:10,746 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:42Z] WARN  17:42:10,757 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T00:42Z] WARN  17:42:10,764 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/14/tx/tmpTa_Z2p/R14-18106_kapa-NGv3-PE100-NGv3-14_19553416_35066851.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T00:42Z] INFO  17:42:10,783 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:42Z] INFO  17:42:10,784 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:42Z] INFO  17:42:10,784 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T00:42Z] INFO  17:42:10,785 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T00:42Z] INFO  17:42:10,785 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T00:42Z] INFO  17:42:10,785 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T00:42Z] INFO  17:42:10,970 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:42Z] INFO  17:42:10,976 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T00:42Z] INFO  17:42:11,147 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T00:42Z] INFO  17:42:11,156 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:42Z] INFO  17:42:11,215 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-15T00:42Z] INFO  17:42:11,232 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T00:42Z] INFO  17:42:11,703 IntervalUtils - Processing 291951 bp from intervals
[2016-04-15T00:42Z] WARN  17:42:11,708 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:42Z] INFO  17:42:11,837 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:42Z] INFO  17:42:11,963 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:42Z] INFO  17:42:11,975 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:42Z] INFO  17:42:11,976 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T00:42Z] INFO  17:42:11,976 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T00:42Z] INFO  17:42:11,988 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T00:42Z] INFO  17:42:11,989 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T00:42Z] INFO  17:42:12,195 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T00:42Z] INFO  17:42:12,276 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.007945742
[2016-04-15T00:42Z] INFO  17:42:12,277 PairHMM - Total compute time in PairHMM computeLikelihoods() : 0.4983748
[2016-04-15T00:42Z] INFO  17:42:12,278 HaplotypeCaller - Ran local assembly on 1538 active regions
[2016-04-15T00:42Z] INFO  17:42:12,321 ProgressMeter -            done     1.17482682E8    47.0 s            0.0 s      100.0%    47.0 s       0.0 s
[2016-04-15T00:42Z] INFO  17:42:12,321 ProgressMeter - Total runtime 47.63 secs, 0.79 min, 0.01 hours
[2016-04-15T00:42Z] INFO  17:42:12,322 MicroScheduler - 19564 reads were filtered out during the traversal out of approximately 256917 total reads (7.61%)
[2016-04-15T00:42Z] INFO  17:42:12,323 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:42Z] INFO  17:42:12,323 MicroScheduler -   -> 19318 reads (7.52% of total) failing DuplicateReadFilter
[2016-04-15T00:42Z] INFO  17:42:12,323 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:42Z] INFO  17:42:12,323 MicroScheduler -   -> 246 reads (0.10% of total) failing HCMappingQualityFilter
[2016-04-15T00:42Z] INFO  17:42:12,324 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:42Z] INFO  17:42:12,324 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:42Z] INFO  17:42:12,324 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:42Z] INFO  17:42:12,324 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:42Z] INFO  17:42:13,085 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:42Z] INFO  17:42:13,088 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:42Z] INFO  17:42:13,089 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:42Z] INFO  17:42:13,090 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:42Z] INFO  17:42:13,094 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/14/R14-18106_kapa-NGv3-PE100-NGv3-sort-14_35072553_50583270-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/14/R14-18106_kapa-NGv3-PE100-NGv3-14_35072553_50583270-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/14/tx/tmptyfz7Q/R14-18106_kapa-NGv3-PE100-NGv3-14_35072553_50583270.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:42Z] INFO  17:42:13,119 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:42Z] INFO  17:42:13,119 HelpFormatter - Date/Time: 2016/04/14 17:42:13
[2016-04-15T00:42Z] INFO  17:42:13,119 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:42Z] INFO  17:42:13,120 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:42Z] INFO  17:42:13,135 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:42Z] INFO  17:42:13,139 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:42Z] INFO  17:42:13,139 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:42Z] INFO  17:42:13,140 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:42Z] INFO  17:42:13,145 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/14/R14-18106_kapa-NGv3-PE100-NGv3-sort-14_50585061_66096324-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/14/R14-18106_kapa-NGv3-PE100-NGv3-14_50585061_66096324-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/14/tx/tmpTPycnB/R14-18106_kapa-NGv3-PE100-NGv3-14_50585061_66096324.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:42Z] INFO  17:42:13,155 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:42Z] WARN  17:42:13,159 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T00:42Z] INFO  17:42:13,161 HelpFormatter - Date/Time: 2016/04/14 17:42:13
[2016-04-15T00:42Z] INFO  17:42:13,161 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:42Z] WARN  17:42:13,162 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/14/tx/tmptyfz7Q/R14-18106_kapa-NGv3-PE100-NGv3-14_35072553_50583270.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T00:42Z] INFO  17:42:13,162 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:42Z] WARN  17:42:13,184 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T00:42Z] WARN  17:42:13,187 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/14/tx/tmpTPycnB/R14-18106_kapa-NGv3-PE100-NGv3-14_50585061_66096324.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T00:42Z] INFO  17:42:13,353 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:42Z] INFO  17:42:13,374 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:42Z] INFO  17:42:13,575 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T00:42Z] INFO  17:42:13,585 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:42Z] INFO  17:42:13,612 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T00:42Z] INFO  17:42:13,622 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:42Z] INFO  17:42:13,665 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-15T00:42Z] INFO  17:42:13,687 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T00:42Z] INFO  17:42:13,696 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:42Z] INFO  17:42:13,704 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-15T00:42Z] INFO  17:42:13,730 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T00:42Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T00:42Z] INFO  17:42:13,859 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T00:42Z] INFO  17:42:13,859 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T00:42Z] GATK: HaplotypeCaller
[2016-04-15T00:42Z] INFO  17:42:14,143 IntervalUtils - Processing 226771 bp from intervals
[2016-04-15T00:42Z] WARN  17:42:14,148 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:42Z] INFO  17:42:14,171 IntervalUtils - Processing 108903 bp from intervals
[2016-04-15T00:42Z] WARN  17:42:14,177 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:42Z] WARN  17:42:14,258 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T00:42Z] WARN  17:42:14,259 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T00:42Z] INFO  17:42:14,260 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:42Z] INFO  17:42:14,301 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:42Z] INFO  17:42:14,359 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:42Z] INFO  17:42:14,360 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:42Z] INFO  17:42:14,360 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T00:42Z] INFO  17:42:14,361 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T00:42Z] INFO  17:42:14,362 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T00:42Z] INFO  17:42:14,362 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T00:42Z] INFO  17:42:14,375 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:42Z] INFO  17:42:14,376 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:42Z] INFO  17:42:14,377 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T00:42Z] INFO  17:42:14,378 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T00:42Z] INFO  17:42:14,379 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T00:42Z] INFO  17:42:14,379 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T00:42Z] INFO  17:42:14,570 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T00:42Z] INFO  17:42:14,620 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T00:42Z] INFO  17:42:15,044 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.021288848000000003
[2016-04-15T00:42Z] INFO  17:42:15,045 PairHMM - Total compute time in PairHMM computeLikelihoods() : 18.797622656
[2016-04-15T00:42Z] INFO  17:42:15,046 HaplotypeCaller - Ran local assembly on 1008 active regions
[2016-04-15T00:42Z] INFO  17:42:15,086 ProgressMeter -            done        4.31997E7    68.0 s            1.0 s      100.0%    68.0 s       0.0 s
[2016-04-15T00:42Z] INFO  17:42:15,087 ProgressMeter - Total runtime 68.45 secs, 1.14 min, 0.02 hours
[2016-04-15T00:42Z] INFO  17:42:15,088 MicroScheduler - 16616 reads were filtered out during the traversal out of approximately 183410 total reads (9.06%)
[2016-04-15T00:42Z] INFO  17:42:15,089 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:42Z] INFO  17:42:15,089 MicroScheduler -   -> 13687 reads (7.46% of total) failing DuplicateReadFilter
[2016-04-15T00:42Z] INFO  17:42:15,090 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:42Z] INFO  17:42:15,091 MicroScheduler -   -> 2929 reads (1.60% of total) failing HCMappingQualityFilter
[2016-04-15T00:42Z] INFO  17:42:15,091 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:42Z] INFO  17:42:15,092 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:42Z] INFO  17:42:15,093 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:42Z] INFO  17:42:15,104 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:42Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T00:42Z] INFO  17:42:15,375 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T00:42Z] INFO  17:42:15,376 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T00:42Z] WARN  17:42:15,892 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T00:42Z] WARN  17:42:15,893 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T00:42Z] INFO  17:42:16,927 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:42Z] GATK: HaplotypeCaller
[2016-04-15T00:42Z] INFO  17:42:17,293 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:42Z] INFO  17:42:17,296 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:42Z] INFO  17:42:17,297 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:42Z] INFO  17:42:17,297 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:42Z] INFO  17:42:17,302 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/14/R14-18106_kapa-NGv3-PE100-NGv3-sort-14_66135960_81646674-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/14/R14-18106_kapa-NGv3-PE100-NGv3-14_66135960_81646674-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/14/tx/tmpSQ1FCg/R14-18106_kapa-NGv3-PE100-NGv3-14_66135960_81646674.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:42Z] INFO  17:42:17,324 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:42Z] INFO  17:42:17,333 HelpFormatter - Date/Time: 2016/04/14 17:42:17
[2016-04-15T00:42Z] INFO  17:42:17,334 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:42Z] INFO  17:42:17,334 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:42Z] WARN  17:42:17,358 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T00:42Z] WARN  17:42:17,361 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/14/tx/tmpSQ1FCg/R14-18106_kapa-NGv3-PE100-NGv3-14_66135960_81646674.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T00:42Z] INFO  17:42:17,568 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:42Z] INFO  17:42:17,715 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T00:42Z] INFO  17:42:17,724 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:42Z] INFO  17:42:17,779 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-15T00:42Z] INFO  17:42:17,809 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T00:42Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T00:42Z] INFO  17:42:18,333 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T00:42Z] INFO  17:42:18,334 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T00:42Z] INFO  17:42:18,360 IntervalUtils - Processing 245410 bp from intervals
[2016-04-15T00:42Z] WARN  17:42:18,365 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:42Z] INFO  17:42:18,441 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:42Z] INFO  17:42:18,646 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:42Z] INFO  17:42:18,647 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:42Z] INFO  17:42:18,647 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T00:42Z] INFO  17:42:18,648 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T00:42Z] WARN  17:42:18,658 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T00:42Z] WARN  17:42:18,660 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T00:42Z] INFO  17:42:18,664 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T00:42Z] INFO  17:42:18,665 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T00:42Z] INFO  17:42:18,835 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T00:42Z] INFO  17:42:18,907 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.008734828
[2016-04-15T00:42Z] INFO  17:42:18,908 PairHMM - Total compute time in PairHMM computeLikelihoods() : 0.47493553000000005
[2016-04-15T00:42Z] INFO  17:42:18,909 HaplotypeCaller - Ran local assembly on 1285 active regions
[2016-04-15T00:42Z] INFO  17:42:18,961 ProgressMeter -            done      7.9081089E7    42.0 s            0.0 s      100.0%    42.0 s       0.0 s
[2016-04-15T00:42Z] INFO  17:42:18,961 ProgressMeter - Total runtime 42.80 secs, 0.71 min, 0.01 hours
[2016-04-15T00:42Z] INFO  17:42:18,962 MicroScheduler - 17208 reads were filtered out during the traversal out of approximately 212957 total reads (8.08%)
[2016-04-15T00:42Z] INFO  17:42:18,963 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:42Z] INFO  17:42:18,963 MicroScheduler -   -> 16390 reads (7.70% of total) failing DuplicateReadFilter
[2016-04-15T00:42Z] INFO  17:42:18,963 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:42Z] INFO  17:42:18,963 MicroScheduler -   -> 818 reads (0.38% of total) failing HCMappingQualityFilter
[2016-04-15T00:42Z] INFO  17:42:18,964 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:42Z] INFO  17:42:18,964 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:42Z] INFO  17:42:18,964 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:42Z] INFO  17:42:18,964 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:42Z] INFO  17:42:19,491 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.004794136
[2016-04-15T00:42Z] INFO  17:42:19,500 PairHMM - Total compute time in PairHMM computeLikelihoods() : 1.188843707
[2016-04-15T00:42Z] INFO  17:42:19,501 HaplotypeCaller - Ran local assembly on 9 active regions
[2016-04-15T00:42Z] INFO  17:42:19,542 ProgressMeter -            done            981.0     8.0 s            2.5 h       99.9%     8.0 s       0.0 s
[2016-04-15T00:42Z] INFO  17:42:19,543 ProgressMeter - Total runtime 8.76 secs, 0.15 min, 0.00 hours
[2016-04-15T00:42Z] INFO  17:42:19,543 MicroScheduler - 1761 reads were filtered out during the traversal out of approximately 3433 total reads (51.30%)
[2016-04-15T00:42Z] INFO  17:42:19,544 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:42Z] INFO  17:42:19,544 MicroScheduler -   -> 138 reads (4.02% of total) failing DuplicateReadFilter
[2016-04-15T00:42Z] INFO  17:42:19,544 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:42Z] INFO  17:42:19,544 MicroScheduler -   -> 1623 reads (47.28% of total) failing HCMappingQualityFilter
[2016-04-15T00:42Z] INFO  17:42:19,545 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:42Z] INFO  17:42:19,545 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:42Z] INFO  17:42:19,545 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:42Z] INFO  17:42:19,546 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:42Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T00:42Z] INFO  17:42:19,723 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T00:42Z] INFO  17:42:19,723 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T00:42Z] WARN  17:42:20,045 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T00:42Z] WARN  17:42:20,056 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T00:42Z] INFO  17:42:20,220 ProgressMeter -     12:11339320     1.90510087E8    90.0 s            0.0 s       84.5%   106.0 s      16.0 s
[2016-04-15T00:42Z] INFO  17:42:20,378 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:42Z] INFO  17:42:20,382 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:42Z] INFO  17:42:20,382 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:42Z] INFO  17:42:20,383 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:42Z] INFO  17:42:20,387 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/14/R14-18106_kapa-NGv3-PE100-NGv3-sort-14_81651874_97299968-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/14/R14-18106_kapa-NGv3-PE100-NGv3-14_81651874_97299968-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/14/tx/tmpctMjEX/R14-18106_kapa-NGv3-PE100-NGv3-14_81651874_97299968.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:42Z] INFO  17:42:20,397 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:42Z] INFO  17:42:20,410 HelpFormatter - Date/Time: 2016/04/14 17:42:20
[2016-04-15T00:42Z] INFO  17:42:20,411 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:42Z] INFO  17:42:20,412 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:42Z] INFO  17:42:20,418 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:42Z] WARN  17:42:20,456 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T00:42Z] WARN  17:42:20,470 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/14/tx/tmpctMjEX/R14-18106_kapa-NGv3-PE100-NGv3-14_81651874_97299968.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T00:42Z] GATK: HaplotypeCaller
[2016-04-15T00:42Z] INFO  17:42:20,742 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:42Z] INFO  17:42:21,001 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T00:42Z] INFO  17:42:21,011 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:42Z] INFO  17:42:21,073 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:42Z] INFO  17:42:21,090 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-15T00:42Z] INFO  17:42:21,116 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T00:42Z] GATK: HaplotypeCaller
[2016-04-15T00:42Z] INFO  17:42:21,676 IntervalUtils - Processing 176504 bp from intervals
[2016-04-15T00:42Z] WARN  17:42:21,689 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:42Z] INFO  17:42:21,770 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:42Z] INFO  17:42:21,894 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:42Z] INFO  17:42:21,895 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:42Z] INFO  17:42:21,896 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T00:42Z] INFO  17:42:21,897 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T00:42Z] INFO  17:42:21,905 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T00:42Z] INFO  17:42:21,906 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T00:42Z] INFO  17:42:22,134 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T00:42Z] INFO  17:42:22,839 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.006719542
[2016-04-15T00:42Z] INFO  17:42:22,840 PairHMM - Total compute time in PairHMM computeLikelihoods() : 0.31993930400000004
[2016-04-15T00:42Z] INFO  17:42:22,840 HaplotypeCaller - Ran local assembly on 587 active regions
[2016-04-15T00:42Z] INFO  17:42:22,894 ProgressMeter -            done      1.7240277E7    27.0 s            1.0 s      100.0%    27.0 s       0.0 s
[2016-04-15T00:42Z] INFO  17:42:22,894 ProgressMeter - Total runtime 27.29 secs, 0.45 min, 0.01 hours
[2016-04-15T00:42Z] INFO  17:42:22,895 MicroScheduler - 8157 reads were filtered out during the traversal out of approximately 105235 total reads (7.75%)
[2016-04-15T00:42Z] INFO  17:42:22,895 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:42Z] INFO  17:42:22,895 MicroScheduler -   -> 8009 reads (7.61% of total) failing DuplicateReadFilter
[2016-04-15T00:42Z] INFO  17:42:22,895 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:42Z] INFO  17:42:22,896 MicroScheduler -   -> 148 reads (0.14% of total) failing HCMappingQualityFilter
[2016-04-15T00:42Z] INFO  17:42:22,896 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:42Z] INFO  17:42:22,896 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:42Z] INFO  17:42:22,896 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:42Z] INFO  17:42:22,897 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:42Z] INFO  17:42:23,801 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:42Z] INFO  17:42:23,803 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:42Z] INFO  17:42:23,804 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:42Z] INFO  17:42:23,804 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:42Z] INFO  17:42:23,808 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/14/R14-18106_kapa-NGv3-PE100-NGv3-sort-14_97304098_107349540-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/14/R14-18106_kapa-NGv3-PE100-NGv3-14_97304098_107349540-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/14/tx/tmpWTSewn/R14-18106_kapa-NGv3-PE100-NGv3-14_97304098_107349540.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:42Z] INFO  17:42:23,831 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:42Z] INFO  17:42:23,832 HelpFormatter - Date/Time: 2016/04/14 17:42:23
[2016-04-15T00:42Z] INFO  17:42:23,832 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:42Z] INFO  17:42:23,832 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:42Z] WARN  17:42:23,874 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T00:42Z] WARN  17:42:23,880 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/14/tx/tmpWTSewn/R14-18106_kapa-NGv3-PE100-NGv3-14_97304098_107349540.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T00:42Z] INFO  17:42:24,204 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:42Z] INFO  17:42:24,295 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:42Z] INFO  17:42:24,443 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T00:42Z] INFO  17:42:24,474 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:42Z] INFO  17:42:24,507 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:42Z] INFO  17:42:24,528 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:42Z] INFO  17:42:24,528 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:42Z] INFO  17:42:24,529 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:42Z] INFO  17:42:24,534 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/15/R14-18106_kapa-NGv3-PE100-NGv3-sort-15_0_20740485-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/15/R14-18106_kapa-NGv3-PE100-NGv3-15_0_20740485-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/15/tx/tmpGD2KZp/R14-18106_kapa-NGv3-PE100-NGv3-15_0_20740485.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:42Z] INFO  17:42:24,547 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:42Z] INFO  17:42:24,548 HelpFormatter - Date/Time: 2016/04/14 17:42:24
[2016-04-15T00:42Z] INFO  17:42:24,549 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:42Z] INFO  17:42:24,549 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:42Z] INFO  17:42:24,551 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-15T00:42Z] WARN  17:42:24,572 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T00:42Z] INFO  17:42:24,574 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T00:42Z] WARN  17:42:24,574 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/15/tx/tmpGD2KZp/R14-18106_kapa-NGv3-PE100-NGv3-15_0_20740485.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T00:42Z] GATK: HaplotypeCaller
[2016-04-15T00:42Z] INFO  17:42:24,739 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:42Z] INFO  17:42:24,837 ProgressMeter -    12:122196457     1.72114114E8    60.0 s            0.0 s       69.2%    86.0 s      26.0 s
[2016-04-15T00:42Z] INFO  17:42:24,950 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T00:42Z] INFO  17:42:24,970 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:42Z] INFO  17:42:25,011 IntervalUtils - Processing 188545 bp from intervals
[2016-04-15T00:42Z] WARN  17:42:25,016 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:42Z] INFO  17:42:25,059 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.09
[2016-04-15T00:42Z] INFO  17:42:25,078 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T00:42Z] INFO  17:42:25,096 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:42Z] INFO  17:42:25,176 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:42Z] INFO  17:42:25,178 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:42Z] INFO  17:42:25,178 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T00:42Z] INFO  17:42:25,179 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T00:42Z] INFO  17:42:25,180 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T00:42Z] INFO  17:42:25,180 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T00:42Z] INFO  17:42:25,343 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T00:42Z] INFO  17:42:25,494 IntervalUtils - Processing 989 bp from intervals
[2016-04-15T00:42Z] WARN  17:42:25,502 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:42Z] INFO  17:42:25,615 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:42Z] INFO  17:42:25,679 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:42Z] INFO  17:42:25,680 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:42Z] INFO  17:42:25,681 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T00:42Z] INFO  17:42:25,681 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T00:42Z] INFO  17:42:25,693 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T00:42Z] INFO  17:42:25,694 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T00:42Z] INFO  17:42:25,947 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T00:42Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T00:42Z] INFO  17:42:26,251 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T00:42Z] INFO  17:42:26,252 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T00:42Z] WARN  17:42:26,520 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T00:42Z] WARN  17:42:26,521 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T00:42Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T00:42Z] INFO  17:42:27,115 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T00:42Z] INFO  17:42:27,116 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T00:42Z] WARN  17:42:27,350 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T00:42Z] WARN  17:42:27,351 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T00:42Z] INFO  17:42:28,022 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:42Z] INFO  17:42:28,025 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:42Z] INFO  17:42:28,025 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:42Z] INFO  17:42:28,025 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:42Z] INFO  17:42:28,029 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/15/R14-18106_kapa-NGv3-PE100-NGv3-sort-15_20741621_36872162-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/15/R14-18106_kapa-NGv3-PE100-NGv3-15_20741621_36872162-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/15/tx/tmpeJSugl/R14-18106_kapa-NGv3-PE100-NGv3-15_20741621_36872162.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:42Z] INFO  17:42:28,069 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:42Z] INFO  17:42:28,069 HelpFormatter - Date/Time: 2016/04/14 17:42:28
[2016-04-15T00:42Z] INFO  17:42:28,075 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:42Z] INFO  17:42:28,075 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:42Z] WARN  17:42:28,098 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T00:42Z] WARN  17:42:28,100 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/15/tx/tmpeJSugl/R14-18106_kapa-NGv3-PE100-NGv3-15_20741621_36872162.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T00:42Z] INFO  17:42:28,294 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:42Z] INFO  17:42:28,379 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.039509452
[2016-04-15T00:42Z] INFO  17:42:28,380 PairHMM - Total compute time in PairHMM computeLikelihoods() : 13.368148391
[2016-04-15T00:42Z] INFO  17:42:28,380 HaplotypeCaller - Ran local assembly on 2339 active regions
[2016-04-15T00:42Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T00:42Z] INFO  17:42:28,423 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T00:42Z] INFO  17:42:28,424 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T00:42Z] INFO  17:42:28,429 ProgressMeter -            done     1.96753928E8   108.0 s            0.0 s      100.0%   108.0 s       0.0 s
[2016-04-15T00:42Z] INFO  17:42:28,429 ProgressMeter - Total runtime 108.99 secs, 1.82 min, 0.03 hours
[2016-04-15T00:42Z] INFO  17:42:28,430 MicroScheduler - 51646 reads were filtered out during the traversal out of approximately 501046 total reads (10.31%)
[2016-04-15T00:42Z] INFO  17:42:28,430 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:42Z] INFO  17:42:28,430 MicroScheduler -   -> 37587 reads (7.50% of total) failing DuplicateReadFilter
[2016-04-15T00:42Z] INFO  17:42:28,430 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:42Z] INFO  17:42:28,431 MicroScheduler -   -> 14059 reads (2.81% of total) failing HCMappingQualityFilter
[2016-04-15T00:42Z] INFO  17:42:28,431 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:42Z] INFO  17:42:28,431 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:42Z] INFO  17:42:28,431 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:42Z] INFO  17:42:28,432 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:42Z] INFO  17:42:28,561 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T00:42Z] INFO  17:42:28,570 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:42Z] WARN  17:42:28,641 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T00:42Z] WARN  17:42:28,642 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T00:42Z] INFO  17:42:28,666 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.09
[2016-04-15T00:42Z] INFO  17:42:28,685 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T00:42Z] INFO  17:42:29,033 IntervalUtils - Processing 177979 bp from intervals
[2016-04-15T00:42Z] WARN  17:42:29,038 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:42Z] INFO  17:42:29,090 ProgressMeter -     13:33703680       8.683956E7    60.0 s            0.0 s       97.8%    61.0 s       1.0 s
[2016-04-15T00:42Z] INFO  17:42:29,121 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:42Z] INFO  17:42:29,223 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:42Z] INFO  17:42:29,224 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:42Z] INFO  17:42:29,225 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T00:42Z] INFO  17:42:29,225 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T00:42Z] INFO  17:42:29,226 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T00:42Z] INFO  17:42:29,226 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T00:42Z] INFO  17:42:29,468 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T00:42Z] INFO  17:42:29,599 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.0010215200000000002
[2016-04-15T00:42Z] INFO  17:42:29,600 PairHMM - Total compute time in PairHMM computeLikelihoods() : 0.013543579
[2016-04-15T00:42Z] INFO  17:42:29,600 HaplotypeCaller - Ran local assembly on 8 active regions
[2016-04-15T00:42Z] INFO  17:42:29,661 ProgressMeter -            done            989.0     3.0 s           67.1 m       99.9%     3.0 s       0.0 s
[2016-04-15T00:42Z] INFO  17:42:29,662 ProgressMeter - Total runtime 3.98 secs, 0.07 min, 0.00 hours
[2016-04-15T00:42Z] INFO  17:42:29,662 MicroScheduler - 1196 reads were filtered out during the traversal out of approximately 1692 total reads (70.69%)
[2016-04-15T00:42Z] INFO  17:42:29,663 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:42Z] INFO  17:42:29,663 MicroScheduler -   -> 33 reads (1.95% of total) failing DuplicateReadFilter
[2016-04-15T00:42Z] INFO  17:42:29,663 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:42Z] INFO  17:42:29,664 MicroScheduler -   -> 1163 reads (68.74% of total) failing HCMappingQualityFilter
[2016-04-15T00:42Z] INFO  17:42:29,664 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:42Z] INFO  17:42:29,664 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:42Z] INFO  17:42:29,664 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:42Z] INFO  17:42:29,665 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:42Z] INFO  17:42:29,767 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:42Z] INFO  17:42:29,857 ProgressMeter -      11:1092874      1.2877009E7   120.0 s            9.0 s       18.8%    10.6 m       8.6 m
[2016-04-15T00:42Z] INFO  17:42:29,874 ProgressMeter -    13:113536127       2.103495E7    30.0 s            1.0 s       66.4%    45.0 s      15.0 s
[2016-04-15T00:42Z] GATK: HaplotypeCaller
[2016-04-15T00:42Z] INFO  17:42:30,448 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.014567416000000001
[2016-04-15T00:42Z] INFO  17:42:30,449 PairHMM - Total compute time in PairHMM computeLikelihoods() : 7.785657049
[2016-04-15T00:42Z] INFO  17:42:30,449 HaplotypeCaller - Ran local assembly on 1418 active regions
[2016-04-15T00:42Z] INFO  17:42:30,484 ProgressMeter -            done      9.1028011E7    61.0 s            0.0 s      100.0%    61.0 s       0.0 s
[2016-04-15T00:42Z] INFO  17:42:30,485 ProgressMeter - Total runtime 61.42 secs, 1.02 min, 0.02 hours
[2016-04-15T00:42Z] INFO  17:42:30,486 MicroScheduler - 19023 reads were filtered out during the traversal out of approximately 232100 total reads (8.20%)
[2016-04-15T00:42Z] INFO  17:42:30,487 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:42Z] INFO  17:42:30,487 MicroScheduler -   -> 17426 reads (7.51% of total) failing DuplicateReadFilter
[2016-04-15T00:42Z] INFO  17:42:30,488 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:42Z] INFO  17:42:30,488 MicroScheduler -   -> 1597 reads (0.69% of total) failing HCMappingQualityFilter
[2016-04-15T00:42Z] INFO  17:42:30,489 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:42Z] INFO  17:42:30,490 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:42Z] INFO  17:42:30,490 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:42Z] INFO  17:42:30,491 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:42Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T00:42Z] INFO  17:42:31,089 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T00:42Z] INFO  17:42:31,090 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T00:42Z] INFO  17:42:31,101 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:42Z] WARN  17:42:31,294 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T00:42Z] WARN  17:42:31,296 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T00:42Z] GATK: HaplotypeCaller
[2016-04-15T00:42Z] INFO  17:42:32,023 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:42Z] GATK: HaplotypeCaller
[2016-04-15T00:42Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T00:42Z] INFO  17:42:33,206 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T00:42Z] INFO  17:42:33,206 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T00:42Z] INFO  17:42:33,346 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:42Z] INFO  17:42:33,349 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:42Z] INFO  17:42:33,349 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:42Z] INFO  17:42:33,349 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:42Z] INFO  17:42:33,353 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/15/R14-18106_kapa-NGv3-PE100-NGv3-sort-15_36887086_52402170-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/15/R14-18106_kapa-NGv3-PE100-NGv3-15_36887086_52402170-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/15/tx/tmpOBjK6E/R14-18106_kapa-NGv3-PE100-NGv3-15_36887086_52402170.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:42Z] INFO  17:42:33,365 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:42Z] INFO  17:42:33,365 HelpFormatter - Date/Time: 2016/04/14 17:42:33
[2016-04-15T00:42Z] INFO  17:42:33,365 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:42Z] INFO  17:42:33,365 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:42Z] WARN  17:42:33,410 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T00:42Z] WARN  17:42:33,424 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/15/tx/tmpOBjK6E/R14-18106_kapa-NGv3-PE100-NGv3-15_36887086_52402170.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T00:42Z] WARN  17:42:33,429 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T00:42Z] WARN  17:42:33,430 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T00:42Z] INFO  17:42:33,681 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:42Z] INFO  17:42:33,857 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T00:42Z] INFO  17:42:33,870 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:42Z] INFO  17:42:33,951 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-15T00:42Z] INFO  17:42:33,971 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T00:42Z] INFO  17:42:34,438 IntervalUtils - Processing 374190 bp from intervals
[2016-04-15T00:42Z] WARN  17:42:34,444 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:42Z] INFO  17:42:34,561 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:42Z] INFO  17:42:34,679 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:42Z] INFO  17:42:34,680 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:42Z] INFO  17:42:34,681 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T00:42Z] INFO  17:42:34,682 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T00:42Z] INFO  17:42:34,682 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:42Z] INFO  17:42:34,685 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:42Z] INFO  17:42:34,685 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:42Z] INFO  17:42:34,686 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:42Z] INFO  17:42:34,690 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/15/R14-18106_kapa-NGv3-PE100-NGv3-sort-15_52404364_67923265-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/15/R14-18106_kapa-NGv3-PE100-NGv3-15_52404364_67923265-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/15/tx/tmpQfSoYE/R14-18106_kapa-NGv3-PE100-NGv3-15_52404364_67923265.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:42Z] INFO  17:42:34,691 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T00:42Z] INFO  17:42:34,691 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T00:42Z] INFO  17:42:34,709 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:42Z] INFO  17:42:34,709 HelpFormatter - Date/Time: 2016/04/14 17:42:34
[2016-04-15T00:42Z] INFO  17:42:34,709 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:42Z] INFO  17:42:34,710 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:42Z] WARN  17:42:34,756 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T00:42Z] WARN  17:42:34,762 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/15/tx/tmpQfSoYE/R14-18106_kapa-NGv3-PE100-NGv3-15_52404364_67923265.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T00:42Z] INFO  17:42:34,958 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T00:42Z] INFO  17:42:35,000 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:42Z] INFO  17:42:35,255 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T00:42Z] INFO  17:42:35,266 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:42Z] INFO  17:42:35,383 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.12
[2016-04-15T00:42Z] INFO  17:42:35,413 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T00:42Z] INFO  17:42:35,425 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:42Z] INFO  17:42:35,427 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:42Z] INFO  17:42:35,428 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:42Z] INFO  17:42:35,428 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:42Z] INFO  17:42:35,445 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/15/R14-18106_kapa-NGv3-PE100-NGv3-sort-15_67932890_83447639-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/15/R14-18106_kapa-NGv3-PE100-NGv3-15_67932890_83447639-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/15/tx/tmpt94kFu/R14-18106_kapa-NGv3-PE100-NGv3-15_67932890_83447639.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:42Z] INFO  17:42:35,458 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:42Z] INFO  17:42:35,459 HelpFormatter - Date/Time: 2016/04/14 17:42:35
[2016-04-15T00:42Z] INFO  17:42:35,460 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:42Z] INFO  17:42:35,469 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:42Z] WARN  17:42:35,500 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T00:42Z] WARN  17:42:35,503 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/15/tx/tmpt94kFu/R14-18106_kapa-NGv3-PE100-NGv3-15_67932890_83447639.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T00:42Z] INFO  17:42:35,726 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:42Z] INFO  17:42:35,815 IntervalUtils - Processing 254619 bp from intervals
[2016-04-15T00:42Z] WARN  17:42:35,820 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:42Z] INFO  17:42:35,910 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:42Z] INFO  17:42:35,981 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T00:42Z] INFO  17:42:36,005 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:42Z] INFO  17:42:36,037 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:42Z] INFO  17:42:36,038 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:42Z] INFO  17:42:36,039 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T00:42Z] INFO  17:42:36,040 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T00:42Z] INFO  17:42:36,041 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T00:42Z] INFO  17:42:36,041 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T00:42Z] INFO  17:42:36,088 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-15T00:42Z] INFO  17:42:36,114 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T00:42Z] INFO  17:42:36,232 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T00:42Z] INFO  17:42:36,538 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.051087971
[2016-04-15T00:42Z] INFO  17:42:36,538 PairHMM - Total compute time in PairHMM computeLikelihoods() : 4.678082323
[2016-04-15T00:42Z] INFO  17:42:36,538 HaplotypeCaller - Ran local assembly on 3833 active regions
[2016-04-15T00:42Z] INFO  17:42:36,588 IntervalUtils - Processing 293221 bp from intervals
[2016-04-15T00:42Z] INFO  17:42:36,598 ProgressMeter -            done     6.10283322E8   117.0 s            0.0 s      100.0%   117.0 s       0.0 s
[2016-04-15T00:42Z] INFO  17:42:36,599 ProgressMeter - Total runtime 117.03 secs, 1.95 min, 0.03 hours
[2016-04-15T00:42Z] INFO  17:42:36,599 MicroScheduler - 66520 reads were filtered out during the traversal out of approximately 833883 total reads (7.98%)
[2016-04-15T00:42Z] WARN  17:42:36,604 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:42Z] INFO  17:42:36,599 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:42Z] INFO  17:42:36,600 MicroScheduler -   -> 63035 reads (7.56% of total) failing DuplicateReadFilter
[2016-04-15T00:42Z] INFO  17:42:36,600 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:42Z] INFO  17:42:36,600 MicroScheduler -   -> 3485 reads (0.42% of total) failing HCMappingQualityFilter
[2016-04-15T00:42Z] INFO  17:42:36,600 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:42Z] INFO  17:42:36,601 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:42Z] INFO  17:42:36,601 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:42Z] INFO  17:42:36,601 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:42Z] INFO  17:42:36,717 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:42Z] INFO  17:42:36,798 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:42Z] INFO  17:42:36,799 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:42Z] INFO  17:42:36,800 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T00:42Z] INFO  17:42:36,801 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T00:42Z] INFO  17:42:36,801 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T00:42Z] INFO  17:42:36,801 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T00:42Z] INFO  17:42:36,985 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T00:42Z] INFO  17:42:37,887 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.027057836000000002
[2016-04-15T00:42Z] INFO  17:42:37,891 PairHMM - Total compute time in PairHMM computeLikelihoods() : 13.580611983
[2016-04-15T00:42Z] INFO  17:42:37,892 HaplotypeCaller - Ran local assembly on 2531 active regions
[2016-04-15T00:42Z] INFO  17:42:37,975 ProgressMeter -            done     2.60606733E8   107.0 s            0.0 s      100.0%   107.0 s       0.0 s
[2016-04-15T00:42Z] INFO  17:42:37,975 ProgressMeter - Total runtime 107.79 secs, 1.80 min, 0.03 hours
[2016-04-15T00:42Z] INFO  17:42:37,976 MicroScheduler - 48583 reads were filtered out during the traversal out of approximately 493656 total reads (9.84%)
[2016-04-15T00:42Z] INFO  17:42:37,976 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:42Z] INFO  17:42:37,976 MicroScheduler -   -> 36406 reads (7.37% of total) failing DuplicateReadFilter
[2016-04-15T00:42Z] INFO  17:42:37,976 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:42Z] INFO  17:42:37,977 MicroScheduler -   -> 12177 reads (2.47% of total) failing HCMappingQualityFilter
[2016-04-15T00:42Z] INFO  17:42:37,977 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:42Z] INFO  17:42:37,977 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:42Z] INFO  17:42:37,977 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:42Z] INFO  17:42:37,978 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:42Z] INFO  17:42:38,037 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:42Z] GATK: HaplotypeCaller
[2016-04-15T00:42Z] INFO  17:42:38,690 ProgressMeter -     12:56999614     3.51390802E8    90.0 s            0.0 s       80.2%   112.0 s      22.0 s
[2016-04-15T00:42Z] INFO  17:42:39,389 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:42Z] GATK: HaplotypeCaller
[2016-04-15T00:42Z] INFO  17:42:40,862 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.029292371
[2016-04-15T00:42Z] INFO  17:42:40,863 PairHMM - Total compute time in PairHMM computeLikelihoods() : 0.54527693
[2016-04-15T00:42Z] INFO  17:42:40,864 HaplotypeCaller - Ran local assembly on 1043 active regions
[2016-04-15T00:42Z] INFO  17:42:40,910 ProgressMeter -            done      4.9965812E7    41.0 s            0.0 s      100.0%    41.0 s       0.0 s
[2016-04-15T00:42Z] INFO  17:42:40,911 ProgressMeter - Total runtime 41.06 secs, 0.68 min, 0.01 hours
[2016-04-15T00:42Z] INFO  17:42:40,912 MicroScheduler - 15352 reads were filtered out during the traversal out of approximately 196975 total reads (7.79%)
[2016-04-15T00:42Z] INFO  17:42:40,912 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:42Z] INFO  17:42:40,912 MicroScheduler -   -> 14845 reads (7.54% of total) failing DuplicateReadFilter
[2016-04-15T00:42Z] INFO  17:42:40,913 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:42Z] INFO  17:42:40,913 MicroScheduler -   -> 507 reads (0.26% of total) failing HCMappingQualityFilter
[2016-04-15T00:42Z] INFO  17:42:40,913 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:42Z] INFO  17:42:40,913 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:42Z] INFO  17:42:40,914 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:42Z] INFO  17:42:40,914 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:42Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T00:42Z] INFO  17:42:40,942 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T00:42Z] INFO  17:42:40,952 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T00:42Z] WARN  17:42:41,172 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T00:42Z] WARN  17:42:41,173 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T00:42Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T00:42Z] INFO  17:42:41,501 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T00:42Z] INFO  17:42:41,502 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T00:42Z] INFO  17:42:41,620 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:42Z] INFO  17:42:41,623 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:42Z] INFO  17:42:41,623 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:42Z] INFO  17:42:41,623 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:42Z] INFO  17:42:41,638 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/15/R14-18106_kapa-NGv3-PE100-NGv3-sort-15_83448996_98982979-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/15/R14-18106_kapa-NGv3-PE100-NGv3-15_83448996_98982979-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/15/tx/tmp195hmD/R14-18106_kapa-NGv3-PE100-NGv3-15_83448996_98982979.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:42Z] INFO  17:42:41,646 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:42Z] INFO  17:42:41,646 HelpFormatter - Date/Time: 2016/04/14 17:42:41
[2016-04-15T00:42Z] INFO  17:42:41,647 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:42Z] INFO  17:42:41,647 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:42Z] WARN  17:42:41,674 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T00:42Z] WARN  17:42:41,681 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/15/tx/tmp195hmD/R14-18106_kapa-NGv3-PE100-NGv3-15_83448996_98982979.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T00:42Z] WARN  17:42:41,864 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T00:42Z] WARN  17:42:41,865 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T00:42Z] INFO  17:42:41,875 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:42Z] INFO  17:42:41,991 ProgressMeter -     14:21831082        8589855.0    30.0 s            3.0 s       23.3%     2.1 m      98.0 s
[2016-04-15T00:42Z] INFO  17:42:42,131 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T00:42Z] INFO  17:42:42,140 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:42Z] INFO  17:42:42,228 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.09
[2016-04-15T00:42Z] INFO  17:42:42,258 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T00:42Z] INFO  17:42:42,473 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:42Z] INFO  17:42:42,741 IntervalUtils - Processing 184993 bp from intervals
[2016-04-15T00:42Z] WARN  17:42:42,756 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:42Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T00:42Z] INFO  17:42:42,829 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T00:42Z] INFO  17:42:42,830 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T00:42Z] GATK: HaplotypeCaller
[2016-04-15T00:42Z] INFO  17:42:42,957 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:42Z] INFO  17:42:43,049 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:42Z] INFO  17:42:43,052 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:42Z] INFO  17:42:43,053 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:42Z] INFO  17:42:43,054 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:42Z] INFO  17:42:43,058 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/15/R14-18106_kapa-NGv3-PE100-NGv3-sort-15_98984299_102531392-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/15/R14-18106_kapa-NGv3-PE100-NGv3-15_98984299_102531392-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/15/tx/tmpts0kan/R14-18106_kapa-NGv3-PE100-NGv3-15_98984299_102531392.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:42Z] INFO  17:42:43,066 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:42Z] INFO  17:42:43,067 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:42Z] INFO  17:42:43,068 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T00:42Z] INFO  17:42:43,069 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T00:42Z] INFO  17:42:43,069 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:42Z] INFO  17:42:43,070 HelpFormatter - Date/Time: 2016/04/14 17:42:43
[2016-04-15T00:42Z] INFO  17:42:43,071 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:42Z] INFO  17:42:43,071 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:42Z] INFO  17:42:43,089 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T00:42Z] INFO  17:42:43,091 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T00:42Z] WARN  17:42:43,116 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T00:42Z] WARN  17:42:43,119 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/15/tx/tmpts0kan/R14-18106_kapa-NGv3-PE100-NGv3-15_98984299_102531392.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T00:42Z] INFO  17:42:43,281 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T00:42Z] WARN  17:42:43,357 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T00:42Z] WARN  17:42:43,363 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T00:42Z] INFO  17:42:43,378 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:42Z] INFO  17:42:43,689 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T00:42Z] INFO  17:42:43,698 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:42Z] INFO  17:42:43,814 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.12
[2016-04-15T00:42Z] INFO  17:42:43,848 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T00:42Z] INFO  17:42:44,305 IntervalUtils - Processing 49123 bp from intervals
[2016-04-15T00:42Z] WARN  17:42:44,310 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:42Z] INFO  17:42:44,386 ProgressMeter -     14:57272099      2.4290402E7    30.0 s            1.0 s       40.4%    74.0 s      44.0 s
[2016-04-15T00:42Z] INFO  17:42:44,391 ProgressMeter -     14:50088600      1.8017267E7    30.0 s            1.0 s       86.2%    34.0 s       4.0 s
[2016-04-15T00:42Z] INFO  17:42:44,464 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:42Z] INFO  17:42:44,553 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:42Z] INFO  17:42:44,554 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:42Z] INFO  17:42:44,555 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T00:42Z] INFO  17:42:44,556 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T00:42Z] INFO  17:42:44,568 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T00:42Z] INFO  17:42:44,569 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T00:42Z] INFO  17:42:44,917 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T00:42Z] INFO  17:42:46,475 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:42Z] INFO  17:42:46,489 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:42Z] INFO  17:42:46,489 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:42Z] INFO  17:42:46,489 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:42Z] INFO  17:42:46,493 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/16/R14-18106_kapa-NGv3-PE100-NGv3-sort-16_0_15528616-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/16/R14-18106_kapa-NGv3-PE100-NGv3-16_0_15528616-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/16/tx/tmp1g9H_R/R14-18106_kapa-NGv3-PE100-NGv3-16_0_15528616.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:42Z] INFO  17:42:46,518 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:42Z] INFO  17:42:46,518 HelpFormatter - Date/Time: 2016/04/14 17:42:46
[2016-04-15T00:42Z] INFO  17:42:46,518 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:42Z] INFO  17:42:46,518 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:42Z] WARN  17:42:46,544 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T00:42Z] WARN  17:42:46,547 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/16/tx/tmp1g9H_R/R14-18106_kapa-NGv3-PE100-NGv3-16_0_15528616.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T00:42Z] INFO  17:42:46,732 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:42Z] INFO  17:42:46,945 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T00:42Z] INFO  17:42:46,972 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:42Z] INFO  17:42:47,024 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-15T00:42Z] INFO  17:42:47,044 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.0056127500000000006
[2016-04-15T00:42Z] INFO  17:42:47,055 PairHMM - Total compute time in PairHMM computeLikelihoods() : 0.317032919
[2016-04-15T00:42Z] INFO  17:42:47,056 HaplotypeCaller - Ran local assembly on 767 active regions
[2016-04-15T00:42Z] INFO  17:42:47,060 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T00:42Z] INFO  17:42:47,222 ProgressMeter -            done      2.6446189E7    32.0 s            1.0 s      100.0%    32.0 s       0.0 s
[2016-04-15T00:42Z] INFO  17:42:47,222 ProgressMeter - Total runtime 32.85 secs, 0.55 min, 0.01 hours
[2016-04-15T00:42Z] INFO  17:42:47,222 MicroScheduler - 9477 reads were filtered out during the traversal out of approximately 113628 total reads (8.34%)
[2016-04-15T00:42Z] INFO  17:42:47,223 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:42Z] INFO  17:42:47,224 MicroScheduler -   -> 8411 reads (7.40% of total) failing DuplicateReadFilter
[2016-04-15T00:42Z] INFO  17:42:47,224 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:42Z] INFO  17:42:47,224 MicroScheduler -   -> 1066 reads (0.94% of total) failing HCMappingQualityFilter
[2016-04-15T00:42Z] INFO  17:42:47,224 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:42Z] INFO  17:42:47,225 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:42Z] INFO  17:42:47,225 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:42Z] INFO  17:42:47,225 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:42Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T00:42Z] INFO  17:42:47,284 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T00:42Z] INFO  17:42:47,285 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T00:42Z] WARN  17:42:47,568 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T00:42Z] WARN  17:42:47,569 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T00:42Z] INFO  17:42:47,601 IntervalUtils - Processing 436708 bp from intervals
[2016-04-15T00:42Z] WARN  17:42:47,607 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:42Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T00:42Z] INFO  17:42:47,633 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T00:42Z] INFO  17:42:47,635 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T00:42Z] INFO  17:42:47,705 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:42Z] INFO  17:42:47,837 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:42Z] INFO  17:42:47,838 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:42Z] INFO  17:42:47,839 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T00:42Z] INFO  17:42:47,840 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T00:42Z] INFO  17:42:47,840 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T00:42Z] INFO  17:42:47,841 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T00:42Z] WARN  17:42:47,923 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T00:42Z] WARN  17:42:47,924 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T00:42Z] INFO  17:42:47,991 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.046942359
[2016-04-15T00:42Z] INFO  17:42:48,002 PairHMM - Total compute time in PairHMM computeLikelihoods() : 2.0760640400000003
[2016-04-15T00:42Z] INFO  17:42:48,003 HaplotypeCaller - Ran local assembly on 2728 active regions
[2016-04-15T00:42Z] INFO  17:42:48,020 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T00:42Z] INFO  17:42:48,055 ProgressMeter -            done     3.54367305E8    83.0 s            0.0 s      100.0%    83.0 s       0.0 s
[2016-04-15T00:42Z] INFO  17:42:48,055 ProgressMeter - Total runtime 83.24 secs, 1.39 min, 0.02 hours
[2016-04-15T00:42Z] INFO  17:42:48,056 MicroScheduler - 44351 reads were filtered out during the traversal out of approximately 562332 total reads (7.89%)
[2016-04-15T00:42Z] INFO  17:42:48,056 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:42Z] INFO  17:42:48,056 MicroScheduler -   -> 42926 reads (7.63% of total) failing DuplicateReadFilter
[2016-04-15T00:42Z] INFO  17:42:48,057 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:42Z] INFO  17:42:48,057 MicroScheduler -   -> 1425 reads (0.25% of total) failing HCMappingQualityFilter
[2016-04-15T00:42Z] INFO  17:42:48,057 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:42Z] INFO  17:42:48,057 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:42Z] INFO  17:42:48,058 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:42Z] INFO  17:42:48,058 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:42Z] INFO  17:42:48,667 ProgressMeter -     14:73007553      1.6926578E7    30.0 s            1.0 s       36.1%    83.0 s      53.0 s
[2016-04-15T00:42Z] INFO  17:42:48,847 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:42Z] GATK: HaplotypeCaller
[2016-04-15T00:42Z] INFO  17:42:49,747 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:42Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T00:42Z] INFO  17:42:49,994 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T00:42Z] INFO  17:42:49,995 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T00:42Z] GATK: HaplotypeCaller
[2016-04-15T00:42Z] WARN  17:42:50,202 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T00:42Z] WARN  17:42:50,213 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T00:42Z] INFO  17:42:51,935 ProgressMeter -     14:92628088      2.1303146E7    30.0 s            1.0 s       50.5%    59.0 s      29.0 s
[2016-04-15T00:42Z] INFO  17:42:52,994 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:42Z] INFO  17:42:53,005 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:42Z] INFO  17:42:53,006 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:42Z] INFO  17:42:53,007 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:42Z] INFO  17:42:53,011 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/16/R14-18106_kapa-NGv3-PE100-NGv3-sort-16_31120544_46629582-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/16/R14-18106_kapa-NGv3-PE100-NGv3-16_31120544_46629582-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/16/tx/tmpGaRdNp/R14-18106_kapa-NGv3-PE100-NGv3-16_31120544_46629582.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:42Z] INFO  17:42:53,021 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:42Z] INFO  17:42:53,032 HelpFormatter - Date/Time: 2016/04/14 17:42:52
[2016-04-15T00:42Z] INFO  17:42:53,033 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:42Z] INFO  17:42:53,034 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:42Z] INFO  17:42:53,032 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:42Z] INFO  17:42:53,035 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:42Z] INFO  17:42:53,035 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:42Z] INFO  17:42:53,036 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:42Z] INFO  17:42:53,040 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/16/R14-18106_kapa-NGv3-PE100-NGv3-sort-16_15596122_31106473-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/16/R14-18106_kapa-NGv3-PE100-NGv3-16_15596122_31106473-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/16/tx/tmpKKx_56/R14-18106_kapa-NGv3-PE100-NGv3-16_15596122_31106473.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:42Z] INFO  17:42:53,072 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:42Z] INFO  17:42:53,073 HelpFormatter - Date/Time: 2016/04/14 17:42:53
[2016-04-15T00:42Z] INFO  17:42:53,074 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:42Z] INFO  17:42:53,078 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:42Z] WARN  17:42:53,079 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T00:42Z] WARN  17:42:53,083 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/16/tx/tmpGaRdNp/R14-18106_kapa-NGv3-PE100-NGv3-16_31120544_46629582.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T00:42Z] WARN  17:42:53,113 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T00:42Z] WARN  17:42:53,116 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/16/tx/tmpKKx_56/R14-18106_kapa-NGv3-PE100-NGv3-16_15596122_31106473.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T00:42Z] INFO  17:42:53,335 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:42Z] INFO  17:42:53,391 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:42Z] INFO  17:42:53,510 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T00:42Z] INFO  17:42:53,520 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:42Z] INFO  17:42:53,608 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.09
[2016-04-15T00:42Z] INFO  17:42:53,613 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T00:42Z] INFO  17:42:53,622 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:42Z] INFO  17:42:53,644 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T00:42Z] INFO  17:42:53,689 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-15T00:42Z] INFO  17:42:53,710 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T00:42Z] INFO  17:42:54,203 IntervalUtils - Processing 400248 bp from intervals
[2016-04-15T00:42Z] WARN  17:42:54,208 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:42Z] INFO  17:42:54,236 IntervalUtils - Processing 40143 bp from intervals
[2016-04-15T00:42Z] WARN  17:42:54,241 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:42Z] INFO  17:42:54,322 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:42Z] INFO  17:42:54,393 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:42Z] INFO  17:42:54,463 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:42Z] INFO  17:42:54,464 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:42Z] INFO  17:42:54,464 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T00:42Z] INFO  17:42:54,465 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T00:42Z] INFO  17:42:54,465 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T00:42Z] INFO  17:42:54,466 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T00:42Z] INFO  17:42:54,535 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:42Z] INFO  17:42:54,536 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:42Z] INFO  17:42:54,536 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T00:42Z] INFO  17:42:54,537 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T00:42Z] INFO  17:42:54,538 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T00:42Z] INFO  17:42:54,538 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T00:42Z] INFO  17:42:54,713 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T00:42Z] INFO  17:42:54,714 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T00:42Z] INFO  17:42:55,198 ProgressMeter -    14:103599161       1.542671E7    30.0 s            1.0 s       47.9%    62.0 s      32.0 s
[2016-04-15T00:42Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T00:42Z] INFO  17:42:56,373 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T00:42Z] INFO  17:42:56,374 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T00:42Z] WARN  17:42:56,729 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T00:42Z] WARN  17:42:56,730 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T00:42Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T00:42Z] INFO  17:42:57,777 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T00:42Z] INFO  17:42:57,778 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T00:42Z] WARN  17:42:58,217 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T00:42Z] WARN  17:42:58,219 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T00:42Z] INFO  17:42:59,248 ProgressMeter -     15:28518039        9293369.0    30.0 s            3.0 s       35.9%    83.0 s      53.0 s
[2016-04-15T00:42Z] INFO  17:42:59,371 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.046211683
[2016-04-15T00:42Z] INFO  17:42:59,371 PairHMM - Total compute time in PairHMM computeLikelihoods() : 1.8113859030000001
[2016-04-15T00:42Z] INFO  17:42:59,371 HaplotypeCaller - Ran local assembly on 3725 active regions
[2016-04-15T00:42Z] INFO  17:42:59,409 ProgressMeter -            done     5.48735474E8   110.0 s            0.0 s      100.0%   110.0 s       0.0 s
[2016-04-15T00:42Z] INFO  17:42:59,409 ProgressMeter - Total runtime 110.74 secs, 1.85 min, 0.03 hours
[2016-04-15T00:42Z] INFO  17:42:59,410 MicroScheduler - 70037 reads were filtered out during the traversal out of approximately 808532 total reads (8.66%)
[2016-04-15T00:42Z] INFO  17:42:59,410 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:42Z] INFO  17:42:59,411 MicroScheduler -   -> 60643 reads (7.50% of total) failing DuplicateReadFilter
[2016-04-15T00:42Z] INFO  17:42:59,411 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:42Z] INFO  17:42:59,411 MicroScheduler -   -> 9394 reads (1.16% of total) failing HCMappingQualityFilter
[2016-04-15T00:42Z] INFO  17:42:59,411 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:42Z] INFO  17:42:59,411 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:42Z] INFO  17:42:59,412 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:42Z] INFO  17:42:59,412 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:42Z] INFO  17:42:59,858 ProgressMeter -      11:1093770      1.2877009E7     2.5 m           11.0 s       19.0%    13.1 m      10.6 m
[2016-04-15T00:43Z] INFO  17:43:01,118 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:43Z] GATK: HaplotypeCaller
[2016-04-15T00:43Z] INFO  17:43:04,404 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:43Z] INFO  17:43:04,407 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:43Z] INFO  17:43:04,408 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:43Z] INFO  17:43:04,408 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:43Z] INFO  17:43:04,413 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/16/R14-18106_kapa-NGv3-PE100-NGv3-sort-16_46633742_64982002-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/16/R14-18106_kapa-NGv3-PE100-NGv3-16_46633742_64982002-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/16/tx/tmpbjaAVC/R14-18106_kapa-NGv3-PE100-NGv3-16_46633742_64982002.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:43Z] INFO  17:43:04,423 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:43Z] INFO  17:43:04,423 HelpFormatter - Date/Time: 2016/04/14 17:43:04
[2016-04-15T00:43Z] INFO  17:43:04,423 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:43Z] INFO  17:43:04,424 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:43Z] WARN  17:43:04,467 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T00:43Z] WARN  17:43:04,480 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/16/tx/tmpbjaAVC/R14-18106_kapa-NGv3-PE100-NGv3-16_46633742_64982002.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T00:43Z] INFO  17:43:04,705 ProgressMeter -     15:41865200      2.3318939E7    30.0 s            1.0 s       26.5%   113.0 s      83.0 s
[2016-04-15T00:43Z] INFO  17:43:04,707 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:43Z] INFO  17:43:04,951 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T00:43Z] INFO  17:43:04,962 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:43Z] INFO  17:43:05,064 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.09
[2016-04-15T00:43Z] INFO  17:43:05,087 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T00:43Z] INFO  17:43:05,480 IntervalUtils - Processing 224129 bp from intervals
[2016-04-15T00:43Z] WARN  17:43:05,486 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:43Z] INFO  17:43:05,599 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:43Z] INFO  17:43:05,703 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:43Z] INFO  17:43:05,704 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:43Z] INFO  17:43:05,705 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T00:43Z] INFO  17:43:05,706 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T00:43Z] INFO  17:43:05,706 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T00:43Z] INFO  17:43:05,707 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T00:43Z] INFO  17:43:05,882 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T00:43Z] INFO  17:43:06,065 ProgressMeter -     15:59225923      1.8359905E7    30.0 s            1.0 s       34.4%    87.0 s      57.0 s
[2016-04-15T00:43Z] INFO  17:43:06,821 ProgressMeter -     15:74336562      2.3341121E7    30.0 s            1.0 s       33.2%    90.0 s      60.0 s
[2016-04-15T00:43Z] INFO  17:43:07,029 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.006901232
[2016-04-15T00:43Z] INFO  17:43:07,030 PairHMM - Total compute time in PairHMM computeLikelihoods() : 0.44772703
[2016-04-15T00:43Z] INFO  17:43:07,031 HaplotypeCaller - Ran local assembly on 369 active regions
[2016-04-15T00:43Z] INFO  17:43:07,107 ProgressMeter -            done        5654523.0    22.0 s            3.0 s      100.0%    22.0 s       0.0 s
[2016-04-15T00:43Z] INFO  17:43:07,107 ProgressMeter - Total runtime 22.55 secs, 0.38 min, 0.01 hours
[2016-04-15T00:43Z] INFO  17:43:07,108 MicroScheduler - 8291 reads were filtered out during the traversal out of approximately 72597 total reads (11.42%)
[2016-04-15T00:43Z] INFO  17:43:07,108 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:43Z] INFO  17:43:07,108 MicroScheduler -   -> 5269 reads (7.26% of total) failing DuplicateReadFilter
[2016-04-15T00:43Z] INFO  17:43:07,109 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:43Z] INFO  17:43:07,109 MicroScheduler -   -> 3022 reads (4.16% of total) failing HCMappingQualityFilter
[2016-04-15T00:43Z] INFO  17:43:07,109 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:43Z] INFO  17:43:07,109 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:43Z] INFO  17:43:07,110 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:43Z] INFO  17:43:07,110 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:43Z] INFO  17:43:08,410 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:43Z] GATK: HaplotypeCaller
[2016-04-15T00:43Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T00:43Z] INFO  17:43:09,225 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T00:43Z] INFO  17:43:09,234 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T00:43Z] WARN  17:43:09,564 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T00:43Z] WARN  17:43:09,565 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T00:43Z] INFO  17:43:11,236 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.026572238
[2016-04-15T00:43Z] INFO  17:43:11,236 PairHMM - Total compute time in PairHMM computeLikelihoods() : 0.7917886150000001
[2016-04-15T00:43Z] INFO  17:43:11,236 HaplotypeCaller - Ran local assembly on 1666 active regions
[2016-04-15T00:43Z] INFO  17:43:11,470 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.004168288
[2016-04-15T00:43Z] INFO  17:43:11,471 PairHMM - Total compute time in PairHMM computeLikelihoods() : 0.172462748
[2016-04-15T00:43Z] INFO  17:43:11,471 HaplotypeCaller - Ran local assembly on 302 active regions
[2016-04-15T00:43Z] INFO  17:43:11,472 ProgressMeter -            done     1.18736277E8    57.0 s            0.0 s      100.0%    57.0 s       0.0 s
[2016-04-15T00:43Z] INFO  17:43:11,473 ProgressMeter - Total runtime 57.11 secs, 0.95 min, 0.02 hours
[2016-04-15T00:43Z] INFO  17:43:11,473 MicroScheduler - 20589 reads were filtered out during the traversal out of approximately 275083 total reads (7.48%)
[2016-04-15T00:43Z] INFO  17:43:11,473 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:43Z] INFO  17:43:11,473 MicroScheduler -   -> 20260 reads (7.37% of total) failing DuplicateReadFilter
[2016-04-15T00:43Z] INFO  17:43:11,475 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:43Z] INFO  17:43:11,476 MicroScheduler -   -> 329 reads (0.12% of total) failing HCMappingQualityFilter
[2016-04-15T00:43Z] INFO  17:43:11,476 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:43Z] INFO  17:43:11,477 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:43Z] INFO  17:43:11,477 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:43Z] INFO  17:43:11,478 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:43Z] INFO  17:43:11,535 ProgressMeter -            done        2938200.0    17.0 s            5.0 s      100.0%    17.0 s       0.0 s
[2016-04-15T00:43Z] INFO  17:43:11,535 ProgressMeter - Total runtime 17.07 secs, 0.28 min, 0.00 hours
[2016-04-15T00:43Z] INFO  17:43:11,536 MicroScheduler - 16867 reads were filtered out during the traversal out of approximately 72750 total reads (23.18%)
[2016-04-15T00:43Z] INFO  17:43:11,536 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:43Z] INFO  17:43:11,536 MicroScheduler -   -> 4528 reads (6.22% of total) failing DuplicateReadFilter
[2016-04-15T00:43Z] INFO  17:43:11,537 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:43Z] INFO  17:43:11,537 MicroScheduler -   -> 12339 reads (16.96% of total) failing HCMappingQualityFilter
[2016-04-15T00:43Z] INFO  17:43:11,537 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:43Z] INFO  17:43:11,537 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:43Z] INFO  17:43:11,538 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:43Z] INFO  17:43:11,538 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:43Z] INFO  17:43:11,571 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:43Z] INFO  17:43:11,575 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:43Z] INFO  17:43:11,575 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:43Z] INFO  17:43:11,576 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:43Z] INFO  17:43:11,581 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/16/R14-18106_kapa-NGv3-PE100-NGv3-sort-16_64982511_80574976-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/16/R14-18106_kapa-NGv3-PE100-NGv3-16_64982511_80574976-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/16/tx/tmpBvXf8u/R14-18106_kapa-NGv3-PE100-NGv3-16_64982511_80574976.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:43Z] INFO  17:43:11,603 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:43Z] INFO  17:43:11,610 HelpFormatter - Date/Time: 2016/04/14 17:43:11
[2016-04-15T00:43Z] INFO  17:43:11,611 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:43Z] INFO  17:43:11,611 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:43Z] INFO  17:43:11,619 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.010924092
[2016-04-15T00:43Z] INFO  17:43:11,620 PairHMM - Total compute time in PairHMM computeLikelihoods() : 0.744438298
[2016-04-15T00:43Z] INFO  17:43:11,621 HaplotypeCaller - Ran local assembly on 1285 active regions
[2016-04-15T00:43Z] WARN  17:43:11,656 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T00:43Z] WARN  17:43:11,658 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/16/tx/tmpBvXf8u/R14-18106_kapa-NGv3-PE100-NGv3-16_64982511_80574976.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T00:43Z] INFO  17:43:11,680 ProgressMeter -            done      7.6164079E7    49.0 s            0.0 s      100.0%    49.0 s       0.0 s
[2016-04-15T00:43Z] INFO  17:43:11,681 ProgressMeter - Total runtime 49.79 secs, 0.83 min, 0.01 hours
[2016-04-15T00:43Z] INFO  17:43:11,681 MicroScheduler - 17528 reads were filtered out during the traversal out of approximately 228257 total reads (7.68%)
[2016-04-15T00:43Z] INFO  17:43:11,682 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:43Z] INFO  17:43:11,682 MicroScheduler -   -> 17207 reads (7.54% of total) failing DuplicateReadFilter
[2016-04-15T00:43Z] INFO  17:43:11,682 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:43Z] INFO  17:43:11,682 MicroScheduler -   -> 321 reads (0.14% of total) failing HCMappingQualityFilter
[2016-04-15T00:43Z] INFO  17:43:11,682 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:43Z] INFO  17:43:11,683 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:43Z] INFO  17:43:11,683 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:43Z] INFO  17:43:11,683 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:43Z] INFO  17:43:11,859 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:43Z] INFO  17:43:12,025 ProgressMeter -     14:24677098      7.0546248E7    60.0 s            0.0 s       68.5%    87.0 s      27.0 s
[2016-04-15T00:43Z] INFO  17:43:12,119 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T00:43Z] INFO  17:43:12,129 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:43Z] INFO  17:43:12,192 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-15T00:43Z] INFO  17:43:12,226 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T00:43Z] INFO  17:43:12,699 IntervalUtils - Processing 344918 bp from intervals
[2016-04-15T00:43Z] WARN  17:43:12,705 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:43Z] INFO  17:43:12,801 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:43Z] INFO  17:43:12,893 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:43Z] INFO  17:43:12,893 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:43Z] INFO  17:43:12,893 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T00:43Z] INFO  17:43:12,894 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T00:43Z] INFO  17:43:12,895 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T00:43Z] INFO  17:43:12,895 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T00:43Z] INFO  17:43:12,926 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:43Z] INFO  17:43:12,997 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:43Z] INFO  17:43:13,032 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T00:43Z] INFO  17:43:13,092 ProgressMeter -     15:89843031      1.6345872E7    30.0 s            1.0 s       47.0%    63.0 s      33.0 s
[2016-04-15T00:43Z] GATK: HaplotypeCaller
[2016-04-15T00:43Z] INFO  17:43:13,157 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:43Z] GATK: HaplotypeCaller
[2016-04-15T00:43Z] GATK: HaplotypeCaller
[2016-04-15T00:43Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T00:43Z] INFO  17:43:16,352 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T00:43Z] INFO  17:43:16,352 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T00:43Z] INFO  17:43:16,600 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:43Z] INFO  17:43:16,603 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:43Z] INFO  17:43:16,604 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:43Z] INFO  17:43:16,604 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:43Z] INFO  17:43:16,609 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/17/R14-18106_kapa-NGv3-PE100-NGv3-sort-17_0_15511002-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/17/R14-18106_kapa-NGv3-PE100-NGv3-17_0_15511002-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/17/tx/tmpvn_8EI/R14-18106_kapa-NGv3-PE100-NGv3-17_0_15511002.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:43Z] INFO  17:43:16,624 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:43Z] INFO  17:43:16,627 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:43Z] INFO  17:43:16,628 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:43Z] INFO  17:43:16,629 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:43Z] INFO  17:43:16,633 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/16/R14-18106_kapa-NGv3-PE100-NGv3-sort-16_80575258_90354753-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/16/R14-18106_kapa-NGv3-PE100-NGv3-16_80575258_90354753-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/16/tx/tmpVTQRb1/R14-18106_kapa-NGv3-PE100-NGv3-16_80575258_90354753.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:43Z] INFO  17:43:16,636 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:43Z] INFO  17:43:16,637 HelpFormatter - Date/Time: 2016/04/14 17:43:16
[2016-04-15T00:43Z] INFO  17:43:16,637 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:43Z] INFO  17:43:16,638 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:43Z] WARN  17:43:16,646 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T00:43Z] WARN  17:43:16,647 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T00:43Z] WARN  17:43:16,663 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T00:43Z] WARN  17:43:16,666 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/17/tx/tmpvn_8EI/R14-18106_kapa-NGv3-PE100-NGv3-17_0_15511002.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T00:43Z] INFO  17:43:16,667 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:43Z] INFO  17:43:16,668 HelpFormatter - Date/Time: 2016/04/14 17:43:16
[2016-04-15T00:43Z] INFO  17:43:16,669 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:43Z] INFO  17:43:16,669 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:43Z] WARN  17:43:16,700 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T00:43Z] WARN  17:43:16,703 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/16/tx/tmpVTQRb1/R14-18106_kapa-NGv3-PE100-NGv3-16_80575258_90354753.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T00:43Z] INFO  17:43:16,818 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:43Z] INFO  17:43:16,867 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:43Z] INFO  17:43:16,870 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:43Z] INFO  17:43:16,871 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:43Z] INFO  17:43:16,871 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:43Z] INFO  17:43:16,875 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:43Z] INFO  17:43:16,875 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/17/R14-18106_kapa-NGv3-PE100-NGv3-sort-17_15515955_31039213-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/17/R14-18106_kapa-NGv3-PE100-NGv3-17_15515955_31039213-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/17/tx/tmpCzXn5X/R14-18106_kapa-NGv3-PE100-NGv3-17_15515955_31039213.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:43Z] INFO  17:43:16,886 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:43Z] INFO  17:43:16,888 HelpFormatter - Date/Time: 2016/04/14 17:43:16
[2016-04-15T00:43Z] INFO  17:43:16,888 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:43Z] INFO  17:43:16,889 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:43Z] WARN  17:43:16,912 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T00:43Z] WARN  17:43:16,929 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/17/tx/tmpCzXn5X/R14-18106_kapa-NGv3-PE100-NGv3-17_15515955_31039213.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T00:43Z] INFO  17:43:17,053 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T00:43Z] INFO  17:43:17,070 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:43Z] INFO  17:43:17,085 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T00:43Z] INFO  17:43:17,106 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:43Z] INFO  17:43:17,129 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-15T00:43Z] INFO  17:43:17,139 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:43Z] INFO  17:43:17,141 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T00:43Z] INFO  17:43:17,173 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-15T00:43Z] INFO  17:43:17,199 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T00:43Z] INFO  17:43:17,358 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T00:43Z] INFO  17:43:17,367 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:43Z] INFO  17:43:17,435 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-15T00:43Z] INFO  17:43:17,467 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T00:43Z] INFO  17:43:17,603 IntervalUtils - Processing 497719 bp from intervals
[2016-04-15T00:43Z] WARN  17:43:17,609 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:43Z] INFO  17:43:17,614 IntervalUtils - Processing 203451 bp from intervals
[2016-04-15T00:43Z] WARN  17:43:17,620 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:43Z] INFO  17:43:17,681 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:43Z] INFO  17:43:17,729 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:43Z] INFO  17:43:17,805 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:43Z] INFO  17:43:17,807 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:43Z] INFO  17:43:17,807 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T00:43Z] INFO  17:43:17,808 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T00:43Z] INFO  17:43:17,809 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T00:43Z] INFO  17:43:17,809 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T00:43Z] INFO  17:43:17,822 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:43Z] INFO  17:43:17,826 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:43Z] INFO  17:43:17,827 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T00:43Z] INFO  17:43:17,828 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T00:43Z] INFO  17:43:17,829 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T00:43Z] INFO  17:43:17,829 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T00:43Z] INFO  17:43:17,860 ProgressMeter -      16:1370960       1.263693E7    30.0 s            2.0 s       21.5%     2.3 m     109.0 s
[2016-04-15T00:43Z] INFO  17:43:17,900 IntervalUtils - Processing 320055 bp from intervals
[2016-04-15T00:43Z] WARN  17:43:17,916 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:43Z] INFO  17:43:18,015 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:43Z] INFO  17:43:18,038 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T00:43Z] INFO  17:43:18,052 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T00:43Z] INFO  17:43:18,135 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:43Z] INFO  17:43:18,135 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:43Z] INFO  17:43:18,136 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T00:43Z] INFO  17:43:18,136 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T00:43Z] INFO  17:43:18,147 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T00:43Z] INFO  17:43:18,148 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T00:43Z] INFO  17:43:18,353 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T00:43Z] INFO  17:43:18,677 ProgressMeter -     14:78710037     1.33729298E8    60.0 s            0.0 s       93.4%    64.0 s       4.0 s
[2016-04-15T00:43Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T00:43Z] INFO  17:43:20,326 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T00:43Z] INFO  17:43:20,338 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T00:43Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T00:43Z] INFO  17:43:20,356 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T00:43Z] INFO  17:43:20,357 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T00:43Z] WARN  17:43:20,641 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T00:43Z] WARN  17:43:20,642 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T00:43Z] WARN  17:43:20,695 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T00:43Z] WARN  17:43:20,696 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T00:43Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T00:43Z] INFO  17:43:21,085 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T00:43Z] INFO  17:43:21,086 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T00:43Z] WARN  17:43:21,400 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T00:43Z] WARN  17:43:21,401 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T00:43Z] INFO  17:43:22,027 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.018064691
[2016-04-15T00:43Z] INFO  17:43:22,038 PairHMM - Total compute time in PairHMM computeLikelihoods() : 4.158296921000001
[2016-04-15T00:43Z] INFO  17:43:22,039 HaplotypeCaller - Ran local assembly on 1328 active regions
[2016-04-15T00:43Z] INFO  17:43:22,087 ProgressMeter -            done      7.2457776E7    52.0 s            0.0 s      100.0%    52.0 s       0.0 s
[2016-04-15T00:43Z] INFO  17:43:22,087 ProgressMeter - Total runtime 52.86 secs, 0.88 min, 0.01 hours
[2016-04-15T00:43Z] INFO  17:43:22,088 MicroScheduler - 89608 reads were filtered out during the traversal out of approximately 290760 total reads (30.82%)
[2016-04-15T00:43Z] INFO  17:43:22,089 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:43Z] INFO  17:43:22,089 MicroScheduler -   -> 16343 reads (5.62% of total) failing DuplicateReadFilter
[2016-04-15T00:43Z] INFO  17:43:22,089 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:43Z] INFO  17:43:22,089 MicroScheduler -   -> 73265 reads (25.20% of total) failing HCMappingQualityFilter
[2016-04-15T00:43Z] INFO  17:43:22,090 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:43Z] INFO  17:43:22,090 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:43Z] INFO  17:43:22,090 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:43Z] INFO  17:43:22,090 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:43Z] INFO  17:43:22,900 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.013700835000000001
[2016-04-15T00:43Z] INFO  17:43:22,901 PairHMM - Total compute time in PairHMM computeLikelihoods() : 1.2323878480000001
[2016-04-15T00:43Z] INFO  17:43:22,901 HaplotypeCaller - Ran local assembly on 1794 active regions
[2016-04-15T00:43Z] INFO  17:43:22,957 ProgressMeter -            done     1.48859234E8    64.0 s            0.0 s      100.0%    64.0 s       0.0 s
[2016-04-15T00:43Z] INFO  17:43:22,957 ProgressMeter - Total runtime 64.31 secs, 1.07 min, 0.02 hours
[2016-04-15T00:43Z] INFO  17:43:22,958 MicroScheduler - 29067 reads were filtered out during the traversal out of approximately 355267 total reads (8.18%)
[2016-04-15T00:43Z] INFO  17:43:22,958 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:43Z] INFO  17:43:22,958 MicroScheduler -   -> 26615 reads (7.49% of total) failing DuplicateReadFilter
[2016-04-15T00:43Z] INFO  17:43:22,959 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:43Z] INFO  17:43:22,959 MicroScheduler -   -> 2452 reads (0.69% of total) failing HCMappingQualityFilter
[2016-04-15T00:43Z] INFO  17:43:22,959 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:43Z] INFO  17:43:22,959 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:43Z] INFO  17:43:22,960 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:43Z] INFO  17:43:22,960 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:43Z] INFO  17:43:23,593 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:43Z] GATK: HaplotypeCaller
[2016-04-15T00:43Z] INFO  17:43:24,344 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:43Z] INFO  17:43:24,543 ProgressMeter -     16:20990702      2.8170704E7    30.0 s            1.0 s       26.6%   112.0 s      82.0 s
[2016-04-15T00:43Z] INFO  17:43:24,560 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.018939205
[2016-04-15T00:43Z] INFO  17:43:24,561 PairHMM - Total compute time in PairHMM computeLikelihoods() : 4.653275634
[2016-04-15T00:43Z] INFO  17:43:24,561 HaplotypeCaller - Ran local assembly on 1342 active regions
[2016-04-15T00:43Z] INFO  17:43:24,613 ProgressMeter -            done      6.4310135E7    59.0 s            0.0 s      100.0%    59.0 s       0.0 s
[2016-04-15T00:43Z] INFO  17:43:24,613 ProgressMeter - Total runtime 59.44 secs, 0.99 min, 0.02 hours
[2016-04-15T00:43Z] INFO  17:43:24,614 MicroScheduler - 24159 reads were filtered out during the traversal out of approximately 303256 total reads (7.97%)
[2016-04-15T00:43Z] INFO  17:43:24,614 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:43Z] INFO  17:43:24,614 MicroScheduler -   -> 23212 reads (7.65% of total) failing DuplicateReadFilter
[2016-04-15T00:43Z] INFO  17:43:24,614 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:43Z] INFO  17:43:24,615 MicroScheduler -   -> 947 reads (0.31% of total) failing HCMappingQualityFilter
[2016-04-15T00:43Z] INFO  17:43:24,615 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:43Z] INFO  17:43:24,615 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:43Z] INFO  17:43:24,615 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:43Z] INFO  17:43:24,616 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:43Z] GATK: HaplotypeCaller
[2016-04-15T00:43Z] INFO  17:43:26,539 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:43Z] GATK: HaplotypeCaller
[2016-04-15T00:43Z] INFO  17:43:27,381 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:43Z] INFO  17:43:27,384 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:43Z] INFO  17:43:27,385 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:43Z] INFO  17:43:27,385 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:43Z] INFO  17:43:27,390 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/17/R14-18106_kapa-NGv3-PE100-NGv3-sort-17_31048040_46607237-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/17/R14-18106_kapa-NGv3-PE100-NGv3-17_31048040_46607237-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/17/tx/tmpUT_mUY/R14-18106_kapa-NGv3-PE100-NGv3-17_31048040_46607237.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:43Z] INFO  17:43:27,421 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:43Z] INFO  17:43:27,422 HelpFormatter - Date/Time: 2016/04/14 17:43:27
[2016-04-15T00:43Z] INFO  17:43:27,423 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:43Z] INFO  17:43:27,423 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:43Z] WARN  17:43:27,491 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T00:43Z] WARN  17:43:27,494 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/17/tx/tmpUT_mUY/R14-18106_kapa-NGv3-PE100-NGv3-17_31048040_46607237.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T00:43Z] INFO  17:43:27,558 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:43Z] INFO  17:43:27,561 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:43Z] INFO  17:43:27,562 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:43Z] INFO  17:43:27,563 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:43Z] INFO  17:43:27,567 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/17/R14-18106_kapa-NGv3-PE100-NGv3-sort-17_46607689_62121560-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/17/R14-18106_kapa-NGv3-PE100-NGv3-17_46607689_62121560-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/17/tx/tmptidXe2/R14-18106_kapa-NGv3-PE100-NGv3-17_46607689_62121560.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:43Z] INFO  17:43:27,589 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:43Z] INFO  17:43:27,590 HelpFormatter - Date/Time: 2016/04/14 17:43:27
[2016-04-15T00:43Z] INFO  17:43:27,590 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:43Z] INFO  17:43:27,590 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:43Z] WARN  17:43:27,625 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T00:43Z] WARN  17:43:27,628 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/17/tx/tmptidXe2/R14-18106_kapa-NGv3-PE100-NGv3-17_46607689_62121560.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T00:43Z] INFO  17:43:27,717 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:43Z] INFO  17:43:27,859 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:43Z] INFO  17:43:27,898 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T00:43Z] INFO  17:43:27,908 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:43Z] INFO  17:43:28,001 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.09
[2016-04-15T00:43Z] INFO  17:43:28,013 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T00:43Z] INFO  17:43:28,078 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T00:43Z] INFO  17:43:28,088 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:43Z] INFO  17:43:28,159 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-15T00:43Z] INFO  17:43:28,182 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T00:43Z] INFO  17:43:28,582 IntervalUtils - Processing 543518 bp from intervals
[2016-04-15T00:43Z] WARN  17:43:28,598 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:43Z] INFO  17:43:28,646 IntervalUtils - Processing 295968 bp from intervals
[2016-04-15T00:43Z] WARN  17:43:28,652 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:43Z] INFO  17:43:28,693 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:43Z] INFO  17:43:28,744 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:43Z] INFO  17:43:28,884 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:43Z] INFO  17:43:28,885 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:43Z] INFO  17:43:28,886 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T00:43Z] INFO  17:43:28,887 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T00:43Z] INFO  17:43:28,887 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T00:43Z] INFO  17:43:28,887 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T00:43Z] INFO  17:43:28,896 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:43Z] INFO  17:43:28,908 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:43Z] INFO  17:43:28,909 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T00:43Z] INFO  17:43:28,909 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T00:43Z] INFO  17:43:28,921 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T00:43Z] INFO  17:43:28,922 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T00:43Z] INFO  17:43:29,082 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T00:43Z] INFO  17:43:29,096 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T00:43Z] INFO  17:43:29,744 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:43Z] INFO  17:43:29,748 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:43Z] INFO  17:43:29,748 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:43Z] INFO  17:43:29,749 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:43Z] INFO  17:43:29,753 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/17/R14-18106_kapa-NGv3-PE100-NGv3-sort-17_62122219_77705154-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/17/R14-18106_kapa-NGv3-PE100-NGv3-17_62122219_77705154-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/17/tx/tmpc4jFYc/R14-18106_kapa-NGv3-PE100-NGv3-17_62122219_77705154.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:43Z] INFO  17:43:29,766 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:43Z] INFO  17:43:29,767 HelpFormatter - Date/Time: 2016/04/14 17:43:29
[2016-04-15T00:43Z] INFO  17:43:29,767 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:43Z] INFO  17:43:29,768 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:43Z] WARN  17:43:29,813 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T00:43Z] WARN  17:43:29,816 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/17/tx/tmpc4jFYc/R14-18106_kapa-NGv3-PE100-NGv3-17_62122219_77705154.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T00:43Z] INFO  17:43:29,859 ProgressMeter -      11:1268876       1.733857E7     3.0 m           10.0 s       23.0%    13.0 m      10.0 m
[2016-04-15T00:43Z] INFO  17:43:30,073 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:43Z] INFO  17:43:30,284 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T00:43Z] INFO  17:43:30,304 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:43Z] INFO  17:43:30,381 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-15T00:43Z] INFO  17:43:30,412 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T00:43Z] INFO  17:43:31,021 IntervalUtils - Processing 345298 bp from intervals
[2016-04-15T00:43Z] WARN  17:43:31,027 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:43Z] INFO  17:43:31,124 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:43Z] INFO  17:43:31,299 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:43Z] INFO  17:43:31,302 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:43Z] INFO  17:43:31,303 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T00:43Z] INFO  17:43:31,304 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T00:43Z] INFO  17:43:31,315 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T00:43Z] INFO  17:43:31,316 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T00:43Z] INFO  17:43:31,557 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T00:43Z] INFO  17:43:32,948 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.031031746000000002
[2016-04-15T00:43Z] INFO  17:43:32,960 PairHMM - Total compute time in PairHMM computeLikelihoods() : 1.8933129830000002
[2016-04-15T00:43Z] INFO  17:43:32,962 HaplotypeCaller - Ran local assembly on 2064 active regions
[2016-04-15T00:43Z] INFO  17:43:33,014 ProgressMeter -            done     1.61002552E8    81.0 s            0.0 s      100.0%    81.0 s       0.0 s
[2016-04-15T00:43Z] INFO  17:43:33,014 ProgressMeter - Total runtime 81.04 secs, 1.35 min, 0.02 hours
[2016-04-15T00:43Z] INFO  17:43:33,015 MicroScheduler - 54601 reads were filtered out during the traversal out of approximately 470077 total reads (11.62%)
[2016-04-15T00:43Z] INFO  17:43:33,015 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:43Z] INFO  17:43:33,015 MicroScheduler -   -> 34748 reads (7.39% of total) failing DuplicateReadFilter
[2016-04-15T00:43Z] INFO  17:43:33,016 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:43Z] INFO  17:43:33,016 MicroScheduler -   -> 19853 reads (4.22% of total) failing HCMappingQualityFilter
[2016-04-15T00:43Z] INFO  17:43:33,016 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:43Z] INFO  17:43:33,017 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:43Z] INFO  17:43:33,017 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:43Z] INFO  17:43:33,017 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:43Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T00:43Z] INFO  17:43:33,220 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T00:43Z] INFO  17:43:33,221 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T00:43Z] WARN  17:43:33,682 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T00:43Z] WARN  17:43:33,684 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T00:43Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T00:43Z] INFO  17:43:33,858 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T00:43Z] INFO  17:43:33,859 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T00:43Z] WARN  17:43:34,144 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T00:43Z] WARN  17:43:34,166 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T00:43Z] INFO  17:43:34,552 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:43Z] INFO  17:43:34,707 ProgressMeter -     15:45879642     1.98686582E8    60.0 s            0.0 s       76.5%    78.0 s      18.0 s
[2016-04-15T00:43Z] GATK: HaplotypeCaller
[2016-04-15T00:43Z] INFO  17:43:35,715 ProgressMeter -     16:55866916      2.6970716E7    30.0 s            1.0 s       48.4%    61.0 s      31.0 s
[2016-04-15T00:43Z] INFO  17:43:36,067 ProgressMeter -     15:66625503     1.38496259E8    60.0 s            0.0 s       93.0%    64.0 s       4.0 s
[2016-04-15T00:43Z] INFO  17:43:36,405 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.023767436000000003
[2016-04-15T00:43Z] INFO  17:43:36,405 PairHMM - Total compute time in PairHMM computeLikelihoods() : 1.124343831
[2016-04-15T00:43Z] INFO  17:43:36,406 HaplotypeCaller - Ran local assembly on 1369 active regions
[2016-04-15T00:43Z] INFO  17:43:36,470 ProgressMeter -            done      8.0187592E7    53.0 s            0.0 s      100.0%    53.0 s       0.0 s
[2016-04-15T00:43Z] INFO  17:43:36,470 ProgressMeter - Total runtime 53.40 secs, 0.89 min, 0.01 hours
[2016-04-15T00:43Z] INFO  17:43:36,471 MicroScheduler - 39922 reads were filtered out during the traversal out of approximately 290372 total reads (13.75%)
[2016-04-15T00:43Z] INFO  17:43:36,472 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:43Z] INFO  17:43:36,472 MicroScheduler -   -> 20209 reads (6.96% of total) failing DuplicateReadFilter
[2016-04-15T00:43Z] INFO  17:43:36,472 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:43Z] INFO  17:43:36,472 MicroScheduler -   -> 19713 reads (6.79% of total) failing HCMappingQualityFilter
[2016-04-15T00:43Z] INFO  17:43:36,473 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:43Z] INFO  17:43:36,473 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:43Z] INFO  17:43:36,473 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:43Z] INFO  17:43:36,473 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:43Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T00:43Z] INFO  17:43:36,607 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T00:43Z] INFO  17:43:36,608 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T00:43Z] INFO  17:43:36,822 ProgressMeter -     15:80259979     1.40248428E8    60.0 s            0.0 s       86.4%    69.0 s       9.0 s
[2016-04-15T00:43Z] WARN  17:43:37,121 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T00:43Z] WARN  17:43:37,122 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T00:43Z] INFO  17:43:37,977 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:43Z] INFO  17:43:38,014 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:43Z] INFO  17:43:38,017 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:43Z] INFO  17:43:38,018 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:43Z] INFO  17:43:38,018 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:43Z] INFO  17:43:38,023 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/17/R14-18106_kapa-NGv3-PE100-NGv3-sort-17_77707305_81195210-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/17/R14-18106_kapa-NGv3-PE100-NGv3-17_77707305_81195210-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/17/tx/tmpPT59im/R14-18106_kapa-NGv3-PE100-NGv3-17_77707305_81195210.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:43Z] INFO  17:43:38,036 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:43Z] INFO  17:43:38,037 HelpFormatter - Date/Time: 2016/04/14 17:43:38
[2016-04-15T00:43Z] INFO  17:43:38,043 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:43Z] INFO  17:43:38,044 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:43Z] WARN  17:43:38,079 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T00:43Z] WARN  17:43:38,090 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/17/tx/tmpPT59im/R14-18106_kapa-NGv3-PE100-NGv3-17_77707305_81195210.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T00:43Z] GATK: HaplotypeCaller
[2016-04-15T00:43Z] INFO  17:43:38,335 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:43Z] INFO  17:43:38,612 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T00:43Z] INFO  17:43:38,643 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:43Z] INFO  17:43:38,730 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.09
[2016-04-15T00:43Z] INFO  17:43:38,767 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T00:43Z] INFO  17:43:39,292 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.018238431000000003
[2016-04-15T00:43Z] INFO  17:43:39,293 PairHMM - Total compute time in PairHMM computeLikelihoods() : 0.826115669
[2016-04-15T00:43Z] INFO  17:43:39,293 HaplotypeCaller - Ran local assembly on 1857 active regions
[2016-04-15T00:43Z] INFO  17:43:39,340 ProgressMeter -            done     1.70188052E8    63.0 s            0.0 s      100.0%    63.0 s       0.0 s
[2016-04-15T00:43Z] INFO  17:43:39,340 ProgressMeter - Total runtime 63.30 secs, 1.06 min, 0.02 hours
[2016-04-15T00:43Z] INFO  17:43:39,340 MicroScheduler - 25524 reads were filtered out during the traversal out of approximately 333127 total reads (7.66%)
[2016-04-15T00:43Z] INFO  17:43:39,341 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:43Z] INFO  17:43:39,341 MicroScheduler -   -> 25021 reads (7.51% of total) failing DuplicateReadFilter
[2016-04-15T00:43Z] INFO  17:43:39,341 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:43Z] INFO  17:43:39,341 MicroScheduler -   -> 503 reads (0.15% of total) failing HCMappingQualityFilter
[2016-04-15T00:43Z] INFO  17:43:39,342 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:43Z] INFO  17:43:39,342 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:43Z] INFO  17:43:39,342 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:43Z] INFO  17:43:39,342 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:43Z] INFO  17:43:39,364 IntervalUtils - Processing 160149 bp from intervals
[2016-04-15T00:43Z] WARN  17:43:39,369 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:43Z] INFO  17:43:39,495 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:43Z] INFO  17:43:39,575 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:43Z] INFO  17:43:39,577 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:43Z] INFO  17:43:39,578 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T00:43Z] INFO  17:43:39,578 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T00:43Z] INFO  17:43:39,579 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T00:43Z] INFO  17:43:39,579 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T00:43Z] INFO  17:43:39,884 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T00:43Z] INFO  17:43:40,882 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:43Z] GATK: HaplotypeCaller
[2016-04-15T00:43Z] INFO  17:43:41,651 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:43Z] INFO  17:43:41,654 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:43Z] INFO  17:43:41,655 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:43Z] INFO  17:43:41,656 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:43Z] INFO  17:43:41,660 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/18/R14-18106_kapa-NGv3-PE100-NGv3-sort-18_0_18531348-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/18/R14-18106_kapa-NGv3-PE100-NGv3-18_0_18531348-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/18/tx/tmprjkde1/R14-18106_kapa-NGv3-PE100-NGv3-18_0_18531348.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:43Z] INFO  17:43:41,669 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:43Z] INFO  17:43:41,669 HelpFormatter - Date/Time: 2016/04/14 17:43:41
[2016-04-15T00:43Z] INFO  17:43:41,670 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:43Z] INFO  17:43:41,670 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:43Z] WARN  17:43:41,731 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T00:43Z] WARN  17:43:41,733 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/18/tx/tmprjkde1/R14-18106_kapa-NGv3-PE100-NGv3-18_0_18531348.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T00:43Z] INFO  17:43:41,953 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:43Z] INFO  17:43:42,115 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T00:43Z] INFO  17:43:42,146 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:43Z] INFO  17:43:42,246 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.10
[2016-04-15T00:43Z] INFO  17:43:42,262 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T00:43Z] INFO  17:43:42,705 IntervalUtils - Processing 162632 bp from intervals
[2016-04-15T00:43Z] WARN  17:43:42,710 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:43Z] INFO  17:43:42,796 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:43Z] INFO  17:43:42,908 ProgressMeter -     16:68056585      2.2717438E7    30.0 s            1.0 s       35.0%    85.0 s      55.0 s
[2016-04-15T00:43Z] INFO  17:43:42,910 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:43Z] INFO  17:43:42,911 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:43Z] INFO  17:43:42,923 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T00:43Z] INFO  17:43:42,924 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T00:43Z] INFO  17:43:42,936 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T00:43Z] INFO  17:43:42,937 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T00:43Z] INFO  17:43:43,152 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T00:43Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T00:43Z] INFO  17:43:43,461 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T00:43Z] INFO  17:43:43,462 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T00:43Z] WARN  17:43:43,712 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T00:43Z] WARN  17:43:43,713 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T00:43Z] INFO  17:43:44,141 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:43Z] INFO  17:43:44,145 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:43Z] INFO  17:43:44,145 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:43Z] INFO  17:43:44,146 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:43Z] INFO  17:43:44,151 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/18/R14-18106_kapa-NGv3-PE100-NGv3-sort-18_18533538_34081962-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/18/R14-18106_kapa-NGv3-PE100-NGv3-18_18533538_34081962-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/18/tx/tmpZJkpmT/R14-18106_kapa-NGv3-PE100-NGv3-18_18533538_34081962.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:43Z] INFO  17:43:44,184 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:43Z] INFO  17:43:44,192 HelpFormatter - Date/Time: 2016/04/14 17:43:44
[2016-04-15T00:43Z] INFO  17:43:44,193 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:43Z] INFO  17:43:44,194 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:43Z] WARN  17:43:44,239 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T00:43Z] WARN  17:43:44,243 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/18/tx/tmpZJkpmT/R14-18106_kapa-NGv3-PE100-NGv3-18_18533538_34081962.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T00:43Z] INFO  17:43:44,475 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:43Z] INFO  17:43:44,680 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T00:43Z] INFO  17:43:44,690 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:43Z] INFO  17:43:44,820 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.13
[2016-04-15T00:43Z] INFO  17:43:44,837 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T00:43Z] INFO  17:43:44,971 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.013804654000000001
[2016-04-15T00:43Z] INFO  17:43:44,972 PairHMM - Total compute time in PairHMM computeLikelihoods() : 1.128834135
[2016-04-15T00:43Z] INFO  17:43:44,973 HaplotypeCaller - Ran local assembly on 2133 active regions
[2016-04-15T00:43Z] INFO  17:43:45,020 ProgressMeter -            done     2.01008217E8    68.0 s            0.0 s      100.0%    68.0 s       0.0 s
[2016-04-15T00:43Z] INFO  17:43:45,020 ProgressMeter - Total runtime 68.22 secs, 1.14 min, 0.02 hours
[2016-04-15T00:43Z] INFO  17:43:45,021 MicroScheduler - 82933 reads were filtered out during the traversal out of approximately 465328 total reads (17.82%)
[2016-04-15T00:43Z] INFO  17:43:45,021 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:43Z] INFO  17:43:45,021 MicroScheduler -   -> 31460 reads (6.76% of total) failing DuplicateReadFilter
[2016-04-15T00:43Z] INFO  17:43:45,021 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:43Z] INFO  17:43:45,021 MicroScheduler -   -> 51473 reads (11.06% of total) failing HCMappingQualityFilter
[2016-04-15T00:43Z] INFO  17:43:45,022 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:43Z] INFO  17:43:45,022 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:43Z] INFO  17:43:45,022 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:43Z] INFO  17:43:45,022 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:43Z] INFO  17:43:45,428 IntervalUtils - Processing 148606 bp from intervals
[2016-04-15T00:43Z] WARN  17:43:45,433 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:43Z] INFO  17:43:45,591 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:43Z] INFO  17:43:45,680 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:43Z] INFO  17:43:45,681 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:43Z] INFO  17:43:45,682 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T00:43Z] INFO  17:43:45,682 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T00:43Z] INFO  17:43:45,683 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T00:43Z] INFO  17:43:45,683 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T00:43Z] INFO  17:43:45,897 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T00:43Z] INFO  17:43:46,292 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:43Z] GATK: HaplotypeCaller
[2016-04-15T00:43Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T00:43Z] INFO  17:43:47,661 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T00:43Z] INFO  17:43:47,663 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T00:43Z] INFO  17:43:47,835 ProgressMeter -      17:2866008      1.5672893E7    30.0 s            1.0 s       17.6%     2.8 m       2.3 m
[2016-04-15T00:43Z] INFO  17:43:47,863 ProgressMeter -      16:3108434       1.008009E8    60.0 s            0.0 s       55.6%   107.0 s      47.0 s
[2016-04-15T00:43Z] INFO  17:43:47,861 ProgressMeter -     16:85496731      1.3904687E7    30.0 s            2.0 s       36.0%    83.0 s      53.0 s
[2016-04-15T00:43Z] WARN  17:43:47,916 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T00:43Z] WARN  17:43:47,917 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T00:43Z] INFO  17:43:48,160 ProgressMeter -     17:18291562      2.0718597E7    30.0 s            1.0 s       30.7%    97.0 s      67.0 s
[2016-04-15T00:43Z] INFO  17:43:49,970 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:43Z] INFO  17:43:49,974 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:43Z] INFO  17:43:49,975 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:43Z] INFO  17:43:49,975 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:43Z] INFO  17:43:49,980 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/18/R14-18106_kapa-NGv3-PE100-NGv3-sort-18_34092400_49867248-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/18/R14-18106_kapa-NGv3-PE100-NGv3-18_34092400_49867248-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/18/tx/tmpXw5Jog/R14-18106_kapa-NGv3-PE100-NGv3-18_34092400_49867248.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:43Z] INFO  17:43:50,037 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:43Z] INFO  17:43:50,050 HelpFormatter - Date/Time: 2016/04/14 17:43:49
[2016-04-15T00:43Z] INFO  17:43:50,051 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:43Z] INFO  17:43:50,051 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:43Z] WARN  17:43:50,106 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T00:43Z] WARN  17:43:50,109 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/18/tx/tmpXw5Jog/R14-18106_kapa-NGv3-PE100-NGv3-18_34092400_49867248.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T00:43Z] INFO  17:43:50,322 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:43Z] INFO  17:43:50,330 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.01237531
[2016-04-15T00:43Z] INFO  17:43:50,331 PairHMM - Total compute time in PairHMM computeLikelihoods() : 0.625999351
[2016-04-15T00:43Z] INFO  17:43:50,331 HaplotypeCaller - Ran local assembly on 2716 active regions
[2016-04-15T00:43Z] INFO  17:43:50,365 ProgressMeter -            done     3.66240357E8    75.0 s            0.0 s      100.0%    75.0 s       0.0 s
[2016-04-15T00:43Z] INFO  17:43:50,366 ProgressMeter - Total runtime 75.69 secs, 1.26 min, 0.02 hours
[2016-04-15T00:43Z] INFO  17:43:50,367 MicroScheduler - 60655 reads were filtered out during the traversal out of approximately 540679 total reads (11.22%)
[2016-04-15T00:43Z] INFO  17:43:50,368 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:43Z] INFO  17:43:50,368 MicroScheduler -   -> 39719 reads (7.35% of total) failing DuplicateReadFilter
[2016-04-15T00:43Z] INFO  17:43:50,369 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:43Z] INFO  17:43:50,369 MicroScheduler -   -> 20936 reads (3.87% of total) failing HCMappingQualityFilter
[2016-04-15T00:43Z] INFO  17:43:50,370 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:43Z] INFO  17:43:50,371 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:43Z] INFO  17:43:50,371 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:43Z] INFO  17:43:50,372 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:43Z] INFO  17:43:50,568 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T00:43Z] INFO  17:43:50,601 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:43Z] INFO  17:43:50,705 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.10
[2016-04-15T00:43Z] INFO  17:43:50,728 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T00:43Z] INFO  17:43:51,096 IntervalUtils - Processing 116317 bp from intervals
[2016-04-15T00:43Z] WARN  17:43:51,102 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:43Z] INFO  17:43:51,234 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:43Z] INFO  17:43:51,322 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:43Z] INFO  17:43:51,322 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:43Z] INFO  17:43:51,323 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T00:43Z] INFO  17:43:51,323 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T00:43Z] INFO  17:43:51,338 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T00:43Z] INFO  17:43:51,339 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T00:43Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T00:43Z] INFO  17:43:51,570 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T00:43Z] INFO  17:43:51,571 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T00:43Z] INFO  17:43:51,619 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T00:43Z] INFO  17:43:51,827 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:43Z] WARN  17:43:51,876 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T00:43Z] WARN  17:43:51,877 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T00:43Z] GATK: HaplotypeCaller
[2016-04-15T00:43Z] INFO  17:43:54,546 ProgressMeter -     16:28618082     1.45732144E8    60.0 s            0.0 s       62.8%    95.0 s      35.0 s
[2016-04-15T00:43Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T00:43Z] INFO  17:43:55,208 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T00:43Z] INFO  17:43:55,208 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T00:43Z] INFO  17:43:55,424 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:43Z] INFO  17:43:55,426 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:43Z] INFO  17:43:55,427 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:43Z] INFO  17:43:55,427 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:43Z] INFO  17:43:55,431 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/18/R14-18106_kapa-NGv3-PE100-NGv3-sort-18_50278423_66344430-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/18/R14-18106_kapa-NGv3-PE100-NGv3-18_50278423_66344430-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/18/tx/tmpbwVw5R/R14-18106_kapa-NGv3-PE100-NGv3-18_50278423_66344430.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:43Z] INFO  17:43:55,452 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:43Z] INFO  17:43:55,452 HelpFormatter - Date/Time: 2016/04/14 17:43:55
[2016-04-15T00:43Z] INFO  17:43:55,453 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:43Z] INFO  17:43:55,454 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:43Z] WARN  17:43:55,476 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T00:43Z] WARN  17:43:55,479 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/18/tx/tmpbwVw5R/R14-18106_kapa-NGv3-PE100-NGv3-18_50278423_66344430.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T00:43Z] INFO  17:43:55,615 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:43Z] WARN  17:43:55,640 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T00:43Z] WARN  17:43:55,641 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T00:43Z] INFO  17:43:55,803 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T00:43Z] INFO  17:43:55,813 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:43Z] INFO  17:43:55,887 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-15T00:43Z] INFO  17:43:55,918 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T00:43Z] INFO  17:43:56,263 IntervalUtils - Processing 111880 bp from intervals
[2016-04-15T00:43Z] WARN  17:43:56,269 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:43Z] INFO  17:43:56,348 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:43Z] INFO  17:43:56,404 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:43Z] INFO  17:43:56,405 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:43Z] INFO  17:43:56,406 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T00:43Z] INFO  17:43:56,406 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T00:43Z] INFO  17:43:56,407 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T00:43Z] INFO  17:43:56,407 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T00:43Z] INFO  17:43:56,560 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T00:43Z] INFO  17:43:58,903 ProgressMeter -     17:49097581      1.9977997E7    30.0 s            1.0 s       31.6%    95.0 s      65.0 s
[2016-04-15T00:43Z] INFO  17:43:58,924 ProgressMeter -     17:35936457      2.5915612E7    30.0 s            1.0 s       17.7%     2.8 m       2.3 m
[2016-04-15T00:43Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T00:43Z] INFO  17:43:59,454 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T00:43Z] INFO  17:43:59,455 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T00:43Z] WARN  17:43:59,846 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T00:43Z] WARN  17:43:59,847 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T00:43Z] INFO  17:43:59,860 ProgressMeter -      11:5020225      7.4283866E7     3.5 m            2.0 s       45.0%     7.8 m       4.3 m
[2016-04-15T00:44Z] INFO  17:44:01,318 ProgressMeter -     17:70845943      3.3110032E7    30.0 s            0.0 s       31.6%    95.0 s      65.0 s
[2016-04-15T00:44Z] INFO  17:44:05,716 ProgressMeter -     16:60393606     1.21426983E8    60.0 s            0.0 s       96.8%    61.0 s       1.0 s
[2016-04-15T00:44Z] INFO  17:44:07,660 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.026586870000000002
[2016-04-15T00:44Z] INFO  17:44:07,660 PairHMM - Total compute time in PairHMM computeLikelihoods() : 2.823501261
[2016-04-15T00:44Z] INFO  17:44:07,660 HaplotypeCaller - Ran local assembly on 1732 active regions
[2016-04-15T00:44Z] INFO  17:44:07,705 ProgressMeter -            done     1.24288875E8    62.0 s            0.0 s      100.0%    62.0 s       0.0 s
[2016-04-15T00:44Z] INFO  17:44:07,706 ProgressMeter - Total runtime 62.00 secs, 1.03 min, 0.02 hours
[2016-04-15T00:44Z] INFO  17:44:07,706 MicroScheduler - 26318 reads were filtered out during the traversal out of approximately 330633 total reads (7.96%)
[2016-04-15T00:44Z] INFO  17:44:07,706 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:44Z] INFO  17:44:07,708 MicroScheduler -   -> 25000 reads (7.56% of total) failing DuplicateReadFilter
[2016-04-15T00:44Z] INFO  17:44:07,708 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:44Z] INFO  17:44:07,708 MicroScheduler -   -> 1318 reads (0.40% of total) failing HCMappingQualityFilter
[2016-04-15T00:44Z] INFO  17:44:07,709 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:44Z] INFO  17:44:07,709 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:44Z] INFO  17:44:07,709 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:44Z] INFO  17:44:07,710 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:44Z] INFO  17:44:09,205 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:44Z] GATK: HaplotypeCaller
[2016-04-15T00:44Z] INFO  17:44:09,606 ProgressMeter -     17:79784256      1.8967223E7    30.0 s            1.0 s       56.5%    53.0 s      23.0 s
[2016-04-15T00:44Z] INFO  17:44:12,591 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:44Z] INFO  17:44:12,600 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:44Z] INFO  17:44:12,600 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:44Z] INFO  17:44:12,600 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:44Z] INFO  17:44:12,604 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/18/R14-18106_kapa-NGv3-PE100-NGv3-sort-18_66346699_78077248-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/18/R14-18106_kapa-NGv3-PE100-NGv3-18_66346699_78077248-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/18/tx/tmpSrfSDg/R14-18106_kapa-NGv3-PE100-NGv3-18_66346699_78077248.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:44Z] INFO  17:44:12,634 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:44Z] INFO  17:44:12,634 HelpFormatter - Date/Time: 2016/04/14 17:44:12
[2016-04-15T00:44Z] INFO  17:44:12,634 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:44Z] INFO  17:44:12,634 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:44Z] WARN  17:44:12,679 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T00:44Z] WARN  17:44:12,682 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/18/tx/tmpSrfSDg/R14-18106_kapa-NGv3-PE100-NGv3-18_66346699_78077248.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T00:44Z] INFO  17:44:12,860 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:44Z] INFO  17:44:12,909 ProgressMeter -     16:72828121     1.63717946E8    60.0 s            0.0 s       79.3%    75.0 s      15.0 s
[2016-04-15T00:44Z] INFO  17:44:12,948 ProgressMeter -      18:9887860      2.2559501E7    30.0 s            1.0 s       60.1%    49.0 s      19.0 s
[2016-04-15T00:44Z] INFO  17:44:13,096 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T00:44Z] INFO  17:44:13,105 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:44Z] INFO  17:44:13,202 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-15T00:44Z] INFO  17:44:13,279 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T00:44Z] INFO  17:44:13,623 IntervalUtils - Processing 87308 bp from intervals
[2016-04-15T00:44Z] WARN  17:44:13,637 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:44Z] INFO  17:44:13,765 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:44Z] INFO  17:44:13,855 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:44Z] INFO  17:44:13,856 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:44Z] INFO  17:44:13,856 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T00:44Z] INFO  17:44:13,857 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T00:44Z] INFO  17:44:13,877 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T00:44Z] INFO  17:44:13,878 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T00:44Z] INFO  17:44:14,099 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T00:44Z] INFO  17:44:15,703 ProgressMeter -     18:31319040      3.3074988E7    30.0 s            0.0 s       74.9%    40.0 s      10.0 s
[2016-04-15T00:44Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T00:44Z] INFO  17:44:16,438 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T00:44Z] INFO  17:44:16,438 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T00:44Z] WARN  17:44:16,772 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T00:44Z] WARN  17:44:16,773 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T00:44Z] INFO  17:44:17,839 ProgressMeter -      17:6021508     1.10618369E8    60.0 s            0.0 s       45.4%     2.2 m      72.0 s
[2016-04-15T00:44Z] INFO  17:44:17,864 ProgressMeter -     16:11035426     2.91641005E8    90.0 s            0.0 s       86.5%   104.0 s      14.0 s
[2016-04-15T00:44Z] INFO  17:44:17,871 ProgressMeter -     16:89783023      6.4360334E7    60.0 s            0.0 s       88.9%    67.0 s       7.0 s
[2016-04-15T00:44Z] INFO  17:44:18,164 ProgressMeter -     17:21319956      5.8118009E7    60.0 s            1.0 s       48.5%     2.1 m      63.0 s
[2016-04-15T00:44Z] INFO  17:44:21,344 ProgressMeter -     18:47797514      2.4618202E7    30.0 s            1.0 s       87.5%    34.0 s       4.0 s
[2016-04-15T00:44Z] INFO  17:44:22,441 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.007726012000000001
[2016-04-15T00:44Z] INFO  17:44:22,443 PairHMM - Total compute time in PairHMM computeLikelihoods() : 0.260117869
[2016-04-15T00:44Z] INFO  17:44:22,443 HaplotypeCaller - Ran local assembly on 1070 active regions
[2016-04-15T00:44Z] INFO  17:44:22,489 ProgressMeter -            done      5.2114591E7    36.0 s            0.0 s      100.0%    36.0 s       0.0 s
[2016-04-15T00:44Z] INFO  17:44:22,489 ProgressMeter - Total runtime 36.81 secs, 0.61 min, 0.01 hours
[2016-04-15T00:44Z] INFO  17:44:22,490 MicroScheduler - 14427 reads were filtered out during the traversal out of approximately 187689 total reads (7.69%)
[2016-04-15T00:44Z] INFO  17:44:22,490 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:44Z] INFO  17:44:22,491 MicroScheduler -   -> 14039 reads (7.48% of total) failing DuplicateReadFilter
[2016-04-15T00:44Z] INFO  17:44:22,491 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:44Z] INFO  17:44:22,491 MicroScheduler -   -> 388 reads (0.21% of total) failing HCMappingQualityFilter
[2016-04-15T00:44Z] INFO  17:44:22,491 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:44Z] INFO  17:44:22,492 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:44Z] INFO  17:44:22,492 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:44Z] INFO  17:44:22,492 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:44Z] INFO  17:44:23,380 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.021857690000000003
[2016-04-15T00:44Z] INFO  17:44:23,381 PairHMM - Total compute time in PairHMM computeLikelihoods() : 2.1540997660000003
[2016-04-15T00:44Z] INFO  17:44:23,382 HaplotypeCaller - Ran local assembly on 2818 active regions
[2016-04-15T00:44Z] INFO  17:44:23,415 ProgressMeter -            done     2.83439102E8    88.0 s            0.0 s      100.0%    88.0 s       0.0 s
[2016-04-15T00:44Z] INFO  17:44:23,416 ProgressMeter - Total runtime 88.88 secs, 1.48 min, 0.02 hours
[2016-04-15T00:44Z] INFO  17:44:23,417 MicroScheduler - 289533 reads were filtered out during the traversal out of approximately 821206 total reads (35.26%)
[2016-04-15T00:44Z] INFO  17:44:23,417 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:44Z] INFO  17:44:23,418 MicroScheduler -   -> 44859 reads (5.46% of total) failing DuplicateReadFilter
[2016-04-15T00:44Z] INFO  17:44:23,419 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:44Z] INFO  17:44:23,419 MicroScheduler -   -> 244674 reads (29.79% of total) failing HCMappingQualityFilter
[2016-04-15T00:44Z] INFO  17:44:23,420 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:44Z] INFO  17:44:23,420 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:44Z] INFO  17:44:23,421 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:44Z] INFO  17:44:23,422 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:44Z] INFO  17:44:23,452 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.024057197000000002
[2016-04-15T00:44Z] INFO  17:44:23,452 PairHMM - Total compute time in PairHMM computeLikelihoods() : 3.184249422
[2016-04-15T00:44Z] INFO  17:44:23,464 HaplotypeCaller - Ran local assembly on 1573 active regions
[2016-04-15T00:44Z] INFO  17:44:23,519 ProgressMeter -            done      8.7428536E7    65.0 s            0.0 s      100.0%    65.0 s       0.0 s
[2016-04-15T00:44Z] INFO  17:44:23,520 ProgressMeter - Total runtime 65.69 secs, 1.09 min, 0.02 hours
[2016-04-15T00:44Z] INFO  17:44:23,520 MicroScheduler - 28570 reads were filtered out during the traversal out of approximately 332515 total reads (8.59%)
[2016-04-15T00:44Z] INFO  17:44:23,520 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:44Z] INFO  17:44:23,521 MicroScheduler -   -> 25586 reads (7.69% of total) failing DuplicateReadFilter
[2016-04-15T00:44Z] INFO  17:44:23,521 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:44Z] INFO  17:44:23,521 MicroScheduler -   -> 2984 reads (0.90% of total) failing HCMappingQualityFilter
[2016-04-15T00:44Z] INFO  17:44:23,521 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:44Z] INFO  17:44:23,522 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:44Z] INFO  17:44:23,522 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:44Z] INFO  17:44:23,522 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:44Z] INFO  17:44:23,824 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:44Z] INFO  17:44:24,091 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.015017633
[2016-04-15T00:44Z] INFO  17:44:24,092 PairHMM - Total compute time in PairHMM computeLikelihoods() : 1.4042159410000001
[2016-04-15T00:44Z] INFO  17:44:24,093 HaplotypeCaller - Ran local assembly on 1234 active regions
[2016-04-15T00:44Z] INFO  17:44:24,127 ProgressMeter -            done      5.7809529E7    44.0 s            0.0 s      100.0%    44.0 s       0.0 s
[2016-04-15T00:44Z] INFO  17:44:24,128 ProgressMeter - Total runtime 44.55 secs, 0.74 min, 0.01 hours
[2016-04-15T00:44Z] INFO  17:44:24,139 MicroScheduler - 21336 reads were filtered out during the traversal out of approximately 267896 total reads (7.96%)
[2016-04-15T00:44Z] INFO  17:44:24,140 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:44Z] INFO  17:44:24,141 MicroScheduler -   -> 20586 reads (7.68% of total) failing DuplicateReadFilter
[2016-04-15T00:44Z] INFO  17:44:24,141 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:44Z] INFO  17:44:24,142 MicroScheduler -   -> 750 reads (0.28% of total) failing HCMappingQualityFilter
[2016-04-15T00:44Z] INFO  17:44:24,142 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:44Z] INFO  17:44:24,143 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:44Z] INFO  17:44:24,144 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:44Z] INFO  17:44:24,144 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:44Z] GATK: HaplotypeCaller
[2016-04-15T00:44Z] INFO  17:44:24,501 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.00767152
[2016-04-15T00:44Z] INFO  17:44:24,513 PairHMM - Total compute time in PairHMM computeLikelihoods() : 0.347157535
[2016-04-15T00:44Z] INFO  17:44:24,514 HaplotypeCaller - Ran local assembly on 805 active regions
[2016-04-15T00:44Z] INFO  17:44:24,546 ProgressMeter -            done      3.1603936E7    33.0 s            1.0 s      100.0%    33.0 s       0.0 s
[2016-04-15T00:44Z] INFO  17:44:24,547 ProgressMeter - Total runtime 33.22 secs, 0.55 min, 0.01 hours
[2016-04-15T00:44Z] INFO  17:44:24,548 MicroScheduler - 75236 reads were filtered out during the traversal out of approximately 225893 total reads (33.31%)
[2016-04-15T00:44Z] INFO  17:44:24,548 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:44Z] INFO  17:44:24,549 MicroScheduler -   -> 12854 reads (5.69% of total) failing DuplicateReadFilter
[2016-04-15T00:44Z] INFO  17:44:24,549 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:44Z] INFO  17:44:24,550 MicroScheduler -   -> 62382 reads (27.62% of total) failing HCMappingQualityFilter
[2016-04-15T00:44Z] INFO  17:44:24,551 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:44Z] INFO  17:44:24,551 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:44Z] INFO  17:44:24,552 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:44Z] INFO  17:44:24,552 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:44Z] INFO  17:44:24,604 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:44Z] GATK: HaplotypeCaller
[2016-04-15T00:44Z] INFO  17:44:24,854 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:44Z] GATK: HaplotypeCaller
[2016-04-15T00:44Z] INFO  17:44:25,505 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:44Z] GATK: HaplotypeCaller
[2016-04-15T00:44Z] INFO  17:44:25,931 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:44Z] GATK: HaplotypeCaller
[2016-04-15T00:44Z] INFO  17:44:26,416 ProgressMeter -     18:61449638      2.3859777E7    30.0 s            1.0 s       87.6%    34.0 s       4.0 s
[2016-04-15T00:44Z] INFO  17:44:27,109 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:44Z] INFO  17:44:27,112 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:44Z] INFO  17:44:27,113 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:44Z] INFO  17:44:27,113 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:44Z] INFO  17:44:27,118 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/19/R14-18106_kapa-NGv3-PE100-NGv3-sort-19_0_15509577-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/19/R14-18106_kapa-NGv3-PE100-NGv3-19_0_15509577-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/19/tx/tmp2iZfjh/R14-18106_kapa-NGv3-PE100-NGv3-19_0_15509577.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:44Z] INFO  17:44:27,128 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:44Z] INFO  17:44:27,133 HelpFormatter - Date/Time: 2016/04/14 17:44:27
[2016-04-15T00:44Z] INFO  17:44:27,134 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:44Z] INFO  17:44:27,134 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:44Z] WARN  17:44:27,175 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T00:44Z] WARN  17:44:27,177 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/19/tx/tmp2iZfjh/R14-18106_kapa-NGv3-PE100-NGv3-19_0_15509577.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T00:44Z] INFO  17:44:27,348 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:44Z] INFO  17:44:27,570 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T00:44Z] INFO  17:44:27,581 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:44Z] INFO  17:44:27,661 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-15T00:44Z] INFO  17:44:27,688 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T00:44Z] INFO  17:44:27,875 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:44Z] INFO  17:44:27,878 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:44Z] INFO  17:44:27,879 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:44Z] INFO  17:44:27,880 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:44Z] INFO  17:44:27,884 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/19/R14-18106_kapa-NGv3-PE100-NGv3-sort-19_15510112_31025906-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/19/R14-18106_kapa-NGv3-PE100-NGv3-19_15510112_31025906-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/19/tx/tmpvJY93Y/R14-18106_kapa-NGv3-PE100-NGv3-19_15510112_31025906.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:44Z] INFO  17:44:27,916 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:44Z] INFO  17:44:27,917 HelpFormatter - Date/Time: 2016/04/14 17:44:27
[2016-04-15T00:44Z] INFO  17:44:27,917 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:44Z] INFO  17:44:27,917 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:44Z] WARN  17:44:27,949 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T00:44Z] WARN  17:44:27,956 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/19/tx/tmpvJY93Y/R14-18106_kapa-NGv3-PE100-NGv3-19_15510112_31025906.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T00:44Z] INFO  17:44:27,957 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:44Z] INFO  17:44:27,961 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:44Z] INFO  17:44:27,961 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:44Z] INFO  17:44:27,962 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:44Z] INFO  17:44:27,966 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/19/R14-18106_kapa-NGv3-PE100-NGv3-sort-19_31038849_46627578-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/19/R14-18106_kapa-NGv3-PE100-NGv3-19_31038849_46627578-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/19/tx/tmpB3y4Qf/R14-18106_kapa-NGv3-PE100-NGv3-19_31038849_46627578.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:44Z] INFO  17:44:27,975 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:44Z] INFO  17:44:27,976 HelpFormatter - Date/Time: 2016/04/14 17:44:27
[2016-04-15T00:44Z] INFO  17:44:27,976 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:44Z] INFO  17:44:27,976 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:44Z] WARN  17:44:28,014 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T00:44Z] WARN  17:44:28,017 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/19/tx/tmpB3y4Qf/R14-18106_kapa-NGv3-PE100-NGv3-19_31038849_46627578.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T00:44Z] INFO  17:44:28,199 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:44Z] INFO  17:44:28,231 IntervalUtils - Processing 793280 bp from intervals
[2016-04-15T00:44Z] WARN  17:44:28,237 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:44Z] INFO  17:44:28,255 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:44Z] INFO  17:44:28,364 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:44Z] INFO  17:44:28,367 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T00:44Z] INFO  17:44:28,378 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:44Z] INFO  17:44:28,437 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T00:44Z] INFO  17:44:28,448 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-15T00:44Z] INFO  17:44:28,451 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:44Z] INFO  17:44:28,464 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T00:44Z] INFO  17:44:28,511 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:44Z] INFO  17:44:28,516 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:44Z] INFO  17:44:28,517 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T00:44Z] INFO  17:44:28,517 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T00:44Z] INFO  17:44:28,518 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T00:44Z] INFO  17:44:28,519 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T00:44Z] INFO  17:44:28,532 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-15T00:44Z] INFO  17:44:28,551 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T00:44Z] INFO  17:44:28,734 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T00:44Z] INFO  17:44:28,864 IntervalUtils - Processing 296880 bp from intervals
[2016-04-15T00:44Z] INFO  17:44:28,868 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:44Z] INFO  17:44:28,872 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:44Z] INFO  17:44:28,873 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:44Z] INFO  17:44:28,874 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:44Z] WARN  17:44:28,881 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:44Z] INFO  17:44:28,879 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/19/R14-18106_kapa-NGv3-PE100-NGv3-sort-19_46627881_59128983-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/19/R14-18106_kapa-NGv3-PE100-NGv3-19_46627881_59128983-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/19/tx/tmpLSPvWI/R14-18106_kapa-NGv3-PE100-NGv3-19_46627881_59128983.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:44Z] INFO  17:44:28,899 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:44Z] INFO  17:44:28,900 HelpFormatter - Date/Time: 2016/04/14 17:44:28
[2016-04-15T00:44Z] INFO  17:44:28,900 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:44Z] INFO  17:44:28,901 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:44Z] INFO  17:44:28,904 ProgressMeter -     17:61457079     1.63617887E8    60.0 s            0.0 s       85.1%    70.0 s      10.0 s
[2016-04-15T00:44Z] INFO  17:44:28,925 ProgressMeter -     17:39296617     1.32103775E8    60.0 s            0.0 s       43.4%     2.3 m      78.0 s
[2016-04-15T00:44Z] WARN  17:44:28,931 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T00:44Z] WARN  17:44:28,945 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/19/tx/tmpLSPvWI/R14-18106_kapa-NGv3-PE100-NGv3-19_46627881_59128983.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T00:44Z] INFO  17:44:28,992 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:44Z] INFO  17:44:29,040 IntervalUtils - Processing 631764 bp from intervals
[2016-04-15T00:44Z] WARN  17:44:29,046 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:44Z] INFO  17:44:29,111 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.016873428
[2016-04-15T00:44Z] INFO  17:44:29,112 PairHMM - Total compute time in PairHMM computeLikelihoods() : 1.7908036900000002
[2016-04-15T00:44Z] INFO  17:44:29,112 HaplotypeCaller - Ran local assembly on 2394 active regions
[2016-04-15T00:44Z] INFO  17:44:29,125 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:44Z] INFO  17:44:29,127 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:44Z] INFO  17:44:29,128 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T00:44Z] INFO  17:44:29,128 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T00:44Z] INFO  17:44:29,129 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T00:44Z] INFO  17:44:29,130 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T00:44Z] INFO  17:44:29,145 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:44Z] INFO  17:44:29,148 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:44Z] INFO  17:44:29,148 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:44Z] INFO  17:44:29,148 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:44Z] INFO  17:44:29,151 ProgressMeter -            done     2.54086229E8    76.0 s            0.0 s      100.0%    76.0 s       0.0 s
[2016-04-15T00:44Z] INFO  17:44:29,152 ProgressMeter - Total runtime 76.26 secs, 1.27 min, 0.02 hours
[2016-04-15T00:44Z] INFO  17:44:29,152 MicroScheduler - 80989 reads were filtered out during the traversal out of approximately 573413 total reads (14.12%)
[2016-04-15T00:44Z] INFO  17:44:29,152 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/20/R14-18106_kapa-NGv3-PE100-NGv3-sort-20_0_15843471-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/20/R14-18106_kapa-NGv3-PE100-NGv3-20_0_15843471-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/20/tx/tmpjpLUjP/R14-18106_kapa-NGv3-PE100-NGv3-20_0_15843471.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:44Z] INFO  17:44:29,154 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:44Z] INFO  17:44:29,161 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:44Z] INFO  17:44:29,161 HelpFormatter - Date/Time: 2016/04/14 17:44:29
[2016-04-15T00:44Z] INFO  17:44:29,161 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:44Z] INFO  17:44:29,152 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:44Z] INFO  17:44:29,161 MicroScheduler -   -> 40941 reads (7.14% of total) failing DuplicateReadFilter
[2016-04-15T00:44Z] INFO  17:44:29,161 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:44Z] INFO  17:44:29,161 MicroScheduler -   -> 40048 reads (6.98% of total) failing HCMappingQualityFilter
[2016-04-15T00:44Z] INFO  17:44:29,162 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:44Z] INFO  17:44:29,162 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:44Z] INFO  17:44:29,162 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:44Z] INFO  17:44:29,161 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:44Z] INFO  17:44:29,174 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:44Z] INFO  17:44:29,178 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:44Z] WARN  17:44:29,206 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T00:44Z] WARN  17:44:29,209 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/20/tx/tmpjpLUjP/R14-18106_kapa-NGv3-PE100-NGv3-20_0_15843471.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T00:44Z] INFO  17:44:29,313 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:44Z] INFO  17:44:29,314 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:44Z] INFO  17:44:29,314 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T00:44Z] INFO  17:44:29,315 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T00:44Z] INFO  17:44:29,316 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T00:44Z] INFO  17:44:29,316 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T00:44Z] INFO  17:44:29,359 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T00:44Z] INFO  17:44:29,383 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T00:44Z] INFO  17:44:29,395 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:44Z] INFO  17:44:29,398 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:44Z] INFO  17:44:29,492 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.10
[2016-04-15T00:44Z] INFO  17:44:29,515 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T00:44Z] INFO  17:44:29,528 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T00:44Z] INFO  17:44:29,645 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T00:44Z] INFO  17:44:29,683 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:44Z] INFO  17:44:29,778 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.09
[2016-04-15T00:44Z] INFO  17:44:29,804 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T00:44Z] INFO  17:44:29,875 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.012412717
[2016-04-15T00:44Z] INFO  17:44:29,876 PairHMM - Total compute time in PairHMM computeLikelihoods() : 0.530145344
[2016-04-15T00:44Z] INFO  17:44:29,876 HaplotypeCaller - Ran local assembly on 840 active regions
[2016-04-15T00:44Z] INFO  17:44:29,941 ProgressMeter -            done      2.9530103E7    33.0 s            1.0 s      100.0%    33.0 s       0.0 s
[2016-04-15T00:44Z] INFO  17:44:29,942 ProgressMeter - Total runtime 33.54 secs, 0.56 min, 0.01 hours
[2016-04-15T00:44Z] INFO  17:44:29,942 MicroScheduler - 10760 reads were filtered out during the traversal out of approximately 138458 total reads (7.77%)
[2016-04-15T00:44Z] INFO  17:44:29,943 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:44Z] INFO  17:44:29,943 MicroScheduler -   -> 10477 reads (7.57% of total) failing DuplicateReadFilter
[2016-04-15T00:44Z] INFO  17:44:29,943 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:44Z] INFO  17:44:29,943 MicroScheduler -   -> 283 reads (0.20% of total) failing HCMappingQualityFilter
[2016-04-15T00:44Z] INFO  17:44:29,944 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:44Z] INFO  17:44:29,944 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:44Z] INFO  17:44:29,944 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:44Z] INFO  17:44:29,944 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:44Z] INFO  17:44:30,088 IntervalUtils - Processing 711484 bp from intervals
[2016-04-15T00:44Z] WARN  17:44:30,093 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:44Z] INFO  17:44:30,127 IntervalUtils - Processing 179899 bp from intervals
[2016-04-15T00:44Z] WARN  17:44:30,133 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:44Z] INFO  17:44:30,217 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:44Z] INFO  17:44:30,228 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:44Z] INFO  17:44:30,232 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.033981932
[2016-04-15T00:44Z] INFO  17:44:30,233 PairHMM - Total compute time in PairHMM computeLikelihoods() : 2.331008311
[2016-04-15T00:44Z] INFO  17:44:30,233 HaplotypeCaller - Ran local assembly on 1206 active regions
[2016-04-15T00:44Z] INFO  17:44:30,263 ProgressMeter -            done      6.3174533E7    47.0 s            0.0 s      100.0%    47.0 s       0.0 s
[2016-04-15T00:44Z] INFO  17:44:30,263 ProgressMeter - Total runtime 47.35 secs, 0.79 min, 0.01 hours
[2016-04-15T00:44Z] INFO  17:44:30,264 MicroScheduler - 19046 reads were filtered out during the traversal out of approximately 213391 total reads (8.93%)
[2016-04-15T00:44Z] INFO  17:44:30,265 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:44Z] INFO  17:44:30,265 MicroScheduler -   -> 16032 reads (7.51% of total) failing DuplicateReadFilter
[2016-04-15T00:44Z] INFO  17:44:30,265 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:44Z] INFO  17:44:30,265 MicroScheduler -   -> 3014 reads (1.41% of total) failing HCMappingQualityFilter
[2016-04-15T00:44Z] INFO  17:44:30,266 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:44Z] INFO  17:44:30,266 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:44Z] INFO  17:44:30,266 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:44Z] INFO  17:44:30,266 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:44Z] INFO  17:44:30,353 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:44Z] INFO  17:44:30,360 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:44Z] INFO  17:44:30,361 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T00:44Z] INFO  17:44:30,362 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T00:44Z] INFO  17:44:30,362 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T00:44Z] INFO  17:44:30,363 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T00:44Z] INFO  17:44:30,422 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:44Z] INFO  17:44:30,423 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:44Z] INFO  17:44:30,424 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T00:44Z] INFO  17:44:30,424 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T00:44Z] INFO  17:44:30,438 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T00:44Z] INFO  17:44:30,439 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T00:44Z] INFO  17:44:30,558 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T00:44Z] INFO  17:44:30,627 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:44Z] INFO  17:44:30,672 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T00:44Z] INFO  17:44:30,970 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.043017393
[2016-04-15T00:44Z] INFO  17:44:30,971 PairHMM - Total compute time in PairHMM computeLikelihoods() : 2.9975342200000004
[2016-04-15T00:44Z] INFO  17:44:30,972 HaplotypeCaller - Ran local assembly on 3287 active regions
[2016-04-15T00:44Z] INFO  17:44:31,010 ProgressMeter -            done     4.23621461E8   103.0 s            0.0 s      100.0%   103.0 s       0.0 s
[2016-04-15T00:44Z] INFO  17:44:31,011 ProgressMeter - Total runtime 103.17 secs, 1.72 min, 0.03 hours
[2016-04-15T00:44Z] INFO  17:44:31,012 MicroScheduler - 113261 reads were filtered out during the traversal out of approximately 774127 total reads (14.63%)
[2016-04-15T00:44Z] INFO  17:44:31,013 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:44Z] INFO  17:44:31,013 MicroScheduler -   -> 55738 reads (7.20% of total) failing DuplicateReadFilter
[2016-04-15T00:44Z] INFO  17:44:31,014 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:44Z] INFO  17:44:31,015 MicroScheduler -   -> 57523 reads (7.43% of total) failing HCMappingQualityFilter
[2016-04-15T00:44Z] INFO  17:44:31,015 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:44Z] INFO  17:44:31,016 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:44Z] INFO  17:44:31,016 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:44Z] INFO  17:44:31,017 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:44Z] GATK: HaplotypeCaller
[2016-04-15T00:44Z] INFO  17:44:31,319 ProgressMeter -     17:74288625     1.50628122E8    60.0 s            0.0 s       74.7%    80.0 s      20.0 s
[2016-04-15T00:44Z] INFO  17:44:31,333 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:44Z] GATK: HaplotypeCaller
[2016-04-15T00:44Z] INFO  17:44:31,675 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:44Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T00:44Z] INFO  17:44:32,014 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T00:44Z] INFO  17:44:32,025 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T00:44Z] GATK: HaplotypeCaller
[2016-04-15T00:44Z] INFO  17:44:32,307 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:44Z] WARN  17:44:32,411 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T00:44Z] WARN  17:44:32,412 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T00:44Z] GATK: HaplotypeCaller
[2016-04-15T00:44Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T00:44Z] INFO  17:44:33,125 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T00:44Z] INFO  17:44:33,126 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T00:44Z] WARN  17:44:33,738 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T00:44Z] WARN  17:44:33,749 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T00:44Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T00:44Z] INFO  17:44:33,965 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T00:44Z] INFO  17:44:33,965 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T00:44Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T00:44Z] INFO  17:44:34,019 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T00:44Z] INFO  17:44:34,020 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T00:44Z] WARN  17:44:34,243 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T00:44Z] WARN  17:44:34,244 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T00:44Z] WARN  17:44:34,295 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T00:44Z] WARN  17:44:34,297 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T00:44Z] INFO  17:44:34,326 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:44Z] INFO  17:44:34,329 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:44Z] INFO  17:44:34,330 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:44Z] INFO  17:44:34,330 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:44Z] INFO  17:44:34,335 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/20/R14-18106_kapa-NGv3-PE100-NGv3-sort-20_15866408_31376818-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/20/R14-18106_kapa-NGv3-PE100-NGv3-20_15866408_31376818-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/20/tx/tmpJkRZjX/R14-18106_kapa-NGv3-PE100-NGv3-20_15866408_31376818.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:44Z] INFO  17:44:34,374 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:44Z] INFO  17:44:34,382 HelpFormatter - Date/Time: 2016/04/14 17:44:34
[2016-04-15T00:44Z] INFO  17:44:34,383 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:44Z] INFO  17:44:34,383 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:44Z] WARN  17:44:34,444 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T00:44Z] WARN  17:44:34,460 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/20/tx/tmpJkRZjX/R14-18106_kapa-NGv3-PE100-NGv3-20_15866408_31376818.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T00:44Z] INFO  17:44:34,719 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:44Z] INFO  17:44:34,828 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:44Z] INFO  17:44:34,840 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:44Z] INFO  17:44:34,841 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:44Z] INFO  17:44:34,842 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:44Z] INFO  17:44:34,846 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/20/R14-18106_kapa-NGv3-PE100-NGv3-sort-20_31379406_47242465-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/20/R14-18106_kapa-NGv3-PE100-NGv3-20_31379406_47242465-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/20/tx/tmp3L4sSz/R14-18106_kapa-NGv3-PE100-NGv3-20_31379406_47242465.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:44Z] INFO  17:44:34,866 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:44Z] INFO  17:44:34,867 HelpFormatter - Date/Time: 2016/04/14 17:44:34
[2016-04-15T00:44Z] INFO  17:44:34,867 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:44Z] INFO  17:44:34,868 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:44Z] WARN  17:44:34,906 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T00:44Z] WARN  17:44:34,920 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/20/tx/tmp3L4sSz/R14-18106_kapa-NGv3-PE100-NGv3-20_31379406_47242465.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T00:44Z] INFO  17:44:34,958 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T00:44Z] INFO  17:44:34,974 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:44Z] INFO  17:44:35,057 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-15T00:44Z] INFO  17:44:35,080 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T00:44Z] INFO  17:44:35,188 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:44Z] INFO  17:44:35,379 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T00:44Z] INFO  17:44:35,392 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:44Z] INFO  17:44:35,477 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-15T00:44Z] INFO  17:44:35,510 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T00:44Z] INFO  17:44:35,524 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:44Z] INFO  17:44:35,528 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:44Z] INFO  17:44:35,528 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:44Z] INFO  17:44:35,529 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:44Z] INFO  17:44:35,533 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/20/R14-18106_kapa-NGv3-PE100-NGv3-sort-20_47244085_62830269-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/20/R14-18106_kapa-NGv3-PE100-NGv3-20_47244085_62830269-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/20/tx/tmpN4anFV/R14-18106_kapa-NGv3-PE100-NGv3-20_47244085_62830269.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:44Z] INFO  17:44:35,568 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:44Z] INFO  17:44:35,569 HelpFormatter - Date/Time: 2016/04/14 17:44:35
[2016-04-15T00:44Z] INFO  17:44:35,569 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:44Z] INFO  17:44:35,570 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:44Z] INFO  17:44:35,615 IntervalUtils - Processing 150913 bp from intervals
[2016-04-15T00:44Z] WARN  17:44:35,618 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T00:44Z] WARN  17:44:35,621 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/20/tx/tmpN4anFV/R14-18106_kapa-NGv3-PE100-NGv3-20_47244085_62830269.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T00:44Z] WARN  17:44:35,628 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:44Z] INFO  17:44:35,791 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:44Z] INFO  17:44:35,906 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:44Z] INFO  17:44:35,907 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:44Z] INFO  17:44:35,918 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:44Z] INFO  17:44:35,919 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T00:44Z] INFO  17:44:35,919 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T00:44Z] INFO  17:44:35,932 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T00:44Z] INFO  17:44:35,933 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T00:44Z] INFO  17:44:36,021 IntervalUtils - Processing 321885 bp from intervals
[2016-04-15T00:44Z] WARN  17:44:36,027 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:44Z] INFO  17:44:36,032 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:44Z] INFO  17:44:36,035 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:44Z] INFO  17:44:36,035 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:44Z] INFO  17:44:36,035 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:44Z] INFO  17:44:36,053 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/20/R14-18106_kapa-NGv3-PE100-NGv3-sort-20_62831244_63025520-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/20/R14-18106_kapa-NGv3-PE100-NGv3-20_62831244_63025520-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/20/tx/tmpCaMQ3P/R14-18106_kapa-NGv3-PE100-NGv3-20_62831244_63025520.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:44Z] INFO  17:44:36,078 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:44Z] INFO  17:44:36,079 HelpFormatter - Date/Time: 2016/04/14 17:44:36
[2016-04-15T00:44Z] INFO  17:44:36,079 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:44Z] INFO  17:44:36,079 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:44Z] INFO  17:44:36,098 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T00:44Z] INFO  17:44:36,107 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:44Z] INFO  17:44:36,126 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:44Z] WARN  17:44:36,136 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T00:44Z] WARN  17:44:36,149 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/20/tx/tmpCaMQ3P/R14-18106_kapa-NGv3-PE100-NGv3-20_62831244_63025520.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T00:44Z] INFO  17:44:36,214 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T00:44Z] INFO  17:44:36,214 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.10
[2016-04-15T00:44Z] INFO  17:44:36,248 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T00:44Z] INFO  17:44:36,271 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:44Z] INFO  17:44:36,272 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:44Z] INFO  17:44:36,272 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T00:44Z] INFO  17:44:36,273 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T00:44Z] INFO  17:44:36,274 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T00:44Z] INFO  17:44:36,274 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T00:44Z] INFO  17:44:36,438 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:44Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T00:44Z] INFO  17:44:36,506 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T00:44Z] INFO  17:44:36,507 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T00:44Z] INFO  17:44:36,534 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T00:44Z] INFO  17:44:36,676 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T00:44Z] INFO  17:44:36,686 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:44Z] INFO  17:44:36,769 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-15T00:44Z] INFO  17:44:36,798 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T00:44Z] INFO  17:44:36,817 IntervalUtils - Processing 269605 bp from intervals
[2016-04-15T00:44Z] WARN  17:44:36,823 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:44Z] WARN  17:44:36,881 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T00:44Z] WARN  17:44:36,882 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T00:44Z] INFO  17:44:36,949 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:44Z] INFO  17:44:37,012 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.025994700000000003
[2016-04-15T00:44Z] INFO  17:44:37,013 PairHMM - Total compute time in PairHMM computeLikelihoods() : 1.042540324
[2016-04-15T00:44Z] INFO  17:44:37,014 HaplotypeCaller - Ran local assembly on 2203 active regions
[2016-04-15T00:44Z] INFO  17:44:37,058 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:44Z] INFO  17:44:37,060 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:44Z] INFO  17:44:37,060 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T00:44Z] INFO  17:44:37,061 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T00:44Z] INFO  17:44:37,062 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T00:44Z] INFO  17:44:37,062 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T00:44Z] INFO  17:44:37,066 ProgressMeter -            done     2.16274885E8    68.0 s            0.0 s      100.0%    68.0 s       0.0 s
[2016-04-15T00:44Z] INFO  17:44:37,067 ProgressMeter - Total runtime 68.18 secs, 1.14 min, 0.02 hours
[2016-04-15T00:44Z] INFO  17:44:37,067 MicroScheduler - 37137 reads were filtered out during the traversal out of approximately 440797 total reads (8.42%)
[2016-04-15T00:44Z] INFO  17:44:37,067 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:44Z] INFO  17:44:37,068 MicroScheduler -   -> 33070 reads (7.50% of total) failing DuplicateReadFilter
[2016-04-15T00:44Z] INFO  17:44:37,068 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:44Z] INFO  17:44:37,068 MicroScheduler -   -> 4067 reads (0.92% of total) failing HCMappingQualityFilter
[2016-04-15T00:44Z] INFO  17:44:37,068 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:44Z] INFO  17:44:37,069 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:44Z] INFO  17:44:37,069 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:44Z] INFO  17:44:37,070 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:44Z] INFO  17:44:37,366 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T00:44Z] INFO  17:44:37,409 IntervalUtils - Processing 4397 bp from intervals
[2016-04-15T00:44Z] WARN  17:44:37,414 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:44Z] INFO  17:44:37,566 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:44Z] INFO  17:44:37,613 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:44Z] INFO  17:44:37,614 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:44Z] INFO  17:44:37,615 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T00:44Z] INFO  17:44:37,616 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T00:44Z] INFO  17:44:37,620 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T00:44Z] INFO  17:44:37,621 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T00:44Z] INFO  17:44:37,866 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T00:44Z] INFO  17:44:38,449 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:44Z] GATK: HaplotypeCaller
[2016-04-15T00:44Z] WARN  17:44:39,011 ExactAFCalculator - this tool is currently set to genotype at most 6 alternate alleles in a given context, but the context at 19:46815969 has 8 alternate alleles so only the top alleles will be used; see the --max_alternate_alleles argument
[2016-04-15T00:44Z] INFO  17:44:39,861 ProgressMeter -      11:9087527     1.93557482E8     4.2 m            1.0 s       79.4%     5.2 m      64.0 s
[2016-04-15T00:44Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T00:44Z] INFO  17:44:40,464 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T00:44Z] INFO  17:44:40,465 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T00:44Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T00:44Z] INFO  17:44:40,607 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T00:44Z] INFO  17:44:40,608 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T00:44Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T00:44Z] WARN  17:44:40,894 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T00:44Z] INFO  17:44:40,899 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T00:44Z] INFO  17:44:40,900 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T00:44Z] WARN  17:44:40,901 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T00:44Z] WARN  17:44:41,042 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T00:44Z] WARN  17:44:41,043 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T00:44Z] WARN  17:44:41,303 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T00:44Z] WARN  17:44:41,304 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T00:44Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T00:44Z] INFO  17:44:41,685 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T00:44Z] INFO  17:44:41,696 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T00:44Z] WARN  17:44:42,184 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T00:44Z] WARN  17:44:42,185 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T00:44Z] INFO  17:44:42,495 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:44Z] INFO  17:44:42,498 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:44Z] INFO  17:44:42,499 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:44Z] INFO  17:44:42,499 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:44Z] INFO  17:44:42,504 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/21/R14-18106_kapa-NGv3-PE100-NGv3-sort-21_0_15517120-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/21/R14-18106_kapa-NGv3-PE100-NGv3-21_0_15517120-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/21/tx/tmpZESqer/R14-18106_kapa-NGv3-PE100-NGv3-21_0_15517120.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:44Z] INFO  17:44:42,533 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:44Z] INFO  17:44:42,534 HelpFormatter - Date/Time: 2016/04/14 17:44:42
[2016-04-15T00:44Z] INFO  17:44:42,534 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:44Z] INFO  17:44:42,535 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:44Z] WARN  17:44:42,609 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T00:44Z] WARN  17:44:42,611 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/21/tx/tmpZESqer/R14-18106_kapa-NGv3-PE100-NGv3-21_0_15517120.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T00:44Z] INFO  17:44:42,956 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:44Z] INFO  17:44:43,219 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T00:44Z] INFO  17:44:43,235 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:44Z] INFO  17:44:43,325 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.09
[2016-04-15T00:44Z] INFO  17:44:43,352 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T00:44Z] INFO  17:44:43,857 IntervalUtils - Processing 4504 bp from intervals
[2016-04-15T00:44Z] WARN  17:44:43,862 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:44Z] INFO  17:44:43,891 ProgressMeter -     18:77918354       1.255032E7    30.0 s            2.0 s       99.5%    30.0 s       0.0 s
[2016-04-15T00:44Z] INFO  17:44:43,958 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:44Z] INFO  17:44:44,004 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:44Z] INFO  17:44:44,005 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:44Z] INFO  17:44:44,006 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T00:44Z] INFO  17:44:44,007 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T00:44Z] INFO  17:44:44,007 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T00:44Z] INFO  17:44:44,008 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T00:44Z] INFO  17:44:44,017 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.015359065000000002
[2016-04-15T00:44Z] INFO  17:44:44,017 PairHMM - Total compute time in PairHMM computeLikelihoods() : 1.089792375
[2016-04-15T00:44Z] INFO  17:44:44,017 HaplotypeCaller - Ran local assembly on 599 active regions
[2016-04-15T00:44Z] INFO  17:44:44,069 ProgressMeter -            done      1.2811877E7    30.0 s            2.0 s      100.0%    30.0 s       0.0 s
[2016-04-15T00:44Z] INFO  17:44:44,069 ProgressMeter - Total runtime 30.21 secs, 0.50 min, 0.01 hours
[2016-04-15T00:44Z] INFO  17:44:44,069 MicroScheduler - 9516 reads were filtered out during the traversal out of approximately 119983 total reads (7.93%)
[2016-04-15T00:44Z] INFO  17:44:44,070 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:44Z] INFO  17:44:44,076 MicroScheduler -   -> 9191 reads (7.66% of total) failing DuplicateReadFilter
[2016-04-15T00:44Z] INFO  17:44:44,076 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:44Z] INFO  17:44:44,076 MicroScheduler -   -> 325 reads (0.27% of total) failing HCMappingQualityFilter
[2016-04-15T00:44Z] INFO  17:44:44,077 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:44Z] INFO  17:44:44,077 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:44Z] INFO  17:44:44,077 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:44Z] INFO  17:44:44,077 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:44Z] INFO  17:44:44,227 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T00:44Z] INFO  17:44:45,098 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.0024573940000000003
[2016-04-15T00:44Z] INFO  17:44:45,099 PairHMM - Total compute time in PairHMM computeLikelihoods() : 0.007616602
[2016-04-15T00:44Z] INFO  17:44:45,099 HaplotypeCaller - Ran local assembly on 33 active regions
[2016-04-15T00:44Z] INFO  17:44:45,145 ProgressMeter -            done          56928.0     7.0 s            2.2 m      100.0%     7.0 s       0.0 s
[2016-04-15T00:44Z] INFO  17:44:45,146 ProgressMeter - Total runtime 7.53 secs, 0.13 min, 0.00 hours
[2016-04-15T00:44Z] INFO  17:44:45,147 MicroScheduler - 461 reads were filtered out during the traversal out of approximately 6985 total reads (6.60%)
[2016-04-15T00:44Z] INFO  17:44:45,148 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:44Z] INFO  17:44:45,149 MicroScheduler -   -> 454 reads (6.50% of total) failing DuplicateReadFilter
[2016-04-15T00:44Z] INFO  17:44:45,149 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:44Z] INFO  17:44:45,150 MicroScheduler -   -> 7 reads (0.10% of total) failing HCMappingQualityFilter
[2016-04-15T00:44Z] INFO  17:44:45,151 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:44Z] INFO  17:44:45,151 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:44Z] INFO  17:44:45,152 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:44Z] INFO  17:44:45,153 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:44Z] INFO  17:44:45,863 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:44Z] GATK: HaplotypeCaller
[2016-04-15T00:44Z] INFO  17:44:46,829 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:44Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T00:44Z] INFO  17:44:47,009 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T00:44Z] INFO  17:44:47,021 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T00:44Z] GATK: HaplotypeCaller
[2016-04-15T00:44Z] WARN  17:44:47,509 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T00:44Z] WARN  17:44:47,511 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T00:44Z] INFO  17:44:47,841 ProgressMeter -      17:7950072     2.49011867E8    90.0 s            0.0 s       72.4%     2.1 m      34.0 s
[2016-04-15T00:44Z] INFO  17:44:48,169 ProgressMeter -     17:30202408      2.1361362E8    90.0 s            0.0 s       94.9%    94.0 s       4.0 s
[2016-04-15T00:44Z] INFO  17:44:49,133 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:44Z] INFO  17:44:49,137 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:44Z] INFO  17:44:49,137 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:44Z] INFO  17:44:49,138 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:44Z] INFO  17:44:49,142 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/21/R14-18106_kapa-NGv3-PE100-NGv3-sort-21_15524893_31045484-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/21/R14-18106_kapa-NGv3-PE100-NGv3-21_15524893_31045484-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/21/tx/tmpZ4Ky_m/R14-18106_kapa-NGv3-PE100-NGv3-21_15524893_31045484.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:44Z] INFO  17:44:49,164 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:44Z] INFO  17:44:49,174 HelpFormatter - Date/Time: 2016/04/14 17:44:49
[2016-04-15T00:44Z] INFO  17:44:49,175 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:44Z] INFO  17:44:49,175 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:44Z] WARN  17:44:49,199 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T00:44Z] WARN  17:44:49,202 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/21/tx/tmpZ4Ky_m/R14-18106_kapa-NGv3-PE100-NGv3-21_15524893_31045484.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T00:44Z] INFO  17:44:49,433 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:44Z] INFO  17:44:49,703 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T00:44Z] INFO  17:44:49,713 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:44Z] INFO  17:44:49,774 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-15T00:44Z] INFO  17:44:49,801 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T00:44Z] INFO  17:44:50,210 IntervalUtils - Processing 58639 bp from intervals
[2016-04-15T00:44Z] WARN  17:44:50,226 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:44Z] INFO  17:44:50,360 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:44Z] INFO  17:44:50,454 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:44Z] INFO  17:44:50,455 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:44Z] INFO  17:44:50,456 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T00:44Z] INFO  17:44:50,457 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T00:44Z] INFO  17:44:50,457 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T00:44Z] INFO  17:44:50,458 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T00:44Z] INFO  17:44:50,616 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T00:44Z] INFO  17:44:50,783 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:44Z] INFO  17:44:50,789 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:44Z] INFO  17:44:50,789 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:44Z] INFO  17:44:50,790 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:44Z] INFO  17:44:50,794 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/21/R14-18106_kapa-NGv3-PE100-NGv3-sort-21_31062047_46591599-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/21/R14-18106_kapa-NGv3-PE100-NGv3-21_31062047_46591599-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/21/tx/tmp11Mk0V/R14-18106_kapa-NGv3-PE100-NGv3-21_31062047_46591599.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:44Z] INFO  17:44:50,817 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:44Z] INFO  17:44:50,818 HelpFormatter - Date/Time: 2016/04/14 17:44:50
[2016-04-15T00:44Z] INFO  17:44:50,818 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:44Z] INFO  17:44:50,819 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:44Z] WARN  17:44:50,853 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T00:44Z] WARN  17:44:50,856 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/21/tx/tmp11Mk0V/R14-18106_kapa-NGv3-PE100-NGv3-21_31062047_46591599.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T00:44Z] INFO  17:44:51,055 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:44Z] INFO  17:44:51,285 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T00:44Z] INFO  17:44:51,290 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.0353185
[2016-04-15T00:44Z] INFO  17:44:51,291 PairHMM - Total compute time in PairHMM computeLikelihoods() : 9.473926064
[2016-04-15T00:44Z] INFO  17:44:51,295 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:44Z] INFO  17:44:51,291 HaplotypeCaller - Ran local assembly on 2287 active regions
[2016-04-15T00:44Z] INFO  17:44:51,338 ProgressMeter -            done     2.48819629E8    93.0 s            0.0 s      100.0%    93.0 s       0.0 s
[2016-04-15T00:44Z] INFO  17:44:51,338 ProgressMeter - Total runtime 93.20 secs, 1.55 min, 0.03 hours
[2016-04-15T00:44Z] INFO  17:44:51,339 MicroScheduler - 55566 reads were filtered out during the traversal out of approximately 520053 total reads (10.68%)
[2016-04-15T00:44Z] INFO  17:44:51,339 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:44Z] INFO  17:44:51,340 MicroScheduler -   -> 38384 reads (7.38% of total) failing DuplicateReadFilter
[2016-04-15T00:44Z] INFO  17:44:51,340 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:44Z] INFO  17:44:51,340 MicroScheduler -   -> 17182 reads (3.30% of total) failing HCMappingQualityFilter
[2016-04-15T00:44Z] INFO  17:44:51,340 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:44Z] INFO  17:44:51,341 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:44Z] INFO  17:44:51,341 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:44Z] INFO  17:44:51,341 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:44Z] INFO  17:44:51,388 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.09
[2016-04-15T00:44Z] INFO  17:44:51,426 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T00:44Z] INFO  17:44:51,978 IntervalUtils - Processing 282111 bp from intervals
[2016-04-15T00:44Z] WARN  17:44:51,983 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:44Z] INFO  17:44:52,058 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:44Z] INFO  17:44:52,178 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:44Z] INFO  17:44:52,180 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:44Z] INFO  17:44:52,180 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T00:44Z] INFO  17:44:52,181 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T00:44Z] INFO  17:44:52,199 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T00:44Z] INFO  17:44:52,201 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T00:44Z] INFO  17:44:52,430 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T00:44Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T00:44Z] INFO  17:44:52,867 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T00:44Z] INFO  17:44:52,868 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T00:44Z] INFO  17:44:52,917 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:44Z] WARN  17:44:53,204 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T00:44Z] WARN  17:44:53,204 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T00:44Z] GATK: HaplotypeCaller
[2016-04-15T00:44Z] INFO  17:44:56,531 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:44Z] INFO  17:44:56,535 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:44Z] INFO  17:44:56,535 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:44Z] INFO  17:44:56,536 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:44Z] INFO  17:44:56,540 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/21/R14-18106_kapa-NGv3-PE100-NGv3-sort-21_46595644_48129895-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/21/R14-18106_kapa-NGv3-PE100-NGv3-21_46595644_48129895-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/21/tx/tmp7NMXOq/R14-18106_kapa-NGv3-PE100-NGv3-21_46595644_48129895.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:44Z] INFO  17:44:56,550 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:44Z] INFO  17:44:56,554 HelpFormatter - Date/Time: 2016/04/14 17:44:56
[2016-04-15T00:44Z] INFO  17:44:56,554 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:44Z] INFO  17:44:56,555 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:44Z] INFO  17:44:56,575 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.006059572
[2016-04-15T00:44Z] INFO  17:44:56,576 PairHMM - Total compute time in PairHMM computeLikelihoods() : 0.7729745760000001
[2016-04-15T00:44Z] INFO  17:44:56,577 HaplotypeCaller - Ran local assembly on 53 active regions
[2016-04-15T00:44Z] WARN  17:44:56,580 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T00:44Z] WARN  17:44:56,583 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/21/tx/tmp7NMXOq/R14-18106_kapa-NGv3-PE100-NGv3-21_46595644_48129895.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T00:44Z] INFO  17:44:56,615 ProgressMeter -            done          75867.0    12.0 s            2.8 m      100.0%    12.0 s       0.0 s
[2016-04-15T00:44Z] INFO  17:44:56,616 ProgressMeter - Total runtime 12.61 secs, 0.21 min, 0.00 hours
[2016-04-15T00:44Z] INFO  17:44:56,617 MicroScheduler - 5105 reads were filtered out during the traversal out of approximately 18848 total reads (27.09%)
[2016-04-15T00:44Z] INFO  17:44:56,618 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:44Z] INFO  17:44:56,618 MicroScheduler -   -> 1156 reads (6.13% of total) failing DuplicateReadFilter
[2016-04-15T00:44Z] INFO  17:44:56,619 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:44Z] INFO  17:44:56,620 MicroScheduler -   -> 3949 reads (20.95% of total) failing HCMappingQualityFilter
[2016-04-15T00:44Z] INFO  17:44:56,625 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:44Z] INFO  17:44:56,626 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:44Z] INFO  17:44:56,627 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:44Z] INFO  17:44:56,628 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:44Z] INFO  17:44:56,908 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:44Z] INFO  17:44:57,112 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T00:44Z] INFO  17:44:57,132 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:44Z] INFO  17:44:57,212 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-15T00:44Z] INFO  17:44:57,242 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T00:44Z] INFO  17:44:57,556 IntervalUtils - Processing 63011 bp from intervals
[2016-04-15T00:44Z] WARN  17:44:57,562 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:44Z] INFO  17:44:57,649 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:44Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T00:44Z] INFO  17:44:57,677 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T00:44Z] INFO  17:44:57,679 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T00:44Z] INFO  17:44:57,708 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:44Z] INFO  17:44:57,710 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:44Z] INFO  17:44:57,710 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T00:44Z] INFO  17:44:57,711 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T00:44Z] INFO  17:44:57,723 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T00:44Z] INFO  17:44:57,735 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T00:44Z] INFO  17:44:57,923 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T00:44Z] WARN  17:44:57,958 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T00:44Z] WARN  17:44:57,959 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T00:44Z] INFO  17:44:58,057 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:44Z] GATK: HaplotypeCaller
[2016-04-15T00:44Z] INFO  17:44:58,520 ProgressMeter -      19:1225548        9660631.0    30.0 s            3.0 s        8.6%     5.8 m       5.3 m
[2016-04-15T00:44Z] INFO  17:44:58,927 ProgressMeter -     17:40695957     2.27345482E8    90.0 s            0.0 s       58.9%     2.5 m      62.0 s
[2016-04-15T00:44Z] INFO  17:44:59,150 ProgressMeter -     19:17370831      1.4683414E7    30.0 s            2.0 s       25.7%   116.0 s      86.0 s
[2016-04-15T00:44Z] INFO  17:44:59,343 ProgressMeter -     19:35541425      1.1230455E7    30.0 s            2.0 s       11.3%     4.4 m       3.9 m
[2016-04-15T00:45Z] INFO  17:45:00,400 ProgressMeter -      20:3096112      1.0353578E7    30.0 s            2.0 s       38.2%    78.0 s      48.0 s
[2016-04-15T00:45Z] INFO  17:45:00,440 ProgressMeter -     19:48305900        9110148.0    30.0 s            3.0 s       10.0%     5.0 m       4.5 m
[2016-04-15T00:45Z] INFO  17:45:00,835 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.023123108
[2016-04-15T00:45Z] INFO  17:45:00,836 PairHMM - Total compute time in PairHMM computeLikelihoods() : 6.333409553
[2016-04-15T00:45Z] INFO  17:45:00,836 HaplotypeCaller - Ran local assembly on 2567 active regions
[2016-04-15T00:45Z] INFO  17:45:00,906 ProgressMeter -            done     2.67239453E8    89.0 s            0.0 s      100.0%    89.0 s       0.0 s
[2016-04-15T00:45Z] INFO  17:45:00,906 ProgressMeter - Total runtime 89.60 secs, 1.49 min, 0.02 hours
[2016-04-15T00:45Z] INFO  17:45:00,906 MicroScheduler - 44754 reads were filtered out during the traversal out of approximately 544865 total reads (8.21%)
[2016-04-15T00:45Z] INFO  17:45:00,907 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:45Z] INFO  17:45:00,907 MicroScheduler -   -> 41837 reads (7.68% of total) failing DuplicateReadFilter
[2016-04-15T00:45Z] INFO  17:45:00,907 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:45Z] INFO  17:45:00,908 MicroScheduler -   -> 2917 reads (0.54% of total) failing HCMappingQualityFilter
[2016-04-15T00:45Z] INFO  17:45:00,908 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:45Z] INFO  17:45:00,908 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:45Z] INFO  17:45:00,908 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:45Z] INFO  17:45:00,909 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:45Z] INFO  17:45:01,242 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:45Z] INFO  17:45:01,245 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:45Z] INFO  17:45:01,246 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:45Z] INFO  17:45:01,247 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:45Z] INFO  17:45:01,251 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/22/R14-18106_kapa-NGv3-PE100-NGv3-sort-22_0_16258303-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/22/R14-18106_kapa-NGv3-PE100-NGv3-22_0_16258303-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/22/tx/tmpo2Fwr8/R14-18106_kapa-NGv3-PE100-NGv3-22_0_16258303.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:45Z] INFO  17:45:01,260 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:45Z] INFO  17:45:01,261 HelpFormatter - Date/Time: 2016/04/14 17:45:01
[2016-04-15T00:45Z] INFO  17:45:01,262 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:45Z] INFO  17:45:01,262 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:45Z] WARN  17:45:01,308 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T00:45Z] WARN  17:45:01,323 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/22/tx/tmpo2Fwr8/R14-18106_kapa-NGv3-PE100-NGv3-22_0_16258303.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T00:45Z] INFO  17:45:01,555 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:45Z] INFO  17:45:01,791 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T00:45Z] INFO  17:45:01,801 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:45Z] INFO  17:45:01,898 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.10
[2016-04-15T00:45Z] INFO  17:45:01,913 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T00:45Z] INFO  17:45:02,293 IntervalUtils - Processing 118 bp from intervals
[2016-04-15T00:45Z] WARN  17:45:02,306 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:45Z] INFO  17:45:02,430 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:45Z] INFO  17:45:02,458 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:45Z] INFO  17:45:02,459 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:45Z] INFO  17:45:02,460 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T00:45Z] INFO  17:45:02,461 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T00:45Z] INFO  17:45:02,461 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T00:45Z] INFO  17:45:02,462 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T00:45Z] INFO  17:45:02,698 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T00:45Z] INFO  17:45:02,768 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:45Z] GATK: HaplotypeCaller
[2016-04-15T00:45Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T00:45Z] INFO  17:45:03,929 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T00:45Z] INFO  17:45:03,941 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T00:45Z] INFO  17:45:03,943 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.0
[2016-04-15T00:45Z] INFO  17:45:03,953 PairHMM - Total compute time in PairHMM computeLikelihoods() : 0.0
[2016-04-15T00:45Z] INFO  17:45:03,954 HaplotypeCaller - Ran local assembly on 1 active regions
[2016-04-15T00:45Z] INFO  17:45:03,990 ProgressMeter -            done            118.0     1.0 s            3.6 h       99.2%     1.0 s       0.0 s
[2016-04-15T00:45Z] INFO  17:45:03,990 ProgressMeter - Total runtime 1.53 secs, 0.03 min, 0.00 hours
[2016-04-15T00:45Z] INFO  17:45:03,991 MicroScheduler - 290 reads were filtered out during the traversal out of approximately 290 total reads (100.00%)
[2016-04-15T00:45Z] INFO  17:45:03,991 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:45Z] INFO  17:45:03,991 MicroScheduler -   -> 0 reads (0.00% of total) failing DuplicateReadFilter
[2016-04-15T00:45Z] INFO  17:45:03,992 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:45Z] INFO  17:45:03,992 MicroScheduler -   -> 290 reads (100.00% of total) failing HCMappingQualityFilter
[2016-04-15T00:45Z] INFO  17:45:03,992 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:45Z] INFO  17:45:04,000 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:45Z] INFO  17:45:04,000 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:45Z] INFO  17:45:04,000 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:45Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T00:45Z] INFO  17:45:04,091 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T00:45Z] INFO  17:45:04,093 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T00:45Z] INFO  17:45:04,169 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.098851824
[2016-04-15T00:45Z] INFO  17:45:04,171 PairHMM - Total compute time in PairHMM computeLikelihoods() : 122.517663118
[2016-04-15T00:45Z] INFO  17:45:04,172 HaplotypeCaller - Ran local assembly on 3217 active regions
[2016-04-15T00:45Z] INFO  17:45:04,211 ProgressMeter -            done     3.81945604E8     4.6 m            0.0 s      100.0%     4.6 m       0.0 s
[2016-04-15T00:45Z] INFO  17:45:04,212 ProgressMeter - Total runtime 274.40 secs, 4.57 min, 0.08 hours
[2016-04-15T00:45Z] INFO  17:45:04,212 MicroScheduler - 87933 reads were filtered out during the traversal out of approximately 737910 total reads (11.92%)
[2016-04-15T00:45Z] INFO  17:45:04,213 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:45Z] INFO  17:45:04,217 MicroScheduler -   -> 56477 reads (7.65% of total) failing DuplicateReadFilter
[2016-04-15T00:45Z] INFO  17:45:04,218 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:45Z] INFO  17:45:04,218 MicroScheduler -   -> 31456 reads (4.26% of total) failing HCMappingQualityFilter
[2016-04-15T00:45Z] INFO  17:45:04,219 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:45Z] INFO  17:45:04,220 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:45Z] INFO  17:45:04,220 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:45Z] INFO  17:45:04,221 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:45Z] WARN  17:45:04,332 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T00:45Z] WARN  17:45:04,333 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T00:45Z] INFO  17:45:05,498 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:45Z] INFO  17:45:05,660 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:45Z] GATK: HaplotypeCaller
[2016-04-15T00:45Z] GATK: HaplotypeCaller
[2016-04-15T00:45Z] INFO  17:45:05,934 ProgressMeter -     20:23966506      1.6734566E7    30.0 s            1.0 s       55.1%    54.0 s      24.0 s
[2016-04-15T00:45Z] INFO  17:45:06,197 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:45Z] INFO  17:45:06,201 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:45Z] INFO  17:45:06,201 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:45Z] INFO  17:45:06,202 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:45Z] INFO  17:45:06,206 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/22/R14-18106_kapa-NGv3-PE100-NGv3-sort-22_16266928_31795711-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/22/R14-18106_kapa-NGv3-PE100-NGv3-22_16266928_31795711-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/22/tx/tmpk5bzGw/R14-18106_kapa-NGv3-PE100-NGv3-22_16266928_31795711.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:45Z] INFO  17:45:06,216 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:45Z] INFO  17:45:06,217 HelpFormatter - Date/Time: 2016/04/14 17:45:06
[2016-04-15T00:45Z] INFO  17:45:06,217 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:45Z] INFO  17:45:06,218 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:45Z] WARN  17:45:06,241 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T00:45Z] WARN  17:45:06,244 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/22/tx/tmpk5bzGw/R14-18106_kapa-NGv3-PE100-NGv3-22_16266928_31795711.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T00:45Z] INFO  17:45:06,292 ProgressMeter -     20:34795371      2.5317788E7    30.0 s            1.0 s       31.8%    94.0 s      64.0 s
[2016-04-15T00:45Z] INFO  17:45:06,429 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:45Z] INFO  17:45:06,656 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T00:45Z] INFO  17:45:06,676 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:45Z] INFO  17:45:06,760 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-15T00:45Z] INFO  17:45:06,781 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T00:45Z] INFO  17:45:07,095 ProgressMeter -     20:55012642      1.3945131E7    30.0 s            2.0 s       31.1%    96.0 s      66.0 s
[2016-04-15T00:45Z] INFO  17:45:07,201 IntervalUtils - Processing 372769 bp from intervals
[2016-04-15T00:45Z] WARN  17:45:07,207 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:45Z] INFO  17:45:07,298 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:45Z] INFO  17:45:07,505 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:45Z] INFO  17:45:07,507 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:45Z] INFO  17:45:07,507 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T00:45Z] INFO  17:45:07,508 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T00:45Z] INFO  17:45:07,533 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T00:45Z] INFO  17:45:07,534 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T00:45Z] INFO  17:45:07,768 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T00:45Z] INFO  17:45:08,841 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:45Z] INFO  17:45:08,844 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:45Z] INFO  17:45:08,844 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:45Z] INFO  17:45:08,844 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:45Z] INFO  17:45:08,848 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/22/R14-18106_kapa-NGv3-PE100-NGv3-sort-22_31796605_47308085-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/22/R14-18106_kapa-NGv3-PE100-NGv3-22_31796605_47308085-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/22/tx/tmpOwEB8g/R14-18106_kapa-NGv3-PE100-NGv3-22_31796605_47308085.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:45Z] INFO  17:45:08,908 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:45Z] INFO  17:45:08,908 HelpFormatter - Date/Time: 2016/04/14 17:45:08
[2016-04-15T00:45Z] INFO  17:45:08,908 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:45Z] INFO  17:45:08,908 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:45Z] WARN  17:45:08,961 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T00:45Z] WARN  17:45:08,964 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/22/tx/tmpOwEB8g/R14-18106_kapa-NGv3-PE100-NGv3-22_31796605_47308085.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T00:45Z] INFO  17:45:09,187 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:45Z] INFO  17:45:09,191 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:45Z] INFO  17:45:09,191 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:45Z] INFO  17:45:09,192 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:45Z] INFO  17:45:09,196 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/22/R14-18106_kapa-NGv3-PE100-NGv3-sort-22_47309229_51304566-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/22/R14-18106_kapa-NGv3-PE100-NGv3-22_47309229_51304566-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/22/tx/tmplCxhj0/R14-18106_kapa-NGv3-PE100-NGv3-22_47309229_51304566.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:45Z] INFO  17:45:09,229 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:45Z] INFO  17:45:09,230 HelpFormatter - Date/Time: 2016/04/14 17:45:09
[2016-04-15T00:45Z] INFO  17:45:09,230 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:45Z] INFO  17:45:09,231 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:45Z] WARN  17:45:09,282 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T00:45Z] WARN  17:45:09,284 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/22/tx/tmplCxhj0/R14-18106_kapa-NGv3-PE100-NGv3-22_47309229_51304566.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T00:45Z] INFO  17:45:09,302 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:45Z] INFO  17:45:09,484 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:45Z] INFO  17:45:09,529 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T00:45Z] INFO  17:45:09,538 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:45Z] INFO  17:45:09,632 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.09
[2016-04-15T00:45Z] INFO  17:45:09,664 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T00:45Z] INFO  17:45:09,691 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T00:45Z] INFO  17:45:09,700 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:45Z] INFO  17:45:09,777 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-15T00:45Z] INFO  17:45:09,796 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T00:45Z] INFO  17:45:10,154 IntervalUtils - Processing 81362 bp from intervals
[2016-04-15T00:45Z] WARN  17:45:10,162 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:45Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T00:45Z] INFO  17:45:10,205 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T00:45Z] INFO  17:45:10,208 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T00:45Z] INFO  17:45:10,214 IntervalUtils - Processing 366557 bp from intervals
[2016-04-15T00:45Z] WARN  17:45:10,219 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:45Z] INFO  17:45:10,302 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:45Z] INFO  17:45:10,337 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:45Z] INFO  17:45:10,378 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:45Z] INFO  17:45:10,379 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:45Z] INFO  17:45:10,380 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T00:45Z] INFO  17:45:10,381 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T00:45Z] INFO  17:45:10,393 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T00:45Z] INFO  17:45:10,394 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T00:45Z] WARN  17:45:10,403 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T00:45Z] WARN  17:45:10,404 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T00:45Z] INFO  17:45:10,499 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:45Z] INFO  17:45:10,500 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:45Z] INFO  17:45:10,501 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T00:45Z] INFO  17:45:10,501 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T00:45Z] INFO  17:45:10,502 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T00:45Z] INFO  17:45:10,502 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T00:45Z] INFO  17:45:10,593 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T00:45Z] INFO  17:45:10,676 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T00:45Z] INFO  17:45:14,093 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.005143894
[2016-04-15T00:45Z] INFO  17:45:14,094 PairHMM - Total compute time in PairHMM computeLikelihoods() : 0.155670302
[2016-04-15T00:45Z] INFO  17:45:14,095 HaplotypeCaller - Ran local assembly on 429 active regions
[2016-04-15T00:45Z] INFO  17:45:14,133 ProgressMeter -            done        8975092.0    23.0 s            2.0 s      100.0%    23.0 s       0.0 s
[2016-04-15T00:45Z] INFO  17:45:14,134 ProgressMeter - Total runtime 23.68 secs, 0.39 min, 0.01 hours
[2016-04-15T00:45Z] INFO  17:45:14,134 MicroScheduler - 5116 reads were filtered out during the traversal out of approximately 66253 total reads (7.72%)
[2016-04-15T00:45Z] INFO  17:45:14,134 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:45Z] INFO  17:45:14,135 MicroScheduler -   -> 4817 reads (7.27% of total) failing DuplicateReadFilter
[2016-04-15T00:45Z] INFO  17:45:14,140 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:45Z] INFO  17:45:14,140 MicroScheduler -   -> 299 reads (0.45% of total) failing HCMappingQualityFilter
[2016-04-15T00:45Z] INFO  17:45:14,140 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:45Z] INFO  17:45:14,141 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:45Z] INFO  17:45:14,141 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:45Z] INFO  17:45:14,141 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:45Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T00:45Z] INFO  17:45:14,764 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T00:45Z] INFO  17:45:14,765 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T00:45Z] WARN  17:45:14,987 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T00:45Z] WARN  17:45:14,988 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T00:45Z] INFO  17:45:15,600 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:45Z] INFO  17:45:15,649 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.031093223000000003
[2016-04-15T00:45Z] INFO  17:45:15,650 PairHMM - Total compute time in PairHMM computeLikelihoods() : 3.9669773420000003
[2016-04-15T00:45Z] INFO  17:45:15,650 HaplotypeCaller - Ran local assembly on 3778 active regions
[2016-04-15T00:45Z] INFO  17:45:15,686 ProgressMeter -            done      5.1376592E8   117.0 s            0.0 s      100.0%   117.0 s       0.0 s
[2016-04-15T00:45Z] INFO  17:45:15,687 ProgressMeter - Total runtime 117.88 secs, 1.96 min, 0.03 hours
[2016-04-15T00:45Z] INFO  17:45:15,688 MicroScheduler - 71063 reads were filtered out during the traversal out of approximately 826260 total reads (8.60%)
[2016-04-15T00:45Z] INFO  17:45:15,689 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:45Z] INFO  17:45:15,690 MicroScheduler -   -> 61864 reads (7.49% of total) failing DuplicateReadFilter
[2016-04-15T00:45Z] INFO  17:45:15,690 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:45Z] INFO  17:45:15,691 MicroScheduler -   -> 9199 reads (1.11% of total) failing HCMappingQualityFilter
[2016-04-15T00:45Z] INFO  17:45:15,691 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:45Z] INFO  17:45:15,692 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:45Z] INFO  17:45:15,692 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:45Z] INFO  17:45:15,693 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:45Z] GATK: HaplotypeCaller
[2016-04-15T00:45Z] INFO  17:45:17,107 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:45Z] GATK: HaplotypeCaller
[2016-04-15T00:45Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T00:45Z] INFO  17:45:18,289 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T00:45Z] INFO  17:45:18,290 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T00:45Z] WARN  17:45:18,828 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T00:45Z] WARN  17:45:18,829 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T00:45Z] INFO  17:45:18,952 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:45Z] INFO  17:45:18,956 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:45Z] INFO  17:45:18,956 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:45Z] INFO  17:45:18,957 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:45Z] INFO  17:45:18,962 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/X/R14-18106_kapa-NGv3-PE100-NGv3-sort-X_0_15509380-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/X/R14-18106_kapa-NGv3-PE100-NGv3-X_0_15509380-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/X/tx/tmpxL4ZNT/R14-18106_kapa-NGv3-PE100-NGv3-X_0_15509380.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:45Z] INFO  17:45:18,976 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:45Z] INFO  17:45:18,977 HelpFormatter - Date/Time: 2016/04/14 17:45:18
[2016-04-15T00:45Z] INFO  17:45:18,977 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:45Z] INFO  17:45:18,978 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:45Z] WARN  17:45:19,028 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T00:45Z] WARN  17:45:19,030 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/X/tx/tmpxL4ZNT/R14-18106_kapa-NGv3-PE100-NGv3-X_0_15509380.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T00:45Z] INFO  17:45:19,328 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:45Z] INFO  17:45:19,597 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T00:45Z] INFO  17:45:19,606 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:45Z] INFO  17:45:19,679 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-15T00:45Z] INFO  17:45:19,713 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T00:45Z] INFO  17:45:20,046 IntervalUtils - Processing 114122 bp from intervals
[2016-04-15T00:45Z] WARN  17:45:20,052 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:45Z] INFO  17:45:20,204 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:45Z] INFO  17:45:20,288 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:45Z] INFO  17:45:20,290 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:45Z] INFO  17:45:20,290 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T00:45Z] INFO  17:45:20,291 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T00:45Z] INFO  17:45:20,307 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T00:45Z] INFO  17:45:20,308 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T00:45Z] INFO  17:45:20,514 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T00:45Z] INFO  17:45:20,800 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:45Z] INFO  17:45:20,803 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:45Z] INFO  17:45:20,804 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:45Z] INFO  17:45:20,805 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:45Z] INFO  17:45:20,809 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/X/R14-18106_kapa-NGv3-PE100-NGv3-sort-X_15518899_31090070-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/X/R14-18106_kapa-NGv3-PE100-NGv3-X_15518899_31090070-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/X/tx/tmp1rzG4n/R14-18106_kapa-NGv3-PE100-NGv3-X_15518899_31090070.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:45Z] INFO  17:45:20,819 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:45Z] INFO  17:45:20,830 HelpFormatter - Date/Time: 2016/04/14 17:45:20
[2016-04-15T00:45Z] INFO  17:45:20,831 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:45Z] INFO  17:45:20,832 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:45Z] INFO  17:45:20,867 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.00988052
[2016-04-15T00:45Z] WARN  17:45:20,877 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T00:45Z] INFO  17:45:20,880 PairHMM - Total compute time in PairHMM computeLikelihoods() : 0.7700802010000001
[2016-04-15T00:45Z] WARN  17:45:20,880 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/X/tx/tmp1rzG4n/R14-18106_kapa-NGv3-PE100-NGv3-X_15518899_31090070.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T00:45Z] INFO  17:45:20,881 HaplotypeCaller - Ran local assembly on 1137 active regions
[2016-04-15T00:45Z] INFO  17:45:20,928 ProgressMeter -            done      5.5115211E7    45.0 s            0.0 s      100.0%    45.0 s       0.0 s
[2016-04-15T00:45Z] INFO  17:45:20,929 ProgressMeter - Total runtime 45.01 secs, 0.75 min, 0.01 hours
[2016-04-15T00:45Z] INFO  17:45:20,930 MicroScheduler - 17279 reads were filtered out during the traversal out of approximately 219635 total reads (7.87%)
[2016-04-15T00:45Z] INFO  17:45:20,930 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:45Z] INFO  17:45:20,930 MicroScheduler -   -> 16494 reads (7.51% of total) failing DuplicateReadFilter
[2016-04-15T00:45Z] INFO  17:45:20,931 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:45Z] INFO  17:45:20,931 MicroScheduler -   -> 785 reads (0.36% of total) failing HCMappingQualityFilter
[2016-04-15T00:45Z] INFO  17:45:20,931 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:45Z] INFO  17:45:20,932 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:45Z] INFO  17:45:20,932 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:45Z] INFO  17:45:20,932 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:45Z] INFO  17:45:21,165 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:45Z] INFO  17:45:21,377 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T00:45Z] INFO  17:45:21,390 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:45Z] INFO  17:45:21,461 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-15T00:45Z] INFO  17:45:21,498 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T00:45Z] INFO  17:45:21,841 IntervalUtils - Processing 133046 bp from intervals
[2016-04-15T00:45Z] WARN  17:45:21,847 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:45Z] INFO  17:45:21,926 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:45Z] INFO  17:45:21,999 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:45Z] INFO  17:45:22,002 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:45Z] INFO  17:45:22,002 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T00:45Z] INFO  17:45:22,002 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T00:45Z] INFO  17:45:22,014 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T00:45Z] INFO  17:45:22,029 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T00:45Z] INFO  17:45:22,202 ProgressMeter -     21:37581013       1.981523E7    30.0 s            1.0 s       36.3%    82.0 s      52.0 s
[2016-04-15T00:45Z] INFO  17:45:22,328 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T00:45Z] INFO  17:45:22,405 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.005874542
[2016-04-15T00:45Z] INFO  17:45:22,406 PairHMM - Total compute time in PairHMM computeLikelihoods() : 0.451395873
[2016-04-15T00:45Z] INFO  17:45:22,407 HaplotypeCaller - Ran local assembly on 459 active regions
[2016-04-15T00:45Z] INFO  17:45:22,464 ProgressMeter -            done        9449583.0    24.0 s            2.0 s      100.0%    24.0 s       0.0 s
[2016-04-15T00:45Z] INFO  17:45:22,465 ProgressMeter - Total runtime 24.76 secs, 0.41 min, 0.01 hours
[2016-04-15T00:45Z] INFO  17:45:22,465 MicroScheduler - 7909 reads were filtered out during the traversal out of approximately 101804 total reads (7.77%)
[2016-04-15T00:45Z] INFO  17:45:22,466 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:45Z] INFO  17:45:22,466 MicroScheduler -   -> 7748 reads (7.61% of total) failing DuplicateReadFilter
[2016-04-15T00:45Z] INFO  17:45:22,467 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:45Z] INFO  17:45:22,467 MicroScheduler -   -> 161 reads (0.16% of total) failing HCMappingQualityFilter
[2016-04-15T00:45Z] INFO  17:45:22,467 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:45Z] INFO  17:45:22,468 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:45Z] INFO  17:45:22,468 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:45Z] INFO  17:45:22,468 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:45Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T00:45Z] INFO  17:45:22,486 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:45Z] INFO  17:45:22,498 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T00:45Z] INFO  17:45:22,500 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T00:45Z] WARN  17:45:22,739 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T00:45Z] WARN  17:45:22,740 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T00:45Z] GATK: HaplotypeCaller
[2016-04-15T00:45Z] INFO  17:45:23,729 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:45Z] INFO  17:45:23,862 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.025837762
[2016-04-15T00:45Z] INFO  17:45:23,863 PairHMM - Total compute time in PairHMM computeLikelihoods() : 1.716224339
[2016-04-15T00:45Z] INFO  17:45:23,863 HaplotypeCaller - Ran local assembly on 1369 active regions
[2016-04-15T00:45Z] INFO  17:45:23,918 ProgressMeter -            done      8.3134367E7    53.0 s            0.0 s      100.0%    53.0 s       0.0 s
[2016-04-15T00:45Z] INFO  17:45:23,918 ProgressMeter - Total runtime 53.56 secs, 0.89 min, 0.01 hours
[2016-04-15T00:45Z] INFO  17:45:23,918 MicroScheduler - 22132 reads were filtered out during the traversal out of approximately 273688 total reads (8.09%)
[2016-04-15T00:45Z] INFO  17:45:23,919 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:45Z] INFO  17:45:23,919 MicroScheduler -   -> 21035 reads (7.69% of total) failing DuplicateReadFilter
[2016-04-15T00:45Z] INFO  17:45:23,919 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:45Z] INFO  17:45:23,919 MicroScheduler -   -> 1097 reads (0.40% of total) failing HCMappingQualityFilter
[2016-04-15T00:45Z] INFO  17:45:23,920 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:45Z] INFO  17:45:23,920 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:45Z] INFO  17:45:23,920 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:45Z] INFO  17:45:23,920 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:45Z] GATK: HaplotypeCaller
[2016-04-15T00:45Z] INFO  17:45:25,404 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:45Z] INFO  17:45:25,579 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:45Z] INFO  17:45:25,582 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:45Z] INFO  17:45:25,583 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:45Z] INFO  17:45:25,584 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:45Z] INFO  17:45:25,588 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/X/R14-18106_kapa-NGv3-PE100-NGv3-sort-X_31139949_46696637-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/X/R14-18106_kapa-NGv3-PE100-NGv3-X_31139949_46696637-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/X/tx/tmpgjYJQY/R14-18106_kapa-NGv3-PE100-NGv3-X_31139949_46696637.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:45Z] INFO  17:45:25,597 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:45Z] INFO  17:45:25,598 HelpFormatter - Date/Time: 2016/04/14 17:45:25
[2016-04-15T00:45Z] INFO  17:45:25,598 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:45Z] INFO  17:45:25,599 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:45Z] WARN  17:45:25,623 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T00:45Z] WARN  17:45:25,626 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/X/tx/tmpgjYJQY/R14-18106_kapa-NGv3-PE100-NGv3-X_31139949_46696637.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T00:45Z] GATK: HaplotypeCaller
[2016-04-15T00:45Z] INFO  17:45:25,826 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:45Z] INFO  17:45:25,967 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T00:45Z] INFO  17:45:25,977 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:45Z] INFO  17:45:26,050 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-15T00:45Z] INFO  17:45:26,085 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T00:45Z] INFO  17:45:26,450 IntervalUtils - Processing 99894 bp from intervals
[2016-04-15T00:45Z] WARN  17:45:26,466 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:45Z] INFO  17:45:26,639 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:45Z] INFO  17:45:26,773 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:45Z] INFO  17:45:26,774 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:45Z] INFO  17:45:26,775 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T00:45Z] INFO  17:45:26,776 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T00:45Z] INFO  17:45:26,792 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T00:45Z] INFO  17:45:26,793 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T00:45Z] INFO  17:45:26,929 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:45Z] INFO  17:45:26,932 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:45Z] INFO  17:45:26,933 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:45Z] INFO  17:45:26,934 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:45Z] INFO  17:45:26,938 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/X/R14-18106_kapa-NGv3-PE100-NGv3-sort-X_46712910_62570698-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/X/R14-18106_kapa-NGv3-PE100-NGv3-X_46712910_62570698-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/X/tx/tmpqEa5_A/R14-18106_kapa-NGv3-PE100-NGv3-X_46712910_62570698.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:45Z] INFO  17:45:26,947 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:45Z] INFO  17:45:26,948 HelpFormatter - Date/Time: 2016/04/14 17:45:26
[2016-04-15T00:45Z] INFO  17:45:26,949 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:45Z] INFO  17:45:26,950 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:45Z] WARN  17:45:26,997 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T00:45Z] WARN  17:45:27,000 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/X/tx/tmpqEa5_A/R14-18106_kapa-NGv3-PE100-NGv3-X_46712910_62570698.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T00:45Z] INFO  17:45:27,054 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T00:45Z] INFO  17:45:27,208 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:45Z] INFO  17:45:27,437 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T00:45Z] INFO  17:45:27,447 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:45Z] INFO  17:45:27,555 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.11
[2016-04-15T00:45Z] INFO  17:45:27,584 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T00:45Z] INFO  17:45:28,034 IntervalUtils - Processing 228299 bp from intervals
[2016-04-15T00:45Z] WARN  17:45:28,050 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:45Z] INFO  17:45:28,135 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:45Z] INFO  17:45:28,239 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:45Z] INFO  17:45:28,242 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:45Z] INFO  17:45:28,243 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T00:45Z] INFO  17:45:28,244 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T00:45Z] INFO  17:45:28,244 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T00:45Z] INFO  17:45:28,244 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T00:45Z] INFO  17:45:28,471 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T00:45Z] INFO  17:45:28,522 ProgressMeter -      19:3638944      8.1085504E7    60.0 s            0.0 s       25.8%     3.9 m       2.9 m
[2016-04-15T00:45Z] INFO  17:45:28,928 ProgressMeter -     17:43339371     4.64655802E8   120.0 s            0.0 s       86.2%     2.3 m      19.0 s
[2016-04-15T00:45Z] INFO  17:45:29,011 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:45Z] INFO  17:45:29,015 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:45Z] INFO  17:45:29,015 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:45Z] INFO  17:45:29,016 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:45Z] INFO  17:45:29,020 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/X/R14-18106_kapa-NGv3-PE100-NGv3-sort-X_62857907_78427545-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/X/R14-18106_kapa-NGv3-PE100-NGv3-X_62857907_78427545-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/X/tx/tmpeJIxd7/R14-18106_kapa-NGv3-PE100-NGv3-X_62857907_78427545.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:45Z] INFO  17:45:29,044 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:45Z] INFO  17:45:29,045 HelpFormatter - Date/Time: 2016/04/14 17:45:29
[2016-04-15T00:45Z] INFO  17:45:29,046 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:45Z] INFO  17:45:29,050 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:45Z] WARN  17:45:29,097 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T00:45Z] WARN  17:45:29,107 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/X/tx/tmpeJIxd7/R14-18106_kapa-NGv3-PE100-NGv3-X_62857907_78427545.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T00:45Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T00:45Z] INFO  17:45:29,151 ProgressMeter -     19:20725667     1.14611271E8    60.0 s            0.0 s       77.5%    77.0 s      17.0 s
[2016-04-15T00:45Z] INFO  17:45:29,151 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T00:45Z] INFO  17:45:29,151 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T00:45Z] INFO  17:45:29,344 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:45Z] INFO  17:45:29,344 ProgressMeter -     19:38380846      6.9392426E7    60.0 s            0.0 s       34.1%     2.9 m     116.0 s
[2016-04-15T00:45Z] WARN  17:45:29,355 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T00:45Z] WARN  17:45:29,356 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T00:45Z] INFO  17:45:29,567 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T00:45Z] INFO  17:45:29,576 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:45Z] INFO  17:45:29,671 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.09
[2016-04-15T00:45Z] INFO  17:45:29,698 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T00:45Z] INFO  17:45:30,273 IntervalUtils - Processing 175038 bp from intervals
[2016-04-15T00:45Z] WARN  17:45:30,279 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:45Z] INFO  17:45:30,405 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:45Z] INFO  17:45:30,441 ProgressMeter -     19:50097954      7.7448263E7    60.0 s            0.0 s       26.4%     3.8 m       2.8 m
[2016-04-15T00:45Z] INFO  17:45:30,491 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:45Z] INFO  17:45:30,493 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:45Z] INFO  17:45:30,493 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T00:45Z] INFO  17:45:30,494 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T00:45Z] INFO  17:45:30,495 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T00:45Z] INFO  17:45:30,495 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T00:45Z] INFO  17:45:30,702 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T00:45Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T00:45Z] INFO  17:45:31,736 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T00:45Z] INFO  17:45:31,747 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T00:45Z] WARN  17:45:31,926 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T00:45Z] WARN  17:45:31,927 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T00:45Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T00:45Z] INFO  17:45:34,435 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T00:45Z] INFO  17:45:34,441 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T00:45Z] WARN  17:45:34,871 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T00:45Z] WARN  17:45:34,872 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T00:45Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T00:45Z] INFO  17:45:35,262 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T00:45Z] INFO  17:45:35,263 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T00:45Z] WARN  17:45:35,539 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T00:45Z] WARN  17:45:35,540 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T00:45Z] INFO  17:45:36,302 ProgressMeter -     20:44048776     1.56261973E8    60.0 s            0.0 s       79.2%    75.0 s      15.0 s
[2016-04-15T00:45Z] INFO  17:45:37,098 ProgressMeter -     20:61981467      9.9829702E7    60.0 s            0.0 s       80.0%    75.0 s      15.0 s
[2016-04-15T00:45Z] INFO  17:45:37,547 ProgressMeter -     22:20302267      2.0110509E7    30.0 s            1.0 s       26.9%   111.0 s      81.0 s
[2016-04-15T00:45Z] INFO  17:45:39,487 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.008575291
[2016-04-15T00:45Z] INFO  17:45:39,488 PairHMM - Total compute time in PairHMM computeLikelihoods() : 0.717728196
[2016-04-15T00:45Z] INFO  17:45:39,489 HaplotypeCaller - Ran local assembly on 632 active regions
[2016-04-15T00:45Z] INFO  17:45:39,566 ProgressMeter -            done      1.1546648E7    29.0 s            2.0 s      100.0%    29.0 s       0.0 s
[2016-04-15T00:45Z] INFO  17:45:39,567 ProgressMeter - Total runtime 29.19 secs, 0.49 min, 0.01 hours
[2016-04-15T00:45Z] INFO  17:45:39,568 MicroScheduler - 11532 reads were filtered out during the traversal out of approximately 138492 total reads (8.33%)
[2016-04-15T00:45Z] INFO  17:45:39,579 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:45Z] INFO  17:45:39,580 MicroScheduler -   -> 10448 reads (7.54% of total) failing DuplicateReadFilter
[2016-04-15T00:45Z] INFO  17:45:39,581 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:45Z] INFO  17:45:39,581 MicroScheduler -   -> 1084 reads (0.78% of total) failing HCMappingQualityFilter
[2016-04-15T00:45Z] INFO  17:45:39,582 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:45Z] INFO  17:45:39,583 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:45Z] INFO  17:45:39,583 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:45Z] INFO  17:45:39,584 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:45Z] INFO  17:45:40,523 ProgressMeter -     22:37770962      2.2668887E7    30.0 s            1.0 s       25.7%   116.0 s      86.0 s
[2016-04-15T00:45Z] INFO  17:45:41,006 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:45Z] GATK: HaplotypeCaller
[2016-04-15T00:45Z] INFO  17:45:44,278 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:45Z] INFO  17:45:44,282 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:45Z] INFO  17:45:44,282 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:45Z] INFO  17:45:44,283 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:45Z] INFO  17:45:44,287 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/X/R14-18106_kapa-NGv3-PE100-NGv3-sort-X_78616585_95940189-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/X/R14-18106_kapa-NGv3-PE100-NGv3-X_78616585_95940189-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/X/tx/tmpyIeJ2U/R14-18106_kapa-NGv3-PE100-NGv3-X_78616585_95940189.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:45Z] INFO  17:45:44,309 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:45Z] INFO  17:45:44,310 HelpFormatter - Date/Time: 2016/04/14 17:45:44
[2016-04-15T00:45Z] INFO  17:45:44,311 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:45Z] INFO  17:45:44,311 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:45Z] WARN  17:45:44,334 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T00:45Z] WARN  17:45:44,337 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/X/tx/tmpyIeJ2U/R14-18106_kapa-NGv3-PE100-NGv3-X_78616585_95940189.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T00:45Z] INFO  17:45:44,481 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:45Z] INFO  17:45:44,688 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T00:45Z] INFO  17:45:44,697 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:45Z] INFO  17:45:44,776 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-15T00:45Z] INFO  17:45:44,806 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T00:45Z] INFO  17:45:45,137 IntervalUtils - Processing 45787 bp from intervals
[2016-04-15T00:45Z] WARN  17:45:45,148 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:45Z] INFO  17:45:45,248 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:45Z] INFO  17:45:45,331 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:45Z] INFO  17:45:45,343 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:45Z] INFO  17:45:45,344 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T00:45Z] INFO  17:45:45,344 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T00:45Z] INFO  17:45:45,345 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T00:45Z] INFO  17:45:45,345 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T00:45Z] INFO  17:45:45,494 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T00:45Z] INFO  17:45:45,702 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.033775206
[2016-04-15T00:45Z] INFO  17:45:45,703 PairHMM - Total compute time in PairHMM computeLikelihoods() : 8.311052754
[2016-04-15T00:45Z] INFO  17:45:45,704 HaplotypeCaller - Ran local assembly on 3969 active regions
[2016-04-15T00:45Z] INFO  17:45:45,746 ProgressMeter -            done     6.43955503E8     2.3 m            0.0 s      100.0%     2.3 m       0.0 s
[2016-04-15T00:45Z] INFO  17:45:45,746 ProgressMeter - Total runtime 136.84 secs, 2.28 min, 0.04 hours
[2016-04-15T00:45Z] INFO  17:45:45,747 MicroScheduler - 183110 reads were filtered out during the traversal out of approximately 979230 total reads (18.70%)
[2016-04-15T00:45Z] INFO  17:45:45,747 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:45Z] INFO  17:45:45,747 MicroScheduler -   -> 67396 reads (6.88% of total) failing DuplicateReadFilter
[2016-04-15T00:45Z] INFO  17:45:45,748 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:45Z] INFO  17:45:45,748 MicroScheduler -   -> 115714 reads (11.82% of total) failing HCMappingQualityFilter
[2016-04-15T00:45Z] INFO  17:45:45,748 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:45Z] INFO  17:45:45,749 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:45Z] INFO  17:45:45,749 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:45Z] INFO  17:45:45,749 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:45Z] INFO  17:45:46,338 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.031756497
[2016-04-15T00:45Z] INFO  17:45:46,339 PairHMM - Total compute time in PairHMM computeLikelihoods() : 1.528872886
[2016-04-15T00:45Z] INFO  17:45:46,340 HaplotypeCaller - Ran local assembly on 2126 active regions
[2016-04-15T00:45Z] INFO  17:45:46,377 ProgressMeter -            done     1.55945449E8    77.0 s            0.0 s      100.0%    77.0 s       0.0 s
[2016-04-15T00:45Z] INFO  17:45:46,377 ProgressMeter - Total runtime 77.25 secs, 1.29 min, 0.02 hours
[2016-04-15T00:45Z] INFO  17:45:46,378 MicroScheduler - 44817 reads were filtered out during the traversal out of approximately 510032 total reads (8.79%)
[2016-04-15T00:45Z] INFO  17:45:46,378 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:45Z] INFO  17:45:46,378 MicroScheduler -   -> 38905 reads (7.63% of total) failing DuplicateReadFilter
[2016-04-15T00:45Z] INFO  17:45:46,378 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:45Z] INFO  17:45:46,379 MicroScheduler -   -> 5912 reads (1.16% of total) failing HCMappingQualityFilter
[2016-04-15T00:45Z] INFO  17:45:46,379 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:45Z] INFO  17:45:46,379 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:45Z] INFO  17:45:46,379 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:45Z] INFO  17:45:46,380 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:45Z] INFO  17:45:47,255 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:45Z] GATK: HaplotypeCaller
[2016-04-15T00:45Z] INFO  17:45:47,830 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:45Z] GATK: HaplotypeCaller
[2016-04-15T00:45Z] INFO  17:45:48,784 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.030981783000000002
[2016-04-15T00:45Z] INFO  17:45:48,784 PairHMM - Total compute time in PairHMM computeLikelihoods() : 1.331206901
[2016-04-15T00:45Z] INFO  17:45:48,785 HaplotypeCaller - Ran local assembly on 1948 active regions
[2016-04-15T00:45Z] INFO  17:45:48,850 ProgressMeter -            done      1.4684951E8    71.0 s            0.0 s      100.0%    71.0 s       0.0 s
[2016-04-15T00:45Z] INFO  17:45:48,850 ProgressMeter - Total runtime 71.79 secs, 1.20 min, 0.02 hours
[2016-04-15T00:45Z] INFO  17:45:48,851 MicroScheduler - 33295 reads were filtered out during the traversal out of approximately 421680 total reads (7.90%)
[2016-04-15T00:45Z] INFO  17:45:48,851 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:45Z] INFO  17:45:48,851 MicroScheduler -   -> 32369 reads (7.68% of total) failing DuplicateReadFilter
[2016-04-15T00:45Z] INFO  17:45:48,852 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:45Z] INFO  17:45:48,852 MicroScheduler -   -> 926 reads (0.22% of total) failing HCMappingQualityFilter
[2016-04-15T00:45Z] INFO  17:45:48,852 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:45Z] INFO  17:45:48,852 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:45Z] INFO  17:45:48,853 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:45Z] INFO  17:45:48,853 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:45Z] INFO  17:45:49,577 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.002103096
[2016-04-15T00:45Z] INFO  17:45:49,577 PairHMM - Total compute time in PairHMM computeLikelihoods() : 0.056059336
[2016-04-15T00:45Z] INFO  17:45:49,577 HaplotypeCaller - Ran local assembly on 637 active regions
[2016-04-15T00:45Z] INFO  17:45:49,632 ProgressMeter -            done      2.4524947E7    22.0 s            0.0 s      100.0%    22.0 s       0.0 s
[2016-04-15T00:45Z] INFO  17:45:49,633 ProgressMeter - Total runtime 22.86 secs, 0.38 min, 0.01 hours
[2016-04-15T00:45Z] INFO  17:45:49,633 MicroScheduler - 5508 reads were filtered out during the traversal out of approximately 67612 total reads (8.15%)
[2016-04-15T00:45Z] INFO  17:45:49,633 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:45Z] INFO  17:45:49,634 MicroScheduler -   -> 5175 reads (7.65% of total) failing DuplicateReadFilter
[2016-04-15T00:45Z] INFO  17:45:49,634 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:45Z] INFO  17:45:49,634 MicroScheduler -   -> 333 reads (0.49% of total) failing HCMappingQualityFilter
[2016-04-15T00:45Z] INFO  17:45:49,634 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:45Z] INFO  17:45:49,635 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:45Z] INFO  17:45:49,635 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:45Z] INFO  17:45:49,635 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:45Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T00:45Z] INFO  17:45:49,689 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T00:45Z] INFO  17:45:49,690 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T00:45Z] INFO  17:45:50,040 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.0021798990000000003
[2016-04-15T00:45Z] INFO  17:45:50,041 PairHMM - Total compute time in PairHMM computeLikelihoods() : 0.023447617
[2016-04-15T00:45Z] INFO  17:45:50,042 HaplotypeCaller - Ran local assembly on 903 active regions
[2016-04-15T00:45Z] WARN  17:45:50,045 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T00:45Z] WARN  17:45:50,046 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T00:45Z] INFO  17:45:50,079 ProgressMeter -            done      4.2176641E7    28.0 s            0.0 s      100.0%    28.0 s       0.0 s
[2016-04-15T00:45Z] INFO  17:45:50,080 ProgressMeter - Total runtime 28.08 secs, 0.47 min, 0.01 hours
[2016-04-15T00:45Z] INFO  17:45:50,080 MicroScheduler - 7143 reads were filtered out during the traversal out of approximately 89356 total reads (7.99%)
[2016-04-15T00:45Z] INFO  17:45:50,081 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:45Z] INFO  17:45:50,081 MicroScheduler -   -> 6701 reads (7.50% of total) failing DuplicateReadFilter
[2016-04-15T00:45Z] INFO  17:45:50,082 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:45Z] INFO  17:45:50,082 MicroScheduler -   -> 442 reads (0.49% of total) failing HCMappingQualityFilter
[2016-04-15T00:45Z] INFO  17:45:50,082 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:45Z] INFO  17:45:50,083 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:45Z] INFO  17:45:50,083 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:45Z] INFO  17:45:50,083 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:45Z] INFO  17:45:50,300 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.005895138
[2016-04-15T00:45Z] INFO  17:45:50,301 PairHMM - Total compute time in PairHMM computeLikelihoods() : 0.374168402
[2016-04-15T00:45Z] INFO  17:45:50,302 HaplotypeCaller - Ran local assembly on 764 active regions
[2016-04-15T00:45Z] INFO  17:45:50,310 ProgressMeter -      X:15509380      2.7778162E7    30.0 s            1.0 s      100.0%    30.0 s       0.0 s
[2016-04-15T00:45Z] INFO  17:45:50,320 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:45Z] INFO  17:45:50,380 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:45Z] INFO  17:45:50,383 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:45Z] INFO  17:45:50,384 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:45Z] INFO  17:45:50,385 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:45Z] INFO  17:45:50,389 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/X/R14-18106_kapa-NGv3-PE100-NGv3-sort-X_95990756_111698889-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/X/R14-18106_kapa-NGv3-PE100-NGv3-X_95990756_111698889-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/X/tx/tmpAcqe9U/R14-18106_kapa-NGv3-PE100-NGv3-X_95990756_111698889.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:45Z] INFO  17:45:50,405 ProgressMeter -            done      2.7892284E7    30.0 s            1.0 s      100.0%    30.0 s       0.0 s
[2016-04-15T00:45Z] INFO  17:45:50,405 ProgressMeter - Total runtime 30.12 secs, 0.50 min, 0.01 hours
[2016-04-15T00:45Z] INFO  17:45:50,406 MicroScheduler - 11981 reads were filtered out during the traversal out of approximately 98056 total reads (12.22%)
[2016-04-15T00:45Z] INFO  17:45:50,409 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:45Z] INFO  17:45:50,409 HelpFormatter - Date/Time: 2016/04/14 17:45:50
[2016-04-15T00:45Z] INFO  17:45:50,406 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:45Z] INFO  17:45:50,409 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:45Z] INFO  17:45:50,408 MicroScheduler -   -> 7116 reads (7.26% of total) failing DuplicateReadFilter
[2016-04-15T00:45Z] INFO  17:45:50,408 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:45Z] INFO  17:45:50,411 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:45Z] INFO  17:45:50,409 MicroScheduler -   -> 4865 reads (4.96% of total) failing HCMappingQualityFilter
[2016-04-15T00:45Z] INFO  17:45:50,409 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:45Z] INFO  17:45:50,409 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:45Z] INFO  17:45:50,410 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:45Z] INFO  17:45:50,410 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:45Z] WARN  17:45:50,439 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T00:45Z] WARN  17:45:50,443 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/X/tx/tmpAcqe9U/R14-18106_kapa-NGv3-PE100-NGv3-X_95990756_111698889.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T00:45Z] GATK: HaplotypeCaller
[2016-04-15T00:45Z] INFO  17:45:50,701 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:45Z] INFO  17:45:50,880 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T00:45Z] INFO  17:45:50,899 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:45Z] INFO  17:45:50,966 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-15T00:45Z] INFO  17:45:50,985 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T00:45Z] INFO  17:45:51,047 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:45Z] INFO  17:45:51,199 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:45Z] INFO  17:45:51,202 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:45Z] INFO  17:45:51,202 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:45Z] INFO  17:45:51,203 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:45Z] INFO  17:45:51,207 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/X/R14-18106_kapa-NGv3-PE100-NGv3-sort-X_111874647_128581278-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/X/R14-18106_kapa-NGv3-PE100-NGv3-X_111874647_128581278-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/X/tx/tmpKqpSKo/R14-18106_kapa-NGv3-PE100-NGv3-X_111874647_128581278.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:45Z] INFO  17:45:51,228 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:45Z] INFO  17:45:51,229 HelpFormatter - Date/Time: 2016/04/14 17:45:51
[2016-04-15T00:45Z] INFO  17:45:51,230 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:45Z] INFO  17:45:51,230 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:45Z] INFO  17:45:51,237 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.013887109000000002
[2016-04-15T00:45Z] INFO  17:45:51,241 PairHMM - Total compute time in PairHMM computeLikelihoods() : 1.211893163
[2016-04-15T00:45Z] INFO  17:45:51,242 HaplotypeCaller - Ran local assembly on 2343 active regions
[2016-04-15T00:45Z] WARN  17:45:51,269 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T00:45Z] WARN  17:45:51,272 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/X/tx/tmpKqpSKo/R14-18106_kapa-NGv3-PE100-NGv3-X_111874647_128581278.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T00:45Z] INFO  17:45:51,300 ProgressMeter -            done     2.49280923E8    75.0 s            0.0 s      100.0%    75.0 s       0.0 s
[2016-04-15T00:45Z] INFO  17:45:51,302 ProgressMeter - Total runtime 75.03 secs, 1.25 min, 0.02 hours
[2016-04-15T00:45Z] INFO  17:45:51,302 MicroScheduler - 40477 reads were filtered out during the traversal out of approximately 522356 total reads (7.75%)
[2016-04-15T00:45Z] INFO  17:45:51,303 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:45Z] INFO  17:45:51,303 MicroScheduler -   -> 39966 reads (7.65% of total) failing DuplicateReadFilter
[2016-04-15T00:45Z] INFO  17:45:51,303 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:45Z] INFO  17:45:51,303 MicroScheduler -   -> 511 reads (0.10% of total) failing HCMappingQualityFilter
[2016-04-15T00:45Z] INFO  17:45:51,303 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:45Z] INFO  17:45:51,304 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:45Z] INFO  17:45:51,304 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:45Z] INFO  17:45:51,304 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:45Z] INFO  17:45:51,314 IntervalUtils - Processing 181656 bp from intervals
[2016-04-15T00:45Z] WARN  17:45:51,319 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:45Z] GATK: HaplotypeCaller
[2016-04-15T00:45Z] INFO  17:45:51,413 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:45Z] INFO  17:45:51,440 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:45Z] INFO  17:45:51,543 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:45Z] INFO  17:45:51,570 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:45Z] INFO  17:45:51,571 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:45Z] INFO  17:45:51,572 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T00:45Z] INFO  17:45:51,572 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T00:45Z] INFO  17:45:51,581 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T00:45Z] INFO  17:45:51,582 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T00:45Z] INFO  17:45:51,624 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:45Z] GATK: HaplotypeCaller
[2016-04-15T00:45Z] INFO  17:45:51,783 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T00:45Z] INFO  17:45:51,803 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:45Z] INFO  17:45:51,825 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T00:45Z] INFO  17:45:51,884 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-15T00:45Z] INFO  17:45:51,904 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T00:45Z] GATK: HaplotypeCaller
[2016-04-15T00:45Z] INFO  17:45:52,211 ProgressMeter -     21:45175916     1.30422714E8    60.0 s            0.0 s       81.9%    73.0 s      13.0 s
[2016-04-15T00:45Z] INFO  17:45:52,289 IntervalUtils - Processing 115535 bp from intervals
[2016-04-15T00:45Z] WARN  17:45:52,294 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:45Z] INFO  17:45:52,439 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:45Z] INFO  17:45:52,533 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:45Z] INFO  17:45:52,534 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:45Z] INFO  17:45:52,535 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T00:45Z] INFO  17:45:52,536 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T00:45Z] INFO  17:45:52,548 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T00:45Z] INFO  17:45:52,549 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T00:45Z] INFO  17:45:52,711 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:45Z] INFO  17:45:52,719 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T00:45Z] GATK: HaplotypeCaller
[2016-04-15T00:45Z] INFO  17:45:53,469 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:45Z] INFO  17:45:53,472 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:45Z] INFO  17:45:53,473 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:45Z] INFO  17:45:53,474 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:45Z] INFO  17:45:53,478 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/X/R14-18106_kapa-NGv3-PE100-NGv3-sort-X_128582278_144329181-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/X/R14-18106_kapa-NGv3-PE100-NGv3-X_128582278_144329181-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/X/tx/tmpiwLOyP/R14-18106_kapa-NGv3-PE100-NGv3-X_128582278_144329181.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:45Z] INFO  17:45:53,492 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:45Z] INFO  17:45:53,493 HelpFormatter - Date/Time: 2016/04/14 17:45:53
[2016-04-15T00:45Z] INFO  17:45:53,494 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:45Z] INFO  17:45:53,494 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:45Z] WARN  17:45:53,517 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T00:45Z] WARN  17:45:53,524 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/X/tx/tmpiwLOyP/R14-18106_kapa-NGv3-PE100-NGv3-X_128582278_144329181.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T00:45Z] INFO  17:45:53,763 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:45Z] INFO  17:45:53,967 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T00:45Z] INFO  17:45:53,983 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:45Z] INFO  17:45:54,068 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-15T00:45Z] INFO  17:45:54,099 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T00:45Z] INFO  17:45:54,474 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:45Z] INFO  17:45:54,477 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:45Z] INFO  17:45:54,477 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:45Z] INFO  17:45:54,477 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:45Z] INFO  17:45:54,481 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/X/R14-18106_kapa-NGv3-PE100-NGv3-sort-X_144337190_155270560-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/X/R14-18106_kapa-NGv3-PE100-NGv3-X_144337190_155270560-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/X/tx/tmpJZtJQ2/R14-18106_kapa-NGv3-PE100-NGv3-X_144337190_155270560.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:45Z] INFO  17:45:54,502 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:45Z] INFO  17:45:54,503 HelpFormatter - Date/Time: 2016/04/14 17:45:54
[2016-04-15T00:45Z] INFO  17:45:54,503 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:45Z] INFO  17:45:54,504 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:45Z] WARN  17:45:54,548 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T00:45Z] WARN  17:45:54,551 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/X/tx/tmpJZtJQ2/R14-18106_kapa-NGv3-PE100-NGv3-X_144337190_155270560.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T00:45Z] INFO  17:45:54,590 IntervalUtils - Processing 143302 bp from intervals
[2016-04-15T00:45Z] WARN  17:45:54,596 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:45Z] INFO  17:45:54,695 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:45Z] INFO  17:45:54,802 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:45Z] INFO  17:45:54,805 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:45Z] INFO  17:45:54,806 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:45Z] INFO  17:45:54,806 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:45Z] INFO  17:45:54,829 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/Y/R14-18106_kapa-NGv3-PE100-NGv3-sort-Y_0_15522993-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/Y/R14-18106_kapa-NGv3-PE100-NGv3-Y_0_15522993-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/Y/tx/tmpCK3b2P/R14-18106_kapa-NGv3-PE100-NGv3-Y_0_15522993.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 1 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:45Z] INFO  17:45:54,864 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:45Z] INFO  17:45:54,865 HelpFormatter - Date/Time: 2016/04/14 17:45:54
[2016-04-15T00:45Z] INFO  17:45:54,866 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:45Z] INFO  17:45:54,866 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:45Z] INFO  17:45:54,884 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:45Z] INFO  17:45:54,895 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:45Z] INFO  17:45:54,896 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T00:45Z] INFO  17:45:54,897 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T00:45Z] INFO  17:45:54,899 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:45Z] INFO  17:45:54,911 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T00:45Z] WARN  17:45:54,918 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T00:45Z] WARN  17:45:54,921 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/Y/tx/tmpCK3b2P/R14-18106_kapa-NGv3-PE100-NGv3-Y_0_15522993.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T00:45Z] INFO  17:45:54,914 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T00:45Z] INFO  17:45:55,100 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:45Z] INFO  17:45:55,157 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T00:45Z] INFO  17:45:55,167 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T00:45Z] INFO  17:45:55,178 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:45Z] INFO  17:45:55,273 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.09
[2016-04-15T00:45Z] INFO  17:45:55,275 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T00:45Z] INFO  17:45:55,285 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:45Z] INFO  17:45:55,292 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T00:45Z] INFO  17:45:55,349 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:45Z] INFO  17:45:55,352 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:45Z] INFO  17:45:55,352 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:45Z] INFO  17:45:55,352 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:45Z] INFO  17:45:55,355 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-15T00:45Z] INFO  17:45:55,357 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/Y/R14-18106_kapa-NGv3-PE100-NGv3-sort-Y_15526614_59222281-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/Y/R14-18106_kapa-NGv3-PE100-NGv3-Y_15526614_59222281-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/Y/tx/tmp43qO5Y/R14-18106_kapa-NGv3-PE100-NGv3-Y_15526614_59222281.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 1 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:45Z] INFO  17:45:55,363 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T00:45Z] INFO  17:45:55,367 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:45Z] INFO  17:45:55,367 HelpFormatter - Date/Time: 2016/04/14 17:45:55
[2016-04-15T00:45Z] INFO  17:45:55,367 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:45Z] INFO  17:45:55,367 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:45Z] WARN  17:45:55,400 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T00:45Z] WARN  17:45:55,403 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/Y/tx/tmp43qO5Y/R14-18106_kapa-NGv3-PE100-NGv3-Y_15526614_59222281.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T00:45Z] INFO  17:45:55,577 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:45Z] INFO  17:45:55,739 IntervalUtils - Processing 184337 bp from intervals
[2016-04-15T00:45Z] WARN  17:45:55,755 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:45Z] INFO  17:45:55,802 IntervalUtils - Processing 52192 bp from intervals
[2016-04-15T00:45Z] INFO  17:45:55,806 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T00:45Z] INFO  17:45:55,815 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:45Z] WARN  17:45:55,818 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:45Z] INFO  17:45:55,863 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:45Z] INFO  17:45:55,966 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:45Z] INFO  17:45:55,969 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:45Z] INFO  17:45:55,970 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:45Z] INFO  17:45:55,971 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T00:45Z] INFO  17:45:55,972 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T00:45Z] INFO  17:45:55,982 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T00:45Z] INFO  17:45:55,982 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T00:45Z] INFO  17:45:56,017 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:45Z] INFO  17:45:56,018 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:45Z] INFO  17:45:56,019 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T00:45Z] INFO  17:45:56,020 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T00:45Z] INFO  17:45:56,021 HaplotypeCaller - Currently, physical phasing is not available when ploidy is different than 2; therefore it won't be performed
[2016-04-15T00:45Z] INFO  17:45:56,021 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T00:45Z] INFO  17:45:56,021 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T00:45Z] INFO  17:45:56,079 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.26
[2016-04-15T00:45Z] INFO  17:45:56,101 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T00:45Z] INFO  17:45:56,243 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T00:45Z] INFO  17:45:56,264 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T00:45Z] INFO  17:45:56,430 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:45Z] INFO  17:45:56,433 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:45Z] INFO  17:45:56,434 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:45Z] INFO  17:45:56,434 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:45Z] INFO  17:45:56,439 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18106_kapa-NGv3-PE100-NGv3/Y/R14-18106_kapa-NGv3-PE100-NGv3-sort-Y_59228291_59373566-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/Y/R14-18106_kapa-NGv3-PE100-NGv3-Y_59228291_59373566-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/Y/tx/tmpNPMnHt/R14-18106_kapa-NGv3-PE100-NGv3-Y_59228291_59373566.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 1 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:45Z] INFO  17:45:56,466 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:45Z] INFO  17:45:56,467 HelpFormatter - Date/Time: 2016/04/14 17:45:56
[2016-04-15T00:45Z] INFO  17:45:56,467 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:45Z] INFO  17:45:56,467 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:45Z] WARN  17:45:56,544 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T00:45Z] INFO  17:45:56,555 IntervalUtils - Processing 44713 bp from intervals
[2016-04-15T00:45Z] WARN  17:45:56,547 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/Y/tx/tmpNPMnHt/R14-18106_kapa-NGv3-PE100-NGv3-Y_59228291_59373566.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T00:45Z] WARN  17:45:56,561 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:45Z] INFO  17:45:56,670 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:45Z] INFO  17:45:56,734 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:45Z] INFO  17:45:56,735 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:45Z] INFO  17:45:56,735 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T00:45Z] INFO  17:45:56,735 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T00:45Z] INFO  17:45:56,741 HaplotypeCaller - Currently, physical phasing is not available when ploidy is different than 2; therefore it won't be performed
[2016-04-15T00:45Z] INFO  17:45:56,741 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T00:45Z] INFO  17:45:56,741 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T00:45Z] INFO  17:45:56,778 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:45Z] INFO  17:45:56,918 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T00:45Z] INFO  17:45:56,951 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T00:45Z] INFO  17:45:56,961 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:45Z] INFO  17:45:57,030 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-15T00:45Z] INFO  17:45:57,038 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T00:45Z] INFO  17:45:57,338 IntervalUtils - Processing 2412 bp from intervals
[2016-04-15T00:45Z] WARN  17:45:57,344 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:45Z] INFO  17:45:57,472 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:45Z] INFO  17:45:57,502 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:45Z] INFO  17:45:57,503 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:45Z] INFO  17:45:57,504 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T00:45Z] INFO  17:45:57,505 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T00:45Z] INFO  17:45:57,505 HaplotypeCaller - Currently, physical phasing is not available when ploidy is different than 2; therefore it won't be performed
[2016-04-15T00:45Z] INFO  17:45:57,506 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T00:45Z] INFO  17:45:57,506 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T00:45Z] INFO  17:45:57,745 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T00:45Z] INFO  17:45:58,255 ProgressMeter -      X:52826314      3.9762158E7    30.0 s            0.0 s       58.5%    51.0 s      21.0 s
[2016-04-15T00:45Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T00:45Z] INFO  17:45:58,382 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T00:45Z] INFO  17:45:58,392 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T00:45Z] INFO  17:45:58,523 ProgressMeter -      19:6678398     2.44765109E8    90.0 s            0.0 s       42.0%     3.6 m       2.1 m
[2016-04-15T00:45Z] WARN  17:45:58,809 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T00:45Z] WARN  17:45:58,810 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T00:45Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T00:45Z] INFO  17:45:59,058 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T00:45Z] INFO  17:45:59,059 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T00:45Z] INFO  17:45:59,060 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.0
[2016-04-15T00:45Z] INFO  17:45:59,061 PairHMM - Total compute time in PairHMM computeLikelihoods() : 0.0
[2016-04-15T00:45Z] INFO  17:45:59,061 HaplotypeCaller - Ran local assembly on 17 active regions
[2016-04-15T00:45Z] INFO  17:45:59,123 ProgressMeter -            done          14930.0     1.0 s          108.0 s      100.0%     1.0 s       0.0 s
[2016-04-15T00:45Z] INFO  17:45:59,123 ProgressMeter - Total runtime 1.62 secs, 0.03 min, 0.00 hours
[2016-04-15T00:45Z] INFO  17:45:59,346 ProgressMeter -     19:40880527      2.2203432E8    90.0 s            0.0 s       55.3%     2.7 m      72.0 s
[2016-04-15T00:46Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T00:46Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T00:46Z] INFO  17:46:00,182 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T00:46Z] INFO  17:46:00,183 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T00:46Z] INFO  17:46:00,195 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T00:46Z] INFO  17:46:00,196 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T00:46Z] INFO  17:46:00,442 ProgressMeter -     19:52395078     2.09254229E8    90.0 s            0.0 s       45.2%     3.3 m     109.0 s
[2016-04-15T00:46Z] WARN  17:46:00,450 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T00:46Z] WARN  17:46:00,451 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T00:46Z] INFO  17:46:00,523 ProgressMeter -      X:76711768      4.6364043E7    30.0 s            0.0 s       86.7%    34.0 s       4.0 s
[2016-04-15T00:46Z] WARN  17:46:00,549 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T00:46Z] WARN  17:46:00,550 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T00:46Z] INFO  17:46:00,737 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:46Z] platypus variant calling
[2016-04-15T00:46Z] INFO  17:46:02,075 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.0012673930000000001
[2016-04-15T00:46Z] INFO  17:46:02,086 PairHMM - Total compute time in PairHMM computeLikelihoods() : 0.016258106
[2016-04-15T00:46Z] INFO  17:46:02,087 HaplotypeCaller - Ran local assembly on 293 active regions
[2016-04-15T00:46Z] INFO  17:46:02,144 ProgressMeter -            done        3554725.0    16.0 s            4.0 s      100.0%    16.0 s       0.0 s
[2016-04-15T00:46Z] INFO  17:46:02,144 ProgressMeter - Total runtime 16.80 secs, 0.28 min, 0.00 hours
[2016-04-15T00:46Z] INFO  17:46:02,145 MicroScheduler - 3307 reads were filtered out during the traversal out of approximately 27720 total reads (11.93%)
[2016-04-15T00:46Z] INFO  17:46:02,145 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:46Z] INFO  17:46:02,145 MicroScheduler -   -> 1970 reads (7.11% of total) failing DuplicateReadFilter
[2016-04-15T00:46Z] INFO  17:46:02,145 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:46Z] INFO  17:46:02,146 MicroScheduler -   -> 1337 reads (4.82% of total) failing HCMappingQualityFilter
[2016-04-15T00:46Z] INFO  17:46:02,146 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:46Z] INFO  17:46:02,146 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:46Z] INFO  17:46:02,146 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:46Z] INFO  17:46:02,147 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:46Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T00:46Z] INFO  17:46:03,519 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T00:46Z] INFO  17:46:03,530 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T00:46Z] INFO  17:46:03,663 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:46Z] WARN  17:46:03,838 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T00:46Z] WARN  17:46:03,839 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T00:46Z] platypus variant calling
[2016-04-15T00:46Z] INFO  17:46:04,119 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.021385263
[2016-04-15T00:46Z] INFO  17:46:04,130 PairHMM - Total compute time in PairHMM computeLikelihoods() : 0.296478406
[2016-04-15T00:46Z] INFO  17:46:04,131 HaplotypeCaller - Ran local assembly on 1116 active regions
[2016-04-15T00:46Z] INFO  17:46:04,171 ProgressMeter -            done      6.1608288E7    33.0 s            0.0 s      100.0%    33.0 s       0.0 s
[2016-04-15T00:46Z] INFO  17:46:04,172 ProgressMeter - Total runtime 33.68 secs, 0.56 min, 0.01 hours
[2016-04-15T00:46Z] INFO  17:46:04,173 MicroScheduler - 19839 reads were filtered out during the traversal out of approximately 138835 total reads (14.29%)
[2016-04-15T00:46Z] INFO  17:46:04,173 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:46Z] INFO  17:46:04,174 MicroScheduler -   -> 9983 reads (7.19% of total) failing DuplicateReadFilter
[2016-04-15T00:46Z] INFO  17:46:04,174 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:46Z] INFO  17:46:04,175 MicroScheduler -   -> 9856 reads (7.10% of total) failing HCMappingQualityFilter
[2016-04-15T00:46Z] INFO  17:46:04,176 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:46Z] INFO  17:46:04,176 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:46Z] INFO  17:46:04,177 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:46Z] INFO  17:46:04,177 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:46Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T00:46Z] INFO  17:46:04,276 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T00:46Z] INFO  17:46:04,277 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T00:46Z] WARN  17:46:05,066 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T00:46Z] WARN  17:46:05,067 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T00:46Z] INFO  17:46:05,628 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:46Z] platypus variant calling
[2016-04-15T00:46Z] INFO  17:46:07,548 ProgressMeter -     22:24898094      9.4151576E7    60.0 s            0.0 s       59.1%   101.0 s      41.0 s
[2016-04-15T00:46Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T00:46Z] INFO  17:46:09,186 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T00:46Z] INFO  17:46:09,187 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T00:46Z] INFO  17:46:09,858 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.001523094
[2016-04-15T00:46Z] INFO  17:46:09,859 PairHMM - Total compute time in PairHMM computeLikelihoods() : 0.27323483200000004
[2016-04-15T00:46Z] INFO  17:46:09,859 HaplotypeCaller - Ran local assembly on 334 active regions
[2016-04-15T00:46Z] INFO  17:46:09,949 ProgressMeter -            done        6560827.0    13.0 s            2.0 s      100.0%    13.0 s       0.0 s
[2016-04-15T00:46Z] INFO  17:46:09,949 ProgressMeter - Total runtime 13.21 secs, 0.22 min, 0.00 hours
[2016-04-15T00:46Z] INFO  17:46:09,950 MicroScheduler - 68259 reads were filtered out during the traversal out of approximately 78382 total reads (87.09%)
[2016-04-15T00:46Z] INFO  17:46:09,950 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:46Z] INFO  17:46:09,951 MicroScheduler -   -> 927 reads (1.18% of total) failing DuplicateReadFilter
[2016-04-15T00:46Z] INFO  17:46:09,951 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:46Z] INFO  17:46:09,951 MicroScheduler -   -> 67332 reads (85.90% of total) failing HCMappingQualityFilter
[2016-04-15T00:46Z] INFO  17:46:09,952 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:46Z] INFO  17:46:09,952 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:46Z] INFO  17:46:09,953 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:46Z] INFO  17:46:09,953 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:46Z] INFO  17:46:10,525 ProgressMeter -     22:41736120     1.27937496E8    60.0 s            0.0 s       63.4%    94.0 s      34.0 s
[2016-04-15T00:46Z] INFO  17:46:11,300 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:46Z] platypus variant calling
[2016-04-15T00:46Z] INFO  17:46:12,450 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.0040954220000000005
[2016-04-15T00:46Z] INFO  17:46:12,450 PairHMM - Total compute time in PairHMM computeLikelihoods() : 0.324106707
[2016-04-15T00:46Z] INFO  17:46:12,450 HaplotypeCaller - Ran local assembly on 1529 active regions
[2016-04-15T00:46Z] INFO  17:46:12,490 ProgressMeter -            done     1.04022591E8    44.0 s            0.0 s      100.0%    44.0 s       0.0 s
[2016-04-15T00:46Z] INFO  17:46:12,490 ProgressMeter - Total runtime 44.25 secs, 0.74 min, 0.01 hours
[2016-04-15T00:46Z] INFO  17:46:12,490 MicroScheduler - 89408 reads were filtered out during the traversal out of approximately 254993 total reads (35.06%)
[2016-04-15T00:46Z] INFO  17:46:12,491 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:46Z] INFO  17:46:12,491 MicroScheduler -   -> 13403 reads (5.26% of total) failing DuplicateReadFilter
[2016-04-15T00:46Z] INFO  17:46:12,491 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:46Z] INFO  17:46:12,492 MicroScheduler -   -> 76005 reads (29.81% of total) failing HCMappingQualityFilter
[2016-04-15T00:46Z] INFO  17:46:12,492 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:46Z] INFO  17:46:12,492 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:46Z] INFO  17:46:12,492 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:46Z] INFO  17:46:12,493 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:46Z] INFO  17:46:12,844 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.001032937
[2016-04-15T00:46Z] INFO  17:46:12,845 PairHMM - Total compute time in PairHMM computeLikelihoods() : 0.032923016
[2016-04-15T00:46Z] INFO  17:46:12,846 HaplotypeCaller - Ran local assembly on 340 active regions
[2016-04-15T00:46Z] INFO  17:46:12,903 ProgressMeter -            done        6359922.0    16.0 s            2.0 s      100.0%    16.0 s       0.0 s
[2016-04-15T00:46Z] INFO  17:46:12,903 ProgressMeter - Total runtime 16.88 secs, 0.28 min, 0.00 hours
[2016-04-15T00:46Z] INFO  17:46:12,904 MicroScheduler - 61013 reads were filtered out during the traversal out of approximately 85327 total reads (71.50%)
[2016-04-15T00:46Z] INFO  17:46:12,904 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:46Z] INFO  17:46:12,904 MicroScheduler -   -> 2112 reads (2.48% of total) failing DuplicateReadFilter
[2016-04-15T00:46Z] INFO  17:46:12,904 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:46Z] INFO  17:46:12,905 MicroScheduler -   -> 58901 reads (69.03% of total) failing HCMappingQualityFilter
[2016-04-15T00:46Z] INFO  17:46:12,906 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:46Z] INFO  17:46:12,906 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:46Z] INFO  17:46:12,906 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:46Z] INFO  17:46:12,907 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:46Z] INFO  17:46:13,807 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:46Z] platypus variant calling
[2016-04-15T00:46Z] INFO  17:46:14,534 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:46Z] platypus variant calling
[2016-04-15T00:46Z] INFO  17:46:16,162 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.035001742
[2016-04-15T00:46Z] INFO  17:46:16,163 PairHMM - Total compute time in PairHMM computeLikelihoods() : 6.487005214000001
[2016-04-15T00:46Z] INFO  17:46:16,163 HaplotypeCaller - Ran local assembly on 2059 active regions
[2016-04-15T00:46Z] INFO  17:46:16,198 ProgressMeter -            done     1.91312624E8    84.0 s            0.0 s      100.0%    84.0 s       0.0 s
[2016-04-15T00:46Z] INFO  17:46:16,199 ProgressMeter - Total runtime 84.02 secs, 1.40 min, 0.02 hours
[2016-04-15T00:46Z] INFO  17:46:16,200 MicroScheduler - 37658 reads were filtered out during the traversal out of approximately 425689 total reads (8.85%)
[2016-04-15T00:46Z] INFO  17:46:16,200 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:46Z] INFO  17:46:16,201 MicroScheduler -   -> 33059 reads (7.77% of total) failing DuplicateReadFilter
[2016-04-15T00:46Z] INFO  17:46:16,201 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:46Z] INFO  17:46:16,201 MicroScheduler -   -> 4599 reads (1.08% of total) failing HCMappingQualityFilter
[2016-04-15T00:46Z] INFO  17:46:16,201 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:46Z] INFO  17:46:16,202 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:46Z] INFO  17:46:16,202 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:46Z] INFO  17:46:16,202 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:46Z] INFO  17:46:17,581 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:46Z] platypus variant calling
[2016-04-15T00:46Z] tabix index R14-18106_kapa-NGv3-PE100-NGv3-1_46715671_62228851.vcf.gz
[2016-04-15T00:46Z] platypus variant calling
[2016-04-15T00:46Z] tabix index R14-18106_kapa-NGv3-PE100-NGv3-1_62231950_77749296.vcf.gz
[2016-04-15T00:46Z] tabix index R14-18106_kapa-NGv3-PE100-NGv3-1_77752625_93297674.vcf.gz
[2016-04-15T00:46Z] platypus variant calling
[2016-04-15T00:46Z] platypus variant calling
[2016-04-15T00:46Z] INFO  17:46:20,799 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.031772817
[2016-04-15T00:46Z] INFO  17:46:20,800 PairHMM - Total compute time in PairHMM computeLikelihoods() : 0.9491473140000001
[2016-04-15T00:46Z] INFO  17:46:20,801 HaplotypeCaller - Ran local assembly on 756 active regions
[2016-04-15T00:46Z] INFO  17:46:20,842 ProgressMeter -            done      2.7516501E7    28.0 s            1.0 s      100.0%    28.0 s       0.0 s
[2016-04-15T00:46Z] INFO  17:46:20,842 ProgressMeter - Total runtime 28.31 secs, 0.47 min, 0.01 hours
[2016-04-15T00:46Z] INFO  17:46:20,843 MicroScheduler - 21750 reads were filtered out during the traversal out of approximately 89259 total reads (24.37%)
[2016-04-15T00:46Z] INFO  17:46:20,843 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:46Z] INFO  17:46:20,843 MicroScheduler -   -> 5420 reads (6.07% of total) failing DuplicateReadFilter
[2016-04-15T00:46Z] INFO  17:46:20,844 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:46Z] INFO  17:46:20,844 MicroScheduler -   -> 16330 reads (18.30% of total) failing HCMappingQualityFilter
[2016-04-15T00:46Z] INFO  17:46:20,844 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:46Z] INFO  17:46:20,844 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:46Z] INFO  17:46:20,845 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:46Z] INFO  17:46:20,845 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:46Z] INFO  17:46:21,594 ProgressMeter -     X:108718436      5.0168705E7    30.0 s            0.0 s       84.0%    35.0 s       5.0 s
[2016-04-15T00:46Z] tabix index R14-18106_kapa-NGv3-PE100-NGv3-1_93298945_108993401.vcf.gz
[2016-04-15T00:46Z] platypus variant calling
[2016-04-15T00:46Z] INFO  17:46:22,338 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:46Z] platypus variant calling
[2016-04-15T00:46Z] tabix index R14-18106_kapa-NGv3-PE100-NGv3-1_0_15541927.vcf.gz
[2016-04-15T00:46Z] platypus variant calling
[2016-04-15T00:46Z] INFO  17:46:24,058 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.004584552
[2016-04-15T00:46Z] INFO  17:46:24,060 PairHMM - Total compute time in PairHMM computeLikelihoods() : 0.43219428000000004
[2016-04-15T00:46Z] INFO  17:46:24,060 HaplotypeCaller - Ran local assembly on 947 active regions
[2016-04-15T00:46Z] INFO  17:46:24,108 ProgressMeter -            done      4.2570099E7    29.0 s            0.0 s      100.0%    29.0 s       0.0 s
[2016-04-15T00:46Z] INFO  17:46:24,109 ProgressMeter - Total runtime 29.21 secs, 0.49 min, 0.01 hours
[2016-04-15T00:46Z] INFO  17:46:24,109 MicroScheduler - 18881 reads were filtered out during the traversal out of approximately 104192 total reads (18.12%)
[2016-04-15T00:46Z] INFO  17:46:24,111 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:46Z] INFO  17:46:24,115 MicroScheduler -   -> 6957 reads (6.68% of total) failing DuplicateReadFilter
[2016-04-15T00:46Z] INFO  17:46:24,121 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:46Z] INFO  17:46:24,122 MicroScheduler -   -> 11924 reads (11.44% of total) failing HCMappingQualityFilter
[2016-04-15T00:46Z] INFO  17:46:24,122 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:46Z] INFO  17:46:24,122 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:46Z] INFO  17:46:24,122 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:46Z] INFO  17:46:24,123 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:46Z] tabix index R14-18106_kapa-NGv3-PE100-NGv3-1_15545821_31186478.vcf.gz
[2016-04-15T00:46Z] INFO  17:46:25,248 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.015083984000000002
[2016-04-15T00:46Z] INFO  17:46:25,249 PairHMM - Total compute time in PairHMM computeLikelihoods() : 0.137664652
[2016-04-15T00:46Z] INFO  17:46:25,250 HaplotypeCaller - Ran local assembly on 1185 active regions
[2016-04-15T00:46Z] INFO  17:46:25,294 ProgressMeter -            done      7.0564604E7    33.0 s            0.0 s      100.0%    33.0 s       0.0 s
[2016-04-15T00:46Z] INFO  17:46:25,295 ProgressMeter - Total runtime 33.72 secs, 0.56 min, 0.01 hours
[2016-04-15T00:46Z] INFO  17:46:25,296 MicroScheduler - 21843 reads were filtered out during the traversal out of approximately 136200 total reads (16.04%)
[2016-04-15T00:46Z] INFO  17:46:25,297 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:46Z] INFO  17:46:25,298 MicroScheduler -   -> 8985 reads (6.60% of total) failing DuplicateReadFilter
[2016-04-15T00:46Z] INFO  17:46:25,298 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:46Z] INFO  17:46:25,299 MicroScheduler -   -> 12858 reads (9.44% of total) failing HCMappingQualityFilter
[2016-04-15T00:46Z] INFO  17:46:25,300 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:46Z] INFO  17:46:25,301 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:46Z] INFO  17:46:25,302 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:46Z] INFO  17:46:25,302 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:46Z] platypus variant calling
[2016-04-15T00:46Z] INFO  17:46:25,416 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:46Z] platypus variant calling
[2016-04-15T00:46Z] INFO  17:46:25,995 ProgressMeter -     X:154159951      5.5331476E7    30.0 s            0.0 s       93.2%    32.0 s       2.0 s
[2016-04-15T00:46Z] INFO  17:46:26,721 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:46Z] INFO  17:46:26,903 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.00434099
[2016-04-15T00:46Z] INFO  17:46:26,903 PairHMM - Total compute time in PairHMM computeLikelihoods() : 0.13115517000000002
[2016-04-15T00:46Z] INFO  17:46:26,904 HaplotypeCaller - Ran local assembly on 1239 active regions
[2016-04-15T00:46Z] tabix index R14-18106_kapa-NGv3-PE100-NGv3-1_31187093_46714270.vcf.gz
[2016-04-15T00:46Z] INFO  17:46:26,951 ProgressMeter -            done      6.5416759E7    30.0 s            0.0 s      100.0%    30.0 s       0.0 s
[2016-04-15T00:46Z] INFO  17:46:26,951 ProgressMeter - Total runtime 30.98 secs, 0.52 min, 0.01 hours
[2016-04-15T00:46Z] INFO  17:46:26,952 MicroScheduler - 32534 reads were filtered out during the traversal out of approximately 162361 total reads (20.04%)
[2016-04-15T00:46Z] INFO  17:46:26,952 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:46Z] INFO  17:46:26,952 MicroScheduler -   -> 11000 reads (6.78% of total) failing DuplicateReadFilter
[2016-04-15T00:46Z] INFO  17:46:26,952 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:46Z] INFO  17:46:26,953 MicroScheduler -   -> 21534 reads (13.26% of total) failing HCMappingQualityFilter
[2016-04-15T00:46Z] INFO  17:46:26,953 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:46Z] INFO  17:46:26,953 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:46Z] INFO  17:46:26,953 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:46Z] INFO  17:46:26,954 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:46Z] platypus variant calling
[2016-04-15T00:46Z] platypus variant calling
[2016-04-15T00:46Z] INFO  17:46:28,220 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:46Z] tabix index R14-18106_kapa-NGv3-PE100-NGv3-1_175048468_192127886.vcf.gz
[2016-04-15T00:46Z] platypus variant calling
[2016-04-15T00:46Z] INFO  17:46:28,524 ProgressMeter -      19:9087978      4.4542652E8   120.0 s            0.0 s       59.6%     3.4 m      81.0 s
[2016-04-15T00:46Z] platypus variant calling
[2016-04-15T00:46Z] tabix index R14-18106_kapa-NGv3-PE100-NGv3-1_207641871_223156451.vcf.gz
[2016-04-15T00:46Z] platypus variant calling
[2016-04-15T00:46Z] INFO  17:46:29,347 ProgressMeter -     19:44047544     4.59750237E8   120.0 s            0.0 s       77.0%     2.6 m      35.0 s
[2016-04-15T00:46Z] tabix index R14-18106_kapa-NGv3-PE100-NGv3-1_159504867_175046963.vcf.gz
[2016-04-15T00:46Z] tabix index R14-18106_kapa-NGv3-PE100-NGv3-1_108994811_143767848.vcf.gz
[2016-04-15T00:46Z] platypus variant calling
[2016-04-15T00:46Z] platypus variant calling
[2016-04-15T00:46Z] tabix index R14-18106_kapa-NGv3-PE100-NGv3-1_240255409_249250621.vcf.gz
[2016-04-15T00:46Z] platypus variant calling
[2016-04-15T00:46Z] INFO  17:46:30,443 ProgressMeter -     19:54746484     3.18648938E8   120.0 s            0.0 s       60.9%     3.3 m      77.0 s
[2016-04-15T00:46Z] tabix index R14-18106_kapa-NGv3-PE100-NGv3-2_0_15514844.vcf.gz
[2016-04-15T00:46Z] platypus variant calling
[2016-04-15T00:46Z] tabix index R14-18106_kapa-NGv3-PE100-NGv3-1_192128349_207640257.vcf.gz
[2016-04-15T00:46Z] tabix index R14-18106_kapa-NGv3-PE100-NGv3-2_46707543_62228117.vcf.gz
[2016-04-15T00:46Z] platypus variant calling
[2016-04-15T00:46Z] platypus variant calling
[2016-04-15T00:46Z] tabix index R14-18106_kapa-NGv3-PE100-NGv3-2_31135088_46706841.vcf.gz
[2016-04-15T00:46Z] INFO  17:46:33,836 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.024587936
[2016-04-15T00:46Z] INFO  17:46:33,837 PairHMM - Total compute time in PairHMM computeLikelihoods() : 3.2805435120000004
[2016-04-15T00:46Z] INFO  17:46:33,838 HaplotypeCaller - Ran local assembly on 2680 active regions
[2016-04-15T00:46Z] INFO  17:46:33,890 ProgressMeter -            done     3.03489097E8    86.0 s            0.0 s      100.0%    86.0 s       0.0 s
[2016-04-15T00:46Z] INFO  17:46:33,891 ProgressMeter - Total runtime 86.38 secs, 1.44 min, 0.02 hours
[2016-04-15T00:46Z] INFO  17:46:33,891 MicroScheduler - 100981 reads were filtered out during the traversal out of approximately 632977 total reads (15.95%)
[2016-04-15T00:46Z] INFO  17:46:33,891 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:46Z] INFO  17:46:33,892 MicroScheduler -   -> 45017 reads (7.11% of total) failing DuplicateReadFilter
[2016-04-15T00:46Z] INFO  17:46:33,892 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:46Z] INFO  17:46:33,892 MicroScheduler -   -> 55964 reads (8.84% of total) failing HCMappingQualityFilter
[2016-04-15T00:46Z] INFO  17:46:33,893 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:46Z] INFO  17:46:33,893 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:46Z] INFO  17:46:33,893 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:46Z] INFO  17:46:33,894 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:46Z] platypus variant calling
[2016-04-15T00:46Z] tabix index R14-18106_kapa-NGv3-PE100-NGv3-2_79253838_95537822.vcf.gz
[2016-04-15T00:46Z] platypus variant calling
[2016-04-15T00:46Z] tabix index R14-18106_kapa-NGv3-PE100-NGv3-2_111281072_127413888.vcf.gz
[2016-04-15T00:46Z] INFO  17:46:35,010 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.023015162000000002
[2016-04-15T00:46Z] INFO  17:46:35,011 PairHMM - Total compute time in PairHMM computeLikelihoods() : 1.719052252
[2016-04-15T00:46Z] INFO  17:46:35,012 HaplotypeCaller - Ran local assembly on 2715 active regions
[2016-04-15T00:46Z] INFO  17:46:35,073 ProgressMeter -            done      3.3533286E8    84.0 s            0.0 s      100.0%    84.0 s       0.0 s
[2016-04-15T00:46Z] INFO  17:46:35,073 ProgressMeter - Total runtime 84.57 secs, 1.41 min, 0.02 hours
[2016-04-15T00:46Z] INFO  17:46:35,074 MicroScheduler - 51454 reads were filtered out during the traversal out of approximately 602586 total reads (8.54%)
[2016-04-15T00:46Z] INFO  17:46:35,074 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:46Z] INFO  17:46:35,075 MicroScheduler -   -> 46094 reads (7.65% of total) failing DuplicateReadFilter
[2016-04-15T00:46Z] INFO  17:46:35,075 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:46Z] INFO  17:46:35,075 MicroScheduler -   -> 5360 reads (0.89% of total) failing HCMappingQualityFilter
[2016-04-15T00:46Z] INFO  17:46:35,075 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:46Z] INFO  17:46:35,076 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:46Z] INFO  17:46:35,076 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:46Z] INFO  17:46:35,076 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:46Z] INFO  17:46:35,253 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:46Z] platypus variant calling
[2016-04-15T00:46Z] tabix index R14-18106_kapa-NGv3-PE100-NGv3-1_223162737_240072524.vcf.gz
[2016-04-15T00:46Z] platypus variant calling
[2016-04-15T00:46Z] platypus variant calling
[2016-04-15T00:46Z] INFO  17:46:36,344 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:46Z] platypus variant calling
[2016-04-15T00:46Z] tabix index R14-18106_kapa-NGv3-PE100-NGv3-2_143676177_159195597.vcf.gz
[2016-04-15T00:46Z] platypus variant calling
[2016-04-15T00:46Z] tabix index R14-18106_kapa-NGv3-PE100-NGv3-2_15519725_31133925.vcf.gz
[2016-04-15T00:46Z] platypus variant calling
[2016-04-15T00:46Z] tabix index R14-18106_kapa-NGv3-PE100-NGv3-2_127433207_143643105.vcf.gz
[2016-04-15T00:46Z] tabix index R14-18106_kapa-NGv3-PE100-NGv3-2_62362965_79253295.vcf.gz
[2016-04-15T00:46Z] platypus variant calling
[2016-04-15T00:46Z] platypus variant calling
[2016-04-15T00:46Z] tabix index R14-18106_kapa-NGv3-PE100-NGv3-3_15515506_31574805.vcf.gz
[2016-04-15T00:46Z] platypus variant calling
[2016-04-15T00:46Z] tabix index R14-18106_kapa-NGv3-PE100-NGv3-2_159196753_174774985.vcf.gz
[2016-04-15T00:46Z] platypus variant calling
[2016-04-15T00:46Z] tabix index R14-18106_kapa-NGv3-PE100-NGv3-2_190313104_205830046.vcf.gz
[2016-04-15T00:46Z] platypus variant calling
[2016-04-15T00:46Z] tabix index R14-18106_kapa-NGv3-PE100-NGv3-3_62739115_78648077.vcf.gz
[2016-04-15T00:46Z] tabix index R14-18106_kapa-NGv3-PE100-NGv3-3_78649262_96533852.vcf.gz
[2016-04-15T00:46Z] platypus variant calling
[2016-04-15T00:46Z] platypus variant calling
[2016-04-15T00:46Z] tabix index R14-18106_kapa-NGv3-PE100-NGv3-2_95538561_111273222.vcf.gz
[2016-04-15T00:46Z] platypus variant calling
[2016-04-15T00:46Z] tabix index R14-18106_kapa-NGv3-PE100-NGv3-2_237995374_243199373.vcf.gz
[2016-04-15T00:46Z] platypus variant calling
[2016-04-15T00:46Z] tabix index R14-18106_kapa-NGv3-PE100-NGv3-2_222291154_237994685.vcf.gz
[2016-04-15T00:46Z] platypus variant calling
[2016-04-15T00:46Z] tabix index R14-18106_kapa-NGv3-PE100-NGv3-3_0_15512123.vcf.gz
[2016-04-15T00:46Z] platypus variant calling
[2016-04-15T00:46Z] tabix index R14-18106_kapa-NGv3-PE100-NGv3-3_158970515_174577240.vcf.gz
[2016-04-15T00:46Z] tabix index R14-18106_kapa-NGv3-PE100-NGv3-3_96585668_112185230.vcf.gz
[2016-04-15T00:46Z] platypus variant calling
[2016-04-15T00:46Z] tabix index R14-18106_kapa-NGv3-PE100-NGv3-2_174777797_190306304.vcf.gz
[2016-04-15T00:46Z] platypus variant calling
[2016-04-15T00:46Z] platypus variant calling
[2016-04-15T00:46Z] tabix index R14-18106_kapa-NGv3-PE100-NGv3-1_143897546_159410511.vcf.gz
[2016-04-15T00:46Z] tabix index R14-18106_kapa-NGv3-PE100-NGv3-2_205912303_222290862.vcf.gz
[2016-04-15T00:46Z] tabix index R14-18106_kapa-NGv3-PE100-NGv3-3_143297426_158963696.vcf.gz
[2016-04-15T00:46Z] platypus variant calling
[2016-04-15T00:46Z] platypus variant calling
[2016-04-15T00:46Z] platypus variant calling
[2016-04-15T00:46Z] tabix index R14-18106_kapa-NGv3-PE100-NGv3-4_15512869_31144471.vcf.gz
[2016-04-15T00:46Z] platypus variant calling
[2016-04-15T00:46Z] tabix index R14-18106_kapa-NGv3-PE100-NGv3-4_52709749_68338393.vcf.gz
[2016-04-15T00:46Z] platypus variant calling
[2016-04-15T00:46Z] tabix index R14-18106_kapa-NGv3-PE100-NGv3-3_31617887_47127804.vcf.gz
[2016-04-15T00:46Z] tabix index R14-18106_kapa-NGv3-PE100-NGv3-3_112188604_127703121.vcf.gz
[2016-04-15T00:46Z] platypus variant calling
[2016-04-15T00:46Z] tabix index R14-18106_kapa-NGv3-PE100-NGv3-3_127770401_143293035.vcf.gz
[2016-04-15T00:46Z] platypus variant calling
[2016-04-15T00:46Z] tabix index R14-18106_kapa-NGv3-PE100-NGv3-4_36069528_52709433.vcf.gz
[2016-04-15T00:46Z] platypus variant calling
[2016-04-15T00:46Z] platypus variant calling
[2016-04-15T00:46Z] tabix index R14-18106_kapa-NGv3-PE100-NGv3-3_174814579_190326970.vcf.gz
[2016-04-15T00:46Z] platypus variant calling
[2016-04-15T00:46Z] tabix index R14-18106_kapa-NGv3-PE100-NGv3-4_99397339_115544957.vcf.gz
[2016-04-15T00:46Z] platypus variant calling
[2016-04-15T00:46Z] tabix index R14-18106_kapa-NGv3-PE100-NGv3-5_15616091_31267808.vcf.gz
[2016-04-15T00:46Z] platypus variant calling
[2016-04-15T00:46Z] tabix index R14-18106_kapa-NGv3-PE100-NGv3-4_165889318_183245405.vcf.gz
[2016-04-15T00:46Z] tabix index R14-18106_kapa-NGv3-PE100-NGv3-4_134075461_150351181.vcf.gz
[2016-04-15T00:46Z] platypus variant calling
[2016-04-15T00:46Z] tabix index R14-18106_kapa-NGv3-PE100-NGv3-4_68340604_83852298.vcf.gz
[2016-04-15T00:46Z] platypus variant calling
[2016-04-15T00:46Z] platypus variant calling
[2016-04-15T00:46Z] tabix index R14-18106_kapa-NGv3-PE100-NGv3-4_150354547_165878648.vcf.gz
[2016-04-15T00:46Z] tabix index R14-18106_kapa-NGv3-PE100-NGv3-4_115584857_134074404.vcf.gz
[2016-04-15T00:46Z] tabix index R14-18106_kapa-NGv3-PE100-NGv3-4_183267803_191154276.vcf.gz
[2016-04-15T00:46Z] platypus variant calling
[2016-04-15T00:46Z] platypus variant calling
[2016-04-15T00:46Z] platypus variant calling
[2016-04-15T00:46Z] tabix index R14-18106_kapa-NGv3-PE100-NGv3-5_96432513_112043579.vcf.gz
[2016-04-15T00:46Z] platypus variant calling
[2016-04-15T00:46Z] tabix index R14-18106_kapa-NGv3-PE100-NGv3-5_0_15580921.vcf.gz
[2016-04-15T00:46Z] INFO  17:46:56,467 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.048103456
[2016-04-15T00:46Z] INFO  17:46:56,468 PairHMM - Total compute time in PairHMM computeLikelihoods() : 3.4459883390000003
[2016-04-15T00:46Z] INFO  17:46:56,468 HaplotypeCaller - Ran local assembly on 4453 active regions
[2016-04-15T00:46Z] INFO  17:46:56,529 ProgressMeter -            done     7.46649334E8     2.5 m            0.0 s      100.0%     2.5 m       0.0 s
[2016-04-15T00:46Z] INFO  17:46:56,529 ProgressMeter - Total runtime 147.22 secs, 2.45 min, 0.04 hours
[2016-04-15T00:46Z] INFO  17:46:56,530 MicroScheduler - 109966 reads were filtered out during the traversal out of approximately 1086516 total reads (10.12%)
[2016-04-15T00:46Z] INFO  17:46:56,530 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:46Z] INFO  17:46:56,531 MicroScheduler -   -> 82047 reads (7.55% of total) failing DuplicateReadFilter
[2016-04-15T00:46Z] INFO  17:46:56,531 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:46Z] INFO  17:46:56,531 MicroScheduler -   -> 27919 reads (2.57% of total) failing HCMappingQualityFilter
[2016-04-15T00:46Z] INFO  17:46:56,531 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:46Z] INFO  17:46:56,532 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:46Z] INFO  17:46:56,532 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:46Z] INFO  17:46:56,532 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:46Z] tabix index R14-18106_kapa-NGv3-PE100-NGv3-5_49695692_65288736.vcf.gz
[2016-04-15T00:46Z] platypus variant calling
[2016-04-15T00:46Z] platypus variant calling
[2016-04-15T00:46Z] tabix index R14-18106_kapa-NGv3-PE100-NGv3-4_0_15511864.vcf.gz
[2016-04-15T00:46Z] tabix index R14-18106_kapa-NGv3-PE100-NGv3-5_80911291_96430739.vcf.gz
[2016-04-15T00:46Z] platypus variant calling
[2016-04-15T00:46Z] platypus variant calling
[2016-04-15T00:46Z] tabix index R14-18106_kapa-NGv3-PE100-NGv3-3_190333063_198022430.vcf.gz
[2016-04-15T00:46Z] tabix index R14-18106_kapa-NGv3-PE100-NGv3-5_112073555_127595521.vcf.gz
[2016-04-15T00:46Z] platypus variant calling
[2016-04-15T00:46Z] tabix index R14-18106_kapa-NGv3-PE100-NGv3-4_83857133_99393738.vcf.gz
[2016-04-15T00:46Z] platypus variant calling
[2016-04-15T00:46Z] tabix index R14-18106_kapa-NGv3-PE100-NGv3-5_31294068_49695124.vcf.gz
[2016-04-15T00:46Z] INFO  17:46:58,319 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:46Z] platypus variant calling
[2016-04-15T00:46Z] platypus variant calling
[2016-04-15T00:46Z] INFO  17:46:58,526 ProgressMeter -     19:12574810     8.12391325E8     2.5 m            0.0 s       82.4%     3.0 m      32.0 s
[2016-04-15T00:46Z] platypus variant calling
[2016-04-15T00:47Z] tabix index R14-18106_kapa-NGv3-PE100-NGv3-5_65290574_80809536.vcf.gz
[2016-04-15T00:47Z] tabix index R14-18106_kapa-NGv3-PE100-NGv3-5_158711911_174870102.vcf.gz
[2016-04-15T00:47Z] platypus variant calling
[2016-04-15T00:47Z] INFO  17:47:00,445 ProgressMeter -     19:56052695     4.90139515E8     2.5 m            0.0 s       73.7%     3.4 m      53.0 s
[2016-04-15T00:47Z] platypus variant calling
[2016-04-15T00:47Z] tabix index R14-18106_kapa-NGv3-PE100-NGv3-6_93955015_109466584.vcf.gz
[2016-04-15T00:47Z] tabix index R14-18106_kapa-NGv3-PE100-NGv3-6_0_15509601.vcf.gz
[2016-04-15T00:47Z] tabix index R14-18106_kapa-NGv3-PE100-NGv3-6_62390867_78173120.vcf.gz
[2016-04-15T00:47Z] platypus variant calling
[2016-04-15T00:47Z] platypus variant calling
[2016-04-15T00:47Z] platypus variant calling
[2016-04-15T00:47Z] tabix index R14-18106_kapa-NGv3-PE100-NGv3-6_78400388_93953258.vcf.gz
[2016-04-15T00:47Z] tabix index R14-18106_kapa-NGv3-PE100-NGv3-6_46598699_62284307.vcf.gz
[2016-04-15T00:47Z] tabix index R14-18106_kapa-NGv3-PE100-NGv3-5_143200044_158710347.vcf.gz
[2016-04-15T00:47Z] platypus variant calling
[2016-04-15T00:47Z] tabix index R14-18106_kapa-NGv3-PE100-NGv3-6_109467960_124979532.vcf.gz
[2016-04-15T00:47Z] tabix index R14-18106_kapa-NGv3-PE100-NGv3-3_47129602_62648069.vcf.gz
[2016-04-15T00:47Z] platypus variant calling
[2016-04-15T00:47Z] platypus variant calling
[2016-04-15T00:47Z] platypus variant calling
[2016-04-15T00:47Z] platypus variant calling
[2016-04-15T00:47Z] tabix index R14-18106_kapa-NGv3-PE100-NGv3-5_174919106_180915260.vcf.gz
[2016-04-15T00:47Z] platypus variant calling
[2016-04-15T00:47Z] tabix index R14-18106_kapa-NGv3-PE100-NGv3-6_125112484_142397186.vcf.gz
[2016-04-15T00:47Z] platypus variant calling
[2016-04-15T00:47Z] tabix index R14-18106_kapa-NGv3-PE100-NGv3-6_142399691_157963777.vcf.gz
[2016-04-15T00:47Z] platypus variant calling
[2016-04-15T00:47Z] tabix index R14-18106_kapa-NGv3-PE100-NGv3-7_47319761_63093154.vcf.gz
[2016-04-15T00:47Z] tabix index R14-18106_kapa-NGv3-PE100-NGv3-6_15511526_31080332.vcf.gz
[2016-04-15T00:47Z] platypus variant calling
[2016-04-15T00:47Z] platypus variant calling
[2016-04-15T00:47Z] tabix index R14-18106_kapa-NGv3-PE100-NGv3-6_158013810_171115067.vcf.gz
[2016-04-15T00:47Z] tabix index R14-18106_kapa-NGv3-PE100-NGv3-7_15599765_31117713.vcf.gz
[2016-04-15T00:47Z] platypus variant calling
[2016-04-15T00:47Z] platypus variant calling
[2016-04-15T00:47Z] tabix index R14-18106_kapa-NGv3-PE100-NGv3-7_110526648_126079222.vcf.gz
[2016-04-15T00:47Z] platypus variant calling
[2016-04-15T00:47Z] tabix index R14-18106_kapa-NGv3-PE100-NGv3-7_157155854_159138663.vcf.gz
[2016-04-15T00:47Z] platypus variant calling
[2016-04-15T00:47Z] tabix index R14-18106_kapa-NGv3-PE100-NGv3-7_79082334_94740703.vcf.gz
[2016-04-15T00:47Z] platypus variant calling
[2016-04-15T00:47Z] tabix index R14-18106_kapa-NGv3-PE100-NGv3-7_31120227_47317818.vcf.gz
[2016-04-15T00:47Z] platypus variant calling
[2016-04-15T00:47Z] tabix index R14-18106_kapa-NGv3-PE100-NGv3-7_0_15584548.vcf.gz
[2016-04-15T00:47Z] platypus variant calling
[2016-04-15T00:47Z] tabix index R14-18106_kapa-NGv3-PE100-NGv3-7_63095909_78636522.vcf.gz
[2016-04-15T00:47Z] platypus variant calling
[2016-04-15T00:47Z] tabix index R14-18106_kapa-NGv3-PE100-NGv3-8_79513976_95140568.vcf.gz
[2016-04-15T00:47Z] tabix index R14-18106_kapa-NGv3-PE100-NGv3-8_48003022_63659688.vcf.gz
[2016-04-15T00:47Z] tabix index R14-18106_kapa-NGv3-PE100-NGv3-8_63775819_79510770.vcf.gz
[2016-04-15T00:47Z] platypus variant calling
[2016-04-15T00:47Z] tabix index R14-18106_kapa-NGv3-PE100-NGv3-8_0_15517156.vcf.gz
[2016-04-15T00:47Z] platypus variant calling
[2016-04-15T00:47Z] platypus variant calling
[2016-04-15T00:47Z] tabix index R14-18106_kapa-NGv3-PE100-NGv3-8_31496910_48001429.vcf.gz
[2016-04-15T00:47Z] tabix index R14-18106_kapa-NGv3-PE100-NGv3-5_127597427_143191869.vcf.gz
[2016-04-15T00:47Z] platypus variant calling
[2016-04-15T00:47Z] platypus variant calling
[2016-04-15T00:47Z] platypus variant calling
[2016-04-15T00:47Z] tabix index R14-18106_kapa-NGv3-PE100-NGv3-8_110656864_126194498.vcf.gz
[2016-04-15T00:47Z] tabix index R14-18106_kapa-NGv3-PE100-NGv3-8_126369460_141889736.vcf.gz
[2016-04-15T00:47Z] platypus variant calling
[2016-04-15T00:47Z] platypus variant calling
[2016-04-15T00:47Z] tabix index R14-18106_kapa-NGv3-PE100-NGv3-7_126086124_141619620.vcf.gz
[2016-04-15T00:47Z] tabix index R14-18106_kapa-NGv3-PE100-NGv3-8_95142853_110655419.vcf.gz
[2016-04-15T00:47Z] platypus variant calling
[2016-04-15T00:47Z] platypus variant calling
[2016-04-15T00:47Z] tabix index R14-18106_kapa-NGv3-PE100-NGv3-9_15564086_32405601.vcf.gz
[2016-04-15T00:47Z] platypus variant calling
[2016-04-15T00:47Z] tabix index R14-18106_kapa-NGv3-PE100-NGv3-8_15519664_31030618.vcf.gz
[2016-04-15T00:47Z] platypus variant calling
[2016-04-15T00:47Z] tabix index R14-18106_kapa-NGv3-PE100-NGv3-9_0_15510186.vcf.gz
[2016-04-15T00:47Z] tabix index R14-18106_kapa-NGv3-PE100-NGv3-9_65507205_82187750.vcf.gz
[2016-04-15T00:47Z] platypus variant calling
[2016-04-15T00:47Z] platypus variant calling
[2016-04-15T00:47Z] tabix index R14-18106_kapa-NGv3-PE100-NGv3-7_141629903_157151331.vcf.gz
[2016-04-15T00:47Z] platypus variant calling
[2016-04-15T00:47Z] tabix index R14-18106_kapa-NGv3-PE100-NGv3-9_82188172_97717561.vcf.gz
[2016-04-15T00:47Z] platypus variant calling
[2016-04-15T00:47Z] tabix index R14-18106_kapa-NGv3-PE100-NGv3-10_31137459_46960129.vcf.gz
[2016-04-15T00:47Z] platypus variant calling
[2016-04-15T00:47Z] tabix index R14-18106_kapa-NGv3-PE100-NGv3-10_0_15559243.vcf.gz
[2016-04-15T00:47Z] tabix index R14-18106_kapa-NGv3-PE100-NGv3-9_97718189_113228306.vcf.gz
[2016-04-15T00:47Z] tabix index R14-18106_kapa-NGv3-PE100-NGv3-10_15561288_31134502.vcf.gz
[2016-04-15T00:47Z] INFO  17:47:21,350 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.061971112
[2016-04-15T00:47Z] INFO  17:47:21,351 PairHMM - Total compute time in PairHMM computeLikelihoods() : 7.009233845000001
[2016-04-15T00:47Z] INFO  17:47:21,351 HaplotypeCaller - Ran local assembly on 5976 active regions
[2016-04-15T00:47Z] platypus variant calling
[2016-04-15T00:47Z] INFO  17:47:21,395 ProgressMeter -            done    1.217430493E9     2.9 m            0.0 s      100.0%     2.9 m       0.0 s
[2016-04-15T00:47Z] INFO  17:47:21,395 ProgressMeter - Total runtime 172.88 secs, 2.88 min, 0.05 hours
[2016-04-15T00:47Z] INFO  17:47:21,396 MicroScheduler - 114307 reads were filtered out during the traversal out of approximately 1353253 total reads (8.45%)
[2016-04-15T00:47Z] INFO  17:47:21,396 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:47Z] INFO  17:47:21,396 MicroScheduler -   -> 102765 reads (7.59% of total) failing DuplicateReadFilter
[2016-04-15T00:47Z] INFO  17:47:21,396 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:47Z] INFO  17:47:21,396 MicroScheduler -   -> 11542 reads (0.85% of total) failing HCMappingQualityFilter
[2016-04-15T00:47Z] INFO  17:47:21,397 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:47Z] INFO  17:47:21,397 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:47Z] INFO  17:47:21,397 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:47Z] INFO  17:47:21,397 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:47Z] platypus variant calling
[2016-04-15T00:47Z] platypus variant calling
[2016-04-15T00:47Z] INFO  17:47:22,673 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:47Z] tabix index R14-18106_kapa-NGv3-PE100-NGv3-9_113231219_129089575.vcf.gz
[2016-04-15T00:47Z] platypus variant calling
[2016-04-15T00:47Z] tabix index R14-18106_kapa-NGv3-PE100-NGv3-9_32407258_65506776.vcf.gz
[2016-04-15T00:47Z] platypus variant calling
[2016-04-15T00:47Z] tabix index R14-18106_kapa-NGv3-PE100-NGv3-10_46960410_62493077.vcf.gz
[2016-04-15T00:47Z] platypus variant calling
[2016-04-15T00:47Z] platypus variant calling
[2016-04-15T00:47Z] tabix index R14-18106_kapa-NGv3-PE100-NGv3-8_141900641_146364022.vcf.gz
[2016-04-15T00:47Z] platypus variant calling
[2016-04-15T00:47Z] tabix index R14-18106_kapa-NGv3-PE100-NGv3-10_78316966_93841258.vcf.gz
[2016-04-15T00:47Z] platypus variant calling
[2016-04-15T00:47Z] tabix index R14-18106_kapa-NGv3-PE100-NGv3-6_31083801_46593245.vcf.gz
[2016-04-15T00:47Z] tabix index R14-18106_kapa-NGv3-PE100-NGv3-7_94750023_110303777.vcf.gz
[2016-04-15T00:47Z] platypus variant calling
[2016-04-15T00:47Z] platypus variant calling
[2016-04-15T00:47Z] tabix index R14-18106_kapa-NGv3-PE100-NGv3-10_127328721_135534747.vcf.gz
[2016-04-15T00:47Z] platypus variant calling
[2016-04-15T00:47Z] tabix index R14-18106_kapa-NGv3-PE100-NGv3-11_16007749_31531554.vcf.gz
[2016-04-15T00:47Z] tabix index R14-18106_kapa-NGv3-PE100-NGv3-10_62539923_78084243.vcf.gz
[2016-04-15T00:47Z] platypus variant calling
[2016-04-15T00:47Z] platypus variant calling
[2016-04-15T00:47Z] tabix index R14-18106_kapa-NGv3-PE100-NGv3-11_78277177_93796886.vcf.gz
[2016-04-15T00:47Z] platypus variant calling
[2016-04-15T00:47Z] tabix index R14-18106_kapa-NGv3-PE100-NGv3-11_93797496_109964158.vcf.gz
[2016-04-15T00:47Z] tabix index R14-18106_kapa-NGv3-PE100-NGv3-11_31541602_47074069.vcf.gz
[2016-04-15T00:47Z] tabix index R14-18106_kapa-NGv3-PE100-NGv3-10_111628371_127265443.vcf.gz
[2016-04-15T00:47Z] platypus variant calling
[2016-04-15T00:47Z] platypus variant calling
[2016-04-15T00:47Z] platypus variant calling
[2016-04-15T00:47Z] tabix index R14-18106_kapa-NGv3-PE100-NGv3-11_125523640_135006516.vcf.gz
[2016-04-15T00:47Z] INFO  17:47:30,446 ProgressMeter -     19:58620240     7.04901185E8     3.0 m            0.0 s       94.9%     3.2 m       9.0 s
[2016-04-15T00:47Z] platypus variant calling
[2016-04-15T00:47Z] tabix index R14-18106_kapa-NGv3-PE100-NGv3-12_15650178_31231471.vcf.gz
[2016-04-15T00:47Z] platypus variant calling
[2016-04-15T00:47Z] tabix index R14-18106_kapa-NGv3-PE100-NGv3-13_0_19748299.vcf.gz
[2016-04-15T00:47Z] platypus variant calling
[2016-04-15T00:47Z] tabix index R14-18106_kapa-NGv3-PE100-NGv3-12_78334098_93863131.vcf.gz
[2016-04-15T00:47Z] tabix index R14-18106_kapa-NGv3-PE100-NGv3-12_62687959_78225484.vcf.gz
[2016-04-15T00:47Z] platypus variant calling
[2016-04-15T00:47Z] platypus variant calling
[2016-04-15T00:47Z] tabix index R14-18106_kapa-NGv3-PE100-NGv3-10_93851586_111625070.vcf.gz
[2016-04-15T00:47Z] platypus variant calling
[2016-04-15T00:47Z] tabix index R14-18106_kapa-NGv3-PE100-NGv3-13_51396767_67205543.vcf.gz
[2016-04-15T00:47Z] platypus variant calling
[2016-04-15T00:47Z] tabix index R14-18106_kapa-NGv3-PE100-NGv3-12_125267228_133851895.vcf.gz
[2016-04-15T00:47Z] platypus variant calling
[2016-04-15T00:47Z] tabix index R14-18106_kapa-NGv3-PE100-NGv3-13_67477635_84455642.vcf.gz
[2016-04-15T00:47Z] platypus variant calling
[2016-04-15T00:47Z] tabix index R14-18106_kapa-NGv3-PE100-NGv3-12_31236746_46754992.vcf.gz
[2016-04-15T00:47Z] tabix index R14-18106_kapa-NGv3-PE100-NGv3-12_93870729_109490566.vcf.gz
[2016-04-15T00:47Z] platypus variant calling
[2016-04-15T00:47Z] tabix index R14-18106_kapa-NGv3-PE100-NGv3-14_0_19378574.vcf.gz
[2016-04-15T00:47Z] platypus variant calling
[2016-04-15T00:47Z] platypus variant calling
[2016-04-15T00:47Z] tabix index R14-18106_kapa-NGv3-PE100-NGv3-11_47158866_62678572.vcf.gz
[2016-04-15T00:47Z] platypus variant calling
[2016-04-15T00:47Z] tabix index R14-18106_kapa-NGv3-PE100-NGv3-11_110001730_125514538.vcf.gz
[2016-04-15T00:47Z] tabix index R14-18106_kapa-NGv3-PE100-NGv3-13_19751066_35517251.vcf.gz
[2016-04-15T00:47Z] tabix index R14-18106_kapa-NGv3-PE100-NGv3-13_86368117_101881935.vcf.gz
[2016-04-15T00:47Z] platypus variant calling
[2016-04-15T00:47Z] platypus variant calling
[2016-04-15T00:47Z] INFO  17:47:38,339 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.086635074
[2016-04-15T00:47Z] INFO  17:47:38,340 PairHMM - Total compute time in PairHMM computeLikelihoods() : 17.717478099
[2016-04-15T00:47Z] INFO  17:47:38,340 HaplotypeCaller - Ran local assembly on 5007 active regions
[2016-04-15T00:47Z] tabix index R14-18106_kapa-NGv3-PE100-NGv3-13_35615069_51287376.vcf.gz
[2016-04-15T00:47Z] INFO  17:47:38,384 ProgressMeter -            done      7.6177958E8     3.1 m            0.0 s      100.0%     3.1 m       0.0 s
[2016-04-15T00:47Z] INFO  17:47:38,385 ProgressMeter - Total runtime 187.96 secs, 3.13 min, 0.05 hours
[2016-04-15T00:47Z] INFO  17:47:38,385 MicroScheduler - 131030 reads were filtered out during the traversal out of approximately 1196576 total reads (10.95%)
[2016-04-15T00:47Z] INFO  17:47:38,385 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:47Z] INFO  17:47:38,386 MicroScheduler -   -> 88942 reads (7.43% of total) failing DuplicateReadFilter
[2016-04-15T00:47Z] INFO  17:47:38,386 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:47Z] INFO  17:47:38,386 MicroScheduler -   -> 42088 reads (3.52% of total) failing HCMappingQualityFilter
[2016-04-15T00:47Z] INFO  17:47:38,387 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:47Z] INFO  17:47:38,387 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:47Z] INFO  17:47:38,387 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:47Z] INFO  17:47:38,388 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:47Z] platypus variant calling
[2016-04-15T00:47Z] platypus variant calling
[2016-04-15T00:47Z] tabix index R14-18106_kapa-NGv3-PE100-NGv3-15_0_20740485.vcf.gz
[2016-04-15T00:47Z] platypus variant calling
[2016-04-15T00:47Z] tabix index R14-18106_kapa-NGv3-PE100-NGv3-9_129097484_141213431.vcf.gz
[2016-04-15T00:47Z] INFO  17:47:39,763 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:47Z] platypus variant calling
[2016-04-15T00:47Z] tabix index R14-18106_kapa-NGv3-PE100-NGv3-14_35072553_50583270.vcf.gz
[2016-04-15T00:47Z] platypus variant calling
[2016-04-15T00:47Z] platypus variant calling
[2016-04-15T00:47Z] tabix index R14-18106_kapa-NGv3-PE100-NGv3-12_0_15637181.vcf.gz
[2016-04-15T00:47Z] platypus variant calling
[2016-04-15T00:47Z] tabix index R14-18106_kapa-NGv3-PE100-NGv3-13_101890105_115169878.vcf.gz
[2016-04-15T00:47Z] platypus variant calling
[2016-04-15T00:47Z] tabix index R14-18106_kapa-NGv3-PE100-NGv3-15_98984299_102531392.vcf.gz
[2016-04-15T00:47Z] platypus variant calling
[2016-04-15T00:47Z] tabix index R14-18106_kapa-NGv3-PE100-NGv3-14_81651874_97299968.vcf.gz
[2016-04-15T00:47Z] tabix index R14-18106_kapa-NGv3-PE100-NGv3-14_50585061_66096324.vcf.gz
[2016-04-15T00:47Z] platypus variant calling
[2016-04-15T00:47Z] platypus variant calling
[2016-04-15T00:47Z] tabix index R14-18106_kapa-NGv3-PE100-NGv3-12_109494486_125263132.vcf.gz
[2016-04-15T00:47Z] platypus variant calling
[2016-04-15T00:47Z] tabix index R14-18106_kapa-NGv3-PE100-NGv3-14_66135960_81646674.vcf.gz
[2016-04-15T00:47Z] tabix index R14-18106_kapa-NGv3-PE100-NGv3-16_31120544_46629582.vcf.gz
[2016-04-15T00:47Z] platypus variant calling
[2016-04-15T00:47Z] tabix index R14-18106_kapa-NGv3-PE100-NGv3-11_0_15994658.vcf.gz
[2016-04-15T00:47Z] tabix index R14-18106_kapa-NGv3-PE100-NGv3-15_20741621_36872162.vcf.gz
[2016-04-15T00:47Z] platypus variant calling
[2016-04-15T00:47Z] platypus variant calling
[2016-04-15T00:47Z] platypus variant calling
[2016-04-15T00:47Z] tabix index R14-18106_kapa-NGv3-PE100-NGv3-14_97304098_107349540.vcf.gz
[2016-04-15T00:47Z] platypus variant calling
[2016-04-15T00:47Z] tabix index R14-18106_kapa-NGv3-PE100-NGv3-15_83448996_98982979.vcf.gz
[2016-04-15T00:47Z] platypus variant calling
[2016-04-15T00:47Z] tabix index R14-18106_kapa-NGv3-PE100-NGv3-11_62744265_78270665.vcf.gz
[2016-04-15T00:47Z] tabix index R14-18106_kapa-NGv3-PE100-NGv3-15_52404364_67923265.vcf.gz
[2016-04-15T00:47Z] platypus variant calling
[2016-04-15T00:47Z] platypus variant calling
[2016-04-15T00:47Z] tabix index R14-18106_kapa-NGv3-PE100-NGv3-14_19553416_35066851.vcf.gz
[2016-04-15T00:47Z] platypus variant calling
[2016-04-15T00:47Z] tabix index R14-18106_kapa-NGv3-PE100-NGv3-15_67932890_83447639.vcf.gz
[2016-04-15T00:47Z] platypus variant calling
[2016-04-15T00:47Z] tabix index R14-18106_kapa-NGv3-PE100-NGv3-16_46633742_64982002.vcf.gz
[2016-04-15T00:47Z] platypus variant calling
[2016-04-15T00:47Z] tabix index R14-18106_kapa-NGv3-PE100-NGv3-18_0_18531348.vcf.gz
[2016-04-15T00:47Z] platypus variant calling
[2016-04-15T00:47Z] tabix index R14-18106_kapa-NGv3-PE100-NGv3-12_46756066_62654284.vcf.gz
[2016-04-15T00:47Z] platypus variant calling
[2016-04-15T00:47Z] tabix index R14-18106_kapa-NGv3-PE100-NGv3-15_36887086_52402170.vcf.gz
[2016-04-15T00:47Z] platypus variant calling
[2016-04-15T00:47Z] tabix index R14-18106_kapa-NGv3-PE100-NGv3-16_80575258_90354753.vcf.gz
[2016-04-15T00:47Z] platypus variant calling
[2016-04-15T00:47Z] tabix index R14-18106_kapa-NGv3-PE100-NGv3-18_34092400_49867248.vcf.gz
[2016-04-15T00:47Z] platypus variant calling
[2016-04-15T00:47Z] tabix index R14-18106_kapa-NGv3-PE100-NGv3-18_18533538_34081962.vcf.gz
[2016-04-15T00:47Z] tabix index R14-18106_kapa-NGv3-PE100-NGv3-18_66346699_78077248.vcf.gz
[2016-04-15T00:47Z] platypus variant calling
[2016-04-15T00:47Z] tabix index R14-18106_kapa-NGv3-PE100-NGv3-17_77707305_81195210.vcf.gz
[2016-04-15T00:47Z] tabix index R14-18106_kapa-NGv3-PE100-NGv3-18_50278423_66344430.vcf.gz
[2016-04-15T00:47Z] platypus variant calling
[2016-04-15T00:47Z] platypus variant calling
[2016-04-15T00:47Z] platypus variant calling
[2016-04-15T00:48Z] tabix index R14-18106_kapa-NGv3-PE100-NGv3-17_46607689_62121560.vcf.gz
[2016-04-15T00:48Z] platypus variant calling
[2016-04-15T00:48Z] tabix index R14-18106_kapa-NGv3-PE100-NGv3-20_62831244_63025520.vcf.gz
[2016-04-15T00:48Z] tabix index R14-18106_kapa-NGv3-PE100-NGv3-16_64982511_80574976.vcf.gz
[2016-04-15T00:48Z] platypus variant calling
[2016-04-15T00:48Z] platypus variant calling
[2016-04-15T00:48Z] tabix index R14-18106_kapa-NGv3-PE100-NGv3-16_15596122_31106473.vcf.gz
[2016-04-15T00:48Z] tabix index R14-18106_kapa-NGv3-PE100-NGv3-21_0_15517120.vcf.gz
[2016-04-15T00:48Z] platypus variant calling
[2016-04-15T00:48Z] platypus variant calling
[2016-04-15T00:48Z] tabix index R14-18106_kapa-NGv3-PE100-NGv3-17_15515955_31039213.vcf.gz
[2016-04-15T00:48Z] platypus variant calling
[2016-04-15T00:48Z] tabix index R14-18106_kapa-NGv3-PE100-NGv3-22_0_16258303.vcf.gz
[2016-04-15T00:48Z] tabix index R14-18106_kapa-NGv3-PE100-NGv3-21_15524893_31045484.vcf.gz
[2016-04-15T00:48Z] platypus variant calling
[2016-04-15T00:48Z] platypus variant calling
[2016-04-15T00:48Z] tabix index R14-18106_kapa-NGv3-PE100-NGv3-20_15866408_31376818.vcf.gz
[2016-04-15T00:48Z] tabix index R14-18106_kapa-NGv3-PE100-NGv3-16_0_15528616.vcf.gz
[2016-04-15T00:48Z] platypus variant calling
[2016-04-15T00:48Z] platypus variant calling
[2016-04-15T00:48Z] tabix index R14-18106_kapa-NGv3-PE100-NGv3-20_0_15843471.vcf.gz
[2016-04-15T00:48Z] tabix index R14-18106_kapa-NGv3-PE100-NGv3-17_62122219_77705154.vcf.gz
[2016-04-15T00:48Z] platypus variant calling
[2016-04-15T00:48Z] platypus variant calling
[2016-04-15T00:48Z] tabix index R14-18106_kapa-NGv3-PE100-NGv3-21_46595644_48129895.vcf.gz
[2016-04-15T00:48Z] platypus variant calling
[2016-04-15T00:48Z] tabix index R14-18106_kapa-NGv3-PE100-NGv3-X_31139949_46696637.vcf.gz
[2016-04-15T00:48Z] tabix index R14-18106_kapa-NGv3-PE100-NGv3-X_0_15509380.vcf.gz
[2016-04-15T00:48Z] platypus variant calling
[2016-04-15T00:48Z] platypus variant calling
[2016-04-15T00:48Z] tabix index R14-18106_kapa-NGv3-PE100-NGv3-X_15518899_31090070.vcf.gz
[2016-04-15T00:48Z] platypus variant calling
[2016-04-15T00:48Z] tabix index R14-18106_kapa-NGv3-PE100-NGv3-19_15510112_31025906.vcf.gz
[2016-04-15T00:48Z] tabix index R14-18106_kapa-NGv3-PE100-NGv3-X_78616585_95940189.vcf.gz
[2016-04-15T00:48Z] platypus variant calling
[2016-04-15T00:48Z] platypus variant calling
[2016-04-15T00:48Z] tabix index R14-18106_kapa-NGv3-PE100-NGv3-22_47309229_51304566.vcf.gz
[2016-04-15T00:48Z] tabix index R14-18106_kapa-NGv3-PE100-NGv3-20_47244085_62830269.vcf.gz
[2016-04-15T00:48Z] platypus variant calling
[2016-04-15T00:48Z] platypus variant calling
[2016-04-15T00:48Z] tabix index R14-18106_kapa-NGv3-PE100-NGv3-X_111874647_128581278.vcf.gz
[2016-04-15T00:48Z] tabix index R14-18106_kapa-NGv3-PE100-NGv3-20_31379406_47242465.vcf.gz
[2016-04-15T00:48Z] tabix index R14-18106_kapa-NGv3-PE100-NGv3-17_0_15511002.vcf.gz
[2016-04-15T00:48Z] platypus variant calling
[2016-04-15T00:48Z] platypus variant calling
[2016-04-15T00:48Z] tabix index R14-18106_kapa-NGv3-PE100-NGv3-Y_0_15522993.vcf.gz
[2016-04-15T00:48Z] GATK: UnifiedGenotyper
[2016-04-15T00:48Z] tabix index R14-18106_kapa-NGv3-PE100-NGv3-Y_59228291_59373566.vcf.gz
[2016-04-15T00:48Z] GATK: UnifiedGenotyper
[2016-04-15T00:48Z] GATK: UnifiedGenotyper
[2016-04-15T00:48Z] tabix index R14-18106_kapa-NGv3-PE100-NGv3-X_62857907_78427545.vcf.gz
[2016-04-15T00:48Z] tabix index R14-18106_kapa-NGv3-PE100-NGv3-X_128582278_144329181.vcf.gz
[2016-04-15T00:48Z] tabix index R14-18106_kapa-NGv3-PE100-NGv3-X_46712910_62570698.vcf.gz
[2016-04-15T00:48Z] GATK: UnifiedGenotyper
[2016-04-15T00:48Z] GATK: UnifiedGenotyper
[2016-04-15T00:48Z] tabix index R14-18106_kapa-NGv3-PE100-NGv3-X_95990756_111698889.vcf.gz
[2016-04-15T00:48Z] GATK: UnifiedGenotyper
[2016-04-15T00:48Z] tabix index R14-18106_kapa-NGv3-PE100-NGv3-17_31048040_46607237.vcf.gz
[2016-04-15T00:48Z] GATK: UnifiedGenotyper
[2016-04-15T00:48Z] tabix index R14-18106_kapa-NGv3-PE100-NGv3-Y_15526614_59222281.vcf.gz
[2016-04-15T00:48Z] GATK: UnifiedGenotyper
[2016-04-15T00:48Z] GATK: UnifiedGenotyper
[2016-04-15T00:48Z] tabix index R14-18106_kapa-NGv3-PE100-NGv3-21_31062047_46591599.vcf.gz
[2016-04-15T00:48Z] GATK: UnifiedGenotyper
[2016-04-15T00:48Z] INFO  17:48:16,827 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:48Z] INFO  17:48:16,842 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:48Z] INFO  17:48:16,843 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:48Z] INFO  17:48:16,844 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:48Z] INFO  17:48:16,849 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/1/R14-18105_kapa-NGv3-PE100-NGv3-sort-1_46715671_62228851-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/1/R14-18105_kapa-NGv3-PE100-NGv3-1_46715671_62228851-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/1/tx/tmp0o65Fw/R14-18105_kapa-NGv3-PE100-NGv3-1_46715671_62228851.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:48Z] INFO  17:48:16,874 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:48Z] INFO  17:48:16,875 HelpFormatter - Date/Time: 2016/04/14 17:48:16
[2016-04-15T00:48Z] INFO  17:48:16,876 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:48Z] INFO  17:48:16,877 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:48Z] INFO  17:48:16,965 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:48Z] INFO  17:48:16,968 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:48Z] INFO  17:48:16,968 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:48Z] INFO  17:48:16,969 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:48Z] INFO  17:48:16,973 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/1/R14-18105_kapa-NGv3-PE100-NGv3-sort-1_77752625_93297674-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/1/R14-18105_kapa-NGv3-PE100-NGv3-1_77752625_93297674-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/1/tx/tmpp2Z93H/R14-18105_kapa-NGv3-PE100-NGv3-1_77752625_93297674.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:48Z] INFO  17:48:17,003 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:48Z] INFO  17:48:17,011 HelpFormatter - Date/Time: 2016/04/14 17:48:16
[2016-04-15T00:48Z] INFO  17:48:17,012 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:48Z] INFO  17:48:17,012 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:48Z] tabix index R14-18106_kapa-NGv3-PE100-NGv3-X_144337190_155270560.vcf.gz
[2016-04-15T00:48Z] INFO  17:48:17,092 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:48Z] INFO  17:48:17,108 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:48Z] INFO  17:48:17,109 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:48Z] INFO  17:48:17,110 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:48Z] INFO  17:48:17,115 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/1/R14-18105_kapa-NGv3-PE100-NGv3-sort-1_62231950_77749296-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/1/R14-18105_kapa-NGv3-PE100-NGv3-1_62231950_77749296-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/1/tx/tmpgaylSe/R14-18105_kapa-NGv3-PE100-NGv3-1_62231950_77749296.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:48Z] INFO  17:48:17,131 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:48Z] INFO  17:48:17,132 HelpFormatter - Date/Time: 2016/04/14 17:48:17
[2016-04-15T00:48Z] INFO  17:48:17,133 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:48Z] INFO  17:48:17,133 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:48Z] INFO  17:48:17,200 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:48Z] INFO  17:48:17,227 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:48Z] INFO  17:48:17,329 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:48Z] INFO  17:48:17,419 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:48Z] INFO  17:48:17,430 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:48Z] INFO  17:48:17,433 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:48Z] INFO  17:48:17,436 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:48Z] INFO  17:48:17,437 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:48Z] INFO  17:48:17,438 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:48Z] INFO  17:48:17,442 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/1/R14-18105_kapa-NGv3-PE100-NGv3-sort-1_31187093_46714270-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/1/R14-18105_kapa-NGv3-PE100-NGv3-1_31187093_46714270-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/1/tx/tmp6nScEY/R14-18105_kapa-NGv3-PE100-NGv3-1_31187093_46714270.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:48Z] INFO  17:48:17,462 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:48Z] INFO  17:48:17,463 HelpFormatter - Date/Time: 2016/04/14 17:48:17
[2016-04-15T00:48Z] INFO  17:48:17,464 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:48Z] INFO  17:48:17,465 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:48Z] GATK: UnifiedGenotyper
[2016-04-15T00:48Z] INFO  17:48:17,492 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-15T00:48Z] INFO  17:48:17,500 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:48Z] INFO  17:48:17,525 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:48Z] INFO  17:48:17,532 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:48Z] INFO  17:48:17,535 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:48Z] INFO  17:48:17,535 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:48Z] INFO  17:48:17,536 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:48Z] INFO  17:48:17,541 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/1/R14-18105_kapa-NGv3-PE100-NGv3-sort-1_143897546_159410511-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/1/R14-18105_kapa-NGv3-PE100-NGv3-1_143897546_159410511-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/1/tx/tmpZ97n2f/R14-18105_kapa-NGv3-PE100-NGv3-1_143897546_159410511.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:48Z] INFO  17:48:17,551 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:48Z] INFO  17:48:17,552 HelpFormatter - Date/Time: 2016/04/14 17:48:17
[2016-04-15T00:48Z] INFO  17:48:17,552 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:48Z] INFO  17:48:17,552 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:48Z] INFO  17:48:17,578 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:48Z] INFO  17:48:17,582 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:48Z] INFO  17:48:17,582 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:48Z] INFO  17:48:17,583 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:48Z] INFO  17:48:17,588 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/1/R14-18105_kapa-NGv3-PE100-NGv3-sort-1_93298945_108993401-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/1/R14-18105_kapa-NGv3-PE100-NGv3-1_93298945_108993401-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/1/tx/tmpfcxjHv/R14-18105_kapa-NGv3-PE100-NGv3-1_93298945_108993401.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:48Z] INFO  17:48:17,604 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-15T00:48Z] INFO  17:48:17,617 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:48Z] INFO  17:48:17,618 HelpFormatter - Date/Time: 2016/04/14 17:48:17
[2016-04-15T00:48Z] INFO  17:48:17,618 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:48Z] INFO  17:48:17,619 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:48Z] INFO  17:48:17,627 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:48Z] INFO  17:48:17,637 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:48Z] INFO  17:48:17,641 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:48Z] INFO  17:48:17,646 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:48Z] INFO  17:48:17,650 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:48Z] INFO  17:48:17,650 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:48Z] INFO  17:48:17,651 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:48Z] INFO  17:48:17,656 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/1/R14-18105_kapa-NGv3-PE100-NGv3-sort-1_0_15541927-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/1/R14-18105_kapa-NGv3-PE100-NGv3-1_0_15541927-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/1/tx/tmpIBPLUO/R14-18105_kapa-NGv3-PE100-NGv3-1_0_15541927.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:48Z] INFO  17:48:17,644 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:48Z] INFO  17:48:17,659 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:48Z] INFO  17:48:17,662 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:48Z] INFO  17:48:17,662 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:48Z] INFO  17:48:17,663 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:48Z] INFO  17:48:17,663 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:48Z] INFO  17:48:17,663 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:48Z] INFO  17:48:17,668 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/1/R14-18105_kapa-NGv3-PE100-NGv3-sort-1_108994811_143767848-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/1/R14-18105_kapa-NGv3-PE100-NGv3-1_108994811_143767848-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/1/tx/tmpImANzJ/R14-18105_kapa-NGv3-PE100-NGv3-1_108994811_143767848.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:48Z] INFO  17:48:17,675 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/1/R14-18105_kapa-NGv3-PE100-NGv3-sort-1_15545821_31186478-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/1/R14-18105_kapa-NGv3-PE100-NGv3-1_15545821_31186478-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/1/tx/tmp5ZuNSh/R14-18105_kapa-NGv3-PE100-NGv3-1_15545821_31186478.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:48Z] INFO  17:48:17,680 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:48Z] INFO  17:48:17,681 HelpFormatter - Date/Time: 2016/04/14 17:48:17
[2016-04-15T00:48Z] INFO  17:48:17,682 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:48Z] INFO  17:48:17,682 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:48Z] INFO  17:48:17,693 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:48Z] INFO  17:48:17,697 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:48Z] INFO  17:48:17,697 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-15T00:48Z] INFO  17:48:17,700 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:48Z] INFO  17:48:17,700 HelpFormatter - Date/Time: 2016/04/14 17:48:17
[2016-04-15T00:48Z] INFO  17:48:17,700 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:48Z] INFO  17:48:17,700 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:48Z] INFO  17:48:17,703 HelpFormatter - Date/Time: 2016/04/14 17:48:17
[2016-04-15T00:48Z] INFO  17:48:17,704 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:48Z] INFO  17:48:17,708 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:48Z] INFO  17:48:17,768 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:48Z] INFO  17:48:17,800 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:48Z] INFO  17:48:17,863 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:48Z] INFO  17:48:17,885 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:48Z] INFO  17:48:17,910 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:48Z] INFO  17:48:17,907 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:48Z] INFO  17:48:17,920 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:48Z] INFO  17:48:17,954 IntervalUtils - Processing 145368 bp from intervals
[2016-04-15T00:48Z] WARN  17:48:17,959 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:48Z] INFO  17:48:17,998 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-15T00:48Z] INFO  17:48:18,031 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:48Z] INFO  17:48:18,046 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:48Z] INFO  17:48:18,060 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:48Z] INFO  17:48:18,069 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:48Z] INFO  17:48:18,090 IntervalUtils - Processing 180557 bp from intervals
[2016-04-15T00:48Z] WARN  17:48:18,096 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:48Z] INFO  17:48:18,098 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:48Z] INFO  17:48:18,122 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:48Z] INFO  17:48:18,131 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:48Z] INFO  17:48:18,132 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-15T00:48Z] INFO  17:48:18,139 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.09
[2016-04-15T00:48Z] INFO  17:48:18,153 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:48Z] INFO  17:48:18,162 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:48Z] INFO  17:48:18,199 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:48Z] INFO  17:48:18,206 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:48Z] INFO  17:48:18,207 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:48Z] INFO  17:48:18,208 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:48Z] INFO  17:48:18,209 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:48Z] INFO  17:48:18,219 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.09
[2016-04-15T00:48Z] INFO  17:48:18,230 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:48Z] INFO  17:48:18,249 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:48Z] INFO  17:48:18,254 IntervalUtils - Processing 150085 bp from intervals
[2016-04-15T00:48Z] INFO  17:48:18,254 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.09
[2016-04-15T00:48Z] INFO  17:48:18,255 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:48Z] INFO  17:48:18,256 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:48Z] WARN  17:48:18,267 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:48Z] INFO  17:48:18,321 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:48Z] INFO  17:48:18,322 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:48Z] INFO  17:48:18,322 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:48Z] INFO  17:48:18,323 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:48Z] INFO  17:48:18,327 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-15T00:48Z] INFO  17:48:18,391 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:48Z] INFO  17:48:18,401 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:48Z] INFO  17:48:18,428 IntervalUtils - Processing 431182 bp from intervals
[2016-04-15T00:48Z] WARN  17:48:18,433 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:48Z] INFO  17:48:18,477 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:48Z] INFO  17:48:18,481 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:48Z] INFO  17:48:18,484 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:48Z] INFO  17:48:18,484 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:48Z] INFO  17:48:18,485 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:48Z] INFO  17:48:18,489 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/1/R14-18105_kapa-NGv3-PE100-NGv3-sort-1_159504867_175046963-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/1/R14-18105_kapa-NGv3-PE100-NGv3-1_159504867_175046963-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/1/tx/tmpl74iCL/R14-18105_kapa-NGv3-PE100-NGv3-1_159504867_175046963.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:48Z] INFO  17:48:18,520 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:48Z] INFO  17:48:18,521 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:48Z] INFO  17:48:18,533 HelpFormatter - Date/Time: 2016/04/14 17:48:18
[2016-04-15T00:48Z] INFO  17:48:18,534 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:48Z] INFO  17:48:18,535 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:48Z] INFO  17:48:18,633 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:48Z] INFO  17:48:18,634 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:48Z] INFO  17:48:18,634 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:48Z] INFO  17:48:18,635 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:48Z] INFO  17:48:18,645 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:48Z] INFO  17:48:18,646 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:48Z] INFO  17:48:18,647 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:48Z] INFO  17:48:18,647 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:48Z] INFO  17:48:18,687 IntervalUtils - Processing 113118 bp from intervals
[2016-04-15T00:48Z] INFO  17:48:18,691 IntervalUtils - Processing 390138 bp from intervals
[2016-04-15T00:48Z] WARN  17:48:18,692 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:48Z] WARN  17:48:18,697 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:48Z] INFO  17:48:18,703 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:48Z] INFO  17:48:18,704 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:48Z] INFO  17:48:18,705 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:48Z] INFO  17:48:18,718 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:48Z] INFO  17:48:18,729 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:48Z] INFO  17:48:18,733 IntervalUtils - Processing 517409 bp from intervals
[2016-04-15T00:48Z] WARN  17:48:18,739 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:48Z] INFO  17:48:18,769 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:48Z] INFO  17:48:18,772 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:48Z] INFO  17:48:18,777 IntervalUtils - Processing 258252 bp from intervals
[2016-04-15T00:48Z] WARN  17:48:18,782 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:48Z] INFO  17:48:18,836 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:48Z] INFO  17:48:18,839 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:48Z] INFO  17:48:18,845 IntervalUtils - Processing 386393 bp from intervals
[2016-04-15T00:48Z] INFO  17:48:18,845 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:48Z] INFO  17:48:18,846 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:48Z] INFO  17:48:18,849 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:48Z] WARN  17:48:18,850 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:48Z] INFO  17:48:18,852 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:48Z] INFO  17:48:18,886 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:48Z] INFO  17:48:18,887 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:48Z] INFO  17:48:18,890 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:48Z] INFO  17:48:18,891 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:48Z] INFO  17:48:18,891 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:48Z] INFO  17:48:18,891 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:48Z] INFO  17:48:18,892 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:48Z] INFO  17:48:18,900 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:48Z] INFO  17:48:18,933 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:48Z] INFO  17:48:18,960 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:48Z] INFO  17:48:18,961 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:48Z] INFO  17:48:18,963 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:48Z] INFO  17:48:18,964 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:48Z] INFO  17:48:18,964 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:48Z] INFO  17:48:18,965 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:48Z] INFO  17:48:18,973 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:48Z] INFO  17:48:18,974 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:48Z] INFO  17:48:18,975 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:48Z] INFO  17:48:18,975 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:48Z] INFO  17:48:18,998 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.10
[2016-04-15T00:48Z] INFO  17:48:19,030 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:48Z] INFO  17:48:19,031 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:48Z] INFO  17:48:19,034 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:48Z] INFO  17:48:19,035 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:48Z] INFO  17:48:19,077 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:48Z] INFO  17:48:19,091 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:48Z] INFO  17:48:19,092 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:48Z] INFO  17:48:19,093 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:48Z] INFO  17:48:19,133 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:48Z] INFO  17:48:19,133 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:48Z] INFO  17:48:19,427 IntervalUtils - Processing 261574 bp from intervals
[2016-04-15T00:48Z] WARN  17:48:19,432 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:48Z] INFO  17:48:19,523 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:48Z] INFO  17:48:19,645 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:48Z] INFO  17:48:19,646 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:48Z] INFO  17:48:19,648 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:48Z] tabix index R14-18106_kapa-NGv3-PE100-NGv3-22_31796605_47308085.vcf.gz
[2016-04-15T00:48Z] INFO  17:48:19,655 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:48Z] INFO  17:48:19,753 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:48Z] INFO  17:48:19,765 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:48Z] GATK: UnifiedGenotyper
[2016-04-15T00:48Z] INFO  17:48:20,394 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:48Z] INFO  17:48:20,397 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:48Z] INFO  17:48:20,398 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:48Z] INFO  17:48:20,399 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:48Z] INFO  17:48:20,404 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/1/R14-18105_kapa-NGv3-PE100-NGv3-sort-1_175048468_192127886-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/1/R14-18105_kapa-NGv3-PE100-NGv3-1_175048468_192127886-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/1/tx/tmp3WBy2T/R14-18105_kapa-NGv3-PE100-NGv3-1_175048468_192127886.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:48Z] INFO  17:48:20,419 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:48Z] INFO  17:48:20,419 HelpFormatter - Date/Time: 2016/04/14 17:48:20
[2016-04-15T00:48Z] INFO  17:48:20,419 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:48Z] INFO  17:48:20,420 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:48Z] INFO  17:48:20,747 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:48Z] INFO  17:48:21,012 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:48Z] INFO  17:48:21,020 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:48Z] INFO  17:48:21,117 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.10
[2016-04-15T00:48Z] tabix index R14-18106_kapa-NGv3-PE100-NGv3-22_16266928_31795711.vcf.gz
[2016-04-15T00:48Z] INFO  17:48:21,607 IntervalUtils - Processing 191568 bp from intervals
[2016-04-15T00:48Z] WARN  17:48:21,612 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:48Z] INFO  17:48:21,742 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:48Z] GATK: UnifiedGenotyper
[2016-04-15T00:48Z] INFO  17:48:21,910 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:48Z] INFO  17:48:21,911 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:48Z] INFO  17:48:21,912 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:48Z] INFO  17:48:21,913 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:48Z] INFO  17:48:22,011 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:48Z] INFO  17:48:22,012 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:48Z] INFO  17:48:23,406 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:48Z] INFO  17:48:23,409 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:48Z] INFO  17:48:23,410 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:48Z] INFO  17:48:23,410 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:48Z] INFO  17:48:23,414 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/1/R14-18105_kapa-NGv3-PE100-NGv3-sort-1_192128349_207640257-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/1/R14-18105_kapa-NGv3-PE100-NGv3-1_192128349_207640257-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/1/tx/tmpGImBUB/R14-18105_kapa-NGv3-PE100-NGv3-1_192128349_207640257.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:48Z] INFO  17:48:23,424 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:48Z] INFO  17:48:23,435 HelpFormatter - Date/Time: 2016/04/14 17:48:23
[2016-04-15T00:48Z] INFO  17:48:23,436 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:48Z] INFO  17:48:23,437 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:48Z] INFO  17:48:23,658 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:48Z] INFO  17:48:23,932 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:48Z] INFO  17:48:23,966 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:48Z] INFO  17:48:24,077 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.11
[2016-04-15T00:48Z] INFO  17:48:24,628 IntervalUtils - Processing 282740 bp from intervals
[2016-04-15T00:48Z] WARN  17:48:24,644 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:48Z] INFO  17:48:24,766 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:48Z] INFO  17:48:24,919 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:48Z] INFO  17:48:24,931 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:48Z] INFO  17:48:24,932 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:48Z] INFO  17:48:24,932 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:48Z] INFO  17:48:25,004 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:48Z] INFO  17:48:25,005 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:48Z] INFO  17:48:25,381 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:48Z] INFO  17:48:25,384 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:48Z] INFO  17:48:25,385 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:48Z] INFO  17:48:25,385 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:48Z] INFO  17:48:25,389 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/1/R14-18105_kapa-NGv3-PE100-NGv3-sort-1_207641871_223156451-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/1/R14-18105_kapa-NGv3-PE100-NGv3-1_207641871_223156451-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/1/tx/tmptpUEUL/R14-18105_kapa-NGv3-PE100-NGv3-1_207641871_223156451.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:48Z] INFO  17:48:25,400 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:48Z] INFO  17:48:25,412 HelpFormatter - Date/Time: 2016/04/14 17:48:25
[2016-04-15T00:48Z] INFO  17:48:25,412 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:48Z] INFO  17:48:25,413 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:48Z] INFO  17:48:25,709 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:48Z] INFO  17:48:26,041 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:48Z] INFO  17:48:26,064 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:48Z] INFO  17:48:26,195 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.13
[2016-04-15T00:48Z] INFO  17:48:26,609 IntervalUtils - Processing 175773 bp from intervals
[2016-04-15T00:48Z] WARN  17:48:26,615 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:48Z] INFO  17:48:26,727 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:48Z] INFO  17:48:26,870 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:48Z] INFO  17:48:26,871 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:48Z] INFO  17:48:26,872 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:48Z] INFO  17:48:26,872 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:48Z] INFO  17:48:26,938 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:48Z] INFO  17:48:26,939 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:48Z] tabix index R14-18106_kapa-NGv3-PE100-NGv3-19_31038849_46627578.vcf.gz
[2016-04-15T00:48Z] GATK: UnifiedGenotyper
[2016-04-15T00:48Z] INFO  17:48:31,256 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:48Z] INFO  17:48:31,259 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:48Z] INFO  17:48:31,260 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:48Z] INFO  17:48:31,260 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:48Z] INFO  17:48:31,265 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/1/R14-18105_kapa-NGv3-PE100-NGv3-sort-1_223162737_240072524-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/1/R14-18105_kapa-NGv3-PE100-NGv3-1_223162737_240072524-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/1/tx/tmp1QOXA1/R14-18105_kapa-NGv3-PE100-NGv3-1_223162737_240072524.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:48Z] INFO  17:48:31,305 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:48Z] INFO  17:48:31,305 HelpFormatter - Date/Time: 2016/04/14 17:48:31
[2016-04-15T00:48Z] INFO  17:48:31,306 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:48Z] INFO  17:48:31,306 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:48Z] INFO  17:48:31,505 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:48Z] INFO  17:48:31,756 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:48Z] INFO  17:48:31,766 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:48Z] INFO  17:48:31,847 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-15T00:48Z] INFO  17:48:32,249 IntervalUtils - Processing 294039 bp from intervals
[2016-04-15T00:48Z] WARN  17:48:32,254 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:48Z] INFO  17:48:32,320 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:48Z] INFO  17:48:32,424 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:48Z] INFO  17:48:32,424 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:48Z] INFO  17:48:32,425 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:48Z] INFO  17:48:32,425 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:48Z] INFO  17:48:32,466 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:48Z] INFO  17:48:32,467 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:48Z] tabix index R14-18106_kapa-NGv3-PE100-NGv3-19_46627881_59128983.vcf.gz
[2016-04-15T00:48Z] GATK: UnifiedGenotyper
[2016-04-15T00:48Z] INFO  17:48:35,727 ProgressMeter -            done    406382.0    17.0 s      43.0 s      100.0%    17.0 s       0.0 s
[2016-04-15T00:48Z] INFO  17:48:35,728 ProgressMeter - Total runtime 17.52 secs, 0.29 min, 0.00 hours
[2016-04-15T00:48Z] INFO  17:48:35,728 MicroScheduler - 12050 reads were filtered out during the traversal out of approximately 151459 total reads (7.96%)
[2016-04-15T00:48Z] INFO  17:48:35,729 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:48Z] INFO  17:48:35,730 MicroScheduler -   -> 234 reads (0.15% of total) failing BadMateFilter
[2016-04-15T00:48Z] INFO  17:48:35,730 MicroScheduler -   -> 11716 reads (7.74% of total) failing DuplicateReadFilter
[2016-04-15T00:48Z] INFO  17:48:35,731 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:48Z] INFO  17:48:35,731 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:48Z] INFO  17:48:35,732 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:48Z] INFO  17:48:35,733 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:48Z] INFO  17:48:35,733 MicroScheduler -   -> 100 reads (0.07% of total) failing UnmappedReadFilter
[2016-04-15T00:48Z] INFO  17:48:35,845 ProgressMeter -            done    343044.0    17.0 s      49.0 s      100.0%    17.0 s       0.0 s
[2016-04-15T00:48Z] INFO  17:48:35,846 ProgressMeter - Total runtime 17.01 secs, 0.28 min, 0.00 hours
[2016-04-15T00:48Z] INFO  17:48:35,847 MicroScheduler - 10918 reads were filtered out during the traversal out of approximately 145738 total reads (7.49%)
[2016-04-15T00:48Z] INFO  17:48:35,847 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:48Z] INFO  17:48:35,847 MicroScheduler -   -> 191 reads (0.13% of total) failing BadMateFilter
[2016-04-15T00:48Z] INFO  17:48:35,848 MicroScheduler -   -> 10634 reads (7.30% of total) failing DuplicateReadFilter
[2016-04-15T00:48Z] INFO  17:48:35,848 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:48Z] INFO  17:48:35,848 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:48Z] INFO  17:48:35,849 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:48Z] INFO  17:48:35,849 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:48Z] INFO  17:48:35,849 MicroScheduler -   -> 93 reads (0.06% of total) failing UnmappedReadFilter
[2016-04-15T00:48Z] INFO  17:48:36,177 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:48Z] INFO  17:48:36,181 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:48Z] INFO  17:48:36,182 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:48Z] INFO  17:48:36,182 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:48Z] INFO  17:48:36,188 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/1/R14-18105_kapa-NGv3-PE100-NGv3-sort-1_240255409_249250621-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/1/R14-18105_kapa-NGv3-PE100-NGv3-1_240255409_249250621-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/1/tx/tmp4v2V5L/R14-18105_kapa-NGv3-PE100-NGv3-1_240255409_249250621.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:48Z] INFO  17:48:36,209 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:48Z] INFO  17:48:36,210 HelpFormatter - Date/Time: 2016/04/14 17:48:36
[2016-04-15T00:48Z] INFO  17:48:36,211 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:48Z] INFO  17:48:36,211 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:48Z] INFO  17:48:36,387 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:48Z] INFO  17:48:36,629 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:48Z] INFO  17:48:36,640 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:48Z] INFO  17:48:36,715 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-15T00:48Z] INFO  17:48:36,860 ProgressMeter -            done    356427.0    18.0 s      51.0 s      100.0%    18.0 s       0.0 s
[2016-04-15T00:48Z] INFO  17:48:36,861 ProgressMeter - Total runtime 18.21 secs, 0.30 min, 0.01 hours
[2016-04-15T00:48Z] INFO  17:48:36,861 MicroScheduler - 13466 reads were filtered out during the traversal out of approximately 162128 total reads (8.31%)
[2016-04-15T00:48Z] INFO  17:48:36,861 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:48Z] INFO  17:48:36,862 MicroScheduler -   -> 199 reads (0.12% of total) failing BadMateFilter
[2016-04-15T00:48Z] INFO  17:48:36,862 MicroScheduler -   -> 13177 reads (8.13% of total) failing DuplicateReadFilter
[2016-04-15T00:48Z] INFO  17:48:36,862 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:48Z] INFO  17:48:36,863 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:48Z] INFO  17:48:36,863 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:48Z] INFO  17:48:36,863 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:48Z] INFO  17:48:36,863 MicroScheduler -   -> 90 reads (0.06% of total) failing UnmappedReadFilter
[2016-04-15T00:48Z] INFO  17:48:37,032 IntervalUtils - Processing 129443 bp from intervals
[2016-04-15T00:48Z] WARN  17:48:37,037 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:48Z] INFO  17:48:37,166 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:48Z] INFO  17:48:37,260 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:48Z] INFO  17:48:37,261 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:48Z] INFO  17:48:37,261 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:48Z] INFO  17:48:37,262 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:48Z] INFO  17:48:37,279 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:48Z] INFO  17:48:37,312 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:48Z] INFO  17:48:37,339 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:48Z] INFO  17:48:37,340 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:48Z] GATK: UnifiedGenotyper
[2016-04-15T00:48Z] GATK: UnifiedGenotyper
[2016-04-15T00:48Z] INFO  17:48:38,199 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:48Z] GATK: UnifiedGenotyper
[2016-04-15T00:48Z] INFO  17:48:40,717 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:48Z] INFO  17:48:40,721 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:48Z] INFO  17:48:40,722 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:48Z] INFO  17:48:40,722 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:48Z] INFO  17:48:40,728 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/2/R14-18105_kapa-NGv3-PE100-NGv3-sort-2_0_15514844-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/2/R14-18105_kapa-NGv3-PE100-NGv3-2_0_15514844-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/2/tx/tmpjghXSb/R14-18105_kapa-NGv3-PE100-NGv3-2_0_15514844.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:48Z] INFO  17:48:40,760 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:48Z] INFO  17:48:40,761 HelpFormatter - Date/Time: 2016/04/14 17:48:40
[2016-04-15T00:48Z] INFO  17:48:40,761 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:48Z] INFO  17:48:40,762 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:48Z] INFO  17:48:40,816 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:48Z] INFO  17:48:40,820 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:48Z] INFO  17:48:40,821 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:48Z] INFO  17:48:40,821 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:48Z] INFO  17:48:40,827 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/2/R14-18105_kapa-NGv3-PE100-NGv3-sort-2_15519725_31133925-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/2/R14-18105_kapa-NGv3-PE100-NGv3-2_15519725_31133925-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/2/tx/tmpbGr2qO/R14-18105_kapa-NGv3-PE100-NGv3-2_15519725_31133925.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:48Z] INFO  17:48:40,838 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:48Z] INFO  17:48:40,839 HelpFormatter - Date/Time: 2016/04/14 17:48:40
[2016-04-15T00:48Z] INFO  17:48:40,839 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:48Z] INFO  17:48:40,839 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:48Z] INFO  17:48:40,980 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:48Z] INFO  17:48:41,005 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:48Z] INFO  17:48:41,225 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:48Z] INFO  17:48:41,236 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:48Z] INFO  17:48:41,280 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:48Z] INFO  17:48:41,290 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:48Z] INFO  17:48:41,309 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-15T00:48Z] INFO  17:48:41,364 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-15T00:48Z] INFO  17:48:41,440 ProgressMeter -            done    578834.0    23.0 s      39.0 s      100.0%    23.0 s       0.0 s
[2016-04-15T00:48Z] INFO  17:48:41,441 ProgressMeter - Total runtime 23.12 secs, 0.39 min, 0.01 hours
[2016-04-15T00:48Z] INFO  17:48:41,441 MicroScheduler - 21555 reads were filtered out during the traversal out of approximately 259684 total reads (8.30%)
[2016-04-15T00:48Z] INFO  17:48:41,442 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:48Z] INFO  17:48:41,442 MicroScheduler -   -> 377 reads (0.15% of total) failing BadMateFilter
[2016-04-15T00:48Z] INFO  17:48:41,442 MicroScheduler -   -> 21019 reads (8.09% of total) failing DuplicateReadFilter
[2016-04-15T00:48Z] INFO  17:48:41,443 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:48Z] INFO  17:48:41,443 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:48Z] INFO  17:48:41,443 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:48Z] INFO  17:48:41,444 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:48Z] INFO  17:48:41,444 MicroScheduler -   -> 159 reads (0.06% of total) failing UnmappedReadFilter
[2016-04-15T00:48Z] INFO  17:48:41,674 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:48Z] INFO  17:48:41,677 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:48Z] INFO  17:48:41,677 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:48Z] INFO  17:48:41,678 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:48Z] INFO  17:48:41,690 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/2/R14-18105_kapa-NGv3-PE100-NGv3-sort-2_31135088_46706841-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/2/R14-18105_kapa-NGv3-PE100-NGv3-2_31135088_46706841-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/2/tx/tmpb8D6Ci/R14-18105_kapa-NGv3-PE100-NGv3-2_31135088_46706841.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:48Z] INFO  17:48:41,723 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:48Z] INFO  17:48:41,730 HelpFormatter - Date/Time: 2016/04/14 17:48:41
[2016-04-15T00:48Z] INFO  17:48:41,731 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:48Z] INFO  17:48:41,731 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:48Z] tabix index R14-18106_kapa-NGv3-PE100-NGv3-19_0_15509577.vcf.gz
[2016-04-15T00:48Z] INFO  17:48:41,825 IntervalUtils - Processing 231513 bp from intervals
[2016-04-15T00:48Z] WARN  17:48:41,830 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:48Z] INFO  17:48:41,896 IntervalUtils - Processing 105700 bp from intervals
[2016-04-15T00:48Z] WARN  17:48:41,901 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:48Z] INFO  17:48:41,953 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:48Z] INFO  17:48:41,956 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:48Z] INFO  17:48:42,044 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:48Z] INFO  17:48:42,044 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:48Z] INFO  17:48:42,045 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:48Z] INFO  17:48:42,046 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:48Z] INFO  17:48:42,046 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:48Z] GATK: UnifiedGenotyper
[2016-04-15T00:48Z] INFO  17:48:42,125 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:48Z] INFO  17:48:42,125 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:48Z] INFO  17:48:42,126 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:48Z] INFO  17:48:42,126 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:48Z] INFO  17:48:42,136 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:48Z] INFO  17:48:42,137 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:48Z] INFO  17:48:42,164 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:48Z] INFO  17:48:42,175 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:48Z] INFO  17:48:42,176 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:48Z] INFO  17:48:42,176 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:48Z] INFO  17:48:42,260 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-15T00:48Z] INFO  17:48:42,664 IntervalUtils - Processing 167641 bp from intervals
[2016-04-15T00:48Z] WARN  17:48:42,669 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:48Z] INFO  17:48:42,744 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:48Z] INFO  17:48:42,802 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:48Z] INFO  17:48:42,832 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:48Z] INFO  17:48:42,832 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:48Z] INFO  17:48:42,833 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:48Z] INFO  17:48:42,833 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:48Z] INFO  17:48:42,875 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:48Z] INFO  17:48:42,876 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:48Z] GATK: UnifiedGenotyper
[2016-04-15T00:48Z] INFO  17:48:43,593 ProgressMeter -            done    638757.0    21.0 s      33.0 s      100.0%    21.0 s       0.0 s
[2016-04-15T00:48Z] INFO  17:48:43,593 ProgressMeter - Total runtime 21.68 secs, 0.36 min, 0.01 hours
[2016-04-15T00:48Z] INFO  17:48:43,594 MicroScheduler - 19400 reads were filtered out during the traversal out of approximately 234843 total reads (8.26%)
[2016-04-15T00:48Z] INFO  17:48:43,594 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:48Z] INFO  17:48:43,594 MicroScheduler -   -> 314 reads (0.13% of total) failing BadMateFilter
[2016-04-15T00:48Z] INFO  17:48:43,595 MicroScheduler -   -> 18942 reads (8.07% of total) failing DuplicateReadFilter
[2016-04-15T00:48Z] INFO  17:48:43,595 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:48Z] INFO  17:48:43,595 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:48Z] INFO  17:48:43,595 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:48Z] INFO  17:48:43,596 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:48Z] INFO  17:48:43,596 MicroScheduler -   -> 144 reads (0.06% of total) failing UnmappedReadFilter
[2016-04-15T00:48Z] INFO  17:48:44,572 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:48Z] INFO  17:48:44,575 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:48Z] INFO  17:48:44,576 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:48Z] INFO  17:48:44,577 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:48Z] INFO  17:48:44,582 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/2/R14-18105_kapa-NGv3-PE100-NGv3-sort-2_46707543_62228117-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/2/R14-18105_kapa-NGv3-PE100-NGv3-2_46707543_62228117-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/2/tx/tmpXAZSiA/R14-18105_kapa-NGv3-PE100-NGv3-2_46707543_62228117.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:48Z] INFO  17:48:44,597 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:48Z] INFO  17:48:44,602 HelpFormatter - Date/Time: 2016/04/14 17:48:44
[2016-04-15T00:48Z] INFO  17:48:44,603 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:48Z] INFO  17:48:44,604 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:48Z] INFO  17:48:44,778 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:48Z] INFO  17:48:44,990 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:48Z] INFO  17:48:44,999 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:48Z] INFO  17:48:45,099 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.10
[2016-04-15T00:48Z] INFO  17:48:45,316 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:48Z] INFO  17:48:45,634 IntervalUtils - Processing 139959 bp from intervals
[2016-04-15T00:48Z] WARN  17:48:45,638 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:48Z] GATK: UnifiedGenotyper
[2016-04-15T00:48Z] INFO  17:48:45,730 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:48Z] INFO  17:48:45,826 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:48Z] INFO  17:48:45,827 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:48Z] INFO  17:48:45,828 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:48Z] INFO  17:48:45,829 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:48Z] INFO  17:48:45,855 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:48Z] INFO  17:48:45,858 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:48Z] INFO  17:48:45,859 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:48Z] INFO  17:48:45,859 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:48Z] INFO  17:48:45,864 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/2/R14-18105_kapa-NGv3-PE100-NGv3-sort-2_62362965_79253295-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/2/R14-18105_kapa-NGv3-PE100-NGv3-2_62362965_79253295-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/2/tx/tmpRgOeVS/R14-18105_kapa-NGv3-PE100-NGv3-2_62362965_79253295.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:48Z] INFO  17:48:45,871 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:48Z] INFO  17:48:45,872 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:48Z] INFO  17:48:45,879 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:48Z] INFO  17:48:45,886 HelpFormatter - Date/Time: 2016/04/14 17:48:45
[2016-04-15T00:48Z] INFO  17:48:45,887 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:48Z] INFO  17:48:45,887 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:48Z] INFO  17:48:46,069 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:48Z] INFO  17:48:46,310 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:48Z] INFO  17:48:46,319 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:48Z] INFO  17:48:46,390 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-15T00:48Z] INFO  17:48:47,046 IntervalUtils - Processing 224219 bp from intervals
[2016-04-15T00:48Z] WARN  17:48:47,052 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:48Z] INFO  17:48:47,151 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:48Z] INFO  17:48:47,216 ProgressMeter -            done    970614.0    28.0 s      29.0 s      100.0%    28.0 s       0.0 s
[2016-04-15T00:48Z] INFO  17:48:47,217 ProgressMeter - Total runtime 28.25 secs, 0.47 min, 0.01 hours
[2016-04-15T00:48Z] INFO  17:48:47,217 MicroScheduler - 29650 reads were filtered out during the traversal out of approximately 359724 total reads (8.24%)
[2016-04-15T00:48Z] INFO  17:48:47,218 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:48Z] INFO  17:48:47,218 MicroScheduler -   -> 489 reads (0.14% of total) failing BadMateFilter
[2016-04-15T00:48Z] INFO  17:48:47,218 MicroScheduler -   -> 28920 reads (8.04% of total) failing DuplicateReadFilter
[2016-04-15T00:48Z] INFO  17:48:47,219 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:48Z] INFO  17:48:47,219 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:48Z] INFO  17:48:47,219 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:48Z] INFO  17:48:47,219 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:48Z] INFO  17:48:47,220 MicroScheduler -   -> 241 reads (0.07% of total) failing UnmappedReadFilter
[2016-04-15T00:48Z] INFO  17:48:47,256 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:48Z] INFO  17:48:47,257 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:48Z] INFO  17:48:47,258 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:48Z] INFO  17:48:47,259 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:48Z] INFO  17:48:47,314 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:48Z] INFO  17:48:47,315 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:48Z] INFO  17:48:47,474 ProgressMeter -            done    540256.0    20.0 s      38.0 s      100.0%    20.0 s       0.0 s
[2016-04-15T00:48Z] INFO  17:48:47,475 ProgressMeter - Total runtime 20.60 secs, 0.34 min, 0.01 hours
[2016-04-15T00:48Z] INFO  17:48:47,475 MicroScheduler - 18410 reads were filtered out during the traversal out of approximately 226301 total reads (8.14%)
[2016-04-15T00:48Z] INFO  17:48:47,476 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:48Z] INFO  17:48:47,476 MicroScheduler -   -> 321 reads (0.14% of total) failing BadMateFilter
[2016-04-15T00:48Z] INFO  17:48:47,476 MicroScheduler -   -> 17938 reads (7.93% of total) failing DuplicateReadFilter
[2016-04-15T00:48Z] INFO  17:48:47,477 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:48Z] INFO  17:48:47,477 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:48Z] INFO  17:48:47,477 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:48Z] INFO  17:48:47,478 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:48Z] INFO  17:48:47,478 MicroScheduler -   -> 151 reads (0.07% of total) failing UnmappedReadFilter
[2016-04-15T00:48Z] INFO  17:48:47,952 ProgressMeter -            done    911237.0    28.0 s      31.0 s      100.0%    28.0 s       0.0 s
[2016-04-15T00:48Z] INFO  17:48:47,953 ProgressMeter - Total runtime 28.31 secs, 0.47 min, 0.01 hours
[2016-04-15T00:48Z] INFO  17:48:47,953 MicroScheduler - 29025 reads were filtered out during the traversal out of approximately 349971 total reads (8.29%)
[2016-04-15T00:48Z] INFO  17:48:47,953 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:48Z] INFO  17:48:47,954 MicroScheduler -   -> 475 reads (0.14% of total) failing BadMateFilter
[2016-04-15T00:48Z] INFO  17:48:47,954 MicroScheduler -   -> 28342 reads (8.10% of total) failing DuplicateReadFilter
[2016-04-15T00:48Z] INFO  17:48:47,954 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:48Z] INFO  17:48:47,954 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:48Z] INFO  17:48:47,955 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:48Z] INFO  17:48:47,955 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:48Z] INFO  17:48:47,955 MicroScheduler -   -> 208 reads (0.06% of total) failing UnmappedReadFilter
[2016-04-15T00:48Z] INFO  17:48:48,355 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:48Z] INFO  17:48:48,357 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:48Z] INFO  17:48:48,358 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:48Z] INFO  17:48:48,358 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:48Z] INFO  17:48:48,362 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/2/R14-18105_kapa-NGv3-PE100-NGv3-sort-2_79253838_95537822-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/2/R14-18105_kapa-NGv3-PE100-NGv3-2_79253838_95537822-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/2/tx/tmpEV2AO_/R14-18105_kapa-NGv3-PE100-NGv3-2_79253838_95537822.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:48Z] INFO  17:48:48,379 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:48Z] INFO  17:48:48,380 HelpFormatter - Date/Time: 2016/04/14 17:48:48
[2016-04-15T00:48Z] INFO  17:48:48,380 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:48Z] INFO  17:48:48,381 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:48Z] INFO  17:48:48,532 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:48Z] INFO  17:48:48,641 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:48Z] INFO  17:48:48,679 ProgressMeter -      1:40776765   1131041.0    30.0 s      26.0 s       63.4%    47.0 s      17.0 s
[2016-04-15T00:48Z] INFO  17:48:48,713 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:48Z] INFO  17:48:48,723 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:48Z] INFO  17:48:48,796 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:48Z] INFO  17:48:48,822 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.10
[2016-04-15T00:48Z] INFO  17:48:48,926 ProgressMeter -      1:10364121   1352666.0    30.0 s      22.0 s       63.8%    47.0 s      17.0 s
[2016-04-15T00:48Z] GATK: UnifiedGenotyper
[2016-04-15T00:48Z] INFO  17:48:49,000 ProgressMeter -     1:152586487    937659.0    30.0 s      32.0 s       42.7%    70.0 s      40.0 s
[2016-04-15T00:48Z] GATK: UnifiedGenotyper
[2016-04-15T00:48Z] INFO  17:48:49,114 ProgressMeter -      1:24069916   1056857.0    30.0 s      28.0 s       58.1%    51.0 s      21.0 s
[2016-04-15T00:48Z] INFO  17:48:49,349 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:48Z] INFO  17:48:49,383 IntervalUtils - Processing 101744 bp from intervals
[2016-04-15T00:48Z] WARN  17:48:49,390 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:48Z] INFO  17:48:49,514 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:48Z] INFO  17:48:49,623 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:48Z] INFO  17:48:49,627 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:48Z] INFO  17:48:49,628 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:48Z] INFO  17:48:49,629 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:48Z] INFO  17:48:49,680 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:48Z] INFO  17:48:49,681 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:48Z] GATK: UnifiedGenotyper
[2016-04-15T00:48Z] INFO  17:48:52,111 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:48Z] INFO  17:48:52,115 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:48Z] INFO  17:48:52,115 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:48Z] INFO  17:48:52,116 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:48Z] INFO  17:48:52,120 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/2/R14-18105_kapa-NGv3-PE100-NGv3-sort-2_111281072_127413888-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/2/R14-18105_kapa-NGv3-PE100-NGv3-2_111281072_127413888-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/2/tx/tmpaOUWXs/R14-18105_kapa-NGv3-PE100-NGv3-2_111281072_127413888.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:48Z] INFO  17:48:52,137 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:48Z] INFO  17:48:52,138 HelpFormatter - Date/Time: 2016/04/14 17:48:52
[2016-04-15T00:48Z] INFO  17:48:52,139 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:48Z] INFO  17:48:52,139 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:48Z] INFO  17:48:52,155 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:48Z] INFO  17:48:52,158 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:48Z] INFO  17:48:52,158 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:48Z] INFO  17:48:52,159 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:48Z] INFO  17:48:52,164 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/2/R14-18105_kapa-NGv3-PE100-NGv3-sort-2_95538561_111273222-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/2/R14-18105_kapa-NGv3-PE100-NGv3-2_95538561_111273222-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/2/tx/tmpT_8GID/R14-18105_kapa-NGv3-PE100-NGv3-2_95538561_111273222.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:48Z] INFO  17:48:52,189 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:48Z] INFO  17:48:52,190 HelpFormatter - Date/Time: 2016/04/14 17:48:52
[2016-04-15T00:48Z] INFO  17:48:52,190 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:48Z] INFO  17:48:52,190 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:48Z] INFO  17:48:52,287 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:48Z] INFO  17:48:52,353 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:48Z] INFO  17:48:52,436 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:48Z] INFO  17:48:52,439 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:48Z] INFO  17:48:52,440 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:48Z] INFO  17:48:52,440 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:48Z] INFO  17:48:52,445 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/2/R14-18105_kapa-NGv3-PE100-NGv3-sort-2_127433207_143643105-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/2/R14-18105_kapa-NGv3-PE100-NGv3-2_127433207_143643105-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/2/tx/tmpvKXjYV/R14-18105_kapa-NGv3-PE100-NGv3-2_127433207_143643105.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:48Z] INFO  17:48:52,467 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:48Z] INFO  17:48:52,467 HelpFormatter - Date/Time: 2016/04/14 17:48:52
[2016-04-15T00:48Z] INFO  17:48:52,467 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:48Z] INFO  17:48:52,467 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:48Z] INFO  17:48:52,517 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:48Z] INFO  17:48:52,525 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:48Z] INFO  17:48:52,581 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-15T00:48Z] INFO  17:48:52,583 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:48Z] INFO  17:48:52,596 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:48Z] INFO  17:48:52,635 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:48Z] INFO  17:48:52,839 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:48Z] INFO  17:48:52,860 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:48Z] INFO  17:48:52,883 IntervalUtils - Processing 123675 bp from intervals
[2016-04-15T00:48Z] WARN  17:48:52,888 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:48Z] INFO  17:48:52,933 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-15T00:48Z] INFO  17:48:52,968 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:48Z] INFO  17:48:53,040 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:48Z] INFO  17:48:53,041 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:48Z] INFO  17:48:53,042 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:48Z] INFO  17:48:53,043 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:48Z] INFO  17:48:53,064 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.47
[2016-04-15T00:48Z] INFO  17:48:53,087 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:48Z] INFO  17:48:53,088 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:48Z] INFO  17:48:53,449 IntervalUtils - Processing 250759 bp from intervals
[2016-04-15T00:48Z] WARN  17:48:53,466 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:48Z] INFO  17:48:53,477 IntervalUtils - Processing 171560 bp from intervals
[2016-04-15T00:48Z] WARN  17:48:53,483 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:48Z] INFO  17:48:53,583 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:48Z] INFO  17:48:53,603 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:48Z] INFO  17:48:53,695 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:48Z] INFO  17:48:53,696 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:48Z] INFO  17:48:53,697 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:48Z] INFO  17:48:53,698 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:48Z] INFO  17:48:53,699 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:48Z] INFO  17:48:53,700 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:48Z] INFO  17:48:53,701 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:48Z] INFO  17:48:53,702 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:48Z] INFO  17:48:53,745 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:48Z] INFO  17:48:53,746 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:48Z] INFO  17:48:53,774 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:48Z] INFO  17:48:53,785 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:48Z] INFO  17:48:53,976 ProgressMeter -            done    991088.0    29.0 s      29.0 s      100.0%    29.0 s       0.0 s
[2016-04-15T00:48Z] INFO  17:48:53,977 ProgressMeter - Total runtime 29.05 secs, 0.48 min, 0.01 hours
[2016-04-15T00:48Z] INFO  17:48:53,977 MicroScheduler - 30545 reads were filtered out during the traversal out of approximately 369579 total reads (8.26%)
[2016-04-15T00:48Z] INFO  17:48:53,978 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:48Z] INFO  17:48:53,978 MicroScheduler -   -> 519 reads (0.14% of total) failing BadMateFilter
[2016-04-15T00:48Z] INFO  17:48:53,978 MicroScheduler -   -> 29803 reads (8.06% of total) failing DuplicateReadFilter
[2016-04-15T00:48Z] INFO  17:48:53,978 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:48Z] INFO  17:48:53,979 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:48Z] INFO  17:48:53,979 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:48Z] INFO  17:48:53,979 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:48Z] INFO  17:48:53,979 MicroScheduler -   -> 223 reads (0.06% of total) failing UnmappedReadFilter
[2016-04-15T00:48Z] INFO  17:48:54,757 ProgressMeter -            done    264653.0    17.0 s      66.0 s      100.0%    17.0 s       0.0 s
[2016-04-15T00:48Z] INFO  17:48:54,757 ProgressMeter - Total runtime 17.50 secs, 0.29 min, 0.00 hours
[2016-04-15T00:48Z] INFO  17:48:54,758 MicroScheduler - 14197 reads were filtered out during the traversal out of approximately 176346 total reads (8.05%)
[2016-04-15T00:48Z] INFO  17:48:54,758 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:48Z] INFO  17:48:54,758 MicroScheduler -   -> 262 reads (0.15% of total) failing BadMateFilter
[2016-04-15T00:48Z] INFO  17:48:54,759 MicroScheduler -   -> 13799 reads (7.82% of total) failing DuplicateReadFilter
[2016-04-15T00:48Z] INFO  17:48:54,759 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:48Z] INFO  17:48:54,759 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:48Z] INFO  17:48:54,760 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:48Z] INFO  17:48:54,760 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:48Z] INFO  17:48:54,760 MicroScheduler -   -> 136 reads (0.08% of total) failing UnmappedReadFilter
[2016-04-15T00:48Z] INFO  17:48:55,477 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:48Z] GATK: UnifiedGenotyper
[2016-04-15T00:48Z] INFO  17:48:56,179 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:48Z] GATK: UnifiedGenotyper
[2016-04-15T00:48Z] INFO  17:48:56,664 ProgressMeter -            done    285546.0    14.0 s      50.0 s      100.0%    14.0 s       0.0 s
[2016-04-15T00:48Z] INFO  17:48:56,665 ProgressMeter - Total runtime 14.54 secs, 0.24 min, 0.00 hours
[2016-04-15T00:48Z] INFO  17:48:56,665 MicroScheduler - 11531 reads were filtered out during the traversal out of approximately 138533 total reads (8.32%)
[2016-04-15T00:48Z] INFO  17:48:56,665 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:48Z] INFO  17:48:56,666 MicroScheduler -   -> 178 reads (0.13% of total) failing BadMateFilter
[2016-04-15T00:48Z] INFO  17:48:56,666 MicroScheduler -   -> 11275 reads (8.14% of total) failing DuplicateReadFilter
[2016-04-15T00:48Z] INFO  17:48:56,666 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:48Z] INFO  17:48:56,666 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:48Z] INFO  17:48:56,667 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:48Z] INFO  17:48:56,667 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:48Z] INFO  17:48:56,667 MicroScheduler -   -> 78 reads (0.06% of total) failing UnmappedReadFilter
[2016-04-15T00:48Z] INFO  17:48:58,126 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:48Z] GATK: UnifiedGenotyper
[2016-04-15T00:48Z] INFO  17:48:58,869 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:48Z] INFO  17:48:58,872 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:48Z] INFO  17:48:58,872 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:48Z] INFO  17:48:58,873 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:48Z] INFO  17:48:58,877 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/2/R14-18105_kapa-NGv3-PE100-NGv3-sort-2_143676177_159195597-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/2/R14-18105_kapa-NGv3-PE100-NGv3-2_143676177_159195597-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/2/tx/tmprXKet5/R14-18105_kapa-NGv3-PE100-NGv3-2_143676177_159195597.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:48Z] INFO  17:48:58,887 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:48Z] INFO  17:48:58,888 HelpFormatter - Date/Time: 2016/04/14 17:48:58
[2016-04-15T00:48Z] INFO  17:48:58,888 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:48Z] INFO  17:48:58,889 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:48Z] INFO  17:48:59,045 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:48Z] INFO  17:48:59,351 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:48Z] INFO  17:48:59,365 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:48Z] INFO  17:48:59,376 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:48Z] INFO  17:48:59,379 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:48Z] INFO  17:48:59,380 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:48Z] INFO  17:48:59,380 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:48Z] INFO  17:48:59,385 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/2/R14-18105_kapa-NGv3-PE100-NGv3-sort-2_159196753_174774985-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/2/R14-18105_kapa-NGv3-PE100-NGv3-2_159196753_174774985-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/2/tx/tmpxlKZp2/R14-18105_kapa-NGv3-PE100-NGv3-2_159196753_174774985.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:48Z] INFO  17:48:59,394 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:48Z] INFO  17:48:59,395 HelpFormatter - Date/Time: 2016/04/14 17:48:59
[2016-04-15T00:48Z] INFO  17:48:59,395 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:48Z] INFO  17:48:59,395 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:48Z] INFO  17:48:59,433 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-15T00:48Z] INFO  17:48:59,524 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:48Z] INFO  17:48:59,771 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:48Z] INFO  17:48:59,791 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:48Z] INFO  17:48:59,854 IntervalUtils - Processing 92555 bp from intervals
[2016-04-15T00:48Z] WARN  17:48:59,859 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:48Z] INFO  17:48:59,889 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.10
[2016-04-15T00:48Z] INFO  17:48:59,954 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:49Z] INFO  17:49:00,033 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:49Z] INFO  17:49:00,034 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:49Z] INFO  17:49:00,035 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:49Z] INFO  17:49:00,036 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:49Z] INFO  17:49:00,094 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:49Z] INFO  17:49:00,095 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:49Z] INFO  17:49:00,286 IntervalUtils - Processing 216485 bp from intervals
[2016-04-15T00:49Z] WARN  17:49:00,291 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:49Z] INFO  17:49:00,364 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:49Z] INFO  17:49:00,449 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:49Z] INFO  17:49:00,450 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:49Z] INFO  17:49:00,451 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:49Z] INFO  17:49:00,452 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:49Z] INFO  17:49:00,512 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:49Z] INFO  17:49:00,513 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:49Z] INFO  17:49:01,262 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:49Z] INFO  17:49:01,266 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:49Z] INFO  17:49:01,266 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:49Z] INFO  17:49:01,267 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:49Z] INFO  17:49:01,271 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/2/R14-18105_kapa-NGv3-PE100-NGv3-sort-2_174777797_190306304-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/2/R14-18105_kapa-NGv3-PE100-NGv3-2_174777797_190306304-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/2/tx/tmp6r3xbb/R14-18105_kapa-NGv3-PE100-NGv3-2_174777797_190306304.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:49Z] INFO  17:49:01,284 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:49Z] INFO  17:49:01,284 HelpFormatter - Date/Time: 2016/04/14 17:49:01
[2016-04-15T00:49Z] INFO  17:49:01,284 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:49Z] INFO  17:49:01,285 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:49Z] INFO  17:49:01,411 ProgressMeter -            done    971140.0    28.0 s      29.0 s      100.0%    28.0 s       0.0 s
[2016-04-15T00:49Z] INFO  17:49:01,412 ProgressMeter - Total runtime 28.99 secs, 0.48 min, 0.01 hours
[2016-04-15T00:49Z] INFO  17:49:01,413 MicroScheduler - 33068 reads were filtered out during the traversal out of approximately 392438 total reads (8.43%)
[2016-04-15T00:49Z] INFO  17:49:01,413 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:49Z] INFO  17:49:01,414 MicroScheduler -   -> 597 reads (0.15% of total) failing BadMateFilter
[2016-04-15T00:49Z] INFO  17:49:01,414 MicroScheduler -   -> 32215 reads (8.21% of total) failing DuplicateReadFilter
[2016-04-15T00:49Z] INFO  17:49:01,414 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:49Z] INFO  17:49:01,415 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:49Z] INFO  17:49:01,415 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:49Z] INFO  17:49:01,415 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:49Z] INFO  17:49:01,415 MicroScheduler -   -> 256 reads (0.07% of total) failing UnmappedReadFilter
[2016-04-15T00:49Z] INFO  17:49:01,454 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:49Z] INFO  17:49:01,627 ProgressMeter -            done    451799.0    15.0 s      34.0 s       99.9%    15.0 s       0.0 s
[2016-04-15T00:49Z] INFO  17:49:01,628 ProgressMeter - Total runtime 15.80 secs, 0.26 min, 0.00 hours
[2016-04-15T00:49Z] INFO  17:49:01,628 MicroScheduler - 13254 reads were filtered out during the traversal out of approximately 163476 total reads (8.11%)
[2016-04-15T00:49Z] INFO  17:49:01,629 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:49Z] INFO  17:49:01,629 MicroScheduler -   -> 208 reads (0.13% of total) failing BadMateFilter
[2016-04-15T00:49Z] INFO  17:49:01,629 MicroScheduler -   -> 12948 reads (7.92% of total) failing DuplicateReadFilter
[2016-04-15T00:49Z] INFO  17:49:01,630 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:49Z] INFO  17:49:01,630 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:49Z] INFO  17:49:01,630 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:49Z] INFO  17:49:01,630 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:49Z] INFO  17:49:01,631 MicroScheduler -   -> 98 reads (0.06% of total) failing UnmappedReadFilter
[2016-04-15T00:49Z] INFO  17:49:01,711 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:49Z] INFO  17:49:01,722 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:49Z] INFO  17:49:01,809 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.09
[2016-04-15T00:49Z] INFO  17:49:01,834 ProgressMeter -            done    491998.0    19.0 s      38.0 s      100.0%    19.0 s       0.0 s
[2016-04-15T00:49Z] INFO  17:49:01,835 ProgressMeter - Total runtime 19.00 secs, 0.32 min, 0.01 hours
[2016-04-15T00:49Z] INFO  17:49:01,835 MicroScheduler - 16352 reads were filtered out during the traversal out of approximately 201121 total reads (8.13%)
[2016-04-15T00:49Z] INFO  17:49:01,835 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:49Z] INFO  17:49:01,836 MicroScheduler -   -> 273 reads (0.14% of total) failing BadMateFilter
[2016-04-15T00:49Z] INFO  17:49:01,836 MicroScheduler -   -> 15961 reads (7.94% of total) failing DuplicateReadFilter
[2016-04-15T00:49Z] INFO  17:49:01,836 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:49Z] INFO  17:49:01,837 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:49Z] INFO  17:49:01,837 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:49Z] INFO  17:49:01,837 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:49Z] INFO  17:49:01,838 MicroScheduler -   -> 118 reads (0.06% of total) failing UnmappedReadFilter
[2016-04-15T00:49Z] INFO  17:49:02,252 ProgressMeter -            done   2049259.0    43.0 s      21.0 s      100.0%    43.0 s       0.0 s
[2016-04-15T00:49Z] INFO  17:49:02,253 ProgressMeter - Total runtime 43.62 secs, 0.73 min, 0.01 hours
[2016-04-15T00:49Z] INFO  17:49:02,253 MicroScheduler - 53757 reads were filtered out during the traversal out of approximately 640719 total reads (8.39%)
[2016-04-15T00:49Z] INFO  17:49:02,254 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:49Z] INFO  17:49:02,254 MicroScheduler -   -> 912 reads (0.14% of total) failing BadMateFilter
[2016-04-15T00:49Z] INFO  17:49:02,254 MicroScheduler -   -> 52454 reads (8.19% of total) failing DuplicateReadFilter
[2016-04-15T00:49Z] INFO  17:49:02,255 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:49Z] INFO  17:49:02,255 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:49Z] INFO  17:49:02,255 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:49Z] INFO  17:49:02,256 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:49Z] INFO  17:49:02,256 MicroScheduler -   -> 391 reads (0.06% of total) failing UnmappedReadFilter
[2016-04-15T00:49Z] INFO  17:49:02,353 IntervalUtils - Processing 253764 bp from intervals
[2016-04-15T00:49Z] WARN  17:49:02,375 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:49Z] INFO  17:49:02,482 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:49Z] INFO  17:49:02,582 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:49Z] INFO  17:49:02,583 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:49Z] INFO  17:49:02,584 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:49Z] INFO  17:49:02,585 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:49Z] INFO  17:49:02,634 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:49Z] INFO  17:49:02,635 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:49Z] INFO  17:49:02,775 ProgressMeter -            done   1670041.0    43.0 s      26.0 s      100.0%    43.0 s       0.0 s
[2016-04-15T00:49Z] INFO  17:49:02,776 ProgressMeter - Total runtime 43.69 secs, 0.73 min, 0.01 hours
[2016-04-15T00:49Z] INFO  17:49:02,777 MicroScheduler - 53392 reads were filtered out during the traversal out of approximately 631526 total reads (8.45%)
[2016-04-15T00:49Z] INFO  17:49:02,778 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:49Z] INFO  17:49:02,779 MicroScheduler -   -> 845 reads (0.13% of total) failing BadMateFilter
[2016-04-15T00:49Z] INFO  17:49:02,780 MicroScheduler -   -> 52162 reads (8.26% of total) failing DuplicateReadFilter
[2016-04-15T00:49Z] INFO  17:49:02,780 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:49Z] INFO  17:49:02,781 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:49Z] INFO  17:49:02,784 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:49Z] INFO  17:49:02,785 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:49Z] INFO  17:49:02,785 MicroScheduler -   -> 385 reads (0.06% of total) failing UnmappedReadFilter
[2016-04-15T00:49Z] INFO  17:49:02,949 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:49Z] INFO  17:49:03,064 ProgressMeter -            done   1809594.0    44.0 s      24.0 s      100.0%    44.0 s       0.0 s
[2016-04-15T00:49Z] INFO  17:49:03,064 ProgressMeter - Total runtime 44.17 secs, 0.74 min, 0.01 hours
[2016-04-15T00:49Z] INFO  17:49:03,065 MicroScheduler - 52733 reads were filtered out during the traversal out of approximately 668288 total reads (7.89%)
[2016-04-15T00:49Z] INFO  17:49:03,066 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:49Z] INFO  17:49:03,066 MicroScheduler -   -> 975 reads (0.15% of total) failing BadMateFilter
[2016-04-15T00:49Z] INFO  17:49:03,066 MicroScheduler -   -> 51331 reads (7.68% of total) failing DuplicateReadFilter
[2016-04-15T00:49Z] INFO  17:49:03,066 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:49Z] INFO  17:49:03,067 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:49Z] INFO  17:49:03,067 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:49Z] INFO  17:49:03,067 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:49Z] INFO  17:49:03,068 MicroScheduler -   -> 427 reads (0.06% of total) failing UnmappedReadFilter
[2016-04-15T00:49Z] INFO  17:49:03,104 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:49Z] GATK: UnifiedGenotyper
[2016-04-15T00:49Z] INFO  17:49:03,289 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:49Z] GATK: UnifiedGenotyper
[2016-04-15T00:49Z] GATK: UnifiedGenotyper
[2016-04-15T00:49Z] INFO  17:49:03,670 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:49Z] GATK: UnifiedGenotyper
[2016-04-15T00:49Z] INFO  17:49:04,076 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:49Z] INFO  17:49:04,388 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:49Z] GATK: UnifiedGenotyper
[2016-04-15T00:49Z] GATK: UnifiedGenotyper
[2016-04-15T00:49Z] INFO  17:49:04,741 ProgressMeter -            done    366382.0    15.0 s      41.0 s       99.9%    15.0 s       0.0 s
[2016-04-15T00:49Z] INFO  17:49:04,742 ProgressMeter - Total runtime 15.11 secs, 0.25 min, 0.00 hours
[2016-04-15T00:49Z] INFO  17:49:04,742 MicroScheduler - 12843 reads were filtered out during the traversal out of approximately 171116 total reads (7.51%)
[2016-04-15T00:49Z] INFO  17:49:04,742 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:49Z] INFO  17:49:04,743 MicroScheduler -   -> 240 reads (0.14% of total) failing BadMateFilter
[2016-04-15T00:49Z] INFO  17:49:04,743 MicroScheduler -   -> 12509 reads (7.31% of total) failing DuplicateReadFilter
[2016-04-15T00:49Z] INFO  17:49:04,743 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:49Z] INFO  17:49:04,743 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:49Z] INFO  17:49:04,744 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:49Z] INFO  17:49:04,744 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:49Z] INFO  17:49:04,744 MicroScheduler -   -> 94 reads (0.05% of total) failing UnmappedReadFilter
[2016-04-15T00:49Z] INFO  17:49:06,118 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:49Z] INFO  17:49:06,384 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:49Z] INFO  17:49:06,387 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:49Z] INFO  17:49:06,388 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:49Z] INFO  17:49:06,388 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:49Z] INFO  17:49:06,393 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/2/R14-18105_kapa-NGv3-PE100-NGv3-sort-2_190313104_205830046-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/2/R14-18105_kapa-NGv3-PE100-NGv3-2_190313104_205830046-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/2/tx/tmpqUjDBZ/R14-18105_kapa-NGv3-PE100-NGv3-2_190313104_205830046.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:49Z] INFO  17:49:06,419 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:49Z] INFO  17:49:06,420 HelpFormatter - Date/Time: 2016/04/14 17:49:06
[2016-04-15T00:49Z] INFO  17:49:06,420 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:49Z] INFO  17:49:06,420 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:49Z] GATK: UnifiedGenotyper
[2016-04-15T00:49Z] INFO  17:49:06,676 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:49Z] INFO  17:49:06,713 ProgressMeter -            done   1055597.0    24.0 s      23.0 s      100.0%    24.0 s       0.0 s
[2016-04-15T00:49Z] INFO  17:49:06,713 ProgressMeter - Total runtime 24.67 secs, 0.41 min, 0.01 hours
[2016-04-15T00:49Z] INFO  17:49:06,713 MicroScheduler - 26612 reads were filtered out during the traversal out of approximately 323002 total reads (8.24%)
[2016-04-15T00:49Z] INFO  17:49:06,714 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:49Z] INFO  17:49:06,714 MicroScheduler -   -> 437 reads (0.14% of total) failing BadMateFilter
[2016-04-15T00:49Z] INFO  17:49:06,714 MicroScheduler -   -> 25985 reads (8.04% of total) failing DuplicateReadFilter
[2016-04-15T00:49Z] INFO  17:49:06,714 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:49Z] INFO  17:49:06,715 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:49Z] INFO  17:49:06,715 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:49Z] INFO  17:49:06,715 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:49Z] INFO  17:49:06,715 MicroScheduler -   -> 190 reads (0.06% of total) failing UnmappedReadFilter
[2016-04-15T00:49Z] INFO  17:49:06,773 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:49Z] INFO  17:49:06,777 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:49Z] INFO  17:49:06,777 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:49Z] INFO  17:49:06,778 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:49Z] INFO  17:49:06,794 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/2/R14-18105_kapa-NGv3-PE100-NGv3-sort-2_222291154_237994685-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/2/R14-18105_kapa-NGv3-PE100-NGv3-2_222291154_237994685-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/2/tx/tmplirnGs/R14-18105_kapa-NGv3-PE100-NGv3-2_222291154_237994685.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:49Z] INFO  17:49:06,825 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:49Z] INFO  17:49:06,826 HelpFormatter - Date/Time: 2016/04/14 17:49:06
[2016-04-15T00:49Z] INFO  17:49:06,826 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:49Z] INFO  17:49:06,827 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:49Z] INFO  17:49:06,932 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:49Z] INFO  17:49:06,935 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:49Z] INFO  17:49:06,936 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:49Z] INFO  17:49:06,936 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:49Z] INFO  17:49:06,941 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/2/R14-18105_kapa-NGv3-PE100-NGv3-sort-2_205912303_222290862-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/2/R14-18105_kapa-NGv3-PE100-NGv3-2_205912303_222290862-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/2/tx/tmpKU6Vtf/R14-18105_kapa-NGv3-PE100-NGv3-2_205912303_222290862.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:49Z] INFO  17:49:06,950 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:49Z] INFO  17:49:06,950 HelpFormatter - Date/Time: 2016/04/14 17:49:06
[2016-04-15T00:49Z] INFO  17:49:06,951 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:49Z] INFO  17:49:06,951 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:49Z] INFO  17:49:06,973 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:49Z] INFO  17:49:06,993 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:49Z] INFO  17:49:07,053 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:49Z] INFO  17:49:07,056 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:49Z] INFO  17:49:07,057 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:49Z] INFO  17:49:07,057 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:49Z] INFO  17:49:07,062 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/2/R14-18105_kapa-NGv3-PE100-NGv3-sort-2_237995374_243199373-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/2/R14-18105_kapa-NGv3-PE100-NGv3-2_237995374_243199373-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/2/tx/tmpr3qKJq/R14-18105_kapa-NGv3-PE100-NGv3-2_237995374_243199373.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:49Z] INFO  17:49:07,065 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:49Z] INFO  17:49:07,081 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.09
[2016-04-15T00:49Z] INFO  17:49:07,096 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:49Z] INFO  17:49:07,096 HelpFormatter - Date/Time: 2016/04/14 17:49:07
[2016-04-15T00:49Z] INFO  17:49:07,097 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:49Z] INFO  17:49:07,097 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:49Z] INFO  17:49:07,163 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:49Z] INFO  17:49:07,291 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:49Z] INFO  17:49:07,301 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:49Z] INFO  17:49:07,346 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:49Z] INFO  17:49:07,410 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.11
[2016-04-15T00:49Z] INFO  17:49:07,422 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:49Z] INFO  17:49:07,431 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:49Z] INFO  17:49:07,519 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.09
[2016-04-15T00:49Z] INFO  17:49:07,559 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:49Z] INFO  17:49:07,561 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:49Z] INFO  17:49:07,561 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:49Z] INFO  17:49:07,561 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:49Z] INFO  17:49:07,565 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/3/R14-18105_kapa-NGv3-PE100-NGv3-sort-3_0_15512123-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/3/R14-18105_kapa-NGv3-PE100-NGv3-3_0_15512123-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/3/tx/tmppAwdK7/R14-18105_kapa-NGv3-PE100-NGv3-3_0_15512123.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:49Z] INFO  17:49:07,573 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:49Z] INFO  17:49:07,574 HelpFormatter - Date/Time: 2016/04/14 17:49:07
[2016-04-15T00:49Z] INFO  17:49:07,574 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:49Z] INFO  17:49:07,575 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:49Z] INFO  17:49:07,635 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:49Z] INFO  17:49:07,644 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:49Z] INFO  17:49:07,722 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-15T00:49Z] INFO  17:49:07,744 IntervalUtils - Processing 204460 bp from intervals
[2016-04-15T00:49Z] INFO  17:49:07,762 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:49Z] WARN  17:49:07,760 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:49Z] INFO  17:49:07,777 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:49Z] INFO  17:49:07,781 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:49Z] INFO  17:49:07,781 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:49Z] INFO  17:49:07,782 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:49Z] INFO  17:49:07,786 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/3/R14-18105_kapa-NGv3-PE100-NGv3-sort-3_15515506_31574805-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/3/R14-18105_kapa-NGv3-PE100-NGv3-3_15515506_31574805-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/3/tx/tmphBr8re/R14-18105_kapa-NGv3-PE100-NGv3-3_15515506_31574805.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:49Z] INFO  17:49:07,796 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:49Z] INFO  17:49:07,796 HelpFormatter - Date/Time: 2016/04/14 17:49:07
[2016-04-15T00:49Z] INFO  17:49:07,796 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:49Z] INFO  17:49:07,796 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:49Z] INFO  17:49:07,834 IntervalUtils - Processing 186854 bp from intervals
[2016-04-15T00:49Z] WARN  17:49:07,842 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:49Z] INFO  17:49:07,893 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:49Z] INFO  17:49:07,967 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:49Z] INFO  17:49:08,027 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:49Z] INFO  17:49:08,035 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:49Z] INFO  17:49:08,040 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:49Z] INFO  17:49:08,041 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:49Z] INFO  17:49:08,042 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:49Z] INFO  17:49:08,044 IntervalUtils - Processing 247026 bp from intervals
[2016-04-15T00:49Z] WARN  17:49:08,049 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:49Z] INFO  17:49:08,054 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:49Z] INFO  17:49:08,073 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:49Z] INFO  17:49:08,100 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:49Z] INFO  17:49:08,101 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:49Z] INFO  17:49:08,102 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:49Z] INFO  17:49:08,102 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:49Z] INFO  17:49:08,103 IntervalUtils - Processing 128077 bp from intervals
[2016-04-15T00:49Z] WARN  17:49:08,108 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:49Z] INFO  17:49:08,102 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-15T00:49Z] INFO  17:49:08,116 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:49Z] INFO  17:49:08,136 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:49Z] INFO  17:49:08,137 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:49Z] INFO  17:49:08,145 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:49Z] INFO  17:49:08,146 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:49Z] INFO  17:49:08,183 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:49Z] INFO  17:49:08,223 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:49Z] INFO  17:49:08,223 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:49Z] INFO  17:49:08,224 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:49Z] INFO  17:49:08,226 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:49Z] INFO  17:49:08,285 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:49Z] INFO  17:49:08,286 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:49Z] INFO  17:49:08,299 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:49Z] INFO  17:49:08,300 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:49Z] INFO  17:49:08,301 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:49Z] INFO  17:49:08,301 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:49Z] INFO  17:49:08,302 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:49Z] INFO  17:49:08,336 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:49Z] INFO  17:49:08,345 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:49Z] INFO  17:49:08,384 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:49Z] INFO  17:49:08,385 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:49Z] INFO  17:49:08,454 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.11
[2016-04-15T00:49Z] INFO  17:49:08,550 IntervalUtils - Processing 188511 bp from intervals
[2016-04-15T00:49Z] WARN  17:49:08,555 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:49Z] GATK: UnifiedGenotyper
[2016-04-15T00:49Z] INFO  17:49:08,642 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:49Z] INFO  17:49:08,711 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:49Z] INFO  17:49:08,712 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:49Z] INFO  17:49:08,713 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:49Z] INFO  17:49:08,713 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:49Z] INFO  17:49:08,734 IntervalUtils - Processing 86168 bp from intervals
[2016-04-15T00:49Z] WARN  17:49:08,739 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:49Z] INFO  17:49:08,766 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:49Z] INFO  17:49:08,767 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:49Z] INFO  17:49:08,818 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:49Z] INFO  17:49:08,871 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:49Z] INFO  17:49:08,872 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:49Z] INFO  17:49:08,873 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:49Z] INFO  17:49:08,874 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:49Z] INFO  17:49:08,965 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:49Z] INFO  17:49:08,966 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:49Z] INFO  17:49:09,300 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:49Z] INFO  17:49:09,313 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:49Z] INFO  17:49:09,314 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:49Z] INFO  17:49:09,315 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:49Z] INFO  17:49:09,319 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/3/R14-18105_kapa-NGv3-PE100-NGv3-sort-3_31617887_47127804-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/3/R14-18105_kapa-NGv3-PE100-NGv3-3_31617887_47127804-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/3/tx/tmpGYyFaO/R14-18105_kapa-NGv3-PE100-NGv3-3_31617887_47127804.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:49Z] INFO  17:49:09,315 ProgressMeter -            done    353576.0    16.0 s      46.0 s       99.9%    16.0 s       0.0 s
[2016-04-15T00:49Z] INFO  17:49:09,316 ProgressMeter - Total runtime 16.27 secs, 0.27 min, 0.00 hours
[2016-04-15T00:49Z] INFO  17:49:09,316 MicroScheduler - 14834 reads were filtered out during the traversal out of approximately 203474 total reads (7.29%)
[2016-04-15T00:49Z] INFO  17:49:09,317 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:49Z] INFO  17:49:09,317 MicroScheduler -   -> 246 reads (0.12% of total) failing BadMateFilter
[2016-04-15T00:49Z] INFO  17:49:09,317 MicroScheduler -   -> 14455 reads (7.10% of total) failing DuplicateReadFilter
[2016-04-15T00:49Z] INFO  17:49:09,318 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:49Z] INFO  17:49:09,318 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:49Z] INFO  17:49:09,318 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:49Z] INFO  17:49:09,319 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:49Z] INFO  17:49:09,319 MicroScheduler -   -> 133 reads (0.07% of total) failing UnmappedReadFilter
[2016-04-15T00:49Z] INFO  17:49:09,332 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:49Z] INFO  17:49:09,333 HelpFormatter - Date/Time: 2016/04/14 17:49:09
[2016-04-15T00:49Z] INFO  17:49:09,334 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:49Z] INFO  17:49:09,335 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:49Z] INFO  17:49:09,570 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:49Z] INFO  17:49:09,895 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:49Z] INFO  17:49:09,906 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:49Z] INFO  17:49:10,384 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.48
[2016-04-15T00:49Z] INFO  17:49:10,976 IntervalUtils - Processing 307437 bp from intervals
[2016-04-15T00:49Z] WARN  17:49:10,982 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:49Z] INFO  17:49:11,019 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:49Z] INFO  17:49:11,107 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:49Z] INFO  17:49:11,239 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:49Z] INFO  17:49:11,240 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:49Z] INFO  17:49:11,241 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:49Z] INFO  17:49:11,242 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:49Z] GATK: UnifiedGenotyper
[2016-04-15T00:49Z] INFO  17:49:11,320 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:49Z] INFO  17:49:11,321 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:49Z] INFO  17:49:11,590 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:49Z] INFO  17:49:11,592 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:49Z] INFO  17:49:11,593 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:49Z] INFO  17:49:11,593 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:49Z] INFO  17:49:11,608 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/3/R14-18105_kapa-NGv3-PE100-NGv3-sort-3_47129602_62648069-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/3/R14-18105_kapa-NGv3-PE100-NGv3-3_47129602_62648069-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/3/tx/tmp88jNmM/R14-18105_kapa-NGv3-PE100-NGv3-3_47129602_62648069.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:49Z] INFO  17:49:11,625 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:49Z] INFO  17:49:11,625 HelpFormatter - Date/Time: 2016/04/14 17:49:11
[2016-04-15T00:49Z] INFO  17:49:11,625 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:49Z] INFO  17:49:11,626 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:49Z] INFO  17:49:11,775 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:49Z] INFO  17:49:11,994 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:49Z] INFO  17:49:12,003 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:49Z] INFO  17:49:12,101 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.10
[2016-04-15T00:49Z] INFO  17:49:12,753 IntervalUtils - Processing 430308 bp from intervals
[2016-04-15T00:49Z] WARN  17:49:12,759 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:49Z] INFO  17:49:12,807 ProgressMeter -            done    769087.0    25.0 s      33.0 s      100.0%    25.0 s       0.0 s
[2016-04-15T00:49Z] INFO  17:49:12,807 ProgressMeter - Total runtime 25.55 secs, 0.43 min, 0.01 hours
[2016-04-15T00:49Z] INFO  17:49:12,808 MicroScheduler - 24804 reads were filtered out during the traversal out of approximately 299497 total reads (8.28%)
[2016-04-15T00:49Z] INFO  17:49:12,808 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:49Z] INFO  17:49:12,808 MicroScheduler -   -> 372 reads (0.12% of total) failing BadMateFilter
[2016-04-15T00:49Z] INFO  17:49:12,808 MicroScheduler -   -> 24243 reads (8.09% of total) failing DuplicateReadFilter
[2016-04-15T00:49Z] INFO  17:49:12,809 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:49Z] INFO  17:49:12,809 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:49Z] INFO  17:49:12,809 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:49Z] INFO  17:49:12,810 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:49Z] INFO  17:49:12,810 MicroScheduler -   -> 189 reads (0.06% of total) failing UnmappedReadFilter
[2016-04-15T00:49Z] INFO  17:49:12,839 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:49Z] INFO  17:49:13,025 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:49Z] INFO  17:49:13,026 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:49Z] INFO  17:49:13,029 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:49Z] INFO  17:49:13,030 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:49Z] INFO  17:49:13,163 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:49Z] INFO  17:49:13,164 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:49Z] INFO  17:49:13,248 ProgressMeter -            done    341277.0    13.0 s      38.0 s       99.9%    13.0 s       0.0 s
[2016-04-15T00:49Z] INFO  17:49:13,249 ProgressMeter - Total runtime 13.21 secs, 0.22 min, 0.00 hours
[2016-04-15T00:49Z] INFO  17:49:13,249 MicroScheduler - 8786 reads were filtered out during the traversal out of approximately 110007 total reads (7.99%)
[2016-04-15T00:49Z] INFO  17:49:13,249 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:49Z] INFO  17:49:13,250 MicroScheduler -   -> 166 reads (0.15% of total) failing BadMateFilter
[2016-04-15T00:49Z] INFO  17:49:13,250 MicroScheduler -   -> 8544 reads (7.77% of total) failing DuplicateReadFilter
[2016-04-15T00:49Z] INFO  17:49:13,250 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:49Z] INFO  17:49:13,250 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:49Z] INFO  17:49:13,251 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:49Z] INFO  17:49:13,251 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:49Z] INFO  17:49:13,251 MicroScheduler -   -> 76 reads (0.07% of total) failing UnmappedReadFilter
[2016-04-15T00:49Z] INFO  17:49:14,346 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:49Z] GATK: UnifiedGenotyper
[2016-04-15T00:49Z] INFO  17:49:14,655 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:49Z] INFO  17:49:14,658 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:49Z] INFO  17:49:14,659 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:49Z] INFO  17:49:14,659 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:49Z] INFO  17:49:14,664 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/3/R14-18105_kapa-NGv3-PE100-NGv3-sort-3_62739115_78648077-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/3/R14-18105_kapa-NGv3-PE100-NGv3-3_62739115_78648077-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/3/tx/tmprs4ItO/R14-18105_kapa-NGv3-PE100-NGv3-3_62739115_78648077.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:49Z] INFO  17:49:14,673 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:49Z] INFO  17:49:14,674 HelpFormatter - Date/Time: 2016/04/14 17:49:14
[2016-04-15T00:49Z] INFO  17:49:14,674 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:49Z] INFO  17:49:14,674 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:49Z] INFO  17:49:14,868 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:49Z] INFO  17:49:14,947 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:49Z] INFO  17:49:15,098 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:49Z] INFO  17:49:15,107 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:49Z] INFO  17:49:15,207 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.10
[2016-04-15T00:49Z] GATK: UnifiedGenotyper
[2016-04-15T00:49Z] INFO  17:49:15,560 IntervalUtils - Processing 82160 bp from intervals
[2016-04-15T00:49Z] WARN  17:49:15,565 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:49Z] INFO  17:49:15,572 ProgressMeter -            done   2535127.0    56.0 s      22.0 s      100.0%    56.0 s       0.0 s
[2016-04-15T00:49Z] INFO  17:49:15,573 ProgressMeter - Total runtime 56.60 secs, 0.94 min, 0.02 hours
[2016-04-15T00:49Z] INFO  17:49:15,573 MicroScheduler - 72716 reads were filtered out during the traversal out of approximately 894805 total reads (8.13%)
[2016-04-15T00:49Z] INFO  17:49:15,573 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:49Z] INFO  17:49:15,574 MicroScheduler -   -> 1163 reads (0.13% of total) failing BadMateFilter
[2016-04-15T00:49Z] INFO  17:49:15,574 MicroScheduler -   -> 71001 reads (7.93% of total) failing DuplicateReadFilter
[2016-04-15T00:49Z] INFO  17:49:15,574 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:49Z] INFO  17:49:15,574 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:49Z] INFO  17:49:15,575 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:49Z] INFO  17:49:15,575 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:49Z] INFO  17:49:15,575 MicroScheduler -   -> 552 reads (0.06% of total) failing UnmappedReadFilter
[2016-04-15T00:49Z] INFO  17:49:15,673 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:49Z] INFO  17:49:15,773 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:49Z] INFO  17:49:15,774 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:49Z] INFO  17:49:15,775 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:49Z] INFO  17:49:15,776 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:49Z] INFO  17:49:15,835 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:49Z] INFO  17:49:15,836 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:49Z] INFO  17:49:16,893 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:49Z] GATK: UnifiedGenotyper
[2016-04-15T00:49Z] INFO  17:49:17,362 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:49Z] INFO  17:49:17,376 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:49Z] INFO  17:49:17,376 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:49Z] INFO  17:49:17,376 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:49Z] INFO  17:49:17,380 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/3/R14-18105_kapa-NGv3-PE100-NGv3-sort-3_78649262_96533852-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/3/R14-18105_kapa-NGv3-PE100-NGv3-3_78649262_96533852-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/3/tx/tmpk4PmXf/R14-18105_kapa-NGv3-PE100-NGv3-3_78649262_96533852.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:49Z] INFO  17:49:17,400 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:49Z] INFO  17:49:17,400 HelpFormatter - Date/Time: 2016/04/14 17:49:17
[2016-04-15T00:49Z] INFO  17:49:17,400 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:49Z] INFO  17:49:17,401 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:49Z] INFO  17:49:17,469 ProgressMeter -            done    525700.0    23.0 s      45.0 s      100.0%    23.0 s       0.0 s
[2016-04-15T00:49Z] INFO  17:49:17,469 ProgressMeter - Total runtime 23.77 secs, 0.40 min, 0.01 hours
[2016-04-15T00:49Z] INFO  17:49:17,470 MicroScheduler - 21821 reads were filtered out during the traversal out of approximately 272774 total reads (8.00%)
[2016-04-15T00:49Z] INFO  17:49:17,470 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:49Z] INFO  17:49:17,470 MicroScheduler -   -> 449 reads (0.16% of total) failing BadMateFilter
[2016-04-15T00:49Z] INFO  17:49:17,470 MicroScheduler -   -> 21191 reads (7.77% of total) failing DuplicateReadFilter
[2016-04-15T00:49Z] INFO  17:49:17,471 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:49Z] INFO  17:49:17,471 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:49Z] INFO  17:49:17,471 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:49Z] INFO  17:49:17,471 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:49Z] INFO  17:49:17,472 MicroScheduler -   -> 181 reads (0.07% of total) failing UnmappedReadFilter
[2016-04-15T00:49Z] INFO  17:49:17,582 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:49Z] INFO  17:49:17,852 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:49Z] INFO  17:49:17,873 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:49Z] INFO  17:49:18,085 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.21
[2016-04-15T00:49Z] INFO  17:49:18,483 IntervalUtils - Processing 30411 bp from intervals
[2016-04-15T00:49Z] WARN  17:49:18,489 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:49Z] INFO  17:49:18,574 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:49Z] INFO  17:49:18,629 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:49Z] INFO  17:49:18,630 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:49Z] INFO  17:49:18,630 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:49Z] INFO  17:49:18,631 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:49Z] INFO  17:49:18,666 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:49Z] INFO  17:49:18,672 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:49Z] INFO  17:49:18,672 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:49Z] INFO  17:49:18,672 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:49Z] INFO  17:49:18,677 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/3/R14-18105_kapa-NGv3-PE100-NGv3-sort-3_96585668_112185230-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/3/R14-18105_kapa-NGv3-PE100-NGv3-3_96585668_112185230-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/3/tx/tmpjLwIs8/R14-18105_kapa-NGv3-PE100-NGv3-3_96585668_112185230.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:49Z] INFO  17:49:18,680 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:49Z] INFO  17:49:18,681 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:49Z] INFO  17:49:18,699 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:49Z] INFO  17:49:18,710 HelpFormatter - Date/Time: 2016/04/14 17:49:18
[2016-04-15T00:49Z] INFO  17:49:18,711 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:49Z] INFO  17:49:18,712 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:49Z] INFO  17:49:18,875 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:49Z] INFO  17:49:19,128 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:49Z] INFO  17:49:19,137 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:49Z] INFO  17:49:19,234 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.10
[2016-04-15T00:49Z] INFO  17:49:19,345 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:49Z] INFO  17:49:19,598 IntervalUtils - Processing 140565 bp from intervals
[2016-04-15T00:49Z] WARN  17:49:19,603 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:49Z] GATK: UnifiedGenotyper
[2016-04-15T00:49Z] INFO  17:49:19,690 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:49Z] INFO  17:49:19,800 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:49Z] INFO  17:49:19,800 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:49Z] INFO  17:49:19,801 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:49Z] INFO  17:49:19,801 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:49Z] INFO  17:49:19,849 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:49Z] INFO  17:49:19,849 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:49Z] INFO  17:49:20,306 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:49Z] INFO  17:49:20,308 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:49Z] INFO  17:49:20,308 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:49Z] INFO  17:49:20,308 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:49Z] INFO  17:49:20,324 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/3/R14-18105_kapa-NGv3-PE100-NGv3-sort-3_112188604_127703121-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/3/R14-18105_kapa-NGv3-PE100-NGv3-3_112188604_127703121-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/3/tx/tmphaiUcb/R14-18105_kapa-NGv3-PE100-NGv3-3_112188604_127703121.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:49Z] INFO  17:49:20,354 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:49Z] INFO  17:49:20,354 HelpFormatter - Date/Time: 2016/04/14 17:49:20
[2016-04-15T00:49Z] INFO  17:49:20,355 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:49Z] INFO  17:49:20,355 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:49Z] INFO  17:49:20,555 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:49Z] INFO  17:49:20,804 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:49Z] INFO  17:49:20,813 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:49Z] INFO  17:49:20,883 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-15T00:49Z] INFO  17:49:21,333 IntervalUtils - Processing 249953 bp from intervals
[2016-04-15T00:49Z] WARN  17:49:21,338 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:49Z] INFO  17:49:21,448 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:49Z] INFO  17:49:21,580 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:49Z] INFO  17:49:21,581 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:49Z] INFO  17:49:21,582 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:49Z] INFO  17:49:21,583 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:49Z] INFO  17:49:21,679 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:49Z] INFO  17:49:21,690 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:49Z] INFO  17:49:22,201 ProgressMeter -            done    206627.0    13.0 s      64.0 s      100.0%    13.0 s       0.0 s
[2016-04-15T00:49Z] INFO  17:49:22,202 ProgressMeter - Total runtime 13.33 secs, 0.22 min, 0.00 hours
[2016-04-15T00:49Z] INFO  17:49:22,202 MicroScheduler - 8185 reads were filtered out during the traversal out of approximately 99056 total reads (8.26%)
[2016-04-15T00:49Z] INFO  17:49:22,202 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:49Z] INFO  17:49:22,203 MicroScheduler -   -> 124 reads (0.13% of total) failing BadMateFilter
[2016-04-15T00:49Z] INFO  17:49:22,203 MicroScheduler -   -> 7994 reads (8.07% of total) failing DuplicateReadFilter
[2016-04-15T00:49Z] INFO  17:49:22,203 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:49Z] INFO  17:49:22,203 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:49Z] INFO  17:49:22,204 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:49Z] INFO  17:49:22,204 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:49Z] INFO  17:49:22,204 MicroScheduler -   -> 67 reads (0.07% of total) failing UnmappedReadFilter
[2016-04-15T00:49Z] INFO  17:49:22,502 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:49Z] INFO  17:49:22,509 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:49Z] INFO  17:49:22,510 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:49Z] INFO  17:49:22,511 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:49Z] INFO  17:49:22,515 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/3/R14-18105_kapa-NGv3-PE100-NGv3-sort-3_127770401_143293035-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/3/R14-18105_kapa-NGv3-PE100-NGv3-3_127770401_143293035-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/3/tx/tmpRPttJR/R14-18105_kapa-NGv3-PE100-NGv3-3_127770401_143293035.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:49Z] INFO  17:49:22,536 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:49Z] INFO  17:49:22,537 HelpFormatter - Date/Time: 2016/04/14 17:49:22
[2016-04-15T00:49Z] INFO  17:49:22,538 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:49Z] INFO  17:49:22,542 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:49Z] INFO  17:49:22,714 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:49Z] INFO  17:49:22,976 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:49Z] INFO  17:49:22,985 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:49Z] INFO  17:49:23,042 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-15T00:49Z] INFO  17:49:23,382 IntervalUtils - Processing 238450 bp from intervals
[2016-04-15T00:49Z] WARN  17:49:23,388 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:49Z] INFO  17:49:23,451 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:49Z] INFO  17:49:23,569 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:49Z] INFO  17:49:23,570 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:49Z] INFO  17:49:23,571 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:49Z] INFO  17:49:23,571 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:49Z] INFO  17:49:23,620 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:49Z] INFO  17:49:23,621 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:49Z] INFO  17:49:23,632 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:49Z] INFO  17:49:23,734 ProgressMeter -     2:110015346    969205.0    30.0 s      30.0 s       93.6%    32.0 s       2.0 s
[2016-04-15T00:49Z] GATK: UnifiedGenotyper
[2016-04-15T00:49Z] INFO  17:49:24,501 ProgressMeter -            done    626517.0    24.0 s      38.0 s      100.0%    24.0 s       0.0 s
[2016-04-15T00:49Z] INFO  17:49:24,502 ProgressMeter - Total runtime 24.05 secs, 0.40 min, 0.01 hours
[2016-04-15T00:49Z] INFO  17:49:24,502 MicroScheduler - 21162 reads were filtered out during the traversal out of approximately 257782 total reads (8.21%)
[2016-04-15T00:49Z] INFO  17:49:24,503 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:49Z] INFO  17:49:24,503 MicroScheduler -   -> 351 reads (0.14% of total) failing BadMateFilter
[2016-04-15T00:49Z] INFO  17:49:24,503 MicroScheduler -   -> 20672 reads (8.02% of total) failing DuplicateReadFilter
[2016-04-15T00:49Z] INFO  17:49:24,504 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:49Z] INFO  17:49:24,504 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:49Z] INFO  17:49:24,504 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:49Z] INFO  17:49:24,505 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:49Z] INFO  17:49:24,505 MicroScheduler -   -> 139 reads (0.05% of total) failing UnmappedReadFilter
[2016-04-15T00:49Z] INFO  17:49:25,823 ProgressMeter -            done   1019400.0    32.0 s      31.0 s      100.0%    32.0 s       0.0 s
[2016-04-15T00:49Z] INFO  17:49:25,824 ProgressMeter - Total runtime 32.12 secs, 0.54 min, 0.01 hours
[2016-04-15T00:49Z] INFO  17:49:25,824 MicroScheduler - 33790 reads were filtered out during the traversal out of approximately 437484 total reads (7.72%)
[2016-04-15T00:49Z] INFO  17:49:25,824 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:49Z] INFO  17:49:25,825 MicroScheduler -   -> 596 reads (0.14% of total) failing BadMateFilter
[2016-04-15T00:49Z] INFO  17:49:25,825 MicroScheduler -   -> 32935 reads (7.53% of total) failing DuplicateReadFilter
[2016-04-15T00:49Z] INFO  17:49:25,825 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:49Z] INFO  17:49:25,825 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:49Z] INFO  17:49:25,826 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:49Z] INFO  17:49:25,826 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:49Z] INFO  17:49:25,826 MicroScheduler -   -> 259 reads (0.06% of total) failing UnmappedReadFilter
[2016-04-15T00:49Z] INFO  17:49:26,005 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:49Z] INFO  17:49:26,016 ProgressMeter -            done     56098.0     7.0 s       2.2 m       99.7%     7.0 s       0.0 s
[2016-04-15T00:49Z] INFO  17:49:26,016 ProgressMeter - Total runtime 7.39 secs, 0.12 min, 0.00 hours
[2016-04-15T00:49Z] INFO  17:49:26,017 MicroScheduler - 3106 reads were filtered out during the traversal out of approximately 36746 total reads (8.45%)
[2016-04-15T00:49Z] INFO  17:49:26,017 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:49Z] INFO  17:49:26,017 MicroScheduler -   -> 58 reads (0.16% of total) failing BadMateFilter
[2016-04-15T00:49Z] INFO  17:49:26,017 MicroScheduler -   -> 3021 reads (8.22% of total) failing DuplicateReadFilter
[2016-04-15T00:49Z] INFO  17:49:26,018 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:49Z] INFO  17:49:26,018 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:49Z] INFO  17:49:26,018 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:49Z] INFO  17:49:26,018 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:49Z] INFO  17:49:26,019 MicroScheduler -   -> 27 reads (0.07% of total) failing UnmappedReadFilter
[2016-04-15T00:49Z] GATK: UnifiedGenotyper
[2016-04-15T00:49Z] INFO  17:49:27,083 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:49Z] INFO  17:49:27,097 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:49Z] INFO  17:49:27,097 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:49Z] INFO  17:49:27,097 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:49Z] INFO  17:49:27,102 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/3/R14-18105_kapa-NGv3-PE100-NGv3-sort-3_143297426_158963696-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/3/R14-18105_kapa-NGv3-PE100-NGv3-3_143297426_158963696-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/3/tx/tmpUFK9wj/R14-18105_kapa-NGv3-PE100-NGv3-3_143297426_158963696.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:49Z] INFO  17:49:27,122 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:49Z] INFO  17:49:27,123 HelpFormatter - Date/Time: 2016/04/14 17:49:27
[2016-04-15T00:49Z] INFO  17:49:27,135 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:49Z] INFO  17:49:27,136 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:49Z] INFO  17:49:27,320 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:49Z] INFO  17:49:27,392 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:49Z] INFO  17:49:27,517 ProgressMeter -            done    469618.0    19.0 s      40.0 s      100.0%    19.0 s       0.0 s
[2016-04-15T00:49Z] INFO  17:49:27,517 ProgressMeter - Total runtime 19.22 secs, 0.32 min, 0.01 hours
[2016-04-15T00:49Z] INFO  17:49:27,518 MicroScheduler - 15744 reads were filtered out during the traversal out of approximately 191047 total reads (8.24%)
[2016-04-15T00:49Z] INFO  17:49:27,518 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:49Z] INFO  17:49:27,519 MicroScheduler -   -> 275 reads (0.14% of total) failing BadMateFilter
[2016-04-15T00:49Z] INFO  17:49:27,519 MicroScheduler -   -> 15365 reads (8.04% of total) failing DuplicateReadFilter
[2016-04-15T00:49Z] INFO  17:49:27,519 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:49Z] INFO  17:49:27,520 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:49Z] INFO  17:49:27,520 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:49Z] INFO  17:49:27,520 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:49Z] INFO  17:49:27,521 MicroScheduler -   -> 104 reads (0.05% of total) failing UnmappedReadFilter
[2016-04-15T00:49Z] GATK: UnifiedGenotyper
[2016-04-15T00:49Z] INFO  17:49:27,634 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:49Z] INFO  17:49:27,644 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:49Z] INFO  17:49:27,724 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-15T00:49Z] INFO  17:49:27,889 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:49Z] INFO  17:49:28,075 IntervalUtils - Processing 125161 bp from intervals
[2016-04-15T00:49Z] WARN  17:49:28,080 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:49Z] INFO  17:49:28,162 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:49Z] GATK: UnifiedGenotyper
[2016-04-15T00:49Z] INFO  17:49:28,263 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:49Z] INFO  17:49:28,264 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:49Z] INFO  17:49:28,265 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:49Z] INFO  17:49:28,265 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:49Z] INFO  17:49:28,306 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:49Z] INFO  17:49:28,307 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:49Z] INFO  17:49:29,148 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:49Z] INFO  17:49:29,172 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:49Z] INFO  17:49:29,175 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:49Z] INFO  17:49:29,176 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:49Z] INFO  17:49:29,177 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:49Z] INFO  17:49:29,182 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/3/R14-18105_kapa-NGv3-PE100-NGv3-sort-3_158970515_174577240-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/3/R14-18105_kapa-NGv3-PE100-NGv3-3_158970515_174577240-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/3/tx/tmpHeJA5I/R14-18105_kapa-NGv3-PE100-NGv3-3_158970515_174577240.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:49Z] INFO  17:49:29,195 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:49Z] INFO  17:49:29,198 HelpFormatter - Date/Time: 2016/04/14 17:49:29
[2016-04-15T00:49Z] INFO  17:49:29,199 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:49Z] INFO  17:49:29,210 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:49Z] INFO  17:49:29,404 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:49Z] GATK: UnifiedGenotyper
[2016-04-15T00:49Z] INFO  17:49:29,646 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:49Z] INFO  17:49:29,656 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:49Z] INFO  17:49:29,726 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-15T00:49Z] INFO  17:49:29,747 ProgressMeter -            done   1634209.0    27.0 s      16.0 s      100.0%    27.0 s       0.0 s
[2016-04-15T00:49Z] INFO  17:49:29,748 ProgressMeter - Total runtime 27.16 secs, 0.45 min, 0.01 hours
[2016-04-15T00:49Z] INFO  17:49:29,748 MicroScheduler - 25793 reads were filtered out during the traversal out of approximately 315630 total reads (8.17%)
[2016-04-15T00:49Z] INFO  17:49:29,748 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:49Z] INFO  17:49:29,749 MicroScheduler -   -> 400 reads (0.13% of total) failing BadMateFilter
[2016-04-15T00:49Z] INFO  17:49:29,749 MicroScheduler -   -> 25190 reads (7.98% of total) failing DuplicateReadFilter
[2016-04-15T00:49Z] INFO  17:49:29,749 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:49Z] INFO  17:49:29,749 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:49Z] INFO  17:49:29,750 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:49Z] INFO  17:49:29,750 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:49Z] INFO  17:49:29,750 MicroScheduler -   -> 203 reads (0.06% of total) failing UnmappedReadFilter
[2016-04-15T00:49Z] INFO  17:49:29,825 ProgressMeter -            done    217382.0    14.0 s      64.0 s      100.0%    14.0 s       0.0 s
[2016-04-15T00:49Z] INFO  17:49:29,826 ProgressMeter - Total runtime 14.05 secs, 0.23 min, 0.00 hours
[2016-04-15T00:49Z] INFO  17:49:29,826 MicroScheduler - 8580 reads were filtered out during the traversal out of approximately 103941 total reads (8.25%)
[2016-04-15T00:49Z] INFO  17:49:29,826 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:49Z] INFO  17:49:29,826 MicroScheduler -   -> 149 reads (0.14% of total) failing BadMateFilter
[2016-04-15T00:49Z] INFO  17:49:29,827 MicroScheduler -   -> 8362 reads (8.04% of total) failing DuplicateReadFilter
[2016-04-15T00:49Z] INFO  17:49:29,827 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:49Z] INFO  17:49:29,827 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:49Z] INFO  17:49:29,828 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:49Z] INFO  17:49:29,828 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:49Z] INFO  17:49:29,828 MicroScheduler -   -> 69 reads (0.07% of total) failing UnmappedReadFilter
[2016-04-15T00:49Z] INFO  17:49:29,939 ProgressMeter -            done    606340.0    21.0 s      36.0 s      100.0%    21.0 s       0.0 s
[2016-04-15T00:49Z] INFO  17:49:29,939 ProgressMeter - Total runtime 21.90 secs, 0.36 min, 0.01 hours
[2016-04-15T00:49Z] INFO  17:49:29,940 MicroScheduler - 18274 reads were filtered out during the traversal out of approximately 221760 total reads (8.24%)
[2016-04-15T00:49Z] INFO  17:49:29,940 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:49Z] INFO  17:49:29,941 MicroScheduler -   -> 312 reads (0.14% of total) failing BadMateFilter
[2016-04-15T00:49Z] INFO  17:49:29,941 MicroScheduler -   -> 17844 reads (8.05% of total) failing DuplicateReadFilter
[2016-04-15T00:49Z] INFO  17:49:29,942 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:49Z] INFO  17:49:29,942 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:49Z] INFO  17:49:29,942 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:49Z] INFO  17:49:29,958 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:49Z] INFO  17:49:29,958 MicroScheduler -   -> 118 reads (0.05% of total) failing UnmappedReadFilter
[2016-04-15T00:49Z] INFO  17:49:30,213 IntervalUtils - Processing 102254 bp from intervals
[2016-04-15T00:49Z] WARN  17:49:30,224 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:49Z] INFO  17:49:30,308 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:49Z] INFO  17:49:30,431 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:49Z] INFO  17:49:30,432 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:49Z] INFO  17:49:30,433 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:49Z] INFO  17:49:30,433 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:49Z] INFO  17:49:30,509 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:49Z] INFO  17:49:30,509 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:49Z] INFO  17:49:30,624 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:49Z] INFO  17:49:30,627 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:49Z] INFO  17:49:30,628 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:49Z] INFO  17:49:30,628 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:49Z] INFO  17:49:30,633 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/3/R14-18105_kapa-NGv3-PE100-NGv3-sort-3_174814579_190326970-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/3/R14-18105_kapa-NGv3-PE100-NGv3-3_174814579_190326970-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/3/tx/tmp0IYhlB/R14-18105_kapa-NGv3-PE100-NGv3-3_174814579_190326970.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:49Z] INFO  17:49:30,667 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:49Z] INFO  17:49:30,668 HelpFormatter - Date/Time: 2016/04/14 17:49:30
[2016-04-15T00:49Z] INFO  17:49:30,668 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:49Z] INFO  17:49:30,669 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:49Z] INFO  17:49:30,811 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:49Z] INFO  17:49:30,993 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:49Z] INFO  17:49:31,004 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:49Z] INFO  17:49:31,116 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.11
[2016-04-15T00:49Z] INFO  17:49:31,150 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:49Z] INFO  17:49:31,156 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:49Z] INFO  17:49:31,157 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:49Z] INFO  17:49:31,158 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:49Z] INFO  17:49:31,162 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/3/R14-18105_kapa-NGv3-PE100-NGv3-sort-3_190333063_198022430-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/3/R14-18105_kapa-NGv3-PE100-NGv3-3_190333063_198022430-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/3/tx/tmpUuXv3w/R14-18105_kapa-NGv3-PE100-NGv3-3_190333063_198022430.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:49Z] INFO  17:49:31,176 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:49Z] INFO  17:49:31,176 HelpFormatter - Date/Time: 2016/04/14 17:49:31
[2016-04-15T00:49Z] INFO  17:49:31,176 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:49Z] INFO  17:49:31,176 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:49Z] INFO  17:49:31,207 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:49Z] INFO  17:49:31,253 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:49Z] INFO  17:49:31,356 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:49Z] INFO  17:49:31,403 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:49Z] GATK: UnifiedGenotyper
[2016-04-15T00:49Z] INFO  17:49:31,508 IntervalUtils - Processing 184739 bp from intervals
[2016-04-15T00:49Z] WARN  17:49:31,513 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:49Z] GATK: UnifiedGenotyper
[2016-04-15T00:49Z] INFO  17:49:31,580 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:49Z] INFO  17:49:31,594 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:49Z] INFO  17:49:31,611 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:49Z] INFO  17:49:31,663 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-15T00:49Z] GATK: UnifiedGenotyper
[2016-04-15T00:49Z] INFO  17:49:31,727 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:49Z] INFO  17:49:31,728 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:49Z] INFO  17:49:31,729 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:49Z] INFO  17:49:31,730 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:49Z] INFO  17:49:31,785 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:49Z] INFO  17:49:31,786 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:49Z] INFO  17:49:32,153 IntervalUtils - Processing 118955 bp from intervals
[2016-04-15T00:49Z] WARN  17:49:32,169 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:49Z] INFO  17:49:32,264 ProgressMeter -            done    666709.0    23.0 s      35.0 s      100.0%    23.0 s       0.0 s
[2016-04-15T00:49Z] INFO  17:49:32,265 ProgressMeter - Total runtime 23.55 secs, 0.39 min, 0.01 hours
[2016-04-15T00:49Z] INFO  17:49:32,265 MicroScheduler - 23368 reads were filtered out during the traversal out of approximately 278818 total reads (8.38%)
[2016-04-15T00:49Z] INFO  17:49:32,266 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:49Z] INFO  17:49:32,266 MicroScheduler -   -> 410 reads (0.15% of total) failing BadMateFilter
[2016-04-15T00:49Z] INFO  17:49:32,266 MicroScheduler -   -> 22794 reads (8.18% of total) failing DuplicateReadFilter
[2016-04-15T00:49Z] INFO  17:49:32,267 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:49Z] INFO  17:49:32,267 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:49Z] INFO  17:49:32,267 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:49Z] INFO  17:49:32,267 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:49Z] INFO  17:49:32,268 MicroScheduler -   -> 164 reads (0.06% of total) failing UnmappedReadFilter
[2016-04-15T00:49Z] INFO  17:49:32,304 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:49Z] INFO  17:49:32,445 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:49Z] INFO  17:49:32,447 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:49Z] INFO  17:49:32,448 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:49Z] INFO  17:49:32,449 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:49Z] INFO  17:49:32,489 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:49Z] INFO  17:49:32,493 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:49Z] INFO  17:49:32,494 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:49Z] INFO  17:49:32,494 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:49Z] INFO  17:49:32,500 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/4/R14-18105_kapa-NGv3-PE100-NGv3-sort-4_0_15511864-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/4/R14-18105_kapa-NGv3-PE100-NGv3-4_0_15511864-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/4/tx/tmpyFIplx/R14-18105_kapa-NGv3-PE100-NGv3-4_0_15511864.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:49Z] INFO  17:49:32,510 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:49Z] INFO  17:49:32,522 HelpFormatter - Date/Time: 2016/04/14 17:49:32
[2016-04-15T00:49Z] INFO  17:49:32,525 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:49Z] INFO  17:49:32,525 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:49Z] INFO  17:49:32,531 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:49Z] INFO  17:49:32,532 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:49Z] INFO  17:49:32,705 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:49Z] INFO  17:49:32,945 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:49Z] INFO  17:49:32,966 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:49Z] INFO  17:49:33,059 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.09
[2016-04-15T00:49Z] INFO  17:49:33,157 ProgressMeter -            done    587434.0    25.0 s      42.0 s      100.0%    25.0 s       0.0 s
[2016-04-15T00:49Z] INFO  17:49:33,158 ProgressMeter - Total runtime 25.06 secs, 0.42 min, 0.01 hours
[2016-04-15T00:49Z] INFO  17:49:33,158 MicroScheduler - 23522 reads were filtered out during the traversal out of approximately 279424 total reads (8.42%)
[2016-04-15T00:49Z] INFO  17:49:33,158 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:49Z] INFO  17:49:33,159 MicroScheduler -   -> 362 reads (0.13% of total) failing BadMateFilter
[2016-04-15T00:49Z] INFO  17:49:33,159 MicroScheduler -   -> 22995 reads (8.23% of total) failing DuplicateReadFilter
[2016-04-15T00:49Z] INFO  17:49:33,159 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:49Z] INFO  17:49:33,160 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:49Z] INFO  17:49:33,160 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:49Z] INFO  17:49:33,160 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:49Z] INFO  17:49:33,161 MicroScheduler -   -> 165 reads (0.06% of total) failing UnmappedReadFilter
[2016-04-15T00:49Z] INFO  17:49:33,595 IntervalUtils - Processing 255565 bp from intervals
[2016-04-15T00:49Z] WARN  17:49:33,601 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:49Z] INFO  17:49:33,691 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:49Z] INFO  17:49:33,778 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:49Z] INFO  17:49:33,779 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:49Z] INFO  17:49:33,780 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:49Z] INFO  17:49:33,781 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:49Z] INFO  17:49:33,793 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:49Z] INFO  17:49:33,824 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:49Z] INFO  17:49:33,825 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:49Z] GATK: UnifiedGenotyper
[2016-04-15T00:49Z] INFO  17:49:34,733 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:49Z] INFO  17:49:34,772 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:49Z] INFO  17:49:34,777 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:49Z] INFO  17:49:34,777 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:49Z] INFO  17:49:34,778 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:49Z] INFO  17:49:34,782 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/4/R14-18105_kapa-NGv3-PE100-NGv3-sort-4_36069528_52709433-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/4/R14-18105_kapa-NGv3-PE100-NGv3-4_36069528_52709433-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/4/tx/tmpsg54mt/R14-18105_kapa-NGv3-PE100-NGv3-4_36069528_52709433.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:49Z] INFO  17:49:34,811 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:49Z] INFO  17:49:34,811 HelpFormatter - Date/Time: 2016/04/14 17:49:34
[2016-04-15T00:49Z] INFO  17:49:34,812 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:49Z] INFO  17:49:34,812 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:49Z] INFO  17:49:34,812 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:49Z] INFO  17:49:34,815 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:49Z] INFO  17:49:34,816 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:49Z] INFO  17:49:34,816 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:49Z] INFO  17:49:34,821 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/4/R14-18105_kapa-NGv3-PE100-NGv3-sort-4_15512869_31144471-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/4/R14-18105_kapa-NGv3-PE100-NGv3-4_15512869_31144471-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/4/tx/tmpvVMvHN/R14-18105_kapa-NGv3-PE100-NGv3-4_15512869_31144471.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:49Z] INFO  17:49:34,829 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:49Z] INFO  17:49:34,832 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:49Z] INFO  17:49:34,833 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:49Z] INFO  17:49:34,833 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:49Z] INFO  17:49:34,838 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/4/R14-18105_kapa-NGv3-PE100-NGv3-sort-4_52709749_68338393-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/4/R14-18105_kapa-NGv3-PE100-NGv3-4_52709749_68338393-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/4/tx/tmpBJURxf/R14-18105_kapa-NGv3-PE100-NGv3-4_52709749_68338393.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:49Z] INFO  17:49:34,851 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:49Z] INFO  17:49:34,859 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:49Z] INFO  17:49:34,860 HelpFormatter - Date/Time: 2016/04/14 17:49:34
[2016-04-15T00:49Z] INFO  17:49:34,861 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:49Z] INFO  17:49:34,862 HelpFormatter - Date/Time: 2016/04/14 17:49:34
[2016-04-15T00:49Z] INFO  17:49:34,863 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:49Z] INFO  17:49:34,863 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:49Z] INFO  17:49:34,863 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:49Z] INFO  17:49:35,008 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:49Z] INFO  17:49:35,027 ProgressMeter -            done    356274.0    15.0 s      42.0 s       99.9%    15.0 s       0.0 s
[2016-04-15T00:49Z] INFO  17:49:35,028 ProgressMeter - Total runtime 15.23 secs, 0.25 min, 0.00 hours
[2016-04-15T00:49Z] INFO  17:49:35,028 MicroScheduler - 12337 reads were filtered out during the traversal out of approximately 150338 total reads (8.21%)
[2016-04-15T00:49Z] INFO  17:49:35,029 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:49Z] INFO  17:49:35,029 MicroScheduler -   -> 214 reads (0.14% of total) failing BadMateFilter
[2016-04-15T00:49Z] INFO  17:49:35,029 MicroScheduler -   -> 12029 reads (8.00% of total) failing DuplicateReadFilter
[2016-04-15T00:49Z] INFO  17:49:35,032 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:49Z] INFO  17:49:35,032 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:49Z] INFO  17:49:35,032 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:49Z] INFO  17:49:35,032 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:49Z] INFO  17:49:35,033 MicroScheduler -   -> 94 reads (0.06% of total) failing UnmappedReadFilter
[2016-04-15T00:49Z] INFO  17:49:35,040 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:49Z] INFO  17:49:35,044 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:49Z] GATK: UnifiedGenotyper
[2016-04-15T00:49Z] INFO  17:49:35,240 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:49Z] INFO  17:49:35,249 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:49Z] INFO  17:49:35,254 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:49Z] INFO  17:49:35,265 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:49Z] INFO  17:49:35,285 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:49Z] INFO  17:49:35,306 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:49Z] INFO  17:49:35,326 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-15T00:49Z] INFO  17:49:35,329 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-15T00:49Z] INFO  17:49:35,409 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.10
[2016-04-15T00:49Z] INFO  17:49:35,668 IntervalUtils - Processing 142047 bp from intervals
[2016-04-15T00:49Z] WARN  17:49:35,673 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:49Z] INFO  17:49:35,799 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:49Z] INFO  17:49:35,811 IntervalUtils - Processing 83782 bp from intervals
[2016-04-15T00:49Z] WARN  17:49:35,835 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:49Z] INFO  17:49:35,874 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:49Z] INFO  17:49:35,874 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:49Z] INFO  17:49:35,875 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:49Z] INFO  17:49:35,875 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:49Z] INFO  17:49:35,919 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:49Z] INFO  17:49:35,920 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:49Z] INFO  17:49:35,926 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:49Z] INFO  17:49:35,986 IntervalUtils - Processing 90668 bp from intervals
[2016-04-15T00:49Z] WARN  17:49:35,992 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:49Z] INFO  17:49:36,027 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:49Z] INFO  17:49:36,028 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:49Z] INFO  17:49:36,029 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:49Z] INFO  17:49:36,029 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:49Z] INFO  17:49:36,124 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:49Z] INFO  17:49:36,125 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:49Z] INFO  17:49:36,126 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:49Z] INFO  17:49:36,214 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:49Z] INFO  17:49:36,216 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:49Z] INFO  17:49:36,216 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:49Z] INFO  17:49:36,217 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:49Z] INFO  17:49:36,284 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:49Z] INFO  17:49:36,284 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:49Z] INFO  17:49:36,406 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:49Z] GATK: UnifiedGenotyper
[2016-04-15T00:49Z] INFO  17:49:36,868 ProgressMeter -            done   1181875.0    28.0 s      24.0 s      100.0%    28.0 s       0.0 s
[2016-04-15T00:49Z] INFO  17:49:36,868 ProgressMeter - Total runtime 28.64 secs, 0.48 min, 0.01 hours
[2016-04-15T00:49Z] INFO  17:49:36,869 MicroScheduler - 30196 reads were filtered out during the traversal out of approximately 360728 total reads (8.37%)
[2016-04-15T00:49Z] INFO  17:49:36,869 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:49Z] INFO  17:49:36,869 MicroScheduler -   -> 510 reads (0.14% of total) failing BadMateFilter
[2016-04-15T00:49Z] INFO  17:49:36,869 MicroScheduler -   -> 29482 reads (8.17% of total) failing DuplicateReadFilter
[2016-04-15T00:49Z] INFO  17:49:36,870 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:49Z] INFO  17:49:36,870 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:49Z] INFO  17:49:36,870 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:49Z] INFO  17:49:36,870 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:49Z] INFO  17:49:36,871 MicroScheduler -   -> 204 reads (0.06% of total) failing UnmappedReadFilter
[2016-04-15T00:49Z] INFO  17:49:36,962 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:49Z] INFO  17:49:36,964 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:49Z] INFO  17:49:36,965 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:49Z] INFO  17:49:36,965 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:49Z] INFO  17:49:36,969 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/4/R14-18105_kapa-NGv3-PE100-NGv3-sort-4_68340604_83852298-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/4/R14-18105_kapa-NGv3-PE100-NGv3-4_68340604_83852298-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/4/tx/tmp4L7Oxu/R14-18105_kapa-NGv3-PE100-NGv3-4_68340604_83852298.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:49Z] INFO  17:49:36,977 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:49Z] INFO  17:49:36,978 HelpFormatter - Date/Time: 2016/04/14 17:49:36
[2016-04-15T00:49Z] INFO  17:49:36,979 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:49Z] INFO  17:49:36,979 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:49Z] INFO  17:49:37,162 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:49Z] INFO  17:49:37,391 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:49Z] INFO  17:49:37,415 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:49Z] INFO  17:49:37,525 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.11
[2016-04-15T00:49Z] INFO  17:49:38,053 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:49Z] INFO  17:49:38,057 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:49Z] INFO  17:49:38,057 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:49Z] INFO  17:49:38,058 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:49Z] INFO  17:49:38,062 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/4/R14-18105_kapa-NGv3-PE100-NGv3-sort-4_83857133_99393738-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/4/R14-18105_kapa-NGv3-PE100-NGv3-4_83857133_99393738-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/4/tx/tmp7qsSe5/R14-18105_kapa-NGv3-PE100-NGv3-4_83857133_99393738.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:49Z] INFO  17:49:38,072 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:49Z] INFO  17:49:38,083 HelpFormatter - Date/Time: 2016/04/14 17:49:38
[2016-04-15T00:49Z] INFO  17:49:38,084 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:49Z] INFO  17:49:38,085 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:49Z] INFO  17:49:38,101 IntervalUtils - Processing 197466 bp from intervals
[2016-04-15T00:49Z] WARN  17:49:38,107 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:49Z] INFO  17:49:38,198 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:49Z] INFO  17:49:38,204 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:49Z] INFO  17:49:38,318 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:49Z] INFO  17:49:38,351 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:49Z] INFO  17:49:38,352 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:49Z] INFO  17:49:38,353 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:49Z] INFO  17:49:38,353 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:49Z] GATK: UnifiedGenotyper
[2016-04-15T00:49Z] INFO  17:49:38,443 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:49Z] INFO  17:49:38,444 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:49Z] INFO  17:49:38,583 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:49Z] INFO  17:49:38,592 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:49Z] INFO  17:49:38,675 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-15T00:49Z] INFO  17:49:39,020 IntervalUtils - Processing 124091 bp from intervals
[2016-04-15T00:49Z] WARN  17:49:39,038 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:49Z] INFO  17:49:39,140 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:49Z] INFO  17:49:39,239 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:49Z] INFO  17:49:39,240 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:49Z] INFO  17:49:39,241 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:49Z] INFO  17:49:39,241 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:49Z] INFO  17:49:39,319 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:49Z] INFO  17:49:39,320 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:49Z] INFO  17:49:39,804 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:49Z] INFO  17:49:39,810 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:49Z] INFO  17:49:39,810 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:49Z] INFO  17:49:39,811 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:49Z] INFO  17:49:39,816 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/4/R14-18105_kapa-NGv3-PE100-NGv3-sort-4_99397339_115544957-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/4/R14-18105_kapa-NGv3-PE100-NGv3-4_99397339_115544957-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/4/tx/tmp7qvK5U/R14-18105_kapa-NGv3-PE100-NGv3-4_99397339_115544957.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:49Z] INFO  17:49:39,826 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:49Z] INFO  17:49:39,837 HelpFormatter - Date/Time: 2016/04/14 17:49:39
[2016-04-15T00:49Z] INFO  17:49:39,838 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:49Z] INFO  17:49:39,839 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:49Z] INFO  17:49:40,028 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:49Z] INFO  17:49:40,340 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:49Z] INFO  17:49:40,349 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:49Z] INFO  17:49:40,420 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-15T00:49Z] INFO  17:49:40,837 IntervalUtils - Processing 153852 bp from intervals
[2016-04-15T00:49Z] WARN  17:49:40,843 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:49Z] INFO  17:49:40,987 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:49Z] INFO  17:49:41,130 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:49Z] INFO  17:49:41,131 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:49Z] INFO  17:49:41,131 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:49Z] INFO  17:49:41,137 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:49Z] INFO  17:49:41,230 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:49Z] INFO  17:49:41,231 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:49Z] INFO  17:49:41,270 ProgressMeter -      3:45804504    819684.0    30.0 s      36.0 s       85.8%    34.0 s       4.0 s
[2016-04-15T00:49Z] INFO  17:49:41,667 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:49Z] INFO  17:49:41,670 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:49Z] INFO  17:49:41,671 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:49Z] INFO  17:49:41,671 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:49Z] INFO  17:49:41,676 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/4/R14-18105_kapa-NGv3-PE100-NGv3-sort-4_115584857_134074404-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/4/R14-18105_kapa-NGv3-PE100-NGv3-4_115584857_134074404-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/4/tx/tmpWgXpGd/R14-18105_kapa-NGv3-PE100-NGv3-4_115584857_134074404.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:49Z] INFO  17:49:41,686 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:49Z] INFO  17:49:41,697 HelpFormatter - Date/Time: 2016/04/14 17:49:41
[2016-04-15T00:49Z] INFO  17:49:41,698 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:49Z] INFO  17:49:41,698 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:49Z] INFO  17:49:41,849 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:49Z] INFO  17:49:42,022 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:49Z] INFO  17:49:42,031 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:49Z] INFO  17:49:42,100 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-15T00:49Z] INFO  17:49:42,562 IntervalUtils - Processing 157938 bp from intervals
[2016-04-15T00:49Z] WARN  17:49:42,571 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:49Z] INFO  17:49:42,690 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:49Z] INFO  17:49:42,774 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:49Z] INFO  17:49:42,775 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:49Z] INFO  17:49:42,776 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:49Z] INFO  17:49:42,776 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:49Z] INFO  17:49:42,844 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:49Z] INFO  17:49:42,845 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:49Z] INFO  17:49:43,048 ProgressMeter -      3:51897003   1816155.0    30.0 s      16.0 s       56.2%    53.0 s      23.0 s
[2016-04-15T00:49Z] INFO  17:49:43,646 ProgressMeter -            done    309734.0    15.0 s      49.0 s       99.9%    15.0 s       0.0 s
[2016-04-15T00:49Z] INFO  17:49:43,647 ProgressMeter - Total runtime 15.38 secs, 0.26 min, 0.00 hours
[2016-04-15T00:49Z] INFO  17:49:43,648 MicroScheduler - 11592 reads were filtered out during the traversal out of approximately 141826 total reads (8.17%)
[2016-04-15T00:49Z] INFO  17:49:43,648 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:49Z] INFO  17:49:43,649 MicroScheduler -   -> 202 reads (0.14% of total) failing BadMateFilter
[2016-04-15T00:49Z] INFO  17:49:43,650 MicroScheduler -   -> 11305 reads (7.97% of total) failing DuplicateReadFilter
[2016-04-15T00:49Z] INFO  17:49:43,650 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:49Z] INFO  17:49:43,651 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:49Z] INFO  17:49:43,651 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:49Z] INFO  17:49:43,652 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:49Z] INFO  17:49:43,652 MicroScheduler -   -> 85 reads (0.06% of total) failing UnmappedReadFilter
[2016-04-15T00:49Z] INFO  17:49:44,283 ProgressMeter -            done    258232.0    13.0 s      53.0 s      100.0%    13.0 s       0.0 s
[2016-04-15T00:49Z] INFO  17:49:44,283 ProgressMeter - Total runtime 13.85 secs, 0.23 min, 0.00 hours
[2016-04-15T00:49Z] INFO  17:49:44,284 MicroScheduler - 9361 reads were filtered out during the traversal out of approximately 114325 total reads (8.19%)
[2016-04-15T00:49Z] INFO  17:49:44,284 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:49Z] INFO  17:49:44,284 MicroScheduler -   -> 174 reads (0.15% of total) failing BadMateFilter
[2016-04-15T00:49Z] INFO  17:49:44,285 MicroScheduler -   -> 9128 reads (7.98% of total) failing DuplicateReadFilter
[2016-04-15T00:49Z] INFO  17:49:44,285 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:49Z] INFO  17:49:44,288 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:49Z] INFO  17:49:44,289 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:49Z] INFO  17:49:44,289 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:49Z] INFO  17:49:44,289 MicroScheduler -   -> 59 reads (0.05% of total) failing UnmappedReadFilter
[2016-04-15T00:49Z] INFO  17:49:44,981 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:49Z] GATK: UnifiedGenotyper
[2016-04-15T00:49Z] INFO  17:49:45,543 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:49Z] INFO  17:49:45,683 ProgressMeter -            done   1082933.0    34.0 s      31.0 s      100.0%    34.0 s       0.0 s
[2016-04-15T00:49Z] INFO  17:49:45,683 ProgressMeter - Total runtime 34.44 secs, 0.57 min, 0.01 hours
[2016-04-15T00:49Z] INFO  17:49:45,683 MicroScheduler - 35468 reads were filtered out during the traversal out of approximately 424505 total reads (8.36%)
[2016-04-15T00:49Z] INFO  17:49:45,684 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:49Z] INFO  17:49:45,684 MicroScheduler -   -> 550 reads (0.13% of total) failing BadMateFilter
[2016-04-15T00:49Z] INFO  17:49:45,684 MicroScheduler -   -> 34653 reads (8.16% of total) failing DuplicateReadFilter
[2016-04-15T00:49Z] INFO  17:49:45,685 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:49Z] INFO  17:49:45,685 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:49Z] INFO  17:49:45,685 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:49Z] INFO  17:49:45,685 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:49Z] INFO  17:49:45,686 MicroScheduler -   -> 265 reads (0.06% of total) failing UnmappedReadFilter
[2016-04-15T00:49Z] GATK: UnifiedGenotyper
[2016-04-15T00:49Z] INFO  17:49:46,911 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:49Z] GATK: UnifiedGenotyper
[2016-04-15T00:49Z] INFO  17:49:48,119 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:49Z] INFO  17:49:48,123 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:49Z] INFO  17:49:48,124 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:49Z] INFO  17:49:48,124 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:49Z] INFO  17:49:48,132 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/4/R14-18105_kapa-NGv3-PE100-NGv3-sort-4_134075461_150351181-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/4/R14-18105_kapa-NGv3-PE100-NGv3-4_134075461_150351181-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/4/tx/tmp6fYTrr/R14-18105_kapa-NGv3-PE100-NGv3-4_134075461_150351181.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:49Z] INFO  17:49:48,137 ProgressMeter -            done    255123.0    12.0 s      47.0 s       99.9%    12.0 s       0.0 s
[2016-04-15T00:49Z] INFO  17:49:48,138 ProgressMeter - Total runtime 12.11 secs, 0.20 min, 0.00 hours
[2016-04-15T00:49Z] INFO  17:49:48,138 MicroScheduler - 7975 reads were filtered out during the traversal out of approximately 97118 total reads (8.21%)
[2016-04-15T00:49Z] INFO  17:49:48,139 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:49Z] INFO  17:49:48,139 MicroScheduler -   -> 152 reads (0.16% of total) failing BadMateFilter
[2016-04-15T00:49Z] INFO  17:49:48,139 MicroScheduler -   -> 7777 reads (8.01% of total) failing DuplicateReadFilter
[2016-04-15T00:49Z] INFO  17:49:48,139 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:49Z] INFO  17:49:48,140 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:49Z] INFO  17:49:48,140 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:49Z] INFO  17:49:48,140 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:49Z] INFO  17:49:48,141 MicroScheduler -   -> 46 reads (0.05% of total) failing UnmappedReadFilter
[2016-04-15T00:49Z] INFO  17:49:48,152 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:49Z] INFO  17:49:48,153 HelpFormatter - Date/Time: 2016/04/14 17:49:48
[2016-04-15T00:49Z] INFO  17:49:48,153 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:49Z] INFO  17:49:48,153 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:49Z] INFO  17:49:48,299 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:49Z] INFO  17:49:48,356 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:49Z] INFO  17:49:48,359 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:49Z] INFO  17:49:48,359 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:49Z] INFO  17:49:48,359 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:49Z] INFO  17:49:48,363 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/4/R14-18105_kapa-NGv3-PE100-NGv3-sort-4_150354547_165878648-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/4/R14-18105_kapa-NGv3-PE100-NGv3-4_150354547_165878648-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/4/tx/tmpCEeQIE/R14-18105_kapa-NGv3-PE100-NGv3-4_150354547_165878648.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:49Z] INFO  17:49:48,383 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:49Z] INFO  17:49:48,383 HelpFormatter - Date/Time: 2016/04/14 17:49:48
[2016-04-15T00:49Z] INFO  17:49:48,384 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:49Z] INFO  17:49:48,384 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:49Z] INFO  17:49:48,466 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:49Z] INFO  17:49:48,474 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:49Z] INFO  17:49:48,527 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-15T00:49Z] INFO  17:49:48,548 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:49Z] INFO  17:49:48,836 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:49Z] INFO  17:49:48,857 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:49Z] INFO  17:49:48,928 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-15T00:49Z] INFO  17:49:49,074 ProgressMeter -            done    230295.0    12.0 s      55.0 s       99.9%    12.0 s       0.0 s
[2016-04-15T00:49Z] INFO  17:49:49,074 ProgressMeter - Total runtime 12.86 secs, 0.21 min, 0.00 hours
[2016-04-15T00:49Z] INFO  17:49:49,075 MicroScheduler - 8520 reads were filtered out during the traversal out of approximately 102111 total reads (8.34%)
[2016-04-15T00:49Z] INFO  17:49:49,075 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:49Z] INFO  17:49:49,079 MicroScheduler -   -> 150 reads (0.15% of total) failing BadMateFilter
[2016-04-15T00:49Z] INFO  17:49:49,079 MicroScheduler -   -> 8313 reads (8.14% of total) failing DuplicateReadFilter
[2016-04-15T00:49Z] INFO  17:49:49,079 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:49Z] INFO  17:49:49,080 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:49Z] INFO  17:49:49,080 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:49Z] INFO  17:49:49,080 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:49Z] INFO  17:49:49,080 MicroScheduler -   -> 57 reads (0.06% of total) failing UnmappedReadFilter
[2016-04-15T00:49Z] INFO  17:49:49,102 IntervalUtils - Processing 86890 bp from intervals
[2016-04-15T00:49Z] WARN  17:49:49,107 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:49Z] INFO  17:49:49,185 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:49Z] INFO  17:49:49,273 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:49Z] INFO  17:49:49,274 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:49Z] INFO  17:49:49,275 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:49Z] INFO  17:49:49,276 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:49Z] INFO  17:49:49,344 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:49Z] INFO  17:49:49,345 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:49Z] INFO  17:49:49,351 IntervalUtils - Processing 119752 bp from intervals
[2016-04-15T00:49Z] WARN  17:49:49,365 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:49Z] INFO  17:49:49,387 ProgressMeter -            done    720572.0    25.0 s      35.0 s      100.0%    25.0 s       0.0 s
[2016-04-15T00:49Z] INFO  17:49:49,387 ProgressMeter - Total runtime 25.82 secs, 0.43 min, 0.01 hours
[2016-04-15T00:49Z] INFO  17:49:49,388 MicroScheduler - 24851 reads were filtered out during the traversal out of approximately 299358 total reads (8.30%)
[2016-04-15T00:49Z] INFO  17:49:49,388 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:49Z] INFO  17:49:49,388 MicroScheduler -   -> 462 reads (0.15% of total) failing BadMateFilter
[2016-04-15T00:49Z] INFO  17:49:49,389 MicroScheduler -   -> 24212 reads (8.09% of total) failing DuplicateReadFilter
[2016-04-15T00:49Z] INFO  17:49:49,389 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:49Z] INFO  17:49:49,389 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:49Z] INFO  17:49:49,389 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:49Z] INFO  17:49:49,390 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:49Z] INFO  17:49:49,390 MicroScheduler -   -> 177 reads (0.06% of total) failing UnmappedReadFilter
[2016-04-15T00:49Z] INFO  17:49:49,468 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:49Z] INFO  17:49:49,495 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:49Z] INFO  17:49:49,501 ProgressMeter -            done    680726.0    27.0 s      41.0 s      100.0%    27.0 s       0.0 s
[2016-04-15T00:49Z] INFO  17:49:49,502 ProgressMeter - Total runtime 27.92 secs, 0.47 min, 0.01 hours
[2016-04-15T00:49Z] INFO  17:49:49,503 MicroScheduler - 26566 reads were filtered out during the traversal out of approximately 320691 total reads (8.28%)
[2016-04-15T00:49Z] INFO  17:49:49,504 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:49Z] INFO  17:49:49,505 MicroScheduler -   -> 450 reads (0.14% of total) failing BadMateFilter
[2016-04-15T00:49Z] INFO  17:49:49,505 MicroScheduler -   -> 25935 reads (8.09% of total) failing DuplicateReadFilter
[2016-04-15T00:49Z] INFO  17:49:49,506 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:49Z] INFO  17:49:49,507 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:49Z] INFO  17:49:49,508 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:49Z] INFO  17:49:49,509 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:49Z] INFO  17:49:49,509 MicroScheduler -   -> 181 reads (0.06% of total) failing UnmappedReadFilter
[2016-04-15T00:49Z] INFO  17:49:49,588 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:49Z] INFO  17:49:49,589 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:49Z] INFO  17:49:49,590 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:49Z] INFO  17:49:49,591 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:49Z] INFO  17:49:49,682 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:49Z] INFO  17:49:49,683 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:49Z] GATK: UnifiedGenotyper
[2016-04-15T00:49Z] INFO  17:49:50,439 ProgressMeter -            done    351075.0    17.0 s      51.0 s       99.9%    17.0 s       0.0 s
[2016-04-15T00:49Z] INFO  17:49:50,439 ProgressMeter - Total runtime 17.99 secs, 0.30 min, 0.00 hours
[2016-04-15T00:49Z] INFO  17:49:50,440 MicroScheduler - 14579 reads were filtered out during the traversal out of approximately 174224 total reads (8.37%)
[2016-04-15T00:49Z] INFO  17:49:50,440 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:49Z] INFO  17:49:50,440 MicroScheduler -   -> 254 reads (0.15% of total) failing BadMateFilter
[2016-04-15T00:49Z] INFO  17:49:50,440 MicroScheduler -   -> 14230 reads (8.17% of total) failing DuplicateReadFilter
[2016-04-15T00:49Z] INFO  17:49:50,441 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:49Z] INFO  17:49:50,441 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:49Z] INFO  17:49:50,441 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:49Z] INFO  17:49:50,441 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:49Z] INFO  17:49:50,442 MicroScheduler -   -> 95 reads (0.05% of total) failing UnmappedReadFilter
[2016-04-15T00:49Z] INFO  17:49:50,451 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:49Z] INFO  17:49:50,679 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:49Z] GATK: UnifiedGenotyper
[2016-04-15T00:49Z] INFO  17:49:50,786 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:49Z] INFO  17:49:50,789 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:49Z] INFO  17:49:50,790 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:49Z] INFO  17:49:50,790 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:49Z] INFO  17:49:50,795 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/4/R14-18105_kapa-NGv3-PE100-NGv3-sort-4_165889318_183245405-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/4/R14-18105_kapa-NGv3-PE100-NGv3-4_165889318_183245405-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/4/tx/tmp1pZQhE/R14-18105_kapa-NGv3-PE100-NGv3-4_165889318_183245405.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:49Z] INFO  17:49:50,817 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:49Z] INFO  17:49:50,818 HelpFormatter - Date/Time: 2016/04/14 17:49:50
[2016-04-15T00:49Z] INFO  17:49:50,818 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:49Z] INFO  17:49:50,818 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:49Z] GATK: UnifiedGenotyper
[2016-04-15T00:49Z] INFO  17:49:50,991 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:49Z] INFO  17:49:51,036 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:49Z] INFO  17:49:51,270 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:49Z] INFO  17:49:51,282 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:49Z] GATK: UnifiedGenotyper
[2016-04-15T00:49Z] INFO  17:49:51,366 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-15T00:49Z] INFO  17:49:51,729 IntervalUtils - Processing 78538 bp from intervals
[2016-04-15T00:49Z] WARN  17:49:51,735 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:49Z] INFO  17:49:51,773 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:49Z] INFO  17:49:51,892 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:49Z] INFO  17:49:51,973 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:49Z] INFO  17:49:51,974 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:49Z] INFO  17:49:51,975 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:49Z] INFO  17:49:51,976 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:49Z] INFO  17:49:52,020 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:49Z] INFO  17:49:52,027 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:49Z] GATK: UnifiedGenotyper
[2016-04-15T00:49Z] INFO  17:49:52,582 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:49Z] INFO  17:49:52,585 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:49Z] INFO  17:49:52,586 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:49Z] INFO  17:49:52,586 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:49Z] INFO  17:49:52,591 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/4/R14-18105_kapa-NGv3-PE100-NGv3-sort-4_183267803_191154276-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/4/R14-18105_kapa-NGv3-PE100-NGv3-4_183267803_191154276-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/4/tx/tmpU5Weha/R14-18105_kapa-NGv3-PE100-NGv3-4_183267803_191154276.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:49Z] INFO  17:49:52,620 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:49Z] INFO  17:49:52,621 HelpFormatter - Date/Time: 2016/04/14 17:49:52
[2016-04-15T00:49Z] INFO  17:49:52,622 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:49Z] INFO  17:49:52,626 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:49Z] INFO  17:49:52,798 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:49Z] INFO  17:49:53,035 ProgressMeter -            done    359128.0    17.0 s      47.0 s      100.0%    17.0 s       0.0 s
[2016-04-15T00:49Z] INFO  17:49:53,035 ProgressMeter - Total runtime 17.16 secs, 0.29 min, 0.00 hours
[2016-04-15T00:49Z] INFO  17:49:53,036 MicroScheduler - 13200 reads were filtered out during the traversal out of approximately 160076 total reads (8.25%)
[2016-04-15T00:49Z] INFO  17:49:53,036 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:49Z] INFO  17:49:53,036 MicroScheduler -   -> 210 reads (0.13% of total) failing BadMateFilter
[2016-04-15T00:49Z] INFO  17:49:53,037 MicroScheduler -   -> 12899 reads (8.06% of total) failing DuplicateReadFilter
[2016-04-15T00:49Z] INFO  17:49:53,037 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:49Z] INFO  17:49:53,037 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:49Z] INFO  17:49:53,037 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:49Z] INFO  17:49:53,038 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:49Z] INFO  17:49:53,038 MicroScheduler -   -> 91 reads (0.06% of total) failing UnmappedReadFilter
[2016-04-15T00:49Z] INFO  17:49:53,053 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:49Z] INFO  17:49:53,075 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:49Z] INFO  17:49:53,183 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.10
[2016-04-15T00:49Z] INFO  17:49:53,512 ProgressMeter -            done    782811.0    21.0 s      27.0 s      100.0%    21.0 s       0.0 s
[2016-04-15T00:49Z] INFO  17:49:53,513 ProgressMeter - Total runtime 21.78 secs, 0.36 min, 0.01 hours
[2016-04-15T00:49Z] INFO  17:49:53,513 MicroScheduler - 20558 reads were filtered out during the traversal out of approximately 252826 total reads (8.13%)
[2016-04-15T00:49Z] INFO  17:49:53,513 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:49Z] INFO  17:49:53,514 MicroScheduler -   -> 325 reads (0.13% of total) failing BadMateFilter
[2016-04-15T00:49Z] INFO  17:49:53,514 MicroScheduler -   -> 20081 reads (7.94% of total) failing DuplicateReadFilter
[2016-04-15T00:49Z] INFO  17:49:53,514 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:49Z] INFO  17:49:53,514 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:49Z] INFO  17:49:53,515 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:49Z] INFO  17:49:53,515 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:49Z] INFO  17:49:53,515 MicroScheduler -   -> 152 reads (0.06% of total) failing UnmappedReadFilter
[2016-04-15T00:49Z] INFO  17:49:53,662 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:49Z] INFO  17:49:53,666 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:49Z] INFO  17:49:53,666 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:49Z] INFO  17:49:53,667 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:49Z] INFO  17:49:53,671 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/5/R14-18105_kapa-NGv3-PE100-NGv3-sort-5_0_15580921-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/5/R14-18105_kapa-NGv3-PE100-NGv3-5_0_15580921-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/5/tx/tmp1dOwqY/R14-18105_kapa-NGv3-PE100-NGv3-5_0_15580921.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:49Z] INFO  17:49:53,696 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:49Z] INFO  17:49:53,697 HelpFormatter - Date/Time: 2016/04/14 17:49:53
[2016-04-15T00:49Z] INFO  17:49:53,697 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:49Z] INFO  17:49:53,697 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:49Z] INFO  17:49:53,704 IntervalUtils - Processing 99602 bp from intervals
[2016-04-15T00:49Z] WARN  17:49:53,709 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:49Z] INFO  17:49:53,825 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:49Z] INFO  17:49:53,891 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:49Z] INFO  17:49:53,899 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:49Z] INFO  17:49:53,903 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:49Z] INFO  17:49:53,904 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:49Z] INFO  17:49:53,905 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:49Z] INFO  17:49:53,940 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:49Z] INFO  17:49:53,944 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:49Z] INFO  17:49:53,944 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:49Z] INFO  17:49:53,945 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:49Z] INFO  17:49:53,949 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/5/R14-18105_kapa-NGv3-PE100-NGv3-sort-5_15616091_31267808-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/5/R14-18105_kapa-NGv3-PE100-NGv3-5_15616091_31267808-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/5/tx/tmpMHNPEy/R14-18105_kapa-NGv3-PE100-NGv3-5_15616091_31267808.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:49Z] INFO  17:49:53,952 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:49Z] INFO  17:49:53,953 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:49Z] INFO  17:49:53,960 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:49Z] INFO  17:49:53,969 HelpFormatter - Date/Time: 2016/04/14 17:49:53
[2016-04-15T00:49Z] INFO  17:49:53,970 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:49Z] INFO  17:49:53,971 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:49Z] INFO  17:49:54,114 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:49Z] INFO  17:49:54,123 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:49Z] INFO  17:49:54,193 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:49Z] INFO  17:49:54,208 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-15T00:49Z] INFO  17:49:54,356 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:49Z] INFO  17:49:54,359 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:49Z] INFO  17:49:54,360 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:49Z] INFO  17:49:54,360 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:49Z] INFO  17:49:54,371 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/5/R14-18105_kapa-NGv3-PE100-NGv3-sort-5_31294068_49695124-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/5/R14-18105_kapa-NGv3-PE100-NGv3-5_31294068_49695124-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/5/tx/tmpErpP0G/R14-18105_kapa-NGv3-PE100-NGv3-5_31294068_49695124.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:49Z] INFO  17:49:54,379 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:49Z] INFO  17:49:54,380 HelpFormatter - Date/Time: 2016/04/14 17:49:54
[2016-04-15T00:49Z] INFO  17:49:54,381 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:49Z] INFO  17:49:54,381 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:49Z] INFO  17:49:54,405 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:49Z] INFO  17:49:54,414 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:49Z] INFO  17:49:54,420 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:49Z] INFO  17:49:54,467 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-15T00:49Z] INFO  17:49:54,553 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:49Z] INFO  17:49:54,582 IntervalUtils - Processing 125185 bp from intervals
[2016-04-15T00:49Z] WARN  17:49:54,587 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:49Z] INFO  17:49:54,698 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:49Z] INFO  17:49:54,777 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:49Z] INFO  17:49:54,778 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:49Z] INFO  17:49:54,790 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:49Z] INFO  17:49:54,791 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:49Z] INFO  17:49:54,790 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:49Z] INFO  17:49:54,811 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:49Z] GATK: UnifiedGenotyper
[2016-04-15T00:49Z] INFO  17:49:54,864 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:49Z] INFO  17:49:54,875 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:49Z] INFO  17:49:54,890 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-15T00:49Z] INFO  17:49:54,982 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:49Z] INFO  17:49:55,017 IntervalUtils - Processing 26887 bp from intervals
[2016-04-15T00:49Z] WARN  17:49:55,023 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:49Z] INFO  17:49:55,095 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:49Z] INFO  17:49:55,098 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:49Z] INFO  17:49:55,098 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:49Z] INFO  17:49:55,099 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:49Z] INFO  17:49:55,103 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/5/R14-18105_kapa-NGv3-PE100-NGv3-sort-5_49695692_65288736-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/5/R14-18105_kapa-NGv3-PE100-NGv3-5_49695692_65288736-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/5/tx/tmpV_NurQ/R14-18105_kapa-NGv3-PE100-NGv3-5_49695692_65288736.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:49Z] INFO  17:49:55,139 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:49Z] INFO  17:49:55,140 HelpFormatter - Date/Time: 2016/04/14 17:49:55
[2016-04-15T00:49Z] INFO  17:49:55,141 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:49Z] INFO  17:49:55,141 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:49Z] INFO  17:49:55,166 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:49Z] INFO  17:49:55,232 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:49Z] INFO  17:49:55,245 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:49Z] INFO  17:49:55,246 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:49Z] INFO  17:49:55,247 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:49Z] INFO  17:49:55,314 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:49Z] INFO  17:49:55,315 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:49Z] INFO  17:49:55,341 IntervalUtils - Processing 183626 bp from intervals
[2016-04-15T00:49Z] GATK: UnifiedGenotyper
[2016-04-15T00:49Z] INFO  17:49:55,347 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:49Z] WARN  17:49:55,358 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:49Z] INFO  17:49:55,489 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:49Z] INFO  17:49:55,623 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:49Z] INFO  17:49:55,625 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:49Z] INFO  17:49:55,625 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:49Z] INFO  17:49:55,627 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:49Z] INFO  17:49:55,648 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:49Z] INFO  17:49:55,659 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:49Z] INFO  17:49:55,670 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:49Z] INFO  17:49:55,671 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:49Z] INFO  17:49:55,754 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.09
[2016-04-15T00:49Z] INFO  17:49:56,252 IntervalUtils - Processing 108713 bp from intervals
[2016-04-15T00:49Z] WARN  17:49:56,262 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:49Z] INFO  17:49:56,377 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:49Z] INFO  17:49:56,490 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:49Z] INFO  17:49:56,496 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:49Z] INFO  17:49:56,497 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:49Z] INFO  17:49:56,498 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:49Z] INFO  17:49:56,570 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:49Z] INFO  17:49:56,570 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:49Z] INFO  17:49:56,592 ProgressMeter -            done    303616.0    17.0 s      57.0 s       99.9%    17.0 s       0.0 s
[2016-04-15T00:49Z] INFO  17:49:56,593 ProgressMeter - Total runtime 17.35 secs, 0.29 min, 0.00 hours
[2016-04-15T00:49Z] INFO  17:49:56,593 MicroScheduler - 12964 reads were filtered out during the traversal out of approximately 150687 total reads (8.60%)
[2016-04-15T00:49Z] INFO  17:49:56,594 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:49Z] INFO  17:49:56,594 MicroScheduler -   -> 180 reads (0.12% of total) failing BadMateFilter
[2016-04-15T00:49Z] INFO  17:49:56,594 MicroScheduler -   -> 12681 reads (8.42% of total) failing DuplicateReadFilter
[2016-04-15T00:49Z] INFO  17:49:56,594 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:49Z] INFO  17:49:56,595 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:49Z] INFO  17:49:56,595 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:49Z] INFO  17:49:56,595 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:49Z] INFO  17:49:56,595 MicroScheduler -   -> 103 reads (0.07% of total) failing UnmappedReadFilter
[2016-04-15T00:49Z] INFO  17:49:58,071 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:49Z] INFO  17:49:58,179 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:49Z] INFO  17:49:58,182 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:49Z] INFO  17:49:58,183 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:49Z] INFO  17:49:58,183 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:49Z] INFO  17:49:58,188 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/5/R14-18105_kapa-NGv3-PE100-NGv3-sort-5_65290574_80809536-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/5/R14-18105_kapa-NGv3-PE100-NGv3-5_65290574_80809536-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/5/tx/tmpWF5e0W/R14-18105_kapa-NGv3-PE100-NGv3-5_65290574_80809536.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:49Z] INFO  17:49:58,220 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:49Z] INFO  17:49:58,221 HelpFormatter - Date/Time: 2016/04/14 17:49:58
[2016-04-15T00:49Z] INFO  17:49:58,222 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:49Z] INFO  17:49:58,222 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:49Z] GATK: UnifiedGenotyper
[2016-04-15T00:49Z] INFO  17:49:58,444 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:49Z] INFO  17:49:58,668 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:49Z] INFO  17:49:58,670 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:49Z] INFO  17:49:58,671 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:49Z] INFO  17:49:58,671 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:49Z] INFO  17:49:58,686 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/5/R14-18105_kapa-NGv3-PE100-NGv3-sort-5_80911291_96430739-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/5/R14-18105_kapa-NGv3-PE100-NGv3-5_80911291_96430739-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/5/tx/tmp2k0UrX/R14-18105_kapa-NGv3-PE100-NGv3-5_80911291_96430739.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:49Z] INFO  17:49:58,701 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:49Z] INFO  17:49:58,702 HelpFormatter - Date/Time: 2016/04/14 17:49:58
[2016-04-15T00:49Z] INFO  17:49:58,703 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:49Z] INFO  17:49:58,723 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:49Z] INFO  17:49:58,739 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:49Z] INFO  17:49:58,750 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:49Z] INFO  17:49:58,820 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-15T00:49Z] INFO  17:49:58,893 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:49Z] INFO  17:49:58,889 ProgressMeter -            done    430817.0    17.0 s      41.0 s      100.0%    17.0 s       0.0 s
[2016-04-15T00:49Z] INFO  17:49:58,890 ProgressMeter - Total runtime 17.76 secs, 0.30 min, 0.00 hours
[2016-04-15T00:49Z] INFO  17:49:58,890 MicroScheduler - 14262 reads were filtered out during the traversal out of approximately 174737 total reads (8.16%)
[2016-04-15T00:49Z] INFO  17:49:58,890 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:49Z] INFO  17:49:58,891 MicroScheduler -   -> 291 reads (0.17% of total) failing BadMateFilter
[2016-04-15T00:49Z] INFO  17:49:58,891 MicroScheduler -   -> 13855 reads (7.93% of total) failing DuplicateReadFilter
[2016-04-15T00:49Z] INFO  17:49:58,891 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:49Z] INFO  17:49:58,891 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:49Z] INFO  17:49:58,892 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:49Z] INFO  17:49:58,892 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:49Z] INFO  17:49:58,892 MicroScheduler -   -> 116 reads (0.07% of total) failing UnmappedReadFilter
[2016-04-15T00:49Z] INFO  17:49:58,906 ProgressMeter -            done    675755.0    16.0 s      23.0 s      100.0%    16.0 s       0.0 s
[2016-04-15T00:49Z] INFO  17:49:58,907 ProgressMeter - Total runtime 16.13 secs, 0.27 min, 0.00 hours
[2016-04-15T00:49Z] INFO  17:49:58,907 MicroScheduler - 12731 reads were filtered out during the traversal out of approximately 154398 total reads (8.25%)
[2016-04-15T00:49Z] INFO  17:49:58,907 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:49Z] INFO  17:49:58,908 MicroScheduler -   -> 227 reads (0.15% of total) failing BadMateFilter
[2016-04-15T00:49Z] INFO  17:49:58,908 MicroScheduler -   -> 12387 reads (8.02% of total) failing DuplicateReadFilter
[2016-04-15T00:49Z] INFO  17:49:58,908 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:49Z] INFO  17:49:58,908 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:49Z] INFO  17:49:58,909 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:49Z] INFO  17:49:58,909 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:49Z] INFO  17:49:58,909 MicroScheduler -   -> 117 reads (0.08% of total) failing UnmappedReadFilter
[2016-04-15T00:49Z] INFO  17:49:59,153 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:49Z] INFO  17:49:59,173 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:49Z] INFO  17:49:59,253 IntervalUtils - Processing 203113 bp from intervals
[2016-04-15T00:49Z] INFO  17:49:59,263 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.09
[2016-04-15T00:49Z] WARN  17:49:59,258 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:49Z] INFO  17:49:59,364 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:49Z] INFO  17:49:59,479 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:49Z] INFO  17:49:59,480 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:49Z] INFO  17:49:59,480 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:49Z] INFO  17:49:59,481 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:49Z] INFO  17:49:59,533 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:49Z] INFO  17:49:59,534 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:49Z] INFO  17:49:59,734 ProgressMeter -            done   2880332.0    46.0 s      16.0 s      100.0%    46.0 s       0.0 s
[2016-04-15T00:49Z] INFO  17:49:59,734 ProgressMeter - Total runtime 46.71 secs, 0.78 min, 0.01 hours
[2016-04-15T00:49Z] INFO  17:49:59,734 MicroScheduler - 56909 reads were filtered out during the traversal out of approximately 680967 total reads (8.36%)
[2016-04-15T00:49Z] INFO  17:49:59,735 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:49Z] INFO  17:49:59,735 MicroScheduler -   -> 1008 reads (0.15% of total) failing BadMateFilter
[2016-04-15T00:49Z] INFO  17:49:59,735 MicroScheduler -   -> 55507 reads (8.15% of total) failing DuplicateReadFilter
[2016-04-15T00:49Z] INFO  17:49:59,735 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:49Z] INFO  17:49:59,736 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:49Z] INFO  17:49:59,736 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:49Z] INFO  17:49:59,736 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:49Z] INFO  17:49:59,737 MicroScheduler -   -> 394 reads (0.06% of total) failing UnmappedReadFilter
[2016-04-15T00:49Z] INFO  17:49:59,760 IntervalUtils - Processing 113632 bp from intervals
[2016-04-15T00:49Z] WARN  17:49:59,765 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:49Z] INFO  17:49:59,866 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:49Z] INFO  17:49:59,992 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:49Z] INFO  17:49:59,993 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:49Z] INFO  17:49:59,993 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:49Z] INFO  17:49:59,994 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:50Z] INFO  17:50:00,079 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:50Z] INFO  17:50:00,080 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:50Z] INFO  17:50:00,240 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:50Z] INFO  17:50:00,291 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:50Z] INFO  17:50:00,417 ProgressMeter -            done    537877.0    22.0 s      41.0 s      100.0%    22.0 s       0.0 s
[2016-04-15T00:50Z] INFO  17:50:00,418 ProgressMeter - Total runtime 22.07 secs, 0.37 min, 0.01 hours
[2016-04-15T00:50Z] INFO  17:50:00,418 MicroScheduler - 19291 reads were filtered out during the traversal out of approximately 235865 total reads (8.18%)
[2016-04-15T00:50Z] INFO  17:50:00,419 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:50Z] INFO  17:50:00,419 MicroScheduler -   -> 354 reads (0.15% of total) failing BadMateFilter
[2016-04-15T00:50Z] INFO  17:50:00,419 MicroScheduler -   -> 18807 reads (7.97% of total) failing DuplicateReadFilter
[2016-04-15T00:50Z] INFO  17:50:00,419 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:50Z] INFO  17:50:00,420 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:50Z] INFO  17:50:00,420 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:50Z] INFO  17:50:00,420 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:50Z] INFO  17:50:00,420 MicroScheduler -   -> 130 reads (0.06% of total) failing UnmappedReadFilter
[2016-04-15T00:50Z] GATK: UnifiedGenotyper
[2016-04-15T00:50Z] GATK: UnifiedGenotyper
[2016-04-15T00:50Z] INFO  17:50:01,330 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:50Z] INFO  17:50:01,527 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:50Z] INFO  17:50:01,531 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:50Z] INFO  17:50:01,532 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:50Z] INFO  17:50:01,533 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:50Z] INFO  17:50:01,538 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/5/R14-18105_kapa-NGv3-PE100-NGv3-sort-5_96432513_112043579-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/5/R14-18105_kapa-NGv3-PE100-NGv3-5_96432513_112043579-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/5/tx/tmpGFVSuz/R14-18105_kapa-NGv3-PE100-NGv3-5_96432513_112043579.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:50Z] INFO  17:50:01,557 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:50Z] INFO  17:50:01,558 HelpFormatter - Date/Time: 2016/04/14 17:50:01
[2016-04-15T00:50Z] INFO  17:50:01,558 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:50Z] INFO  17:50:01,558 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:50Z] GATK: UnifiedGenotyper
[2016-04-15T00:50Z] INFO  17:50:01,793 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:50Z] INFO  17:50:01,885 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:50Z] INFO  17:50:02,025 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:50Z] INFO  17:50:02,062 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:50Z] INFO  17:50:02,131 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-15T00:50Z] GATK: UnifiedGenotyper
[2016-04-15T00:50Z] INFO  17:50:02,447 IntervalUtils - Processing 57322 bp from intervals
[2016-04-15T00:50Z] WARN  17:50:02,452 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:50Z] INFO  17:50:02,488 ProgressMeter -            done     60320.0     7.0 s     120.0 s       99.9%     7.0 s       0.0 s
[2016-04-15T00:50Z] INFO  17:50:02,489 ProgressMeter - Total runtime 7.24 secs, 0.12 min, 0.00 hours
[2016-04-15T00:50Z] INFO  17:50:02,490 MicroScheduler - 3001 reads were filtered out during the traversal out of approximately 35048 total reads (8.56%)
[2016-04-15T00:50Z] INFO  17:50:02,490 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:50Z] INFO  17:50:02,491 MicroScheduler -   -> 55 reads (0.16% of total) failing BadMateFilter
[2016-04-15T00:50Z] INFO  17:50:02,492 MicroScheduler -   -> 2922 reads (8.34% of total) failing DuplicateReadFilter
[2016-04-15T00:50Z] INFO  17:50:02,492 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:50Z] INFO  17:50:02,493 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:50Z] INFO  17:50:02,494 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:50Z] INFO  17:50:02,494 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:50Z] INFO  17:50:02,495 MicroScheduler -   -> 24 reads (0.07% of total) failing UnmappedReadFilter
[2016-04-15T00:50Z] INFO  17:50:02,522 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:50Z] INFO  17:50:02,607 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:50Z] INFO  17:50:02,608 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:50Z] INFO  17:50:02,608 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:50Z] INFO  17:50:02,608 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:50Z] INFO  17:50:02,706 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:50Z] INFO  17:50:02,707 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:50Z] INFO  17:50:03,188 ProgressMeter -            done    205394.0    13.0 s      67.0 s       99.9%    13.0 s       0.0 s
[2016-04-15T00:50Z] INFO  17:50:03,189 ProgressMeter - Total runtime 13.91 secs, 0.23 min, 0.00 hours
[2016-04-15T00:50Z] INFO  17:50:03,189 MicroScheduler - 8669 reads were filtered out during the traversal out of approximately 105495 total reads (8.22%)
[2016-04-15T00:50Z] INFO  17:50:03,190 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:50Z] INFO  17:50:03,190 MicroScheduler -   -> 153 reads (0.15% of total) failing BadMateFilter
[2016-04-15T00:50Z] INFO  17:50:03,190 MicroScheduler -   -> 8449 reads (8.01% of total) failing DuplicateReadFilter
[2016-04-15T00:50Z] INFO  17:50:03,191 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:50Z] INFO  17:50:03,191 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:50Z] INFO  17:50:03,191 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:50Z] INFO  17:50:03,191 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:50Z] INFO  17:50:03,192 MicroScheduler -   -> 67 reads (0.06% of total) failing UnmappedReadFilter
[2016-04-15T00:50Z] INFO  17:50:03,658 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:50Z] INFO  17:50:03,662 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:50Z] INFO  17:50:03,662 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:50Z] INFO  17:50:03,663 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:50Z] INFO  17:50:03,668 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/5/R14-18105_kapa-NGv3-PE100-NGv3-sort-5_112073555_127595521-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/5/R14-18105_kapa-NGv3-PE100-NGv3-5_112073555_127595521-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/5/tx/tmp3QvHzE/R14-18105_kapa-NGv3-PE100-NGv3-5_112073555_127595521.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:50Z] INFO  17:50:03,687 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:50Z] INFO  17:50:03,688 HelpFormatter - Date/Time: 2016/04/14 17:50:03
[2016-04-15T00:50Z] INFO  17:50:03,689 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:50Z] INFO  17:50:03,690 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:50Z] INFO  17:50:03,797 ProgressMeter -      4:11401706    762870.0    30.0 s      39.0 s       92.5%    32.0 s       2.0 s
[2016-04-15T00:50Z] INFO  17:50:03,799 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:50Z] INFO  17:50:03,803 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:50Z] INFO  17:50:03,803 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:50Z] INFO  17:50:03,804 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:50Z] INFO  17:50:03,808 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/5/R14-18105_kapa-NGv3-PE100-NGv3-sort-5_127597427_143191869-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/5/R14-18105_kapa-NGv3-PE100-NGv3-5_127597427_143191869-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/5/tx/tmpmHEWJV/R14-18105_kapa-NGv3-PE100-NGv3-5_127597427_143191869.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:50Z] INFO  17:50:03,821 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:50Z] INFO  17:50:03,822 HelpFormatter - Date/Time: 2016/04/14 17:50:03
[2016-04-15T00:50Z] INFO  17:50:03,823 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:50Z] INFO  17:50:03,823 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:50Z] INFO  17:50:03,905 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:50Z] INFO  17:50:04,022 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:50Z] INFO  17:50:04,108 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:50Z] INFO  17:50:04,136 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:50Z] INFO  17:50:04,144 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:50Z] INFO  17:50:04,213 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-15T00:50Z] INFO  17:50:04,258 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:50Z] INFO  17:50:04,290 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:50Z] INFO  17:50:04,376 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.09
[2016-04-15T00:50Z] GATK: UnifiedGenotyper
[2016-04-15T00:50Z] INFO  17:50:04,624 IntervalUtils - Processing 103986 bp from intervals
[2016-04-15T00:50Z] WARN  17:50:04,629 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:50Z] INFO  17:50:04,746 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:50Z] INFO  17:50:04,768 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:50Z] INFO  17:50:04,781 IntervalUtils - Processing 393653 bp from intervals
[2016-04-15T00:50Z] WARN  17:50:04,786 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:50Z] INFO  17:50:04,850 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:50Z] INFO  17:50:04,851 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:50Z] INFO  17:50:04,852 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:50Z] INFO  17:50:04,853 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:50Z] INFO  17:50:04,873 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:50Z] INFO  17:50:04,877 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:50Z] INFO  17:50:04,877 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:50Z] INFO  17:50:04,878 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:50Z] INFO  17:50:04,882 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/5/R14-18105_kapa-NGv3-PE100-NGv3-sort-5_143200044_158710347-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/5/R14-18105_kapa-NGv3-PE100-NGv3-5_143200044_158710347-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/5/tx/tmpVP7sB_/R14-18105_kapa-NGv3-PE100-NGv3-5_143200044_158710347.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:50Z] INFO  17:50:04,895 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:50Z] INFO  17:50:04,915 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:50Z] INFO  17:50:04,915 HelpFormatter - Date/Time: 2016/04/14 17:50:04
[2016-04-15T00:50Z] INFO  17:50:04,915 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:50Z] INFO  17:50:04,915 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:50Z] INFO  17:50:04,930 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:50Z] INFO  17:50:04,931 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:50Z] INFO  17:50:04,974 ProgressMeter -            done    829685.0    31.0 s      37.0 s      100.0%    31.0 s       0.0 s
[2016-04-15T00:50Z] INFO  17:50:04,975 ProgressMeter - Total runtime 31.20 secs, 0.52 min, 0.01 hours
[2016-04-15T00:50Z] INFO  17:50:04,975 MicroScheduler - 32716 reads were filtered out during the traversal out of approximately 410428 total reads (7.97%)
[2016-04-15T00:50Z] INFO  17:50:04,976 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:50Z] INFO  17:50:04,976 MicroScheduler -   -> 653 reads (0.16% of total) failing BadMateFilter
[2016-04-15T00:50Z] INFO  17:50:04,976 MicroScheduler -   -> 31774 reads (7.74% of total) failing DuplicateReadFilter
[2016-04-15T00:50Z] INFO  17:50:04,976 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:50Z] INFO  17:50:04,977 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:50Z] INFO  17:50:04,977 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:50Z] INFO  17:50:04,977 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:50Z] INFO  17:50:04,977 MicroScheduler -   -> 289 reads (0.07% of total) failing UnmappedReadFilter
[2016-04-15T00:50Z] INFO  17:50:05,000 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:50Z] INFO  17:50:05,001 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:50Z] INFO  17:50:05,002 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:50Z] INFO  17:50:05,002 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:50Z] INFO  17:50:05,005 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:50Z] INFO  17:50:05,008 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:50Z] INFO  17:50:05,009 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:50Z] INFO  17:50:05,009 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:50Z] INFO  17:50:05,014 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/5/R14-18105_kapa-NGv3-PE100-NGv3-sort-5_158711911_174870102-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/5/R14-18105_kapa-NGv3-PE100-NGv3-5_158711911_174870102-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/5/tx/tmpwF6GcK/R14-18105_kapa-NGv3-PE100-NGv3-5_158711911_174870102.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:50Z] INFO  17:50:05,036 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:50Z] INFO  17:50:05,038 HelpFormatter - Date/Time: 2016/04/14 17:50:05
[2016-04-15T00:50Z] INFO  17:50:05,039 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:50Z] INFO  17:50:05,039 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:50Z] INFO  17:50:05,049 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:50Z] INFO  17:50:05,050 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:50Z] INFO  17:50:05,104 ProgressMeter -            done    310683.0    15.0 s      49.0 s       99.9%    15.0 s       0.0 s
[2016-04-15T00:50Z] INFO  17:50:05,104 ProgressMeter - Total runtime 15.51 secs, 0.26 min, 0.00 hours
[2016-04-15T00:50Z] INFO  17:50:05,104 MicroScheduler - 11174 reads were filtered out during the traversal out of approximately 134921 total reads (8.28%)
[2016-04-15T00:50Z] INFO  17:50:05,105 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:50Z] INFO  17:50:05,105 MicroScheduler -   -> 190 reads (0.14% of total) failing BadMateFilter
[2016-04-15T00:50Z] INFO  17:50:05,105 MicroScheduler -   -> 10903 reads (8.08% of total) failing DuplicateReadFilter
[2016-04-15T00:50Z] INFO  17:50:05,105 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:50Z] INFO  17:50:05,106 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:50Z] INFO  17:50:05,106 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:50Z] INFO  17:50:05,106 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:50Z] INFO  17:50:05,106 MicroScheduler -   -> 81 reads (0.06% of total) failing UnmappedReadFilter
[2016-04-15T00:50Z] GATK: UnifiedGenotyper
[2016-04-15T00:50Z] INFO  17:50:05,114 ProgressMeter -            done    172946.0    13.0 s      75.0 s      100.0%    13.0 s       0.0 s
[2016-04-15T00:50Z] INFO  17:50:05,115 ProgressMeter - Total runtime 13.14 secs, 0.22 min, 0.00 hours
[2016-04-15T00:50Z] INFO  17:50:05,116 MicroScheduler - 6806 reads were filtered out during the traversal out of approximately 83383 total reads (8.16%)
[2016-04-15T00:50Z] INFO  17:50:05,117 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:50Z] INFO  17:50:05,117 MicroScheduler -   -> 131 reads (0.16% of total) failing BadMateFilter
[2016-04-15T00:50Z] INFO  17:50:05,118 MicroScheduler -   -> 6626 reads (7.95% of total) failing DuplicateReadFilter
[2016-04-15T00:50Z] INFO  17:50:05,119 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:50Z] INFO  17:50:05,119 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:50Z] INFO  17:50:05,119 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:50Z] INFO  17:50:05,120 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:50Z] INFO  17:50:05,121 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:50Z] INFO  17:50:05,121 MicroScheduler -   -> 49 reads (0.06% of total) failing UnmappedReadFilter
[2016-04-15T00:50Z] INFO  17:50:05,237 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:50Z] INFO  17:50:05,325 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:50Z] INFO  17:50:05,337 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:50Z] INFO  17:50:05,445 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.11
[2016-04-15T00:50Z] INFO  17:50:05,471 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:50Z] INFO  17:50:05,481 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:50Z] INFO  17:50:05,562 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-15T00:50Z] INFO  17:50:05,977 IntervalUtils - Processing 205172 bp from intervals
[2016-04-15T00:50Z] WARN  17:50:05,995 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:50Z] INFO  17:50:06,110 IntervalUtils - Processing 104189 bp from intervals
[2016-04-15T00:50Z] WARN  17:50:06,116 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:50Z] INFO  17:50:06,182 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:50Z] INFO  17:50:06,223 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:50Z] INFO  17:50:06,344 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:50Z] INFO  17:50:06,345 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:50Z] INFO  17:50:06,346 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:50Z] INFO  17:50:06,347 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:50Z] INFO  17:50:06,381 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:50Z] INFO  17:50:06,382 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:50Z] INFO  17:50:06,383 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:50Z] INFO  17:50:06,384 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:50Z] INFO  17:50:06,387 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:50Z] INFO  17:50:06,388 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:50Z] INFO  17:50:06,425 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:50Z] INFO  17:50:06,426 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:50Z] INFO  17:50:06,439 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:50Z] INFO  17:50:06,450 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:50Z] INFO  17:50:06,572 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:50Z] GATK: UnifiedGenotyper
[2016-04-15T00:50Z] GATK: UnifiedGenotyper
[2016-04-15T00:50Z] GATK: UnifiedGenotyper
[2016-04-15T00:50Z] INFO  17:50:07,396 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:50Z] INFO  17:50:07,399 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:50Z] INFO  17:50:07,400 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:50Z] INFO  17:50:07,400 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:50Z] INFO  17:50:07,405 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/5/R14-18105_kapa-NGv3-PE100-NGv3-sort-5_174919106_180915260-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/5/R14-18105_kapa-NGv3-PE100-NGv3-5_174919106_180915260-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/5/tx/tmpill1QF/R14-18105_kapa-NGv3-PE100-NGv3-5_174919106_180915260.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:50Z] INFO  17:50:07,414 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:50Z] INFO  17:50:07,425 HelpFormatter - Date/Time: 2016/04/14 17:50:07
[2016-04-15T00:50Z] INFO  17:50:07,426 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:50Z] INFO  17:50:07,427 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:50Z] INFO  17:50:07,596 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:50Z] INFO  17:50:07,796 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:50Z] INFO  17:50:07,813 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:50Z] INFO  17:50:07,903 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.09
[2016-04-15T00:50Z] INFO  17:50:08,235 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:50Z] INFO  17:50:08,238 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:50Z] INFO  17:50:08,239 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:50Z] INFO  17:50:08,239 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:50Z] INFO  17:50:08,244 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/6/R14-18105_kapa-NGv3-PE100-NGv3-sort-6_0_15509601-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/6/R14-18105_kapa-NGv3-PE100-NGv3-6_0_15509601-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/6/tx/tmpTor8cF/R14-18105_kapa-NGv3-PE100-NGv3-6_0_15509601.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:50Z] INFO  17:50:08,255 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:50Z] INFO  17:50:08,256 HelpFormatter - Date/Time: 2016/04/14 17:50:08
[2016-04-15T00:50Z] INFO  17:50:08,257 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:50Z] INFO  17:50:08,257 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:50Z] INFO  17:50:08,356 ProgressMeter -            done    326544.0    14.0 s      44.0 s       99.9%    14.0 s       0.0 s
[2016-04-15T00:50Z] INFO  17:50:08,356 ProgressMeter - Total runtime 14.45 secs, 0.24 min, 0.00 hours
[2016-04-15T00:50Z] INFO  17:50:08,356 MicroScheduler - 10718 reads were filtered out during the traversal out of approximately 129600 total reads (8.27%)
[2016-04-15T00:50Z] INFO  17:50:08,357 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:50Z] INFO  17:50:08,357 MicroScheduler -   -> 195 reads (0.15% of total) failing BadMateFilter
[2016-04-15T00:50Z] INFO  17:50:08,357 MicroScheduler -   -> 10462 reads (8.07% of total) failing DuplicateReadFilter
[2016-04-15T00:50Z] INFO  17:50:08,357 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:50Z] INFO  17:50:08,358 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:50Z] INFO  17:50:08,358 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:50Z] INFO  17:50:08,358 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:50Z] INFO  17:50:08,358 MicroScheduler -   -> 61 reads (0.05% of total) failing UnmappedReadFilter
[2016-04-15T00:50Z] INFO  17:50:08,458 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:50Z] INFO  17:50:08,466 IntervalUtils - Processing 163171 bp from intervals
[2016-04-15T00:50Z] WARN  17:50:08,480 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:50Z] INFO  17:50:08,635 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:50Z] INFO  17:50:08,704 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:50Z] INFO  17:50:08,705 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:50Z] INFO  17:50:08,706 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:50Z] INFO  17:50:08,718 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:50Z] INFO  17:50:08,720 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:50Z] INFO  17:50:08,734 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:50Z] INFO  17:50:08,777 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:50Z] INFO  17:50:08,778 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:50Z] INFO  17:50:08,831 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.10
[2016-04-15T00:50Z] INFO  17:50:09,333 IntervalUtils - Processing 139546 bp from intervals
[2016-04-15T00:50Z] WARN  17:50:09,337 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:50Z] INFO  17:50:09,473 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:50Z] INFO  17:50:09,552 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:50Z] INFO  17:50:09,553 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:50Z] INFO  17:50:09,554 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:50Z] INFO  17:50:09,555 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:50Z] INFO  17:50:09,630 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:50Z] INFO  17:50:09,630 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:50Z] INFO  17:50:09,796 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:50Z] INFO  17:50:09,799 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:50Z] INFO  17:50:09,799 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:50Z] INFO  17:50:09,799 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:50Z] INFO  17:50:09,803 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/6/R14-18105_kapa-NGv3-PE100-NGv3-sort-6_15511526_31080332-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/6/R14-18105_kapa-NGv3-PE100-NGv3-6_15511526_31080332-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/6/tx/tmpcsjXzN/R14-18105_kapa-NGv3-PE100-NGv3-6_15511526_31080332.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:50Z] INFO  17:50:09,829 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:50Z] INFO  17:50:09,830 HelpFormatter - Date/Time: 2016/04/14 17:50:09
[2016-04-15T00:50Z] INFO  17:50:09,830 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:50Z] INFO  17:50:09,831 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:50Z] INFO  17:50:09,899 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:50Z] INFO  17:50:10,021 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:50Z] INFO  17:50:10,199 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:50Z] INFO  17:50:10,208 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:50Z] INFO  17:50:10,282 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-15T00:50Z] INFO  17:50:10,282 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:50Z] INFO  17:50:10,284 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:50Z] INFO  17:50:10,284 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:50Z] INFO  17:50:10,285 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:50Z] INFO  17:50:10,289 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/6/R14-18105_kapa-NGv3-PE100-NGv3-sort-6_46598699_62284307-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/6/R14-18105_kapa-NGv3-PE100-NGv3-6_46598699_62284307-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/6/tx/tmp2ChFmz/R14-18105_kapa-NGv3-PE100-NGv3-6_46598699_62284307.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:50Z] GATK: UnifiedGenotyper
[2016-04-15T00:50Z] INFO  17:50:10,308 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:50Z] INFO  17:50:10,309 HelpFormatter - Date/Time: 2016/04/14 17:50:10
[2016-04-15T00:50Z] INFO  17:50:10,310 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:50Z] INFO  17:50:10,310 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:50Z] INFO  17:50:10,418 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:50Z] INFO  17:50:10,421 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:50Z] INFO  17:50:10,422 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:50Z] INFO  17:50:10,422 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:50Z] INFO  17:50:10,427 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/6/R14-18105_kapa-NGv3-PE100-NGv3-sort-6_31083801_46593245-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/6/R14-18105_kapa-NGv3-PE100-NGv3-6_31083801_46593245-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/6/tx/tmpMLU9mQ/R14-18105_kapa-NGv3-PE100-NGv3-6_31083801_46593245.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:50Z] INFO  17:50:10,436 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:50Z] INFO  17:50:10,437 HelpFormatter - Date/Time: 2016/04/14 17:50:10
[2016-04-15T00:50Z] INFO  17:50:10,438 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:50Z] INFO  17:50:10,438 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:50Z] INFO  17:50:10,500 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:50Z] INFO  17:50:10,619 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:50Z] INFO  17:50:10,772 IntervalUtils - Processing 239663 bp from intervals
[2016-04-15T00:50Z] WARN  17:50:10,778 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:50Z] INFO  17:50:10,803 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:50Z] INFO  17:50:10,833 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:50Z] INFO  17:50:10,883 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:50Z] INFO  17:50:10,917 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-15T00:50Z] INFO  17:50:10,929 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:50Z] INFO  17:50:10,953 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:50Z] INFO  17:50:11,037 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:50Z] INFO  17:50:11,038 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:50Z] INFO  17:50:11,039 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:50Z] INFO  17:50:11,040 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:50Z] INFO  17:50:11,065 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.11
[2016-04-15T00:50Z] INFO  17:50:11,110 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:50Z] INFO  17:50:11,111 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:50Z] INFO  17:50:11,216 ProgressMeter -            done    292827.0    14.0 s      50.0 s       99.9%    14.0 s       0.0 s
[2016-04-15T00:50Z] INFO  17:50:11,216 ProgressMeter - Total runtime 14.72 secs, 0.25 min, 0.00 hours
[2016-04-15T00:50Z] INFO  17:50:11,216 MicroScheduler - 9936 reads were filtered out during the traversal out of approximately 119802 total reads (8.29%)
[2016-04-15T00:50Z] INFO  17:50:11,217 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:50Z] INFO  17:50:11,217 MicroScheduler -   -> 176 reads (0.15% of total) failing BadMateFilter
[2016-04-15T00:50Z] INFO  17:50:11,217 MicroScheduler -   -> 9697 reads (8.09% of total) failing DuplicateReadFilter
[2016-04-15T00:50Z] INFO  17:50:11,217 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:50Z] INFO  17:50:11,218 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:50Z] INFO  17:50:11,218 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:50Z] INFO  17:50:11,218 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:50Z] INFO  17:50:11,218 MicroScheduler -   -> 63 reads (0.05% of total) failing UnmappedReadFilter
[2016-04-15T00:50Z] INFO  17:50:11,462 IntervalUtils - Processing 157522 bp from intervals
[2016-04-15T00:50Z] WARN  17:50:11,469 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:50Z] INFO  17:50:11,575 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:50Z] INFO  17:50:11,666 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:50Z] INFO  17:50:11,667 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:50Z] INFO  17:50:11,668 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:50Z] INFO  17:50:11,669 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:50Z] INFO  17:50:11,709 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:50Z] INFO  17:50:11,710 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:50Z] INFO  17:50:11,801 IntervalUtils - Processing 501134 bp from intervals
[2016-04-15T00:50Z] WARN  17:50:11,807 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:50Z] INFO  17:50:11,904 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:50Z] INFO  17:50:12,132 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:50Z] INFO  17:50:12,133 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:50Z] INFO  17:50:12,133 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:50Z] INFO  17:50:12,134 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:50Z] INFO  17:50:12,229 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:50Z] INFO  17:50:12,230 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:50Z] INFO  17:50:12,638 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:50Z] GATK: UnifiedGenotyper
[2016-04-15T00:50Z] INFO  17:50:13,107 ProgressMeter -            done    152663.0    10.0 s      68.0 s       99.9%    10.0 s       0.0 s
[2016-04-15T00:50Z] INFO  17:50:13,107 ProgressMeter - Total runtime 10.50 secs, 0.17 min, 0.00 hours
[2016-04-15T00:50Z] INFO  17:50:13,108 MicroScheduler - 4415 reads were filtered out during the traversal out of approximately 55628 total reads (7.94%)
[2016-04-15T00:50Z] INFO  17:50:13,108 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:50Z] INFO  17:50:13,108 MicroScheduler -   -> 61 reads (0.11% of total) failing BadMateFilter
[2016-04-15T00:50Z] INFO  17:50:13,108 MicroScheduler -   -> 4327 reads (7.78% of total) failing DuplicateReadFilter
[2016-04-15T00:50Z] INFO  17:50:13,109 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:50Z] INFO  17:50:13,109 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:50Z] INFO  17:50:13,109 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:50Z] INFO  17:50:13,109 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:50Z] INFO  17:50:13,110 MicroScheduler -   -> 27 reads (0.05% of total) failing UnmappedReadFilter
[2016-04-15T00:50Z] INFO  17:50:13,534 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:50Z] INFO  17:50:13,537 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:50Z] INFO  17:50:13,538 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:50Z] INFO  17:50:13,538 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:50Z] INFO  17:50:13,543 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/6/R14-18105_kapa-NGv3-PE100-NGv3-sort-6_62390867_78173120-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/6/R14-18105_kapa-NGv3-PE100-NGv3-6_62390867_78173120-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/6/tx/tmpUz7DGI/R14-18105_kapa-NGv3-PE100-NGv3-6_62390867_78173120.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:50Z] INFO  17:50:13,551 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:50Z] INFO  17:50:13,551 HelpFormatter - Date/Time: 2016/04/14 17:50:13
[2016-04-15T00:50Z] INFO  17:50:13,552 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:50Z] INFO  17:50:13,553 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:50Z] INFO  17:50:13,781 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:50Z] INFO  17:50:14,002 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:50Z] INFO  17:50:14,011 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:50Z] INFO  17:50:14,102 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.09
[2016-04-15T00:50Z] INFO  17:50:14,154 ProgressMeter -            done    392693.0    19.0 s      49.0 s       99.9%    19.0 s       0.0 s
[2016-04-15T00:50Z] INFO  17:50:14,154 ProgressMeter - Total runtime 19.38 secs, 0.32 min, 0.01 hours
[2016-04-15T00:50Z] INFO  17:50:14,155 MicroScheduler - 15966 reads were filtered out during the traversal out of approximately 187732 total reads (8.50%)
[2016-04-15T00:50Z] INFO  17:50:14,155 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:50Z] INFO  17:50:14,155 MicroScheduler -   -> 283 reads (0.15% of total) failing BadMateFilter
[2016-04-15T00:50Z] INFO  17:50:14,156 MicroScheduler -   -> 15524 reads (8.27% of total) failing DuplicateReadFilter
[2016-04-15T00:50Z] INFO  17:50:14,156 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:50Z] INFO  17:50:14,156 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:50Z] INFO  17:50:14,156 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:50Z] INFO  17:50:14,157 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:50Z] INFO  17:50:14,157 MicroScheduler -   -> 159 reads (0.08% of total) failing UnmappedReadFilter
[2016-04-15T00:50Z] INFO  17:50:14,450 IntervalUtils - Processing 103397 bp from intervals
[2016-04-15T00:50Z] WARN  17:50:14,455 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:50Z] INFO  17:50:14,455 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:50Z] INFO  17:50:14,540 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:50Z] INFO  17:50:14,644 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:50Z] INFO  17:50:14,645 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:50Z] INFO  17:50:14,645 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:50Z] INFO  17:50:14,646 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:50Z] INFO  17:50:14,708 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:50Z] INFO  17:50:14,709 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:50Z] GATK: UnifiedGenotyper
[2016-04-15T00:50Z] INFO  17:50:15,721 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:50Z] INFO  17:50:15,923 ProgressMeter -            done    373968.0    15.0 s      42.0 s       99.9%    15.0 s       0.0 s
[2016-04-15T00:50Z] INFO  17:50:15,923 ProgressMeter - Total runtime 15.93 secs, 0.27 min, 0.00 hours
[2016-04-15T00:50Z] INFO  17:50:15,924 MicroScheduler - 9813 reads were filtered out during the traversal out of approximately 120877 total reads (8.12%)
[2016-04-15T00:50Z] INFO  17:50:15,924 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:50Z] INFO  17:50:15,924 MicroScheduler -   -> 160 reads (0.13% of total) failing BadMateFilter
[2016-04-15T00:50Z] INFO  17:50:15,925 MicroScheduler -   -> 9577 reads (7.92% of total) failing DuplicateReadFilter
[2016-04-15T00:50Z] INFO  17:50:15,925 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:50Z] INFO  17:50:15,925 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:50Z] INFO  17:50:15,925 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:50Z] INFO  17:50:15,926 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:50Z] INFO  17:50:15,926 MicroScheduler -   -> 76 reads (0.06% of total) failing UnmappedReadFilter
[2016-04-15T00:50Z] GATK: UnifiedGenotyper
[2016-04-15T00:50Z] INFO  17:50:16,426 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:50Z] INFO  17:50:16,429 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:50Z] INFO  17:50:16,430 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:50Z] INFO  17:50:16,430 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:50Z] INFO  17:50:16,435 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/6/R14-18105_kapa-NGv3-PE100-NGv3-sort-6_78400388_93953258-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/6/R14-18105_kapa-NGv3-PE100-NGv3-6_78400388_93953258-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/6/tx/tmpHcUJLQ/R14-18105_kapa-NGv3-PE100-NGv3-6_78400388_93953258.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:50Z] INFO  17:50:16,465 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:50Z] INFO  17:50:16,466 HelpFormatter - Date/Time: 2016/04/14 17:50:16
[2016-04-15T00:50Z] INFO  17:50:16,467 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:50Z] INFO  17:50:16,467 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:50Z] INFO  17:50:16,575 ProgressMeter -            done    536506.0    20.0 s      39.0 s      100.0%    20.0 s       0.0 s
[2016-04-15T00:50Z] INFO  17:50:16,575 ProgressMeter - Total runtime 20.95 secs, 0.35 min, 0.01 hours
[2016-04-15T00:50Z] INFO  17:50:16,576 MicroScheduler - 16702 reads were filtered out during the traversal out of approximately 206430 total reads (8.09%)
[2016-04-15T00:50Z] INFO  17:50:16,576 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:50Z] INFO  17:50:16,576 MicroScheduler -   -> 270 reads (0.13% of total) failing BadMateFilter
[2016-04-15T00:50Z] INFO  17:50:16,577 MicroScheduler -   -> 16304 reads (7.90% of total) failing DuplicateReadFilter
[2016-04-15T00:50Z] INFO  17:50:16,577 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:50Z] INFO  17:50:16,577 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:50Z] INFO  17:50:16,577 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:50Z] INFO  17:50:16,578 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:50Z] INFO  17:50:16,578 MicroScheduler -   -> 128 reads (0.06% of total) failing UnmappedReadFilter
[2016-04-15T00:50Z] INFO  17:50:16,756 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:50Z] INFO  17:50:16,990 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:50Z] INFO  17:50:16,999 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:50Z] INFO  17:50:17,096 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.10
[2016-04-15T00:50Z] INFO  17:50:17,320 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:50Z] INFO  17:50:17,530 IntervalUtils - Processing 131721 bp from intervals
[2016-04-15T00:50Z] WARN  17:50:17,535 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:50Z] GATK: UnifiedGenotyper
[2016-04-15T00:50Z] INFO  17:50:17,674 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:50Z] INFO  17:50:17,784 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:50Z] INFO  17:50:17,785 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:50Z] INFO  17:50:17,786 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:50Z] INFO  17:50:17,787 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:50Z] INFO  17:50:17,845 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:50Z] INFO  17:50:17,846 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:50Z] INFO  17:50:17,971 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:50Z] INFO  17:50:17,989 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:50Z] INFO  17:50:17,992 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:50Z] INFO  17:50:17,993 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:50Z] INFO  17:50:17,994 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:50Z] INFO  17:50:17,998 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/6/R14-18105_kapa-NGv3-PE100-NGv3-sort-6_93955015_109466584-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/6/R14-18105_kapa-NGv3-PE100-NGv3-6_93955015_109466584-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/6/tx/tmpSL3SNQ/R14-18105_kapa-NGv3-PE100-NGv3-6_93955015_109466584.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:50Z] INFO  17:50:18,023 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:50Z] INFO  17:50:18,023 HelpFormatter - Date/Time: 2016/04/14 17:50:17
[2016-04-15T00:50Z] INFO  17:50:18,023 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:50Z] INFO  17:50:18,024 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:50Z] INFO  17:50:18,175 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:50Z] GATK: UnifiedGenotyper
[2016-04-15T00:50Z] INFO  17:50:18,442 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:50Z] INFO  17:50:18,450 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:50Z] INFO  17:50:18,529 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-15T00:50Z] INFO  17:50:19,029 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:50Z] INFO  17:50:19,033 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:50Z] INFO  17:50:19,033 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:50Z] INFO  17:50:19,034 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:50Z] INFO  17:50:19,038 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/6/R14-18105_kapa-NGv3-PE100-NGv3-sort-6_109467960_124979532-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/6/R14-18105_kapa-NGv3-PE100-NGv3-6_109467960_124979532-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/6/tx/tmpzX1R3Y/R14-18105_kapa-NGv3-PE100-NGv3-6_109467960_124979532.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:50Z] INFO  17:50:19,057 IntervalUtils - Processing 95525 bp from intervals
[2016-04-15T00:50Z] WARN  17:50:19,062 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:50Z] INFO  17:50:19,064 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:50Z] INFO  17:50:19,065 HelpFormatter - Date/Time: 2016/04/14 17:50:19
[2016-04-15T00:50Z] INFO  17:50:19,065 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:50Z] INFO  17:50:19,066 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:50Z] INFO  17:50:19,186 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:50Z] INFO  17:50:19,290 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:50Z] INFO  17:50:19,290 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:50Z] INFO  17:50:19,291 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:50Z] INFO  17:50:19,291 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:50Z] INFO  17:50:19,293 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:50Z] INFO  17:50:19,359 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:50Z] INFO  17:50:19,359 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:50Z] INFO  17:50:19,496 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:50Z] INFO  17:50:19,505 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:50Z] INFO  17:50:19,590 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-15T00:50Z] INFO  17:50:20,002 IntervalUtils - Processing 147815 bp from intervals
[2016-04-15T00:50Z] WARN  17:50:20,015 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:50Z] INFO  17:50:20,110 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:50Z] INFO  17:50:20,223 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:50Z] INFO  17:50:20,224 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:50Z] INFO  17:50:20,224 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:50Z] INFO  17:50:20,225 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:50Z] INFO  17:50:20,312 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:50Z] INFO  17:50:20,313 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:50Z] INFO  17:50:20,659 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:50Z] INFO  17:50:20,663 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:50Z] INFO  17:50:20,663 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:50Z] INFO  17:50:20,664 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:50Z] INFO  17:50:20,669 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/6/R14-18105_kapa-NGv3-PE100-NGv3-sort-6_125112484_142397186-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/6/R14-18105_kapa-NGv3-PE100-NGv3-6_125112484_142397186-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/6/tx/tmpcJG0ng/R14-18105_kapa-NGv3-PE100-NGv3-6_125112484_142397186.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:50Z] INFO  17:50:20,689 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:50Z] INFO  17:50:20,689 HelpFormatter - Date/Time: 2016/04/14 17:50:20
[2016-04-15T00:50Z] INFO  17:50:20,689 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:50Z] INFO  17:50:20,690 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:50Z] INFO  17:50:20,855 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:50Z] INFO  17:50:21,036 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:50Z] INFO  17:50:21,047 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:50Z] INFO  17:50:21,110 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-15T00:50Z] INFO  17:50:21,170 ProgressMeter -            done    235248.0    16.0 s      69.0 s       99.9%    16.0 s       0.0 s
[2016-04-15T00:50Z] INFO  17:50:21,171 ProgressMeter - Total runtime 16.32 secs, 0.27 min, 0.00 hours
[2016-04-15T00:50Z] INFO  17:50:21,171 MicroScheduler - 10259 reads were filtered out during the traversal out of approximately 123497 total reads (8.31%)
[2016-04-15T00:50Z] INFO  17:50:21,172 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:50Z] INFO  17:50:21,173 MicroScheduler -   -> 237 reads (0.19% of total) failing BadMateFilter
[2016-04-15T00:50Z] INFO  17:50:21,173 MicroScheduler -   -> 9939 reads (8.05% of total) failing DuplicateReadFilter
[2016-04-15T00:50Z] INFO  17:50:21,174 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:50Z] INFO  17:50:21,175 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:50Z] INFO  17:50:21,175 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:50Z] INFO  17:50:21,176 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:50Z] INFO  17:50:21,176 MicroScheduler -   -> 83 reads (0.07% of total) failing UnmappedReadFilter
[2016-04-15T00:50Z] INFO  17:50:21,384 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:50Z] INFO  17:50:21,387 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:50Z] INFO  17:50:21,388 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:50Z] INFO  17:50:21,389 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:50Z] INFO  17:50:21,393 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/6/R14-18105_kapa-NGv3-PE100-NGv3-sort-6_142399691_157963777-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/6/R14-18105_kapa-NGv3-PE100-NGv3-6_142399691_157963777-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/6/tx/tmpPJCoh6/R14-18105_kapa-NGv3-PE100-NGv3-6_142399691_157963777.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:50Z] INFO  17:50:21,423 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:50Z] INFO  17:50:21,424 HelpFormatter - Date/Time: 2016/04/14 17:50:21
[2016-04-15T00:50Z] INFO  17:50:21,424 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:50Z] INFO  17:50:21,424 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:50Z] INFO  17:50:21,497 ProgressMeter -            done    554557.0    22.0 s      39.0 s      100.0%    22.0 s       0.0 s
[2016-04-15T00:50Z] INFO  17:50:21,497 ProgressMeter - Total runtime 22.02 secs, 0.37 min, 0.01 hours
[2016-04-15T00:50Z] INFO  17:50:21,497 MicroScheduler - 17645 reads were filtered out during the traversal out of approximately 225654 total reads (7.82%)
[2016-04-15T00:50Z] INFO  17:50:21,498 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:50Z] INFO  17:50:21,498 MicroScheduler -   -> 290 reads (0.13% of total) failing BadMateFilter
[2016-04-15T00:50Z] INFO  17:50:21,498 MicroScheduler -   -> 17217 reads (7.63% of total) failing DuplicateReadFilter
[2016-04-15T00:50Z] INFO  17:50:21,498 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:50Z] INFO  17:50:21,499 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:50Z] INFO  17:50:21,499 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:50Z] INFO  17:50:21,499 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:50Z] INFO  17:50:21,499 MicroScheduler -   -> 138 reads (0.06% of total) failing UnmappedReadFilter
[2016-04-15T00:50Z] INFO  17:50:21,634 IntervalUtils - Processing 156964 bp from intervals
[2016-04-15T00:50Z] WARN  17:50:21,639 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:50Z] INFO  17:50:21,672 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:50Z] INFO  17:50:21,786 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:50Z] INFO  17:50:21,933 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:50Z] INFO  17:50:21,950 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:50Z] INFO  17:50:21,951 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:50Z] INFO  17:50:21,951 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:50Z] INFO  17:50:21,951 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:50Z] INFO  17:50:21,961 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:50Z] INFO  17:50:22,002 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:50Z] INFO  17:50:22,011 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:50Z] INFO  17:50:22,054 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.09
[2016-04-15T00:50Z] INFO  17:50:22,490 IntervalUtils - Processing 183871 bp from intervals
[2016-04-15T00:50Z] WARN  17:50:22,499 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:50Z] INFO  17:50:22,579 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:50Z] INFO  17:50:22,589 ProgressMeter -            done    237846.0    16.0 s      68.0 s      100.0%    16.0 s       0.0 s
[2016-04-15T00:50Z] INFO  17:50:22,589 ProgressMeter - Total runtime 16.24 secs, 0.27 min, 0.00 hours
[2016-04-15T00:50Z] INFO  17:50:22,590 MicroScheduler - 12375 reads were filtered out during the traversal out of approximately 145859 total reads (8.48%)
[2016-04-15T00:50Z] INFO  17:50:22,590 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:50Z] INFO  17:50:22,590 MicroScheduler -   -> 216 reads (0.15% of total) failing BadMateFilter
[2016-04-15T00:50Z] INFO  17:50:22,590 MicroScheduler -   -> 12071 reads (8.28% of total) failing DuplicateReadFilter
[2016-04-15T00:50Z] INFO  17:50:22,591 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:50Z] INFO  17:50:22,591 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:50Z] INFO  17:50:22,591 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:50Z] INFO  17:50:22,591 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:50Z] INFO  17:50:22,592 MicroScheduler -   -> 88 reads (0.06% of total) failing UnmappedReadFilter
[2016-04-15T00:50Z] INFO  17:50:22,655 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:50Z] INFO  17:50:22,699 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:50Z] INFO  17:50:22,701 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:50Z] INFO  17:50:22,701 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:50Z] INFO  17:50:22,702 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:50Z] INFO  17:50:22,790 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:50Z] INFO  17:50:22,791 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:50Z] INFO  17:50:22,958 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:50Z] GATK: UnifiedGenotyper
[2016-04-15T00:50Z] GATK: UnifiedGenotyper
[2016-04-15T00:50Z] INFO  17:50:24,015 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:50Z] GATK: UnifiedGenotyper
[2016-04-15T00:50Z] INFO  17:50:26,063 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:50Z] INFO  17:50:26,067 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:50Z] INFO  17:50:26,067 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:50Z] INFO  17:50:26,068 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:50Z] INFO  17:50:26,072 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/7/R14-18105_kapa-NGv3-PE100-NGv3-sort-7_0_15584548-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/7/R14-18105_kapa-NGv3-PE100-NGv3-7_0_15584548-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/7/tx/tmppXVHww/R14-18105_kapa-NGv3-PE100-NGv3-7_0_15584548.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:50Z] INFO  17:50:26,102 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:50Z] INFO  17:50:26,111 HelpFormatter - Date/Time: 2016/04/14 17:50:26
[2016-04-15T00:50Z] INFO  17:50:26,112 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:50Z] INFO  17:50:26,113 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:50Z] INFO  17:50:26,139 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:50Z] INFO  17:50:26,142 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:50Z] INFO  17:50:26,143 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:50Z] INFO  17:50:26,143 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:50Z] INFO  17:50:26,148 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/6/R14-18105_kapa-NGv3-PE100-NGv3-sort-6_158013810_171115067-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/6/R14-18105_kapa-NGv3-PE100-NGv3-6_158013810_171115067-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/6/tx/tmp6zzkdO/R14-18105_kapa-NGv3-PE100-NGv3-6_158013810_171115067.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:50Z] INFO  17:50:26,163 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:50Z] INFO  17:50:26,164 HelpFormatter - Date/Time: 2016/04/14 17:50:26
[2016-04-15T00:50Z] INFO  17:50:26,165 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:50Z] INFO  17:50:26,165 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:50Z] INFO  17:50:26,288 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:50Z] INFO  17:50:26,351 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:50Z] INFO  17:50:26,527 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:50Z] INFO  17:50:26,536 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:50Z] INFO  17:50:26,561 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:50Z] INFO  17:50:26,571 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:50Z] INFO  17:50:26,610 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-15T00:50Z] INFO  17:50:26,637 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-15T00:50Z] INFO  17:50:27,013 IntervalUtils - Processing 187602 bp from intervals
[2016-04-15T00:50Z] WARN  17:50:27,030 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:50Z] INFO  17:50:27,121 IntervalUtils - Processing 143202 bp from intervals
[2016-04-15T00:50Z] WARN  17:50:27,126 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:50Z] INFO  17:50:27,132 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:50Z] INFO  17:50:27,146 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:50Z] INFO  17:50:27,149 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:50Z] INFO  17:50:27,150 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:50Z] INFO  17:50:27,150 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:50Z] INFO  17:50:27,155 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/7/R14-18105_kapa-NGv3-PE100-NGv3-sort-7_15599765_31117713-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/7/R14-18105_kapa-NGv3-PE100-NGv3-7_15599765_31117713-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/7/tx/tmpP2lXcw/R14-18105_kapa-NGv3-PE100-NGv3-7_15599765_31117713.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:50Z] INFO  17:50:27,164 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:50Z] INFO  17:50:27,165 HelpFormatter - Date/Time: 2016/04/14 17:50:27
[2016-04-15T00:50Z] INFO  17:50:27,166 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:50Z] INFO  17:50:27,167 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:50Z] INFO  17:50:27,222 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:50Z] INFO  17:50:27,223 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:50Z] INFO  17:50:27,224 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:50Z] INFO  17:50:27,225 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:50Z] INFO  17:50:27,258 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:50Z] INFO  17:50:27,301 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:50Z] INFO  17:50:27,302 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:50Z] INFO  17:50:27,370 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:50Z] INFO  17:50:27,378 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:50Z] INFO  17:50:27,379 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:50Z] INFO  17:50:27,379 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:50Z] INFO  17:50:27,379 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:50Z] INFO  17:50:27,432 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:50Z] INFO  17:50:27,432 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:50Z] INFO  17:50:27,631 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:50Z] INFO  17:50:27,650 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:50Z] INFO  17:50:27,728 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-15T00:50Z] INFO  17:50:28,039 IntervalUtils - Processing 149727 bp from intervals
[2016-04-15T00:50Z] WARN  17:50:28,044 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:50Z] INFO  17:50:28,113 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:50Z] INFO  17:50:28,191 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:50Z] INFO  17:50:28,192 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:50Z] INFO  17:50:28,193 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:50Z] INFO  17:50:28,193 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:50Z] INFO  17:50:28,235 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:50Z] INFO  17:50:28,236 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:50Z] INFO  17:50:28,237 ProgressMeter -            done    269142.0    13.0 s      50.0 s       99.9%    13.0 s       0.0 s
[2016-04-15T00:50Z] INFO  17:50:28,237 ProgressMeter - Total runtime 13.59 secs, 0.23 min, 0.00 hours
[2016-04-15T00:50Z] INFO  17:50:28,238 MicroScheduler - 9177 reads were filtered out during the traversal out of approximately 112470 total reads (8.16%)
[2016-04-15T00:50Z] INFO  17:50:28,238 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:50Z] INFO  17:50:28,238 MicroScheduler -   -> 165 reads (0.15% of total) failing BadMateFilter
[2016-04-15T00:50Z] INFO  17:50:28,238 MicroScheduler -   -> 8962 reads (7.97% of total) failing DuplicateReadFilter
[2016-04-15T00:50Z] INFO  17:50:28,239 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:50Z] INFO  17:50:28,239 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:50Z] INFO  17:50:28,239 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:50Z] INFO  17:50:28,239 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:50Z] INFO  17:50:28,240 MicroScheduler -   -> 50 reads (0.04% of total) failing UnmappedReadFilter
[2016-04-15T00:50Z] INFO  17:50:29,650 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:50Z] GATK: UnifiedGenotyper
[2016-04-15T00:50Z] INFO  17:50:30,299 ProgressMeter -            done    472667.0    18.0 s      39.0 s      100.0%    18.0 s       0.0 s
[2016-04-15T00:50Z] INFO  17:50:30,299 ProgressMeter - Total runtime 18.63 secs, 0.31 min, 0.01 hours
[2016-04-15T00:50Z] INFO  17:50:30,299 MicroScheduler - 14230 reads were filtered out during the traversal out of approximately 175534 total reads (8.11%)
[2016-04-15T00:50Z] INFO  17:50:30,300 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:50Z] INFO  17:50:30,300 MicroScheduler -   -> 248 reads (0.14% of total) failing BadMateFilter
[2016-04-15T00:50Z] INFO  17:50:30,300 MicroScheduler -   -> 13888 reads (7.91% of total) failing DuplicateReadFilter
[2016-04-15T00:50Z] INFO  17:50:30,300 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:50Z] INFO  17:50:30,301 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:50Z] INFO  17:50:30,301 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:50Z] INFO  17:50:30,301 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:50Z] INFO  17:50:30,301 MicroScheduler -   -> 94 reads (0.05% of total) failing UnmappedReadFilter
[2016-04-15T00:50Z] INFO  17:50:30,585 ProgressMeter -            done    712768.0    21.0 s      30.0 s      100.0%    21.0 s       0.0 s
[2016-04-15T00:50Z] INFO  17:50:30,586 ProgressMeter - Total runtime 21.88 secs, 0.36 min, 0.01 hours
[2016-04-15T00:50Z] INFO  17:50:30,586 MicroScheduler - 21471 reads were filtered out during the traversal out of approximately 260469 total reads (8.24%)
[2016-04-15T00:50Z] INFO  17:50:30,586 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:50Z] INFO  17:50:30,587 MicroScheduler -   -> 411 reads (0.16% of total) failing BadMateFilter
[2016-04-15T00:50Z] INFO  17:50:30,587 MicroScheduler -   -> 20895 reads (8.02% of total) failing DuplicateReadFilter
[2016-04-15T00:50Z] INFO  17:50:30,587 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:50Z] INFO  17:50:30,587 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:50Z] INFO  17:50:30,588 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:50Z] INFO  17:50:30,588 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:50Z] INFO  17:50:30,588 MicroScheduler -   -> 165 reads (0.06% of total) failing UnmappedReadFilter
[2016-04-15T00:50Z] INFO  17:50:31,237 ProgressMeter -            done    349428.0    21.0 s      62.0 s      100.0%    21.0 s       0.0 s
[2016-04-15T00:50Z] INFO  17:50:31,238 ProgressMeter - Total runtime 21.68 secs, 0.36 min, 0.01 hours
[2016-04-15T00:50Z] INFO  17:50:31,238 MicroScheduler - 15428 reads were filtered out during the traversal out of approximately 185438 total reads (8.32%)
[2016-04-15T00:50Z] INFO  17:50:31,238 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:50Z] INFO  17:50:31,239 MicroScheduler -   -> 212 reads (0.11% of total) failing BadMateFilter
[2016-04-15T00:50Z] INFO  17:50:31,239 MicroScheduler -   -> 15102 reads (8.14% of total) failing DuplicateReadFilter
[2016-04-15T00:50Z] INFO  17:50:31,239 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:50Z] INFO  17:50:31,239 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:50Z] INFO  17:50:31,240 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:50Z] INFO  17:50:31,240 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:50Z] INFO  17:50:31,240 MicroScheduler -   -> 114 reads (0.06% of total) failing UnmappedReadFilter
[2016-04-15T00:50Z] INFO  17:50:31,678 ProgressMeter -            done    639654.0    25.0 s      39.0 s      100.0%    25.0 s       0.0 s
[2016-04-15T00:50Z] INFO  17:50:31,678 ProgressMeter - Total runtime 25.30 secs, 0.42 min, 0.01 hours
[2016-04-15T00:50Z] INFO  17:50:31,679 MicroScheduler - 23999 reads were filtered out during the traversal out of approximately 288678 total reads (8.31%)
[2016-04-15T00:50Z] INFO  17:50:31,679 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:50Z] INFO  17:50:31,679 MicroScheduler -   -> 405 reads (0.14% of total) failing BadMateFilter
[2016-04-15T00:50Z] INFO  17:50:31,679 MicroScheduler -   -> 23422 reads (8.11% of total) failing DuplicateReadFilter
[2016-04-15T00:50Z] INFO  17:50:31,680 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:50Z] INFO  17:50:31,680 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:50Z] INFO  17:50:31,680 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:50Z] INFO  17:50:31,680 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:50Z] INFO  17:50:31,681 MicroScheduler -   -> 172 reads (0.06% of total) failing UnmappedReadFilter
[2016-04-15T00:50Z] INFO  17:50:31,806 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:50Z] INFO  17:50:31,969 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:50Z] INFO  17:50:32,031 ProgressMeter -            done    213234.0    12.0 s      59.0 s       99.9%    12.0 s       0.0 s
[2016-04-15T00:50Z] INFO  17:50:32,032 ProgressMeter - Total runtime 12.74 secs, 0.21 min, 0.00 hours
[2016-04-15T00:50Z] INFO  17:50:32,032 MicroScheduler - 8448 reads were filtered out during the traversal out of approximately 103703 total reads (8.15%)
[2016-04-15T00:50Z] INFO  17:50:32,032 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:50Z] INFO  17:50:32,033 MicroScheduler -   -> 153 reads (0.15% of total) failing BadMateFilter
[2016-04-15T00:50Z] INFO  17:50:32,033 MicroScheduler -   -> 8229 reads (7.94% of total) failing DuplicateReadFilter
[2016-04-15T00:50Z] INFO  17:50:32,033 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:50Z] INFO  17:50:32,033 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:50Z] INFO  17:50:32,034 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:50Z] INFO  17:50:32,034 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:50Z] INFO  17:50:32,034 MicroScheduler -   -> 66 reads (0.06% of total) failing UnmappedReadFilter
[2016-04-15T00:50Z] GATK: UnifiedGenotyper
[2016-04-15T00:50Z] INFO  17:50:32,164 ProgressMeter -            done    399770.0    14.0 s      35.0 s      100.0%    14.0 s       0.0 s
[2016-04-15T00:50Z] INFO  17:50:32,164 ProgressMeter - Total runtime 14.38 secs, 0.24 min, 0.00 hours
[2016-04-15T00:50Z] INFO  17:50:32,164 MicroScheduler - 11454 reads were filtered out during the traversal out of approximately 141173 total reads (8.11%)
[2016-04-15T00:50Z] INFO  17:50:32,165 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:50Z] INFO  17:50:32,165 MicroScheduler -   -> 192 reads (0.14% of total) failing BadMateFilter
[2016-04-15T00:50Z] INFO  17:50:32,165 MicroScheduler -   -> 11176 reads (7.92% of total) failing DuplicateReadFilter
[2016-04-15T00:50Z] INFO  17:50:32,166 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:50Z] INFO  17:50:32,166 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:50Z] INFO  17:50:32,166 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:50Z] INFO  17:50:32,166 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:50Z] INFO  17:50:32,167 MicroScheduler -   -> 86 reads (0.06% of total) failing UnmappedReadFilter
[2016-04-15T00:50Z] GATK: UnifiedGenotyper
[2016-04-15T00:50Z] INFO  17:50:32,711 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:50Z] INFO  17:50:32,918 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:50Z] INFO  17:50:32,921 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:50Z] INFO  17:50:32,922 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:50Z] INFO  17:50:32,922 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:50Z] INFO  17:50:32,927 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/7/R14-18105_kapa-NGv3-PE100-NGv3-sort-7_31120227_47317818-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/7/R14-18105_kapa-NGv3-PE100-NGv3-7_31120227_47317818-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/7/tx/tmpvVMEi4/R14-18105_kapa-NGv3-PE100-NGv3-7_31120227_47317818.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:50Z] INFO  17:50:32,970 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:50Z] INFO  17:50:32,971 HelpFormatter - Date/Time: 2016/04/14 17:50:32
[2016-04-15T00:50Z] INFO  17:50:32,972 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:50Z] INFO  17:50:32,972 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:50Z] GATK: UnifiedGenotyper
[2016-04-15T00:50Z] INFO  17:50:33,162 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:50Z] INFO  17:50:33,181 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:50Z] INFO  17:50:33,390 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:50Z] INFO  17:50:33,399 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:50Z] INFO  17:50:33,423 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:50Z] GATK: UnifiedGenotyper
[2016-04-15T00:50Z] INFO  17:50:33,462 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-15T00:50Z] INFO  17:50:33,504 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:50Z] GATK: UnifiedGenotyper
[2016-04-15T00:50Z] GATK: UnifiedGenotyper
[2016-04-15T00:50Z] INFO  17:50:33,935 IntervalUtils - Processing 138106 bp from intervals
[2016-04-15T00:50Z] WARN  17:50:33,963 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:50Z] INFO  17:50:34,100 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:50Z] INFO  17:50:34,224 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:50Z] INFO  17:50:34,225 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:50Z] INFO  17:50:34,226 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:50Z] INFO  17:50:34,227 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:50Z] INFO  17:50:34,330 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:50Z] INFO  17:50:34,331 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:50Z] INFO  17:50:35,021 ProgressMeter -     5:140476617    948516.0    30.0 s      31.0 s       65.9%    45.0 s      15.0 s
[2016-04-15T00:50Z] INFO  17:50:35,195 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:50Z] INFO  17:50:35,198 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:50Z] INFO  17:50:35,198 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:50Z] INFO  17:50:35,198 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:50Z] INFO  17:50:35,202 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/7/R14-18105_kapa-NGv3-PE100-NGv3-sort-7_47319761_63093154-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/7/R14-18105_kapa-NGv3-PE100-NGv3-7_47319761_63093154-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/7/tx/tmp193gPR/R14-18105_kapa-NGv3-PE100-NGv3-7_47319761_63093154.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:50Z] INFO  17:50:35,222 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:50Z] INFO  17:50:35,223 HelpFormatter - Date/Time: 2016/04/14 17:50:35
[2016-04-15T00:50Z] INFO  17:50:35,223 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:50Z] INFO  17:50:35,223 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:50Z] INFO  17:50:35,448 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:50Z] INFO  17:50:35,571 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:50Z] INFO  17:50:35,573 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:50Z] INFO  17:50:35,574 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:50Z] INFO  17:50:35,574 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:50Z] INFO  17:50:35,578 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/7/R14-18105_kapa-NGv3-PE100-NGv3-sort-7_63095909_78636522-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/7/R14-18105_kapa-NGv3-PE100-NGv3-7_63095909_78636522-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/7/tx/tmpRdFdY6/R14-18105_kapa-NGv3-PE100-NGv3-7_63095909_78636522.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:50Z] INFO  17:50:35,597 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:50Z] INFO  17:50:35,598 HelpFormatter - Date/Time: 2016/04/14 17:50:35
[2016-04-15T00:50Z] INFO  17:50:35,599 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:50Z] INFO  17:50:35,599 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:50Z] INFO  17:50:35,634 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:50Z] INFO  17:50:35,643 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:50Z] INFO  17:50:35,713 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-15T00:50Z] INFO  17:50:35,782 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:50Z] INFO  17:50:36,058 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:50Z] INFO  17:50:36,068 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:50Z] INFO  17:50:36,106 IntervalUtils - Processing 74873 bp from intervals
[2016-04-15T00:50Z] WARN  17:50:36,117 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:50Z] INFO  17:50:36,123 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:50Z] INFO  17:50:36,126 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:50Z] INFO  17:50:36,126 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:50Z] INFO  17:50:36,127 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:50Z] INFO  17:50:36,131 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/7/R14-18105_kapa-NGv3-PE100-NGv3-sort-7_79082334_94740703-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/7/R14-18105_kapa-NGv3-PE100-NGv3-7_79082334_94740703-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/7/tx/tmpdGCJ7r/R14-18105_kapa-NGv3-PE100-NGv3-7_79082334_94740703.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:50Z] INFO  17:50:36,159 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:50Z] INFO  17:50:36,160 HelpFormatter - Date/Time: 2016/04/14 17:50:36
[2016-04-15T00:50Z] INFO  17:50:36,160 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:50Z] INFO  17:50:36,161 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:50Z] INFO  17:50:36,171 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.10
[2016-04-15T00:50Z] INFO  17:50:36,228 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:50Z] INFO  17:50:36,282 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:50Z] INFO  17:50:36,283 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:50Z] INFO  17:50:36,283 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:50Z] INFO  17:50:36,284 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:50Z] INFO  17:50:36,364 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:50Z] INFO  17:50:36,365 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:50Z] INFO  17:50:36,366 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:50Z] INFO  17:50:36,592 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:50Z] INFO  17:50:36,595 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:50Z] INFO  17:50:36,596 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:50Z] INFO  17:50:36,596 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:50Z] INFO  17:50:36,601 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/7/R14-18105_kapa-NGv3-PE100-NGv3-sort-7_94750023_110303777-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/7/R14-18105_kapa-NGv3-PE100-NGv3-7_94750023_110303777-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/7/tx/tmpanf6o1/R14-18105_kapa-NGv3-PE100-NGv3-7_94750023_110303777.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:50Z] INFO  17:50:36,602 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:50Z] INFO  17:50:36,611 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:50Z] INFO  17:50:36,618 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:50Z] INFO  17:50:36,622 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:50Z] INFO  17:50:36,622 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:50Z] INFO  17:50:36,623 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:50Z] INFO  17:50:36,627 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/7/R14-18105_kapa-NGv3-PE100-NGv3-sort-7_110526648_126079222-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/7/R14-18105_kapa-NGv3-PE100-NGv3-7_110526648_126079222-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/7/tx/tmpI1Y2u_/R14-18105_kapa-NGv3-PE100-NGv3-7_110526648_126079222.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:50Z] INFO  17:50:36,640 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:50Z] INFO  17:50:36,640 HelpFormatter - Date/Time: 2016/04/14 17:50:36
[2016-04-15T00:50Z] INFO  17:50:36,641 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:50Z] INFO  17:50:36,642 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:50Z] INFO  17:50:36,654 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:50Z] INFO  17:50:36,655 HelpFormatter - Date/Time: 2016/04/14 17:50:36
[2016-04-15T00:50Z] INFO  17:50:36,655 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:50Z] INFO  17:50:36,656 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:50Z] INFO  17:50:36,713 IntervalUtils - Processing 152751 bp from intervals
[2016-04-15T00:50Z] WARN  17:50:36,718 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:50Z] INFO  17:50:36,721 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.11
[2016-04-15T00:50Z] INFO  17:50:36,778 ProgressMeter -            done    414458.0    16.0 s      39.0 s      100.0%    16.0 s       0.0 s
[2016-04-15T00:50Z] INFO  17:50:36,778 ProgressMeter - Total runtime 16.55 secs, 0.28 min, 0.00 hours
[2016-04-15T00:50Z] INFO  17:50:36,779 MicroScheduler - 13328 reads were filtered out during the traversal out of approximately 164678 total reads (8.09%)
[2016-04-15T00:50Z] INFO  17:50:36,779 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:50Z] INFO  17:50:36,779 MicroScheduler -   -> 247 reads (0.15% of total) failing BadMateFilter
[2016-04-15T00:50Z] INFO  17:50:36,779 MicroScheduler -   -> 13001 reads (7.89% of total) failing DuplicateReadFilter
[2016-04-15T00:50Z] INFO  17:50:36,780 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:50Z] INFO  17:50:36,780 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:50Z] INFO  17:50:36,780 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:50Z] INFO  17:50:36,780 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:50Z] INFO  17:50:36,781 MicroScheduler -   -> 80 reads (0.05% of total) failing UnmappedReadFilter
[2016-04-15T00:50Z] INFO  17:50:36,794 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:50Z] INFO  17:50:36,798 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:50Z] INFO  17:50:36,816 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:50Z] INFO  17:50:36,902 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:50Z] INFO  17:50:36,902 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:50Z] INFO  17:50:36,902 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:50Z] INFO  17:50:36,903 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:50Z] INFO  17:50:37,008 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:50Z] INFO  17:50:37,009 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:50Z] INFO  17:50:37,010 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:50Z] INFO  17:50:37,013 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:50Z] INFO  17:50:37,014 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:50Z] INFO  17:50:37,014 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:50Z] INFO  17:50:37,019 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/7/R14-18105_kapa-NGv3-PE100-NGv3-sort-7_126086124_141619620-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/7/R14-18105_kapa-NGv3-PE100-NGv3-7_126086124_141619620-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/7/tx/tmp9je7gX/R14-18105_kapa-NGv3-PE100-NGv3-7_126086124_141619620.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:50Z] INFO  17:50:37,028 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:50Z] INFO  17:50:37,029 HelpFormatter - Date/Time: 2016/04/14 17:50:37
[2016-04-15T00:50Z] INFO  17:50:37,029 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:50Z] INFO  17:50:37,029 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:50Z] INFO  17:50:37,089 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:50Z] INFO  17:50:37,103 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:50Z] INFO  17:50:37,104 IntervalUtils - Processing 163786 bp from intervals
[2016-04-15T00:50Z] INFO  17:50:37,106 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:50Z] WARN  17:50:37,109 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:50Z] INFO  17:50:37,120 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:50Z] INFO  17:50:37,186 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:50Z] INFO  17:50:37,197 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:50Z] INFO  17:50:37,218 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.10
[2016-04-15T00:50Z] INFO  17:50:37,263 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:50Z] INFO  17:50:37,264 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:50Z] INFO  17:50:37,265 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:50Z] INFO  17:50:37,266 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:50Z] INFO  17:50:37,319 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:50Z] INFO  17:50:37,320 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:50Z] INFO  17:50:37,424 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:50Z] INFO  17:50:37,432 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:50Z] INFO  17:50:37,510 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-15T00:50Z] INFO  17:50:37,622 IntervalUtils - Processing 352548 bp from intervals
[2016-04-15T00:50Z] WARN  17:50:37,628 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:50Z] INFO  17:50:37,691 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.57
[2016-04-15T00:50Z] INFO  17:50:37,760 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:50Z] INFO  17:50:37,895 IntervalUtils - Processing 219678 bp from intervals
[2016-04-15T00:50Z] WARN  17:50:37,900 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:50Z] INFO  17:50:37,924 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:50Z] INFO  17:50:37,926 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:50Z] INFO  17:50:37,926 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:50Z] INFO  17:50:37,927 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:50Z] INFO  17:50:37,971 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:50Z] INFO  17:50:37,972 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:50Z] INFO  17:50:37,991 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:50Z] INFO  17:50:38,137 IntervalUtils - Processing 97998 bp from intervals
[2016-04-15T00:50Z] WARN  17:50:38,143 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:50Z] INFO  17:50:38,142 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:50Z] INFO  17:50:38,159 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:50Z] INFO  17:50:38,160 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:50Z] INFO  17:50:38,161 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:50Z] INFO  17:50:38,161 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:50Z] INFO  17:50:38,202 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:50Z] INFO  17:50:38,203 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:50Z] INFO  17:50:38,298 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:50Z] INFO  17:50:38,413 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:50Z] INFO  17:50:38,414 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:50Z] INFO  17:50:38,414 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:50Z] INFO  17:50:38,414 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:50Z] INFO  17:50:38,476 ProgressMeter -            done    821918.0    27.0 s      33.0 s      100.0%    27.0 s       0.0 s
[2016-04-15T00:50Z] INFO  17:50:38,477 ProgressMeter - Total runtime 27.44 secs, 0.46 min, 0.01 hours
[2016-04-15T00:50Z] INFO  17:50:38,478 MicroScheduler - 28442 reads were filtered out during the traversal out of approximately 342033 total reads (8.32%)
[2016-04-15T00:50Z] INFO  17:50:38,478 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:50Z] INFO  17:50:38,478 MicroScheduler -   -> 514 reads (0.15% of total) failing BadMateFilter
[2016-04-15T00:50Z] INFO  17:50:38,479 MicroScheduler -   -> 27701 reads (8.10% of total) failing DuplicateReadFilter
[2016-04-15T00:50Z] INFO  17:50:38,479 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:50Z] INFO  17:50:38,479 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:50Z] INFO  17:50:38,479 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:50Z] INFO  17:50:38,480 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:50Z] INFO  17:50:38,480 MicroScheduler -   -> 227 reads (0.07% of total) failing UnmappedReadFilter
[2016-04-15T00:50Z] INFO  17:50:38,510 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:50Z] INFO  17:50:38,510 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:50Z] GATK: UnifiedGenotyper
[2016-04-15T00:50Z] INFO  17:50:39,863 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:50Z] GATK: UnifiedGenotyper
[2016-04-15T00:50Z] INFO  17:50:41,481 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:50Z] INFO  17:50:41,486 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:50Z] INFO  17:50:41,487 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:50Z] INFO  17:50:41,487 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:50Z] INFO  17:50:41,492 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/7/R14-18105_kapa-NGv3-PE100-NGv3-sort-7_141629903_157151331-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/7/R14-18105_kapa-NGv3-PE100-NGv3-7_141629903_157151331-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/7/tx/tmpqTWOVX/R14-18105_kapa-NGv3-PE100-NGv3-7_141629903_157151331.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:50Z] INFO  17:50:41,502 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:50Z] INFO  17:50:41,503 HelpFormatter - Date/Time: 2016/04/14 17:50:41
[2016-04-15T00:50Z] INFO  17:50:41,503 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:50Z] INFO  17:50:41,503 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:50Z] INFO  17:50:41,655 ProgressMeter -            done    394136.0    19.0 s      49.0 s      100.0%    19.0 s       0.0 s
[2016-04-15T00:50Z] INFO  17:50:41,655 ProgressMeter - Total runtime 19.70 secs, 0.33 min, 0.01 hours
[2016-04-15T00:50Z] INFO  17:50:41,656 MicroScheduler - 15902 reads were filtered out during the traversal out of approximately 193743 total reads (8.21%)
[2016-04-15T00:50Z] INFO  17:50:41,656 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:50Z] INFO  17:50:41,656 MicroScheduler -   -> 310 reads (0.16% of total) failing BadMateFilter
[2016-04-15T00:50Z] INFO  17:50:41,656 MicroScheduler -   -> 15459 reads (7.98% of total) failing DuplicateReadFilter
[2016-04-15T00:50Z] INFO  17:50:41,657 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:50Z] INFO  17:50:41,657 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:50Z] INFO  17:50:41,657 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:50Z] INFO  17:50:41,657 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:50Z] INFO  17:50:41,658 MicroScheduler -   -> 133 reads (0.07% of total) failing UnmappedReadFilter
[2016-04-15T00:50Z] INFO  17:50:41,716 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:50Z] INFO  17:50:41,955 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:50Z] INFO  17:50:41,964 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:50Z] INFO  17:50:42,027 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-15T00:50Z] INFO  17:50:42,147 ProgressMeter -      6:35436574   1965804.0    30.0 s      15.0 s       48.2%    62.0 s      32.0 s
[2016-04-15T00:50Z] INFO  17:50:42,412 IntervalUtils - Processing 248696 bp from intervals
[2016-04-15T00:50Z] WARN  17:50:42,420 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:50Z] INFO  17:50:42,528 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:50Z] INFO  17:50:42,633 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:50Z] INFO  17:50:42,634 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:50Z] INFO  17:50:42,634 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:50Z] INFO  17:50:42,635 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:50Z] INFO  17:50:42,770 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:50Z] INFO  17:50:42,771 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:50Z] INFO  17:50:43,189 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:50Z] INFO  17:50:43,192 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:50Z] INFO  17:50:43,193 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:50Z] INFO  17:50:43,193 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:50Z] INFO  17:50:43,198 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/7/R14-18105_kapa-NGv3-PE100-NGv3-sort-7_157155854_159138663-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/7/R14-18105_kapa-NGv3-PE100-NGv3-7_157155854_159138663-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/7/tx/tmp6AV558/R14-18105_kapa-NGv3-PE100-NGv3-7_157155854_159138663.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:50Z] INFO  17:50:43,210 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:50Z] INFO  17:50:43,221 HelpFormatter - Date/Time: 2016/04/14 17:50:43
[2016-04-15T00:50Z] INFO  17:50:43,222 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:50Z] INFO  17:50:43,223 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:50Z] INFO  17:50:43,283 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:50Z] INFO  17:50:43,427 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:50Z] GATK: UnifiedGenotyper
[2016-04-15T00:50Z] INFO  17:50:43,684 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:50Z] INFO  17:50:43,703 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:50Z] INFO  17:50:43,865 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.16
[2016-04-15T00:50Z] INFO  17:50:44,243 IntervalUtils - Processing 17619 bp from intervals
[2016-04-15T00:50Z] WARN  17:50:44,256 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:50Z] INFO  17:50:44,372 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:50Z] INFO  17:50:44,473 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:50Z] INFO  17:50:44,474 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:50Z] INFO  17:50:44,475 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:50Z] INFO  17:50:44,476 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:50Z] INFO  17:50:44,575 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:50Z] INFO  17:50:44,577 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:50Z] INFO  17:50:44,672 ProgressMeter -            done    448393.0    21.0 s      48.0 s      100.0%    21.0 s       0.0 s
[2016-04-15T00:50Z] INFO  17:50:44,673 ProgressMeter - Total runtime 21.97 secs, 0.37 min, 0.01 hours
[2016-04-15T00:50Z] INFO  17:50:44,674 MicroScheduler - 19076 reads were filtered out during the traversal out of approximately 232383 total reads (8.21%)
[2016-04-15T00:50Z] INFO  17:50:44,674 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:50Z] INFO  17:50:44,674 MicroScheduler -   -> 329 reads (0.14% of total) failing BadMateFilter
[2016-04-15T00:50Z] INFO  17:50:44,674 MicroScheduler -   -> 18605 reads (8.01% of total) failing DuplicateReadFilter
[2016-04-15T00:50Z] INFO  17:50:44,675 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:50Z] INFO  17:50:44,675 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:50Z] INFO  17:50:44,675 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:50Z] INFO  17:50:44,676 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:50Z] INFO  17:50:44,676 MicroScheduler -   -> 142 reads (0.06% of total) failing UnmappedReadFilter
[2016-04-15T00:50Z] INFO  17:50:46,063 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:50Z] INFO  17:50:46,306 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:50Z] INFO  17:50:46,309 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:50Z] INFO  17:50:46,309 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:50Z] INFO  17:50:46,310 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:50Z] INFO  17:50:46,335 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/8/R14-18105_kapa-NGv3-PE100-NGv3-sort-8_0_15517156-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/8/R14-18105_kapa-NGv3-PE100-NGv3-8_0_15517156-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/8/tx/tmpEes3Y7/R14-18105_kapa-NGv3-PE100-NGv3-8_0_15517156.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:50Z] INFO  17:50:46,362 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:50Z] INFO  17:50:46,363 HelpFormatter - Date/Time: 2016/04/14 17:50:46
[2016-04-15T00:50Z] INFO  17:50:46,364 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:50Z] INFO  17:50:46,365 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:50Z] GATK: UnifiedGenotyper
[2016-04-15T00:50Z] INFO  17:50:46,653 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:50Z] INFO  17:50:46,697 ProgressMeter -            done    357849.0    18.0 s      51.0 s      100.0%    18.0 s       0.0 s
[2016-04-15T00:50Z] INFO  17:50:46,697 ProgressMeter - Total runtime 18.51 secs, 0.31 min, 0.01 hours
[2016-04-15T00:50Z] INFO  17:50:46,698 MicroScheduler - 14803 reads were filtered out during the traversal out of approximately 177858 total reads (8.32%)
[2016-04-15T00:50Z] INFO  17:50:46,698 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:50Z] INFO  17:50:46,698 MicroScheduler -   -> 276 reads (0.16% of total) failing BadMateFilter
[2016-04-15T00:50Z] INFO  17:50:46,699 MicroScheduler -   -> 14414 reads (8.10% of total) failing DuplicateReadFilter
[2016-04-15T00:50Z] INFO  17:50:46,699 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:50Z] INFO  17:50:46,699 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:50Z] INFO  17:50:46,699 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:50Z] INFO  17:50:46,700 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:50Z] INFO  17:50:46,700 MicroScheduler -   -> 113 reads (0.06% of total) failing UnmappedReadFilter
[2016-04-15T00:50Z] INFO  17:50:46,882 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:50Z] INFO  17:50:46,891 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:50Z] INFO  17:50:46,965 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-15T00:50Z] INFO  17:50:47,328 IntervalUtils - Processing 115548 bp from intervals
[2016-04-15T00:50Z] WARN  17:50:47,333 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:50Z] INFO  17:50:47,435 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:50Z] INFO  17:50:47,447 ProgressMeter -            done    442893.0    20.0 s      45.0 s       99.9%    20.0 s       0.0 s
[2016-04-15T00:50Z] INFO  17:50:47,447 ProgressMeter - Total runtime 20.07 secs, 0.33 min, 0.01 hours
[2016-04-15T00:50Z] INFO  17:50:47,448 MicroScheduler - 17173 reads were filtered out during the traversal out of approximately 206740 total reads (8.31%)
[2016-04-15T00:50Z] INFO  17:50:47,448 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:50Z] INFO  17:50:47,448 MicroScheduler -   -> 251 reads (0.12% of total) failing BadMateFilter
[2016-04-15T00:50Z] INFO  17:50:47,449 MicroScheduler -   -> 16786 reads (8.12% of total) failing DuplicateReadFilter
[2016-04-15T00:50Z] INFO  17:50:47,449 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:50Z] INFO  17:50:47,449 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:50Z] INFO  17:50:47,449 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:50Z] INFO  17:50:47,450 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:50Z] INFO  17:50:47,450 MicroScheduler -   -> 136 reads (0.07% of total) failing UnmappedReadFilter
[2016-04-15T00:50Z] INFO  17:50:47,553 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:50Z] INFO  17:50:47,554 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:50Z] INFO  17:50:47,555 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:50Z] INFO  17:50:47,555 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:50Z] INFO  17:50:47,596 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:50Z] INFO  17:50:47,597 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:50Z] INFO  17:50:48,022 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:50Z] GATK: UnifiedGenotyper
[2016-04-15T00:50Z] INFO  17:50:48,701 ProgressMeter -            done    186536.0    12.0 s      66.0 s       99.9%    12.0 s       0.0 s
[2016-04-15T00:50Z] INFO  17:50:48,701 ProgressMeter - Total runtime 12.42 secs, 0.21 min, 0.00 hours
[2016-04-15T00:50Z] INFO  17:50:48,701 MicroScheduler - 8385 reads were filtered out during the traversal out of approximately 104057 total reads (8.06%)
[2016-04-15T00:50Z] INFO  17:50:48,702 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:50Z] INFO  17:50:48,702 MicroScheduler -   -> 138 reads (0.13% of total) failing BadMateFilter
[2016-04-15T00:50Z] INFO  17:50:48,702 MicroScheduler -   -> 8171 reads (7.85% of total) failing DuplicateReadFilter
[2016-04-15T00:50Z] INFO  17:50:48,702 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:50Z] INFO  17:50:48,703 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:50Z] INFO  17:50:48,703 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:50Z] INFO  17:50:48,703 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:50Z] INFO  17:50:48,703 MicroScheduler -   -> 76 reads (0.07% of total) failing UnmappedReadFilter
[2016-04-15T00:50Z] INFO  17:50:48,925 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:50Z] INFO  17:50:49,082 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:50Z] INFO  17:50:49,086 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:50Z] INFO  17:50:49,086 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:50Z] INFO  17:50:49,087 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:50Z] INFO  17:50:49,092 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/8/R14-18105_kapa-NGv3-PE100-NGv3-sort-8_15519664_31030618-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/8/R14-18105_kapa-NGv3-PE100-NGv3-8_15519664_31030618-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/8/tx/tmpJpfJ0e/R14-18105_kapa-NGv3-PE100-NGv3-8_15519664_31030618.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:50Z] INFO  17:50:49,125 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:50Z] INFO  17:50:49,126 HelpFormatter - Date/Time: 2016/04/14 17:50:49
[2016-04-15T00:50Z] INFO  17:50:49,126 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:50Z] INFO  17:50:49,131 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:50Z] GATK: UnifiedGenotyper
[2016-04-15T00:50Z] INFO  17:50:49,288 ProgressMeter -            done   1343007.0    44.0 s      32.0 s      100.0%    44.0 s       0.0 s
[2016-04-15T00:50Z] INFO  17:50:49,289 ProgressMeter - Total runtime 44.29 secs, 0.74 min, 0.01 hours
[2016-04-15T00:50Z] INFO  17:50:49,289 MicroScheduler - 58335 reads were filtered out during the traversal out of approximately 657842 total reads (8.87%)
[2016-04-15T00:50Z] INFO  17:50:49,289 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:50Z] INFO  17:50:49,290 MicroScheduler -   -> 904 reads (0.14% of total) failing BadMateFilter
[2016-04-15T00:50Z] INFO  17:50:49,290 MicroScheduler -   -> 56974 reads (8.66% of total) failing DuplicateReadFilter
[2016-04-15T00:50Z] INFO  17:50:49,290 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:50Z] INFO  17:50:49,290 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:50Z] INFO  17:50:49,291 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:50Z] INFO  17:50:49,291 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:50Z] INFO  17:50:49,291 MicroScheduler -   -> 457 reads (0.07% of total) failing UnmappedReadFilter
[2016-04-15T00:50Z] INFO  17:50:49,338 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:50Z] INFO  17:50:49,551 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:50Z] INFO  17:50:49,560 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:50Z] INFO  17:50:49,636 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-15T00:50Z] INFO  17:50:49,758 ProgressMeter -            done     46373.0     5.0 s     113.0 s       99.7%     5.0 s       0.0 s
[2016-04-15T00:50Z] INFO  17:50:49,759 ProgressMeter - Total runtime 5.28 secs, 0.09 min, 0.00 hours
[2016-04-15T00:50Z] INFO  17:50:49,759 MicroScheduler - 2004 reads were filtered out during the traversal out of approximately 24263 total reads (8.26%)
[2016-04-15T00:50Z] INFO  17:50:49,759 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:50Z] INFO  17:50:49,759 MicroScheduler -   -> 29 reads (0.12% of total) failing BadMateFilter
[2016-04-15T00:50Z] INFO  17:50:49,760 MicroScheduler -   -> 1965 reads (8.10% of total) failing DuplicateReadFilter
[2016-04-15T00:50Z] INFO  17:50:49,760 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:50Z] INFO  17:50:49,760 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:50Z] INFO  17:50:49,761 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:50Z] INFO  17:50:49,761 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:50Z] INFO  17:50:49,761 MicroScheduler -   -> 10 reads (0.04% of total) failing UnmappedReadFilter
[2016-04-15T00:50Z] INFO  17:50:50,073 IntervalUtils - Processing 233081 bp from intervals
[2016-04-15T00:50Z] WARN  17:50:50,078 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:50Z] INFO  17:50:50,112 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:50Z] INFO  17:50:50,184 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:50Z] INFO  17:50:50,305 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:50Z] INFO  17:50:50,306 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:50Z] INFO  17:50:50,306 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:50Z] INFO  17:50:50,307 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:50Z] INFO  17:50:50,358 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:50Z] INFO  17:50:50,359 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:50Z] GATK: UnifiedGenotyper
[2016-04-15T00:50Z] INFO  17:50:50,669 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:50Z] INFO  17:50:50,965 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:50Z] GATK: UnifiedGenotyper
[2016-04-15T00:50Z] INFO  17:50:51,151 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:50Z] INFO  17:50:51,154 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:50Z] INFO  17:50:51,155 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:50Z] INFO  17:50:51,155 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:50Z] INFO  17:50:51,160 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/8/R14-18105_kapa-NGv3-PE100-NGv3-sort-8_31496910_48001429-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/8/R14-18105_kapa-NGv3-PE100-NGv3-8_31496910_48001429-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/8/tx/tmpElnKMU/R14-18105_kapa-NGv3-PE100-NGv3-8_31496910_48001429.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:50Z] INFO  17:50:51,171 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:50Z] INFO  17:50:51,172 HelpFormatter - Date/Time: 2016/04/14 17:50:51
[2016-04-15T00:50Z] INFO  17:50:51,172 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:50Z] INFO  17:50:51,172 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:50Z] GATK: UnifiedGenotyper
[2016-04-15T00:50Z] INFO  17:50:51,399 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:50Z] INFO  17:50:51,413 ProgressMeter -            done    637397.0    24.0 s      37.0 s      100.0%    24.0 s       0.0 s
[2016-04-15T00:50Z] INFO  17:50:51,414 ProgressMeter - Total runtime 24.19 secs, 0.40 min, 0.01 hours
[2016-04-15T00:50Z] INFO  17:50:51,414 MicroScheduler - 22914 reads were filtered out during the traversal out of approximately 279389 total reads (8.20%)
[2016-04-15T00:50Z] INFO  17:50:51,414 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:50Z] INFO  17:50:51,415 MicroScheduler -   -> 472 reads (0.17% of total) failing BadMateFilter
[2016-04-15T00:50Z] INFO  17:50:51,415 MicroScheduler -   -> 22263 reads (7.97% of total) failing DuplicateReadFilter
[2016-04-15T00:50Z] INFO  17:50:51,415 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:50Z] INFO  17:50:51,416 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:50Z] INFO  17:50:51,416 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:50Z] INFO  17:50:51,416 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:50Z] INFO  17:50:51,417 MicroScheduler -   -> 179 reads (0.06% of total) failing UnmappedReadFilter
[2016-04-15T00:50Z] INFO  17:50:51,680 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:50Z] INFO  17:50:51,697 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:50Z] INFO  17:50:51,765 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-15T00:50Z] INFO  17:50:51,965 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:50Z] INFO  17:50:51,969 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:50Z] INFO  17:50:51,970 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:50Z] INFO  17:50:51,971 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:50Z] INFO  17:50:51,976 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/8/R14-18105_kapa-NGv3-PE100-NGv3-sort-8_48003022_63659688-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/8/R14-18105_kapa-NGv3-PE100-NGv3-8_48003022_63659688-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/8/tx/tmpd_Tdjp/R14-18105_kapa-NGv3-PE100-NGv3-8_48003022_63659688.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:50Z] INFO  17:50:52,002 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:50Z] INFO  17:50:52,009 HelpFormatter - Date/Time: 2016/04/14 17:50:51
[2016-04-15T00:50Z] INFO  17:50:52,010 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:50Z] INFO  17:50:52,011 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:50Z] INFO  17:50:52,103 ProgressMeter -            done    214671.0    13.0 s      63.0 s       99.9%    13.0 s       0.0 s
[2016-04-15T00:50Z] INFO  17:50:52,104 ProgressMeter - Total runtime 13.69 secs, 0.23 min, 0.00 hours
[2016-04-15T00:50Z] INFO  17:50:52,104 MicroScheduler - 9115 reads were filtered out during the traversal out of approximately 109887 total reads (8.29%)
[2016-04-15T00:50Z] INFO  17:50:52,105 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:50Z] INFO  17:50:52,105 MicroScheduler -   -> 146 reads (0.13% of total) failing BadMateFilter
[2016-04-15T00:50Z] INFO  17:50:52,105 MicroScheduler -   -> 8901 reads (8.10% of total) failing DuplicateReadFilter
[2016-04-15T00:50Z] INFO  17:50:52,106 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:50Z] INFO  17:50:52,106 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:50Z] INFO  17:50:52,106 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:50Z] INFO  17:50:52,107 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:50Z] INFO  17:50:52,107 MicroScheduler -   -> 68 reads (0.06% of total) failing UnmappedReadFilter
[2016-04-15T00:50Z] INFO  17:50:52,235 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:50Z] INFO  17:50:52,254 IntervalUtils - Processing 125262 bp from intervals
[2016-04-15T00:50Z] WARN  17:50:52,259 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:50Z] INFO  17:50:52,371 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:50Z] INFO  17:50:52,467 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:50Z] INFO  17:50:52,477 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:50Z] INFO  17:50:52,478 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:50Z] INFO  17:50:52,479 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:50Z] INFO  17:50:52,513 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:50Z] INFO  17:50:52,523 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:50Z] INFO  17:50:52,585 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:50Z] INFO  17:50:52,586 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:50Z] INFO  17:50:52,623 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.10
[2016-04-15T00:50Z] INFO  17:50:53,035 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:50Z] INFO  17:50:53,081 IntervalUtils - Processing 104159 bp from intervals
[2016-04-15T00:50Z] WARN  17:50:53,086 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:50Z] INFO  17:50:53,149 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:50Z] INFO  17:50:53,152 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:50Z] INFO  17:50:53,153 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:50Z] INFO  17:50:53,153 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:50Z] INFO  17:50:53,158 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/8/R14-18105_kapa-NGv3-PE100-NGv3-sort-8_63775819_79510770-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/8/R14-18105_kapa-NGv3-PE100-NGv3-8_63775819_79510770-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/8/tx/tmpmO5tdO/R14-18105_kapa-NGv3-PE100-NGv3-8_63775819_79510770.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:50Z] INFO  17:50:53,167 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:50Z] INFO  17:50:53,168 HelpFormatter - Date/Time: 2016/04/14 17:50:53
[2016-04-15T00:50Z] INFO  17:50:53,169 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:50Z] INFO  17:50:53,169 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:50Z] INFO  17:50:53,238 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:50Z] GATK: UnifiedGenotyper
[2016-04-15T00:50Z] INFO  17:50:53,333 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:50Z] INFO  17:50:53,343 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:50Z] INFO  17:50:53,344 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:50Z] INFO  17:50:53,345 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:50Z] INFO  17:50:53,380 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:50Z] INFO  17:50:53,395 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:50Z] INFO  17:50:53,396 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:50Z] INFO  17:50:53,579 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:50Z] INFO  17:50:53,602 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:50Z] INFO  17:50:53,608 ProgressMeter -            done    438420.0    19.0 s      44.0 s      100.0%    19.0 s       0.0 s
[2016-04-15T00:50Z] INFO  17:50:53,609 ProgressMeter - Total runtime 19.38 secs, 0.32 min, 0.01 hours
[2016-04-15T00:50Z] INFO  17:50:53,609 MicroScheduler - 17552 reads were filtered out during the traversal out of approximately 209201 total reads (8.39%)
[2016-04-15T00:50Z] INFO  17:50:53,609 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:50Z] INFO  17:50:53,609 MicroScheduler -   -> 311 reads (0.15% of total) failing BadMateFilter
[2016-04-15T00:50Z] INFO  17:50:53,610 MicroScheduler -   -> 17105 reads (8.18% of total) failing DuplicateReadFilter
[2016-04-15T00:50Z] INFO  17:50:53,610 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:50Z] INFO  17:50:53,610 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:50Z] INFO  17:50:53,610 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:50Z] INFO  17:50:53,611 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:50Z] INFO  17:50:53,611 MicroScheduler -   -> 136 reads (0.07% of total) failing UnmappedReadFilter
[2016-04-15T00:50Z] INFO  17:50:53,619 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:50Z] INFO  17:50:53,708 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.11
[2016-04-15T00:50Z] GATK: UnifiedGenotyper
[2016-04-15T00:50Z] INFO  17:50:54,159 IntervalUtils - Processing 117209 bp from intervals
[2016-04-15T00:50Z] INFO  17:50:54,156 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:50Z] INFO  17:50:54,160 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:50Z] WARN  17:50:54,166 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:50Z] INFO  17:50:54,167 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:50Z] INFO  17:50:54,168 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:50Z] INFO  17:50:54,172 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/8/R14-18105_kapa-NGv3-PE100-NGv3-sort-8_79513976_95140568-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/8/R14-18105_kapa-NGv3-PE100-NGv3-8_79513976_95140568-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/8/tx/tmpwiMDJ1/R14-18105_kapa-NGv3-PE100-NGv3-8_79513976_95140568.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:50Z] INFO  17:50:54,197 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:50Z] INFO  17:50:54,198 HelpFormatter - Date/Time: 2016/04/14 17:50:54
[2016-04-15T00:50Z] INFO  17:50:54,199 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:50Z] INFO  17:50:54,199 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:50Z] INFO  17:50:54,299 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:50Z] INFO  17:50:54,365 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:50Z] INFO  17:50:54,394 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:50Z] INFO  17:50:54,396 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:50Z] INFO  17:50:54,397 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:50Z] INFO  17:50:54,398 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:50Z] INFO  17:50:54,445 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:50Z] INFO  17:50:54,448 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:50Z] INFO  17:50:54,449 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:50Z] INFO  17:50:54,449 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:50Z] INFO  17:50:54,454 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/8/R14-18105_kapa-NGv3-PE100-NGv3-sort-8_95142853_110655419-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/8/R14-18105_kapa-NGv3-PE100-NGv3-8_95142853_110655419-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/8/tx/tmpkBB8nd/R14-18105_kapa-NGv3-PE100-NGv3-8_95142853_110655419.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:50Z] INFO  17:50:54,476 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:50Z] INFO  17:50:54,484 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:50Z] INFO  17:50:54,485 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:50Z] INFO  17:50:54,477 HelpFormatter - Date/Time: 2016/04/14 17:50:54
[2016-04-15T00:50Z] INFO  17:50:54,489 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:50Z] INFO  17:50:54,494 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:50Z] INFO  17:50:54,601 ProgressMeter -            done    434204.0    17.0 s      39.0 s      100.0%    17.0 s       0.0 s
[2016-04-15T00:50Z] INFO  17:50:54,602 ProgressMeter - Total runtime 17.34 secs, 0.29 min, 0.00 hours
[2016-04-15T00:50Z] INFO  17:50:54,602 MicroScheduler - 12927 reads were filtered out during the traversal out of approximately 159728 total reads (8.09%)
[2016-04-15T00:50Z] INFO  17:50:54,603 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:50Z] INFO  17:50:54,603 MicroScheduler -   -> 244 reads (0.15% of total) failing BadMateFilter
[2016-04-15T00:50Z] INFO  17:50:54,603 MicroScheduler -   -> 12564 reads (7.87% of total) failing DuplicateReadFilter
[2016-04-15T00:50Z] INFO  17:50:54,603 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:50Z] INFO  17:50:54,604 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:50Z] INFO  17:50:54,604 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:50Z] INFO  17:50:54,604 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:50Z] INFO  17:50:54,604 MicroScheduler -   -> 119 reads (0.07% of total) failing UnmappedReadFilter
[2016-04-15T00:50Z] INFO  17:50:54,633 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:50Z] INFO  17:50:54,670 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:50Z] INFO  17:50:54,675 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:50Z] INFO  17:50:54,753 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-15T00:50Z] INFO  17:50:54,910 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:50Z] INFO  17:50:54,919 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:50Z] INFO  17:50:54,995 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-15T00:50Z] INFO  17:50:55,076 IntervalUtils - Processing 78340 bp from intervals
[2016-04-15T00:50Z] WARN  17:50:55,080 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:50Z] INFO  17:50:55,085 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:50Z] INFO  17:50:55,218 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:50Z] INFO  17:50:55,332 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:50Z] INFO  17:50:55,333 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:50Z] INFO  17:50:55,334 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:50Z] INFO  17:50:55,334 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:50Z] INFO  17:50:55,349 IntervalUtils - Processing 161638 bp from intervals
[2016-04-15T00:50Z] WARN  17:50:55,353 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:50Z] INFO  17:50:55,376 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:50Z] INFO  17:50:55,377 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:50Z] INFO  17:50:55,423 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:50Z] GATK: UnifiedGenotyper
[2016-04-15T00:50Z] INFO  17:50:55,543 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:50Z] INFO  17:50:55,544 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:50Z] INFO  17:50:55,545 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:50Z] INFO  17:50:55,546 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:50Z] INFO  17:50:55,594 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:50Z] INFO  17:50:55,595 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:50Z] INFO  17:50:55,993 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:50Z] INFO  17:50:55,997 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:50Z] INFO  17:50:55,998 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:50Z] INFO  17:50:55,998 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:50Z] INFO  17:50:56,004 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/8/R14-18105_kapa-NGv3-PE100-NGv3-sort-8_110656864_126194498-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/8/R14-18105_kapa-NGv3-PE100-NGv3-8_110656864_126194498-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/8/tx/tmpgdV7ul/R14-18105_kapa-NGv3-PE100-NGv3-8_110656864_126194498.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:50Z] INFO  17:50:56,014 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:50Z] INFO  17:50:56,015 HelpFormatter - Date/Time: 2016/04/14 17:50:55
[2016-04-15T00:50Z] INFO  17:50:56,016 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:50Z] INFO  17:50:56,017 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:50Z] INFO  17:50:56,046 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:50Z] INFO  17:50:56,345 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:50Z] GATK: UnifiedGenotyper
[2016-04-15T00:50Z] INFO  17:50:56,606 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:50Z] INFO  17:50:56,617 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:50Z] INFO  17:50:56,750 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.13
[2016-04-15T00:50Z] INFO  17:50:56,866 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:50Z] INFO  17:50:56,869 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:50Z] INFO  17:50:56,870 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:50Z] INFO  17:50:56,870 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:50Z] INFO  17:50:56,875 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/8/R14-18105_kapa-NGv3-PE100-NGv3-sort-8_126369460_141889736-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/8/R14-18105_kapa-NGv3-PE100-NGv3-8_126369460_141889736-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/8/tx/tmpDLO_LB/R14-18105_kapa-NGv3-PE100-NGv3-8_126369460_141889736.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:50Z] INFO  17:50:56,905 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:50Z] INFO  17:50:56,905 HelpFormatter - Date/Time: 2016/04/14 17:50:56
[2016-04-15T00:50Z] INFO  17:50:56,906 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:50Z] INFO  17:50:56,907 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:50Z] INFO  17:50:57,105 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:50Z] INFO  17:50:57,210 IntervalUtils - Processing 102393 bp from intervals
[2016-04-15T00:50Z] WARN  17:50:57,216 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:50Z] INFO  17:50:57,410 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:50Z] INFO  17:50:57,412 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:50Z] INFO  17:50:57,439 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:50Z] INFO  17:50:57,507 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:50Z] INFO  17:50:57,508 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:50Z] INFO  17:50:57,509 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:50Z] INFO  17:50:57,510 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:50Z] INFO  17:50:57,521 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-15T00:50Z] INFO  17:50:57,558 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:50Z] INFO  17:50:57,559 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:50Z] INFO  17:50:58,031 IntervalUtils - Processing 72911 bp from intervals
[2016-04-15T00:50Z] WARN  17:50:58,036 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:50Z] INFO  17:50:58,163 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:50Z] INFO  17:50:58,261 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:50Z] INFO  17:50:58,262 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:50Z] INFO  17:50:58,263 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:50Z] INFO  17:50:58,264 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:50Z] INFO  17:50:58,352 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:50Z] INFO  17:50:58,353 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:50Z] INFO  17:50:58,506 ProgressMeter -            done    457571.0    21.0 s      47.0 s      100.0%    21.0 s       0.0 s
[2016-04-15T00:50Z] INFO  17:50:58,506 ProgressMeter - Total runtime 21.60 secs, 0.36 min, 0.01 hours
[2016-04-15T00:50Z] INFO  17:50:58,507 MicroScheduler - 18933 reads were filtered out during the traversal out of approximately 240734 total reads (7.86%)
[2016-04-15T00:50Z] INFO  17:50:58,507 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:50Z] INFO  17:50:58,507 MicroScheduler -   -> 377 reads (0.16% of total) failing BadMateFilter
[2016-04-15T00:50Z] INFO  17:50:58,508 MicroScheduler -   -> 18418 reads (7.65% of total) failing DuplicateReadFilter
[2016-04-15T00:50Z] INFO  17:50:58,508 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:50Z] INFO  17:50:58,508 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:50Z] INFO  17:50:58,508 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:50Z] INFO  17:50:58,509 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:50Z] INFO  17:50:58,509 MicroScheduler -   -> 138 reads (0.06% of total) failing UnmappedReadFilter
[2016-04-15T00:50Z] INFO  17:50:59,102 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:50Z] INFO  17:50:59,105 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:50Z] INFO  17:50:59,106 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:50Z] INFO  17:50:59,106 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:50Z] INFO  17:50:59,111 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/8/R14-18105_kapa-NGv3-PE100-NGv3-sort-8_141900641_146364022-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/8/R14-18105_kapa-NGv3-PE100-NGv3-8_141900641_146364022-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/8/tx/tmpX0lY62/R14-18105_kapa-NGv3-PE100-NGv3-8_141900641_146364022.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:50Z] INFO  17:50:59,119 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:50Z] INFO  17:50:59,131 HelpFormatter - Date/Time: 2016/04/14 17:50:59
[2016-04-15T00:50Z] INFO  17:50:59,132 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:50Z] INFO  17:50:59,132 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:50Z] INFO  17:50:59,244 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:50Z] INFO  17:50:59,246 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:50Z] INFO  17:50:59,247 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:50Z] INFO  17:50:59,247 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:50Z] INFO  17:50:59,251 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/9/R14-18105_kapa-NGv3-PE100-NGv3-sort-9_0_15510186-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/9/R14-18105_kapa-NGv3-PE100-NGv3-9_0_15510186-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/9/tx/tmpgNpucm/R14-18105_kapa-NGv3-PE100-NGv3-9_0_15510186.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:50Z] INFO  17:50:59,268 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:50Z] INFO  17:50:59,269 HelpFormatter - Date/Time: 2016/04/14 17:50:59
[2016-04-15T00:50Z] INFO  17:50:59,269 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:50Z] INFO  17:50:59,269 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:50Z] INFO  17:50:59,276 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:50Z] INFO  17:50:59,520 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:50Z] INFO  17:50:59,583 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:50Z] INFO  17:50:59,592 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:50Z] INFO  17:50:59,677 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.09
[2016-04-15T00:50Z] INFO  17:50:59,747 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:50Z] INFO  17:50:59,756 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:50Z] INFO  17:50:59,826 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-15T00:50Z] INFO  17:50:59,830 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:51Z] INFO  17:51:00,131 IntervalUtils - Processing 204618 bp from intervals
[2016-04-15T00:51Z] WARN  17:51:00,137 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:51Z] GATK: UnifiedGenotyper
[2016-04-15T00:51Z] INFO  17:51:00,238 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:51Z] INFO  17:51:00,273 IntervalUtils - Processing 123193 bp from intervals
[2016-04-15T00:51Z] WARN  17:51:00,278 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:51Z] INFO  17:51:00,337 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:51Z] INFO  17:51:00,338 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:51Z] INFO  17:51:00,338 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:51Z] INFO  17:51:00,338 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:51Z] INFO  17:51:00,378 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:51Z] INFO  17:51:00,391 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:51Z] INFO  17:51:00,392 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:51Z] INFO  17:51:00,463 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:51Z] INFO  17:51:00,464 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:51Z] INFO  17:51:00,465 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:51Z] INFO  17:51:00,466 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:51Z] INFO  17:51:00,513 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:51Z] INFO  17:51:00,514 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:51Z] INFO  17:51:02,919 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:51Z] INFO  17:51:02,922 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:51Z] INFO  17:51:02,922 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:51Z] INFO  17:51:02,923 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:51Z] INFO  17:51:02,927 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/9/R14-18105_kapa-NGv3-PE100-NGv3-sort-9_15564086_32405601-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/9/R14-18105_kapa-NGv3-PE100-NGv3-9_15564086_32405601-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/9/tx/tmphvC_nV/R14-18105_kapa-NGv3-PE100-NGv3-9_15564086_32405601.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:51Z] INFO  17:51:02,955 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:51Z] INFO  17:51:02,955 HelpFormatter - Date/Time: 2016/04/14 17:51:02
[2016-04-15T00:51Z] INFO  17:51:02,955 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:51Z] INFO  17:51:02,956 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:51Z] INFO  17:51:03,166 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:51Z] INFO  17:51:03,390 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:51Z] INFO  17:51:03,408 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:51Z] INFO  17:51:03,490 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-15T00:51Z] INFO  17:51:03,808 IntervalUtils - Processing 89361 bp from intervals
[2016-04-15T00:51Z] WARN  17:51:03,820 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:51Z] INFO  17:51:03,942 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:51Z] INFO  17:51:04,001 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:51Z] INFO  17:51:04,002 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:51Z] INFO  17:51:04,003 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:51Z] INFO  17:51:04,004 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:51Z] INFO  17:51:04,061 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:51Z] INFO  17:51:04,062 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:51Z] INFO  17:51:04,516 ProgressMeter -            done    735970.0    26.0 s      35.0 s      100.0%    26.0 s       0.0 s
[2016-04-15T00:51Z] INFO  17:51:04,517 ProgressMeter - Total runtime 26.36 secs, 0.44 min, 0.01 hours
[2016-04-15T00:51Z] INFO  17:51:04,518 MicroScheduler - 24570 reads were filtered out during the traversal out of approximately 295312 total reads (8.32%)
[2016-04-15T00:51Z] INFO  17:51:04,519 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:51Z] INFO  17:51:04,520 MicroScheduler -   -> 471 reads (0.16% of total) failing BadMateFilter
[2016-04-15T00:51Z] INFO  17:51:04,520 MicroScheduler -   -> 23948 reads (8.11% of total) failing DuplicateReadFilter
[2016-04-15T00:51Z] INFO  17:51:04,521 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:51Z] INFO  17:51:04,522 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:51Z] INFO  17:51:04,523 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:51Z] INFO  17:51:04,523 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:51Z] INFO  17:51:04,524 MicroScheduler -   -> 151 reads (0.05% of total) failing UnmappedReadFilter
[2016-04-15T00:51Z] INFO  17:51:05,755 ProgressMeter -            done    239009.0    18.0 s      76.0 s      100.0%    18.0 s       0.0 s
[2016-04-15T00:51Z] INFO  17:51:05,756 ProgressMeter - Total runtime 18.20 secs, 0.30 min, 0.01 hours
[2016-04-15T00:51Z] INFO  17:51:05,756 MicroScheduler - 15492 reads were filtered out during the traversal out of approximately 197379 total reads (7.85%)
[2016-04-15T00:51Z] INFO  17:51:05,757 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:51Z] INFO  17:51:05,757 MicroScheduler -   -> 270 reads (0.14% of total) failing BadMateFilter
[2016-04-15T00:51Z] INFO  17:51:05,757 MicroScheduler -   -> 15096 reads (7.65% of total) failing DuplicateReadFilter
[2016-04-15T00:51Z] INFO  17:51:05,758 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:51Z] INFO  17:51:05,758 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:51Z] INFO  17:51:05,758 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:51Z] INFO  17:51:05,756 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:51Z] INFO  17:51:05,759 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:51Z] INFO  17:51:05,759 MicroScheduler -   -> 126 reads (0.06% of total) failing UnmappedReadFilter
[2016-04-15T00:51Z] INFO  17:51:05,882 ProgressMeter -            done   3191514.0    53.0 s      16.0 s      100.0%    53.0 s       0.0 s
[2016-04-15T00:51Z] INFO  17:51:05,883 ProgressMeter - Total runtime 53.75 secs, 0.90 min, 0.01 hours
[2016-04-15T00:51Z] INFO  17:51:05,883 MicroScheduler - 62933 reads were filtered out during the traversal out of approximately 776624 total reads (8.10%)
[2016-04-15T00:51Z] INFO  17:51:05,884 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:51Z] INFO  17:51:05,884 MicroScheduler -   -> 1121 reads (0.14% of total) failing BadMateFilter
[2016-04-15T00:51Z] INFO  17:51:05,884 MicroScheduler -   -> 61322 reads (7.90% of total) failing DuplicateReadFilter
[2016-04-15T00:51Z] INFO  17:51:05,885 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:51Z] INFO  17:51:05,885 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:51Z] INFO  17:51:05,885 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:51Z] INFO  17:51:05,885 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:51Z] INFO  17:51:05,886 MicroScheduler -   -> 490 reads (0.06% of total) failing UnmappedReadFilter
[2016-04-15T00:51Z] GATK: UnifiedGenotyper
[2016-04-15T00:51Z] INFO  17:51:07,101 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:51Z] INFO  17:51:07,258 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:51Z] GATK: UnifiedGenotyper
[2016-04-15T00:51Z] GATK: UnifiedGenotyper
[2016-04-15T00:51Z] INFO  17:51:07,964 ProgressMeter -     7:101256755   1023602.0    30.0 s      29.0 s       60.8%    49.0 s      19.0 s
[2016-04-15T00:51Z] INFO  17:51:08,048 ProgressMeter -            done    185097.0    12.0 s      68.0 s      100.0%    12.0 s       0.0 s
[2016-04-15T00:51Z] INFO  17:51:08,049 ProgressMeter - Total runtime 12.72 secs, 0.21 min, 0.00 hours
[2016-04-15T00:51Z] INFO  17:51:08,049 MicroScheduler - 6911 reads were filtered out during the traversal out of approximately 85601 total reads (8.07%)
[2016-04-15T00:51Z] INFO  17:51:08,050 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:51Z] INFO  17:51:08,050 MicroScheduler -   -> 131 reads (0.15% of total) failing BadMateFilter
[2016-04-15T00:51Z] INFO  17:51:08,050 MicroScheduler -   -> 6725 reads (7.86% of total) failing DuplicateReadFilter
[2016-04-15T00:51Z] INFO  17:51:08,051 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:51Z] INFO  17:51:08,051 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:51Z] INFO  17:51:08,051 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:51Z] INFO  17:51:08,052 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:51Z] INFO  17:51:08,052 MicroScheduler -   -> 55 reads (0.06% of total) failing UnmappedReadFilter
[2016-04-15T00:51Z] INFO  17:51:08,101 ProgressMeter -            done    284373.0    14.0 s      51.0 s       99.9%    14.0 s       0.0 s
[2016-04-15T00:51Z] INFO  17:51:08,102 ProgressMeter - Total runtime 14.76 secs, 0.25 min, 0.00 hours
[2016-04-15T00:51Z] INFO  17:51:08,103 MicroScheduler - 10079 reads were filtered out during the traversal out of approximately 121835 total reads (8.27%)
[2016-04-15T00:51Z] INFO  17:51:08,104 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:51Z] INFO  17:51:08,105 MicroScheduler -   -> 172 reads (0.14% of total) failing BadMateFilter
[2016-04-15T00:51Z] INFO  17:51:08,106 MicroScheduler -   -> 9827 reads (8.07% of total) failing DuplicateReadFilter
[2016-04-15T00:51Z] INFO  17:51:08,106 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:51Z] INFO  17:51:08,107 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:51Z] INFO  17:51:08,108 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:51Z] INFO  17:51:08,109 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:51Z] INFO  17:51:08,109 MicroScheduler -   -> 80 reads (0.07% of total) failing UnmappedReadFilter
[2016-04-15T00:51Z] INFO  17:51:08,511 ProgressMeter -            done    405639.0    16.0 s      39.0 s      100.0%    16.0 s       0.0 s
[2016-04-15T00:51Z] INFO  17:51:08,511 ProgressMeter - Total runtime 16.03 secs, 0.27 min, 0.00 hours
[2016-04-15T00:51Z] INFO  17:51:08,512 MicroScheduler - 13757 reads were filtered out during the traversal out of approximately 162195 total reads (8.48%)
[2016-04-15T00:51Z] INFO  17:51:08,512 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:51Z] INFO  17:51:08,513 MicroScheduler -   -> 233 reads (0.14% of total) failing BadMateFilter
[2016-04-15T00:51Z] INFO  17:51:08,513 MicroScheduler -   -> 13433 reads (8.28% of total) failing DuplicateReadFilter
[2016-04-15T00:51Z] INFO  17:51:08,513 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:51Z] INFO  17:51:08,513 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:51Z] INFO  17:51:08,514 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:51Z] INFO  17:51:08,514 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:51Z] INFO  17:51:08,514 MicroScheduler -   -> 91 reads (0.06% of total) failing UnmappedReadFilter
[2016-04-15T00:51Z] INFO  17:51:09,377 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:51Z] INFO  17:51:09,381 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:51Z] INFO  17:51:09,381 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:51Z] INFO  17:51:09,382 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:51Z] INFO  17:51:09,387 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/9/R14-18105_kapa-NGv3-PE100-NGv3-sort-9_32407258_65506776-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/9/R14-18105_kapa-NGv3-PE100-NGv3-9_32407258_65506776-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/9/tx/tmp2_rIaA/R14-18105_kapa-NGv3-PE100-NGv3-9_32407258_65506776.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:51Z] INFO  17:51:09,399 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:51Z] INFO  17:51:09,401 HelpFormatter - Date/Time: 2016/04/14 17:51:09
[2016-04-15T00:51Z] INFO  17:51:09,402 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:51Z] INFO  17:51:09,403 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:51Z] INFO  17:51:09,525 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:51Z] INFO  17:51:09,580 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:51Z] INFO  17:51:09,640 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:51Z] INFO  17:51:09,810 ProgressMeter -            done    175776.0    11.0 s      65.0 s       99.9%    11.0 s       0.0 s
[2016-04-15T00:51Z] INFO  17:51:09,811 ProgressMeter - Total runtime 11.55 secs, 0.19 min, 0.00 hours
[2016-04-15T00:51Z] INFO  17:51:09,811 MicroScheduler - 8727 reads were filtered out during the traversal out of approximately 104897 total reads (8.32%)
[2016-04-15T00:51Z] INFO  17:51:09,811 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:51Z] INFO  17:51:09,812 MicroScheduler -   -> 167 reads (0.16% of total) failing BadMateFilter
[2016-04-15T00:51Z] INFO  17:51:09,812 MicroScheduler -   -> 8506 reads (8.11% of total) failing DuplicateReadFilter
[2016-04-15T00:51Z] INFO  17:51:09,812 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:51Z] INFO  17:51:09,812 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:51Z] INFO  17:51:09,813 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:51Z] INFO  17:51:09,813 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:51Z] INFO  17:51:09,813 MicroScheduler -   -> 54 reads (0.05% of total) failing UnmappedReadFilter
[2016-04-15T00:51Z] INFO  17:51:09,824 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:51Z] GATK: UnifiedGenotyper
[2016-04-15T00:51Z] INFO  17:51:09,833 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:51Z] GATK: UnifiedGenotyper
[2016-04-15T00:51Z] INFO  17:51:09,897 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-15T00:51Z] INFO  17:51:10,076 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:51Z] INFO  17:51:10,196 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:51Z] INFO  17:51:10,199 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:51Z] INFO  17:51:10,200 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:51Z] INFO  17:51:10,200 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:51Z] INFO  17:51:10,205 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/9/R14-18105_kapa-NGv3-PE100-NGv3-sort-9_65507205_82187750-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/9/R14-18105_kapa-NGv3-PE100-NGv3-9_65507205_82187750-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/9/tx/tmp4Rd5Fh/R14-18105_kapa-NGv3-PE100-NGv3-9_65507205_82187750.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:51Z] INFO  17:51:10,231 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:51Z] INFO  17:51:10,243 HelpFormatter - Date/Time: 2016/04/14 17:51:10
[2016-04-15T00:51Z] INFO  17:51:10,244 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:51Z] INFO  17:51:10,244 IntervalUtils - Processing 223679 bp from intervals
[2016-04-15T00:51Z] INFO  17:51:10,245 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:51Z] WARN  17:51:10,250 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:51Z] INFO  17:51:10,316 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:51Z] INFO  17:51:10,334 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:51Z] INFO  17:51:10,338 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:51Z] INFO  17:51:10,338 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:51Z] INFO  17:51:10,339 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:51Z] INFO  17:51:10,343 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/9/R14-18105_kapa-NGv3-PE100-NGv3-sort-9_82188172_97717561-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/9/R14-18105_kapa-NGv3-PE100-NGv3-9_82188172_97717561-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/9/tx/tmpWuKxaK/R14-18105_kapa-NGv3-PE100-NGv3-9_82188172_97717561.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:51Z] INFO  17:51:10,370 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:51Z] INFO  17:51:10,371 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:51Z] INFO  17:51:10,372 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:51Z] INFO  17:51:10,373 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:51Z] INFO  17:51:10,375 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:51Z] INFO  17:51:10,376 HelpFormatter - Date/Time: 2016/04/14 17:51:10
[2016-04-15T00:51Z] INFO  17:51:10,377 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:51Z] INFO  17:51:10,377 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:51Z] INFO  17:51:10,389 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:51Z] INFO  17:51:10,428 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:51Z] INFO  17:51:10,429 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:51Z] GATK: UnifiedGenotyper
[2016-04-15T00:51Z] INFO  17:51:10,543 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:51Z] INFO  17:51:10,597 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:51Z] INFO  17:51:10,606 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:51Z] INFO  17:51:10,697 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-15T00:51Z] INFO  17:51:10,698 ProgressMeter -            done    271335.0    16.0 s      60.0 s      100.0%    16.0 s       0.0 s
[2016-04-15T00:51Z] INFO  17:51:10,699 ProgressMeter - Total runtime 16.30 secs, 0.27 min, 0.00 hours
[2016-04-15T00:51Z] INFO  17:51:10,700 MicroScheduler - 10892 reads were filtered out during the traversal out of approximately 131694 total reads (8.27%)
[2016-04-15T00:51Z] INFO  17:51:10,700 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:51Z] INFO  17:51:10,701 MicroScheduler -   -> 212 reads (0.16% of total) failing BadMateFilter
[2016-04-15T00:51Z] INFO  17:51:10,702 MicroScheduler -   -> 10593 reads (8.04% of total) failing DuplicateReadFilter
[2016-04-15T00:51Z] INFO  17:51:10,702 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:51Z] INFO  17:51:10,703 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:51Z] INFO  17:51:10,703 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:51Z] INFO  17:51:10,704 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:51Z] INFO  17:51:10,705 MicroScheduler -   -> 87 reads (0.07% of total) failing UnmappedReadFilter
[2016-04-15T00:51Z] INFO  17:51:10,756 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:51Z] INFO  17:51:10,765 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:51Z] INFO  17:51:10,848 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-15T00:51Z] INFO  17:51:11,022 IntervalUtils - Processing 119378 bp from intervals
[2016-04-15T00:51Z] WARN  17:51:11,038 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:51Z] INFO  17:51:11,126 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:51Z] INFO  17:51:11,197 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:51Z] INFO  17:51:11,198 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:51Z] INFO  17:51:11,199 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:51Z] INFO  17:51:11,200 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:51Z] INFO  17:51:11,240 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:51Z] INFO  17:51:11,241 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:51Z] INFO  17:51:11,264 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:51Z] INFO  17:51:11,281 IntervalUtils - Processing 181286 bp from intervals
[2016-04-15T00:51Z] WARN  17:51:11,297 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:51Z] INFO  17:51:11,383 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:51Z] INFO  17:51:11,467 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:51Z] INFO  17:51:11,469 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:51Z] INFO  17:51:11,469 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:51Z] INFO  17:51:11,470 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:51Z] INFO  17:51:11,510 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:51Z] INFO  17:51:11,511 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:51Z] GATK: UnifiedGenotyper
[2016-04-15T00:51Z] INFO  17:51:11,881 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:51Z] INFO  17:51:11,932 ProgressMeter -            done    255372.0    14.0 s      56.0 s       99.9%    14.0 s       0.0 s
[2016-04-15T00:51Z] INFO  17:51:11,933 ProgressMeter - Total runtime 14.42 secs, 0.24 min, 0.00 hours
[2016-04-15T00:51Z] INFO  17:51:11,933 MicroScheduler - 10171 reads were filtered out during the traversal out of approximately 125342 total reads (8.11%)
[2016-04-15T00:51Z] INFO  17:51:11,933 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:51Z] INFO  17:51:11,934 MicroScheduler -   -> 152 reads (0.12% of total) failing BadMateFilter
[2016-04-15T00:51Z] INFO  17:51:11,934 MicroScheduler -   -> 9937 reads (7.93% of total) failing DuplicateReadFilter
[2016-04-15T00:51Z] INFO  17:51:11,934 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:51Z] INFO  17:51:11,934 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:51Z] INFO  17:51:11,935 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:51Z] INFO  17:51:11,935 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:51Z] INFO  17:51:11,935 MicroScheduler -   -> 82 reads (0.07% of total) failing UnmappedReadFilter
[2016-04-15T00:51Z] GATK: UnifiedGenotyper
[2016-04-15T00:51Z] INFO  17:51:12,450 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:51Z] INFO  17:51:12,454 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:51Z] INFO  17:51:12,454 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:51Z] INFO  17:51:12,455 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:51Z] INFO  17:51:12,459 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/9/R14-18105_kapa-NGv3-PE100-NGv3-sort-9_113231219_129089575-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/9/R14-18105_kapa-NGv3-PE100-NGv3-9_113231219_129089575-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/9/tx/tmpYMc2dF/R14-18105_kapa-NGv3-PE100-NGv3-9_113231219_129089575.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:51Z] INFO  17:51:12,478 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:51Z] INFO  17:51:12,479 HelpFormatter - Date/Time: 2016/04/14 17:51:12
[2016-04-15T00:51Z] INFO  17:51:12,479 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:51Z] INFO  17:51:12,480 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:51Z] INFO  17:51:12,570 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:51Z] INFO  17:51:12,573 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:51Z] INFO  17:51:12,574 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:51Z] INFO  17:51:12,574 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:51Z] INFO  17:51:12,579 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/9/R14-18105_kapa-NGv3-PE100-NGv3-sort-9_97718189_113228306-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/9/R14-18105_kapa-NGv3-PE100-NGv3-9_97718189_113228306-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/9/tx/tmpwzgEn4/R14-18105_kapa-NGv3-PE100-NGv3-9_97718189_113228306.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:51Z] INFO  17:51:12,592 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:51Z] INFO  17:51:12,592 HelpFormatter - Date/Time: 2016/04/14 17:51:12
[2016-04-15T00:51Z] INFO  17:51:12,593 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:51Z] INFO  17:51:12,593 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:51Z] INFO  17:51:12,656 ProgressMeter -     7:157046648   1157051.0    30.0 s      25.0 s       99.7%    30.0 s       0.0 s
[2016-04-15T00:51Z] INFO  17:51:12,697 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:51Z] INFO  17:51:12,743 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:51Z] INFO  17:51:12,799 ProgressMeter -            done   1158758.0    30.0 s      26.0 s      100.0%    30.0 s       0.0 s
[2016-04-15T00:51Z] INFO  17:51:12,800 ProgressMeter - Total runtime 30.17 secs, 0.50 min, 0.01 hours
[2016-04-15T00:51Z] INFO  17:51:12,800 MicroScheduler - 31141 reads were filtered out during the traversal out of approximately 402130 total reads (7.74%)
[2016-04-15T00:51Z] INFO  17:51:12,801 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:51Z] INFO  17:51:12,801 MicroScheduler -   -> 583 reads (0.14% of total) failing BadMateFilter
[2016-04-15T00:51Z] INFO  17:51:12,801 MicroScheduler -   -> 30296 reads (7.53% of total) failing DuplicateReadFilter
[2016-04-15T00:51Z] INFO  17:51:12,801 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:51Z] INFO  17:51:12,802 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:51Z] INFO  17:51:12,802 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:51Z] INFO  17:51:12,802 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:51Z] INFO  17:51:12,803 MicroScheduler -   -> 262 reads (0.07% of total) failing UnmappedReadFilter
[2016-04-15T00:51Z] INFO  17:51:12,997 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:51Z] INFO  17:51:13,016 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:51Z] INFO  17:51:13,089 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-15T00:51Z] INFO  17:51:13,103 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:51Z] INFO  17:51:13,124 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:51Z] INFO  17:51:13,210 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-15T00:51Z] INFO  17:51:13,257 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:51Z] INFO  17:51:13,489 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:51Z] INFO  17:51:13,492 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:51Z] INFO  17:51:13,493 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:51Z] INFO  17:51:13,493 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:51Z] INFO  17:51:13,498 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/9/R14-18105_kapa-NGv3-PE100-NGv3-sort-9_129097484_141213431-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/9/R14-18105_kapa-NGv3-PE100-NGv3-9_129097484_141213431-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/9/tx/tmputm0CN/R14-18105_kapa-NGv3-PE100-NGv3-9_129097484_141213431.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:51Z] INFO  17:51:13,501 IntervalUtils - Processing 199321 bp from intervals
[2016-04-15T00:51Z] INFO  17:51:13,518 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:51Z] INFO  17:51:13,519 HelpFormatter - Date/Time: 2016/04/14 17:51:13
[2016-04-15T00:51Z] INFO  17:51:13,519 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:51Z] INFO  17:51:13,524 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:51Z] WARN  17:51:13,539 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:51Z] GATK: UnifiedGenotyper
[2016-04-15T00:51Z] INFO  17:51:13,620 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:51Z] INFO  17:51:13,753 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:51Z] INFO  17:51:13,754 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:51Z] INFO  17:51:13,754 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:51Z] INFO  17:51:13,755 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:51Z] INFO  17:51:13,768 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:51Z] INFO  17:51:13,803 IntervalUtils - Processing 228449 bp from intervals
[2016-04-15T00:51Z] WARN  17:51:13,819 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:51Z] INFO  17:51:13,837 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:51Z] INFO  17:51:13,837 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:51Z] INFO  17:51:13,979 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:51Z] INFO  17:51:14,026 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:51Z] INFO  17:51:14,038 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:51Z] INFO  17:51:14,101 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:51Z] INFO  17:51:14,102 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:51Z] INFO  17:51:14,102 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:51Z] INFO  17:51:14,104 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:51Z] INFO  17:51:14,113 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-15T00:51Z] INFO  17:51:14,144 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:51Z] INFO  17:51:14,145 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:51Z] INFO  17:51:14,244 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:51Z] INFO  17:51:14,276 ProgressMeter -            done    445208.0    18.0 s      42.0 s      100.0%    18.0 s       0.0 s
[2016-04-15T00:51Z] INFO  17:51:14,276 ProgressMeter - Total runtime 18.73 secs, 0.31 min, 0.01 hours
[2016-04-15T00:51Z] INFO  17:51:14,277 MicroScheduler - 15105 reads were filtered out during the traversal out of approximately 184781 total reads (8.17%)
[2016-04-15T00:51Z] INFO  17:51:14,277 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:51Z] INFO  17:51:14,277 MicroScheduler -   -> 257 reads (0.14% of total) failing BadMateFilter
[2016-04-15T00:51Z] INFO  17:51:14,277 MicroScheduler -   -> 14742 reads (7.98% of total) failing DuplicateReadFilter
[2016-04-15T00:51Z] INFO  17:51:14,278 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:51Z] INFO  17:51:14,278 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:51Z] INFO  17:51:14,278 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:51Z] INFO  17:51:14,278 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:51Z] INFO  17:51:14,279 MicroScheduler -   -> 106 reads (0.06% of total) failing UnmappedReadFilter
[2016-04-15T00:51Z] GATK: UnifiedGenotyper
[2016-04-15T00:51Z] INFO  17:51:14,605 IntervalUtils - Processing 455246 bp from intervals
[2016-04-15T00:51Z] WARN  17:51:14,611 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:51Z] INFO  17:51:14,711 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:51Z] INFO  17:51:14,851 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:51Z] INFO  17:51:14,852 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:51Z] INFO  17:51:14,853 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:51Z] INFO  17:51:14,854 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:51Z] INFO  17:51:14,870 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:51Z] INFO  17:51:14,873 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:51Z] INFO  17:51:14,874 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:51Z] INFO  17:51:14,874 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:51Z] INFO  17:51:14,879 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/10/R14-18105_kapa-NGv3-PE100-NGv3-sort-10_0_15559243-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/10/R14-18105_kapa-NGv3-PE100-NGv3-10_0_15559243-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/10/tx/tmp4HTLUa/R14-18105_kapa-NGv3-PE100-NGv3-10_0_15559243.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:51Z] INFO  17:51:14,894 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:51Z] INFO  17:51:14,895 HelpFormatter - Date/Time: 2016/04/14 17:51:14
[2016-04-15T00:51Z] INFO  17:51:14,896 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:51Z] INFO  17:51:14,896 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:51Z] INFO  17:51:14,934 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:51Z] INFO  17:51:14,934 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:51Z] INFO  17:51:15,157 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:51Z] INFO  17:51:15,200 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:51Z] INFO  17:51:15,203 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:51Z] INFO  17:51:15,203 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:51Z] INFO  17:51:15,204 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:51Z] INFO  17:51:15,208 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/10/R14-18105_kapa-NGv3-PE100-NGv3-sort-10_15561288_31134502-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/10/R14-18105_kapa-NGv3-PE100-NGv3-10_15561288_31134502-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/10/tx/tmpIOriQH/R14-18105_kapa-NGv3-PE100-NGv3-10_15561288_31134502.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:51Z] INFO  17:51:15,238 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:51Z] INFO  17:51:15,246 HelpFormatter - Date/Time: 2016/04/14 17:51:15
[2016-04-15T00:51Z] INFO  17:51:15,247 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:51Z] INFO  17:51:15,248 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:51Z] INFO  17:51:15,441 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:51Z] INFO  17:51:15,464 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:51Z] INFO  17:51:15,473 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:51Z] INFO  17:51:15,580 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.11
[2016-04-15T00:51Z] INFO  17:51:15,639 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:51Z] INFO  17:51:15,636 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:51Z] INFO  17:51:15,660 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:51Z] INFO  17:51:15,755 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.09
[2016-04-15T00:51Z] GATK: UnifiedGenotyper
[2016-04-15T00:51Z] INFO  17:51:16,078 IntervalUtils - Processing 145147 bp from intervals
[2016-04-15T00:51Z] WARN  17:51:16,082 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:51Z] INFO  17:51:16,193 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:51Z] INFO  17:51:16,240 IntervalUtils - Processing 156629 bp from intervals
[2016-04-15T00:51Z] WARN  17:51:16,246 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:51Z] INFO  17:51:16,309 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:51Z] INFO  17:51:16,322 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:51Z] INFO  17:51:16,337 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:51Z] INFO  17:51:16,338 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:51Z] INFO  17:51:16,339 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:51Z] INFO  17:51:16,399 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:51Z] INFO  17:51:16,400 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:51Z] INFO  17:51:16,401 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:51Z] INFO  17:51:16,401 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:51Z] INFO  17:51:16,407 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:51Z] INFO  17:51:16,408 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:51Z] INFO  17:51:16,447 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:51Z] INFO  17:51:16,448 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:51Z] INFO  17:51:16,587 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:51Z] INFO  17:51:16,591 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:51Z] INFO  17:51:16,591 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:51Z] INFO  17:51:16,592 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:51Z] INFO  17:51:16,596 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/10/R14-18105_kapa-NGv3-PE100-NGv3-sort-10_31137459_46960129-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/10/R14-18105_kapa-NGv3-PE100-NGv3-10_31137459_46960129-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/10/tx/tmp9giApo/R14-18105_kapa-NGv3-PE100-NGv3-10_31137459_46960129.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:51Z] INFO  17:51:16,629 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:51Z] INFO  17:51:16,630 HelpFormatter - Date/Time: 2016/04/14 17:51:16
[2016-04-15T00:51Z] INFO  17:51:16,631 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:51Z] INFO  17:51:16,631 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:51Z] INFO  17:51:16,851 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:51Z] INFO  17:51:17,132 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:51Z] INFO  17:51:17,152 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:51Z] INFO  17:51:17,181 ProgressMeter -            done    316474.0    16.0 s      52.0 s       99.9%    16.0 s       0.0 s
[2016-04-15T00:51Z] INFO  17:51:17,182 ProgressMeter - Total runtime 16.72 secs, 0.28 min, 0.00 hours
[2016-04-15T00:51Z] INFO  17:51:17,182 MicroScheduler - 13185 reads were filtered out during the traversal out of approximately 159932 total reads (8.24%)
[2016-04-15T00:51Z] INFO  17:51:17,183 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:51Z] INFO  17:51:17,183 MicroScheduler -   -> 259 reads (0.16% of total) failing BadMateFilter
[2016-04-15T00:51Z] INFO  17:51:17,183 MicroScheduler -   -> 12837 reads (8.03% of total) failing DuplicateReadFilter
[2016-04-15T00:51Z] INFO  17:51:17,183 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:51Z] INFO  17:51:17,184 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:51Z] INFO  17:51:17,184 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:51Z] INFO  17:51:17,184 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:51Z] INFO  17:51:17,184 MicroScheduler -   -> 89 reads (0.06% of total) failing UnmappedReadFilter
[2016-04-15T00:51Z] INFO  17:51:17,240 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-15T00:51Z] INFO  17:51:17,272 ProgressMeter -            done    186579.0    13.0 s      71.0 s       99.9%    13.0 s       0.0 s
[2016-04-15T00:51Z] INFO  17:51:17,273 ProgressMeter - Total runtime 13.27 secs, 0.22 min, 0.00 hours
[2016-04-15T00:51Z] INFO  17:51:17,274 MicroScheduler - 8803 reads were filtered out during the traversal out of approximately 111692 total reads (7.88%)
[2016-04-15T00:51Z] INFO  17:51:17,274 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:51Z] INFO  17:51:17,275 MicroScheduler -   -> 186 reads (0.17% of total) failing BadMateFilter
[2016-04-15T00:51Z] INFO  17:51:17,276 MicroScheduler -   -> 8550 reads (7.65% of total) failing DuplicateReadFilter
[2016-04-15T00:51Z] INFO  17:51:17,276 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:51Z] INFO  17:51:17,277 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:51Z] INFO  17:51:17,277 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:51Z] INFO  17:51:17,278 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:51Z] INFO  17:51:17,279 MicroScheduler -   -> 67 reads (0.06% of total) failing UnmappedReadFilter
[2016-04-15T00:51Z] INFO  17:51:17,597 IntervalUtils - Processing 103621 bp from intervals
[2016-04-15T00:51Z] WARN  17:51:17,602 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:51Z] INFO  17:51:17,692 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:51Z] INFO  17:51:17,744 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:51Z] INFO  17:51:17,747 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:51Z] INFO  17:51:17,748 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:51Z] INFO  17:51:17,748 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:51Z] INFO  17:51:17,753 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/10/R14-18105_kapa-NGv3-PE100-NGv3-sort-10_46960410_62493077-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/10/R14-18105_kapa-NGv3-PE100-NGv3-10_46960410_62493077-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/10/tx/tmpdEK64a/R14-18105_kapa-NGv3-PE100-NGv3-10_46960410_62493077.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:51Z] INFO  17:51:17,761 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:51Z] INFO  17:51:17,770 HelpFormatter - Date/Time: 2016/04/14 17:51:17
[2016-04-15T00:51Z] INFO  17:51:17,770 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:51Z] INFO  17:51:17,771 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:51Z] INFO  17:51:17,779 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:51Z] INFO  17:51:17,791 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:51Z] INFO  17:51:17,792 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:51Z] INFO  17:51:17,793 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:51Z] INFO  17:51:17,838 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:51Z] INFO  17:51:17,839 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:51Z] INFO  17:51:17,924 ProgressMeter -            done    771215.0    27.0 s      35.0 s      100.0%    27.0 s       0.0 s
[2016-04-15T00:51Z] INFO  17:51:17,925 ProgressMeter - Total runtime 27.62 secs, 0.46 min, 0.01 hours
[2016-04-15T00:51Z] INFO  17:51:17,925 MicroScheduler - 26178 reads were filtered out during the traversal out of approximately 309687 total reads (8.45%)
[2016-04-15T00:51Z] INFO  17:51:17,925 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:51Z] INFO  17:51:17,926 MicroScheduler -   -> 472 reads (0.15% of total) failing BadMateFilter
[2016-04-15T00:51Z] INFO  17:51:17,926 MicroScheduler -   -> 25519 reads (8.24% of total) failing DuplicateReadFilter
[2016-04-15T00:51Z] INFO  17:51:17,926 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:51Z] INFO  17:51:17,926 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:51Z] INFO  17:51:17,926 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:51Z] INFO  17:51:17,927 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:51Z] INFO  17:51:17,927 MicroScheduler -   -> 187 reads (0.06% of total) failing UnmappedReadFilter
[2016-04-15T00:51Z] INFO  17:51:17,993 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:51Z] INFO  17:51:18,268 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:51Z] INFO  17:51:18,277 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:51Z] INFO  17:51:18,374 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.10
[2016-04-15T00:51Z] INFO  17:51:18,852 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:51Z] INFO  17:51:18,852 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:51Z] INFO  17:51:18,880 IntervalUtils - Processing 143638 bp from intervals
[2016-04-15T00:51Z] WARN  17:51:18,901 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:51Z] INFO  17:51:18,980 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:51Z] INFO  17:51:18,984 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:51Z] INFO  17:51:18,985 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:51Z] INFO  17:51:18,986 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:51Z] INFO  17:51:18,991 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/10/R14-18105_kapa-NGv3-PE100-NGv3-sort-10_62539923_78084243-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/10/R14-18105_kapa-NGv3-PE100-NGv3-10_62539923_78084243-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/10/tx/tmpuSVLxW/R14-18105_kapa-NGv3-PE100-NGv3-10_62539923_78084243.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:51Z] INFO  17:51:19,024 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:51Z] INFO  17:51:19,024 HelpFormatter - Date/Time: 2016/04/14 17:51:18
[2016-04-15T00:51Z] INFO  17:51:19,024 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:51Z] INFO  17:51:19,025 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:51Z] INFO  17:51:19,065 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:51Z] GATK: UnifiedGenotyper
[2016-04-15T00:51Z] INFO  17:51:19,208 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:51Z] INFO  17:51:19,209 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:51Z] INFO  17:51:19,210 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:51Z] INFO  17:51:19,211 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:51Z] GATK: UnifiedGenotyper
[2016-04-15T00:51Z] INFO  17:51:19,286 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:51Z] INFO  17:51:19,316 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:51Z] INFO  17:51:19,317 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:51Z] INFO  17:51:19,445 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:51Z] INFO  17:51:19,588 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:51Z] INFO  17:51:19,599 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:51Z] INFO  17:51:19,722 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.12
[2016-04-15T00:51Z] GATK: UnifiedGenotyper
[2016-04-15T00:51Z] INFO  17:51:20,257 IntervalUtils - Processing 230109 bp from intervals
[2016-04-15T00:51Z] WARN  17:51:20,263 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:51Z] INFO  17:51:20,388 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:51Z] INFO  17:51:20,521 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:51Z] INFO  17:51:20,522 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:51Z] INFO  17:51:20,523 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:51Z] INFO  17:51:20,524 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:51Z] INFO  17:51:20,541 ProgressMeter -            done   1463815.0    42.0 s      29.0 s      100.0%    42.0 s       0.0 s
[2016-04-15T00:51Z] INFO  17:51:20,542 ProgressMeter - Total runtime 42.62 secs, 0.71 min, 0.01 hours
[2016-04-15T00:51Z] INFO  17:51:20,542 MicroScheduler - 51075 reads were filtered out during the traversal out of approximately 638501 total reads (8.00%)
[2016-04-15T00:51Z] INFO  17:51:20,543 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:51Z] INFO  17:51:20,543 MicroScheduler -   -> 917 reads (0.14% of total) failing BadMateFilter
[2016-04-15T00:51Z] INFO  17:51:20,543 MicroScheduler -   -> 49716 reads (7.79% of total) failing DuplicateReadFilter
[2016-04-15T00:51Z] INFO  17:51:20,543 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:51Z] INFO  17:51:20,544 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:51Z] INFO  17:51:20,544 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:51Z] INFO  17:51:20,544 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:51Z] INFO  17:51:20,544 MicroScheduler -   -> 442 reads (0.07% of total) failing UnmappedReadFilter
[2016-04-15T00:51Z] INFO  17:51:20,576 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:51Z] INFO  17:51:20,577 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:51Z] INFO  17:51:22,129 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:51Z] GATK: UnifiedGenotyper
[2016-04-15T00:51Z] INFO  17:51:22,518 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:51Z] INFO  17:51:22,521 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:51Z] INFO  17:51:22,521 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:51Z] INFO  17:51:22,522 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:51Z] INFO  17:51:22,526 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/10/R14-18105_kapa-NGv3-PE100-NGv3-sort-10_93851586_111625070-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/10/R14-18105_kapa-NGv3-PE100-NGv3-10_93851586_111625070-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/10/tx/tmpoqtkRp/R14-18105_kapa-NGv3-PE100-NGv3-10_93851586_111625070.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:51Z] INFO  17:51:22,554 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:51Z] INFO  17:51:22,565 HelpFormatter - Date/Time: 2016/04/14 17:51:22
[2016-04-15T00:51Z] INFO  17:51:22,566 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:51Z] INFO  17:51:22,566 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:51Z] INFO  17:51:22,795 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:51Z] INFO  17:51:22,818 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:51Z] INFO  17:51:22,821 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:51Z] INFO  17:51:22,822 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:51Z] INFO  17:51:22,822 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:51Z] INFO  17:51:22,827 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/10/R14-18105_kapa-NGv3-PE100-NGv3-sort-10_78316966_93841258-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/10/R14-18105_kapa-NGv3-PE100-NGv3-10_78316966_93841258-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/10/tx/tmpFYNCYl/R14-18105_kapa-NGv3-PE100-NGv3-10_78316966_93841258.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:51Z] INFO  17:51:22,842 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:51Z] INFO  17:51:22,843 HelpFormatter - Date/Time: 2016/04/14 17:51:22
[2016-04-15T00:51Z] INFO  17:51:22,843 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:51Z] INFO  17:51:22,841 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:51Z] INFO  17:51:22,844 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:51Z] INFO  17:51:22,844 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:51Z] INFO  17:51:22,847 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:51Z] INFO  17:51:22,854 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:51Z] INFO  17:51:22,864 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/10/R14-18105_kapa-NGv3-PE100-NGv3-sort-10_111628371_127265443-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/10/R14-18105_kapa-NGv3-PE100-NGv3-10_111628371_127265443-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/10/tx/tmpIsMCSe/R14-18105_kapa-NGv3-PE100-NGv3-10_111628371_127265443.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:51Z] INFO  17:51:22,883 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:51Z] INFO  17:51:22,884 HelpFormatter - Date/Time: 2016/04/14 17:51:22
[2016-04-15T00:51Z] INFO  17:51:22,884 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:51Z] INFO  17:51:22,885 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:51Z] INFO  17:51:23,034 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:51Z] INFO  17:51:23,056 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:51Z] INFO  17:51:23,062 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:51Z] INFO  17:51:23,098 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:51Z] INFO  17:51:23,174 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.12
[2016-04-15T00:51Z] INFO  17:51:23,280 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:51Z] INFO  17:51:23,310 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:51Z] INFO  17:51:23,317 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:51Z] INFO  17:51:23,337 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:51Z] INFO  17:51:23,402 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.09
[2016-04-15T00:51Z] INFO  17:51:23,413 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-15T00:51Z] INFO  17:51:23,602 IntervalUtils - Processing 335852 bp from intervals
[2016-04-15T00:51Z] WARN  17:51:23,615 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:51Z] INFO  17:51:23,748 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:51Z] INFO  17:51:23,823 IntervalUtils - Processing 148808 bp from intervals
[2016-04-15T00:51Z] WARN  17:51:23,829 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:51Z] INFO  17:51:23,942 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:51Z] INFO  17:51:23,943 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:51Z] INFO  17:51:23,944 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:51Z] INFO  17:51:23,945 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:51Z] INFO  17:51:23,947 IntervalUtils - Processing 210787 bp from intervals
[2016-04-15T00:51Z] WARN  17:51:23,952 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:51Z] INFO  17:51:23,986 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:51Z] INFO  17:51:23,992 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:51Z] INFO  17:51:23,993 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:51Z] INFO  17:51:24,058 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:51Z] INFO  17:51:24,059 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:51Z] INFO  17:51:24,060 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:51Z] INFO  17:51:24,060 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:51Z] INFO  17:51:24,095 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:51Z] INFO  17:51:24,110 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:51Z] INFO  17:51:24,111 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:51Z] INFO  17:51:24,214 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:51Z] INFO  17:51:24,214 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:51Z] INFO  17:51:24,215 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:51Z] INFO  17:51:24,215 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:51Z] INFO  17:51:24,297 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:51Z] INFO  17:51:24,298 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:51Z] INFO  17:51:25,113 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:51Z] INFO  17:51:25,117 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:51Z] INFO  17:51:25,117 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:51Z] INFO  17:51:25,118 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:51Z] INFO  17:51:25,123 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/10/R14-18105_kapa-NGv3-PE100-NGv3-sort-10_127328721_135534747-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/10/R14-18105_kapa-NGv3-PE100-NGv3-10_127328721_135534747-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/10/tx/tmpL0Cll6/R14-18105_kapa-NGv3-PE100-NGv3-10_127328721_135534747.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:51Z] INFO  17:51:25,135 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:51Z] INFO  17:51:25,136 HelpFormatter - Date/Time: 2016/04/14 17:51:25
[2016-04-15T00:51Z] INFO  17:51:25,136 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:51Z] INFO  17:51:25,137 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:51Z] INFO  17:51:25,305 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:51Z] INFO  17:51:25,547 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:51Z] INFO  17:51:25,557 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:51Z] INFO  17:51:25,638 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-15T00:51Z] INFO  17:51:25,859 ProgressMeter -            done   1313389.0    25.0 s      19.0 s      100.0%    25.0 s       0.0 s
[2016-04-15T00:51Z] INFO  17:51:25,861 ProgressMeter - Total runtime 25.52 secs, 0.43 min, 0.01 hours
[2016-04-15T00:51Z] INFO  17:51:25,865 MicroScheduler - 30058 reads were filtered out during the traversal out of approximately 355025 total reads (8.47%)
[2016-04-15T00:51Z] INFO  17:51:25,866 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:51Z] INFO  17:51:25,866 MicroScheduler -   -> 550 reads (0.15% of total) failing BadMateFilter
[2016-04-15T00:51Z] INFO  17:51:25,867 MicroScheduler -   -> 29174 reads (8.22% of total) failing DuplicateReadFilter
[2016-04-15T00:51Z] INFO  17:51:25,867 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:51Z] INFO  17:51:25,867 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:51Z] INFO  17:51:25,867 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:51Z] INFO  17:51:25,868 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:51Z] INFO  17:51:25,872 MicroScheduler -   -> 334 reads (0.09% of total) failing UnmappedReadFilter
[2016-04-15T00:51Z] INFO  17:51:26,084 IntervalUtils - Processing 102137 bp from intervals
[2016-04-15T00:51Z] WARN  17:51:26,095 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:51Z] INFO  17:51:26,211 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:51Z] INFO  17:51:26,342 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:51Z] INFO  17:51:26,342 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:51Z] INFO  17:51:26,343 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:51Z] INFO  17:51:26,343 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:51Z] INFO  17:51:26,388 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:51Z] INFO  17:51:26,389 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:51Z] INFO  17:51:27,268 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:51Z] GATK: UnifiedGenotyper
[2016-04-15T00:51Z] INFO  17:51:27,657 ProgressMeter -            done    294057.0    16.0 s      55.0 s      100.0%    16.0 s       0.0 s
[2016-04-15T00:51Z] INFO  17:51:27,657 ProgressMeter - Total runtime 16.46 secs, 0.27 min, 0.00 hours
[2016-04-15T00:51Z] INFO  17:51:27,657 MicroScheduler - 13279 reads were filtered out during the traversal out of approximately 181240 total reads (7.33%)
[2016-04-15T00:51Z] INFO  17:51:27,658 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:51Z] INFO  17:51:27,658 MicroScheduler -   -> 270 reads (0.15% of total) failing BadMateFilter
[2016-04-15T00:51Z] INFO  17:51:27,658 MicroScheduler -   -> 12892 reads (7.11% of total) failing DuplicateReadFilter
[2016-04-15T00:51Z] INFO  17:51:27,658 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:51Z] INFO  17:51:27,659 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:51Z] INFO  17:51:27,659 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:51Z] INFO  17:51:27,659 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:51Z] INFO  17:51:27,659 MicroScheduler -   -> 117 reads (0.06% of total) failing UnmappedReadFilter
[2016-04-15T00:51Z] INFO  17:51:29,059 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:51Z] GATK: UnifiedGenotyper
[2016-04-15T00:51Z] INFO  17:51:30,305 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:51Z] INFO  17:51:30,308 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:51Z] INFO  17:51:30,308 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:51Z] INFO  17:51:30,309 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:51Z] INFO  17:51:30,313 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/11/R14-18105_kapa-NGv3-PE100-NGv3-sort-11_0_15994658-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/11/R14-18105_kapa-NGv3-PE100-NGv3-11_0_15994658-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/11/tx/tmpAufpPQ/R14-18105_kapa-NGv3-PE100-NGv3-11_0_15994658.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:51Z] INFO  17:51:30,335 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:51Z] INFO  17:51:30,336 HelpFormatter - Date/Time: 2016/04/14 17:51:30
[2016-04-15T00:51Z] INFO  17:51:30,336 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:51Z] INFO  17:51:30,337 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:51Z] INFO  17:51:30,504 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:51Z] INFO  17:51:30,749 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:51Z] INFO  17:51:30,760 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:51Z] INFO  17:51:30,843 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-15T00:51Z] INFO  17:51:31,328 IntervalUtils - Processing 438345 bp from intervals
[2016-04-15T00:51Z] WARN  17:51:31,334 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:51Z] INFO  17:51:31,406 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:51Z] INFO  17:51:31,515 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:51Z] INFO  17:51:31,515 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:51Z] INFO  17:51:31,516 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:51Z] INFO  17:51:31,516 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:51Z] INFO  17:51:31,564 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:51Z] INFO  17:51:31,565 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:51Z] INFO  17:51:32,167 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:51Z] INFO  17:51:32,170 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:51Z] INFO  17:51:32,171 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:51Z] INFO  17:51:32,171 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:51Z] INFO  17:51:32,176 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/11/R14-18105_kapa-NGv3-PE100-NGv3-sort-11_16007749_31531554-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/11/R14-18105_kapa-NGv3-PE100-NGv3-11_16007749_31531554-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/11/tx/tmpM6sNE2/R14-18105_kapa-NGv3-PE100-NGv3-11_16007749_31531554.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:51Z] INFO  17:51:32,186 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:51Z] INFO  17:51:32,197 HelpFormatter - Date/Time: 2016/04/14 17:51:32
[2016-04-15T00:51Z] INFO  17:51:32,198 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:51Z] INFO  17:51:32,199 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:51Z] INFO  17:51:32,355 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:51Z] INFO  17:51:32,431 ProgressMeter -            done    272797.0    14.0 s      53.0 s       99.9%    14.0 s       0.0 s
[2016-04-15T00:51Z] INFO  17:51:32,432 ProgressMeter - Total runtime 14.64 secs, 0.24 min, 0.00 hours
[2016-04-15T00:51Z] INFO  17:51:32,432 MicroScheduler - 11379 reads were filtered out during the traversal out of approximately 146170 total reads (7.78%)
[2016-04-15T00:51Z] INFO  17:51:32,432 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:51Z] INFO  17:51:32,433 MicroScheduler -   -> 190 reads (0.13% of total) failing BadMateFilter
[2016-04-15T00:51Z] INFO  17:51:32,433 MicroScheduler -   -> 11098 reads (7.59% of total) failing DuplicateReadFilter
[2016-04-15T00:51Z] INFO  17:51:32,433 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:51Z] INFO  17:51:32,433 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:51Z] INFO  17:51:32,434 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:51Z] INFO  17:51:32,434 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:51Z] INFO  17:51:32,434 MicroScheduler -   -> 91 reads (0.06% of total) failing UnmappedReadFilter
[2016-04-15T00:51Z] INFO  17:51:32,577 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:51Z] INFO  17:51:32,592 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:51Z] INFO  17:51:32,654 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-15T00:51Z] INFO  17:51:33,149 IntervalUtils - Processing 144906 bp from intervals
[2016-04-15T00:51Z] WARN  17:51:33,166 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:51Z] INFO  17:51:33,261 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:51Z] INFO  17:51:33,327 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:51Z] INFO  17:51:33,329 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:51Z] INFO  17:51:33,330 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:51Z] INFO  17:51:33,330 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:51Z] INFO  17:51:33,382 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:51Z] INFO  17:51:33,383 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:51Z] INFO  17:51:34,033 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:51Z] GATK: UnifiedGenotyper
[2016-04-15T00:51Z] INFO  17:51:35,493 ProgressMeter -            done    421173.0    19.0 s      45.0 s      100.0%    19.0 s       0.0 s
[2016-04-15T00:51Z] INFO  17:51:35,494 ProgressMeter - Total runtime 19.09 secs, 0.32 min, 0.01 hours
[2016-04-15T00:51Z] INFO  17:51:35,494 MicroScheduler - 14686 reads were filtered out during the traversal out of approximately 177342 total reads (8.28%)
[2016-04-15T00:51Z] INFO  17:51:35,495 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:51Z] INFO  17:51:35,495 MicroScheduler -   -> 240 reads (0.14% of total) failing BadMateFilter
[2016-04-15T00:51Z] INFO  17:51:35,495 MicroScheduler -   -> 14329 reads (8.08% of total) failing DuplicateReadFilter
[2016-04-15T00:51Z] INFO  17:51:35,496 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:51Z] INFO  17:51:35,496 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:51Z] INFO  17:51:35,496 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:51Z] INFO  17:51:35,497 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:51Z] INFO  17:51:35,497 MicroScheduler -   -> 117 reads (0.07% of total) failing UnmappedReadFilter
[2016-04-15T00:51Z] INFO  17:51:35,662 ProgressMeter -            done    477875.0    24.0 s      50.0 s      100.0%    24.0 s       0.0 s
[2016-04-15T00:51Z] INFO  17:51:35,663 ProgressMeter - Total runtime 24.19 secs, 0.40 min, 0.01 hours
[2016-04-15T00:51Z] INFO  17:51:35,663 MicroScheduler - 22205 reads were filtered out during the traversal out of approximately 267716 total reads (8.29%)
[2016-04-15T00:51Z] INFO  17:51:35,663 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:51Z] INFO  17:51:35,664 MicroScheduler -   -> 388 reads (0.14% of total) failing BadMateFilter
[2016-04-15T00:51Z] INFO  17:51:35,664 MicroScheduler -   -> 21594 reads (8.07% of total) failing DuplicateReadFilter
[2016-04-15T00:51Z] INFO  17:51:35,664 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:51Z] INFO  17:51:35,664 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:51Z] INFO  17:51:35,665 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:51Z] INFO  17:51:35,665 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:51Z] INFO  17:51:35,665 MicroScheduler -   -> 223 reads (0.08% of total) failing UnmappedReadFilter
[2016-04-15T00:51Z] INFO  17:51:36,633 ProgressMeter -            done    465734.0    20.0 s      43.0 s       99.9%    20.0 s       0.0 s
[2016-04-15T00:51Z] INFO  17:51:36,634 ProgressMeter - Total runtime 20.30 secs, 0.34 min, 0.01 hours
[2016-04-15T00:51Z] INFO  17:51:36,634 MicroScheduler - 16284 reads were filtered out during the traversal out of approximately 197351 total reads (8.25%)
[2016-04-15T00:51Z] INFO  17:51:36,634 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:51Z] INFO  17:51:36,635 MicroScheduler -   -> 292 reads (0.15% of total) failing BadMateFilter
[2016-04-15T00:51Z] INFO  17:51:36,635 MicroScheduler -   -> 15874 reads (8.04% of total) failing DuplicateReadFilter
[2016-04-15T00:51Z] INFO  17:51:36,635 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:51Z] INFO  17:51:36,635 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:51Z] INFO  17:51:36,636 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:51Z] INFO  17:51:36,636 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:51Z] INFO  17:51:36,636 MicroScheduler -   -> 118 reads (0.06% of total) failing UnmappedReadFilter
[2016-04-15T00:51Z] INFO  17:51:36,749 ProgressMeter -            done    539922.0    22.0 s      42.0 s      100.0%    22.0 s       0.0 s
[2016-04-15T00:51Z] INFO  17:51:36,749 ProgressMeter - Total runtime 23.00 secs, 0.38 min, 0.01 hours
[2016-04-15T00:51Z] INFO  17:51:36,750 MicroScheduler - 21940 reads were filtered out during the traversal out of approximately 261786 total reads (8.38%)
[2016-04-15T00:51Z] INFO  17:51:36,750 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:51Z] INFO  17:51:36,750 MicroScheduler -   -> 382 reads (0.15% of total) failing BadMateFilter
[2016-04-15T00:51Z] INFO  17:51:36,751 MicroScheduler -   -> 21361 reads (8.16% of total) failing DuplicateReadFilter
[2016-04-15T00:51Z] INFO  17:51:36,751 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:51Z] INFO  17:51:36,751 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:51Z] INFO  17:51:36,752 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:51Z] INFO  17:51:36,752 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:51Z] INFO  17:51:36,752 MicroScheduler -   -> 197 reads (0.08% of total) failing UnmappedReadFilter
[2016-04-15T00:51Z] INFO  17:51:36,882 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:51Z] INFO  17:51:36,989 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:51Z] GATK: UnifiedGenotyper
[2016-04-15T00:51Z] INFO  17:51:37,219 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:51Z] INFO  17:51:37,222 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:51Z] INFO  17:51:37,223 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:51Z] INFO  17:51:37,223 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:51Z] INFO  17:51:37,228 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/11/R14-18105_kapa-NGv3-PE100-NGv3-sort-11_31541602_47074069-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/11/R14-18105_kapa-NGv3-PE100-NGv3-11_31541602_47074069-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/11/tx/tmptavTdv/R14-18105_kapa-NGv3-PE100-NGv3-11_31541602_47074069.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:51Z] INFO  17:51:37,242 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:51Z] INFO  17:51:37,243 HelpFormatter - Date/Time: 2016/04/14 17:51:37
[2016-04-15T00:51Z] INFO  17:51:37,243 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:51Z] INFO  17:51:37,244 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:51Z] GATK: UnifiedGenotyper
[2016-04-15T00:51Z] INFO  17:51:37,388 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:51Z] INFO  17:51:37,670 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:51Z] INFO  17:51:37,684 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:51Z] INFO  17:51:37,765 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-15T00:51Z] INFO  17:51:37,774 ProgressMeter -            done    946777.0    27.0 s      28.0 s      100.0%    27.0 s       0.0 s
[2016-04-15T00:51Z] INFO  17:51:37,774 ProgressMeter - Total runtime 27.40 secs, 0.46 min, 0.01 hours
[2016-04-15T00:51Z] INFO  17:51:37,775 MicroScheduler - 29123 reads were filtered out during the traversal out of approximately 407747 total reads (7.14%)
[2016-04-15T00:51Z] INFO  17:51:37,775 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:51Z] INFO  17:51:37,775 MicroScheduler -   -> 586 reads (0.14% of total) failing BadMateFilter
[2016-04-15T00:51Z] INFO  17:51:37,776 MicroScheduler -   -> 28255 reads (6.93% of total) failing DuplicateReadFilter
[2016-04-15T00:51Z] INFO  17:51:37,776 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:51Z] INFO  17:51:37,776 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:51Z] INFO  17:51:37,777 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:51Z] INFO  17:51:37,777 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:51Z] INFO  17:51:37,777 MicroScheduler -   -> 282 reads (0.07% of total) failing UnmappedReadFilter
[2016-04-15T00:51Z] INFO  17:51:37,979 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:51Z] INFO  17:51:38,136 IntervalUtils - Processing 150047 bp from intervals
[2016-04-15T00:51Z] WARN  17:51:38,143 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:51Z] INFO  17:51:38,222 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:51Z] GATK: UnifiedGenotyper
[2016-04-15T00:51Z] INFO  17:51:38,284 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:51Z] INFO  17:51:38,368 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:51Z] INFO  17:51:38,376 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:51Z] INFO  17:51:38,377 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:51Z] INFO  17:51:38,378 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:51Z] INFO  17:51:38,461 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:51Z] INFO  17:51:38,462 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:51Z] GATK: UnifiedGenotyper
[2016-04-15T00:51Z] INFO  17:51:39,528 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:51Z] INFO  17:51:39,530 ProgressMeter -            done    678904.0    25.0 s      37.0 s      100.0%    25.0 s       0.0 s
[2016-04-15T00:51Z] INFO  17:51:39,530 ProgressMeter - Total runtime 25.43 secs, 0.42 min, 0.01 hours
[2016-04-15T00:51Z] INFO  17:51:39,530 MicroScheduler - 26146 reads were filtered out during the traversal out of approximately 316143 total reads (8.27%)
[2016-04-15T00:51Z] INFO  17:51:39,531 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:51Z] INFO  17:51:39,531 MicroScheduler -   -> 446 reads (0.14% of total) failing BadMateFilter
[2016-04-15T00:51Z] INFO  17:51:39,531 MicroScheduler -   -> 25507 reads (8.07% of total) failing DuplicateReadFilter
[2016-04-15T00:51Z] INFO  17:51:39,531 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:51Z] INFO  17:51:39,532 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:51Z] INFO  17:51:39,532 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:51Z] INFO  17:51:39,532 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:51Z] INFO  17:51:39,532 MicroScheduler -   -> 193 reads (0.06% of total) failing UnmappedReadFilter
[2016-04-15T00:51Z] GATK: UnifiedGenotyper
[2016-04-15T00:51Z] INFO  17:51:40,281 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:51Z] INFO  17:51:40,284 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:51Z] INFO  17:51:40,284 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:51Z] INFO  17:51:40,284 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:51Z] INFO  17:51:40,288 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/11/R14-18105_kapa-NGv3-PE100-NGv3-sort-11_47158866_62678572-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/11/R14-18105_kapa-NGv3-PE100-NGv3-11_47158866_62678572-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/11/tx/tmpGVmpU3/R14-18105_kapa-NGv3-PE100-NGv3-11_47158866_62678572.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:51Z] INFO  17:51:40,317 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:51Z] INFO  17:51:40,317 HelpFormatter - Date/Time: 2016/04/14 17:51:40
[2016-04-15T00:51Z] INFO  17:51:40,317 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:51Z] INFO  17:51:40,318 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:51Z] INFO  17:51:40,339 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:51Z] INFO  17:51:40,342 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:51Z] INFO  17:51:40,343 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:51Z] INFO  17:51:40,344 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:51Z] INFO  17:51:40,348 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/11/R14-18105_kapa-NGv3-PE100-NGv3-sort-11_62744265_78270665-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/11/R14-18105_kapa-NGv3-PE100-NGv3-11_62744265_78270665-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/11/tx/tmpqcKGJ3/R14-18105_kapa-NGv3-PE100-NGv3-11_62744265_78270665.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:51Z] INFO  17:51:40,358 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:51Z] INFO  17:51:40,358 HelpFormatter - Date/Time: 2016/04/14 17:51:40
[2016-04-15T00:51Z] INFO  17:51:40,358 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:51Z] INFO  17:51:40,359 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:51Z] INFO  17:51:40,513 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:51Z] INFO  17:51:40,613 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:51Z] INFO  17:51:40,746 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:51Z] INFO  17:51:40,756 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:51Z] INFO  17:51:40,819 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-15T00:51Z] INFO  17:51:40,827 ProgressMeter -            done    405882.0    21.0 s      53.0 s      100.0%    21.0 s       0.0 s
[2016-04-15T00:51Z] INFO  17:51:40,828 ProgressMeter - Total runtime 21.62 secs, 0.36 min, 0.01 hours
[2016-04-15T00:51Z] INFO  17:51:40,829 MicroScheduler - 20925 reads were filtered out during the traversal out of approximately 274374 total reads (7.63%)
[2016-04-15T00:51Z] INFO  17:51:40,829 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:51Z] INFO  17:51:40,830 MicroScheduler -   -> 375 reads (0.14% of total) failing BadMateFilter
[2016-04-15T00:51Z] INFO  17:51:40,831 MicroScheduler -   -> 20351 reads (7.42% of total) failing DuplicateReadFilter
[2016-04-15T00:51Z] INFO  17:51:40,831 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:51Z] INFO  17:51:40,832 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:51Z] INFO  17:51:40,832 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:51Z] INFO  17:51:40,833 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:51Z] INFO  17:51:40,834 MicroScheduler -   -> 199 reads (0.07% of total) failing UnmappedReadFilter
[2016-04-15T00:51Z] INFO  17:51:40,892 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:51Z] INFO  17:51:40,915 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:51Z] INFO  17:51:41,003 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-15T00:51Z] INFO  17:51:41,056 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:51Z] INFO  17:51:41,059 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:51Z] INFO  17:51:41,059 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:51Z] INFO  17:51:41,060 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:51Z] INFO  17:51:41,066 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/11/R14-18105_kapa-NGv3-PE100-NGv3-sort-11_78277177_93796886-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/11/R14-18105_kapa-NGv3-PE100-NGv3-11_78277177_93796886-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/11/tx/tmpb6rqdq/R14-18105_kapa-NGv3-PE100-NGv3-11_78277177_93796886.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:51Z] INFO  17:51:41,080 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:51Z] INFO  17:51:41,085 HelpFormatter - Date/Time: 2016/04/14 17:51:41
[2016-04-15T00:51Z] INFO  17:51:41,085 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:51Z] INFO  17:51:41,086 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:51Z] INFO  17:51:41,199 IntervalUtils - Processing 330540 bp from intervals
[2016-04-15T00:51Z] INFO  17:51:41,201 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:51Z] WARN  17:51:41,204 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:51Z] INFO  17:51:41,268 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:51Z] INFO  17:51:41,271 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:51Z] INFO  17:51:41,272 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:51Z] INFO  17:51:41,272 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:51Z] INFO  17:51:41,277 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/11/R14-18105_kapa-NGv3-PE100-NGv3-sort-11_93797496_109964158-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/11/R14-18105_kapa-NGv3-PE100-NGv3-11_93797496_109964158-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/11/tx/tmpnvWKMU/R14-18105_kapa-NGv3-PE100-NGv3-11_93797496_109964158.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:51Z] INFO  17:51:41,285 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:51Z] INFO  17:51:41,295 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:51Z] INFO  17:51:41,297 HelpFormatter - Date/Time: 2016/04/14 17:51:41
[2016-04-15T00:51Z] INFO  17:51:41,305 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:51Z] INFO  17:51:41,306 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:51Z] INFO  17:51:41,292 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:51Z] INFO  17:51:41,363 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:51Z] INFO  17:51:41,364 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:51Z] INFO  17:51:41,364 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:51Z] INFO  17:51:41,365 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:51Z] INFO  17:51:41,409 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:51Z] INFO  17:51:41,410 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:51Z] INFO  17:51:41,459 ProgressMeter -            done    360383.0    15.0 s      41.0 s       99.9%    15.0 s       0.0 s
[2016-04-15T00:51Z] INFO  17:51:41,459 ProgressMeter - Total runtime 15.12 secs, 0.25 min, 0.00 hours
[2016-04-15T00:51Z] INFO  17:51:41,459 MicroScheduler - 12767 reads were filtered out during the traversal out of approximately 154821 total reads (8.25%)
[2016-04-15T00:51Z] INFO  17:51:41,460 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:51Z] INFO  17:51:41,460 MicroScheduler -   -> 222 reads (0.14% of total) failing BadMateFilter
[2016-04-15T00:51Z] INFO  17:51:41,460 MicroScheduler -   -> 12456 reads (8.05% of total) failing DuplicateReadFilter
[2016-04-15T00:51Z] INFO  17:51:41,460 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:51Z] INFO  17:51:41,461 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:51Z] INFO  17:51:41,461 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:51Z] INFO  17:51:41,461 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:51Z] INFO  17:51:41,461 MicroScheduler -   -> 89 reads (0.06% of total) failing UnmappedReadFilter
[2016-04-15T00:51Z] INFO  17:51:41,491 IntervalUtils - Processing 515206 bp from intervals
[2016-04-15T00:51Z] INFO  17:51:41,489 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:51Z] WARN  17:51:41,497 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:51Z] GATK: UnifiedGenotyper
[2016-04-15T00:51Z] INFO  17:51:41,565 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:51Z] INFO  17:51:41,574 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:51Z] INFO  17:51:41,607 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:51Z] INFO  17:51:41,682 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.11
[2016-04-15T00:51Z] INFO  17:51:41,739 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:51Z] INFO  17:51:41,750 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:51Z] INFO  17:51:41,797 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:51Z] INFO  17:51:41,797 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:51Z] INFO  17:51:41,798 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:51Z] INFO  17:51:41,798 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:51Z] INFO  17:51:41,853 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.10
[2016-04-15T00:51Z] INFO  17:51:41,895 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:51Z] INFO  17:51:41,895 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:51Z] INFO  17:51:42,132 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:51Z] INFO  17:51:42,141 IntervalUtils - Processing 119993 bp from intervals
[2016-04-15T00:51Z] WARN  17:51:42,151 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:51Z] INFO  17:51:42,279 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:51Z] INFO  17:51:42,347 IntervalUtils - Processing 148585 bp from intervals
[2016-04-15T00:51Z] WARN  17:51:42,360 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:51Z] INFO  17:51:42,391 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:51Z] INFO  17:51:42,392 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:51Z] INFO  17:51:42,393 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:51Z] INFO  17:51:42,405 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:51Z] GATK: UnifiedGenotyper
[2016-04-15T00:51Z] INFO  17:51:42,493 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:51Z] INFO  17:51:42,517 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:51Z] INFO  17:51:42,524 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:51Z] INFO  17:51:42,605 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:51Z] INFO  17:51:42,607 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:51Z] INFO  17:51:42,608 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:51Z] INFO  17:51:42,608 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:51Z] INFO  17:51:42,661 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:51Z] INFO  17:51:42,662 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:51Z] INFO  17:51:42,776 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:51Z] INFO  17:51:42,880 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:51Z] INFO  17:51:42,883 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:51Z] INFO  17:51:42,883 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:51Z] INFO  17:51:42,884 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:51Z] INFO  17:51:42,888 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/11/R14-18105_kapa-NGv3-PE100-NGv3-sort-11_110001730_125514538-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/11/R14-18105_kapa-NGv3-PE100-NGv3-11_110001730_125514538-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/11/tx/tmprT8HIv/R14-18105_kapa-NGv3-PE100-NGv3-11_110001730_125514538.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:51Z] INFO  17:51:42,900 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:51Z] INFO  17:51:42,901 HelpFormatter - Date/Time: 2016/04/14 17:51:42
[2016-04-15T00:51Z] INFO  17:51:42,912 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:51Z] INFO  17:51:42,913 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:51Z] INFO  17:51:43,123 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:51Z] GATK: UnifiedGenotyper
[2016-04-15T00:51Z] INFO  17:51:43,355 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:51Z] INFO  17:51:43,364 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:51Z] INFO  17:51:43,454 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.09
[2016-04-15T00:51Z] INFO  17:51:43,987 IntervalUtils - Processing 318135 bp from intervals
[2016-04-15T00:51Z] WARN  17:51:44,003 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:51Z] INFO  17:51:44,137 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:51Z] INFO  17:51:44,224 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:51Z] INFO  17:51:44,227 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:51Z] INFO  17:51:44,228 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:51Z] INFO  17:51:44,228 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:51Z] INFO  17:51:44,233 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/11/R14-18105_kapa-NGv3-PE100-NGv3-sort-11_125523640_135006516-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/11/R14-18105_kapa-NGv3-PE100-NGv3-11_125523640_135006516-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/11/tx/tmpL5dUxg/R14-18105_kapa-NGv3-PE100-NGv3-11_125523640_135006516.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:51Z] INFO  17:51:44,248 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:51Z] INFO  17:51:44,259 HelpFormatter - Date/Time: 2016/04/14 17:51:44
[2016-04-15T00:51Z] INFO  17:51:44,260 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:51Z] INFO  17:51:44,261 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:51Z] INFO  17:51:44,276 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:51Z] INFO  17:51:44,288 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:51Z] INFO  17:51:44,289 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:51Z] INFO  17:51:44,300 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:51Z] INFO  17:51:44,390 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:51Z] INFO  17:51:44,391 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:51Z] INFO  17:51:44,417 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:51Z] INFO  17:51:44,425 ProgressMeter -            done    459685.0    20.0 s      44.0 s       99.9%    20.0 s       0.0 s
[2016-04-15T00:51Z] INFO  17:51:44,425 ProgressMeter - Total runtime 20.37 secs, 0.34 min, 0.01 hours
[2016-04-15T00:51Z] INFO  17:51:44,426 MicroScheduler - 16689 reads were filtered out during the traversal out of approximately 203682 total reads (8.19%)
[2016-04-15T00:51Z] INFO  17:51:44,426 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:51Z] INFO  17:51:44,426 MicroScheduler -   -> 281 reads (0.14% of total) failing BadMateFilter
[2016-04-15T00:51Z] INFO  17:51:44,427 MicroScheduler -   -> 16275 reads (7.99% of total) failing DuplicateReadFilter
[2016-04-15T00:51Z] INFO  17:51:44,427 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:51Z] INFO  17:51:44,427 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:51Z] INFO  17:51:44,427 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:51Z] INFO  17:51:44,427 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:51Z] INFO  17:51:44,428 MicroScheduler -   -> 133 reads (0.07% of total) failing UnmappedReadFilter
[2016-04-15T00:51Z] INFO  17:51:44,566 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:51Z] INFO  17:51:44,576 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:51Z] INFO  17:51:44,655 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-15T00:51Z] INFO  17:51:44,876 ProgressMeter -     9:136325189   1263276.0    30.0 s      23.0 s       55.4%    54.0 s      24.0 s
[2016-04-15T00:51Z] INFO  17:51:45,071 IntervalUtils - Processing 106404 bp from intervals
[2016-04-15T00:51Z] WARN  17:51:45,083 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:51Z] INFO  17:51:45,201 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:51Z] INFO  17:51:45,295 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:51Z] INFO  17:51:45,296 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:51Z] INFO  17:51:45,297 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:51Z] INFO  17:51:45,297 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:51Z] INFO  17:51:45,363 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:51Z] INFO  17:51:45,365 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:51Z] INFO  17:51:45,722 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:51Z] INFO  17:51:45,724 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:51Z] INFO  17:51:45,724 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:51Z] INFO  17:51:45,725 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:51Z] INFO  17:51:45,729 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/12/R14-18105_kapa-NGv3-PE100-NGv3-sort-12_0_15637181-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/12/R14-18105_kapa-NGv3-PE100-NGv3-12_0_15637181-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/12/tx/tmpjp_gTq/R14-18105_kapa-NGv3-PE100-NGv3-12_0_15637181.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:51Z] INFO  17:51:45,751 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:51Z] INFO  17:51:45,762 HelpFormatter - Date/Time: 2016/04/14 17:51:45
[2016-04-15T00:51Z] INFO  17:51:45,763 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:51Z] INFO  17:51:45,764 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:51Z] INFO  17:51:45,964 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:51Z] INFO  17:51:46,015 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:51Z] INFO  17:51:46,201 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:51Z] INFO  17:51:46,222 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:51Z] INFO  17:51:46,263 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:51Z] INFO  17:51:46,266 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:51Z] INFO  17:51:46,266 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:51Z] INFO  17:51:46,267 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:51Z] INFO  17:51:46,272 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/12/R14-18105_kapa-NGv3-PE100-NGv3-sort-12_15650178_31231471-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/12/R14-18105_kapa-NGv3-PE100-NGv3-12_15650178_31231471-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/12/tx/tmp4hLDWq/R14-18105_kapa-NGv3-PE100-NGv3-12_15650178_31231471.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:51Z] GATK: UnifiedGenotyper
[2016-04-15T00:51Z] INFO  17:51:46,281 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:51Z] INFO  17:51:46,282 HelpFormatter - Date/Time: 2016/04/14 17:51:46
[2016-04-15T00:51Z] INFO  17:51:46,282 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:51Z] INFO  17:51:46,283 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:51Z] INFO  17:51:46,318 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.10
[2016-04-15T00:51Z] INFO  17:51:46,439 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:51Z] INFO  17:51:46,679 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:51Z] INFO  17:51:46,688 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:51Z] INFO  17:51:46,749 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-15T00:51Z] INFO  17:51:46,777 IntervalUtils - Processing 329920 bp from intervals
[2016-04-15T00:51Z] WARN  17:51:46,784 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:51Z] INFO  17:51:46,908 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:51Z] INFO  17:51:47,086 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:51Z] INFO  17:51:47,087 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:51Z] INFO  17:51:47,087 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:51Z] INFO  17:51:47,088 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:51Z] INFO  17:51:47,164 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:51Z] INFO  17:51:47,165 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:51Z] INFO  17:51:47,260 IntervalUtils - Processing 134686 bp from intervals
[2016-04-15T00:51Z] WARN  17:51:47,275 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:51Z] INFO  17:51:47,348 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:51Z] INFO  17:51:47,487 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:51Z] INFO  17:51:47,488 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:51Z] INFO  17:51:47,489 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:51Z] INFO  17:51:47,489 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:51Z] INFO  17:51:47,586 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:51Z] INFO  17:51:47,587 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:51Z] INFO  17:51:47,938 ProgressMeter -            done    818570.0    27.0 s      33.0 s      100.0%    27.0 s       0.0 s
[2016-04-15T00:51Z] INFO  17:51:47,939 ProgressMeter - Total runtime 27.42 secs, 0.46 min, 0.01 hours
[2016-04-15T00:51Z] INFO  17:51:47,940 MicroScheduler - 26527 reads were filtered out during the traversal out of approximately 322662 total reads (8.22%)
[2016-04-15T00:51Z] INFO  17:51:47,941 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:51Z] INFO  17:51:47,941 MicroScheduler -   -> 452 reads (0.14% of total) failing BadMateFilter
[2016-04-15T00:51Z] INFO  17:51:47,942 MicroScheduler -   -> 25887 reads (8.02% of total) failing DuplicateReadFilter
[2016-04-15T00:51Z] INFO  17:51:47,943 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:51Z] INFO  17:51:47,943 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:51Z] INFO  17:51:47,944 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:51Z] INFO  17:51:47,944 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:51Z] INFO  17:51:47,945 MicroScheduler -   -> 188 reads (0.06% of total) failing UnmappedReadFilter
[2016-04-15T00:51Z] INFO  17:51:48,592 ProgressMeter -            done    665309.0    24.0 s      36.0 s      100.0%    24.0 s       0.0 s
[2016-04-15T00:51Z] INFO  17:51:48,593 ProgressMeter - Total runtime 24.38 secs, 0.41 min, 0.01 hours
[2016-04-15T00:51Z] INFO  17:51:48,593 MicroScheduler - 22485 reads were filtered out during the traversal out of approximately 271496 total reads (8.28%)
[2016-04-15T00:51Z] INFO  17:51:48,593 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:51Z] INFO  17:51:48,594 MicroScheduler -   -> 394 reads (0.15% of total) failing BadMateFilter
[2016-04-15T00:51Z] INFO  17:51:48,594 MicroScheduler -   -> 21942 reads (8.08% of total) failing DuplicateReadFilter
[2016-04-15T00:51Z] INFO  17:51:48,594 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:51Z] INFO  17:51:48,594 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:51Z] INFO  17:51:48,595 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:51Z] INFO  17:51:48,595 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:51Z] INFO  17:51:48,595 MicroScheduler -   -> 149 reads (0.05% of total) failing UnmappedReadFilter
[2016-04-15T00:51Z] INFO  17:51:49,271 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:51Z] INFO  17:51:49,274 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:51Z] INFO  17:51:49,274 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:51Z] INFO  17:51:49,274 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:51Z] INFO  17:51:49,278 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/12/R14-18105_kapa-NGv3-PE100-NGv3-sort-12_31236746_46754992-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/12/R14-18105_kapa-NGv3-PE100-NGv3-12_31236746_46754992-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/12/tx/tmpiL299D/R14-18105_kapa-NGv3-PE100-NGv3-12_31236746_46754992.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:51Z] INFO  17:51:49,301 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:51Z] INFO  17:51:49,301 HelpFormatter - Date/Time: 2016/04/14 17:51:49
[2016-04-15T00:51Z] INFO  17:51:49,301 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:51Z] INFO  17:51:49,301 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:51Z] INFO  17:51:49,473 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:51Z] INFO  17:51:49,514 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:51Z] INFO  17:51:49,704 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:51Z] INFO  17:51:49,725 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:51Z] INFO  17:51:49,833 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.11
[2016-04-15T00:51Z] GATK: UnifiedGenotyper
[2016-04-15T00:51Z] INFO  17:51:50,103 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:51Z] INFO  17:51:50,296 IntervalUtils - Processing 136917 bp from intervals
[2016-04-15T00:51Z] WARN  17:51:50,301 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:51Z] INFO  17:51:50,382 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:51Z] GATK: UnifiedGenotyper
[2016-04-15T00:51Z] INFO  17:51:50,483 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:51Z] INFO  17:51:50,484 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:51Z] INFO  17:51:50,485 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:51Z] INFO  17:51:50,486 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:51Z] INFO  17:51:50,532 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:51Z] INFO  17:51:50,533 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:51Z] INFO  17:51:50,925 ProgressMeter -            done    449347.0    17.0 s      39.0 s      100.0%    17.0 s       0.0 s
[2016-04-15T00:51Z] INFO  17:51:50,925 ProgressMeter - Total runtime 17.60 secs, 0.29 min, 0.00 hours
[2016-04-15T00:51Z] INFO  17:51:50,925 MicroScheduler - 14894 reads were filtered out during the traversal out of approximately 180746 total reads (8.24%)
[2016-04-15T00:51Z] INFO  17:51:50,926 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:51Z] INFO  17:51:50,926 MicroScheduler -   -> 252 reads (0.14% of total) failing BadMateFilter
[2016-04-15T00:51Z] INFO  17:51:50,926 MicroScheduler -   -> 14528 reads (8.04% of total) failing DuplicateReadFilter
[2016-04-15T00:51Z] INFO  17:51:50,927 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:51Z] INFO  17:51:50,927 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:51Z] INFO  17:51:50,927 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:51Z] INFO  17:51:50,927 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:51Z] INFO  17:51:50,927 MicroScheduler -   -> 114 reads (0.06% of total) failing UnmappedReadFilter
[2016-04-15T00:51Z] INFO  17:51:52,410 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:51Z] GATK: UnifiedGenotyper
[2016-04-15T00:51Z] INFO  17:51:52,920 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:51Z] INFO  17:51:52,933 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:51Z] INFO  17:51:52,933 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:51Z] INFO  17:51:52,933 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:51Z] INFO  17:51:52,938 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/12/R14-18105_kapa-NGv3-PE100-NGv3-sort-12_46756066_62654284-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/12/R14-18105_kapa-NGv3-PE100-NGv3-12_46756066_62654284-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/12/tx/tmpHQU8Ug/R14-18105_kapa-NGv3-PE100-NGv3-12_46756066_62654284.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:51Z] INFO  17:51:52,957 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:51Z] INFO  17:51:52,957 HelpFormatter - Date/Time: 2016/04/14 17:51:52
[2016-04-15T00:51Z] INFO  17:51:52,958 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:51Z] INFO  17:51:52,958 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:51Z] INFO  17:51:53,127 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:51Z] INFO  17:51:53,353 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:51Z] INFO  17:51:53,361 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:51Z] INFO  17:51:53,422 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-15T00:51Z] INFO  17:51:53,436 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:51Z] INFO  17:51:53,439 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:51Z] INFO  17:51:53,440 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:51Z] INFO  17:51:53,440 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:51Z] INFO  17:51:53,445 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/12/R14-18105_kapa-NGv3-PE100-NGv3-sort-12_62687959_78225484-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/12/R14-18105_kapa-NGv3-PE100-NGv3-12_62687959_78225484-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/12/tx/tmpZG3gNM/R14-18105_kapa-NGv3-PE100-NGv3-12_62687959_78225484.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:51Z] INFO  17:51:53,461 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:51Z] INFO  17:51:53,462 HelpFormatter - Date/Time: 2016/04/14 17:51:53
[2016-04-15T00:51Z] INFO  17:51:53,463 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:51Z] INFO  17:51:53,463 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:51Z] INFO  17:51:53,621 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:51Z] INFO  17:51:53,877 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:51Z] INFO  17:51:53,886 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:51Z] INFO  17:51:53,945 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-15T00:51Z] INFO  17:51:53,963 ProgressMeter -    10:105207109   1176521.0    30.0 s      25.0 s       87.8%    34.0 s       4.0 s
[2016-04-15T00:51Z] INFO  17:51:54,004 IntervalUtils - Processing 504306 bp from intervals
[2016-04-15T00:51Z] WARN  17:51:54,009 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:51Z] INFO  17:51:54,114 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:51Z] INFO  17:51:54,314 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:51Z] INFO  17:51:54,316 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:51Z] INFO  17:51:54,317 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:51Z] INFO  17:51:54,318 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:51Z] INFO  17:51:54,359 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:51Z] INFO  17:51:54,360 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:51Z] INFO  17:51:54,424 IntervalUtils - Processing 146919 bp from intervals
[2016-04-15T00:51Z] WARN  17:51:54,429 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:51Z] INFO  17:51:54,511 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:51Z] INFO  17:51:54,602 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:51Z] INFO  17:51:54,602 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:51Z] INFO  17:51:54,603 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:51Z] INFO  17:51:54,603 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:51Z] INFO  17:51:54,659 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:51Z] INFO  17:51:54,660 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:51Z] INFO  17:51:55,700 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:51Z] INFO  17:51:55,704 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:51Z] INFO  17:51:55,704 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:51Z] INFO  17:51:55,705 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:51Z] INFO  17:51:55,709 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/12/R14-18105_kapa-NGv3-PE100-NGv3-sort-12_78334098_93863131-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/12/R14-18105_kapa-NGv3-PE100-NGv3-12_78334098_93863131-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/12/tx/tmpIcz0h0/R14-18105_kapa-NGv3-PE100-NGv3-12_78334098_93863131.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:51Z] INFO  17:51:55,719 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:51Z] INFO  17:51:55,719 HelpFormatter - Date/Time: 2016/04/14 17:51:55
[2016-04-15T00:51Z] INFO  17:51:55,719 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:51Z] INFO  17:51:55,719 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:51Z] INFO  17:51:55,916 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:51Z] INFO  17:51:56,032 ProgressMeter -            done    576314.0    17.0 s      30.0 s      100.0%    17.0 s       0.0 s
[2016-04-15T00:51Z] INFO  17:51:56,032 ProgressMeter - Total runtime 17.66 secs, 0.29 min, 0.00 hours
[2016-04-15T00:51Z] INFO  17:51:56,033 MicroScheduler - 17568 reads were filtered out during the traversal out of approximately 211260 total reads (8.32%)
[2016-04-15T00:51Z] INFO  17:51:56,033 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:51Z] INFO  17:51:56,033 MicroScheduler -   -> 302 reads (0.14% of total) failing BadMateFilter
[2016-04-15T00:51Z] INFO  17:51:56,034 MicroScheduler -   -> 17139 reads (8.11% of total) failing DuplicateReadFilter
[2016-04-15T00:51Z] INFO  17:51:56,034 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:51Z] INFO  17:51:56,034 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:51Z] INFO  17:51:56,034 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:51Z] INFO  17:51:56,035 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:51Z] INFO  17:51:56,035 MicroScheduler -   -> 127 reads (0.06% of total) failing UnmappedReadFilter
[2016-04-15T00:51Z] INFO  17:51:56,121 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:51Z] INFO  17:51:56,138 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:51Z] INFO  17:51:56,224 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.09
[2016-04-15T00:51Z] INFO  17:51:56,565 IntervalUtils - Processing 88957 bp from intervals
[2016-04-15T00:51Z] WARN  17:51:56,570 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:51Z] INFO  17:51:56,708 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:51Z] INFO  17:51:56,756 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:51Z] INFO  17:51:56,757 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:51Z] INFO  17:51:56,780 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:51Z] INFO  17:51:56,781 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:51Z] INFO  17:51:56,834 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:51Z] INFO  17:51:56,835 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:51Z] INFO  17:51:57,348 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:51Z] GATK: UnifiedGenotyper
[2016-04-15T00:51Z] INFO  17:51:57,806 ProgressMeter -            done   1324132.0    33.0 s      25.0 s      100.0%    33.0 s       0.0 s
[2016-04-15T00:51Z] INFO  17:51:57,806 ProgressMeter - Total runtime 33.86 secs, 0.56 min, 0.01 hours
[2016-04-15T00:51Z] INFO  17:51:57,807 MicroScheduler - 37437 reads were filtered out during the traversal out of approximately 452056 total reads (8.28%)
[2016-04-15T00:51Z] INFO  17:51:57,807 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:51Z] INFO  17:51:57,807 MicroScheduler -   -> 657 reads (0.15% of total) failing BadMateFilter
[2016-04-15T00:51Z] INFO  17:51:57,808 MicroScheduler -   -> 36529 reads (8.08% of total) failing DuplicateReadFilter
[2016-04-15T00:51Z] INFO  17:51:57,808 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:51Z] INFO  17:51:57,808 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:51Z] INFO  17:51:57,808 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:51Z] INFO  17:51:57,808 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:51Z] INFO  17:51:57,809 MicroScheduler -   -> 251 reads (0.06% of total) failing UnmappedReadFilter
[2016-04-15T00:51Z] INFO  17:51:59,078 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:51Z] GATK: UnifiedGenotyper
[2016-04-15T00:51Z] INFO  17:51:59,475 ProgressMeter -            done    278160.0    17.0 s      61.0 s      100.0%    17.0 s       0.0 s
[2016-04-15T00:51Z] INFO  17:51:59,476 ProgressMeter - Total runtime 17.08 secs, 0.28 min, 0.00 hours
[2016-04-15T00:51Z] INFO  17:51:59,476 MicroScheduler - 12314 reads were filtered out during the traversal out of approximately 157625 total reads (7.81%)
[2016-04-15T00:51Z] INFO  17:51:59,477 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:51Z] INFO  17:51:59,477 MicroScheduler -   -> 241 reads (0.15% of total) failing BadMateFilter
[2016-04-15T00:51Z] INFO  17:51:59,477 MicroScheduler -   -> 11982 reads (7.60% of total) failing DuplicateReadFilter
[2016-04-15T00:51Z] INFO  17:51:59,477 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:51Z] INFO  17:51:59,478 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:51Z] INFO  17:51:59,478 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:51Z] INFO  17:51:59,478 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:51Z] INFO  17:51:59,478 MicroScheduler -   -> 91 reads (0.06% of total) failing UnmappedReadFilter
[2016-04-15T00:51Z] INFO  17:51:59,909 ProgressMeter -            done    400167.0    17.0 s      43.0 s      100.0%    17.0 s       0.0 s
[2016-04-15T00:51Z] INFO  17:51:59,910 ProgressMeter - Total runtime 17.30 secs, 0.29 min, 0.00 hours
[2016-04-15T00:51Z] INFO  17:51:59,910 MicroScheduler - 13577 reads were filtered out during the traversal out of approximately 164965 total reads (8.23%)
[2016-04-15T00:51Z] INFO  17:51:59,910 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:51Z] INFO  17:51:59,910 MicroScheduler -   -> 222 reads (0.13% of total) failing BadMateFilter
[2016-04-15T00:51Z] INFO  17:51:59,911 MicroScheduler -   -> 13247 reads (8.03% of total) failing DuplicateReadFilter
[2016-04-15T00:51Z] INFO  17:51:59,911 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:51Z] INFO  17:51:59,911 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:51Z] INFO  17:51:59,911 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:51Z] INFO  17:51:59,912 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:51Z] INFO  17:51:59,912 MicroScheduler -   -> 108 reads (0.07% of total) failing UnmappedReadFilter
[2016-04-15T00:52Z] INFO  17:52:00,574 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:52Z] INFO  17:52:00,577 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:52Z] INFO  17:52:00,577 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:52Z] INFO  17:52:00,578 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:52Z] INFO  17:52:00,582 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/12/R14-18105_kapa-NGv3-PE100-NGv3-sort-12_93870729_109490566-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/12/R14-18105_kapa-NGv3-PE100-NGv3-12_93870729_109490566-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/12/tx/tmp8TxqMW/R14-18105_kapa-NGv3-PE100-NGv3-12_93870729_109490566.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:52Z] INFO  17:52:00,596 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:52Z] INFO  17:52:00,597 HelpFormatter - Date/Time: 2016/04/14 17:52:00
[2016-04-15T00:52Z] INFO  17:52:00,597 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:52Z] INFO  17:52:00,598 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:52Z] INFO  17:52:00,757 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:52Z] INFO  17:52:00,799 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:52Z] INFO  17:52:00,990 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:52Z] INFO  17:52:00,999 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:52Z] INFO  17:52:01,059 ProgressMeter -            done    387169.0    15.0 s      40.0 s       99.9%    15.0 s       0.0 s
[2016-04-15T00:52Z] INFO  17:52:01,059 ProgressMeter - Total runtime 15.76 secs, 0.26 min, 0.00 hours
[2016-04-15T00:52Z] INFO  17:52:01,060 MicroScheduler - 12997 reads were filtered out during the traversal out of approximately 154660 total reads (8.40%)
[2016-04-15T00:52Z] INFO  17:52:01,060 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:52Z] INFO  17:52:01,060 MicroScheduler -   -> 213 reads (0.14% of total) failing BadMateFilter
[2016-04-15T00:52Z] INFO  17:52:01,060 MicroScheduler -   -> 12696 reads (8.21% of total) failing DuplicateReadFilter
[2016-04-15T00:52Z] INFO  17:52:01,061 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:52Z] INFO  17:52:01,061 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:52Z] INFO  17:52:01,061 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:52Z] INFO  17:52:01,061 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:52Z] INFO  17:52:01,062 MicroScheduler -   -> 88 reads (0.06% of total) failing UnmappedReadFilter
[2016-04-15T00:52Z] GATK: UnifiedGenotyper
[2016-04-15T00:52Z] INFO  17:52:01,093 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.09
[2016-04-15T00:52Z] INFO  17:52:01,265 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:52Z] GATK: UnifiedGenotyper
[2016-04-15T00:52Z] INFO  17:52:01,520 ProgressMeter -      11:6048678   1342714.0    30.0 s      22.0 s       54.5%    55.0 s      25.0 s
[2016-04-15T00:52Z] INFO  17:52:01,534 IntervalUtils - Processing 201796 bp from intervals
[2016-04-15T00:52Z] WARN  17:52:01,551 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:52Z] INFO  17:52:01,625 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:52Z] INFO  17:52:01,734 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:52Z] INFO  17:52:01,735 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:52Z] INFO  17:52:01,736 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:52Z] INFO  17:52:01,737 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:52Z] INFO  17:52:01,804 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:52Z] INFO  17:52:01,806 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:52Z] INFO  17:52:01,963 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:52Z] INFO  17:52:01,977 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:52Z] INFO  17:52:01,977 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:52Z] INFO  17:52:01,977 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:52Z] INFO  17:52:01,983 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/12/R14-18105_kapa-NGv3-PE100-NGv3-sort-12_109494486_125263132-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/12/R14-18105_kapa-NGv3-PE100-NGv3-12_109494486_125263132-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/12/tx/tmpg0chVA/R14-18105_kapa-NGv3-PE100-NGv3-12_109494486_125263132.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:52Z] INFO  17:52:02,010 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:52Z] INFO  17:52:02,021 HelpFormatter - Date/Time: 2016/04/14 17:52:01
[2016-04-15T00:52Z] INFO  17:52:02,022 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:52Z] INFO  17:52:02,023 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:52Z] INFO  17:52:02,234 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:52Z] INFO  17:52:02,512 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:52Z] INFO  17:52:02,524 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:52Z] INFO  17:52:02,600 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-15T00:52Z] INFO  17:52:02,665 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:52Z] INFO  17:52:02,949 ProgressMeter -            done    352890.0    15.0 s      43.0 s      100.0%    15.0 s       0.0 s
[2016-04-15T00:52Z] INFO  17:52:02,950 ProgressMeter - Total runtime 15.46 secs, 0.26 min, 0.00 hours
[2016-04-15T00:52Z] INFO  17:52:02,950 MicroScheduler - 11616 reads were filtered out during the traversal out of approximately 138139 total reads (8.41%)
[2016-04-15T00:52Z] INFO  17:52:02,950 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:52Z] INFO  17:52:02,951 MicroScheduler -   -> 220 reads (0.16% of total) failing BadMateFilter
[2016-04-15T00:52Z] INFO  17:52:02,951 MicroScheduler -   -> 11329 reads (8.20% of total) failing DuplicateReadFilter
[2016-04-15T00:52Z] INFO  17:52:02,951 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:52Z] INFO  17:52:02,952 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:52Z] INFO  17:52:02,952 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:52Z] INFO  17:52:02,952 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:52Z] INFO  17:52:02,952 MicroScheduler -   -> 67 reads (0.05% of total) failing UnmappedReadFilter
[2016-04-15T00:52Z] GATK: UnifiedGenotyper
[2016-04-15T00:52Z] INFO  17:52:03,177 IntervalUtils - Processing 364987 bp from intervals
[2016-04-15T00:52Z] WARN  17:52:03,191 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:52Z] INFO  17:52:03,334 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:52Z] INFO  17:52:03,495 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:52Z] INFO  17:52:03,497 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:52Z] INFO  17:52:03,508 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:52Z] INFO  17:52:03,509 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:52Z] INFO  17:52:03,578 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:52Z] INFO  17:52:03,579 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:52Z] INFO  17:52:03,638 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:52Z] INFO  17:52:03,641 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:52Z] INFO  17:52:03,641 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:52Z] INFO  17:52:03,642 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:52Z] INFO  17:52:03,646 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/12/R14-18105_kapa-NGv3-PE100-NGv3-sort-12_125267228_133851895-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/12/R14-18105_kapa-NGv3-PE100-NGv3-12_125267228_133851895-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/12/tx/tmpj8Gpew/R14-18105_kapa-NGv3-PE100-NGv3-12_125267228_133851895.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:52Z] INFO  17:52:03,668 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:52Z] INFO  17:52:03,672 HelpFormatter - Date/Time: 2016/04/14 17:52:03
[2016-04-15T00:52Z] INFO  17:52:03,672 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:52Z] INFO  17:52:03,677 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:52Z] INFO  17:52:03,830 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:52Z] INFO  17:52:04,072 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:52Z] INFO  17:52:04,082 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:52Z] INFO  17:52:04,101 ProgressMeter -            done   2509744.0    49.0 s      19.0 s      100.0%    49.0 s       0.0 s
[2016-04-15T00:52Z] INFO  17:52:04,102 ProgressMeter - Total runtime 49.25 secs, 0.82 min, 0.01 hours
[2016-04-15T00:52Z] INFO  17:52:04,102 MicroScheduler - 61119 reads were filtered out during the traversal out of approximately 735672 total reads (8.31%)
[2016-04-15T00:52Z] INFO  17:52:04,102 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:52Z] INFO  17:52:04,103 MicroScheduler -   -> 1041 reads (0.14% of total) failing BadMateFilter
[2016-04-15T00:52Z] INFO  17:52:04,103 MicroScheduler -   -> 59654 reads (8.11% of total) failing DuplicateReadFilter
[2016-04-15T00:52Z] INFO  17:52:04,103 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:52Z] INFO  17:52:04,103 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:52Z] INFO  17:52:04,103 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:52Z] INFO  17:52:04,104 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:52Z] INFO  17:52:04,104 MicroScheduler -   -> 424 reads (0.06% of total) failing UnmappedReadFilter
[2016-04-15T00:52Z] INFO  17:52:04,159 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-15T00:52Z] INFO  17:52:04,305 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:52Z] INFO  17:52:04,415 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:52Z] INFO  17:52:04,418 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:52Z] INFO  17:52:04,419 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:52Z] INFO  17:52:04,420 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:52Z] INFO  17:52:04,424 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/13/R14-18105_kapa-NGv3-PE100-NGv3-sort-13_0_19748299-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/13/R14-18105_kapa-NGv3-PE100-NGv3-13_0_19748299-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/13/tx/tmpZeRpKe/R14-18105_kapa-NGv3-PE100-NGv3-13_0_19748299.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:52Z] INFO  17:52:04,439 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:52Z] INFO  17:52:04,440 HelpFormatter - Date/Time: 2016/04/14 17:52:04
[2016-04-15T00:52Z] INFO  17:52:04,440 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:52Z] INFO  17:52:04,441 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:52Z] INFO  17:52:04,565 IntervalUtils - Processing 106872 bp from intervals
[2016-04-15T00:52Z] WARN  17:52:04,581 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:52Z] INFO  17:52:04,610 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:52Z] INFO  17:52:04,657 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:52Z] GATK: UnifiedGenotyper
[2016-04-15T00:52Z] INFO  17:52:04,721 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:52Z] INFO  17:52:04,722 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:52Z] INFO  17:52:04,723 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:52Z] INFO  17:52:04,723 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:52Z] INFO  17:52:04,801 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:52Z] INFO  17:52:04,802 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:52Z] INFO  17:52:04,807 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:52Z] INFO  17:52:04,833 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:52Z] INFO  17:52:04,904 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-15T00:52Z] INFO  17:52:05,356 IntervalUtils - Processing 297 bp from intervals
[2016-04-15T00:52Z] WARN  17:52:05,361 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:52Z] INFO  17:52:05,444 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:52Z] INFO  17:52:05,499 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:52Z] INFO  17:52:05,500 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:52Z] INFO  17:52:05,500 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:52Z] INFO  17:52:05,500 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:52Z] INFO  17:52:05,539 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:52Z] INFO  17:52:05,590 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:52Z] INFO  17:52:05,591 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:52Z] GATK: UnifiedGenotyper
[2016-04-15T00:52Z] INFO  17:52:05,873 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:52Z] INFO  17:52:05,891 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:52Z] INFO  17:52:05,891 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:52Z] INFO  17:52:05,891 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:52Z] INFO  17:52:05,896 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/13/R14-18105_kapa-NGv3-PE100-NGv3-sort-13_19751066_35517251-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/13/R14-18105_kapa-NGv3-PE100-NGv3-13_19751066_35517251-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/13/tx/tmpwUhbtV/R14-18105_kapa-NGv3-PE100-NGv3-13_19751066_35517251.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:52Z] INFO  17:52:05,923 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:52Z] INFO  17:52:05,923 HelpFormatter - Date/Time: 2016/04/14 17:52:05
[2016-04-15T00:52Z] INFO  17:52:05,923 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:52Z] INFO  17:52:05,924 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:52Z] INFO  17:52:06,188 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:52Z] INFO  17:52:06,373 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:52Z] INFO  17:52:06,395 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:52Z] INFO  17:52:06,485 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.09
[2016-04-15T00:52Z] INFO  17:52:06,904 ProgressMeter -            done       297.0     1.0 s      78.7 m       67.3%     1.0 s       0.0 s
[2016-04-15T00:52Z] INFO  17:52:06,904 ProgressMeter - Total runtime 1.40 secs, 0.02 min, 0.00 hours
[2016-04-15T00:52Z] INFO  17:52:06,905 MicroScheduler - 105 reads were filtered out during the traversal out of approximately 996 total reads (10.54%)
[2016-04-15T00:52Z] INFO  17:52:06,905 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:52Z] INFO  17:52:06,905 MicroScheduler -   -> 1 reads (0.10% of total) failing BadMateFilter
[2016-04-15T00:52Z] INFO  17:52:06,906 MicroScheduler -   -> 103 reads (10.34% of total) failing DuplicateReadFilter
[2016-04-15T00:52Z] INFO  17:52:06,906 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:52Z] INFO  17:52:06,906 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:52Z] INFO  17:52:06,907 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:52Z] INFO  17:52:06,907 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:52Z] INFO  17:52:06,907 MicroScheduler -   -> 1 reads (0.10% of total) failing UnmappedReadFilter
[2016-04-15T00:52Z] INFO  17:52:06,909 IntervalUtils - Processing 201552 bp from intervals
[2016-04-15T00:52Z] WARN  17:52:06,926 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:52Z] INFO  17:52:07,051 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:52Z] INFO  17:52:07,166 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:52Z] INFO  17:52:07,167 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:52Z] INFO  17:52:07,167 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:52Z] INFO  17:52:07,167 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:52Z] INFO  17:52:07,225 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:52Z] INFO  17:52:07,226 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:52Z] INFO  17:52:07,529 ProgressMeter -            done    441963.0    17.0 s      38.0 s       99.9%    17.0 s       0.0 s
[2016-04-15T00:52Z] INFO  17:52:07,530 ProgressMeter - Total runtime 17.05 secs, 0.28 min, 0.00 hours
[2016-04-15T00:52Z] INFO  17:52:07,530 MicroScheduler - 14560 reads were filtered out during the traversal out of approximately 178587 total reads (8.15%)
[2016-04-15T00:52Z] INFO  17:52:07,531 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:52Z] INFO  17:52:07,531 MicroScheduler -   -> 251 reads (0.14% of total) failing BadMateFilter
[2016-04-15T00:52Z] INFO  17:52:07,531 MicroScheduler -   -> 14210 reads (7.96% of total) failing DuplicateReadFilter
[2016-04-15T00:52Z] INFO  17:52:07,531 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:52Z] INFO  17:52:07,532 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:52Z] INFO  17:52:07,532 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:52Z] INFO  17:52:07,532 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:52Z] INFO  17:52:07,532 MicroScheduler -   -> 99 reads (0.06% of total) failing UnmappedReadFilter
[2016-04-15T00:52Z] INFO  17:52:07,920 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:52Z] INFO  17:52:07,930 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:52Z] INFO  17:52:07,931 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:52Z] INFO  17:52:07,931 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:52Z] INFO  17:52:07,936 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/13/R14-18105_kapa-NGv3-PE100-NGv3-sort-13_35615069_51287376-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/13/R14-18105_kapa-NGv3-PE100-NGv3-13_35615069_51287376-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/13/tx/tmpsmvUxy/R14-18105_kapa-NGv3-PE100-NGv3-13_35615069_51287376.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:52Z] INFO  17:52:07,967 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:52Z] INFO  17:52:07,968 HelpFormatter - Date/Time: 2016/04/14 17:52:07
[2016-04-15T00:52Z] INFO  17:52:07,969 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:52Z] INFO  17:52:07,969 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:52Z] INFO  17:52:08,182 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:52Z] INFO  17:52:08,352 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:52Z] INFO  17:52:08,371 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:52Z] INFO  17:52:08,372 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:52Z] INFO  17:52:08,430 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-15T00:52Z] INFO  17:52:08,492 ProgressMeter -            done    243833.0    11.0 s      48.0 s       99.9%    11.0 s       0.0 s
[2016-04-15T00:52Z] INFO  17:52:08,493 ProgressMeter - Total runtime 11.74 secs, 0.20 min, 0.00 hours
[2016-04-15T00:52Z] INFO  17:52:08,493 MicroScheduler - 7178 reads were filtered out during the traversal out of approximately 86211 total reads (8.33%)
[2016-04-15T00:52Z] INFO  17:52:08,493 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:52Z] INFO  17:52:08,494 MicroScheduler -   -> 130 reads (0.15% of total) failing BadMateFilter
[2016-04-15T00:52Z] INFO  17:52:08,494 MicroScheduler -   -> 6997 reads (8.12% of total) failing DuplicateReadFilter
[2016-04-15T00:52Z] INFO  17:52:08,494 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:52Z] INFO  17:52:08,494 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:52Z] INFO  17:52:08,495 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:52Z] INFO  17:52:08,495 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:52Z] INFO  17:52:08,495 MicroScheduler -   -> 51 reads (0.06% of total) failing UnmappedReadFilter
[2016-04-15T00:52Z] GATK: UnifiedGenotyper
[2016-04-15T00:52Z] INFO  17:52:08,823 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:52Z] INFO  17:52:08,826 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:52Z] INFO  17:52:08,827 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:52Z] INFO  17:52:08,827 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:52Z] INFO  17:52:08,832 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/13/R14-18105_kapa-NGv3-PE100-NGv3-sort-13_51396767_67205543-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/13/R14-18105_kapa-NGv3-PE100-NGv3-13_51396767_67205543-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/13/tx/tmpjlPV3h/R14-18105_kapa-NGv3-PE100-NGv3-13_51396767_67205543.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:52Z] INFO  17:52:08,865 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:52Z] INFO  17:52:08,866 HelpFormatter - Date/Time: 2016/04/14 17:52:08
[2016-04-15T00:52Z] INFO  17:52:08,866 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:52Z] INFO  17:52:08,871 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:52Z] INFO  17:52:08,898 IntervalUtils - Processing 179232 bp from intervals
[2016-04-15T00:52Z] WARN  17:52:08,904 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:52Z] INFO  17:52:08,921 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:52Z] INFO  17:52:08,998 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:52Z] INFO  17:52:09,042 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:52Z] INFO  17:52:09,087 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:52Z] INFO  17:52:09,089 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:52Z] INFO  17:52:09,089 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:52Z] INFO  17:52:09,090 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:52Z] INFO  17:52:09,138 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:52Z] INFO  17:52:09,139 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:52Z] GATK: UnifiedGenotyper
[2016-04-15T00:52Z] INFO  17:52:09,305 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:52Z] INFO  17:52:09,337 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:52Z] INFO  17:52:09,419 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-15T00:52Z] INFO  17:52:09,757 IntervalUtils - Processing 59966 bp from intervals
[2016-04-15T00:52Z] WARN  17:52:09,762 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:52Z] INFO  17:52:09,827 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:52Z] INFO  17:52:09,879 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:52Z] INFO  17:52:09,880 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:52Z] INFO  17:52:09,881 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:52Z] INFO  17:52:09,882 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:52Z] INFO  17:52:09,926 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:52Z] INFO  17:52:09,927 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:52Z] INFO  17:52:09,932 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:52Z] GATK: UnifiedGenotyper
[2016-04-15T00:52Z] INFO  17:52:10,706 ProgressMeter -            done    406794.0    16.0 s      39.0 s      100.0%    16.0 s       0.0 s
[2016-04-15T00:52Z] INFO  17:52:10,706 ProgressMeter - Total runtime 16.10 secs, 0.27 min, 0.00 hours
[2016-04-15T00:52Z] INFO  17:52:10,707 MicroScheduler - 13085 reads were filtered out during the traversal out of approximately 157958 total reads (8.28%)
[2016-04-15T00:52Z] INFO  17:52:10,707 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:52Z] INFO  17:52:10,707 MicroScheduler -   -> 241 reads (0.15% of total) failing BadMateFilter
[2016-04-15T00:52Z] INFO  17:52:10,707 MicroScheduler -   -> 12758 reads (8.08% of total) failing DuplicateReadFilter
[2016-04-15T00:52Z] INFO  17:52:10,708 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:52Z] INFO  17:52:10,708 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:52Z] INFO  17:52:10,708 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:52Z] INFO  17:52:10,708 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:52Z] INFO  17:52:10,709 MicroScheduler -   -> 86 reads (0.05% of total) failing UnmappedReadFilter
[2016-04-15T00:52Z] INFO  17:52:11,242 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:52Z] INFO  17:52:11,246 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:52Z] INFO  17:52:11,247 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:52Z] INFO  17:52:11,247 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:52Z] INFO  17:52:11,252 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/13/R14-18105_kapa-NGv3-PE100-NGv3-sort-13_67477635_84455642-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/13/R14-18105_kapa-NGv3-PE100-NGv3-13_67477635_84455642-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/13/tx/tmpQSPky6/R14-18105_kapa-NGv3-PE100-NGv3-13_67477635_84455642.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:52Z] INFO  17:52:11,262 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:52Z] INFO  17:52:11,264 HelpFormatter - Date/Time: 2016/04/14 17:52:11
[2016-04-15T00:52Z] INFO  17:52:11,265 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:52Z] INFO  17:52:11,266 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:52Z] INFO  17:52:11,371 ProgressMeter -     11:62289274    958393.0    30.0 s      31.0 s       83.6%    35.0 s       5.0 s
[2016-04-15T00:52Z] INFO  17:52:11,434 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:52Z] INFO  17:52:11,587 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:52Z] INFO  17:52:11,596 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:52Z] INFO  17:52:11,663 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-15T00:52Z] INFO  17:52:11,829 ProgressMeter -     11:67057300   1714624.0    30.0 s      17.0 s       50.0%    59.0 s      29.0 s
[2016-04-15T00:52Z] INFO  17:52:12,103 IntervalUtils - Processing 69582 bp from intervals
[2016-04-15T00:52Z] WARN  17:52:12,108 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:52Z] INFO  17:52:12,129 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:52Z] INFO  17:52:12,202 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:52Z] INFO  17:52:12,269 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:52Z] INFO  17:52:12,279 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:52Z] INFO  17:52:12,280 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:52Z] INFO  17:52:12,281 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:52Z] INFO  17:52:12,389 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:52Z] INFO  17:52:12,390 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:52Z] INFO  17:52:12,456 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:52Z] INFO  17:52:12,458 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:52Z] INFO  17:52:12,459 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:52Z] INFO  17:52:12,459 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:52Z] INFO  17:52:12,474 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/13/R14-18105_kapa-NGv3-PE100-NGv3-sort-13_86368117_101881935-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/13/R14-18105_kapa-NGv3-PE100-NGv3-13_86368117_101881935-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/13/tx/tmp2029Wj/R14-18105_kapa-NGv3-PE100-NGv3-13_86368117_101881935.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:52Z] INFO  17:52:12,486 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:52Z] INFO  17:52:12,486 HelpFormatter - Date/Time: 2016/04/14 17:52:12
[2016-04-15T00:52Z] INFO  17:52:12,486 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:52Z] INFO  17:52:12,487 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:52Z] GATK: UnifiedGenotyper
[2016-04-15T00:52Z] INFO  17:52:12,706 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:52Z] INFO  17:52:12,961 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:52Z] INFO  17:52:12,970 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:52Z] INFO  17:52:13,013 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:52Z] INFO  17:52:13,016 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:52Z] INFO  17:52:13,017 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:52Z] INFO  17:52:13,018 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:52Z] INFO  17:52:13,022 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/13/R14-18105_kapa-NGv3-PE100-NGv3-sort-13_101890105_115169878-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/13/R14-18105_kapa-NGv3-PE100-NGv3-13_101890105_115169878-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/13/tx/tmpgviFL5/R14-18105_kapa-NGv3-PE100-NGv3-13_101890105_115169878.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:52Z] INFO  17:52:13,027 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-15T00:52Z] INFO  17:52:13,035 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:52Z] INFO  17:52:13,036 HelpFormatter - Date/Time: 2016/04/14 17:52:13
[2016-04-15T00:52Z] INFO  17:52:13,037 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:52Z] INFO  17:52:13,038 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:52Z] INFO  17:52:13,175 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:52Z] INFO  17:52:13,413 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:52Z] INFO  17:52:13,421 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:52Z] INFO  17:52:13,450 IntervalUtils - Processing 75123 bp from intervals
[2016-04-15T00:52Z] WARN  17:52:13,462 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:52Z] INFO  17:52:13,507 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.09
[2016-04-15T00:52Z] INFO  17:52:13,600 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:52Z] INFO  17:52:13,718 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:52Z] INFO  17:52:13,719 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:52Z] INFO  17:52:13,719 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:52Z] INFO  17:52:13,720 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:52Z] INFO  17:52:13,827 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:52Z] INFO  17:52:13,828 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:52Z] INFO  17:52:13,935 IntervalUtils - Processing 144481 bp from intervals
[2016-04-15T00:52Z] WARN  17:52:13,941 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:52Z] INFO  17:52:14,045 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:52Z] INFO  17:52:14,183 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:52Z] INFO  17:52:14,184 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:52Z] INFO  17:52:14,184 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:52Z] INFO  17:52:14,185 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:52Z] INFO  17:52:14,255 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:52Z] INFO  17:52:14,256 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:52Z] INFO  17:52:14,325 ProgressMeter -    11:123597305   1116873.0    30.0 s      26.0 s       81.9%    36.0 s       6.0 s
[2016-04-15T00:52Z] INFO  17:52:15,468 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:52Z] INFO  17:52:15,470 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:52Z] INFO  17:52:15,471 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:52Z] INFO  17:52:15,471 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:52Z] INFO  17:52:15,477 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/14/R14-18105_kapa-NGv3-PE100-NGv3-sort-14_0_19378574-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/14/R14-18105_kapa-NGv3-PE100-NGv3-14_0_19378574-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/14/tx/tmpVbJdZ5/R14-18105_kapa-NGv3-PE100-NGv3-14_0_19378574.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:52Z] INFO  17:52:15,495 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:52Z] INFO  17:52:15,495 HelpFormatter - Date/Time: 2016/04/14 17:52:15
[2016-04-15T00:52Z] INFO  17:52:15,495 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:52Z] INFO  17:52:15,496 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:52Z] INFO  17:52:15,666 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:52Z] INFO  17:52:15,927 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:52Z] INFO  17:52:15,938 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:52Z] INFO  17:52:16,012 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-15T00:52Z] INFO  17:52:16,383 IntervalUtils - Processing 981 bp from intervals
[2016-04-15T00:52Z] WARN  17:52:16,388 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:52Z] INFO  17:52:16,520 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:52Z] INFO  17:52:16,547 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:52Z] INFO  17:52:16,559 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:52Z] INFO  17:52:16,560 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:52Z] INFO  17:52:16,560 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:52Z] INFO  17:52:16,616 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:52Z] INFO  17:52:16,617 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:52Z] INFO  17:52:16,861 ProgressMeter -            done   1302582.0    35.0 s      27.0 s      100.0%    35.0 s       0.0 s
[2016-04-15T00:52Z] INFO  17:52:16,861 ProgressMeter - Total runtime 35.50 secs, 0.59 min, 0.01 hours
[2016-04-15T00:52Z] INFO  17:52:16,862 MicroScheduler - 40138 reads were filtered out during the traversal out of approximately 486886 total reads (8.24%)
[2016-04-15T00:52Z] INFO  17:52:16,862 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:52Z] INFO  17:52:16,862 MicroScheduler -   -> 654 reads (0.13% of total) failing BadMateFilter
[2016-04-15T00:52Z] INFO  17:52:16,863 MicroScheduler -   -> 39184 reads (8.05% of total) failing DuplicateReadFilter
[2016-04-15T00:52Z] INFO  17:52:16,863 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:52Z] INFO  17:52:16,863 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:52Z] INFO  17:52:16,863 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:52Z] INFO  17:52:16,864 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:52Z] INFO  17:52:16,864 MicroScheduler -   -> 300 reads (0.06% of total) failing UnmappedReadFilter
[2016-04-15T00:52Z] INFO  17:52:17,103 ProgressMeter -     12:10541370   1150575.0    30.0 s      26.0 s       78.3%    38.0 s       8.0 s
[2016-04-15T00:52Z] INFO  17:52:18,452 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:52Z] INFO  17:52:18,677 ProgressMeter -            done       981.0     2.0 s      36.0 m       91.7%     2.0 s       0.0 s
[2016-04-15T00:52Z] INFO  17:52:18,678 ProgressMeter - Total runtime 2.12 secs, 0.04 min, 0.00 hours
[2016-04-15T00:52Z] INFO  17:52:18,679 MicroScheduler - 272 reads were filtered out during the traversal out of approximately 3213 total reads (8.47%)
[2016-04-15T00:52Z] INFO  17:52:18,680 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:52Z] INFO  17:52:18,681 MicroScheduler -   -> 7 reads (0.22% of total) failing BadMateFilter
[2016-04-15T00:52Z] INFO  17:52:18,681 MicroScheduler -   -> 263 reads (8.19% of total) failing DuplicateReadFilter
[2016-04-15T00:52Z] INFO  17:52:18,682 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:52Z] INFO  17:52:18,682 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:52Z] INFO  17:52:18,683 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:52Z] INFO  17:52:18,684 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:52Z] INFO  17:52:18,684 MicroScheduler -   -> 2 reads (0.06% of total) failing UnmappedReadFilter
[2016-04-15T00:52Z] GATK: UnifiedGenotyper
[2016-04-15T00:52Z] INFO  17:52:19,464 ProgressMeter -            done   1335468.0    35.0 s      26.0 s      100.0%    35.0 s       0.0 s
[2016-04-15T00:52Z] INFO  17:52:19,464 ProgressMeter - Total runtime 35.18 secs, 0.59 min, 0.01 hours
[2016-04-15T00:52Z] INFO  17:52:19,465 MicroScheduler - 38163 reads were filtered out during the traversal out of approximately 457301 total reads (8.35%)
[2016-04-15T00:52Z] INFO  17:52:19,465 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:52Z] INFO  17:52:19,465 MicroScheduler -   -> 657 reads (0.14% of total) failing BadMateFilter
[2016-04-15T00:52Z] INFO  17:52:19,466 MicroScheduler -   -> 37225 reads (8.14% of total) failing DuplicateReadFilter
[2016-04-15T00:52Z] INFO  17:52:19,466 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:52Z] INFO  17:52:19,466 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:52Z] INFO  17:52:19,466 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:52Z] INFO  17:52:19,467 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:52Z] INFO  17:52:19,467 MicroScheduler -   -> 281 reads (0.06% of total) failing UnmappedReadFilter
[2016-04-15T00:52Z] INFO  17:52:19,569 ProgressMeter -            done   2117017.0    48.0 s      22.0 s      100.0%    48.0 s       0.0 s
[2016-04-15T00:52Z] INFO  17:52:19,569 ProgressMeter - Total runtime 48.05 secs, 0.80 min, 0.01 hours
[2016-04-15T00:52Z] INFO  17:52:19,569 MicroScheduler - 65933 reads were filtered out during the traversal out of approximately 734174 total reads (8.98%)
[2016-04-15T00:52Z] INFO  17:52:19,570 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:52Z] INFO  17:52:19,570 MicroScheduler -   -> 1188 reads (0.16% of total) failing BadMateFilter
[2016-04-15T00:52Z] INFO  17:52:19,570 MicroScheduler -   -> 64150 reads (8.74% of total) failing DuplicateReadFilter
[2016-04-15T00:52Z] INFO  17:52:19,570 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:52Z] INFO  17:52:19,571 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:52Z] INFO  17:52:19,571 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:52Z] INFO  17:52:19,571 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:52Z] INFO  17:52:19,571 MicroScheduler -   -> 595 reads (0.08% of total) failing UnmappedReadFilter
[2016-04-15T00:52Z] INFO  17:52:20,050 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:52Z] INFO  17:52:20,167 ProgressMeter -            done    144034.0    10.0 s      71.0 s      100.0%    10.0 s       0.0 s
[2016-04-15T00:52Z] INFO  17:52:20,168 ProgressMeter - Total runtime 10.29 secs, 0.17 min, 0.00 hours
[2016-04-15T00:52Z] INFO  17:52:20,169 MicroScheduler - 6473 reads were filtered out during the traversal out of approximately 89248 total reads (7.25%)
[2016-04-15T00:52Z] INFO  17:52:20,169 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:52Z] INFO  17:52:20,170 MicroScheduler -   -> 145 reads (0.16% of total) failing BadMateFilter
[2016-04-15T00:52Z] INFO  17:52:20,178 MicroScheduler -   -> 6269 reads (7.02% of total) failing DuplicateReadFilter
[2016-04-15T00:52Z] INFO  17:52:20,179 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:52Z] INFO  17:52:20,179 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:52Z] INFO  17:52:20,180 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:52Z] INFO  17:52:20,181 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:52Z] INFO  17:52:20,181 MicroScheduler -   -> 59 reads (0.07% of total) failing UnmappedReadFilter
[2016-04-15T00:52Z] INFO  17:52:20,414 ProgressMeter -            done    370183.0    15.0 s      42.0 s      100.0%    15.0 s       0.0 s
[2016-04-15T00:52Z] INFO  17:52:20,415 ProgressMeter - Total runtime 15.69 secs, 0.26 min, 0.00 hours
[2016-04-15T00:52Z] INFO  17:52:20,416 MicroScheduler - 15038 reads were filtered out during the traversal out of approximately 180560 total reads (8.33%)
[2016-04-15T00:52Z] INFO  17:52:20,416 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:52Z] INFO  17:52:20,417 MicroScheduler -   -> 297 reads (0.16% of total) failing BadMateFilter
[2016-04-15T00:52Z] INFO  17:52:20,418 MicroScheduler -   -> 14611 reads (8.09% of total) failing DuplicateReadFilter
[2016-04-15T00:52Z] INFO  17:52:20,418 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:52Z] INFO  17:52:20,419 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:52Z] INFO  17:52:20,420 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:52Z] INFO  17:52:20,420 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:52Z] INFO  17:52:20,421 MicroScheduler -   -> 130 reads (0.07% of total) failing UnmappedReadFilter
[2016-04-15T00:52Z] GATK: UnifiedGenotyper
[2016-04-15T00:52Z] INFO  17:52:20,859 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:52Z] GATK: UnifiedGenotyper
[2016-04-15T00:52Z] INFO  17:52:21,130 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:52Z] GATK: UnifiedGenotyper
[2016-04-15T00:52Z] INFO  17:52:21,522 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:52Z] INFO  17:52:21,767 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:52Z] INFO  17:52:21,770 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:52Z] INFO  17:52:21,770 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:52Z] INFO  17:52:21,771 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:52Z] GATK: UnifiedGenotyper
[2016-04-15T00:52Z] INFO  17:52:21,776 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/14/R14-18105_kapa-NGv3-PE100-NGv3-sort-14_19553416_35066851-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/14/R14-18105_kapa-NGv3-PE100-NGv3-14_19553416_35066851-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/14/tx/tmpiMemPK/R14-18105_kapa-NGv3-PE100-NGv3-14_19553416_35066851.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:52Z] INFO  17:52:21,786 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:52Z] INFO  17:52:21,801 HelpFormatter - Date/Time: 2016/04/14 17:52:21
[2016-04-15T00:52Z] INFO  17:52:21,801 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:52Z] INFO  17:52:21,802 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:52Z] INFO  17:52:21,803 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:52Z] INFO  17:52:21,995 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:52Z] GATK: UnifiedGenotyper
[2016-04-15T00:52Z] INFO  17:52:22,228 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:52Z] INFO  17:52:22,239 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:52Z] INFO  17:52:22,331 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.09
[2016-04-15T00:52Z] INFO  17:52:22,825 IntervalUtils - Processing 291951 bp from intervals
[2016-04-15T00:52Z] WARN  17:52:22,842 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:52Z] INFO  17:52:22,961 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:52Z] INFO  17:52:23,067 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:52Z] INFO  17:52:23,068 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:52Z] INFO  17:52:23,069 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:52Z] INFO  17:52:23,070 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:52Z] INFO  17:52:23,140 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:52Z] INFO  17:52:23,141 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:52Z] INFO  17:52:23,164 ProgressMeter -            done    188528.0    10.0 s      57.0 s       99.9%    10.0 s       0.0 s
[2016-04-15T00:52Z] INFO  17:52:23,164 ProgressMeter - Total runtime 10.89 secs, 0.18 min, 0.00 hours
[2016-04-15T00:52Z] INFO  17:52:23,165 MicroScheduler - 6605 reads were filtered out during the traversal out of approximately 77847 total reads (8.48%)
[2016-04-15T00:52Z] INFO  17:52:23,165 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:52Z] INFO  17:52:23,165 MicroScheduler -   -> 123 reads (0.16% of total) failing BadMateFilter
[2016-04-15T00:52Z] INFO  17:52:23,166 MicroScheduler -   -> 6437 reads (8.27% of total) failing DuplicateReadFilter
[2016-04-15T00:52Z] INFO  17:52:23,166 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:52Z] INFO  17:52:23,166 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:52Z] INFO  17:52:23,167 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:52Z] INFO  17:52:23,167 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:52Z] INFO  17:52:23,167 MicroScheduler -   -> 45 reads (0.06% of total) failing UnmappedReadFilter
[2016-04-15T00:52Z] INFO  17:52:23,774 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:52Z] INFO  17:52:23,777 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:52Z] INFO  17:52:23,778 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:52Z] INFO  17:52:23,779 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:52Z] INFO  17:52:23,783 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/14/R14-18105_kapa-NGv3-PE100-NGv3-sort-14_35072553_50583270-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/14/R14-18105_kapa-NGv3-PE100-NGv3-14_35072553_50583270-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/14/tx/tmpurEZvr/R14-18105_kapa-NGv3-PE100-NGv3-14_35072553_50583270.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:52Z] INFO  17:52:23,805 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:52Z] INFO  17:52:23,806 HelpFormatter - Date/Time: 2016/04/14 17:52:23
[2016-04-15T00:52Z] INFO  17:52:23,806 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:52Z] INFO  17:52:23,806 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:52Z] INFO  17:52:24,001 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:52Z] INFO  17:52:24,187 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:52Z] INFO  17:52:24,196 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:52Z] INFO  17:52:24,222 ProgressMeter -            done   1314614.0    37.0 s      28.0 s      100.0%    37.0 s       0.0 s
[2016-04-15T00:52Z] INFO  17:52:24,222 ProgressMeter - Total runtime 37.14 secs, 0.62 min, 0.01 hours
[2016-04-15T00:52Z] INFO  17:52:24,223 MicroScheduler - 38357 reads were filtered out during the traversal out of approximately 467259 total reads (8.21%)
[2016-04-15T00:52Z] INFO  17:52:24,223 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:52Z] INFO  17:52:24,223 MicroScheduler -   -> 708 reads (0.15% of total) failing BadMateFilter
[2016-04-15T00:52Z] INFO  17:52:24,223 MicroScheduler -   -> 37384 reads (8.00% of total) failing DuplicateReadFilter
[2016-04-15T00:52Z] INFO  17:52:24,224 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:52Z] INFO  17:52:24,224 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:52Z] INFO  17:52:24,224 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:52Z] INFO  17:52:24,224 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:52Z] INFO  17:52:24,225 MicroScheduler -   -> 265 reads (0.06% of total) failing UnmappedReadFilter
[2016-04-15T00:52Z] INFO  17:52:24,241 ProgressMeter -            done    596495.0    22.0 s      37.0 s      100.0%    22.0 s       0.0 s
[2016-04-15T00:52Z] INFO  17:52:24,241 ProgressMeter - Total runtime 22.51 secs, 0.38 min, 0.01 hours
[2016-04-15T00:52Z] INFO  17:52:24,241 MicroScheduler - 20221 reads were filtered out during the traversal out of approximately 245570 total reads (8.23%)
[2016-04-15T00:52Z] INFO  17:52:24,242 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:52Z] INFO  17:52:24,242 MicroScheduler -   -> 341 reads (0.14% of total) failing BadMateFilter
[2016-04-15T00:52Z] INFO  17:52:24,242 MicroScheduler -   -> 19756 reads (8.04% of total) failing DuplicateReadFilter
[2016-04-15T00:52Z] INFO  17:52:24,242 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:52Z] INFO  17:52:24,243 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:52Z] INFO  17:52:24,243 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:52Z] INFO  17:52:24,243 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:52Z] INFO  17:52:24,243 MicroScheduler -   -> 124 reads (0.05% of total) failing UnmappedReadFilter
[2016-04-15T00:52Z] INFO  17:52:24,274 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-15T00:52Z] INFO  17:52:24,339 ProgressMeter -     12:53899633   1523825.0    30.0 s      19.0 s       55.6%    54.0 s      24.0 s
[2016-04-15T00:52Z] INFO  17:52:24,418 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:52Z] INFO  17:52:24,422 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:52Z] INFO  17:52:24,422 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:52Z] INFO  17:52:24,423 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:52Z] INFO  17:52:24,429 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/14/R14-18105_kapa-NGv3-PE100-NGv3-sort-14_50585061_66096324-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/14/R14-18105_kapa-NGv3-PE100-NGv3-14_50585061_66096324-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/14/tx/tmpXSZyDq/R14-18105_kapa-NGv3-PE100-NGv3-14_50585061_66096324.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:52Z] INFO  17:52:24,444 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:52Z] INFO  17:52:24,453 HelpFormatter - Date/Time: 2016/04/14 17:52:24
[2016-04-15T00:52Z] INFO  17:52:24,453 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:52Z] INFO  17:52:24,454 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:52Z] INFO  17:52:24,502 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:52Z] INFO  17:52:24,505 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:52Z] INFO  17:52:24,506 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:52Z] INFO  17:52:24,507 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:52Z] INFO  17:52:24,511 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/14/R14-18105_kapa-NGv3-PE100-NGv3-sort-14_66135960_81646674-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/14/R14-18105_kapa-NGv3-PE100-NGv3-14_66135960_81646674-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/14/tx/tmpgQpjWO/R14-18105_kapa-NGv3-PE100-NGv3-14_66135960_81646674.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:52Z] INFO  17:52:24,527 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:52Z] INFO  17:52:24,528 HelpFormatter - Date/Time: 2016/04/14 17:52:24
[2016-04-15T00:52Z] INFO  17:52:24,528 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:52Z] INFO  17:52:24,529 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:52Z] INFO  17:52:24,579 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:52Z] INFO  17:52:24,666 IntervalUtils - Processing 108903 bp from intervals
[2016-04-15T00:52Z] INFO  17:52:24,666 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:52Z] WARN  17:52:24,678 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:52Z] INFO  17:52:24,734 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:52Z] INFO  17:52:24,746 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:52Z] INFO  17:52:24,750 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:52Z] INFO  17:52:24,750 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:52Z] INFO  17:52:24,751 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:52Z] INFO  17:52:24,748 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:52Z] INFO  17:52:24,755 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/14/R14-18105_kapa-NGv3-PE100-NGv3-sort-14_81651874_97299968-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/14/R14-18105_kapa-NGv3-PE100-NGv3-14_81651874_97299968-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/14/tx/tmpjTWgrc/R14-18105_kapa-NGv3-PE100-NGv3-14_81651874_97299968.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:52Z] INFO  17:52:24,766 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:52Z] INFO  17:52:24,773 HelpFormatter - Date/Time: 2016/04/14 17:52:24
[2016-04-15T00:52Z] INFO  17:52:24,774 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:52Z] INFO  17:52:24,774 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:52Z] GATK: UnifiedGenotyper
[2016-04-15T00:52Z] INFO  17:52:24,842 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:52Z] INFO  17:52:24,844 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:52Z] INFO  17:52:24,844 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:52Z] INFO  17:52:24,845 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:52Z] INFO  17:52:24,882 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:52Z] INFO  17:52:24,888 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:52Z] INFO  17:52:24,889 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:52Z] INFO  17:52:24,912 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:52Z] INFO  17:52:24,942 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:52Z] INFO  17:52:24,946 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:52Z] INFO  17:52:24,955 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:52Z] INFO  17:52:24,987 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-15T00:52Z] INFO  17:52:25,018 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-15T00:52Z] INFO  17:52:25,111 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:52Z] INFO  17:52:25,114 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:52Z] INFO  17:52:25,114 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:52Z] INFO  17:52:25,114 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:52Z] INFO  17:52:25,118 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/14/R14-18105_kapa-NGv3-PE100-NGv3-sort-14_97304098_107349540-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/14/R14-18105_kapa-NGv3-PE100-NGv3-14_97304098_107349540-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/14/tx/tmpd0yROo/R14-18105_kapa-NGv3-PE100-NGv3-14_97304098_107349540.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:52Z] INFO  17:52:25,156 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:52Z] INFO  17:52:25,157 HelpFormatter - Date/Time: 2016/04/14 17:52:25
[2016-04-15T00:52Z] INFO  17:52:25,158 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:52Z] INFO  17:52:25,158 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:52Z] INFO  17:52:25,197 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:52Z] INFO  17:52:25,206 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:52Z] INFO  17:52:25,303 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.10
[2016-04-15T00:52Z] INFO  17:52:25,418 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:52Z] INFO  17:52:25,480 IntervalUtils - Processing 245410 bp from intervals
[2016-04-15T00:52Z] WARN  17:52:25,486 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:52Z] INFO  17:52:25,529 IntervalUtils - Processing 226771 bp from intervals
[2016-04-15T00:52Z] WARN  17:52:25,545 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:52Z] INFO  17:52:25,599 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:52Z] INFO  17:52:25,635 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:52Z] INFO  17:52:25,654 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:52Z] INFO  17:52:25,680 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:52Z] INFO  17:52:25,697 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:52Z] INFO  17:52:25,707 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:52Z] INFO  17:52:25,737 IntervalUtils - Processing 176504 bp from intervals
[2016-04-15T00:52Z] WARN  17:52:25,743 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:52Z] INFO  17:52:25,750 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:52Z] INFO  17:52:25,751 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:52Z] INFO  17:52:25,752 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:52Z] INFO  17:52:25,753 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:52Z] INFO  17:52:25,769 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:52Z] INFO  17:52:25,769 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:52Z] INFO  17:52:25,770 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:52Z] INFO  17:52:25,770 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:52Z] INFO  17:52:25,794 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.09
[2016-04-15T00:52Z] INFO  17:52:25,805 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:52Z] INFO  17:52:25,806 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:52Z] INFO  17:52:25,844 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:52Z] INFO  17:52:25,845 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:52Z] INFO  17:52:25,851 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:52Z] GATK: UnifiedGenotyper
[2016-04-15T00:52Z] INFO  17:52:25,957 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:52Z] INFO  17:52:25,963 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:52Z] INFO  17:52:25,964 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:52Z] INFO  17:52:25,976 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:52Z] GATK: UnifiedGenotyper
[2016-04-15T00:52Z] INFO  17:52:26,047 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:52Z] INFO  17:52:26,047 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:52Z] INFO  17:52:26,152 IntervalUtils - Processing 188545 bp from intervals
[2016-04-15T00:52Z] WARN  17:52:26,157 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:52Z] INFO  17:52:26,234 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:52Z] INFO  17:52:26,351 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:52Z] INFO  17:52:26,352 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:52Z] INFO  17:52:26,352 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:52Z] INFO  17:52:26,365 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:52Z] INFO  17:52:26,417 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:52Z] INFO  17:52:26,417 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:52Z] INFO  17:52:26,720 ProgressMeter -            done    183411.0    12.0 s      70.0 s       99.9%    12.0 s       0.0 s
[2016-04-15T00:52Z] INFO  17:52:26,720 ProgressMeter - Total runtime 13.00 secs, 0.22 min, 0.00 hours
[2016-04-15T00:52Z] INFO  17:52:26,721 MicroScheduler - 8696 reads were filtered out during the traversal out of approximately 101391 total reads (8.58%)
[2016-04-15T00:52Z] INFO  17:52:26,721 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:52Z] INFO  17:52:26,721 MicroScheduler -   -> 176 reads (0.17% of total) failing BadMateFilter
[2016-04-15T00:52Z] INFO  17:52:26,722 MicroScheduler -   -> 8452 reads (8.34% of total) failing DuplicateReadFilter
[2016-04-15T00:52Z] INFO  17:52:26,722 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:52Z] INFO  17:52:26,722 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:52Z] INFO  17:52:26,722 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:52Z] INFO  17:52:26,723 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:52Z] INFO  17:52:26,723 MicroScheduler -   -> 68 reads (0.07% of total) failing UnmappedReadFilter
[2016-04-15T00:52Z] INFO  17:52:27,979 ProgressMeter -            done    504383.0    20.0 s      41.0 s      100.0%    20.0 s       0.0 s
[2016-04-15T00:52Z] INFO  17:52:27,979 ProgressMeter - Total runtime 20.81 secs, 0.35 min, 0.01 hours
[2016-04-15T00:52Z] INFO  17:52:27,980 MicroScheduler - 18480 reads were filtered out during the traversal out of approximately 226933 total reads (8.14%)
[2016-04-15T00:52Z] INFO  17:52:27,980 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:52Z] INFO  17:52:27,980 MicroScheduler -   -> 343 reads (0.15% of total) failing BadMateFilter
[2016-04-15T00:52Z] INFO  17:52:27,980 MicroScheduler -   -> 18005 reads (7.93% of total) failing DuplicateReadFilter
[2016-04-15T00:52Z] INFO  17:52:27,981 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:52Z] INFO  17:52:27,981 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:52Z] INFO  17:52:27,981 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:52Z] INFO  17:52:27,981 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:52Z] INFO  17:52:27,982 MicroScheduler -   -> 132 reads (0.06% of total) failing UnmappedReadFilter
[2016-04-15T00:52Z] INFO  17:52:28,158 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:52Z] INFO  17:52:28,161 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:52Z] INFO  17:52:28,161 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:52Z] INFO  17:52:28,162 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:52Z] INFO  17:52:28,170 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/15/R14-18105_kapa-NGv3-PE100-NGv3-sort-15_0_20740485-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/15/R14-18105_kapa-NGv3-PE100-NGv3-15_0_20740485-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/15/tx/tmp_0oya3/R14-18105_kapa-NGv3-PE100-NGv3-15_0_20740485.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:52Z] INFO  17:52:28,180 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:52Z] INFO  17:52:28,181 HelpFormatter - Date/Time: 2016/04/14 17:52:28
[2016-04-15T00:52Z] INFO  17:52:28,182 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:52Z] INFO  17:52:28,182 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:52Z] INFO  17:52:28,298 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:52Z] INFO  17:52:28,424 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:52Z] GATK: UnifiedGenotyper
[2016-04-15T00:52Z] INFO  17:52:28,653 ProgressMeter -            done    469270.0    19.0 s      41.0 s      100.0%    19.0 s       0.0 s
[2016-04-15T00:52Z] INFO  17:52:28,653 ProgressMeter - Total runtime 19.56 secs, 0.33 min, 0.01 hours
[2016-04-15T00:52Z] INFO  17:52:28,653 MicroScheduler - 16797 reads were filtered out during the traversal out of approximately 204814 total reads (8.20%)
[2016-04-15T00:52Z] INFO  17:52:28,654 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:52Z] INFO  17:52:28,654 MicroScheduler -   -> 312 reads (0.15% of total) failing BadMateFilter
[2016-04-15T00:52Z] INFO  17:52:28,654 MicroScheduler -   -> 16371 reads (7.99% of total) failing DuplicateReadFilter
[2016-04-15T00:52Z] INFO  17:52:28,655 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:52Z] INFO  17:52:28,655 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:52Z] INFO  17:52:28,655 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:52Z] INFO  17:52:28,655 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:52Z] INFO  17:52:28,656 MicroScheduler -   -> 114 reads (0.06% of total) failing UnmappedReadFilter
[2016-04-15T00:52Z] INFO  17:52:28,700 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:52Z] INFO  17:52:28,719 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:52Z] INFO  17:52:28,795 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-15T00:52Z] INFO  17:52:28,818 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:52Z] INFO  17:52:28,821 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:52Z] INFO  17:52:28,821 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:52Z] INFO  17:52:28,821 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:52Z] INFO  17:52:28,827 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/15/R14-18105_kapa-NGv3-PE100-NGv3-sort-15_20741621_36872162-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/15/R14-18105_kapa-NGv3-PE100-NGv3-15_20741621_36872162-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/15/tx/tmpuEfMtC/R14-18105_kapa-NGv3-PE100-NGv3-15_20741621_36872162.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:52Z] INFO  17:52:28,837 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:52Z] INFO  17:52:28,838 HelpFormatter - Date/Time: 2016/04/14 17:52:28
[2016-04-15T00:52Z] INFO  17:52:28,839 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:52Z] INFO  17:52:28,839 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:52Z] INFO  17:52:28,996 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:52Z] INFO  17:52:29,206 IntervalUtils - Processing 989 bp from intervals
[2016-04-15T00:52Z] WARN  17:52:29,232 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:52Z] INFO  17:52:29,292 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:52Z] INFO  17:52:29,301 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:52Z] INFO  17:52:29,308 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:52Z] INFO  17:52:29,311 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:52Z] INFO  17:52:29,312 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:52Z] INFO  17:52:29,312 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:52Z] INFO  17:52:29,316 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/15/R14-18105_kapa-NGv3-PE100-NGv3-sort-15_36887086_52402170-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/15/R14-18105_kapa-NGv3-PE100-NGv3-15_36887086_52402170-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/15/tx/tmpNRPZjA/R14-18105_kapa-NGv3-PE100-NGv3-15_36887086_52402170.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:52Z] INFO  17:52:29,353 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:52Z] INFO  17:52:29,354 HelpFormatter - Date/Time: 2016/04/14 17:52:29
[2016-04-15T00:52Z] INFO  17:52:29,354 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:52Z] INFO  17:52:29,354 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:52Z] INFO  17:52:29,362 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:52Z] INFO  17:52:29,384 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:52Z] INFO  17:52:29,404 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.10
[2016-04-15T00:52Z] INFO  17:52:29,413 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:52Z] INFO  17:52:29,414 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:52Z] INFO  17:52:29,415 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:52Z] INFO  17:52:29,416 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:52Z] INFO  17:52:29,479 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:52Z] INFO  17:52:29,480 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:52Z] INFO  17:52:29,551 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:52Z] GATK: UnifiedGenotyper
[2016-04-15T00:52Z] INFO  17:52:29,865 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:52Z] INFO  17:52:29,873 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:52Z] INFO  17:52:29,949 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-15T00:52Z] INFO  17:52:29,981 IntervalUtils - Processing 177979 bp from intervals
[2016-04-15T00:52Z] WARN  17:52:29,986 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:52Z] INFO  17:52:30,012 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:52Z] INFO  17:52:30,089 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:52Z] INFO  17:52:30,207 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:52Z] INFO  17:52:30,207 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:52Z] INFO  17:52:30,208 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:52Z] INFO  17:52:30,208 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:52Z] INFO  17:52:30,288 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:52Z] INFO  17:52:30,292 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:52Z] GATK: UnifiedGenotyper
[2016-04-15T00:52Z] INFO  17:52:30,494 IntervalUtils - Processing 374190 bp from intervals
[2016-04-15T00:52Z] WARN  17:52:30,499 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:52Z] INFO  17:52:30,581 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:52Z] INFO  17:52:30,675 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:52Z] INFO  17:52:30,676 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:52Z] INFO  17:52:30,677 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:52Z] INFO  17:52:30,678 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:52Z] INFO  17:52:30,756 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:52Z] INFO  17:52:30,757 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:52Z] INFO  17:52:31,681 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:52Z] INFO  17:52:31,684 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:52Z] INFO  17:52:31,684 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:52Z] INFO  17:52:31,685 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:52Z] INFO  17:52:31,700 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/15/R14-18105_kapa-NGv3-PE100-NGv3-sort-15_52404364_67923265-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/15/R14-18105_kapa-NGv3-PE100-NGv3-15_52404364_67923265-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/15/tx/tmpX5p1n7/R14-18105_kapa-NGv3-PE100-NGv3-15_52404364_67923265.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:52Z] INFO  17:52:31,740 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:52Z] INFO  17:52:31,741 HelpFormatter - Date/Time: 2016/04/14 17:52:31
[2016-04-15T00:52Z] INFO  17:52:31,742 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:52Z] INFO  17:52:31,742 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:52Z] INFO  17:52:31,818 ProgressMeter -            done       989.0     2.0 s      40.5 m       91.0%     2.0 s       0.0 s
[2016-04-15T00:52Z] INFO  17:52:31,819 ProgressMeter - Total runtime 2.40 secs, 0.04 min, 0.00 hours
[2016-04-15T00:52Z] INFO  17:52:31,820 MicroScheduler - 103 reads were filtered out during the traversal out of approximately 2094 total reads (4.92%)
[2016-04-15T00:52Z] INFO  17:52:31,820 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:52Z] INFO  17:52:31,821 MicroScheduler -   -> 8 reads (0.38% of total) failing BadMateFilter
[2016-04-15T00:52Z] INFO  17:52:31,822 MicroScheduler -   -> 95 reads (4.54% of total) failing DuplicateReadFilter
[2016-04-15T00:52Z] INFO  17:52:31,823 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:52Z] INFO  17:52:31,823 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:52Z] INFO  17:52:31,824 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:52Z] INFO  17:52:31,825 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:52Z] INFO  17:52:31,825 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:52Z] INFO  17:52:31,915 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:52Z] INFO  17:52:32,264 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:52Z] INFO  17:52:32,284 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:52Z] INFO  17:52:32,388 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.10
[2016-04-15T00:52Z] INFO  17:52:32,819 IntervalUtils - Processing 254619 bp from intervals
[2016-04-15T00:52Z] WARN  17:52:32,838 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:52Z] INFO  17:52:32,915 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:52Z] INFO  17:52:32,989 ProgressMeter -            done    399815.0    18.0 s      47.0 s      100.0%    18.0 s       0.0 s
[2016-04-15T00:52Z] INFO  17:52:32,989 ProgressMeter - Total runtime 18.81 secs, 0.31 min, 0.01 hours
[2016-04-15T00:52Z] INFO  17:52:32,990 MicroScheduler - 15807 reads were filtered out during the traversal out of approximately 190425 total reads (8.30%)
[2016-04-15T00:52Z] INFO  17:52:32,990 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:52Z] INFO  17:52:32,990 MicroScheduler -   -> 286 reads (0.15% of total) failing BadMateFilter
[2016-04-15T00:52Z] INFO  17:52:32,991 MicroScheduler -   -> 15382 reads (8.08% of total) failing DuplicateReadFilter
[2016-04-15T00:52Z] INFO  17:52:32,991 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:52Z] INFO  17:52:32,991 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:52Z] INFO  17:52:32,991 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:52Z] INFO  17:52:32,992 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:52Z] INFO  17:52:32,992 MicroScheduler -   -> 139 reads (0.07% of total) failing UnmappedReadFilter
[2016-04-15T00:52Z] INFO  17:52:33,008 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:52Z] INFO  17:52:33,009 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:52Z] INFO  17:52:33,010 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:52Z] INFO  17:52:33,011 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:52Z] INFO  17:52:33,031 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:52Z] INFO  17:52:33,034 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:52Z] INFO  17:52:33,035 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:52Z] INFO  17:52:33,035 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:52Z] INFO  17:52:33,040 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/15/R14-18105_kapa-NGv3-PE100-NGv3-sort-15_67932890_83447639-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/15/R14-18105_kapa-NGv3-PE100-NGv3-15_67932890_83447639-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/15/tx/tmpxDzvZi/R14-18105_kapa-NGv3-PE100-NGv3-15_67932890_83447639.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:52Z] INFO  17:52:33,056 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:52Z] INFO  17:52:33,057 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:52Z] INFO  17:52:33,058 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:52Z] INFO  17:52:33,059 HelpFormatter - Date/Time: 2016/04/14 17:52:33
[2016-04-15T00:52Z] INFO  17:52:33,059 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:52Z] INFO  17:52:33,060 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:52Z] INFO  17:52:33,297 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:52Z] INFO  17:52:33,306 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:52Z] INFO  17:52:33,420 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:52Z] INFO  17:52:33,424 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:52Z] INFO  17:52:33,425 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:52Z] INFO  17:52:33,425 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:52Z] INFO  17:52:33,430 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/15/R14-18105_kapa-NGv3-PE100-NGv3-sort-15_83448996_98982979-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/15/R14-18105_kapa-NGv3-PE100-NGv3-15_83448996_98982979-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/15/tx/tmpRDNMtg/R14-18105_kapa-NGv3-PE100-NGv3-15_83448996_98982979.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:52Z] INFO  17:52:33,447 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:52Z] INFO  17:52:33,448 HelpFormatter - Date/Time: 2016/04/14 17:52:33
[2016-04-15T00:52Z] INFO  17:52:33,448 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:52Z] INFO  17:52:33,449 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:52Z] INFO  17:52:33,514 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:52Z] INFO  17:52:33,525 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:52Z] INFO  17:52:33,532 ProgressMeter -    12:122614454    945971.0    30.0 s      31.0 s       73.6%    40.0 s      10.0 s
[2016-04-15T00:52Z] GATK: UnifiedGenotyper
[2016-04-15T00:52Z] INFO  17:52:33,598 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-15T00:52Z] INFO  17:52:33,603 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:52Z] INFO  17:52:33,832 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:52Z] INFO  17:52:33,846 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:52Z] INFO  17:52:33,928 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-15T00:52Z] INFO  17:52:34,107 IntervalUtils - Processing 293221 bp from intervals
[2016-04-15T00:52Z] WARN  17:52:34,112 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:52Z] INFO  17:52:34,194 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:52Z] INFO  17:52:34,313 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:52Z] INFO  17:52:34,314 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:52Z] INFO  17:52:34,314 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:52Z] INFO  17:52:34,315 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:52Z] INFO  17:52:34,367 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:52Z] INFO  17:52:34,368 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:52Z] INFO  17:52:34,476 IntervalUtils - Processing 184993 bp from intervals
[2016-04-15T00:52Z] WARN  17:52:34,483 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:52Z] INFO  17:52:34,502 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:52Z] INFO  17:52:34,633 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:52Z] INFO  17:52:34,712 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:52Z] INFO  17:52:34,713 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:52Z] INFO  17:52:34,714 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:52Z] INFO  17:52:34,715 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:52Z] INFO  17:52:34,758 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:52Z] INFO  17:52:34,758 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:52Z] GATK: UnifiedGenotyper
[2016-04-15T00:52Z] INFO  17:52:36,079 ProgressMeter -            done   2754858.0    54.0 s      19.0 s      100.0%    54.0 s       0.0 s
[2016-04-15T00:52Z] INFO  17:52:36,079 ProgressMeter - Total runtime 54.28 secs, 0.90 min, 0.02 hours
[2016-04-15T00:52Z] INFO  17:52:36,080 MicroScheduler - 67917 reads were filtered out during the traversal out of approximately 807892 total reads (8.41%)
[2016-04-15T00:52Z] INFO  17:52:36,080 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:52Z] INFO  17:52:36,081 MicroScheduler -   -> 1235 reads (0.15% of total) failing BadMateFilter
[2016-04-15T00:52Z] INFO  17:52:36,081 MicroScheduler -   -> 66198 reads (8.19% of total) failing DuplicateReadFilter
[2016-04-15T00:52Z] INFO  17:52:36,081 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:52Z] INFO  17:52:36,082 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:52Z] INFO  17:52:36,082 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:52Z] INFO  17:52:36,082 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:52Z] INFO  17:52:36,090 MicroScheduler -   -> 484 reads (0.06% of total) failing UnmappedReadFilter
[2016-04-15T00:52Z] INFO  17:52:36,455 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:52Z] INFO  17:52:36,458 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:52Z] INFO  17:52:36,459 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:52Z] INFO  17:52:36,460 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:52Z] INFO  17:52:36,465 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/15/R14-18105_kapa-NGv3-PE100-NGv3-sort-15_98984299_102531392-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/15/R14-18105_kapa-NGv3-PE100-NGv3-15_98984299_102531392-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/15/tx/tmpzG1nco/R14-18105_kapa-NGv3-PE100-NGv3-15_98984299_102531392.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:52Z] INFO  17:52:36,505 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:52Z] INFO  17:52:36,506 HelpFormatter - Date/Time: 2016/04/14 17:52:36
[2016-04-15T00:52Z] INFO  17:52:36,506 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:52Z] INFO  17:52:36,506 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:52Z] INFO  17:52:36,774 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:52Z] INFO  17:52:36,996 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:52Z] INFO  17:52:37,012 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:52Z] INFO  17:52:37,094 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-15T00:52Z] INFO  17:52:37,532 IntervalUtils - Processing 49123 bp from intervals
[2016-04-15T00:52Z] WARN  17:52:37,537 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:52Z] INFO  17:52:37,551 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:52Z] INFO  17:52:37,668 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:52Z] INFO  17:52:37,746 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:52Z] INFO  17:52:37,747 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:52Z] INFO  17:52:37,748 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:52Z] INFO  17:52:37,748 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:52Z] INFO  17:52:37,808 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:52Z] INFO  17:52:37,809 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:52Z] GATK: UnifiedGenotyper
[2016-04-15T00:52Z] INFO  17:52:37,951 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:52Z] INFO  17:52:37,955 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:52Z] INFO  17:52:37,955 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:52Z] INFO  17:52:37,956 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:52Z] INFO  17:52:37,960 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/16/R14-18105_kapa-NGv3-PE100-NGv3-sort-16_0_15528616-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/16/R14-18105_kapa-NGv3-PE100-NGv3-16_0_15528616-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/16/tx/tmpAYKG4h/R14-18105_kapa-NGv3-PE100-NGv3-16_0_15528616.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:52Z] INFO  17:52:37,974 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:52Z] INFO  17:52:37,975 HelpFormatter - Date/Time: 2016/04/14 17:52:37
[2016-04-15T00:52Z] INFO  17:52:37,975 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:52Z] INFO  17:52:37,976 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:52Z] INFO  17:52:38,155 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:52Z] INFO  17:52:38,379 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:52Z] INFO  17:52:38,389 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:52Z] INFO  17:52:38,498 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.11
[2016-04-15T00:52Z] INFO  17:52:38,981 IntervalUtils - Processing 436708 bp from intervals
[2016-04-15T00:52Z] WARN  17:52:38,990 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:52Z] INFO  17:52:39,097 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:52Z] INFO  17:52:39,234 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:52Z] INFO  17:52:39,235 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:52Z] INFO  17:52:39,236 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:52Z] INFO  17:52:39,237 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:52Z] INFO  17:52:39,265 ProgressMeter -            done    291019.0    14.0 s      49.0 s       99.9%    14.0 s       0.0 s
[2016-04-15T00:52Z] INFO  17:52:39,266 ProgressMeter - Total runtime 14.42 secs, 0.24 min, 0.00 hours
[2016-04-15T00:52Z] INFO  17:52:39,266 MicroScheduler - 8899 reads were filtered out during the traversal out of approximately 110505 total reads (8.05%)
[2016-04-15T00:52Z] INFO  17:52:39,266 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:52Z] INFO  17:52:39,267 MicroScheduler -   -> 155 reads (0.14% of total) failing BadMateFilter
[2016-04-15T00:52Z] INFO  17:52:39,267 MicroScheduler -   -> 8673 reads (7.85% of total) failing DuplicateReadFilter
[2016-04-15T00:52Z] INFO  17:52:39,267 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:52Z] INFO  17:52:39,267 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:52Z] INFO  17:52:39,268 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:52Z] INFO  17:52:39,268 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:52Z] INFO  17:52:39,268 MicroScheduler -   -> 71 reads (0.06% of total) failing UnmappedReadFilter
[2016-04-15T00:52Z] INFO  17:52:39,310 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:52Z] INFO  17:52:39,311 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:52Z] INFO  17:52:40,598 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:52Z] GATK: UnifiedGenotyper
[2016-04-15T00:52Z] INFO  17:52:41,199 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:52Z] INFO  17:52:41,203 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:52Z] INFO  17:52:41,203 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:52Z] INFO  17:52:41,204 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:52Z] INFO  17:52:41,209 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/16/R14-18105_kapa-NGv3-PE100-NGv3-sort-16_15596122_31106473-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/16/R14-18105_kapa-NGv3-PE100-NGv3-16_15596122_31106473-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/16/tx/tmpGw4ZEz/R14-18105_kapa-NGv3-PE100-NGv3-16_15596122_31106473.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:52Z] INFO  17:52:41,221 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:52Z] INFO  17:52:41,223 HelpFormatter - Date/Time: 2016/04/14 17:52:41
[2016-04-15T00:52Z] INFO  17:52:41,223 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:52Z] INFO  17:52:41,224 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:52Z] INFO  17:52:41,370 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:52Z] INFO  17:52:41,676 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:52Z] INFO  17:52:41,696 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:52Z] INFO  17:52:41,783 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.09
[2016-04-15T00:52Z] INFO  17:52:42,252 IntervalUtils - Processing 400248 bp from intervals
[2016-04-15T00:52Z] WARN  17:52:42,257 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:52Z] INFO  17:52:42,334 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:52Z] INFO  17:52:42,431 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:52Z] INFO  17:52:42,433 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:52Z] INFO  17:52:42,433 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:52Z] INFO  17:52:42,434 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:52Z] INFO  17:52:42,476 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:52Z] INFO  17:52:42,477 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:52Z] INFO  17:52:42,998 ProgressMeter -            done   1353894.0    39.0 s      29.0 s      100.0%    39.0 s       0.0 s
[2016-04-15T00:52Z] INFO  17:52:42,998 ProgressMeter - Total runtime 39.50 secs, 0.66 min, 0.01 hours
[2016-04-15T00:52Z] INFO  17:52:42,999 MicroScheduler - 43924 reads were filtered out during the traversal out of approximately 532507 total reads (8.25%)
[2016-04-15T00:52Z] INFO  17:52:42,999 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:52Z] INFO  17:52:42,999 MicroScheduler -   -> 713 reads (0.13% of total) failing BadMateFilter
[2016-04-15T00:52Z] INFO  17:52:42,999 MicroScheduler -   -> 42873 reads (8.05% of total) failing DuplicateReadFilter
[2016-04-15T00:52Z] INFO  17:52:43,000 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:52Z] INFO  17:52:43,000 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:52Z] INFO  17:52:43,000 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:52Z] INFO  17:52:43,000 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:52Z] INFO  17:52:43,001 MicroScheduler -   -> 338 reads (0.06% of total) failing UnmappedReadFilter
[2016-04-15T00:52Z] INFO  17:52:43,505 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:52Z] INFO  17:52:43,509 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:52Z] INFO  17:52:43,509 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:52Z] INFO  17:52:43,510 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:52Z] INFO  17:52:43,514 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/16/R14-18105_kapa-NGv3-PE100-NGv3-sort-16_31120544_46629582-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/16/R14-18105_kapa-NGv3-PE100-NGv3-16_31120544_46629582-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/16/tx/tmpKGEC5p/R14-18105_kapa-NGv3-PE100-NGv3-16_31120544_46629582.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:52Z] INFO  17:52:43,522 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:52Z] INFO  17:52:43,523 HelpFormatter - Date/Time: 2016/04/14 17:52:43
[2016-04-15T00:52Z] INFO  17:52:43,523 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:52Z] INFO  17:52:43,523 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:52Z] INFO  17:52:43,672 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:52Z] INFO  17:52:43,776 ProgressMeter -            done   3065212.0    49.0 s      16.0 s      100.0%    49.0 s       0.0 s
[2016-04-15T00:52Z] INFO  17:52:43,776 ProgressMeter - Total runtime 49.46 secs, 0.82 min, 0.01 hours
[2016-04-15T00:52Z] INFO  17:52:43,776 MicroScheduler - 64718 reads were filtered out during the traversal out of approximately 780214 total reads (8.29%)
[2016-04-15T00:52Z] INFO  17:52:43,777 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:52Z] INFO  17:52:43,777 MicroScheduler -   -> 1094 reads (0.14% of total) failing BadMateFilter
[2016-04-15T00:52Z] INFO  17:52:43,777 MicroScheduler -   -> 63127 reads (8.09% of total) failing DuplicateReadFilter
[2016-04-15T00:52Z] INFO  17:52:43,777 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:52Z] INFO  17:52:43,778 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:52Z] INFO  17:52:43,778 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:52Z] INFO  17:52:43,778 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:52Z] INFO  17:52:43,778 MicroScheduler -   -> 497 reads (0.06% of total) failing UnmappedReadFilter
[2016-04-15T00:52Z] INFO  17:52:43,909 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:52Z] INFO  17:52:43,920 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:52Z] INFO  17:52:43,999 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-15T00:52Z] INFO  17:52:44,379 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:52Z] INFO  17:52:44,451 IntervalUtils - Processing 40143 bp from intervals
[2016-04-15T00:52Z] WARN  17:52:44,456 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:52Z] INFO  17:52:44,541 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:52Z] INFO  17:52:44,604 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:52Z] INFO  17:52:44,606 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:52Z] INFO  17:52:44,606 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:52Z] INFO  17:52:44,607 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:52Z] INFO  17:52:44,663 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:52Z] INFO  17:52:44,663 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:52Z] GATK: UnifiedGenotyper
[2016-04-15T00:52Z] INFO  17:52:45,012 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:52Z] GATK: UnifiedGenotyper
[2016-04-15T00:52Z] INFO  17:52:47,000 ProgressMeter -            done    545455.0    21.0 s      38.0 s      100.0%    21.0 s       0.0 s
[2016-04-15T00:52Z] INFO  17:52:47,000 ProgressMeter - Total runtime 21.04 secs, 0.35 min, 0.01 hours
[2016-04-15T00:52Z] INFO  17:52:47,001 MicroScheduler - 18327 reads were filtered out during the traversal out of approximately 221577 total reads (8.27%)
[2016-04-15T00:52Z] INFO  17:52:47,001 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:52Z] INFO  17:52:47,001 MicroScheduler -   -> 300 reads (0.14% of total) failing BadMateFilter
[2016-04-15T00:52Z] INFO  17:52:47,001 MicroScheduler -   -> 17906 reads (8.08% of total) failing DuplicateReadFilter
[2016-04-15T00:52Z] INFO  17:52:47,002 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:52Z] INFO  17:52:47,002 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:52Z] INFO  17:52:47,002 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:52Z] INFO  17:52:47,002 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:52Z] INFO  17:52:47,003 MicroScheduler -   -> 121 reads (0.05% of total) failing UnmappedReadFilter
[2016-04-15T00:52Z] INFO  17:52:47,426 ProgressMeter -            done    131383.0     9.0 s      73.0 s      100.0%     9.0 s       0.0 s
[2016-04-15T00:52Z] INFO  17:52:47,427 ProgressMeter - Total runtime 9.68 secs, 0.16 min, 0.00 hours
[2016-04-15T00:52Z] INFO  17:52:47,427 MicroScheduler - 6060 reads were filtered out during the traversal out of approximately 71548 total reads (8.47%)
[2016-04-15T00:52Z] INFO  17:52:47,427 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:52Z] INFO  17:52:47,428 MicroScheduler -   -> 108 reads (0.15% of total) failing BadMateFilter
[2016-04-15T00:52Z] INFO  17:52:47,428 MicroScheduler -   -> 5909 reads (8.26% of total) failing DuplicateReadFilter
[2016-04-15T00:52Z] INFO  17:52:47,428 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:52Z] INFO  17:52:47,428 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:52Z] INFO  17:52:47,429 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:52Z] INFO  17:52:47,429 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:52Z] INFO  17:52:47,429 MicroScheduler -   -> 43 reads (0.06% of total) failing UnmappedReadFilter
[2016-04-15T00:52Z] INFO  17:52:47,577 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:52Z] INFO  17:52:47,580 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:52Z] INFO  17:52:47,580 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:52Z] INFO  17:52:47,580 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:52Z] INFO  17:52:47,584 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/16/R14-18105_kapa-NGv3-PE100-NGv3-sort-16_46633742_64982002-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/16/R14-18105_kapa-NGv3-PE100-NGv3-16_46633742_64982002-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/16/tx/tmp7anLQ_/R14-18105_kapa-NGv3-PE100-NGv3-16_46633742_64982002.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:52Z] INFO  17:52:47,609 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:52Z] INFO  17:52:47,609 HelpFormatter - Date/Time: 2016/04/14 17:52:47
[2016-04-15T00:52Z] INFO  17:52:47,609 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:52Z] INFO  17:52:47,610 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:52Z] INFO  17:52:47,803 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:52Z] INFO  17:52:47,979 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:52Z] INFO  17:52:47,988 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:52Z] INFO  17:52:48,054 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-15T00:52Z] INFO  17:52:48,333 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:52Z] INFO  17:52:48,649 IntervalUtils - Processing 224129 bp from intervals
[2016-04-15T00:52Z] WARN  17:52:48,654 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:52Z] GATK: UnifiedGenotyper
[2016-04-15T00:52Z] INFO  17:52:48,703 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:52Z] INFO  17:52:48,707 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:52Z] INFO  17:52:48,707 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:52Z] INFO  17:52:48,708 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:52Z] INFO  17:52:48,713 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/16/R14-18105_kapa-NGv3-PE100-NGv3-sort-16_64982511_80574976-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/16/R14-18105_kapa-NGv3-PE100-NGv3-16_64982511_80574976-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/16/tx/tmpIzUKnh/R14-18105_kapa-NGv3-PE100-NGv3-16_64982511_80574976.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:52Z] INFO  17:52:48,730 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:52Z] INFO  17:52:48,730 HelpFormatter - Date/Time: 2016/04/14 17:52:48
[2016-04-15T00:52Z] INFO  17:52:48,730 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:52Z] INFO  17:52:48,731 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:52Z] INFO  17:52:48,745 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:52Z] INFO  17:52:48,829 ProgressMeter -            done    695639.0    23.0 s      33.0 s      100.0%    23.0 s       0.0 s
[2016-04-15T00:52Z] INFO  17:52:48,829 ProgressMeter - Total runtime 23.06 secs, 0.38 min, 0.01 hours
[2016-04-15T00:52Z] INFO  17:52:48,830 MicroScheduler - 21881 reads were filtered out during the traversal out of approximately 264915 total reads (8.26%)
[2016-04-15T00:52Z] INFO  17:52:48,830 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:52Z] INFO  17:52:48,830 MicroScheduler -   -> 368 reads (0.14% of total) failing BadMateFilter
[2016-04-15T00:52Z] INFO  17:52:48,830 MicroScheduler -   -> 21351 reads (8.06% of total) failing DuplicateReadFilter
[2016-04-15T00:52Z] INFO  17:52:48,831 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:52Z] INFO  17:52:48,831 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:52Z] INFO  17:52:48,831 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:52Z] INFO  17:52:48,831 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:52Z] INFO  17:52:48,832 MicroScheduler -   -> 162 reads (0.06% of total) failing UnmappedReadFilter
[2016-04-15T00:52Z] INFO  17:52:48,841 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:52Z] INFO  17:52:48,842 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:52Z] INFO  17:52:48,843 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:52Z] INFO  17:52:48,843 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:52Z] INFO  17:52:48,877 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:52Z] INFO  17:52:48,883 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:52Z] INFO  17:52:48,893 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:52Z] INFO  17:52:48,894 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:52Z] INFO  17:52:49,118 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:52Z] INFO  17:52:49,127 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:52Z] INFO  17:52:49,231 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.10
[2016-04-15T00:52Z] GATK: UnifiedGenotyper
[2016-04-15T00:52Z] INFO  17:52:49,817 IntervalUtils - Processing 344918 bp from intervals
[2016-04-15T00:52Z] WARN  17:52:49,824 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:52Z] INFO  17:52:49,858 ProgressMeter -            done    817418.0    23.0 s      28.0 s      100.0%    23.0 s       0.0 s
[2016-04-15T00:52Z] INFO  17:52:49,859 ProgressMeter - Total runtime 23.51 secs, 0.39 min, 0.01 hours
[2016-04-15T00:52Z] INFO  17:52:49,859 MicroScheduler - 25581 reads were filtered out during the traversal out of approximately 300278 total reads (8.52%)
[2016-04-15T00:52Z] INFO  17:52:49,860 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:52Z] INFO  17:52:49,860 MicroScheduler -   -> 438 reads (0.15% of total) failing BadMateFilter
[2016-04-15T00:52Z] INFO  17:52:49,860 MicroScheduler -   -> 24930 reads (8.30% of total) failing DuplicateReadFilter
[2016-04-15T00:52Z] INFO  17:52:49,860 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:52Z] INFO  17:52:49,861 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:52Z] INFO  17:52:49,861 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:52Z] INFO  17:52:49,861 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:52Z] INFO  17:52:49,861 MicroScheduler -   -> 213 reads (0.07% of total) failing UnmappedReadFilter
[2016-04-15T00:52Z] INFO  17:52:49,906 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:52Z] INFO  17:52:50,053 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:52Z] INFO  17:52:50,054 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:52Z] INFO  17:52:50,054 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:52Z] INFO  17:52:50,055 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:52Z] INFO  17:52:50,110 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:52Z] INFO  17:52:50,122 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:52Z] INFO  17:52:50,277 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:52Z] GATK: UnifiedGenotyper
[2016-04-15T00:52Z] INFO  17:52:51,232 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:52Z] GATK: UnifiedGenotyper
[2016-04-15T00:52Z] INFO  17:52:51,787 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:52Z] INFO  17:52:51,793 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:52Z] INFO  17:52:51,794 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:52Z] INFO  17:52:51,794 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:52Z] INFO  17:52:51,799 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/16/R14-18105_kapa-NGv3-PE100-NGv3-sort-16_80575258_90354753-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/16/R14-18105_kapa-NGv3-PE100-NGv3-16_80575258_90354753-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/16/tx/tmpafoCsZ/R14-18105_kapa-NGv3-PE100-NGv3-16_80575258_90354753.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:52Z] INFO  17:52:51,813 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:52Z] INFO  17:52:51,814 HelpFormatter - Date/Time: 2016/04/14 17:52:51
[2016-04-15T00:52Z] INFO  17:52:51,814 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:52Z] INFO  17:52:51,815 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:52Z] INFO  17:52:51,964 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:52Z] INFO  17:52:52,064 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:52Z] INFO  17:52:52,067 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:52Z] INFO  17:52:52,068 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:52Z] INFO  17:52:52,068 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:52Z] INFO  17:52:52,073 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/17/R14-18105_kapa-NGv3-PE100-NGv3-sort-17_0_15511002-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/17/R14-18105_kapa-NGv3-PE100-NGv3-17_0_15511002-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/17/tx/tmpKIYmPv/R14-18105_kapa-NGv3-PE100-NGv3-17_0_15511002.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:52Z] INFO  17:52:52,082 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:52Z] INFO  17:52:52,083 HelpFormatter - Date/Time: 2016/04/14 17:52:52
[2016-04-15T00:52Z] INFO  17:52:52,083 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:52Z] INFO  17:52:52,084 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:52Z] INFO  17:52:52,192 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:52Z] INFO  17:52:52,201 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:52Z] INFO  17:52:52,267 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:52Z] INFO  17:52:52,298 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.10
[2016-04-15T00:52Z] INFO  17:52:52,550 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:52Z] INFO  17:52:52,562 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:52Z] INFO  17:52:52,648 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-15T00:52Z] INFO  17:52:52,769 IntervalUtils - Processing 203451 bp from intervals
[2016-04-15T00:52Z] WARN  17:52:52,775 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:52Z] INFO  17:52:52,802 ProgressMeter -            done    240450.0     8.0 s      34.0 s      100.0%     8.0 s       0.0 s
[2016-04-15T00:52Z] INFO  17:52:52,803 ProgressMeter - Total runtime 8.20 secs, 0.14 min, 0.00 hours
[2016-04-15T00:52Z] INFO  17:52:52,804 MicroScheduler - 5297 reads were filtered out during the traversal out of approximately 70499 total reads (7.51%)
[2016-04-15T00:52Z] INFO  17:52:52,805 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:52Z] INFO  17:52:52,806 MicroScheduler -   -> 127 reads (0.18% of total) failing BadMateFilter
[2016-04-15T00:52Z] INFO  17:52:52,806 MicroScheduler -   -> 5125 reads (7.27% of total) failing DuplicateReadFilter
[2016-04-15T00:52Z] INFO  17:52:52,807 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:52Z] INFO  17:52:52,808 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:52Z] INFO  17:52:52,808 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:52Z] INFO  17:52:52,809 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:52Z] INFO  17:52:52,810 MicroScheduler -   -> 45 reads (0.06% of total) failing UnmappedReadFilter
[2016-04-15T00:52Z] INFO  17:52:52,896 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:52Z] INFO  17:52:53,002 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:52Z] INFO  17:52:53,003 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:52Z] INFO  17:52:53,004 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:52Z] INFO  17:52:53,005 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:52Z] INFO  17:52:53,057 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:52Z] INFO  17:52:53,058 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:52Z] INFO  17:52:53,093 ProgressMeter -     14:25325242   1549526.0    30.0 s      19.0 s       82.1%    36.0 s       6.0 s
[2016-04-15T00:52Z] INFO  17:52:53,182 IntervalUtils - Processing 497719 bp from intervals
[2016-04-15T00:52Z] WARN  17:52:53,189 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:52Z] INFO  17:52:53,307 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:52Z] INFO  17:52:53,457 ProgressMeter -            done    633510.0    23.0 s      36.0 s      100.0%    23.0 s       0.0 s
[2016-04-15T00:52Z] INFO  17:52:53,457 ProgressMeter - Total runtime 23.25 secs, 0.39 min, 0.01 hours
[2016-04-15T00:52Z] INFO  17:52:53,458 MicroScheduler - 20668 reads were filtered out during the traversal out of approximately 281073 total reads (7.35%)
[2016-04-15T00:52Z] INFO  17:52:53,458 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:52Z] INFO  17:52:53,458 MicroScheduler -   -> 452 reads (0.16% of total) failing BadMateFilter
[2016-04-15T00:52Z] INFO  17:52:53,458 MicroScheduler -   -> 20052 reads (7.13% of total) failing DuplicateReadFilter
[2016-04-15T00:52Z] INFO  17:52:53,459 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:52Z] INFO  17:52:53,459 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:52Z] INFO  17:52:53,459 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:52Z] INFO  17:52:53,459 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:52Z] INFO  17:52:53,460 MicroScheduler -   -> 164 reads (0.06% of total) failing UnmappedReadFilter
[2016-04-15T00:52Z] INFO  17:52:53,479 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:52Z] INFO  17:52:53,485 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:52Z] INFO  17:52:53,486 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:52Z] INFO  17:52:53,488 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:52Z] INFO  17:52:53,485 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:52Z] INFO  17:52:53,489 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:52Z] INFO  17:52:53,489 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:52Z] INFO  17:52:53,490 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:52Z] INFO  17:52:53,494 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/17/R14-18105_kapa-NGv3-PE100-NGv3-sort-17_15515955_31039213-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/17/R14-18105_kapa-NGv3-PE100-NGv3-17_15515955_31039213-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/17/tx/tmpbV37L8/R14-18105_kapa-NGv3-PE100-NGv3-17_15515955_31039213.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:52Z] INFO  17:52:53,519 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:52Z] INFO  17:52:53,520 HelpFormatter - Date/Time: 2016/04/14 17:52:53
[2016-04-15T00:52Z] INFO  17:52:53,520 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:52Z] INFO  17:52:53,521 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:52Z] INFO  17:52:53,538 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:52Z] INFO  17:52:53,539 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:52Z] INFO  17:52:53,711 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:52Z] INFO  17:52:54,055 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:52Z] INFO  17:52:54,070 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:52Z] INFO  17:52:54,148 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-15T00:52Z] INFO  17:52:54,310 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:52Z] INFO  17:52:54,601 ProgressMeter -            done    727916.0    28.0 s      39.0 s      100.0%    28.0 s       0.0 s
[2016-04-15T00:52Z] INFO  17:52:54,601 ProgressMeter - Total runtime 28.85 secs, 0.48 min, 0.01 hours
[2016-04-15T00:52Z] INFO  17:52:54,602 MicroScheduler - 28652 reads were filtered out during the traversal out of approximately 340548 total reads (8.41%)
[2016-04-15T00:52Z] INFO  17:52:54,602 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:52Z] INFO  17:52:54,602 MicroScheduler -   -> 464 reads (0.14% of total) failing BadMateFilter
[2016-04-15T00:52Z] INFO  17:52:54,603 MicroScheduler -   -> 27993 reads (8.22% of total) failing DuplicateReadFilter
[2016-04-15T00:52Z] INFO  17:52:54,603 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:52Z] INFO  17:52:54,603 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:52Z] INFO  17:52:54,604 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:52Z] INFO  17:52:54,604 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:52Z] INFO  17:52:54,604 MicroScheduler -   -> 195 reads (0.06% of total) failing UnmappedReadFilter
[2016-04-15T00:52Z] INFO  17:52:54,619 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:52Z] INFO  17:52:54,634 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:52Z] INFO  17:52:54,635 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:52Z] INFO  17:52:54,636 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:52Z] INFO  17:52:54,642 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/17/R14-18105_kapa-NGv3-PE100-NGv3-sort-17_31048040_46607237-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/17/R14-18105_kapa-NGv3-PE100-NGv3-17_31048040_46607237-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/17/tx/tmpIb9AgN/R14-18105_kapa-NGv3-PE100-NGv3-17_31048040_46607237.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:52Z] INFO  17:52:54,661 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:52Z] INFO  17:52:54,662 HelpFormatter - Date/Time: 2016/04/14 17:52:54
[2016-04-15T00:52Z] INFO  17:52:54,663 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:52Z] INFO  17:52:54,663 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:52Z] INFO  17:52:54,669 IntervalUtils - Processing 320055 bp from intervals
[2016-04-15T00:52Z] WARN  17:52:54,674 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:52Z] GATK: UnifiedGenotyper
[2016-04-15T00:52Z] INFO  17:52:54,741 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:52Z] INFO  17:52:54,819 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:52Z] INFO  17:52:54,819 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:52Z] INFO  17:52:54,820 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:52Z] INFO  17:52:54,820 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:52Z] INFO  17:52:54,864 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:52Z] INFO  17:52:54,878 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:52Z] INFO  17:52:54,879 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:52Z] INFO  17:52:54,931 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:52Z] INFO  17:52:55,073 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:52Z] INFO  17:52:55,082 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:52Z] INFO  17:52:55,159 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-15T00:52Z] GATK: UnifiedGenotyper
[2016-04-15T00:52Z] INFO  17:52:55,729 IntervalUtils - Processing 543518 bp from intervals
[2016-04-15T00:52Z] WARN  17:52:55,748 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:52Z] INFO  17:52:55,826 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:52Z] INFO  17:52:55,963 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:52Z] INFO  17:52:55,964 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:52Z] INFO  17:52:55,964 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:52Z] INFO  17:52:55,965 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:52Z] INFO  17:52:56,009 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:52Z] INFO  17:52:56,010 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:52Z] INFO  17:52:56,054 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:52Z] GATK: UnifiedGenotyper
[2016-04-15T00:52Z] INFO  17:52:57,046 ProgressMeter -            done   1676712.0    33.0 s      20.0 s      100.0%    33.0 s       0.0 s
[2016-04-15T00:52Z] INFO  17:52:57,046 ProgressMeter - Total runtime 33.98 secs, 0.57 min, 0.01 hours
[2016-04-15T00:52Z] INFO  17:52:57,047 MicroScheduler - 37954 reads were filtered out during the traversal out of approximately 455471 total reads (8.33%)
[2016-04-15T00:52Z] INFO  17:52:57,047 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:52Z] INFO  17:52:57,047 MicroScheduler -   -> 686 reads (0.15% of total) failing BadMateFilter
[2016-04-15T00:52Z] INFO  17:52:57,048 MicroScheduler -   -> 36994 reads (8.12% of total) failing DuplicateReadFilter
[2016-04-15T00:52Z] INFO  17:52:57,048 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:52Z] INFO  17:52:57,048 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:52Z] INFO  17:52:57,048 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:52Z] INFO  17:52:57,048 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:52Z] INFO  17:52:57,049 MicroScheduler -   -> 274 reads (0.06% of total) failing UnmappedReadFilter
[2016-04-15T00:52Z] INFO  17:52:57,589 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:52Z] INFO  17:52:57,592 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:52Z] INFO  17:52:57,592 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:52Z] INFO  17:52:57,592 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:52Z] INFO  17:52:57,596 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/17/R14-18105_kapa-NGv3-PE100-NGv3-sort-17_46607689_62121560-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/17/R14-18105_kapa-NGv3-PE100-NGv3-17_46607689_62121560-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/17/tx/tmpbITl3S/R14-18105_kapa-NGv3-PE100-NGv3-17_46607689_62121560.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:52Z] INFO  17:52:57,627 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:52Z] INFO  17:52:57,628 HelpFormatter - Date/Time: 2016/04/14 17:52:57
[2016-04-15T00:52Z] INFO  17:52:57,629 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:52Z] INFO  17:52:57,630 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:52Z] INFO  17:52:57,806 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:52Z] INFO  17:52:58,019 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:52Z] INFO  17:52:58,028 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:52Z] INFO  17:52:58,037 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:52Z] INFO  17:52:58,040 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:52Z] INFO  17:52:58,041 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:52Z] INFO  17:52:58,041 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:52Z] INFO  17:52:58,046 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/17/R14-18105_kapa-NGv3-PE100-NGv3-sort-17_62122219_77705154-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/17/R14-18105_kapa-NGv3-PE100-NGv3-17_62122219_77705154-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/17/tx/tmp82pKGv/R14-18105_kapa-NGv3-PE100-NGv3-17_62122219_77705154.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:52Z] INFO  17:52:58,057 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:52Z] INFO  17:52:58,058 HelpFormatter - Date/Time: 2016/04/14 17:52:58
[2016-04-15T00:52Z] INFO  17:52:58,059 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:52Z] INFO  17:52:58,059 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:52Z] INFO  17:52:58,132 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.10
[2016-04-15T00:52Z] INFO  17:52:58,223 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:52Z] INFO  17:52:58,233 ProgressMeter -            done    711142.0    23.0 s      33.0 s      100.0%    23.0 s       0.0 s
[2016-04-15T00:52Z] INFO  17:52:58,234 ProgressMeter - Total runtime 23.52 secs, 0.39 min, 0.01 hours
[2016-04-15T00:52Z] INFO  17:52:58,234 MicroScheduler - 22442 reads were filtered out during the traversal out of approximately 279688 total reads (8.02%)
[2016-04-15T00:52Z] INFO  17:52:58,235 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:52Z] INFO  17:52:58,235 MicroScheduler -   -> 358 reads (0.13% of total) failing BadMateFilter
[2016-04-15T00:52Z] INFO  17:52:58,235 MicroScheduler -   -> 21898 reads (7.83% of total) failing DuplicateReadFilter
[2016-04-15T00:52Z] INFO  17:52:58,235 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:52Z] INFO  17:52:58,236 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:52Z] INFO  17:52:58,236 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:52Z] INFO  17:52:58,236 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:52Z] INFO  17:52:58,236 MicroScheduler -   -> 186 reads (0.07% of total) failing UnmappedReadFilter
[2016-04-15T00:52Z] INFO  17:52:58,432 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:52Z] INFO  17:52:58,437 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:52Z] INFO  17:52:58,447 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:52Z] INFO  17:52:58,577 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.13
[2016-04-15T00:52Z] INFO  17:52:58,633 IntervalUtils - Processing 295968 bp from intervals
[2016-04-15T00:52Z] WARN  17:52:58,638 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:52Z] GATK: UnifiedGenotyper
[2016-04-15T00:52Z] INFO  17:52:58,709 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:52Z] INFO  17:52:58,842 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:52Z] INFO  17:52:58,842 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:52Z] INFO  17:52:58,843 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:52Z] INFO  17:52:58,843 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:52Z] INFO  17:52:58,905 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:52Z] INFO  17:52:58,906 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:52Z] INFO  17:52:59,129 IntervalUtils - Processing 345298 bp from intervals
[2016-04-15T00:52Z] WARN  17:52:59,134 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:52Z] INFO  17:52:59,240 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:52Z] INFO  17:52:59,347 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:52Z] INFO  17:52:59,348 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:52Z] INFO  17:52:59,348 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:52Z] INFO  17:52:59,349 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:52Z] INFO  17:52:59,372 ProgressMeter -            done    802075.0    26.0 s      32.0 s      100.0%    26.0 s       0.0 s
[2016-04-15T00:52Z] INFO  17:52:59,372 ProgressMeter - Total runtime 26.36 secs, 0.44 min, 0.01 hours
[2016-04-15T00:52Z] INFO  17:52:59,372 MicroScheduler - 25967 reads were filtered out during the traversal out of approximately 318905 total reads (8.14%)
[2016-04-15T00:52Z] INFO  17:52:59,373 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:52Z] INFO  17:52:59,373 MicroScheduler -   -> 438 reads (0.14% of total) failing BadMateFilter
[2016-04-15T00:52Z] INFO  17:52:59,373 MicroScheduler -   -> 25332 reads (7.94% of total) failing DuplicateReadFilter
[2016-04-15T00:52Z] INFO  17:52:59,373 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:52Z] INFO  17:52:59,374 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:52Z] INFO  17:52:59,374 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:52Z] INFO  17:52:59,374 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:52Z] INFO  17:52:59,374 MicroScheduler -   -> 197 reads (0.06% of total) failing UnmappedReadFilter
[2016-04-15T00:52Z] INFO  17:52:59,394 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:52Z] INFO  17:52:59,395 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:52Z] INFO  17:52:59,704 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:52Z] INFO  17:52:59,715 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:52Z] INFO  17:52:59,716 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:52Z] INFO  17:52:59,716 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:52Z] INFO  17:52:59,720 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/17/R14-18105_kapa-NGv3-PE100-NGv3-sort-17_77707305_81195210-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/17/R14-18105_kapa-NGv3-PE100-NGv3-17_77707305_81195210-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/17/tx/tmphuISls/R14-18105_kapa-NGv3-PE100-NGv3-17_77707305_81195210.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:52Z] INFO  17:52:59,745 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:52Z] INFO  17:52:59,741 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:52Z] INFO  17:52:59,748 HelpFormatter - Date/Time: 2016/04/14 17:52:59
[2016-04-15T00:52Z] INFO  17:52:59,748 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:52Z] INFO  17:52:59,757 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:52Z] INFO  17:52:59,946 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:53Z] GATK: UnifiedGenotyper
[2016-04-15T00:53Z] INFO  17:53:00,229 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:53Z] INFO  17:53:00,238 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:53Z] INFO  17:53:00,320 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-15T00:53Z] INFO  17:53:00,686 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:53Z] INFO  17:53:00,702 ProgressMeter -     15:45491070   1497573.0    30.0 s      20.0 s       74.5%    40.0 s      10.0 s
[2016-04-15T00:53Z] INFO  17:53:00,862 IntervalUtils - Processing 160149 bp from intervals
[2016-04-15T00:53Z] WARN  17:53:00,868 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:53Z] INFO  17:53:00,958 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:53Z] GATK: UnifiedGenotyper
[2016-04-15T00:53Z] INFO  17:53:01,015 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:53Z] INFO  17:53:01,016 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:53Z] INFO  17:53:01,016 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:53Z] INFO  17:53:01,017 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:53Z] INFO  17:53:01,060 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:53Z] INFO  17:53:01,061 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:53Z] INFO  17:53:02,033 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:53Z] INFO  17:53:02,051 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:53Z] INFO  17:53:02,052 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:53Z] INFO  17:53:02,053 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:53Z] INFO  17:53:02,058 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/18/R14-18105_kapa-NGv3-PE100-NGv3-sort-18_0_18531348-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/18/R14-18105_kapa-NGv3-PE100-NGv3-18_0_18531348-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/18/tx/tmpMP8AdK/R14-18105_kapa-NGv3-PE100-NGv3-18_0_18531348.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:53Z] INFO  17:53:02,079 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:53Z] INFO  17:53:02,080 HelpFormatter - Date/Time: 2016/04/14 17:53:02
[2016-04-15T00:53Z] INFO  17:53:02,080 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:53Z] INFO  17:53:02,080 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:53Z] INFO  17:53:02,313 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:53Z] INFO  17:53:02,507 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:53Z] INFO  17:53:02,518 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:53Z] INFO  17:53:02,591 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-15T00:53Z] INFO  17:53:03,137 IntervalUtils - Processing 162632 bp from intervals
[2016-04-15T00:53Z] WARN  17:53:03,154 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:53Z] INFO  17:53:03,282 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:53Z] INFO  17:53:03,392 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:53Z] INFO  17:53:03,404 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:53Z] INFO  17:53:03,404 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:53Z] INFO  17:53:03,405 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:53Z] INFO  17:53:03,492 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:53Z] INFO  17:53:03,502 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:53Z] INFO  17:53:03,719 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:53Z] INFO  17:53:03,722 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:53Z] INFO  17:53:03,722 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:53Z] INFO  17:53:03,723 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:53Z] INFO  17:53:03,728 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/18/R14-18105_kapa-NGv3-PE100-NGv3-sort-18_18533538_34081962-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/18/R14-18105_kapa-NGv3-PE100-NGv3-18_18533538_34081962-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/18/tx/tmp4H943a/R14-18105_kapa-NGv3-PE100-NGv3-18_18533538_34081962.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:53Z] INFO  17:53:03,760 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:53Z] INFO  17:53:03,761 HelpFormatter - Date/Time: 2016/04/14 17:53:03
[2016-04-15T00:53Z] INFO  17:53:03,766 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:53Z] INFO  17:53:03,766 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:53Z] INFO  17:53:03,961 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:53Z] INFO  17:53:04,215 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:53Z] INFO  17:53:04,247 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:53Z] INFO  17:53:04,245 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:53Z] INFO  17:53:04,249 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:53Z] INFO  17:53:04,249 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:53Z] INFO  17:53:04,250 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:53Z] INFO  17:53:04,254 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/18/R14-18105_kapa-NGv3-PE100-NGv3-sort-18_34092400_49867248-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/18/R14-18105_kapa-NGv3-PE100-NGv3-18_34092400_49867248-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/18/tx/tmpQCR6In/R14-18105_kapa-NGv3-PE100-NGv3-18_34092400_49867248.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:53Z] INFO  17:53:04,275 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:53Z] INFO  17:53:04,276 HelpFormatter - Date/Time: 2016/04/14 17:53:04
[2016-04-15T00:53Z] INFO  17:53:04,276 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:53Z] INFO  17:53:04,276 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:53Z] INFO  17:53:04,340 ProgressMeter -     15:81614849    968187.0    30.0 s      31.0 s       92.4%    32.0 s       2.0 s
[2016-04-15T00:53Z] INFO  17:53:04,355 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.11
[2016-04-15T00:53Z] INFO  17:53:04,442 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:53Z] INFO  17:53:04,703 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:53Z] INFO  17:53:04,714 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:53Z] INFO  17:53:04,797 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-15T00:53Z] INFO  17:53:04,815 IntervalUtils - Processing 148606 bp from intervals
[2016-04-15T00:53Z] WARN  17:53:04,821 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:53Z] INFO  17:53:04,942 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:53Z] INFO  17:53:05,047 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:53Z] INFO  17:53:05,048 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:53Z] INFO  17:53:05,048 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:53Z] INFO  17:53:05,049 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:53Z] INFO  17:53:05,096 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:53Z] INFO  17:53:05,097 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:53Z] INFO  17:53:05,314 IntervalUtils - Processing 116317 bp from intervals
[2016-04-15T00:53Z] WARN  17:53:05,323 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:53Z] INFO  17:53:05,397 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:53Z] INFO  17:53:05,481 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:53Z] INFO  17:53:05,482 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:53Z] INFO  17:53:05,483 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:53Z] INFO  17:53:05,484 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:53Z] INFO  17:53:05,552 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:53Z] INFO  17:53:05,563 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:53Z] INFO  17:53:06,657 ProgressMeter -            done   1052407.0    32.0 s      30.0 s      100.0%    32.0 s       0.0 s
[2016-04-15T00:53Z] INFO  17:53:06,658 ProgressMeter - Total runtime 32.34 secs, 0.54 min, 0.01 hours
[2016-04-15T00:53Z] INFO  17:53:06,658 MicroScheduler - 34647 reads were filtered out during the traversal out of approximately 438419 total reads (7.90%)
[2016-04-15T00:53Z] INFO  17:53:06,658 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:53Z] INFO  17:53:06,659 MicroScheduler -   -> 657 reads (0.15% of total) failing BadMateFilter
[2016-04-15T00:53Z] INFO  17:53:06,659 MicroScheduler -   -> 33744 reads (7.70% of total) failing DuplicateReadFilter
[2016-04-15T00:53Z] INFO  17:53:06,659 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:53Z] INFO  17:53:06,659 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:53Z] INFO  17:53:06,660 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:53Z] INFO  17:53:06,660 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:53Z] INFO  17:53:06,663 MicroScheduler -   -> 246 reads (0.06% of total) failing UnmappedReadFilter
[2016-04-15T00:53Z] INFO  17:53:08,182 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:53Z] GATK: UnifiedGenotyper
[2016-04-15T00:53Z] INFO  17:53:08,463 ProgressMeter -            done   1805916.0    37.0 s      20.0 s      100.0%    37.0 s       0.0 s
[2016-04-15T00:53Z] INFO  17:53:08,463 ProgressMeter - Total runtime 37.79 secs, 0.63 min, 0.01 hours
[2016-04-15T00:53Z] INFO  17:53:08,463 MicroScheduler - 42120 reads were filtered out during the traversal out of approximately 519972 total reads (8.10%)
[2016-04-15T00:53Z] INFO  17:53:08,464 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:53Z] INFO  17:53:08,464 MicroScheduler -   -> 809 reads (0.16% of total) failing BadMateFilter
[2016-04-15T00:53Z] INFO  17:53:08,464 MicroScheduler -   -> 41027 reads (7.89% of total) failing DuplicateReadFilter
[2016-04-15T00:53Z] INFO  17:53:08,464 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:53Z] INFO  17:53:08,465 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:53Z] INFO  17:53:08,465 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:53Z] INFO  17:53:08,465 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:53Z] INFO  17:53:08,466 MicroScheduler -   -> 284 reads (0.05% of total) failing UnmappedReadFilter
[2016-04-15T00:53Z] INFO  17:53:09,261 ProgressMeter -      16:3169006   1894719.0    30.0 s      15.0 s       56.6%    53.0 s      23.0 s
[2016-04-15T00:53Z] INFO  17:53:09,874 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:53Z] GATK: UnifiedGenotyper
[2016-04-15T00:53Z] INFO  17:53:11,618 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:53Z] INFO  17:53:11,621 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:53Z] INFO  17:53:11,622 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:53Z] INFO  17:53:11,622 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:53Z] INFO  17:53:11,627 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/18/R14-18105_kapa-NGv3-PE100-NGv3-sort-18_50278423_66344430-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/18/R14-18105_kapa-NGv3-PE100-NGv3-18_50278423_66344430-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/18/tx/tmpgzdJkp/R14-18105_kapa-NGv3-PE100-NGv3-18_50278423_66344430.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:53Z] INFO  17:53:11,640 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:53Z] INFO  17:53:11,641 HelpFormatter - Date/Time: 2016/04/14 17:53:11
[2016-04-15T00:53Z] INFO  17:53:11,650 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:53Z] INFO  17:53:11,651 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:53Z] INFO  17:53:11,861 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:53Z] INFO  17:53:12,130 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:53Z] INFO  17:53:12,142 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:53Z] INFO  17:53:12,231 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.09
[2016-04-15T00:53Z] INFO  17:53:12,455 ProgressMeter -     16:28620029    920275.0    30.0 s      32.0 s       62.9%    47.0 s      17.0 s
[2016-04-15T00:53Z] INFO  17:53:12,620 IntervalUtils - Processing 111880 bp from intervals
[2016-04-15T00:53Z] WARN  17:53:12,627 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:53Z] INFO  17:53:12,710 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:53Z] INFO  17:53:12,816 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:53Z] INFO  17:53:12,818 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:53Z] INFO  17:53:12,819 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:53Z] INFO  17:53:12,820 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:53Z] INFO  17:53:12,880 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:53Z] INFO  17:53:12,881 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:53Z] INFO  17:53:13,250 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:53Z] INFO  17:53:13,254 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:53Z] INFO  17:53:13,255 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:53Z] INFO  17:53:13,255 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:53Z] INFO  17:53:13,265 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/18/R14-18105_kapa-NGv3-PE100-NGv3-sort-18_66346699_78077248-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/18/R14-18105_kapa-NGv3-PE100-NGv3-18_66346699_78077248-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/18/tx/tmpSRppie/R14-18105_kapa-NGv3-PE100-NGv3-18_66346699_78077248.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:53Z] INFO  17:53:13,309 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:53Z] INFO  17:53:13,310 HelpFormatter - Date/Time: 2016/04/14 17:53:13
[2016-04-15T00:53Z] INFO  17:53:13,310 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:53Z] INFO  17:53:13,310 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:53Z] INFO  17:53:13,522 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:53Z] INFO  17:53:13,720 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:53Z] INFO  17:53:13,732 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:53Z] INFO  17:53:13,922 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.19
[2016-04-15T00:53Z] INFO  17:53:14,396 IntervalUtils - Processing 87308 bp from intervals
[2016-04-15T00:53Z] WARN  17:53:14,403 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:53Z] INFO  17:53:14,514 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:53Z] INFO  17:53:14,635 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:53Z] INFO  17:53:14,637 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:53Z] INFO  17:53:14,638 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:53Z] INFO  17:53:14,638 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:53Z] INFO  17:53:14,697 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:53Z] INFO  17:53:14,698 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:53Z] INFO  17:53:15,665 ProgressMeter -            done    892419.0    26.0 s      30.0 s      100.0%    26.0 s       0.0 s
[2016-04-15T00:53Z] INFO  17:53:15,665 ProgressMeter - Total runtime 26.82 secs, 0.45 min, 0.01 hours
[2016-04-15T00:53Z] INFO  17:53:15,666 MicroScheduler - 26497 reads were filtered out during the traversal out of approximately 315470 total reads (8.40%)
[2016-04-15T00:53Z] INFO  17:53:15,666 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:53Z] INFO  17:53:15,667 MicroScheduler -   -> 459 reads (0.15% of total) failing BadMateFilter
[2016-04-15T00:53Z] INFO  17:53:15,668 MicroScheduler -   -> 25836 reads (8.19% of total) failing DuplicateReadFilter
[2016-04-15T00:53Z] INFO  17:53:15,668 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:53Z] INFO  17:53:15,669 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:53Z] INFO  17:53:15,670 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:53Z] INFO  17:53:15,671 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:53Z] INFO  17:53:15,671 MicroScheduler -   -> 202 reads (0.06% of total) failing UnmappedReadFilter
[2016-04-15T00:53Z] INFO  17:53:17,112 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:53Z] GATK: UnifiedGenotyper
[2016-04-15T00:53Z] INFO  17:53:20,071 ProgressMeter -     16:72142699   1422843.0    30.0 s      21.0 s       77.3%    38.0 s       8.0 s
[2016-04-15T00:53Z] INFO  17:53:20,372 ProgressMeter -            done    861644.0    27.0 s      31.0 s      100.0%    27.0 s       0.0 s
[2016-04-15T00:53Z] INFO  17:53:20,373 ProgressMeter - Total runtime 27.37 secs, 0.46 min, 0.01 hours
[2016-04-15T00:53Z] INFO  17:53:20,373 MicroScheduler - 27788 reads were filtered out during the traversal out of approximately 324950 total reads (8.55%)
[2016-04-15T00:53Z] INFO  17:53:20,374 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:53Z] INFO  17:53:20,374 MicroScheduler -   -> 490 reads (0.15% of total) failing BadMateFilter
[2016-04-15T00:53Z] INFO  17:53:20,374 MicroScheduler -   -> 27106 reads (8.34% of total) failing DuplicateReadFilter
[2016-04-15T00:53Z] INFO  17:53:20,375 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:53Z] INFO  17:53:20,375 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:53Z] INFO  17:53:20,375 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:53Z] INFO  17:53:20,376 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:53Z] INFO  17:53:20,376 MicroScheduler -   -> 192 reads (0.06% of total) failing UnmappedReadFilter
[2016-04-15T00:53Z] INFO  17:53:20,544 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:53Z] INFO  17:53:20,548 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:53Z] INFO  17:53:20,549 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:53Z] INFO  17:53:20,549 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:53Z] INFO  17:53:20,555 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/19/R14-18105_kapa-NGv3-PE100-NGv3-sort-19_0_15509577-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/19/R14-18105_kapa-NGv3-PE100-NGv3-19_0_15509577-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/19/tx/tmpUz9jq_/R14-18105_kapa-NGv3-PE100-NGv3-19_0_15509577.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:53Z] INFO  17:53:20,575 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:53Z] INFO  17:53:20,585 HelpFormatter - Date/Time: 2016/04/14 17:53:20
[2016-04-15T00:53Z] INFO  17:53:20,586 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:53Z] INFO  17:53:20,586 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:53Z] INFO  17:53:20,761 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:53Z] INFO  17:53:21,072 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:53Z] INFO  17:53:21,081 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:53Z] INFO  17:53:21,164 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-15T00:53Z] INFO  17:53:21,609 ProgressMeter -            done    934025.0    20.0 s      22.0 s      100.0%    20.0 s       0.0 s
[2016-04-15T00:53Z] INFO  17:53:21,609 ProgressMeter - Total runtime 20.59 secs, 0.34 min, 0.01 hours
[2016-04-15T00:53Z] INFO  17:53:21,610 MicroScheduler - 22222 reads were filtered out during the traversal out of approximately 261841 total reads (8.49%)
[2016-04-15T00:53Z] INFO  17:53:21,610 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:53Z] INFO  17:53:21,611 MicroScheduler -   -> 397 reads (0.15% of total) failing BadMateFilter
[2016-04-15T00:53Z] INFO  17:53:21,611 MicroScheduler -   -> 21650 reads (8.27% of total) failing DuplicateReadFilter
[2016-04-15T00:53Z] INFO  17:53:21,611 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:53Z] INFO  17:53:21,612 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:53Z] INFO  17:53:21,612 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:53Z] INFO  17:53:21,612 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:53Z] INFO  17:53:21,612 MicroScheduler -   -> 175 reads (0.07% of total) failing UnmappedReadFilter
[2016-04-15T00:53Z] INFO  17:53:21,686 IntervalUtils - Processing 793280 bp from intervals
[2016-04-15T00:53Z] WARN  17:53:21,692 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:53Z] INFO  17:53:21,792 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:53Z] INFO  17:53:21,917 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:53Z] INFO  17:53:21,918 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:53Z] INFO  17:53:21,919 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:53Z] INFO  17:53:21,919 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:53Z] INFO  17:53:21,935 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:53Z] INFO  17:53:21,967 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:53Z] INFO  17:53:21,968 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:53Z] INFO  17:53:22,133 ProgressMeter -            done    322965.0    16.0 s      51.0 s       99.9%    16.0 s       0.0 s
[2016-04-15T00:53Z] INFO  17:53:22,134 ProgressMeter - Total runtime 16.65 secs, 0.28 min, 0.00 hours
[2016-04-15T00:53Z] INFO  17:53:22,134 MicroScheduler - 16563 reads were filtered out during the traversal out of approximately 208253 total reads (7.95%)
[2016-04-15T00:53Z] INFO  17:53:22,135 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:53Z] INFO  17:53:22,135 MicroScheduler -   -> 311 reads (0.15% of total) failing BadMateFilter
[2016-04-15T00:53Z] INFO  17:53:22,135 MicroScheduler -   -> 16115 reads (7.74% of total) failing DuplicateReadFilter
[2016-04-15T00:53Z] INFO  17:53:22,135 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:53Z] INFO  17:53:22,136 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:53Z] INFO  17:53:22,136 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:53Z] INFO  17:53:22,136 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:53Z] INFO  17:53:22,136 MicroScheduler -   -> 137 reads (0.07% of total) failing UnmappedReadFilter
[2016-04-15T00:53Z] GATK: UnifiedGenotyper
[2016-04-15T00:53Z] INFO  17:53:22,635 ProgressMeter -            done    391274.0    17.0 s      44.0 s      100.0%    17.0 s       0.0 s
[2016-04-15T00:53Z] INFO  17:53:22,636 ProgressMeter - Total runtime 17.59 secs, 0.29 min, 0.00 hours
[2016-04-15T00:53Z] INFO  17:53:22,637 MicroScheduler - 15028 reads were filtered out during the traversal out of approximately 181501 total reads (8.28%)
[2016-04-15T00:53Z] INFO  17:53:22,638 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:53Z] INFO  17:53:22,638 MicroScheduler -   -> 281 reads (0.15% of total) failing BadMateFilter
[2016-04-15T00:53Z] INFO  17:53:22,639 MicroScheduler -   -> 14639 reads (8.07% of total) failing DuplicateReadFilter
[2016-04-15T00:53Z] INFO  17:53:22,640 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:53Z] INFO  17:53:22,640 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:53Z] INFO  17:53:22,641 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:53Z] INFO  17:53:22,652 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:53Z] INFO  17:53:22,652 MicroScheduler -   -> 108 reads (0.06% of total) failing UnmappedReadFilter
[2016-04-15T00:53Z] INFO  17:53:22,797 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:53Z] GATK: UnifiedGenotyper
[2016-04-15T00:53Z] INFO  17:53:23,267 ProgressMeter -            done    443441.0    19.0 s      44.0 s      100.0%    19.0 s       0.0 s
[2016-04-15T00:53Z] INFO  17:53:23,268 ProgressMeter - Total runtime 19.86 secs, 0.33 min, 0.01 hours
[2016-04-15T00:53Z] INFO  17:53:23,268 MicroScheduler - 16994 reads were filtered out during the traversal out of approximately 206779 total reads (8.22%)
[2016-04-15T00:53Z] INFO  17:53:23,268 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:53Z] INFO  17:53:23,269 MicroScheduler -   -> 300 reads (0.15% of total) failing BadMateFilter
[2016-04-15T00:53Z] INFO  17:53:23,269 MicroScheduler -   -> 16553 reads (8.01% of total) failing DuplicateReadFilter
[2016-04-15T00:53Z] INFO  17:53:23,269 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:53Z] INFO  17:53:23,270 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:53Z] INFO  17:53:23,270 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:53Z] INFO  17:53:23,270 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:53Z] INFO  17:53:23,270 MicroScheduler -   -> 141 reads (0.07% of total) failing UnmappedReadFilter
[2016-04-15T00:53Z] INFO  17:53:23,473 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:53Z] INFO  17:53:23,492 ProgressMeter -      17:7157902   1437409.0    30.0 s      20.0 s       53.5%    56.0 s      26.0 s
[2016-04-15T00:53Z] GATK: UnifiedGenotyper
[2016-04-15T00:53Z] INFO  17:53:24,281 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:53Z] GATK: UnifiedGenotyper
[2016-04-15T00:53Z] INFO  17:53:24,836 ProgressMeter -     17:27893204   1200677.0    30.0 s      24.0 s       76.7%    39.0 s       9.0 s
[2016-04-15T00:53Z] INFO  17:53:25,011 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:53Z] INFO  17:53:25,015 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:53Z] INFO  17:53:25,015 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:53Z] INFO  17:53:25,016 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:53Z] INFO  17:53:25,022 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/19/R14-18105_kapa-NGv3-PE100-NGv3-sort-19_15510112_31025906-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/19/R14-18105_kapa-NGv3-PE100-NGv3-19_15510112_31025906-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/19/tx/tmpA7HGv2/R14-18105_kapa-NGv3-PE100-NGv3-19_15510112_31025906.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:53Z] INFO  17:53:25,033 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:53Z] INFO  17:53:25,043 HelpFormatter - Date/Time: 2016/04/14 17:53:25
[2016-04-15T00:53Z] INFO  17:53:25,044 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:53Z] INFO  17:53:25,045 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:53Z] INFO  17:53:25,246 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:53Z] INFO  17:53:25,423 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:53Z] INFO  17:53:25,534 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:53Z] INFO  17:53:25,545 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:53Z] INFO  17:53:25,623 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-15T00:53Z] GATK: UnifiedGenotyper
[2016-04-15T00:53Z] INFO  17:53:25,851 ProgressMeter -            done    242253.0    13.0 s      53.0 s       99.9%    13.0 s       0.0 s
[2016-04-15T00:53Z] INFO  17:53:25,852 ProgressMeter - Total runtime 13.03 secs, 0.22 min, 0.00 hours
[2016-04-15T00:53Z] INFO  17:53:25,852 MicroScheduler - 10895 reads were filtered out during the traversal out of approximately 134313 total reads (8.11%)
[2016-04-15T00:53Z] INFO  17:53:25,853 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:53Z] INFO  17:53:25,853 MicroScheduler -   -> 198 reads (0.15% of total) failing BadMateFilter
[2016-04-15T00:53Z] INFO  17:53:25,853 MicroScheduler -   -> 10604 reads (7.89% of total) failing DuplicateReadFilter
[2016-04-15T00:53Z] INFO  17:53:25,854 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:53Z] INFO  17:53:25,854 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:53Z] INFO  17:53:25,854 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:53Z] INFO  17:53:25,855 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:53Z] INFO  17:53:25,855 MicroScheduler -   -> 93 reads (0.07% of total) failing UnmappedReadFilter
[2016-04-15T00:53Z] INFO  17:53:25,872 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:53Z] INFO  17:53:25,875 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:53Z] INFO  17:53:25,875 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:53Z] INFO  17:53:25,875 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:53Z] INFO  17:53:25,879 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/19/R14-18105_kapa-NGv3-PE100-NGv3-sort-19_31038849_46627578-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/19/R14-18105_kapa-NGv3-PE100-NGv3-19_31038849_46627578-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/19/tx/tmp_G6RV3/R14-18105_kapa-NGv3-PE100-NGv3-19_31038849_46627578.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:53Z] INFO  17:53:25,915 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:53Z] INFO  17:53:25,916 HelpFormatter - Date/Time: 2016/04/14 17:53:25
[2016-04-15T00:53Z] INFO  17:53:25,917 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:53Z] INFO  17:53:25,917 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:53Z] INFO  17:53:25,974 ProgressMeter -     17:39768510   1010252.0    30.0 s      29.0 s       48.9%    61.0 s      31.0 s
[2016-04-15T00:53Z] INFO  17:53:26,096 IntervalUtils - Processing 296880 bp from intervals
[2016-04-15T00:53Z] WARN  17:53:26,103 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:53Z] INFO  17:53:26,164 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:53Z] INFO  17:53:26,208 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:53Z] INFO  17:53:26,350 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:53Z] INFO  17:53:26,351 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:53Z] INFO  17:53:26,352 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:53Z] INFO  17:53:26,353 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:53Z] INFO  17:53:26,407 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:53Z] INFO  17:53:26,416 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:53Z] INFO  17:53:26,425 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:53Z] INFO  17:53:26,426 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:53Z] INFO  17:53:26,482 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-15T00:53Z] INFO  17:53:26,759 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:53Z] INFO  17:53:26,762 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:53Z] INFO  17:53:26,763 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:53Z] INFO  17:53:26,764 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:53Z] INFO  17:53:26,768 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/19/R14-18105_kapa-NGv3-PE100-NGv3-sort-19_46627881_59128983-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/19/R14-18105_kapa-NGv3-PE100-NGv3-19_46627881_59128983-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/19/tx/tmpG9vTNu/R14-18105_kapa-NGv3-PE100-NGv3-19_46627881_59128983.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:53Z] INFO  17:53:26,788 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:53Z] INFO  17:53:26,789 HelpFormatter - Date/Time: 2016/04/14 17:53:26
[2016-04-15T00:53Z] INFO  17:53:26,789 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:53Z] INFO  17:53:26,789 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:53Z] INFO  17:53:26,893 ProgressMeter -            done   1795980.0    44.0 s      24.0 s      100.0%    44.0 s       0.0 s
[2016-04-15T00:53Z] INFO  17:53:26,893 ProgressMeter - Total runtime 44.46 secs, 0.74 min, 0.01 hours
[2016-04-15T00:53Z] INFO  17:53:26,894 MicroScheduler - 59685 reads were filtered out during the traversal out of approximately 813244 total reads (7.34%)
[2016-04-15T00:53Z] INFO  17:53:26,894 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:53Z] INFO  17:53:26,894 MicroScheduler -   -> 1224 reads (0.15% of total) failing BadMateFilter
[2016-04-15T00:53Z] INFO  17:53:26,895 MicroScheduler -   -> 57968 reads (7.13% of total) failing DuplicateReadFilter
[2016-04-15T00:53Z] INFO  17:53:26,895 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:53Z] INFO  17:53:26,895 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:53Z] INFO  17:53:26,895 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:53Z] INFO  17:53:26,896 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:53Z] INFO  17:53:26,897 MicroScheduler -   -> 493 reads (0.06% of total) failing UnmappedReadFilter
[2016-04-15T00:53Z] INFO  17:53:26,956 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:53Z] INFO  17:53:26,998 IntervalUtils - Processing 631764 bp from intervals
[2016-04-15T00:53Z] WARN  17:53:27,004 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:53Z] INFO  17:53:27,087 ProgressMeter -            done    175642.0    12.0 s      70.0 s       99.9%    12.0 s       0.0 s
[2016-04-15T00:53Z] INFO  17:53:27,088 ProgressMeter - Total runtime 12.45 secs, 0.21 min, 0.00 hours
[2016-04-15T00:53Z] INFO  17:53:27,088 MicroScheduler - 10019 reads were filtered out during the traversal out of approximately 118788 total reads (8.43%)
[2016-04-15T00:53Z] INFO  17:53:27,088 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:53Z] INFO  17:53:27,089 MicroScheduler -   -> 166 reads (0.14% of total) failing BadMateFilter
[2016-04-15T00:53Z] INFO  17:53:27,089 MicroScheduler -   -> 9755 reads (8.21% of total) failing DuplicateReadFilter
[2016-04-15T00:53Z] INFO  17:53:27,089 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:53Z] INFO  17:53:27,089 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:53Z] INFO  17:53:27,090 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:53Z] INFO  17:53:27,090 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:53Z] INFO  17:53:27,090 MicroScheduler -   -> 98 reads (0.08% of total) failing UnmappedReadFilter
[2016-04-15T00:53Z] INFO  17:53:27,098 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:53Z] INFO  17:53:27,220 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:53Z] INFO  17:53:27,229 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:53Z] INFO  17:53:27,252 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:53Z] INFO  17:53:27,253 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:53Z] INFO  17:53:27,254 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:53Z] INFO  17:53:27,254 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:53Z] INFO  17:53:27,294 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:53Z] INFO  17:53:27,294 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:53Z] INFO  17:53:27,300 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-15T00:53Z] INFO  17:53:27,420 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:53Z] INFO  17:53:27,474 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:53Z] INFO  17:53:27,477 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:53Z] INFO  17:53:27,478 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:53Z] INFO  17:53:27,478 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:53Z] INFO  17:53:27,483 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/20/R14-18105_kapa-NGv3-PE100-NGv3-sort-20_0_15843471-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/20/R14-18105_kapa-NGv3-PE100-NGv3-20_0_15843471-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/20/tx/tmpHdPlfS/R14-18105_kapa-NGv3-PE100-NGv3-20_0_15843471.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:53Z] INFO  17:53:27,492 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:53Z] INFO  17:53:27,503 HelpFormatter - Date/Time: 2016/04/14 17:53:27
[2016-04-15T00:53Z] INFO  17:53:27,504 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:53Z] INFO  17:53:27,504 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:53Z] INFO  17:53:27,697 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:53Z] GATK: UnifiedGenotyper
[2016-04-15T00:53Z] INFO  17:53:27,852 IntervalUtils - Processing 711484 bp from intervals
[2016-04-15T00:53Z] WARN  17:53:27,858 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:53Z] INFO  17:53:27,944 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:53Z] INFO  17:53:27,948 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:53Z] INFO  17:53:27,958 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:53Z] INFO  17:53:27,967 ProgressMeter -            done   1653515.0    37.0 s      22.0 s      100.0%    37.0 s       0.0 s
[2016-04-15T00:53Z] INFO  17:53:27,968 ProgressMeter - Total runtime 37.91 secs, 0.63 min, 0.01 hours
[2016-04-15T00:53Z] INFO  17:53:27,968 MicroScheduler - 48756 reads were filtered out during the traversal out of approximately 590869 total reads (8.25%)
[2016-04-15T00:53Z] INFO  17:53:27,969 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:53Z] INFO  17:53:27,969 MicroScheduler -   -> 809 reads (0.14% of total) failing BadMateFilter
[2016-04-15T00:53Z] INFO  17:53:27,969 MicroScheduler -   -> 47566 reads (8.05% of total) failing DuplicateReadFilter
[2016-04-15T00:53Z] INFO  17:53:27,969 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:53Z] INFO  17:53:27,970 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:53Z] INFO  17:53:27,970 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:53Z] INFO  17:53:27,970 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:53Z] INFO  17:53:27,970 MicroScheduler -   -> 381 reads (0.06% of total) failing UnmappedReadFilter
[2016-04-15T00:53Z] INFO  17:53:28,054 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.10
[2016-04-15T00:53Z] INFO  17:53:28,101 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:53Z] INFO  17:53:28,102 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:53Z] INFO  17:53:28,103 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:53Z] INFO  17:53:28,104 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:53Z] INFO  17:53:28,157 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:53Z] INFO  17:53:28,158 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:53Z] INFO  17:53:28,312 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:53Z] INFO  17:53:28,424 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:53Z] INFO  17:53:28,427 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:53Z] INFO  17:53:28,428 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:53Z] INFO  17:53:28,429 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:53Z] INFO  17:53:28,433 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/20/R14-18105_kapa-NGv3-PE100-NGv3-sort-20_15866408_31376818-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/20/R14-18105_kapa-NGv3-PE100-NGv3-20_15866408_31376818-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/20/tx/tmpmTjeBG/R14-18105_kapa-NGv3-PE100-NGv3-20_15866408_31376818.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:53Z] INFO  17:53:28,448 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:53Z] INFO  17:53:28,449 HelpFormatter - Date/Time: 2016/04/14 17:53:28
[2016-04-15T00:53Z] INFO  17:53:28,450 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:53Z] INFO  17:53:28,450 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:53Z] INFO  17:53:28,530 IntervalUtils - Processing 179899 bp from intervals
[2016-04-15T00:53Z] WARN  17:53:28,535 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:53Z] GATK: UnifiedGenotyper
[2016-04-15T00:53Z] INFO  17:53:28,625 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:53Z] INFO  17:53:28,650 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:53Z] INFO  17:53:28,667 ProgressMeter -            done   2608342.0    49.0 s      18.0 s      100.0%    49.0 s       0.0 s
[2016-04-15T00:53Z] INFO  17:53:28,667 ProgressMeter - Total runtime 49.43 secs, 0.82 min, 0.01 hours
[2016-04-15T00:53Z] INFO  17:53:28,667 MicroScheduler - 61665 reads were filtered out during the traversal out of approximately 760156 total reads (8.11%)
[2016-04-15T00:53Z] INFO  17:53:28,668 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:53Z] INFO  17:53:28,668 MicroScheduler -   -> 1224 reads (0.16% of total) failing BadMateFilter
[2016-04-15T00:53Z] INFO  17:53:28,668 MicroScheduler -   -> 59915 reads (7.88% of total) failing DuplicateReadFilter
[2016-04-15T00:53Z] INFO  17:53:28,668 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:53Z] INFO  17:53:28,669 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:53Z] INFO  17:53:28,669 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:53Z] INFO  17:53:28,669 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:53Z] INFO  17:53:28,669 MicroScheduler -   -> 526 reads (0.07% of total) failing UnmappedReadFilter
[2016-04-15T00:53Z] INFO  17:53:28,727 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:53Z] INFO  17:53:28,728 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:53Z] INFO  17:53:28,729 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:53Z] INFO  17:53:28,736 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:53Z] INFO  17:53:28,782 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:53Z] INFO  17:53:28,791 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:53Z] INFO  17:53:28,792 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:53Z] INFO  17:53:28,810 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:53Z] INFO  17:53:28,824 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:53Z] INFO  17:53:28,861 ProgressMeter -     17:61972460   1248405.0    30.0 s      24.0 s       96.4%    31.0 s       1.0 s
[2016-04-15T00:53Z] INFO  17:53:28,949 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.13
[2016-04-15T00:53Z] GATK: UnifiedGenotyper
[2016-04-15T00:53Z] INFO  17:53:29,363 ProgressMeter -     17:75484809   1441520.0    30.0 s      20.0 s       85.3%    35.0 s       5.0 s
[2016-04-15T00:53Z] INFO  17:53:29,384 IntervalUtils - Processing 150913 bp from intervals
[2016-04-15T00:53Z] WARN  17:53:29,400 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:53Z] INFO  17:53:29,467 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:53Z] INFO  17:53:29,497 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:53Z] INFO  17:53:29,607 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:53Z] INFO  17:53:29,608 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:53Z] INFO  17:53:29,612 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:53Z] INFO  17:53:29,613 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:53Z] INFO  17:53:29,694 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:53Z] INFO  17:53:29,694 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:53Z] GATK: UnifiedGenotyper
[2016-04-15T00:53Z] INFO  17:53:30,012 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:53Z] INFO  17:53:30,259 ProgressMeter -            done   1302364.0    31.0 s      24.0 s      100.0%    31.0 s       0.0 s
[2016-04-15T00:53Z] INFO  17:53:30,260 ProgressMeter - Total runtime 31.42 secs, 0.52 min, 0.01 hours
[2016-04-15T00:53Z] INFO  17:53:30,260 MicroScheduler - 35281 reads were filtered out during the traversal out of approximately 427338 total reads (8.26%)
[2016-04-15T00:53Z] INFO  17:53:30,260 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:53Z] INFO  17:53:30,260 MicroScheduler -   -> 651 reads (0.15% of total) failing BadMateFilter
[2016-04-15T00:53Z] INFO  17:53:30,261 MicroScheduler -   -> 34341 reads (8.04% of total) failing DuplicateReadFilter
[2016-04-15T00:53Z] INFO  17:53:30,261 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:53Z] INFO  17:53:30,261 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:53Z] INFO  17:53:30,261 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:53Z] INFO  17:53:30,262 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:53Z] INFO  17:53:30,262 MicroScheduler -   -> 289 reads (0.07% of total) failing UnmappedReadFilter
[2016-04-15T00:53Z] GATK: UnifiedGenotyper
[2016-04-15T00:53Z] INFO  17:53:30,437 ProgressMeter -            done   1490193.0    35.0 s      23.0 s      100.0%    35.0 s       0.0 s
[2016-04-15T00:53Z] INFO  17:53:30,437 ProgressMeter - Total runtime 35.62 secs, 0.59 min, 0.01 hours
[2016-04-15T00:53Z] INFO  17:53:30,438 MicroScheduler - 41318 reads were filtered out during the traversal out of approximately 498815 total reads (8.28%)
[2016-04-15T00:53Z] INFO  17:53:30,438 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:53Z] INFO  17:53:30,438 MicroScheduler -   -> 758 reads (0.15% of total) failing BadMateFilter
[2016-04-15T00:53Z] INFO  17:53:30,439 MicroScheduler -   -> 40241 reads (8.07% of total) failing DuplicateReadFilter
[2016-04-15T00:53Z] INFO  17:53:30,439 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:53Z] INFO  17:53:30,439 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:53Z] INFO  17:53:30,439 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:53Z] INFO  17:53:30,439 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:53Z] INFO  17:53:30,440 MicroScheduler -   -> 319 reads (0.06% of total) failing UnmappedReadFilter
[2016-04-15T00:53Z] INFO  17:53:30,686 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:53Z] INFO  17:53:30,693 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:53Z] INFO  17:53:30,693 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:53Z] INFO  17:53:30,694 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:53Z] INFO  17:53:30,698 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/20/R14-18105_kapa-NGv3-PE100-NGv3-sort-20_31379406_47242465-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/20/R14-18105_kapa-NGv3-PE100-NGv3-20_31379406_47242465-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/20/tx/tmpqdUwYI/R14-18105_kapa-NGv3-PE100-NGv3-20_31379406_47242465.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:53Z] INFO  17:53:30,724 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:53Z] INFO  17:53:30,725 HelpFormatter - Date/Time: 2016/04/14 17:53:30
[2016-04-15T00:53Z] INFO  17:53:30,726 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:53Z] INFO  17:53:30,730 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:53Z] INFO  17:53:30,974 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:53Z] INFO  17:53:31,216 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:53Z] INFO  17:53:31,225 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:53Z] INFO  17:53:31,310 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-15T00:53Z] INFO  17:53:31,351 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:53Z] INFO  17:53:31,355 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:53Z] INFO  17:53:31,355 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:53Z] INFO  17:53:31,356 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:53Z] INFO  17:53:31,360 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/20/R14-18105_kapa-NGv3-PE100-NGv3-sort-20_47244085_62830269-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/20/R14-18105_kapa-NGv3-PE100-NGv3-20_47244085_62830269-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/20/tx/tmpnhCqWt/R14-18105_kapa-NGv3-PE100-NGv3-20_47244085_62830269.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:53Z] INFO  17:53:31,370 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:53Z] INFO  17:53:31,371 HelpFormatter - Date/Time: 2016/04/14 17:53:31
[2016-04-15T00:53Z] INFO  17:53:31,371 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:53Z] INFO  17:53:31,372 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:53Z] INFO  17:53:31,604 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:53Z] INFO  17:53:31,857 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:53Z] INFO  17:53:31,872 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:53Z] INFO  17:53:31,872 IntervalUtils - Processing 321885 bp from intervals
[2016-04-15T00:53Z] WARN  17:53:31,878 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:53Z] INFO  17:53:31,910 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:53Z] INFO  17:53:31,963 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:53Z] INFO  17:53:31,991 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.12
[2016-04-15T00:53Z] INFO  17:53:32,078 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:53Z] INFO  17:53:32,079 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:53Z] INFO  17:53:32,080 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:53Z] INFO  17:53:32,080 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:53Z] INFO  17:53:32,083 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:53Z] INFO  17:53:32,139 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:53Z] INFO  17:53:32,140 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:53Z] GATK: UnifiedGenotyper
[2016-04-15T00:53Z] INFO  17:53:32,390 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:53Z] INFO  17:53:32,393 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:53Z] INFO  17:53:32,393 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:53Z] INFO  17:53:32,394 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:53Z] INFO  17:53:32,398 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/20/R14-18105_kapa-NGv3-PE100-NGv3-sort-20_62831244_63025520-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/20/R14-18105_kapa-NGv3-PE100-NGv3-20_62831244_63025520-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/20/tx/tmpp8Y67M/R14-18105_kapa-NGv3-PE100-NGv3-20_62831244_63025520.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:53Z] INFO  17:53:32,414 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:53Z] INFO  17:53:32,415 HelpFormatter - Date/Time: 2016/04/14 17:53:32
[2016-04-15T00:53Z] INFO  17:53:32,415 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:53Z] INFO  17:53:32,416 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:53Z] INFO  17:53:32,527 IntervalUtils - Processing 269605 bp from intervals
[2016-04-15T00:53Z] WARN  17:53:32,545 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:53Z] GATK: UnifiedGenotyper
[2016-04-15T00:53Z] INFO  17:53:32,597 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:53Z] INFO  17:53:32,645 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:53Z] INFO  17:53:32,764 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:53Z] INFO  17:53:32,765 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:53Z] INFO  17:53:32,766 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:53Z] INFO  17:53:32,766 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:53Z] INFO  17:53:32,812 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:53Z] INFO  17:53:32,813 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:53Z] INFO  17:53:32,844 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:53Z] INFO  17:53:32,847 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:53Z] INFO  17:53:32,848 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:53Z] INFO  17:53:32,848 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:53Z] INFO  17:53:32,852 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/21/R14-18105_kapa-NGv3-PE100-NGv3-sort-21_0_15517120-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/21/R14-18105_kapa-NGv3-PE100-NGv3-21_0_15517120-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/21/tx/tmp9XsLOF/R14-18105_kapa-NGv3-PE100-NGv3-21_0_15517120.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:53Z] INFO  17:53:32,862 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:53Z] INFO  17:53:32,874 HelpFormatter - Date/Time: 2016/04/14 17:53:32
[2016-04-15T00:53Z] INFO  17:53:32,875 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:53Z] INFO  17:53:32,876 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:53Z] INFO  17:53:32,883 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:53Z] INFO  17:53:32,903 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:53Z] INFO  17:53:33,000 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.10
[2016-04-15T00:53Z] INFO  17:53:33,090 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:53Z] INFO  17:53:33,184 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:53Z] INFO  17:53:33,187 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:53Z] INFO  17:53:33,188 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:53Z] INFO  17:53:33,188 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:53Z] INFO  17:53:33,193 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/21/R14-18105_kapa-NGv3-PE100-NGv3-sort-21_15524893_31045484-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/21/R14-18105_kapa-NGv3-PE100-NGv3-21_15524893_31045484-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/21/tx/tmps2c864/R14-18105_kapa-NGv3-PE100-NGv3-21_15524893_31045484.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:53Z] INFO  17:53:33,237 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:53Z] INFO  17:53:33,245 HelpFormatter - Date/Time: 2016/04/14 17:53:33
[2016-04-15T00:53Z] INFO  17:53:33,246 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:53Z] INFO  17:53:33,247 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:53Z] INFO  17:53:33,345 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:53Z] INFO  17:53:33,368 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:53Z] INFO  17:53:33,438 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:53Z] INFO  17:53:33,463 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.09
[2016-04-15T00:53Z] INFO  17:53:33,490 ProgressMeter -            done   1664309.0    34.0 s      20.0 s      100.0%    34.0 s       0.0 s
[2016-04-15T00:53Z] INFO  17:53:33,490 ProgressMeter - Total runtime 34.14 secs, 0.57 min, 0.01 hours
[2016-04-15T00:53Z] INFO  17:53:33,490 MicroScheduler - 43929 reads were filtered out during the traversal out of approximately 524711 total reads (8.37%)
[2016-04-15T00:53Z] INFO  17:53:33,491 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:53Z] INFO  17:53:33,491 MicroScheduler -   -> 781 reads (0.15% of total) failing BadMateFilter
[2016-04-15T00:53Z] INFO  17:53:33,491 MicroScheduler -   -> 42785 reads (8.15% of total) failing DuplicateReadFilter
[2016-04-15T00:53Z] INFO  17:53:33,491 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:53Z] INFO  17:53:33,492 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:53Z] INFO  17:53:33,492 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:53Z] INFO  17:53:33,492 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:53Z] INFO  17:53:33,492 MicroScheduler -   -> 363 reads (0.07% of total) failing UnmappedReadFilter
[2016-04-15T00:53Z] INFO  17:53:33,566 IntervalUtils - Processing 4397 bp from intervals
[2016-04-15T00:53Z] WARN  17:53:33,571 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:53Z] INFO  17:53:33,696 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:53Z] INFO  17:53:33,708 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:53Z] INFO  17:53:33,716 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:53Z] INFO  17:53:33,766 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:53Z] INFO  17:53:33,767 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:53Z] INFO  17:53:33,767 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:53Z] INFO  17:53:33,767 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:53Z] INFO  17:53:33,794 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.09
[2016-04-15T00:53Z] INFO  17:53:33,895 IntervalUtils - Processing 4504 bp from intervals
[2016-04-15T00:53Z] WARN  17:53:33,900 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:53Z] INFO  17:53:33,931 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:53Z] INFO  17:53:33,932 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:53Z] INFO  17:53:34,017 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:53Z] INFO  17:53:34,045 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:53Z] INFO  17:53:34,046 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:53Z] INFO  17:53:34,047 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:53Z] INFO  17:53:34,047 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:53Z] INFO  17:53:34,096 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:53Z] INFO  17:53:34,097 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:53Z] INFO  17:53:34,218 IntervalUtils - Processing 58639 bp from intervals
[2016-04-15T00:53Z] WARN  17:53:34,223 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:53Z] INFO  17:53:34,305 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:53Z] INFO  17:53:34,389 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:53Z] INFO  17:53:34,390 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:53Z] INFO  17:53:34,391 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:53Z] INFO  17:53:34,391 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:53Z] INFO  17:53:34,532 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:53Z] INFO  17:53:34,533 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:53Z] INFO  17:53:34,929 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:53Z] GATK: UnifiedGenotyper
[2016-04-15T00:53Z] INFO  17:53:35,321 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:53Z] INFO  17:53:35,324 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:53Z] INFO  17:53:35,325 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:53Z] INFO  17:53:35,325 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:53Z] INFO  17:53:35,330 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/21/R14-18105_kapa-NGv3-PE100-NGv3-sort-21_31062047_46591599-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/21/R14-18105_kapa-NGv3-PE100-NGv3-21_31062047_46591599-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/21/tx/tmptcgJGq/R14-18105_kapa-NGv3-PE100-NGv3-21_31062047_46591599.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:53Z] INFO  17:53:35,351 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:53Z] INFO  17:53:35,352 HelpFormatter - Date/Time: 2016/04/14 17:53:35
[2016-04-15T00:53Z] INFO  17:53:35,353 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:53Z] INFO  17:53:35,354 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:53Z] INFO  17:53:35,379 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:53Z] INFO  17:53:35,382 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:53Z] INFO  17:53:35,383 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:53Z] INFO  17:53:35,384 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:53Z] INFO  17:53:35,388 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/21/R14-18105_kapa-NGv3-PE100-NGv3-sort-21_46595644_48129895-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/21/R14-18105_kapa-NGv3-PE100-NGv3-21_46595644_48129895-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/21/tx/tmpIuyCr0/R14-18105_kapa-NGv3-PE100-NGv3-21_46595644_48129895.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:53Z] INFO  17:53:35,405 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:53Z] INFO  17:53:35,406 HelpFormatter - Date/Time: 2016/04/14 17:53:35
[2016-04-15T00:53Z] INFO  17:53:35,406 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:53Z] INFO  17:53:35,407 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:53Z] INFO  17:53:35,626 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:53Z] INFO  17:53:35,682 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:53Z] INFO  17:53:35,855 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:53Z] INFO  17:53:35,865 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:53Z] INFO  17:53:35,941 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:53Z] INFO  17:53:35,954 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.09
[2016-04-15T00:53Z] INFO  17:53:35,981 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:53Z] INFO  17:53:36,071 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.09
[2016-04-15T00:53Z] INFO  17:53:36,586 IntervalUtils - Processing 282111 bp from intervals
[2016-04-15T00:53Z] WARN  17:53:36,591 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:53Z] INFO  17:53:36,602 IntervalUtils - Processing 63011 bp from intervals
[2016-04-15T00:53Z] WARN  17:53:36,616 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:53Z] INFO  17:53:36,663 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:53Z] INFO  17:53:36,723 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:53Z] INFO  17:53:36,779 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:53Z] INFO  17:53:36,780 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:53Z] INFO  17:53:36,781 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:53Z] INFO  17:53:36,782 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:53Z] INFO  17:53:36,804 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:53Z] INFO  17:53:36,805 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:53Z] INFO  17:53:36,806 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:53Z] INFO  17:53:36,807 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:53Z] INFO  17:53:36,837 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:53Z] INFO  17:53:36,839 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:53Z] INFO  17:53:36,899 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:53Z] INFO  17:53:36,900 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:53Z] INFO  17:53:37,128 ProgressMeter -            done     15700.0     3.0 s       3.6 m       98.2%     3.0 s       0.0 s
[2016-04-15T00:53Z] INFO  17:53:37,129 ProgressMeter - Total runtime 3.36 secs, 0.06 min, 0.00 hours
[2016-04-15T00:53Z] INFO  17:53:37,130 MicroScheduler - 543 reads were filtered out during the traversal out of approximately 6421 total reads (8.46%)
[2016-04-15T00:53Z] INFO  17:53:37,131 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:53Z] INFO  17:53:37,132 MicroScheduler -   -> 13 reads (0.20% of total) failing BadMateFilter
[2016-04-15T00:53Z] INFO  17:53:37,132 MicroScheduler -   -> 527 reads (8.21% of total) failing DuplicateReadFilter
[2016-04-15T00:53Z] INFO  17:53:37,133 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:53Z] INFO  17:53:37,133 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:53Z] INFO  17:53:37,134 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:53Z] INFO  17:53:37,135 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:53Z] INFO  17:53:37,135 MicroScheduler -   -> 3 reads (0.05% of total) failing UnmappedReadFilter
[2016-04-15T00:53Z] INFO  17:53:38,310 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:53Z] INFO  17:53:38,313 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:53Z] INFO  17:53:38,314 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:53Z] INFO  17:53:38,314 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:53Z] INFO  17:53:38,318 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/22/R14-18105_kapa-NGv3-PE100-NGv3-sort-22_0_16258303-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/22/R14-18105_kapa-NGv3-PE100-NGv3-22_0_16258303-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/22/tx/tmp1Bv8Ck/R14-18105_kapa-NGv3-PE100-NGv3-22_0_16258303.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:53Z] INFO  17:53:38,330 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:53Z] INFO  17:53:38,331 HelpFormatter - Date/Time: 2016/04/14 17:53:38
[2016-04-15T00:53Z] INFO  17:53:38,332 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:53Z] INFO  17:53:38,332 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:53Z] INFO  17:53:38,558 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:53Z] INFO  17:53:38,694 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:53Z] INFO  17:53:38,802 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:53Z] INFO  17:53:38,811 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:53Z] INFO  17:53:38,878 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-15T00:53Z] INFO  17:53:39,143 IntervalUtils - Processing 118 bp from intervals
[2016-04-15T00:53Z] GATK: UnifiedGenotyper
[2016-04-15T00:53Z] WARN  17:53:39,148 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:53Z] INFO  17:53:39,250 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:53Z] INFO  17:53:39,247 ProgressMeter -            done     11154.0     5.0 s       7.8 m       98.3%     5.0 s       0.0 s
[2016-04-15T00:53Z] INFO  17:53:39,248 ProgressMeter - Total runtime 5.20 secs, 0.09 min, 0.00 hours
[2016-04-15T00:53Z] INFO  17:53:39,248 MicroScheduler - 1333 reads were filtered out during the traversal out of approximately 15364 total reads (8.68%)
[2016-04-15T00:53Z] INFO  17:53:39,249 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:53Z] INFO  17:53:39,249 MicroScheduler -   -> 48 reads (0.31% of total) failing BadMateFilter
[2016-04-15T00:53Z] INFO  17:53:39,249 MicroScheduler -   -> 1283 reads (8.35% of total) failing DuplicateReadFilter
[2016-04-15T00:53Z] INFO  17:53:39,249 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:53Z] INFO  17:53:39,250 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:53Z] INFO  17:53:39,250 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:53Z] INFO  17:53:39,250 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:53Z] INFO  17:53:39,251 MicroScheduler -   -> 2 reads (0.01% of total) failing UnmappedReadFilter
[2016-04-15T00:53Z] INFO  17:53:39,287 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:53Z] INFO  17:53:39,287 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:53Z] INFO  17:53:39,288 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:53Z] INFO  17:53:39,288 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:53Z] INFO  17:53:39,336 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:53Z] INFO  17:53:39,337 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:53Z] INFO  17:53:40,556 ProgressMeter -            done       118.0     1.0 s       3.0 h       84.7%     1.0 s       0.0 s
[2016-04-15T00:53Z] INFO  17:53:40,557 ProgressMeter - Total runtime 1.27 secs, 0.02 min, 0.00 hours
[2016-04-15T00:53Z] INFO  17:53:40,557 MicroScheduler - 1 reads were filtered out during the traversal out of approximately 230 total reads (0.43%)
[2016-04-15T00:53Z] INFO  17:53:40,557 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:53Z] INFO  17:53:40,558 MicroScheduler -   -> 1 reads (0.43% of total) failing BadMateFilter
[2016-04-15T00:53Z] INFO  17:53:40,558 MicroScheduler -   -> 0 reads (0.00% of total) failing DuplicateReadFilter
[2016-04-15T00:53Z] INFO  17:53:40,558 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:53Z] INFO  17:53:40,559 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:53Z] INFO  17:53:40,559 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:53Z] INFO  17:53:40,559 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:53Z] INFO  17:53:40,559 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:53Z] INFO  17:53:40,715 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:53Z] GATK: UnifiedGenotyper
[2016-04-15T00:53Z] INFO  17:53:41,863 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:53Z] INFO  17:53:42,053 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:53Z] INFO  17:53:42,058 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:53Z] INFO  17:53:42,058 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:53Z] INFO  17:53:42,059 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:53Z] INFO  17:53:42,064 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/22/R14-18105_kapa-NGv3-PE100-NGv3-sort-22_16266928_31795711-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/22/R14-18105_kapa-NGv3-PE100-NGv3-22_16266928_31795711-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/22/tx/tmpijF_xg/R14-18105_kapa-NGv3-PE100-NGv3-22_16266928_31795711.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:53Z] INFO  17:53:42,075 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:53Z] INFO  17:53:42,086 HelpFormatter - Date/Time: 2016/04/14 17:53:42
[2016-04-15T00:53Z] INFO  17:53:42,087 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:53Z] INFO  17:53:42,088 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:53Z] GATK: UnifiedGenotyper
[2016-04-15T00:53Z] INFO  17:53:42,255 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:53Z] INFO  17:53:42,453 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:53Z] INFO  17:53:42,486 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:53Z] INFO  17:53:42,578 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.09
[2016-04-15T00:53Z] INFO  17:53:42,985 IntervalUtils - Processing 372769 bp from intervals
[2016-04-15T00:53Z] WARN  17:53:42,991 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:53Z] INFO  17:53:43,118 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:53Z] INFO  17:53:43,287 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:53Z] INFO  17:53:43,288 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:53Z] INFO  17:53:43,288 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:53Z] INFO  17:53:43,289 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:53Z] INFO  17:53:43,356 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:53Z] INFO  17:53:43,357 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:53Z] INFO  17:53:43,950 ProgressMeter -            done   2975101.0    50.0 s      16.0 s      100.0%    50.0 s       0.0 s
[2016-04-15T00:53Z] INFO  17:53:43,951 ProgressMeter - Total runtime 50.47 secs, 0.84 min, 0.01 hours
[2016-04-15T00:53Z] INFO  17:53:43,952 MicroScheduler - 66484 reads were filtered out during the traversal out of approximately 800532 total reads (8.30%)
[2016-04-15T00:53Z] INFO  17:53:43,953 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:53Z] INFO  17:53:43,950 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:53Z] INFO  17:53:43,953 MicroScheduler -   -> 1149 reads (0.14% of total) failing BadMateFilter
[2016-04-15T00:53Z] INFO  17:53:43,953 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:53Z] INFO  17:53:43,954 MicroScheduler -   -> 64834 reads (8.10% of total) failing DuplicateReadFilter
[2016-04-15T00:53Z] INFO  17:53:43,954 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:53Z] INFO  17:53:43,955 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:53Z] INFO  17:53:43,955 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:53Z] INFO  17:53:43,956 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:53Z] INFO  17:53:43,954 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:53Z] INFO  17:53:43,955 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:53Z] INFO  17:53:43,957 MicroScheduler -   -> 501 reads (0.06% of total) failing UnmappedReadFilter
[2016-04-15T00:53Z] INFO  17:53:43,977 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/22/R14-18105_kapa-NGv3-PE100-NGv3-sort-22_31796605_47308085-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/22/R14-18105_kapa-NGv3-PE100-NGv3-22_31796605_47308085-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/22/tx/tmpYlsoXS/R14-18105_kapa-NGv3-PE100-NGv3-22_31796605_47308085.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:53Z] INFO  17:53:43,994 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:53Z] INFO  17:53:43,994 HelpFormatter - Date/Time: 2016/04/14 17:53:43
[2016-04-15T00:53Z] INFO  17:53:43,994 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:53Z] INFO  17:53:43,995 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:53Z] INFO  17:53:44,078 ProgressMeter -            done    144598.0     9.0 s      66.0 s       99.9%     9.0 s       0.0 s
[2016-04-15T00:53Z] INFO  17:53:44,079 ProgressMeter - Total runtime 9.69 secs, 0.16 min, 0.00 hours
[2016-04-15T00:53Z] INFO  17:53:44,080 MicroScheduler - 5201 reads were filtered out during the traversal out of approximately 63284 total reads (8.22%)
[2016-04-15T00:53Z] INFO  17:53:44,081 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:53Z] INFO  17:53:44,081 MicroScheduler -   -> 75 reads (0.12% of total) failing BadMateFilter
[2016-04-15T00:53Z] INFO  17:53:44,082 MicroScheduler -   -> 5089 reads (8.04% of total) failing DuplicateReadFilter
[2016-04-15T00:53Z] INFO  17:53:44,082 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:53Z] INFO  17:53:44,083 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:53Z] INFO  17:53:44,084 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:53Z] INFO  17:53:44,084 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:53Z] INFO  17:53:44,085 MicroScheduler -   -> 37 reads (0.06% of total) failing UnmappedReadFilter
[2016-04-15T00:53Z] INFO  17:53:44,154 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:53Z] INFO  17:53:44,350 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:53Z] INFO  17:53:44,360 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:53Z] INFO  17:53:44,462 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.10
[2016-04-15T00:53Z] INFO  17:53:45,036 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:53Z] INFO  17:53:45,040 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:53Z] INFO  17:53:45,040 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:53Z] INFO  17:53:45,041 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:53Z] INFO  17:53:45,047 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/22/R14-18105_kapa-NGv3-PE100-NGv3-sort-22_47309229_51304566-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/22/R14-18105_kapa-NGv3-PE100-NGv3-22_47309229_51304566-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/22/tx/tmp6fS1OR/R14-18105_kapa-NGv3-PE100-NGv3-22_47309229_51304566.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:53Z] INFO  17:53:45,050 IntervalUtils - Processing 366557 bp from intervals
[2016-04-15T00:53Z] WARN  17:53:45,057 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:53Z] INFO  17:53:45,059 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:53Z] INFO  17:53:45,070 HelpFormatter - Date/Time: 2016/04/14 17:53:45
[2016-04-15T00:53Z] INFO  17:53:45,071 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:53Z] INFO  17:53:45,072 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:53Z] INFO  17:53:45,191 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:53Z] INFO  17:53:45,291 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:53Z] INFO  17:53:45,296 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:53Z] INFO  17:53:45,368 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:53Z] INFO  17:53:45,369 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:53Z] INFO  17:53:45,370 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:53Z] INFO  17:53:45,371 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:53Z] INFO  17:53:45,427 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:53Z] INFO  17:53:45,428 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:53Z] GATK: UnifiedGenotyper
[2016-04-15T00:53Z] INFO  17:53:45,584 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:53Z] INFO  17:53:45,595 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:53Z] INFO  17:53:45,660 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-15T00:53Z] INFO  17:53:45,793 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:53Z] INFO  17:53:46,032 IntervalUtils - Processing 81362 bp from intervals
[2016-04-15T00:53Z] WARN  17:53:46,037 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:53Z] INFO  17:53:46,128 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:53Z] GATK: UnifiedGenotyper
[2016-04-15T00:53Z] INFO  17:53:46,189 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:53Z] INFO  17:53:46,190 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:53Z] INFO  17:53:46,191 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:53Z] INFO  17:53:46,192 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:53Z] INFO  17:53:46,234 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:53Z] INFO  17:53:46,235 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:53Z] INFO  17:53:48,264 ProgressMeter -            done    403180.0    18.0 s      46.0 s      100.0%    18.0 s       0.0 s
[2016-04-15T00:53Z] INFO  17:53:48,265 ProgressMeter - Total runtime 18.66 secs, 0.31 min, 0.01 hours
[2016-04-15T00:53Z] INFO  17:53:48,265 MicroScheduler - 17631 reads were filtered out during the traversal out of approximately 212741 total reads (8.29%)
[2016-04-15T00:53Z] INFO  17:53:48,266 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:53Z] INFO  17:53:48,266 MicroScheduler -   -> 299 reads (0.14% of total) failing BadMateFilter
[2016-04-15T00:53Z] INFO  17:53:48,266 MicroScheduler -   -> 17221 reads (8.09% of total) failing DuplicateReadFilter
[2016-04-15T00:53Z] INFO  17:53:48,266 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:53Z] INFO  17:53:48,267 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:53Z] INFO  17:53:48,267 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:53Z] INFO  17:53:48,267 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:53Z] INFO  17:53:48,267 MicroScheduler -   -> 111 reads (0.05% of total) failing UnmappedReadFilter
[2016-04-15T00:53Z] INFO  17:53:48,514 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:53Z] INFO  17:53:48,517 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:53Z] INFO  17:53:48,518 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:53Z] INFO  17:53:48,518 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:53Z] INFO  17:53:48,523 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/X/R14-18105_kapa-NGv3-PE100-NGv3-sort-X_0_15509380-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/X/R14-18105_kapa-NGv3-PE100-NGv3-X_0_15509380-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/X/tx/tmpOzLQJB/R14-18105_kapa-NGv3-PE100-NGv3-X_0_15509380.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:53Z] INFO  17:53:48,537 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:53Z] INFO  17:53:48,537 HelpFormatter - Date/Time: 2016/04/14 17:53:48
[2016-04-15T00:53Z] INFO  17:53:48,537 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:53Z] INFO  17:53:48,538 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:53Z] INFO  17:53:48,770 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:53Z] INFO  17:53:48,955 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:53Z] INFO  17:53:48,959 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:53Z] INFO  17:53:48,959 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:53Z] INFO  17:53:48,960 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:53Z] INFO  17:53:48,960 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:53Z] INFO  17:53:48,964 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/X/R14-18105_kapa-NGv3-PE100-NGv3-sort-X_15518899_31090070-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/X/R14-18105_kapa-NGv3-PE100-NGv3-X_15518899_31090070-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/X/tx/tmpbzB8c3/R14-18105_kapa-NGv3-PE100-NGv3-X_15518899_31090070.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:53Z] INFO  17:53:48,969 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:53Z] INFO  17:53:48,974 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:53Z] INFO  17:53:48,985 HelpFormatter - Date/Time: 2016/04/14 17:53:48
[2016-04-15T00:53Z] INFO  17:53:48,986 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:53Z] INFO  17:53:48,987 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:53Z] INFO  17:53:49,060 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.09
[2016-04-15T00:53Z] INFO  17:53:49,220 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:53Z] INFO  17:53:49,461 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:53Z] INFO  17:53:49,481 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:53Z] INFO  17:53:49,498 IntervalUtils - Processing 114122 bp from intervals
[2016-04-15T00:53Z] WARN  17:53:49,506 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:53Z] INFO  17:53:49,516 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:53Z] INFO  17:53:49,575 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.09
[2016-04-15T00:53Z] INFO  17:53:49,604 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:53Z] INFO  17:53:49,605 ProgressMeter -            done    282818.0    12.0 s      45.0 s       99.9%    12.0 s       0.0 s
[2016-04-15T00:53Z] INFO  17:53:49,605 ProgressMeter - Total runtime 12.83 secs, 0.21 min, 0.00 hours
[2016-04-15T00:53Z] INFO  17:53:49,606 MicroScheduler - 8250 reads were filtered out during the traversal out of approximately 98532 total reads (8.37%)
[2016-04-15T00:53Z] INFO  17:53:49,606 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:53Z] INFO  17:53:49,606 MicroScheduler -   -> 155 reads (0.16% of total) failing BadMateFilter
[2016-04-15T00:53Z] INFO  17:53:49,607 MicroScheduler -   -> 8022 reads (8.14% of total) failing DuplicateReadFilter
[2016-04-15T00:53Z] INFO  17:53:49,607 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:53Z] INFO  17:53:49,607 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:53Z] INFO  17:53:49,607 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:53Z] INFO  17:53:49,608 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:53Z] INFO  17:53:49,608 MicroScheduler -   -> 73 reads (0.07% of total) failing UnmappedReadFilter
[2016-04-15T00:53Z] INFO  17:53:49,652 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:53Z] INFO  17:53:49,653 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:53Z] INFO  17:53:49,654 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:53Z] INFO  17:53:49,655 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:53Z] INFO  17:53:49,698 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:53Z] INFO  17:53:49,699 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:53Z] GATK: UnifiedGenotyper
[2016-04-15T00:53Z] INFO  17:53:49,909 IntervalUtils - Processing 133046 bp from intervals
[2016-04-15T00:53Z] WARN  17:53:49,915 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:53Z] INFO  17:53:49,978 ProgressMeter -            done   2489748.0    54.0 s      21.0 s      100.0%    54.0 s       0.0 s
[2016-04-15T00:53Z] INFO  17:53:49,979 ProgressMeter - Total runtime 54.01 secs, 0.90 min, 0.02 hours
[2016-04-15T00:53Z] INFO  17:53:49,979 MicroScheduler - 75982 reads were filtered out during the traversal out of approximately 942866 total reads (8.06%)
[2016-04-15T00:53Z] INFO  17:53:49,979 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:53Z] INFO  17:53:49,980 MicroScheduler -   -> 1414 reads (0.15% of total) failing BadMateFilter
[2016-04-15T00:53Z] INFO  17:53:49,980 MicroScheduler -   -> 73956 reads (7.84% of total) failing DuplicateReadFilter
[2016-04-15T00:53Z] INFO  17:53:49,980 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:53Z] INFO  17:53:49,980 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:53Z] INFO  17:53:49,980 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:53Z] INFO  17:53:49,981 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:53Z] INFO  17:53:49,981 MicroScheduler -   -> 612 reads (0.06% of total) failing UnmappedReadFilter
[2016-04-15T00:53Z] INFO  17:53:50,035 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:53Z] INFO  17:53:50,119 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:53Z] INFO  17:53:50,123 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:53Z] INFO  17:53:50,135 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:53Z] INFO  17:53:50,136 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:53Z] INFO  17:53:50,222 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:53Z] INFO  17:53:50,223 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:53Z] INFO  17:53:51,010 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:53Z] GATK: UnifiedGenotyper
[2016-04-15T00:53Z] INFO  17:53:51,425 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:53Z] GATK: UnifiedGenotyper
[2016-04-15T00:53Z] INFO  17:53:51,938 ProgressMeter -      19:4513458   1339718.0    30.0 s      22.0 s       32.0%    93.0 s      63.0 s
[2016-04-15T00:53Z] INFO  17:53:52,440 ProgressMeter -            done    626912.0    23.0 s      37.0 s      100.0%    23.0 s       0.0 s
[2016-04-15T00:53Z] INFO  17:53:52,440 ProgressMeter - Total runtime 23.71 secs, 0.40 min, 0.01 hours
[2016-04-15T00:53Z] INFO  17:53:52,441 MicroScheduler - 22360 reads were filtered out during the traversal out of approximately 265243 total reads (8.43%)
[2016-04-15T00:53Z] INFO  17:53:52,441 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:53Z] INFO  17:53:52,442 MicroScheduler -   -> 384 reads (0.14% of total) failing BadMateFilter
[2016-04-15T00:53Z] INFO  17:53:52,442 MicroScheduler -   -> 21800 reads (8.22% of total) failing DuplicateReadFilter
[2016-04-15T00:53Z] INFO  17:53:52,442 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:53Z] INFO  17:53:52,442 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:53Z] INFO  17:53:52,443 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:53Z] INFO  17:53:52,443 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:53Z] INFO  17:53:52,443 MicroScheduler -   -> 176 reads (0.07% of total) failing UnmappedReadFilter
[2016-04-15T00:53Z] INFO  17:53:52,542 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:53Z] INFO  17:53:52,546 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:53Z] INFO  17:53:52,546 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:53Z] INFO  17:53:52,547 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:53Z] INFO  17:53:52,553 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/X/R14-18105_kapa-NGv3-PE100-NGv3-sort-X_31139949_46696637-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/X/R14-18105_kapa-NGv3-PE100-NGv3-X_31139949_46696637-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/X/tx/tmpX0sCrm/R14-18105_kapa-NGv3-PE100-NGv3-X_31139949_46696637.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:53Z] INFO  17:53:52,579 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:53Z] INFO  17:53:52,581 HelpFormatter - Date/Time: 2016/04/14 17:53:52
[2016-04-15T00:53Z] INFO  17:53:52,582 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:53Z] INFO  17:53:52,583 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:53Z] INFO  17:53:52,839 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:53Z] INFO  17:53:53,092 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:53Z] INFO  17:53:53,100 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:53Z] INFO  17:53:53,232 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.13
[2016-04-15T00:53Z] INFO  17:53:53,679 IntervalUtils - Processing 99894 bp from intervals
[2016-04-15T00:53Z] WARN  17:53:53,685 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:53Z] INFO  17:53:53,799 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:53Z] INFO  17:53:53,891 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:53Z] INFO  17:53:53,903 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:53Z] INFO  17:53:53,904 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:53Z] INFO  17:53:53,905 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:53Z] INFO  17:53:53,923 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:53Z] INFO  17:53:53,975 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:53Z] INFO  17:53:53,976 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:53Z] GATK: UnifiedGenotyper
[2016-04-15T00:53Z] INFO  17:53:54,271 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:53Z] INFO  17:53:54,274 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:53Z] INFO  17:53:54,275 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:53Z] INFO  17:53:54,275 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:53Z] INFO  17:53:54,280 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/X/R14-18105_kapa-NGv3-PE100-NGv3-sort-X_46712910_62570698-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/X/R14-18105_kapa-NGv3-PE100-NGv3-X_46712910_62570698-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/X/tx/tmpxlm3zI/R14-18105_kapa-NGv3-PE100-NGv3-X_46712910_62570698.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:53Z] INFO  17:53:54,288 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:53Z] INFO  17:53:54,289 HelpFormatter - Date/Time: 2016/04/14 17:53:54
[2016-04-15T00:53Z] INFO  17:53:54,290 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:53Z] INFO  17:53:54,291 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:53Z] INFO  17:53:54,481 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:53Z] INFO  17:53:54,679 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:53Z] INFO  17:53:54,689 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:53Z] INFO  17:53:54,731 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:53Z] INFO  17:53:54,734 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:53Z] INFO  17:53:54,734 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:53Z] INFO  17:53:54,735 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:53Z] INFO  17:53:54,739 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/X/R14-18105_kapa-NGv3-PE100-NGv3-sort-X_62857907_78427545-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/X/R14-18105_kapa-NGv3-PE100-NGv3-X_62857907_78427545-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/X/tx/tmp88pird/R14-18105_kapa-NGv3-PE100-NGv3-X_62857907_78427545.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:53Z] INFO  17:53:54,767 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:53Z] INFO  17:53:54,768 HelpFormatter - Date/Time: 2016/04/14 17:53:54
[2016-04-15T00:53Z] INFO  17:53:54,769 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:53Z] INFO  17:53:54,769 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:53Z] INFO  17:53:54,809 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.12
[2016-04-15T00:53Z] INFO  17:53:55,015 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:53Z] INFO  17:53:55,250 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:53Z] INFO  17:53:55,259 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:53Z] INFO  17:53:55,266 IntervalUtils - Processing 228299 bp from intervals
[2016-04-15T00:53Z] WARN  17:53:55,273 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:53Z] INFO  17:53:55,349 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.09
[2016-04-15T00:53Z] INFO  17:53:55,366 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:53Z] INFO  17:53:55,494 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:53Z] INFO  17:53:55,495 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:53Z] INFO  17:53:55,496 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:53Z] INFO  17:53:55,496 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:53Z] INFO  17:53:55,550 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:53Z] INFO  17:53:55,551 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:53Z] INFO  17:53:55,676 IntervalUtils - Processing 175038 bp from intervals
[2016-04-15T00:53Z] WARN  17:53:55,681 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:53Z] INFO  17:53:55,769 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:53Z] INFO  17:53:55,856 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:53Z] INFO  17:53:55,857 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:53Z] INFO  17:53:55,857 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:53Z] INFO  17:53:55,858 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:53Z] INFO  17:53:55,917 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:53Z] INFO  17:53:55,918 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:53Z] INFO  17:53:56,370 ProgressMeter -     19:21992209   1084824.0    30.0 s      27.0 s       85.5%    35.0 s       5.0 s
[2016-04-15T00:53Z] INFO  17:53:56,917 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:53Z] INFO  17:53:56,920 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:53Z] INFO  17:53:56,920 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:53Z] INFO  17:53:56,920 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:53Z] INFO  17:53:56,944 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/X/R14-18105_kapa-NGv3-PE100-NGv3-sort-X_78616585_95940189-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/X/R14-18105_kapa-NGv3-PE100-NGv3-X_78616585_95940189-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/X/tx/tmpSJhmY5/R14-18105_kapa-NGv3-PE100-NGv3-X_78616585_95940189.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:53Z] INFO  17:53:56,966 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:53Z] INFO  17:53:56,967 HelpFormatter - Date/Time: 2016/04/14 17:53:56
[2016-04-15T00:53Z] INFO  17:53:56,967 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:53Z] INFO  17:53:56,967 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:53Z] INFO  17:53:57,179 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:53Z] INFO  17:53:57,263 ProgressMeter -     19:39371740   1259435.0    30.0 s      23.0 s       43.0%    69.0 s      39.0 s
[2016-04-15T00:53Z] INFO  17:53:57,364 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:53Z] INFO  17:53:57,373 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:53Z] INFO  17:53:57,439 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-15T00:53Z] INFO  17:53:57,816 IntervalUtils - Processing 45787 bp from intervals
[2016-04-15T00:53Z] WARN  17:53:57,821 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:53Z] INFO  17:53:57,946 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:53Z] INFO  17:53:57,998 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:53Z] INFO  17:53:57,999 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:53Z] INFO  17:53:58,000 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:53Z] INFO  17:53:58,000 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:53Z] INFO  17:53:58,045 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:53Z] INFO  17:53:58,046 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:53Z] INFO  17:53:58,127 ProgressMeter -     19:51205724   1218987.0    30.0 s      24.0 s       37.5%    80.0 s      50.0 s
[2016-04-15T00:53Z] INFO  17:53:59,565 ProgressMeter -            done    613276.0    13.0 s      21.0 s      100.0%    13.0 s       0.0 s
[2016-04-15T00:53Z] INFO  17:53:59,565 ProgressMeter - Total runtime 13.38 secs, 0.22 min, 0.00 hours
[2016-04-15T00:53Z] INFO  17:53:59,566 MicroScheduler - 11778 reads were filtered out during the traversal out of approximately 140307 total reads (8.39%)
[2016-04-15T00:53Z] INFO  17:53:59,566 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:53Z] INFO  17:53:59,566 MicroScheduler -   -> 238 reads (0.17% of total) failing BadMateFilter
[2016-04-15T00:53Z] INFO  17:53:59,566 MicroScheduler -   -> 11451 reads (8.16% of total) failing DuplicateReadFilter
[2016-04-15T00:53Z] INFO  17:53:59,567 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:53Z] INFO  17:53:59,567 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:53Z] INFO  17:53:59,567 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:53Z] INFO  17:53:59,568 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:53Z] INFO  17:53:59,568 MicroScheduler -   -> 89 reads (0.06% of total) failing UnmappedReadFilter
[2016-04-15T00:54Z] INFO  17:54:00,797 ProgressMeter -            done   1154024.0    34.0 s      29.0 s      100.0%    34.0 s       0.0 s
[2016-04-15T00:54Z] INFO  17:54:00,798 ProgressMeter - Total runtime 34.45 secs, 0.57 min, 0.01 hours
[2016-04-15T00:54Z] INFO  17:54:00,798 MicroScheduler - 42251 reads were filtered out during the traversal out of approximately 495325 total reads (8.53%)
[2016-04-15T00:54Z] INFO  17:54:00,798 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:54Z] INFO  17:54:00,799 MicroScheduler -   -> 815 reads (0.16% of total) failing BadMateFilter
[2016-04-15T00:54Z] INFO  17:54:00,799 MicroScheduler -   -> 41143 reads (8.31% of total) failing DuplicateReadFilter
[2016-04-15T00:54Z] INFO  17:54:00,799 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:54Z] INFO  17:54:00,800 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:54Z] INFO  17:54:00,800 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:54Z] INFO  17:54:00,800 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:54Z] INFO  17:54:00,800 MicroScheduler -   -> 293 reads (0.06% of total) failing UnmappedReadFilter
[2016-04-15T00:54Z] INFO  17:54:01,009 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:54Z] INFO  17:54:01,265 ProgressMeter -            done    281084.0    11.0 s      41.0 s       99.9%    11.0 s       0.0 s
[2016-04-15T00:54Z] INFO  17:54:01,265 ProgressMeter - Total runtime 11.61 secs, 0.19 min, 0.00 hours
[2016-04-15T00:54Z] INFO  17:54:01,265 MicroScheduler - 7623 reads were filtered out during the traversal out of approximately 92602 total reads (8.23%)
[2016-04-15T00:54Z] INFO  17:54:01,266 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:54Z] INFO  17:54:01,266 MicroScheduler -   -> 183 reads (0.20% of total) failing BadMateFilter
[2016-04-15T00:54Z] INFO  17:54:01,266 MicroScheduler -   -> 7374 reads (7.96% of total) failing DuplicateReadFilter
[2016-04-15T00:54Z] INFO  17:54:01,267 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:54Z] INFO  17:54:01,267 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:54Z] INFO  17:54:01,267 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:54Z] INFO  17:54:01,267 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:54Z] INFO  17:54:01,267 MicroScheduler -   -> 66 reads (0.07% of total) failing UnmappedReadFilter
[2016-04-15T00:54Z] GATK: UnifiedGenotyper
[2016-04-15T00:54Z] INFO  17:54:02,105 ProgressMeter -     20:44472266    901677.0    30.0 s      33.0 s       82.9%    36.0 s       6.0 s
[2016-04-15T00:54Z] INFO  17:54:02,203 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:54Z] INFO  17:54:02,274 ProgressMeter -            done    312881.0    12.0 s      38.0 s      100.0%    12.0 s       0.0 s
[2016-04-15T00:54Z] INFO  17:54:02,274 ProgressMeter - Total runtime 12.15 secs, 0.20 min, 0.00 hours
[2016-04-15T00:54Z] INFO  17:54:02,275 MicroScheduler - 6955 reads were filtered out during the traversal out of approximately 85906 total reads (8.10%)
[2016-04-15T00:54Z] INFO  17:54:02,275 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:54Z] INFO  17:54:02,275 MicroScheduler -   -> 139 reads (0.16% of total) failing BadMateFilter
[2016-04-15T00:54Z] INFO  17:54:02,276 MicroScheduler -   -> 6763 reads (7.87% of total) failing DuplicateReadFilter
[2016-04-15T00:54Z] INFO  17:54:02,276 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:54Z] INFO  17:54:02,276 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:54Z] INFO  17:54:02,277 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:54Z] INFO  17:54:02,277 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:54Z] INFO  17:54:02,277 MicroScheduler -   -> 53 reads (0.06% of total) failing UnmappedReadFilter
[2016-04-15T00:54Z] GATK: UnifiedGenotyper
[2016-04-15T00:54Z] INFO  17:54:02,747 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:54Z] INFO  17:54:02,780 ProgressMeter -     20:62333488   1091886.0    30.0 s      27.0 s       90.9%    33.0 s       3.0 s
[2016-04-15T00:54Z] GATK: UnifiedGenotyper
[2016-04-15T00:54Z] INFO  17:54:03,638 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:54Z] GATK: UnifiedGenotyper
[2016-04-15T00:54Z] INFO  17:54:04,022 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:54Z] INFO  17:54:04,025 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:54Z] INFO  17:54:04,026 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:54Z] INFO  17:54:04,046 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:54Z] INFO  17:54:04,050 ProgressMeter -            done    248425.0    10.0 s      40.0 s      100.0%    10.0 s       0.0 s
[2016-04-15T00:54Z] INFO  17:54:04,050 ProgressMeter - Total runtime 10.15 secs, 0.17 min, 0.00 hours
[2016-04-15T00:54Z] INFO  17:54:04,051 MicroScheduler - 5447 reads were filtered out during the traversal out of approximately 65208 total reads (8.35%)
[2016-04-15T00:54Z] INFO  17:54:04,051 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:54Z] INFO  17:54:04,051 MicroScheduler -   -> 91 reads (0.14% of total) failing BadMateFilter
[2016-04-15T00:54Z] INFO  17:54:04,051 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/X/R14-18105_kapa-NGv3-PE100-NGv3-sort-X_95990756_111698889-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/X/R14-18105_kapa-NGv3-PE100-NGv3-X_95990756_111698889-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/X/tx/tmpXZ91L8/R14-18105_kapa-NGv3-PE100-NGv3-X_95990756_111698889.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:54Z] INFO  17:54:04,052 MicroScheduler -   -> 5316 reads (8.15% of total) failing DuplicateReadFilter
[2016-04-15T00:54Z] INFO  17:54:04,052 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:54Z] INFO  17:54:04,052 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:54Z] INFO  17:54:04,053 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:54Z] INFO  17:54:04,053 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:54Z] INFO  17:54:04,053 MicroScheduler -   -> 40 reads (0.06% of total) failing UnmappedReadFilter
[2016-04-15T00:54Z] INFO  17:54:04,061 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:54Z] INFO  17:54:04,062 HelpFormatter - Date/Time: 2016/04/14 17:54:04
[2016-04-15T00:54Z] INFO  17:54:04,063 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:54Z] INFO  17:54:04,063 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:54Z] INFO  17:54:04,233 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:54Z] INFO  17:54:04,458 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:54Z] INFO  17:54:04,468 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:54Z] INFO  17:54:04,543 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-15T00:54Z] INFO  17:54:05,002 IntervalUtils - Processing 181656 bp from intervals
[2016-04-15T00:54Z] WARN  17:54:05,009 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:54Z] INFO  17:54:05,130 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:54Z] INFO  17:54:05,227 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:54Z] INFO  17:54:05,236 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:54Z] INFO  17:54:05,237 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:54Z] INFO  17:54:05,238 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:54Z] INFO  17:54:05,256 ProgressMeter -            done   1223679.0    32.0 s      26.0 s      100.0%    32.0 s       0.0 s
[2016-04-15T00:54Z] INFO  17:54:05,256 ProgressMeter - Total runtime 32.49 secs, 0.54 min, 0.01 hours
[2016-04-15T00:54Z] INFO  17:54:05,256 MicroScheduler - 34785 reads were filtered out during the traversal out of approximately 412632 total reads (8.43%)
[2016-04-15T00:54Z] INFO  17:54:05,257 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:54Z] INFO  17:54:05,257 MicroScheduler -   -> 592 reads (0.14% of total) failing BadMateFilter
[2016-04-15T00:54Z] INFO  17:54:05,257 MicroScheduler -   -> 33925 reads (8.22% of total) failing DuplicateReadFilter
[2016-04-15T00:54Z] INFO  17:54:05,258 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:54Z] INFO  17:54:05,258 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:54Z] INFO  17:54:05,258 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:54Z] INFO  17:54:05,259 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:54Z] INFO  17:54:05,259 MicroScheduler -   -> 268 reads (0.06% of total) failing UnmappedReadFilter
[2016-04-15T00:54Z] INFO  17:54:05,280 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:54Z] INFO  17:54:05,284 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:54Z] INFO  17:54:05,285 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:54Z] INFO  17:54:05,286 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:54Z] INFO  17:54:05,291 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/X/R14-18105_kapa-NGv3-PE100-NGv3-sort-X_111874647_128581278-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/X/R14-18105_kapa-NGv3-PE100-NGv3-X_111874647_128581278-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/X/tx/tmpFEiUQO/R14-18105_kapa-NGv3-PE100-NGv3-X_111874647_128581278.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:54Z] INFO  17:54:05,292 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:54Z] INFO  17:54:05,293 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:54Z] INFO  17:54:05,318 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:54Z] INFO  17:54:05,319 HelpFormatter - Date/Time: 2016/04/14 17:54:05
[2016-04-15T00:54Z] INFO  17:54:05,319 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:54Z] INFO  17:54:05,319 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:54Z] INFO  17:54:05,491 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:54Z] INFO  17:54:05,545 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:54Z] INFO  17:54:05,710 ProgressMeter -            done    104106.0     7.0 s      74.0 s       99.9%     7.0 s       0.0 s
[2016-04-15T00:54Z] INFO  17:54:05,711 ProgressMeter - Total runtime 7.71 secs, 0.13 min, 0.00 hours
[2016-04-15T00:54Z] INFO  17:54:05,711 MicroScheduler - 2090 reads were filtered out during the traversal out of approximately 27121 total reads (7.71%)
[2016-04-15T00:54Z] INFO  17:54:05,711 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:54Z] INFO  17:54:05,712 MicroScheduler -   -> 41 reads (0.15% of total) failing BadMateFilter
[2016-04-15T00:54Z] INFO  17:54:05,712 MicroScheduler -   -> 2034 reads (7.50% of total) failing DuplicateReadFilter
[2016-04-15T00:54Z] INFO  17:54:05,712 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:54Z] INFO  17:54:05,712 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:54Z] INFO  17:54:05,713 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:54Z] INFO  17:54:05,713 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:54Z] INFO  17:54:05,713 MicroScheduler -   -> 15 reads (0.06% of total) failing UnmappedReadFilter
[2016-04-15T00:54Z] INFO  17:54:05,777 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:54Z] GATK: UnifiedGenotyper
[2016-04-15T00:54Z] INFO  17:54:05,797 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:54Z] INFO  17:54:05,851 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-15T00:54Z] INFO  17:54:05,893 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:54Z] INFO  17:54:05,896 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:54Z] INFO  17:54:05,896 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:54Z] INFO  17:54:05,897 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:54Z] INFO  17:54:05,901 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/X/R14-18105_kapa-NGv3-PE100-NGv3-sort-X_128582278_144329181-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/X/R14-18105_kapa-NGv3-PE100-NGv3-X_128582278_144329181-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/X/tx/tmpYashXP/R14-18105_kapa-NGv3-PE100-NGv3-X_128582278_144329181.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:54Z] INFO  17:54:05,910 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:54Z] INFO  17:54:05,911 HelpFormatter - Date/Time: 2016/04/14 17:54:05
[2016-04-15T00:54Z] INFO  17:54:05,911 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:54Z] INFO  17:54:05,912 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:54Z] INFO  17:54:06,075 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:54Z] INFO  17:54:06,243 IntervalUtils - Processing 115535 bp from intervals
[2016-04-15T00:54Z] WARN  17:54:06,264 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:54Z] INFO  17:54:06,366 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:54Z] INFO  17:54:06,373 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:54Z] INFO  17:54:06,386 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:54Z] INFO  17:54:06,452 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:54Z] INFO  17:54:06,453 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:54Z] INFO  17:54:06,454 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:54Z] INFO  17:54:06,455 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:54Z] INFO  17:54:06,468 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-15T00:54Z] INFO  17:54:06,519 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:54Z] INFO  17:54:06,519 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:54Z] INFO  17:54:06,617 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:54Z] INFO  17:54:06,619 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:54Z] INFO  17:54:06,620 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:54Z] INFO  17:54:06,620 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:54Z] INFO  17:54:06,640 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:54Z] INFO  17:54:06,641 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/X/R14-18105_kapa-NGv3-PE100-NGv3-sort-X_144337190_155270560-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/X/R14-18105_kapa-NGv3-PE100-NGv3-X_144337190_155270560-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/X/tx/tmp5Fq2Um/R14-18105_kapa-NGv3-PE100-NGv3-X_144337190_155270560.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:54Z] INFO  17:54:06,661 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:54Z] INFO  17:54:06,662 HelpFormatter - Date/Time: 2016/04/14 17:54:06
[2016-04-15T00:54Z] INFO  17:54:06,662 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:54Z] INFO  17:54:06,663 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:54Z] INFO  17:54:06,834 ProgressMeter -     21:46226866    846390.0    30.0 s      35.0 s       98.2%    30.0 s       0.0 s
[2016-04-15T00:54Z] INFO  17:54:06,838 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:54Z] GATK: UnifiedGenotyper
[2016-04-15T00:54Z] INFO  17:54:07,024 IntervalUtils - Processing 143302 bp from intervals
[2016-04-15T00:54Z] WARN  17:54:07,029 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:54Z] INFO  17:54:07,047 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:54Z] INFO  17:54:07,062 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:54Z] INFO  17:54:07,096 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:54Z] INFO  17:54:07,147 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-15T00:54Z] INFO  17:54:07,159 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:54Z] INFO  17:54:07,160 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:54Z] INFO  17:54:07,161 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:54Z] INFO  17:54:07,162 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:54Z] INFO  17:54:07,192 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:54Z] INFO  17:54:07,214 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:54Z] INFO  17:54:07,215 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:54Z] INFO  17:54:07,361 ProgressMeter -            done    861650.0    30.0 s      35.0 s      100.0%    30.0 s       0.0 s
[2016-04-15T00:54Z] INFO  17:54:07,372 ProgressMeter - Total runtime 30.57 secs, 0.51 min, 0.01 hours
[2016-04-15T00:54Z] INFO  17:54:07,374 MicroScheduler - 35625 reads were filtered out during the traversal out of approximately 413376 total reads (8.62%)
[2016-04-15T00:54Z] INFO  17:54:07,374 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:54Z] INFO  17:54:07,375 MicroScheduler -   -> 616 reads (0.15% of total) failing BadMateFilter
[2016-04-15T00:54Z] INFO  17:54:07,376 MicroScheduler -   -> 34703 reads (8.40% of total) failing DuplicateReadFilter
[2016-04-15T00:54Z] INFO  17:54:07,376 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:54Z] INFO  17:54:07,377 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:54Z] INFO  17:54:07,377 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:54Z] INFO  17:54:07,378 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:54Z] INFO  17:54:07,379 MicroScheduler -   -> 306 reads (0.07% of total) failing UnmappedReadFilter
[2016-04-15T00:54Z] GATK: UnifiedGenotyper
[2016-04-15T00:54Z] INFO  17:54:07,549 IntervalUtils - Processing 184337 bp from intervals
[2016-04-15T00:54Z] WARN  17:54:07,554 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:54Z] INFO  17:54:07,657 ProgressMeter -            done   1208060.0    35.0 s      29.0 s      100.0%    35.0 s       0.0 s
[2016-04-15T00:54Z] INFO  17:54:07,657 ProgressMeter - Total runtime 35.58 secs, 0.59 min, 0.01 hours
[2016-04-15T00:54Z] INFO  17:54:07,658 MicroScheduler - 41763 reads were filtered out during the traversal out of approximately 498760 total reads (8.37%)
[2016-04-15T00:54Z] INFO  17:54:07,658 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:54Z] INFO  17:54:07,658 MicroScheduler -   -> 768 reads (0.15% of total) failing BadMateFilter
[2016-04-15T00:54Z] INFO  17:54:07,659 MicroScheduler -   -> 40715 reads (8.16% of total) failing DuplicateReadFilter
[2016-04-15T00:54Z] INFO  17:54:07,659 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:54Z] INFO  17:54:07,659 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:54Z] INFO  17:54:07,660 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:54Z] INFO  17:54:07,660 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:54Z] INFO  17:54:07,660 MicroScheduler -   -> 280 reads (0.06% of total) failing UnmappedReadFilter
[2016-04-15T00:54Z] INFO  17:54:07,667 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:54Z] INFO  17:54:07,786 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:54Z] INFO  17:54:07,787 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:54Z] INFO  17:54:07,787 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:54Z] INFO  17:54:07,788 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:54Z] INFO  17:54:07,851 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:54Z] INFO  17:54:07,852 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:54Z] INFO  17:54:08,575 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:54Z] INFO  17:54:08,579 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:54Z] INFO  17:54:08,579 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:54Z] INFO  17:54:08,580 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:54Z] INFO  17:54:08,584 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/Y/R14-18105_kapa-NGv3-PE100-NGv3-sort-Y_0_15522993-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/Y/R14-18105_kapa-NGv3-PE100-NGv3-Y_0_15522993-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/Y/tx/tmpqfs8xo/R14-18105_kapa-NGv3-PE100-NGv3-Y_0_15522993.vcf.gz -ploidy 1 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:54Z] INFO  17:54:08,601 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:54Z] INFO  17:54:08,603 HelpFormatter - Date/Time: 2016/04/14 17:54:08
[2016-04-15T00:54Z] INFO  17:54:08,603 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:54Z] INFO  17:54:08,604 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:54Z] INFO  17:54:08,765 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:54Z] INFO  17:54:08,956 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:54Z] INFO  17:54:09,013 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:54Z] INFO  17:54:09,034 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:54Z] INFO  17:54:09,113 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-15T00:54Z] GATK: HaplotypeCaller
[2016-04-15T00:54Z] INFO  17:54:09,450 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:54Z] INFO  17:54:09,486 IntervalUtils - Processing 52192 bp from intervals
[2016-04-15T00:54Z] WARN  17:54:09,491 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:54Z] INFO  17:54:09,584 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:54Z] INFO  17:54:09,665 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:54Z] INFO  17:54:09,666 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:54Z] INFO  17:54:09,667 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:54Z] INFO  17:54:09,668 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:54Z] INFO  17:54:09,720 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:54Z] INFO  17:54:09,721 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:54Z] GATK: HaplotypeCaller
[2016-04-15T00:54Z] INFO  17:54:09,808 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:54Z] INFO  17:54:09,812 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:54Z] INFO  17:54:09,813 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:54Z] INFO  17:54:09,813 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:54Z] INFO  17:54:09,819 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/Y/R14-18105_kapa-NGv3-PE100-NGv3-sort-Y_15526614_59222281-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/Y/R14-18105_kapa-NGv3-PE100-NGv3-Y_15526614_59222281-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/Y/tx/tmp9fZ_eB/R14-18105_kapa-NGv3-PE100-NGv3-Y_15526614_59222281.vcf.gz -ploidy 1 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:54Z] INFO  17:54:09,830 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:54Z] INFO  17:54:09,831 HelpFormatter - Date/Time: 2016/04/14 17:54:09
[2016-04-15T00:54Z] INFO  17:54:09,831 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:54Z] INFO  17:54:09,832 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:54Z] INFO  17:54:10,029 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:54Z] INFO  17:54:10,255 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:54Z] INFO  17:54:10,272 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:54Z] INFO  17:54:10,372 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.10
[2016-04-15T00:54Z] INFO  17:54:10,438 ProgressMeter -            done    626722.0    14.0 s      23.0 s      100.0%    14.0 s       0.0 s
[2016-04-15T00:54Z] INFO  17:54:10,439 ProgressMeter - Total runtime 14.58 secs, 0.24 min, 0.00 hours
[2016-04-15T00:54Z] INFO  17:54:10,441 MicroScheduler - 10603 reads were filtered out during the traversal out of approximately 132731 total reads (7.99%)
[2016-04-15T00:54Z] INFO  17:54:10,442 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:54Z] INFO  17:54:10,443 MicroScheduler -   -> 205 reads (0.15% of total) failing BadMateFilter
[2016-04-15T00:54Z] INFO  17:54:10,444 MicroScheduler -   -> 10307 reads (7.77% of total) failing DuplicateReadFilter
[2016-04-15T00:54Z] INFO  17:54:10,444 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:54Z] INFO  17:54:10,445 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:54Z] INFO  17:54:10,446 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:54Z] INFO  17:54:10,447 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:54Z] INFO  17:54:10,448 MicroScheduler -   -> 91 reads (0.07% of total) failing UnmappedReadFilter
[2016-04-15T00:54Z] INFO  17:54:10,655 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:54Z] INFO  17:54:10,665 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:54Z] INFO  17:54:10,666 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:54Z] INFO  17:54:10,666 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:54Z] INFO  17:54:10,671 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/Y/R14-18105_kapa-NGv3-PE100-NGv3-sort-Y_59228291_59373566-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/Y/R14-18105_kapa-NGv3-PE100-NGv3-Y_59228291_59373566-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/Y/tx/tmpq03NSk/R14-18105_kapa-NGv3-PE100-NGv3-Y_59228291_59373566.vcf.gz -ploidy 1 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:54Z] INFO  17:54:10,702 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:54Z] INFO  17:54:10,712 HelpFormatter - Date/Time: 2016/04/14 17:54:10
[2016-04-15T00:54Z] INFO  17:54:10,713 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:54Z] INFO  17:54:10,713 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:54Z] INFO  17:54:10,809 IntervalUtils - Processing 44713 bp from intervals
[2016-04-15T00:54Z] WARN  17:54:10,825 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:54Z] INFO  17:54:10,893 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:54Z] INFO  17:54:10,913 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:54Z] INFO  17:54:10,995 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:54Z] INFO  17:54:10,996 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:54Z] INFO  17:54:10,997 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:54Z] INFO  17:54:10,997 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:54Z] INFO  17:54:11,096 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:54Z] INFO  17:54:11,097 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:54Z] INFO  17:54:11,151 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T00:54Z] INFO  17:54:11,169 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:54Z] INFO  17:54:11,281 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.11
[2016-04-15T00:54Z] INFO  17:54:11,774 IntervalUtils - Processing 2412 bp from intervals
[2016-04-15T00:54Z] WARN  17:54:11,778 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:54Z] INFO  17:54:11,873 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:54Z] INFO  17:54:11,897 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:54Z] INFO  17:54:11,898 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:54Z] INFO  17:54:11,898 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T00:54Z] INFO  17:54:11,899 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T00:54Z] INFO  17:54:11,941 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:54Z] INFO  17:54:11,942 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T00:54Z] INFO  17:54:12,053 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:54Z] INFO  17:54:12,203 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:54Z] INFO  17:54:12,206 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:54Z] INFO  17:54:12,207 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:54Z] INFO  17:54:12,207 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:54Z] INFO  17:54:12,212 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/1/R14-18105_kapa-NGv3-PE100-NGv3-sort-1_0_15541927-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/1/R14-18105_kapa-NGv3-PE100-NGv3-1_0_15541927-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/1/tx/tmp9Crokg/R14-18105_kapa-NGv3-PE100-NGv3-1_0_15541927.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:54Z] INFO  17:54:12,231 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:54Z] INFO  17:54:12,232 HelpFormatter - Date/Time: 2016/04/14 17:54:12
[2016-04-15T00:54Z] INFO  17:54:12,232 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:54Z] INFO  17:54:12,233 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:54Z] WARN  17:54:12,278 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T00:54Z] WARN  17:54:12,281 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/1/tx/tmp9Crokg/R14-18105_kapa-NGv3-PE100-NGv3-1_0_15541927.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T00:54Z] INFO  17:54:12,557 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:54Z] GATK: HaplotypeCaller
[2016-04-15T00:54Z] INFO  17:54:12,711 ProgressMeter -            done     16030.0     0.0 s      50.0 s       96.1%     0.0 s       0.0 s
[2016-04-15T00:54Z] INFO  17:54:12,712 ProgressMeter - Total runtime 0.81 secs, 0.01 min, 0.00 hours
[2016-04-15T00:54Z] INFO  17:54:12,748 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T00:54Z] INFO  17:54:12,758 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:54Z] INFO  17:54:12,839 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-15T00:54Z] INFO  17:54:12,874 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T00:54Z] INFO  17:54:13,140 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:54Z] INFO  17:54:13,144 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:54Z] INFO  17:54:13,144 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:54Z] INFO  17:54:13,145 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:54Z] INFO  17:54:13,149 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/1/R14-18105_kapa-NGv3-PE100-NGv3-sort-1_15545821_31186478-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/1/R14-18105_kapa-NGv3-PE100-NGv3-1_15545821_31186478-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/1/tx/tmpdaCPdp/R14-18105_kapa-NGv3-PE100-NGv3-1_15545821_31186478.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:54Z] INFO  17:54:13,180 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:54Z] INFO  17:54:13,181 HelpFormatter - Date/Time: 2016/04/14 17:54:13
[2016-04-15T00:54Z] INFO  17:54:13,181 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:54Z] INFO  17:54:13,182 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:54Z] WARN  17:54:13,209 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T00:54Z] WARN  17:54:13,211 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/1/tx/tmpdaCPdp/R14-18105_kapa-NGv3-PE100-NGv3-1_15545821_31186478.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T00:54Z] INFO  17:54:13,310 ProgressMeter -     22:25436527    835950.0    30.0 s      35.0 s       63.6%    47.0 s      17.0 s
[2016-04-15T00:54Z] INFO  17:54:13,321 IntervalUtils - Processing 390138 bp from intervals
[2016-04-15T00:54Z] WARN  17:54:13,337 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:54Z] INFO  17:54:13,417 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:54Z] INFO  17:54:13,429 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:54Z] INFO  17:54:13,543 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:54Z] INFO  17:54:13,544 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:54Z] INFO  17:54:13,544 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T00:54Z] INFO  17:54:13,544 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T00:54Z] INFO  17:54:13,545 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T00:54Z] INFO  17:54:13,545 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T00:54Z] INFO  17:54:13,573 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T00:54Z] INFO  17:54:13,585 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:54Z] INFO  17:54:13,670 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-15T00:54Z] INFO  17:54:13,699 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T00:54Z] INFO  17:54:13,791 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T00:54Z] INFO  17:54:14,086 IntervalUtils - Processing 386393 bp from intervals
[2016-04-15T00:54Z] WARN  17:54:14,092 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:54Z] INFO  17:54:14,127 ProgressMeter -            done   1090417.0    18.0 s      17.0 s      100.0%    18.0 s       0.0 s
[2016-04-15T00:54Z] INFO  17:54:14,127 ProgressMeter - Total runtime 18.63 secs, 0.31 min, 0.01 hours
[2016-04-15T00:54Z] INFO  17:54:14,128 MicroScheduler - 17138 reads were filtered out during the traversal out of approximately 227141 total reads (7.55%)
[2016-04-15T00:54Z] INFO  17:54:14,128 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:54Z] INFO  17:54:14,129 MicroScheduler -   -> 329 reads (0.14% of total) failing BadMateFilter
[2016-04-15T00:54Z] INFO  17:54:14,129 MicroScheduler -   -> 16676 reads (7.34% of total) failing DuplicateReadFilter
[2016-04-15T00:54Z] INFO  17:54:14,129 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:54Z] INFO  17:54:14,129 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:54Z] INFO  17:54:14,130 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:54Z] INFO  17:54:14,130 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:54Z] INFO  17:54:14,130 MicroScheduler -   -> 133 reads (0.06% of total) failing UnmappedReadFilter
[2016-04-15T00:54Z] INFO  17:54:14,192 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:54Z] INFO  17:54:14,341 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:54Z] INFO  17:54:14,341 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:54Z] INFO  17:54:14,341 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T00:54Z] INFO  17:54:14,342 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T00:54Z] INFO  17:54:14,350 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T00:54Z] INFO  17:54:14,350 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T00:54Z] INFO  17:54:14,361 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:54Z] INFO  17:54:14,565 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T00:54Z] GATK: HaplotypeCaller
[2016-04-15T00:54Z] INFO  17:54:15,300 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:54Z] INFO  17:54:15,303 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:54Z] INFO  17:54:15,303 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:54Z] INFO  17:54:15,303 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:54Z] INFO  17:54:15,307 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/1/R14-18105_kapa-NGv3-PE100-NGv3-sort-1_31187093_46714270-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/1/R14-18105_kapa-NGv3-PE100-NGv3-1_31187093_46714270-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/1/tx/tmpOA_HtM/R14-18105_kapa-NGv3-PE100-NGv3-1_31187093_46714270.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:54Z] INFO  17:54:15,316 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:54Z] INFO  17:54:15,317 HelpFormatter - Date/Time: 2016/04/14 17:54:15
[2016-04-15T00:54Z] INFO  17:54:15,318 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:54Z] INFO  17:54:15,318 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:54Z] WARN  17:54:15,352 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T00:54Z] WARN  17:54:15,355 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/1/tx/tmpOA_HtM/R14-18105_kapa-NGv3-PE100-NGv3-1_31187093_46714270.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T00:54Z] INFO  17:54:15,385 ProgressMeter -     22:42180343    904619.0    30.0 s      33.0 s       68.1%    44.0 s      14.0 s
[2016-04-15T00:54Z] INFO  17:54:15,497 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:54Z] INFO  17:54:15,562 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:54Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T00:54Z] INFO  17:54:15,696 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T00:54Z] INFO  17:54:15,703 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T00:54Z] INFO  17:54:15,772 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T00:54Z] INFO  17:54:15,781 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:54Z] GATK: HaplotypeCaller
[2016-04-15T00:54Z] WARN  17:54:15,892 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T00:54Z] WARN  17:54:15,893 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T00:54Z] INFO  17:54:16,211 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.43
[2016-04-15T00:54Z] INFO  17:54:16,244 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T00:54Z] INFO  17:54:16,861 IntervalUtils - Processing 431182 bp from intervals
[2016-04-15T00:54Z] WARN  17:54:16,868 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:54Z] INFO  17:54:17,013 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:54Z] INFO  17:54:17,161 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:54Z] INFO  17:54:17,162 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:54Z] INFO  17:54:17,163 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T00:54Z] INFO  17:54:17,163 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T00:54Z] INFO  17:54:17,175 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T00:54Z] INFO  17:54:17,176 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T00:54Z] INFO  17:54:17,378 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T00:54Z] INFO  17:54:17,697 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:54Z] INFO  17:54:17,701 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:54Z] INFO  17:54:17,701 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:54Z] INFO  17:54:17,702 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:54Z] INFO  17:54:17,706 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/1/R14-18105_kapa-NGv3-PE100-NGv3-sort-1_46715671_62228851-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/1/R14-18105_kapa-NGv3-PE100-NGv3-1_46715671_62228851-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/1/tx/tmpceeyNE/R14-18105_kapa-NGv3-PE100-NGv3-1_46715671_62228851.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:54Z] INFO  17:54:17,736 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:54Z] INFO  17:54:17,746 HelpFormatter - Date/Time: 2016/04/14 17:54:17
[2016-04-15T00:54Z] INFO  17:54:17,747 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:54Z] INFO  17:54:17,752 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:54Z] WARN  17:54:17,794 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T00:54Z] WARN  17:54:17,797 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/1/tx/tmpceeyNE/R14-18105_kapa-NGv3-PE100-NGv3-1_46715671_62228851.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T00:54Z] INFO  17:54:18,023 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:54Z] INFO  17:54:18,237 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T00:54Z] INFO  17:54:18,260 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:54Z] INFO  17:54:18,331 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-15T00:54Z] INFO  17:54:18,359 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T00:54Z] INFO  17:54:18,718 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:54Z] INFO  17:54:18,721 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:54Z] INFO  17:54:18,722 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:54Z] INFO  17:54:18,722 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:54Z] INFO  17:54:18,727 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/1/R14-18105_kapa-NGv3-PE100-NGv3-sort-1_62231950_77749296-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/1/R14-18105_kapa-NGv3-PE100-NGv3-1_62231950_77749296-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/1/tx/tmpeWcTvR/R14-18105_kapa-NGv3-PE100-NGv3-1_62231950_77749296.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:54Z] INFO  17:54:18,755 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:54Z] INFO  17:54:18,756 HelpFormatter - Date/Time: 2016/04/14 17:54:18
[2016-04-15T00:54Z] INFO  17:54:18,757 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:54Z] INFO  17:54:18,757 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:54Z] WARN  17:54:18,809 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T00:54Z] WARN  17:54:18,812 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/1/tx/tmpeWcTvR/R14-18105_kapa-NGv3-PE100-NGv3-1_62231950_77749296.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T00:54Z] INFO  17:54:18,838 ProgressMeter -            done   1149428.0     9.0 s       7.0 s      100.0%     9.0 s       0.0 s
[2016-04-15T00:54Z] INFO  17:54:18,841 IntervalUtils - Processing 180557 bp from intervals
[2016-04-15T00:54Z] INFO  17:54:18,839 ProgressMeter - Total runtime 9.17 secs, 0.15 min, 0.00 hours
[2016-04-15T00:54Z] INFO  17:54:18,839 MicroScheduler - 4316 reads were filtered out during the traversal out of approximately 82212 total reads (5.25%)
[2016-04-15T00:54Z] INFO  17:54:18,840 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:54Z] INFO  17:54:18,840 MicroScheduler -   -> 122 reads (0.15% of total) failing BadMateFilter
[2016-04-15T00:54Z] INFO  17:54:18,840 MicroScheduler -   -> 4150 reads (5.05% of total) failing DuplicateReadFilter
[2016-04-15T00:54Z] INFO  17:54:18,840 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:54Z] INFO  17:54:18,841 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:54Z] INFO  17:54:18,841 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:54Z] INFO  17:54:18,841 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:54Z] INFO  17:54:18,841 MicroScheduler -   -> 44 reads (0.05% of total) failing UnmappedReadFilter
[2016-04-15T00:54Z] WARN  17:54:18,857 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:54Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T00:54Z] INFO  17:54:18,965 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T00:54Z] INFO  17:54:18,977 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T00:54Z] INFO  17:54:18,979 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:54Z] INFO  17:54:19,045 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:54Z] INFO  17:54:19,115 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:54Z] INFO  17:54:19,116 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:54Z] INFO  17:54:19,116 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T00:54Z] INFO  17:54:19,117 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T00:54Z] INFO  17:54:19,118 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T00:54Z] INFO  17:54:19,118 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T00:54Z] WARN  17:54:19,167 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T00:54Z] WARN  17:54:19,168 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T00:54Z] INFO  17:54:19,252 ProgressMeter -            done    306895.0    12.0 s      41.0 s      100.0%    12.0 s       0.0 s
[2016-04-15T00:54Z] INFO  17:54:19,252 ProgressMeter - Total runtime 12.80 secs, 0.21 min, 0.00 hours
[2016-04-15T00:54Z] INFO  17:54:19,252 MicroScheduler - 5926 reads were filtered out during the traversal out of approximately 85463 total reads (6.93%)
[2016-04-15T00:54Z] INFO  17:54:19,253 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:54Z] INFO  17:54:19,253 MicroScheduler -   -> 128 reads (0.15% of total) failing BadMateFilter
[2016-04-15T00:54Z] INFO  17:54:19,253 MicroScheduler -   -> 5736 reads (6.71% of total) failing DuplicateReadFilter
[2016-04-15T00:54Z] INFO  17:54:19,254 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:54Z] INFO  17:54:19,254 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:54Z] INFO  17:54:19,254 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:54Z] INFO  17:54:19,254 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:54Z] INFO  17:54:19,255 MicroScheduler -   -> 62 reads (0.07% of total) failing UnmappedReadFilter
[2016-04-15T00:54Z] INFO  17:54:19,292 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T00:54Z] INFO  17:54:19,310 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:54Z] INFO  17:54:19,336 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T00:54Z] INFO  17:54:19,392 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-15T00:54Z] INFO  17:54:19,430 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T00:54Z] INFO  17:54:19,684 ProgressMeter -            done    518040.0    14.0 s      27.0 s      100.0%    14.0 s       0.0 s
[2016-04-15T00:54Z] INFO  17:54:19,685 ProgressMeter - Total runtime 14.45 secs, 0.24 min, 0.00 hours
[2016-04-15T00:54Z] INFO  17:54:19,685 MicroScheduler - 10106 reads were filtered out during the traversal out of approximately 130593 total reads (7.74%)
[2016-04-15T00:54Z] INFO  17:54:19,685 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:54Z] INFO  17:54:19,686 MicroScheduler -   -> 204 reads (0.16% of total) failing BadMateFilter
[2016-04-15T00:54Z] INFO  17:54:19,686 MicroScheduler -   -> 9825 reads (7.52% of total) failing DuplicateReadFilter
[2016-04-15T00:54Z] INFO  17:54:19,686 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:54Z] INFO  17:54:19,687 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:54Z] INFO  17:54:19,687 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:54Z] INFO  17:54:19,687 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:54Z] INFO  17:54:19,687 MicroScheduler -   -> 77 reads (0.06% of total) failing UnmappedReadFilter
[2016-04-15T00:54Z] INFO  17:54:19,793 IntervalUtils - Processing 150085 bp from intervals
[2016-04-15T00:54Z] WARN  17:54:19,808 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:54Z] INFO  17:54:19,893 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:54Z] INFO  17:54:20,000 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:54Z] INFO  17:54:20,001 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:54Z] INFO  17:54:20,002 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T00:54Z] INFO  17:54:20,002 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T00:54Z] INFO  17:54:20,003 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T00:54Z] INFO  17:54:20,003 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T00:54Z] INFO  17:54:20,137 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:54Z] INFO  17:54:20,216 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T00:54Z] GATK: HaplotypeCaller
[2016-04-15T00:54Z] INFO  17:54:20,494 ProgressMeter -            done    145748.0     9.0 s      65.0 s       99.9%     9.0 s       0.0 s
[2016-04-15T00:54Z] INFO  17:54:20,495 ProgressMeter - Total runtime 9.50 secs, 0.16 min, 0.00 hours
[2016-04-15T00:54Z] INFO  17:54:20,495 MicroScheduler - 2923 reads were filtered out during the traversal out of approximately 74793 total reads (3.91%)
[2016-04-15T00:54Z] INFO  17:54:20,496 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:54Z] INFO  17:54:20,496 MicroScheduler -   -> 120 reads (0.16% of total) failing BadMateFilter
[2016-04-15T00:54Z] INFO  17:54:20,496 MicroScheduler -   -> 2739 reads (3.66% of total) failing DuplicateReadFilter
[2016-04-15T00:54Z] INFO  17:54:20,496 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:54Z] INFO  17:54:20,497 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:54Z] INFO  17:54:20,497 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:54Z] INFO  17:54:20,497 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:54Z] INFO  17:54:20,497 MicroScheduler -   -> 64 reads (0.09% of total) failing UnmappedReadFilter
[2016-04-15T00:54Z] INFO  17:54:20,852 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:54Z] INFO  17:54:20,857 ProgressMeter -            done    411488.0    13.0 s      33.0 s       99.9%    13.0 s       0.0 s
[2016-04-15T00:54Z] INFO  17:54:20,857 ProgressMeter - Total runtime 13.70 secs, 0.23 min, 0.00 hours
[2016-04-15T00:54Z] INFO  17:54:20,858 MicroScheduler - 8223 reads were filtered out during the traversal out of approximately 109422 total reads (7.51%)
[2016-04-15T00:54Z] INFO  17:54:20,858 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:54Z] INFO  17:54:20,858 MicroScheduler -   -> 163 reads (0.15% of total) failing BadMateFilter
[2016-04-15T00:54Z] INFO  17:54:20,859 MicroScheduler -   -> 7987 reads (7.30% of total) failing DuplicateReadFilter
[2016-04-15T00:54Z] INFO  17:54:20,859 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:54Z] INFO  17:54:20,859 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:54Z] INFO  17:54:20,859 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:54Z] INFO  17:54:20,860 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:54Z] INFO  17:54:20,860 MicroScheduler -   -> 73 reads (0.07% of total) failing UnmappedReadFilter
[2016-04-15T00:54Z] GATK: HaplotypeCaller
[2016-04-15T00:54Z] INFO  17:54:21,878 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:54Z] INFO  17:54:21,940 ProgressMeter -     19:10792669   2907859.0    60.0 s      20.0 s       71.1%    84.0 s      24.0 s
[2016-04-15T00:54Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T00:54Z] INFO  17:54:22,062 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T00:54Z] INFO  17:54:22,063 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T00:54Z] GATK: HaplotypeCaller
[2016-04-15T00:54Z] INFO  17:54:22,197 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:54Z] WARN  17:54:22,305 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T00:54Z] WARN  17:54:22,306 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T00:54Z] INFO  17:54:22,346 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:54Z] GATK: HaplotypeCaller
[2016-04-15T00:54Z] GATK: HaplotypeCaller
[2016-04-15T00:54Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T00:54Z] INFO  17:54:22,742 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T00:54Z] INFO  17:54:22,743 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T00:54Z] WARN  17:54:23,043 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T00:54Z] WARN  17:54:23,044 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T00:54Z] INFO  17:54:23,440 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:54Z] INFO  17:54:23,461 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:54Z] INFO  17:54:23,462 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:54Z] INFO  17:54:23,463 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:54Z] INFO  17:54:23,468 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/1/R14-18105_kapa-NGv3-PE100-NGv3-sort-1_77752625_93297674-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/1/R14-18105_kapa-NGv3-PE100-NGv3-1_77752625_93297674-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/1/tx/tmpzsdisR/R14-18105_kapa-NGv3-PE100-NGv3-1_77752625_93297674.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:54Z] INFO  17:54:23,503 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:54Z] INFO  17:54:23,504 HelpFormatter - Date/Time: 2016/04/14 17:54:23
[2016-04-15T00:54Z] INFO  17:54:23,513 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:54Z] INFO  17:54:23,514 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:54Z] INFO  17:54:23,518 ProgressMeter -            done   1018074.0    15.0 s      15.0 s      100.0%    15.0 s       0.0 s
[2016-04-15T00:54Z] INFO  17:54:23,518 ProgressMeter - Total runtime 15.73 secs, 0.26 min, 0.00 hours
[2016-04-15T00:54Z] INFO  17:54:23,518 MicroScheduler - 12200 reads were filtered out during the traversal out of approximately 156612 total reads (7.79%)
[2016-04-15T00:54Z] INFO  17:54:23,519 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:54Z] INFO  17:54:23,519 MicroScheduler -   -> 255 reads (0.16% of total) failing BadMateFilter
[2016-04-15T00:54Z] INFO  17:54:23,519 MicroScheduler -   -> 11831 reads (7.55% of total) failing DuplicateReadFilter
[2016-04-15T00:54Z] INFO  17:54:23,520 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:54Z] INFO  17:54:23,520 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:54Z] INFO  17:54:23,520 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:54Z] INFO  17:54:23,520 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:54Z] INFO  17:54:23,521 MicroScheduler -   -> 114 reads (0.07% of total) failing UnmappedReadFilter
[2016-04-15T00:54Z] WARN  17:54:23,585 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T00:54Z] WARN  17:54:23,588 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/1/tx/tmpzsdisR/R14-18105_kapa-NGv3-PE100-NGv3-1_77752625_93297674.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T00:54Z] INFO  17:54:23,781 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:54Z] INFO  17:54:24,067 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T00:54Z] INFO  17:54:24,091 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:54Z] INFO  17:54:24,173 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-15T00:54Z] INFO  17:54:24,209 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T00:54Z] INFO  17:54:24,498 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:54Z] INFO  17:54:24,501 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:54Z] INFO  17:54:24,502 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:54Z] INFO  17:54:24,503 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:54Z] INFO  17:54:24,507 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/1/R14-18105_kapa-NGv3-PE100-NGv3-sort-1_93298945_108993401-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/1/R14-18105_kapa-NGv3-PE100-NGv3-1_93298945_108993401-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/1/tx/tmpaBJ6_1/R14-18105_kapa-NGv3-PE100-NGv3-1_93298945_108993401.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:54Z] INFO  17:54:24,540 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:54Z] INFO  17:54:24,541 HelpFormatter - Date/Time: 2016/04/14 17:54:24
[2016-04-15T00:54Z] INFO  17:54:24,542 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:54Z] INFO  17:54:24,542 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:54Z] WARN  17:54:24,577 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T00:54Z] WARN  17:54:24,580 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/1/tx/tmpaBJ6_1/R14-18105_kapa-NGv3-PE100-NGv3-1_93298945_108993401.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T00:54Z] INFO  17:54:24,746 IntervalUtils - Processing 145368 bp from intervals
[2016-04-15T00:54Z] WARN  17:54:24,766 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:54Z] INFO  17:54:24,881 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:54Z] INFO  17:54:24,920 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:54Z] INFO  17:54:24,943 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:54Z] INFO  17:54:25,007 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:54Z] INFO  17:54:25,009 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:54Z] INFO  17:54:25,009 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T00:54Z] INFO  17:54:25,010 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T00:54Z] INFO  17:54:25,011 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T00:54Z] INFO  17:54:25,011 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T00:54Z] INFO  17:54:25,111 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T00:54Z] INFO  17:54:25,129 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:54Z] INFO  17:54:25,194 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T00:54Z] INFO  17:54:25,240 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.11
[2016-04-15T00:54Z] INFO  17:54:25,267 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T00:54Z] GATK: HaplotypeCaller
[2016-04-15T00:54Z] INFO  17:54:25,769 IntervalUtils - Processing 113118 bp from intervals
[2016-04-15T00:54Z] WARN  17:54:25,785 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:54Z] INFO  17:54:25,763 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:54Z] INFO  17:54:25,788 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:54Z] INFO  17:54:25,789 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:54Z] INFO  17:54:25,789 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:54Z] INFO  17:54:25,793 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/1/R14-18105_kapa-NGv3-PE100-NGv3-sort-1_108994811_143767848-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/1/R14-18105_kapa-NGv3-PE100-NGv3-1_108994811_143767848-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/1/tx/tmpepRMua/R14-18105_kapa-NGv3-PE100-NGv3-1_108994811_143767848.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:54Z] INFO  17:54:25,820 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:54Z] INFO  17:54:25,827 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:54Z] INFO  17:54:25,830 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:54Z] INFO  17:54:25,831 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:54Z] INFO  17:54:25,831 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:54Z] INFO  17:54:25,831 HelpFormatter - Date/Time: 2016/04/14 17:54:25
[2016-04-15T00:54Z] INFO  17:54:25,832 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:54Z] INFO  17:54:25,833 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:54Z] INFO  17:54:25,836 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/1/R14-18105_kapa-NGv3-PE100-NGv3-sort-1_143897546_159410511-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/1/R14-18105_kapa-NGv3-PE100-NGv3-1_143897546_159410511-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/1/tx/tmps6tBvB/R14-18105_kapa-NGv3-PE100-NGv3-1_143897546_159410511.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:54Z] WARN  17:54:25,861 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T00:54Z] WARN  17:54:25,864 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/1/tx/tmpepRMua/R14-18105_kapa-NGv3-PE100-NGv3-1_108994811_143767848.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T00:54Z] INFO  17:54:25,865 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:54Z] INFO  17:54:25,868 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:54Z] INFO  17:54:25,868 HelpFormatter - Date/Time: 2016/04/14 17:54:25
[2016-04-15T00:54Z] INFO  17:54:25,869 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:54Z] INFO  17:54:25,869 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:54Z] WARN  17:54:25,902 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T00:54Z] WARN  17:54:25,905 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/1/tx/tmps6tBvB/R14-18105_kapa-NGv3-PE100-NGv3-1_143897546_159410511.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T00:54Z] INFO  17:54:25,925 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:54Z] INFO  17:54:25,927 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:54Z] INFO  17:54:25,927 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T00:54Z] INFO  17:54:25,928 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T00:54Z] INFO  17:54:25,929 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T00:54Z] INFO  17:54:25,929 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T00:54Z] INFO  17:54:26,061 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:54Z] INFO  17:54:26,070 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:54Z] INFO  17:54:26,126 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:54Z] INFO  17:54:26,129 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:54Z] INFO  17:54:26,129 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:54Z] INFO  17:54:26,130 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:54Z] INFO  17:54:26,133 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T00:54Z] INFO  17:54:26,134 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/1/R14-18105_kapa-NGv3-PE100-NGv3-sort-1_159504867_175046963-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/1/R14-18105_kapa-NGv3-PE100-NGv3-1_159504867_175046963-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/1/tx/tmp3v1Wdh/R14-18105_kapa-NGv3-PE100-NGv3-1_159504867_175046963.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:54Z] INFO  17:54:26,143 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:54Z] INFO  17:54:26,158 HelpFormatter - Date/Time: 2016/04/14 17:54:26
[2016-04-15T00:54Z] INFO  17:54:26,159 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:54Z] INFO  17:54:26,159 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:54Z] WARN  17:54:26,205 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T00:54Z] WARN  17:54:26,233 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/1/tx/tmp3v1Wdh/R14-18105_kapa-NGv3-PE100-NGv3-1_159504867_175046963.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T00:54Z] INFO  17:54:26,254 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T00:54Z] INFO  17:54:26,264 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:54Z] INFO  17:54:26,350 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T00:54Z] INFO  17:54:26,362 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:54Z] INFO  17:54:26,381 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.12
[2016-04-15T00:54Z] INFO  17:54:26,409 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T00:54Z] INFO  17:54:26,441 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-15T00:54Z] INFO  17:54:26,453 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:54Z] INFO  17:54:26,485 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T00:54Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T00:54Z] INFO  17:54:26,498 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T00:54Z] INFO  17:54:26,498 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T00:54Z] INFO  17:54:26,527 ProgressMeter -            done   1247079.0    41.0 s      33.0 s      100.0%    41.0 s       0.0 s
[2016-04-15T00:54Z] INFO  17:54:26,527 ProgressMeter - Total runtime 41.16 secs, 0.69 min, 0.01 hours
[2016-04-15T00:54Z] INFO  17:54:26,527 MicroScheduler - 47625 reads were filtered out during the traversal out of approximately 570863 total reads (8.34%)
[2016-04-15T00:54Z] INFO  17:54:26,528 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:54Z] INFO  17:54:26,528 MicroScheduler -   -> 827 reads (0.14% of total) failing BadMateFilter
[2016-04-15T00:54Z] INFO  17:54:26,528 MicroScheduler -   -> 46423 reads (8.13% of total) failing DuplicateReadFilter
[2016-04-15T00:54Z] INFO  17:54:26,528 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:54Z] INFO  17:54:26,529 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:54Z] INFO  17:54:26,529 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:54Z] INFO  17:54:26,529 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:54Z] INFO  17:54:26,529 MicroScheduler -   -> 375 reads (0.07% of total) failing UnmappedReadFilter
[2016-04-15T00:54Z] INFO  17:54:26,718 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T00:54Z] INFO  17:54:26,730 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:54Z] INFO  17:54:26,804 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-15T00:54Z] INFO  17:54:26,844 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T00:54Z] WARN  17:54:26,903 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T00:54Z] WARN  17:54:26,904 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T00:54Z] INFO  17:54:26,983 IntervalUtils - Processing 517409 bp from intervals
[2016-04-15T00:54Z] WARN  17:54:26,989 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:54Z] INFO  17:54:27,020 IntervalUtils - Processing 258252 bp from intervals
[2016-04-15T00:54Z] WARN  17:54:27,025 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:54Z] INFO  17:54:27,048 ProgressMeter -            done   1359359.0    43.0 s      32.0 s      100.0%    43.0 s       0.0 s
[2016-04-15T00:54Z] INFO  17:54:27,048 ProgressMeter - Total runtime 43.76 secs, 0.73 min, 0.01 hours
[2016-04-15T00:54Z] INFO  17:54:27,048 MicroScheduler - 52022 reads were filtered out during the traversal out of approximately 639231 total reads (8.14%)
[2016-04-15T00:54Z] INFO  17:54:27,049 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:54Z] INFO  17:54:27,049 MicroScheduler -   -> 885 reads (0.14% of total) failing BadMateFilter
[2016-04-15T00:54Z] INFO  17:54:27,049 MicroScheduler -   -> 50747 reads (7.94% of total) failing DuplicateReadFilter
[2016-04-15T00:54Z] INFO  17:54:27,049 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:54Z] INFO  17:54:27,050 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:54Z] INFO  17:54:27,050 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:54Z] INFO  17:54:27,050 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:54Z] INFO  17:54:27,050 MicroScheduler -   -> 390 reads (0.06% of total) failing UnmappedReadFilter
[2016-04-15T00:54Z] INFO  17:54:27,088 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:54Z] INFO  17:54:27,178 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:54Z] INFO  17:54:27,244 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:54Z] INFO  17:54:27,245 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:54Z] INFO  17:54:27,265 ProgressMeter -     19:45643494   2471873.0    60.0 s      24.0 s       90.2%    66.0 s       6.0 s
[2016-04-15T00:54Z] INFO  17:54:27,268 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T00:54Z] INFO  17:54:27,269 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T00:54Z] INFO  17:54:27,277 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T00:54Z] INFO  17:54:27,277 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T00:54Z] INFO  17:54:27,298 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:54Z] INFO  17:54:27,299 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:54Z] INFO  17:54:27,300 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T00:54Z] INFO  17:54:27,300 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T00:54Z] INFO  17:54:27,301 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T00:54Z] INFO  17:54:27,301 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T00:54Z] INFO  17:54:27,410 IntervalUtils - Processing 261574 bp from intervals
[2016-04-15T00:54Z] WARN  17:54:27,415 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:54Z] INFO  17:54:27,507 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:54Z] INFO  17:54:27,540 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T00:54Z] INFO  17:54:27,549 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T00:54Z] INFO  17:54:27,624 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:54Z] INFO  17:54:27,626 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:54Z] INFO  17:54:27,626 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T00:54Z] INFO  17:54:27,627 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T00:54Z] INFO  17:54:27,627 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T00:54Z] INFO  17:54:27,628 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T00:54Z] INFO  17:54:27,893 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T00:54Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T00:54Z] INFO  17:54:27,994 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T00:54Z] INFO  17:54:27,994 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T00:54Z] INFO  17:54:28,128 ProgressMeter -     19:56300695   2307230.0    60.0 s      26.0 s       76.7%    78.0 s      18.0 s
[2016-04-15T00:54Z] WARN  17:54:28,283 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T00:54Z] WARN  17:54:28,284 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T00:54Z] INFO  17:54:28,353 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:54Z] INFO  17:54:28,517 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:54Z] INFO  17:54:28,520 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:54Z] INFO  17:54:28,521 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:54Z] INFO  17:54:28,521 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:54Z] INFO  17:54:28,528 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/1/R14-18105_kapa-NGv3-PE100-NGv3-sort-1_175048468_192127886-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/1/R14-18105_kapa-NGv3-PE100-NGv3-1_175048468_192127886-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/1/tx/tmpmwIzhm/R14-18105_kapa-NGv3-PE100-NGv3-1_175048468_192127886.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:54Z] INFO  17:54:28,540 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:54Z] INFO  17:54:28,541 HelpFormatter - Date/Time: 2016/04/14 17:54:28
[2016-04-15T00:54Z] INFO  17:54:28,542 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:54Z] INFO  17:54:28,553 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:54Z] WARN  17:54:28,590 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T00:54Z] WARN  17:54:28,603 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/1/tx/tmpmwIzhm/R14-18105_kapa-NGv3-PE100-NGv3-1_175048468_192127886.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T00:54Z] GATK: HaplotypeCaller
[2016-04-15T00:54Z] INFO  17:54:28,750 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:54Z] INFO  17:54:28,899 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:54Z] GATK: HaplotypeCaller
[2016-04-15T00:54Z] INFO  17:54:29,186 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T00:54Z] INFO  17:54:29,206 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:54Z] INFO  17:54:29,305 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.10
[2016-04-15T00:54Z] INFO  17:54:29,348 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T00:54Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T00:54Z] INFO  17:54:29,760 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T00:54Z] INFO  17:54:29,761 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T00:54Z] INFO  17:54:29,926 IntervalUtils - Processing 191568 bp from intervals
[2016-04-15T00:54Z] WARN  17:54:29,943 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:54Z] INFO  17:54:30,082 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:54Z] WARN  17:54:30,126 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T00:54Z] WARN  17:54:30,127 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T00:54Z] INFO  17:54:30,204 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:54Z] INFO  17:54:30,205 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:54Z] INFO  17:54:30,206 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T00:54Z] INFO  17:54:30,207 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T00:54Z] INFO  17:54:30,208 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T00:54Z] INFO  17:54:30,208 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T00:54Z] INFO  17:54:30,435 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T00:54Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T00:54Z] INFO  17:54:31,166 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T00:54Z] INFO  17:54:31,166 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T00:54Z] WARN  17:54:31,627 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T00:54Z] WARN  17:54:31,629 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T00:54Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T00:54Z] INFO  17:54:31,706 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T00:54Z] INFO  17:54:31,707 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T00:54Z] WARN  17:54:32,278 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T00:54Z] WARN  17:54:32,279 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T00:54Z] INFO  17:54:32,562 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:54Z] INFO  17:54:32,565 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:54Z] INFO  17:54:32,566 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:54Z] INFO  17:54:32,567 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:54Z] INFO  17:54:32,571 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/1/R14-18105_kapa-NGv3-PE100-NGv3-sort-1_192128349_207640257-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/1/R14-18105_kapa-NGv3-PE100-NGv3-1_192128349_207640257-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/1/tx/tmpxP9C6_/R14-18105_kapa-NGv3-PE100-NGv3-1_192128349_207640257.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:54Z] INFO  17:54:32,597 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:54Z] INFO  17:54:32,598 HelpFormatter - Date/Time: 2016/04/14 17:54:32
[2016-04-15T00:54Z] INFO  17:54:32,599 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:54Z] INFO  17:54:32,599 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:54Z] WARN  17:54:32,637 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T00:54Z] WARN  17:54:32,651 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/1/tx/tmpxP9C6_/R14-18105_kapa-NGv3-PE100-NGv3-1_192128349_207640257.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T00:54Z] INFO  17:54:32,878 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:54Z] INFO  17:54:32,941 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:54Z] INFO  17:54:32,943 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:54Z] INFO  17:54:32,943 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:54Z] INFO  17:54:32,944 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:54Z] INFO  17:54:32,962 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/1/R14-18105_kapa-NGv3-PE100-NGv3-sort-1_207641871_223156451-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/1/R14-18105_kapa-NGv3-PE100-NGv3-1_207641871_223156451-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/1/tx/tmpWRA2th/R14-18105_kapa-NGv3-PE100-NGv3-1_207641871_223156451.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:54Z] INFO  17:54:32,970 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:54Z] INFO  17:54:32,971 HelpFormatter - Date/Time: 2016/04/14 17:54:32
[2016-04-15T00:54Z] INFO  17:54:32,971 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:54Z] INFO  17:54:32,972 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:54Z] WARN  17:54:32,995 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T00:54Z] WARN  17:54:32,998 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/1/tx/tmpWRA2th/R14-18105_kapa-NGv3-PE100-NGv3-1_207641871_223156451.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T00:54Z] INFO  17:54:33,140 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T00:54Z] INFO  17:54:33,150 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:54Z] INFO  17:54:33,283 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:54Z] INFO  17:54:33,279 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.13
[2016-04-15T00:54Z] INFO  17:54:33,318 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T00:54Z] INFO  17:54:33,483 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T00:54Z] INFO  17:54:33,494 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:54Z] INFO  17:54:33,596 ProgressMeter -            done   2766033.0    66.0 s      23.0 s      100.0%    66.0 s       0.0 s
[2016-04-15T00:54Z] INFO  17:54:33,586 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.09
[2016-04-15T00:54Z] INFO  17:54:33,597 ProgressMeter - Total runtime 66.34 secs, 1.11 min, 0.02 hours
[2016-04-15T00:54Z] INFO  17:54:33,597 MicroScheduler - 88322 reads were filtered out during the traversal out of approximately 1063447 total reads (8.31%)
[2016-04-15T00:54Z] INFO  17:54:33,597 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:54Z] INFO  17:54:33,598 MicroScheduler -   -> 1544 reads (0.15% of total) failing BadMateFilter
[2016-04-15T00:54Z] INFO  17:54:33,598 MicroScheduler -   -> 86116 reads (8.10% of total) failing DuplicateReadFilter
[2016-04-15T00:54Z] INFO  17:54:33,598 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:54Z] INFO  17:54:33,598 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:54Z] INFO  17:54:33,599 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:54Z] INFO  17:54:33,599 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:54Z] INFO  17:54:33,599 MicroScheduler -   -> 662 reads (0.06% of total) failing UnmappedReadFilter
[2016-04-15T00:54Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T00:54Z] INFO  17:54:33,631 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T00:54Z] INFO  17:54:33,640 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T00:54Z] INFO  17:54:33,638 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T00:54Z] INFO  17:54:33,791 IntervalUtils - Processing 282740 bp from intervals
[2016-04-15T00:54Z] WARN  17:54:33,797 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:54Z] INFO  17:54:33,906 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:54Z] WARN  17:54:34,000 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T00:54Z] WARN  17:54:34,000 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T00:54Z] INFO  17:54:34,076 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:54Z] INFO  17:54:34,077 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:54Z] INFO  17:54:34,077 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T00:54Z] INFO  17:54:34,084 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T00:54Z] INFO  17:54:34,092 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T00:54Z] INFO  17:54:34,093 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T00:54Z] INFO  17:54:34,390 IntervalUtils - Processing 175773 bp from intervals
[2016-04-15T00:54Z] WARN  17:54:34,395 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:54Z] INFO  17:54:34,426 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T00:54Z] INFO  17:54:34,524 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:54Z] INFO  17:54:34,660 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:54Z] INFO  17:54:34,661 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:54Z] INFO  17:54:34,662 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T00:54Z] INFO  17:54:34,662 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T00:54Z] INFO  17:54:34,675 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T00:54Z] INFO  17:54:34,678 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T00:54Z] INFO  17:54:34,959 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T00:54Z] INFO  17:54:35,190 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:54Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T00:54Z] INFO  17:54:35,415 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T00:54Z] INFO  17:54:35,416 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T00:54Z] GATK: HaplotypeCaller
[2016-04-15T00:54Z] WARN  17:54:35,810 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T00:54Z] WARN  17:54:35,811 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T00:54Z] INFO  17:54:39,268 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:54Z] INFO  17:54:39,271 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:54Z] INFO  17:54:39,271 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:54Z] INFO  17:54:39,272 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:54Z] INFO  17:54:39,276 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/1/R14-18105_kapa-NGv3-PE100-NGv3-sort-1_223162737_240072524-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/1/R14-18105_kapa-NGv3-PE100-NGv3-1_223162737_240072524-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/1/tx/tmp9piAjx/R14-18105_kapa-NGv3-PE100-NGv3-1_223162737_240072524.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:54Z] INFO  17:54:39,285 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:54Z] INFO  17:54:39,286 HelpFormatter - Date/Time: 2016/04/14 17:54:39
[2016-04-15T00:54Z] INFO  17:54:39,287 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:54Z] INFO  17:54:39,287 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:54Z] WARN  17:54:39,352 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T00:54Z] WARN  17:54:39,361 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/1/tx/tmp9piAjx/R14-18105_kapa-NGv3-PE100-NGv3-1_223162737_240072524.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T00:54Z] INFO  17:54:39,576 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:54Z] INFO  17:54:39,872 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T00:54Z] INFO  17:54:39,882 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:54Z] INFO  17:54:39,965 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-15T00:54Z] INFO  17:54:39,989 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T00:54Z] INFO  17:54:40,370 IntervalUtils - Processing 294039 bp from intervals
[2016-04-15T00:54Z] WARN  17:54:40,381 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:54Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T00:54Z] INFO  17:54:40,454 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:54Z] INFO  17:54:40,464 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T00:54Z] INFO  17:54:40,465 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T00:54Z] INFO  17:54:40,607 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:54Z] INFO  17:54:40,608 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:54Z] INFO  17:54:40,608 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T00:54Z] INFO  17:54:40,609 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T00:54Z] INFO  17:54:40,622 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T00:54Z] INFO  17:54:40,623 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T00:54Z] WARN  17:54:40,756 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T00:54Z] WARN  17:54:40,756 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T00:54Z] INFO  17:54:40,888 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T00:54Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T00:54Z] INFO  17:54:42,901 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T00:54Z] INFO  17:54:42,910 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T00:54Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T00:54Z] INFO  17:54:42,959 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T00:54Z] INFO  17:54:42,959 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T00:54Z] WARN  17:54:43,299 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T00:54Z] WARN  17:54:43,300 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T00:54Z] INFO  17:54:43,547 ProgressMeter -       1:1685006      1.2212465E7    30.0 s            2.0 s       21.0%     2.4 m     112.0 s
[2016-04-15T00:54Z] WARN  17:54:43,995 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T00:54Z] WARN  17:54:43,996 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T00:54Z] INFO  17:54:44,363 ProgressMeter -      1:17084961        7036865.0    30.0 s            4.0 s       15.1%     3.3 m       2.8 m
[2016-04-15T00:54Z] INFO  17:54:47,172 ProgressMeter -            done   2732198.0    79.0 s      28.0 s      100.0%    79.0 s       0.0 s
[2016-04-15T00:54Z] INFO  17:54:47,173 ProgressMeter - Total runtime 79.07 secs, 1.32 min, 0.02 hours
[2016-04-15T00:54Z] INFO  17:54:47,173 MicroScheduler - 98246 reads were filtered out during the traversal out of approximately 1184848 total reads (8.29%)
[2016-04-15T00:54Z] INFO  17:54:47,173 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:54Z] INFO  17:54:47,174 MicroScheduler -   -> 1855 reads (0.16% of total) failing BadMateFilter
[2016-04-15T00:54Z] INFO  17:54:47,174 MicroScheduler -   -> 95563 reads (8.07% of total) failing DuplicateReadFilter
[2016-04-15T00:54Z] INFO  17:54:47,174 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:54Z] INFO  17:54:47,174 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:54Z] INFO  17:54:47,174 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:54Z] INFO  17:54:47,175 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:54Z] INFO  17:54:47,175 MicroScheduler -   -> 828 reads (0.07% of total) failing UnmappedReadFilter
[2016-04-15T00:54Z] INFO  17:54:47,193 ProgressMeter -      1:33985118      1.6588176E7    30.0 s            1.0 s       20.8%     2.4 m     113.0 s
[2016-04-15T00:54Z] INFO  17:54:47,913 ProgressMeter -            done   4005652.0    85.0 s      21.0 s      100.0%    85.0 s       0.0 s
[2016-04-15T00:54Z] INFO  17:54:47,914 ProgressMeter - Total runtime 86.00 secs, 1.43 min, 0.02 hours
[2016-04-15T00:54Z] INFO  17:54:47,914 MicroScheduler - 112536 reads were filtered out during the traversal out of approximately 1326558 total reads (8.48%)
[2016-04-15T00:54Z] INFO  17:54:47,915 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:54Z] INFO  17:54:47,915 MicroScheduler -   -> 2115 reads (0.16% of total) failing BadMateFilter
[2016-04-15T00:54Z] INFO  17:54:47,915 MicroScheduler -   -> 109515 reads (8.26% of total) failing DuplicateReadFilter
[2016-04-15T00:54Z] INFO  17:54:47,915 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:54Z] INFO  17:54:47,916 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:54Z] INFO  17:54:47,916 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:54Z] INFO  17:54:47,916 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:54Z] INFO  17:54:47,916 MicroScheduler -   -> 906 reads (0.07% of total) failing UnmappedReadFilter
[2016-04-15T00:54Z] INFO  17:54:48,541 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:54Z] GATK: HaplotypeCaller
[2016-04-15T00:54Z] INFO  17:54:49,131 ProgressMeter -      1:52195486      1.0149282E7    30.0 s            2.0 s       32.9%    91.0 s      61.0 s
[2016-04-15T00:54Z] INFO  17:54:49,449 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:54Z] GATK: HaplotypeCaller
[2016-04-15T00:54Z] INFO  17:54:50,016 ProgressMeter -      1:67816553      1.7571168E7    30.0 s            1.0 s       54.3%    55.0 s      25.0 s
[2016-04-15T00:54Z] INFO  17:54:52,020 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:54Z] INFO  17:54:52,024 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:54Z] INFO  17:54:52,025 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:54Z] INFO  17:54:52,025 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:54Z] INFO  17:54:52,030 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/1/R14-18105_kapa-NGv3-PE100-NGv3-sort-1_240255409_249250621-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/1/R14-18105_kapa-NGv3-PE100-NGv3-1_240255409_249250621-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/1/tx/tmpaffvxD/R14-18105_kapa-NGv3-PE100-NGv3-1_240255409_249250621.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:54Z] INFO  17:54:52,053 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:54Z] INFO  17:54:52,054 HelpFormatter - Date/Time: 2016/04/14 17:54:52
[2016-04-15T00:54Z] INFO  17:54:52,055 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:54Z] INFO  17:54:52,055 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:54Z] WARN  17:54:52,089 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T00:54Z] WARN  17:54:52,092 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/1/tx/tmpaffvxD/R14-18105_kapa-NGv3-PE100-NGv3-1_240255409_249250621.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T00:54Z] INFO  17:54:52,351 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:54Z] INFO  17:54:52,587 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T00:54Z] INFO  17:54:52,596 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:54Z] INFO  17:54:52,692 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.09
[2016-04-15T00:54Z] INFO  17:54:52,716 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T00:54Z] INFO  17:54:53,109 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:54Z] INFO  17:54:53,111 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:54Z] INFO  17:54:53,111 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:54Z] INFO  17:54:53,111 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:54Z] INFO  17:54:53,115 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/2/R14-18105_kapa-NGv3-PE100-NGv3-sort-2_0_15514844-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/2/R14-18105_kapa-NGv3-PE100-NGv3-2_0_15514844-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/2/tx/tmpSOSxim/R14-18105_kapa-NGv3-PE100-NGv3-2_0_15514844.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:54Z] INFO  17:54:53,124 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:54Z] INFO  17:54:53,125 HelpFormatter - Date/Time: 2016/04/14 17:54:53
[2016-04-15T00:54Z] INFO  17:54:53,125 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:54Z] INFO  17:54:53,126 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:54Z] WARN  17:54:53,173 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T00:54Z] WARN  17:54:53,176 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/2/tx/tmpSOSxim/R14-18105_kapa-NGv3-PE100-NGv3-2_0_15514844.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T00:54Z] INFO  17:54:53,208 IntervalUtils - Processing 129443 bp from intervals
[2016-04-15T00:54Z] WARN  17:54:53,214 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:54Z] INFO  17:54:53,350 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:54Z] INFO  17:54:53,351 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:54Z] INFO  17:54:53,458 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:54Z] INFO  17:54:53,459 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:54Z] INFO  17:54:53,460 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T00:54Z] INFO  17:54:53,461 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T00:54Z] INFO  17:54:53,461 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T00:54Z] INFO  17:54:53,462 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T00:54Z] INFO  17:54:53,573 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T00:54Z] INFO  17:54:53,582 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:54Z] INFO  17:54:53,663 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-15T00:54Z] INFO  17:54:53,699 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T00:54Z] INFO  17:54:53,743 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T00:54Z] INFO  17:54:54,100 IntervalUtils - Processing 105700 bp from intervals
[2016-04-15T00:54Z] WARN  17:54:54,105 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:54Z] INFO  17:54:54,198 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:54Z] INFO  17:54:54,291 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:54Z] INFO  17:54:54,292 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:54Z] INFO  17:54:54,293 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T00:54Z] INFO  17:54:54,293 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T00:54Z] INFO  17:54:54,294 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T00:54Z] INFO  17:54:54,294 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T00:54Z] INFO  17:54:54,465 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T00:54Z] INFO  17:54:55,036 ProgressMeter -      1:89523675      2.4211835E7    30.0 s            1.0 s       63.3%    47.0 s      17.0 s
[2016-04-15T00:54Z] INFO  17:54:55,949 ProgressMeter -     1:103380301      2.2248705E7    30.0 s            1.0 s       77.9%    38.0 s       8.0 s
[2016-04-15T00:54Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T00:54Z] INFO  17:54:56,097 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T00:54Z] INFO  17:54:56,098 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T00:54Z] WARN  17:54:56,973 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T00:54Z] WARN  17:54:56,974 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T00:54Z] INFO  17:54:57,299 ProgressMeter -     1:145075630         426418.0    30.0 s           70.0 s        3.0%    16.8 m      16.3 m
[2016-04-15T00:54Z] INFO  17:54:57,321 ProgressMeter -     1:110993839      1.4838851E7    30.0 s            2.0 s       31.0%    96.0 s      66.0 s
[2016-04-15T00:54Z] INFO  17:54:57,634 ProgressMeter -     1:161599803      1.8317893E7    30.0 s            1.0 s       33.6%    89.0 s      59.0 s
[2016-04-15T00:54Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T00:54Z] INFO  17:54:59,448 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T00:54Z] INFO  17:54:59,463 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T00:54Z] WARN  17:54:59,740 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T00:54Z] WARN  17:54:59,742 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T00:55Z] INFO  17:55:00,226 ProgressMeter -     1:180904951      1.5332926E7    30.0 s            1.0 s       42.4%    70.0 s      40.0 s
[2016-04-15T00:55Z] INFO  17:55:01,143 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.006549892000000001
[2016-04-15T00:55Z] INFO  17:55:01,144 PairHMM - Total compute time in PairHMM computeLikelihoods() : 0.40168249300000003
[2016-04-15T00:55Z] INFO  17:55:01,145 HaplotypeCaller - Ran local assembly on 888 active regions
[2016-04-15T00:55Z] INFO  17:55:01,203 ProgressMeter -            done       3.770404E7    35.0 s            0.0 s      100.0%    35.0 s       0.0 s
[2016-04-15T00:55Z] INFO  17:55:01,204 ProgressMeter - Total runtime 35.28 secs, 0.59 min, 0.01 hours
[2016-04-15T00:55Z] INFO  17:55:01,205 MicroScheduler - 37163 reads were filtered out during the traversal out of approximately 161269 total reads (23.04%)
[2016-04-15T00:55Z] INFO  17:55:01,205 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:55Z] INFO  17:55:01,205 MicroScheduler -   -> 10535 reads (6.53% of total) failing DuplicateReadFilter
[2016-04-15T00:55Z] INFO  17:55:01,206 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:55Z] INFO  17:55:01,206 MicroScheduler -   -> 26628 reads (16.51% of total) failing HCMappingQualityFilter
[2016-04-15T00:55Z] INFO  17:55:01,206 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:55Z] INFO  17:55:01,206 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:55Z] INFO  17:55:01,206 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:55Z] INFO  17:55:01,207 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:55Z] INFO  17:55:02,574 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:55Z] GATK: HaplotypeCaller
[2016-04-15T00:55Z] INFO  17:55:04,126 ProgressMeter -     1:201176078      2.1984258E7    30.0 s            1.0 s       34.3%    87.0 s      57.0 s
[2016-04-15T00:55Z] INFO  17:55:04,680 ProgressMeter -     1:213056713      1.3603664E7    30.0 s            2.0 s       45.6%    65.0 s      35.0 s
[2016-04-15T00:55Z] INFO  17:55:04,747 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.007016905
[2016-04-15T00:55Z] INFO  17:55:04,748 PairHMM - Total compute time in PairHMM computeLikelihoods() : 0.809343436
[2016-04-15T00:55Z] INFO  17:55:04,748 HaplotypeCaller - Ran local assembly on 1093 active regions
[2016-04-15T00:55Z] INFO  17:55:04,801 ProgressMeter -            done      5.3650037E7    39.0 s            0.0 s      100.0%    39.0 s       0.0 s
[2016-04-15T00:55Z] INFO  17:55:04,801 ProgressMeter - Total runtime 39.79 secs, 0.66 min, 0.01 hours
[2016-04-15T00:55Z] INFO  17:55:04,806 MicroScheduler - 12730 reads were filtered out during the traversal out of approximately 164577 total reads (7.73%)
[2016-04-15T00:55Z] INFO  17:55:04,806 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:55Z] INFO  17:55:04,806 MicroScheduler -   -> 12512 reads (7.60% of total) failing DuplicateReadFilter
[2016-04-15T00:55Z] INFO  17:55:04,806 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:55Z] INFO  17:55:04,807 MicroScheduler -   -> 218 reads (0.13% of total) failing HCMappingQualityFilter
[2016-04-15T00:55Z] INFO  17:55:04,807 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:55Z] INFO  17:55:04,807 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:55Z] INFO  17:55:04,807 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:55Z] INFO  17:55:04,807 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:55Z] INFO  17:55:05,402 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.008166011
[2016-04-15T00:55Z] INFO  17:55:05,403 PairHMM - Total compute time in PairHMM computeLikelihoods() : 0.5915010340000001
[2016-04-15T00:55Z] INFO  17:55:05,404 HaplotypeCaller - Ran local assembly on 1095 active regions
[2016-04-15T00:55Z] INFO  17:55:05,463 ProgressMeter -            done      5.6255126E7    45.0 s            0.0 s      100.0%    45.0 s       0.0 s
[2016-04-15T00:55Z] INFO  17:55:05,463 ProgressMeter - Total runtime 45.46 secs, 0.76 min, 0.01 hours
[2016-04-15T00:55Z] INFO  17:55:05,463 MicroScheduler - 14519 reads were filtered out during the traversal out of approximately 177784 total reads (8.17%)
[2016-04-15T00:55Z] INFO  17:55:05,464 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:55Z] INFO  17:55:05,464 MicroScheduler -   -> 14190 reads (7.98% of total) failing DuplicateReadFilter
[2016-04-15T00:55Z] INFO  17:55:05,465 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:55Z] INFO  17:55:05,465 MicroScheduler -   -> 329 reads (0.19% of total) failing HCMappingQualityFilter
[2016-04-15T00:55Z] INFO  17:55:05,466 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:55Z] INFO  17:55:05,466 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:55Z] INFO  17:55:05,466 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:55Z] INFO  17:55:05,466 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:55Z] INFO  17:55:05,867 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:55Z] INFO  17:55:05,870 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:55Z] INFO  17:55:05,871 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:55Z] INFO  17:55:05,871 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:55Z] INFO  17:55:05,876 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/2/R14-18105_kapa-NGv3-PE100-NGv3-sort-2_15519725_31133925-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/2/R14-18105_kapa-NGv3-PE100-NGv3-2_15519725_31133925-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/2/tx/tmpJGV_l3/R14-18105_kapa-NGv3-PE100-NGv3-2_15519725_31133925.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:55Z] INFO  17:55:05,898 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:55Z] INFO  17:55:05,899 HelpFormatter - Date/Time: 2016/04/14 17:55:05
[2016-04-15T00:55Z] INFO  17:55:05,900 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:55Z] INFO  17:55:05,900 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:55Z] WARN  17:55:05,935 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T00:55Z] WARN  17:55:05,938 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/2/tx/tmpJGV_l3/R14-18105_kapa-NGv3-PE100-NGv3-2_15519725_31133925.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T00:55Z] INFO  17:55:06,106 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:55Z] INFO  17:55:06,206 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:55Z] INFO  17:55:06,332 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T00:55Z] INFO  17:55:06,342 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:55Z] INFO  17:55:06,431 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.09
[2016-04-15T00:55Z] INFO  17:55:06,459 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T00:55Z] GATK: HaplotypeCaller
[2016-04-15T00:55Z] INFO  17:55:06,793 IntervalUtils - Processing 231513 bp from intervals
[2016-04-15T00:55Z] WARN  17:55:06,801 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:55Z] INFO  17:55:06,892 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:55Z] INFO  17:55:06,955 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:55Z] INFO  17:55:07,013 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:55Z] INFO  17:55:07,015 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:55Z] INFO  17:55:07,015 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T00:55Z] INFO  17:55:07,016 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T00:55Z] INFO  17:55:07,017 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T00:55Z] INFO  17:55:07,017 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T00:55Z] INFO  17:55:07,215 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T00:55Z] GATK: HaplotypeCaller
[2016-04-15T00:55Z] INFO  17:55:09,377 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:55Z] INFO  17:55:09,380 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:55Z] INFO  17:55:09,380 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:55Z] INFO  17:55:09,380 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:55Z] INFO  17:55:09,396 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/2/R14-18105_kapa-NGv3-PE100-NGv3-sort-2_31135088_46706841-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/2/R14-18105_kapa-NGv3-PE100-NGv3-2_31135088_46706841-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/2/tx/tmpjhwB3D/R14-18105_kapa-NGv3-PE100-NGv3-2_31135088_46706841.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:55Z] INFO  17:55:09,415 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:55Z] INFO  17:55:09,416 HelpFormatter - Date/Time: 2016/04/14 17:55:09
[2016-04-15T00:55Z] INFO  17:55:09,417 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:55Z] INFO  17:55:09,417 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:55Z] WARN  17:55:09,447 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T00:55Z] WARN  17:55:09,450 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/2/tx/tmpjhwB3D/R14-18105_kapa-NGv3-PE100-NGv3-2_31135088_46706841.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T00:55Z] INFO  17:55:09,680 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:55Z] INFO  17:55:09,945 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T00:55Z] INFO  17:55:09,968 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:55Z] INFO  17:55:10,060 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.09
[2016-04-15T00:55Z] INFO  17:55:10,085 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T00:55Z] INFO  17:55:10,256 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:55Z] INFO  17:55:10,259 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:55Z] INFO  17:55:10,260 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:55Z] INFO  17:55:10,261 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:55Z] INFO  17:55:10,265 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/2/R14-18105_kapa-NGv3-PE100-NGv3-sort-2_46707543_62228117-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/2/R14-18105_kapa-NGv3-PE100-NGv3-2_46707543_62228117-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/2/tx/tmpjWUCUg/R14-18105_kapa-NGv3-PE100-NGv3-2_46707543_62228117.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:55Z] INFO  17:55:10,274 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:55Z] INFO  17:55:10,274 HelpFormatter - Date/Time: 2016/04/14 17:55:10
[2016-04-15T00:55Z] INFO  17:55:10,274 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:55Z] INFO  17:55:10,274 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:55Z] WARN  17:55:10,325 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T00:55Z] WARN  17:55:10,327 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/2/tx/tmpjWUCUg/R14-18105_kapa-NGv3-PE100-NGv3-2_46707543_62228117.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T00:55Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T00:55Z] INFO  17:55:10,459 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T00:55Z] INFO  17:55:10,461 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T00:55Z] INFO  17:55:10,474 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:55Z] INFO  17:55:10,494 IntervalUtils - Processing 167641 bp from intervals
[2016-04-15T00:55Z] WARN  17:55:10,500 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:55Z] INFO  17:55:10,601 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:55Z] INFO  17:55:10,634 ProgressMeter -     1:228362823      2.2214915E7    30.0 s            1.0 s       32.7%    91.0 s      61.0 s
[2016-04-15T00:55Z] INFO  17:55:10,664 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T00:55Z] INFO  17:55:10,674 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:55Z] INFO  17:55:10,715 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:55Z] INFO  17:55:10,716 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:55Z] INFO  17:55:10,717 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T00:55Z] INFO  17:55:10,717 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T00:55Z] INFO  17:55:10,717 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T00:55Z] INFO  17:55:10,717 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T00:55Z] WARN  17:55:10,756 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T00:55Z] INFO  17:55:10,757 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-15T00:55Z] WARN  17:55:10,757 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T00:55Z] INFO  17:55:10,794 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T00:55Z] INFO  17:55:10,881 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T00:55Z] INFO  17:55:11,187 IntervalUtils - Processing 139959 bp from intervals
[2016-04-15T00:55Z] WARN  17:55:11,203 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:55Z] INFO  17:55:11,330 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:55Z] INFO  17:55:11,413 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:55Z] INFO  17:55:11,414 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:55Z] INFO  17:55:11,415 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T00:55Z] INFO  17:55:11,417 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T00:55Z] INFO  17:55:11,418 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T00:55Z] INFO  17:55:11,418 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T00:55Z] INFO  17:55:11,560 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T00:55Z] INFO  17:55:13,554 ProgressMeter -       1:6948213      9.0874705E7    60.0 s            0.0 s       49.9%   120.0 s      60.0 s
[2016-04-15T00:55Z] INFO  17:55:14,368 ProgressMeter -      1:17952482      1.9208782E7    60.0 s            3.0 s       22.0%     4.5 m       3.5 m
[2016-04-15T00:55Z] INFO  17:55:14,783 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.031834251
[2016-04-15T00:55Z] INFO  17:55:14,784 PairHMM - Total compute time in PairHMM computeLikelihoods() : 0.614516421
[2016-04-15T00:55Z] INFO  17:55:14,785 HaplotypeCaller - Ran local assembly on 1425 active regions
[2016-04-15T00:55Z] INFO  17:55:14,847 ProgressMeter -            done      9.8875698E7    55.0 s            0.0 s      100.0%    55.0 s       0.0 s
[2016-04-15T00:55Z] INFO  17:55:14,847 ProgressMeter - Total runtime 55.73 secs, 0.93 min, 0.02 hours
[2016-04-15T00:55Z] INFO  17:55:14,847 MicroScheduler - 25045 reads were filtered out during the traversal out of approximately 294098 total reads (8.52%)
[2016-04-15T00:55Z] INFO  17:55:14,848 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:55Z] INFO  17:55:14,848 MicroScheduler -   -> 23139 reads (7.87% of total) failing DuplicateReadFilter
[2016-04-15T00:55Z] INFO  17:55:14,849 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:55Z] INFO  17:55:14,849 MicroScheduler -   -> 1906 reads (0.65% of total) failing HCMappingQualityFilter
[2016-04-15T00:55Z] INFO  17:55:14,849 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:55Z] INFO  17:55:14,849 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:55Z] INFO  17:55:14,850 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:55Z] INFO  17:55:14,850 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:55Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T00:55Z] INFO  17:55:15,805 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T00:55Z] INFO  17:55:15,816 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T00:55Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T00:55Z] INFO  17:55:15,960 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T00:55Z] INFO  17:55:15,961 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T00:55Z] WARN  17:55:16,096 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T00:55Z] WARN  17:55:16,097 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T00:55Z] WARN  17:55:16,218 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T00:55Z] WARN  17:55:16,219 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T00:55Z] INFO  17:55:16,308 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:55Z] GATK: HaplotypeCaller
[2016-04-15T00:55Z] INFO  17:55:17,194 ProgressMeter -      1:40236927     1.33009203E8    60.0 s            0.0 s       58.9%   101.0 s      41.0 s
[2016-04-15T00:55Z] INFO  17:55:19,648 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:55Z] INFO  17:55:19,651 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:55Z] INFO  17:55:19,652 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:55Z] INFO  17:55:19,652 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:55Z] INFO  17:55:19,657 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/2/R14-18105_kapa-NGv3-PE100-NGv3-sort-2_62362965_79253295-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/2/R14-18105_kapa-NGv3-PE100-NGv3-2_62362965_79253295-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/2/tx/tmp1JRUGd/R14-18105_kapa-NGv3-PE100-NGv3-2_62362965_79253295.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:55Z] INFO  17:55:19,667 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:55Z] INFO  17:55:19,668 HelpFormatter - Date/Time: 2016/04/14 17:55:19
[2016-04-15T00:55Z] INFO  17:55:19,668 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:55Z] INFO  17:55:19,669 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:55Z] WARN  17:55:19,698 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T00:55Z] WARN  17:55:19,702 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/2/tx/tmp1JRUGd/R14-18105_kapa-NGv3-PE100-NGv3-2_62362965_79253295.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T00:55Z] INFO  17:55:19,878 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:55Z] INFO  17:55:20,030 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T00:55Z] INFO  17:55:20,040 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:55Z] INFO  17:55:20,120 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-15T00:55Z] INFO  17:55:20,152 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T00:55Z] INFO  17:55:20,524 IntervalUtils - Processing 224219 bp from intervals
[2016-04-15T00:55Z] WARN  17:55:20,529 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:55Z] INFO  17:55:20,636 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:55Z] INFO  17:55:20,764 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:55Z] INFO  17:55:20,766 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:55Z] INFO  17:55:20,767 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T00:55Z] INFO  17:55:20,768 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T00:55Z] INFO  17:55:20,768 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T00:55Z] INFO  17:55:20,769 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T00:55Z] INFO  17:55:20,970 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T00:55Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T00:55Z] INFO  17:55:22,581 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T00:55Z] INFO  17:55:22,582 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T00:55Z] WARN  17:55:22,797 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T00:55Z] WARN  17:55:22,798 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T00:55Z] INFO  17:55:23,481 ProgressMeter -     1:247769425      1.5758557E7    30.0 s            1.0 s       67.6%    44.0 s      14.0 s
[2016-04-15T00:55Z] INFO  17:55:23,929 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.009068771
[2016-04-15T00:55Z] INFO  17:55:23,930 PairHMM - Total compute time in PairHMM computeLikelihoods() : 0.8125136580000001
[2016-04-15T00:55Z] INFO  17:55:23,931 HaplotypeCaller - Ran local assembly on 1219 active regions
[2016-04-15T00:55Z] INFO  17:55:23,987 ProgressMeter -            done      7.1291223E7    49.0 s            0.0 s      100.0%    49.0 s       0.0 s
[2016-04-15T00:55Z] INFO  17:55:23,987 ProgressMeter - Total runtime 49.33 secs, 0.82 min, 0.01 hours
[2016-04-15T00:55Z] INFO  17:55:23,987 MicroScheduler - 34706 reads were filtered out during the traversal out of approximately 247508 total reads (14.02%)
[2016-04-15T00:55Z] INFO  17:55:23,988 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:55Z] INFO  17:55:23,988 MicroScheduler -   -> 18500 reads (7.47% of total) failing DuplicateReadFilter
[2016-04-15T00:55Z] INFO  17:55:23,988 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:55Z] INFO  17:55:23,988 MicroScheduler -   -> 16206 reads (6.55% of total) failing HCMappingQualityFilter
[2016-04-15T00:55Z] INFO  17:55:23,988 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:55Z] INFO  17:55:23,989 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:55Z] INFO  17:55:23,989 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:55Z] INFO  17:55:23,989 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:55Z] INFO  17:55:24,314 ProgressMeter -      2:11736268      2.4448068E7    30.0 s            1.0 s       86.5%    34.0 s       4.0 s
[2016-04-15T00:55Z] INFO  17:55:24,835 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.010942682
[2016-04-15T00:55Z] INFO  17:55:24,835 PairHMM - Total compute time in PairHMM computeLikelihoods() : 0.900132911
[2016-04-15T00:55Z] INFO  17:55:24,836 HaplotypeCaller - Ran local assembly on 1369 active regions
[2016-04-15T00:55Z] INFO  17:55:24,898 ProgressMeter -            done      9.8539022E7    54.0 s            0.0 s      100.0%    54.0 s       0.0 s
[2016-04-15T00:55Z] INFO  17:55:24,899 ProgressMeter - Total runtime 54.69 secs, 0.91 min, 0.02 hours
[2016-04-15T00:55Z] INFO  17:55:24,899 MicroScheduler - 20624 reads were filtered out during the traversal out of approximately 258128 total reads (7.99%)
[2016-04-15T00:55Z] INFO  17:55:24,899 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:55Z] INFO  17:55:24,900 MicroScheduler -   -> 20366 reads (7.89% of total) failing DuplicateReadFilter
[2016-04-15T00:55Z] INFO  17:55:24,900 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:55Z] INFO  17:55:24,900 MicroScheduler -   -> 258 reads (0.10% of total) failing HCMappingQualityFilter
[2016-04-15T00:55Z] INFO  17:55:24,900 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:55Z] INFO  17:55:24,901 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:55Z] INFO  17:55:24,901 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:55Z] INFO  17:55:24,901 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:55Z] INFO  17:55:25,776 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:55Z] GATK: HaplotypeCaller
[2016-04-15T00:55Z] INFO  17:55:26,199 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:55Z] GATK: HaplotypeCaller
[2016-04-15T00:55Z] INFO  17:55:27,301 ProgressMeter -     1:149895434      1.2842027E7    60.0 s            4.0 s       14.8%     6.8 m       5.8 m
[2016-04-15T00:55Z] INFO  17:55:27,326 ProgressMeter -     1:118550746      1.2070155E8    60.0 s            0.0 s       86.9%    69.0 s       9.0 s
[2016-04-15T00:55Z] INFO  17:55:27,635 ProgressMeter -     1:172512194     1.28331674E8    60.0 s            0.0 s       86.5%    69.0 s       9.0 s
[2016-04-15T00:55Z] INFO  17:55:27,951 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.009912691000000001
[2016-04-15T00:55Z] INFO  17:55:27,952 PairHMM - Total compute time in PairHMM computeLikelihoods() : 0.60770755
[2016-04-15T00:55Z] INFO  17:55:27,953 HaplotypeCaller - Ran local assembly on 837 active regions
[2016-04-15T00:55Z] INFO  17:55:27,989 ProgressMeter -            done      3.2059538E7    33.0 s            1.0 s      100.0%    33.0 s       0.0 s
[2016-04-15T00:55Z] INFO  17:55:27,989 ProgressMeter - Total runtime 33.70 secs, 0.56 min, 0.01 hours
[2016-04-15T00:55Z] INFO  17:55:27,990 MicroScheduler - 12555 reads were filtered out during the traversal out of approximately 155221 total reads (8.09%)
[2016-04-15T00:55Z] INFO  17:55:27,990 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:55Z] INFO  17:55:27,991 MicroScheduler -   -> 12353 reads (7.96% of total) failing DuplicateReadFilter
[2016-04-15T00:55Z] INFO  17:55:27,991 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:55Z] INFO  17:55:27,991 MicroScheduler -   -> 202 reads (0.13% of total) failing HCMappingQualityFilter
[2016-04-15T00:55Z] INFO  17:55:27,992 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:55Z] INFO  17:55:27,992 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:55Z] INFO  17:55:27,992 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:55Z] INFO  17:55:27,992 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:55Z] INFO  17:55:29,209 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:55Z] INFO  17:55:29,213 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:55Z] INFO  17:55:29,214 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:55Z] INFO  17:55:29,215 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:55Z] INFO  17:55:29,234 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/2/R14-18105_kapa-NGv3-PE100-NGv3-sort-2_79253838_95537822-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/2/R14-18105_kapa-NGv3-PE100-NGv3-2_79253838_95537822-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/2/tx/tmpDqcttH/R14-18105_kapa-NGv3-PE100-NGv3-2_79253838_95537822.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:55Z] INFO  17:55:29,245 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:55Z] INFO  17:55:29,246 HelpFormatter - Date/Time: 2016/04/14 17:55:29
[2016-04-15T00:55Z] INFO  17:55:29,246 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:55Z] INFO  17:55:29,247 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:55Z] WARN  17:55:29,274 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T00:55Z] WARN  17:55:29,278 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/2/tx/tmpDqcttH/R14-18105_kapa-NGv3-PE100-NGv3-2_79253838_95537822.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T00:55Z] INFO  17:55:29,463 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:55Z] INFO  17:55:29,492 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:55Z] INFO  17:55:29,632 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:55Z] INFO  17:55:29,635 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:55Z] INFO  17:55:29,636 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:55Z] INFO  17:55:29,636 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:55Z] INFO  17:55:29,641 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/2/R14-18105_kapa-NGv3-PE100-NGv3-sort-2_95538561_111273222-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/2/R14-18105_kapa-NGv3-PE100-NGv3-2_95538561_111273222-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/2/tx/tmp19_GpU/R14-18105_kapa-NGv3-PE100-NGv3-2_95538561_111273222.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:55Z] INFO  17:55:29,664 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:55Z] INFO  17:55:29,664 HelpFormatter - Date/Time: 2016/04/14 17:55:29
[2016-04-15T00:55Z] INFO  17:55:29,665 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:55Z] INFO  17:55:29,665 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:55Z] INFO  17:55:29,702 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T00:55Z] WARN  17:55:29,694 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T00:55Z] WARN  17:55:29,706 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/2/tx/tmp19_GpU/R14-18105_kapa-NGv3-PE100-NGv3-2_95538561_111273222.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T00:55Z] INFO  17:55:29,714 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:55Z] INFO  17:55:29,794 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-15T00:55Z] GATK: HaplotypeCaller
[2016-04-15T00:55Z] INFO  17:55:29,823 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T00:55Z] INFO  17:55:29,869 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:55Z] INFO  17:55:30,079 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T00:55Z] INFO  17:55:30,089 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:55Z] INFO  17:55:30,153 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-15T00:55Z] INFO  17:55:30,181 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T00:55Z] INFO  17:55:30,348 IntervalUtils - Processing 101744 bp from intervals
[2016-04-15T00:55Z] WARN  17:55:30,365 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:55Z] INFO  17:55:30,530 IntervalUtils - Processing 250759 bp from intervals
[2016-04-15T00:55Z] WARN  17:55:30,537 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:55Z] INFO  17:55:30,550 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:55Z] INFO  17:55:30,620 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:55Z] INFO  17:55:30,658 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:55Z] INFO  17:55:30,658 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:55Z] INFO  17:55:30,659 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T00:55Z] INFO  17:55:30,659 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T00:55Z] INFO  17:55:30,671 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T00:55Z] INFO  17:55:30,674 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T00:55Z] INFO  17:55:30,715 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:55Z] INFO  17:55:30,716 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:55Z] INFO  17:55:30,716 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T00:55Z] INFO  17:55:30,717 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T00:55Z] INFO  17:55:30,718 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T00:55Z] INFO  17:55:30,718 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T00:55Z] INFO  17:55:30,878 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T00:55Z] INFO  17:55:30,881 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T00:55Z] INFO  17:55:33,031 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:55Z] INFO  17:55:33,035 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:55Z] INFO  17:55:33,035 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:55Z] INFO  17:55:33,036 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:55Z] INFO  17:55:33,040 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/2/R14-18105_kapa-NGv3-PE100-NGv3-sort-2_111281072_127413888-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/2/R14-18105_kapa-NGv3-PE100-NGv3-2_111281072_127413888-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/2/tx/tmpP5trhz/R14-18105_kapa-NGv3-PE100-NGv3-2_111281072_127413888.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:55Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T00:55Z] INFO  17:55:33,058 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:55Z] INFO  17:55:33,059 HelpFormatter - Date/Time: 2016/04/14 17:55:33
[2016-04-15T00:55Z] INFO  17:55:33,059 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:55Z] INFO  17:55:33,060 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:55Z] INFO  17:55:33,062 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T00:55Z] INFO  17:55:33,063 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T00:55Z] INFO  17:55:33,070 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.015031133
[2016-04-15T00:55Z] INFO  17:55:33,072 PairHMM - Total compute time in PairHMM computeLikelihoods() : 1.418499975
[2016-04-15T00:55Z] INFO  17:55:33,072 HaplotypeCaller - Ran local assembly on 1905 active regions
[2016-04-15T00:55Z] WARN  17:55:33,107 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T00:55Z] WARN  17:55:33,110 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/2/tx/tmpP5trhz/R14-18105_kapa-NGv3-PE100-NGv3-2_111281072_127413888.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T00:55Z] INFO  17:55:33,137 ProgressMeter -            done     1.74572625E8    65.0 s            0.0 s      100.0%    65.0 s       0.0 s
[2016-04-15T00:55Z] INFO  17:55:33,138 ProgressMeter - Total runtime 65.51 secs, 1.09 min, 0.02 hours
[2016-04-15T00:55Z] INFO  17:55:33,138 MicroScheduler - 34082 reads were filtered out during the traversal out of approximately 389248 total reads (8.76%)
[2016-04-15T00:55Z] INFO  17:55:33,138 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:55Z] INFO  17:55:33,139 MicroScheduler -   -> 30685 reads (7.88% of total) failing DuplicateReadFilter
[2016-04-15T00:55Z] INFO  17:55:33,139 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:55Z] INFO  17:55:33,139 MicroScheduler -   -> 3397 reads (0.87% of total) failing HCMappingQualityFilter
[2016-04-15T00:55Z] INFO  17:55:33,139 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:55Z] INFO  17:55:33,140 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:55Z] INFO  17:55:33,140 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:55Z] INFO  17:55:33,140 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:55Z] INFO  17:55:33,298 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:55Z] WARN  17:55:33,363 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T00:55Z] WARN  17:55:33,364 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T00:55Z] INFO  17:55:33,553 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T00:55Z] INFO  17:55:33,562 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:55Z] INFO  17:55:33,661 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.10
[2016-04-15T00:55Z] INFO  17:55:33,688 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T00:55Z] INFO  17:55:34,136 ProgressMeter -     1:205809380     1.39277113E8    60.0 s            0.0 s       84.9%    70.0 s      10.0 s
[2016-04-15T00:55Z] INFO  17:55:34,158 IntervalUtils - Processing 123675 bp from intervals
[2016-04-15T00:55Z] WARN  17:55:34,185 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:55Z] INFO  17:55:34,309 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:55Z] INFO  17:55:34,385 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:55Z] INFO  17:55:34,386 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:55Z] INFO  17:55:34,387 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T00:55Z] INFO  17:55:34,387 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T00:55Z] INFO  17:55:34,388 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T00:55Z] INFO  17:55:34,388 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T00:55Z] INFO  17:55:34,571 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T00:55Z] INFO  17:55:34,598 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:55Z] GATK: HaplotypeCaller
[2016-04-15T00:55Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T00:55Z] INFO  17:55:35,612 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T00:55Z] INFO  17:55:35,612 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T00:55Z] WARN  17:55:35,816 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T00:55Z] WARN  17:55:35,817 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T00:55Z] INFO  17:55:37,038 ProgressMeter -      2:26257604      2.6899404E7    30.0 s            1.0 s       44.7%    67.0 s      37.0 s
[2016-04-15T00:55Z] INFO  17:55:38,043 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:55Z] INFO  17:55:38,046 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:55Z] INFO  17:55:38,047 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:55Z] INFO  17:55:38,047 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:55Z] INFO  17:55:38,052 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/2/R14-18105_kapa-NGv3-PE100-NGv3-sort-2_127433207_143643105-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/2/R14-18105_kapa-NGv3-PE100-NGv3-2_127433207_143643105-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/2/tx/tmpH8x3xo/R14-18105_kapa-NGv3-PE100-NGv3-2_127433207_143643105.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:55Z] INFO  17:55:38,069 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:55Z] INFO  17:55:38,070 HelpFormatter - Date/Time: 2016/04/14 17:55:38
[2016-04-15T00:55Z] INFO  17:55:38,070 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:55Z] INFO  17:55:38,071 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:55Z] WARN  17:55:38,121 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T00:55Z] WARN  17:55:38,129 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/2/tx/tmpH8x3xo/R14-18105_kapa-NGv3-PE100-NGv3-2_127433207_143643105.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T00:55Z] INFO  17:55:38,413 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:55Z] INFO  17:55:38,598 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T00:55Z] INFO  17:55:38,607 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:55Z] INFO  17:55:38,709 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.10
[2016-04-15T00:55Z] INFO  17:55:38,751 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T00:55Z] INFO  17:55:39,193 IntervalUtils - Processing 171560 bp from intervals
[2016-04-15T00:55Z] WARN  17:55:39,214 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:55Z] INFO  17:55:39,348 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:55Z] INFO  17:55:39,475 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:55Z] INFO  17:55:39,475 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:55Z] INFO  17:55:39,476 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T00:55Z] INFO  17:55:39,476 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T00:55Z] INFO  17:55:39,476 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T00:55Z] INFO  17:55:39,477 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T00:55Z] INFO  17:55:39,643 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T00:55Z] INFO  17:55:40,187 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.014032415000000001
[2016-04-15T00:55Z] INFO  17:55:40,188 PairHMM - Total compute time in PairHMM computeLikelihoods() : 2.7134198130000002
[2016-04-15T00:55Z] INFO  17:55:40,189 HaplotypeCaller - Ran local assembly on 889 active regions
[2016-04-15T00:55Z] INFO  17:55:40,254 ProgressMeter -            done      2.1915914E7    46.0 s            2.0 s      100.0%    46.0 s       0.0 s
[2016-04-15T00:55Z] INFO  17:55:40,255 ProgressMeter - Total runtime 46.80 secs, 0.78 min, 0.01 hours
[2016-04-15T00:55Z] INFO  17:55:40,259 MicroScheduler - 27246 reads were filtered out during the traversal out of approximately 186515 total reads (14.61%)
[2016-04-15T00:55Z] INFO  17:55:40,260 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:55Z] INFO  17:55:40,260 MicroScheduler -   -> 13781 reads (7.39% of total) failing DuplicateReadFilter
[2016-04-15T00:55Z] INFO  17:55:40,260 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:55Z] INFO  17:55:40,260 MicroScheduler -   -> 13465 reads (7.22% of total) failing HCMappingQualityFilter
[2016-04-15T00:55Z] INFO  17:55:40,261 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:55Z] INFO  17:55:40,261 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:55Z] INFO  17:55:40,261 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:55Z] INFO  17:55:40,261 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:55Z] INFO  17:55:40,635 ProgressMeter -     1:235345300     1.06886334E8    60.0 s            0.0 s       78.5%    76.0 s      16.0 s
[2016-04-15T00:55Z] INFO  17:55:40,721 ProgressMeter -      2:42284743       3.460349E7    30.0 s            0.0 s       65.6%    45.0 s      15.0 s
[2016-04-15T00:55Z] INFO  17:55:41,431 ProgressMeter -      2:56611490      2.4314061E7    30.0 s            1.0 s       69.4%    43.0 s      13.0 s
[2016-04-15T00:55Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T00:55Z] INFO  17:55:41,592 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T00:55Z] INFO  17:55:41,593 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T00:55Z] INFO  17:55:41,778 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:55Z] WARN  17:55:42,010 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T00:55Z] WARN  17:55:42,011 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T00:55Z] GATK: HaplotypeCaller
[2016-04-15T00:55Z] INFO  17:55:42,571 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.015157137000000001
[2016-04-15T00:55Z] INFO  17:55:42,572 PairHMM - Total compute time in PairHMM computeLikelihoods() : 1.554319835
[2016-04-15T00:55Z] INFO  17:55:42,573 HaplotypeCaller - Ran local assembly on 2013 active regions
[2016-04-15T00:55Z] INFO  17:55:42,643 ProgressMeter -            done     1.89229853E8    68.0 s            0.0 s      100.0%    68.0 s       0.0 s
[2016-04-15T00:55Z] INFO  17:55:42,644 ProgressMeter - Total runtime 68.57 secs, 1.14 min, 0.02 hours
[2016-04-15T00:55Z] INFO  17:55:42,644 MicroScheduler - 37221 reads were filtered out during the traversal out of approximately 411362 total reads (9.05%)
[2016-04-15T00:55Z] INFO  17:55:42,644 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:55Z] INFO  17:55:42,645 MicroScheduler -   -> 32315 reads (7.86% of total) failing DuplicateReadFilter
[2016-04-15T00:55Z] INFO  17:55:42,645 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:55Z] INFO  17:55:42,645 MicroScheduler -   -> 4906 reads (1.19% of total) failing HCMappingQualityFilter
[2016-04-15T00:55Z] INFO  17:55:42,645 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:55Z] INFO  17:55:42,646 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:55Z] INFO  17:55:42,646 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:55Z] INFO  17:55:42,646 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:55Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T00:55Z] INFO  17:55:42,891 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T00:55Z] INFO  17:55:42,893 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T00:55Z] WARN  17:55:43,288 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T00:55Z] WARN  17:55:43,289 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T00:55Z] INFO  17:55:43,555 ProgressMeter -      1:12353581     2.62103127E8    90.0 s            0.0 s       83.5%   107.0 s      17.0 s
[2016-04-15T00:55Z] INFO  17:55:44,034 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:55Z] INFO  17:55:44,178 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.026749834
[2016-04-15T00:55Z] INFO  17:55:44,179 PairHMM - Total compute time in PairHMM computeLikelihoods() : 7.613786909000001
[2016-04-15T00:55Z] INFO  17:55:44,189 HaplotypeCaller - Ran local assembly on 1807 active regions
[2016-04-15T00:55Z] INFO  17:55:44,238 ProgressMeter -            done     1.55311872E8    76.0 s            0.0 s      100.0%    76.0 s       0.0 s
[2016-04-15T00:55Z] INFO  17:55:44,239 ProgressMeter - Total runtime 76.94 secs, 1.28 min, 0.02 hours
[2016-04-15T00:55Z] INFO  17:55:44,240 MicroScheduler - 40076 reads were filtered out during the traversal out of approximately 396042 total reads (10.12%)
[2016-04-15T00:55Z] INFO  17:55:44,241 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:55Z] INFO  17:55:44,241 MicroScheduler -   -> 30901 reads (7.80% of total) failing DuplicateReadFilter
[2016-04-15T00:55Z] INFO  17:55:44,242 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:55Z] INFO  17:55:44,243 MicroScheduler -   -> 9175 reads (2.32% of total) failing HCMappingQualityFilter
[2016-04-15T00:55Z] INFO  17:55:44,243 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:55Z] INFO  17:55:44,244 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:55Z] INFO  17:55:44,245 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:55Z] INFO  17:55:44,245 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:55Z] GATK: HaplotypeCaller
[2016-04-15T00:55Z] INFO  17:55:44,381 ProgressMeter -      1:23398648     1.16750975E8    90.0 s            0.0 s       53.9%     2.8 m      76.0 s
[2016-04-15T00:55Z] INFO  17:55:45,205 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:55Z] INFO  17:55:45,210 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:55Z] INFO  17:55:45,210 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:55Z] INFO  17:55:45,211 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:55Z] INFO  17:55:45,216 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/2/R14-18105_kapa-NGv3-PE100-NGv3-sort-2_143676177_159195597-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/2/R14-18105_kapa-NGv3-PE100-NGv3-2_143676177_159195597-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/2/tx/tmp3y1jNE/R14-18105_kapa-NGv3-PE100-NGv3-2_143676177_159195597.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:55Z] INFO  17:55:45,234 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:55Z] INFO  17:55:45,246 HelpFormatter - Date/Time: 2016/04/14 17:55:45
[2016-04-15T00:55Z] INFO  17:55:45,247 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:55Z] INFO  17:55:45,248 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:55Z] WARN  17:55:45,271 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T00:55Z] WARN  17:55:45,274 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/2/tx/tmp3y1jNE/R14-18105_kapa-NGv3-PE100-NGv3-2_143676177_159195597.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T00:55Z] INFO  17:55:45,488 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:55Z] INFO  17:55:45,689 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T00:55Z] INFO  17:55:45,699 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:55Z] INFO  17:55:45,780 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-15T00:55Z] INFO  17:55:45,795 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T00:55Z] INFO  17:55:45,812 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:55Z] INFO  17:55:46,127 IntervalUtils - Processing 92555 bp from intervals
[2016-04-15T00:55Z] WARN  17:55:46,143 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:55Z] GATK: HaplotypeCaller
[2016-04-15T00:55Z] INFO  17:55:46,275 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:55Z] INFO  17:55:46,417 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:55Z] INFO  17:55:46,418 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:55Z] INFO  17:55:46,419 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T00:55Z] INFO  17:55:46,420 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T00:55Z] INFO  17:55:46,428 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T00:55Z] INFO  17:55:46,428 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T00:55Z] INFO  17:55:46,654 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T00:55Z] INFO  17:55:47,195 ProgressMeter -      1:46485268     3.78913869E8    90.0 s            0.0 s       97.4%    92.0 s       2.0 s
[2016-04-15T00:55Z] INFO  17:55:47,495 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:55Z] INFO  17:55:47,498 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:55Z] INFO  17:55:47,498 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:55Z] INFO  17:55:47,498 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:55Z] INFO  17:55:47,512 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/2/R14-18105_kapa-NGv3-PE100-NGv3-sort-2_159196753_174774985-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/2/R14-18105_kapa-NGv3-PE100-NGv3-2_159196753_174774985-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/2/tx/tmpftITAs/R14-18105_kapa-NGv3-PE100-NGv3-2_159196753_174774985.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:55Z] INFO  17:55:47,539 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:55Z] INFO  17:55:47,539 HelpFormatter - Date/Time: 2016/04/14 17:55:47
[2016-04-15T00:55Z] INFO  17:55:47,539 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:55Z] INFO  17:55:47,540 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:55Z] WARN  17:55:47,589 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T00:55Z] WARN  17:55:47,591 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/2/tx/tmpftITAs/R14-18105_kapa-NGv3-PE100-NGv3-2_159196753_174774985.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T00:55Z] INFO  17:55:47,881 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:55Z] INFO  17:55:48,074 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T00:55Z] INFO  17:55:48,084 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:55Z] INFO  17:55:48,151 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-15T00:55Z] INFO  17:55:48,178 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T00:55Z] INFO  17:55:48,642 IntervalUtils - Processing 216485 bp from intervals
[2016-04-15T00:55Z] WARN  17:55:48,647 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:55Z] INFO  17:55:48,749 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:55Z] INFO  17:55:48,876 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:55Z] INFO  17:55:48,877 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:55Z] INFO  17:55:48,878 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T00:55Z] INFO  17:55:48,878 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T00:55Z] INFO  17:55:48,881 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.014422021
[2016-04-15T00:55Z] INFO  17:55:48,882 PairHMM - Total compute time in PairHMM computeLikelihoods() : 1.02381446
[2016-04-15T00:55Z] INFO  17:55:48,883 HaplotypeCaller - Ran local assembly on 3031 active regions
[2016-04-15T00:55Z] INFO  17:55:48,888 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T00:55Z] INFO  17:55:48,888 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T00:55Z] INFO  17:55:48,930 ProgressMeter -            done     3.97207864E8    91.0 s            0.0 s      100.0%    91.0 s       0.0 s
[2016-04-15T00:55Z] INFO  17:55:48,931 ProgressMeter - Total runtime 91.77 secs, 1.53 min, 0.03 hours
[2016-04-15T00:55Z] INFO  17:55:48,931 MicroScheduler - 62895 reads were filtered out during the traversal out of approximately 714564 total reads (8.80%)
[2016-04-15T00:55Z] INFO  17:55:48,931 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:55Z] INFO  17:55:48,931 MicroScheduler -   -> 57151 reads (8.00% of total) failing DuplicateReadFilter
[2016-04-15T00:55Z] INFO  17:55:48,932 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:55Z] INFO  17:55:48,932 MicroScheduler -   -> 5744 reads (0.80% of total) failing HCMappingQualityFilter
[2016-04-15T00:55Z] INFO  17:55:48,932 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:55Z] INFO  17:55:48,932 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:55Z] INFO  17:55:48,933 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:55Z] INFO  17:55:48,933 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:55Z] INFO  17:55:49,078 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T00:55Z] INFO  17:55:49,277 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:55Z] INFO  17:55:49,280 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:55Z] INFO  17:55:49,281 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:55Z] INFO  17:55:49,281 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:55Z] INFO  17:55:49,285 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/2/R14-18105_kapa-NGv3-PE100-NGv3-sort-2_174777797_190306304-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/2/R14-18105_kapa-NGv3-PE100-NGv3-2_174777797_190306304-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/2/tx/tmpnRNkbd/R14-18105_kapa-NGv3-PE100-NGv3-2_174777797_190306304.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:55Z] INFO  17:55:49,296 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:55Z] INFO  17:55:49,297 HelpFormatter - Date/Time: 2016/04/14 17:55:49
[2016-04-15T00:55Z] INFO  17:55:49,297 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:55Z] INFO  17:55:49,298 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:55Z] WARN  17:55:49,331 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T00:55Z] WARN  17:55:49,336 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/2/tx/tmpnRNkbd/R14-18105_kapa-NGv3-PE100-NGv3-2_174777797_190306304.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T00:55Z] INFO  17:55:49,605 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.006865961
[2016-04-15T00:55Z] INFO  17:55:49,606 PairHMM - Total compute time in PairHMM computeLikelihoods() : 0.31663133400000004
[2016-04-15T00:55Z] INFO  17:55:49,607 HaplotypeCaller - Ran local assembly on 1037 active regions
[2016-04-15T00:55Z] INFO  17:55:49,613 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:55Z] INFO  17:55:49,655 ProgressMeter -            done       4.967453E7    38.0 s            0.0 s      100.0%    38.0 s       0.0 s
[2016-04-15T00:55Z] INFO  17:55:49,656 ProgressMeter - Total runtime 38.24 secs, 0.64 min, 0.01 hours
[2016-04-15T00:55Z] INFO  17:55:49,656 MicroScheduler - 14118 reads were filtered out during the traversal out of approximately 178593 total reads (7.91%)
[2016-04-15T00:55Z] INFO  17:55:49,656 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:55Z] INFO  17:55:49,657 MicroScheduler -   -> 13929 reads (7.80% of total) failing DuplicateReadFilter
[2016-04-15T00:55Z] INFO  17:55:49,657 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:55Z] INFO  17:55:49,657 MicroScheduler -   -> 189 reads (0.11% of total) failing HCMappingQualityFilter
[2016-04-15T00:55Z] INFO  17:55:49,657 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:55Z] INFO  17:55:49,658 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:55Z] INFO  17:55:49,660 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:55Z] INFO  17:55:49,661 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:55Z] INFO  17:55:49,798 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T00:55Z] INFO  17:55:49,818 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:55Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T00:55Z] INFO  17:55:49,899 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T00:55Z] INFO  17:55:49,900 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T00:55Z] INFO  17:55:49,911 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.09
[2016-04-15T00:55Z] INFO  17:55:49,942 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T00:55Z] WARN  17:55:50,220 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T00:55Z] WARN  17:55:50,221 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T00:55Z] INFO  17:55:50,466 IntervalUtils - Processing 253764 bp from intervals
[2016-04-15T00:55Z] WARN  17:55:50,470 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:55Z] INFO  17:55:50,565 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:55Z] INFO  17:55:50,591 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:55Z] INFO  17:55:50,683 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:55Z] INFO  17:55:50,685 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:55Z] INFO  17:55:50,685 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T00:55Z] INFO  17:55:50,686 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T00:55Z] INFO  17:55:50,687 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T00:55Z] INFO  17:55:50,687 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T00:55Z] INFO  17:55:50,786 ProgressMeter -      2:71004499      1.8307829E7    30.0 s            1.0 s       40.2%    74.0 s      44.0 s
[2016-04-15T00:55Z] GATK: HaplotypeCaller
[2016-04-15T00:55Z] INFO  17:55:50,973 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T00:55Z] INFO  17:55:51,243 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:55Z] INFO  17:55:51,274 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.017362040000000002
[2016-04-15T00:55Z] INFO  17:55:51,275 PairHMM - Total compute time in PairHMM computeLikelihoods() : 0.248413923
[2016-04-15T00:55Z] INFO  17:55:51,275 HaplotypeCaller - Ran local assembly on 1251 active regions
[2016-04-15T00:55Z] INFO  17:55:51,315 ProgressMeter -            done       7.519483E7    40.0 s            0.0 s      100.0%    40.0 s       0.0 s
[2016-04-15T00:55Z] INFO  17:55:51,315 ProgressMeter - Total runtime 40.60 secs, 0.68 min, 0.01 hours
[2016-04-15T00:55Z] INFO  17:55:51,316 MicroScheduler - 17641 reads were filtered out during the traversal out of approximately 222859 total reads (7.92%)
[2016-04-15T00:55Z] INFO  17:55:51,316 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:55Z] INFO  17:55:51,316 MicroScheduler -   -> 17343 reads (7.78% of total) failing DuplicateReadFilter
[2016-04-15T00:55Z] INFO  17:55:51,318 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:55Z] INFO  17:55:51,318 MicroScheduler -   -> 298 reads (0.13% of total) failing HCMappingQualityFilter
[2016-04-15T00:55Z] INFO  17:55:51,319 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:55Z] INFO  17:55:51,319 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:55Z] INFO  17:55:51,319 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:55Z] INFO  17:55:51,319 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:55Z] GATK: HaplotypeCaller
[2016-04-15T00:55Z] INFO  17:55:52,860 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:55Z] GATK: HaplotypeCaller
[2016-04-15T00:55Z] INFO  17:55:53,596 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.051228313000000004
[2016-04-15T00:55Z] INFO  17:55:53,597 PairHMM - Total compute time in PairHMM computeLikelihoods() : 1.131185503
[2016-04-15T00:55Z] INFO  17:55:53,597 HaplotypeCaller - Ran local assembly on 2090 active regions
[2016-04-15T00:55Z] INFO  17:55:53,648 ProgressMeter -            done     2.06201078E8    73.0 s            0.0 s      100.0%    73.0 s       0.0 s
[2016-04-15T00:55Z] INFO  17:55:53,649 ProgressMeter - Total runtime 73.04 secs, 1.22 min, 0.02 hours
[2016-04-15T00:55Z] INFO  17:55:53,649 MicroScheduler - 36465 reads were filtered out during the traversal out of approximately 432418 total reads (8.43%)
[2016-04-15T00:55Z] INFO  17:55:53,649 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:55Z] INFO  17:55:53,649 MicroScheduler -   -> 34790 reads (8.05% of total) failing DuplicateReadFilter
[2016-04-15T00:55Z] INFO  17:55:53,650 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:55Z] INFO  17:55:53,650 MicroScheduler -   -> 1675 reads (0.39% of total) failing HCMappingQualityFilter
[2016-04-15T00:55Z] INFO  17:55:53,650 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:55Z] INFO  17:55:53,650 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:55Z] INFO  17:55:53,651 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:55Z] INFO  17:55:53,651 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:55Z] INFO  17:55:54,007 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:55Z] INFO  17:55:54,016 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:55Z] INFO  17:55:54,017 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:55Z] INFO  17:55:54,028 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:55Z] INFO  17:55:54,033 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/2/R14-18105_kapa-NGv3-PE100-NGv3-sort-2_190313104_205830046-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/2/R14-18105_kapa-NGv3-PE100-NGv3-2_190313104_205830046-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/2/tx/tmp4c4prm/R14-18105_kapa-NGv3-PE100-NGv3-2_190313104_205830046.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:55Z] INFO  17:55:54,073 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:55Z] INFO  17:55:54,074 HelpFormatter - Date/Time: 2016/04/14 17:55:54
[2016-04-15T00:55Z] INFO  17:55:54,075 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:55Z] INFO  17:55:54,075 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:55Z] WARN  17:55:54,180 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T00:55Z] WARN  17:55:54,183 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/2/tx/tmp4c4prm/R14-18105_kapa-NGv3-PE100-NGv3-2_190313104_205830046.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T00:55Z] INFO  17:55:54,487 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:55Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T00:55Z] INFO  17:55:54,556 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T00:55Z] INFO  17:55:54,568 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T00:55Z] INFO  17:55:54,701 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T00:55Z] INFO  17:55:54,732 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:55Z] INFO  17:55:54,822 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.09
[2016-04-15T00:55Z] WARN  17:55:54,845 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T00:55Z] WARN  17:55:54,846 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T00:55Z] INFO  17:55:54,850 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T00:55Z] INFO  17:55:54,859 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:55Z] INFO  17:55:54,862 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:55Z] INFO  17:55:54,863 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:55Z] INFO  17:55:54,863 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:55Z] INFO  17:55:54,867 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/2/R14-18105_kapa-NGv3-PE100-NGv3-sort-2_205912303_222290862-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/2/R14-18105_kapa-NGv3-PE100-NGv3-2_205912303_222290862-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/2/tx/tmpEOW5Zg/R14-18105_kapa-NGv3-PE100-NGv3-2_205912303_222290862.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:55Z] INFO  17:55:54,897 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:55Z] INFO  17:55:54,905 HelpFormatter - Date/Time: 2016/04/14 17:55:54
[2016-04-15T00:55Z] INFO  17:55:54,906 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:55Z] INFO  17:55:54,911 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:55Z] WARN  17:55:54,967 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T00:55Z] WARN  17:55:54,970 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/2/tx/tmpEOW5Zg/R14-18105_kapa-NGv3-PE100-NGv3-2_205912303_222290862.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T00:55Z] INFO  17:55:55,222 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:55Z] INFO  17:55:55,261 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:55Z] INFO  17:55:55,357 IntervalUtils - Processing 204460 bp from intervals
[2016-04-15T00:55Z] WARN  17:55:55,373 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:55Z] INFO  17:55:55,487 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T00:55Z] INFO  17:55:55,496 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:55Z] INFO  17:55:55,534 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:55Z] INFO  17:55:55,621 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.09
[2016-04-15T00:55Z] INFO  17:55:55,645 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:55Z] INFO  17:55:55,654 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:55Z] INFO  17:55:55,655 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T00:55Z] INFO  17:55:55,656 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T00:55Z] GATK: HaplotypeCaller
[2016-04-15T00:55Z] INFO  17:55:55,673 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T00:55Z] INFO  17:55:55,670 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T00:55Z] INFO  17:55:55,671 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T00:55Z] INFO  17:55:55,940 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T00:55Z] INFO  17:55:56,177 IntervalUtils - Processing 247026 bp from intervals
[2016-04-15T00:55Z] WARN  17:55:56,183 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:55Z] INFO  17:55:56,267 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:55Z] INFO  17:55:56,392 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:55Z] INFO  17:55:56,393 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:55Z] INFO  17:55:56,394 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T00:55Z] INFO  17:55:56,395 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T00:55Z] INFO  17:55:56,396 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T00:55Z] INFO  17:55:56,396 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T00:55Z] INFO  17:55:56,544 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T00:55Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T00:55Z] INFO  17:55:56,604 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T00:55Z] INFO  17:55:56,604 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T00:55Z] INFO  17:55:56,780 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:55Z] INFO  17:55:56,801 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:55Z] INFO  17:55:56,801 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:55Z] INFO  17:55:56,801 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:55Z] INFO  17:55:56,805 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/2/R14-18105_kapa-NGv3-PE100-NGv3-sort-2_222291154_237994685-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/2/R14-18105_kapa-NGv3-PE100-NGv3-2_222291154_237994685-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/2/tx/tmpjfB7Xn/R14-18105_kapa-NGv3-PE100-NGv3-2_222291154_237994685.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:55Z] INFO  17:55:56,819 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:55Z] INFO  17:55:56,820 HelpFormatter - Date/Time: 2016/04/14 17:55:56
[2016-04-15T00:55Z] INFO  17:55:56,820 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:55Z] INFO  17:55:56,820 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:55Z] WARN  17:55:56,870 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T00:55Z] WARN  17:55:56,875 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/2/tx/tmpjfB7Xn/R14-18105_kapa-NGv3-PE100-NGv3-2_222291154_237994685.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T00:55Z] WARN  17:55:56,914 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T00:55Z] WARN  17:55:56,915 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T00:55Z] INFO  17:55:57,082 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:55Z] INFO  17:55:57,286 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T00:55Z] INFO  17:55:57,300 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:55Z] INFO  17:55:57,302 ProgressMeter -     1:152187546      7.4636378E7    90.0 s            1.0 s       37.1%     4.0 m       2.5 m
[2016-04-15T00:55Z] INFO  17:55:57,411 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.11
[2016-04-15T00:55Z] INFO  17:55:57,441 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T00:55Z] INFO  17:55:57,914 IntervalUtils - Processing 186854 bp from intervals
[2016-04-15T00:55Z] WARN  17:55:57,931 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:55Z] INFO  17:55:58,067 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:55Z] INFO  17:55:58,217 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:55Z] INFO  17:55:58,218 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:55Z] INFO  17:55:58,219 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T00:55Z] INFO  17:55:58,220 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T00:55Z] INFO  17:55:58,244 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T00:55Z] INFO  17:55:58,245 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T00:55Z] INFO  17:55:58,430 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T00:55Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T00:55Z] INFO  17:55:58,456 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T00:55Z] INFO  17:55:58,457 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T00:55Z] WARN  17:55:58,734 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T00:55Z] WARN  17:55:58,735 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T00:55Z] INFO  17:55:58,958 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:55Z] INFO  17:55:58,961 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:55Z] INFO  17:55:58,962 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:55Z] INFO  17:55:58,962 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:55Z] INFO  17:55:58,968 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/2/R14-18105_kapa-NGv3-PE100-NGv3-sort-2_237995374_243199373-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/2/R14-18105_kapa-NGv3-PE100-NGv3-2_237995374_243199373-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/2/tx/tmpOZHV9b/R14-18105_kapa-NGv3-PE100-NGv3-2_237995374_243199373.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:55Z] INFO  17:55:59,001 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:55Z] INFO  17:55:59,002 HelpFormatter - Date/Time: 2016/04/14 17:55:58
[2016-04-15T00:55Z] INFO  17:55:59,002 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:55Z] INFO  17:55:59,003 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:55Z] WARN  17:55:59,058 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T00:55Z] WARN  17:55:59,065 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/2/tx/tmpOZHV9b/R14-18105_kapa-NGv3-PE100-NGv3-2_237995374_243199373.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T00:55Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T00:55Z] INFO  17:55:59,250 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T00:55Z] INFO  17:55:59,251 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T00:55Z] INFO  17:55:59,319 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:55Z] WARN  17:55:59,517 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T00:55Z] WARN  17:55:59,517 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T00:55Z] INFO  17:55:59,527 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T00:55Z] INFO  17:55:59,538 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:55Z] INFO  17:55:59,649 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.11
[2016-04-15T00:55Z] INFO  17:55:59,682 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T00:55Z] INFO  17:55:59,945 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.015399039000000002
[2016-04-15T00:55Z] INFO  17:55:59,946 PairHMM - Total compute time in PairHMM computeLikelihoods() : 0.20633474100000002
[2016-04-15T00:55Z] INFO  17:55:59,946 HaplotypeCaller - Ran local assembly on 764 active regions
[2016-04-15T00:55Z] INFO  17:55:59,998 ProgressMeter -            done      2.4918497E7    29.0 s            1.0 s      100.0%    29.0 s       0.0 s
[2016-04-15T00:56Z] INFO  17:55:59,998 ProgressMeter - Total runtime 29.34 secs, 0.49 min, 0.01 hours
[2016-04-15T00:56Z] INFO  17:55:59,999 MicroScheduler - 62180 reads were filtered out during the traversal out of approximately 189329 total reads (32.84%)
[2016-04-15T00:56Z] INFO  17:56:00,000 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:56Z] INFO  17:56:00,000 MicroScheduler -   -> 11260 reads (5.95% of total) failing DuplicateReadFilter
[2016-04-15T00:56Z] INFO  17:56:00,000 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:56Z] INFO  17:56:00,000 MicroScheduler -   -> 50920 reads (26.89% of total) failing HCMappingQualityFilter
[2016-04-15T00:56Z] INFO  17:56:00,001 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:56Z] INFO  17:56:00,001 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:56Z] INFO  17:56:00,001 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:56Z] INFO  17:56:00,001 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:56Z] INFO  17:56:00,241 IntervalUtils - Processing 128077 bp from intervals
[2016-04-15T00:56Z] WARN  17:56:00,247 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:56Z] INFO  17:56:00,348 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:56Z] INFO  17:56:00,439 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:56Z] INFO  17:56:00,440 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:56Z] INFO  17:56:00,440 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T00:56Z] INFO  17:56:00,440 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T00:56Z] INFO  17:56:00,452 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T00:56Z] INFO  17:56:00,453 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T00:56Z] INFO  17:56:00,717 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T00:56Z] INFO  17:56:00,737 ProgressMeter -      2:97560798      1.0354872E7    30.0 s            2.0 s       27.6%   108.0 s      78.0 s
[2016-04-15T00:56Z] INFO  17:56:01,498 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:56Z] GATK: HaplotypeCaller
[2016-04-15T00:56Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T00:56Z] INFO  17:56:04,381 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T00:56Z] INFO  17:56:04,382 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T00:56Z] INFO  17:56:04,408 ProgressMeter -     2:120012260      1.9779018E7    30.0 s            1.0 s       69.7%    43.0 s      13.0 s
[2016-04-15T00:56Z] WARN  17:56:05,146 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T00:56Z] WARN  17:56:05,147 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T00:56Z] INFO  17:56:05,164 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:56Z] INFO  17:56:05,167 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:56Z] INFO  17:56:05,168 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:56Z] INFO  17:56:05,169 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:56Z] INFO  17:56:05,173 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/3/R14-18105_kapa-NGv3-PE100-NGv3-sort-3_0_15512123-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/3/R14-18105_kapa-NGv3-PE100-NGv3-3_0_15512123-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/3/tx/tmpLgfWUC/R14-18105_kapa-NGv3-PE100-NGv3-3_0_15512123.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:56Z] INFO  17:56:05,183 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:56Z] INFO  17:56:05,194 HelpFormatter - Date/Time: 2016/04/14 17:56:05
[2016-04-15T00:56Z] INFO  17:56:05,195 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:56Z] INFO  17:56:05,196 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:56Z] WARN  17:56:05,241 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T00:56Z] WARN  17:56:05,244 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/3/tx/tmpLgfWUC/R14-18105_kapa-NGv3-PE100-NGv3-3_0_15512123.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T00:56Z] INFO  17:56:05,538 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.022197563
[2016-04-15T00:56Z] INFO  17:56:05,539 PairHMM - Total compute time in PairHMM computeLikelihoods() : 1.064931651
[2016-04-15T00:56Z] INFO  17:56:05,540 HaplotypeCaller - Ran local assembly on 1737 active regions
[2016-04-15T00:56Z] INFO  17:56:05,572 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:56Z] INFO  17:56:05,603 ProgressMeter -            done      1.3985948E8    58.0 s            0.0 s      100.0%    58.0 s       0.0 s
[2016-04-15T00:56Z] INFO  17:56:05,604 ProgressMeter - Total runtime 58.59 secs, 0.98 min, 0.02 hours
[2016-04-15T00:56Z] INFO  17:56:05,604 MicroScheduler - 28927 reads were filtered out during the traversal out of approximately 361955 total reads (7.99%)
[2016-04-15T00:56Z] INFO  17:56:05,604 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:56Z] INFO  17:56:05,605 MicroScheduler -   -> 28567 reads (7.89% of total) failing DuplicateReadFilter
[2016-04-15T00:56Z] INFO  17:56:05,605 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:56Z] INFO  17:56:05,605 MicroScheduler -   -> 360 reads (0.10% of total) failing HCMappingQualityFilter
[2016-04-15T00:56Z] INFO  17:56:05,605 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:56Z] INFO  17:56:05,606 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:56Z] INFO  17:56:05,606 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:56Z] INFO  17:56:05,606 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:56Z] INFO  17:56:05,764 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T00:56Z] INFO  17:56:05,773 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:56Z] INFO  17:56:05,868 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.09
[2016-04-15T00:56Z] INFO  17:56:05,904 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T00:56Z] INFO  17:56:06,480 IntervalUtils - Processing 188511 bp from intervals
[2016-04-15T00:56Z] WARN  17:56:06,485 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:56Z] INFO  17:56:06,577 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:56Z] INFO  17:56:06,659 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:56Z] INFO  17:56:06,660 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:56Z] INFO  17:56:06,661 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T00:56Z] INFO  17:56:06,662 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T00:56Z] INFO  17:56:06,674 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T00:56Z] INFO  17:56:06,675 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T00:56Z] INFO  17:56:06,944 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T00:56Z] INFO  17:56:07,162 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:56Z] GATK: HaplotypeCaller
[2016-04-15T00:56Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T00:56Z] INFO  17:56:08,639 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T00:56Z] INFO  17:56:08,640 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T00:56Z] WARN  17:56:08,948 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T00:56Z] WARN  17:56:08,949 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T00:56Z] INFO  17:56:09,501 ProgressMeter -     2:131520646      1.1112518E7    30.0 s            2.0 s       41.7%    71.0 s      41.0 s
[2016-04-15T00:56Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T00:56Z] INFO  17:56:10,417 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T00:56Z] INFO  17:56:10,420 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T00:56Z] WARN  17:56:10,679 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T00:56Z] WARN  17:56:10,680 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T00:56Z] INFO  17:56:11,156 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:56Z] INFO  17:56:11,170 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:56Z] INFO  17:56:11,171 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:56Z] INFO  17:56:11,171 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:56Z] INFO  17:56:11,176 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/3/R14-18105_kapa-NGv3-PE100-NGv3-sort-3_15515506_31574805-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/3/R14-18105_kapa-NGv3-PE100-NGv3-3_15515506_31574805-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/3/tx/tmpP5URWw/R14-18105_kapa-NGv3-PE100-NGv3-3_15515506_31574805.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:56Z] INFO  17:56:11,197 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:56Z] INFO  17:56:11,198 HelpFormatter - Date/Time: 2016/04/14 17:56:11
[2016-04-15T00:56Z] INFO  17:56:11,198 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:56Z] INFO  17:56:11,198 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:56Z] WARN  17:56:11,231 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T00:56Z] WARN  17:56:11,248 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/3/tx/tmpP5URWw/R14-18105_kapa-NGv3-PE100-NGv3-3_15515506_31574805.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T00:56Z] INFO  17:56:11,498 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:56Z] INFO  17:56:11,779 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T00:56Z] INFO  17:56:11,792 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:56Z] INFO  17:56:11,871 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-15T00:56Z] INFO  17:56:11,892 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T00:56Z] INFO  17:56:12,400 IntervalUtils - Processing 86168 bp from intervals
[2016-04-15T00:56Z] WARN  17:56:12,417 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:56Z] INFO  17:56:12,538 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:56Z] INFO  17:56:12,645 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:56Z] INFO  17:56:12,646 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:56Z] INFO  17:56:12,646 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T00:56Z] INFO  17:56:12,646 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T00:56Z] INFO  17:56:12,660 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T00:56Z] INFO  17:56:12,661 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T00:56Z] INFO  17:56:12,870 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T00:56Z] INFO  17:56:13,556 ProgressMeter -      1:13183802     2.96147518E8   120.0 s            0.0 s       91.2%     2.2 m      11.0 s
[2016-04-15T00:56Z] INFO  17:56:14,382 ProgressMeter -      1:27687648     2.76433961E8   120.0 s            0.0 s       85.9%     2.3 m      19.0 s
[2016-04-15T00:56Z] INFO  17:56:15,432 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.008705602
[2016-04-15T00:56Z] INFO  17:56:15,433 PairHMM - Total compute time in PairHMM computeLikelihoods() : 0.8751264750000001
[2016-04-15T00:56Z] INFO  17:56:15,433 HaplotypeCaller - Ran local assembly on 956 active regions
[2016-04-15T00:56Z] INFO  17:56:15,494 ProgressMeter -            done      4.1916896E7    41.0 s            0.0 s      100.0%    41.0 s       0.0 s
[2016-04-15T00:56Z] INFO  17:56:15,494 ProgressMeter - Total runtime 41.11 secs, 0.69 min, 0.01 hours
[2016-04-15T00:56Z] INFO  17:56:15,495 MicroScheduler - 73052 reads were filtered out during the traversal out of approximately 222937 total reads (32.77%)
[2016-04-15T00:56Z] INFO  17:56:15,496 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:56Z] INFO  17:56:15,496 MicroScheduler -   -> 13284 reads (5.96% of total) failing DuplicateReadFilter
[2016-04-15T00:56Z] INFO  17:56:15,496 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:56Z] INFO  17:56:15,496 MicroScheduler -   -> 59768 reads (26.81% of total) failing HCMappingQualityFilter
[2016-04-15T00:56Z] INFO  17:56:15,497 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:56Z] INFO  17:56:15,497 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:56Z] INFO  17:56:15,497 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:56Z] INFO  17:56:15,497 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:56Z] INFO  17:56:16,019 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.00576804
[2016-04-15T00:56Z] INFO  17:56:16,020 PairHMM - Total compute time in PairHMM computeLikelihoods() : 0.306174053
[2016-04-15T00:56Z] INFO  17:56:16,021 HaplotypeCaller - Ran local assembly on 698 active regions
[2016-04-15T00:56Z] INFO  17:56:16,059 ProgressMeter -            done      2.4452471E7    29.0 s            1.0 s      100.0%    29.0 s       0.0 s
[2016-04-15T00:56Z] INFO  17:56:16,060 ProgressMeter - Total runtime 29.64 secs, 0.49 min, 0.01 hours
[2016-04-15T00:56Z] INFO  17:56:16,061 MicroScheduler - 19628 reads were filtered out during the traversal out of approximately 120277 total reads (16.32%)
[2016-04-15T00:56Z] INFO  17:56:16,062 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:56Z] INFO  17:56:16,062 MicroScheduler -   -> 8653 reads (7.19% of total) failing DuplicateReadFilter
[2016-04-15T00:56Z] INFO  17:56:16,063 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:56Z] INFO  17:56:16,064 MicroScheduler -   -> 10975 reads (9.12% of total) failing HCMappingQualityFilter
[2016-04-15T00:56Z] INFO  17:56:16,064 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:56Z] INFO  17:56:16,065 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:56Z] INFO  17:56:16,066 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:56Z] INFO  17:56:16,066 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:56Z] INFO  17:56:16,955 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:56Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T00:56Z] INFO  17:56:17,025 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T00:56Z] INFO  17:56:17,026 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T00:56Z] GATK: HaplotypeCaller
[2016-04-15T00:56Z] WARN  17:56:17,258 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T00:56Z] WARN  17:56:17,259 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T00:56Z] INFO  17:56:17,612 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:56Z] GATK: HaplotypeCaller
[2016-04-15T00:56Z] INFO  17:56:18,890 ProgressMeter -     2:167334206      3.1262466E7    30.0 s            0.0 s       51.9%    57.0 s      27.0 s
[2016-04-15T00:56Z] INFO  17:56:20,249 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:56Z] INFO  17:56:20,253 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:56Z] INFO  17:56:20,253 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:56Z] INFO  17:56:20,253 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:56Z] INFO  17:56:20,265 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/3/R14-18105_kapa-NGv3-PE100-NGv3-sort-3_31617887_47127804-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/3/R14-18105_kapa-NGv3-PE100-NGv3-3_31617887_47127804-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/3/tx/tmp4UPVVD/R14-18105_kapa-NGv3-PE100-NGv3-3_31617887_47127804.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:56Z] INFO  17:56:20,281 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:56Z] INFO  17:56:20,281 HelpFormatter - Date/Time: 2016/04/14 17:56:20
[2016-04-15T00:56Z] INFO  17:56:20,282 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:56Z] INFO  17:56:20,282 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:56Z] WARN  17:56:20,331 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T00:56Z] WARN  17:56:20,335 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/3/tx/tmp4UPVVD/R14-18105_kapa-NGv3-PE100-NGv3-3_31617887_47127804.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T00:56Z] INFO  17:56:20,549 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:56Z] INFO  17:56:20,723 ProgressMeter -     2:179449402        8839612.0    30.0 s            3.0 s       39.2%    76.0 s      46.0 s
[2016-04-15T00:56Z] INFO  17:56:20,782 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T00:56Z] INFO  17:56:20,787 ProgressMeter -      2:77746304      9.9926326E7    60.0 s            0.0 s       99.7%    60.0 s       0.0 s
[2016-04-15T00:56Z] INFO  17:56:20,803 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:56Z] INFO  17:56:20,888 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-15T00:56Z] INFO  17:56:20,911 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:56Z] INFO  17:56:20,915 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:56Z] INFO  17:56:20,915 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:56Z] INFO  17:56:20,915 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:56Z] INFO  17:56:20,912 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T00:56Z] INFO  17:56:20,919 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/3/R14-18105_kapa-NGv3-PE100-NGv3-sort-3_47129602_62648069-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/3/R14-18105_kapa-NGv3-PE100-NGv3-3_47129602_62648069-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/3/tx/tmpg22Dly/R14-18105_kapa-NGv3-PE100-NGv3-3_47129602_62648069.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:56Z] INFO  17:56:20,924 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.065380611
[2016-04-15T00:56Z] INFO  17:56:20,925 PairHMM - Total compute time in PairHMM computeLikelihoods() : 16.151961899
[2016-04-15T00:56Z] INFO  17:56:20,926 HaplotypeCaller - Ran local assembly on 2810 active regions
[2016-04-15T00:56Z] INFO  17:56:20,933 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:56Z] INFO  17:56:20,934 HelpFormatter - Date/Time: 2016/04/14 17:56:20
[2016-04-15T00:56Z] INFO  17:56:20,935 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:56Z] INFO  17:56:20,935 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:56Z] WARN  17:56:20,968 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T00:56Z] WARN  17:56:20,971 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/3/tx/tmpg22Dly/R14-18105_kapa-NGv3-PE100-NGv3-3_47129602_62648069.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T00:56Z] INFO  17:56:20,973 ProgressMeter -            done     3.27575124E8     2.1 m            0.0 s      100.0%     2.1 m       0.0 s
[2016-04-15T00:56Z] INFO  17:56:20,973 ProgressMeter - Total runtime 127.43 secs, 2.12 min, 0.04 hours
[2016-04-15T00:56Z] INFO  17:56:20,974 MicroScheduler - 148791 reads were filtered out during the traversal out of approximately 745916 total reads (19.95%)
[2016-04-15T00:56Z] INFO  17:56:20,974 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:56Z] INFO  17:56:20,974 MicroScheduler -   -> 52561 reads (7.05% of total) failing DuplicateReadFilter
[2016-04-15T00:56Z] INFO  17:56:20,975 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:56Z] INFO  17:56:20,975 MicroScheduler -   -> 96230 reads (12.90% of total) failing HCMappingQualityFilter
[2016-04-15T00:56Z] INFO  17:56:20,975 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:56Z] INFO  17:56:20,975 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:56Z] INFO  17:56:20,976 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:56Z] INFO  17:56:20,976 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:56Z] INFO  17:56:21,182 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:56Z] INFO  17:56:21,289 IntervalUtils - Processing 307437 bp from intervals
[2016-04-15T00:56Z] WARN  17:56:21,295 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:56Z] INFO  17:56:21,368 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.021713633000000003
[2016-04-15T00:56Z] INFO  17:56:21,369 PairHMM - Total compute time in PairHMM computeLikelihoods() : 1.430367396
[2016-04-15T00:56Z] INFO  17:56:21,369 HaplotypeCaller - Ran local assembly on 1553 active regions
[2016-04-15T00:56Z] INFO  17:56:21,386 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:56Z] INFO  17:56:21,388 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T00:56Z] INFO  17:56:21,397 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:56Z] INFO  17:56:21,446 ProgressMeter -            done     1.00598827E8    60.0 s            0.0 s      100.0%    60.0 s       0.0 s
[2016-04-15T00:56Z] INFO  17:56:21,447 ProgressMeter - Total runtime 60.68 secs, 1.01 min, 0.02 hours
[2016-04-15T00:56Z] INFO  17:56:21,447 MicroScheduler - 26936 reads were filtered out during the traversal out of approximately 329972 total reads (8.16%)
[2016-04-15T00:56Z] INFO  17:56:21,448 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:56Z] INFO  17:56:21,451 MicroScheduler -   -> 26237 reads (7.95% of total) failing DuplicateReadFilter
[2016-04-15T00:56Z] INFO  17:56:21,451 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:56Z] INFO  17:56:21,451 MicroScheduler -   -> 699 reads (0.21% of total) failing HCMappingQualityFilter
[2016-04-15T00:56Z] INFO  17:56:21,452 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:56Z] INFO  17:56:21,452 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:56Z] INFO  17:56:21,452 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:56Z] INFO  17:56:21,452 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:56Z] INFO  17:56:21,493 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.10
[2016-04-15T00:56Z] INFO  17:56:21,523 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T00:56Z] INFO  17:56:21,543 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:56Z] INFO  17:56:21,544 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:56Z] INFO  17:56:21,545 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T00:56Z] INFO  17:56:21,546 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T00:56Z] INFO  17:56:21,546 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T00:56Z] INFO  17:56:21,547 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T00:56Z] INFO  17:56:21,709 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T00:56Z] INFO  17:56:22,022 IntervalUtils - Processing 430308 bp from intervals
[2016-04-15T00:56Z] WARN  17:56:22,028 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:56Z] INFO  17:56:22,148 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:56Z] INFO  17:56:22,319 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:56Z] INFO  17:56:22,321 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:56Z] INFO  17:56:22,321 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T00:56Z] INFO  17:56:22,322 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T00:56Z] INFO  17:56:22,323 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T00:56Z] INFO  17:56:22,323 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T00:56Z] INFO  17:56:22,432 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:56Z] INFO  17:56:22,494 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T00:56Z] GATK: HaplotypeCaller
[2016-04-15T00:56Z] INFO  17:56:22,966 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:56Z] GATK: HaplotypeCaller
[2016-04-15T00:56Z] INFO  17:56:25,673 ProgressMeter -     2:200245087      2.8955599E7    30.0 s            1.0 s       51.4%    58.0 s      28.0 s
[2016-04-15T00:56Z] INFO  17:56:25,874 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:56Z] INFO  17:56:25,877 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:56Z] INFO  17:56:25,878 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:56Z] INFO  17:56:25,879 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:56Z] INFO  17:56:25,883 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/3/R14-18105_kapa-NGv3-PE100-NGv3-sort-3_62739115_78648077-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/3/R14-18105_kapa-NGv3-PE100-NGv3-3_62739115_78648077-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/3/tx/tmpmoRnmB/R14-18105_kapa-NGv3-PE100-NGv3-3_62739115_78648077.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:56Z] INFO  17:56:25,899 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:56Z] INFO  17:56:25,903 HelpFormatter - Date/Time: 2016/04/14 17:56:25
[2016-04-15T00:56Z] INFO  17:56:25,903 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:56Z] INFO  17:56:25,904 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:56Z] INFO  17:56:25,945 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.034542341000000004
[2016-04-15T00:56Z] INFO  17:56:25,946 PairHMM - Total compute time in PairHMM computeLikelihoods() : 18.800546365000002
[2016-04-15T00:56Z] INFO  17:56:25,947 HaplotypeCaller - Ran local assembly on 2980 active regions
[2016-04-15T00:56Z] WARN  17:56:25,973 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T00:56Z] INFO  17:56:25,975 ProgressMeter -            done     3.72740812E8     2.2 m            0.0 s      100.0%     2.2 m       0.0 s
[2016-04-15T00:56Z] WARN  17:56:25,976 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/3/tx/tmpmoRnmB/R14-18105_kapa-NGv3-PE100-NGv3-3_62739115_78648077.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T00:56Z] INFO  17:56:25,977 ProgressMeter - Total runtime 131.64 secs, 2.19 min, 0.04 hours
[2016-04-15T00:56Z] INFO  17:56:25,977 MicroScheduler - 67011 reads were filtered out during the traversal out of approximately 715368 total reads (9.37%)
[2016-04-15T00:56Z] INFO  17:56:25,978 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:56Z] INFO  17:56:25,979 MicroScheduler -   -> 57407 reads (8.02% of total) failing DuplicateReadFilter
[2016-04-15T00:56Z] INFO  17:56:25,979 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:56Z] INFO  17:56:25,980 MicroScheduler -   -> 9604 reads (1.34% of total) failing HCMappingQualityFilter
[2016-04-15T00:56Z] INFO  17:56:25,981 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:56Z] INFO  17:56:25,981 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:56Z] INFO  17:56:25,982 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:56Z] INFO  17:56:25,983 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:56Z] INFO  17:56:26,208 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:56Z] INFO  17:56:26,212 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:56Z] INFO  17:56:26,212 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:56Z] INFO  17:56:26,213 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:56Z] INFO  17:56:26,218 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/3/R14-18105_kapa-NGv3-PE100-NGv3-sort-3_78649262_96533852-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/3/R14-18105_kapa-NGv3-PE100-NGv3-3_78649262_96533852-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/3/tx/tmpyAyC53/R14-18105_kapa-NGv3-PE100-NGv3-3_78649262_96533852.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:56Z] INFO  17:56:26,233 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:56Z] INFO  17:56:26,234 HelpFormatter - Date/Time: 2016/04/14 17:56:26
[2016-04-15T00:56Z] INFO  17:56:26,234 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:56Z] INFO  17:56:26,235 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:56Z] INFO  17:56:26,241 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:56Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T00:56Z] WARN  17:56:26,269 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T00:56Z] WARN  17:56:26,272 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/3/tx/tmpyAyC53/R14-18105_kapa-NGv3-PE100-NGv3-3_78649262_96533852.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T00:56Z] INFO  17:56:26,278 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T00:56Z] INFO  17:56:26,289 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T00:56Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T00:56Z] INFO  17:56:26,317 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T00:56Z] INFO  17:56:26,319 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T00:56Z] INFO  17:56:26,416 ProgressMeter -     2:214794869      2.4146157E7    30.0 s            1.0 s       37.0%    81.0 s      51.0 s
[2016-04-15T00:56Z] INFO  17:56:26,455 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T00:56Z] INFO  17:56:26,464 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:56Z] INFO  17:56:26,472 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:56Z] WARN  17:56:26,550 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T00:56Z] WARN  17:56:26,555 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T00:56Z] INFO  17:56:26,567 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.09
[2016-04-15T00:56Z] INFO  17:56:26,606 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T00:56Z] WARN  17:56:26,613 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T00:56Z] WARN  17:56:26,613 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T00:56Z] INFO  17:56:26,680 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T00:56Z] INFO  17:56:26,690 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:56Z] INFO  17:56:26,768 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-15T00:56Z] INFO  17:56:26,790 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T00:56Z] INFO  17:56:27,094 IntervalUtils - Processing 30411 bp from intervals
[2016-04-15T00:56Z] WARN  17:56:27,099 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:56Z] INFO  17:56:27,129 IntervalUtils - Processing 82160 bp from intervals
[2016-04-15T00:56Z] WARN  17:56:27,148 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:56Z] INFO  17:56:27,195 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:56Z] INFO  17:56:27,262 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:56Z] INFO  17:56:27,263 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:56Z] INFO  17:56:27,263 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T00:56Z] INFO  17:56:27,263 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T00:56Z] INFO  17:56:27,274 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T00:56Z] INFO  17:56:27,275 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T00:56Z] INFO  17:56:27,302 ProgressMeter -     1:152276946      7.5033226E7   120.0 s            1.0 s       38.7%     5.2 m       3.2 m
[2016-04-15T00:56Z] INFO  17:56:27,307 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:56Z] INFO  17:56:27,371 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:56Z] INFO  17:56:27,373 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:56Z] INFO  17:56:27,373 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T00:56Z] INFO  17:56:27,374 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T00:56Z] INFO  17:56:27,375 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T00:56Z] INFO  17:56:27,375 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T00:56Z] INFO  17:56:27,462 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T00:56Z] INFO  17:56:27,512 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:56Z] INFO  17:56:27,583 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T00:56Z] GATK: HaplotypeCaller
[2016-04-15T00:56Z] INFO  17:56:28,247 ProgressMeter -     2:231407661      2.4918415E7    30.0 s            1.0 s       47.5%    63.0 s      33.0 s
[2016-04-15T00:56Z] INFO  17:56:30,455 ProgressMeter -     2:241872287      1.4529545E7    30.0 s            2.0 s       58.6%    51.0 s      21.0 s
[2016-04-15T00:56Z] INFO  17:56:30,736 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:56Z] INFO  17:56:30,739 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:56Z] INFO  17:56:30,740 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:56Z] INFO  17:56:30,740 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:56Z] INFO  17:56:30,744 ProgressMeter -     2:106015299      8.9617966E7    60.0 s            0.0 s       75.9%    79.0 s      19.0 s
[2016-04-15T00:56Z] INFO  17:56:30,745 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/3/R14-18105_kapa-NGv3-PE100-NGv3-sort-3_96585668_112185230-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/3/R14-18105_kapa-NGv3-PE100-NGv3-3_96585668_112185230-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/3/tx/tmptYH0U4/R14-18105_kapa-NGv3-PE100-NGv3-3_96585668_112185230.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:56Z] INFO  17:56:30,769 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:56Z] INFO  17:56:30,770 HelpFormatter - Date/Time: 2016/04/14 17:56:30
[2016-04-15T00:56Z] INFO  17:56:30,770 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:56Z] INFO  17:56:30,771 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:56Z] WARN  17:56:30,829 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T00:56Z] WARN  17:56:30,832 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/3/tx/tmptYH0U4/R14-18105_kapa-NGv3-PE100-NGv3-3_96585668_112185230.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T00:56Z] INFO  17:56:31,023 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:56Z] INFO  17:56:31,267 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T00:56Z] INFO  17:56:31,277 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:56Z] INFO  17:56:31,374 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.10
[2016-04-15T00:56Z] INFO  17:56:31,402 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T00:56Z] INFO  17:56:31,758 IntervalUtils - Processing 140565 bp from intervals
[2016-04-15T00:56Z] WARN  17:56:31,775 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:56Z] INFO  17:56:31,925 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:56Z] INFO  17:56:32,035 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:56Z] INFO  17:56:32,036 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:56Z] INFO  17:56:32,037 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T00:56Z] INFO  17:56:32,037 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T00:56Z] INFO  17:56:32,038 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T00:56Z] INFO  17:56:32,038 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T00:56Z] INFO  17:56:32,203 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T00:56Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T00:56Z] INFO  17:56:33,327 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T00:56Z] INFO  17:56:33,327 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T00:56Z] WARN  17:56:33,545 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T00:56Z] WARN  17:56:33,546 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T00:56Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T00:56Z] INFO  17:56:33,806 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T00:56Z] INFO  17:56:33,806 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T00:56Z] WARN  17:56:34,686 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T00:56Z] WARN  17:56:34,686 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T00:56Z] INFO  17:56:36,688 ProgressMeter -      3:10089601      1.8102063E7    30.0 s            1.0 s       46.3%    64.0 s      34.0 s
[2016-04-15T00:56Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T00:56Z] INFO  17:56:38,578 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T00:56Z] INFO  17:56:38,579 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T00:56Z] WARN  17:56:38,788 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T00:56Z] WARN  17:56:38,789 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T00:56Z] INFO  17:56:39,511 ProgressMeter -     2:138163377      4.7585359E7    60.0 s            1.0 s       88.7%    67.0 s       7.0 s
[2016-04-15T00:56Z] INFO  17:56:39,617 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.007940715000000001
[2016-04-15T00:56Z] INFO  17:56:39,618 PairHMM - Total compute time in PairHMM computeLikelihoods() : 0.41037909
[2016-04-15T00:56Z] INFO  17:56:39,618 HaplotypeCaller - Ran local assembly on 1563 active regions
[2016-04-15T00:56Z] INFO  17:56:39,684 ProgressMeter -            done     1.25465506E8    50.0 s            0.0 s      100.0%    50.0 s       0.0 s
[2016-04-15T00:56Z] INFO  17:56:39,684 ProgressMeter - Total runtime 50.81 secs, 0.85 min, 0.01 hours
[2016-04-15T00:56Z] INFO  17:56:39,685 MicroScheduler - 22834 reads were filtered out during the traversal out of approximately 282698 total reads (8.08%)
[2016-04-15T00:56Z] INFO  17:56:39,685 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:56Z] INFO  17:56:39,685 MicroScheduler -   -> 22182 reads (7.85% of total) failing DuplicateReadFilter
[2016-04-15T00:56Z] INFO  17:56:39,685 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:56Z] INFO  17:56:39,686 MicroScheduler -   -> 652 reads (0.23% of total) failing HCMappingQualityFilter
[2016-04-15T00:56Z] INFO  17:56:39,686 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:56Z] INFO  17:56:39,686 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:56Z] INFO  17:56:39,686 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:56Z] INFO  17:56:39,687 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:56Z] INFO  17:56:41,061 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:56Z] GATK: HaplotypeCaller
[2016-04-15T00:56Z] INFO  17:56:41,568 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.011623644
[2016-04-15T00:56Z] INFO  17:56:41,569 PairHMM - Total compute time in PairHMM computeLikelihoods() : 0.8413080070000001
[2016-04-15T00:56Z] INFO  17:56:41,569 HaplotypeCaller - Ran local assembly on 960 active regions
[2016-04-15T00:56Z] INFO  17:56:41,623 ProgressMeter -            done      3.8908959E7    41.0 s            1.0 s      100.0%    41.0 s       0.0 s
[2016-04-15T00:56Z] INFO  17:56:41,624 ProgressMeter - Total runtime 41.18 secs, 0.69 min, 0.01 hours
[2016-04-15T00:56Z] INFO  17:56:41,624 MicroScheduler - 23091 reads were filtered out during the traversal out of approximately 215354 total reads (10.72%)
[2016-04-15T00:56Z] INFO  17:56:41,625 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:56Z] INFO  17:56:41,625 MicroScheduler -   -> 16637 reads (7.73% of total) failing DuplicateReadFilter
[2016-04-15T00:56Z] INFO  17:56:41,625 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:56Z] INFO  17:56:41,625 MicroScheduler -   -> 6454 reads (3.00% of total) failing HCMappingQualityFilter
[2016-04-15T00:56Z] INFO  17:56:41,626 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:56Z] INFO  17:56:41,626 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:56Z] INFO  17:56:41,626 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:56Z] INFO  17:56:41,626 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:56Z] INFO  17:56:42,082 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.018566031
[2016-04-15T00:56Z] INFO  17:56:42,082 PairHMM - Total compute time in PairHMM computeLikelihoods() : 0.20909316600000002
[2016-04-15T00:56Z] INFO  17:56:42,083 HaplotypeCaller - Ran local assembly on 626 active regions
[2016-04-15T00:56Z] INFO  17:56:42,141 ProgressMeter -            done      2.0117694E7    29.0 s            1.0 s      100.0%    29.0 s       0.0 s
[2016-04-15T00:56Z] INFO  17:56:42,142 ProgressMeter - Total runtime 29.50 secs, 0.49 min, 0.01 hours
[2016-04-15T00:56Z] INFO  17:56:42,143 MicroScheduler - 8789 reads were filtered out during the traversal out of approximately 108975 total reads (8.07%)
[2016-04-15T00:56Z] INFO  17:56:42,144 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:56Z] INFO  17:56:42,145 MicroScheduler -   -> 8584 reads (7.88% of total) failing DuplicateReadFilter
[2016-04-15T00:56Z] INFO  17:56:42,145 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:56Z] INFO  17:56:42,146 MicroScheduler -   -> 205 reads (0.19% of total) failing HCMappingQualityFilter
[2016-04-15T00:56Z] INFO  17:56:42,147 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:56Z] INFO  17:56:42,148 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:56Z] INFO  17:56:42,148 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:56Z] INFO  17:56:42,149 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:56Z] INFO  17:56:43,205 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:56Z] GATK: HaplotypeCaller
[2016-04-15T00:56Z] INFO  17:56:43,529 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.01610296
[2016-04-15T00:56Z] INFO  17:56:43,530 PairHMM - Total compute time in PairHMM computeLikelihoods() : 5.250828602
[2016-04-15T00:56Z] INFO  17:56:43,530 HaplotypeCaller - Ran local assembly on 1883 active regions
[2016-04-15T00:56Z] INFO  17:56:43,568 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.008556278
[2016-04-15T00:56Z] INFO  17:56:43,568 PairHMM - Total compute time in PairHMM computeLikelihoods() : 0.34326542200000004
[2016-04-15T00:56Z] INFO  17:56:43,568 HaplotypeCaller - Ran local assembly on 1506 active regions
[2016-04-15T00:56Z] INFO  17:56:43,599 ProgressMeter -            done     1.46584651E8    72.0 s            0.0 s      100.0%    72.0 s       0.0 s
[2016-04-15T00:56Z] INFO  17:56:43,600 ProgressMeter - Total runtime 72.88 secs, 1.21 min, 0.02 hours
[2016-04-15T00:56Z] INFO  17:56:43,600 MicroScheduler - 120348 reads were filtered out during the traversal out of approximately 483457 total reads (24.89%)
[2016-04-15T00:56Z] INFO  17:56:43,600 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:56Z] INFO  17:56:43,601 MicroScheduler -   -> 31999 reads (6.62% of total) failing DuplicateReadFilter
[2016-04-15T00:56Z] INFO  17:56:43,601 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:56Z] INFO  17:56:43,601 MicroScheduler -   -> 88349 reads (18.27% of total) failing HCMappingQualityFilter
[2016-04-15T00:56Z] INFO  17:56:43,601 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:56Z] INFO  17:56:43,602 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:56Z] INFO  17:56:43,602 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:56Z] INFO  17:56:43,602 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:56Z] INFO  17:56:43,646 ProgressMeter -            done     1.12411448E8    47.0 s            0.0 s      100.0%    47.0 s       0.0 s
[2016-04-15T00:56Z] INFO  17:56:43,647 ProgressMeter - Total runtime 47.99 secs, 0.80 min, 0.01 hours
[2016-04-15T00:56Z] INFO  17:56:43,648 MicroScheduler - 19515 reads were filtered out during the traversal out of approximately 242123 total reads (8.06%)
[2016-04-15T00:56Z] INFO  17:56:43,648 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:56Z] INFO  17:56:43,648 MicroScheduler -   -> 19083 reads (7.88% of total) failing DuplicateReadFilter
[2016-04-15T00:56Z] INFO  17:56:43,648 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:56Z] INFO  17:56:43,649 MicroScheduler -   -> 432 reads (0.18% of total) failing HCMappingQualityFilter
[2016-04-15T00:56Z] INFO  17:56:43,649 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:56Z] INFO  17:56:43,649 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:56Z] INFO  17:56:43,649 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:56Z] INFO  17:56:43,649 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:56Z] INFO  17:56:44,123 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.002049113
[2016-04-15T00:56Z] INFO  17:56:44,124 PairHMM - Total compute time in PairHMM computeLikelihoods() : 0.032852136000000004
[2016-04-15T00:56Z] INFO  17:56:44,125 HaplotypeCaller - Ran local assembly on 199 active regions
[2016-04-15T00:56Z] INFO  17:56:44,190 ProgressMeter -            done        2089463.0    16.0 s            8.0 s      100.0%    16.0 s       0.0 s
[2016-04-15T00:56Z] INFO  17:56:44,190 ProgressMeter - Total runtime 16.93 secs, 0.28 min, 0.00 hours
[2016-04-15T00:56Z] INFO  17:56:44,191 MicroScheduler - 3261 reads were filtered out during the traversal out of approximately 39853 total reads (8.18%)
[2016-04-15T00:56Z] INFO  17:56:44,191 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:56Z] INFO  17:56:44,191 MicroScheduler -   -> 3208 reads (8.05% of total) failing DuplicateReadFilter
[2016-04-15T00:56Z] INFO  17:56:44,192 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:56Z] INFO  17:56:44,192 MicroScheduler -   -> 53 reads (0.13% of total) failing HCMappingQualityFilter
[2016-04-15T00:56Z] INFO  17:56:44,192 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:56Z] INFO  17:56:44,193 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:56Z] INFO  17:56:44,193 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:56Z] INFO  17:56:44,193 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:56Z] INFO  17:56:44,247 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:56Z] INFO  17:56:44,522 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.030177226
[2016-04-15T00:56Z] INFO  17:56:44,524 PairHMM - Total compute time in PairHMM computeLikelihoods() : 6.942251362
[2016-04-15T00:56Z] INFO  17:56:44,524 HaplotypeCaller - Ran local assembly on 1243 active regions
[2016-04-15T00:56Z] INFO  17:56:44,525 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:56Z] INFO  17:56:44,529 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:56Z] INFO  17:56:44,530 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:56Z] INFO  17:56:44,531 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:56Z] INFO  17:56:44,536 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/3/R14-18105_kapa-NGv3-PE100-NGv3-sort-3_112188604_127703121-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/3/R14-18105_kapa-NGv3-PE100-NGv3-3_112188604_127703121-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/3/tx/tmpBbkIOn/R14-18105_kapa-NGv3-PE100-NGv3-3_112188604_127703121.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:56Z] INFO  17:56:44,582 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:56Z] INFO  17:56:44,583 HelpFormatter - Date/Time: 2016/04/14 17:56:44
[2016-04-15T00:56Z] INFO  17:56:44,584 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:56Z] INFO  17:56:44,585 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:56Z] INFO  17:56:44,592 ProgressMeter -            done      6.7478645E7    65.0 s            0.0 s      100.0%    65.0 s       0.0 s
[2016-04-15T00:56Z] INFO  17:56:44,593 ProgressMeter - Total runtime 65.12 secs, 1.09 min, 0.02 hours
[2016-04-15T00:56Z] INFO  17:56:44,594 MicroScheduler - 64326 reads were filtered out during the traversal out of approximately 299144 total reads (21.50%)
[2016-04-15T00:56Z] INFO  17:56:44,594 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:56Z] INFO  17:56:44,594 MicroScheduler -   -> 20764 reads (6.94% of total) failing DuplicateReadFilter
[2016-04-15T00:56Z] INFO  17:56:44,594 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:56Z] INFO  17:56:44,595 MicroScheduler -   -> 43562 reads (14.56% of total) failing HCMappingQualityFilter
[2016-04-15T00:56Z] INFO  17:56:44,595 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:56Z] INFO  17:56:44,595 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:56Z] INFO  17:56:44,596 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:56Z] INFO  17:56:44,596 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:56Z] GATK: HaplotypeCaller
[2016-04-15T00:56Z] WARN  17:56:44,641 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T00:56Z] WARN  17:56:44,655 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/3/tx/tmpBbkIOn/R14-18105_kapa-NGv3-PE100-NGv3-3_112188604_127703121.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T00:56Z] INFO  17:56:44,875 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:56Z] INFO  17:56:44,930 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:56Z] INFO  17:56:45,071 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T00:56Z] INFO  17:56:45,080 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:56Z] INFO  17:56:45,091 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:56Z] INFO  17:56:45,163 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-15T00:56Z] INFO  17:56:45,192 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T00:56Z] GATK: HaplotypeCaller
[2016-04-15T00:56Z] GATK: HaplotypeCaller
[2016-04-15T00:56Z] INFO  17:56:45,565 IntervalUtils - Processing 249953 bp from intervals
[2016-04-15T00:56Z] WARN  17:56:45,571 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:56Z] INFO  17:56:45,578 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:56Z] INFO  17:56:45,691 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:56Z] INFO  17:56:45,851 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:56Z] INFO  17:56:45,852 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:56Z] INFO  17:56:45,853 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T00:56Z] INFO  17:56:45,854 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T00:56Z] INFO  17:56:45,855 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T00:56Z] INFO  17:56:45,855 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T00:56Z] GATK: HaplotypeCaller
[2016-04-15T00:56Z] INFO  17:56:46,048 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T00:56Z] INFO  17:56:46,094 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:56Z] INFO  17:56:46,403 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:56Z] INFO  17:56:46,406 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:56Z] INFO  17:56:46,406 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:56Z] INFO  17:56:46,406 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:56Z] INFO  17:56:46,410 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/3/R14-18105_kapa-NGv3-PE100-NGv3-sort-3_127770401_143293035-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/3/R14-18105_kapa-NGv3-PE100-NGv3-3_127770401_143293035-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/3/tx/tmprSHdls/R14-18105_kapa-NGv3-PE100-NGv3-3_127770401_143293035.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:56Z] INFO  17:56:46,420 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:56Z] INFO  17:56:46,421 HelpFormatter - Date/Time: 2016/04/14 17:56:46
[2016-04-15T00:56Z] INFO  17:56:46,421 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:56Z] INFO  17:56:46,422 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:56Z] WARN  17:56:46,450 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T00:56Z] WARN  17:56:46,457 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/3/tx/tmprSHdls/R14-18105_kapa-NGv3-PE100-NGv3-3_127770401_143293035.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T00:56Z] GATK: HaplotypeCaller
[2016-04-15T00:56Z] INFO  17:56:46,733 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:56Z] INFO  17:56:46,913 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T00:56Z] INFO  17:56:46,937 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:56Z] INFO  17:56:47,012 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-15T00:56Z] INFO  17:56:47,032 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T00:56Z] INFO  17:56:47,558 IntervalUtils - Processing 238450 bp from intervals
[2016-04-15T00:56Z] WARN  17:56:47,564 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:56Z] INFO  17:56:47,579 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:56Z] INFO  17:56:47,582 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:56Z] INFO  17:56:47,583 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:56Z] INFO  17:56:47,584 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:56Z] INFO  17:56:47,588 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/3/R14-18105_kapa-NGv3-PE100-NGv3-sort-3_143297426_158963696-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/3/R14-18105_kapa-NGv3-PE100-NGv3-3_143297426_158963696-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/3/tx/tmp_3W1Ac/R14-18105_kapa-NGv3-PE100-NGv3-3_143297426_158963696.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:56Z] INFO  17:56:47,603 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:56Z] INFO  17:56:47,604 HelpFormatter - Date/Time: 2016/04/14 17:56:47
[2016-04-15T00:56Z] INFO  17:56:47,604 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:56Z] INFO  17:56:47,605 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:56Z] WARN  17:56:47,669 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T00:56Z] WARN  17:56:47,688 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/3/tx/tmp_3W1Ac/R14-18105_kapa-NGv3-PE100-NGv3-3_143297426_158963696.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T00:56Z] INFO  17:56:47,729 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:56Z] INFO  17:56:47,902 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:56Z] INFO  17:56:47,903 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:56Z] INFO  17:56:47,903 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T00:56Z] INFO  17:56:47,903 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T00:56Z] INFO  17:56:47,913 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T00:56Z] INFO  17:56:47,913 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T00:56Z] INFO  17:56:47,920 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:56Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T00:56Z] INFO  17:56:48,036 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T00:56Z] INFO  17:56:48,037 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T00:56Z] INFO  17:56:48,156 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T00:56Z] INFO  17:56:48,169 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:56Z] INFO  17:56:48,177 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T00:56Z] INFO  17:56:48,242 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-15T00:56Z] INFO  17:56:48,257 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T00:56Z] WARN  17:56:48,361 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T00:56Z] WARN  17:56:48,362 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T00:56Z] INFO  17:56:48,378 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:56Z] INFO  17:56:48,380 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:56Z] INFO  17:56:48,380 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:56Z] INFO  17:56:48,381 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:56Z] INFO  17:56:48,396 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/3/R14-18105_kapa-NGv3-PE100-NGv3-sort-3_158970515_174577240-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/3/R14-18105_kapa-NGv3-PE100-NGv3-3_158970515_174577240-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/3/tx/tmpPicIWo/R14-18105_kapa-NGv3-PE100-NGv3-3_158970515_174577240.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:56Z] INFO  17:56:48,419 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:56Z] INFO  17:56:48,419 HelpFormatter - Date/Time: 2016/04/14 17:56:48
[2016-04-15T00:56Z] INFO  17:56:48,419 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:56Z] INFO  17:56:48,420 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:56Z] WARN  17:56:48,453 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T00:56Z] WARN  17:56:48,456 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/3/tx/tmpPicIWo/R14-18105_kapa-NGv3-PE100-NGv3-3_158970515_174577240.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T00:56Z] INFO  17:56:48,567 IntervalUtils - Processing 125161 bp from intervals
[2016-04-15T00:56Z] WARN  17:56:48,573 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:56Z] INFO  17:56:48,604 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:56Z] INFO  17:56:48,607 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:56Z] INFO  17:56:48,608 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:56Z] INFO  17:56:48,608 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:56Z] INFO  17:56:48,613 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/3/R14-18105_kapa-NGv3-PE100-NGv3-sort-3_174814579_190326970-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/3/R14-18105_kapa-NGv3-PE100-NGv3-3_174814579_190326970-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/3/tx/tmp1HDV6I/R14-18105_kapa-NGv3-PE100-NGv3-3_174814579_190326970.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:56Z] INFO  17:56:48,652 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:56Z] INFO  17:56:48,653 HelpFormatter - Date/Time: 2016/04/14 17:56:48
[2016-04-15T00:56Z] INFO  17:56:48,653 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:56Z] INFO  17:56:48,658 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:56Z] INFO  17:56:48,674 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:56Z] WARN  17:56:48,681 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T00:56Z] WARN  17:56:48,683 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/3/tx/tmp1HDV6I/R14-18105_kapa-NGv3-PE100-NGv3-3_174814579_190326970.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T00:56Z] INFO  17:56:48,694 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:56Z] INFO  17:56:48,785 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:56Z] INFO  17:56:48,795 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:56Z] INFO  17:56:48,796 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T00:56Z] INFO  17:56:48,796 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T00:56Z] INFO  17:56:48,797 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T00:56Z] INFO  17:56:48,797 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T00:56Z] INFO  17:56:48,836 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:56Z] INFO  17:56:48,889 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T00:56Z] INFO  17:56:48,899 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:56Z] INFO  17:56:48,974 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-15T00:56Z] INFO  17:56:48,988 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T00:56Z] INFO  17:56:49,001 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T00:56Z] INFO  17:56:49,047 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T00:56Z] INFO  17:56:49,066 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:56Z] INFO  17:56:49,145 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-15T00:56Z] INFO  17:56:49,186 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T00:56Z] INFO  17:56:49,220 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:56Z] INFO  17:56:49,224 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:56Z] INFO  17:56:49,224 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:56Z] INFO  17:56:49,225 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:56Z] INFO  17:56:49,229 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/3/R14-18105_kapa-NGv3-PE100-NGv3-sort-3_190333063_198022430-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/3/R14-18105_kapa-NGv3-PE100-NGv3-3_190333063_198022430-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/3/tx/tmpxidqd_/R14-18105_kapa-NGv3-PE100-NGv3-3_190333063_198022430.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:56Z] INFO  17:56:49,239 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:56Z] INFO  17:56:49,245 HelpFormatter - Date/Time: 2016/04/14 17:56:49
[2016-04-15T00:56Z] INFO  17:56:49,246 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:56Z] INFO  17:56:49,246 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:56Z] WARN  17:56:49,291 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T00:56Z] WARN  17:56:49,307 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/3/tx/tmpxidqd_/R14-18105_kapa-NGv3-PE100-NGv3-3_190333063_198022430.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T00:56Z] INFO  17:56:49,410 IntervalUtils - Processing 102254 bp from intervals
[2016-04-15T00:56Z] WARN  17:56:49,426 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:56Z] INFO  17:56:49,522 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:56Z] INFO  17:56:49,526 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:56Z] INFO  17:56:49,526 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:56Z] INFO  17:56:49,527 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:56Z] INFO  17:56:49,531 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/4/R14-18105_kapa-NGv3-PE100-NGv3-sort-4_0_15511864-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/4/R14-18105_kapa-NGv3-PE100-NGv3-4_0_15511864-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/4/tx/tmpeDF2gm/R14-18105_kapa-NGv3-PE100-NGv3-4_0_15511864.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:56Z] INFO  17:56:49,534 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:56Z] INFO  17:56:49,540 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:56Z] INFO  17:56:49,541 HelpFormatter - Date/Time: 2016/04/14 17:56:49
[2016-04-15T00:56Z] INFO  17:56:49,541 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:56Z] INFO  17:56:49,541 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:56Z] WARN  17:56:49,587 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T00:56Z] WARN  17:56:49,590 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/4/tx/tmpeDF2gm/R14-18105_kapa-NGv3-PE100-NGv3-4_0_15511864.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T00:56Z] INFO  17:56:49,600 IntervalUtils - Processing 184739 bp from intervals
[2016-04-15T00:56Z] WARN  17:56:49,606 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:56Z] INFO  17:56:49,631 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:56Z] INFO  17:56:49,660 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:56Z] INFO  17:56:49,661 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:56Z] INFO  17:56:49,662 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T00:56Z] INFO  17:56:49,663 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T00:56Z] INFO  17:56:49,678 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T00:56Z] INFO  17:56:49,678 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T00:56Z] INFO  17:56:49,686 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:56Z] INFO  17:56:49,795 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:56Z] INFO  17:56:49,796 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:56Z] INFO  17:56:49,796 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T00:56Z] INFO  17:56:49,797 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T00:56Z] INFO  17:56:49,798 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T00:56Z] INFO  17:56:49,798 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T00:56Z] INFO  17:56:49,837 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T00:56Z] INFO  17:56:49,853 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:56Z] INFO  17:56:49,869 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:56Z] INFO  17:56:49,892 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T00:56Z] INFO  17:56:49,955 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.09
[2016-04-15T00:56Z] INFO  17:56:49,974 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T00:56Z] INFO  17:56:49,981 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T00:56Z] INFO  17:56:50,042 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T00:56Z] INFO  17:56:50,051 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:56Z] INFO  17:56:50,104 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-15T00:56Z] INFO  17:56:50,122 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T00:56Z] INFO  17:56:50,481 IntervalUtils - Processing 118955 bp from intervals
[2016-04-15T00:56Z] WARN  17:56:50,487 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:56Z] INFO  17:56:50,626 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:56Z] INFO  17:56:50,685 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:56Z] INFO  17:56:50,686 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:56Z] INFO  17:56:50,687 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T00:56Z] INFO  17:56:50,688 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T00:56Z] INFO  17:56:50,688 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T00:56Z] INFO  17:56:50,688 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T00:56Z] INFO  17:56:50,702 IntervalUtils - Processing 255565 bp from intervals
[2016-04-15T00:56Z] WARN  17:56:50,718 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:56Z] INFO  17:56:50,724 ProgressMeter -     2:189851785      9.8747871E7    60.0 s            0.0 s       96.6%    62.0 s       2.0 s
[2016-04-15T00:56Z] INFO  17:56:50,868 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T00:56Z] INFO  17:56:50,898 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:56Z] INFO  17:56:51,026 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:56Z] INFO  17:56:51,027 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:56Z] INFO  17:56:51,029 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T00:56Z] INFO  17:56:51,029 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T00:56Z] INFO  17:56:51,037 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T00:56Z] INFO  17:56:51,037 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T00:56Z] INFO  17:56:51,321 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T00:56Z] INFO  17:56:51,551 ProgressMeter -      3:38740000      3.0708938E7    30.0 s            0.0 s       36.2%    82.0 s      52.0 s
[2016-04-15T00:56Z] INFO  17:56:52,345 ProgressMeter -      3:49060509      2.0797469E7    30.0 s            1.0 s       25.6%   117.0 s      87.0 s
[2016-04-15T00:56Z] INFO  17:56:52,457 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.010889419000000001
[2016-04-15T00:56Z] INFO  17:56:52,458 PairHMM - Total compute time in PairHMM computeLikelihoods() : 0.642758818
[2016-04-15T00:56Z] INFO  17:56:52,458 HaplotypeCaller - Ran local assembly on 1660 active regions
[2016-04-15T00:56Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T00:56Z] INFO  17:56:52,536 ProgressMeter -            done     1.20474354E8    61.0 s            0.0 s      100.0%    61.0 s       0.0 s
[2016-04-15T00:56Z] INFO  17:56:52,537 ProgressMeter - Total runtime 61.85 secs, 1.03 min, 0.02 hours
[2016-04-15T00:56Z] INFO  17:56:52,537 MicroScheduler - 32900 reads were filtered out during the traversal out of approximately 333548 total reads (9.86%)
[2016-04-15T00:56Z] INFO  17:56:52,537 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:56Z] INFO  17:56:52,538 MicroScheduler -   -> 26081 reads (7.82% of total) failing DuplicateReadFilter
[2016-04-15T00:56Z] INFO  17:56:52,538 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:56Z] INFO  17:56:52,538 MicroScheduler -   -> 6819 reads (2.04% of total) failing HCMappingQualityFilter
[2016-04-15T00:56Z] INFO  17:56:52,538 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:56Z] INFO  17:56:52,539 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:56Z] INFO  17:56:52,539 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:56Z] INFO  17:56:52,539 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:56Z] INFO  17:56:52,535 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T00:56Z] INFO  17:56:52,547 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T00:56Z] WARN  17:56:52,813 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T00:56Z] WARN  17:56:52,817 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T00:56Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T00:56Z] INFO  17:56:52,982 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T00:56Z] INFO  17:56:52,993 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T00:56Z] WARN  17:56:53,248 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T00:56Z] WARN  17:56:53,250 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T00:56Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T00:56Z] INFO  17:56:53,310 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T00:56Z] INFO  17:56:53,311 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T00:56Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T00:56Z] WARN  17:56:53,553 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T00:56Z] WARN  17:56:53,554 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T00:56Z] INFO  17:56:53,559 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T00:56Z] INFO  17:56:53,560 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T00:56Z] WARN  17:56:53,848 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T00:56Z] WARN  17:56:53,849 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T00:56Z] INFO  17:56:54,017 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:56Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T00:56Z] INFO  17:56:54,182 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T00:56Z] INFO  17:56:54,183 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T00:56Z] GATK: HaplotypeCaller
[2016-04-15T00:56Z] WARN  17:56:54,599 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T00:56Z] WARN  17:56:54,600 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T00:56Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T00:56Z] INFO  17:56:55,290 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T00:56Z] INFO  17:56:55,301 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T00:56Z] WARN  17:56:55,832 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T00:56Z] WARN  17:56:55,833 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T00:56Z] INFO  17:56:56,417 ProgressMeter -     2:220309883     1.14366377E8    60.0 s            0.0 s       86.3%    69.0 s       9.0 s
[2016-04-15T00:56Z] INFO  17:56:57,303 ProgressMeter -     1:153122365       8.356281E7     2.5 m            1.0 s       44.9%     5.6 m       3.1 m
[2016-04-15T00:56Z] INFO  17:56:57,402 ProgressMeter -      3:75787170      1.3758296E7    30.0 s            2.0 s       91.8%    32.0 s       2.0 s
[2016-04-15T00:56Z] INFO  17:56:57,572 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:56Z] INFO  17:56:57,575 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:56Z] INFO  17:56:57,576 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:56Z] INFO  17:56:57,576 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:56Z] INFO  17:56:57,581 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/4/R14-18105_kapa-NGv3-PE100-NGv3-sort-4_15512869_31144471-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/4/R14-18105_kapa-NGv3-PE100-NGv3-4_15512869_31144471-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/4/tx/tmpeY9Eg2/R14-18105_kapa-NGv3-PE100-NGv3-4_15512869_31144471.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:56Z] INFO  17:56:57,612 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:56Z] INFO  17:56:57,620 HelpFormatter - Date/Time: 2016/04/14 17:56:57
[2016-04-15T00:56Z] INFO  17:56:57,621 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:56Z] INFO  17:56:57,622 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:56Z] WARN  17:56:57,662 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T00:56Z] WARN  17:56:57,665 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/4/tx/tmpeY9Eg2/R14-18105_kapa-NGv3-PE100-NGv3-4_15512869_31144471.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T00:56Z] INFO  17:56:57,920 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:56Z] INFO  17:56:58,152 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T00:56Z] INFO  17:56:58,163 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:56Z] INFO  17:56:58,246 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-15T00:56Z] INFO  17:56:58,259 ProgressMeter -     2:236945205      8.5569488E7    60.0 s            0.0 s       96.2%    62.0 s       2.0 s
[2016-04-15T00:56Z] INFO  17:56:58,273 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T00:56Z] INFO  17:56:58,771 IntervalUtils - Processing 90668 bp from intervals
[2016-04-15T00:56Z] WARN  17:56:58,779 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:56Z] INFO  17:56:58,930 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:56Z] INFO  17:56:59,010 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:56Z] INFO  17:56:59,011 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:56Z] INFO  17:56:59,012 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T00:56Z] INFO  17:56:59,013 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T00:56Z] INFO  17:56:59,014 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T00:56Z] INFO  17:56:59,014 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T00:56Z] INFO  17:56:59,201 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T00:57Z] INFO  17:57:00,126 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.034781076
[2016-04-15T00:57Z] INFO  17:57:00,127 PairHMM - Total compute time in PairHMM computeLikelihoods() : 3.85545074
[2016-04-15T00:57Z] INFO  17:57:00,128 HaplotypeCaller - Ran local assembly on 1475 active regions
[2016-04-15T00:57Z] INFO  17:57:00,190 ProgressMeter -            done      9.2172487E7    61.0 s            0.0 s      100.0%    61.0 s       0.0 s
[2016-04-15T00:57Z] INFO  17:57:00,191 ProgressMeter - Total runtime 61.97 secs, 1.03 min, 0.02 hours
[2016-04-15T00:57Z] INFO  17:57:00,192 MicroScheduler - 28449 reads were filtered out during the traversal out of approximately 310046 total reads (9.18%)
[2016-04-15T00:57Z] INFO  17:57:00,192 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:57Z] INFO  17:57:00,193 MicroScheduler -   -> 24810 reads (8.00% of total) failing DuplicateReadFilter
[2016-04-15T00:57Z] INFO  17:57:00,194 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:57Z] INFO  17:57:00,194 MicroScheduler -   -> 3639 reads (1.17% of total) failing HCMappingQualityFilter
[2016-04-15T00:57Z] INFO  17:57:00,195 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:57Z] INFO  17:57:00,195 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:57Z] INFO  17:57:00,196 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:57Z] INFO  17:57:00,197 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:57Z] INFO  17:57:00,647 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.017617321000000002
[2016-04-15T00:57Z] INFO  17:57:00,647 PairHMM - Total compute time in PairHMM computeLikelihoods() : 1.5716379660000002
[2016-04-15T00:57Z] INFO  17:57:00,647 HaplotypeCaller - Ran local assembly on 581 active regions
[2016-04-15T00:57Z] INFO  17:57:00,736 ProgressMeter -            done      1.6464959E7    33.0 s            2.0 s      100.0%    33.0 s       0.0 s
[2016-04-15T00:57Z] INFO  17:57:00,736 ProgressMeter - Total runtime 33.36 secs, 0.56 min, 0.01 hours
[2016-04-15T00:57Z] INFO  17:57:00,737 MicroScheduler - 12600 reads were filtered out during the traversal out of approximately 114543 total reads (11.00%)
[2016-04-15T00:57Z] INFO  17:57:00,738 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:57Z] INFO  17:57:00,738 MicroScheduler -   -> 8934 reads (7.80% of total) failing DuplicateReadFilter
[2016-04-15T00:57Z] INFO  17:57:00,738 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:57Z] INFO  17:57:00,739 MicroScheduler -   -> 3666 reads (3.20% of total) failing HCMappingQualityFilter
[2016-04-15T00:57Z] INFO  17:57:00,739 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:57Z] INFO  17:57:00,739 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:57Z] INFO  17:57:00,739 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:57Z] INFO  17:57:00,740 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:57Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T00:57Z] INFO  17:57:01,222 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T00:57Z] INFO  17:57:01,222 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T00:57Z] INFO  17:57:01,750 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:57Z] WARN  17:57:01,790 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T00:57Z] WARN  17:57:01,791 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T00:57Z] INFO  17:57:02,053 ProgressMeter -     3:105588289      2.0589327E7    30.0 s            1.0 s       63.2%    47.0 s      17.0 s
[2016-04-15T00:57Z] GATK: HaplotypeCaller
[2016-04-15T00:57Z] INFO  17:57:02,307 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:57Z] GATK: HaplotypeCaller
[2016-04-15T00:57Z] INFO  17:57:03,666 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.013882784
[2016-04-15T00:57Z] INFO  17:57:03,667 PairHMM - Total compute time in PairHMM computeLikelihoods() : 1.164441437
[2016-04-15T00:57Z] INFO  17:57:03,668 HaplotypeCaller - Ran local assembly on 1428 active regions
[2016-04-15T00:57Z] INFO  17:57:03,733 ProgressMeter -            done      9.3035935E7    57.0 s            0.0 s      100.0%    57.0 s       0.0 s
[2016-04-15T00:57Z] INFO  17:57:03,733 ProgressMeter - Total runtime 57.07 secs, 0.95 min, 0.02 hours
[2016-04-15T00:57Z] INFO  17:57:03,734 MicroScheduler - 25909 reads were filtered out during the traversal out of approximately 315145 total reads (8.22%)
[2016-04-15T00:57Z] INFO  17:57:03,735 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:57Z] INFO  17:57:03,735 MicroScheduler -   -> 25306 reads (8.03% of total) failing DuplicateReadFilter
[2016-04-15T00:57Z] INFO  17:57:03,735 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:57Z] INFO  17:57:03,736 MicroScheduler -   -> 603 reads (0.19% of total) failing HCMappingQualityFilter
[2016-04-15T00:57Z] INFO  17:57:03,736 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:57Z] INFO  17:57:03,736 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:57Z] INFO  17:57:03,736 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:57Z] INFO  17:57:03,737 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:57Z] INFO  17:57:05,100 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.019331468
[2016-04-15T00:57Z] INFO  17:57:05,100 PairHMM - Total compute time in PairHMM computeLikelihoods() : 1.361683328
[2016-04-15T00:57Z] INFO  17:57:05,100 HaplotypeCaller - Ran local assembly on 1852 active regions
[2016-04-15T00:57Z] INFO  17:57:05,182 ProgressMeter -            done     1.39336955E8    68.0 s            0.0 s      100.0%    68.0 s       0.0 s
[2016-04-15T00:57Z] INFO  17:57:05,182 ProgressMeter - Total runtime 68.79 secs, 1.15 min, 0.02 hours
[2016-04-15T00:57Z] INFO  17:57:05,183 MicroScheduler - 32558 reads were filtered out during the traversal out of approximately 402002 total reads (8.10%)
[2016-04-15T00:57Z] INFO  17:57:05,183 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:57Z] INFO  17:57:05,183 MicroScheduler -   -> 32182 reads (8.01% of total) failing DuplicateReadFilter
[2016-04-15T00:57Z] INFO  17:57:05,184 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:57Z] INFO  17:57:05,184 MicroScheduler -   -> 376 reads (0.09% of total) failing HCMappingQualityFilter
[2016-04-15T00:57Z] INFO  17:57:05,184 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:57Z] INFO  17:57:05,184 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:57Z] INFO  17:57:05,185 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:57Z] INFO  17:57:05,185 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:57Z] INFO  17:57:05,459 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:57Z] INFO  17:57:05,463 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:57Z] INFO  17:57:05,463 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:57Z] INFO  17:57:05,464 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:57Z] INFO  17:57:05,468 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/4/R14-18105_kapa-NGv3-PE100-NGv3-sort-4_36069528_52709433-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/4/R14-18105_kapa-NGv3-PE100-NGv3-4_36069528_52709433-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/4/tx/tmpZWkH0P/R14-18105_kapa-NGv3-PE100-NGv3-4_36069528_52709433.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:57Z] INFO  17:57:05,473 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:57Z] INFO  17:57:05,488 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:57Z] INFO  17:57:05,493 HelpFormatter - Date/Time: 2016/04/14 17:57:05
[2016-04-15T00:57Z] INFO  17:57:05,494 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:57Z] INFO  17:57:05,494 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:57Z] WARN  17:57:05,539 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T00:57Z] WARN  17:57:05,546 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/4/tx/tmpZWkH0P/R14-18105_kapa-NGv3-PE100-NGv3-4_36069528_52709433.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T00:57Z] GATK: HaplotypeCaller
[2016-04-15T00:57Z] INFO  17:57:05,741 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:57Z] INFO  17:57:05,977 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T00:57Z] INFO  17:57:05,998 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:57Z] INFO  17:57:06,026 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:57Z] INFO  17:57:06,040 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:57Z] INFO  17:57:06,041 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:57Z] INFO  17:57:06,042 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:57Z] INFO  17:57:06,046 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/4/R14-18105_kapa-NGv3-PE100-NGv3-sort-4_52709749_68338393-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/4/R14-18105_kapa-NGv3-PE100-NGv3-4_52709749_68338393-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/4/tx/tmp1BdZG_/R14-18105_kapa-NGv3-PE100-NGv3-4_52709749_68338393.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:57Z] INFO  17:57:06,078 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:57Z] INFO  17:57:06,079 HelpFormatter - Date/Time: 2016/04/14 17:57:06
[2016-04-15T00:57Z] INFO  17:57:06,080 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:57Z] INFO  17:57:06,084 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:57Z] INFO  17:57:06,087 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.09
[2016-04-15T00:57Z] INFO  17:57:06,108 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T00:57Z] WARN  17:57:06,131 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T00:57Z] WARN  17:57:06,144 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/4/tx/tmp1BdZG_/R14-18105_kapa-NGv3-PE100-NGv3-4_52709749_68338393.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T00:57Z] INFO  17:57:06,415 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:57Z] INFO  17:57:06,648 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T00:57Z] INFO  17:57:06,658 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:57Z] INFO  17:57:06,681 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:57Z] INFO  17:57:06,730 IntervalUtils - Processing 142047 bp from intervals
[2016-04-15T00:57Z] WARN  17:57:06,736 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:57Z] INFO  17:57:06,753 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.09
[2016-04-15T00:57Z] INFO  17:57:06,777 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T00:57Z] INFO  17:57:06,877 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:57Z] GATK: HaplotypeCaller
[2016-04-15T00:57Z] INFO  17:57:07,000 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:57Z] INFO  17:57:07,012 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:57Z] INFO  17:57:07,012 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T00:57Z] INFO  17:57:07,013 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T00:57Z] INFO  17:57:07,023 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T00:57Z] INFO  17:57:07,024 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T00:57Z] INFO  17:57:07,228 IntervalUtils - Processing 83782 bp from intervals
[2016-04-15T00:57Z] WARN  17:57:07,234 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:57Z] INFO  17:57:07,335 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T00:57Z] INFO  17:57:07,347 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:57Z] INFO  17:57:07,426 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:57Z] INFO  17:57:07,427 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:57Z] INFO  17:57:07,428 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T00:57Z] INFO  17:57:07,429 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T00:57Z] INFO  17:57:07,430 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T00:57Z] INFO  17:57:07,430 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T00:57Z] INFO  17:57:07,684 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T00:57Z] INFO  17:57:08,612 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:57Z] INFO  17:57:08,623 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:57Z] INFO  17:57:08,623 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:57Z] INFO  17:57:08,624 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:57Z] INFO  17:57:08,629 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/4/R14-18105_kapa-NGv3-PE100-NGv3-sort-4_68340604_83852298-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/4/R14-18105_kapa-NGv3-PE100-NGv3-4_68340604_83852298-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/4/tx/tmppPzUn1/R14-18105_kapa-NGv3-PE100-NGv3-4_68340604_83852298.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:57Z] INFO  17:57:08,639 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:57Z] INFO  17:57:08,639 HelpFormatter - Date/Time: 2016/04/14 17:57:08
[2016-04-15T00:57Z] INFO  17:57:08,639 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:57Z] INFO  17:57:08,640 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:57Z] WARN  17:57:08,687 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T00:57Z] WARN  17:57:08,690 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/4/tx/tmppPzUn1/R14-18105_kapa-NGv3-PE100-NGv3-4_68340604_83852298.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T00:57Z] INFO  17:57:08,840 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:57Z] INFO  17:57:09,045 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T00:57Z] INFO  17:57:09,054 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:57Z] INFO  17:57:09,173 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.12
[2016-04-15T00:57Z] INFO  17:57:09,199 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T00:57Z] INFO  17:57:09,713 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:57Z] INFO  17:57:09,716 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:57Z] INFO  17:57:09,717 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:57Z] INFO  17:57:09,717 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:57Z] INFO  17:57:09,722 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/4/R14-18105_kapa-NGv3-PE100-NGv3-sort-4_83857133_99393738-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/4/R14-18105_kapa-NGv3-PE100-NGv3-4_83857133_99393738-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/4/tx/tmpYhSHyi/R14-18105_kapa-NGv3-PE100-NGv3-4_83857133_99393738.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:57Z] INFO  17:57:09,725 IntervalUtils - Processing 197466 bp from intervals
[2016-04-15T00:57Z] WARN  17:57:09,730 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:57Z] INFO  17:57:09,754 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:57Z] INFO  17:57:09,762 HelpFormatter - Date/Time: 2016/04/14 17:57:09
[2016-04-15T00:57Z] INFO  17:57:09,763 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:57Z] INFO  17:57:09,764 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:57Z] WARN  17:57:09,811 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T00:57Z] WARN  17:57:09,821 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/4/tx/tmpYhSHyi/R14-18105_kapa-NGv3-PE100-NGv3-4_83857133_99393738.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T00:57Z] INFO  17:57:09,849 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:57Z] INFO  17:57:09,983 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:57Z] INFO  17:57:09,995 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:57Z] INFO  17:57:09,996 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T00:57Z] INFO  17:57:09,996 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T00:57Z] INFO  17:57:10,004 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T00:57Z] INFO  17:57:10,005 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T00:57Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T00:57Z] INFO  17:57:10,050 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T00:57Z] INFO  17:57:10,051 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T00:57Z] INFO  17:57:10,053 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:57Z] INFO  17:57:10,168 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T00:57Z] INFO  17:57:10,220 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T00:57Z] INFO  17:57:10,229 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:57Z] INFO  17:57:10,305 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-15T00:57Z] INFO  17:57:10,333 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T00:57Z] WARN  17:57:10,362 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T00:57Z] WARN  17:57:10,363 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T00:57Z] INFO  17:57:10,704 IntervalUtils - Processing 124091 bp from intervals
[2016-04-15T00:57Z] WARN  17:57:10,710 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:57Z] INFO  17:57:10,835 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:57Z] INFO  17:57:10,967 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:57Z] INFO  17:57:10,968 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:57Z] INFO  17:57:10,968 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T00:57Z] INFO  17:57:10,969 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T00:57Z] INFO  17:57:10,980 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T00:57Z] INFO  17:57:10,981 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T00:57Z] INFO  17:57:11,227 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T00:57Z] INFO  17:57:12,467 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.007826093000000001
[2016-04-15T00:57Z] INFO  17:57:12,468 PairHMM - Total compute time in PairHMM computeLikelihoods() : 0.6477125850000001
[2016-04-15T00:57Z] INFO  17:57:12,468 HaplotypeCaller - Ran local assembly on 1067 active regions
[2016-04-15T00:57Z] INFO  17:57:12,513 ProgressMeter -            done      5.7451533E7    40.0 s            0.0 s      100.0%    40.0 s       0.0 s
[2016-04-15T00:57Z] INFO  17:57:12,514 ProgressMeter - Total runtime 40.48 secs, 0.67 min, 0.01 hours
[2016-04-15T00:57Z] INFO  17:57:12,515 MicroScheduler - 13587 reads were filtered out during the traversal out of approximately 164833 total reads (8.24%)
[2016-04-15T00:57Z] INFO  17:57:12,515 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:57Z] INFO  17:57:12,516 MicroScheduler -   -> 12879 reads (7.81% of total) failing DuplicateReadFilter
[2016-04-15T00:57Z] INFO  17:57:12,517 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:57Z] INFO  17:57:12,518 MicroScheduler -   -> 708 reads (0.43% of total) failing HCMappingQualityFilter
[2016-04-15T00:57Z] INFO  17:57:12,518 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:57Z] INFO  17:57:12,519 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:57Z] INFO  17:57:12,519 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:57Z] INFO  17:57:12,520 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:57Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T00:57Z] INFO  17:57:13,242 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T00:57Z] INFO  17:57:13,243 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T00:57Z] WARN  17:57:13,660 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T00:57Z] WARN  17:57:13,661 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T00:57Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T00:57Z] INFO  17:57:13,903 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T00:57Z] INFO  17:57:13,904 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T00:57Z] INFO  17:57:14,045 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:57Z] WARN  17:57:14,143 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T00:57Z] WARN  17:57:14,144 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T00:57Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T00:57Z] INFO  17:57:14,231 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T00:57Z] INFO  17:57:14,232 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T00:57Z] GATK: HaplotypeCaller
[2016-04-15T00:57Z] WARN  17:57:14,488 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T00:57Z] WARN  17:57:14,489 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T00:57Z] INFO  17:57:15,908 ProgressMeter -     3:120500204      2.0111212E7    30.0 s            1.0 s       36.2%    82.0 s      52.0 s
[2016-04-15T00:57Z] INFO  17:57:17,611 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:57Z] INFO  17:57:17,615 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:57Z] INFO  17:57:17,615 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:57Z] INFO  17:57:17,616 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:57Z] INFO  17:57:17,620 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/4/R14-18105_kapa-NGv3-PE100-NGv3-sort-4_99397339_115544957-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/4/R14-18105_kapa-NGv3-PE100-NGv3-4_99397339_115544957-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/4/tx/tmpLrc2sg/R14-18105_kapa-NGv3-PE100-NGv3-4_99397339_115544957.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:57Z] INFO  17:57:17,636 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:57Z] INFO  17:57:17,637 HelpFormatter - Date/Time: 2016/04/14 17:57:17
[2016-04-15T00:57Z] INFO  17:57:17,638 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:57Z] INFO  17:57:17,639 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:57Z] WARN  17:57:17,664 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T00:57Z] WARN  17:57:17,669 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/4/tx/tmpLrc2sg/R14-18105_kapa-NGv3-PE100-NGv3-4_99397339_115544957.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T00:57Z] INFO  17:57:17,872 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:57Z] INFO  17:57:17,918 ProgressMeter -     3:132245022      2.0889247E7    30.0 s            1.0 s       36.9%    81.0 s      51.0 s
[2016-04-15T00:57Z] INFO  17:57:18,141 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T00:57Z] INFO  17:57:18,152 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:57Z] INFO  17:57:18,274 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.12
[2016-04-15T00:57Z] INFO  17:57:18,312 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T00:57Z] INFO  17:57:18,808 ProgressMeter -     3:154139114      1.3768699E7    30.0 s            2.0 s       65.5%    45.0 s      15.0 s
[2016-04-15T00:57Z] INFO  17:57:18,827 IntervalUtils - Processing 153852 bp from intervals
[2016-04-15T00:57Z] WARN  17:57:18,843 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:57Z] INFO  17:57:18,962 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:57Z] INFO  17:57:19,105 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:57Z] INFO  17:57:19,117 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:57Z] INFO  17:57:19,118 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T00:57Z] INFO  17:57:19,119 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T00:57Z] INFO  17:57:19,134 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T00:57Z] INFO  17:57:19,134 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T00:57Z] INFO  17:57:19,350 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T00:57Z] INFO  17:57:19,684 ProgressMeter -     3:172634271      2.6224773E7    30.0 s            1.0 s       96.0%    31.0 s       1.0 s
[2016-04-15T00:57Z] INFO  17:57:19,818 ProgressMeter -     3:183995254      2.0148655E7    30.0 s            1.0 s       50.7%    59.0 s      29.0 s
[2016-04-15T00:57Z] INFO  17:57:20,697 ProgressMeter -     3:195506145        7445396.0    30.0 s            4.0 s       45.9%    65.0 s      35.0 s
[2016-04-15T00:57Z] INFO  17:57:21,050 ProgressMeter -       4:1389354        5377855.0    30.0 s            5.0 s       21.9%     2.3 m     107.0 s
[2016-04-15T00:57Z] INFO  17:57:21,118 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.0038468340000000004
[2016-04-15T00:57Z] INFO  17:57:21,119 PairHMM - Total compute time in PairHMM computeLikelihoods() : 0.31324725200000003
[2016-04-15T00:57Z] INFO  17:57:21,120 HaplotypeCaller - Ran local assembly on 721 active regions
[2016-04-15T00:57Z] INFO  17:57:21,186 ProgressMeter -            done      2.7921091E7    31.0 s            1.0 s      100.0%    31.0 s       0.0 s
[2016-04-15T00:57Z] INFO  17:57:21,186 ProgressMeter - Total runtime 31.52 secs, 0.53 min, 0.01 hours
[2016-04-15T00:57Z] INFO  17:57:21,187 MicroScheduler - 9790 reads were filtered out during the traversal out of approximately 124323 total reads (7.87%)
[2016-04-15T00:57Z] INFO  17:57:21,187 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:57Z] INFO  17:57:21,187 MicroScheduler -   -> 9687 reads (7.79% of total) failing DuplicateReadFilter
[2016-04-15T00:57Z] INFO  17:57:21,188 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:57Z] INFO  17:57:21,188 MicroScheduler -   -> 103 reads (0.08% of total) failing HCMappingQualityFilter
[2016-04-15T00:57Z] INFO  17:57:21,188 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:57Z] INFO  17:57:21,188 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:57Z] INFO  17:57:21,189 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:57Z] INFO  17:57:21,189 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:57Z] INFO  17:57:21,554 ProgressMeter -      3:44943190     1.10297166E8    60.0 s            0.0 s       78.4%    76.0 s      16.0 s
[2016-04-15T00:57Z] INFO  17:57:22,349 ProgressMeter -      3:52022592     1.16967526E8    60.0 s            0.0 s       58.6%   102.0 s      42.0 s
[2016-04-15T00:57Z] INFO  17:57:22,730 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:57Z] GATK: HaplotypeCaller
[2016-04-15T00:57Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T00:57Z] INFO  17:57:24,091 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T00:57Z] INFO  17:57:24,102 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T00:57Z] WARN  17:57:24,446 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T00:57Z] WARN  17:57:24,447 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T00:57Z] INFO  17:57:26,234 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:57Z] INFO  17:57:26,238 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:57Z] INFO  17:57:26,238 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:57Z] INFO  17:57:26,239 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:57Z] INFO  17:57:26,244 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/4/R14-18105_kapa-NGv3-PE100-NGv3-sort-4_115584857_134074404-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/4/R14-18105_kapa-NGv3-PE100-NGv3-4_115584857_134074404-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/4/tx/tmpGa3XLw/R14-18105_kapa-NGv3-PE100-NGv3-4_115584857_134074404.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:57Z] INFO  17:57:26,272 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:57Z] INFO  17:57:26,272 HelpFormatter - Date/Time: 2016/04/14 17:57:26
[2016-04-15T00:57Z] INFO  17:57:26,273 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:57Z] INFO  17:57:26,273 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:57Z] WARN  17:57:26,337 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T00:57Z] WARN  17:57:26,345 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/4/tx/tmpGa3XLw/R14-18105_kapa-NGv3-PE100-NGv3-4_115584857_134074404.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T00:57Z] INFO  17:57:26,515 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:57Z] INFO  17:57:26,800 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T00:57Z] INFO  17:57:26,809 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:57Z] INFO  17:57:26,926 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.12
[2016-04-15T00:57Z] INFO  17:57:26,956 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T00:57Z] INFO  17:57:27,309 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.017149503
[2016-04-15T00:57Z] INFO  17:57:27,304 ProgressMeter -     1:155658478     2.53222157E8     3.0 m            0.0 s       71.3%     4.2 m      72.0 s
[2016-04-15T00:57Z] INFO  17:57:27,324 PairHMM - Total compute time in PairHMM computeLikelihoods() : 0.267231392
[2016-04-15T00:57Z] INFO  17:57:27,325 HaplotypeCaller - Ran local assembly on 666 active regions
[2016-04-15T00:57Z] INFO  17:57:27,332 IntervalUtils - Processing 157938 bp from intervals
[2016-04-15T00:57Z] WARN  17:57:27,337 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:57Z] INFO  17:57:27,379 ProgressMeter -            done      2.0932049E7    28.0 s            1.0 s      100.0%    28.0 s       0.0 s
[2016-04-15T00:57Z] INFO  17:57:27,380 ProgressMeter - Total runtime 28.37 secs, 0.47 min, 0.01 hours
[2016-04-15T00:57Z] INFO  17:57:27,380 MicroScheduler - 9087 reads were filtered out during the traversal out of approximately 112746 total reads (8.06%)
[2016-04-15T00:57Z] INFO  17:57:27,381 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:57Z] INFO  17:57:27,381 MicroScheduler -   -> 8962 reads (7.95% of total) failing DuplicateReadFilter
[2016-04-15T00:57Z] INFO  17:57:27,381 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:57Z] INFO  17:57:27,381 MicroScheduler -   -> 125 reads (0.11% of total) failing HCMappingQualityFilter
[2016-04-15T00:57Z] INFO  17:57:27,382 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:57Z] INFO  17:57:27,382 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:57Z] INFO  17:57:27,382 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:57Z] INFO  17:57:27,382 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:57Z] INFO  17:57:27,452 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:57Z] INFO  17:57:27,537 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:57Z] INFO  17:57:27,538 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:57Z] INFO  17:57:27,539 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T00:57Z] INFO  17:57:27,539 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T00:57Z] INFO  17:57:27,540 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T00:57Z] INFO  17:57:27,540 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T00:57Z] INFO  17:57:27,736 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T00:57Z] INFO  17:57:28,201 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.006866865000000001
[2016-04-15T00:57Z] INFO  17:57:28,202 PairHMM - Total compute time in PairHMM computeLikelihoods() : 0.6710025460000001
[2016-04-15T00:57Z] INFO  17:57:28,203 HaplotypeCaller - Ran local assembly on 874 active regions
[2016-04-15T00:57Z] INFO  17:57:28,257 ProgressMeter -            done      3.5894583E7    39.0 s            1.0 s      100.0%    39.0 s       0.0 s
[2016-04-15T00:57Z] INFO  17:57:28,258 ProgressMeter - Total runtime 39.46 secs, 0.66 min, 0.01 hours
[2016-04-15T00:57Z] INFO  17:57:28,258 MicroScheduler - 12688 reads were filtered out during the traversal out of approximately 153067 total reads (8.29%)
[2016-04-15T00:57Z] INFO  17:57:28,258 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:57Z] INFO  17:57:28,258 MicroScheduler -   -> 12002 reads (7.84% of total) failing DuplicateReadFilter
[2016-04-15T00:57Z] INFO  17:57:28,259 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:57Z] INFO  17:57:28,259 MicroScheduler -   -> 686 reads (0.45% of total) failing HCMappingQualityFilter
[2016-04-15T00:57Z] INFO  17:57:28,259 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:57Z] INFO  17:57:28,259 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:57Z] INFO  17:57:28,260 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:57Z] INFO  17:57:28,260 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:57Z] INFO  17:57:28,892 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:57Z] GATK: HaplotypeCaller
[2016-04-15T00:57Z] INFO  17:57:29,620 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:57Z] GATK: HaplotypeCaller
[2016-04-15T00:57Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T00:57Z] INFO  17:57:30,083 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T00:57Z] INFO  17:57:30,094 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T00:57Z] WARN  17:57:30,279 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T00:57Z] WARN  17:57:30,280 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T00:57Z] INFO  17:57:32,144 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:57Z] INFO  17:57:32,147 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:57Z] INFO  17:57:32,147 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:57Z] INFO  17:57:32,147 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:57Z] INFO  17:57:32,168 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/4/R14-18105_kapa-NGv3-PE100-NGv3-sort-4_134075461_150351181-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/4/R14-18105_kapa-NGv3-PE100-NGv3-4_134075461_150351181-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/4/tx/tmpU1RtLM/R14-18105_kapa-NGv3-PE100-NGv3-4_134075461_150351181.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:57Z] INFO  17:57:32,185 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:57Z] INFO  17:57:32,186 HelpFormatter - Date/Time: 2016/04/14 17:57:32
[2016-04-15T00:57Z] INFO  17:57:32,186 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:57Z] INFO  17:57:32,186 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:57Z] WARN  17:57:32,220 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T00:57Z] WARN  17:57:32,223 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/4/tx/tmpU1RtLM/R14-18105_kapa-NGv3-PE100-NGv3-4_134075461_150351181.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T00:57Z] INFO  17:57:32,452 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:57Z] INFO  17:57:32,606 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T00:57Z] INFO  17:57:32,634 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:57Z] INFO  17:57:32,715 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-15T00:57Z] INFO  17:57:32,734 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T00:57Z] INFO  17:57:32,747 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:57Z] INFO  17:57:32,750 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:57Z] INFO  17:57:32,750 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:57Z] INFO  17:57:32,751 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:57Z] INFO  17:57:32,756 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/4/R14-18105_kapa-NGv3-PE100-NGv3-sort-4_150354547_165878648-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/4/R14-18105_kapa-NGv3-PE100-NGv3-4_150354547_165878648-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/4/tx/tmpFFFxBz/R14-18105_kapa-NGv3-PE100-NGv3-4_150354547_165878648.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:57Z] INFO  17:57:32,766 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:57Z] INFO  17:57:32,777 HelpFormatter - Date/Time: 2016/04/14 17:57:32
[2016-04-15T00:57Z] INFO  17:57:32,778 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:57Z] INFO  17:57:32,779 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:57Z] WARN  17:57:32,808 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T00:57Z] WARN  17:57:32,811 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/4/tx/tmpFFFxBz/R14-18105_kapa-NGv3-PE100-NGv3-4_150354547_165878648.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T00:57Z] INFO  17:57:33,065 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:57Z] INFO  17:57:33,114 IntervalUtils - Processing 86890 bp from intervals
[2016-04-15T00:57Z] WARN  17:57:33,120 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:57Z] INFO  17:57:33,214 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:57Z] INFO  17:57:33,228 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T00:57Z] INFO  17:57:33,238 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:57Z] INFO  17:57:33,278 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:57Z] INFO  17:57:33,289 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:57Z] INFO  17:57:33,289 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T00:57Z] INFO  17:57:33,289 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T00:57Z] INFO  17:57:33,298 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T00:57Z] INFO  17:57:33,298 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T00:57Z] INFO  17:57:33,323 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-15T00:57Z] INFO  17:57:33,340 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T00:57Z] INFO  17:57:33,528 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T00:57Z] INFO  17:57:33,721 IntervalUtils - Processing 119752 bp from intervals
[2016-04-15T00:57Z] WARN  17:57:33,738 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:57Z] INFO  17:57:33,906 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:57Z] INFO  17:57:33,985 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:57Z] INFO  17:57:33,986 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:57Z] INFO  17:57:33,987 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T00:57Z] INFO  17:57:33,988 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T00:57Z] INFO  17:57:33,989 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T00:57Z] INFO  17:57:33,989 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T00:57Z] INFO  17:57:34,194 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T00:57Z] INFO  17:57:35,506 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.01664368
[2016-04-15T00:57Z] INFO  17:57:35,507 PairHMM - Total compute time in PairHMM computeLikelihoods() : 1.843943345
[2016-04-15T00:57Z] INFO  17:57:35,508 HaplotypeCaller - Ran local assembly on 2093 active regions
[2016-04-15T00:57Z] INFO  17:57:35,606 ProgressMeter -            done     1.83827552E8    74.0 s            0.0 s      100.0%    74.0 s       0.0 s
[2016-04-15T00:57Z] INFO  17:57:35,606 ProgressMeter - Total runtime 74.06 secs, 1.23 min, 0.02 hours
[2016-04-15T00:57Z] INFO  17:57:35,607 MicroScheduler - 38635 reads were filtered out during the traversal out of approximately 465736 total reads (8.30%)
[2016-04-15T00:57Z] INFO  17:57:35,607 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:57Z] INFO  17:57:35,607 MicroScheduler -   -> 37473 reads (8.05% of total) failing DuplicateReadFilter
[2016-04-15T00:57Z] INFO  17:57:35,607 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:57Z] INFO  17:57:35,608 MicroScheduler -   -> 1162 reads (0.25% of total) failing HCMappingQualityFilter
[2016-04-15T00:57Z] INFO  17:57:35,608 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:57Z] INFO  17:57:35,608 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:57Z] INFO  17:57:35,608 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:57Z] INFO  17:57:35,609 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:57Z] INFO  17:57:36,295 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.005823974
[2016-04-15T00:57Z] INFO  17:57:36,295 PairHMM - Total compute time in PairHMM computeLikelihoods() : 0.424337071
[2016-04-15T00:57Z] INFO  17:57:36,295 HaplotypeCaller - Ran local assembly on 623 active regions
[2016-04-15T00:57Z] INFO  17:57:36,338 ProgressMeter -            done      1.8095278E7    28.0 s            1.0 s      100.0%    28.0 s       0.0 s
[2016-04-15T00:57Z] INFO  17:57:36,338 ProgressMeter - Total runtime 28.91 secs, 0.48 min, 0.01 hours
[2016-04-15T00:57Z] INFO  17:57:36,339 MicroScheduler - 8451 reads were filtered out during the traversal out of approximately 106770 total reads (7.92%)
[2016-04-15T00:57Z] INFO  17:57:36,339 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:57Z] INFO  17:57:36,339 MicroScheduler -   -> 8354 reads (7.82% of total) failing DuplicateReadFilter
[2016-04-15T00:57Z] INFO  17:57:36,340 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:57Z] INFO  17:57:36,340 MicroScheduler -   -> 97 reads (0.09% of total) failing HCMappingQualityFilter
[2016-04-15T00:57Z] INFO  17:57:36,340 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:57Z] INFO  17:57:36,341 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:57Z] INFO  17:57:36,341 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:57Z] INFO  17:57:36,341 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:57Z] INFO  17:57:36,817 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:57Z] INFO  17:57:37,026 ProgressMeter -      4:44706739      2.4012124E7    30.0 s            1.0 s       68.2%    44.0 s      14.0 s
[2016-04-15T00:57Z] GATK: HaplotypeCaller
[2016-04-15T00:57Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T00:57Z] INFO  17:57:37,215 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T00:57Z] INFO  17:57:37,216 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T00:57Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T00:57Z] INFO  17:57:37,457 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T00:57Z] INFO  17:57:37,457 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T00:57Z] WARN  17:57:37,488 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T00:57Z] WARN  17:57:37,489 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T00:57Z] WARN  17:57:37,716 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T00:57Z] WARN  17:57:37,717 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T00:57Z] INFO  17:57:37,799 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:57Z] GATK: HaplotypeCaller
[2016-04-15T00:57Z] INFO  17:57:40,025 ProgressMeter -      4:76507043      2.8579321E7    30.0 s            1.0 s       51.8%    57.0 s      27.0 s
[2016-04-15T00:57Z] INFO  17:57:40,324 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:57Z] INFO  17:57:40,328 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:57Z] INFO  17:57:40,342 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:57Z] INFO  17:57:40,342 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:57Z] INFO  17:57:40,347 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/4/R14-18105_kapa-NGv3-PE100-NGv3-sort-4_165889318_183245405-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/4/R14-18105_kapa-NGv3-PE100-NGv3-4_165889318_183245405-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/4/tx/tmpCRxGTd/R14-18105_kapa-NGv3-PE100-NGv3-4_165889318_183245405.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:57Z] INFO  17:57:40,390 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:57Z] INFO  17:57:40,391 HelpFormatter - Date/Time: 2016/04/14 17:57:40
[2016-04-15T00:57Z] INFO  17:57:40,391 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:57Z] INFO  17:57:40,392 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:57Z] WARN  17:57:40,437 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T00:57Z] WARN  17:57:40,452 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/4/tx/tmpCRxGTd/R14-18105_kapa-NGv3-PE100-NGv3-4_165889318_183245405.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T00:57Z] INFO  17:57:40,657 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.038848621
[2016-04-15T00:57Z] INFO  17:57:40,658 PairHMM - Total compute time in PairHMM computeLikelihoods() : 0.65890722
[2016-04-15T00:57Z] INFO  17:57:40,659 HaplotypeCaller - Ran local assembly on 1407 active regions
[2016-04-15T00:57Z] INFO  17:57:40,687 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:57Z] INFO  17:57:40,732 ProgressMeter -            done      8.1782422E7    50.0 s            0.0 s      100.0%    50.0 s       0.0 s
[2016-04-15T00:57Z] INFO  17:57:40,733 ProgressMeter - Total runtime 50.94 secs, 0.85 min, 0.01 hours
[2016-04-15T00:57Z] INFO  17:57:40,734 MicroScheduler - 22467 reads were filtered out during the traversal out of approximately 280088 total reads (8.02%)
[2016-04-15T00:57Z] INFO  17:57:40,734 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:57Z] INFO  17:57:40,734 MicroScheduler -   -> 21730 reads (7.76% of total) failing DuplicateReadFilter
[2016-04-15T00:57Z] INFO  17:57:40,734 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:57Z] INFO  17:57:40,735 MicroScheduler -   -> 737 reads (0.26% of total) failing HCMappingQualityFilter
[2016-04-15T00:57Z] INFO  17:57:40,739 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:57Z] INFO  17:57:40,739 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:57Z] INFO  17:57:40,739 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:57Z] INFO  17:57:40,739 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:57Z] INFO  17:57:40,902 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T00:57Z] INFO  17:57:40,911 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:57Z] INFO  17:57:40,960 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-15T00:57Z] INFO  17:57:40,978 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T00:57Z] INFO  17:57:40,991 ProgressMeter -      4:88537179        8706540.0    30.0 s            3.0 s       46.9%    63.0 s      33.0 s
[2016-04-15T00:57Z] INFO  17:57:41,254 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:57Z] INFO  17:57:41,256 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:57Z] INFO  17:57:41,257 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:57Z] INFO  17:57:41,257 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:57Z] INFO  17:57:41,272 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/4/R14-18105_kapa-NGv3-PE100-NGv3-sort-4_183267803_191154276-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/4/R14-18105_kapa-NGv3-PE100-NGv3-4_183267803_191154276-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/4/tx/tmpjjGvc6/R14-18105_kapa-NGv3-PE100-NGv3-4_183267803_191154276.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:57Z] INFO  17:57:41,286 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:57Z] INFO  17:57:41,286 HelpFormatter - Date/Time: 2016/04/14 17:57:41
[2016-04-15T00:57Z] INFO  17:57:41,286 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:57Z] INFO  17:57:41,286 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:57Z] WARN  17:57:41,331 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T00:57Z] WARN  17:57:41,334 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/4/tx/tmpjjGvc6/R14-18105_kapa-NGv3-PE100-NGv3-4_183267803_191154276.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T00:57Z] INFO  17:57:41,362 IntervalUtils - Processing 78538 bp from intervals
[2016-04-15T00:57Z] WARN  17:57:41,368 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:57Z] INFO  17:57:41,466 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:57Z] INFO  17:57:41,576 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:57Z] INFO  17:57:41,576 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:57Z] INFO  17:57:41,576 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T00:57Z] INFO  17:57:41,577 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T00:57Z] INFO  17:57:41,581 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T00:57Z] INFO  17:57:41,581 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T00:57Z] INFO  17:57:41,601 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:57Z] INFO  17:57:41,819 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T00:57Z] INFO  17:57:41,837 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T00:57Z] INFO  17:57:41,838 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:57Z] INFO  17:57:41,924 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.09
[2016-04-15T00:57Z] INFO  17:57:41,957 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T00:57Z] INFO  17:57:42,257 IntervalUtils - Processing 99602 bp from intervals
[2016-04-15T00:57Z] WARN  17:57:42,262 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:57Z] INFO  17:57:42,283 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:57Z] INFO  17:57:42,422 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:57Z] INFO  17:57:42,494 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:57Z] INFO  17:57:42,494 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:57Z] INFO  17:57:42,495 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T00:57Z] INFO  17:57:42,496 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T00:57Z] INFO  17:57:42,501 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T00:57Z] INFO  17:57:42,501 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T00:57Z] GATK: HaplotypeCaller
[2016-04-15T00:57Z] INFO  17:57:42,717 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T00:57Z] INFO  17:57:45,865 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:57Z] INFO  17:57:45,867 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:57Z] INFO  17:57:45,867 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:57Z] INFO  17:57:45,868 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:57Z] INFO  17:57:45,882 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/5/R14-18105_kapa-NGv3-PE100-NGv3-sort-5_0_15580921-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/5/R14-18105_kapa-NGv3-PE100-NGv3-5_0_15580921-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/5/tx/tmpzOjf7m/R14-18105_kapa-NGv3-PE100-NGv3-5_0_15580921.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:57Z] INFO  17:57:45,904 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:57Z] INFO  17:57:45,904 HelpFormatter - Date/Time: 2016/04/14 17:57:45
[2016-04-15T00:57Z] INFO  17:57:45,904 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:57Z] INFO  17:57:45,905 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:57Z] INFO  17:57:45,910 ProgressMeter -     3:127398828     1.39451785E8    60.0 s            0.0 s       98.5%    60.0 s       0.0 s
[2016-04-15T00:57Z] WARN  17:57:45,949 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T00:57Z] WARN  17:57:45,952 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/5/tx/tmpzOjf7m/R14-18105_kapa-NGv3-PE100-NGv3-5_0_15580921.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T00:57Z] INFO  17:57:46,211 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:57Z] INFO  17:57:46,458 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T00:57Z] INFO  17:57:46,467 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:57Z] INFO  17:57:46,540 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-15T00:57Z] INFO  17:57:46,558 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T00:57Z] INFO  17:57:46,668 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.019000695
[2016-04-15T00:57Z] INFO  17:57:46,670 PairHMM - Total compute time in PairHMM computeLikelihoods() : 0.342654829
[2016-04-15T00:57Z] INFO  17:57:46,671 HaplotypeCaller - Ran local assembly on 1035 active regions
[2016-04-15T00:57Z] INFO  17:57:46,743 ProgressMeter -            done      5.6156843E7    39.0 s            0.0 s      100.0%    39.0 s       0.0 s
[2016-04-15T00:57Z] INFO  17:57:46,743 ProgressMeter - Total runtime 39.73 secs, 0.66 min, 0.01 hours
[2016-04-15T00:57Z] INFO  17:57:46,744 MicroScheduler - 14182 reads were filtered out during the traversal out of approximately 174575 total reads (8.12%)
[2016-04-15T00:57Z] INFO  17:57:46,744 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:57Z] INFO  17:57:46,744 MicroScheduler -   -> 13805 reads (7.91% of total) failing DuplicateReadFilter
[2016-04-15T00:57Z] INFO  17:57:46,745 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:57Z] INFO  17:57:46,745 MicroScheduler -   -> 377 reads (0.22% of total) failing HCMappingQualityFilter
[2016-04-15T00:57Z] INFO  17:57:46,745 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:57Z] INFO  17:57:46,745 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:57Z] INFO  17:57:46,746 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:57Z] INFO  17:57:46,746 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:57Z] INFO  17:57:46,749 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.054815291
[2016-04-15T00:57Z] INFO  17:57:46,750 PairHMM - Total compute time in PairHMM computeLikelihoods() : 0.759929826
[2016-04-15T00:57Z] INFO  17:57:46,751 HaplotypeCaller - Ran local assembly on 1763 active regions
[2016-04-15T00:57Z] INFO  17:57:46,806 ProgressMeter -            done     1.43172621E8    60.0 s            0.0 s      100.0%    60.0 s       0.0 s
[2016-04-15T00:57Z] INFO  17:57:46,807 ProgressMeter - Total runtime 60.95 secs, 1.02 min, 0.02 hours
[2016-04-15T00:57Z] INFO  17:57:46,807 MicroScheduler - 29534 reads were filtered out during the traversal out of approximately 354532 total reads (8.33%)
[2016-04-15T00:57Z] INFO  17:57:46,807 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:57Z] INFO  17:57:46,808 MicroScheduler -   -> 28081 reads (7.92% of total) failing DuplicateReadFilter
[2016-04-15T00:57Z] INFO  17:57:46,808 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:57Z] INFO  17:57:46,808 MicroScheduler -   -> 1453 reads (0.41% of total) failing HCMappingQualityFilter
[2016-04-15T00:57Z] INFO  17:57:46,808 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:57Z] INFO  17:57:46,809 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:57Z] INFO  17:57:46,809 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:57Z] INFO  17:57:46,809 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:57Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T00:57Z] INFO  17:57:46,950 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T00:57Z] INFO  17:57:46,950 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T00:57Z] INFO  17:57:46,999 IntervalUtils - Processing 125185 bp from intervals
[2016-04-15T00:57Z] WARN  17:57:47,015 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:57Z] INFO  17:57:47,115 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:57Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T00:57Z] INFO  17:57:47,138 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T00:57Z] INFO  17:57:47,139 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T00:57Z] INFO  17:57:47,195 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:57Z] INFO  17:57:47,196 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:57Z] INFO  17:57:47,196 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T00:57Z] INFO  17:57:47,197 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T00:57Z] INFO  17:57:47,198 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T00:57Z] INFO  17:57:47,198 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T00:57Z] WARN  17:57:47,242 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T00:57Z] WARN  17:57:47,243 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T00:57Z] INFO  17:57:47,379 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T00:57Z] WARN  17:57:47,453 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T00:57Z] WARN  17:57:47,455 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T00:57Z] INFO  17:57:47,919 ProgressMeter -     3:142741695     1.39401158E8    60.0 s            0.0 s       98.0%    61.0 s       1.0 s
[2016-04-15T00:57Z] INFO  17:57:48,189 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:57Z] INFO  17:57:48,309 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:57Z] GATK: HaplotypeCaller
[2016-04-15T00:57Z] GATK: HaplotypeCaller
[2016-04-15T00:57Z] INFO  17:57:49,143 ProgressMeter -     4:110452678      2.9481079E7    30.0 s            1.0 s       65.5%    45.0 s      15.0 s
[2016-04-15T00:57Z] INFO  17:57:49,152 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.021589338000000003
[2016-04-15T00:57Z] INFO  17:57:49,174 PairHMM - Total compute time in PairHMM computeLikelihoods() : 0.8210194120000001
[2016-04-15T00:57Z] INFO  17:57:49,175 HaplotypeCaller - Ran local assembly on 1778 active regions
[2016-04-15T00:57Z] INFO  17:57:49,210 ProgressMeter -            done      1.4553848E8    61.0 s            0.0 s      100.0%    61.0 s       0.0 s
[2016-04-15T00:57Z] INFO  17:57:49,211 ProgressMeter - Total runtime 61.31 secs, 1.02 min, 0.02 hours
[2016-04-15T00:57Z] INFO  17:57:49,211 MicroScheduler - 27300 reads were filtered out during the traversal out of approximately 330698 total reads (8.26%)
[2016-04-15T00:57Z] INFO  17:57:49,212 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:57Z] INFO  17:57:49,213 MicroScheduler -   -> 26183 reads (7.92% of total) failing DuplicateReadFilter
[2016-04-15T00:57Z] INFO  17:57:49,213 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:57Z] INFO  17:57:49,214 MicroScheduler -   -> 1117 reads (0.34% of total) failing HCMappingQualityFilter
[2016-04-15T00:57Z] INFO  17:57:49,215 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:57Z] INFO  17:57:49,215 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:57Z] INFO  17:57:49,216 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:57Z] INFO  17:57:49,217 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:57Z] INFO  17:57:50,698 ProgressMeter -     3:195594838        7646000.0    60.0 s            7.0 s       56.9%   105.0 s      45.0 s
[2016-04-15T00:57Z] INFO  17:57:50,898 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:57Z] INFO  17:57:51,052 ProgressMeter -       4:5785407      5.5471455E7    60.0 s            1.0 s       60.6%    99.0 s      39.0 s
[2016-04-15T00:57Z] GATK: HaplotypeCaller
[2016-04-15T00:57Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T00:57Z] INFO  17:57:51,633 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T00:57Z] INFO  17:57:51,633 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T00:57Z] WARN  17:57:51,959 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T00:57Z] WARN  17:57:51,960 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T00:57Z] INFO  17:57:52,026 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:57Z] INFO  17:57:52,029 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:57Z] INFO  17:57:52,030 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:57Z] INFO  17:57:52,031 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:57Z] INFO  17:57:52,035 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/5/R14-18105_kapa-NGv3-PE100-NGv3-sort-5_31294068_49695124-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/5/R14-18105_kapa-NGv3-PE100-NGv3-5_31294068_49695124-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/5/tx/tmpNqV9Cw/R14-18105_kapa-NGv3-PE100-NGv3-5_31294068_49695124.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:57Z] INFO  17:57:52,064 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:57Z] INFO  17:57:52,065 HelpFormatter - Date/Time: 2016/04/14 17:57:52
[2016-04-15T00:57Z] INFO  17:57:52,066 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:57Z] INFO  17:57:52,066 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:57Z] INFO  17:57:52,078 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:57Z] INFO  17:57:52,081 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:57Z] INFO  17:57:52,082 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:57Z] INFO  17:57:52,082 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:57Z] INFO  17:57:52,087 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/5/R14-18105_kapa-NGv3-PE100-NGv3-sort-5_15616091_31267808-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/5/R14-18105_kapa-NGv3-PE100-NGv3-5_15616091_31267808-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/5/tx/tmpfQs08m/R14-18105_kapa-NGv3-PE100-NGv3-5_15616091_31267808.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:57Z] WARN  17:57:52,099 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T00:57Z] WARN  17:57:52,102 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/5/tx/tmpNqV9Cw/R14-18105_kapa-NGv3-PE100-NGv3-5_31294068_49695124.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T00:57Z] INFO  17:57:52,105 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:57Z] INFO  17:57:52,106 HelpFormatter - Date/Time: 2016/04/14 17:57:52
[2016-04-15T00:57Z] INFO  17:57:52,107 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:57Z] INFO  17:57:52,107 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:57Z] WARN  17:57:52,135 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T00:57Z] WARN  17:57:52,138 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/5/tx/tmpfQs08m/R14-18105_kapa-NGv3-PE100-NGv3-5_15616091_31267808.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T00:57Z] INFO  17:57:52,315 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:57Z] INFO  17:57:52,338 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:57Z] INFO  17:57:52,353 ProgressMeter -      3:58193945     3.87381064E8    90.0 s            0.0 s       93.6%    96.0 s       6.0 s
[2016-04-15T00:57Z] INFO  17:57:52,517 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T00:57Z] INFO  17:57:52,527 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:57Z] INFO  17:57:52,574 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T00:57Z] INFO  17:57:52,584 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:57Z] INFO  17:57:52,585 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-15T00:57Z] INFO  17:57:52,606 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T00:57Z] INFO  17:57:52,671 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.09
[2016-04-15T00:57Z] INFO  17:57:52,687 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T00:57Z] INFO  17:57:52,910 IntervalUtils - Processing 26887 bp from intervals
[2016-04-15T00:57Z] WARN  17:57:52,918 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:57Z] INFO  17:57:53,050 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:57Z] INFO  17:57:53,119 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:57Z] INFO  17:57:53,121 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:57Z] INFO  17:57:53,121 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T00:57Z] INFO  17:57:53,122 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T00:57Z] INFO  17:57:53,123 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T00:57Z] INFO  17:57:53,123 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T00:57Z] INFO  17:57:53,130 IntervalUtils - Processing 183626 bp from intervals
[2016-04-15T00:57Z] WARN  17:57:53,136 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:57Z] INFO  17:57:53,284 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:57Z] INFO  17:57:53,312 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T00:57Z] INFO  17:57:53,398 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:57Z] INFO  17:57:53,410 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:57Z] INFO  17:57:53,411 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T00:57Z] INFO  17:57:53,411 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T00:57Z] INFO  17:57:53,412 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T00:57Z] INFO  17:57:53,412 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T00:57Z] INFO  17:57:53,595 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T00:57Z] INFO  17:57:54,543 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:57Z] INFO  17:57:54,557 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:57Z] INFO  17:57:54,558 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:57Z] INFO  17:57:54,559 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:57Z] INFO  17:57:54,564 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/5/R14-18105_kapa-NGv3-PE100-NGv3-sort-5_49695692_65288736-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/5/R14-18105_kapa-NGv3-PE100-NGv3-5_49695692_65288736-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/5/tx/tmpvoOCdR/R14-18105_kapa-NGv3-PE100-NGv3-5_49695692_65288736.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:57Z] INFO  17:57:54,584 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:57Z] INFO  17:57:54,585 HelpFormatter - Date/Time: 2016/04/14 17:57:54
[2016-04-15T00:57Z] INFO  17:57:54,585 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:57Z] INFO  17:57:54,585 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:57Z] WARN  17:57:54,629 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T00:57Z] WARN  17:57:54,648 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/5/tx/tmpvoOCdR/R14-18105_kapa-NGv3-PE100-NGv3-5_49695692_65288736.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T00:57Z] INFO  17:57:54,900 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:57Z] INFO  17:57:55,122 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T00:57Z] INFO  17:57:55,147 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:57Z] INFO  17:57:55,228 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-15T00:57Z] INFO  17:57:55,245 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T00:57Z] INFO  17:57:55,813 IntervalUtils - Processing 108713 bp from intervals
[2016-04-15T00:57Z] WARN  17:57:55,829 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:57Z] INFO  17:57:55,976 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:57Z] INFO  17:57:56,061 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:57Z] INFO  17:57:56,062 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:57Z] INFO  17:57:56,063 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T00:57Z] INFO  17:57:56,064 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T00:57Z] INFO  17:57:56,066 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T00:57Z] INFO  17:57:56,066 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T00:57Z] INFO  17:57:56,232 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T00:57Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T00:57Z] INFO  17:57:56,503 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T00:57Z] INFO  17:57:56,504 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T00:57Z] WARN  17:57:56,922 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T00:57Z] WARN  17:57:56,923 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T00:57Z] INFO  17:57:57,314 ProgressMeter -     1:159283860     5.33453718E8     3.5 m            0.0 s       99.7%     3.5 m       0.0 s
[2016-04-15T00:57Z] INFO  17:57:57,558 ProgressMeter -     4:124323706      2.2137322E7    30.0 s            1.0 s       67.0%    44.0 s      14.0 s
[2016-04-15T00:57Z] INFO  17:57:57,778 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.11068369400000001
[2016-04-15T00:57Z] INFO  17:57:57,780 PairHMM - Total compute time in PairHMM computeLikelihoods() : 48.233514896
[2016-04-15T00:57Z] INFO  17:57:57,780 HaplotypeCaller - Ran local assembly on 3765 active regions
[2016-04-15T00:57Z] INFO  17:57:57,833 ProgressMeter -            done     5.34487573E8     3.5 m            0.0 s      100.0%     3.5 m       0.0 s
[2016-04-15T00:57Z] INFO  17:57:57,834 ProgressMeter - Total runtime 210.59 secs, 3.51 min, 0.06 hours
[2016-04-15T00:57Z] INFO  17:57:57,834 MicroScheduler - 169741 reads were filtered out during the traversal out of approximately 981772 total reads (17.29%)
[2016-04-15T00:57Z] INFO  17:57:57,835 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:57Z] INFO  17:57:57,835 MicroScheduler -   -> 71239 reads (7.26% of total) failing DuplicateReadFilter
[2016-04-15T00:57Z] INFO  17:57:57,835 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:57Z] INFO  17:57:57,836 MicroScheduler -   -> 98502 reads (10.03% of total) failing HCMappingQualityFilter
[2016-04-15T00:57Z] INFO  17:57:57,836 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:57Z] INFO  17:57:57,836 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:57Z] INFO  17:57:57,837 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:57Z] INFO  17:57:57,837 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:57Z] INFO  17:57:59,143 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:57Z] GATK: HaplotypeCaller
[2016-04-15T00:57Z] INFO  17:57:59,839 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.016283599
[2016-04-15T00:57Z] INFO  17:57:59,840 PairHMM - Total compute time in PairHMM computeLikelihoods() : 0.9048509480000001
[2016-04-15T00:57Z] INFO  17:57:59,840 HaplotypeCaller - Ran local assembly on 3230 active regions
[2016-04-15T00:57Z] INFO  17:57:59,902 ProgressMeter -            done     4.57477008E8    97.0 s            0.0 s      100.0%    97.0 s       0.0 s
[2016-04-15T00:57Z] INFO  17:57:59,903 ProgressMeter - Total runtime 97.58 secs, 1.63 min, 0.03 hours
[2016-04-15T00:57Z] INFO  17:57:59,903 MicroScheduler - 62376 reads were filtered out during the traversal out of approximately 755412 total reads (8.26%)
[2016-04-15T00:57Z] INFO  17:57:59,904 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:57Z] INFO  17:57:59,904 MicroScheduler -   -> 60620 reads (8.02% of total) failing DuplicateReadFilter
[2016-04-15T00:57Z] INFO  17:57:59,904 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:57Z] INFO  17:57:59,904 MicroScheduler -   -> 1756 reads (0.23% of total) failing HCMappingQualityFilter
[2016-04-15T00:57Z] INFO  17:57:59,905 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:57Z] INFO  17:57:59,905 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:57Z] INFO  17:57:59,905 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:57Z] INFO  17:57:59,905 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:58Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T00:58Z] INFO  17:58:00,053 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T00:58Z] INFO  17:58:00,054 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T00:58Z] INFO  17:58:00,105 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.011126395
[2016-04-15T00:58Z] INFO  17:58:00,106 PairHMM - Total compute time in PairHMM computeLikelihoods() : 0.529213468
[2016-04-15T00:58Z] INFO  17:58:00,106 HaplotypeCaller - Ran local assembly on 1469 active regions
[2016-04-15T00:58Z] INFO  17:58:00,150 ProgressMeter -            done      9.7624838E7    50.0 s            0.0 s      100.0%    50.0 s       0.0 s
[2016-04-15T00:58Z] INFO  17:58:00,151 ProgressMeter - Total runtime 50.16 secs, 0.84 min, 0.01 hours
[2016-04-15T00:58Z] INFO  17:58:00,151 MicroScheduler - 22651 reads were filtered out during the traversal out of approximately 258254 total reads (8.77%)
[2016-04-15T00:58Z] INFO  17:58:00,151 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:58Z] INFO  17:58:00,152 MicroScheduler -   -> 20027 reads (7.75% of total) failing DuplicateReadFilter
[2016-04-15T00:58Z] INFO  17:58:00,152 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:58Z] INFO  17:58:00,153 MicroScheduler -   -> 2624 reads (1.02% of total) failing HCMappingQualityFilter
[2016-04-15T00:58Z] INFO  17:58:00,153 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:58Z] INFO  17:58:00,153 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:58Z] INFO  17:58:00,153 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:58Z] INFO  17:58:00,154 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:58Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T00:58Z] INFO  17:58:00,200 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T00:58Z] INFO  17:58:00,201 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T00:58Z] WARN  17:58:00,279 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T00:58Z] WARN  17:58:00,280 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T00:58Z] INFO  17:58:00,492 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.019275263
[2016-04-15T00:58Z] INFO  17:58:00,493 PairHMM - Total compute time in PairHMM computeLikelihoods() : 0.37148341
[2016-04-15T00:58Z] INFO  17:58:00,493 HaplotypeCaller - Ran local assembly on 1152 active regions
[2016-04-15T00:58Z] WARN  17:58:00,499 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T00:58Z] WARN  17:58:00,500 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T00:58Z] INFO  17:58:00,536 ProgressMeter -            done      5.9405179E7    41.0 s            0.0 s      100.0%    41.0 s       0.0 s
[2016-04-15T00:58Z] INFO  17:58:00,537 ProgressMeter - Total runtime 41.42 secs, 0.69 min, 0.01 hours
[2016-04-15T00:58Z] INFO  17:58:00,538 MicroScheduler - 15495 reads were filtered out during the traversal out of approximately 191792 total reads (8.08%)
[2016-04-15T00:58Z] INFO  17:58:00,538 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:58Z] INFO  17:58:00,539 MicroScheduler -   -> 14901 reads (7.77% of total) failing DuplicateReadFilter
[2016-04-15T00:58Z] INFO  17:58:00,540 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:58Z] INFO  17:58:00,540 MicroScheduler -   -> 594 reads (0.31% of total) failing HCMappingQualityFilter
[2016-04-15T00:58Z] INFO  17:58:00,541 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:58Z] INFO  17:58:00,541 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:58Z] INFO  17:58:00,542 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:58Z] INFO  17:58:00,543 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:58Z] INFO  17:58:01,559 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:58Z] INFO  17:58:01,686 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:58Z] GATK: HaplotypeCaller
[2016-04-15T00:58Z] INFO  17:58:01,931 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.024958049000000003
[2016-04-15T00:58Z] INFO  17:58:01,932 PairHMM - Total compute time in PairHMM computeLikelihoods() : 19.088153615
[2016-04-15T00:58Z] INFO  17:58:01,933 HaplotypeCaller - Ran local assembly on 906 active regions
[2016-04-15T00:58Z] INFO  17:58:01,986 ProgressMeter -            done      3.3552483E7    71.0 s            2.0 s      100.0%    71.0 s       0.0 s
[2016-04-15T00:58Z] INFO  17:58:01,991 ProgressMeter - Total runtime 71.31 secs, 1.19 min, 0.02 hours
[2016-04-15T00:58Z] INFO  17:58:01,991 MicroScheduler - 30487 reads were filtered out during the traversal out of approximately 188663 total reads (16.16%)
[2016-04-15T00:58Z] INFO  17:58:01,992 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:58Z] INFO  17:58:01,992 MicroScheduler -   -> 13986 reads (7.41% of total) failing DuplicateReadFilter
[2016-04-15T00:58Z] INFO  17:58:01,992 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:58Z] INFO  17:58:01,992 MicroScheduler -   -> 16501 reads (8.75% of total) failing HCMappingQualityFilter
[2016-04-15T00:58Z] INFO  17:58:01,993 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:58Z] INFO  17:58:01,993 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:58Z] INFO  17:58:01,993 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:58Z] INFO  17:58:01,994 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:58Z] INFO  17:58:02,100 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:58Z] GATK: HaplotypeCaller
[2016-04-15T00:58Z] GATK: HaplotypeCaller
[2016-04-15T00:58Z] INFO  17:58:02,488 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:58Z] INFO  17:58:02,491 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:58Z] INFO  17:58:02,499 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:58Z] INFO  17:58:02,500 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:58Z] INFO  17:58:02,505 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/5/R14-18105_kapa-NGv3-PE100-NGv3-sort-5_65290574_80809536-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/5/R14-18105_kapa-NGv3-PE100-NGv3-5_65290574_80809536-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/5/tx/tmpef56aY/R14-18105_kapa-NGv3-PE100-NGv3-5_65290574_80809536.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:58Z] INFO  17:58:02,527 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:58Z] INFO  17:58:02,528 HelpFormatter - Date/Time: 2016/04/14 17:58:02
[2016-04-15T00:58Z] INFO  17:58:02,528 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:58Z] INFO  17:58:02,529 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:58Z] WARN  17:58:02,556 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T00:58Z] WARN  17:58:02,559 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/5/tx/tmpef56aY/R14-18105_kapa-NGv3-PE100-NGv3-5_65290574_80809536.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T00:58Z] INFO  17:58:02,829 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:58Z] INFO  17:58:03,059 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T00:58Z] INFO  17:58:03,080 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:58Z] INFO  17:58:03,164 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-15T00:58Z] INFO  17:58:03,199 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T00:58Z] INFO  17:58:03,310 ProgressMeter -     4:149363826      1.8896086E7    30.0 s            1.0 s       98.1%    30.0 s       0.0 s
[2016-04-15T00:58Z] INFO  17:58:03,323 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:58Z] GATK: HaplotypeCaller
[2016-04-15T00:58Z] INFO  17:58:03,736 IntervalUtils - Processing 203113 bp from intervals
[2016-04-15T00:58Z] WARN  17:58:03,741 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:58Z] INFO  17:58:03,769 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.019786994000000002
[2016-04-15T00:58Z] INFO  17:58:03,770 PairHMM - Total compute time in PairHMM computeLikelihoods() : 0.719537207
[2016-04-15T00:58Z] INFO  17:58:03,771 HaplotypeCaller - Ran local assembly on 611 active regions
[2016-04-15T00:58Z] INFO  17:58:03,817 ProgressMeter -            done      1.9501835E7    30.0 s            1.0 s      100.0%    30.0 s       0.0 s
[2016-04-15T00:58Z] INFO  17:58:03,817 ProgressMeter - Total runtime 30.54 secs, 0.51 min, 0.01 hours
[2016-04-15T00:58Z] INFO  17:58:03,817 MicroScheduler - 9373 reads were filtered out during the traversal out of approximately 114512 total reads (8.19%)
[2016-04-15T00:58Z] INFO  17:58:03,818 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:58Z] INFO  17:58:03,818 MicroScheduler -   -> 9005 reads (7.86% of total) failing DuplicateReadFilter
[2016-04-15T00:58Z] INFO  17:58:03,818 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:58Z] INFO  17:58:03,818 MicroScheduler -   -> 368 reads (0.32% of total) failing HCMappingQualityFilter
[2016-04-15T00:58Z] INFO  17:58:03,819 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:58Z] INFO  17:58:03,819 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:58Z] INFO  17:58:03,819 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:58Z] INFO  17:58:03,819 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:58Z] INFO  17:58:03,822 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:58Z] INFO  17:58:03,936 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:58Z] INFO  17:58:03,938 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:58Z] INFO  17:58:03,938 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T00:58Z] INFO  17:58:03,939 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T00:58Z] INFO  17:58:03,940 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T00:58Z] INFO  17:58:03,940 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T00:58Z] INFO  17:58:04,001 ProgressMeter -     4:164247514      3.0180931E7    30.0 s            0.0 s       93.6%    32.0 s       2.0 s
[2016-04-15T00:58Z] INFO  17:58:04,128 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T00:58Z] INFO  17:58:05,101 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:58Z] INFO  17:58:05,149 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:58Z] INFO  17:58:05,152 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:58Z] INFO  17:58:05,152 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:58Z] INFO  17:58:05,153 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:58Z] INFO  17:58:05,157 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/5/R14-18105_kapa-NGv3-PE100-NGv3-sort-5_80911291_96430739-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/5/R14-18105_kapa-NGv3-PE100-NGv3-5_80911291_96430739-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/5/tx/tmp2tmRn_/R14-18105_kapa-NGv3-PE100-NGv3-5_80911291_96430739.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:58Z] INFO  17:58:05,170 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:58Z] INFO  17:58:05,171 HelpFormatter - Date/Time: 2016/04/14 17:58:05
[2016-04-15T00:58Z] INFO  17:58:05,171 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:58Z] INFO  17:58:05,172 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:58Z] INFO  17:58:05,217 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:58Z] WARN  17:58:05,221 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T00:58Z] WARN  17:58:05,224 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/5/tx/tmp2tmRn_/R14-18105_kapa-NGv3-PE100-NGv3-5_80911291_96430739.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T00:58Z] INFO  17:58:05,230 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:58Z] INFO  17:58:05,231 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:58Z] INFO  17:58:05,232 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:58Z] INFO  17:58:05,236 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/5/R14-18105_kapa-NGv3-PE100-NGv3-sort-5_96432513_112043579-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/5/R14-18105_kapa-NGv3-PE100-NGv3-5_96432513_112043579-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/5/tx/tmp7Jsvfv/R14-18105_kapa-NGv3-PE100-NGv3-5_96432513_112043579.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:58Z] INFO  17:58:05,262 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:58Z] INFO  17:58:05,262 HelpFormatter - Date/Time: 2016/04/14 17:58:05
[2016-04-15T00:58Z] INFO  17:58:05,262 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:58Z] INFO  17:58:05,262 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:58Z] WARN  17:58:05,314 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T00:58Z] WARN  17:58:05,334 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/5/tx/tmp7Jsvfv/R14-18105_kapa-NGv3-PE100-NGv3-5_96432513_112043579.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T00:58Z] INFO  17:58:05,456 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:58Z] INFO  17:58:05,472 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:58Z] INFO  17:58:05,475 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:58Z] INFO  17:58:05,476 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:58Z] INFO  17:58:05,476 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:58Z] INFO  17:58:05,481 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/5/R14-18105_kapa-NGv3-PE100-NGv3-sort-5_112073555_127595521-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/5/R14-18105_kapa-NGv3-PE100-NGv3-5_112073555_127595521-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/5/tx/tmpb5B3KB/R14-18105_kapa-NGv3-PE100-NGv3-5_112073555_127595521.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:58Z] INFO  17:58:05,489 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:58Z] INFO  17:58:05,493 HelpFormatter - Date/Time: 2016/04/14 17:58:05
[2016-04-15T00:58Z] INFO  17:58:05,493 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:58Z] INFO  17:58:05,494 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:58Z] GATK: HaplotypeCaller
[2016-04-15T00:58Z] WARN  17:58:05,537 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T00:58Z] WARN  17:58:05,551 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/5/tx/tmpb5B3KB/R14-18105_kapa-NGv3-PE100-NGv3-5_112073555_127595521.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T00:58Z] INFO  17:58:05,565 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:58Z] INFO  17:58:05,639 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T00:58Z] INFO  17:58:05,659 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:58Z] INFO  17:58:05,760 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.10
[2016-04-15T00:58Z] INFO  17:58:05,784 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T00:58Z] INFO  17:58:05,790 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T00:58Z] INFO  17:58:05,792 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:58Z] INFO  17:58:05,817 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:58Z] INFO  17:58:05,900 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-15T00:58Z] INFO  17:58:05,928 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T00:58Z] INFO  17:58:06,053 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T00:58Z] INFO  17:58:06,083 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:58Z] INFO  17:58:06,143 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.006300874000000001
[2016-04-15T00:58Z] INFO  17:58:06,154 PairHMM - Total compute time in PairHMM computeLikelihoods() : 0.45732292700000005
[2016-04-15T00:58Z] INFO  17:58:06,156 HaplotypeCaller - Ran local assembly on 834 active regions
[2016-04-15T00:58Z] INFO  17:58:06,197 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.11
[2016-04-15T00:58Z] INFO  17:58:06,209 ProgressMeter -            done      3.2744349E7    32.0 s            0.0 s      100.0%    32.0 s       0.0 s
[2016-04-15T00:58Z] INFO  17:58:06,209 ProgressMeter - Total runtime 32.22 secs, 0.54 min, 0.01 hours
[2016-04-15T00:58Z] INFO  17:58:06,210 MicroScheduler - 11766 reads were filtered out during the traversal out of approximately 146298 total reads (8.04%)
[2016-04-15T00:58Z] INFO  17:58:06,210 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:58Z] INFO  17:58:06,210 MicroScheduler -   -> 11600 reads (7.93% of total) failing DuplicateReadFilter
[2016-04-15T00:58Z] INFO  17:58:06,211 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:58Z] INFO  17:58:06,211 MicroScheduler -   -> 166 reads (0.11% of total) failing HCMappingQualityFilter
[2016-04-15T00:58Z] INFO  17:58:06,211 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:58Z] INFO  17:58:06,211 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:58Z] INFO  17:58:06,212 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:58Z] INFO  17:58:06,212 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:58Z] INFO  17:58:06,235 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T00:58Z] INFO  17:58:06,266 IntervalUtils - Processing 113632 bp from intervals
[2016-04-15T00:58Z] WARN  17:58:06,271 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:58Z] INFO  17:58:06,311 IntervalUtils - Processing 57322 bp from intervals
[2016-04-15T00:58Z] WARN  17:58:06,336 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:58Z] INFO  17:58:06,409 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:58Z] INFO  17:58:06,456 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:58Z] INFO  17:58:06,478 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:58Z] INFO  17:58:06,479 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:58Z] INFO  17:58:06,480 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T00:58Z] INFO  17:58:06,481 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T00:58Z] INFO  17:58:06,481 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T00:58Z] INFO  17:58:06,482 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T00:58Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T00:58Z] INFO  17:58:06,512 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T00:58Z] INFO  17:58:06,523 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T00:58Z] INFO  17:58:06,570 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:58Z] INFO  17:58:06,571 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:58Z] INFO  17:58:06,572 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T00:58Z] INFO  17:58:06,573 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T00:58Z] INFO  17:58:06,584 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T00:58Z] INFO  17:58:06,585 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T00:58Z] INFO  17:58:06,637 IntervalUtils - Processing 103986 bp from intervals
[2016-04-15T00:58Z] INFO  17:58:06,641 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T00:58Z] WARN  17:58:06,642 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:58Z] INFO  17:58:06,771 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:58Z] WARN  17:58:06,787 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T00:58Z] WARN  17:58:06,788 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T00:58Z] INFO  17:58:06,827 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T00:58Z] INFO  17:58:06,833 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:58Z] INFO  17:58:06,835 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:58Z] INFO  17:58:06,836 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:58Z] INFO  17:58:06,836 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:58Z] INFO  17:58:06,840 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/5/R14-18105_kapa-NGv3-PE100-NGv3-sort-5_127597427_143191869-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/5/R14-18105_kapa-NGv3-PE100-NGv3-5_127597427_143191869-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/5/tx/tmpgn71NG/R14-18105_kapa-NGv3-PE100-NGv3-5_127597427_143191869.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:58Z] INFO  17:58:06,865 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:58Z] INFO  17:58:06,865 HelpFormatter - Date/Time: 2016/04/14 17:58:06
[2016-04-15T00:58Z] INFO  17:58:06,865 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:58Z] INFO  17:58:06,866 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:58Z] INFO  17:58:06,866 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:58Z] INFO  17:58:06,867 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:58Z] INFO  17:58:06,868 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T00:58Z] INFO  17:58:06,869 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T00:58Z] INFO  17:58:06,869 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T00:58Z] INFO  17:58:06,870 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T00:58Z] WARN  17:58:06,911 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T00:58Z] WARN  17:58:06,920 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/5/tx/tmpgn71NG/R14-18105_kapa-NGv3-PE100-NGv3-5_127597427_143191869.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T00:58Z] INFO  17:58:07,088 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T00:58Z] INFO  17:58:07,088 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:58Z] INFO  17:58:07,267 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T00:58Z] INFO  17:58:07,278 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:58Z] INFO  17:58:07,417 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.14
[2016-04-15T00:58Z] INFO  17:58:07,434 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T00:58Z] INFO  17:58:07,797 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:58Z] INFO  17:58:07,879 IntervalUtils - Processing 393653 bp from intervals
[2016-04-15T00:58Z] WARN  17:58:07,885 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:58Z] INFO  17:58:07,975 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:58Z] INFO  17:58:08,163 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:58Z] INFO  17:58:08,166 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:58Z] INFO  17:58:08,167 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T00:58Z] INFO  17:58:08,168 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T00:58Z] GATK: HaplotypeCaller
[2016-04-15T00:58Z] INFO  17:58:08,168 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T00:58Z] INFO  17:58:08,169 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T00:58Z] INFO  17:58:08,475 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T00:58Z] INFO  17:58:08,805 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:58Z] INFO  17:58:08,807 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:58Z] INFO  17:58:08,808 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:58Z] INFO  17:58:08,808 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:58Z] INFO  17:58:08,812 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/5/R14-18105_kapa-NGv3-PE100-NGv3-sort-5_143200044_158710347-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/5/R14-18105_kapa-NGv3-PE100-NGv3-5_143200044_158710347-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/5/tx/tmpIn7mZj/R14-18105_kapa-NGv3-PE100-NGv3-5_143200044_158710347.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:58Z] INFO  17:58:08,821 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.019495633000000002
[2016-04-15T00:58Z] INFO  17:58:08,825 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:58Z] INFO  17:58:08,822 PairHMM - Total compute time in PairHMM computeLikelihoods() : 0.848855482
[2016-04-15T00:58Z] INFO  17:58:08,833 HelpFormatter - Date/Time: 2016/04/14 17:58:08
[2016-04-15T00:58Z] INFO  17:58:08,836 HaplotypeCaller - Ran local assembly on 1023 active regions
[2016-04-15T00:58Z] INFO  17:58:08,844 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:58Z] INFO  17:58:08,845 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:58Z] WARN  17:58:08,868 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T00:58Z] WARN  17:58:08,875 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/5/tx/tmpIn7mZj/R14-18105_kapa-NGv3-PE100-NGv3-5_143200044_158710347.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T00:58Z] INFO  17:58:08,898 ProgressMeter -            done      4.4117255E7    41.0 s            0.0 s      100.0%    41.0 s       0.0 s
[2016-04-15T00:58Z] INFO  17:58:08,898 ProgressMeter - Total runtime 41.36 secs, 0.69 min, 0.01 hours
[2016-04-15T00:58Z] INFO  17:58:08,898 MicroScheduler - 13171 reads were filtered out during the traversal out of approximately 164210 total reads (8.02%)
[2016-04-15T00:58Z] INFO  17:58:08,899 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:58Z] INFO  17:58:08,899 MicroScheduler -   -> 13007 reads (7.92% of total) failing DuplicateReadFilter
[2016-04-15T00:58Z] INFO  17:58:08,899 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:58Z] INFO  17:58:08,899 MicroScheduler -   -> 164 reads (0.10% of total) failing HCMappingQualityFilter
[2016-04-15T00:58Z] INFO  17:58:08,900 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:58Z] INFO  17:58:08,900 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:58Z] INFO  17:58:08,900 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:58Z] INFO  17:58:08,900 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:58Z] INFO  17:58:09,043 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:58Z] INFO  17:58:09,322 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T00:58Z] INFO  17:58:09,331 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:58Z] INFO  17:58:09,403 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-15T00:58Z] INFO  17:58:09,420 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T00:58Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T00:58Z] INFO  17:58:09,781 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T00:58Z] INFO  17:58:09,782 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T00:58Z] INFO  17:58:09,866 IntervalUtils - Processing 205172 bp from intervals
[2016-04-15T00:58Z] WARN  17:58:09,872 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:58Z] INFO  17:58:09,998 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:58Z] WARN  17:58:10,061 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T00:58Z] WARN  17:58:10,078 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T00:58Z] INFO  17:58:10,154 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:58Z] INFO  17:58:10,155 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:58Z] INFO  17:58:10,155 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T00:58Z] INFO  17:58:10,156 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T00:58Z] INFO  17:58:10,165 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T00:58Z] INFO  17:58:10,165 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T00:58Z] INFO  17:58:10,329 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T00:58Z] INFO  17:58:10,471 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:58Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T00:58Z] INFO  17:58:10,522 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T00:58Z] INFO  17:58:10,523 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T00:58Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T00:58Z] INFO  17:58:10,584 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T00:58Z] INFO  17:58:10,584 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T00:58Z] GATK: HaplotypeCaller
[2016-04-15T00:58Z] WARN  17:58:10,799 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T00:58Z] WARN  17:58:10,799 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T00:58Z] WARN  17:58:10,828 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T00:58Z] WARN  17:58:10,829 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T00:58Z] INFO  17:58:10,895 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.018270813
[2016-04-15T00:58Z] INFO  17:58:10,896 PairHMM - Total compute time in PairHMM computeLikelihoods() : 16.877392019000002
[2016-04-15T00:58Z] INFO  17:58:10,897 HaplotypeCaller - Ran local assembly on 906 active regions
[2016-04-15T00:58Z] INFO  17:58:10,951 ProgressMeter -            done      3.7254023E7    59.0 s            1.0 s      100.0%    59.0 s       0.0 s
[2016-04-15T00:58Z] INFO  17:58:10,951 ProgressMeter - Total runtime 59.98 secs, 1.00 min, 0.02 hours
[2016-04-15T00:58Z] INFO  17:58:10,952 MicroScheduler - 14069 reads were filtered out during the traversal out of approximately 163053 total reads (8.63%)
[2016-04-15T00:58Z] INFO  17:58:10,952 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:58Z] INFO  17:58:10,952 MicroScheduler -   -> 13391 reads (8.21% of total) failing DuplicateReadFilter
[2016-04-15T00:58Z] INFO  17:58:10,953 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:58Z] INFO  17:58:10,953 MicroScheduler -   -> 678 reads (0.42% of total) failing HCMappingQualityFilter
[2016-04-15T00:58Z] INFO  17:58:10,953 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:58Z] INFO  17:58:10,953 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:58Z] INFO  17:58:10,954 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:58Z] INFO  17:58:10,954 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:58Z] INFO  17:58:11,381 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:58Z] INFO  17:58:11,384 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:58Z] INFO  17:58:11,384 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:58Z] INFO  17:58:11,385 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:58Z] INFO  17:58:11,389 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/5/R14-18105_kapa-NGv3-PE100-NGv3-sort-5_158711911_174870102-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/5/R14-18105_kapa-NGv3-PE100-NGv3-5_158711911_174870102-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/5/tx/tmpzXuIr6/R14-18105_kapa-NGv3-PE100-NGv3-5_158711911_174870102.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:58Z] INFO  17:58:11,418 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:58Z] INFO  17:58:11,428 HelpFormatter - Date/Time: 2016/04/14 17:58:11
[2016-04-15T00:58Z] INFO  17:58:11,429 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:58Z] INFO  17:58:11,430 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:58Z] WARN  17:58:11,477 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T00:58Z] WARN  17:58:11,480 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/5/tx/tmpzXuIr6/R14-18105_kapa-NGv3-PE100-NGv3-5_158711911_174870102.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T00:58Z] INFO  17:58:11,598 ProgressMeter -     4:178597044      1.6184159E7    30.0 s            1.0 s       99.7%    30.0 s       0.0 s
[2016-04-15T00:58Z] INFO  17:58:11,716 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:58Z] INFO  17:58:11,920 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T00:58Z] INFO  17:58:11,930 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:58Z] INFO  17:58:12,007 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-15T00:58Z] INFO  17:58:12,034 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T00:58Z] INFO  17:58:12,325 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.005460917
[2016-04-15T00:58Z] INFO  17:58:12,326 PairHMM - Total compute time in PairHMM computeLikelihoods() : 0.306227588
[2016-04-15T00:58Z] INFO  17:58:12,337 HaplotypeCaller - Ran local assembly on 595 active regions
[2016-04-15T00:58Z] INFO  17:58:12,370 IntervalUtils - Processing 104189 bp from intervals
[2016-04-15T00:58Z] INFO  17:58:12,379 ProgressMeter -            done      1.6341003E7    30.0 s            1.0 s      100.0%    30.0 s       0.0 s
[2016-04-15T00:58Z] INFO  17:58:12,380 ProgressMeter - Total runtime 30.80 secs, 0.51 min, 0.01 hours
[2016-04-15T00:58Z] INFO  17:58:12,381 MicroScheduler - 7636 reads were filtered out during the traversal out of approximately 91623 total reads (8.33%)
[2016-04-15T00:58Z] INFO  17:58:12,381 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:58Z] INFO  17:58:12,382 MicroScheduler -   -> 7114 reads (7.76% of total) failing DuplicateReadFilter
[2016-04-15T00:58Z] INFO  17:58:12,383 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:58Z] INFO  17:58:12,383 MicroScheduler -   -> 522 reads (0.57% of total) failing HCMappingQualityFilter
[2016-04-15T00:58Z] INFO  17:58:12,384 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:58Z] INFO  17:58:12,384 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:58Z] INFO  17:58:12,385 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:58Z] INFO  17:58:12,386 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:58Z] WARN  17:58:12,391 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:58Z] INFO  17:58:12,476 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:58Z] INFO  17:58:12,517 ProgressMeter -     4:187524188      1.4154824E7    30.0 s            2.0 s       83.2%    36.0 s       6.0 s
[2016-04-15T00:58Z] INFO  17:58:12,592 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:58Z] INFO  17:58:12,593 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:58Z] INFO  17:58:12,594 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T00:58Z] INFO  17:58:12,594 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T00:58Z] INFO  17:58:12,605 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T00:58Z] INFO  17:58:12,606 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T00:58Z] INFO  17:58:12,672 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:58Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T00:58Z] INFO  17:58:12,712 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T00:58Z] INFO  17:58:12,724 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T00:58Z] INFO  17:58:12,726 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.0016382200000000001
[2016-04-15T00:58Z] INFO  17:58:12,727 PairHMM - Total compute time in PairHMM computeLikelihoods() : 0.040182374
[2016-04-15T00:58Z] INFO  17:58:12,728 HaplotypeCaller - Ran local assembly on 166 active regions
[2016-04-15T00:58Z] INFO  17:58:12,786 ProgressMeter -            done        1678889.0    19.0 s           11.0 s      100.0%    19.0 s       0.0 s
[2016-04-15T00:58Z] INFO  17:58:12,786 ProgressMeter - Total runtime 19.67 secs, 0.33 min, 0.01 hours
[2016-04-15T00:58Z] INFO  17:58:12,787 MicroScheduler - 4919 reads were filtered out during the traversal out of approximately 37640 total reads (13.07%)
[2016-04-15T00:58Z] INFO  17:58:12,788 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:58Z] INFO  17:58:12,788 MicroScheduler -   -> 2920 reads (7.76% of total) failing DuplicateReadFilter
[2016-04-15T00:58Z] INFO  17:58:12,788 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:58Z] INFO  17:58:12,789 MicroScheduler -   -> 1999 reads (5.31% of total) failing HCMappingQualityFilter
[2016-04-15T00:58Z] INFO  17:58:12,789 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:58Z] INFO  17:58:12,789 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:58Z] INFO  17:58:12,789 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:58Z] INFO  17:58:12,790 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:58Z] INFO  17:58:12,922 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T00:58Z] WARN  17:58:13,015 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T00:58Z] WARN  17:58:13,016 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T00:58Z] GATK: HaplotypeCaller
[2016-04-15T00:58Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T00:58Z] INFO  17:58:13,482 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T00:58Z] INFO  17:58:13,482 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T00:58Z] WARN  17:58:13,699 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T00:58Z] WARN  17:58:13,700 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T00:58Z] INFO  17:58:13,882 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:58Z] INFO  17:58:14,123 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:58Z] GATK: HaplotypeCaller
[2016-04-15T00:58Z] INFO  17:58:14,397 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:58Z] INFO  17:58:14,400 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:58Z] INFO  17:58:14,401 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:58Z] INFO  17:58:14,401 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:58Z] INFO  17:58:14,406 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/5/R14-18105_kapa-NGv3-PE100-NGv3-sort-5_174919106_180915260-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/5/R14-18105_kapa-NGv3-PE100-NGv3-5_174919106_180915260-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/5/tx/tmpqciWxa/R14-18105_kapa-NGv3-PE100-NGv3-5_174919106_180915260.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:58Z] INFO  17:58:14,415 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:58Z] INFO  17:58:14,427 HelpFormatter - Date/Time: 2016/04/14 17:58:14
[2016-04-15T00:58Z] INFO  17:58:14,428 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:58Z] INFO  17:58:14,429 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:58Z] WARN  17:58:14,472 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T00:58Z] WARN  17:58:14,474 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/5/tx/tmpqciWxa/R14-18105_kapa-NGv3-PE100-NGv3-5_174919106_180915260.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T00:58Z] GATK: HaplotypeCaller
[2016-04-15T00:58Z] INFO  17:58:14,801 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:58Z] INFO  17:58:15,043 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T00:58Z] INFO  17:58:15,063 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:58Z] INFO  17:58:15,152 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.09
[2016-04-15T00:58Z] INFO  17:58:15,176 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T00:58Z] INFO  17:58:15,755 IntervalUtils - Processing 163171 bp from intervals
[2016-04-15T00:58Z] WARN  17:58:15,761 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:58Z] INFO  17:58:15,924 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:58Z] INFO  17:58:16,069 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:58Z] INFO  17:58:16,078 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:58Z] INFO  17:58:16,079 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T00:58Z] INFO  17:58:16,079 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T00:58Z] INFO  17:58:16,091 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T00:58Z] INFO  17:58:16,092 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T00:58Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T00:58Z] INFO  17:58:16,458 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T00:58Z] INFO  17:58:16,458 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T00:58Z] INFO  17:58:16,459 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T00:58Z] INFO  17:58:16,630 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:58Z] INFO  17:58:16,633 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:58Z] INFO  17:58:16,633 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:58Z] INFO  17:58:16,633 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:58Z] INFO  17:58:16,648 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/6/R14-18105_kapa-NGv3-PE100-NGv3-sort-6_0_15509601-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/6/R14-18105_kapa-NGv3-PE100-NGv3-6_0_15509601-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/6/tx/tmpzPEqZV/R14-18105_kapa-NGv3-PE100-NGv3-6_0_15509601.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:58Z] INFO  17:58:16,656 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:58Z] INFO  17:58:16,657 HelpFormatter - Date/Time: 2016/04/14 17:58:16
[2016-04-15T00:58Z] INFO  17:58:16,657 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:58Z] INFO  17:58:16,657 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:58Z] WARN  17:58:16,702 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T00:58Z] WARN  17:58:16,709 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/6/tx/tmpzPEqZV/R14-18105_kapa-NGv3-PE100-NGv3-6_0_15509601.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T00:58Z] WARN  17:58:16,811 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T00:58Z] WARN  17:58:16,824 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T00:58Z] INFO  17:58:17,001 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:58Z] INFO  17:58:17,209 ProgressMeter -       5:6449228      1.0865598E7    30.0 s            2.0 s       52.4%    57.0 s      27.0 s
[2016-04-15T00:58Z] INFO  17:58:17,293 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T00:58Z] INFO  17:58:17,303 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:58Z] INFO  17:58:17,416 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.11
[2016-04-15T00:58Z] INFO  17:58:17,453 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T00:58Z] INFO  17:58:18,056 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:58Z] INFO  17:58:18,069 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:58Z] INFO  17:58:18,070 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:58Z] INFO  17:58:18,071 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:58Z] INFO  17:58:18,075 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/6/R14-18105_kapa-NGv3-PE100-NGv3-sort-6_15511526_31080332-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/6/R14-18105_kapa-NGv3-PE100-NGv3-6_15511526_31080332-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/6/tx/tmpiG9wcd/R14-18105_kapa-NGv3-PE100-NGv3-6_15511526_31080332.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:58Z] INFO  17:58:18,094 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:58Z] INFO  17:58:18,095 HelpFormatter - Date/Time: 2016/04/14 17:58:18
[2016-04-15T00:58Z] INFO  17:58:18,095 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:58Z] INFO  17:58:18,096 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:58Z] INFO  17:58:18,096 IntervalUtils - Processing 139546 bp from intervals
[2016-04-15T00:58Z] WARN  17:58:18,101 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:58Z] WARN  17:58:18,142 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T00:58Z] WARN  17:58:18,145 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/6/tx/tmpiG9wcd/R14-18105_kapa-NGv3-PE100-NGv3-6_15511526_31080332.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T00:58Z] INFO  17:58:18,217 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:58Z] INFO  17:58:18,363 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:58Z] INFO  17:58:18,364 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:58Z] INFO  17:58:18,364 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T00:58Z] INFO  17:58:18,365 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T00:58Z] INFO  17:58:18,379 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T00:58Z] INFO  17:58:18,387 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T00:58Z] INFO  17:58:18,427 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:58Z] INFO  17:58:18,648 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T00:58Z] INFO  17:58:18,657 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:58Z] INFO  17:58:18,694 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:58Z] INFO  17:58:18,697 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:58Z] INFO  17:58:18,697 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:58Z] INFO  17:58:18,698 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:58Z] INFO  17:58:18,702 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/6/R14-18105_kapa-NGv3-PE100-NGv3-sort-6_31083801_46593245-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/6/R14-18105_kapa-NGv3-PE100-NGv3-6_31083801_46593245-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/6/tx/tmpCrt4Qj/R14-18105_kapa-NGv3-PE100-NGv3-6_31083801_46593245.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:58Z] INFO  17:58:18,727 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T00:58Z] INFO  17:58:18,732 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:58Z] INFO  17:58:18,742 HelpFormatter - Date/Time: 2016/04/14 17:58:18
[2016-04-15T00:58Z] INFO  17:58:18,743 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:58Z] INFO  17:58:18,743 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:58Z] INFO  17:58:18,776 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.12
[2016-04-15T00:58Z] WARN  17:58:18,792 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T00:58Z] WARN  17:58:18,795 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/6/tx/tmpCrt4Qj/R14-18105_kapa-NGv3-PE100-NGv3-6_31083801_46593245.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T00:58Z] INFO  17:58:18,807 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T00:58Z] INFO  17:58:19,033 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:58Z] INFO  17:58:19,170 IntervalUtils - Processing 239663 bp from intervals
[2016-04-15T00:58Z] WARN  17:58:19,175 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:58Z] INFO  17:58:19,272 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T00:58Z] INFO  17:58:19,281 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:58Z] INFO  17:58:19,317 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:58Z] INFO  17:58:19,348 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-15T00:58Z] INFO  17:58:19,383 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T00:58Z] INFO  17:58:19,441 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:58Z] INFO  17:58:19,442 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:58Z] INFO  17:58:19,443 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T00:58Z] INFO  17:58:19,443 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T00:58Z] INFO  17:58:19,458 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T00:58Z] INFO  17:58:19,458 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T00:58Z] INFO  17:58:19,727 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T00:58Z] INFO  17:58:20,009 IntervalUtils - Processing 501134 bp from intervals
[2016-04-15T00:58Z] WARN  17:58:20,019 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:58Z] INFO  17:58:20,104 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:58Z] INFO  17:58:20,304 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:58Z] INFO  17:58:20,306 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:58Z] INFO  17:58:20,306 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T00:58Z] INFO  17:58:20,307 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T00:58Z] INFO  17:58:20,325 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T00:58Z] INFO  17:58:20,326 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T00:58Z] INFO  17:58:20,562 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T00:58Z] INFO  17:58:21,053 ProgressMeter -      4:15005093     1.32047721E8    90.0 s            0.0 s       98.3%    91.0 s       1.0 s
[2016-04-15T00:58Z] INFO  17:58:21,513 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.021326064000000002
[2016-04-15T00:58Z] INFO  17:58:21,521 PairHMM - Total compute time in PairHMM computeLikelihoods() : 1.2611630120000001
[2016-04-15T00:58Z] INFO  17:58:21,522 HaplotypeCaller - Ran local assembly on 708 active regions
[2016-04-15T00:58Z] INFO  17:58:21,580 ProgressMeter -            done      1.8181148E7    39.0 s            2.0 s      100.0%    39.0 s       0.0 s
[2016-04-15T00:58Z] INFO  17:58:21,580 ProgressMeter - Total runtime 39.09 secs, 0.65 min, 0.01 hours
[2016-04-15T00:58Z] INFO  17:58:21,580 MicroScheduler - 13819 reads were filtered out during the traversal out of approximately 140029 total reads (9.87%)
[2016-04-15T00:58Z] INFO  17:58:21,581 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:58Z] INFO  17:58:21,581 MicroScheduler -   -> 11055 reads (7.89% of total) failing DuplicateReadFilter
[2016-04-15T00:58Z] INFO  17:58:21,581 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:58Z] INFO  17:58:21,582 MicroScheduler -   -> 2764 reads (1.97% of total) failing HCMappingQualityFilter
[2016-04-15T00:58Z] INFO  17:58:21,582 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:58Z] INFO  17:58:21,582 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:58Z] INFO  17:58:21,582 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:58Z] INFO  17:58:21,582 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:58Z] INFO  17:58:22,340 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.038190014
[2016-04-15T00:58Z] INFO  17:58:22,351 PairHMM - Total compute time in PairHMM computeLikelihoods() : 10.220454937000001
[2016-04-15T00:58Z] INFO  17:58:22,352 HaplotypeCaller - Ran local assembly on 1819 active regions
[2016-04-15T00:58Z] INFO  17:58:22,408 ProgressMeter -            done     1.38636459E8    91.0 s            0.0 s      100.0%    91.0 s       0.0 s
[2016-04-15T00:58Z] INFO  17:58:22,409 ProgressMeter - Total runtime 91.38 secs, 1.52 min, 0.03 hours
[2016-04-15T00:58Z] INFO  17:58:22,410 MicroScheduler - 68810 reads were filtered out during the traversal out of approximately 452477 total reads (15.21%)
[2016-04-15T00:58Z] INFO  17:58:22,410 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:58Z] INFO  17:58:22,410 MicroScheduler -   -> 33495 reads (7.40% of total) failing DuplicateReadFilter
[2016-04-15T00:58Z] INFO  17:58:22,411 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:58Z] INFO  17:58:22,411 MicroScheduler -   -> 35315 reads (7.80% of total) failing HCMappingQualityFilter
[2016-04-15T00:58Z] INFO  17:58:22,411 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:58Z] INFO  17:58:22,411 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:58Z] INFO  17:58:22,412 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:58Z] INFO  17:58:22,412 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:58Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T00:58Z] INFO  17:58:23,004 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T00:58Z] INFO  17:58:23,016 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T00:58Z] WARN  17:58:23,414 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T00:58Z] WARN  17:58:23,415 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T00:58Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T00:58Z] INFO  17:58:23,443 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T00:58Z] INFO  17:58:23,445 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T00:58Z] INFO  17:58:23,447 ProgressMeter -      5:37107605      1.9570197E7    30.0 s            1.0 s       48.4%    62.0 s      32.0 s
[2016-04-15T00:58Z] INFO  17:58:23,484 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:58Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T00:58Z] INFO  17:58:23,608 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T00:58Z] INFO  17:58:23,612 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T00:58Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T00:58Z] WARN  17:58:23,723 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T00:58Z] WARN  17:58:23,724 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T00:58Z] INFO  17:58:23,734 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T00:58Z] INFO  17:58:23,746 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T00:58Z] GATK: HaplotypeCaller
[2016-04-15T00:58Z] WARN  17:58:24,021 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T00:58Z] WARN  17:58:24,023 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T00:58Z] WARN  17:58:24,256 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T00:58Z] WARN  17:58:24,267 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T00:58Z] INFO  17:58:25,486 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:58Z] GATK: HaplotypeCaller
[2016-04-15T00:58Z] INFO  17:58:26,086 ProgressMeter -      5:63894192      2.1916594E7    30.0 s            1.0 s       82.1%    36.0 s       6.0 s
[2016-04-15T00:58Z] INFO  17:58:27,305 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:58Z] INFO  17:58:27,318 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:58Z] INFO  17:58:27,319 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:58Z] INFO  17:58:27,320 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:58Z] INFO  17:58:27,325 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/6/R14-18105_kapa-NGv3-PE100-NGv3-sort-6_46598699_62284307-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/6/R14-18105_kapa-NGv3-PE100-NGv3-6_46598699_62284307-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/6/tx/tmp5XDOJn/R14-18105_kapa-NGv3-PE100-NGv3-6_46598699_62284307.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:58Z] INFO  17:58:27,348 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:58Z] INFO  17:58:27,349 HelpFormatter - Date/Time: 2016/04/14 17:58:27
[2016-04-15T00:58Z] INFO  17:58:27,350 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:58Z] INFO  17:58:27,350 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:58Z] WARN  17:58:27,397 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T00:58Z] WARN  17:58:27,400 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/6/tx/tmp5XDOJn/R14-18105_kapa-NGv3-PE100-NGv3-6_46598699_62284307.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T00:58Z] INFO  17:58:27,615 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:58Z] INFO  17:58:27,806 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T00:58Z] INFO  17:58:27,820 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:58Z] INFO  17:58:27,910 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.09
[2016-04-15T00:58Z] INFO  17:58:27,928 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T00:58Z] INFO  17:58:28,453 IntervalUtils - Processing 157522 bp from intervals
[2016-04-15T00:58Z] WARN  17:58:28,458 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:58Z] INFO  17:58:28,610 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:58Z] INFO  17:58:28,729 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:58Z] INFO  17:58:28,741 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:58Z] INFO  17:58:28,741 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T00:58Z] INFO  17:58:28,742 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T00:58Z] INFO  17:58:28,751 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T00:58Z] INFO  17:58:28,752 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T00:58Z] INFO  17:58:29,008 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T00:58Z] INFO  17:58:29,257 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:58Z] INFO  17:58:29,260 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:58Z] INFO  17:58:29,260 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:58Z] INFO  17:58:29,260 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:58Z] INFO  17:58:29,264 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/6/R14-18105_kapa-NGv3-PE100-NGv3-sort-6_62390867_78173120-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/6/R14-18105_kapa-NGv3-PE100-NGv3-6_62390867_78173120-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/6/tx/tmpMP6eJb/R14-18105_kapa-NGv3-PE100-NGv3-6_62390867_78173120.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:58Z] INFO  17:58:29,276 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:58Z] INFO  17:58:29,276 HelpFormatter - Date/Time: 2016/04/14 17:58:29
[2016-04-15T00:58Z] INFO  17:58:29,276 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:58Z] INFO  17:58:29,276 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:58Z] WARN  17:58:29,320 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T00:58Z] WARN  17:58:29,333 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/6/tx/tmpMP6eJb/R14-18105_kapa-NGv3-PE100-NGv3-6_62390867_78173120.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T00:58Z] INFO  17:58:29,547 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:58Z] INFO  17:58:29,756 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T00:58Z] INFO  17:58:29,765 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:58Z] INFO  17:58:29,853 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.09
[2016-04-15T00:58Z] INFO  17:58:29,878 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T00:58Z] INFO  17:58:30,449 IntervalUtils - Processing 103397 bp from intervals
[2016-04-15T00:58Z] WARN  17:58:30,454 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:58Z] INFO  17:58:30,595 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:58Z] INFO  17:58:30,684 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:58Z] INFO  17:58:30,686 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:58Z] INFO  17:58:30,686 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T00:58Z] INFO  17:58:30,687 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T00:58Z] INFO  17:58:30,688 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T00:58Z] INFO  17:58:30,688 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T00:58Z] INFO  17:58:30,889 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T00:58Z] INFO  17:58:30,998 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.006307994000000001
[2016-04-15T00:58Z] INFO  17:58:30,999 PairHMM - Total compute time in PairHMM computeLikelihoods() : 0.280580838
[2016-04-15T00:58Z] INFO  17:58:30,999 HaplotypeCaller - Ran local assembly on 843 active regions
[2016-04-15T00:58Z] INFO  17:58:31,056 ProgressMeter -            done      3.3641126E7    34.0 s            1.0 s      100.0%    34.0 s       0.0 s
[2016-04-15T00:58Z] INFO  17:58:31,056 ProgressMeter - Total runtime 34.99 secs, 0.58 min, 0.01 hours
[2016-04-15T00:58Z] INFO  17:58:31,057 MicroScheduler - 10618 reads were filtered out during the traversal out of approximately 132369 total reads (8.02%)
[2016-04-15T00:58Z] INFO  17:58:31,058 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:58Z] INFO  17:58:31,058 MicroScheduler -   -> 10479 reads (7.92% of total) failing DuplicateReadFilter
[2016-04-15T00:58Z] INFO  17:58:31,058 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:58Z] INFO  17:58:31,058 MicroScheduler -   -> 139 reads (0.11% of total) failing HCMappingQualityFilter
[2016-04-15T00:58Z] INFO  17:58:31,059 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:58Z] INFO  17:58:31,059 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:58Z] INFO  17:58:31,059 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:58Z] INFO  17:58:31,059 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:58Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T00:58Z] INFO  17:58:31,773 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T00:58Z] INFO  17:58:31,774 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T00:58Z] WARN  17:58:32,100 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T00:58Z] WARN  17:58:32,101 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T00:58Z] INFO  17:58:32,747 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:58Z] GATK: HaplotypeCaller
[2016-04-15T00:58Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T00:58Z] INFO  17:58:33,187 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T00:58Z] INFO  17:58:33,188 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T00:58Z] WARN  17:58:33,484 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T00:58Z] WARN  17:58:33,484 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T00:58Z] INFO  17:58:33,962 ProgressMeter -      5:73236838      2.0368445E7    30.0 s            1.0 s       43.0%    69.0 s      39.0 s
[2016-04-15T00:58Z] INFO  17:58:34,384 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.004936984
[2016-04-15T00:58Z] INFO  17:58:34,385 PairHMM - Total compute time in PairHMM computeLikelihoods() : 0.13726645
[2016-04-15T00:58Z] INFO  17:58:34,386 HaplotypeCaller - Ran local assembly on 430 active regions
[2016-04-15T00:58Z] INFO  17:58:34,460 ProgressMeter -            done        9535184.0    27.0 s            2.0 s      100.0%    27.0 s       0.0 s
[2016-04-15T00:58Z] INFO  17:58:34,461 ProgressMeter - Total runtime 27.89 secs, 0.46 min, 0.01 hours
[2016-04-15T00:58Z] INFO  17:58:34,461 MicroScheduler - 4690 reads were filtered out during the traversal out of approximately 60497 total reads (7.75%)
[2016-04-15T00:58Z] INFO  17:58:34,462 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:58Z] INFO  17:58:34,462 MicroScheduler -   -> 4630 reads (7.65% of total) failing DuplicateReadFilter
[2016-04-15T00:58Z] INFO  17:58:34,462 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:58Z] INFO  17:58:34,462 MicroScheduler -   -> 60 reads (0.10% of total) failing HCMappingQualityFilter
[2016-04-15T00:58Z] INFO  17:58:34,463 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:58Z] INFO  17:58:34,463 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:58Z] INFO  17:58:34,463 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:58Z] INFO  17:58:34,463 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:58Z] INFO  17:58:34,780 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.021359288
[2016-04-15T00:58Z] INFO  17:58:34,792 PairHMM - Total compute time in PairHMM computeLikelihoods() : 1.3762142210000001
[2016-04-15T00:58Z] INFO  17:58:34,792 HaplotypeCaller - Ran local assembly on 949 active regions
[2016-04-15T00:58Z] INFO  17:58:34,820 ProgressMeter -            done      4.4963609E7    47.0 s            1.0 s      100.0%    47.0 s       0.0 s
[2016-04-15T00:58Z] INFO  17:58:34,821 ProgressMeter - Total runtime 47.63 secs, 0.79 min, 0.01 hours
[2016-04-15T00:58Z] INFO  17:58:34,822 MicroScheduler - 21139 reads were filtered out during the traversal out of approximately 212934 total reads (9.93%)
[2016-04-15T00:58Z] INFO  17:58:34,823 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:58Z] INFO  17:58:34,823 MicroScheduler -   -> 17103 reads (8.03% of total) failing DuplicateReadFilter
[2016-04-15T00:58Z] INFO  17:58:34,824 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:58Z] INFO  17:58:34,825 MicroScheduler -   -> 4036 reads (1.90% of total) failing HCMappingQualityFilter
[2016-04-15T00:58Z] INFO  17:58:34,825 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:58Z] INFO  17:58:34,826 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:58Z] INFO  17:58:34,826 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:58Z] INFO  17:58:34,827 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:58Z] INFO  17:58:35,934 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:58Z] INFO  17:58:36,067 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:58Z] INFO  17:58:36,070 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:58Z] INFO  17:58:36,071 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:58Z] INFO  17:58:36,071 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:58Z] INFO  17:58:36,076 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/6/R14-18105_kapa-NGv3-PE100-NGv3-sort-6_78400388_93953258-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/6/R14-18105_kapa-NGv3-PE100-NGv3-6_78400388_93953258-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/6/tx/tmpNeiRF4/R14-18105_kapa-NGv3-PE100-NGv3-6_78400388_93953258.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:58Z] INFO  17:58:36,085 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:58Z] INFO  17:58:36,086 HelpFormatter - Date/Time: 2016/04/14 17:58:36
[2016-04-15T00:58Z] INFO  17:58:36,087 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:58Z] INFO  17:58:36,087 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:58Z] WARN  17:58:36,110 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T00:58Z] WARN  17:58:36,113 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/6/tx/tmpNeiRF4/R14-18105_kapa-NGv3-PE100-NGv3-6_78400388_93953258.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T00:58Z] GATK: HaplotypeCaller
[2016-04-15T00:58Z] INFO  17:58:36,288 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:58Z] INFO  17:58:36,355 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:58Z] INFO  17:58:36,513 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T00:58Z] INFO  17:58:36,500 ProgressMeter -      5:93807171      1.0445829E7    30.0 s            2.0 s       62.9%    47.0 s      17.0 s
[2016-04-15T00:58Z] INFO  17:58:36,523 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:58Z] INFO  17:58:36,601 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-15T00:58Z] GATK: HaplotypeCaller
[2016-04-15T00:58Z] INFO  17:58:36,640 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T00:58Z] INFO  17:58:36,878 ProgressMeter -     5:122130961      1.1354936E7    30.0 s            2.0 s       65.4%    45.0 s      15.0 s
[2016-04-15T00:58Z] INFO  17:58:37,132 IntervalUtils - Processing 131721 bp from intervals
[2016-04-15T00:58Z] WARN  17:58:37,152 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:58Z] INFO  17:58:37,302 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:58Z] INFO  17:58:37,391 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:58Z] INFO  17:58:37,395 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:58Z] INFO  17:58:37,397 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T00:58Z] INFO  17:58:37,397 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T00:58Z] INFO  17:58:37,398 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T00:58Z] INFO  17:58:37,398 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T00:58Z] INFO  17:58:37,613 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T00:58Z] INFO  17:58:38,187 ProgressMeter -     5:133862076       1.730355E7    30.0 s            1.0 s       21.0%     2.4 m     112.0 s
[2016-04-15T00:58Z] INFO  17:58:39,692 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:58Z] INFO  17:58:39,708 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:58Z] INFO  17:58:39,709 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:58Z] INFO  17:58:39,710 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:58Z] INFO  17:58:39,733 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/6/R14-18105_kapa-NGv3-PE100-NGv3-sort-6_93955015_109466584-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/6/R14-18105_kapa-NGv3-PE100-NGv3-6_93955015_109466584-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/6/tx/tmploFjMg/R14-18105_kapa-NGv3-PE100-NGv3-6_93955015_109466584.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:58Z] INFO  17:58:39,758 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:58Z] INFO  17:58:39,759 HelpFormatter - Date/Time: 2016/04/14 17:58:39
[2016-04-15T00:58Z] INFO  17:58:39,759 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:58Z] INFO  17:58:39,759 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:58Z] WARN  17:58:39,785 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T00:58Z] WARN  17:58:39,788 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/6/tx/tmploFjMg/R14-18105_kapa-NGv3-PE100-NGv3-6_93955015_109466584.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T00:58Z] INFO  17:58:39,827 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:58Z] INFO  17:58:39,831 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:58Z] INFO  17:58:39,832 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:58Z] INFO  17:58:39,832 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:58Z] INFO  17:58:39,837 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/6/R14-18105_kapa-NGv3-PE100-NGv3-sort-6_109467960_124979532-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/6/R14-18105_kapa-NGv3-PE100-NGv3-6_109467960_124979532-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/6/tx/tmpAuLLkP/R14-18105_kapa-NGv3-PE100-NGv3-6_109467960_124979532.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:58Z] INFO  17:58:39,849 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:58Z] INFO  17:58:39,849 HelpFormatter - Date/Time: 2016/04/14 17:58:39
[2016-04-15T00:58Z] INFO  17:58:39,849 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:58Z] INFO  17:58:39,850 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:58Z] WARN  17:58:39,909 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T00:58Z] WARN  17:58:39,912 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/6/tx/tmpAuLLkP/R14-18105_kapa-NGv3-PE100-NGv3-6_109467960_124979532.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T00:58Z] INFO  17:58:39,957 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:58Z] INFO  17:58:40,100 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:58Z] INFO  17:58:40,178 ProgressMeter -     5:149227021      1.2290756E7    30.0 s            2.0 s       34.2%    87.0 s      57.0 s
[2016-04-15T00:58Z] INFO  17:58:40,191 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T00:58Z] INFO  17:58:40,213 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:58Z] INFO  17:58:40,297 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T00:58Z] INFO  17:58:40,307 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:58Z] INFO  17:58:40,322 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.11
[2016-04-15T00:58Z] INFO  17:58:40,347 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T00:58Z] INFO  17:58:40,420 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.11
[2016-04-15T00:58Z] INFO  17:58:40,454 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T00:58Z] INFO  17:58:40,634 IntervalUtils - Processing 95525 bp from intervals
[2016-04-15T00:58Z] WARN  17:58:40,639 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:58Z] INFO  17:58:40,728 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:58Z] INFO  17:58:40,793 IntervalUtils - Processing 147815 bp from intervals
[2016-04-15T00:58Z] WARN  17:58:40,799 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:58Z] INFO  17:58:40,823 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:58Z] INFO  17:58:40,824 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:58Z] INFO  17:58:40,825 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T00:58Z] INFO  17:58:40,826 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T00:58Z] INFO  17:58:40,831 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T00:58Z] INFO  17:58:40,831 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T00:58Z] INFO  17:58:40,888 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:58Z] INFO  17:58:40,982 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:58Z] INFO  17:58:40,983 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:58Z] INFO  17:58:40,984 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T00:58Z] INFO  17:58:40,985 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T00:58Z] INFO  17:58:40,985 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T00:58Z] INFO  17:58:40,986 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T00:58Z] INFO  17:58:41,048 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T00:58Z] INFO  17:58:41,154 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T00:58Z] INFO  17:58:42,618 ProgressMeter -     5:170736708      1.5979312E7    30.0 s            1.0 s       67.7%    44.0 s      14.0 s
[2016-04-15T00:58Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T00:58Z] INFO  17:58:42,804 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T00:58Z] INFO  17:58:42,805 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T00:58Z] WARN  17:58:43,044 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T00:58Z] WARN  17:58:43,044 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T00:58Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T00:58Z] INFO  17:58:43,525 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T00:58Z] INFO  17:58:43,527 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T00:58Z] WARN  17:58:43,795 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T00:58Z] WARN  17:58:43,796 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T00:58Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T00:58Z] INFO  17:58:44,295 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T00:58Z] INFO  17:58:44,296 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T00:58Z] WARN  17:58:44,565 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T00:58Z] WARN  17:58:44,565 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T00:58Z] INFO  17:58:44,715 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.033702082
[2016-04-15T00:58Z] INFO  17:58:44,715 PairHMM - Total compute time in PairHMM computeLikelihoods() : 0.388927593
[2016-04-15T00:58Z] INFO  17:58:44,716 HaplotypeCaller - Ran local assembly on 1314 active regions
[2016-04-15T00:58Z] INFO  17:58:44,752 ProgressMeter -            done      8.6588753E7    51.0 s            0.0 s      100.0%    51.0 s       0.0 s
[2016-04-15T00:58Z] INFO  17:58:44,753 ProgressMeter - Total runtime 51.34 secs, 0.86 min, 0.01 hours
[2016-04-15T00:58Z] INFO  17:58:44,754 MicroScheduler - 17894 reads were filtered out during the traversal out of approximately 226538 total reads (7.90%)
[2016-04-15T00:58Z] INFO  17:58:44,754 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:58Z] INFO  17:58:44,755 MicroScheduler -   -> 17650 reads (7.79% of total) failing DuplicateReadFilter
[2016-04-15T00:58Z] INFO  17:58:44,756 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:58Z] INFO  17:58:44,758 MicroScheduler -   -> 244 reads (0.11% of total) failing HCMappingQualityFilter
[2016-04-15T00:58Z] INFO  17:58:44,759 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:58Z] INFO  17:58:44,759 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:58Z] INFO  17:58:44,760 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:58Z] INFO  17:58:44,760 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:58Z] INFO  17:58:45,231 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.029530658
[2016-04-15T00:58Z] INFO  17:58:45,231 PairHMM - Total compute time in PairHMM computeLikelihoods() : 0.6711197130000001
[2016-04-15T00:58Z] INFO  17:58:45,231 HaplotypeCaller - Ran local assembly on 809 active regions
[2016-04-15T00:58Z] INFO  17:58:45,293 ProgressMeter -            done      3.2848972E7    38.0 s            1.0 s      100.0%    38.0 s       0.0 s
[2016-04-15T00:58Z] INFO  17:58:45,294 ProgressMeter - Total runtime 38.81 secs, 0.65 min, 0.01 hours
[2016-04-15T00:58Z] INFO  17:58:45,294 MicroScheduler - 10320 reads were filtered out during the traversal out of approximately 130591 total reads (7.90%)
[2016-04-15T00:58Z] INFO  17:58:45,295 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:58Z] INFO  17:58:45,295 MicroScheduler -   -> 10175 reads (7.79% of total) failing DuplicateReadFilter
[2016-04-15T00:58Z] INFO  17:58:45,295 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:58Z] INFO  17:58:45,295 MicroScheduler -   -> 145 reads (0.11% of total) failing HCMappingQualityFilter
[2016-04-15T00:58Z] INFO  17:58:45,296 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:58Z] INFO  17:58:45,296 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:58Z] INFO  17:58:45,296 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:58Z] INFO  17:58:45,296 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:58Z] INFO  17:58:45,919 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.007547647
[2016-04-15T00:58Z] INFO  17:58:45,920 PairHMM - Total compute time in PairHMM computeLikelihoods() : 0.959751067
[2016-04-15T00:58Z] INFO  17:58:45,921 HaplotypeCaller - Ran local assembly on 763 active regions
[2016-04-15T00:58Z] INFO  17:58:45,968 ProgressMeter -            done      2.8586597E7    39.0 s            1.0 s      100.0%    39.0 s       0.0 s
[2016-04-15T00:58Z] INFO  17:58:45,968 ProgressMeter - Total runtime 39.10 secs, 0.65 min, 0.01 hours
[2016-04-15T00:58Z] INFO  17:58:45,969 MicroScheduler - 10776 reads were filtered out during the traversal out of approximately 134761 total reads (8.00%)
[2016-04-15T00:58Z] INFO  17:58:45,970 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:58Z] INFO  17:58:45,970 MicroScheduler -   -> 10658 reads (7.91% of total) failing DuplicateReadFilter
[2016-04-15T00:58Z] INFO  17:58:45,970 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:58Z] INFO  17:58:45,970 MicroScheduler -   -> 118 reads (0.09% of total) failing HCMappingQualityFilter
[2016-04-15T00:58Z] INFO  17:58:45,971 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:58Z] INFO  17:58:45,971 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:58Z] INFO  17:58:45,971 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:58Z] INFO  17:58:45,971 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:58Z] INFO  17:58:46,094 ProgressMeter -     5:177652430      1.3193134E7    30.0 s            2.0 s       48.6%    61.0 s      31.0 s
[2016-04-15T00:58Z] INFO  17:58:46,189 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:58Z] GATK: HaplotypeCaller
[2016-04-15T00:58Z] INFO  17:58:46,763 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:58Z] GATK: HaplotypeCaller
[2016-04-15T00:58Z] INFO  17:58:47,319 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:58Z] GATK: HaplotypeCaller
[2016-04-15T00:58Z] INFO  17:58:48,396 ProgressMeter -       6:7569419       1.158049E7    30.0 s            2.0 s       50.1%    59.0 s      29.0 s
[2016-04-15T00:58Z] INFO  17:58:49,460 ProgressMeter -      6:25652632      1.4023051E7    30.0 s            2.0 s       29.3%   102.0 s      72.0 s
[2016-04-15T00:58Z] INFO  17:58:49,699 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:58Z] INFO  17:58:49,702 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:58Z] INFO  17:58:49,703 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:58Z] INFO  17:58:49,703 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:58Z] INFO  17:58:49,708 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/6/R14-18105_kapa-NGv3-PE100-NGv3-sort-6_125112484_142397186-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/6/R14-18105_kapa-NGv3-PE100-NGv3-6_125112484_142397186-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/6/tx/tmpKenGkl/R14-18105_kapa-NGv3-PE100-NGv3-6_125112484_142397186.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:58Z] INFO  17:58:49,723 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:58Z] INFO  17:58:49,724 HelpFormatter - Date/Time: 2016/04/14 17:58:49
[2016-04-15T00:58Z] INFO  17:58:49,725 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:58Z] INFO  17:58:49,726 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:58Z] WARN  17:58:49,770 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T00:58Z] WARN  17:58:49,786 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/6/tx/tmpKenGkl/R14-18105_kapa-NGv3-PE100-NGv3-6_125112484_142397186.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T00:58Z] INFO  17:58:50,077 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:58Z] INFO  17:58:50,284 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T00:58Z] INFO  17:58:50,294 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:58Z] INFO  17:58:50,330 ProgressMeter -      6:31549345         703126.0    30.0 s           42.0 s        3.8%    13.1 m      12.6 m
[2016-04-15T00:58Z] INFO  17:58:50,422 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.12
[2016-04-15T00:58Z] INFO  17:58:50,449 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T00:58Z] INFO  17:58:50,727 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:58Z] INFO  17:58:50,729 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:58Z] INFO  17:58:50,730 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:58Z] INFO  17:58:50,730 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:58Z] INFO  17:58:50,734 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/6/R14-18105_kapa-NGv3-PE100-NGv3-sort-6_142399691_157963777-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/6/R14-18105_kapa-NGv3-PE100-NGv3-6_142399691_157963777-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/6/tx/tmpn9jV8Q/R14-18105_kapa-NGv3-PE100-NGv3-6_142399691_157963777.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:58Z] INFO  17:58:50,760 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:58Z] INFO  17:58:50,760 HelpFormatter - Date/Time: 2016/04/14 17:58:50
[2016-04-15T00:58Z] INFO  17:58:50,760 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:58Z] INFO  17:58:50,761 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:58Z] WARN  17:58:50,810 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T00:58Z] WARN  17:58:50,816 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/6/tx/tmpn9jV8Q/R14-18105_kapa-NGv3-PE100-NGv3-6_142399691_157963777.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T00:58Z] INFO  17:58:50,889 IntervalUtils - Processing 156964 bp from intervals
[2016-04-15T00:58Z] WARN  17:58:50,895 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:58Z] INFO  17:58:50,958 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:58Z] INFO  17:58:50,961 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:58Z] INFO  17:58:50,962 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:58Z] INFO  17:58:50,962 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:58Z] INFO  17:58:50,967 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/6/R14-18105_kapa-NGv3-PE100-NGv3-sort-6_158013810_171115067-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/6/R14-18105_kapa-NGv3-PE100-NGv3-6_158013810_171115067-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/6/tx/tmpFouyeK/R14-18105_kapa-NGv3-PE100-NGv3-6_158013810_171115067.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:58Z] INFO  17:58:50,981 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:58Z] INFO  17:58:50,982 HelpFormatter - Date/Time: 2016/04/14 17:58:50
[2016-04-15T00:58Z] INFO  17:58:50,982 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:58Z] INFO  17:58:50,983 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:58Z] INFO  17:58:51,007 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:58Z] WARN  17:58:51,039 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T00:58Z] WARN  17:58:51,041 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/6/tx/tmpFouyeK/R14-18105_kapa-NGv3-PE100-NGv3-6_158013810_171115067.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T00:58Z] INFO  17:58:51,055 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:58Z] INFO  17:58:51,125 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:58Z] INFO  17:58:51,137 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:58Z] INFO  17:58:51,138 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T00:58Z] INFO  17:58:51,139 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T00:58Z] INFO  17:58:51,147 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T00:58Z] INFO  17:58:51,147 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T00:58Z] INFO  17:58:51,264 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:58Z] INFO  17:58:51,264 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T00:58Z] INFO  17:58:51,289 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:58Z] INFO  17:58:51,380 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.09
[2016-04-15T00:58Z] INFO  17:58:51,409 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T00:58Z] INFO  17:58:51,410 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T00:58Z] INFO  17:58:51,455 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T00:58Z] INFO  17:58:51,464 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:58Z] INFO  17:58:51,553 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.09
[2016-04-15T00:58Z] INFO  17:58:51,589 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T00:58Z] INFO  17:58:51,809 IntervalUtils - Processing 183871 bp from intervals
[2016-04-15T00:58Z] WARN  17:58:51,815 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:58Z] INFO  17:58:51,907 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:58Z] INFO  17:58:52,011 IntervalUtils - Processing 143202 bp from intervals
[2016-04-15T00:58Z] WARN  17:58:52,016 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:58Z] INFO  17:58:52,036 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:58Z] INFO  17:58:52,037 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:58Z] INFO  17:58:52,038 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T00:58Z] INFO  17:58:52,038 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T00:58Z] INFO  17:58:52,039 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T00:58Z] INFO  17:58:52,039 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T00:58Z] INFO  17:58:52,121 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:58Z] INFO  17:58:52,246 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:58Z] INFO  17:58:52,247 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:58Z] INFO  17:58:52,247 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T00:58Z] INFO  17:58:52,248 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T00:58Z] INFO  17:58:52,249 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T00:58Z] INFO  17:58:52,249 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T00:58Z] INFO  17:58:52,274 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T00:58Z] INFO  17:58:52,485 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T00:58Z] INFO  17:58:54,532 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.007948984000000001
[2016-04-15T00:58Z] INFO  17:58:54,533 PairHMM - Total compute time in PairHMM computeLikelihoods() : 2.583297609
[2016-04-15T00:58Z] INFO  17:58:54,534 HaplotypeCaller - Ran local assembly on 770 active regions
[2016-04-15T00:58Z] INFO  17:58:54,577 ProgressMeter -            done      2.8976366E7    41.0 s            1.0 s      100.0%    41.0 s       0.0 s
[2016-04-15T00:58Z] INFO  17:58:54,578 ProgressMeter - Total runtime 41.98 secs, 0.70 min, 0.01 hours
[2016-04-15T00:58Z] INFO  17:58:54,578 MicroScheduler - 13458 reads were filtered out during the traversal out of approximately 163955 total reads (8.21%)
[2016-04-15T00:58Z] INFO  17:58:54,578 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:58Z] INFO  17:58:54,590 MicroScheduler -   -> 13279 reads (8.10% of total) failing DuplicateReadFilter
[2016-04-15T00:58Z] INFO  17:58:54,590 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:58Z] INFO  17:58:54,590 MicroScheduler -   -> 179 reads (0.11% of total) failing HCMappingQualityFilter
[2016-04-15T00:58Z] INFO  17:58:54,590 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:58Z] INFO  17:58:54,591 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:58Z] INFO  17:58:54,591 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:58Z] INFO  17:58:54,591 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:58Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T00:58Z] INFO  17:58:55,391 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T00:58Z] INFO  17:58:55,392 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T00:58Z] WARN  17:58:55,714 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T00:58Z] WARN  17:58:55,716 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T00:58Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T00:58Z] INFO  17:58:55,962 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T00:58Z] INFO  17:58:55,963 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T00:58Z] INFO  17:58:56,125 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:58Z] WARN  17:58:56,191 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T00:58Z] WARN  17:58:56,192 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T00:58Z] GATK: HaplotypeCaller
[2016-04-15T00:58Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T00:58Z] INFO  17:58:57,245 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T00:58Z] INFO  17:58:57,246 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T00:58Z] INFO  17:58:57,639 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.01101007
[2016-04-15T00:58Z] INFO  17:58:57,640 PairHMM - Total compute time in PairHMM computeLikelihoods() : 0.755452242
[2016-04-15T00:58Z] INFO  17:58:57,641 HaplotypeCaller - Ran local assembly on 1491 active regions
[2016-04-15T00:58Z] WARN  17:58:57,680 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T00:58Z] WARN  17:58:57,681 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T00:58Z] INFO  17:58:57,704 ProgressMeter -            done     1.03497862E8    53.0 s            0.0 s      100.0%    53.0 s       0.0 s
[2016-04-15T00:58Z] INFO  17:58:57,704 ProgressMeter - Total runtime 53.77 secs, 0.90 min, 0.01 hours
[2016-04-15T00:58Z] INFO  17:58:57,705 MicroScheduler - 31444 reads were filtered out during the traversal out of approximately 247055 total reads (12.73%)
[2016-04-15T00:58Z] INFO  17:58:57,705 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:58Z] INFO  17:58:57,706 MicroScheduler -   -> 18009 reads (7.29% of total) failing DuplicateReadFilter
[2016-04-15T00:58Z] INFO  17:58:57,706 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:58Z] INFO  17:58:57,706 MicroScheduler -   -> 13435 reads (5.44% of total) failing HCMappingQualityFilter
[2016-04-15T00:58Z] INFO  17:58:57,706 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:58Z] INFO  17:58:57,706 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:58Z] INFO  17:58:57,707 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:58Z] INFO  17:58:57,707 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:58Z] INFO  17:58:58,757 ProgressMeter -      6:54002594      2.1967485E7    30.0 s            1.0 s       56.9%    52.0 s      22.0 s
[2016-04-15T00:58Z] INFO  17:58:59,106 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:58Z] GATK: HaplotypeCaller
[2016-04-15T00:58Z] INFO  17:58:59,453 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:58Z] INFO  17:58:59,456 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:58Z] INFO  17:58:59,456 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:58Z] INFO  17:58:59,457 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:58Z] INFO  17:58:59,462 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/7/R14-18105_kapa-NGv3-PE100-NGv3-sort-7_0_15584548-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/7/R14-18105_kapa-NGv3-PE100-NGv3-7_0_15584548-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/7/tx/tmpPuhBs3/R14-18105_kapa-NGv3-PE100-NGv3-7_0_15584548.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:58Z] INFO  17:58:59,475 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:58Z] INFO  17:58:59,475 HelpFormatter - Date/Time: 2016/04/14 17:58:59
[2016-04-15T00:58Z] INFO  17:58:59,476 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:58Z] INFO  17:58:59,476 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:58Z] WARN  17:58:59,521 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T00:58Z] WARN  17:58:59,524 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/7/tx/tmpPuhBs3/R14-18105_kapa-NGv3-PE100-NGv3-7_0_15584548.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T00:58Z] INFO  17:58:59,719 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:58Z] INFO  17:58:59,962 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T00:58Z] INFO  17:58:59,983 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:59Z] INFO  17:59:00,114 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.13
[2016-04-15T00:59Z] INFO  17:59:00,139 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T00:59Z] INFO  17:59:00,505 IntervalUtils - Processing 187602 bp from intervals
[2016-04-15T00:59Z] WARN  17:59:00,510 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:59Z] INFO  17:59:00,633 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:59Z] INFO  17:59:00,702 ProgressMeter -      6:76657031      2.7947838E7    30.0 s            1.0 s       96.9%    30.0 s       0.0 s
[2016-04-15T00:59Z] INFO  17:59:00,767 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:59Z] INFO  17:59:00,768 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:59Z] INFO  17:59:00,768 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T00:59Z] INFO  17:59:00,769 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T00:59Z] INFO  17:59:00,770 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T00:59Z] INFO  17:59:00,770 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T00:59Z] INFO  17:59:00,961 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T00:59Z] INFO  17:59:01,976 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.034280585
[2016-04-15T00:59Z] INFO  17:59:01,977 PairHMM - Total compute time in PairHMM computeLikelihoods() : 0.32241421000000003
[2016-04-15T00:59Z] INFO  17:59:01,978 HaplotypeCaller - Ran local assembly on 772 active regions
[2016-04-15T00:59Z] INFO  17:59:02,035 ProgressMeter -            done      2.9471788E7    31.0 s            1.0 s      100.0%    31.0 s       0.0 s
[2016-04-15T00:59Z] INFO  17:59:02,035 ProgressMeter - Total runtime 31.35 secs, 0.52 min, 0.01 hours
[2016-04-15T00:59Z] INFO  17:59:02,036 MicroScheduler - 11261 reads were filtered out during the traversal out of approximately 122409 total reads (9.20%)
[2016-04-15T00:59Z] INFO  17:59:02,037 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:59Z] INFO  17:59:02,037 MicroScheduler -   -> 9490 reads (7.75% of total) failing DuplicateReadFilter
[2016-04-15T00:59Z] INFO  17:59:02,037 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:59Z] INFO  17:59:02,037 MicroScheduler -   -> 1771 reads (1.45% of total) failing HCMappingQualityFilter
[2016-04-15T00:59Z] INFO  17:59:02,038 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:59Z] INFO  17:59:02,038 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:59Z] INFO  17:59:02,038 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:59Z] INFO  17:59:02,038 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:59Z] INFO  17:59:02,497 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:59Z] INFO  17:59:02,500 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:59Z] INFO  17:59:02,501 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:59Z] INFO  17:59:02,501 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:59Z] INFO  17:59:02,506 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/7/R14-18105_kapa-NGv3-PE100-NGv3-sort-7_15599765_31117713-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/7/R14-18105_kapa-NGv3-PE100-NGv3-7_15599765_31117713-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/7/tx/tmpmknkCm/R14-18105_kapa-NGv3-PE100-NGv3-7_15599765_31117713.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:59Z] INFO  17:59:02,524 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:59Z] INFO  17:59:02,524 HelpFormatter - Date/Time: 2016/04/14 17:59:02
[2016-04-15T00:59Z] INFO  17:59:02,525 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:59Z] INFO  17:59:02,525 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:59Z] WARN  17:59:02,571 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T00:59Z] WARN  17:59:02,573 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/7/tx/tmpmknkCm/R14-18105_kapa-NGv3-PE100-NGv3-7_15599765_31117713.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T00:59Z] INFO  17:59:02,821 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:59Z] INFO  17:59:03,045 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T00:59Z] INFO  17:59:03,059 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:59Z] INFO  17:59:03,153 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.09
[2016-04-15T00:59Z] INFO  17:59:03,184 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T00:59Z] INFO  17:59:03,466 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:59Z] INFO  17:59:03,636 IntervalUtils - Processing 149727 bp from intervals
[2016-04-15T00:59Z] WARN  17:59:03,641 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:59Z] INFO  17:59:03,725 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:59Z] INFO  17:59:03,794 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:59Z] INFO  17:59:03,796 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:59Z] INFO  17:59:03,796 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T00:59Z] INFO  17:59:03,797 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T00:59Z] INFO  17:59:03,798 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T00:59Z] INFO  17:59:03,798 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T00:59Z] GATK: HaplotypeCaller
[2016-04-15T00:59Z] INFO  17:59:04,045 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T00:59Z] INFO  17:59:04,646 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.012110172
[2016-04-15T00:59Z] INFO  17:59:04,658 PairHMM - Total compute time in PairHMM computeLikelihoods() : 0.8973705780000001
[2016-04-15T00:59Z] INFO  17:59:04,658 HaplotypeCaller - Ran local assembly on 983 active regions
[2016-04-15T00:59Z] INFO  17:59:04,693 ProgressMeter -            done      4.2296058E7    46.0 s            1.0 s      100.0%    46.0 s       0.0 s
[2016-04-15T00:59Z] INFO  17:59:04,694 ProgressMeter - Total runtime 46.33 secs, 0.77 min, 0.01 hours
[2016-04-15T00:59Z] INFO  17:59:04,694 MicroScheduler - 22934 reads were filtered out during the traversal out of approximately 202093 total reads (11.35%)
[2016-04-15T00:59Z] INFO  17:59:04,695 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:59Z] INFO  17:59:04,696 MicroScheduler -   -> 15842 reads (7.84% of total) failing DuplicateReadFilter
[2016-04-15T00:59Z] INFO  17:59:04,696 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:59Z] INFO  17:59:04,697 MicroScheduler -   -> 7092 reads (3.51% of total) failing HCMappingQualityFilter
[2016-04-15T00:59Z] INFO  17:59:04,697 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:59Z] INFO  17:59:04,698 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:59Z] INFO  17:59:04,699 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:59Z] INFO  17:59:04,699 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:59Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T00:59Z] INFO  17:59:05,563 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T00:59Z] INFO  17:59:05,564 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T00:59Z] INFO  17:59:05,605 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.015918294
[2016-04-15T00:59Z] INFO  17:59:05,619 PairHMM - Total compute time in PairHMM computeLikelihoods() : 1.250986575
[2016-04-15T00:59Z] INFO  17:59:05,620 HaplotypeCaller - Ran local assembly on 1199 active regions
[2016-04-15T00:59Z] INFO  17:59:05,674 ProgressMeter -            done      5.3274727E7    49.0 s            0.0 s      100.0%    49.0 s       0.0 s
[2016-04-15T00:59Z] INFO  17:59:05,674 ProgressMeter - Total runtime 49.60 secs, 0.83 min, 0.01 hours
[2016-04-15T00:59Z] INFO  17:59:05,674 MicroScheduler - 34697 reads were filtered out during the traversal out of approximately 290019 total reads (11.96%)
[2016-04-15T00:59Z] INFO  17:59:05,675 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:59Z] INFO  17:59:05,675 MicroScheduler -   -> 22436 reads (7.74% of total) failing DuplicateReadFilter
[2016-04-15T00:59Z] INFO  17:59:05,675 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:59Z] INFO  17:59:05,675 MicroScheduler -   -> 12261 reads (4.23% of total) failing HCMappingQualityFilter
[2016-04-15T00:59Z] INFO  17:59:05,676 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:59Z] INFO  17:59:05,676 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:59Z] INFO  17:59:05,676 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:59Z] INFO  17:59:05,676 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:59Z] INFO  17:59:05,935 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:59Z] WARN  17:59:05,979 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T00:59Z] WARN  17:59:06,002 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T00:59Z] GATK: HaplotypeCaller
[2016-04-15T00:59Z] INFO  17:59:06,867 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:59Z] INFO  17:59:06,870 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:59Z] INFO  17:59:06,871 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:59Z] INFO  17:59:06,872 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:59Z] INFO  17:59:06,876 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/7/R14-18105_kapa-NGv3-PE100-NGv3-sort-7_31120227_47317818-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/7/R14-18105_kapa-NGv3-PE100-NGv3-7_31120227_47317818-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/7/tx/tmp6GirR4/R14-18105_kapa-NGv3-PE100-NGv3-7_31120227_47317818.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:59Z] INFO  17:59:06,887 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:59Z] INFO  17:59:06,895 HelpFormatter - Date/Time: 2016/04/14 17:59:06
[2016-04-15T00:59Z] INFO  17:59:06,895 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:59Z] INFO  17:59:06,896 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:59Z] WARN  17:59:06,930 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T00:59Z] WARN  17:59:06,933 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/7/tx/tmp6GirR4/R14-18105_kapa-NGv3-PE100-NGv3-7_31120227_47317818.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T00:59Z] INFO  17:59:07,039 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:59Z] INFO  17:59:07,152 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:59Z] INFO  17:59:07,351 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T00:59Z] INFO  17:59:07,364 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:59Z] INFO  17:59:07,408 ProgressMeter -      6:90121712      2.5092156E7    30.0 s            1.0 s       75.5%    39.0 s       9.0 s
[2016-04-15T00:59Z] GATK: HaplotypeCaller
[2016-04-15T00:59Z] INFO  17:59:07,467 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.09
[2016-04-15T00:59Z] INFO  17:59:07,490 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T00:59Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T00:59Z] INFO  17:59:07,828 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T00:59Z] INFO  17:59:07,840 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T00:59Z] INFO  17:59:07,901 IntervalUtils - Processing 138106 bp from intervals
[2016-04-15T00:59Z] WARN  17:59:07,906 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:59Z] INFO  17:59:08,003 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:59Z] INFO  17:59:08,120 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:59Z] INFO  17:59:08,121 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:59Z] INFO  17:59:08,122 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T00:59Z] INFO  17:59:08,122 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T00:59Z] INFO  17:59:08,123 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T00:59Z] INFO  17:59:08,123 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T00:59Z] INFO  17:59:08,197 ProgressMeter -     5:140187300     1.08321246E8    60.0 s            0.0 s       56.4%   106.0 s      46.0 s
[2016-04-15T00:59Z] INFO  17:59:08,297 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T00:59Z] WARN  17:59:08,568 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T00:59Z] WARN  17:59:08,569 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T00:59Z] INFO  17:59:08,994 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.010441369
[2016-04-15T00:59Z] INFO  17:59:08,995 PairHMM - Total compute time in PairHMM computeLikelihoods() : 0.285289053
[2016-04-15T00:59Z] INFO  17:59:08,996 HaplotypeCaller - Ran local assembly on 679 active regions
[2016-04-15T00:59Z] INFO  17:59:09,042 ProgressMeter -            done      2.2700296E7    28.0 s            1.0 s      100.0%    28.0 s       0.0 s
[2016-04-15T00:59Z] INFO  17:59:09,043 ProgressMeter - Total runtime 28.22 secs, 0.47 min, 0.01 hours
[2016-04-15T00:59Z] INFO  17:59:09,044 MicroScheduler - 9779 reads were filtered out during the traversal out of approximately 112758 total reads (8.67%)
[2016-04-15T00:59Z] INFO  17:59:09,045 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:59Z] INFO  17:59:09,045 MicroScheduler -   -> 8734 reads (7.75% of total) failing DuplicateReadFilter
[2016-04-15T00:59Z] INFO  17:59:09,047 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:59Z] INFO  17:59:09,048 MicroScheduler -   -> 1045 reads (0.93% of total) failing HCMappingQualityFilter
[2016-04-15T00:59Z] INFO  17:59:09,048 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:59Z] INFO  17:59:09,049 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:59Z] INFO  17:59:09,050 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:59Z] INFO  17:59:09,050 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:59Z] INFO  17:59:09,415 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:59Z] INFO  17:59:09,418 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:59Z] INFO  17:59:09,419 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:59Z] INFO  17:59:09,420 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:59Z] INFO  17:59:09,424 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/7/R14-18105_kapa-NGv3-PE100-NGv3-sort-7_47319761_63093154-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/7/R14-18105_kapa-NGv3-PE100-NGv3-7_47319761_63093154-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/7/tx/tmpabwLUI/R14-18105_kapa-NGv3-PE100-NGv3-7_47319761_63093154.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:59Z] INFO  17:59:09,434 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:59Z] INFO  17:59:09,445 HelpFormatter - Date/Time: 2016/04/14 17:59:09
[2016-04-15T00:59Z] INFO  17:59:09,446 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:59Z] INFO  17:59:09,447 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:59Z] WARN  17:59:09,490 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T00:59Z] WARN  17:59:09,493 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/7/tx/tmpabwLUI/R14-18105_kapa-NGv3-PE100-NGv3-7_47319761_63093154.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T00:59Z] INFO  17:59:09,770 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:59Z] INFO  17:59:10,003 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T00:59Z] INFO  17:59:10,023 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:59Z] INFO  17:59:10,093 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-15T00:59Z] INFO  17:59:10,123 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T00:59Z] INFO  17:59:10,179 ProgressMeter -     5:156905951      8.5852586E7    60.0 s            0.0 s       91.4%    65.0 s       5.0 s
[2016-04-15T00:59Z] INFO  17:59:10,335 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:59Z] INFO  17:59:10,536 IntervalUtils - Processing 74873 bp from intervals
[2016-04-15T00:59Z] WARN  17:59:10,541 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:59Z] GATK: HaplotypeCaller
[2016-04-15T00:59Z] INFO  17:59:10,682 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:59Z] INFO  17:59:10,755 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:59Z] INFO  17:59:10,756 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:59Z] INFO  17:59:10,756 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T00:59Z] INFO  17:59:10,757 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T00:59Z] INFO  17:59:10,769 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T00:59Z] INFO  17:59:10,770 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T00:59Z] INFO  17:59:10,778 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:59Z] INFO  17:59:10,781 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:59Z] INFO  17:59:10,782 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:59Z] INFO  17:59:10,782 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:59Z] INFO  17:59:10,787 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/7/R14-18105_kapa-NGv3-PE100-NGv3-sort-7_63095909_78636522-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/7/R14-18105_kapa-NGv3-PE100-NGv3-7_63095909_78636522-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/7/tx/tmpVEPQB6/R14-18105_kapa-NGv3-PE100-NGv3-7_63095909_78636522.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:59Z] INFO  17:59:10,795 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:59Z] INFO  17:59:10,796 HelpFormatter - Date/Time: 2016/04/14 17:59:10
[2016-04-15T00:59Z] INFO  17:59:10,796 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:59Z] INFO  17:59:10,796 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:59Z] WARN  17:59:10,839 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T00:59Z] WARN  17:59:10,842 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/7/tx/tmpVEPQB6/R14-18105_kapa-NGv3-PE100-NGv3-7_63095909_78636522.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T00:59Z] INFO  17:59:10,973 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T00:59Z] INFO  17:59:10,993 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:59Z] INFO  17:59:10,995 ProgressMeter -     6:117709176      2.4080517E7    30.0 s            1.0 s       68.3%    43.0 s      13.0 s
[2016-04-15T00:59Z] INFO  17:59:11,237 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T00:59Z] INFO  17:59:11,266 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:59Z] INFO  17:59:11,361 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.09
[2016-04-15T00:59Z] INFO  17:59:11,376 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T00:59Z] INFO  17:59:11,759 IntervalUtils - Processing 152751 bp from intervals
[2016-04-15T00:59Z] WARN  17:59:11,764 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:59Z] INFO  17:59:11,921 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:59Z] INFO  17:59:12,057 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:59Z] INFO  17:59:12,059 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:59Z] INFO  17:59:12,060 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T00:59Z] INFO  17:59:12,061 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T00:59Z] INFO  17:59:12,071 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T00:59Z] INFO  17:59:12,072 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T00:59Z] INFO  17:59:12,262 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T00:59Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T00:59Z] INFO  17:59:13,313 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T00:59Z] INFO  17:59:13,314 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T00:59Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T00:59Z] INFO  17:59:13,447 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T00:59Z] INFO  17:59:13,447 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T00:59Z] WARN  17:59:13,530 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T00:59Z] WARN  17:59:13,532 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T00:59Z] INFO  17:59:13,554 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.025100764
[2016-04-15T00:59Z] INFO  17:59:13,555 PairHMM - Total compute time in PairHMM computeLikelihoods() : 2.2027226140000002
[2016-04-15T00:59Z] INFO  17:59:13,556 HaplotypeCaller - Ran local assembly on 1490 active regions
[2016-04-15T00:59Z] INFO  17:59:13,612 ProgressMeter -            done     1.03846414E8    63.0 s            0.0 s      100.0%    63.0 s       0.0 s
[2016-04-15T00:59Z] INFO  17:59:13,612 ProgressMeter - Total runtime 63.46 secs, 1.06 min, 0.02 hours
[2016-04-15T00:59Z] INFO  17:59:13,612 MicroScheduler - 25880 reads were filtered out during the traversal out of approximately 321743 total reads (8.04%)
[2016-04-15T00:59Z] INFO  17:59:13,613 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:59Z] INFO  17:59:13,613 MicroScheduler -   -> 25595 reads (7.96% of total) failing DuplicateReadFilter
[2016-04-15T00:59Z] INFO  17:59:13,613 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:59Z] INFO  17:59:13,613 MicroScheduler -   -> 285 reads (0.09% of total) failing HCMappingQualityFilter
[2016-04-15T00:59Z] INFO  17:59:13,614 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:59Z] INFO  17:59:13,614 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:59Z] INFO  17:59:13,614 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:59Z] INFO  17:59:13,614 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:59Z] WARN  17:59:13,707 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T00:59Z] WARN  17:59:13,708 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T00:59Z] INFO  17:59:13,757 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:59Z] INFO  17:59:13,760 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:59Z] INFO  17:59:13,760 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:59Z] INFO  17:59:13,761 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:59Z] INFO  17:59:13,765 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/7/R14-18105_kapa-NGv3-PE100-NGv3-sort-7_79082334_94740703-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/7/R14-18105_kapa-NGv3-PE100-NGv3-7_79082334_94740703-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/7/tx/tmpERa87M/R14-18105_kapa-NGv3-PE100-NGv3-7_79082334_94740703.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:59Z] INFO  17:59:13,790 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:59Z] INFO  17:59:13,798 HelpFormatter - Date/Time: 2016/04/14 17:59:13
[2016-04-15T00:59Z] INFO  17:59:13,798 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:59Z] INFO  17:59:13,799 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:59Z] WARN  17:59:13,843 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T00:59Z] WARN  17:59:13,857 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/7/tx/tmpERa87M/R14-18105_kapa-NGv3-PE100-NGv3-7_79082334_94740703.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T00:59Z] INFO  17:59:14,137 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:59Z] INFO  17:59:14,395 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T00:59Z] INFO  17:59:14,441 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:59Z] INFO  17:59:14,516 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-15T00:59Z] INFO  17:59:14,566 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T00:59Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T00:59Z] INFO  17:59:14,824 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T00:59Z] INFO  17:59:14,825 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T00:59Z] INFO  17:59:14,913 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.014401507000000001
[2016-04-15T00:59Z] INFO  17:59:14,914 PairHMM - Total compute time in PairHMM computeLikelihoods() : 0.33424249
[2016-04-15T00:59Z] INFO  17:59:14,915 HaplotypeCaller - Ran local assembly on 929 active regions
[2016-04-15T00:59Z] INFO  17:59:14,966 ProgressMeter -            done      4.2012935E7    37.0 s            0.0 s      100.0%    37.0 s       0.0 s
[2016-04-15T00:59Z] INFO  17:59:14,967 ProgressMeter - Total runtime 37.57 secs, 0.63 min, 0.01 hours
[2016-04-15T00:59Z] INFO  17:59:14,967 MicroScheduler - 12073 reads were filtered out during the traversal out of approximately 153547 total reads (7.86%)
[2016-04-15T00:59Z] INFO  17:59:14,967 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:59Z] INFO  17:59:14,968 MicroScheduler -   -> 11915 reads (7.76% of total) failing DuplicateReadFilter
[2016-04-15T00:59Z] INFO  17:59:14,968 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:59Z] INFO  17:59:14,968 MicroScheduler -   -> 158 reads (0.10% of total) failing HCMappingQualityFilter
[2016-04-15T00:59Z] INFO  17:59:14,968 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:59Z] INFO  17:59:14,969 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:59Z] INFO  17:59:14,969 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:59Z] INFO  17:59:14,969 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:59Z] WARN  17:59:15,076 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T00:59Z] WARN  17:59:15,078 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T00:59Z] INFO  17:59:15,116 IntervalUtils - Processing 163786 bp from intervals
[2016-04-15T00:59Z] WARN  17:59:15,122 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:59Z] INFO  17:59:15,243 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:59Z] INFO  17:59:15,348 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:59Z] INFO  17:59:15,349 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:59Z] INFO  17:59:15,349 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T00:59Z] INFO  17:59:15,350 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T00:59Z] INFO  17:59:15,361 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T00:59Z] INFO  17:59:15,362 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T00:59Z] INFO  17:59:15,628 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T00:59Z] INFO  17:59:15,932 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:59Z] GATK: HaplotypeCaller
[2016-04-15T00:59Z] INFO  17:59:16,386 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:59Z] INFO  17:59:16,521 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.010039634
[2016-04-15T00:59Z] INFO  17:59:16,521 PairHMM - Total compute time in PairHMM computeLikelihoods() : 2.070227377
[2016-04-15T00:59Z] INFO  17:59:16,521 HaplotypeCaller - Ran local assembly on 1068 active regions
[2016-04-15T00:59Z] INFO  17:59:16,575 ProgressMeter -            done      4.9918554E7    47.0 s            0.0 s      100.0%    47.0 s       0.0 s
[2016-04-15T00:59Z] INFO  17:59:16,575 ProgressMeter - Total runtime 47.85 secs, 0.80 min, 0.01 hours
[2016-04-15T00:59Z] INFO  17:59:16,576 MicroScheduler - 15538 reads were filtered out during the traversal out of approximately 190210 total reads (8.17%)
[2016-04-15T00:59Z] INFO  17:59:16,577 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:59Z] INFO  17:59:16,577 MicroScheduler -   -> 14789 reads (7.78% of total) failing DuplicateReadFilter
[2016-04-15T00:59Z] INFO  17:59:16,577 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:59Z] INFO  17:59:16,577 MicroScheduler -   -> 749 reads (0.39% of total) failing HCMappingQualityFilter
[2016-04-15T00:59Z] INFO  17:59:16,578 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:59Z] INFO  17:59:16,578 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:59Z] INFO  17:59:16,578 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:59Z] INFO  17:59:16,578 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:59Z] GATK: HaplotypeCaller
[2016-04-15T00:59Z] INFO  17:59:18,037 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:59Z] GATK: HaplotypeCaller
[2016-04-15T00:59Z] INFO  17:59:19,330 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:59Z] INFO  17:59:19,333 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:59Z] INFO  17:59:19,334 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:59Z] INFO  17:59:19,334 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:59Z] INFO  17:59:19,339 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/7/R14-18105_kapa-NGv3-PE100-NGv3-sort-7_94750023_110303777-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/7/R14-18105_kapa-NGv3-PE100-NGv3-7_94750023_110303777-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/7/tx/tmpZGppQb/R14-18105_kapa-NGv3-PE100-NGv3-7_94750023_110303777.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:59Z] INFO  17:59:19,347 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:59Z] INFO  17:59:19,348 HelpFormatter - Date/Time: 2016/04/14 17:59:19
[2016-04-15T00:59Z] INFO  17:59:19,349 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:59Z] INFO  17:59:19,349 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:59Z] WARN  17:59:19,371 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T00:59Z] WARN  17:59:19,374 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/7/tx/tmpZGppQb/R14-18105_kapa-NGv3-PE100-NGv3-7_94750023_110303777.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T00:59Z] INFO  17:59:19,461 ProgressMeter -      6:29911045      5.1195021E7    60.0 s            1.0 s       73.9%    81.0 s      21.0 s
[2016-04-15T00:59Z] INFO  17:59:19,608 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:59Z] INFO  17:59:19,799 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T00:59Z] INFO  17:59:19,819 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:59Z] INFO  17:59:19,911 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.09
[2016-04-15T00:59Z] INFO  17:59:19,944 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T00:59Z] INFO  17:59:20,129 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:59Z] INFO  17:59:20,132 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:59Z] INFO  17:59:20,132 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:59Z] INFO  17:59:20,133 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:59Z] INFO  17:59:20,137 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/7/R14-18105_kapa-NGv3-PE100-NGv3-sort-7_110526648_126079222-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/7/R14-18105_kapa-NGv3-PE100-NGv3-7_110526648_126079222-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/7/tx/tmpONA9dk/R14-18105_kapa-NGv3-PE100-NGv3-7_110526648_126079222.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:59Z] INFO  17:59:20,177 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:59Z] INFO  17:59:20,178 HelpFormatter - Date/Time: 2016/04/14 17:59:20
[2016-04-15T00:59Z] INFO  17:59:20,178 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:59Z] INFO  17:59:20,183 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:59Z] WARN  17:59:20,239 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T00:59Z] WARN  17:59:20,242 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/7/tx/tmpONA9dk/R14-18105_kapa-NGv3-PE100-NGv3-7_110526648_126079222.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T00:59Z] INFO  17:59:20,334 ProgressMeter -      6:32551886      2.8415957E7    60.0 s            2.0 s       26.3%     3.8 m       2.8 m
[2016-04-15T00:59Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T00:59Z] INFO  17:59:20,416 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T00:59Z] INFO  17:59:20,426 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T00:59Z] INFO  17:59:20,430 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:59Z] INFO  17:59:20,496 IntervalUtils - Processing 352548 bp from intervals
[2016-04-15T00:59Z] WARN  17:59:20,502 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:59Z] INFO  17:59:20,634 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T00:59Z] INFO  17:59:20,644 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:59Z] INFO  17:59:20,645 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:59Z] INFO  17:59:20,700 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-15T00:59Z] INFO  17:59:20,728 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T00:59Z] WARN  17:59:20,743 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T00:59Z] WARN  17:59:20,744 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T00:59Z] INFO  17:59:20,853 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:59Z] INFO  17:59:20,854 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:59Z] INFO  17:59:20,855 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T00:59Z] INFO  17:59:20,855 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T00:59Z] INFO  17:59:20,881 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T00:59Z] INFO  17:59:20,881 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T00:59Z] INFO  17:59:21,046 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T00:59Z] INFO  17:59:21,163 ProgressMeter -     6:135375829       2.382467E7    30.0 s            1.0 s       62.2%    48.0 s      18.0 s
[2016-04-15T00:59Z] INFO  17:59:21,211 IntervalUtils - Processing 97998 bp from intervals
[2016-04-15T00:59Z] WARN  17:59:21,216 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:59Z] INFO  17:59:21,337 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:59Z] INFO  17:59:21,400 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:59Z] INFO  17:59:21,401 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:59Z] INFO  17:59:21,402 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T00:59Z] INFO  17:59:21,402 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T00:59Z] INFO  17:59:21,403 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T00:59Z] INFO  17:59:21,403 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T00:59Z] INFO  17:59:21,506 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.007979319
[2016-04-15T00:59Z] INFO  17:59:21,507 PairHMM - Total compute time in PairHMM computeLikelihoods() : 0.48966365600000006
[2016-04-15T00:59Z] INFO  17:59:21,507 HaplotypeCaller - Ran local assembly on 1058 active regions
[2016-04-15T00:59Z] INFO  17:59:21,557 ProgressMeter -            done      5.3468356E7    40.0 s            0.0 s      100.0%    40.0 s       0.0 s
[2016-04-15T00:59Z] INFO  17:59:21,558 ProgressMeter - Total runtime 40.58 secs, 0.68 min, 0.01 hours
[2016-04-15T00:59Z] INFO  17:59:21,559 MicroScheduler - 14270 reads were filtered out during the traversal out of approximately 179945 total reads (7.93%)
[2016-04-15T00:59Z] INFO  17:59:21,560 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:59Z] INFO  17:59:21,560 MicroScheduler -   -> 13928 reads (7.74% of total) failing DuplicateReadFilter
[2016-04-15T00:59Z] INFO  17:59:21,561 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:59Z] INFO  17:59:21,561 MicroScheduler -   -> 342 reads (0.19% of total) failing HCMappingQualityFilter
[2016-04-15T00:59Z] INFO  17:59:21,562 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:59Z] INFO  17:59:21,563 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:59Z] INFO  17:59:21,563 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:59Z] INFO  17:59:21,564 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:59Z] INFO  17:59:21,598 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T00:59Z] INFO  17:59:21,640 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:59Z] INFO  17:59:21,644 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:59Z] INFO  17:59:21,644 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:59Z] INFO  17:59:21,645 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:59Z] INFO  17:59:21,649 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/7/R14-18105_kapa-NGv3-PE100-NGv3-sort-7_126086124_141619620-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/7/R14-18105_kapa-NGv3-PE100-NGv3-7_126086124_141619620-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/7/tx/tmpuz6u8a/R14-18105_kapa-NGv3-PE100-NGv3-7_126086124_141619620.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:59Z] INFO  17:59:21,658 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:59Z] INFO  17:59:21,659 HelpFormatter - Date/Time: 2016/04/14 17:59:21
[2016-04-15T00:59Z] INFO  17:59:21,660 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:59Z] INFO  17:59:21,661 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:59Z] WARN  17:59:21,692 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T00:59Z] WARN  17:59:21,695 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/7/tx/tmpuz6u8a/R14-18105_kapa-NGv3-PE100-NGv3-7_126086124_141619620.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T00:59Z] INFO  17:59:21,925 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:59Z] INFO  17:59:22,066 ProgressMeter -     6:150385782      2.0563749E7    30.0 s            1.0 s       52.2%    57.0 s      27.0 s
[2016-04-15T00:59Z] INFO  17:59:22,107 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T00:59Z] INFO  17:59:22,117 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:59Z] INFO  17:59:22,201 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-15T00:59Z] INFO  17:59:22,216 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T00:59Z] INFO  17:59:22,268 ProgressMeter -     6:163235313        1.48841E7    30.0 s            2.0 s       49.7%    60.0 s      30.0 s
[2016-04-15T00:59Z] INFO  17:59:22,704 IntervalUtils - Processing 219678 bp from intervals
[2016-04-15T00:59Z] WARN  17:59:22,720 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:59Z] INFO  17:59:22,830 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:59Z] INFO  17:59:22,919 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:59Z] INFO  17:59:22,920 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:59Z] INFO  17:59:22,921 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T00:59Z] INFO  17:59:22,921 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T00:59Z] INFO  17:59:22,922 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T00:59Z] INFO  17:59:22,922 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T00:59Z] INFO  17:59:23,145 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T00:59Z] INFO  17:59:23,204 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:59Z] GATK: HaplotypeCaller
[2016-04-15T00:59Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T00:59Z] INFO  17:59:23,905 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T00:59Z] INFO  17:59:23,916 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T00:59Z] WARN  17:59:24,284 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T00:59Z] WARN  17:59:24,285 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T00:59Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T00:59Z] INFO  17:59:24,843 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T00:59Z] INFO  17:59:24,844 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T00:59Z] WARN  17:59:25,122 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T00:59Z] WARN  17:59:25,124 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T00:59Z] INFO  17:59:26,922 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:59Z] INFO  17:59:26,942 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:59Z] INFO  17:59:26,947 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:59Z] INFO  17:59:26,947 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:59Z] INFO  17:59:26,952 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/7/R14-18105_kapa-NGv3-PE100-NGv3-sort-7_141629903_157151331-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/7/R14-18105_kapa-NGv3-PE100-NGv3-7_141629903_157151331-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/7/tx/tmpQHJhrx/R14-18105_kapa-NGv3-PE100-NGv3-7_141629903_157151331.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:59Z] INFO  17:59:26,996 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:59Z] INFO  17:59:26,997 HelpFormatter - Date/Time: 2016/04/14 17:59:26
[2016-04-15T00:59Z] INFO  17:59:26,997 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:59Z] INFO  17:59:26,997 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:59Z] WARN  17:59:27,045 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T00:59Z] WARN  17:59:27,048 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/7/tx/tmpQHJhrx/R14-18105_kapa-NGv3-PE100-NGv3-7_141629903_157151331.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T00:59Z] INFO  17:59:27,226 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:59Z] INFO  17:59:27,412 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T00:59Z] INFO  17:59:27,422 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:59Z] INFO  17:59:27,516 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.09
[2016-04-15T00:59Z] INFO  17:59:27,548 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T00:59Z] INFO  17:59:27,967 IntervalUtils - Processing 248696 bp from intervals
[2016-04-15T00:59Z] WARN  17:59:27,972 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:59Z] INFO  17:59:28,117 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:59Z] INFO  17:59:28,281 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:59Z] INFO  17:59:28,282 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:59Z] INFO  17:59:28,292 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T00:59Z] INFO  17:59:28,293 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T00:59Z] INFO  17:59:28,309 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T00:59Z] INFO  17:59:28,310 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T00:59Z] INFO  17:59:28,515 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T00:59Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T00:59Z] INFO  17:59:30,590 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T00:59Z] INFO  17:59:30,591 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T00:59Z] INFO  17:59:30,787 ProgressMeter -       7:4845478      1.5065872E7    30.0 s            1.0 s       42.1%    71.0 s      41.0 s
[2016-04-15T00:59Z] WARN  17:59:31,012 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T00:59Z] WARN  17:59:31,013 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T00:59Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T00:59Z] INFO  17:59:31,801 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T00:59Z] INFO  17:59:31,807 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T00:59Z] WARN  17:59:32,170 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T00:59Z] WARN  17:59:32,171 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T00:59Z] INFO  17:59:33,856 ProgressMeter -      7:25019682      2.1332022E7    30.0 s            1.0 s       57.3%    52.0 s      22.0 s
[2016-04-15T00:59Z] INFO  17:59:34,869 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.008914152
[2016-04-15T00:59Z] INFO  17:59:34,890 PairHMM - Total compute time in PairHMM computeLikelihoods() : 1.103636706
[2016-04-15T00:59Z] INFO  17:59:34,891 HaplotypeCaller - Ran local assembly on 1119 active regions
[2016-04-15T00:59Z] INFO  17:59:34,948 ProgressMeter -            done      5.9409326E7    43.0 s            0.0 s      100.0%    43.0 s       0.0 s
[2016-04-15T00:59Z] INFO  17:59:34,949 ProgressMeter - Total runtime 43.81 secs, 0.73 min, 0.01 hours
[2016-04-15T00:59Z] INFO  17:59:34,950 MicroScheduler - 23710 reads were filtered out during the traversal out of approximately 210435 total reads (11.27%)
[2016-04-15T00:59Z] INFO  17:59:34,951 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:59Z] INFO  17:59:34,951 MicroScheduler -   -> 16241 reads (7.72% of total) failing DuplicateReadFilter
[2016-04-15T00:59Z] INFO  17:59:34,952 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:59Z] INFO  17:59:34,953 MicroScheduler -   -> 7469 reads (3.55% of total) failing HCMappingQualityFilter
[2016-04-15T00:59Z] INFO  17:59:34,953 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:59Z] INFO  17:59:34,954 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:59Z] INFO  17:59:34,955 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:59Z] INFO  17:59:34,955 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:59Z] INFO  17:59:36,311 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:59Z] GATK: HaplotypeCaller
[2016-04-15T00:59Z] INFO  17:59:38,135 ProgressMeter -      7:43508519      1.7463161E7    30.0 s            1.0 s       57.2%    52.0 s      22.0 s
[2016-04-15T00:59Z] INFO  17:59:38,198 ProgressMeter -     5:140563937     1.15039024E8    90.0 s            0.0 s       70.1%     2.1 m      38.0 s
[2016-04-15T00:59Z] INFO  17:59:39,645 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:59Z] INFO  17:59:39,649 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:59Z] INFO  17:59:39,649 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:59Z] INFO  17:59:39,650 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:59Z] INFO  17:59:39,654 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/7/R14-18105_kapa-NGv3-PE100-NGv3-sort-7_157155854_159138663-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/7/R14-18105_kapa-NGv3-PE100-NGv3-7_157155854_159138663-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/7/tx/tmp7h0SUj/R14-18105_kapa-NGv3-PE100-NGv3-7_157155854_159138663.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:59Z] INFO  17:59:39,684 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:59Z] INFO  17:59:39,685 HelpFormatter - Date/Time: 2016/04/14 17:59:39
[2016-04-15T00:59Z] INFO  17:59:39,685 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:59Z] INFO  17:59:39,686 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:59Z] WARN  17:59:39,710 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T00:59Z] WARN  17:59:39,718 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/7/tx/tmp7h0SUj/R14-18105_kapa-NGv3-PE100-NGv3-7_157155854_159138663.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T00:59Z] INFO  17:59:39,899 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:59Z] INFO  17:59:40,120 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T00:59Z] INFO  17:59:40,131 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:59Z] INFO  17:59:40,207 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-15T00:59Z] INFO  17:59:40,244 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T00:59Z] INFO  17:59:40,640 IntervalUtils - Processing 17619 bp from intervals
[2016-04-15T00:59Z] WARN  17:59:40,645 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:59Z] INFO  17:59:40,742 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:59Z] INFO  17:59:40,783 ProgressMeter -      7:56878876      1.3283768E7    30.0 s            2.0 s       93.3%    32.0 s       2.0 s
[2016-04-15T00:59Z] INFO  17:59:40,814 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:59Z] INFO  17:59:40,814 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:59Z] INFO  17:59:40,815 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T00:59Z] INFO  17:59:40,816 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T00:59Z] INFO  17:59:40,816 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T00:59Z] INFO  17:59:40,817 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T00:59Z] INFO  17:59:41,009 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T00:59Z] INFO  17:59:41,399 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.010256350000000001
[2016-04-15T00:59Z] INFO  17:59:41,400 PairHMM - Total compute time in PairHMM computeLikelihoods() : 0.329675953
[2016-04-15T00:59Z] INFO  17:59:41,401 HaplotypeCaller - Ran local assembly on 1258 active regions
[2016-04-15T00:59Z] INFO  17:59:41,468 ProgressMeter -            done      7.7025077E7    49.0 s            0.0 s      100.0%    49.0 s       0.0 s
[2016-04-15T00:59Z] INFO  17:59:41,469 ProgressMeter - Total runtime 49.43 secs, 0.82 min, 0.01 hours
[2016-04-15T00:59Z] INFO  17:59:41,475 MicroScheduler - 22685 reads were filtered out during the traversal out of approximately 253195 total reads (8.96%)
[2016-04-15T00:59Z] INFO  17:59:41,475 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:59Z] INFO  17:59:41,475 MicroScheduler -   -> 19829 reads (7.83% of total) failing DuplicateReadFilter
[2016-04-15T00:59Z] INFO  17:59:41,476 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:59Z] INFO  17:59:41,476 MicroScheduler -   -> 2856 reads (1.13% of total) failing HCMappingQualityFilter
[2016-04-15T00:59Z] INFO  17:59:41,476 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:59Z] INFO  17:59:41,476 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:59Z] INFO  17:59:41,477 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:59Z] INFO  17:59:41,477 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:59Z] INFO  17:59:42,012 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.012959842000000001
[2016-04-15T00:59Z] INFO  17:59:42,012 PairHMM - Total compute time in PairHMM computeLikelihoods() : 1.7171252840000002
[2016-04-15T00:59Z] INFO  17:59:42,013 HaplotypeCaller - Ran local assembly on 1074 active regions
[2016-04-15T00:59Z] INFO  17:59:42,075 ProgressMeter -      7:73663550       1.697401E7    30.0 s            1.0 s       54.5%    55.0 s      25.0 s
[2016-04-15T00:59Z] INFO  17:59:42,097 ProgressMeter -            done      5.0541583E7    49.0 s            0.0 s      100.0%    49.0 s       0.0 s
[2016-04-15T00:59Z] INFO  17:59:42,097 ProgressMeter - Total runtime 49.85 secs, 0.83 min, 0.01 hours
[2016-04-15T00:59Z] INFO  17:59:42,098 MicroScheduler - 22303 reads were filtered out during the traversal out of approximately 230211 total reads (9.69%)
[2016-04-15T00:59Z] INFO  17:59:42,098 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:59Z] INFO  17:59:42,098 MicroScheduler -   -> 18153 reads (7.89% of total) failing DuplicateReadFilter
[2016-04-15T00:59Z] INFO  17:59:42,098 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:59Z] INFO  17:59:42,099 MicroScheduler -   -> 4150 reads (1.80% of total) failing HCMappingQualityFilter
[2016-04-15T00:59Z] INFO  17:59:42,099 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:59Z] INFO  17:59:42,099 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:59Z] INFO  17:59:42,099 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:59Z] INFO  17:59:42,100 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:59Z] INFO  17:59:42,825 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.035414429000000004
[2016-04-15T00:59Z] INFO  17:59:42,826 PairHMM - Total compute time in PairHMM computeLikelihoods() : 7.503573327000001
[2016-04-15T00:59Z] INFO  17:59:42,827 HaplotypeCaller - Ran local assembly on 1690 active regions
[2016-04-15T00:59Z] INFO  17:59:42,883 ProgressMeter -            done      9.0413204E7    83.0 s            0.0 s      100.0%    83.0 s       0.0 s
[2016-04-15T00:59Z] INFO  17:59:42,884 ProgressMeter - Total runtime 83.44 secs, 1.39 min, 0.02 hours
[2016-04-15T00:59Z] INFO  17:59:42,884 MicroScheduler - 35173 reads were filtered out during the traversal out of approximately 370500 total reads (9.49%)
[2016-04-15T00:59Z] INFO  17:59:42,885 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:59Z] INFO  17:59:42,885 MicroScheduler -   -> 29335 reads (7.92% of total) failing DuplicateReadFilter
[2016-04-15T00:59Z] INFO  17:59:42,885 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:59Z] INFO  17:59:42,885 MicroScheduler -   -> 5838 reads (1.58% of total) failing HCMappingQualityFilter
[2016-04-15T00:59Z] INFO  17:59:42,886 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:59Z] INFO  17:59:42,886 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:59Z] INFO  17:59:42,886 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:59Z] INFO  17:59:42,886 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:59Z] INFO  17:59:42,909 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:59Z] INFO  17:59:43,131 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.009369671000000001
[2016-04-15T00:59Z] INFO  17:59:43,132 PairHMM - Total compute time in PairHMM computeLikelihoods() : 0.58010406
[2016-04-15T00:59Z] INFO  17:59:43,132 HaplotypeCaller - Ran local assembly on 594 active regions
[2016-04-15T00:59Z] INFO  17:59:43,176 ProgressMeter -            done      1.4657262E7    32.0 s            2.0 s      100.0%    32.0 s       0.0 s
[2016-04-15T00:59Z] INFO  17:59:43,177 ProgressMeter - Total runtime 32.42 secs, 0.54 min, 0.01 hours
[2016-04-15T00:59Z] INFO  17:59:43,177 MicroScheduler - 13187 reads were filtered out during the traversal out of approximately 116759 total reads (11.29%)
[2016-04-15T00:59Z] INFO  17:59:43,178 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:59Z] INFO  17:59:43,179 MicroScheduler -   -> 8844 reads (7.57% of total) failing DuplicateReadFilter
[2016-04-15T00:59Z] INFO  17:59:43,179 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:59Z] INFO  17:59:43,180 MicroScheduler -   -> 4343 reads (3.72% of total) failing HCMappingQualityFilter
[2016-04-15T00:59Z] INFO  17:59:43,181 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:59Z] INFO  17:59:43,181 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:59Z] INFO  17:59:43,182 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:59Z] INFO  17:59:43,182 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:59Z] GATK: HaplotypeCaller
[2016-04-15T00:59Z] INFO  17:59:43,380 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:59Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T00:59Z] INFO  17:59:43,622 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T00:59Z] INFO  17:59:43,623 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T00:59Z] GATK: HaplotypeCaller
[2016-04-15T00:59Z] WARN  17:59:43,853 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T00:59Z] WARN  17:59:43,854 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T00:59Z] INFO  17:59:44,204 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:59Z] GATK: HaplotypeCaller
[2016-04-15T00:59Z] INFO  17:59:44,566 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:59Z] GATK: HaplotypeCaller
[2016-04-15T00:59Z] INFO  17:59:45,374 ProgressMeter -      7:90747495      2.1081767E7    30.0 s            1.0 s       58.3%    51.0 s      21.0 s
[2016-04-15T00:59Z] INFO  17:59:45,909 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:59Z] INFO  17:59:45,911 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:59Z] INFO  17:59:45,911 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:59Z] INFO  17:59:45,912 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:59Z] INFO  17:59:45,918 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/8/R14-18105_kapa-NGv3-PE100-NGv3-sort-8_0_15517156-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/8/R14-18105_kapa-NGv3-PE100-NGv3-8_0_15517156-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/8/tx/tmpZzDGYK/R14-18105_kapa-NGv3-PE100-NGv3-8_0_15517156.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:59Z] INFO  17:59:45,945 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:59Z] INFO  17:59:45,946 HelpFormatter - Date/Time: 2016/04/14 17:59:45
[2016-04-15T00:59Z] INFO  17:59:45,946 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:59Z] INFO  17:59:45,946 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:59Z] WARN  17:59:45,977 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T00:59Z] WARN  17:59:45,980 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/8/tx/tmpZzDGYK/R14-18105_kapa-NGv3-PE100-NGv3-8_0_15517156.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T00:59Z] INFO  17:59:46,234 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:59Z] INFO  17:59:46,462 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T00:59Z] INFO  17:59:46,472 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:59Z] INFO  17:59:46,531 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-15T00:59Z] INFO  17:59:46,559 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T00:59Z] INFO  17:59:46,584 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:59Z] INFO  17:59:46,587 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:59Z] INFO  17:59:46,588 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:59Z] INFO  17:59:46,588 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:59Z] INFO  17:59:46,593 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/8/R14-18105_kapa-NGv3-PE100-NGv3-sort-8_15519664_31030618-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/8/R14-18105_kapa-NGv3-PE100-NGv3-8_15519664_31030618-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/8/tx/tmpqDBLTL/R14-18105_kapa-NGv3-PE100-NGv3-8_15519664_31030618.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:59Z] INFO  17:59:46,601 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:59Z] INFO  17:59:46,602 HelpFormatter - Date/Time: 2016/04/14 17:59:46
[2016-04-15T00:59Z] INFO  17:59:46,614 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:59Z] INFO  17:59:46,619 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:59Z] WARN  17:59:46,674 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T00:59Z] WARN  17:59:46,677 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/8/tx/tmpqDBLTL/R14-18105_kapa-NGv3-PE100-NGv3-8_15519664_31030618.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T00:59Z] INFO  17:59:46,876 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:59Z] INFO  17:59:47,036 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T00:59Z] INFO  17:59:47,046 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:59Z] INFO  17:59:47,052 IntervalUtils - Processing 115548 bp from intervals
[2016-04-15T00:59Z] WARN  17:59:47,058 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:59Z] INFO  17:59:47,129 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-15T00:59Z] INFO  17:59:47,164 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T00:59Z] INFO  17:59:47,202 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:59Z] INFO  17:59:47,296 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:59Z] INFO  17:59:47,299 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:59Z] INFO  17:59:47,300 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:59Z] INFO  17:59:47,300 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:59Z] INFO  17:59:47,305 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/8/R14-18105_kapa-NGv3-PE100-NGv3-sort-8_31496910_48001429-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/8/R14-18105_kapa-NGv3-PE100-NGv3-8_31496910_48001429-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/8/tx/tmphq6lGq/R14-18105_kapa-NGv3-PE100-NGv3-8_31496910_48001429.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:59Z] INFO  17:59:47,317 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:59Z] INFO  17:59:47,319 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:59Z] INFO  17:59:47,319 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T00:59Z] INFO  17:59:47,320 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T00:59Z] INFO  17:59:47,321 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T00:59Z] INFO  17:59:47,321 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T00:59Z] INFO  17:59:47,338 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:59Z] INFO  17:59:47,338 HelpFormatter - Date/Time: 2016/04/14 17:59:47
[2016-04-15T00:59Z] INFO  17:59:47,338 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:59Z] INFO  17:59:47,338 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:59Z] WARN  17:59:47,378 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T00:59Z] WARN  17:59:47,380 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/8/tx/tmphq6lGq/R14-18105_kapa-NGv3-PE100-NGv3-8_31496910_48001429.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T00:59Z] INFO  17:59:47,513 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T00:59Z] INFO  17:59:47,626 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:59Z] INFO  17:59:47,729 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:59Z] INFO  17:59:47,733 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:59Z] INFO  17:59:47,733 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:59Z] INFO  17:59:47,734 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:59Z] INFO  17:59:47,739 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/8/R14-18105_kapa-NGv3-PE100-NGv3-sort-8_48003022_63659688-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/8/R14-18105_kapa-NGv3-PE100-NGv3-8_48003022_63659688-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/8/tx/tmpcnlD9A/R14-18105_kapa-NGv3-PE100-NGv3-8_48003022_63659688.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:59Z] INFO  17:59:47,746 IntervalUtils - Processing 233081 bp from intervals
[2016-04-15T00:59Z] INFO  17:59:47,764 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:59Z] INFO  17:59:47,765 HelpFormatter - Date/Time: 2016/04/14 17:59:47
[2016-04-15T00:59Z] INFO  17:59:47,765 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:59Z] INFO  17:59:47,765 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:59Z] WARN  17:59:47,777 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:59Z] WARN  17:59:47,804 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T00:59Z] WARN  17:59:47,807 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/8/tx/tmpcnlD9A/R14-18105_kapa-NGv3-PE100-NGv3-8_48003022_63659688.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T00:59Z] INFO  17:59:47,844 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T00:59Z] INFO  17:59:47,857 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:59Z] INFO  17:59:47,896 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:59Z] INFO  17:59:47,927 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-15T00:59Z] INFO  17:59:47,978 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T00:59Z] INFO  17:59:47,998 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:59Z] INFO  17:59:48,012 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.012740433
[2016-04-15T00:59Z] INFO  17:59:48,013 PairHMM - Total compute time in PairHMM computeLikelihoods() : 0.501544049
[2016-04-15T00:59Z] INFO  17:59:48,014 HaplotypeCaller - Ran local assembly on 1108 active regions
[2016-04-15T00:59Z] INFO  17:59:48,025 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:59Z] INFO  17:59:48,027 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:59Z] INFO  17:59:48,027 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T00:59Z] INFO  17:59:48,028 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T00:59Z] INFO  17:59:48,040 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T00:59Z] INFO  17:59:48,041 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T00:59Z] INFO  17:59:48,051 ProgressMeter -            done       5.703208E7    44.0 s            0.0 s      100.0%    44.0 s       0.0 s
[2016-04-15T00:59Z] INFO  17:59:48,052 ProgressMeter - Total runtime 44.26 secs, 0.74 min, 0.01 hours
[2016-04-15T00:59Z] INFO  17:59:48,063 MicroScheduler - 16038 reads were filtered out during the traversal out of approximately 197168 total reads (8.13%)
[2016-04-15T00:59Z] INFO  17:59:48,064 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:59Z] INFO  17:59:48,065 MicroScheduler -   -> 15640 reads (7.93% of total) failing DuplicateReadFilter
[2016-04-15T00:59Z] INFO  17:59:48,065 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:59Z] INFO  17:59:48,066 MicroScheduler -   -> 398 reads (0.20% of total) failing HCMappingQualityFilter
[2016-04-15T00:59Z] INFO  17:59:48,067 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:59Z] INFO  17:59:48,067 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:59Z] INFO  17:59:48,068 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:59Z] INFO  17:59:48,069 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:59Z] INFO  17:59:48,190 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T00:59Z] INFO  17:59:48,219 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:59Z] INFO  17:59:48,229 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T00:59Z] INFO  17:59:48,314 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.09
[2016-04-15T00:59Z] INFO  17:59:48,338 IntervalUtils - Processing 125262 bp from intervals
[2016-04-15T00:59Z] WARN  17:59:48,343 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:59Z] INFO  17:59:48,352 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T00:59Z] INFO  17:59:48,420 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:59Z] INFO  17:59:48,528 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:59Z] INFO  17:59:48,529 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:59Z] INFO  17:59:48,540 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T00:59Z] INFO  17:59:48,541 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T00:59Z] INFO  17:59:48,551 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T00:59Z] INFO  17:59:48,551 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T00:59Z] INFO  17:59:48,679 IntervalUtils - Processing 104159 bp from intervals
[2016-04-15T00:59Z] WARN  17:59:48,684 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:59Z] INFO  17:59:48,832 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T00:59Z] INFO  17:59:48,859 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:59Z] INFO  17:59:48,944 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:59Z] INFO  17:59:48,945 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:59Z] INFO  17:59:48,946 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T00:59Z] INFO  17:59:48,946 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T00:59Z] INFO  17:59:48,947 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T00:59Z] INFO  17:59:48,948 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T00:59Z] INFO  17:59:49,133 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T00:59Z] INFO  17:59:49,614 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:59Z] GATK: HaplotypeCaller
[2016-04-15T00:59Z] INFO  17:59:50,335 ProgressMeter -      6:33656187      6.7475088E7    90.0 s            1.0 s       39.6%     3.8 m       2.3 m
[2016-04-15T00:59Z] INFO  17:59:50,413 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.004940168
[2016-04-15T00:59Z] INFO  17:59:50,414 PairHMM - Total compute time in PairHMM computeLikelihoods() : 0.11732328500000001
[2016-04-15T00:59Z] INFO  17:59:50,414 HaplotypeCaller - Ran local assembly on 701 active regions
[2016-04-15T00:59Z] INFO  17:59:50,471 ProgressMeter -            done      2.3520612E7    29.0 s            1.0 s      100.0%    29.0 s       0.0 s
[2016-04-15T00:59Z] INFO  17:59:50,472 ProgressMeter - Total runtime 29.07 secs, 0.48 min, 0.01 hours
[2016-04-15T00:59Z] INFO  17:59:50,472 MicroScheduler - 9699 reads were filtered out during the traversal out of approximately 120294 total reads (8.06%)
[2016-04-15T00:59Z] INFO  17:59:50,473 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:59Z] INFO  17:59:50,474 MicroScheduler -   -> 9546 reads (7.94% of total) failing DuplicateReadFilter
[2016-04-15T00:59Z] INFO  17:59:50,474 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:59Z] INFO  17:59:50,475 MicroScheduler -   -> 153 reads (0.13% of total) failing HCMappingQualityFilter
[2016-04-15T00:59Z] INFO  17:59:50,475 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:59Z] INFO  17:59:50,476 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:59Z] INFO  17:59:50,477 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:59Z] INFO  17:59:50,477 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:59Z] INFO  17:59:50,808 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.0017678420000000002
[2016-04-15T00:59Z] INFO  17:59:50,809 PairHMM - Total compute time in PairHMM computeLikelihoods() : 0.014603307000000001
[2016-04-15T00:59Z] INFO  17:59:50,810 HaplotypeCaller - Ran local assembly on 149 active regions
[2016-04-15T00:59Z] INFO  17:59:50,883 ProgressMeter -      7:99754570      2.2452396E7    30.0 s            1.0 s       29.7%   100.0 s      70.0 s
[2016-04-15T00:59Z] INFO  17:59:50,892 ProgressMeter -            done        1060833.0    10.0 s            9.0 s      100.0%    10.0 s       0.0 s
[2016-04-15T00:59Z] INFO  17:59:50,893 ProgressMeter - Total runtime 10.08 secs, 0.17 min, 0.00 hours
[2016-04-15T00:59Z] INFO  17:59:50,893 MicroScheduler - 2472 reads were filtered out during the traversal out of approximately 28003 total reads (8.83%)
[2016-04-15T00:59Z] INFO  17:59:50,893 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:59Z] INFO  17:59:50,894 MicroScheduler -   -> 2202 reads (7.86% of total) failing DuplicateReadFilter
[2016-04-15T00:59Z] INFO  17:59:50,894 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:59Z] INFO  17:59:50,894 MicroScheduler -   -> 270 reads (0.96% of total) failing HCMappingQualityFilter
[2016-04-15T00:59Z] INFO  17:59:50,894 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:59Z] INFO  17:59:50,895 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:59Z] INFO  17:59:50,895 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:59Z] INFO  17:59:50,895 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:59Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T00:59Z] INFO  17:59:51,488 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T00:59Z] INFO  17:59:51,499 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T00:59Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T00:59Z] INFO  17:59:51,632 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T00:59Z] INFO  17:59:51,633 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T00:59Z] WARN  17:59:51,750 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T00:59Z] WARN  17:59:51,751 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T00:59Z] WARN  17:59:51,883 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T00:59Z] WARN  17:59:51,884 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T00:59Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T00:59Z] INFO  17:59:51,986 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T00:59Z] INFO  17:59:51,997 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T00:59Z] INFO  17:59:52,063 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:59Z] WARN  17:59:52,215 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T00:59Z] WARN  17:59:52,216 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T00:59Z] INFO  17:59:52,390 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:59Z] GATK: HaplotypeCaller
[2016-04-15T00:59Z] GATK: HaplotypeCaller
[2016-04-15T00:59Z] INFO  17:59:52,758 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:59Z] INFO  17:59:52,762 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:59Z] INFO  17:59:52,762 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:59Z] INFO  17:59:52,763 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:59Z] INFO  17:59:52,767 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/8/R14-18105_kapa-NGv3-PE100-NGv3-sort-8_63775819_79510770-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/8/R14-18105_kapa-NGv3-PE100-NGv3-8_63775819_79510770-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/8/tx/tmpJi0lY4/R14-18105_kapa-NGv3-PE100-NGv3-8_63775819_79510770.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:59Z] INFO  17:59:52,776 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:59Z] INFO  17:59:52,788 HelpFormatter - Date/Time: 2016/04/14 17:59:52
[2016-04-15T00:59Z] INFO  17:59:52,789 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:59Z] INFO  17:59:52,790 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:59Z] WARN  17:59:52,830 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T00:59Z] WARN  17:59:52,838 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/8/tx/tmpJi0lY4/R14-18105_kapa-NGv3-PE100-NGv3-8_63775819_79510770.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T00:59Z] INFO  17:59:52,942 ProgressMeter -     7:132261323      2.4258864E7    30.0 s            1.0 s       42.4%    70.0 s      40.0 s
[2016-04-15T00:59Z] INFO  17:59:53,035 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:59Z] INFO  17:59:53,214 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T00:59Z] INFO  17:59:53,234 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:59Z] INFO  17:59:53,320 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.09
[2016-04-15T00:59Z] INFO  17:59:53,337 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T00:59Z] INFO  17:59:53,680 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.012737451
[2016-04-15T00:59Z] INFO  17:59:53,691 PairHMM - Total compute time in PairHMM computeLikelihoods() : 0.803144665
[2016-04-15T00:59Z] INFO  17:59:53,693 HaplotypeCaller - Ran local assembly on 1125 active regions
[2016-04-15T00:59Z] INFO  17:59:53,739 ProgressMeter -            done      4.9480485E7    45.0 s            0.0 s      100.0%    45.0 s       0.0 s
[2016-04-15T00:59Z] INFO  17:59:53,740 ProgressMeter - Total runtime 45.62 secs, 0.76 min, 0.01 hours
[2016-04-15T00:59Z] INFO  17:59:53,740 MicroScheduler - 26812 reads were filtered out during the traversal out of approximately 235136 total reads (11.40%)
[2016-04-15T00:59Z] INFO  17:59:53,741 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:59Z] INFO  17:59:53,742 MicroScheduler -   -> 18210 reads (7.74% of total) failing DuplicateReadFilter
[2016-04-15T00:59Z] INFO  17:59:53,742 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:59Z] INFO  17:59:53,743 MicroScheduler -   -> 8602 reads (3.66% of total) failing HCMappingQualityFilter
[2016-04-15T00:59Z] INFO  17:59:53,744 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:59Z] INFO  17:59:53,744 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:59Z] INFO  17:59:53,745 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:59Z] INFO  17:59:53,745 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:59Z] INFO  17:59:53,751 IntervalUtils - Processing 117209 bp from intervals
[2016-04-15T00:59Z] WARN  17:59:53,756 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:59Z] INFO  17:59:53,885 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:59Z] INFO  17:59:53,973 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:59Z] INFO  17:59:53,974 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:59Z] INFO  17:59:53,975 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T00:59Z] INFO  17:59:53,975 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T00:59Z] INFO  17:59:53,976 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T00:59Z] INFO  17:59:53,976 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T00:59Z] INFO  17:59:54,146 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T00:59Z] INFO  17:59:55,250 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:59Z] GATK: HaplotypeCaller
[2016-04-15T00:59Z] INFO  17:59:55,627 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:59Z] INFO  17:59:55,630 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:59Z] INFO  17:59:55,631 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:59Z] INFO  17:59:55,632 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:59Z] INFO  17:59:55,636 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/8/R14-18105_kapa-NGv3-PE100-NGv3-sort-8_79513976_95140568-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/8/R14-18105_kapa-NGv3-PE100-NGv3-8_79513976_95140568-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/8/tx/tmp75SVem/R14-18105_kapa-NGv3-PE100-NGv3-8_79513976_95140568.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:59Z] INFO  17:59:55,654 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:59Z] INFO  17:59:55,655 HelpFormatter - Date/Time: 2016/04/14 17:59:55
[2016-04-15T00:59Z] INFO  17:59:55,656 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:59Z] INFO  17:59:55,656 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:59Z] WARN  17:59:55,679 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T00:59Z] WARN  17:59:55,682 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/8/tx/tmp75SVem/R14-18105_kapa-NGv3-PE100-NGv3-8_79513976_95140568.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T00:59Z] INFO  17:59:55,871 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:59Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T00:59Z] INFO  17:59:56,073 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T00:59Z] INFO  17:59:56,081 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T00:59Z] INFO  17:59:56,118 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.014686094
[2016-04-15T00:59Z] INFO  17:59:56,119 PairHMM - Total compute time in PairHMM computeLikelihoods() : 0.933343236
[2016-04-15T00:59Z] INFO  17:59:56,119 HaplotypeCaller - Ran local assembly on 1392 active regions
[2016-04-15T00:59Z] INFO  17:59:56,145 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T00:59Z] INFO  17:59:56,154 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:59Z] INFO  17:59:56,157 ProgressMeter -            done      8.7090457E7    55.0 s            0.0 s      100.0%    55.0 s       0.0 s
[2016-04-15T00:59Z] INFO  17:59:56,158 ProgressMeter - Total runtime 55.39 secs, 0.92 min, 0.02 hours
[2016-04-15T00:59Z] INFO  17:59:56,159 MicroScheduler - 39617 reads were filtered out during the traversal out of approximately 313440 total reads (12.64%)
[2016-04-15T00:59Z] INFO  17:59:56,160 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:59Z] INFO  17:59:56,168 MicroScheduler -   -> 23757 reads (7.58% of total) failing DuplicateReadFilter
[2016-04-15T00:59Z] INFO  17:59:56,169 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:59Z] INFO  17:59:56,169 MicroScheduler -   -> 15860 reads (5.06% of total) failing HCMappingQualityFilter
[2016-04-15T00:59Z] INFO  17:59:56,170 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:59Z] INFO  17:59:56,171 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:59Z] INFO  17:59:56,168 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:59Z] INFO  17:59:56,172 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:59Z] INFO  17:59:56,172 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:59Z] INFO  17:59:56,172 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:59Z] INFO  17:59:56,172 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:59Z] INFO  17:59:56,173 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:59Z] INFO  17:59:56,177 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/8/R14-18105_kapa-NGv3-PE100-NGv3-sort-8_95142853_110655419-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/8/R14-18105_kapa-NGv3-PE100-NGv3-8_95142853_110655419-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/8/tx/tmpk2910K/R14-18105_kapa-NGv3-PE100-NGv3-8_95142853_110655419.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:59Z] INFO  17:59:56,205 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:59Z] INFO  17:59:56,206 HelpFormatter - Date/Time: 2016/04/14 17:59:56
[2016-04-15T00:59Z] INFO  17:59:56,207 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:59Z] INFO  17:59:56,207 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:59Z] WARN  17:59:56,234 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T00:59Z] WARN  17:59:56,237 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/8/tx/tmpk2910K/R14-18105_kapa-NGv3-PE100-NGv3-8_95142853_110655419.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T00:59Z] INFO  17:59:56,267 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.11
[2016-04-15T00:59Z] INFO  17:59:56,284 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T00:59Z] INFO  17:59:56,514 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:59Z] WARN  17:59:56,565 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T00:59Z] WARN  17:59:56,566 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T00:59Z] INFO  17:59:56,745 IntervalUtils - Processing 78340 bp from intervals
[2016-04-15T00:59Z] WARN  17:59:56,750 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:59Z] INFO  17:59:56,753 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T00:59Z] INFO  17:59:56,773 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:59Z] INFO  17:59:56,864 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.09
[2016-04-15T00:59Z] INFO  17:59:56,876 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T00:59Z] INFO  17:59:56,902 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:59Z] INFO  17:59:57,009 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:59Z] INFO  17:59:57,010 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:59Z] INFO  17:59:57,010 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T00:59Z] INFO  17:59:57,011 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T00:59Z] INFO  17:59:57,029 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T00:59Z] INFO  17:59:57,030 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T00:59Z] INFO  17:59:57,215 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.006984901000000001
[2016-04-15T00:59Z] INFO  17:59:57,216 PairHMM - Total compute time in PairHMM computeLikelihoods() : 0.707532518
[2016-04-15T00:59Z] INFO  17:59:57,217 HaplotypeCaller - Ran local assembly on 1137 active regions
[2016-04-15T00:59Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T00:59Z] INFO  17:59:57,273 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T00:59Z] INFO  17:59:57,274 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T00:59Z] INFO  17:59:57,276 ProgressMeter -            done      6.0270329E7    41.0 s            0.0 s      100.0%    41.0 s       0.0 s
[2016-04-15T00:59Z] INFO  17:59:57,276 ProgressMeter - Total runtime 41.93 secs, 0.70 min, 0.01 hours
[2016-04-15T00:59Z] INFO  17:59:57,277 MicroScheduler - 13718 reads were filtered out during the traversal out of approximately 172478 total reads (7.95%)
[2016-04-15T00:59Z] INFO  17:59:57,277 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:59Z] INFO  17:59:57,278 MicroScheduler -   -> 13331 reads (7.73% of total) failing DuplicateReadFilter
[2016-04-15T00:59Z] INFO  17:59:57,278 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:59Z] INFO  17:59:57,278 MicroScheduler -   -> 387 reads (0.22% of total) failing HCMappingQualityFilter
[2016-04-15T00:59Z] INFO  17:59:57,278 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:59Z] INFO  17:59:57,279 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:59Z] INFO  17:59:57,279 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:59Z] INFO  17:59:57,279 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:59Z] INFO  17:59:57,307 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T00:59Z] INFO  17:59:57,379 IntervalUtils - Processing 161638 bp from intervals
[2016-04-15T00:59Z] WARN  17:59:57,384 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T00:59Z] INFO  17:59:57,498 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T00:59Z] INFO  17:59:57,542 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:59Z] INFO  17:59:57,597 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T00:59Z] INFO  17:59:57,598 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T00:59Z] INFO  17:59:57,599 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T00:59Z] INFO  17:59:57,600 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T00:59Z] INFO  17:59:57,600 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T00:59Z] INFO  17:59:57,601 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T00:59Z] INFO  17:59:57,692 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.037397815
[2016-04-15T00:59Z] INFO  17:59:57,693 PairHMM - Total compute time in PairHMM computeLikelihoods() : 1.3649949620000001
[2016-04-15T00:59Z] INFO  17:59:57,693 HaplotypeCaller - Ran local assembly on 1174 active regions
[2016-04-15T00:59Z] INFO  17:59:57,723 ProgressMeter -            done      6.3591551E7    45.0 s            0.0 s      100.0%    45.0 s       0.0 s
[2016-04-15T00:59Z] INFO  17:59:57,724 ProgressMeter - Total runtime 45.67 secs, 0.76 min, 0.01 hours
[2016-04-15T00:59Z] INFO  17:59:57,725 MicroScheduler - 56679 reads were filtered out during the traversal out of approximately 271665 total reads (20.86%)
[2016-04-15T00:59Z] INFO  17:59:57,726 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T00:59Z] INFO  17:59:57,727 MicroScheduler -   -> 18811 reads (6.92% of total) failing DuplicateReadFilter
[2016-04-15T00:59Z] INFO  17:59:57,727 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T00:59Z] INFO  17:59:57,728 MicroScheduler -   -> 37868 reads (13.94% of total) failing HCMappingQualityFilter
[2016-04-15T00:59Z] INFO  17:59:57,728 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T00:59Z] INFO  17:59:57,729 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T00:59Z] INFO  17:59:57,730 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T00:59Z] INFO  17:59:57,730 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T00:59Z] WARN  17:59:57,763 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T00:59Z] WARN  17:59:57,764 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T00:59Z] GATK: HaplotypeCaller
[2016-04-15T00:59Z] INFO  17:59:57,846 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T00:59Z] INFO  17:59:58,321 ProgressMeter -     7:148801529       1.473339E7    30.0 s            2.0 s       36.6%    81.0 s      51.0 s
[2016-04-15T00:59Z] INFO  17:59:58,819 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:59Z] INFO  17:59:59,030 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:59Z] INFO  17:59:59,033 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T00:59Z] INFO  17:59:59,034 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T00:59Z] INFO  17:59:59,034 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T00:59Z] INFO  17:59:59,039 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/8/R14-18105_kapa-NGv3-PE100-NGv3-sort-8_110656864_126194498-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/8/R14-18105_kapa-NGv3-PE100-NGv3-8_110656864_126194498-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/8/tx/tmplZF_cl/R14-18105_kapa-NGv3-PE100-NGv3-8_110656864_126194498.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T00:59Z] INFO  17:59:59,078 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T00:59Z] INFO  17:59:59,079 HelpFormatter - Date/Time: 2016/04/14 17:59:59
[2016-04-15T00:59Z] INFO  17:59:59,079 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:59Z] INFO  17:59:59,080 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T00:59Z] WARN  17:59:59,109 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T00:59Z] WARN  17:59:59,113 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/8/tx/tmplZF_cl/R14-18105_kapa-NGv3-PE100-NGv3-8_110656864_126194498.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T00:59Z] GATK: HaplotypeCaller
[2016-04-15T00:59Z] INFO  17:59:59,177 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T00:59Z] INFO  17:59:59,361 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T00:59Z] INFO  17:59:59,528 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T00:59Z] INFO  17:59:59,537 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T00:59Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T00:59Z] INFO  17:59:59,560 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T00:59Z] INFO  17:59:59,561 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T00:59Z] GATK: HaplotypeCaller
[2016-04-15T00:59Z] INFO  17:59:59,625 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-15T00:59Z] INFO  17:59:59,651 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T00:59Z] WARN  17:59:59,875 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T00:59Z] WARN  17:59:59,877 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T01:00Z] INFO  18:00:00,009 IntervalUtils - Processing 102393 bp from intervals
[2016-04-15T01:00Z] WARN  18:00:00,014 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:00Z] INFO  18:00:00,112 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:00Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T01:00Z] INFO  18:00:00,187 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T01:00Z] INFO  18:00:00,199 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T01:00Z] INFO  18:00:00,209 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:00Z] INFO  18:00:00,212 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:00Z] INFO  18:00:00,213 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T01:00Z] INFO  18:00:00,214 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T01:00Z] INFO  18:00:00,214 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T01:00Z] INFO  18:00:00,215 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T01:00Z] WARN  18:00:00,562 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T01:00Z] WARN  18:00:00,563 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T01:00Z] INFO  18:00:00,570 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T01:00Z] INFO  18:00:01,218 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:00Z] INFO  18:00:01,227 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:00Z] INFO  18:00:01,227 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:00Z] INFO  18:00:01,228 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:00Z] INFO  18:00:01,232 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/8/R14-18105_kapa-NGv3-PE100-NGv3-sort-8_126369460_141889736-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/8/R14-18105_kapa-NGv3-PE100-NGv3-8_126369460_141889736-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/8/tx/tmpam4naf/R14-18105_kapa-NGv3-PE100-NGv3-8_126369460_141889736.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:00Z] INFO  18:00:01,251 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:00Z] INFO  18:00:01,252 HelpFormatter - Date/Time: 2016/04/14 18:00:01
[2016-04-15T01:00Z] INFO  18:00:01,253 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:00Z] INFO  18:00:01,254 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:00Z] WARN  18:00:01,314 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T01:00Z] WARN  18:00:01,329 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/8/tx/tmpam4naf/R14-18105_kapa-NGv3-PE100-NGv3-8_126369460_141889736.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T01:00Z] INFO  18:00:01,577 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:00Z] INFO  18:00:01,810 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T01:00Z] INFO  18:00:01,820 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:00Z] INFO  18:00:01,898 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-15T01:00Z] INFO  18:00:01,923 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T01:00Z] INFO  18:00:02,431 IntervalUtils - Processing 72911 bp from intervals
[2016-04-15T01:00Z] WARN  18:00:02,437 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:00Z] INFO  18:00:02,582 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:00Z] INFO  18:00:02,691 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:00Z] INFO  18:00:02,692 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:00Z] INFO  18:00:02,704 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T01:00Z] INFO  18:00:02,705 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T01:00Z] INFO  18:00:02,717 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T01:00Z] INFO  18:00:02,718 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T01:00Z] INFO  18:00:02,768 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:00Z] INFO  18:00:02,771 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:00Z] INFO  18:00:02,772 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:00Z] INFO  18:00:02,772 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:00Z] INFO  18:00:02,777 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/8/R14-18105_kapa-NGv3-PE100-NGv3-sort-8_141900641_146364022-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/8/R14-18105_kapa-NGv3-PE100-NGv3-8_141900641_146364022-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/8/tx/tmpISdSOE/R14-18105_kapa-NGv3-PE100-NGv3-8_141900641_146364022.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:00Z] INFO  18:00:02,819 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:00Z] INFO  18:00:02,819 HelpFormatter - Date/Time: 2016/04/14 18:00:02
[2016-04-15T01:00Z] INFO  18:00:02,820 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:00Z] INFO  18:00:02,820 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:00Z] WARN  18:00:02,872 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T01:00Z] WARN  18:00:02,876 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/8/tx/tmpISdSOE/R14-18105_kapa-NGv3-PE100-NGv3-8_141900641_146364022.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T01:00Z] INFO  18:00:02,942 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T01:00Z] INFO  18:00:03,053 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:00Z] INFO  18:00:03,220 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:00Z] INFO  18:00:03,223 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:00Z] INFO  18:00:03,224 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:00Z] INFO  18:00:03,224 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:00Z] INFO  18:00:03,229 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/9/R14-18105_kapa-NGv3-PE100-NGv3-sort-9_0_15510186-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/9/R14-18105_kapa-NGv3-PE100-NGv3-9_0_15510186-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/9/tx/tmpKWqtTR/R14-18105_kapa-NGv3-PE100-NGv3-9_0_15510186.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:00Z] INFO  18:00:03,244 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:00Z] INFO  18:00:03,245 HelpFormatter - Date/Time: 2016/04/14 18:00:03
[2016-04-15T01:00Z] INFO  18:00:03,245 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:00Z] INFO  18:00:03,246 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:00Z] INFO  18:00:03,292 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T01:00Z] WARN  18:00:03,294 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T01:00Z] WARN  18:00:03,297 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/9/tx/tmpKWqtTR/R14-18105_kapa-NGv3-PE100-NGv3-9_0_15510186.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T01:00Z] INFO  18:00:03,301 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:00Z] INFO  18:00:03,389 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.09
[2016-04-15T01:00Z] INFO  18:00:03,421 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T01:00Z] INFO  18:00:03,459 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:00Z] INFO  18:00:03,669 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T01:00Z] INFO  18:00:03,679 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:00Z] INFO  18:00:03,777 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.10
[2016-04-15T01:00Z] INFO  18:00:03,806 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T01:00Z] INFO  18:00:03,840 IntervalUtils - Processing 204618 bp from intervals
[2016-04-15T01:00Z] WARN  18:00:03,845 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:00Z] INFO  18:00:03,952 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:00Z] INFO  18:00:04,071 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:00Z] INFO  18:00:04,071 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:00Z] INFO  18:00:04,071 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T01:00Z] INFO  18:00:04,072 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T01:00Z] INFO  18:00:04,079 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T01:00Z] INFO  18:00:04,080 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T01:00Z] INFO  18:00:04,270 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T01:00Z] INFO  18:00:04,353 IntervalUtils - Processing 123193 bp from intervals
[2016-04-15T01:00Z] WARN  18:00:04,358 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:00Z] INFO  18:00:04,513 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:00Z] INFO  18:00:04,623 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:00Z] INFO  18:00:04,624 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:00Z] INFO  18:00:04,625 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T01:00Z] INFO  18:00:04,626 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T01:00Z] INFO  18:00:04,637 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T01:00Z] INFO  18:00:04,638 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T01:00Z] INFO  18:00:04,914 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T01:00Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T01:00Z] INFO  18:00:05,487 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T01:00Z] INFO  18:00:05,488 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T01:00Z] WARN  18:00:05,873 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T01:00Z] WARN  18:00:05,874 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T01:00Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T01:00Z] INFO  18:00:06,092 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T01:00Z] INFO  18:00:06,093 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T01:00Z] WARN  18:00:06,580 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T01:00Z] WARN  18:00:06,581 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T01:00Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T01:00Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T01:00Z] INFO  18:00:07,898 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T01:00Z] INFO  18:00:07,899 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T01:00Z] INFO  18:00:07,908 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T01:00Z] INFO  18:00:07,909 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T01:00Z] WARN  18:00:08,146 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T01:00Z] WARN  18:00:08,147 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T01:00Z] INFO  18:00:08,202 ProgressMeter -     5:142784715     1.85320462E8   120.0 s            0.0 s       99.7%   120.0 s       0.0 s
[2016-04-15T01:00Z] WARN  18:00:08,225 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T01:00Z] WARN  18:00:08,226 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T01:00Z] INFO  18:00:08,634 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.036861426
[2016-04-15T01:00Z] INFO  18:00:08,654 PairHMM - Total compute time in PairHMM computeLikelihoods() : 9.421480278
[2016-04-15T01:00Z] INFO  18:00:08,655 HaplotypeCaller - Ran local assembly on 2488 active regions
[2016-04-15T01:00Z] INFO  18:00:08,711 ProgressMeter -            done     1.86500366E8   120.0 s            0.0 s      100.0%   120.0 s       0.0 s
[2016-04-15T01:00Z] INFO  18:00:08,712 ProgressMeter - Total runtime 120.55 secs, 2.01 min, 0.03 hours
[2016-04-15T01:00Z] INFO  18:00:08,712 MicroScheduler - 78013 reads were filtered out during the traversal out of approximately 695373 total reads (11.22%)
[2016-04-15T01:00Z] INFO  18:00:08,713 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:00Z] INFO  18:00:08,713 MicroScheduler -   -> 58188 reads (8.37% of total) failing DuplicateReadFilter
[2016-04-15T01:00Z] INFO  18:00:08,713 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:00Z] INFO  18:00:08,713 MicroScheduler -   -> 19825 reads (2.85% of total) failing HCMappingQualityFilter
[2016-04-15T01:00Z] INFO  18:00:08,714 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:00Z] INFO  18:00:08,714 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:00Z] INFO  18:00:08,714 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:00Z] INFO  18:00:08,714 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T01:00Z] INFO  18:00:10,279 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:00Z] GATK: HaplotypeCaller
[2016-04-15T01:00Z] INFO  18:00:14,223 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:00Z] INFO  18:00:14,226 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:00Z] INFO  18:00:14,226 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:00Z] INFO  18:00:14,226 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:00Z] INFO  18:00:14,230 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/9/R14-18105_kapa-NGv3-PE100-NGv3-sort-9_15564086_32405601-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/9/R14-18105_kapa-NGv3-PE100-NGv3-9_15564086_32405601-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/9/tx/tmpUW8BAF/R14-18105_kapa-NGv3-PE100-NGv3-9_15564086_32405601.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:00Z] INFO  18:00:14,248 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:00Z] INFO  18:00:14,249 HelpFormatter - Date/Time: 2016/04/14 18:00:14
[2016-04-15T01:00Z] INFO  18:00:14,249 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:00Z] INFO  18:00:14,249 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:00Z] WARN  18:00:14,290 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T01:00Z] WARN  18:00:14,303 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/9/tx/tmpUW8BAF/R14-18105_kapa-NGv3-PE100-NGv3-9_15564086_32405601.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T01:00Z] INFO  18:00:14,553 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:00Z] INFO  18:00:14,804 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T01:00Z] INFO  18:00:14,825 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:00Z] INFO  18:00:14,906 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-15T01:00Z] INFO  18:00:14,934 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T01:00Z] INFO  18:00:15,404 IntervalUtils - Processing 89361 bp from intervals
[2016-04-15T01:00Z] WARN  18:00:15,409 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:00Z] INFO  18:00:15,586 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:00Z] INFO  18:00:15,674 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:00Z] INFO  18:00:15,676 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:00Z] INFO  18:00:15,676 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T01:00Z] INFO  18:00:15,677 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T01:00Z] INFO  18:00:15,678 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T01:00Z] INFO  18:00:15,678 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T01:00Z] INFO  18:00:15,904 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T01:00Z] INFO  18:00:17,341 ProgressMeter -       8:8748550        8683160.0    30.0 s            3.0 s       52.3%    57.0 s      27.0 s
[2016-04-15T01:00Z] INFO  18:00:18,043 ProgressMeter -      8:22105484       1.499115E7    30.0 s            2.0 s       32.4%    92.0 s      62.0 s
[2016-04-15T01:00Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T01:00Z] INFO  18:00:18,284 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T01:00Z] INFO  18:00:18,285 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T01:00Z] WARN  18:00:18,527 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T01:00Z] WARN  18:00:18,529 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T01:00Z] INFO  18:00:18,570 ProgressMeter -      8:41552695      2.2107505E7    30.0 s            1.0 s       70.0%    42.0 s      12.0 s
[2016-04-15T01:00Z] INFO  18:00:18,950 ProgressMeter -      8:59571810      1.6158098E7    30.0 s            1.0 s       78.6%    38.0 s       8.0 s
[2016-04-15T01:00Z] INFO  18:00:20,336 ProgressMeter -      6:39284558     2.44484017E8   120.0 s            0.0 s       65.5%     3.1 m      63.0 s
[2016-04-15T01:00Z] INFO  18:00:20,889 ProgressMeter -     7:100552881      5.4804197E7    60.0 s            1.0 s       48.2%     2.1 m      64.0 s
[2016-04-15T01:00Z] INFO  18:00:22,062 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.012122474000000001
[2016-04-15T01:00Z] INFO  18:00:22,063 PairHMM - Total compute time in PairHMM computeLikelihoods() : 0.922613576
[2016-04-15T01:00Z] INFO  18:00:22,064 HaplotypeCaller - Ran local assembly on 1618 active regions
[2016-04-15T01:00Z] INFO  18:00:22,128 ProgressMeter -            done      1.2205741E8    59.0 s            0.0 s      100.0%    59.0 s       0.0 s
[2016-04-15T01:00Z] INFO  18:00:22,128 ProgressMeter - Total runtime 59.21 secs, 0.99 min, 0.02 hours
[2016-04-15T01:00Z] INFO  18:00:22,129 MicroScheduler - 27274 reads were filtered out during the traversal out of approximately 329857 total reads (8.27%)
[2016-04-15T01:00Z] INFO  18:00:22,129 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:00Z] INFO  18:00:22,130 MicroScheduler -   -> 26170 reads (7.93% of total) failing DuplicateReadFilter
[2016-04-15T01:00Z] INFO  18:00:22,130 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:00Z] INFO  18:00:22,130 MicroScheduler -   -> 1104 reads (0.33% of total) failing HCMappingQualityFilter
[2016-04-15T01:00Z] INFO  18:00:22,130 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:00Z] INFO  18:00:22,131 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:00Z] INFO  18:00:22,131 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:00Z] INFO  18:00:22,131 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T01:00Z] INFO  18:00:23,140 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.004084692
[2016-04-15T01:00Z] INFO  18:00:23,141 PairHMM - Total compute time in PairHMM computeLikelihoods() : 1.006009462
[2016-04-15T01:00Z] INFO  18:00:23,142 HaplotypeCaller - Ran local assembly on 707 active regions
[2016-04-15T01:00Z] INFO  18:00:23,177 ProgressMeter -            done      2.5170077E7    34.0 s            1.0 s      100.0%    34.0 s       0.0 s
[2016-04-15T01:00Z] INFO  18:00:23,177 ProgressMeter - Total runtime 34.23 secs, 0.57 min, 0.01 hours
[2016-04-15T01:00Z] INFO  18:00:23,178 MicroScheduler - 11251 reads were filtered out during the traversal out of approximately 133520 total reads (8.43%)
[2016-04-15T01:00Z] INFO  18:00:23,178 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:00Z] INFO  18:00:23,179 MicroScheduler -   -> 10546 reads (7.90% of total) failing DuplicateReadFilter
[2016-04-15T01:00Z] INFO  18:00:23,180 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:00Z] INFO  18:00:23,180 MicroScheduler -   -> 705 reads (0.53% of total) failing HCMappingQualityFilter
[2016-04-15T01:00Z] INFO  18:00:23,181 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:00Z] INFO  18:00:23,181 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:00Z] INFO  18:00:23,181 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:00Z] INFO  18:00:23,181 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T01:00Z] INFO  18:00:23,815 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:00Z] INFO  18:00:24,013 ProgressMeter -      8:74701115      2.0870956E7    30.0 s            1.0 s       77.7%    38.0 s       8.0 s
[2016-04-15T01:00Z] GATK: HaplotypeCaller
[2016-04-15T01:00Z] INFO  18:00:24,583 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:00Z] GATK: HaplotypeCaller
[2016-04-15T01:00Z] INFO  18:00:25,412 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.004365361
[2016-04-15T01:00Z] INFO  18:00:25,413 PairHMM - Total compute time in PairHMM computeLikelihoods() : 0.09511599700000001
[2016-04-15T01:00Z] INFO  18:00:25,413 HaplotypeCaller - Ran local assembly on 607 active regions
[2016-04-15T01:00Z] INFO  18:00:25,459 ProgressMeter -            done      1.7516305E7    28.0 s            1.0 s      100.0%    28.0 s       0.0 s
[2016-04-15T01:00Z] INFO  18:00:25,460 ProgressMeter - Total runtime 28.45 secs, 0.47 min, 0.01 hours
[2016-04-15T01:00Z] INFO  18:00:25,460 MicroScheduler - 7403 reads were filtered out during the traversal out of approximately 94278 total reads (7.85%)
[2016-04-15T01:00Z] INFO  18:00:25,461 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:00Z] INFO  18:00:25,461 MicroScheduler -   -> 7280 reads (7.72% of total) failing DuplicateReadFilter
[2016-04-15T01:00Z] INFO  18:00:25,461 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:00Z] INFO  18:00:25,461 MicroScheduler -   -> 123 reads (0.13% of total) failing HCMappingQualityFilter
[2016-04-15T01:00Z] INFO  18:00:25,462 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:00Z] INFO  18:00:25,462 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:00Z] INFO  18:00:25,462 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:00Z] INFO  18:00:25,462 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T01:00Z] INFO  18:00:26,230 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.029650197000000003
[2016-04-15T01:00Z] INFO  18:00:26,231 PairHMM - Total compute time in PairHMM computeLikelihoods() : 0.491694083
[2016-04-15T01:00Z] INFO  18:00:26,231 HaplotypeCaller - Ran local assembly on 902 active regions
[2016-04-15T01:00Z] INFO  18:00:26,284 ProgressMeter -            done      4.4752116E7    37.0 s            0.0 s      100.0%    37.0 s       0.0 s
[2016-04-15T01:00Z] INFO  18:00:26,285 ProgressMeter - Total runtime 37.76 secs, 0.63 min, 0.01 hours
[2016-04-15T01:00Z] INFO  18:00:26,286 MicroScheduler - 14735 reads were filtered out during the traversal out of approximately 179647 total reads (8.20%)
[2016-04-15T01:00Z] INFO  18:00:26,286 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:00Z] INFO  18:00:26,287 MicroScheduler -   -> 14588 reads (8.12% of total) failing DuplicateReadFilter
[2016-04-15T01:00Z] INFO  18:00:26,288 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:00Z] INFO  18:00:26,288 MicroScheduler -   -> 147 reads (0.08% of total) failing HCMappingQualityFilter
[2016-04-15T01:00Z] INFO  18:00:26,289 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:00Z] INFO  18:00:26,290 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:00Z] INFO  18:00:26,290 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:00Z] INFO  18:00:26,291 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T01:00Z] INFO  18:00:27,081 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:00Z] INFO  18:00:27,084 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:00Z] INFO  18:00:27,085 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:00Z] INFO  18:00:27,086 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:00Z] INFO  18:00:27,090 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/9/R14-18105_kapa-NGv3-PE100-NGv3-sort-9_32407258_65506776-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/9/R14-18105_kapa-NGv3-PE100-NGv3-9_32407258_65506776-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/9/tx/tmphkuOl3/R14-18105_kapa-NGv3-PE100-NGv3-9_32407258_65506776.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:00Z] INFO  18:00:27,098 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:00Z] INFO  18:00:27,105 HelpFormatter - Date/Time: 2016/04/14 18:00:27
[2016-04-15T01:00Z] INFO  18:00:27,106 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:00Z] INFO  18:00:27,106 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:00Z] WARN  18:00:27,128 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T01:00Z] WARN  18:00:27,131 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/9/tx/tmphkuOl3/R14-18105_kapa-NGv3-PE100-NGv3-9_32407258_65506776.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T01:00Z] INFO  18:00:27,369 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:00Z] INFO  18:00:27,443 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:00Z] INFO  18:00:27,512 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T01:00Z] INFO  18:00:27,521 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:00Z] INFO  18:00:27,615 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.09
[2016-04-15T01:00Z] INFO  18:00:27,626 ProgressMeter -     8:101724590      1.8770485E7    30.0 s            1.0 s       53.0%    56.0 s      26.0 s
[2016-04-15T01:00Z] INFO  18:00:27,640 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T01:00Z] INFO  18:00:27,674 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:00Z] GATK: HaplotypeCaller
[2016-04-15T01:00Z] INFO  18:00:27,765 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:00Z] INFO  18:00:27,768 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:00Z] INFO  18:00:27,768 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:00Z] INFO  18:00:27,769 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:00Z] INFO  18:00:27,773 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/9/R14-18105_kapa-NGv3-PE100-NGv3-sort-9_65507205_82187750-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/9/R14-18105_kapa-NGv3-PE100-NGv3-9_65507205_82187750-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/9/tx/tmpbdLZWf/R14-18105_kapa-NGv3-PE100-NGv3-9_65507205_82187750.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:00Z] INFO  18:00:27,783 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:00Z] INFO  18:00:27,784 HelpFormatter - Date/Time: 2016/04/14 18:00:27
[2016-04-15T01:00Z] INFO  18:00:27,784 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:00Z] INFO  18:00:27,785 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:00Z] WARN  18:00:27,810 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T01:00Z] WARN  18:00:27,813 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/9/tx/tmpbdLZWf/R14-18105_kapa-NGv3-PE100-NGv3-9_65507205_82187750.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T01:00Z] GATK: HaplotypeCaller
[2016-04-15T01:00Z] INFO  18:00:27,949 IntervalUtils - Processing 223679 bp from intervals
[2016-04-15T01:00Z] WARN  18:00:27,955 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:00Z] INFO  18:00:27,976 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:00Z] INFO  18:00:28,066 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:00Z] INFO  18:00:28,131 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:00Z] INFO  18:00:28,132 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:00Z] INFO  18:00:28,133 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T01:00Z] INFO  18:00:28,133 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T01:00Z] INFO  18:00:28,134 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T01:00Z] INFO  18:00:28,134 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T01:00Z] INFO  18:00:28,185 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T01:00Z] INFO  18:00:28,211 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:00Z] INFO  18:00:28,302 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.09
[2016-04-15T01:00Z] INFO  18:00:28,307 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T01:00Z] INFO  18:00:28,330 ProgressMeter -     7:151815763      7.1081995E7    60.0 s            0.0 s       82.9%    72.0 s      12.0 s
[2016-04-15T01:00Z] INFO  18:00:28,326 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T01:00Z] INFO  18:00:28,829 IntervalUtils - Processing 119378 bp from intervals
[2016-04-15T01:00Z] WARN  18:00:28,845 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:00Z] INFO  18:00:28,953 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:00Z] INFO  18:00:29,028 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:00Z] INFO  18:00:29,030 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:00Z] INFO  18:00:29,031 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T01:00Z] INFO  18:00:29,032 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T01:00Z] INFO  18:00:29,032 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T01:00Z] INFO  18:00:29,032 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T01:00Z] INFO  18:00:29,118 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.016885445000000002
[2016-04-15T01:00Z] INFO  18:00:29,119 PairHMM - Total compute time in PairHMM computeLikelihoods() : 0.191356996
[2016-04-15T01:00Z] INFO  18:00:29,120 HaplotypeCaller - Ran local assembly on 778 active regions
[2016-04-15T01:00Z] INFO  18:00:29,184 ProgressMeter -            done      2.8015737E7    35.0 s            1.0 s      100.0%    35.0 s       0.0 s
[2016-04-15T01:00Z] INFO  18:00:29,185 ProgressMeter - Total runtime 35.21 secs, 0.59 min, 0.01 hours
[2016-04-15T01:00Z] INFO  18:00:29,185 MicroScheduler - 11570 reads were filtered out during the traversal out of approximately 142581 total reads (8.11%)
[2016-04-15T01:00Z] INFO  18:00:29,185 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:00Z] INFO  18:00:29,186 MicroScheduler -   -> 11297 reads (7.92% of total) failing DuplicateReadFilter
[2016-04-15T01:00Z] INFO  18:00:29,186 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:00Z] INFO  18:00:29,186 MicroScheduler -   -> 273 reads (0.19% of total) failing HCMappingQualityFilter
[2016-04-15T01:00Z] INFO  18:00:29,186 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:00Z] INFO  18:00:29,187 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:00Z] INFO  18:00:29,187 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:00Z] INFO  18:00:29,187 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T01:00Z] INFO  18:00:29,214 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T01:00Z] INFO  18:00:30,236 ProgressMeter -     8:125076775      2.0083041E7    30.0 s            1.0 s       82.3%    36.0 s       6.0 s
[2016-04-15T01:00Z] INFO  18:00:30,644 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:00Z] INFO  18:00:30,696 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:00Z] INFO  18:00:30,699 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:00Z] INFO  18:00:30,700 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:00Z] INFO  18:00:30,700 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:00Z] INFO  18:00:30,705 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/9/R14-18105_kapa-NGv3-PE100-NGv3-sort-9_82188172_97717561-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/9/R14-18105_kapa-NGv3-PE100-NGv3-9_82188172_97717561-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/9/tx/tmpxxUeR2/R14-18105_kapa-NGv3-PE100-NGv3-9_82188172_97717561.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:00Z] INFO  18:00:30,721 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:00Z] INFO  18:00:30,722 HelpFormatter - Date/Time: 2016/04/14 18:00:30
[2016-04-15T01:00Z] INFO  18:00:30,723 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:00Z] INFO  18:00:30,723 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:00Z] WARN  18:00:30,775 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T01:00Z] WARN  18:00:30,777 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/9/tx/tmpxxUeR2/R14-18105_kapa-NGv3-PE100-NGv3-9_82188172_97717561.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T01:00Z] INFO  18:00:30,799 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:00Z] INFO  18:00:30,802 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:00Z] INFO  18:00:30,803 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:00Z] INFO  18:00:30,803 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:00Z] INFO  18:00:30,808 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/9/R14-18105_kapa-NGv3-PE100-NGv3-sort-9_97718189_113228306-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/9/R14-18105_kapa-NGv3-PE100-NGv3-9_97718189_113228306-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/9/tx/tmpYUvOyz/R14-18105_kapa-NGv3-PE100-NGv3-9_97718189_113228306.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:00Z] INFO  18:00:30,820 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:00Z] INFO  18:00:30,821 HelpFormatter - Date/Time: 2016/04/14 18:00:30
[2016-04-15T01:00Z] INFO  18:00:30,821 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:00Z] INFO  18:00:30,822 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:00Z] WARN  18:00:30,845 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T01:00Z] WARN  18:00:30,848 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/9/tx/tmpYUvOyz/R14-18105_kapa-NGv3-PE100-NGv3-9_97718189_113228306.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T01:00Z] INFO  18:00:30,981 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:00Z] GATK: HaplotypeCaller
[2016-04-15T01:00Z] INFO  18:00:31,025 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:00Z] INFO  18:00:31,163 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T01:00Z] INFO  18:00:31,172 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:00Z] INFO  18:00:31,208 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T01:00Z] INFO  18:00:31,224 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:00Z] INFO  18:00:31,240 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-15T01:00Z] INFO  18:00:31,258 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T01:00Z] INFO  18:00:31,329 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.10
[2016-04-15T01:00Z] INFO  18:00:31,362 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T01:00Z] INFO  18:00:31,367 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.0063895010000000006
[2016-04-15T01:00Z] INFO  18:00:31,368 PairHMM - Total compute time in PairHMM computeLikelihoods() : 0.348765674
[2016-04-15T01:00Z] INFO  18:00:31,368 HaplotypeCaller - Ran local assembly on 602 active regions
[2016-04-15T01:00Z] INFO  18:00:31,443 ProgressMeter -            done      1.8346896E7    28.0 s            1.0 s      100.0%    28.0 s       0.0 s
[2016-04-15T01:00Z] INFO  18:00:31,443 ProgressMeter - Total runtime 28.75 secs, 0.48 min, 0.01 hours
[2016-04-15T01:00Z] INFO  18:00:31,444 MicroScheduler - 9611 reads were filtered out during the traversal out of approximately 119603 total reads (8.04%)
[2016-04-15T01:00Z] INFO  18:00:31,445 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:00Z] INFO  18:00:31,445 MicroScheduler -   -> 9484 reads (7.93% of total) failing DuplicateReadFilter
[2016-04-15T01:00Z] INFO  18:00:31,446 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:00Z] INFO  18:00:31,446 MicroScheduler -   -> 127 reads (0.11% of total) failing HCMappingQualityFilter
[2016-04-15T01:00Z] INFO  18:00:31,446 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:00Z] INFO  18:00:31,446 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:00Z] INFO  18:00:31,447 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:00Z] INFO  18:00:31,447 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T01:00Z] INFO  18:00:31,693 IntervalUtils - Processing 181286 bp from intervals
[2016-04-15T01:00Z] WARN  18:00:31,698 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:00Z] INFO  18:00:31,770 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:00Z] INFO  18:00:31,859 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:00Z] INFO  18:00:31,860 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:00Z] INFO  18:00:31,861 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T01:00Z] INFO  18:00:31,861 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T01:00Z] INFO  18:00:31,861 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T01:00Z] INFO  18:00:31,861 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T01:00Z] INFO  18:00:31,869 IntervalUtils - Processing 199321 bp from intervals
[2016-04-15T01:00Z] WARN  18:00:31,875 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:00Z] INFO  18:00:32,043 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:00Z] INFO  18:00:32,079 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T01:00Z] INFO  18:00:32,181 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:00Z] INFO  18:00:32,182 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:00Z] INFO  18:00:32,183 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T01:00Z] INFO  18:00:32,183 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T01:00Z] INFO  18:00:32,194 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T01:00Z] INFO  18:00:32,195 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T01:00Z] INFO  18:00:32,418 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T01:00Z] INFO  18:00:32,795 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:00Z] GATK: HaplotypeCaller
[2016-04-15T01:00Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T01:00Z] INFO  18:00:33,400 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T01:00Z] INFO  18:00:33,412 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T01:00Z] INFO  18:00:33,932 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.040725071
[2016-04-15T01:00Z] INFO  18:00:33,943 PairHMM - Total compute time in PairHMM computeLikelihoods() : 1.221557209
[2016-04-15T01:00Z] INFO  18:00:33,944 HaplotypeCaller - Ran local assembly on 838 active regions
[2016-04-15T01:00Z] WARN  18:00:33,965 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T01:00Z] WARN  18:00:33,966 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T01:00Z] INFO  18:00:33,987 ProgressMeter -            done      2.7109958E7    46.0 s            1.0 s      100.0%    46.0 s       0.0 s
[2016-04-15T01:00Z] INFO  18:00:33,993 ProgressMeter - Total runtime 46.67 secs, 0.78 min, 0.01 hours
[2016-04-15T01:00Z] INFO  18:00:33,993 MicroScheduler - 58993 reads were filtered out during the traversal out of approximately 218854 total reads (26.96%)
[2016-04-15T01:00Z] INFO  18:00:33,994 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:00Z] INFO  18:00:33,995 MicroScheduler -   -> 14153 reads (6.47% of total) failing DuplicateReadFilter
[2016-04-15T01:00Z] INFO  18:00:33,995 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:00Z] INFO  18:00:33,996 MicroScheduler -   -> 44840 reads (20.49% of total) failing HCMappingQualityFilter
[2016-04-15T01:00Z] INFO  18:00:33,997 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:00Z] INFO  18:00:33,997 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:00Z] INFO  18:00:33,998 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:00Z] INFO  18:00:33,998 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T01:00Z] INFO  18:00:34,092 ProgressMeter -     8:144657683        7922395.0    30.0 s            3.0 s       34.3%    87.0 s      57.0 s
[2016-04-15T01:00Z] INFO  18:00:34,253 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:00Z] INFO  18:00:34,256 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:00Z] INFO  18:00:34,256 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:00Z] INFO  18:00:34,257 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:00Z] INFO  18:00:34,261 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/9/R14-18105_kapa-NGv3-PE100-NGv3-sort-9_113231219_129089575-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/9/R14-18105_kapa-NGv3-PE100-NGv3-9_113231219_129089575-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/9/tx/tmp7diJBz/R14-18105_kapa-NGv3-PE100-NGv3-9_113231219_129089575.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:00Z] INFO  18:00:34,279 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:00Z] INFO  18:00:34,280 HelpFormatter - Date/Time: 2016/04/14 18:00:34
[2016-04-15T01:00Z] INFO  18:00:34,281 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:00Z] INFO  18:00:34,282 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:00Z] WARN  18:00:34,305 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T01:00Z] INFO  18:00:34,322 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.023208306
[2016-04-15T01:00Z] WARN  18:00:34,329 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/9/tx/tmp7diJBz/R14-18105_kapa-NGv3-PE100-NGv3-9_113231219_129089575.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T01:00Z] INFO  18:00:34,333 PairHMM - Total compute time in PairHMM computeLikelihoods() : 0.5687584880000001
[2016-04-15T01:00Z] INFO  18:00:34,334 HaplotypeCaller - Ran local assembly on 754 active regions
[2016-04-15T01:00Z] INFO  18:00:34,365 ProgressMeter -            done       2.937439E7    34.0 s            1.0 s      100.0%    34.0 s       0.0 s
[2016-04-15T01:00Z] INFO  18:00:34,366 ProgressMeter - Total runtime 34.15 secs, 0.57 min, 0.01 hours
[2016-04-15T01:00Z] INFO  18:00:34,367 MicroScheduler - 10857 reads were filtered out during the traversal out of approximately 137899 total reads (7.87%)
[2016-04-15T01:00Z] INFO  18:00:34,368 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:00Z] INFO  18:00:34,368 MicroScheduler -   -> 10722 reads (7.78% of total) failing DuplicateReadFilter
[2016-04-15T01:00Z] INFO  18:00:34,369 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:00Z] INFO  18:00:34,370 MicroScheduler -   -> 135 reads (0.10% of total) failing HCMappingQualityFilter
[2016-04-15T01:00Z] INFO  18:00:34,370 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:00Z] INFO  18:00:34,371 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:00Z] INFO  18:00:34,371 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:00Z] INFO  18:00:34,372 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T01:00Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T01:00Z] INFO  18:00:34,396 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T01:00Z] INFO  18:00:34,397 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T01:00Z] INFO  18:00:34,614 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:00Z] INFO  18:00:34,652 ProgressMeter -       9:7799502      1.8362102E7    30.0 s            1.0 s       73.1%    41.0 s      11.0 s
[2016-04-15T01:00Z] WARN  18:00:34,704 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T01:00Z] WARN  18:00:34,705 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T01:00Z] INFO  18:00:34,763 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T01:00Z] INFO  18:00:34,772 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:00Z] INFO  18:00:34,838 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-15T01:00Z] INFO  18:00:34,856 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T01:00Z] INFO  18:00:35,444 IntervalUtils - Processing 228449 bp from intervals
[2016-04-15T01:00Z] WARN  18:00:35,460 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:00Z] INFO  18:00:35,567 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:00Z] INFO  18:00:35,583 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:00Z] INFO  18:00:35,722 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:00Z] INFO  18:00:35,722 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:00Z] INFO  18:00:35,722 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T01:00Z] INFO  18:00:35,723 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T01:00Z] INFO  18:00:35,733 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T01:00Z] INFO  18:00:35,734 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T01:00Z] GATK: HaplotypeCaller
[2016-04-15T01:00Z] INFO  18:00:35,909 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:00Z] INFO  18:00:35,974 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T01:00Z] INFO  18:00:36,148 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:00Z] INFO  18:00:36,151 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:00Z] INFO  18:00:36,152 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:00Z] INFO  18:00:36,152 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:00Z] INFO  18:00:36,157 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/9/R14-18105_kapa-NGv3-PE100-NGv3-sort-9_129097484_141213431-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/9/R14-18105_kapa-NGv3-PE100-NGv3-9_129097484_141213431-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/9/tx/tmpvNMgtg/R14-18105_kapa-NGv3-PE100-NGv3-9_129097484_141213431.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:00Z] INFO  18:00:36,176 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:00Z] INFO  18:00:36,180 HelpFormatter - Date/Time: 2016/04/14 18:00:36
[2016-04-15T01:00Z] INFO  18:00:36,180 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:00Z] INFO  18:00:36,181 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:00Z] GATK: HaplotypeCaller
[2016-04-15T01:00Z] WARN  18:00:36,227 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T01:00Z] WARN  18:00:36,230 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/9/tx/tmpvNMgtg/R14-18105_kapa-NGv3-PE100-NGv3-9_129097484_141213431.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T01:00Z] INFO  18:00:36,511 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:00Z] INFO  18:00:36,715 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T01:00Z] INFO  18:00:36,732 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:00Z] INFO  18:00:36,827 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.09
[2016-04-15T01:00Z] INFO  18:00:36,860 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T01:00Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T01:00Z] INFO  18:00:37,108 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T01:00Z] INFO  18:00:37,109 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T01:00Z] WARN  18:00:37,405 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T01:00Z] WARN  18:00:37,406 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T01:00Z] INFO  18:00:37,582 IntervalUtils - Processing 455246 bp from intervals
[2016-04-15T01:00Z] WARN  18:00:37,588 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:00Z] INFO  18:00:37,735 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:00Z] INFO  18:00:37,981 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:00Z] INFO  18:00:37,983 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:00Z] INFO  18:00:37,990 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T01:00Z] INFO  18:00:37,996 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T01:00Z] INFO  18:00:38,006 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T01:00Z] INFO  18:00:38,006 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T01:00Z] INFO  18:00:38,279 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T01:00Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T01:00Z] INFO  18:00:38,334 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T01:00Z] INFO  18:00:38,337 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T01:00Z] WARN  18:00:38,778 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T01:00Z] WARN  18:00:38,779 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T01:00Z] INFO  18:00:38,826 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:00Z] INFO  18:00:38,829 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:00Z] INFO  18:00:38,830 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:00Z] INFO  18:00:38,831 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:00Z] INFO  18:00:38,835 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/10/R14-18105_kapa-NGv3-PE100-NGv3-sort-10_0_15559243-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/10/R14-18105_kapa-NGv3-PE100-NGv3-10_0_15559243-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/10/tx/tmp_lb8UB/R14-18105_kapa-NGv3-PE100-NGv3-10_0_15559243.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:00Z] INFO  18:00:38,847 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:00Z] INFO  18:00:38,862 HelpFormatter - Date/Time: 2016/04/14 18:00:38
[2016-04-15T01:00Z] INFO  18:00:38,863 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:00Z] INFO  18:00:38,871 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:00Z] WARN  18:00:38,906 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T01:00Z] WARN  18:00:38,908 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/10/tx/tmp_lb8UB/R14-18105_kapa-NGv3-PE100-NGv3-10_0_15559243.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T01:00Z] INFO  18:00:39,142 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:00Z] INFO  18:00:39,341 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T01:00Z] INFO  18:00:39,351 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:00Z] INFO  18:00:39,471 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.12
[2016-04-15T01:00Z] INFO  18:00:39,500 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T01:00Z] INFO  18:00:39,712 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:00Z] INFO  18:00:39,716 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:00Z] INFO  18:00:39,716 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:00Z] INFO  18:00:39,717 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:00Z] INFO  18:00:39,721 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/10/R14-18105_kapa-NGv3-PE100-NGv3-sort-10_15561288_31134502-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/10/R14-18105_kapa-NGv3-PE100-NGv3-10_15561288_31134502-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/10/tx/tmpFjczGO/R14-18105_kapa-NGv3-PE100-NGv3-10_15561288_31134502.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:00Z] INFO  18:00:39,739 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:00Z] INFO  18:00:39,739 HelpFormatter - Date/Time: 2016/04/14 18:00:39
[2016-04-15T01:00Z] INFO  18:00:39,740 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:00Z] INFO  18:00:39,741 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:00Z] WARN  18:00:39,786 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T01:00Z] WARN  18:00:39,793 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/10/tx/tmpFjczGO/R14-18105_kapa-NGv3-PE100-NGv3-10_15561288_31134502.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T01:00Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T01:00Z] INFO  18:00:39,944 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T01:00Z] INFO  18:00:39,946 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T01:00Z] INFO  18:00:40,058 IntervalUtils - Processing 145147 bp from intervals
[2016-04-15T01:00Z] WARN  18:00:40,075 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:00Z] INFO  18:00:40,089 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:00Z] INFO  18:00:40,235 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:00Z] WARN  18:00:40,299 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T01:00Z] WARN  18:00:40,300 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T01:00Z] INFO  18:00:40,371 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T01:00Z] INFO  18:00:40,381 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:00Z] INFO  18:00:40,402 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:00Z] INFO  18:00:40,402 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:00Z] INFO  18:00:40,403 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T01:00Z] INFO  18:00:40,403 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T01:00Z] INFO  18:00:40,414 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T01:00Z] INFO  18:00:40,414 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T01:00Z] INFO  18:00:40,484 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.10
[2016-04-15T01:00Z] INFO  18:00:40,521 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T01:00Z] INFO  18:00:40,733 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T01:00Z] INFO  18:00:41,029 IntervalUtils - Processing 156629 bp from intervals
[2016-04-15T01:00Z] WARN  18:00:41,034 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:00Z] INFO  18:00:41,155 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:00Z] INFO  18:00:41,266 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:00Z] INFO  18:00:41,267 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:00Z] INFO  18:00:41,268 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T01:00Z] INFO  18:00:41,269 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T01:00Z] INFO  18:00:41,269 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T01:00Z] INFO  18:00:41,270 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T01:00Z] INFO  18:00:41,475 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T01:00Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T01:00Z] INFO  18:00:42,105 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T01:00Z] INFO  18:00:42,120 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T01:00Z] WARN  18:00:42,734 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T01:00Z] WARN  18:00:42,735 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T01:00Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T01:00Z] INFO  18:00:43,702 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T01:00Z] INFO  18:00:43,703 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T01:00Z] WARN  18:00:43,908 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T01:00Z] WARN  18:00:43,909 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T01:00Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T01:00Z] INFO  18:00:44,310 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T01:00Z] INFO  18:00:44,310 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T01:00Z] INFO  18:00:44,431 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.021775202
[2016-04-15T01:00Z] INFO  18:00:44,431 PairHMM - Total compute time in PairHMM computeLikelihoods() : 0.514889126
[2016-04-15T01:00Z] INFO  18:00:44,431 HaplotypeCaller - Ran local assembly on 902 active regions
[2016-04-15T01:00Z] INFO  18:00:44,495 ProgressMeter -            done      3.9438501E7    39.0 s            1.0 s      100.0%    39.0 s       0.0 s
[2016-04-15T01:00Z] INFO  18:00:44,495 ProgressMeter - Total runtime 39.87 secs, 0.66 min, 0.01 hours
[2016-04-15T01:00Z] INFO  18:00:44,496 MicroScheduler - 24412 reads were filtered out during the traversal out of approximately 176486 total reads (13.83%)
[2016-04-15T01:00Z] INFO  18:00:44,496 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:00Z] INFO  18:00:44,496 MicroScheduler -   -> 13349 reads (7.56% of total) failing DuplicateReadFilter
[2016-04-15T01:00Z] INFO  18:00:44,496 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:00Z] INFO  18:00:44,497 MicroScheduler -   -> 11063 reads (6.27% of total) failing HCMappingQualityFilter
[2016-04-15T01:00Z] INFO  18:00:44,497 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:00Z] INFO  18:00:44,497 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:00Z] INFO  18:00:44,497 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:00Z] INFO  18:00:44,498 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T01:00Z] WARN  18:00:44,655 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T01:00Z] WARN  18:00:44,656 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T01:00Z] INFO  18:00:44,755 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.06335562
[2016-04-15T01:00Z] INFO  18:00:44,756 PairHMM - Total compute time in PairHMM computeLikelihoods() : 7.192595528
[2016-04-15T01:00Z] INFO  18:00:44,757 HaplotypeCaller - Ran local assembly on 1705 active regions
[2016-04-15T01:00Z] INFO  18:00:44,812 ProgressMeter -            done     1.17619154E8    76.0 s            0.0 s      100.0%    76.0 s       0.0 s
[2016-04-15T01:00Z] INFO  18:00:44,813 ProgressMeter - Total runtime 76.53 secs, 1.28 min, 0.02 hours
[2016-04-15T01:00Z] INFO  18:00:44,813 MicroScheduler - 87494 reads were filtered out during the traversal out of approximately 437957 total reads (19.98%)
[2016-04-15T01:00Z] INFO  18:00:44,814 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:00Z] INFO  18:00:44,814 MicroScheduler -   -> 30363 reads (6.93% of total) failing DuplicateReadFilter
[2016-04-15T01:00Z] INFO  18:00:44,814 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:00Z] INFO  18:00:44,814 MicroScheduler -   -> 57131 reads (13.04% of total) failing HCMappingQualityFilter
[2016-04-15T01:00Z] INFO  18:00:44,815 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:00Z] INFO  18:00:44,815 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:00Z] INFO  18:00:44,815 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:00Z] INFO  18:00:44,815 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T01:00Z] INFO  18:00:45,700 ProgressMeter -      9:26905509      1.0778361E7    30.0 s            2.0 s       80.8%    37.0 s       7.0 s
[2016-04-15T01:00Z] WARN  18:00:45,922 ExactAFCalculator - this tool is currently set to genotype at most 6 alternate alleles in a given context, but the context at 6:43238152 has 8 alternate alleles so only the top alleles will be used; see the --max_alternate_alleles argument
[2016-04-15T01:00Z] INFO  18:00:46,182 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:00Z] INFO  18:00:46,330 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:00Z] GATK: HaplotypeCaller
[2016-04-15T01:00Z] GATK: HaplotypeCaller
[2016-04-15T01:00Z] INFO  18:00:46,983 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.009422719000000001
[2016-04-15T01:00Z] INFO  18:00:46,983 PairHMM - Total compute time in PairHMM computeLikelihoods() : 4.179151745
[2016-04-15T01:00Z] INFO  18:00:46,984 HaplotypeCaller - Ran local assembly on 1145 active regions
[2016-04-15T01:00Z] INFO  18:00:47,043 ProgressMeter -            done      6.7177744E7    49.0 s            0.0 s      100.0%    49.0 s       0.0 s
[2016-04-15T01:00Z] INFO  18:00:47,043 ProgressMeter - Total runtime 49.45 secs, 0.82 min, 0.01 hours
[2016-04-15T01:00Z] INFO  18:00:47,044 MicroScheduler - 15975 reads were filtered out during the traversal out of approximately 200766 total reads (7.96%)
[2016-04-15T01:00Z] INFO  18:00:47,044 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:00Z] INFO  18:00:47,044 MicroScheduler -   -> 15701 reads (7.82% of total) failing DuplicateReadFilter
[2016-04-15T01:00Z] INFO  18:00:47,045 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:00Z] INFO  18:00:47,045 MicroScheduler -   -> 274 reads (0.14% of total) failing HCMappingQualityFilter
[2016-04-15T01:00Z] INFO  18:00:47,045 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:00Z] INFO  18:00:47,045 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:00Z] INFO  18:00:47,046 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:00Z] INFO  18:00:47,046 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T01:00Z] INFO  18:00:48,047 ProgressMeter -      8:30038104     1.14751698E8    60.0 s            0.0 s       90.3%    66.0 s       6.0 s
[2016-04-15T01:00Z] INFO  18:00:48,705 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:00Z] GATK: HaplotypeCaller
[2016-04-15T01:00Z] INFO  18:00:49,789 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:00Z] INFO  18:00:49,792 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:00Z] INFO  18:00:49,793 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:00Z] INFO  18:00:49,793 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:00Z] INFO  18:00:49,798 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/10/R14-18105_kapa-NGv3-PE100-NGv3-sort-10_31137459_46960129-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/10/R14-18105_kapa-NGv3-PE100-NGv3-10_31137459_46960129-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/10/tx/tmpAEG2g8/R14-18105_kapa-NGv3-PE100-NGv3-10_31137459_46960129.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:00Z] INFO  18:00:49,811 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:00Z] INFO  18:00:49,812 HelpFormatter - Date/Time: 2016/04/14 18:00:49
[2016-04-15T01:00Z] INFO  18:00:49,812 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:00Z] INFO  18:00:49,813 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:00Z] WARN  18:00:49,856 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T01:00Z] WARN  18:00:49,858 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/10/tx/tmpAEG2g8/R14-18105_kapa-NGv3-PE100-NGv3-10_31137459_46960129.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T01:00Z] INFO  18:00:50,040 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:00Z] INFO  18:00:50,116 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:00Z] INFO  18:00:50,118 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:00Z] INFO  18:00:50,118 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:00Z] INFO  18:00:50,118 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:00Z] INFO  18:00:50,134 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/10/R14-18105_kapa-NGv3-PE100-NGv3-sort-10_46960410_62493077-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/10/R14-18105_kapa-NGv3-PE100-NGv3-10_46960410_62493077-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/10/tx/tmpO7lU3U/R14-18105_kapa-NGv3-PE100-NGv3-10_46960410_62493077.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:00Z] INFO  18:00:50,160 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:00Z] INFO  18:00:50,161 HelpFormatter - Date/Time: 2016/04/14 18:00:50
[2016-04-15T01:00Z] INFO  18:00:50,161 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:00Z] INFO  18:00:50,161 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:00Z] WARN  18:00:50,207 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T01:00Z] WARN  18:00:50,210 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/10/tx/tmpO7lU3U/R14-18105_kapa-NGv3-PE100-NGv3-10_46960410_62493077.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T01:00Z] INFO  18:00:50,296 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T01:00Z] INFO  18:00:50,315 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:00Z] INFO  18:00:50,337 ProgressMeter -      6:43400276     4.22898131E8     2.5 m            0.0 s       88.5%     2.8 m      19.0 s
[2016-04-15T01:00Z] INFO  18:00:50,406 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.09
[2016-04-15T01:00Z] INFO  18:00:50,432 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T01:00Z] INFO  18:00:50,479 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:00Z] INFO  18:00:50,720 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T01:00Z] INFO  18:00:50,739 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:00Z] INFO  18:00:50,840 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.10
[2016-04-15T01:00Z] INFO  18:00:50,881 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T01:00Z] INFO  18:00:50,890 ProgressMeter -     7:101991168      8.3661526E7    90.0 s            1.0 s       65.9%     2.3 m      46.0 s
[2016-04-15T01:00Z] INFO  18:00:50,941 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.009940948
[2016-04-15T01:00Z] INFO  18:00:50,942 PairHMM - Total compute time in PairHMM computeLikelihoods() : 1.367679828
[2016-04-15T01:00Z] INFO  18:00:50,943 HaplotypeCaller - Ran local assembly on 634 active regions
[2016-04-15T01:00Z] INFO  18:00:51,006 ProgressMeter -            done      1.7418853E7    35.0 s            2.0 s      100.0%    35.0 s       0.0 s
[2016-04-15T01:00Z] INFO  18:00:51,007 ProgressMeter - Total runtime 35.33 secs, 0.59 min, 0.01 hours
[2016-04-15T01:00Z] INFO  18:00:51,007 MicroScheduler - 12156 reads were filtered out during the traversal out of approximately 120683 total reads (10.07%)
[2016-04-15T01:00Z] INFO  18:00:51,007 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:00Z] INFO  18:00:51,007 MicroScheduler -   -> 8961 reads (7.43% of total) failing DuplicateReadFilter
[2016-04-15T01:00Z] INFO  18:00:51,008 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:00Z] INFO  18:00:51,008 MicroScheduler -   -> 3195 reads (2.65% of total) failing HCMappingQualityFilter
[2016-04-15T01:00Z] INFO  18:00:51,008 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:00Z] INFO  18:00:51,008 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:00Z] INFO  18:00:51,009 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:00Z] INFO  18:00:51,009 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T01:00Z] INFO  18:00:51,017 IntervalUtils - Processing 103621 bp from intervals
[2016-04-15T01:00Z] WARN  18:00:51,022 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:00Z] INFO  18:00:51,130 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:00Z] INFO  18:00:51,208 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:00Z] INFO  18:00:51,209 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:00Z] INFO  18:00:51,210 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T01:00Z] INFO  18:00:51,211 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T01:00Z] INFO  18:00:51,229 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T01:00Z] INFO  18:00:51,230 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T01:00Z] INFO  18:00:51,286 IntervalUtils - Processing 143638 bp from intervals
[2016-04-15T01:00Z] WARN  18:00:51,291 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:00Z] INFO  18:00:51,396 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:00Z] INFO  18:00:51,469 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T01:00Z] INFO  18:00:51,502 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:00Z] INFO  18:00:51,503 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:00Z] INFO  18:00:51,504 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T01:00Z] INFO  18:00:51,505 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T01:00Z] INFO  18:00:51,506 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T01:00Z] INFO  18:00:51,506 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T01:00Z] INFO  18:00:51,718 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T01:00Z] INFO  18:00:51,911 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.014984800000000001
[2016-04-15T01:00Z] INFO  18:00:51,912 PairHMM - Total compute time in PairHMM computeLikelihoods() : 1.4194010970000002
[2016-04-15T01:00Z] INFO  18:00:51,913 HaplotypeCaller - Ran local assembly on 1800 active regions
[2016-04-15T01:00Z] INFO  18:00:51,955 ProgressMeter -            done     1.35599805E8    63.0 s            0.0 s      100.0%    63.0 s       0.0 s
[2016-04-15T01:00Z] INFO  18:00:51,956 ProgressMeter - Total runtime 63.93 secs, 1.07 min, 0.02 hours
[2016-04-15T01:00Z] INFO  18:00:51,956 MicroScheduler - 29256 reads were filtered out during the traversal out of approximately 344751 total reads (8.49%)
[2016-04-15T01:00Z] INFO  18:00:51,957 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:00Z] INFO  18:00:51,958 MicroScheduler -   -> 27802 reads (8.06% of total) failing DuplicateReadFilter
[2016-04-15T01:00Z] INFO  18:00:51,958 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:00Z] INFO  18:00:51,958 MicroScheduler -   -> 1454 reads (0.42% of total) failing HCMappingQualityFilter
[2016-04-15T01:00Z] INFO  18:00:51,958 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:00Z] INFO  18:00:51,959 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:00Z] INFO  18:00:51,959 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:00Z] INFO  18:00:51,959 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T01:00Z] INFO  18:00:52,358 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:00Z] INFO  18:00:52,361 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:00Z] INFO  18:00:52,362 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:00Z] INFO  18:00:52,362 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:00Z] INFO  18:00:52,367 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/10/R14-18105_kapa-NGv3-PE100-NGv3-sort-10_62539923_78084243-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/10/R14-18105_kapa-NGv3-PE100-NGv3-10_62539923_78084243-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/10/tx/tmpsyZf_l/R14-18105_kapa-NGv3-PE100-NGv3-10_62539923_78084243.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:00Z] INFO  18:00:52,386 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:00Z] INFO  18:00:52,387 HelpFormatter - Date/Time: 2016/04/14 18:00:52
[2016-04-15T01:00Z] INFO  18:00:52,387 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:00Z] INFO  18:00:52,388 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:00Z] WARN  18:00:52,430 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T01:00Z] WARN  18:00:52,433 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/10/tx/tmpsyZf_l/R14-18105_kapa-NGv3-PE100-NGv3-10_62539923_78084243.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T01:00Z] INFO  18:00:52,470 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:00Z] INFO  18:00:52,690 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:00Z] GATK: HaplotypeCaller
[2016-04-15T01:00Z] INFO  18:00:52,832 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T01:00Z] INFO  18:00:52,842 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:00Z] INFO  18:00:52,921 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-15T01:00Z] INFO  18:00:52,960 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T01:00Z] INFO  18:00:53,470 IntervalUtils - Processing 230109 bp from intervals
[2016-04-15T01:00Z] WARN  18:00:53,476 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:00Z] INFO  18:00:53,558 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:00Z] INFO  18:00:53,561 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:00Z] INFO  18:00:53,691 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:00Z] INFO  18:00:53,691 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:00Z] INFO  18:00:53,692 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T01:00Z] INFO  18:00:53,692 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T01:00Z] INFO  18:00:53,695 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T01:00Z] INFO  18:00:53,695 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T01:00Z] GATK: HaplotypeCaller
[2016-04-15T01:00Z] INFO  18:00:53,884 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T01:00Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T01:00Z] INFO  18:00:54,001 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T01:00Z] INFO  18:00:54,002 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T01:00Z] WARN  18:00:54,284 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T01:00Z] WARN  18:00:54,286 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T01:00Z] INFO  18:00:56,006 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:00Z] INFO  18:00:56,009 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:00Z] INFO  18:00:56,010 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:00Z] INFO  18:00:56,010 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:00Z] INFO  18:00:56,015 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/10/R14-18105_kapa-NGv3-PE100-NGv3-sort-10_78316966_93841258-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/10/R14-18105_kapa-NGv3-PE100-NGv3-10_78316966_93841258-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/10/tx/tmpP_GT8v/R14-18105_kapa-NGv3-PE100-NGv3-10_78316966_93841258.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:00Z] INFO  18:00:56,025 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:00Z] INFO  18:00:56,036 HelpFormatter - Date/Time: 2016/04/14 18:00:56
[2016-04-15T01:00Z] INFO  18:00:56,037 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:00Z] INFO  18:00:56,038 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:00Z] WARN  18:00:56,061 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T01:00Z] WARN  18:00:56,063 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/10/tx/tmpP_GT8v/R14-18105_kapa-NGv3-PE100-NGv3-10_78316966_93841258.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T01:00Z] INFO  18:00:56,286 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:00Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T01:00Z] INFO  18:00:56,311 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T01:00Z] INFO  18:00:56,322 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T01:00Z] INFO  18:00:56,456 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T01:00Z] INFO  18:00:56,465 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:00Z] INFO  18:00:56,563 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.10
[2016-04-15T01:00Z] INFO  18:00:56,591 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T01:00Z] WARN  18:00:56,622 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T01:00Z] WARN  18:00:56,623 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T01:00Z] INFO  18:00:57,031 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:00Z] INFO  18:00:57,034 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:00Z] INFO  18:00:57,034 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:00Z] INFO  18:00:57,035 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:00Z] INFO  18:00:57,039 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/10/R14-18105_kapa-NGv3-PE100-NGv3-sort-10_93851586_111625070-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/10/R14-18105_kapa-NGv3-PE100-NGv3-10_93851586_111625070-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/10/tx/tmptf9EAf/R14-18105_kapa-NGv3-PE100-NGv3-10_93851586_111625070.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:00Z] INFO  18:00:57,072 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:00Z] INFO  18:00:57,073 HelpFormatter - Date/Time: 2016/04/14 18:00:57
[2016-04-15T01:00Z] INFO  18:00:57,074 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:00Z] INFO  18:00:57,074 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:00Z] INFO  18:00:57,095 IntervalUtils - Processing 148808 bp from intervals
[2016-04-15T01:00Z] WARN  18:00:57,101 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:00Z] WARN  18:00:57,125 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T01:00Z] WARN  18:00:57,154 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/10/tx/tmptf9EAf/R14-18105_kapa-NGv3-PE100-NGv3-10_93851586_111625070.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T01:00Z] INFO  18:00:57,249 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:00Z] INFO  18:00:57,343 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:00Z] INFO  18:00:57,344 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:00Z] INFO  18:00:57,344 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T01:00Z] INFO  18:00:57,345 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T01:00Z] INFO  18:00:57,346 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T01:00Z] INFO  18:00:57,346 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T01:00Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T01:00Z] INFO  18:00:57,464 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T01:00Z] INFO  18:00:57,465 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T01:00Z] INFO  18:00:57,468 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:00Z] INFO  18:00:57,525 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T01:00Z] INFO  18:00:57,648 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T01:00Z] INFO  18:00:57,658 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:00Z] INFO  18:00:57,718 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-15T01:00Z] INFO  18:00:57,741 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T01:00Z] INFO  18:00:58,159 ProgressMeter -      9:34972350      1.0336108E7    30.0 s            2.0 s       30.2%    99.0 s      69.0 s
[2016-04-15T01:00Z] INFO  18:00:58,359 IntervalUtils - Processing 335852 bp from intervals
[2016-04-15T01:00Z] WARN  18:00:58,365 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:00Z] INFO  18:00:58,479 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:00Z] WARN  18:00:58,512 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T01:00Z] WARN  18:00:58,513 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T01:00Z] INFO  18:00:58,708 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:00Z] INFO  18:00:58,709 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:00Z] INFO  18:00:58,709 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T01:00Z] INFO  18:00:58,710 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T01:00Z] INFO  18:00:58,721 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T01:00Z] INFO  18:00:58,722 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T01:00Z] INFO  18:00:58,967 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T01:00Z] INFO  18:00:59,051 ProgressMeter -      9:77377615      1.5192807E7    30.0 s            1.0 s       64.1%    46.0 s      16.0 s
[2016-04-15T01:01Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T01:01Z] INFO  18:01:00,659 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T01:01Z] INFO  18:01:00,660 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T01:01Z] WARN  18:01:00,955 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T01:01Z] WARN  18:01:00,955 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T01:01Z] INFO  18:01:01,882 ProgressMeter -      9:90747881      1.3946502E7    30.0 s            2.0 s       49.9%    60.0 s      30.0 s
[2016-04-15T01:01Z] INFO  18:01:02,198 ProgressMeter -     9:104032162      2.2185472E7    30.0 s            1.0 s       47.4%    63.0 s      33.0 s
[2016-04-15T01:01Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T01:01Z] INFO  18:01:02,470 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T01:01Z] INFO  18:01:02,471 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T01:01Z] WARN  18:01:02,801 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T01:01Z] WARN  18:01:02,803 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T01:01Z] INFO  18:01:04,094 ProgressMeter -     8:146025867      4.2030178E7    60.0 s            1.0 s       95.2%    63.0 s       3.0 s
[2016-04-15T01:01Z] INFO  18:01:05,001 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.060118063000000006
[2016-04-15T01:01Z] INFO  18:01:05,002 PairHMM - Total compute time in PairHMM computeLikelihoods() : 19.283691024
[2016-04-15T01:01Z] INFO  18:01:05,002 HaplotypeCaller - Ran local assembly on 3765 active regions
[2016-04-15T01:01Z] INFO  18:01:05,058 ProgressMeter -            done     5.57488561E8     2.7 m            0.0 s      100.0%     2.7 m       0.0 s
[2016-04-15T01:01Z] INFO  18:01:05,058 ProgressMeter - Total runtime 164.75 secs, 2.75 min, 0.05 hours
[2016-04-15T01:01Z] INFO  18:01:05,058 MicroScheduler - 94919 reads were filtered out during the traversal out of approximately 861880 total reads (11.01%)
[2016-04-15T01:01Z] INFO  18:01:05,059 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:01Z] INFO  18:01:05,059 MicroScheduler -   -> 65594 reads (7.61% of total) failing DuplicateReadFilter
[2016-04-15T01:01Z] INFO  18:01:05,059 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:01Z] INFO  18:01:05,059 MicroScheduler -   -> 29325 reads (3.40% of total) failing HCMappingQualityFilter
[2016-04-15T01:01Z] INFO  18:01:05,059 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:01Z] INFO  18:01:05,060 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:01Z] INFO  18:01:05,060 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:01Z] INFO  18:01:05,060 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T01:01Z] INFO  18:01:05,736 ProgressMeter -     9:117663825      2.1992876E7    30.0 s            1.0 s       38.4%    78.0 s      48.0 s
[2016-04-15T01:01Z] INFO  18:01:06,552 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:01Z] INFO  18:01:06,647 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.021241252000000002
[2016-04-15T01:01Z] INFO  18:01:06,653 PairHMM - Total compute time in PairHMM computeLikelihoods() : 3.0910781820000004
[2016-04-15T01:01Z] INFO  18:01:06,664 HaplotypeCaller - Ran local assembly on 1403 active regions
[2016-04-15T01:01Z] INFO  18:01:06,712 ProgressMeter -            done      4.6020795E7    62.0 s            1.0 s      100.0%    62.0 s       0.0 s
[2016-04-15T01:01Z] INFO  18:01:06,712 ProgressMeter - Total runtime 62.64 secs, 1.04 min, 0.02 hours
[2016-04-15T01:01Z] INFO  18:01:06,713 MicroScheduler - 37727 reads were filtered out during the traversal out of approximately 383067 total reads (9.85%)
[2016-04-15T01:01Z] INFO  18:01:06,713 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:01Z] INFO  18:01:06,713 MicroScheduler -   -> 30790 reads (8.04% of total) failing DuplicateReadFilter
[2016-04-15T01:01Z] INFO  18:01:06,714 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:01Z] INFO  18:01:06,714 MicroScheduler -   -> 6937 reads (1.81% of total) failing HCMappingQualityFilter
[2016-04-15T01:01Z] INFO  18:01:06,714 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:01Z] INFO  18:01:06,714 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:01Z] INFO  18:01:06,715 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:01Z] INFO  18:01:06,715 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T01:01Z] GATK: HaplotypeCaller
[2016-04-15T01:01Z] INFO  18:01:08,014 ProgressMeter -     9:131418989      2.1658479E7    30.0 s            1.0 s       19.9%     2.5 m     120.0 s
[2016-04-15T01:01Z] INFO  18:01:08,218 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:01Z] GATK: HaplotypeCaller
[2016-04-15T01:01Z] INFO  18:01:09,832 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.011343111000000001
[2016-04-15T01:01Z] INFO  18:01:09,833 PairHMM - Total compute time in PairHMM computeLikelihoods() : 0.903386036
[2016-04-15T01:01Z] INFO  18:01:09,834 HaplotypeCaller - Ran local assembly on 921 active regions
[2016-04-15T01:01Z] INFO  18:01:09,910 ProgressMeter -            done      3.7646403E7    40.0 s            1.0 s      100.0%    40.0 s       0.0 s
[2016-04-15T01:01Z] INFO  18:01:09,910 ProgressMeter - Total runtime 40.88 secs, 0.68 min, 0.01 hours
[2016-04-15T01:01Z] INFO  18:01:09,910 MicroScheduler - 66915 reads were filtered out during the traversal out of approximately 199484 total reads (33.54%)
[2016-04-15T01:01Z] INFO  18:01:09,911 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:01Z] INFO  18:01:09,911 MicroScheduler -   -> 11574 reads (5.80% of total) failing DuplicateReadFilter
[2016-04-15T01:01Z] INFO  18:01:09,911 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:01Z] INFO  18:01:09,912 MicroScheduler -   -> 55341 reads (27.74% of total) failing HCMappingQualityFilter
[2016-04-15T01:01Z] INFO  18:01:09,912 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:01Z] INFO  18:01:09,912 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:01Z] INFO  18:01:09,912 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:01Z] INFO  18:01:09,912 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T01:01Z] INFO  18:01:09,933 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:01Z] INFO  18:01:09,947 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:01Z] INFO  18:01:09,948 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:01Z] INFO  18:01:09,948 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:01Z] INFO  18:01:09,953 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/10/R14-18105_kapa-NGv3-PE100-NGv3-sort-10_111628371_127265443-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/10/R14-18105_kapa-NGv3-PE100-NGv3-10_111628371_127265443-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/10/tx/tmpOEkSv7/R14-18105_kapa-NGv3-PE100-NGv3-10_111628371_127265443.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:01Z] INFO  18:01:09,986 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:01Z] INFO  18:01:09,996 HelpFormatter - Date/Time: 2016/04/14 18:01:09
[2016-04-15T01:01Z] INFO  18:01:09,996 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:01Z] INFO  18:01:09,996 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:01Z] WARN  18:01:10,048 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T01:01Z] WARN  18:01:10,057 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/10/tx/tmpOEkSv7/R14-18105_kapa-NGv3-PE100-NGv3-10_111628371_127265443.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T01:01Z] INFO  18:01:10,284 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:01Z] INFO  18:01:10,416 ProgressMeter -      10:7285578      1.2970956E7    30.0 s            2.0 s       47.8%    62.0 s      32.0 s
[2016-04-15T01:01Z] INFO  18:01:10,439 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T01:01Z] INFO  18:01:10,448 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:01Z] INFO  18:01:10,528 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-15T01:01Z] INFO  18:01:10,559 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T01:01Z] INFO  18:01:11,030 IntervalUtils - Processing 210787 bp from intervals
[2016-04-15T01:01Z] WARN  18:01:11,035 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:01Z] INFO  18:01:11,159 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:01Z] INFO  18:01:11,289 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:01Z] INFO  18:01:11,290 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:01Z] INFO  18:01:11,291 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T01:01Z] INFO  18:01:11,291 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T01:01Z] INFO  18:01:11,292 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T01:01Z] INFO  18:01:11,292 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T01:01Z] INFO  18:01:11,312 ProgressMeter -     10:24910273      1.9586926E7    30.0 s            1.0 s       58.8%    50.0 s      20.0 s
[2016-04-15T01:01Z] INFO  18:01:11,320 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:01Z] INFO  18:01:11,470 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:01Z] INFO  18:01:11,473 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:01Z] INFO  18:01:11,473 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:01Z] INFO  18:01:11,474 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:01Z] INFO  18:01:11,478 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/10/R14-18105_kapa-NGv3-PE100-NGv3-sort-10_127328721_135534747-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/10/R14-18105_kapa-NGv3-PE100-NGv3-10_127328721_135534747-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/10/tx/tmpSKbg3v/R14-18105_kapa-NGv3-PE100-NGv3-10_127328721_135534747.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:01Z] INFO  18:01:11,483 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T01:01Z] INFO  18:01:11,490 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:01Z] INFO  18:01:11,496 HelpFormatter - Date/Time: 2016/04/14 18:01:11
[2016-04-15T01:01Z] INFO  18:01:11,497 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:01Z] INFO  18:01:11,497 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:01Z] WARN  18:01:11,531 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T01:01Z] WARN  18:01:11,534 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/10/tx/tmpSKbg3v/R14-18105_kapa-NGv3-PE100-NGv3-10_127328721_135534747.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T01:01Z] GATK: HaplotypeCaller
[2016-04-15T01:01Z] INFO  18:01:11,708 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:01Z] INFO  18:01:11,919 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T01:01Z] INFO  18:01:11,932 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:01Z] INFO  18:01:12,030 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.10
[2016-04-15T01:01Z] INFO  18:01:12,054 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T01:01Z] INFO  18:01:12,528 IntervalUtils - Processing 102137 bp from intervals
[2016-04-15T01:01Z] WARN  18:01:12,544 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:01Z] INFO  18:01:12,689 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:01Z] INFO  18:01:12,763 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:01Z] INFO  18:01:12,764 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:01Z] INFO  18:01:12,765 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T01:01Z] INFO  18:01:12,766 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T01:01Z] INFO  18:01:12,766 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T01:01Z] INFO  18:01:12,767 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T01:01Z] INFO  18:01:12,991 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T01:01Z] INFO  18:01:14,709 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:01Z] INFO  18:01:14,712 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:01Z] INFO  18:01:14,713 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:01Z] INFO  18:01:14,713 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:01Z] INFO  18:01:14,718 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/11/R14-18105_kapa-NGv3-PE100-NGv3-sort-11_0_15994658-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/11/R14-18105_kapa-NGv3-PE100-NGv3-11_0_15994658-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/11/tx/tmpOz15N2/R14-18105_kapa-NGv3-PE100-NGv3-11_0_15994658.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:01Z] INFO  18:01:14,734 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:01Z] INFO  18:01:14,745 HelpFormatter - Date/Time: 2016/04/14 18:01:14
[2016-04-15T01:01Z] INFO  18:01:14,746 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:01Z] INFO  18:01:14,747 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:01Z] WARN  18:01:14,797 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T01:01Z] WARN  18:01:14,800 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/11/tx/tmpOz15N2/R14-18105_kapa-NGv3-PE100-NGv3-11_0_15994658.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T01:01Z] INFO  18:01:14,996 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:01Z] INFO  18:01:15,225 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T01:01Z] INFO  18:01:15,239 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:01Z] INFO  18:01:15,349 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.11
[2016-04-15T01:01Z] INFO  18:01:15,386 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T01:01Z] INFO  18:01:15,838 IntervalUtils - Processing 438345 bp from intervals
[2016-04-15T01:01Z] WARN  18:01:15,844 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:01Z] INFO  18:01:15,946 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:01Z] INFO  18:01:16,063 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:01Z] INFO  18:01:16,064 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:01Z] INFO  18:01:16,065 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T01:01Z] INFO  18:01:16,065 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T01:01Z] INFO  18:01:16,066 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T01:01Z] INFO  18:01:16,066 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T01:01Z] INFO  18:01:16,351 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T01:01Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T01:01Z] INFO  18:01:18,080 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T01:01Z] INFO  18:01:18,091 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T01:01Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T01:01Z] INFO  18:01:18,319 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T01:01Z] INFO  18:01:18,320 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T01:01Z] WARN  18:01:18,362 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T01:01Z] WARN  18:01:18,363 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T01:01Z] WARN  18:01:18,661 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T01:01Z] WARN  18:01:18,663 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T01:01Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T01:01Z] INFO  18:01:19,544 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T01:01Z] INFO  18:01:19,545 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T01:01Z] WARN  18:01:19,854 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T01:01Z] WARN  18:01:19,862 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T01:01Z] INFO  18:01:20,891 ProgressMeter -     7:107743489     2.51061779E8   120.0 s            0.0 s       97.0%     2.1 m       3.0 s
[2016-04-15T01:01Z] INFO  18:01:21,232 ProgressMeter -     10:44872553      1.2761679E7    30.0 s            2.0 s       79.0%    37.0 s       7.0 s
[2016-04-15T01:01Z] INFO  18:01:21,527 ProgressMeter -     10:49447648        2563722.0    30.0 s           11.0 s       22.3%     2.2 m     104.0 s
[2016-04-15T01:01Z] INFO  18:01:23,492 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.067538534
[2016-04-15T01:01Z] INFO  18:01:23,493 PairHMM - Total compute time in PairHMM computeLikelihoods() : 19.493857242
[2016-04-15T01:01Z] INFO  18:01:23,493 HaplotypeCaller - Ran local assembly on 2487 active regions
[2016-04-15T01:01Z] INFO  18:01:23,541 ProgressMeter -            done      2.7011063E8     2.0 m            0.0 s      100.0%     2.0 m       0.0 s
[2016-04-15T01:01Z] INFO  18:01:23,542 ProgressMeter - Total runtime 122.69 secs, 2.04 min, 0.03 hours
[2016-04-15T01:01Z] INFO  18:01:23,542 MicroScheduler - 171918 reads were filtered out during the traversal out of approximately 699023 total reads (24.59%)
[2016-04-15T01:01Z] INFO  18:01:23,542 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:01Z] INFO  18:01:23,543 MicroScheduler -   -> 47355 reads (6.77% of total) failing DuplicateReadFilter
[2016-04-15T01:01Z] INFO  18:01:23,543 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:01Z] INFO  18:01:23,544 MicroScheduler -   -> 124563 reads (17.82% of total) failing HCMappingQualityFilter
[2016-04-15T01:01Z] INFO  18:01:23,544 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:01Z] INFO  18:01:23,544 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:01Z] INFO  18:01:23,545 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:01Z] INFO  18:01:23,545 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T01:01Z] INFO  18:01:23,697 ProgressMeter -     10:71211344      2.2318029E7    30.0 s            1.0 s       42.7%    70.0 s      40.0 s
[2016-04-15T01:01Z] INFO  18:01:23,930 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.010061237
[2016-04-15T01:01Z] INFO  18:01:23,941 PairHMM - Total compute time in PairHMM computeLikelihoods() : 0.8033418090000001
[2016-04-15T01:01Z] INFO  18:01:23,943 HaplotypeCaller - Ran local assembly on 1188 active regions
[2016-04-15T01:01Z] INFO  18:01:24,001 ProgressMeter -            done      6.7952989E7    52.0 s            0.0 s      100.0%    52.0 s       0.0 s
[2016-04-15T01:01Z] INFO  18:01:24,001 ProgressMeter - Total runtime 52.14 secs, 0.87 min, 0.01 hours
[2016-04-15T01:01Z] INFO  18:01:24,001 MicroScheduler - 44383 reads were filtered out during the traversal out of approximately 290873 total reads (15.26%)
[2016-04-15T01:01Z] INFO  18:01:24,002 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:01Z] INFO  18:01:24,002 MicroScheduler -   -> 22050 reads (7.58% of total) failing DuplicateReadFilter
[2016-04-15T01:01Z] INFO  18:01:24,002 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:01Z] INFO  18:01:24,002 MicroScheduler -   -> 22333 reads (7.68% of total) failing HCMappingQualityFilter
[2016-04-15T01:01Z] INFO  18:01:24,003 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:01Z] INFO  18:01:24,003 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:01Z] INFO  18:01:24,003 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:01Z] INFO  18:01:24,003 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T01:01Z] INFO  18:01:25,063 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:01Z] GATK: HaplotypeCaller
[2016-04-15T01:01Z] INFO  18:01:25,488 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.049109011
[2016-04-15T01:01Z] INFO  18:01:25,489 PairHMM - Total compute time in PairHMM computeLikelihoods() : 1.633466032
[2016-04-15T01:01Z] INFO  18:01:25,489 HaplotypeCaller - Ran local assembly on 1362 active regions
[2016-04-15T01:01Z] INFO  18:01:25,530 ProgressMeter -            done      8.2992301E7    53.0 s            0.0 s      100.0%    53.0 s       0.0 s
[2016-04-15T01:01Z] INFO  18:01:25,531 ProgressMeter - Total runtime 53.35 secs, 0.89 min, 0.01 hours
[2016-04-15T01:01Z] INFO  18:01:25,532 MicroScheduler - 26990 reads were filtered out during the traversal out of approximately 287493 total reads (9.39%)
[2016-04-15T01:01Z] INFO  18:01:25,533 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:01Z] INFO  18:01:25,533 MicroScheduler -   -> 22902 reads (7.97% of total) failing DuplicateReadFilter
[2016-04-15T01:01Z] INFO  18:01:25,534 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:01Z] INFO  18:01:25,535 MicroScheduler -   -> 4088 reads (1.42% of total) failing HCMappingQualityFilter
[2016-04-15T01:01Z] INFO  18:01:25,535 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:01Z] INFO  18:01:25,536 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:01Z] INFO  18:01:25,536 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:01Z] INFO  18:01:25,537 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T01:01Z] INFO  18:01:25,550 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:01Z] GATK: HaplotypeCaller
[2016-04-15T01:01Z] INFO  18:01:26,661 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.01061128
[2016-04-15T01:01Z] INFO  18:01:26,661 PairHMM - Total compute time in PairHMM computeLikelihoods() : 0.67829653
[2016-04-15T01:01Z] INFO  18:01:26,661 HaplotypeCaller - Ran local assembly on 1178 active regions
[2016-04-15T01:01Z] INFO  18:01:26,705 ProgressMeter -            done      6.1102753E7    45.0 s            0.0 s      100.0%    45.0 s       0.0 s
[2016-04-15T01:01Z] INFO  18:01:26,706 ProgressMeter - Total runtime 45.44 secs, 0.76 min, 0.01 hours
[2016-04-15T01:01Z] INFO  18:01:26,706 MicroScheduler - 16961 reads were filtered out during the traversal out of approximately 193635 total reads (8.76%)
[2016-04-15T01:01Z] INFO  18:01:26,706 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:01Z] INFO  18:01:26,707 MicroScheduler -   -> 15277 reads (7.89% of total) failing DuplicateReadFilter
[2016-04-15T01:01Z] INFO  18:01:26,707 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:01Z] INFO  18:01:26,707 MicroScheduler -   -> 1684 reads (0.87% of total) failing HCMappingQualityFilter
[2016-04-15T01:01Z] INFO  18:01:26,707 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:01Z] INFO  18:01:26,708 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:01Z] INFO  18:01:26,708 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:01Z] INFO  18:01:26,708 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T01:01Z] INFO  18:01:26,780 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.008275617
[2016-04-15T01:01Z] INFO  18:01:26,781 PairHMM - Total compute time in PairHMM computeLikelihoods() : 0.48733210000000005
[2016-04-15T01:01Z] INFO  18:01:26,781 HaplotypeCaller - Ran local assembly on 746 active regions
[2016-04-15T01:01Z] INFO  18:01:26,837 ProgressMeter -            done      2.2800337E7    35.0 s            1.0 s      100.0%    35.0 s       0.0 s
[2016-04-15T01:01Z] INFO  18:01:26,838 ProgressMeter - Total runtime 35.63 secs, 0.59 min, 0.01 hours
[2016-04-15T01:01Z] INFO  18:01:26,838 MicroScheduler - 32223 reads were filtered out during the traversal out of approximately 159030 total reads (20.26%)
[2016-04-15T01:01Z] INFO  18:01:26,839 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:01Z] INFO  18:01:26,839 MicroScheduler -   -> 11030 reads (6.94% of total) failing DuplicateReadFilter
[2016-04-15T01:01Z] INFO  18:01:26,839 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:01Z] INFO  18:01:26,839 MicroScheduler -   -> 21193 reads (13.33% of total) failing HCMappingQualityFilter
[2016-04-15T01:01Z] INFO  18:01:26,840 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:01Z] INFO  18:01:26,840 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:01Z] INFO  18:01:26,840 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:01Z] INFO  18:01:26,840 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T01:01Z] INFO  18:01:27,055 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:01Z] INFO  18:01:27,375 ProgressMeter -     10:88718110      1.3712441E7    30.0 s            2.0 s       52.4%    57.0 s      27.0 s
[2016-04-15T01:01Z] GATK: HaplotypeCaller
[2016-04-15T01:01Z] INFO  18:01:27,961 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:01Z] INFO  18:01:28,161 ProgressMeter -      9:43915826      8.4756919E7    60.0 s            0.0 s       98.5%    60.0 s       0.0 s
[2016-04-15T01:01Z] GATK: HaplotypeCaller
[2016-04-15T01:01Z] INFO  18:01:28,358 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:01Z] INFO  18:01:28,538 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:01Z] INFO  18:01:28,542 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:01Z] INFO  18:01:28,543 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:01Z] INFO  18:01:28,543 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:01Z] INFO  18:01:28,547 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/11/R14-18105_kapa-NGv3-PE100-NGv3-sort-11_16007749_31531554-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/11/R14-18105_kapa-NGv3-PE100-NGv3-11_16007749_31531554-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/11/tx/tmprAK5Rq/R14-18105_kapa-NGv3-PE100-NGv3-11_16007749_31531554.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:01Z] GATK: HaplotypeCaller
[2016-04-15T01:01Z] INFO  18:01:28,578 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:01Z] INFO  18:01:28,578 HelpFormatter - Date/Time: 2016/04/14 18:01:28
[2016-04-15T01:01Z] INFO  18:01:28,579 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:01Z] INFO  18:01:28,579 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:01Z] INFO  18:01:28,600 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:01Z] INFO  18:01:28,603 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:01Z] INFO  18:01:28,605 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:01Z] INFO  18:01:28,605 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:01Z] INFO  18:01:28,610 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/11/R14-18105_kapa-NGv3-PE100-NGv3-sort-11_31541602_47074069-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/11/R14-18105_kapa-NGv3-PE100-NGv3-11_31541602_47074069-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/11/tx/tmpk6z6GJ/R14-18105_kapa-NGv3-PE100-NGv3-11_31541602_47074069.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:01Z] WARN  18:01:28,612 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T01:01Z] INFO  18:01:28,618 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:01Z] WARN  18:01:28,627 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/11/tx/tmprAK5Rq/R14-18105_kapa-NGv3-PE100-NGv3-11_16007749_31531554.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T01:01Z] INFO  18:01:28,629 HelpFormatter - Date/Time: 2016/04/14 18:01:28
[2016-04-15T01:01Z] INFO  18:01:28,630 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:01Z] INFO  18:01:28,631 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:01Z] WARN  18:01:28,671 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T01:01Z] WARN  18:01:28,673 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/11/tx/tmpk6z6GJ/R14-18105_kapa-NGv3-PE100-NGv3-11_31541602_47074069.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T01:01Z] INFO  18:01:28,728 ProgressMeter -     10:98803199      2.7486276E7    30.0 s            1.0 s       31.9%    94.0 s      64.0 s
[2016-04-15T01:01Z] INFO  18:01:28,880 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:01Z] INFO  18:01:28,918 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:01Z] INFO  18:01:29,069 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T01:01Z] INFO  18:01:29,094 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.012204191000000001
[2016-04-15T01:01Z] INFO  18:01:29,095 PairHMM - Total compute time in PairHMM computeLikelihoods() : 0.9455001550000001
[2016-04-15T01:01Z] INFO  18:01:29,095 HaplotypeCaller - Ran local assembly on 1176 active regions
[2016-04-15T01:01Z] INFO  18:01:29,098 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:01Z] INFO  18:01:29,127 ProgressMeter -            done      5.6897824E7    48.0 s            0.0 s      100.0%    48.0 s       0.0 s
[2016-04-15T01:01Z] INFO  18:01:29,127 ProgressMeter - Total runtime 48.72 secs, 0.81 min, 0.01 hours
[2016-04-15T01:01Z] INFO  18:01:29,138 MicroScheduler - 20900 reads were filtered out during the traversal out of approximately 222350 total reads (9.40%)
[2016-04-15T01:01Z] INFO  18:01:29,138 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:01Z] INFO  18:01:29,138 MicroScheduler -   -> 17342 reads (7.80% of total) failing DuplicateReadFilter
[2016-04-15T01:01Z] INFO  18:01:29,139 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:01Z] INFO  18:01:29,139 MicroScheduler -   -> 3558 reads (1.60% of total) failing HCMappingQualityFilter
[2016-04-15T01:01Z] INFO  18:01:29,139 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:01Z] INFO  18:01:29,139 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:01Z] INFO  18:01:29,140 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:01Z] INFO  18:01:29,140 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T01:01Z] INFO  18:01:29,158 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T01:01Z] INFO  18:01:29,171 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:01Z] INFO  18:01:29,188 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.09
[2016-04-15T01:01Z] INFO  18:01:29,236 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T01:01Z] INFO  18:01:29,270 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.10
[2016-04-15T01:01Z] INFO  18:01:29,298 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T01:01Z] INFO  18:01:29,440 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.034685343
[2016-04-15T01:01Z] INFO  18:01:29,441 PairHMM - Total compute time in PairHMM computeLikelihoods() : 4.700565548
[2016-04-15T01:01Z] INFO  18:01:29,441 HaplotypeCaller - Ran local assembly on 1489 active regions
[2016-04-15T01:01Z] INFO  18:01:29,496 ProgressMeter -            done      8.5421311E7    61.0 s            0.0 s      100.0%    61.0 s       0.0 s
[2016-04-15T01:01Z] INFO  18:01:29,496 ProgressMeter - Total runtime 61.36 secs, 1.02 min, 0.02 hours
[2016-04-15T01:01Z] INFO  18:01:29,496 MicroScheduler - 138974 reads were filtered out during the traversal out of approximately 441916 total reads (31.45%)
[2016-04-15T01:01Z] INFO  18:01:29,497 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:01Z] INFO  18:01:29,497 MicroScheduler -   -> 26431 reads (5.98% of total) failing DuplicateReadFilter
[2016-04-15T01:01Z] INFO  18:01:29,497 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:01Z] INFO  18:01:29,497 MicroScheduler -   -> 112543 reads (25.47% of total) failing HCMappingQualityFilter
[2016-04-15T01:01Z] INFO  18:01:29,498 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:01Z] INFO  18:01:29,498 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:01Z] INFO  18:01:29,498 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:01Z] INFO  18:01:29,498 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T01:01Z] INFO  18:01:29,696 IntervalUtils - Processing 144906 bp from intervals
[2016-04-15T01:01Z] WARN  18:01:29,701 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:01Z] INFO  18:01:29,819 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:01Z] INFO  18:01:29,821 IntervalUtils - Processing 150047 bp from intervals
[2016-04-15T01:01Z] WARN  18:01:29,837 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:01Z] INFO  18:01:29,929 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:01Z] INFO  18:01:29,929 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:01Z] INFO  18:01:29,930 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T01:01Z] INFO  18:01:29,930 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T01:01Z] INFO  18:01:29,936 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T01:01Z] INFO  18:01:29,936 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T01:01Z] INFO  18:01:29,953 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:01Z] INFO  18:01:30,075 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:01Z] INFO  18:01:30,076 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:01Z] INFO  18:01:30,077 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T01:01Z] INFO  18:01:30,078 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T01:01Z] INFO  18:01:30,088 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T01:01Z] INFO  18:01:30,089 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T01:01Z] INFO  18:01:30,101 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T01:01Z] INFO  18:01:30,216 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:01Z] INFO  18:01:30,219 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:01Z] INFO  18:01:30,220 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:01Z] INFO  18:01:30,220 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:01Z] INFO  18:01:30,226 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/11/R14-18105_kapa-NGv3-PE100-NGv3-sort-11_47158866_62678572-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/11/R14-18105_kapa-NGv3-PE100-NGv3-11_47158866_62678572-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/11/tx/tmpyiihPN/R14-18105_kapa-NGv3-PE100-NGv3-11_47158866_62678572.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:01Z] INFO  18:01:30,236 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:01Z] INFO  18:01:30,236 HelpFormatter - Date/Time: 2016/04/14 18:01:30
[2016-04-15T01:01Z] INFO  18:01:30,236 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:01Z] INFO  18:01:30,237 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:01Z] WARN  18:01:30,273 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T01:01Z] WARN  18:01:30,276 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/11/tx/tmpyiihPN/R14-18105_kapa-NGv3-PE100-NGv3-11_47158866_62678572.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T01:01Z] INFO  18:01:30,311 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T01:01Z] INFO  18:01:30,473 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:01Z] INFO  18:01:30,495 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:01Z] INFO  18:01:30,675 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T01:01Z] INFO  18:01:30,685 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:01Z] INFO  18:01:30,778 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-15T01:01Z] INFO  18:01:30,795 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:01Z] INFO  18:01:30,812 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T01:01Z] GATK: HaplotypeCaller
[2016-04-15T01:01Z] GATK: HaplotypeCaller
[2016-04-15T01:01Z] INFO  18:01:31,326 IntervalUtils - Processing 330540 bp from intervals
[2016-04-15T01:01Z] WARN  18:01:31,331 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:01Z] INFO  18:01:31,462 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:01Z] INFO  18:01:31,466 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:01Z] INFO  18:01:31,466 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:01Z] INFO  18:01:31,467 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:01Z] INFO  18:01:31,471 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/11/R14-18105_kapa-NGv3-PE100-NGv3-sort-11_62744265_78270665-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/11/R14-18105_kapa-NGv3-PE100-NGv3-11_62744265_78270665-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/11/tx/tmpeirIn3/R14-18105_kapa-NGv3-PE100-NGv3-11_62744265_78270665.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:01Z] INFO  18:01:31,481 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:01Z] INFO  18:01:31,492 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:01Z] INFO  18:01:31,492 HelpFormatter - Date/Time: 2016/04/14 18:01:31
[2016-04-15T01:01Z] INFO  18:01:31,493 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:01Z] INFO  18:01:31,494 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:01Z] WARN  18:01:31,529 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T01:01Z] WARN  18:01:31,532 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/11/tx/tmpeirIn3/R14-18105_kapa-NGv3-PE100-NGv3-11_62744265_78270665.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T01:01Z] INFO  18:01:31,642 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:01Z] INFO  18:01:31,643 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:01Z] INFO  18:01:31,643 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T01:01Z] INFO  18:01:31,655 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T01:01Z] INFO  18:01:31,663 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T01:01Z] INFO  18:01:31,663 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T01:01Z] INFO  18:01:31,708 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:01Z] INFO  18:01:31,901 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:01Z] INFO  18:01:31,904 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:01Z] INFO  18:01:31,905 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:01Z] INFO  18:01:31,905 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:01Z] INFO  18:01:31,908 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T01:01Z] INFO  18:01:31,910 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/11/R14-18105_kapa-NGv3-PE100-NGv3-sort-11_78277177_93796886-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/11/R14-18105_kapa-NGv3-PE100-NGv3-11_78277177_93796886-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/11/tx/tmpV5u7DR/R14-18105_kapa-NGv3-PE100-NGv3-11_78277177_93796886.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:01Z] INFO  18:01:31,931 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:01Z] INFO  18:01:31,932 HelpFormatter - Date/Time: 2016/04/14 18:01:31
[2016-04-15T01:01Z] INFO  18:01:31,932 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:01Z] INFO  18:01:31,933 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:01Z] INFO  18:01:31,941 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T01:01Z] INFO  18:01:31,959 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:01Z] WARN  18:01:31,986 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T01:01Z] WARN  18:01:31,989 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/11/tx/tmpV5u7DR/R14-18105_kapa-NGv3-PE100-NGv3-11_78277177_93796886.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T01:01Z] INFO  18:01:32,033 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-15T01:01Z] INFO  18:01:32,062 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T01:01Z] INFO  18:01:32,276 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:01Z] INFO  18:01:32,506 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T01:01Z] INFO  18:01:32,515 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:01Z] INFO  18:01:32,619 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.10
[2016-04-15T01:01Z] INFO  18:01:32,650 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T01:01Z] INFO  18:01:32,658 IntervalUtils - Processing 515206 bp from intervals
[2016-04-15T01:01Z] WARN  18:01:32,675 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:01Z] INFO  18:01:32,824 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:01Z] INFO  18:01:32,964 IntervalUtils - Processing 119993 bp from intervals
[2016-04-15T01:01Z] WARN  18:01:32,969 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:01Z] INFO  18:01:32,981 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:01Z] INFO  18:01:32,981 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:01Z] INFO  18:01:32,982 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T01:01Z] INFO  18:01:32,982 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T01:01Z] INFO  18:01:32,983 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T01:01Z] INFO  18:01:32,983 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T01:01Z] INFO  18:01:33,053 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:01Z] INFO  18:01:33,124 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:01Z] INFO  18:01:33,125 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:01Z] INFO  18:01:33,127 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T01:01Z] INFO  18:01:33,128 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T01:01Z] INFO  18:01:33,129 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T01:01Z] INFO  18:01:33,129 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T01:01Z] INFO  18:01:33,215 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T01:01Z] INFO  18:01:33,293 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T01:01Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T01:01Z] INFO  18:01:33,346 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T01:01Z] INFO  18:01:33,346 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T01:01Z] WARN  18:01:33,575 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T01:01Z] WARN  18:01:33,575 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T01:01Z] INFO  18:01:33,983 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:01Z] INFO  18:01:33,986 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:01Z] INFO  18:01:33,987 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:01Z] INFO  18:01:33,987 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:01Z] INFO  18:01:33,992 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/11/R14-18105_kapa-NGv3-PE100-NGv3-sort-11_93797496_109964158-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/11/R14-18105_kapa-NGv3-PE100-NGv3-11_93797496_109964158-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/11/tx/tmp4VjoWq/R14-18105_kapa-NGv3-PE100-NGv3-11_93797496_109964158.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:01Z] INFO  18:01:34,031 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:01Z] INFO  18:01:34,031 HelpFormatter - Date/Time: 2016/04/14 18:01:33
[2016-04-15T01:01Z] INFO  18:01:34,032 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:01Z] INFO  18:01:34,032 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:01Z] WARN  18:01:34,065 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T01:01Z] WARN  18:01:34,068 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/11/tx/tmp4VjoWq/R14-18105_kapa-NGv3-PE100-NGv3-11_93797496_109964158.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T01:01Z] INFO  18:01:34,240 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:01Z] INFO  18:01:34,244 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:01Z] INFO  18:01:34,244 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:01Z] INFO  18:01:34,245 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:01Z] INFO  18:01:34,250 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/11/R14-18105_kapa-NGv3-PE100-NGv3-sort-11_110001730_125514538-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/11/R14-18105_kapa-NGv3-PE100-NGv3-11_110001730_125514538-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/11/tx/tmpiIsDQJ/R14-18105_kapa-NGv3-PE100-NGv3-11_110001730_125514538.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:01Z] INFO  18:01:34,268 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:01Z] INFO  18:01:34,278 HelpFormatter - Date/Time: 2016/04/14 18:01:34
[2016-04-15T01:01Z] INFO  18:01:34,279 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:01Z] INFO  18:01:34,280 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:01Z] INFO  18:01:34,310 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:01Z] WARN  18:01:34,316 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T01:01Z] WARN  18:01:34,330 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/11/tx/tmpiIsDQJ/R14-18105_kapa-NGv3-PE100-NGv3-11_110001730_125514538.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T01:01Z] INFO  18:01:34,479 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T01:01Z] INFO  18:01:34,499 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:01Z] INFO  18:01:34,551 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:01Z] INFO  18:01:34,608 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.11
[2016-04-15T01:01Z] INFO  18:01:34,633 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T01:01Z] INFO  18:01:34,810 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T01:01Z] INFO  18:01:34,833 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:01Z] INFO  18:01:34,938 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.10
[2016-04-15T01:01Z] INFO  18:01:34,960 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T01:01Z] INFO  18:01:35,123 IntervalUtils - Processing 148585 bp from intervals
[2016-04-15T01:01Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T01:01Z] WARN  18:01:35,129 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:01Z] INFO  18:01:35,137 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T01:01Z] INFO  18:01:35,146 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T01:01Z] INFO  18:01:35,217 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:01Z] INFO  18:01:35,305 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:01Z] INFO  18:01:35,306 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:01Z] INFO  18:01:35,307 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T01:01Z] INFO  18:01:35,317 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T01:01Z] INFO  18:01:35,318 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T01:01Z] INFO  18:01:35,318 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T01:01Z] INFO  18:01:35,368 IntervalUtils - Processing 318135 bp from intervals
[2016-04-15T01:01Z] WARN  18:01:35,373 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:01Z] WARN  18:01:35,450 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T01:01Z] WARN  18:01:35,451 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T01:01Z] INFO  18:01:35,498 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T01:01Z] INFO  18:01:35,522 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:01Z] INFO  18:01:35,686 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:01Z] INFO  18:01:35,687 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:01Z] INFO  18:01:35,699 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T01:01Z] INFO  18:01:35,700 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T01:01Z] INFO  18:01:35,713 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T01:01Z] INFO  18:01:35,714 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T01:01Z] INFO  18:01:35,739 ProgressMeter -     9:127951198     1.14138979E8    60.0 s            0.0 s       95.0%    63.0 s       3.0 s
[2016-04-15T01:01Z] INFO  18:01:35,880 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T01:01Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T01:01Z] INFO  18:01:36,023 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T01:01Z] INFO  18:01:36,024 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T01:01Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T01:01Z] INFO  18:01:36,062 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T01:01Z] INFO  18:01:36,063 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T01:01Z] WARN  18:01:36,344 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T01:01Z] WARN  18:01:36,345 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T01:01Z] WARN  18:01:36,364 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T01:01Z] WARN  18:01:36,365 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T01:01Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T01:01Z] INFO  18:01:37,400 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T01:01Z] INFO  18:01:37,401 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T01:01Z] WARN  18:01:37,655 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T01:01Z] WARN  18:01:37,656 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T01:01Z] INFO  18:01:38,025 ProgressMeter -     9:135906551     1.27405993E8    60.0 s            0.0 s       48.6%     2.1 m      63.0 s
[2016-04-15T01:01Z] INFO  18:01:38,116 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.026099229
[2016-04-15T01:01Z] INFO  18:01:38,117 PairHMM - Total compute time in PairHMM computeLikelihoods() : 1.365152033
[2016-04-15T01:01Z] INFO  18:01:38,117 HaplotypeCaller - Ran local assembly on 1691 active regions
[2016-04-15T01:01Z] INFO  18:01:38,182 ProgressMeter -            done     1.27765104E8    62.0 s            0.0 s      100.0%    62.0 s       0.0 s
[2016-04-15T01:01Z] INFO  18:01:38,183 ProgressMeter - Total runtime 62.46 secs, 1.04 min, 0.02 hours
[2016-04-15T01:01Z] INFO  18:01:38,183 MicroScheduler - 29412 reads were filtered out during the traversal out of approximately 352663 total reads (8.34%)
[2016-04-15T01:01Z] INFO  18:01:38,183 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:01Z] INFO  18:01:38,183 MicroScheduler -   -> 27796 reads (7.88% of total) failing DuplicateReadFilter
[2016-04-15T01:01Z] INFO  18:01:38,184 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:01Z] INFO  18:01:38,184 MicroScheduler -   -> 1616 reads (0.46% of total) failing HCMappingQualityFilter
[2016-04-15T01:01Z] INFO  18:01:38,184 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:01Z] INFO  18:01:38,184 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:01Z] INFO  18:01:38,185 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:01Z] INFO  18:01:38,185 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T01:01Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T01:01Z] INFO  18:01:38,516 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T01:01Z] INFO  18:01:38,516 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T01:01Z] WARN  18:01:38,808 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T01:01Z] WARN  18:01:38,809 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T01:01Z] INFO  18:01:39,630 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:01Z] GATK: HaplotypeCaller
[2016-04-15T01:01Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T01:01Z] INFO  18:01:40,521 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T01:01Z] INFO  18:01:40,521 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T01:01Z] WARN  18:01:41,116 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T01:01Z] WARN  18:01:41,116 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T01:01Z] INFO  18:01:41,308 ProgressMeter -    10:118893594      2.7994252E7    30.0 s            1.0 s       46.8%    64.0 s      34.0 s
[2016-04-15T01:01Z] INFO  18:01:42,801 ProgressMeter -    10:134893791      1.4982953E7    30.0 s            2.0 s       73.0%    41.0 s      11.0 s
[2016-04-15T01:01Z] INFO  18:01:43,293 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:01Z] INFO  18:01:43,296 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:01Z] INFO  18:01:43,296 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:01Z] INFO  18:01:43,296 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:01Z] INFO  18:01:43,312 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/11/R14-18105_kapa-NGv3-PE100-NGv3-sort-11_125523640_135006516-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/11/R14-18105_kapa-NGv3-PE100-NGv3-11_125523640_135006516-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/11/tx/tmpfUq3_4/R14-18105_kapa-NGv3-PE100-NGv3-11_125523640_135006516.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:01Z] INFO  18:01:43,320 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:01Z] INFO  18:01:43,321 HelpFormatter - Date/Time: 2016/04/14 18:01:43
[2016-04-15T01:01Z] INFO  18:01:43,322 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:01Z] INFO  18:01:43,332 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:01Z] WARN  18:01:43,356 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T01:01Z] WARN  18:01:43,359 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/11/tx/tmpfUq3_4/R14-18105_kapa-NGv3-PE100-NGv3-11_125523640_135006516.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T01:01Z] INFO  18:01:43,531 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:01Z] INFO  18:01:43,748 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T01:01Z] INFO  18:01:43,758 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:01Z] INFO  18:01:43,837 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-15T01:01Z] INFO  18:01:43,862 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.055176821
[2016-04-15T01:01Z] INFO  18:01:43,862 PairHMM - Total compute time in PairHMM computeLikelihoods() : 0.824857222
[2016-04-15T01:01Z] INFO  18:01:43,863 HaplotypeCaller - Ran local assembly on 1111 active regions
[2016-04-15T01:01Z] INFO  18:01:43,865 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T01:01Z] INFO  18:01:43,924 ProgressMeter -            done      5.4493851E7    46.0 s            0.0 s      100.0%    46.0 s       0.0 s
[2016-04-15T01:01Z] INFO  18:01:43,924 ProgressMeter - Total runtime 46.58 secs, 0.78 min, 0.01 hours
[2016-04-15T01:01Z] INFO  18:01:43,926 MicroScheduler - 31226 reads were filtered out during the traversal out of approximately 226501 total reads (13.79%)
[2016-04-15T01:01Z] INFO  18:01:43,927 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:01Z] INFO  18:01:43,927 MicroScheduler -   -> 17044 reads (7.52% of total) failing DuplicateReadFilter
[2016-04-15T01:01Z] INFO  18:01:43,927 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:01Z] INFO  18:01:43,927 MicroScheduler -   -> 14182 reads (6.26% of total) failing HCMappingQualityFilter
[2016-04-15T01:01Z] INFO  18:01:43,928 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:01Z] INFO  18:01:43,928 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:01Z] INFO  18:01:43,928 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:01Z] INFO  18:01:43,928 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T01:01Z] INFO  18:01:44,252 IntervalUtils - Processing 106404 bp from intervals
[2016-04-15T01:01Z] WARN  18:01:44,268 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:01Z] INFO  18:01:44,408 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:01Z] INFO  18:01:44,534 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:01Z] INFO  18:01:44,536 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:01Z] INFO  18:01:44,536 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T01:01Z] INFO  18:01:44,537 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T01:01Z] INFO  18:01:44,549 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T01:01Z] INFO  18:01:44,550 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T01:01Z] INFO  18:01:44,783 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T01:01Z] INFO  18:01:45,601 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:01Z] GATK: HaplotypeCaller
[2016-04-15T01:01Z] INFO  18:01:46,091 ProgressMeter -      11:1016891        9985430.0    30.0 s            3.0 s       16.4%     3.0 m       2.5 m
[2016-04-15T01:01Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T01:01Z] INFO  18:01:46,712 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T01:01Z] INFO  18:01:46,713 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T01:01Z] WARN  18:01:46,916 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T01:01Z] WARN  18:01:46,917 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T01:01Z] INFO  18:01:48,910 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:01Z] INFO  18:01:48,913 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:01Z] INFO  18:01:48,914 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:01Z] INFO  18:01:48,914 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:01Z] INFO  18:01:48,919 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/12/R14-18105_kapa-NGv3-PE100-NGv3-sort-12_0_15637181-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/12/R14-18105_kapa-NGv3-PE100-NGv3-12_0_15637181-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/12/tx/tmpsOlbgi/R14-18105_kapa-NGv3-PE100-NGv3-12_0_15637181.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:01Z] INFO  18:01:48,939 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:01Z] INFO  18:01:48,940 HelpFormatter - Date/Time: 2016/04/14 18:01:48
[2016-04-15T01:01Z] INFO  18:01:48,941 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:01Z] INFO  18:01:48,941 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:01Z] WARN  18:01:48,970 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T01:01Z] WARN  18:01:48,973 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/12/tx/tmpsOlbgi/R14-18105_kapa-NGv3-PE100-NGv3-12_0_15637181.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T01:01Z] INFO  18:01:49,261 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:01Z] INFO  18:01:49,454 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T01:01Z] INFO  18:01:49,464 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:01Z] INFO  18:01:49,566 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.10
[2016-04-15T01:01Z] INFO  18:01:49,584 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T01:01Z] INFO  18:01:50,007 IntervalUtils - Processing 329920 bp from intervals
[2016-04-15T01:01Z] WARN  18:01:50,013 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:01Z] INFO  18:01:50,102 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:01Z] INFO  18:01:50,285 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:01Z] INFO  18:01:50,291 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:01Z] INFO  18:01:50,292 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T01:01Z] INFO  18:01:50,292 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T01:01Z] INFO  18:01:50,293 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T01:01Z] INFO  18:01:50,293 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T01:01Z] INFO  18:01:50,438 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T01:01Z] INFO  18:01:51,528 ProgressMeter -     10:55973696      3.0223163E7    60.0 s            1.0 s       77.8%    77.0 s      17.0 s
[2016-04-15T01:01Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T01:01Z] INFO  18:01:52,690 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T01:01Z] INFO  18:01:52,691 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T01:01Z] WARN  18:01:52,968 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T01:01Z] WARN  18:01:52,968 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T01:01Z] INFO  18:01:53,698 ProgressMeter -     10:76158229     1.13034298E8    60.0 s            0.0 s       92.8%    64.0 s       4.0 s
[2016-04-15T01:01Z] INFO  18:01:56,345 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.013554625
[2016-04-15T01:01Z] INFO  18:01:56,346 PairHMM - Total compute time in PairHMM computeLikelihoods() : 6.0436843410000005
[2016-04-15T01:01Z] INFO  18:01:56,346 HaplotypeCaller - Ran local assembly on 835 active regions
[2016-04-15T01:01Z] INFO  18:01:56,421 ProgressMeter -            done      2.7883461E7    43.0 s            1.0 s      100.0%    43.0 s       0.0 s
[2016-04-15T01:01Z] INFO  18:01:56,422 ProgressMeter - Total runtime 43.66 secs, 0.73 min, 0.01 hours
[2016-04-15T01:01Z] INFO  18:01:56,422 MicroScheduler - 15532 reads were filtered out during the traversal out of approximately 176485 total reads (8.80%)
[2016-04-15T01:01Z] INFO  18:01:56,422 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:01Z] INFO  18:01:56,423 MicroScheduler -   -> 13876 reads (7.86% of total) failing DuplicateReadFilter
[2016-04-15T01:01Z] INFO  18:01:56,423 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:01Z] INFO  18:01:56,423 MicroScheduler -   -> 1656 reads (0.94% of total) failing HCMappingQualityFilter
[2016-04-15T01:01Z] INFO  18:01:56,424 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:01Z] INFO  18:01:56,424 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:01Z] INFO  18:01:56,424 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:01Z] INFO  18:01:56,424 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T01:01Z] INFO  18:01:57,795 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:01Z] GATK: HaplotypeCaller
[2016-04-15T01:01Z] INFO  18:01:58,113 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.013524669000000001
[2016-04-15T01:01Z] INFO  18:01:58,115 PairHMM - Total compute time in PairHMM computeLikelihoods() : 1.42732393
[2016-04-15T01:01Z] INFO  18:01:58,115 HaplotypeCaller - Ran local assembly on 1626 active regions
[2016-04-15T01:01Z] INFO  18:01:58,163 ProgressMeter -            done     1.26783317E8    64.0 s            0.0 s      100.0%    64.0 s       0.0 s
[2016-04-15T01:01Z] INFO  18:01:58,164 ProgressMeter - Total runtime 64.47 secs, 1.07 min, 0.02 hours
[2016-04-15T01:01Z] INFO  18:01:58,165 MicroScheduler - 35276 reads were filtered out during the traversal out of approximately 357214 total reads (9.88%)
[2016-04-15T01:01Z] INFO  18:01:58,165 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:01Z] INFO  18:01:58,165 MicroScheduler -   -> 27933 reads (7.82% of total) failing DuplicateReadFilter
[2016-04-15T01:01Z] INFO  18:01:58,165 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:01Z] INFO  18:01:58,166 MicroScheduler -   -> 7343 reads (2.06% of total) failing HCMappingQualityFilter
[2016-04-15T01:01Z] INFO  18:01:58,166 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:01Z] INFO  18:01:58,166 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:01Z] INFO  18:01:58,166 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:01Z] INFO  18:01:58,167 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T01:01Z] INFO  18:01:58,731 ProgressMeter -    10:104164940     1.53585773E8    60.0 s            0.0 s       76.5%    78.0 s      18.0 s
[2016-04-15T01:01Z] INFO  18:01:59,457 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:01Z] INFO  18:01:59,672 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.055996170000000005
[2016-04-15T01:01Z] INFO  18:01:59,673 PairHMM - Total compute time in PairHMM computeLikelihoods() : 11.320880936
[2016-04-15T01:01Z] INFO  18:01:59,674 HaplotypeCaller - Ran local assembly on 1089 active regions
[2016-04-15T01:01Z] GATK: HaplotypeCaller
[2016-04-15T01:01Z] INFO  18:01:59,728 ProgressMeter -            done      4.8765504E7    68.0 s            1.0 s      100.0%    68.0 s       0.0 s
[2016-04-15T01:01Z] INFO  18:01:59,733 ProgressMeter - Total runtime 68.23 secs, 1.14 min, 0.02 hours
[2016-04-15T01:01Z] INFO  18:01:59,734 MicroScheduler - 100265 reads were filtered out during the traversal out of approximately 302866 total reads (33.11%)
[2016-04-15T01:01Z] INFO  18:01:59,734 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:01Z] INFO  18:01:59,734 MicroScheduler -   -> 18444 reads (6.09% of total) failing DuplicateReadFilter
[2016-04-15T01:01Z] INFO  18:01:59,735 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:01Z] INFO  18:01:59,735 MicroScheduler -   -> 81821 reads (27.02% of total) failing HCMappingQualityFilter
[2016-04-15T01:01Z] INFO  18:01:59,735 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:01Z] INFO  18:01:59,735 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:01Z] INFO  18:01:59,736 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:01Z] INFO  18:01:59,736 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T01:01Z] INFO  18:01:59,952 ProgressMeter -     11:20623043      2.1549561E7    30.0 s            1.0 s       63.8%    46.0 s      16.0 s
[2016-04-15T01:02Z] INFO  18:02:00,100 ProgressMeter -     11:44105245      1.9894165E7    30.0 s            1.0 s       58.2%    51.0 s      21.0 s
[2016-04-15T01:02Z] INFO  18:02:01,022 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:02Z] INFO  18:02:01,025 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:02Z] INFO  18:02:01,026 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:02Z] INFO  18:02:01,026 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:02Z] INFO  18:02:01,031 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/12/R14-18105_kapa-NGv3-PE100-NGv3-sort-12_15650178_31231471-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/12/R14-18105_kapa-NGv3-PE100-NGv3-12_15650178_31231471-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/12/tx/tmpeXS85c/R14-18105_kapa-NGv3-PE100-NGv3-12_15650178_31231471.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:02Z] INFO  18:02:01,041 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:02Z] INFO  18:02:01,041 HelpFormatter - Date/Time: 2016/04/14 18:02:01
[2016-04-15T01:02Z] INFO  18:02:01,041 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:02Z] INFO  18:02:01,042 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:02Z] WARN  18:02:01,067 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T01:02Z] WARN  18:02:01,069 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/12/tx/tmpeXS85c/R14-18105_kapa-NGv3-PE100-NGv3-12_15650178_31231471.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T01:02Z] INFO  18:02:01,152 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:02Z] INFO  18:02:01,227 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:02Z] INFO  18:02:01,396 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T01:02Z] INFO  18:02:01,406 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:02Z] INFO  18:02:01,484 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-15T01:02Z] INFO  18:02:01,499 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T01:02Z] GATK: HaplotypeCaller
[2016-04-15T01:02Z] INFO  18:02:01,670 ProgressMeter -     11:48373671        6934557.0    30.0 s            4.0 s       16.8%     3.0 m       2.5 m
[2016-04-15T01:02Z] INFO  18:02:01,957 IntervalUtils - Processing 134686 bp from intervals
[2016-04-15T01:02Z] WARN  18:02:01,962 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:02Z] INFO  18:02:02,048 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:02Z] INFO  18:02:02,160 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:02Z] INFO  18:02:02,172 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:02Z] INFO  18:02:02,173 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T01:02Z] INFO  18:02:02,173 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T01:02Z] INFO  18:02:02,181 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T01:02Z] INFO  18:02:02,182 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T01:02Z] INFO  18:02:02,262 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:02Z] INFO  18:02:02,266 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:02Z] INFO  18:02:02,266 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:02Z] INFO  18:02:02,267 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:02Z] INFO  18:02:02,271 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/12/R14-18105_kapa-NGv3-PE100-NGv3-sort-12_31236746_46754992-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/12/R14-18105_kapa-NGv3-PE100-NGv3-12_31236746_46754992-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/12/tx/tmp7HtZj1/R14-18105_kapa-NGv3-PE100-NGv3-12_31236746_46754992.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:02Z] INFO  18:02:02,294 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:02Z] INFO  18:02:02,295 HelpFormatter - Date/Time: 2016/04/14 18:02:02
[2016-04-15T01:02Z] INFO  18:02:02,295 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:02Z] INFO  18:02:02,296 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:02Z] WARN  18:02:02,341 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T01:02Z] WARN  18:02:02,356 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/12/tx/tmp7HtZj1/R14-18105_kapa-NGv3-PE100-NGv3-12_31236746_46754992.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T01:02Z] INFO  18:02:02,356 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T01:02Z] INFO  18:02:02,550 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:02Z] INFO  18:02:02,711 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T01:02Z] INFO  18:02:02,726 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:02Z] INFO  18:02:02,789 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-15T01:02Z] INFO  18:02:02,802 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T01:02Z] INFO  18:02:02,994 ProgressMeter -     11:64627658      1.6604705E7    30.0 s            1.0 s       17.8%     2.8 m       2.3 m
[2016-04-15T01:02Z] INFO  18:02:03,162 ProgressMeter -     11:89956122      1.8040819E7    30.0 s            1.0 s       71.2%    42.0 s      12.0 s
[2016-04-15T01:02Z] INFO  18:02:03,169 IntervalUtils - Processing 136917 bp from intervals
[2016-04-15T01:02Z] WARN  18:02:03,174 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:02Z] INFO  18:02:03,318 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:02Z] INFO  18:02:03,378 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:02Z] INFO  18:02:03,379 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:02Z] INFO  18:02:03,379 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T01:02Z] INFO  18:02:03,380 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T01:02Z] INFO  18:02:03,396 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T01:02Z] INFO  18:02:03,397 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T01:02Z] INFO  18:02:03,627 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T01:02Z] INFO  18:02:04,384 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:02Z] INFO  18:02:04,387 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:02Z] INFO  18:02:04,388 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:02Z] INFO  18:02:04,388 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:02Z] INFO  18:02:04,395 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/12/R14-18105_kapa-NGv3-PE100-NGv3-sort-12_46756066_62654284-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/12/R14-18105_kapa-NGv3-PE100-NGv3-12_46756066_62654284-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/12/tx/tmp5KN_bK/R14-18105_kapa-NGv3-PE100-NGv3-12_46756066_62654284.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:02Z] INFO  18:02:04,429 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:02Z] INFO  18:02:04,437 HelpFormatter - Date/Time: 2016/04/14 18:02:04
[2016-04-15T01:02Z] INFO  18:02:04,438 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:02Z] INFO  18:02:04,438 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:02Z] WARN  18:02:04,467 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T01:02Z] WARN  18:02:04,474 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/12/tx/tmp5KN_bK/R14-18105_kapa-NGv3-PE100-NGv3-12_46756066_62654284.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T01:02Z] INFO  18:02:04,654 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:02Z] INFO  18:02:04,887 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T01:02Z] INFO  18:02:04,896 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:02Z] INFO  18:02:04,959 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-15T01:02Z] INFO  18:02:04,971 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T01:02Z] INFO  18:02:05,341 ProgressMeter -    11:105782602      2.6813227E7    30.0 s            1.0 s       66.3%    45.0 s      15.0 s
[2016-04-15T01:02Z] INFO  18:02:05,406 IntervalUtils - Processing 504306 bp from intervals
[2016-04-15T01:02Z] WARN  18:02:05,412 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:02Z] INFO  18:02:05,532 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:02Z] INFO  18:02:05,677 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:02Z] INFO  18:02:05,677 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:02Z] INFO  18:02:05,677 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T01:02Z] INFO  18:02:05,678 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T01:02Z] INFO  18:02:05,692 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T01:02Z] INFO  18:02:05,693 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T01:02Z] INFO  18:02:05,716 ProgressMeter -    11:116633419      1.7598804E7    30.0 s            1.0 s       26.5%   113.0 s      83.0 s
[2016-04-15T01:02Z] INFO  18:02:05,921 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T01:02Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T01:02Z] INFO  18:02:07,202 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T01:02Z] INFO  18:02:07,213 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T01:02Z] WARN  18:02:07,477 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T01:02Z] WARN  18:02:07,478 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T01:02Z] INFO  18:02:08,026 ProgressMeter -     9:139379352     2.94100993E8    90.0 s            0.0 s       75.4%   119.0 s      29.0 s
[2016-04-15T01:02Z] INFO  18:02:09,247 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.015304344000000001
[2016-04-15T01:02Z] INFO  18:02:09,258 PairHMM - Total compute time in PairHMM computeLikelihoods() : 2.7460618610000003
[2016-04-15T01:02Z] INFO  18:02:09,259 HaplotypeCaller - Ran local assembly on 1597 active regions
[2016-04-15T01:02Z] INFO  18:02:09,309 ProgressMeter -            done     1.10097324E8    58.0 s            0.0 s      100.0%    58.0 s       0.0 s
[2016-04-15T01:02Z] INFO  18:02:09,310 ProgressMeter - Total runtime 58.02 secs, 0.97 min, 0.02 hours
[2016-04-15T01:02Z] INFO  18:02:09,310 MicroScheduler - 32344 reads were filtered out during the traversal out of approximately 301581 total reads (10.72%)
[2016-04-15T01:02Z] INFO  18:02:09,322 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:02Z] INFO  18:02:09,323 MicroScheduler -   -> 23531 reads (7.80% of total) failing DuplicateReadFilter
[2016-04-15T01:02Z] INFO  18:02:09,323 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:02Z] INFO  18:02:09,324 MicroScheduler -   -> 8813 reads (2.92% of total) failing HCMappingQualityFilter
[2016-04-15T01:02Z] INFO  18:02:09,324 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:02Z] INFO  18:02:09,325 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:02Z] INFO  18:02:09,326 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:02Z] INFO  18:02:09,326 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T01:02Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T01:02Z] INFO  18:02:09,581 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T01:02Z] INFO  18:02:09,582 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T01:02Z] WARN  18:02:09,818 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T01:02Z] WARN  18:02:09,819 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T01:02Z] INFO  18:02:10,025 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.007446149000000001
[2016-04-15T01:02Z] INFO  18:02:10,025 PairHMM - Total compute time in PairHMM computeLikelihoods() : 0.32819621400000004
[2016-04-15T01:02Z] INFO  18:02:10,026 HaplotypeCaller - Ran local assembly on 795 active regions
[2016-04-15T01:02Z] INFO  18:02:10,061 ProgressMeter -            done      2.9891248E7    36.0 s            1.0 s      100.0%    36.0 s       0.0 s
[2016-04-15T01:02Z] INFO  18:02:10,062 ProgressMeter - Total runtime 36.94 secs, 0.62 min, 0.01 hours
[2016-04-15T01:02Z] INFO  18:02:10,071 MicroScheduler - 33110 reads were filtered out during the traversal out of approximately 169334 total reads (19.55%)
[2016-04-15T01:02Z] INFO  18:02:10,071 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:02Z] INFO  18:02:10,071 MicroScheduler -   -> 11700 reads (6.91% of total) failing DuplicateReadFilter
[2016-04-15T01:02Z] INFO  18:02:10,071 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:02Z] INFO  18:02:10,072 MicroScheduler -   -> 21410 reads (12.64% of total) failing HCMappingQualityFilter
[2016-04-15T01:02Z] INFO  18:02:10,072 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:02Z] INFO  18:02:10,072 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:02Z] INFO  18:02:10,072 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:02Z] INFO  18:02:10,073 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T01:02Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T01:02Z] INFO  18:02:10,687 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T01:02Z] INFO  18:02:10,688 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T01:02Z] INFO  18:02:11,032 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:02Z] WARN  18:02:11,037 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T01:02Z] WARN  18:02:11,043 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T01:02Z] GATK: HaplotypeCaller
[2016-04-15T01:02Z] INFO  18:02:11,716 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:02Z] GATK: HaplotypeCaller
[2016-04-15T01:02Z] INFO  18:02:12,547 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.011656061
[2016-04-15T01:02Z] INFO  18:02:12,548 PairHMM - Total compute time in PairHMM computeLikelihoods() : 0.550389024
[2016-04-15T01:02Z] INFO  18:02:12,549 HaplotypeCaller - Ran local assembly on 1110 active regions
[2016-04-15T01:02Z] INFO  18:02:12,580 ProgressMeter -            done      5.2775059E7    42.0 s            0.0 s      100.0%    42.0 s       0.0 s
[2016-04-15T01:02Z] INFO  18:02:12,581 ProgressMeter - Total runtime 42.65 secs, 0.71 min, 0.01 hours
[2016-04-15T01:02Z] INFO  18:02:12,582 MicroScheduler - 16635 reads were filtered out during the traversal out of approximately 200317 total reads (8.30%)
[2016-04-15T01:02Z] INFO  18:02:12,582 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:02Z] INFO  18:02:12,583 MicroScheduler -   -> 15815 reads (7.89% of total) failing DuplicateReadFilter
[2016-04-15T01:02Z] INFO  18:02:12,584 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:02Z] INFO  18:02:12,584 MicroScheduler -   -> 820 reads (0.41% of total) failing HCMappingQualityFilter
[2016-04-15T01:02Z] INFO  18:02:12,585 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:02Z] INFO  18:02:12,585 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:02Z] INFO  18:02:12,586 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:02Z] INFO  18:02:12,586 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T01:02Z] INFO  18:02:13,405 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.0076215810000000005
[2016-04-15T01:02Z] INFO  18:02:13,406 PairHMM - Total compute time in PairHMM computeLikelihoods() : 0.341755289
[2016-04-15T01:02Z] INFO  18:02:13,407 HaplotypeCaller - Ran local assembly on 1064 active regions
[2016-04-15T01:02Z] INFO  18:02:13,459 ProgressMeter -            done      5.3488435E7    43.0 s            0.0 s      100.0%    43.0 s       0.0 s
[2016-04-15T01:02Z] INFO  18:02:13,460 ProgressMeter - Total runtime 43.38 secs, 0.72 min, 0.01 hours
[2016-04-15T01:02Z] INFO  18:02:13,460 MicroScheduler - 19106 reads were filtered out during the traversal out of approximately 235059 total reads (8.13%)
[2016-04-15T01:02Z] INFO  18:02:13,460 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:02Z] INFO  18:02:13,460 MicroScheduler -   -> 18649 reads (7.93% of total) failing DuplicateReadFilter
[2016-04-15T01:02Z] INFO  18:02:13,461 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:02Z] INFO  18:02:13,462 MicroScheduler -   -> 457 reads (0.19% of total) failing HCMappingQualityFilter
[2016-04-15T01:02Z] INFO  18:02:13,462 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:02Z] INFO  18:02:13,462 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:02Z] INFO  18:02:13,462 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:02Z] INFO  18:02:13,463 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T01:02Z] INFO  18:02:13,621 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.015559630000000001
[2016-04-15T01:02Z] INFO  18:02:13,622 PairHMM - Total compute time in PairHMM computeLikelihoods() : 1.082909635
[2016-04-15T01:02Z] INFO  18:02:13,623 HaplotypeCaller - Ran local assembly on 2466 active regions
[2016-04-15T01:02Z] INFO  18:02:13,667 ProgressMeter -            done     2.79147334E8    74.0 s            0.0 s      100.0%    74.0 s       0.0 s
[2016-04-15T01:02Z] INFO  18:02:13,670 ProgressMeter - Total runtime 74.96 secs, 1.25 min, 0.02 hours
[2016-04-15T01:02Z] INFO  18:02:13,671 MicroScheduler - 41057 reads were filtered out during the traversal out of approximately 506028 total reads (8.11%)
[2016-04-15T01:02Z] INFO  18:02:13,672 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:02Z] INFO  18:02:13,672 MicroScheduler -   -> 40104 reads (7.93% of total) failing DuplicateReadFilter
[2016-04-15T01:02Z] INFO  18:02:13,673 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:02Z] INFO  18:02:13,673 MicroScheduler -   -> 953 reads (0.19% of total) failing HCMappingQualityFilter
[2016-04-15T01:02Z] INFO  18:02:13,674 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:02Z] INFO  18:02:13,675 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:02Z] INFO  18:02:13,675 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:02Z] INFO  18:02:13,676 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T01:02Z] INFO  18:02:14,020 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:02Z] INFO  18:02:14,365 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:02Z] INFO  18:02:14,368 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:02Z] INFO  18:02:14,368 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:02Z] INFO  18:02:14,368 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:02Z] INFO  18:02:14,372 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/12/R14-18105_kapa-NGv3-PE100-NGv3-sort-12_62687959_78225484-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/12/R14-18105_kapa-NGv3-PE100-NGv3-12_62687959_78225484-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/12/tx/tmp8tz2Gt/R14-18105_kapa-NGv3-PE100-NGv3-12_62687959_78225484.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:02Z] INFO  18:02:14,392 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:02Z] INFO  18:02:14,393 HelpFormatter - Date/Time: 2016/04/14 18:02:14
[2016-04-15T01:02Z] INFO  18:02:14,393 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:02Z] INFO  18:02:14,394 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:02Z] WARN  18:02:14,434 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T01:02Z] GATK: HaplotypeCaller
[2016-04-15T01:02Z] WARN  18:02:14,449 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/12/tx/tmp8tz2Gt/R14-18105_kapa-NGv3-PE100-NGv3-12_62687959_78225484.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T01:02Z] INFO  18:02:14,552 ProgressMeter -    11:134120169      1.9943661E7    30.0 s            1.0 s       91.8%    32.0 s       2.0 s
[2016-04-15T01:02Z] INFO  18:02:14,604 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.052944788000000007
[2016-04-15T01:02Z] INFO  18:02:14,605 PairHMM - Total compute time in PairHMM computeLikelihoods() : 0.48069058400000003
[2016-04-15T01:02Z] INFO  18:02:14,606 HaplotypeCaller - Ran local assembly on 1061 active regions
[2016-04-15T01:02Z] INFO  18:02:14,657 ProgressMeter -            done      5.5507672E7    39.0 s            0.0 s      100.0%    39.0 s       0.0 s
[2016-04-15T01:02Z] INFO  18:02:14,657 ProgressMeter - Total runtime 39.35 secs, 0.66 min, 0.01 hours
[2016-04-15T01:02Z] INFO  18:02:14,665 MicroScheduler - 14432 reads were filtered out during the traversal out of approximately 179681 total reads (8.03%)
[2016-04-15T01:02Z] INFO  18:02:14,665 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:02Z] INFO  18:02:14,665 MicroScheduler -   -> 14115 reads (7.86% of total) failing DuplicateReadFilter
[2016-04-15T01:02Z] INFO  18:02:14,666 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:02Z] INFO  18:02:14,666 MicroScheduler -   -> 317 reads (0.18% of total) failing HCMappingQualityFilter
[2016-04-15T01:02Z] INFO  18:02:14,666 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:02Z] INFO  18:02:14,666 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:02Z] INFO  18:02:14,666 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:02Z] INFO  18:02:14,667 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T01:02Z] INFO  18:02:14,728 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:02Z] INFO  18:02:14,916 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T01:02Z] INFO  18:02:14,936 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:02Z] INFO  18:02:15,011 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-15T01:02Z] INFO  18:02:15,045 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:02Z] INFO  18:02:15,053 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T01:02Z] INFO  18:02:15,192 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:02Z] INFO  18:02:15,196 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:02Z] INFO  18:02:15,196 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:02Z] INFO  18:02:15,197 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:02Z] INFO  18:02:15,202 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/12/R14-18105_kapa-NGv3-PE100-NGv3-sort-12_78334098_93863131-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/12/R14-18105_kapa-NGv3-PE100-NGv3-12_78334098_93863131-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/12/tx/tmpY4ZVlf/R14-18105_kapa-NGv3-PE100-NGv3-12_78334098_93863131.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:02Z] INFO  18:02:15,233 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:02Z] INFO  18:02:15,234 HelpFormatter - Date/Time: 2016/04/14 18:02:15
[2016-04-15T01:02Z] INFO  18:02:15,234 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:02Z] INFO  18:02:15,239 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:02Z] INFO  18:02:15,247 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:02Z] WARN  18:02:15,290 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T01:02Z] WARN  18:02:15,293 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/12/tx/tmpY4ZVlf/R14-18105_kapa-NGv3-PE100-NGv3-12_78334098_93863131.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T01:02Z] GATK: HaplotypeCaller
[2016-04-15T01:02Z] INFO  18:02:15,383 IntervalUtils - Processing 146919 bp from intervals
[2016-04-15T01:02Z] WARN  18:02:15,399 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:02Z] INFO  18:02:15,434 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:02Z] INFO  18:02:15,485 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:02Z] GATK: HaplotypeCaller
[2016-04-15T01:02Z] INFO  18:02:15,590 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:02Z] INFO  18:02:15,591 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:02Z] INFO  18:02:15,592 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T01:02Z] INFO  18:02:15,593 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T01:02Z] INFO  18:02:15,593 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T01:02Z] INFO  18:02:15,594 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T01:02Z] INFO  18:02:15,763 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T01:02Z] INFO  18:02:15,798 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:02Z] INFO  18:02:15,833 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T01:02Z] INFO  18:02:15,892 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.09
[2016-04-15T01:02Z] INFO  18:02:15,921 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T01:02Z] INFO  18:02:16,092 ProgressMeter -      11:1017239        9985430.0    60.0 s            6.0 s       16.5%     6.1 m       5.1 m
[2016-04-15T01:02Z] INFO  18:02:16,132 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:02Z] INFO  18:02:16,288 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.008005605
[2016-04-15T01:02Z] INFO  18:02:16,289 PairHMM - Total compute time in PairHMM computeLikelihoods() : 0.41851108400000003
[2016-04-15T01:02Z] INFO  18:02:16,290 HaplotypeCaller - Ran local assembly on 749 active regions
[2016-04-15T01:02Z] INFO  18:02:16,293 IntervalUtils - Processing 88957 bp from intervals
[2016-04-15T01:02Z] WARN  18:02:16,299 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:02Z] INFO  18:02:16,338 ProgressMeter -            done      2.5784333E7    31.0 s            1.0 s      100.0%    31.0 s       0.0 s
[2016-04-15T01:02Z] INFO  18:02:16,339 ProgressMeter - Total runtime 31.80 secs, 0.53 min, 0.01 hours
[2016-04-15T01:02Z] INFO  18:02:16,340 MicroScheduler - 14627 reads were filtered out during the traversal out of approximately 172575 total reads (8.48%)
[2016-04-15T01:02Z] INFO  18:02:16,340 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:02Z] INFO  18:02:16,341 MicroScheduler -   -> 13915 reads (8.06% of total) failing DuplicateReadFilter
[2016-04-15T01:02Z] INFO  18:02:16,341 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:02Z] INFO  18:02:16,341 MicroScheduler -   -> 712 reads (0.41% of total) failing HCMappingQualityFilter
[2016-04-15T01:02Z] INFO  18:02:16,341 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:02Z] INFO  18:02:16,342 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:02Z] INFO  18:02:16,342 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:02Z] INFO  18:02:16,342 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T01:02Z] INFO  18:02:16,436 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:02Z] GATK: HaplotypeCaller
[2016-04-15T01:02Z] INFO  18:02:16,548 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:02Z] INFO  18:02:16,549 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:02Z] INFO  18:02:16,550 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T01:02Z] INFO  18:02:16,551 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T01:02Z] INFO  18:02:16,552 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T01:02Z] INFO  18:02:16,552 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T01:02Z] INFO  18:02:16,738 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T01:02Z] INFO  18:02:17,159 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:02Z] INFO  18:02:17,162 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:02Z] INFO  18:02:17,163 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:02Z] INFO  18:02:17,164 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:02Z] INFO  18:02:17,168 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/12/R14-18105_kapa-NGv3-PE100-NGv3-sort-12_93870729_109490566-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/12/R14-18105_kapa-NGv3-PE100-NGv3-12_93870729_109490566-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/12/tx/tmpkXT5J1/R14-18105_kapa-NGv3-PE100-NGv3-12_93870729_109490566.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:02Z] INFO  18:02:17,184 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:02Z] INFO  18:02:17,185 HelpFormatter - Date/Time: 2016/04/14 18:02:17
[2016-04-15T01:02Z] INFO  18:02:17,185 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:02Z] INFO  18:02:17,186 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:02Z] WARN  18:02:17,236 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T01:02Z] WARN  18:02:17,238 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/12/tx/tmpkXT5J1/R14-18105_kapa-NGv3-PE100-NGv3-12_93870729_109490566.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T01:02Z] INFO  18:02:17,537 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:02Z] INFO  18:02:17,811 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T01:02Z] INFO  18:02:17,812 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:02Z] INFO  18:02:17,821 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:02Z] INFO  18:02:17,939 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.12
[2016-04-15T01:02Z] INFO  18:02:17,962 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T01:02Z] GATK: HaplotypeCaller
[2016-04-15T01:02Z] INFO  18:02:18,577 IntervalUtils - Processing 201796 bp from intervals
[2016-04-15T01:02Z] WARN  18:02:18,593 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:02Z] INFO  18:02:18,703 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:02Z] INFO  18:02:18,832 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:02Z] INFO  18:02:18,832 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:02Z] INFO  18:02:18,832 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T01:02Z] INFO  18:02:18,833 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T01:02Z] INFO  18:02:18,843 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T01:02Z] INFO  18:02:18,844 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T01:02Z] INFO  18:02:19,111 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:02Z] INFO  18:02:19,124 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:02Z] INFO  18:02:19,125 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:02Z] INFO  18:02:19,126 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:02Z] INFO  18:02:19,130 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/12/R14-18105_kapa-NGv3-PE100-NGv3-sort-12_109494486_125263132-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/12/R14-18105_kapa-NGv3-PE100-NGv3-12_109494486_125263132-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/12/tx/tmpCChAkO/R14-18105_kapa-NGv3-PE100-NGv3-12_109494486_125263132.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:02Z] INFO  18:02:19,152 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:02Z] INFO  18:02:19,153 HelpFormatter - Date/Time: 2016/04/14 18:02:19
[2016-04-15T01:02Z] INFO  18:02:19,153 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:02Z] INFO  18:02:19,154 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:02Z] INFO  18:02:19,156 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T01:02Z] WARN  18:02:19,188 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T01:02Z] WARN  18:02:19,203 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/12/tx/tmpCChAkO/R14-18105_kapa-NGv3-PE100-NGv3-12_109494486_125263132.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T01:02Z] INFO  18:02:19,323 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:02Z] INFO  18:02:19,337 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:02Z] INFO  18:02:19,338 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:02Z] INFO  18:02:19,339 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:02Z] INFO  18:02:19,343 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/12/R14-18105_kapa-NGv3-PE100-NGv3-sort-12_125267228_133851895-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/12/R14-18105_kapa-NGv3-PE100-NGv3-12_125267228_133851895-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/12/tx/tmpHPa3AO/R14-18105_kapa-NGv3-PE100-NGv3-12_125267228_133851895.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:02Z] INFO  18:02:19,388 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:02Z] INFO  18:02:19,389 HelpFormatter - Date/Time: 2016/04/14 18:02:19
[2016-04-15T01:02Z] INFO  18:02:19,390 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:02Z] INFO  18:02:19,390 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:02Z] WARN  18:02:19,434 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T01:02Z] WARN  18:02:19,447 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/12/tx/tmpHPa3AO/R14-18105_kapa-NGv3-PE100-NGv3-12_125267228_133851895.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T01:02Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T01:02Z] INFO  18:02:19,491 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T01:02Z] INFO  18:02:19,491 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T01:02Z] INFO  18:02:19,550 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:02Z] INFO  18:02:19,647 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:02Z] INFO  18:02:19,762 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T01:02Z] INFO  18:02:19,775 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:02Z] WARN  18:02:19,809 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T01:02Z] WARN  18:02:19,810 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T01:02Z] INFO  18:02:19,863 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.09
[2016-04-15T01:02Z] INFO  18:02:19,892 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T01:02Z] INFO  18:02:19,888 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T01:02Z] INFO  18:02:19,912 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:02Z] INFO  18:02:19,926 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:02Z] INFO  18:02:19,939 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:02Z] INFO  18:02:19,940 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:02Z] INFO  18:02:19,941 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:02Z] INFO  18:02:19,945 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/13/R14-18105_kapa-NGv3-PE100-NGv3-sort-13_0_19748299-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/13/R14-18105_kapa-NGv3-PE100-NGv3-13_0_19748299-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/13/tx/tmpNbdTtS/R14-18105_kapa-NGv3-PE100-NGv3-13_0_19748299.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:02Z] INFO  18:02:19,965 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:02Z] INFO  18:02:19,966 HelpFormatter - Date/Time: 2016/04/14 18:02:19
[2016-04-15T01:02Z] INFO  18:02:19,967 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:02Z] INFO  18:02:19,967 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:02Z] WARN  18:02:20,013 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T01:02Z] INFO  18:02:20,021 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.11
[2016-04-15T01:02Z] WARN  18:02:20,026 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/13/tx/tmpNbdTtS/R14-18105_kapa-NGv3-PE100-NGv3-13_0_19748299.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T01:02Z] INFO  18:02:20,040 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T01:02Z] INFO  18:02:20,299 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:02Z] INFO  18:02:20,313 ProgressMeter -      12:5687624       2.160439E7    30.0 s            1.0 s       28.6%   104.0 s      74.0 s
[2016-04-15T01:02Z] INFO  18:02:20,411 IntervalUtils - Processing 364987 bp from intervals
[2016-04-15T01:02Z] WARN  18:02:20,423 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:02Z] INFO  18:02:20,545 IntervalUtils - Processing 106872 bp from intervals
[2016-04-15T01:02Z] INFO  18:02:20,552 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T01:02Z] WARN  18:02:20,563 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:02Z] INFO  18:02:20,568 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:02Z] INFO  18:02:20,574 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:02Z] INFO  18:02:20,662 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.09
[2016-04-15T01:02Z] INFO  18:02:20,670 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T01:02Z] INFO  18:02:20,697 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:02Z] INFO  18:02:20,729 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:02Z] INFO  18:02:20,730 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:02Z] INFO  18:02:20,731 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T01:02Z] INFO  18:02:20,732 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T01:02Z] INFO  18:02:20,732 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T01:02Z] INFO  18:02:20,733 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T01:02Z] INFO  18:02:20,814 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:02Z] INFO  18:02:20,815 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:02Z] INFO  18:02:20,816 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T01:02Z] INFO  18:02:20,816 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T01:02Z] INFO  18:02:20,833 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T01:02Z] INFO  18:02:20,834 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T01:02Z] INFO  18:02:20,964 IntervalUtils - Processing 297 bp from intervals
[2016-04-15T01:02Z] WARN  18:02:20,969 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:02Z] INFO  18:02:20,988 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T01:02Z] INFO  18:02:21,021 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T01:02Z] INFO  18:02:21,134 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:02Z] INFO  18:02:21,165 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:02Z] INFO  18:02:21,167 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:02Z] INFO  18:02:21,167 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T01:02Z] INFO  18:02:21,168 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T01:02Z] INFO  18:02:21,169 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T01:02Z] INFO  18:02:21,169 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T01:02Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T01:02Z] INFO  18:02:21,270 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T01:02Z] INFO  18:02:21,272 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T01:02Z] INFO  18:02:21,333 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:02Z] INFO  18:02:21,342 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:02Z] INFO  18:02:21,342 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:02Z] INFO  18:02:21,343 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:02Z] INFO  18:02:21,348 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/13/R14-18105_kapa-NGv3-PE100-NGv3-sort-13_19751066_35517251-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/13/R14-18105_kapa-NGv3-PE100-NGv3-13_19751066_35517251-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/13/tx/tmpvy64j6/R14-18105_kapa-NGv3-PE100-NGv3-13_19751066_35517251.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:02Z] INFO  18:02:21,372 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:02Z] INFO  18:02:21,372 HelpFormatter - Date/Time: 2016/04/14 18:02:21
[2016-04-15T01:02Z] INFO  18:02:21,372 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:02Z] INFO  18:02:21,373 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:02Z] INFO  18:02:21,382 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T01:02Z] WARN  18:02:21,422 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T01:02Z] WARN  18:02:21,425 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/13/tx/tmpvy64j6/R14-18105_kapa-NGv3-PE100-NGv3-13_19751066_35517251.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T01:02Z] WARN  18:02:21,511 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T01:02Z] WARN  18:02:21,512 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T01:02Z] INFO  18:02:21,632 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:02Z] INFO  18:02:21,809 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T01:02Z] INFO  18:02:21,818 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:02Z] INFO  18:02:21,898 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-15T01:02Z] INFO  18:02:21,934 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T01:02Z] INFO  18:02:22,431 IntervalUtils - Processing 201552 bp from intervals
[2016-04-15T01:02Z] WARN  18:02:22,437 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:02Z] INFO  18:02:22,531 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:02Z] INFO  18:02:22,647 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:02Z] INFO  18:02:22,648 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:02Z] INFO  18:02:22,648 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T01:02Z] INFO  18:02:22,649 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T01:02Z] INFO  18:02:22,660 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T01:02Z] INFO  18:02:22,661 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T01:02Z] INFO  18:02:22,934 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T01:02Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T01:02Z] INFO  18:02:23,859 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T01:02Z] INFO  18:02:23,859 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T01:02Z] INFO  18:02:23,860 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.0
[2016-04-15T01:02Z] INFO  18:02:23,860 PairHMM - Total compute time in PairHMM computeLikelihoods() : 0.0
[2016-04-15T01:02Z] INFO  18:02:23,861 HaplotypeCaller - Ran local assembly on 1 active regions
[2016-04-15T01:02Z] INFO  18:02:23,906 ProgressMeter -            done            297.0     2.0 s            2.6 h       99.7%     2.0 s       0.0 s
[2016-04-15T01:02Z] INFO  18:02:23,907 ProgressMeter - Total runtime 2.74 secs, 0.05 min, 0.00 hours
[2016-04-15T01:02Z] INFO  18:02:23,907 MicroScheduler - 110 reads were filtered out during the traversal out of approximately 1041 total reads (10.57%)
[2016-04-15T01:02Z] INFO  18:02:23,908 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:02Z] INFO  18:02:23,908 MicroScheduler -   -> 109 reads (10.47% of total) failing DuplicateReadFilter
[2016-04-15T01:02Z] INFO  18:02:23,909 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:02Z] INFO  18:02:23,910 MicroScheduler -   -> 1 reads (0.10% of total) failing HCMappingQualityFilter
[2016-04-15T01:02Z] INFO  18:02:23,910 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:02Z] INFO  18:02:23,911 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:02Z] INFO  18:02:23,912 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:02Z] INFO  18:02:23,917 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T01:02Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T01:02Z] INFO  18:02:23,961 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T01:02Z] INFO  18:02:23,961 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T01:02Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T01:02Z] INFO  18:02:24,247 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T01:02Z] INFO  18:02:24,250 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T01:02Z] WARN  18:02:24,287 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T01:02Z] WARN  18:02:24,287 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T01:02Z] WARN  18:02:24,547 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T01:02Z] WARN  18:02:24,548 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T01:02Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T01:02Z] INFO  18:02:24,596 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T01:02Z] INFO  18:02:24,608 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T01:02Z] WARN  18:02:24,934 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T01:02Z] WARN  18:02:24,946 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T01:02Z] INFO  18:02:25,402 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:02Z] GATK: HaplotypeCaller
[2016-04-15T01:02Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T01:02Z] INFO  18:02:28,462 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T01:02Z] INFO  18:02:28,463 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T01:02Z] WARN  18:02:28,697 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T01:02Z] WARN  18:02:28,698 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T01:02Z] INFO  18:02:29,247 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:02Z] INFO  18:02:29,262 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:02Z] INFO  18:02:29,263 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:02Z] INFO  18:02:29,263 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:02Z] INFO  18:02:29,268 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/13/R14-18105_kapa-NGv3-PE100-NGv3-sort-13_35615069_51287376-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/13/R14-18105_kapa-NGv3-PE100-NGv3-13_35615069_51287376-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/13/tx/tmpN_ewT9/R14-18105_kapa-NGv3-PE100-NGv3-13_35615069_51287376.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:02Z] INFO  18:02:29,287 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:02Z] INFO  18:02:29,288 HelpFormatter - Date/Time: 2016/04/14 18:02:29
[2016-04-15T01:02Z] INFO  18:02:29,289 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:02Z] INFO  18:02:29,289 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:02Z] WARN  18:02:29,338 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T01:02Z] WARN  18:02:29,340 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/13/tx/tmpN_ewT9/R14-18105_kapa-NGv3-PE100-NGv3-13_35615069_51287376.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T01:02Z] INFO  18:02:29,534 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:02Z] INFO  18:02:29,774 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T01:02Z] INFO  18:02:29,784 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:02Z] INFO  18:02:29,890 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.10
[2016-04-15T01:02Z] INFO  18:02:29,919 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T01:02Z] INFO  18:02:30,287 IntervalUtils - Processing 179232 bp from intervals
[2016-04-15T01:02Z] WARN  18:02:30,292 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:02Z] INFO  18:02:30,446 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:02Z] INFO  18:02:30,563 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:02Z] INFO  18:02:30,565 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:02Z] INFO  18:02:30,565 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T01:02Z] INFO  18:02:30,566 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T01:02Z] INFO  18:02:30,567 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T01:02Z] INFO  18:02:30,567 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T01:02Z] INFO  18:02:30,859 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T01:02Z] INFO  18:02:31,671 ProgressMeter -     11:56510304       1.384399E7    60.0 s            4.0 s       32.9%     3.0 m       2.0 m
[2016-04-15T01:02Z] INFO  18:02:32,184 ProgressMeter -     12:26878698      2.5941236E7    30.0 s            1.0 s       70.9%    42.0 s      12.0 s
[2016-04-15T01:02Z] INFO  18:02:33,004 ProgressMeter -     11:66457514     1.00004363E8    60.0 s            0.0 s       45.5%     2.2 m      71.0 s
[2016-04-15T01:02Z] INFO  18:02:33,398 ProgressMeter -     12:40873641      1.2833395E7    30.0 s            2.0 s       49.8%    60.0 s      30.0 s
[2016-04-15T01:02Z] INFO  18:02:35,709 ProgressMeter -     12:49721108       1.325327E7    30.0 s            2.0 s       17.7%     2.8 m       2.3 m
[2016-04-15T01:02Z] INFO  18:02:35,721 ProgressMeter -    11:119228300      9.5420171E7    60.0 s            0.0 s       65.4%    91.0 s      31.0 s
[2016-04-15T01:02Z] INFO  18:02:36,715 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.042761876000000004
[2016-04-15T01:02Z] INFO  18:02:36,716 PairHMM - Total compute time in PairHMM computeLikelihoods() : 2.467253916
[2016-04-15T01:02Z] INFO  18:02:36,717 HaplotypeCaller - Ran local assembly on 3584 active regions
[2016-04-15T01:02Z] INFO  18:02:36,761 ProgressMeter -            done     4.74191826E8   118.0 s            0.0 s      100.0%   118.0 s       0.0 s
[2016-04-15T01:02Z] INFO  18:02:36,762 ProgressMeter - Total runtime 118.78 secs, 1.98 min, 0.03 hours
[2016-04-15T01:02Z] INFO  18:02:36,763 MicroScheduler - 73289 reads were filtered out during the traversal out of approximately 834602 total reads (8.78%)
[2016-04-15T01:02Z] INFO  18:02:36,764 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:02Z] INFO  18:02:36,771 MicroScheduler -   -> 66152 reads (7.93% of total) failing DuplicateReadFilter
[2016-04-15T01:02Z] INFO  18:02:36,771 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:02Z] INFO  18:02:36,771 MicroScheduler -   -> 7137 reads (0.86% of total) failing HCMappingQualityFilter
[2016-04-15T01:02Z] INFO  18:02:36,771 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:02Z] INFO  18:02:36,772 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:02Z] INFO  18:02:36,772 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:02Z] INFO  18:02:36,772 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T01:02Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T01:02Z] INFO  18:02:37,662 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T01:02Z] INFO  18:02:37,663 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T01:02Z] WARN  18:02:37,962 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T01:02Z] WARN  18:02:37,963 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T01:02Z] INFO  18:02:38,737 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:02Z] GATK: HaplotypeCaller
[2016-04-15T01:02Z] INFO  18:02:41,070 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.007123209
[2016-04-15T01:02Z] INFO  18:02:41,070 PairHMM - Total compute time in PairHMM computeLikelihoods() : 0.411250516
[2016-04-15T01:02Z] INFO  18:02:41,070 HaplotypeCaller - Ran local assembly on 1064 active regions
[2016-04-15T01:02Z] INFO  18:02:41,112 ProgressMeter -            done      5.5983758E7    38.0 s            0.0 s      100.0%    38.0 s       0.0 s
[2016-04-15T01:02Z] INFO  18:02:41,113 ProgressMeter - Total runtime 38.94 secs, 0.65 min, 0.01 hours
[2016-04-15T01:02Z] INFO  18:02:41,113 MicroScheduler - 12418 reads were filtered out during the traversal out of approximately 152867 total reads (8.12%)
[2016-04-15T01:02Z] INFO  18:02:41,113 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:02Z] INFO  18:02:41,114 MicroScheduler -   -> 12170 reads (7.96% of total) failing DuplicateReadFilter
[2016-04-15T01:02Z] INFO  18:02:41,114 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:02Z] INFO  18:02:41,114 MicroScheduler -   -> 248 reads (0.16% of total) failing HCMappingQualityFilter
[2016-04-15T01:02Z] INFO  18:02:41,115 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:02Z] INFO  18:02:41,115 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:02Z] INFO  18:02:41,115 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:02Z] INFO  18:02:41,115 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T01:02Z] INFO  18:02:42,027 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:02Z] INFO  18:02:42,030 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:02Z] INFO  18:02:42,031 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:02Z] INFO  18:02:42,031 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:02Z] INFO  18:02:42,036 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/13/R14-18105_kapa-NGv3-PE100-NGv3-sort-13_51396767_67205543-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/13/R14-18105_kapa-NGv3-PE100-NGv3-13_51396767_67205543-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/13/tx/tmpGq34LS/R14-18105_kapa-NGv3-PE100-NGv3-13_51396767_67205543.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:02Z] INFO  18:02:42,047 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:02Z] INFO  18:02:42,059 HelpFormatter - Date/Time: 2016/04/14 18:02:42
[2016-04-15T01:02Z] INFO  18:02:42,060 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:02Z] INFO  18:02:42,061 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:02Z] WARN  18:02:42,104 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T01:02Z] WARN  18:02:42,106 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/13/tx/tmpGq34LS/R14-18105_kapa-NGv3-PE100-NGv3-13_51396767_67205543.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T01:02Z] INFO  18:02:42,380 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:02Z] INFO  18:02:42,636 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T01:02Z] INFO  18:02:42,646 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:02Z] INFO  18:02:42,647 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:02Z] INFO  18:02:42,719 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-15T01:02Z] INFO  18:02:42,741 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T01:02Z] GATK: HaplotypeCaller
[2016-04-15T01:02Z] INFO  18:02:43,145 IntervalUtils - Processing 59966 bp from intervals
[2016-04-15T01:02Z] WARN  18:02:43,162 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:02Z] INFO  18:02:43,235 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:02Z] INFO  18:02:43,316 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:02Z] INFO  18:02:43,316 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:02Z] INFO  18:02:43,334 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T01:02Z] INFO  18:02:43,334 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T01:02Z] INFO  18:02:43,341 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T01:02Z] INFO  18:02:43,342 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T01:02Z] INFO  18:02:43,550 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T01:02Z] INFO  18:02:45,192 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.004558207
[2016-04-15T01:02Z] INFO  18:02:45,193 PairHMM - Total compute time in PairHMM computeLikelihoods() : 0.312391112
[2016-04-15T01:02Z] INFO  18:02:45,194 HaplotypeCaller - Ran local assembly on 652 active regions
[2016-04-15T01:02Z] INFO  18:02:45,243 ProgressMeter -            done        2.16241E7    28.0 s            1.0 s      100.0%    28.0 s       0.0 s
[2016-04-15T01:02Z] INFO  18:02:45,244 ProgressMeter - Total runtime 28.69 secs, 0.48 min, 0.01 hours
[2016-04-15T01:02Z] INFO  18:02:45,244 MicroScheduler - 7617 reads were filtered out during the traversal out of approximately 93842 total reads (8.12%)
[2016-04-15T01:02Z] INFO  18:02:45,244 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:02Z] INFO  18:02:45,245 MicroScheduler -   -> 7455 reads (7.94% of total) failing DuplicateReadFilter
[2016-04-15T01:02Z] INFO  18:02:45,245 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:02Z] INFO  18:02:45,245 MicroScheduler -   -> 162 reads (0.17% of total) failing HCMappingQualityFilter
[2016-04-15T01:02Z] INFO  18:02:45,245 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:02Z] INFO  18:02:45,246 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:02Z] INFO  18:02:45,246 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:02Z] INFO  18:02:45,246 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T01:02Z] INFO  18:02:45,603 ProgressMeter -     12:71946853      2.7298339E7    30.0 s            1.0 s       68.0%    44.0 s      14.0 s
[2016-04-15T01:02Z] INFO  18:02:46,093 ProgressMeter -      11:1017933        9985430.0    90.0 s            9.0 s       16.6%     9.0 m       7.5 m
[2016-04-15T01:02Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T01:02Z] INFO  18:02:46,125 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T01:02Z] INFO  18:02:46,126 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T01:02Z] WARN  18:02:46,388 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T01:02Z] WARN  18:02:46,389 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T01:02Z] INFO  18:02:46,494 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:02Z] INFO  18:02:46,498 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:02Z] INFO  18:02:46,498 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:02Z] INFO  18:02:46,499 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:02Z] INFO  18:02:46,504 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/13/R14-18105_kapa-NGv3-PE100-NGv3-sort-13_67477635_84455642-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/13/R14-18105_kapa-NGv3-PE100-NGv3-13_67477635_84455642-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/13/tx/tmpkgiLqi/R14-18105_kapa-NGv3-PE100-NGv3-13_67477635_84455642.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:02Z] INFO  18:02:46,555 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:02Z] INFO  18:02:46,555 HelpFormatter - Date/Time: 2016/04/14 18:02:46
[2016-04-15T01:02Z] INFO  18:02:46,555 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:02Z] INFO  18:02:46,556 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:02Z] WARN  18:02:46,593 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T01:02Z] WARN  18:02:46,596 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/13/tx/tmpkgiLqi/R14-18105_kapa-NGv3-PE100-NGv3-13_67477635_84455642.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T01:02Z] INFO  18:02:46,776 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:02Z] INFO  18:02:46,777 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:02Z] INFO  18:02:47,012 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T01:02Z] INFO  18:02:47,022 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:02Z] GATK: HaplotypeCaller
[2016-04-15T01:02Z] INFO  18:02:47,109 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.09
[2016-04-15T01:02Z] INFO  18:02:47,138 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T01:02Z] INFO  18:02:47,439 IntervalUtils - Processing 69582 bp from intervals
[2016-04-15T01:02Z] WARN  18:02:47,466 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:02Z] INFO  18:02:47,584 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:02Z] INFO  18:02:47,699 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:02Z] INFO  18:02:47,700 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:02Z] INFO  18:02:47,701 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T01:02Z] INFO  18:02:47,701 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T01:02Z] INFO  18:02:47,711 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T01:02Z] INFO  18:02:47,712 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T01:02Z] INFO  18:02:47,889 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T01:02Z] INFO  18:02:48,858 ProgressMeter -    12:102590044      3.9888049E7    30.0 s            0.0 s       56.4%    53.0 s      23.0 s
[2016-04-15T01:02Z] INFO  18:02:50,314 ProgressMeter -      12:8375131     1.00643534E8    60.0 s            0.0 s       63.8%    94.0 s      34.0 s
[2016-04-15T01:02Z] INFO  18:02:50,317 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:02Z] INFO  18:02:50,320 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:02Z] INFO  18:02:50,320 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:02Z] INFO  18:02:50,320 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:02Z] INFO  18:02:50,324 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/13/R14-18105_kapa-NGv3-PE100-NGv3-sort-13_86368117_101881935-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/13/R14-18105_kapa-NGv3-PE100-NGv3-13_86368117_101881935-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/13/tx/tmpAhXRnk/R14-18105_kapa-NGv3-PE100-NGv3-13_86368117_101881935.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:02Z] INFO  18:02:50,334 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:02Z] INFO  18:02:50,335 HelpFormatter - Date/Time: 2016/04/14 18:02:50
[2016-04-15T01:02Z] INFO  18:02:50,335 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:02Z] INFO  18:02:50,335 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:02Z] WARN  18:02:50,389 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T01:02Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T01:02Z] WARN  18:02:50,392 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/13/tx/tmpAhXRnk/R14-18105_kapa-NGv3-PE100-NGv3-13_86368117_101881935.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T01:02Z] INFO  18:02:50,405 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T01:02Z] INFO  18:02:50,405 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T01:02Z] INFO  18:02:50,592 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:02Z] WARN  18:02:50,612 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T01:02Z] WARN  18:02:50,613 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T01:02Z] INFO  18:02:50,730 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T01:02Z] INFO  18:02:50,750 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:02Z] INFO  18:02:50,761 ProgressMeter -    12:113385751      3.5846298E7    30.0 s            0.0 s       30.4%    98.0 s      68.0 s
[2016-04-15T01:02Z] INFO  18:02:50,827 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-15T01:02Z] INFO  18:02:50,836 ProgressMeter -    12:133249329      1.2873422E7    30.0 s            2.0 s       72.6%    41.0 s      11.0 s
[2016-04-15T01:02Z] INFO  18:02:50,855 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T01:02Z] INFO  18:02:51,223 IntervalUtils - Processing 75123 bp from intervals
[2016-04-15T01:02Z] WARN  18:02:51,239 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:02Z] INFO  18:02:51,333 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:02Z] INFO  18:02:51,426 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:02Z] INFO  18:02:51,427 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:02Z] INFO  18:02:51,428 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T01:02Z] INFO  18:02:51,429 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T01:02Z] INFO  18:02:51,430 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T01:02Z] INFO  18:02:51,430 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T01:02Z] INFO  18:02:51,585 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T01:02Z] INFO  18:02:52,670 ProgressMeter -     13:25671555       1.610196E7    30.0 s            1.0 s       43.2%    69.0 s      39.0 s
[2016-04-15T01:02Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T01:02Z] INFO  18:02:54,759 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T01:02Z] INFO  18:02:54,760 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T01:02Z] INFO  18:02:54,922 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.007532550000000001
[2016-04-15T01:02Z] INFO  18:02:54,923 PairHMM - Total compute time in PairHMM computeLikelihoods() : 0.365250984
[2016-04-15T01:02Z] INFO  18:02:54,923 HaplotypeCaller - Ran local assembly on 1096 active regions
[2016-04-15T01:02Z] INFO  18:02:54,976 ProgressMeter -            done       5.533073E7    39.0 s            0.0 s      100.0%    39.0 s       0.0 s
[2016-04-15T01:02Z] INFO  18:02:54,976 ProgressMeter - Total runtime 39.39 secs, 0.66 min, 0.01 hours
[2016-04-15T01:02Z] INFO  18:02:54,977 MicroScheduler - 14142 reads were filtered out during the traversal out of approximately 173025 total reads (8.17%)
[2016-04-15T01:02Z] INFO  18:02:54,977 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:02Z] INFO  18:02:54,977 MicroScheduler -   -> 13670 reads (7.90% of total) failing DuplicateReadFilter
[2016-04-15T01:02Z] INFO  18:02:54,978 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:02Z] INFO  18:02:54,978 MicroScheduler -   -> 472 reads (0.27% of total) failing HCMappingQualityFilter
[2016-04-15T01:02Z] INFO  18:02:54,978 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:02Z] INFO  18:02:54,978 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:02Z] INFO  18:02:54,979 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:02Z] INFO  18:02:54,979 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T01:02Z] WARN  18:02:55,058 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T01:02Z] WARN  18:02:55,059 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T01:02Z] INFO  18:02:55,500 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.021023548000000003
[2016-04-15T01:02Z] INFO  18:02:55,501 PairHMM - Total compute time in PairHMM computeLikelihoods() : 1.058857758
[2016-04-15T01:02Z] INFO  18:02:55,502 HaplotypeCaller - Ran local assembly on 784 active regions
[2016-04-15T01:02Z] INFO  18:02:55,566 ProgressMeter -            done      2.2806798E7    34.0 s            1.0 s      100.0%    34.0 s       0.0 s
[2016-04-15T01:02Z] INFO  18:02:55,566 ProgressMeter - Total runtime 34.75 secs, 0.58 min, 0.01 hours
[2016-04-15T01:02Z] INFO  18:02:55,567 MicroScheduler - 25818 reads were filtered out during the traversal out of approximately 201181 total reads (12.83%)
[2016-04-15T01:02Z] INFO  18:02:55,567 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:02Z] INFO  18:02:55,567 MicroScheduler -   -> 15445 reads (7.68% of total) failing DuplicateReadFilter
[2016-04-15T01:02Z] INFO  18:02:55,567 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:02Z] INFO  18:02:55,568 MicroScheduler -   -> 10373 reads (5.16% of total) failing HCMappingQualityFilter
[2016-04-15T01:02Z] INFO  18:02:55,568 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:02Z] INFO  18:02:55,568 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:02Z] INFO  18:02:55,568 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:02Z] INFO  18:02:55,569 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T01:02Z] INFO  18:02:56,321 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:02Z] GATK: HaplotypeCaller
[2016-04-15T01:02Z] INFO  18:02:56,902 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:02Z] GATK: HaplotypeCaller
[2016-04-15T01:02Z] INFO  18:02:59,629 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:02Z] INFO  18:02:59,632 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:02Z] INFO  18:02:59,633 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:02Z] INFO  18:02:59,634 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:02Z] INFO  18:02:59,638 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/13/R14-18105_kapa-NGv3-PE100-NGv3-sort-13_101890105_115169878-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/13/R14-18105_kapa-NGv3-PE100-NGv3-13_101890105_115169878-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/13/tx/tmplUpOE0/R14-18105_kapa-NGv3-PE100-NGv3-13_101890105_115169878.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:02Z] INFO  18:02:59,667 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:02Z] INFO  18:02:59,668 HelpFormatter - Date/Time: 2016/04/14 18:02:59
[2016-04-15T01:02Z] INFO  18:02:59,668 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:02Z] INFO  18:02:59,668 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:02Z] WARN  18:02:59,701 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T01:02Z] WARN  18:02:59,705 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/13/tx/tmplUpOE0/R14-18105_kapa-NGv3-PE100-NGv3-13_101890105_115169878.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T01:02Z] INFO  18:02:59,873 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:03Z] INFO  18:03:00,104 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T01:03Z] INFO  18:03:00,119 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:03Z] INFO  18:03:00,193 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-15T01:03Z] INFO  18:03:00,207 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T01:03Z] INFO  18:03:00,258 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:03Z] INFO  18:03:00,262 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:03Z] INFO  18:03:00,262 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:03Z] INFO  18:03:00,263 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:03Z] INFO  18:03:00,267 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/14/R14-18105_kapa-NGv3-PE100-NGv3-sort-14_0_19378574-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/14/R14-18105_kapa-NGv3-PE100-NGv3-14_0_19378574-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/14/tx/tmpKDz5Bl/R14-18105_kapa-NGv3-PE100-NGv3-14_0_19378574.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:03Z] INFO  18:03:00,283 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:03Z] INFO  18:03:00,284 HelpFormatter - Date/Time: 2016/04/14 18:03:00
[2016-04-15T01:03Z] INFO  18:03:00,284 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:03Z] INFO  18:03:00,285 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:03Z] WARN  18:03:00,332 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T01:03Z] WARN  18:03:00,335 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/14/tx/tmpKDz5Bl/R14-18105_kapa-NGv3-PE100-NGv3-14_0_19378574.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T01:03Z] INFO  18:03:00,522 IntervalUtils - Processing 144481 bp from intervals
[2016-04-15T01:03Z] WARN  18:03:00,528 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:03Z] INFO  18:03:00,604 ProgressMeter -     13:44462893      2.4574788E7    30.0 s            1.0 s       55.2%    54.0 s      24.0 s
[2016-04-15T01:03Z] INFO  18:03:00,646 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:03Z] INFO  18:03:00,647 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:03Z] INFO  18:03:00,756 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:03Z] INFO  18:03:00,757 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:03Z] INFO  18:03:00,758 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T01:03Z] INFO  18:03:00,759 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T01:03Z] INFO  18:03:00,773 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T01:03Z] INFO  18:03:00,774 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T01:03Z] INFO  18:03:00,811 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T01:03Z] INFO  18:03:00,821 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:03Z] INFO  18:03:00,894 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-15T01:03Z] INFO  18:03:00,915 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T01:03Z] INFO  18:03:00,989 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T01:03Z] INFO  18:03:01,180 IntervalUtils - Processing 981 bp from intervals
[2016-04-15T01:03Z] WARN  18:03:01,186 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:03Z] INFO  18:03:01,211 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.033006538
[2016-04-15T01:03Z] INFO  18:03:01,212 PairHMM - Total compute time in PairHMM computeLikelihoods() : 2.869968039
[2016-04-15T01:03Z] INFO  18:03:01,213 HaplotypeCaller - Ran local assembly on 2312 active regions
[2016-04-15T01:03Z] INFO  18:03:01,280 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:03Z] INFO  18:03:01,285 ProgressMeter -            done     2.23715124E8    85.0 s            0.0 s      100.0%    85.0 s       0.0 s
[2016-04-15T01:03Z] INFO  18:03:01,286 ProgressMeter - Total runtime 85.60 secs, 1.43 min, 0.02 hours
[2016-04-15T01:03Z] INFO  18:03:01,287 MicroScheduler - 43951 reads were filtered out during the traversal out of approximately 507867 total reads (8.65%)
[2016-04-15T01:03Z] INFO  18:03:01,287 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:03Z] INFO  18:03:01,288 MicroScheduler -   -> 40469 reads (7.97% of total) failing DuplicateReadFilter
[2016-04-15T01:03Z] INFO  18:03:01,288 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:03Z] INFO  18:03:01,289 MicroScheduler -   -> 3482 reads (0.69% of total) failing HCMappingQualityFilter
[2016-04-15T01:03Z] INFO  18:03:01,290 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:03Z] INFO  18:03:01,290 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:03Z] INFO  18:03:01,291 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:03Z] INFO  18:03:01,292 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T01:03Z] INFO  18:03:01,312 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:03Z] INFO  18:03:01,313 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:03Z] INFO  18:03:01,314 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T01:03Z] INFO  18:03:01,314 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T01:03Z] INFO  18:03:01,315 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T01:03Z] INFO  18:03:01,315 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T01:03Z] INFO  18:03:01,514 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T01:03Z] INFO  18:03:02,581 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:03Z] GATK: HaplotypeCaller
[2016-04-15T01:03Z] INFO  18:03:03,005 ProgressMeter -     11:71806265     2.86892797E8    90.0 s            0.0 s       72.0%     2.1 m      34.0 s
[2016-04-15T01:03Z] INFO  18:03:03,403 ProgressMeter -     12:40884404      1.2902841E7    60.0 s            4.0 s       57.4%   104.0 s      44.0 s
[2016-04-15T01:03Z] WARN  18:03:03,936 ExactAFCalculator - this tool is currently set to genotype at most 6 alternate alleles in a given context, but the context at 12:117646196 has 9 alternate alleles so only the top alleles will be used; see the --max_alternate_alleles argument
[2016-04-15T01:03Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T01:03Z] INFO  18:03:04,554 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T01:03Z] INFO  18:03:04,555 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T01:03Z] INFO  18:03:04,844 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.0036292110000000002
[2016-04-15T01:03Z] INFO  18:03:04,845 PairHMM - Total compute time in PairHMM computeLikelihoods() : 0.072001994
[2016-04-15T01:03Z] WARN  18:03:04,845 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T01:03Z] INFO  18:03:04,845 HaplotypeCaller - Ran local assembly on 383 active regions
[2016-04-15T01:03Z] WARN  18:03:04,846 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T01:03Z] INFO  18:03:04,897 ProgressMeter -            done        7043015.0    21.0 s            3.0 s      100.0%    21.0 s       0.0 s
[2016-04-15T01:03Z] INFO  18:03:04,898 ProgressMeter - Total runtime 21.58 secs, 0.36 min, 0.01 hours
[2016-04-15T01:03Z] INFO  18:03:04,899 MicroScheduler - 25038 reads were filtered out during the traversal out of approximately 95992 total reads (26.08%)
[2016-04-15T01:03Z] INFO  18:03:04,900 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:03Z] INFO  18:03:04,900 MicroScheduler -   -> 6118 reads (6.37% of total) failing DuplicateReadFilter
[2016-04-15T01:03Z] INFO  18:03:04,901 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:03Z] INFO  18:03:04,902 MicroScheduler -   -> 18920 reads (19.71% of total) failing HCMappingQualityFilter
[2016-04-15T01:03Z] INFO  18:03:04,902 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:03Z] INFO  18:03:04,903 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:03Z] INFO  18:03:04,904 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:03Z] INFO  18:03:04,904 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T01:03Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T01:03Z] INFO  18:03:05,318 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T01:03Z] INFO  18:03:05,319 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T01:03Z] WARN  18:03:05,544 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T01:03Z] WARN  18:03:05,545 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T01:03Z] INFO  18:03:05,713 ProgressMeter -     12:53039203     1.09407055E8    60.0 s            0.0 s       44.1%     2.3 m      75.0 s
[2016-04-15T01:03Z] INFO  18:03:06,063 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:03Z] INFO  18:03:06,066 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:03Z] INFO  18:03:06,067 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:03Z] INFO  18:03:06,067 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:03Z] INFO  18:03:06,072 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/14/R14-18105_kapa-NGv3-PE100-NGv3-sort-14_19553416_35066851-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/14/R14-18105_kapa-NGv3-PE100-NGv3-14_19553416_35066851-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/14/tx/tmpQq8nmv/R14-18105_kapa-NGv3-PE100-NGv3-14_19553416_35066851.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:03Z] INFO  18:03:06,102 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:03Z] INFO  18:03:06,112 HelpFormatter - Date/Time: 2016/04/14 18:03:06
[2016-04-15T01:03Z] INFO  18:03:06,113 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:03Z] INFO  18:03:06,118 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:03Z] WARN  18:03:06,165 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T01:03Z] WARN  18:03:06,168 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/14/tx/tmpQq8nmv/R14-18105_kapa-NGv3-PE100-NGv3-14_19553416_35066851.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T01:03Z] INFO  18:03:06,391 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:03Z] INFO  18:03:06,488 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:03Z] INFO  18:03:06,612 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T01:03Z] INFO  18:03:06,624 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:03Z] INFO  18:03:06,722 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.10
[2016-04-15T01:03Z] INFO  18:03:06,739 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T01:03Z] GATK: HaplotypeCaller
[2016-04-15T01:03Z] INFO  18:03:07,125 IntervalUtils - Processing 291951 bp from intervals
[2016-04-15T01:03Z] WARN  18:03:07,130 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:03Z] INFO  18:03:07,203 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:03Z] INFO  18:03:07,351 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:03Z] INFO  18:03:07,363 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:03Z] INFO  18:03:07,364 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T01:03Z] INFO  18:03:07,364 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T01:03Z] INFO  18:03:07,371 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T01:03Z] INFO  18:03:07,372 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T01:03Z] INFO  18:03:07,540 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T01:03Z] INFO  18:03:08,911 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.019160784
[2016-04-15T01:03Z] INFO  18:03:08,916 PairHMM - Total compute time in PairHMM computeLikelihoods() : 0.580226459
[2016-04-15T01:03Z] INFO  18:03:08,917 HaplotypeCaller - Ran local assembly on 1537 active regions
[2016-04-15T01:03Z] INFO  18:03:08,966 ProgressMeter -            done     1.17482682E8    50.0 s            0.0 s      100.0%    50.0 s       0.0 s
[2016-04-15T01:03Z] INFO  18:03:08,966 ProgressMeter - Total runtime 50.13 secs, 0.84 min, 0.01 hours
[2016-04-15T01:03Z] INFO  18:03:08,967 MicroScheduler - 21808 reads were filtered out during the traversal out of approximately 272865 total reads (7.99%)
[2016-04-15T01:03Z] INFO  18:03:08,967 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:03Z] INFO  18:03:08,967 MicroScheduler -   -> 21536 reads (7.89% of total) failing DuplicateReadFilter
[2016-04-15T01:03Z] INFO  18:03:08,968 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:03Z] INFO  18:03:08,968 MicroScheduler -   -> 272 reads (0.10% of total) failing HCMappingQualityFilter
[2016-04-15T01:03Z] INFO  18:03:08,968 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:03Z] INFO  18:03:08,968 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:03Z] INFO  18:03:08,969 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:03Z] INFO  18:03:08,969 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T01:03Z] INFO  18:03:09,317 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.004553229000000001
[2016-04-15T01:03Z] INFO  18:03:09,317 PairHMM - Total compute time in PairHMM computeLikelihoods() : 0.767692459
[2016-04-15T01:03Z] INFO  18:03:09,317 HaplotypeCaller - Ran local assembly on 9 active regions
[2016-04-15T01:03Z] INFO  18:03:09,387 ProgressMeter -            done            981.0     8.0 s            2.3 h       99.9%     8.0 s       0.0 s
[2016-04-15T01:03Z] INFO  18:03:09,388 ProgressMeter - Total runtime 8.08 secs, 0.13 min, 0.00 hours
[2016-04-15T01:03Z] INFO  18:03:09,388 MicroScheduler - 1704 reads were filtered out during the traversal out of approximately 3252 total reads (52.40%)
[2016-04-15T01:03Z] INFO  18:03:09,389 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:03Z] INFO  18:03:09,389 MicroScheduler -   -> 178 reads (5.47% of total) failing DuplicateReadFilter
[2016-04-15T01:03Z] INFO  18:03:09,389 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:03Z] INFO  18:03:09,389 MicroScheduler -   -> 1526 reads (46.92% of total) failing HCMappingQualityFilter
[2016-04-15T01:03Z] INFO  18:03:09,390 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:03Z] INFO  18:03:09,390 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:03Z] INFO  18:03:09,390 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:03Z] INFO  18:03:09,391 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T01:03Z] INFO  18:03:09,719 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:03Z] INFO  18:03:09,722 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:03Z] INFO  18:03:09,722 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:03Z] INFO  18:03:09,722 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:03Z] INFO  18:03:09,737 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/14/R14-18105_kapa-NGv3-PE100-NGv3-sort-14_35072553_50583270-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/14/R14-18105_kapa-NGv3-PE100-NGv3-14_35072553_50583270-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/14/tx/tmpRiczQm/R14-18105_kapa-NGv3-PE100-NGv3-14_35072553_50583270.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:03Z] INFO  18:03:09,757 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:03Z] INFO  18:03:09,758 HelpFormatter - Date/Time: 2016/04/14 18:03:09
[2016-04-15T01:03Z] INFO  18:03:09,758 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:03Z] INFO  18:03:09,758 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:03Z] WARN  18:03:09,814 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T01:03Z] WARN  18:03:09,817 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/14/tx/tmpRiczQm/R14-18105_kapa-NGv3-PE100-NGv3-14_35072553_50583270.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T01:03Z] INFO  18:03:10,056 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:03Z] INFO  18:03:10,151 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.003966622
[2016-04-15T01:03Z] INFO  18:03:10,152 PairHMM - Total compute time in PairHMM computeLikelihoods() : 0.10404883000000001
[2016-04-15T01:03Z] INFO  18:03:10,152 HaplotypeCaller - Ran local assembly on 469 active regions
[2016-04-15T01:03Z] INFO  18:03:10,227 ProgressMeter -            done      1.1587684E7    22.0 s            1.0 s      100.0%    22.0 s       0.0 s
[2016-04-15T01:03Z] INFO  18:03:10,227 ProgressMeter - Total runtime 22.53 secs, 0.38 min, 0.01 hours
[2016-04-15T01:03Z] INFO  18:03:10,228 MicroScheduler - 6921 reads were filtered out during the traversal out of approximately 84292 total reads (8.21%)
[2016-04-15T01:03Z] INFO  18:03:10,228 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:03Z] INFO  18:03:10,228 MicroScheduler -   -> 6866 reads (8.15% of total) failing DuplicateReadFilter
[2016-04-15T01:03Z] INFO  18:03:10,229 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:03Z] INFO  18:03:10,229 MicroScheduler -   -> 55 reads (0.07% of total) failing HCMappingQualityFilter
[2016-04-15T01:03Z] INFO  18:03:10,229 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:03Z] INFO  18:03:10,229 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:03Z] INFO  18:03:10,230 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:03Z] INFO  18:03:10,230 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T01:03Z] INFO  18:03:10,272 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T01:03Z] INFO  18:03:10,282 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:03Z] INFO  18:03:10,372 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:03Z] INFO  18:03:10,403 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.12
[2016-04-15T01:03Z] INFO  18:03:10,439 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T01:03Z] GATK: HaplotypeCaller
[2016-04-15T01:03Z] INFO  18:03:10,778 IntervalUtils - Processing 108903 bp from intervals
[2016-04-15T01:03Z] WARN  18:03:10,783 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:03Z] INFO  18:03:10,877 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:03Z] INFO  18:03:10,907 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:03Z] INFO  18:03:10,957 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:03Z] INFO  18:03:10,958 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:03Z] INFO  18:03:10,958 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T01:03Z] INFO  18:03:10,958 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T01:03Z] INFO  18:03:10,960 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T01:03Z] INFO  18:03:10,960 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T01:03Z] GATK: HaplotypeCaller
[2016-04-15T01:03Z] INFO  18:03:11,173 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T01:03Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T01:03Z] INFO  18:03:11,287 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T01:03Z] INFO  18:03:11,287 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T01:03Z] INFO  18:03:11,546 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:03Z] INFO  18:03:11,672 ProgressMeter -     11:62300251     1.53436111E8   100.0 s            0.0 s       86.9%   115.0 s      15.0 s
[2016-04-15T01:03Z] GATK: HaplotypeCaller
[2016-04-15T01:03Z] WARN  18:03:12,366 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T01:03Z] WARN  18:03:12,367 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T01:03Z] INFO  18:03:13,624 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:03Z] INFO  18:03:13,627 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:03Z] INFO  18:03:13,627 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:03Z] INFO  18:03:13,627 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:03Z] INFO  18:03:13,643 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/14/R14-18105_kapa-NGv3-PE100-NGv3-sort-14_50585061_66096324-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/14/R14-18105_kapa-NGv3-PE100-NGv3-14_50585061_66096324-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/14/tx/tmpSWOUje/R14-18105_kapa-NGv3-PE100-NGv3-14_50585061_66096324.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:03Z] INFO  18:03:13,664 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:03Z] INFO  18:03:13,664 HelpFormatter - Date/Time: 2016/04/14 18:03:13
[2016-04-15T01:03Z] INFO  18:03:13,664 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:03Z] INFO  18:03:13,665 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:03Z] WARN  18:03:13,705 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T01:03Z] WARN  18:03:13,717 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/14/tx/tmpSWOUje/R14-18105_kapa-NGv3-PE100-NGv3-14_50585061_66096324.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T01:03Z] INFO  18:03:13,939 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:03Z] INFO  18:03:14,037 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:03Z] INFO  18:03:14,040 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:03Z] INFO  18:03:14,041 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:03Z] INFO  18:03:14,041 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:03Z] INFO  18:03:14,046 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/14/R14-18105_kapa-NGv3-PE100-NGv3-sort-14_66135960_81646674-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/14/R14-18105_kapa-NGv3-PE100-NGv3-14_66135960_81646674-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/14/tx/tmpViV4rj/R14-18105_kapa-NGv3-PE100-NGv3-14_66135960_81646674.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:03Z] INFO  18:03:14,064 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:03Z] INFO  18:03:14,065 HelpFormatter - Date/Time: 2016/04/14 18:03:14
[2016-04-15T01:03Z] INFO  18:03:14,066 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:03Z] INFO  18:03:14,066 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:03Z] WARN  18:03:14,101 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T01:03Z] WARN  18:03:14,103 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/14/tx/tmpViV4rj/R14-18105_kapa-NGv3-PE100-NGv3-14_66135960_81646674.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T01:03Z] INFO  18:03:14,118 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T01:03Z] INFO  18:03:14,138 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:03Z] INFO  18:03:14,231 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.09
[2016-04-15T01:03Z] INFO  18:03:14,259 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T01:03Z] INFO  18:03:14,269 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:03Z] INFO  18:03:14,470 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T01:03Z] INFO  18:03:14,480 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:03Z] INFO  18:03:14,556 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-15T01:03Z] INFO  18:03:14,583 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T01:03Z] INFO  18:03:14,670 IntervalUtils - Processing 226771 bp from intervals
[2016-04-15T01:03Z] WARN  18:03:14,677 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:03Z] INFO  18:03:14,737 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:03Z] INFO  18:03:14,740 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:03Z] INFO  18:03:14,741 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:03Z] INFO  18:03:14,741 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:03Z] INFO  18:03:14,746 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/14/R14-18105_kapa-NGv3-PE100-NGv3-sort-14_81651874_97299968-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/14/R14-18105_kapa-NGv3-PE100-NGv3-14_81651874_97299968-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/14/tx/tmpq_bEqL/R14-18105_kapa-NGv3-PE100-NGv3-14_81651874_97299968.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:03Z] INFO  18:03:14,753 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:03Z] INFO  18:03:14,755 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:03Z] INFO  18:03:14,766 HelpFormatter - Date/Time: 2016/04/14 18:03:14
[2016-04-15T01:03Z] INFO  18:03:14,767 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:03Z] INFO  18:03:14,768 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:03Z] WARN  18:03:14,790 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T01:03Z] WARN  18:03:14,797 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/14/tx/tmpq_bEqL/R14-18105_kapa-NGv3-PE100-NGv3-14_81651874_97299968.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T01:03Z] INFO  18:03:14,859 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:03Z] INFO  18:03:14,860 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:03Z] INFO  18:03:14,861 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T01:03Z] INFO  18:03:14,862 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T01:03Z] INFO  18:03:14,862 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T01:03Z] INFO  18:03:14,863 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T01:03Z] INFO  18:03:14,950 IntervalUtils - Processing 245410 bp from intervals
[2016-04-15T01:03Z] WARN  18:03:14,956 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:03Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T01:03Z] INFO  18:03:14,972 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:03Z] INFO  18:03:14,974 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T01:03Z] INFO  18:03:14,975 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T01:03Z] INFO  18:03:15,074 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:03Z] INFO  18:03:15,101 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T01:03Z] INFO  18:03:15,187 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:03Z] INFO  18:03:15,188 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:03Z] INFO  18:03:15,188 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T01:03Z] INFO  18:03:15,204 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T01:03Z] INFO  18:03:15,210 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T01:03Z] INFO  18:03:15,216 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T01:03Z] INFO  18:03:15,217 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T01:03Z] INFO  18:03:15,219 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:03Z] WARN  18:03:15,244 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T01:03Z] WARN  18:03:15,245 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T01:03Z] INFO  18:03:15,281 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-15T01:03Z] INFO  18:03:15,300 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T01:03Z] INFO  18:03:15,425 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T01:03Z] INFO  18:03:15,683 IntervalUtils - Processing 176504 bp from intervals
[2016-04-15T01:03Z] WARN  18:03:15,688 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:03Z] INFO  18:03:15,784 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:03Z] INFO  18:03:15,953 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:03Z] INFO  18:03:15,954 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:03Z] INFO  18:03:15,955 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T01:03Z] INFO  18:03:15,955 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T01:03Z] INFO  18:03:15,956 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T01:03Z] INFO  18:03:15,956 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T01:03Z] INFO  18:03:16,094 ProgressMeter -      11:1093806      1.2877009E7   120.0 s            9.0 s       19.0%    10.5 m       8.5 m
[2016-04-15T01:03Z] INFO  18:03:16,179 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T01:03Z] INFO  18:03:17,028 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.009094852
[2016-04-15T01:03Z] INFO  18:03:17,029 PairHMM - Total compute time in PairHMM computeLikelihoods() : 0.710695779
[2016-04-15T01:03Z] INFO  18:03:17,029 HaplotypeCaller - Ran local assembly on 1288 active regions
[2016-04-15T01:03Z] INFO  18:03:17,072 ProgressMeter -            done      7.9081089E7    46.0 s            0.0 s      100.0%    46.0 s       0.0 s
[2016-04-15T01:03Z] INFO  18:03:17,073 ProgressMeter - Total runtime 46.51 secs, 0.78 min, 0.01 hours
[2016-04-15T01:03Z] INFO  18:03:17,073 MicroScheduler - 18293 reads were filtered out during the traversal out of approximately 222290 total reads (8.23%)
[2016-04-15T01:03Z] INFO  18:03:17,074 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:03Z] INFO  18:03:17,075 MicroScheduler -   -> 17445 reads (7.85% of total) failing DuplicateReadFilter
[2016-04-15T01:03Z] INFO  18:03:17,075 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:03Z] INFO  18:03:17,076 MicroScheduler -   -> 848 reads (0.38% of total) failing HCMappingQualityFilter
[2016-04-15T01:03Z] INFO  18:03:17,077 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:03Z] INFO  18:03:17,077 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:03Z] INFO  18:03:17,078 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:03Z] INFO  18:03:17,078 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T01:03Z] INFO  18:03:17,389 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.005479157
[2016-04-15T01:03Z] INFO  18:03:17,390 PairHMM - Total compute time in PairHMM computeLikelihoods() : 0.328856036
[2016-04-15T01:03Z] INFO  18:03:17,391 HaplotypeCaller - Ran local assembly on 582 active regions
[2016-04-15T01:03Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T01:03Z] INFO  18:03:17,434 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T01:03Z] INFO  18:03:17,434 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T01:03Z] INFO  18:03:17,437 ProgressMeter -            done      1.7240277E7    26.0 s            1.0 s      100.0%    26.0 s       0.0 s
[2016-04-15T01:03Z] INFO  18:03:17,438 ProgressMeter - Total runtime 26.01 secs, 0.43 min, 0.01 hours
[2016-04-15T01:03Z] INFO  18:03:17,439 MicroScheduler - 9310 reads were filtered out during the traversal out of approximately 112307 total reads (8.29%)
[2016-04-15T01:03Z] INFO  18:03:17,440 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:03Z] INFO  18:03:17,440 MicroScheduler -   -> 9165 reads (8.16% of total) failing DuplicateReadFilter
[2016-04-15T01:03Z] INFO  18:03:17,441 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:03Z] INFO  18:03:17,442 MicroScheduler -   -> 145 reads (0.13% of total) failing HCMappingQualityFilter
[2016-04-15T01:03Z] INFO  18:03:17,443 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:03Z] INFO  18:03:17,443 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:03Z] INFO  18:03:17,444 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:03Z] INFO  18:03:17,444 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T01:03Z] INFO  18:03:17,607 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.037064042000000005
[2016-04-15T01:03Z] INFO  18:03:17,608 PairHMM - Total compute time in PairHMM computeLikelihoods() : 17.177461189000002
[2016-04-15T01:03Z] INFO  18:03:17,609 HaplotypeCaller - Ran local assembly on 1048 active regions
[2016-04-15T01:03Z] INFO  18:03:17,642 ProgressMeter -            done        4.31997E7    74.0 s            1.0 s      100.0%    74.0 s       0.0 s
[2016-04-15T01:03Z] INFO  18:03:17,644 ProgressMeter - Total runtime 74.26 secs, 1.24 min, 0.02 hours
[2016-04-15T01:03Z] INFO  18:03:17,644 MicroScheduler - 18169 reads were filtered out during the traversal out of approximately 191773 total reads (9.47%)
[2016-04-15T01:03Z] INFO  18:03:17,645 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:03Z] INFO  18:03:17,646 MicroScheduler -   -> 14772 reads (7.70% of total) failing DuplicateReadFilter
[2016-04-15T01:03Z] INFO  18:03:17,646 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:03Z] INFO  18:03:17,647 MicroScheduler -   -> 3397 reads (1.77% of total) failing HCMappingQualityFilter
[2016-04-15T01:03Z] INFO  18:03:17,648 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:03Z] INFO  18:03:17,648 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:03Z] INFO  18:03:17,648 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:03Z] INFO  18:03:17,648 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T01:03Z] WARN  18:03:17,832 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T01:03Z] WARN  18:03:17,833 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T01:03Z] INFO  18:03:18,527 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:03Z] GATK: HaplotypeCaller
[2016-04-15T01:03Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T01:03Z] INFO  18:03:18,906 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:03Z] INFO  18:03:18,912 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T01:03Z] INFO  18:03:18,913 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T01:03Z] INFO  18:03:19,043 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:03Z] GATK: HaplotypeCaller
[2016-04-15T01:03Z] WARN  18:03:19,284 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T01:03Z] WARN  18:03:19,285 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T01:03Z] GATK: HaplotypeCaller
[2016-04-15T01:03Z] INFO  18:03:19,460 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.032715216000000005
[2016-04-15T01:03Z] INFO  18:03:19,461 PairHMM - Total compute time in PairHMM computeLikelihoods() : 11.847212941
[2016-04-15T01:03Z] INFO  18:03:19,461 HaplotypeCaller - Ran local assembly on 2366 active regions
[2016-04-15T01:03Z] INFO  18:03:19,508 ProgressMeter -            done     1.96753928E8   107.0 s            0.0 s      100.0%   107.0 s       0.0 s
[2016-04-15T01:03Z] INFO  18:03:19,508 ProgressMeter - Total runtime 107.87 secs, 1.80 min, 0.03 hours
[2016-04-15T01:03Z] INFO  18:03:19,508 MicroScheduler - 52539 reads were filtered out during the traversal out of approximately 530379 total reads (9.91%)
[2016-04-15T01:03Z] INFO  18:03:19,509 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:03Z] INFO  18:03:19,509 MicroScheduler -   -> 41676 reads (7.86% of total) failing DuplicateReadFilter
[2016-04-15T01:03Z] INFO  18:03:19,509 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:03Z] INFO  18:03:19,510 MicroScheduler -   -> 10863 reads (2.05% of total) failing HCMappingQualityFilter
[2016-04-15T01:03Z] INFO  18:03:19,510 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:03Z] INFO  18:03:19,510 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:03Z] INFO  18:03:19,510 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:03Z] INFO  18:03:19,511 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T01:03Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T01:03Z] INFO  18:03:19,753 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T01:03Z] INFO  18:03:19,753 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T01:03Z] WARN  18:03:20,047 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T01:03Z] WARN  18:03:20,048 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T01:03Z] INFO  18:03:20,282 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.011136348
[2016-04-15T01:03Z] INFO  18:03:20,283 PairHMM - Total compute time in PairHMM computeLikelihoods() : 5.093436517000001
[2016-04-15T01:03Z] INFO  18:03:20,283 HaplotypeCaller - Ran local assembly on 1414 active regions
[2016-04-15T01:03Z] INFO  18:03:20,315 ProgressMeter -     12:12976804     2.13724473E8    90.0 s            0.0 s       91.3%    98.0 s       8.0 s
[2016-04-15T01:03Z] INFO  18:03:20,358 ProgressMeter -            done      9.1028011E7    57.0 s            0.0 s      100.0%    57.0 s       0.0 s
[2016-04-15T01:03Z] INFO  18:03:20,358 ProgressMeter - Total runtime 57.71 secs, 0.96 min, 0.02 hours
[2016-04-15T01:03Z] INFO  18:03:20,359 MicroScheduler - 20613 reads were filtered out during the traversal out of approximately 246779 total reads (8.35%)
[2016-04-15T01:03Z] INFO  18:03:20,359 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:03Z] INFO  18:03:20,360 MicroScheduler -   -> 19086 reads (7.73% of total) failing DuplicateReadFilter
[2016-04-15T01:03Z] INFO  18:03:20,360 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:03Z] INFO  18:03:20,360 MicroScheduler -   -> 1527 reads (0.62% of total) failing HCMappingQualityFilter
[2016-04-15T01:03Z] INFO  18:03:20,360 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:03Z] INFO  18:03:20,361 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:03Z] INFO  18:03:20,361 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:03Z] INFO  18:03:20,361 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T01:03Z] INFO  18:03:20,763 ProgressMeter -    12:121593039     1.49156731E8    60.0 s            0.0 s       64.7%    92.0 s      32.0 s
[2016-04-15T01:03Z] INFO  18:03:20,985 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:03Z] GATK: HaplotypeCaller
[2016-04-15T01:03Z] INFO  18:03:21,852 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:03Z] GATK: HaplotypeCaller
[2016-04-15T01:03Z] INFO  18:03:22,368 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:03Z] INFO  18:03:22,372 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:03Z] INFO  18:03:22,372 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:03Z] INFO  18:03:22,373 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:03Z] INFO  18:03:22,377 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/14/R14-18105_kapa-NGv3-PE100-NGv3-sort-14_97304098_107349540-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/14/R14-18105_kapa-NGv3-PE100-NGv3-14_97304098_107349540-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/14/tx/tmp5T_GnN/R14-18105_kapa-NGv3-PE100-NGv3-14_97304098_107349540.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:03Z] INFO  18:03:22,398 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:03Z] INFO  18:03:22,399 HelpFormatter - Date/Time: 2016/04/14 18:03:22
[2016-04-15T01:03Z] INFO  18:03:22,399 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:03Z] INFO  18:03:22,400 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:03Z] WARN  18:03:22,422 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T01:03Z] WARN  18:03:22,430 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/14/tx/tmp5T_GnN/R14-18105_kapa-NGv3-PE100-NGv3-14_97304098_107349540.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T01:03Z] INFO  18:03:22,550 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:03Z] INFO  18:03:22,552 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:03Z] INFO  18:03:22,553 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:03Z] INFO  18:03:22,553 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:03Z] INFO  18:03:22,557 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/15/R14-18105_kapa-NGv3-PE100-NGv3-sort-15_0_20740485-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/15/R14-18105_kapa-NGv3-PE100-NGv3-15_0_20740485-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/15/tx/tmpxbC5Tc/R14-18105_kapa-NGv3-PE100-NGv3-15_0_20740485.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:03Z] INFO  18:03:22,574 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:03Z] INFO  18:03:22,575 HelpFormatter - Date/Time: 2016/04/14 18:03:22
[2016-04-15T01:03Z] INFO  18:03:22,575 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:03Z] INFO  18:03:22,576 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:03Z] WARN  18:03:22,655 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T01:03Z] WARN  18:03:22,665 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/15/tx/tmpxbC5Tc/R14-18105_kapa-NGv3-PE100-NGv3-15_0_20740485.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T01:03Z] INFO  18:03:22,743 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:03Z] INFO  18:03:22,750 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:03Z] INFO  18:03:22,754 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:03Z] INFO  18:03:22,754 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:03Z] INFO  18:03:22,755 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:03Z] INFO  18:03:22,759 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/15/R14-18105_kapa-NGv3-PE100-NGv3-sort-15_20741621_36872162-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/15/R14-18105_kapa-NGv3-PE100-NGv3-15_20741621_36872162-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/15/tx/tmpnNa_5m/R14-18105_kapa-NGv3-PE100-NGv3-15_20741621_36872162.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:03Z] INFO  18:03:22,798 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:03Z] INFO  18:03:22,799 HelpFormatter - Date/Time: 2016/04/14 18:03:22
[2016-04-15T01:03Z] INFO  18:03:22,800 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:03Z] INFO  18:03:22,800 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:03Z] WARN  18:03:22,844 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T01:03Z] WARN  18:03:22,855 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/15/tx/tmpnNa_5m/R14-18105_kapa-NGv3-PE100-NGv3-15_20741621_36872162.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T01:03Z] INFO  18:03:22,916 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:03Z] INFO  18:03:22,969 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T01:03Z] INFO  18:03:22,979 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:03Z] INFO  18:03:23,076 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-15T01:03Z] INFO  18:03:23,118 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T01:03Z] INFO  18:03:23,126 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:03Z] INFO  18:03:23,137 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T01:03Z] INFO  18:03:23,146 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:03Z] INFO  18:03:23,229 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-15T01:03Z] INFO  18:03:23,261 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T01:03Z] INFO  18:03:23,395 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T01:03Z] INFO  18:03:23,405 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:03Z] INFO  18:03:23,513 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.11
[2016-04-15T01:03Z] INFO  18:03:23,533 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T01:03Z] INFO  18:03:23,708 IntervalUtils - Processing 188545 bp from intervals
[2016-04-15T01:03Z] WARN  18:03:23,713 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:03Z] INFO  18:03:23,722 IntervalUtils - Processing 989 bp from intervals
[2016-04-15T01:03Z] WARN  18:03:23,727 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:03Z] INFO  18:03:23,835 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:03Z] INFO  18:03:23,864 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:03Z] INFO  18:03:23,901 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:03Z] INFO  18:03:23,902 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:03Z] INFO  18:03:23,903 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T01:03Z] INFO  18:03:23,904 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T01:03Z] INFO  18:03:23,904 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T01:03Z] INFO  18:03:23,905 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T01:03Z] INFO  18:03:23,947 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:03Z] INFO  18:03:23,949 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:03Z] INFO  18:03:23,950 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T01:03Z] INFO  18:03:23,950 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T01:03Z] INFO  18:03:23,957 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T01:03Z] INFO  18:03:23,958 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T01:03Z] INFO  18:03:24,048 IntervalUtils - Processing 177979 bp from intervals
[2016-04-15T01:03Z] WARN  18:03:24,053 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:03Z] INFO  18:03:24,138 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:03Z] INFO  18:03:24,142 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T01:03Z] INFO  18:03:24,235 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:03Z] INFO  18:03:24,237 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:03Z] INFO  18:03:24,237 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T01:03Z] INFO  18:03:24,238 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T01:03Z] INFO  18:03:24,239 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T01:03Z] INFO  18:03:24,239 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T01:03Z] INFO  18:03:24,239 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T01:03Z] INFO  18:03:24,343 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:03Z] INFO  18:03:24,346 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:03Z] INFO  18:03:24,347 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:03Z] INFO  18:03:24,348 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:03Z] INFO  18:03:24,352 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/15/R14-18105_kapa-NGv3-PE100-NGv3-sort-15_36887086_52402170-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/15/R14-18105_kapa-NGv3-PE100-NGv3-15_36887086_52402170-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/15/tx/tmpeusLR6/R14-18105_kapa-NGv3-PE100-NGv3-15_36887086_52402170.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:03Z] INFO  18:03:24,372 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:03Z] INFO  18:03:24,373 HelpFormatter - Date/Time: 2016/04/14 18:03:24
[2016-04-15T01:03Z] INFO  18:03:24,373 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:03Z] INFO  18:03:24,374 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:03Z] WARN  18:03:24,402 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T01:03Z] WARN  18:03:24,404 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/15/tx/tmpeusLR6/R14-18105_kapa-NGv3-PE100-NGv3-15_36887086_52402170.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T01:03Z] INFO  18:03:24,500 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T01:03Z] INFO  18:03:24,630 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:03Z] INFO  18:03:24,849 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T01:03Z] INFO  18:03:24,890 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:03Z] INFO  18:03:24,959 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-15T01:03Z] INFO  18:03:24,993 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T01:03Z] INFO  18:03:25,575 IntervalUtils - Processing 374190 bp from intervals
[2016-04-15T01:03Z] WARN  18:03:25,592 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:03Z] INFO  18:03:25,700 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:03Z] INFO  18:03:25,878 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:03Z] INFO  18:03:25,879 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:03Z] INFO  18:03:25,880 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T01:03Z] INFO  18:03:25,880 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T01:03Z] INFO  18:03:25,881 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T01:03Z] INFO  18:03:25,881 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T01:03Z] INFO  18:03:26,024 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:03Z] INFO  18:03:26,037 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:03Z] INFO  18:03:26,038 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:03Z] INFO  18:03:26,038 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:03Z] INFO  18:03:26,043 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/15/R14-18105_kapa-NGv3-PE100-NGv3-sort-15_52404364_67923265-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/15/R14-18105_kapa-NGv3-PE100-NGv3-15_52404364_67923265-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/15/tx/tmpMpqVYD/R14-18105_kapa-NGv3-PE100-NGv3-15_52404364_67923265.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:03Z] INFO  18:03:26,062 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:03Z] INFO  18:03:26,063 HelpFormatter - Date/Time: 2016/04/14 18:03:26
[2016-04-15T01:03Z] INFO  18:03:26,064 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:03Z] INFO  18:03:26,064 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:03Z] WARN  18:03:26,109 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T01:03Z] WARN  18:03:26,116 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/15/tx/tmpMpqVYD/R14-18105_kapa-NGv3-PE100-NGv3-15_52404364_67923265.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T01:03Z] INFO  18:03:26,136 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T01:03Z] INFO  18:03:26,397 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:03Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T01:03Z] INFO  18:03:26,545 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T01:03Z] INFO  18:03:26,546 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T01:03Z] INFO  18:03:26,717 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T01:03Z] INFO  18:03:26,735 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:03Z] WARN  18:03:26,770 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T01:03Z] WARN  18:03:26,771 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T01:03Z] INFO  18:03:26,812 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-15T01:03Z] INFO  18:03:26,834 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T01:03Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T01:03Z] INFO  18:03:27,064 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T01:03Z] INFO  18:03:27,065 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T01:03Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T01:03Z] INFO  18:03:27,296 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T01:03Z] INFO  18:03:27,297 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T01:03Z] WARN  18:03:27,313 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T01:03Z] WARN  18:03:27,314 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T01:03Z] INFO  18:03:27,386 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.050535971000000006
[2016-04-15T01:03Z] INFO  18:03:27,387 PairHMM - Total compute time in PairHMM computeLikelihoods() : 8.058539467000001
[2016-04-15T01:03Z] INFO  18:03:27,387 HaplotypeCaller - Ran local assembly on 2522 active regions
[2016-04-15T01:03Z] INFO  18:03:27,397 IntervalUtils - Processing 254619 bp from intervals
[2016-04-15T01:03Z] WARN  18:03:27,402 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:03Z] INFO  18:03:27,453 ProgressMeter -            done     2.60606733E8    97.0 s            0.0 s      100.0%    97.0 s       0.0 s
[2016-04-15T01:03Z] INFO  18:03:27,454 ProgressMeter - Total runtime 97.16 secs, 1.62 min, 0.03 hours
[2016-04-15T01:03Z] INFO  18:03:27,455 MicroScheduler - 51124 reads were filtered out during the traversal out of approximately 519228 total reads (9.85%)
[2016-04-15T01:03Z] INFO  18:03:27,455 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:03Z] INFO  18:03:27,456 MicroScheduler -   -> 40202 reads (7.74% of total) failing DuplicateReadFilter
[2016-04-15T01:03Z] INFO  18:03:27,456 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:03Z] INFO  18:03:27,456 MicroScheduler -   -> 10922 reads (2.10% of total) failing HCMappingQualityFilter
[2016-04-15T01:03Z] INFO  18:03:27,456 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:03Z] INFO  18:03:27,457 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:03Z] INFO  18:03:27,457 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:03Z] INFO  18:03:27,457 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T01:03Z] INFO  18:03:27,503 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:03Z] INFO  18:03:27,628 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:03Z] INFO  18:03:27,640 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:03Z] INFO  18:03:27,641 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T01:03Z] INFO  18:03:27,641 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T01:03Z] INFO  18:03:27,657 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T01:03Z] INFO  18:03:27,657 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T01:03Z] WARN  18:03:27,830 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T01:03Z] WARN  18:03:27,831 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T01:03Z] INFO  18:03:27,912 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T01:03Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T01:03Z] INFO  18:03:28,626 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T01:03Z] INFO  18:03:28,627 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T01:03Z] WARN  18:03:28,956 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T01:03Z] WARN  18:03:28,957 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T01:03Z] INFO  18:03:29,038 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:03Z] GATK: HaplotypeCaller
[2016-04-15T01:03Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T01:03Z] INFO  18:03:30,753 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T01:03Z] INFO  18:03:30,762 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T01:03Z] INFO  18:03:30,784 ProgressMeter -    13:113478739      1.9164163E7    30.0 s            1.0 s       63.8%    47.0 s      17.0 s
[2016-04-15T01:03Z] INFO  18:03:30,886 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.003390839
[2016-04-15T01:03Z] INFO  18:03:30,887 PairHMM - Total compute time in PairHMM computeLikelihoods() : 0.809993097
[2016-04-15T01:03Z] INFO  18:03:30,888 HaplotypeCaller - Ran local assembly on 14 active regions
[2016-04-15T01:03Z] INFO  18:03:30,922 ProgressMeter -            done            989.0     7.0 s          118.3 m       99.9%     7.0 s       0.0 s
[2016-04-15T01:03Z] INFO  18:03:30,923 ProgressMeter - Total runtime 7.02 secs, 0.12 min, 0.00 hours
[2016-04-15T01:03Z] INFO  18:03:30,924 MicroScheduler - 1355 reads were filtered out during the traversal out of approximately 2157 total reads (62.82%)
[2016-04-15T01:03Z] INFO  18:03:30,936 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:03Z] INFO  18:03:30,936 MicroScheduler -   -> 56 reads (2.60% of total) failing DuplicateReadFilter
[2016-04-15T01:03Z] INFO  18:03:30,937 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:03Z] INFO  18:03:30,938 MicroScheduler -   -> 1299 reads (60.22% of total) failing HCMappingQualityFilter
[2016-04-15T01:03Z] INFO  18:03:30,938 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:03Z] INFO  18:03:30,939 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:03Z] INFO  18:03:30,940 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:03Z] INFO  18:03:30,940 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T01:03Z] WARN  18:03:31,221 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T01:03Z] WARN  18:03:31,222 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T01:03Z] INFO  18:03:32,325 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:03Z] GATK: HaplotypeCaller
[2016-04-15T01:03Z] INFO  18:03:32,793 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:03Z] INFO  18:03:32,797 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:03Z] INFO  18:03:32,797 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:03Z] INFO  18:03:32,798 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:03Z] INFO  18:03:32,802 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/15/R14-18105_kapa-NGv3-PE100-NGv3-sort-15_67932890_83447639-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/15/R14-18105_kapa-NGv3-PE100-NGv3-15_67932890_83447639-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/15/tx/tmp1ICKqQ/R14-18105_kapa-NGv3-PE100-NGv3-15_67932890_83447639.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:03Z] INFO  18:03:32,820 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:03Z] INFO  18:03:32,821 HelpFormatter - Date/Time: 2016/04/14 18:03:32
[2016-04-15T01:03Z] INFO  18:03:32,822 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:03Z] INFO  18:03:32,822 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:03Z] WARN  18:03:32,862 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T01:03Z] WARN  18:03:32,865 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/15/tx/tmp1ICKqQ/R14-18105_kapa-NGv3-PE100-NGv3-15_67932890_83447639.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T01:03Z] INFO  18:03:33,007 ProgressMeter -     11:77907575     5.94389089E8   120.0 s            0.0 s       98.9%     2.0 m       1.0 s
[2016-04-15T01:03Z] INFO  18:03:33,108 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:03Z] INFO  18:03:33,418 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T01:03Z] INFO  18:03:33,439 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:03Z] INFO  18:03:33,543 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.10
[2016-04-15T01:03Z] INFO  18:03:33,571 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T01:03Z] WARN  18:03:33,706 ExactAFCalculator - this tool is currently set to genotype at most 6 alternate alleles in a given context, but the context at 12:56415078 has 8 alternate alleles so only the top alleles will be used; see the --max_alternate_alleles argument
[2016-04-15T01:03Z] INFO  18:03:34,044 IntervalUtils - Processing 293221 bp from intervals
[2016-04-15T01:03Z] WARN  18:03:34,050 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:03Z] INFO  18:03:34,139 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:03Z] INFO  18:03:34,283 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:03Z] INFO  18:03:34,284 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:03Z] INFO  18:03:34,286 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T01:03Z] INFO  18:03:34,287 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T01:03Z] INFO  18:03:34,296 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T01:03Z] INFO  18:03:34,296 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T01:03Z] INFO  18:03:34,563 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T01:03Z] INFO  18:03:34,682 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.064831838
[2016-04-15T01:03Z] INFO  18:03:34,683 PairHMM - Total compute time in PairHMM computeLikelihoods() : 3.301990709
[2016-04-15T01:03Z] INFO  18:03:34,694 HaplotypeCaller - Ran local assembly on 3822 active regions
[2016-04-15T01:03Z] INFO  18:03:34,727 ProgressMeter -            done     6.10283322E8     2.0 m            0.0 s      100.0%     2.0 m       0.0 s
[2016-04-15T01:03Z] INFO  18:03:34,727 ProgressMeter - Total runtime 121.75 secs, 2.03 min, 0.03 hours
[2016-04-15T01:03Z] INFO  18:03:34,728 MicroScheduler - 76221 reads were filtered out during the traversal out of approximately 903037 total reads (8.44%)
[2016-04-15T01:03Z] INFO  18:03:34,728 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:03Z] INFO  18:03:34,728 MicroScheduler -   -> 72496 reads (8.03% of total) failing DuplicateReadFilter
[2016-04-15T01:03Z] INFO  18:03:34,728 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:03Z] INFO  18:03:34,729 MicroScheduler -   -> 3725 reads (0.41% of total) failing HCMappingQualityFilter
[2016-04-15T01:03Z] INFO  18:03:34,729 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:03Z] INFO  18:03:34,729 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:03Z] INFO  18:03:34,729 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:03Z] INFO  18:03:34,730 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T01:03Z] INFO  18:03:35,714 ProgressMeter -     12:56524366     2.81878632E8    90.0 s            0.0 s       72.2%     2.1 m      34.0 s
[2016-04-15T01:03Z] INFO  18:03:35,886 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:03Z] INFO  18:03:35,902 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:03Z] INFO  18:03:35,903 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:03Z] INFO  18:03:35,903 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:03Z] INFO  18:03:35,908 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/15/R14-18105_kapa-NGv3-PE100-NGv3-sort-15_83448996_98982979-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/15/R14-18105_kapa-NGv3-PE100-NGv3-15_83448996_98982979-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/15/tx/tmp8Sx53J/R14-18105_kapa-NGv3-PE100-NGv3-15_83448996_98982979.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:03Z] INFO  18:03:35,937 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:03Z] INFO  18:03:35,938 HelpFormatter - Date/Time: 2016/04/14 18:03:35
[2016-04-15T01:03Z] INFO  18:03:35,938 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:03Z] INFO  18:03:35,939 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:03Z] WARN  18:03:35,995 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T01:03Z] WARN  18:03:35,998 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/15/tx/tmp8Sx53J/R14-18105_kapa-NGv3-PE100-NGv3-15_83448996_98982979.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T01:03Z] INFO  18:03:36,213 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:03Z] INFO  18:03:36,434 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T01:03Z] INFO  18:03:36,444 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:03Z] INFO  18:03:36,449 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:03Z] INFO  18:03:36,523 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-15T01:03Z] INFO  18:03:36,559 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T01:03Z] GATK: HaplotypeCaller
[2016-04-15T01:03Z] INFO  18:03:37,057 IntervalUtils - Processing 184993 bp from intervals
[2016-04-15T01:03Z] WARN  18:03:37,062 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:03Z] INFO  18:03:37,223 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:03Z] INFO  18:03:37,332 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:03Z] INFO  18:03:37,344 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:03Z] INFO  18:03:37,345 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T01:03Z] INFO  18:03:37,345 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T01:03Z] INFO  18:03:37,360 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T01:03Z] INFO  18:03:37,361 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T01:03Z] INFO  18:03:37,381 ProgressMeter -     14:21216169        2760984.0    30.0 s           10.0 s       14.7%     3.4 m       2.9 m
[2016-04-15T01:03Z] INFO  18:03:37,599 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T01:03Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T01:03Z] INFO  18:03:38,900 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T01:03Z] INFO  18:03:38,901 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T01:03Z] WARN  18:03:39,164 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T01:03Z] WARN  18:03:39,165 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T01:03Z] INFO  18:03:39,790 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:03Z] INFO  18:03:39,793 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:03Z] INFO  18:03:39,794 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:03Z] INFO  18:03:39,795 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:03Z] INFO  18:03:39,799 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/15/R14-18105_kapa-NGv3-PE100-NGv3-sort-15_98984299_102531392-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/15/R14-18105_kapa-NGv3-PE100-NGv3-15_98984299_102531392-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/15/tx/tmprsytDK/R14-18105_kapa-NGv3-PE100-NGv3-15_98984299_102531392.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:03Z] INFO  18:03:39,808 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:03Z] INFO  18:03:39,819 HelpFormatter - Date/Time: 2016/04/14 18:03:39
[2016-04-15T01:03Z] INFO  18:03:39,820 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:03Z] INFO  18:03:39,821 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:03Z] WARN  18:03:39,865 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T01:03Z] WARN  18:03:39,868 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/15/tx/tmprsytDK/R14-18105_kapa-NGv3-PE100-NGv3-15_98984299_102531392.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T01:03Z] INFO  18:03:40,135 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:03Z] INFO  18:03:40,359 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T01:03Z] INFO  18:03:40,369 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:03Z] INFO  18:03:40,454 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-15T01:03Z] INFO  18:03:40,494 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T01:03Z] INFO  18:03:40,832 IntervalUtils - Processing 49123 bp from intervals
[2016-04-15T01:03Z] WARN  18:03:40,837 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:03Z] INFO  18:03:40,938 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:03Z] INFO  18:03:40,973 ProgressMeter -     14:50088016      1.8017267E7    30.0 s            1.0 s       85.7%    35.0 s       5.0 s
[2016-04-15T01:03Z] INFO  18:03:41,008 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:03Z] INFO  18:03:41,009 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:03Z] INFO  18:03:41,009 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T01:03Z] INFO  18:03:41,010 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T01:03Z] INFO  18:03:41,011 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T01:03Z] INFO  18:03:41,011 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T01:03Z] INFO  18:03:41,248 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T01:03Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T01:03Z] INFO  18:03:41,707 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T01:03Z] INFO  18:03:41,708 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T01:03Z] WARN  18:03:41,997 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T01:03Z] WARN  18:03:41,999 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T01:03Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T01:03Z] INFO  18:03:43,663 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T01:03Z] INFO  18:03:43,663 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T01:03Z] INFO  18:03:43,975 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.0066342250000000005
[2016-04-15T01:03Z] INFO  18:03:43,977 PairHMM - Total compute time in PairHMM computeLikelihoods() : 0.34193641900000005
[2016-04-15T01:03Z] INFO  18:03:43,987 HaplotypeCaller - Ran local assembly on 779 active regions
[2016-04-15T01:03Z] INFO  18:03:44,032 ProgressMeter -            done      2.6446189E7    33.0 s            1.0 s      100.0%    33.0 s       0.0 s
[2016-04-15T01:03Z] INFO  18:03:44,033 ProgressMeter - Total runtime 33.08 secs, 0.55 min, 0.01 hours
[2016-04-15T01:03Z] WARN  18:03:44,031 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T01:03Z] INFO  18:03:44,033 MicroScheduler - 10211 reads were filtered out during the traversal out of approximately 118795 total reads (8.60%)
[2016-04-15T01:03Z] WARN  18:03:44,034 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T01:03Z] INFO  18:03:44,033 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:03Z] INFO  18:03:44,033 MicroScheduler -   -> 9143 reads (7.70% of total) failing DuplicateReadFilter
[2016-04-15T01:03Z] INFO  18:03:44,034 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:03Z] INFO  18:03:44,034 MicroScheduler -   -> 1068 reads (0.90% of total) failing HCMappingQualityFilter
[2016-04-15T01:03Z] INFO  18:03:44,034 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:03Z] INFO  18:03:44,035 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:03Z] INFO  18:03:44,035 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:03Z] INFO  18:03:44,035 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T01:03Z] INFO  18:03:44,872 ProgressMeter -     14:56083235      1.8638422E7    30.0 s            1.0 s       36.8%    81.0 s      51.0 s
[2016-04-15T01:03Z] INFO  18:03:45,001 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.025007086
[2016-04-15T01:03Z] INFO  18:03:45,012 PairHMM - Total compute time in PairHMM computeLikelihoods() : 0.763835738
[2016-04-15T01:03Z] INFO  18:03:45,013 HaplotypeCaller - Ran local assembly on 1045 active regions
[2016-04-15T01:03Z] INFO  18:03:45,054 ProgressMeter -            done      4.9965812E7    44.0 s            0.0 s      100.0%    44.0 s       0.0 s
[2016-04-15T01:03Z] INFO  18:03:45,054 ProgressMeter - Total runtime 44.30 secs, 0.74 min, 0.01 hours
[2016-04-15T01:03Z] INFO  18:03:45,054 MicroScheduler - 17264 reads were filtered out during the traversal out of approximately 210581 total reads (8.20%)
[2016-04-15T01:03Z] INFO  18:03:45,055 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:03Z] INFO  18:03:45,055 MicroScheduler -   -> 16627 reads (7.90% of total) failing DuplicateReadFilter
[2016-04-15T01:03Z] INFO  18:03:45,055 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:03Z] INFO  18:03:45,055 MicroScheduler -   -> 637 reads (0.30% of total) failing HCMappingQualityFilter
[2016-04-15T01:03Z] INFO  18:03:45,056 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:03Z] INFO  18:03:45,056 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:03Z] INFO  18:03:45,056 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:03Z] INFO  18:03:45,056 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T01:03Z] INFO  18:03:45,230 ProgressMeter -     14:72176339      1.4927867E7    30.0 s            2.0 s       34.8%    86.0 s      56.0 s
[2016-04-15T01:03Z] INFO  18:03:45,680 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:03Z] INFO  18:03:45,975 ProgressMeter -     14:93170608      2.4142446E7    30.0 s            1.0 s       54.1%    55.0 s      25.0 s
[2016-04-15T01:03Z] INFO  18:03:46,095 ProgressMeter -      11:1264994       1.733857E7     2.5 m            8.0 s       22.1%    11.3 m       8.8 m
[2016-04-15T01:03Z] GATK: HaplotypeCaller
[2016-04-15T01:03Z] INFO  18:03:46,603 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:03Z] GATK: HaplotypeCaller
[2016-04-15T01:03Z] INFO  18:03:49,631 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:03Z] INFO  18:03:49,644 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:03Z] INFO  18:03:49,644 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:03Z] INFO  18:03:49,645 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:03Z] INFO  18:03:49,649 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/16/R14-18105_kapa-NGv3-PE100-NGv3-sort-16_0_15528616-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/16/R14-18105_kapa-NGv3-PE100-NGv3-16_0_15528616-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/16/tx/tmpfmxOEx/R14-18105_kapa-NGv3-PE100-NGv3-16_0_15528616.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:03Z] INFO  18:03:49,666 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:03Z] INFO  18:03:49,666 HelpFormatter - Date/Time: 2016/04/14 18:03:49
[2016-04-15T01:03Z] INFO  18:03:49,667 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:03Z] INFO  18:03:49,667 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:03Z] WARN  18:03:49,712 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T01:03Z] WARN  18:03:49,714 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/16/tx/tmpfmxOEx/R14-18105_kapa-NGv3-PE100-NGv3-16_0_15528616.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T01:03Z] INFO  18:03:49,722 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:03Z] INFO  18:03:49,726 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:03Z] INFO  18:03:49,726 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:03Z] INFO  18:03:49,727 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:03Z] INFO  18:03:49,731 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/16/R14-18105_kapa-NGv3-PE100-NGv3-sort-16_15596122_31106473-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/16/R14-18105_kapa-NGv3-PE100-NGv3-16_15596122_31106473-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/16/tx/tmpaig0sX/R14-18105_kapa-NGv3-PE100-NGv3-16_15596122_31106473.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:03Z] INFO  18:03:49,740 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:03Z] INFO  18:03:49,751 HelpFormatter - Date/Time: 2016/04/14 18:03:49
[2016-04-15T01:03Z] INFO  18:03:49,752 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:03Z] INFO  18:03:49,753 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:03Z] WARN  18:03:49,786 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T01:03Z] WARN  18:03:49,800 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/16/tx/tmpaig0sX/R14-18105_kapa-NGv3-PE100-NGv3-16_15596122_31106473.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T01:03Z] INFO  18:03:49,987 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:03Z] INFO  18:03:50,080 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:03Z] INFO  18:03:50,178 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.018164901
[2016-04-15T01:03Z] INFO  18:03:50,190 PairHMM - Total compute time in PairHMM computeLikelihoods() : 3.0480668730000002
[2016-04-15T01:03Z] INFO  18:03:50,191 HaplotypeCaller - Ran local assembly on 2734 active regions
[2016-04-15T01:03Z] INFO  18:03:50,213 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T01:03Z] INFO  18:03:50,232 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:03Z] INFO  18:03:50,247 ProgressMeter -            done     3.54367305E8    89.0 s            0.0 s      100.0%    89.0 s       0.0 s
[2016-04-15T01:03Z] INFO  18:03:50,248 ProgressMeter - Total runtime 89.52 secs, 1.49 min, 0.02 hours
[2016-04-15T01:03Z] INFO  18:03:50,248 MicroScheduler - 48892 reads were filtered out during the traversal out of approximately 601018 total reads (8.13%)
[2016-04-15T01:03Z] INFO  18:03:50,248 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:03Z] INFO  18:03:50,249 MicroScheduler -   -> 47322 reads (7.87% of total) failing DuplicateReadFilter
[2016-04-15T01:03Z] INFO  18:03:50,249 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:03Z] INFO  18:03:50,249 MicroScheduler -   -> 1570 reads (0.26% of total) failing HCMappingQualityFilter
[2016-04-15T01:03Z] INFO  18:03:50,249 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:03Z] INFO  18:03:50,250 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:03Z] INFO  18:03:50,250 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:03Z] INFO  18:03:50,250 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T01:03Z] INFO  18:03:50,320 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.09
[2016-04-15T01:03Z] INFO  18:03:50,339 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T01:03Z] INFO  18:03:50,351 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T01:03Z] INFO  18:03:50,359 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:03Z] INFO  18:03:50,456 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.10
[2016-04-15T01:03Z] INFO  18:03:50,472 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T01:03Z] INFO  18:03:50,893 IntervalUtils - Processing 436708 bp from intervals
[2016-04-15T01:03Z] WARN  18:03:50,898 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:03Z] INFO  18:03:50,974 IntervalUtils - Processing 400248 bp from intervals
[2016-04-15T01:03Z] WARN  18:03:50,979 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:03Z] INFO  18:03:50,987 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:03Z] INFO  18:03:51,084 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:03Z] INFO  18:03:51,115 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:03Z] INFO  18:03:51,116 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:03Z] INFO  18:03:51,116 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T01:03Z] INFO  18:03:51,117 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T01:03Z] INFO  18:03:51,118 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T01:03Z] INFO  18:03:51,118 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T01:03Z] INFO  18:03:51,206 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:03Z] INFO  18:03:51,207 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:03Z] INFO  18:03:51,208 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T01:03Z] INFO  18:03:51,209 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T01:03Z] INFO  18:03:51,226 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T01:03Z] INFO  18:03:51,226 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T01:03Z] INFO  18:03:51,308 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T01:03Z] INFO  18:03:51,407 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T01:03Z] INFO  18:03:51,860 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:03Z] GATK: HaplotypeCaller
[2016-04-15T01:03Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T01:03Z] INFO  18:03:53,276 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T01:03Z] INFO  18:03:53,277 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T01:03Z] WARN  18:03:53,501 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T01:03Z] WARN  18:03:53,502 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T01:03Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T01:03Z] INFO  18:03:53,657 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T01:03Z] INFO  18:03:53,657 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T01:03Z] WARN  18:03:53,887 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T01:03Z] WARN  18:03:53,888 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T01:03Z] INFO  18:03:53,982 ProgressMeter -    14:103442021      1.3331423E7    30.0 s            2.0 s       44.4%    67.0 s      37.0 s
[2016-04-15T01:03Z] INFO  18:03:54,257 ProgressMeter -     15:30033535      1.3510288E7    30.0 s            2.0 s       43.3%    69.0 s      39.0 s
[2016-04-15T01:03Z] INFO  18:03:55,194 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:03Z] INFO  18:03:55,197 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:03Z] INFO  18:03:55,198 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:03Z] INFO  18:03:55,198 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:03Z] INFO  18:03:55,203 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/16/R14-18105_kapa-NGv3-PE100-NGv3-sort-16_31120544_46629582-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/16/R14-18105_kapa-NGv3-PE100-NGv3-16_31120544_46629582-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/16/tx/tmpslmgJA/R14-18105_kapa-NGv3-PE100-NGv3-16_31120544_46629582.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:03Z] INFO  18:03:55,213 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:03Z] INFO  18:03:55,224 HelpFormatter - Date/Time: 2016/04/14 18:03:55
[2016-04-15T01:03Z] INFO  18:03:55,225 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:03Z] INFO  18:03:55,225 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:03Z] WARN  18:03:55,248 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T01:03Z] WARN  18:03:55,251 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/16/tx/tmpslmgJA/R14-18105_kapa-NGv3-PE100-NGv3-16_31120544_46629582.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T01:03Z] INFO  18:03:55,476 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:03Z] INFO  18:03:55,682 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T01:03Z] INFO  18:03:55,705 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:03Z] INFO  18:03:55,767 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-15T01:03Z] INFO  18:03:55,802 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T01:03Z] INFO  18:03:55,901 ProgressMeter -     15:41624472      1.6253058E7    30.0 s            1.0 s       22.5%     2.2 m     103.0 s
[2016-04-15T01:03Z] INFO  18:03:56,274 IntervalUtils - Processing 40143 bp from intervals
[2016-04-15T01:03Z] WARN  18:03:56,291 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:03Z] INFO  18:03:56,414 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:03Z] INFO  18:03:56,480 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:03Z] INFO  18:03:56,481 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:03Z] INFO  18:03:56,482 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T01:03Z] INFO  18:03:56,483 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T01:03Z] INFO  18:03:56,492 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T01:03Z] INFO  18:03:56,493 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T01:03Z] INFO  18:03:56,715 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T01:03Z] INFO  18:03:57,661 ProgressMeter -     15:59102587      1.6388743E7    30.0 s            1.0 s       32.9%    91.0 s      61.0 s
[2016-04-15T01:03Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T01:03Z] INFO  18:03:59,472 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T01:03Z] INFO  18:03:59,474 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T01:03Z] WARN  18:03:59,765 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T01:03Z] WARN  18:03:59,766 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T01:04Z] INFO  18:04:02,002 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.026738581
[2016-04-15T01:04Z] INFO  18:04:02,003 PairHMM - Total compute time in PairHMM computeLikelihoods() : 2.87747336
[2016-04-15T01:04Z] INFO  18:04:02,004 HaplotypeCaller - Ran local assembly on 3754 active regions
[2016-04-15T01:04Z] INFO  18:04:02,053 ProgressMeter -            done     5.48735474E8   116.0 s            0.0 s      100.0%   116.0 s       0.0 s
[2016-04-15T01:04Z] INFO  18:04:02,053 ProgressMeter - Total runtime 116.38 secs, 1.94 min, 0.03 hours
[2016-04-15T01:04Z] INFO  18:04:02,053 MicroScheduler - 79446 reads were filtered out during the traversal out of approximately 870489 total reads (9.13%)
[2016-04-15T01:04Z] INFO  18:04:02,054 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:04Z] INFO  18:04:02,054 MicroScheduler -   -> 68423 reads (7.86% of total) failing DuplicateReadFilter
[2016-04-15T01:04Z] INFO  18:04:02,054 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:04Z] INFO  18:04:02,054 MicroScheduler -   -> 11023 reads (1.27% of total) failing HCMappingQualityFilter
[2016-04-15T01:04Z] INFO  18:04:02,055 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:04Z] INFO  18:04:02,056 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:04Z] INFO  18:04:02,056 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:04Z] INFO  18:04:02,057 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T01:04Z] INFO  18:04:03,190 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.017008781
[2016-04-15T01:04Z] INFO  18:04:03,191 PairHMM - Total compute time in PairHMM computeLikelihoods() : 0.43424990900000005
[2016-04-15T01:04Z] INFO  18:04:03,191 HaplotypeCaller - Ran local assembly on 358 active regions
[2016-04-15T01:04Z] INFO  18:04:03,243 ProgressMeter -            done        5654523.0    22.0 s            3.0 s      100.0%    22.0 s       0.0 s
[2016-04-15T01:04Z] INFO  18:04:03,244 ProgressMeter - Total runtime 22.24 secs, 0.37 min, 0.01 hours
[2016-04-15T01:04Z] INFO  18:04:03,245 MicroScheduler - 9912 reads were filtered out during the traversal out of approximately 78877 total reads (12.57%)
[2016-04-15T01:04Z] INFO  18:04:03,246 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:04Z] INFO  18:04:03,246 MicroScheduler -   -> 6210 reads (7.87% of total) failing DuplicateReadFilter
[2016-04-15T01:04Z] INFO  18:04:03,247 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:04Z] INFO  18:04:03,248 MicroScheduler -   -> 3702 reads (4.69% of total) failing HCMappingQualityFilter
[2016-04-15T01:04Z] INFO  18:04:03,248 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:04Z] INFO  18:04:03,249 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:04Z] INFO  18:04:03,250 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:04Z] INFO  18:04:03,250 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T01:04Z] INFO  18:04:03,468 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:04Z] INFO  18:04:03,560 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.01070012
[2016-04-15T01:04Z] INFO  18:04:03,561 PairHMM - Total compute time in PairHMM computeLikelihoods() : 0.768328562
[2016-04-15T01:04Z] INFO  18:04:03,562 HaplotypeCaller - Ran local assembly on 1256 active regions
[2016-04-15T01:04Z] INFO  18:04:03,601 ProgressMeter -            done      7.6164079E7    47.0 s            0.0 s      100.0%    47.0 s       0.0 s
[2016-04-15T01:04Z] INFO  18:04:03,602 ProgressMeter - Total runtime 47.65 secs, 0.79 min, 0.01 hours
[2016-04-15T01:04Z] INFO  18:04:03,603 MicroScheduler - 19762 reads were filtered out during the traversal out of approximately 244722 total reads (8.08%)
[2016-04-15T01:04Z] INFO  18:04:03,603 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:04Z] INFO  18:04:03,604 MicroScheduler -   -> 19391 reads (7.92% of total) failing DuplicateReadFilter
[2016-04-15T01:04Z] INFO  18:04:03,604 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:04Z] INFO  18:04:03,605 MicroScheduler -   -> 371 reads (0.15% of total) failing HCMappingQualityFilter
[2016-04-15T01:04Z] INFO  18:04:03,606 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:04Z] INFO  18:04:03,606 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:04Z] INFO  18:04:03,607 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:04Z] INFO  18:04:03,607 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T01:04Z] GATK: HaplotypeCaller
[2016-04-15T01:04Z] INFO  18:04:04,321 ProgressMeter -     15:74363720      2.3439241E7    30.0 s            1.0 s       33.6%    89.0 s      59.0 s
[2016-04-15T01:04Z] INFO  18:04:04,632 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:04Z] GATK: HaplotypeCaller
[2016-04-15T01:04Z] INFO  18:04:05,061 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:04Z] GATK: HaplotypeCaller
[2016-04-15T01:04Z] INFO  18:04:06,769 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:04Z] INFO  18:04:06,772 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:04Z] INFO  18:04:06,773 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:04Z] INFO  18:04:06,774 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:04Z] INFO  18:04:06,778 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/16/R14-18105_kapa-NGv3-PE100-NGv3-sort-16_46633742_64982002-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/16/R14-18105_kapa-NGv3-PE100-NGv3-16_46633742_64982002-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/16/tx/tmpLX8iTo/R14-18105_kapa-NGv3-PE100-NGv3-16_46633742_64982002.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:04Z] INFO  18:04:06,799 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:04Z] INFO  18:04:06,800 HelpFormatter - Date/Time: 2016/04/14 18:04:06
[2016-04-15T01:04Z] INFO  18:04:06,800 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:04Z] INFO  18:04:06,801 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:04Z] WARN  18:04:06,851 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T01:04Z] WARN  18:04:06,853 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/16/tx/tmpLX8iTo/R14-18105_kapa-NGv3-PE100-NGv3-16_46633742_64982002.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T01:04Z] INFO  18:04:07,014 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:04Z] INFO  18:04:07,197 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T01:04Z] INFO  18:04:07,207 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:04Z] INFO  18:04:07,266 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-15T01:04Z] INFO  18:04:07,302 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T01:04Z] INFO  18:04:07,363 ProgressMeter -     15:89865246      1.7670652E7    30.0 s            1.0 s       48.7%    61.0 s      31.0 s
[2016-04-15T01:04Z] INFO  18:04:07,382 ProgressMeter -     14:24003194      4.3657966E7    60.0 s            1.0 s       54.3%   110.0 s      50.0 s
[2016-04-15T01:04Z] INFO  18:04:07,749 IntervalUtils - Processing 224129 bp from intervals
[2016-04-15T01:04Z] WARN  18:04:07,763 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:04Z] INFO  18:04:07,838 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:04Z] INFO  18:04:07,847 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:04Z] INFO  18:04:07,850 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:04Z] INFO  18:04:07,851 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:04Z] INFO  18:04:07,851 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:04Z] INFO  18:04:07,856 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/16/R14-18105_kapa-NGv3-PE100-NGv3-sort-16_64982511_80574976-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/16/R14-18105_kapa-NGv3-PE100-NGv3-16_64982511_80574976-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/16/tx/tmpwxpLSy/R14-18105_kapa-NGv3-PE100-NGv3-16_64982511_80574976.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:04Z] INFO  18:04:07,864 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:04Z] INFO  18:04:07,876 HelpFormatter - Date/Time: 2016/04/14 18:04:07
[2016-04-15T01:04Z] INFO  18:04:07,877 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:04Z] INFO  18:04:07,878 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:04Z] WARN  18:04:07,912 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T01:04Z] WARN  18:04:07,915 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/16/tx/tmpwxpLSy/R14-18105_kapa-NGv3-PE100-NGv3-16_64982511_80574976.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T01:04Z] INFO  18:04:07,954 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:04Z] INFO  18:04:07,954 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:04Z] INFO  18:04:07,956 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T01:04Z] INFO  18:04:07,957 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T01:04Z] INFO  18:04:07,957 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T01:04Z] INFO  18:04:07,957 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T01:04Z] INFO  18:04:08,108 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:04Z] INFO  18:04:08,144 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T01:04Z] INFO  18:04:08,272 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:04Z] INFO  18:04:08,275 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:04Z] INFO  18:04:08,276 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:04Z] INFO  18:04:08,282 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:04Z] INFO  18:04:08,287 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/16/R14-18105_kapa-NGv3-PE100-NGv3-sort-16_80575258_90354753-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/16/R14-18105_kapa-NGv3-PE100-NGv3-16_80575258_90354753-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/16/tx/tmpAs9rwF/R14-18105_kapa-NGv3-PE100-NGv3-16_80575258_90354753.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:04Z] INFO  18:04:08,306 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:04Z] INFO  18:04:08,307 HelpFormatter - Date/Time: 2016/04/14 18:04:08
[2016-04-15T01:04Z] INFO  18:04:08,307 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:04Z] INFO  18:04:08,308 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:04Z] WARN  18:04:08,345 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T01:04Z] INFO  18:04:08,352 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T01:04Z] WARN  18:04:08,358 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/16/tx/tmpAs9rwF/R14-18105_kapa-NGv3-PE100-NGv3-16_80575258_90354753.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T01:04Z] INFO  18:04:08,380 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:04Z] INFO  18:04:08,450 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-15T01:04Z] INFO  18:04:08,490 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T01:04Z] INFO  18:04:08,619 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:04Z] INFO  18:04:08,832 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T01:04Z] INFO  18:04:08,861 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:04Z] INFO  18:04:08,943 IntervalUtils - Processing 344918 bp from intervals
[2016-04-15T01:04Z] WARN  18:04:08,949 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:04Z] INFO  18:04:08,963 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.10
[2016-04-15T01:04Z] INFO  18:04:08,993 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T01:04Z] INFO  18:04:09,031 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:04Z] INFO  18:04:09,175 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:04Z] INFO  18:04:09,176 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:04Z] INFO  18:04:09,177 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T01:04Z] INFO  18:04:09,178 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T01:04Z] INFO  18:04:09,178 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T01:04Z] INFO  18:04:09,179 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T01:04Z] INFO  18:04:09,384 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T01:04Z] INFO  18:04:09,506 IntervalUtils - Processing 203451 bp from intervals
[2016-04-15T01:04Z] WARN  18:04:09,519 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:04Z] INFO  18:04:09,615 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:04Z] INFO  18:04:09,718 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:04Z] INFO  18:04:09,719 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:04Z] INFO  18:04:09,720 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T01:04Z] INFO  18:04:09,721 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T01:04Z] INFO  18:04:09,738 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T01:04Z] INFO  18:04:09,739 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T01:04Z] INFO  18:04:09,993 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T01:04Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T01:04Z] INFO  18:04:11,702 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T01:04Z] INFO  18:04:11,703 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T01:04Z] WARN  18:04:12,051 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T01:04Z] WARN  18:04:12,053 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T01:04Z] INFO  18:04:12,828 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.003606742
[2016-04-15T01:04Z] INFO  18:04:12,829 PairHMM - Total compute time in PairHMM computeLikelihoods() : 0.065974904
[2016-04-15T01:04Z] INFO  18:04:12,830 HaplotypeCaller - Ran local assembly on 299 active regions
[2016-04-15T01:04Z] INFO  18:04:12,888 ProgressMeter -            done        2938200.0    16.0 s            5.0 s      100.0%    16.0 s       0.0 s
[2016-04-15T01:04Z] INFO  18:04:12,889 ProgressMeter - Total runtime 16.41 secs, 0.27 min, 0.00 hours
[2016-04-15T01:04Z] INFO  18:04:12,889 MicroScheduler - 17869 reads were filtered out during the traversal out of approximately 77911 total reads (22.94%)
[2016-04-15T01:04Z] INFO  18:04:12,889 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:04Z] INFO  18:04:12,890 MicroScheduler -   -> 5165 reads (6.63% of total) failing DuplicateReadFilter
[2016-04-15T01:04Z] INFO  18:04:12,900 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:04Z] INFO  18:04:12,900 MicroScheduler -   -> 12704 reads (16.31% of total) failing HCMappingQualityFilter
[2016-04-15T01:04Z] INFO  18:04:12,900 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:04Z] INFO  18:04:12,901 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:04Z] INFO  18:04:12,901 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:04Z] INFO  18:04:12,901 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T01:04Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T01:04Z] INFO  18:04:12,979 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T01:04Z] INFO  18:04:12,980 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T01:04Z] WARN  18:04:13,263 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T01:04Z] WARN  18:04:13,264 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T01:04Z] INFO  18:04:13,902 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.013106242
[2016-04-15T01:04Z] INFO  18:04:13,903 PairHMM - Total compute time in PairHMM computeLikelihoods() : 0.897064772
[2016-04-15T01:04Z] INFO  18:04:13,904 HaplotypeCaller - Ran local assembly on 1307 active regions
[2016-04-15T01:04Z] INFO  18:04:13,953 ProgressMeter -            done      7.2457776E7    49.0 s            0.0 s      100.0%    49.0 s       0.0 s
[2016-04-15T01:04Z] INFO  18:04:13,954 ProgressMeter - Total runtime 49.72 secs, 0.83 min, 0.01 hours
[2016-04-15T01:04Z] INFO  18:04:13,954 MicroScheduler - 97847 reads were filtered out during the traversal out of approximately 314099 total reads (31.15%)
[2016-04-15T01:04Z] INFO  18:04:13,954 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:04Z] INFO  18:04:13,955 MicroScheduler -   -> 18782 reads (5.98% of total) failing DuplicateReadFilter
[2016-04-15T01:04Z] INFO  18:04:13,955 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:04Z] INFO  18:04:13,955 MicroScheduler -   -> 79065 reads (25.17% of total) failing HCMappingQualityFilter
[2016-04-15T01:04Z] INFO  18:04:13,955 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:04Z] INFO  18:04:13,956 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:04Z] INFO  18:04:13,956 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:04Z] INFO  18:04:13,956 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T01:04Z] INFO  18:04:14,333 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:04Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T01:04Z] INFO  18:04:14,577 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T01:04Z] INFO  18:04:14,578 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T01:04Z] INFO  18:04:14,631 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.021889322000000003
[2016-04-15T01:04Z] INFO  18:04:14,642 PairHMM - Total compute time in PairHMM computeLikelihoods() : 1.3980385000000002
[2016-04-15T01:04Z] INFO  18:04:14,643 HaplotypeCaller - Ran local assembly on 1664 active regions
[2016-04-15T01:04Z] GATK: HaplotypeCaller
[2016-04-15T01:04Z] INFO  18:04:14,689 ProgressMeter -            done     1.18736277E8    59.0 s            0.0 s      100.0%    59.0 s       0.0 s
[2016-04-15T01:04Z] INFO  18:04:14,689 ProgressMeter - Total runtime 59.83 secs, 1.00 min, 0.02 hours
[2016-04-15T01:04Z] INFO  18:04:14,690 MicroScheduler - 23385 reads were filtered out during the traversal out of approximately 290795 total reads (8.04%)
[2016-04-15T01:04Z] INFO  18:04:14,690 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:04Z] INFO  18:04:14,690 MicroScheduler -   -> 23079 reads (7.94% of total) failing DuplicateReadFilter
[2016-04-15T01:04Z] INFO  18:04:14,691 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:04Z] INFO  18:04:14,691 MicroScheduler -   -> 306 reads (0.11% of total) failing HCMappingQualityFilter
[2016-04-15T01:04Z] INFO  18:04:14,691 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:04Z] INFO  18:04:14,691 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:04Z] INFO  18:04:14,692 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:04Z] INFO  18:04:14,692 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T01:04Z] WARN  18:04:14,955 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T01:04Z] WARN  18:04:14,958 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T01:04Z] INFO  18:04:15,231 ProgressMeter -     14:77808330     1.12474214E8    60.0 s            0.0 s       86.9%    69.0 s       9.0 s
[2016-04-15T01:04Z] INFO  18:04:15,472 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:04Z] GATK: HaplotypeCaller
[2016-04-15T01:04Z] INFO  18:04:16,242 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:04Z] GATK: HaplotypeCaller
[2016-04-15T01:04Z] INFO  18:04:18,029 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:04Z] INFO  18:04:18,032 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:04Z] INFO  18:04:18,033 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:04Z] INFO  18:04:18,033 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:04Z] INFO  18:04:18,038 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/17/R14-18105_kapa-NGv3-PE100-NGv3-sort-17_0_15511002-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/17/R14-18105_kapa-NGv3-PE100-NGv3-17_0_15511002-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/17/tx/tmp7_kmmv/R14-18105_kapa-NGv3-PE100-NGv3-17_0_15511002.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:04Z] INFO  18:04:18,047 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:04Z] INFO  18:04:18,048 HelpFormatter - Date/Time: 2016/04/14 18:04:18
[2016-04-15T01:04Z] INFO  18:04:18,048 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:04Z] INFO  18:04:18,049 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:04Z] WARN  18:04:18,083 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T01:04Z] WARN  18:04:18,086 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/17/tx/tmp7_kmmv/R14-18105_kapa-NGv3-PE100-NGv3-17_0_15511002.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T01:04Z] INFO  18:04:18,264 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:04Z] INFO  18:04:18,383 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T01:04Z] INFO  18:04:18,394 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:04Z] INFO  18:04:18,470 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-15T01:04Z] INFO  18:04:18,489 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T01:04Z] INFO  18:04:18,829 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:04Z] INFO  18:04:18,833 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:04Z] INFO  18:04:18,833 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:04Z] INFO  18:04:18,834 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:04Z] INFO  18:04:18,838 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/17/R14-18105_kapa-NGv3-PE100-NGv3-sort-17_15515955_31039213-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/17/R14-18105_kapa-NGv3-PE100-NGv3-17_15515955_31039213-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/17/tx/tmpqbv198/R14-18105_kapa-NGv3-PE100-NGv3-17_15515955_31039213.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:04Z] INFO  18:04:18,871 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:04Z] INFO  18:04:18,876 HelpFormatter - Date/Time: 2016/04/14 18:04:18
[2016-04-15T01:04Z] INFO  18:04:18,877 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:04Z] INFO  18:04:18,877 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:04Z] WARN  18:04:18,913 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T01:04Z] WARN  18:04:18,916 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/17/tx/tmpqbv198/R14-18105_kapa-NGv3-PE100-NGv3-17_15515955_31039213.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T01:04Z] INFO  18:04:19,042 IntervalUtils - Processing 497719 bp from intervals
[2016-04-15T01:04Z] WARN  18:04:19,048 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:04Z] INFO  18:04:19,051 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:04Z] INFO  18:04:19,129 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:04Z] INFO  18:04:19,237 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T01:04Z] INFO  18:04:19,247 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:04Z] INFO  18:04:19,317 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-15T01:04Z] INFO  18:04:19,323 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:04Z] INFO  18:04:19,323 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:04Z] INFO  18:04:19,323 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T01:04Z] INFO  18:04:19,335 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T01:04Z] INFO  18:04:19,345 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T01:04Z] INFO  18:04:19,346 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T01:04Z] INFO  18:04:19,366 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T01:04Z] INFO  18:04:19,647 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T01:04Z] INFO  18:04:19,754 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:04Z] INFO  18:04:19,757 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:04Z] INFO  18:04:19,758 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:04Z] INFO  18:04:19,758 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:04Z] INFO  18:04:19,763 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/17/R14-18105_kapa-NGv3-PE100-NGv3-sort-17_31048040_46607237-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/17/R14-18105_kapa-NGv3-PE100-NGv3-17_31048040_46607237-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/17/tx/tmphKu5Pb/R14-18105_kapa-NGv3-PE100-NGv3-17_31048040_46607237.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:04Z] INFO  18:04:19,773 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:04Z] INFO  18:04:19,782 HelpFormatter - Date/Time: 2016/04/14 18:04:19
[2016-04-15T01:04Z] INFO  18:04:19,783 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:04Z] INFO  18:04:19,783 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:04Z] WARN  18:04:19,829 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T01:04Z] WARN  18:04:19,832 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/17/tx/tmphKu5Pb/R14-18105_kapa-NGv3-PE100-NGv3-17_31048040_46607237.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T01:04Z] INFO  18:04:19,971 IntervalUtils - Processing 320055 bp from intervals
[2016-04-15T01:04Z] WARN  18:04:19,988 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:04Z] INFO  18:04:20,105 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:04Z] INFO  18:04:20,153 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:04Z] INFO  18:04:20,284 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:04Z] INFO  18:04:20,296 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:04Z] INFO  18:04:20,297 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T01:04Z] INFO  18:04:20,297 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T01:04Z] INFO  18:04:20,305 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T01:04Z] INFO  18:04:20,303 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T01:04Z] INFO  18:04:20,304 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T01:04Z] INFO  18:04:20,315 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:04Z] INFO  18:04:20,387 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-15T01:04Z] INFO  18:04:20,403 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T01:04Z] INFO  18:04:20,531 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T01:04Z] INFO  18:04:20,793 IntervalUtils - Processing 543518 bp from intervals
[2016-04-15T01:04Z] WARN  18:04:20,799 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:04Z] INFO  18:04:20,885 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:04Z] INFO  18:04:21,103 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:04Z] INFO  18:04:21,105 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:04Z] INFO  18:04:21,106 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T01:04Z] INFO  18:04:21,106 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T01:04Z] INFO  18:04:21,107 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T01:04Z] INFO  18:04:21,107 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T01:04Z] INFO  18:04:21,146 ProgressMeter -      16:1306798      1.2264522E7    30.0 s            2.0 s       21.2%     2.4 m     111.0 s
[2016-04-15T01:04Z] INFO  18:04:21,231 ProgressMeter -     16:20818276      2.4626672E7    30.0 s            1.0 s       24.6%     2.0 m      92.0 s
[2016-04-15T01:04Z] INFO  18:04:21,305 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T01:04Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T01:04Z] INFO  18:04:22,035 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T01:04Z] INFO  18:04:22,035 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T01:04Z] INFO  18:04:22,160 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.014816810000000001
[2016-04-15T01:04Z] INFO  18:04:22,161 PairHMM - Total compute time in PairHMM computeLikelihoods() : 1.9037359850000002
[2016-04-15T01:04Z] INFO  18:04:22,161 HaplotypeCaller - Ran local assembly on 1784 active regions
[2016-04-15T01:04Z] INFO  18:04:22,207 ProgressMeter -            done     1.48859234E8    67.0 s            0.0 s      100.0%    67.0 s       0.0 s
[2016-04-15T01:04Z] INFO  18:04:22,208 ProgressMeter - Total runtime 67.02 secs, 1.12 min, 0.02 hours
[2016-04-15T01:04Z] INFO  18:04:22,209 MicroScheduler - 32533 reads were filtered out during the traversal out of approximately 378137 total reads (8.60%)
[2016-04-15T01:04Z] INFO  18:04:22,209 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:04Z] INFO  18:04:22,210 MicroScheduler -   -> 30402 reads (8.04% of total) failing DuplicateReadFilter
[2016-04-15T01:04Z] INFO  18:04:22,211 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:04Z] INFO  18:04:22,211 MicroScheduler -   -> 2131 reads (0.56% of total) failing HCMappingQualityFilter
[2016-04-15T01:04Z] INFO  18:04:22,212 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:04Z] INFO  18:04:22,212 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:04Z] INFO  18:04:22,213 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:04Z] INFO  18:04:22,214 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T01:04Z] WARN  18:04:22,528 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T01:04Z] WARN  18:04:22,529 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T01:04Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T01:04Z] INFO  18:04:22,552 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T01:04Z] INFO  18:04:22,552 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T01:04Z] WARN  18:04:22,815 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T01:04Z] WARN  18:04:22,816 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T01:04Z] INFO  18:04:23,512 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:04Z] GATK: HaplotypeCaller
[2016-04-15T01:04Z] INFO  18:04:23,991 ProgressMeter -    14:105939838      6.0590975E7    60.0 s            0.0 s       97.3%    61.0 s       1.0 s
[2016-04-15T01:04Z] INFO  18:04:25,559 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.021318718
[2016-04-15T01:04Z] INFO  18:04:25,560 PairHMM - Total compute time in PairHMM computeLikelihoods() : 3.6459146710000003
[2016-04-15T01:04Z] INFO  18:04:25,561 HaplotypeCaller - Ran local assembly on 1354 active regions
[2016-04-15T01:04Z] INFO  18:04:25,601 ProgressMeter -            done      6.4310135E7    61.0 s            0.0 s      100.0%    61.0 s       0.0 s
[2016-04-15T01:04Z] INFO  18:04:25,602 ProgressMeter - Total runtime 61.65 secs, 1.03 min, 0.02 hours
[2016-04-15T01:04Z] INFO  18:04:25,602 MicroScheduler - 27787 reads were filtered out during the traversal out of approximately 329664 total reads (8.43%)
[2016-04-15T01:04Z] INFO  18:04:25,603 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:04Z] INFO  18:04:25,603 MicroScheduler -   -> 26894 reads (8.16% of total) failing DuplicateReadFilter
[2016-04-15T01:04Z] INFO  18:04:25,603 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:04Z] INFO  18:04:25,603 MicroScheduler -   -> 893 reads (0.27% of total) failing HCMappingQualityFilter
[2016-04-15T01:04Z] INFO  18:04:25,604 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:04Z] INFO  18:04:25,604 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:04Z] INFO  18:04:25,604 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:04Z] INFO  18:04:25,604 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T01:04Z] INFO  18:04:25,902 ProgressMeter -     15:44067920     1.28124139E8    60.0 s            0.0 s       63.9%    93.0 s      33.0 s
[2016-04-15T01:04Z] INFO  18:04:26,096 ProgressMeter -      11:5345129      7.7734422E7     3.2 m            2.0 s       47.1%     6.7 m       3.6 m
[2016-04-15T01:04Z] INFO  18:04:26,569 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:04Z] INFO  18:04:26,573 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:04Z] INFO  18:04:26,573 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:04Z] INFO  18:04:26,574 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:04Z] INFO  18:04:26,586 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/17/R14-18105_kapa-NGv3-PE100-NGv3-sort-17_46607689_62121560-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/17/R14-18105_kapa-NGv3-PE100-NGv3-17_46607689_62121560-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/17/tx/tmpcqOG91/R14-18105_kapa-NGv3-PE100-NGv3-17_46607689_62121560.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:04Z] INFO  18:04:26,604 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:04Z] INFO  18:04:26,605 HelpFormatter - Date/Time: 2016/04/14 18:04:26
[2016-04-15T01:04Z] INFO  18:04:26,606 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:04Z] INFO  18:04:26,606 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:04Z] WARN  18:04:26,646 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T01:04Z] WARN  18:04:26,661 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/17/tx/tmpcqOG91/R14-18105_kapa-NGv3-PE100-NGv3-17_46607689_62121560.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T01:04Z] INFO  18:04:26,933 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:04Z] INFO  18:04:27,022 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:04Z] INFO  18:04:27,148 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T01:04Z] INFO  18:04:27,169 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:04Z] INFO  18:04:27,285 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.12
[2016-04-15T01:04Z] INFO  18:04:27,321 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T01:04Z] GATK: HaplotypeCaller
[2016-04-15T01:04Z] INFO  18:04:27,662 ProgressMeter -     15:66624213      1.3825981E8    60.0 s            0.0 s       92.8%    64.0 s       4.0 s
[2016-04-15T01:04Z] INFO  18:04:27,833 IntervalUtils - Processing 295968 bp from intervals
[2016-04-15T01:04Z] WARN  18:04:27,852 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:04Z] INFO  18:04:27,962 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:04Z] INFO  18:04:28,119 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:04Z] INFO  18:04:28,119 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:04Z] INFO  18:04:28,131 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T01:04Z] INFO  18:04:28,131 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T01:04Z] INFO  18:04:28,132 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T01:04Z] INFO  18:04:28,132 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T01:04Z] INFO  18:04:28,407 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T01:04Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T01:04Z] INFO  18:04:28,825 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T01:04Z] INFO  18:04:28,826 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T01:04Z] WARN  18:04:29,090 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T01:04Z] WARN  18:04:29,091 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T01:04Z] INFO  18:04:30,055 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:04Z] INFO  18:04:30,059 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:04Z] INFO  18:04:30,059 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:04Z] INFO  18:04:30,060 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:04Z] INFO  18:04:30,065 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/17/R14-18105_kapa-NGv3-PE100-NGv3-sort-17_62122219_77705154-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/17/R14-18105_kapa-NGv3-PE100-NGv3-17_62122219_77705154-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/17/tx/tmpvXPCyQ/R14-18105_kapa-NGv3-PE100-NGv3-17_62122219_77705154.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:04Z] INFO  18:04:30,106 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:04Z] INFO  18:04:30,113 HelpFormatter - Date/Time: 2016/04/14 18:04:30
[2016-04-15T01:04Z] INFO  18:04:30,114 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:04Z] INFO  18:04:30,115 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:04Z] WARN  18:04:30,143 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T01:04Z] WARN  18:04:30,146 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/17/tx/tmpvXPCyQ/R14-18105_kapa-NGv3-PE100-NGv3-17_62122219_77705154.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T01:04Z] INFO  18:04:30,183 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.016200501000000003
[2016-04-15T01:04Z] INFO  18:04:30,184 PairHMM - Total compute time in PairHMM computeLikelihoods() : 1.4876200910000001
[2016-04-15T01:04Z] INFO  18:04:30,185 HaplotypeCaller - Ran local assembly on 1382 active regions
[2016-04-15T01:04Z] INFO  18:04:30,226 ProgressMeter -            done      8.0187592E7    52.0 s            0.0 s      100.0%    52.0 s       0.0 s
[2016-04-15T01:04Z] INFO  18:04:30,227 ProgressMeter - Total runtime 52.88 secs, 0.88 min, 0.01 hours
[2016-04-15T01:04Z] INFO  18:04:30,231 MicroScheduler - 42067 reads were filtered out during the traversal out of approximately 310894 total reads (13.53%)
[2016-04-15T01:04Z] INFO  18:04:30,231 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:04Z] INFO  18:04:30,232 MicroScheduler -   -> 23180 reads (7.46% of total) failing DuplicateReadFilter
[2016-04-15T01:04Z] INFO  18:04:30,232 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:04Z] INFO  18:04:30,232 MicroScheduler -   -> 18887 reads (6.08% of total) failing HCMappingQualityFilter
[2016-04-15T01:04Z] INFO  18:04:30,233 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:04Z] INFO  18:04:30,233 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:04Z] INFO  18:04:30,233 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:04Z] INFO  18:04:30,233 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T01:04Z] INFO  18:04:30,384 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:04Z] INFO  18:04:30,614 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T01:04Z] INFO  18:04:30,623 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:04Z] INFO  18:04:30,746 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.12
[2016-04-15T01:04Z] INFO  18:04:30,770 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T01:04Z] INFO  18:04:31,367 IntervalUtils - Processing 345298 bp from intervals
[2016-04-15T01:04Z] WARN  18:04:31,387 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:04Z] INFO  18:04:31,478 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:04Z] INFO  18:04:31,551 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.012099994000000001
[2016-04-15T01:04Z] INFO  18:04:31,552 PairHMM - Total compute time in PairHMM computeLikelihoods() : 0.8796920720000001
[2016-04-15T01:04Z] INFO  18:04:31,552 HaplotypeCaller - Ran local assembly on 1856 active regions
[2016-04-15T01:04Z] INFO  18:04:31,608 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:04Z] INFO  18:04:31,613 ProgressMeter -            done     1.70188052E8    63.0 s            0.0 s      100.0%    63.0 s       0.0 s
[2016-04-15T01:04Z] INFO  18:04:31,613 ProgressMeter - Total runtime 63.97 secs, 1.07 min, 0.02 hours
[2016-04-15T01:04Z] INFO  18:04:31,613 MicroScheduler - 28062 reads were filtered out during the traversal out of approximately 353171 total reads (7.95%)
[2016-04-15T01:04Z] INFO  18:04:31,614 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:04Z] INFO  18:04:31,614 MicroScheduler -   -> 27543 reads (7.80% of total) failing DuplicateReadFilter
[2016-04-15T01:04Z] INFO  18:04:31,614 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:04Z] INFO  18:04:31,614 MicroScheduler -   -> 519 reads (0.15% of total) failing HCMappingQualityFilter
[2016-04-15T01:04Z] INFO  18:04:31,615 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:04Z] INFO  18:04:31,615 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:04Z] INFO  18:04:31,615 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:04Z] INFO  18:04:31,615 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T01:04Z] INFO  18:04:31,634 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:04Z] INFO  18:04:31,634 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:04Z] INFO  18:04:31,635 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T01:04Z] INFO  18:04:31,635 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T01:04Z] INFO  18:04:31,649 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T01:04Z] INFO  18:04:31,649 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T01:04Z] INFO  18:04:31,927 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T01:04Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T01:04Z] INFO  18:04:31,943 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T01:04Z] INFO  18:04:31,944 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T01:04Z] GATK: HaplotypeCaller
[2016-04-15T01:04Z] WARN  18:04:32,366 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T01:04Z] WARN  18:04:32,367 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T01:04Z] INFO  18:04:33,089 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:04Z] GATK: HaplotypeCaller
[2016-04-15T01:04Z] INFO  18:04:34,330 ProgressMeter -     15:79586027     1.36983547E8    60.0 s            0.0 s       84.2%    71.0 s      11.0 s
[2016-04-15T01:04Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T01:04Z] INFO  18:04:34,576 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T01:04Z] INFO  18:04:34,576 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T01:04Z] WARN  18:04:34,835 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T01:04Z] WARN  18:04:34,836 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T01:04Z] INFO  18:04:34,982 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:04Z] INFO  18:04:34,996 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:04Z] INFO  18:04:34,996 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:04Z] INFO  18:04:34,997 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:04Z] INFO  18:04:35,001 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/17/R14-18105_kapa-NGv3-PE100-NGv3-sort-17_77707305_81195210-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/17/R14-18105_kapa-NGv3-PE100-NGv3-17_77707305_81195210-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/17/tx/tmpdh_lGZ/R14-18105_kapa-NGv3-PE100-NGv3-17_77707305_81195210.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:04Z] INFO  18:04:35,018 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:04Z] INFO  18:04:35,019 HelpFormatter - Date/Time: 2016/04/14 18:04:34
[2016-04-15T01:04Z] INFO  18:04:35,020 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:04Z] INFO  18:04:35,020 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:04Z] WARN  18:04:35,058 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T01:04Z] WARN  18:04:35,067 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/17/tx/tmpdh_lGZ/R14-18105_kapa-NGv3-PE100-NGv3-17_77707305_81195210.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T01:04Z] INFO  18:04:35,285 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:04Z] INFO  18:04:35,481 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T01:04Z] INFO  18:04:35,499 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:04Z] INFO  18:04:35,630 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.13
[2016-04-15T01:04Z] INFO  18:04:35,653 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T01:04Z] INFO  18:04:36,111 IntervalUtils - Processing 160149 bp from intervals
[2016-04-15T01:04Z] WARN  18:04:36,122 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:04Z] INFO  18:04:36,233 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:04Z] INFO  18:04:36,307 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:04Z] INFO  18:04:36,308 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:04Z] INFO  18:04:36,309 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T01:04Z] INFO  18:04:36,309 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T01:04Z] INFO  18:04:36,310 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T01:04Z] INFO  18:04:36,310 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T01:04Z] INFO  18:04:36,355 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:04Z] INFO  18:04:36,370 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:04Z] INFO  18:04:36,371 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:04Z] INFO  18:04:36,371 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:04Z] INFO  18:04:36,376 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/18/R14-18105_kapa-NGv3-PE100-NGv3-sort-18_0_18531348-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/18/R14-18105_kapa-NGv3-PE100-NGv3-18_0_18531348-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/18/tx/tmps3jdLm/R14-18105_kapa-NGv3-PE100-NGv3-18_0_18531348.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:04Z] INFO  18:04:36,414 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:04Z] INFO  18:04:36,415 HelpFormatter - Date/Time: 2016/04/14 18:04:36
[2016-04-15T01:04Z] INFO  18:04:36,415 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:04Z] INFO  18:04:36,415 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:04Z] WARN  18:04:36,461 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T01:04Z] WARN  18:04:36,464 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/18/tx/tmps3jdLm/R14-18105_kapa-NGv3-PE100-NGv3-18_0_18531348.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T01:04Z] INFO  18:04:36,569 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T01:04Z] INFO  18:04:36,666 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:04Z] INFO  18:04:36,872 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T01:04Z] INFO  18:04:36,881 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:04Z] INFO  18:04:36,948 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-15T01:04Z] INFO  18:04:36,962 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T01:04Z] INFO  18:04:37,383 ProgressMeter -     14:34029416     1.52882643E8    90.0 s            0.0 s       98.4%    91.0 s       1.0 s
[2016-04-15T01:04Z] INFO  18:04:37,422 IntervalUtils - Processing 162632 bp from intervals
[2016-04-15T01:04Z] WARN  18:04:37,441 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:04Z] INFO  18:04:37,526 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:04Z] INFO  18:04:37,620 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:04Z] INFO  18:04:37,621 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:04Z] INFO  18:04:37,622 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T01:04Z] INFO  18:04:37,623 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T01:04Z] INFO  18:04:37,624 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T01:04Z] INFO  18:04:37,624 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T01:04Z] INFO  18:04:37,835 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T01:04Z] INFO  18:04:37,964 ProgressMeter -     16:55737017      2.5357145E7    30.0 s            1.0 s       47.3%    63.0 s      33.0 s
[2016-04-15T01:04Z] INFO  18:04:38,716 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.05839464900000001
[2016-04-15T01:04Z] INFO  18:04:38,739 PairHMM - Total compute time in PairHMM computeLikelihoods() : 5.090171307
[2016-04-15T01:04Z] INFO  18:04:38,740 HaplotypeCaller - Ran local assembly on 2094 active regions
[2016-04-15T01:04Z] INFO  18:04:38,779 ProgressMeter -            done     1.61002552E8    91.0 s            0.0 s      100.0%    91.0 s       0.0 s
[2016-04-15T01:04Z] INFO  18:04:38,780 ProgressMeter - Total runtime 91.42 secs, 1.52 min, 0.03 hours
[2016-04-15T01:04Z] INFO  18:04:38,780 MicroScheduler - 59070 reads were filtered out during the traversal out of approximately 498107 total reads (11.86%)
[2016-04-15T01:04Z] INFO  18:04:38,781 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:04Z] INFO  18:04:38,781 MicroScheduler -   -> 38579 reads (7.75% of total) failing DuplicateReadFilter
[2016-04-15T01:04Z] INFO  18:04:38,793 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:04Z] INFO  18:04:38,794 MicroScheduler -   -> 20491 reads (4.11% of total) failing HCMappingQualityFilter
[2016-04-15T01:04Z] INFO  18:04:38,795 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:04Z] INFO  18:04:38,795 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:04Z] INFO  18:04:38,796 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:04Z] INFO  18:04:38,797 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T01:04Z] INFO  18:04:39,187 ProgressMeter -     16:68027811      2.2121346E7    30.0 s            1.0 s       34.2%    87.0 s      57.0 s
[2016-04-15T01:04Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T01:04Z] INFO  18:04:39,698 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T01:04Z] INFO  18:04:39,710 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T01:04Z] INFO  18:04:39,741 ProgressMeter -     16:85205413       1.375854E7    30.0 s            2.0 s       35.9%    83.0 s      53.0 s
[2016-04-15T01:04Z] WARN  18:04:40,021 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T01:04Z] WARN  18:04:40,029 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T01:04Z] INFO  18:04:40,293 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:04Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T01:04Z] INFO  18:04:40,439 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T01:04Z] INFO  18:04:40,440 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T01:04Z] GATK: HaplotypeCaller
[2016-04-15T01:04Z] WARN  18:04:40,766 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T01:04Z] WARN  18:04:40,767 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T01:04Z] INFO  18:04:43,776 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:04Z] INFO  18:04:43,779 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:04Z] INFO  18:04:43,779 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:04Z] INFO  18:04:43,779 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:04Z] INFO  18:04:43,794 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/18/R14-18105_kapa-NGv3-PE100-NGv3-sort-18_18533538_34081962-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/18/R14-18105_kapa-NGv3-PE100-NGv3-18_18533538_34081962-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/18/tx/tmpF3WTxp/R14-18105_kapa-NGv3-PE100-NGv3-18_18533538_34081962.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:04Z] INFO  18:04:43,803 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:04Z] INFO  18:04:43,814 HelpFormatter - Date/Time: 2016/04/14 18:04:43
[2016-04-15T01:04Z] INFO  18:04:43,815 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:04Z] INFO  18:04:43,816 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:04Z] WARN  18:04:43,862 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T01:04Z] WARN  18:04:43,865 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/18/tx/tmpF3WTxp/R14-18105_kapa-NGv3-PE100-NGv3-18_18533538_34081962.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T01:04Z] INFO  18:04:44,185 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:04Z] INFO  18:04:44,455 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T01:04Z] INFO  18:04:44,475 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:04Z] INFO  18:04:44,565 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.09
[2016-04-15T01:04Z] INFO  18:04:44,593 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T01:04Z] INFO  18:04:44,656 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.01695414
[2016-04-15T01:04Z] INFO  18:04:44,657 PairHMM - Total compute time in PairHMM computeLikelihoods() : 1.069189368
[2016-04-15T01:04Z] INFO  18:04:44,658 HaplotypeCaller - Ran local assembly on 2145 active regions
[2016-04-15T01:04Z] INFO  18:04:44,716 ProgressMeter -            done     2.01008217E8    70.0 s            0.0 s      100.0%    70.0 s       0.0 s
[2016-04-15T01:04Z] INFO  18:04:44,716 ProgressMeter - Total runtime 70.43 secs, 1.17 min, 0.02 hours
[2016-04-15T01:04Z] INFO  18:04:44,717 MicroScheduler - 82189 reads were filtered out during the traversal out of approximately 490774 total reads (16.75%)
[2016-04-15T01:04Z] INFO  18:04:44,717 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:04Z] INFO  18:04:44,717 MicroScheduler -   -> 35281 reads (7.19% of total) failing DuplicateReadFilter
[2016-04-15T01:04Z] INFO  18:04:44,717 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:04Z] INFO  18:04:44,718 MicroScheduler -   -> 46908 reads (9.56% of total) failing HCMappingQualityFilter
[2016-04-15T01:04Z] INFO  18:04:44,718 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:04Z] INFO  18:04:44,718 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:04Z] INFO  18:04:44,718 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:04Z] INFO  18:04:44,719 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T01:04Z] INFO  18:04:45,195 IntervalUtils - Processing 148606 bp from intervals
[2016-04-15T01:04Z] WARN  18:04:45,216 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:04Z] INFO  18:04:45,360 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:04Z] INFO  18:04:45,484 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:04Z] INFO  18:04:45,485 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:04Z] INFO  18:04:45,486 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T01:04Z] INFO  18:04:45,487 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T01:04Z] INFO  18:04:45,487 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T01:04Z] INFO  18:04:45,487 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T01:04Z] INFO  18:04:45,721 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T01:04Z] INFO  18:04:46,211 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:04Z] GATK: HaplotypeCaller
[2016-04-15T01:04Z] INFO  18:04:49,360 ProgressMeter -      17:2596090      1.3624185E7    30.0 s            2.0 s       16.4%     3.0 m       2.5 m
[2016-04-15T01:04Z] INFO  18:04:49,587 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:04Z] INFO  18:04:49,590 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:04Z] INFO  18:04:49,591 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:04Z] INFO  18:04:49,591 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:04Z] INFO  18:04:49,596 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/18/R14-18105_kapa-NGv3-PE100-NGv3-sort-18_34092400_49867248-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/18/R14-18105_kapa-NGv3-PE100-NGv3-18_34092400_49867248-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/18/tx/tmpBykaJN/R14-18105_kapa-NGv3-PE100-NGv3-18_34092400_49867248.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:04Z] INFO  18:04:49,607 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:04Z] INFO  18:04:49,608 HelpFormatter - Date/Time: 2016/04/14 18:04:49
[2016-04-15T01:04Z] INFO  18:04:49,608 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:04Z] INFO  18:04:49,609 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:04Z] WARN  18:04:49,631 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T01:04Z] WARN  18:04:49,634 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/18/tx/tmpBykaJN/R14-18105_kapa-NGv3-PE100-NGv3-18_34092400_49867248.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T01:04Z] INFO  18:04:49,840 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:04Z] INFO  18:04:50,021 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T01:04Z] INFO  18:04:50,050 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:04Z] INFO  18:04:50,136 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.09
[2016-04-15T01:04Z] INFO  18:04:50,165 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T01:04Z] INFO  18:04:50,327 ProgressMeter -     17:18220404      1.9168794E7    30.0 s            1.0 s       29.5%   101.0 s      71.0 s
[2016-04-15T01:04Z] INFO  18:04:50,517 IntervalUtils - Processing 116317 bp from intervals
[2016-04-15T01:04Z] WARN  18:04:50,532 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:04Z] INFO  18:04:50,660 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:04Z] INFO  18:04:50,780 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:04Z] INFO  18:04:50,781 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:04Z] INFO  18:04:50,782 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T01:04Z] INFO  18:04:50,782 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T01:04Z] INFO  18:04:50,783 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T01:04Z] INFO  18:04:50,783 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T01:04Z] INFO  18:04:50,943 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T01:04Z] INFO  18:04:51,116 ProgressMeter -     17:35901144      2.5152744E7    30.0 s            1.0 s       17.2%     2.9 m       2.4 m
[2016-04-15T01:04Z] INFO  18:04:51,148 ProgressMeter -      16:2813977       8.544875E7    60.0 s            0.0 s       50.2%   119.0 s      59.0 s
[2016-04-15T01:04Z] INFO  18:04:51,232 ProgressMeter -     16:28495439     1.39773824E8    60.0 s            0.0 s       61.0%    98.0 s      38.0 s
[2016-04-15T01:04Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T01:04Z] INFO  18:04:51,482 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T01:04Z] INFO  18:04:51,483 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T01:04Z] WARN  18:04:51,746 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T01:04Z] WARN  18:04:51,747 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T01:04Z] INFO  18:04:51,795 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.025546848
[2016-04-15T01:04Z] INFO  18:04:51,795 PairHMM - Total compute time in PairHMM computeLikelihoods() : 0.7136708310000001
[2016-04-15T01:04Z] INFO  18:04:51,796 HaplotypeCaller - Ran local assembly on 2729 active regions
[2016-04-15T01:04Z] INFO  18:04:51,862 ProgressMeter -            done     3.66240357E8    85.0 s            0.0 s      100.0%    85.0 s       0.0 s
[2016-04-15T01:04Z] INFO  18:04:51,863 ProgressMeter - Total runtime 85.98 secs, 1.43 min, 0.02 hours
[2016-04-15T01:04Z] INFO  18:04:51,863 MicroScheduler - 66828 reads were filtered out during the traversal out of approximately 578257 total reads (11.56%)
[2016-04-15T01:04Z] INFO  18:04:51,863 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:04Z] INFO  18:04:51,864 MicroScheduler -   -> 43804 reads (7.58% of total) failing DuplicateReadFilter
[2016-04-15T01:04Z] INFO  18:04:51,864 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:04Z] INFO  18:04:51,864 MicroScheduler -   -> 23024 reads (3.98% of total) failing HCMappingQualityFilter
[2016-04-15T01:04Z] INFO  18:04:51,864 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:04Z] INFO  18:04:51,865 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:04Z] INFO  18:04:51,865 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:04Z] INFO  18:04:51,865 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T01:04Z] INFO  18:04:53,373 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:04Z] GATK: HaplotypeCaller
[2016-04-15T01:04Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T01:04Z] INFO  18:04:55,070 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T01:04Z] INFO  18:04:55,071 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T01:04Z] WARN  18:04:55,615 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T01:04Z] WARN  18:04:55,616 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T01:04Z] INFO  18:04:56,098 ProgressMeter -      11:7064118     1.24422576E8     3.7 m            1.0 s       69.5%     5.3 m      96.0 s
[2016-04-15T01:04Z] INFO  18:04:56,593 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:04Z] INFO  18:04:56,596 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:04Z] INFO  18:04:56,596 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:04Z] INFO  18:04:56,597 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:04Z] INFO  18:04:56,602 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/18/R14-18105_kapa-NGv3-PE100-NGv3-sort-18_50278423_66344430-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/18/R14-18105_kapa-NGv3-PE100-NGv3-18_50278423_66344430-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/18/tx/tmpWJ0NmB/R14-18105_kapa-NGv3-PE100-NGv3-18_50278423_66344430.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:04Z] INFO  18:04:56,634 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:04Z] INFO  18:04:56,635 HelpFormatter - Date/Time: 2016/04/14 18:04:56
[2016-04-15T01:04Z] INFO  18:04:56,635 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:04Z] INFO  18:04:56,636 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:04Z] WARN  18:04:56,709 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T01:04Z] WARN  18:04:56,724 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/18/tx/tmpWJ0NmB/R14-18105_kapa-NGv3-PE100-NGv3-18_50278423_66344430.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T01:04Z] INFO  18:04:56,959 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:04Z] INFO  18:04:57,100 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T01:04Z] INFO  18:04:57,110 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:04Z] INFO  18:04:57,170 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-15T01:04Z] INFO  18:04:57,210 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T01:04Z] INFO  18:04:57,654 IntervalUtils - Processing 111880 bp from intervals
[2016-04-15T01:04Z] WARN  18:04:57,659 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:04Z] INFO  18:04:57,825 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:04Z] INFO  18:04:57,905 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:04Z] INFO  18:04:57,918 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:04Z] INFO  18:04:57,918 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T01:04Z] INFO  18:04:57,919 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T01:04Z] INFO  18:04:57,928 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T01:04Z] INFO  18:04:57,929 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T01:04Z] INFO  18:04:58,104 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T01:04Z] INFO  18:04:58,134 ProgressMeter -     17:49270789      2.1973092E7    30.0 s            1.0 s       32.6%    92.0 s      62.0 s
[2016-04-15T01:05Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T01:05Z] INFO  18:05:01,196 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T01:05Z] INFO  18:05:01,197 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T01:05Z] WARN  18:05:01,492 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T01:05Z] WARN  18:05:01,493 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T01:05Z] INFO  18:05:01,651 ProgressMeter -     17:71204429       3.500341E7    30.0 s            0.0 s       33.0%    90.0 s      60.0 s
[2016-04-15T01:05Z] INFO  18:05:06,323 ProgressMeter -     17:79818202      1.9881121E7    30.0 s            1.0 s       57.7%    52.0 s      22.0 s
[2016-04-15T01:05Z] INFO  18:05:07,644 ProgressMeter -      18:9887757      2.2559501E7    30.0 s            1.0 s       60.1%    49.0 s      19.0 s
[2016-04-15T01:05Z] INFO  18:05:07,965 ProgressMeter -     16:60392493     1.21426983E8    60.0 s            0.0 s       96.3%    62.0 s       2.0 s
[2016-04-15T01:05Z] INFO  18:05:09,189 ProgressMeter -     16:71768601     1.30415495E8    60.0 s            0.0 s       71.4%    84.0 s      24.0 s
[2016-04-15T01:05Z] INFO  18:05:09,755 ProgressMeter -     16:89713735      5.8859742E7    60.0 s            1.0 s       85.9%    69.0 s       9.0 s
[2016-04-15T01:05Z] INFO  18:05:10,377 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.045014289000000006
[2016-04-15T01:05Z] INFO  18:05:10,377 PairHMM - Total compute time in PairHMM computeLikelihoods() : 2.7149189750000002
[2016-04-15T01:05Z] INFO  18:05:10,378 HaplotypeCaller - Ran local assembly on 1719 active regions
[2016-04-15T01:05Z] INFO  18:05:10,427 ProgressMeter -            done     1.24288875E8    62.0 s            0.0 s      100.0%    62.0 s       0.0 s
[2016-04-15T01:05Z] INFO  18:05:10,428 ProgressMeter - Total runtime 62.47 secs, 1.04 min, 0.02 hours
[2016-04-15T01:05Z] INFO  18:05:10,428 MicroScheduler - 29705 reads were filtered out during the traversal out of approximately 354816 total reads (8.37%)
[2016-04-15T01:05Z] INFO  18:05:10,429 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:05Z] INFO  18:05:10,429 MicroScheduler -   -> 28342 reads (7.99% of total) failing DuplicateReadFilter
[2016-04-15T01:05Z] INFO  18:05:10,429 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:05Z] INFO  18:05:10,429 MicroScheduler -   -> 1363 reads (0.38% of total) failing HCMappingQualityFilter
[2016-04-15T01:05Z] INFO  18:05:10,429 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:05Z] INFO  18:05:10,430 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:05Z] INFO  18:05:10,430 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:05Z] INFO  18:05:10,430 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T01:05Z] INFO  18:05:12,041 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:05Z] GATK: HaplotypeCaller
[2016-04-15T01:05Z] INFO  18:05:15,234 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:05Z] INFO  18:05:15,237 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:05Z] INFO  18:05:15,238 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:05Z] INFO  18:05:15,239 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:05Z] INFO  18:05:15,243 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/18/R14-18105_kapa-NGv3-PE100-NGv3-sort-18_66346699_78077248-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/18/R14-18105_kapa-NGv3-PE100-NGv3-18_66346699_78077248-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/18/tx/tmph994m1/R14-18105_kapa-NGv3-PE100-NGv3-18_66346699_78077248.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:05Z] INFO  18:05:15,262 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:05Z] INFO  18:05:15,263 HelpFormatter - Date/Time: 2016/04/14 18:05:15
[2016-04-15T01:05Z] INFO  18:05:15,263 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:05Z] INFO  18:05:15,264 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:05Z] WARN  18:05:15,309 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T01:05Z] WARN  18:05:15,312 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/18/tx/tmph994m1/R14-18105_kapa-NGv3-PE100-NGv3-18_66346699_78077248.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T01:05Z] INFO  18:05:15,457 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:05Z] INFO  18:05:15,508 ProgressMeter -     18:29797919      2.8120147E7    30.0 s            1.0 s       69.0%    43.0 s      13.0 s
[2016-04-15T01:05Z] INFO  18:05:15,702 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T01:05Z] INFO  18:05:15,728 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:05Z] INFO  18:05:15,826 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.10
[2016-04-15T01:05Z] INFO  18:05:15,841 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T01:05Z] INFO  18:05:16,097 IntervalUtils - Processing 87308 bp from intervals
[2016-04-15T01:05Z] WARN  18:05:16,103 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:05Z] INFO  18:05:16,182 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:05Z] INFO  18:05:16,235 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:05Z] INFO  18:05:16,236 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:05Z] INFO  18:05:16,237 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T01:05Z] INFO  18:05:16,238 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T01:05Z] INFO  18:05:16,238 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T01:05Z] INFO  18:05:16,239 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T01:05Z] INFO  18:05:16,386 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T01:05Z] INFO  18:05:16,575 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.024888859000000003
[2016-04-15T01:05Z] INFO  18:05:16,576 PairHMM - Total compute time in PairHMM computeLikelihoods() : 3.1752062010000004
[2016-04-15T01:05Z] INFO  18:05:16,576 HaplotypeCaller - Ran local assembly on 1571 active regions
[2016-04-15T01:05Z] INFO  18:05:16,641 ProgressMeter -            done      8.7428536E7    66.0 s            0.0 s      100.0%    66.0 s       0.0 s
[2016-04-15T01:05Z] INFO  18:05:16,642 ProgressMeter - Total runtime 66.92 secs, 1.12 min, 0.02 hours
[2016-04-15T01:05Z] INFO  18:05:16,642 MicroScheduler - 32514 reads were filtered out during the traversal out of approximately 361689 total reads (8.99%)
[2016-04-15T01:05Z] INFO  18:05:16,643 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:05Z] INFO  18:05:16,643 MicroScheduler -   -> 29389 reads (8.13% of total) failing DuplicateReadFilter
[2016-04-15T01:05Z] INFO  18:05:16,643 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:05Z] INFO  18:05:16,644 MicroScheduler -   -> 3125 reads (0.86% of total) failing HCMappingQualityFilter
[2016-04-15T01:05Z] INFO  18:05:16,644 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:05Z] INFO  18:05:16,644 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:05Z] INFO  18:05:16,644 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:05Z] INFO  18:05:16,645 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T01:05Z] INFO  18:05:18,008 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:05Z] GATK: HaplotypeCaller
[2016-04-15T01:05Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T01:05Z] INFO  18:05:18,507 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T01:05Z] INFO  18:05:18,510 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T01:05Z] WARN  18:05:18,724 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T01:05Z] WARN  18:05:18,725 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T01:05Z] INFO  18:05:19,361 ProgressMeter -      17:6329508      1.1129696E8    60.0 s            0.0 s       45.5%     2.2 m      71.0 s
[2016-04-15T01:05Z] INFO  18:05:20,328 ProgressMeter -     17:21319956      5.8118009E7    60.0 s            1.0 s       48.5%     2.1 m      63.0 s
[2016-04-15T01:05Z] INFO  18:05:20,764 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.014583768
[2016-04-15T01:05Z] INFO  18:05:20,765 PairHMM - Total compute time in PairHMM computeLikelihoods() : 1.2516708600000002
[2016-04-15T01:05Z] INFO  18:05:20,766 HaplotypeCaller - Ran local assembly on 1211 active regions
[2016-04-15T01:05Z] INFO  18:05:20,800 ProgressMeter -     18:47116892       1.861685E7    30.0 s            1.0 s       79.4%    37.0 s       7.0 s
[2016-04-15T01:05Z] INFO  18:05:20,809 ProgressMeter -            done      5.7809529E7    44.0 s            0.0 s      100.0%    44.0 s       0.0 s
[2016-04-15T01:05Z] INFO  18:05:20,810 ProgressMeter - Total runtime 44.50 secs, 0.74 min, 0.01 hours
[2016-04-15T01:05Z] INFO  18:05:20,810 MicroScheduler - 24888 reads were filtered out during the traversal out of approximately 294405 total reads (8.45%)
[2016-04-15T01:05Z] INFO  18:05:20,811 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:05Z] INFO  18:05:20,818 MicroScheduler -   -> 23846 reads (8.10% of total) failing DuplicateReadFilter
[2016-04-15T01:05Z] INFO  18:05:20,818 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:05Z] INFO  18:05:20,818 MicroScheduler -   -> 1042 reads (0.35% of total) failing HCMappingQualityFilter
[2016-04-15T01:05Z] INFO  18:05:20,819 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:05Z] INFO  18:05:20,819 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:05Z] INFO  18:05:20,819 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:05Z] INFO  18:05:20,819 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T01:05Z] INFO  18:05:21,117 ProgressMeter -     17:39296500     1.32103775E8    60.0 s            0.0 s       43.3%     2.3 m      78.0 s
[2016-04-15T01:05Z] INFO  18:05:21,149 ProgressMeter -      16:7760747     2.39170471E8    90.0 s            0.0 s       80.6%   111.0 s      21.0 s
[2016-04-15T01:05Z] INFO  18:05:21,233 ProgressMeter -     16:30964757      2.6678203E8    90.0 s            0.0 s       94.6%    95.0 s       5.0 s
[2016-04-15T01:05Z] INFO  18:05:21,250 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:05Z] INFO  18:05:21,253 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:05Z] INFO  18:05:21,254 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:05Z] INFO  18:05:21,254 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:05Z] INFO  18:05:21,259 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/19/R14-18105_kapa-NGv3-PE100-NGv3-sort-19_0_15509577-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/19/R14-18105_kapa-NGv3-PE100-NGv3-19_0_15509577-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/19/tx/tmpMeAZSM/R14-18105_kapa-NGv3-PE100-NGv3-19_0_15509577.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:05Z] INFO  18:05:21,268 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:05Z] INFO  18:05:21,268 HelpFormatter - Date/Time: 2016/04/14 18:05:21
[2016-04-15T01:05Z] INFO  18:05:21,268 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:05Z] INFO  18:05:21,268 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:05Z] WARN  18:05:21,291 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T01:05Z] WARN  18:05:21,294 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/19/tx/tmpMeAZSM/R14-18105_kapa-NGv3-PE100-NGv3-19_0_15509577.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T01:05Z] INFO  18:05:21,529 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:05Z] INFO  18:05:21,708 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T01:05Z] INFO  18:05:21,718 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:05Z] INFO  18:05:21,797 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-15T01:05Z] INFO  18:05:21,821 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T01:05Z] INFO  18:05:22,278 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:05Z] INFO  18:05:22,409 IntervalUtils - Processing 793280 bp from intervals
[2016-04-15T01:05Z] WARN  18:05:22,416 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:05Z] INFO  18:05:22,569 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:05Z] GATK: HaplotypeCaller
[2016-04-15T01:05Z] INFO  18:05:22,747 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:05Z] INFO  18:05:22,748 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:05Z] INFO  18:05:22,749 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T01:05Z] INFO  18:05:22,750 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T01:05Z] INFO  18:05:22,750 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T01:05Z] INFO  18:05:22,750 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T01:05Z] INFO  18:05:22,908 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T01:05Z] INFO  18:05:24,939 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.015845178
[2016-04-15T01:05Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T01:05Z] INFO  18:05:24,940 PairHMM - Total compute time in PairHMM computeLikelihoods() : 0.33421363200000004
[2016-04-15T01:05Z] INFO  18:05:24,940 HaplotypeCaller - Ran local assembly on 1071 active regions
[2016-04-15T01:05Z] INFO  18:05:24,950 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T01:05Z] INFO  18:05:24,951 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T01:05Z] INFO  18:05:24,978 ProgressMeter -            done      5.2114591E7    39.0 s            0.0 s      100.0%    39.0 s       0.0 s
[2016-04-15T01:05Z] INFO  18:05:24,978 ProgressMeter - Total runtime 39.49 secs, 0.66 min, 0.01 hours
[2016-04-15T01:05Z] INFO  18:05:24,983 MicroScheduler - 16011 reads were filtered out during the traversal out of approximately 197599 total reads (8.10%)
[2016-04-15T01:05Z] INFO  18:05:24,984 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:05Z] INFO  18:05:24,984 MicroScheduler -   -> 15623 reads (7.91% of total) failing DuplicateReadFilter
[2016-04-15T01:05Z] INFO  18:05:24,985 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:05Z] INFO  18:05:24,985 MicroScheduler -   -> 388 reads (0.20% of total) failing HCMappingQualityFilter
[2016-04-15T01:05Z] INFO  18:05:24,986 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:05Z] INFO  18:05:24,987 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:05Z] INFO  18:05:24,987 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:05Z] INFO  18:05:24,988 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T01:05Z] WARN  18:05:25,212 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T01:05Z] WARN  18:05:25,213 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T01:05Z] INFO  18:05:25,468 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:05Z] INFO  18:05:25,472 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:05Z] INFO  18:05:25,472 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:05Z] INFO  18:05:25,473 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:05Z] INFO  18:05:25,478 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/19/R14-18105_kapa-NGv3-PE100-NGv3-sort-19_15510112_31025906-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/19/R14-18105_kapa-NGv3-PE100-NGv3-19_15510112_31025906-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/19/tx/tmpWbRaG6/R14-18105_kapa-NGv3-PE100-NGv3-19_15510112_31025906.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:05Z] INFO  18:05:25,488 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:05Z] INFO  18:05:25,490 HelpFormatter - Date/Time: 2016/04/14 18:05:25
[2016-04-15T01:05Z] INFO  18:05:25,491 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:05Z] INFO  18:05:25,491 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:05Z] WARN  18:05:25,519 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T01:05Z] WARN  18:05:25,522 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/19/tx/tmpWbRaG6/R14-18105_kapa-NGv3-PE100-NGv3-19_15510112_31025906.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T01:05Z] INFO  18:05:25,737 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:05Z] INFO  18:05:25,876 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T01:05Z] INFO  18:05:25,886 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:05Z] INFO  18:05:25,908 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.00958848
[2016-04-15T01:05Z] INFO  18:05:25,909 PairHMM - Total compute time in PairHMM computeLikelihoods() : 1.115848882
[2016-04-15T01:05Z] INFO  18:05:25,909 HaplotypeCaller - Ran local assembly on 813 active regions
[2016-04-15T01:05Z] INFO  18:05:25,951 ProgressMeter -            done      3.1603936E7    35.0 s            1.0 s      100.0%    35.0 s       0.0 s
[2016-04-15T01:05Z] INFO  18:05:25,952 ProgressMeter - Total runtime 35.17 secs, 0.59 min, 0.01 hours
[2016-04-15T01:05Z] INFO  18:05:25,952 MicroScheduler - 69730 reads were filtered out during the traversal out of approximately 225171 total reads (30.97%)
[2016-04-15T01:05Z] INFO  18:05:25,952 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:05Z] INFO  18:05:25,953 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-15T01:05Z] INFO  18:05:25,953 MicroScheduler -   -> 13716 reads (6.09% of total) failing DuplicateReadFilter
[2016-04-15T01:05Z] INFO  18:05:25,953 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:05Z] INFO  18:05:25,953 MicroScheduler -   -> 56014 reads (24.88% of total) failing HCMappingQualityFilter
[2016-04-15T01:05Z] INFO  18:05:25,953 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:05Z] INFO  18:05:25,954 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:05Z] INFO  18:05:25,954 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:05Z] INFO  18:05:25,954 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T01:05Z] INFO  18:05:25,972 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T01:05Z] INFO  18:05:26,083 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.022054194000000003
[2016-04-15T01:05Z] INFO  18:05:26,083 PairHMM - Total compute time in PairHMM computeLikelihoods() : 2.283875728
[2016-04-15T01:05Z] INFO  18:05:26,083 HaplotypeCaller - Ran local assembly on 2816 active regions
[2016-04-15T01:05Z] INFO  18:05:26,099 ProgressMeter -     11:14913751     3.71466099E8     4.2 m            0.0 s       99.2%     4.2 m       2.0 s
[2016-04-15T01:05Z] INFO  18:05:26,119 ProgressMeter -            done     2.83439102E8    94.0 s            0.0 s      100.0%    94.0 s       0.0 s
[2016-04-15T01:05Z] INFO  18:05:26,120 ProgressMeter - Total runtime 94.91 secs, 1.58 min, 0.03 hours
[2016-04-15T01:05Z] INFO  18:05:26,121 MicroScheduler - 325353 reads were filtered out during the traversal out of approximately 897034 total reads (36.27%)
[2016-04-15T01:05Z] INFO  18:05:26,121 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:05Z] INFO  18:05:26,121 MicroScheduler -   -> 50574 reads (5.64% of total) failing DuplicateReadFilter
[2016-04-15T01:05Z] INFO  18:05:26,121 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:05Z] INFO  18:05:26,122 MicroScheduler -   -> 274779 reads (30.63% of total) failing HCMappingQualityFilter
[2016-04-15T01:05Z] INFO  18:05:26,122 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:05Z] INFO  18:05:26,122 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:05Z] INFO  18:05:26,122 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:05Z] INFO  18:05:26,123 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T01:05Z] INFO  18:05:26,285 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:05Z] INFO  18:05:26,408 IntervalUtils - Processing 296880 bp from intervals
[2016-04-15T01:05Z] WARN  18:05:26,424 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:05Z] INFO  18:05:26,562 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:05Z] INFO  18:05:26,696 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:05Z] INFO  18:05:26,696 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:05Z] INFO  18:05:26,697 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T01:05Z] INFO  18:05:26,699 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T01:05Z] INFO  18:05:26,706 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T01:05Z] INFO  18:05:26,707 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T01:05Z] GATK: HaplotypeCaller
[2016-04-15T01:05Z] INFO  18:05:26,916 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T01:05Z] INFO  18:05:27,067 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.091202638
[2016-04-15T01:05Z] INFO  18:05:27,069 PairHMM - Total compute time in PairHMM computeLikelihoods() : 99.608453417
[2016-04-15T01:05Z] INFO  18:05:27,070 HaplotypeCaller - Ran local assembly on 3208 active regions
[2016-04-15T01:05Z] INFO  18:05:27,112 ProgressMeter -            done     3.81945604E8     4.2 m            0.0 s      100.0%     4.2 m       0.0 s
[2016-04-15T01:05Z] INFO  18:05:27,113 ProgressMeter - Total runtime 251.05 secs, 4.18 min, 0.07 hours
[2016-04-15T01:05Z] INFO  18:05:27,114 MicroScheduler - 97817 reads were filtered out during the traversal out of approximately 797305 total reads (12.27%)
[2016-04-15T01:05Z] INFO  18:05:27,115 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:05Z] INFO  18:05:27,115 MicroScheduler -   -> 64495 reads (8.09% of total) failing DuplicateReadFilter
[2016-04-15T01:05Z] INFO  18:05:27,116 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:05Z] INFO  18:05:27,117 MicroScheduler -   -> 33322 reads (4.18% of total) failing HCMappingQualityFilter
[2016-04-15T01:05Z] INFO  18:05:27,118 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:05Z] INFO  18:05:27,119 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:05Z] INFO  18:05:27,120 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:05Z] INFO  18:05:27,121 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T01:05Z] INFO  18:05:27,264 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:05Z] INFO  18:05:27,391 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:05Z] GATK: HaplotypeCaller
[2016-04-15T01:05Z] GATK: HaplotypeCaller
[2016-04-15T01:05Z] INFO  18:05:27,945 ProgressMeter -     18:61326761       2.298545E7    30.0 s            1.0 s       86.3%    34.0 s       4.0 s
[2016-04-15T01:05Z] INFO  18:05:28,135 ProgressMeter -     17:61391937     1.62361668E8    60.0 s            0.0 s       84.7%    70.0 s      10.0 s
[2016-04-15T01:05Z] INFO  18:05:28,568 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:05Z] GATK: HaplotypeCaller
[2016-04-15T01:05Z] INFO  18:05:29,795 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:05Z] INFO  18:05:29,798 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:05Z] INFO  18:05:29,799 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:05Z] INFO  18:05:29,799 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:05Z] INFO  18:05:29,804 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/19/R14-18105_kapa-NGv3-PE100-NGv3-sort-19_31038849_46627578-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/19/R14-18105_kapa-NGv3-PE100-NGv3-19_31038849_46627578-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/19/tx/tmpgItRyF/R14-18105_kapa-NGv3-PE100-NGv3-19_31038849_46627578.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:05Z] INFO  18:05:29,813 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:05Z] INFO  18:05:29,824 HelpFormatter - Date/Time: 2016/04/14 18:05:29
[2016-04-15T01:05Z] INFO  18:05:29,825 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:05Z] INFO  18:05:29,826 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:05Z] WARN  18:05:29,859 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T01:05Z] WARN  18:05:29,872 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/19/tx/tmpgItRyF/R14-18105_kapa-NGv3-PE100-NGv3-19_31038849_46627578.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T01:05Z] INFO  18:05:30,135 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:05Z] INFO  18:05:30,343 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T01:05Z] INFO  18:05:30,353 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:05Z] INFO  18:05:30,466 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.11
[2016-04-15T01:05Z] INFO  18:05:30,481 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T01:05Z] INFO  18:05:30,828 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:05Z] INFO  18:05:30,832 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:05Z] INFO  18:05:30,832 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:05Z] INFO  18:05:30,833 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:05Z] INFO  18:05:30,837 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/19/R14-18105_kapa-NGv3-PE100-NGv3-sort-19_46627881_59128983-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/19/R14-18105_kapa-NGv3-PE100-NGv3-19_46627881_59128983-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/19/tx/tmpfM0vKi/R14-18105_kapa-NGv3-PE100-NGv3-19_46627881_59128983.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:05Z] INFO  18:05:30,868 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:05Z] INFO  18:05:30,869 HelpFormatter - Date/Time: 2016/04/14 18:05:30
[2016-04-15T01:05Z] INFO  18:05:30,870 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:05Z] INFO  18:05:30,870 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:05Z] WARN  18:05:30,925 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T01:05Z] WARN  18:05:30,929 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/19/tx/tmpfM0vKi/R14-18105_kapa-NGv3-PE100-NGv3-19_46627881_59128983.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T01:05Z] INFO  18:05:31,049 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:05Z] INFO  18:05:31,052 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:05Z] INFO  18:05:31,053 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:05Z] INFO  18:05:31,053 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:05Z] INFO  18:05:31,058 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/20/R14-18105_kapa-NGv3-PE100-NGv3-sort-20_0_15843471-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/20/R14-18105_kapa-NGv3-PE100-NGv3-20_0_15843471-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/20/tx/tmpCGC_zK/R14-18105_kapa-NGv3-PE100-NGv3-20_0_15843471.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:05Z] INFO  18:05:31,095 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:05Z] INFO  18:05:31,096 HelpFormatter - Date/Time: 2016/04/14 18:05:31
[2016-04-15T01:05Z] INFO  18:05:31,097 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:05Z] INFO  18:05:31,101 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:05Z] INFO  18:05:31,109 IntervalUtils - Processing 631764 bp from intervals
[2016-04-15T01:05Z] WARN  18:05:31,115 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:05Z] WARN  18:05:31,146 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T01:05Z] WARN  18:05:31,149 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/20/tx/tmpCGC_zK/R14-18105_kapa-NGv3-PE100-NGv3-20_0_15843471.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T01:05Z] INFO  18:05:31,188 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:05Z] INFO  18:05:31,294 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:05Z] INFO  18:05:31,401 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:05Z] INFO  18:05:31,406 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T01:05Z] INFO  18:05:31,415 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:05Z] INFO  18:05:31,437 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:05Z] INFO  18:05:31,438 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:05Z] INFO  18:05:31,438 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T01:05Z] INFO  18:05:31,439 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T01:05Z] INFO  18:05:31,439 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T01:05Z] INFO  18:05:31,439 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T01:05Z] INFO  18:05:31,497 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-15T01:05Z] INFO  18:05:31,528 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T01:05Z] INFO  18:05:31,599 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T01:05Z] INFO  18:05:31,609 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:05Z] INFO  18:05:31,652 ProgressMeter -     17:74381689      1.5454131E8    60.0 s            0.0 s       76.1%    78.0 s      18.0 s
[2016-04-15T01:05Z] INFO  18:05:31,694 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-15T01:05Z] INFO  18:05:31,717 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T01:05Z] INFO  18:05:31,726 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T01:05Z] INFO  18:05:31,912 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:05Z] INFO  18:05:31,915 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:05Z] INFO  18:05:31,915 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:05Z] INFO  18:05:31,915 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:05Z] INFO  18:05:31,920 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/20/R14-18105_kapa-NGv3-PE100-NGv3-sort-20_15866408_31376818-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/20/R14-18105_kapa-NGv3-PE100-NGv3-20_15866408_31376818-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/20/tx/tmp21oq2v/R14-18105_kapa-NGv3-PE100-NGv3-20_15866408_31376818.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:05Z] INFO  18:05:31,932 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:05Z] INFO  18:05:31,934 HelpFormatter - Date/Time: 2016/04/14 18:05:31
[2016-04-15T01:05Z] INFO  18:05:31,935 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:05Z] INFO  18:05:31,942 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:05Z] WARN  18:05:31,966 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T01:05Z] WARN  18:05:31,969 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/20/tx/tmp21oq2v/R14-18105_kapa-NGv3-PE100-NGv3-20_15866408_31376818.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T01:05Z] INFO  18:05:31,998 IntervalUtils - Processing 711484 bp from intervals
[2016-04-15T01:05Z] WARN  18:05:32,004 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:05Z] INFO  18:05:32,120 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:05Z] INFO  18:05:32,137 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:05Z] INFO  18:05:32,185 IntervalUtils - Processing 179899 bp from intervals
[2016-04-15T01:05Z] WARN  18:05:32,190 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:05Z] INFO  18:05:32,325 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:05Z] INFO  18:05:32,326 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T01:05Z] INFO  18:05:32,335 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:05Z] INFO  18:05:32,338 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:05Z] INFO  18:05:32,338 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:05Z] INFO  18:05:32,339 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T01:05Z] INFO  18:05:32,339 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T01:05Z] INFO  18:05:32,347 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T01:05Z] INFO  18:05:32,347 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T01:05Z] INFO  18:05:32,391 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:05Z] INFO  18:05:32,392 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:05Z] INFO  18:05:32,393 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T01:05Z] INFO  18:05:32,393 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T01:05Z] INFO  18:05:32,394 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T01:05Z] INFO  18:05:32,394 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T01:05Z] INFO  18:05:32,403 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-15T01:05Z] INFO  18:05:32,426 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T01:05Z] INFO  18:05:32,493 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.009960319
[2016-04-15T01:05Z] INFO  18:05:32,493 PairHMM - Total compute time in PairHMM computeLikelihoods() : 0.573363061
[2016-04-15T01:05Z] INFO  18:05:32,494 HaplotypeCaller - Ran local assembly on 835 active regions
[2016-04-15T01:05Z] INFO  18:05:32,545 ProgressMeter -            done      2.9530103E7    34.0 s            1.0 s      100.0%    34.0 s       0.0 s
[2016-04-15T01:05Z] INFO  18:05:32,546 ProgressMeter - Total runtime 34.63 secs, 0.58 min, 0.01 hours
[2016-04-15T01:05Z] INFO  18:05:32,549 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T01:05Z] INFO  18:05:32,546 MicroScheduler - 11622 reads were filtered out during the traversal out of approximately 146785 total reads (7.92%)
[2016-04-15T01:05Z] INFO  18:05:32,546 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:05Z] INFO  18:05:32,547 MicroScheduler -   -> 11352 reads (7.73% of total) failing DuplicateReadFilter
[2016-04-15T01:05Z] INFO  18:05:32,547 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:05Z] INFO  18:05:32,547 MicroScheduler -   -> 270 reads (0.18% of total) failing HCMappingQualityFilter
[2016-04-15T01:05Z] INFO  18:05:32,547 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:05Z] INFO  18:05:32,548 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:05Z] INFO  18:05:32,548 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:05Z] INFO  18:05:32,548 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T01:05Z] INFO  18:05:32,599 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T01:05Z] INFO  18:05:32,967 IntervalUtils - Processing 150913 bp from intervals
[2016-04-15T01:05Z] WARN  18:05:32,981 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:05Z] INFO  18:05:33,126 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:05Z] INFO  18:05:33,182 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.036474658
[2016-04-15T01:05Z] INFO  18:05:33,183 PairHMM - Total compute time in PairHMM computeLikelihoods() : 8.39778896
[2016-04-15T01:05Z] INFO  18:05:33,183 HaplotypeCaller - Ran local assembly on 1199 active regions
[2016-04-15T01:05Z] INFO  18:05:33,206 ProgressMeter -            done      6.3174533E7    55.0 s            0.0 s      100.0%    55.0 s       0.0 s
[2016-04-15T01:05Z] INFO  18:05:33,207 ProgressMeter - Total runtime 55.59 secs, 0.93 min, 0.02 hours
[2016-04-15T01:05Z] INFO  18:05:33,208 MicroScheduler - 21045 reads were filtered out during the traversal out of approximately 227135 total reads (9.27%)
[2016-04-15T01:05Z] INFO  18:05:33,209 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:05Z] INFO  18:05:33,209 MicroScheduler -   -> 17668 reads (7.78% of total) failing DuplicateReadFilter
[2016-04-15T01:05Z] INFO  18:05:33,210 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:05Z] INFO  18:05:33,211 MicroScheduler -   -> 3377 reads (1.49% of total) failing HCMappingQualityFilter
[2016-04-15T01:05Z] INFO  18:05:33,211 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:05Z] INFO  18:05:33,212 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:05Z] INFO  18:05:33,213 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:05Z] INFO  18:05:33,213 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T01:05Z] INFO  18:05:33,224 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:05Z] INFO  18:05:33,225 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:05Z] INFO  18:05:33,226 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T01:05Z] INFO  18:05:33,226 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T01:05Z] INFO  18:05:33,227 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T01:05Z] INFO  18:05:33,227 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T01:05Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T01:05Z] INFO  18:05:33,342 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T01:05Z] INFO  18:05:33,347 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T01:05Z] INFO  18:05:33,452 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T01:05Z] WARN  18:05:34,002 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T01:05Z] WARN  18:05:34,004 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T01:05Z] INFO  18:05:34,066 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:05Z] GATK: HaplotypeCaller
[2016-04-15T01:05Z] INFO  18:05:34,775 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:05Z] GATK: HaplotypeCaller
[2016-04-15T01:05Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T01:05Z] INFO  18:05:35,182 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T01:05Z] INFO  18:05:35,183 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T01:05Z] WARN  18:05:35,524 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T01:05Z] WARN  18:05:35,525 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T01:05Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T01:05Z] INFO  18:05:36,001 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T01:05Z] INFO  18:05:36,002 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T01:05Z] WARN  18:05:36,213 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T01:05Z] WARN  18:05:36,214 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T01:05Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T01:05Z] INFO  18:05:37,143 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T01:05Z] INFO  18:05:37,144 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T01:05Z] WARN  18:05:37,356 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T01:05Z] WARN  18:05:37,357 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T01:05Z] INFO  18:05:37,610 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:05Z] INFO  18:05:37,613 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:05Z] INFO  18:05:37,613 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:05Z] INFO  18:05:37,614 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:05Z] INFO  18:05:37,618 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/20/R14-18105_kapa-NGv3-PE100-NGv3-sort-20_31379406_47242465-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/20/R14-18105_kapa-NGv3-PE100-NGv3-20_31379406_47242465-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/20/tx/tmpDDCme2/R14-18105_kapa-NGv3-PE100-NGv3-20_31379406_47242465.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:05Z] INFO  18:05:37,642 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:05Z] INFO  18:05:37,643 HelpFormatter - Date/Time: 2016/04/14 18:05:37
[2016-04-15T01:05Z] INFO  18:05:37,643 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:05Z] INFO  18:05:37,644 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:05Z] WARN  18:05:37,721 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T01:05Z] WARN  18:05:37,730 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/20/tx/tmpDDCme2/R14-18105_kapa-NGv3-PE100-NGv3-20_31379406_47242465.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T01:05Z] INFO  18:05:37,752 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.014285493000000002
[2016-04-15T01:05Z] INFO  18:05:37,753 PairHMM - Total compute time in PairHMM computeLikelihoods() : 1.1749583350000001
[2016-04-15T01:05Z] INFO  18:05:37,754 HaplotypeCaller - Ran local assembly on 2179 active regions
[2016-04-15T01:05Z] INFO  18:05:37,807 ProgressMeter -            done     2.16274885E8    69.0 s            0.0 s      100.0%    69.0 s       0.0 s
[2016-04-15T01:05Z] INFO  18:05:37,808 ProgressMeter - Total runtime 69.69 secs, 1.16 min, 0.02 hours
[2016-04-15T01:05Z] INFO  18:05:37,808 MicroScheduler - 42530 reads were filtered out during the traversal out of approximately 476628 total reads (8.92%)
[2016-04-15T01:05Z] INFO  18:05:37,809 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:05Z] INFO  18:05:37,810 MicroScheduler -   -> 37278 reads (7.82% of total) failing DuplicateReadFilter
[2016-04-15T01:05Z] INFO  18:05:37,810 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:05Z] INFO  18:05:37,810 MicroScheduler -   -> 5252 reads (1.10% of total) failing HCMappingQualityFilter
[2016-04-15T01:05Z] INFO  18:05:37,810 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:05Z] INFO  18:05:37,811 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:05Z] INFO  18:05:37,811 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:05Z] INFO  18:05:37,811 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T01:05Z] INFO  18:05:37,871 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.034397538000000005
[2016-04-15T01:05Z] INFO  18:05:37,872 PairHMM - Total compute time in PairHMM computeLikelihoods() : 5.723012575
[2016-04-15T01:05Z] INFO  18:05:37,877 HaplotypeCaller - Ran local assembly on 2395 active regions
[2016-04-15T01:05Z] INFO  18:05:37,922 ProgressMeter -            done     2.54086229E8    88.0 s            0.0 s      100.0%    88.0 s       0.0 s
[2016-04-15T01:05Z] INFO  18:05:37,923 ProgressMeter - Total runtime 88.75 secs, 1.48 min, 0.02 hours
[2016-04-15T01:05Z] INFO  18:05:37,923 MicroScheduler - 108527 reads were filtered out during the traversal out of approximately 655895 total reads (16.55%)
[2016-04-15T01:05Z] INFO  18:05:37,923 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:05Z] INFO  18:05:37,924 MicroScheduler -   -> 48676 reads (7.42% of total) failing DuplicateReadFilter
[2016-04-15T01:05Z] INFO  18:05:37,924 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:05Z] INFO  18:05:37,925 MicroScheduler -   -> 59851 reads (9.13% of total) failing HCMappingQualityFilter
[2016-04-15T01:05Z] INFO  18:05:37,925 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:05Z] INFO  18:05:37,925 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:05Z] INFO  18:05:37,925 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:05Z] INFO  18:05:37,926 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T01:05Z] INFO  18:05:37,992 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:05Z] INFO  18:05:38,196 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T01:05Z] INFO  18:05:38,227 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:05Z] INFO  18:05:38,297 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-15T01:05Z] INFO  18:05:38,325 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T01:05Z] INFO  18:05:38,386 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:05Z] INFO  18:05:38,393 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:05Z] INFO  18:05:38,394 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:05Z] INFO  18:05:38,394 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:05Z] INFO  18:05:38,399 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/20/R14-18105_kapa-NGv3-PE100-NGv3-sort-20_47244085_62830269-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/20/R14-18105_kapa-NGv3-PE100-NGv3-20_47244085_62830269-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/20/tx/tmpGHeYNg/R14-18105_kapa-NGv3-PE100-NGv3-20_47244085_62830269.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:05Z] INFO  18:05:38,412 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:05Z] INFO  18:05:38,413 HelpFormatter - Date/Time: 2016/04/14 18:05:38
[2016-04-15T01:05Z] INFO  18:05:38,414 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:05Z] INFO  18:05:38,414 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:05Z] WARN  18:05:38,446 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T01:05Z] WARN  18:05:38,449 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/20/tx/tmpGHeYNg/R14-18105_kapa-NGv3-PE100-NGv3-20_47244085_62830269.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T01:05Z] INFO  18:05:38,597 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:05Z] INFO  18:05:38,769 IntervalUtils - Processing 321885 bp from intervals
[2016-04-15T01:05Z] WARN  18:05:38,774 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:05Z] INFO  18:05:38,848 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T01:05Z] INFO  18:05:38,865 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:05Z] INFO  18:05:38,909 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:05Z] INFO  18:05:38,948 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-15T01:05Z] INFO  18:05:38,974 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T01:05Z] INFO  18:05:39,078 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:05Z] INFO  18:05:39,079 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:05Z] INFO  18:05:39,080 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T01:05Z] INFO  18:05:39,080 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T01:05Z] INFO  18:05:39,089 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T01:05Z] INFO  18:05:39,089 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T01:05Z] INFO  18:05:39,271 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T01:05Z] INFO  18:05:39,290 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:05Z] INFO  18:05:39,431 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:05Z] INFO  18:05:39,506 IntervalUtils - Processing 269605 bp from intervals
[2016-04-15T01:05Z] WARN  18:05:39,512 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:05Z] GATK: HaplotypeCaller
[2016-04-15T01:05Z] INFO  18:05:39,615 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:05Z] GATK: HaplotypeCaller
[2016-04-15T01:05Z] INFO  18:05:39,735 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:05Z] INFO  18:05:39,736 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:05Z] INFO  18:05:39,737 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T01:05Z] INFO  18:05:39,738 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T01:05Z] INFO  18:05:39,738 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T01:05Z] INFO  18:05:39,739 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T01:05Z] INFO  18:05:39,973 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T01:05Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T01:05Z] INFO  18:05:40,402 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T01:05Z] INFO  18:05:40,404 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T01:05Z] WARN  18:05:41,016 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T01:05Z] WARN  18:05:41,017 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T01:05Z] INFO  18:05:43,049 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:05Z] INFO  18:05:43,066 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:05Z] INFO  18:05:43,067 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:05Z] INFO  18:05:43,068 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:05Z] INFO  18:05:43,072 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/20/R14-18105_kapa-NGv3-PE100-NGv3-sort-20_62831244_63025520-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/20/R14-18105_kapa-NGv3-PE100-NGv3-20_62831244_63025520-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/20/tx/tmpJPNkfg/R14-18105_kapa-NGv3-PE100-NGv3-20_62831244_63025520.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:05Z] INFO  18:05:43,091 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:05Z] INFO  18:05:43,092 HelpFormatter - Date/Time: 2016/04/14 18:05:43
[2016-04-15T01:05Z] INFO  18:05:43,092 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:05Z] INFO  18:05:43,093 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:05Z] WARN  18:05:43,169 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T01:05Z] WARN  18:05:43,173 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/20/tx/tmpJPNkfg/R14-18105_kapa-NGv3-PE100-NGv3-20_62831244_63025520.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T01:05Z] INFO  18:05:43,499 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:05Z] INFO  18:05:43,509 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:05Z] INFO  18:05:43,512 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:05Z] INFO  18:05:43,512 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:05Z] INFO  18:05:43,513 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:05Z] INFO  18:05:43,517 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/21/R14-18105_kapa-NGv3-PE100-NGv3-sort-21_0_15517120-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/21/R14-18105_kapa-NGv3-PE100-NGv3-21_0_15517120-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/21/tx/tmp4dLFtd/R14-18105_kapa-NGv3-PE100-NGv3-21_0_15517120.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:05Z] INFO  18:05:43,560 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:05Z] INFO  18:05:43,560 HelpFormatter - Date/Time: 2016/04/14 18:05:43
[2016-04-15T01:05Z] INFO  18:05:43,561 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:05Z] INFO  18:05:43,561 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:05Z] WARN  18:05:43,607 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T01:05Z] WARN  18:05:43,618 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/21/tx/tmp4dLFtd/R14-18105_kapa-NGv3-PE100-NGv3-21_0_15517120.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T01:05Z] INFO  18:05:43,706 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T01:05Z] INFO  18:05:43,715 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:05Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T01:05Z] INFO  18:05:43,749 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T01:05Z] INFO  18:05:43,752 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T01:05Z] INFO  18:05:43,813 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.10
[2016-04-15T01:05Z] INFO  18:05:43,844 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T01:05Z] INFO  18:05:43,859 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:05Z] INFO  18:05:44,181 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T01:05Z] WARN  18:05:44,188 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T01:05Z] WARN  18:05:44,189 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T01:05Z] INFO  18:05:44,190 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:05Z] INFO  18:05:44,286 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.10
[2016-04-15T01:05Z] INFO  18:05:44,305 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T01:05Z] INFO  18:05:44,319 IntervalUtils - Processing 4397 bp from intervals
[2016-04-15T01:05Z] WARN  18:05:44,324 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:05Z] INFO  18:05:44,415 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:05Z] INFO  18:05:44,464 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:05Z] INFO  18:05:44,465 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:05Z] INFO  18:05:44,465 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T01:05Z] INFO  18:05:44,466 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T01:05Z] INFO  18:05:44,467 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T01:05Z] INFO  18:05:44,467 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T01:05Z] INFO  18:05:44,681 IntervalUtils - Processing 4504 bp from intervals
[2016-04-15T01:05Z] WARN  18:05:44,697 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:05Z] INFO  18:05:44,719 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T01:05Z] INFO  18:05:44,796 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:05Z] INFO  18:05:44,831 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:05Z] INFO  18:05:44,832 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:05Z] INFO  18:05:44,832 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T01:05Z] INFO  18:05:44,833 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T01:05Z] INFO  18:05:44,836 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T01:05Z] INFO  18:05:44,836 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T01:05Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T01:05Z] INFO  18:05:44,974 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T01:05Z] INFO  18:05:44,975 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T01:05Z] INFO  18:05:45,016 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T01:05Z] WARN  18:05:45,261 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T01:05Z] WARN  18:05:45,261 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T01:05Z] INFO  18:05:45,698 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.036901988000000004
[2016-04-15T01:05Z] INFO  18:05:45,699 PairHMM - Total compute time in PairHMM computeLikelihoods() : 4.509664281
[2016-04-15T01:05Z] INFO  18:05:45,700 HaplotypeCaller - Ran local assembly on 3240 active regions
[2016-04-15T01:05Z] INFO  18:05:45,737 ProgressMeter -            done     4.23621461E8   114.0 s            0.0 s      100.0%   114.0 s       0.0 s
[2016-04-15T01:05Z] INFO  18:05:45,738 ProgressMeter - Total runtime 114.62 secs, 1.91 min, 0.03 hours
[2016-04-15T01:05Z] INFO  18:05:45,738 MicroScheduler - 128744 reads were filtered out during the traversal out of approximately 847797 total reads (15.19%)
[2016-04-15T01:05Z] INFO  18:05:45,738 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:05Z] INFO  18:05:45,739 MicroScheduler -   -> 63459 reads (7.49% of total) failing DuplicateReadFilter
[2016-04-15T01:05Z] INFO  18:05:45,739 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:05Z] INFO  18:05:45,739 MicroScheduler -   -> 65285 reads (7.70% of total) failing HCMappingQualityFilter
[2016-04-15T01:05Z] INFO  18:05:45,739 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:05Z] INFO  18:05:45,740 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:05Z] INFO  18:05:45,740 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:05Z] INFO  18:05:45,740 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T01:05Z] INFO  18:05:46,105 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.019294168
[2016-04-15T01:05Z] INFO  18:05:46,106 PairHMM - Total compute time in PairHMM computeLikelihoods() : 0.741227743
[2016-04-15T01:05Z] INFO  18:05:46,107 HaplotypeCaller - Ran local assembly on 583 active regions
[2016-04-15T01:05Z] INFO  18:05:46,157 ProgressMeter -            done      1.2811877E7    29.0 s            2.0 s      100.0%    29.0 s       0.0 s
[2016-04-15T01:05Z] INFO  18:05:46,158 ProgressMeter - Total runtime 29.92 secs, 0.50 min, 0.01 hours
[2016-04-15T01:05Z] INFO  18:05:46,159 MicroScheduler - 10740 reads were filtered out during the traversal out of approximately 128827 total reads (8.34%)
[2016-04-15T01:05Z] INFO  18:05:46,160 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:05Z] INFO  18:05:46,160 MicroScheduler -   -> 10392 reads (8.07% of total) failing DuplicateReadFilter
[2016-04-15T01:05Z] INFO  18:05:46,161 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:05Z] INFO  18:05:46,161 MicroScheduler -   -> 348 reads (0.27% of total) failing HCMappingQualityFilter
[2016-04-15T01:05Z] INFO  18:05:46,162 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:05Z] INFO  18:05:46,163 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:05Z] INFO  18:05:46,163 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:05Z] INFO  18:05:46,164 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T01:05Z] INFO  18:05:47,540 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:05Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T01:05Z] INFO  18:05:47,650 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T01:05Z] INFO  18:05:47,662 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T01:05Z] INFO  18:05:47,704 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:05Z] GATK: HaplotypeCaller
[2016-04-15T01:05Z] GATK: HaplotypeCaller
[2016-04-15T01:05Z] WARN  18:05:48,154 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T01:05Z] WARN  18:05:48,166 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T01:05Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T01:05Z] INFO  18:05:48,444 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T01:05Z] INFO  18:05:48,445 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T01:05Z] WARN  18:05:48,738 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T01:05Z] WARN  18:05:48,739 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T01:05Z] INFO  18:05:49,362 ProgressMeter -      17:7837864     2.37962442E8    90.0 s            0.0 s       70.9%     2.1 m      36.0 s
[2016-04-15T01:05Z] INFO  18:05:50,329 ProgressMeter -     17:29220712     1.80511636E8    90.0 s            0.0 s       88.0%   102.0 s      12.0 s
[2016-04-15T01:05Z] INFO  18:05:50,432 VectorLoglessPairHMM - Time spent in setup for JNI call : 6.79626E-4
[2016-04-15T01:05Z] INFO  18:05:50,433 PairHMM - Total compute time in PairHMM computeLikelihoods() : 0.009684921
[2016-04-15T01:05Z] INFO  18:05:50,433 HaplotypeCaller - Ran local assembly on 31 active regions
[2016-04-15T01:05Z] INFO  18:05:50,514 ProgressMeter -            done          56928.0     6.0 s          106.0 s      100.0%     6.0 s       0.0 s
[2016-04-15T01:05Z] INFO  18:05:50,515 ProgressMeter - Total runtime 6.05 secs, 0.10 min, 0.00 hours
[2016-04-15T01:05Z] INFO  18:05:50,515 MicroScheduler - 614 reads were filtered out during the traversal out of approximately 7534 total reads (8.15%)
[2016-04-15T01:05Z] INFO  18:05:50,515 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:05Z] INFO  18:05:50,516 MicroScheduler -   -> 603 reads (8.00% of total) failing DuplicateReadFilter
[2016-04-15T01:05Z] INFO  18:05:50,516 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:05Z] INFO  18:05:50,516 MicroScheduler -   -> 11 reads (0.15% of total) failing HCMappingQualityFilter
[2016-04-15T01:05Z] INFO  18:05:50,516 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:05Z] INFO  18:05:50,517 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:05Z] INFO  18:05:50,517 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:05Z] INFO  18:05:50,517 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T01:05Z] INFO  18:05:51,052 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:05Z] INFO  18:05:51,055 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:05Z] INFO  18:05:51,055 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:05Z] INFO  18:05:51,056 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:05Z] INFO  18:05:51,060 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/21/R14-18105_kapa-NGv3-PE100-NGv3-sort-21_15524893_31045484-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/21/R14-18105_kapa-NGv3-PE100-NGv3-21_15524893_31045484-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/21/tx/tmpazFfez/R14-18105_kapa-NGv3-PE100-NGv3-21_15524893_31045484.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:05Z] INFO  18:05:51,069 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:05Z] INFO  18:05:51,070 HelpFormatter - Date/Time: 2016/04/14 18:05:51
[2016-04-15T01:05Z] INFO  18:05:51,070 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:05Z] INFO  18:05:51,071 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:05Z] WARN  18:05:51,093 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T01:05Z] WARN  18:05:51,096 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/21/tx/tmpazFfez/R14-18105_kapa-NGv3-PE100-NGv3-21_15524893_31045484.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T01:05Z] INFO  18:05:51,118 ProgressMeter -     17:40766862     2.37746908E8    90.0 s            0.0 s       60.4%     2.5 m      59.0 s
[2016-04-15T01:05Z] INFO  18:05:51,223 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:05Z] INFO  18:05:51,226 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:05Z] INFO  18:05:51,227 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:05Z] INFO  18:05:51,227 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:05Z] INFO  18:05:51,231 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/21/R14-18105_kapa-NGv3-PE100-NGv3-sort-21_31062047_46591599-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/21/R14-18105_kapa-NGv3-PE100-NGv3-21_31062047_46591599-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/21/tx/tmpV6A2w3/R14-18105_kapa-NGv3-PE100-NGv3-21_31062047_46591599.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:05Z] INFO  18:05:51,242 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:05Z] INFO  18:05:51,242 HelpFormatter - Date/Time: 2016/04/14 18:05:51
[2016-04-15T01:05Z] INFO  18:05:51,243 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:05Z] INFO  18:05:51,244 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:05Z] WARN  18:05:51,288 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T01:05Z] WARN  18:05:51,291 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/21/tx/tmpV6A2w3/R14-18105_kapa-NGv3-PE100-NGv3-21_31062047_46591599.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T01:05Z] INFO  18:05:51,299 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:05Z] INFO  18:05:51,548 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T01:05Z] INFO  18:05:51,557 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:05Z] INFO  18:05:51,570 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:05Z] INFO  18:05:51,649 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.09
[2016-04-15T01:05Z] INFO  18:05:51,688 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T01:05Z] INFO  18:05:51,805 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T01:05Z] INFO  18:05:51,829 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:05Z] INFO  18:05:51,907 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:05Z] INFO  18:05:51,909 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-15T01:05Z] INFO  18:05:51,934 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T01:05Z] INFO  18:05:52,191 IntervalUtils - Processing 58639 bp from intervals
[2016-04-15T01:05Z] WARN  18:05:52,197 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:05Z] GATK: HaplotypeCaller
[2016-04-15T01:05Z] INFO  18:05:52,317 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:05Z] INFO  18:05:52,421 IntervalUtils - Processing 282111 bp from intervals
[2016-04-15T01:05Z] INFO  18:05:52,424 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:05Z] INFO  18:05:52,425 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:05Z] INFO  18:05:52,425 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T01:05Z] INFO  18:05:52,426 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T01:05Z] WARN  18:05:52,426 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:05Z] INFO  18:05:52,438 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T01:05Z] INFO  18:05:52,439 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T01:05Z] INFO  18:05:52,509 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:05Z] INFO  18:05:52,661 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:05Z] INFO  18:05:52,662 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:05Z] INFO  18:05:52,663 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T01:05Z] INFO  18:05:52,665 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T01:05Z] INFO  18:05:52,677 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T01:05Z] INFO  18:05:52,678 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T01:05Z] INFO  18:05:52,711 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T01:05Z] INFO  18:05:52,760 ProgressMeter -      19:1224337        9592068.0    30.0 s            3.0 s        8.5%     5.9 m       5.4 m
[2016-04-15T01:05Z] INFO  18:05:52,845 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T01:05Z] INFO  18:05:55,336 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:05Z] INFO  18:05:55,339 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:05Z] INFO  18:05:55,340 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:05Z] INFO  18:05:55,340 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:05Z] INFO  18:05:55,345 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/21/R14-18105_kapa-NGv3-PE100-NGv3-sort-21_46595644_48129895-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/21/R14-18105_kapa-NGv3-PE100-NGv3-21_46595644_48129895-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/21/tx/tmp06vYPy/R14-18105_kapa-NGv3-PE100-NGv3-21_46595644_48129895.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:05Z] INFO  18:05:55,354 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:05Z] INFO  18:05:55,355 HelpFormatter - Date/Time: 2016/04/14 18:05:55
[2016-04-15T01:05Z] INFO  18:05:55,356 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:05Z] INFO  18:05:55,356 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:05Z] WARN  18:05:55,392 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T01:05Z] WARN  18:05:55,395 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/21/tx/tmp06vYPy/R14-18105_kapa-NGv3-PE100-NGv3-21_46595644_48129895.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T01:05Z] INFO  18:05:55,633 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:05Z] INFO  18:05:55,883 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T01:05Z] INFO  18:05:55,893 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:05Z] INFO  18:05:55,978 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-15T01:05Z] INFO  18:05:56,003 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T01:05Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T01:05Z] INFO  18:05:56,213 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T01:05Z] INFO  18:05:56,224 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T01:05Z] INFO  18:05:56,369 IntervalUtils - Processing 63011 bp from intervals
[2016-04-15T01:05Z] WARN  18:05:56,375 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:05Z] INFO  18:05:56,467 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:05Z] WARN  18:05:56,524 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T01:05Z] WARN  18:05:56,525 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T01:05Z] INFO  18:05:56,556 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:05Z] INFO  18:05:56,556 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:05Z] INFO  18:05:56,557 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T01:05Z] INFO  18:05:56,557 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T01:05Z] INFO  18:05:56,562 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T01:05Z] INFO  18:05:56,563 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T01:05Z] INFO  18:05:56,720 ProgressMeter -     19:17394898      1.5535635E7    30.0 s            1.0 s       26.7%   112.0 s      82.0 s
[2016-04-15T01:05Z] INFO  18:05:56,815 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T01:05Z] INFO  18:05:56,886 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.025093594
[2016-04-15T01:05Z] INFO  18:05:56,887 PairHMM - Total compute time in PairHMM computeLikelihoods() : 8.701955176
[2016-04-15T01:05Z] INFO  18:05:56,888 HaplotypeCaller - Ran local assembly on 2315 active regions
[2016-04-15T01:05Z] INFO  18:05:56,953 ProgressMeter -            done     2.48819629E8    96.0 s            0.0 s      100.0%    96.0 s       0.0 s
[2016-04-15T01:05Z] INFO  18:05:56,954 ProgressMeter - Total runtime 96.66 secs, 1.61 min, 0.03 hours
[2016-04-15T01:05Z] INFO  18:05:56,955 MicroScheduler - 62062 reads were filtered out during the traversal out of approximately 556448 total reads (11.15%)
[2016-04-15T01:05Z] INFO  18:05:56,955 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:05Z] INFO  18:05:56,955 MicroScheduler -   -> 43103 reads (7.75% of total) failing DuplicateReadFilter
[2016-04-15T01:05Z] INFO  18:05:56,955 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:05Z] INFO  18:05:56,956 MicroScheduler -   -> 18959 reads (3.41% of total) failing HCMappingQualityFilter
[2016-04-15T01:05Z] INFO  18:05:56,956 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:05Z] INFO  18:05:56,956 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:05Z] INFO  18:05:56,957 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:05Z] INFO  18:05:56,957 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T01:05Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T01:05Z] INFO  18:05:57,443 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T01:05Z] INFO  18:05:57,444 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T01:05Z] WARN  18:05:57,713 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T01:05Z] WARN  18:05:57,714 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T01:05Z] WARN  18:05:57,770 ExactAFCalculator - this tool is currently set to genotype at most 6 alternate alleles in a given context, but the context at 19:17397501 has 10 alternate alleles so only the top alleles will be used; see the --max_alternate_alleles argument
[2016-04-15T01:05Z] INFO  18:05:57,811 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.006576796
[2016-04-15T01:05Z] INFO  18:05:57,812 PairHMM - Total compute time in PairHMM computeLikelihoods() : 0.632417491
[2016-04-15T01:05Z] INFO  18:05:57,820 HaplotypeCaller - Ran local assembly on 53 active regions
[2016-04-15T01:05Z] INFO  18:05:57,869 ProgressMeter -            done          75867.0    13.0 s            2.9 m      100.0%    13.0 s       0.0 s
[2016-04-15T01:05Z] INFO  18:05:57,870 ProgressMeter - Total runtime 13.04 secs, 0.22 min, 0.00 hours
[2016-04-15T01:05Z] INFO  18:05:57,871 MicroScheduler - 5254 reads were filtered out during the traversal out of approximately 17757 total reads (29.59%)
[2016-04-15T01:05Z] INFO  18:05:57,871 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:05Z] INFO  18:05:57,872 MicroScheduler -   -> 1209 reads (6.81% of total) failing DuplicateReadFilter
[2016-04-15T01:05Z] INFO  18:05:57,872 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:05Z] INFO  18:05:57,873 MicroScheduler -   -> 4045 reads (22.78% of total) failing HCMappingQualityFilter
[2016-04-15T01:05Z] INFO  18:05:57,874 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:05Z] INFO  18:05:57,874 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:05Z] INFO  18:05:57,875 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:05Z] INFO  18:05:57,876 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T01:05Z] INFO  18:05:58,472 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:05Z] GATK: HaplotypeCaller
[2016-04-15T01:05Z] INFO  18:05:59,246 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:05Z] GATK: HaplotypeCaller
[2016-04-15T01:06Z] INFO  18:06:00,825 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.023322613000000002
[2016-04-15T01:06Z] INFO  18:06:00,837 PairHMM - Total compute time in PairHMM computeLikelihoods() : 8.708248647000001
[2016-04-15T01:06Z] INFO  18:06:00,838 HaplotypeCaller - Ran local assembly on 2544 active regions
[2016-04-15T01:06Z] INFO  18:06:00,888 ProgressMeter -            done     2.67239453E8    89.0 s            0.0 s      100.0%    89.0 s       0.0 s
[2016-04-15T01:06Z] INFO  18:06:00,889 ProgressMeter - Total runtime 89.25 secs, 1.49 min, 0.02 hours
[2016-04-15T01:06Z] INFO  18:06:00,889 MicroScheduler - 50133 reads were filtered out during the traversal out of approximately 586591 total reads (8.55%)
[2016-04-15T01:06Z] INFO  18:06:00,889 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:06Z] INFO  18:06:00,890 MicroScheduler -   -> 46799 reads (7.98% of total) failing DuplicateReadFilter
[2016-04-15T01:06Z] INFO  18:06:00,891 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:06Z] INFO  18:06:00,891 MicroScheduler -   -> 3334 reads (0.57% of total) failing HCMappingQualityFilter
[2016-04-15T01:06Z] INFO  18:06:00,891 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:06Z] INFO  18:06:00,891 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:06Z] INFO  18:06:00,892 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:06Z] INFO  18:06:00,892 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T01:06Z] INFO  18:06:01,454 ProgressMeter -     19:35617776      1.1893791E7    30.0 s            2.0 s       12.0%     4.2 m       3.7 m
[2016-04-15T01:06Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T01:06Z] INFO  18:06:01,497 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T01:06Z] INFO  18:06:01,498 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T01:06Z] WARN  18:06:01,824 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T01:06Z] WARN  18:06:01,825 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T01:06Z] INFO  18:06:02,353 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:06Z] INFO  18:06:02,356 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:06Z] INFO  18:06:02,357 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:06Z] INFO  18:06:02,357 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:06Z] INFO  18:06:02,362 ProgressMeter -     19:48305908        9110148.0    30.0 s            3.0 s       10.0%     5.0 m       4.5 m
[2016-04-15T01:06Z] INFO  18:06:02,362 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/22/R14-18105_kapa-NGv3-PE100-NGv3-sort-22_0_16258303-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/22/R14-18105_kapa-NGv3-PE100-NGv3-22_0_16258303-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/22/tx/tmpFbe91z/R14-18105_kapa-NGv3-PE100-NGv3-22_0_16258303.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:06Z] INFO  18:06:02,401 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:06Z] INFO  18:06:02,401 HelpFormatter - Date/Time: 2016/04/14 18:06:02
[2016-04-15T01:06Z] INFO  18:06:02,402 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:06Z] INFO  18:06:02,406 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:06Z] INFO  18:06:02,407 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:06Z] INFO  18:06:02,420 ProgressMeter -      20:2637047        6213398.0    30.0 s            4.0 s       29.1%   103.0 s      73.0 s
[2016-04-15T01:06Z] WARN  18:06:02,458 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T01:06Z] WARN  18:06:02,461 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/22/tx/tmpFbe91z/R14-18105_kapa-NGv3-PE100-NGv3-22_0_16258303.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T01:06Z] INFO  18:06:02,715 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:06Z] INFO  18:06:02,765 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:06Z] INFO  18:06:02,768 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:06Z] INFO  18:06:02,769 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:06Z] INFO  18:06:02,770 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:06Z] INFO  18:06:02,774 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/22/R14-18105_kapa-NGv3-PE100-NGv3-sort-22_16266928_31795711-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/22/R14-18105_kapa-NGv3-PE100-NGv3-22_16266928_31795711-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/22/tx/tmp5RQlco/R14-18105_kapa-NGv3-PE100-NGv3-22_16266928_31795711.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:06Z] INFO  18:06:02,797 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:06Z] GATK: HaplotypeCaller
[2016-04-15T01:06Z] INFO  18:06:02,803 HelpFormatter - Date/Time: 2016/04/14 18:06:02
[2016-04-15T01:06Z] INFO  18:06:02,804 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:06Z] INFO  18:06:02,804 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:06Z] WARN  18:06:02,828 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T01:06Z] WARN  18:06:02,831 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/22/tx/tmp5RQlco/R14-18105_kapa-NGv3-PE100-NGv3-22_16266928_31795711.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T01:06Z] INFO  18:06:02,891 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T01:06Z] INFO  18:06:02,914 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:06Z] INFO  18:06:02,990 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-15T01:06Z] INFO  18:06:03,007 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T01:06Z] INFO  18:06:03,055 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:06Z] INFO  18:06:03,240 ProgressMeter -     20:24959403      1.8004836E7    30.0 s            1.0 s       56.8%    52.0 s      22.0 s
[2016-04-15T01:06Z] INFO  18:06:03,276 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T01:06Z] INFO  18:06:03,285 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:06Z] INFO  18:06:03,360 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-15T01:06Z] INFO  18:06:03,366 IntervalUtils - Processing 118 bp from intervals
[2016-04-15T01:06Z] WARN  18:06:03,371 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:06Z] INFO  18:06:03,399 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T01:06Z] INFO  18:06:03,520 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:06Z] INFO  18:06:03,570 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:06Z] INFO  18:06:03,571 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:06Z] INFO  18:06:03,572 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T01:06Z] INFO  18:06:03,572 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T01:06Z] INFO  18:06:03,587 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T01:06Z] INFO  18:06:03,588 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T01:06Z] INFO  18:06:03,795 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T01:06Z] INFO  18:06:03,925 IntervalUtils - Processing 372769 bp from intervals
[2016-04-15T01:06Z] WARN  18:06:03,931 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:06Z] INFO  18:06:04,091 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:06Z] INFO  18:06:04,239 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:06Z] INFO  18:06:04,239 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:06Z] INFO  18:06:04,239 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T01:06Z] INFO  18:06:04,240 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T01:06Z] INFO  18:06:04,250 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T01:06Z] INFO  18:06:04,251 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T01:06Z] INFO  18:06:04,425 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T01:06Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T01:06Z] INFO  18:06:04,980 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T01:06Z] INFO  18:06:04,980 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T01:06Z] INFO  18:06:04,981 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.0
[2016-04-15T01:06Z] INFO  18:06:04,982 PairHMM - Total compute time in PairHMM computeLikelihoods() : 0.0
[2016-04-15T01:06Z] INFO  18:06:04,982 HaplotypeCaller - Ran local assembly on 1 active regions
[2016-04-15T01:06Z] INFO  18:06:05,027 ProgressMeter -            done            118.0     1.0 s            3.4 h       99.2%     1.0 s       0.0 s
[2016-04-15T01:06Z] INFO  18:06:05,028 ProgressMeter - Total runtime 1.46 secs, 0.02 min, 0.00 hours
[2016-04-15T01:06Z] INFO  18:06:05,036 MicroScheduler - 228 reads were filtered out during the traversal out of approximately 231 total reads (98.70%)
[2016-04-15T01:06Z] INFO  18:06:05,036 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:06Z] INFO  18:06:05,037 MicroScheduler -   -> 0 reads (0.00% of total) failing DuplicateReadFilter
[2016-04-15T01:06Z] INFO  18:06:05,037 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:06Z] INFO  18:06:05,037 MicroScheduler -   -> 228 reads (98.70% of total) failing HCMappingQualityFilter
[2016-04-15T01:06Z] INFO  18:06:05,038 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:06Z] INFO  18:06:05,038 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:06Z] INFO  18:06:05,038 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:06Z] INFO  18:06:05,038 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T01:06Z] INFO  18:06:05,744 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:06Z] INFO  18:06:05,747 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:06Z] INFO  18:06:05,748 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:06Z] INFO  18:06:05,748 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:06Z] INFO  18:06:05,753 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/22/R14-18105_kapa-NGv3-PE100-NGv3-sort-22_31796605_47308085-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/22/R14-18105_kapa-NGv3-PE100-NGv3-22_31796605_47308085-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/22/tx/tmpjClBHX/R14-18105_kapa-NGv3-PE100-NGv3-22_31796605_47308085.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:06Z] INFO  18:06:05,768 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:06Z] INFO  18:06:05,768 HelpFormatter - Date/Time: 2016/04/14 18:06:05
[2016-04-15T01:06Z] INFO  18:06:05,768 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:06Z] INFO  18:06:05,769 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:06Z] WARN  18:06:05,830 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T01:06Z] WARN  18:06:05,833 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/22/tx/tmpjClBHX/R14-18105_kapa-NGv3-PE100-NGv3-22_31796605_47308085.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T01:06Z] INFO  18:06:06,104 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:06Z] INFO  18:06:06,314 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T01:06Z] INFO  18:06:06,324 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:06Z] INFO  18:06:06,415 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.09
[2016-04-15T01:06Z] INFO  18:06:06,443 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T01:06Z] INFO  18:06:06,592 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:06Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T01:06Z] INFO  18:06:06,808 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T01:06Z] INFO  18:06:06,808 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T01:06Z] INFO  18:06:06,862 IntervalUtils - Processing 366557 bp from intervals
[2016-04-15T01:06Z] WARN  18:06:06,869 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:06Z] GATK: HaplotypeCaller
[2016-04-15T01:06Z] INFO  18:06:07,026 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:06Z] WARN  18:06:07,070 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T01:06Z] WARN  18:06:07,071 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T01:06Z] INFO  18:06:07,230 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:06Z] INFO  18:06:07,231 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:06Z] INFO  18:06:07,232 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T01:06Z] INFO  18:06:07,232 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T01:06Z] INFO  18:06:07,233 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T01:06Z] INFO  18:06:07,233 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T01:06Z] INFO  18:06:07,486 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T01:06Z] INFO  18:06:09,114 ProgressMeter -     20:35128602       2.762943E7    30.0 s            1.0 s       33.7%    89.0 s      59.0 s
[2016-04-15T01:06Z] INFO  18:06:09,785 ProgressMeter -     20:55803477      1.6851644E7    30.0 s            1.0 s       34.0%    88.0 s      58.0 s
[2016-04-15T01:06Z] INFO  18:06:10,047 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:06Z] INFO  18:06:10,055 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:06Z] INFO  18:06:10,056 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:06Z] INFO  18:06:10,056 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:06Z] INFO  18:06:10,070 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/22/R14-18105_kapa-NGv3-PE100-NGv3-sort-22_47309229_51304566-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/22/R14-18105_kapa-NGv3-PE100-NGv3-22_47309229_51304566-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/22/tx/tmptQUYOT/R14-18105_kapa-NGv3-PE100-NGv3-22_47309229_51304566.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:06Z] INFO  18:06:10,093 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:06Z] INFO  18:06:10,094 HelpFormatter - Date/Time: 2016/04/14 18:06:10
[2016-04-15T01:06Z] INFO  18:06:10,095 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:06Z] INFO  18:06:10,096 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:06Z] WARN  18:06:10,118 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T01:06Z] WARN  18:06:10,121 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/22/tx/tmptQUYOT/R14-18105_kapa-NGv3-PE100-NGv3-22_47309229_51304566.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T01:06Z] INFO  18:06:10,314 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:06Z] INFO  18:06:10,609 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T01:06Z] INFO  18:06:10,639 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:06Z] INFO  18:06:10,746 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.11
[2016-04-15T01:06Z] INFO  18:06:10,757 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T01:06Z] INFO  18:06:11,103 IntervalUtils - Processing 81362 bp from intervals
[2016-04-15T01:06Z] WARN  18:06:11,108 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:06Z] INFO  18:06:11,229 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:06Z] INFO  18:06:11,319 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:06Z] INFO  18:06:11,320 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:06Z] INFO  18:06:11,320 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T01:06Z] INFO  18:06:11,321 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T01:06Z] INFO  18:06:11,338 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T01:06Z] INFO  18:06:11,339 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T01:06Z] INFO  18:06:11,542 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T01:06Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T01:06Z] INFO  18:06:11,665 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T01:06Z] INFO  18:06:11,666 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T01:06Z] WARN  18:06:11,915 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T01:06Z] WARN  18:06:11,915 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T01:06Z] INFO  18:06:17,182 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.020806459000000003
[2016-04-15T01:06Z] INFO  18:06:17,183 PairHMM - Total compute time in PairHMM computeLikelihoods() : 0.662852086
[2016-04-15T01:06Z] INFO  18:06:17,183 HaplotypeCaller - Ran local assembly on 1128 active regions
[2016-04-15T01:06Z] INFO  18:06:17,227 ProgressMeter -            done      5.5115211E7    44.0 s            0.0 s      100.0%    44.0 s       0.0 s
[2016-04-15T01:06Z] INFO  18:06:17,227 ProgressMeter - Total runtime 44.00 secs, 0.73 min, 0.01 hours
[2016-04-15T01:06Z] INFO  18:06:17,228 MicroScheduler - 19521 reads were filtered out during the traversal out of approximately 237335 total reads (8.23%)
[2016-04-15T01:06Z] INFO  18:06:17,228 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:06Z] INFO  18:06:17,229 MicroScheduler -   -> 18730 reads (7.89% of total) failing DuplicateReadFilter
[2016-04-15T01:06Z] INFO  18:06:17,229 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:06Z] INFO  18:06:17,229 MicroScheduler -   -> 791 reads (0.33% of total) failing HCMappingQualityFilter
[2016-04-15T01:06Z] INFO  18:06:17,230 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:06Z] INFO  18:06:17,230 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:06Z] INFO  18:06:17,230 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:06Z] INFO  18:06:17,230 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T01:06Z] INFO  18:06:17,269 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.005082945
[2016-04-15T01:06Z] INFO  18:06:17,270 PairHMM - Total compute time in PairHMM computeLikelihoods() : 0.18102289600000002
[2016-04-15T01:06Z] INFO  18:06:17,270 HaplotypeCaller - Ran local assembly on 425 active regions
[2016-04-15T01:06Z] INFO  18:06:17,316 ProgressMeter -            done        8975092.0    24.0 s            2.0 s      100.0%    24.0 s       0.0 s
[2016-04-15T01:06Z] INFO  18:06:17,317 ProgressMeter - Total runtime 24.89 secs, 0.41 min, 0.01 hours
[2016-04-15T01:06Z] INFO  18:06:17,317 MicroScheduler - 5703 reads were filtered out during the traversal out of approximately 69086 total reads (8.25%)
[2016-04-15T01:06Z] INFO  18:06:17,318 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:06Z] INFO  18:06:17,318 MicroScheduler -   -> 5401 reads (7.82% of total) failing DuplicateReadFilter
[2016-04-15T01:06Z] INFO  18:06:17,318 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:06Z] INFO  18:06:17,319 MicroScheduler -   -> 302 reads (0.44% of total) failing HCMappingQualityFilter
[2016-04-15T01:06Z] INFO  18:06:17,319 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:06Z] INFO  18:06:17,319 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:06Z] INFO  18:06:17,319 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:06Z] INFO  18:06:17,320 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T01:06Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T01:06Z] INFO  18:06:18,260 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T01:06Z] INFO  18:06:18,260 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T01:06Z] WARN  18:06:18,517 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T01:06Z] WARN  18:06:18,518 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T01:06Z] INFO  18:06:18,595 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:06Z] INFO  18:06:18,623 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:06Z] GATK: HaplotypeCaller
[2016-04-15T01:06Z] GATK: HaplotypeCaller
[2016-04-15T01:06Z] INFO  18:06:19,364 ProgressMeter -     17:15498013     5.11279245E8   120.0 s            0.0 s       99.8%   120.0 s       0.0 s
[2016-04-15T01:06Z] INFO  18:06:19,669 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.0333144
[2016-04-15T01:06Z] INFO  18:06:19,671 PairHMM - Total compute time in PairHMM computeLikelihoods() : 4.307893340000001
[2016-04-15T01:06Z] INFO  18:06:19,671 HaplotypeCaller - Ran local assembly on 3762 active regions
[2016-04-15T01:06Z] INFO  18:06:19,707 ProgressMeter -            done      5.1376592E8   120.0 s            0.0 s      100.0%   120.0 s       0.0 s
[2016-04-15T01:06Z] INFO  18:06:19,708 ProgressMeter - Total runtime 120.39 secs, 2.01 min, 0.03 hours
[2016-04-15T01:06Z] INFO  18:06:19,709 MicroScheduler - 79981 reads were filtered out during the traversal out of approximately 890428 total reads (8.98%)
[2016-04-15T01:06Z] INFO  18:06:19,709 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:06Z] INFO  18:06:19,710 MicroScheduler -   -> 70245 reads (7.89% of total) failing DuplicateReadFilter
[2016-04-15T01:06Z] INFO  18:06:19,711 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:06Z] INFO  18:06:19,711 MicroScheduler -   -> 9736 reads (1.09% of total) failing HCMappingQualityFilter
[2016-04-15T01:06Z] INFO  18:06:19,712 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:06Z] INFO  18:06:19,713 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:06Z] INFO  18:06:19,713 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:06Z] INFO  18:06:19,714 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T01:06Z] INFO  18:06:21,120 ProgressMeter -     17:43922974     4.87893068E8   120.0 s            0.0 s       88.3%     2.3 m      15.0 s
[2016-04-15T01:06Z] INFO  18:06:21,315 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:06Z] GATK: HaplotypeCaller
[2016-04-15T01:06Z] INFO  18:06:21,682 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:06Z] INFO  18:06:21,684 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:06Z] INFO  18:06:21,684 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:06Z] INFO  18:06:21,685 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:06Z] INFO  18:06:21,689 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/X/R14-18105_kapa-NGv3-PE100-NGv3-sort-X_0_15509380-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/X/R14-18105_kapa-NGv3-PE100-NGv3-X_0_15509380-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/X/tx/tmpctHIY3/R14-18105_kapa-NGv3-PE100-NGv3-X_0_15509380.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:06Z] INFO  18:06:21,711 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:06Z] INFO  18:06:21,712 HelpFormatter - Date/Time: 2016/04/14 18:06:21
[2016-04-15T01:06Z] INFO  18:06:21,713 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:06Z] INFO  18:06:21,714 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:06Z] WARN  18:06:21,763 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T01:06Z] WARN  18:06:21,766 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/X/tx/tmpctHIY3/R14-18105_kapa-NGv3-PE100-NGv3-X_0_15509380.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T01:06Z] INFO  18:06:21,896 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:06Z] INFO  18:06:21,899 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:06Z] INFO  18:06:21,900 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:06Z] INFO  18:06:21,900 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:06Z] INFO  18:06:21,905 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/X/R14-18105_kapa-NGv3-PE100-NGv3-sort-X_15518899_31090070-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/X/R14-18105_kapa-NGv3-PE100-NGv3-X_15518899_31090070-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/X/tx/tmpzX76ug/R14-18105_kapa-NGv3-PE100-NGv3-X_15518899_31090070.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:06Z] INFO  18:06:21,930 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:06Z] INFO  18:06:21,931 HelpFormatter - Date/Time: 2016/04/14 18:06:21
[2016-04-15T01:06Z] INFO  18:06:21,932 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:06Z] INFO  18:06:21,933 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:06Z] WARN  18:06:21,976 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T01:06Z] WARN  18:06:21,980 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/X/tx/tmpzX76ug/R14-18105_kapa-NGv3-PE100-NGv3-X_15518899_31090070.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T01:06Z] INFO  18:06:22,014 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:06Z] INFO  18:06:22,204 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:06Z] INFO  18:06:22,249 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T01:06Z] INFO  18:06:22,260 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:06Z] INFO  18:06:22,373 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.10
[2016-04-15T01:06Z] INFO  18:06:22,398 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T01:06Z] INFO  18:06:22,473 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T01:06Z] INFO  18:06:22,496 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:06Z] INFO  18:06:22,598 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.10
[2016-04-15T01:06Z] INFO  18:06:22,637 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T01:06Z] INFO  18:06:22,680 ProgressMeter -     21:36260889      1.7229002E7    30.0 s            1.0 s       34.4%    87.0 s      57.0 s
[2016-04-15T01:06Z] INFO  18:06:22,758 IntervalUtils - Processing 114122 bp from intervals
[2016-04-15T01:06Z] INFO  18:06:22,761 ProgressMeter -      19:3492445      7.1720785E7    60.0 s            0.0 s       23.8%     4.2 m       3.2 m
[2016-04-15T01:06Z] WARN  18:06:22,763 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:06Z] INFO  18:06:22,850 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:06Z] INFO  18:06:22,949 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:06Z] INFO  18:06:22,949 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:06Z] INFO  18:06:22,950 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T01:06Z] INFO  18:06:22,950 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T01:06Z] INFO  18:06:22,952 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T01:06Z] INFO  18:06:22,953 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T01:06Z] INFO  18:06:22,983 IntervalUtils - Processing 133046 bp from intervals
[2016-04-15T01:06Z] WARN  18:06:22,988 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:06Z] INFO  18:06:23,093 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:06Z] INFO  18:06:23,151 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T01:06Z] INFO  18:06:23,215 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:06Z] INFO  18:06:23,215 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:06Z] INFO  18:06:23,216 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T01:06Z] INFO  18:06:23,216 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T01:06Z] INFO  18:06:23,225 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T01:06Z] INFO  18:06:23,226 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T01:06Z] INFO  18:06:23,311 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.01047755
[2016-04-15T01:06Z] INFO  18:06:23,312 PairHMM - Total compute time in PairHMM computeLikelihoods() : 0.617754639
[2016-04-15T01:06Z] INFO  18:06:23,313 HaplotypeCaller - Ran local assembly on 488 active regions
[2016-04-15T01:06Z] INFO  18:06:23,362 ProgressMeter -            done        9449583.0    26.0 s            2.0 s      100.0%    26.0 s       0.0 s
[2016-04-15T01:06Z] INFO  18:06:23,363 ProgressMeter - Total runtime 26.81 secs, 0.45 min, 0.01 hours
[2016-04-15T01:06Z] INFO  18:06:23,364 MicroScheduler - 9011 reads were filtered out during the traversal out of approximately 111436 total reads (8.09%)
[2016-04-15T01:06Z] INFO  18:06:23,365 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:06Z] INFO  18:06:23,366 MicroScheduler -   -> 8829 reads (7.92% of total) failing DuplicateReadFilter
[2016-04-15T01:06Z] INFO  18:06:23,366 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:06Z] INFO  18:06:23,367 MicroScheduler -   -> 182 reads (0.16% of total) failing HCMappingQualityFilter
[2016-04-15T01:06Z] INFO  18:06:23,367 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:06Z] INFO  18:06:23,368 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:06Z] INFO  18:06:23,368 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:06Z] INFO  18:06:23,368 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T01:06Z] INFO  18:06:23,407 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T01:06Z] INFO  18:06:24,686 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:06Z] INFO  18:06:24,689 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:06Z] INFO  18:06:24,690 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:06Z] INFO  18:06:24,690 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:06Z] INFO  18:06:24,695 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/X/R14-18105_kapa-NGv3-PE100-NGv3-sort-X_31139949_46696637-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/X/R14-18105_kapa-NGv3-PE100-NGv3-X_31139949_46696637-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/X/tx/tmppxxDmz/R14-18105_kapa-NGv3-PE100-NGv3-X_31139949_46696637.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:06Z] INFO  18:06:24,717 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:06Z] INFO  18:06:24,718 HelpFormatter - Date/Time: 2016/04/14 18:06:24
[2016-04-15T01:06Z] INFO  18:06:24,718 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:06Z] INFO  18:06:24,719 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:06Z] WARN  18:06:24,759 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T01:06Z] WARN  18:06:24,778 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/X/tx/tmppxxDmz/R14-18105_kapa-NGv3-PE100-NGv3-X_31139949_46696637.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T01:06Z] INFO  18:06:24,936 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:06Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T01:06Z] INFO  18:06:24,976 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:06Z] INFO  18:06:24,981 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T01:06Z] INFO  18:06:24,982 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T01:06Z] INFO  18:06:25,149 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T01:06Z] INFO  18:06:25,174 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:06Z] INFO  18:06:25,248 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-15T01:06Z] GATK: HaplotypeCaller
[2016-04-15T01:06Z] INFO  18:06:25,270 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T01:06Z] WARN  18:06:25,411 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T01:06Z] WARN  18:06:25,412 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T01:06Z] INFO  18:06:25,647 IntervalUtils - Processing 99894 bp from intervals
[2016-04-15T01:06Z] WARN  18:06:25,652 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:06Z] INFO  18:06:25,745 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:06Z] INFO  18:06:25,831 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:06Z] INFO  18:06:25,831 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:06Z] INFO  18:06:25,832 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T01:06Z] INFO  18:06:25,832 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T01:06Z] INFO  18:06:25,844 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T01:06Z] INFO  18:06:25,844 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T01:06Z] INFO  18:06:26,047 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T01:06Z] INFO  18:06:26,721 ProgressMeter -     19:20117446     1.10320723E8    60.0 s            0.0 s       75.0%    80.0 s      20.0 s
[2016-04-15T01:06Z] INFO  18:06:28,366 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:06Z] INFO  18:06:28,370 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:06Z] INFO  18:06:28,371 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:06Z] INFO  18:06:28,372 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:06Z] INFO  18:06:28,377 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/X/R14-18105_kapa-NGv3-PE100-NGv3-sort-X_46712910_62570698-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/X/R14-18105_kapa-NGv3-PE100-NGv3-X_46712910_62570698-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/X/tx/tmpelSw_o/R14-18105_kapa-NGv3-PE100-NGv3-X_46712910_62570698.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:06Z] INFO  18:06:28,393 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:06Z] INFO  18:06:28,395 HelpFormatter - Date/Time: 2016/04/14 18:06:28
[2016-04-15T01:06Z] INFO  18:06:28,395 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:06Z] INFO  18:06:28,396 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:06Z] WARN  18:06:28,450 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T01:06Z] WARN  18:06:28,452 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/X/tx/tmpelSw_o/R14-18105_kapa-NGv3-PE100-NGv3-X_46712910_62570698.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T01:06Z] INFO  18:06:28,712 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:06Z] INFO  18:06:28,923 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T01:06Z] INFO  18:06:28,937 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:06Z] INFO  18:06:28,994 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-15T01:06Z] INFO  18:06:29,024 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T01:06Z] INFO  18:06:29,546 IntervalUtils - Processing 228299 bp from intervals
[2016-04-15T01:06Z] WARN  18:06:29,551 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:06Z] INFO  18:06:29,655 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:06Z] INFO  18:06:29,763 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:06Z] INFO  18:06:29,764 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:06Z] INFO  18:06:29,765 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T01:06Z] INFO  18:06:29,765 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T01:06Z] INFO  18:06:29,766 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T01:06Z] INFO  18:06:29,766 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T01:06Z] INFO  18:06:29,997 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T01:06Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T01:06Z] INFO  18:06:30,631 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T01:06Z] INFO  18:06:30,631 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T01:06Z] WARN  18:06:30,855 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T01:06Z] WARN  18:06:30,856 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T01:06Z] INFO  18:06:30,953 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.013577553000000001
[2016-04-15T01:06Z] INFO  18:06:30,954 PairHMM - Total compute time in PairHMM computeLikelihoods() : 5.742575639
[2016-04-15T01:06Z] INFO  18:06:30,954 HaplotypeCaller - Ran local assembly on 1348 active regions
[2016-04-15T01:06Z] INFO  18:06:31,016 ProgressMeter -            done      8.3134367E7    58.0 s            0.0 s      100.0%    58.0 s       0.0 s
[2016-04-15T01:06Z] INFO  18:06:31,017 ProgressMeter - Total runtime 58.63 secs, 0.98 min, 0.02 hours
[2016-04-15T01:06Z] INFO  18:06:31,018 MicroScheduler - 24787 reads were filtered out during the traversal out of approximately 293884 total reads (8.43%)
[2016-04-15T01:06Z] INFO  18:06:31,019 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:06Z] INFO  18:06:31,019 MicroScheduler -   -> 23749 reads (8.08% of total) failing DuplicateReadFilter
[2016-04-15T01:06Z] INFO  18:06:31,020 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:06Z] INFO  18:06:31,021 MicroScheduler -   -> 1038 reads (0.35% of total) failing HCMappingQualityFilter
[2016-04-15T01:06Z] INFO  18:06:31,021 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:06Z] INFO  18:06:31,022 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:06Z] INFO  18:06:31,022 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:06Z] INFO  18:06:31,023 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T01:06Z] INFO  18:06:31,455 ProgressMeter -     19:38260645      6.8340715E7    60.0 s            0.0 s       33.2%     3.0 m     120.0 s
[2016-04-15T01:06Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T01:06Z] INFO  18:06:31,934 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T01:06Z] INFO  18:06:31,935 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T01:06Z] WARN  18:06:32,194 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T01:06Z] WARN  18:06:32,202 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T01:06Z] INFO  18:06:32,364 ProgressMeter -     19:49995067      7.2269505E7    60.0 s            0.0 s       25.6%     3.9 m       2.9 m
[2016-04-15T01:06Z] INFO  18:06:32,564 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:06Z] GATK: HaplotypeCaller
[2016-04-15T01:06Z] INFO  18:06:34,268 ProgressMeter -     22:20132752      1.9518184E7    30.0 s            1.0 s       25.6%   117.0 s      87.0 s
[2016-04-15T01:06Z] INFO  18:06:35,913 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.039389060000000004
[2016-04-15T01:06Z] INFO  18:06:35,913 PairHMM - Total compute time in PairHMM computeLikelihoods() : 5.955498712000001
[2016-04-15T01:06Z] INFO  18:06:35,914 HaplotypeCaller - Ran local assembly on 3957 active regions
[2016-04-15T01:06Z] INFO  18:06:35,958 ProgressMeter -            done     6.43955503E8     2.2 m            0.0 s      100.0%     2.2 m       0.0 s
[2016-04-15T01:06Z] INFO  18:06:35,959 ProgressMeter - Total runtime 134.85 secs, 2.25 min, 0.04 hours
[2016-04-15T01:06Z] INFO  18:06:35,967 MicroScheduler - 202752 reads were filtered out during the traversal out of approximately 1056456 total reads (19.19%)
[2016-04-15T01:06Z] INFO  18:06:35,967 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:06Z] INFO  18:06:35,967 MicroScheduler -   -> 75890 reads (7.18% of total) failing DuplicateReadFilter
[2016-04-15T01:06Z] INFO  18:06:35,968 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:06Z] INFO  18:06:35,968 MicroScheduler -   -> 126862 reads (12.01% of total) failing HCMappingQualityFilter
[2016-04-15T01:06Z] INFO  18:06:35,968 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:06Z] INFO  18:06:35,969 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:06Z] INFO  18:06:35,969 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:06Z] INFO  18:06:35,969 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T01:06Z] INFO  18:06:35,992 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:06Z] INFO  18:06:35,994 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:06Z] INFO  18:06:35,995 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:06Z] INFO  18:06:35,995 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:06Z] INFO  18:06:36,012 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/X/R14-18105_kapa-NGv3-PE100-NGv3-sort-X_62857907_78427545-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/X/R14-18105_kapa-NGv3-PE100-NGv3-X_62857907_78427545-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/X/tx/tmpFz8rOy/R14-18105_kapa-NGv3-PE100-NGv3-X_62857907_78427545.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:06Z] INFO  18:06:36,029 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:06Z] INFO  18:06:36,029 HelpFormatter - Date/Time: 2016/04/14 18:06:35
[2016-04-15T01:06Z] INFO  18:06:36,029 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:06Z] INFO  18:06:36,030 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:06Z] WARN  18:06:36,070 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T01:06Z] WARN  18:06:36,084 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/X/tx/tmpFz8rOy/R14-18105_kapa-NGv3-PE100-NGv3-X_62857907_78427545.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T01:06Z] INFO  18:06:36,316 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:06Z] INFO  18:06:36,525 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T01:06Z] INFO  18:06:36,546 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:06Z] INFO  18:06:36,625 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-15T01:06Z] INFO  18:06:36,646 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T01:06Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T01:06Z] INFO  18:06:36,700 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T01:06Z] INFO  18:06:36,701 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T01:06Z] WARN  18:06:37,030 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T01:06Z] WARN  18:06:37,035 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T01:06Z] INFO  18:06:37,190 IntervalUtils - Processing 175038 bp from intervals
[2016-04-15T01:06Z] WARN  18:06:37,227 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:06Z] INFO  18:06:37,260 ProgressMeter -     22:37622713      2.0927487E7    30.0 s            1.0 s       24.8%     2.0 m      91.0 s
[2016-04-15T01:06Z] INFO  18:06:37,358 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:06Z] INFO  18:06:37,426 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:06Z] INFO  18:06:37,512 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:06Z] INFO  18:06:37,513 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:06Z] INFO  18:06:37,514 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T01:06Z] INFO  18:06:37,515 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T01:06Z] INFO  18:06:37,516 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T01:06Z] INFO  18:06:37,516 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T01:06Z] GATK: HaplotypeCaller
[2016-04-15T01:06Z] INFO  18:06:37,840 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T01:06Z] INFO  18:06:39,115 ProgressMeter -     20:44258453     1.63207279E8    60.0 s            0.0 s       80.4%    74.0 s      14.0 s
[2016-04-15T01:06Z] INFO  18:06:39,792 ProgressMeter -     20:62172544     1.09539962E8    60.0 s            0.0 s       83.6%    71.0 s      11.0 s
[2016-04-15T01:06Z] INFO  18:06:40,664 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:06Z] INFO  18:06:40,667 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:06Z] INFO  18:06:40,667 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:06Z] INFO  18:06:40,667 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:06Z] INFO  18:06:40,671 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/X/R14-18105_kapa-NGv3-PE100-NGv3-sort-X_78616585_95940189-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/X/R14-18105_kapa-NGv3-PE100-NGv3-X_78616585_95940189-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/X/tx/tmpNnDzyj/R14-18105_kapa-NGv3-PE100-NGv3-X_78616585_95940189.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:06Z] INFO  18:06:40,693 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:06Z] INFO  18:06:40,693 HelpFormatter - Date/Time: 2016/04/14 18:06:40
[2016-04-15T01:06Z] INFO  18:06:40,694 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:06Z] INFO  18:06:40,694 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:06Z] WARN  18:06:40,750 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T01:06Z] WARN  18:06:40,752 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/X/tx/tmpNnDzyj/R14-18105_kapa-NGv3-PE100-NGv3-X_78616585_95940189.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T01:06Z] INFO  18:06:41,020 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:06Z] INFO  18:06:41,257 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T01:06Z] INFO  18:06:41,266 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:06Z] INFO  18:06:41,340 ProgressMeter -     22:51117740        9435315.0    30.0 s            3.0 s       92.1%    32.0 s       2.0 s
[2016-04-15T01:06Z] INFO  18:06:41,342 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-15T01:06Z] INFO  18:06:41,358 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T01:06Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T01:06Z] INFO  18:06:41,642 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T01:06Z] INFO  18:06:41,643 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T01:06Z] INFO  18:06:41,750 IntervalUtils - Processing 45787 bp from intervals
[2016-04-15T01:06Z] WARN  18:06:41,779 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:06Z] INFO  18:06:41,883 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:06Z] INFO  18:06:41,963 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:06Z] INFO  18:06:41,964 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:06Z] INFO  18:06:41,965 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T01:06Z] INFO  18:06:41,966 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T01:06Z] INFO  18:06:41,974 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T01:06Z] INFO  18:06:41,975 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T01:06Z] WARN  18:06:42,139 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T01:06Z] WARN  18:06:42,139 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T01:06Z] INFO  18:06:42,253 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T01:06Z] INFO  18:06:42,740 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.009428274
[2016-04-15T01:06Z] INFO  18:06:42,741 PairHMM - Total compute time in PairHMM computeLikelihoods() : 0.7111283770000001
[2016-04-15T01:06Z] INFO  18:06:42,742 HaplotypeCaller - Ran local assembly on 650 active regions
[2016-04-15T01:06Z] INFO  18:06:42,780 ProgressMeter -            done      1.1546648E7    31.0 s            2.0 s      100.0%    31.0 s       0.0 s
[2016-04-15T01:06Z] INFO  18:06:42,781 ProgressMeter - Total runtime 31.46 secs, 0.52 min, 0.01 hours
[2016-04-15T01:06Z] INFO  18:06:42,782 MicroScheduler - 13563 reads were filtered out during the traversal out of approximately 154129 total reads (8.80%)
[2016-04-15T01:06Z] INFO  18:06:42,782 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:06Z] INFO  18:06:42,783 MicroScheduler -   -> 12352 reads (8.01% of total) failing DuplicateReadFilter
[2016-04-15T01:06Z] INFO  18:06:42,783 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:06Z] INFO  18:06:42,783 MicroScheduler -   -> 1211 reads (0.79% of total) failing HCMappingQualityFilter
[2016-04-15T01:06Z] INFO  18:06:42,784 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:06Z] INFO  18:06:42,784 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:06Z] INFO  18:06:42,784 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:06Z] INFO  18:06:42,785 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T01:06Z] INFO  18:06:44,250 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:06Z] GATK: HaplotypeCaller
[2016-04-15T01:06Z] INFO  18:06:46,083 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.038816621
[2016-04-15T01:06Z] INFO  18:06:46,084 PairHMM - Total compute time in PairHMM computeLikelihoods() : 1.619211801
[2016-04-15T01:06Z] INFO  18:06:46,085 HaplotypeCaller - Ran local assembly on 2104 active regions
[2016-04-15T01:06Z] INFO  18:06:46,130 ProgressMeter -            done     1.55945449E8    79.0 s            0.0 s      100.0%    79.0 s       0.0 s
[2016-04-15T01:06Z] INFO  18:06:46,131 ProgressMeter - Total runtime 79.43 secs, 1.32 min, 0.02 hours
[2016-04-15T01:06Z] INFO  18:06:46,131 MicroScheduler - 50581 reads were filtered out during the traversal out of approximately 549520 total reads (9.20%)
[2016-04-15T01:06Z] INFO  18:06:46,132 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:06Z] INFO  18:06:46,132 MicroScheduler -   -> 44539 reads (8.11% of total) failing DuplicateReadFilter
[2016-04-15T01:06Z] INFO  18:06:46,132 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:06Z] INFO  18:06:46,132 MicroScheduler -   -> 6042 reads (1.10% of total) failing HCMappingQualityFilter
[2016-04-15T01:06Z] INFO  18:06:46,133 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:06Z] INFO  18:06:46,133 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:06Z] INFO  18:06:46,133 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:06Z] INFO  18:06:46,133 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T01:06Z] INFO  18:06:47,443 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:06Z] INFO  18:06:47,447 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:06Z] INFO  18:06:47,447 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:06Z] INFO  18:06:47,448 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:06Z] INFO  18:06:47,453 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/X/R14-18105_kapa-NGv3-PE100-NGv3-sort-X_95990756_111698889-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/X/R14-18105_kapa-NGv3-PE100-NGv3-X_95990756_111698889-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/X/tx/tmpLMxtLJ/R14-18105_kapa-NGv3-PE100-NGv3-X_95990756_111698889.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:06Z] INFO  18:06:47,454 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:06Z] INFO  18:06:47,463 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:06Z] INFO  18:06:47,464 HelpFormatter - Date/Time: 2016/04/14 18:06:47
[2016-04-15T01:06Z] INFO  18:06:47,464 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:06Z] INFO  18:06:47,464 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:06Z] WARN  18:06:47,507 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T01:06Z] WARN  18:06:47,510 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/X/tx/tmpLMxtLJ/R14-18105_kapa-NGv3-PE100-NGv3-X_95990756_111698889.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T01:06Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T01:06Z] INFO  18:06:47,536 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T01:06Z] INFO  18:06:47,537 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T01:06Z] INFO  18:06:47,671 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:06Z] GATK: HaplotypeCaller
[2016-04-15T01:06Z] WARN  18:06:47,725 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T01:06Z] WARN  18:06:47,726 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T01:06Z] INFO  18:06:47,857 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T01:06Z] INFO  18:06:47,877 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:06Z] INFO  18:06:47,956 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-15T01:06Z] INFO  18:06:47,972 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T01:06Z] INFO  18:06:48,346 IntervalUtils - Processing 181656 bp from intervals
[2016-04-15T01:06Z] WARN  18:06:48,354 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:06Z] INFO  18:06:48,450 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:06Z] INFO  18:06:48,533 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:06Z] INFO  18:06:48,534 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:06Z] INFO  18:06:48,535 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T01:06Z] INFO  18:06:48,536 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T01:06Z] INFO  18:06:48,536 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T01:06Z] INFO  18:06:48,536 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T01:06Z] INFO  18:06:48,737 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T01:06Z] INFO  18:06:49,589 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.019245683
[2016-04-15T01:06Z] INFO  18:06:49,590 PairHMM - Total compute time in PairHMM computeLikelihoods() : 1.2162019210000001
[2016-04-15T01:06Z] INFO  18:06:49,590 HaplotypeCaller - Ran local assembly on 1957 active regions
[2016-04-15T01:06Z] INFO  18:06:49,625 ProgressMeter -            done      1.4684951E8    69.0 s            0.0 s      100.0%    69.0 s       0.0 s
[2016-04-15T01:06Z] INFO  18:06:49,627 ProgressMeter - Total runtime 69.89 secs, 1.16 min, 0.02 hours
[2016-04-15T01:06Z] INFO  18:06:49,627 MicroScheduler - 38023 reads were filtered out during the traversal out of approximately 458115 total reads (8.30%)
[2016-04-15T01:06Z] INFO  18:06:49,628 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:06Z] INFO  18:06:49,629 MicroScheduler -   -> 37030 reads (8.08% of total) failing DuplicateReadFilter
[2016-04-15T01:06Z] INFO  18:06:49,629 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:06Z] INFO  18:06:49,630 MicroScheduler -   -> 993 reads (0.22% of total) failing HCMappingQualityFilter
[2016-04-15T01:06Z] INFO  18:06:49,630 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:06Z] INFO  18:06:49,631 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:06Z] INFO  18:06:49,632 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:06Z] INFO  18:06:49,632 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T01:06Z] INFO  18:06:50,181 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.0030647720000000003
[2016-04-15T01:06Z] INFO  18:06:50,182 PairHMM - Total compute time in PairHMM computeLikelihoods() : 0.064718628
[2016-04-15T01:06Z] INFO  18:06:50,183 HaplotypeCaller - Ran local assembly on 647 active regions
[2016-04-15T01:06Z] INFO  18:06:50,230 ProgressMeter -            done      2.4524947E7    24.0 s            0.0 s      100.0%    24.0 s       0.0 s
[2016-04-15T01:06Z] INFO  18:06:50,231 ProgressMeter - Total runtime 24.40 secs, 0.41 min, 0.01 hours
[2016-04-15T01:06Z] INFO  18:06:50,231 MicroScheduler - 6061 reads were filtered out during the traversal out of approximately 71174 total reads (8.52%)
[2016-04-15T01:06Z] INFO  18:06:50,232 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:06Z] INFO  18:06:50,232 MicroScheduler -   -> 5705 reads (8.02% of total) failing DuplicateReadFilter
[2016-04-15T01:06Z] INFO  18:06:50,232 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:06Z] INFO  18:06:50,233 MicroScheduler -   -> 356 reads (0.50% of total) failing HCMappingQualityFilter
[2016-04-15T01:06Z] INFO  18:06:50,233 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:06Z] INFO  18:06:50,233 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:06Z] INFO  18:06:50,234 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:06Z] INFO  18:06:50,234 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T01:06Z] INFO  18:06:50,601 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.002265842
[2016-04-15T01:06Z] INFO  18:06:50,602 PairHMM - Total compute time in PairHMM computeLikelihoods() : 0.030836066000000002
[2016-04-15T01:06Z] INFO  18:06:50,603 HaplotypeCaller - Ran local assembly on 898 active regions
[2016-04-15T01:06Z] INFO  18:06:50,667 ProgressMeter -            done      4.2176641E7    27.0 s            0.0 s      100.0%    27.0 s       0.0 s
[2016-04-15T01:06Z] INFO  18:06:50,668 ProgressMeter - Total runtime 27.45 secs, 0.46 min, 0.01 hours
[2016-04-15T01:06Z] INFO  18:06:50,668 MicroScheduler - 7750 reads were filtered out during the traversal out of approximately 94628 total reads (8.19%)
[2016-04-15T01:06Z] INFO  18:06:50,669 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:06Z] INFO  18:06:50,669 MicroScheduler -   -> 7292 reads (7.71% of total) failing DuplicateReadFilter
[2016-04-15T01:06Z] INFO  18:06:50,669 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:06Z] INFO  18:06:50,671 MicroScheduler -   -> 458 reads (0.48% of total) failing HCMappingQualityFilter
[2016-04-15T01:06Z] INFO  18:06:50,671 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:06Z] INFO  18:06:50,672 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:06Z] INFO  18:06:50,672 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:06Z] INFO  18:06:50,672 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T01:06Z] INFO  18:06:50,694 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:06Z] INFO  18:06:50,698 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:06Z] INFO  18:06:50,699 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:06Z] INFO  18:06:50,700 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:06Z] INFO  18:06:50,705 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/X/R14-18105_kapa-NGv3-PE100-NGv3-sort-X_111874647_128581278-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/X/R14-18105_kapa-NGv3-PE100-NGv3-X_111874647_128581278-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/X/tx/tmp4UCK4J/R14-18105_kapa-NGv3-PE100-NGv3-X_111874647_128581278.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:06Z] INFO  18:06:50,736 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:06Z] INFO  18:06:50,737 HelpFormatter - Date/Time: 2016/04/14 18:06:50
[2016-04-15T01:06Z] INFO  18:06:50,737 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:06Z] INFO  18:06:50,738 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:06Z] WARN  18:06:50,779 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T01:06Z] WARN  18:06:50,782 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/X/tx/tmp4UCK4J/R14-18105_kapa-NGv3-PE100-NGv3-X_111874647_128581278.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T01:06Z] INFO  18:06:51,043 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:06Z] INFO  18:06:51,155 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:06Z] INFO  18:06:51,241 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T01:06Z] INFO  18:06:51,265 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:06Z] INFO  18:06:51,353 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.09
[2016-04-15T01:06Z] INFO  18:06:51,388 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T01:06Z] GATK: HaplotypeCaller
[2016-04-15T01:06Z] INFO  18:06:51,741 IntervalUtils - Processing 115535 bp from intervals
[2016-04-15T01:06Z] WARN  18:06:51,747 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:06Z] INFO  18:06:51,784 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:06Z] INFO  18:06:51,821 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:06Z] INFO  18:06:51,923 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:06Z] INFO  18:06:51,924 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:06Z] INFO  18:06:51,924 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T01:06Z] INFO  18:06:51,925 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T01:06Z] INFO  18:06:51,932 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T01:06Z] INFO  18:06:51,932 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T01:06Z] GATK: HaplotypeCaller
[2016-04-15T01:06Z] INFO  18:06:52,103 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T01:06Z] INFO  18:06:52,234 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:06Z] GATK: HaplotypeCaller
[2016-04-15T01:06Z] INFO  18:06:52,682 ProgressMeter -     21:44482421     1.15562248E8    60.0 s            0.0 s       77.9%    77.0 s      17.0 s
[2016-04-15T01:06Z] INFO  18:06:52,762 ProgressMeter -      19:5867017     2.00982646E8    90.0 s            0.0 s       38.2%     3.9 m       2.4 m
[2016-04-15T01:06Z] INFO  18:06:52,954 ProgressMeter -      X:15307692      2.4745951E7    30.0 s            1.0 s       96.3%    31.0 s       1.0 s
[2016-04-15T01:06Z] INFO  18:06:53,544 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.006704422000000001
[2016-04-15T01:06Z] INFO  18:06:53,545 PairHMM - Total compute time in PairHMM computeLikelihoods() : 0.670903076
[2016-04-15T01:06Z] INFO  18:06:53,545 HaplotypeCaller - Ran local assembly on 767 active regions
[2016-04-15T01:06Z] INFO  18:06:53,586 ProgressMeter -            done      2.7892284E7    30.0 s            1.0 s      100.0%    30.0 s       0.0 s
[2016-04-15T01:06Z] INFO  18:06:53,586 ProgressMeter - Total runtime 30.64 secs, 0.51 min, 0.01 hours
[2016-04-15T01:06Z] INFO  18:06:53,586 MicroScheduler - 12978 reads were filtered out during the traversal out of approximately 102534 total reads (12.66%)
[2016-04-15T01:06Z] INFO  18:06:53,587 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:06Z] INFO  18:06:53,587 MicroScheduler -   -> 7752 reads (7.56% of total) failing DuplicateReadFilter
[2016-04-15T01:06Z] INFO  18:06:53,587 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:06Z] INFO  18:06:53,587 MicroScheduler -   -> 5226 reads (5.10% of total) failing HCMappingQualityFilter
[2016-04-15T01:06Z] INFO  18:06:53,588 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:06Z] INFO  18:06:53,588 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:06Z] INFO  18:06:53,588 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:06Z] INFO  18:06:53,588 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T01:06Z] INFO  18:06:54,386 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:06Z] INFO  18:06:54,389 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:06Z] INFO  18:06:54,390 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:06Z] INFO  18:06:54,391 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:06Z] INFO  18:06:54,395 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/X/R14-18105_kapa-NGv3-PE100-NGv3-sort-X_128582278_144329181-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/X/R14-18105_kapa-NGv3-PE100-NGv3-X_128582278_144329181-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/X/tx/tmpqMWNkf/R14-18105_kapa-NGv3-PE100-NGv3-X_128582278_144329181.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:06Z] INFO  18:06:54,406 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:06Z] INFO  18:06:54,409 HelpFormatter - Date/Time: 2016/04/14 18:06:54
[2016-04-15T01:06Z] INFO  18:06:54,420 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:06Z] INFO  18:06:54,421 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:06Z] INFO  18:06:54,427 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.014440063000000001
[2016-04-15T01:06Z] INFO  18:06:54,428 PairHMM - Total compute time in PairHMM computeLikelihoods() : 0.9765102520000001
[2016-04-15T01:06Z] INFO  18:06:54,429 HaplotypeCaller - Ran local assembly on 2351 active regions
[2016-04-15T01:06Z] WARN  18:06:54,459 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T01:06Z] WARN  18:06:54,462 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/X/tx/tmpqMWNkf/R14-18105_kapa-NGv3-PE100-NGv3-X_128582278_144329181.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T01:06Z] INFO  18:06:54,474 ProgressMeter -            done     2.49280923E8    75.0 s            0.0 s      100.0%    75.0 s       0.0 s
[2016-04-15T01:06Z] INFO  18:06:54,475 ProgressMeter - Total runtime 75.40 secs, 1.26 min, 0.02 hours
[2016-04-15T01:06Z] INFO  18:06:54,475 MicroScheduler - 45638 reads were filtered out during the traversal out of approximately 562342 total reads (8.12%)
[2016-04-15T01:06Z] INFO  18:06:54,475 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:06Z] INFO  18:06:54,475 MicroScheduler -   -> 45114 reads (8.02% of total) failing DuplicateReadFilter
[2016-04-15T01:06Z] INFO  18:06:54,476 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:06Z] INFO  18:06:54,476 MicroScheduler -   -> 524 reads (0.09% of total) failing HCMappingQualityFilter
[2016-04-15T01:06Z] INFO  18:06:54,476 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:06Z] INFO  18:06:54,476 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:06Z] INFO  18:06:54,477 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:06Z] INFO  18:06:54,477 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T01:06Z] INFO  18:06:54,714 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:06Z] INFO  18:06:54,908 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T01:06Z] INFO  18:06:54,918 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:06Z] INFO  18:06:54,997 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-15T01:06Z] INFO  18:06:55,016 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T01:06Z] INFO  18:06:55,132 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:06Z] INFO  18:06:55,136 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:06Z] INFO  18:06:55,136 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:06Z] INFO  18:06:55,137 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:06Z] INFO  18:06:55,141 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/X/R14-18105_kapa-NGv3-PE100-NGv3-sort-X_144337190_155270560-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/X/R14-18105_kapa-NGv3-PE100-NGv3-X_144337190_155270560-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/X/tx/tmpbuIRv9/R14-18105_kapa-NGv3-PE100-NGv3-X_144337190_155270560.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:06Z] INFO  18:06:55,183 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:06Z] INFO  18:06:55,184 HelpFormatter - Date/Time: 2016/04/14 18:06:55
[2016-04-15T01:06Z] INFO  18:06:55,185 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:06Z] INFO  18:06:55,189 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:06Z] INFO  18:06:55,190 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:06Z] WARN  18:06:55,236 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T01:06Z] WARN  18:06:55,238 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/X/tx/tmpbuIRv9/R14-18105_kapa-NGv3-PE100-NGv3-X_144337190_155270560.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T01:06Z] INFO  18:06:55,390 IntervalUtils - Processing 143302 bp from intervals
[2016-04-15T01:06Z] WARN  18:06:55,406 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:06Z] INFO  18:06:55,411 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:06Z] INFO  18:06:55,414 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:06Z] INFO  18:06:55,415 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:06Z] INFO  18:06:55,417 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:06Z] INFO  18:06:55,427 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/Y/R14-18105_kapa-NGv3-PE100-NGv3-sort-Y_0_15522993-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/Y/R14-18105_kapa-NGv3-PE100-NGv3-Y_0_15522993-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/Y/tx/tmpviHahb/R14-18105_kapa-NGv3-PE100-NGv3-Y_0_15522993.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 1 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:06Z] INFO  18:06:55,448 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:06Z] INFO  18:06:55,455 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:06Z] INFO  18:06:55,456 HelpFormatter - Date/Time: 2016/04/14 18:06:55
[2016-04-15T01:06Z] INFO  18:06:55,457 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:06Z] INFO  18:06:55,457 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:06Z] GATK: HaplotypeCaller
[2016-04-15T01:06Z] WARN  18:06:55,495 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T01:06Z] WARN  18:06:55,498 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/Y/tx/tmpviHahb/R14-18105_kapa-NGv3-PE100-NGv3-Y_0_15522993.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T01:06Z] INFO  18:06:55,541 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:06Z] INFO  18:06:55,630 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T01:06Z] INFO  18:06:55,640 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:06Z] INFO  18:06:55,656 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:06Z] INFO  18:06:55,657 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:06Z] INFO  18:06:55,658 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T01:06Z] INFO  18:06:55,659 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T01:06Z] INFO  18:06:55,659 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T01:06Z] INFO  18:06:55,660 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T01:06Z] INFO  18:06:55,729 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.09
[2016-04-15T01:06Z] INFO  18:06:55,737 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:06Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T01:06Z] INFO  18:06:55,746 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T01:06Z] INFO  18:06:55,754 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T01:06Z] INFO  18:06:55,754 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T01:06Z] INFO  18:06:55,872 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T01:06Z] WARN  18:06:55,964 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T01:06Z] WARN  18:06:55,966 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T01:06Z] INFO  18:06:55,965 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:06Z] INFO  18:06:55,966 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T01:06Z] INFO  18:06:55,991 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:06Z] INFO  18:06:56,070 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-15T01:06Z] INFO  18:06:56,097 IntervalUtils - Processing 184337 bp from intervals
[2016-04-15T01:06Z] INFO  18:06:56,101 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T01:06Z] WARN  18:06:56,103 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:06Z] INFO  18:06:56,256 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:06Z] INFO  18:06:56,381 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:06Z] INFO  18:06:56,382 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:06Z] INFO  18:06:56,383 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T01:06Z] INFO  18:06:56,383 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T01:06Z] INFO  18:06:56,387 IntervalUtils - Processing 52192 bp from intervals
[2016-04-15T01:06Z] WARN  18:06:56,392 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:06Z] INFO  18:06:56,395 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T01:06Z] INFO  18:06:56,396 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T01:06Z] GATK: HaplotypeCaller
[2016-04-15T01:06Z] INFO  18:06:56,505 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:06Z] INFO  18:06:56,607 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:06Z] INFO  18:06:56,608 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:06Z] INFO  18:06:56,609 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T01:06Z] INFO  18:06:56,610 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T01:06Z] INFO  18:06:56,610 HaplotypeCaller - Currently, physical phasing is not available when ploidy is different than 2; therefore it won't be performed
[2016-04-15T01:06Z] INFO  18:06:56,611 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T01:06Z] INFO  18:06:56,611 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T01:06Z] INFO  18:06:56,674 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T01:06Z] INFO  18:06:56,880 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T01:06Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T01:06Z] INFO  18:06:57,694 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T01:06Z] INFO  18:06:57,705 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T01:06Z] WARN  18:06:57,954 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T01:06Z] WARN  18:06:57,955 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T01:06Z] INFO  18:06:58,413 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.0012325180000000002
[2016-04-15T01:06Z] INFO  18:06:58,424 PairHMM - Total compute time in PairHMM computeLikelihoods() : 0.01283685
[2016-04-15T01:06Z] INFO  18:06:58,425 HaplotypeCaller - Ran local assembly on 296 active regions
[2016-04-15T01:06Z] INFO  18:06:58,476 ProgressMeter -            done        3554725.0    16.0 s            4.0 s      100.0%    16.0 s       0.0 s
[2016-04-15T01:06Z] INFO  18:06:58,477 ProgressMeter - Total runtime 16.51 secs, 0.28 min, 0.00 hours
[2016-04-15T01:06Z] INFO  18:06:58,478 MicroScheduler - 3391 reads were filtered out during the traversal out of approximately 29078 total reads (11.66%)
[2016-04-15T01:06Z] INFO  18:06:58,478 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:06Z] INFO  18:06:58,478 MicroScheduler -   -> 2065 reads (7.10% of total) failing DuplicateReadFilter
[2016-04-15T01:06Z] INFO  18:06:58,478 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:06Z] INFO  18:06:58,479 MicroScheduler -   -> 1326 reads (4.56% of total) failing HCMappingQualityFilter
[2016-04-15T01:06Z] INFO  18:06:58,479 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:06Z] INFO  18:06:58,479 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:06Z] INFO  18:06:58,479 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:06Z] INFO  18:06:58,480 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T01:06Z] INFO  18:06:58,966 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:06Z] INFO  18:06:58,969 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:06Z] INFO  18:06:58,969 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:06Z] INFO  18:06:58,970 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:06Z] INFO  18:06:58,974 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/Y/R14-18105_kapa-NGv3-PE100-NGv3-sort-Y_15526614_59222281-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/Y/R14-18105_kapa-NGv3-PE100-NGv3-Y_15526614_59222281-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/Y/tx/tmpgyCx19/R14-18105_kapa-NGv3-PE100-NGv3-Y_15526614_59222281.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 1 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:06Z] INFO  18:06:58,983 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:06Z] INFO  18:06:58,984 HelpFormatter - Date/Time: 2016/04/14 18:06:58
[2016-04-15T01:06Z] INFO  18:06:58,985 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:06Z] INFO  18:06:58,986 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:06Z] WARN  18:06:59,053 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T01:06Z] WARN  18:06:59,072 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/Y/tx/tmpgyCx19/R14-18105_kapa-NGv3-PE100-NGv3-Y_15526614_59222281.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T01:06Z] INFO  18:06:59,391 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:06Z] INFO  18:06:59,662 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T01:06Z] INFO  18:06:59,679 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:06Z] INFO  18:06:59,772 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.09
[2016-04-15T01:06Z] INFO  18:06:59,786 ProgressMeter -      X:52113158      3.6457498E7    30.0 s            0.0 s       57.3%    52.0 s      22.0 s
[2016-04-15T01:06Z] INFO  18:06:59,807 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T01:06Z] INFO  18:06:59,815 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:06Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T01:06Z] INFO  18:06:59,818 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:06Z] INFO  18:06:59,819 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:06Z] INFO  18:06:59,820 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:06Z] INFO  18:06:59,824 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18105_kapa-NGv3-PE100-NGv3/Y/R14-18105_kapa-NGv3-PE100-NGv3-sort-Y_59228291_59373566-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/Y/R14-18105_kapa-NGv3-PE100-NGv3-Y_59228291_59373566-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/Y/tx/tmpgi8JeD/R14-18105_kapa-NGv3-PE100-NGv3-Y_59228291_59373566.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 1 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:06Z] INFO  18:06:59,839 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T01:06Z] INFO  18:06:59,841 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T01:06Z] INFO  18:06:59,843 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:06Z] INFO  18:06:59,844 HelpFormatter - Date/Time: 2016/04/14 18:06:59
[2016-04-15T01:06Z] INFO  18:06:59,844 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:06Z] INFO  18:06:59,845 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:06Z] WARN  18:06:59,867 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T01:06Z] WARN  18:06:59,870 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/Y/tx/tmpgi8JeD/R14-18105_kapa-NGv3-PE100-NGv3-Y_59228291_59373566.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T01:07Z] INFO  18:07:00,075 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:07Z] INFO  18:07:00,078 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:07Z] WARN  18:07:00,144 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T01:07Z] WARN  18:07:00,146 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T01:07Z] INFO  18:07:00,213 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T01:07Z] INFO  18:07:00,223 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:07Z] INFO  18:07:00,279 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-15T01:07Z] INFO  18:07:00,287 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T01:07Z] INFO  18:07:00,296 IntervalUtils - Processing 44713 bp from intervals
[2016-04-15T01:07Z] WARN  18:07:00,301 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:07Z] INFO  18:07:00,451 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:07Z] platypus variant calling
[2016-04-15T01:07Z] INFO  18:07:00,535 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:07Z] INFO  18:07:00,547 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:07Z] INFO  18:07:00,548 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T01:07Z] INFO  18:07:00,549 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T01:07Z] INFO  18:07:00,556 IntervalUtils - Processing 2412 bp from intervals
[2016-04-15T01:07Z] WARN  18:07:00,561 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:07Z] INFO  18:07:00,559 HaplotypeCaller - Currently, physical phasing is not available when ploidy is different than 2; therefore it won't be performed
[2016-04-15T01:07Z] INFO  18:07:00,560 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T01:07Z] INFO  18:07:00,560 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T01:07Z] INFO  18:07:00,686 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:07Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T01:07Z] INFO  18:07:00,709 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:07Z] INFO  18:07:00,710 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:07Z] INFO  18:07:00,711 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T01:07Z] INFO  18:07:00,711 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T01:07Z] INFO  18:07:00,712 HaplotypeCaller - Currently, physical phasing is not available when ploidy is different than 2; therefore it won't be performed
[2016-04-15T01:07Z] INFO  18:07:00,715 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T01:07Z] INFO  18:07:00,712 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T01:07Z] INFO  18:07:00,712 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T01:07Z] INFO  18:07:00,716 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T01:07Z] INFO  18:07:00,886 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T01:07Z] INFO  18:07:00,899 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T01:07Z] WARN  18:07:00,910 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T01:07Z] WARN  18:07:00,911 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T01:07Z] INFO  18:07:01,456 ProgressMeter -     19:40581912      2.0756351E8    90.0 s            0.0 s       53.7%     2.8 m      77.0 s
[2016-04-15T01:07Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T01:07Z] INFO  18:07:02,280 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T01:07Z] INFO  18:07:02,281 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T01:07Z] INFO  18:07:02,282 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.0
[2016-04-15T01:07Z] INFO  18:07:02,282 PairHMM - Total compute time in PairHMM computeLikelihoods() : 0.0
[2016-04-15T01:07Z] INFO  18:07:02,282 HaplotypeCaller - Ran local assembly on 17 active regions
[2016-04-15T01:07Z] INFO  18:07:02,340 ProgressMeter -            done          14930.0     1.0 s          109.0 s      100.0%     1.0 s       0.0 s
[2016-04-15T01:07Z] INFO  18:07:02,341 ProgressMeter - Total runtime 1.63 secs, 0.03 min, 0.00 hours
[2016-04-15T01:07Z] INFO  18:07:02,365 ProgressMeter -     19:52272312     2.07335497E8    90.0 s            0.0 s       44.6%     3.4 m     111.0 s
[2016-04-15T01:07Z] INFO  18:07:03,948 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:07Z] INFO  18:07:04,270 ProgressMeter -     22:23966073      6.4138358E7    60.0 s            0.0 s       49.5%     2.0 m      61.0 s
[2016-04-15T01:07Z] platypus variant calling
[2016-04-15T01:07Z] INFO  18:07:07,264 ProgressMeter -     22:41605955     1.17881858E8    60.0 s            0.0 s       61.1%    98.0 s      38.0 s
[2016-04-15T01:07Z] INFO  18:07:07,537 ProgressMeter -      X:74641825      4.3710006E7    30.0 s            0.0 s       83.1%    36.0 s       6.0 s
[2016-04-15T01:07Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T01:07Z] INFO  18:07:07,980 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T01:07Z] INFO  18:07:07,981 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T01:07Z] WARN  18:07:08,444 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T01:07Z] WARN  18:07:08,444 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T01:07Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T01:07Z] INFO  18:07:10,028 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T01:07Z] INFO  18:07:10,029 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T01:07Z] INFO  18:07:11,885 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.003492948
[2016-04-15T01:07Z] INFO  18:07:11,886 PairHMM - Total compute time in PairHMM computeLikelihoods() : 0.272376281
[2016-04-15T01:07Z] INFO  18:07:11,887 HaplotypeCaller - Ran local assembly on 1105 active regions
[2016-04-15T01:07Z] INFO  18:07:11,936 ProgressMeter -            done      6.1608288E7    34.0 s            0.0 s      100.0%    34.0 s       0.0 s
[2016-04-15T01:07Z] INFO  18:07:11,936 ProgressMeter - Total runtime 34.42 secs, 0.57 min, 0.01 hours
[2016-04-15T01:07Z] INFO  18:07:11,937 MicroScheduler - 21196 reads were filtered out during the traversal out of approximately 146141 total reads (14.50%)
[2016-04-15T01:07Z] INFO  18:07:11,937 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:07Z] INFO  18:07:11,938 MicroScheduler -   -> 10595 reads (7.25% of total) failing DuplicateReadFilter
[2016-04-15T01:07Z] INFO  18:07:11,938 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:07Z] INFO  18:07:11,938 MicroScheduler -   -> 10601 reads (7.25% of total) failing HCMappingQualityFilter
[2016-04-15T01:07Z] INFO  18:07:11,938 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:07Z] INFO  18:07:11,939 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:07Z] INFO  18:07:11,939 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:07Z] INFO  18:07:11,939 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T01:07Z] INFO  18:07:13,109 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.001697855
[2016-04-15T01:07Z] INFO  18:07:13,110 PairHMM - Total compute time in PairHMM computeLikelihoods() : 0.054005081
[2016-04-15T01:07Z] INFO  18:07:13,111 HaplotypeCaller - Ran local assembly on 339 active regions
[2016-04-15T01:07Z] INFO  18:07:13,190 ProgressMeter -            done        6359922.0    16.0 s            2.0 s      100.0%    16.0 s       0.0 s
[2016-04-15T01:07Z] INFO  18:07:13,191 ProgressMeter - Total runtime 16.58 secs, 0.28 min, 0.00 hours
[2016-04-15T01:07Z] INFO  18:07:13,191 MicroScheduler - 65184 reads were filtered out during the traversal out of approximately 90713 total reads (71.86%)
[2016-04-15T01:07Z] INFO  18:07:13,191 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:07Z] INFO  18:07:13,192 MicroScheduler -   -> 2382 reads (2.63% of total) failing DuplicateReadFilter
[2016-04-15T01:07Z] INFO  18:07:13,192 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:07Z] INFO  18:07:13,193 MicroScheduler -   -> 62802 reads (69.23% of total) failing HCMappingQualityFilter
[2016-04-15T01:07Z] INFO  18:07:13,193 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:07Z] INFO  18:07:13,193 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:07Z] INFO  18:07:13,194 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:07Z] INFO  18:07:13,194 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T01:07Z] INFO  18:07:13,276 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:07Z] INFO  18:07:13,510 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.0016660450000000001
[2016-04-15T01:07Z] INFO  18:07:13,511 PairHMM - Total compute time in PairHMM computeLikelihoods() : 0.214416299
[2016-04-15T01:07Z] INFO  18:07:13,512 HaplotypeCaller - Ran local assembly on 334 active regions
[2016-04-15T01:07Z] INFO  18:07:13,592 ProgressMeter -            done        6560827.0    13.0 s            1.0 s      100.0%    13.0 s       0.0 s
[2016-04-15T01:07Z] INFO  18:07:13,593 ProgressMeter - Total runtime 13.05 secs, 0.22 min, 0.00 hours
[2016-04-15T01:07Z] INFO  18:07:13,593 MicroScheduler - 72340 reads were filtered out during the traversal out of approximately 82895 total reads (87.27%)
[2016-04-15T01:07Z] INFO  18:07:13,594 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:07Z] INFO  18:07:13,594 MicroScheduler -   -> 971 reads (1.17% of total) failing DuplicateReadFilter
[2016-04-15T01:07Z] INFO  18:07:13,594 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:07Z] INFO  18:07:13,595 MicroScheduler -   -> 71369 reads (86.10% of total) failing HCMappingQualityFilter
[2016-04-15T01:07Z] INFO  18:07:13,595 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:07Z] INFO  18:07:13,595 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:07Z] INFO  18:07:13,596 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:07Z] INFO  18:07:13,596 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T01:07Z] platypus variant calling
[2016-04-15T01:07Z] INFO  18:07:14,349 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.003765366
[2016-04-15T01:07Z] INFO  18:07:14,350 PairHMM - Total compute time in PairHMM computeLikelihoods() : 0.5763111910000001
[2016-04-15T01:07Z] INFO  18:07:14,351 HaplotypeCaller - Ran local assembly on 1532 active regions
[2016-04-15T01:07Z] INFO  18:07:14,391 ProgressMeter -            done     1.04022591E8    44.0 s            0.0 s      100.0%    44.0 s       0.0 s
[2016-04-15T01:07Z] INFO  18:07:14,391 ProgressMeter - Total runtime 44.63 secs, 0.74 min, 0.01 hours
[2016-04-15T01:07Z] INFO  18:07:14,392 MicroScheduler - 79281 reads were filtered out during the traversal out of approximately 255003 total reads (31.09%)
[2016-04-15T01:07Z] INFO  18:07:14,393 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:07Z] INFO  18:07:14,393 MicroScheduler -   -> 15151 reads (5.94% of total) failing DuplicateReadFilter
[2016-04-15T01:07Z] INFO  18:07:14,393 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:07Z] INFO  18:07:14,393 MicroScheduler -   -> 64130 reads (25.15% of total) failing HCMappingQualityFilter
[2016-04-15T01:07Z] INFO  18:07:14,394 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:07Z] INFO  18:07:14,394 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:07Z] INFO  18:07:14,394 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:07Z] INFO  18:07:14,394 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T01:07Z] INFO  18:07:14,739 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:07Z] INFO  18:07:14,933 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:07Z] platypus variant calling
[2016-04-15T01:07Z] platypus variant calling
[2016-04-15T01:07Z] INFO  18:07:15,795 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:07Z] platypus variant calling
[2016-04-15T01:07Z] INFO  18:07:18,556 ProgressMeter -     X:107978277      4.7449804E7    30.0 s            0.0 s       81.7%    36.0 s       6.0 s
[2016-04-15T01:07Z] tabix index R14-18105_kapa-NGv3-PE100-NGv3-1_62231950_77749296.vcf.gz
[2016-04-15T01:07Z] platypus variant calling
[2016-04-15T01:07Z] tabix index R14-18105_kapa-NGv3-PE100-NGv3-1_77752625_93297674.vcf.gz
[2016-04-15T01:07Z] platypus variant calling
[2016-04-15T01:07Z] INFO  18:07:21,934 ProgressMeter -     X:125686591      2.6944553E7    30.0 s            1.0 s       98.1%    30.0 s       0.0 s
[2016-04-15T01:07Z] INFO  18:07:22,447 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.004242495000000001
[2016-04-15T01:07Z] INFO  18:07:22,447 PairHMM - Total compute time in PairHMM computeLikelihoods() : 0.148323263
[2016-04-15T01:07Z] INFO  18:07:22,448 HaplotypeCaller - Ran local assembly on 1181 active regions
[2016-04-15T01:07Z] INFO  18:07:22,490 ProgressMeter -            done      7.0564604E7    33.0 s            0.0 s      100.0%    33.0 s       0.0 s
[2016-04-15T01:07Z] INFO  18:07:22,490 ProgressMeter - Total runtime 33.96 secs, 0.57 min, 0.01 hours
[2016-04-15T01:07Z] INFO  18:07:22,490 MicroScheduler - 23883 reads were filtered out during the traversal out of approximately 143591 total reads (16.63%)
[2016-04-15T01:07Z] INFO  18:07:22,491 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:07Z] INFO  18:07:22,491 MicroScheduler -   -> 9968 reads (6.94% of total) failing DuplicateReadFilter
[2016-04-15T01:07Z] INFO  18:07:22,492 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:07Z] INFO  18:07:22,492 MicroScheduler -   -> 13915 reads (9.69% of total) failing HCMappingQualityFilter
[2016-04-15T01:07Z] INFO  18:07:22,492 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:07Z] INFO  18:07:22,493 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:07Z] INFO  18:07:22,493 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:07Z] INFO  18:07:22,494 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T01:07Z] tabix index R14-18105_kapa-NGv3-PE100-NGv3-1_46715671_62228851.vcf.gz
[2016-04-15T01:07Z] INFO  18:07:22,609 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.003734607
[2016-04-15T01:07Z] INFO  18:07:22,610 PairHMM - Total compute time in PairHMM computeLikelihoods() : 1.4030938560000001
[2016-04-15T01:07Z] INFO  18:07:22,611 HaplotypeCaller - Ran local assembly on 735 active regions
[2016-04-15T01:07Z] INFO  18:07:22,650 ProgressMeter -            done      2.7516501E7    30.0 s            1.0 s      100.0%    30.0 s       0.0 s
[2016-04-15T01:07Z] INFO  18:07:22,650 ProgressMeter - Total runtime 30.73 secs, 0.51 min, 0.01 hours
[2016-04-15T01:07Z] INFO  18:07:22,651 MicroScheduler - 21110 reads were filtered out during the traversal out of approximately 92756 total reads (22.76%)
[2016-04-15T01:07Z] INFO  18:07:22,651 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:07Z] INFO  18:07:22,651 MicroScheduler -   -> 5828 reads (6.28% of total) failing DuplicateReadFilter
[2016-04-15T01:07Z] INFO  18:07:22,652 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:07Z] INFO  18:07:22,652 MicroScheduler -   -> 15282 reads (16.48% of total) failing HCMappingQualityFilter
[2016-04-15T01:07Z] INFO  18:07:22,652 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:07Z] INFO  18:07:22,652 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:07Z] INFO  18:07:22,653 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:07Z] INFO  18:07:22,653 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T01:07Z] INFO  18:07:22,687 ProgressMeter -     21:46320235     1.87371946E8    90.0 s            0.0 s       99.4%    90.0 s       0.0 s
[2016-04-15T01:07Z] INFO  18:07:22,763 ProgressMeter -      19:8809051     4.11968573E8   120.0 s            0.0 s       54.4%     3.7 m     100.0 s
[2016-04-15T01:07Z] platypus variant calling
[2016-04-15T01:07Z] INFO  18:07:23,056 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.031777006000000003
[2016-04-15T01:07Z] INFO  18:07:23,057 PairHMM - Total compute time in PairHMM computeLikelihoods() : 8.765598636
[2016-04-15T01:07Z] INFO  18:07:23,058 HaplotypeCaller - Ran local assembly on 2061 active regions
[2016-04-15T01:07Z] INFO  18:07:23,093 ProgressMeter -            done     1.91312624E8    90.0 s            0.0 s      100.0%    90.0 s       0.0 s
[2016-04-15T01:07Z] INFO  18:07:23,094 ProgressMeter - Total runtime 90.43 secs, 1.51 min, 0.03 hours
[2016-04-15T01:07Z] INFO  18:07:23,094 MicroScheduler - 41941 reads were filtered out during the traversal out of approximately 458289 total reads (9.15%)
[2016-04-15T01:07Z] INFO  18:07:23,094 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:07Z] INFO  18:07:23,095 MicroScheduler -   -> 37534 reads (8.19% of total) failing DuplicateReadFilter
[2016-04-15T01:07Z] INFO  18:07:23,095 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:07Z] INFO  18:07:23,095 MicroScheduler -   -> 4407 reads (0.96% of total) failing HCMappingQualityFilter
[2016-04-15T01:07Z] INFO  18:07:23,095 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:07Z] INFO  18:07:23,096 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:07Z] INFO  18:07:23,096 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:07Z] INFO  18:07:23,096 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T01:07Z] INFO  18:07:23,811 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:07Z] tabix index R14-18105_kapa-NGv3-PE100-NGv3-1_0_15541927.vcf.gz
[2016-04-15T01:07Z] INFO  18:07:24,061 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:07Z] platypus variant calling
[2016-04-15T01:07Z] INFO  18:07:24,231 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:07Z] platypus variant calling
[2016-04-15T01:07Z] platypus variant calling
[2016-04-15T01:07Z] platypus variant calling
[2016-04-15T01:07Z] INFO  18:07:24,469 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.0035578220000000004
[2016-04-15T01:07Z] INFO  18:07:24,470 PairHMM - Total compute time in PairHMM computeLikelihoods() : 0.350861331
[2016-04-15T01:07Z] INFO  18:07:24,471 HaplotypeCaller - Ran local assembly on 939 active regions
[2016-04-15T01:07Z] INFO  18:07:24,496 ProgressMeter -            done      4.2570099E7    28.0 s            0.0 s      100.0%    28.0 s       0.0 s
[2016-04-15T01:07Z] INFO  18:07:24,497 ProgressMeter - Total runtime 28.84 secs, 0.48 min, 0.01 hours
[2016-04-15T01:07Z] INFO  18:07:24,498 MicroScheduler - 29658 reads were filtered out during the traversal out of approximately 120472 total reads (24.62%)
[2016-04-15T01:07Z] INFO  18:07:24,498 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:07Z] INFO  18:07:24,499 MicroScheduler -   -> 7734 reads (6.42% of total) failing DuplicateReadFilter
[2016-04-15T01:07Z] INFO  18:07:24,500 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:07Z] INFO  18:07:24,501 MicroScheduler -   -> 21924 reads (18.20% of total) failing HCMappingQualityFilter
[2016-04-15T01:07Z] INFO  18:07:24,501 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:07Z] INFO  18:07:24,502 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:07Z] INFO  18:07:24,502 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:07Z] INFO  18:07:24,503 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T01:07Z] tabix index R14-18105_kapa-NGv3-PE100-NGv3-1_93298945_108993401.vcf.gz
[2016-04-15T01:07Z] platypus variant calling
[2016-04-15T01:07Z] INFO  18:07:25,880 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:07Z] platypus variant calling
[2016-04-15T01:07Z] INFO  18:07:26,408 ProgressMeter -     X:154132571      5.4826119E7    30.0 s            0.0 s       91.2%    32.0 s       2.0 s
[2016-04-15T01:07Z] tabix index R14-18105_kapa-NGv3-PE100-NGv3-1_15545821_31186478.vcf.gz
[2016-04-15T01:07Z] platypus variant calling
[2016-04-15T01:07Z] INFO  18:07:27,896 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.004701689
[2016-04-15T01:07Z] INFO  18:07:27,896 PairHMM - Total compute time in PairHMM computeLikelihoods() : 0.149909698
[2016-04-15T01:07Z] INFO  18:07:27,896 HaplotypeCaller - Ran local assembly on 1237 active regions
[2016-04-15T01:07Z] INFO  18:07:27,931 ProgressMeter -            done      6.5416759E7    31.0 s            0.0 s      100.0%    31.0 s       0.0 s
[2016-04-15T01:07Z] INFO  18:07:27,932 ProgressMeter - Total runtime 31.55 secs, 0.53 min, 0.01 hours
[2016-04-15T01:07Z] INFO  18:07:27,932 MicroScheduler - 36089 reads were filtered out during the traversal out of approximately 174114 total reads (20.73%)
[2016-04-15T01:07Z] INFO  18:07:27,933 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:07Z] INFO  18:07:27,933 MicroScheduler -   -> 12020 reads (6.90% of total) failing DuplicateReadFilter
[2016-04-15T01:07Z] INFO  18:07:27,933 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:07Z] INFO  18:07:27,934 MicroScheduler -   -> 24069 reads (13.82% of total) failing HCMappingQualityFilter
[2016-04-15T01:07Z] INFO  18:07:27,934 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:07Z] INFO  18:07:27,934 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:07Z] INFO  18:07:27,934 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:07Z] INFO  18:07:27,935 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T01:07Z] INFO  18:07:29,217 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:07Z] platypus variant calling
[2016-04-15T01:07Z] tabix index R14-18105_kapa-NGv3-PE100-NGv3-1_207641871_223156451.vcf.gz
[2016-04-15T01:07Z] tabix index R14-18105_kapa-NGv3-PE100-NGv3-1_240255409_249250621.vcf.gz
[2016-04-15T01:07Z] platypus variant calling
[2016-04-15T01:07Z] platypus variant calling
[2016-04-15T01:07Z] tabix index R14-18105_kapa-NGv3-PE100-NGv3-2_0_15514844.vcf.gz
[2016-04-15T01:07Z] tabix index R14-18105_kapa-NGv3-PE100-NGv3-1_108994811_143767848.vcf.gz
[2016-04-15T01:07Z] platypus variant calling
[2016-04-15T01:07Z] INFO  18:07:31,458 ProgressMeter -     19:43441165     4.29519756E8   120.0 s            0.0 s       74.8%     2.7 m      40.0 s
[2016-04-15T01:07Z] tabix index R14-18105_kapa-NGv3-PE100-NGv3-1_175048468_192127886.vcf.gz
[2016-04-15T01:07Z] platypus variant calling
[2016-04-15T01:07Z] platypus variant calling
[2016-04-15T01:07Z] INFO  18:07:32,366 ProgressMeter -     19:54783930     3.26470971E8   120.0 s            0.0 s       61.4%     3.3 m      75.0 s
[2016-04-15T01:07Z] tabix index R14-18105_kapa-NGv3-PE100-NGv3-1_31187093_46714270.vcf.gz
[2016-04-15T01:07Z] platypus variant calling
[2016-04-15T01:07Z] INFO  18:07:34,271 ProgressMeter -     22:30985178     2.61244871E8    90.0 s            0.0 s       92.4%    97.0 s       7.0 s
[2016-04-15T01:07Z] tabix index R14-18105_kapa-NGv3-PE100-NGv3-1_159504867_175046963.vcf.gz
[2016-04-15T01:07Z] platypus variant calling
[2016-04-15T01:07Z] tabix index R14-18105_kapa-NGv3-PE100-NGv3-1_192128349_207640257.vcf.gz
[2016-04-15T01:07Z] platypus variant calling
[2016-04-15T01:07Z] INFO  18:07:35,582 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.023272865
[2016-04-15T01:07Z] INFO  18:07:35,583 PairHMM - Total compute time in PairHMM computeLikelihoods() : 2.310445967
[2016-04-15T01:07Z] INFO  18:07:35,583 HaplotypeCaller - Ran local assembly on 2710 active regions
[2016-04-15T01:07Z] INFO  18:07:35,613 ProgressMeter -            done      3.3533286E8    88.0 s            0.0 s      100.0%    88.0 s       0.0 s
[2016-04-15T01:07Z] INFO  18:07:35,614 ProgressMeter - Total runtime 88.38 secs, 1.47 min, 0.02 hours
[2016-04-15T01:07Z] INFO  18:07:35,615 MicroScheduler - 56937 reads were filtered out during the traversal out of approximately 646426 total reads (8.81%)
[2016-04-15T01:07Z] INFO  18:07:35,616 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:07Z] INFO  18:07:35,616 MicroScheduler -   -> 51267 reads (7.93% of total) failing DuplicateReadFilter
[2016-04-15T01:07Z] INFO  18:07:35,617 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:07Z] INFO  18:07:35,618 MicroScheduler -   -> 5670 reads (0.88% of total) failing HCMappingQualityFilter
[2016-04-15T01:07Z] INFO  18:07:35,618 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:07Z] INFO  18:07:35,619 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:07Z] INFO  18:07:35,619 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:07Z] INFO  18:07:35,620 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T01:07Z] tabix index R14-18105_kapa-NGv3-PE100-NGv3-1_223162737_240072524.vcf.gz
[2016-04-15T01:07Z] tabix index R14-18105_kapa-NGv3-PE100-NGv3-2_46707543_62228117.vcf.gz
[2016-04-15T01:07Z] tabix index R14-18105_kapa-NGv3-PE100-NGv3-2_31135088_46706841.vcf.gz
[2016-04-15T01:07Z] platypus variant calling
[2016-04-15T01:07Z] platypus variant calling
[2016-04-15T01:07Z] tabix index R14-18105_kapa-NGv3-PE100-NGv3-2_79253838_95537822.vcf.gz
[2016-04-15T01:07Z] platypus variant calling
[2016-04-15T01:07Z] platypus variant calling
[2016-04-15T01:07Z] INFO  18:07:36,894 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:07Z] platypus variant calling
[2016-04-15T01:07Z] INFO  18:07:39,001 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.060323958000000004
[2016-04-15T01:07Z] INFO  18:07:39,002 PairHMM - Total compute time in PairHMM computeLikelihoods() : 4.655900900000001
[2016-04-15T01:07Z] INFO  18:07:39,003 HaplotypeCaller - Ran local assembly on 2679 active regions
[2016-04-15T01:07Z] INFO  18:07:39,047 ProgressMeter -            done     3.03489097E8    94.0 s            0.0 s      100.0%    94.0 s       0.0 s
[2016-04-15T01:07Z] INFO  18:07:39,048 ProgressMeter - Total runtime 94.81 secs, 1.58 min, 0.03 hours
[2016-04-15T01:07Z] INFO  18:07:39,048 MicroScheduler - 125575 reads were filtered out during the traversal out of approximately 708728 total reads (17.72%)
[2016-04-15T01:07Z] INFO  18:07:39,049 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:07Z] INFO  18:07:39,049 MicroScheduler -   -> 52153 reads (7.36% of total) failing DuplicateReadFilter
[2016-04-15T01:07Z] INFO  18:07:39,049 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:07Z] INFO  18:07:39,050 MicroScheduler -   -> 73422 reads (10.36% of total) failing HCMappingQualityFilter
[2016-04-15T01:07Z] INFO  18:07:39,050 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:07Z] INFO  18:07:39,050 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:07Z] INFO  18:07:39,051 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:07Z] INFO  18:07:39,051 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T01:07Z] tabix index R14-18105_kapa-NGv3-PE100-NGv3-2_143676177_159195597.vcf.gz
[2016-04-15T01:07Z] tabix index R14-18105_kapa-NGv3-PE100-NGv3-2_111281072_127413888.vcf.gz
[2016-04-15T01:07Z] platypus variant calling
[2016-04-15T01:07Z] platypus variant calling
[2016-04-15T01:07Z] tabix index R14-18105_kapa-NGv3-PE100-NGv3-2_62362965_79253295.vcf.gz
[2016-04-15T01:07Z] platypus variant calling
[2016-04-15T01:07Z] INFO  18:07:40,402 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:07Z] tabix index R14-18105_kapa-NGv3-PE100-NGv3-2_15519725_31133925.vcf.gz
[2016-04-15T01:07Z] platypus variant calling
[2016-04-15T01:07Z] platypus variant calling
[2016-04-15T01:07Z] tabix index R14-18105_kapa-NGv3-PE100-NGv3-2_127433207_143643105.vcf.gz
[2016-04-15T01:07Z] platypus variant calling
[2016-04-15T01:07Z] tabix index R14-18105_kapa-NGv3-PE100-NGv3-3_15515506_31574805.vcf.gz
[2016-04-15T01:07Z] tabix index R14-18105_kapa-NGv3-PE100-NGv3-2_190313104_205830046.vcf.gz
[2016-04-15T01:07Z] platypus variant calling
[2016-04-15T01:07Z] platypus variant calling
[2016-04-15T01:07Z] tabix index R14-18105_kapa-NGv3-PE100-NGv3-2_159196753_174774985.vcf.gz
[2016-04-15T01:07Z] tabix index R14-18105_kapa-NGv3-PE100-NGv3-3_78649262_96533852.vcf.gz
[2016-04-15T01:07Z] platypus variant calling
[2016-04-15T01:07Z] tabix index R14-18105_kapa-NGv3-PE100-NGv3-2_95538561_111273222.vcf.gz
[2016-04-15T01:07Z] platypus variant calling
[2016-04-15T01:07Z] platypus variant calling
[2016-04-15T01:07Z] tabix index R14-18105_kapa-NGv3-PE100-NGv3-2_222291154_237994685.vcf.gz
[2016-04-15T01:07Z] platypus variant calling
[2016-04-15T01:07Z] tabix index R14-18105_kapa-NGv3-PE100-NGv3-3_62739115_78648077.vcf.gz
[2016-04-15T01:07Z] tabix index R14-18105_kapa-NGv3-PE100-NGv3-2_237995374_243199373.vcf.gz
[2016-04-15T01:07Z] platypus variant calling
[2016-04-15T01:07Z] platypus variant calling
[2016-04-15T01:07Z] tabix index R14-18105_kapa-NGv3-PE100-NGv3-3_0_15512123.vcf.gz
[2016-04-15T01:07Z] tabix index R14-18105_kapa-NGv3-PE100-NGv3-3_96585668_112185230.vcf.gz
[2016-04-15T01:07Z] platypus variant calling
[2016-04-15T01:07Z] platypus variant calling
[2016-04-15T01:07Z] tabix index R14-18105_kapa-NGv3-PE100-NGv3-2_174777797_190306304.vcf.gz
[2016-04-15T01:07Z] platypus variant calling
[2016-04-15T01:07Z] tabix index R14-18105_kapa-NGv3-PE100-NGv3-2_205912303_222290862.vcf.gz
[2016-04-15T01:07Z] platypus variant calling
[2016-04-15T01:07Z] tabix index R14-18105_kapa-NGv3-PE100-NGv3-3_158970515_174577240.vcf.gz
[2016-04-15T01:07Z] tabix index R14-18105_kapa-NGv3-PE100-NGv3-3_143297426_158963696.vcf.gz
[2016-04-15T01:07Z] platypus variant calling
[2016-04-15T01:07Z] platypus variant calling
[2016-04-15T01:07Z] tabix index R14-18105_kapa-NGv3-PE100-NGv3-4_15512869_31144471.vcf.gz
[2016-04-15T01:07Z] platypus variant calling
[2016-04-15T01:07Z] tabix index R14-18105_kapa-NGv3-PE100-NGv3-4_52709749_68338393.vcf.gz
[2016-04-15T01:07Z] tabix index R14-18105_kapa-NGv3-PE100-NGv3-1_143897546_159410511.vcf.gz
[2016-04-15T01:07Z] platypus variant calling
[2016-04-15T01:07Z] INFO  18:07:52,764 ProgressMeter -     19:10822975     6.17078526E8     2.5 m            0.0 s       71.5%     3.5 m      59.0 s
[2016-04-15T01:07Z] tabix index R14-18105_kapa-NGv3-PE100-NGv3-3_31617887_47127804.vcf.gz
[2016-04-15T01:07Z] platypus variant calling
[2016-04-15T01:07Z] platypus variant calling
[2016-04-15T01:07Z] tabix index R14-18105_kapa-NGv3-PE100-NGv3-4_36069528_52709433.vcf.gz
[2016-04-15T01:07Z] tabix index R14-18105_kapa-NGv3-PE100-NGv3-3_127770401_143293035.vcf.gz
[2016-04-15T01:07Z] tabix index R14-18105_kapa-NGv3-PE100-NGv3-3_112188604_127703121.vcf.gz
[2016-04-15T01:07Z] platypus variant calling
[2016-04-15T01:07Z] platypus variant calling
[2016-04-15T01:07Z] platypus variant calling
[2016-04-15T01:07Z] tabix index R14-18105_kapa-NGv3-PE100-NGv3-3_174814579_190326970.vcf.gz
[2016-04-15T01:07Z] platypus variant calling
[2016-04-15T01:07Z] tabix index R14-18105_kapa-NGv3-PE100-NGv3-4_165889318_183245405.vcf.gz
[2016-04-15T01:07Z] tabix index R14-18105_kapa-NGv3-PE100-NGv3-4_134075461_150351181.vcf.gz
[2016-04-15T01:07Z] platypus variant calling
[2016-04-15T01:07Z] tabix index R14-18105_kapa-NGv3-PE100-NGv3-5_15616091_31267808.vcf.gz
[2016-04-15T01:07Z] tabix index R14-18105_kapa-NGv3-PE100-NGv3-4_68340604_83852298.vcf.gz
[2016-04-15T01:07Z] platypus variant calling
[2016-04-15T01:07Z] platypus variant calling
[2016-04-15T01:07Z] platypus variant calling
[2016-04-15T01:07Z] tabix index R14-18105_kapa-NGv3-PE100-NGv3-4_150354547_165878648.vcf.gz
[2016-04-15T01:07Z] platypus variant calling
[2016-04-15T01:07Z] tabix index R14-18105_kapa-NGv3-PE100-NGv3-4_99397339_115544957.vcf.gz
[2016-04-15T01:07Z] tabix index R14-18105_kapa-NGv3-PE100-NGv3-4_183267803_191154276.vcf.gz
[2016-04-15T01:07Z] tabix index R14-18105_kapa-NGv3-PE100-NGv3-4_115584857_134074404.vcf.gz
[2016-04-15T01:07Z] platypus variant calling
[2016-04-15T01:07Z] platypus variant calling
[2016-04-15T01:07Z] platypus variant calling
[2016-04-15T01:07Z] tabix index R14-18105_kapa-NGv3-PE100-NGv3-3_190333063_198022430.vcf.gz
[2016-04-15T01:07Z] platypus variant calling
[2016-04-15T01:07Z] tabix index R14-18105_kapa-NGv3-PE100-NGv3-5_96432513_112043579.vcf.gz
[2016-04-15T01:07Z] tabix index R14-18105_kapa-NGv3-PE100-NGv3-5_0_15580921.vcf.gz
[2016-04-15T01:08Z] platypus variant calling
[2016-04-15T01:08Z] platypus variant calling
[2016-04-15T01:08Z] tabix index R14-18105_kapa-NGv3-PE100-NGv3-5_49695692_65288736.vcf.gz
[2016-04-15T01:08Z] platypus variant calling
[2016-04-15T01:08Z] tabix index R14-18105_kapa-NGv3-PE100-NGv3-5_80911291_96430739.vcf.gz
[2016-04-15T01:08Z] tabix index R14-18105_kapa-NGv3-PE100-NGv3-4_0_15511864.vcf.gz
[2016-04-15T01:08Z] INFO  18:08:01,459 ProgressMeter -     19:46269608     7.02504167E8     2.5 m            0.0 s       96.6%     2.6 m       5.0 s
[2016-04-15T01:08Z] platypus variant calling
[2016-04-15T01:08Z] platypus variant calling
[2016-04-15T01:08Z] tabix index R14-18105_kapa-NGv3-PE100-NGv3-5_112073555_127595521.vcf.gz
[2016-04-15T01:08Z] platypus variant calling
[2016-04-15T01:08Z] INFO  18:08:02,368 ProgressMeter -     19:56089718     4.92238551E8     2.5 m            0.0 s       73.8%     3.4 m      53.0 s
[2016-04-15T01:08Z] tabix index R14-18105_kapa-NGv3-PE100-NGv3-5_31294068_49695124.vcf.gz
[2016-04-15T01:08Z] platypus variant calling
[2016-04-15T01:08Z] tabix index R14-18105_kapa-NGv3-PE100-NGv3-5_158711911_174870102.vcf.gz
[2016-04-15T01:08Z] tabix index R14-18105_kapa-NGv3-PE100-NGv3-4_83857133_99393738.vcf.gz
[2016-04-15T01:08Z] platypus variant calling
[2016-04-15T01:08Z] platypus variant calling
[2016-04-15T01:08Z] tabix index R14-18105_kapa-NGv3-PE100-NGv3-5_65290574_80809536.vcf.gz
[2016-04-15T01:08Z] platypus variant calling
[2016-04-15T01:08Z] tabix index R14-18105_kapa-NGv3-PE100-NGv3-6_0_15509601.vcf.gz
[2016-04-15T01:08Z] INFO  18:08:05,400 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.043140712000000005
[2016-04-15T01:08Z] INFO  18:08:05,406 PairHMM - Total compute time in PairHMM computeLikelihoods() : 5.012952639
[2016-04-15T01:08Z] INFO  18:08:05,406 HaplotypeCaller - Ran local assembly on 4483 active regions
[2016-04-15T01:08Z] INFO  18:08:05,465 ProgressMeter -            done     7.46649334E8     2.6 m            0.0 s      100.0%     2.6 m       0.0 s
[2016-04-15T01:08Z] INFO  18:08:05,465 ProgressMeter - Total runtime 154.03 secs, 2.57 min, 0.04 hours
[2016-04-15T01:08Z] INFO  18:08:05,466 MicroScheduler - 122795 reads were filtered out during the traversal out of approximately 1174982 total reads (10.45%)
[2016-04-15T01:08Z] INFO  18:08:05,466 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:08Z] INFO  18:08:05,466 MicroScheduler -   -> 92274 reads (7.85% of total) failing DuplicateReadFilter
[2016-04-15T01:08Z] INFO  18:08:05,467 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:08Z] INFO  18:08:05,467 MicroScheduler -   -> 30521 reads (2.60% of total) failing HCMappingQualityFilter
[2016-04-15T01:08Z] INFO  18:08:05,467 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:08Z] INFO  18:08:05,468 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:08Z] INFO  18:08:05,468 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:08Z] INFO  18:08:05,468 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T01:08Z] platypus variant calling
[2016-04-15T01:08Z] tabix index R14-18105_kapa-NGv3-PE100-NGv3-6_62390867_78173120.vcf.gz
[2016-04-15T01:08Z] platypus variant calling
[2016-04-15T01:08Z] tabix index R14-18105_kapa-NGv3-PE100-NGv3-6_93955015_109466584.vcf.gz
[2016-04-15T01:08Z] tabix index R14-18105_kapa-NGv3-PE100-NGv3-5_143200044_158710347.vcf.gz
[2016-04-15T01:08Z] tabix index R14-18105_kapa-NGv3-PE100-NGv3-6_46598699_62284307.vcf.gz
[2016-04-15T01:08Z] INFO  18:08:07,290 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:08Z] platypus variant calling
[2016-04-15T01:08Z] platypus variant calling
[2016-04-15T01:08Z] platypus variant calling
[2016-04-15T01:08Z] platypus variant calling
[2016-04-15T01:08Z] tabix index R14-18105_kapa-NGv3-PE100-NGv3-3_47129602_62648069.vcf.gz
[2016-04-15T01:08Z] platypus variant calling
[2016-04-15T01:08Z] tabix index R14-18105_kapa-NGv3-PE100-NGv3-6_78400388_93953258.vcf.gz
[2016-04-15T01:08Z] platypus variant calling
[2016-04-15T01:08Z] tabix index R14-18105_kapa-NGv3-PE100-NGv3-5_174919106_180915260.vcf.gz
[2016-04-15T01:08Z] platypus variant calling
[2016-04-15T01:08Z] tabix index R14-18105_kapa-NGv3-PE100-NGv3-6_109467960_124979532.vcf.gz
[2016-04-15T01:08Z] platypus variant calling
[2016-04-15T01:08Z] tabix index R14-18105_kapa-NGv3-PE100-NGv3-6_125112484_142397186.vcf.gz
[2016-04-15T01:08Z] platypus variant calling
[2016-04-15T01:08Z] tabix index R14-18105_kapa-NGv3-PE100-NGv3-7_47319761_63093154.vcf.gz
[2016-04-15T01:08Z] platypus variant calling
[2016-04-15T01:08Z] tabix index R14-18105_kapa-NGv3-PE100-NGv3-6_15511526_31080332.vcf.gz
[2016-04-15T01:08Z] platypus variant calling
[2016-04-15T01:08Z] tabix index R14-18105_kapa-NGv3-PE100-NGv3-6_142399691_157963777.vcf.gz
[2016-04-15T01:08Z] tabix index R14-18105_kapa-NGv3-PE100-NGv3-6_158013810_171115067.vcf.gz
[2016-04-15T01:08Z] platypus variant calling
[2016-04-15T01:08Z] tabix index R14-18105_kapa-NGv3-PE100-NGv3-7_110526648_126079222.vcf.gz
[2016-04-15T01:08Z] tabix index R14-18105_kapa-NGv3-PE100-NGv3-7_15599765_31117713.vcf.gz
[2016-04-15T01:08Z] platypus variant calling
[2016-04-15T01:08Z] platypus variant calling
[2016-04-15T01:08Z] tabix index R14-18105_kapa-NGv3-PE100-NGv3-7_157155854_159138663.vcf.gz
[2016-04-15T01:08Z] platypus variant calling
[2016-04-15T01:08Z] platypus variant calling
[2016-04-15T01:08Z] tabix index R14-18105_kapa-NGv3-PE100-NGv3-7_79082334_94740703.vcf.gz
[2016-04-15T01:08Z] platypus variant calling
[2016-04-15T01:08Z] tabix index R14-18105_kapa-NGv3-PE100-NGv3-7_31120227_47317818.vcf.gz
[2016-04-15T01:08Z] platypus variant calling
[2016-04-15T01:08Z] tabix index R14-18105_kapa-NGv3-PE100-NGv3-7_63095909_78636522.vcf.gz
[2016-04-15T01:08Z] platypus variant calling
[2016-04-15T01:08Z] tabix index R14-18105_kapa-NGv3-PE100-NGv3-7_0_15584548.vcf.gz
[2016-04-15T01:08Z] platypus variant calling
[2016-04-15T01:08Z] tabix index R14-18105_kapa-NGv3-PE100-NGv3-8_48003022_63659688.vcf.gz
[2016-04-15T01:08Z] tabix index R14-18105_kapa-NGv3-PE100-NGv3-8_79513976_95140568.vcf.gz
[2016-04-15T01:08Z] platypus variant calling
[2016-04-15T01:08Z] platypus variant calling
[2016-04-15T01:08Z] tabix index R14-18105_kapa-NGv3-PE100-NGv3-8_63775819_79510770.vcf.gz
[2016-04-15T01:08Z] tabix index R14-18105_kapa-NGv3-PE100-NGv3-5_127597427_143191869.vcf.gz
[2016-04-15T01:08Z] platypus variant calling
[2016-04-15T01:08Z] tabix index R14-18105_kapa-NGv3-PE100-NGv3-8_0_15517156.vcf.gz
[2016-04-15T01:08Z] platypus variant calling
[2016-04-15T01:08Z] platypus variant calling
[2016-04-15T01:08Z] tabix index R14-18105_kapa-NGv3-PE100-NGv3-8_31496910_48001429.vcf.gz
[2016-04-15T01:08Z] platypus variant calling
[2016-04-15T01:08Z] tabix index R14-18105_kapa-NGv3-PE100-NGv3-7_126086124_141619620.vcf.gz
[2016-04-15T01:08Z] platypus variant calling
[2016-04-15T01:08Z] tabix index R14-18105_kapa-NGv3-PE100-NGv3-8_110656864_126194498.vcf.gz
[2016-04-15T01:08Z] tabix index R14-18105_kapa-NGv3-PE100-NGv3-8_126369460_141889736.vcf.gz
[2016-04-15T01:08Z] tabix index R14-18105_kapa-NGv3-PE100-NGv3-8_95142853_110655419.vcf.gz
[2016-04-15T01:08Z] platypus variant calling
[2016-04-15T01:08Z] platypus variant calling
[2016-04-15T01:08Z] platypus variant calling
[2016-04-15T01:08Z] tabix index R14-18105_kapa-NGv3-PE100-NGv3-9_15564086_32405601.vcf.gz
[2016-04-15T01:08Z] platypus variant calling
[2016-04-15T01:08Z] tabix index R14-18105_kapa-NGv3-PE100-NGv3-9_0_15510186.vcf.gz
[2016-04-15T01:08Z] platypus variant calling
[2016-04-15T01:08Z] tabix index R14-18105_kapa-NGv3-PE100-NGv3-8_15519664_31030618.vcf.gz
[2016-04-15T01:08Z] platypus variant calling
[2016-04-15T01:08Z] tabix index R14-18105_kapa-NGv3-PE100-NGv3-9_65507205_82187750.vcf.gz
[2016-04-15T01:08Z] platypus variant calling
[2016-04-15T01:08Z] INFO  18:08:22,766 ProgressMeter -     19:14267848    1.053669734E9     3.0 m            0.0 s       93.4%     3.2 m      12.0 s
[2016-04-15T01:08Z] tabix index R14-18105_kapa-NGv3-PE100-NGv3-7_141629903_157151331.vcf.gz
[2016-04-15T01:08Z] platypus variant calling
[2016-04-15T01:08Z] tabix index R14-18105_kapa-NGv3-PE100-NGv3-9_82188172_97717561.vcf.gz
[2016-04-15T01:08Z] platypus variant calling
[2016-04-15T01:08Z] tabix index R14-18105_kapa-NGv3-PE100-NGv3-10_31137459_46960129.vcf.gz
[2016-04-15T01:08Z] tabix index R14-18105_kapa-NGv3-PE100-NGv3-10_0_15559243.vcf.gz
[2016-04-15T01:08Z] platypus variant calling
[2016-04-15T01:08Z] platypus variant calling
[2016-04-15T01:08Z] tabix index R14-18105_kapa-NGv3-PE100-NGv3-10_15561288_31134502.vcf.gz
[2016-04-15T01:08Z] platypus variant calling
[2016-04-15T01:08Z] tabix index R14-18105_kapa-NGv3-PE100-NGv3-9_97718189_113228306.vcf.gz
[2016-04-15T01:08Z] platypus variant calling
[2016-04-15T01:08Z] tabix index R14-18105_kapa-NGv3-PE100-NGv3-9_32407258_65506776.vcf.gz
[2016-04-15T01:08Z] platypus variant calling
[2016-04-15T01:08Z] tabix index R14-18105_kapa-NGv3-PE100-NGv3-9_113231219_129089575.vcf.gz
[2016-04-15T01:08Z] tabix index R14-18105_kapa-NGv3-PE100-NGv3-10_46960410_62493077.vcf.gz
[2016-04-15T01:08Z] platypus variant calling
[2016-04-15T01:08Z] tabix index R14-18105_kapa-NGv3-PE100-NGv3-8_141900641_146364022.vcf.gz
[2016-04-15T01:08Z] platypus variant calling
[2016-04-15T01:08Z] tabix index R14-18105_kapa-NGv3-PE100-NGv3-10_78316966_93841258.vcf.gz
[2016-04-15T01:08Z] platypus variant calling
[2016-04-15T01:08Z] platypus variant calling
[2016-04-15T01:08Z] tabix index R14-18105_kapa-NGv3-PE100-NGv3-7_94750023_110303777.vcf.gz
[2016-04-15T01:08Z] platypus variant calling
[2016-04-15T01:08Z] tabix index R14-18105_kapa-NGv3-PE100-NGv3-6_31083801_46593245.vcf.gz
[2016-04-15T01:08Z] platypus variant calling
[2016-04-15T01:08Z] tabix index R14-18105_kapa-NGv3-PE100-NGv3-10_127328721_135534747.vcf.gz
[2016-04-15T01:08Z] platypus variant calling
[2016-04-15T01:08Z] tabix index R14-18105_kapa-NGv3-PE100-NGv3-10_62539923_78084243.vcf.gz
[2016-04-15T01:08Z] platypus variant calling
[2016-04-15T01:08Z] INFO  18:08:32,369 ProgressMeter -     19:58773817     7.14394379E8     3.0 m            0.0 s       95.8%     3.1 m       7.0 s
[2016-04-15T01:08Z] tabix index R14-18105_kapa-NGv3-PE100-NGv3-11_16007749_31531554.vcf.gz
[2016-04-15T01:08Z] platypus variant calling
[2016-04-15T01:08Z] tabix index R14-18105_kapa-NGv3-PE100-NGv3-11_78277177_93796886.vcf.gz
[2016-04-15T01:08Z] INFO  18:08:33,800 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.081325699
[2016-04-15T01:08Z] INFO  18:08:33,801 PairHMM - Total compute time in PairHMM computeLikelihoods() : 9.793902714000001
[2016-04-15T01:08Z] INFO  18:08:33,802 HaplotypeCaller - Ran local assembly on 5964 active regions
[2016-04-15T01:08Z] INFO  18:08:33,856 ProgressMeter -            done    1.217430493E9     3.2 m            0.0 s      100.0%     3.2 m       0.0 s
[2016-04-15T01:08Z] INFO  18:08:33,857 ProgressMeter - Total runtime 191.11 secs, 3.19 min, 0.05 hours
[2016-04-15T01:08Z] INFO  18:08:33,857 MicroScheduler - 131935 reads were filtered out during the traversal out of approximately 1472858 total reads (8.96%)
[2016-04-15T01:08Z] INFO  18:08:33,857 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:08Z] INFO  18:08:33,858 MicroScheduler -   -> 119081 reads (8.09% of total) failing DuplicateReadFilter
[2016-04-15T01:08Z] INFO  18:08:33,858 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:08Z] INFO  18:08:33,858 MicroScheduler -   -> 12854 reads (0.87% of total) failing HCMappingQualityFilter
[2016-04-15T01:08Z] INFO  18:08:33,859 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:08Z] INFO  18:08:33,859 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:08Z] INFO  18:08:33,859 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:08Z] INFO  18:08:33,859 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T01:08Z] platypus variant calling
[2016-04-15T01:08Z] tabix index R14-18105_kapa-NGv3-PE100-NGv3-10_111628371_127265443.vcf.gz
[2016-04-15T01:08Z] platypus variant calling
[2016-04-15T01:08Z] tabix index R14-18105_kapa-NGv3-PE100-NGv3-11_93797496_109964158.vcf.gz
[2016-04-15T01:08Z] platypus variant calling
[2016-04-15T01:08Z] INFO  18:08:35,159 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:08Z] tabix index R14-18105_kapa-NGv3-PE100-NGv3-11_31541602_47074069.vcf.gz
[2016-04-15T01:08Z] platypus variant calling
[2016-04-15T01:08Z] platypus variant calling
[2016-04-15T01:08Z] tabix index R14-18105_kapa-NGv3-PE100-NGv3-11_125523640_135006516.vcf.gz
[2016-04-15T01:08Z] platypus variant calling
[2016-04-15T01:08Z] tabix index R14-18105_kapa-NGv3-PE100-NGv3-12_15650178_31231471.vcf.gz
[2016-04-15T01:08Z] platypus variant calling
[2016-04-15T01:08Z] tabix index R14-18105_kapa-NGv3-PE100-NGv3-13_0_19748299.vcf.gz
[2016-04-15T01:08Z] tabix index R14-18105_kapa-NGv3-PE100-NGv3-12_78334098_93863131.vcf.gz
[2016-04-15T01:08Z] platypus variant calling
[2016-04-15T01:08Z] platypus variant calling
[2016-04-15T01:08Z] INFO  18:08:38,815 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.091255863
[2016-04-15T01:08Z] INFO  18:08:38,816 PairHMM - Total compute time in PairHMM computeLikelihoods() : 19.247691997
[2016-04-15T01:08Z] INFO  18:08:38,816 HaplotypeCaller - Ran local assembly on 4915 active regions
[2016-04-15T01:08Z] INFO  18:08:38,851 ProgressMeter -            done      7.6177958E8     3.1 m            0.0 s      100.0%     3.1 m       0.0 s
[2016-04-15T01:08Z] INFO  18:08:38,862 ProgressMeter - Total runtime 186.52 secs, 3.11 min, 0.05 hours
[2016-04-15T01:08Z] INFO  18:08:38,863 MicroScheduler - 148289 reads were filtered out during the traversal out of approximately 1301861 total reads (11.39%)
[2016-04-15T01:08Z] INFO  18:08:38,864 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:08Z] INFO  18:08:38,865 MicroScheduler -   -> 101423 reads (7.79% of total) failing DuplicateReadFilter
[2016-04-15T01:08Z] INFO  18:08:38,866 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:08Z] INFO  18:08:38,867 MicroScheduler -   -> 46866 reads (3.60% of total) failing HCMappingQualityFilter
[2016-04-15T01:08Z] INFO  18:08:38,867 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:08Z] INFO  18:08:38,868 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:08Z] INFO  18:08:38,869 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:08Z] INFO  18:08:38,870 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T01:08Z] tabix index R14-18105_kapa-NGv3-PE100-NGv3-12_62687959_78225484.vcf.gz
[2016-04-15T01:08Z] platypus variant calling
[2016-04-15T01:08Z] tabix index R14-18105_kapa-NGv3-PE100-NGv3-10_93851586_111625070.vcf.gz
[2016-04-15T01:08Z] platypus variant calling
[2016-04-15T01:08Z] INFO  18:08:40,161 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:08Z] platypus variant calling
[2016-04-15T01:08Z] tabix index R14-18105_kapa-NGv3-PE100-NGv3-12_125267228_133851895.vcf.gz
[2016-04-15T01:08Z] platypus variant calling
[2016-04-15T01:08Z] tabix index R14-18105_kapa-NGv3-PE100-NGv3-13_51396767_67205543.vcf.gz
[2016-04-15T01:08Z] platypus variant calling
[2016-04-15T01:08Z] tabix index R14-18105_kapa-NGv3-PE100-NGv3-13_67477635_84455642.vcf.gz
[2016-04-15T01:08Z] tabix index R14-18105_kapa-NGv3-PE100-NGv3-14_0_19378574.vcf.gz
[2016-04-15T01:08Z] platypus variant calling
[2016-04-15T01:08Z] tabix index R14-18105_kapa-NGv3-PE100-NGv3-12_93870729_109490566.vcf.gz
[2016-04-15T01:08Z] platypus variant calling
[2016-04-15T01:08Z] platypus variant calling
[2016-04-15T01:08Z] tabix index R14-18105_kapa-NGv3-PE100-NGv3-13_86368117_101881935.vcf.gz
[2016-04-15T01:08Z] platypus variant calling
[2016-04-15T01:08Z] tabix index R14-18105_kapa-NGv3-PE100-NGv3-13_35615069_51287376.vcf.gz
[2016-04-15T01:08Z] tabix index R14-18105_kapa-NGv3-PE100-NGv3-11_47158866_62678572.vcf.gz
[2016-04-15T01:08Z] platypus variant calling
[2016-04-15T01:08Z] platypus variant calling
[2016-04-15T01:08Z] tabix index R14-18105_kapa-NGv3-PE100-NGv3-13_19751066_35517251.vcf.gz
[2016-04-15T01:08Z] platypus variant calling
[2016-04-15T01:08Z] tabix index R14-18105_kapa-NGv3-PE100-NGv3-11_110001730_125514538.vcf.gz
[2016-04-15T01:08Z] platypus variant calling
[2016-04-15T01:08Z] tabix index R14-18105_kapa-NGv3-PE100-NGv3-15_0_20740485.vcf.gz
[2016-04-15T01:08Z] platypus variant calling
[2016-04-15T01:08Z] tabix index R14-18105_kapa-NGv3-PE100-NGv3-14_35072553_50583270.vcf.gz
[2016-04-15T01:08Z] tabix index R14-18105_kapa-NGv3-PE100-NGv3-9_129097484_141213431.vcf.gz
[2016-04-15T01:08Z] platypus variant calling
[2016-04-15T01:08Z] platypus variant calling
[2016-04-15T01:08Z] tabix index R14-18105_kapa-NGv3-PE100-NGv3-12_31236746_46754992.vcf.gz
[2016-04-15T01:08Z] platypus variant calling
[2016-04-15T01:08Z] tabix index R14-18105_kapa-NGv3-PE100-NGv3-13_101890105_115169878.vcf.gz
[2016-04-15T01:08Z] platypus variant calling
[2016-04-15T01:08Z] tabix index R14-18105_kapa-NGv3-PE100-NGv3-12_0_15637181.vcf.gz
[2016-04-15T01:08Z] platypus variant calling
[2016-04-15T01:08Z] tabix index R14-18105_kapa-NGv3-PE100-NGv3-15_98984299_102531392.vcf.gz
[2016-04-15T01:08Z] platypus variant calling
[2016-04-15T01:08Z] tabix index R14-18105_kapa-NGv3-PE100-NGv3-14_81651874_97299968.vcf.gz
[2016-04-15T01:08Z] tabix index R14-18105_kapa-NGv3-PE100-NGv3-14_50585061_66096324.vcf.gz
[2016-04-15T01:08Z] platypus variant calling
[2016-04-15T01:08Z] platypus variant calling
[2016-04-15T01:08Z] tabix index R14-18105_kapa-NGv3-PE100-NGv3-12_109494486_125263132.vcf.gz
[2016-04-15T01:08Z] platypus variant calling
[2016-04-15T01:08Z] tabix index R14-18105_kapa-NGv3-PE100-NGv3-15_20741621_36872162.vcf.gz
[2016-04-15T01:08Z] platypus variant calling
[2016-04-15T01:08Z] tabix index R14-18105_kapa-NGv3-PE100-NGv3-14_66135960_81646674.vcf.gz
[2016-04-15T01:08Z] tabix index R14-18105_kapa-NGv3-PE100-NGv3-16_31120544_46629582.vcf.gz
[2016-04-15T01:08Z] platypus variant calling
[2016-04-15T01:08Z] platypus variant calling
[2016-04-15T01:08Z] tabix index R14-18105_kapa-NGv3-PE100-NGv3-11_0_15994658.vcf.gz
[2016-04-15T01:08Z] tabix index R14-18105_kapa-NGv3-PE100-NGv3-14_97304098_107349540.vcf.gz
[2016-04-15T01:08Z] platypus variant calling
[2016-04-15T01:08Z] platypus variant calling
[2016-04-15T01:08Z] tabix index R14-18105_kapa-NGv3-PE100-NGv3-15_83448996_98982979.vcf.gz
[2016-04-15T01:08Z] platypus variant calling
[2016-04-15T01:08Z] tabix index R14-18105_kapa-NGv3-PE100-NGv3-15_52404364_67923265.vcf.gz
[2016-04-15T01:08Z] tabix index R14-18105_kapa-NGv3-PE100-NGv3-11_62744265_78270665.vcf.gz
[2016-04-15T01:08Z] platypus variant calling
[2016-04-15T01:08Z] platypus variant calling
[2016-04-15T01:08Z] tabix index R14-18105_kapa-NGv3-PE100-NGv3-14_19553416_35066851.vcf.gz
[2016-04-15T01:08Z] platypus variant calling
[2016-04-15T01:08Z] tabix index R14-18105_kapa-NGv3-PE100-NGv3-15_67932890_83447639.vcf.gz
[2016-04-15T01:08Z] platypus variant calling
[2016-04-15T01:09Z] tabix index R14-18105_kapa-NGv3-PE100-NGv3-16_46633742_64982002.vcf.gz
[2016-04-15T01:09Z] platypus variant calling
[2016-04-15T01:09Z] tabix index R14-18105_kapa-NGv3-PE100-NGv3-18_0_18531348.vcf.gz
[2016-04-15T01:09Z] platypus variant calling
[2016-04-15T01:09Z] tabix index R14-18105_kapa-NGv3-PE100-NGv3-15_36887086_52402170.vcf.gz
[2016-04-15T01:09Z] platypus variant calling
[2016-04-15T01:09Z] tabix index R14-18105_kapa-NGv3-PE100-NGv3-18_18533538_34081962.vcf.gz
[2016-04-15T01:09Z] tabix index R14-18105_kapa-NGv3-PE100-NGv3-12_46756066_62654284.vcf.gz
[2016-04-15T01:09Z] tabix index R14-18105_kapa-NGv3-PE100-NGv3-16_80575258_90354753.vcf.gz
[2016-04-15T01:09Z] platypus variant calling
[2016-04-15T01:09Z] platypus variant calling
[2016-04-15T01:09Z] platypus variant calling
[2016-04-15T01:09Z] tabix index R14-18105_kapa-NGv3-PE100-NGv3-18_34092400_49867248.vcf.gz
[2016-04-15T01:09Z] platypus variant calling
[2016-04-15T01:09Z] tabix index R14-18105_kapa-NGv3-PE100-NGv3-17_77707305_81195210.vcf.gz
[2016-04-15T01:09Z] platypus variant calling
[2016-04-15T01:09Z] tabix index R14-18105_kapa-NGv3-PE100-NGv3-18_66346699_78077248.vcf.gz
[2016-04-15T01:09Z] tabix index R14-18105_kapa-NGv3-PE100-NGv3-18_50278423_66344430.vcf.gz
[2016-04-15T01:09Z] platypus variant calling
[2016-04-15T01:09Z] platypus variant calling
[2016-04-15T01:09Z] tabix index R14-18105_kapa-NGv3-PE100-NGv3-17_46607689_62121560.vcf.gz
[2016-04-15T01:09Z] platypus variant calling
[2016-04-15T01:09Z] tabix index R14-18105_kapa-NGv3-PE100-NGv3-20_62831244_63025520.vcf.gz
[2016-04-15T01:09Z] platypus variant calling
[2016-04-15T01:09Z] tabix index R14-18105_kapa-NGv3-PE100-NGv3-17_15515955_31039213.vcf.gz
[2016-04-15T01:09Z] platypus variant calling
[2016-04-15T01:09Z] tabix index R14-18105_kapa-NGv3-PE100-NGv3-21_0_15517120.vcf.gz
[2016-04-15T01:09Z] platypus variant calling
[2016-04-15T01:09Z] tabix index R14-18105_kapa-NGv3-PE100-NGv3-16_64982511_80574976.vcf.gz
[2016-04-15T01:09Z] platypus variant calling
[2016-04-15T01:09Z] tabix index R14-18105_kapa-NGv3-PE100-NGv3-16_15596122_31106473.vcf.gz
[2016-04-15T01:09Z] platypus variant calling
[2016-04-15T01:09Z] tabix index R14-18105_kapa-NGv3-PE100-NGv3-22_0_16258303.vcf.gz
[2016-04-15T01:09Z] tabix index R14-18105_kapa-NGv3-PE100-NGv3-21_15524893_31045484.vcf.gz
[2016-04-15T01:09Z] platypus variant calling
[2016-04-15T01:09Z] tabix index R14-18105_kapa-NGv3-PE100-NGv3-20_15866408_31376818.vcf.gz
[2016-04-15T01:09Z] tabix index R14-18105_kapa-NGv3-PE100-NGv3-20_0_15843471.vcf.gz
[2016-04-15T01:09Z] platypus variant calling
[2016-04-15T01:09Z] platypus variant calling
[2016-04-15T01:09Z] platypus variant calling
[2016-04-15T01:09Z] tabix index R14-18105_kapa-NGv3-PE100-NGv3-17_62122219_77705154.vcf.gz
[2016-04-15T01:09Z] platypus variant calling
[2016-04-15T01:09Z] tabix index R14-18105_kapa-NGv3-PE100-NGv3-16_0_15528616.vcf.gz
[2016-04-15T01:09Z] tabix index R14-18105_kapa-NGv3-PE100-NGv3-21_46595644_48129895.vcf.gz
[2016-04-15T01:09Z] platypus variant calling
[2016-04-15T01:09Z] platypus variant calling
[2016-04-15T01:09Z] tabix index R14-18105_kapa-NGv3-PE100-NGv3-X_0_15509380.vcf.gz
[2016-04-15T01:09Z] platypus variant calling
[2016-04-15T01:09Z] tabix index R14-18105_kapa-NGv3-PE100-NGv3-X_15518899_31090070.vcf.gz
[2016-04-15T01:09Z] tabix index R14-18105_kapa-NGv3-PE100-NGv3-X_31139949_46696637.vcf.gz
[2016-04-15T01:09Z] platypus variant calling
[2016-04-15T01:09Z] platypus variant calling
[2016-04-15T01:09Z] tabix index R14-18105_kapa-NGv3-PE100-NGv3-X_78616585_95940189.vcf.gz
[2016-04-15T01:09Z] tabix index R14-18105_kapa-NGv3-PE100-NGv3-22_47309229_51304566.vcf.gz
[2016-04-15T01:09Z] platypus variant calling
[2016-04-15T01:09Z] platypus variant calling
[2016-04-15T01:09Z] tabix index R14-18105_kapa-NGv3-PE100-NGv3-20_47244085_62830269.vcf.gz
[2016-04-15T01:09Z] tabix index R14-18105_kapa-NGv3-PE100-NGv3-19_15510112_31025906.vcf.gz
[2016-04-15T01:09Z] platypus variant calling
[2016-04-15T01:09Z] platypus variant calling
[2016-04-15T01:09Z] tabix index R14-18105_kapa-NGv3-PE100-NGv3-17_0_15511002.vcf.gz
[2016-04-15T01:09Z] tabix index R14-18105_kapa-NGv3-PE100-NGv3-20_31379406_47242465.vcf.gz
[2016-04-15T01:09Z] tabix index R14-18105_kapa-NGv3-PE100-NGv3-Y_0_15522993.vcf.gz
[2016-04-15T01:09Z] platypus variant calling
[2016-04-15T01:09Z] tabix index R14-18105_kapa-NGv3-PE100-NGv3-X_62857907_78427545.vcf.gz
[2016-04-15T01:09Z] platypus variant calling
[2016-04-15T01:09Z] tabix index R14-18105_kapa-NGv3-PE100-NGv3-Y_59228291_59373566.vcf.gz
[2016-04-15T01:09Z] GATK: UnifiedGenotyper
[2016-04-15T01:09Z] GATK: UnifiedGenotyper
[2016-04-15T01:09Z] tabix index R14-18105_kapa-NGv3-PE100-NGv3-X_111874647_128581278.vcf.gz
[2016-04-15T01:09Z] GATK: UnifiedGenotyper
[2016-04-15T01:09Z] GATK: UnifiedGenotyper
[2016-04-15T01:09Z] tabix index R14-18105_kapa-NGv3-PE100-NGv3-X_95990756_111698889.vcf.gz
[2016-04-15T01:09Z] tabix index R14-18105_kapa-NGv3-PE100-NGv3-X_46712910_62570698.vcf.gz
[2016-04-15T01:09Z] tabix index R14-18105_kapa-NGv3-PE100-NGv3-X_128582278_144329181.vcf.gz
[2016-04-15T01:09Z] GATK: UnifiedGenotyper
[2016-04-15T01:09Z] GATK: UnifiedGenotyper
[2016-04-15T01:09Z] GATK: UnifiedGenotyper
[2016-04-15T01:09Z] tabix index R14-18105_kapa-NGv3-PE100-NGv3-Y_15526614_59222281.vcf.gz
[2016-04-15T01:09Z] GATK: UnifiedGenotyper
[2016-04-15T01:09Z] tabix index R14-18105_kapa-NGv3-PE100-NGv3-17_31048040_46607237.vcf.gz
[2016-04-15T01:09Z] GATK: UnifiedGenotyper
[2016-04-15T01:09Z] tabix index R14-18105_kapa-NGv3-PE100-NGv3-21_31062047_46591599.vcf.gz
[2016-04-15T01:09Z] GATK: UnifiedGenotyper
[2016-04-15T01:09Z] INFO  18:09:25,185 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:09Z] INFO  18:09:25,189 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:09Z] INFO  18:09:25,190 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:09Z] INFO  18:09:25,191 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:09Z] INFO  18:09:25,196 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/1/R14-18102_kapa-NGv3-PE100-NGv3-sort-1_46715671_62228851-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/1/R14-18102_kapa-NGv3-PE100-NGv3-1_46715671_62228851-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/1/tx/tmpfob9Rs/R14-18102_kapa-NGv3-PE100-NGv3-1_46715671_62228851.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:09Z] INFO  18:09:25,236 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:09Z] INFO  18:09:25,236 HelpFormatter - Date/Time: 2016/04/14 18:09:25
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[2016-04-15T01:09Z] INFO  18:09:25,237 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:09Z] INFO  18:09:25,548 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:09Z] INFO  18:09:25,770 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T01:09Z] INFO  18:09:25,779 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:09Z] tabix index R14-18105_kapa-NGv3-PE100-NGv3-X_144337190_155270560.vcf.gz
[2016-04-15T01:09Z] INFO  18:09:25,862 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-15T01:09Z] INFO  18:09:25,882 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:09Z] INFO  18:09:25,887 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:09Z] INFO  18:09:25,888 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:09Z] INFO  18:09:25,888 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:09Z] INFO  18:09:25,893 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/1/R14-18102_kapa-NGv3-PE100-NGv3-sort-1_62231950_77749296-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/1/R14-18102_kapa-NGv3-PE100-NGv3-1_62231950_77749296-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/1/tx/tmp2k60so/R14-18102_kapa-NGv3-PE100-NGv3-1_62231950_77749296.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:09Z] INFO  18:09:25,912 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:09Z] INFO  18:09:25,913 HelpFormatter - Date/Time: 2016/04/14 18:09:25
[2016-04-15T01:09Z] INFO  18:09:25,914 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:09Z] INFO  18:09:25,914 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:09Z] INFO  18:09:26,040 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:09Z] INFO  18:09:26,043 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:09Z] INFO  18:09:26,044 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:09Z] INFO  18:09:26,044 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:09Z] INFO  18:09:26,048 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/1/R14-18102_kapa-NGv3-PE100-NGv3-sort-1_0_15541927-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/1/R14-18102_kapa-NGv3-PE100-NGv3-1_0_15541927-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/1/tx/tmpD5CzmF/R14-18102_kapa-NGv3-PE100-NGv3-1_0_15541927.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:09Z] INFO  18:09:26,058 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:09Z] INFO  18:09:26,064 HelpFormatter - Date/Time: 2016/04/14 18:09:26
[2016-04-15T01:09Z] INFO  18:09:26,064 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:09Z] INFO  18:09:26,065 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:09Z] INFO  18:09:26,087 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:09Z] INFO  18:09:26,117 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:09Z] INFO  18:09:26,121 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:09Z] INFO  18:09:26,121 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:09Z] INFO  18:09:26,122 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:09Z] INFO  18:09:26,126 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/1/R14-18102_kapa-NGv3-PE100-NGv3-sort-1_77752625_93297674-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/1/R14-18102_kapa-NGv3-PE100-NGv3-1_77752625_93297674-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/1/tx/tmpU1kuxq/R14-18102_kapa-NGv3-PE100-NGv3-1_77752625_93297674.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:09Z] GATK: UnifiedGenotyper
[2016-04-15T01:09Z] INFO  18:09:26,133 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:09Z] INFO  18:09:26,135 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:09Z] INFO  18:09:26,135 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:09Z] INFO  18:09:26,136 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:09Z] INFO  18:09:26,137 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:09Z] INFO  18:09:26,141 HelpFormatter - Date/Time: 2016/04/14 18:09:26
[2016-04-15T01:09Z] INFO  18:09:26,142 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:09Z] INFO  18:09:26,142 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:09Z] INFO  18:09:26,150 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/1/R14-18102_kapa-NGv3-PE100-NGv3-sort-1_31187093_46714270-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/1/R14-18102_kapa-NGv3-PE100-NGv3-1_31187093_46714270-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/1/tx/tmpyyoJrZ/R14-18102_kapa-NGv3-PE100-NGv3-1_31187093_46714270.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:09Z] INFO  18:09:26,173 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:09Z] INFO  18:09:26,176 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:09Z] INFO  18:09:26,176 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:09Z] INFO  18:09:26,177 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:09Z] INFO  18:09:26,177 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:09Z] INFO  18:09:26,180 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:09Z] INFO  18:09:26,180 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:09Z] INFO  18:09:26,180 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:09Z] INFO  18:09:26,180 HelpFormatter - Date/Time: 2016/04/14 18:09:26
[2016-04-15T01:09Z] INFO  18:09:26,180 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:09Z] INFO  18:09:26,181 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:09Z] INFO  18:09:26,180 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/1/R14-18102_kapa-NGv3-PE100-NGv3-sort-1_15545821_31186478-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/1/R14-18102_kapa-NGv3-PE100-NGv3-1_15545821_31186478-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/1/tx/tmpNly3ut/R14-18102_kapa-NGv3-PE100-NGv3-1_15545821_31186478.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:09Z] INFO  18:09:26,180 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:09Z] INFO  18:09:26,184 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/1/R14-18102_kapa-NGv3-PE100-NGv3-sort-1_93298945_108993401-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/1/R14-18102_kapa-NGv3-PE100-NGv3-1_93298945_108993401-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/1/tx/tmp6z4hDg/R14-18102_kapa-NGv3-PE100-NGv3-1_93298945_108993401.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:09Z] INFO  18:09:26,193 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:09Z] INFO  18:09:26,199 HelpFormatter - Date/Time: 2016/04/14 18:09:26
[2016-04-15T01:09Z] INFO  18:09:26,199 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:09Z] INFO  18:09:26,199 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:09Z] INFO  18:09:26,208 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:09Z] INFO  18:09:26,215 HelpFormatter - Date/Time: 2016/04/14 18:09:26
[2016-04-15T01:09Z] INFO  18:09:26,215 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:09Z] INFO  18:09:26,216 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:09Z] INFO  18:09:26,248 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:09Z] INFO  18:09:26,340 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T01:09Z] INFO  18:09:26,346 IntervalUtils - Processing 180557 bp from intervals
[2016-04-15T01:09Z] WARN  18:09:26,351 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:09Z] INFO  18:09:26,354 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:09Z] INFO  18:09:26,373 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:09Z] INFO  18:09:26,383 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:09Z] INFO  18:09:26,417 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:09Z] INFO  18:09:26,456 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.10
[2016-04-15T01:09Z] INFO  18:09:26,459 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:09Z] INFO  18:09:26,526 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T01:09Z] INFO  18:09:26,539 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:09Z] INFO  18:09:26,554 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:09Z] INFO  18:09:26,616 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T01:09Z] INFO  18:09:26,629 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:09Z] INFO  18:09:26,628 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:09Z] INFO  18:09:26,631 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:09Z] INFO  18:09:26,632 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:09Z] INFO  18:09:26,632 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:09Z] INFO  18:09:26,632 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:09Z] INFO  18:09:26,633 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:09Z] INFO  18:09:26,633 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T01:09Z] INFO  18:09:26,634 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T01:09Z] INFO  18:09:26,637 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/1/R14-18102_kapa-NGv3-PE100-NGv3-sort-1_108994811_143767848-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/1/R14-18102_kapa-NGv3-PE100-NGv3-1_108994811_143767848-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/1/tx/tmpjMZouT/R14-18102_kapa-NGv3-PE100-NGv3-1_108994811_143767848.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:09Z] INFO  18:09:26,648 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:09Z] INFO  18:09:26,652 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T01:09Z] INFO  18:09:26,658 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.12
[2016-04-15T01:09Z] INFO  18:09:26,658 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T01:09Z] INFO  18:09:26,659 HelpFormatter - Date/Time: 2016/04/14 18:09:26
[2016-04-15T01:09Z] INFO  18:09:26,659 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:09Z] INFO  18:09:26,661 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:09Z] INFO  18:09:26,661 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:09Z] INFO  18:09:26,671 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T01:09Z] INFO  18:09:26,677 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:09Z] INFO  18:09:26,681 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:09Z] INFO  18:09:26,695 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:09Z] INFO  18:09:26,696 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:09Z] INFO  18:09:26,704 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-15T01:09Z] INFO  18:09:26,719 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-15T01:09Z] INFO  18:09:26,742 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-15T01:09Z] INFO  18:09:26,755 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-15T01:09Z] INFO  18:09:26,884 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:09Z] INFO  18:09:26,888 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:09Z] INFO  18:09:26,891 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:09Z] INFO  18:09:26,892 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:09Z] INFO  18:09:26,892 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:09Z] INFO  18:09:26,897 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/1/R14-18102_kapa-NGv3-PE100-NGv3-sort-1_143897546_159410511-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/1/R14-18102_kapa-NGv3-PE100-NGv3-1_143897546_159410511-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/1/tx/tmpAzUGAB/R14-18102_kapa-NGv3-PE100-NGv3-1_143897546_159410511.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:09Z] INFO  18:09:26,909 IntervalUtils - Processing 150085 bp from intervals
[2016-04-15T01:09Z] INFO  18:09:26,916 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:09Z] INFO  18:09:26,917 HelpFormatter - Date/Time: 2016/04/14 18:09:26
[2016-04-15T01:09Z] INFO  18:09:26,917 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:09Z] INFO  18:09:26,918 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:09Z] WARN  18:09:26,925 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:09Z] INFO  18:09:27,032 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:09Z] INFO  18:09:27,134 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:09Z] INFO  18:09:27,163 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:09Z] INFO  18:09:27,164 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:09Z] INFO  18:09:27,165 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T01:09Z] INFO  18:09:27,166 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T01:09Z] INFO  18:09:27,198 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T01:09Z] INFO  18:09:27,205 IntervalUtils - Processing 390138 bp from intervals
[2016-04-15T01:09Z] INFO  18:09:27,209 IntervalUtils - Processing 386393 bp from intervals
[2016-04-15T01:09Z] WARN  18:09:27,211 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:09Z] INFO  18:09:27,210 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:09Z] WARN  18:09:27,214 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:09Z] INFO  18:09:27,254 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:09Z] INFO  18:09:27,255 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:09Z] INFO  18:09:27,280 IntervalUtils - Processing 145368 bp from intervals
[2016-04-15T01:09Z] WARN  18:09:27,285 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:09Z] INFO  18:09:27,289 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:09Z] INFO  18:09:27,294 IntervalUtils - Processing 113118 bp from intervals
[2016-04-15T01:09Z] WARN  18:09:27,298 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:09Z] INFO  18:09:27,304 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:09Z] INFO  18:09:27,324 IntervalUtils - Processing 431182 bp from intervals
[2016-04-15T01:09Z] WARN  18:09:27,329 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:09Z] INFO  18:09:27,365 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T01:09Z] INFO  18:09:27,373 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:09Z] INFO  18:09:27,374 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:09Z] INFO  18:09:27,385 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:09Z] INFO  18:09:27,401 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:09Z] INFO  18:09:27,402 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:09Z] INFO  18:09:27,402 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T01:09Z] INFO  18:09:27,403 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T01:09Z] INFO  18:09:27,410 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:09Z] INFO  18:09:27,421 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:09Z] INFO  18:09:27,422 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:09Z] INFO  18:09:27,423 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T01:09Z] INFO  18:09:27,424 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T01:09Z] INFO  18:09:27,425 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.21
[2016-04-15T01:09Z] INFO  18:09:27,446 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:09Z] INFO  18:09:27,447 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:09Z] INFO  18:09:27,458 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:09Z] INFO  18:09:27,459 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:09Z] INFO  18:09:27,459 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T01:09Z] INFO  18:09:27,460 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T01:09Z] INFO  18:09:27,452 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:09Z] INFO  18:09:27,466 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:09Z] INFO  18:09:27,468 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T01:09Z] INFO  18:09:27,467 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.09
[2016-04-15T01:09Z] INFO  18:09:27,482 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:09Z] INFO  18:09:27,483 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T01:09Z] INFO  18:09:27,483 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:09Z] INFO  18:09:27,499 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:09Z] INFO  18:09:27,502 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:09Z] INFO  18:09:27,512 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:09Z] INFO  18:09:27,513 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:09Z] INFO  18:09:27,514 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T01:09Z] INFO  18:09:27,514 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T01:09Z] INFO  18:09:27,563 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:09Z] INFO  18:09:27,564 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:09Z] INFO  18:09:27,577 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:09Z] INFO  18:09:27,578 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:09Z] INFO  18:09:27,735 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:09Z] INFO  18:09:27,738 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:09Z] INFO  18:09:27,739 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:09Z] INFO  18:09:27,739 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:09Z] INFO  18:09:27,744 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/1/R14-18102_kapa-NGv3-PE100-NGv3-sort-1_159504867_175046963-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/1/R14-18102_kapa-NGv3-PE100-NGv3-1_159504867_175046963-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/1/tx/tmp66ybOD/R14-18102_kapa-NGv3-PE100-NGv3-1_159504867_175046963.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:09Z] INFO  18:09:27,756 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:09Z] INFO  18:09:27,758 HelpFormatter - Date/Time: 2016/04/14 18:09:27
[2016-04-15T01:09Z] INFO  18:09:27,758 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:09Z] INFO  18:09:27,759 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:09Z] INFO  18:09:27,883 IntervalUtils - Processing 258252 bp from intervals
[2016-04-15T01:09Z] WARN  18:09:27,889 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:09Z] INFO  18:09:27,930 IntervalUtils - Processing 517409 bp from intervals
[2016-04-15T01:09Z] WARN  18:09:27,936 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:09Z] INFO  18:09:27,943 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:09Z] INFO  18:09:27,957 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:09Z] INFO  18:09:28,002 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:09Z] INFO  18:09:28,034 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:09Z] INFO  18:09:28,040 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:09Z] INFO  18:09:28,040 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T01:09Z] INFO  18:09:28,041 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T01:09Z] INFO  18:09:28,092 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:09Z] INFO  18:09:28,092 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:09Z] INFO  18:09:28,100 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:09Z] INFO  18:09:28,104 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:09Z] INFO  18:09:28,105 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T01:09Z] INFO  18:09:28,106 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T01:09Z] INFO  18:09:28,113 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T01:09Z] INFO  18:09:28,122 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:09Z] INFO  18:09:28,164 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:09Z] INFO  18:09:28,165 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:09Z] INFO  18:09:28,192 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-15T01:09Z] INFO  18:09:28,815 IntervalUtils - Processing 261574 bp from intervals
[2016-04-15T01:09Z] WARN  18:09:28,827 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:09Z] INFO  18:09:28,990 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:09Z] INFO  18:09:29,077 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:09Z] INFO  18:09:29,078 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:09Z] INFO  18:09:29,079 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T01:09Z] INFO  18:09:29,080 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T01:09Z] INFO  18:09:29,080 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:09Z] INFO  18:09:29,084 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:09Z] INFO  18:09:29,085 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:09Z] INFO  18:09:29,085 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:09Z] INFO  18:09:29,090 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/1/R14-18102_kapa-NGv3-PE100-NGv3-sort-1_175048468_192127886-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/1/R14-18102_kapa-NGv3-PE100-NGv3-1_175048468_192127886-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/1/tx/tmpFP8g4b/R14-18102_kapa-NGv3-PE100-NGv3-1_175048468_192127886.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:09Z] INFO  18:09:29,101 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:09Z] INFO  18:09:29,113 HelpFormatter - Date/Time: 2016/04/14 18:09:29
[2016-04-15T01:09Z] INFO  18:09:29,114 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:09Z] INFO  18:09:29,115 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:09Z] INFO  18:09:29,134 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:09Z] INFO  18:09:29,135 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:09Z] tabix index R14-18105_kapa-NGv3-PE100-NGv3-22_31796605_47308085.vcf.gz
[2016-04-15T01:09Z] INFO  18:09:29,366 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:09Z] INFO  18:09:29,680 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T01:09Z] INFO  18:09:29,701 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:09Z] GATK: UnifiedGenotyper
[2016-04-15T01:09Z] INFO  18:09:29,792 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.09
[2016-04-15T01:09Z] INFO  18:09:30,413 IntervalUtils - Processing 191568 bp from intervals
[2016-04-15T01:09Z] WARN  18:09:30,418 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:09Z] INFO  18:09:30,569 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:09Z] INFO  18:09:30,720 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:09Z] INFO  18:09:30,721 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:09Z] INFO  18:09:30,722 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T01:09Z] INFO  18:09:30,723 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T01:09Z] INFO  18:09:30,803 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:09Z] INFO  18:09:30,814 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:09Z] tabix index R14-18105_kapa-NGv3-PE100-NGv3-22_16266928_31795711.vcf.gz
[2016-04-15T01:09Z] GATK: UnifiedGenotyper
[2016-04-15T01:09Z] INFO  18:09:33,137 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:09Z] INFO  18:09:33,146 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:09Z] INFO  18:09:33,147 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:09Z] INFO  18:09:33,147 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:09Z] INFO  18:09:33,156 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/1/R14-18102_kapa-NGv3-PE100-NGv3-sort-1_192128349_207640257-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/1/R14-18102_kapa-NGv3-PE100-NGv3-1_192128349_207640257-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/1/tx/tmpwPur4A/R14-18102_kapa-NGv3-PE100-NGv3-1_192128349_207640257.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:09Z] INFO  18:09:33,170 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:09Z] INFO  18:09:33,171 HelpFormatter - Date/Time: 2016/04/14 18:09:33
[2016-04-15T01:09Z] INFO  18:09:33,172 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:09Z] INFO  18:09:33,172 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:09Z] INFO  18:09:33,393 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:09Z] INFO  18:09:33,665 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T01:09Z] INFO  18:09:33,685 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:09Z] INFO  18:09:33,766 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-15T01:09Z] INFO  18:09:34,408 IntervalUtils - Processing 282740 bp from intervals
[2016-04-15T01:09Z] WARN  18:09:34,413 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:09Z] INFO  18:09:34,552 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:09Z] INFO  18:09:34,685 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:09Z] INFO  18:09:34,686 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:09Z] INFO  18:09:34,687 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T01:09Z] INFO  18:09:34,687 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T01:09Z] INFO  18:09:34,729 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:09Z] INFO  18:09:34,730 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:09Z] INFO  18:09:35,787 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:09Z] INFO  18:09:35,790 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:09Z] INFO  18:09:35,791 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:09Z] INFO  18:09:35,792 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:09Z] INFO  18:09:35,796 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/1/R14-18102_kapa-NGv3-PE100-NGv3-sort-1_207641871_223156451-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/1/R14-18102_kapa-NGv3-PE100-NGv3-1_207641871_223156451-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/1/tx/tmptgeyyx/R14-18102_kapa-NGv3-PE100-NGv3-1_207641871_223156451.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:09Z] INFO  18:09:35,822 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:09Z] INFO  18:09:35,823 HelpFormatter - Date/Time: 2016/04/14 18:09:35
[2016-04-15T01:09Z] INFO  18:09:35,824 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:09Z] INFO  18:09:35,824 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:09Z] INFO  18:09:36,051 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:09Z] INFO  18:09:36,261 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T01:09Z] INFO  18:09:36,285 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:09Z] INFO  18:09:36,395 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.11
[2016-04-15T01:09Z] INFO  18:09:36,908 IntervalUtils - Processing 175773 bp from intervals
[2016-04-15T01:09Z] WARN  18:09:36,924 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:09Z] INFO  18:09:37,045 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:09Z] INFO  18:09:37,163 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:09Z] INFO  18:09:37,164 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:09Z] INFO  18:09:37,164 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T01:09Z] INFO  18:09:37,165 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T01:09Z] INFO  18:09:37,224 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:09Z] INFO  18:09:37,224 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:09Z] tabix index R14-18105_kapa-NGv3-PE100-NGv3-19_31038849_46627578.vcf.gz
[2016-04-15T01:09Z] GATK: UnifiedGenotyper
[2016-04-15T01:09Z] INFO  18:09:42,173 ProgressMeter -            done    343044.0    14.0 s      42.0 s      100.0%    14.0 s       0.0 s
[2016-04-15T01:09Z] INFO  18:09:42,174 ProgressMeter - Total runtime 14.71 secs, 0.25 min, 0.00 hours
[2016-04-15T01:09Z] INFO  18:09:42,175 MicroScheduler - 11683 reads were filtered out during the traversal out of approximately 151666 total reads (7.70%)
[2016-04-15T01:09Z] INFO  18:09:42,175 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:09Z] INFO  18:09:42,176 MicroScheduler -   -> 202 reads (0.13% of total) failing BadMateFilter
[2016-04-15T01:09Z] INFO  18:09:42,177 MicroScheduler -   -> 11365 reads (7.49% of total) failing DuplicateReadFilter
[2016-04-15T01:09Z] INFO  18:09:42,177 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:09Z] INFO  18:09:42,178 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:09Z] INFO  18:09:42,178 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:09Z] INFO  18:09:42,180 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:09Z] INFO  18:09:42,181 MicroScheduler -   -> 116 reads (0.08% of total) failing UnmappedReadFilter
[2016-04-15T01:09Z] INFO  18:09:42,565 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:09Z] INFO  18:09:42,568 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:09Z] INFO  18:09:42,569 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:09Z] INFO  18:09:42,570 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:09Z] INFO  18:09:42,574 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/1/R14-18102_kapa-NGv3-PE100-NGv3-sort-1_223162737_240072524-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/1/R14-18102_kapa-NGv3-PE100-NGv3-1_223162737_240072524-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/1/tx/tmp_9fbHt/R14-18102_kapa-NGv3-PE100-NGv3-1_223162737_240072524.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:09Z] tabix index R14-18105_kapa-NGv3-PE100-NGv3-19_46627881_59128983.vcf.gz
[2016-04-15T01:09Z] INFO  18:09:42,597 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:09Z] INFO  18:09:42,598 HelpFormatter - Date/Time: 2016/04/14 18:09:42
[2016-04-15T01:09Z] INFO  18:09:42,599 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:09Z] INFO  18:09:42,599 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:09Z] INFO  18:09:42,746 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:09Z] GATK: UnifiedGenotyper
[2016-04-15T01:09Z] INFO  18:09:43,019 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T01:09Z] INFO  18:09:43,030 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:09Z] INFO  18:09:43,148 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.12
[2016-04-15T01:09Z] INFO  18:09:43,560 IntervalUtils - Processing 294039 bp from intervals
[2016-04-15T01:09Z] WARN  18:09:43,567 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:09Z] INFO  18:09:43,652 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:09Z] INFO  18:09:43,813 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:09Z] INFO  18:09:43,814 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:09Z] INFO  18:09:43,826 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T01:09Z] INFO  18:09:43,826 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T01:09Z] INFO  18:09:43,858 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:09Z] INFO  18:09:43,890 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:09Z] INFO  18:09:43,891 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:09Z] GATK: UnifiedGenotyper
[2016-04-15T01:09Z] INFO  18:09:45,155 ProgressMeter -            done    356392.0    17.0 s      50.0 s      100.0%    17.0 s       0.0 s
[2016-04-15T01:09Z] INFO  18:09:45,156 ProgressMeter - Total runtime 17.99 secs, 0.30 min, 0.00 hours
[2016-04-15T01:09Z] INFO  18:09:45,157 MicroScheduler - 13190 reads were filtered out during the traversal out of approximately 158798 total reads (8.31%)
[2016-04-15T01:09Z] INFO  18:09:45,157 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:09Z] INFO  18:09:45,158 MicroScheduler -   -> 225 reads (0.14% of total) failing BadMateFilter
[2016-04-15T01:09Z] INFO  18:09:45,159 MicroScheduler -   -> 12861 reads (8.10% of total) failing DuplicateReadFilter
[2016-04-15T01:09Z] INFO  18:09:45,159 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:09Z] INFO  18:09:45,160 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:09Z] INFO  18:09:45,160 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:09Z] INFO  18:09:45,161 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:09Z] INFO  18:09:45,162 MicroScheduler -   -> 104 reads (0.07% of total) failing UnmappedReadFilter
[2016-04-15T01:09Z] INFO  18:09:45,211 ProgressMeter -            done    406382.0    17.0 s      43.0 s      100.0%    17.0 s       0.0 s
[2016-04-15T01:09Z] INFO  18:09:45,212 ProgressMeter - Total runtime 17.75 secs, 0.30 min, 0.00 hours
[2016-04-15T01:09Z] INFO  18:09:45,213 MicroScheduler - 12308 reads were filtered out during the traversal out of approximately 148915 total reads (8.27%)
[2016-04-15T01:09Z] INFO  18:09:45,213 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:09Z] INFO  18:09:45,214 MicroScheduler -   -> 214 reads (0.14% of total) failing BadMateFilter
[2016-04-15T01:09Z] INFO  18:09:45,214 MicroScheduler -   -> 11977 reads (8.04% of total) failing DuplicateReadFilter
[2016-04-15T01:09Z] INFO  18:09:45,215 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:09Z] INFO  18:09:45,216 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:09Z] INFO  18:09:45,216 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:09Z] INFO  18:09:45,217 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:09Z] INFO  18:09:45,218 MicroScheduler -   -> 117 reads (0.08% of total) failing UnmappedReadFilter
[2016-04-15T01:09Z] INFO  18:09:45,865 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:09Z] INFO  18:09:45,870 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:09Z] INFO  18:09:45,870 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:09Z] INFO  18:09:45,871 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:09Z] INFO  18:09:45,875 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/1/R14-18102_kapa-NGv3-PE100-NGv3-sort-1_240255409_249250621-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/1/R14-18102_kapa-NGv3-PE100-NGv3-1_240255409_249250621-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/1/tx/tmp2xJE4f/R14-18102_kapa-NGv3-PE100-NGv3-1_240255409_249250621.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:09Z] INFO  18:09:45,894 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:09Z] INFO  18:09:45,895 HelpFormatter - Date/Time: 2016/04/14 18:09:45
[2016-04-15T01:09Z] INFO  18:09:45,895 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:09Z] INFO  18:09:45,895 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:09Z] INFO  18:09:46,053 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:09Z] INFO  18:09:46,261 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T01:09Z] INFO  18:09:46,270 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:09Z] INFO  18:09:46,337 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-15T01:09Z] INFO  18:09:46,538 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:09Z] INFO  18:09:46,618 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:09Z] INFO  18:09:46,670 IntervalUtils - Processing 129443 bp from intervals
[2016-04-15T01:09Z] WARN  18:09:46,675 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:09Z] INFO  18:09:46,737 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:09Z] INFO  18:09:46,741 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:09Z] INFO  18:09:46,742 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:09Z] INFO  18:09:46,743 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:09Z] INFO  18:09:46,748 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/2/R14-18102_kapa-NGv3-PE100-NGv3-sort-2_0_15514844-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/2/R14-18102_kapa-NGv3-PE100-NGv3-2_0_15514844-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/2/tx/tmpCvmTEL/R14-18102_kapa-NGv3-PE100-NGv3-2_0_15514844.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:09Z] INFO  18:09:46,763 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:09Z] INFO  18:09:46,764 HelpFormatter - Date/Time: 2016/04/14 18:09:46
[2016-04-15T01:09Z] INFO  18:09:46,764 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:09Z] INFO  18:09:46,764 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:09Z] INFO  18:09:46,795 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:09Z] GATK: UnifiedGenotyper
[2016-04-15T01:09Z] GATK: UnifiedGenotyper
[2016-04-15T01:09Z] INFO  18:09:46,926 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:09Z] INFO  18:09:46,938 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:09Z] INFO  18:09:46,939 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T01:09Z] INFO  18:09:46,940 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T01:09Z] INFO  18:09:47,010 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:09Z] INFO  18:09:47,011 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:09Z] INFO  18:09:47,034 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:09Z] INFO  18:09:47,288 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T01:09Z] INFO  18:09:47,299 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:09Z] INFO  18:09:47,418 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.12
[2016-04-15T01:09Z] INFO  18:09:47,836 IntervalUtils - Processing 105700 bp from intervals
[2016-04-15T01:09Z] WARN  18:09:47,852 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:09Z] INFO  18:09:47,951 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:09Z] INFO  18:09:48,048 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:09Z] INFO  18:09:48,049 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:09Z] INFO  18:09:48,057 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T01:09Z] INFO  18:09:48,058 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T01:09Z] INFO  18:09:48,147 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:09Z] INFO  18:09:48,148 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:09Z] INFO  18:09:49,723 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:09Z] INFO  18:09:49,726 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:09Z] INFO  18:09:49,727 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:09Z] INFO  18:09:49,727 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:09Z] INFO  18:09:49,733 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/2/R14-18102_kapa-NGv3-PE100-NGv3-sort-2_31135088_46706841-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/2/R14-18102_kapa-NGv3-PE100-NGv3-2_31135088_46706841-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/2/tx/tmp_jDXz2/R14-18102_kapa-NGv3-PE100-NGv3-2_31135088_46706841.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:09Z] INFO  18:09:49,750 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:09Z] INFO  18:09:49,751 HelpFormatter - Date/Time: 2016/04/14 18:09:49
[2016-04-15T01:09Z] INFO  18:09:49,752 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:09Z] INFO  18:09:49,752 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:09Z] INFO  18:09:49,844 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:09Z] INFO  18:09:49,847 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:09Z] INFO  18:09:49,847 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:09Z] INFO  18:09:49,847 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:09Z] INFO  18:09:49,852 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/2/R14-18102_kapa-NGv3-PE100-NGv3-sort-2_15519725_31133925-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/2/R14-18102_kapa-NGv3-PE100-NGv3-2_15519725_31133925-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/2/tx/tmp1IS4e7/R14-18102_kapa-NGv3-PE100-NGv3-2_15519725_31133925.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:09Z] INFO  18:09:49,886 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:09Z] INFO  18:09:49,897 HelpFormatter - Date/Time: 2016/04/14 18:09:49
[2016-04-15T01:09Z] INFO  18:09:49,898 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:09Z] INFO  18:09:49,899 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:09Z] INFO  18:09:49,958 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:09Z] INFO  18:09:50,138 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:09Z] INFO  18:09:50,199 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T01:09Z] INFO  18:09:50,210 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:09Z] INFO  18:09:50,314 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.10
[2016-04-15T01:09Z] INFO  18:09:50,347 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T01:09Z] INFO  18:09:50,377 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:09Z] INFO  18:09:50,423 ProgressMeter -            done    578834.0    23.0 s      41.0 s      100.0%    23.0 s       0.0 s
[2016-04-15T01:09Z] INFO  18:09:50,423 ProgressMeter - Total runtime 23.79 secs, 0.40 min, 0.01 hours
[2016-04-15T01:09Z] INFO  18:09:50,424 MicroScheduler - 21365 reads were filtered out during the traversal out of approximately 252594 total reads (8.46%)
[2016-04-15T01:09Z] INFO  18:09:50,424 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:09Z] INFO  18:09:50,424 MicroScheduler -   -> 356 reads (0.14% of total) failing BadMateFilter
[2016-04-15T01:09Z] INFO  18:09:50,425 MicroScheduler -   -> 20816 reads (8.24% of total) failing DuplicateReadFilter
[2016-04-15T01:09Z] INFO  18:09:50,425 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:09Z] INFO  18:09:50,425 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:09Z] INFO  18:09:50,426 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:09Z] INFO  18:09:50,426 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:09Z] INFO  18:09:50,430 MicroScheduler -   -> 193 reads (0.08% of total) failing UnmappedReadFilter
[2016-04-15T01:09Z] INFO  18:09:50,596 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.22
[2016-04-15T01:09Z] INFO  18:09:50,742 IntervalUtils - Processing 167641 bp from intervals
[2016-04-15T01:09Z] WARN  18:09:50,749 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:09Z] INFO  18:09:50,838 ProgressMeter -            done    638757.0    20.0 s      31.0 s      100.0%    20.0 s       0.0 s
[2016-04-15T01:09Z] INFO  18:09:50,839 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:09Z] INFO  18:09:50,848 ProgressMeter - Total runtime 20.13 secs, 0.34 min, 0.01 hours
[2016-04-15T01:09Z] INFO  18:09:50,849 MicroScheduler - 18834 reads were filtered out during the traversal out of approximately 229599 total reads (8.20%)
[2016-04-15T01:09Z] INFO  18:09:50,850 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:09Z] INFO  18:09:50,851 MicroScheduler -   -> 334 reads (0.15% of total) failing BadMateFilter
[2016-04-15T01:09Z] INFO  18:09:50,851 MicroScheduler -   -> 18314 reads (7.98% of total) failing DuplicateReadFilter
[2016-04-15T01:09Z] INFO  18:09:50,852 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:09Z] INFO  18:09:50,853 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:09Z] INFO  18:09:50,854 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:09Z] INFO  18:09:50,854 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:09Z] INFO  18:09:50,855 MicroScheduler -   -> 186 reads (0.08% of total) failing UnmappedReadFilter
[2016-04-15T01:09Z] INFO  18:09:50,959 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:09Z] INFO  18:09:50,966 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:09Z] INFO  18:09:50,967 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T01:09Z] INFO  18:09:50,967 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T01:09Z] INFO  18:09:51,065 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:09Z] INFO  18:09:51,066 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:09Z] INFO  18:09:51,117 IntervalUtils - Processing 231513 bp from intervals
[2016-04-15T01:09Z] WARN  18:09:51,124 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:09Z] INFO  18:09:51,261 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:09Z] INFO  18:09:51,377 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:09Z] INFO  18:09:51,378 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:09Z] INFO  18:09:51,379 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T01:09Z] INFO  18:09:51,380 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T01:09Z] INFO  18:09:51,444 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:09Z] INFO  18:09:51,445 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:09Z] INFO  18:09:52,011 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:09Z] INFO  18:09:52,212 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:09Z] GATK: UnifiedGenotyper
[2016-04-15T01:09Z] GATK: UnifiedGenotyper
[2016-04-15T01:09Z] tabix index R14-18105_kapa-NGv3-PE100-NGv3-19_0_15509577.vcf.gz
[2016-04-15T01:09Z] GATK: UnifiedGenotyper
[2016-04-15T01:09Z] INFO  18:09:55,451 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:09Z] INFO  18:09:55,454 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:09Z] INFO  18:09:55,454 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:09Z] INFO  18:09:55,454 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:09Z] INFO  18:09:55,471 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/2/R14-18102_kapa-NGv3-PE100-NGv3-sort-2_46707543_62228117-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/2/R14-18102_kapa-NGv3-PE100-NGv3-2_46707543_62228117-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/2/tx/tmpBvUkAw/R14-18102_kapa-NGv3-PE100-NGv3-2_46707543_62228117.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:09Z] INFO  18:09:55,492 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:09Z] INFO  18:09:55,493 HelpFormatter - Date/Time: 2016/04/14 18:09:55
[2016-04-15T01:09Z] INFO  18:09:55,494 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:09Z] INFO  18:09:55,494 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:09Z] INFO  18:09:55,533 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:09Z] INFO  18:09:55,536 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:09Z] INFO  18:09:55,536 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:09Z] INFO  18:09:55,537 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:09Z] INFO  18:09:55,553 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/2/R14-18102_kapa-NGv3-PE100-NGv3-sort-2_62362965_79253295-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/2/R14-18102_kapa-NGv3-PE100-NGv3-2_62362965_79253295-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/2/tx/tmpZMiE8I/R14-18102_kapa-NGv3-PE100-NGv3-2_62362965_79253295.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:09Z] INFO  18:09:55,572 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:09Z] INFO  18:09:55,572 HelpFormatter - Date/Time: 2016/04/14 18:09:55
[2016-04-15T01:09Z] INFO  18:09:55,572 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:09Z] INFO  18:09:55,572 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:09Z] INFO  18:09:55,752 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:09Z] INFO  18:09:55,837 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:09Z] INFO  18:09:56,030 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T01:09Z] INFO  18:09:56,041 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:09Z] INFO  18:09:56,075 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T01:09Z] INFO  18:09:56,087 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:09Z] INFO  18:09:56,136 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.09
[2016-04-15T01:09Z] INFO  18:09:56,164 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-15T01:09Z] INFO  18:09:56,606 IntervalUtils - Processing 139959 bp from intervals
[2016-04-15T01:09Z] WARN  18:09:56,613 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:09Z] INFO  18:09:56,680 IntervalUtils - Processing 224219 bp from intervals
[2016-04-15T01:09Z] WARN  18:09:56,699 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:09Z] INFO  18:09:56,753 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:09Z] INFO  18:09:56,831 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:09Z] INFO  18:09:56,832 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:09Z] INFO  18:09:56,833 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T01:09Z] INFO  18:09:56,834 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T01:09Z] INFO  18:09:56,839 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:09Z] INFO  18:09:56,890 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:09Z] INFO  18:09:56,891 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:09Z] INFO  18:09:56,978 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:09Z] INFO  18:09:56,978 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:09Z] INFO  18:09:56,978 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T01:09Z] INFO  18:09:56,979 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T01:09Z] INFO  18:09:57,021 ProgressMeter -            done    540256.0    19.0 s      36.0 s      100.0%    19.0 s       0.0 s
[2016-04-15T01:09Z] INFO  18:09:57,021 ProgressMeter - Total runtime 19.86 secs, 0.33 min, 0.01 hours
[2016-04-15T01:09Z] INFO  18:09:57,021 MicroScheduler - 17619 reads were filtered out during the traversal out of approximately 212325 total reads (8.30%)
[2016-04-15T01:09Z] INFO  18:09:57,022 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:09Z] INFO  18:09:57,022 MicroScheduler -   -> 340 reads (0.16% of total) failing BadMateFilter
[2016-04-15T01:09Z] INFO  18:09:57,023 MicroScheduler -   -> 17112 reads (8.06% of total) failing DuplicateReadFilter
[2016-04-15T01:09Z] INFO  18:09:57,023 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:09Z] INFO  18:09:57,023 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:09Z] INFO  18:09:57,024 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:09Z] INFO  18:09:57,024 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:09Z] INFO  18:09:57,024 MicroScheduler -   -> 167 reads (0.08% of total) failing UnmappedReadFilter
[2016-04-15T01:09Z] INFO  18:09:57,069 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:09Z] INFO  18:09:57,070 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:09Z] INFO  18:09:57,079 ProgressMeter -            done    970614.0    29.0 s      29.0 s      100.0%    29.0 s       0.0 s
[2016-04-15T01:09Z] INFO  18:09:57,080 ProgressMeter - Total runtime 29.04 secs, 0.48 min, 0.01 hours
[2016-04-15T01:09Z] INFO  18:09:57,080 MicroScheduler - 29708 reads were filtered out during the traversal out of approximately 352802 total reads (8.42%)
[2016-04-15T01:09Z] INFO  18:09:57,081 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:09Z] INFO  18:09:57,082 MicroScheduler -   -> 471 reads (0.13% of total) failing BadMateFilter
[2016-04-15T01:09Z] INFO  18:09:57,082 MicroScheduler -   -> 28947 reads (8.20% of total) failing DuplicateReadFilter
[2016-04-15T01:09Z] INFO  18:09:57,083 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:09Z] INFO  18:09:57,083 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:09Z] INFO  18:09:57,084 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:09Z] INFO  18:09:57,085 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:09Z] INFO  18:09:57,085 MicroScheduler -   -> 290 reads (0.08% of total) failing UnmappedReadFilter
[2016-04-15T01:09Z] INFO  18:09:57,249 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:09Z] INFO  18:09:57,251 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:09Z] INFO  18:09:57,251 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:09Z] INFO  18:09:57,251 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:09Z] INFO  18:09:57,255 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/2/R14-18102_kapa-NGv3-PE100-NGv3-sort-2_79253838_95537822-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/2/R14-18102_kapa-NGv3-PE100-NGv3-2_79253838_95537822-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/2/tx/tmpFGkiCd/R14-18102_kapa-NGv3-PE100-NGv3-2_79253838_95537822.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:09Z] INFO  18:09:57,264 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:09Z] INFO  18:09:57,265 HelpFormatter - Date/Time: 2016/04/14 18:09:57
[2016-04-15T01:09Z] INFO  18:09:57,265 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:09Z] INFO  18:09:57,266 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:09Z] INFO  18:09:57,422 ProgressMeter -       1:9663727   1271636.0    30.0 s      23.0 s       58.9%    50.0 s      20.0 s
[2016-04-15T01:09Z] INFO  18:09:57,424 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:09Z] INFO  18:09:57,441 ProgressMeter -      1:24401809   1120372.0    30.0 s      26.0 s       61.6%    48.0 s      18.0 s
[2016-04-15T01:09Z] INFO  18:09:57,536 ProgressMeter -      1:40433476   1080397.0    30.0 s      27.0 s       60.5%    49.0 s      19.0 s
[2016-04-15T01:09Z] INFO  18:09:57,655 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T01:09Z] INFO  18:09:57,664 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:09Z] INFO  18:09:57,762 ProgressMeter -            done    911237.0    28.0 s      31.0 s      100.0%    28.0 s       0.0 s
[2016-04-15T01:09Z] INFO  18:09:57,763 ProgressMeter - Total runtime 28.69 secs, 0.48 min, 0.01 hours
[2016-04-15T01:09Z] INFO  18:09:57,764 MicroScheduler - 28426 reads were filtered out during the traversal out of approximately 343793 total reads (8.27%)
[2016-04-15T01:09Z] INFO  18:09:57,765 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:09Z] INFO  18:09:57,765 MicroScheduler -   -> 491 reads (0.14% of total) failing BadMateFilter
[2016-04-15T01:09Z] INFO  18:09:57,765 MicroScheduler -   -> 27639 reads (8.04% of total) failing DuplicateReadFilter
[2016-04-15T01:09Z] INFO  18:09:57,766 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:09Z] INFO  18:09:57,766 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:09Z] INFO  18:09:57,766 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:09Z] INFO  18:09:57,768 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:09Z] INFO  18:09:57,768 MicroScheduler -   -> 296 reads (0.09% of total) failing UnmappedReadFilter
[2016-04-15T01:09Z] INFO  18:09:57,919 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.25
[2016-04-15T01:09Z] INFO  18:09:58,124 ProgressMeter -     1:152595510    937947.0    30.0 s      32.0 s       42.8%    70.0 s      40.0 s
[2016-04-15T01:09Z] INFO  18:09:58,290 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:09Z] INFO  18:09:58,374 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:09Z] INFO  18:09:58,484 IntervalUtils - Processing 101744 bp from intervals
[2016-04-15T01:09Z] WARN  18:09:58,489 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:09Z] GATK: UnifiedGenotyper
[2016-04-15T01:09Z] INFO  18:09:58,645 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:09Z] GATK: UnifiedGenotyper
[2016-04-15T01:09Z] INFO  18:09:58,743 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:09Z] INFO  18:09:58,744 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:09Z] INFO  18:09:58,745 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T01:09Z] INFO  18:09:58,746 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T01:09Z] INFO  18:09:58,827 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:09Z] INFO  18:09:58,829 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:09Z] INFO  18:09:59,077 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:09Z] GATK: UnifiedGenotyper
[2016-04-15T01:10Z] INFO  18:10:01,597 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:10Z] INFO  18:10:01,601 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:10Z] INFO  18:10:01,601 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:10Z] INFO  18:10:01,602 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:10Z] INFO  18:10:01,606 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/2/R14-18102_kapa-NGv3-PE100-NGv3-sort-2_95538561_111273222-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/2/R14-18102_kapa-NGv3-PE100-NGv3-2_95538561_111273222-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/2/tx/tmpNAb9Rb/R14-18102_kapa-NGv3-PE100-NGv3-2_95538561_111273222.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:10Z] INFO  18:10:01,636 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:10Z] INFO  18:10:01,640 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:10Z] INFO  18:10:01,640 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:10Z] INFO  18:10:01,641 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:10Z] INFO  18:10:01,645 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/2/R14-18102_kapa-NGv3-PE100-NGv3-sort-2_111281072_127413888-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/2/R14-18102_kapa-NGv3-PE100-NGv3-2_111281072_127413888-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/2/tx/tmp1GeVWB/R14-18102_kapa-NGv3-PE100-NGv3-2_111281072_127413888.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:10Z] INFO  18:10:01,649 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:10Z] INFO  18:10:01,649 HelpFormatter - Date/Time: 2016/04/14 18:10:01
[2016-04-15T01:10Z] INFO  18:10:01,649 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:10Z] INFO  18:10:01,649 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:10Z] INFO  18:10:01,665 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:10Z] INFO  18:10:01,666 HelpFormatter - Date/Time: 2016/04/14 18:10:01
[2016-04-15T01:10Z] INFO  18:10:01,666 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:10Z] INFO  18:10:01,667 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:10Z] INFO  18:10:01,797 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:10Z] INFO  18:10:01,829 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:10Z] INFO  18:10:02,008 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T01:10Z] INFO  18:10:02,017 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:10Z] INFO  18:10:02,064 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T01:10Z] INFO  18:10:02,074 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:10Z] INFO  18:10:02,094 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-15T01:10Z] INFO  18:10:02,140 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-15T01:10Z] INFO  18:10:02,312 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:10Z] INFO  18:10:02,315 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:10Z] INFO  18:10:02,315 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:10Z] INFO  18:10:02,316 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:10Z] INFO  18:10:02,324 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/2/R14-18102_kapa-NGv3-PE100-NGv3-sort-2_127433207_143643105-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/2/R14-18102_kapa-NGv3-PE100-NGv3-2_127433207_143643105-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/2/tx/tmpOoCnn6/R14-18102_kapa-NGv3-PE100-NGv3-2_127433207_143643105.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:10Z] INFO  18:10:02,350 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:10Z] INFO  18:10:02,350 HelpFormatter - Date/Time: 2016/04/14 18:10:02
[2016-04-15T01:10Z] INFO  18:10:02,350 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:10Z] INFO  18:10:02,350 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:10Z] INFO  18:10:02,461 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:10Z] INFO  18:10:02,519 IntervalUtils - Processing 250759 bp from intervals
[2016-04-15T01:10Z] WARN  18:10:02,525 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:10Z] INFO  18:10:02,658 IntervalUtils - Processing 123675 bp from intervals
[2016-04-15T01:10Z] WARN  18:10:02,663 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:10Z] INFO  18:10:02,679 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T01:10Z] INFO  18:10:02,683 ProgressMeter -            done    285546.0    14.0 s      51.0 s      100.0%    14.0 s       0.0 s
[2016-04-15T01:10Z] INFO  18:10:02,684 ProgressMeter - Total runtime 14.63 secs, 0.24 min, 0.00 hours
[2016-04-15T01:10Z] INFO  18:10:02,684 MicroScheduler - 11197 reads were filtered out during the traversal out of approximately 133413 total reads (8.39%)
[2016-04-15T01:10Z] INFO  18:10:02,684 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:10Z] INFO  18:10:02,685 MicroScheduler -   -> 205 reads (0.15% of total) failing BadMateFilter
[2016-04-15T01:10Z] INFO  18:10:02,685 MicroScheduler -   -> 10885 reads (8.16% of total) failing DuplicateReadFilter
[2016-04-15T01:10Z] INFO  18:10:02,685 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:10Z] INFO  18:10:02,686 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:10Z] INFO  18:10:02,686 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:10Z] INFO  18:10:02,686 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:10Z] INFO  18:10:02,686 MicroScheduler -   -> 107 reads (0.08% of total) failing UnmappedReadFilter
[2016-04-15T01:10Z] INFO  18:10:02,687 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:10Z] INFO  18:10:02,692 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:10Z] INFO  18:10:02,778 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.09
[2016-04-15T01:10Z] INFO  18:10:02,815 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:10Z] INFO  18:10:02,841 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:10Z] INFO  18:10:02,848 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:10Z] INFO  18:10:02,848 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T01:10Z] INFO  18:10:02,849 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T01:10Z] INFO  18:10:02,935 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:10Z] INFO  18:10:02,940 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:10Z] INFO  18:10:02,974 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:10Z] INFO  18:10:02,975 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:10Z] INFO  18:10:02,976 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T01:10Z] INFO  18:10:02,977 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T01:10Z] INFO  18:10:03,072 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:10Z] INFO  18:10:03,073 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:10Z] INFO  18:10:03,169 IntervalUtils - Processing 171560 bp from intervals
[2016-04-15T01:10Z] WARN  18:10:03,175 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:10Z] INFO  18:10:03,237 ProgressMeter -            done    991088.0    28.0 s      28.0 s      100.0%    28.0 s       0.0 s
[2016-04-15T01:10Z] INFO  18:10:03,238 ProgressMeter - Total runtime 28.55 secs, 0.48 min, 0.01 hours
[2016-04-15T01:10Z] INFO  18:10:03,238 MicroScheduler - 29944 reads were filtered out during the traversal out of approximately 359598 total reads (8.33%)
[2016-04-15T01:10Z] INFO  18:10:03,238 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:10Z] INFO  18:10:03,239 MicroScheduler -   -> 509 reads (0.14% of total) failing BadMateFilter
[2016-04-15T01:10Z] INFO  18:10:03,239 MicroScheduler -   -> 29184 reads (8.12% of total) failing DuplicateReadFilter
[2016-04-15T01:10Z] INFO  18:10:03,239 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:10Z] INFO  18:10:03,240 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:10Z] INFO  18:10:03,240 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:10Z] INFO  18:10:03,240 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:10Z] INFO  18:10:03,242 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:10Z] INFO  18:10:03,241 MicroScheduler -   -> 251 reads (0.07% of total) failing UnmappedReadFilter
[2016-04-15T01:10Z] INFO  18:10:03,316 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:10Z] INFO  18:10:03,317 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:10Z] INFO  18:10:03,318 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T01:10Z] INFO  18:10:03,319 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T01:10Z] INFO  18:10:03,362 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:10Z] INFO  18:10:03,363 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:10Z] INFO  18:10:04,204 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:10Z] GATK: UnifiedGenotyper
[2016-04-15T01:10Z] INFO  18:10:04,915 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:10Z] GATK: UnifiedGenotyper
[2016-04-15T01:10Z] INFO  18:10:05,543 ProgressMeter -            done    264653.0    18.0 s      70.0 s      100.0%    18.0 s       0.0 s
[2016-04-15T01:10Z] INFO  18:10:05,543 ProgressMeter - Total runtime 18.61 secs, 0.31 min, 0.01 hours
[2016-04-15T01:10Z] INFO  18:10:05,544 MicroScheduler - 14090 reads were filtered out during the traversal out of approximately 172307 total reads (8.18%)
[2016-04-15T01:10Z] INFO  18:10:05,544 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:10Z] INFO  18:10:05,544 MicroScheduler -   -> 251 reads (0.15% of total) failing BadMateFilter
[2016-04-15T01:10Z] INFO  18:10:05,545 MicroScheduler -   -> 13689 reads (7.94% of total) failing DuplicateReadFilter
[2016-04-15T01:10Z] INFO  18:10:05,545 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:10Z] INFO  18:10:05,545 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:10Z] INFO  18:10:05,545 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:10Z] INFO  18:10:05,546 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:10Z] INFO  18:10:05,546 MicroScheduler -   -> 150 reads (0.09% of total) failing UnmappedReadFilter
[2016-04-15T01:10Z] INFO  18:10:06,988 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:10Z] GATK: UnifiedGenotyper
[2016-04-15T01:10Z] INFO  18:10:07,520 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:10Z] INFO  18:10:07,524 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:10Z] INFO  18:10:07,524 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:10Z] INFO  18:10:07,525 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:10Z] INFO  18:10:07,529 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/2/R14-18102_kapa-NGv3-PE100-NGv3-sort-2_143676177_159195597-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/2/R14-18102_kapa-NGv3-PE100-NGv3-2_143676177_159195597-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/2/tx/tmpXv5L9e/R14-18102_kapa-NGv3-PE100-NGv3-2_143676177_159195597.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:10Z] INFO  18:10:07,539 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:10Z] INFO  18:10:07,540 HelpFormatter - Date/Time: 2016/04/14 18:10:07
[2016-04-15T01:10Z] INFO  18:10:07,545 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:10Z] INFO  18:10:07,545 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:10Z] INFO  18:10:07,737 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:10Z] INFO  18:10:08,043 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T01:10Z] INFO  18:10:08,052 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:10Z] INFO  18:10:08,070 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:10Z] INFO  18:10:08,073 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:10Z] INFO  18:10:08,074 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:10Z] INFO  18:10:08,074 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:10Z] INFO  18:10:08,079 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/2/R14-18102_kapa-NGv3-PE100-NGv3-sort-2_159196753_174774985-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/2/R14-18102_kapa-NGv3-PE100-NGv3-2_159196753_174774985-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/2/tx/tmpALEc1A/R14-18102_kapa-NGv3-PE100-NGv3-2_159196753_174774985.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:10Z] INFO  18:10:08,096 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:10Z] INFO  18:10:08,097 HelpFormatter - Date/Time: 2016/04/14 18:10:08
[2016-04-15T01:10Z] INFO  18:10:08,098 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:10Z] INFO  18:10:08,098 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:10Z] INFO  18:10:08,169 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.10
[2016-04-15T01:10Z] INFO  18:10:08,235 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:10Z] INFO  18:10:08,477 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T01:10Z] INFO  18:10:08,490 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:10Z] INFO  18:10:08,559 ProgressMeter -            done    491998.0    17.0 s      35.0 s      100.0%    17.0 s       0.0 s
[2016-04-15T01:10Z] INFO  18:10:08,559 ProgressMeter - Total runtime 17.59 secs, 0.29 min, 0.00 hours
[2016-04-15T01:10Z] INFO  18:10:08,560 MicroScheduler - 16336 reads were filtered out during the traversal out of approximately 195914 total reads (8.34%)
[2016-04-15T01:10Z] INFO  18:10:08,560 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:10Z] INFO  18:10:08,560 MicroScheduler -   -> 291 reads (0.15% of total) failing BadMateFilter
[2016-04-15T01:10Z] INFO  18:10:08,561 MicroScheduler -   -> 15911 reads (8.12% of total) failing DuplicateReadFilter
[2016-04-15T01:10Z] INFO  18:10:08,561 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:10Z] INFO  18:10:08,561 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:10Z] INFO  18:10:08,561 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:10Z] INFO  18:10:08,562 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:10Z] INFO  18:10:08,562 MicroScheduler -   -> 134 reads (0.07% of total) failing UnmappedReadFilter
[2016-04-15T01:10Z] INFO  18:10:08,570 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-15T01:10Z] INFO  18:10:08,623 IntervalUtils - Processing 92555 bp from intervals
[2016-04-15T01:10Z] WARN  18:10:08,629 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:10Z] INFO  18:10:08,820 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:10Z] INFO  18:10:08,935 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:10Z] INFO  18:10:08,936 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:10Z] INFO  18:10:08,937 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T01:10Z] INFO  18:10:08,937 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T01:10Z] INFO  18:10:08,943 IntervalUtils - Processing 216485 bp from intervals
[2016-04-15T01:10Z] WARN  18:10:08,949 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:10Z] INFO  18:10:09,021 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:10Z] INFO  18:10:09,039 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:10Z] INFO  18:10:09,040 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:10Z] INFO  18:10:09,146 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:10Z] INFO  18:10:09,147 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:10Z] INFO  18:10:09,148 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T01:10Z] INFO  18:10:09,149 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T01:10Z] INFO  18:10:09,173 ProgressMeter -            done   1670041.0    41.0 s      24.0 s      100.0%    41.0 s       0.0 s
[2016-04-15T01:10Z] INFO  18:10:09,173 ProgressMeter - Total runtime 41.75 secs, 0.70 min, 0.01 hours
[2016-04-15T01:10Z] INFO  18:10:09,174 MicroScheduler - 51398 reads were filtered out during the traversal out of approximately 607689 total reads (8.46%)
[2016-04-15T01:10Z] INFO  18:10:09,174 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:10Z] INFO  18:10:09,174 MicroScheduler -   -> 894 reads (0.15% of total) failing BadMateFilter
[2016-04-15T01:10Z] INFO  18:10:09,175 MicroScheduler -   -> 50029 reads (8.23% of total) failing DuplicateReadFilter
[2016-04-15T01:10Z] INFO  18:10:09,175 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:10Z] INFO  18:10:09,175 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:10Z] INFO  18:10:09,175 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:10Z] INFO  18:10:09,176 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:10Z] INFO  18:10:09,176 MicroScheduler -   -> 475 reads (0.08% of total) failing UnmappedReadFilter
[2016-04-15T01:10Z] INFO  18:10:09,191 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:10Z] INFO  18:10:09,192 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:10Z] INFO  18:10:10,008 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:10Z] INFO  18:10:10,121 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:10Z] INFO  18:10:10,125 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:10Z] INFO  18:10:10,125 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:10Z] INFO  18:10:10,126 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:10Z] INFO  18:10:10,130 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/2/R14-18102_kapa-NGv3-PE100-NGv3-sort-2_174777797_190306304-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/2/R14-18102_kapa-NGv3-PE100-NGv3-2_174777797_190306304-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/2/tx/tmpaxC1AO/R14-18102_kapa-NGv3-PE100-NGv3-2_174777797_190306304.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:10Z] INFO  18:10:10,161 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:10Z] INFO  18:10:10,162 HelpFormatter - Date/Time: 2016/04/14 18:10:10
[2016-04-15T01:10Z] INFO  18:10:10,163 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:10Z] INFO  18:10:10,163 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:10Z] GATK: UnifiedGenotyper
[2016-04-15T01:10Z] INFO  18:10:10,377 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:10Z] INFO  18:10:10,556 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:10Z] INFO  18:10:10,637 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T01:10Z] INFO  18:10:10,646 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:10Z] INFO  18:10:10,724 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-15T01:10Z] GATK: UnifiedGenotyper
[2016-04-15T01:10Z] INFO  18:10:11,151 IntervalUtils - Processing 253764 bp from intervals
[2016-04-15T01:10Z] WARN  18:10:11,170 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:10Z] INFO  18:10:11,242 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:10Z] INFO  18:10:11,339 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:10Z] INFO  18:10:11,340 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:10Z] INFO  18:10:11,341 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T01:10Z] INFO  18:10:11,342 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T01:10Z] INFO  18:10:11,387 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:10Z] INFO  18:10:11,388 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:10Z] INFO  18:10:11,587 ProgressMeter -            done   2049259.0    44.0 s      21.0 s      100.0%    44.0 s       0.0 s
[2016-04-15T01:10Z] INFO  18:10:11,588 ProgressMeter - Total runtime 44.07 secs, 0.73 min, 0.01 hours
[2016-04-15T01:10Z] INFO  18:10:11,588 MicroScheduler - 52062 reads were filtered out during the traversal out of approximately 620770 total reads (8.39%)
[2016-04-15T01:10Z] INFO  18:10:11,589 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:10Z] INFO  18:10:11,589 MicroScheduler -   -> 881 reads (0.14% of total) failing BadMateFilter
[2016-04-15T01:10Z] INFO  18:10:11,589 MicroScheduler -   -> 50741 reads (8.17% of total) failing DuplicateReadFilter
[2016-04-15T01:10Z] INFO  18:10:11,589 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:10Z] INFO  18:10:11,590 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:10Z] INFO  18:10:11,590 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:10Z] INFO  18:10:11,590 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:10Z] INFO  18:10:11,590 MicroScheduler -   -> 440 reads (0.07% of total) failing UnmappedReadFilter
[2016-04-15T01:10Z] INFO  18:10:12,458 ProgressMeter -            done   1809594.0    45.0 s      24.0 s      100.0%    45.0 s       0.0 s
[2016-04-15T01:10Z] INFO  18:10:12,459 ProgressMeter - Total runtime 45.06 secs, 0.75 min, 0.01 hours
[2016-04-15T01:10Z] INFO  18:10:12,459 MicroScheduler - 50567 reads were filtered out during the traversal out of approximately 627802 total reads (8.05%)
[2016-04-15T01:10Z] INFO  18:10:12,460 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:10Z] INFO  18:10:12,460 MicroScheduler -   -> 1068 reads (0.17% of total) failing BadMateFilter
[2016-04-15T01:10Z] INFO  18:10:12,460 MicroScheduler -   -> 49005 reads (7.81% of total) failing DuplicateReadFilter
[2016-04-15T01:10Z] INFO  18:10:12,460 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:10Z] INFO  18:10:12,461 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:10Z] INFO  18:10:12,461 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:10Z] INFO  18:10:12,461 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:10Z] INFO  18:10:12,461 MicroScheduler -   -> 494 reads (0.08% of total) failing UnmappedReadFilter
[2016-04-15T01:10Z] INFO  18:10:12,743 ProgressMeter -            done    971140.0    28.0 s      29.0 s      100.0%    28.0 s       0.0 s
[2016-04-15T01:10Z] INFO  18:10:12,743 ProgressMeter - Total runtime 28.93 secs, 0.48 min, 0.01 hours
[2016-04-15T01:10Z] INFO  18:10:12,744 MicroScheduler - 32326 reads were filtered out during the traversal out of approximately 381374 total reads (8.48%)
[2016-04-15T01:10Z] INFO  18:10:12,744 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:10Z] INFO  18:10:12,744 MicroScheduler -   -> 577 reads (0.15% of total) failing BadMateFilter
[2016-04-15T01:10Z] INFO  18:10:12,745 MicroScheduler -   -> 31469 reads (8.25% of total) failing DuplicateReadFilter
[2016-04-15T01:10Z] INFO  18:10:12,745 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:10Z] INFO  18:10:12,745 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:10Z] INFO  18:10:12,745 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:10Z] INFO  18:10:12,746 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:10Z] INFO  18:10:12,746 MicroScheduler -   -> 280 reads (0.07% of total) failing UnmappedReadFilter
[2016-04-15T01:10Z] INFO  18:10:13,011 ProgressMeter -            done    451799.0    16.0 s      35.0 s       99.9%    16.0 s       0.0 s
[2016-04-15T01:10Z] INFO  18:10:13,011 ProgressMeter - Total runtime 16.18 secs, 0.27 min, 0.00 hours
[2016-04-15T01:10Z] INFO  18:10:13,011 MicroScheduler - 13052 reads were filtered out during the traversal out of approximately 159590 total reads (8.18%)
[2016-04-15T01:10Z] INFO  18:10:13,012 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:10Z] INFO  18:10:13,012 MicroScheduler -   -> 208 reads (0.13% of total) failing BadMateFilter
[2016-04-15T01:10Z] INFO  18:10:13,012 MicroScheduler -   -> 12722 reads (7.97% of total) failing DuplicateReadFilter
[2016-04-15T01:10Z] INFO  18:10:13,013 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:10Z] INFO  18:10:13,013 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:10Z] INFO  18:10:13,013 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:10Z] INFO  18:10:13,013 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:10Z] INFO  18:10:13,014 MicroScheduler -   -> 122 reads (0.08% of total) failing UnmappedReadFilter
[2016-04-15T01:10Z] INFO  18:10:13,033 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:10Z] INFO  18:10:13,036 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:10Z] INFO  18:10:13,037 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:10Z] INFO  18:10:13,037 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:10Z] INFO  18:10:13,045 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:10Z] INFO  18:10:13,042 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/2/R14-18102_kapa-NGv3-PE100-NGv3-sort-2_190313104_205830046-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/2/R14-18102_kapa-NGv3-PE100-NGv3-2_190313104_205830046-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/2/tx/tmpewOj3k/R14-18102_kapa-NGv3-PE100-NGv3-2_190313104_205830046.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:10Z] INFO  18:10:13,061 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:10Z] INFO  18:10:13,068 HelpFormatter - Date/Time: 2016/04/14 18:10:13
[2016-04-15T01:10Z] INFO  18:10:13,069 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:10Z] INFO  18:10:13,074 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:10Z] INFO  18:10:13,235 ProgressMeter -            done    366382.0    14.0 s      39.0 s       99.9%    14.0 s       0.0 s
[2016-04-15T01:10Z] INFO  18:10:13,236 ProgressMeter - Total runtime 14.49 secs, 0.24 min, 0.00 hours
[2016-04-15T01:10Z] INFO  18:10:13,236 MicroScheduler - 12532 reads were filtered out during the traversal out of approximately 166590 total reads (7.52%)
[2016-04-15T01:10Z] INFO  18:10:13,237 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:10Z] INFO  18:10:13,237 MicroScheduler -   -> 238 reads (0.14% of total) failing BadMateFilter
[2016-04-15T01:10Z] INFO  18:10:13,237 MicroScheduler -   -> 12188 reads (7.32% of total) failing DuplicateReadFilter
[2016-04-15T01:10Z] INFO  18:10:13,237 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:10Z] INFO  18:10:13,238 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:10Z] INFO  18:10:13,238 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:10Z] INFO  18:10:13,238 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:10Z] INFO  18:10:13,238 MicroScheduler -   -> 106 reads (0.06% of total) failing UnmappedReadFilter
[2016-04-15T01:10Z] INFO  18:10:13,256 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:10Z] GATK: UnifiedGenotyper
[2016-04-15T01:10Z] INFO  18:10:13,456 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T01:10Z] INFO  18:10:13,466 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:10Z] INFO  18:10:13,540 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-15T01:10Z] INFO  18:10:13,804 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:10Z] INFO  18:10:13,808 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:10Z] INFO  18:10:13,808 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:10Z] INFO  18:10:13,809 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:10Z] INFO  18:10:13,813 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/2/R14-18102_kapa-NGv3-PE100-NGv3-sort-2_205912303_222290862-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/2/R14-18102_kapa-NGv3-PE100-NGv3-2_205912303_222290862-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/2/tx/tmpEeoK54/R14-18102_kapa-NGv3-PE100-NGv3-2_205912303_222290862.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:10Z] INFO  18:10:13,824 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:10Z] INFO  18:10:13,837 HelpFormatter - Date/Time: 2016/04/14 18:10:13
[2016-04-15T01:10Z] INFO  18:10:13,838 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:10Z] INFO  18:10:13,838 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:10Z] INFO  18:10:13,963 IntervalUtils - Processing 204460 bp from intervals
[2016-04-15T01:10Z] WARN  18:10:13,968 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:10Z] INFO  18:10:13,983 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:10Z] INFO  18:10:14,054 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:10Z] INFO  18:10:14,089 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:10Z] INFO  18:10:14,112 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:10Z] INFO  18:10:14,184 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:10Z] INFO  18:10:14,185 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:10Z] INFO  18:10:14,186 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T01:10Z] INFO  18:10:14,186 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T01:10Z] GATK: UnifiedGenotyper
[2016-04-15T01:10Z] INFO  18:10:14,227 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:10Z] INFO  18:10:14,227 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:10Z] INFO  18:10:14,229 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T01:10Z] INFO  18:10:14,242 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:10Z] INFO  18:10:14,330 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.09
[2016-04-15T01:10Z] INFO  18:10:14,350 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:10Z] GATK: UnifiedGenotyper
[2016-04-15T01:10Z] GATK: UnifiedGenotyper
[2016-04-15T01:10Z] INFO  18:10:14,809 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:10Z] INFO  18:10:14,842 IntervalUtils - Processing 247026 bp from intervals
[2016-04-15T01:10Z] WARN  18:10:14,859 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:10Z] INFO  18:10:14,966 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:10Z] INFO  18:10:15,093 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:10Z] INFO  18:10:15,093 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:10Z] INFO  18:10:15,094 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T01:10Z] INFO  18:10:15,094 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T01:10Z] GATK: UnifiedGenotyper
[2016-04-15T01:10Z] INFO  18:10:15,181 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:10Z] INFO  18:10:15,181 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:10Z] INFO  18:10:15,478 ProgressMeter -            done   1055597.0    24.0 s      22.0 s      100.0%    24.0 s       0.0 s
[2016-04-15T01:10Z] INFO  18:10:15,478 ProgressMeter - Total runtime 24.10 secs, 0.40 min, 0.01 hours
[2016-04-15T01:10Z] INFO  18:10:15,479 MicroScheduler - 26329 reads were filtered out during the traversal out of approximately 313150 total reads (8.41%)
[2016-04-15T01:10Z] INFO  18:10:15,479 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:10Z] INFO  18:10:15,479 MicroScheduler -   -> 467 reads (0.15% of total) failing BadMateFilter
[2016-04-15T01:10Z] INFO  18:10:15,480 MicroScheduler -   -> 25642 reads (8.19% of total) failing DuplicateReadFilter
[2016-04-15T01:10Z] INFO  18:10:15,480 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:10Z] INFO  18:10:15,480 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:10Z] INFO  18:10:15,480 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:10Z] INFO  18:10:15,481 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:10Z] INFO  18:10:15,481 MicroScheduler -   -> 220 reads (0.07% of total) failing UnmappedReadFilter
[2016-04-15T01:10Z] INFO  18:10:16,120 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:10Z] INFO  18:10:16,124 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:10Z] INFO  18:10:16,125 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:10Z] INFO  18:10:16,125 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:10Z] INFO  18:10:16,129 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/2/R14-18102_kapa-NGv3-PE100-NGv3-sort-2_222291154_237994685-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/2/R14-18102_kapa-NGv3-PE100-NGv3-2_222291154_237994685-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/2/tx/tmp3Y5LDj/R14-18102_kapa-NGv3-PE100-NGv3-2_222291154_237994685.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:10Z] INFO  18:10:16,140 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:10Z] INFO  18:10:16,140 HelpFormatter - Date/Time: 2016/04/14 18:10:16
[2016-04-15T01:10Z] INFO  18:10:16,140 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:10Z] INFO  18:10:16,140 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:10Z] INFO  18:10:16,336 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:10Z] INFO  18:10:16,578 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T01:10Z] INFO  18:10:16,587 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:10Z] INFO  18:10:16,665 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-15T01:10Z] INFO  18:10:16,854 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:10Z] INFO  18:10:16,857 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:10Z] INFO  18:10:16,858 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:10Z] INFO  18:10:16,858 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:10Z] INFO  18:10:16,863 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/2/R14-18102_kapa-NGv3-PE100-NGv3-sort-2_237995374_243199373-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/2/R14-18102_kapa-NGv3-PE100-NGv3-2_237995374_243199373-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/2/tx/tmp_6VYPt/R14-18102_kapa-NGv3-PE100-NGv3-2_237995374_243199373.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:10Z] INFO  18:10:16,873 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:10Z] INFO  18:10:16,884 HelpFormatter - Date/Time: 2016/04/14 18:10:16
[2016-04-15T01:10Z] INFO  18:10:16,885 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:10Z] INFO  18:10:16,886 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:10Z] INFO  18:10:16,957 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:10Z] INFO  18:10:17,036 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:10Z] INFO  18:10:17,078 IntervalUtils - Processing 186854 bp from intervals
[2016-04-15T01:10Z] WARN  18:10:17,083 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:10Z] INFO  18:10:17,229 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:10Z] INFO  18:10:17,281 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T01:10Z] INFO  18:10:17,291 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:10Z] INFO  18:10:17,354 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:10Z] INFO  18:10:17,355 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:10Z] INFO  18:10:17,359 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T01:10Z] INFO  18:10:17,359 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T01:10Z] GATK: UnifiedGenotyper
[2016-04-15T01:10Z] INFO  18:10:17,408 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.12
[2016-04-15T01:10Z] INFO  18:10:17,409 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:10Z] INFO  18:10:17,410 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:10Z] INFO  18:10:17,803 IntervalUtils - Processing 128077 bp from intervals
[2016-04-15T01:10Z] WARN  18:10:17,808 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:10Z] INFO  18:10:17,885 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:10Z] INFO  18:10:17,889 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:10Z] INFO  18:10:17,889 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:10Z] INFO  18:10:17,890 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:10Z] INFO  18:10:17,894 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/3/R14-18102_kapa-NGv3-PE100-NGv3-sort-3_15515506_31574805-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/3/R14-18102_kapa-NGv3-PE100-NGv3-3_15515506_31574805-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/3/tx/tmpi5JYpq/R14-18102_kapa-NGv3-PE100-NGv3-3_15515506_31574805.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:10Z] INFO  18:10:17,893 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:10Z] INFO  18:10:17,896 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:10Z] INFO  18:10:17,897 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:10Z] INFO  18:10:17,897 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:10Z] INFO  18:10:17,904 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:10Z] INFO  18:10:17,904 HelpFormatter - Date/Time: 2016/04/14 18:10:17
[2016-04-15T01:10Z] INFO  18:10:17,904 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:10Z] INFO  18:10:17,904 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:10Z] INFO  18:10:17,901 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/3/R14-18102_kapa-NGv3-PE100-NGv3-sort-3_31617887_47127804-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/3/R14-18102_kapa-NGv3-PE100-NGv3-3_31617887_47127804-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/3/tx/tmpvkzFoS/R14-18102_kapa-NGv3-PE100-NGv3-3_31617887_47127804.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:10Z] INFO  18:10:17,912 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:10Z] INFO  18:10:17,920 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:10Z] INFO  18:10:17,921 HelpFormatter - Date/Time: 2016/04/14 18:10:17
[2016-04-15T01:10Z] INFO  18:10:17,927 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:10Z] INFO  18:10:17,928 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:10Z] INFO  18:10:17,981 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:10Z] INFO  18:10:17,984 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:10Z] INFO  18:10:17,985 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:10Z] INFO  18:10:17,985 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:10Z] INFO  18:10:17,990 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/3/R14-18102_kapa-NGv3-PE100-NGv3-sort-3_0_15512123-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/3/R14-18102_kapa-NGv3-PE100-NGv3-3_0_15512123-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/3/tx/tmpKvitwI/R14-18102_kapa-NGv3-PE100-NGv3-3_0_15512123.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:10Z] INFO  18:10:18,005 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:10Z] INFO  18:10:18,006 HelpFormatter - Date/Time: 2016/04/14 18:10:17
[2016-04-15T01:10Z] INFO  18:10:18,007 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:10Z] INFO  18:10:18,007 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:10Z] INFO  18:10:18,018 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:10Z] INFO  18:10:18,020 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:10Z] INFO  18:10:18,020 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T01:10Z] INFO  18:10:18,021 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T01:10Z] INFO  18:10:18,110 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:10Z] INFO  18:10:18,111 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:10Z] INFO  18:10:18,131 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:10Z] INFO  18:10:18,155 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:10Z] INFO  18:10:18,250 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:10Z] INFO  18:10:18,404 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T01:10Z] INFO  18:10:18,413 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T01:10Z] INFO  18:10:18,420 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:10Z] INFO  18:10:18,427 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:10Z] INFO  18:10:18,451 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T01:10Z] INFO  18:10:18,468 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:10Z] INFO  18:10:18,501 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-15T01:10Z] INFO  18:10:18,529 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.10
[2016-04-15T01:10Z] INFO  18:10:18,569 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.10
[2016-04-15T01:10Z] INFO  18:10:18,739 ProgressMeter -            done    353576.0    15.0 s      44.0 s       99.9%    15.0 s       0.0 s
[2016-04-15T01:10Z] INFO  18:10:18,740 ProgressMeter - Total runtime 15.76 secs, 0.26 min, 0.00 hours
[2016-04-15T01:10Z] INFO  18:10:18,740 MicroScheduler - 14286 reads were filtered out during the traversal out of approximately 196629 total reads (7.27%)
[2016-04-15T01:10Z] INFO  18:10:18,740 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:10Z] INFO  18:10:18,740 MicroScheduler -   -> 260 reads (0.13% of total) failing BadMateFilter
[2016-04-15T01:10Z] INFO  18:10:18,741 MicroScheduler -   -> 13908 reads (7.07% of total) failing DuplicateReadFilter
[2016-04-15T01:10Z] INFO  18:10:18,741 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:10Z] INFO  18:10:18,741 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:10Z] INFO  18:10:18,741 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:10Z] INFO  18:10:18,742 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:10Z] INFO  18:10:18,742 MicroScheduler -   -> 118 reads (0.06% of total) failing UnmappedReadFilter
[2016-04-15T01:10Z] INFO  18:10:18,956 IntervalUtils - Processing 188511 bp from intervals
[2016-04-15T01:10Z] WARN  18:10:18,961 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:10Z] INFO  18:10:19,040 IntervalUtils - Processing 86168 bp from intervals
[2016-04-15T01:10Z] INFO  18:10:19,054 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:10Z] WARN  18:10:19,056 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:10Z] INFO  18:10:19,145 IntervalUtils - Processing 307437 bp from intervals
[2016-04-15T01:10Z] WARN  18:10:19,161 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:10Z] INFO  18:10:19,166 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:10Z] INFO  18:10:19,178 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:10Z] INFO  18:10:19,179 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T01:10Z] INFO  18:10:19,180 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T01:10Z] INFO  18:10:19,223 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:10Z] INFO  18:10:19,270 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:10Z] INFO  18:10:19,281 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:10Z] INFO  18:10:19,313 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:10Z] INFO  18:10:19,313 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:10Z] INFO  18:10:19,332 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:10Z] INFO  18:10:19,333 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T01:10Z] INFO  18:10:19,334 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T01:10Z] INFO  18:10:19,411 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:10Z] INFO  18:10:19,412 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:10Z] INFO  18:10:19,422 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:10Z] INFO  18:10:19,423 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:10Z] INFO  18:10:19,424 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T01:10Z] INFO  18:10:19,425 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T01:10Z] INFO  18:10:19,509 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:10Z] INFO  18:10:19,509 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:10Z] INFO  18:10:20,269 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:10Z] INFO  18:10:20,322 ProgressMeter -            done    769087.0    23.0 s      30.0 s      100.0%    23.0 s       0.0 s
[2016-04-15T01:10Z] INFO  18:10:20,323 ProgressMeter - Total runtime 23.34 secs, 0.39 min, 0.01 hours
[2016-04-15T01:10Z] INFO  18:10:20,323 MicroScheduler - 24502 reads were filtered out during the traversal out of approximately 290389 total reads (8.44%)
[2016-04-15T01:10Z] INFO  18:10:20,323 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:10Z] INFO  18:10:20,324 MicroScheduler -   -> 391 reads (0.13% of total) failing BadMateFilter
[2016-04-15T01:10Z] INFO  18:10:20,324 MicroScheduler -   -> 23874 reads (8.22% of total) failing DuplicateReadFilter
[2016-04-15T01:10Z] INFO  18:10:20,324 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:10Z] INFO  18:10:20,324 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:10Z] INFO  18:10:20,324 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:10Z] INFO  18:10:20,325 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:10Z] INFO  18:10:20,325 MicroScheduler -   -> 237 reads (0.08% of total) failing UnmappedReadFilter
[2016-04-15T01:10Z] INFO  18:10:20,327 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:10Z] INFO  18:10:20,330 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:10Z] INFO  18:10:20,331 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:10Z] INFO  18:10:20,332 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:10Z] INFO  18:10:20,336 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/3/R14-18102_kapa-NGv3-PE100-NGv3-sort-3_47129602_62648069-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/3/R14-18102_kapa-NGv3-PE100-NGv3-3_47129602_62648069-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/3/tx/tmpEzJluD/R14-18102_kapa-NGv3-PE100-NGv3-3_47129602_62648069.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:10Z] INFO  18:10:20,345 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:10Z] INFO  18:10:20,346 HelpFormatter - Date/Time: 2016/04/14 18:10:20
[2016-04-15T01:10Z] INFO  18:10:20,346 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:10Z] INFO  18:10:20,347 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:10Z] INFO  18:10:20,510 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:10Z] GATK: UnifiedGenotyper
[2016-04-15T01:10Z] INFO  18:10:20,787 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T01:10Z] INFO  18:10:20,796 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:10Z] INFO  18:10:20,893 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.10
[2016-04-15T01:10Z] INFO  18:10:21,611 IntervalUtils - Processing 430308 bp from intervals
[2016-04-15T01:10Z] WARN  18:10:21,617 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:10Z] INFO  18:10:21,728 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:10Z] INFO  18:10:21,822 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:10Z] INFO  18:10:21,905 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:10Z] INFO  18:10:21,905 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:10Z] INFO  18:10:21,906 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T01:10Z] INFO  18:10:21,906 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T01:10Z] INFO  18:10:21,974 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:10Z] INFO  18:10:21,975 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:10Z] GATK: UnifiedGenotyper
[2016-04-15T01:10Z] INFO  18:10:22,303 ProgressMeter -            done    341277.0    13.0 s      39.0 s       99.9%    13.0 s       0.0 s
[2016-04-15T01:10Z] INFO  18:10:22,304 ProgressMeter - Total runtime 13.37 secs, 0.22 min, 0.00 hours
[2016-04-15T01:10Z] INFO  18:10:22,305 MicroScheduler - 8706 reads were filtered out during the traversal out of approximately 107895 total reads (8.07%)
[2016-04-15T01:10Z] INFO  18:10:22,306 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:10Z] INFO  18:10:22,306 MicroScheduler -   -> 178 reads (0.16% of total) failing BadMateFilter
[2016-04-15T01:10Z] INFO  18:10:22,307 MicroScheduler -   -> 8450 reads (7.83% of total) failing DuplicateReadFilter
[2016-04-15T01:10Z] INFO  18:10:22,307 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:10Z] INFO  18:10:22,308 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:10Z] INFO  18:10:22,309 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:10Z] INFO  18:10:22,309 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:10Z] INFO  18:10:22,310 MicroScheduler -   -> 78 reads (0.07% of total) failing UnmappedReadFilter
[2016-04-15T01:10Z] INFO  18:10:23,931 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:10Z] INFO  18:10:23,935 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:10Z] INFO  18:10:23,936 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:10Z] INFO  18:10:23,937 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:10Z] INFO  18:10:23,941 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/3/R14-18102_kapa-NGv3-PE100-NGv3-sort-3_62739115_78648077-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/3/R14-18102_kapa-NGv3-PE100-NGv3-3_62739115_78648077-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/3/tx/tmpY8i5jf/R14-18102_kapa-NGv3-PE100-NGv3-3_62739115_78648077.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:10Z] INFO  18:10:23,962 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:10Z] INFO  18:10:23,962 HelpFormatter - Date/Time: 2016/04/14 18:10:23
[2016-04-15T01:10Z] INFO  18:10:23,962 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:10Z] INFO  18:10:23,963 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:10Z] INFO  18:10:23,968 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:10Z] INFO  18:10:24,120 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:10Z] GATK: UnifiedGenotyper
[2016-04-15T01:10Z] INFO  18:10:24,260 ProgressMeter -            done   2535127.0    56.0 s      22.0 s      100.0%    56.0 s       0.0 s
[2016-04-15T01:10Z] INFO  18:10:24,260 ProgressMeter - Total runtime 56.16 secs, 0.94 min, 0.02 hours
[2016-04-15T01:10Z] INFO  18:10:24,261 MicroScheduler - 71388 reads were filtered out during the traversal out of approximately 860574 total reads (8.30%)
[2016-04-15T01:10Z] INFO  18:10:24,261 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:10Z] INFO  18:10:24,261 MicroScheduler -   -> 1243 reads (0.14% of total) failing BadMateFilter
[2016-04-15T01:10Z] INFO  18:10:24,262 MicroScheduler -   -> 69469 reads (8.07% of total) failing DuplicateReadFilter
[2016-04-15T01:10Z] INFO  18:10:24,262 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:10Z] INFO  18:10:24,262 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:10Z] INFO  18:10:24,262 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:10Z] INFO  18:10:24,263 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:10Z] INFO  18:10:24,263 MicroScheduler -   -> 676 reads (0.08% of total) failing UnmappedReadFilter
[2016-04-15T01:10Z] INFO  18:10:24,295 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T01:10Z] INFO  18:10:24,304 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:10Z] INFO  18:10:24,367 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-15T01:10Z] INFO  18:10:24,778 IntervalUtils - Processing 82160 bp from intervals
[2016-04-15T01:10Z] WARN  18:10:24,796 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:10Z] INFO  18:10:24,970 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:10Z] INFO  18:10:24,978 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:10Z] INFO  18:10:24,981 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:10Z] INFO  18:10:24,981 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:10Z] INFO  18:10:24,982 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:10Z] INFO  18:10:24,986 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/3/R14-18102_kapa-NGv3-PE100-NGv3-sort-3_78649262_96533852-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/3/R14-18102_kapa-NGv3-PE100-NGv3-3_78649262_96533852-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/3/tx/tmpEtb5HG/R14-18102_kapa-NGv3-PE100-NGv3-3_78649262_96533852.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:10Z] INFO  18:10:25,002 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:10Z] INFO  18:10:25,003 HelpFormatter - Date/Time: 2016/04/14 18:10:24
[2016-04-15T01:10Z] INFO  18:10:25,004 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:10Z] INFO  18:10:25,004 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:10Z] INFO  18:10:25,085 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:10Z] INFO  18:10:25,086 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:10Z] INFO  18:10:25,086 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T01:10Z] INFO  18:10:25,087 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T01:10Z] INFO  18:10:25,143 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:10Z] INFO  18:10:25,143 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:10Z] INFO  18:10:25,160 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:10Z] INFO  18:10:25,366 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T01:10Z] INFO  18:10:25,375 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:10Z] INFO  18:10:25,457 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-15T01:10Z] INFO  18:10:25,497 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:10Z] GATK: UnifiedGenotyper
[2016-04-15T01:10Z] INFO  18:10:25,912 IntervalUtils - Processing 30411 bp from intervals
[2016-04-15T01:10Z] WARN  18:10:25,929 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:10Z] INFO  18:10:25,935 ProgressMeter -            done    525700.0    22.0 s      43.0 s      100.0%    22.0 s       0.0 s
[2016-04-15T01:10Z] INFO  18:10:25,936 ProgressMeter - Total runtime 22.62 secs, 0.38 min, 0.01 hours
[2016-04-15T01:10Z] INFO  18:10:25,936 MicroScheduler - 22269 reads were filtered out during the traversal out of approximately 266690 total reads (8.35%)
[2016-04-15T01:10Z] INFO  18:10:25,936 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:10Z] INFO  18:10:25,937 MicroScheduler -   -> 388 reads (0.15% of total) failing BadMateFilter
[2016-04-15T01:10Z] INFO  18:10:25,937 MicroScheduler -   -> 21660 reads (8.12% of total) failing DuplicateReadFilter
[2016-04-15T01:10Z] INFO  18:10:25,937 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:10Z] INFO  18:10:25,938 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:10Z] INFO  18:10:25,938 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:10Z] INFO  18:10:25,938 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:10Z] INFO  18:10:25,939 MicroScheduler -   -> 221 reads (0.08% of total) failing UnmappedReadFilter
[2016-04-15T01:10Z] INFO  18:10:26,036 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:10Z] INFO  18:10:26,094 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:10Z] INFO  18:10:26,095 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:10Z] INFO  18:10:26,096 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T01:10Z] INFO  18:10:26,101 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T01:10Z] INFO  18:10:26,198 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:10Z] INFO  18:10:26,199 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:10Z] INFO  18:10:26,927 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:10Z] INFO  18:10:26,941 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:10Z] INFO  18:10:26,942 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:10Z] INFO  18:10:26,942 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:10Z] INFO  18:10:26,947 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/3/R14-18102_kapa-NGv3-PE100-NGv3-sort-3_96585668_112185230-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/3/R14-18102_kapa-NGv3-PE100-NGv3-3_96585668_112185230-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/3/tx/tmpkMtR3c/R14-18102_kapa-NGv3-PE100-NGv3-3_96585668_112185230.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:10Z] INFO  18:10:26,981 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:10Z] INFO  18:10:26,982 HelpFormatter - Date/Time: 2016/04/14 18:10:26
[2016-04-15T01:10Z] INFO  18:10:26,983 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:10Z] INFO  18:10:26,983 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:10Z] INFO  18:10:27,121 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:10Z] INFO  18:10:27,288 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T01:10Z] INFO  18:10:27,298 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:10Z] INFO  18:10:27,374 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:10Z] INFO  18:10:27,396 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.10
[2016-04-15T01:10Z] GATK: UnifiedGenotyper
[2016-04-15T01:10Z] INFO  18:10:27,813 IntervalUtils - Processing 140565 bp from intervals
[2016-04-15T01:10Z] WARN  18:10:27,818 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:10Z] INFO  18:10:27,907 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:10Z] INFO  18:10:27,991 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:10Z] INFO  18:10:27,992 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:10Z] INFO  18:10:27,993 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T01:10Z] INFO  18:10:27,993 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T01:10Z] INFO  18:10:28,066 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:10Z] INFO  18:10:28,077 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:10Z] INFO  18:10:28,539 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:10Z] INFO  18:10:28,543 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:10Z] INFO  18:10:28,543 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:10Z] INFO  18:10:28,544 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:10Z] INFO  18:10:28,548 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/3/R14-18102_kapa-NGv3-PE100-NGv3-sort-3_112188604_127703121-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/3/R14-18102_kapa-NGv3-PE100-NGv3-3_112188604_127703121-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/3/tx/tmp1YneT5/R14-18102_kapa-NGv3-PE100-NGv3-3_112188604_127703121.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:10Z] INFO  18:10:28,557 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:10Z] INFO  18:10:28,558 HelpFormatter - Date/Time: 2016/04/14 18:10:28
[2016-04-15T01:10Z] INFO  18:10:28,559 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:10Z] INFO  18:10:28,559 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:10Z] INFO  18:10:28,738 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:10Z] INFO  18:10:28,962 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T01:10Z] INFO  18:10:28,972 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:10Z] INFO  18:10:29,043 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-15T01:10Z] INFO  18:10:29,465 IntervalUtils - Processing 249953 bp from intervals
[2016-04-15T01:10Z] WARN  18:10:29,471 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:10Z] INFO  18:10:29,563 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:10Z] INFO  18:10:29,676 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:10Z] INFO  18:10:29,677 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:10Z] INFO  18:10:29,677 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T01:10Z] INFO  18:10:29,678 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T01:10Z] INFO  18:10:29,728 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:10Z] INFO  18:10:29,729 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:10Z] INFO  18:10:30,329 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:10Z] INFO  18:10:30,335 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:10Z] INFO  18:10:30,336 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:10Z] INFO  18:10:30,337 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:10Z] INFO  18:10:30,341 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/3/R14-18102_kapa-NGv3-PE100-NGv3-sort-3_127770401_143293035-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/3/R14-18102_kapa-NGv3-PE100-NGv3-3_127770401_143293035-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/3/tx/tmpOzCuMX/R14-18102_kapa-NGv3-PE100-NGv3-3_127770401_143293035.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:10Z] INFO  18:10:30,353 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:10Z] INFO  18:10:30,364 HelpFormatter - Date/Time: 2016/04/14 18:10:30
[2016-04-15T01:10Z] INFO  18:10:30,365 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:10Z] INFO  18:10:30,366 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:10Z] INFO  18:10:30,531 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:10Z] INFO  18:10:30,788 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T01:10Z] INFO  18:10:30,799 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:10Z] INFO  18:10:30,887 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.09
[2016-04-15T01:10Z] INFO  18:10:31,286 IntervalUtils - Processing 238450 bp from intervals
[2016-04-15T01:10Z] WARN  18:10:31,292 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:10Z] INFO  18:10:31,362 ProgressMeter -            done   1019400.0    28.0 s      27.0 s      100.0%    28.0 s       0.0 s
[2016-04-15T01:10Z] INFO  18:10:31,363 ProgressMeter - Total runtime 28.52 secs, 0.48 min, 0.01 hours
[2016-04-15T01:10Z] INFO  18:10:31,363 MicroScheduler - 33474 reads were filtered out during the traversal out of approximately 426198 total reads (7.85%)
[2016-04-15T01:10Z] INFO  18:10:31,364 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:10Z] INFO  18:10:31,364 MicroScheduler -   -> 623 reads (0.15% of total) failing BadMateFilter
[2016-04-15T01:10Z] INFO  18:10:31,364 MicroScheduler -   -> 32549 reads (7.64% of total) failing DuplicateReadFilter
[2016-04-15T01:10Z] INFO  18:10:31,365 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:10Z] INFO  18:10:31,365 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:10Z] INFO  18:10:31,365 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:10Z] INFO  18:10:31,366 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:10Z] INFO  18:10:31,366 MicroScheduler -   -> 302 reads (0.07% of total) failing UnmappedReadFilter
[2016-04-15T01:10Z] INFO  18:10:31,377 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:10Z] INFO  18:10:31,512 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:10Z] INFO  18:10:31,513 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:10Z] INFO  18:10:31,514 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T01:10Z] INFO  18:10:31,515 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T01:10Z] INFO  18:10:31,562 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:10Z] INFO  18:10:31,563 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:10Z] INFO  18:10:32,051 ProgressMeter -            done    626517.0    22.0 s      36.0 s      100.0%    22.0 s       0.0 s
[2016-04-15T01:10Z] INFO  18:10:32,052 ProgressMeter - Total runtime 22.90 secs, 0.38 min, 0.01 hours
[2016-04-15T01:10Z] INFO  18:10:32,052 MicroScheduler - 21235 reads were filtered out during the traversal out of approximately 254484 total reads (8.34%)
[2016-04-15T01:10Z] INFO  18:10:32,052 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:10Z] INFO  18:10:32,053 MicroScheduler -   -> 340 reads (0.13% of total) failing BadMateFilter
[2016-04-15T01:10Z] INFO  18:10:32,053 MicroScheduler -   -> 20680 reads (8.13% of total) failing DuplicateReadFilter
[2016-04-15T01:10Z] INFO  18:10:32,053 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:10Z] INFO  18:10:32,054 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:10Z] INFO  18:10:32,054 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:10Z] INFO  18:10:32,054 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:10Z] INFO  18:10:32,055 MicroScheduler -   -> 215 reads (0.08% of total) failing UnmappedReadFilter
[2016-04-15T01:10Z] INFO  18:10:33,012 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:10Z] INFO  18:10:33,023 ProgressMeter -            done     56098.0     6.0 s       2.1 m       99.7%     6.0 s       0.0 s
[2016-04-15T01:10Z] INFO  18:10:33,023 ProgressMeter - Total runtime 6.93 secs, 0.12 min, 0.00 hours
[2016-04-15T01:10Z] INFO  18:10:33,024 MicroScheduler - 3043 reads were filtered out during the traversal out of approximately 35792 total reads (8.50%)
[2016-04-15T01:10Z] INFO  18:10:33,024 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:10Z] INFO  18:10:33,025 MicroScheduler -   -> 46 reads (0.13% of total) failing BadMateFilter
[2016-04-15T01:10Z] INFO  18:10:33,025 MicroScheduler -   -> 2961 reads (8.27% of total) failing DuplicateReadFilter
[2016-04-15T01:10Z] INFO  18:10:33,025 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:10Z] INFO  18:10:33,026 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:10Z] INFO  18:10:33,026 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:10Z] INFO  18:10:33,033 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:10Z] INFO  18:10:33,033 MicroScheduler -   -> 36 reads (0.10% of total) failing UnmappedReadFilter
[2016-04-15T01:10Z] INFO  18:10:33,261 ProgressMeter -            done    206627.0    13.0 s      67.0 s      100.0%    13.0 s       0.0 s
[2016-04-15T01:10Z] INFO  18:10:33,262 ProgressMeter - Total runtime 13.93 secs, 0.23 min, 0.00 hours
[2016-04-15T01:10Z] INFO  18:10:33,263 MicroScheduler - 8219 reads were filtered out during the traversal out of approximately 97516 total reads (8.43%)
[2016-04-15T01:10Z] INFO  18:10:33,264 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:10Z] INFO  18:10:33,265 MicroScheduler -   -> 158 reads (0.16% of total) failing BadMateFilter
[2016-04-15T01:10Z] INFO  18:10:33,266 MicroScheduler -   -> 7995 reads (8.20% of total) failing DuplicateReadFilter
[2016-04-15T01:10Z] INFO  18:10:33,266 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:10Z] INFO  18:10:33,267 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:10Z] INFO  18:10:33,268 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:10Z] INFO  18:10:33,269 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:10Z] INFO  18:10:33,269 MicroScheduler -   -> 66 reads (0.07% of total) failing UnmappedReadFilter
[2016-04-15T01:10Z] GATK: UnifiedGenotyper
[2016-04-15T01:10Z] INFO  18:10:33,339 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:10Z] GATK: UnifiedGenotyper
[2016-04-15T01:10Z] INFO  18:10:34,776 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:10Z] GATK: UnifiedGenotyper
[2016-04-15T01:10Z] INFO  18:10:35,076 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:10Z] GATK: UnifiedGenotyper
[2016-04-15T01:10Z] INFO  18:10:35,549 ProgressMeter -            done    606340.0    21.0 s      35.0 s      100.0%    21.0 s       0.0 s
[2016-04-15T01:10Z] INFO  18:10:35,550 ProgressMeter - Total runtime 21.37 secs, 0.36 min, 0.01 hours
[2016-04-15T01:10Z] INFO  18:10:35,550 MicroScheduler - 17903 reads were filtered out during the traversal out of approximately 217219 total reads (8.24%)
[2016-04-15T01:10Z] INFO  18:10:35,551 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:10Z] INFO  18:10:35,551 MicroScheduler -   -> 295 reads (0.14% of total) failing BadMateFilter
[2016-04-15T01:10Z] INFO  18:10:35,551 MicroScheduler -   -> 17450 reads (8.03% of total) failing DuplicateReadFilter
[2016-04-15T01:10Z] INFO  18:10:35,551 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:10Z] INFO  18:10:35,552 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:10Z] INFO  18:10:35,552 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:10Z] INFO  18:10:35,552 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:10Z] INFO  18:10:35,552 MicroScheduler -   -> 158 reads (0.07% of total) failing UnmappedReadFilter
[2016-04-15T01:10Z] INFO  18:10:35,670 ProgressMeter -            done    469618.0    17.0 s      37.0 s      100.0%    17.0 s       0.0 s
[2016-04-15T01:10Z] INFO  18:10:35,670 ProgressMeter - Total runtime 17.65 secs, 0.29 min, 0.00 hours
[2016-04-15T01:10Z] INFO  18:10:35,671 MicroScheduler - 15479 reads were filtered out during the traversal out of approximately 183482 total reads (8.44%)
[2016-04-15T01:10Z] INFO  18:10:35,671 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:10Z] INFO  18:10:35,671 MicroScheduler -   -> 239 reads (0.13% of total) failing BadMateFilter
[2016-04-15T01:10Z] INFO  18:10:35,671 MicroScheduler -   -> 15095 reads (8.23% of total) failing DuplicateReadFilter
[2016-04-15T01:10Z] INFO  18:10:35,672 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:10Z] INFO  18:10:35,672 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:10Z] INFO  18:10:35,673 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:10Z] INFO  18:10:35,673 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:10Z] INFO  18:10:35,673 MicroScheduler -   -> 145 reads (0.08% of total) failing UnmappedReadFilter
[2016-04-15T01:10Z] INFO  18:10:36,508 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:10Z] INFO  18:10:36,512 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:10Z] INFO  18:10:36,512 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:10Z] INFO  18:10:36,513 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:10Z] INFO  18:10:36,518 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/3/R14-18102_kapa-NGv3-PE100-NGv3-sort-3_143297426_158963696-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/3/R14-18102_kapa-NGv3-PE100-NGv3-3_143297426_158963696-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/3/tx/tmpDv5ymG/R14-18102_kapa-NGv3-PE100-NGv3-3_143297426_158963696.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:10Z] INFO  18:10:36,518 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:10Z] INFO  18:10:36,521 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:10Z] INFO  18:10:36,522 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:10Z] INFO  18:10:36,523 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:10Z] INFO  18:10:36,528 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/3/R14-18102_kapa-NGv3-PE100-NGv3-sort-3_158970515_174577240-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/3/R14-18102_kapa-NGv3-PE100-NGv3-3_158970515_174577240-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/3/tx/tmpYkifr2/R14-18102_kapa-NGv3-PE100-NGv3-3_158970515_174577240.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:10Z] INFO  18:10:36,529 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:10Z] INFO  18:10:36,530 HelpFormatter - Date/Time: 2016/04/14 18:10:36
[2016-04-15T01:10Z] INFO  18:10:36,539 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:10Z] INFO  18:10:36,550 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:10Z] INFO  18:10:36,563 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:10Z] INFO  18:10:36,564 HelpFormatter - Date/Time: 2016/04/14 18:10:36
[2016-04-15T01:10Z] INFO  18:10:36,564 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:10Z] INFO  18:10:36,564 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:10Z] INFO  18:10:36,750 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:10Z] INFO  18:10:36,766 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:10Z] INFO  18:10:36,890 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:10Z] INFO  18:10:36,941 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T01:10Z] INFO  18:10:36,950 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:10Z] INFO  18:10:36,958 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T01:10Z] INFO  18:10:36,967 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:10Z] INFO  18:10:37,034 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-15T01:10Z] INFO  18:10:37,036 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.09
[2016-04-15T01:10Z] INFO  18:10:37,049 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:10Z] GATK: UnifiedGenotyper
[2016-04-15T01:10Z] GATK: UnifiedGenotyper
[2016-04-15T01:10Z] INFO  18:10:37,445 IntervalUtils - Processing 102254 bp from intervals
[2016-04-15T01:10Z] WARN  18:10:37,451 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:10Z] INFO  18:10:37,454 IntervalUtils - Processing 125161 bp from intervals
[2016-04-15T01:10Z] WARN  18:10:37,464 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:10Z] INFO  18:10:37,557 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:10Z] INFO  18:10:37,572 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:10Z] INFO  18:10:37,661 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:10Z] INFO  18:10:37,662 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:10Z] INFO  18:10:37,663 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T01:10Z] INFO  18:10:37,663 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:10Z] INFO  18:10:37,663 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T01:10Z] INFO  18:10:37,664 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:10Z] INFO  18:10:37,664 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T01:10Z] INFO  18:10:37,665 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T01:10Z] INFO  18:10:37,710 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:10Z] INFO  18:10:37,721 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:10Z] INFO  18:10:37,747 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:10Z] INFO  18:10:37,752 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:10Z] INFO  18:10:38,139 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:10Z] INFO  18:10:38,143 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:10Z] INFO  18:10:38,148 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:10Z] INFO  18:10:38,149 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:10Z] INFO  18:10:38,150 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:10Z] INFO  18:10:38,154 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:10Z] INFO  18:10:38,155 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:10Z] INFO  18:10:38,155 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/3/R14-18102_kapa-NGv3-PE100-NGv3-sort-3_174814579_190326970-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/3/R14-18102_kapa-NGv3-PE100-NGv3-3_174814579_190326970-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/3/tx/tmpnerUl0/R14-18102_kapa-NGv3-PE100-NGv3-3_174814579_190326970.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:10Z] INFO  18:10:38,155 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:10Z] INFO  18:10:38,161 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/3/R14-18102_kapa-NGv3-PE100-NGv3-sort-3_190333063_198022430-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/3/R14-18102_kapa-NGv3-PE100-NGv3-3_190333063_198022430-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/3/tx/tmp7XZ283/R14-18102_kapa-NGv3-PE100-NGv3-3_190333063_198022430.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:10Z] INFO  18:10:38,166 ProgressMeter -            done    217382.0    13.0 s      60.0 s      100.0%    13.0 s       0.0 s
[2016-04-15T01:10Z] INFO  18:10:38,170 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:10Z] INFO  18:10:38,175 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:10Z] INFO  18:10:38,167 ProgressMeter - Total runtime 13.08 secs, 0.22 min, 0.00 hours
[2016-04-15T01:10Z] INFO  18:10:38,171 HelpFormatter - Date/Time: 2016/04/14 18:10:38
[2016-04-15T01:10Z] INFO  18:10:38,176 HelpFormatter - Date/Time: 2016/04/14 18:10:38
[2016-04-15T01:10Z] INFO  18:10:38,176 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:10Z] INFO  18:10:38,176 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:10Z] INFO  18:10:38,167 MicroScheduler - 8021 reads were filtered out during the traversal out of approximately 98860 total reads (8.11%)
[2016-04-15T01:10Z] INFO  18:10:38,172 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:10Z] INFO  18:10:38,168 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:10Z] INFO  18:10:38,173 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:10Z] INFO  18:10:38,168 MicroScheduler -   -> 126 reads (0.13% of total) failing BadMateFilter
[2016-04-15T01:10Z] INFO  18:10:38,168 MicroScheduler -   -> 7817 reads (7.91% of total) failing DuplicateReadFilter
[2016-04-15T01:10Z] INFO  18:10:38,168 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:10Z] INFO  18:10:38,169 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:10Z] INFO  18:10:38,169 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:10Z] INFO  18:10:38,169 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:10Z] INFO  18:10:38,169 MicroScheduler -   -> 78 reads (0.08% of total) failing UnmappedReadFilter
[2016-04-15T01:10Z] INFO  18:10:38,297 ProgressMeter -            done   1634209.0    26.0 s      16.0 s      100.0%    26.0 s       0.0 s
[2016-04-15T01:10Z] INFO  18:10:38,297 ProgressMeter - Total runtime 26.96 secs, 0.45 min, 0.01 hours
[2016-04-15T01:10Z] INFO  18:10:38,297 MicroScheduler - 25500 reads were filtered out during the traversal out of approximately 310745 total reads (8.21%)
[2016-04-15T01:10Z] INFO  18:10:38,298 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:10Z] INFO  18:10:38,298 MicroScheduler -   -> 421 reads (0.14% of total) failing BadMateFilter
[2016-04-15T01:10Z] INFO  18:10:38,298 MicroScheduler -   -> 24805 reads (7.98% of total) failing DuplicateReadFilter
[2016-04-15T01:10Z] INFO  18:10:38,299 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:10Z] INFO  18:10:38,299 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:10Z] INFO  18:10:38,299 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:10Z] INFO  18:10:38,299 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:10Z] INFO  18:10:38,300 MicroScheduler -   -> 274 reads (0.09% of total) failing UnmappedReadFilter
[2016-04-15T01:10Z] INFO  18:10:38,346 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:10Z] INFO  18:10:38,381 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:10Z] INFO  18:10:38,582 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T01:10Z] INFO  18:10:38,594 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:10Z] INFO  18:10:38,632 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T01:10Z] INFO  18:10:38,650 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:10Z] INFO  18:10:38,704 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.11
[2016-04-15T01:10Z] INFO  18:10:38,737 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.09
[2016-04-15T01:10Z] INFO  18:10:39,196 IntervalUtils - Processing 184739 bp from intervals
[2016-04-15T01:10Z] WARN  18:10:39,201 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:10Z] INFO  18:10:39,245 IntervalUtils - Processing 118955 bp from intervals
[2016-04-15T01:10Z] WARN  18:10:39,250 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:10Z] INFO  18:10:39,343 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:10Z] INFO  18:10:39,398 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:10Z] INFO  18:10:39,473 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:10Z] INFO  18:10:39,474 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:10Z] INFO  18:10:39,475 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T01:10Z] INFO  18:10:39,475 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T01:10Z] INFO  18:10:39,507 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:10Z] INFO  18:10:39,508 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:10Z] INFO  18:10:39,509 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T01:10Z] INFO  18:10:39,510 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T01:10Z] INFO  18:10:39,550 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:10Z] INFO  18:10:39,551 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:10Z] INFO  18:10:39,562 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:10Z] INFO  18:10:39,563 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:10Z] INFO  18:10:39,593 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:10Z] INFO  18:10:39,799 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:10Z] GATK: UnifiedGenotyper
[2016-04-15T01:10Z] GATK: UnifiedGenotyper
[2016-04-15T01:10Z] INFO  18:10:40,254 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:10Z] INFO  18:10:40,257 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:10Z] INFO  18:10:40,258 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:10Z] INFO  18:10:40,258 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:10Z] INFO  18:10:40,263 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/4/R14-18102_kapa-NGv3-PE100-NGv3-sort-4_0_15511864-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/4/R14-18102_kapa-NGv3-PE100-NGv3-4_0_15511864-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/4/tx/tmpxCu3PW/R14-18102_kapa-NGv3-PE100-NGv3-4_0_15511864.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:10Z] INFO  18:10:40,298 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:10Z] INFO  18:10:40,300 HelpFormatter - Date/Time: 2016/04/14 18:10:40
[2016-04-15T01:10Z] INFO  18:10:40,301 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:10Z] INFO  18:10:40,305 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:10Z] INFO  18:10:40,373 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:10Z] INFO  18:10:40,376 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:10Z] INFO  18:10:40,377 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:10Z] INFO  18:10:40,377 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:10Z] INFO  18:10:40,382 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/4/R14-18102_kapa-NGv3-PE100-NGv3-sort-4_15512869_31144471-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/4/R14-18102_kapa-NGv3-PE100-NGv3-4_15512869_31144471-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/4/tx/tmpzgm5mC/R14-18102_kapa-NGv3-PE100-NGv3-4_15512869_31144471.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:10Z] INFO  18:10:40,394 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:10Z] INFO  18:10:40,395 HelpFormatter - Date/Time: 2016/04/14 18:10:40
[2016-04-15T01:10Z] INFO  18:10:40,396 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:10Z] INFO  18:10:40,396 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:10Z] INFO  18:10:40,500 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:10Z] INFO  18:10:40,542 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:10Z] INFO  18:10:40,778 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T01:10Z] INFO  18:10:40,787 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:10Z] INFO  18:10:40,800 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T01:10Z] INFO  18:10:40,819 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:10Z] INFO  18:10:40,886 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.10
[2016-04-15T01:10Z] INFO  18:10:40,936 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.12
[2016-04-15T01:10Z] INFO  18:10:41,394 IntervalUtils - Processing 90668 bp from intervals
[2016-04-15T01:10Z] WARN  18:10:41,413 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:10Z] INFO  18:10:41,436 IntervalUtils - Processing 255565 bp from intervals
[2016-04-15T01:10Z] WARN  18:10:41,441 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:10Z] INFO  18:10:41,518 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:10Z] INFO  18:10:41,573 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:10Z] INFO  18:10:41,616 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:10Z] INFO  18:10:41,617 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:10Z] INFO  18:10:41,618 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T01:10Z] INFO  18:10:41,619 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T01:10Z] INFO  18:10:41,676 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:10Z] INFO  18:10:41,678 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:10Z] INFO  18:10:41,681 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T01:10Z] INFO  18:10:41,682 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T01:10Z] INFO  18:10:41,690 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:10Z] INFO  18:10:41,691 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:10Z] INFO  18:10:41,746 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:10Z] INFO  18:10:41,747 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:10Z] INFO  18:10:42,566 ProgressMeter -            done    587434.0    25.0 s      42.0 s      100.0%    25.0 s       0.0 s
[2016-04-15T01:10Z] INFO  18:10:42,567 ProgressMeter - Total runtime 25.21 secs, 0.42 min, 0.01 hours
[2016-04-15T01:10Z] INFO  18:10:42,567 MicroScheduler - 23012 reads were filtered out during the traversal out of approximately 268924 total reads (8.56%)
[2016-04-15T01:10Z] INFO  18:10:42,568 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:10Z] INFO  18:10:42,568 MicroScheduler -   -> 394 reads (0.15% of total) failing BadMateFilter
[2016-04-15T01:10Z] INFO  18:10:42,568 MicroScheduler -   -> 22394 reads (8.33% of total) failing DuplicateReadFilter
[2016-04-15T01:10Z] INFO  18:10:42,568 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:10Z] INFO  18:10:42,569 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:10Z] INFO  18:10:42,569 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:10Z] INFO  18:10:42,569 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:10Z] INFO  18:10:42,569 MicroScheduler -   -> 224 reads (0.08% of total) failing UnmappedReadFilter
[2016-04-15T01:10Z] INFO  18:10:42,847 ProgressMeter -            done    666709.0    23.0 s      35.0 s      100.0%    23.0 s       0.0 s
[2016-04-15T01:10Z] INFO  18:10:42,847 ProgressMeter - Total runtime 23.67 secs, 0.39 min, 0.01 hours
[2016-04-15T01:10Z] INFO  18:10:42,848 MicroScheduler - 23349 reads were filtered out during the traversal out of approximately 270481 total reads (8.63%)
[2016-04-15T01:10Z] INFO  18:10:42,848 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:10Z] INFO  18:10:42,848 MicroScheduler -   -> 404 reads (0.15% of total) failing BadMateFilter
[2016-04-15T01:10Z] INFO  18:10:42,848 MicroScheduler -   -> 22730 reads (8.40% of total) failing DuplicateReadFilter
[2016-04-15T01:10Z] INFO  18:10:42,849 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:10Z] INFO  18:10:42,849 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:10Z] INFO  18:10:42,849 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:10Z] INFO  18:10:42,849 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:10Z] INFO  18:10:42,850 MicroScheduler -   -> 215 reads (0.08% of total) failing UnmappedReadFilter
[2016-04-15T01:10Z] INFO  18:10:42,913 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:10Z] INFO  18:10:42,916 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:10Z] INFO  18:10:42,917 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:10Z] INFO  18:10:42,917 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:10Z] INFO  18:10:42,922 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/4/R14-18102_kapa-NGv3-PE100-NGv3-sort-4_36069528_52709433-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/4/R14-18102_kapa-NGv3-PE100-NGv3-4_36069528_52709433-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/4/tx/tmpOB7PNE/R14-18102_kapa-NGv3-PE100-NGv3-4_36069528_52709433.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:10Z] INFO  18:10:42,935 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:10Z] INFO  18:10:42,946 HelpFormatter - Date/Time: 2016/04/14 18:10:42
[2016-04-15T01:10Z] INFO  18:10:42,947 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:10Z] INFO  18:10:42,948 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:10Z] INFO  18:10:43,046 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:10Z] INFO  18:10:43,050 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:10Z] INFO  18:10:43,050 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:10Z] INFO  18:10:43,051 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:10Z] INFO  18:10:43,055 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/4/R14-18102_kapa-NGv3-PE100-NGv3-sort-4_52709749_68338393-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/4/R14-18102_kapa-NGv3-PE100-NGv3-4_52709749_68338393-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/4/tx/tmp5ibyC0/R14-18102_kapa-NGv3-PE100-NGv3-4_52709749_68338393.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:10Z] INFO  18:10:43,067 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:10Z] INFO  18:10:43,068 HelpFormatter - Date/Time: 2016/04/14 18:10:43
[2016-04-15T01:10Z] INFO  18:10:43,069 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:10Z] INFO  18:10:43,069 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:10Z] INFO  18:10:43,225 ProgressMeter -            done    356274.0    15.0 s      42.0 s       99.9%    15.0 s       0.0 s
[2016-04-15T01:10Z] INFO  18:10:43,226 ProgressMeter - Total runtime 15.23 secs, 0.25 min, 0.00 hours
[2016-04-15T01:10Z] INFO  18:10:43,226 MicroScheduler - 11967 reads were filtered out during the traversal out of approximately 147673 total reads (8.10%)
[2016-04-15T01:10Z] INFO  18:10:43,226 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:10Z] INFO  18:10:43,226 MicroScheduler -   -> 220 reads (0.15% of total) failing BadMateFilter
[2016-04-15T01:10Z] INFO  18:10:43,227 MicroScheduler -   -> 11647 reads (7.89% of total) failing DuplicateReadFilter
[2016-04-15T01:10Z] INFO  18:10:43,227 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:10Z] INFO  18:10:43,227 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:10Z] INFO  18:10:43,227 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:10Z] INFO  18:10:43,228 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:10Z] INFO  18:10:43,228 MicroScheduler -   -> 100 reads (0.07% of total) failing UnmappedReadFilter
[2016-04-15T01:10Z] INFO  18:10:43,256 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:10Z] INFO  18:10:43,266 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:10Z] INFO  18:10:43,545 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T01:10Z] INFO  18:10:43,554 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:10Z] INFO  18:10:43,621 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T01:10Z] INFO  18:10:43,632 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:10Z] INFO  18:10:43,675 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.12
[2016-04-15T01:10Z] INFO  18:10:43,737 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.10
[2016-04-15T01:10Z] INFO  18:10:44,092 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:10Z] INFO  18:10:44,102 IntervalUtils - Processing 142047 bp from intervals
[2016-04-15T01:10Z] WARN  18:10:44,107 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:10Z] INFO  18:10:44,162 IntervalUtils - Processing 83782 bp from intervals
[2016-04-15T01:10Z] WARN  18:10:44,175 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:10Z] INFO  18:10:44,212 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:10Z] INFO  18:10:44,281 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:10Z] INFO  18:10:44,288 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:10Z] INFO  18:10:44,289 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:10Z] INFO  18:10:44,290 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T01:10Z] INFO  18:10:44,291 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T01:10Z] INFO  18:10:44,332 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:10Z] INFO  18:10:44,332 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:10Z] INFO  18:10:44,344 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:10Z] GATK: UnifiedGenotyper
[2016-04-15T01:10Z] INFO  18:10:44,362 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:10Z] INFO  18:10:44,363 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T01:10Z] INFO  18:10:44,364 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T01:10Z] INFO  18:10:44,383 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:10Z] INFO  18:10:44,436 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:10Z] INFO  18:10:44,437 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:10Z] GATK: UnifiedGenotyper
[2016-04-15T01:10Z] INFO  18:10:44,784 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:10Z] INFO  18:10:44,856 ProgressMeter -            done   1181875.0    29.0 s      25.0 s      100.0%    29.0 s       0.0 s
[2016-04-15T01:10Z] INFO  18:10:44,857 ProgressMeter - Total runtime 29.76 secs, 0.50 min, 0.01 hours
[2016-04-15T01:10Z] INFO  18:10:44,858 MicroScheduler - 29200 reads were filtered out during the traversal out of approximately 349697 total reads (8.35%)
[2016-04-15T01:10Z] INFO  18:10:44,858 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:10Z] INFO  18:10:44,859 MicroScheduler -   -> 518 reads (0.15% of total) failing BadMateFilter
[2016-04-15T01:10Z] INFO  18:10:44,860 MicroScheduler -   -> 28395 reads (8.12% of total) failing DuplicateReadFilter
[2016-04-15T01:10Z] INFO  18:10:44,860 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:10Z] INFO  18:10:44,861 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:10Z] INFO  18:10:44,861 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:10Z] INFO  18:10:44,862 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:10Z] INFO  18:10:44,863 MicroScheduler -   -> 287 reads (0.08% of total) failing UnmappedReadFilter
[2016-04-15T01:10Z] GATK: UnifiedGenotyper
[2016-04-15T01:10Z] INFO  18:10:46,329 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:10Z] GATK: UnifiedGenotyper
[2016-04-15T01:10Z] INFO  18:10:47,320 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:10Z] INFO  18:10:47,324 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:10Z] INFO  18:10:47,324 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:10Z] INFO  18:10:47,325 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:10Z] INFO  18:10:47,329 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/4/R14-18102_kapa-NGv3-PE100-NGv3-sort-4_68340604_83852298-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/4/R14-18102_kapa-NGv3-PE100-NGv3-4_68340604_83852298-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/4/tx/tmpLgKENE/R14-18102_kapa-NGv3-PE100-NGv3-4_68340604_83852298.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:10Z] INFO  18:10:47,346 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:10Z] INFO  18:10:47,346 HelpFormatter - Date/Time: 2016/04/14 18:10:47
[2016-04-15T01:10Z] INFO  18:10:47,346 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:10Z] INFO  18:10:47,347 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:10Z] INFO  18:10:47,508 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:10Z] INFO  18:10:47,699 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T01:10Z] INFO  18:10:47,709 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:10Z] INFO  18:10:47,785 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-15T01:10Z] INFO  18:10:47,844 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:10Z] INFO  18:10:47,849 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:10Z] INFO  18:10:47,850 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:10Z] INFO  18:10:47,851 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:10Z] INFO  18:10:47,876 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/4/R14-18102_kapa-NGv3-PE100-NGv3-sort-4_83857133_99393738-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/4/R14-18102_kapa-NGv3-PE100-NGv3-4_83857133_99393738-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/4/tx/tmp_qFw6b/R14-18102_kapa-NGv3-PE100-NGv3-4_83857133_99393738.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:10Z] INFO  18:10:47,887 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:10Z] INFO  18:10:47,898 HelpFormatter - Date/Time: 2016/04/14 18:10:47
[2016-04-15T01:10Z] INFO  18:10:47,899 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:10Z] INFO  18:10:47,900 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:10Z] INFO  18:10:48,033 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:10Z] INFO  18:10:48,042 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:10Z] INFO  18:10:48,043 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:10Z] INFO  18:10:48,043 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:10Z] INFO  18:10:48,048 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/4/R14-18102_kapa-NGv3-PE100-NGv3-sort-4_99397339_115544957-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/4/R14-18102_kapa-NGv3-PE100-NGv3-4_99397339_115544957-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/4/tx/tmp6KVcig/R14-18102_kapa-NGv3-PE100-NGv3-4_99397339_115544957.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:10Z] INFO  18:10:48,064 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:10Z] INFO  18:10:48,065 HelpFormatter - Date/Time: 2016/04/14 18:10:48
[2016-04-15T01:10Z] INFO  18:10:48,066 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:10Z] INFO  18:10:48,067 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:10Z] INFO  18:10:48,165 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:10Z] INFO  18:10:48,241 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:10Z] INFO  18:10:48,409 IntervalUtils - Processing 197466 bp from intervals
[2016-04-15T01:10Z] WARN  18:10:48,415 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:10Z] INFO  18:10:48,499 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T01:10Z] INFO  18:10:48,515 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:10Z] INFO  18:10:48,518 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T01:10Z] INFO  18:10:48,538 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:10Z] INFO  18:10:48,590 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:10Z] INFO  18:10:48,615 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.10
[2016-04-15T01:10Z] INFO  18:10:48,621 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-15T01:10Z] INFO  18:10:48,732 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:10Z] INFO  18:10:48,732 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:10Z] INFO  18:10:48,733 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T01:10Z] INFO  18:10:48,733 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T01:10Z] INFO  18:10:48,798 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:10Z] INFO  18:10:48,799 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:10Z] INFO  18:10:48,996 IntervalUtils - Processing 153852 bp from intervals
[2016-04-15T01:10Z] WARN  18:10:49,002 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:10Z] INFO  18:10:49,007 IntervalUtils - Processing 124091 bp from intervals
[2016-04-15T01:10Z] WARN  18:10:49,011 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:10Z] INFO  18:10:49,078 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:10Z] INFO  18:10:49,080 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:10Z] INFO  18:10:49,165 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:10Z] INFO  18:10:49,166 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:10Z] INFO  18:10:49,167 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T01:10Z] INFO  18:10:49,167 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T01:10Z] INFO  18:10:49,177 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:10Z] INFO  18:10:49,178 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:10Z] INFO  18:10:49,179 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T01:10Z] INFO  18:10:49,180 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T01:10Z] INFO  18:10:49,220 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:10Z] INFO  18:10:49,225 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:10Z] INFO  18:10:49,236 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:10Z] INFO  18:10:49,237 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:10Z] INFO  18:10:49,431 ProgressMeter -      3:46621229    875749.0    30.0 s      34.0 s       92.7%    32.0 s       2.0 s
[2016-04-15T01:10Z] INFO  18:10:49,969 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:10Z] INFO  18:10:49,972 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:10Z] INFO  18:10:49,973 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:10Z] INFO  18:10:49,973 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:10Z] INFO  18:10:49,978 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/4/R14-18102_kapa-NGv3-PE100-NGv3-sort-4_115584857_134074404-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/4/R14-18102_kapa-NGv3-PE100-NGv3-4_115584857_134074404-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/4/tx/tmp58UWKm/R14-18102_kapa-NGv3-PE100-NGv3-4_115584857_134074404.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:10Z] INFO  18:10:50,000 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:10Z] INFO  18:10:50,002 HelpFormatter - Date/Time: 2016/04/14 18:10:49
[2016-04-15T01:10Z] INFO  18:10:50,003 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:10Z] INFO  18:10:50,004 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:10Z] INFO  18:10:50,199 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:10Z] INFO  18:10:50,458 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T01:10Z] INFO  18:10:50,466 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:10Z] INFO  18:10:50,541 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-15T01:10Z] INFO  18:10:50,919 IntervalUtils - Processing 157938 bp from intervals
[2016-04-15T01:10Z] WARN  18:10:50,925 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:10Z] INFO  18:10:51,007 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:10Z] INFO  18:10:51,062 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:10Z] INFO  18:10:51,064 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:10Z] INFO  18:10:51,064 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T01:10Z] INFO  18:10:51,065 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T01:10Z] INFO  18:10:51,106 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:10Z] INFO  18:10:51,107 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:10Z] INFO  18:10:51,331 ProgressMeter -            done   1082933.0    31.0 s      29.0 s      100.0%    31.0 s       0.0 s
[2016-04-15T01:10Z] INFO  18:10:51,332 ProgressMeter - Total runtime 31.91 secs, 0.53 min, 0.01 hours
[2016-04-15T01:10Z] INFO  18:10:51,332 MicroScheduler - 34606 reads were filtered out during the traversal out of approximately 411635 total reads (8.41%)
[2016-04-15T01:10Z] INFO  18:10:51,332 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:10Z] INFO  18:10:51,333 MicroScheduler -   -> 583 reads (0.14% of total) failing BadMateFilter
[2016-04-15T01:10Z] INFO  18:10:51,333 MicroScheduler -   -> 33692 reads (8.18% of total) failing DuplicateReadFilter
[2016-04-15T01:10Z] INFO  18:10:51,333 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:10Z] INFO  18:10:51,333 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:10Z] INFO  18:10:51,334 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:10Z] INFO  18:10:51,334 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:10Z] INFO  18:10:51,334 MicroScheduler -   -> 331 reads (0.08% of total) failing UnmappedReadFilter
[2016-04-15T01:10Z] INFO  18:10:51,713 ProgressMeter -            done    258232.0    14.0 s      54.0 s      100.0%    14.0 s       0.0 s
[2016-04-15T01:10Z] INFO  18:10:51,713 ProgressMeter - Total runtime 14.05 secs, 0.23 min, 0.00 hours
[2016-04-15T01:10Z] INFO  18:10:51,713 MicroScheduler - 9223 reads were filtered out during the traversal out of approximately 111031 total reads (8.31%)
[2016-04-15T01:10Z] INFO  18:10:51,714 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:10Z] INFO  18:10:51,714 MicroScheduler -   -> 168 reads (0.15% of total) failing BadMateFilter
[2016-04-15T01:10Z] INFO  18:10:51,714 MicroScheduler -   -> 8972 reads (8.08% of total) failing DuplicateReadFilter
[2016-04-15T01:10Z] INFO  18:10:51,714 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:10Z] INFO  18:10:51,715 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:10Z] INFO  18:10:51,715 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:10Z] INFO  18:10:51,715 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:10Z] INFO  18:10:51,715 MicroScheduler -   -> 83 reads (0.07% of total) failing UnmappedReadFilter
[2016-04-15T01:10Z] INFO  18:10:51,937 ProgressMeter -      3:52392674   1980542.0    30.0 s      15.0 s       62.8%    47.0 s      17.0 s
[2016-04-15T01:10Z] INFO  18:10:52,728 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:10Z] INFO  18:10:52,759 ProgressMeter -            done    309734.0    15.0 s      48.0 s       99.9%    15.0 s       0.0 s
[2016-04-15T01:10Z] INFO  18:10:52,759 ProgressMeter - Total runtime 15.10 secs, 0.25 min, 0.00 hours
[2016-04-15T01:10Z] INFO  18:10:52,760 MicroScheduler - 11626 reads were filtered out during the traversal out of approximately 139087 total reads (8.36%)
[2016-04-15T01:10Z] INFO  18:10:52,760 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:10Z] INFO  18:10:52,760 MicroScheduler -   -> 195 reads (0.14% of total) failing BadMateFilter
[2016-04-15T01:10Z] INFO  18:10:52,761 MicroScheduler -   -> 11316 reads (8.14% of total) failing DuplicateReadFilter
[2016-04-15T01:10Z] INFO  18:10:52,761 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:10Z] INFO  18:10:52,761 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:10Z] INFO  18:10:52,761 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:10Z] INFO  18:10:52,762 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:10Z] INFO  18:10:52,762 MicroScheduler -   -> 115 reads (0.08% of total) failing UnmappedReadFilter
[2016-04-15T01:10Z] GATK: UnifiedGenotyper
[2016-04-15T01:10Z] INFO  18:10:53,263 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:10Z] GATK: UnifiedGenotyper
[2016-04-15T01:10Z] INFO  18:10:54,073 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:10Z] GATK: UnifiedGenotyper
[2016-04-15T01:10Z] INFO  18:10:54,979 ProgressMeter -            done    230295.0    13.0 s      57.0 s       99.9%    13.0 s       0.0 s
[2016-04-15T01:10Z] INFO  18:10:54,985 ProgressMeter - Total runtime 13.31 secs, 0.22 min, 0.00 hours
[2016-04-15T01:10Z] INFO  18:10:54,985 MicroScheduler - 8241 reads were filtered out during the traversal out of approximately 99484 total reads (8.28%)
[2016-04-15T01:10Z] INFO  18:10:54,986 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:10Z] INFO  18:10:54,986 MicroScheduler -   -> 129 reads (0.13% of total) failing BadMateFilter
[2016-04-15T01:10Z] INFO  18:10:54,986 MicroScheduler -   -> 8045 reads (8.09% of total) failing DuplicateReadFilter
[2016-04-15T01:10Z] INFO  18:10:54,987 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:10Z] INFO  18:10:54,987 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:10Z] INFO  18:10:54,987 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:10Z] INFO  18:10:54,988 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:10Z] INFO  18:10:54,988 MicroScheduler -   -> 67 reads (0.07% of total) failing UnmappedReadFilter
[2016-04-15T01:10Z] INFO  18:10:55,899 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:10Z] INFO  18:10:55,903 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:10Z] INFO  18:10:55,904 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:10Z] INFO  18:10:55,904 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:10Z] INFO  18:10:55,910 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/4/R14-18102_kapa-NGv3-PE100-NGv3-sort-4_134075461_150351181-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/4/R14-18102_kapa-NGv3-PE100-NGv3-4_134075461_150351181-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/4/tx/tmpzKizwU/R14-18102_kapa-NGv3-PE100-NGv3-4_134075461_150351181.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:10Z] INFO  18:10:55,943 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:10Z] INFO  18:10:55,945 HelpFormatter - Date/Time: 2016/04/14 18:10:55
[2016-04-15T01:10Z] INFO  18:10:55,945 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:10Z] INFO  18:10:55,946 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:10Z] INFO  18:10:56,167 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:10Z] INFO  18:10:56,256 ProgressMeter -            done    720572.0    24.0 s      34.0 s      100.0%    24.0 s       0.0 s
[2016-04-15T01:10Z] INFO  18:10:56,257 ProgressMeter - Total runtime 24.74 secs, 0.41 min, 0.01 hours
[2016-04-15T01:10Z] INFO  18:10:56,257 MicroScheduler - 24832 reads were filtered out during the traversal out of approximately 293125 total reads (8.47%)
[2016-04-15T01:10Z] INFO  18:10:56,258 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:10Z] INFO  18:10:56,258 MicroScheduler -   -> 469 reads (0.16% of total) failing BadMateFilter
[2016-04-15T01:10Z] INFO  18:10:56,258 MicroScheduler -   -> 24136 reads (8.23% of total) failing DuplicateReadFilter
[2016-04-15T01:10Z] INFO  18:10:56,259 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:10Z] INFO  18:10:56,259 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:10Z] INFO  18:10:56,259 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:10Z] INFO  18:10:56,260 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:10Z] INFO  18:10:56,260 MicroScheduler -   -> 227 reads (0.08% of total) failing UnmappedReadFilter
[2016-04-15T01:10Z] INFO  18:10:56,444 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T01:10Z] INFO  18:10:56,455 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:10Z] INFO  18:10:56,548 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.09
[2016-04-15T01:10Z] INFO  18:10:56,575 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:10Z] INFO  18:10:56,579 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:10Z] INFO  18:10:56,580 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:10Z] INFO  18:10:56,581 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:10Z] INFO  18:10:56,586 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/4/R14-18102_kapa-NGv3-PE100-NGv3-sort-4_150354547_165878648-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/4/R14-18102_kapa-NGv3-PE100-NGv3-4_150354547_165878648-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/4/tx/tmppZtEkg/R14-18102_kapa-NGv3-PE100-NGv3-4_150354547_165878648.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:10Z] INFO  18:10:56,602 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:10Z] INFO  18:10:56,603 HelpFormatter - Date/Time: 2016/04/14 18:10:56
[2016-04-15T01:10Z] INFO  18:10:56,603 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:10Z] INFO  18:10:56,603 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:10Z] INFO  18:10:56,789 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:10Z] INFO  18:10:56,854 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:10Z] INFO  18:10:56,945 ProgressMeter -            done    255123.0    12.0 s      49.0 s       99.9%    12.0 s       0.0 s
[2016-04-15T01:10Z] INFO  18:10:56,946 ProgressMeter - Total runtime 12.60 secs, 0.21 min, 0.00 hours
[2016-04-15T01:10Z] INFO  18:10:56,946 MicroScheduler - 8123 reads were filtered out during the traversal out of approximately 95300 total reads (8.52%)
[2016-04-15T01:10Z] INFO  18:10:56,947 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:10Z] INFO  18:10:56,947 MicroScheduler -   -> 165 reads (0.17% of total) failing BadMateFilter
[2016-04-15T01:10Z] INFO  18:10:56,947 MicroScheduler -   -> 7878 reads (8.27% of total) failing DuplicateReadFilter
[2016-04-15T01:10Z] INFO  18:10:56,948 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:10Z] INFO  18:10:56,948 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:10Z] INFO  18:10:56,948 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:10Z] INFO  18:10:56,949 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:10Z] INFO  18:10:56,949 MicroScheduler -   -> 80 reads (0.08% of total) failing UnmappedReadFilter
[2016-04-15T01:10Z] INFO  18:10:56,954 IntervalUtils - Processing 86890 bp from intervals
[2016-04-15T01:10Z] INFO  18:10:56,968 ProgressMeter -            done    680726.0    27.0 s      40.0 s      100.0%    27.0 s       0.0 s
[2016-04-15T01:10Z] INFO  18:10:56,969 ProgressMeter - Total runtime 27.29 secs, 0.45 min, 0.01 hours
[2016-04-15T01:10Z] INFO  18:10:56,969 MicroScheduler - 25925 reads were filtered out during the traversal out of approximately 312324 total reads (8.30%)
[2016-04-15T01:10Z] INFO  18:10:56,969 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:10Z] INFO  18:10:56,970 MicroScheduler -   -> 451 reads (0.14% of total) failing BadMateFilter
[2016-04-15T01:10Z] INFO  18:10:56,970 MicroScheduler -   -> 25270 reads (8.09% of total) failing DuplicateReadFilter
[2016-04-15T01:10Z] INFO  18:10:56,970 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:10Z] WARN  18:10:56,972 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:10Z] INFO  18:10:56,970 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:10Z] INFO  18:10:56,970 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:10Z] INFO  18:10:56,971 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:10Z] INFO  18:10:56,971 MicroScheduler -   -> 204 reads (0.07% of total) failing UnmappedReadFilter
[2016-04-15T01:10Z] INFO  18:10:57,033 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T01:10Z] INFO  18:10:57,045 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:10Z] INFO  18:10:57,077 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:10Z] INFO  18:10:57,161 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.11
[2016-04-15T01:10Z] INFO  18:10:57,189 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:10Z] INFO  18:10:57,190 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:10Z] INFO  18:10:57,190 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T01:10Z] INFO  18:10:57,190 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T01:10Z] GATK: UnifiedGenotyper
[2016-04-15T01:10Z] INFO  18:10:57,258 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:10Z] INFO  18:10:57,259 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:10Z] INFO  18:10:57,576 IntervalUtils - Processing 119752 bp from intervals
[2016-04-15T01:10Z] WARN  18:10:57,593 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:10Z] INFO  18:10:57,687 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:10Z] INFO  18:10:57,689 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:10Z] INFO  18:10:57,692 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:10Z] INFO  18:10:57,692 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:10Z] INFO  18:10:57,693 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:10Z] INFO  18:10:57,697 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/4/R14-18102_kapa-NGv3-PE100-NGv3-sort-4_165889318_183245405-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/4/R14-18102_kapa-NGv3-PE100-NGv3-4_165889318_183245405-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/4/tx/tmprbL59A/R14-18102_kapa-NGv3-PE100-NGv3-4_165889318_183245405.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:10Z] INFO  18:10:57,733 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:10Z] INFO  18:10:57,733 HelpFormatter - Date/Time: 2016/04/14 18:10:57
[2016-04-15T01:10Z] INFO  18:10:57,734 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:10Z] INFO  18:10:57,735 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:10Z] INFO  18:10:57,798 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:10Z] INFO  18:10:57,798 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:10Z] INFO  18:10:57,799 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T01:10Z] INFO  18:10:57,799 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T01:10Z] INFO  18:10:57,843 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:10Z] INFO  18:10:57,843 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:10Z] INFO  18:10:57,888 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:10Z] INFO  18:10:57,969 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:10Z] INFO  18:10:58,115 ProgressMeter -            done    351075.0    18.0 s      52.0 s       99.9%    18.0 s       0.0 s
[2016-04-15T01:10Z] INFO  18:10:58,116 ProgressMeter - Total runtime 18.61 secs, 0.31 min, 0.01 hours
[2016-04-15T01:10Z] INFO  18:10:58,116 MicroScheduler - 15836 reads were filtered out during the traversal out of approximately 184518 total reads (8.58%)
[2016-04-15T01:10Z] INFO  18:10:58,116 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:10Z] INFO  18:10:58,116 MicroScheduler -   -> 308 reads (0.17% of total) failing BadMateFilter
[2016-04-15T01:10Z] INFO  18:10:58,117 MicroScheduler -   -> 15365 reads (8.33% of total) failing DuplicateReadFilter
[2016-04-15T01:10Z] INFO  18:10:58,117 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:10Z] INFO  18:10:58,117 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:10Z] INFO  18:10:58,117 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:10Z] INFO  18:10:58,118 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:10Z] INFO  18:10:58,118 MicroScheduler -   -> 163 reads (0.09% of total) failing UnmappedReadFilter
[2016-04-15T01:10Z] INFO  18:10:58,142 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T01:10Z] INFO  18:10:58,156 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:10Z] INFO  18:10:58,211 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-15T01:10Z] GATK: UnifiedGenotyper
[2016-04-15T01:10Z] INFO  18:10:58,371 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:10Z] INFO  18:10:58,454 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:10Z] INFO  18:10:58,575 IntervalUtils - Processing 78538 bp from intervals
[2016-04-15T01:10Z] WARN  18:10:58,580 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:10Z] GATK: UnifiedGenotyper
[2016-04-15T01:10Z] INFO  18:10:58,682 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:10Z] GATK: UnifiedGenotyper
[2016-04-15T01:10Z] INFO  18:10:58,777 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:10Z] INFO  18:10:58,778 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:10Z] INFO  18:10:58,778 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T01:10Z] INFO  18:10:58,778 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T01:10Z] INFO  18:10:58,830 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:10Z] INFO  18:10:58,831 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:10Z] INFO  18:10:59,579 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:10Z] GATK: UnifiedGenotyper
[2016-04-15T01:11Z] INFO  18:11:00,259 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:11Z] INFO  18:11:00,262 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:11Z] INFO  18:11:00,263 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:11Z] INFO  18:11:00,263 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:11Z] INFO  18:11:00,268 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/4/R14-18102_kapa-NGv3-PE100-NGv3-sort-4_183267803_191154276-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/4/R14-18102_kapa-NGv3-PE100-NGv3-4_183267803_191154276-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/4/tx/tmpknSPlN/R14-18102_kapa-NGv3-PE100-NGv3-4_183267803_191154276.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:11Z] INFO  18:11:00,287 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:11Z] INFO  18:11:00,288 HelpFormatter - Date/Time: 2016/04/14 18:11:00
[2016-04-15T01:11Z] INFO  18:11:00,288 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:11Z] INFO  18:11:00,289 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:11Z] INFO  18:11:00,494 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:11Z] INFO  18:11:00,715 ProgressMeter -            done    359128.0    16.0 s      45.0 s      100.0%    16.0 s       0.0 s
[2016-04-15T01:11Z] INFO  18:11:00,716 ProgressMeter - Total runtime 16.43 secs, 0.27 min, 0.00 hours
[2016-04-15T01:11Z] INFO  18:11:00,716 MicroScheduler - 12812 reads were filtered out during the traversal out of approximately 155778 total reads (8.22%)
[2016-04-15T01:11Z] INFO  18:11:00,716 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:11Z] INFO  18:11:00,716 MicroScheduler -   -> 225 reads (0.14% of total) failing BadMateFilter
[2016-04-15T01:11Z] INFO  18:11:00,717 MicroScheduler -   -> 12466 reads (8.00% of total) failing DuplicateReadFilter
[2016-04-15T01:11Z] INFO  18:11:00,717 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:11Z] INFO  18:11:00,717 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:11Z] INFO  18:11:00,717 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:11Z] INFO  18:11:00,718 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:11Z] INFO  18:11:00,718 MicroScheduler -   -> 121 reads (0.08% of total) failing UnmappedReadFilter
[2016-04-15T01:11Z] INFO  18:11:00,719 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T01:11Z] INFO  18:11:00,733 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:11Z] INFO  18:11:00,818 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-15T01:11Z] INFO  18:11:01,366 IntervalUtils - Processing 99602 bp from intervals
[2016-04-15T01:11Z] WARN  18:11:01,370 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:11Z] INFO  18:11:01,485 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:11Z] INFO  18:11:01,500 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:11Z] INFO  18:11:01,500 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:11Z] INFO  18:11:01,501 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:11Z] INFO  18:11:01,502 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:11Z] INFO  18:11:01,507 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/5/R14-18102_kapa-NGv3-PE100-NGv3-sort-5_0_15580921-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/5/R14-18102_kapa-NGv3-PE100-NGv3-5_0_15580921-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/5/tx/tmpCplhlb/R14-18102_kapa-NGv3-PE100-NGv3-5_0_15580921.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:11Z] INFO  18:11:01,539 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:11Z] INFO  18:11:01,539 HelpFormatter - Date/Time: 2016/04/14 18:11:01
[2016-04-15T01:11Z] INFO  18:11:01,539 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:11Z] INFO  18:11:01,540 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:11Z] INFO  18:11:01,587 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:11Z] INFO  18:11:01,588 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:11Z] INFO  18:11:01,588 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T01:11Z] INFO  18:11:01,589 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T01:11Z] INFO  18:11:01,642 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:11Z] INFO  18:11:01,645 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:11Z] INFO  18:11:01,645 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:11Z] INFO  18:11:01,645 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:11Z] INFO  18:11:01,649 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/5/R14-18102_kapa-NGv3-PE100-NGv3-sort-5_15616091_31267808-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/5/R14-18102_kapa-NGv3-PE100-NGv3-5_15616091_31267808-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/5/tx/tmpmroPrd/R14-18102_kapa-NGv3-PE100-NGv3-5_15616091_31267808.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:11Z] INFO  18:11:01,656 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:11Z] INFO  18:11:01,657 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:11Z] INFO  18:11:01,658 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:11Z] INFO  18:11:01,658 HelpFormatter - Date/Time: 2016/04/14 18:11:01
[2016-04-15T01:11Z] INFO  18:11:01,659 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:11Z] INFO  18:11:01,659 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:11Z] INFO  18:11:01,685 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:11Z] INFO  18:11:01,688 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:11Z] INFO  18:11:01,689 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:11Z] INFO  18:11:01,689 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:11Z] INFO  18:11:01,694 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/5/R14-18102_kapa-NGv3-PE100-NGv3-sort-5_31294068_49695124-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/5/R14-18102_kapa-NGv3-PE100-NGv3-5_31294068_49695124-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/5/tx/tmpigcgfQ/R14-18102_kapa-NGv3-PE100-NGv3-5_31294068_49695124.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:11Z] INFO  18:11:01,700 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:11Z] INFO  18:11:01,721 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:11Z] INFO  18:11:01,729 HelpFormatter - Date/Time: 2016/04/14 18:11:01
[2016-04-15T01:11Z] INFO  18:11:01,730 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:11Z] INFO  18:11:01,730 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:11Z] INFO  18:11:01,828 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:11Z] INFO  18:11:01,921 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:11Z] INFO  18:11:02,000 ProgressMeter -            done    782811.0    22.0 s      28.0 s      100.0%    22.0 s       0.0 s
[2016-04-15T01:11Z] INFO  18:11:02,001 ProgressMeter - Total runtime 22.53 secs, 0.38 min, 0.01 hours
[2016-04-15T01:11Z] INFO  18:11:02,001 MicroScheduler - 21259 reads were filtered out during the traversal out of approximately 248058 total reads (8.57%)
[2016-04-15T01:11Z] INFO  18:11:02,001 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:11Z] INFO  18:11:02,002 MicroScheduler -   -> 338 reads (0.14% of total) failing BadMateFilter
[2016-04-15T01:11Z] INFO  18:11:02,002 MicroScheduler -   -> 20751 reads (8.37% of total) failing DuplicateReadFilter
[2016-04-15T01:11Z] INFO  18:11:02,002 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:11Z] INFO  18:11:02,002 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:11Z] INFO  18:11:02,002 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:11Z] INFO  18:11:02,003 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:11Z] INFO  18:11:02,003 MicroScheduler -   -> 170 reads (0.07% of total) failing UnmappedReadFilter
[2016-04-15T01:11Z] INFO  18:11:02,020 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T01:11Z] INFO  18:11:02,029 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:11Z] INFO  18:11:02,064 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T01:11Z] INFO  18:11:02,073 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:11Z] INFO  18:11:02,109 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-15T01:11Z] INFO  18:11:02,154 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-15T01:11Z] INFO  18:11:02,179 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T01:11Z] INFO  18:11:02,200 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:11Z] INFO  18:11:02,242 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:11Z] INFO  18:11:02,274 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-15T01:11Z] INFO  18:11:02,529 IntervalUtils - Processing 125185 bp from intervals
[2016-04-15T01:11Z] WARN  18:11:02,535 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:11Z] INFO  18:11:02,600 IntervalUtils - Processing 26887 bp from intervals
[2016-04-15T01:11Z] WARN  18:11:02,605 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:11Z] GATK: UnifiedGenotyper
[2016-04-15T01:11Z] INFO  18:11:02,649 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:11Z] INFO  18:11:02,676 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:11Z] INFO  18:11:02,736 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:11Z] INFO  18:11:02,737 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:11Z] INFO  18:11:02,738 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T01:11Z] INFO  18:11:02,739 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T01:11Z] INFO  18:11:02,741 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:11Z] INFO  18:11:02,742 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:11Z] INFO  18:11:02,743 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T01:11Z] INFO  18:11:02,743 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T01:11Z] INFO  18:11:02,784 IntervalUtils - Processing 183626 bp from intervals
[2016-04-15T01:11Z] WARN  18:11:02,790 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:11Z] INFO  18:11:02,825 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:11Z] INFO  18:11:02,826 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:11Z] INFO  18:11:02,833 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:11Z] INFO  18:11:02,834 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:11Z] INFO  18:11:02,869 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:11Z] INFO  18:11:02,956 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:11Z] INFO  18:11:02,957 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:11Z] INFO  18:11:02,957 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T01:11Z] INFO  18:11:02,958 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T01:11Z] INFO  18:11:03,001 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:11Z] INFO  18:11:03,008 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:11Z] INFO  18:11:03,008 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:11Z] INFO  18:11:03,009 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:11Z] INFO  18:11:03,013 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/5/R14-18102_kapa-NGv3-PE100-NGv3-sort-5_49695692_65288736-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/5/R14-18102_kapa-NGv3-PE100-NGv3-5_49695692_65288736-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/5/tx/tmp60wxP2/R14-18102_kapa-NGv3-PE100-NGv3-5_49695692_65288736.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:11Z] INFO  18:11:03,016 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:11Z] INFO  18:11:03,017 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:11Z] INFO  18:11:03,036 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:11Z] INFO  18:11:03,037 HelpFormatter - Date/Time: 2016/04/14 18:11:03
[2016-04-15T01:11Z] INFO  18:11:03,037 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:11Z] INFO  18:11:03,038 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:11Z] INFO  18:11:03,293 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:11Z] INFO  18:11:03,500 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T01:11Z] INFO  18:11:03,509 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:11Z] INFO  18:11:03,531 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:11Z] INFO  18:11:03,570 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-15T01:11Z] GATK: UnifiedGenotyper
[2016-04-15T01:11Z] INFO  18:11:04,061 IntervalUtils - Processing 108713 bp from intervals
[2016-04-15T01:11Z] WARN  18:11:04,068 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:11Z] INFO  18:11:04,197 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:11Z] INFO  18:11:04,233 ProgressMeter -            done    303616.0    15.0 s      49.0 s       99.9%    15.0 s       0.0 s
[2016-04-15T01:11Z] INFO  18:11:04,235 ProgressMeter - Total runtime 15.06 secs, 0.25 min, 0.00 hours
[2016-04-15T01:11Z] INFO  18:11:04,236 MicroScheduler - 12892 reads were filtered out during the traversal out of approximately 146809 total reads (8.78%)
[2016-04-15T01:11Z] INFO  18:11:04,237 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:11Z] INFO  18:11:04,237 MicroScheduler -   -> 210 reads (0.14% of total) failing BadMateFilter
[2016-04-15T01:11Z] INFO  18:11:04,238 MicroScheduler -   -> 12555 reads (8.55% of total) failing DuplicateReadFilter
[2016-04-15T01:11Z] INFO  18:11:04,239 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:11Z] INFO  18:11:04,239 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:11Z] INFO  18:11:04,240 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:11Z] INFO  18:11:04,240 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:11Z] INFO  18:11:04,241 MicroScheduler -   -> 127 reads (0.09% of total) failing UnmappedReadFilter
[2016-04-15T01:11Z] INFO  18:11:04,305 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:11Z] INFO  18:11:04,307 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:11Z] INFO  18:11:04,308 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T01:11Z] INFO  18:11:04,308 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T01:11Z] INFO  18:11:04,365 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:11Z] INFO  18:11:04,366 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:11Z] INFO  18:11:05,732 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:11Z] INFO  18:11:05,746 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:11Z] INFO  18:11:05,746 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:11Z] INFO  18:11:05,747 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:11Z] INFO  18:11:05,751 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/5/R14-18102_kapa-NGv3-PE100-NGv3-sort-5_65290574_80809536-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/5/R14-18102_kapa-NGv3-PE100-NGv3-5_65290574_80809536-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/5/tx/tmp3ePjl1/R14-18102_kapa-NGv3-PE100-NGv3-5_65290574_80809536.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:11Z] INFO  18:11:05,756 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:11Z] INFO  18:11:05,773 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:11Z] INFO  18:11:05,774 HelpFormatter - Date/Time: 2016/04/14 18:11:05
[2016-04-15T01:11Z] INFO  18:11:05,774 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:11Z] INFO  18:11:05,775 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:11Z] INFO  18:11:05,781 ProgressMeter -            done    430821.0    16.0 s      38.0 s      100.0%    16.0 s       0.0 s
[2016-04-15T01:11Z] INFO  18:11:05,782 ProgressMeter - Total runtime 16.62 secs, 0.28 min, 0.00 hours
[2016-04-15T01:11Z] INFO  18:11:05,783 MicroScheduler - 14151 reads were filtered out during the traversal out of approximately 171359 total reads (8.26%)
[2016-04-15T01:11Z] INFO  18:11:05,783 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:11Z] INFO  18:11:05,784 MicroScheduler -   -> 279 reads (0.16% of total) failing BadMateFilter
[2016-04-15T01:11Z] INFO  18:11:05,785 MicroScheduler -   -> 13752 reads (8.03% of total) failing DuplicateReadFilter
[2016-04-15T01:11Z] INFO  18:11:05,785 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:11Z] INFO  18:11:05,786 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:11Z] INFO  18:11:05,787 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:11Z] INFO  18:11:05,787 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:11Z] INFO  18:11:05,788 MicroScheduler -   -> 120 reads (0.07% of total) failing UnmappedReadFilter
[2016-04-15T01:11Z] INFO  18:11:05,843 ProgressMeter -            done   2880332.0    43.0 s      15.0 s      100.0%    43.0 s       0.0 s
[2016-04-15T01:11Z] INFO  18:11:05,843 ProgressMeter - Total runtime 43.94 secs, 0.73 min, 0.01 hours
[2016-04-15T01:11Z] INFO  18:11:05,844 MicroScheduler - 56019 reads were filtered out during the traversal out of approximately 660188 total reads (8.49%)
[2016-04-15T01:11Z] INFO  18:11:05,844 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:11Z] INFO  18:11:05,845 MicroScheduler -   -> 1032 reads (0.16% of total) failing BadMateFilter
[2016-04-15T01:11Z] INFO  18:11:05,845 MicroScheduler -   -> 54530 reads (8.26% of total) failing DuplicateReadFilter
[2016-04-15T01:11Z] INFO  18:11:05,845 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:11Z] INFO  18:11:05,845 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:11Z] INFO  18:11:05,846 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:11Z] INFO  18:11:05,846 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:11Z] INFO  18:11:05,846 MicroScheduler -   -> 457 reads (0.07% of total) failing UnmappedReadFilter
[2016-04-15T01:11Z] INFO  18:11:05,964 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:11Z] GATK: UnifiedGenotyper
[2016-04-15T01:11Z] INFO  18:11:06,226 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T01:11Z] INFO  18:11:06,235 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:11Z] INFO  18:11:06,324 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.09
[2016-04-15T01:11Z] INFO  18:11:06,767 IntervalUtils - Processing 203113 bp from intervals
[2016-04-15T01:11Z] WARN  18:11:06,772 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:11Z] INFO  18:11:06,846 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:11Z] INFO  18:11:06,926 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:11Z] INFO  18:11:06,929 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:11Z] INFO  18:11:06,930 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:11Z] INFO  18:11:06,930 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:11Z] INFO  18:11:06,935 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/5/R14-18102_kapa-NGv3-PE100-NGv3-sort-5_80911291_96430739-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/5/R14-18102_kapa-NGv3-PE100-NGv3-5_80911291_96430739-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/5/tx/tmpoEtPia/R14-18102_kapa-NGv3-PE100-NGv3-5_80911291_96430739.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:11Z] INFO  18:11:06,943 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:11Z] INFO  18:11:06,944 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:11Z] INFO  18:11:06,945 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T01:11Z] INFO  18:11:06,945 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T01:11Z] INFO  18:11:06,955 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:11Z] INFO  18:11:06,956 HelpFormatter - Date/Time: 2016/04/14 18:11:06
[2016-04-15T01:11Z] INFO  18:11:06,956 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:11Z] INFO  18:11:06,956 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:11Z] INFO  18:11:07,029 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:11Z] INFO  18:11:07,040 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:11Z] INFO  18:11:07,117 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:11Z] INFO  18:11:07,360 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T01:11Z] INFO  18:11:07,375 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:11Z] INFO  18:11:07,406 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:11Z] INFO  18:11:07,480 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.09
[2016-04-15T01:11Z] GATK: UnifiedGenotyper
[2016-04-15T01:11Z] INFO  18:11:07,794 ProgressMeter -            done    675755.0    16.0 s      24.0 s      100.0%    16.0 s       0.0 s
[2016-04-15T01:11Z] INFO  18:11:07,795 ProgressMeter - Total runtime 16.73 secs, 0.28 min, 0.00 hours
[2016-04-15T01:11Z] INFO  18:11:07,795 MicroScheduler - 12413 reads were filtered out during the traversal out of approximately 151239 total reads (8.21%)
[2016-04-15T01:11Z] INFO  18:11:07,796 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:11Z] INFO  18:11:07,796 MicroScheduler -   -> 218 reads (0.14% of total) failing BadMateFilter
[2016-04-15T01:11Z] INFO  18:11:07,796 MicroScheduler -   -> 12074 reads (7.98% of total) failing DuplicateReadFilter
[2016-04-15T01:11Z] INFO  18:11:07,796 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:11Z] INFO  18:11:07,797 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:11Z] INFO  18:11:07,797 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:11Z] INFO  18:11:07,797 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:11Z] INFO  18:11:07,798 MicroScheduler -   -> 121 reads (0.08% of total) failing UnmappedReadFilter
[2016-04-15T01:11Z] INFO  18:11:07,823 IntervalUtils - Processing 113632 bp from intervals
[2016-04-15T01:11Z] WARN  18:11:07,829 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:11Z] INFO  18:11:07,914 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:11Z] INFO  18:11:07,927 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:11Z] INFO  18:11:08,008 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:11Z] INFO  18:11:08,013 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:11Z] INFO  18:11:08,014 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T01:11Z] INFO  18:11:08,016 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T01:11Z] INFO  18:11:08,084 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:11Z] INFO  18:11:08,085 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:11Z] GATK: UnifiedGenotyper
[2016-04-15T01:11Z] INFO  18:11:09,232 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:11Z] INFO  18:11:09,236 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:11Z] INFO  18:11:09,236 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:11Z] INFO  18:11:09,237 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:11Z] INFO  18:11:09,242 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/5/R14-18102_kapa-NGv3-PE100-NGv3-sort-5_96432513_112043579-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/5/R14-18102_kapa-NGv3-PE100-NGv3-5_96432513_112043579-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/5/tx/tmp2tk7Yd/R14-18102_kapa-NGv3-PE100-NGv3-5_96432513_112043579.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:11Z] INFO  18:11:09,256 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:11Z] INFO  18:11:09,257 HelpFormatter - Date/Time: 2016/04/14 18:11:09
[2016-04-15T01:11Z] INFO  18:11:09,258 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:11Z] INFO  18:11:09,258 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:11Z] INFO  18:11:09,400 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:11Z] INFO  18:11:09,633 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T01:11Z] INFO  18:11:09,642 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:11Z] INFO  18:11:09,708 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-15T01:11Z] INFO  18:11:09,952 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:11Z] INFO  18:11:10,124 IntervalUtils - Processing 57322 bp from intervals
[2016-04-15T01:11Z] WARN  18:11:10,134 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:11Z] GATK: UnifiedGenotyper
[2016-04-15T01:11Z] INFO  18:11:10,232 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:11Z] INFO  18:11:10,321 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:11Z] INFO  18:11:10,324 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:11Z] INFO  18:11:10,325 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:11Z] INFO  18:11:10,325 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:11Z] INFO  18:11:10,330 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/5/R14-18102_kapa-NGv3-PE100-NGv3-sort-5_112073555_127595521-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/5/R14-18102_kapa-NGv3-PE100-NGv3-5_112073555_127595521-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/5/tx/tmpIopTdl/R14-18102_kapa-NGv3-PE100-NGv3-5_112073555_127595521.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:11Z] INFO  18:11:10,340 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:11Z] INFO  18:11:10,341 HelpFormatter - Date/Time: 2016/04/14 18:11:10
[2016-04-15T01:11Z] INFO  18:11:10,341 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:11Z] INFO  18:11:10,341 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:11Z] INFO  18:11:10,365 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:11Z] INFO  18:11:10,365 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:11Z] INFO  18:11:10,366 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T01:11Z] INFO  18:11:10,366 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T01:11Z] INFO  18:11:10,421 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:11Z] INFO  18:11:10,422 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:11Z] INFO  18:11:10,471 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:11Z] INFO  18:11:10,669 ProgressMeter -            done     60320.0     7.0 s       2.2 m       99.9%     7.0 s       0.0 s
[2016-04-15T01:11Z] INFO  18:11:10,671 ProgressMeter - Total runtime 7.93 secs, 0.13 min, 0.00 hours
[2016-04-15T01:11Z] INFO  18:11:10,672 MicroScheduler - 2937 reads were filtered out during the traversal out of approximately 34081 total reads (8.62%)
[2016-04-15T01:11Z] INFO  18:11:10,673 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:11Z] INFO  18:11:10,674 MicroScheduler -   -> 60 reads (0.18% of total) failing BadMateFilter
[2016-04-15T01:11Z] INFO  18:11:10,675 MicroScheduler -   -> 2844 reads (8.34% of total) failing DuplicateReadFilter
[2016-04-15T01:11Z] INFO  18:11:10,675 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:11Z] INFO  18:11:10,676 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:11Z] INFO  18:11:10,698 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:11Z] INFO  18:11:10,699 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:11Z] INFO  18:11:10,699 MicroScheduler -   -> 33 reads (0.10% of total) failing UnmappedReadFilter
[2016-04-15T01:11Z] INFO  18:11:10,731 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T01:11Z] INFO  18:11:10,743 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:11Z] INFO  18:11:10,810 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-15T01:11Z] INFO  18:11:10,876 ProgressMeter -            done    538645.0    22.0 s      41.0 s      100.0%    22.0 s       0.0 s
[2016-04-15T01:11Z] INFO  18:11:10,878 ProgressMeter - Total runtime 22.15 secs, 0.37 min, 0.01 hours
[2016-04-15T01:11Z] INFO  18:11:10,878 MicroScheduler - 19841 reads were filtered out during the traversal out of approximately 236234 total reads (8.40%)
[2016-04-15T01:11Z] INFO  18:11:10,879 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:11Z] INFO  18:11:10,880 MicroScheduler -   -> 361 reads (0.15% of total) failing BadMateFilter
[2016-04-15T01:11Z] INFO  18:11:10,881 MicroScheduler -   -> 19308 reads (8.17% of total) failing DuplicateReadFilter
[2016-04-15T01:11Z] INFO  18:11:10,882 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:11Z] INFO  18:11:10,882 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:11Z] INFO  18:11:10,883 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:11Z] INFO  18:11:10,884 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:11Z] INFO  18:11:10,885 MicroScheduler -   -> 172 reads (0.07% of total) failing UnmappedReadFilter
[2016-04-15T01:11Z] INFO  18:11:11,206 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:11Z] INFO  18:11:11,210 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:11Z] INFO  18:11:11,211 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:11Z] INFO  18:11:11,212 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:11Z] INFO  18:11:11,217 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/5/R14-18102_kapa-NGv3-PE100-NGv3-sort-5_127597427_143191869-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/5/R14-18102_kapa-NGv3-PE100-NGv3-5_127597427_143191869-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/5/tx/tmpdbg0cZ/R14-18102_kapa-NGv3-PE100-NGv3-5_127597427_143191869.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:11Z] INFO  18:11:11,237 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:11Z] INFO  18:11:11,246 HelpFormatter - Date/Time: 2016/04/14 18:11:11
[2016-04-15T01:11Z] INFO  18:11:11,253 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:11Z] INFO  18:11:11,254 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:11Z] INFO  18:11:11,376 IntervalUtils - Processing 103986 bp from intervals
[2016-04-15T01:11Z] WARN  18:11:11,382 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:11Z] INFO  18:11:11,414 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:11Z] INFO  18:11:11,483 ProgressMeter -            done    207309.0    14.0 s      68.0 s       99.9%    14.0 s       0.0 s
[2016-04-15T01:11Z] INFO  18:11:11,484 ProgressMeter - Total runtime 14.29 secs, 0.24 min, 0.00 hours
[2016-04-15T01:11Z] INFO  18:11:11,484 MicroScheduler - 8605 reads were filtered out during the traversal out of approximately 103187 total reads (8.34%)
[2016-04-15T01:11Z] INFO  18:11:11,485 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:11Z] INFO  18:11:11,489 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:11Z] INFO  18:11:11,485 MicroScheduler -   -> 162 reads (0.16% of total) failing BadMateFilter
[2016-04-15T01:11Z] INFO  18:11:11,485 MicroScheduler -   -> 8343 reads (8.09% of total) failing DuplicateReadFilter
[2016-04-15T01:11Z] INFO  18:11:11,485 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:11Z] INFO  18:11:11,486 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:11Z] INFO  18:11:11,486 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:11Z] INFO  18:11:11,486 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:11Z] INFO  18:11:11,487 MicroScheduler -   -> 100 reads (0.10% of total) failing UnmappedReadFilter
[2016-04-15T01:11Z] INFO  18:11:11,618 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:11Z] INFO  18:11:11,618 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:11Z] INFO  18:11:11,619 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T01:11Z] INFO  18:11:11,619 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T01:11Z] INFO  18:11:11,660 ProgressMeter -      4:10445428    757095.0    30.0 s      39.0 s       90.6%    33.0 s       3.0 s
[2016-04-15T01:11Z] INFO  18:11:11,665 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T01:11Z] INFO  18:11:11,680 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:11Z] INFO  18:11:11,691 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:11Z] INFO  18:11:11,692 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:11Z] INFO  18:11:11,814 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.13
[2016-04-15T01:11Z] INFO  18:11:11,822 ProgressMeter -            done    172946.0    13.0 s      75.0 s      100.0%    13.0 s       0.0 s
[2016-04-15T01:11Z] INFO  18:11:11,822 ProgressMeter - Total runtime 13.04 secs, 0.22 min, 0.00 hours
[2016-04-15T01:11Z] INFO  18:11:11,822 MicroScheduler - 7076 reads were filtered out during the traversal out of approximately 82891 total reads (8.54%)
[2016-04-15T01:11Z] INFO  18:11:11,823 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:11Z] INFO  18:11:11,823 MicroScheduler -   -> 118 reads (0.14% of total) failing BadMateFilter
[2016-04-15T01:11Z] INFO  18:11:11,823 MicroScheduler -   -> 6894 reads (8.32% of total) failing DuplicateReadFilter
[2016-04-15T01:11Z] INFO  18:11:11,824 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:11Z] INFO  18:11:11,824 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:11Z] INFO  18:11:11,824 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:11Z] INFO  18:11:11,824 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:11Z] INFO  18:11:11,825 MicroScheduler -   -> 64 reads (0.08% of total) failing UnmappedReadFilter
[2016-04-15T01:11Z] INFO  18:11:12,242 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:11Z] INFO  18:11:12,250 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:11Z] INFO  18:11:12,252 IntervalUtils - Processing 393653 bp from intervals
[2016-04-15T01:11Z] WARN  18:11:12,263 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:11Z] INFO  18:11:12,375 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:11Z] GATK: UnifiedGenotyper
[2016-04-15T01:11Z] INFO  18:11:12,493 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:11Z] INFO  18:11:12,494 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:11Z] INFO  18:11:12,495 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T01:11Z] INFO  18:11:12,496 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T01:11Z] INFO  18:11:12,540 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:11Z] INFO  18:11:12,541 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:11Z] GATK: UnifiedGenotyper
[2016-04-15T01:11Z] INFO  18:11:12,752 ProgressMeter -            done    310683.0    14.0 s      48.0 s       99.9%    14.0 s       0.0 s
[2016-04-15T01:11Z] INFO  18:11:12,752 ProgressMeter - Total runtime 14.95 secs, 0.25 min, 0.00 hours
[2016-04-15T01:11Z] INFO  18:11:12,753 MicroScheduler - 11166 reads were filtered out during the traversal out of approximately 132659 total reads (8.42%)
[2016-04-15T01:11Z] INFO  18:11:12,753 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:11Z] INFO  18:11:12,754 MicroScheduler -   -> 214 reads (0.16% of total) failing BadMateFilter
[2016-04-15T01:11Z] INFO  18:11:12,754 MicroScheduler -   -> 10836 reads (8.17% of total) failing DuplicateReadFilter
[2016-04-15T01:11Z] INFO  18:11:12,755 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:11Z] INFO  18:11:12,755 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:11Z] INFO  18:11:12,756 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:11Z] INFO  18:11:12,757 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:11Z] INFO  18:11:12,757 MicroScheduler -   -> 116 reads (0.09% of total) failing UnmappedReadFilter
[2016-04-15T01:11Z] INFO  18:11:12,866 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:11Z] INFO  18:11:13,125 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:11Z] INFO  18:11:13,129 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:11Z] INFO  18:11:13,129 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:11Z] INFO  18:11:13,130 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:11Z] INFO  18:11:13,134 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/5/R14-18102_kapa-NGv3-PE100-NGv3-sort-5_143200044_158710347-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/5/R14-18102_kapa-NGv3-PE100-NGv3-5_143200044_158710347-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/5/tx/tmp7UjSeh/R14-18102_kapa-NGv3-PE100-NGv3-5_143200044_158710347.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:11Z] INFO  18:11:13,149 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:11Z] INFO  18:11:13,152 HelpFormatter - Date/Time: 2016/04/14 18:11:13
[2016-04-15T01:11Z] INFO  18:11:13,152 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:11Z] INFO  18:11:13,153 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:11Z] GATK: UnifiedGenotyper
[2016-04-15T01:11Z] INFO  18:11:13,243 ProgressMeter -            done    829685.0    31.0 s      38.0 s      100.0%    31.0 s       0.0 s
[2016-04-15T01:11Z] INFO  18:11:13,243 ProgressMeter - Total runtime 31.63 secs, 0.53 min, 0.01 hours
[2016-04-15T01:11Z] INFO  18:11:13,243 MicroScheduler - 33029 reads were filtered out during the traversal out of approximately 405277 total reads (8.15%)
[2016-04-15T01:11Z] INFO  18:11:13,244 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:11Z] INFO  18:11:13,244 MicroScheduler -   -> 696 reads (0.17% of total) failing BadMateFilter
[2016-04-15T01:11Z] INFO  18:11:13,244 MicroScheduler -   -> 32013 reads (7.90% of total) failing DuplicateReadFilter
[2016-04-15T01:11Z] INFO  18:11:13,244 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:11Z] INFO  18:11:13,245 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:11Z] INFO  18:11:13,245 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:11Z] INFO  18:11:13,245 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:11Z] INFO  18:11:13,246 MicroScheduler -   -> 320 reads (0.08% of total) failing UnmappedReadFilter
[2016-04-15T01:11Z] INFO  18:11:13,306 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:11Z] INFO  18:11:13,359 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:11Z] INFO  18:11:13,651 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T01:11Z] INFO  18:11:13,661 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:11Z] GATK: UnifiedGenotyper
[2016-04-15T01:11Z] INFO  18:11:13,756 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.09
[2016-04-15T01:11Z] INFO  18:11:14,429 IntervalUtils - Processing 205172 bp from intervals
[2016-04-15T01:11Z] WARN  18:11:14,435 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:11Z] INFO  18:11:14,561 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:11Z] INFO  18:11:14,573 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:11Z] INFO  18:11:14,733 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:11Z] INFO  18:11:14,745 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:11Z] INFO  18:11:14,746 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T01:11Z] INFO  18:11:14,746 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T01:11Z] INFO  18:11:14,848 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:11Z] INFO  18:11:14,859 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:11Z] INFO  18:11:14,920 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:11Z] GATK: UnifiedGenotyper
[2016-04-15T01:11Z] GATK: UnifiedGenotyper
[2016-04-15T01:11Z] INFO  18:11:15,549 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:11Z] INFO  18:11:15,552 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:11Z] INFO  18:11:15,553 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:11Z] INFO  18:11:15,554 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:11Z] INFO  18:11:15,558 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/5/R14-18102_kapa-NGv3-PE100-NGv3-sort-5_158711911_174870102-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/5/R14-18102_kapa-NGv3-PE100-NGv3-5_158711911_174870102-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/5/tx/tmppjON8z/R14-18102_kapa-NGv3-PE100-NGv3-5_158711911_174870102.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:11Z] INFO  18:11:15,567 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:11Z] INFO  18:11:15,567 HelpFormatter - Date/Time: 2016/04/14 18:11:15
[2016-04-15T01:11Z] INFO  18:11:15,567 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:11Z] INFO  18:11:15,567 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:11Z] INFO  18:11:15,708 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:11Z] INFO  18:11:15,711 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:11Z] INFO  18:11:15,712 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:11Z] INFO  18:11:15,712 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:11Z] INFO  18:11:15,717 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/5/R14-18102_kapa-NGv3-PE100-NGv3-sort-5_174919106_180915260-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/5/R14-18102_kapa-NGv3-PE100-NGv3-5_174919106_180915260-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/5/tx/tmpjRjS4I/R14-18102_kapa-NGv3-PE100-NGv3-5_174919106_180915260.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:11Z] INFO  18:11:15,733 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:11Z] INFO  18:11:15,749 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:11Z] INFO  18:11:15,763 HelpFormatter - Date/Time: 2016/04/14 18:11:15
[2016-04-15T01:11Z] INFO  18:11:15,764 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:11Z] INFO  18:11:15,765 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:11Z] INFO  18:11:15,933 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:11Z] INFO  18:11:15,988 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T01:11Z] INFO  18:11:16,000 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:11Z] INFO  18:11:16,019 ProgressMeter -            done    326544.0    14.0 s      44.0 s       99.9%    14.0 s       0.0 s
[2016-04-15T01:11Z] INFO  18:11:16,019 ProgressMeter - Total runtime 14.43 secs, 0.24 min, 0.00 hours
[2016-04-15T01:11Z] INFO  18:11:16,019 MicroScheduler - 10466 reads were filtered out during the traversal out of approximately 126223 total reads (8.29%)
[2016-04-15T01:11Z] INFO  18:11:16,020 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:11Z] INFO  18:11:16,020 MicroScheduler -   -> 197 reads (0.16% of total) failing BadMateFilter
[2016-04-15T01:11Z] INFO  18:11:16,020 MicroScheduler -   -> 10160 reads (8.05% of total) failing DuplicateReadFilter
[2016-04-15T01:11Z] INFO  18:11:16,020 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:11Z] INFO  18:11:16,021 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:11Z] INFO  18:11:16,021 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:11Z] INFO  18:11:16,021 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:11Z] INFO  18:11:16,021 MicroScheduler -   -> 109 reads (0.09% of total) failing UnmappedReadFilter
[2016-04-15T01:11Z] INFO  18:11:16,109 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.11
[2016-04-15T01:11Z] INFO  18:11:16,113 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:11Z] INFO  18:11:16,115 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:11Z] INFO  18:11:16,116 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:11Z] INFO  18:11:16,116 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:11Z] INFO  18:11:16,131 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/6/R14-18102_kapa-NGv3-PE100-NGv3-sort-6_0_15509601-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/6/R14-18102_kapa-NGv3-PE100-NGv3-6_0_15509601-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/6/tx/tmp5g5aw8/R14-18102_kapa-NGv3-PE100-NGv3-6_0_15509601.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:11Z] INFO  18:11:16,138 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T01:11Z] INFO  18:11:16,141 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:11Z] INFO  18:11:16,152 HelpFormatter - Date/Time: 2016/04/14 18:11:16
[2016-04-15T01:11Z] INFO  18:11:16,153 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:11Z] INFO  18:11:16,153 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:11Z] INFO  18:11:16,154 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:11Z] INFO  18:11:16,269 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.11
[2016-04-15T01:11Z] INFO  18:11:16,336 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:11Z] INFO  18:11:16,518 IntervalUtils - Processing 104189 bp from intervals
[2016-04-15T01:11Z] WARN  18:11:16,523 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:11Z] INFO  18:11:16,589 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T01:11Z] INFO  18:11:16,597 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:11Z] INFO  18:11:16,598 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:11Z] INFO  18:11:16,679 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-15T01:11Z] INFO  18:11:16,768 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:11Z] INFO  18:11:16,769 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:11Z] INFO  18:11:16,770 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T01:11Z] INFO  18:11:16,770 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T01:11Z] INFO  18:11:16,817 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:11Z] INFO  18:11:16,820 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:11Z] INFO  18:11:16,821 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:11Z] INFO  18:11:16,821 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:11Z] INFO  18:11:16,825 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/6/R14-18102_kapa-NGv3-PE100-NGv3-sort-6_15511526_31080332-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/6/R14-18102_kapa-NGv3-PE100-NGv3-6_15511526_31080332-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/6/tx/tmp1gYW81/R14-18102_kapa-NGv3-PE100-NGv3-6_15511526_31080332.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:11Z] INFO  18:11:16,830 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:11Z] INFO  18:11:16,831 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:11Z] INFO  18:11:16,841 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:11Z] INFO  18:11:16,842 HelpFormatter - Date/Time: 2016/04/14 18:11:16
[2016-04-15T01:11Z] INFO  18:11:16,842 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:11Z] INFO  18:11:16,843 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:11Z] INFO  18:11:16,849 IntervalUtils - Processing 163171 bp from intervals
[2016-04-15T01:11Z] WARN  18:11:16,855 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:11Z] INFO  18:11:16,952 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:11Z] INFO  18:11:17,086 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:11Z] INFO  18:11:17,116 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:11Z] INFO  18:11:17,117 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:11Z] INFO  18:11:17,118 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T01:11Z] INFO  18:11:17,119 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T01:11Z] INFO  18:11:17,184 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:11Z] INFO  18:11:17,185 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:11Z] INFO  18:11:17,280 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T01:11Z] INFO  18:11:17,290 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:11Z] INFO  18:11:17,353 IntervalUtils - Processing 139546 bp from intervals
[2016-04-15T01:11Z] WARN  18:11:17,358 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:11Z] INFO  18:11:17,364 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-15T01:11Z] INFO  18:11:17,461 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:11Z] INFO  18:11:17,516 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:11Z] INFO  18:11:17,518 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:11Z] INFO  18:11:17,518 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T01:11Z] INFO  18:11:17,519 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T01:11Z] INFO  18:11:17,578 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:11Z] INFO  18:11:17,579 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:11Z] INFO  18:11:17,775 IntervalUtils - Processing 239663 bp from intervals
[2016-04-15T01:11Z] INFO  18:11:17,780 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:11Z] WARN  18:11:17,780 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:11Z] INFO  18:11:17,870 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:11Z] INFO  18:11:17,954 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:11Z] INFO  18:11:17,955 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:11Z] INFO  18:11:17,956 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T01:11Z] INFO  18:11:17,957 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T01:11Z] INFO  18:11:18,006 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:11Z] INFO  18:11:18,007 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:11Z] INFO  18:11:18,008 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:11Z] INFO  18:11:18,011 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:11Z] INFO  18:11:18,011 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:11Z] INFO  18:11:18,012 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:11Z] INFO  18:11:18,017 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/6/R14-18102_kapa-NGv3-PE100-NGv3-sort-6_31083801_46593245-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/6/R14-18102_kapa-NGv3-PE100-NGv3-6_31083801_46593245-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/6/tx/tmpwDsV59/R14-18102_kapa-NGv3-PE100-NGv3-6_31083801_46593245.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:11Z] INFO  18:11:18,043 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:11Z] INFO  18:11:18,052 HelpFormatter - Date/Time: 2016/04/14 18:11:18
[2016-04-15T01:11Z] INFO  18:11:18,053 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:11Z] INFO  18:11:18,054 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:11Z] GATK: UnifiedGenotyper
[2016-04-15T01:11Z] INFO  18:11:18,306 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:11Z] INFO  18:11:18,556 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T01:11Z] INFO  18:11:18,576 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:11Z] INFO  18:11:18,672 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.10
[2016-04-15T01:11Z] INFO  18:11:18,754 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:11Z] INFO  18:11:18,757 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:11Z] INFO  18:11:18,758 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:11Z] INFO  18:11:18,758 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:11Z] INFO  18:11:18,763 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/6/R14-18102_kapa-NGv3-PE100-NGv3-sort-6_46598699_62284307-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/6/R14-18102_kapa-NGv3-PE100-NGv3-6_46598699_62284307-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/6/tx/tmplc82lo/R14-18102_kapa-NGv3-PE100-NGv3-6_46598699_62284307.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:11Z] INFO  18:11:18,779 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:11Z] INFO  18:11:18,786 HelpFormatter - Date/Time: 2016/04/14 18:11:18
[2016-04-15T01:11Z] INFO  18:11:18,787 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:11Z] INFO  18:11:18,788 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:11Z] INFO  18:11:18,976 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:11Z] INFO  18:11:19,251 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T01:11Z] INFO  18:11:19,261 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:11Z] INFO  18:11:19,314 IntervalUtils - Processing 501134 bp from intervals
[2016-04-15T01:11Z] WARN  18:11:19,320 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:11Z] INFO  18:11:19,343 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-15T01:11Z] INFO  18:11:19,385 ProgressMeter -            done    292827.0    15.0 s      51.0 s       99.9%    15.0 s       0.0 s
[2016-04-15T01:11Z] INFO  18:11:19,385 ProgressMeter - Total runtime 15.08 secs, 0.25 min, 0.00 hours
[2016-04-15T01:11Z] INFO  18:11:19,386 MicroScheduler - 10030 reads were filtered out during the traversal out of approximately 117739 total reads (8.52%)
[2016-04-15T01:11Z] INFO  18:11:19,386 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:11Z] INFO  18:11:19,386 MicroScheduler -   -> 150 reads (0.13% of total) failing BadMateFilter
[2016-04-15T01:11Z] INFO  18:11:19,386 MicroScheduler -   -> 9782 reads (8.31% of total) failing DuplicateReadFilter
[2016-04-15T01:11Z] INFO  18:11:19,387 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:11Z] INFO  18:11:19,387 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:11Z] INFO  18:11:19,387 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:11Z] INFO  18:11:19,387 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:11Z] INFO  18:11:19,388 MicroScheduler -   -> 98 reads (0.08% of total) failing UnmappedReadFilter
[2016-04-15T01:11Z] INFO  18:11:19,432 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:11Z] INFO  18:11:19,577 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:11Z] INFO  18:11:19,578 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:11Z] INFO  18:11:19,579 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T01:11Z] INFO  18:11:19,580 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T01:11Z] INFO  18:11:19,623 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:11Z] INFO  18:11:19,624 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:11Z] INFO  18:11:19,828 IntervalUtils - Processing 157522 bp from intervals
[2016-04-15T01:11Z] WARN  18:11:19,834 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:11Z] INFO  18:11:19,954 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:11Z] INFO  18:11:20,028 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:11Z] INFO  18:11:20,030 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:11Z] INFO  18:11:20,030 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T01:11Z] INFO  18:11:20,031 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T01:11Z] INFO  18:11:20,076 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:11Z] INFO  18:11:20,076 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:11Z] INFO  18:11:20,683 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:11Z] GATK: UnifiedGenotyper
[2016-04-15T01:11Z] INFO  18:11:21,043 ProgressMeter -            done    152663.0    10.0 s      69.0 s       99.9%    10.0 s       0.0 s
[2016-04-15T01:11Z] INFO  18:11:21,044 ProgressMeter - Total runtime 10.68 secs, 0.18 min, 0.00 hours
[2016-04-15T01:11Z] INFO  18:11:21,044 MicroScheduler - 4502 reads were filtered out during the traversal out of approximately 54470 total reads (8.27%)
[2016-04-15T01:11Z] INFO  18:11:21,044 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:11Z] INFO  18:11:21,045 MicroScheduler -   -> 83 reads (0.15% of total) failing BadMateFilter
[2016-04-15T01:11Z] INFO  18:11:21,045 MicroScheduler -   -> 4371 reads (8.02% of total) failing DuplicateReadFilter
[2016-04-15T01:11Z] INFO  18:11:21,045 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:11Z] INFO  18:11:21,046 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:11Z] INFO  18:11:21,046 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:11Z] INFO  18:11:21,046 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:11Z] INFO  18:11:21,046 MicroScheduler -   -> 48 reads (0.09% of total) failing UnmappedReadFilter
[2016-04-15T01:11Z] INFO  18:11:21,271 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:11Z] INFO  18:11:21,275 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:11Z] INFO  18:11:21,275 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:11Z] INFO  18:11:21,275 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:11Z] INFO  18:11:21,279 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/6/R14-18102_kapa-NGv3-PE100-NGv3-sort-6_62390867_78173120-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/6/R14-18102_kapa-NGv3-PE100-NGv3-6_62390867_78173120-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/6/tx/tmpFtmwfD/R14-18102_kapa-NGv3-PE100-NGv3-6_62390867_78173120.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:11Z] INFO  18:11:21,302 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:11Z] INFO  18:11:21,302 HelpFormatter - Date/Time: 2016/04/14 18:11:21
[2016-04-15T01:11Z] INFO  18:11:21,302 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:11Z] INFO  18:11:21,303 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:11Z] INFO  18:11:21,337 ProgressMeter -            done    392693.0    18.0 s      47.0 s       99.9%    18.0 s       0.0 s
[2016-04-15T01:11Z] INFO  18:11:21,337 ProgressMeter - Total runtime 18.60 secs, 0.31 min, 0.01 hours
[2016-04-15T01:11Z] INFO  18:11:21,338 MicroScheduler - 15874 reads were filtered out during the traversal out of approximately 181040 total reads (8.77%)
[2016-04-15T01:11Z] INFO  18:11:21,338 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:11Z] INFO  18:11:21,338 MicroScheduler -   -> 339 reads (0.19% of total) failing BadMateFilter
[2016-04-15T01:11Z] INFO  18:11:21,339 MicroScheduler -   -> 15320 reads (8.46% of total) failing DuplicateReadFilter
[2016-04-15T01:11Z] INFO  18:11:21,339 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:11Z] INFO  18:11:21,339 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:11Z] INFO  18:11:21,339 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:11Z] INFO  18:11:21,352 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:11Z] INFO  18:11:21,352 MicroScheduler -   -> 215 reads (0.12% of total) failing UnmappedReadFilter
[2016-04-15T01:11Z] INFO  18:11:21,509 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:11Z] INFO  18:11:21,807 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T01:11Z] INFO  18:11:21,817 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:11Z] INFO  18:11:21,915 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.10
[2016-04-15T01:11Z] INFO  18:11:22,485 IntervalUtils - Processing 103397 bp from intervals
[2016-04-15T01:11Z] WARN  18:11:22,490 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:11Z] INFO  18:11:22,635 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:11Z] INFO  18:11:22,740 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:11Z] INFO  18:11:22,741 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:11Z] INFO  18:11:22,742 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T01:11Z] INFO  18:11:22,742 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T01:11Z] INFO  18:11:22,844 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:11Z] INFO  18:11:22,844 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:11Z] INFO  18:11:22,927 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:11Z] INFO  18:11:23,068 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:11Z] GATK: UnifiedGenotyper
[2016-04-15T01:11Z] GATK: UnifiedGenotyper
[2016-04-15T01:11Z] INFO  18:11:23,493 ProgressMeter -            done    373968.0    15.0 s      41.0 s       99.9%    15.0 s       0.0 s
[2016-04-15T01:11Z] INFO  18:11:23,494 ProgressMeter - Total runtime 15.48 secs, 0.26 min, 0.00 hours
[2016-04-15T01:11Z] INFO  18:11:23,495 MicroScheduler - 9755 reads were filtered out during the traversal out of approximately 117473 total reads (8.30%)
[2016-04-15T01:11Z] INFO  18:11:23,496 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:11Z] INFO  18:11:23,496 MicroScheduler -   -> 170 reads (0.14% of total) failing BadMateFilter
[2016-04-15T01:11Z] INFO  18:11:23,497 MicroScheduler -   -> 9496 reads (8.08% of total) failing DuplicateReadFilter
[2016-04-15T01:11Z] INFO  18:11:23,498 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:11Z] INFO  18:11:23,498 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:11Z] INFO  18:11:23,499 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:11Z] INFO  18:11:23,499 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:11Z] INFO  18:11:23,500 MicroScheduler -   -> 89 reads (0.08% of total) failing UnmappedReadFilter
[2016-04-15T01:11Z] INFO  18:11:24,220 ProgressMeter -            done    536506.0    21.0 s      39.0 s      100.0%    21.0 s       0.0 s
[2016-04-15T01:11Z] INFO  18:11:24,221 ProgressMeter - Total runtime 21.26 secs, 0.35 min, 0.01 hours
[2016-04-15T01:11Z] INFO  18:11:24,222 MicroScheduler - 17131 reads were filtered out during the traversal out of approximately 202889 total reads (8.44%)
[2016-04-15T01:11Z] INFO  18:11:24,222 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:11Z] INFO  18:11:24,223 MicroScheduler -   -> 299 reads (0.15% of total) failing BadMateFilter
[2016-04-15T01:11Z] INFO  18:11:24,224 MicroScheduler -   -> 16697 reads (8.23% of total) failing DuplicateReadFilter
[2016-04-15T01:11Z] INFO  18:11:24,224 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:11Z] INFO  18:11:24,225 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:11Z] INFO  18:11:24,225 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:11Z] INFO  18:11:24,226 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:11Z] INFO  18:11:24,227 MicroScheduler -   -> 135 reads (0.07% of total) failing UnmappedReadFilter
[2016-04-15T01:11Z] INFO  18:11:24,310 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:11Z] INFO  18:11:24,312 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:11Z] INFO  18:11:24,313 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:11Z] INFO  18:11:24,313 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:11Z] INFO  18:11:24,341 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/6/R14-18102_kapa-NGv3-PE100-NGv3-sort-6_78400388_93953258-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/6/R14-18102_kapa-NGv3-PE100-NGv3-6_78400388_93953258-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/6/tx/tmph7lgI8/R14-18102_kapa-NGv3-PE100-NGv3-6_78400388_93953258.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:11Z] INFO  18:11:24,353 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:11Z] INFO  18:11:24,354 HelpFormatter - Date/Time: 2016/04/14 18:11:24
[2016-04-15T01:11Z] INFO  18:11:24,355 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:11Z] INFO  18:11:24,355 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:11Z] INFO  18:11:24,540 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:11Z] INFO  18:11:24,852 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T01:11Z] INFO  18:11:24,871 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:11Z] INFO  18:11:24,872 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:11Z] INFO  18:11:24,961 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.09
[2016-04-15T01:11Z] GATK: UnifiedGenotyper
[2016-04-15T01:11Z] INFO  18:11:25,350 IntervalUtils - Processing 131721 bp from intervals
[2016-04-15T01:11Z] WARN  18:11:25,354 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:11Z] INFO  18:11:25,430 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:11Z] INFO  18:11:25,489 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:11Z] INFO  18:11:25,490 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:11Z] INFO  18:11:25,491 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T01:11Z] INFO  18:11:25,492 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T01:11Z] INFO  18:11:25,537 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:11Z] INFO  18:11:25,538 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:11Z] INFO  18:11:25,739 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:11Z] GATK: UnifiedGenotyper
[2016-04-15T01:11Z] INFO  18:11:26,101 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:11Z] INFO  18:11:26,103 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:11Z] INFO  18:11:26,104 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:11Z] INFO  18:11:26,104 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:11Z] INFO  18:11:26,108 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/6/R14-18102_kapa-NGv3-PE100-NGv3-sort-6_93955015_109466584-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/6/R14-18102_kapa-NGv3-PE100-NGv3-6_93955015_109466584-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/6/tx/tmp41Lgh3/R14-18102_kapa-NGv3-PE100-NGv3-6_93955015_109466584.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:11Z] INFO  18:11:26,147 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:11Z] INFO  18:11:26,148 HelpFormatter - Date/Time: 2016/04/14 18:11:26
[2016-04-15T01:11Z] INFO  18:11:26,149 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:11Z] INFO  18:11:26,149 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:11Z] INFO  18:11:26,345 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:11Z] INFO  18:11:26,535 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T01:11Z] INFO  18:11:26,544 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:11Z] INFO  18:11:26,569 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:11Z] INFO  18:11:26,572 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:11Z] INFO  18:11:26,573 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:11Z] INFO  18:11:26,573 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:11Z] INFO  18:11:26,578 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/6/R14-18102_kapa-NGv3-PE100-NGv3-sort-6_109467960_124979532-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/6/R14-18102_kapa-NGv3-PE100-NGv3-6_109467960_124979532-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/6/tx/tmpL0SxpV/R14-18102_kapa-NGv3-PE100-NGv3-6_109467960_124979532.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:11Z] INFO  18:11:26,610 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:11Z] INFO  18:11:26,610 HelpFormatter - Date/Time: 2016/04/14 18:11:26
[2016-04-15T01:11Z] INFO  18:11:26,610 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:11Z] INFO  18:11:26,611 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:11Z] INFO  18:11:26,654 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.11
[2016-04-15T01:11Z] INFO  18:11:26,804 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:11Z] INFO  18:11:26,938 ProgressMeter -            done    235248.0    15.0 s      65.0 s       99.9%    15.0 s       0.0 s
[2016-04-15T01:11Z] INFO  18:11:26,938 ProgressMeter - Total runtime 15.32 secs, 0.26 min, 0.00 hours
[2016-04-15T01:11Z] INFO  18:11:26,939 MicroScheduler - 10240 reads were filtered out during the traversal out of approximately 119779 total reads (8.55%)
[2016-04-15T01:11Z] INFO  18:11:26,939 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:11Z] INFO  18:11:26,939 MicroScheduler -   -> 267 reads (0.22% of total) failing BadMateFilter
[2016-04-15T01:11Z] INFO  18:11:26,939 MicroScheduler -   -> 9844 reads (8.22% of total) failing DuplicateReadFilter
[2016-04-15T01:11Z] INFO  18:11:26,940 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:11Z] INFO  18:11:26,940 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:11Z] INFO  18:11:26,941 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:11Z] INFO  18:11:26,941 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:11Z] INFO  18:11:26,941 MicroScheduler -   -> 129 reads (0.11% of total) failing UnmappedReadFilter
[2016-04-15T01:11Z] INFO  18:11:27,036 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T01:11Z] INFO  18:11:27,053 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:11Z] INFO  18:11:27,122 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-15T01:11Z] INFO  18:11:27,128 IntervalUtils - Processing 95525 bp from intervals
[2016-04-15T01:11Z] WARN  18:11:27,134 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:11Z] INFO  18:11:27,214 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:11Z] INFO  18:11:27,317 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:11Z] INFO  18:11:27,318 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:11Z] INFO  18:11:27,319 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T01:11Z] INFO  18:11:27,320 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T01:11Z] INFO  18:11:27,408 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:11Z] INFO  18:11:27,409 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:11Z] INFO  18:11:27,506 IntervalUtils - Processing 147815 bp from intervals
[2016-04-15T01:11Z] WARN  18:11:27,511 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:11Z] INFO  18:11:27,618 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:11Z] INFO  18:11:27,628 ProgressMeter -            done    554557.0    20.0 s      37.0 s      100.0%    20.0 s       0.0 s
[2016-04-15T01:11Z] INFO  18:11:27,629 ProgressMeter - Total runtime 20.69 secs, 0.34 min, 0.01 hours
[2016-04-15T01:11Z] INFO  18:11:27,629 MicroScheduler - 17252 reads were filtered out during the traversal out of approximately 218239 total reads (7.91%)
[2016-04-15T01:11Z] INFO  18:11:27,630 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:11Z] INFO  18:11:27,630 MicroScheduler -   -> 335 reads (0.15% of total) failing BadMateFilter
[2016-04-15T01:11Z] INFO  18:11:27,630 MicroScheduler -   -> 16758 reads (7.68% of total) failing DuplicateReadFilter
[2016-04-15T01:11Z] INFO  18:11:27,630 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:11Z] INFO  18:11:27,631 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:11Z] INFO  18:11:27,631 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:11Z] INFO  18:11:27,631 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:11Z] INFO  18:11:27,631 MicroScheduler -   -> 159 reads (0.07% of total) failing UnmappedReadFilter
[2016-04-15T01:11Z] INFO  18:11:27,681 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:11Z] INFO  18:11:27,681 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:11Z] INFO  18:11:27,682 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T01:11Z] INFO  18:11:27,683 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T01:11Z] INFO  18:11:27,729 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:11Z] INFO  18:11:27,730 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:11Z] INFO  18:11:28,074 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:11Z] INFO  18:11:28,078 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:11Z] INFO  18:11:28,079 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:11Z] INFO  18:11:28,080 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:11Z] INFO  18:11:28,085 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/6/R14-18102_kapa-NGv3-PE100-NGv3-sort-6_125112484_142397186-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/6/R14-18102_kapa-NGv3-PE100-NGv3-6_125112484_142397186-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/6/tx/tmpP6D1QR/R14-18102_kapa-NGv3-PE100-NGv3-6_125112484_142397186.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:11Z] INFO  18:11:28,096 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:11Z] INFO  18:11:28,097 HelpFormatter - Date/Time: 2016/04/14 18:11:28
[2016-04-15T01:11Z] INFO  18:11:28,098 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:11Z] INFO  18:11:28,099 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:11Z] INFO  18:11:28,320 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:11Z] INFO  18:11:28,402 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:11Z] INFO  18:11:28,653 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T01:11Z] INFO  18:11:28,664 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:11Z] INFO  18:11:28,726 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-15T01:11Z] GATK: UnifiedGenotyper
[2016-04-15T01:11Z] INFO  18:11:29,075 IntervalUtils - Processing 156964 bp from intervals
[2016-04-15T01:11Z] WARN  18:11:29,082 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:11Z] INFO  18:11:29,086 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:11Z] INFO  18:11:29,162 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:11Z] INFO  18:11:29,319 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:11Z] INFO  18:11:29,319 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:11Z] INFO  18:11:29,320 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T01:11Z] INFO  18:11:29,320 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T01:11Z] INFO  18:11:29,375 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:11Z] INFO  18:11:29,376 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:11Z] GATK: UnifiedGenotyper
[2016-04-15T01:11Z] INFO  18:11:29,611 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:11Z] INFO  18:11:29,615 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:11Z] INFO  18:11:29,615 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:11Z] INFO  18:11:29,616 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:11Z] INFO  18:11:29,621 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/6/R14-18102_kapa-NGv3-PE100-NGv3-sort-6_142399691_157963777-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/6/R14-18102_kapa-NGv3-PE100-NGv3-6_142399691_157963777-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/6/tx/tmpHmkwNS/R14-18102_kapa-NGv3-PE100-NGv3-6_142399691_157963777.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:11Z] INFO  18:11:29,633 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:11Z] INFO  18:11:29,644 HelpFormatter - Date/Time: 2016/04/14 18:11:29
[2016-04-15T01:11Z] INFO  18:11:29,645 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:11Z] INFO  18:11:29,646 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:11Z] INFO  18:11:29,810 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:11Z] INFO  18:11:30,046 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T01:11Z] INFO  18:11:30,055 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:11Z] INFO  18:11:30,178 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.12
[2016-04-15T01:11Z] INFO  18:11:30,676 IntervalUtils - Processing 183871 bp from intervals
[2016-04-15T01:11Z] WARN  18:11:30,682 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:11Z] INFO  18:11:30,798 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:11Z] INFO  18:11:30,899 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:11Z] INFO  18:11:30,900 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:11Z] INFO  18:11:30,900 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T01:11Z] INFO  18:11:30,901 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T01:11Z] INFO  18:11:30,991 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:11Z] INFO  18:11:30,992 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:11Z] INFO  18:11:31,610 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:11Z] INFO  18:11:31,613 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:11Z] INFO  18:11:31,614 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:11Z] INFO  18:11:31,614 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:11Z] INFO  18:11:31,618 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/6/R14-18102_kapa-NGv3-PE100-NGv3-sort-6_158013810_171115067-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/6/R14-18102_kapa-NGv3-PE100-NGv3-6_158013810_171115067-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/6/tx/tmpR3UIwb/R14-18102_kapa-NGv3-PE100-NGv3-6_158013810_171115067.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:11Z] INFO  18:11:31,628 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:11Z] INFO  18:11:31,629 HelpFormatter - Date/Time: 2016/04/14 18:11:31
[2016-04-15T01:11Z] INFO  18:11:31,640 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:11Z] INFO  18:11:31,641 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:11Z] INFO  18:11:31,800 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:11Z] INFO  18:11:32,086 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T01:11Z] INFO  18:11:32,108 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:11Z] INFO  18:11:32,172 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:11Z] INFO  18:11:32,175 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:11Z] INFO  18:11:32,176 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:11Z] INFO  18:11:32,176 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:11Z] INFO  18:11:32,181 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/7/R14-18102_kapa-NGv3-PE100-NGv3-sort-7_0_15584548-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/7/R14-18102_kapa-NGv3-PE100-NGv3-7_0_15584548-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/7/tx/tmp3vqmpN/R14-18102_kapa-NGv3-PE100-NGv3-7_0_15584548.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:11Z] INFO  18:11:32,196 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:11Z] INFO  18:11:32,197 HelpFormatter - Date/Time: 2016/04/14 18:11:32
[2016-04-15T01:11Z] INFO  18:11:32,198 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:11Z] INFO  18:11:32,198 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:11Z] INFO  18:11:32,222 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.11
[2016-04-15T01:11Z] INFO  18:11:32,364 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:11Z] INFO  18:11:32,458 ProgressMeter -            done    237846.0    15.0 s      65.0 s      100.0%    15.0 s       0.0 s
[2016-04-15T01:11Z] INFO  18:11:32,458 ProgressMeter - Total runtime 15.69 secs, 0.26 min, 0.00 hours
[2016-04-15T01:11Z] INFO  18:11:32,459 MicroScheduler - 11936 reads were filtered out during the traversal out of approximately 141972 total reads (8.41%)
[2016-04-15T01:11Z] INFO  18:11:32,459 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:11Z] INFO  18:11:32,459 MicroScheduler -   -> 227 reads (0.16% of total) failing BadMateFilter
[2016-04-15T01:11Z] INFO  18:11:32,460 MicroScheduler -   -> 11614 reads (8.18% of total) failing DuplicateReadFilter
[2016-04-15T01:11Z] INFO  18:11:32,460 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:11Z] INFO  18:11:32,460 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:11Z] INFO  18:11:32,460 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:11Z] INFO  18:11:32,461 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:11Z] INFO  18:11:32,461 MicroScheduler -   -> 95 reads (0.07% of total) failing UnmappedReadFilter
[2016-04-15T01:11Z] INFO  18:11:32,635 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T01:11Z] INFO  18:11:32,643 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:11Z] INFO  18:11:32,655 IntervalUtils - Processing 143202 bp from intervals
[2016-04-15T01:11Z] WARN  18:11:32,660 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:11Z] INFO  18:11:32,730 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:11Z] INFO  18:11:32,769 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.13
[2016-04-15T01:11Z] INFO  18:11:32,827 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:11Z] INFO  18:11:32,829 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:11Z] INFO  18:11:32,830 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T01:11Z] INFO  18:11:32,830 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T01:11Z] INFO  18:11:32,871 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:11Z] INFO  18:11:32,872 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:11Z] INFO  18:11:33,118 IntervalUtils - Processing 187602 bp from intervals
[2016-04-15T01:11Z] WARN  18:11:33,136 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:11Z] INFO  18:11:33,207 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:11Z] INFO  18:11:33,274 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:11Z] INFO  18:11:33,275 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:11Z] INFO  18:11:33,276 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T01:11Z] INFO  18:11:33,277 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T01:11Z] INFO  18:11:33,364 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:11Z] INFO  18:11:33,375 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:11Z] INFO  18:11:34,003 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:11Z] GATK: UnifiedGenotyper
[2016-04-15T01:11Z] INFO  18:11:36,262 ProgressMeter -            done    269142.0    13.0 s      50.0 s       99.9%    13.0 s       0.0 s
[2016-04-15T01:11Z] INFO  18:11:36,263 ProgressMeter - Total runtime 13.52 secs, 0.23 min, 0.00 hours
[2016-04-15T01:11Z] INFO  18:11:36,263 MicroScheduler - 9089 reads were filtered out during the traversal out of approximately 109229 total reads (8.32%)
[2016-04-15T01:11Z] INFO  18:11:36,263 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:11Z] INFO  18:11:36,264 MicroScheduler -   -> 160 reads (0.15% of total) failing BadMateFilter
[2016-04-15T01:11Z] INFO  18:11:36,264 MicroScheduler -   -> 8840 reads (8.09% of total) failing DuplicateReadFilter
[2016-04-15T01:11Z] INFO  18:11:36,264 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:11Z] INFO  18:11:36,264 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:11Z] INFO  18:11:36,265 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:11Z] INFO  18:11:36,265 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:11Z] INFO  18:11:36,265 MicroScheduler -   -> 89 reads (0.08% of total) failing UnmappedReadFilter
[2016-04-15T01:11Z] INFO  18:11:37,191 ProgressMeter -            done    349428.0    19.0 s      56.0 s      100.0%    19.0 s       0.0 s
[2016-04-15T01:11Z] INFO  18:11:37,192 ProgressMeter - Total runtime 19.67 secs, 0.33 min, 0.01 hours
[2016-04-15T01:11Z] INFO  18:11:37,192 MicroScheduler - 14893 reads were filtered out during the traversal out of approximately 177686 total reads (8.38%)
[2016-04-15T01:11Z] INFO  18:11:37,192 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:11Z] INFO  18:11:37,193 MicroScheduler -   -> 285 reads (0.16% of total) failing BadMateFilter
[2016-04-15T01:11Z] INFO  18:11:37,193 MicroScheduler -   -> 14462 reads (8.14% of total) failing DuplicateReadFilter
[2016-04-15T01:11Z] INFO  18:11:37,193 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:11Z] INFO  18:11:37,193 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:11Z] INFO  18:11:37,194 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:11Z] INFO  18:11:37,194 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:11Z] INFO  18:11:37,194 MicroScheduler -   -> 146 reads (0.08% of total) failing UnmappedReadFilter
[2016-04-15T01:11Z] INFO  18:11:37,201 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:11Z] INFO  18:11:37,204 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:11Z] INFO  18:11:37,204 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:11Z] INFO  18:11:37,205 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:11Z] INFO  18:11:37,212 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/7/R14-18102_kapa-NGv3-PE100-NGv3-sort-7_15599765_31117713-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/7/R14-18102_kapa-NGv3-PE100-NGv3-7_15599765_31117713-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/7/tx/tmpPZqQ14/R14-18102_kapa-NGv3-PE100-NGv3-7_15599765_31117713.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:11Z] INFO  18:11:37,247 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:11Z] INFO  18:11:37,247 HelpFormatter - Date/Time: 2016/04/14 18:11:37
[2016-04-15T01:11Z] INFO  18:11:37,248 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:11Z] INFO  18:11:37,248 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:11Z] INFO  18:11:37,420 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:11Z] INFO  18:11:37,674 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T01:11Z] INFO  18:11:37,683 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:11Z] INFO  18:11:37,765 ProgressMeter -            done    472667.0    17.0 s      37.0 s      100.0%    17.0 s       0.0 s
[2016-04-15T01:11Z] INFO  18:11:37,766 ProgressMeter - Total runtime 17.74 secs, 0.30 min, 0.00 hours
[2016-04-15T01:11Z] INFO  18:11:37,766 MicroScheduler - 14560 reads were filtered out during the traversal out of approximately 174127 total reads (8.36%)
[2016-04-15T01:11Z] INFO  18:11:37,766 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:11Z] INFO  18:11:37,767 MicroScheduler -   -> 281 reads (0.16% of total) failing BadMateFilter
[2016-04-15T01:11Z] INFO  18:11:37,767 MicroScheduler -   -> 14138 reads (8.12% of total) failing DuplicateReadFilter
[2016-04-15T01:11Z] INFO  18:11:37,767 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:11Z] INFO  18:11:37,767 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:11Z] INFO  18:11:37,768 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:11Z] INFO  18:11:37,768 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:11Z] INFO  18:11:37,769 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-15T01:11Z] INFO  18:11:37,768 MicroScheduler -   -> 141 reads (0.08% of total) failing UnmappedReadFilter
[2016-04-15T01:11Z] INFO  18:11:37,798 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:11Z] INFO  18:11:38,106 IntervalUtils - Processing 149727 bp from intervals
[2016-04-15T01:11Z] WARN  18:11:38,111 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:11Z] GATK: UnifiedGenotyper
[2016-04-15T01:11Z] INFO  18:11:38,192 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:11Z] INFO  18:11:38,277 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:11Z] INFO  18:11:38,278 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:11Z] INFO  18:11:38,278 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T01:11Z] INFO  18:11:38,278 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T01:11Z] INFO  18:11:38,335 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:11Z] INFO  18:11:38,336 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:11Z] INFO  18:11:38,468 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:11Z] INFO  18:11:38,496 ProgressMeter -            done    712768.0    21.0 s      29.0 s      100.0%    21.0 s       0.0 s
[2016-04-15T01:11Z] INFO  18:11:38,498 ProgressMeter - Total runtime 21.38 secs, 0.36 min, 0.01 hours
[2016-04-15T01:11Z] INFO  18:11:38,498 MicroScheduler - 21241 reads were filtered out during the traversal out of approximately 253171 total reads (8.39%)
[2016-04-15T01:11Z] INFO  18:11:38,499 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:11Z] INFO  18:11:38,500 MicroScheduler -   -> 403 reads (0.16% of total) failing BadMateFilter
[2016-04-15T01:11Z] INFO  18:11:38,500 MicroScheduler -   -> 20644 reads (8.15% of total) failing DuplicateReadFilter
[2016-04-15T01:11Z] INFO  18:11:38,500 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:11Z] INFO  18:11:38,500 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:11Z] INFO  18:11:38,501 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:11Z] INFO  18:11:38,501 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:11Z] INFO  18:11:38,501 MicroScheduler -   -> 194 reads (0.08% of total) failing UnmappedReadFilter
[2016-04-15T01:11Z] GATK: UnifiedGenotyper
[2016-04-15T01:11Z] INFO  18:11:38,930 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:11Z] GATK: UnifiedGenotyper
[2016-04-15T01:11Z] INFO  18:11:39,270 ProgressMeter -            done    639654.0    24.0 s      38.0 s      100.0%    24.0 s       0.0 s
[2016-04-15T01:11Z] INFO  18:11:39,271 ProgressMeter - Total runtime 24.53 secs, 0.41 min, 0.01 hours
[2016-04-15T01:11Z] INFO  18:11:39,271 MicroScheduler - 23548 reads were filtered out during the traversal out of approximately 281411 total reads (8.37%)
[2016-04-15T01:11Z] INFO  18:11:39,272 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:11Z] INFO  18:11:39,272 MicroScheduler -   -> 395 reads (0.14% of total) failing BadMateFilter
[2016-04-15T01:11Z] INFO  18:11:39,272 MicroScheduler -   -> 22943 reads (8.15% of total) failing DuplicateReadFilter
[2016-04-15T01:11Z] INFO  18:11:39,273 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:11Z] INFO  18:11:39,273 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:11Z] INFO  18:11:39,273 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:11Z] INFO  18:11:39,273 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:11Z] INFO  18:11:39,274 MicroScheduler -   -> 210 reads (0.07% of total) failing UnmappedReadFilter
[2016-04-15T01:11Z] INFO  18:11:39,805 ProgressMeter -            done    213234.0    12.0 s      58.0 s       99.9%    12.0 s       0.0 s
[2016-04-15T01:11Z] INFO  18:11:39,805 ProgressMeter - Total runtime 12.49 secs, 0.21 min, 0.00 hours
[2016-04-15T01:11Z] INFO  18:11:39,805 MicroScheduler - 8114 reads were filtered out during the traversal out of approximately 100954 total reads (8.04%)
[2016-04-15T01:11Z] INFO  18:11:39,806 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:11Z] INFO  18:11:39,806 MicroScheduler -   -> 154 reads (0.15% of total) failing BadMateFilter
[2016-04-15T01:11Z] INFO  18:11:39,806 MicroScheduler -   -> 7878 reads (7.80% of total) failing DuplicateReadFilter
[2016-04-15T01:11Z] INFO  18:11:39,806 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:11Z] INFO  18:11:39,807 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:11Z] INFO  18:11:39,807 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:11Z] INFO  18:11:39,807 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:11Z] INFO  18:11:39,807 MicroScheduler -   -> 82 reads (0.08% of total) failing UnmappedReadFilter
[2016-04-15T01:11Z] INFO  18:11:39,914 ProgressMeter -            done    399770.0    14.0 s      36.0 s      100.0%    14.0 s       0.0 s
[2016-04-15T01:11Z] INFO  18:11:39,914 ProgressMeter - Total runtime 14.42 secs, 0.24 min, 0.00 hours
[2016-04-15T01:11Z] INFO  18:11:39,915 MicroScheduler - 11483 reads were filtered out during the traversal out of approximately 138600 total reads (8.28%)
[2016-04-15T01:11Z] INFO  18:11:39,915 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:11Z] INFO  18:11:39,915 MicroScheduler -   -> 198 reads (0.14% of total) failing BadMateFilter
[2016-04-15T01:11Z] INFO  18:11:39,915 MicroScheduler -   -> 11172 reads (8.06% of total) failing DuplicateReadFilter
[2016-04-15T01:11Z] INFO  18:11:39,916 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:11Z] INFO  18:11:39,916 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:11Z] INFO  18:11:39,916 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:11Z] INFO  18:11:39,916 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:11Z] INFO  18:11:39,917 MicroScheduler -   -> 113 reads (0.08% of total) failing UnmappedReadFilter
[2016-04-15T01:11Z] INFO  18:11:40,104 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:11Z] GATK: UnifiedGenotyper
[2016-04-15T01:11Z] INFO  18:11:40,917 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:11Z] INFO  18:11:41,026 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:11Z] INFO  18:11:41,029 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:11Z] INFO  18:11:41,030 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:11Z] INFO  18:11:41,030 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:11Z] INFO  18:11:41,035 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/7/R14-18102_kapa-NGv3-PE100-NGv3-sort-7_31120227_47317818-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/7/R14-18102_kapa-NGv3-PE100-NGv3-7_31120227_47317818-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/7/tx/tmpppcpFH/R14-18102_kapa-NGv3-PE100-NGv3-7_31120227_47317818.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:11Z] INFO  18:11:41,046 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:11Z] INFO  18:11:41,047 HelpFormatter - Date/Time: 2016/04/14 18:11:41
[2016-04-15T01:11Z] INFO  18:11:41,047 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:11Z] INFO  18:11:41,048 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:11Z] INFO  18:11:41,284 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:11Z] GATK: UnifiedGenotyper
[2016-04-15T01:11Z] INFO  18:11:41,415 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:11Z] INFO  18:11:41,546 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T01:11Z] INFO  18:11:41,563 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:11Z] INFO  18:11:41,566 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:11Z] INFO  18:11:41,637 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-15T01:11Z] GATK: UnifiedGenotyper
[2016-04-15T01:11Z] GATK: UnifiedGenotyper
[2016-04-15T01:11Z] INFO  18:11:41,918 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:11Z] INFO  18:11:41,921 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:11Z] INFO  18:11:41,922 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:11Z] INFO  18:11:41,922 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:11Z] INFO  18:11:41,927 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/7/R14-18102_kapa-NGv3-PE100-NGv3-sort-7_47319761_63093154-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/7/R14-18102_kapa-NGv3-PE100-NGv3-7_47319761_63093154-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/7/tx/tmpsmIgYn/R14-18102_kapa-NGv3-PE100-NGv3-7_47319761_63093154.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:11Z] INFO  18:11:41,949 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:11Z] INFO  18:11:41,950 HelpFormatter - Date/Time: 2016/04/14 18:11:41
[2016-04-15T01:11Z] INFO  18:11:41,951 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:11Z] INFO  18:11:41,951 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:11Z] INFO  18:11:42,106 IntervalUtils - Processing 138106 bp from intervals
[2016-04-15T01:11Z] WARN  18:11:42,119 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:11Z] INFO  18:11:42,140 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:11Z] INFO  18:11:42,143 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:11Z] INFO  18:11:42,143 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:11Z] INFO  18:11:42,143 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:11Z] INFO  18:11:42,148 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/7/R14-18102_kapa-NGv3-PE100-NGv3-sort-7_63095909_78636522-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/7/R14-18102_kapa-NGv3-PE100-NGv3-7_63095909_78636522-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/7/tx/tmpayf4A7/R14-18102_kapa-NGv3-PE100-NGv3-7_63095909_78636522.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:11Z] INFO  18:11:42,159 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:11Z] INFO  18:11:42,186 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:11Z] INFO  18:11:42,187 HelpFormatter - Date/Time: 2016/04/14 18:11:42
[2016-04-15T01:11Z] INFO  18:11:42,188 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:11Z] INFO  18:11:42,188 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:11Z] INFO  18:11:42,253 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:11Z] INFO  18:11:42,340 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T01:11Z] INFO  18:11:42,349 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:11Z] INFO  18:11:42,349 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:11Z] INFO  18:11:42,351 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:11Z] INFO  18:11:42,352 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T01:11Z] INFO  18:11:42,352 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T01:11Z] INFO  18:11:42,376 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:11Z] INFO  18:11:42,430 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-15T01:11Z] INFO  18:11:42,443 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:11Z] INFO  18:11:42,444 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:11Z] INFO  18:11:42,509 ProgressMeter -     5:140474975    944597.0    30.0 s      31.0 s       65.5%    45.0 s      15.0 s
[2016-04-15T01:11Z] INFO  18:11:42,669 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T01:11Z] INFO  18:11:42,689 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:11Z] INFO  18:11:42,781 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.09
[2016-04-15T01:11Z] INFO  18:11:42,870 IntervalUtils - Processing 74873 bp from intervals
[2016-04-15T01:11Z] WARN  18:11:42,875 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:11Z] INFO  18:11:42,952 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:11Z] INFO  18:11:43,048 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:11Z] INFO  18:11:43,049 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:11Z] INFO  18:11:43,049 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T01:11Z] INFO  18:11:43,049 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T01:11Z] INFO  18:11:43,097 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:11Z] INFO  18:11:43,098 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:11Z] INFO  18:11:43,231 IntervalUtils - Processing 152751 bp from intervals
[2016-04-15T01:11Z] WARN  18:11:43,264 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:11Z] INFO  18:11:43,364 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:11Z] INFO  18:11:43,413 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:11Z] INFO  18:11:43,416 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:11Z] INFO  18:11:43,417 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:11Z] INFO  18:11:43,418 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:11Z] INFO  18:11:43,422 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/7/R14-18102_kapa-NGv3-PE100-NGv3-sort-7_79082334_94740703-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/7/R14-18102_kapa-NGv3-PE100-NGv3-7_79082334_94740703-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/7/tx/tmp0KBkuZ/R14-18102_kapa-NGv3-PE100-NGv3-7_79082334_94740703.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:11Z] INFO  18:11:43,460 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:11Z] INFO  18:11:43,461 HelpFormatter - Date/Time: 2016/04/14 18:11:43
[2016-04-15T01:11Z] INFO  18:11:43,461 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:11Z] INFO  18:11:43,472 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:11Z] INFO  18:11:43,512 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:11Z] INFO  18:11:43,513 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:11Z] INFO  18:11:43,514 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T01:11Z] INFO  18:11:43,514 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T01:11Z] INFO  18:11:43,563 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:11Z] INFO  18:11:43,564 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:11Z] INFO  18:11:43,717 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:11Z] INFO  18:11:43,956 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T01:11Z] INFO  18:11:43,967 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:11Z] INFO  18:11:44,033 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-15T01:11Z] INFO  18:11:44,459 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:11Z] INFO  18:11:44,462 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:11Z] INFO  18:11:44,462 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:11Z] INFO  18:11:44,462 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:11Z] INFO  18:11:44,469 IntervalUtils - Processing 163786 bp from intervals
[2016-04-15T01:11Z] WARN  18:11:44,475 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:11Z] INFO  18:11:44,478 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/7/R14-18102_kapa-NGv3-PE100-NGv3-sort-7_94750023_110303777-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/7/R14-18102_kapa-NGv3-PE100-NGv3-7_94750023_110303777-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/7/tx/tmpVkUYCc/R14-18102_kapa-NGv3-PE100-NGv3-7_94750023_110303777.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:11Z] INFO  18:11:44,518 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:11Z] INFO  18:11:44,527 HelpFormatter - Date/Time: 2016/04/14 18:11:44
[2016-04-15T01:11Z] INFO  18:11:44,527 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:11Z] INFO  18:11:44,527 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:11Z] INFO  18:11:44,557 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:11Z] INFO  18:11:44,721 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:11Z] INFO  18:11:44,722 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:11Z] INFO  18:11:44,723 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T01:11Z] INFO  18:11:44,724 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T01:11Z] INFO  18:11:44,756 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:11Z] INFO  18:11:44,765 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:11Z] INFO  18:11:44,766 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:11Z] INFO  18:11:44,889 ProgressMeter -            done    414458.0    17.0 s      41.0 s      100.0%    17.0 s       0.0 s
[2016-04-15T01:11Z] INFO  18:11:44,889 ProgressMeter - Total runtime 17.21 secs, 0.29 min, 0.00 hours
[2016-04-15T01:11Z] INFO  18:11:44,890 MicroScheduler - 13174 reads were filtered out during the traversal out of approximately 160454 total reads (8.21%)
[2016-04-15T01:11Z] INFO  18:11:44,890 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:11Z] INFO  18:11:44,890 MicroScheduler -   -> 220 reads (0.14% of total) failing BadMateFilter
[2016-04-15T01:11Z] INFO  18:11:44,890 MicroScheduler -   -> 12845 reads (8.01% of total) failing DuplicateReadFilter
[2016-04-15T01:11Z] INFO  18:11:44,891 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:11Z] INFO  18:11:44,891 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:11Z] INFO  18:11:44,891 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:11Z] INFO  18:11:44,891 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:11Z] INFO  18:11:44,892 MicroScheduler -   -> 109 reads (0.07% of total) failing UnmappedReadFilter
[2016-04-15T01:11Z] INFO  18:11:45,012 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T01:11Z] INFO  18:11:45,024 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:11Z] INFO  18:11:45,103 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:11Z] INFO  18:11:45,106 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:11Z] INFO  18:11:45,107 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:11Z] INFO  18:11:45,107 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:11Z] INFO  18:11:45,112 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/7/R14-18102_kapa-NGv3-PE100-NGv3-sort-7_126086124_141619620-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/7/R14-18102_kapa-NGv3-PE100-NGv3-7_126086124_141619620-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/7/tx/tmp8a_Lx8/R14-18102_kapa-NGv3-PE100-NGv3-7_126086124_141619620.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:11Z] INFO  18:11:45,125 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:11Z] INFO  18:11:45,126 HelpFormatter - Date/Time: 2016/04/14 18:11:45
[2016-04-15T01:11Z] INFO  18:11:45,126 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:11Z] INFO  18:11:45,127 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:11Z] INFO  18:11:45,133 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.11
[2016-04-15T01:11Z] INFO  18:11:45,136 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:11Z] INFO  18:11:45,140 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:11Z] INFO  18:11:45,140 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:11Z] INFO  18:11:45,141 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:11Z] INFO  18:11:45,145 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/7/R14-18102_kapa-NGv3-PE100-NGv3-sort-7_110526648_126079222-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/7/R14-18102_kapa-NGv3-PE100-NGv3-7_110526648_126079222-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/7/tx/tmpHQUOUD/R14-18102_kapa-NGv3-PE100-NGv3-7_110526648_126079222.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:11Z] INFO  18:11:45,158 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:11Z] INFO  18:11:45,159 HelpFormatter - Date/Time: 2016/04/14 18:11:45
[2016-04-15T01:11Z] INFO  18:11:45,160 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:11Z] INFO  18:11:45,160 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:11Z] INFO  18:11:45,288 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:11Z] INFO  18:11:45,346 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:11Z] INFO  18:11:45,546 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T01:11Z] INFO  18:11:45,555 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:11Z] INFO  18:11:45,625 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T01:11Z] INFO  18:11:45,634 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:11Z] INFO  18:11:45,655 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.10
[2016-04-15T01:11Z] INFO  18:11:45,667 IntervalUtils - Processing 352548 bp from intervals
[2016-04-15T01:11Z] WARN  18:11:45,675 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:11Z] INFO  18:11:45,726 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.09
[2016-04-15T01:11Z] INFO  18:11:45,757 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:11Z] INFO  18:11:45,932 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:11Z] INFO  18:11:45,934 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:11Z] INFO  18:11:45,934 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T01:11Z] INFO  18:11:45,935 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T01:11Z] INFO  18:11:46,018 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:11Z] INFO  18:11:46,018 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:11Z] INFO  18:11:46,141 IntervalUtils - Processing 219678 bp from intervals
[2016-04-15T01:11Z] WARN  18:11:46,158 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:11Z] INFO  18:11:46,263 IntervalUtils - Processing 97998 bp from intervals
[2016-04-15T01:11Z] WARN  18:11:46,268 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:11Z] INFO  18:11:46,290 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:11Z] INFO  18:11:46,352 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:11Z] INFO  18:11:46,428 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:11Z] INFO  18:11:46,424 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:11Z] INFO  18:11:46,425 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:11Z] INFO  18:11:46,442 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T01:11Z] INFO  18:11:46,443 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T01:11Z] INFO  18:11:46,488 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:11Z] INFO  18:11:46,489 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:11Z] INFO  18:11:46,508 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:11Z] INFO  18:11:46,509 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:11Z] INFO  18:11:46,526 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T01:11Z] INFO  18:11:46,527 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T01:11Z] INFO  18:11:46,593 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:11Z] INFO  18:11:46,594 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:11Z] GATK: UnifiedGenotyper
[2016-04-15T01:11Z] INFO  18:11:47,798 ProgressMeter -            done    394136.0    18.0 s      46.0 s      100.0%    18.0 s       0.0 s
[2016-04-15T01:11Z] INFO  18:11:47,798 ProgressMeter - Total runtime 18.48 secs, 0.31 min, 0.01 hours
[2016-04-15T01:11Z] INFO  18:11:47,799 MicroScheduler - 15386 reads were filtered out during the traversal out of approximately 187510 total reads (8.21%)
[2016-04-15T01:11Z] INFO  18:11:47,799 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:11Z] INFO  18:11:47,799 MicroScheduler -   -> 308 reads (0.16% of total) failing BadMateFilter
[2016-04-15T01:11Z] INFO  18:11:47,799 MicroScheduler -   -> 14964 reads (7.98% of total) failing DuplicateReadFilter
[2016-04-15T01:11Z] INFO  18:11:47,800 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:11Z] INFO  18:11:47,800 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:11Z] INFO  18:11:47,800 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:11Z] INFO  18:11:47,800 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:11Z] INFO  18:11:47,801 MicroScheduler -   -> 114 reads (0.06% of total) failing UnmappedReadFilter
[2016-04-15T01:11Z] INFO  18:11:47,829 ProgressMeter -            done    821918.0    29.0 s      36.0 s      100.0%    29.0 s       0.0 s
[2016-04-15T01:11Z] INFO  18:11:47,830 ProgressMeter - Total runtime 29.87 secs, 0.50 min, 0.01 hours
[2016-04-15T01:11Z] INFO  18:11:47,830 MicroScheduler - 28439 reads were filtered out during the traversal out of approximately 334958 total reads (8.49%)
[2016-04-15T01:11Z] INFO  18:11:47,831 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:11Z] INFO  18:11:47,831 MicroScheduler -   -> 533 reads (0.16% of total) failing BadMateFilter
[2016-04-15T01:11Z] INFO  18:11:47,831 MicroScheduler -   -> 27588 reads (8.24% of total) failing DuplicateReadFilter
[2016-04-15T01:11Z] INFO  18:11:47,831 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:11Z] INFO  18:11:47,832 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:11Z] INFO  18:11:47,832 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:11Z] INFO  18:11:47,832 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:11Z] INFO  18:11:47,832 MicroScheduler -   -> 318 reads (0.09% of total) failing UnmappedReadFilter
[2016-04-15T01:11Z] INFO  18:11:49,143 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:11Z] INFO  18:11:49,314 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:11Z] GATK: UnifiedGenotyper
[2016-04-15T01:11Z] INFO  18:11:49,594 ProgressMeter -      6:35443213   1976479.0    30.0 s      15.0 s       48.4%    61.0 s      31.0 s
[2016-04-15T01:11Z] GATK: UnifiedGenotyper
[2016-04-15T01:11Z] INFO  18:11:49,747 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:11Z] INFO  18:11:49,750 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:11Z] INFO  18:11:49,751 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:11Z] INFO  18:11:49,751 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:11Z] INFO  18:11:49,756 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/7/R14-18102_kapa-NGv3-PE100-NGv3-sort-7_141629903_157151331-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/7/R14-18102_kapa-NGv3-PE100-NGv3-7_141629903_157151331-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/7/tx/tmp6v_sdG/R14-18102_kapa-NGv3-PE100-NGv3-7_141629903_157151331.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:11Z] INFO  18:11:49,766 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:11Z] INFO  18:11:49,777 HelpFormatter - Date/Time: 2016/04/14 18:11:49
[2016-04-15T01:11Z] INFO  18:11:49,778 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:11Z] INFO  18:11:49,778 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:11Z] INFO  18:11:49,936 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:11Z] INFO  18:11:50,178 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T01:11Z] INFO  18:11:50,187 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:11Z] INFO  18:11:50,264 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-15T01:11Z] INFO  18:11:50,637 IntervalUtils - Processing 248696 bp from intervals
[2016-04-15T01:11Z] WARN  18:11:50,642 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:11Z] INFO  18:11:50,725 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:11Z] INFO  18:11:50,840 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:11Z] INFO  18:11:50,852 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:11Z] INFO  18:11:50,853 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T01:11Z] INFO  18:11:50,853 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T01:11Z] INFO  18:11:50,919 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:11Z] INFO  18:11:50,920 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:11Z] INFO  18:11:52,265 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:11Z] INFO  18:11:52,270 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:11Z] INFO  18:11:52,271 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:11Z] INFO  18:11:52,271 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:11Z] INFO  18:11:52,276 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/7/R14-18102_kapa-NGv3-PE100-NGv3-sort-7_157155854_159138663-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/7/R14-18102_kapa-NGv3-PE100-NGv3-7_157155854_159138663-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/7/tx/tmp85yDsn/R14-18102_kapa-NGv3-PE100-NGv3-7_157155854_159138663.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:11Z] INFO  18:11:52,287 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:11Z] INFO  18:11:52,287 HelpFormatter - Date/Time: 2016/04/14 18:11:52
[2016-04-15T01:11Z] INFO  18:11:52,287 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:11Z] INFO  18:11:52,287 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:11Z] INFO  18:11:52,382 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:11Z] INFO  18:11:52,385 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:11Z] INFO  18:11:52,386 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:11Z] INFO  18:11:52,386 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:11Z] INFO  18:11:52,391 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/8/R14-18102_kapa-NGv3-PE100-NGv3-sort-8_0_15517156-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/8/R14-18102_kapa-NGv3-PE100-NGv3-8_0_15517156-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/8/tx/tmpCrL_1q/R14-18102_kapa-NGv3-PE100-NGv3-8_0_15517156.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:11Z] INFO  18:11:52,410 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:11Z] INFO  18:11:52,411 HelpFormatter - Date/Time: 2016/04/14 18:11:52
[2016-04-15T01:11Z] INFO  18:11:52,412 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:11Z] INFO  18:11:52,413 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:11Z] INFO  18:11:52,474 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:11Z] INFO  18:11:52,636 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:11Z] INFO  18:11:52,651 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T01:11Z] INFO  18:11:52,661 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:11Z] INFO  18:11:52,753 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.09
[2016-04-15T01:11Z] INFO  18:11:52,857 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T01:11Z] INFO  18:11:52,873 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:11Z] INFO  18:11:52,964 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.09
[2016-04-15T01:11Z] INFO  18:11:53,005 ProgressMeter -            done    448393.0    22.0 s      49.0 s      100.0%    22.0 s       0.0 s
[2016-04-15T01:11Z] INFO  18:11:53,007 ProgressMeter - Total runtime 22.11 secs, 0.37 min, 0.01 hours
[2016-04-15T01:11Z] INFO  18:11:53,008 MicroScheduler - 18607 reads were filtered out during the traversal out of approximately 226831 total reads (8.20%)
[2016-04-15T01:11Z] INFO  18:11:53,009 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:11Z] INFO  18:11:53,009 MicroScheduler -   -> 308 reads (0.14% of total) failing BadMateFilter
[2016-04-15T01:11Z] INFO  18:11:53,010 MicroScheduler -   -> 18113 reads (7.99% of total) failing DuplicateReadFilter
[2016-04-15T01:11Z] INFO  18:11:53,011 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:11Z] INFO  18:11:53,012 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:11Z] INFO  18:11:53,012 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:11Z] INFO  18:11:53,013 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:11Z] INFO  18:11:53,014 MicroScheduler -   -> 186 reads (0.08% of total) failing UnmappedReadFilter
[2016-04-15T01:11Z] INFO  18:11:53,187 IntervalUtils - Processing 17619 bp from intervals
[2016-04-15T01:11Z] WARN  18:11:53,193 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:11Z] INFO  18:11:53,279 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:11Z] INFO  18:11:53,332 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:11Z] INFO  18:11:53,333 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:11Z] INFO  18:11:53,334 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T01:11Z] INFO  18:11:53,335 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T01:11Z] INFO  18:11:53,375 IntervalUtils - Processing 115548 bp from intervals
[2016-04-15T01:11Z] WARN  18:11:53,382 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:11Z] INFO  18:11:53,390 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:11Z] INFO  18:11:53,390 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:11Z] INFO  18:11:53,504 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:11Z] INFO  18:11:53,540 ProgressMeter -            done    442893.0    20.0 s      46.0 s       99.9%    20.0 s       0.0 s
[2016-04-15T01:11Z] INFO  18:11:53,540 ProgressMeter - Total runtime 20.71 secs, 0.35 min, 0.01 hours
[2016-04-15T01:11Z] INFO  18:11:53,541 MicroScheduler - 16728 reads were filtered out during the traversal out of approximately 198726 total reads (8.42%)
[2016-04-15T01:11Z] INFO  18:11:53,541 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:11Z] INFO  18:11:53,542 MicroScheduler -   -> 309 reads (0.16% of total) failing BadMateFilter
[2016-04-15T01:11Z] INFO  18:11:53,542 MicroScheduler -   -> 16259 reads (8.18% of total) failing DuplicateReadFilter
[2016-04-15T01:11Z] INFO  18:11:53,542 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:11Z] INFO  18:11:53,543 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:11Z] INFO  18:11:53,543 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:11Z] INFO  18:11:53,543 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:11Z] INFO  18:11:53,543 MicroScheduler -   -> 160 reads (0.08% of total) failing UnmappedReadFilter
[2016-04-15T01:11Z] INFO  18:11:53,593 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:11Z] INFO  18:11:53,594 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:11Z] INFO  18:11:53,595 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T01:11Z] INFO  18:11:53,596 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T01:11Z] INFO  18:11:53,654 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:11Z] INFO  18:11:53,655 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:11Z] INFO  18:11:54,511 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:11Z] GATK: UnifiedGenotyper
[2016-04-15T01:11Z] INFO  18:11:55,231 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:11Z] GATK: UnifiedGenotyper
[2016-04-15T01:11Z] INFO  18:11:55,775 ProgressMeter -            done    186536.0    12.0 s      68.0 s       99.9%    12.0 s       0.0 s
[2016-04-15T01:11Z] INFO  18:11:55,775 ProgressMeter - Total runtime 12.73 secs, 0.21 min, 0.00 hours
[2016-04-15T01:11Z] INFO  18:11:55,776 MicroScheduler - 8353 reads were filtered out during the traversal out of approximately 100661 total reads (8.30%)
[2016-04-15T01:11Z] INFO  18:11:55,776 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:11Z] INFO  18:11:55,776 MicroScheduler -   -> 153 reads (0.15% of total) failing BadMateFilter
[2016-04-15T01:11Z] INFO  18:11:55,777 MicroScheduler -   -> 8117 reads (8.06% of total) failing DuplicateReadFilter
[2016-04-15T01:11Z] INFO  18:11:55,777 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:11Z] INFO  18:11:55,777 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:11Z] INFO  18:11:55,777 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:11Z] INFO  18:11:55,778 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:11Z] INFO  18:11:55,778 MicroScheduler -   -> 83 reads (0.08% of total) failing UnmappedReadFilter
[2016-04-15T01:11Z] INFO  18:11:56,019 ProgressMeter -            done    637397.0    22.0 s      35.0 s      100.0%    22.0 s       0.0 s
[2016-04-15T01:11Z] INFO  18:11:56,020 ProgressMeter - Total runtime 22.74 secs, 0.38 min, 0.01 hours
[2016-04-15T01:11Z] INFO  18:11:56,020 MicroScheduler - 22333 reads were filtered out during the traversal out of approximately 268570 total reads (8.32%)
[2016-04-15T01:11Z] INFO  18:11:56,020 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:11Z] INFO  18:11:56,021 MicroScheduler -   -> 509 reads (0.19% of total) failing BadMateFilter
[2016-04-15T01:11Z] INFO  18:11:56,021 MicroScheduler -   -> 21587 reads (8.04% of total) failing DuplicateReadFilter
[2016-04-15T01:11Z] INFO  18:11:56,021 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:11Z] INFO  18:11:56,021 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:11Z] INFO  18:11:56,022 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:11Z] INFO  18:11:56,022 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:11Z] INFO  18:11:56,022 MicroScheduler -   -> 237 reads (0.09% of total) failing UnmappedReadFilter
[2016-04-15T01:11Z] INFO  18:11:56,879 ProgressMeter -            done    357873.0    18.0 s      51.0 s      100.0%    18.0 s       0.0 s
[2016-04-15T01:11Z] INFO  18:11:56,880 ProgressMeter - Total runtime 18.60 secs, 0.31 min, 0.01 hours
[2016-04-15T01:11Z] INFO  18:11:56,880 MicroScheduler - 14193 reads were filtered out during the traversal out of approximately 172789 total reads (8.21%)
[2016-04-15T01:11Z] INFO  18:11:56,880 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:11Z] INFO  18:11:56,881 MicroScheduler -   -> 275 reads (0.16% of total) failing BadMateFilter
[2016-04-15T01:11Z] INFO  18:11:56,881 MicroScheduler -   -> 13777 reads (7.97% of total) failing DuplicateReadFilter
[2016-04-15T01:11Z] INFO  18:11:56,881 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:11Z] INFO  18:11:56,881 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:11Z] INFO  18:11:56,881 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:11Z] INFO  18:11:56,882 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:11Z] INFO  18:11:56,882 MicroScheduler -   -> 141 reads (0.08% of total) failing UnmappedReadFilter
[2016-04-15T01:11Z] INFO  18:11:56,900 ProgressMeter -            done   1341130.0    44.0 s      33.0 s      100.0%    44.0 s       0.0 s
[2016-04-15T01:11Z] INFO  18:11:56,901 ProgressMeter - Total runtime 44.41 secs, 0.74 min, 0.01 hours
[2016-04-15T01:11Z] INFO  18:11:56,901 MicroScheduler - 56140 reads were filtered out during the traversal out of approximately 627556 total reads (8.95%)
[2016-04-15T01:11Z] INFO  18:11:56,901 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:11Z] INFO  18:11:56,902 MicroScheduler -   -> 923 reads (0.15% of total) failing BadMateFilter
[2016-04-15T01:11Z] INFO  18:11:56,902 MicroScheduler -   -> 54702 reads (8.72% of total) failing DuplicateReadFilter
[2016-04-15T01:11Z] INFO  18:11:56,902 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:11Z] INFO  18:11:56,902 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:11Z] INFO  18:11:56,902 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:11Z] INFO  18:11:56,903 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:11Z] INFO  18:11:56,903 MicroScheduler -   -> 515 reads (0.08% of total) failing UnmappedReadFilter
[2016-04-15T01:11Z] INFO  18:11:57,310 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:11Z] INFO  18:11:57,418 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:11Z] GATK: UnifiedGenotyper
[2016-04-15T01:11Z] GATK: UnifiedGenotyper
[2016-04-15T01:11Z] INFO  18:11:57,744 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:11Z] INFO  18:11:57,748 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:11Z] INFO  18:11:57,749 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:11Z] INFO  18:11:57,749 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:11Z] INFO  18:11:57,754 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/8/R14-18102_kapa-NGv3-PE100-NGv3-sort-8_15519664_31030618-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/8/R14-18102_kapa-NGv3-PE100-NGv3-8_15519664_31030618-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/8/tx/tmpWmN42h/R14-18102_kapa-NGv3-PE100-NGv3-8_15519664_31030618.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:11Z] INFO  18:11:57,791 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:11Z] INFO  18:11:57,803 HelpFormatter - Date/Time: 2016/04/14 18:11:57
[2016-04-15T01:11Z] INFO  18:11:57,804 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:11Z] INFO  18:11:57,805 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:11Z] INFO  18:11:58,001 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:11Z] INFO  18:11:58,069 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:11Z] INFO  18:11:58,073 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:11Z] INFO  18:11:58,074 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:11Z] INFO  18:11:58,074 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:11Z] INFO  18:11:58,080 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/8/R14-18102_kapa-NGv3-PE100-NGv3-sort-8_31496910_48001429-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/8/R14-18102_kapa-NGv3-PE100-NGv3-8_31496910_48001429-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/8/tx/tmpFTHP6s/R14-18102_kapa-NGv3-PE100-NGv3-8_31496910_48001429.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:11Z] INFO  18:11:58,099 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:11Z] INFO  18:11:58,100 HelpFormatter - Date/Time: 2016/04/14 18:11:58
[2016-04-15T01:11Z] INFO  18:11:58,101 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:11Z] INFO  18:11:58,101 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:11Z] INFO  18:11:58,195 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:11Z] INFO  18:11:58,203 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:11Z] INFO  18:11:58,208 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T01:11Z] INFO  18:11:58,220 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:11Z] INFO  18:11:58,290 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-15T01:11Z] INFO  18:11:58,344 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:11Z] GATK: UnifiedGenotyper
[2016-04-15T01:11Z] GATK: UnifiedGenotyper
[2016-04-15T01:11Z] INFO  18:11:58,617 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T01:11Z] INFO  18:11:58,629 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:11Z] INFO  18:11:58,695 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-15T01:11Z] INFO  18:11:58,740 IntervalUtils - Processing 233081 bp from intervals
[2016-04-15T01:11Z] WARN  18:11:58,749 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:11Z] INFO  18:11:58,784 ProgressMeter -            done     46373.0     5.0 s     117.0 s       99.7%     5.0 s       0.0 s
[2016-04-15T01:11Z] INFO  18:11:58,785 ProgressMeter - Total runtime 5.45 secs, 0.09 min, 0.00 hours
[2016-04-15T01:11Z] INFO  18:11:58,785 MicroScheduler - 2009 reads were filtered out during the traversal out of approximately 23824 total reads (8.43%)
[2016-04-15T01:11Z] INFO  18:11:58,785 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:11Z] INFO  18:11:58,786 MicroScheduler -   -> 48 reads (0.20% of total) failing BadMateFilter
[2016-04-15T01:11Z] INFO  18:11:58,786 MicroScheduler -   -> 1949 reads (8.18% of total) failing DuplicateReadFilter
[2016-04-15T01:11Z] INFO  18:11:58,786 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:11Z] INFO  18:11:58,786 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:11Z] INFO  18:11:58,787 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:11Z] INFO  18:11:58,787 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:11Z] INFO  18:11:58,787 MicroScheduler -   -> 12 reads (0.05% of total) failing UnmappedReadFilter
[2016-04-15T01:11Z] INFO  18:11:58,825 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:11Z] INFO  18:11:58,921 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:11Z] INFO  18:11:58,922 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:11Z] INFO  18:11:58,923 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T01:11Z] INFO  18:11:58,924 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T01:11Z] INFO  18:11:58,981 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:11Z] INFO  18:11:58,982 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:11Z] INFO  18:11:59,075 IntervalUtils - Processing 125262 bp from intervals
[2016-04-15T01:11Z] WARN  18:11:59,091 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:11Z] INFO  18:11:59,171 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:11Z] INFO  18:11:59,277 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:11Z] INFO  18:11:59,279 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:11Z] INFO  18:11:59,286 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T01:11Z] INFO  18:11:59,287 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T01:11Z] INFO  18:11:59,371 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:11Z] INFO  18:11:59,372 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:12Z] INFO  18:12:00,272 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:12Z] INFO  18:12:00,447 ProgressMeter -            done    214671.0    13.0 s      64.0 s       99.9%    13.0 s       0.0 s
[2016-04-15T01:12Z] INFO  18:12:00,448 ProgressMeter - Total runtime 13.94 secs, 0.23 min, 0.00 hours
[2016-04-15T01:12Z] INFO  18:12:00,448 MicroScheduler - 8854 reads were filtered out during the traversal out of approximately 107781 total reads (8.21%)
[2016-04-15T01:12Z] INFO  18:12:00,448 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:12Z] INFO  18:12:00,449 MicroScheduler -   -> 170 reads (0.16% of total) failing BadMateFilter
[2016-04-15T01:12Z] INFO  18:12:00,449 MicroScheduler -   -> 8605 reads (7.98% of total) failing DuplicateReadFilter
[2016-04-15T01:12Z] INFO  18:12:00,449 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:12Z] INFO  18:12:00,450 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:12Z] INFO  18:12:00,450 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:12Z] INFO  18:12:00,450 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:12Z] INFO  18:12:00,451 MicroScheduler -   -> 79 reads (0.07% of total) failing UnmappedReadFilter
[2016-04-15T01:12Z] GATK: UnifiedGenotyper
[2016-04-15T01:12Z] INFO  18:12:00,826 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:12Z] INFO  18:12:00,830 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:12Z] INFO  18:12:00,830 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:12Z] INFO  18:12:00,831 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:12Z] INFO  18:12:00,835 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/8/R14-18102_kapa-NGv3-PE100-NGv3-sort-8_48003022_63659688-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/8/R14-18102_kapa-NGv3-PE100-NGv3-8_48003022_63659688-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/8/tx/tmpvJakIR/R14-18102_kapa-NGv3-PE100-NGv3-8_48003022_63659688.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:12Z] INFO  18:12:00,854 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:12Z] INFO  18:12:00,855 HelpFormatter - Date/Time: 2016/04/14 18:12:00
[2016-04-15T01:12Z] INFO  18:12:00,862 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:12Z] INFO  18:12:00,863 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:12Z] INFO  18:12:00,960 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:12Z] INFO  18:12:00,963 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:12Z] INFO  18:12:00,964 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:12Z] INFO  18:12:00,964 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:12Z] INFO  18:12:00,969 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/8/R14-18102_kapa-NGv3-PE100-NGv3-sort-8_63775819_79510770-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/8/R14-18102_kapa-NGv3-PE100-NGv3-8_63775819_79510770-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/8/tx/tmpZvuass/R14-18102_kapa-NGv3-PE100-NGv3-8_63775819_79510770.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:12Z] INFO  18:12:00,978 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:12Z] INFO  18:12:00,986 HelpFormatter - Date/Time: 2016/04/14 18:12:00
[2016-04-15T01:12Z] INFO  18:12:00,987 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:12Z] INFO  18:12:00,987 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:12Z] INFO  18:12:01,098 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:12Z] INFO  18:12:01,319 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:12Z] INFO  18:12:01,357 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T01:12Z] INFO  18:12:01,377 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:12Z] INFO  18:12:01,460 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-15T01:12Z] INFO  18:12:01,575 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T01:12Z] INFO  18:12:01,585 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:12Z] INFO  18:12:01,614 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:12Z] INFO  18:12:01,618 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:12Z] INFO  18:12:01,619 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:12Z] INFO  18:12:01,619 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:12Z] INFO  18:12:01,625 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/8/R14-18102_kapa-NGv3-PE100-NGv3-sort-8_79513976_95140568-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/8/R14-18102_kapa-NGv3-PE100-NGv3-8_79513976_95140568-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/8/tx/tmplD8gfX/R14-18102_kapa-NGv3-PE100-NGv3-8_79513976_95140568.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:12Z] INFO  18:12:01,626 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:12Z] INFO  18:12:01,630 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:12Z] INFO  18:12:01,631 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:12Z] INFO  18:12:01,631 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:12Z] INFO  18:12:01,635 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:12Z] INFO  18:12:01,636 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/8/R14-18102_kapa-NGv3-PE100-NGv3-sort-8_95142853_110655419-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/8/R14-18102_kapa-NGv3-PE100-NGv3-8_95142853_110655419-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/8/tx/tmpF_WWF6/R14-18102_kapa-NGv3-PE100-NGv3-8_95142853_110655419.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:12Z] INFO  18:12:01,637 HelpFormatter - Date/Time: 2016/04/14 18:12:01
[2016-04-15T01:12Z] INFO  18:12:01,637 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:12Z] INFO  18:12:01,637 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:12Z] INFO  18:12:01,665 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:12Z] INFO  18:12:01,666 HelpFormatter - Date/Time: 2016/04/14 18:12:01
[2016-04-15T01:12Z] INFO  18:12:01,667 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:12Z] INFO  18:12:01,667 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-15T01:12Z] INFO  18:12:01,667 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:12Z] INFO  18:12:01,758 ProgressMeter -            done    438420.0    19.0 s      44.0 s      100.0%    19.0 s       0.0 s
[2016-04-15T01:12Z] INFO  18:12:01,758 ProgressMeter - Total runtime 19.41 secs, 0.32 min, 0.01 hours
[2016-04-15T01:12Z] INFO  18:12:01,759 MicroScheduler - 17463 reads were filtered out during the traversal out of approximately 204715 total reads (8.53%)
[2016-04-15T01:12Z] INFO  18:12:01,759 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:12Z] INFO  18:12:01,759 MicroScheduler -   -> 298 reads (0.15% of total) failing BadMateFilter
[2016-04-15T01:12Z] INFO  18:12:01,760 MicroScheduler -   -> 17023 reads (8.32% of total) failing DuplicateReadFilter
[2016-04-15T01:12Z] INFO  18:12:01,760 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:12Z] INFO  18:12:01,760 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:12Z] INFO  18:12:01,760 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:12Z] INFO  18:12:01,760 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:12Z] INFO  18:12:01,761 MicroScheduler -   -> 142 reads (0.07% of total) failing UnmappedReadFilter
[2016-04-15T01:12Z] INFO  18:12:01,882 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:12Z] INFO  18:12:01,904 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:12Z] INFO  18:12:01,961 IntervalUtils - Processing 104159 bp from intervals
[2016-04-15T01:12Z] WARN  18:12:01,973 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:12Z] INFO  18:12:02,039 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:12Z] INFO  18:12:02,077 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:12Z] INFO  18:12:02,111 ProgressMeter -            done    434204.0    17.0 s      40.0 s      100.0%    17.0 s       0.0 s
[2016-04-15T01:12Z] INFO  18:12:02,111 ProgressMeter - Total runtime 17.39 secs, 0.29 min, 0.00 hours
[2016-04-15T01:12Z] INFO  18:12:02,111 MicroScheduler - 12835 reads were filtered out during the traversal out of approximately 157331 total reads (8.16%)
[2016-04-15T01:12Z] INFO  18:12:02,112 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:12Z] INFO  18:12:02,112 MicroScheduler -   -> 250 reads (0.16% of total) failing BadMateFilter
[2016-04-15T01:12Z] INFO  18:12:02,112 MicroScheduler -   -> 12468 reads (7.92% of total) failing DuplicateReadFilter
[2016-04-15T01:12Z] INFO  18:12:02,112 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:12Z] INFO  18:12:02,113 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:12Z] INFO  18:12:02,113 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:12Z] INFO  18:12:02,113 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:12Z] INFO  18:12:02,113 MicroScheduler -   -> 117 reads (0.07% of total) failing UnmappedReadFilter
[2016-04-15T01:12Z] INFO  18:12:02,130 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T01:12Z] INFO  18:12:02,136 IntervalUtils - Processing 117209 bp from intervals
[2016-04-15T01:12Z] WARN  18:12:02,142 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:12Z] INFO  18:12:02,151 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:12Z] INFO  18:12:02,152 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:12Z] INFO  18:12:02,153 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T01:12Z] INFO  18:12:02,153 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T01:12Z] INFO  18:12:02,156 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:12Z] INFO  18:12:02,201 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:12Z] INFO  18:12:02,201 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:12Z] INFO  18:12:02,220 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T01:12Z] INFO  18:12:02,228 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:12Z] INFO  18:12:02,229 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:12Z] INFO  18:12:02,244 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.09
[2016-04-15T01:12Z] GATK: UnifiedGenotyper
[2016-04-15T01:12Z] INFO  18:12:02,302 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-15T01:12Z] INFO  18:12:02,328 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:12Z] INFO  18:12:02,328 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:12Z] INFO  18:12:02,329 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T01:12Z] INFO  18:12:02,329 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T01:12Z] INFO  18:12:02,385 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:12Z] INFO  18:12:02,386 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:12Z] INFO  18:12:02,728 IntervalUtils - Processing 78340 bp from intervals
[2016-04-15T01:12Z] WARN  18:12:02,733 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:12Z] INFO  18:12:02,800 IntervalUtils - Processing 161638 bp from intervals
[2016-04-15T01:12Z] WARN  18:12:02,805 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:12Z] INFO  18:12:02,851 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:12Z] INFO  18:12:02,871 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:12Z] INFO  18:12:02,960 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:12Z] INFO  18:12:02,960 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:12Z] INFO  18:12:02,961 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T01:12Z] INFO  18:12:02,961 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T01:12Z] INFO  18:12:02,989 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:12Z] INFO  18:12:02,989 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:12Z] INFO  18:12:02,992 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T01:12Z] INFO  18:12:02,992 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T01:12Z] INFO  18:12:03,042 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:12Z] INFO  18:12:03,054 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:12Z] INFO  18:12:03,064 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:12Z] INFO  18:12:03,087 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:12Z] INFO  18:12:03,087 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:12Z] GATK: UnifiedGenotyper
[2016-04-15T01:12Z] INFO  18:12:03,400 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:12Z] GATK: UnifiedGenotyper
[2016-04-15T01:12Z] INFO  18:12:03,762 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:12Z] INFO  18:12:03,766 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:12Z] INFO  18:12:03,766 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:12Z] INFO  18:12:03,767 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:12Z] INFO  18:12:03,772 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/8/R14-18102_kapa-NGv3-PE100-NGv3-sort-8_110656864_126194498-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/8/R14-18102_kapa-NGv3-PE100-NGv3-8_110656864_126194498-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/8/tx/tmpBYCAL5/R14-18102_kapa-NGv3-PE100-NGv3-8_110656864_126194498.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:12Z] INFO  18:12:03,782 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:12Z] INFO  18:12:03,789 HelpFormatter - Date/Time: 2016/04/14 18:12:03
[2016-04-15T01:12Z] INFO  18:12:03,790 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:12Z] INFO  18:12:03,790 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:12Z] INFO  18:12:03,910 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:12Z] INFO  18:12:04,160 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T01:12Z] INFO  18:12:04,169 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:12Z] INFO  18:12:04,264 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.09
[2016-04-15T01:12Z] INFO  18:12:04,607 IntervalUtils - Processing 102393 bp from intervals
[2016-04-15T01:12Z] WARN  18:12:04,613 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:12Z] INFO  18:12:04,637 ProgressMeter -            done    457571.0    21.0 s      46.0 s      100.0%    21.0 s       0.0 s
[2016-04-15T01:12Z] INFO  18:12:04,637 ProgressMeter - Total runtime 21.12 secs, 0.35 min, 0.01 hours
[2016-04-15T01:12Z] INFO  18:12:04,637 MicroScheduler - 18660 reads were filtered out during the traversal out of approximately 235952 total reads (7.91%)
[2016-04-15T01:12Z] INFO  18:12:04,638 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:12Z] INFO  18:12:04,638 MicroScheduler -   -> 372 reads (0.16% of total) failing BadMateFilter
[2016-04-15T01:12Z] INFO  18:12:04,638 MicroScheduler -   -> 18104 reads (7.67% of total) failing DuplicateReadFilter
[2016-04-15T01:12Z] INFO  18:12:04,639 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:12Z] INFO  18:12:04,639 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:12Z] INFO  18:12:04,639 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:12Z] INFO  18:12:04,639 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:12Z] INFO  18:12:04,640 MicroScheduler -   -> 184 reads (0.08% of total) failing UnmappedReadFilter
[2016-04-15T01:12Z] INFO  18:12:04,717 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:12Z] INFO  18:12:04,803 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:12Z] INFO  18:12:04,804 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:12Z] INFO  18:12:04,805 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T01:12Z] INFO  18:12:04,806 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T01:12Z] INFO  18:12:04,846 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:12Z] INFO  18:12:04,847 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:12Z] INFO  18:12:05,581 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:12Z] INFO  18:12:05,584 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:12Z] INFO  18:12:05,585 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:12Z] INFO  18:12:05,585 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:12Z] INFO  18:12:05,590 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/8/R14-18102_kapa-NGv3-PE100-NGv3-sort-8_126369460_141889736-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/8/R14-18102_kapa-NGv3-PE100-NGv3-8_126369460_141889736-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/8/tx/tmpYbDsxn/R14-18102_kapa-NGv3-PE100-NGv3-8_126369460_141889736.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:12Z] INFO  18:12:05,615 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:12Z] INFO  18:12:05,623 HelpFormatter - Date/Time: 2016/04/14 18:12:05
[2016-04-15T01:12Z] INFO  18:12:05,624 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:12Z] INFO  18:12:05,625 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:12Z] INFO  18:12:05,781 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:12Z] INFO  18:12:06,011 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T01:12Z] INFO  18:12:06,020 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:12Z] INFO  18:12:06,081 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:12Z] INFO  18:12:06,128 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.11
[2016-04-15T01:12Z] INFO  18:12:06,370 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:12Z] INFO  18:12:06,373 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:12Z] INFO  18:12:06,373 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:12Z] INFO  18:12:06,373 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:12Z] GATK: UnifiedGenotyper
[2016-04-15T01:12Z] INFO  18:12:06,377 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/8/R14-18102_kapa-NGv3-PE100-NGv3-sort-8_141900641_146364022-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/8/R14-18102_kapa-NGv3-PE100-NGv3-8_141900641_146364022-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/8/tx/tmpSs71OX/R14-18102_kapa-NGv3-PE100-NGv3-8_141900641_146364022.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:12Z] INFO  18:12:06,410 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:12Z] INFO  18:12:06,411 HelpFormatter - Date/Time: 2016/04/14 18:12:06
[2016-04-15T01:12Z] INFO  18:12:06,412 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:12Z] INFO  18:12:06,412 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:12Z] INFO  18:12:06,563 IntervalUtils - Processing 72911 bp from intervals
[2016-04-15T01:12Z] WARN  18:12:06,569 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:12Z] INFO  18:12:06,660 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:12Z] INFO  18:12:06,721 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:12Z] INFO  18:12:06,821 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:12Z] INFO  18:12:06,822 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:12Z] INFO  18:12:06,823 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T01:12Z] INFO  18:12:06,824 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T01:12Z] INFO  18:12:06,921 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:12Z] INFO  18:12:06,922 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:12Z] INFO  18:12:06,965 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:12Z] INFO  18:12:06,968 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:12Z] INFO  18:12:06,969 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:12Z] INFO  18:12:06,969 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:12Z] INFO  18:12:06,973 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/9/R14-18102_kapa-NGv3-PE100-NGv3-sort-9_0_15510186-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/9/R14-18102_kapa-NGv3-PE100-NGv3-9_0_15510186-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/9/tx/tmpLjATFc/R14-18102_kapa-NGv3-PE100-NGv3-9_0_15510186.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:12Z] INFO  18:12:07,001 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:12Z] INFO  18:12:07,002 HelpFormatter - Date/Time: 2016/04/14 18:12:06
[2016-04-15T01:12Z] INFO  18:12:07,003 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:12Z] INFO  18:12:07,003 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:12Z] INFO  18:12:07,023 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T01:12Z] INFO  18:12:07,045 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:12Z] INFO  18:12:07,144 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.10
[2016-04-15T01:12Z] INFO  18:12:07,269 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:12Z] INFO  18:12:07,516 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T01:12Z] INFO  18:12:07,560 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:12Z] INFO  18:12:07,643 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-15T01:12Z] INFO  18:12:07,745 IntervalUtils - Processing 204618 bp from intervals
[2016-04-15T01:12Z] WARN  18:12:07,750 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:12Z] INFO  18:12:07,840 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:12Z] INFO  18:12:07,920 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:12Z] INFO  18:12:07,921 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:12Z] INFO  18:12:07,922 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T01:12Z] INFO  18:12:07,923 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T01:12Z] INFO  18:12:07,970 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:12Z] INFO  18:12:07,971 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:12Z] INFO  18:12:08,101 IntervalUtils - Processing 123193 bp from intervals
[2016-04-15T01:12Z] WARN  18:12:08,106 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:12Z] INFO  18:12:08,239 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:12Z] INFO  18:12:08,338 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:12Z] INFO  18:12:08,339 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:12Z] INFO  18:12:08,339 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T01:12Z] INFO  18:12:08,339 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T01:12Z] INFO  18:12:08,423 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:12Z] INFO  18:12:08,423 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:12Z] INFO  18:12:09,748 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:12Z] INFO  18:12:09,752 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:12Z] INFO  18:12:09,752 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:12Z] INFO  18:12:09,753 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:12Z] INFO  18:12:09,757 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/9/R14-18102_kapa-NGv3-PE100-NGv3-sort-9_15564086_32405601-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/9/R14-18102_kapa-NGv3-PE100-NGv3-9_15564086_32405601-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/9/tx/tmpZ5e2O4/R14-18102_kapa-NGv3-PE100-NGv3-9_15564086_32405601.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:12Z] INFO  18:12:09,769 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:12Z] INFO  18:12:09,777 HelpFormatter - Date/Time: 2016/04/14 18:12:09
[2016-04-15T01:12Z] INFO  18:12:09,778 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:12Z] INFO  18:12:09,778 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:12Z] INFO  18:12:09,895 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:12Z] INFO  18:12:10,190 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T01:12Z] INFO  18:12:10,211 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:12Z] INFO  18:12:10,301 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.09
[2016-04-15T01:12Z] INFO  18:12:10,696 IntervalUtils - Processing 89361 bp from intervals
[2016-04-15T01:12Z] WARN  18:12:10,701 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:12Z] INFO  18:12:10,786 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:12Z] INFO  18:12:10,850 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:12Z] INFO  18:12:10,851 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:12Z] INFO  18:12:10,851 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T01:12Z] INFO  18:12:10,852 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T01:12Z] INFO  18:12:10,898 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:12Z] INFO  18:12:10,898 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:12Z] INFO  18:12:11,541 ProgressMeter -            done    735970.0    25.0 s      34.0 s      100.0%    25.0 s       0.0 s
[2016-04-15T01:12Z] INFO  18:12:11,542 ProgressMeter - Total runtime 25.12 secs, 0.42 min, 0.01 hours
[2016-04-15T01:12Z] INFO  18:12:11,542 MicroScheduler - 24003 reads were filtered out during the traversal out of approximately 287223 total reads (8.36%)
[2016-04-15T01:12Z] INFO  18:12:11,542 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:12Z] INFO  18:12:11,543 MicroScheduler -   -> 447 reads (0.16% of total) failing BadMateFilter
[2016-04-15T01:12Z] INFO  18:12:11,543 MicroScheduler -   -> 23356 reads (8.13% of total) failing DuplicateReadFilter
[2016-04-15T01:12Z] INFO  18:12:11,543 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:12Z] INFO  18:12:11,544 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:12Z] INFO  18:12:11,544 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:12Z] INFO  18:12:11,544 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:12Z] INFO  18:12:11,544 MicroScheduler -   -> 200 reads (0.07% of total) failing UnmappedReadFilter
[2016-04-15T01:12Z] INFO  18:12:12,343 ProgressMeter -            done    239009.0    18.0 s      78.0 s      100.0%    18.0 s       0.0 s
[2016-04-15T01:12Z] INFO  18:12:12,344 ProgressMeter - Total runtime 18.75 secs, 0.31 min, 0.01 hours
[2016-04-15T01:12Z] INFO  18:12:12,344 MicroScheduler - 14902 reads were filtered out during the traversal out of approximately 189752 total reads (7.85%)
[2016-04-15T01:12Z] INFO  18:12:12,344 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:12Z] INFO  18:12:12,345 MicroScheduler -   -> 271 reads (0.14% of total) failing BadMateFilter
[2016-04-15T01:12Z] INFO  18:12:12,345 MicroScheduler -   -> 14497 reads (7.64% of total) failing DuplicateReadFilter
[2016-04-15T01:12Z] INFO  18:12:12,345 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:12Z] INFO  18:12:12,346 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:12Z] INFO  18:12:12,346 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:12Z] INFO  18:12:12,346 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:12Z] INFO  18:12:12,347 MicroScheduler -   -> 134 reads (0.07% of total) failing UnmappedReadFilter
[2016-04-15T01:12Z] INFO  18:12:13,009 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:12Z] GATK: UnifiedGenotyper
[2016-04-15T01:12Z] INFO  18:12:13,460 ProgressMeter -            done   3191514.0    53.0 s      16.0 s      100.0%    53.0 s       0.0 s
[2016-04-15T01:12Z] INFO  18:12:13,460 ProgressMeter - Total runtime 53.88 secs, 0.90 min, 0.01 hours
[2016-04-15T01:12Z] INFO  18:12:13,461 MicroScheduler - 63867 reads were filtered out during the traversal out of approximately 767536 total reads (8.32%)
[2016-04-15T01:12Z] INFO  18:12:13,461 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:12Z] INFO  18:12:13,462 MicroScheduler -   -> 1223 reads (0.16% of total) failing BadMateFilter
[2016-04-15T01:12Z] INFO  18:12:13,462 MicroScheduler -   -> 62069 reads (8.09% of total) failing DuplicateReadFilter
[2016-04-15T01:12Z] INFO  18:12:13,462 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:12Z] INFO  18:12:13,462 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:12Z] INFO  18:12:13,463 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:12Z] INFO  18:12:13,463 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:12Z] INFO  18:12:13,466 MicroScheduler -   -> 575 reads (0.07% of total) failing UnmappedReadFilter
[2016-04-15T01:12Z] INFO  18:12:13,821 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:12Z] GATK: UnifiedGenotyper
[2016-04-15T01:12Z] INFO  18:12:14,709 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:12Z] GATK: UnifiedGenotyper
[2016-04-15T01:12Z] INFO  18:12:15,419 ProgressMeter -            done    184917.0    12.0 s      67.0 s      100.0%    12.0 s       0.0 s
[2016-04-15T01:12Z] INFO  18:12:15,419 ProgressMeter - Total runtime 12.46 secs, 0.21 min, 0.00 hours
[2016-04-15T01:12Z] INFO  18:12:15,420 MicroScheduler - 6838 reads were filtered out during the traversal out of approximately 83952 total reads (8.15%)
[2016-04-15T01:12Z] INFO  18:12:15,420 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:12Z] INFO  18:12:15,420 MicroScheduler -   -> 141 reads (0.17% of total) failing BadMateFilter
[2016-04-15T01:12Z] INFO  18:12:15,421 MicroScheduler -   -> 6632 reads (7.90% of total) failing DuplicateReadFilter
[2016-04-15T01:12Z] INFO  18:12:15,421 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:12Z] INFO  18:12:15,421 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:12Z] INFO  18:12:15,422 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:12Z] INFO  18:12:15,422 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:12Z] INFO  18:12:15,422 MicroScheduler -   -> 65 reads (0.08% of total) failing UnmappedReadFilter
[2016-04-15T01:12Z] INFO  18:12:15,974 ProgressMeter -     7:101893697   1035159.0    30.0 s      29.0 s       62.9%    47.0 s      17.0 s
[2016-04-15T01:12Z] INFO  18:12:16,054 ProgressMeter -            done    405639.0    16.0 s      41.0 s      100.0%    16.0 s       0.0 s
[2016-04-15T01:12Z] INFO  18:12:16,054 ProgressMeter - Total runtime 16.78 secs, 0.28 min, 0.00 hours
[2016-04-15T01:12Z] INFO  18:12:16,054 MicroScheduler - 13099 reads were filtered out during the traversal out of approximately 155752 total reads (8.41%)
[2016-04-15T01:12Z] INFO  18:12:16,055 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:12Z] INFO  18:12:16,055 MicroScheduler -   -> 232 reads (0.15% of total) failing BadMateFilter
[2016-04-15T01:12Z] INFO  18:12:16,055 MicroScheduler -   -> 12756 reads (8.19% of total) failing DuplicateReadFilter
[2016-04-15T01:12Z] INFO  18:12:16,055 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:12Z] INFO  18:12:16,056 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:12Z] INFO  18:12:16,056 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:12Z] INFO  18:12:16,056 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:12Z] INFO  18:12:16,056 MicroScheduler -   -> 111 reads (0.07% of total) failing UnmappedReadFilter
[2016-04-15T01:12Z] INFO  18:12:16,281 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:12Z] INFO  18:12:16,284 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:12Z] INFO  18:12:16,284 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:12Z] INFO  18:12:16,285 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:12Z] INFO  18:12:16,291 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/9/R14-18102_kapa-NGv3-PE100-NGv3-sort-9_32407258_65506776-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/9/R14-18102_kapa-NGv3-PE100-NGv3-9_32407258_65506776-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/9/tx/tmp69m9s4/R14-18102_kapa-NGv3-PE100-NGv3-9_32407258_65506776.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:12Z] INFO  18:12:16,303 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:12Z] INFO  18:12:16,304 HelpFormatter - Date/Time: 2016/04/14 18:12:16
[2016-04-15T01:12Z] INFO  18:12:16,304 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:12Z] INFO  18:12:16,305 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:12Z] INFO  18:12:16,438 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:12Z] INFO  18:12:16,643 ProgressMeter -            done    284373.0    14.0 s      50.0 s       99.9%    14.0 s       0.0 s
[2016-04-15T01:12Z] INFO  18:12:16,644 ProgressMeter - Total runtime 14.49 secs, 0.24 min, 0.00 hours
[2016-04-15T01:12Z] INFO  18:12:16,644 MicroScheduler - 9910 reads were filtered out during the traversal out of approximately 118377 total reads (8.37%)
[2016-04-15T01:12Z] INFO  18:12:16,645 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:12Z] INFO  18:12:16,646 MicroScheduler -   -> 166 reads (0.14% of total) failing BadMateFilter
[2016-04-15T01:12Z] INFO  18:12:16,646 MicroScheduler -   -> 9645 reads (8.15% of total) failing DuplicateReadFilter
[2016-04-15T01:12Z] INFO  18:12:16,647 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:12Z] INFO  18:12:16,647 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:12Z] INFO  18:12:16,647 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:12Z] INFO  18:12:16,647 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:12Z] INFO  18:12:16,648 MicroScheduler -   -> 99 reads (0.08% of total) failing UnmappedReadFilter
[2016-04-15T01:12Z] INFO  18:12:16,671 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T01:12Z] INFO  18:12:16,685 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:12Z] INFO  18:12:16,758 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-15T01:12Z] INFO  18:12:17,012 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:12Z] INFO  18:12:17,020 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:12Z] INFO  18:12:17,023 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:12Z] INFO  18:12:17,024 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:12Z] INFO  18:12:17,024 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:12Z] INFO  18:12:17,029 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/9/R14-18102_kapa-NGv3-PE100-NGv3-sort-9_65507205_82187750-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/9/R14-18102_kapa-NGv3-PE100-NGv3-9_65507205_82187750-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/9/tx/tmpVHHjq5/R14-18102_kapa-NGv3-PE100-NGv3-9_65507205_82187750.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:12Z] INFO  18:12:17,045 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:12Z] INFO  18:12:17,046 HelpFormatter - Date/Time: 2016/04/14 18:12:17
[2016-04-15T01:12Z] INFO  18:12:17,047 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:12Z] INFO  18:12:17,048 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:12Z] INFO  18:12:17,302 IntervalUtils - Processing 223679 bp from intervals
[2016-04-15T01:12Z] WARN  18:12:17,309 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:12Z] INFO  18:12:17,319 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:12Z] INFO  18:12:17,465 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:12Z] GATK: UnifiedGenotyper
[2016-04-15T01:12Z] INFO  18:12:17,539 ProgressMeter -            done    271335.0    15.0 s      56.0 s      100.0%    15.0 s       0.0 s
[2016-04-15T01:12Z] INFO  18:12:17,540 ProgressMeter - Total runtime 15.21 secs, 0.25 min, 0.00 hours
[2016-04-15T01:12Z] INFO  18:12:17,541 MicroScheduler - 10741 reads were filtered out during the traversal out of approximately 128004 total reads (8.39%)
[2016-04-15T01:12Z] INFO  18:12:17,543 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:12Z] INFO  18:12:17,543 MicroScheduler -   -> 213 reads (0.17% of total) failing BadMateFilter
[2016-04-15T01:12Z] INFO  18:12:17,544 MicroScheduler -   -> 10431 reads (8.15% of total) failing DuplicateReadFilter
[2016-04-15T01:12Z] INFO  18:12:17,545 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:12Z] INFO  18:12:17,545 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:12Z] INFO  18:12:17,546 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:12Z] INFO  18:12:17,547 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:12Z] INFO  18:12:17,547 MicroScheduler -   -> 97 reads (0.08% of total) failing UnmappedReadFilter
[2016-04-15T01:12Z] INFO  18:12:17,567 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T01:12Z] INFO  18:12:17,578 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:12Z] INFO  18:12:17,592 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:12Z] INFO  18:12:17,604 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:12Z] INFO  18:12:17,605 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T01:12Z] INFO  18:12:17,606 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T01:12Z] INFO  18:12:17,674 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:12Z] INFO  18:12:17,675 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:12Z] INFO  18:12:17,702 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.12
[2016-04-15T01:12Z] INFO  18:12:17,740 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:12Z] GATK: UnifiedGenotyper
[2016-04-15T01:12Z] INFO  18:12:18,092 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:12Z] INFO  18:12:18,095 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:12Z] INFO  18:12:18,096 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:12Z] INFO  18:12:18,096 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:12Z] INFO  18:12:18,101 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/9/R14-18102_kapa-NGv3-PE100-NGv3-sort-9_82188172_97717561-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/9/R14-18102_kapa-NGv3-PE100-NGv3-9_82188172_97717561-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/9/tx/tmpzhjEDG/R14-18102_kapa-NGv3-PE100-NGv3-9_82188172_97717561.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:12Z] INFO  18:12:18,109 IntervalUtils - Processing 119378 bp from intervals
[2016-04-15T01:12Z] WARN  18:12:18,116 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:12Z] INFO  18:12:18,140 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:12Z] INFO  18:12:18,141 HelpFormatter - Date/Time: 2016/04/14 18:12:18
[2016-04-15T01:12Z] INFO  18:12:18,141 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:12Z] INFO  18:12:18,142 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:12Z] INFO  18:12:18,143 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:12Z] INFO  18:12:18,205 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:12Z] INFO  18:12:18,269 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:12Z] INFO  18:12:18,270 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:12Z] INFO  18:12:18,271 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T01:12Z] INFO  18:12:18,272 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T01:12Z] INFO  18:12:18,278 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:12Z] INFO  18:12:18,314 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:12Z] INFO  18:12:18,315 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:12Z] GATK: UnifiedGenotyper
[2016-04-15T01:12Z] INFO  18:12:18,506 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T01:12Z] INFO  18:12:18,515 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:12Z] INFO  18:12:18,587 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-15T01:12Z] INFO  18:12:18,859 ProgressMeter -            done    175776.0    12.0 s      68.0 s       99.9%    12.0 s       0.0 s
[2016-04-15T01:12Z] INFO  18:12:18,859 ProgressMeter - Total runtime 12.04 secs, 0.20 min, 0.00 hours
[2016-04-15T01:12Z] INFO  18:12:18,860 MicroScheduler - 8561 reads were filtered out during the traversal out of approximately 101093 total reads (8.47%)
[2016-04-15T01:12Z] INFO  18:12:18,860 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:12Z] INFO  18:12:18,860 MicroScheduler -   -> 149 reads (0.15% of total) failing BadMateFilter
[2016-04-15T01:12Z] INFO  18:12:18,860 MicroScheduler -   -> 8342 reads (8.25% of total) failing DuplicateReadFilter
[2016-04-15T01:12Z] INFO  18:12:18,861 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:12Z] INFO  18:12:18,861 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:12Z] INFO  18:12:18,861 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:12Z] INFO  18:12:18,861 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:12Z] INFO  18:12:18,862 MicroScheduler -   -> 70 reads (0.07% of total) failing UnmappedReadFilter
[2016-04-15T01:12Z] INFO  18:12:18,942 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:12Z] INFO  18:12:18,956 IntervalUtils - Processing 181286 bp from intervals
[2016-04-15T01:12Z] WARN  18:12:18,961 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:12Z] INFO  18:12:18,974 ProgressMeter -            done    255372.0    14.0 s      55.0 s       99.9%    14.0 s       0.0 s
[2016-04-15T01:12Z] INFO  18:12:18,974 ProgressMeter - Total runtime 14.17 secs, 0.24 min, 0.00 hours
[2016-04-15T01:12Z] INFO  18:12:18,975 MicroScheduler - 10148 reads were filtered out during the traversal out of approximately 123249 total reads (8.23%)
[2016-04-15T01:12Z] INFO  18:12:18,975 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:12Z] INFO  18:12:18,975 MicroScheduler -   -> 170 reads (0.14% of total) failing BadMateFilter
[2016-04-15T01:12Z] INFO  18:12:18,976 MicroScheduler -   -> 9886 reads (8.02% of total) failing DuplicateReadFilter
[2016-04-15T01:12Z] INFO  18:12:18,976 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:12Z] INFO  18:12:18,976 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:12Z] INFO  18:12:18,976 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:12Z] INFO  18:12:18,977 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:12Z] INFO  18:12:18,977 MicroScheduler -   -> 92 reads (0.07% of total) failing UnmappedReadFilter
[2016-04-15T01:12Z] INFO  18:12:19,089 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:12Z] INFO  18:12:19,231 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:12Z] INFO  18:12:19,232 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:12Z] INFO  18:12:19,233 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T01:12Z] INFO  18:12:19,233 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T01:12Z] GATK: UnifiedGenotyper
[2016-04-15T01:12Z] INFO  18:12:19,278 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:12Z] INFO  18:12:19,279 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:12Z] INFO  18:12:20,166 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:12Z] INFO  18:12:20,170 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:12Z] INFO  18:12:20,170 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:12Z] INFO  18:12:20,171 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:12Z] INFO  18:12:20,175 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/9/R14-18102_kapa-NGv3-PE100-NGv3-sort-9_97718189_113228306-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/9/R14-18102_kapa-NGv3-PE100-NGv3-9_97718189_113228306-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/9/tx/tmphlPRkI/R14-18102_kapa-NGv3-PE100-NGv3-9_97718189_113228306.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:12Z] INFO  18:12:20,189 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:12Z] INFO  18:12:20,190 HelpFormatter - Date/Time: 2016/04/14 18:12:20
[2016-04-15T01:12Z] INFO  18:12:20,190 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:12Z] INFO  18:12:20,191 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:12Z] INFO  18:12:20,219 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:12Z] INFO  18:12:20,325 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:12Z] INFO  18:12:20,325 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:12Z] GATK: UnifiedGenotyper
[2016-04-15T01:12Z] GATK: UnifiedGenotyper
[2016-04-15T01:12Z] INFO  18:12:20,607 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T01:12Z] INFO  18:12:20,616 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:12Z] INFO  18:12:20,620 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:12Z] INFO  18:12:20,623 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:12Z] INFO  18:12:20,624 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:12Z] INFO  18:12:20,624 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:12Z] INFO  18:12:20,629 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/9/R14-18102_kapa-NGv3-PE100-NGv3-sort-9_113231219_129089575-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/9/R14-18102_kapa-NGv3-PE100-NGv3-9_113231219_129089575-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/9/tx/tmplsEL9b/R14-18102_kapa-NGv3-PE100-NGv3-9_113231219_129089575.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:12Z] INFO  18:12:20,642 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:12Z] INFO  18:12:20,642 HelpFormatter - Date/Time: 2016/04/14 18:12:20
[2016-04-15T01:12Z] INFO  18:12:20,642 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:12Z] INFO  18:12:20,643 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:12Z] INFO  18:12:20,671 ProgressMeter -            done   1158758.0    29.0 s      25.0 s      100.0%    29.0 s       0.0 s
[2016-04-15T01:12Z] INFO  18:12:20,671 ProgressMeter - Total runtime 29.82 secs, 0.50 min, 0.01 hours
[2016-04-15T01:12Z] INFO  18:12:20,672 MicroScheduler - 30682 reads were filtered out during the traversal out of approximately 386665 total reads (7.94%)
[2016-04-15T01:12Z] INFO  18:12:20,672 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:12Z] INFO  18:12:20,672 MicroScheduler -   -> 607 reads (0.16% of total) failing BadMateFilter
[2016-04-15T01:12Z] INFO  18:12:20,673 MicroScheduler -   -> 29768 reads (7.70% of total) failing DuplicateReadFilter
[2016-04-15T01:12Z] INFO  18:12:20,673 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:12Z] INFO  18:12:20,673 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:12Z] INFO  18:12:20,673 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:12Z] INFO  18:12:20,674 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:12Z] INFO  18:12:20,674 MicroScheduler -   -> 307 reads (0.08% of total) failing UnmappedReadFilter
[2016-04-15T01:12Z] INFO  18:12:20,677 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-15T01:12Z] INFO  18:12:20,818 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:12Z] INFO  18:12:21,115 IntervalUtils - Processing 199321 bp from intervals
[2016-04-15T01:12Z] INFO  18:12:21,111 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T01:12Z] WARN  18:12:21,128 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:12Z] INFO  18:12:21,132 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:12Z] INFO  18:12:21,225 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-15T01:12Z] INFO  18:12:21,238 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:12Z] INFO  18:12:21,350 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:12Z] INFO  18:12:21,354 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:12Z] INFO  18:12:21,354 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:12Z] INFO  18:12:21,355 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:12Z] INFO  18:12:21,359 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/9/R14-18102_kapa-NGv3-PE100-NGv3-sort-9_129097484_141213431-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/9/R14-18102_kapa-NGv3-PE100-NGv3-9_129097484_141213431-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/9/tx/tmpMUKIas/R14-18102_kapa-NGv3-PE100-NGv3-9_129097484_141213431.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:12Z] INFO  18:12:21,368 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:12Z] INFO  18:12:21,373 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:12Z] INFO  18:12:21,374 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:12Z] INFO  18:12:21,375 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T01:12Z] INFO  18:12:21,376 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T01:12Z] INFO  18:12:21,369 HelpFormatter - Date/Time: 2016/04/14 18:12:21
[2016-04-15T01:12Z] INFO  18:12:21,380 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:12Z] INFO  18:12:21,381 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:12Z] INFO  18:12:21,467 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:12Z] INFO  18:12:21,467 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:12Z] INFO  18:12:21,642 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:12Z] INFO  18:12:21,667 IntervalUtils - Processing 228449 bp from intervals
[2016-04-15T01:12Z] WARN  18:12:21,692 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:12Z] INFO  18:12:21,783 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:12Z] INFO  18:12:21,879 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T01:12Z] INFO  18:12:21,889 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:12Z] INFO  18:12:21,920 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:12Z] INFO  18:12:21,921 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:12Z] INFO  18:12:21,922 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T01:12Z] INFO  18:12:21,923 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T01:12Z] INFO  18:12:21,958 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-15T01:12Z] INFO  18:12:21,978 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:12Z] INFO  18:12:21,979 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:12Z] INFO  18:12:22,116 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:12Z] INFO  18:12:22,318 ProgressMeter -            done    445208.0    19.0 s      43.0 s      100.0%    19.0 s       0.0 s
[2016-04-15T01:12Z] INFO  18:12:22,318 ProgressMeter - Total runtime 19.33 secs, 0.32 min, 0.01 hours
[2016-04-15T01:12Z] INFO  18:12:22,319 MicroScheduler - 15257 reads were filtered out during the traversal out of approximately 180815 total reads (8.44%)
[2016-04-15T01:12Z] INFO  18:12:22,319 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:12Z] INFO  18:12:22,319 MicroScheduler -   -> 284 reads (0.16% of total) failing BadMateFilter
[2016-04-15T01:12Z] INFO  18:12:22,320 MicroScheduler -   -> 14827 reads (8.20% of total) failing DuplicateReadFilter
[2016-04-15T01:12Z] INFO  18:12:22,320 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:12Z] INFO  18:12:22,320 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:12Z] INFO  18:12:22,320 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:12Z] INFO  18:12:22,321 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:12Z] INFO  18:12:22,321 MicroScheduler -   -> 146 reads (0.08% of total) failing UnmappedReadFilter
[2016-04-15T01:12Z] INFO  18:12:22,345 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:12Z] INFO  18:12:22,348 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:12Z] INFO  18:12:22,349 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:12Z] INFO  18:12:22,350 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:12Z] INFO  18:12:22,354 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/10/R14-18102_kapa-NGv3-PE100-NGv3-sort-10_0_15559243-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/10/R14-18102_kapa-NGv3-PE100-NGv3-10_0_15559243-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/10/tx/tmpoPx_PI/R14-18102_kapa-NGv3-PE100-NGv3-10_0_15559243.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:12Z] INFO  18:12:22,363 IntervalUtils - Processing 455246 bp from intervals
[2016-04-15T01:12Z] INFO  18:12:22,364 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:12Z] INFO  18:12:22,365 HelpFormatter - Date/Time: 2016/04/14 18:12:22
[2016-04-15T01:12Z] INFO  18:12:22,366 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:12Z] INFO  18:12:22,366 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:12Z] WARN  18:12:22,368 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:12Z] GATK: UnifiedGenotyper
[2016-04-15T01:12Z] INFO  18:12:22,446 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:12Z] INFO  18:12:22,568 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:12Z] INFO  18:12:22,572 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:12Z] INFO  18:12:22,573 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:12Z] INFO  18:12:22,574 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T01:12Z] INFO  18:12:22,574 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T01:12Z] INFO  18:12:22,649 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:12Z] INFO  18:12:22,650 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:12Z] INFO  18:12:22,824 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T01:12Z] INFO  18:12:22,853 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:12Z] INFO  18:12:22,949 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.10
[2016-04-15T01:12Z] INFO  18:12:23,422 IntervalUtils - Processing 145147 bp from intervals
[2016-04-15T01:12Z] WARN  18:12:23,427 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:12Z] INFO  18:12:23,523 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:12Z] INFO  18:12:23,631 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:12Z] INFO  18:12:23,631 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:12Z] INFO  18:12:23,633 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T01:12Z] INFO  18:12:23,634 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T01:12Z] INFO  18:12:23,675 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:12Z] INFO  18:12:23,676 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:12Z] INFO  18:12:23,776 ProgressMeter -            done    316474.0    15.0 s      48.0 s       99.9%    15.0 s       0.0 s
[2016-04-15T01:12Z] INFO  18:12:23,776 ProgressMeter - Total runtime 15.44 secs, 0.26 min, 0.00 hours
[2016-04-15T01:12Z] INFO  18:12:23,777 MicroScheduler - 13162 reads were filtered out during the traversal out of approximately 155781 total reads (8.45%)
[2016-04-15T01:12Z] INFO  18:12:23,777 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:12Z] INFO  18:12:23,777 MicroScheduler -   -> 266 reads (0.17% of total) failing BadMateFilter
[2016-04-15T01:12Z] INFO  18:12:23,778 MicroScheduler -   -> 12768 reads (8.20% of total) failing DuplicateReadFilter
[2016-04-15T01:12Z] INFO  18:12:23,778 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:12Z] INFO  18:12:23,778 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:12Z] INFO  18:12:23,778 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:12Z] INFO  18:12:23,779 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:12Z] INFO  18:12:23,779 MicroScheduler -   -> 128 reads (0.08% of total) failing UnmappedReadFilter
[2016-04-15T01:12Z] INFO  18:12:23,825 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:12Z] INFO  18:12:23,828 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:12Z] INFO  18:12:23,829 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:12Z] INFO  18:12:23,829 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:12Z] INFO  18:12:23,834 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/10/R14-18102_kapa-NGv3-PE100-NGv3-sort-10_31137459_46960129-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/10/R14-18102_kapa-NGv3-PE100-NGv3-10_31137459_46960129-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/10/tx/tmp_Ls_al/R14-18102_kapa-NGv3-PE100-NGv3-10_31137459_46960129.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:12Z] INFO  18:12:23,844 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:12Z] INFO  18:12:23,849 HelpFormatter - Date/Time: 2016/04/14 18:12:23
[2016-04-15T01:12Z] INFO  18:12:23,850 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:12Z] INFO  18:12:23,851 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:12Z] INFO  18:12:23,866 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:12Z] INFO  18:12:23,953 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:12Z] INFO  18:12:23,956 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:12Z] INFO  18:12:23,957 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:12Z] INFO  18:12:23,957 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:12Z] INFO  18:12:23,961 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/10/R14-18102_kapa-NGv3-PE100-NGv3-sort-10_15561288_31134502-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/10/R14-18102_kapa-NGv3-PE100-NGv3-10_15561288_31134502-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/10/tx/tmpgccAaa/R14-18102_kapa-NGv3-PE100-NGv3-10_15561288_31134502.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:12Z] INFO  18:12:23,979 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:12Z] INFO  18:12:23,980 HelpFormatter - Date/Time: 2016/04/14 18:12:23
[2016-04-15T01:12Z] INFO  18:12:23,981 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:12Z] INFO  18:12:23,981 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:12Z] INFO  18:12:24,081 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:12Z] GATK: UnifiedGenotyper
[2016-04-15T01:12Z] INFO  18:12:24,161 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:12Z] INFO  18:12:24,277 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T01:12Z] INFO  18:12:24,286 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:12Z] INFO  18:12:24,364 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-15T01:12Z] INFO  18:12:24,400 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T01:12Z] INFO  18:12:24,409 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:12Z] INFO  18:12:24,434 ProgressMeter -            done    186579.0    13.0 s      72.0 s       99.9%    13.0 s       0.0 s
[2016-04-15T01:12Z] INFO  18:12:24,435 ProgressMeter - Total runtime 13.58 secs, 0.23 min, 0.00 hours
[2016-04-15T01:12Z] INFO  18:12:24,436 MicroScheduler - 9191 reads were filtered out during the traversal out of approximately 109726 total reads (8.38%)
[2016-04-15T01:12Z] INFO  18:12:24,436 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:12Z] INFO  18:12:24,437 MicroScheduler -   -> 157 reads (0.14% of total) failing BadMateFilter
[2016-04-15T01:12Z] INFO  18:12:24,438 MicroScheduler -   -> 8951 reads (8.16% of total) failing DuplicateReadFilter
[2016-04-15T01:12Z] INFO  18:12:24,438 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:12Z] INFO  18:12:24,439 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:12Z] INFO  18:12:24,439 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:12Z] INFO  18:12:24,440 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:12Z] INFO  18:12:24,440 MicroScheduler -   -> 83 reads (0.08% of total) failing UnmappedReadFilter
[2016-04-15T01:12Z] INFO  18:12:24,517 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.11
[2016-04-15T01:12Z] INFO  18:12:24,877 IntervalUtils - Processing 156629 bp from intervals
[2016-04-15T01:12Z] INFO  18:12:24,901 IntervalUtils - Processing 103621 bp from intervals
[2016-04-15T01:12Z] WARN  18:12:24,907 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:12Z] WARN  18:12:24,914 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:12Z] INFO  18:12:25,005 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:12Z] INFO  18:12:25,036 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:12Z] INFO  18:12:25,083 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:12Z] INFO  18:12:25,084 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:12Z] INFO  18:12:25,085 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T01:12Z] INFO  18:12:25,086 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T01:12Z] INFO  18:12:25,103 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:12Z] INFO  18:12:25,104 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:12Z] INFO  18:12:25,105 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T01:12Z] INFO  18:12:25,106 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T01:12Z] INFO  18:12:25,154 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:12Z] INFO  18:12:25,159 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:12Z] INFO  18:12:25,160 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:12Z] INFO  18:12:25,165 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:12Z] INFO  18:12:25,205 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:12Z] INFO  18:12:25,300 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:12Z] INFO  18:12:25,303 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:12Z] INFO  18:12:25,304 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:12Z] INFO  18:12:25,304 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:12Z] INFO  18:12:25,309 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/10/R14-18102_kapa-NGv3-PE100-NGv3-sort-10_46960410_62493077-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/10/R14-18102_kapa-NGv3-PE100-NGv3-10_46960410_62493077-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/10/tx/tmpIGue8I/R14-18102_kapa-NGv3-PE100-NGv3-10_46960410_62493077.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:12Z] INFO  18:12:25,320 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:12Z] INFO  18:12:25,323 HelpFormatter - Date/Time: 2016/04/14 18:12:25
[2016-04-15T01:12Z] INFO  18:12:25,324 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:12Z] INFO  18:12:25,324 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:12Z] GATK: UnifiedGenotyper
[2016-04-15T01:12Z] INFO  18:12:25,546 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:12Z] INFO  18:12:25,760 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T01:12Z] INFO  18:12:25,772 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:12Z] INFO  18:12:25,843 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-15T01:12Z] INFO  18:12:26,040 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:12Z] INFO  18:12:26,354 IntervalUtils - Processing 143638 bp from intervals
[2016-04-15T01:12Z] WARN  18:12:26,370 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:12Z] INFO  18:12:26,478 ProgressMeter -            done    771215.0    27.0 s      35.0 s      100.0%    27.0 s       0.0 s
[2016-04-15T01:12Z] INFO  18:12:26,479 ProgressMeter - Total runtime 27.56 secs, 0.46 min, 0.01 hours
[2016-04-15T01:12Z] INFO  18:12:26,479 MicroScheduler - 24706 reads were filtered out during the traversal out of approximately 301713 total reads (8.19%)
[2016-04-15T01:12Z] INFO  18:12:26,480 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:12Z] INFO  18:12:26,481 MicroScheduler -   -> 463 reads (0.15% of total) failing BadMateFilter
[2016-04-15T01:12Z] INFO  18:12:26,481 MicroScheduler -   -> 24032 reads (7.97% of total) failing DuplicateReadFilter
[2016-04-15T01:12Z] INFO  18:12:26,482 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:12Z] INFO  18:12:26,483 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:12Z] INFO  18:12:26,483 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:12Z] INFO  18:12:26,484 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:12Z] INFO  18:12:26,485 MicroScheduler -   -> 211 reads (0.07% of total) failing UnmappedReadFilter
[2016-04-15T01:12Z] INFO  18:12:26,503 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:12Z] GATK: UnifiedGenotyper
[2016-04-15T01:12Z] INFO  18:12:26,608 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:12Z] INFO  18:12:26,610 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:12Z] INFO  18:12:26,610 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T01:12Z] INFO  18:12:26,621 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T01:12Z] INFO  18:12:26,700 ProgressMeter -            done   1463815.0    40.0 s      27.0 s      100.0%    40.0 s       0.0 s
[2016-04-15T01:12Z] INFO  18:12:26,703 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:12Z] INFO  18:12:26,704 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:12Z] INFO  18:12:26,700 ProgressMeter - Total runtime 40.77 secs, 0.68 min, 0.01 hours
[2016-04-15T01:12Z] INFO  18:12:26,700 MicroScheduler - 52546 reads were filtered out during the traversal out of approximately 634006 total reads (8.29%)
[2016-04-15T01:12Z] INFO  18:12:26,701 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:12Z] INFO  18:12:26,701 MicroScheduler -   -> 992 reads (0.16% of total) failing BadMateFilter
[2016-04-15T01:12Z] INFO  18:12:26,701 MicroScheduler -   -> 51016 reads (8.05% of total) failing DuplicateReadFilter
[2016-04-15T01:12Z] INFO  18:12:26,701 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:12Z] INFO  18:12:26,702 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:12Z] INFO  18:12:26,702 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:12Z] INFO  18:12:26,702 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:12Z] INFO  18:12:26,703 MicroScheduler -   -> 538 reads (0.08% of total) failing UnmappedReadFilter
[2016-04-15T01:12Z] INFO  18:12:27,317 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:12Z] INFO  18:12:27,320 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:12Z] INFO  18:12:27,321 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:12Z] INFO  18:12:27,321 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:12Z] INFO  18:12:27,326 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/10/R14-18102_kapa-NGv3-PE100-NGv3-sort-10_62539923_78084243-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/10/R14-18102_kapa-NGv3-PE100-NGv3-10_62539923_78084243-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/10/tx/tmpF_PZX6/R14-18102_kapa-NGv3-PE100-NGv3-10_62539923_78084243.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:12Z] INFO  18:12:27,342 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:12Z] INFO  18:12:27,343 HelpFormatter - Date/Time: 2016/04/14 18:12:27
[2016-04-15T01:12Z] INFO  18:12:27,343 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:12Z] INFO  18:12:27,344 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:12Z] INFO  18:12:27,531 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:12Z] INFO  18:12:27,774 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T01:12Z] INFO  18:12:27,784 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:12Z] INFO  18:12:27,884 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.10
[2016-04-15T01:12Z] INFO  18:12:28,016 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:12Z] INFO  18:12:28,278 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:12Z] GATK: UnifiedGenotyper
[2016-04-15T01:12Z] INFO  18:12:28,379 IntervalUtils - Processing 230109 bp from intervals
[2016-04-15T01:12Z] WARN  18:12:28,393 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:12Z] INFO  18:12:28,490 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:12Z] GATK: UnifiedGenotyper
[2016-04-15T01:12Z] INFO  18:12:28,607 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:12Z] INFO  18:12:28,607 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:12Z] INFO  18:12:28,607 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T01:12Z] INFO  18:12:28,608 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T01:12Z] INFO  18:12:28,696 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:12Z] INFO  18:12:28,697 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:12Z] INFO  18:12:28,726 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:12Z] INFO  18:12:28,729 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:12Z] INFO  18:12:28,730 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:12Z] INFO  18:12:28,730 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:12Z] INFO  18:12:28,735 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/10/R14-18102_kapa-NGv3-PE100-NGv3-sort-10_78316966_93841258-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/10/R14-18102_kapa-NGv3-PE100-NGv3-10_78316966_93841258-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/10/tx/tmpw0EfXE/R14-18102_kapa-NGv3-PE100-NGv3-10_78316966_93841258.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:12Z] INFO  18:12:28,745 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:12Z] INFO  18:12:28,746 HelpFormatter - Date/Time: 2016/04/14 18:12:28
[2016-04-15T01:12Z] INFO  18:12:28,746 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:12Z] INFO  18:12:28,747 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:12Z] INFO  18:12:28,961 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:12Z] INFO  18:12:29,196 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T01:12Z] INFO  18:12:29,208 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:12Z] INFO  18:12:29,317 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.11
[2016-04-15T01:12Z] INFO  18:12:29,649 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:12Z] INFO  18:12:29,652 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:12Z] INFO  18:12:29,653 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:12Z] INFO  18:12:29,653 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:12Z] INFO  18:12:29,658 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/10/R14-18102_kapa-NGv3-PE100-NGv3-sort-10_93851586_111625070-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/10/R14-18102_kapa-NGv3-PE100-NGv3-10_93851586_111625070-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/10/tx/tmpjiKaJV/R14-18102_kapa-NGv3-PE100-NGv3-10_93851586_111625070.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:12Z] INFO  18:12:29,681 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:12Z] INFO  18:12:29,682 HelpFormatter - Date/Time: 2016/04/14 18:12:29
[2016-04-15T01:12Z] INFO  18:12:29,683 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:12Z] INFO  18:12:29,683 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:12Z] INFO  18:12:29,835 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:12Z] INFO  18:12:29,910 IntervalUtils - Processing 148808 bp from intervals
[2016-04-15T01:12Z] WARN  18:12:29,915 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:12Z] INFO  18:12:30,035 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:12Z] INFO  18:12:30,097 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T01:12Z] INFO  18:12:30,107 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:12Z] INFO  18:12:30,137 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:12Z] INFO  18:12:30,138 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:12Z] INFO  18:12:30,139 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T01:12Z] INFO  18:12:30,140 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T01:12Z] INFO  18:12:30,201 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:12Z] INFO  18:12:30,212 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.10
[2016-04-15T01:12Z] INFO  18:12:30,213 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:12Z] INFO  18:12:30,607 IntervalUtils - Processing 335852 bp from intervals
[2016-04-15T01:12Z] WARN  18:12:30,613 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:12Z] INFO  18:12:30,702 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:12Z] INFO  18:12:30,867 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:12Z] INFO  18:12:30,868 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:12Z] INFO  18:12:30,869 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T01:12Z] INFO  18:12:30,870 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T01:12Z] INFO  18:12:30,913 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:12Z] INFO  18:12:30,914 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:12Z] INFO  18:12:31,421 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:12Z] INFO  18:12:31,424 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:12Z] INFO  18:12:31,425 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:12Z] INFO  18:12:31,425 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:12Z] INFO  18:12:31,429 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/10/R14-18102_kapa-NGv3-PE100-NGv3-sort-10_111628371_127265443-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/10/R14-18102_kapa-NGv3-PE100-NGv3-10_111628371_127265443-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/10/tx/tmpBtQscy/R14-18102_kapa-NGv3-PE100-NGv3-10_111628371_127265443.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:12Z] INFO  18:12:31,427 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:12Z] INFO  18:12:31,430 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:12Z] INFO  18:12:31,431 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:12Z] INFO  18:12:31,432 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:12Z] INFO  18:12:31,436 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/10/R14-18102_kapa-NGv3-PE100-NGv3-sort-10_127328721_135534747-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/10/R14-18102_kapa-NGv3-PE100-NGv3-10_127328721_135534747-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/10/tx/tmpuWHZ2j/R14-18102_kapa-NGv3-PE100-NGv3-10_127328721_135534747.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:12Z] INFO  18:12:31,441 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:12Z] INFO  18:12:31,442 HelpFormatter - Date/Time: 2016/04/14 18:12:31
[2016-04-15T01:12Z] INFO  18:12:31,443 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:12Z] INFO  18:12:31,443 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:12Z] INFO  18:12:31,448 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:12Z] INFO  18:12:31,450 HelpFormatter - Date/Time: 2016/04/14 18:12:31
[2016-04-15T01:12Z] INFO  18:12:31,450 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:12Z] INFO  18:12:31,451 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:12Z] INFO  18:12:31,625 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:12Z] INFO  18:12:31,648 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:12Z] INFO  18:12:31,912 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T01:12Z] INFO  18:12:31,933 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:12Z] INFO  18:12:32,020 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T01:12Z] INFO  18:12:32,008 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-15T01:12Z] INFO  18:12:32,037 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:12Z] INFO  18:12:32,130 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.09
[2016-04-15T01:12Z] INFO  18:12:32,488 IntervalUtils - Processing 210787 bp from intervals
[2016-04-15T01:12Z] WARN  18:12:32,504 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:12Z] INFO  18:12:32,580 IntervalUtils - Processing 102137 bp from intervals
[2016-04-15T01:12Z] WARN  18:12:32,585 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:12Z] INFO  18:12:32,624 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:12Z] INFO  18:12:32,652 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:12Z] INFO  18:12:32,707 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:12Z] INFO  18:12:32,708 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:12Z] INFO  18:12:32,709 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T01:12Z] INFO  18:12:32,710 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T01:12Z] INFO  18:12:32,725 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:12Z] INFO  18:12:32,726 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:12Z] INFO  18:12:32,727 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T01:12Z] INFO  18:12:32,728 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T01:12Z] INFO  18:12:32,752 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:12Z] INFO  18:12:32,752 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:12Z] INFO  18:12:32,779 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:12Z] INFO  18:12:32,780 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:12Z] INFO  18:12:35,224 ProgressMeter -            done   1313389.0    27.0 s      20.0 s      100.0%    27.0 s       0.0 s
[2016-04-15T01:12Z] INFO  18:12:35,230 ProgressMeter - Total runtime 27.31 secs, 0.46 min, 0.01 hours
[2016-04-15T01:12Z] INFO  18:12:35,232 MicroScheduler - 30121 reads were filtered out during the traversal out of approximately 343689 total reads (8.76%)
[2016-04-15T01:12Z] INFO  18:12:35,232 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:12Z] INFO  18:12:35,233 MicroScheduler -   -> 578 reads (0.17% of total) failing BadMateFilter
[2016-04-15T01:12Z] INFO  18:12:35,233 MicroScheduler -   -> 29132 reads (8.48% of total) failing DuplicateReadFilter
[2016-04-15T01:12Z] INFO  18:12:35,234 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:12Z] INFO  18:12:35,235 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:12Z] INFO  18:12:35,235 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:12Z] INFO  18:12:35,247 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:12Z] INFO  18:12:35,248 MicroScheduler -   -> 411 reads (0.12% of total) failing UnmappedReadFilter
[2016-04-15T01:12Z] INFO  18:12:35,436 ProgressMeter -            done    294057.0    17.0 s      58.0 s      100.0%    17.0 s       0.0 s
[2016-04-15T01:12Z] INFO  18:12:35,436 ProgressMeter - Total runtime 17.17 secs, 0.29 min, 0.00 hours
[2016-04-15T01:12Z] INFO  18:12:35,437 MicroScheduler - 13169 reads were filtered out during the traversal out of approximately 176151 total reads (7.48%)
[2016-04-15T01:12Z] INFO  18:12:35,437 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:12Z] INFO  18:12:35,437 MicroScheduler -   -> 261 reads (0.15% of total) failing BadMateFilter
[2016-04-15T01:12Z] INFO  18:12:35,438 MicroScheduler -   -> 12790 reads (7.26% of total) failing DuplicateReadFilter
[2016-04-15T01:12Z] INFO  18:12:35,438 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:12Z] INFO  18:12:35,438 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:12Z] INFO  18:12:35,438 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:12Z] INFO  18:12:35,439 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:12Z] INFO  18:12:35,439 MicroScheduler -   -> 118 reads (0.07% of total) failing UnmappedReadFilter
[2016-04-15T01:12Z] INFO  18:12:36,568 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:12Z] INFO  18:12:36,769 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:12Z] GATK: UnifiedGenotyper
[2016-04-15T01:12Z] GATK: UnifiedGenotyper
[2016-04-15T01:12Z] INFO  18:12:39,370 ProgressMeter -            done    272797.0    14.0 s      52.0 s       99.9%    14.0 s       0.0 s
[2016-04-15T01:12Z] INFO  18:12:39,371 ProgressMeter - Total runtime 14.29 secs, 0.24 min, 0.00 hours
[2016-04-15T01:12Z] INFO  18:12:39,371 MicroScheduler - 11032 reads were filtered out during the traversal out of approximately 140807 total reads (7.83%)
[2016-04-15T01:12Z] INFO  18:12:39,371 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:12Z] INFO  18:12:39,372 MicroScheduler -   -> 202 reads (0.14% of total) failing BadMateFilter
[2016-04-15T01:12Z] INFO  18:12:39,372 MicroScheduler -   -> 10701 reads (7.60% of total) failing DuplicateReadFilter
[2016-04-15T01:12Z] INFO  18:12:39,372 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:12Z] INFO  18:12:39,373 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:12Z] INFO  18:12:39,373 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:12Z] INFO  18:12:39,373 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:12Z] INFO  18:12:39,374 MicroScheduler -   -> 129 reads (0.09% of total) failing UnmappedReadFilter
[2016-04-15T01:12Z] INFO  18:12:39,887 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:12Z] INFO  18:12:39,889 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:12Z] INFO  18:12:39,889 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:12Z] INFO  18:12:39,889 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:12Z] INFO  18:12:39,893 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/11/R14-18102_kapa-NGv3-PE100-NGv3-sort-11_16007749_31531554-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/11/R14-18102_kapa-NGv3-PE100-NGv3-11_16007749_31531554-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/11/tx/tmpNPwJsg/R14-18102_kapa-NGv3-PE100-NGv3-11_16007749_31531554.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:12Z] INFO  18:12:39,915 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:12Z] INFO  18:12:39,916 HelpFormatter - Date/Time: 2016/04/14 18:12:39
[2016-04-15T01:12Z] INFO  18:12:39,917 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:12Z] INFO  18:12:39,917 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:12Z] INFO  18:12:39,922 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:12Z] INFO  18:12:39,925 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:12Z] INFO  18:12:39,926 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:12Z] INFO  18:12:39,926 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:12Z] INFO  18:12:39,931 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/11/R14-18102_kapa-NGv3-PE100-NGv3-sort-11_0_15994658-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/11/R14-18102_kapa-NGv3-PE100-NGv3-11_0_15994658-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/11/tx/tmpICPd4h/R14-18102_kapa-NGv3-PE100-NGv3-11_0_15994658.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:12Z] INFO  18:12:39,941 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:12Z] INFO  18:12:39,941 HelpFormatter - Date/Time: 2016/04/14 18:12:39
[2016-04-15T01:12Z] INFO  18:12:39,941 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:12Z] INFO  18:12:39,941 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:12Z] INFO  18:12:40,067 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:12Z] INFO  18:12:40,148 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:12Z] INFO  18:12:40,300 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T01:12Z] INFO  18:12:40,312 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T01:12Z] INFO  18:12:40,320 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:12Z] INFO  18:12:40,321 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:12Z] INFO  18:12:40,393 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-15T01:12Z] INFO  18:12:40,417 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.10
[2016-04-15T01:12Z] INFO  18:12:40,698 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:12Z] INFO  18:12:40,793 IntervalUtils - Processing 144906 bp from intervals
[2016-04-15T01:12Z] WARN  18:12:40,799 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:12Z] INFO  18:12:40,860 IntervalUtils - Processing 438345 bp from intervals
[2016-04-15T01:12Z] WARN  18:12:40,867 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:12Z] INFO  18:12:40,920 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:12Z] GATK: UnifiedGenotyper
[2016-04-15T01:12Z] INFO  18:12:40,966 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:12Z] INFO  18:12:40,985 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:12Z] INFO  18:12:40,987 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:12Z] INFO  18:12:40,988 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T01:12Z] INFO  18:12:40,989 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T01:12Z] INFO  18:12:41,039 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:12Z] INFO  18:12:41,040 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:12Z] INFO  18:12:41,130 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:12Z] INFO  18:12:41,132 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:12Z] INFO  18:12:41,133 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T01:12Z] INFO  18:12:41,134 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T01:12Z] INFO  18:12:41,185 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:12Z] INFO  18:12:41,186 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:12Z] INFO  18:12:41,990 ProgressMeter -            done    477875.0    22.0 s      47.0 s      100.0%    22.0 s       0.0 s
[2016-04-15T01:12Z] INFO  18:12:41,991 ProgressMeter - Total runtime 22.76 secs, 0.38 min, 0.01 hours
[2016-04-15T01:12Z] INFO  18:12:41,992 MicroScheduler - 21934 reads were filtered out during the traversal out of approximately 265446 total reads (8.26%)
[2016-04-15T01:12Z] INFO  18:12:41,993 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:12Z] INFO  18:12:41,993 MicroScheduler -   -> 392 reads (0.15% of total) failing BadMateFilter
[2016-04-15T01:12Z] INFO  18:12:41,994 MicroScheduler -   -> 21313 reads (8.03% of total) failing DuplicateReadFilter
[2016-04-15T01:12Z] INFO  18:12:41,994 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:12Z] INFO  18:12:41,994 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:12Z] INFO  18:12:41,995 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:12Z] INFO  18:12:41,995 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:12Z] INFO  18:12:41,995 MicroScheduler -   -> 229 reads (0.09% of total) failing UnmappedReadFilter
[2016-04-15T01:12Z] INFO  18:12:42,721 ProgressMeter -            done    465734.0    19.0 s      40.0 s       99.9%    19.0 s       0.0 s
[2016-04-15T01:12Z] INFO  18:12:42,722 ProgressMeter - Total runtime 19.09 secs, 0.32 min, 0.01 hours
[2016-04-15T01:12Z] INFO  18:12:42,723 MicroScheduler - 15957 reads were filtered out during the traversal out of approximately 191260 total reads (8.34%)
[2016-04-15T01:12Z] INFO  18:12:42,724 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:12Z] INFO  18:12:42,725 MicroScheduler -   -> 329 reads (0.17% of total) failing BadMateFilter
[2016-04-15T01:12Z] INFO  18:12:42,726 MicroScheduler -   -> 15474 reads (8.09% of total) failing DuplicateReadFilter
[2016-04-15T01:12Z] INFO  18:12:42,726 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:12Z] INFO  18:12:42,727 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:12Z] INFO  18:12:42,728 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:12Z] INFO  18:12:42,728 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:12Z] INFO  18:12:42,729 MicroScheduler -   -> 154 reads (0.08% of total) failing UnmappedReadFilter
[2016-04-15T01:12Z] INFO  18:12:43,510 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:12Z] INFO  18:12:43,559 ProgressMeter -            done    539922.0    22.0 s      41.0 s      100.0%    22.0 s       0.0 s
[2016-04-15T01:12Z] INFO  18:12:43,561 ProgressMeter - Total runtime 22.19 secs, 0.37 min, 0.01 hours
[2016-04-15T01:12Z] INFO  18:12:43,562 MicroScheduler - 21333 reads were filtered out during the traversal out of approximately 254671 total reads (8.38%)
[2016-04-15T01:12Z] INFO  18:12:43,563 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:12Z] INFO  18:12:43,563 MicroScheduler -   -> 373 reads (0.15% of total) failing BadMateFilter
[2016-04-15T01:12Z] INFO  18:12:43,563 MicroScheduler -   -> 20750 reads (8.15% of total) failing DuplicateReadFilter
[2016-04-15T01:12Z] INFO  18:12:43,564 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:12Z] INFO  18:12:43,564 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:12Z] INFO  18:12:43,564 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:12Z] INFO  18:12:43,564 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:12Z] INFO  18:12:43,565 MicroScheduler -   -> 210 reads (0.08% of total) failing UnmappedReadFilter
[2016-04-15T01:12Z] INFO  18:12:43,698 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:12Z] INFO  18:12:43,702 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:12Z] INFO  18:12:43,703 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:12Z] INFO  18:12:43,704 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:12Z] INFO  18:12:43,709 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/11/R14-18102_kapa-NGv3-PE100-NGv3-sort-11_31541602_47074069-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/11/R14-18102_kapa-NGv3-PE100-NGv3-11_31541602_47074069-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/11/tx/tmpdiSXbu/R14-18102_kapa-NGv3-PE100-NGv3-11_31541602_47074069.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:12Z] INFO  18:12:43,722 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:12Z] INFO  18:12:43,726 HelpFormatter - Date/Time: 2016/04/14 18:12:43
[2016-04-15T01:12Z] INFO  18:12:43,727 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:12Z] INFO  18:12:43,728 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:12Z] GATK: UnifiedGenotyper
[2016-04-15T01:12Z] INFO  18:12:43,916 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:12Z] INFO  18:12:44,090 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T01:12Z] INFO  18:12:44,100 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:12Z] INFO  18:12:44,180 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-15T01:12Z] INFO  18:12:44,203 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:12Z] INFO  18:12:44,551 IntervalUtils - Processing 150047 bp from intervals
[2016-04-15T01:12Z] WARN  18:12:44,567 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:12Z] GATK: UnifiedGenotyper
[2016-04-15T01:12Z] INFO  18:12:44,652 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:12Z] INFO  18:12:44,751 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:12Z] INFO  18:12:44,752 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:12Z] INFO  18:12:44,760 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T01:12Z] INFO  18:12:44,761 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T01:12Z] INFO  18:12:44,812 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:12Z] INFO  18:12:44,812 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:12Z] INFO  18:12:44,825 ProgressMeter -            done    421173.0    19.0 s      46.0 s      100.0%    19.0 s       0.0 s
[2016-04-15T01:12Z] INFO  18:12:44,826 ProgressMeter - Total runtime 19.72 secs, 0.33 min, 0.01 hours
[2016-04-15T01:12Z] INFO  18:12:44,827 MicroScheduler - 14554 reads were filtered out during the traversal out of approximately 173940 total reads (8.37%)
[2016-04-15T01:12Z] INFO  18:12:44,827 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:12Z] INFO  18:12:44,828 MicroScheduler -   -> 265 reads (0.15% of total) failing BadMateFilter
[2016-04-15T01:12Z] INFO  18:12:44,829 MicroScheduler -   -> 14161 reads (8.14% of total) failing DuplicateReadFilter
[2016-04-15T01:12Z] INFO  18:12:44,829 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:12Z] INFO  18:12:44,830 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:12Z] INFO  18:12:44,830 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:12Z] INFO  18:12:44,831 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:12Z] INFO  18:12:44,831 MicroScheduler -   -> 128 reads (0.07% of total) failing UnmappedReadFilter
[2016-04-15T01:12Z] INFO  18:12:44,842 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:12Z] GATK: UnifiedGenotyper
[2016-04-15T01:12Z] INFO  18:12:45,903 ProgressMeter -            done    946777.0    28.0 s      29.0 s      100.0%    28.0 s       0.0 s
[2016-04-15T01:12Z] INFO  18:12:45,903 ProgressMeter - Total runtime 28.30 secs, 0.47 min, 0.01 hours
[2016-04-15T01:12Z] INFO  18:12:45,904 MicroScheduler - 29516 reads were filtered out during the traversal out of approximately 396866 total reads (7.44%)
[2016-04-15T01:12Z] INFO  18:12:45,904 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:12Z] INFO  18:12:45,905 MicroScheduler -   -> 650 reads (0.16% of total) failing BadMateFilter
[2016-04-15T01:12Z] INFO  18:12:45,905 MicroScheduler -   -> 28508 reads (7.18% of total) failing DuplicateReadFilter
[2016-04-15T01:12Z] INFO  18:12:45,905 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:12Z] INFO  18:12:45,906 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:12Z] INFO  18:12:45,906 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:12Z] INFO  18:12:45,906 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:12Z] INFO  18:12:45,906 MicroScheduler -   -> 358 reads (0.09% of total) failing UnmappedReadFilter
[2016-04-15T01:12Z] INFO  18:12:46,388 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:12Z] INFO  18:12:46,729 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:12Z] INFO  18:12:46,732 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:12Z] INFO  18:12:46,732 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:12Z] INFO  18:12:46,733 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:12Z] INFO  18:12:46,737 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/11/R14-18102_kapa-NGv3-PE100-NGv3-sort-11_47158866_62678572-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/11/R14-18102_kapa-NGv3-PE100-NGv3-11_47158866_62678572-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/11/tx/tmp8PkTMa/R14-18102_kapa-NGv3-PE100-NGv3-11_47158866_62678572.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:12Z] INFO  18:12:46,750 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:12Z] INFO  18:12:46,759 HelpFormatter - Date/Time: 2016/04/14 18:12:46
[2016-04-15T01:12Z] INFO  18:12:46,760 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:12Z] GATK: UnifiedGenotyper
[2016-04-15T01:12Z] INFO  18:12:46,760 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:12Z] INFO  18:12:46,929 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:12Z] INFO  18:12:47,181 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T01:12Z] INFO  18:12:47,190 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:12Z] INFO  18:12:47,259 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-15T01:12Z] INFO  18:12:47,408 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:12Z] INFO  18:12:47,469 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:12Z] INFO  18:12:47,476 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:12Z] INFO  18:12:47,477 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:12Z] INFO  18:12:47,477 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:12Z] INFO  18:12:47,482 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/11/R14-18102_kapa-NGv3-PE100-NGv3-sort-11_62744265_78270665-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/11/R14-18102_kapa-NGv3-PE100-NGv3-11_62744265_78270665-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/11/tx/tmpibgeKK/R14-18102_kapa-NGv3-PE100-NGv3-11_62744265_78270665.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:12Z] INFO  18:12:47,494 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:12Z] INFO  18:12:47,494 HelpFormatter - Date/Time: 2016/04/14 18:12:47
[2016-04-15T01:12Z] INFO  18:12:47,494 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:12Z] INFO  18:12:47,494 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:12Z] INFO  18:12:47,653 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:12Z] INFO  18:12:47,732 IntervalUtils - Processing 330540 bp from intervals
[2016-04-15T01:12Z] GATK: UnifiedGenotyper
[2016-04-15T01:12Z] WARN  18:12:47,737 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:12Z] INFO  18:12:47,807 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:12Z] INFO  18:12:47,819 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T01:12Z] INFO  18:12:47,830 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:12Z] INFO  18:12:47,894 ProgressMeter -            done    678904.0    25.0 s      38.0 s      100.0%    25.0 s       0.0 s
[2016-04-15T01:12Z] INFO  18:12:47,895 ProgressMeter - Total runtime 25.97 secs, 0.43 min, 0.01 hours
[2016-04-15T01:12Z] INFO  18:12:47,895 MicroScheduler - 25578 reads were filtered out during the traversal out of approximately 306061 total reads (8.36%)
[2016-04-15T01:12Z] INFO  18:12:47,896 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:12Z] INFO  18:12:47,896 MicroScheduler -   -> 446 reads (0.15% of total) failing BadMateFilter
[2016-04-15T01:12Z] INFO  18:12:47,896 MicroScheduler -   -> 24868 reads (8.13% of total) failing DuplicateReadFilter
[2016-04-15T01:12Z] INFO  18:12:47,897 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:12Z] INFO  18:12:47,897 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:12Z] INFO  18:12:47,897 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:12Z] INFO  18:12:47,899 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:12Z] INFO  18:12:47,899 MicroScheduler -   -> 264 reads (0.09% of total) failing UnmappedReadFilter
[2016-04-15T01:12Z] INFO  18:12:47,915 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-15T01:12Z] INFO  18:12:47,919 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:12Z] INFO  18:12:47,921 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:12Z] INFO  18:12:47,921 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T01:12Z] INFO  18:12:47,922 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T01:12Z] INFO  18:12:47,959 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:12Z] INFO  18:12:47,963 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:12Z] INFO  18:12:47,963 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:12Z] INFO  18:12:47,964 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:12Z] INFO  18:12:47,968 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/11/R14-18102_kapa-NGv3-PE100-NGv3-sort-11_78277177_93796886-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/11/R14-18102_kapa-NGv3-PE100-NGv3-11_78277177_93796886-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/11/tx/tmp1I4gU9/R14-18102_kapa-NGv3-PE100-NGv3-11_78277177_93796886.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:12Z] INFO  18:12:47,978 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:12Z] INFO  18:12:47,979 HelpFormatter - Date/Time: 2016/04/14 18:12:47
[2016-04-15T01:12Z] INFO  18:12:47,979 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:12Z] INFO  18:12:47,980 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:12Z] INFO  18:12:47,982 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:12Z] INFO  18:12:47,983 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:12Z] INFO  18:12:48,060 ProgressMeter -            done    360383.0    15.0 s      42.0 s       99.9%    15.0 s       0.0 s
[2016-04-15T01:12Z] INFO  18:12:48,061 ProgressMeter - Total runtime 15.35 secs, 0.26 min, 0.00 hours
[2016-04-15T01:12Z] INFO  18:12:48,061 MicroScheduler - 12826 reads were filtered out during the traversal out of approximately 149691 total reads (8.57%)
[2016-04-15T01:12Z] INFO  18:12:48,062 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:12Z] INFO  18:12:48,062 MicroScheduler -   -> 277 reads (0.19% of total) failing BadMateFilter
[2016-04-15T01:12Z] INFO  18:12:48,062 MicroScheduler -   -> 12442 reads (8.31% of total) failing DuplicateReadFilter
[2016-04-15T01:12Z] INFO  18:12:48,062 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:12Z] INFO  18:12:48,063 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:12Z] INFO  18:12:48,063 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:12Z] INFO  18:12:48,063 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:12Z] INFO  18:12:48,063 MicroScheduler -   -> 107 reads (0.07% of total) failing UnmappedReadFilter
[2016-04-15T01:12Z] INFO  18:12:48,132 ProgressMeter -            done    405882.0    21.0 s      53.0 s      100.0%    21.0 s       0.0 s
[2016-04-15T01:12Z] INFO  18:12:48,132 ProgressMeter - Total runtime 21.52 secs, 0.36 min, 0.01 hours
[2016-04-15T01:12Z] INFO  18:12:48,132 MicroScheduler - 19191 reads were filtered out during the traversal out of approximately 247498 total reads (7.75%)
[2016-04-15T01:12Z] INFO  18:12:48,133 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:12Z] INFO  18:12:48,133 MicroScheduler -   -> 402 reads (0.16% of total) failing BadMateFilter
[2016-04-15T01:12Z] INFO  18:12:48,133 MicroScheduler -   -> 18591 reads (7.51% of total) failing DuplicateReadFilter
[2016-04-15T01:12Z] INFO  18:12:48,133 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:12Z] INFO  18:12:48,134 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:12Z] INFO  18:12:48,134 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:12Z] INFO  18:12:48,134 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:12Z] INFO  18:12:48,134 MicroScheduler -   -> 198 reads (0.08% of total) failing UnmappedReadFilter
[2016-04-15T01:12Z] INFO  18:12:48,203 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:12Z] INFO  18:12:48,441 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T01:12Z] INFO  18:12:48,461 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:12Z] INFO  18:12:48,534 IntervalUtils - Processing 515206 bp from intervals
[2016-04-15T01:12Z] WARN  18:12:48,541 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:12Z] INFO  18:12:48,562 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.10
[2016-04-15T01:12Z] INFO  18:12:48,637 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:12Z] INFO  18:12:48,666 ProgressMeter -            done    459685.0    18.0 s      40.0 s       99.9%    18.0 s       0.0 s
[2016-04-15T01:12Z] INFO  18:12:48,666 ProgressMeter - Total runtime 18.53 secs, 0.31 min, 0.01 hours
[2016-04-15T01:12Z] INFO  18:12:48,666 MicroScheduler - 16090 reads were filtered out during the traversal out of approximately 196998 total reads (8.17%)
[2016-04-15T01:12Z] INFO  18:12:48,667 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:12Z] INFO  18:12:48,667 MicroScheduler -   -> 309 reads (0.16% of total) failing BadMateFilter
[2016-04-15T01:12Z] INFO  18:12:48,667 MicroScheduler -   -> 15635 reads (7.94% of total) failing DuplicateReadFilter
[2016-04-15T01:12Z] INFO  18:12:48,667 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:12Z] INFO  18:12:48,668 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:12Z] INFO  18:12:48,668 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:12Z] INFO  18:12:48,668 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:12Z] INFO  18:12:48,668 MicroScheduler -   -> 146 reads (0.07% of total) failing UnmappedReadFilter
[2016-04-15T01:12Z] INFO  18:12:48,740 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:12Z] INFO  18:12:48,742 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:12Z] INFO  18:12:48,742 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T01:12Z] INFO  18:12:48,743 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T01:12Z] INFO  18:12:48,783 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:12Z] INFO  18:12:48,784 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:12Z] INFO  18:12:49,101 IntervalUtils - Processing 119993 bp from intervals
[2016-04-15T01:12Z] WARN  18:12:49,114 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:12Z] INFO  18:12:49,210 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:12Z] INFO  18:12:49,270 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:12Z] INFO  18:12:49,271 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:12Z] INFO  18:12:49,271 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T01:12Z] INFO  18:12:49,272 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T01:12Z] INFO  18:12:49,308 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:12Z] INFO  18:12:49,315 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:12Z] INFO  18:12:49,316 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:12Z] INFO  18:12:49,551 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:12Z] GATK: UnifiedGenotyper
[2016-04-15T01:12Z] INFO  18:12:49,627 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:12Z] INFO  18:12:49,672 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:12Z] INFO  18:12:49,675 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:12Z] INFO  18:12:49,676 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:12Z] INFO  18:12:49,676 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:12Z] INFO  18:12:49,681 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/11/R14-18102_kapa-NGv3-PE100-NGv3-sort-11_93797496_109964158-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/11/R14-18102_kapa-NGv3-PE100-NGv3-11_93797496_109964158-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/11/tx/tmpT1VQpf/R14-18102_kapa-NGv3-PE100-NGv3-11_93797496_109964158.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:12Z] INFO  18:12:49,695 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:12Z] INFO  18:12:49,695 HelpFormatter - Date/Time: 2016/04/14 18:12:49
[2016-04-15T01:12Z] INFO  18:12:49,695 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:12Z] INFO  18:12:49,696 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:12Z] INFO  18:12:49,957 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:12Z] GATK: UnifiedGenotyper
[2016-04-15T01:12Z] GATK: UnifiedGenotyper
[2016-04-15T01:12Z] INFO  18:12:49,987 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:12Z] INFO  18:12:50,220 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T01:12Z] INFO  18:12:50,248 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:12Z] INFO  18:12:50,346 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.09
[2016-04-15T01:12Z] GATK: UnifiedGenotyper
[2016-04-15T01:12Z] INFO  18:12:50,664 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:12Z] INFO  18:12:50,668 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:12Z] INFO  18:12:50,668 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:12Z] INFO  18:12:50,668 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:12Z] INFO  18:12:50,674 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/11/R14-18102_kapa-NGv3-PE100-NGv3-sort-11_110001730_125514538-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/11/R14-18102_kapa-NGv3-PE100-NGv3-11_110001730_125514538-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/11/tx/tmpPe89fS/R14-18102_kapa-NGv3-PE100-NGv3-11_110001730_125514538.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:12Z] INFO  18:12:50,687 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:12Z] INFO  18:12:50,688 HelpFormatter - Date/Time: 2016/04/14 18:12:50
[2016-04-15T01:12Z] INFO  18:12:50,689 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:12Z] INFO  18:12:50,689 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:12Z] INFO  18:12:50,891 IntervalUtils - Processing 148585 bp from intervals
[2016-04-15T01:12Z] WARN  18:12:50,896 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:12Z] INFO  18:12:50,920 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:12Z] INFO  18:12:50,987 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:12Z] INFO  18:12:51,091 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:12Z] INFO  18:12:51,092 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:12Z] INFO  18:12:51,093 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T01:12Z] INFO  18:12:51,094 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T01:12Z] INFO  18:12:51,184 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:12Z] INFO  18:12:51,184 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:12Z] INFO  18:12:51,195 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T01:12Z] INFO  18:12:51,205 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:12Z] INFO  18:12:51,321 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.12
[2016-04-15T01:12Z] INFO  18:12:51,836 IntervalUtils - Processing 318135 bp from intervals
[2016-04-15T01:12Z] WARN  18:12:51,841 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:12Z] INFO  18:12:51,948 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:12Z] INFO  18:12:52,088 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:12Z] INFO  18:12:52,100 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:12Z] INFO  18:12:52,101 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T01:12Z] INFO  18:12:52,102 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T01:12Z] INFO  18:12:52,178 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:12Z] INFO  18:12:52,189 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:12Z] INFO  18:12:52,578 ProgressMeter -     9:136279885   1236392.0    30.0 s      24.0 s       54.3%    55.0 s      25.0 s
[2016-04-15T01:12Z] INFO  18:12:52,627 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:12Z] INFO  18:12:52,630 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:12Z] INFO  18:12:52,631 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:12Z] INFO  18:12:52,631 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:12Z] INFO  18:12:52,636 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/11/R14-18102_kapa-NGv3-PE100-NGv3-sort-11_125523640_135006516-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/11/R14-18102_kapa-NGv3-PE100-NGv3-11_125523640_135006516-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/11/tx/tmpARB8Mb/R14-18102_kapa-NGv3-PE100-NGv3-11_125523640_135006516.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:12Z] INFO  18:12:52,673 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:12Z] INFO  18:12:52,673 HelpFormatter - Date/Time: 2016/04/14 18:12:52
[2016-04-15T01:12Z] INFO  18:12:52,673 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:12Z] INFO  18:12:52,674 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:12Z] INFO  18:12:52,902 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:12Z] INFO  18:12:53,149 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T01:12Z] INFO  18:12:53,176 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:12Z] INFO  18:12:53,207 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:12Z] INFO  18:12:53,211 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:12Z] INFO  18:12:53,211 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:12Z] INFO  18:12:53,212 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:12Z] INFO  18:12:53,217 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/12/R14-18102_kapa-NGv3-PE100-NGv3-sort-12_0_15637181-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/12/R14-18102_kapa-NGv3-PE100-NGv3-12_0_15637181-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/12/tx/tmpa166TQ/R14-18102_kapa-NGv3-PE100-NGv3-12_0_15637181.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:12Z] INFO  18:12:53,235 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:12Z] INFO  18:12:53,236 HelpFormatter - Date/Time: 2016/04/14 18:12:53
[2016-04-15T01:12Z] INFO  18:12:53,237 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:12Z] INFO  18:12:53,237 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:12Z] INFO  18:12:53,262 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.09
[2016-04-15T01:12Z] INFO  18:12:53,302 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:12Z] INFO  18:12:53,305 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:12Z] INFO  18:12:53,306 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:12Z] INFO  18:12:53,306 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:12Z] INFO  18:12:53,311 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/12/R14-18102_kapa-NGv3-PE100-NGv3-sort-12_15650178_31231471-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/12/R14-18102_kapa-NGv3-PE100-NGv3-12_15650178_31231471-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/12/tx/tmpmD_hrI/R14-18102_kapa-NGv3-PE100-NGv3-12_15650178_31231471.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:12Z] INFO  18:12:53,332 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:12Z] INFO  18:12:53,333 HelpFormatter - Date/Time: 2016/04/14 18:12:53
[2016-04-15T01:12Z] INFO  18:12:53,333 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:12Z] INFO  18:12:53,334 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:12Z] INFO  18:12:53,375 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:12Z] INFO  18:12:53,378 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:12Z] INFO  18:12:53,378 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:12Z] INFO  18:12:53,379 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:12Z] INFO  18:12:53,383 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/12/R14-18102_kapa-NGv3-PE100-NGv3-sort-12_31236746_46754992-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/12/R14-18102_kapa-NGv3-PE100-NGv3-12_31236746_46754992-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/12/tx/tmp76nVnu/R14-18102_kapa-NGv3-PE100-NGv3-12_31236746_46754992.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:12Z] INFO  18:12:53,410 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:12Z] INFO  18:12:53,425 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:12Z] INFO  18:12:53,433 HelpFormatter - Date/Time: 2016/04/14 18:12:53
[2016-04-15T01:12Z] INFO  18:12:53,433 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:12Z] INFO  18:12:53,434 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:12Z] INFO  18:12:53,488 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:12Z] INFO  18:12:53,613 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:12Z] INFO  18:12:53,671 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T01:12Z] INFO  18:12:53,680 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:12Z] INFO  18:12:53,741 IntervalUtils - Processing 106404 bp from intervals
[2016-04-15T01:12Z] WARN  18:12:53,745 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:12Z] INFO  18:12:53,759 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T01:12Z] INFO  18:12:53,768 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:12Z] INFO  18:12:53,772 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.09
[2016-04-15T01:12Z] INFO  18:12:53,839 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:12Z] INFO  18:12:53,882 ProgressMeter -            done    818570.0    25.0 s      30.0 s      100.0%    25.0 s       0.0 s
[2016-04-15T01:12Z] INFO  18:12:53,883 ProgressMeter - Total runtime 25.28 secs, 0.42 min, 0.01 hours
[2016-04-15T01:12Z] INFO  18:12:53,883 MicroScheduler - 26103 reads were filtered out during the traversal out of approximately 311352 total reads (8.38%)
[2016-04-15T01:12Z] INFO  18:12:53,883 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:12Z] INFO  18:12:53,884 MicroScheduler -   -> 460 reads (0.15% of total) failing BadMateFilter
[2016-04-15T01:12Z] INFO  18:12:53,884 MicroScheduler -   -> 25385 reads (8.15% of total) failing DuplicateReadFilter
[2016-04-15T01:12Z] INFO  18:12:53,884 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:12Z] INFO  18:12:53,879 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.11
[2016-04-15T01:12Z] INFO  18:12:53,884 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:12Z] INFO  18:12:53,885 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:12Z] INFO  18:12:53,885 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:12Z] INFO  18:12:53,885 MicroScheduler -   -> 258 reads (0.08% of total) failing UnmappedReadFilter
[2016-04-15T01:12Z] INFO  18:12:53,911 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T01:12Z] INFO  18:12:53,930 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:12Z] INFO  18:12:53,937 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:12Z] INFO  18:12:53,938 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:12Z] INFO  18:12:53,938 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T01:12Z] INFO  18:12:53,939 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T01:12Z] INFO  18:12:53,985 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:12Z] INFO  18:12:53,986 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:12Z] INFO  18:12:54,011 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-15T01:12Z] INFO  18:12:54,307 IntervalUtils - Processing 134686 bp from intervals
[2016-04-15T01:12Z] WARN  18:12:54,313 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:12Z] INFO  18:12:54,355 IntervalUtils - Processing 329920 bp from intervals
[2016-04-15T01:12Z] WARN  18:12:54,362 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:12Z] INFO  18:12:54,431 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:12Z] INFO  18:12:54,431 IntervalUtils - Processing 136917 bp from intervals
[2016-04-15T01:12Z] WARN  18:12:54,436 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:12Z] INFO  18:12:54,486 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:12Z] INFO  18:12:54,487 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:12Z] INFO  18:12:54,488 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T01:12Z] INFO  18:12:54,489 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T01:12Z] INFO  18:12:54,500 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:12Z] INFO  18:12:54,531 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:12Z] INFO  18:12:54,532 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:12Z] INFO  18:12:54,560 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:12Z] INFO  18:12:54,632 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:12Z] INFO  18:12:54,633 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:12Z] INFO  18:12:54,634 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T01:12Z] INFO  18:12:54,634 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T01:12Z] INFO  18:12:54,660 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:12Z] INFO  18:12:54,661 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:12Z] INFO  18:12:54,661 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T01:12Z] INFO  18:12:54,662 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T01:12Z] INFO  18:12:54,682 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:12Z] INFO  18:12:54,683 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:12Z] INFO  18:12:54,703 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:12Z] INFO  18:12:54,704 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:12Z] INFO  18:12:55,251 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:12Z] GATK: UnifiedGenotyper
[2016-04-15T01:12Z] INFO  18:12:56,584 ProgressMeter -            done    665309.0    23.0 s      35.0 s      100.0%    23.0 s       0.0 s
[2016-04-15T01:12Z] INFO  18:12:56,585 ProgressMeter - Total runtime 23.86 secs, 0.40 min, 0.01 hours
[2016-04-15T01:12Z] INFO  18:12:56,585 MicroScheduler - 22280 reads were filtered out during the traversal out of approximately 267019 total reads (8.34%)
[2016-04-15T01:12Z] INFO  18:12:56,586 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:12Z] INFO  18:12:56,586 MicroScheduler -   -> 402 reads (0.15% of total) failing BadMateFilter
[2016-04-15T01:12Z] INFO  18:12:56,586 MicroScheduler -   -> 21663 reads (8.11% of total) failing DuplicateReadFilter
[2016-04-15T01:12Z] INFO  18:12:56,586 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:12Z] INFO  18:12:56,587 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:12Z] INFO  18:12:56,587 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:12Z] INFO  18:12:56,587 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:12Z] INFO  18:12:56,587 MicroScheduler -   -> 215 reads (0.08% of total) failing UnmappedReadFilter
[2016-04-15T01:12Z] INFO  18:12:57,882 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:12Z] INFO  18:12:57,951 ProgressMeter -            done    449347.0    16.0 s      37.0 s      100.0%    16.0 s       0.0 s
[2016-04-15T01:12Z] INFO  18:12:57,952 ProgressMeter - Total runtime 16.97 secs, 0.28 min, 0.00 hours
[2016-04-15T01:12Z] INFO  18:12:57,952 MicroScheduler - 14807 reads were filtered out during the traversal out of approximately 175494 total reads (8.44%)
[2016-04-15T01:12Z] INFO  18:12:57,953 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:12Z] INFO  18:12:57,954 MicroScheduler -   -> 268 reads (0.15% of total) failing BadMateFilter
[2016-04-15T01:12Z] INFO  18:12:57,954 MicroScheduler -   -> 14420 reads (8.22% of total) failing DuplicateReadFilter
[2016-04-15T01:12Z] INFO  18:12:57,955 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:12Z] INFO  18:12:57,955 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:12Z] INFO  18:12:57,956 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:12Z] INFO  18:12:57,957 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:12Z] INFO  18:12:57,957 MicroScheduler -   -> 119 reads (0.07% of total) failing UnmappedReadFilter
[2016-04-15T01:12Z] GATK: UnifiedGenotyper
[2016-04-15T01:12Z] INFO  18:12:59,278 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:12Z] INFO  18:12:59,281 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:12Z] INFO  18:12:59,282 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:12Z] INFO  18:12:59,282 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:12Z] INFO  18:12:59,287 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/12/R14-18102_kapa-NGv3-PE100-NGv3-sort-12_46756066_62654284-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/12/R14-18102_kapa-NGv3-PE100-NGv3-12_46756066_62654284-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/12/tx/tmpdqyW66/R14-18102_kapa-NGv3-PE100-NGv3-12_46756066_62654284.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:12Z] INFO  18:12:59,314 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:12Z] INFO  18:12:59,318 HelpFormatter - Date/Time: 2016/04/14 18:12:59
[2016-04-15T01:12Z] INFO  18:12:59,318 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:12Z] INFO  18:12:59,319 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:12Z] INFO  18:12:59,532 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:12Z] INFO  18:12:59,665 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:12Z] INFO  18:12:59,717 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T01:12Z] INFO  18:12:59,726 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:12Z] INFO  18:12:59,809 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-15T01:13Z] GATK: UnifiedGenotyper
[2016-04-15T01:13Z] INFO  18:13:00,278 IntervalUtils - Processing 504306 bp from intervals
[2016-04-15T01:13Z] WARN  18:13:00,284 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:13Z] INFO  18:13:00,414 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:13Z] INFO  18:13:00,502 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:13Z] INFO  18:13:00,503 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:13Z] INFO  18:13:00,504 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T01:13Z] INFO  18:13:00,505 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T01:13Z] INFO  18:13:00,562 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:13Z] INFO  18:13:00,563 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:13Z] INFO  18:13:00,889 ProgressMeter -    10:105809167   1252563.0    30.0 s      23.0 s       92.5%    32.0 s       2.0 s
[2016-04-15T01:13Z] INFO  18:13:01,535 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:13Z] INFO  18:13:01,539 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:13Z] INFO  18:13:01,539 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:13Z] INFO  18:13:01,540 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:13Z] INFO  18:13:01,544 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/12/R14-18102_kapa-NGv3-PE100-NGv3-sort-12_62687959_78225484-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/12/R14-18102_kapa-NGv3-PE100-NGv3-12_62687959_78225484-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/12/tx/tmpXHEPt8/R14-18102_kapa-NGv3-PE100-NGv3-12_62687959_78225484.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:13Z] INFO  18:13:01,565 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:13Z] INFO  18:13:01,566 HelpFormatter - Date/Time: 2016/04/14 18:13:01
[2016-04-15T01:13Z] INFO  18:13:01,574 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:13Z] INFO  18:13:01,574 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:13Z] INFO  18:13:01,838 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:13Z] INFO  18:13:02,017 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T01:13Z] INFO  18:13:02,035 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:13Z] INFO  18:13:02,120 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-15T01:13Z] INFO  18:13:02,488 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:13Z] INFO  18:13:02,491 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:13Z] INFO  18:13:02,492 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:13Z] INFO  18:13:02,492 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:13Z] INFO  18:13:02,497 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/12/R14-18102_kapa-NGv3-PE100-NGv3-sort-12_78334098_93863131-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/12/R14-18102_kapa-NGv3-PE100-NGv3-12_78334098_93863131-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/12/tx/tmpVYwShF/R14-18102_kapa-NGv3-PE100-NGv3-12_78334098_93863131.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:13Z] INFO  18:13:02,516 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:13Z] INFO  18:13:02,516 HelpFormatter - Date/Time: 2016/04/14 18:13:02
[2016-04-15T01:13Z] INFO  18:13:02,517 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:13Z] INFO  18:13:02,517 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:13Z] INFO  18:13:02,557 IntervalUtils - Processing 146919 bp from intervals
[2016-04-15T01:13Z] WARN  18:13:02,563 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:13Z] INFO  18:13:02,635 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:13Z] INFO  18:13:02,704 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:13Z] INFO  18:13:02,711 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:13Z] INFO  18:13:02,712 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:13Z] INFO  18:13:02,713 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T01:13Z] INFO  18:13:02,714 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T01:13Z] INFO  18:13:02,769 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:13Z] INFO  18:13:02,770 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:13Z] INFO  18:13:02,970 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T01:13Z] INFO  18:13:02,981 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:13Z] INFO  18:13:03,049 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-15T01:13Z] INFO  18:13:03,130 ProgressMeter -            done    576314.0    18.0 s      31.0 s      100.0%    18.0 s       0.0 s
[2016-04-15T01:13Z] INFO  18:13:03,136 ProgressMeter - Total runtime 18.38 secs, 0.31 min, 0.01 hours
[2016-04-15T01:13Z] INFO  18:13:03,138 MicroScheduler - 17613 reads were filtered out during the traversal out of approximately 206566 total reads (8.53%)
[2016-04-15T01:13Z] INFO  18:13:03,138 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:13Z] INFO  18:13:03,139 MicroScheduler -   -> 314 reads (0.15% of total) failing BadMateFilter
[2016-04-15T01:13Z] INFO  18:13:03,146 MicroScheduler -   -> 17139 reads (8.30% of total) failing DuplicateReadFilter
[2016-04-15T01:13Z] INFO  18:13:03,146 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:13Z] INFO  18:13:03,147 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:13Z] INFO  18:13:03,147 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:13Z] INFO  18:13:03,147 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:13Z] INFO  18:13:03,147 MicroScheduler -   -> 160 reads (0.08% of total) failing UnmappedReadFilter
[2016-04-15T01:13Z] INFO  18:13:03,181 ProgressMeter -            done   1324364.0    32.0 s      24.0 s      100.0%    32.0 s       0.0 s
[2016-04-15T01:13Z] INFO  18:13:03,181 ProgressMeter - Total runtime 32.31 secs, 0.54 min, 0.01 hours
[2016-04-15T01:13Z] INFO  18:13:03,182 MicroScheduler - 36428 reads were filtered out during the traversal out of approximately 438196 total reads (8.31%)
[2016-04-15T01:13Z] INFO  18:13:03,182 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:13Z] INFO  18:13:03,183 MicroScheduler -   -> 695 reads (0.16% of total) failing BadMateFilter
[2016-04-15T01:13Z] INFO  18:13:03,183 MicroScheduler -   -> 35362 reads (8.07% of total) failing DuplicateReadFilter
[2016-04-15T01:13Z] INFO  18:13:03,184 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:13Z] INFO  18:13:03,184 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:13Z] INFO  18:13:03,185 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:13Z] INFO  18:13:03,185 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:13Z] INFO  18:13:03,185 MicroScheduler -   -> 371 reads (0.08% of total) failing UnmappedReadFilter
[2016-04-15T01:13Z] INFO  18:13:03,448 IntervalUtils - Processing 88957 bp from intervals
[2016-04-15T01:13Z] WARN  18:13:03,461 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:13Z] INFO  18:13:03,539 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:13Z] INFO  18:13:03,665 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:13Z] INFO  18:13:03,666 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:13Z] INFO  18:13:03,667 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T01:13Z] INFO  18:13:03,668 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T01:13Z] INFO  18:13:03,731 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:13Z] INFO  18:13:03,732 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:13Z] INFO  18:13:04,689 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:13Z] INFO  18:13:04,785 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:13Z] GATK: UnifiedGenotyper
[2016-04-15T01:13Z] GATK: UnifiedGenotyper
[2016-04-15T01:13Z] INFO  18:13:05,639 ProgressMeter -            done    278160.0    16.0 s      58.0 s      100.0%    16.0 s       0.0 s
[2016-04-15T01:13Z] INFO  18:13:05,640 ProgressMeter - Total runtime 16.37 secs, 0.27 min, 0.00 hours
[2016-04-15T01:13Z] INFO  18:13:05,640 MicroScheduler - 12719 reads were filtered out during the traversal out of approximately 155634 total reads (8.17%)
[2016-04-15T01:13Z] INFO  18:13:05,641 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:13Z] INFO  18:13:05,641 MicroScheduler -   -> 221 reads (0.14% of total) failing BadMateFilter
[2016-04-15T01:13Z] INFO  18:13:05,641 MicroScheduler -   -> 12359 reads (7.94% of total) failing DuplicateReadFilter
[2016-04-15T01:13Z] INFO  18:13:05,641 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:13Z] INFO  18:13:05,642 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:13Z] INFO  18:13:05,642 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:13Z] INFO  18:13:05,642 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:13Z] INFO  18:13:05,643 MicroScheduler -   -> 139 reads (0.09% of total) failing UnmappedReadFilter
[2016-04-15T01:13Z] INFO  18:13:07,191 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:13Z] GATK: UnifiedGenotyper
[2016-04-15T01:13Z] INFO  18:13:07,970 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:13Z] INFO  18:13:07,973 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:13Z] INFO  18:13:07,974 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:13Z] INFO  18:13:07,974 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:13Z] INFO  18:13:07,979 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/12/R14-18102_kapa-NGv3-PE100-NGv3-sort-12_93870729_109490566-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/12/R14-18102_kapa-NGv3-PE100-NGv3-12_93870729_109490566-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/12/tx/tmpgYcQJT/R14-18102_kapa-NGv3-PE100-NGv3-12_93870729_109490566.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:13Z] INFO  18:13:08,009 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:13Z] INFO  18:13:08,010 HelpFormatter - Date/Time: 2016/04/14 18:13:07
[2016-04-15T01:13Z] INFO  18:13:08,010 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:13Z] INFO  18:13:08,010 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:13Z] INFO  18:13:08,057 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:13Z] INFO  18:13:08,060 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:13Z] INFO  18:13:08,060 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:13Z] INFO  18:13:08,061 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:13Z] INFO  18:13:08,065 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/12/R14-18102_kapa-NGv3-PE100-NGv3-sort-12_109494486_125263132-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/12/R14-18102_kapa-NGv3-PE100-NGv3-12_109494486_125263132-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/12/tx/tmpssNZDV/R14-18102_kapa-NGv3-PE100-NGv3-12_109494486_125263132.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:13Z] INFO  18:13:08,077 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:13Z] INFO  18:13:08,078 HelpFormatter - Date/Time: 2016/04/14 18:13:08
[2016-04-15T01:13Z] INFO  18:13:08,078 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:13Z] INFO  18:13:08,078 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:13Z] INFO  18:13:08,182 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:13Z] INFO  18:13:08,261 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:13Z] INFO  18:13:08,429 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T01:13Z] INFO  18:13:08,438 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:13Z] INFO  18:13:08,487 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T01:13Z] INFO  18:13:08,495 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:13Z] INFO  18:13:08,536 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.10
[2016-04-15T01:13Z] INFO  18:13:08,584 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.09
[2016-04-15T01:13Z] INFO  18:13:09,048 IntervalUtils - Processing 201796 bp from intervals
[2016-04-15T01:13Z] WARN  18:13:09,055 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:13Z] INFO  18:13:09,136 IntervalUtils - Processing 364987 bp from intervals
[2016-04-15T01:13Z] WARN  18:13:09,143 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:13Z] INFO  18:13:09,175 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:13Z] INFO  18:13:09,247 ProgressMeter -            done    400167.0    18.0 s      45.0 s      100.0%    18.0 s       0.0 s
[2016-04-15T01:13Z] INFO  18:13:09,247 ProgressMeter - Total runtime 18.16 secs, 0.30 min, 0.01 hours
[2016-04-15T01:13Z] INFO  18:13:09,248 MicroScheduler - 13295 reads were filtered out during the traversal out of approximately 161717 total reads (8.22%)
[2016-04-15T01:13Z] INFO  18:13:09,248 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:13Z] INFO  18:13:09,248 MicroScheduler -   -> 238 reads (0.15% of total) failing BadMateFilter
[2016-04-15T01:13Z] INFO  18:13:09,248 MicroScheduler -   -> 12940 reads (8.00% of total) failing DuplicateReadFilter
[2016-04-15T01:13Z] INFO  18:13:09,249 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:13Z] INFO  18:13:09,249 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:13Z] INFO  18:13:09,249 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:13Z] INFO  18:13:09,249 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:13Z] INFO  18:13:09,250 MicroScheduler -   -> 117 reads (0.07% of total) failing UnmappedReadFilter
[2016-04-15T01:13Z] INFO  18:13:09,286 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:13Z] INFO  18:13:09,288 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:13Z] INFO  18:13:09,289 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T01:13Z] INFO  18:13:09,289 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T01:13Z] INFO  18:13:09,290 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:13Z] INFO  18:13:09,341 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:13Z] INFO  18:13:09,343 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:13Z] INFO  18:13:09,414 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:13Z] INFO  18:13:09,416 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:13Z] INFO  18:13:09,417 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T01:13Z] INFO  18:13:09,418 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T01:13Z] INFO  18:13:09,479 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:13Z] INFO  18:13:09,481 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:13Z] INFO  18:13:10,076 ProgressMeter -            done    387169.0    16.0 s      41.0 s       99.9%    16.0 s       0.0 s
[2016-04-15T01:13Z] INFO  18:13:10,076 ProgressMeter - Total runtime 16.14 secs, 0.27 min, 0.00 hours
[2016-04-15T01:13Z] INFO  18:13:10,077 MicroScheduler - 12533 reads were filtered out during the traversal out of approximately 148946 total reads (8.41%)
[2016-04-15T01:13Z] INFO  18:13:10,077 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:13Z] INFO  18:13:10,077 MicroScheduler -   -> 222 reads (0.15% of total) failing BadMateFilter
[2016-04-15T01:13Z] INFO  18:13:10,077 MicroScheduler -   -> 12197 reads (8.19% of total) failing DuplicateReadFilter
[2016-04-15T01:13Z] INFO  18:13:10,078 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:13Z] INFO  18:13:10,078 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:13Z] INFO  18:13:10,078 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:13Z] INFO  18:13:10,078 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:13Z] INFO  18:13:10,079 MicroScheduler -   -> 114 reads (0.08% of total) failing UnmappedReadFilter
[2016-04-15T01:13Z] INFO  18:13:10,147 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:13Z] INFO  18:13:10,149 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:13Z] INFO  18:13:10,149 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:13Z] INFO  18:13:10,150 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:13Z] INFO  18:13:10,153 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/12/R14-18102_kapa-NGv3-PE100-NGv3-sort-12_125267228_133851895-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/12/R14-18102_kapa-NGv3-PE100-NGv3-12_125267228_133851895-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/12/tx/tmpNwR5XP/R14-18102_kapa-NGv3-PE100-NGv3-12_125267228_133851895.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:13Z] INFO  18:13:10,162 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:13Z] INFO  18:13:10,163 HelpFormatter - Date/Time: 2016/04/14 18:13:10
[2016-04-15T01:13Z] INFO  18:13:10,163 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:13Z] INFO  18:13:10,164 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:13Z] INFO  18:13:10,310 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:13Z] INFO  18:13:10,505 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T01:13Z] INFO  18:13:10,513 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:13Z] INFO  18:13:10,607 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.09
[2016-04-15T01:13Z] INFO  18:13:10,721 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:13Z] INFO  18:13:10,941 IntervalUtils - Processing 106872 bp from intervals
[2016-04-15T01:13Z] WARN  18:13:10,947 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:13Z] INFO  18:13:11,035 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:13Z] GATK: UnifiedGenotyper
[2016-04-15T01:13Z] INFO  18:13:11,114 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:13Z] INFO  18:13:11,115 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:13Z] INFO  18:13:11,116 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T01:13Z] INFO  18:13:11,116 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T01:13Z] INFO  18:13:11,148 ProgressMeter -      11:5686341   1317964.0    30.0 s      22.0 s       51.2%    58.0 s      28.0 s
[2016-04-15T01:13Z] INFO  18:13:11,164 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:13Z] INFO  18:13:11,165 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:13Z] INFO  18:13:11,322 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:13Z] INFO  18:13:11,635 ProgressMeter -            done    352890.0    17.0 s      48.0 s      100.0%    17.0 s       0.0 s
[2016-04-15T01:13Z] INFO  18:13:11,637 ProgressMeter - Total runtime 17.15 secs, 0.29 min, 0.00 hours
[2016-04-15T01:13Z] INFO  18:13:11,637 MicroScheduler - 11168 reads were filtered out during the traversal out of approximately 134751 total reads (8.29%)
[2016-04-15T01:13Z] INFO  18:13:11,638 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:13Z] INFO  18:13:11,639 MicroScheduler -   -> 222 reads (0.16% of total) failing BadMateFilter
[2016-04-15T01:13Z] INFO  18:13:11,640 MicroScheduler -   -> 10848 reads (8.05% of total) failing DuplicateReadFilter
[2016-04-15T01:13Z] INFO  18:13:11,641 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:13Z] INFO  18:13:11,641 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:13Z] INFO  18:13:11,642 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:13Z] INFO  18:13:11,643 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:13Z] INFO  18:13:11,644 MicroScheduler -   -> 98 reads (0.07% of total) failing UnmappedReadFilter
[2016-04-15T01:13Z] GATK: UnifiedGenotyper
[2016-04-15T01:13Z] INFO  18:13:13,074 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:13Z] GATK: UnifiedGenotyper
[2016-04-15T01:13Z] INFO  18:13:13,849 ProgressMeter -            done    441963.0    19.0 s      43.0 s       99.9%    19.0 s       0.0 s
[2016-04-15T01:13Z] INFO  18:13:13,850 ProgressMeter - Total runtime 19.22 secs, 0.32 min, 0.01 hours
[2016-04-15T01:13Z] INFO  18:13:13,850 MicroScheduler - 14749 reads were filtered out during the traversal out of approximately 171007 total reads (8.62%)
[2016-04-15T01:13Z] INFO  18:13:13,851 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:13Z] INFO  18:13:13,851 MicroScheduler -   -> 265 reads (0.15% of total) failing BadMateFilter
[2016-04-15T01:13Z] INFO  18:13:13,851 MicroScheduler -   -> 14343 reads (8.39% of total) failing DuplicateReadFilter
[2016-04-15T01:13Z] INFO  18:13:13,851 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:13Z] INFO  18:13:13,852 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:13Z] INFO  18:13:13,852 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:13Z] INFO  18:13:13,852 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:13Z] INFO  18:13:13,852 MicroScheduler -   -> 141 reads (0.08% of total) failing UnmappedReadFilter
[2016-04-15T01:13Z] INFO  18:13:14,073 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:13Z] INFO  18:13:14,077 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:13Z] INFO  18:13:14,077 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:13Z] INFO  18:13:14,078 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:13Z] INFO  18:13:14,083 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/13/R14-18102_kapa-NGv3-PE100-NGv3-sort-13_0_19748299-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/13/R14-18102_kapa-NGv3-PE100-NGv3-13_0_19748299-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/13/tx/tmpbp81oP/R14-18102_kapa-NGv3-PE100-NGv3-13_0_19748299.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:13Z] INFO  18:13:14,094 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:13Z] INFO  18:13:14,095 HelpFormatter - Date/Time: 2016/04/14 18:13:14
[2016-04-15T01:13Z] INFO  18:13:14,095 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:13Z] INFO  18:13:14,096 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:13Z] INFO  18:13:14,253 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:13Z] INFO  18:13:14,366 ProgressMeter -            done   2509744.0    51.0 s      20.0 s      100.0%    51.0 s       0.0 s
[2016-04-15T01:13Z] INFO  18:13:14,366 ProgressMeter - Total runtime 51.79 secs, 0.86 min, 0.01 hours
[2016-04-15T01:13Z] INFO  18:13:14,367 MicroScheduler - 60237 reads were filtered out during the traversal out of approximately 708260 total reads (8.50%)
[2016-04-15T01:13Z] INFO  18:13:14,367 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:13Z] INFO  18:13:14,367 MicroScheduler -   -> 1177 reads (0.17% of total) failing BadMateFilter
[2016-04-15T01:13Z] INFO  18:13:14,367 MicroScheduler -   -> 58530 reads (8.26% of total) failing DuplicateReadFilter
[2016-04-15T01:13Z] INFO  18:13:14,368 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:13Z] INFO  18:13:14,368 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:13Z] INFO  18:13:14,368 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:13Z] INFO  18:13:14,368 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:13Z] INFO  18:13:14,369 MicroScheduler -   -> 530 reads (0.07% of total) failing UnmappedReadFilter
[2016-04-15T01:13Z] INFO  18:13:14,495 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T01:13Z] INFO  18:13:14,503 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:13Z] INFO  18:13:14,571 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-15T01:13Z] INFO  18:13:14,591 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:13Z] INFO  18:13:14,595 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:13Z] INFO  18:13:14,595 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:13Z] INFO  18:13:14,596 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:13Z] INFO  18:13:14,600 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/13/R14-18102_kapa-NGv3-PE100-NGv3-sort-13_19751066_35517251-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/13/R14-18102_kapa-NGv3-PE100-NGv3-13_19751066_35517251-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/13/tx/tmp3qs8Sz/R14-18102_kapa-NGv3-PE100-NGv3-13_19751066_35517251.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:13Z] INFO  18:13:14,615 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:13Z] INFO  18:13:14,616 HelpFormatter - Date/Time: 2016/04/14 18:13:14
[2016-04-15T01:13Z] INFO  18:13:14,617 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:13Z] INFO  18:13:14,617 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:13Z] INFO  18:13:14,744 ProgressMeter -            done    243833.0    11.0 s      45.0 s       99.9%    11.0 s       0.0 s
[2016-04-15T01:13Z] INFO  18:13:14,745 ProgressMeter - Total runtime 11.08 secs, 0.18 min, 0.00 hours
[2016-04-15T01:13Z] INFO  18:13:14,746 MicroScheduler - 6915 reads were filtered out during the traversal out of approximately 84929 total reads (8.14%)
[2016-04-15T01:13Z] INFO  18:13:14,747 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:13Z] INFO  18:13:14,747 MicroScheduler -   -> 137 reads (0.16% of total) failing BadMateFilter
[2016-04-15T01:13Z] INFO  18:13:14,748 MicroScheduler -   -> 6711 reads (7.90% of total) failing DuplicateReadFilter
[2016-04-15T01:13Z] INFO  18:13:14,749 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:13Z] INFO  18:13:14,749 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:13Z] INFO  18:13:14,750 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:13Z] INFO  18:13:14,751 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:13Z] INFO  18:13:14,751 MicroScheduler -   -> 67 reads (0.08% of total) failing UnmappedReadFilter
[2016-04-15T01:13Z] INFO  18:13:14,767 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:13Z] INFO  18:13:15,022 IntervalUtils - Processing 297 bp from intervals
[2016-04-15T01:13Z] WARN  18:13:15,027 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:13Z] INFO  18:13:15,043 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T01:13Z] INFO  18:13:15,052 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:13Z] INFO  18:13:15,119 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:13Z] INFO  18:13:15,123 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-15T01:13Z] INFO  18:13:15,173 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:13Z] INFO  18:13:15,173 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:13Z] INFO  18:13:15,174 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T01:13Z] INFO  18:13:15,174 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T01:13Z] INFO  18:13:15,238 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:13Z] INFO  18:13:15,239 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:13Z] INFO  18:13:15,365 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:13Z] INFO  18:13:15,498 IntervalUtils - Processing 201552 bp from intervals
[2016-04-15T01:13Z] WARN  18:13:15,504 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:13Z] INFO  18:13:15,578 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:13Z] INFO  18:13:15,679 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:13Z] INFO  18:13:15,681 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:13Z] INFO  18:13:15,681 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T01:13Z] INFO  18:13:15,682 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T01:13Z] GATK: UnifiedGenotyper
[2016-04-15T01:13Z] INFO  18:13:15,729 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:13Z] INFO  18:13:15,730 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:13Z] INFO  18:13:15,911 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:13Z] INFO  18:13:16,126 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:13Z] INFO  18:13:16,128 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:13Z] INFO  18:13:16,129 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:13Z] INFO  18:13:16,129 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:13Z] INFO  18:13:16,133 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/13/R14-18102_kapa-NGv3-PE100-NGv3-sort-13_35615069_51287376-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/13/R14-18102_kapa-NGv3-PE100-NGv3-13_35615069_51287376-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/13/tx/tmpoQQex0/R14-18102_kapa-NGv3-PE100-NGv3-13_35615069_51287376.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:13Z] INFO  18:13:16,154 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:13Z] INFO  18:13:16,155 HelpFormatter - Date/Time: 2016/04/14 18:13:16
[2016-04-15T01:13Z] INFO  18:13:16,155 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:13Z] INFO  18:13:16,155 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:13Z] GATK: UnifiedGenotyper
[2016-04-15T01:13Z] INFO  18:13:16,217 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:13Z] INFO  18:13:16,414 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:13Z] INFO  18:13:16,449 ProgressMeter -            done       297.0     1.0 s      71.5 m       67.3%     1.0 s       0.0 s
[2016-04-15T01:13Z] INFO  18:13:16,450 ProgressMeter - Total runtime 1.28 secs, 0.02 min, 0.00 hours
[2016-04-15T01:13Z] INFO  18:13:16,450 MicroScheduler - 98 reads were filtered out during the traversal out of approximately 805 total reads (12.17%)
[2016-04-15T01:13Z] INFO  18:13:16,450 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:13Z] INFO  18:13:16,451 MicroScheduler -   -> 0 reads (0.00% of total) failing BadMateFilter
[2016-04-15T01:13Z] INFO  18:13:16,451 MicroScheduler -   -> 98 reads (12.17% of total) failing DuplicateReadFilter
[2016-04-15T01:13Z] INFO  18:13:16,451 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:13Z] INFO  18:13:16,452 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:13Z] INFO  18:13:16,452 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:13Z] INFO  18:13:16,452 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:13Z] INFO  18:13:16,452 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T01:13Z] GATK: UnifiedGenotyper
[2016-04-15T01:13Z] INFO  18:13:16,637 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T01:13Z] INFO  18:13:16,647 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:13Z] INFO  18:13:16,722 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-15T01:13Z] INFO  18:13:17,345 IntervalUtils - Processing 179232 bp from intervals
[2016-04-15T01:13Z] WARN  18:13:17,352 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:13Z] INFO  18:13:17,432 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:13Z] INFO  18:13:17,576 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:13Z] INFO  18:13:17,577 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:13Z] INFO  18:13:17,578 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T01:13Z] INFO  18:13:17,579 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T01:13Z] INFO  18:13:17,657 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:13Z] INFO  18:13:17,658 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:13Z] INFO  18:13:17,949 ProgressMeter -     11:61674038    907675.0    30.0 s      33.0 s       78.3%    38.0 s       8.0 s
[2016-04-15T01:13Z] INFO  18:13:17,999 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:13Z] GATK: UnifiedGenotyper
[2016-04-15T01:13Z] INFO  18:13:18,705 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:13Z] INFO  18:13:18,708 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:13Z] INFO  18:13:18,708 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:13Z] INFO  18:13:18,709 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:13Z] INFO  18:13:18,713 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/13/R14-18102_kapa-NGv3-PE100-NGv3-sort-13_51396767_67205543-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/13/R14-18102_kapa-NGv3-PE100-NGv3-13_51396767_67205543-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/13/tx/tmpWwI2WO/R14-18102_kapa-NGv3-PE100-NGv3-13_51396767_67205543.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:13Z] INFO  18:13:18,722 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:13Z] INFO  18:13:18,723 HelpFormatter - Date/Time: 2016/04/14 18:13:18
[2016-04-15T01:13Z] INFO  18:13:18,723 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:13Z] INFO  18:13:18,724 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:13Z] INFO  18:13:18,757 ProgressMeter -     11:67135631   1755432.0    30.0 s      17.0 s       51.1%    58.0 s      28.0 s
[2016-04-15T01:13Z] INFO  18:13:18,965 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:13Z] INFO  18:13:19,258 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T01:13Z] INFO  18:13:19,269 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:13Z] INFO  18:13:19,370 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.10
[2016-04-15T01:13Z] INFO  18:13:19,598 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:13Z] INFO  18:13:19,601 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:13Z] INFO  18:13:19,601 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:13Z] INFO  18:13:19,602 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:13Z] INFO  18:13:19,617 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/13/R14-18102_kapa-NGv3-PE100-NGv3-sort-13_67477635_84455642-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/13/R14-18102_kapa-NGv3-PE100-NGv3-13_67477635_84455642-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/13/tx/tmpkxvsfW/R14-18102_kapa-NGv3-PE100-NGv3-13_67477635_84455642.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:13Z] INFO  18:13:19,617 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:13Z] INFO  18:13:19,621 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:13Z] INFO  18:13:19,622 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:13Z] INFO  18:13:19,622 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:13Z] INFO  18:13:19,628 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/13/R14-18102_kapa-NGv3-PE100-NGv3-sort-13_86368117_101881935-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/13/R14-18102_kapa-NGv3-PE100-NGv3-13_86368117_101881935-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/13/tx/tmpsWUdHN/R14-18102_kapa-NGv3-PE100-NGv3-13_86368117_101881935.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:13Z] INFO  18:13:19,640 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:13Z] INFO  18:13:19,641 HelpFormatter - Date/Time: 2016/04/14 18:13:19
[2016-04-15T01:13Z] INFO  18:13:19,642 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:13Z] INFO  18:13:19,642 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:13Z] INFO  18:13:19,667 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:13Z] INFO  18:13:19,668 HelpFormatter - Date/Time: 2016/04/14 18:13:19
[2016-04-15T01:13Z] INFO  18:13:19,683 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:13Z] INFO  18:13:19,684 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:13Z] INFO  18:13:19,856 IntervalUtils - Processing 59966 bp from intervals
[2016-04-15T01:13Z] WARN  18:13:19,861 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:13Z] INFO  18:13:19,862 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:13Z] INFO  18:13:19,865 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:13Z] INFO  18:13:19,937 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:13Z] INFO  18:13:19,978 ProgressMeter -            done    406794.0    17.0 s      42.0 s      100.0%    17.0 s       0.0 s
[2016-04-15T01:13Z] INFO  18:13:19,979 ProgressMeter - Total runtime 17.27 secs, 0.29 min, 0.00 hours
[2016-04-15T01:13Z] INFO  18:13:19,980 MicroScheduler - 12846 reads were filtered out during the traversal out of approximately 154465 total reads (8.32%)
[2016-04-15T01:13Z] INFO  18:13:19,981 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:13Z] INFO  18:13:19,982 MicroScheduler -   -> 245 reads (0.16% of total) failing BadMateFilter
[2016-04-15T01:13Z] INFO  18:13:19,982 MicroScheduler -   -> 12492 reads (8.09% of total) failing DuplicateReadFilter
[2016-04-15T01:13Z] INFO  18:13:19,983 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:13Z] INFO  18:13:19,983 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:13Z] INFO  18:13:19,984 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:13Z] INFO  18:13:19,985 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:13Z] INFO  18:13:19,985 MicroScheduler -   -> 109 reads (0.07% of total) failing UnmappedReadFilter
[2016-04-15T01:13Z] INFO  18:13:20,013 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:13Z] INFO  18:13:20,014 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:13Z] INFO  18:13:20,014 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T01:13Z] INFO  18:13:20,015 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T01:13Z] INFO  18:13:20,103 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T01:13Z] INFO  18:13:20,112 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T01:13Z] INFO  18:13:20,114 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:13Z] INFO  18:13:20,115 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:13Z] INFO  18:13:20,119 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:13Z] INFO  18:13:20,121 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:13Z] INFO  18:13:20,200 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-15T01:13Z] INFO  18:13:20,220 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.10
[2016-04-15T01:13Z] INFO  18:13:20,549 IntervalUtils - Processing 75123 bp from intervals
[2016-04-15T01:13Z] WARN  18:13:20,554 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:13Z] INFO  18:13:20,589 IntervalUtils - Processing 69582 bp from intervals
[2016-04-15T01:13Z] WARN  18:13:20,593 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:13Z] INFO  18:13:20,632 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:13Z] INFO  18:13:20,724 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:13Z] INFO  18:13:20,725 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:13Z] INFO  18:13:20,725 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T01:13Z] INFO  18:13:20,726 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T01:13Z] INFO  18:13:20,732 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:13Z] INFO  18:13:20,786 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:13Z] INFO  18:13:20,787 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:13Z] INFO  18:13:20,852 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:13Z] INFO  18:13:20,852 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:13Z] INFO  18:13:20,853 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T01:13Z] INFO  18:13:20,853 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T01:13Z] INFO  18:13:20,940 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:13Z] INFO  18:13:20,941 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:13Z] INFO  18:13:21,330 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:13Z] INFO  18:13:21,345 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:13Z] INFO  18:13:21,348 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:13Z] INFO  18:13:21,349 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:13Z] INFO  18:13:21,349 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:13Z] INFO  18:13:21,354 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/13/R14-18102_kapa-NGv3-PE100-NGv3-sort-13_101890105_115169878-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/13/R14-18102_kapa-NGv3-PE100-NGv3-13_101890105_115169878-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/13/tx/tmphNrg6Q/R14-18102_kapa-NGv3-PE100-NGv3-13_101890105_115169878.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:13Z] INFO  18:13:21,368 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:13Z] INFO  18:13:21,368 HelpFormatter - Date/Time: 2016/04/14 18:13:21
[2016-04-15T01:13Z] INFO  18:13:21,368 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:13Z] INFO  18:13:21,369 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:13Z] INFO  18:13:21,516 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:13Z] GATK: UnifiedGenotyper
[2016-04-15T01:13Z] INFO  18:13:21,787 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T01:13Z] INFO  18:13:21,807 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:13Z] INFO  18:13:21,891 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-15T01:13Z] INFO  18:13:22,138 ProgressMeter -    11:123483469   1109858.0    30.0 s      27.0 s       81.2%    36.0 s       6.0 s
[2016-04-15T01:13Z] INFO  18:13:22,312 IntervalUtils - Processing 144481 bp from intervals
[2016-04-15T01:13Z] WARN  18:13:22,318 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:13Z] INFO  18:13:22,418 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:13Z] INFO  18:13:22,515 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:13Z] INFO  18:13:22,532 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:13Z] INFO  18:13:22,533 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T01:13Z] INFO  18:13:22,534 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T01:13Z] INFO  18:13:22,635 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:13Z] INFO  18:13:22,636 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:13Z] INFO  18:13:24,190 ProgressMeter -            done   1302582.0    36.0 s      27.0 s      100.0%    36.0 s       0.0 s
[2016-04-15T01:13Z] INFO  18:13:24,202 ProgressMeter - Total runtime 36.28 secs, 0.60 min, 0.01 hours
[2016-04-15T01:13Z] INFO  18:13:24,203 MicroScheduler - 40323 reads were filtered out during the traversal out of approximately 478718 total reads (8.42%)
[2016-04-15T01:13Z] INFO  18:13:24,203 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:13Z] INFO  18:13:24,204 MicroScheduler -   -> 718 reads (0.15% of total) failing BadMateFilter
[2016-04-15T01:13Z] INFO  18:13:24,204 MicroScheduler -   -> 39225 reads (8.19% of total) failing DuplicateReadFilter
[2016-04-15T01:13Z] INFO  18:13:24,205 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:13Z] INFO  18:13:24,206 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:13Z] INFO  18:13:24,206 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:13Z] INFO  18:13:24,207 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:13Z] INFO  18:13:24,207 MicroScheduler -   -> 380 reads (0.08% of total) failing UnmappedReadFilter
[2016-04-15T01:13Z] INFO  18:13:24,441 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:13Z] INFO  18:13:24,444 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:13Z] INFO  18:13:24,444 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:13Z] INFO  18:13:24,445 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:13Z] INFO  18:13:24,449 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/14/R14-18102_kapa-NGv3-PE100-NGv3-sort-14_0_19378574-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/14/R14-18102_kapa-NGv3-PE100-NGv3-14_0_19378574-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/14/tx/tmpIp6vEI/R14-18102_kapa-NGv3-PE100-NGv3-14_0_19378574.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:13Z] INFO  18:13:24,481 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:13Z] INFO  18:13:24,487 HelpFormatter - Date/Time: 2016/04/14 18:13:24
[2016-04-15T01:13Z] INFO  18:13:24,488 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:13Z] INFO  18:13:24,492 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:13Z] INFO  18:13:24,676 ProgressMeter -     12:10568383   1151818.0    30.0 s      26.0 s       78.5%    38.0 s       8.0 s
[2016-04-15T01:13Z] INFO  18:13:24,682 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:13Z] INFO  18:13:24,963 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T01:13Z] INFO  18:13:24,985 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:13Z] INFO  18:13:25,131 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.14
[2016-04-15T01:13Z] INFO  18:13:25,469 IntervalUtils - Processing 981 bp from intervals
[2016-04-15T01:13Z] WARN  18:13:25,476 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:13Z] INFO  18:13:25,556 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:13Z] INFO  18:13:25,577 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:13Z] INFO  18:13:25,578 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:13Z] INFO  18:13:25,579 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T01:13Z] INFO  18:13:25,580 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T01:13Z] INFO  18:13:25,630 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:13Z] INFO  18:13:25,631 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:13Z] INFO  18:13:25,801 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:13Z] GATK: UnifiedGenotyper
[2016-04-15T01:13Z] INFO  18:13:27,648 ProgressMeter -            done    370183.0    16.0 s      44.0 s      100.0%    16.0 s       0.0 s
[2016-04-15T01:13Z] INFO  18:13:27,649 ProgressMeter - Total runtime 16.53 secs, 0.28 min, 0.00 hours
[2016-04-15T01:13Z] INFO  18:13:27,649 MicroScheduler - 15158 reads were filtered out during the traversal out of approximately 178793 total reads (8.48%)
[2016-04-15T01:13Z] INFO  18:13:27,650 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:13Z] INFO  18:13:27,650 MicroScheduler -   -> 291 reads (0.16% of total) failing BadMateFilter
[2016-04-15T01:13Z] INFO  18:13:27,650 MicroScheduler -   -> 14729 reads (8.24% of total) failing DuplicateReadFilter
[2016-04-15T01:13Z] INFO  18:13:27,650 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:13Z] INFO  18:13:27,651 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:13Z] INFO  18:13:27,651 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:13Z] INFO  18:13:27,651 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:13Z] INFO  18:13:27,651 MicroScheduler -   -> 138 reads (0.08% of total) failing UnmappedReadFilter
[2016-04-15T01:13Z] INFO  18:13:27,799 ProgressMeter -            done       981.0     2.0 s      37.7 m       91.7%     2.0 s       0.0 s
[2016-04-15T01:13Z] INFO  18:13:27,799 ProgressMeter - Total runtime 2.22 secs, 0.04 min, 0.00 hours
[2016-04-15T01:13Z] INFO  18:13:27,800 MicroScheduler - 245 reads were filtered out during the traversal out of approximately 2961 total reads (8.27%)
[2016-04-15T01:13Z] INFO  18:13:27,800 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:13Z] INFO  18:13:27,800 MicroScheduler -   -> 4 reads (0.14% of total) failing BadMateFilter
[2016-04-15T01:13Z] INFO  18:13:27,801 MicroScheduler -   -> 236 reads (7.97% of total) failing DuplicateReadFilter
[2016-04-15T01:13Z] INFO  18:13:27,801 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:13Z] INFO  18:13:27,802 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:13Z] INFO  18:13:27,808 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:13Z] INFO  18:13:27,809 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:13Z] INFO  18:13:27,809 MicroScheduler -   -> 5 reads (0.17% of total) failing UnmappedReadFilter
[2016-04-15T01:13Z] INFO  18:13:27,870 ProgressMeter -            done   1335468.0    35.0 s      26.0 s      100.0%    35.0 s       0.0 s
[2016-04-15T01:13Z] INFO  18:13:27,871 ProgressMeter - Total runtime 35.77 secs, 0.60 min, 0.01 hours
[2016-04-15T01:13Z] INFO  18:13:27,872 MicroScheduler - 37568 reads were filtered out during the traversal out of approximately 446592 total reads (8.41%)
[2016-04-15T01:13Z] INFO  18:13:27,873 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:13Z] INFO  18:13:27,873 MicroScheduler -   -> 643 reads (0.14% of total) failing BadMateFilter
[2016-04-15T01:13Z] INFO  18:13:27,873 MicroScheduler -   -> 36594 reads (8.19% of total) failing DuplicateReadFilter
[2016-04-15T01:13Z] INFO  18:13:27,873 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:13Z] INFO  18:13:27,874 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:13Z] INFO  18:13:27,874 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:13Z] INFO  18:13:27,874 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:13Z] INFO  18:13:27,875 MicroScheduler -   -> 331 reads (0.07% of total) failing UnmappedReadFilter
[2016-04-15T01:13Z] INFO  18:13:29,028 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:13Z] INFO  18:13:29,032 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:13Z] INFO  18:13:29,033 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:13Z] INFO  18:13:29,034 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:13Z] INFO  18:13:29,039 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/14/R14-18102_kapa-NGv3-PE100-NGv3-sort-14_19553416_35066851-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/14/R14-18102_kapa-NGv3-PE100-NGv3-14_19553416_35066851-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/14/tx/tmpQpLwT6/R14-18102_kapa-NGv3-PE100-NGv3-14_19553416_35066851.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:13Z] INFO  18:13:29,056 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:13Z] INFO  18:13:29,058 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:13Z] INFO  18:13:29,064 HelpFormatter - Date/Time: 2016/04/14 18:13:29
[2016-04-15T01:13Z] INFO  18:13:29,065 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:13Z] INFO  18:13:29,066 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:13Z] INFO  18:13:29,228 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:13Z] INFO  18:13:29,274 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:13Z] GATK: UnifiedGenotyper
[2016-04-15T01:13Z] INFO  18:13:29,352 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:13Z] INFO  18:13:29,501 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T01:13Z] INFO  18:13:29,511 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:13Z] GATK: UnifiedGenotyper
[2016-04-15T01:13Z] INFO  18:13:29,586 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-15T01:13Z] GATK: UnifiedGenotyper
[2016-04-15T01:13Z] INFO  18:13:30,154 IntervalUtils - Processing 291951 bp from intervals
[2016-04-15T01:13Z] WARN  18:13:30,160 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:13Z] INFO  18:13:30,274 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:13Z] INFO  18:13:30,289 ProgressMeter -            done    144034.0    10.0 s      71.0 s      100.0%    10.0 s       0.0 s
[2016-04-15T01:13Z] INFO  18:13:30,290 ProgressMeter - Total runtime 10.28 secs, 0.17 min, 0.00 hours
[2016-04-15T01:13Z] INFO  18:13:30,290 MicroScheduler - 6560 reads were filtered out during the traversal out of approximately 93541 total reads (7.01%)
[2016-04-15T01:13Z] INFO  18:13:30,291 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:13Z] INFO  18:13:30,291 MicroScheduler -   -> 136 reads (0.15% of total) failing BadMateFilter
[2016-04-15T01:13Z] INFO  18:13:30,291 MicroScheduler -   -> 6350 reads (6.79% of total) failing DuplicateReadFilter
[2016-04-15T01:13Z] INFO  18:13:30,292 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:13Z] INFO  18:13:30,292 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:13Z] INFO  18:13:30,292 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:13Z] INFO  18:13:30,293 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:13Z] INFO  18:13:30,293 MicroScheduler -   -> 74 reads (0.08% of total) failing UnmappedReadFilter
[2016-04-15T01:13Z] INFO  18:13:30,437 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:13Z] INFO  18:13:30,439 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:13Z] INFO  18:13:30,440 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T01:13Z] INFO  18:13:30,440 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T01:13Z] INFO  18:13:30,489 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:13Z] INFO  18:13:30,490 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:13Z] INFO  18:13:30,527 ProgressMeter -            done   2117017.0    49.0 s      23.0 s      100.0%    49.0 s       0.0 s
[2016-04-15T01:13Z] INFO  18:13:30,527 ProgressMeter - Total runtime 49.40 secs, 0.82 min, 0.01 hours
[2016-04-15T01:13Z] INFO  18:13:30,528 MicroScheduler - 66242 reads were filtered out during the traversal out of approximately 718370 total reads (9.22%)
[2016-04-15T01:13Z] INFO  18:13:30,528 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:13Z] INFO  18:13:30,528 MicroScheduler -   -> 1247 reads (0.17% of total) failing BadMateFilter
[2016-04-15T01:13Z] INFO  18:13:30,528 ProgressMeter -     12:53608330   1377319.0    30.0 s      21.0 s       50.8%    59.0 s      29.0 s
[2016-04-15T01:13Z] INFO  18:13:30,529 MicroScheduler -   -> 64317 reads (8.95% of total) failing DuplicateReadFilter
[2016-04-15T01:13Z] INFO  18:13:30,529 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:13Z] INFO  18:13:30,529 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:13Z] INFO  18:13:30,530 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:13Z] INFO  18:13:30,530 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:13Z] INFO  18:13:30,530 MicroScheduler -   -> 678 reads (0.09% of total) failing UnmappedReadFilter
[2016-04-15T01:13Z] INFO  18:13:31,415 ProgressMeter -            done    596495.0    22.0 s      37.0 s      100.0%    22.0 s       0.0 s
[2016-04-15T01:13Z] INFO  18:13:31,415 ProgressMeter - Total runtime 22.13 secs, 0.37 min, 0.01 hours
[2016-04-15T01:13Z] INFO  18:13:31,416 MicroScheduler - 20155 reads were filtered out during the traversal out of approximately 238833 total reads (8.44%)
[2016-04-15T01:13Z] INFO  18:13:31,416 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:13Z] INFO  18:13:31,417 MicroScheduler -   -> 352 reads (0.15% of total) failing BadMateFilter
[2016-04-15T01:13Z] INFO  18:13:31,417 MicroScheduler -   -> 19631 reads (8.22% of total) failing DuplicateReadFilter
[2016-04-15T01:13Z] INFO  18:13:31,417 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:13Z] INFO  18:13:31,418 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:13Z] INFO  18:13:31,418 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:13Z] INFO  18:13:31,418 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:13Z] INFO  18:13:31,418 MicroScheduler -   -> 172 reads (0.07% of total) failing UnmappedReadFilter
[2016-04-15T01:13Z] INFO  18:13:31,552 ProgressMeter -            done    188528.0    10.0 s      56.0 s       99.9%    10.0 s       0.0 s
[2016-04-15T01:13Z] INFO  18:13:31,553 ProgressMeter - Total runtime 10.70 secs, 0.18 min, 0.00 hours
[2016-04-15T01:13Z] INFO  18:13:31,553 MicroScheduler - 6370 reads were filtered out during the traversal out of approximately 76742 total reads (8.30%)
[2016-04-15T01:13Z] INFO  18:13:31,554 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:13Z] INFO  18:13:31,554 MicroScheduler -   -> 122 reads (0.16% of total) failing BadMateFilter
[2016-04-15T01:13Z] INFO  18:13:31,554 MicroScheduler -   -> 6196 reads (8.07% of total) failing DuplicateReadFilter
[2016-04-15T01:13Z] INFO  18:13:31,555 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:13Z] INFO  18:13:31,555 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:13Z] INFO  18:13:31,555 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:13Z] INFO  18:13:31,556 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:13Z] INFO  18:13:31,556 MicroScheduler -   -> 52 reads (0.07% of total) failing UnmappedReadFilter
[2016-04-15T01:13Z] INFO  18:13:31,691 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:13Z] INFO  18:13:31,819 ProgressMeter -            done   1314614.0    37.0 s      28.0 s      100.0%    37.0 s       0.0 s
[2016-04-15T01:13Z] INFO  18:13:31,819 ProgressMeter - Total runtime 37.16 secs, 0.62 min, 0.01 hours
[2016-04-15T01:13Z] INFO  18:13:31,820 MicroScheduler - 38637 reads were filtered out during the traversal out of approximately 463695 total reads (8.33%)
[2016-04-15T01:13Z] INFO  18:13:31,820 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:13Z] INFO  18:13:31,820 MicroScheduler -   -> 711 reads (0.15% of total) failing BadMateFilter
[2016-04-15T01:13Z] INFO  18:13:31,820 MicroScheduler -   -> 37560 reads (8.10% of total) failing DuplicateReadFilter
[2016-04-15T01:13Z] INFO  18:13:31,821 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:13Z] INFO  18:13:31,821 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:13Z] INFO  18:13:31,821 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:13Z] INFO  18:13:31,821 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:13Z] INFO  18:13:31,822 MicroScheduler -   -> 366 reads (0.08% of total) failing UnmappedReadFilter
[2016-04-15T01:13Z] INFO  18:13:31,933 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:13Z] GATK: UnifiedGenotyper
[2016-04-15T01:13Z] GATK: UnifiedGenotyper
[2016-04-15T01:13Z] INFO  18:13:32,468 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:13Z] INFO  18:13:32,472 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:13Z] INFO  18:13:32,472 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:13Z] INFO  18:13:32,473 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:13Z] INFO  18:13:32,477 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/14/R14-18102_kapa-NGv3-PE100-NGv3-sort-14_35072553_50583270-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/14/R14-18102_kapa-NGv3-PE100-NGv3-14_35072553_50583270-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/14/tx/tmpDgY98L/R14-18102_kapa-NGv3-PE100-NGv3-14_35072553_50583270.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:13Z] INFO  18:13:32,487 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:13Z] INFO  18:13:32,487 HelpFormatter - Date/Time: 2016/04/14 18:13:32
[2016-04-15T01:13Z] INFO  18:13:32,488 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:13Z] INFO  18:13:32,488 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:13Z] INFO  18:13:32,532 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:13Z] INFO  18:13:32,537 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:13Z] INFO  18:13:32,541 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:13Z] INFO  18:13:32,552 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:13Z] INFO  18:13:32,557 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/14/R14-18102_kapa-NGv3-PE100-NGv3-sort-14_50585061_66096324-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/14/R14-18102_kapa-NGv3-PE100-NGv3-14_50585061_66096324-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/14/tx/tmp83cyxk/R14-18102_kapa-NGv3-PE100-NGv3-14_50585061_66096324.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:13Z] INFO  18:13:32,571 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:13Z] INFO  18:13:32,572 HelpFormatter - Date/Time: 2016/04/14 18:13:32
[2016-04-15T01:13Z] INFO  18:13:32,572 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:13Z] INFO  18:13:32,573 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:13Z] INFO  18:13:32,665 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:13Z] INFO  18:13:32,666 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:13Z] INFO  18:13:32,669 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:13Z] INFO  18:13:32,669 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:13Z] INFO  18:13:32,669 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:13Z] INFO  18:13:32,673 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/14/R14-18102_kapa-NGv3-PE100-NGv3-sort-14_66135960_81646674-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/14/R14-18102_kapa-NGv3-PE100-NGv3-14_66135960_81646674-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/14/tx/tmpsoOIdg/R14-18102_kapa-NGv3-PE100-NGv3-14_66135960_81646674.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:13Z] INFO  18:13:32,690 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:13Z] INFO  18:13:32,691 HelpFormatter - Date/Time: 2016/04/14 18:13:32
[2016-04-15T01:13Z] INFO  18:13:32,691 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:13Z] INFO  18:13:32,692 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:13Z] INFO  18:13:32,706 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:13Z] INFO  18:13:32,835 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:13Z] INFO  18:13:32,888 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T01:13Z] INFO  18:13:32,898 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:13Z] INFO  18:13:32,914 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:13Z] INFO  18:13:32,928 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:13Z] INFO  18:13:32,936 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T01:13Z] INFO  18:13:32,947 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:13Z] INFO  18:13:33,012 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.11
[2016-04-15T01:13Z] INFO  18:13:33,026 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-15T01:13Z] GATK: UnifiedGenotyper
[2016-04-15T01:13Z] GATK: UnifiedGenotyper
[2016-04-15T01:13Z] INFO  18:13:33,219 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:13Z] INFO  18:13:33,255 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T01:13Z] INFO  18:13:33,270 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:13Z] INFO  18:13:33,362 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.09
[2016-04-15T01:13Z] INFO  18:13:33,466 IntervalUtils - Processing 108903 bp from intervals
[2016-04-15T01:13Z] WARN  18:13:33,472 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:13Z] INFO  18:13:33,557 IntervalUtils - Processing 226771 bp from intervals
[2016-04-15T01:13Z] WARN  18:13:33,564 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:13Z] GATK: UnifiedGenotyper
[2016-04-15T01:13Z] INFO  18:13:33,647 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:13Z] INFO  18:13:33,659 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:13Z] INFO  18:13:33,736 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:13Z] INFO  18:13:33,738 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:13Z] INFO  18:13:33,738 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T01:13Z] INFO  18:13:33,739 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T01:13Z] INFO  18:13:33,750 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:13Z] INFO  18:13:33,751 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:13Z] INFO  18:13:33,752 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T01:13Z] INFO  18:13:33,753 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T01:13Z] INFO  18:13:33,769 IntervalUtils - Processing 245410 bp from intervals
[2016-04-15T01:13Z] WARN  18:13:33,774 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:13Z] INFO  18:13:33,804 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:13Z] INFO  18:13:33,805 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:13Z] INFO  18:13:33,834 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:13Z] INFO  18:13:33,834 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:13Z] INFO  18:13:33,871 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:13Z] INFO  18:13:34,019 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:13Z] INFO  18:13:34,020 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:13Z] INFO  18:13:34,020 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T01:13Z] INFO  18:13:34,021 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T01:13Z] INFO  18:13:34,043 ProgressMeter -            done    183411.0    13.0 s      72.0 s       99.9%    13.0 s       0.0 s
[2016-04-15T01:13Z] INFO  18:13:34,044 ProgressMeter - Total runtime 13.32 secs, 0.22 min, 0.00 hours
[2016-04-15T01:13Z] INFO  18:13:34,045 MicroScheduler - 8436 reads were filtered out during the traversal out of approximately 98748 total reads (8.54%)
[2016-04-15T01:13Z] INFO  18:13:34,046 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:13Z] INFO  18:13:34,046 MicroScheduler -   -> 154 reads (0.16% of total) failing BadMateFilter
[2016-04-15T01:13Z] INFO  18:13:34,047 MicroScheduler -   -> 8212 reads (8.32% of total) failing DuplicateReadFilter
[2016-04-15T01:13Z] INFO  18:13:34,048 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:13Z] INFO  18:13:34,048 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:13Z] INFO  18:13:34,049 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:13Z] INFO  18:13:34,049 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:13Z] INFO  18:13:34,050 MicroScheduler -   -> 70 reads (0.07% of total) failing UnmappedReadFilter
[2016-04-15T01:13Z] INFO  18:13:34,089 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:13Z] INFO  18:13:34,090 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:13Z] INFO  18:13:35,319 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:13Z] INFO  18:13:35,377 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:13Z] INFO  18:13:35,380 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:13Z] INFO  18:13:35,380 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:13Z] INFO  18:13:35,381 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:13Z] INFO  18:13:35,385 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/14/R14-18102_kapa-NGv3-PE100-NGv3-sort-14_81651874_97299968-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/14/R14-18102_kapa-NGv3-PE100-NGv3-14_81651874_97299968-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/14/tx/tmpULRf5j/R14-18102_kapa-NGv3-PE100-NGv3-14_81651874_97299968.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:13Z] INFO  18:13:35,395 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:13Z] INFO  18:13:35,406 HelpFormatter - Date/Time: 2016/04/14 18:13:35
[2016-04-15T01:13Z] INFO  18:13:35,407 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:13Z] INFO  18:13:35,408 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:13Z] INFO  18:13:35,484 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:13Z] INFO  18:13:35,486 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:13Z] INFO  18:13:35,487 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:13Z] INFO  18:13:35,487 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:13Z] INFO  18:13:35,497 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/14/R14-18102_kapa-NGv3-PE100-NGv3-sort-14_97304098_107349540-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/14/R14-18102_kapa-NGv3-PE100-NGv3-14_97304098_107349540-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/14/tx/tmpfJ1moo/R14-18102_kapa-NGv3-PE100-NGv3-14_97304098_107349540.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:13Z] INFO  18:13:35,516 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:13Z] INFO  18:13:35,517 HelpFormatter - Date/Time: 2016/04/14 18:13:35
[2016-04-15T01:13Z] INFO  18:13:35,518 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:13Z] INFO  18:13:35,518 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:13Z] INFO  18:13:35,607 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:13Z] GATK: UnifiedGenotyper
[2016-04-15T01:13Z] INFO  18:13:35,760 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:13Z] INFO  18:13:35,829 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T01:13Z] INFO  18:13:35,838 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:13Z] INFO  18:13:35,918 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-15T01:13Z] INFO  18:13:36,048 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T01:13Z] INFO  18:13:36,057 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:13Z] INFO  18:13:36,167 ProgressMeter -            done    469270.0    18.0 s      39.0 s      100.0%    18.0 s       0.0 s
[2016-04-15T01:13Z] INFO  18:13:36,167 ProgressMeter - Total runtime 18.59 secs, 0.31 min, 0.01 hours
[2016-04-15T01:13Z] INFO  18:13:36,168 MicroScheduler - 16668 reads were filtered out during the traversal out of approximately 201036 total reads (8.29%)
[2016-04-15T01:13Z] INFO  18:13:36,168 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:13Z] INFO  18:13:36,168 MicroScheduler -   -> 279 reads (0.14% of total) failing BadMateFilter
[2016-04-15T01:13Z] INFO  18:13:36,168 MicroScheduler -   -> 16238 reads (8.08% of total) failing DuplicateReadFilter
[2016-04-15T01:13Z] INFO  18:13:36,169 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:13Z] INFO  18:13:36,169 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:13Z] INFO  18:13:36,169 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:13Z] INFO  18:13:36,169 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:13Z] INFO  18:13:36,170 MicroScheduler -   -> 151 reads (0.08% of total) failing UnmappedReadFilter
[2016-04-15T01:13Z] INFO  18:13:36,177 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:13Z] INFO  18:13:36,180 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:13Z] INFO  18:13:36,181 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:13Z] INFO  18:13:36,181 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:13Z] INFO  18:13:36,185 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/15/R14-18102_kapa-NGv3-PE100-NGv3-sort-15_0_20740485-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/15/R14-18102_kapa-NGv3-PE100-NGv3-15_0_20740485-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/15/tx/tmprzc77d/R14-18102_kapa-NGv3-PE100-NGv3-15_0_20740485.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:13Z] INFO  18:13:36,204 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:13Z] INFO  18:13:36,204 HelpFormatter - Date/Time: 2016/04/14 18:13:36
[2016-04-15T01:13Z] INFO  18:13:36,204 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:13Z] INFO  18:13:36,205 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:13Z] INFO  18:13:36,295 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.24
[2016-04-15T01:13Z] INFO  18:13:36,341 IntervalUtils - Processing 176504 bp from intervals
[2016-04-15T01:13Z] WARN  18:13:36,346 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:13Z] INFO  18:13:36,348 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:13Z] INFO  18:13:36,350 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:13Z] INFO  18:13:36,350 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:13Z] INFO  18:13:36,351 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:13Z] INFO  18:13:36,356 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/15/R14-18102_kapa-NGv3-PE100-NGv3-sort-15_20741621_36872162-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/15/R14-18102_kapa-NGv3-PE100-NGv3-15_20741621_36872162-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/15/tx/tmpCFFofW/R14-18102_kapa-NGv3-PE100-NGv3-15_20741621_36872162.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:13Z] INFO  18:13:36,370 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:13Z] INFO  18:13:36,371 HelpFormatter - Date/Time: 2016/04/14 18:13:36
[2016-04-15T01:13Z] INFO  18:13:36,372 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:13Z] INFO  18:13:36,372 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:13Z] INFO  18:13:36,374 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:13Z] INFO  18:13:36,420 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:13Z] INFO  18:13:36,504 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:13Z] INFO  18:13:36,504 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:13Z] INFO  18:13:36,505 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T01:13Z] INFO  18:13:36,505 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T01:13Z] INFO  18:13:36,545 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:13Z] INFO  18:13:36,572 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:13Z] INFO  18:13:36,573 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:13Z] INFO  18:13:36,641 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T01:13Z] INFO  18:13:36,655 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:13Z] INFO  18:13:36,736 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-15T01:13Z] INFO  18:13:36,742 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T01:13Z] INFO  18:13:36,762 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:13Z] INFO  18:13:36,773 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:13Z] INFO  18:13:36,775 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:13Z] INFO  18:13:36,776 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:13Z] INFO  18:13:36,776 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:13Z] INFO  18:13:36,786 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/15/R14-18102_kapa-NGv3-PE100-NGv3-sort-15_36887086_52402170-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/15/R14-18102_kapa-NGv3-PE100-NGv3-15_36887086_52402170-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/15/tx/tmpX06AJQ/R14-18102_kapa-NGv3-PE100-NGv3-15_36887086_52402170.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:13Z] INFO  18:13:36,820 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:13Z] INFO  18:13:36,821 HelpFormatter - Date/Time: 2016/04/14 18:13:36
[2016-04-15T01:13Z] INFO  18:13:36,821 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:13Z] INFO  18:13:36,821 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:13Z] INFO  18:13:36,882 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.12
[2016-04-15T01:13Z] INFO  18:13:36,916 IntervalUtils - Processing 188545 bp from intervals
[2016-04-15T01:13Z] WARN  18:13:36,932 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:13Z] INFO  18:13:37,002 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:13Z] INFO  18:13:37,071 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:13Z] INFO  18:13:37,135 IntervalUtils - Processing 989 bp from intervals
[2016-04-15T01:13Z] WARN  18:13:37,140 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:13Z] INFO  18:13:37,209 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:13Z] INFO  18:13:37,211 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:13Z] INFO  18:13:37,211 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T01:13Z] INFO  18:13:37,212 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T01:13Z] INFO  18:13:37,253 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T01:13Z] INFO  18:13:37,258 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:13Z] INFO  18:13:37,262 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:13Z] INFO  18:13:37,301 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:13Z] INFO  18:13:37,302 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:13Z] INFO  18:13:37,298 IntervalUtils - Processing 177979 bp from intervals
[2016-04-15T01:13Z] WARN  18:13:37,318 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:13Z] INFO  18:13:37,304 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:13Z] INFO  18:13:37,323 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:13Z] INFO  18:13:37,324 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T01:13Z] INFO  18:13:37,325 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T01:13Z] INFO  18:13:37,364 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.10
[2016-04-15T01:13Z] INFO  18:13:37,403 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:13Z] INFO  18:13:37,415 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:13Z] INFO  18:13:37,447 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:13Z] INFO  18:13:37,581 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:13Z] INFO  18:13:37,582 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:13Z] INFO  18:13:37,582 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T01:13Z] INFO  18:13:37,582 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T01:13Z] INFO  18:13:37,630 ProgressMeter -            done    504383.0    21.0 s      43.0 s      100.0%    21.0 s       0.0 s
[2016-04-15T01:13Z] INFO  18:13:37,632 ProgressMeter - Total runtime 21.95 secs, 0.37 min, 0.01 hours
[2016-04-15T01:13Z] INFO  18:13:37,632 MicroScheduler - 18456 reads were filtered out during the traversal out of approximately 219621 total reads (8.40%)
[2016-04-15T01:13Z] INFO  18:13:37,633 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:13Z] INFO  18:13:37,633 MicroScheduler -   -> 371 reads (0.17% of total) failing BadMateFilter
[2016-04-15T01:13Z] INFO  18:13:37,634 MicroScheduler -   -> 17907 reads (8.15% of total) failing DuplicateReadFilter
[2016-04-15T01:13Z] INFO  18:13:37,635 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:13Z] INFO  18:13:37,635 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:13Z] INFO  18:13:37,636 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:13Z] INFO  18:13:37,636 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:13Z] INFO  18:13:37,637 MicroScheduler -   -> 178 reads (0.08% of total) failing UnmappedReadFilter
[2016-04-15T01:13Z] INFO  18:13:37,676 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:13Z] INFO  18:13:37,677 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:13Z] INFO  18:13:37,705 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:13Z] INFO  18:13:37,905 IntervalUtils - Processing 374190 bp from intervals
[2016-04-15T01:13Z] WARN  18:13:37,921 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:13Z] GATK: UnifiedGenotyper
[2016-04-15T01:13Z] INFO  18:13:38,036 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:13Z] INFO  18:13:38,177 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:13Z] INFO  18:13:38,179 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:13Z] INFO  18:13:38,179 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T01:13Z] INFO  18:13:38,180 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T01:13Z] INFO  18:13:38,265 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:13Z] INFO  18:13:38,266 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:13Z] INFO  18:13:38,926 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:13Z] INFO  18:13:38,929 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:13Z] INFO  18:13:38,930 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:13Z] INFO  18:13:38,931 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:13Z] INFO  18:13:38,956 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/15/R14-18102_kapa-NGv3-PE100-NGv3-sort-15_52404364_67923265-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/15/R14-18102_kapa-NGv3-PE100-NGv3-15_52404364_67923265-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/15/tx/tmpH728Py/R14-18102_kapa-NGv3-PE100-NGv3-15_52404364_67923265.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:13Z] INFO  18:13:38,987 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:13Z] INFO  18:13:38,987 HelpFormatter - Date/Time: 2016/04/14 18:13:38
[2016-04-15T01:13Z] INFO  18:13:38,987 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:13Z] INFO  18:13:38,988 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:13Z] INFO  18:13:39,160 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:13Z] INFO  18:13:39,173 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:13Z] INFO  18:13:39,389 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T01:13Z] INFO  18:13:39,397 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:13Z] GATK: UnifiedGenotyper
[2016-04-15T01:13Z] INFO  18:13:39,430 ProgressMeter -    12:122260496    908946.0    30.0 s      33.0 s       70.8%    42.0 s      12.0 s
[2016-04-15T01:13Z] INFO  18:13:39,523 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.12
[2016-04-15T01:13Z] INFO  18:13:39,826 ProgressMeter -            done    399815.0    17.0 s      43.0 s      100.0%    17.0 s       0.0 s
[2016-04-15T01:13Z] INFO  18:13:39,826 ProgressMeter - Total runtime 17.29 secs, 0.29 min, 0.00 hours
[2016-04-15T01:13Z] INFO  18:13:39,826 MicroScheduler - 15635 reads were filtered out during the traversal out of approximately 186840 total reads (8.37%)
[2016-04-15T01:13Z] INFO  18:13:39,827 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:13Z] INFO  18:13:39,827 MicroScheduler -   -> 314 reads (0.17% of total) failing BadMateFilter
[2016-04-15T01:13Z] INFO  18:13:39,827 MicroScheduler -   -> 15152 reads (8.11% of total) failing DuplicateReadFilter
[2016-04-15T01:13Z] INFO  18:13:39,827 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:13Z] INFO  18:13:39,828 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:13Z] INFO  18:13:39,828 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:13Z] INFO  18:13:39,828 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:13Z] INFO  18:13:39,828 MicroScheduler -   -> 169 reads (0.09% of total) failing UnmappedReadFilter
[2016-04-15T01:13Z] INFO  18:13:39,988 IntervalUtils - Processing 254619 bp from intervals
[2016-04-15T01:13Z] WARN  18:13:40,009 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:13Z] INFO  18:13:40,037 ProgressMeter -            done       989.0     2.0 s      45.7 m       91.0%     2.0 s       0.0 s
[2016-04-15T01:13Z] INFO  18:13:40,037 ProgressMeter - Total runtime 2.71 secs, 0.05 min, 0.00 hours
[2016-04-15T01:13Z] INFO  18:13:40,038 MicroScheduler - 133 reads were filtered out during the traversal out of approximately 2590 total reads (5.14%)
[2016-04-15T01:13Z] INFO  18:13:40,038 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:13Z] INFO  18:13:40,038 MicroScheduler -   -> 5 reads (0.19% of total) failing BadMateFilter
[2016-04-15T01:13Z] INFO  18:13:40,039 MicroScheduler -   -> 124 reads (4.79% of total) failing DuplicateReadFilter
[2016-04-15T01:13Z] INFO  18:13:40,039 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:13Z] INFO  18:13:40,039 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:13Z] INFO  18:13:40,040 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:13Z] INFO  18:13:40,040 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:13Z] INFO  18:13:40,040 MicroScheduler -   -> 4 reads (0.15% of total) failing UnmappedReadFilter
[2016-04-15T01:13Z] INFO  18:13:40,092 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:13Z] INFO  18:13:40,229 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:13Z] INFO  18:13:40,231 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:13Z] INFO  18:13:40,231 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T01:13Z] INFO  18:13:40,232 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T01:13Z] INFO  18:13:40,327 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:13Z] INFO  18:13:40,328 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:13Z] INFO  18:13:41,255 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:13Z] GATK: UnifiedGenotyper
[2016-04-15T01:13Z] INFO  18:13:41,528 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:13Z] INFO  18:13:41,676 ProgressMeter -            done   2754858.0    52.0 s      19.0 s      100.0%    52.0 s       0.0 s
[2016-04-15T01:13Z] INFO  18:13:41,678 ProgressMeter - Total runtime 52.94 secs, 0.88 min, 0.01 hours
[2016-04-15T01:13Z] INFO  18:13:41,679 MicroScheduler - 66250 reads were filtered out during the traversal out of approximately 781599 total reads (8.48%)
[2016-04-15T01:13Z] INFO  18:13:41,679 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:13Z] INFO  18:13:41,680 MicroScheduler -   -> 1276 reads (0.16% of total) failing BadMateFilter
[2016-04-15T01:13Z] INFO  18:13:41,683 MicroScheduler -   -> 64363 reads (8.23% of total) failing DuplicateReadFilter
[2016-04-15T01:13Z] INFO  18:13:41,684 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:13Z] INFO  18:13:41,684 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:13Z] INFO  18:13:41,685 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:13Z] INFO  18:13:41,685 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:13Z] INFO  18:13:41,686 MicroScheduler -   -> 611 reads (0.08% of total) failing UnmappedReadFilter
[2016-04-15T01:13Z] INFO  18:13:41,783 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:13Z] INFO  18:13:41,787 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:13Z] INFO  18:13:41,787 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:13Z] INFO  18:13:41,788 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:13Z] INFO  18:13:41,793 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/15/R14-18102_kapa-NGv3-PE100-NGv3-sort-15_67932890_83447639-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/15/R14-18102_kapa-NGv3-PE100-NGv3-15_67932890_83447639-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/15/tx/tmpcM9Ng1/R14-18102_kapa-NGv3-PE100-NGv3-15_67932890_83447639.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:13Z] INFO  18:13:41,808 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:13Z] INFO  18:13:41,808 HelpFormatter - Date/Time: 2016/04/14 18:13:41
[2016-04-15T01:13Z] INFO  18:13:41,809 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:13Z] INFO  18:13:41,809 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:13Z] GATK: UnifiedGenotyper
[2016-04-15T01:13Z] INFO  18:13:42,016 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:13Z] INFO  18:13:42,323 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T01:13Z] INFO  18:13:42,343 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:13Z] INFO  18:13:42,408 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:13Z] INFO  18:13:42,411 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:13Z] INFO  18:13:42,411 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:13Z] INFO  18:13:42,412 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:13Z] INFO  18:13:42,416 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/15/R14-18102_kapa-NGv3-PE100-NGv3-sort-15_83448996_98982979-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/15/R14-18102_kapa-NGv3-PE100-NGv3-15_83448996_98982979-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/15/tx/tmpi1fO6M/R14-18102_kapa-NGv3-PE100-NGv3-15_83448996_98982979.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:13Z] INFO  18:13:42,431 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.09
[2016-04-15T01:13Z] INFO  18:13:42,450 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:13Z] INFO  18:13:42,450 HelpFormatter - Date/Time: 2016/04/14 18:13:42
[2016-04-15T01:13Z] INFO  18:13:42,451 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:13Z] INFO  18:13:42,452 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:13Z] INFO  18:13:42,619 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:13Z] INFO  18:13:42,831 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T01:13Z] INFO  18:13:42,840 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:13Z] INFO  18:13:42,919 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-15T01:13Z] INFO  18:13:42,986 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:13Z] INFO  18:13:42,997 IntervalUtils - Processing 293221 bp from intervals
[2016-04-15T01:13Z] WARN  18:13:43,002 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:13Z] INFO  18:13:43,118 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:13Z] INFO  18:13:43,254 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:13Z] INFO  18:13:43,255 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:13Z] INFO  18:13:43,256 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T01:13Z] INFO  18:13:43,257 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T01:13Z] INFO  18:13:43,302 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:13Z] INFO  18:13:43,303 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:13Z] INFO  18:13:43,359 IntervalUtils - Processing 184993 bp from intervals
[2016-04-15T01:13Z] WARN  18:13:43,364 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:13Z] GATK: UnifiedGenotyper
[2016-04-15T01:13Z] INFO  18:13:43,437 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:13Z] INFO  18:13:43,551 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:13Z] INFO  18:13:43,552 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:13Z] INFO  18:13:43,553 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T01:13Z] INFO  18:13:43,553 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T01:13Z] INFO  18:13:43,618 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:13Z] INFO  18:13:43,619 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:13Z] INFO  18:13:44,315 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:13Z] INFO  18:13:44,318 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:13Z] INFO  18:13:44,318 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:13Z] INFO  18:13:44,318 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:13Z] INFO  18:13:44,333 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/15/R14-18102_kapa-NGv3-PE100-NGv3-sort-15_98984299_102531392-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/15/R14-18102_kapa-NGv3-PE100-NGv3-15_98984299_102531392-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/15/tx/tmp6s5Icx/R14-18102_kapa-NGv3-PE100-NGv3-15_98984299_102531392.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:13Z] INFO  18:13:44,344 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:13Z] INFO  18:13:44,344 HelpFormatter - Date/Time: 2016/04/14 18:13:44
[2016-04-15T01:13Z] INFO  18:13:44,345 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:13Z] INFO  18:13:44,346 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:13Z] INFO  18:13:44,537 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:13Z] INFO  18:13:44,786 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T01:13Z] INFO  18:13:44,807 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:13Z] INFO  18:13:44,921 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.11
[2016-04-15T01:13Z] INFO  18:13:44,994 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:13Z] INFO  18:13:44,998 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:13Z] INFO  18:13:44,999 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:13Z] INFO  18:13:45,000 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:13Z] INFO  18:13:45,005 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/16/R14-18102_kapa-NGv3-PE100-NGv3-sort-16_0_15528616-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/16/R14-18102_kapa-NGv3-PE100-NGv3-16_0_15528616-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/16/tx/tmpIb6EdV/R14-18102_kapa-NGv3-PE100-NGv3-16_0_15528616.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:13Z] INFO  18:13:45,033 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:13Z] INFO  18:13:45,041 HelpFormatter - Date/Time: 2016/04/14 18:13:44
[2016-04-15T01:13Z] INFO  18:13:45,042 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:13Z] INFO  18:13:45,042 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:13Z] INFO  18:13:45,403 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:13Z] INFO  18:13:45,542 IntervalUtils - Processing 49123 bp from intervals
[2016-04-15T01:13Z] WARN  18:13:45,548 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:13Z] INFO  18:13:45,627 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:13Z] INFO  18:13:45,632 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T01:13Z] INFO  18:13:45,641 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:13Z] INFO  18:13:45,716 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:13Z] INFO  18:13:45,717 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:13Z] INFO  18:13:45,717 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T01:13Z] INFO  18:13:45,717 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T01:13Z] INFO  18:13:45,724 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-15T01:13Z] INFO  18:13:45,772 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:13Z] INFO  18:13:45,773 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:13Z] INFO  18:13:46,184 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:13Z] INFO  18:13:46,187 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:13Z] INFO  18:13:46,187 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:13Z] INFO  18:13:46,187 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:13Z] INFO  18:13:46,201 IntervalUtils - Processing 436708 bp from intervals
[2016-04-15T01:13Z] INFO  18:13:46,202 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/16/R14-18102_kapa-NGv3-PE100-NGv3-sort-16_15596122_31106473-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/16/R14-18102_kapa-NGv3-PE100-NGv3-16_15596122_31106473-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/16/tx/tmpNVB2d6/R14-18102_kapa-NGv3-PE100-NGv3-16_15596122_31106473.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:13Z] WARN  18:13:46,206 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:13Z] INFO  18:13:46,212 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:13Z] INFO  18:13:46,213 HelpFormatter - Date/Time: 2016/04/14 18:13:46
[2016-04-15T01:13Z] INFO  18:13:46,213 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:13Z] INFO  18:13:46,213 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:13Z] INFO  18:13:46,289 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:13Z] INFO  18:13:46,401 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:13Z] INFO  18:13:46,446 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:13Z] INFO  18:13:46,447 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:13Z] INFO  18:13:46,447 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T01:13Z] INFO  18:13:46,448 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T01:13Z] INFO  18:13:46,567 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:13Z] INFO  18:13:46,568 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:13Z] INFO  18:13:46,628 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T01:13Z] INFO  18:13:46,643 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:13Z] INFO  18:13:46,726 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-15T01:13Z] INFO  18:13:47,103 IntervalUtils - Processing 400248 bp from intervals
[2016-04-15T01:13Z] WARN  18:13:47,108 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:13Z] INFO  18:13:47,215 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:13Z] INFO  18:13:47,316 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:13Z] INFO  18:13:47,317 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:13Z] INFO  18:13:47,317 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T01:13Z] INFO  18:13:47,318 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T01:13Z] INFO  18:13:47,365 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:13Z] INFO  18:13:47,366 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:13Z] INFO  18:13:48,162 ProgressMeter -            done    291019.0    14.0 s      49.0 s       99.9%    14.0 s       0.0 s
[2016-04-15T01:13Z] INFO  18:13:48,162 ProgressMeter - Total runtime 14.42 secs, 0.24 min, 0.00 hours
[2016-04-15T01:13Z] INFO  18:13:48,163 MicroScheduler - 8965 reads were filtered out during the traversal out of approximately 108090 total reads (8.29%)
[2016-04-15T01:13Z] INFO  18:13:48,163 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:13Z] INFO  18:13:48,163 MicroScheduler -   -> 184 reads (0.17% of total) failing BadMateFilter
[2016-04-15T01:13Z] INFO  18:13:48,164 MicroScheduler -   -> 8687 reads (8.04% of total) failing DuplicateReadFilter
[2016-04-15T01:13Z] INFO  18:13:48,164 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:13Z] INFO  18:13:48,164 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:13Z] INFO  18:13:48,165 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:13Z] INFO  18:13:48,165 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:13Z] INFO  18:13:48,165 MicroScheduler -   -> 94 reads (0.09% of total) failing UnmappedReadFilter
[2016-04-15T01:13Z] INFO  18:13:49,188 ProgressMeter -            done   1353894.0    39.0 s      29.0 s      100.0%    39.0 s       0.0 s
[2016-04-15T01:13Z] INFO  18:13:49,189 ProgressMeter - Total runtime 39.77 secs, 0.66 min, 0.01 hours
[2016-04-15T01:13Z] INFO  18:13:49,189 MicroScheduler - 43961 reads were filtered out during the traversal out of approximately 516994 total reads (8.50%)
[2016-04-15T01:13Z] INFO  18:13:49,189 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:13Z] INFO  18:13:49,189 MicroScheduler -   -> 827 reads (0.16% of total) failing BadMateFilter
[2016-04-15T01:13Z] INFO  18:13:49,190 MicroScheduler -   -> 42690 reads (8.26% of total) failing DuplicateReadFilter
[2016-04-15T01:13Z] INFO  18:13:49,190 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:13Z] INFO  18:13:49,190 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:13Z] INFO  18:13:49,190 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:13Z] INFO  18:13:49,191 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:13Z] INFO  18:13:49,191 MicroScheduler -   -> 444 reads (0.09% of total) failing UnmappedReadFilter
[2016-04-15T01:13Z] INFO  18:13:49,519 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:13Z] GATK: UnifiedGenotyper
[2016-04-15T01:13Z] INFO  18:13:50,565 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:13Z] GATK: UnifiedGenotyper
[2016-04-15T01:13Z] INFO  18:13:52,681 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:13Z] INFO  18:13:52,684 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:13Z] INFO  18:13:52,684 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:13Z] INFO  18:13:52,684 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:13Z] INFO  18:13:52,688 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/16/R14-18102_kapa-NGv3-PE100-NGv3-sort-16_31120544_46629582-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/16/R14-18102_kapa-NGv3-PE100-NGv3-16_31120544_46629582-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/16/tx/tmpflDWYM/R14-18102_kapa-NGv3-PE100-NGv3-16_31120544_46629582.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:13Z] INFO  18:13:52,716 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:13Z] INFO  18:13:52,716 HelpFormatter - Date/Time: 2016/04/14 18:13:52
[2016-04-15T01:13Z] INFO  18:13:52,716 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:13Z] INFO  18:13:52,716 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:13Z] INFO  18:13:52,919 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:13Z] INFO  18:13:53,032 ProgressMeter -            done   3065212.0    52.0 s      17.0 s      100.0%    52.0 s       0.0 s
[2016-04-15T01:13Z] INFO  18:13:53,032 ProgressMeter - Total runtime 52.53 secs, 0.88 min, 0.01 hours
[2016-04-15T01:13Z] INFO  18:13:53,033 MicroScheduler - 63548 reads were filtered out during the traversal out of approximately 755818 total reads (8.41%)
[2016-04-15T01:13Z] INFO  18:13:53,033 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:13Z] INFO  18:13:53,033 MicroScheduler -   -> 1196 reads (0.16% of total) failing BadMateFilter
[2016-04-15T01:13Z] INFO  18:13:53,034 MicroScheduler -   -> 61729 reads (8.17% of total) failing DuplicateReadFilter
[2016-04-15T01:13Z] INFO  18:13:53,034 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:13Z] INFO  18:13:53,034 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:13Z] INFO  18:13:53,034 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:13Z] INFO  18:13:53,034 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:13Z] INFO  18:13:53,035 MicroScheduler -   -> 623 reads (0.08% of total) failing UnmappedReadFilter
[2016-04-15T01:13Z] INFO  18:13:53,101 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T01:13Z] INFO  18:13:53,121 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:13Z] INFO  18:13:53,188 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-15T01:13Z] INFO  18:13:53,513 IntervalUtils - Processing 40143 bp from intervals
[2016-04-15T01:13Z] WARN  18:13:53,518 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:13Z] INFO  18:13:53,624 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:13Z] INFO  18:13:53,661 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:13Z] INFO  18:13:53,662 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:13Z] INFO  18:13:53,662 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T01:13Z] INFO  18:13:53,663 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T01:13Z] INFO  18:13:53,730 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:13Z] INFO  18:13:53,738 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:13Z] INFO  18:13:53,844 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:13Z] INFO  18:13:53,847 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:13Z] INFO  18:13:53,848 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:13Z] INFO  18:13:53,848 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:13Z] INFO  18:13:53,853 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/16/R14-18102_kapa-NGv3-PE100-NGv3-sort-16_46633742_64982002-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/16/R14-18102_kapa-NGv3-PE100-NGv3-16_46633742_64982002-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/16/tx/tmp95ZQBZ/R14-18102_kapa-NGv3-PE100-NGv3-16_46633742_64982002.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:13Z] INFO  18:13:53,869 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:13Z] INFO  18:13:53,870 HelpFormatter - Date/Time: 2016/04/14 18:13:53
[2016-04-15T01:13Z] INFO  18:13:53,870 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:13Z] INFO  18:13:53,871 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:13Z] INFO  18:13:54,091 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:13Z] INFO  18:13:54,355 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T01:13Z] INFO  18:13:54,366 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:13Z] INFO  18:13:54,469 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.10
[2016-04-15T01:13Z] INFO  18:13:54,514 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:13Z] GATK: UnifiedGenotyper
[2016-04-15T01:13Z] INFO  18:13:54,918 IntervalUtils - Processing 224129 bp from intervals
[2016-04-15T01:13Z] WARN  18:13:54,924 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:13Z] INFO  18:13:55,003 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:13Z] INFO  18:13:55,097 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:13Z] INFO  18:13:55,098 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:13Z] INFO  18:13:55,099 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T01:13Z] INFO  18:13:55,100 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T01:13Z] INFO  18:13:55,185 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:13Z] INFO  18:13:55,186 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:13Z] INFO  18:13:56,128 ProgressMeter -            done    545455.0    19.0 s      35.0 s      100.0%    19.0 s       0.0 s
[2016-04-15T01:13Z] INFO  18:13:56,128 ProgressMeter - Total runtime 19.62 secs, 0.33 min, 0.01 hours
[2016-04-15T01:13Z] INFO  18:13:56,129 MicroScheduler - 17706 reads were filtered out during the traversal out of approximately 213884 total reads (8.28%)
[2016-04-15T01:13Z] INFO  18:13:56,129 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:13Z] INFO  18:13:56,130 MicroScheduler -   -> 306 reads (0.14% of total) failing BadMateFilter
[2016-04-15T01:13Z] INFO  18:13:56,130 MicroScheduler -   -> 17233 reads (8.06% of total) failing DuplicateReadFilter
[2016-04-15T01:13Z] INFO  18:13:56,130 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:13Z] INFO  18:13:56,131 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:13Z] INFO  18:13:56,131 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:13Z] INFO  18:13:56,131 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:13Z] INFO  18:13:56,131 MicroScheduler -   -> 167 reads (0.08% of total) failing UnmappedReadFilter
[2016-04-15T01:13Z] INFO  18:13:56,584 ProgressMeter -            done    695639.0    22.0 s      32.0 s      100.0%    22.0 s       0.0 s
[2016-04-15T01:13Z] INFO  18:13:56,585 ProgressMeter - Total runtime 22.83 secs, 0.38 min, 0.01 hours
[2016-04-15T01:13Z] INFO  18:13:56,585 MicroScheduler - 21700 reads were filtered out during the traversal out of approximately 258780 total reads (8.39%)
[2016-04-15T01:13Z] INFO  18:13:56,586 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:13Z] INFO  18:13:56,586 MicroScheduler -   -> 409 reads (0.16% of total) failing BadMateFilter
[2016-04-15T01:13Z] INFO  18:13:56,586 MicroScheduler -   -> 21102 reads (8.15% of total) failing DuplicateReadFilter
[2016-04-15T01:13Z] INFO  18:13:56,586 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:13Z] INFO  18:13:56,587 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:13Z] INFO  18:13:56,587 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:13Z] INFO  18:13:56,587 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:13Z] INFO  18:13:56,588 MicroScheduler -   -> 189 reads (0.07% of total) failing UnmappedReadFilter
[2016-04-15T01:13Z] INFO  18:13:56,699 ProgressMeter -            done    131383.0    10.0 s      83.0 s      100.0%    10.0 s       0.0 s
[2016-04-15T01:13Z] INFO  18:13:56,700 ProgressMeter - Total runtime 10.98 secs, 0.18 min, 0.00 hours
[2016-04-15T01:13Z] INFO  18:13:56,700 MicroScheduler - 5487 reads were filtered out during the traversal out of approximately 68064 total reads (8.06%)
[2016-04-15T01:13Z] INFO  18:13:56,701 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:13Z] INFO  18:13:56,701 MicroScheduler -   -> 103 reads (0.15% of total) failing BadMateFilter
[2016-04-15T01:13Z] INFO  18:13:56,701 MicroScheduler -   -> 5334 reads (7.84% of total) failing DuplicateReadFilter
[2016-04-15T01:13Z] INFO  18:13:56,702 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:13Z] INFO  18:13:56,702 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:13Z] INFO  18:13:56,702 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:13Z] INFO  18:13:56,703 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:13Z] INFO  18:13:56,703 MicroScheduler -   -> 50 reads (0.07% of total) failing UnmappedReadFilter
[2016-04-15T01:13Z] INFO  18:13:57,758 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:13Z] INFO  18:13:57,752 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:13Z] INFO  18:13:57,765 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:13Z] INFO  18:13:57,766 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:13Z] INFO  18:13:57,766 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:13Z] INFO  18:13:57,770 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/16/R14-18102_kapa-NGv3-PE100-NGv3-sort-16_64982511_80574976-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/16/R14-18102_kapa-NGv3-PE100-NGv3-16_64982511_80574976-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/16/tx/tmp6K2X_y/R14-18102_kapa-NGv3-PE100-NGv3-16_64982511_80574976.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:13Z] INFO  18:13:57,780 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:13Z] INFO  18:13:57,792 HelpFormatter - Date/Time: 2016/04/14 18:13:57
[2016-04-15T01:13Z] INFO  18:13:57,793 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:13Z] INFO  18:13:57,794 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:13Z] INFO  18:13:57,875 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:13Z] INFO  18:13:57,965 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:13Z] GATK: UnifiedGenotyper
[2016-04-15T01:13Z] INFO  18:13:58,078 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:13Z] INFO  18:13:58,162 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T01:13Z] INFO  18:13:58,170 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:13Z] INFO  18:13:58,236 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-15T01:13Z] GATK: UnifiedGenotyper
[2016-04-15T01:13Z] GATK: UnifiedGenotyper
[2016-04-15T01:13Z] INFO  18:13:58,746 IntervalUtils - Processing 344918 bp from intervals
[2016-04-15T01:13Z] WARN  18:13:58,753 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:13Z] INFO  18:13:58,842 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:13Z] INFO  18:13:59,008 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:13Z] INFO  18:13:59,009 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:13Z] INFO  18:13:59,010 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T01:13Z] INFO  18:13:59,011 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T01:13Z] INFO  18:13:59,086 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:13Z] INFO  18:13:59,087 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:14Z] INFO  18:14:00,444 ProgressMeter -     14:31381313   1589837.0    30.0 s      18.0 s       87.5%    34.0 s       4.0 s
[2016-04-15T01:14Z] INFO  18:14:01,225 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:14Z] INFO  18:14:01,228 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:14Z] INFO  18:14:01,229 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:14Z] INFO  18:14:01,230 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:14Z] INFO  18:14:01,235 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/16/R14-18102_kapa-NGv3-PE100-NGv3-sort-16_80575258_90354753-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/16/R14-18102_kapa-NGv3-PE100-NGv3-16_80575258_90354753-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/16/tx/tmpb2Osal/R14-18102_kapa-NGv3-PE100-NGv3-16_80575258_90354753.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:14Z] INFO  18:14:01,246 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:14Z] INFO  18:14:01,247 HelpFormatter - Date/Time: 2016/04/14 18:14:01
[2016-04-15T01:14Z] INFO  18:14:01,247 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:14Z] INFO  18:14:01,247 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:14Z] INFO  18:14:01,285 ProgressMeter -            done    633510.0    23.0 s      37.0 s      100.0%    23.0 s       0.0 s
[2016-04-15T01:14Z] INFO  18:14:01,286 ProgressMeter - Total runtime 23.70 secs, 0.40 min, 0.01 hours
[2016-04-15T01:14Z] INFO  18:14:01,286 MicroScheduler - 21583 reads were filtered out during the traversal out of approximately 295554 total reads (7.30%)
[2016-04-15T01:14Z] INFO  18:14:01,287 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:14Z] INFO  18:14:01,287 MicroScheduler -   -> 520 reads (0.18% of total) failing BadMateFilter
[2016-04-15T01:14Z] INFO  18:14:01,287 MicroScheduler -   -> 20815 reads (7.04% of total) failing DuplicateReadFilter
[2016-04-15T01:14Z] INFO  18:14:01,287 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:14Z] INFO  18:14:01,288 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:14Z] INFO  18:14:01,288 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:14Z] INFO  18:14:01,288 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:14Z] INFO  18:14:01,288 MicroScheduler -   -> 248 reads (0.08% of total) failing UnmappedReadFilter
[2016-04-15T01:14Z] INFO  18:14:01,325 ProgressMeter -            done    817418.0    24.0 s      29.0 s      100.0%    24.0 s       0.0 s
[2016-04-15T01:14Z] INFO  18:14:01,326 ProgressMeter - Total runtime 24.12 secs, 0.40 min, 0.01 hours
[2016-04-15T01:14Z] INFO  18:14:01,326 MicroScheduler - 25197 reads were filtered out during the traversal out of approximately 289460 total reads (8.70%)
[2016-04-15T01:14Z] INFO  18:14:01,326 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:14Z] INFO  18:14:01,327 MicroScheduler -   -> 492 reads (0.17% of total) failing BadMateFilter
[2016-04-15T01:14Z] INFO  18:14:01,327 MicroScheduler -   -> 24483 reads (8.46% of total) failing DuplicateReadFilter
[2016-04-15T01:14Z] INFO  18:14:01,327 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:14Z] INFO  18:14:01,327 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:14Z] INFO  18:14:01,328 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:14Z] INFO  18:14:01,328 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:14Z] INFO  18:14:01,328 MicroScheduler -   -> 222 reads (0.08% of total) failing UnmappedReadFilter
[2016-04-15T01:14Z] INFO  18:14:01,422 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:14Z] INFO  18:14:01,465 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:14Z] INFO  18:14:01,469 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:14Z] INFO  18:14:01,469 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:14Z] INFO  18:14:01,469 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:14Z] INFO  18:14:01,473 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/17/R14-18102_kapa-NGv3-PE100-NGv3-sort-17_0_15511002-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/17/R14-18102_kapa-NGv3-PE100-NGv3-17_0_15511002-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/17/tx/tmpX_slss/R14-18102_kapa-NGv3-PE100-NGv3-17_0_15511002.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:14Z] INFO  18:14:01,489 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:14Z] INFO  18:14:01,490 HelpFormatter - Date/Time: 2016/04/14 18:14:01
[2016-04-15T01:14Z] INFO  18:14:01,490 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:14Z] INFO  18:14:01,491 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:14Z] INFO  18:14:01,509 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:14Z] INFO  18:14:01,512 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:14Z] INFO  18:14:01,513 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:14Z] INFO  18:14:01,513 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:14Z] INFO  18:14:01,518 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/17/R14-18102_kapa-NGv3-PE100-NGv3-sort-17_15515955_31039213-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/17/R14-18102_kapa-NGv3-PE100-NGv3-17_15515955_31039213-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/17/tx/tmpP35vzv/R14-18102_kapa-NGv3-PE100-NGv3-17_15515955_31039213.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:14Z] INFO  18:14:01,531 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:14Z] INFO  18:14:01,532 HelpFormatter - Date/Time: 2016/04/14 18:14:01
[2016-04-15T01:14Z] INFO  18:14:01,533 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:14Z] INFO  18:14:01,534 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:14Z] INFO  18:14:01,590 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T01:14Z] INFO  18:14:01,599 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:14Z] INFO  18:14:01,640 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:14Z] INFO  18:14:01,672 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-15T01:14Z] INFO  18:14:01,705 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:14Z] INFO  18:14:01,830 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T01:14Z] INFO  18:14:01,842 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:14Z] INFO  18:14:01,886 ProgressMeter -            done    727916.0    27.0 s      38.0 s      100.0%    27.0 s       0.0 s
[2016-04-15T01:14Z] INFO  18:14:01,887 ProgressMeter - Total runtime 27.87 secs, 0.46 min, 0.01 hours
[2016-04-15T01:14Z] INFO  18:14:01,888 MicroScheduler - 28034 reads were filtered out during the traversal out of approximately 332064 total reads (8.44%)
[2016-04-15T01:14Z] INFO  18:14:01,889 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:14Z] INFO  18:14:01,890 MicroScheduler -   -> 536 reads (0.16% of total) failing BadMateFilter
[2016-04-15T01:14Z] INFO  18:14:01,891 MicroScheduler -   -> 27205 reads (8.19% of total) failing DuplicateReadFilter
[2016-04-15T01:14Z] INFO  18:14:01,891 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:14Z] INFO  18:14:01,892 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:14Z] INFO  18:14:01,893 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:14Z] INFO  18:14:01,894 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:14Z] INFO  18:14:01,895 MicroScheduler -   -> 293 reads (0.09% of total) failing UnmappedReadFilter
[2016-04-15T01:14Z] INFO  18:14:01,902 ProgressMeter -            done    240450.0     8.0 s      34.0 s      100.0%     8.0 s       0.0 s
[2016-04-15T01:14Z] INFO  18:14:01,903 ProgressMeter - Total runtime 8.24 secs, 0.14 min, 0.00 hours
[2016-04-15T01:14Z] INFO  18:14:01,904 MicroScheduler - 5306 reads were filtered out during the traversal out of approximately 68892 total reads (7.70%)
[2016-04-15T01:14Z] INFO  18:14:01,905 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:14Z] INFO  18:14:01,905 MicroScheduler -   -> 115 reads (0.17% of total) failing BadMateFilter
[2016-04-15T01:14Z] INFO  18:14:01,906 MicroScheduler -   -> 5140 reads (7.46% of total) failing DuplicateReadFilter
[2016-04-15T01:14Z] INFO  18:14:01,907 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:14Z] INFO  18:14:01,908 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:14Z] INFO  18:14:01,908 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:14Z] INFO  18:14:01,909 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:14Z] INFO  18:14:01,910 MicroScheduler -   -> 51 reads (0.07% of total) failing UnmappedReadFilter
[2016-04-15T01:14Z] INFO  18:14:01,955 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T01:14Z] INFO  18:14:01,961 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.12
[2016-04-15T01:14Z] INFO  18:14:01,966 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:14Z] INFO  18:14:02,058 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.09
[2016-04-15T01:14Z] INFO  18:14:02,085 IntervalUtils - Processing 203451 bp from intervals
[2016-04-15T01:14Z] WARN  18:14:02,091 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:14Z] INFO  18:14:02,174 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:14Z] INFO  18:14:02,286 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:14Z] INFO  18:14:02,288 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:14Z] INFO  18:14:02,288 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T01:14Z] INFO  18:14:02,289 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T01:14Z] INFO  18:14:02,450 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:14Z] INFO  18:14:02,451 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:14Z] INFO  18:14:02,585 IntervalUtils - Processing 320055 bp from intervals
[2016-04-15T01:14Z] WARN  18:14:02,595 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:14Z] INFO  18:14:02,698 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:14Z] INFO  18:14:02,737 IntervalUtils - Processing 497719 bp from intervals
[2016-04-15T01:14Z] WARN  18:14:02,743 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:14Z] INFO  18:14:02,803 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:14Z] INFO  18:14:02,812 ProgressMeter -            done   1676712.0    32.0 s      19.0 s      100.0%    32.0 s       0.0 s
[2016-04-15T01:14Z] INFO  18:14:02,813 ProgressMeter - Total runtime 32.37 secs, 0.54 min, 0.01 hours
[2016-04-15T01:14Z] INFO  18:14:02,813 MicroScheduler - 36349 reads were filtered out during the traversal out of approximately 435790 total reads (8.34%)
[2016-04-15T01:14Z] INFO  18:14:02,814 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:14Z] INFO  18:14:02,815 MicroScheduler -   -> 680 reads (0.16% of total) failing BadMateFilter
[2016-04-15T01:14Z] INFO  18:14:02,815 MicroScheduler -   -> 35334 reads (8.11% of total) failing DuplicateReadFilter
[2016-04-15T01:14Z] INFO  18:14:02,816 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:14Z] INFO  18:14:02,816 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:14Z] INFO  18:14:02,817 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:14Z] INFO  18:14:02,818 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:14Z] INFO  18:14:02,818 MicroScheduler -   -> 335 reads (0.08% of total) failing UnmappedReadFilter
[2016-04-15T01:14Z] INFO  18:14:02,821 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:14Z] INFO  18:14:02,827 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:14Z] INFO  18:14:02,828 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:14Z] INFO  18:14:02,829 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T01:14Z] INFO  18:14:02,830 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T01:14Z] INFO  18:14:02,873 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:14Z] INFO  18:14:02,874 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:14Z] INFO  18:14:02,887 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:14Z] INFO  18:14:02,955 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:14Z] INFO  18:14:02,956 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:14Z] INFO  18:14:02,957 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T01:14Z] INFO  18:14:02,958 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T01:14Z] INFO  18:14:03,065 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:14Z] INFO  18:14:03,066 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:14Z] GATK: UnifiedGenotyper
[2016-04-15T01:14Z] GATK: UnifiedGenotyper
[2016-04-15T01:14Z] INFO  18:14:03,502 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:14Z] INFO  18:14:03,551 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:14Z] GATK: UnifiedGenotyper
[2016-04-15T01:14Z] GATK: UnifiedGenotyper
[2016-04-15T01:14Z] INFO  18:14:04,177 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:14Z] GATK: UnifiedGenotyper
[2016-04-15T01:14Z] INFO  18:14:05,882 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:14Z] INFO  18:14:05,885 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:14Z] INFO  18:14:05,886 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:14Z] INFO  18:14:05,887 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:14Z] INFO  18:14:05,891 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/17/R14-18102_kapa-NGv3-PE100-NGv3-sort-17_46607689_62121560-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/17/R14-18102_kapa-NGv3-PE100-NGv3-17_46607689_62121560-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/17/tx/tmp5T0g35/R14-18102_kapa-NGv3-PE100-NGv3-17_46607689_62121560.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:14Z] INFO  18:14:05,902 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:14Z] INFO  18:14:05,917 HelpFormatter - Date/Time: 2016/04/14 18:14:05
[2016-04-15T01:14Z] INFO  18:14:05,918 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:14Z] INFO  18:14:05,919 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:14Z] INFO  18:14:06,150 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:14Z] INFO  18:14:06,198 ProgressMeter -            done    802075.0    25.0 s      32.0 s      100.0%    25.0 s       0.0 s
[2016-04-15T01:14Z] INFO  18:14:06,198 ProgressMeter - Total runtime 25.97 secs, 0.43 min, 0.01 hours
[2016-04-15T01:14Z] INFO  18:14:06,198 MicroScheduler - 26301 reads were filtered out during the traversal out of approximately 310014 total reads (8.48%)
[2016-04-15T01:14Z] INFO  18:14:06,199 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:14Z] INFO  18:14:06,199 MicroScheduler -   -> 470 reads (0.15% of total) failing BadMateFilter
[2016-04-15T01:14Z] INFO  18:14:06,199 MicroScheduler -   -> 25590 reads (8.25% of total) failing DuplicateReadFilter
[2016-04-15T01:14Z] INFO  18:14:06,200 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:14Z] INFO  18:14:06,200 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:14Z] INFO  18:14:06,200 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:14Z] INFO  18:14:06,200 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:14Z] INFO  18:14:06,201 MicroScheduler -   -> 241 reads (0.08% of total) failing UnmappedReadFilter
[2016-04-15T01:14Z] INFO  18:14:06,399 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T01:14Z] INFO  18:14:06,408 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:14Z] INFO  18:14:06,411 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:14Z] INFO  18:14:06,412 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:14Z] INFO  18:14:06,412 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:14Z] INFO  18:14:06,417 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/17/R14-18102_kapa-NGv3-PE100-NGv3-sort-17_31048040_46607237-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/17/R14-18102_kapa-NGv3-PE100-NGv3-17_31048040_46607237-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/17/tx/tmp6cg02w/R14-18102_kapa-NGv3-PE100-NGv3-17_31048040_46607237.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:14Z] INFO  18:14:06,432 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:14Z] INFO  18:14:06,442 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:14Z] INFO  18:14:06,442 HelpFormatter - Date/Time: 2016/04/14 18:14:06
[2016-04-15T01:14Z] INFO  18:14:06,442 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:14Z] INFO  18:14:06,442 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:14Z] INFO  18:14:06,516 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-15T01:14Z] INFO  18:14:06,634 ProgressMeter -            done    711142.0    23.0 s      32.0 s      100.0%    23.0 s       0.0 s
[2016-04-15T01:14Z] INFO  18:14:06,634 ProgressMeter - Total runtime 23.08 secs, 0.38 min, 0.01 hours
[2016-04-15T01:14Z] INFO  18:14:06,635 MicroScheduler - 22105 reads were filtered out during the traversal out of approximately 272035 total reads (8.13%)
[2016-04-15T01:14Z] INFO  18:14:06,635 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:14Z] INFO  18:14:06,635 MicroScheduler -   -> 398 reads (0.15% of total) failing BadMateFilter
[2016-04-15T01:14Z] INFO  18:14:06,635 MicroScheduler -   -> 21505 reads (7.91% of total) failing DuplicateReadFilter
[2016-04-15T01:14Z] INFO  18:14:06,636 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:14Z] INFO  18:14:06,636 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:14Z] INFO  18:14:06,636 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:14Z] INFO  18:14:06,636 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:14Z] INFO  18:14:06,637 MicroScheduler -   -> 202 reads (0.07% of total) failing UnmappedReadFilter
[2016-04-15T01:14Z] INFO  18:14:06,679 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:14Z] INFO  18:14:06,908 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T01:14Z] INFO  18:14:06,920 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:14Z] INFO  18:14:06,985 IntervalUtils - Processing 295968 bp from intervals
[2016-04-15T01:14Z] WARN  18:14:06,990 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:14Z] INFO  18:14:07,012 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.09
[2016-04-15T01:14Z] INFO  18:14:07,073 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:14Z] INFO  18:14:07,143 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:14Z] INFO  18:14:07,146 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:14Z] INFO  18:14:07,147 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:14Z] INFO  18:14:07,147 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:14Z] INFO  18:14:07,152 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/17/R14-18102_kapa-NGv3-PE100-NGv3-sort-17_62122219_77705154-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/17/R14-18102_kapa-NGv3-PE100-NGv3-17_62122219_77705154-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/17/tx/tmprfVByh/R14-18102_kapa-NGv3-PE100-NGv3-17_62122219_77705154.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:14Z] INFO  18:14:07,174 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:14Z] INFO  18:14:07,175 HelpFormatter - Date/Time: 2016/04/14 18:14:07
[2016-04-15T01:14Z] INFO  18:14:07,176 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:14Z] INFO  18:14:07,177 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:14Z] INFO  18:14:07,192 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:14Z] INFO  18:14:07,193 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:14Z] INFO  18:14:07,194 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T01:14Z] INFO  18:14:07,195 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T01:14Z] INFO  18:14:07,207 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:14Z] INFO  18:14:07,210 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:14Z] INFO  18:14:07,211 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:14Z] INFO  18:14:07,211 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:14Z] INFO  18:14:07,216 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/17/R14-18102_kapa-NGv3-PE100-NGv3-sort-17_77707305_81195210-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/17/R14-18102_kapa-NGv3-PE100-NGv3-17_77707305_81195210-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/17/tx/tmpnZ208H/R14-18102_kapa-NGv3-PE100-NGv3-17_77707305_81195210.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:14Z] INFO  18:14:07,241 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:14Z] INFO  18:14:07,242 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:14Z] INFO  18:14:07,248 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:14Z] INFO  18:14:07,253 HelpFormatter - Date/Time: 2016/04/14 18:14:07
[2016-04-15T01:14Z] INFO  18:14:07,254 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:14Z] INFO  18:14:07,259 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:14Z] INFO  18:14:07,336 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:14Z] INFO  18:14:07,429 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:14Z] INFO  18:14:07,575 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T01:14Z] INFO  18:14:07,585 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:14Z] INFO  18:14:07,618 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T01:14Z] INFO  18:14:07,630 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:14Z] INFO  18:14:07,644 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-15T01:14Z] INFO  18:14:07,698 IntervalUtils - Processing 543518 bp from intervals
[2016-04-15T01:14Z] WARN  18:14:07,714 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:14Z] INFO  18:14:07,706 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-15T01:14Z] INFO  18:14:07,720 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:14Z] INFO  18:14:07,723 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:14Z] INFO  18:14:07,724 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:14Z] INFO  18:14:07,724 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:14Z] INFO  18:14:07,729 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/18/R14-18102_kapa-NGv3-PE100-NGv3-sort-18_0_18531348-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/18/R14-18102_kapa-NGv3-PE100-NGv3-18_0_18531348-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/18/tx/tmpmTpueW/R14-18102_kapa-NGv3-PE100-NGv3-18_0_18531348.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:14Z] INFO  18:14:07,740 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:14Z] INFO  18:14:07,761 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:14Z] INFO  18:14:07,762 HelpFormatter - Date/Time: 2016/04/14 18:14:07
[2016-04-15T01:14Z] INFO  18:14:07,763 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:14Z] INFO  18:14:07,763 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:14Z] INFO  18:14:07,814 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:14Z] INFO  18:14:07,903 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:14Z] INFO  18:14:07,904 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:14Z] INFO  18:14:07,905 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T01:14Z] INFO  18:14:07,906 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T01:14Z] INFO  18:14:07,948 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:14Z] INFO  18:14:07,951 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:14Z] INFO  18:14:07,952 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:14Z] GATK: UnifiedGenotyper
[2016-04-15T01:14Z] INFO  18:14:08,149 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T01:14Z] INFO  18:14:08,157 IntervalUtils - Processing 345298 bp from intervals
[2016-04-15T01:14Z] INFO  18:14:08,159 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:14Z] WARN  18:14:08,162 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:14Z] INFO  18:14:08,194 IntervalUtils - Processing 160149 bp from intervals
[2016-04-15T01:14Z] WARN  18:14:08,200 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:14Z] INFO  18:14:08,200 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:14Z] INFO  18:14:08,203 ProgressMeter -     15:48058302   1538083.0    30.0 s      19.0 s       77.6%    38.0 s       8.0 s
[2016-04-15T01:14Z] INFO  18:14:08,233 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:14Z] INFO  18:14:08,250 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.09
[2016-04-15T01:14Z] INFO  18:14:08,267 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:14Z] INFO  18:14:08,363 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:14Z] INFO  18:14:08,364 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:14Z] INFO  18:14:08,364 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T01:14Z] INFO  18:14:08,364 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:14Z] INFO  18:14:08,365 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T01:14Z] INFO  18:14:08,365 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:14Z] INFO  18:14:08,366 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T01:14Z] INFO  18:14:08,367 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T01:14Z] INFO  18:14:08,430 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:14Z] INFO  18:14:08,431 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:14Z] INFO  18:14:08,435 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:14Z] INFO  18:14:08,436 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:14Z] GATK: UnifiedGenotyper
[2016-04-15T01:14Z] INFO  18:14:08,640 IntervalUtils - Processing 162632 bp from intervals
[2016-04-15T01:14Z] WARN  18:14:08,646 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:14Z] INFO  18:14:08,787 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:14Z] INFO  18:14:08,913 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:14Z] INFO  18:14:08,914 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:14Z] INFO  18:14:08,915 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T01:14Z] INFO  18:14:08,915 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T01:14Z] INFO  18:14:08,961 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:14Z] INFO  18:14:08,962 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:14Z] INFO  18:14:10,899 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:14Z] INFO  18:14:10,912 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:14Z] INFO  18:14:10,913 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:14Z] INFO  18:14:10,914 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:14Z] INFO  18:14:10,919 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/18/R14-18102_kapa-NGv3-PE100-NGv3-sort-18_18533538_34081962-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/18/R14-18102_kapa-NGv3-PE100-NGv3-18_18533538_34081962-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/18/tx/tmphGTKw_/R14-18102_kapa-NGv3-PE100-NGv3-18_18533538_34081962.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:14Z] INFO  18:14:10,953 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:14Z] INFO  18:14:10,954 HelpFormatter - Date/Time: 2016/04/14 18:14:10
[2016-04-15T01:14Z] INFO  18:14:10,955 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:14Z] INFO  18:14:10,955 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:14Z] INFO  18:14:11,187 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:14Z] INFO  18:14:11,487 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T01:14Z] INFO  18:14:11,496 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:14Z] INFO  18:14:11,585 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.09
[2016-04-15T01:14Z] INFO  18:14:11,617 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:14Z] INFO  18:14:11,620 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:14Z] INFO  18:14:11,621 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:14Z] INFO  18:14:11,621 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:14Z] INFO  18:14:11,626 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/18/R14-18102_kapa-NGv3-PE100-NGv3-sort-18_34092400_49867248-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/18/R14-18102_kapa-NGv3-PE100-NGv3-18_34092400_49867248-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/18/tx/tmpl83Xo_/R14-18102_kapa-NGv3-PE100-NGv3-18_34092400_49867248.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:14Z] INFO  18:14:11,639 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:14Z] INFO  18:14:11,650 HelpFormatter - Date/Time: 2016/04/14 18:14:11
[2016-04-15T01:14Z] INFO  18:14:11,651 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:14Z] INFO  18:14:11,652 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:14Z] INFO  18:14:11,891 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:14Z] INFO  18:14:12,150 IntervalUtils - Processing 148606 bp from intervals
[2016-04-15T01:14Z] WARN  18:14:12,155 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:14Z] INFO  18:14:12,179 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T01:14Z] INFO  18:14:12,188 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:14Z] INFO  18:14:12,269 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-15T01:14Z] INFO  18:14:12,277 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:14Z] INFO  18:14:12,385 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:14Z] INFO  18:14:12,386 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:14Z] INFO  18:14:12,387 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T01:14Z] INFO  18:14:12,387 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T01:14Z] INFO  18:14:12,478 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:14Z] INFO  18:14:12,478 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:14Z] INFO  18:14:12,858 IntervalUtils - Processing 116317 bp from intervals
[2016-04-15T01:14Z] WARN  18:14:12,862 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:14Z] INFO  18:14:12,955 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:14Z] INFO  18:14:13,015 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:14Z] INFO  18:14:13,016 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:14Z] INFO  18:14:13,017 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T01:14Z] INFO  18:14:13,018 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T01:14Z] INFO  18:14:13,061 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:14Z] INFO  18:14:13,062 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:14Z] INFO  18:14:13,287 ProgressMeter -     15:81625489    970244.0    30.0 s      30.0 s       92.8%    32.0 s       2.0 s
[2016-04-15T01:14Z] INFO  18:14:14,408 ProgressMeter -            done   1805916.0    36.0 s      20.0 s      100.0%    36.0 s       0.0 s
[2016-04-15T01:14Z] INFO  18:14:14,409 ProgressMeter - Total runtime 36.23 secs, 0.60 min, 0.01 hours
[2016-04-15T01:14Z] INFO  18:14:14,409 MicroScheduler - 41812 reads were filtered out during the traversal out of approximately 505632 total reads (8.27%)
[2016-04-15T01:14Z] INFO  18:14:14,410 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:14Z] INFO  18:14:14,411 MicroScheduler -   -> 822 reads (0.16% of total) failing BadMateFilter
[2016-04-15T01:14Z] INFO  18:14:14,411 MicroScheduler -   -> 40629 reads (8.04% of total) failing DuplicateReadFilter
[2016-04-15T01:14Z] INFO  18:14:14,412 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:14Z] INFO  18:14:14,412 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:14Z] INFO  18:14:14,413 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:14Z] INFO  18:14:14,414 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:14Z] INFO  18:14:14,425 MicroScheduler -   -> 361 reads (0.07% of total) failing UnmappedReadFilter
[2016-04-15T01:14Z] INFO  18:14:15,578 ProgressMeter -            done   1052407.0    32.0 s      30.0 s      100.0%    32.0 s       0.0 s
[2016-04-15T01:14Z] INFO  18:14:15,578 ProgressMeter - Total runtime 32.32 secs, 0.54 min, 0.01 hours
[2016-04-15T01:14Z] INFO  18:14:15,578 MicroScheduler - 35390 reads were filtered out during the traversal out of approximately 440552 total reads (8.03%)
[2016-04-15T01:14Z] INFO  18:14:15,579 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:14Z] INFO  18:14:15,579 MicroScheduler -   -> 716 reads (0.16% of total) failing BadMateFilter
[2016-04-15T01:14Z] INFO  18:14:15,579 MicroScheduler -   -> 34334 reads (7.79% of total) failing DuplicateReadFilter
[2016-04-15T01:14Z] INFO  18:14:15,580 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:14Z] INFO  18:14:15,580 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:14Z] INFO  18:14:15,580 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:14Z] INFO  18:14:15,581 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:14Z] INFO  18:14:15,581 MicroScheduler -   -> 340 reads (0.08% of total) failing UnmappedReadFilter
[2016-04-15T01:14Z] INFO  18:14:15,812 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:14Z] GATK: UnifiedGenotyper
[2016-04-15T01:14Z] INFO  18:14:16,464 ProgressMeter -      16:3165356   1893601.0    30.0 s      15.0 s       56.5%    53.0 s      23.0 s
[2016-04-15T01:14Z] INFO  18:14:17,066 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:14Z] INFO  18:14:17,322 ProgressMeter -     16:28844580    968180.0    30.0 s      30.0 s       65.7%    45.0 s      15.0 s
[2016-04-15T01:14Z] GATK: UnifiedGenotyper
[2016-04-15T01:14Z] INFO  18:14:18,780 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:14Z] INFO  18:14:18,783 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:14Z] INFO  18:14:18,784 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:14Z] INFO  18:14:18,784 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:14Z] INFO  18:14:18,789 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/18/R14-18102_kapa-NGv3-PE100-NGv3-sort-18_50278423_66344430-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/18/R14-18102_kapa-NGv3-PE100-NGv3-18_50278423_66344430-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/18/tx/tmpLrDHBg/R14-18102_kapa-NGv3-PE100-NGv3-18_50278423_66344430.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:14Z] INFO  18:14:18,803 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:14Z] INFO  18:14:18,803 HelpFormatter - Date/Time: 2016/04/14 18:14:18
[2016-04-15T01:14Z] INFO  18:14:18,804 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:14Z] INFO  18:14:18,804 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:14Z] INFO  18:14:18,939 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:14Z] INFO  18:14:19,173 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T01:14Z] INFO  18:14:19,182 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:14Z] INFO  18:14:19,285 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.10
[2016-04-15T01:14Z] INFO  18:14:19,587 IntervalUtils - Processing 111880 bp from intervals
[2016-04-15T01:14Z] WARN  18:14:19,593 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:14Z] INFO  18:14:19,659 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:14Z] INFO  18:14:19,731 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:14Z] INFO  18:14:19,732 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:14Z] INFO  18:14:19,733 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T01:14Z] INFO  18:14:19,734 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T01:14Z] INFO  18:14:19,779 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:14Z] INFO  18:14:19,780 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:14Z] INFO  18:14:20,234 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:14Z] INFO  18:14:20,236 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:14Z] INFO  18:14:20,236 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:14Z] INFO  18:14:20,237 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:14Z] INFO  18:14:20,241 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/18/R14-18102_kapa-NGv3-PE100-NGv3-sort-18_66346699_78077248-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/18/R14-18102_kapa-NGv3-PE100-NGv3-18_66346699_78077248-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/18/tx/tmphq25nb/R14-18102_kapa-NGv3-PE100-NGv3-18_66346699_78077248.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:14Z] INFO  18:14:20,250 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:14Z] INFO  18:14:20,251 HelpFormatter - Date/Time: 2016/04/14 18:14:20
[2016-04-15T01:14Z] INFO  18:14:20,251 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:14Z] INFO  18:14:20,252 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:14Z] INFO  18:14:20,375 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:14Z] INFO  18:14:20,561 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T01:14Z] INFO  18:14:20,581 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:14Z] INFO  18:14:20,654 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-15T01:14Z] INFO  18:14:20,995 IntervalUtils - Processing 87308 bp from intervals
[2016-04-15T01:14Z] WARN  18:14:21,000 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:14Z] INFO  18:14:21,070 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:14Z] INFO  18:14:21,153 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:14Z] INFO  18:14:21,154 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:14Z] INFO  18:14:21,154 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T01:14Z] INFO  18:14:21,155 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T01:14Z] INFO  18:14:21,217 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:14Z] INFO  18:14:21,218 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:14Z] INFO  18:14:21,754 ProgressMeter -            done    892419.0    26.0 s      29.0 s      100.0%    26.0 s       0.0 s
[2016-04-15T01:14Z] INFO  18:14:21,755 ProgressMeter - Total runtime 26.66 secs, 0.44 min, 0.01 hours
[2016-04-15T01:14Z] INFO  18:14:21,755 MicroScheduler - 26102 reads were filtered out during the traversal out of approximately 305236 total reads (8.55%)
[2016-04-15T01:14Z] INFO  18:14:21,756 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:14Z] INFO  18:14:21,756 MicroScheduler -   -> 487 reads (0.16% of total) failing BadMateFilter
[2016-04-15T01:14Z] INFO  18:14:21,756 MicroScheduler -   -> 25365 reads (8.31% of total) failing DuplicateReadFilter
[2016-04-15T01:14Z] INFO  18:14:21,757 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:14Z] INFO  18:14:21,757 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:14Z] INFO  18:14:21,757 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:14Z] INFO  18:14:21,757 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:14Z] INFO  18:14:21,758 MicroScheduler -   -> 250 reads (0.08% of total) failing UnmappedReadFilter
[2016-04-15T01:14Z] INFO  18:14:23,212 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:14Z] GATK: UnifiedGenotyper
[2016-04-15T01:14Z] INFO  18:14:26,259 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:14Z] INFO  18:14:26,263 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:14Z] INFO  18:14:26,263 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:14Z] INFO  18:14:26,263 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:14Z] INFO  18:14:26,267 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/19/R14-18102_kapa-NGv3-PE100-NGv3-sort-19_0_15509577-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/19/R14-18102_kapa-NGv3-PE100-NGv3-19_0_15509577-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/19/tx/tmpRn4ulR/R14-18102_kapa-NGv3-PE100-NGv3-19_0_15509577.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:14Z] INFO  18:14:26,289 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:14Z] INFO  18:14:26,290 HelpFormatter - Date/Time: 2016/04/14 18:14:26
[2016-04-15T01:14Z] INFO  18:14:26,291 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:14Z] INFO  18:14:26,291 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:14Z] INFO  18:14:26,499 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:14Z] INFO  18:14:26,746 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T01:14Z] INFO  18:14:26,757 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:14Z] INFO  18:14:26,830 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-15T01:14Z] INFO  18:14:27,312 IntervalUtils - Processing 793280 bp from intervals
[2016-04-15T01:14Z] WARN  18:14:27,319 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:14Z] INFO  18:14:27,426 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:14Z] INFO  18:14:27,527 ProgressMeter -            done    861644.0    25.0 s      29.0 s      100.0%    25.0 s       0.0 s
[2016-04-15T01:14Z] INFO  18:14:27,528 ProgressMeter - Total runtime 25.24 secs, 0.42 min, 0.01 hours
[2016-04-15T01:14Z] INFO  18:14:27,528 MicroScheduler - 26976 reads were filtered out during the traversal out of approximately 311701 total reads (8.65%)
[2016-04-15T01:14Z] INFO  18:14:27,529 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:14Z] INFO  18:14:27,529 MicroScheduler -   -> 552 reads (0.18% of total) failing BadMateFilter
[2016-04-15T01:14Z] INFO  18:14:27,529 MicroScheduler -   -> 26168 reads (8.40% of total) failing DuplicateReadFilter
[2016-04-15T01:14Z] INFO  18:14:27,530 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:14Z] INFO  18:14:27,530 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:14Z] INFO  18:14:27,530 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:14Z] INFO  18:14:27,530 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:14Z] INFO  18:14:27,531 MicroScheduler -   -> 256 reads (0.08% of total) failing UnmappedReadFilter
[2016-04-15T01:14Z] INFO  18:14:27,597 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:14Z] INFO  18:14:27,610 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:14Z] INFO  18:14:27,611 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T01:14Z] INFO  18:14:27,611 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T01:14Z] INFO  18:14:27,674 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:14Z] INFO  18:14:27,675 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:14Z] INFO  18:14:28,233 ProgressMeter -            done    443441.0    19.0 s      43.0 s      100.0%    19.0 s       0.0 s
[2016-04-15T01:14Z] INFO  18:14:28,234 ProgressMeter - Total runtime 19.32 secs, 0.32 min, 0.01 hours
[2016-04-15T01:14Z] INFO  18:14:28,234 MicroScheduler - 17089 reads were filtered out during the traversal out of approximately 201841 total reads (8.47%)
[2016-04-15T01:14Z] INFO  18:14:28,234 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:14Z] INFO  18:14:28,235 MicroScheduler -   -> 301 reads (0.15% of total) failing BadMateFilter
[2016-04-15T01:14Z] INFO  18:14:28,235 MicroScheduler -   -> 16623 reads (8.24% of total) failing DuplicateReadFilter
[2016-04-15T01:14Z] INFO  18:14:28,235 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:14Z] INFO  18:14:28,236 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:14Z] INFO  18:14:28,236 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:14Z] INFO  18:14:28,236 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:14Z] INFO  18:14:28,236 MicroScheduler -   -> 165 reads (0.08% of total) failing UnmappedReadFilter
[2016-04-15T01:14Z] INFO  18:14:29,018 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:14Z] INFO  18:14:29,025 ProgressMeter -     16:72993826   1460312.0    30.0 s      20.0 s       81.7%    36.0 s       6.0 s
[2016-04-15T01:14Z] INFO  18:14:29,157 ProgressMeter -            done    391308.0    16.0 s      42.0 s      100.0%    16.0 s       0.0 s
[2016-04-15T01:14Z] INFO  18:14:29,157 ProgressMeter - Total runtime 16.77 secs, 0.28 min, 0.00 hours
[2016-04-15T01:14Z] INFO  18:14:29,158 MicroScheduler - 15099 reads were filtered out during the traversal out of approximately 177943 total reads (8.49%)
[2016-04-15T01:14Z] INFO  18:14:29,158 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:14Z] INFO  18:14:29,158 MicroScheduler -   -> 280 reads (0.16% of total) failing BadMateFilter
[2016-04-15T01:14Z] INFO  18:14:29,159 MicroScheduler -   -> 14674 reads (8.25% of total) failing DuplicateReadFilter
[2016-04-15T01:14Z] INFO  18:14:29,159 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:14Z] INFO  18:14:29,159 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:14Z] INFO  18:14:29,159 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:14Z] INFO  18:14:29,160 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:14Z] INFO  18:14:29,160 MicroScheduler -   -> 145 reads (0.08% of total) failing UnmappedReadFilter
[2016-04-15T01:14Z] GATK: UnifiedGenotyper
[2016-04-15T01:14Z] INFO  18:14:29,369 ProgressMeter -            done    934025.0    21.0 s      22.0 s      100.0%    21.0 s       0.0 s
[2016-04-15T01:14Z] INFO  18:14:29,371 ProgressMeter - Total runtime 21.01 secs, 0.35 min, 0.01 hours
[2016-04-15T01:14Z] INFO  18:14:29,371 MicroScheduler - 21550 reads were filtered out during the traversal out of approximately 251920 total reads (8.55%)
[2016-04-15T01:14Z] INFO  18:14:29,372 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:14Z] INFO  18:14:29,373 MicroScheduler -   -> 385 reads (0.15% of total) failing BadMateFilter
[2016-04-15T01:14Z] INFO  18:14:29,373 MicroScheduler -   -> 20979 reads (8.33% of total) failing DuplicateReadFilter
[2016-04-15T01:14Z] INFO  18:14:29,374 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:14Z] INFO  18:14:29,375 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:14Z] INFO  18:14:29,375 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:14Z] INFO  18:14:29,376 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:14Z] INFO  18:14:29,376 MicroScheduler -   -> 186 reads (0.07% of total) failing UnmappedReadFilter
[2016-04-15T01:14Z] INFO  18:14:29,502 ProgressMeter -            done    322965.0    16.0 s      51.0 s       99.9%    16.0 s       0.0 s
[2016-04-15T01:14Z] INFO  18:14:29,503 ProgressMeter - Total runtime 16.49 secs, 0.27 min, 0.00 hours
[2016-04-15T01:14Z] INFO  18:14:29,503 MicroScheduler - 18736 reads were filtered out during the traversal out of approximately 226269 total reads (8.28%)
[2016-04-15T01:14Z] INFO  18:14:29,503 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:14Z] INFO  18:14:29,503 MicroScheduler -   -> 380 reads (0.17% of total) failing BadMateFilter
[2016-04-15T01:14Z] INFO  18:14:29,504 MicroScheduler -   -> 18166 reads (8.03% of total) failing DuplicateReadFilter
[2016-04-15T01:14Z] INFO  18:14:29,504 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:14Z] INFO  18:14:29,504 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:14Z] INFO  18:14:29,504 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:14Z] INFO  18:14:29,505 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:14Z] INFO  18:14:29,505 MicroScheduler -   -> 190 reads (0.08% of total) failing UnmappedReadFilter
[2016-04-15T01:14Z] INFO  18:14:29,540 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:14Z] GATK: UnifiedGenotyper
[2016-04-15T01:14Z] INFO  18:14:30,092 ProgressMeter -            done   1795980.0    42.0 s      23.0 s      100.0%    42.0 s       0.0 s
[2016-04-15T01:14Z] INFO  18:14:30,092 ProgressMeter - Total runtime 42.78 secs, 0.71 min, 0.01 hours
[2016-04-15T01:14Z] INFO  18:14:30,092 MicroScheduler - 57793 reads were filtered out during the traversal out of approximately 776724 total reads (7.44%)
[2016-04-15T01:14Z] INFO  18:14:30,093 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:14Z] INFO  18:14:30,093 MicroScheduler -   -> 1193 reads (0.15% of total) failing BadMateFilter
[2016-04-15T01:14Z] INFO  18:14:30,094 MicroScheduler -   -> 55980 reads (7.21% of total) failing DuplicateReadFilter
[2016-04-15T01:14Z] INFO  18:14:30,094 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:14Z] INFO  18:14:30,094 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:14Z] INFO  18:14:30,094 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:14Z] INFO  18:14:30,095 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:14Z] INFO  18:14:30,095 MicroScheduler -   -> 620 reads (0.08% of total) failing UnmappedReadFilter
[2016-04-15T01:14Z] INFO  18:14:30,756 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:14Z] INFO  18:14:30,887 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:14Z] GATK: UnifiedGenotyper
[2016-04-15T01:14Z] GATK: UnifiedGenotyper
[2016-04-15T01:14Z] INFO  18:14:31,649 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:14Z] INFO  18:14:31,712 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:14Z] GATK: UnifiedGenotyper
[2016-04-15T01:14Z] INFO  18:14:32,127 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:14Z] INFO  18:14:32,131 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:14Z] INFO  18:14:32,132 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:14Z] INFO  18:14:32,133 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:14Z] INFO  18:14:32,138 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/19/R14-18102_kapa-NGv3-PE100-NGv3-sort-19_15510112_31025906-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/19/R14-18102_kapa-NGv3-PE100-NGv3-19_15510112_31025906-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/19/tx/tmpzzDljP/R14-18102_kapa-NGv3-PE100-NGv3-19_15510112_31025906.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:14Z] INFO  18:14:32,155 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:14Z] INFO  18:14:32,156 HelpFormatter - Date/Time: 2016/04/14 18:14:32
[2016-04-15T01:14Z] INFO  18:14:32,156 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:14Z] INFO  18:14:32,157 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:14Z] GATK: UnifiedGenotyper
[2016-04-15T01:14Z] INFO  18:14:32,366 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:14Z] INFO  18:14:32,621 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T01:14Z] INFO  18:14:32,631 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:14Z] INFO  18:14:32,725 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.09
[2016-04-15T01:14Z] INFO  18:14:32,855 ProgressMeter -     17:28783480   1337181.0    30.0 s      22.0 s       85.3%    35.0 s       5.0 s
[2016-04-15T01:14Z] INFO  18:14:32,896 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:14Z] INFO  18:14:32,898 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:14Z] INFO  18:14:32,898 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:14Z] INFO  18:14:32,899 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:14Z] INFO  18:14:32,903 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/19/R14-18102_kapa-NGv3-PE100-NGv3-sort-19_31038849_46627578-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/19/R14-18102_kapa-NGv3-PE100-NGv3-19_31038849_46627578-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/19/tx/tmppKXX_G/R14-18102_kapa-NGv3-PE100-NGv3-19_31038849_46627578.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:14Z] INFO  18:14:32,923 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:14Z] INFO  18:14:32,924 HelpFormatter - Date/Time: 2016/04/14 18:14:32
[2016-04-15T01:14Z] INFO  18:14:32,924 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:14Z] INFO  18:14:32,925 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:14Z] INFO  18:14:33,014 ProgressMeter -      17:7246698   1584075.0    30.0 s      18.0 s       56.2%    53.0 s      23.0 s
[2016-04-15T01:14Z] INFO  18:14:33,099 IntervalUtils - Processing 296880 bp from intervals
[2016-04-15T01:14Z] WARN  18:14:33,104 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:14Z] INFO  18:14:33,135 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:14Z] INFO  18:14:33,182 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:14Z] INFO  18:14:33,191 ProgressMeter -            done    242253.0    13.0 s      55.0 s       99.9%    13.0 s       0.0 s
[2016-04-15T01:14Z] INFO  18:14:33,192 ProgressMeter - Total runtime 13.46 secs, 0.22 min, 0.00 hours
[2016-04-15T01:14Z] INFO  18:14:33,192 MicroScheduler - 11102 reads were filtered out during the traversal out of approximately 132890 total reads (8.35%)
[2016-04-15T01:14Z] INFO  18:14:33,192 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:14Z] INFO  18:14:33,193 MicroScheduler -   -> 188 reads (0.14% of total) failing BadMateFilter
[2016-04-15T01:14Z] INFO  18:14:33,193 MicroScheduler -   -> 10795 reads (8.12% of total) failing DuplicateReadFilter
[2016-04-15T01:14Z] INFO  18:14:33,193 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:14Z] INFO  18:14:33,193 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:14Z] INFO  18:14:33,194 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:14Z] INFO  18:14:33,194 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:14Z] INFO  18:14:33,194 MicroScheduler -   -> 119 reads (0.09% of total) failing UnmappedReadFilter
[2016-04-15T01:14Z] INFO  18:14:33,253 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:14Z] INFO  18:14:33,254 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:14Z] INFO  18:14:33,255 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T01:14Z] INFO  18:14:33,256 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T01:14Z] INFO  18:14:33,300 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:14Z] INFO  18:14:33,300 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:14Z] INFO  18:14:33,359 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T01:14Z] INFO  18:14:33,380 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:14Z] INFO  18:14:33,498 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.12
[2016-04-15T01:14Z] INFO  18:14:33,866 ProgressMeter -            done    175642.0    12.0 s      72.0 s       99.9%    12.0 s       0.0 s
[2016-04-15T01:14Z] INFO  18:14:33,867 ProgressMeter - Total runtime 12.71 secs, 0.21 min, 0.00 hours
[2016-04-15T01:14Z] INFO  18:14:33,867 MicroScheduler - 10020 reads were filtered out during the traversal out of approximately 116092 total reads (8.63%)
[2016-04-15T01:14Z] INFO  18:14:33,867 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:14Z] INFO  18:14:33,868 MicroScheduler -   -> 193 reads (0.17% of total) failing BadMateFilter
[2016-04-15T01:14Z] INFO  18:14:33,868 MicroScheduler -   -> 9726 reads (8.38% of total) failing DuplicateReadFilter
[2016-04-15T01:14Z] INFO  18:14:33,868 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:14Z] INFO  18:14:33,869 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:14Z] INFO  18:14:33,869 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:14Z] INFO  18:14:33,869 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:14Z] INFO  18:14:33,869 MicroScheduler -   -> 101 reads (0.09% of total) failing UnmappedReadFilter
[2016-04-15T01:14Z] INFO  18:14:33,995 IntervalUtils - Processing 631764 bp from intervals
[2016-04-15T01:14Z] WARN  18:14:34,001 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:14Z] INFO  18:14:34,106 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:14Z] INFO  18:14:34,154 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:14Z] INFO  18:14:34,158 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:14Z] INFO  18:14:34,158 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:14Z] INFO  18:14:34,159 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:14Z] INFO  18:14:34,163 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/19/R14-18102_kapa-NGv3-PE100-NGv3-sort-19_46627881_59128983-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/19/R14-18102_kapa-NGv3-PE100-NGv3-19_46627881_59128983-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/19/tx/tmpBxIxHf/R14-18102_kapa-NGv3-PE100-NGv3-19_46627881_59128983.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:14Z] INFO  18:14:34,172 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:14Z] INFO  18:14:34,176 HelpFormatter - Date/Time: 2016/04/14 18:14:34
[2016-04-15T01:14Z] INFO  18:14:34,177 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:14Z] INFO  18:14:34,177 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:14Z] INFO  18:14:34,242 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:14Z] INFO  18:14:34,243 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:14Z] INFO  18:14:34,244 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T01:14Z] INFO  18:14:34,244 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T01:14Z] INFO  18:14:34,250 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:14Z] INFO  18:14:34,252 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:14Z] INFO  18:14:34,252 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:14Z] INFO  18:14:34,253 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:14Z] INFO  18:14:34,257 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/20/R14-18102_kapa-NGv3-PE100-NGv3-sort-20_0_15843471-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/20/R14-18102_kapa-NGv3-PE100-NGv3-20_0_15843471-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/20/tx/tmpSLNYkY/R14-18102_kapa-NGv3-PE100-NGv3-20_0_15843471.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:14Z] INFO  18:14:34,287 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:14Z] INFO  18:14:34,288 HelpFormatter - Date/Time: 2016/04/14 18:14:34
[2016-04-15T01:14Z] INFO  18:14:34,288 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:14Z] INFO  18:14:34,289 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:14Z] INFO  18:14:34,291 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:14Z] INFO  18:14:34,292 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:14Z] INFO  18:14:34,406 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:14Z] INFO  18:14:34,434 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:14Z] INFO  18:14:34,515 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:14Z] INFO  18:14:34,627 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T01:14Z] INFO  18:14:34,637 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:14Z] INFO  18:14:34,646 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T01:14Z] INFO  18:14:34,655 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:14Z] INFO  18:14:34,731 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-15T01:14Z] INFO  18:14:34,744 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.11
[2016-04-15T01:14Z] INFO  18:14:34,756 ProgressMeter -            done   2608342.0    48.0 s      18.0 s      100.0%    48.0 s       0.0 s
[2016-04-15T01:14Z] INFO  18:14:34,756 ProgressMeter - Total runtime 48.31 secs, 0.81 min, 0.01 hours
[2016-04-15T01:14Z] INFO  18:14:34,757 MicroScheduler - 60390 reads were filtered out during the traversal out of approximately 730104 total reads (8.27%)
[2016-04-15T01:14Z] INFO  18:14:34,757 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:14Z] INFO  18:14:34,757 MicroScheduler -   -> 1233 reads (0.17% of total) failing BadMateFilter
[2016-04-15T01:14Z] INFO  18:14:34,757 MicroScheduler -   -> 58556 reads (8.02% of total) failing DuplicateReadFilter
[2016-04-15T01:14Z] INFO  18:14:34,758 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:14Z] INFO  18:14:34,758 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:14Z] INFO  18:14:34,758 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:14Z] INFO  18:14:34,758 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:14Z] INFO  18:14:34,759 MicroScheduler -   -> 601 reads (0.08% of total) failing UnmappedReadFilter
[2016-04-15T01:14Z] INFO  18:14:34,775 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:14Z] INFO  18:14:34,778 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:14Z] INFO  18:14:34,779 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:14Z] INFO  18:14:34,779 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:14Z] INFO  18:14:34,784 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/20/R14-18102_kapa-NGv3-PE100-NGv3-sort-20_15866408_31376818-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/20/R14-18102_kapa-NGv3-PE100-NGv3-20_15866408_31376818-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/20/tx/tmp12PThY/R14-18102_kapa-NGv3-PE100-NGv3-20_15866408_31376818.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:14Z] INFO  18:14:34,799 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:14Z] GATK: UnifiedGenotyper
[2016-04-15T01:14Z] INFO  18:14:34,800 HelpFormatter - Date/Time: 2016/04/14 18:14:34
[2016-04-15T01:14Z] INFO  18:14:34,808 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:14Z] INFO  18:14:34,821 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:14Z] INFO  18:14:34,969 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:14Z] INFO  18:14:34,972 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:14Z] INFO  18:14:34,973 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:14Z] INFO  18:14:34,973 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:14Z] INFO  18:14:34,978 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/20/R14-18102_kapa-NGv3-PE100-NGv3-sort-20_31379406_47242465-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/20/R14-18102_kapa-NGv3-PE100-NGv3-20_31379406_47242465-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/20/tx/tmpn0TfhI/R14-18102_kapa-NGv3-PE100-NGv3-20_31379406_47242465.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:14Z] INFO  18:14:35,002 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:14Z] INFO  18:14:35,007 HelpFormatter - Date/Time: 2016/04/14 18:14:34
[2016-04-15T01:14Z] INFO  18:14:35,008 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:14Z] INFO  18:14:35,008 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:14Z] INFO  18:14:35,080 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:14Z] INFO  18:14:35,094 ProgressMeter -            done   1653515.0    36.0 s      21.0 s      100.0%    36.0 s       0.0 s
[2016-04-15T01:14Z] INFO  18:14:35,094 ProgressMeter - Total runtime 36.08 secs, 0.60 min, 0.01 hours
[2016-04-15T01:14Z] INFO  18:14:35,094 MicroScheduler - 45000 reads were filtered out during the traversal out of approximately 539976 total reads (8.33%)
[2016-04-15T01:14Z] INFO  18:14:35,095 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:14Z] INFO  18:14:35,095 MicroScheduler -   -> 895 reads (0.17% of total) failing BadMateFilter
[2016-04-15T01:14Z] INFO  18:14:35,095 MicroScheduler -   -> 43645 reads (8.08% of total) failing DuplicateReadFilter
[2016-04-15T01:14Z] INFO  18:14:35,095 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:14Z] INFO  18:14:35,096 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:14Z] INFO  18:14:35,096 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:14Z] INFO  18:14:35,096 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:14Z] INFO  18:14:35,096 MicroScheduler -   -> 460 reads (0.09% of total) failing UnmappedReadFilter
[2016-04-15T01:14Z] INFO  18:14:35,113 IntervalUtils - Processing 179899 bp from intervals
[2016-04-15T01:14Z] WARN  18:14:35,118 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:14Z] INFO  18:14:35,181 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:14Z] INFO  18:14:35,244 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:14Z] INFO  18:14:35,328 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T01:14Z] INFO  18:14:35,335 IntervalUtils - Processing 711484 bp from intervals
[2016-04-15T01:14Z] WARN  18:14:35,340 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:14Z] INFO  18:14:35,347 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:14Z] INFO  18:14:35,352 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T01:14Z] INFO  18:14:35,361 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:14Z] INFO  18:14:35,366 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:14Z] INFO  18:14:35,367 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:14Z] INFO  18:14:35,368 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T01:14Z] INFO  18:14:35,369 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T01:14Z] INFO  18:14:35,410 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:14Z] INFO  18:14:35,413 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-15T01:14Z] INFO  18:14:35,417 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:14Z] INFO  18:14:35,418 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:14Z] INFO  18:14:35,427 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:14Z] INFO  18:14:35,431 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-15T01:14Z] INFO  18:14:35,641 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:14Z] INFO  18:14:35,641 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:14Z] INFO  18:14:35,642 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T01:14Z] INFO  18:14:35,642 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T01:14Z] GATK: UnifiedGenotyper
[2016-04-15T01:14Z] INFO  18:14:35,695 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:14Z] INFO  18:14:35,696 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:14Z] INFO  18:14:35,740 IntervalUtils - Processing 150913 bp from intervals
[2016-04-15T01:14Z] WARN  18:14:35,746 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:14Z] INFO  18:14:35,816 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:14Z] INFO  18:14:35,890 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:14Z] INFO  18:14:35,892 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:14Z] INFO  18:14:35,892 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T01:14Z] INFO  18:14:35,893 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T01:14Z] INFO  18:14:35,939 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:14Z] INFO  18:14:35,939 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:14Z] INFO  18:14:35,974 IntervalUtils - Processing 321885 bp from intervals
[2016-04-15T01:14Z] WARN  18:14:35,980 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:14Z] INFO  18:14:36,068 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:14Z] INFO  18:14:36,112 ProgressMeter -            done   1490193.0    33.0 s      22.0 s      100.0%    33.0 s       0.0 s
[2016-04-15T01:14Z] INFO  18:14:36,113 ProgressMeter - Total runtime 33.28 secs, 0.55 min, 0.01 hours
[2016-04-15T01:14Z] INFO  18:14:36,114 MicroScheduler - 40800 reads were filtered out during the traversal out of approximately 482775 total reads (8.45%)
[2016-04-15T01:14Z] INFO  18:14:36,114 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:14Z] INFO  18:14:36,115 MicroScheduler -   -> 763 reads (0.16% of total) failing BadMateFilter
[2016-04-15T01:14Z] INFO  18:14:36,115 MicroScheduler -   -> 39661 reads (8.22% of total) failing DuplicateReadFilter
[2016-04-15T01:14Z] INFO  18:14:36,115 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:14Z] INFO  18:14:36,116 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:14Z] INFO  18:14:36,116 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:14Z] INFO  18:14:36,116 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:14Z] INFO  18:14:36,117 MicroScheduler -   -> 376 reads (0.08% of total) failing UnmappedReadFilter
[2016-04-15T01:14Z] INFO  18:14:36,171 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:14Z] INFO  18:14:36,172 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:14Z] INFO  18:14:36,173 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T01:14Z] INFO  18:14:36,173 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T01:14Z] INFO  18:14:36,214 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:14Z] INFO  18:14:36,215 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:14Z] INFO  18:14:36,400 ProgressMeter -            done   1302364.0    29.0 s      22.0 s      100.0%    29.0 s       0.0 s
[2016-04-15T01:14Z] INFO  18:14:36,400 ProgressMeter - Total runtime 29.21 secs, 0.49 min, 0.01 hours
[2016-04-15T01:14Z] INFO  18:14:36,401 MicroScheduler - 34963 reads were filtered out during the traversal out of approximately 413321 total reads (8.46%)
[2016-04-15T01:14Z] INFO  18:14:36,401 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:14Z] INFO  18:14:36,401 MicroScheduler -   -> 686 reads (0.17% of total) failing BadMateFilter
[2016-04-15T01:14Z] INFO  18:14:36,402 MicroScheduler -   -> 33932 reads (8.21% of total) failing DuplicateReadFilter
[2016-04-15T01:14Z] INFO  18:14:36,402 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:14Z] INFO  18:14:36,402 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:14Z] INFO  18:14:36,402 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:14Z] INFO  18:14:36,403 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:14Z] INFO  18:14:36,403 MicroScheduler -   -> 345 reads (0.08% of total) failing UnmappedReadFilter
[2016-04-15T01:14Z] INFO  18:14:36,500 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:14Z] INFO  18:14:36,533 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:14Z] GATK: UnifiedGenotyper
[2016-04-15T01:14Z] GATK: UnifiedGenotyper
[2016-04-15T01:14Z] INFO  18:14:37,507 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:14Z] INFO  18:14:37,799 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:14Z] GATK: UnifiedGenotyper
[2016-04-15T01:14Z] INFO  18:14:37,878 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:14Z] INFO  18:14:37,882 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:14Z] INFO  18:14:37,883 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:14Z] INFO  18:14:37,883 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:14Z] INFO  18:14:37,888 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/20/R14-18102_kapa-NGv3-PE100-NGv3-sort-20_47244085_62830269-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/20/R14-18102_kapa-NGv3-PE100-NGv3-20_47244085_62830269-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/20/tx/tmpQsZCT0/R14-18102_kapa-NGv3-PE100-NGv3-20_47244085_62830269.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:14Z] INFO  18:14:37,907 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:14Z] INFO  18:14:37,908 HelpFormatter - Date/Time: 2016/04/14 18:14:37
[2016-04-15T01:14Z] INFO  18:14:37,909 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:14Z] INFO  18:14:37,909 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:14Z] INFO  18:14:37,927 ProgressMeter -     17:39680395    989053.0    30.0 s      30.0 s       48.0%    62.0 s      32.0 s
[2016-04-15T01:14Z] INFO  18:14:38,113 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:14Z] GATK: UnifiedGenotyper
[2016-04-15T01:14Z] INFO  18:14:38,379 ProgressMeter -     17:75369372   1436541.0    30.0 s      20.0 s       84.4%    35.0 s       5.0 s
[2016-04-15T01:14Z] INFO  18:14:38,397 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T01:14Z] INFO  18:14:38,417 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:14Z] INFO  18:14:38,545 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.13
[2016-04-15T01:14Z] INFO  18:14:38,992 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:14Z] INFO  18:14:38,996 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:14Z] INFO  18:14:38,997 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:14Z] INFO  18:14:38,997 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:14Z] INFO  18:14:39,002 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/20/R14-18102_kapa-NGv3-PE100-NGv3-sort-20_62831244_63025520-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/20/R14-18102_kapa-NGv3-PE100-NGv3-20_62831244_63025520-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/20/tx/tmpkhE9TQ/R14-18102_kapa-NGv3-PE100-NGv3-20_62831244_63025520.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:14Z] INFO  18:14:39,050 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:14Z] INFO  18:14:39,050 HelpFormatter - Date/Time: 2016/04/14 18:14:38
[2016-04-15T01:14Z] INFO  18:14:39,051 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:14Z] INFO  18:14:39,051 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:14Z] INFO  18:14:39,093 IntervalUtils - Processing 269605 bp from intervals
[2016-04-15T01:14Z] WARN  18:14:39,099 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:14Z] INFO  18:14:39,235 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:14Z] INFO  18:14:39,312 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:14Z] INFO  18:14:39,347 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:14Z] INFO  18:14:39,348 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:14Z] INFO  18:14:39,349 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T01:14Z] INFO  18:14:39,349 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T01:14Z] INFO  18:14:39,430 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:14Z] INFO  18:14:39,431 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:14Z] INFO  18:14:39,592 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T01:14Z] INFO  18:14:39,615 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:14Z] INFO  18:14:39,738 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.12
[2016-04-15T01:14Z] INFO  18:14:40,222 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:14Z] INFO  18:14:40,225 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:14Z] INFO  18:14:40,226 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:14Z] INFO  18:14:40,226 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:14Z] INFO  18:14:40,231 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/21/R14-18102_kapa-NGv3-PE100-NGv3-sort-21_15524893_31045484-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/21/R14-18102_kapa-NGv3-PE100-NGv3-21_15524893_31045484-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/21/tx/tmpYdmmG1/R14-18102_kapa-NGv3-PE100-NGv3-21_15524893_31045484.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:14Z] INFO  18:14:40,260 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:14Z] INFO  18:14:40,265 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:14Z] INFO  18:14:40,273 HelpFormatter - Date/Time: 2016/04/14 18:14:40
[2016-04-15T01:14Z] INFO  18:14:40,274 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:14Z] INFO  18:14:40,275 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:14Z] INFO  18:14:40,276 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:14Z] INFO  18:14:40,274 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:14Z] INFO  18:14:40,279 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:14Z] INFO  18:14:40,280 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/21/R14-18102_kapa-NGv3-PE100-NGv3-sort-21_0_15517120-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/21/R14-18102_kapa-NGv3-PE100-NGv3-21_0_15517120-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/21/tx/tmpSQn_Lp/R14-18102_kapa-NGv3-PE100-NGv3-21_0_15517120.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:14Z] INFO  18:14:40,301 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:14Z] INFO  18:14:40,302 HelpFormatter - Date/Time: 2016/04/14 18:14:40
[2016-04-15T01:14Z] INFO  18:14:40,302 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:14Z] INFO  18:14:40,303 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:14Z] INFO  18:14:40,306 IntervalUtils - Processing 4397 bp from intervals
[2016-04-15T01:14Z] WARN  18:14:40,311 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:14Z] INFO  18:14:40,383 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:14Z] INFO  18:14:40,443 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:14Z] INFO  18:14:40,444 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:14Z] INFO  18:14:40,444 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T01:14Z] INFO  18:14:40,445 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T01:14Z] INFO  18:14:40,501 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:14Z] INFO  18:14:40,512 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:14Z] INFO  18:14:40,513 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:14Z] INFO  18:14:40,538 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:14Z] INFO  18:14:40,677 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T01:14Z] INFO  18:14:40,686 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:14Z] INFO  18:14:40,728 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T01:14Z] INFO  18:14:40,737 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:14Z] INFO  18:14:40,748 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-15T01:14Z] INFO  18:14:40,826 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.09
[2016-04-15T01:14Z] INFO  18:14:40,944 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:14Z] INFO  18:14:40,948 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:14Z] INFO  18:14:40,949 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:14Z] INFO  18:14:40,950 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:14Z] INFO  18:14:40,954 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/21/R14-18102_kapa-NGv3-PE100-NGv3-sort-21_31062047_46591599-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/21/R14-18102_kapa-NGv3-PE100-NGv3-21_31062047_46591599-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/21/tx/tmpzOshAf/R14-18102_kapa-NGv3-PE100-NGv3-21_31062047_46591599.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:14Z] INFO  18:14:40,969 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:14Z] INFO  18:14:40,970 HelpFormatter - Date/Time: 2016/04/14 18:14:40
[2016-04-15T01:14Z] INFO  18:14:40,970 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:14Z] INFO  18:14:40,970 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:14Z] INFO  18:14:41,182 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:14Z] INFO  18:14:41,314 IntervalUtils - Processing 58639 bp from intervals
[2016-04-15T01:14Z] WARN  18:14:41,319 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:14Z] INFO  18:14:41,341 IntervalUtils - Processing 4504 bp from intervals
[2016-04-15T01:14Z] WARN  18:14:41,357 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:14Z] INFO  18:14:41,373 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:14Z] INFO  18:14:41,377 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:14Z] INFO  18:14:41,377 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:14Z] INFO  18:14:41,378 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:14Z] INFO  18:14:41,386 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/21/R14-18102_kapa-NGv3-PE100-NGv3-sort-21_46595644_48129895-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/21/R14-18102_kapa-NGv3-PE100-NGv3-21_46595644_48129895-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/21/tx/tmpull5sD/R14-18102_kapa-NGv3-PE100-NGv3-21_46595644_48129895.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:14Z] INFO  18:14:41,421 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:14Z] INFO  18:14:41,429 HelpFormatter - Date/Time: 2016/04/14 18:14:41
[2016-04-15T01:14Z] INFO  18:14:41,429 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:14Z] INFO  18:14:41,430 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:14Z] INFO  18:14:41,444 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:14Z] INFO  18:14:41,478 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T01:14Z] INFO  18:14:41,497 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:14Z] INFO  18:14:41,498 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:14Z] INFO  18:14:41,513 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:14Z] INFO  18:14:41,514 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:14Z] INFO  18:14:41,515 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T01:14Z] INFO  18:14:41,516 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T01:14Z] INFO  18:14:41,534 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:14Z] INFO  18:14:41,535 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:14Z] INFO  18:14:41,536 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T01:14Z] INFO  18:14:41,537 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T01:14Z] INFO  18:14:41,588 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.09
[2016-04-15T01:14Z] INFO  18:14:41,613 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:14Z] INFO  18:14:41,614 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:14Z] INFO  18:14:41,628 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:14Z] INFO  18:14:41,633 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:14Z] INFO  18:14:41,634 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:14Z] INFO  18:14:41,932 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T01:14Z] INFO  18:14:41,940 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:14Z] INFO  18:14:42,030 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.09
[2016-04-15T01:14Z] INFO  18:14:42,220 IntervalUtils - Processing 282111 bp from intervals
[2016-04-15T01:14Z] WARN  18:14:42,236 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:14Z] INFO  18:14:42,338 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:14Z] INFO  18:14:42,437 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:14Z] INFO  18:14:42,438 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:14Z] INFO  18:14:42,439 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T01:14Z] INFO  18:14:42,440 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T01:14Z] INFO  18:14:42,446 IntervalUtils - Processing 63011 bp from intervals
[2016-04-15T01:14Z] WARN  18:14:42,451 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:14Z] INFO  18:14:42,493 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:14Z] INFO  18:14:42,494 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:14Z] INFO  18:14:42,554 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:14Z] INFO  18:14:42,603 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:14Z] INFO  18:14:42,615 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:14Z] INFO  18:14:42,616 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T01:14Z] INFO  18:14:42,616 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T01:14Z] INFO  18:14:42,701 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:14Z] INFO  18:14:42,702 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:14Z] INFO  18:14:43,808 ProgressMeter -            done     15700.0     3.0 s       3.6 m       98.2%     3.0 s       0.0 s
[2016-04-15T01:14Z] INFO  18:14:43,809 ProgressMeter - Total runtime 3.37 secs, 0.06 min, 0.00 hours
[2016-04-15T01:14Z] INFO  18:14:43,809 MicroScheduler - 485 reads were filtered out during the traversal out of approximately 6135 total reads (7.91%)
[2016-04-15T01:14Z] INFO  18:14:43,810 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:14Z] INFO  18:14:43,810 MicroScheduler -   -> 5 reads (0.08% of total) failing BadMateFilter
[2016-04-15T01:14Z] INFO  18:14:43,811 MicroScheduler -   -> 473 reads (7.71% of total) failing DuplicateReadFilter
[2016-04-15T01:14Z] INFO  18:14:43,811 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:14Z] INFO  18:14:43,811 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:14Z] INFO  18:14:43,812 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:14Z] INFO  18:14:43,812 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:14Z] INFO  18:14:43,812 MicroScheduler -   -> 7 reads (0.11% of total) failing UnmappedReadFilter
[2016-04-15T01:14Z] INFO  18:14:43,821 ProgressMeter -            done   1664309.0    35.0 s      21.0 s      100.0%    35.0 s       0.0 s
[2016-04-15T01:14Z] INFO  18:14:43,822 ProgressMeter - Total runtime 35.46 secs, 0.59 min, 0.01 hours
[2016-04-15T01:14Z] INFO  18:14:43,822 MicroScheduler - 43336 reads were filtered out during the traversal out of approximately 509133 total reads (8.51%)
[2016-04-15T01:14Z] INFO  18:14:43,822 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:14Z] INFO  18:14:43,823 MicroScheduler -   -> 836 reads (0.16% of total) failing BadMateFilter
[2016-04-15T01:14Z] INFO  18:14:43,823 MicroScheduler -   -> 42079 reads (8.26% of total) failing DuplicateReadFilter
[2016-04-15T01:14Z] INFO  18:14:43,823 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:14Z] INFO  18:14:43,823 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:14Z] INFO  18:14:43,824 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:14Z] INFO  18:14:43,824 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:14Z] INFO  18:14:43,824 MicroScheduler -   -> 421 reads (0.08% of total) failing UnmappedReadFilter
[2016-04-15T01:14Z] INFO  18:14:45,254 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:14Z] INFO  18:14:45,355 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:14Z] GATK: UnifiedGenotyper
[2016-04-15T01:14Z] GATK: UnifiedGenotyper
[2016-04-15T01:14Z] INFO  18:14:46,745 ProgressMeter -            done     11154.0     5.0 s       7.8 m       98.3%     5.0 s       0.0 s
[2016-04-15T01:14Z] INFO  18:14:46,749 ProgressMeter - Total runtime 5.21 secs, 0.09 min, 0.00 hours
[2016-04-15T01:14Z] INFO  18:14:46,750 MicroScheduler - 1484 reads were filtered out during the traversal out of approximately 17298 total reads (8.58%)
[2016-04-15T01:14Z] INFO  18:14:46,751 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:14Z] INFO  18:14:46,751 MicroScheduler -   -> 43 reads (0.25% of total) failing BadMateFilter
[2016-04-15T01:14Z] INFO  18:14:46,752 MicroScheduler -   -> 1428 reads (8.26% of total) failing DuplicateReadFilter
[2016-04-15T01:14Z] INFO  18:14:46,761 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:14Z] INFO  18:14:46,762 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:14Z] INFO  18:14:46,762 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:14Z] INFO  18:14:46,763 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:14Z] INFO  18:14:46,764 MicroScheduler -   -> 13 reads (0.08% of total) failing UnmappedReadFilter
[2016-04-15T01:14Z] INFO  18:14:48,295 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:14Z] GATK: UnifiedGenotyper
[2016-04-15T01:14Z] INFO  18:14:48,589 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:14Z] INFO  18:14:48,592 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:14Z] INFO  18:14:48,593 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:14Z] INFO  18:14:48,593 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:14Z] INFO  18:14:48,598 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/22/R14-18102_kapa-NGv3-PE100-NGv3-sort-22_0_16258303-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/22/R14-18102_kapa-NGv3-PE100-NGv3-22_0_16258303-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/22/tx/tmp89RbiH/R14-18102_kapa-NGv3-PE100-NGv3-22_0_16258303.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:14Z] INFO  18:14:48,608 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:14Z] INFO  18:14:48,620 HelpFormatter - Date/Time: 2016/04/14 18:14:48
[2016-04-15T01:14Z] INFO  18:14:48,621 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:14Z] INFO  18:14:48,622 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:14Z] INFO  18:14:48,639 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:14Z] INFO  18:14:48,642 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:14Z] INFO  18:14:48,643 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:14Z] INFO  18:14:48,643 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:14Z] INFO  18:14:48,669 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/22/R14-18102_kapa-NGv3-PE100-NGv3-sort-22_16266928_31795711-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/22/R14-18102_kapa-NGv3-PE100-NGv3-22_16266928_31795711-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/22/tx/tmpDlLUK0/R14-18102_kapa-NGv3-PE100-NGv3-22_16266928_31795711.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:14Z] INFO  18:14:48,687 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:14Z] INFO  18:14:48,688 HelpFormatter - Date/Time: 2016/04/14 18:14:48
[2016-04-15T01:14Z] INFO  18:14:48,688 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:14Z] INFO  18:14:48,689 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:14Z] INFO  18:14:48,795 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:14Z] INFO  18:14:48,842 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:14Z] INFO  18:14:49,063 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T01:14Z] INFO  18:14:49,084 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:14Z] INFO  18:14:49,090 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T01:14Z] INFO  18:14:49,101 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:14Z] INFO  18:14:49,156 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-15T01:14Z] INFO  18:14:49,185 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-15T01:14Z] INFO  18:14:49,597 IntervalUtils - Processing 118 bp from intervals
[2016-04-15T01:14Z] WARN  18:14:49,603 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:14Z] INFO  18:14:49,702 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:14Z] INFO  18:14:49,727 IntervalUtils - Processing 372769 bp from intervals
[2016-04-15T01:14Z] WARN  18:14:49,733 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:14Z] INFO  18:14:49,735 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:14Z] INFO  18:14:49,736 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:14Z] INFO  18:14:49,737 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T01:14Z] INFO  18:14:49,738 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T01:14Z] INFO  18:14:49,790 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:14Z] INFO  18:14:49,791 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:14Z] INFO  18:14:49,834 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:14Z] INFO  18:14:49,923 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:14Z] INFO  18:14:49,924 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:14Z] INFO  18:14:49,924 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T01:14Z] INFO  18:14:49,936 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T01:14Z] INFO  18:14:49,987 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:14Z] INFO  18:14:49,988 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:14Z] INFO  18:14:51,054 ProgressMeter -            done    144412.0     9.0 s      66.0 s       99.9%     9.0 s       0.0 s
[2016-04-15T01:14Z] INFO  18:14:51,055 ProgressMeter - Total runtime 9.54 secs, 0.16 min, 0.00 hours
[2016-04-15T01:14Z] INFO  18:14:51,056 MicroScheduler - 5257 reads were filtered out during the traversal out of approximately 61735 total reads (8.52%)
[2016-04-15T01:14Z] INFO  18:14:51,057 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:14Z] INFO  18:14:51,058 MicroScheduler -   -> 84 reads (0.14% of total) failing BadMateFilter
[2016-04-15T01:14Z] INFO  18:14:51,058 MicroScheduler -   -> 5124 reads (8.30% of total) failing DuplicateReadFilter
[2016-04-15T01:14Z] INFO  18:14:51,059 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:14Z] INFO  18:14:51,060 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:14Z] INFO  18:14:51,061 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:14Z] INFO  18:14:51,061 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:14Z] INFO  18:14:51,062 MicroScheduler -   -> 49 reads (0.08% of total) failing UnmappedReadFilter
[2016-04-15T01:14Z] INFO  18:14:51,106 ProgressMeter -            done       118.0     1.0 s       3.2 h       84.7%     1.0 s       0.0 s
[2016-04-15T01:14Z] INFO  18:14:51,107 ProgressMeter - Total runtime 1.37 secs, 0.02 min, 0.00 hours
[2016-04-15T01:14Z] INFO  18:14:51,108 MicroScheduler - 8 reads were filtered out during the traversal out of approximately 165 total reads (4.85%)
[2016-04-15T01:14Z] INFO  18:14:51,108 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:14Z] INFO  18:14:51,108 MicroScheduler -   -> 0 reads (0.00% of total) failing BadMateFilter
[2016-04-15T01:14Z] INFO  18:14:51,109 MicroScheduler -   -> 8 reads (4.85% of total) failing DuplicateReadFilter
[2016-04-15T01:14Z] INFO  18:14:51,109 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:14Z] INFO  18:14:51,110 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:14Z] INFO  18:14:51,110 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:14Z] INFO  18:14:51,110 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:14Z] INFO  18:14:51,111 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T01:14Z] INFO  18:14:51,953 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:14Z] INFO  18:14:51,957 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:14Z] INFO  18:14:51,958 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:14Z] INFO  18:14:51,958 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:14Z] INFO  18:14:51,964 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/22/R14-18102_kapa-NGv3-PE100-NGv3-sort-22_31796605_47308085-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/22/R14-18102_kapa-NGv3-PE100-NGv3-22_31796605_47308085-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/22/tx/tmpCEb1uv/R14-18102_kapa-NGv3-PE100-NGv3-22_31796605_47308085.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:14Z] INFO  18:14:51,975 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:14Z] INFO  18:14:51,976 HelpFormatter - Date/Time: 2016/04/14 18:14:51
[2016-04-15T01:14Z] INFO  18:14:51,977 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:14Z] INFO  18:14:51,977 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:14Z] INFO  18:14:52,182 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:14Z] INFO  18:14:52,396 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T01:14Z] INFO  18:14:52,405 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:14Z] INFO  18:14:52,464 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-15T01:14Z] INFO  18:14:52,656 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:14Z] INFO  18:14:52,672 ProgressMeter -            done   2975101.0    49.0 s      16.0 s      100.0%    49.0 s       0.0 s
[2016-04-15T01:14Z] INFO  18:14:52,672 ProgressMeter - Total runtime 49.72 secs, 0.83 min, 0.01 hours
[2016-04-15T01:14Z] INFO  18:14:52,673 MicroScheduler - 65926 reads were filtered out during the traversal out of approximately 776811 total reads (8.49%)
[2016-04-15T01:14Z] INFO  18:14:52,673 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:14Z] INFO  18:14:52,673 MicroScheduler -   -> 1269 reads (0.16% of total) failing BadMateFilter
[2016-04-15T01:14Z] INFO  18:14:52,673 MicroScheduler -   -> 64086 reads (8.25% of total) failing DuplicateReadFilter
[2016-04-15T01:14Z] INFO  18:14:52,673 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:14Z] INFO  18:14:52,674 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:14Z] INFO  18:14:52,674 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:14Z] INFO  18:14:52,674 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:14Z] INFO  18:14:52,675 MicroScheduler -   -> 571 reads (0.07% of total) failing UnmappedReadFilter
[2016-04-15T01:14Z] INFO  18:14:52,710 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:14Z] INFO  18:14:52,905 IntervalUtils - Processing 366557 bp from intervals
[2016-04-15T01:14Z] WARN  18:14:52,911 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:14Z] GATK: UnifiedGenotyper
[2016-04-15T01:14Z] INFO  18:14:53,054 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:14Z] GATK: UnifiedGenotyper
[2016-04-15T01:14Z] INFO  18:14:53,205 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:14Z] INFO  18:14:53,207 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:14Z] INFO  18:14:53,208 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T01:14Z] INFO  18:14:53,208 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T01:14Z] INFO  18:14:53,267 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:14Z] INFO  18:14:53,268 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:14Z] INFO  18:14:54,129 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:14Z] GATK: UnifiedGenotyper
[2016-04-15T01:14Z] INFO  18:14:55,136 ProgressMeter -            done    282818.0    12.0 s      44.0 s       99.9%    12.0 s       0.0 s
[2016-04-15T01:14Z] INFO  18:14:55,137 ProgressMeter - Total runtime 12.52 secs, 0.21 min, 0.00 hours
[2016-04-15T01:14Z] INFO  18:14:55,138 MicroScheduler - 8002 reads were filtered out during the traversal out of approximately 94009 total reads (8.51%)
[2016-04-15T01:14Z] INFO  18:14:55,139 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:14Z] INFO  18:14:55,139 MicroScheduler -   -> 165 reads (0.18% of total) failing BadMateFilter
[2016-04-15T01:14Z] INFO  18:14:55,140 MicroScheduler -   -> 7759 reads (8.25% of total) failing DuplicateReadFilter
[2016-04-15T01:14Z] INFO  18:14:55,140 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:14Z] INFO  18:14:55,141 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:14Z] INFO  18:14:55,142 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:14Z] INFO  18:14:55,142 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:14Z] INFO  18:14:55,143 MicroScheduler -   -> 78 reads (0.08% of total) failing UnmappedReadFilter
[2016-04-15T01:14Z] INFO  18:14:55,835 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:14Z] INFO  18:14:55,838 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:14Z] INFO  18:14:55,838 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:14Z] INFO  18:14:55,839 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:14Z] INFO  18:14:55,843 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/X/R14-18102_kapa-NGv3-PE100-NGv3-sort-X_0_15509380-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/X/R14-18102_kapa-NGv3-PE100-NGv3-X_0_15509380-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/X/tx/tmpFX7JU8/R14-18102_kapa-NGv3-PE100-NGv3-X_0_15509380.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:14Z] INFO  18:14:55,879 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:14Z] INFO  18:14:55,880 HelpFormatter - Date/Time: 2016/04/14 18:14:55
[2016-04-15T01:14Z] INFO  18:14:55,881 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:14Z] INFO  18:14:55,881 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:14Z] INFO  18:14:56,030 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:14Z] INFO  18:14:56,034 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:14Z] INFO  18:14:56,034 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:14Z] INFO  18:14:56,035 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:14Z] INFO  18:14:56,041 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/22/R14-18102_kapa-NGv3-PE100-NGv3-sort-22_47309229_51304566-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/22/R14-18102_kapa-NGv3-PE100-NGv3-22_47309229_51304566-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/22/tx/tmpBOMS9h/R14-18102_kapa-NGv3-PE100-NGv3-22_47309229_51304566.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:14Z] INFO  18:14:56,059 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:14Z] INFO  18:14:56,060 HelpFormatter - Date/Time: 2016/04/14 18:14:56
[2016-04-15T01:14Z] INFO  18:14:56,061 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:14Z] INFO  18:14:56,061 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:14Z] INFO  18:14:56,070 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:14Z] INFO  18:14:56,219 ProgressMeter -            done    403180.0    20.0 s      50.0 s      100.0%    20.0 s       0.0 s
[2016-04-15T01:14Z] INFO  18:14:56,220 ProgressMeter - Total runtime 20.33 secs, 0.34 min, 0.01 hours
[2016-04-15T01:14Z] INFO  18:14:56,220 MicroScheduler - 17577 reads were filtered out during the traversal out of approximately 205756 total reads (8.54%)
[2016-04-15T01:14Z] INFO  18:14:56,221 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:14Z] INFO  18:14:56,223 MicroScheduler -   -> 319 reads (0.16% of total) failing BadMateFilter
[2016-04-15T01:14Z] INFO  18:14:56,223 MicroScheduler -   -> 17083 reads (8.30% of total) failing DuplicateReadFilter
[2016-04-15T01:14Z] INFO  18:14:56,223 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:14Z] INFO  18:14:56,224 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:14Z] INFO  18:14:56,224 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:14Z] INFO  18:14:56,224 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:14Z] INFO  18:14:56,225 MicroScheduler -   -> 175 reads (0.09% of total) failing UnmappedReadFilter
[2016-04-15T01:14Z] INFO  18:14:56,327 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:14Z] INFO  18:14:56,350 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:14Z] INFO  18:14:56,358 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T01:14Z] INFO  18:14:56,369 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:14Z] INFO  18:14:56,458 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.09
[2016-04-15T01:14Z] INFO  18:14:56,591 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T01:14Z] INFO  18:14:56,613 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:14Z] GATK: UnifiedGenotyper
[2016-04-15T01:14Z] INFO  18:14:56,694 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-15T01:14Z] INFO  18:14:56,943 IntervalUtils - Processing 114122 bp from intervals
[2016-04-15T01:14Z] WARN  18:14:56,950 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:14Z] INFO  18:14:57,094 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:14Z] INFO  18:14:57,157 IntervalUtils - Processing 81362 bp from intervals
[2016-04-15T01:14Z] INFO  18:14:57,161 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:14Z] INFO  18:14:57,162 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:14Z] INFO  18:14:57,162 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T01:14Z] INFO  18:14:57,163 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T01:14Z] WARN  18:14:57,176 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:14Z] INFO  18:14:57,234 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:14Z] INFO  18:14:57,236 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:14Z] INFO  18:14:57,345 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:14Z] INFO  18:14:57,394 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:14Z] INFO  18:14:57,396 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:14Z] INFO  18:14:57,397 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T01:14Z] INFO  18:14:57,398 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T01:14Z] INFO  18:14:57,449 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:14Z] INFO  18:14:57,450 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:14Z] INFO  18:14:57,558 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:14Z] INFO  18:14:57,561 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:14Z] INFO  18:14:57,561 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:14Z] INFO  18:14:57,562 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:14Z] INFO  18:14:57,566 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/X/R14-18102_kapa-NGv3-PE100-NGv3-sort-X_15518899_31090070-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/X/R14-18102_kapa-NGv3-PE100-NGv3-X_15518899_31090070-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/X/tx/tmp8bqg5Q/R14-18102_kapa-NGv3-PE100-NGv3-X_15518899_31090070.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:14Z] INFO  18:14:57,590 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:14Z] INFO  18:14:57,601 HelpFormatter - Date/Time: 2016/04/14 18:14:57
[2016-04-15T01:14Z] INFO  18:14:57,602 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:14Z] INFO  18:14:57,602 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:14Z] INFO  18:14:57,623 ProgressMeter -      19:4318343   1274028.0    30.0 s      23.0 s       30.1%    99.0 s      69.0 s
[2016-04-15T01:14Z] INFO  18:14:57,702 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:14Z] INFO  18:14:57,781 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:14Z] INFO  18:14:57,945 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T01:14Z] INFO  18:14:57,954 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:14Z] GATK: UnifiedGenotyper
[2016-04-15T01:14Z] INFO  18:14:58,040 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-15T01:14Z] INFO  18:14:58,121 ProgressMeter -            done    626854.0    22.0 s      36.0 s      100.0%    22.0 s       0.0 s
[2016-04-15T01:14Z] INFO  18:14:58,122 ProgressMeter - Total runtime 22.75 secs, 0.38 min, 0.01 hours
[2016-04-15T01:14Z] INFO  18:14:58,122 MicroScheduler - 21869 reads were filtered out during the traversal out of approximately 257658 total reads (8.49%)
[2016-04-15T01:14Z] INFO  18:14:58,123 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:14Z] INFO  18:14:58,123 MicroScheduler -   -> 383 reads (0.15% of total) failing BadMateFilter
[2016-04-15T01:14Z] INFO  18:14:58,123 MicroScheduler -   -> 21297 reads (8.27% of total) failing DuplicateReadFilter
[2016-04-15T01:14Z] INFO  18:14:58,123 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:14Z] INFO  18:14:58,124 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:14Z] INFO  18:14:58,124 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:14Z] INFO  18:14:58,124 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:14Z] INFO  18:14:58,124 MicroScheduler -   -> 189 reads (0.07% of total) failing UnmappedReadFilter
[2016-04-15T01:14Z] INFO  18:14:58,402 IntervalUtils - Processing 133046 bp from intervals
[2016-04-15T01:14Z] WARN  18:14:58,419 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:14Z] INFO  18:14:58,522 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:14Z] INFO  18:14:58,610 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:14Z] INFO  18:14:58,611 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:14Z] INFO  18:14:58,612 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T01:14Z] INFO  18:14:58,612 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T01:14Z] INFO  18:14:58,658 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:14Z] INFO  18:14:58,659 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:14Z] INFO  18:14:59,469 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:14Z] INFO  18:14:59,473 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:14Z] INFO  18:14:59,474 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:14Z] INFO  18:14:59,474 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:14Z] INFO  18:14:59,480 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/X/R14-18102_kapa-NGv3-PE100-NGv3-sort-X_31139949_46696637-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/X/R14-18102_kapa-NGv3-PE100-NGv3-X_31139949_46696637-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/X/tx/tmpCJMo8n/R14-18102_kapa-NGv3-PE100-NGv3-X_31139949_46696637.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:14Z] INFO  18:14:59,495 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:14Z] INFO  18:14:59,496 HelpFormatter - Date/Time: 2016/04/14 18:14:59
[2016-04-15T01:14Z] INFO  18:14:59,497 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:14Z] INFO  18:14:59,498 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:14Z] INFO  18:14:59,558 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:14Z] INFO  18:14:59,757 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:14Z] GATK: UnifiedGenotyper
[2016-04-15T01:14Z] INFO  18:14:59,936 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T01:14Z] INFO  18:14:59,956 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:15Z] INFO  18:15:00,057 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.10
[2016-04-15T01:15Z] INFO  18:15:00,457 IntervalUtils - Processing 99894 bp from intervals
[2016-04-15T01:15Z] WARN  18:15:00,462 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:15Z] INFO  18:15:00,581 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:15Z] INFO  18:15:00,649 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:15Z] INFO  18:15:00,649 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:15Z] INFO  18:15:00,650 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T01:15Z] INFO  18:15:00,650 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T01:15Z] INFO  18:15:00,732 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:15Z] INFO  18:15:00,745 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:15Z] INFO  18:15:00,944 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:15Z] INFO  18:15:00,948 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:15Z] INFO  18:15:00,948 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:15Z] INFO  18:15:00,949 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:15Z] INFO  18:15:00,953 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/X/R14-18102_kapa-NGv3-PE100-NGv3-sort-X_46712910_62570698-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/X/R14-18102_kapa-NGv3-PE100-NGv3-X_46712910_62570698-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/X/tx/tmptWbo9_/R14-18102_kapa-NGv3-PE100-NGv3-X_46712910_62570698.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:15Z] INFO  18:15:00,974 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:15Z] INFO  18:15:00,975 HelpFormatter - Date/Time: 2016/04/14 18:15:00
[2016-04-15T01:15Z] INFO  18:15:00,975 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:15Z] INFO  18:15:00,980 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:15Z] INFO  18:15:01,147 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:15Z] INFO  18:15:01,348 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T01:15Z] INFO  18:15:01,379 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:15Z] INFO  18:15:01,578 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.20
[2016-04-15T01:15Z] INFO  18:15:02,027 IntervalUtils - Processing 228299 bp from intervals
[2016-04-15T01:15Z] WARN  18:15:02,033 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:15Z] INFO  18:15:02,155 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:15Z] INFO  18:15:02,238 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:15Z] INFO  18:15:02,240 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:15Z] INFO  18:15:02,240 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T01:15Z] INFO  18:15:02,241 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T01:15Z] INFO  18:15:02,301 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:15Z] INFO  18:15:02,312 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:15Z] INFO  18:15:02,762 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:15Z] INFO  18:15:02,765 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:15Z] INFO  18:15:02,766 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:15Z] INFO  18:15:02,767 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:15Z] INFO  18:15:02,771 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/X/R14-18102_kapa-NGv3-PE100-NGv3-sort-X_62857907_78427545-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/X/R14-18102_kapa-NGv3-PE100-NGv3-X_62857907_78427545-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/X/tx/tmpD1GxGK/R14-18102_kapa-NGv3-PE100-NGv3-X_62857907_78427545.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:15Z] INFO  18:15:02,783 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:15Z] INFO  18:15:02,784 HelpFormatter - Date/Time: 2016/04/14 18:15:02
[2016-04-15T01:15Z] INFO  18:15:02,785 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:15Z] INFO  18:15:02,786 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:15Z] INFO  18:15:03,031 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:15Z] INFO  18:15:03,229 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T01:15Z] INFO  18:15:03,249 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:15Z] INFO  18:15:03,270 ProgressMeter -     19:22940116   1107583.0    30.0 s      27.0 s       90.7%    33.0 s       3.0 s
[2016-04-15T01:15Z] INFO  18:15:03,333 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-15T01:15Z] INFO  18:15:03,917 IntervalUtils - Processing 175038 bp from intervals
[2016-04-15T01:15Z] WARN  18:15:03,922 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:15Z] INFO  18:15:04,072 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:15Z] INFO  18:15:04,151 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:15Z] INFO  18:15:04,153 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:15Z] INFO  18:15:04,153 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T01:15Z] INFO  18:15:04,154 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T01:15Z] INFO  18:15:04,208 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:15Z] INFO  18:15:04,209 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:15Z] INFO  18:15:04,257 ProgressMeter -     19:39234769   1211707.0    30.0 s      24.0 s       41.8%    71.0 s      41.0 s
[2016-04-15T01:15Z] INFO  18:15:04,489 ProgressMeter -            done   2489748.0    56.0 s      22.0 s      100.0%    56.0 s       0.0 s
[2016-04-15T01:15Z] INFO  18:15:04,489 ProgressMeter - Total runtime 56.59 secs, 0.94 min, 0.02 hours
[2016-04-15T01:15Z] INFO  18:15:04,490 MicroScheduler - 76138 reads were filtered out during the traversal out of approximately 944207 total reads (8.06%)
[2016-04-15T01:15Z] INFO  18:15:04,490 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:15Z] INFO  18:15:04,490 MicroScheduler -   -> 1452 reads (0.15% of total) failing BadMateFilter
[2016-04-15T01:15Z] INFO  18:15:04,491 MicroScheduler -   -> 73964 reads (7.83% of total) failing DuplicateReadFilter
[2016-04-15T01:15Z] INFO  18:15:04,491 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:15Z] INFO  18:15:04,491 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:15Z] INFO  18:15:04,491 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:15Z] INFO  18:15:04,491 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:15Z] INFO  18:15:04,501 MicroScheduler -   -> 722 reads (0.08% of total) failing UnmappedReadFilter
[2016-04-15T01:15Z] INFO  18:15:05,657 ProgressMeter -     19:51228530   1229526.0    30.0 s      24.0 s       37.8%    79.0 s      49.0 s
[2016-04-15T01:15Z] INFO  18:15:05,928 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:15Z] INFO  18:15:06,194 ProgressMeter -     20:44258453    877953.0    30.0 s      34.0 s       80.4%    37.0 s       7.0 s
[2016-04-15T01:15Z] GATK: UnifiedGenotyper
[2016-04-15T01:15Z] INFO  18:15:06,252 ProgressMeter -            done   1154024.0    32.0 s      28.0 s      100.0%    32.0 s       0.0 s
[2016-04-15T01:15Z] INFO  18:15:06,253 ProgressMeter - Total runtime 33.00 secs, 0.55 min, 0.01 hours
[2016-04-15T01:15Z] INFO  18:15:06,253 MicroScheduler - 40959 reads were filtered out during the traversal out of approximately 478848 total reads (8.55%)
[2016-04-15T01:15Z] INFO  18:15:06,254 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:15Z] INFO  18:15:06,255 MicroScheduler -   -> 756 reads (0.16% of total) failing BadMateFilter
[2016-04-15T01:15Z] INFO  18:15:06,256 MicroScheduler -   -> 39808 reads (8.31% of total) failing DuplicateReadFilter
[2016-04-15T01:15Z] INFO  18:15:06,257 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:15Z] INFO  18:15:06,257 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:15Z] INFO  18:15:06,258 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:15Z] INFO  18:15:06,259 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:15Z] INFO  18:15:06,260 MicroScheduler -   -> 395 reads (0.08% of total) failing UnmappedReadFilter
[2016-04-15T01:15Z] INFO  18:15:07,750 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:15Z] GATK: UnifiedGenotyper
[2016-04-15T01:15Z] INFO  18:15:09,320 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:15Z] INFO  18:15:09,324 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:15Z] INFO  18:15:09,324 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:15Z] INFO  18:15:09,325 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:15Z] INFO  18:15:09,330 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/X/R14-18102_kapa-NGv3-PE100-NGv3-sort-X_78616585_95940189-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/X/R14-18102_kapa-NGv3-PE100-NGv3-X_78616585_95940189-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/X/tx/tmp1RSPHp/R14-18102_kapa-NGv3-PE100-NGv3-X_78616585_95940189.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:15Z] INFO  18:15:09,355 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:15Z] INFO  18:15:09,356 HelpFormatter - Date/Time: 2016/04/14 18:15:09
[2016-04-15T01:15Z] INFO  18:15:09,356 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:15Z] INFO  18:15:09,357 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:15Z] INFO  18:15:09,391 ProgressMeter -     20:62729255   1220920.0    30.0 s      24.0 s       99.3%    30.0 s       0.0 s
[2016-04-15T01:15Z] INFO  18:15:09,506 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:15Z] INFO  18:15:09,557 ProgressMeter -            done   1223679.0    30.0 s      24.0 s      100.0%    30.0 s       0.0 s
[2016-04-15T01:15Z] INFO  18:15:09,557 ProgressMeter - Total runtime 30.21 secs, 0.50 min, 0.01 hours
[2016-04-15T01:15Z] INFO  18:15:09,558 MicroScheduler - 34205 reads were filtered out during the traversal out of approximately 396777 total reads (8.62%)
[2016-04-15T01:15Z] INFO  18:15:09,558 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:15Z] INFO  18:15:09,558 MicroScheduler -   -> 655 reads (0.17% of total) failing BadMateFilter
[2016-04-15T01:15Z] INFO  18:15:09,558 MicroScheduler -   -> 33203 reads (8.37% of total) failing DuplicateReadFilter
[2016-04-15T01:15Z] INFO  18:15:09,559 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:15Z] INFO  18:15:09,559 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:15Z] INFO  18:15:09,559 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:15Z] INFO  18:15:09,559 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:15Z] INFO  18:15:09,560 MicroScheduler -   -> 347 reads (0.09% of total) failing UnmappedReadFilter
[2016-04-15T01:15Z] INFO  18:15:09,701 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T01:15Z] INFO  18:15:09,727 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:15Z] INFO  18:15:09,837 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.11
[2016-04-15T01:15Z] INFO  18:15:10,408 IntervalUtils - Processing 45787 bp from intervals
[2016-04-15T01:15Z] WARN  18:15:10,414 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:15Z] INFO  18:15:10,584 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:15Z] INFO  18:15:10,679 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:15Z] INFO  18:15:10,681 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:15Z] INFO  18:15:10,682 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T01:15Z] INFO  18:15:10,683 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T01:15Z] INFO  18:15:10,745 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:15Z] INFO  18:15:10,746 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:15Z] INFO  18:15:10,777 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:15Z] INFO  18:15:10,780 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:15Z] INFO  18:15:10,781 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:15Z] INFO  18:15:10,782 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:15Z] INFO  18:15:10,786 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/X/R14-18102_kapa-NGv3-PE100-NGv3-sort-X_95990756_111698889-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/X/R14-18102_kapa-NGv3-PE100-NGv3-X_95990756_111698889-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/X/tx/tmp1Op5e_/R14-18102_kapa-NGv3-PE100-NGv3-X_95990756_111698889.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:15Z] INFO  18:15:10,797 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:15Z] INFO  18:15:10,798 HelpFormatter - Date/Time: 2016/04/14 18:15:10
[2016-04-15T01:15Z] INFO  18:15:10,799 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:15Z] INFO  18:15:10,799 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:15Z] INFO  18:15:10,892 ProgressMeter -            done    613276.0    13.0 s      22.0 s      100.0%    13.0 s       0.0 s
[2016-04-15T01:15Z] INFO  18:15:10,892 ProgressMeter - Total runtime 13.50 secs, 0.22 min, 0.00 hours
[2016-04-15T01:15Z] INFO  18:15:10,893 MicroScheduler - 11458 reads were filtered out during the traversal out of approximately 133227 total reads (8.60%)
[2016-04-15T01:15Z] INFO  18:15:10,893 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:15Z] INFO  18:15:10,894 MicroScheduler -   -> 252 reads (0.19% of total) failing BadMateFilter
[2016-04-15T01:15Z] INFO  18:15:10,894 MicroScheduler -   -> 11098 reads (8.33% of total) failing DuplicateReadFilter
[2016-04-15T01:15Z] INFO  18:15:10,894 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:15Z] INFO  18:15:10,894 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:15Z] INFO  18:15:10,895 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:15Z] INFO  18:15:10,895 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:15Z] INFO  18:15:10,895 MicroScheduler -   -> 108 reads (0.08% of total) failing UnmappedReadFilter
[2016-04-15T01:15Z] INFO  18:15:10,932 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:15Z] INFO  18:15:11,065 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:15Z] INFO  18:15:11,118 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T01:15Z] INFO  18:15:11,127 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:15Z] GATK: UnifiedGenotyper
[2016-04-15T01:15Z] INFO  18:15:11,429 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.30
[2016-04-15T01:15Z] INFO  18:15:11,912 IntervalUtils - Processing 181656 bp from intervals
[2016-04-15T01:15Z] WARN  18:15:11,920 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:15Z] INFO  18:15:12,016 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:15Z] INFO  18:15:12,089 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:15Z] INFO  18:15:12,091 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:15Z] INFO  18:15:12,092 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T01:15Z] INFO  18:15:12,092 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T01:15Z] INFO  18:15:12,127 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:15Z] INFO  18:15:12,170 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:15Z] INFO  18:15:12,171 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:15Z] GATK: UnifiedGenotyper
[2016-04-15T01:15Z] INFO  18:15:12,463 ProgressMeter -     21:45994336    831354.0    30.0 s      36.0 s       94.8%    31.0 s       1.0 s
[2016-04-15T01:15Z] INFO  18:15:12,572 ProgressMeter -            done    281084.0    15.0 s      54.0 s       99.9%    15.0 s       0.0 s
[2016-04-15T01:15Z] INFO  18:15:12,573 ProgressMeter - Total runtime 15.41 secs, 0.26 min, 0.00 hours
[2016-04-15T01:15Z] INFO  18:15:12,573 MicroScheduler - 13912 reads were filtered out during the traversal out of approximately 164270 total reads (8.47%)
[2016-04-15T01:15Z] INFO  18:15:12,573 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:15Z] INFO  18:15:12,574 MicroScheduler -   -> 261 reads (0.16% of total) failing BadMateFilter
[2016-04-15T01:15Z] INFO  18:15:12,574 MicroScheduler -   -> 13525 reads (8.23% of total) failing DuplicateReadFilter
[2016-04-15T01:15Z] INFO  18:15:12,574 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:15Z] INFO  18:15:12,574 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:15Z] INFO  18:15:12,575 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:15Z] INFO  18:15:12,575 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:15Z] INFO  18:15:12,575 MicroScheduler -   -> 126 reads (0.08% of total) failing UnmappedReadFilter
[2016-04-15T01:15Z] INFO  18:15:12,600 ProgressMeter -            done   1208060.0    36.0 s      30.0 s      100.0%    36.0 s       0.0 s
[2016-04-15T01:15Z] INFO  18:15:12,600 ProgressMeter - Total runtime 36.43 secs, 0.61 min, 0.01 hours
[2016-04-15T01:15Z] INFO  18:15:12,601 MicroScheduler - 40311 reads were filtered out during the traversal out of approximately 479337 total reads (8.41%)
[2016-04-15T01:15Z] INFO  18:15:12,601 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:15Z] INFO  18:15:12,601 MicroScheduler -   -> 698 reads (0.15% of total) failing BadMateFilter
[2016-04-15T01:15Z] INFO  18:15:12,602 MicroScheduler -   -> 39269 reads (8.19% of total) failing DuplicateReadFilter
[2016-04-15T01:15Z] INFO  18:15:12,602 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:15Z] INFO  18:15:12,602 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:15Z] INFO  18:15:12,603 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:15Z] INFO  18:15:12,603 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:15Z] INFO  18:15:12,603 MicroScheduler -   -> 344 reads (0.07% of total) failing UnmappedReadFilter
[2016-04-15T01:15Z] INFO  18:15:13,181 ProgressMeter -            done    248425.0    12.0 s      50.0 s      100.0%    12.0 s       0.0 s
[2016-04-15T01:15Z] INFO  18:15:13,182 ProgressMeter - Total runtime 12.53 secs, 0.21 min, 0.00 hours
[2016-04-15T01:15Z] INFO  18:15:13,182 MicroScheduler - 10678 reads were filtered out during the traversal out of approximately 127072 total reads (8.40%)
[2016-04-15T01:15Z] INFO  18:15:13,182 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:15Z] INFO  18:15:13,183 MicroScheduler -   -> 197 reads (0.16% of total) failing BadMateFilter
[2016-04-15T01:15Z] INFO  18:15:13,183 MicroScheduler -   -> 10390 reads (8.18% of total) failing DuplicateReadFilter
[2016-04-15T01:15Z] INFO  18:15:13,183 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:15Z] INFO  18:15:13,183 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:15Z] INFO  18:15:13,184 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:15Z] INFO  18:15:13,184 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:15Z] INFO  18:15:13,184 MicroScheduler -   -> 91 reads (0.07% of total) failing UnmappedReadFilter
[2016-04-15T01:15Z] INFO  18:15:14,089 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:15Z] INFO  18:15:14,098 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:15Z] INFO  18:15:14,101 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:15Z] INFO  18:15:14,102 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:15Z] INFO  18:15:14,103 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:15Z] INFO  18:15:14,106 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:15Z] INFO  18:15:14,109 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/X/R14-18102_kapa-NGv3-PE100-NGv3-sort-X_111874647_128581278-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/X/R14-18102_kapa-NGv3-PE100-NGv3-X_111874647_128581278-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/X/tx/tmpag6kME/R14-18102_kapa-NGv3-PE100-NGv3-X_111874647_128581278.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:15Z] INFO  18:15:14,147 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:15Z] INFO  18:15:14,154 HelpFormatter - Date/Time: 2016/04/14 18:15:14
[2016-04-15T01:15Z] INFO  18:15:14,155 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:15Z] INFO  18:15:14,155 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:15Z] GATK: UnifiedGenotyper
[2016-04-15T01:15Z] GATK: UnifiedGenotyper
[2016-04-15T01:15Z] INFO  18:15:14,416 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:15Z] INFO  18:15:14,480 ProgressMeter -            done    312881.0    15.0 s      50.0 s      100.0%    15.0 s       0.0 s
[2016-04-15T01:15Z] INFO  18:15:14,481 ProgressMeter - Total runtime 15.87 secs, 0.26 min, 0.00 hours
[2016-04-15T01:15Z] INFO  18:15:14,482 MicroScheduler - 14036 reads were filtered out during the traversal out of approximately 166241 total reads (8.44%)
[2016-04-15T01:15Z] INFO  18:15:14,483 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:15Z] INFO  18:15:14,483 MicroScheduler -   -> 212 reads (0.13% of total) failing BadMateFilter
[2016-04-15T01:15Z] INFO  18:15:14,484 MicroScheduler -   -> 13708 reads (8.25% of total) failing DuplicateReadFilter
[2016-04-15T01:15Z] INFO  18:15:14,485 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:15Z] INFO  18:15:14,485 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:15Z] INFO  18:15:14,486 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:15Z] INFO  18:15:14,487 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:15Z] INFO  18:15:14,488 MicroScheduler -   -> 116 reads (0.07% of total) failing UnmappedReadFilter
[2016-04-15T01:15Z] INFO  18:15:14,607 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:15Z] INFO  18:15:14,661 ProgressMeter -            done    861650.0    32.0 s      37.0 s      100.0%    32.0 s       0.0 s
[2016-04-15T01:15Z] INFO  18:15:14,662 ProgressMeter - Total runtime 32.22 secs, 0.54 min, 0.01 hours
[2016-04-15T01:15Z] INFO  18:15:14,663 MicroScheduler - 34881 reads were filtered out during the traversal out of approximately 401846 total reads (8.68%)
[2016-04-15T01:15Z] INFO  18:15:14,667 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:15Z] INFO  18:15:14,668 MicroScheduler -   -> 622 reads (0.15% of total) failing BadMateFilter
[2016-04-15T01:15Z] INFO  18:15:14,668 MicroScheduler -   -> 33953 reads (8.45% of total) failing DuplicateReadFilter
[2016-04-15T01:15Z] INFO  18:15:14,669 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:15Z] INFO  18:15:14,670 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:15Z] INFO  18:15:14,670 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:15Z] INFO  18:15:14,671 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:15Z] INFO  18:15:14,672 MicroScheduler -   -> 306 reads (0.08% of total) failing UnmappedReadFilter
[2016-04-15T01:15Z] INFO  18:15:14,689 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T01:15Z] INFO  18:15:14,711 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:15Z] INFO  18:15:14,774 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-15T01:15Z] GATK: UnifiedGenotyper
[2016-04-15T01:15Z] INFO  18:15:15,203 IntervalUtils - Processing 115535 bp from intervals
[2016-04-15T01:15Z] WARN  18:15:15,208 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:15Z] INFO  18:15:15,290 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:15Z] INFO  18:15:15,292 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:15Z] INFO  18:15:15,295 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:15Z] INFO  18:15:15,296 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:15Z] INFO  18:15:15,296 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:15Z] INFO  18:15:15,301 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/X/R14-18102_kapa-NGv3-PE100-NGv3-sort-X_128582278_144329181-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/X/R14-18102_kapa-NGv3-PE100-NGv3-X_128582278_144329181-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/X/tx/tmpyLMNyg/R14-18102_kapa-NGv3-PE100-NGv3-X_128582278_144329181.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:15Z] INFO  18:15:15,310 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:15Z] INFO  18:15:15,311 HelpFormatter - Date/Time: 2016/04/14 18:15:15
[2016-04-15T01:15Z] INFO  18:15:15,311 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:15Z] INFO  18:15:15,312 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:15Z] INFO  18:15:15,400 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:15Z] INFO  18:15:15,402 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:15Z] INFO  18:15:15,402 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T01:15Z] INFO  18:15:15,403 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T01:15Z] INFO  18:15:15,501 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:15Z] INFO  18:15:15,502 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:15Z] INFO  18:15:15,503 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:15Z] INFO  18:15:15,719 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T01:15Z] INFO  18:15:15,736 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:15Z] INFO  18:15:15,770 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:15Z] INFO  18:15:15,816 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-15T01:15Z] GATK: UnifiedGenotyper
[2016-04-15T01:15Z] INFO  18:15:16,148 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:15Z] INFO  18:15:16,280 IntervalUtils - Processing 143302 bp from intervals
[2016-04-15T01:15Z] WARN  18:15:16,286 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:15Z] INFO  18:15:16,381 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:15Z] INFO  18:15:16,523 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:15Z] INFO  18:15:16,523 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:15Z] INFO  18:15:16,524 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T01:15Z] INFO  18:15:16,524 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T01:15Z] INFO  18:15:16,621 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:15Z] INFO  18:15:16,624 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:15Z] GATK: HaplotypeCaller
[2016-04-15T01:15Z] INFO  18:15:17,244 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:15Z] INFO  18:15:17,265 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:15Z] INFO  18:15:17,265 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:15Z] INFO  18:15:17,265 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:15Z] INFO  18:15:17,270 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/Y/R14-18102_kapa-NGv3-PE100-NGv3-sort-Y_0_15522993-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/Y/R14-18102_kapa-NGv3-PE100-NGv3-Y_0_15522993-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/Y/tx/tmpYvgUwe/R14-18102_kapa-NGv3-PE100-NGv3-Y_0_15522993.vcf.gz -ploidy 1 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:15Z] INFO  18:15:17,286 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:15Z] INFO  18:15:17,286 HelpFormatter - Date/Time: 2016/04/14 18:15:17
[2016-04-15T01:15Z] INFO  18:15:17,287 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:15Z] INFO  18:15:17,287 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:15Z] INFO  18:15:17,381 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:15Z] INFO  18:15:17,384 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:15Z] INFO  18:15:17,385 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:15Z] INFO  18:15:17,386 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:15Z] INFO  18:15:17,390 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/X/R14-18102_kapa-NGv3-PE100-NGv3-sort-X_144337190_155270560-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/X/R14-18102_kapa-NGv3-PE100-NGv3-X_144337190_155270560-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/X/tx/tmpxECwJz/R14-18102_kapa-NGv3-PE100-NGv3-X_144337190_155270560.vcf.gz -ploidy 2 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:15Z] INFO  18:15:17,422 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:15Z] INFO  18:15:17,433 HelpFormatter - Date/Time: 2016/04/14 18:15:17
[2016-04-15T01:15Z] INFO  18:15:17,434 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:15Z] INFO  18:15:17,435 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:15Z] INFO  18:15:17,468 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:15Z] INFO  18:15:17,622 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:15Z] INFO  18:15:17,689 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T01:15Z] INFO  18:15:17,720 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:15Z] INFO  18:15:17,794 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-15T01:15Z] INFO  18:15:17,915 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T01:15Z] INFO  18:15:17,924 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:15Z] INFO  18:15:18,002 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-15T01:15Z] INFO  18:15:18,119 IntervalUtils - Processing 52192 bp from intervals
[2016-04-15T01:15Z] WARN  18:15:18,124 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:15Z] INFO  18:15:18,190 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:15Z] INFO  18:15:18,204 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:15Z] INFO  18:15:18,205 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:15Z] INFO  18:15:18,206 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:15Z] INFO  18:15:18,212 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/Y/R14-18102_kapa-NGv3-PE100-NGv3-sort-Y_15526614_59222281-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/Y/R14-18102_kapa-NGv3-PE100-NGv3-Y_15526614_59222281-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/Y/tx/tmpPDm0wx/R14-18102_kapa-NGv3-PE100-NGv3-Y_15526614_59222281.vcf.gz -ploidy 1 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:15Z] INFO  18:15:18,233 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:15Z] INFO  18:15:18,234 HelpFormatter - Date/Time: 2016/04/14 18:15:18
[2016-04-15T01:15Z] INFO  18:15:18,234 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:15Z] INFO  18:15:18,235 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:15Z] INFO  18:15:18,231 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:15Z] INFO  18:15:18,316 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:15Z] INFO  18:15:18,318 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:15Z] INFO  18:15:18,318 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T01:15Z] INFO  18:15:18,319 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T01:15Z] INFO  18:15:18,367 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:15Z] INFO  18:15:18,368 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:15Z] INFO  18:15:18,434 IntervalUtils - Processing 184337 bp from intervals
[2016-04-15T01:15Z] WARN  18:15:18,440 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:15Z] INFO  18:15:18,504 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:15Z] INFO  18:15:18,532 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:15Z] INFO  18:15:18,658 ProgressMeter -            done    104106.0     7.0 s      76.0 s       99.9%     7.0 s       0.0 s
[2016-04-15T01:15Z] INFO  18:15:18,659 ProgressMeter - Total runtime 7.98 secs, 0.13 min, 0.00 hours
[2016-04-15T01:15Z] INFO  18:15:18,659 MicroScheduler - 4442 reads were filtered out during the traversal out of approximately 51468 total reads (8.63%)
[2016-04-15T01:15Z] INFO  18:15:18,660 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:15Z] INFO  18:15:18,661 MicroScheduler -   -> 72 reads (0.14% of total) failing BadMateFilter
[2016-04-15T01:15Z] INFO  18:15:18,661 MicroScheduler -   -> 4329 reads (8.41% of total) failing DuplicateReadFilter
[2016-04-15T01:15Z] INFO  18:15:18,662 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:15Z] INFO  18:15:18,663 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:15Z] INFO  18:15:18,663 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:15Z] INFO  18:15:18,664 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:15Z] INFO  18:15:18,664 MicroScheduler -   -> 41 reads (0.08% of total) failing UnmappedReadFilter
[2016-04-15T01:15Z] INFO  18:15:18,667 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:15Z] INFO  18:15:18,668 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:15Z] INFO  18:15:18,669 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T01:15Z] INFO  18:15:18,670 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T01:15Z] INFO  18:15:18,734 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:15Z] INFO  18:15:18,735 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:15Z] INFO  18:15:18,752 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T01:15Z] INFO  18:15:18,763 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:15Z] INFO  18:15:18,841 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-15T01:15Z] INFO  18:15:19,204 IntervalUtils - Processing 44713 bp from intervals
[2016-04-15T01:15Z] WARN  18:15:19,209 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:15Z] INFO  18:15:19,226 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:15Z] INFO  18:15:19,230 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:15Z] INFO  18:15:19,230 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:15Z] INFO  18:15:19,231 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:15Z] INFO  18:15:19,249 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/Y/R14-18102_kapa-NGv3-PE100-NGv3-sort-Y_59228291_59373566-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/Y/R14-18102_kapa-NGv3-PE100-NGv3-Y_59228291_59373566-regions.bed --interval_set_rule INTERSECTION -T UnifiedGenotyper -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/Y/tx/tmpuHBzBd/R14-18102_kapa-NGv3-PE100-NGv3-Y_59228291_59373566.vcf.gz -ploidy 1 --genotype_likelihoods_model BOTH -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:15Z] INFO  18:15:19,259 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:15Z] INFO  18:15:19,279 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:15Z] INFO  18:15:19,281 HelpFormatter - Date/Time: 2016/04/14 18:15:19
[2016-04-15T01:15Z] INFO  18:15:19,282 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:15Z] INFO  18:15:19,287 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:15Z] INFO  18:15:19,312 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:15Z] INFO  18:15:19,313 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:15Z] INFO  18:15:19,314 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T01:15Z] INFO  18:15:19,315 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T01:15Z] INFO  18:15:19,355 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:15Z] INFO  18:15:19,356 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:15Z] INFO  18:15:19,526 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:15Z] INFO  18:15:19,529 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:15Z] INFO  18:15:19,529 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:15Z] INFO  18:15:19,530 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:15Z] INFO  18:15:19,530 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:15Z] INFO  18:15:19,535 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/1/R14-18102_kapa-NGv3-PE100-NGv3-sort-1_0_15541927-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/1/R14-18102_kapa-NGv3-PE100-NGv3-1_0_15541927-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/1/tx/tmp8BvQSN/R14-18102_kapa-NGv3-PE100-NGv3-1_0_15541927.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:15Z] INFO  18:15:19,545 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:15Z] INFO  18:15:19,546 HelpFormatter - Date/Time: 2016/04/14 18:15:19
[2016-04-15T01:15Z] INFO  18:15:19,546 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:15Z] INFO  18:15:19,546 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:15Z] WARN  18:15:19,597 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T01:15Z] WARN  18:15:19,600 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/1/tx/tmp8BvQSN/R14-18102_kapa-NGv3-PE100-NGv3-1_0_15541927.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T01:15Z] INFO  18:15:19,776 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
[2016-04-15T01:15Z] INFO  18:15:19,795 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:15Z] INFO  18:15:19,853 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:15Z] INFO  18:15:19,872 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-15T01:15Z] INFO  18:15:19,941 ProgressMeter -     22:26164182    850996.0    30.0 s      35.0 s       65.5%    45.0 s      15.0 s
[2016-04-15T01:15Z] INFO  18:15:20,091 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T01:15Z] INFO  18:15:20,101 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:15Z] INFO  18:15:20,185 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-15T01:15Z] INFO  18:15:20,185 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:15Z] INFO  18:15:20,210 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T01:15Z] INFO  18:15:20,405 IntervalUtils - Processing 2412 bp from intervals
[2016-04-15T01:15Z] WARN  18:15:20,410 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:15Z] INFO  18:15:20,487 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:15Z] INFO  18:15:20,511 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:15Z] INFO  18:15:20,512 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:15Z] INFO  18:15:20,513 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T01:15Z] INFO  18:15:20,513 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T01:15Z] INFO  18:15:20,571 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:15Z] INFO  18:15:20,572 StrandBiasTest - SAM/BAM data was found. Attempting to use read data to calculate strand bias annotations values.
[2016-04-15T01:15Z] GATK: HaplotypeCaller
[2016-04-15T01:15Z] INFO  18:15:20,687 IntervalUtils - Processing 390138 bp from intervals
[2016-04-15T01:15Z] WARN  18:15:20,693 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:15Z] INFO  18:15:20,825 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:15Z] INFO  18:15:20,946 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:15Z] INFO  18:15:20,946 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:15Z] INFO  18:15:20,946 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T01:15Z] INFO  18:15:20,947 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T01:15Z] INFO  18:15:20,954 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T01:15Z] INFO  18:15:20,955 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T01:15Z] INFO  18:15:21,178 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T01:15Z] INFO  18:15:21,186 ProgressMeter -            done     16030.0     0.0 s      41.0 s       96.1%     0.0 s       0.0 s
[2016-04-15T01:15Z] INFO  18:15:21,186 ProgressMeter - Total runtime 0.67 secs, 0.01 min, 0.00 hours
[2016-04-15T01:15Z] INFO  18:15:22,642 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:15Z] GATK: HaplotypeCaller
[2016-04-15T01:15Z] INFO  18:15:22,978 ProgressMeter -            done   1172190.0     4.0 s       3.0 s      100.0%     4.0 s       0.0 s
[2016-04-15T01:15Z] INFO  18:15:22,979 ProgressMeter - Total runtime 4.66 secs, 0.08 min, 0.00 hours
[2016-04-15T01:15Z] INFO  18:15:22,980 MicroScheduler - 59 reads were filtered out during the traversal out of approximately 1455 total reads (4.05%)
[2016-04-15T01:15Z] INFO  18:15:22,980 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:15Z] INFO  18:15:22,980 MicroScheduler -   -> 10 reads (0.69% of total) failing BadMateFilter
[2016-04-15T01:15Z] INFO  18:15:22,981 MicroScheduler -   -> 40 reads (2.75% of total) failing DuplicateReadFilter
[2016-04-15T01:15Z] INFO  18:15:22,981 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:15Z] INFO  18:15:22,981 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:15Z] INFO  18:15:22,982 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:15Z] INFO  18:15:22,982 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:15Z] INFO  18:15:22,982 MicroScheduler -   -> 9 reads (0.62% of total) failing UnmappedReadFilter
[2016-04-15T01:15Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T01:15Z] INFO  18:15:23,223 ProgressMeter -     22:42987961    979065.0    30.0 s      30.0 s       75.3%    39.0 s       9.0 s
[2016-04-15T01:15Z] INFO  18:15:23,225 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T01:15Z] INFO  18:15:23,226 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T01:15Z] WARN  18:15:23,368 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T01:15Z] WARN  18:15:23,369 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T01:15Z] INFO  18:15:23,433 ProgressMeter -            done    166188.0     4.0 s      24.0 s       99.9%     4.0 s       0.0 s
[2016-04-15T01:15Z] INFO  18:15:23,433 ProgressMeter - Total runtime 4.12 secs, 0.07 min, 0.00 hours
[2016-04-15T01:15Z] INFO  18:15:23,433 MicroScheduler - 132 reads were filtered out during the traversal out of approximately 1375 total reads (9.60%)
[2016-04-15T01:15Z] INFO  18:15:23,434 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:15Z] INFO  18:15:23,434 MicroScheduler -   -> 13 reads (0.95% of total) failing BadMateFilter
[2016-04-15T01:15Z] INFO  18:15:23,434 MicroScheduler -   -> 85 reads (6.18% of total) failing DuplicateReadFilter
[2016-04-15T01:15Z] INFO  18:15:23,435 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:15Z] INFO  18:15:23,435 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:15Z] INFO  18:15:23,435 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:15Z] INFO  18:15:23,435 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:15Z] INFO  18:15:23,436 MicroScheduler -   -> 34 reads (2.47% of total) failing UnmappedReadFilter
[2016-04-15T01:15Z] INFO  18:15:24,128 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:15Z] INFO  18:15:24,143 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:15Z] INFO  18:15:24,144 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:15Z] INFO  18:15:24,144 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:15Z] INFO  18:15:24,149 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/1/R14-18102_kapa-NGv3-PE100-NGv3-sort-1_15545821_31186478-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/1/R14-18102_kapa-NGv3-PE100-NGv3-1_15545821_31186478-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/1/tx/tmpuRoCV4/R14-18102_kapa-NGv3-PE100-NGv3-1_15545821_31186478.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:15Z] INFO  18:15:24,158 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:15Z] INFO  18:15:24,159 HelpFormatter - Date/Time: 2016/04/14 18:15:24
[2016-04-15T01:15Z] INFO  18:15:24,160 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:15Z] INFO  18:15:24,160 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:15Z] WARN  18:15:24,206 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T01:15Z] WARN  18:15:24,209 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/1/tx/tmpuRoCV4/R14-18102_kapa-NGv3-PE100-NGv3-1_15545821_31186478.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T01:15Z] INFO  18:15:24,469 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:15Z] INFO  18:15:24,530 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:15Z] INFO  18:15:24,620 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T01:15Z] INFO  18:15:24,629 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:15Z] INFO  18:15:24,690 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-15T01:15Z] INFO  18:15:24,706 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T01:15Z] INFO  18:15:24,821 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:15Z] GATK: HaplotypeCaller
[2016-04-15T01:15Z] GATK: HaplotypeCaller
[2016-04-15T01:15Z] INFO  18:15:25,235 IntervalUtils - Processing 386393 bp from intervals
[2016-04-15T01:15Z] WARN  18:15:25,241 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:15Z] INFO  18:15:25,325 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:15Z] INFO  18:15:25,439 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:15Z] INFO  18:15:25,440 ProgressMeter -            done    626722.0    21.0 s      33.0 s      100.0%    21.0 s       0.0 s
[2016-04-15T01:15Z] INFO  18:15:25,440 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:15Z] INFO  18:15:25,441 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T01:15Z] INFO  18:15:25,441 ProgressMeter - Total runtime 21.29 secs, 0.35 min, 0.01 hours
[2016-04-15T01:15Z] INFO  18:15:25,442 MicroScheduler - 21406 reads were filtered out during the traversal out of approximately 257732 total reads (8.31%)
[2016-04-15T01:15Z] INFO  18:15:25,442 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T01:15Z] INFO  18:15:25,442 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:15Z] INFO  18:15:25,442 MicroScheduler -   -> 382 reads (0.15% of total) failing BadMateFilter
[2016-04-15T01:15Z] INFO  18:15:25,442 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T01:15Z] INFO  18:15:25,442 MicroScheduler -   -> 20852 reads (8.09% of total) failing DuplicateReadFilter
[2016-04-15T01:15Z] INFO  18:15:25,443 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:15Z] INFO  18:15:25,443 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:15Z] INFO  18:15:25,443 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:15Z] INFO  18:15:25,443 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:15Z] INFO  18:15:25,444 MicroScheduler -   -> 172 reads (0.07% of total) failing UnmappedReadFilter
[2016-04-15T01:15Z] INFO  18:15:25,443 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T01:15Z] INFO  18:15:25,596 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T01:15Z] INFO  18:15:25,617 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:15Z] INFO  18:15:25,620 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:15Z] INFO  18:15:25,621 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:15Z] INFO  18:15:25,621 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:15Z] INFO  18:15:25,626 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/1/R14-18102_kapa-NGv3-PE100-NGv3-sort-1_31187093_46714270-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/1/R14-18102_kapa-NGv3-PE100-NGv3-1_31187093_46714270-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/1/tx/tmp993B5W/R14-18102_kapa-NGv3-PE100-NGv3-1_31187093_46714270.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:15Z] INFO  18:15:25,660 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:15Z] INFO  18:15:25,661 HelpFormatter - Date/Time: 2016/04/14 18:15:25
[2016-04-15T01:15Z] INFO  18:15:25,662 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:15Z] INFO  18:15:25,662 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:15Z] WARN  18:15:25,717 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T01:15Z] WARN  18:15:25,720 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/1/tx/tmp993B5W/R14-18102_kapa-NGv3-PE100-NGv3-1_31187093_46714270.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T01:15Z] INFO  18:15:25,921 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:15Z] INFO  18:15:26,163 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T01:15Z] INFO  18:15:26,174 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:15Z] INFO  18:15:26,242 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-15T01:15Z] INFO  18:15:26,266 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T01:15Z] INFO  18:15:26,756 IntervalUtils - Processing 431182 bp from intervals
[2016-04-15T01:15Z] WARN  18:15:26,772 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:15Z] INFO  18:15:26,902 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:15Z] INFO  18:15:27,086 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:15Z] INFO  18:15:27,087 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:15Z] INFO  18:15:27,087 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T01:15Z] INFO  18:15:27,088 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T01:15Z] INFO  18:15:27,089 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T01:15Z] INFO  18:15:27,089 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T01:15Z] INFO  18:15:27,269 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T01:15Z] INFO  18:15:27,562 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:15Z] INFO  18:15:27,625 ProgressMeter -     19:10599868   2837022.0    60.0 s      21.0 s       69.5%    86.0 s      26.0 s
[2016-04-15T01:15Z] GATK: HaplotypeCaller
[2016-04-15T01:15Z] INFO  18:15:27,987 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:15Z] INFO  18:15:27,990 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:15Z] INFO  18:15:27,991 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:15Z] INFO  18:15:27,991 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:15Z] INFO  18:15:27,996 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/1/R14-18102_kapa-NGv3-PE100-NGv3-sort-1_46715671_62228851-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/1/R14-18102_kapa-NGv3-PE100-NGv3-1_46715671_62228851-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/1/tx/tmpwnY46g/R14-18102_kapa-NGv3-PE100-NGv3-1_46715671_62228851.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:15Z] INFO  18:15:28,008 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:15Z] INFO  18:15:28,009 HelpFormatter - Date/Time: 2016/04/14 18:15:27
[2016-04-15T01:15Z] INFO  18:15:28,010 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:15Z] INFO  18:15:28,010 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:15Z] WARN  18:15:28,032 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T01:15Z] WARN  18:15:28,035 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/1/tx/tmpwnY46g/R14-18102_kapa-NGv3-PE100-NGv3-1_46715671_62228851.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T01:15Z] INFO  18:15:28,093 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:15Z] INFO  18:15:28,096 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:15Z] INFO  18:15:28,097 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:15Z] INFO  18:15:28,097 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:15Z] INFO  18:15:28,102 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/1/R14-18102_kapa-NGv3-PE100-NGv3-sort-1_62231950_77749296-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/1/R14-18102_kapa-NGv3-PE100-NGv3-1_62231950_77749296-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/1/tx/tmp9KlkXX/R14-18102_kapa-NGv3-PE100-NGv3-1_62231950_77749296.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:15Z] INFO  18:15:28,133 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:15Z] INFO  18:15:28,133 HelpFormatter - Date/Time: 2016/04/14 18:15:28
[2016-04-15T01:15Z] INFO  18:15:28,133 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:15Z] INFO  18:15:28,134 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:15Z] WARN  18:15:28,178 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T01:15Z] WARN  18:15:28,181 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/1/tx/tmp9KlkXX/R14-18102_kapa-NGv3-PE100-NGv3-1_62231950_77749296.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T01:15Z] INFO  18:15:28,226 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:15Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T01:15Z] INFO  18:15:28,405 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T01:15Z] INFO  18:15:28,417 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T01:15Z] INFO  18:15:28,475 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:15Z] INFO  18:15:28,496 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T01:15Z] INFO  18:15:28,517 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:15Z] INFO  18:15:28,606 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.09
[2016-04-15T01:15Z] INFO  18:15:28,636 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T01:15Z] INFO  18:15:28,680 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T01:15Z] INFO  18:15:28,689 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:15Z] WARN  18:15:28,744 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T01:15Z] WARN  18:15:28,745 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T01:15Z] INFO  18:15:28,771 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-15T01:15Z] INFO  18:15:28,810 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T01:15Z] INFO  18:15:29,037 IntervalUtils - Processing 180557 bp from intervals
[2016-04-15T01:15Z] WARN  18:15:29,042 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:15Z] INFO  18:15:29,164 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:15Z] INFO  18:15:29,318 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:15Z] INFO  18:15:29,318 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:15Z] INFO  18:15:29,319 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T01:15Z] INFO  18:15:29,319 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T01:15Z] INFO  18:15:29,331 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T01:15Z] INFO  18:15:29,332 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T01:15Z] INFO  18:15:29,366 IntervalUtils - Processing 150085 bp from intervals
[2016-04-15T01:15Z] WARN  18:15:29,371 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:15Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T01:15Z] INFO  18:15:29,445 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T01:15Z] INFO  18:15:29,446 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T01:15Z] INFO  18:15:29,505 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:15Z] INFO  18:15:29,534 ProgressMeter -            done   1090417.0    27.0 s      25.0 s      100.0%    27.0 s       0.0 s
[2016-04-15T01:15Z] INFO  18:15:29,535 ProgressMeter - Total runtime 27.30 secs, 0.45 min, 0.01 hours
[2016-04-15T01:15Z] INFO  18:15:29,536 MicroScheduler - 36440 reads were filtered out during the traversal out of approximately 448585 total reads (8.12%)
[2016-04-15T01:15Z] INFO  18:15:29,537 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:15Z] INFO  18:15:29,537 MicroScheduler -   -> 691 reads (0.15% of total) failing BadMateFilter
[2016-04-15T01:15Z] INFO  18:15:29,538 MicroScheduler -   -> 35432 reads (7.90% of total) failing DuplicateReadFilter
[2016-04-15T01:15Z] INFO  18:15:29,539 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:15Z] INFO  18:15:29,539 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:15Z] INFO  18:15:29,540 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:15Z] INFO  18:15:29,540 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:15Z] INFO  18:15:29,541 MicroScheduler -   -> 317 reads (0.07% of total) failing UnmappedReadFilter
[2016-04-15T01:15Z] INFO  18:15:29,561 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T01:15Z] INFO  18:15:29,622 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:15Z] INFO  18:15:29,623 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:15Z] INFO  18:15:29,624 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T01:15Z] INFO  18:15:29,624 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T01:15Z] INFO  18:15:29,625 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T01:15Z] INFO  18:15:29,625 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T01:15Z] WARN  18:15:29,740 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T01:15Z] WARN  18:15:29,742 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T01:15Z] INFO  18:15:29,862 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T01:15Z] INFO  18:15:30,912 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:15Z] INFO  18:15:31,013 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:15Z] INFO  18:15:31,017 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:15Z] INFO  18:15:31,018 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:15Z] INFO  18:15:31,018 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:15Z] INFO  18:15:31,024 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/1/R14-18102_kapa-NGv3-PE100-NGv3-sort-1_77752625_93297674-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/1/R14-18102_kapa-NGv3-PE100-NGv3-1_77752625_93297674-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/1/tx/tmpsJphfn/R14-18102_kapa-NGv3-PE100-NGv3-1_77752625_93297674.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:15Z] INFO  18:15:31,053 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:15Z] INFO  18:15:31,061 HelpFormatter - Date/Time: 2016/04/14 18:15:31
[2016-04-15T01:15Z] INFO  18:15:31,062 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:15Z] INFO  18:15:31,063 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:15Z] WARN  18:15:31,094 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T01:15Z] WARN  18:15:31,109 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/1/tx/tmpsJphfn/R14-18102_kapa-NGv3-PE100-NGv3-1_77752625_93297674.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T01:15Z] GATK: HaplotypeCaller
[2016-04-15T01:15Z] INFO  18:15:31,390 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:15Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T01:15Z] INFO  18:15:31,566 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T01:15Z] INFO  18:15:31,567 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T01:15Z] INFO  18:15:31,655 ProgressMeter -            done   1247079.0    38.0 s      30.0 s      100.0%    38.0 s       0.0 s
[2016-04-15T01:15Z] INFO  18:15:31,656 ProgressMeter - Total runtime 38.45 secs, 0.64 min, 0.01 hours
[2016-04-15T01:15Z] INFO  18:15:31,656 MicroScheduler - 47093 reads were filtered out during the traversal out of approximately 551435 total reads (8.54%)
[2016-04-15T01:15Z] INFO  18:15:31,657 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:15Z] INFO  18:15:31,657 MicroScheduler -   -> 876 reads (0.16% of total) failing BadMateFilter
[2016-04-15T01:15Z] INFO  18:15:31,657 MicroScheduler -   -> 45799 reads (8.31% of total) failing DuplicateReadFilter
[2016-04-15T01:15Z] INFO  18:15:31,657 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:15Z] INFO  18:15:31,658 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:15Z] INFO  18:15:31,658 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:15Z] INFO  18:15:31,658 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:15Z] INFO  18:15:31,659 MicroScheduler -   -> 418 reads (0.08% of total) failing UnmappedReadFilter
[2016-04-15T01:15Z] INFO  18:15:31,661 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T01:15Z] INFO  18:15:31,671 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:15Z] INFO  18:15:31,771 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.10
[2016-04-15T01:15Z] WARN  18:15:31,781 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T01:15Z] WARN  18:15:31,782 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T01:15Z] INFO  18:15:31,792 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T01:15Z] INFO  18:15:32,191 ProgressMeter -            done   1359315.0    42.0 s      31.0 s      100.0%    42.0 s       0.0 s
[2016-04-15T01:15Z] INFO  18:15:32,191 ProgressMeter - Total runtime 42.27 secs, 0.70 min, 0.01 hours
[2016-04-15T01:15Z] INFO  18:15:32,192 MicroScheduler - 49411 reads were filtered out during the traversal out of approximately 594707 total reads (8.31%)
[2016-04-15T01:15Z] INFO  18:15:32,192 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:15Z] INFO  18:15:32,192 MicroScheduler -   -> 969 reads (0.16% of total) failing BadMateFilter
[2016-04-15T01:15Z] INFO  18:15:32,193 MicroScheduler -   -> 47966 reads (8.07% of total) failing DuplicateReadFilter
[2016-04-15T01:15Z] INFO  18:15:32,193 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:15Z] INFO  18:15:32,193 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:15Z] INFO  18:15:32,193 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:15Z] INFO  18:15:32,194 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:15Z] INFO  18:15:32,194 MicroScheduler -   -> 476 reads (0.08% of total) failing UnmappedReadFilter
[2016-04-15T01:15Z] INFO  18:15:32,210 IntervalUtils - Processing 145368 bp from intervals
[2016-04-15T01:15Z] WARN  18:15:32,214 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:15Z] INFO  18:15:32,304 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:15Z] INFO  18:15:32,416 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:15Z] INFO  18:15:32,426 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:15Z] INFO  18:15:32,431 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T01:15Z] INFO  18:15:32,432 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T01:15Z] INFO  18:15:32,433 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T01:15Z] INFO  18:15:32,433 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T01:15Z] INFO  18:15:32,470 ProgressMeter -            done    306895.0    17.0 s      55.0 s      100.0%    17.0 s       0.0 s
[2016-04-15T01:15Z] INFO  18:15:32,471 ProgressMeter - Total runtime 17.07 secs, 0.28 min, 0.00 hours
[2016-04-15T01:15Z] INFO  18:15:32,471 MicroScheduler - 12476 reads were filtered out during the traversal out of approximately 169009 total reads (7.38%)
[2016-04-15T01:15Z] INFO  18:15:32,471 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:15Z] INFO  18:15:32,472 MicroScheduler -   -> 255 reads (0.15% of total) failing BadMateFilter
[2016-04-15T01:15Z] INFO  18:15:32,472 MicroScheduler -   -> 12106 reads (7.16% of total) failing DuplicateReadFilter
[2016-04-15T01:15Z] INFO  18:15:32,472 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:15Z] INFO  18:15:32,472 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:15Z] INFO  18:15:32,473 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:15Z] INFO  18:15:32,473 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:15Z] INFO  18:15:32,473 MicroScheduler -   -> 115 reads (0.07% of total) failing UnmappedReadFilter
[2016-04-15T01:15Z] INFO  18:15:32,661 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T01:15Z] INFO  18:15:33,006 ProgressMeter -            done    518040.0    20.0 s      40.0 s      100.0%    20.0 s       0.0 s
[2016-04-15T01:15Z] INFO  18:15:33,007 ProgressMeter - Total runtime 20.92 secs, 0.35 min, 0.01 hours
[2016-04-15T01:15Z] INFO  18:15:33,007 MicroScheduler - 20425 reads were filtered out during the traversal out of approximately 254054 total reads (8.04%)
[2016-04-15T01:15Z] INFO  18:15:33,008 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:15Z] INFO  18:15:33,008 MicroScheduler -   -> 340 reads (0.13% of total) failing BadMateFilter
[2016-04-15T01:15Z] INFO  18:15:33,008 MicroScheduler -   -> 19898 reads (7.83% of total) failing DuplicateReadFilter
[2016-04-15T01:15Z] INFO  18:15:33,008 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:15Z] INFO  18:15:33,009 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:15Z] INFO  18:15:33,009 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:15Z] INFO  18:15:33,009 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:15Z] INFO  18:15:33,010 MicroScheduler -   -> 187 reads (0.07% of total) failing UnmappedReadFilter
[2016-04-15T01:15Z] INFO  18:15:33,265 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:15Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T01:15Z] INFO  18:15:33,587 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T01:15Z] INFO  18:15:33,588 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T01:15Z] INFO  18:15:33,632 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:15Z] GATK: HaplotypeCaller
[2016-04-15T01:15Z] WARN  18:15:33,899 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T01:15Z] WARN  18:15:33,900 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T01:15Z] INFO  18:15:34,069 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:15Z] GATK: HaplotypeCaller
[2016-04-15T01:15Z] INFO  18:15:34,259 ProgressMeter -     19:45811667   2501399.0    60.0 s      23.0 s       91.7%    65.0 s       5.0 s
[2016-04-15T01:15Z] INFO  18:15:34,320 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:15Z] INFO  18:15:34,323 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:15Z] INFO  18:15:34,323 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:15Z] INFO  18:15:34,324 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:15Z] INFO  18:15:34,329 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/1/R14-18102_kapa-NGv3-PE100-NGv3-sort-1_93298945_108993401-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/1/R14-18102_kapa-NGv3-PE100-NGv3-1_93298945_108993401-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/1/tx/tmp1Q2Uv6/R14-18102_kapa-NGv3-PE100-NGv3-1_93298945_108993401.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:15Z] INFO  18:15:34,338 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:15Z] INFO  18:15:34,338 HelpFormatter - Date/Time: 2016/04/14 18:15:34
[2016-04-15T01:15Z] INFO  18:15:34,338 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:15Z] INFO  18:15:34,338 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:15Z] WARN  18:15:34,398 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T01:15Z] WARN  18:15:34,402 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/1/tx/tmp1Q2Uv6/R14-18102_kapa-NGv3-PE100-NGv3-1_93298945_108993401.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T01:15Z] INFO  18:15:34,474 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:15Z] GATK: HaplotypeCaller
[2016-04-15T01:15Z] INFO  18:15:34,579 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:15Z] INFO  18:15:34,686 ProgressMeter -            done    405872.0    18.0 s      44.0 s       99.9%    18.0 s       0.0 s
[2016-04-15T01:15Z] INFO  18:15:34,687 ProgressMeter - Total runtime 18.16 secs, 0.30 min, 0.01 hours
[2016-04-15T01:15Z] INFO  18:15:34,687 MicroScheduler - 16159 reads were filtered out during the traversal out of approximately 204777 total reads (7.89%)
[2016-04-15T01:15Z] INFO  18:15:34,687 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:15Z] INFO  18:15:34,688 MicroScheduler -   -> 285 reads (0.14% of total) failing BadMateFilter
[2016-04-15T01:15Z] INFO  18:15:34,688 MicroScheduler -   -> 15743 reads (7.69% of total) failing DuplicateReadFilter
[2016-04-15T01:15Z] INFO  18:15:34,688 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:15Z] INFO  18:15:34,688 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:15Z] INFO  18:15:34,689 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:15Z] INFO  18:15:34,689 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:15Z] INFO  18:15:34,689 MicroScheduler -   -> 131 reads (0.06% of total) failing UnmappedReadFilter
[2016-04-15T01:15Z] GATK: HaplotypeCaller
[2016-04-15T01:15Z] INFO  18:15:34,851 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T01:15Z] INFO  18:15:34,873 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:15Z] INFO  18:15:34,970 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.09
[2016-04-15T01:15Z] INFO  18:15:34,999 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T01:15Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T01:15Z] INFO  18:15:35,459 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T01:15Z] INFO  18:15:35,460 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T01:15Z] INFO  18:15:35,574 IntervalUtils - Processing 113118 bp from intervals
[2016-04-15T01:15Z] WARN  18:15:35,579 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:15Z] INFO  18:15:35,658 ProgressMeter -     19:57093417   2401041.0    60.0 s      24.0 s       82.2%    73.0 s      13.0 s
[2016-04-15T01:15Z] INFO  18:15:35,742 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:15Z] WARN  18:15:35,747 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T01:15Z] WARN  18:15:35,754 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T01:15Z] INFO  18:15:35,844 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:15Z] INFO  18:15:35,845 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:15Z] INFO  18:15:35,846 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T01:15Z] INFO  18:15:35,846 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T01:15Z] INFO  18:15:35,847 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T01:15Z] INFO  18:15:35,847 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T01:15Z] INFO  18:15:36,033 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T01:15Z] INFO  18:15:36,646 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:15Z] GATK: HaplotypeCaller
[2016-04-15T01:15Z] INFO  18:15:37,536 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:15Z] INFO  18:15:37,539 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:15Z] INFO  18:15:37,539 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:15Z] INFO  18:15:37,539 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:15Z] INFO  18:15:37,552 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/1/R14-18102_kapa-NGv3-PE100-NGv3-sort-1_108994811_143767848-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/1/R14-18102_kapa-NGv3-PE100-NGv3-1_108994811_143767848-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/1/tx/tmpb9bIl6/R14-18102_kapa-NGv3-PE100-NGv3-1_108994811_143767848.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:15Z] INFO  18:15:37,568 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:15Z] INFO  18:15:37,569 HelpFormatter - Date/Time: 2016/04/14 18:15:37
[2016-04-15T01:15Z] INFO  18:15:37,570 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:15Z] INFO  18:15:37,570 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:15Z] INFO  18:15:37,612 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:15Z] WARN  18:15:37,614 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T01:15Z] INFO  18:15:37,615 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:15Z] INFO  18:15:37,616 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:15Z] INFO  18:15:37,616 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:15Z] WARN  18:15:37,617 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/1/tx/tmpb9bIl6/R14-18102_kapa-NGv3-PE100-NGv3-1_108994811_143767848.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T01:15Z] INFO  18:15:37,621 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/1/R14-18102_kapa-NGv3-PE100-NGv3-sort-1_159504867_175046963-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/1/R14-18102_kapa-NGv3-PE100-NGv3-1_159504867_175046963-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/1/tx/tmptlCGdI/R14-18102_kapa-NGv3-PE100-NGv3-1_159504867_175046963.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:15Z] INFO  18:15:37,650 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:15Z] INFO  18:15:37,651 HelpFormatter - Date/Time: 2016/04/14 18:15:37
[2016-04-15T01:15Z] INFO  18:15:37,651 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:15Z] INFO  18:15:37,651 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:15Z] WARN  18:15:37,701 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T01:15Z] WARN  18:15:37,714 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/1/tx/tmptlCGdI/R14-18102_kapa-NGv3-PE100-NGv3-1_159504867_175046963.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T01:15Z] INFO  18:15:37,771 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:15Z] INFO  18:15:37,774 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:15Z] INFO  18:15:37,774 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:15Z] INFO  18:15:37,775 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:15Z] INFO  18:15:37,779 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/1/R14-18102_kapa-NGv3-PE100-NGv3-sort-1_143897546_159410511-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/1/R14-18102_kapa-NGv3-PE100-NGv3-1_143897546_159410511-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/1/tx/tmpCcD1FU/R14-18102_kapa-NGv3-PE100-NGv3-1_143897546_159410511.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:15Z] INFO  18:15:37,787 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:15Z] INFO  18:15:37,798 HelpFormatter - Date/Time: 2016/04/14 18:15:37
[2016-04-15T01:15Z] INFO  18:15:37,798 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:15Z] INFO  18:15:37,799 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:15Z] WARN  18:15:37,833 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T01:15Z] WARN  18:15:37,836 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/1/tx/tmpCcD1FU/R14-18102_kapa-NGv3-PE100-NGv3-1_143897546_159410511.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T01:15Z] INFO  18:15:37,862 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:15Z] INFO  18:15:38,036 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:15Z] INFO  18:15:38,037 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:15Z] INFO  18:15:38,095 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T01:15Z] INFO  18:15:38,104 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:15Z] WARN  18:15:38,153 ExactAFCalculator - this tool is currently set to genotype at most 6 alternate alleles in a given context, but the context at 1:31887268 has 11 alternate alleles so only the top alleles will be used; see the --max_alternate_alleles argument
[2016-04-15T01:15Z] WARN  18:15:38,159 ExactAFCalculator - this tool is currently set to genotype at most 6 alternate alleles in a given context, but the context at 1:31887301 has 9 alternate alleles so only the top alleles will be used; see the --max_alternate_alleles argument
[2016-04-15T01:15Z] INFO  18:15:38,191 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.09
[2016-04-15T01:15Z] INFO  18:15:38,224 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T01:15Z] INFO  18:15:38,231 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T01:15Z] INFO  18:15:38,252 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:15Z] INFO  18:15:38,310 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T01:15Z] INFO  18:15:38,330 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:15Z] INFO  18:15:38,336 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-15T01:15Z] INFO  18:15:38,363 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T01:15Z] INFO  18:15:38,420 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:15Z] INFO  18:15:38,424 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:15Z] INFO  18:15:38,424 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:15Z] INFO  18:15:38,425 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:15Z] INFO  18:15:38,428 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-15T01:15Z] INFO  18:15:38,429 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/1/R14-18102_kapa-NGv3-PE100-NGv3-sort-1_175048468_192127886-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/1/R14-18102_kapa-NGv3-PE100-NGv3-1_175048468_192127886-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/1/tx/tmpsU1O0N/R14-18102_kapa-NGv3-PE100-NGv3-1_175048468_192127886.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:15Z] INFO  18:15:38,459 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:15Z] INFO  18:15:38,460 HelpFormatter - Date/Time: 2016/04/14 18:15:38
[2016-04-15T01:15Z] INFO  18:15:38,460 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:15Z] INFO  18:15:38,460 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:15Z] INFO  18:15:38,460 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T01:15Z] WARN  18:15:38,533 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T01:15Z] WARN  18:15:38,535 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/1/tx/tmpsU1O0N/R14-18102_kapa-NGv3-PE100-NGv3-1_175048468_192127886.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T01:15Z] INFO  18:15:38,809 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:15Z] INFO  18:15:38,848 IntervalUtils - Processing 258252 bp from intervals
[2016-04-15T01:15Z] WARN  18:15:38,861 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:15Z] INFO  18:15:38,940 IntervalUtils - Processing 261574 bp from intervals
[2016-04-15T01:15Z] WARN  18:15:38,956 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:15Z] INFO  18:15:39,034 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T01:15Z] INFO  18:15:39,042 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:15Z] INFO  18:15:39,047 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:15Z] INFO  18:15:39,118 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:15Z] INFO  18:15:39,136 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.09
[2016-04-15T01:15Z] INFO  18:15:39,140 IntervalUtils - Processing 517409 bp from intervals
[2016-04-15T01:15Z] WARN  18:15:39,148 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:15Z] INFO  18:15:39,154 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T01:15Z] INFO  18:15:39,155 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:15Z] INFO  18:15:39,156 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:15Z] INFO  18:15:39,156 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T01:15Z] INFO  18:15:39,156 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T01:15Z] INFO  18:15:39,157 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T01:15Z] INFO  18:15:39,157 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T01:15Z] INFO  18:15:39,217 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:15Z] INFO  18:15:39,274 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:15Z] INFO  18:15:39,275 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:15Z] INFO  18:15:39,275 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T01:15Z] INFO  18:15:39,275 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T01:15Z] INFO  18:15:39,302 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T01:15Z] INFO  18:15:39,302 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T01:15Z] INFO  18:15:39,341 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:15Z] INFO  18:15:39,342 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:15Z] INFO  18:15:39,356 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T01:15Z] INFO  18:15:39,357 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T01:15Z] INFO  18:15:39,366 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T01:15Z] INFO  18:15:39,366 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T01:15Z] INFO  18:15:39,401 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T01:15Z] INFO  18:15:39,588 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T01:15Z] INFO  18:15:39,594 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T01:15Z] INFO  18:15:39,678 ProgressMeter -            done   2766033.0    65.0 s      23.0 s      100.0%    65.0 s       0.0 s
[2016-04-15T01:15Z] INFO  18:15:39,679 ProgressMeter - Total runtime 65.44 secs, 1.09 min, 0.02 hours
[2016-04-15T01:15Z] INFO  18:15:39,679 MicroScheduler - 87211 reads were filtered out during the traversal out of approximately 1030634 total reads (8.46%)
[2016-04-15T01:15Z] INFO  18:15:39,679 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:15Z] INFO  18:15:39,680 MicroScheduler -   -> 1583 reads (0.15% of total) failing BadMateFilter
[2016-04-15T01:15Z] INFO  18:15:39,680 MicroScheduler -   -> 84833 reads (8.23% of total) failing DuplicateReadFilter
[2016-04-15T01:15Z] INFO  18:15:39,680 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:15Z] INFO  18:15:39,680 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:15Z] INFO  18:15:39,681 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:15Z] INFO  18:15:39,681 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:15Z] INFO  18:15:39,681 MicroScheduler -   -> 795 reads (0.08% of total) failing UnmappedReadFilter
[2016-04-15T01:15Z] INFO  18:15:39,717 IntervalUtils - Processing 191568 bp from intervals
[2016-04-15T01:15Z] WARN  18:15:39,723 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:15Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T01:15Z] INFO  18:15:39,796 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T01:15Z] INFO  18:15:39,797 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T01:15Z] INFO  18:15:39,841 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:15Z] INFO  18:15:39,959 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:15Z] INFO  18:15:39,961 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:15Z] INFO  18:15:39,961 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T01:15Z] INFO  18:15:39,962 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T01:15Z] INFO  18:15:39,972 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T01:15Z] INFO  18:15:39,973 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T01:15Z] WARN  18:15:40,084 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T01:15Z] WARN  18:15:40,085 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T01:15Z] INFO  18:15:40,231 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T01:15Z] INFO  18:15:40,585 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:15Z] INFO  18:15:40,589 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:15Z] INFO  18:15:40,589 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:15Z] INFO  18:15:40,590 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:15Z] INFO  18:15:40,594 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/1/R14-18102_kapa-NGv3-PE100-NGv3-sort-1_192128349_207640257-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/1/R14-18102_kapa-NGv3-PE100-NGv3-1_192128349_207640257-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/1/tx/tmp07CreB/R14-18102_kapa-NGv3-PE100-NGv3-1_192128349_207640257.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:15Z] INFO  18:15:40,637 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:15Z] INFO  18:15:40,638 HelpFormatter - Date/Time: 2016/04/14 18:15:40
[2016-04-15T01:15Z] INFO  18:15:40,639 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:15Z] INFO  18:15:40,640 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:15Z] WARN  18:15:40,710 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T01:15Z] WARN  18:15:40,727 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/1/tx/tmp07CreB/R14-18102_kapa-NGv3-PE100-NGv3-1_192128349_207640257.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T01:15Z] INFO  18:15:41,093 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:15Z] INFO  18:15:41,408 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T01:15Z] INFO  18:15:41,418 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:15Z] INFO  18:15:41,526 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.11
[2016-04-15T01:15Z] INFO  18:15:41,545 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:15Z] INFO  18:15:41,569 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T01:15Z] GATK: HaplotypeCaller
[2016-04-15T01:15Z] INFO  18:15:42,201 IntervalUtils - Processing 282740 bp from intervals
[2016-04-15T01:15Z] WARN  18:15:42,206 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:15Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T01:15Z] INFO  18:15:42,268 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T01:15Z] INFO  18:15:42,279 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T01:15Z] INFO  18:15:42,296 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:15Z] INFO  18:15:42,300 ProgressMeter -            done   1018074.0    23.0 s      23.0 s      100.0%    23.0 s       0.0 s
[2016-04-15T01:15Z] INFO  18:15:42,300 ProgressMeter - Total runtime 23.63 secs, 0.39 min, 0.01 hours
[2016-04-15T01:15Z] INFO  18:15:42,300 MicroScheduler - 24204 reads were filtered out during the traversal out of approximately 298784 total reads (8.10%)
[2016-04-15T01:15Z] INFO  18:15:42,301 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:15Z] INFO  18:15:42,301 MicroScheduler -   -> 498 reads (0.17% of total) failing BadMateFilter
[2016-04-15T01:15Z] INFO  18:15:42,301 MicroScheduler -   -> 23494 reads (7.86% of total) failing DuplicateReadFilter
[2016-04-15T01:15Z] INFO  18:15:42,301 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:15Z] INFO  18:15:42,302 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:15Z] INFO  18:15:42,302 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:15Z] INFO  18:15:42,302 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:15Z] INFO  18:15:42,302 MicroScheduler -   -> 212 reads (0.07% of total) failing UnmappedReadFilter
[2016-04-15T01:15Z] INFO  18:15:42,416 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:15Z] INFO  18:15:42,417 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:15Z] INFO  18:15:42,418 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T01:15Z] INFO  18:15:42,418 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T01:15Z] INFO  18:15:42,419 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T01:15Z] INFO  18:15:42,419 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T01:15Z] WARN  18:15:42,636 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T01:15Z] WARN  18:15:42,638 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T01:15Z] INFO  18:15:42,673 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T01:15Z] INFO  18:15:43,725 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:15Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T01:15Z] INFO  18:15:43,764 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T01:15Z] INFO  18:15:43,765 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T01:15Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T01:15Z] INFO  18:15:43,934 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T01:15Z] INFO  18:15:43,935 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T01:15Z] WARN  18:15:44,012 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T01:15Z] WARN  18:15:44,013 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T01:15Z] GATK: HaplotypeCaller
[2016-04-15T01:15Z] WARN  18:15:44,329 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T01:15Z] WARN  18:15:44,330 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T01:15Z] INFO  18:15:45,203 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:15Z] INFO  18:15:45,206 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:15Z] INFO  18:15:45,207 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:15Z] INFO  18:15:45,207 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:15Z] INFO  18:15:45,212 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/1/R14-18102_kapa-NGv3-PE100-NGv3-sort-1_207641871_223156451-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/1/R14-18102_kapa-NGv3-PE100-NGv3-1_207641871_223156451-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/1/tx/tmpL0fcWM/R14-18102_kapa-NGv3-PE100-NGv3-1_207641871_223156451.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:15Z] INFO  18:15:45,252 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:15Z] INFO  18:15:45,260 HelpFormatter - Date/Time: 2016/04/14 18:15:45
[2016-04-15T01:15Z] INFO  18:15:45,261 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:15Z] INFO  18:15:45,266 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:15Z] WARN  18:15:45,325 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T01:15Z] WARN  18:15:45,328 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/1/tx/tmpL0fcWM/R14-18102_kapa-NGv3-PE100-NGv3-1_207641871_223156451.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T01:15Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T01:15Z] INFO  18:15:45,581 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T01:15Z] INFO  18:15:45,581 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T01:15Z] INFO  18:15:45,618 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:15Z] WARN  18:15:45,846 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T01:15Z] WARN  18:15:45,847 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T01:15Z] INFO  18:15:45,938 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T01:15Z] INFO  18:15:45,947 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:15Z] INFO  18:15:46,044 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.10
[2016-04-15T01:15Z] INFO  18:15:46,083 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T01:15Z] INFO  18:15:46,662 IntervalUtils - Processing 175773 bp from intervals
[2016-04-15T01:15Z] WARN  18:15:46,667 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:15Z] INFO  18:15:46,821 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:15Z] INFO  18:15:46,940 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:15Z] INFO  18:15:46,952 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:15Z] INFO  18:15:46,953 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T01:15Z] INFO  18:15:46,954 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T01:15Z] INFO  18:15:46,965 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T01:15Z] INFO  18:15:46,966 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T01:15Z] INFO  18:15:47,245 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T01:15Z] INFO  18:15:47,471 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:15Z] INFO  18:15:47,474 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:15Z] INFO  18:15:47,475 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:15Z] INFO  18:15:47,475 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:15Z] INFO  18:15:47,479 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/1/R14-18102_kapa-NGv3-PE100-NGv3-sort-1_223162737_240072524-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/1/R14-18102_kapa-NGv3-PE100-NGv3-1_223162737_240072524-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/1/tx/tmpZwNGpr/R14-18102_kapa-NGv3-PE100-NGv3-1_223162737_240072524.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:15Z] INFO  18:15:47,498 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:15Z] INFO  18:15:47,499 HelpFormatter - Date/Time: 2016/04/14 18:15:47
[2016-04-15T01:15Z] INFO  18:15:47,499 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:15Z] INFO  18:15:47,500 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:15Z] WARN  18:15:47,533 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T01:15Z] WARN  18:15:47,547 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/1/tx/tmpZwNGpr/R14-18102_kapa-NGv3-PE100-NGv3-1_223162737_240072524.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T01:15Z] INFO  18:15:47,835 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:15Z] INFO  18:15:48,036 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T01:15Z] INFO  18:15:48,045 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:15Z] INFO  18:15:48,130 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-15T01:15Z] INFO  18:15:48,169 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T01:15Z] INFO  18:15:48,648 IntervalUtils - Processing 294039 bp from intervals
[2016-04-15T01:15Z] WARN  18:15:48,653 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:15Z] INFO  18:15:48,739 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:15Z] INFO  18:15:48,900 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:15Z] INFO  18:15:48,900 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:15Z] INFO  18:15:48,900 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T01:15Z] INFO  18:15:48,901 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T01:15Z] INFO  18:15:48,924 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T01:15Z] INFO  18:15:48,925 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T01:15Z] INFO  18:15:49,176 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T01:15Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T01:15Z] INFO  18:15:50,289 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T01:15Z] INFO  18:15:50,301 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T01:15Z] WARN  18:15:50,743 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T01:15Z] WARN  18:15:50,744 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T01:15Z] INFO  18:15:50,973 ProgressMeter -       1:1670796      1.2048466E7    30.0 s            2.0 s       20.9%     2.4 m     113.0 s
[2016-04-15T01:15Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T01:15Z] INFO  18:15:51,464 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T01:15Z] INFO  18:15:51,476 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T01:15Z] INFO  18:15:51,490 ProgressMeter -            done   2732198.0    75.0 s      27.0 s      100.0%    75.0 s       0.0 s
[2016-04-15T01:15Z] INFO  18:15:51,491 ProgressMeter - Total runtime 75.85 secs, 1.26 min, 0.02 hours
[2016-04-15T01:15Z] INFO  18:15:51,491 MicroScheduler - 96571 reads were filtered out during the traversal out of approximately 1140000 total reads (8.47%)
[2016-04-15T01:15Z] INFO  18:15:51,491 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:15Z] INFO  18:15:51,491 MicroScheduler -   -> 1860 reads (0.16% of total) failing BadMateFilter
[2016-04-15T01:15Z] INFO  18:15:51,492 MicroScheduler -   -> 93752 reads (8.22% of total) failing DuplicateReadFilter
[2016-04-15T01:15Z] INFO  18:15:51,492 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:15Z] INFO  18:15:51,492 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:15Z] INFO  18:15:51,492 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:15Z] INFO  18:15:51,500 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:15Z] INFO  18:15:51,500 MicroScheduler -   -> 959 reads (0.08% of total) failing UnmappedReadFilter
[2016-04-15T01:15Z] WARN  18:15:51,952 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T01:15Z] WARN  18:15:51,953 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T01:15Z] INFO  18:15:53,308 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:15Z] INFO  18:15:53,458 ProgressMeter -            done   4005652.0    85.0 s      21.0 s      100.0%    85.0 s       0.0 s
[2016-04-15T01:15Z] INFO  18:15:53,459 ProgressMeter - Total runtime 85.85 secs, 1.43 min, 0.02 hours
[2016-04-15T01:15Z] INFO  18:15:53,460 MicroScheduler - 109193 reads were filtered out during the traversal out of approximately 1279255 total reads (8.54%)
[2016-04-15T01:15Z] INFO  18:15:53,461 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:15Z] INFO  18:15:53,461 MicroScheduler -   -> 2240 reads (0.18% of total) failing BadMateFilter
[2016-04-15T01:15Z] INFO  18:15:53,461 MicroScheduler -   -> 105872 reads (8.28% of total) failing DuplicateReadFilter
[2016-04-15T01:15Z] INFO  18:15:53,461 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:15Z] INFO  18:15:53,462 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:15Z] INFO  18:15:53,462 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:15Z] INFO  18:15:53,462 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:15Z] INFO  18:15:53,462 MicroScheduler -   -> 1081 reads (0.08% of total) failing UnmappedReadFilter
[2016-04-15T01:15Z] GATK: HaplotypeCaller
[2016-04-15T01:15Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T01:15Z] INFO  18:15:54,218 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T01:15Z] INFO  18:15:54,218 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T01:15Z] WARN  18:15:54,657 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T01:15Z] WARN  18:15:54,658 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T01:15Z] INFO  18:15:54,865 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:15Z] GATK: HaplotypeCaller
[2016-04-15T01:15Z] INFO  18:15:55,464 ProgressMeter -      1:17084553        6978609.0    30.0 s            4.0 s       15.1%     3.3 m       2.8 m
[2016-04-15T01:15Z] INFO  18:15:57,048 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:15Z] INFO  18:15:57,051 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:15Z] INFO  18:15:57,052 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:15Z] INFO  18:15:57,052 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:15Z] INFO  18:15:57,057 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/1/R14-18102_kapa-NGv3-PE100-NGv3-sort-1_240255409_249250621-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/1/R14-18102_kapa-NGv3-PE100-NGv3-1_240255409_249250621-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/1/tx/tmppsk_77/R14-18102_kapa-NGv3-PE100-NGv3-1_240255409_249250621.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:15Z] INFO  18:15:57,077 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:15Z] INFO  18:15:57,077 HelpFormatter - Date/Time: 2016/04/14 18:15:57
[2016-04-15T01:15Z] INFO  18:15:57,077 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:15Z] INFO  18:15:57,077 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:15Z] INFO  18:15:57,091 ProgressMeter -      1:33477612       1.190367E7    30.0 s            2.0 s       17.0%     2.9 m       2.4 m
[2016-04-15T01:15Z] WARN  18:15:57,130 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T01:15Z] WARN  18:15:57,132 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/1/tx/tmppsk_77/R14-18102_kapa-NGv3-PE100-NGv3-1_240255409_249250621.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T01:15Z] INFO  18:15:57,494 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:15Z] INFO  18:15:57,728 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T01:15Z] INFO  18:15:57,755 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:15Z] INFO  18:15:57,846 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.09
[2016-04-15T01:15Z] INFO  18:15:57,884 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T01:15Z] INFO  18:15:58,206 IntervalUtils - Processing 129443 bp from intervals
[2016-04-15T01:15Z] WARN  18:15:58,211 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:15Z] INFO  18:15:58,302 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:15Z] INFO  18:15:58,413 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:15Z] INFO  18:15:58,414 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:15Z] INFO  18:15:58,415 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T01:15Z] INFO  18:15:58,416 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T01:15Z] INFO  18:15:58,416 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T01:15Z] INFO  18:15:58,416 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T01:15Z] INFO  18:15:58,654 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T01:15Z] INFO  18:15:58,920 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:15Z] INFO  18:15:58,923 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:15Z] INFO  18:15:58,924 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:15Z] INFO  18:15:58,925 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:15Z] INFO  18:15:58,929 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/2/R14-18102_kapa-NGv3-PE100-NGv3-sort-2_0_15514844-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/2/R14-18102_kapa-NGv3-PE100-NGv3-2_0_15514844-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/2/tx/tmp5BhtIC/R14-18102_kapa-NGv3-PE100-NGv3-2_0_15514844.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:15Z] INFO  18:15:58,938 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:15Z] INFO  18:15:58,947 HelpFormatter - Date/Time: 2016/04/14 18:15:58
[2016-04-15T01:15Z] INFO  18:15:58,947 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:15Z] INFO  18:15:58,947 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:15Z] WARN  18:15:58,994 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T01:15Z] WARN  18:15:59,003 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/2/tx/tmp5BhtIC/R14-18102_kapa-NGv3-PE100-NGv3-2_0_15514844.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T01:15Z] INFO  18:15:59,219 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:15Z] INFO  18:15:59,334 ProgressMeter -      1:52823370      1.6165529E7    30.0 s            1.0 s       41.6%    72.0 s      42.0 s
[2016-04-15T01:15Z] INFO  18:15:59,394 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T01:15Z] INFO  18:15:59,404 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:15Z] INFO  18:15:59,517 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.11
[2016-04-15T01:15Z] INFO  18:15:59,546 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T01:15Z] INFO  18:15:59,661 ProgressMeter -      1:68512291      1.9325199E7    30.0 s            1.0 s       56.8%    52.0 s      22.0 s
[2016-04-15T01:15Z] INFO  18:15:59,946 IntervalUtils - Processing 105700 bp from intervals
[2016-04-15T01:15Z] WARN  18:15:59,952 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:16Z] INFO  18:16:00,106 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:16Z] INFO  18:16:00,220 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:16Z] INFO  18:16:00,222 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:16Z] INFO  18:16:00,222 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T01:16Z] INFO  18:16:00,223 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T01:16Z] INFO  18:16:00,235 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T01:16Z] INFO  18:16:00,236 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T01:16Z] INFO  18:16:00,501 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T01:16Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T01:16Z] INFO  18:16:00,894 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T01:16Z] INFO  18:16:00,895 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T01:16Z] WARN  18:16:01,443 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T01:16Z] WARN  18:16:01,444 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T01:16Z] INFO  18:16:02,453 ProgressMeter -      1:89329676      2.1543797E7    30.0 s            1.0 s       59.4%    50.0 s      20.0 s
[2016-04-15T01:16Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T01:16Z] INFO  18:16:05,168 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T01:16Z] INFO  18:16:05,169 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T01:16Z] WARN  18:16:05,559 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T01:16Z] WARN  18:16:05,560 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T01:16Z] INFO  18:16:05,867 ProgressMeter -     1:103412512      2.3044665E7    30.0 s            1.0 s       78.5%    38.0 s       8.0 s
[2016-04-15T01:16Z] INFO  18:16:09,174 ProgressMeter -     1:111144889      1.5330903E7    30.0 s            1.0 s       34.7%    86.0 s      56.0 s
[2016-04-15T01:16Z] INFO  18:16:09,307 ProgressMeter -     1:161495403      1.7021644E7    30.0 s            1.0 s       32.2%    93.0 s      63.0 s
[2016-04-15T01:16Z] INFO  18:16:09,388 ProgressMeter -     1:144931693         310245.0    30.0 s           96.0 s        2.5%    20.3 m      19.8 m
[2016-04-15T01:16Z] INFO  18:16:09,979 ProgressMeter -     1:181762801      2.1028275E7    30.0 s            1.0 s       48.1%    62.0 s      32.0 s
[2016-04-15T01:16Z] INFO  18:16:11,165 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.005719636
[2016-04-15T01:16Z] INFO  18:16:11,166 PairHMM - Total compute time in PairHMM computeLikelihoods() : 0.285458251
[2016-04-15T01:16Z] INFO  18:16:11,166 HaplotypeCaller - Ran local assembly on 878 active regions
[2016-04-15T01:16Z] INFO  18:16:11,203 ProgressMeter -            done       3.770404E7    35.0 s            0.0 s      100.0%    35.0 s       0.0 s
[2016-04-15T01:16Z] INFO  18:16:11,205 ProgressMeter - Total runtime 35.36 secs, 0.59 min, 0.01 hours
[2016-04-15T01:16Z] INFO  18:16:11,205 MicroScheduler - 45461 reads were filtered out during the traversal out of approximately 168154 total reads (27.04%)
[2016-04-15T01:16Z] INFO  18:16:11,206 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:16Z] INFO  18:16:11,207 MicroScheduler -   -> 10831 reads (6.44% of total) failing DuplicateReadFilter
[2016-04-15T01:16Z] INFO  18:16:11,207 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:16Z] INFO  18:16:11,208 MicroScheduler -   -> 34630 reads (20.59% of total) failing HCMappingQualityFilter
[2016-04-15T01:16Z] INFO  18:16:11,209 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:16Z] INFO  18:16:11,209 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:16Z] INFO  18:16:11,210 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:16Z] INFO  18:16:11,210 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T01:16Z] INFO  18:16:12,440 ProgressMeter -     1:201060768      2.0090799E7    30.0 s            1.0 s       32.8%    91.0 s      61.0 s
[2016-04-15T01:16Z] INFO  18:16:12,633 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:16Z] GATK: HaplotypeCaller
[2016-04-15T01:16Z] INFO  18:16:13,644 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.007111513000000001
[2016-04-15T01:16Z] INFO  18:16:13,645 PairHMM - Total compute time in PairHMM computeLikelihoods() : 0.663154503
[2016-04-15T01:16Z] INFO  18:16:13,645 HaplotypeCaller - Ran local assembly on 1093 active regions
[2016-04-15T01:16Z] INFO  18:16:13,699 ProgressMeter -            done      5.3650037E7    41.0 s            0.0 s      100.0%    41.0 s       0.0 s
[2016-04-15T01:16Z] INFO  18:16:13,699 ProgressMeter - Total runtime 41.28 secs, 0.69 min, 0.01 hours
[2016-04-15T01:16Z] INFO  18:16:13,700 MicroScheduler - 13002 reads were filtered out during the traversal out of approximately 161980 total reads (8.03%)
[2016-04-15T01:16Z] INFO  18:16:13,700 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:16Z] INFO  18:16:13,701 MicroScheduler -   -> 12749 reads (7.87% of total) failing DuplicateReadFilter
[2016-04-15T01:16Z] INFO  18:16:13,701 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:16Z] INFO  18:16:13,701 MicroScheduler -   -> 253 reads (0.16% of total) failing HCMappingQualityFilter
[2016-04-15T01:16Z] INFO  18:16:13,702 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:16Z] INFO  18:16:13,702 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:16Z] INFO  18:16:13,702 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:16Z] INFO  18:16:13,702 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T01:16Z] INFO  18:16:14,070 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.007767851
[2016-04-15T01:16Z] INFO  18:16:14,071 PairHMM - Total compute time in PairHMM computeLikelihoods() : 0.7005857480000001
[2016-04-15T01:16Z] INFO  18:16:14,072 HaplotypeCaller - Ran local assembly on 1115 active regions
[2016-04-15T01:16Z] INFO  18:16:14,109 ProgressMeter -            done      5.6255126E7    44.0 s            0.0 s      100.0%    44.0 s       0.0 s
[2016-04-15T01:16Z] INFO  18:16:14,110 ProgressMeter - Total runtime 44.49 secs, 0.74 min, 0.01 hours
[2016-04-15T01:16Z] INFO  18:16:14,111 MicroScheduler - 14217 reads were filtered out during the traversal out of approximately 174482 total reads (8.15%)
[2016-04-15T01:16Z] INFO  18:16:14,112 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:16Z] INFO  18:16:14,112 MicroScheduler -   -> 13908 reads (7.97% of total) failing DuplicateReadFilter
[2016-04-15T01:16Z] INFO  18:16:14,113 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:16Z] INFO  18:16:14,113 MicroScheduler -   -> 309 reads (0.18% of total) failing HCMappingQualityFilter
[2016-04-15T01:16Z] INFO  18:16:14,114 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:16Z] INFO  18:16:14,115 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:16Z] INFO  18:16:14,115 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:16Z] INFO  18:16:14,116 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T01:16Z] INFO  18:16:15,034 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:16Z] GATK: HaplotypeCaller
[2016-04-15T01:16Z] INFO  18:16:15,523 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:16Z] INFO  18:16:15,763 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:16Z] INFO  18:16:15,765 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:16Z] INFO  18:16:15,765 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:16Z] INFO  18:16:15,766 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:16Z] INFO  18:16:15,770 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/2/R14-18102_kapa-NGv3-PE100-NGv3-sort-2_15519725_31133925-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/2/R14-18102_kapa-NGv3-PE100-NGv3-2_15519725_31133925-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/2/tx/tmp3K7fkW/R14-18102_kapa-NGv3-PE100-NGv3-2_15519725_31133925.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:16Z] INFO  18:16:15,789 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:16Z] INFO  18:16:15,790 HelpFormatter - Date/Time: 2016/04/14 18:16:15
[2016-04-15T01:16Z] INFO  18:16:15,790 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:16Z] INFO  18:16:15,791 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:16Z] WARN  18:16:15,814 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T01:16Z] WARN  18:16:15,817 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/2/tx/tmp3K7fkW/R14-18102_kapa-NGv3-PE100-NGv3-2_15519725_31133925.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T01:16Z] GATK: HaplotypeCaller
[2016-04-15T01:16Z] INFO  18:16:16,033 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:16Z] INFO  18:16:16,273 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T01:16Z] INFO  18:16:16,294 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:16Z] INFO  18:16:16,455 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.16
[2016-04-15T01:16Z] INFO  18:16:16,490 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T01:16Z] INFO  18:16:16,884 IntervalUtils - Processing 231513 bp from intervals
[2016-04-15T01:16Z] WARN  18:16:16,892 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:16Z] INFO  18:16:16,980 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:16Z] INFO  18:16:16,974 ProgressMeter -     1:214454598      1.7530289E7    30.0 s            1.0 s       52.2%    57.0 s      27.0 s
[2016-04-15T01:16Z] INFO  18:16:17,094 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:16Z] INFO  18:16:17,096 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:16Z] INFO  18:16:17,097 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T01:16Z] INFO  18:16:17,114 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T01:16Z] INFO  18:16:17,126 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T01:16Z] INFO  18:16:17,127 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T01:16Z] INFO  18:16:17,343 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T01:16Z] INFO  18:16:18,132 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:16Z] INFO  18:16:18,135 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:16Z] INFO  18:16:18,136 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:16Z] INFO  18:16:18,136 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:16Z] INFO  18:16:18,141 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/2/R14-18102_kapa-NGv3-PE100-NGv3-sort-2_31135088_46706841-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/2/R14-18102_kapa-NGv3-PE100-NGv3-2_31135088_46706841-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/2/tx/tmpv5dVQ3/R14-18102_kapa-NGv3-PE100-NGv3-2_31135088_46706841.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:16Z] INFO  18:16:18,153 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:16Z] INFO  18:16:18,165 HelpFormatter - Date/Time: 2016/04/14 18:16:18
[2016-04-15T01:16Z] INFO  18:16:18,166 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:16Z] INFO  18:16:18,167 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:16Z] WARN  18:16:18,214 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T01:16Z] WARN  18:16:18,223 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/2/tx/tmpv5dVQ3/R14-18102_kapa-NGv3-PE100-NGv3-2_31135088_46706841.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T01:16Z] INFO  18:16:18,446 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:16Z] INFO  18:16:18,487 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:16Z] INFO  18:16:18,491 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:16Z] INFO  18:16:18,491 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:16Z] INFO  18:16:18,492 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:16Z] INFO  18:16:18,497 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/2/R14-18102_kapa-NGv3-PE100-NGv3-sort-2_46707543_62228117-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/2/R14-18102_kapa-NGv3-PE100-NGv3-2_46707543_62228117-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/2/tx/tmpMjUKnr/R14-18102_kapa-NGv3-PE100-NGv3-2_46707543_62228117.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:16Z] INFO  18:16:18,511 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:16Z] INFO  18:16:18,512 HelpFormatter - Date/Time: 2016/04/14 18:16:18
[2016-04-15T01:16Z] INFO  18:16:18,512 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:16Z] INFO  18:16:18,513 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:16Z] WARN  18:16:18,553 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T01:16Z] WARN  18:16:18,567 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/2/tx/tmpMjUKnr/R14-18102_kapa-NGv3-PE100-NGv3-2_46707543_62228117.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T01:16Z] INFO  18:16:18,647 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T01:16Z] INFO  18:16:18,663 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:16Z] INFO  18:16:18,755 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.09
[2016-04-15T01:16Z] INFO  18:16:18,790 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:16Z] INFO  18:16:18,789 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T01:16Z] INFO  18:16:18,927 ProgressMeter -     1:228402491      2.2605316E7    30.0 s            1.0 s       33.4%    89.0 s      59.0 s
[2016-04-15T01:16Z] INFO  18:16:18,960 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T01:16Z] INFO  18:16:18,969 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:16Z] INFO  18:16:19,033 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-15T01:16Z] INFO  18:16:19,051 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T01:16Z] INFO  18:16:19,293 IntervalUtils - Processing 167641 bp from intervals
[2016-04-15T01:16Z] WARN  18:16:19,315 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:16Z] INFO  18:16:19,437 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:16Z] INFO  18:16:19,532 IntervalUtils - Processing 139959 bp from intervals
[2016-04-15T01:16Z] WARN  18:16:19,538 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:16Z] INFO  18:16:19,569 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:16Z] INFO  18:16:19,571 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:16Z] INFO  18:16:19,571 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T01:16Z] INFO  18:16:19,572 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T01:16Z] INFO  18:16:19,573 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T01:16Z] INFO  18:16:19,573 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T01:16Z] INFO  18:16:19,625 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:16Z] INFO  18:16:19,737 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:16Z] INFO  18:16:19,748 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:16Z] INFO  18:16:19,749 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T01:16Z] INFO  18:16:19,750 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T01:16Z] INFO  18:16:19,751 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T01:16Z] INFO  18:16:19,751 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T01:16Z] INFO  18:16:19,765 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T01:16Z] INFO  18:16:19,904 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T01:16Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T01:16Z] INFO  18:16:20,145 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T01:16Z] INFO  18:16:20,146 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T01:16Z] WARN  18:16:20,362 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T01:16Z] WARN  18:16:20,363 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T01:16Z] INFO  18:16:20,980 ProgressMeter -       1:8037799     1.03723163E8    60.0 s            0.0 s       52.6%   114.0 s      54.0 s
[2016-04-15T01:16Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T01:16Z] INFO  18:16:21,433 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T01:16Z] INFO  18:16:21,434 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T01:16Z] WARN  18:16:21,786 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T01:16Z] WARN  18:16:21,787 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T01:16Z] INFO  18:16:22,335 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.022592161000000003
[2016-04-15T01:16Z] INFO  18:16:22,336 PairHMM - Total compute time in PairHMM computeLikelihoods() : 0.8841394250000001
[2016-04-15T01:16Z] INFO  18:16:22,337 HaplotypeCaller - Ran local assembly on 1437 active regions
[2016-04-15T01:16Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T01:16Z] INFO  18:16:22,392 ProgressMeter -            done      9.8875698E7    53.0 s            0.0 s      100.0%    53.0 s       0.0 s
[2016-04-15T01:16Z] INFO  18:16:22,392 ProgressMeter - Total runtime 53.07 secs, 0.88 min, 0.01 hours
[2016-04-15T01:16Z] INFO  18:16:22,393 MicroScheduler - 24913 reads were filtered out during the traversal out of approximately 286471 total reads (8.70%)
[2016-04-15T01:16Z] INFO  18:16:22,393 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:16Z] INFO  18:16:22,393 MicroScheduler -   -> 22994 reads (8.03% of total) failing DuplicateReadFilter
[2016-04-15T01:16Z] INFO  18:16:22,394 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:16Z] INFO  18:16:22,394 MicroScheduler -   -> 1919 reads (0.67% of total) failing HCMappingQualityFilter
[2016-04-15T01:16Z] INFO  18:16:22,394 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:16Z] INFO  18:16:22,394 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:16Z] INFO  18:16:22,395 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:16Z] INFO  18:16:22,395 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T01:16Z] INFO  18:16:22,402 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T01:16Z] INFO  18:16:22,403 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T01:16Z] WARN  18:16:23,166 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T01:16Z] WARN  18:16:23,177 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T01:16Z] INFO  18:16:23,888 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:16Z] GATK: HaplotypeCaller
[2016-04-15T01:16Z] INFO  18:16:25,467 ProgressMeter -      1:19775519      4.3053144E7    60.0 s            1.0 s       32.3%     3.1 m       2.1 m
[2016-04-15T01:16Z] INFO  18:16:27,023 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:16Z] INFO  18:16:27,026 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:16Z] INFO  18:16:27,027 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:16Z] INFO  18:16:27,027 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:16Z] INFO  18:16:27,032 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/2/R14-18102_kapa-NGv3-PE100-NGv3-sort-2_62362965_79253295-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/2/R14-18102_kapa-NGv3-PE100-NGv3-2_62362965_79253295-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/2/tx/tmp7UGyZ0/R14-18102_kapa-NGv3-PE100-NGv3-2_62362965_79253295.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:16Z] INFO  18:16:27,045 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:16Z] INFO  18:16:27,046 HelpFormatter - Date/Time: 2016/04/14 18:16:27
[2016-04-15T01:16Z] INFO  18:16:27,056 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:16Z] INFO  18:16:27,057 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:16Z] WARN  18:16:27,081 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T01:16Z] WARN  18:16:27,084 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/2/tx/tmp7UGyZ0/R14-18102_kapa-NGv3-PE100-NGv3-2_62362965_79253295.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T01:16Z] INFO  18:16:27,092 ProgressMeter -      1:39909185     1.15874509E8    60.0 s            0.0 s       55.4%   108.0 s      48.0 s
[2016-04-15T01:16Z] INFO  18:16:27,290 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:16Z] INFO  18:16:27,492 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T01:16Z] INFO  18:16:27,502 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:16Z] INFO  18:16:27,594 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.09
[2016-04-15T01:16Z] INFO  18:16:27,637 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T01:16Z] INFO  18:16:28,128 IntervalUtils - Processing 224219 bp from intervals
[2016-04-15T01:16Z] WARN  18:16:28,134 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:16Z] INFO  18:16:28,230 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:16Z] INFO  18:16:28,321 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:16Z] INFO  18:16:28,329 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:16Z] INFO  18:16:28,330 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T01:16Z] INFO  18:16:28,331 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T01:16Z] INFO  18:16:28,342 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T01:16Z] INFO  18:16:28,343 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T01:16Z] INFO  18:16:28,459 ProgressMeter -     1:248005082      1.6207159E7    30.0 s            1.0 s       71.4%    42.0 s      12.0 s
[2016-04-15T01:16Z] INFO  18:16:28,610 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T01:16Z] INFO  18:16:30,238 ProgressMeter -      2:11809758      2.6701323E7    30.0 s            1.0 s       91.1%    32.0 s       2.0 s
[2016-04-15T01:16Z] INFO  18:16:31,295 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.009035006
[2016-04-15T01:16Z] INFO  18:16:31,296 PairHMM - Total compute time in PairHMM computeLikelihoods() : 0.47562786100000004
[2016-04-15T01:16Z] INFO  18:16:31,296 HaplotypeCaller - Ran local assembly on 1357 active regions
[2016-04-15T01:16Z] INFO  18:16:31,344 ProgressMeter -            done      9.8539022E7    51.0 s            0.0 s      100.0%    51.0 s       0.0 s
[2016-04-15T01:16Z] INFO  18:16:31,345 ProgressMeter - Total runtime 51.38 secs, 0.86 min, 0.01 hours
[2016-04-15T01:16Z] INFO  18:16:31,345 MicroScheduler - 20144 reads were filtered out during the traversal out of approximately 253001 total reads (7.96%)
[2016-04-15T01:16Z] INFO  18:16:31,345 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:16Z] INFO  18:16:31,345 MicroScheduler -   -> 19812 reads (7.83% of total) failing DuplicateReadFilter
[2016-04-15T01:16Z] INFO  18:16:31,346 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:16Z] INFO  18:16:31,346 MicroScheduler -   -> 332 reads (0.13% of total) failing HCMappingQualityFilter
[2016-04-15T01:16Z] INFO  18:16:31,346 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:16Z] INFO  18:16:31,346 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:16Z] INFO  18:16:31,347 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:16Z] INFO  18:16:31,347 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T01:16Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T01:16Z] INFO  18:16:32,382 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T01:16Z] INFO  18:16:32,383 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T01:16Z] INFO  18:16:32,459 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.01884649
[2016-04-15T01:16Z] INFO  18:16:32,460 PairHMM - Total compute time in PairHMM computeLikelihoods() : 0.6361694560000001
[2016-04-15T01:16Z] INFO  18:16:32,460 HaplotypeCaller - Ran local assembly on 796 active regions
[2016-04-15T01:16Z] INFO  18:16:32,509 ProgressMeter -            done      3.2059538E7    32.0 s            1.0 s      100.0%    32.0 s       0.0 s
[2016-04-15T01:16Z] INFO  18:16:32,510 ProgressMeter - Total runtime 32.29 secs, 0.54 min, 0.01 hours
[2016-04-15T01:16Z] INFO  18:16:32,511 MicroScheduler - 12310 reads were filtered out during the traversal out of approximately 149779 total reads (8.22%)
[2016-04-15T01:16Z] INFO  18:16:32,511 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:16Z] INFO  18:16:32,512 MicroScheduler -   -> 12043 reads (8.04% of total) failing DuplicateReadFilter
[2016-04-15T01:16Z] INFO  18:16:32,513 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:16Z] INFO  18:16:32,513 MicroScheduler -   -> 267 reads (0.18% of total) failing HCMappingQualityFilter
[2016-04-15T01:16Z] INFO  18:16:32,514 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:16Z] INFO  18:16:32,514 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:16Z] INFO  18:16:32,515 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:16Z] INFO  18:16:32,516 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T01:16Z] WARN  18:16:32,542 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T01:16Z] WARN  18:16:32,543 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T01:16Z] INFO  18:16:32,747 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:16Z] GATK: HaplotypeCaller
[2016-04-15T01:16Z] INFO  18:16:33,792 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:16Z] GATK: HaplotypeCaller
[2016-04-15T01:16Z] INFO  18:16:35,350 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.010980173000000001
[2016-04-15T01:16Z] INFO  18:16:35,351 PairHMM - Total compute time in PairHMM computeLikelihoods() : 0.675724638
[2016-04-15T01:16Z] INFO  18:16:35,351 HaplotypeCaller - Ran local assembly on 1237 active regions
[2016-04-15T01:16Z] INFO  18:16:35,419 ProgressMeter -            done      7.1291223E7    48.0 s            0.0 s      100.0%    48.0 s       0.0 s
[2016-04-15T01:16Z] INFO  18:16:35,419 ProgressMeter - Total runtime 48.47 secs, 0.81 min, 0.01 hours
[2016-04-15T01:16Z] INFO  18:16:35,420 MicroScheduler - 25906 reads were filtered out during the traversal out of approximately 232516 total reads (11.14%)
[2016-04-15T01:16Z] INFO  18:16:35,420 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:16Z] INFO  18:16:35,420 MicroScheduler -   -> 18134 reads (7.80% of total) failing DuplicateReadFilter
[2016-04-15T01:16Z] INFO  18:16:35,420 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:16Z] INFO  18:16:35,421 MicroScheduler -   -> 7772 reads (3.34% of total) failing HCMappingQualityFilter
[2016-04-15T01:16Z] INFO  18:16:35,421 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:16Z] INFO  18:16:35,421 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:16Z] INFO  18:16:35,421 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:16Z] INFO  18:16:35,422 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T01:16Z] INFO  18:16:35,838 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:16Z] INFO  18:16:35,842 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:16Z] INFO  18:16:35,842 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:16Z] INFO  18:16:35,843 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:16Z] INFO  18:16:35,852 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/2/R14-18102_kapa-NGv3-PE100-NGv3-sort-2_79253838_95537822-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/2/R14-18102_kapa-NGv3-PE100-NGv3-2_79253838_95537822-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/2/tx/tmps14lAs/R14-18102_kapa-NGv3-PE100-NGv3-2_79253838_95537822.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:16Z] INFO  18:16:35,865 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:16Z] INFO  18:16:35,866 HelpFormatter - Date/Time: 2016/04/14 18:16:35
[2016-04-15T01:16Z] INFO  18:16:35,866 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:16Z] INFO  18:16:35,867 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:16Z] WARN  18:16:35,912 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T01:16Z] WARN  18:16:35,925 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/2/tx/tmps14lAs/R14-18102_kapa-NGv3-PE100-NGv3-2_79253838_95537822.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T01:16Z] INFO  18:16:36,192 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:16Z] INFO  18:16:36,365 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T01:16Z] INFO  18:16:36,387 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:16Z] INFO  18:16:36,483 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.10
[2016-04-15T01:16Z] INFO  18:16:36,505 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T01:16Z] INFO  18:16:36,835 IntervalUtils - Processing 101744 bp from intervals
[2016-04-15T01:16Z] WARN  18:16:36,839 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:16Z] INFO  18:16:36,927 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:16Z] INFO  18:16:36,971 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:16Z] INFO  18:16:37,041 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:16Z] INFO  18:16:37,042 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:16Z] INFO  18:16:37,045 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T01:16Z] INFO  18:16:37,046 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T01:16Z] INFO  18:16:37,057 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T01:16Z] INFO  18:16:37,057 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T01:16Z] GATK: HaplotypeCaller
[2016-04-15T01:16Z] INFO  18:16:37,223 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:16Z] INFO  18:16:37,226 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:16Z] INFO  18:16:37,226 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:16Z] INFO  18:16:37,227 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:16Z] INFO  18:16:37,231 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/2/R14-18102_kapa-NGv3-PE100-NGv3-sort-2_95538561_111273222-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/2/R14-18102_kapa-NGv3-PE100-NGv3-2_95538561_111273222-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/2/tx/tmpOHV11q/R14-18102_kapa-NGv3-PE100-NGv3-2_95538561_111273222.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:16Z] INFO  18:16:37,261 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:16Z] INFO  18:16:37,272 HelpFormatter - Date/Time: 2016/04/14 18:16:37
[2016-04-15T01:16Z] INFO  18:16:37,273 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:16Z] INFO  18:16:37,274 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:16Z] WARN  18:16:37,308 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T01:16Z] WARN  18:16:37,311 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/2/tx/tmpOHV11q/R14-18102_kapa-NGv3-PE100-NGv3-2_95538561_111273222.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T01:16Z] INFO  18:16:37,335 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T01:16Z] INFO  18:16:37,517 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:16Z] INFO  18:16:37,732 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T01:16Z] INFO  18:16:37,742 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:16Z] INFO  18:16:37,833 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.09
[2016-04-15T01:16Z] INFO  18:16:37,851 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T01:16Z] INFO  18:16:38,334 IntervalUtils - Processing 250759 bp from intervals
[2016-04-15T01:16Z] WARN  18:16:38,339 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:16Z] INFO  18:16:38,431 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:16Z] INFO  18:16:38,571 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:16Z] INFO  18:16:38,572 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:16Z] INFO  18:16:38,572 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T01:16Z] INFO  18:16:38,573 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T01:16Z] INFO  18:16:38,585 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T01:16Z] INFO  18:16:38,586 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T01:16Z] INFO  18:16:38,838 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T01:16Z] INFO  18:16:39,175 ProgressMeter -     1:120466425     1.44661097E8    60.0 s            0.0 s       96.4%    62.0 s       2.0 s
[2016-04-15T01:16Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T01:16Z] INFO  18:16:39,215 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T01:16Z] INFO  18:16:39,216 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T01:16Z] INFO  18:16:39,324 ProgressMeter -     1:172348322     1.24309589E8    60.0 s            0.0 s       83.2%    72.0 s      12.0 s
[2016-04-15T01:16Z] INFO  18:16:39,389 ProgressMeter -     1:150235441      1.7968593E7    60.0 s            3.0 s       16.9%     5.9 m       4.9 m
[2016-04-15T01:16Z] WARN  18:16:39,435 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T01:16Z] WARN  18:16:39,436 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T01:16Z] INFO  18:16:40,018 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:16Z] INFO  18:16:40,021 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:16Z] INFO  18:16:40,022 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:16Z] INFO  18:16:40,022 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:16Z] INFO  18:16:40,027 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/2/R14-18102_kapa-NGv3-PE100-NGv3-sort-2_111281072_127413888-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/2/R14-18102_kapa-NGv3-PE100-NGv3-2_111281072_127413888-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/2/tx/tmpZwOIEb/R14-18102_kapa-NGv3-PE100-NGv3-2_111281072_127413888.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:16Z] INFO  18:16:40,050 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:16Z] INFO  18:16:40,051 HelpFormatter - Date/Time: 2016/04/14 18:16:40
[2016-04-15T01:16Z] INFO  18:16:40,052 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:16Z] INFO  18:16:40,052 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:16Z] WARN  18:16:40,080 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T01:16Z] WARN  18:16:40,083 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/2/tx/tmpZwOIEb/R14-18102_kapa-NGv3-PE100-NGv3-2_111281072_127413888.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T01:16Z] INFO  18:16:40,332 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:16Z] INFO  18:16:40,563 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T01:16Z] INFO  18:16:40,577 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:16Z] INFO  18:16:40,664 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.09
[2016-04-15T01:16Z] INFO  18:16:40,692 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T01:16Z] INFO  18:16:41,021 IntervalUtils - Processing 123675 bp from intervals
[2016-04-15T01:16Z] WARN  18:16:41,027 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:16Z] INFO  18:16:41,134 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:16Z] INFO  18:16:41,253 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:16Z] INFO  18:16:41,255 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:16Z] INFO  18:16:41,255 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T01:16Z] INFO  18:16:41,256 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T01:16Z] INFO  18:16:41,257 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T01:16Z] INFO  18:16:41,257 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T01:16Z] INFO  18:16:41,410 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T01:16Z] INFO  18:16:42,446 ProgressMeter -     1:205719101     1.34755838E8    60.0 s            0.0 s       83.6%    71.0 s      11.0 s
[2016-04-15T01:16Z] INFO  18:16:42,864 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.028615135000000003
[2016-04-15T01:16Z] INFO  18:16:42,866 PairHMM - Total compute time in PairHMM computeLikelihoods() : 1.9018608750000001
[2016-04-15T01:16Z] INFO  18:16:42,866 HaplotypeCaller - Ran local assembly on 880 active regions
[2016-04-15T01:16Z] INFO  18:16:42,931 ProgressMeter -            done      2.1915914E7    44.0 s            2.0 s      100.0%    44.0 s       0.0 s
[2016-04-15T01:16Z] INFO  18:16:42,932 ProgressMeter - Total runtime 44.52 secs, 0.74 min, 0.01 hours
[2016-04-15T01:16Z] INFO  18:16:42,933 MicroScheduler - 27315 reads were filtered out during the traversal out of approximately 182762 total reads (14.95%)
[2016-04-15T01:16Z] INFO  18:16:42,933 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:16Z] INFO  18:16:42,933 MicroScheduler -   -> 13674 reads (7.48% of total) failing DuplicateReadFilter
[2016-04-15T01:16Z] INFO  18:16:42,934 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:16Z] INFO  18:16:42,934 MicroScheduler -   -> 13641 reads (7.46% of total) failing HCMappingQualityFilter
[2016-04-15T01:16Z] INFO  18:16:42,934 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:16Z] INFO  18:16:42,934 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:16Z] INFO  18:16:42,935 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:16Z] INFO  18:16:42,935 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T01:16Z] WARN  18:16:42,979 ExactAFCalculator - this tool is currently set to genotype at most 6 alternate alleles in a given context, but the context at 1:120612040 has 8 alternate alleles so only the top alleles will be used; see the --max_alternate_alleles argument
[2016-04-15T01:16Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T01:16Z] INFO  18:16:43,016 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T01:16Z] INFO  18:16:43,017 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T01:16Z] WARN  18:16:43,379 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T01:16Z] WARN  18:16:43,380 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T01:16Z] INFO  18:16:44,367 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:16Z] GATK: HaplotypeCaller
[2016-04-15T01:16Z] INFO  18:16:47,132 ProgressMeter -      2:26405966      2.7940469E7    30.0 s            1.0 s       45.5%    66.0 s      36.0 s
[2016-04-15T01:16Z] INFO  18:16:47,639 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.020612441000000002
[2016-04-15T01:16Z] INFO  18:16:47,640 PairHMM - Total compute time in PairHMM computeLikelihoods() : 0.987573188
[2016-04-15T01:16Z] INFO  18:16:47,640 HaplotypeCaller - Ran local assembly on 1922 active regions
[2016-04-15T01:16Z] INFO  18:16:47,698 ProgressMeter -            done     1.74572625E8    68.0 s            0.0 s      100.0%    68.0 s       0.0 s
[2016-04-15T01:16Z] INFO  18:16:47,698 ProgressMeter - Total runtime 68.42 secs, 1.14 min, 0.02 hours
[2016-04-15T01:16Z] INFO  18:16:47,699 MicroScheduler - 34894 reads were filtered out during the traversal out of approximately 383635 total reads (9.10%)
[2016-04-15T01:16Z] INFO  18:16:47,699 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:16Z] INFO  18:16:47,699 MicroScheduler -   -> 30040 reads (7.83% of total) failing DuplicateReadFilter
[2016-04-15T01:16Z] INFO  18:16:47,700 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:16Z] INFO  18:16:47,700 MicroScheduler -   -> 4854 reads (1.27% of total) failing HCMappingQualityFilter
[2016-04-15T01:16Z] INFO  18:16:47,700 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:16Z] INFO  18:16:47,700 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:16Z] INFO  18:16:47,701 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:16Z] INFO  18:16:47,701 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T01:16Z] INFO  18:16:47,716 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:16Z] INFO  18:16:47,719 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:16Z] INFO  18:16:47,720 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:16Z] INFO  18:16:47,720 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:16Z] INFO  18:16:47,725 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/2/R14-18102_kapa-NGv3-PE100-NGv3-sort-2_127433207_143643105-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/2/R14-18102_kapa-NGv3-PE100-NGv3-2_127433207_143643105-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/2/tx/tmp2RCkCo/R14-18102_kapa-NGv3-PE100-NGv3-2_127433207_143643105.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:16Z] INFO  18:16:47,741 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:16Z] INFO  18:16:47,742 HelpFormatter - Date/Time: 2016/04/14 18:16:47
[2016-04-15T01:16Z] INFO  18:16:47,743 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:16Z] INFO  18:16:47,743 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:16Z] WARN  18:16:47,796 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T01:16Z] WARN  18:16:47,798 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/2/tx/tmp2RCkCo/R14-18102_kapa-NGv3-PE100-NGv3-2_127433207_143643105.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T01:16Z] INFO  18:16:48,080 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:16Z] INFO  18:16:48,281 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T01:16Z] INFO  18:16:48,291 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:16Z] INFO  18:16:48,376 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-15T01:16Z] INFO  18:16:48,414 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T01:16Z] INFO  18:16:48,785 IntervalUtils - Processing 171560 bp from intervals
[2016-04-15T01:16Z] WARN  18:16:48,790 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:16Z] INFO  18:16:48,879 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:16Z] INFO  18:16:48,928 ProgressMeter -     1:235920581     1.26343552E8    60.0 s            0.0 s       83.0%    72.0 s      12.0 s
[2016-04-15T01:16Z] INFO  18:16:48,972 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:16Z] INFO  18:16:48,973 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:16Z] INFO  18:16:48,974 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T01:16Z] INFO  18:16:48,975 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T01:16Z] INFO  18:16:48,976 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T01:16Z] INFO  18:16:48,976 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T01:16Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T01:16Z] INFO  18:16:49,035 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T01:16Z] INFO  18:16:49,036 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T01:16Z] INFO  18:16:49,131 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:16Z] INFO  18:16:49,145 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T01:16Z] WARN  18:16:49,343 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T01:16Z] WARN  18:16:49,343 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T01:16Z] GATK: HaplotypeCaller
[2016-04-15T01:16Z] INFO  18:16:49,594 ProgressMeter -      2:42483641      3.4933798E7    30.0 s            0.0 s       65.8%    45.0 s      15.0 s
[2016-04-15T01:16Z] INFO  18:16:49,760 ProgressMeter -      2:56145354      2.3072215E7    30.0 s            1.0 s       67.1%    44.0 s      14.0 s
[2016-04-15T01:16Z] INFO  18:16:50,945 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.02524969
[2016-04-15T01:16Z] INFO  18:16:50,954 PairHMM - Total compute time in PairHMM computeLikelihoods() : 6.518764395000001
[2016-04-15T01:16Z] INFO  18:16:50,955 HaplotypeCaller - Ran local assembly on 1802 active regions
[2016-04-15T01:16Z] INFO  18:16:50,981 ProgressMeter -      1:12835229     2.83999625E8    90.0 s            0.0 s       86.7%   103.0 s      13.0 s
[2016-04-15T01:16Z] INFO  18:16:50,996 ProgressMeter -            done     1.55311872E8    71.0 s            0.0 s      100.0%    71.0 s       0.0 s
[2016-04-15T01:16Z] INFO  18:16:50,997 ProgressMeter - Total runtime 71.84 secs, 1.20 min, 0.02 hours
[2016-04-15T01:16Z] INFO  18:16:50,997 MicroScheduler - 40453 reads were filtered out during the traversal out of approximately 389165 total reads (10.39%)
[2016-04-15T01:16Z] INFO  18:16:50,997 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:16Z] INFO  18:16:50,998 MicroScheduler -   -> 30887 reads (7.94% of total) failing DuplicateReadFilter
[2016-04-15T01:16Z] INFO  18:16:50,998 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:16Z] INFO  18:16:50,998 MicroScheduler -   -> 9566 reads (2.46% of total) failing HCMappingQualityFilter
[2016-04-15T01:16Z] INFO  18:16:50,998 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:16Z] INFO  18:16:50,999 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:16Z] INFO  18:16:50,999 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:16Z] INFO  18:16:50,999 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T01:16Z] INFO  18:16:51,275 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.015135904
[2016-04-15T01:16Z] INFO  18:16:51,276 PairHMM - Total compute time in PairHMM computeLikelihoods() : 1.3211700080000002
[2016-04-15T01:16Z] INFO  18:16:51,277 HaplotypeCaller - Ran local assembly on 2039 active regions
[2016-04-15T01:16Z] INFO  18:16:51,336 ProgressMeter -            done     1.89229853E8    68.0 s            0.0 s      100.0%    68.0 s       0.0 s
[2016-04-15T01:16Z] INFO  18:16:51,336 ProgressMeter - Total runtime 68.92 secs, 1.15 min, 0.02 hours
[2016-04-15T01:16Z] INFO  18:16:51,336 MicroScheduler - 36659 reads were filtered out during the traversal out of approximately 401545 total reads (9.13%)
[2016-04-15T01:16Z] INFO  18:16:51,337 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:16Z] INFO  18:16:51,337 MicroScheduler -   -> 31805 reads (7.92% of total) failing DuplicateReadFilter
[2016-04-15T01:16Z] INFO  18:16:51,337 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:16Z] INFO  18:16:51,337 MicroScheduler -   -> 4854 reads (1.21% of total) failing HCMappingQualityFilter
[2016-04-15T01:16Z] INFO  18:16:51,338 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:16Z] INFO  18:16:51,338 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:16Z] INFO  18:16:51,338 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:16Z] INFO  18:16:51,338 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T01:16Z] INFO  18:16:52,286 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:16Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T01:16Z] INFO  18:16:52,595 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T01:16Z] GATK: HaplotypeCaller
[2016-04-15T01:16Z] INFO  18:16:52,607 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T01:16Z] INFO  18:16:52,700 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:16Z] INFO  18:16:52,703 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:16Z] INFO  18:16:52,704 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:16Z] INFO  18:16:52,704 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:16Z] INFO  18:16:52,709 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/2/R14-18102_kapa-NGv3-PE100-NGv3-sort-2_143676177_159195597-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/2/R14-18102_kapa-NGv3-PE100-NGv3-2_143676177_159195597-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/2/tx/tmpR1JhvQ/R14-18102_kapa-NGv3-PE100-NGv3-2_143676177_159195597.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:16Z] INFO  18:16:52,720 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:16Z] INFO  18:16:52,721 HelpFormatter - Date/Time: 2016/04/14 18:16:52
[2016-04-15T01:16Z] INFO  18:16:52,721 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:16Z] INFO  18:16:52,722 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:16Z] INFO  18:16:52,749 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:16Z] WARN  18:16:52,749 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T01:16Z] WARN  18:16:52,754 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/2/tx/tmpR1JhvQ/R14-18102_kapa-NGv3-PE100-NGv3-2_143676177_159195597.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T01:16Z] WARN  18:16:52,864 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T01:16Z] WARN  18:16:52,864 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T01:16Z] INFO  18:16:53,042 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:16Z] GATK: HaplotypeCaller
[2016-04-15T01:16Z] INFO  18:16:53,260 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T01:16Z] INFO  18:16:53,270 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:16Z] INFO  18:16:53,362 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.09
[2016-04-15T01:16Z] INFO  18:16:53,402 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T01:16Z] INFO  18:16:53,792 IntervalUtils - Processing 92555 bp from intervals
[2016-04-15T01:16Z] WARN  18:16:53,798 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:16Z] INFO  18:16:53,915 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:16Z] INFO  18:16:53,977 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:16Z] INFO  18:16:53,978 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:16Z] INFO  18:16:53,979 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T01:16Z] INFO  18:16:53,979 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T01:16Z] INFO  18:16:53,980 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T01:16Z] INFO  18:16:53,980 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T01:16Z] INFO  18:16:54,150 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T01:16Z] INFO  18:16:55,468 ProgressMeter -      1:25893375     1.88135064E8    90.0 s            0.0 s       68.8%     2.2 m      40.0 s
[2016-04-15T01:16Z] INFO  18:16:55,915 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:16Z] INFO  18:16:55,918 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:16Z] INFO  18:16:55,918 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:16Z] INFO  18:16:55,918 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:16Z] INFO  18:16:55,922 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/2/R14-18102_kapa-NGv3-PE100-NGv3-sort-2_159196753_174774985-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/2/R14-18102_kapa-NGv3-PE100-NGv3-2_159196753_174774985-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/2/tx/tmp37ikSm/R14-18102_kapa-NGv3-PE100-NGv3-2_159196753_174774985.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:16Z] INFO  18:16:55,958 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:16Z] INFO  18:16:55,959 HelpFormatter - Date/Time: 2016/04/14 18:16:55
[2016-04-15T01:16Z] INFO  18:16:55,959 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:16Z] INFO  18:16:55,959 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:16Z] INFO  18:16:56,037 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:16Z] INFO  18:16:56,040 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:16Z] INFO  18:16:56,041 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:16Z] INFO  18:16:56,041 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:16Z] INFO  18:16:56,046 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/2/R14-18102_kapa-NGv3-PE100-NGv3-sort-2_174777797_190306304-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/2/R14-18102_kapa-NGv3-PE100-NGv3-2_174777797_190306304-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/2/tx/tmp8bLc9z/R14-18102_kapa-NGv3-PE100-NGv3-2_174777797_190306304.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:16Z] WARN  18:16:56,042 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T01:16Z] WARN  18:16:56,050 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/2/tx/tmp37ikSm/R14-18102_kapa-NGv3-PE100-NGv3-2_159196753_174774985.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T01:16Z] INFO  18:16:56,068 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:16Z] INFO  18:16:56,071 HelpFormatter - Date/Time: 2016/04/14 18:16:56
[2016-04-15T01:16Z] INFO  18:16:56,072 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:16Z] INFO  18:16:56,072 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:16Z] WARN  18:16:56,099 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T01:16Z] WARN  18:16:56,102 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/2/tx/tmp8bLc9z/R14-18102_kapa-NGv3-PE100-NGv3-2_174777797_190306304.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T01:16Z] INFO  18:16:56,226 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:16Z] INFO  18:16:56,367 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:16Z] INFO  18:16:56,471 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T01:16Z] INFO  18:16:56,497 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:16Z] INFO  18:16:56,546 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T01:16Z] INFO  18:16:56,561 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:16Z] INFO  18:16:56,605 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.11
[2016-04-15T01:16Z] INFO  18:16:56,630 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T01:16Z] INFO  18:16:56,644 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-15T01:16Z] INFO  18:16:56,672 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T01:16Z] INFO  18:16:57,093 ProgressMeter -      1:45294880      3.2630886E8    90.0 s            0.0 s       90.0%   100.0 s      10.0 s
[2016-04-15T01:16Z] INFO  18:16:57,100 IntervalUtils - Processing 253764 bp from intervals
[2016-04-15T01:16Z] WARN  18:16:57,116 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:16Z] INFO  18:16:57,143 IntervalUtils - Processing 216485 bp from intervals
[2016-04-15T01:16Z] WARN  18:16:57,160 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:16Z] INFO  18:16:57,204 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:16Z] INFO  18:16:57,228 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:16Z] INFO  18:16:57,329 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:16Z] INFO  18:16:57,338 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:16Z] INFO  18:16:57,339 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T01:16Z] INFO  18:16:57,339 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T01:16Z] INFO  18:16:57,352 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:16Z] INFO  18:16:57,353 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T01:16Z] INFO  18:16:57,353 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T01:16Z] INFO  18:16:57,371 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:16Z] INFO  18:16:57,372 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T01:16Z] INFO  18:16:57,372 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T01:16Z] INFO  18:16:57,374 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T01:16Z] INFO  18:16:57,374 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T01:16Z] INFO  18:16:57,592 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T01:16Z] INFO  18:16:57,629 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T01:16Z] INFO  18:16:58,345 ProgressMeter -      2:71633389      2.7480805E7    30.0 s            1.0 s       48.3%    62.0 s      32.0 s
[2016-04-15T01:16Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T01:16Z] INFO  18:16:58,626 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T01:16Z] INFO  18:16:58,638 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T01:16Z] INFO  18:16:58,669 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.009257837000000001
[2016-04-15T01:16Z] INFO  18:16:58,680 PairHMM - Total compute time in PairHMM computeLikelihoods() : 0.428269204
[2016-04-15T01:16Z] INFO  18:16:58,681 HaplotypeCaller - Ran local assembly on 1021 active regions
[2016-04-15T01:16Z] INFO  18:16:58,727 ProgressMeter -            done       4.967453E7    38.0 s            0.0 s      100.0%    38.0 s       0.0 s
[2016-04-15T01:16Z] INFO  18:16:58,728 ProgressMeter - Total runtime 38.99 secs, 0.65 min, 0.01 hours
[2016-04-15T01:16Z] INFO  18:16:58,728 MicroScheduler - 13912 reads were filtered out during the traversal out of approximately 174831 total reads (7.96%)
[2016-04-15T01:16Z] INFO  18:16:58,728 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:16Z] INFO  18:16:58,729 MicroScheduler -   -> 13713 reads (7.84% of total) failing DuplicateReadFilter
[2016-04-15T01:16Z] INFO  18:16:58,729 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:16Z] INFO  18:16:58,729 MicroScheduler -   -> 199 reads (0.11% of total) failing HCMappingQualityFilter
[2016-04-15T01:16Z] INFO  18:16:58,729 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:16Z] INFO  18:16:58,730 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:16Z] INFO  18:16:58,730 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:16Z] INFO  18:16:58,730 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T01:16Z] WARN  18:16:58,997 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T01:16Z] WARN  18:16:58,998 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T01:16Z] INFO  18:16:59,450 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.025123794
[2016-04-15T01:16Z] INFO  18:16:59,451 PairHMM - Total compute time in PairHMM computeLikelihoods() : 1.137742035
[2016-04-15T01:16Z] INFO  18:16:59,451 HaplotypeCaller - Ran local assembly on 2058 active regions
[2016-04-15T01:16Z] INFO  18:16:59,519 ProgressMeter -            done     2.06201078E8    70.0 s            0.0 s      100.0%    70.0 s       0.0 s
[2016-04-15T01:16Z] INFO  18:16:59,525 ProgressMeter - Total runtime 70.62 secs, 1.18 min, 0.02 hours
[2016-04-15T01:16Z] INFO  18:16:59,525 MicroScheduler - 35800 reads were filtered out during the traversal out of approximately 421364 total reads (8.50%)
[2016-04-15T01:16Z] INFO  18:16:59,525 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:16Z] INFO  18:16:59,526 MicroScheduler -   -> 34135 reads (8.10% of total) failing DuplicateReadFilter
[2016-04-15T01:16Z] INFO  18:16:59,526 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:16Z] INFO  18:16:59,526 MicroScheduler -   -> 1665 reads (0.40% of total) failing HCMappingQualityFilter
[2016-04-15T01:16Z] INFO  18:16:59,526 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:16Z] INFO  18:16:59,526 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:16Z] INFO  18:16:59,527 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:16Z] INFO  18:16:59,527 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T01:17Z] INFO  18:17:00,243 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:17Z] GATK: HaplotypeCaller
[2016-04-15T01:17Z] INFO  18:17:01,065 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:17Z] INFO  18:17:01,073 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.008637059
[2016-04-15T01:17Z] INFO  18:17:01,084 PairHMM - Total compute time in PairHMM computeLikelihoods() : 0.284201596
[2016-04-15T01:17Z] INFO  18:17:01,085 HaplotypeCaller - Ran local assembly on 1271 active regions
[2016-04-15T01:17Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T01:17Z] INFO  18:17:01,136 ProgressMeter -            done       7.519483E7    41.0 s            0.0 s      100.0%    41.0 s       0.0 s
[2016-04-15T01:17Z] INFO  18:17:01,137 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T01:17Z] INFO  18:17:01,138 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T01:17Z] INFO  18:17:01,136 ProgressMeter - Total runtime 41.57 secs, 0.69 min, 0.01 hours
[2016-04-15T01:17Z] INFO  18:17:01,137 MicroScheduler - 17631 reads were filtered out during the traversal out of approximately 217603 total reads (8.10%)
[2016-04-15T01:17Z] INFO  18:17:01,137 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:17Z] INFO  18:17:01,137 MicroScheduler -   -> 17302 reads (7.95% of total) failing DuplicateReadFilter
[2016-04-15T01:17Z] INFO  18:17:01,138 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:17Z] INFO  18:17:01,138 MicroScheduler -   -> 329 reads (0.15% of total) failing HCMappingQualityFilter
[2016-04-15T01:17Z] INFO  18:17:01,138 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:17Z] INFO  18:17:01,139 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:17Z] INFO  18:17:01,139 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:17Z] INFO  18:17:01,139 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T01:17Z] WARN  18:17:01,428 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T01:17Z] WARN  18:17:01,429 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T01:17Z] GATK: HaplotypeCaller
[2016-04-15T01:17Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T01:17Z] INFO  18:17:02,274 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T01:17Z] INFO  18:17:02,285 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T01:17Z] WARN  18:17:02,615 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T01:17Z] WARN  18:17:02,619 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T01:17Z] INFO  18:17:02,683 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:17Z] GATK: HaplotypeCaller
[2016-04-15T01:17Z] INFO  18:17:03,673 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:17Z] INFO  18:17:03,676 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:17Z] INFO  18:17:03,677 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:17Z] INFO  18:17:03,677 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:17Z] INFO  18:17:03,682 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/2/R14-18102_kapa-NGv3-PE100-NGv3-sort-2_190313104_205830046-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/2/R14-18102_kapa-NGv3-PE100-NGv3-2_190313104_205830046-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/2/tx/tmpZHjumA/R14-18102_kapa-NGv3-PE100-NGv3-2_190313104_205830046.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:17Z] INFO  18:17:03,692 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:17Z] INFO  18:17:03,696 HelpFormatter - Date/Time: 2016/04/14 18:17:03
[2016-04-15T01:17Z] INFO  18:17:03,697 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:17Z] INFO  18:17:03,698 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:17Z] WARN  18:17:03,747 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T01:17Z] WARN  18:17:03,750 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/2/tx/tmpZHjumA/R14-18102_kapa-NGv3-PE100-NGv3-2_190313104_205830046.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T01:17Z] INFO  18:17:03,905 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:17Z] INFO  18:17:04,179 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T01:17Z] INFO  18:17:04,191 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:17Z] INFO  18:17:04,255 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-15T01:17Z] INFO  18:17:04,292 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T01:17Z] INFO  18:17:04,285 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:17Z] INFO  18:17:04,315 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:17Z] INFO  18:17:04,315 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:17Z] INFO  18:17:04,316 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:17Z] INFO  18:17:04,321 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/2/R14-18102_kapa-NGv3-PE100-NGv3-sort-2_205912303_222290862-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/2/R14-18102_kapa-NGv3-PE100-NGv3-2_205912303_222290862-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/2/tx/tmpzi8v_S/R14-18102_kapa-NGv3-PE100-NGv3-2_205912303_222290862.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:17Z] INFO  18:17:04,331 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:17Z] INFO  18:17:04,332 HelpFormatter - Date/Time: 2016/04/14 18:17:04
[2016-04-15T01:17Z] INFO  18:17:04,333 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:17Z] INFO  18:17:04,333 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:17Z] WARN  18:17:04,381 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T01:17Z] WARN  18:17:04,384 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/2/tx/tmpzi8v_S/R14-18102_kapa-NGv3-PE100-NGv3-2_205912303_222290862.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T01:17Z] INFO  18:17:04,582 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:17Z] INFO  18:17:04,687 IntervalUtils - Processing 204460 bp from intervals
[2016-04-15T01:17Z] WARN  18:17:04,693 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:17Z] INFO  18:17:04,772 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:17Z] INFO  18:17:04,854 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T01:17Z] INFO  18:17:04,864 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:17Z] INFO  18:17:04,953 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-15T01:17Z] INFO  18:17:04,964 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:17Z] INFO  18:17:04,965 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:17Z] INFO  18:17:04,966 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T01:17Z] INFO  18:17:04,966 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T01:17Z] INFO  18:17:04,966 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T01:17Z] INFO  18:17:04,967 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T01:17Z] INFO  18:17:04,980 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T01:17Z] INFO  18:17:05,213 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T01:17Z] INFO  18:17:05,437 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.031335151
[2016-04-15T01:17Z] INFO  18:17:05,438 PairHMM - Total compute time in PairHMM computeLikelihoods() : 1.595780664
[2016-04-15T01:17Z] INFO  18:17:05,438 HaplotypeCaller - Ran local assembly on 3086 active regions
[2016-04-15T01:17Z] INFO  18:17:05,497 ProgressMeter -            done     3.97207864E8    98.0 s            0.0 s      100.0%    98.0 s       0.0 s
[2016-04-15T01:17Z] INFO  18:17:05,498 ProgressMeter - Total runtime 98.41 secs, 1.64 min, 0.03 hours
[2016-04-15T01:17Z] INFO  18:17:05,498 MicroScheduler - 61279 reads were filtered out during the traversal out of approximately 693902 total reads (8.83%)
[2016-04-15T01:17Z] INFO  18:17:05,498 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:17Z] INFO  18:17:05,498 MicroScheduler -   -> 55594 reads (8.01% of total) failing DuplicateReadFilter
[2016-04-15T01:17Z] INFO  18:17:05,499 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:17Z] INFO  18:17:05,499 MicroScheduler -   -> 5685 reads (0.82% of total) failing HCMappingQualityFilter
[2016-04-15T01:17Z] INFO  18:17:05,499 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:17Z] INFO  18:17:05,499 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:17Z] INFO  18:17:05,500 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:17Z] INFO  18:17:05,500 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T01:17Z] INFO  18:17:05,597 IntervalUtils - Processing 247026 bp from intervals
[2016-04-15T01:17Z] WARN  18:17:05,603 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:17Z] INFO  18:17:05,709 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:17Z] INFO  18:17:05,861 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:17Z] INFO  18:17:05,862 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:17Z] INFO  18:17:05,862 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T01:17Z] INFO  18:17:05,863 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T01:17Z] INFO  18:17:05,877 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T01:17Z] INFO  18:17:05,878 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T01:17Z] INFO  18:17:06,009 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:17Z] INFO  18:17:06,012 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:17Z] INFO  18:17:06,013 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:17Z] INFO  18:17:06,014 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:17Z] INFO  18:17:06,018 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/2/R14-18102_kapa-NGv3-PE100-NGv3-sort-2_222291154_237994685-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/2/R14-18102_kapa-NGv3-PE100-NGv3-2_222291154_237994685-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/2/tx/tmpGRGFX7/R14-18102_kapa-NGv3-PE100-NGv3-2_222291154_237994685.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:17Z] INFO  18:17:06,049 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:17Z] INFO  18:17:06,050 HelpFormatter - Date/Time: 2016/04/14 18:17:06
[2016-04-15T01:17Z] INFO  18:17:06,051 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:17Z] INFO  18:17:06,052 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:17Z] WARN  18:17:06,107 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T01:17Z] WARN  18:17:06,110 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/2/tx/tmpGRGFX7/R14-18102_kapa-NGv3-PE100-NGv3-2_222291154_237994685.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T01:17Z] INFO  18:17:06,124 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T01:17Z] INFO  18:17:06,290 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:17Z] INFO  18:17:06,479 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T01:17Z] INFO  18:17:06,509 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:17Z] INFO  18:17:06,593 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-15T01:17Z] INFO  18:17:06,613 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T01:17Z] INFO  18:17:06,622 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.006534884
[2016-04-15T01:17Z] INFO  18:17:06,623 PairHMM - Total compute time in PairHMM computeLikelihoods() : 0.366357792
[2016-04-15T01:17Z] INFO  18:17:06,623 HaplotypeCaller - Ran local assembly on 755 active regions
[2016-04-15T01:17Z] INFO  18:17:06,664 ProgressMeter -            done      2.4918497E7    29.0 s            1.0 s      100.0%    29.0 s       0.0 s
[2016-04-15T01:17Z] INFO  18:17:06,665 ProgressMeter - Total runtime 29.62 secs, 0.49 min, 0.01 hours
[2016-04-15T01:17Z] INFO  18:17:06,665 MicroScheduler - 61324 reads were filtered out during the traversal out of approximately 184815 total reads (33.18%)
[2016-04-15T01:17Z] INFO  18:17:06,665 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:17Z] INFO  18:17:06,666 MicroScheduler -   -> 11123 reads (6.02% of total) failing DuplicateReadFilter
[2016-04-15T01:17Z] INFO  18:17:06,666 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:17Z] INFO  18:17:06,666 MicroScheduler -   -> 50201 reads (27.16% of total) failing HCMappingQualityFilter
[2016-04-15T01:17Z] INFO  18:17:06,666 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:17Z] INFO  18:17:06,667 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:17Z] INFO  18:17:06,667 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:17Z] INFO  18:17:06,667 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T01:17Z] INFO  18:17:07,023 IntervalUtils - Processing 186854 bp from intervals
[2016-04-15T01:17Z] INFO  18:17:07,038 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:17Z] WARN  18:17:07,039 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:17Z] INFO  18:17:07,175 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:17Z] GATK: HaplotypeCaller
[2016-04-15T01:17Z] INFO  18:17:07,329 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:17Z] INFO  18:17:07,329 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:17Z] INFO  18:17:07,330 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T01:17Z] INFO  18:17:07,330 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T01:17Z] INFO  18:17:07,338 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T01:17Z] INFO  18:17:07,339 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T01:17Z] INFO  18:17:07,569 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T01:17Z] INFO  18:17:08,058 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:17Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T01:17Z] INFO  18:17:08,309 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T01:17Z] INFO  18:17:08,310 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T01:17Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T01:17Z] INFO  18:17:08,346 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T01:17Z] INFO  18:17:08,358 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T01:17Z] GATK: HaplotypeCaller
[2016-04-15T01:17Z] WARN  18:17:08,577 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T01:17Z] WARN  18:17:08,578 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T01:17Z] INFO  18:17:08,601 ProgressMeter -      2:97364814        7210559.0    30.0 s            4.0 s       21.1%     2.4 m     111.0 s
[2016-04-15T01:17Z] WARN  18:17:08,764 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T01:17Z] WARN  18:17:08,765 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T01:17Z] INFO  18:17:09,393 ProgressMeter -     1:152189250      7.4636378E7    90.0 s            1.0 s       37.4%     4.0 m       2.5 m
[2016-04-15T01:17Z] INFO  18:17:10,468 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:17Z] INFO  18:17:10,471 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:17Z] INFO  18:17:10,472 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:17Z] INFO  18:17:10,472 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:17Z] INFO  18:17:10,477 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/2/R14-18102_kapa-NGv3-PE100-NGv3-sort-2_237995374_243199373-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/2/R14-18102_kapa-NGv3-PE100-NGv3-2_237995374_243199373-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/2/tx/tmp4sdQZc/R14-18102_kapa-NGv3-PE100-NGv3-2_237995374_243199373.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:17Z] INFO  18:17:10,515 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:17Z] INFO  18:17:10,523 HelpFormatter - Date/Time: 2016/04/14 18:17:10
[2016-04-15T01:17Z] INFO  18:17:10,524 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:17Z] INFO  18:17:10,525 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:17Z] WARN  18:17:10,587 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T01:17Z] WARN  18:17:10,604 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/2/tx/tmp4sdQZc/R14-18102_kapa-NGv3-PE100-NGv3-2_237995374_243199373.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T01:17Z] INFO  18:17:10,918 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:17Z] INFO  18:17:11,169 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T01:17Z] INFO  18:17:11,184 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:17Z] INFO  18:17:11,274 ProgressMeter -     2:120395835      2.3648509E7    30.0 s            1.0 s       75.4%    39.0 s       9.0 s
[2016-04-15T01:17Z] INFO  18:17:11,308 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.12
[2016-04-15T01:17Z] INFO  18:17:11,345 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T01:17Z] INFO  18:17:11,719 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:17Z] INFO  18:17:11,722 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:17Z] INFO  18:17:11,723 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:17Z] INFO  18:17:11,723 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:17Z] INFO  18:17:11,728 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/3/R14-18102_kapa-NGv3-PE100-NGv3-sort-3_0_15512123-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/3/R14-18102_kapa-NGv3-PE100-NGv3-3_0_15512123-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/3/tx/tmpgOvrt9/R14-18102_kapa-NGv3-PE100-NGv3-3_0_15512123.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:17Z] INFO  18:17:11,746 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:17Z] INFO  18:17:11,747 HelpFormatter - Date/Time: 2016/04/14 18:17:11
[2016-04-15T01:17Z] INFO  18:17:11,747 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:17Z] INFO  18:17:11,748 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:17Z] WARN  18:17:11,793 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T01:17Z] WARN  18:17:11,796 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/3/tx/tmpgOvrt9/R14-18102_kapa-NGv3-PE100-NGv3-3_0_15512123.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T01:17Z] INFO  18:17:11,808 IntervalUtils - Processing 128077 bp from intervals
[2016-04-15T01:17Z] WARN  18:17:11,814 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:17Z] INFO  18:17:11,896 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:17Z] INFO  18:17:12,080 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:17Z] INFO  18:17:12,081 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:17Z] INFO  18:17:12,082 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T01:17Z] INFO  18:17:12,073 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:17Z] INFO  18:17:12,092 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T01:17Z] INFO  18:17:12,103 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T01:17Z] INFO  18:17:12,104 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T01:17Z] INFO  18:17:12,302 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T01:17Z] INFO  18:17:12,313 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T01:17Z] INFO  18:17:12,344 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:17Z] INFO  18:17:12,430 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.09
[2016-04-15T01:17Z] INFO  18:17:12,465 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T01:17Z] INFO  18:17:12,812 IntervalUtils - Processing 188511 bp from intervals
[2016-04-15T01:17Z] WARN  18:17:12,829 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:17Z] INFO  18:17:12,992 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:17Z] INFO  18:17:13,174 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:17Z] INFO  18:17:13,176 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:17Z] INFO  18:17:13,176 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T01:17Z] INFO  18:17:13,177 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T01:17Z] INFO  18:17:13,196 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T01:17Z] INFO  18:17:13,196 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T01:17Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T01:17Z] INFO  18:17:13,275 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T01:17Z] INFO  18:17:13,276 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T01:17Z] INFO  18:17:13,435 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T01:17Z] WARN  18:17:13,788 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T01:17Z] WARN  18:17:13,789 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T01:17Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T01:17Z] INFO  18:17:14,772 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T01:17Z] INFO  18:17:14,792 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T01:17Z] WARN  18:17:15,107 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T01:17Z] WARN  18:17:15,118 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T01:17Z] INFO  18:17:16,525 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.012331507
[2016-04-15T01:17Z] INFO  18:17:16,526 PairHMM - Total compute time in PairHMM computeLikelihoods() : 0.6399826540000001
[2016-04-15T01:17Z] INFO  18:17:16,526 HaplotypeCaller - Ran local assembly on 1781 active regions
[2016-04-15T01:17Z] INFO  18:17:16,581 ProgressMeter -            done      1.3985948E8    59.0 s            0.0 s      100.0%    59.0 s       0.0 s
[2016-04-15T01:17Z] INFO  18:17:16,581 ProgressMeter - Total runtime 59.49 secs, 0.99 min, 0.02 hours
[2016-04-15T01:17Z] INFO  18:17:16,582 MicroScheduler - 28653 reads were filtered out during the traversal out of approximately 351812 total reads (8.14%)
[2016-04-15T01:17Z] INFO  18:17:16,582 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:17Z] INFO  18:17:16,582 MicroScheduler -   -> 28250 reads (8.03% of total) failing DuplicateReadFilter
[2016-04-15T01:17Z] INFO  18:17:16,583 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:17Z] INFO  18:17:16,583 MicroScheduler -   -> 403 reads (0.11% of total) failing HCMappingQualityFilter
[2016-04-15T01:17Z] INFO  18:17:16,583 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:17Z] INFO  18:17:16,584 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:17Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T01:17Z] INFO  18:17:16,584 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:17Z] INFO  18:17:16,584 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T01:17Z] INFO  18:17:16,617 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T01:17Z] INFO  18:17:16,624 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T01:17Z] WARN  18:17:16,989 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T01:17Z] WARN  18:17:17,000 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T01:17Z] INFO  18:17:17,945 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.039454292
[2016-04-15T01:17Z] INFO  18:17:17,947 PairHMM - Total compute time in PairHMM computeLikelihoods() : 11.976485178
[2016-04-15T01:17Z] INFO  18:17:17,947 HaplotypeCaller - Ran local assembly on 2781 active regions
[2016-04-15T01:17Z] INFO  18:17:18,000 ProgressMeter -            done     3.27575124E8   117.0 s            0.0 s      100.0%   117.0 s       0.0 s
[2016-04-15T01:17Z] INFO  18:17:18,000 ProgressMeter - Total runtime 117.05 secs, 1.95 min, 0.03 hours
[2016-04-15T01:17Z] INFO  18:17:18,001 MicroScheduler - 135042 reads were filtered out during the traversal out of approximately 702318 total reads (19.23%)
[2016-04-15T01:17Z] INFO  18:17:18,001 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:17Z] INFO  18:17:18,002 MicroScheduler -   -> 50514 reads (7.19% of total) failing DuplicateReadFilter
[2016-04-15T01:17Z] INFO  18:17:18,002 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:17Z] INFO  18:17:18,002 MicroScheduler -   -> 84528 reads (12.04% of total) failing HCMappingQualityFilter
[2016-04-15T01:17Z] INFO  18:17:18,002 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:17Z] INFO  18:17:18,003 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:17Z] INFO  18:17:18,003 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:17Z] INFO  18:17:18,003 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T01:17Z] INFO  18:17:18,190 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:17Z] GATK: HaplotypeCaller
[2016-04-15T01:17Z] INFO  18:17:18,983 ProgressMeter -     2:131377724      1.0227166E7    30.0 s            2.0 s       39.2%    76.0 s      46.0 s
[2016-04-15T01:17Z] INFO  18:17:19,775 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:17Z] GATK: HaplotypeCaller
[2016-04-15T01:17Z] INFO  18:17:20,138 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.007382458000000001
[2016-04-15T01:17Z] INFO  18:17:20,139 PairHMM - Total compute time in PairHMM computeLikelihoods() : 0.356641645
[2016-04-15T01:17Z] INFO  18:17:20,139 HaplotypeCaller - Ran local assembly on 948 active regions
[2016-04-15T01:17Z] INFO  18:17:20,200 ProgressMeter -            done      4.1916896E7    38.0 s            0.0 s      100.0%    38.0 s       0.0 s
[2016-04-15T01:17Z] INFO  18:17:20,201 ProgressMeter - Total runtime 38.95 secs, 0.65 min, 0.01 hours
[2016-04-15T01:17Z] INFO  18:17:20,201 MicroScheduler - 71018 reads were filtered out during the traversal out of approximately 216197 total reads (32.85%)
[2016-04-15T01:17Z] INFO  18:17:20,201 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:17Z] INFO  18:17:20,201 MicroScheduler -   -> 12790 reads (5.92% of total) failing DuplicateReadFilter
[2016-04-15T01:17Z] INFO  18:17:20,202 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:17Z] INFO  18:17:20,202 MicroScheduler -   -> 58228 reads (26.93% of total) failing HCMappingQualityFilter
[2016-04-15T01:17Z] INFO  18:17:20,202 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:17Z] INFO  18:17:20,202 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:17Z] INFO  18:17:20,203 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:17Z] INFO  18:17:20,203 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T01:17Z] INFO  18:17:21,420 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:17Z] INFO  18:17:21,423 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:17Z] INFO  18:17:21,424 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:17Z] INFO  18:17:21,425 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:17Z] INFO  18:17:21,429 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/3/R14-18102_kapa-NGv3-PE100-NGv3-sort-3_15515506_31574805-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/3/R14-18102_kapa-NGv3-PE100-NGv3-3_15515506_31574805-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/3/tx/tmpG5vDjE/R14-18102_kapa-NGv3-PE100-NGv3-3_15515506_31574805.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:17Z] INFO  18:17:21,442 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:17Z] INFO  18:17:21,443 HelpFormatter - Date/Time: 2016/04/14 18:17:21
[2016-04-15T01:17Z] INFO  18:17:21,444 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:17Z] INFO  18:17:21,451 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:17Z] WARN  18:17:21,476 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T01:17Z] WARN  18:17:21,479 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/3/tx/tmpG5vDjE/R14-18102_kapa-NGv3-PE100-NGv3-3_15515506_31574805.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T01:17Z] INFO  18:17:21,634 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:17Z] INFO  18:17:21,708 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:17Z] INFO  18:17:21,848 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T01:17Z] INFO  18:17:21,879 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:17Z] INFO  18:17:21,941 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-15T01:17Z] INFO  18:17:21,987 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T01:17Z] GATK: HaplotypeCaller
[2016-04-15T01:17Z] INFO  18:17:22,317 IntervalUtils - Processing 86168 bp from intervals
[2016-04-15T01:17Z] WARN  18:17:22,323 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:17Z] INFO  18:17:22,451 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:17Z] INFO  18:17:22,556 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:17Z] INFO  18:17:22,556 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:17Z] INFO  18:17:22,557 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T01:17Z] INFO  18:17:22,558 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T01:17Z] INFO  18:17:22,569 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T01:17Z] INFO  18:17:22,570 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T01:17Z] INFO  18:17:22,704 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.031318806000000005
[2016-04-15T01:17Z] INFO  18:17:22,705 PairHMM - Total compute time in PairHMM computeLikelihoods() : 9.594084686
[2016-04-15T01:17Z] INFO  18:17:22,706 HaplotypeCaller - Ran local assembly on 3014 active regions
[2016-04-15T01:17Z] INFO  18:17:22,731 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.00476925
[2016-04-15T01:17Z] INFO  18:17:22,732 PairHMM - Total compute time in PairHMM computeLikelihoods() : 0.147513745
[2016-04-15T01:17Z] INFO  18:17:22,733 HaplotypeCaller - Ran local assembly on 697 active regions
[2016-04-15T01:17Z] INFO  18:17:22,755 ProgressMeter -            done     3.72740812E8   117.0 s            0.0 s      100.0%   117.0 s       0.0 s
[2016-04-15T01:17Z] INFO  18:17:22,755 ProgressMeter - Total runtime 117.32 secs, 1.96 min, 0.03 hours
[2016-04-15T01:17Z] INFO  18:17:22,756 MicroScheduler - 64992 reads were filtered out during the traversal out of approximately 689935 total reads (9.42%)
[2016-04-15T01:17Z] INFO  18:17:22,756 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:17Z] INFO  18:17:22,757 MicroScheduler -   -> 55234 reads (8.01% of total) failing DuplicateReadFilter
[2016-04-15T01:17Z] INFO  18:17:22,757 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:17Z] INFO  18:17:22,757 MicroScheduler -   -> 9758 reads (1.41% of total) failing HCMappingQualityFilter
[2016-04-15T01:17Z] INFO  18:17:22,758 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:17Z] INFO  18:17:22,758 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:17Z] INFO  18:17:22,758 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:17Z] INFO  18:17:22,758 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T01:17Z] INFO  18:17:22,779 ProgressMeter -            done      2.4452471E7    28.0 s            1.0 s      100.0%    28.0 s       0.0 s
[2016-04-15T01:17Z] INFO  18:17:22,780 ProgressMeter - Total runtime 28.80 secs, 0.48 min, 0.01 hours
[2016-04-15T01:17Z] INFO  18:17:22,781 MicroScheduler - 19295 reads were filtered out during the traversal out of approximately 118049 total reads (16.34%)
[2016-04-15T01:17Z] INFO  18:17:22,782 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:17Z] INFO  18:17:22,782 MicroScheduler -   -> 8675 reads (7.35% of total) failing DuplicateReadFilter
[2016-04-15T01:17Z] INFO  18:17:22,783 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:17Z] INFO  18:17:22,784 MicroScheduler -   -> 10620 reads (9.00% of total) failing HCMappingQualityFilter
[2016-04-15T01:17Z] INFO  18:17:22,784 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:17Z] INFO  18:17:22,785 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:17Z] INFO  18:17:22,785 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:17Z] INFO  18:17:22,786 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T01:17Z] INFO  18:17:22,815 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T01:17Z] INFO  18:17:22,875 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.012490037
[2016-04-15T01:17Z] INFO  18:17:22,876 PairHMM - Total compute time in PairHMM computeLikelihoods() : 0.689104127
[2016-04-15T01:17Z] INFO  18:17:22,876 HaplotypeCaller - Ran local assembly on 1529 active regions
[2016-04-15T01:17Z] INFO  18:17:22,926 ProgressMeter -            done     1.00598827E8    54.0 s            0.0 s      100.0%    54.0 s       0.0 s
[2016-04-15T01:17Z] INFO  18:17:22,928 ProgressMeter - Total runtime 54.60 secs, 0.91 min, 0.02 hours
[2016-04-15T01:17Z] INFO  18:17:22,929 MicroScheduler - 26707 reads were filtered out during the traversal out of approximately 320639 total reads (8.33%)
[2016-04-15T01:17Z] INFO  18:17:22,929 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:17Z] INFO  18:17:22,930 MicroScheduler -   -> 25889 reads (8.07% of total) failing DuplicateReadFilter
[2016-04-15T01:17Z] INFO  18:17:22,931 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:17Z] INFO  18:17:22,931 MicroScheduler -   -> 818 reads (0.26% of total) failing HCMappingQualityFilter
[2016-04-15T01:17Z] INFO  18:17:22,932 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:17Z] INFO  18:17:22,932 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:17Z] INFO  18:17:22,933 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:17Z] INFO  18:17:22,934 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T01:17Z] INFO  18:17:23,332 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:17Z] INFO  18:17:23,335 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:17Z] INFO  18:17:23,336 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:17Z] INFO  18:17:23,336 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:17Z] INFO  18:17:23,341 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/3/R14-18102_kapa-NGv3-PE100-NGv3-sort-3_31617887_47127804-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/3/R14-18102_kapa-NGv3-PE100-NGv3-3_31617887_47127804-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/3/tx/tmprcCxxx/R14-18102_kapa-NGv3-PE100-NGv3-3_31617887_47127804.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:17Z] INFO  18:17:23,354 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:17Z] INFO  18:17:23,355 HelpFormatter - Date/Time: 2016/04/14 18:17:23
[2016-04-15T01:17Z] INFO  18:17:23,355 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:17Z] INFO  18:17:23,356 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:17Z] WARN  18:17:23,389 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T01:17Z] WARN  18:17:23,392 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/3/tx/tmprcCxxx/R14-18102_kapa-NGv3-PE100-NGv3-3_31617887_47127804.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T01:17Z] INFO  18:17:23,621 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:17Z] INFO  18:17:23,809 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T01:17Z] INFO  18:17:23,819 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:17Z] INFO  18:17:23,906 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.09
[2016-04-15T01:17Z] INFO  18:17:23,927 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T01:17Z] INFO  18:17:24,263 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:17Z] INFO  18:17:24,360 IntervalUtils - Processing 307437 bp from intervals
[2016-04-15T01:17Z] WARN  18:17:24,365 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:17Z] INFO  18:17:24,422 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:17Z] INFO  18:17:24,434 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:17Z] INFO  18:17:24,451 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:17Z] INFO  18:17:24,552 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:17Z] INFO  18:17:24,553 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:17Z] INFO  18:17:24,554 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T01:17Z] INFO  18:17:24,555 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T01:17Z] INFO  18:17:24,556 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T01:17Z] INFO  18:17:24,556 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T01:17Z] GATK: HaplotypeCaller
[2016-04-15T01:17Z] GATK: HaplotypeCaller
[2016-04-15T01:17Z] GATK: HaplotypeCaller
[2016-04-15T01:17Z] INFO  18:17:24,897 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T01:17Z] INFO  18:17:25,232 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:17Z] INFO  18:17:25,235 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:17Z] INFO  18:17:25,236 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:17Z] INFO  18:17:25,236 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:17Z] INFO  18:17:25,241 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/3/R14-18102_kapa-NGv3-PE100-NGv3-sort-3_47129602_62648069-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/3/R14-18102_kapa-NGv3-PE100-NGv3-3_47129602_62648069-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/3/tx/tmpVgc89J/R14-18102_kapa-NGv3-PE100-NGv3-3_47129602_62648069.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:17Z] INFO  18:17:25,256 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:17Z] INFO  18:17:25,257 HelpFormatter - Date/Time: 2016/04/14 18:17:25
[2016-04-15T01:17Z] INFO  18:17:25,257 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:17Z] INFO  18:17:25,257 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:17Z] WARN  18:17:25,281 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T01:17Z] WARN  18:17:25,284 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/3/tx/tmpVgc89J/R14-18102_kapa-NGv3-PE100-NGv3-3_47129602_62648069.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T01:17Z] INFO  18:17:25,528 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:17Z] INFO  18:17:25,740 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T01:17Z] INFO  18:17:25,750 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:17Z] INFO  18:17:25,838 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.09
[2016-04-15T01:17Z] INFO  18:17:25,855 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T01:17Z] INFO  18:17:26,357 IntervalUtils - Processing 430308 bp from intervals
[2016-04-15T01:17Z] WARN  18:17:26,373 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:17Z] INFO  18:17:26,492 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:17Z] INFO  18:17:26,637 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:17Z] INFO  18:17:26,638 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:17Z] INFO  18:17:26,639 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T01:17Z] INFO  18:17:26,639 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T01:17Z] INFO  18:17:26,640 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T01:17Z] INFO  18:17:26,640 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T01:17Z] INFO  18:17:26,832 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T01:17Z] INFO  18:17:27,355 ProgressMeter -     2:179466391        9570177.0    30.0 s            3.0 s       42.9%    69.0 s      39.0 s
[2016-04-15T01:17Z] INFO  18:17:27,397 ProgressMeter -     2:167285679      2.9706839E7    30.0 s            1.0 s       50.6%    59.0 s      29.0 s
[2016-04-15T01:17Z] INFO  18:17:28,072 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:17Z] INFO  18:17:28,086 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:17Z] INFO  18:17:28,086 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:17Z] INFO  18:17:28,086 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:17Z] INFO  18:17:28,090 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/3/R14-18102_kapa-NGv3-PE100-NGv3-sort-3_96585668_112185230-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/3/R14-18102_kapa-NGv3-PE100-NGv3-3_96585668_112185230-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/3/tx/tmpPezjQN/R14-18102_kapa-NGv3-PE100-NGv3-3_96585668_112185230.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:17Z] INFO  18:17:28,111 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:17Z] INFO  18:17:28,111 HelpFormatter - Date/Time: 2016/04/14 18:17:28
[2016-04-15T01:17Z] INFO  18:17:28,112 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:17Z] INFO  18:17:28,112 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:17Z] WARN  18:17:28,160 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T01:17Z] WARN  18:17:28,162 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/3/tx/tmpPezjQN/R14-18102_kapa-NGv3-PE100-NGv3-3_96585668_112185230.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T01:17Z] INFO  18:17:28,396 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:17Z] INFO  18:17:28,399 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:17Z] INFO  18:17:28,424 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:17Z] INFO  18:17:28,425 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:17Z] INFO  18:17:28,429 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/3/R14-18102_kapa-NGv3-PE100-NGv3-sort-3_78649262_96533852-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/3/R14-18102_kapa-NGv3-PE100-NGv3-3_78649262_96533852-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/3/tx/tmplHL5aL/R14-18102_kapa-NGv3-PE100-NGv3-3_78649262_96533852.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:17Z] INFO  18:17:28,449 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:17Z] INFO  18:17:28,450 HelpFormatter - Date/Time: 2016/04/14 18:17:28
[2016-04-15T01:17Z] INFO  18:17:28,450 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:17Z] INFO  18:17:28,451 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:17Z] INFO  18:17:28,451 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:17Z] INFO  18:17:28,481 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:17Z] INFO  18:17:28,485 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:17Z] INFO  18:17:28,485 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:17Z] INFO  18:17:28,486 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:17Z] INFO  18:17:28,491 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/3/R14-18102_kapa-NGv3-PE100-NGv3-sort-3_62739115_78648077-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/3/R14-18102_kapa-NGv3-PE100-NGv3-3_62739115_78648077-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/3/tx/tmpmpbXRc/R14-18102_kapa-NGv3-PE100-NGv3-3_62739115_78648077.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:17Z] WARN  18:17:28,495 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T01:17Z] WARN  18:17:28,508 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/3/tx/tmplHL5aL/R14-18102_kapa-NGv3-PE100-NGv3-3_78649262_96533852.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T01:17Z] INFO  18:17:28,514 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:17Z] INFO  18:17:28,526 HelpFormatter - Date/Time: 2016/04/14 18:17:28
[2016-04-15T01:17Z] INFO  18:17:28,526 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:17Z] INFO  18:17:28,527 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:17Z] WARN  18:17:28,561 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T01:17Z] WARN  18:17:28,564 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/3/tx/tmpmpbXRc/R14-18102_kapa-NGv3-PE100-NGv3-3_62739115_78648077.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T01:17Z] INFO  18:17:28,671 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T01:17Z] INFO  18:17:28,685 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:17Z] INFO  18:17:28,693 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:17Z] INFO  18:17:28,743 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:17Z] INFO  18:17:28,796 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.11
[2016-04-15T01:17Z] INFO  18:17:28,824 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T01:17Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T01:17Z] INFO  18:17:28,906 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T01:17Z] INFO  18:17:28,915 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:17Z] INFO  18:17:28,924 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T01:17Z] INFO  18:17:28,925 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T01:17Z] INFO  18:17:28,936 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T01:17Z] INFO  18:17:28,945 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:17Z] INFO  18:17:29,002 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.09
[2016-04-15T01:17Z] INFO  18:17:29,003 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-15T01:17Z] INFO  18:17:29,026 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T01:17Z] INFO  18:17:29,065 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T01:17Z] INFO  18:17:29,303 IntervalUtils - Processing 140565 bp from intervals
[2016-04-15T01:17Z] WARN  18:17:29,308 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:17Z] WARN  18:17:29,362 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T01:17Z] WARN  18:17:29,363 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T01:17Z] INFO  18:17:29,404 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:17Z] INFO  18:17:29,500 IntervalUtils - Processing 30411 bp from intervals
[2016-04-15T01:17Z] WARN  18:17:29,505 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:17Z] INFO  18:17:29,505 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:17Z] INFO  18:17:29,507 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:17Z] INFO  18:17:29,507 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T01:17Z] INFO  18:17:29,508 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T01:17Z] INFO  18:17:29,509 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T01:17Z] INFO  18:17:29,509 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T01:17Z] INFO  18:17:29,574 IntervalUtils - Processing 82160 bp from intervals
[2016-04-15T01:17Z] WARN  18:17:29,579 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:17Z] INFO  18:17:29,587 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:17Z] INFO  18:17:29,676 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:17Z] INFO  18:17:29,677 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:17Z] INFO  18:17:29,677 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T01:17Z] INFO  18:17:29,677 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T01:17Z] INFO  18:17:29,681 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:17Z] INFO  18:17:29,689 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T01:17Z] INFO  18:17:29,690 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T01:17Z] INFO  18:17:29,790 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T01:17Z] INFO  18:17:29,794 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:17Z] INFO  18:17:29,807 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:17Z] INFO  18:17:29,808 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T01:17Z] INFO  18:17:29,809 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T01:17Z] INFO  18:17:29,821 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T01:17Z] INFO  18:17:29,821 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T01:17Z] INFO  18:17:29,938 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T01:17Z] INFO  18:17:30,051 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T01:17Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T01:17Z] INFO  18:17:30,882 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T01:17Z] INFO  18:17:30,882 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T01:17Z] WARN  18:17:31,200 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T01:17Z] WARN  18:17:31,201 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T01:17Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T01:17Z] INFO  18:17:31,600 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T01:17Z] INFO  18:17:31,601 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T01:17Z] WARN  18:17:31,929 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T01:17Z] WARN  18:17:31,930 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T01:17Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T01:17Z] INFO  18:17:34,491 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T01:17Z] INFO  18:17:34,504 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T01:17Z] WARN  18:17:34,819 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T01:17Z] WARN  18:17:34,820 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T01:17Z] INFO  18:17:35,025 ProgressMeter -     2:201303845      3.1983967E7    30.0 s            0.0 s       54.1%    55.0 s      25.0 s
[2016-04-15T01:17Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T01:17Z] INFO  18:17:35,137 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T01:17Z] INFO  18:17:35,138 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T01:17Z] WARN  18:17:35,485 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T01:17Z] WARN  18:17:35,486 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T01:17Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T01:17Z] INFO  18:17:35,564 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T01:17Z] INFO  18:17:35,564 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T01:17Z] WARN  18:17:35,867 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T01:17Z] WARN  18:17:35,868 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T01:17Z] INFO  18:17:35,882 ProgressMeter -     2:215279307      2.4604248E7    30.0 s            1.0 s       37.4%    80.0 s      50.0 s
[2016-04-15T01:17Z] INFO  18:17:37,343 ProgressMeter -     2:231333758      2.3521573E7    30.0 s            1.0 s       46.0%    65.0 s      35.0 s
[2016-04-15T01:17Z] INFO  18:17:38,636 ProgressMeter -     2:103125320      7.7975891E7    60.0 s            0.0 s       69.2%    86.0 s      26.0 s
[2016-04-15T01:17Z] INFO  18:17:39,394 ProgressMeter -     1:152284912      7.5033226E7   120.0 s            1.0 s       40.2%     5.0 m       3.0 m
[2016-04-15T01:17Z] INFO  18:17:42,107 ProgressMeter -     2:241889020      1.5135473E7    30.0 s            1.0 s       59.7%    50.0 s      20.0 s
[2016-04-15T01:17Z] INFO  18:17:43,200 ProgressMeter -       3:9991799      1.6036776E7    30.0 s            1.0 s       44.7%    67.0 s      37.0 s
[2016-04-15T01:17Z] INFO  18:17:47,817 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.0035681980000000003
[2016-04-15T01:17Z] INFO  18:17:47,818 PairHMM - Total compute time in PairHMM computeLikelihoods() : 0.09782581600000001
[2016-04-15T01:17Z] INFO  18:17:47,818 HaplotypeCaller - Ran local assembly on 206 active regions
[2016-04-15T01:17Z] INFO  18:17:47,926 ProgressMeter -            done        2089463.0    18.0 s            8.0 s      100.0%    18.0 s       0.0 s
[2016-04-15T01:17Z] INFO  18:17:47,934 ProgressMeter - Total runtime 18.26 secs, 0.30 min, 0.01 hours
[2016-04-15T01:17Z] INFO  18:17:47,934 MicroScheduler - 3231 reads were filtered out during the traversal out of approximately 38793 total reads (8.33%)
[2016-04-15T01:17Z] INFO  18:17:47,935 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:17Z] INFO  18:17:47,935 MicroScheduler -   -> 3167 reads (8.16% of total) failing DuplicateReadFilter
[2016-04-15T01:17Z] INFO  18:17:47,935 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:17Z] INFO  18:17:47,935 MicroScheduler -   -> 64 reads (0.16% of total) failing HCMappingQualityFilter
[2016-04-15T01:17Z] INFO  18:17:47,936 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:17Z] INFO  18:17:47,936 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:17Z] INFO  18:17:47,936 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:17Z] INFO  18:17:47,936 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T01:17Z] INFO  18:17:48,984 ProgressMeter -     2:135102501      2.0329277E7    60.0 s            2.0 s       62.6%    95.0 s      35.0 s
[2016-04-15T01:17Z] INFO  18:17:49,407 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:17Z] GATK: HaplotypeCaller
[2016-04-15T01:17Z] INFO  18:17:49,702 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.008287297
[2016-04-15T01:17Z] INFO  18:17:49,703 PairHMM - Total compute time in PairHMM computeLikelihoods() : 0.329732181
[2016-04-15T01:17Z] INFO  18:17:49,704 HaplotypeCaller - Ran local assembly on 1572 active regions
[2016-04-15T01:17Z] INFO  18:17:49,748 ProgressMeter -            done     1.25465506E8    52.0 s            0.0 s      100.0%    52.0 s       0.0 s
[2016-04-15T01:17Z] INFO  18:17:49,749 ProgressMeter - Total runtime 52.38 secs, 0.87 min, 0.01 hours
[2016-04-15T01:17Z] INFO  18:17:49,750 MicroScheduler - 22998 reads were filtered out during the traversal out of approximately 279592 total reads (8.23%)
[2016-04-15T01:17Z] INFO  18:17:49,750 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:17Z] INFO  18:17:49,750 MicroScheduler -   -> 22235 reads (7.95% of total) failing DuplicateReadFilter
[2016-04-15T01:17Z] INFO  18:17:49,751 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:17Z] INFO  18:17:49,751 MicroScheduler -   -> 763 reads (0.27% of total) failing HCMappingQualityFilter
[2016-04-15T01:17Z] INFO  18:17:49,751 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:17Z] INFO  18:17:49,751 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:17Z] INFO  18:17:49,751 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:17Z] INFO  18:17:49,752 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T01:17Z] INFO  18:17:50,704 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.020083877
[2016-04-15T01:17Z] INFO  18:17:50,705 PairHMM - Total compute time in PairHMM computeLikelihoods() : 0.46836392600000004
[2016-04-15T01:17Z] INFO  18:17:50,705 HaplotypeCaller - Ran local assembly on 1503 active regions
[2016-04-15T01:17Z] INFO  18:17:50,754 ProgressMeter -            done     1.12411448E8    45.0 s            0.0 s      100.0%    45.0 s       0.0 s
[2016-04-15T01:17Z] INFO  18:17:50,755 ProgressMeter - Total runtime 45.79 secs, 0.76 min, 0.01 hours
[2016-04-15T01:17Z] INFO  18:17:50,755 MicroScheduler - 19170 reads were filtered out during the traversal out of approximately 237661 total reads (8.07%)
[2016-04-15T01:17Z] INFO  18:17:50,755 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:17Z] INFO  18:17:50,756 MicroScheduler -   -> 18718 reads (7.88% of total) failing DuplicateReadFilter
[2016-04-15T01:17Z] INFO  18:17:50,757 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:17Z] INFO  18:17:50,757 MicroScheduler -   -> 452 reads (0.19% of total) failing HCMappingQualityFilter
[2016-04-15T01:17Z] INFO  18:17:50,758 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:17Z] INFO  18:17:50,758 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:17Z] INFO  18:17:50,758 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:17Z] INFO  18:17:50,758 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T01:17Z] INFO  18:17:51,215 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:17Z] GATK: HaplotypeCaller
[2016-04-15T01:17Z] INFO  18:17:52,145 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:17Z] INFO  18:17:52,322 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:17Z] INFO  18:17:52,327 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:17Z] INFO  18:17:52,328 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:17Z] INFO  18:17:52,328 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:17Z] INFO  18:17:52,332 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/3/R14-18102_kapa-NGv3-PE100-NGv3-sort-3_112188604_127703121-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/3/R14-18102_kapa-NGv3-PE100-NGv3-3_112188604_127703121-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/3/tx/tmpANSj7s/R14-18102_kapa-NGv3-PE100-NGv3-3_112188604_127703121.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:17Z] INFO  18:17:52,344 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:17Z] INFO  18:17:52,345 HelpFormatter - Date/Time: 2016/04/14 18:17:52
[2016-04-15T01:17Z] INFO  18:17:52,345 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:17Z] INFO  18:17:52,345 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:17Z] WARN  18:17:52,395 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T01:17Z] WARN  18:17:52,398 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/3/tx/tmpANSj7s/R14-18102_kapa-NGv3-PE100-NGv3-3_112188604_127703121.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T01:17Z] GATK: HaplotypeCaller
[2016-04-15T01:17Z] INFO  18:17:52,572 ProgressMeter -      3:30664765      1.8254663E7    30.0 s            1.0 s       95.9%    31.0 s       1.0 s
[2016-04-15T01:17Z] INFO  18:17:52,575 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:17Z] INFO  18:17:52,821 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T01:17Z] INFO  18:17:52,835 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:17Z] INFO  18:17:52,957 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.12
[2016-04-15T01:17Z] INFO  18:17:52,989 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T01:17Z] INFO  18:17:53,331 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.013183437000000001
[2016-04-15T01:17Z] INFO  18:17:53,343 PairHMM - Total compute time in PairHMM computeLikelihoods() : 1.2439486670000002
[2016-04-15T01:17Z] INFO  18:17:53,344 HaplotypeCaller - Ran local assembly on 982 active regions
[2016-04-15T01:17Z] INFO  18:17:53,401 ProgressMeter -            done      3.8908959E7    41.0 s            1.0 s      100.0%    41.0 s       0.0 s
[2016-04-15T01:17Z] INFO  18:17:53,402 ProgressMeter - Total runtime 41.32 secs, 0.69 min, 0.01 hours
[2016-04-15T01:17Z] INFO  18:17:53,403 MicroScheduler - 22740 reads were filtered out during the traversal out of approximately 207327 total reads (10.97%)
[2016-04-15T01:17Z] INFO  18:17:53,404 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:17Z] INFO  18:17:53,405 MicroScheduler -   -> 16416 reads (7.92% of total) failing DuplicateReadFilter
[2016-04-15T01:17Z] INFO  18:17:53,405 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:17Z] INFO  18:17:53,405 MicroScheduler -   -> 6324 reads (3.05% of total) failing HCMappingQualityFilter
[2016-04-15T01:17Z] INFO  18:17:53,406 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:17Z] INFO  18:17:53,406 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:17Z] INFO  18:17:53,406 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:17Z] INFO  18:17:53,407 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T01:17Z] INFO  18:17:53,533 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.005538189000000001
[2016-04-15T01:17Z] INFO  18:17:53,533 PairHMM - Total compute time in PairHMM computeLikelihoods() : 0.30553439000000004
[2016-04-15T01:17Z] INFO  18:17:53,533 HaplotypeCaller - Ran local assembly on 623 active regions
[2016-04-15T01:17Z] INFO  18:17:53,599 ProgressMeter -            done      2.0117694E7    31.0 s            1.0 s      100.0%    31.0 s       0.0 s
[2016-04-15T01:17Z] INFO  18:17:53,600 ProgressMeter - Total runtime 31.04 secs, 0.52 min, 0.01 hours
[2016-04-15T01:17Z] INFO  18:17:53,600 MicroScheduler - 8825 reads were filtered out during the traversal out of approximately 107417 total reads (8.22%)
[2016-04-15T01:17Z] INFO  18:17:53,600 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:17Z] INFO  18:17:53,601 MicroScheduler -   -> 8610 reads (8.02% of total) failing DuplicateReadFilter
[2016-04-15T01:17Z] INFO  18:17:53,603 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:17Z] INFO  18:17:53,603 MicroScheduler -   -> 215 reads (0.20% of total) failing HCMappingQualityFilter
[2016-04-15T01:17Z] INFO  18:17:53,603 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:17Z] INFO  18:17:53,604 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:17Z] INFO  18:17:53,604 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:17Z] INFO  18:17:53,604 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T01:17Z] INFO  18:17:53,611 IntervalUtils - Processing 249953 bp from intervals
[2016-04-15T01:17Z] WARN  18:17:53,617 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:17Z] INFO  18:17:53,705 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:17Z] INFO  18:17:53,817 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:17Z] INFO  18:17:53,818 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:17Z] INFO  18:17:53,819 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T01:17Z] INFO  18:17:53,820 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T01:17Z] INFO  18:17:53,820 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T01:17Z] INFO  18:17:53,820 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T01:17Z] INFO  18:17:53,985 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T01:17Z] INFO  18:17:54,032 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:17Z] INFO  18:17:54,034 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:17Z] INFO  18:17:54,035 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:17Z] INFO  18:17:54,035 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:17Z] INFO  18:17:54,039 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/3/R14-18102_kapa-NGv3-PE100-NGv3-sort-3_127770401_143293035-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/3/R14-18102_kapa-NGv3-PE100-NGv3-3_127770401_143293035-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/3/tx/tmpwj0zfV/R14-18102_kapa-NGv3-PE100-NGv3-3_127770401_143293035.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:17Z] INFO  18:17:54,055 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:17Z] INFO  18:17:54,058 HelpFormatter - Date/Time: 2016/04/14 18:17:54
[2016-04-15T01:17Z] INFO  18:17:54,059 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:17Z] INFO  18:17:54,060 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:17Z] WARN  18:17:54,093 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T01:17Z] WARN  18:17:54,103 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/3/tx/tmpwj0zfV/R14-18102_kapa-NGv3-PE100-NGv3-3_127770401_143293035.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T01:17Z] INFO  18:17:54,291 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:17Z] INFO  18:17:54,551 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T01:17Z] INFO  18:17:54,561 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:17Z] INFO  18:17:54,566 ProgressMeter -      3:38359689      2.4238874E7    30.0 s            1.0 s       31.4%    95.0 s      65.0 s
[2016-04-15T01:17Z] INFO  18:17:54,573 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.015617547
[2016-04-15T01:17Z] INFO  18:17:54,573 PairHMM - Total compute time in PairHMM computeLikelihoods() : 7.174541212
[2016-04-15T01:17Z] INFO  18:17:54,574 HaplotypeCaller - Ran local assembly on 1900 active regions
[2016-04-15T01:17Z] INFO  18:17:54,615 ProgressMeter -            done     1.46584651E8    76.0 s            0.0 s      100.0%    76.0 s       0.0 s
[2016-04-15T01:17Z] INFO  18:17:54,615 ProgressMeter - Total runtime 76.04 secs, 1.27 min, 0.02 hours
[2016-04-15T01:17Z] INFO  18:17:54,615 MicroScheduler - 117034 reads were filtered out during the traversal out of approximately 472020 total reads (24.79%)
[2016-04-15T01:17Z] INFO  18:17:54,616 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:17Z] INFO  18:17:54,616 MicroScheduler -   -> 31763 reads (6.73% of total) failing DuplicateReadFilter
[2016-04-15T01:17Z] INFO  18:17:54,616 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:17Z] INFO  18:17:54,617 MicroScheduler -   -> 85271 reads (18.07% of total) failing HCMappingQualityFilter
[2016-04-15T01:17Z] INFO  18:17:54,617 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:17Z] INFO  18:17:54,617 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:17Z] INFO  18:17:54,617 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:17Z] INFO  18:17:54,618 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T01:17Z] INFO  18:17:54,652 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.09
[2016-04-15T01:17Z] INFO  18:17:54,689 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T01:17Z] INFO  18:17:54,726 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:17Z] INFO  18:17:54,841 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:17Z] GATK: HaplotypeCaller
[2016-04-15T01:17Z] INFO  18:17:55,126 IntervalUtils - Processing 238450 bp from intervals
[2016-04-15T01:17Z] WARN  18:17:55,157 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:17Z] GATK: HaplotypeCaller
[2016-04-15T01:17Z] INFO  18:17:55,307 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:17Z] INFO  18:17:55,346 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:17Z] INFO  18:17:55,350 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:17Z] INFO  18:17:55,350 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:17Z] INFO  18:17:55,351 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:17Z] INFO  18:17:55,360 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/3/R14-18102_kapa-NGv3-PE100-NGv3-sort-3_143297426_158963696-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/3/R14-18102_kapa-NGv3-PE100-NGv3-3_143297426_158963696-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/3/tx/tmpiQc5u7/R14-18102_kapa-NGv3-PE100-NGv3-3_143297426_158963696.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:17Z] INFO  18:17:55,376 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:17Z] INFO  18:17:55,377 HelpFormatter - Date/Time: 2016/04/14 18:17:55
[2016-04-15T01:17Z] INFO  18:17:55,377 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:17Z] INFO  18:17:55,377 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:17Z] INFO  18:17:55,420 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:17Z] INFO  18:17:55,422 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:17Z] INFO  18:17:55,425 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T01:17Z] INFO  18:17:55,426 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T01:17Z] INFO  18:17:55,427 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T01:17Z] INFO  18:17:55,427 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T01:17Z] WARN  18:17:55,437 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T01:17Z] WARN  18:17:55,451 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/3/tx/tmpiQc5u7/R14-18102_kapa-NGv3-PE100-NGv3-3_143297426_158963696.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T01:17Z] INFO  18:17:55,636 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T01:17Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T01:17Z] INFO  18:17:55,780 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:17Z] INFO  18:17:55,788 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T01:17Z] INFO  18:17:55,789 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T01:17Z] INFO  18:17:56,024 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.01144381
[2016-04-15T01:17Z] INFO  18:17:56,025 PairHMM - Total compute time in PairHMM computeLikelihoods() : 1.1681634790000002
[2016-04-15T01:17Z] INFO  18:17:56,026 HaplotypeCaller - Ran local assembly on 1657 active regions
[2016-04-15T01:17Z] WARN  18:17:56,061 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T01:17Z] WARN  18:17:56,062 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T01:17Z] INFO  18:17:56,065 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T01:17Z] INFO  18:17:56,074 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:17Z] INFO  18:17:56,079 ProgressMeter -            done     1.20474354E8    58.0 s            0.0 s      100.0%    58.0 s       0.0 s
[2016-04-15T01:17Z] INFO  18:17:56,080 ProgressMeter - Total runtime 58.74 secs, 0.98 min, 0.02 hours
[2016-04-15T01:17Z] INFO  18:17:56,080 MicroScheduler - 33355 reads were filtered out during the traversal out of approximately 328496 total reads (10.15%)
[2016-04-15T01:17Z] INFO  18:17:56,081 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:17Z] INFO  18:17:56,082 MicroScheduler -   -> 25653 reads (7.81% of total) failing DuplicateReadFilter
[2016-04-15T01:17Z] INFO  18:17:56,082 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:17Z] INFO  18:17:56,083 MicroScheduler -   -> 7702 reads (2.34% of total) failing HCMappingQualityFilter
[2016-04-15T01:17Z] INFO  18:17:56,084 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:17Z] INFO  18:17:56,084 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:17Z] INFO  18:17:56,085 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:17Z] INFO  18:17:56,085 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T01:17Z] INFO  18:17:56,088 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:17Z] INFO  18:17:56,195 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.12
[2016-04-15T01:17Z] INFO  18:17:56,223 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T01:17Z] GATK: HaplotypeCaller
[2016-04-15T01:17Z] INFO  18:17:56,593 IntervalUtils - Processing 125161 bp from intervals
[2016-04-15T01:17Z] WARN  18:17:56,598 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:17Z] INFO  18:17:56,665 ProgressMeter -      3:49053874      2.0579312E7    30.0 s            1.0 s       25.1%   119.0 s      89.0 s
[2016-04-15T01:17Z] INFO  18:17:56,690 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:17Z] INFO  18:17:56,785 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:17Z] INFO  18:17:56,787 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:17Z] INFO  18:17:56,787 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T01:17Z] INFO  18:17:56,788 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T01:17Z] INFO  18:17:56,789 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T01:17Z] INFO  18:17:56,789 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T01:17Z] INFO  18:17:56,982 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T01:17Z] INFO  18:17:57,539 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:17Z] GATK: HaplotypeCaller
[2016-04-15T01:17Z] INFO  18:17:57,880 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:17Z] INFO  18:17:57,884 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:17Z] INFO  18:17:57,884 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:17Z] INFO  18:17:57,885 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:17Z] INFO  18:17:57,889 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/3/R14-18102_kapa-NGv3-PE100-NGv3-sort-3_158970515_174577240-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/3/R14-18102_kapa-NGv3-PE100-NGv3-3_158970515_174577240-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/3/tx/tmpkKzNFh/R14-18102_kapa-NGv3-PE100-NGv3-3_158970515_174577240.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:17Z] INFO  18:17:57,926 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:17Z] INFO  18:17:57,935 HelpFormatter - Date/Time: 2016/04/14 18:17:57
[2016-04-15T01:17Z] INFO  18:17:57,935 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:17Z] INFO  18:17:57,935 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:17Z] WARN  18:17:58,003 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T01:17Z] WARN  18:17:58,005 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/3/tx/tmpkKzNFh/R14-18102_kapa-NGv3-PE100-NGv3-3_158970515_174577240.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T01:17Z] INFO  18:17:58,225 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:17Z] INFO  18:17:58,228 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:17Z] INFO  18:17:58,229 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:17Z] INFO  18:17:58,229 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:17Z] INFO  18:17:58,233 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/3/R14-18102_kapa-NGv3-PE100-NGv3-sort-3_174814579_190326970-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/3/R14-18102_kapa-NGv3-PE100-NGv3-3_174814579_190326970-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/3/tx/tmp_ojjJh/R14-18102_kapa-NGv3-PE100-NGv3-3_174814579_190326970.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:17Z] INFO  18:17:58,268 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:17Z] INFO  18:17:58,269 HelpFormatter - Date/Time: 2016/04/14 18:17:58
[2016-04-15T01:17Z] INFO  18:17:58,270 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:17Z] INFO  18:17:58,274 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:17Z] INFO  18:17:58,270 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:17Z] WARN  18:17:58,320 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T01:17Z] WARN  18:17:58,330 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/3/tx/tmp_ojjJh/R14-18102_kapa-NGv3-PE100-NGv3-3_174814579_190326970.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T01:17Z] INFO  18:17:58,454 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T01:17Z] INFO  18:17:58,464 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:17Z] INFO  18:17:58,550 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.09
[2016-04-15T01:17Z] INFO  18:17:58,577 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T01:17Z] INFO  18:17:58,579 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:17Z] INFO  18:17:58,782 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T01:17Z] INFO  18:17:58,792 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:17Z] INFO  18:17:58,888 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.10
[2016-04-15T01:17Z] INFO  18:17:58,919 IntervalUtils - Processing 102254 bp from intervals
[2016-04-15T01:17Z] WARN  18:17:58,924 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:17Z] INFO  18:17:58,926 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T01:17Z] INFO  18:17:59,085 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:17Z] INFO  18:17:59,118 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:17Z] INFO  18:17:59,131 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:17Z] INFO  18:17:59,132 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:17Z] INFO  18:17:59,133 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:17Z] INFO  18:17:59,137 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/3/R14-18102_kapa-NGv3-PE100-NGv3-sort-3_190333063_198022430-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/3/R14-18102_kapa-NGv3-PE100-NGv3-3_190333063_198022430-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/3/tx/tmpaROGrA/R14-18102_kapa-NGv3-PE100-NGv3-3_190333063_198022430.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:17Z] INFO  18:17:59,150 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:17Z] INFO  18:17:59,151 HelpFormatter - Date/Time: 2016/04/14 18:17:59
[2016-04-15T01:17Z] INFO  18:17:59,152 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:17Z] INFO  18:17:59,153 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:17Z] INFO  18:17:59,164 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:17Z] INFO  18:17:59,165 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:17Z] INFO  18:17:59,166 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T01:17Z] INFO  18:17:59,167 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T01:17Z] INFO  18:17:59,168 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T01:17Z] INFO  18:17:59,168 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T01:17Z] WARN  18:17:59,176 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T01:17Z] WARN  18:17:59,179 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/3/tx/tmpaROGrA/R14-18102_kapa-NGv3-PE100-NGv3-3_190333063_198022430.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T01:17Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T01:17Z] INFO  18:17:59,202 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T01:17Z] INFO  18:17:59,203 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T01:17Z] INFO  18:17:59,404 IntervalUtils - Processing 184739 bp from intervals
[2016-04-15T01:17Z] INFO  18:17:59,420 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T01:17Z] WARN  18:17:59,419 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:17Z] INFO  18:17:59,470 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:17Z] WARN  18:17:59,540 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T01:17Z] WARN  18:17:59,541 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T01:17Z] INFO  18:17:59,537 ProgressMeter -     3:108381055      3.3325723E7    30.0 s            0.0 s       76.5%    39.0 s       9.0 s
[2016-04-15T01:17Z] INFO  18:17:59,564 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:17Z] INFO  18:17:59,656 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T01:17Z] INFO  18:17:59,665 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:17Z] INFO  18:17:59,694 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:17Z] INFO  18:17:59,695 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:17Z] INFO  18:17:59,696 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T01:17Z] INFO  18:17:59,697 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T01:17Z] INFO  18:17:59,698 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T01:17Z] INFO  18:17:59,698 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T01:17Z] INFO  18:17:59,752 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-15T01:17Z] INFO  18:17:59,778 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T01:17Z] INFO  18:17:59,823 ProgressMeter -      3:77089246      1.4142952E7    30.0 s            2.0 s       93.9%    31.0 s       1.0 s
[2016-04-15T01:17Z] INFO  18:17:59,890 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T01:18Z] INFO  18:18:00,085 IntervalUtils - Processing 118955 bp from intervals
[2016-04-15T01:18Z] WARN  18:18:00,090 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:18Z] INFO  18:18:00,240 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:18Z] INFO  18:18:00,335 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:18Z] INFO  18:18:00,336 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:18Z] INFO  18:18:00,337 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T01:18Z] INFO  18:18:00,337 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T01:18Z] INFO  18:18:00,345 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T01:18Z] INFO  18:18:00,346 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T01:18Z] INFO  18:18:00,566 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T01:18Z] INFO  18:18:00,776 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.022837279000000002
[2016-04-15T01:18Z] INFO  18:18:00,787 PairHMM - Total compute time in PairHMM computeLikelihoods() : 11.569162442000001
[2016-04-15T01:18Z] INFO  18:18:00,789 HaplotypeCaller - Ran local assembly on 1273 active regions
[2016-04-15T01:18Z] INFO  18:18:00,844 ProgressMeter -            done      6.7478645E7    71.0 s            1.0 s      100.0%    71.0 s       0.0 s
[2016-04-15T01:18Z] INFO  18:18:00,844 ProgressMeter - Total runtime 71.87 secs, 1.20 min, 0.02 hours
[2016-04-15T01:18Z] INFO  18:18:00,845 MicroScheduler - 64508 reads were filtered out during the traversal out of approximately 292769 total reads (22.03%)
[2016-04-15T01:18Z] INFO  18:18:00,845 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:18Z] INFO  18:18:00,850 MicroScheduler -   -> 21155 reads (7.23% of total) failing DuplicateReadFilter
[2016-04-15T01:18Z] INFO  18:18:00,851 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:18Z] INFO  18:18:00,861 MicroScheduler -   -> 43353 reads (14.81% of total) failing HCMappingQualityFilter
[2016-04-15T01:18Z] INFO  18:18:00,862 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:18Z] INFO  18:18:00,862 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:18Z] INFO  18:18:00,862 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:18Z] INFO  18:18:00,863 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T01:18Z] INFO  18:18:00,954 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:18Z] INFO  18:18:00,957 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:18Z] INFO  18:18:00,958 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:18Z] INFO  18:18:00,959 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:18Z] INFO  18:18:00,967 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/4/R14-18102_kapa-NGv3-PE100-NGv3-sort-4_0_15511864-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/4/R14-18102_kapa-NGv3-PE100-NGv3-4_0_15511864-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/4/tx/tmpf9hEa3/R14-18102_kapa-NGv3-PE100-NGv3-4_0_15511864.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:18Z] INFO  18:18:00,979 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:18Z] INFO  18:18:00,980 HelpFormatter - Date/Time: 2016/04/14 18:18:00
[2016-04-15T01:18Z] INFO  18:18:00,980 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:18Z] INFO  18:18:00,981 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:18Z] WARN  18:18:01,026 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T01:18Z] INFO  18:18:01,026 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.013844480000000001
[2016-04-15T01:18Z] INFO  18:18:01,027 PairHMM - Total compute time in PairHMM computeLikelihoods() : 1.2135154750000001
[2016-04-15T01:18Z] INFO  18:18:01,028 HaplotypeCaller - Ran local assembly on 1439 active regions
[2016-04-15T01:18Z] WARN  18:18:01,033 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/4/tx/tmpf9hEa3/R14-18102_kapa-NGv3-PE100-NGv3-4_0_15511864.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T01:18Z] INFO  18:18:01,077 ProgressMeter -            done      9.2172487E7    53.0 s            0.0 s      100.0%    53.0 s       0.0 s
[2016-04-15T01:18Z] INFO  18:18:01,077 ProgressMeter - Total runtime 53.75 secs, 0.90 min, 0.01 hours
[2016-04-15T01:18Z] INFO  18:18:01,078 MicroScheduler - 27139 reads were filtered out during the traversal out of approximately 299036 total reads (9.08%)
[2016-04-15T01:18Z] INFO  18:18:01,078 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:18Z] INFO  18:18:01,078 MicroScheduler -   -> 24343 reads (8.14% of total) failing DuplicateReadFilter
[2016-04-15T01:18Z] INFO  18:18:01,079 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:18Z] INFO  18:18:01,079 MicroScheduler -   -> 2796 reads (0.94% of total) failing HCMappingQualityFilter
[2016-04-15T01:18Z] INFO  18:18:01,079 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:18Z] INFO  18:18:01,079 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:18Z] INFO  18:18:01,080 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:18Z] INFO  18:18:01,080 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T01:18Z] INFO  18:18:01,266 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.004969702
[2016-04-15T01:18Z] INFO  18:18:01,267 PairHMM - Total compute time in PairHMM computeLikelihoods() : 1.031686794
[2016-04-15T01:18Z] INFO  18:18:01,267 HaplotypeCaller - Ran local assembly on 587 active regions
[2016-04-15T01:18Z] INFO  18:18:01,289 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:18Z] INFO  18:18:01,328 ProgressMeter -            done      1.6464959E7    31.0 s            1.0 s      100.0%    31.0 s       0.0 s
[2016-04-15T01:18Z] INFO  18:18:01,329 ProgressMeter - Total runtime 31.52 secs, 0.53 min, 0.01 hours
[2016-04-15T01:18Z] INFO  18:18:01,330 MicroScheduler - 11638 reads were filtered out during the traversal out of approximately 109242 total reads (10.65%)
[2016-04-15T01:18Z] INFO  18:18:01,331 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:18Z] INFO  18:18:01,331 MicroScheduler -   -> 8363 reads (7.66% of total) failing DuplicateReadFilter
[2016-04-15T01:18Z] INFO  18:18:01,332 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:18Z] INFO  18:18:01,333 MicroScheduler -   -> 3275 reads (3.00% of total) failing HCMappingQualityFilter
[2016-04-15T01:18Z] INFO  18:18:01,333 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:18Z] INFO  18:18:01,334 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:18Z] INFO  18:18:01,334 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:18Z] INFO  18:18:01,335 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T01:18Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T01:18Z] INFO  18:18:01,507 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T01:18Z] INFO  18:18:01,508 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T01:18Z] INFO  18:18:01,537 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T01:18Z] INFO  18:18:01,546 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:18Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T01:18Z] INFO  18:18:01,584 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T01:18Z] INFO  18:18:01,585 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T01:18Z] INFO  18:18:01,621 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-15T01:18Z] INFO  18:18:01,644 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T01:18Z] WARN  18:18:01,762 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T01:18Z] WARN  18:18:01,763 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T01:18Z] WARN  18:18:01,920 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T01:18Z] WARN  18:18:01,931 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T01:18Z] INFO  18:18:02,179 IntervalUtils - Processing 255565 bp from intervals
[2016-04-15T01:18Z] WARN  18:18:02,184 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:18Z] INFO  18:18:02,282 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:18Z] INFO  18:18:02,377 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:18Z] INFO  18:18:02,537 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:18Z] INFO  18:18:02,538 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:18Z] INFO  18:18:02,539 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T01:18Z] INFO  18:18:02,540 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T01:18Z] INFO  18:18:02,540 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T01:18Z] INFO  18:18:02,541 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T01:18Z] INFO  18:18:02,606 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:18Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T01:18Z] INFO  18:18:02,698 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T01:18Z] INFO  18:18:02,699 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T01:18Z] GATK: HaplotypeCaller
[2016-04-15T01:18Z] INFO  18:18:02,739 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T01:18Z] INFO  18:18:02,827 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:18Z] WARN  18:18:02,962 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T01:18Z] WARN  18:18:02,963 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T01:18Z] GATK: HaplotypeCaller
[2016-04-15T01:18Z] GATK: HaplotypeCaller
[2016-04-15T01:18Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T01:18Z] INFO  18:18:03,228 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T01:18Z] INFO  18:18:03,229 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T01:18Z] WARN  18:18:03,625 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T01:18Z] WARN  18:18:03,636 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T01:18Z] INFO  18:18:05,847 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.006713552
[2016-04-15T01:18Z] INFO  18:18:05,858 PairHMM - Total compute time in PairHMM computeLikelihoods() : 0.39959329200000004
[2016-04-15T01:18Z] INFO  18:18:05,859 HaplotypeCaller - Ran local assembly on 1048 active regions
[2016-04-15T01:18Z] INFO  18:18:05,883 ProgressMeter -     2:220412438     1.26360356E8    60.0 s            0.0 s       93.5%    64.0 s       4.0 s
[2016-04-15T01:18Z] INFO  18:18:05,916 ProgressMeter -            done      5.7451533E7    36.0 s            0.0 s      100.0%    36.0 s       0.0 s
[2016-04-15T01:18Z] INFO  18:18:05,916 ProgressMeter - Total runtime 36.41 secs, 0.61 min, 0.01 hours
[2016-04-15T01:18Z] INFO  18:18:05,917 MicroScheduler - 13306 reads were filtered out during the traversal out of approximately 162459 total reads (8.19%)
[2016-04-15T01:18Z] INFO  18:18:05,918 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:18Z] INFO  18:18:05,918 MicroScheduler -   -> 12513 reads (7.70% of total) failing DuplicateReadFilter
[2016-04-15T01:18Z] INFO  18:18:05,918 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:18Z] INFO  18:18:05,918 MicroScheduler -   -> 793 reads (0.49% of total) failing HCMappingQualityFilter
[2016-04-15T01:18Z] INFO  18:18:05,919 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:18Z] INFO  18:18:05,919 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:18Z] INFO  18:18:05,919 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:18Z] INFO  18:18:05,919 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T01:18Z] INFO  18:18:06,380 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:18Z] INFO  18:18:06,383 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:18Z] INFO  18:18:06,384 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:18Z] INFO  18:18:06,384 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:18Z] INFO  18:18:06,388 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/4/R14-18102_kapa-NGv3-PE100-NGv3-sort-4_15512869_31144471-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/4/R14-18102_kapa-NGv3-PE100-NGv3-4_15512869_31144471-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/4/tx/tmpsfIhqN/R14-18102_kapa-NGv3-PE100-NGv3-4_15512869_31144471.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:18Z] INFO  18:18:06,418 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:18Z] INFO  18:18:06,419 HelpFormatter - Date/Time: 2016/04/14 18:18:06
[2016-04-15T01:18Z] INFO  18:18:06,420 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:18Z] INFO  18:18:06,420 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:18Z] WARN  18:18:06,463 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T01:18Z] WARN  18:18:06,476 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/4/tx/tmpsfIhqN/R14-18102_kapa-NGv3-PE100-NGv3-4_15512869_31144471.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T01:18Z] INFO  18:18:06,656 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:18Z] INFO  18:18:06,793 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:18Z] INFO  18:18:06,796 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:18Z] INFO  18:18:06,797 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:18Z] INFO  18:18:06,797 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:18Z] INFO  18:18:06,802 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/4/R14-18102_kapa-NGv3-PE100-NGv3-sort-4_36069528_52709433-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/4/R14-18102_kapa-NGv3-PE100-NGv3-4_36069528_52709433-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/4/tx/tmp7VSBXn/R14-18102_kapa-NGv3-PE100-NGv3-4_36069528_52709433.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:18Z] INFO  18:18:06,842 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:18Z] INFO  18:18:06,842 HelpFormatter - Date/Time: 2016/04/14 18:18:06
[2016-04-15T01:18Z] INFO  18:18:06,843 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:18Z] INFO  18:18:06,843 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:18Z] WARN  18:18:06,898 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T01:18Z] WARN  18:18:06,912 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/4/tx/tmp7VSBXn/R14-18102_kapa-NGv3-PE100-NGv3-4_36069528_52709433.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T01:18Z] INFO  18:18:06,945 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T01:18Z] INFO  18:18:06,954 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:18Z] INFO  18:18:06,966 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:18Z] INFO  18:18:06,969 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:18Z] INFO  18:18:06,970 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:18Z] INFO  18:18:06,970 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:18Z] INFO  18:18:06,981 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/4/R14-18102_kapa-NGv3-PE100-NGv3-sort-4_52709749_68338393-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/4/R14-18102_kapa-NGv3-PE100-NGv3-4_52709749_68338393-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/4/tx/tmpL4uyFv/R14-18102_kapa-NGv3-PE100-NGv3-4_52709749_68338393.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:18Z] INFO  18:18:07,003 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:18Z] INFO  18:18:07,004 HelpFormatter - Date/Time: 2016/04/14 18:18:06
[2016-04-15T01:18Z] INFO  18:18:07,005 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:18Z] INFO  18:18:07,005 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:18Z] WARN  18:18:07,038 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T01:18Z] WARN  18:18:07,041 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/4/tx/tmpL4uyFv/R14-18102_kapa-NGv3-PE100-NGv3-4_52709749_68338393.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T01:18Z] INFO  18:18:07,058 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.10
[2016-04-15T01:18Z] INFO  18:18:07,082 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T01:18Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T01:18Z] INFO  18:18:07,094 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T01:18Z] INFO  18:18:07,095 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T01:18Z] INFO  18:18:07,101 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:18Z] INFO  18:18:07,300 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:18Z] INFO  18:18:07,351 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T01:18Z] INFO  18:18:07,364 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:18Z] INFO  18:18:07,418 IntervalUtils - Processing 90668 bp from intervals
[2016-04-15T01:18Z] WARN  18:18:07,423 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:18Z] INFO  18:18:07,446 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-15T01:18Z] INFO  18:18:07,477 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T01:18Z] INFO  18:18:07,512 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T01:18Z] INFO  18:18:07,521 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:18Z] INFO  18:18:07,527 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:18Z] INFO  18:18:07,554 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:18Z] INFO  18:18:07,611 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-15T01:18Z] INFO  18:18:07,628 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T01:18Z] INFO  18:18:07,648 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:18Z] INFO  18:18:07,649 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:18Z] INFO  18:18:07,650 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T01:18Z] INFO  18:18:07,650 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T01:18Z] WARN  18:18:07,654 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T01:18Z] WARN  18:18:07,655 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T01:18Z] INFO  18:18:07,666 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T01:18Z] INFO  18:18:07,667 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T01:18Z] GATK: HaplotypeCaller
[2016-04-15T01:18Z] INFO  18:18:07,909 IntervalUtils - Processing 142047 bp from intervals
[2016-04-15T01:18Z] WARN  18:18:07,915 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:18Z] INFO  18:18:07,953 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T01:18Z] INFO  18:18:08,055 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.038007650000000004
[2016-04-15T01:18Z] INFO  18:18:08,067 PairHMM - Total compute time in PairHMM computeLikelihoods() : 0.8047101080000001
[2016-04-15T01:18Z] INFO  18:18:08,068 HaplotypeCaller - Ran local assembly on 1423 active regions
[2016-04-15T01:18Z] INFO  18:18:08,088 IntervalUtils - Processing 83782 bp from intervals
[2016-04-15T01:18Z] WARN  18:18:08,110 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:18Z] INFO  18:18:08,115 ProgressMeter -            done      9.3035935E7    54.0 s            0.0 s      100.0%    54.0 s       0.0 s
[2016-04-15T01:18Z] INFO  18:18:08,115 ProgressMeter - Total runtime 54.94 secs, 0.92 min, 0.02 hours
[2016-04-15T01:18Z] INFO  18:18:08,120 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:18Z] INFO  18:18:08,116 MicroScheduler - 25791 reads were filtered out during the traversal out of approximately 306669 total reads (8.41%)
[2016-04-15T01:18Z] INFO  18:18:08,116 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:18Z] INFO  18:18:08,117 MicroScheduler -   -> 25248 reads (8.23% of total) failing DuplicateReadFilter
[2016-04-15T01:18Z] INFO  18:18:08,117 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:18Z] INFO  18:18:08,117 MicroScheduler -   -> 543 reads (0.18% of total) failing HCMappingQualityFilter
[2016-04-15T01:18Z] INFO  18:18:08,117 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:18Z] INFO  18:18:08,118 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:18Z] INFO  18:18:08,118 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:18Z] INFO  18:18:08,118 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T01:18Z] INFO  18:18:08,231 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:18Z] INFO  18:18:08,232 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:18Z] INFO  18:18:08,233 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T01:18Z] INFO  18:18:08,233 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T01:18Z] INFO  18:18:08,240 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:18Z] INFO  18:18:08,243 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T01:18Z] INFO  18:18:08,244 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T01:18Z] INFO  18:18:08,346 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:18Z] INFO  18:18:08,346 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:18Z] INFO  18:18:08,347 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T01:18Z] INFO  18:18:08,348 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T01:18Z] INFO  18:18:08,352 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T01:18Z] INFO  18:18:08,353 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T01:18Z] INFO  18:18:08,473 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T01:18Z] INFO  18:18:08,558 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T01:18Z] INFO  18:18:09,411 ProgressMeter -     1:155156305     2.12887667E8     2.5 m            0.0 s       63.9%     3.9 m      84.0 s
[2016-04-15T01:18Z] INFO  18:18:09,528 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:18Z] GATK: HaplotypeCaller
[2016-04-15T01:18Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T01:18Z] INFO  18:18:09,952 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T01:18Z] INFO  18:18:09,952 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T01:18Z] WARN  18:18:10,503 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T01:18Z] WARN  18:18:10,504 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T01:18Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T01:18Z] INFO  18:18:11,166 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T01:18Z] INFO  18:18:11,172 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T01:18Z] WARN  18:18:11,538 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T01:18Z] WARN  18:18:11,539 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T01:18Z] INFO  18:18:11,692 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.016103059
[2016-04-15T01:18Z] INFO  18:18:11,693 PairHMM - Total compute time in PairHMM computeLikelihoods() : 1.0221705
[2016-04-15T01:18Z] INFO  18:18:11,694 HaplotypeCaller - Ran local assembly on 1854 active regions
[2016-04-15T01:18Z] INFO  18:18:11,749 ProgressMeter -            done     1.39336955E8    65.0 s            0.0 s      100.0%    65.0 s       0.0 s
[2016-04-15T01:18Z] INFO  18:18:11,750 ProgressMeter - Total runtime 65.89 secs, 1.10 min, 0.02 hours
[2016-04-15T01:18Z] INFO  18:18:11,751 MicroScheduler - 31687 reads were filtered out during the traversal out of approximately 390836 total reads (8.11%)
[2016-04-15T01:18Z] INFO  18:18:11,751 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:18Z] INFO  18:18:11,752 MicroScheduler -   -> 31174 reads (7.98% of total) failing DuplicateReadFilter
[2016-04-15T01:18Z] INFO  18:18:11,752 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:18Z] INFO  18:18:11,753 MicroScheduler -   -> 513 reads (0.13% of total) failing HCMappingQualityFilter
[2016-04-15T01:18Z] INFO  18:18:11,754 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:18Z] INFO  18:18:11,754 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:18Z] INFO  18:18:11,755 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:18Z] INFO  18:18:11,755 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T01:18Z] INFO  18:18:11,829 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:18Z] INFO  18:18:11,832 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:18Z] INFO  18:18:11,833 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:18Z] INFO  18:18:11,834 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:18Z] INFO  18:18:11,838 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/4/R14-18102_kapa-NGv3-PE100-NGv3-sort-4_68340604_83852298-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/4/R14-18102_kapa-NGv3-PE100-NGv3-4_68340604_83852298-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/4/tx/tmpzGnn79/R14-18102_kapa-NGv3-PE100-NGv3-4_68340604_83852298.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:18Z] INFO  18:18:11,874 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:18Z] INFO  18:18:11,878 HelpFormatter - Date/Time: 2016/04/14 18:18:11
[2016-04-15T01:18Z] INFO  18:18:11,879 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:18Z] INFO  18:18:11,880 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:18Z] WARN  18:18:11,924 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T01:18Z] WARN  18:18:11,928 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/4/tx/tmpzGnn79/R14-18102_kapa-NGv3-PE100-NGv3-4_68340604_83852298.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T01:18Z] INFO  18:18:12,211 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:18Z] INFO  18:18:12,473 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T01:18Z] INFO  18:18:12,485 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:18Z] INFO  18:18:12,573 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.09
[2016-04-15T01:18Z] INFO  18:18:12,612 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T01:18Z] INFO  18:18:13,255 IntervalUtils - Processing 197466 bp from intervals
[2016-04-15T01:18Z] WARN  18:18:13,260 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:18Z] INFO  18:18:13,373 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:18Z] INFO  18:18:13,376 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:18Z] INFO  18:18:13,376 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:18Z] INFO  18:18:13,377 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:18Z] INFO  18:18:13,377 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:18Z] INFO  18:18:13,381 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/4/R14-18102_kapa-NGv3-PE100-NGv3-sort-4_83857133_99393738-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/4/R14-18102_kapa-NGv3-PE100-NGv3-4_83857133_99393738-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/4/tx/tmp9g_n3s/R14-18102_kapa-NGv3-PE100-NGv3-4_83857133_99393738.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:18Z] INFO  18:18:13,408 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:18Z] INFO  18:18:13,408 HelpFormatter - Date/Time: 2016/04/14 18:18:13
[2016-04-15T01:18Z] INFO  18:18:13,408 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:18Z] INFO  18:18:13,408 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:18Z] WARN  18:18:13,452 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T01:18Z] WARN  18:18:13,459 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/4/tx/tmp9g_n3s/R14-18102_kapa-NGv3-PE100-NGv3-4_83857133_99393738.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T01:18Z] INFO  18:18:13,514 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:18Z] INFO  18:18:13,515 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:18Z] INFO  18:18:13,516 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T01:18Z] INFO  18:18:13,516 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T01:18Z] INFO  18:18:13,526 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T01:18Z] INFO  18:18:13,527 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T01:18Z] INFO  18:18:13,568 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:18Z] INFO  18:18:13,659 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:18Z] INFO  18:18:13,795 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T01:18Z] INFO  18:18:13,864 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T01:18Z] INFO  18:18:13,883 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:18Z] GATK: HaplotypeCaller
[2016-04-15T01:18Z] INFO  18:18:13,972 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.09
[2016-04-15T01:18Z] INFO  18:18:14,033 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T01:18Z] INFO  18:18:14,518 IntervalUtils - Processing 124091 bp from intervals
[2016-04-15T01:18Z] WARN  18:18:14,536 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:18Z] INFO  18:18:14,678 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:18Z] INFO  18:18:14,795 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:18Z] INFO  18:18:14,796 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:18Z] INFO  18:18:14,799 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T01:18Z] INFO  18:18:14,800 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T01:18Z] INFO  18:18:14,800 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T01:18Z] INFO  18:18:14,801 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T01:18Z] INFO  18:18:14,970 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T01:18Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T01:18Z] INFO  18:18:15,659 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T01:18Z] INFO  18:18:15,660 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T01:18Z] WARN  18:18:15,954 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T01:18Z] WARN  18:18:15,955 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T01:18Z] INFO  18:18:17,583 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:18Z] INFO  18:18:17,586 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:18Z] INFO  18:18:17,587 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:18Z] INFO  18:18:17,587 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:18Z] INFO  18:18:17,592 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/4/R14-18102_kapa-NGv3-PE100-NGv3-sort-4_99397339_115544957-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/4/R14-18102_kapa-NGv3-PE100-NGv3-4_99397339_115544957-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/4/tx/tmpcwlsic/R14-18102_kapa-NGv3-PE100-NGv3-4_99397339_115544957.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:18Z] INFO  18:18:17,610 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:18Z] INFO  18:18:17,611 HelpFormatter - Date/Time: 2016/04/14 18:18:17
[2016-04-15T01:18Z] INFO  18:18:17,611 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:18Z] INFO  18:18:17,612 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:18Z] WARN  18:18:17,647 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T01:18Z] WARN  18:18:17,650 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/4/tx/tmpcwlsic/R14-18102_kapa-NGv3-PE100-NGv3-4_99397339_115544957.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T01:18Z] INFO  18:18:17,999 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:18Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T01:18Z] INFO  18:18:18,132 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T01:18Z] INFO  18:18:18,133 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T01:18Z] INFO  18:18:18,234 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T01:18Z] INFO  18:18:18,244 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:18Z] INFO  18:18:18,332 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.09
[2016-04-15T01:18Z] INFO  18:18:18,362 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T01:18Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T01:18Z] WARN  18:18:18,444 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T01:18Z] WARN  18:18:18,445 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T01:18Z] INFO  18:18:18,453 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T01:18Z] INFO  18:18:18,454 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T01:18Z] WARN  18:18:18,684 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T01:18Z] WARN  18:18:18,685 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T01:18Z] INFO  18:18:18,936 IntervalUtils - Processing 153852 bp from intervals
[2016-04-15T01:18Z] WARN  18:18:18,997 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:18Z] INFO  18:18:19,133 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:18Z] INFO  18:18:19,265 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:18Z] INFO  18:18:19,266 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:18Z] INFO  18:18:19,266 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T01:18Z] INFO  18:18:19,266 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T01:18Z] INFO  18:18:19,282 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T01:18Z] INFO  18:18:19,283 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T01:18Z] INFO  18:18:19,606 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T01:18Z] INFO  18:18:23,824 ProgressMeter -     3:119904146      1.6035883E7    30.0 s            1.0 s       33.1%    90.0 s      60.0 s
[2016-04-15T01:18Z] INFO  18:18:24,577 ProgressMeter -      3:44496665      9.4592077E7    60.0 s            0.0 s       71.5%    83.0 s      23.0 s
[2016-04-15T01:18Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T01:18Z] INFO  18:18:24,832 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T01:18Z] INFO  18:18:24,835 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T01:18Z] WARN  18:18:25,387 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T01:18Z] WARN  18:18:25,388 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T01:18Z] INFO  18:18:25,450 ProgressMeter -     3:132203432      1.8903194E7    30.0 s            1.0 s       35.6%    84.0 s      54.0 s
[2016-04-15T01:18Z] INFO  18:18:26,678 ProgressMeter -      3:51978794     1.10487906E8    60.0 s            0.0 s       57.1%   105.0 s      45.0 s
[2016-04-15T01:18Z] INFO  18:18:26,804 ProgressMeter -     3:154886578      1.5196272E7    30.0 s            1.0 s       68.1%    44.0 s      14.0 s
[2016-04-15T01:18Z] INFO  18:18:29,182 ProgressMeter -     3:172353706      2.3628766E7    30.0 s            1.0 s       91.7%    32.0 s       2.0 s
[2016-04-15T01:18Z] INFO  18:18:29,703 ProgressMeter -     3:183904295      1.7474341E7    30.0 s            1.0 s       45.7%    65.0 s      35.0 s
[2016-04-15T01:18Z] INFO  18:18:30,348 ProgressMeter -     3:195506754        7445396.0    30.0 s            4.0 s       46.4%    64.0 s      34.0 s
[2016-04-15T01:18Z] INFO  18:18:31,061 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.0056359190000000005
[2016-04-15T01:18Z] INFO  18:18:31,062 PairHMM - Total compute time in PairHMM computeLikelihoods() : 0.24342238300000002
[2016-04-15T01:18Z] INFO  18:18:31,063 HaplotypeCaller - Ran local assembly on 738 active regions
[2016-04-15T01:18Z] INFO  18:18:31,117 ProgressMeter -            done      2.7921091E7    31.0 s            1.0 s      100.0%    31.0 s       0.0 s
[2016-04-15T01:18Z] INFO  18:18:31,118 ProgressMeter - Total runtime 31.95 secs, 0.53 min, 0.01 hours
[2016-04-15T01:18Z] INFO  18:18:31,118 MicroScheduler - 9663 reads were filtered out during the traversal out of approximately 120914 total reads (7.99%)
[2016-04-15T01:18Z] INFO  18:18:31,118 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:18Z] INFO  18:18:31,119 MicroScheduler -   -> 9536 reads (7.89% of total) failing DuplicateReadFilter
[2016-04-15T01:18Z] INFO  18:18:31,119 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:18Z] INFO  18:18:31,119 MicroScheduler -   -> 127 reads (0.11% of total) failing HCMappingQualityFilter
[2016-04-15T01:18Z] INFO  18:18:31,119 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:18Z] INFO  18:18:31,120 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:18Z] INFO  18:18:31,120 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:18Z] INFO  18:18:31,120 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T01:18Z] INFO  18:18:32,586 ProgressMeter -       4:1388694        5377855.0    30.0 s            5.0 s       21.6%     2.3 m     108.0 s
[2016-04-15T01:18Z] INFO  18:18:32,799 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:18Z] GATK: HaplotypeCaller
[2016-04-15T01:18Z] INFO  18:18:34,584 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.007942626000000001
[2016-04-15T01:18Z] INFO  18:18:34,584 PairHMM - Total compute time in PairHMM computeLikelihoods() : 0.338079638
[2016-04-15T01:18Z] INFO  18:18:34,585 HaplotypeCaller - Ran local assembly on 882 active regions
[2016-04-15T01:18Z] INFO  18:18:34,648 ProgressMeter -            done      3.5894583E7    37.0 s            1.0 s      100.0%    37.0 s       0.0 s
[2016-04-15T01:18Z] INFO  18:18:34,648 ProgressMeter - Total runtime 37.86 secs, 0.63 min, 0.01 hours
[2016-04-15T01:18Z] INFO  18:18:34,649 MicroScheduler - 12700 reads were filtered out during the traversal out of approximately 150561 total reads (8.44%)
[2016-04-15T01:18Z] INFO  18:18:34,649 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:18Z] INFO  18:18:34,649 MicroScheduler -   -> 12021 reads (7.98% of total) failing DuplicateReadFilter
[2016-04-15T01:18Z] INFO  18:18:34,650 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:18Z] INFO  18:18:34,650 MicroScheduler -   -> 679 reads (0.45% of total) failing HCMappingQualityFilter
[2016-04-15T01:18Z] INFO  18:18:34,650 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:18Z] INFO  18:18:34,650 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:18Z] INFO  18:18:34,651 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:18Z] INFO  18:18:34,651 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T01:18Z] INFO  18:18:35,912 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:18Z] INFO  18:18:35,916 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:18Z] INFO  18:18:35,916 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:18Z] INFO  18:18:35,917 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:18Z] INFO  18:18:35,921 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/4/R14-18102_kapa-NGv3-PE100-NGv3-sort-4_115584857_134074404-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/4/R14-18102_kapa-NGv3-PE100-NGv3-4_115584857_134074404-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/4/tx/tmpLzrxGf/R14-18102_kapa-NGv3-PE100-NGv3-4_115584857_134074404.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:18Z] INFO  18:18:35,932 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:18Z] INFO  18:18:35,940 HelpFormatter - Date/Time: 2016/04/14 18:18:35
[2016-04-15T01:18Z] INFO  18:18:35,941 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:18Z] INFO  18:18:35,941 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:18Z] WARN  18:18:35,970 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T01:18Z] WARN  18:18:35,973 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/4/tx/tmpLzrxGf/R14-18102_kapa-NGv3-PE100-NGv3-4_115584857_134074404.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T01:18Z] INFO  18:18:36,138 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:18Z] INFO  18:18:36,181 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:18Z] INFO  18:18:36,316 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T01:18Z] INFO  18:18:36,326 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:18Z] GATK: HaplotypeCaller
[2016-04-15T01:18Z] INFO  18:18:36,399 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-15T01:18Z] INFO  18:18:36,414 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T01:18Z] INFO  18:18:36,813 IntervalUtils - Processing 157938 bp from intervals
[2016-04-15T01:18Z] WARN  18:18:36,818 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:18Z] INFO  18:18:36,919 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:18Z] INFO  18:18:37,027 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:18Z] INFO  18:18:37,028 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:18Z] INFO  18:18:37,029 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T01:18Z] INFO  18:18:37,029 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T01:18Z] INFO  18:18:37,040 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T01:18Z] INFO  18:18:37,041 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T01:18Z] INFO  18:18:37,188 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.00598046
[2016-04-15T01:18Z] INFO  18:18:37,189 PairHMM - Total compute time in PairHMM computeLikelihoods() : 0.314447122
[2016-04-15T01:18Z] INFO  18:18:37,190 HaplotypeCaller - Ran local assembly on 671 active regions
[2016-04-15T01:18Z] INFO  18:18:37,217 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T01:18Z] INFO  18:18:37,255 ProgressMeter -            done      2.0932049E7    29.0 s            1.0 s      100.0%    29.0 s       0.0 s
[2016-04-15T01:18Z] INFO  18:18:37,255 ProgressMeter - Total runtime 29.61 secs, 0.49 min, 0.01 hours
[2016-04-15T01:18Z] INFO  18:18:37,255 MicroScheduler - 8865 reads were filtered out during the traversal out of approximately 110041 total reads (8.06%)
[2016-04-15T01:18Z] INFO  18:18:37,256 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:18Z] INFO  18:18:37,256 MicroScheduler -   -> 8724 reads (7.93% of total) failing DuplicateReadFilter
[2016-04-15T01:18Z] INFO  18:18:37,256 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:18Z] INFO  18:18:37,256 MicroScheduler -   -> 141 reads (0.13% of total) failing HCMappingQualityFilter
[2016-04-15T01:18Z] INFO  18:18:37,257 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:18Z] INFO  18:18:37,257 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:18Z] INFO  18:18:37,257 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:18Z] INFO  18:18:37,257 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T01:18Z] INFO  18:18:38,250 ProgressMeter -      4:43032557      2.1702587E7    30.0 s            1.0 s       63.1%    47.0 s      17.0 s
[2016-04-15T01:18Z] INFO  18:18:38,411 ProgressMeter -      4:66197069      1.6616459E7    30.0 s            1.0 s       95.5%    31.0 s       1.0 s
[2016-04-15T01:18Z] INFO  18:18:38,794 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:18Z] GATK: HaplotypeCaller
[2016-04-15T01:18Z] INFO  18:18:39,089 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:18Z] INFO  18:18:39,093 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:18Z] INFO  18:18:39,093 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:18Z] INFO  18:18:39,094 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:18Z] INFO  18:18:39,099 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/4/R14-18102_kapa-NGv3-PE100-NGv3-sort-4_134075461_150351181-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/4/R14-18102_kapa-NGv3-PE100-NGv3-4_134075461_150351181-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/4/tx/tmpB_2JtX/R14-18102_kapa-NGv3-PE100-NGv3-4_134075461_150351181.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:18Z] INFO  18:18:39,122 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:18Z] INFO  18:18:39,123 HelpFormatter - Date/Time: 2016/04/14 18:18:39
[2016-04-15T01:18Z] INFO  18:18:39,124 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:18Z] INFO  18:18:39,129 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:18Z] WARN  18:18:39,175 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T01:18Z] WARN  18:18:39,187 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/4/tx/tmpB_2JtX/R14-18102_kapa-NGv3-PE100-NGv3-4_134075461_150351181.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T01:18Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T01:18Z] INFO  18:18:39,229 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T01:18Z] INFO  18:18:39,229 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T01:18Z] INFO  18:18:39,353 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:18Z] WARN  18:18:39,392 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T01:18Z] WARN  18:18:39,392 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T01:18Z] INFO  18:18:39,412 ProgressMeter -     1:158045925     4.61288416E8     3.0 m            0.0 s       92.4%     3.2 m      14.0 s
[2016-04-15T01:18Z] INFO  18:18:39,549 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.005735715000000001
[2016-04-15T01:18Z] INFO  18:18:39,550 PairHMM - Total compute time in PairHMM computeLikelihoods() : 0.44979471200000004
[2016-04-15T01:18Z] INFO  18:18:39,550 HaplotypeCaller - Ran local assembly on 631 active regions
[2016-04-15T01:18Z] INFO  18:18:39,598 ProgressMeter -            done      1.8095278E7    31.0 s            1.0 s      100.0%    31.0 s       0.0 s
[2016-04-15T01:18Z] INFO  18:18:39,598 ProgressMeter - Total runtime 31.25 secs, 0.52 min, 0.01 hours
[2016-04-15T01:18Z] INFO  18:18:39,598 MicroScheduler - 8648 reads were filtered out during the traversal out of approximately 104890 total reads (8.24%)
[2016-04-15T01:18Z] INFO  18:18:39,599 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:18Z] INFO  18:18:39,599 MicroScheduler -   -> 8494 reads (8.10% of total) failing DuplicateReadFilter
[2016-04-15T01:18Z] INFO  18:18:39,599 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:18Z] INFO  18:18:39,599 MicroScheduler -   -> 154 reads (0.15% of total) failing HCMappingQualityFilter
[2016-04-15T01:18Z] INFO  18:18:39,600 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:18Z] INFO  18:18:39,600 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:18Z] INFO  18:18:39,600 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:18Z] INFO  18:18:39,600 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T01:18Z] INFO  18:18:39,616 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T01:18Z] INFO  18:18:39,626 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:18Z] INFO  18:18:39,693 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-15T01:18Z] INFO  18:18:39,714 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T01:18Z] INFO  18:18:40,013 IntervalUtils - Processing 86890 bp from intervals
[2016-04-15T01:18Z] WARN  18:18:40,017 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:18Z] INFO  18:18:40,144 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:18Z] INFO  18:18:40,238 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:18Z] INFO  18:18:40,251 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:18Z] INFO  18:18:40,252 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T01:18Z] INFO  18:18:40,253 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T01:18Z] INFO  18:18:40,253 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T01:18Z] INFO  18:18:40,254 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T01:18Z] INFO  18:18:40,427 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T01:18Z] INFO  18:18:41,101 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:18Z] GATK: HaplotypeCaller
[2016-04-15T01:18Z] INFO  18:18:41,891 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:18Z] INFO  18:18:41,895 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:18Z] INFO  18:18:41,895 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:18Z] INFO  18:18:41,896 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:18Z] INFO  18:18:41,900 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/4/R14-18102_kapa-NGv3-PE100-NGv3-sort-4_150354547_165878648-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/4/R14-18102_kapa-NGv3-PE100-NGv3-4_150354547_165878648-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/4/tx/tmp3b8mjS/R14-18102_kapa-NGv3-PE100-NGv3-4_150354547_165878648.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:18Z] INFO  18:18:41,916 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:18Z] INFO  18:18:41,917 HelpFormatter - Date/Time: 2016/04/14 18:18:41
[2016-04-15T01:18Z] INFO  18:18:41,918 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:18Z] INFO  18:18:41,919 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:18Z] WARN  18:18:41,965 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T01:18Z] WARN  18:18:41,980 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/4/tx/tmp3b8mjS/R14-18102_kapa-NGv3-PE100-NGv3-4_150354547_165878648.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T01:18Z] INFO  18:18:42,178 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:18Z] INFO  18:18:42,408 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T01:18Z] INFO  18:18:42,429 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:18Z] INFO  18:18:42,517 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.09
[2016-04-15T01:18Z] INFO  18:18:42,546 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T01:18Z] INFO  18:18:42,903 IntervalUtils - Processing 119752 bp from intervals
[2016-04-15T01:18Z] WARN  18:18:42,909 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:18Z] INFO  18:18:42,993 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:18Z] INFO  18:18:43,080 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:18Z] INFO  18:18:43,082 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:18Z] INFO  18:18:43,082 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T01:18Z] INFO  18:18:43,083 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T01:18Z] INFO  18:18:43,084 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T01:18Z] INFO  18:18:43,084 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T01:18Z] INFO  18:18:43,208 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.029717097
[2016-04-15T01:18Z] INFO  18:18:43,209 PairHMM - Total compute time in PairHMM computeLikelihoods() : 2.126816096
[2016-04-15T01:18Z] INFO  18:18:43,210 HaplotypeCaller - Ran local assembly on 2146 active regions
[2016-04-15T01:18Z] INFO  18:18:43,275 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T01:18Z] INFO  18:18:43,359 ProgressMeter -            done     1.83827552E8    78.0 s            0.0 s      100.0%    78.0 s       0.0 s
[2016-04-15T01:18Z] INFO  18:18:43,360 ProgressMeter - Total runtime 78.81 secs, 1.31 min, 0.02 hours
[2016-04-15T01:18Z] INFO  18:18:43,360 MicroScheduler - 37918 reads were filtered out during the traversal out of approximately 452783 total reads (8.37%)
[2016-04-15T01:18Z] INFO  18:18:43,360 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:18Z] INFO  18:18:43,360 MicroScheduler -   -> 36478 reads (8.06% of total) failing DuplicateReadFilter
[2016-04-15T01:18Z] INFO  18:18:43,361 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:18Z] INFO  18:18:43,361 MicroScheduler -   -> 1440 reads (0.32% of total) failing HCMappingQualityFilter
[2016-04-15T01:18Z] INFO  18:18:43,361 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:18Z] INFO  18:18:43,361 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:18Z] INFO  18:18:43,362 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:18Z] INFO  18:18:43,362 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T01:18Z] INFO  18:18:43,535 ProgressMeter -      4:76453512      2.7968686E7    30.0 s            1.0 s       50.8%    59.0 s      29.0 s
[2016-04-15T01:18Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T01:18Z] INFO  18:18:43,662 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T01:18Z] INFO  18:18:43,663 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T01:18Z] WARN  18:18:43,964 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T01:18Z] WARN  18:18:43,965 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T01:18Z] INFO  18:18:44,303 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:18Z] INFO  18:18:44,322 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:18Z] INFO  18:18:44,323 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:18Z] INFO  18:18:44,324 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:18Z] INFO  18:18:44,328 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/4/R14-18102_kapa-NGv3-PE100-NGv3-sort-4_165889318_183245405-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/4/R14-18102_kapa-NGv3-PE100-NGv3-4_165889318_183245405-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/4/tx/tmpcKiOO_/R14-18102_kapa-NGv3-PE100-NGv3-4_165889318_183245405.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:18Z] INFO  18:18:44,356 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:18Z] INFO  18:18:44,356 HelpFormatter - Date/Time: 2016/04/14 18:18:44
[2016-04-15T01:18Z] INFO  18:18:44,356 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:18Z] INFO  18:18:44,357 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:18Z] WARN  18:18:44,401 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T01:18Z] WARN  18:18:44,404 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/4/tx/tmpcKiOO_/R14-18102_kapa-NGv3-PE100-NGv3-4_165889318_183245405.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T01:18Z] INFO  18:18:44,591 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:18Z] INFO  18:18:44,801 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T01:18Z] INFO  18:18:44,810 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:18Z] INFO  18:18:44,821 ProgressMeter -      4:88537424        8706540.0    30.0 s            3.0 s       47.1%    63.0 s      33.0 s
[2016-04-15T01:18Z] INFO  18:18:44,860 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-15T01:18Z] INFO  18:18:44,878 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:18Z] INFO  18:18:44,903 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T01:18Z] GATK: HaplotypeCaller
[2016-04-15T01:18Z] INFO  18:18:45,280 IntervalUtils - Processing 78538 bp from intervals
[2016-04-15T01:18Z] WARN  18:18:45,285 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:18Z] INFO  18:18:45,373 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:18Z] INFO  18:18:45,480 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:18Z] INFO  18:18:45,481 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:18Z] INFO  18:18:45,481 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T01:18Z] INFO  18:18:45,482 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T01:18Z] INFO  18:18:45,483 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T01:18Z] INFO  18:18:45,483 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T01:18Z] INFO  18:18:45,667 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T01:18Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T01:18Z] INFO  18:18:46,776 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T01:18Z] INFO  18:18:46,777 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T01:18Z] WARN  18:18:47,015 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T01:18Z] WARN  18:18:47,016 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T01:18Z] INFO  18:18:48,094 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:18Z] INFO  18:18:48,098 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:18Z] INFO  18:18:48,098 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:18Z] INFO  18:18:48,099 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:18Z] INFO  18:18:48,103 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/4/R14-18102_kapa-NGv3-PE100-NGv3-sort-4_183267803_191154276-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/4/R14-18102_kapa-NGv3-PE100-NGv3-4_183267803_191154276-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/4/tx/tmpn46YuU/R14-18102_kapa-NGv3-PE100-NGv3-4_183267803_191154276.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:18Z] INFO  18:18:48,134 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:18Z] INFO  18:18:48,134 HelpFormatter - Date/Time: 2016/04/14 18:18:48
[2016-04-15T01:18Z] INFO  18:18:48,134 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:18Z] INFO  18:18:48,135 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:18Z] WARN  18:18:48,170 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T01:18Z] WARN  18:18:48,183 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/4/tx/tmpn46YuU/R14-18102_kapa-NGv3-PE100-NGv3-4_183267803_191154276.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T01:18Z] INFO  18:18:48,387 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:18Z] INFO  18:18:48,568 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.06708301600000001
[2016-04-15T01:18Z] INFO  18:18:48,569 PairHMM - Total compute time in PairHMM computeLikelihoods() : 38.309417489000005
[2016-04-15T01:18Z] INFO  18:18:48,570 HaplotypeCaller - Ran local assembly on 3722 active regions
[2016-04-15T01:18Z] INFO  18:18:48,615 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T01:18Z] INFO  18:18:48,624 ProgressMeter -            done     5.34487573E8     3.2 m            0.0 s      100.0%     3.2 m       0.0 s
[2016-04-15T01:18Z] INFO  18:18:48,625 ProgressMeter - Total runtime 189.28 secs, 3.15 min, 0.05 hours
[2016-04-15T01:18Z] INFO  18:18:48,625 MicroScheduler - 163010 reads were filtered out during the traversal out of approximately 947638 total reads (17.20%)
[2016-04-15T01:18Z] INFO  18:18:48,626 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:18Z] INFO  18:18:48,626 MicroScheduler -   -> 70108 reads (7.40% of total) failing DuplicateReadFilter
[2016-04-15T01:18Z] INFO  18:18:48,626 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:18Z] INFO  18:18:48,627 MicroScheduler -   -> 92902 reads (9.80% of total) failing HCMappingQualityFilter
[2016-04-15T01:18Z] INFO  18:18:48,627 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:18Z] INFO  18:18:48,627 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:18Z] INFO  18:18:48,627 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:18Z] INFO  18:18:48,628 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T01:18Z] INFO  18:18:48,635 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:18Z] INFO  18:18:48,715 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-15T01:18Z] INFO  18:18:48,744 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T01:18Z] INFO  18:18:49,163 IntervalUtils - Processing 99602 bp from intervals
[2016-04-15T01:18Z] WARN  18:18:49,169 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:18Z] INFO  18:18:49,295 ProgressMeter -     4:110663685       3.203948E7    30.0 s            0.0 s       67.8%    44.0 s      14.0 s
[2016-04-15T01:18Z] INFO  18:18:49,316 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:18Z] INFO  18:18:49,393 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:18Z] INFO  18:18:49,394 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:18Z] INFO  18:18:49,395 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T01:18Z] INFO  18:18:49,396 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T01:18Z] INFO  18:18:49,396 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T01:18Z] INFO  18:18:49,397 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T01:18Z] INFO  18:18:49,546 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T01:18Z] INFO  18:18:49,553 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.009229462
[2016-04-15T01:18Z] INFO  18:18:49,554 PairHMM - Total compute time in PairHMM computeLikelihoods() : 0.373974786
[2016-04-15T01:18Z] INFO  18:18:49,566 HaplotypeCaller - Ran local assembly on 1054 active regions
[2016-04-15T01:18Z] INFO  18:18:49,600 ProgressMeter -            done      5.6156843E7    41.0 s            0.0 s      100.0%    41.0 s       0.0 s
[2016-04-15T01:18Z] INFO  18:18:49,600 ProgressMeter - Total runtime 41.37 secs, 0.69 min, 0.01 hours
[2016-04-15T01:18Z] INFO  18:18:49,600 MicroScheduler - 13767 reads were filtered out during the traversal out of approximately 170175 total reads (8.09%)
[2016-04-15T01:18Z] INFO  18:18:49,601 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:18Z] INFO  18:18:49,601 MicroScheduler -   -> 13322 reads (7.83% of total) failing DuplicateReadFilter
[2016-04-15T01:18Z] INFO  18:18:49,601 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:18Z] INFO  18:18:49,601 MicroScheduler -   -> 445 reads (0.26% of total) failing HCMappingQualityFilter
[2016-04-15T01:18Z] INFO  18:18:49,602 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:18Z] INFO  18:18:49,602 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:18Z] INFO  18:18:49,602 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:18Z] INFO  18:18:49,602 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T01:18Z] INFO  18:18:50,134 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:18Z] GATK: HaplotypeCaller
[2016-04-15T01:18Z] INFO  18:18:51,118 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:18Z] GATK: HaplotypeCaller
[2016-04-15T01:18Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T01:18Z] INFO  18:18:51,699 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T01:18Z] INFO  18:18:51,700 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T01:18Z] WARN  18:18:51,910 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T01:18Z] WARN  18:18:51,911 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T01:18Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T01:18Z] INFO  18:18:53,496 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:18Z] INFO  18:18:53,499 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:18Z] INFO  18:18:53,500 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:18Z] INFO  18:18:53,500 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:18Z] INFO  18:18:53,505 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/5/R14-18102_kapa-NGv3-PE100-NGv3-sort-5_0_15580921-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/5/R14-18102_kapa-NGv3-PE100-NGv3-5_0_15580921-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/5/tx/tmpveeFaD/R14-18102_kapa-NGv3-PE100-NGv3-5_0_15580921.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:18Z] INFO  18:18:53,506 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T01:18Z] INFO  18:18:53,507 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T01:18Z] INFO  18:18:53,513 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:18Z] INFO  18:18:53,514 HelpFormatter - Date/Time: 2016/04/14 18:18:53
[2016-04-15T01:18Z] INFO  18:18:53,514 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:18Z] INFO  18:18:53,515 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:18Z] WARN  18:18:53,537 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T01:18Z] WARN  18:18:53,540 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/5/tx/tmpveeFaD/R14-18102_kapa-NGv3-PE100-NGv3-5_0_15580921.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T01:18Z] INFO  18:18:53,692 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:18Z] INFO  18:18:53,713 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.011662106
[2016-04-15T01:18Z] INFO  18:18:53,724 PairHMM - Total compute time in PairHMM computeLikelihoods() : 0.817663452
[2016-04-15T01:18Z] INFO  18:18:53,725 HaplotypeCaller - Ran local assembly on 1423 active regions
[2016-04-15T01:18Z] INFO  18:18:53,777 ProgressMeter -            done      8.1782422E7    54.0 s            0.0 s      100.0%    54.0 s       0.0 s
[2016-04-15T01:18Z] INFO  18:18:53,778 ProgressMeter - Total runtime 54.08 secs, 0.90 min, 0.02 hours
[2016-04-15T01:18Z] INFO  18:18:53,778 MicroScheduler - 23247 reads were filtered out during the traversal out of approximately 275551 total reads (8.44%)
[2016-04-15T01:18Z] INFO  18:18:53,778 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:18Z] INFO  18:18:53,779 MicroScheduler -   -> 22545 reads (8.18% of total) failing DuplicateReadFilter
[2016-04-15T01:18Z] INFO  18:18:53,780 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:18Z] INFO  18:18:53,780 MicroScheduler -   -> 702 reads (0.25% of total) failing HCMappingQualityFilter
[2016-04-15T01:18Z] INFO  18:18:53,780 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:18Z] INFO  18:18:53,780 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:18Z] INFO  18:18:53,781 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:18Z] INFO  18:18:53,781 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T01:18Z] INFO  18:18:53,825 ProgressMeter -     3:126220061     1.16386062E8    60.0 s            0.0 s       90.5%    66.0 s       6.0 s
[2016-04-15T01:18Z] WARN  18:18:53,866 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T01:18Z] WARN  18:18:53,867 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T01:18Z] INFO  18:18:53,906 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T01:18Z] INFO  18:18:53,915 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:18Z] INFO  18:18:53,987 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-15T01:18Z] INFO  18:18:54,004 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T01:18Z] INFO  18:18:54,388 IntervalUtils - Processing 125185 bp from intervals
[2016-04-15T01:18Z] WARN  18:18:54,398 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:18Z] INFO  18:18:54,531 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:18Z] INFO  18:18:54,616 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:18Z] INFO  18:18:54,616 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:18Z] INFO  18:18:54,619 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:18Z] INFO  18:18:54,620 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:18Z] INFO  18:18:54,620 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:18Z] INFO  18:18:54,620 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:18Z] INFO  18:18:54,623 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T01:18Z] INFO  18:18:54,625 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/5/R14-18102_kapa-NGv3-PE100-NGv3-sort-5_15616091_31267808-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/5/R14-18102_kapa-NGv3-PE100-NGv3-5_15616091_31267808-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/5/tx/tmpXMcusH/R14-18102_kapa-NGv3-PE100-NGv3-5_15616091_31267808.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:18Z] INFO  18:18:54,629 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T01:18Z] INFO  18:18:54,630 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T01:18Z] INFO  18:18:54,630 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T01:18Z] INFO  18:18:54,634 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:18Z] INFO  18:18:54,635 HelpFormatter - Date/Time: 2016/04/14 18:18:54
[2016-04-15T01:18Z] INFO  18:18:54,636 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:18Z] INFO  18:18:54,637 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:18Z] WARN  18:18:54,698 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T01:18Z] WARN  18:18:54,712 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/5/tx/tmpXMcusH/R14-18102_kapa-NGv3-PE100-NGv3-5_15616091_31267808.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T01:18Z] INFO  18:18:54,761 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T01:18Z] INFO  18:18:54,961 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:18Z] INFO  18:18:55,165 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T01:18Z] INFO  18:18:55,183 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:18Z] INFO  18:18:55,257 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-15T01:18Z] INFO  18:18:55,266 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:18Z] INFO  18:18:55,288 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T01:18Z] INFO  18:18:55,451 ProgressMeter -     3:142756174     1.41276066E8    60.0 s            0.0 s       98.5%    60.0 s       0.0 s
[2016-04-15T01:18Z] GATK: HaplotypeCaller
[2016-04-15T01:18Z] INFO  18:18:55,680 IntervalUtils - Processing 26887 bp from intervals
[2016-04-15T01:18Z] WARN  18:18:55,696 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:18Z] INFO  18:18:55,799 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:18Z] INFO  18:18:55,861 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:18Z] INFO  18:18:55,862 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:18Z] INFO  18:18:55,863 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T01:18Z] INFO  18:18:55,875 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T01:18Z] INFO  18:18:55,888 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T01:18Z] INFO  18:18:55,888 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T01:18Z] INFO  18:18:56,060 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T01:18Z] INFO  18:18:56,401 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.011286069000000001
[2016-04-15T01:18Z] INFO  18:18:56,412 PairHMM - Total compute time in PairHMM computeLikelihoods() : 0.9146427730000001
[2016-04-15T01:18Z] INFO  18:18:56,413 HaplotypeCaller - Ran local assembly on 1735 active regions
[2016-04-15T01:18Z] INFO  18:18:56,466 ProgressMeter -            done      1.4553848E8    61.0 s            0.0 s      100.0%    61.0 s       0.0 s
[2016-04-15T01:18Z] INFO  18:18:56,466 ProgressMeter - Total runtime 61.04 secs, 1.02 min, 0.02 hours
[2016-04-15T01:18Z] INFO  18:18:56,467 MicroScheduler - 27253 reads were filtered out during the traversal out of approximately 324704 total reads (8.39%)
[2016-04-15T01:18Z] INFO  18:18:56,467 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:18Z] INFO  18:18:56,467 MicroScheduler -   -> 26177 reads (8.06% of total) failing DuplicateReadFilter
[2016-04-15T01:18Z] INFO  18:18:56,467 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:18Z] INFO  18:18:56,468 MicroScheduler -   -> 1076 reads (0.33% of total) failing HCMappingQualityFilter
[2016-04-15T01:18Z] INFO  18:18:56,468 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:18Z] INFO  18:18:56,468 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:18Z] INFO  18:18:56,468 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:18Z] INFO  18:18:56,472 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T01:18Z] INFO  18:18:56,679 ProgressMeter -      3:58154385     3.83762529E8    90.0 s            0.0 s       93.3%    96.0 s       6.0 s
[2016-04-15T01:18Z] INFO  18:18:57,978 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:18Z] GATK: HaplotypeCaller
[2016-04-15T01:18Z] INFO  18:18:58,631 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:18Z] INFO  18:18:58,634 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:18Z] INFO  18:18:58,634 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:18Z] INFO  18:18:58,634 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:18Z] INFO  18:18:58,650 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/5/R14-18102_kapa-NGv3-PE100-NGv3-sort-5_31294068_49695124-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/5/R14-18102_kapa-NGv3-PE100-NGv3-5_31294068_49695124-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/5/tx/tmpf3V8_F/R14-18102_kapa-NGv3-PE100-NGv3-5_31294068_49695124.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:18Z] INFO  18:18:58,665 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:18Z] INFO  18:18:58,666 HelpFormatter - Date/Time: 2016/04/14 18:18:58
[2016-04-15T01:18Z] INFO  18:18:58,666 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:18Z] INFO  18:18:58,667 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:18Z] WARN  18:18:58,700 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T01:18Z] WARN  18:18:58,705 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/5/tx/tmpf3V8_F/R14-18102_kapa-NGv3-PE100-NGv3-5_31294068_49695124.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T01:18Z] INFO  18:18:58,763 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.007221499
[2016-04-15T01:18Z] INFO  18:18:58,775 PairHMM - Total compute time in PairHMM computeLikelihoods() : 0.8020780670000001
[2016-04-15T01:18Z] INFO  18:18:58,775 HaplotypeCaller - Ran local assembly on 1099 active regions
[2016-04-15T01:18Z] INFO  18:18:58,838 ProgressMeter -            done      5.9405179E7    39.0 s            0.0 s      100.0%    39.0 s       0.0 s
[2016-04-15T01:18Z] INFO  18:18:58,838 ProgressMeter - Total runtime 39.57 secs, 0.66 min, 0.01 hours
[2016-04-15T01:18Z] INFO  18:18:58,839 MicroScheduler - 15575 reads were filtered out during the traversal out of approximately 188628 total reads (8.26%)
[2016-04-15T01:18Z] INFO  18:18:58,839 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:18Z] INFO  18:18:58,839 MicroScheduler -   -> 14818 reads (7.86% of total) failing DuplicateReadFilter
[2016-04-15T01:18Z] INFO  18:18:58,840 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:18Z] INFO  18:18:58,840 MicroScheduler -   -> 757 reads (0.40% of total) failing HCMappingQualityFilter
[2016-04-15T01:18Z] INFO  18:18:58,840 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:18Z] INFO  18:18:58,840 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:18Z] INFO  18:18:58,841 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:18Z] INFO  18:18:58,841 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T01:18Z] INFO  18:18:59,011 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:18Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T01:18Z] INFO  18:18:59,203 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T01:18Z] INFO  18:18:59,224 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:18Z] INFO  18:18:59,225 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T01:18Z] INFO  18:18:59,226 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T01:18Z] INFO  18:18:59,297 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-15T01:18Z] INFO  18:18:59,326 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T01:18Z] INFO  18:18:59,502 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.024530864000000003
[2016-04-15T01:18Z] INFO  18:18:59,503 PairHMM - Total compute time in PairHMM computeLikelihoods() : 0.8971003710000001
[2016-04-15T01:18Z] INFO  18:18:59,504 HaplotypeCaller - Ran local assembly on 1775 active regions
[2016-04-15T01:18Z] INFO  18:18:59,570 ProgressMeter -            done     1.43172621E8    65.0 s            0.0 s      100.0%    65.0 s       0.0 s
[2016-04-15T01:18Z] INFO  18:18:59,570 ProgressMeter - Total runtime 65.75 secs, 1.10 min, 0.02 hours
[2016-04-15T01:18Z] INFO  18:18:59,570 MicroScheduler - 28960 reads were filtered out during the traversal out of approximately 345775 total reads (8.38%)
[2016-04-15T01:18Z] INFO  18:18:59,571 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:18Z] INFO  18:18:59,571 MicroScheduler -   -> 27519 reads (7.96% of total) failing DuplicateReadFilter
[2016-04-15T01:18Z] INFO  18:18:59,571 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:18Z] INFO  18:18:59,572 MicroScheduler -   -> 1441 reads (0.42% of total) failing HCMappingQualityFilter
[2016-04-15T01:18Z] INFO  18:18:59,572 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:18Z] INFO  18:18:59,572 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:18Z] INFO  18:18:59,572 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:18Z] INFO  18:18:59,572 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T01:18Z] WARN  18:18:59,600 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T01:18Z] WARN  18:18:59,601 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T01:18Z] INFO  18:18:59,798 IntervalUtils - Processing 183626 bp from intervals
[2016-04-15T01:18Z] WARN  18:18:59,814 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:18Z] INFO  18:18:59,962 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:19Z] INFO  18:19:00,053 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:19Z] INFO  18:19:00,054 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:19Z] INFO  18:19:00,055 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T01:19Z] INFO  18:19:00,056 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T01:19Z] INFO  18:19:00,057 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T01:19Z] INFO  18:19:00,057 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T01:19Z] INFO  18:19:00,258 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:19Z] INFO  18:19:00,275 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T01:19Z] INFO  18:19:00,349 ProgressMeter -     3:195509332        7445396.0    60.0 s            8.0 s       48.6%     2.1 m      63.0 s
[2016-04-15T01:19Z] GATK: HaplotypeCaller
[2016-04-15T01:19Z] INFO  18:19:01,169 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:19Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T01:19Z] INFO  18:19:01,208 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T01:19Z] INFO  18:19:01,210 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T01:19Z] INFO  18:19:01,331 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:19Z] INFO  18:19:01,334 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:19Z] INFO  18:19:01,335 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:19Z] INFO  18:19:01,335 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:19Z] INFO  18:19:01,340 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/5/R14-18102_kapa-NGv3-PE100-NGv3-sort-5_49695692_65288736-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/5/R14-18102_kapa-NGv3-PE100-NGv3-5_49695692_65288736-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/5/tx/tmpGJzc63/R14-18102_kapa-NGv3-PE100-NGv3-5_49695692_65288736.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:19Z] INFO  18:19:01,352 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:19Z] INFO  18:19:01,363 HelpFormatter - Date/Time: 2016/04/14 18:19:01
[2016-04-15T01:19Z] INFO  18:19:01,364 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:19Z] INFO  18:19:01,365 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:19Z] WARN  18:19:01,390 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T01:19Z] WARN  18:19:01,393 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/5/tx/tmpGJzc63/R14-18102_kapa-NGv3-PE100-NGv3-5_49695692_65288736.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T01:19Z] WARN  18:19:01,506 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T01:19Z] WARN  18:19:01,507 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T01:19Z] GATK: HaplotypeCaller
[2016-04-15T01:19Z] INFO  18:19:01,672 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:19Z] INFO  18:19:01,874 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T01:19Z] INFO  18:19:01,889 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:19Z] INFO  18:19:01,981 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.09
[2016-04-15T01:19Z] INFO  18:19:02,022 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T01:19Z] INFO  18:19:02,568 IntervalUtils - Processing 108713 bp from intervals
[2016-04-15T01:19Z] WARN  18:19:02,581 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:19Z] INFO  18:19:02,600 ProgressMeter -       4:5754648      5.5007765E7    60.0 s            1.0 s       60.4%    99.0 s      39.0 s
[2016-04-15T01:19Z] INFO  18:19:02,712 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:19Z] INFO  18:19:02,829 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:19Z] INFO  18:19:02,830 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:19Z] INFO  18:19:02,842 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T01:19Z] INFO  18:19:02,843 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T01:19Z] INFO  18:19:02,845 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T01:19Z] INFO  18:19:02,846 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T01:19Z] INFO  18:19:03,065 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T01:19Z] INFO  18:19:03,165 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.017160328000000002
[2016-04-15T01:19Z] INFO  18:19:03,166 PairHMM - Total compute time in PairHMM computeLikelihoods() : 0.8512374410000001
[2016-04-15T01:19Z] INFO  18:19:03,166 HaplotypeCaller - Ran local assembly on 3242 active regions
[2016-04-15T01:19Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T01:19Z] INFO  18:19:03,215 ProgressMeter -            done     4.57477008E8    96.0 s            0.0 s      100.0%    96.0 s       0.0 s
[2016-04-15T01:19Z] INFO  18:19:03,215 ProgressMeter - Total runtime 96.58 secs, 1.61 min, 0.03 hours
[2016-04-15T01:19Z] INFO  18:19:03,216 MicroScheduler - 61276 reads were filtered out during the traversal out of approximately 733035 total reads (8.36%)
[2016-04-15T01:19Z] INFO  18:19:03,216 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:19Z] INFO  18:19:03,216 MicroScheduler -   -> 59500 reads (8.12% of total) failing DuplicateReadFilter
[2016-04-15T01:19Z] INFO  18:19:03,216 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:19Z] INFO  18:19:03,217 MicroScheduler -   -> 1776 reads (0.24% of total) failing HCMappingQualityFilter
[2016-04-15T01:19Z] INFO  18:19:03,217 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:19Z] INFO  18:19:03,217 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:19Z] INFO  18:19:03,217 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:19Z] INFO  18:19:03,218 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T01:19Z] INFO  18:19:03,244 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T01:19Z] INFO  18:19:03,244 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T01:19Z] WARN  18:19:03,523 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T01:19Z] WARN  18:19:03,524 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T01:19Z] INFO  18:19:03,688 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:19Z] INFO  18:19:03,691 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:19Z] INFO  18:19:03,691 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:19Z] INFO  18:19:03,691 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:19Z] INFO  18:19:03,695 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/5/R14-18102_kapa-NGv3-PE100-NGv3-sort-5_65290574_80809536-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/5/R14-18102_kapa-NGv3-PE100-NGv3-5_65290574_80809536-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/5/tx/tmpItc43p/R14-18102_kapa-NGv3-PE100-NGv3-5_65290574_80809536.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:19Z] INFO  18:19:03,725 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:19Z] INFO  18:19:03,726 HelpFormatter - Date/Time: 2016/04/14 18:19:03
[2016-04-15T01:19Z] INFO  18:19:03,726 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:19Z] INFO  18:19:03,727 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:19Z] WARN  18:19:03,774 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T01:19Z] WARN  18:19:03,776 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/5/tx/tmpItc43p/R14-18102_kapa-NGv3-PE100-NGv3-5_65290574_80809536.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T01:19Z] INFO  18:19:04,063 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:19Z] INFO  18:19:04,186 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.011849791
[2016-04-15T01:19Z] INFO  18:19:04,187 PairHMM - Total compute time in PairHMM computeLikelihoods() : 0.978069681
[2016-04-15T01:19Z] INFO  18:19:04,188 HaplotypeCaller - Ran local assembly on 1471 active regions
[2016-04-15T01:19Z] INFO  18:19:04,235 ProgressMeter -            done      9.7624838E7    50.0 s            0.0 s      100.0%    50.0 s       0.0 s
[2016-04-15T01:19Z] INFO  18:19:04,236 ProgressMeter - Total runtime 50.72 secs, 0.85 min, 0.01 hours
[2016-04-15T01:19Z] INFO  18:19:04,236 MicroScheduler - 23940 reads were filtered out during the traversal out of approximately 259197 total reads (9.24%)
[2016-04-15T01:19Z] INFO  18:19:04,237 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:19Z] INFO  18:19:04,237 MicroScheduler -   -> 20583 reads (7.94% of total) failing DuplicateReadFilter
[2016-04-15T01:19Z] INFO  18:19:04,237 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:19Z] INFO  18:19:04,237 MicroScheduler -   -> 3357 reads (1.30% of total) failing HCMappingQualityFilter
[2016-04-15T01:19Z] INFO  18:19:04,238 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:19Z] INFO  18:19:04,238 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:19Z] INFO  18:19:04,238 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:19Z] INFO  18:19:04,238 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T01:19Z] INFO  18:19:04,245 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T01:19Z] INFO  18:19:04,255 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:19Z] INFO  18:19:04,363 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.11
[2016-04-15T01:19Z] INFO  18:19:04,396 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T01:19Z] INFO  18:19:04,671 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:19Z] INFO  18:19:04,954 IntervalUtils - Processing 203113 bp from intervals
[2016-04-15T01:19Z] WARN  18:19:04,980 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:19Z] INFO  18:19:04,986 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:19Z] INFO  18:19:04,989 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:19Z] INFO  18:19:04,990 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:19Z] INFO  18:19:04,990 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:19Z] INFO  18:19:04,995 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/5/R14-18102_kapa-NGv3-PE100-NGv3-sort-5_80911291_96430739-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/5/R14-18102_kapa-NGv3-PE100-NGv3-5_80911291_96430739-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/5/tx/tmpf2iW4C/R14-18102_kapa-NGv3-PE100-NGv3-5_80911291_96430739.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:19Z] INFO  18:19:05,004 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:19Z] INFO  18:19:05,006 HelpFormatter - Date/Time: 2016/04/14 18:19:04
[2016-04-15T01:19Z] INFO  18:19:05,007 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:19Z] INFO  18:19:05,015 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:19Z] WARN  18:19:05,043 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T01:19Z] WARN  18:19:05,046 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/5/tx/tmpf2iW4C/R14-18102_kapa-NGv3-PE100-NGv3-5_80911291_96430739.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T01:19Z] GATK: HaplotypeCaller
[2016-04-15T01:19Z] INFO  18:19:05,119 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:19Z] INFO  18:19:05,226 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:19Z] INFO  18:19:05,242 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:19Z] INFO  18:19:05,243 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:19Z] INFO  18:19:05,244 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T01:19Z] INFO  18:19:05,244 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T01:19Z] INFO  18:19:05,255 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T01:19Z] INFO  18:19:05,256 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T01:19Z] INFO  18:19:05,419 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T01:19Z] INFO  18:19:05,432 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:19Z] INFO  18:19:05,497 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-15T01:19Z] INFO  18:19:05,512 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T01:19Z] INFO  18:19:05,526 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T01:19Z] INFO  18:19:05,747 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:19Z] INFO  18:19:05,987 IntervalUtils - Processing 113632 bp from intervals
[2016-04-15T01:19Z] WARN  18:19:05,992 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:19Z] GATK: HaplotypeCaller
[2016-04-15T01:19Z] INFO  18:19:06,089 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:19Z] INFO  18:19:06,182 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:19Z] INFO  18:19:06,184 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:19Z] INFO  18:19:06,185 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T01:19Z] INFO  18:19:06,185 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T01:19Z] INFO  18:19:06,197 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T01:19Z] INFO  18:19:06,197 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T01:19Z] INFO  18:19:06,461 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T01:19Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T01:19Z] INFO  18:19:06,863 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T01:19Z] INFO  18:19:06,864 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T01:19Z] INFO  18:19:07,042 ProgressMeter -     4:125593689      2.2243201E7    30.0 s            1.0 s       69.3%    43.0 s      13.0 s
[2016-04-15T01:19Z] WARN  18:19:07,192 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T01:19Z] WARN  18:19:07,192 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T01:19Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T01:19Z] INFO  18:19:07,308 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T01:19Z] INFO  18:19:07,309 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T01:19Z] WARN  18:19:07,556 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T01:19Z] WARN  18:19:07,557 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T01:19Z] INFO  18:19:08,106 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:19Z] INFO  18:19:08,112 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:19Z] INFO  18:19:08,113 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:19Z] INFO  18:19:08,113 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:19Z] INFO  18:19:08,118 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/5/R14-18102_kapa-NGv3-PE100-NGv3-sort-5_96432513_112043579-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/5/R14-18102_kapa-NGv3-PE100-NGv3-5_96432513_112043579-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/5/tx/tmpsDuDcC/R14-18102_kapa-NGv3-PE100-NGv3-5_96432513_112043579.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:19Z] INFO  18:19:08,146 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:19Z] INFO  18:19:08,147 HelpFormatter - Date/Time: 2016/04/14 18:19:08
[2016-04-15T01:19Z] INFO  18:19:08,147 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:19Z] INFO  18:19:08,147 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:19Z] WARN  18:19:08,203 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T01:19Z] WARN  18:19:08,206 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/5/tx/tmpsDuDcC/R14-18102_kapa-NGv3-PE100-NGv3-5_96432513_112043579.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T01:19Z] INFO  18:19:08,384 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:19Z] INFO  18:19:08,594 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T01:19Z] INFO  18:19:08,604 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:19Z] INFO  18:19:08,677 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-15T01:19Z] INFO  18:19:08,708 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T01:19Z] INFO  18:19:09,254 IntervalUtils - Processing 57322 bp from intervals
[2016-04-15T01:19Z] WARN  18:19:09,259 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:19Z] INFO  18:19:09,369 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:19Z] INFO  18:19:09,449 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:19Z] INFO  18:19:09,462 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:19Z] INFO  18:19:09,463 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:19Z] INFO  18:19:09,463 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:19Z] INFO  18:19:09,468 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/5/R14-18102_kapa-NGv3-PE100-NGv3-sort-5_112073555_127595521-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/5/R14-18102_kapa-NGv3-PE100-NGv3-5_112073555_127595521-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/5/tx/tmpxgDzAG/R14-18102_kapa-NGv3-PE100-NGv3-5_112073555_127595521.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:19Z] INFO  18:19:09,474 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:19Z] INFO  18:19:09,475 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:19Z] INFO  18:19:09,476 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T01:19Z] INFO  18:19:09,476 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T01:19Z] INFO  18:19:09,477 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T01:19Z] INFO  18:19:09,482 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:19Z] INFO  18:19:09,483 HelpFormatter - Date/Time: 2016/04/14 18:19:09
[2016-04-15T01:19Z] INFO  18:19:09,483 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:19Z] INFO  18:19:09,483 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:19Z] INFO  18:19:09,477 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T01:19Z] WARN  18:19:09,532 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T01:19Z] WARN  18:19:09,539 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/5/tx/tmpxgDzAG/R14-18102_kapa-NGv3-PE100-NGv3-5_112073555_127595521.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T01:19Z] INFO  18:19:09,607 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.014250202000000002
[2016-04-15T01:19Z] INFO  18:19:09,608 PairHMM - Total compute time in PairHMM computeLikelihoods() : 0.470560234
[2016-04-15T01:19Z] INFO  18:19:09,609 HaplotypeCaller - Ran local assembly on 611 active regions
[2016-04-15T01:19Z] INFO  18:19:09,659 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T01:19Z] INFO  18:19:09,662 ProgressMeter -            done      1.9501835E7    29.0 s            1.0 s      100.0%    29.0 s       0.0 s
[2016-04-15T01:19Z] INFO  18:19:09,662 ProgressMeter - Total runtime 29.41 secs, 0.49 min, 0.01 hours
[2016-04-15T01:19Z] INFO  18:19:09,663 MicroScheduler - 9443 reads were filtered out during the traversal out of approximately 112244 total reads (8.41%)
[2016-04-15T01:19Z] INFO  18:19:09,663 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:19Z] INFO  18:19:09,663 MicroScheduler -   -> 8955 reads (7.98% of total) failing DuplicateReadFilter
[2016-04-15T01:19Z] INFO  18:19:09,663 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:19Z] INFO  18:19:09,664 MicroScheduler -   -> 488 reads (0.43% of total) failing HCMappingQualityFilter
[2016-04-15T01:19Z] INFO  18:19:09,664 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:19Z] INFO  18:19:09,664 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:19Z] INFO  18:19:09,664 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:19Z] INFO  18:19:09,665 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T01:19Z] INFO  18:19:09,792 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:19Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T01:19Z] INFO  18:19:09,994 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T01:19Z] INFO  18:19:09,995 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T01:19Z] INFO  18:19:10,027 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T01:19Z] INFO  18:19:10,043 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:19Z] INFO  18:19:10,143 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.09
[2016-04-15T01:19Z] INFO  18:19:10,167 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T01:19Z] WARN  18:19:10,236 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T01:19Z] WARN  18:19:10,237 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T01:19Z] INFO  18:19:10,557 IntervalUtils - Processing 103986 bp from intervals
[2016-04-15T01:19Z] WARN  18:19:10,562 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:19Z] INFO  18:19:10,686 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:19Z] INFO  18:19:10,797 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:19Z] INFO  18:19:10,798 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:19Z] INFO  18:19:10,799 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T01:19Z] INFO  18:19:10,799 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T01:19Z] INFO  18:19:10,811 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T01:19Z] INFO  18:19:10,812 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T01:19Z] INFO  18:19:10,967 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.011094623000000001
[2016-04-15T01:19Z] INFO  18:19:10,968 PairHMM - Total compute time in PairHMM computeLikelihoods() : 15.604253710000002
[2016-04-15T01:19Z] INFO  18:19:10,969 HaplotypeCaller - Ran local assembly on 887 active regions
[2016-04-15T01:19Z] INFO  18:19:11,008 ProgressMeter -            done      3.7254023E7    56.0 s            1.0 s      100.0%    56.0 s       0.0 s
[2016-04-15T01:19Z] INFO  18:19:11,009 ProgressMeter - Total runtime 56.21 secs, 0.94 min, 0.02 hours
[2016-04-15T01:19Z] INFO  18:19:11,010 MicroScheduler - 13829 reads were filtered out during the traversal out of approximately 159226 total reads (8.69%)
[2016-04-15T01:19Z] INFO  18:19:11,011 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:19Z] INFO  18:19:11,012 MicroScheduler -   -> 13286 reads (8.34% of total) failing DuplicateReadFilter
[2016-04-15T01:19Z] INFO  18:19:11,012 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:19Z] INFO  18:19:11,013 MicroScheduler -   -> 543 reads (0.34% of total) failing HCMappingQualityFilter
[2016-04-15T01:19Z] INFO  18:19:11,014 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:19Z] INFO  18:19:11,014 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:19Z] INFO  18:19:11,015 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:19Z] INFO  18:19:11,016 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T01:19Z] INFO  18:19:11,145 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T01:19Z] INFO  18:19:11,300 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:19Z] GATK: HaplotypeCaller
[2016-04-15T01:19Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T01:19Z] INFO  18:19:12,227 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T01:19Z] INFO  18:19:12,228 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T01:19Z] WARN  18:19:12,519 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T01:19Z] WARN  18:19:12,521 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T01:19Z] INFO  18:19:12,605 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:19Z] GATK: HaplotypeCaller
[2016-04-15T01:19Z] INFO  18:19:13,104 ProgressMeter -     4:160253849      2.5979651E7    30.0 s            1.0 s       86.6%    34.0 s       4.0 s
[2016-04-15T01:19Z] INFO  18:19:14,039 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.002062468
[2016-04-15T01:19Z] INFO  18:19:14,040 PairHMM - Total compute time in PairHMM computeLikelihoods() : 0.106794864
[2016-04-15T01:19Z] INFO  18:19:14,041 HaplotypeCaller - Ran local assembly on 171 active regions
[2016-04-15T01:19Z] INFO  18:19:14,100 ProgressMeter -            done        1678889.0    18.0 s           10.0 s      100.0%    18.0 s       0.0 s
[2016-04-15T01:19Z] INFO  18:19:14,100 ProgressMeter - Total runtime 18.24 secs, 0.30 min, 0.01 hours
[2016-04-15T01:19Z] INFO  18:19:14,100 MicroScheduler - 4836 reads were filtered out during the traversal out of approximately 36707 total reads (13.17%)
[2016-04-15T01:19Z] INFO  18:19:14,101 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:19Z] INFO  18:19:14,101 MicroScheduler -   -> 2796 reads (7.62% of total) failing DuplicateReadFilter
[2016-04-15T01:19Z] INFO  18:19:14,102 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:19Z] INFO  18:19:14,102 MicroScheduler -   -> 2040 reads (5.56% of total) failing HCMappingQualityFilter
[2016-04-15T01:19Z] INFO  18:19:14,102 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:19Z] INFO  18:19:14,103 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:19Z] INFO  18:19:14,103 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:19Z] INFO  18:19:14,103 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T01:19Z] INFO  18:19:15,103 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:19Z] INFO  18:19:15,106 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:19Z] INFO  18:19:15,107 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:19Z] INFO  18:19:15,107 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:19Z] INFO  18:19:15,112 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/5/R14-18102_kapa-NGv3-PE100-NGv3-sort-5_127597427_143191869-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/5/R14-18102_kapa-NGv3-PE100-NGv3-5_127597427_143191869-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/5/tx/tmpyeSp2p/R14-18102_kapa-NGv3-PE100-NGv3-5_127597427_143191869.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:19Z] INFO  18:19:15,145 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:19Z] INFO  18:19:15,146 HelpFormatter - Date/Time: 2016/04/14 18:19:15
[2016-04-15T01:19Z] INFO  18:19:15,146 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:19Z] INFO  18:19:15,146 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:19Z] WARN  18:19:15,191 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T01:19Z] WARN  18:19:15,194 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/5/tx/tmpyeSp2p/R14-18102_kapa-NGv3-PE100-NGv3-5_127597427_143191869.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T01:19Z] INFO  18:19:15,367 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:19Z] INFO  18:19:15,430 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:19Z] INFO  18:19:15,507 ProgressMeter -     4:178514700      1.6105907E7    30.0 s            1.0 s       99.6%    30.0 s       0.0 s
[2016-04-15T01:19Z] INFO  18:19:15,703 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T01:19Z] INFO  18:19:15,715 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:19Z] GATK: HaplotypeCaller
[2016-04-15T01:19Z] INFO  18:19:15,815 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.10
[2016-04-15T01:19Z] INFO  18:19:15,843 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T01:19Z] INFO  18:19:15,995 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:19Z] INFO  18:19:15,998 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:19Z] INFO  18:19:15,998 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:19Z] INFO  18:19:15,999 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:19Z] INFO  18:19:16,003 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/5/R14-18102_kapa-NGv3-PE100-NGv3-sort-5_143200044_158710347-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/5/R14-18102_kapa-NGv3-PE100-NGv3-5_143200044_158710347-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/5/tx/tmpB50tbg/R14-18102_kapa-NGv3-PE100-NGv3-5_143200044_158710347.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:19Z] INFO  18:19:16,017 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:19Z] INFO  18:19:16,018 HelpFormatter - Date/Time: 2016/04/14 18:19:15
[2016-04-15T01:19Z] INFO  18:19:16,019 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:19Z] INFO  18:19:16,019 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:19Z] WARN  18:19:16,051 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T01:19Z] WARN  18:19:16,064 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/5/tx/tmpB50tbg/R14-18102_kapa-NGv3-PE100-NGv3-5_143200044_158710347.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T01:19Z] INFO  18:19:16,366 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:19Z] INFO  18:19:16,417 IntervalUtils - Processing 393653 bp from intervals
[2016-04-15T01:19Z] WARN  18:19:16,423 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:19Z] INFO  18:19:16,499 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T01:19Z] INFO  18:19:16,509 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:19Z] INFO  18:19:16,581 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-15T01:19Z] INFO  18:19:16,599 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:19Z] INFO  18:19:16,619 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T01:19Z] INFO  18:19:16,792 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:19Z] INFO  18:19:16,792 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:19Z] INFO  18:19:16,793 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T01:19Z] INFO  18:19:16,793 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T01:19Z] INFO  18:19:16,806 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T01:19Z] INFO  18:19:16,807 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T01:19Z] INFO  18:19:16,854 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.005405909
[2016-04-15T01:19Z] INFO  18:19:16,855 PairHMM - Total compute time in PairHMM computeLikelihoods() : 0.396959204
[2016-04-15T01:19Z] INFO  18:19:16,855 HaplotypeCaller - Ran local assembly on 602 active regions
[2016-04-15T01:19Z] INFO  18:19:16,936 ProgressMeter -            done      1.6341003E7    31.0 s            1.0 s      100.0%    31.0 s       0.0 s
[2016-04-15T01:19Z] INFO  18:19:16,937 ProgressMeter - Total runtime 31.46 secs, 0.52 min, 0.01 hours
[2016-04-15T01:19Z] INFO  18:19:16,945 MicroScheduler - 7955 reads were filtered out during the traversal out of approximately 91366 total reads (8.71%)
[2016-04-15T01:19Z] INFO  18:19:16,946 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:19Z] INFO  18:19:16,946 MicroScheduler -   -> 7400 reads (8.10% of total) failing DuplicateReadFilter
[2016-04-15T01:19Z] INFO  18:19:16,947 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:19Z] INFO  18:19:16,948 MicroScheduler -   -> 555 reads (0.61% of total) failing HCMappingQualityFilter
[2016-04-15T01:19Z] INFO  18:19:16,948 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:19Z] INFO  18:19:16,953 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:19Z] INFO  18:19:16,954 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:19Z] INFO  18:19:16,955 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T01:19Z] INFO  18:19:17,083 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T01:19Z] INFO  18:19:17,125 IntervalUtils - Processing 205172 bp from intervals
[2016-04-15T01:19Z] WARN  18:19:17,131 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:19Z] INFO  18:19:17,289 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:19Z] INFO  18:19:17,449 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:19Z] INFO  18:19:17,466 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:19Z] INFO  18:19:17,467 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T01:19Z] INFO  18:19:17,468 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T01:19Z] INFO  18:19:17,480 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T01:19Z] INFO  18:19:17,511 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T01:19Z] INFO  18:19:17,814 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T01:19Z] INFO  18:19:18,463 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:19Z] INFO  18:19:18,680 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.008998243000000001
[2016-04-15T01:19Z] INFO  18:19:18,681 PairHMM - Total compute time in PairHMM computeLikelihoods() : 0.759466019
[2016-04-15T01:19Z] INFO  18:19:18,682 HaplotypeCaller - Ran local assembly on 1045 active regions
[2016-04-15T01:19Z] INFO  18:19:18,725 ProgressMeter -            done      4.4117255E7    41.0 s            0.0 s      100.0%    41.0 s       0.0 s
[2016-04-15T01:19Z] INFO  18:19:18,726 ProgressMeter - Total runtime 41.70 secs, 0.69 min, 0.01 hours
[2016-04-15T01:19Z] INFO  18:19:18,727 MicroScheduler - 12810 reads were filtered out during the traversal out of approximately 160906 total reads (7.96%)
[2016-04-15T01:19Z] INFO  18:19:18,727 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:19Z] INFO  18:19:18,728 MicroScheduler -   -> 12638 reads (7.85% of total) failing DuplicateReadFilter
[2016-04-15T01:19Z] INFO  18:19:18,729 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:19Z] INFO  18:19:18,729 MicroScheduler -   -> 172 reads (0.11% of total) failing HCMappingQualityFilter
[2016-04-15T01:19Z] INFO  18:19:18,730 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:19Z] INFO  18:19:18,730 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:19Z] INFO  18:19:18,731 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:19Z] INFO  18:19:18,732 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T01:19Z] GATK: HaplotypeCaller
[2016-04-15T01:19Z] INFO  18:19:18,971 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:19Z] INFO  18:19:18,974 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:19Z] INFO  18:19:18,974 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:19Z] INFO  18:19:18,975 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:19Z] INFO  18:19:18,979 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/5/R14-18102_kapa-NGv3-PE100-NGv3-sort-5_158711911_174870102-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/5/R14-18102_kapa-NGv3-PE100-NGv3-5_158711911_174870102-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/5/tx/tmpjslVfe/R14-18102_kapa-NGv3-PE100-NGv3-5_158711911_174870102.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:19Z] INFO  18:19:19,019 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:19Z] INFO  18:19:19,020 HelpFormatter - Date/Time: 2016/04/14 18:19:18
[2016-04-15T01:19Z] INFO  18:19:19,020 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:19Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T01:19Z] INFO  18:19:19,021 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:19Z] INFO  18:19:19,044 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T01:19Z] INFO  18:19:19,044 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T01:19Z] WARN  18:19:19,086 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T01:19Z] WARN  18:19:19,088 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/5/tx/tmpjslVfe/R14-18102_kapa-NGv3-PE100-NGv3-5_158711911_174870102.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T01:19Z] INFO  18:19:19,219 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.00642544
[2016-04-15T01:19Z] INFO  18:19:19,220 PairHMM - Total compute time in PairHMM computeLikelihoods() : 0.36418411500000003
[2016-04-15T01:19Z] INFO  18:19:19,220 HaplotypeCaller - Ran local assembly on 835 active regions
[2016-04-15T01:19Z] INFO  18:19:19,288 ProgressMeter -            done      3.2744349E7    36.0 s            1.0 s      100.0%    36.0 s       0.0 s
[2016-04-15T01:19Z] INFO  18:19:19,288 ProgressMeter - Total runtime 36.21 secs, 0.60 min, 0.01 hours
[2016-04-15T01:19Z] INFO  18:19:19,289 MicroScheduler - 11822 reads were filtered out during the traversal out of approximately 144276 total reads (8.19%)
[2016-04-15T01:19Z] INFO  18:19:19,289 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:19Z] INFO  18:19:19,289 MicroScheduler -   -> 11604 reads (8.04% of total) failing DuplicateReadFilter
[2016-04-15T01:19Z] INFO  18:19:19,289 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:19Z] INFO  18:19:19,290 MicroScheduler -   -> 218 reads (0.15% of total) failing HCMappingQualityFilter
[2016-04-15T01:19Z] INFO  18:19:19,290 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:19Z] INFO  18:19:19,290 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:19Z] INFO  18:19:19,290 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:19Z] INFO  18:19:19,291 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T01:19Z] INFO  18:19:19,386 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:19Z] INFO  18:19:19,421 ProgressMeter -     4:187629860      1.5547155E7    30.0 s            1.0 s       93.5%    32.0 s       2.0 s
[2016-04-15T01:19Z] WARN  18:19:19,513 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T01:19Z] WARN  18:19:19,513 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T01:19Z] INFO  18:19:19,595 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T01:19Z] INFO  18:19:19,604 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:19Z] INFO  18:19:19,702 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.10
[2016-04-15T01:19Z] INFO  18:19:19,719 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T01:19Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T01:19Z] INFO  18:19:19,841 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T01:19Z] INFO  18:19:19,842 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T01:19Z] INFO  18:19:20,043 IntervalUtils - Processing 104189 bp from intervals
[2016-04-15T01:19Z] WARN  18:19:20,048 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:19Z] WARN  18:19:20,056 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T01:19Z] WARN  18:19:20,057 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T01:19Z] INFO  18:19:20,139 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:19Z] INFO  18:19:20,209 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:19Z] INFO  18:19:20,221 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:19Z] INFO  18:19:20,222 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:19Z] INFO  18:19:20,223 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T01:19Z] INFO  18:19:20,224 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T01:19Z] INFO  18:19:20,225 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T01:19Z] INFO  18:19:20,225 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T01:19Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T01:19Z] INFO  18:19:20,342 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T01:19Z] INFO  18:19:20,350 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T01:19Z] INFO  18:19:20,506 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T01:19Z] GATK: HaplotypeCaller
[2016-04-15T01:19Z] WARN  18:19:20,712 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T01:19Z] WARN  18:19:20,724 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T01:19Z] INFO  18:19:20,935 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:19Z] GATK: HaplotypeCaller
[2016-04-15T01:19Z] INFO  18:19:22,147 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:19Z] INFO  18:19:22,150 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:19Z] INFO  18:19:22,151 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:19Z] INFO  18:19:22,151 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:19Z] INFO  18:19:22,155 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/5/R14-18102_kapa-NGv3-PE100-NGv3-sort-5_174919106_180915260-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/5/R14-18102_kapa-NGv3-PE100-NGv3-5_174919106_180915260-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/5/tx/tmppYOtjW/R14-18102_kapa-NGv3-PE100-NGv3-5_174919106_180915260.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:19Z] INFO  18:19:22,166 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:19Z] INFO  18:19:22,178 HelpFormatter - Date/Time: 2016/04/14 18:19:22
[2016-04-15T01:19Z] INFO  18:19:22,179 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:19Z] INFO  18:19:22,180 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:19Z] WARN  18:19:22,225 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T01:19Z] WARN  18:19:22,228 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/5/tx/tmppYOtjW/R14-18102_kapa-NGv3-PE100-NGv3-5_174919106_180915260.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T01:19Z] INFO  18:19:22,499 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:19Z] INFO  18:19:22,779 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T01:19Z] INFO  18:19:22,789 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:19Z] INFO  18:19:22,884 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.09
[2016-04-15T01:19Z] INFO  18:19:22,908 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T01:19Z] INFO  18:19:23,446 IntervalUtils - Processing 163171 bp from intervals
[2016-04-15T01:19Z] WARN  18:19:23,462 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:19Z] INFO  18:19:23,601 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:19Z] INFO  18:19:23,728 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:19Z] INFO  18:19:23,730 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:19Z] INFO  18:19:23,730 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T01:19Z] INFO  18:19:23,731 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T01:19Z] INFO  18:19:23,746 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T01:19Z] INFO  18:19:23,747 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T01:19Z] INFO  18:19:24,127 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T01:19Z] INFO  18:19:24,497 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:19Z] INFO  18:19:24,500 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:19Z] INFO  18:19:24,500 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:19Z] INFO  18:19:24,501 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:19Z] INFO  18:19:24,505 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/6/R14-18102_kapa-NGv3-PE100-NGv3-sort-6_0_15509601-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/6/R14-18102_kapa-NGv3-PE100-NGv3-6_0_15509601-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/6/tx/tmpMQysEl/R14-18102_kapa-NGv3-PE100-NGv3-6_0_15509601.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:19Z] INFO  18:19:24,535 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:19Z] INFO  18:19:24,538 HelpFormatter - Date/Time: 2016/04/14 18:19:24
[2016-04-15T01:19Z] INFO  18:19:24,539 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:19Z] INFO  18:19:24,540 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:19Z] INFO  18:19:24,564 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.008228639000000001
[2016-04-15T01:19Z] INFO  18:19:24,564 PairHMM - Total compute time in PairHMM computeLikelihoods() : 0.9484645810000001
[2016-04-15T01:19Z] INFO  18:19:24,564 HaplotypeCaller - Ran local assembly on 701 active regions
[2016-04-15T01:19Z] WARN  18:19:24,593 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T01:19Z] WARN  18:19:24,596 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/6/tx/tmpMQysEl/R14-18102_kapa-NGv3-PE100-NGv3-6_0_15509601.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T01:19Z] INFO  18:19:24,645 ProgressMeter -       5:6607497      1.1395856E7    30.0 s            2.0 s       53.4%    56.0 s      26.0 s
[2016-04-15T01:19Z] INFO  18:19:24,707 ProgressMeter -            done      1.8181148E7    35.0 s            1.0 s      100.0%    35.0 s       0.0 s
[2016-04-15T01:19Z] INFO  18:19:24,708 ProgressMeter - Total runtime 35.31 secs, 0.59 min, 0.01 hours
[2016-04-15T01:19Z] INFO  18:19:24,708 MicroScheduler - 13392 reads were filtered out during the traversal out of approximately 136394 total reads (9.82%)
[2016-04-15T01:19Z] INFO  18:19:24,708 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:19Z] INFO  18:19:24,709 MicroScheduler -   -> 10741 reads (7.87% of total) failing DuplicateReadFilter
[2016-04-15T01:19Z] INFO  18:19:24,709 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:19Z] INFO  18:19:24,709 MicroScheduler -   -> 2651 reads (1.94% of total) failing HCMappingQualityFilter
[2016-04-15T01:19Z] INFO  18:19:24,710 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:19Z] INFO  18:19:24,710 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:19Z] INFO  18:19:24,710 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:19Z] INFO  18:19:24,710 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T01:19Z] INFO  18:19:24,878 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:19Z] INFO  18:19:25,114 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T01:19Z] INFO  18:19:25,146 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:19Z] INFO  18:19:25,200 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:19Z] INFO  18:19:25,203 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:19Z] INFO  18:19:25,204 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:19Z] INFO  18:19:25,204 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:19Z] INFO  18:19:25,209 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/6/R14-18102_kapa-NGv3-PE100-NGv3-sort-6_15511526_31080332-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/6/R14-18102_kapa-NGv3-PE100-NGv3-6_15511526_31080332-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/6/tx/tmp95UpnW/R14-18102_kapa-NGv3-PE100-NGv3-6_15511526_31080332.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:19Z] INFO  18:19:25,256 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:19Z] INFO  18:19:25,257 HelpFormatter - Date/Time: 2016/04/14 18:19:25
[2016-04-15T01:19Z] INFO  18:19:25,258 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:19Z] INFO  18:19:25,258 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:19Z] INFO  18:19:25,259 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.11
[2016-04-15T01:19Z] WARN  18:19:25,294 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T01:19Z] WARN  18:19:25,297 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/6/tx/tmp95UpnW/R14-18102_kapa-NGv3-PE100-NGv3-6_15511526_31080332.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T01:19Z] INFO  18:19:25,296 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T01:19Z] INFO  18:19:25,534 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:19Z] INFO  18:19:25,805 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T01:19Z] INFO  18:19:25,815 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:19Z] INFO  18:19:25,932 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.10
[2016-04-15T01:19Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T01:19Z] INFO  18:19:25,952 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T01:19Z] INFO  18:19:25,973 IntervalUtils - Processing 139546 bp from intervals
[2016-04-15T01:19Z] INFO  18:19:25,975 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T01:19Z] INFO  18:19:25,976 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T01:19Z] WARN  18:19:25,986 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:19Z] INFO  18:19:26,177 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:19Z] INFO  18:19:26,258 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:19Z] INFO  18:19:26,259 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:19Z] INFO  18:19:26,260 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T01:19Z] INFO  18:19:26,261 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T01:19Z] INFO  18:19:26,278 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T01:19Z] INFO  18:19:26,279 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T01:19Z] INFO  18:19:26,325 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:19Z] WARN  18:19:26,330 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T01:19Z] WARN  18:19:26,331 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T01:19Z] INFO  18:19:26,436 IntervalUtils - Processing 239663 bp from intervals
[2016-04-15T01:19Z] WARN  18:19:26,442 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:19Z] INFO  18:19:26,520 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:19Z] INFO  18:19:26,590 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T01:19Z] INFO  18:19:26,663 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:19Z] INFO  18:19:26,664 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:19Z] INFO  18:19:26,665 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T01:19Z] INFO  18:19:26,666 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T01:19Z] INFO  18:19:26,692 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T01:19Z] INFO  18:19:26,693 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T01:19Z] GATK: HaplotypeCaller
[2016-04-15T01:19Z] INFO  18:19:26,923 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T01:19Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T01:19Z] INFO  18:19:26,993 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T01:19Z] INFO  18:19:26,994 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T01:19Z] WARN  18:19:27,326 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T01:19Z] WARN  18:19:27,327 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T01:19Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T01:19Z] INFO  18:19:29,877 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T01:19Z] INFO  18:19:29,878 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T01:19Z] INFO  18:19:30,068 ProgressMeter -      5:36976279      1.6619893E7    30.0 s            1.0 s       43.7%    68.0 s      38.0 s
[2016-04-15T01:19Z] WARN  18:19:30,204 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T01:19Z] WARN  18:19:30,205 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T01:19Z] INFO  18:19:30,258 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:19Z] INFO  18:19:30,272 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:19Z] INFO  18:19:30,272 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:19Z] INFO  18:19:30,272 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:19Z] INFO  18:19:30,277 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/6/R14-18102_kapa-NGv3-PE100-NGv3-sort-6_31083801_46593245-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/6/R14-18102_kapa-NGv3-PE100-NGv3-6_31083801_46593245-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/6/tx/tmpS_uWg3/R14-18102_kapa-NGv3-PE100-NGv3-6_31083801_46593245.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:19Z] INFO  18:19:30,300 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:19Z] INFO  18:19:30,301 HelpFormatter - Date/Time: 2016/04/14 18:19:30
[2016-04-15T01:19Z] INFO  18:19:30,301 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:19Z] INFO  18:19:30,302 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:19Z] WARN  18:19:30,343 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T01:19Z] INFO  18:19:30,350 ProgressMeter -     3:196613053       1.678364E7    90.0 s            5.0 s       76.2%   118.0 s      28.0 s
[2016-04-15T01:19Z] WARN  18:19:30,345 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/6/tx/tmpS_uWg3/R14-18102_kapa-NGv3-PE100-NGv3-6_31083801_46593245.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T01:19Z] INFO  18:19:30,633 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:19Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T01:19Z] INFO  18:19:30,680 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T01:19Z] INFO  18:19:30,680 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T01:19Z] INFO  18:19:30,867 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T01:19Z] INFO  18:19:30,877 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:19Z] INFO  18:19:30,967 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.09
[2016-04-15T01:19Z] INFO  18:19:31,009 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T01:19Z] WARN  18:19:31,211 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T01:19Z] WARN  18:19:31,212 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T01:19Z] INFO  18:19:31,606 IntervalUtils - Processing 501134 bp from intervals
[2016-04-15T01:19Z] WARN  18:19:31,611 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:19Z] INFO  18:19:31,769 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:19Z] INFO  18:19:31,937 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.026161139
[2016-04-15T01:19Z] INFO  18:19:31,938 PairHMM - Total compute time in PairHMM computeLikelihoods() : 8.592643119
[2016-04-15T01:19Z] INFO  18:19:31,939 HaplotypeCaller - Ran local assembly on 1860 active regions
[2016-04-15T01:19Z] INFO  18:19:32,004 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:19Z] INFO  18:19:32,005 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:19Z] INFO  18:19:32,005 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T01:19Z] INFO  18:19:32,006 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T01:19Z] INFO  18:19:32,007 ProgressMeter -            done     1.38636459E8    89.0 s            0.0 s      100.0%    89.0 s       0.0 s
[2016-04-15T01:19Z] INFO  18:19:32,008 ProgressMeter - Total runtime 89.47 secs, 1.49 min, 0.02 hours
[2016-04-15T01:19Z] INFO  18:19:32,009 MicroScheduler - 78997 reads were filtered out during the traversal out of approximately 447472 total reads (17.65%)
[2016-04-15T01:19Z] INFO  18:19:32,009 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:19Z] INFO  18:19:32,009 MicroScheduler -   -> 33217 reads (7.42% of total) failing DuplicateReadFilter
[2016-04-15T01:19Z] INFO  18:19:32,009 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:19Z] INFO  18:19:32,010 MicroScheduler -   -> 45780 reads (10.23% of total) failing HCMappingQualityFilter
[2016-04-15T01:19Z] INFO  18:19:32,010 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:19Z] INFO  18:19:32,010 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:19Z] INFO  18:19:32,011 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:19Z] INFO  18:19:32,011 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T01:19Z] INFO  18:19:32,016 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T01:19Z] INFO  18:19:32,017 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T01:19Z] INFO  18:19:32,336 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T01:19Z] INFO  18:19:32,848 ProgressMeter -      5:61688061      1.7912911E7    30.0 s            1.0 s       73.5%    40.0 s      10.0 s
[2016-04-15T01:19Z] INFO  18:19:33,621 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:19Z] GATK: HaplotypeCaller
[2016-04-15T01:19Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T01:19Z] INFO  18:19:34,446 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T01:19Z] INFO  18:19:34,447 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T01:19Z] WARN  18:19:34,802 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T01:19Z] WARN  18:19:34,804 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T01:19Z] INFO  18:19:35,265 ProgressMeter -      5:73931189      2.0455779E7    30.0 s            1.0 s       43.3%    69.0 s      39.0 s
[2016-04-15T01:19Z] INFO  18:19:35,784 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.018273039
[2016-04-15T01:19Z] INFO  18:19:35,785 PairHMM - Total compute time in PairHMM computeLikelihoods() : 0.111804544
[2016-04-15T01:19Z] INFO  18:19:35,786 HaplotypeCaller - Ran local assembly on 423 active regions
[2016-04-15T01:19Z] INFO  18:19:35,849 ProgressMeter -            done        9535184.0    26.0 s            2.0 s      100.0%    26.0 s       0.0 s
[2016-04-15T01:19Z] INFO  18:19:35,849 ProgressMeter - Total runtime 26.37 secs, 0.44 min, 0.01 hours
[2016-04-15T01:19Z] INFO  18:19:35,850 MicroScheduler - 4790 reads were filtered out during the traversal out of approximately 59544 total reads (8.04%)
[2016-04-15T01:19Z] INFO  18:19:35,850 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:19Z] INFO  18:19:35,850 MicroScheduler -   -> 4693 reads (7.88% of total) failing DuplicateReadFilter
[2016-04-15T01:19Z] INFO  18:19:35,851 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:19Z] INFO  18:19:35,851 MicroScheduler -   -> 97 reads (0.16% of total) failing HCMappingQualityFilter
[2016-04-15T01:19Z] INFO  18:19:35,851 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:19Z] INFO  18:19:35,851 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:19Z] INFO  18:19:35,852 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:19Z] INFO  18:19:35,852 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T01:19Z] INFO  18:19:36,205 ProgressMeter -      5:94955980      1.9121756E7    30.0 s            1.0 s       78.5%    38.0 s       8.0 s
[2016-04-15T01:19Z] INFO  18:19:36,280 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.029918354
[2016-04-15T01:19Z] INFO  18:19:36,281 PairHMM - Total compute time in PairHMM computeLikelihoods() : 38.169100650000004
[2016-04-15T01:19Z] INFO  18:19:36,282 HaplotypeCaller - Ran local assembly on 896 active regions
[2016-04-15T01:19Z] INFO  18:19:36,330 ProgressMeter -            done      3.3552483E7    95.0 s            2.0 s      100.0%    95.0 s       0.0 s
[2016-04-15T01:19Z] INFO  18:19:36,331 ProgressMeter - Total runtime 96.00 secs, 1.60 min, 0.03 hours
[2016-04-15T01:19Z] INFO  18:19:36,332 MicroScheduler - 30336 reads were filtered out during the traversal out of approximately 198584 total reads (15.28%)
[2016-04-15T01:19Z] INFO  18:19:36,332 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:19Z] INFO  18:19:36,333 MicroScheduler -   -> 15426 reads (7.77% of total) failing DuplicateReadFilter
[2016-04-15T01:19Z] INFO  18:19:36,334 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:19Z] INFO  18:19:36,335 MicroScheduler -   -> 14910 reads (7.51% of total) failing HCMappingQualityFilter
[2016-04-15T01:19Z] INFO  18:19:36,335 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:19Z] INFO  18:19:36,336 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:19Z] INFO  18:19:36,337 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:19Z] INFO  18:19:36,337 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T01:19Z] INFO  18:19:37,244 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:19Z] INFO  18:19:37,247 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:19Z] INFO  18:19:37,248 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:19Z] INFO  18:19:37,248 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:19Z] INFO  18:19:37,253 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/6/R14-18102_kapa-NGv3-PE100-NGv3-sort-6_46598699_62284307-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/6/R14-18102_kapa-NGv3-PE100-NGv3-6_46598699_62284307-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/6/tx/tmp7jFRIS/R14-18102_kapa-NGv3-PE100-NGv3-6_46598699_62284307.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:19Z] INFO  18:19:37,262 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:19Z] INFO  18:19:37,263 HelpFormatter - Date/Time: 2016/04/14 18:19:37
[2016-04-15T01:19Z] INFO  18:19:37,264 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:19Z] INFO  18:19:37,264 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:19Z] WARN  18:19:37,310 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T01:19Z] WARN  18:19:37,327 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/6/tx/tmp7jFRIS/R14-18102_kapa-NGv3-PE100-NGv3-6_46598699_62284307.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T01:19Z] INFO  18:19:37,529 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:19Z] INFO  18:19:37,567 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:19Z] INFO  18:19:37,727 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:19Z] INFO  18:19:37,841 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T01:19Z] INFO  18:19:37,862 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:19Z] GATK: HaplotypeCaller
[2016-04-15T01:19Z] INFO  18:19:37,951 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-15T01:19Z] INFO  18:19:37,978 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T01:19Z] GATK: HaplotypeCaller
[2016-04-15T01:19Z] INFO  18:19:38,318 IntervalUtils - Processing 157522 bp from intervals
[2016-04-15T01:19Z] WARN  18:19:38,323 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:19Z] INFO  18:19:38,448 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:19Z] INFO  18:19:38,572 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:19Z] INFO  18:19:38,573 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:19Z] INFO  18:19:38,573 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T01:19Z] INFO  18:19:38,575 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T01:19Z] INFO  18:19:38,583 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T01:19Z] INFO  18:19:38,586 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T01:19Z] INFO  18:19:38,674 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.040513583000000006
[2016-04-15T01:19Z] INFO  18:19:38,675 PairHMM - Total compute time in PairHMM computeLikelihoods() : 0.289839897
[2016-04-15T01:19Z] INFO  18:19:38,675 HaplotypeCaller - Ran local assembly on 835 active regions
[2016-04-15T01:19Z] INFO  18:19:38,754 ProgressMeter -            done      3.3641126E7    35.0 s            1.0 s      100.0%    35.0 s       0.0 s
[2016-04-15T01:19Z] INFO  18:19:38,755 ProgressMeter - Total runtime 35.93 secs, 0.60 min, 0.01 hours
[2016-04-15T01:19Z] INFO  18:19:38,756 MicroScheduler - 10776 reads were filtered out during the traversal out of approximately 130287 total reads (8.27%)
[2016-04-15T01:19Z] INFO  18:19:38,756 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:19Z] INFO  18:19:38,756 MicroScheduler -   -> 10600 reads (8.14% of total) failing DuplicateReadFilter
[2016-04-15T01:19Z] INFO  18:19:38,756 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:19Z] INFO  18:19:38,757 MicroScheduler -   -> 176 reads (0.14% of total) failing HCMappingQualityFilter
[2016-04-15T01:19Z] INFO  18:19:38,757 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:19Z] INFO  18:19:38,757 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:19Z] INFO  18:19:38,757 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:19Z] INFO  18:19:38,758 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T01:19Z] INFO  18:19:38,861 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T01:19Z] INFO  18:19:40,195 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:19Z] GATK: HaplotypeCaller
[2016-04-15T01:19Z] INFO  18:19:40,828 ProgressMeter -     5:122491578      1.3312315E7    30.0 s            2.0 s       69.8%    42.0 s      12.0 s
[2016-04-15T01:19Z] INFO  18:19:41,177 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.010954851
[2016-04-15T01:19Z] INFO  18:19:41,178 PairHMM - Total compute time in PairHMM computeLikelihoods() : 0.677974739
[2016-04-15T01:19Z] INFO  18:19:41,178 HaplotypeCaller - Ran local assembly on 953 active regions
[2016-04-15T01:19Z] INFO  18:19:41,177 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:19Z] INFO  18:19:41,180 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:19Z] INFO  18:19:41,181 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:19Z] INFO  18:19:41,181 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:19Z] INFO  18:19:41,186 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/6/R14-18102_kapa-NGv3-PE100-NGv3-sort-6_62390867_78173120-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/6/R14-18102_kapa-NGv3-PE100-NGv3-6_62390867_78173120-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/6/tx/tmpy6yjKE/R14-18102_kapa-NGv3-PE100-NGv3-6_62390867_78173120.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:19Z] INFO  18:19:41,204 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:19Z] INFO  18:19:41,205 HelpFormatter - Date/Time: 2016/04/14 18:19:41
[2016-04-15T01:19Z] INFO  18:19:41,205 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:19Z] INFO  18:19:41,206 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:19Z] INFO  18:19:41,222 ProgressMeter -            done      4.4963609E7    46.0 s            1.0 s      100.0%    46.0 s       0.0 s
[2016-04-15T01:19Z] INFO  18:19:41,223 ProgressMeter - Total runtime 46.60 secs, 0.78 min, 0.01 hours
[2016-04-15T01:19Z] INFO  18:19:41,223 MicroScheduler - 20636 reads were filtered out during the traversal out of approximately 205462 total reads (10.04%)
[2016-04-15T01:19Z] INFO  18:19:41,224 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:19Z] INFO  18:19:41,230 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:19Z] WARN  18:19:41,233 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T01:19Z] INFO  18:19:41,234 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:19Z] INFO  18:19:41,224 MicroScheduler -   -> 16821 reads (8.19% of total) failing DuplicateReadFilter
[2016-04-15T01:19Z] INFO  18:19:41,224 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:19Z] INFO  18:19:41,225 MicroScheduler -   -> 3815 reads (1.86% of total) failing HCMappingQualityFilter
[2016-04-15T01:19Z] INFO  18:19:41,225 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:19Z] INFO  18:19:41,225 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:19Z] INFO  18:19:41,225 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:19Z] INFO  18:19:41,226 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T01:19Z] INFO  18:19:41,234 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:19Z] INFO  18:19:41,235 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:19Z] WARN  18:19:41,236 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/6/tx/tmpy6yjKE/R14-18102_kapa-NGv3-PE100-NGv3-6_62390867_78173120.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T01:19Z] INFO  18:19:41,239 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/6/R14-18102_kapa-NGv3-PE100-NGv3-sort-6_78400388_93953258-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/6/R14-18102_kapa-NGv3-PE100-NGv3-6_78400388_93953258-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/6/tx/tmpvZhTLw/R14-18102_kapa-NGv3-PE100-NGv3-6_78400388_93953258.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:19Z] INFO  18:19:41,249 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:19Z] INFO  18:19:41,256 HelpFormatter - Date/Time: 2016/04/14 18:19:41
[2016-04-15T01:19Z] INFO  18:19:41,256 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:19Z] INFO  18:19:41,257 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:19Z] WARN  18:19:41,315 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T01:19Z] WARN  18:19:41,317 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/6/tx/tmpvZhTLw/R14-18102_kapa-NGv3-PE100-NGv3-6_78400388_93953258.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T01:19Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T01:19Z] INFO  18:19:41,445 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T01:19Z] INFO  18:19:41,445 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T01:19Z] INFO  18:19:41,446 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:19Z] INFO  18:19:41,595 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T01:19Z] INFO  18:19:41,604 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:19Z] INFO  18:19:41,678 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:19Z] INFO  18:19:41,687 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-15T01:19Z] INFO  18:19:41,707 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T01:19Z] WARN  18:19:41,741 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T01:19Z] WARN  18:19:41,741 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T01:19Z] INFO  18:19:41,916 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T01:19Z] INFO  18:19:41,928 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:19Z] INFO  18:19:41,989 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-15T01:19Z] INFO  18:19:42,032 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T01:19Z] INFO  18:19:42,183 IntervalUtils - Processing 103397 bp from intervals
[2016-04-15T01:19Z] WARN  18:19:42,189 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:19Z] INFO  18:19:42,327 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:19Z] INFO  18:19:42,432 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:19Z] INFO  18:19:42,433 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:19Z] INFO  18:19:42,434 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T01:19Z] INFO  18:19:42,434 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T01:19Z] INFO  18:19:42,446 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T01:19Z] INFO  18:19:42,447 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T01:19Z] INFO  18:19:42,554 IntervalUtils - Processing 131721 bp from intervals
[2016-04-15T01:19Z] WARN  18:19:42,559 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:19Z] INFO  18:19:42,722 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T01:19Z] INFO  18:19:42,732 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:19Z] INFO  18:19:42,826 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:19Z] INFO  18:19:42,827 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:19Z] INFO  18:19:42,832 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T01:19Z] INFO  18:19:42,833 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T01:19Z] INFO  18:19:42,834 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T01:19Z] INFO  18:19:42,834 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T01:19Z] INFO  18:19:42,866 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:19Z] INFO  18:19:43,058 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T01:19Z] GATK: HaplotypeCaller
[2016-04-15T01:19Z] INFO  18:19:43,870 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.015894943
[2016-04-15T01:19Z] INFO  18:19:43,871 PairHMM - Total compute time in PairHMM computeLikelihoods() : 1.7242144480000001
[2016-04-15T01:19Z] INFO  18:19:43,872 HaplotypeCaller - Ran local assembly on 824 active regions
[2016-04-15T01:19Z] INFO  18:19:43,916 ProgressMeter -            done      3.2848972E7    37.0 s            1.0 s      100.0%    37.0 s       0.0 s
[2016-04-15T01:19Z] INFO  18:19:43,918 ProgressMeter - Total runtime 37.73 secs, 0.63 min, 0.01 hours
[2016-04-15T01:19Z] INFO  18:19:43,917 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:19Z] INFO  18:19:43,921 MicroScheduler - 10283 reads were filtered out during the traversal out of approximately 127440 total reads (8.07%)
[2016-04-15T01:19Z] INFO  18:19:43,921 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:19Z] INFO  18:19:43,921 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:19Z] INFO  18:19:43,921 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:19Z] INFO  18:19:43,922 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:19Z] INFO  18:19:43,923 MicroScheduler -   -> 10114 reads (7.94% of total) failing DuplicateReadFilter
[2016-04-15T01:19Z] INFO  18:19:43,923 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:19Z] INFO  18:19:43,924 MicroScheduler -   -> 169 reads (0.13% of total) failing HCMappingQualityFilter
[2016-04-15T01:19Z] INFO  18:19:43,935 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:19Z] INFO  18:19:43,937 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:19Z] INFO  18:19:43,937 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:19Z] INFO  18:19:43,938 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T01:19Z] INFO  18:19:43,941 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/6/R14-18102_kapa-NGv3-PE100-NGv3-sort-6_93955015_109466584-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/6/R14-18102_kapa-NGv3-PE100-NGv3-6_93955015_109466584-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/6/tx/tmpiKi3vx/R14-18102_kapa-NGv3-PE100-NGv3-6_93955015_109466584.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:19Z] INFO  18:19:43,976 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:19Z] INFO  18:19:43,977 HelpFormatter - Date/Time: 2016/04/14 18:19:43
[2016-04-15T01:19Z] INFO  18:19:43,978 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:19Z] INFO  18:19:43,978 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:19Z] WARN  18:19:44,017 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T01:19Z] WARN  18:19:44,020 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/6/tx/tmpiKi3vx/R14-18102_kapa-NGv3-PE100-NGv3-6_93955015_109466584.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T01:19Z] INFO  18:19:44,293 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:19Z] INFO  18:19:44,533 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T01:19Z] INFO  18:19:44,543 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:19Z] INFO  18:19:44,613 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-15T01:19Z] INFO  18:19:44,648 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T01:19Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T01:19Z] INFO  18:19:44,857 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T01:19Z] INFO  18:19:44,858 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T01:19Z] INFO  18:19:44,964 IntervalUtils - Processing 95525 bp from intervals
[2016-04-15T01:19Z] WARN  18:19:44,969 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:19Z] INFO  18:19:45,055 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:19Z] WARN  18:19:45,117 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T01:19Z] WARN  18:19:45,121 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T01:19Z] INFO  18:19:45,165 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:19Z] INFO  18:19:45,166 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:19Z] INFO  18:19:45,166 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T01:19Z] INFO  18:19:45,167 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T01:19Z] INFO  18:19:45,168 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T01:19Z] INFO  18:19:45,168 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T01:19Z] INFO  18:19:45,403 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:19Z] INFO  18:19:45,435 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T01:19Z] GATK: HaplotypeCaller
[2016-04-15T01:19Z] INFO  18:19:46,487 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:19Z] INFO  18:19:46,491 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:19Z] INFO  18:19:46,492 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:19Z] INFO  18:19:46,492 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:19Z] INFO  18:19:46,498 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/6/R14-18102_kapa-NGv3-PE100-NGv3-sort-6_109467960_124979532-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/6/R14-18102_kapa-NGv3-PE100-NGv3-6_109467960_124979532-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/6/tx/tmpRCaWag/R14-18102_kapa-NGv3-PE100-NGv3-6_109467960_124979532.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:19Z] INFO  18:19:46,519 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:19Z] INFO  18:19:46,520 HelpFormatter - Date/Time: 2016/04/14 18:19:46
[2016-04-15T01:19Z] INFO  18:19:46,521 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:19Z] INFO  18:19:46,522 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:19Z] WARN  18:19:46,546 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T01:19Z] WARN  18:19:46,549 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/6/tx/tmpRCaWag/R14-18102_kapa-NGv3-PE100-NGv3-6_109467960_124979532.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T01:19Z] INFO  18:19:46,794 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:19Z] INFO  18:19:46,809 ProgressMeter -     5:134366966      2.5409044E7    30.0 s            1.0 s       25.3%   118.0 s      88.0 s
[2016-04-15T01:19Z] INFO  18:19:47,046 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T01:19Z] INFO  18:19:47,056 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:19Z] INFO  18:19:47,124 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-15T01:19Z] INFO  18:19:47,142 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T01:19Z] INFO  18:19:47,519 ProgressMeter -     5:149431660      1.5353833E7    30.0 s            1.0 s       39.3%    76.0 s      46.0 s
[2016-04-15T01:19Z] INFO  18:19:47,610 IntervalUtils - Processing 147815 bp from intervals
[2016-04-15T01:19Z] WARN  18:19:47,627 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:19Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T01:19Z] INFO  18:19:47,710 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T01:19Z] INFO  18:19:47,722 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T01:19Z] INFO  18:19:47,732 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:19Z] INFO  18:19:47,834 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:19Z] INFO  18:19:47,835 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:19Z] INFO  18:19:47,836 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T01:19Z] INFO  18:19:47,837 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T01:19Z] INFO  18:19:47,837 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T01:19Z] INFO  18:19:47,838 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T01:19Z] INFO  18:19:47,895 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.007683042
[2016-04-15T01:19Z] INFO  18:19:47,895 PairHMM - Total compute time in PairHMM computeLikelihoods() : 0.49535964400000004
[2016-04-15T01:19Z] INFO  18:19:47,896 HaplotypeCaller - Ran local assembly on 750 active regions
[2016-04-15T01:19Z] WARN  18:19:48,003 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T01:19Z] WARN  18:19:48,003 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T01:19Z] INFO  18:19:48,124 ProgressMeter -            done      2.8586597E7    37.0 s            1.0 s      100.0%    37.0 s       0.0 s
[2016-04-15T01:19Z] INFO  18:19:48,125 ProgressMeter - Total runtime 37.33 secs, 0.62 min, 0.01 hours
[2016-04-15T01:19Z] INFO  18:19:48,125 MicroScheduler - 10826 reads were filtered out during the traversal out of approximately 131242 total reads (8.25%)
[2016-04-15T01:19Z] INFO  18:19:48,126 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:19Z] INFO  18:19:48,126 MicroScheduler -   -> 10617 reads (8.09% of total) failing DuplicateReadFilter
[2016-04-15T01:19Z] INFO  18:19:48,126 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:19Z] INFO  18:19:48,126 MicroScheduler -   -> 209 reads (0.16% of total) failing HCMappingQualityFilter
[2016-04-15T01:19Z] INFO  18:19:48,127 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:19Z] INFO  18:19:48,127 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:19Z] INFO  18:19:48,127 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:19Z] INFO  18:19:48,127 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T01:19Z] INFO  18:19:48,136 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T01:19Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T01:19Z] INFO  18:19:48,338 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T01:19Z] INFO  18:19:48,339 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T01:19Z] WARN  18:19:48,674 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T01:19Z] WARN  18:19:48,676 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T01:19Z] INFO  18:19:49,049 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:19Z] INFO  18:19:49,052 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:19Z] INFO  18:19:49,052 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:19Z] INFO  18:19:49,052 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:19Z] INFO  18:19:49,067 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/6/R14-18102_kapa-NGv3-PE100-NGv3-sort-6_125112484_142397186-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/6/R14-18102_kapa-NGv3-PE100-NGv3-6_125112484_142397186-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/6/tx/tmpxVIfbF/R14-18102_kapa-NGv3-PE100-NGv3-6_125112484_142397186.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:19Z] INFO  18:19:49,094 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:19Z] INFO  18:19:49,095 HelpFormatter - Date/Time: 2016/04/14 18:19:49
[2016-04-15T01:19Z] INFO  18:19:49,095 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:19Z] INFO  18:19:49,100 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:19Z] WARN  18:19:49,141 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T01:19Z] WARN  18:19:49,145 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/6/tx/tmpxVIfbF/R14-18102_kapa-NGv3-PE100-NGv3-6_125112484_142397186.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T01:19Z] INFO  18:19:49,404 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:19Z] INFO  18:19:49,536 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:19Z] INFO  18:19:49,592 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T01:19Z] INFO  18:19:49,601 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:19Z] INFO  18:19:49,682 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-15T01:19Z] INFO  18:19:49,717 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T01:19Z] GATK: HaplotypeCaller
[2016-04-15T01:19Z] INFO  18:19:50,217 IntervalUtils - Processing 156964 bp from intervals
[2016-04-15T01:19Z] WARN  18:19:50,222 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:19Z] INFO  18:19:50,247 ProgressMeter -     5:170597207      1.5076241E7    30.0 s            1.0 s       66.0%    45.0 s      15.0 s
[2016-04-15T01:19Z] INFO  18:19:50,332 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.007767230000000001
[2016-04-15T01:19Z] INFO  18:19:50,345 PairHMM - Total compute time in PairHMM computeLikelihoods() : 0.472600585
[2016-04-15T01:19Z] INFO  18:19:50,346 HaplotypeCaller - Ran local assembly on 1318 active regions
[2016-04-15T01:19Z] INFO  18:19:50,356 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:19Z] INFO  18:19:50,381 ProgressMeter -            done      8.6588753E7    50.0 s            0.0 s      100.0%    50.0 s       0.0 s
[2016-04-15T01:19Z] INFO  18:19:50,382 ProgressMeter - Total runtime 50.33 secs, 0.84 min, 0.01 hours
[2016-04-15T01:19Z] INFO  18:19:50,382 MicroScheduler - 18305 reads were filtered out during the traversal out of approximately 222896 total reads (8.21%)
[2016-04-15T01:19Z] INFO  18:19:50,382 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:19Z] INFO  18:19:50,388 MicroScheduler -   -> 18036 reads (8.09% of total) failing DuplicateReadFilter
[2016-04-15T01:19Z] INFO  18:19:50,388 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:19Z] INFO  18:19:50,388 MicroScheduler -   -> 269 reads (0.12% of total) failing HCMappingQualityFilter
[2016-04-15T01:19Z] INFO  18:19:50,388 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:19Z] INFO  18:19:50,389 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:19Z] INFO  18:19:50,389 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:19Z] INFO  18:19:50,389 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T01:19Z] INFO  18:19:50,480 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:19Z] INFO  18:19:50,481 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:19Z] INFO  18:19:50,481 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T01:19Z] INFO  18:19:50,482 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T01:19Z] INFO  18:19:50,488 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T01:19Z] INFO  18:19:50,488 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T01:19Z] INFO  18:19:50,683 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T01:19Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T01:19Z] INFO  18:19:51,363 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T01:19Z] INFO  18:19:51,364 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T01:19Z] WARN  18:19:51,642 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T01:19Z] WARN  18:19:51,643 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T01:19Z] INFO  18:19:51,937 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:19Z] GATK: HaplotypeCaller
[2016-04-15T01:19Z] INFO  18:19:52,797 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:19Z] INFO  18:19:52,799 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:19Z] INFO  18:19:52,799 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:19Z] INFO  18:19:52,800 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:19Z] INFO  18:19:52,811 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/6/R14-18102_kapa-NGv3-PE100-NGv3-sort-6_142399691_157963777-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/6/R14-18102_kapa-NGv3-PE100-NGv3-6_142399691_157963777-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/6/tx/tmp_u7XED/R14-18102_kapa-NGv3-PE100-NGv3-6_142399691_157963777.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:19Z] INFO  18:19:52,828 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:19Z] INFO  18:19:52,829 HelpFormatter - Date/Time: 2016/04/14 18:19:52
[2016-04-15T01:19Z] INFO  18:19:52,830 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:19Z] INFO  18:19:52,830 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:19Z] WARN  18:19:52,857 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T01:19Z] WARN  18:19:52,860 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/6/tx/tmp_u7XED/R14-18102_kapa-NGv3-PE100-NGv3-6_142399691_157963777.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T01:19Z] INFO  18:19:53,063 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:19Z] INFO  18:19:53,307 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T01:19Z] INFO  18:19:53,328 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:19Z] INFO  18:19:53,412 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-15T01:19Z] INFO  18:19:53,438 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T01:19Z] INFO  18:19:53,754 ProgressMeter -     5:177733920      1.5544927E7    30.0 s            1.0 s       50.2%    59.0 s      29.0 s
[2016-04-15T01:19Z] INFO  18:19:53,894 IntervalUtils - Processing 183871 bp from intervals
[2016-04-15T01:19Z] WARN  18:19:53,910 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:19Z] INFO  18:19:54,004 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:19Z] INFO  18:19:54,144 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:19Z] INFO  18:19:54,145 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:19Z] INFO  18:19:54,146 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T01:19Z] INFO  18:19:54,146 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T01:19Z] INFO  18:19:54,148 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T01:19Z] INFO  18:19:54,148 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T01:19Z] INFO  18:19:54,395 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T01:19Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T01:19Z] INFO  18:19:54,669 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T01:19Z] INFO  18:19:54,670 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T01:19Z] WARN  18:19:55,048 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T01:19Z] WARN  18:19:55,049 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T01:19Z] INFO  18:19:55,854 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:19Z] INFO  18:19:55,873 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:19Z] INFO  18:19:55,874 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:19Z] INFO  18:19:55,875 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:19Z] INFO  18:19:55,880 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/6/R14-18102_kapa-NGv3-PE100-NGv3-sort-6_158013810_171115067-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/6/R14-18102_kapa-NGv3-PE100-NGv3-6_158013810_171115067-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/6/tx/tmpTfXVf5/R14-18102_kapa-NGv3-PE100-NGv3-6_158013810_171115067.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:19Z] INFO  18:19:55,914 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:19Z] INFO  18:19:55,915 HelpFormatter - Date/Time: 2016/04/14 18:19:55
[2016-04-15T01:19Z] INFO  18:19:55,916 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:19Z] INFO  18:19:55,919 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:19Z] WARN  18:19:55,967 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T01:19Z] WARN  18:19:55,970 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/6/tx/tmpTfXVf5/R14-18102_kapa-NGv3-PE100-NGv3-6_158013810_171115067.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T01:19Z] INFO  18:19:56,246 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:19Z] INFO  18:19:56,281 ProgressMeter -       6:7601569      1.2899121E7    30.0 s            2.0 s       55.9%    53.0 s      23.0 s
[2016-04-15T01:19Z] INFO  18:19:56,477 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T01:19Z] INFO  18:19:56,486 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:19Z] INFO  18:19:56,588 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.10
[2016-04-15T01:19Z] INFO  18:19:56,617 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T01:19Z] INFO  18:19:56,708 ProgressMeter -      6:25701443      1.4729017E7    30.0 s            2.0 s       29.6%   101.0 s      71.0 s
[2016-04-15T01:19Z] INFO  18:19:57,058 IntervalUtils - Processing 143202 bp from intervals
[2016-04-15T01:19Z] WARN  18:19:57,063 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:19Z] INFO  18:19:57,150 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:19Z] INFO  18:19:57,240 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:19Z] INFO  18:19:57,241 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:19Z] INFO  18:19:57,242 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T01:19Z] INFO  18:19:57,242 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T01:19Z] INFO  18:19:57,243 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T01:19Z] INFO  18:19:57,243 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T01:19Z] INFO  18:19:57,454 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T01:19Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T01:19Z] INFO  18:19:59,072 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T01:19Z] INFO  18:19:59,073 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T01:19Z] INFO  18:19:59,108 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.008206424
[2016-04-15T01:19Z] INFO  18:19:59,119 PairHMM - Total compute time in PairHMM computeLikelihoods() : 0.6768954810000001
[2016-04-15T01:19Z] INFO  18:19:59,120 HaplotypeCaller - Ran local assembly on 1454 active regions
[2016-04-15T01:19Z] INFO  18:19:59,167 ProgressMeter -            done     1.03497862E8    53.0 s            0.0 s      100.0%    53.0 s       0.0 s
[2016-04-15T01:19Z] INFO  18:19:59,167 ProgressMeter - Total runtime 53.92 secs, 0.90 min, 0.01 hours
[2016-04-15T01:19Z] INFO  18:19:59,168 MicroScheduler - 30252 reads were filtered out during the traversal out of approximately 238911 total reads (12.66%)
[2016-04-15T01:19Z] INFO  18:19:59,169 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:19Z] INFO  18:19:59,169 MicroScheduler -   -> 17597 reads (7.37% of total) failing DuplicateReadFilter
[2016-04-15T01:19Z] INFO  18:19:59,169 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:19Z] INFO  18:19:59,169 MicroScheduler -   -> 12655 reads (5.30% of total) failing HCMappingQualityFilter
[2016-04-15T01:19Z] INFO  18:19:59,170 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:19Z] INFO  18:19:59,170 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:19Z] INFO  18:19:59,170 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:19Z] INFO  18:19:59,170 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T01:19Z] WARN  18:19:59,426 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T01:19Z] WARN  18:19:59,438 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T01:20Z] INFO  18:20:00,852 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:20Z] GATK: HaplotypeCaller
[2016-04-15T01:20Z] INFO  18:20:01,522 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.009453165000000001
[2016-04-15T01:20Z] INFO  18:20:01,523 PairHMM - Total compute time in PairHMM computeLikelihoods() : 0.9648021170000001
[2016-04-15T01:20Z] INFO  18:20:01,523 HaplotypeCaller - Ran local assembly on 773 active regions
[2016-04-15T01:20Z] INFO  18:20:01,577 ProgressMeter -            done      2.8976366E7    41.0 s            1.0 s      100.0%    41.0 s       0.0 s
[2016-04-15T01:20Z] INFO  18:20:01,578 ProgressMeter - Total runtime 41.36 secs, 0.69 min, 0.01 hours
[2016-04-15T01:20Z] INFO  18:20:01,579 MicroScheduler - 12987 reads were filtered out during the traversal out of approximately 159639 total reads (8.14%)
[2016-04-15T01:20Z] INFO  18:20:01,579 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:20Z] INFO  18:20:01,579 MicroScheduler -   -> 12799 reads (8.02% of total) failing DuplicateReadFilter
[2016-04-15T01:20Z] INFO  18:20:01,580 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:20Z] INFO  18:20:01,580 MicroScheduler -   -> 188 reads (0.12% of total) failing HCMappingQualityFilter
[2016-04-15T01:20Z] INFO  18:20:01,580 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:20Z] INFO  18:20:01,580 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:20Z] INFO  18:20:01,581 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:20Z] INFO  18:20:01,581 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T01:20Z] INFO  18:20:02,019 ProgressMeter -      6:31516075         558998.0    30.0 s           53.0 s        3.3%    15.2 m      14.7 m
[2016-04-15T01:20Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T01:20Z] INFO  18:20:02,300 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T01:20Z] INFO  18:20:02,301 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T01:20Z] WARN  18:20:02,595 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T01:20Z] WARN  18:20:02,596 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T01:20Z] INFO  18:20:02,955 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:20Z] GATK: HaplotypeCaller
[2016-04-15T01:20Z] INFO  18:20:04,146 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:20Z] INFO  18:20:04,159 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:20Z] INFO  18:20:04,160 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:20Z] INFO  18:20:04,160 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:20Z] INFO  18:20:04,164 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/7/R14-18102_kapa-NGv3-PE100-NGv3-sort-7_0_15584548-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/7/R14-18102_kapa-NGv3-PE100-NGv3-7_0_15584548-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/7/tx/tmpiUxffE/R14-18102_kapa-NGv3-PE100-NGv3-7_0_15584548.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:20Z] INFO  18:20:04,179 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:20Z] INFO  18:20:04,179 HelpFormatter - Date/Time: 2016/04/14 18:20:04
[2016-04-15T01:20Z] INFO  18:20:04,179 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:20Z] INFO  18:20:04,180 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:20Z] WARN  18:20:04,226 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T01:20Z] WARN  18:20:04,229 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/7/tx/tmpiUxffE/R14-18102_kapa-NGv3-PE100-NGv3-7_0_15584548.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T01:20Z] INFO  18:20:04,451 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:20Z] INFO  18:20:04,624 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T01:20Z] INFO  18:20:04,637 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:20Z] INFO  18:20:04,734 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.10
[2016-04-15T01:20Z] INFO  18:20:04,755 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T01:20Z] INFO  18:20:05,149 IntervalUtils - Processing 187602 bp from intervals
[2016-04-15T01:20Z] WARN  18:20:05,155 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:20Z] INFO  18:20:05,264 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:20Z] INFO  18:20:05,385 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:20Z] INFO  18:20:05,386 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:20Z] INFO  18:20:05,387 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T01:20Z] INFO  18:20:05,388 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T01:20Z] INFO  18:20:05,389 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T01:20Z] INFO  18:20:05,389 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T01:20Z] INFO  18:20:05,578 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T01:20Z] INFO  18:20:06,396 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:20Z] INFO  18:20:06,399 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:20Z] INFO  18:20:06,399 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:20Z] INFO  18:20:06,400 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:20Z] INFO  18:20:06,416 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/7/R14-18102_kapa-NGv3-PE100-NGv3-sort-7_15599765_31117713-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/7/R14-18102_kapa-NGv3-PE100-NGv3-7_15599765_31117713-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/7/tx/tmpkf9bpk/R14-18102_kapa-NGv3-PE100-NGv3-7_15599765_31117713.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:20Z] INFO  18:20:06,444 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:20Z] INFO  18:20:06,444 HelpFormatter - Date/Time: 2016/04/14 18:20:06
[2016-04-15T01:20Z] INFO  18:20:06,444 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:20Z] INFO  18:20:06,445 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:20Z] WARN  18:20:06,504 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T01:20Z] WARN  18:20:06,522 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/7/tx/tmpkf9bpk/R14-18102_kapa-NGv3-PE100-NGv3-7_15599765_31117713.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T01:20Z] INFO  18:20:06,835 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:20Z] INFO  18:20:07,008 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T01:20Z] INFO  18:20:07,017 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:20Z] INFO  18:20:07,099 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-15T01:20Z] INFO  18:20:07,123 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T01:20Z] INFO  18:20:07,516 IntervalUtils - Processing 149727 bp from intervals
[2016-04-15T01:20Z] WARN  18:20:07,523 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:20Z] INFO  18:20:07,635 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:20Z] INFO  18:20:07,761 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:20Z] INFO  18:20:07,762 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:20Z] INFO  18:20:07,762 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T01:20Z] INFO  18:20:07,762 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T01:20Z] INFO  18:20:07,770 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T01:20Z] INFO  18:20:07,771 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T01:20Z] INFO  18:20:08,095 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T01:20Z] INFO  18:20:08,593 ProgressMeter -      6:53706929      2.0396742E7    30.0 s            1.0 s       54.8%    54.0 s      24.0 s
[2016-04-15T01:20Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T01:20Z] INFO  18:20:09,096 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T01:20Z] INFO  18:20:09,108 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T01:20Z] WARN  18:20:09,421 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T01:20Z] WARN  18:20:09,423 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T01:20Z] INFO  18:20:11,725 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.023198311000000003
[2016-04-15T01:20Z] INFO  18:20:11,726 PairHMM - Total compute time in PairHMM computeLikelihoods() : 0.813339079
[2016-04-15T01:20Z] INFO  18:20:11,727 HaplotypeCaller - Ran local assembly on 990 active regions
[2016-04-15T01:20Z] INFO  18:20:11,773 ProgressMeter -            done      4.2296058E7    45.0 s            1.0 s      100.0%    45.0 s       0.0 s
[2016-04-15T01:20Z] INFO  18:20:11,773 ProgressMeter - Total runtime 45.51 secs, 0.76 min, 0.01 hours
[2016-04-15T01:20Z] INFO  18:20:11,774 MicroScheduler - 22024 reads were filtered out during the traversal out of approximately 194001 total reads (11.35%)
[2016-04-15T01:20Z] INFO  18:20:11,774 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:20Z] INFO  18:20:11,774 MicroScheduler -   -> 15167 reads (7.82% of total) failing DuplicateReadFilter
[2016-04-15T01:20Z] INFO  18:20:11,774 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:20Z] INFO  18:20:11,775 MicroScheduler -   -> 6857 reads (3.53% of total) failing HCMappingQualityFilter
[2016-04-15T01:20Z] INFO  18:20:11,775 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:20Z] INFO  18:20:11,775 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:20Z] INFO  18:20:11,775 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:20Z] INFO  18:20:11,776 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T01:20Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T01:20Z] INFO  18:20:11,820 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T01:20Z] INFO  18:20:11,821 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T01:20Z] INFO  18:20:12,449 ProgressMeter -      6:76072633      2.1972844E7    30.0 s            1.0 s       89.2%    33.0 s       3.0 s
[2016-04-15T01:20Z] INFO  18:20:12,499 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.011378273000000001
[2016-04-15T01:20Z] INFO  18:20:12,500 PairHMM - Total compute time in PairHMM computeLikelihoods() : 0.8634839160000001
[2016-04-15T01:20Z] INFO  18:20:12,501 HaplotypeCaller - Ran local assembly on 1196 active regions
[2016-04-15T01:20Z] INFO  18:20:12,546 ProgressMeter -            done      5.3274727E7    48.0 s            0.0 s      100.0%    48.0 s       0.0 s
[2016-04-15T01:20Z] INFO  18:20:12,547 ProgressMeter - Total runtime 48.82 secs, 0.81 min, 0.01 hours
[2016-04-15T01:20Z] INFO  18:20:12,548 MicroScheduler - 33516 reads were filtered out during the traversal out of approximately 282085 total reads (11.88%)
[2016-04-15T01:20Z] INFO  18:20:12,548 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:20Z] INFO  18:20:12,549 MicroScheduler -   -> 22109 reads (7.84% of total) failing DuplicateReadFilter
[2016-04-15T01:20Z] INFO  18:20:12,549 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:20Z] INFO  18:20:12,550 MicroScheduler -   -> 11407 reads (4.04% of total) failing HCMappingQualityFilter
[2016-04-15T01:20Z] INFO  18:20:12,551 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:20Z] INFO  18:20:12,551 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:20Z] INFO  18:20:12,552 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:20Z] INFO  18:20:12,552 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T01:20Z] WARN  18:20:12,577 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T01:20Z] WARN  18:20:12,589 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T01:20Z] INFO  18:20:12,845 ProgressMeter -      6:90042805      2.3911149E7    30.0 s            1.0 s       74.1%    40.0 s      10.0 s
[2016-04-15T01:20Z] INFO  18:20:13,289 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:20Z] GATK: HaplotypeCaller
[2016-04-15T01:20Z] INFO  18:20:14,123 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:20Z] GATK: HaplotypeCaller
[2016-04-15T01:20Z] INFO  18:20:14,635 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.006698835
[2016-04-15T01:20Z] INFO  18:20:14,637 PairHMM - Total compute time in PairHMM computeLikelihoods() : 0.262583805
[2016-04-15T01:20Z] INFO  18:20:14,637 HaplotypeCaller - Ran local assembly on 780 active regions
[2016-04-15T01:20Z] INFO  18:20:14,692 ProgressMeter -            done      2.9471788E7    32.0 s            1.0 s      100.0%    32.0 s       0.0 s
[2016-04-15T01:20Z] INFO  18:20:14,692 ProgressMeter - Total runtime 32.26 secs, 0.54 min, 0.01 hours
[2016-04-15T01:20Z] INFO  18:20:14,693 MicroScheduler - 11244 reads were filtered out during the traversal out of approximately 119330 total reads (9.42%)
[2016-04-15T01:20Z] INFO  18:20:14,693 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:20Z] INFO  18:20:14,693 MicroScheduler -   -> 9461 reads (7.93% of total) failing DuplicateReadFilter
[2016-04-15T01:20Z] INFO  18:20:14,693 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:20Z] INFO  18:20:14,694 MicroScheduler -   -> 1783 reads (1.49% of total) failing HCMappingQualityFilter
[2016-04-15T01:20Z] INFO  18:20:14,694 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:20Z] INFO  18:20:14,694 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:20Z] INFO  18:20:14,694 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:20Z] INFO  18:20:14,695 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T01:20Z] INFO  18:20:15,190 ProgressMeter -     6:109282794      2.0826723E7    30.0 s            1.0 s       96.4%    31.0 s       1.0 s
[2016-04-15T01:20Z] INFO  18:20:15,719 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.005896972
[2016-04-15T01:20Z] INFO  18:20:15,720 PairHMM - Total compute time in PairHMM computeLikelihoods() : 0.24557699100000002
[2016-04-15T01:20Z] INFO  18:20:15,720 HaplotypeCaller - Ran local assembly on 668 active regions
[2016-04-15T01:20Z] INFO  18:20:15,774 ProgressMeter -            done      2.2700296E7    30.0 s            1.0 s      100.0%    30.0 s       0.0 s
[2016-04-15T01:20Z] INFO  18:20:15,774 ProgressMeter - Total runtime 30.61 secs, 0.51 min, 0.01 hours
[2016-04-15T01:20Z] INFO  18:20:15,775 MicroScheduler - 9284 reads were filtered out during the traversal out of approximately 110121 total reads (8.43%)
[2016-04-15T01:20Z] INFO  18:20:15,776 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:20Z] INFO  18:20:15,776 MicroScheduler -   -> 8466 reads (7.69% of total) failing DuplicateReadFilter
[2016-04-15T01:20Z] INFO  18:20:15,776 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:20Z] INFO  18:20:15,776 MicroScheduler -   -> 818 reads (0.74% of total) failing HCMappingQualityFilter
[2016-04-15T01:20Z] INFO  18:20:15,777 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:20Z] INFO  18:20:15,777 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:20Z] INFO  18:20:15,777 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:20Z] INFO  18:20:15,777 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T01:20Z] INFO  18:20:15,979 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:20Z] GATK: HaplotypeCaller
[2016-04-15T01:20Z] INFO  18:20:16,613 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:20Z] INFO  18:20:16,631 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:20Z] INFO  18:20:16,632 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:20Z] INFO  18:20:16,632 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:20Z] INFO  18:20:16,636 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/7/R14-18102_kapa-NGv3-PE100-NGv3-sort-7_31120227_47317818-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/7/R14-18102_kapa-NGv3-PE100-NGv3-7_31120227_47317818-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/7/tx/tmp9EUhhR/R14-18102_kapa-NGv3-PE100-NGv3-7_31120227_47317818.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:20Z] INFO  18:20:16,660 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:20Z] INFO  18:20:16,660 HelpFormatter - Date/Time: 2016/04/14 18:20:16
[2016-04-15T01:20Z] INFO  18:20:16,660 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:20Z] INFO  18:20:16,664 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:20Z] WARN  18:20:16,693 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T01:20Z] WARN  18:20:16,696 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/7/tx/tmp9EUhhR/R14-18102_kapa-NGv3-PE100-NGv3-7_31120227_47317818.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T01:20Z] INFO  18:20:16,827 ProgressMeter -     5:140182464     1.07878626E8    60.0 s            0.0 s       55.9%   107.0 s      47.0 s
[2016-04-15T01:20Z] INFO  18:20:16,987 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:20Z] INFO  18:20:17,162 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T01:20Z] INFO  18:20:17,173 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:20Z] INFO  18:20:17,245 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-15T01:20Z] INFO  18:20:17,279 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T01:20Z] INFO  18:20:17,365 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:20Z] INFO  18:20:17,520 ProgressMeter -     5:157178398      9.3183694E7    60.0 s            0.0 s       96.0%    62.0 s       2.0 s
[2016-04-15T01:20Z] INFO  18:20:17,574 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:20Z] INFO  18:20:17,587 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:20Z] INFO  18:20:17,588 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:20Z] INFO  18:20:17,589 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:20Z] INFO  18:20:17,593 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/7/R14-18102_kapa-NGv3-PE100-NGv3-sort-7_47319761_63093154-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/7/R14-18102_kapa-NGv3-PE100-NGv3-7_47319761_63093154-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/7/tx/tmp2BgNUO/R14-18102_kapa-NGv3-PE100-NGv3-7_47319761_63093154.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:20Z] INFO  18:20:17,616 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:20Z] INFO  18:20:17,617 HelpFormatter - Date/Time: 2016/04/14 18:20:17
[2016-04-15T01:20Z] INFO  18:20:17,617 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:20Z] INFO  18:20:17,617 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:20Z] GATK: HaplotypeCaller
[2016-04-15T01:20Z] WARN  18:20:17,665 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T01:20Z] WARN  18:20:17,671 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/7/tx/tmp2BgNUO/R14-18102_kapa-NGv3-PE100-NGv3-7_47319761_63093154.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T01:20Z] INFO  18:20:17,702 IntervalUtils - Processing 138106 bp from intervals
[2016-04-15T01:20Z] WARN  18:20:17,707 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:20Z] INFO  18:20:17,784 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:20Z] INFO  18:20:17,857 ProgressMeter -     6:117674236      2.2784598E7    30.0 s            1.0 s       66.6%    45.0 s      15.0 s
[2016-04-15T01:20Z] INFO  18:20:17,893 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:20Z] INFO  18:20:17,894 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:20Z] INFO  18:20:17,897 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T01:20Z] INFO  18:20:17,898 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T01:20Z] INFO  18:20:17,899 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T01:20Z] INFO  18:20:17,899 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T01:20Z] INFO  18:20:17,958 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:20Z] INFO  18:20:18,118 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T01:20Z] INFO  18:20:18,131 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T01:20Z] INFO  18:20:18,140 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:20Z] INFO  18:20:18,196 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-15T01:20Z] INFO  18:20:18,236 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T01:20Z] INFO  18:20:18,651 IntervalUtils - Processing 74873 bp from intervals
[2016-04-15T01:20Z] WARN  18:20:18,656 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:20Z] INFO  18:20:18,776 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:20Z] INFO  18:20:18,848 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:20Z] INFO  18:20:18,848 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:20Z] INFO  18:20:18,848 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T01:20Z] INFO  18:20:18,849 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T01:20Z] INFO  18:20:18,859 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T01:20Z] INFO  18:20:18,860 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T01:20Z] INFO  18:20:19,131 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T01:20Z] INFO  18:20:19,143 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:20Z] INFO  18:20:19,145 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:20Z] INFO  18:20:19,145 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:20Z] INFO  18:20:19,167 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:20Z] INFO  18:20:19,172 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/7/R14-18102_kapa-NGv3-PE100-NGv3-sort-7_63095909_78636522-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/7/R14-18102_kapa-NGv3-PE100-NGv3-7_63095909_78636522-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/7/tx/tmp5hXazo/R14-18102_kapa-NGv3-PE100-NGv3-7_63095909_78636522.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:20Z] INFO  18:20:19,181 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:20Z] INFO  18:20:19,182 HelpFormatter - Date/Time: 2016/04/14 18:20:19
[2016-04-15T01:20Z] INFO  18:20:19,182 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:20Z] INFO  18:20:19,182 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:20Z] WARN  18:20:19,232 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T01:20Z] WARN  18:20:19,235 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/7/tx/tmp5hXazo/R14-18102_kapa-NGv3-PE100-NGv3-7_63095909_78636522.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T01:20Z] INFO  18:20:19,340 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.024484329000000003
[2016-04-15T01:20Z] INFO  18:20:19,341 PairHMM - Total compute time in PairHMM computeLikelihoods() : 2.8890821850000004
[2016-04-15T01:20Z] INFO  18:20:19,343 HaplotypeCaller - Ran local assembly on 1509 active regions
[2016-04-15T01:20Z] INFO  18:20:19,402 ProgressMeter -            done     1.03846414E8    61.0 s            0.0 s      100.0%    61.0 s       0.0 s
[2016-04-15T01:20Z] INFO  18:20:19,403 ProgressMeter - Total runtime 61.94 secs, 1.03 min, 0.02 hours
[2016-04-15T01:20Z] INFO  18:20:19,403 MicroScheduler - 25535 reads were filtered out during the traversal out of approximately 314405 total reads (8.12%)
[2016-04-15T01:20Z] INFO  18:20:19,403 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:20Z] INFO  18:20:19,404 MicroScheduler -   -> 25208 reads (8.02% of total) failing DuplicateReadFilter
[2016-04-15T01:20Z] INFO  18:20:19,404 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:20Z] INFO  18:20:19,404 MicroScheduler -   -> 327 reads (0.10% of total) failing HCMappingQualityFilter
[2016-04-15T01:20Z] INFO  18:20:19,404 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:20Z] INFO  18:20:19,405 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:20Z] INFO  18:20:19,405 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:20Z] INFO  18:20:19,405 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T01:20Z] INFO  18:20:19,459 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:20Z] INFO  18:20:19,660 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T01:20Z] INFO  18:20:19,670 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:20Z] INFO  18:20:19,715 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.013788965
[2016-04-15T01:20Z] INFO  18:20:19,724 PairHMM - Total compute time in PairHMM computeLikelihoods() : 0.367114361
[2016-04-15T01:20Z] INFO  18:20:19,725 HaplotypeCaller - Ran local assembly on 928 active regions
[2016-04-15T01:20Z] INFO  18:20:19,760 ProgressMeter -            done      4.2012935E7    36.0 s            0.0 s      100.0%    36.0 s       0.0 s
[2016-04-15T01:20Z] INFO  18:20:19,760 ProgressMeter - Total runtime 36.93 secs, 0.62 min, 0.01 hours
[2016-04-15T01:20Z] INFO  18:20:19,772 MicroScheduler - 12113 reads were filtered out during the traversal out of approximately 150887 total reads (8.03%)
[2016-04-15T01:20Z] INFO  18:20:19,772 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:20Z] INFO  18:20:19,772 MicroScheduler -   -> 11920 reads (7.90% of total) failing DuplicateReadFilter
[2016-04-15T01:20Z] INFO  18:20:19,773 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:20Z] INFO  18:20:19,773 MicroScheduler -   -> 193 reads (0.13% of total) failing HCMappingQualityFilter
[2016-04-15T01:20Z] INFO  18:20:19,773 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:20Z] INFO  18:20:19,774 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.10
[2016-04-15T01:20Z] INFO  18:20:19,773 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:20Z] INFO  18:20:19,774 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:20Z] INFO  18:20:19,774 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T01:20Z] INFO  18:20:19,800 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T01:20Z] INFO  18:20:20,263 IntervalUtils - Processing 152751 bp from intervals
[2016-04-15T01:20Z] WARN  18:20:20,269 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:20Z] INFO  18:20:20,360 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:20Z] INFO  18:20:20,494 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:20Z] INFO  18:20:20,501 ProgressMeter -     6:135639657       2.601037E7    30.0 s            1.0 s       65.6%    45.0 s      15.0 s
[2016-04-15T01:20Z] INFO  18:20:20,506 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:20Z] INFO  18:20:20,507 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T01:20Z] INFO  18:20:20,508 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T01:20Z] INFO  18:20:20,520 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T01:20Z] INFO  18:20:20,521 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T01:20Z] INFO  18:20:20,562 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:20Z] INFO  18:20:20,572 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:20Z] INFO  18:20:20,573 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:20Z] INFO  18:20:20,574 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:20Z] INFO  18:20:20,589 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/7/R14-18102_kapa-NGv3-PE100-NGv3-sort-7_79082334_94740703-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/7/R14-18102_kapa-NGv3-PE100-NGv3-7_79082334_94740703-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/7/tx/tmpCLMECW/R14-18102_kapa-NGv3-PE100-NGv3-7_79082334_94740703.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:20Z] INFO  18:20:20,607 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:20Z] INFO  18:20:20,608 HelpFormatter - Date/Time: 2016/04/14 18:20:20
[2016-04-15T01:20Z] INFO  18:20:20,609 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:20Z] INFO  18:20:20,609 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:20Z] WARN  18:20:20,632 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T01:20Z] WARN  18:20:20,635 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/7/tx/tmpCLMECW/R14-18102_kapa-NGv3-PE100-NGv3-7_79082334_94740703.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T01:20Z] INFO  18:20:20,685 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T01:20Z] INFO  18:20:20,784 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:20Z] INFO  18:20:20,858 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:20Z] INFO  18:20:21,009 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T01:20Z] INFO  18:20:21,021 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:20Z] INFO  18:20:21,103 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-15T01:20Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T01:20Z] INFO  18:20:21,122 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T01:20Z] INFO  18:20:21,123 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T01:20Z] INFO  18:20:21,126 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T01:20Z] INFO  18:20:21,217 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:20Z] GATK: HaplotypeCaller
[2016-04-15T01:20Z] WARN  18:20:21,361 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T01:20Z] WARN  18:20:21,363 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T01:20Z] GATK: HaplotypeCaller
[2016-04-15T01:20Z] INFO  18:20:21,533 IntervalUtils - Processing 163786 bp from intervals
[2016-04-15T01:20Z] WARN  18:20:21,538 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:20Z] INFO  18:20:21,614 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:20Z] INFO  18:20:21,720 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:20Z] INFO  18:20:21,721 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:20Z] INFO  18:20:21,722 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T01:20Z] INFO  18:20:21,723 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T01:20Z] INFO  18:20:21,723 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T01:20Z] INFO  18:20:21,724 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T01:20Z] INFO  18:20:21,912 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T01:20Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T01:20Z] INFO  18:20:22,593 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T01:20Z] INFO  18:20:22,594 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T01:20Z] WARN  18:20:22,857 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T01:20Z] WARN  18:20:22,858 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T01:20Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T01:20Z] INFO  18:20:23,018 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T01:20Z] INFO  18:20:23,029 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T01:20Z] WARN  18:20:23,387 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T01:20Z] WARN  18:20:23,388 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T01:20Z] INFO  18:20:24,174 ProgressMeter -     6:150390595      2.0949273E7    30.0 s            1.0 s       52.6%    57.0 s      27.0 s
[2016-04-15T01:20Z] INFO  18:20:24,435 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:20Z] INFO  18:20:24,438 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:20Z] INFO  18:20:24,439 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:20Z] INFO  18:20:24,439 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:20Z] INFO  18:20:24,444 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/7/R14-18102_kapa-NGv3-PE100-NGv3-sort-7_94750023_110303777-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/7/R14-18102_kapa-NGv3-PE100-NGv3-7_94750023_110303777-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/7/tx/tmp_wSpgt/R14-18102_kapa-NGv3-PE100-NGv3-7_94750023_110303777.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:20Z] INFO  18:20:24,462 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:20Z] INFO  18:20:24,463 HelpFormatter - Date/Time: 2016/04/14 18:20:24
[2016-04-15T01:20Z] INFO  18:20:24,463 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:20Z] INFO  18:20:24,464 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:20Z] WARN  18:20:24,509 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T01:20Z] WARN  18:20:24,512 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/7/tx/tmp_wSpgt/R14-18102_kapa-NGv3-PE100-NGv3-7_94750023_110303777.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T01:20Z] INFO  18:20:24,629 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:20Z] INFO  18:20:24,632 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:20Z] INFO  18:20:24,632 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:20Z] INFO  18:20:24,633 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:20Z] INFO  18:20:24,637 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/7/R14-18102_kapa-NGv3-PE100-NGv3-sort-7_110526648_126079222-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/7/R14-18102_kapa-NGv3-PE100-NGv3-7_110526648_126079222-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/7/tx/tmprjmMs2/R14-18102_kapa-NGv3-PE100-NGv3-7_110526648_126079222.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:20Z] INFO  18:20:24,646 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:20Z] INFO  18:20:24,653 HelpFormatter - Date/Time: 2016/04/14 18:20:24
[2016-04-15T01:20Z] INFO  18:20:24,654 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:20Z] INFO  18:20:24,654 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:20Z] WARN  18:20:24,682 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T01:20Z] WARN  18:20:24,685 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/7/tx/tmprjmMs2/R14-18102_kapa-NGv3-PE100-NGv3-7_110526648_126079222.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T01:20Z] INFO  18:20:24,721 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:20Z] INFO  18:20:24,898 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:20Z] INFO  18:20:24,931 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T01:20Z] INFO  18:20:24,940 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:20Z] INFO  18:20:25,023 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-15T01:20Z] INFO  18:20:25,043 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T01:20Z] INFO  18:20:25,127 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T01:20Z] INFO  18:20:25,147 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:20Z] INFO  18:20:25,238 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.09
[2016-04-15T01:20Z] INFO  18:20:25,264 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T01:20Z] INFO  18:20:25,520 IntervalUtils - Processing 352548 bp from intervals
[2016-04-15T01:20Z] WARN  18:20:25,525 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:20Z] INFO  18:20:25,641 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:20Z] INFO  18:20:25,736 IntervalUtils - Processing 97998 bp from intervals
[2016-04-15T01:20Z] WARN  18:20:25,741 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:20Z] INFO  18:20:25,819 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:20Z] INFO  18:20:25,821 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:20Z] INFO  18:20:25,821 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T01:20Z] INFO  18:20:25,822 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T01:20Z] INFO  18:20:25,823 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:20Z] INFO  18:20:25,823 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T01:20Z] INFO  18:20:25,823 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T01:20Z] INFO  18:20:25,942 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:20Z] INFO  18:20:25,944 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:20Z] INFO  18:20:25,945 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T01:20Z] INFO  18:20:25,945 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T01:20Z] INFO  18:20:25,946 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T01:20Z] INFO  18:20:25,946 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T01:20Z] INFO  18:20:26,088 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T01:20Z] INFO  18:20:26,127 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T01:20Z] INFO  18:20:26,710 ProgressMeter -      6:29911045      5.1195021E7    60.0 s            1.0 s       73.9%    81.0 s      21.0 s
[2016-04-15T01:20Z] INFO  18:20:27,272 ProgressMeter -     6:166721107      1.8992716E7    30.0 s            1.0 s       60.1%    49.0 s      19.0 s
[2016-04-15T01:20Z] INFO  18:20:27,959 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.010106228
[2016-04-15T01:20Z] INFO  18:20:27,960 PairHMM - Total compute time in PairHMM computeLikelihoods() : 3.5438778070000003
[2016-04-15T01:20Z] INFO  18:20:27,961 HaplotypeCaller - Ran local assembly on 1085 active regions
[2016-04-15T01:20Z] INFO  18:20:27,998 ProgressMeter -            done      4.9918554E7    49.0 s            0.0 s      100.0%    49.0 s       0.0 s
[2016-04-15T01:20Z] INFO  18:20:27,999 ProgressMeter - Total runtime 49.43 secs, 0.82 min, 0.01 hours
[2016-04-15T01:20Z] INFO  18:20:27,999 MicroScheduler - 15904 reads were filtered out during the traversal out of approximately 188978 total reads (8.42%)
[2016-04-15T01:20Z] INFO  18:20:28,000 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:20Z] INFO  18:20:28,000 MicroScheduler -   -> 15074 reads (7.98% of total) failing DuplicateReadFilter
[2016-04-15T01:20Z] INFO  18:20:28,000 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:20Z] INFO  18:20:28,000 MicroScheduler -   -> 830 reads (0.44% of total) failing HCMappingQualityFilter
[2016-04-15T01:20Z] INFO  18:20:28,000 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:20Z] INFO  18:20:28,001 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:20Z] INFO  18:20:28,001 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:20Z] INFO  18:20:28,001 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T01:20Z] INFO  18:20:28,278 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.027897573000000002
[2016-04-15T01:20Z] INFO  18:20:28,284 PairHMM - Total compute time in PairHMM computeLikelihoods() : 0.384969928
[2016-04-15T01:20Z] INFO  18:20:28,285 HaplotypeCaller - Ran local assembly on 1071 active regions
[2016-04-15T01:20Z] INFO  18:20:28,333 ProgressMeter -            done      5.3468356E7    40.0 s            0.0 s      100.0%    40.0 s       0.0 s
[2016-04-15T01:20Z] INFO  18:20:28,334 ProgressMeter - Total runtime 40.50 secs, 0.67 min, 0.01 hours
[2016-04-15T01:20Z] INFO  18:20:28,335 MicroScheduler - 14214 reads were filtered out during the traversal out of approximately 175725 total reads (8.09%)
[2016-04-15T01:20Z] INFO  18:20:28,335 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:20Z] INFO  18:20:28,335 MicroScheduler -   -> 13807 reads (7.86% of total) failing DuplicateReadFilter
[2016-04-15T01:20Z] INFO  18:20:28,335 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:20Z] INFO  18:20:28,336 MicroScheduler -   -> 407 reads (0.23% of total) failing HCMappingQualityFilter
[2016-04-15T01:20Z] INFO  18:20:28,336 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:20Z] INFO  18:20:28,336 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:20Z] INFO  18:20:28,336 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:20Z] INFO  18:20:28,337 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T01:20Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T01:20Z] INFO  18:20:28,615 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T01:20Z] INFO  18:20:28,642 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T01:20Z] WARN  18:20:28,964 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T01:20Z] WARN  18:20:28,965 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T01:20Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T01:20Z] INFO  18:20:29,009 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T01:20Z] INFO  18:20:29,010 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T01:20Z] WARN  18:20:29,313 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T01:20Z] WARN  18:20:29,315 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T01:20Z] INFO  18:20:29,559 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:20Z] INFO  18:20:29,788 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:20Z] GATK: HaplotypeCaller
[2016-04-15T01:20Z] GATK: HaplotypeCaller
[2016-04-15T01:20Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T01:20Z] INFO  18:20:31,232 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T01:20Z] INFO  18:20:31,244 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T01:20Z] WARN  18:20:31,784 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T01:20Z] WARN  18:20:31,785 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T01:20Z] INFO  18:20:32,020 ProgressMeter -      6:32610387      2.9078768E7    60.0 s            2.0 s       26.5%     3.8 m       2.8 m
[2016-04-15T01:20Z] INFO  18:20:33,113 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:20Z] INFO  18:20:33,127 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:20Z] INFO  18:20:33,128 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:20Z] INFO  18:20:33,129 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:20Z] INFO  18:20:33,133 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/7/R14-18102_kapa-NGv3-PE100-NGv3-sort-7_141629903_157151331-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/7/R14-18102_kapa-NGv3-PE100-NGv3-7_141629903_157151331-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/7/tx/tmpPTwW8Q/R14-18102_kapa-NGv3-PE100-NGv3-7_141629903_157151331.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:20Z] INFO  18:20:33,169 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:20Z] INFO  18:20:33,170 HelpFormatter - Date/Time: 2016/04/14 18:20:33
[2016-04-15T01:20Z] INFO  18:20:33,171 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:20Z] INFO  18:20:33,171 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:20Z] WARN  18:20:33,208 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T01:20Z] INFO  18:20:33,208 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:20Z] WARN  18:20:33,221 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/7/tx/tmpPTwW8Q/R14-18102_kapa-NGv3-PE100-NGv3-7_141629903_157151331.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T01:20Z] INFO  18:20:33,222 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:20Z] INFO  18:20:33,223 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:20Z] INFO  18:20:33,224 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:20Z] INFO  18:20:33,228 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/7/R14-18102_kapa-NGv3-PE100-NGv3-sort-7_126086124_141619620-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/7/R14-18102_kapa-NGv3-PE100-NGv3-7_126086124_141619620-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/7/tx/tmpiyWkai/R14-18102_kapa-NGv3-PE100-NGv3-7_126086124_141619620.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:20Z] INFO  18:20:33,258 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:20Z] INFO  18:20:33,259 HelpFormatter - Date/Time: 2016/04/14 18:20:33
[2016-04-15T01:20Z] INFO  18:20:33,260 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:20Z] INFO  18:20:33,260 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:20Z] WARN  18:20:33,294 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T01:20Z] WARN  18:20:33,307 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/7/tx/tmpiyWkai/R14-18102_kapa-NGv3-PE100-NGv3-7_126086124_141619620.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T01:20Z] INFO  18:20:33,436 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:20Z] INFO  18:20:33,548 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.007197599000000001
[2016-04-15T01:20Z] INFO  18:20:33,553 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:20Z] INFO  18:20:33,557 PairHMM - Total compute time in PairHMM computeLikelihoods() : 0.42648953700000003
[2016-04-15T01:20Z] INFO  18:20:33,558 HaplotypeCaller - Ran local assembly on 1093 active regions
[2016-04-15T01:20Z] INFO  18:20:33,621 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T01:20Z] INFO  18:20:33,627 ProgressMeter -            done      5.9409326E7    43.0 s            0.0 s      100.0%    43.0 s       0.0 s
[2016-04-15T01:20Z] INFO  18:20:33,631 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:20Z] INFO  18:20:33,627 ProgressMeter - Total runtime 43.15 secs, 0.72 min, 0.01 hours
[2016-04-15T01:20Z] INFO  18:20:33,628 MicroScheduler - 22009 reads were filtered out during the traversal out of approximately 204124 total reads (10.78%)
[2016-04-15T01:20Z] INFO  18:20:33,628 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:20Z] INFO  18:20:33,629 MicroScheduler -   -> 15837 reads (7.76% of total) failing DuplicateReadFilter
[2016-04-15T01:20Z] INFO  18:20:33,629 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:20Z] INFO  18:20:33,629 MicroScheduler -   -> 6172 reads (3.02% of total) failing HCMappingQualityFilter
[2016-04-15T01:20Z] INFO  18:20:33,629 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:20Z] INFO  18:20:33,630 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:20Z] INFO  18:20:33,630 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:20Z] INFO  18:20:33,630 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T01:20Z] INFO  18:20:33,715 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-15T01:20Z] INFO  18:20:33,753 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T01:20Z] INFO  18:20:33,750 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T01:20Z] INFO  18:20:33,762 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:20Z] INFO  18:20:33,871 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.11
[2016-04-15T01:20Z] INFO  18:20:33,894 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T01:20Z] INFO  18:20:34,290 IntervalUtils - Processing 248696 bp from intervals
[2016-04-15T01:20Z] WARN  18:20:34,306 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:20Z] INFO  18:20:34,402 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:20Z] INFO  18:20:34,479 IntervalUtils - Processing 219678 bp from intervals
[2016-04-15T01:20Z] WARN  18:20:34,486 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:20Z] INFO  18:20:34,542 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:20Z] INFO  18:20:34,543 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:20Z] INFO  18:20:34,543 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T01:20Z] INFO  18:20:34,544 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T01:20Z] INFO  18:20:34,545 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T01:20Z] INFO  18:20:34,545 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T01:20Z] INFO  18:20:34,648 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:20Z] INFO  18:20:34,808 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T01:20Z] INFO  18:20:34,809 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:20Z] INFO  18:20:34,810 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:20Z] INFO  18:20:34,810 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T01:20Z] INFO  18:20:34,811 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T01:20Z] INFO  18:20:34,824 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T01:20Z] INFO  18:20:34,825 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T01:20Z] INFO  18:20:35,043 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T01:20Z] INFO  18:20:35,210 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:20Z] INFO  18:20:35,398 ProgressMeter -       7:5270578      1.8122015E7    30.0 s            1.0 s       47.5%    63.0 s      33.0 s
[2016-04-15T01:20Z] GATK: HaplotypeCaller
[2016-04-15T01:20Z] INFO  18:20:37,801 ProgressMeter -      7:27169737      2.7453372E7    30.0 s            1.0 s       67.1%    44.0 s      14.0 s
[2016-04-15T01:20Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T01:20Z] INFO  18:20:38,045 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T01:20Z] INFO  18:20:38,045 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T01:20Z] WARN  18:20:38,457 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T01:20Z] WARN  18:20:38,458 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T01:20Z] INFO  18:20:38,760 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:20Z] INFO  18:20:38,763 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:20Z] INFO  18:20:38,764 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:20Z] INFO  18:20:38,764 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:20Z] INFO  18:20:38,769 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/7/R14-18102_kapa-NGv3-PE100-NGv3-sort-7_157155854_159138663-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/7/R14-18102_kapa-NGv3-PE100-NGv3-7_157155854_159138663-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/7/tx/tmpLkgQJW/R14-18102_kapa-NGv3-PE100-NGv3-7_157155854_159138663.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:20Z] INFO  18:20:38,782 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:20Z] INFO  18:20:38,786 HelpFormatter - Date/Time: 2016/04/14 18:20:38
[2016-04-15T01:20Z] INFO  18:20:38,787 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:20Z] INFO  18:20:38,788 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:20Z] WARN  18:20:38,811 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T01:20Z] WARN  18:20:38,816 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/7/tx/tmpLkgQJW/R14-18102_kapa-NGv3-PE100-NGv3-7_157155854_159138663.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T01:20Z] INFO  18:20:38,989 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:20Z] INFO  18:20:39,212 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T01:20Z] INFO  18:20:39,225 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:20Z] INFO  18:20:39,300 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-15T01:20Z] INFO  18:20:39,320 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T01:20Z] INFO  18:20:39,620 IntervalUtils - Processing 17619 bp from intervals
[2016-04-15T01:20Z] WARN  18:20:39,636 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:20Z] INFO  18:20:39,755 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:20Z] INFO  18:20:39,817 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:20Z] INFO  18:20:39,819 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:20Z] INFO  18:20:39,827 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T01:20Z] INFO  18:20:39,827 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T01:20Z] INFO  18:20:39,845 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T01:20Z] INFO  18:20:39,846 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T01:20Z] INFO  18:20:40,075 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T01:20Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T01:20Z] INFO  18:20:42,866 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T01:20Z] INFO  18:20:42,866 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T01:20Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T01:20Z] INFO  18:20:43,187 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T01:20Z] INFO  18:20:43,188 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T01:20Z] WARN  18:20:43,250 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T01:20Z] WARN  18:20:43,251 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T01:20Z] WARN  18:20:43,433 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T01:20Z] WARN  18:20:43,435 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T01:20Z] INFO  18:20:46,034 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.017389357
[2016-04-15T01:20Z] INFO  18:20:46,035 PairHMM - Total compute time in PairHMM computeLikelihoods() : 0.397135234
[2016-04-15T01:20Z] INFO  18:20:46,036 HaplotypeCaller - Ran local assembly on 1260 active regions
[2016-04-15T01:20Z] INFO  18:20:46,125 ProgressMeter -            done      7.7025077E7    51.0 s            0.0 s      100.0%    51.0 s       0.0 s
[2016-04-15T01:20Z] INFO  18:20:46,125 ProgressMeter - Total runtime 51.98 secs, 0.87 min, 0.01 hours
[2016-04-15T01:20Z] INFO  18:20:46,126 MicroScheduler - 22213 reads were filtered out during the traversal out of approximately 247795 total reads (8.96%)
[2016-04-15T01:20Z] INFO  18:20:46,126 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:20Z] INFO  18:20:46,126 MicroScheduler -   -> 19275 reads (7.78% of total) failing DuplicateReadFilter
[2016-04-15T01:20Z] INFO  18:20:46,127 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:20Z] INFO  18:20:46,127 MicroScheduler -   -> 2938 reads (1.19% of total) failing HCMappingQualityFilter
[2016-04-15T01:20Z] INFO  18:20:46,127 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:20Z] INFO  18:20:46,128 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:20Z] INFO  18:20:46,128 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:20Z] INFO  18:20:46,128 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T01:20Z] INFO  18:20:46,647 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.040388643
[2016-04-15T01:20Z] INFO  18:20:46,648 PairHMM - Total compute time in PairHMM computeLikelihoods() : 2.038972096
[2016-04-15T01:20Z] INFO  18:20:46,649 HaplotypeCaller - Ran local assembly on 1116 active regions
[2016-04-15T01:20Z] INFO  18:20:46,707 ProgressMeter -            done      5.0541583E7    49.0 s            0.0 s      100.0%    49.0 s       0.0 s
[2016-04-15T01:20Z] INFO  18:20:46,708 ProgressMeter - Total runtime 49.47 secs, 0.82 min, 0.01 hours
[2016-04-15T01:20Z] INFO  18:20:46,709 MicroScheduler - 20898 reads were filtered out during the traversal out of approximately 221808 total reads (9.42%)
[2016-04-15T01:20Z] INFO  18:20:46,710 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:20Z] INFO  18:20:46,710 MicroScheduler -   -> 17691 reads (7.98% of total) failing DuplicateReadFilter
[2016-04-15T01:20Z] INFO  18:20:46,711 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:20Z] INFO  18:20:46,712 MicroScheduler -   -> 3207 reads (1.45% of total) failing HCMappingQualityFilter
[2016-04-15T01:20Z] INFO  18:20:46,712 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:20Z] INFO  18:20:46,713 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:20Z] INFO  18:20:46,713 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:20Z] INFO  18:20:46,714 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T01:20Z] INFO  18:20:46,828 ProgressMeter -     5:140588474     1.16717259E8    90.0 s            0.0 s       72.3%     2.1 m      34.0 s
[2016-04-15T01:20Z] INFO  18:20:47,708 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:20Z] INFO  18:20:47,920 ProgressMeter -      7:43664117      1.9070306E7    30.0 s            1.0 s       59.2%    50.0 s      20.0 s
[2016-04-15T01:20Z] GATK: HaplotypeCaller
[2016-04-15T01:20Z] INFO  18:20:47,985 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:20Z] GATK: HaplotypeCaller
[2016-04-15T01:20Z] INFO  18:20:48,871 ProgressMeter -      7:57529655      1.4507685E7    30.0 s            2.0 s       99.8%    30.0 s       0.0 s
[2016-04-15T01:20Z] INFO  18:20:49,327 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.021561001
[2016-04-15T01:20Z] INFO  18:20:49,327 PairHMM - Total compute time in PairHMM computeLikelihoods() : 0.5272663870000001
[2016-04-15T01:20Z] INFO  18:20:49,327 HaplotypeCaller - Ran local assembly on 1098 active regions
[2016-04-15T01:20Z] INFO  18:20:49,371 ProgressMeter -            done       5.703208E7    41.0 s            0.0 s      100.0%    41.0 s       0.0 s
[2016-04-15T01:20Z] INFO  18:20:49,371 ProgressMeter - Total runtime 41.61 secs, 0.69 min, 0.01 hours
[2016-04-15T01:20Z] INFO  18:20:49,372 MicroScheduler - 15307 reads were filtered out during the traversal out of approximately 191908 total reads (7.98%)
[2016-04-15T01:20Z] INFO  18:20:49,372 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:20Z] INFO  18:20:49,372 MicroScheduler -   -> 14960 reads (7.80% of total) failing DuplicateReadFilter
[2016-04-15T01:20Z] INFO  18:20:49,372 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:20Z] INFO  18:20:49,373 MicroScheduler -   -> 347 reads (0.18% of total) failing HCMappingQualityFilter
[2016-04-15T01:20Z] INFO  18:20:49,373 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:20Z] INFO  18:20:49,373 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:20Z] INFO  18:20:49,373 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:20Z] INFO  18:20:49,374 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T01:20Z] INFO  18:20:49,504 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.014238289000000001
[2016-04-15T01:20Z] INFO  18:20:49,505 PairHMM - Total compute time in PairHMM computeLikelihoods() : 0.300864191
[2016-04-15T01:20Z] INFO  18:20:49,505 HaplotypeCaller - Ran local assembly on 595 active regions
[2016-04-15T01:20Z] INFO  18:20:49,569 ProgressMeter -            done      1.4657262E7    30.0 s            2.0 s      100.0%    30.0 s       0.0 s
[2016-04-15T01:20Z] INFO  18:20:49,570 ProgressMeter - Total runtime 30.72 secs, 0.51 min, 0.01 hours
[2016-04-15T01:20Z] INFO  18:20:49,571 MicroScheduler - 12859 reads were filtered out during the traversal out of approximately 113344 total reads (11.35%)
[2016-04-15T01:20Z] INFO  18:20:49,572 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:20Z] INFO  18:20:49,573 MicroScheduler -   -> 8784 reads (7.75% of total) failing DuplicateReadFilter
[2016-04-15T01:20Z] INFO  18:20:49,573 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:20Z] INFO  18:20:49,574 MicroScheduler -   -> 4075 reads (3.60% of total) failing HCMappingQualityFilter
[2016-04-15T01:20Z] INFO  18:20:49,575 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:20Z] INFO  18:20:49,575 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:20Z] INFO  18:20:49,576 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:20Z] INFO  18:20:49,577 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T01:20Z] INFO  18:20:49,610 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.028552751
[2016-04-15T01:20Z] INFO  18:20:49,610 PairHMM - Total compute time in PairHMM computeLikelihoods() : 8.583591657000001
[2016-04-15T01:20Z] INFO  18:20:49,611 HaplotypeCaller - Ran local assembly on 1718 active regions
[2016-04-15T01:20Z] INFO  18:20:49,665 ProgressMeter -            done      9.0413204E7    83.0 s            0.0 s      100.0%    83.0 s       0.0 s
[2016-04-15T01:20Z] INFO  18:20:49,666 ProgressMeter - Total runtime 83.00 secs, 1.38 min, 0.02 hours
[2016-04-15T01:20Z] INFO  18:20:49,666 MicroScheduler - 34453 reads were filtered out during the traversal out of approximately 362867 total reads (9.49%)
[2016-04-15T01:20Z] INFO  18:20:49,667 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:20Z] INFO  18:20:49,667 MicroScheduler -   -> 29165 reads (8.04% of total) failing DuplicateReadFilter
[2016-04-15T01:20Z] INFO  18:20:49,667 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:20Z] INFO  18:20:49,668 MicroScheduler -   -> 5288 reads (1.46% of total) failing HCMappingQualityFilter
[2016-04-15T01:20Z] INFO  18:20:49,668 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:20Z] INFO  18:20:49,668 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:20Z] INFO  18:20:49,668 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:20Z] INFO  18:20:49,669 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T01:20Z] INFO  18:20:50,523 ProgressMeter -      7:73731899      1.7307181E7    30.0 s            1.0 s       54.6%    54.0 s      24.0 s
[2016-04-15T01:20Z] INFO  18:20:50,796 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:20Z] INFO  18:20:50,937 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.003164361
[2016-04-15T01:20Z] INFO  18:20:50,938 PairHMM - Total compute time in PairHMM computeLikelihoods() : 0.066873683
[2016-04-15T01:20Z] INFO  18:20:50,939 HaplotypeCaller - Ran local assembly on 157 active regions
[2016-04-15T01:20Z] INFO  18:20:50,953 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:20Z] INFO  18:20:50,956 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:20Z] INFO  18:20:50,957 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:20Z] INFO  18:20:50,957 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:20Z] INFO  18:20:50,962 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/8/R14-18102_kapa-NGv3-PE100-NGv3-sort-8_0_15517156-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/8/R14-18102_kapa-NGv3-PE100-NGv3-8_0_15517156-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/8/tx/tmpQMYTxy/R14-18102_kapa-NGv3-PE100-NGv3-8_0_15517156.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:20Z] INFO  18:20:50,977 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:20Z] INFO  18:20:50,978 HelpFormatter - Date/Time: 2016/04/14 18:20:50
[2016-04-15T01:20Z] INFO  18:20:50,985 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:20Z] INFO  18:20:50,985 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:20Z] INFO  18:20:50,996 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:20Z] INFO  18:20:51,000 ProgressMeter -            done        1060833.0    11.0 s           10.0 s      100.0%    11.0 s       0.0 s
[2016-04-15T01:20Z] INFO  18:20:51,001 ProgressMeter - Total runtime 11.18 secs, 0.19 min, 0.00 hours
[2016-04-15T01:20Z] INFO  18:20:51,002 MicroScheduler - 2472 reads were filtered out during the traversal out of approximately 27522 total reads (8.98%)
[2016-04-15T01:20Z] INFO  18:20:51,003 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:20Z] INFO  18:20:51,003 MicroScheduler -   -> 2197 reads (7.98% of total) failing DuplicateReadFilter
[2016-04-15T01:20Z] INFO  18:20:51,004 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:20Z] INFO  18:20:51,005 MicroScheduler -   -> 275 reads (1.00% of total) failing HCMappingQualityFilter
[2016-04-15T01:20Z] INFO  18:20:51,005 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:20Z] INFO  18:20:51,006 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:20Z] INFO  18:20:51,007 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:20Z] INFO  18:20:51,007 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T01:20Z] WARN  18:20:51,009 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T01:20Z] WARN  18:20:51,012 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/8/tx/tmpQMYTxy/R14-18102_kapa-NGv3-PE100-NGv3-8_0_15517156.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T01:20Z] INFO  18:20:51,065 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:20Z] GATK: HaplotypeCaller
[2016-04-15T01:20Z] INFO  18:20:51,168 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:20Z] GATK: HaplotypeCaller
[2016-04-15T01:20Z] INFO  18:20:51,312 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:20Z] INFO  18:20:51,315 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:20Z] INFO  18:20:51,316 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:20Z] INFO  18:20:51,316 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:20Z] INFO  18:20:51,321 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/8/R14-18102_kapa-NGv3-PE100-NGv3-sort-8_15519664_31030618-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/8/R14-18102_kapa-NGv3-PE100-NGv3-8_15519664_31030618-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/8/tx/tmpzOO_LW/R14-18102_kapa-NGv3-PE100-NGv3-8_15519664_31030618.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:20Z] INFO  18:20:51,338 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:20Z] INFO  18:20:51,339 HelpFormatter - Date/Time: 2016/04/14 18:20:51
[2016-04-15T01:20Z] INFO  18:20:51,340 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:20Z] INFO  18:20:51,340 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:20Z] INFO  18:20:51,369 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T01:20Z] WARN  18:20:51,376 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T01:20Z] INFO  18:20:51,379 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:20Z] WARN  18:20:51,380 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/8/tx/tmpzOO_LW/R14-18102_kapa-NGv3-PE100-NGv3-8_15519664_31030618.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T01:20Z] GATK: HaplotypeCaller
[2016-04-15T01:20Z] INFO  18:20:51,455 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-15T01:20Z] INFO  18:20:51,472 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T01:20Z] INFO  18:20:51,580 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:20Z] INFO  18:20:51,722 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T01:20Z] INFO  18:20:51,737 ProgressMeter -      7:91503072      2.1274671E7    30.0 s            1.0 s       59.6%    50.0 s      20.0 s
[2016-04-15T01:20Z] INFO  18:20:51,742 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:20Z] INFO  18:20:51,835 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.09
[2016-04-15T01:20Z] INFO  18:20:51,852 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T01:20Z] INFO  18:20:51,918 IntervalUtils - Processing 115548 bp from intervals
[2016-04-15T01:20Z] WARN  18:20:51,934 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:20Z] INFO  18:20:52,059 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:20Z] INFO  18:20:52,136 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:20Z] INFO  18:20:52,137 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:20Z] INFO  18:20:52,137 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T01:20Z] INFO  18:20:52,138 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T01:20Z] INFO  18:20:52,150 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T01:20Z] INFO  18:20:52,150 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T01:20Z] INFO  18:20:52,223 IntervalUtils - Processing 233081 bp from intervals
[2016-04-15T01:20Z] WARN  18:20:52,228 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:20Z] INFO  18:20:52,291 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:20Z] INFO  18:20:52,354 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:20Z] INFO  18:20:52,372 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T01:20Z] INFO  18:20:52,456 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:20Z] INFO  18:20:52,457 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:20Z] INFO  18:20:52,458 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T01:20Z] INFO  18:20:52,459 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T01:20Z] INFO  18:20:52,475 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T01:20Z] INFO  18:20:52,476 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T01:20Z] GATK: HaplotypeCaller
[2016-04-15T01:20Z] INFO  18:20:52,684 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T01:20Z] INFO  18:20:53,802 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:20Z] INFO  18:20:53,806 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:20Z] INFO  18:20:53,806 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:20Z] INFO  18:20:53,807 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:20Z] INFO  18:20:53,811 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/8/R14-18102_kapa-NGv3-PE100-NGv3-sort-8_31496910_48001429-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/8/R14-18102_kapa-NGv3-PE100-NGv3-8_31496910_48001429-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/8/tx/tmpKFH2hU/R14-18102_kapa-NGv3-PE100-NGv3-8_31496910_48001429.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:20Z] INFO  18:20:53,859 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:20Z] INFO  18:20:53,860 HelpFormatter - Date/Time: 2016/04/14 18:20:53
[2016-04-15T01:20Z] INFO  18:20:53,861 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:20Z] INFO  18:20:53,862 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:20Z] WARN  18:20:53,899 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T01:20Z] WARN  18:20:53,902 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/8/tx/tmpKFH2hU/R14-18102_kapa-NGv3-PE100-NGv3-8_31496910_48001429.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T01:20Z] INFO  18:20:54,075 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:20Z] INFO  18:20:54,286 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T01:20Z] INFO  18:20:54,306 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:20Z] INFO  18:20:54,367 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-15T01:20Z] INFO  18:20:54,393 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T01:20Z] INFO  18:20:54,634 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:20Z] INFO  18:20:54,637 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:20Z] INFO  18:20:54,638 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:20Z] INFO  18:20:54,638 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:20Z] INFO  18:20:54,643 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/8/R14-18102_kapa-NGv3-PE100-NGv3-sort-8_48003022_63659688-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/8/R14-18102_kapa-NGv3-PE100-NGv3-8_48003022_63659688-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/8/tx/tmpphn0rR/R14-18102_kapa-NGv3-PE100-NGv3-8_48003022_63659688.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:20Z] INFO  18:20:54,652 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:20Z] INFO  18:20:54,653 HelpFormatter - Date/Time: 2016/04/14 18:20:54
[2016-04-15T01:20Z] INFO  18:20:54,654 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:20Z] INFO  18:20:54,654 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:20Z] INFO  18:20:54,658 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:20Z] INFO  18:20:54,661 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:20Z] INFO  18:20:54,662 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:20Z] INFO  18:20:54,662 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:20Z] INFO  18:20:54,667 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/8/R14-18102_kapa-NGv3-PE100-NGv3-sort-8_63775819_79510770-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/8/R14-18102_kapa-NGv3-PE100-NGv3-8_63775819_79510770-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/8/tx/tmpu_DirR/R14-18102_kapa-NGv3-PE100-NGv3-8_63775819_79510770.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:20Z] INFO  18:20:54,684 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:20Z] INFO  18:20:54,685 HelpFormatter - Date/Time: 2016/04/14 18:20:54
[2016-04-15T01:20Z] INFO  18:20:54,686 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:20Z] INFO  18:20:54,687 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:20Z] WARN  18:20:54,699 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T01:20Z] WARN  18:20:54,702 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/8/tx/tmpphn0rR/R14-18102_kapa-NGv3-PE100-NGv3-8_48003022_63659688.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T01:20Z] WARN  18:20:54,709 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T01:20Z] WARN  18:20:54,712 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/8/tx/tmpu_DirR/R14-18102_kapa-NGv3-PE100-NGv3-8_63775819_79510770.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T01:20Z] INFO  18:20:54,755 IntervalUtils - Processing 125262 bp from intervals
[2016-04-15T01:20Z] WARN  18:20:54,761 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:20Z] INFO  18:20:54,838 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:20Z] INFO  18:20:54,914 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:20Z] INFO  18:20:54,916 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:20Z] INFO  18:20:54,916 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T01:20Z] INFO  18:20:54,917 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T01:20Z] INFO  18:20:54,918 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T01:20Z] INFO  18:20:54,918 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T01:20Z] INFO  18:20:54,957 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:20Z] INFO  18:20:54,987 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:20Z] INFO  18:20:55,081 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T01:20Z] INFO  18:20:55,125 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T01:20Z] INFO  18:20:55,134 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:20Z] INFO  18:20:55,166 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T01:20Z] INFO  18:20:55,176 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:20Z] INFO  18:20:55,196 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-15T01:20Z] INFO  18:20:55,232 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T01:20Z] INFO  18:20:55,270 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.09
[2016-04-15T01:20Z] INFO  18:20:55,296 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T01:20Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T01:20Z] INFO  18:20:55,590 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T01:20Z] INFO  18:20:55,592 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T01:20Z] INFO  18:20:55,713 IntervalUtils - Processing 117209 bp from intervals
[2016-04-15T01:20Z] INFO  18:20:55,729 IntervalUtils - Processing 104159 bp from intervals
[2016-04-15T01:20Z] WARN  18:20:55,735 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:20Z] WARN  18:20:55,741 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:20Z] WARN  18:20:55,867 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T01:20Z] WARN  18:20:55,868 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T01:20Z] INFO  18:20:55,871 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:20Z] INFO  18:20:55,868 ProgressMeter -      7:99668188       1.789314E7    30.0 s            1.0 s       26.2%   114.0 s      84.0 s
[2016-04-15T01:20Z] INFO  18:20:55,896 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:20Z] INFO  18:20:55,928 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:20Z] INFO  18:20:55,929 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:20Z] INFO  18:20:55,929 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T01:20Z] INFO  18:20:55,930 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T01:20Z] INFO  18:20:55,931 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T01:20Z] INFO  18:20:55,931 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T01:20Z] INFO  18:20:55,956 ProgressMeter -     7:124537227      2.3324666E7    30.0 s            1.0 s       99.9%    30.0 s       0.0 s
[2016-04-15T01:20Z] INFO  18:20:56,005 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:20Z] INFO  18:20:56,011 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:20Z] INFO  18:20:56,012 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:20Z] INFO  18:20:56,013 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:20Z] INFO  18:20:56,018 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/8/R14-18102_kapa-NGv3-PE100-NGv3-sort-8_79513976_95140568-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/8/R14-18102_kapa-NGv3-PE100-NGv3-8_79513976_95140568-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/8/tx/tmpYkA6Sx/R14-18102_kapa-NGv3-PE100-NGv3-8_79513976_95140568.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:20Z] INFO  18:20:56,022 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:20Z] INFO  18:20:56,022 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:20Z] INFO  18:20:56,023 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T01:20Z] INFO  18:20:56,023 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T01:20Z] INFO  18:20:56,034 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:20Z] INFO  18:20:56,035 HelpFormatter - Date/Time: 2016/04/14 18:20:56
[2016-04-15T01:20Z] INFO  18:20:56,035 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:20Z] INFO  18:20:56,035 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:20Z] INFO  18:20:56,039 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T01:20Z] INFO  18:20:56,040 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T01:20Z] WARN  18:20:56,058 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T01:20Z] WARN  18:20:56,061 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/8/tx/tmpYkA6Sx/R14-18102_kapa-NGv3-PE100-NGv3-8_79513976_95140568.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T01:20Z] INFO  18:20:56,127 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T01:20Z] INFO  18:20:56,244 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:20Z] INFO  18:20:56,264 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T01:20Z] INFO  18:20:56,423 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T01:20Z] INFO  18:20:56,433 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:20Z] INFO  18:20:56,504 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.005992833
[2016-04-15T01:20Z] INFO  18:20:56,504 PairHMM - Total compute time in PairHMM computeLikelihoods() : 0.269106925
[2016-04-15T01:20Z] INFO  18:20:56,504 HaplotypeCaller - Ran local assembly on 698 active regions
[2016-04-15T01:20Z] INFO  18:20:56,513 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-15T01:20Z] INFO  18:20:56,550 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T01:20Z] INFO  18:20:56,570 ProgressMeter -            done      2.3520612E7    30.0 s            1.0 s      100.0%    30.0 s       0.0 s
[2016-04-15T01:20Z] INFO  18:20:56,571 ProgressMeter - Total runtime 30.63 secs, 0.51 min, 0.01 hours
[2016-04-15T01:20Z] INFO  18:20:56,572 MicroScheduler - 9408 reads were filtered out during the traversal out of approximately 118010 total reads (7.97%)
[2016-04-15T01:20Z] INFO  18:20:56,572 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:20Z] INFO  18:20:56,572 MicroScheduler -   -> 9247 reads (7.84% of total) failing DuplicateReadFilter
[2016-04-15T01:20Z] INFO  18:20:56,573 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:20Z] INFO  18:20:56,573 MicroScheduler -   -> 161 reads (0.14% of total) failing HCMappingQualityFilter
[2016-04-15T01:20Z] INFO  18:20:56,573 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:20Z] INFO  18:20:56,573 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:20Z] INFO  18:20:56,573 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:20Z] INFO  18:20:56,574 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T01:20Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T01:20Z] INFO  18:20:56,888 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T01:20Z] INFO  18:20:56,889 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T01:20Z] INFO  18:20:56,995 IntervalUtils - Processing 78340 bp from intervals
[2016-04-15T01:20Z] WARN  18:20:57,001 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:20Z] INFO  18:20:57,168 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:20Z] WARN  18:20:57,218 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T01:20Z] WARN  18:20:57,218 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T01:20Z] INFO  18:20:57,271 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:20Z] INFO  18:20:57,272 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:20Z] INFO  18:20:57,273 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T01:20Z] INFO  18:20:57,274 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T01:20Z] INFO  18:20:57,281 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T01:20Z] INFO  18:20:57,282 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T01:20Z] INFO  18:20:57,522 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T01:20Z] INFO  18:20:58,210 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.042367655000000004
[2016-04-15T01:20Z] INFO  18:20:58,211 PairHMM - Total compute time in PairHMM computeLikelihoods() : 0.8257848600000001
[2016-04-15T01:20Z] INFO  18:20:58,212 HaplotypeCaller - Ran local assembly on 1384 active regions
[2016-04-15T01:20Z] INFO  18:20:58,249 ProgressMeter -            done      8.7090457E7    52.0 s            0.0 s      100.0%    52.0 s       0.0 s
[2016-04-15T01:20Z] INFO  18:20:58,250 ProgressMeter - Total runtime 52.86 secs, 0.88 min, 0.01 hours
[2016-04-15T01:20Z] INFO  18:20:58,251 MicroScheduler - 39053 reads were filtered out during the traversal out of approximately 302451 total reads (12.91%)
[2016-04-15T01:20Z] INFO  18:20:58,251 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:20Z] INFO  18:20:58,252 MicroScheduler -   -> 23129 reads (7.65% of total) failing DuplicateReadFilter
[2016-04-15T01:20Z] INFO  18:20:58,252 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:20Z] INFO  18:20:58,253 MicroScheduler -   -> 15924 reads (5.26% of total) failing HCMappingQualityFilter
[2016-04-15T01:20Z] INFO  18:20:58,254 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:20Z] INFO  18:20:58,254 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:20Z] INFO  18:20:58,255 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:20Z] INFO  18:20:58,255 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T01:20Z] INFO  18:20:58,307 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:20Z] GATK: HaplotypeCaller
[2016-04-15T01:20Z] INFO  18:20:59,518 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:20Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T01:20Z] INFO  18:20:59,732 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T01:20Z] INFO  18:20:59,732 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T01:20Z] GATK: HaplotypeCaller
[2016-04-15T01:21Z] WARN  18:21:00,045 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T01:21Z] WARN  18:21:00,046 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T01:21Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T01:21Z] INFO  18:21:00,871 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T01:21Z] INFO  18:21:00,872 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T01:21Z] WARN  18:21:01,076 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T01:21Z] WARN  18:21:01,080 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T01:21Z] INFO  18:21:01,486 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.021377402
[2016-04-15T01:21Z] INFO  18:21:01,486 PairHMM - Total compute time in PairHMM computeLikelihoods() : 0.626090471
[2016-04-15T01:21Z] INFO  18:21:01,487 HaplotypeCaller - Ran local assembly on 1115 active regions
[2016-04-15T01:21Z] INFO  18:21:01,578 ProgressMeter -            done      4.9480485E7    43.0 s            0.0 s      100.0%    43.0 s       0.0 s
[2016-04-15T01:21Z] INFO  18:21:01,578 ProgressMeter - Total runtime 43.68 secs, 0.73 min, 0.01 hours
[2016-04-15T01:21Z] INFO  18:21:01,578 MicroScheduler - 26564 reads were filtered out during the traversal out of approximately 230637 total reads (11.52%)
[2016-04-15T01:21Z] INFO  18:21:01,579 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:21Z] INFO  18:21:01,579 MicroScheduler -   -> 18234 reads (7.91% of total) failing DuplicateReadFilter
[2016-04-15T01:21Z] INFO  18:21:01,579 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:21Z] INFO  18:21:01,580 MicroScheduler -   -> 8330 reads (3.61% of total) failing HCMappingQualityFilter
[2016-04-15T01:21Z] INFO  18:21:01,580 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:21Z] INFO  18:21:01,580 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:21Z] INFO  18:21:01,580 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:21Z] INFO  18:21:01,581 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T01:21Z] INFO  18:21:02,021 ProgressMeter -      6:35207529     1.00120735E8    90.0 s            0.0 s       46.1%     3.3 m     105.0 s
[2016-04-15T01:21Z] INFO  18:21:02,172 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:21Z] INFO  18:21:02,175 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:21Z] INFO  18:21:02,176 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:21Z] INFO  18:21:02,176 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:21Z] INFO  18:21:02,181 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/8/R14-18102_kapa-NGv3-PE100-NGv3-sort-8_95142853_110655419-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/8/R14-18102_kapa-NGv3-PE100-NGv3-8_95142853_110655419-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/8/tx/tmpb8pxuS/R14-18102_kapa-NGv3-PE100-NGv3-8_95142853_110655419.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:21Z] INFO  18:21:02,209 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:21Z] INFO  18:21:02,210 HelpFormatter - Date/Time: 2016/04/14 18:21:02
[2016-04-15T01:21Z] INFO  18:21:02,211 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:21Z] INFO  18:21:02,212 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:21Z] WARN  18:21:02,252 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T01:21Z] WARN  18:21:02,254 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/8/tx/tmpb8pxuS/R14-18102_kapa-NGv3-PE100-NGv3-8_95142853_110655419.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T01:21Z] INFO  18:21:02,299 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.008023402
[2016-04-15T01:21Z] INFO  18:21:02,300 PairHMM - Total compute time in PairHMM computeLikelihoods() : 0.18699172
[2016-04-15T01:21Z] INFO  18:21:02,300 HaplotypeCaller - Ran local assembly on 1146 active regions
[2016-04-15T01:21Z] INFO  18:21:02,350 ProgressMeter -            done      6.0270329E7    40.0 s            0.0 s      100.0%    40.0 s       0.0 s
[2016-04-15T01:21Z] INFO  18:21:02,350 ProgressMeter - Total runtime 40.63 secs, 0.68 min, 0.01 hours
[2016-04-15T01:21Z] INFO  18:21:02,350 MicroScheduler - 13579 reads were filtered out during the traversal out of approximately 169918 total reads (7.99%)
[2016-04-15T01:21Z] INFO  18:21:02,351 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:21Z] INFO  18:21:02,351 MicroScheduler -   -> 13274 reads (7.81% of total) failing DuplicateReadFilter
[2016-04-15T01:21Z] INFO  18:21:02,351 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:21Z] INFO  18:21:02,351 MicroScheduler -   -> 305 reads (0.18% of total) failing HCMappingQualityFilter
[2016-04-15T01:21Z] INFO  18:21:02,352 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:21Z] INFO  18:21:02,352 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:21Z] INFO  18:21:02,352 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:21Z] INFO  18:21:02,352 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T01:21Z] INFO  18:21:02,472 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:21Z] INFO  18:21:02,707 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T01:21Z] INFO  18:21:02,717 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:21Z] INFO  18:21:02,807 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.09
[2016-04-15T01:21Z] INFO  18:21:02,836 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T01:21Z] INFO  18:21:03,146 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:21Z] INFO  18:21:03,275 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:21Z] INFO  18:21:03,288 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:21Z] INFO  18:21:03,289 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:21Z] INFO  18:21:03,289 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:21Z] INFO  18:21:03,294 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/8/R14-18102_kapa-NGv3-PE100-NGv3-sort-8_110656864_126194498-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/8/R14-18102_kapa-NGv3-PE100-NGv3-8_110656864_126194498-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/8/tx/tmp3CYSww/R14-18102_kapa-NGv3-PE100-NGv3-8_110656864_126194498.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:21Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T01:21Z] INFO  18:21:03,317 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T01:21Z] INFO  18:21:03,318 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T01:21Z] INFO  18:21:03,325 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:21Z] INFO  18:21:03,326 HelpFormatter - Date/Time: 2016/04/14 18:21:03
[2016-04-15T01:21Z] INFO  18:21:03,326 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:21Z] INFO  18:21:03,327 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:21Z] WARN  18:21:03,385 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T01:21Z] WARN  18:21:03,388 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/8/tx/tmp3CYSww/R14-18102_kapa-NGv3-PE100-NGv3-8_110656864_126194498.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T01:21Z] INFO  18:21:03,452 IntervalUtils - Processing 161638 bp from intervals
[2016-04-15T01:21Z] WARN  18:21:03,457 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:21Z] GATK: HaplotypeCaller
[2016-04-15T01:21Z] INFO  18:21:03,552 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:21Z] INFO  18:21:03,646 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:21Z] INFO  18:21:03,672 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:21Z] INFO  18:21:03,674 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:21Z] INFO  18:21:03,674 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T01:21Z] WARN  18:21:03,674 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T01:21Z] INFO  18:21:03,675 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T01:21Z] WARN  18:21:03,675 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T01:21Z] INFO  18:21:03,687 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T01:21Z] INFO  18:21:03,688 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T01:21Z] INFO  18:21:03,894 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:21Z] INFO  18:21:03,902 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T01:21Z] INFO  18:21:03,912 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:21Z] INFO  18:21:03,945 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T01:21Z] INFO  18:21:04,015 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.10
[2016-04-15T01:21Z] INFO  18:21:04,043 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T01:21Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T01:21Z] INFO  18:21:04,240 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T01:21Z] INFO  18:21:04,251 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T01:21Z] GATK: HaplotypeCaller
[2016-04-15T01:21Z] INFO  18:21:04,506 IntervalUtils - Processing 102393 bp from intervals
[2016-04-15T01:21Z] WARN  18:21:04,511 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:21Z] INFO  18:21:04,571 ProgressMeter -     7:149156758      1.8012852E7    30.0 s            1.0 s       41.4%    72.0 s      42.0 s
[2016-04-15T01:21Z] INFO  18:21:04,633 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:21Z] INFO  18:21:04,745 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:21Z] INFO  18:21:04,746 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:21Z] INFO  18:21:04,747 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T01:21Z] INFO  18:21:04,748 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T01:21Z] INFO  18:21:04,756 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T01:21Z] INFO  18:21:04,757 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T01:21Z] WARN  18:21:04,823 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T01:21Z] WARN  18:21:04,824 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T01:21Z] INFO  18:21:04,830 ProgressMeter -     7:131241118       2.300277E7    30.0 s            1.0 s       40.2%    74.0 s      44.0 s
[2016-04-15T01:21Z] INFO  18:21:05,047 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T01:21Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T01:21Z] INFO  18:21:06,236 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T01:21Z] INFO  18:21:06,248 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T01:21Z] WARN  18:21:06,620 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T01:21Z] WARN  18:21:06,621 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T01:21Z] INFO  18:21:07,062 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.029705274
[2016-04-15T01:21Z] INFO  18:21:07,063 PairHMM - Total compute time in PairHMM computeLikelihoods() : 1.003141348
[2016-04-15T01:21Z] INFO  18:21:07,063 HaplotypeCaller - Ran local assembly on 1182 active regions
[2016-04-15T01:21Z] INFO  18:21:07,128 ProgressMeter -            done      6.3591551E7    46.0 s            0.0 s      100.0%    46.0 s       0.0 s
[2016-04-15T01:21Z] INFO  18:21:07,128 ProgressMeter - Total runtime 46.62 secs, 0.78 min, 0.01 hours
[2016-04-15T01:21Z] INFO  18:21:07,128 MicroScheduler - 57169 reads were filtered out during the traversal out of approximately 266740 total reads (21.43%)
[2016-04-15T01:21Z] INFO  18:21:07,129 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:21Z] INFO  18:21:07,129 MicroScheduler -   -> 18453 reads (6.92% of total) failing DuplicateReadFilter
[2016-04-15T01:21Z] INFO  18:21:07,130 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:21Z] INFO  18:21:07,130 MicroScheduler -   -> 38716 reads (14.51% of total) failing HCMappingQualityFilter
[2016-04-15T01:21Z] INFO  18:21:07,130 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:21Z] INFO  18:21:07,130 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:21Z] INFO  18:21:07,131 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:21Z] INFO  18:21:07,131 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T01:21Z] INFO  18:21:07,262 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:21Z] INFO  18:21:07,265 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:21Z] INFO  18:21:07,266 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:21Z] INFO  18:21:07,266 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:21Z] INFO  18:21:07,271 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/8/R14-18102_kapa-NGv3-PE100-NGv3-sort-8_126369460_141889736-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/8/R14-18102_kapa-NGv3-PE100-NGv3-8_126369460_141889736-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/8/tx/tmpdU3TSw/R14-18102_kapa-NGv3-PE100-NGv3-8_126369460_141889736.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:21Z] INFO  18:21:07,279 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:21Z] INFO  18:21:07,280 HelpFormatter - Date/Time: 2016/04/14 18:21:07
[2016-04-15T01:21Z] INFO  18:21:07,281 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:21Z] INFO  18:21:07,281 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:21Z] WARN  18:21:07,336 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T01:21Z] WARN  18:21:07,353 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/8/tx/tmpdU3TSw/R14-18102_kapa-NGv3-PE100-NGv3-8_126369460_141889736.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T01:21Z] INFO  18:21:07,665 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:21Z] INFO  18:21:07,749 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:21Z] INFO  18:21:07,752 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:21Z] INFO  18:21:07,752 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:21Z] INFO  18:21:07,753 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:21Z] INFO  18:21:07,757 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/8/R14-18102_kapa-NGv3-PE100-NGv3-sort-8_141900641_146364022-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/8/R14-18102_kapa-NGv3-PE100-NGv3-8_141900641_146364022-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/8/tx/tmpdKCQId/R14-18102_kapa-NGv3-PE100-NGv3-8_141900641_146364022.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:21Z] INFO  18:21:07,767 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:21Z] INFO  18:21:07,778 HelpFormatter - Date/Time: 2016/04/14 18:21:07
[2016-04-15T01:21Z] INFO  18:21:07,779 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:21Z] INFO  18:21:07,780 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:21Z] WARN  18:21:07,814 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T01:21Z] WARN  18:21:07,817 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/8/tx/tmpdKCQId/R14-18102_kapa-NGv3-PE100-NGv3-8_141900641_146364022.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T01:21Z] INFO  18:21:07,931 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T01:21Z] INFO  18:21:07,941 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:21Z] INFO  18:21:08,001 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:21Z] INFO  18:21:08,029 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.09
[2016-04-15T01:21Z] INFO  18:21:08,051 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T01:21Z] INFO  18:21:08,154 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T01:21Z] INFO  18:21:08,162 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:21Z] INFO  18:21:08,217 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-15T01:21Z] INFO  18:21:08,243 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T01:21Z] INFO  18:21:08,600 IntervalUtils - Processing 72911 bp from intervals
[2016-04-15T01:21Z] WARN  18:21:08,605 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:21Z] INFO  18:21:08,609 IntervalUtils - Processing 204618 bp from intervals
[2016-04-15T01:21Z] WARN  18:21:08,615 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:21Z] INFO  18:21:08,681 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:21Z] INFO  18:21:08,716 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:21Z] INFO  18:21:08,743 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:21Z] INFO  18:21:08,808 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:21Z] INFO  18:21:08,809 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:21Z] INFO  18:21:08,810 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T01:21Z] INFO  18:21:08,811 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T01:21Z] INFO  18:21:08,812 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T01:21Z] INFO  18:21:08,812 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T01:21Z] INFO  18:21:08,829 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:21Z] INFO  18:21:08,830 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:21Z] INFO  18:21:08,831 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T01:21Z] INFO  18:21:08,832 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T01:21Z] INFO  18:21:08,832 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T01:21Z] INFO  18:21:08,833 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T01:21Z] GATK: HaplotypeCaller
[2016-04-15T01:21Z] INFO  18:21:09,031 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T01:21Z] INFO  18:21:09,044 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T01:21Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T01:21Z] INFO  18:21:09,867 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T01:21Z] INFO  18:21:09,868 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T01:21Z] WARN  18:21:10,155 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T01:21Z] WARN  18:21:10,156 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T01:21Z] INFO  18:21:10,828 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.04438338
[2016-04-15T01:21Z] INFO  18:21:10,829 PairHMM - Total compute time in PairHMM computeLikelihoods() : 5.719760138000001
[2016-04-15T01:21Z] INFO  18:21:10,829 HaplotypeCaller - Ran local assembly on 2435 active regions
[2016-04-15T01:21Z] INFO  18:21:10,882 ProgressMeter -            done     1.86500366E8   114.0 s            0.0 s      100.0%   114.0 s       0.0 s
[2016-04-15T01:21Z] INFO  18:21:10,883 ProgressMeter - Total runtime 114.09 secs, 1.90 min, 0.03 hours
[2016-04-15T01:21Z] INFO  18:21:10,883 MicroScheduler - 74748 reads were filtered out during the traversal out of approximately 665440 total reads (11.23%)
[2016-04-15T01:21Z] INFO  18:21:10,883 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:21Z] INFO  18:21:10,884 MicroScheduler -   -> 56012 reads (8.42% of total) failing DuplicateReadFilter
[2016-04-15T01:21Z] INFO  18:21:10,887 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:21Z] INFO  18:21:10,888 MicroScheduler -   -> 18736 reads (2.82% of total) failing HCMappingQualityFilter
[2016-04-15T01:21Z] INFO  18:21:10,888 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:21Z] INFO  18:21:10,889 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:21Z] INFO  18:21:10,889 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:21Z] INFO  18:21:10,889 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T01:21Z] INFO  18:21:11,835 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:21Z] INFO  18:21:11,849 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:21Z] INFO  18:21:11,850 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:21Z] INFO  18:21:11,851 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:21Z] INFO  18:21:11,855 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/9/R14-18102_kapa-NGv3-PE100-NGv3-sort-9_0_15510186-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/9/R14-18102_kapa-NGv3-PE100-NGv3-9_0_15510186-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/9/tx/tmph6YMNf/R14-18102_kapa-NGv3-PE100-NGv3-9_0_15510186.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:21Z] INFO  18:21:11,886 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:21Z] INFO  18:21:11,887 HelpFormatter - Date/Time: 2016/04/14 18:21:11
[2016-04-15T01:21Z] INFO  18:21:11,887 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:21Z] INFO  18:21:11,888 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:21Z] WARN  18:21:11,945 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T01:21Z] WARN  18:21:11,948 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/9/tx/tmph6YMNf/R14-18102_kapa-NGv3-PE100-NGv3-9_0_15510186.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T01:21Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T01:21Z] INFO  18:21:11,998 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T01:21Z] INFO  18:21:11,999 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T01:21Z] INFO  18:21:12,135 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:21Z] WARN  18:21:12,292 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T01:21Z] WARN  18:21:12,303 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T01:21Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T01:21Z] INFO  18:21:12,339 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T01:21Z] INFO  18:21:12,340 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T01:21Z] INFO  18:21:12,355 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T01:21Z] INFO  18:21:12,365 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:21Z] INFO  18:21:12,395 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:21Z] INFO  18:21:12,464 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.10
[2016-04-15T01:21Z] INFO  18:21:12,484 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T01:21Z] GATK: HaplotypeCaller
[2016-04-15T01:21Z] WARN  18:21:12,715 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T01:21Z] WARN  18:21:12,716 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T01:21Z] INFO  18:21:12,857 IntervalUtils - Processing 123193 bp from intervals
[2016-04-15T01:21Z] WARN  18:21:12,862 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:21Z] INFO  18:21:12,965 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:21Z] INFO  18:21:13,047 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:21Z] INFO  18:21:13,048 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:21Z] INFO  18:21:13,048 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T01:21Z] INFO  18:21:13,049 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T01:21Z] INFO  18:21:13,050 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T01:21Z] INFO  18:21:13,050 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T01:21Z] INFO  18:21:13,272 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T01:21Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T01:21Z] INFO  18:21:16,065 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T01:21Z] INFO  18:21:16,080 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T01:21Z] INFO  18:21:16,142 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:21Z] INFO  18:21:16,146 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:21Z] INFO  18:21:16,146 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:21Z] INFO  18:21:16,147 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:21Z] INFO  18:21:16,151 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/9/R14-18102_kapa-NGv3-PE100-NGv3-sort-9_15564086_32405601-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/9/R14-18102_kapa-NGv3-PE100-NGv3-9_15564086_32405601-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/9/tx/tmpC90ocG/R14-18102_kapa-NGv3-PE100-NGv3-9_15564086_32405601.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:21Z] INFO  18:21:16,163 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:21Z] INFO  18:21:16,164 HelpFormatter - Date/Time: 2016/04/14 18:21:16
[2016-04-15T01:21Z] INFO  18:21:16,164 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:21Z] INFO  18:21:16,165 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:21Z] WARN  18:21:16,187 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T01:21Z] WARN  18:21:16,190 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/9/tx/tmpC90ocG/R14-18102_kapa-NGv3-PE100-NGv3-9_15564086_32405601.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T01:21Z] WARN  18:21:16,360 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T01:21Z] WARN  18:21:16,361 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T01:21Z] INFO  18:21:16,461 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:21Z] INFO  18:21:16,667 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T01:21Z] INFO  18:21:16,677 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:21Z] INFO  18:21:16,774 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.10
[2016-04-15T01:21Z] INFO  18:21:16,817 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T01:21Z] INFO  18:21:17,167 IntervalUtils - Processing 89361 bp from intervals
[2016-04-15T01:21Z] WARN  18:21:17,172 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:21Z] INFO  18:21:17,255 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:21Z] INFO  18:21:17,345 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:21Z] INFO  18:21:17,357 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:21Z] INFO  18:21:17,358 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T01:21Z] INFO  18:21:17,358 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T01:21Z] INFO  18:21:17,371 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T01:21Z] INFO  18:21:17,372 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T01:21Z] INFO  18:21:17,621 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T01:21Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T01:21Z] INFO  18:21:20,000 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T01:21Z] INFO  18:21:20,001 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T01:21Z] WARN  18:21:20,295 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T01:21Z] WARN  18:21:20,296 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T01:21Z] INFO  18:21:22,152 ProgressMeter -       8:8234248        8329832.0    30.0 s            3.0 s       49.0%    61.0 s      31.0 s
[2016-04-15T01:21Z] INFO  18:21:22,478 ProgressMeter -      8:22412376      1.9271351E7    30.0 s            1.0 s       37.1%    80.0 s      50.0 s
[2016-04-15T01:21Z] INFO  18:21:24,937 ProgressMeter -      8:41574491      2.3348597E7    30.0 s            1.0 s       71.4%    42.0 s      12.0 s
[2016-04-15T01:21Z] INFO  18:21:25,824 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.003617238
[2016-04-15T01:21Z] INFO  18:21:25,825 PairHMM - Total compute time in PairHMM computeLikelihoods() : 0.15913711800000002
[2016-04-15T01:21Z] INFO  18:21:25,825 HaplotypeCaller - Ran local assembly on 598 active regions
[2016-04-15T01:21Z] INFO  18:21:25,875 ProgressMeter -            done      1.7516305E7    28.0 s            1.0 s      100.0%    28.0 s       0.0 s
[2016-04-15T01:21Z] INFO  18:21:25,875 ProgressMeter - Total runtime 28.60 secs, 0.48 min, 0.01 hours
[2016-04-15T01:21Z] INFO  18:21:25,876 MicroScheduler - 7329 reads were filtered out during the traversal out of approximately 92671 total reads (7.91%)
[2016-04-15T01:21Z] INFO  18:21:25,877 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:21Z] INFO  18:21:25,877 MicroScheduler -   -> 7176 reads (7.74% of total) failing DuplicateReadFilter
[2016-04-15T01:21Z] INFO  18:21:25,878 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:21Z] INFO  18:21:25,878 MicroScheduler -   -> 153 reads (0.17% of total) failing HCMappingQualityFilter
[2016-04-15T01:21Z] INFO  18:21:25,878 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:21Z] INFO  18:21:25,879 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:21Z] INFO  18:21:25,879 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:21Z] INFO  18:21:25,880 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T01:21Z] INFO  18:21:25,883 ProgressMeter -     7:100551998      5.4804197E7    60.0 s            1.0 s       48.0%     2.1 m      64.0 s
[2016-04-15T01:21Z] INFO  18:21:25,952 ProgressMeter -      8:57228809      1.1783204E7    30.0 s            2.0 s       69.4%    43.0 s      13.0 s
[2016-04-15T01:21Z] INFO  18:21:26,042 ProgressMeter -      8:74903678      2.2409173E7    30.0 s            1.0 s       83.3%    36.0 s       6.0 s
[2016-04-15T01:21Z] INFO  18:21:27,224 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:21Z] GATK: HaplotypeCaller
[2016-04-15T01:21Z] INFO  18:21:30,481 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:21Z] INFO  18:21:30,484 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:21Z] INFO  18:21:30,484 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:21Z] INFO  18:21:30,484 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:21Z] INFO  18:21:30,488 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/9/R14-18102_kapa-NGv3-PE100-NGv3-sort-9_32407258_65506776-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/9/R14-18102_kapa-NGv3-PE100-NGv3-9_32407258_65506776-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/9/tx/tmpo0G9ww/R14-18102_kapa-NGv3-PE100-NGv3-9_32407258_65506776.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:21Z] INFO  18:21:30,505 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:21Z] INFO  18:21:30,506 HelpFormatter - Date/Time: 2016/04/14 18:21:30
[2016-04-15T01:21Z] INFO  18:21:30,507 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:21Z] INFO  18:21:30,507 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:21Z] WARN  18:21:30,530 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T01:21Z] WARN  18:21:30,533 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/9/tx/tmpo0G9ww/R14-18102_kapa-NGv3-PE100-NGv3-9_32407258_65506776.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T01:21Z] INFO  18:21:30,715 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:21Z] INFO  18:21:30,734 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.005519307
[2016-04-15T01:21Z] INFO  18:21:30,735 PairHMM - Total compute time in PairHMM computeLikelihoods() : 0.246648054
[2016-04-15T01:21Z] INFO  18:21:30,736 HaplotypeCaller - Ran local assembly on 787 active regions
[2016-04-15T01:21Z] INFO  18:21:30,826 ProgressMeter -            done      2.8015737E7    34.0 s            1.0 s      100.0%    34.0 s       0.0 s
[2016-04-15T01:21Z] INFO  18:21:30,827 ProgressMeter - Total runtime 34.80 secs, 0.58 min, 0.01 hours
[2016-04-15T01:21Z] INFO  18:21:30,832 MicroScheduler - 11452 reads were filtered out during the traversal out of approximately 138941 total reads (8.24%)
[2016-04-15T01:21Z] INFO  18:21:30,832 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:21Z] INFO  18:21:30,833 MicroScheduler -   -> 11147 reads (8.02% of total) failing DuplicateReadFilter
[2016-04-15T01:21Z] INFO  18:21:30,834 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:21Z] INFO  18:21:30,835 MicroScheduler -   -> 305 reads (0.22% of total) failing HCMappingQualityFilter
[2016-04-15T01:21Z] INFO  18:21:30,835 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:21Z] INFO  18:21:30,839 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:21Z] INFO  18:21:30,851 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:21Z] INFO  18:21:30,853 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T01:21Z] INFO  18:21:30,899 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T01:21Z] INFO  18:21:30,909 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:21Z] INFO  18:21:30,991 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-15T01:21Z] INFO  18:21:31,004 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T01:21Z] INFO  18:21:31,363 IntervalUtils - Processing 223679 bp from intervals
[2016-04-15T01:21Z] WARN  18:21:31,368 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:21Z] INFO  18:21:31,448 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:21Z] INFO  18:21:31,560 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:21Z] INFO  18:21:31,561 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:21Z] INFO  18:21:31,562 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T01:21Z] INFO  18:21:31,563 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T01:21Z] INFO  18:21:31,565 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T01:21Z] INFO  18:21:31,565 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T01:21Z] INFO  18:21:31,808 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T01:21Z] INFO  18:21:32,024 ProgressMeter -      6:41552533     2.83748621E8   120.0 s            0.0 s       70.0%     2.9 m      51.0 s
[2016-04-15T01:21Z] INFO  18:21:32,121 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.028168428000000002
[2016-04-15T01:21Z] INFO  18:21:32,122 PairHMM - Total compute time in PairHMM computeLikelihoods() : 0.28028879100000004
[2016-04-15T01:21Z] INFO  18:21:32,122 HaplotypeCaller - Ran local assembly on 916 active regions
[2016-04-15T01:21Z] INFO  18:21:32,176 ProgressMeter -            done      4.4752116E7    37.0 s            0.0 s      100.0%    37.0 s       0.0 s
[2016-04-15T01:21Z] INFO  18:21:32,178 ProgressMeter - Total runtime 37.26 secs, 0.62 min, 0.01 hours
[2016-04-15T01:21Z] INFO  18:21:32,178 MicroScheduler - 14123 reads were filtered out during the traversal out of approximately 173043 total reads (8.16%)
[2016-04-15T01:21Z] INFO  18:21:32,179 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:21Z] INFO  18:21:32,179 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:21Z] INFO  18:21:32,179 MicroScheduler -   -> 13931 reads (8.05% of total) failing DuplicateReadFilter
[2016-04-15T01:21Z] INFO  18:21:32,179 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:21Z] INFO  18:21:32,180 MicroScheduler -   -> 192 reads (0.11% of total) failing HCMappingQualityFilter
[2016-04-15T01:21Z] INFO  18:21:32,180 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:21Z] INFO  18:21:32,181 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:21Z] INFO  18:21:32,181 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:21Z] INFO  18:21:32,181 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T01:21Z] INFO  18:21:32,400 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.005241315000000001
[2016-04-15T01:21Z] INFO  18:21:32,401 PairHMM - Total compute time in PairHMM computeLikelihoods() : 1.9828489280000001
[2016-04-15T01:21Z] INFO  18:21:32,402 HaplotypeCaller - Ran local assembly on 724 active regions
[2016-04-15T01:21Z] INFO  18:21:32,427 ProgressMeter -            done      2.5170077E7    36.0 s            1.0 s      100.0%    36.0 s       0.0 s
[2016-04-15T01:21Z] INFO  18:21:32,428 ProgressMeter - Total runtime 36.50 secs, 0.61 min, 0.01 hours
[2016-04-15T01:21Z] INFO  18:21:32,428 MicroScheduler - 10950 reads were filtered out during the traversal out of approximately 130087 total reads (8.42%)
[2016-04-15T01:21Z] INFO  18:21:32,429 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:21Z] INFO  18:21:32,429 MicroScheduler -   -> 10371 reads (7.97% of total) failing DuplicateReadFilter
[2016-04-15T01:21Z] INFO  18:21:32,430 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:21Z] INFO  18:21:32,430 MicroScheduler -   -> 579 reads (0.45% of total) failing HCMappingQualityFilter
[2016-04-15T01:21Z] INFO  18:21:32,430 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:21Z] INFO  18:21:32,430 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:21Z] INFO  18:21:32,431 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:21Z] INFO  18:21:32,431 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T01:21Z] GATK: HaplotypeCaller
[2016-04-15T01:21Z] INFO  18:21:33,688 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:21Z] INFO  18:21:33,710 ProgressMeter -     8:102705019      2.1888203E7    30.0 s            1.0 s       57.8%    51.0 s      21.0 s
[2016-04-15T01:21Z] INFO  18:21:33,851 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:21Z] GATK: HaplotypeCaller
[2016-04-15T01:21Z] GATK: HaplotypeCaller
[2016-04-15T01:21Z] INFO  18:21:34,586 ProgressMeter -     7:151945387      8.0663527E7    60.0 s            0.0 s       88.2%    68.0 s       8.0 s
[2016-04-15T01:21Z] INFO  18:21:34,776 ProgressMeter -     8:125132031      2.1360478E7    30.0 s            1.0 s       84.3%    35.0 s       5.0 s
[2016-04-15T01:21Z] INFO  18:21:34,841 ProgressMeter -     7:141464325      1.1987934E8    60.0 s            0.0 s       97.9%    61.0 s       1.0 s
[2016-04-15T01:21Z] INFO  18:21:35,715 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:21Z] INFO  18:21:35,719 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:21Z] INFO  18:21:35,719 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:21Z] INFO  18:21:35,720 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:21Z] INFO  18:21:35,724 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/9/R14-18102_kapa-NGv3-PE100-NGv3-sort-9_65507205_82187750-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/9/R14-18102_kapa-NGv3-PE100-NGv3-9_65507205_82187750-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/9/tx/tmpO5XVIi/R14-18102_kapa-NGv3-PE100-NGv3-9_65507205_82187750.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:21Z] INFO  18:21:35,733 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:21Z] INFO  18:21:35,734 HelpFormatter - Date/Time: 2016/04/14 18:21:35
[2016-04-15T01:21Z] INFO  18:21:35,734 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:21Z] INFO  18:21:35,735 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:21Z] WARN  18:21:35,774 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T01:21Z] WARN  18:21:35,777 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/9/tx/tmpO5XVIi/R14-18102_kapa-NGv3-PE100-NGv3-9_65507205_82187750.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T01:21Z] INFO  18:21:35,990 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:21Z] INFO  18:21:36,123 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.017982574
[2016-04-15T01:21Z] INFO  18:21:36,124 PairHMM - Total compute time in PairHMM computeLikelihoods() : 0.8250486250000001
[2016-04-15T01:21Z] INFO  18:21:36,124 HaplotypeCaller - Ran local assembly on 1617 active regions
[2016-04-15T01:21Z] INFO  18:21:36,202 ProgressMeter -            done      1.2205741E8    61.0 s            0.0 s      100.0%    61.0 s       0.0 s
[2016-04-15T01:21Z] INFO  18:21:36,202 ProgressMeter - Total runtime 61.39 secs, 1.02 min, 0.02 hours
[2016-04-15T01:21Z] INFO  18:21:36,203 MicroScheduler - 26710 reads were filtered out during the traversal out of approximately 321300 total reads (8.31%)
[2016-04-15T01:21Z] INFO  18:21:36,203 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:21Z] INFO  18:21:36,203 MicroScheduler -   -> 25649 reads (7.98% of total) failing DuplicateReadFilter
[2016-04-15T01:21Z] INFO  18:21:36,203 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:21Z] INFO  18:21:36,204 MicroScheduler -   -> 1061 reads (0.33% of total) failing HCMappingQualityFilter
[2016-04-15T01:21Z] INFO  18:21:36,204 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:21Z] INFO  18:21:36,204 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:21Z] INFO  18:21:36,204 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:21Z] INFO  18:21:36,205 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T01:21Z] INFO  18:21:36,205 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T01:21Z] INFO  18:21:36,215 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:21Z] INFO  18:21:36,272 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-15T01:21Z] INFO  18:21:36,299 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T01:21Z] INFO  18:21:36,677 IntervalUtils - Processing 119378 bp from intervals
[2016-04-15T01:21Z] WARN  18:21:36,696 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:21Z] INFO  18:21:36,821 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:21Z] INFO  18:21:36,885 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:21Z] INFO  18:21:36,889 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:21Z] INFO  18:21:36,889 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:21Z] INFO  18:21:36,890 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:21Z] INFO  18:21:36,900 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/9/R14-18102_kapa-NGv3-PE100-NGv3-sort-9_82188172_97717561-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/9/R14-18102_kapa-NGv3-PE100-NGv3-9_82188172_97717561-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/9/tx/tmp06LDpj/R14-18102_kapa-NGv3-PE100-NGv3-9_82188172_97717561.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:21Z] INFO  18:21:36,904 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:21Z] INFO  18:21:36,905 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:21Z] INFO  18:21:36,906 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T01:21Z] INFO  18:21:36,907 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T01:21Z] INFO  18:21:36,907 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T01:21Z] INFO  18:21:36,907 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T01:21Z] INFO  18:21:36,917 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:21Z] INFO  18:21:36,917 HelpFormatter - Date/Time: 2016/04/14 18:21:36
[2016-04-15T01:21Z] INFO  18:21:36,917 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:21Z] INFO  18:21:36,918 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:21Z] WARN  18:21:36,939 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T01:21Z] WARN  18:21:36,942 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/9/tx/tmp06LDpj/R14-18102_kapa-NGv3-PE100-NGv3-9_82188172_97717561.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T01:21Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T01:21Z] INFO  18:21:37,079 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T01:21Z] INFO  18:21:37,079 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T01:21Z] INFO  18:21:37,109 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T01:21Z] INFO  18:21:37,168 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:21Z] INFO  18:21:37,343 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:21Z] INFO  18:21:37,346 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:21Z] INFO  18:21:37,347 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:21Z] INFO  18:21:37,347 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:21Z] INFO  18:21:37,352 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/9/R14-18102_kapa-NGv3-PE100-NGv3-sort-9_97718189_113228306-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/9/R14-18102_kapa-NGv3-PE100-NGv3-9_97718189_113228306-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/9/tx/tmp6GfkzV/R14-18102_kapa-NGv3-PE100-NGv3-9_97718189_113228306.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:21Z] INFO  18:21:37,361 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:21Z] INFO  18:21:37,362 HelpFormatter - Date/Time: 2016/04/14 18:21:37
[2016-04-15T01:21Z] INFO  18:21:37,363 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:21Z] INFO  18:21:37,364 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:21Z] INFO  18:21:37,365 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T01:21Z] INFO  18:21:37,375 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:21Z] WARN  18:21:37,395 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T01:21Z] WARN  18:21:37,398 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/9/tx/tmp6GfkzV/R14-18102_kapa-NGv3-PE100-NGv3-9_97718189_113228306.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T01:21Z] INFO  18:21:37,434 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-15T01:21Z] WARN  18:21:37,435 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T01:21Z] WARN  18:21:37,435 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T01:21Z] INFO  18:21:37,465 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T01:21Z] INFO  18:21:37,601 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:21Z] INFO  18:21:37,625 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:21Z] INFO  18:21:37,797 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.00706277
[2016-04-15T01:21Z] INFO  18:21:37,798 PairHMM - Total compute time in PairHMM computeLikelihoods() : 0.434571792
[2016-04-15T01:21Z] INFO  18:21:37,799 HaplotypeCaller - Ran local assembly on 605 active regions
[2016-04-15T01:21Z] INFO  18:21:37,809 IntervalUtils - Processing 181286 bp from intervals
[2016-04-15T01:21Z] WARN  18:21:37,814 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:21Z] INFO  18:21:37,852 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T01:21Z] INFO  18:21:37,854 ProgressMeter -            done      1.8346896E7    29.0 s            1.0 s      100.0%    29.0 s       0.0 s
[2016-04-15T01:21Z] INFO  18:21:37,856 ProgressMeter - Total runtime 29.05 secs, 0.48 min, 0.01 hours
[2016-04-15T01:21Z] INFO  18:21:37,856 MicroScheduler - 9470 reads were filtered out during the traversal out of approximately 115477 total reads (8.20%)
[2016-04-15T01:21Z] INFO  18:21:37,857 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:21Z] INFO  18:21:37,858 MicroScheduler -   -> 9326 reads (8.08% of total) failing DuplicateReadFilter
[2016-04-15T01:21Z] INFO  18:21:37,862 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:21Z] INFO  18:21:37,858 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:21Z] INFO  18:21:37,859 MicroScheduler -   -> 144 reads (0.12% of total) failing HCMappingQualityFilter
[2016-04-15T01:21Z] INFO  18:21:37,859 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:21Z] INFO  18:21:37,859 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:21Z] INFO  18:21:37,859 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:21Z] INFO  18:21:37,860 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T01:21Z] INFO  18:21:37,925 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:21Z] INFO  18:21:37,926 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-15T01:21Z] GATK: HaplotypeCaller
[2016-04-15T01:21Z] INFO  18:21:37,969 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T01:21Z] INFO  18:21:38,044 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:21Z] INFO  18:21:38,045 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:21Z] INFO  18:21:38,046 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T01:21Z] INFO  18:21:38,046 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T01:21Z] INFO  18:21:38,065 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T01:21Z] INFO  18:21:38,065 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T01:21Z] INFO  18:21:38,226 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.007532131
[2016-04-15T01:21Z] INFO  18:21:38,227 PairHMM - Total compute time in PairHMM computeLikelihoods() : 0.41787104500000005
[2016-04-15T01:21Z] INFO  18:21:38,228 HaplotypeCaller - Ran local assembly on 762 active regions
[2016-04-15T01:21Z] INFO  18:21:38,268 ProgressMeter -            done       2.937439E7    33.0 s            1.0 s      100.0%    33.0 s       0.0 s
[2016-04-15T01:21Z] INFO  18:21:38,268 ProgressMeter - Total runtime 33.52 secs, 0.56 min, 0.01 hours
[2016-04-15T01:21Z] INFO  18:21:38,269 MicroScheduler - 10895 reads were filtered out during the traversal out of approximately 136021 total reads (8.01%)
[2016-04-15T01:21Z] INFO  18:21:38,269 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:21Z] INFO  18:21:38,269 MicroScheduler -   -> 10747 reads (7.90% of total) failing DuplicateReadFilter
[2016-04-15T01:21Z] INFO  18:21:38,269 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:21Z] INFO  18:21:38,270 IntervalUtils - Processing 199321 bp from intervals
[2016-04-15T01:21Z] INFO  18:21:38,270 MicroScheduler -   -> 148 reads (0.11% of total) failing HCMappingQualityFilter
[2016-04-15T01:21Z] INFO  18:21:38,270 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:21Z] INFO  18:21:38,270 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:21Z] INFO  18:21:38,270 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:21Z] INFO  18:21:38,271 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T01:21Z] WARN  18:21:38,275 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:21Z] INFO  18:21:38,284 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T01:21Z] INFO  18:21:38,357 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:21Z] INFO  18:21:38,426 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:21Z] INFO  18:21:38,427 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:21Z] INFO  18:21:38,428 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T01:21Z] INFO  18:21:38,428 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T01:21Z] INFO  18:21:38,429 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T01:21Z] INFO  18:21:38,430 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T01:21Z] INFO  18:21:38,722 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T01:21Z] INFO  18:21:38,856 ProgressMeter -     8:144458823        5591755.0    30.0 s            5.0 s       29.2%   102.0 s      72.0 s
[2016-04-15T01:21Z] INFO  18:21:39,167 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:21Z] GATK: HaplotypeCaller
[2016-04-15T01:21Z] INFO  18:21:39,832 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:21Z] GATK: HaplotypeCaller
[2016-04-15T01:21Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T01:21Z] INFO  18:21:40,446 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T01:21Z] INFO  18:21:40,466 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T01:21Z] WARN  18:21:40,728 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T01:21Z] WARN  18:21:40,729 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T01:21Z] INFO  18:21:40,858 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:21Z] INFO  18:21:40,872 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:21Z] INFO  18:21:40,873 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:21Z] INFO  18:21:40,874 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:21Z] INFO  18:21:40,878 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/9/R14-18102_kapa-NGv3-PE100-NGv3-sort-9_113231219_129089575-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/9/R14-18102_kapa-NGv3-PE100-NGv3-9_113231219_129089575-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/9/tx/tmprkchB_/R14-18102_kapa-NGv3-PE100-NGv3-9_113231219_129089575.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:21Z] INFO  18:21:40,897 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:21Z] INFO  18:21:40,898 HelpFormatter - Date/Time: 2016/04/14 18:21:40
[2016-04-15T01:21Z] INFO  18:21:40,898 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:21Z] INFO  18:21:40,899 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:21Z] WARN  18:21:40,933 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T01:21Z] WARN  18:21:40,946 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/9/tx/tmprkchB_/R14-18102_kapa-NGv3-PE100-NGv3-9_113231219_129089575.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T01:21Z] INFO  18:21:41,145 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:21Z] INFO  18:21:41,330 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T01:21Z] INFO  18:21:41,349 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:21Z] INFO  18:21:41,414 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-15T01:21Z] INFO  18:21:41,451 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T01:21Z] INFO  18:21:41,796 IntervalUtils - Processing 228449 bp from intervals
[2016-04-15T01:21Z] WARN  18:21:41,801 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:21Z] INFO  18:21:41,875 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:21Z] INFO  18:21:42,002 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:21Z] INFO  18:21:42,004 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:21Z] INFO  18:21:42,004 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T01:21Z] INFO  18:21:42,005 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T01:21Z] INFO  18:21:42,006 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T01:21Z] INFO  18:21:42,006 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T01:21Z] INFO  18:21:42,232 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T01:21Z] INFO  18:21:42,650 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:21Z] INFO  18:21:42,653 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:21Z] INFO  18:21:42,654 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:21Z] INFO  18:21:42,654 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:21Z] INFO  18:21:42,658 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/9/R14-18102_kapa-NGv3-PE100-NGv3-sort-9_129097484_141213431-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/9/R14-18102_kapa-NGv3-PE100-NGv3-9_129097484_141213431-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/9/tx/tmpPbKmiD/R14-18102_kapa-NGv3-PE100-NGv3-9_129097484_141213431.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:21Z] INFO  18:21:42,668 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:21Z] INFO  18:21:42,675 HelpFormatter - Date/Time: 2016/04/14 18:21:42
[2016-04-15T01:21Z] INFO  18:21:42,676 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:21Z] INFO  18:21:42,676 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:21Z] WARN  18:21:42,702 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T01:21Z] WARN  18:21:42,705 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/9/tx/tmpPbKmiD/R14-18102_kapa-NGv3-PE100-NGv3-9_129097484_141213431.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T01:21Z] INFO  18:21:42,907 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:21Z] INFO  18:21:43,069 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T01:21Z] INFO  18:21:43,070 ProgressMeter -       9:8733843      2.1806577E7    30.0 s            1.0 s       78.0%    38.0 s       8.0 s
[2016-04-15T01:21Z] INFO  18:21:43,080 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:21Z] INFO  18:21:43,154 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-15T01:21Z] INFO  18:21:43,179 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T01:21Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T01:21Z] INFO  18:21:43,210 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T01:21Z] INFO  18:21:43,211 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T01:21Z] INFO  18:21:43,247 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:21Z] INFO  18:21:43,250 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:21Z] INFO  18:21:43,251 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:21Z] INFO  18:21:43,251 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:21Z] INFO  18:21:43,256 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/10/R14-18102_kapa-NGv3-PE100-NGv3-sort-10_0_15559243-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/10/R14-18102_kapa-NGv3-PE100-NGv3-10_0_15559243-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/10/tx/tmp3bh447/R14-18102_kapa-NGv3-PE100-NGv3-10_0_15559243.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:21Z] INFO  18:21:43,280 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:21Z] INFO  18:21:43,280 HelpFormatter - Date/Time: 2016/04/14 18:21:43
[2016-04-15T01:21Z] INFO  18:21:43,281 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:21Z] INFO  18:21:43,281 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:21Z] WARN  18:21:43,308 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T01:21Z] WARN  18:21:43,311 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/10/tx/tmp3bh447/R14-18102_kapa-NGv3-PE100-NGv3-10_0_15559243.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T01:21Z] INFO  18:21:43,556 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:21Z] WARN  18:21:43,562 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T01:21Z] WARN  18:21:43,564 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T01:21Z] INFO  18:21:43,734 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T01:21Z] INFO  18:21:43,756 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:21Z] INFO  18:21:43,775 IntervalUtils - Processing 455246 bp from intervals
[2016-04-15T01:21Z] WARN  18:21:43,791 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:21Z] INFO  18:21:43,838 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-15T01:21Z] INFO  18:21:43,870 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T01:21Z] INFO  18:21:43,945 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:21Z] INFO  18:21:44,173 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:21Z] INFO  18:21:44,174 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:21Z] INFO  18:21:44,174 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T01:21Z] INFO  18:21:44,175 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T01:21Z] INFO  18:21:44,186 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T01:21Z] INFO  18:21:44,187 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T01:21Z] INFO  18:21:44,288 IntervalUtils - Processing 145147 bp from intervals
[2016-04-15T01:21Z] WARN  18:21:44,293 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:21Z] INFO  18:21:44,419 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:21Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T01:21Z] INFO  18:21:44,435 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T01:21Z] INFO  18:21:44,436 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T01:21Z] INFO  18:21:44,448 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T01:21Z] INFO  18:21:44,509 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:21Z] INFO  18:21:44,521 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:21Z] INFO  18:21:44,522 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T01:21Z] INFO  18:21:44,522 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T01:21Z] INFO  18:21:44,539 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T01:21Z] INFO  18:21:44,540 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T01:21Z] WARN  18:21:44,692 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T01:21Z] WARN  18:21:44,693 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T01:21Z] INFO  18:21:44,798 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T01:21Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T01:21Z] INFO  18:21:44,976 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T01:21Z] INFO  18:21:44,977 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T01:21Z] WARN  18:21:45,242 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T01:21Z] WARN  18:21:45,242 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T01:21Z] INFO  18:21:45,465 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.036200731
[2016-04-15T01:21Z] INFO  18:21:45,465 PairHMM - Total compute time in PairHMM computeLikelihoods() : 3.5071866930000004
[2016-04-15T01:21Z] INFO  18:21:45,476 HaplotypeCaller - Ran local assembly on 866 active regions
[2016-04-15T01:21Z] INFO  18:21:45,524 ProgressMeter -            done      2.7109958E7    53.0 s            1.0 s      100.0%    53.0 s       0.0 s
[2016-04-15T01:21Z] INFO  18:21:45,524 ProgressMeter - Total runtime 53.39 secs, 0.89 min, 0.01 hours
[2016-04-15T01:21Z] INFO  18:21:45,525 MicroScheduler - 57502 reads were filtered out during the traversal out of approximately 210692 total reads (27.29%)
[2016-04-15T01:21Z] INFO  18:21:45,525 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:21Z] INFO  18:21:45,525 MicroScheduler -   -> 13751 reads (6.53% of total) failing DuplicateReadFilter
[2016-04-15T01:21Z] INFO  18:21:45,526 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:21Z] INFO  18:21:45,526 MicroScheduler -   -> 43751 reads (20.77% of total) failing HCMappingQualityFilter
[2016-04-15T01:21Z] INFO  18:21:45,526 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:21Z] INFO  18:21:45,527 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:21Z] INFO  18:21:45,527 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:21Z] INFO  18:21:45,527 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T01:21Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T01:21Z] INFO  18:21:47,098 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:21Z] INFO  18:21:47,102 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T01:21Z] INFO  18:21:47,103 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T01:21Z] INFO  18:21:47,423 ProgressMeter -      9:27950669      1.7240228E7    30.0 s            1.0 s       99.9%    30.0 s       0.0 s
[2016-04-15T01:21Z] WARN  18:21:47,495 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T01:21Z] WARN  18:21:47,496 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T01:21Z] GATK: HaplotypeCaller
[2016-04-15T01:21Z] INFO  18:21:47,668 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.012160007
[2016-04-15T01:21Z] INFO  18:21:47,670 PairHMM - Total compute time in PairHMM computeLikelihoods() : 0.25239366
[2016-04-15T01:21Z] INFO  18:21:47,670 HaplotypeCaller - Ran local assembly on 609 active regions
[2016-04-15T01:21Z] INFO  18:21:47,723 ProgressMeter -            done      1.7418853E7    30.0 s            1.0 s      100.0%    30.0 s       0.0 s
[2016-04-15T01:21Z] INFO  18:21:47,724 ProgressMeter - Total runtime 30.37 secs, 0.51 min, 0.01 hours
[2016-04-15T01:21Z] INFO  18:21:47,725 MicroScheduler - 12165 reads were filtered out during the traversal out of approximately 118786 total reads (10.24%)
[2016-04-15T01:21Z] INFO  18:21:47,725 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:21Z] INFO  18:21:47,726 MicroScheduler -   -> 9424 reads (7.93% of total) failing DuplicateReadFilter
[2016-04-15T01:21Z] INFO  18:21:47,726 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:21Z] INFO  18:21:47,726 MicroScheduler -   -> 2741 reads (2.31% of total) failing HCMappingQualityFilter
[2016-04-15T01:21Z] INFO  18:21:47,726 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:21Z] INFO  18:21:47,727 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:21Z] INFO  18:21:47,727 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:21Z] INFO  18:21:47,727 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T01:21Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T01:21Z] INFO  18:21:48,363 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T01:21Z] INFO  18:21:48,364 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T01:21Z] WARN  18:21:48,730 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T01:21Z] WARN  18:21:48,731 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T01:21Z] INFO  18:21:49,174 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.019669214
[2016-04-15T01:21Z] INFO  18:21:49,174 PairHMM - Total compute time in PairHMM computeLikelihoods() : 1.297701918
[2016-04-15T01:21Z] INFO  18:21:49,174 HaplotypeCaller - Ran local assembly on 1140 active regions
[2016-04-15T01:21Z] INFO  18:21:49,210 ProgressMeter -            done      6.7177744E7    45.0 s            0.0 s      100.0%    45.0 s       0.0 s
[2016-04-15T01:21Z] INFO  18:21:49,221 ProgressMeter - Total runtime 45.55 secs, 0.76 min, 0.01 hours
[2016-04-15T01:21Z] INFO  18:21:49,221 MicroScheduler - 16114 reads were filtered out during the traversal out of approximately 196849 total reads (8.19%)
[2016-04-15T01:21Z] INFO  18:21:49,222 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:21Z] INFO  18:21:49,222 MicroScheduler -   -> 15802 reads (8.03% of total) failing DuplicateReadFilter
[2016-04-15T01:21Z] INFO  18:21:49,222 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:21Z] INFO  18:21:49,222 MicroScheduler -   -> 312 reads (0.16% of total) failing HCMappingQualityFilter
[2016-04-15T01:21Z] INFO  18:21:49,222 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:21Z] INFO  18:21:49,223 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:21Z] INFO  18:21:49,223 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:21Z] INFO  18:21:49,223 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T01:21Z] INFO  18:21:49,837 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.027737287000000003
[2016-04-15T01:21Z] INFO  18:21:49,838 PairHMM - Total compute time in PairHMM computeLikelihoods() : 7.959956062000001
[2016-04-15T01:21Z] INFO  18:21:49,839 HaplotypeCaller - Ran local assembly on 1684 active regions
[2016-04-15T01:21Z] INFO  18:21:49,896 ProgressMeter -            done     1.17619154E8    75.0 s            0.0 s      100.0%    75.0 s       0.0 s
[2016-04-15T01:21Z] INFO  18:21:49,896 ProgressMeter - Total runtime 75.35 secs, 1.26 min, 0.02 hours
[2016-04-15T01:21Z] INFO  18:21:49,897 MicroScheduler - 81371 reads were filtered out during the traversal out of approximately 421913 total reads (19.29%)
[2016-04-15T01:21Z] INFO  18:21:49,897 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:21Z] INFO  18:21:49,898 MicroScheduler -   -> 30057 reads (7.12% of total) failing DuplicateReadFilter
[2016-04-15T01:21Z] INFO  18:21:49,898 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:21Z] INFO  18:21:49,898 MicroScheduler -   -> 51314 reads (12.16% of total) failing HCMappingQualityFilter
[2016-04-15T01:21Z] INFO  18:21:49,898 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:21Z] INFO  18:21:49,899 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:21Z] INFO  18:21:49,899 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:21Z] INFO  18:21:49,899 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T01:21Z] INFO  18:21:50,090 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:21Z] GATK: HaplotypeCaller
[2016-04-15T01:21Z] INFO  18:21:50,488 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.007527022
[2016-04-15T01:21Z] INFO  18:21:50,489 PairHMM - Total compute time in PairHMM computeLikelihoods() : 0.41446532900000005
[2016-04-15T01:21Z] INFO  18:21:50,490 HaplotypeCaller - Ran local assembly on 887 active regions
[2016-04-15T01:21Z] INFO  18:21:50,547 ProgressMeter -            done      3.9438501E7    37.0 s            0.0 s      100.0%    37.0 s       0.0 s
[2016-04-15T01:21Z] INFO  18:21:50,547 ProgressMeter - Total runtime 37.50 secs, 0.62 min, 0.01 hours
[2016-04-15T01:21Z] INFO  18:21:50,548 MicroScheduler - 23054 reads were filtered out during the traversal out of approximately 172493 total reads (13.37%)
[2016-04-15T01:21Z] INFO  18:21:50,549 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:21Z] INFO  18:21:50,549 MicroScheduler -   -> 13482 reads (7.82% of total) failing DuplicateReadFilter
[2016-04-15T01:21Z] INFO  18:21:50,550 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:21Z] INFO  18:21:50,551 MicroScheduler -   -> 9572 reads (5.55% of total) failing HCMappingQualityFilter
[2016-04-15T01:21Z] INFO  18:21:50,551 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:21Z] INFO  18:21:50,552 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:21Z] INFO  18:21:50,553 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:21Z] INFO  18:21:50,553 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T01:21Z] INFO  18:21:50,626 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:21Z] INFO  18:21:50,629 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:21Z] INFO  18:21:50,630 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:21Z] INFO  18:21:50,630 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:21Z] INFO  18:21:50,635 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/10/R14-18102_kapa-NGv3-PE100-NGv3-sort-10_15561288_31134502-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/10/R14-18102_kapa-NGv3-PE100-NGv3-10_15561288_31134502-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/10/tx/tmpXtQyFX/R14-18102_kapa-NGv3-PE100-NGv3-10_15561288_31134502.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:21Z] INFO  18:21:50,652 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:21Z] INFO  18:21:50,653 HelpFormatter - Date/Time: 2016/04/14 18:21:50
[2016-04-15T01:21Z] INFO  18:21:50,654 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:21Z] INFO  18:21:50,654 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:21Z] WARN  18:21:50,699 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T01:21Z] INFO  18:21:50,701 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:21Z] WARN  18:21:50,710 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/10/tx/tmpXtQyFX/R14-18102_kapa-NGv3-PE100-NGv3-10_15561288_31134502.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T01:21Z] INFO  18:21:50,865 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:21Z] GATK: HaplotypeCaller
[2016-04-15T01:21Z] INFO  18:21:51,099 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T01:21Z] INFO  18:21:51,119 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:21Z] INFO  18:21:51,218 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.10
[2016-04-15T01:21Z] INFO  18:21:51,247 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T01:21Z] INFO  18:21:51,289 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:21Z] GATK: HaplotypeCaller
[2016-04-15T01:21Z] INFO  18:21:51,733 IntervalUtils - Processing 156629 bp from intervals
[2016-04-15T01:21Z] WARN  18:21:51,738 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:21Z] INFO  18:21:51,849 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:21Z] INFO  18:21:51,915 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:21Z] INFO  18:21:51,982 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:21Z] INFO  18:21:51,983 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:21Z] INFO  18:21:51,984 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T01:21Z] INFO  18:21:51,984 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T01:21Z] INFO  18:21:51,997 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T01:21Z] INFO  18:21:51,998 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T01:21Z] GATK: HaplotypeCaller
[2016-04-15T01:21Z] INFO  18:21:52,247 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T01:21Z] INFO  18:21:52,479 ProgressMeter -      8:28902878     1.00023966E8    60.0 s            0.0 s       83.9%    71.0 s      11.0 s
[2016-04-15T01:21Z] INFO  18:21:53,562 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:21Z] INFO  18:21:53,566 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:21Z] INFO  18:21:53,566 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:21Z] INFO  18:21:53,567 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:21Z] INFO  18:21:53,571 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/10/R14-18102_kapa-NGv3-PE100-NGv3-sort-10_31137459_46960129-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/10/R14-18102_kapa-NGv3-PE100-NGv3-10_31137459_46960129-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/10/tx/tmps93dNQ/R14-18102_kapa-NGv3-PE100-NGv3-10_31137459_46960129.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:21Z] INFO  18:21:53,603 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:21Z] INFO  18:21:53,604 HelpFormatter - Date/Time: 2016/04/14 18:21:53
[2016-04-15T01:21Z] INFO  18:21:53,604 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:21Z] INFO  18:21:53,605 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:21Z] WARN  18:21:53,630 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T01:21Z] WARN  18:21:53,633 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/10/tx/tmps93dNQ/R14-18102_kapa-NGv3-PE100-NGv3-10_31137459_46960129.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T01:21Z] INFO  18:21:53,916 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:21Z] INFO  18:21:54,087 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T01:21Z] INFO  18:21:54,096 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:21Z] INFO  18:21:54,193 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.10
[2016-04-15T01:21Z] INFO  18:21:54,225 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T01:21Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T01:21Z] INFO  18:21:54,386 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T01:21Z] INFO  18:21:54,387 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T01:21Z] INFO  18:21:54,537 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:21Z] INFO  18:21:54,539 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:21Z] INFO  18:21:54,539 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:21Z] INFO  18:21:54,540 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:21Z] INFO  18:21:54,544 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/10/R14-18102_kapa-NGv3-PE100-NGv3-sort-10_46960410_62493077-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/10/R14-18102_kapa-NGv3-PE100-NGv3-10_46960410_62493077-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/10/tx/tmpWgALTN/R14-18102_kapa-NGv3-PE100-NGv3-10_46960410_62493077.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:21Z] INFO  18:21:54,556 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:21Z] INFO  18:21:54,556 HelpFormatter - Date/Time: 2016/04/14 18:21:54
[2016-04-15T01:21Z] INFO  18:21:54,556 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:21Z] INFO  18:21:54,557 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:21Z] WARN  18:21:54,596 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T01:21Z] WARN  18:21:54,614 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/10/tx/tmpWgALTN/R14-18102_kapa-NGv3-PE100-NGv3-10_46960410_62493077.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T01:21Z] WARN  18:21:54,642 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T01:21Z] WARN  18:21:54,643 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T01:21Z] INFO  18:21:54,761 IntervalUtils - Processing 103621 bp from intervals
[2016-04-15T01:21Z] WARN  18:21:54,766 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:21Z] INFO  18:21:54,845 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:21Z] INFO  18:21:54,884 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:21Z] INFO  18:21:54,933 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:21Z] INFO  18:21:54,933 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:21Z] INFO  18:21:54,934 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T01:21Z] INFO  18:21:54,934 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T01:21Z] INFO  18:21:54,947 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T01:21Z] INFO  18:21:54,948 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T01:21Z] INFO  18:21:55,004 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:21Z] INFO  18:21:55,018 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:21Z] INFO  18:21:55,019 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:21Z] INFO  18:21:55,020 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:21Z] INFO  18:21:55,025 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/10/R14-18102_kapa-NGv3-PE100-NGv3-sort-10_62539923_78084243-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/10/R14-18102_kapa-NGv3-PE100-NGv3-10_62539923_78084243-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/10/tx/tmplU7QuW/R14-18102_kapa-NGv3-PE100-NGv3-10_62539923_78084243.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:21Z] INFO  18:21:55,073 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:21Z] INFO  18:21:55,074 HelpFormatter - Date/Time: 2016/04/14 18:21:55
[2016-04-15T01:21Z] INFO  18:21:55,074 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:21Z] INFO  18:21:55,074 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:21Z] WARN  18:21:55,124 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T01:21Z] INFO  18:21:55,126 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T01:21Z] WARN  18:21:55,137 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/10/tx/tmplU7QuW/R14-18102_kapa-NGv3-PE100-NGv3-10_62539923_78084243.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T01:21Z] INFO  18:21:55,147 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:21Z] INFO  18:21:55,222 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T01:21Z] INFO  18:21:55,260 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.11
[2016-04-15T01:21Z] INFO  18:21:55,273 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T01:21Z] INFO  18:21:55,374 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:21Z] INFO  18:21:55,611 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T01:21Z] INFO  18:21:55,620 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:21Z] INFO  18:21:55,738 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.12
[2016-04-15T01:21Z] INFO  18:21:55,759 IntervalUtils - Processing 143638 bp from intervals
[2016-04-15T01:21Z] WARN  18:21:55,764 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:21Z] INFO  18:21:55,767 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T01:21Z] INFO  18:21:55,834 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:21Z] INFO  18:21:55,884 ProgressMeter -     7:100682125      5.8414959E7    90.0 s            1.0 s       55.1%     2.7 m      73.0 s
[2016-04-15T01:21Z] INFO  18:21:55,895 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:21Z] INFO  18:21:55,896 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:21Z] INFO  18:21:55,897 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T01:21Z] INFO  18:21:55,897 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T01:21Z] INFO  18:21:55,898 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T01:21Z] INFO  18:21:55,898 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T01:21Z] INFO  18:21:56,135 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:21Z] INFO  18:21:56,139 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:21Z] INFO  18:21:56,139 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:21Z] INFO  18:21:56,140 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:21Z] INFO  18:21:56,141 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T01:21Z] INFO  18:21:56,144 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/10/R14-18102_kapa-NGv3-PE100-NGv3-sort-10_78316966_93841258-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/10/R14-18102_kapa-NGv3-PE100-NGv3-10_78316966_93841258-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/10/tx/tmpu6HolT/R14-18102_kapa-NGv3-PE100-NGv3-10_78316966_93841258.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:21Z] INFO  18:21:56,153 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:21Z] INFO  18:21:56,154 HelpFormatter - Date/Time: 2016/04/14 18:21:56
[2016-04-15T01:21Z] INFO  18:21:56,154 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:21Z] INFO  18:21:56,154 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:21Z] WARN  18:21:56,186 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T01:21Z] WARN  18:21:56,188 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/10/tx/tmpu6HolT/R14-18102_kapa-NGv3-PE100-NGv3-10_78316966_93841258.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T01:21Z] INFO  18:21:56,193 IntervalUtils - Processing 230109 bp from intervals
[2016-04-15T01:21Z] WARN  18:21:56,209 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:21Z] INFO  18:21:56,291 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:21Z] INFO  18:21:56,419 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:21Z] INFO  18:21:56,420 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:21Z] INFO  18:21:56,420 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T01:21Z] INFO  18:21:56,420 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T01:21Z] INFO  18:21:56,427 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T01:21Z] INFO  18:21:56,428 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T01:21Z] INFO  18:21:56,446 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:21Z] INFO  18:21:56,629 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T01:21Z] INFO  18:21:56,639 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:21Z] INFO  18:21:56,677 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T01:21Z] INFO  18:21:56,729 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.09
[2016-04-15T01:21Z] INFO  18:21:56,749 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T01:21Z] INFO  18:21:57,352 IntervalUtils - Processing 148808 bp from intervals
[2016-04-15T01:21Z] WARN  18:21:57,371 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:21Z] INFO  18:21:57,502 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:21Z] INFO  18:21:57,589 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:21Z] INFO  18:21:57,590 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:21Z] INFO  18:21:57,590 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T01:21Z] INFO  18:21:57,591 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T01:21Z] INFO  18:21:57,592 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T01:21Z] INFO  18:21:57,592 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T01:21Z] INFO  18:21:57,899 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T01:21Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T01:21Z] INFO  18:21:59,173 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T01:21Z] INFO  18:21:59,174 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T01:21Z] WARN  18:21:59,478 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T01:21Z] WARN  18:21:59,479 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T01:22Z] INFO  18:22:00,967 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.028526686000000002
[2016-04-15T01:22Z] INFO  18:22:00,968 PairHMM - Total compute time in PairHMM computeLikelihoods() : 3.356258775
[2016-04-15T01:22Z] INFO  18:22:00,969 HaplotypeCaller - Ran local assembly on 1799 active regions
[2016-04-15T01:22Z] INFO  18:22:01,007 ProgressMeter -            done     1.35599805E8    68.0 s            0.0 s      100.0%    68.0 s       0.0 s
[2016-04-15T01:22Z] INFO  18:22:01,008 ProgressMeter - Total runtime 68.55 secs, 1.14 min, 0.02 hours
[2016-04-15T01:22Z] INFO  18:22:01,009 MicroScheduler - 27953 reads were filtered out during the traversal out of approximately 336573 total reads (8.31%)
[2016-04-15T01:22Z] INFO  18:22:01,009 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:22Z] INFO  18:22:01,010 MicroScheduler -   -> 26261 reads (7.80% of total) failing DuplicateReadFilter
[2016-04-15T01:22Z] INFO  18:22:01,010 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:22Z] INFO  18:22:01,011 MicroScheduler -   -> 1692 reads (0.50% of total) failing HCMappingQualityFilter
[2016-04-15T01:22Z] INFO  18:22:01,012 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:22Z] INFO  18:22:01,012 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:22Z] INFO  18:22:01,013 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:22Z] INFO  18:22:01,013 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T01:22Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T01:22Z] INFO  18:22:01,083 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T01:22Z] INFO  18:22:01,083 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T01:22Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T01:22Z] INFO  18:22:01,216 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T01:22Z] INFO  18:22:01,217 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T01:22Z] WARN  18:22:01,303 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T01:22Z] WARN  18:22:01,303 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T01:22Z] INFO  18:22:01,584 ProgressMeter -      9:34726525       1.000006E7    30.0 s            3.0 s       29.7%   100.0 s      70.0 s
[2016-04-15T01:22Z] WARN  18:22:01,724 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T01:22Z] WARN  18:22:01,726 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T01:22Z] INFO  18:22:02,025 ProgressMeter -      6:44278036     5.16161507E8     2.5 m            0.0 s       96.8%     2.6 m       4.0 s
[2016-04-15T01:22Z] INFO  18:22:02,381 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:22Z] GATK: HaplotypeCaller
[2016-04-15T01:22Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T01:22Z] INFO  18:22:03,023 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T01:22Z] INFO  18:22:03,024 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T01:22Z] WARN  18:22:03,321 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T01:22Z] WARN  18:22:03,322 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T01:22Z] INFO  18:22:05,850 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:22Z] INFO  18:22:05,852 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:22Z] INFO  18:22:05,863 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:22Z] INFO  18:22:05,864 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:22Z] INFO  18:22:05,868 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/10/R14-18102_kapa-NGv3-PE100-NGv3-sort-10_93851586_111625070-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/10/R14-18102_kapa-NGv3-PE100-NGv3-10_93851586_111625070-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/10/tx/tmp1ht146/R14-18102_kapa-NGv3-PE100-NGv3-10_93851586_111625070.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:22Z] INFO  18:22:05,898 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:22Z] INFO  18:22:05,899 HelpFormatter - Date/Time: 2016/04/14 18:22:05
[2016-04-15T01:22Z] INFO  18:22:05,900 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:22Z] INFO  18:22:05,900 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:22Z] WARN  18:22:05,950 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T01:22Z] WARN  18:22:05,953 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/10/tx/tmp1ht146/R14-18102_kapa-NGv3-PE100-NGv3-10_93851586_111625070.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T01:22Z] INFO  18:22:06,229 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:22Z] INFO  18:22:06,446 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T01:22Z] INFO  18:22:06,455 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:22Z] INFO  18:22:06,568 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.11
[2016-04-15T01:22Z] INFO  18:22:06,594 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T01:22Z] INFO  18:22:06,926 ProgressMeter -      9:77415302      1.5891753E7    30.0 s            1.0 s       65.7%    45.0 s      15.0 s
[2016-04-15T01:22Z] INFO  18:22:06,949 IntervalUtils - Processing 335852 bp from intervals
[2016-04-15T01:22Z] WARN  18:22:06,955 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:22Z] INFO  18:22:07,063 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:22Z] INFO  18:22:07,225 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:22Z] INFO  18:22:07,226 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:22Z] INFO  18:22:07,227 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T01:22Z] INFO  18:22:07,228 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T01:22Z] INFO  18:22:07,229 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T01:22Z] INFO  18:22:07,229 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T01:22Z] INFO  18:22:07,363 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.053596468
[2016-04-15T01:22Z] INFO  18:22:07,364 PairHMM - Total compute time in PairHMM computeLikelihoods() : 15.608885158000001
[2016-04-15T01:22Z] INFO  18:22:07,365 HaplotypeCaller - Ran local assembly on 3720 active regions
[2016-04-15T01:22Z] INFO  18:22:07,414 ProgressMeter -            done     5.57488561E8     2.6 m            0.0 s      100.0%     2.6 m       0.0 s
[2016-04-15T01:22Z] INFO  18:22:07,415 ProgressMeter - Total runtime 155.41 secs, 2.59 min, 0.04 hours
[2016-04-15T01:22Z] INFO  18:22:07,415 MicroScheduler - 105753 reads were filtered out during the traversal out of approximately 852854 total reads (12.40%)
[2016-04-15T01:22Z] INFO  18:22:07,416 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:22Z] INFO  18:22:07,416 MicroScheduler -   -> 65943 reads (7.73% of total) failing DuplicateReadFilter
[2016-04-15T01:22Z] INFO  18:22:07,416 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:22Z] INFO  18:22:07,416 MicroScheduler -   -> 39810 reads (4.67% of total) failing HCMappingQualityFilter
[2016-04-15T01:22Z] INFO  18:22:07,417 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:22Z] INFO  18:22:07,417 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:22Z] INFO  18:22:07,417 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:22Z] INFO  18:22:07,417 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T01:22Z] INFO  18:22:07,451 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T01:22Z] INFO  18:22:08,071 ProgressMeter -      9:91159294      1.4857861E7    30.0 s            2.0 s       50.8%    59.0 s      29.0 s
[2016-04-15T01:22Z] INFO  18:22:08,449 ProgressMeter -     9:103312442      2.1530842E7    30.0 s            1.0 s       46.6%    64.0 s      34.0 s
[2016-04-15T01:22Z] INFO  18:22:08,872 ProgressMeter -     8:145621563      2.7387553E7    60.0 s            2.0 s       76.9%    78.0 s      18.0 s
[2016-04-15T01:22Z] INFO  18:22:08,904 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:22Z] GATK: HaplotypeCaller
[2016-04-15T01:22Z] INFO  18:22:12,029 ProgressMeter -     9:117852841      2.4835421E7    30.0 s            1.0 s       42.0%    71.0 s      41.0 s
[2016-04-15T01:22Z] INFO  18:22:12,352 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:22Z] INFO  18:22:12,355 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:22Z] INFO  18:22:12,356 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:22Z] INFO  18:22:12,356 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:22Z] INFO  18:22:12,361 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/10/R14-18102_kapa-NGv3-PE100-NGv3-sort-10_111628371_127265443-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/10/R14-18102_kapa-NGv3-PE100-NGv3-10_111628371_127265443-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/10/tx/tmpYgqkwz/R14-18102_kapa-NGv3-PE100-NGv3-10_111628371_127265443.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:22Z] INFO  18:22:12,384 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:22Z] INFO  18:22:12,385 HelpFormatter - Date/Time: 2016/04/14 18:22:12
[2016-04-15T01:22Z] INFO  18:22:12,386 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:22Z] INFO  18:22:12,386 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:22Z] WARN  18:22:12,437 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T01:22Z] WARN  18:22:12,440 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/10/tx/tmpYgqkwz/R14-18102_kapa-NGv3-PE100-NGv3-10_111628371_127265443.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T01:22Z] INFO  18:22:12,724 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:22Z] INFO  18:22:12,944 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T01:22Z] INFO  18:22:12,954 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:22Z] INFO  18:22:13,022 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-15T01:22Z] INFO  18:22:13,059 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T01:22Z] INFO  18:22:13,547 IntervalUtils - Processing 210787 bp from intervals
[2016-04-15T01:22Z] WARN  18:22:13,562 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:22Z] INFO  18:22:13,636 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:22Z] INFO  18:22:13,745 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:22Z] INFO  18:22:13,745 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:22Z] INFO  18:22:13,746 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T01:22Z] INFO  18:22:13,746 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T01:22Z] INFO  18:22:13,758 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T01:22Z] INFO  18:22:13,758 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T01:22Z] INFO  18:22:14,008 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T01:22Z] INFO  18:22:14,189 ProgressMeter -     9:131151288      1.3430786E7    30.0 s            2.0 s       15.9%     3.1 m       2.6 m
[2016-04-15T01:22Z] INFO  18:22:14,542 ProgressMeter -      10:7245644      1.2152325E7    30.0 s            2.0 s       45.3%    66.0 s      36.0 s
[2016-04-15T01:22Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T01:22Z] INFO  18:22:14,840 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T01:22Z] INFO  18:22:14,841 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T01:22Z] WARN  18:22:15,642 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T01:22Z] WARN  18:22:15,643 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T01:22Z] INFO  18:22:16,096 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.009702778
[2016-04-15T01:22Z] INFO  18:22:16,107 PairHMM - Total compute time in PairHMM computeLikelihoods() : 1.023993157
[2016-04-15T01:22Z] INFO  18:22:16,108 HaplotypeCaller - Ran local assembly on 911 active regions
[2016-04-15T01:22Z] INFO  18:22:16,147 ProgressMeter -            done      3.7646403E7    39.0 s            1.0 s      100.0%    39.0 s       0.0 s
[2016-04-15T01:22Z] INFO  18:22:16,147 ProgressMeter - Total runtime 39.24 secs, 0.65 min, 0.01 hours
[2016-04-15T01:22Z] INFO  18:22:16,159 MicroScheduler - 65403 reads were filtered out during the traversal out of approximately 193830 total reads (33.74%)
[2016-04-15T01:22Z] INFO  18:22:16,159 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:22Z] INFO  18:22:16,159 MicroScheduler -   -> 11448 reads (5.91% of total) failing DuplicateReadFilter
[2016-04-15T01:22Z] INFO  18:22:16,160 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:22Z] INFO  18:22:16,160 MicroScheduler -   -> 53955 reads (27.84% of total) failing HCMappingQualityFilter
[2016-04-15T01:22Z] INFO  18:22:16,160 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:22Z] INFO  18:22:16,160 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:22Z] INFO  18:22:16,161 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:22Z] INFO  18:22:16,161 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T01:22Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T01:22Z] INFO  18:22:16,658 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T01:22Z] INFO  18:22:16,659 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T01:22Z] WARN  18:22:16,963 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T01:22Z] WARN  18:22:16,964 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T01:22Z] INFO  18:22:17,492 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:22Z] GATK: HaplotypeCaller
[2016-04-15T01:22Z] INFO  18:22:19,541 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.050063774000000005
[2016-04-15T01:22Z] INFO  18:22:19,542 PairHMM - Total compute time in PairHMM computeLikelihoods() : 5.141234753
[2016-04-15T01:22Z] INFO  18:22:19,542 HaplotypeCaller - Ran local assembly on 1467 active regions
[2016-04-15T01:22Z] INFO  18:22:19,609 ProgressMeter -            done      4.6020795E7    70.0 s            1.0 s      100.0%    70.0 s       0.0 s
[2016-04-15T01:22Z] INFO  18:22:19,609 ProgressMeter - Total runtime 70.78 secs, 1.18 min, 0.02 hours
[2016-04-15T01:22Z] INFO  18:22:19,610 MicroScheduler - 37966 reads were filtered out during the traversal out of approximately 371434 total reads (10.22%)
[2016-04-15T01:22Z] INFO  18:22:19,610 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:22Z] INFO  18:22:19,610 MicroScheduler -   -> 30828 reads (8.30% of total) failing DuplicateReadFilter
[2016-04-15T01:22Z] INFO  18:22:19,611 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:22Z] INFO  18:22:19,611 MicroScheduler -   -> 7138 reads (1.92% of total) failing HCMappingQualityFilter
[2016-04-15T01:22Z] INFO  18:22:19,611 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:22Z] INFO  18:22:19,612 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:22Z] INFO  18:22:19,612 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:22Z] INFO  18:22:19,612 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T01:22Z] INFO  18:22:20,896 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:22Z] INFO  18:22:20,899 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:22Z] INFO  18:22:20,899 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:22Z] INFO  18:22:20,899 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:22Z] INFO  18:22:20,903 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/10/R14-18102_kapa-NGv3-PE100-NGv3-sort-10_127328721_135534747-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/10/R14-18102_kapa-NGv3-PE100-NGv3-10_127328721_135534747-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/10/tx/tmpzzaYyc/R14-18102_kapa-NGv3-PE100-NGv3-10_127328721_135534747.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:22Z] INFO  18:22:20,928 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:22Z] INFO  18:22:20,929 HelpFormatter - Date/Time: 2016/04/14 18:22:20
[2016-04-15T01:22Z] INFO  18:22:20,929 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:22Z] INFO  18:22:20,929 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:22Z] WARN  18:22:20,959 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T01:22Z] WARN  18:22:20,979 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/10/tx/tmpzzaYyc/R14-18102_kapa-NGv3-PE100-NGv3-10_127328721_135534747.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T01:22Z] INFO  18:22:21,055 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:22Z] INFO  18:22:21,215 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:22Z] INFO  18:22:21,437 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T01:22Z] GATK: HaplotypeCaller
[2016-04-15T01:22Z] INFO  18:22:21,448 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:22Z] INFO  18:22:21,510 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-15T01:22Z] INFO  18:22:21,557 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T01:22Z] INFO  18:22:21,935 IntervalUtils - Processing 102137 bp from intervals
[2016-04-15T01:22Z] WARN  18:22:21,940 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:22Z] INFO  18:22:22,019 ProgressMeter -     10:25160992      2.0883211E7    30.0 s            1.0 s       59.4%    50.0 s      20.0 s
[2016-04-15T01:22Z] INFO  18:22:22,057 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:22Z] INFO  18:22:22,161 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:22Z] INFO  18:22:22,164 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:22Z] INFO  18:22:22,165 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T01:22Z] INFO  18:22:22,166 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T01:22Z] INFO  18:22:22,167 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T01:22Z] INFO  18:22:22,167 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T01:22Z] INFO  18:22:22,336 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T01:22Z] INFO  18:22:24,452 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:22Z] INFO  18:22:24,456 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:22Z] INFO  18:22:24,456 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:22Z] INFO  18:22:24,457 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:22Z] INFO  18:22:24,461 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/11/R14-18102_kapa-NGv3-PE100-NGv3-sort-11_0_15994658-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/11/R14-18102_kapa-NGv3-PE100-NGv3-11_0_15994658-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/11/tx/tmpHBV_Ym/R14-18102_kapa-NGv3-PE100-NGv3-11_0_15994658.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:22Z] INFO  18:22:24,470 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:22Z] INFO  18:22:24,471 HelpFormatter - Date/Time: 2016/04/14 18:22:24
[2016-04-15T01:22Z] INFO  18:22:24,472 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:22Z] INFO  18:22:24,472 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:22Z] WARN  18:22:24,518 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T01:22Z] WARN  18:22:24,521 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/11/tx/tmpHBV_Ym/R14-18102_kapa-NGv3-PE100-NGv3-11_0_15994658.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T01:22Z] INFO  18:22:24,772 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:22Z] INFO  18:22:24,940 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T01:22Z] INFO  18:22:24,949 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:22Z] INFO  18:22:24,955 ProgressMeter -     10:45480298        1.38579E7    30.0 s            2.0 s       82.6%    36.0 s       6.0 s
[2016-04-15T01:22Z] INFO  18:22:25,010 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-15T01:22Z] INFO  18:22:25,045 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T01:22Z] INFO  18:22:25,596 IntervalUtils - Processing 438345 bp from intervals
[2016-04-15T01:22Z] WARN  18:22:25,604 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:22Z] INFO  18:22:25,726 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:22Z] INFO  18:22:25,884 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:22Z] INFO  18:22:25,885 ProgressMeter -     7:107800865     2.55177037E8   120.0 s            0.0 s       97.5%     2.1 m       3.0 s
[2016-04-15T01:22Z] INFO  18:22:25,886 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:22Z] INFO  18:22:25,887 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T01:22Z] INFO  18:22:25,887 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T01:22Z] INFO  18:22:25,888 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T01:22Z] INFO  18:22:25,888 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T01:22Z] INFO  18:22:25,931 ProgressMeter -     10:50690733        8346628.0    30.0 s            3.0 s       41.2%    72.0 s      42.0 s
[2016-04-15T01:22Z] INFO  18:22:26,159 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T01:22Z] INFO  18:22:26,445 ProgressMeter -     10:71255350      2.2712765E7    30.0 s            1.0 s       43.0%    69.0 s      39.0 s
[2016-04-15T01:22Z] INFO  18:22:27,615 ProgressMeter -     10:88946842      1.6800878E7    30.0 s            1.0 s       57.6%    52.0 s      22.0 s
[2016-04-15T01:22Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T01:22Z] INFO  18:22:27,797 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T01:22Z] INFO  18:22:27,798 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T01:22Z] INFO  18:22:28,039 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.006427661
[2016-04-15T01:22Z] INFO  18:22:28,041 PairHMM - Total compute time in PairHMM computeLikelihoods() : 0.33246535800000004
[2016-04-15T01:22Z] INFO  18:22:28,041 HaplotypeCaller - Ran local assembly on 723 active regions
[2016-04-15T01:22Z] WARN  18:22:28,076 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T01:22Z] WARN  18:22:28,077 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T01:22Z] INFO  18:22:28,087 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.066606594
[2016-04-15T01:22Z] INFO  18:22:28,087 PairHMM - Total compute time in PairHMM computeLikelihoods() : 13.406482856
[2016-04-15T01:22Z] INFO  18:22:28,088 HaplotypeCaller - Ran local assembly on 2488 active regions
[2016-04-15T01:22Z] INFO  18:22:28,092 ProgressMeter -            done      2.2800337E7    33.0 s            1.0 s      100.0%    33.0 s       0.0 s
[2016-04-15T01:22Z] INFO  18:22:28,092 ProgressMeter - Total runtime 33.16 secs, 0.55 min, 0.01 hours
[2016-04-15T01:22Z] INFO  18:22:28,093 MicroScheduler - 30235 reads were filtered out during the traversal out of approximately 153550 total reads (19.69%)
[2016-04-15T01:22Z] INFO  18:22:28,093 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:22Z] INFO  18:22:28,093 MicroScheduler -   -> 10779 reads (7.02% of total) failing DuplicateReadFilter
[2016-04-15T01:22Z] INFO  18:22:28,094 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:22Z] INFO  18:22:28,094 MicroScheduler -   -> 19456 reads (12.67% of total) failing HCMappingQualityFilter
[2016-04-15T01:22Z] INFO  18:22:28,094 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:22Z] INFO  18:22:28,094 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:22Z] INFO  18:22:28,095 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:22Z] INFO  18:22:28,095 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T01:22Z] INFO  18:22:28,131 ProgressMeter -            done      2.7011063E8     2.0 m            0.0 s      100.0%     2.0 m       0.0 s
[2016-04-15T01:22Z] INFO  18:22:28,132 ProgressMeter - Total runtime 122.31 secs, 2.04 min, 0.03 hours
[2016-04-15T01:22Z] INFO  18:22:28,132 MicroScheduler - 178445 reads were filtered out during the traversal out of approximately 692639 total reads (25.76%)
[2016-04-15T01:22Z] INFO  18:22:28,132 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:22Z] INFO  18:22:28,133 MicroScheduler -   -> 47826 reads (6.90% of total) failing DuplicateReadFilter
[2016-04-15T01:22Z] INFO  18:22:28,133 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:22Z] INFO  18:22:28,133 MicroScheduler -   -> 130619 reads (18.86% of total) failing HCMappingQualityFilter
[2016-04-15T01:22Z] INFO  18:22:28,133 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:22Z] INFO  18:22:28,134 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:22Z] INFO  18:22:28,134 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:22Z] INFO  18:22:28,134 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T01:22Z] INFO  18:22:28,235 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.019849991
[2016-04-15T01:22Z] INFO  18:22:28,236 PairHMM - Total compute time in PairHMM computeLikelihoods() : 0.672405232
[2016-04-15T01:22Z] INFO  18:22:28,236 HaplotypeCaller - Ran local assembly on 1183 active regions
[2016-04-15T01:22Z] INFO  18:22:28,288 ProgressMeter -            done      6.7952989E7    50.0 s            0.0 s      100.0%    50.0 s       0.0 s
[2016-04-15T01:22Z] INFO  18:22:28,289 ProgressMeter - Total runtime 50.24 secs, 0.84 min, 0.01 hours
[2016-04-15T01:22Z] INFO  18:22:28,289 MicroScheduler - 47812 reads were filtered out during the traversal out of approximately 288322 total reads (16.58%)
[2016-04-15T01:22Z] INFO  18:22:28,289 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:22Z] INFO  18:22:28,289 MicroScheduler -   -> 21536 reads (7.47% of total) failing DuplicateReadFilter
[2016-04-15T01:22Z] INFO  18:22:28,290 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:22Z] INFO  18:22:28,290 MicroScheduler -   -> 26276 reads (9.11% of total) failing HCMappingQualityFilter
[2016-04-15T01:22Z] INFO  18:22:28,290 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:22Z] INFO  18:22:28,290 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:22Z] INFO  18:22:28,291 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:22Z] INFO  18:22:28,291 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T01:22Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T01:22Z] INFO  18:22:28,408 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T01:22Z] INFO  18:22:28,409 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T01:22Z] WARN  18:22:28,733 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T01:22Z] WARN  18:22:28,734 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T01:22Z] INFO  18:22:29,479 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:22Z] INFO  18:22:29,554 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:22Z] GATK: HaplotypeCaller
[2016-04-15T01:22Z] INFO  18:22:29,728 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:22Z] GATK: HaplotypeCaller
[2016-04-15T01:22Z] GATK: HaplotypeCaller
[2016-04-15T01:22Z] INFO  18:22:31,585 ProgressMeter -      9:43627791      7.9087043E7    60.0 s            0.0 s       96.4%    62.0 s       2.0 s
[2016-04-15T01:22Z] INFO  18:22:32,704 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.020235644
[2016-04-15T01:22Z] INFO  18:22:32,715 PairHMM - Total compute time in PairHMM computeLikelihoods() : 0.896493234
[2016-04-15T01:22Z] INFO  18:22:32,716 HaplotypeCaller - Ran local assembly on 1354 active regions
[2016-04-15T01:22Z] INFO  18:22:32,729 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:22Z] INFO  18:22:32,733 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:22Z] INFO  18:22:32,733 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:22Z] INFO  18:22:32,734 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:22Z] INFO  18:22:32,738 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/11/R14-18102_kapa-NGv3-PE100-NGv3-sort-11_16007749_31531554-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/11/R14-18102_kapa-NGv3-PE100-NGv3-11_16007749_31531554-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/11/tx/tmpqxbWA7/R14-18102_kapa-NGv3-PE100-NGv3-11_16007749_31531554.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:22Z] INFO  18:22:32,748 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:22Z] INFO  18:22:32,753 HelpFormatter - Date/Time: 2016/04/14 18:22:32
[2016-04-15T01:22Z] INFO  18:22:32,753 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:22Z] INFO  18:22:32,754 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:22Z] INFO  18:22:32,768 ProgressMeter -            done      8.2992301E7    54.0 s            0.0 s      100.0%    54.0 s       0.0 s
[2016-04-15T01:22Z] INFO  18:22:32,769 ProgressMeter - Total runtime 54.34 secs, 0.91 min, 0.02 hours
[2016-04-15T01:22Z] INFO  18:22:32,769 MicroScheduler - 26330 reads were filtered out during the traversal out of approximately 280100 total reads (9.40%)
[2016-04-15T01:22Z] INFO  18:22:32,769 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:22Z] INFO  18:22:32,770 MicroScheduler -   -> 22316 reads (7.97% of total) failing DuplicateReadFilter
[2016-04-15T01:22Z] INFO  18:22:32,770 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:22Z] INFO  18:22:32,770 MicroScheduler -   -> 4014 reads (1.43% of total) failing HCMappingQualityFilter
[2016-04-15T01:22Z] INFO  18:22:32,770 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:22Z] INFO  18:22:32,771 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:22Z] INFO  18:22:32,771 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:22Z] INFO  18:22:32,771 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T01:22Z] WARN  18:22:32,778 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T01:22Z] WARN  18:22:32,780 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/11/tx/tmpqxbWA7/R14-18102_kapa-NGv3-PE100-NGv3-11_16007749_31531554.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T01:22Z] INFO  18:22:32,982 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:22Z] INFO  18:22:33,173 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:22Z] INFO  18:22:33,175 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T01:22Z] INFO  18:22:33,177 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:22Z] INFO  18:22:33,177 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:22Z] INFO  18:22:33,178 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:22Z] INFO  18:22:33,182 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/11/R14-18102_kapa-NGv3-PE100-NGv3-sort-11_31541602_47074069-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/11/R14-18102_kapa-NGv3-PE100-NGv3-11_31541602_47074069-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/11/tx/tmp4f_7gG/R14-18102_kapa-NGv3-PE100-NGv3-11_31541602_47074069.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:22Z] INFO  18:22:33,185 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:22Z] INFO  18:22:33,190 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:22Z] INFO  18:22:33,193 HelpFormatter - Date/Time: 2016/04/14 18:22:33
[2016-04-15T01:22Z] INFO  18:22:33,194 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:22Z] INFO  18:22:33,194 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:22Z] WARN  18:22:33,216 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T01:22Z] WARN  18:22:33,219 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/11/tx/tmp4f_7gG/R14-18102_kapa-NGv3-PE100-NGv3-11_31541602_47074069.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T01:22Z] INFO  18:22:33,270 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-15T01:22Z] INFO  18:22:33,312 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T01:22Z] INFO  18:22:33,386 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:22Z] INFO  18:22:33,389 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:22Z] INFO  18:22:33,389 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:22Z] INFO  18:22:33,389 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:22Z] INFO  18:22:33,393 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/11/R14-18102_kapa-NGv3-PE100-NGv3-sort-11_47158866_62678572-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/11/R14-18102_kapa-NGv3-PE100-NGv3-11_47158866_62678572-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/11/tx/tmp0ZB5PA/R14-18102_kapa-NGv3-PE100-NGv3-11_47158866_62678572.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:22Z] INFO  18:22:33,405 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:22Z] INFO  18:22:33,406 HelpFormatter - Date/Time: 2016/04/14 18:22:33
[2016-04-15T01:22Z] INFO  18:22:33,406 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:22Z] INFO  18:22:33,406 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:22Z] INFO  18:22:33,428 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:22Z] WARN  18:22:33,441 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T01:22Z] WARN  18:22:33,444 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/11/tx/tmp0ZB5PA/R14-18102_kapa-NGv3-PE100-NGv3-11_47158866_62678572.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T01:22Z] INFO  18:22:33,590 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T01:22Z] INFO  18:22:33,599 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:22Z] INFO  18:22:33,617 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:22Z] INFO  18:22:33,679 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-15T01:22Z] INFO  18:22:33,698 IntervalUtils - Processing 144906 bp from intervals
[2016-04-15T01:22Z] INFO  18:22:33,703 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T01:22Z] WARN  18:22:33,714 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:22Z] INFO  18:22:33,830 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:22Z] INFO  18:22:33,840 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T01:22Z] INFO  18:22:33,855 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.028488028000000002
[2016-04-15T01:22Z] INFO  18:22:33,856 PairHMM - Total compute time in PairHMM computeLikelihoods() : 0.758386179
[2016-04-15T01:22Z] INFO  18:22:33,857 HaplotypeCaller - Ran local assembly on 1163 active regions
[2016-04-15T01:22Z] INFO  18:22:33,860 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:22Z] INFO  18:22:33,906 ProgressMeter -            done      5.6897824E7    49.0 s            0.0 s      100.0%    49.0 s       0.0 s
[2016-04-15T01:22Z] INFO  18:22:33,906 ProgressMeter - Total runtime 49.39 secs, 0.82 min, 0.01 hours
[2016-04-15T01:22Z] INFO  18:22:33,906 MicroScheduler - 20628 reads were filtered out during the traversal out of approximately 216340 total reads (9.53%)
[2016-04-15T01:22Z] INFO  18:22:33,907 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:22Z] INFO  18:22:33,908 MicroScheduler -   -> 17043 reads (7.88% of total) failing DuplicateReadFilter
[2016-04-15T01:22Z] INFO  18:22:33,908 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:22Z] INFO  18:22:33,908 MicroScheduler -   -> 3585 reads (1.66% of total) failing HCMappingQualityFilter
[2016-04-15T01:22Z] INFO  18:22:33,908 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:22Z] INFO  18:22:33,909 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:22Z] INFO  18:22:33,909 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:22Z] INFO  18:22:33,909 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T01:22Z] INFO  18:22:33,938 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-15T01:22Z] INFO  18:22:33,972 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:22Z] INFO  18:22:33,966 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T01:22Z] INFO  18:22:33,974 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:22Z] INFO  18:22:33,974 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T01:22Z] INFO  18:22:33,975 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T01:22Z] INFO  18:22:33,976 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T01:22Z] INFO  18:22:33,976 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T01:22Z] INFO  18:22:34,145 IntervalUtils - Processing 150047 bp from intervals
[2016-04-15T01:22Z] WARN  18:22:34,151 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:22Z] INFO  18:22:34,161 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:22Z] INFO  18:22:34,173 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T01:22Z] INFO  18:22:34,244 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:22Z] INFO  18:22:34,328 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:22Z] INFO  18:22:34,329 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:22Z] INFO  18:22:34,329 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T01:22Z] INFO  18:22:34,330 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T01:22Z] INFO  18:22:34,331 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T01:22Z] INFO  18:22:34,331 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T01:22Z] INFO  18:22:34,463 IntervalUtils - Processing 330540 bp from intervals
[2016-04-15T01:22Z] WARN  18:22:34,468 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:22Z] INFO  18:22:34,553 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T01:22Z] INFO  18:22:34,557 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.014987152
[2016-04-15T01:22Z] INFO  18:22:34,558 PairHMM - Total compute time in PairHMM computeLikelihoods() : 3.633937335
[2016-04-15T01:22Z] INFO  18:22:34,559 HaplotypeCaller - Ran local assembly on 1517 active regions
[2016-04-15T01:22Z] GATK: HaplotypeCaller
[2016-04-15T01:22Z] INFO  18:22:34,605 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:22Z] INFO  18:22:34,616 ProgressMeter -            done      8.5421311E7    63.0 s            0.0 s      100.0%    63.0 s       0.0 s
[2016-04-15T01:22Z] INFO  18:22:34,616 ProgressMeter - Total runtime 63.06 secs, 1.05 min, 0.02 hours
[2016-04-15T01:22Z] INFO  18:22:34,617 MicroScheduler - 132797 reads were filtered out during the traversal out of approximately 431240 total reads (30.79%)
[2016-04-15T01:22Z] INFO  18:22:34,617 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:22Z] INFO  18:22:34,617 MicroScheduler -   -> 26675 reads (6.19% of total) failing DuplicateReadFilter
[2016-04-15T01:22Z] INFO  18:22:34,617 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:22Z] INFO  18:22:34,618 MicroScheduler -   -> 106122 reads (24.61% of total) failing HCMappingQualityFilter
[2016-04-15T01:22Z] INFO  18:22:34,618 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:22Z] INFO  18:22:34,618 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:22Z] INFO  18:22:34,618 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:22Z] INFO  18:22:34,619 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T01:22Z] INFO  18:22:34,759 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:22Z] INFO  18:22:34,760 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:22Z] INFO  18:22:34,761 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T01:22Z] INFO  18:22:34,762 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T01:22Z] INFO  18:22:34,773 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T01:22Z] INFO  18:22:34,774 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T01:22Z] INFO  18:22:34,955 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T01:22Z] INFO  18:22:35,251 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:22Z] GATK: HaplotypeCaller
[2016-04-15T01:22Z] INFO  18:22:35,996 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:22Z] GATK: HaplotypeCaller
[2016-04-15T01:22Z] INFO  18:22:36,889 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.010662309
[2016-04-15T01:22Z] INFO  18:22:36,890 PairHMM - Total compute time in PairHMM computeLikelihoods() : 0.770238033
[2016-04-15T01:22Z] INFO  18:22:36,891 HaplotypeCaller - Ran local assembly on 1182 active regions
[2016-04-15T01:22Z] INFO  18:22:36,929 ProgressMeter -            done      6.1102753E7    44.0 s            0.0 s      100.0%    44.0 s       0.0 s
[2016-04-15T01:22Z] INFO  18:22:36,930 ProgressMeter - Total runtime 44.95 secs, 0.75 min, 0.01 hours
[2016-04-15T01:22Z] INFO  18:22:36,931 MicroScheduler - 16822 reads were filtered out during the traversal out of approximately 190445 total reads (8.83%)
[2016-04-15T01:22Z] INFO  18:22:36,932 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:22Z] INFO  18:22:36,932 MicroScheduler -   -> 15245 reads (8.00% of total) failing DuplicateReadFilter
[2016-04-15T01:22Z] INFO  18:22:36,933 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:22Z] INFO  18:22:36,933 MicroScheduler -   -> 1577 reads (0.83% of total) failing HCMappingQualityFilter
[2016-04-15T01:22Z] INFO  18:22:36,934 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:22Z] INFO  18:22:36,940 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:22Z] INFO  18:22:36,948 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:22Z] INFO  18:22:36,949 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T01:22Z] INFO  18:22:37,248 ProgressMeter -     10:99093872      3.0866766E7    30.0 s            0.0 s       33.3%    90.0 s      60.0 s
[2016-04-15T01:22Z] INFO  18:22:37,556 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:22Z] INFO  18:22:37,559 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:22Z] INFO  18:22:37,560 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:22Z] INFO  18:22:37,560 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:22Z] INFO  18:22:37,565 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/11/R14-18102_kapa-NGv3-PE100-NGv3-sort-11_62744265_78270665-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/11/R14-18102_kapa-NGv3-PE100-NGv3-11_62744265_78270665-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/11/tx/tmpkHnLq8/R14-18102_kapa-NGv3-PE100-NGv3-11_62744265_78270665.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:22Z] INFO  18:22:37,574 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:22Z] INFO  18:22:37,574 HelpFormatter - Date/Time: 2016/04/14 18:22:37
[2016-04-15T01:22Z] INFO  18:22:37,575 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:22Z] INFO  18:22:37,575 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:22Z] WARN  18:22:37,607 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T01:22Z] WARN  18:22:37,610 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/11/tx/tmpkHnLq8/R14-18102_kapa-NGv3-PE100-NGv3-11_62744265_78270665.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T01:22Z] INFO  18:22:37,776 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:22Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T01:22Z] INFO  18:22:38,036 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T01:22Z] INFO  18:22:38,037 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T01:22Z] INFO  18:22:38,057 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T01:22Z] INFO  18:22:38,067 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:22Z] INFO  18:22:38,188 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.12
[2016-04-15T01:22Z] INFO  18:22:38,210 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T01:22Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T01:22Z] INFO  18:22:38,320 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T01:22Z] INFO  18:22:38,321 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T01:22Z] WARN  18:22:38,339 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T01:22Z] WARN  18:22:38,340 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T01:22Z] INFO  18:22:38,362 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:22Z] INFO  18:22:38,365 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:22Z] INFO  18:22:38,365 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:22Z] INFO  18:22:38,366 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:22Z] INFO  18:22:38,370 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/11/R14-18102_kapa-NGv3-PE100-NGv3-sort-11_78277177_93796886-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/11/R14-18102_kapa-NGv3-PE100-NGv3-11_78277177_93796886-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/11/tx/tmpL09xi8/R14-18102_kapa-NGv3-PE100-NGv3-11_78277177_93796886.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:22Z] INFO  18:22:38,401 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:22Z] INFO  18:22:38,402 HelpFormatter - Date/Time: 2016/04/14 18:22:38
[2016-04-15T01:22Z] INFO  18:22:38,402 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:22Z] INFO  18:22:38,403 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:22Z] WARN  18:22:38,442 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T01:22Z] WARN  18:22:38,445 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/11/tx/tmpL09xi8/R14-18102_kapa-NGv3-PE100-NGv3-11_78277177_93796886.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T01:22Z] INFO  18:22:38,587 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:22Z] INFO  18:22:38,614 IntervalUtils - Processing 515206 bp from intervals
[2016-04-15T01:22Z] WARN  18:22:38,620 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:22Z] INFO  18:22:38,627 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:22Z] INFO  18:22:38,680 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.012695310000000001
[2016-04-15T01:22Z] INFO  18:22:38,681 PairHMM - Total compute time in PairHMM computeLikelihoods() : 0.7059696910000001
[2016-04-15T01:22Z] INFO  18:22:38,682 HaplotypeCaller - Ran local assembly on 1652 active regions
[2016-04-15T01:22Z] WARN  18:22:38,689 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T01:22Z] WARN  18:22:38,695 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T01:22Z] INFO  18:22:38,732 ProgressMeter -            done     1.27765104E8    56.0 s            0.0 s      100.0%    56.0 s       0.0 s
[2016-04-15T01:22Z] INFO  18:22:38,733 ProgressMeter - Total runtime 56.73 secs, 0.95 min, 0.02 hours
[2016-04-15T01:22Z] INFO  18:22:38,734 MicroScheduler - 28969 reads were filtered out during the traversal out of approximately 342367 total reads (8.46%)
[2016-04-15T01:22Z] INFO  18:22:38,734 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:22Z] INFO  18:22:38,735 MicroScheduler -   -> 27233 reads (7.95% of total) failing DuplicateReadFilter
[2016-04-15T01:22Z] INFO  18:22:38,736 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:22Z] INFO  18:22:38,736 MicroScheduler -   -> 1736 reads (0.51% of total) failing HCMappingQualityFilter
[2016-04-15T01:22Z] INFO  18:22:38,737 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:22Z] INFO  18:22:38,737 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:22Z] INFO  18:22:38,738 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:22Z] INFO  18:22:38,739 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T01:22Z] INFO  18:22:38,768 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:22Z] GATK: HaplotypeCaller
[2016-04-15T01:22Z] INFO  18:22:38,861 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T01:22Z] INFO  18:22:38,878 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:22Z] INFO  18:22:38,961 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:22Z] INFO  18:22:38,962 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:22Z] INFO  18:22:38,962 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T01:22Z] INFO  18:22:38,962 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T01:22Z] INFO  18:22:38,972 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.09
[2016-04-15T01:22Z] INFO  18:22:38,977 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T01:22Z] INFO  18:22:38,977 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T01:22Z] INFO  18:22:39,013 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T01:22Z] INFO  18:22:39,108 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.019418025000000002
[2016-04-15T01:22Z] INFO  18:22:39,109 PairHMM - Total compute time in PairHMM computeLikelihoods() : 0.30512946700000004
[2016-04-15T01:22Z] INFO  18:22:39,109 HaplotypeCaller - Ran local assembly on 1078 active regions
[2016-04-15T01:22Z] INFO  18:22:39,135 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T01:22Z] INFO  18:22:39,171 ProgressMeter -            done      5.4493851E7    41.0 s            0.0 s      100.0%    41.0 s       0.0 s
[2016-04-15T01:22Z] INFO  18:22:39,172 ProgressMeter - Total runtime 41.58 secs, 0.69 min, 0.01 hours
[2016-04-15T01:22Z] INFO  18:22:39,172 MicroScheduler - 29917 reads were filtered out during the traversal out of approximately 219555 total reads (13.63%)
[2016-04-15T01:22Z] INFO  18:22:39,172 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:22Z] INFO  18:22:39,173 MicroScheduler -   -> 16576 reads (7.55% of total) failing DuplicateReadFilter
[2016-04-15T01:22Z] INFO  18:22:39,173 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:22Z] INFO  18:22:39,173 MicroScheduler -   -> 13341 reads (6.08% of total) failing HCMappingQualityFilter
[2016-04-15T01:22Z] INFO  18:22:39,173 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:22Z] INFO  18:22:39,174 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:22Z] INFO  18:22:39,174 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:22Z] INFO  18:22:39,174 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T01:22Z] INFO  18:22:39,405 IntervalUtils - Processing 119993 bp from intervals
[2016-04-15T01:22Z] WARN  18:22:39,410 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:22Z] INFO  18:22:39,502 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:22Z] INFO  18:22:39,579 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:22Z] INFO  18:22:39,580 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:22Z] INFO  18:22:39,581 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T01:22Z] INFO  18:22:39,581 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:22Z] INFO  18:22:39,585 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:22Z] INFO  18:22:39,585 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:22Z] INFO  18:22:39,586 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:22Z] INFO  18:22:39,590 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/11/R14-18102_kapa-NGv3-PE100-NGv3-sort-11_93797496_109964158-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/11/R14-18102_kapa-NGv3-PE100-NGv3-11_93797496_109964158-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/11/tx/tmpRSPCOg/R14-18102_kapa-NGv3-PE100-NGv3-11_93797496_109964158.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:22Z] INFO  18:22:39,593 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T01:22Z] INFO  18:22:39,600 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T01:22Z] INFO  18:22:39,601 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T01:22Z] INFO  18:22:39,600 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:22Z] INFO  18:22:39,601 HelpFormatter - Date/Time: 2016/04/14 18:22:39
[2016-04-15T01:22Z] INFO  18:22:39,601 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:22Z] INFO  18:22:39,602 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:22Z] WARN  18:22:39,631 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T01:22Z] WARN  18:22:39,646 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/11/tx/tmpRSPCOg/R14-18102_kapa-NGv3-PE100-NGv3-11_93797496_109964158.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T01:22Z] INFO  18:22:39,843 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:22Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T01:22Z] INFO  18:22:39,876 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T01:22Z] INFO  18:22:39,877 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T01:22Z] INFO  18:22:39,877 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T01:22Z] INFO  18:22:40,005 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T01:22Z] INFO  18:22:40,015 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:22Z] INFO  18:22:40,110 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.09
[2016-04-15T01:22Z] INFO  18:22:40,147 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T01:22Z] WARN  18:22:40,179 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T01:22Z] WARN  18:22:40,180 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T01:22Z] INFO  18:22:40,190 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:22Z] GATK: HaplotypeCaller
[2016-04-15T01:22Z] INFO  18:22:40,572 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:22Z] INFO  18:22:40,587 IntervalUtils - Processing 148585 bp from intervals
[2016-04-15T01:22Z] WARN  18:22:40,592 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:22Z] INFO  18:22:40,687 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:22Z] INFO  18:22:40,809 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:22Z] INFO  18:22:40,821 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:22Z] INFO  18:22:40,822 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T01:22Z] INFO  18:22:40,823 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T01:22Z] INFO  18:22:40,842 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T01:22Z] INFO  18:22:40,842 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T01:22Z] GATK: HaplotypeCaller
[2016-04-15T01:22Z] INFO  18:22:41,104 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T01:22Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T01:22Z] INFO  18:22:41,762 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T01:22Z] INFO  18:22:41,762 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T01:22Z] INFO  18:22:41,947 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:22Z] INFO  18:22:41,951 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:22Z] INFO  18:22:41,958 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:22Z] INFO  18:22:41,958 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:22Z] INFO  18:22:41,963 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/11/R14-18102_kapa-NGv3-PE100-NGv3-sort-11_110001730_125514538-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/11/R14-18102_kapa-NGv3-PE100-NGv3-11_110001730_125514538-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/11/tx/tmpJCPK_V/R14-18102_kapa-NGv3-PE100-NGv3-11_110001730_125514538.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:22Z] INFO  18:22:41,982 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:22Z] INFO  18:22:41,983 HelpFormatter - Date/Time: 2016/04/14 18:22:41
[2016-04-15T01:22Z] INFO  18:22:41,983 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:22Z] INFO  18:22:41,984 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:22Z] WARN  18:22:42,030 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T01:22Z] WARN  18:22:42,033 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/11/tx/tmpJCPK_V/R14-18102_kapa-NGv3-PE100-NGv3-11_110001730_125514538.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T01:22Z] WARN  18:22:42,131 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T01:22Z] WARN  18:22:42,131 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T01:22Z] INFO  18:22:42,300 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:22Z] INFO  18:22:42,552 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T01:22Z] INFO  18:22:42,561 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:22Z] INFO  18:22:42,648 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.09
[2016-04-15T01:22Z] INFO  18:22:42,682 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T01:22Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T01:22Z] INFO  18:22:43,017 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T01:22Z] INFO  18:22:43,028 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T01:22Z] INFO  18:22:43,282 IntervalUtils - Processing 318135 bp from intervals
[2016-04-15T01:22Z] WARN  18:22:43,287 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:22Z] INFO  18:22:43,453 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:22Z] WARN  18:22:43,458 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T01:22Z] WARN  18:22:43,459 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T01:22Z] INFO  18:22:43,625 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:22Z] INFO  18:22:43,625 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:22Z] INFO  18:22:43,626 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T01:22Z] INFO  18:22:43,636 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T01:22Z] INFO  18:22:43,684 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T01:22Z] INFO  18:22:43,685 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T01:22Z] INFO  18:22:43,768 ProgressMeter -    10:119302844      3.0341502E7    30.0 s            0.0 s       50.3%    59.0 s      29.0 s
[2016-04-15T01:22Z] INFO  18:22:43,798 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:22Z] INFO  18:22:43,801 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:22Z] INFO  18:22:43,802 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:22Z] INFO  18:22:43,802 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:22Z] INFO  18:22:43,807 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/11/R14-18102_kapa-NGv3-PE100-NGv3-sort-11_125523640_135006516-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/11/R14-18102_kapa-NGv3-PE100-NGv3-11_125523640_135006516-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/11/tx/tmpz1Bohm/R14-18102_kapa-NGv3-PE100-NGv3-11_125523640_135006516.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:22Z] INFO  18:22:43,816 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:22Z] INFO  18:22:43,827 HelpFormatter - Date/Time: 2016/04/14 18:22:43
[2016-04-15T01:22Z] INFO  18:22:43,828 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:22Z] INFO  18:22:43,829 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:22Z] WARN  18:22:43,864 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T01:22Z] WARN  18:22:43,876 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/11/tx/tmpz1Bohm/R14-18102_kapa-NGv3-PE100-NGv3-11_125523640_135006516.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T01:22Z] INFO  18:22:43,931 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T01:22Z] INFO  18:22:44,107 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:22Z] INFO  18:22:44,132 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:22Z] INFO  18:22:44,135 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:22Z] INFO  18:22:44,136 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:22Z] INFO  18:22:44,136 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:22Z] INFO  18:22:44,141 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/12/R14-18102_kapa-NGv3-PE100-NGv3-sort-12_0_15637181-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/12/R14-18102_kapa-NGv3-PE100-NGv3-12_0_15637181-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/12/tx/tmpt38TJS/R14-18102_kapa-NGv3-PE100-NGv3-12_0_15637181.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:22Z] INFO  18:22:44,159 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:22Z] INFO  18:22:44,160 HelpFormatter - Date/Time: 2016/04/14 18:22:44
[2016-04-15T01:22Z] INFO  18:22:44,161 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:22Z] INFO  18:22:44,161 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:22Z] INFO  18:22:44,198 ProgressMeter -     9:135205535      1.0710826E8    60.0 s            0.0 s       44.1%     2.3 m      75.0 s
[2016-04-15T01:22Z] WARN  18:22:44,207 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T01:22Z] WARN  18:22:44,214 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/12/tx/tmpt38TJS/R14-18102_kapa-NGv3-PE100-NGv3-12_0_15637181.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T01:22Z] INFO  18:22:44,300 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T01:22Z] INFO  18:22:44,310 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:22Z] INFO  18:22:44,392 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-15T01:22Z] INFO  18:22:44,409 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T01:22Z] INFO  18:22:44,475 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:22Z] INFO  18:22:44,721 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T01:22Z] INFO  18:22:44,730 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:22Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T01:22Z] INFO  18:22:44,766 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T01:22Z] INFO  18:22:44,767 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T01:22Z] INFO  18:22:44,818 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.09
[2016-04-15T01:22Z] INFO  18:22:44,852 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T01:22Z] INFO  18:22:44,929 IntervalUtils - Processing 106404 bp from intervals
[2016-04-15T01:22Z] WARN  18:22:44,942 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:22Z] INFO  18:22:45,057 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:22Z] WARN  18:22:45,071 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T01:22Z] WARN  18:22:45,082 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T01:22Z] INFO  18:22:45,138 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:22Z] INFO  18:22:45,140 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:22Z] INFO  18:22:45,140 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T01:22Z] INFO  18:22:45,141 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T01:22Z] INFO  18:22:45,142 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T01:22Z] INFO  18:22:45,142 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T01:22Z] INFO  18:22:45,462 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T01:22Z] INFO  18:22:45,577 IntervalUtils - Processing 329920 bp from intervals
[2016-04-15T01:22Z] WARN  18:22:45,582 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:22Z] INFO  18:22:45,758 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:22Z] INFO  18:22:45,911 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:22Z] INFO  18:22:45,913 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:22Z] INFO  18:22:45,913 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T01:22Z] INFO  18:22:45,914 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T01:22Z] INFO  18:22:45,915 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T01:22Z] INFO  18:22:45,915 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T01:22Z] INFO  18:22:46,117 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T01:22Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T01:22Z] INFO  18:22:47,369 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T01:22Z] INFO  18:22:47,381 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T01:22Z] WARN  18:22:47,744 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T01:22Z] WARN  18:22:47,745 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T01:22Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T01:22Z] INFO  18:22:48,671 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T01:22Z] INFO  18:22:48,683 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T01:22Z] WARN  18:22:49,185 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T01:22Z] WARN  18:22:49,186 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T01:22Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T01:22Z] INFO  18:22:49,644 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T01:22Z] INFO  18:22:49,645 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T01:22Z] WARN  18:22:50,019 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T01:22Z] WARN  18:22:50,020 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T01:22Z] INFO  18:22:50,610 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.030556257000000003
[2016-04-15T01:22Z] INFO  18:22:50,610 PairHMM - Total compute time in PairHMM computeLikelihoods() : 3.4783484230000004
[2016-04-15T01:22Z] INFO  18:22:50,611 HaplotypeCaller - Ran local assembly on 1062 active regions
[2016-04-15T01:22Z] INFO  18:22:50,678 ProgressMeter -            done      4.8765504E7    54.0 s            1.0 s      100.0%    54.0 s       0.0 s
[2016-04-15T01:22Z] INFO  18:22:50,678 ProgressMeter - Total runtime 54.78 secs, 0.91 min, 0.02 hours
[2016-04-15T01:22Z] INFO  18:22:50,679 MicroScheduler - 85542 reads were filtered out during the traversal out of approximately 273417 total reads (31.29%)
[2016-04-15T01:22Z] INFO  18:22:50,679 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:22Z] INFO  18:22:50,679 MicroScheduler -   -> 17353 reads (6.35% of total) failing DuplicateReadFilter
[2016-04-15T01:22Z] INFO  18:22:50,680 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:22Z] INFO  18:22:50,680 MicroScheduler -   -> 68189 reads (24.94% of total) failing HCMappingQualityFilter
[2016-04-15T01:22Z] INFO  18:22:50,680 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:22Z] INFO  18:22:50,680 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:22Z] INFO  18:22:50,681 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:22Z] INFO  18:22:50,681 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T01:22Z] INFO  18:22:52,189 ProgressMeter -    10:134909155      1.5511121E7    30.0 s            1.0 s       74.7%    40.0 s      10.0 s
[2016-04-15T01:22Z] INFO  18:22:52,435 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:22Z] GATK: HaplotypeCaller
[2016-04-15T01:22Z] INFO  18:22:55,909 ProgressMeter -      11:1016372        9985430.0    30.0 s            3.0 s       16.3%     3.1 m       2.6 m
[2016-04-15T01:22Z] INFO  18:22:56,449 ProgressMeter -     10:76784716     1.17556495E8    60.0 s            0.0 s       94.5%    63.0 s       3.0 s
[2016-04-15T01:22Z] INFO  18:22:56,474 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:22Z] INFO  18:22:56,476 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:22Z] INFO  18:22:56,477 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:22Z] INFO  18:22:56,477 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:22Z] INFO  18:22:56,488 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/12/R14-18102_kapa-NGv3-PE100-NGv3-sort-12_15650178_31231471-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/12/R14-18102_kapa-NGv3-PE100-NGv3-12_15650178_31231471-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/12/tx/tmphVuPty/R14-18102_kapa-NGv3-PE100-NGv3-12_15650178_31231471.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:22Z] INFO  18:22:56,508 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:22Z] INFO  18:22:56,508 HelpFormatter - Date/Time: 2016/04/14 18:22:56
[2016-04-15T01:22Z] INFO  18:22:56,509 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:22Z] INFO  18:22:56,510 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:22Z] WARN  18:22:56,550 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T01:22Z] WARN  18:22:56,563 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/12/tx/tmphVuPty/R14-18102_kapa-NGv3-PE100-NGv3-12_15650178_31231471.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T01:22Z] INFO  18:22:56,818 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:22Z] INFO  18:22:57,041 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T01:22Z] INFO  18:22:57,061 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:22Z] INFO  18:22:57,157 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.10
[2016-04-15T01:22Z] INFO  18:22:57,185 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T01:22Z] INFO  18:22:57,633 IntervalUtils - Processing 134686 bp from intervals
[2016-04-15T01:22Z] WARN  18:22:57,649 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:22Z] INFO  18:22:57,810 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:22Z] INFO  18:22:57,939 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:22Z] INFO  18:22:57,940 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:22Z] INFO  18:22:57,941 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T01:22Z] INFO  18:22:57,941 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T01:22Z] INFO  18:22:57,950 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T01:22Z] INFO  18:22:57,950 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T01:22Z] INFO  18:22:58,210 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T01:22Z] INFO  18:22:59,468 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.013048404000000001
[2016-04-15T01:22Z] INFO  18:22:59,469 PairHMM - Total compute time in PairHMM computeLikelihoods() : 1.242166007
[2016-04-15T01:22Z] INFO  18:22:59,470 HaplotypeCaller - Ran local assembly on 1613 active regions
[2016-04-15T01:22Z] INFO  18:22:59,512 ProgressMeter -            done     1.26783317E8    63.0 s            0.0 s      100.0%    63.0 s       0.0 s
[2016-04-15T01:22Z] INFO  18:22:59,513 ProgressMeter - Total runtime 63.09 secs, 1.05 min, 0.02 hours
[2016-04-15T01:22Z] INFO  18:22:59,514 MicroScheduler - 33556 reads were filtered out during the traversal out of approximately 344934 total reads (9.73%)
[2016-04-15T01:22Z] INFO  18:22:59,515 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:22Z] INFO  18:22:59,515 MicroScheduler -   -> 27418 reads (7.95% of total) failing DuplicateReadFilter
[2016-04-15T01:22Z] INFO  18:22:59,516 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:22Z] INFO  18:22:59,517 MicroScheduler -   -> 6138 reads (1.78% of total) failing HCMappingQualityFilter
[2016-04-15T01:22Z] INFO  18:22:59,517 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:22Z] INFO  18:22:59,518 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:22Z] INFO  18:22:59,518 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:22Z] INFO  18:22:59,519 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T01:23Z] INFO  18:23:00,582 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.010197375
[2016-04-15T01:23Z] INFO  18:23:00,583 PairHMM - Total compute time in PairHMM computeLikelihoods() : 1.742902006
[2016-04-15T01:23Z] INFO  18:23:00,584 HaplotypeCaller - Ran local assembly on 834 active regions
[2016-04-15T01:23Z] INFO  18:23:00,624 ProgressMeter -            done      2.7883461E7    38.0 s            1.0 s      100.0%    38.0 s       0.0 s
[2016-04-15T01:23Z] INFO  18:23:00,625 ProgressMeter - Total runtime 38.46 secs, 0.64 min, 0.01 hours
[2016-04-15T01:23Z] INFO  18:23:00,626 MicroScheduler - 15378 reads were filtered out during the traversal out of approximately 170778 total reads (9.00%)
[2016-04-15T01:23Z] INFO  18:23:00,627 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:23Z] INFO  18:23:00,638 MicroScheduler -   -> 13876 reads (8.13% of total) failing DuplicateReadFilter
[2016-04-15T01:23Z] INFO  18:23:00,639 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:23Z] INFO  18:23:00,640 MicroScheduler -   -> 1502 reads (0.88% of total) failing HCMappingQualityFilter
[2016-04-15T01:23Z] INFO  18:23:00,640 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:23Z] INFO  18:23:00,641 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:23Z] INFO  18:23:00,641 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:23Z] INFO  18:23:00,642 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T01:23Z] INFO  18:23:00,905 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:23Z] GATK: HaplotypeCaller
[2016-04-15T01:23Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T01:23Z] INFO  18:23:01,899 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T01:23Z] INFO  18:23:01,900 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T01:23Z] INFO  18:23:02,080 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:23Z] WARN  18:23:02,160 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T01:23Z] WARN  18:23:02,161 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T01:23Z] GATK: HaplotypeCaller
[2016-04-15T01:23Z] INFO  18:23:03,997 ProgressMeter -     11:20066514      1.7039175E7    30.0 s            1.0 s       57.8%    51.0 s      21.0 s
[2016-04-15T01:23Z] INFO  18:23:04,069 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:23Z] INFO  18:23:04,072 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:23Z] INFO  18:23:04,073 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:23Z] INFO  18:23:04,073 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:23Z] INFO  18:23:04,078 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/12/R14-18102_kapa-NGv3-PE100-NGv3-sort-12_31236746_46754992-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/12/R14-18102_kapa-NGv3-PE100-NGv3-12_31236746_46754992-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/12/tx/tmpc6TclC/R14-18102_kapa-NGv3-PE100-NGv3-12_31236746_46754992.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:23Z] INFO  18:23:04,091 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:23Z] INFO  18:23:04,100 HelpFormatter - Date/Time: 2016/04/14 18:23:04
[2016-04-15T01:23Z] INFO  18:23:04,100 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:23Z] INFO  18:23:04,100 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:23Z] WARN  18:23:04,166 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T01:23Z] WARN  18:23:04,168 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/12/tx/tmpc6TclC/R14-18102_kapa-NGv3-PE100-NGv3-12_31236746_46754992.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T01:23Z] INFO  18:23:04,351 ProgressMeter -     11:44076752      1.8776766E7    30.0 s            1.0 s       56.5%    53.0 s      23.0 s
[2016-04-15T01:23Z] INFO  18:23:04,449 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:23Z] INFO  18:23:04,635 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T01:23Z] INFO  18:23:04,644 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:23Z] INFO  18:23:04,728 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-15T01:23Z] INFO  18:23:04,752 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T01:23Z] INFO  18:23:04,776 ProgressMeter -     11:48373671        6934557.0    30.0 s            4.0 s       16.8%     3.0 m       2.5 m
[2016-04-15T01:23Z] INFO  18:23:05,013 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:23Z] INFO  18:23:05,016 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:23Z] INFO  18:23:05,017 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:23Z] INFO  18:23:05,017 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:23Z] INFO  18:23:05,021 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/12/R14-18102_kapa-NGv3-PE100-NGv3-sort-12_46756066_62654284-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/12/R14-18102_kapa-NGv3-PE100-NGv3-12_46756066_62654284-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/12/tx/tmpDl0lJK/R14-18102_kapa-NGv3-PE100-NGv3-12_46756066_62654284.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:23Z] INFO  18:23:05,040 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:23Z] INFO  18:23:05,040 HelpFormatter - Date/Time: 2016/04/14 18:23:05
[2016-04-15T01:23Z] INFO  18:23:05,041 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:23Z] INFO  18:23:05,042 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:23Z] WARN  18:23:05,064 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T01:23Z] WARN  18:23:05,067 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/12/tx/tmpDl0lJK/R14-18102_kapa-NGv3-PE100-NGv3-12_46756066_62654284.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T01:23Z] INFO  18:23:05,098 IntervalUtils - Processing 136917 bp from intervals
[2016-04-15T01:23Z] WARN  18:23:05,102 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:23Z] INFO  18:23:05,184 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:23Z] INFO  18:23:05,236 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:23Z] INFO  18:23:05,285 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:23Z] INFO  18:23:05,285 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:23Z] INFO  18:23:05,285 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T01:23Z] INFO  18:23:05,286 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T01:23Z] INFO  18:23:05,287 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T01:23Z] INFO  18:23:05,288 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T01:23Z] INFO  18:23:05,445 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T01:23Z] INFO  18:23:05,456 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:23Z] INFO  18:23:05,513 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-15T01:23Z] INFO  18:23:05,545 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T01:23Z] INFO  18:23:05,547 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T01:23Z] INFO  18:23:06,031 IntervalUtils - Processing 504306 bp from intervals
[2016-04-15T01:23Z] WARN  18:23:06,038 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:23Z] INFO  18:23:06,146 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:23Z] INFO  18:23:06,297 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:23Z] INFO  18:23:06,298 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:23Z] INFO  18:23:06,299 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T01:23Z] INFO  18:23:06,300 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T01:23Z] INFO  18:23:06,301 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T01:23Z] INFO  18:23:06,301 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T01:23Z] INFO  18:23:06,509 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T01:23Z] INFO  18:23:07,250 ProgressMeter -    10:103919196     1.40305381E8    60.0 s            0.0 s       72.9%    82.0 s      22.0 s
[2016-04-15T01:23Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T01:23Z] INFO  18:23:08,148 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T01:23Z] INFO  18:23:08,160 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T01:23Z] WARN  18:23:08,372 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T01:23Z] WARN  18:23:08,374 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T01:23Z] INFO  18:23:08,979 ProgressMeter -     11:64677153      1.8212179E7    30.0 s            1.0 s       18.8%     2.7 m       2.2 m
[2016-04-15T01:23Z] INFO  18:23:09,615 ProgressMeter -     11:92533040      1.8928552E7    30.0 s            1.0 s       77.0%    38.0 s       8.0 s
[2016-04-15T01:23Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T01:23Z] INFO  18:23:10,819 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T01:23Z] INFO  18:23:10,820 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T01:23Z] INFO  18:23:10,847 ProgressMeter -    11:105774614         2.6518E7    30.0 s            1.0 s       66.1%    45.0 s      15.0 s
[2016-04-15T01:23Z] WARN  18:23:11,083 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T01:23Z] WARN  18:23:11,084 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T01:23Z] INFO  18:23:13,033 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.035597167
[2016-04-15T01:23Z] INFO  18:23:13,043 PairHMM - Total compute time in PairHMM computeLikelihoods() : 3.4110873510000004
[2016-04-15T01:23Z] INFO  18:23:13,044 HaplotypeCaller - Ran local assembly on 1621 active regions
[2016-04-15T01:23Z] INFO  18:23:13,098 ProgressMeter -            done     1.10097324E8    59.0 s            0.0 s      100.0%    59.0 s       0.0 s
[2016-04-15T01:23Z] INFO  18:23:13,098 ProgressMeter - Total runtime 59.35 secs, 0.99 min, 0.02 hours
[2016-04-15T01:23Z] INFO  18:23:13,099 MicroScheduler - 32231 reads were filtered out during the traversal out of approximately 296721 total reads (10.86%)
[2016-04-15T01:23Z] INFO  18:23:13,100 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:23Z] INFO  18:23:13,100 MicroScheduler -   -> 23257 reads (7.84% of total) failing DuplicateReadFilter
[2016-04-15T01:23Z] INFO  18:23:13,100 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:23Z] INFO  18:23:13,100 MicroScheduler -   -> 8974 reads (3.02% of total) failing HCMappingQualityFilter
[2016-04-15T01:23Z] INFO  18:23:13,101 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:23Z] INFO  18:23:13,101 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:23Z] INFO  18:23:13,101 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:23Z] INFO  18:23:13,101 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T01:23Z] INFO  18:23:13,715 ProgressMeter -    11:114424777      1.5177528E7    30.0 s            1.0 s       23.7%     2.1 m      96.0 s
[2016-04-15T01:23Z] INFO  18:23:14,200 ProgressMeter -     9:139090766     2.52890807E8    90.0 s            0.0 s       68.5%     2.2 m      41.0 s
[2016-04-15T01:23Z] INFO  18:23:14,419 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:23Z] GATK: HaplotypeCaller
[2016-04-15T01:23Z] INFO  18:23:15,056 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.005826989
[2016-04-15T01:23Z] INFO  18:23:15,057 PairHMM - Total compute time in PairHMM computeLikelihoods() : 0.22356249800000003
[2016-04-15T01:23Z] INFO  18:23:15,057 HaplotypeCaller - Ran local assembly on 771 active regions
[2016-04-15T01:23Z] INFO  18:23:15,111 ProgressMeter -            done      2.9891248E7    35.0 s            1.0 s      100.0%    35.0 s       0.0 s
[2016-04-15T01:23Z] INFO  18:23:15,112 ProgressMeter - Total runtime 35.53 secs, 0.59 min, 0.01 hours
[2016-04-15T01:23Z] INFO  18:23:15,112 MicroScheduler - 33138 reads were filtered out during the traversal out of approximately 167588 total reads (19.77%)
[2016-04-15T01:23Z] INFO  18:23:15,113 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:23Z] INFO  18:23:15,113 MicroScheduler -   -> 12097 reads (7.22% of total) failing DuplicateReadFilter
[2016-04-15T01:23Z] INFO  18:23:15,113 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:23Z] INFO  18:23:15,113 MicroScheduler -   -> 21041 reads (12.56% of total) failing HCMappingQualityFilter
[2016-04-15T01:23Z] INFO  18:23:15,114 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:23Z] INFO  18:23:15,114 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:23Z] INFO  18:23:15,114 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:23Z] INFO  18:23:15,114 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T01:23Z] INFO  18:23:15,172 ProgressMeter -    11:133293024      1.3304674E7    30.0 s            2.0 s       80.2%    37.0 s       7.0 s
[2016-04-15T01:23Z] INFO  18:23:15,935 ProgressMeter -      12:5153314      2.0949238E7    30.0 s            1.0 s       27.5%   109.0 s      79.0 s
[2016-04-15T01:23Z] INFO  18:23:16,716 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:23Z] GATK: HaplotypeCaller
[2016-04-15T01:23Z] INFO  18:23:17,875 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:23Z] INFO  18:23:17,877 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:23Z] INFO  18:23:17,877 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:23Z] INFO  18:23:17,877 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:23Z] INFO  18:23:17,882 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/12/R14-18102_kapa-NGv3-PE100-NGv3-sort-12_62687959_78225484-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/12/R14-18102_kapa-NGv3-PE100-NGv3-12_62687959_78225484-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/12/tx/tmpxAcbaK/R14-18102_kapa-NGv3-PE100-NGv3-12_62687959_78225484.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:23Z] INFO  18:23:17,892 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:23Z] INFO  18:23:17,893 HelpFormatter - Date/Time: 2016/04/14 18:23:17
[2016-04-15T01:23Z] INFO  18:23:17,893 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:23Z] INFO  18:23:17,894 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:23Z] WARN  18:23:17,939 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T01:23Z] WARN  18:23:17,952 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/12/tx/tmpxAcbaK/R14-18102_kapa-NGv3-PE100-NGv3-12_62687959_78225484.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T01:23Z] INFO  18:23:18,136 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:23Z] INFO  18:23:18,353 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T01:23Z] INFO  18:23:18,362 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:23Z] INFO  18:23:18,441 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-15T01:23Z] INFO  18:23:18,455 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T01:23Z] INFO  18:23:18,834 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.007923861
[2016-04-15T01:23Z] INFO  18:23:18,840 IntervalUtils - Processing 146919 bp from intervals
[2016-04-15T01:23Z] WARN  18:23:18,847 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:23Z] INFO  18:23:18,848 PairHMM - Total compute time in PairHMM computeLikelihoods() : 0.735973074
[2016-04-15T01:23Z] INFO  18:23:18,849 HaplotypeCaller - Ran local assembly on 1077 active regions
[2016-04-15T01:23Z] INFO  18:23:18,901 ProgressMeter -            done      5.3488435E7    44.0 s            0.0 s      100.0%    44.0 s       0.0 s
[2016-04-15T01:23Z] INFO  18:23:18,902 ProgressMeter - Total runtime 44.57 secs, 0.74 min, 0.01 hours
[2016-04-15T01:23Z] INFO  18:23:18,903 MicroScheduler - 19292 reads were filtered out during the traversal out of approximately 230625 total reads (8.37%)
[2016-04-15T01:23Z] INFO  18:23:18,903 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:23Z] INFO  18:23:18,903 MicroScheduler -   -> 18788 reads (8.15% of total) failing DuplicateReadFilter
[2016-04-15T01:23Z] INFO  18:23:18,904 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:23Z] INFO  18:23:18,904 MicroScheduler -   -> 504 reads (0.22% of total) failing HCMappingQualityFilter
[2016-04-15T01:23Z] INFO  18:23:18,905 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:23Z] INFO  18:23:18,906 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:23Z] INFO  18:23:18,906 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:23Z] INFO  18:23:18,906 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T01:23Z] INFO  18:23:18,997 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:23Z] INFO  18:23:19,061 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.019601244
[2016-04-15T01:23Z] INFO  18:23:19,062 PairHMM - Total compute time in PairHMM computeLikelihoods() : 0.398360794
[2016-04-15T01:23Z] INFO  18:23:19,063 HaplotypeCaller - Ran local assembly on 760 active regions
[2016-04-15T01:23Z] INFO  18:23:19,111 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:23Z] INFO  18:23:19,113 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:23Z] INFO  18:23:19,113 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T01:23Z] INFO  18:23:19,114 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T01:23Z] INFO  18:23:19,116 ProgressMeter -            done      2.5784333E7    33.0 s            1.0 s      100.0%    33.0 s       0.0 s
[2016-04-15T01:23Z] INFO  18:23:19,116 ProgressMeter - Total runtime 33.98 secs, 0.57 min, 0.01 hours
[2016-04-15T01:23Z] INFO  18:23:19,117 MicroScheduler - 14149 reads were filtered out during the traversal out of approximately 166816 total reads (8.48%)
[2016-04-15T01:23Z] INFO  18:23:19,117 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:23Z] INFO  18:23:19,118 MicroScheduler -   -> 13365 reads (8.01% of total) failing DuplicateReadFilter
[2016-04-15T01:23Z] INFO  18:23:19,118 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:23Z] INFO  18:23:19,118 MicroScheduler -   -> 784 reads (0.47% of total) failing HCMappingQualityFilter
[2016-04-15T01:23Z] INFO  18:23:19,119 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:23Z] INFO  18:23:19,119 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:23Z] INFO  18:23:19,119 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:23Z] INFO  18:23:19,120 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T01:23Z] INFO  18:23:19,115 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T01:23Z] INFO  18:23:19,115 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T01:23Z] INFO  18:23:19,347 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T01:23Z] INFO  18:23:19,781 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:23Z] INFO  18:23:19,784 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:23Z] INFO  18:23:19,785 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:23Z] INFO  18:23:19,785 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:23Z] INFO  18:23:19,790 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/12/R14-18102_kapa-NGv3-PE100-NGv3-sort-12_78334098_93863131-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/12/R14-18102_kapa-NGv3-PE100-NGv3-12_78334098_93863131-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/12/tx/tmpgd3WMd/R14-18102_kapa-NGv3-PE100-NGv3-12_78334098_93863131.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:23Z] INFO  18:23:19,805 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:23Z] INFO  18:23:19,806 HelpFormatter - Date/Time: 2016/04/14 18:23:19
[2016-04-15T01:23Z] INFO  18:23:19,806 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:23Z] INFO  18:23:19,807 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:23Z] WARN  18:23:19,852 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T01:23Z] WARN  18:23:19,855 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/12/tx/tmpgd3WMd/R14-18102_kapa-NGv3-PE100-NGv3-12_78334098_93863131.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T01:23Z] INFO  18:23:20,110 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:23Z] INFO  18:23:20,287 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T01:23Z] INFO  18:23:20,296 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:23Z] INFO  18:23:20,315 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:23Z] INFO  18:23:20,342 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.007505693000000001
[2016-04-15T01:23Z] INFO  18:23:20,343 PairHMM - Total compute time in PairHMM computeLikelihoods() : 0.31175388400000004
[2016-04-15T01:23Z] INFO  18:23:20,344 HaplotypeCaller - Ran local assembly on 1067 active regions
[2016-04-15T01:23Z] INFO  18:23:20,353 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.020960186000000002
[2016-04-15T01:23Z] INFO  18:23:20,354 PairHMM - Total compute time in PairHMM computeLikelihoods() : 0.603904815
[2016-04-15T01:23Z] INFO  18:23:20,355 HaplotypeCaller - Ran local assembly on 1106 active regions
[2016-04-15T01:23Z] INFO  18:23:20,370 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-15T01:23Z] INFO  18:23:20,391 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T01:23Z] INFO  18:23:20,396 ProgressMeter -            done      5.5507672E7    39.0 s            0.0 s      100.0%    39.0 s       0.0 s
[2016-04-15T01:23Z] INFO  18:23:20,397 ProgressMeter -            done      5.2775059E7    46.0 s            0.0 s      100.0%    46.0 s       0.0 s
[2016-04-15T01:23Z] INFO  18:23:20,398 ProgressMeter - Total runtime 46.42 secs, 0.77 min, 0.01 hours
[2016-04-15T01:23Z] INFO  18:23:20,399 MicroScheduler - 16527 reads were filtered out during the traversal out of approximately 195389 total reads (8.46%)
[2016-04-15T01:23Z] INFO  18:23:20,399 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:23Z] INFO  18:23:20,396 ProgressMeter - Total runtime 39.58 secs, 0.66 min, 0.01 hours
[2016-04-15T01:23Z] INFO  18:23:20,400 MicroScheduler - 14174 reads were filtered out during the traversal out of approximately 176722 total reads (8.02%)
[2016-04-15T01:23Z] INFO  18:23:20,400 MicroScheduler -   -> 15736 reads (8.05% of total) failing DuplicateReadFilter
[2016-04-15T01:23Z] INFO  18:23:20,400 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:23Z] INFO  18:23:20,401 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:23Z] INFO  18:23:20,401 MicroScheduler -   -> 13857 reads (7.84% of total) failing DuplicateReadFilter
[2016-04-15T01:23Z] INFO  18:23:20,401 MicroScheduler -   -> 791 reads (0.40% of total) failing HCMappingQualityFilter
[2016-04-15T01:23Z] INFO  18:23:20,401 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:23Z] INFO  18:23:20,401 MicroScheduler -   -> 317 reads (0.18% of total) failing HCMappingQualityFilter
[2016-04-15T01:23Z] INFO  18:23:20,402 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:23Z] INFO  18:23:20,401 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:23Z] INFO  18:23:20,402 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:23Z] INFO  18:23:20,402 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:23Z] INFO  18:23:20,403 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:23Z] INFO  18:23:20,403 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T01:23Z] INFO  18:23:20,402 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:23Z] INFO  18:23:20,402 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T01:23Z] INFO  18:23:20,489 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:23Z] GATK: HaplotypeCaller
[2016-04-15T01:23Z] GATK: HaplotypeCaller
[2016-04-15T01:23Z] INFO  18:23:20,790 IntervalUtils - Processing 88957 bp from intervals
[2016-04-15T01:23Z] WARN  18:23:20,795 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:23Z] INFO  18:23:20,954 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:23Z] INFO  18:23:21,052 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:23Z] INFO  18:23:21,052 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:23Z] INFO  18:23:21,053 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T01:23Z] INFO  18:23:21,064 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T01:23Z] INFO  18:23:21,075 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T01:23Z] INFO  18:23:21,076 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T01:23Z] INFO  18:23:21,321 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T01:23Z] INFO  18:23:21,861 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:23Z] INFO  18:23:21,901 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:23Z] GATK: HaplotypeCaller
[2016-04-15T01:23Z] GATK: HaplotypeCaller
[2016-04-15T01:23Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T01:23Z] INFO  18:23:22,416 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T01:23Z] INFO  18:23:22,417 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T01:23Z] WARN  18:23:22,689 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T01:23Z] WARN  18:23:22,691 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T01:23Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T01:23Z] INFO  18:23:23,040 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T01:23Z] INFO  18:23:23,051 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T01:23Z] INFO  18:23:23,295 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:23Z] INFO  18:23:23,298 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:23Z] INFO  18:23:23,298 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:23Z] INFO  18:23:23,298 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:23Z] INFO  18:23:23,312 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/12/R14-18102_kapa-NGv3-PE100-NGv3-sort-12_93870729_109490566-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/12/R14-18102_kapa-NGv3-PE100-NGv3-12_93870729_109490566-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/12/tx/tmph6ioWT/R14-18102_kapa-NGv3-PE100-NGv3-12_93870729_109490566.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:23Z] INFO  18:23:23,339 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:23Z] INFO  18:23:23,346 HelpFormatter - Date/Time: 2016/04/14 18:23:23
[2016-04-15T01:23Z] INFO  18:23:23,347 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:23Z] INFO  18:23:23,347 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:23Z] WARN  18:23:23,387 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T01:23Z] WARN  18:23:23,390 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/12/tx/tmph6ioWT/R14-18102_kapa-NGv3-PE100-NGv3-12_93870729_109490566.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T01:23Z] WARN  18:23:23,434 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T01:23Z] WARN  18:23:23,446 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T01:23Z] INFO  18:23:23,662 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:23Z] INFO  18:23:23,683 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:23Z] INFO  18:23:23,686 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:23Z] INFO  18:23:23,686 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:23Z] INFO  18:23:23,686 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:23Z] INFO  18:23:23,690 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/12/R14-18102_kapa-NGv3-PE100-NGv3-sort-12_109494486_125263132-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/12/R14-18102_kapa-NGv3-PE100-NGv3-12_109494486_125263132-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/12/tx/tmpJI9tUb/R14-18102_kapa-NGv3-PE100-NGv3-12_109494486_125263132.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:23Z] INFO  18:23:23,713 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:23Z] INFO  18:23:23,714 HelpFormatter - Date/Time: 2016/04/14 18:23:23
[2016-04-15T01:23Z] INFO  18:23:23,714 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:23Z] INFO  18:23:23,715 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:23Z] WARN  18:23:23,759 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T01:23Z] WARN  18:23:23,796 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/12/tx/tmpJI9tUb/R14-18102_kapa-NGv3-PE100-NGv3-12_109494486_125263132.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T01:23Z] INFO  18:23:23,900 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T01:23Z] INFO  18:23:23,918 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:23Z] INFO  18:23:24,006 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.09
[2016-04-15T01:23Z] INFO  18:23:24,026 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T01:23Z] INFO  18:23:24,043 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:23Z] INFO  18:23:24,217 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T01:23Z] INFO  18:23:24,227 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:23Z] INFO  18:23:24,296 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-15T01:23Z] INFO  18:23:24,334 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T01:23Z] INFO  18:23:24,534 IntervalUtils - Processing 201796 bp from intervals
[2016-04-15T01:23Z] WARN  18:23:24,540 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:23Z] INFO  18:23:24,638 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:23Z] INFO  18:23:24,771 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:23Z] INFO  18:23:24,771 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:23Z] INFO  18:23:24,772 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T01:23Z] INFO  18:23:24,772 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T01:23Z] INFO  18:23:24,785 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T01:23Z] INFO  18:23:24,786 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T01:23Z] INFO  18:23:24,937 IntervalUtils - Processing 364987 bp from intervals
[2016-04-15T01:23Z] WARN  18:23:24,953 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:23Z] INFO  18:23:25,039 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T01:23Z] INFO  18:23:25,073 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:23Z] INFO  18:23:25,207 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:23Z] INFO  18:23:25,208 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:23Z] INFO  18:23:25,209 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T01:23Z] INFO  18:23:25,209 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T01:23Z] INFO  18:23:25,210 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T01:23Z] INFO  18:23:25,210 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T01:23Z] INFO  18:23:25,324 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:23Z] INFO  18:23:25,328 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:23Z] INFO  18:23:25,328 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:23Z] INFO  18:23:25,328 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:23Z] INFO  18:23:25,332 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/12/R14-18102_kapa-NGv3-PE100-NGv3-sort-12_125267228_133851895-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/12/R14-18102_kapa-NGv3-PE100-NGv3-12_125267228_133851895-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/12/tx/tmpexXuBe/R14-18102_kapa-NGv3-PE100-NGv3-12_125267228_133851895.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:23Z] INFO  18:23:25,342 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:23Z] INFO  18:23:25,345 HelpFormatter - Date/Time: 2016/04/14 18:23:25
[2016-04-15T01:23Z] INFO  18:23:25,346 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:23Z] INFO  18:23:25,346 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:23Z] WARN  18:23:25,369 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T01:23Z] WARN  18:23:25,372 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/12/tx/tmpexXuBe/R14-18102_kapa-NGv3-PE100-NGv3-12_125267228_133851895.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T01:23Z] INFO  18:23:25,404 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T01:23Z] INFO  18:23:25,633 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:23Z] INFO  18:23:25,786 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T01:23Z] INFO  18:23:25,796 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:23Z] INFO  18:23:25,794 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:23Z] INFO  18:23:25,797 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:23Z] INFO  18:23:25,798 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:23Z] INFO  18:23:25,798 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:23Z] INFO  18:23:25,803 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/13/R14-18102_kapa-NGv3-PE100-NGv3-sort-13_0_19748299-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/13/R14-18102_kapa-NGv3-PE100-NGv3-13_0_19748299-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/13/tx/tmpwqCowv/R14-18102_kapa-NGv3-PE100-NGv3-13_0_19748299.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:23Z] INFO  18:23:25,822 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:23Z] INFO  18:23:25,822 HelpFormatter - Date/Time: 2016/04/14 18:23:25
[2016-04-15T01:23Z] INFO  18:23:25,822 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:23Z] INFO  18:23:25,823 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:23Z] WARN  18:23:25,845 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T01:23Z] WARN  18:23:25,848 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/13/tx/tmpwqCowv/R14-18102_kapa-NGv3-PE100-NGv3-13_0_19748299.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T01:23Z] INFO  18:23:25,874 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-15T01:23Z] INFO  18:23:25,899 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T01:23Z] INFO  18:23:25,937 ProgressMeter -      11:1017237        9985430.0    60.0 s            6.0 s       16.5%     6.1 m       5.1 m
[2016-04-15T01:23Z] INFO  18:23:26,050 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:23Z] INFO  18:23:26,229 IntervalUtils - Processing 106872 bp from intervals
[2016-04-15T01:23Z] WARN  18:23:26,234 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:23Z] INFO  18:23:26,298 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T01:23Z] INFO  18:23:26,322 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:23Z] INFO  18:23:26,338 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:23Z] INFO  18:23:26,409 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:23Z] INFO  18:23:26,410 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:23Z] INFO  18:23:26,410 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T01:23Z] INFO  18:23:26,411 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T01:23Z] INFO  18:23:26,412 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T01:23Z] INFO  18:23:26,412 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T01:23Z] INFO  18:23:26,423 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.10
[2016-04-15T01:23Z] INFO  18:23:26,433 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T01:23Z] INFO  18:23:26,629 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T01:23Z] INFO  18:23:26,752 IntervalUtils - Processing 297 bp from intervals
[2016-04-15T01:23Z] WARN  18:23:26,757 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:23Z] INFO  18:23:26,833 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:23Z] INFO  18:23:26,863 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:23Z] INFO  18:23:26,865 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:23Z] INFO  18:23:26,865 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T01:23Z] INFO  18:23:26,866 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T01:23Z] INFO  18:23:26,867 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T01:23Z] INFO  18:23:26,867 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T01:23Z] INFO  18:23:27,126 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T01:23Z] INFO  18:23:27,145 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.022035986
[2016-04-15T01:23Z] INFO  18:23:27,176 PairHMM - Total compute time in PairHMM computeLikelihoods() : 1.911999511
[2016-04-15T01:23Z] INFO  18:23:27,177 HaplotypeCaller - Ran local assembly on 2479 active regions
[2016-04-15T01:23Z] INFO  18:23:27,209 ProgressMeter -            done     2.79147334E8    79.0 s            0.0 s      100.0%    79.0 s       0.0 s
[2016-04-15T01:23Z] INFO  18:23:27,210 ProgressMeter - Total runtime 79.98 secs, 1.33 min, 0.02 hours
[2016-04-15T01:23Z] INFO  18:23:27,210 MicroScheduler - 40106 reads were filtered out during the traversal out of approximately 491699 total reads (8.16%)
[2016-04-15T01:23Z] INFO  18:23:27,211 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:23Z] INFO  18:23:27,212 MicroScheduler -   -> 39000 reads (7.93% of total) failing DuplicateReadFilter
[2016-04-15T01:23Z] INFO  18:23:27,213 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:23Z] INFO  18:23:27,213 MicroScheduler -   -> 1106 reads (0.22% of total) failing HCMappingQualityFilter
[2016-04-15T01:23Z] INFO  18:23:27,214 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:23Z] INFO  18:23:27,214 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:23Z] INFO  18:23:27,215 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:23Z] INFO  18:23:27,215 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T01:23Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T01:23Z] INFO  18:23:27,919 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T01:23Z] INFO  18:23:27,920 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T01:23Z] INFO  18:23:27,952 ProgressMeter -     12:29446400       4.061054E7    30.0 s            0.0 s       87.9%    34.0 s       4.0 s
[2016-04-15T01:23Z] WARN  18:23:28,224 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T01:23Z] WARN  18:23:28,225 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T01:23Z] INFO  18:23:28,760 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:23Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T01:23Z] INFO  18:23:28,942 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T01:23Z] INFO  18:23:28,943 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T01:23Z] INFO  18:23:28,945 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.0
[2016-04-15T01:23Z] INFO  18:23:28,945 PairHMM - Total compute time in PairHMM computeLikelihoods() : 0.0
[2016-04-15T01:23Z] INFO  18:23:28,946 HaplotypeCaller - Ran local assembly on 1 active regions
[2016-04-15T01:23Z] INFO  18:23:28,987 ProgressMeter -            done            297.0     2.0 s          119.0 m       99.7%     2.0 s       0.0 s
[2016-04-15T01:23Z] INFO  18:23:28,987 ProgressMeter - Total runtime 2.12 secs, 0.04 min, 0.00 hours
[2016-04-15T01:23Z] INFO  18:23:28,988 MicroScheduler - 100 reads were filtered out during the traversal out of approximately 831 total reads (12.03%)
[2016-04-15T01:23Z] INFO  18:23:28,989 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:23Z] INFO  18:23:28,989 MicroScheduler -   -> 100 reads (12.03% of total) failing DuplicateReadFilter
[2016-04-15T01:23Z] INFO  18:23:28,989 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:23Z] INFO  18:23:28,989 MicroScheduler -   -> 0 reads (0.00% of total) failing HCMappingQualityFilter
[2016-04-15T01:23Z] INFO  18:23:28,990 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:23Z] INFO  18:23:28,990 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:23Z] INFO  18:23:28,990 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:23Z] INFO  18:23:28,991 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T01:23Z] GATK: HaplotypeCaller
[2016-04-15T01:23Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T01:23Z] INFO  18:23:29,709 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T01:23Z] INFO  18:23:29,710 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T01:23Z] WARN  18:23:30,002 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T01:23Z] WARN  18:23:30,003 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T01:23Z] INFO  18:23:30,471 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:23Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T01:23Z] INFO  18:23:30,589 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T01:23Z] INFO  18:23:30,590 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T01:23Z] GATK: HaplotypeCaller
[2016-04-15T01:23Z] WARN  18:23:30,928 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T01:23Z] WARN  18:23:30,929 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T01:23Z] INFO  18:23:31,250 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.009425349000000001
[2016-04-15T01:23Z] INFO  18:23:31,251 PairHMM - Total compute time in PairHMM computeLikelihoods() : 0.437556955
[2016-04-15T01:23Z] INFO  18:23:31,252 HaplotypeCaller - Ran local assembly on 1089 active regions
[2016-04-15T01:23Z] INFO  18:23:31,292 ProgressMeter -            done      5.5983758E7    33.0 s            0.0 s      100.0%    33.0 s       0.0 s
[2016-04-15T01:23Z] INFO  18:23:31,292 ProgressMeter - Total runtime 33.35 secs, 0.56 min, 0.01 hours
[2016-04-15T01:23Z] INFO  18:23:31,293 MicroScheduler - 12110 reads were filtered out during the traversal out of approximately 149562 total reads (8.10%)
[2016-04-15T01:23Z] INFO  18:23:31,293 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:23Z] INFO  18:23:31,293 MicroScheduler -   -> 11787 reads (7.88% of total) failing DuplicateReadFilter
[2016-04-15T01:23Z] INFO  18:23:31,294 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:23Z] INFO  18:23:31,294 MicroScheduler -   -> 323 reads (0.22% of total) failing HCMappingQualityFilter
[2016-04-15T01:23Z] INFO  18:23:31,294 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:23Z] INFO  18:23:31,294 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:23Z] INFO  18:23:31,294 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:23Z] INFO  18:23:31,295 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T01:23Z] INFO  18:23:32,853 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:23Z] INFO  18:23:33,002 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:23Z] INFO  18:23:33,016 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:23Z] INFO  18:23:33,017 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:23Z] INFO  18:23:33,018 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:23Z] INFO  18:23:33,022 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/13/R14-18102_kapa-NGv3-PE100-NGv3-sort-13_19751066_35517251-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/13/R14-18102_kapa-NGv3-PE100-NGv3-13_19751066_35517251-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/13/tx/tmpFns68U/R14-18102_kapa-NGv3-PE100-NGv3-13_19751066_35517251.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:23Z] INFO  18:23:33,047 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:23Z] INFO  18:23:33,048 HelpFormatter - Date/Time: 2016/04/14 18:23:33
[2016-04-15T01:23Z] INFO  18:23:33,049 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:23Z] INFO  18:23:33,050 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:23Z] WARN  18:23:33,113 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T01:23Z] WARN  18:23:33,129 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/13/tx/tmpFns68U/R14-18102_kapa-NGv3-PE100-NGv3-13_19751066_35517251.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T01:23Z] GATK: HaplotypeCaller
[2016-04-15T01:23Z] INFO  18:23:33,452 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:23Z] INFO  18:23:33,746 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T01:23Z] INFO  18:23:33,767 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:23Z] INFO  18:23:33,865 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.10
[2016-04-15T01:23Z] INFO  18:23:33,892 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T01:23Z] INFO  18:23:34,516 IntervalUtils - Processing 201552 bp from intervals
[2016-04-15T01:23Z] WARN  18:23:34,522 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:23Z] INFO  18:23:34,603 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:23Z] INFO  18:23:34,718 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:23Z] INFO  18:23:34,719 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:23Z] INFO  18:23:34,720 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T01:23Z] INFO  18:23:34,721 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T01:23Z] INFO  18:23:34,732 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T01:23Z] INFO  18:23:34,732 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T01:23Z] INFO  18:23:34,746 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:23Z] INFO  18:23:34,766 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:23Z] INFO  18:23:34,766 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:23Z] INFO  18:23:34,767 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:23Z] INFO  18:23:34,771 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/13/R14-18102_kapa-NGv3-PE100-NGv3-sort-13_35615069_51287376-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/13/R14-18102_kapa-NGv3-PE100-NGv3-13_35615069_51287376-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/13/tx/tmpXluImX/R14-18102_kapa-NGv3-PE100-NGv3-13_35615069_51287376.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:23Z] INFO  18:23:34,777 ProgressMeter -     11:56510304       1.384399E7    60.0 s            4.0 s       32.9%     3.0 m       2.0 m
[2016-04-15T01:23Z] INFO  18:23:34,790 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:23Z] INFO  18:23:34,790 HelpFormatter - Date/Time: 2016/04/14 18:23:34
[2016-04-15T01:23Z] INFO  18:23:34,790 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:23Z] INFO  18:23:34,790 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:23Z] WARN  18:23:34,814 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T01:23Z] WARN  18:23:34,817 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/13/tx/tmpXluImX/R14-18102_kapa-NGv3-PE100-NGv3-13_35615069_51287376.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T01:23Z] INFO  18:23:35,046 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T01:23Z] INFO  18:23:35,084 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:23Z] INFO  18:23:35,318 ProgressMeter -     12:40881343      1.2902841E7    30.0 s            2.0 s       55.2%    54.0 s      24.0 s
[2016-04-15T01:23Z] INFO  18:23:35,369 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T01:23Z] INFO  18:23:35,379 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:23Z] INFO  18:23:35,499 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.12
[2016-04-15T01:23Z] INFO  18:23:35,514 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T01:23Z] INFO  18:23:36,089 IntervalUtils - Processing 179232 bp from intervals
[2016-04-15T01:23Z] WARN  18:23:36,095 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:23Z] INFO  18:23:36,245 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:23Z] INFO  18:23:36,316 ProgressMeter -     12:50026797      1.8440868E7    30.0 s            1.0 s       20.4%     2.4 m     116.0 s
[2016-04-15T01:23Z] INFO  18:23:36,375 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:23Z] INFO  18:23:36,377 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:23Z] INFO  18:23:36,377 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T01:23Z] INFO  18:23:36,378 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T01:23Z] INFO  18:23:36,387 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T01:23Z] INFO  18:23:36,388 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T01:23Z] INFO  18:23:36,489 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:23Z] INFO  18:23:36,492 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:23Z] INFO  18:23:36,493 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:23Z] INFO  18:23:36,493 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:23Z] INFO  18:23:36,498 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/13/R14-18102_kapa-NGv3-PE100-NGv3-sort-13_51396767_67205543-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/13/R14-18102_kapa-NGv3-PE100-NGv3-13_51396767_67205543-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/13/tx/tmpSctaIC/R14-18102_kapa-NGv3-PE100-NGv3-13_51396767_67205543.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:23Z] INFO  18:23:36,513 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:23Z] INFO  18:23:36,514 HelpFormatter - Date/Time: 2016/04/14 18:23:36
[2016-04-15T01:23Z] INFO  18:23:36,514 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:23Z] INFO  18:23:36,515 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:23Z] WARN  18:23:36,558 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T01:23Z] WARN  18:23:36,561 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/13/tx/tmpSctaIC/R14-18102_kapa-NGv3-PE100-NGv3-13_51396767_67205543.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T01:23Z] INFO  18:23:36,633 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T01:23Z] INFO  18:23:36,810 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:23Z] INFO  18:23:37,003 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T01:23Z] INFO  18:23:37,012 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:23Z] INFO  18:23:37,102 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.09
[2016-04-15T01:23Z] INFO  18:23:37,124 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T01:23Z] INFO  18:23:37,514 IntervalUtils - Processing 59966 bp from intervals
[2016-04-15T01:23Z] WARN  18:23:37,519 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:23Z] INFO  18:23:37,644 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:23Z] INFO  18:23:37,712 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:23Z] INFO  18:23:37,713 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:23Z] INFO  18:23:37,714 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T01:23Z] INFO  18:23:37,715 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T01:23Z] INFO  18:23:37,715 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T01:23Z] INFO  18:23:37,716 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T01:23Z] INFO  18:23:37,932 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T01:23Z] INFO  18:23:38,980 ProgressMeter -     11:66618511     1.11028328E8    60.0 s            0.0 s       47.5%     2.1 m      66.0 s
[2016-04-15T01:23Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T01:23Z] INFO  18:23:39,074 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T01:23Z] INFO  18:23:39,075 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T01:23Z] WARN  18:23:39,590 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T01:23Z] WARN  18:23:39,591 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T01:23Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T01:23Z] INFO  18:23:43,107 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T01:23Z] INFO  18:23:43,119 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T01:23Z] WARN  18:23:43,359 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T01:23Z] WARN  18:23:43,360 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T01:23Z] INFO  18:23:43,716 ProgressMeter -    11:118978452      8.1410848E7    60.0 s            0.0 s       58.7%   102.0 s      42.0 s
[2016-04-15T01:23Z] INFO  18:23:44,201 ProgressMeter -     9:140331321     4.06955696E8   120.0 s            0.0 s       94.0%     2.1 m       7.0 s
[2016-04-15T01:23Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T01:23Z] INFO  18:23:45,508 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T01:23Z] INFO  18:23:45,509 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T01:23Z] WARN  18:23:45,756 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T01:23Z] WARN  18:23:45,757 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T01:23Z] INFO  18:23:45,947 ProgressMeter -      12:8374418     1.00643534E8    60.0 s            0.0 s       63.5%    94.0 s      34.0 s
[2016-04-15T01:23Z] INFO  18:23:49,135 ProgressMeter -     12:71978428      2.8404788E7    30.0 s            1.0 s       69.5%    43.0 s      13.0 s
[2016-04-15T01:23Z] INFO  18:23:49,363 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.004389828
[2016-04-15T01:23Z] INFO  18:23:49,364 PairHMM - Total compute time in PairHMM computeLikelihoods() : 0.132176292
[2016-04-15T01:23Z] INFO  18:23:49,364 HaplotypeCaller - Ran local assembly on 655 active regions
[2016-04-15T01:23Z] INFO  18:23:49,428 ProgressMeter -            done        2.16241E7    28.0 s            1.0 s      100.0%    28.0 s       0.0 s
[2016-04-15T01:23Z] INFO  18:23:49,428 ProgressMeter - Total runtime 28.38 secs, 0.47 min, 0.01 hours
[2016-04-15T01:23Z] INFO  18:23:49,429 MicroScheduler - 7340 reads were filtered out during the traversal out of approximately 92542 total reads (7.93%)
[2016-04-15T01:23Z] INFO  18:23:49,429 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:23Z] INFO  18:23:49,429 MicroScheduler -   -> 7182 reads (7.76% of total) failing DuplicateReadFilter
[2016-04-15T01:23Z] INFO  18:23:49,430 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:23Z] INFO  18:23:49,430 MicroScheduler -   -> 158 reads (0.17% of total) failing HCMappingQualityFilter
[2016-04-15T01:23Z] INFO  18:23:49,430 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:23Z] INFO  18:23:49,430 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:23Z] INFO  18:23:49,431 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:23Z] INFO  18:23:49,431 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T01:23Z] INFO  18:23:50,667 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.039475933000000005
[2016-04-15T01:23Z] INFO  18:23:50,668 PairHMM - Total compute time in PairHMM computeLikelihoods() : 2.6134161700000003
[2016-04-15T01:23Z] INFO  18:23:50,678 HaplotypeCaller - Ran local assembly on 3573 active regions
[2016-04-15T01:23Z] INFO  18:23:50,742 ProgressMeter -            done     4.74191826E8     2.1 m            0.0 s      100.0%     2.1 m       0.0 s
[2016-04-15T01:23Z] INFO  18:23:50,743 ProgressMeter - Total runtime 126.57 secs, 2.11 min, 0.04 hours
[2016-04-15T01:23Z] INFO  18:23:50,743 MicroScheduler - 72263 reads were filtered out during the traversal out of approximately 805069 total reads (8.98%)
[2016-04-15T01:23Z] INFO  18:23:50,744 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:23Z] INFO  18:23:50,744 MicroScheduler -   -> 64996 reads (8.07% of total) failing DuplicateReadFilter
[2016-04-15T01:23Z] INFO  18:23:50,744 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:23Z] INFO  18:23:50,745 MicroScheduler -   -> 7267 reads (0.90% of total) failing HCMappingQualityFilter
[2016-04-15T01:23Z] INFO  18:23:50,745 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:23Z] INFO  18:23:50,745 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:23Z] INFO  18:23:50,746 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:23Z] INFO  18:23:50,746 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T01:23Z] INFO  18:23:50,805 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:23Z] GATK: HaplotypeCaller
[2016-04-15T01:23Z] INFO  18:23:52,103 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:23Z] GATK: HaplotypeCaller
[2016-04-15T01:23Z] INFO  18:23:54,021 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:23Z] INFO  18:23:54,024 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:23Z] INFO  18:23:54,025 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:23Z] INFO  18:23:54,026 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:23Z] INFO  18:23:54,030 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/13/R14-18102_kapa-NGv3-PE100-NGv3-sort-13_67477635_84455642-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/13/R14-18102_kapa-NGv3-PE100-NGv3-13_67477635_84455642-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/13/tx/tmpKX8c6F/R14-18102_kapa-NGv3-PE100-NGv3-13_67477635_84455642.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:23Z] INFO  18:23:54,055 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:23Z] INFO  18:23:54,056 HelpFormatter - Date/Time: 2016/04/14 18:23:54
[2016-04-15T01:23Z] INFO  18:23:54,056 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:23Z] INFO  18:23:54,057 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:23Z] WARN  18:23:54,091 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T01:23Z] WARN  18:23:54,094 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/13/tx/tmpKX8c6F/R14-18102_kapa-NGv3-PE100-NGv3-13_67477635_84455642.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T01:23Z] INFO  18:23:54,274 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:23Z] INFO  18:23:54,428 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T01:23Z] INFO  18:23:54,439 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:23Z] INFO  18:23:54,493 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05
[2016-04-15T01:23Z] INFO  18:23:54,512 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T01:23Z] INFO  18:23:54,794 IntervalUtils - Processing 69582 bp from intervals
[2016-04-15T01:23Z] INFO  18:23:54,797 ProgressMeter -    12:102071013      3.1541137E7    30.0 s            0.0 s       50.9%    58.0 s      28.0 s
[2016-04-15T01:23Z] WARN  18:23:54,800 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:23Z] INFO  18:23:54,891 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:23Z] INFO  18:23:54,973 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:23Z] INFO  18:23:54,974 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:23Z] INFO  18:23:54,974 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T01:23Z] INFO  18:23:54,974 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T01:23Z] INFO  18:23:54,975 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T01:23Z] INFO  18:23:54,975 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T01:23Z] INFO  18:23:55,090 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:23Z] INFO  18:23:55,094 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:23Z] INFO  18:23:55,094 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:23Z] INFO  18:23:55,095 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:23Z] INFO  18:23:55,099 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/13/R14-18102_kapa-NGv3-PE100-NGv3-sort-13_86368117_101881935-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/13/R14-18102_kapa-NGv3-PE100-NGv3-13_86368117_101881935-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/13/tx/tmp6W76bf/R14-18102_kapa-NGv3-PE100-NGv3-13_86368117_101881935.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:23Z] INFO  18:23:55,120 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:23Z] INFO  18:23:55,140 HelpFormatter - Date/Time: 2016/04/14 18:23:55
[2016-04-15T01:23Z] INFO  18:23:55,141 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:23Z] INFO  18:23:55,141 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:23Z] INFO  18:23:55,163 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T01:23Z] WARN  18:23:55,185 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T01:23Z] WARN  18:23:55,188 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/13/tx/tmp6W76bf/R14-18102_kapa-NGv3-PE100-NGv3-13_86368117_101881935.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T01:23Z] INFO  18:23:55,231 ProgressMeter -    12:113447241      3.8350294E7    30.0 s            0.0 s       32.0%    93.0 s      63.0 s
[2016-04-15T01:23Z] INFO  18:23:55,436 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:23Z] INFO  18:23:55,670 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T01:23Z] INFO  18:23:55,679 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:23Z] INFO  18:23:55,748 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-15T01:23Z] INFO  18:23:55,763 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T01:23Z] INFO  18:23:55,938 ProgressMeter -      11:1018096        9985430.0    90.0 s            9.0 s       16.7%     9.0 m       7.5 m
[2016-04-15T01:23Z] INFO  18:23:56,149 IntervalUtils - Processing 75123 bp from intervals
[2016-04-15T01:23Z] WARN  18:23:56,157 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:23Z] INFO  18:23:56,230 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:23Z] INFO  18:23:56,286 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:23Z] INFO  18:23:56,288 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:23Z] INFO  18:23:56,288 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T01:23Z] INFO  18:23:56,289 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T01:23Z] INFO  18:23:56,289 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T01:23Z] INFO  18:23:56,290 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T01:23Z] INFO  18:23:56,435 ProgressMeter -    12:133067157        9524618.0    30.0 s            3.0 s       57.8%    51.0 s      21.0 s
[2016-04-15T01:23Z] INFO  18:23:56,484 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T01:23Z] INFO  18:23:56,891 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.0063316660000000006
[2016-04-15T01:23Z] INFO  18:23:56,892 PairHMM - Total compute time in PairHMM computeLikelihoods() : 0.35574015800000003
[2016-04-15T01:23Z] INFO  18:23:56,893 HaplotypeCaller - Ran local assembly on 1096 active regions
[2016-04-15T01:23Z] INFO  18:23:56,933 ProgressMeter -            done       5.533073E7    37.0 s            0.0 s      100.0%    37.0 s       0.0 s
[2016-04-15T01:23Z] INFO  18:23:56,933 ProgressMeter - Total runtime 37.82 secs, 0.63 min, 0.01 hours
[2016-04-15T01:23Z] INFO  18:23:56,934 MicroScheduler - 13876 reads were filtered out during the traversal out of approximately 169584 total reads (8.18%)
[2016-04-15T01:23Z] INFO  18:23:56,934 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:23Z] INFO  18:23:56,935 MicroScheduler -   -> 13425 reads (7.92% of total) failing DuplicateReadFilter
[2016-04-15T01:23Z] INFO  18:23:56,935 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:23Z] INFO  18:23:56,935 MicroScheduler -   -> 451 reads (0.27% of total) failing HCMappingQualityFilter
[2016-04-15T01:23Z] INFO  18:23:56,935 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:23Z] INFO  18:23:56,936 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:23Z] INFO  18:23:56,936 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:23Z] INFO  18:23:56,936 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T01:23Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T01:23Z] INFO  18:23:57,260 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T01:23Z] INFO  18:23:57,271 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T01:23Z] WARN  18:23:57,441 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T01:23Z] WARN  18:23:57,442 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T01:23Z] INFO  18:23:58,350 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:23Z] GATK: HaplotypeCaller
[2016-04-15T01:23Z] INFO  18:23:59,047 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.012795986
[2016-04-15T01:23Z] INFO  18:23:59,048 PairHMM - Total compute time in PairHMM computeLikelihoods() : 0.043321178
[2016-04-15T01:23Z] INFO  18:23:59,049 HaplotypeCaller - Ran local assembly on 380 active regions
[2016-04-15T01:23Z] INFO  18:23:59,097 ProgressMeter -            done        7043015.0    21.0 s            3.0 s      100.0%    21.0 s       0.0 s
[2016-04-15T01:23Z] INFO  18:23:59,098 ProgressMeter - Total runtime 21.38 secs, 0.36 min, 0.01 hours
[2016-04-15T01:23Z] INFO  18:23:59,098 MicroScheduler - 31605 reads were filtered out during the traversal out of approximately 100798 total reads (31.35%)
[2016-04-15T01:23Z] INFO  18:23:59,099 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:23Z] INFO  18:23:59,099 MicroScheduler -   -> 5987 reads (5.94% of total) failing DuplicateReadFilter
[2016-04-15T01:23Z] INFO  18:23:59,099 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:23Z] INFO  18:23:59,099 MicroScheduler -   -> 25618 reads (25.42% of total) failing HCMappingQualityFilter
[2016-04-15T01:23Z] INFO  18:23:59,102 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:23Z] INFO  18:23:59,103 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:23Z] INFO  18:23:59,103 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:23Z] INFO  18:23:59,103 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T01:23Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T01:23Z] INFO  18:23:59,118 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T01:23Z] INFO  18:23:59,119 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T01:23Z] WARN  18:23:59,434 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T01:23Z] WARN  18:23:59,435 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T01:24Z] INFO  18:24:00,536 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:24Z] GATK: HaplotypeCaller
[2016-04-15T01:24Z] INFO  18:24:01,818 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:24Z] INFO  18:24:01,821 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:24Z] INFO  18:24:01,822 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:24Z] INFO  18:24:01,823 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:24Z] INFO  18:24:01,827 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/13/R14-18102_kapa-NGv3-PE100-NGv3-sort-13_101890105_115169878-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/13/R14-18102_kapa-NGv3-PE100-NGv3-13_101890105_115169878-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/13/tx/tmpttiZlp/R14-18102_kapa-NGv3-PE100-NGv3-13_101890105_115169878.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:24Z] INFO  18:24:01,846 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:24Z] INFO  18:24:01,857 HelpFormatter - Date/Time: 2016/04/14 18:24:01
[2016-04-15T01:24Z] INFO  18:24:01,858 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:24Z] INFO  18:24:01,859 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:24Z] WARN  18:24:01,905 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T01:24Z] WARN  18:24:01,907 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/13/tx/tmpttiZlp/R14-18102_kapa-NGv3-PE100-NGv3-13_101890105_115169878.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T01:24Z] INFO  18:24:02,096 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:24Z] INFO  18:24:02,355 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T01:24Z] INFO  18:24:02,364 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:24Z] INFO  18:24:02,427 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-15T01:24Z] INFO  18:24:02,446 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T01:24Z] INFO  18:24:02,783 IntervalUtils - Processing 144481 bp from intervals
[2016-04-15T01:24Z] WARN  18:24:02,799 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:24Z] INFO  18:24:02,933 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:24Z] INFO  18:24:03,062 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:24Z] INFO  18:24:03,074 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:24Z] INFO  18:24:03,075 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T01:24Z] INFO  18:24:03,076 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T01:24Z] INFO  18:24:03,088 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T01:24Z] INFO  18:24:03,089 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T01:24Z] INFO  18:24:03,369 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T01:24Z] INFO  18:24:03,644 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:24Z] INFO  18:24:03,647 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:24Z] INFO  18:24:03,648 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:24Z] INFO  18:24:03,649 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:24Z] INFO  18:24:03,653 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/14/R14-18102_kapa-NGv3-PE100-NGv3-sort-14_0_19378574-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/14/R14-18102_kapa-NGv3-PE100-NGv3-14_0_19378574-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/14/tx/tmpHJ2LcM/R14-18102_kapa-NGv3-PE100-NGv3-14_0_19378574.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:24Z] INFO  18:24:03,663 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:24Z] INFO  18:24:03,664 HelpFormatter - Date/Time: 2016/04/14 18:24:03
[2016-04-15T01:24Z] INFO  18:24:03,664 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:24Z] INFO  18:24:03,664 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:24Z] WARN  18:24:03,708 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T01:24Z] WARN  18:24:03,711 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/14/tx/tmpHJ2LcM/R14-18102_kapa-NGv3-PE100-NGv3-14_0_19378574.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T01:24Z] INFO  18:24:03,969 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:24Z] INFO  18:24:04,161 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T01:24Z] INFO  18:24:04,175 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:24Z] INFO  18:24:04,265 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.09
[2016-04-15T01:24Z] INFO  18:24:04,295 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T01:24Z] INFO  18:24:04,703 IntervalUtils - Processing 981 bp from intervals
[2016-04-15T01:24Z] WARN  18:24:04,719 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:24Z] INFO  18:24:04,739 ProgressMeter -     13:25671560       1.610196E7    30.0 s            1.0 s       43.2%    69.0 s      39.0 s
[2016-04-15T01:24Z] INFO  18:24:04,778 ProgressMeter -     11:61308138     1.16647001E8    90.0 s            0.0 s       73.7%     2.0 m      32.0 s
[2016-04-15T01:24Z] INFO  18:24:04,833 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:24Z] INFO  18:24:04,873 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:24Z] INFO  18:24:04,874 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:24Z] INFO  18:24:04,875 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T01:24Z] INFO  18:24:04,876 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T01:24Z] INFO  18:24:04,878 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T01:24Z] INFO  18:24:04,878 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T01:24Z] INFO  18:24:05,113 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T01:24Z] INFO  18:24:05,319 ProgressMeter -     12:41582905      1.9580031E7    60.0 s            3.0 s       64.4%    93.0 s      33.0 s
[2016-04-15T01:24Z] INFO  18:24:06,204 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.018622301
[2016-04-15T01:24Z] INFO  18:24:06,205 PairHMM - Total compute time in PairHMM computeLikelihoods() : 2.9929322540000003
[2016-04-15T01:24Z] INFO  18:24:06,206 HaplotypeCaller - Ran local assembly on 770 active regions
[2016-04-15T01:24Z] INFO  18:24:06,246 ProgressMeter -            done      2.2806798E7    39.0 s            1.0 s      100.0%    39.0 s       0.0 s
[2016-04-15T01:24Z] INFO  18:24:06,247 ProgressMeter - Total runtime 39.84 secs, 0.66 min, 0.01 hours
[2016-04-15T01:24Z] INFO  18:24:06,248 MicroScheduler - 27797 reads were filtered out during the traversal out of approximately 199539 total reads (13.93%)
[2016-04-15T01:24Z] INFO  18:24:06,248 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:24Z] INFO  18:24:06,249 MicroScheduler -   -> 15430 reads (7.73% of total) failing DuplicateReadFilter
[2016-04-15T01:24Z] INFO  18:24:06,250 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:24Z] INFO  18:24:06,251 MicroScheduler -   -> 12367 reads (6.20% of total) failing HCMappingQualityFilter
[2016-04-15T01:24Z] INFO  18:24:06,251 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:24Z] INFO  18:24:06,252 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:24Z] INFO  18:24:06,253 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:24Z] INFO  18:24:06,253 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T01:24Z] INFO  18:24:06,317 ProgressMeter -     12:53457666     1.34201254E8    60.0 s            0.0 s       48.7%     2.1 m      63.0 s
[2016-04-15T01:24Z] INFO  18:24:06,419 ProgressMeter -     13:45149499      2.5982553E7    30.0 s            1.0 s       59.6%    50.0 s      20.0 s
[2016-04-15T01:24Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T01:24Z] INFO  18:24:07,374 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T01:24Z] INFO  18:24:07,385 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T01:24Z] WARN  18:24:07,751 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T01:24Z] WARN  18:24:07,752 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T01:24Z] INFO  18:24:07,815 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:24Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T01:24Z] INFO  18:24:07,964 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T01:24Z] INFO  18:24:07,965 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T01:24Z] GATK: HaplotypeCaller
[2016-04-15T01:24Z] WARN  18:24:08,481 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T01:24Z] WARN  18:24:08,485 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T01:24Z] INFO  18:24:08,981 ProgressMeter -     11:71952146     3.00804376E8    90.0 s            0.0 s       74.0%     2.0 m      31.0 s
[2016-04-15T01:24Z] INFO  18:24:09,798 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.0023289590000000002
[2016-04-15T01:24Z] INFO  18:24:09,798 PairHMM - Total compute time in PairHMM computeLikelihoods() : 0.052805248000000006
[2016-04-15T01:24Z] INFO  18:24:09,798 HaplotypeCaller - Ran local assembly on 8 active regions
[2016-04-15T01:24Z] INFO  18:24:09,851 ProgressMeter -            done            981.0     4.0 s           84.5 m       99.9%     4.0 s       0.0 s
[2016-04-15T01:24Z] INFO  18:24:09,853 ProgressMeter - Total runtime 4.98 secs, 0.08 min, 0.00 hours
[2016-04-15T01:24Z] INFO  18:24:09,853 MicroScheduler - 1418 reads were filtered out during the traversal out of approximately 3005 total reads (47.19%)
[2016-04-15T01:24Z] INFO  18:24:09,854 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:24Z] INFO  18:24:09,855 MicroScheduler -   -> 176 reads (5.86% of total) failing DuplicateReadFilter
[2016-04-15T01:24Z] INFO  18:24:09,856 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:24Z] INFO  18:24:09,856 MicroScheduler -   -> 1242 reads (41.33% of total) failing HCMappingQualityFilter
[2016-04-15T01:24Z] INFO  18:24:09,857 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:24Z] INFO  18:24:09,857 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:24Z] INFO  18:24:09,857 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:24Z] INFO  18:24:09,857 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T01:24Z] INFO  18:24:11,094 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:24Z] INFO  18:24:11,098 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:24Z] INFO  18:24:11,098 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:24Z] INFO  18:24:11,099 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:24Z] INFO  18:24:11,103 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/14/R14-18102_kapa-NGv3-PE100-NGv3-sort-14_19553416_35066851-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/14/R14-18102_kapa-NGv3-PE100-NGv3-14_19553416_35066851-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/14/tx/tmpnn9x7g/R14-18102_kapa-NGv3-PE100-NGv3-14_19553416_35066851.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:24Z] INFO  18:24:11,114 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:24Z] INFO  18:24:11,121 HelpFormatter - Date/Time: 2016/04/14 18:24:11
[2016-04-15T01:24Z] INFO  18:24:11,122 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:24Z] INFO  18:24:11,123 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:24Z] WARN  18:24:11,168 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T01:24Z] WARN  18:24:11,187 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/14/tx/tmpnn9x7g/R14-18102_kapa-NGv3-PE100-NGv3-14_19553416_35066851.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T01:24Z] INFO  18:24:11,223 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:24Z] INFO  18:24:11,409 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:24Z] GATK: HaplotypeCaller
[2016-04-15T01:24Z] INFO  18:24:11,601 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T01:24Z] INFO  18:24:11,605 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.048858473000000006
[2016-04-15T01:24Z] INFO  18:24:11,606 PairHMM - Total compute time in PairHMM computeLikelihoods() : 4.58477882
[2016-04-15T01:24Z] INFO  18:24:11,607 HaplotypeCaller - Ran local assembly on 2349 active regions
[2016-04-15T01:24Z] INFO  18:24:11,621 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:24Z] INFO  18:24:11,670 ProgressMeter -            done     2.23715124E8    88.0 s            0.0 s      100.0%    88.0 s       0.0 s
[2016-04-15T01:24Z] INFO  18:24:11,670 ProgressMeter - Total runtime 88.05 secs, 1.47 min, 0.02 hours
[2016-04-15T01:24Z] INFO  18:24:11,671 MicroScheduler - 43036 reads were filtered out during the traversal out of approximately 496757 total reads (8.66%)
[2016-04-15T01:24Z] INFO  18:24:11,671 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:24Z] INFO  18:24:11,671 MicroScheduler -   -> 39720 reads (8.00% of total) failing DuplicateReadFilter
[2016-04-15T01:24Z] INFO  18:24:11,672 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:24Z] INFO  18:24:11,672 MicroScheduler -   -> 3316 reads (0.67% of total) failing HCMappingQualityFilter
[2016-04-15T01:24Z] INFO  18:24:11,672 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:24Z] INFO  18:24:11,672 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:24Z] INFO  18:24:11,672 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:24Z] INFO  18:24:11,673 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T01:24Z] INFO  18:24:11,684 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-15T01:24Z] INFO  18:24:11,720 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T01:24Z] INFO  18:24:12,156 IntervalUtils - Processing 291951 bp from intervals
[2016-04-15T01:24Z] WARN  18:24:12,161 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:24Z] INFO  18:24:12,235 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:24Z] INFO  18:24:12,361 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:24Z] INFO  18:24:12,361 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:24Z] INFO  18:24:12,362 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T01:24Z] INFO  18:24:12,362 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T01:24Z] INFO  18:24:12,365 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T01:24Z] INFO  18:24:12,365 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T01:24Z] INFO  18:24:12,545 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T01:24Z] INFO  18:24:13,139 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:24Z] GATK: HaplotypeCaller
[2016-04-15T01:24Z] INFO  18:24:14,088 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:24Z] INFO  18:24:14,091 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:24Z] INFO  18:24:14,092 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:24Z] INFO  18:24:14,092 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:24Z] INFO  18:24:14,100 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/14/R14-18102_kapa-NGv3-PE100-NGv3-sort-14_35072553_50583270-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/14/R14-18102_kapa-NGv3-PE100-NGv3-14_35072553_50583270-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/14/tx/tmpEWYQgi/R14-18102_kapa-NGv3-PE100-NGv3-14_35072553_50583270.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:24Z] INFO  18:24:14,110 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:24Z] INFO  18:24:14,111 HelpFormatter - Date/Time: 2016/04/14 18:24:14
[2016-04-15T01:24Z] INFO  18:24:14,112 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:24Z] INFO  18:24:14,112 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:24Z] WARN  18:24:14,136 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T01:24Z] WARN  18:24:14,139 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/14/tx/tmpEWYQgi/R14-18102_kapa-NGv3-PE100-NGv3-14_35072553_50583270.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T01:24Z] INFO  18:24:14,342 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:24Z] INFO  18:24:14,532 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T01:24Z] INFO  18:24:14,542 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:24Z] INFO  18:24:14,589 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.015884147
[2016-04-15T01:24Z] INFO  18:24:14,591 PairHMM - Total compute time in PairHMM computeLikelihoods() : 0.6285736620000001
[2016-04-15T01:24Z] INFO  18:24:14,591 HaplotypeCaller - Ran local assembly on 1562 active regions
[2016-04-15T01:24Z] INFO  18:24:14,647 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.10
[2016-04-15T01:24Z] INFO  18:24:14,647 ProgressMeter -            done     1.17482682E8    49.0 s            0.0 s      100.0%    49.0 s       0.0 s
[2016-04-15T01:24Z] INFO  18:24:14,647 ProgressMeter - Total runtime 49.88 secs, 0.83 min, 0.01 hours
[2016-04-15T01:24Z] INFO  18:24:14,648 MicroScheduler - 21786 reads were filtered out during the traversal out of approximately 266279 total reads (8.18%)
[2016-04-15T01:24Z] INFO  18:24:14,648 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:24Z] INFO  18:24:14,648 MicroScheduler -   -> 21480 reads (8.07% of total) failing DuplicateReadFilter
[2016-04-15T01:24Z] INFO  18:24:14,649 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:24Z] INFO  18:24:14,650 MicroScheduler -   -> 306 reads (0.11% of total) failing HCMappingQualityFilter
[2016-04-15T01:24Z] INFO  18:24:14,650 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:24Z] INFO  18:24:14,650 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:24Z] INFO  18:24:14,650 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:24Z] INFO  18:24:14,651 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T01:24Z] INFO  18:24:14,671 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T01:24Z] INFO  18:24:14,772 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.023227916
[2016-04-15T01:24Z] INFO  18:24:14,773 PairHMM - Total compute time in PairHMM computeLikelihoods() : 20.858593045000003
[2016-04-15T01:24Z] INFO  18:24:14,773 HaplotypeCaller - Ran local assembly on 1024 active regions
[2016-04-15T01:24Z] INFO  18:24:14,839 ProgressMeter -            done        4.31997E7    69.0 s            1.0 s      100.0%    69.0 s       0.0 s
[2016-04-15T01:24Z] INFO  18:24:14,840 ProgressMeter - Total runtime 69.55 secs, 1.16 min, 0.02 hours
[2016-04-15T01:24Z] INFO  18:24:14,840 MicroScheduler - 17680 reads were filtered out during the traversal out of approximately 184211 total reads (9.60%)
[2016-04-15T01:24Z] INFO  18:24:14,841 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:24Z] INFO  18:24:14,841 MicroScheduler -   -> 15063 reads (8.18% of total) failing DuplicateReadFilter
[2016-04-15T01:24Z] INFO  18:24:14,841 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:24Z] INFO  18:24:14,841 MicroScheduler -   -> 2617 reads (1.42% of total) failing HCMappingQualityFilter
[2016-04-15T01:24Z] INFO  18:24:14,842 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:24Z] INFO  18:24:14,842 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:24Z] INFO  18:24:14,842 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:24Z] INFO  18:24:14,843 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T01:24Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T01:24Z] INFO  18:24:15,002 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T01:24Z] INFO  18:24:15,003 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T01:24Z] INFO  18:24:15,009 IntervalUtils - Processing 108903 bp from intervals
[2016-04-15T01:24Z] WARN  18:24:15,015 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:24Z] INFO  18:24:15,097 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:24Z] INFO  18:24:15,172 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:24Z] INFO  18:24:15,173 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:24Z] INFO  18:24:15,174 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T01:24Z] INFO  18:24:15,175 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T01:24Z] INFO  18:24:15,176 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T01:24Z] INFO  18:24:15,176 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T01:24Z] INFO  18:24:15,365 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T01:24Z] WARN  18:24:15,486 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T01:24Z] WARN  18:24:15,487 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T01:24Z] INFO  18:24:15,948 ProgressMeter -     12:12248254     1.97289592E8    90.0 s            0.0 s       86.6%   103.0 s      13.0 s
[2016-04-15T01:24Z] INFO  18:24:16,153 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:24Z] INFO  18:24:16,209 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:24Z] GATK: HaplotypeCaller
[2016-04-15T01:24Z] GATK: HaplotypeCaller
[2016-04-15T01:24Z] INFO  18:24:16,611 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:24Z] INFO  18:24:16,614 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:24Z] INFO  18:24:16,615 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:24Z] INFO  18:24:16,615 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:24Z] INFO  18:24:16,620 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/14/R14-18102_kapa-NGv3-PE100-NGv3-sort-14_50585061_66096324-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/14/R14-18102_kapa-NGv3-PE100-NGv3-14_50585061_66096324-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/14/tx/tmpXMpbb1/R14-18102_kapa-NGv3-PE100-NGv3-14_50585061_66096324.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:24Z] INFO  18:24:16,633 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:24Z] INFO  18:24:16,633 HelpFormatter - Date/Time: 2016/04/14 18:24:16
[2016-04-15T01:24Z] INFO  18:24:16,633 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:24Z] INFO  18:24:16,634 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:24Z] WARN  18:24:16,711 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T01:24Z] WARN  18:24:16,713 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/14/tx/tmpXMpbb1/R14-18102_kapa-NGv3-PE100-NGv3-14_50585061_66096324.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T01:24Z] INFO  18:24:16,987 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:24Z] INFO  18:24:17,224 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T01:24Z] INFO  18:24:17,241 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:24Z] INFO  18:24:17,326 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-15T01:24Z] INFO  18:24:17,346 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T01:24Z] INFO  18:24:17,928 IntervalUtils - Processing 226771 bp from intervals
[2016-04-15T01:24Z] WARN  18:24:17,945 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:24Z] INFO  18:24:17,987 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.005762139
[2016-04-15T01:24Z] INFO  18:24:17,988 PairHMM - Total compute time in PairHMM computeLikelihoods() : 0.081774124
[2016-04-15T01:24Z] INFO  18:24:17,988 HaplotypeCaller - Ran local assembly on 476 active regions
[2016-04-15T01:24Z] INFO  18:24:18,037 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:24Z] INFO  18:24:18,078 ProgressMeter -            done      1.1587684E7    23.0 s            1.0 s      100.0%    23.0 s       0.0 s
[2016-04-15T01:24Z] INFO  18:24:18,078 ProgressMeter - Total runtime 23.10 secs, 0.39 min, 0.01 hours
[2016-04-15T01:24Z] INFO  18:24:18,079 MicroScheduler - 6697 reads were filtered out during the traversal out of approximately 83012 total reads (8.07%)
[2016-04-15T01:24Z] INFO  18:24:18,079 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:24Z] INFO  18:24:18,079 MicroScheduler -   -> 6615 reads (7.97% of total) failing DuplicateReadFilter
[2016-04-15T01:24Z] INFO  18:24:18,079 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:24Z] INFO  18:24:18,080 MicroScheduler -   -> 82 reads (0.10% of total) failing HCMappingQualityFilter
[2016-04-15T01:24Z] INFO  18:24:18,080 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:24Z] INFO  18:24:18,080 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:24Z] INFO  18:24:18,080 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:24Z] INFO  18:24:18,081 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T01:24Z] INFO  18:24:18,171 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:24Z] INFO  18:24:18,172 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:24Z] INFO  18:24:18,173 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T01:24Z] INFO  18:24:18,180 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T01:24Z] INFO  18:24:18,185 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T01:24Z] INFO  18:24:18,201 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T01:24Z] INFO  18:24:18,387 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T01:24Z] INFO  18:24:19,401 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:24Z] INFO  18:24:19,404 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:24Z] INFO  18:24:19,405 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:24Z] INFO  18:24:19,405 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:24Z] INFO  18:24:19,412 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/14/R14-18102_kapa-NGv3-PE100-NGv3-sort-14_81651874_97299968-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/14/R14-18102_kapa-NGv3-PE100-NGv3-14_81651874_97299968-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/14/tx/tmpzuVGYS/R14-18102_kapa-NGv3-PE100-NGv3-14_81651874_97299968.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:24Z] INFO  18:24:19,422 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:24Z] INFO  18:24:19,423 HelpFormatter - Date/Time: 2016/04/14 18:24:19
[2016-04-15T01:24Z] INFO  18:24:19,423 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:24Z] INFO  18:24:19,423 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:24Z] WARN  18:24:19,452 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T01:24Z] INFO  18:24:19,450 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:24Z] INFO  18:24:19,453 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:24Z] INFO  18:24:19,453 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:24Z] INFO  18:24:19,454 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:24Z] WARN  18:24:19,454 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/14/tx/tmpzuVGYS/R14-18102_kapa-NGv3-PE100-NGv3-14_81651874_97299968.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T01:24Z] INFO  18:24:19,458 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/14/R14-18102_kapa-NGv3-PE100-NGv3-sort-14_66135960_81646674-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/14/R14-18102_kapa-NGv3-PE100-NGv3-14_66135960_81646674-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/14/tx/tmpmsIssz/R14-18102_kapa-NGv3-PE100-NGv3-14_66135960_81646674.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:24Z] INFO  18:24:19,488 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:24Z] INFO  18:24:19,489 HelpFormatter - Date/Time: 2016/04/14 18:24:19
[2016-04-15T01:24Z] INFO  18:24:19,490 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:24Z] INFO  18:24:19,491 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:24Z] INFO  18:24:19,508 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:24Z] WARN  18:24:19,514 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T01:24Z] WARN  18:24:19,517 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/14/tx/tmpmsIssz/R14-18102_kapa-NGv3-PE100-NGv3-14_66135960_81646674.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T01:24Z] INFO  18:24:19,681 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:24Z] INFO  18:24:19,686 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:24Z] GATK: HaplotypeCaller
[2016-04-15T01:24Z] INFO  18:24:19,885 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T01:24Z] INFO  18:24:19,895 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:24Z] INFO  18:24:19,902 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T01:24Z] INFO  18:24:19,912 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:24Z] INFO  18:24:19,954 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-15T01:24Z] INFO  18:24:19,969 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T01:24Z] INFO  18:24:20,005 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.09
[2016-04-15T01:24Z] INFO  18:24:20,045 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T01:24Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T01:24Z] INFO  18:24:20,133 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T01:24Z] INFO  18:24:20,134 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T01:24Z] WARN  18:24:20,339 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T01:24Z] WARN  18:24:20,340 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T01:24Z] INFO  18:24:20,394 IntervalUtils - Processing 245410 bp from intervals
[2016-04-15T01:24Z] WARN  18:24:20,399 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:24Z] INFO  18:24:20,471 IntervalUtils - Processing 176504 bp from intervals
[2016-04-15T01:24Z] WARN  18:24:20,476 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:24Z] INFO  18:24:20,500 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:24Z] INFO  18:24:20,583 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:24Z] INFO  18:24:20,592 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:24Z] INFO  18:24:20,593 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:24Z] INFO  18:24:20,593 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T01:24Z] INFO  18:24:20,594 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T01:24Z] INFO  18:24:20,595 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T01:24Z] INFO  18:24:20,595 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T01:24Z] INFO  18:24:20,637 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.036046519
[2016-04-15T01:24Z] INFO  18:24:20,638 PairHMM - Total compute time in PairHMM computeLikelihoods() : 12.763785403
[2016-04-15T01:24Z] INFO  18:24:20,639 HaplotypeCaller - Ran local assembly on 2299 active regions
[2016-04-15T01:24Z] INFO  18:24:20,681 ProgressMeter -            done     1.96753928E8   105.0 s            0.0 s      100.0%   105.0 s       0.0 s
[2016-04-15T01:24Z] INFO  18:24:20,682 ProgressMeter - Total runtime 105.92 secs, 1.77 min, 0.03 hours
[2016-04-15T01:24Z] INFO  18:24:20,683 MicroScheduler - 57909 reads were filtered out during the traversal out of approximately 522256 total reads (11.09%)
[2016-04-15T01:24Z] INFO  18:24:20,686 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:24Z] INFO  18:24:20,686 MicroScheduler -   -> 41419 reads (7.93% of total) failing DuplicateReadFilter
[2016-04-15T01:24Z] INFO  18:24:20,686 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:24Z] INFO  18:24:20,686 MicroScheduler -   -> 16490 reads (3.16% of total) failing HCMappingQualityFilter
[2016-04-15T01:24Z] INFO  18:24:20,687 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:24Z] INFO  18:24:20,687 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:24Z] INFO  18:24:20,687 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:24Z] INFO  18:24:20,687 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T01:24Z] INFO  18:24:20,692 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:24Z] INFO  18:24:20,694 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:24Z] INFO  18:24:20,695 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T01:24Z] INFO  18:24:20,695 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T01:24Z] INFO  18:24:20,696 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T01:24Z] INFO  18:24:20,696 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T01:24Z] INFO  18:24:20,856 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T01:24Z] INFO  18:24:20,958 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T01:24Z] INFO  18:24:21,596 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.008367411
[2016-04-15T01:24Z] INFO  18:24:21,598 PairHMM - Total compute time in PairHMM computeLikelihoods() : 0.457996577
[2016-04-15T01:24Z] INFO  18:24:21,599 HaplotypeCaller - Ran local assembly on 1274 active regions
[2016-04-15T01:24Z] INFO  18:24:21,644 ProgressMeter -            done      7.9081089E7    45.0 s            0.0 s      100.0%    45.0 s       0.0 s
[2016-04-15T01:24Z] INFO  18:24:21,644 ProgressMeter - Total runtime 45.27 secs, 0.75 min, 0.01 hours
[2016-04-15T01:24Z] INFO  18:24:21,644 MicroScheduler - 18284 reads were filtered out during the traversal out of approximately 218479 total reads (8.37%)
[2016-04-15T01:24Z] INFO  18:24:21,645 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:24Z] INFO  18:24:21,645 MicroScheduler -   -> 17312 reads (7.92% of total) failing DuplicateReadFilter
[2016-04-15T01:24Z] INFO  18:24:21,645 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:24Z] INFO  18:24:21,645 MicroScheduler -   -> 972 reads (0.44% of total) failing HCMappingQualityFilter
[2016-04-15T01:24Z] INFO  18:24:21,646 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:24Z] INFO  18:24:21,646 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:24Z] INFO  18:24:21,646 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:24Z] INFO  18:24:21,646 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T01:24Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T01:24Z] INFO  18:24:22,030 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T01:24Z] INFO  18:24:22,031 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T01:24Z] INFO  18:24:22,242 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:24Z] WARN  18:24:22,490 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T01:24Z] WARN  18:24:22,491 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T01:24Z] GATK: HaplotypeCaller
[2016-04-15T01:24Z] INFO  18:24:23,063 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:24Z] INFO  18:24:23,141 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:24Z] INFO  18:24:23,145 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:24Z] INFO  18:24:23,145 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:24Z] INFO  18:24:23,146 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:24Z] INFO  18:24:23,150 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/14/R14-18102_kapa-NGv3-PE100-NGv3-sort-14_97304098_107349540-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/14/R14-18102_kapa-NGv3-PE100-NGv3-14_97304098_107349540-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/14/tx/tmpkeLofW/R14-18102_kapa-NGv3-PE100-NGv3-14_97304098_107349540.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:24Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T01:24Z] INFO  18:24:23,162 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T01:24Z] INFO  18:24:23,164 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T01:24Z] INFO  18:24:23,175 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:24Z] INFO  18:24:23,176 HelpFormatter - Date/Time: 2016/04/14 18:24:23
[2016-04-15T01:24Z] INFO  18:24:23,177 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:24Z] INFO  18:24:23,178 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:24Z] WARN  18:24:23,211 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T01:24Z] WARN  18:24:23,225 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/14/tx/tmpkeLofW/R14-18102_kapa-NGv3-PE100-NGv3-14_97304098_107349540.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T01:24Z] GATK: HaplotypeCaller
[2016-04-15T01:24Z] INFO  18:24:23,344 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.004884019000000001
[2016-04-15T01:24Z] INFO  18:24:23,345 PairHMM - Total compute time in PairHMM computeLikelihoods() : 0.34585725100000003
[2016-04-15T01:24Z] INFO  18:24:23,345 HaplotypeCaller - Ran local assembly on 594 active regions
[2016-04-15T01:24Z] INFO  18:24:23,399 ProgressMeter -            done      1.7240277E7    27.0 s            1.0 s      100.0%    27.0 s       0.0 s
[2016-04-15T01:24Z] INFO  18:24:23,399 ProgressMeter - Total runtime 27.11 secs, 0.45 min, 0.01 hours
[2016-04-15T01:24Z] INFO  18:24:23,400 MicroScheduler - 9080 reads were filtered out during the traversal out of approximately 109609 total reads (8.28%)
[2016-04-15T01:24Z] INFO  18:24:23,400 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:24Z] INFO  18:24:23,400 MicroScheduler -   -> 8919 reads (8.14% of total) failing DuplicateReadFilter
[2016-04-15T01:24Z] INFO  18:24:23,401 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:24Z] INFO  18:24:23,401 MicroScheduler -   -> 161 reads (0.15% of total) failing HCMappingQualityFilter
[2016-04-15T01:24Z] INFO  18:24:23,401 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:24Z] INFO  18:24:23,402 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:24Z] INFO  18:24:23,402 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:24Z] INFO  18:24:23,402 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T01:24Z] WARN  18:24:23,400 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T01:24Z] WARN  18:24:23,413 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T01:24Z] INFO  18:24:23,437 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:24Z] INFO  18:24:23,609 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T01:24Z] INFO  18:24:23,619 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:24Z] INFO  18:24:23,716 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.09
[2016-04-15T01:24Z] INFO  18:24:23,734 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T01:24Z] INFO  18:24:24,187 IntervalUtils - Processing 188545 bp from intervals
[2016-04-15T01:24Z] WARN  18:24:24,192 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:24Z] INFO  18:24:24,311 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:24Z] INFO  18:24:24,409 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:24Z] INFO  18:24:24,411 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:24Z] INFO  18:24:24,411 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T01:24Z] INFO  18:24:24,412 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T01:24Z] INFO  18:24:24,438 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T01:24Z] INFO  18:24:24,439 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T01:24Z] INFO  18:24:24,649 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T01:24Z] INFO  18:24:24,815 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:24Z] GATK: HaplotypeCaller
[2016-04-15T01:24Z] INFO  18:24:25,232 ProgressMeter -    12:122248192     1.76178326E8    60.0 s            0.0 s       70.1%    85.0 s      25.0 s
[2016-04-15T01:24Z] INFO  18:24:25,443 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.037758083000000005
[2016-04-15T01:24Z] INFO  18:24:25,444 PairHMM - Total compute time in PairHMM computeLikelihoods() : 8.926130338
[2016-04-15T01:24Z] INFO  18:24:25,445 HaplotypeCaller - Ran local assembly on 2529 active regions
[2016-04-15T01:24Z] INFO  18:24:25,487 ProgressMeter -            done     2.60606733E8    99.0 s            0.0 s      100.0%    99.0 s       0.0 s
[2016-04-15T01:24Z] INFO  18:24:25,488 ProgressMeter - Total runtime 99.58 secs, 1.66 min, 0.03 hours
[2016-04-15T01:24Z] INFO  18:24:25,488 MicroScheduler - 52459 reads were filtered out during the traversal out of approximately 515734 total reads (10.17%)
[2016-04-15T01:24Z] INFO  18:24:25,489 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:24Z] INFO  18:24:25,490 MicroScheduler -   -> 40365 reads (7.83% of total) failing DuplicateReadFilter
[2016-04-15T01:24Z] INFO  18:24:25,490 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:24Z] INFO  18:24:25,491 MicroScheduler -   -> 12094 reads (2.35% of total) failing HCMappingQualityFilter
[2016-04-15T01:24Z] INFO  18:24:25,492 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:24Z] INFO  18:24:25,492 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:24Z] INFO  18:24:25,493 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:24Z] INFO  18:24:25,493 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T01:24Z] INFO  18:24:25,545 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:24Z] INFO  18:24:25,547 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:24Z] INFO  18:24:25,547 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:24Z] INFO  18:24:25,553 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:24Z] INFO  18:24:25,578 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/15/R14-18102_kapa-NGv3-PE100-NGv3-sort-15_0_20740485-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/15/R14-18102_kapa-NGv3-PE100-NGv3-15_0_20740485-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/15/tx/tmpS44UbH/R14-18102_kapa-NGv3-PE100-NGv3-15_0_20740485.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:24Z] INFO  18:24:25,602 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:24Z] INFO  18:24:25,602 HelpFormatter - Date/Time: 2016/04/14 18:24:25
[2016-04-15T01:24Z] INFO  18:24:25,602 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:24Z] INFO  18:24:25,602 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:24Z] WARN  18:24:25,672 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T01:24Z] WARN  18:24:25,674 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/15/tx/tmpS44UbH/R14-18102_kapa-NGv3-PE100-NGv3-15_0_20740485.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T01:24Z] INFO  18:24:25,936 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:24Z] INFO  18:24:25,940 ProgressMeter -      11:1092899      1.2877009E7   120.0 s            9.0 s       18.8%    10.6 m       8.6 m
[2016-04-15T01:24Z] INFO  18:24:26,133 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T01:24Z] INFO  18:24:26,142 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:24Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T01:24Z] INFO  18:24:26,177 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T01:24Z] INFO  18:24:26,178 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T01:24Z] INFO  18:24:26,226 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-15T01:24Z] INFO  18:24:26,240 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T01:24Z] WARN  18:24:26,428 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T01:24Z] WARN  18:24:26,440 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T01:24Z] INFO  18:24:26,679 IntervalUtils - Processing 989 bp from intervals
[2016-04-15T01:24Z] WARN  18:24:26,683 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:24Z] INFO  18:24:26,794 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:24Z] INFO  18:24:26,815 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:24Z] INFO  18:24:26,819 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:24Z] INFO  18:24:26,819 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:24Z] INFO  18:24:26,820 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:24Z] INFO  18:24:26,824 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/15/R14-18102_kapa-NGv3-PE100-NGv3-sort-15_20741621_36872162-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/15/R14-18102_kapa-NGv3-PE100-NGv3-15_20741621_36872162-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/15/tx/tmpcaJoCs/R14-18102_kapa-NGv3-PE100-NGv3-15_20741621_36872162.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:24Z] INFO  18:24:26,844 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:24Z] INFO  18:24:26,871 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:24Z] INFO  18:24:26,872 HelpFormatter - Date/Time: 2016/04/14 18:24:26
[2016-04-15T01:24Z] INFO  18:24:26,873 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:24Z] INFO  18:24:26,873 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:24Z] INFO  18:24:26,880 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:24Z] INFO  18:24:26,881 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:24Z] INFO  18:24:26,882 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T01:24Z] INFO  18:24:26,882 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T01:24Z] INFO  18:24:26,895 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T01:24Z] INFO  18:24:26,896 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T01:24Z] WARN  18:24:26,908 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T01:24Z] WARN  18:24:26,926 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/15/tx/tmpcaJoCs/R14-18102_kapa-NGv3-PE100-NGv3-15_20741621_36872162.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T01:24Z] GATK: HaplotypeCaller
[2016-04-15T01:24Z] INFO  18:24:27,128 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T01:24Z] INFO  18:24:27,180 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:24Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T01:24Z] INFO  18:24:27,328 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T01:24Z] INFO  18:24:27,328 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T01:24Z] INFO  18:24:27,442 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T01:24Z] INFO  18:24:27,451 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:24Z] INFO  18:24:27,536 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-15T01:24Z] INFO  18:24:27,563 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T01:24Z] WARN  18:24:27,844 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T01:24Z] WARN  18:24:27,845 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T01:24Z] INFO  18:24:28,070 IntervalUtils - Processing 177979 bp from intervals
[2016-04-15T01:24Z] WARN  18:24:28,075 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:24Z] INFO  18:24:28,166 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:24Z] INFO  18:24:28,255 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:24Z] INFO  18:24:28,256 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:24Z] INFO  18:24:28,257 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T01:24Z] INFO  18:24:28,258 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T01:24Z] INFO  18:24:28,259 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T01:24Z] INFO  18:24:28,259 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T01:24Z] INFO  18:24:28,451 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T01:24Z] INFO  18:24:28,648 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:24Z] INFO  18:24:28,656 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:24Z] INFO  18:24:28,657 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:24Z] INFO  18:24:28,658 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:24Z] INFO  18:24:28,662 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/15/R14-18102_kapa-NGv3-PE100-NGv3-sort-15_36887086_52402170-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/15/R14-18102_kapa-NGv3-PE100-NGv3-15_36887086_52402170-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/15/tx/tmptPyhDT/R14-18102_kapa-NGv3-PE100-NGv3-15_36887086_52402170.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:24Z] INFO  18:24:28,688 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:24Z] INFO  18:24:28,688 HelpFormatter - Date/Time: 2016/04/14 18:24:28
[2016-04-15T01:24Z] INFO  18:24:28,689 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:24Z] INFO  18:24:28,689 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:24Z] WARN  18:24:28,734 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T01:24Z] WARN  18:24:28,739 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/15/tx/tmptPyhDT/R14-18102_kapa-NGv3-PE100-NGv3-15_36887086_52402170.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T01:24Z] INFO  18:24:29,003 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:24Z] INFO  18:24:29,364 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T01:24Z] INFO  18:24:29,386 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:24Z] INFO  18:24:29,498 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.10
[2016-04-15T01:24Z] INFO  18:24:29,522 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T01:24Z] INFO  18:24:30,197 IntervalUtils - Processing 374190 bp from intervals
[2016-04-15T01:24Z] WARN  18:24:30,203 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:24Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T01:24Z] INFO  18:24:30,341 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T01:24Z] INFO  18:24:30,341 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T01:24Z] INFO  18:24:30,353 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:24Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T01:24Z] INFO  18:24:30,447 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T01:24Z] INFO  18:24:30,457 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T01:24Z] WARN  18:24:30,496 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T01:24Z] WARN  18:24:30,497 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T01:24Z] INFO  18:24:30,554 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:24Z] INFO  18:24:30,554 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:24Z] INFO  18:24:30,555 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T01:24Z] INFO  18:24:30,555 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T01:24Z] INFO  18:24:30,567 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T01:24Z] INFO  18:24:30,568 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T01:24Z] INFO  18:24:30,654 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:24Z] INFO  18:24:30,658 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:24Z] INFO  18:24:30,658 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:24Z] INFO  18:24:30,659 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:24Z] INFO  18:24:30,663 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/15/R14-18102_kapa-NGv3-PE100-NGv3-sort-15_52404364_67923265-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/15/R14-18102_kapa-NGv3-PE100-NGv3-15_52404364_67923265-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/15/tx/tmpfa2JlB/R14-18102_kapa-NGv3-PE100-NGv3-15_52404364_67923265.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:24Z] INFO  18:24:30,673 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:24Z] INFO  18:24:30,674 HelpFormatter - Date/Time: 2016/04/14 18:24:30
[2016-04-15T01:24Z] INFO  18:24:30,674 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:24Z] INFO  18:24:30,675 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:24Z] WARN  18:24:30,698 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T01:24Z] WARN  18:24:30,701 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/15/tx/tmpfa2JlB/R14-18102_kapa-NGv3-PE100-NGv3-15_52404364_67923265.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T01:24Z] WARN  18:24:30,891 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T01:24Z] INFO  18:24:30,891 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:24Z] WARN  18:24:30,892 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T01:24Z] INFO  18:24:30,914 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T01:24Z] INFO  18:24:31,090 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T01:24Z] INFO  18:24:31,100 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:24Z] INFO  18:24:31,209 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.10
[2016-04-15T01:24Z] INFO  18:24:31,233 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T01:24Z] INFO  18:24:31,815 IntervalUtils - Processing 254619 bp from intervals
[2016-04-15T01:24Z] WARN  18:24:31,821 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:24Z] INFO  18:24:31,909 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:24Z] INFO  18:24:32,060 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:24Z] INFO  18:24:32,061 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:24Z] INFO  18:24:32,062 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T01:24Z] INFO  18:24:32,063 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T01:24Z] INFO  18:24:32,064 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T01:24Z] INFO  18:24:32,064 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T01:24Z] INFO  18:24:32,266 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T01:24Z] INFO  18:24:32,547 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.0026871660000000004
[2016-04-15T01:24Z] INFO  18:24:32,549 PairHMM - Total compute time in PairHMM computeLikelihoods() : 0.087905383
[2016-04-15T01:24Z] INFO  18:24:32,549 HaplotypeCaller - Ran local assembly on 7 active regions
[2016-04-15T01:24Z] INFO  18:24:32,598 ProgressMeter -            done            989.0     5.0 s           96.3 m       99.9%     5.0 s       0.0 s
[2016-04-15T01:24Z] INFO  18:24:32,599 ProgressMeter - Total runtime 5.72 secs, 0.10 min, 0.00 hours
[2016-04-15T01:24Z] INFO  18:24:32,599 MicroScheduler - 1727 reads were filtered out during the traversal out of approximately 2695 total reads (64.08%)
[2016-04-15T01:24Z] INFO  18:24:32,599 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:24Z] INFO  18:24:32,600 MicroScheduler -   -> 70 reads (2.60% of total) failing DuplicateReadFilter
[2016-04-15T01:24Z] INFO  18:24:32,600 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:24Z] INFO  18:24:32,600 MicroScheduler -   -> 1657 reads (61.48% of total) failing HCMappingQualityFilter
[2016-04-15T01:24Z] INFO  18:24:32,601 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:24Z] INFO  18:24:32,601 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:24Z] INFO  18:24:32,601 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:24Z] INFO  18:24:32,601 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T01:24Z] INFO  18:24:33,090 ProgressMeter -    13:113745032      2.3899994E7    30.0 s            1.0 s       70.4%    42.0 s      12.0 s
[2016-04-15T01:24Z] INFO  18:24:34,050 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:24Z] INFO  18:24:34,359 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.010502625
[2016-04-15T01:24Z] INFO  18:24:34,370 PairHMM - Total compute time in PairHMM computeLikelihoods() : 6.176230022
[2016-04-15T01:24Z] INFO  18:24:34,371 HaplotypeCaller - Ran local assembly on 1407 active regions
[2016-04-15T01:24Z] INFO  18:24:34,402 ProgressMeter -            done      9.1028011E7    59.0 s            0.0 s      100.0%    59.0 s       0.0 s
[2016-04-15T01:24Z] INFO  18:24:34,402 ProgressMeter - Total runtime 59.68 secs, 0.99 min, 0.02 hours
[2016-04-15T01:24Z] INFO  18:24:34,403 MicroScheduler - 20924 reads were filtered out during the traversal out of approximately 239313 total reads (8.74%)
[2016-04-15T01:24Z] INFO  18:24:34,403 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:24Z] INFO  18:24:34,403 MicroScheduler -   -> 19125 reads (7.99% of total) failing DuplicateReadFilter
[2016-04-15T01:24Z] INFO  18:24:34,404 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:24Z] INFO  18:24:34,404 MicroScheduler -   -> 1799 reads (0.75% of total) failing HCMappingQualityFilter
[2016-04-15T01:24Z] INFO  18:24:34,404 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:24Z] INFO  18:24:34,404 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:24Z] INFO  18:24:34,405 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:24Z] INFO  18:24:34,405 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T01:24Z] GATK: HaplotypeCaller
[2016-04-15T01:24Z] INFO  18:24:35,877 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:24Z] GATK: HaplotypeCaller
[2016-04-15T01:24Z] INFO  18:24:36,318 ProgressMeter -     12:56869408     3.40574599E8    90.0 s            0.0 s       79.0%   113.0 s      23.0 s
[2016-04-15T01:24Z] INFO  18:24:36,903 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.03435077
[2016-04-15T01:24Z] INFO  18:24:36,904 PairHMM - Total compute time in PairHMM computeLikelihoods() : 4.119882684
[2016-04-15T01:24Z] INFO  18:24:36,904 HaplotypeCaller - Ran local assembly on 3832 active regions
[2016-04-15T01:24Z] INFO  18:24:36,957 ProgressMeter -            done     6.10283322E8   117.0 s            0.0 s      100.0%   117.0 s       0.0 s
[2016-04-15T01:24Z] INFO  18:24:36,958 ProgressMeter - Total runtime 118.00 secs, 1.97 min, 0.03 hours
[2016-04-15T01:24Z] INFO  18:24:36,959 MicroScheduler - 74882 reads were filtered out during the traversal out of approximately 875530 total reads (8.55%)
[2016-04-15T01:24Z] INFO  18:24:36,959 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:24Z] INFO  18:24:36,959 MicroScheduler -   -> 70805 reads (8.09% of total) failing DuplicateReadFilter
[2016-04-15T01:24Z] INFO  18:24:36,960 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:24Z] INFO  18:24:36,960 MicroScheduler -   -> 4077 reads (0.47% of total) failing HCMappingQualityFilter
[2016-04-15T01:24Z] INFO  18:24:36,960 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:24Z] INFO  18:24:36,960 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:24Z] INFO  18:24:36,961 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:24Z] INFO  18:24:36,961 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T01:24Z] INFO  18:24:38,039 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:24Z] INFO  18:24:38,042 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:24Z] INFO  18:24:38,043 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:24Z] INFO  18:24:38,043 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:24Z] INFO  18:24:38,048 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/15/R14-18102_kapa-NGv3-PE100-NGv3-sort-15_67932890_83447639-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/15/R14-18102_kapa-NGv3-PE100-NGv3-15_67932890_83447639-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/15/tx/tmpRxX4Fa/R14-18102_kapa-NGv3-PE100-NGv3-15_67932890_83447639.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:24Z] INFO  18:24:38,078 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:24Z] INFO  18:24:38,079 HelpFormatter - Date/Time: 2016/04/14 18:24:38
[2016-04-15T01:24Z] INFO  18:24:38,080 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:24Z] INFO  18:24:38,080 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:24Z] WARN  18:24:38,125 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T01:24Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T01:24Z] WARN  18:24:38,140 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/15/tx/tmpRxX4Fa/R14-18102_kapa-NGv3-PE100-NGv3-15_67932890_83447639.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T01:24Z] INFO  18:24:38,147 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T01:24Z] INFO  18:24:38,148 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T01:24Z] INFO  18:24:38,334 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:24Z] INFO  18:24:38,456 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:24Z] WARN  18:24:38,526 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T01:24Z] WARN  18:24:38,527 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T01:24Z] INFO  18:24:38,535 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T01:24Z] INFO  18:24:38,544 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:24Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T01:24Z] INFO  18:24:38,593 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T01:24Z] INFO  18:24:38,594 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T01:24Z] INFO  18:24:38,657 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.11
[2016-04-15T01:24Z] INFO  18:24:38,680 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T01:24Z] GATK: HaplotypeCaller
[2016-04-15T01:24Z] WARN  18:24:38,896 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T01:24Z] WARN  18:24:38,897 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T01:24Z] INFO  18:24:39,201 IntervalUtils - Processing 293221 bp from intervals
[2016-04-15T01:24Z] WARN  18:24:39,207 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:24Z] INFO  18:24:39,299 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:24Z] INFO  18:24:39,473 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:24Z] INFO  18:24:39,473 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:24Z] INFO  18:24:39,474 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T01:24Z] INFO  18:24:39,488 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T01:24Z] INFO  18:24:39,518 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T01:24Z] INFO  18:24:39,519 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T01:24Z] INFO  18:24:39,701 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:24Z] INFO  18:24:39,703 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:24Z] INFO  18:24:39,703 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:24Z] INFO  18:24:39,703 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:24Z] INFO  18:24:39,727 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/15/R14-18102_kapa-NGv3-PE100-NGv3-sort-15_83448996_98982979-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/15/R14-18102_kapa-NGv3-PE100-NGv3-15_83448996_98982979-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/15/tx/tmpVcn72l/R14-18102_kapa-NGv3-PE100-NGv3-15_83448996_98982979.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:24Z] INFO  18:24:39,741 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:24Z] INFO  18:24:39,741 HelpFormatter - Date/Time: 2016/04/14 18:24:39
[2016-04-15T01:24Z] INFO  18:24:39,741 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:24Z] INFO  18:24:39,742 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:24Z] INFO  18:24:39,771 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T01:24Z] WARN  18:24:39,783 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T01:24Z] WARN  18:24:39,785 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/15/tx/tmpVcn72l/R14-18102_kapa-NGv3-PE100-NGv3-15_83448996_98982979.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T01:24Z] INFO  18:24:40,062 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:24Z] INFO  18:24:40,251 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T01:24Z] INFO  18:24:40,272 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:24Z] INFO  18:24:40,357 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-15T01:24Z] INFO  18:24:40,381 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T01:24Z] INFO  18:24:40,880 IntervalUtils - Processing 184993 bp from intervals
[2016-04-15T01:24Z] WARN  18:24:40,885 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:24Z] INFO  18:24:40,956 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:24Z] INFO  18:24:41,070 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:24Z] INFO  18:24:41,071 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:24Z] INFO  18:24:41,072 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T01:24Z] INFO  18:24:41,073 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T01:24Z] INFO  18:24:41,074 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T01:24Z] INFO  18:24:41,074 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T01:24Z] INFO  18:24:41,314 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T01:24Z] INFO  18:24:42,139 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:24Z] INFO  18:24:42,143 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:24Z] INFO  18:24:42,143 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:24Z] INFO  18:24:42,165 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:24Z] INFO  18:24:42,170 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/15/R14-18102_kapa-NGv3-PE100-NGv3-sort-15_98984299_102531392-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/15/R14-18102_kapa-NGv3-PE100-NGv3-15_98984299_102531392-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/15/tx/tmpQoIRMt/R14-18102_kapa-NGv3-PE100-NGv3-15_98984299_102531392.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:24Z] INFO  18:24:42,210 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:24Z] INFO  18:24:42,211 HelpFormatter - Date/Time: 2016/04/14 18:24:42
[2016-04-15T01:24Z] INFO  18:24:42,215 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:24Z] INFO  18:24:42,220 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:24Z] WARN  18:24:42,279 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T01:24Z] WARN  18:24:42,283 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/15/tx/tmpQoIRMt/R14-18102_kapa-NGv3-PE100-NGv3-15_98984299_102531392.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T01:24Z] INFO  18:24:42,391 ProgressMeter -     14:21896162      1.1260782E7    30.0 s            2.0 s       26.0%   115.0 s      85.0 s
[2016-04-15T01:24Z] INFO  18:24:42,576 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:24Z] INFO  18:24:42,744 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.011540080000000001
[2016-04-15T01:24Z] INFO  18:24:42,745 PairHMM - Total compute time in PairHMM computeLikelihoods() : 0.406969399
[2016-04-15T01:24Z] INFO  18:24:42,746 HaplotypeCaller - Ran local assembly on 1034 active regions
[2016-04-15T01:24Z] INFO  18:24:42,791 ProgressMeter -            done      4.9965812E7    39.0 s            0.0 s      100.0%    39.0 s       0.0 s
[2016-04-15T01:24Z] INFO  18:24:42,791 ProgressMeter - Total runtime 39.72 secs, 0.66 min, 0.01 hours
[2016-04-15T01:24Z] INFO  18:24:42,792 MicroScheduler - 17037 reads were filtered out during the traversal out of approximately 206724 total reads (8.24%)
[2016-04-15T01:24Z] INFO  18:24:42,792 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:24Z] INFO  18:24:42,793 MicroScheduler -   -> 16457 reads (7.96% of total) failing DuplicateReadFilter
[2016-04-15T01:24Z] INFO  18:24:42,793 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:24Z] INFO  18:24:42,793 MicroScheduler -   -> 580 reads (0.28% of total) failing HCMappingQualityFilter
[2016-04-15T01:24Z] INFO  18:24:42,794 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:24Z] INFO  18:24:42,794 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:24Z] INFO  18:24:42,794 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:24Z] INFO  18:24:42,794 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T01:24Z] INFO  18:24:42,887 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T01:24Z] INFO  18:24:42,905 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:24Z] INFO  18:24:42,989 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-15T01:24Z] INFO  18:24:43,036 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T01:24Z] INFO  18:24:43,463 IntervalUtils - Processing 49123 bp from intervals
[2016-04-15T01:24Z] WARN  18:24:43,469 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:24Z] INFO  18:24:43,596 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:24Z] INFO  18:24:43,670 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:24Z] INFO  18:24:43,671 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:24Z] INFO  18:24:43,671 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T01:24Z] INFO  18:24:43,672 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T01:24Z] INFO  18:24:43,687 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T01:24Z] INFO  18:24:43,687 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T01:24Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T01:24Z] INFO  18:24:43,884 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T01:24Z] INFO  18:24:43,885 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T01:24Z] INFO  18:24:43,926 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T01:24Z] INFO  18:24:44,112 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:24Z] WARN  18:24:44,116 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T01:24Z] WARN  18:24:44,118 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T01:24Z] GATK: HaplotypeCaller
[2016-04-15T01:24Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T01:24Z] INFO  18:24:45,113 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T01:24Z] INFO  18:24:45,121 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T01:24Z] INFO  18:24:45,193 ProgressMeter -     14:50044530      1.6913418E7    30.0 s            1.0 s       83.7%    35.0 s       5.0 s
[2016-04-15T01:24Z] WARN  18:24:45,499 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T01:24Z] WARN  18:24:45,504 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T01:24Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T01:24Z] INFO  18:24:45,932 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T01:24Z] INFO  18:24:45,933 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T01:24Z] WARN  18:24:46,235 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T01:24Z] WARN  18:24:46,236 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T01:24Z] INFO  18:24:47,185 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:24Z] INFO  18:24:47,188 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:24Z] INFO  18:24:47,189 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:24Z] INFO  18:24:47,189 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:24Z] INFO  18:24:47,193 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/16/R14-18102_kapa-NGv3-PE100-NGv3-sort-16_0_15528616-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/16/R14-18102_kapa-NGv3-PE100-NGv3-16_0_15528616-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/16/tx/tmplFjqvp/R14-18102_kapa-NGv3-PE100-NGv3-16_0_15528616.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:24Z] INFO  18:24:47,216 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:24Z] INFO  18:24:47,216 HelpFormatter - Date/Time: 2016/04/14 18:24:47
[2016-04-15T01:24Z] INFO  18:24:47,216 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:24Z] INFO  18:24:47,217 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:24Z] WARN  18:24:47,244 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T01:24Z] WARN  18:24:47,247 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/16/tx/tmplFjqvp/R14-18102_kapa-NGv3-PE100-NGv3-16_0_15528616.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T01:24Z] INFO  18:24:47,424 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:24Z] INFO  18:24:47,684 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T01:24Z] INFO  18:24:47,693 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:24Z] INFO  18:24:47,828 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.13
[2016-04-15T01:24Z] INFO  18:24:47,855 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T01:24Z] INFO  18:24:48,191 ProgressMeter -     14:58675771      2.9705521E7    30.0 s            1.0 s       45.2%    66.0 s      36.0 s
[2016-04-15T01:24Z] INFO  18:24:48,381 IntervalUtils - Processing 436708 bp from intervals
[2016-04-15T01:24Z] WARN  18:24:48,386 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:24Z] INFO  18:24:48,533 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:24Z] INFO  18:24:48,705 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:24Z] INFO  18:24:48,706 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:24Z] INFO  18:24:48,706 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T01:24Z] INFO  18:24:48,706 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T01:24Z] INFO  18:24:48,718 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T01:24Z] INFO  18:24:48,719 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T01:24Z] INFO  18:24:48,803 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.030059019000000003
[2016-04-15T01:24Z] INFO  18:24:48,804 PairHMM - Total compute time in PairHMM computeLikelihoods() : 2.263470029
[2016-04-15T01:24Z] INFO  18:24:48,804 HaplotypeCaller - Ran local assembly on 2718 active regions
[2016-04-15T01:24Z] INFO  18:24:48,868 ProgressMeter -            done     3.54367305E8    83.0 s            0.0 s      100.0%    83.0 s       0.0 s
[2016-04-15T01:24Z] INFO  18:24:48,869 ProgressMeter - Total runtime 83.66 secs, 1.39 min, 0.02 hours
[2016-04-15T01:24Z] INFO  18:24:48,869 MicroScheduler - 48936 reads were filtered out during the traversal out of approximately 585549 total reads (8.36%)
[2016-04-15T01:24Z] INFO  18:24:48,871 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:24Z] INFO  18:24:48,871 MicroScheduler -   -> 47304 reads (8.08% of total) failing DuplicateReadFilter
[2016-04-15T01:24Z] INFO  18:24:48,871 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:24Z] INFO  18:24:48,871 MicroScheduler -   -> 1632 reads (0.28% of total) failing HCMappingQualityFilter
[2016-04-15T01:24Z] INFO  18:24:48,872 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:24Z] INFO  18:24:48,872 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:24Z] INFO  18:24:48,872 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:24Z] INFO  18:24:48,872 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T01:24Z] INFO  18:24:48,983 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T01:24Z] INFO  18:24:49,407 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.006067925
[2016-04-15T01:24Z] INFO  18:24:49,408 PairHMM - Total compute time in PairHMM computeLikelihoods() : 0.296930913
[2016-04-15T01:24Z] INFO  18:24:49,408 HaplotypeCaller - Ran local assembly on 765 active regions
[2016-04-15T01:24Z] INFO  18:24:49,618 ProgressMeter -            done      2.6446189E7    34.0 s            1.0 s      100.0%    34.0 s       0.0 s
[2016-04-15T01:24Z] INFO  18:24:49,618 ProgressMeter - Total runtime 34.44 secs, 0.57 min, 0.01 hours
[2016-04-15T01:24Z] INFO  18:24:49,619 MicroScheduler - 10320 reads were filtered out during the traversal out of approximately 116451 total reads (8.86%)
[2016-04-15T01:24Z] INFO  18:24:49,619 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:24Z] INFO  18:24:49,619 MicroScheduler -   -> 9190 reads (7.89% of total) failing DuplicateReadFilter
[2016-04-15T01:24Z] INFO  18:24:49,619 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:24Z] INFO  18:24:49,620 MicroScheduler -   -> 1130 reads (0.97% of total) failing HCMappingQualityFilter
[2016-04-15T01:24Z] INFO  18:24:49,620 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:24Z] INFO  18:24:49,620 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:24Z] INFO  18:24:49,620 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:24Z] INFO  18:24:49,620 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T01:24Z] INFO  18:24:50,464 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:24Z] INFO  18:24:50,617 ProgressMeter -     14:71429048      1.1022885E7    30.0 s            2.0 s       30.3%    98.0 s      68.0 s
[2016-04-15T01:24Z] INFO  18:24:50,715 ProgressMeter -     14:92548776      1.9297129E7    30.0 s            1.0 s       48.6%    61.0 s      31.0 s
[2016-04-15T01:24Z] GATK: HaplotypeCaller
[2016-04-15T01:24Z] INFO  18:24:51,192 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:24Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T01:24Z] INFO  18:24:51,380 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T01:24Z] INFO  18:24:51,381 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T01:24Z] GATK: HaplotypeCaller
[2016-04-15T01:24Z] WARN  18:24:51,608 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T01:24Z] WARN  18:24:51,609 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T01:24Z] INFO  18:24:53,798 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:24Z] INFO  18:24:53,812 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:24Z] INFO  18:24:53,813 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:24Z] INFO  18:24:53,814 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:24Z] INFO  18:24:53,819 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/16/R14-18102_kapa-NGv3-PE100-NGv3-sort-16_15596122_31106473-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/16/R14-18102_kapa-NGv3-PE100-NGv3-16_15596122_31106473-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/16/tx/tmpTcHe37/R14-18102_kapa-NGv3-PE100-NGv3-16_15596122_31106473.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:24Z] INFO  18:24:53,839 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:24Z] INFO  18:24:53,840 HelpFormatter - Date/Time: 2016/04/14 18:24:53
[2016-04-15T01:24Z] INFO  18:24:53,840 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:24Z] INFO  18:24:53,840 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:24Z] WARN  18:24:53,870 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T01:24Z] WARN  18:24:53,873 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/16/tx/tmpTcHe37/R14-18102_kapa-NGv3-PE100-NGv3-16_15596122_31106473.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T01:24Z] INFO  18:24:54,136 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:24Z] INFO  18:24:54,344 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T01:24Z] INFO  18:24:54,364 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:24Z] INFO  18:24:54,440 ProgressMeter -    14:103410929      1.1866348E7    30.0 s            2.0 s       42.1%    71.0 s      41.0 s
[2016-04-15T01:24Z] INFO  18:24:54,444 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-15T01:24Z] INFO  18:24:54,467 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T01:24Z] INFO  18:24:54,764 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:24Z] INFO  18:24:54,767 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:24Z] INFO  18:24:54,767 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:24Z] INFO  18:24:54,768 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:24Z] INFO  18:24:54,772 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/16/R14-18102_kapa-NGv3-PE100-NGv3-sort-16_31120544_46629582-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/16/R14-18102_kapa-NGv3-PE100-NGv3-16_31120544_46629582-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/16/tx/tmpO_3pVE/R14-18102_kapa-NGv3-PE100-NGv3-16_31120544_46629582.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:24Z] INFO  18:24:54,819 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:24Z] INFO  18:24:54,820 HelpFormatter - Date/Time: 2016/04/14 18:24:54
[2016-04-15T01:24Z] INFO  18:24:54,820 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:24Z] INFO  18:24:54,820 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:24Z] WARN  18:24:54,865 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T01:24Z] WARN  18:24:54,878 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/16/tx/tmpO_3pVE/R14-18102_kapa-NGv3-PE100-NGv3-16_31120544_46629582.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T01:24Z] INFO  18:24:55,052 IntervalUtils - Processing 400248 bp from intervals
[2016-04-15T01:24Z] WARN  18:24:55,057 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:24Z] INFO  18:24:55,139 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:24Z] INFO  18:24:55,150 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:24Z] INFO  18:24:55,311 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T01:24Z] INFO  18:24:55,315 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:24Z] INFO  18:24:55,316 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:24Z] INFO  18:24:55,316 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T01:24Z] INFO  18:24:55,316 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T01:24Z] INFO  18:24:55,321 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:24Z] INFO  18:24:55,327 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T01:24Z] INFO  18:24:55,337 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T01:24Z] INFO  18:24:55,383 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-15T01:24Z] INFO  18:24:55,397 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T01:24Z] INFO  18:24:55,578 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T01:24Z] INFO  18:24:55,697 IntervalUtils - Processing 40143 bp from intervals
[2016-04-15T01:24Z] WARN  18:24:55,702 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:24Z] INFO  18:24:55,796 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:24Z] INFO  18:24:55,853 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:24Z] INFO  18:24:55,854 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:24Z] INFO  18:24:55,855 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T01:24Z] INFO  18:24:55,855 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T01:24Z] INFO  18:24:55,856 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T01:24Z] INFO  18:24:55,856 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T01:24Z] INFO  18:24:55,941 ProgressMeter -      11:1263732       1.733857E7     2.5 m            8.0 s       21.8%    11.5 m       9.0 m
[2016-04-15T01:24Z] INFO  18:24:56,089 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T01:24Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T01:24Z] INFO  18:24:57,087 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T01:24Z] INFO  18:24:57,088 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T01:24Z] WARN  18:24:57,440 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T01:24Z] WARN  18:24:57,441 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T01:24Z] INFO  18:24:58,294 ProgressMeter -     15:28117009        4494115.0    30.0 s            6.0 s       26.9%   111.0 s      81.0 s
[2016-04-15T01:24Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T01:24Z] INFO  18:24:58,709 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T01:24Z] INFO  18:24:58,710 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T01:24Z] WARN  18:24:59,066 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T01:24Z] WARN  18:24:59,077 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T01:24Z] INFO  18:24:59,646 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.036822104
[2016-04-15T01:24Z] INFO  18:24:59,647 PairHMM - Total compute time in PairHMM computeLikelihoods() : 1.686964605
[2016-04-15T01:24Z] INFO  18:24:59,648 HaplotypeCaller - Ran local assembly on 3729 active regions
[2016-04-15T01:24Z] INFO  18:24:59,680 ProgressMeter -            done     5.48735474E8   113.0 s            0.0 s      100.0%   113.0 s       0.0 s
[2016-04-15T01:24Z] INFO  18:24:59,680 ProgressMeter - Total runtime 113.38 secs, 1.89 min, 0.03 hours
[2016-04-15T01:24Z] INFO  18:24:59,681 MicroScheduler - 77779 reads were filtered out during the traversal out of approximately 845347 total reads (9.20%)
[2016-04-15T01:24Z] INFO  18:24:59,681 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:24Z] INFO  18:24:59,681 MicroScheduler -   -> 67341 reads (7.97% of total) failing DuplicateReadFilter
[2016-04-15T01:24Z] INFO  18:24:59,681 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:24Z] INFO  18:24:59,682 MicroScheduler -   -> 10438 reads (1.23% of total) failing HCMappingQualityFilter
[2016-04-15T01:24Z] INFO  18:24:59,682 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:24Z] INFO  18:24:59,682 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:24Z] INFO  18:24:59,682 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:24Z] INFO  18:24:59,683 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T01:25Z] INFO  18:25:00,571 ProgressMeter -     15:41319934      1.2503078E7    30.0 s            2.0 s       21.0%     2.4 m     113.0 s
[2016-04-15T01:25Z] INFO  18:25:01,251 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:25Z] GATK: HaplotypeCaller
[2016-04-15T01:25Z] INFO  18:25:02,096 ProgressMeter -     15:59450486      2.0628455E7    30.0 s            1.0 s       36.4%    82.0 s      52.0 s
[2016-04-15T01:25Z] INFO  18:25:04,847 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:25Z] INFO  18:25:04,850 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:25Z] INFO  18:25:04,851 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:25Z] INFO  18:25:04,852 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:25Z] INFO  18:25:04,856 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/16/R14-18102_kapa-NGv3-PE100-NGv3-sort-16_46633742_64982002-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/16/R14-18102_kapa-NGv3-PE100-NGv3-16_46633742_64982002-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/16/tx/tmpoOFvXv/R14-18102_kapa-NGv3-PE100-NGv3-16_46633742_64982002.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:25Z] INFO  18:25:04,867 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:25Z] INFO  18:25:04,868 HelpFormatter - Date/Time: 2016/04/14 18:25:04
[2016-04-15T01:25Z] INFO  18:25:04,868 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:25Z] INFO  18:25:04,869 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:25Z] INFO  18:25:04,921 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.016918744
[2016-04-15T01:25Z] INFO  18:25:04,922 PairHMM - Total compute time in PairHMM computeLikelihoods() : 0.339171027
[2016-04-15T01:25Z] WARN  18:25:04,922 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T01:25Z] INFO  18:25:04,923 HaplotypeCaller - Ran local assembly on 364 active regions
[2016-04-15T01:25Z] WARN  18:25:04,925 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/16/tx/tmpoOFvXv/R14-18102_kapa-NGv3-PE100-NGv3-16_46633742_64982002.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T01:25Z] INFO  18:25:05,008 ProgressMeter -            done        5654523.0    21.0 s            3.0 s      100.0%    21.0 s       0.0 s
[2016-04-15T01:25Z] INFO  18:25:05,008 ProgressMeter - Total runtime 21.34 secs, 0.36 min, 0.01 hours
[2016-04-15T01:25Z] INFO  18:25:05,008 MicroScheduler - 8374 reads were filtered out during the traversal out of approximately 75297 total reads (11.12%)
[2016-04-15T01:25Z] INFO  18:25:05,009 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:25Z] INFO  18:25:05,009 MicroScheduler -   -> 5683 reads (7.55% of total) failing DuplicateReadFilter
[2016-04-15T01:25Z] INFO  18:25:05,009 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:25Z] INFO  18:25:05,010 MicroScheduler -   -> 2691 reads (3.57% of total) failing HCMappingQualityFilter
[2016-04-15T01:25Z] INFO  18:25:05,010 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:25Z] INFO  18:25:05,010 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:25Z] INFO  18:25:05,010 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:25Z] INFO  18:25:05,011 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T01:25Z] INFO  18:25:05,136 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:25Z] INFO  18:25:05,391 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T01:25Z] INFO  18:25:05,400 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:25Z] INFO  18:25:05,472 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-15T01:25Z] INFO  18:25:05,487 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T01:25Z] INFO  18:25:05,851 IntervalUtils - Processing 224129 bp from intervals
[2016-04-15T01:25Z] WARN  18:25:05,864 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:25Z] INFO  18:25:06,002 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:25Z] INFO  18:25:06,141 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:25Z] INFO  18:25:06,142 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:25Z] INFO  18:25:06,142 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T01:25Z] INFO  18:25:06,142 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T01:25Z] INFO  18:25:06,158 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T01:25Z] INFO  18:25:06,159 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T01:25Z] INFO  18:25:06,366 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T01:25Z] INFO  18:25:06,466 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:25Z] GATK: HaplotypeCaller
[2016-04-15T01:25Z] INFO  18:25:09,417 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:25Z] INFO  18:25:09,421 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:25Z] INFO  18:25:09,421 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:25Z] INFO  18:25:09,422 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:25Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T01:25Z] INFO  18:25:09,426 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/16/R14-18102_kapa-NGv3-PE100-NGv3-sort-16_64982511_80574976-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/16/R14-18102_kapa-NGv3-PE100-NGv3-16_64982511_80574976-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/16/tx/tmp7qGl9z/R14-18102_kapa-NGv3-PE100-NGv3-16_64982511_80574976.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:25Z] INFO  18:25:09,447 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:25Z] INFO  18:25:09,448 HelpFormatter - Date/Time: 2016/04/14 18:25:09
[2016-04-15T01:25Z] INFO  18:25:09,449 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:25Z] INFO  18:25:09,449 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:25Z] INFO  18:25:09,446 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T01:25Z] INFO  18:25:09,447 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T01:25Z] WARN  18:25:09,490 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T01:25Z] WARN  18:25:09,493 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/16/tx/tmp7qGl9z/R14-18102_kapa-NGv3-PE100-NGv3-16_64982511_80574976.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T01:25Z] INFO  18:25:09,521 ProgressMeter -     15:74369359      2.4033167E7    30.0 s            1.0 s       34.0%    88.0 s      58.0 s
[2016-04-15T01:25Z] INFO  18:25:09,753 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:25Z] WARN  18:25:09,789 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T01:25Z] WARN  18:25:09,789 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T01:25Z] INFO  18:25:09,915 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T01:25Z] INFO  18:25:09,925 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:25Z] INFO  18:25:10,003 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-15T01:25Z] INFO  18:25:10,026 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T01:25Z] INFO  18:25:10,411 IntervalUtils - Processing 344918 bp from intervals
[2016-04-15T01:25Z] WARN  18:25:10,416 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:25Z] INFO  18:25:10,485 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:25Z] INFO  18:25:10,575 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:25Z] INFO  18:25:10,576 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:25Z] INFO  18:25:10,577 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T01:25Z] INFO  18:25:10,577 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T01:25Z] INFO  18:25:10,578 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T01:25Z] INFO  18:25:10,578 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T01:25Z] INFO  18:25:10,766 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T01:25Z] INFO  18:25:11,003 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.011640745000000001
[2016-04-15T01:25Z] INFO  18:25:11,004 PairHMM - Total compute time in PairHMM computeLikelihoods() : 0.7476280860000001
[2016-04-15T01:25Z] INFO  18:25:11,005 HaplotypeCaller - Ran local assembly on 1292 active regions
[2016-04-15T01:25Z] INFO  18:25:11,069 ProgressMeter -            done      7.6164079E7    50.0 s            0.0 s      100.0%    50.0 s       0.0 s
[2016-04-15T01:25Z] INFO  18:25:11,069 ProgressMeter - Total runtime 50.38 secs, 0.84 min, 0.01 hours
[2016-04-15T01:25Z] INFO  18:25:11,069 MicroScheduler - 19156 reads were filtered out during the traversal out of approximately 236937 total reads (8.08%)
[2016-04-15T01:25Z] INFO  18:25:11,070 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:25Z] INFO  18:25:11,070 MicroScheduler -   -> 18760 reads (7.92% of total) failing DuplicateReadFilter
[2016-04-15T01:25Z] INFO  18:25:11,070 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:25Z] INFO  18:25:11,071 MicroScheduler -   -> 396 reads (0.17% of total) failing HCMappingQualityFilter
[2016-04-15T01:25Z] INFO  18:25:11,071 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:25Z] INFO  18:25:11,071 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:25Z] INFO  18:25:11,072 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:25Z] INFO  18:25:11,072 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T01:25Z] INFO  18:25:11,095 ProgressMeter -     15:89843031      1.6345872E7    30.0 s            1.0 s       47.0%    63.0 s      33.0 s
[2016-04-15T01:25Z] INFO  18:25:12,116 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.00428461
[2016-04-15T01:25Z] INFO  18:25:12,117 PairHMM - Total compute time in PairHMM computeLikelihoods() : 0.096287146
[2016-04-15T01:25Z] INFO  18:25:12,117 HaplotypeCaller - Ran local assembly on 303 active regions
[2016-04-15T01:25Z] INFO  18:25:12,162 ProgressMeter -            done        2938200.0    16.0 s            5.0 s      100.0%    16.0 s       0.0 s
[2016-04-15T01:25Z] INFO  18:25:12,163 ProgressMeter - Total runtime 16.31 secs, 0.27 min, 0.00 hours
[2016-04-15T01:25Z] INFO  18:25:12,164 MicroScheduler - 18180 reads were filtered out during the traversal out of approximately 76303 total reads (23.83%)
[2016-04-15T01:25Z] INFO  18:25:12,164 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:25Z] INFO  18:25:12,165 MicroScheduler -   -> 5197 reads (6.81% of total) failing DuplicateReadFilter
[2016-04-15T01:25Z] INFO  18:25:12,176 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:25Z] INFO  18:25:12,177 MicroScheduler -   -> 12983 reads (17.02% of total) failing HCMappingQualityFilter
[2016-04-15T01:25Z] INFO  18:25:12,178 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:25Z] INFO  18:25:12,178 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:25Z] INFO  18:25:12,179 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:25Z] INFO  18:25:12,180 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T01:25Z] INFO  18:25:12,397 ProgressMeter -     14:24736866      7.6464434E7    60.0 s            0.0 s       71.3%    84.0 s      24.0 s
[2016-04-15T01:25Z] INFO  18:25:12,410 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:25Z] GATK: HaplotypeCaller
[2016-04-15T01:25Z] INFO  18:25:13,470 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.025133854
[2016-04-15T01:25Z] INFO  18:25:13,471 PairHMM - Total compute time in PairHMM computeLikelihoods() : 0.715778437
[2016-04-15T01:25Z] INFO  18:25:13,472 HaplotypeCaller - Ran local assembly on 1654 active regions
[2016-04-15T01:25Z] INFO  18:25:13,502 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:25Z] INFO  18:25:13,530 ProgressMeter -            done     1.18736277E8    55.0 s            0.0 s      100.0%    55.0 s       0.0 s
[2016-04-15T01:25Z] INFO  18:25:13,531 ProgressMeter - Total runtime 55.36 secs, 0.92 min, 0.02 hours
[2016-04-15T01:25Z] INFO  18:25:13,532 MicroScheduler - 23218 reads were filtered out during the traversal out of approximately 285063 total reads (8.14%)
[2016-04-15T01:25Z] INFO  18:25:13,533 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:25Z] INFO  18:25:13,533 MicroScheduler -   -> 22860 reads (8.02% of total) failing DuplicateReadFilter
[2016-04-15T01:25Z] INFO  18:25:13,533 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:25Z] INFO  18:25:13,534 MicroScheduler -   -> 358 reads (0.13% of total) failing HCMappingQualityFilter
[2016-04-15T01:25Z] INFO  18:25:13,534 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:25Z] INFO  18:25:13,534 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:25Z] INFO  18:25:13,534 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:25Z] INFO  18:25:13,535 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T01:25Z] GATK: HaplotypeCaller
[2016-04-15T01:25Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T01:25Z] INFO  18:25:14,114 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T01:25Z] INFO  18:25:14,116 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T01:25Z] WARN  18:25:14,307 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T01:25Z] WARN  18:25:14,307 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T01:25Z] INFO  18:25:14,864 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:25Z] GATK: HaplotypeCaller
[2016-04-15T01:25Z] INFO  18:25:15,777 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:25Z] INFO  18:25:15,780 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:25Z] INFO  18:25:15,780 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:25Z] INFO  18:25:15,780 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:25Z] INFO  18:25:15,796 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/16/R14-18102_kapa-NGv3-PE100-NGv3-sort-16_80575258_90354753-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/16/R14-18102_kapa-NGv3-PE100-NGv3-16_80575258_90354753-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/16/tx/tmphlFjaz/R14-18102_kapa-NGv3-PE100-NGv3-16_80575258_90354753.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:25Z] INFO  18:25:15,833 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:25Z] INFO  18:25:15,833 HelpFormatter - Date/Time: 2016/04/14 18:25:15
[2016-04-15T01:25Z] INFO  18:25:15,834 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:25Z] INFO  18:25:15,839 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:25Z] WARN  18:25:15,895 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T01:25Z] WARN  18:25:15,899 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/16/tx/tmphlFjaz/R14-18102_kapa-NGv3-PE100-NGv3-16_80575258_90354753.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T01:25Z] INFO  18:25:16,099 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:25Z] INFO  18:25:16,319 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T01:25Z] INFO  18:25:16,331 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:25Z] INFO  18:25:16,397 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-15T01:25Z] INFO  18:25:16,422 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T01:25Z] INFO  18:25:16,564 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:25Z] INFO  18:25:16,567 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:25Z] INFO  18:25:16,568 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:25Z] INFO  18:25:16,568 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:25Z] INFO  18:25:16,573 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/17/R14-18102_kapa-NGv3-PE100-NGv3-sort-17_0_15511002-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/17/R14-18102_kapa-NGv3-PE100-NGv3-17_0_15511002-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/17/tx/tmpuLXVl2/R14-18102_kapa-NGv3-PE100-NGv3-17_0_15511002.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:25Z] INFO  18:25:16,597 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:25Z] INFO  18:25:16,598 HelpFormatter - Date/Time: 2016/04/14 18:25:16
[2016-04-15T01:25Z] INFO  18:25:16,598 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:25Z] INFO  18:25:16,599 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:25Z] WARN  18:25:16,649 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T01:25Z] WARN  18:25:16,652 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/17/tx/tmpuLXVl2/R14-18102_kapa-NGv3-PE100-NGv3-17_0_15511002.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T01:25Z] INFO  18:25:16,926 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:25Z] INFO  18:25:16,984 IntervalUtils - Processing 203451 bp from intervals
[2016-04-15T01:25Z] WARN  18:25:16,989 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:25Z] INFO  18:25:17,108 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:25Z] INFO  18:25:17,097 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T01:25Z] INFO  18:25:17,128 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:25Z] INFO  18:25:17,182 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:25Z] INFO  18:25:17,183 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:25Z] INFO  18:25:17,184 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T01:25Z] INFO  18:25:17,184 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T01:25Z] INFO  18:25:17,185 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T01:25Z] INFO  18:25:17,185 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T01:25Z] INFO  18:25:17,212 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-15T01:25Z] INFO  18:25:17,241 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T01:25Z] INFO  18:25:17,441 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T01:25Z] INFO  18:25:17,659 IntervalUtils - Processing 497719 bp from intervals
[2016-04-15T01:25Z] WARN  18:25:17,665 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:25Z] INFO  18:25:17,779 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:25Z] INFO  18:25:17,970 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:25Z] INFO  18:25:17,971 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:25Z] INFO  18:25:17,972 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T01:25Z] INFO  18:25:17,973 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T01:25Z] INFO  18:25:17,973 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T01:25Z] INFO  18:25:17,973 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T01:25Z] INFO  18:25:18,165 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:25Z] INFO  18:25:18,168 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:25Z] INFO  18:25:18,169 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:25Z] INFO  18:25:18,169 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:25Z] INFO  18:25:18,178 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/17/R14-18102_kapa-NGv3-PE100-NGv3-sort-17_15515955_31039213-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/17/R14-18102_kapa-NGv3-PE100-NGv3-17_15515955_31039213-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/17/tx/tmpxqXu_2/R14-18102_kapa-NGv3-PE100-NGv3-17_15515955_31039213.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:25Z] INFO  18:25:18,188 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:25Z] INFO  18:25:18,198 HelpFormatter - Date/Time: 2016/04/14 18:25:18
[2016-04-15T01:25Z] INFO  18:25:18,199 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:25Z] INFO  18:25:18,200 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:25Z] INFO  18:25:18,206 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T01:25Z] WARN  18:25:18,245 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T01:25Z] WARN  18:25:18,248 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/17/tx/tmpxqXu_2/R14-18102_kapa-NGv3-PE100-NGv3-17_15515955_31039213.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T01:25Z] INFO  18:25:18,530 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:25Z] INFO  18:25:18,723 ProgressMeter -      16:1268220      1.1361429E7    30.0 s            2.0 s       20.2%     2.5 m     118.0 s
[2016-04-15T01:25Z] INFO  18:25:18,741 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T01:25Z] INFO  18:25:18,751 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:25Z] INFO  18:25:18,846 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.10
[2016-04-15T01:25Z] INFO  18:25:18,868 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T01:25Z] INFO  18:25:19,440 IntervalUtils - Processing 320055 bp from intervals
[2016-04-15T01:25Z] WARN  18:25:19,446 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:25Z] INFO  18:25:19,520 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:25Z] INFO  18:25:19,676 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:25Z] INFO  18:25:19,688 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:25Z] INFO  18:25:19,689 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T01:25Z] INFO  18:25:19,690 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T01:25Z] INFO  18:25:19,701 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T01:25Z] INFO  18:25:19,702 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T01:25Z] INFO  18:25:19,947 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T01:25Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T01:25Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T01:25Z] INFO  18:25:20,270 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T01:25Z] INFO  18:25:20,271 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T01:25Z] INFO  18:25:20,278 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T01:25Z] INFO  18:25:20,279 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T01:25Z] WARN  18:25:20,534 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T01:25Z] WARN  18:25:20,535 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T01:25Z] INFO  18:25:20,618 ProgressMeter -     14:77797412     1.12261122E8    60.0 s            0.0 s       86.8%    69.0 s       9.0 s
[2016-04-15T01:25Z] WARN  18:25:20,628 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T01:25Z] WARN  18:25:20,629 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T01:25Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T01:25Z] INFO  18:25:21,773 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T01:25Z] INFO  18:25:21,774 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T01:25Z] WARN  18:25:22,076 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T01:25Z] WARN  18:25:22,078 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T01:25Z] INFO  18:25:24,442 ProgressMeter -    14:105996131       6.412159E7    60.0 s            0.0 s      100.0%    60.0 s       0.0 s
[2016-04-15T01:25Z] INFO  18:25:24,492 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.030494835
[2016-04-15T01:25Z] INFO  18:25:24,493 PairHMM - Total compute time in PairHMM computeLikelihoods() : 2.0375629770000003
[2016-04-15T01:25Z] INFO  18:25:24,494 HaplotypeCaller - Ran local assembly on 1349 active regions
[2016-04-15T01:25Z] INFO  18:25:24,527 ProgressMeter -            done      6.4310135E7    60.0 s            0.0 s      100.0%    60.0 s       0.0 s
[2016-04-15T01:25Z] INFO  18:25:24,538 ProgressMeter - Total runtime 60.13 secs, 1.00 min, 0.02 hours
[2016-04-15T01:25Z] INFO  18:25:24,538 MicroScheduler - 27402 reads were filtered out during the traversal out of approximately 318375 total reads (8.61%)
[2016-04-15T01:25Z] INFO  18:25:24,539 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:25Z] INFO  18:25:24,539 MicroScheduler -   -> 26472 reads (8.31% of total) failing DuplicateReadFilter
[2016-04-15T01:25Z] INFO  18:25:24,539 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:25Z] INFO  18:25:24,539 MicroScheduler -   -> 930 reads (0.29% of total) failing HCMappingQualityFilter
[2016-04-15T01:25Z] INFO  18:25:24,540 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:25Z] INFO  18:25:24,540 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:25Z] INFO  18:25:24,540 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:25Z] INFO  18:25:24,540 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T01:25Z] INFO  18:25:25,339 ProgressMeter -     16:20975906      2.7852489E7    30.0 s            1.0 s       26.2%   114.0 s      84.0 s
[2016-04-15T01:25Z] INFO  18:25:25,470 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.014003117
[2016-04-15T01:25Z] INFO  18:25:25,470 PairHMM - Total compute time in PairHMM computeLikelihoods() : 5.589583394
[2016-04-15T01:25Z] INFO  18:25:25,470 HaplotypeCaller - Ran local assembly on 1316 active regions
[2016-04-15T01:25Z] INFO  18:25:25,521 ProgressMeter -            done      7.2457776E7    57.0 s            0.0 s      100.0%    57.0 s       0.0 s
[2016-04-15T01:25Z] INFO  18:25:25,522 ProgressMeter - Total runtime 57.27 secs, 0.95 min, 0.02 hours
[2016-04-15T01:25Z] INFO  18:25:25,522 MicroScheduler - 117051 reads were filtered out during the traversal out of approximately 331563 total reads (35.30%)
[2016-04-15T01:25Z] INFO  18:25:25,522 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:25Z] INFO  18:25:25,523 MicroScheduler -   -> 18938 reads (5.71% of total) failing DuplicateReadFilter
[2016-04-15T01:25Z] INFO  18:25:25,523 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:25Z] INFO  18:25:25,523 MicroScheduler -   -> 98113 reads (29.59% of total) failing HCMappingQualityFilter
[2016-04-15T01:25Z] INFO  18:25:25,523 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:25Z] INFO  18:25:25,524 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:25Z] INFO  18:25:25,524 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:25Z] INFO  18:25:25,524 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T01:25Z] INFO  18:25:25,945 ProgressMeter -      11:4080626      6.2214696E7     3.0 m            2.0 s       38.9%     7.7 m       4.7 m
[2016-04-15T01:25Z] INFO  18:25:25,956 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:25Z] GATK: HaplotypeCaller
[2016-04-15T01:25Z] INFO  18:25:26,879 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:25Z] GATK: HaplotypeCaller
[2016-04-15T01:25Z] INFO  18:25:28,209 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.014623919
[2016-04-15T01:25Z] INFO  18:25:28,210 PairHMM - Total compute time in PairHMM computeLikelihoods() : 2.116284718
[2016-04-15T01:25Z] INFO  18:25:28,211 HaplotypeCaller - Ran local assembly on 1800 active regions
[2016-04-15T01:25Z] INFO  18:25:28,247 ProgressMeter -            done     1.48859234E8    67.0 s            0.0 s      100.0%    67.0 s       0.0 s
[2016-04-15T01:25Z] INFO  18:25:28,248 ProgressMeter - Total runtime 67.66 secs, 1.13 min, 0.02 hours
[2016-04-15T01:25Z] INFO  18:25:28,248 MicroScheduler - 31741 reads were filtered out during the traversal out of approximately 369770 total reads (8.58%)
[2016-04-15T01:25Z] INFO  18:25:28,248 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:25Z] INFO  18:25:28,249 MicroScheduler -   -> 29650 reads (8.02% of total) failing DuplicateReadFilter
[2016-04-15T01:25Z] INFO  18:25:28,249 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:25Z] INFO  18:25:28,249 MicroScheduler -   -> 2091 reads (0.57% of total) failing HCMappingQualityFilter
[2016-04-15T01:25Z] INFO  18:25:28,249 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:25Z] INFO  18:25:28,249 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:25Z] INFO  18:25:28,250 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:25Z] INFO  18:25:28,253 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T01:25Z] INFO  18:25:29,416 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:25Z] INFO  18:25:29,419 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:25Z] INFO  18:25:29,420 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:25Z] INFO  18:25:29,420 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:25Z] INFO  18:25:29,425 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/17/R14-18102_kapa-NGv3-PE100-NGv3-sort-17_31048040_46607237-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/17/R14-18102_kapa-NGv3-PE100-NGv3-17_31048040_46607237-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/17/tx/tmpabya5N/R14-18102_kapa-NGv3-PE100-NGv3-17_31048040_46607237.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:25Z] INFO  18:25:29,436 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:25Z] INFO  18:25:29,441 HelpFormatter - Date/Time: 2016/04/14 18:25:29
[2016-04-15T01:25Z] INFO  18:25:29,441 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:25Z] INFO  18:25:29,442 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:25Z] WARN  18:25:29,465 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T01:25Z] WARN  18:25:29,468 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/17/tx/tmpabya5N/R14-18102_kapa-NGv3-PE100-NGv3-17_31048040_46607237.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T01:25Z] INFO  18:25:29,691 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:25Z] INFO  18:25:29,706 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:25Z] INFO  18:25:29,950 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T01:25Z] GATK: HaplotypeCaller
[2016-04-15T01:25Z] INFO  18:25:29,984 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:25Z] INFO  18:25:30,063 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-15T01:25Z] INFO  18:25:30,084 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T01:25Z] INFO  18:25:30,283 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:25Z] INFO  18:25:30,289 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:25Z] INFO  18:25:30,290 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:25Z] INFO  18:25:30,290 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:25Z] INFO  18:25:30,295 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/17/R14-18102_kapa-NGv3-PE100-NGv3-sort-17_46607689_62121560-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/17/R14-18102_kapa-NGv3-PE100-NGv3-17_46607689_62121560-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/17/tx/tmpnBRilS/R14-18102_kapa-NGv3-PE100-NGv3-17_46607689_62121560.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:25Z] INFO  18:25:30,316 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:25Z] INFO  18:25:30,317 HelpFormatter - Date/Time: 2016/04/14 18:25:30
[2016-04-15T01:25Z] INFO  18:25:30,317 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:25Z] INFO  18:25:30,318 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:25Z] WARN  18:25:30,347 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T01:25Z] WARN  18:25:30,350 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/17/tx/tmpnBRilS/R14-18102_kapa-NGv3-PE100-NGv3-17_46607689_62121560.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T01:25Z] INFO  18:25:30,497 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:25Z] INFO  18:25:30,573 ProgressMeter -     15:44106699     1.32949855E8    60.0 s            0.0 s       65.0%    92.0 s      32.0 s
[2016-04-15T01:25Z] INFO  18:25:30,632 IntervalUtils - Processing 543518 bp from intervals
[2016-04-15T01:25Z] WARN  18:25:30,638 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:25Z] INFO  18:25:30,716 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T01:25Z] INFO  18:25:30,733 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:25Z] INFO  18:25:30,737 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:25Z] INFO  18:25:30,825 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.09
[2016-04-15T01:25Z] INFO  18:25:30,854 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:25Z] INFO  18:25:30,855 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:25Z] INFO  18:25:30,856 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T01:25Z] INFO  18:25:30,854 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T01:25Z] INFO  18:25:30,877 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T01:25Z] INFO  18:25:30,890 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T01:25Z] INFO  18:25:30,891 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T01:25Z] INFO  18:25:31,098 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T01:25Z] INFO  18:25:31,233 IntervalUtils - Processing 295968 bp from intervals
[2016-04-15T01:25Z] WARN  18:25:31,239 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:25Z] INFO  18:25:31,348 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:25Z] INFO  18:25:31,503 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:25Z] INFO  18:25:31,503 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:25Z] INFO  18:25:31,504 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T01:25Z] INFO  18:25:31,504 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T01:25Z] INFO  18:25:31,504 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T01:25Z] INFO  18:25:31,504 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T01:25Z] INFO  18:25:31,680 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T01:25Z] INFO  18:25:31,784 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.031935722
[2016-04-15T01:25Z] INFO  18:25:31,784 PairHMM - Total compute time in PairHMM computeLikelihoods() : 2.3010335470000003
[2016-04-15T01:25Z] INFO  18:25:31,785 HaplotypeCaller - Ran local assembly on 2074 active regions
[2016-04-15T01:25Z] INFO  18:25:31,821 ProgressMeter -            done     1.61002552E8    79.0 s            0.0 s      100.0%    79.0 s       0.0 s
[2016-04-15T01:25Z] INFO  18:25:31,822 ProgressMeter - Total runtime 79.46 secs, 1.32 min, 0.02 hours
[2016-04-15T01:25Z] INFO  18:25:31,823 MicroScheduler - 52965 reads were filtered out during the traversal out of approximately 477893 total reads (11.08%)
[2016-04-15T01:25Z] INFO  18:25:31,824 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:25Z] INFO  18:25:31,828 MicroScheduler -   -> 37319 reads (7.81% of total) failing DuplicateReadFilter
[2016-04-15T01:25Z] INFO  18:25:31,828 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:25Z] INFO  18:25:31,829 MicroScheduler -   -> 15646 reads (3.27% of total) failing HCMappingQualityFilter
[2016-04-15T01:25Z] INFO  18:25:31,830 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:25Z] INFO  18:25:31,830 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:25Z] INFO  18:25:31,831 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:25Z] INFO  18:25:31,832 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T01:25Z] INFO  18:25:32,108 ProgressMeter -     15:67500909     1.59100939E8    60.0 s            0.0 s       97.7%    61.0 s       1.0 s
[2016-04-15T01:25Z] INFO  18:25:32,728 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:25Z] INFO  18:25:32,731 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:25Z] INFO  18:25:32,731 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:25Z] INFO  18:25:32,732 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:25Z] INFO  18:25:32,737 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/17/R14-18102_kapa-NGv3-PE100-NGv3-sort-17_62122219_77705154-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/17/R14-18102_kapa-NGv3-PE100-NGv3-17_62122219_77705154-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/17/tx/tmpdOmZW7/R14-18102_kapa-NGv3-PE100-NGv3-17_62122219_77705154.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:25Z] INFO  18:25:32,754 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:25Z] INFO  18:25:32,755 HelpFormatter - Date/Time: 2016/04/14 18:25:32
[2016-04-15T01:25Z] INFO  18:25:32,755 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:25Z] INFO  18:25:32,755 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:25Z] WARN  18:25:32,782 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T01:25Z] WARN  18:25:32,786 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/17/tx/tmpdOmZW7/R14-18102_kapa-NGv3-PE100-NGv3-17_62122219_77705154.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T01:25Z] INFO  18:25:32,989 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:25Z] INFO  18:25:33,212 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T01:25Z] INFO  18:25:33,221 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:25Z] INFO  18:25:33,230 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.010946893000000001
[2016-04-15T01:25Z] INFO  18:25:33,231 PairHMM - Total compute time in PairHMM computeLikelihoods() : 0.557150253
[2016-04-15T01:25Z] INFO  18:25:33,232 HaplotypeCaller - Ran local assembly on 1846 active regions
[2016-04-15T01:25Z] INFO  18:25:33,242 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:25Z] INFO  18:25:33,301 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-15T01:25Z] INFO  18:25:33,309 ProgressMeter -            done     1.70188052E8    61.0 s            0.0 s      100.0%    61.0 s       0.0 s
[2016-04-15T01:25Z] INFO  18:25:33,310 ProgressMeter - Total runtime 61.25 secs, 1.02 min, 0.02 hours
[2016-04-15T01:25Z] INFO  18:25:33,310 MicroScheduler - 28415 reads were filtered out during the traversal out of approximately 344388 total reads (8.25%)
[2016-04-15T01:25Z] INFO  18:25:33,311 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:25Z] INFO  18:25:33,311 MicroScheduler -   -> 27810 reads (8.08% of total) failing DuplicateReadFilter
[2016-04-15T01:25Z] INFO  18:25:33,311 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:25Z] INFO  18:25:33,312 MicroScheduler -   -> 605 reads (0.18% of total) failing HCMappingQualityFilter
[2016-04-15T01:25Z] INFO  18:25:33,312 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:25Z] INFO  18:25:33,312 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:25Z] INFO  18:25:33,312 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:25Z] INFO  18:25:33,313 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T01:25Z] INFO  18:25:33,327 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T01:25Z] GATK: HaplotypeCaller
[2016-04-15T01:25Z] INFO  18:25:33,839 IntervalUtils - Processing 345298 bp from intervals
[2016-04-15T01:25Z] WARN  18:25:33,845 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:25Z] INFO  18:25:33,951 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:25Z] INFO  18:25:34,136 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:25Z] INFO  18:25:34,137 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:25Z] INFO  18:25:34,138 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T01:25Z] INFO  18:25:34,138 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T01:25Z] INFO  18:25:34,145 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T01:25Z] INFO  18:25:34,155 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.025147819000000002
[2016-04-15T01:25Z] INFO  18:25:34,156 PairHMM - Total compute time in PairHMM computeLikelihoods() : 1.349969594
[2016-04-15T01:25Z] INFO  18:25:34,157 HaplotypeCaller - Ran local assembly on 1350 active regions
[2016-04-15T01:25Z] INFO  18:25:34,159 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T01:25Z] INFO  18:25:34,205 ProgressMeter -            done      8.0187592E7    53.0 s            0.0 s      100.0%    53.0 s       0.0 s
[2016-04-15T01:25Z] INFO  18:25:34,206 ProgressMeter - Total runtime 53.13 secs, 0.89 min, 0.01 hours
[2016-04-15T01:25Z] INFO  18:25:34,207 MicroScheduler - 44051 reads were filtered out during the traversal out of approximately 302642 total reads (14.56%)
[2016-04-15T01:25Z] INFO  18:25:34,207 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:25Z] INFO  18:25:34,208 MicroScheduler -   -> 22611 reads (7.47% of total) failing DuplicateReadFilter
[2016-04-15T01:25Z] INFO  18:25:34,209 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:25Z] INFO  18:25:34,209 MicroScheduler -   -> 21440 reads (7.08% of total) failing HCMappingQualityFilter
[2016-04-15T01:25Z] INFO  18:25:34,210 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:25Z] INFO  18:25:34,210 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:25Z] INFO  18:25:34,211 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:25Z] INFO  18:25:34,212 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T01:25Z] INFO  18:25:34,361 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T01:25Z] INFO  18:25:34,719 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:25Z] GATK: HaplotypeCaller
[2016-04-15T01:25Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T01:25Z] INFO  18:25:35,514 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T01:25Z] INFO  18:25:35,517 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T01:25Z] INFO  18:25:35,541 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:25Z] GATK: HaplotypeCaller
[2016-04-15T01:25Z] WARN  18:25:35,875 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T01:25Z] WARN  18:25:35,886 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T01:25Z] INFO  18:25:36,161 ProgressMeter -     16:55854284      2.6429935E7    30.0 s            1.0 s       48.1%    62.0 s      32.0 s
[2016-04-15T01:25Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T01:25Z] INFO  18:25:36,547 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T01:25Z] INFO  18:25:36,549 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T01:25Z] WARN  18:25:36,755 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T01:25Z] WARN  18:25:36,756 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T01:25Z] INFO  18:25:36,906 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:25Z] INFO  18:25:36,921 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:25Z] INFO  18:25:36,921 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:25Z] INFO  18:25:36,922 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:25Z] INFO  18:25:36,926 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/17/R14-18102_kapa-NGv3-PE100-NGv3-sort-17_77707305_81195210-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/17/R14-18102_kapa-NGv3-PE100-NGv3-17_77707305_81195210-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/17/tx/tmpHgVUfW/R14-18102_kapa-NGv3-PE100-NGv3-17_77707305_81195210.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:25Z] INFO  18:25:36,950 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:25Z] INFO  18:25:36,961 HelpFormatter - Date/Time: 2016/04/14 18:25:36
[2016-04-15T01:25Z] INFO  18:25:36,962 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:25Z] INFO  18:25:36,963 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:25Z] WARN  18:25:36,986 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T01:25Z] WARN  18:25:36,989 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/17/tx/tmpHgVUfW/R14-18102_kapa-NGv3-PE100-NGv3-17_77707305_81195210.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T01:25Z] INFO  18:25:37,214 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:25Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T01:25Z] INFO  18:25:37,265 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T01:25Z] INFO  18:25:37,277 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T01:25Z] INFO  18:25:37,424 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T01:25Z] INFO  18:25:37,443 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:25Z] INFO  18:25:37,519 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-15T01:25Z] INFO  18:25:37,549 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T01:25Z] WARN  18:25:37,679 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T01:25Z] WARN  18:25:37,680 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T01:25Z] INFO  18:25:37,831 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:25Z] INFO  18:25:37,834 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:25Z] INFO  18:25:37,835 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:25Z] INFO  18:25:37,835 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:25Z] INFO  18:25:37,840 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/18/R14-18102_kapa-NGv3-PE100-NGv3-sort-18_0_18531348-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/18/R14-18102_kapa-NGv3-PE100-NGv3-18_0_18531348-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/18/tx/tmpuaZLik/R14-18102_kapa-NGv3-PE100-NGv3-18_0_18531348.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:25Z] INFO  18:25:37,856 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:25Z] INFO  18:25:37,857 HelpFormatter - Date/Time: 2016/04/14 18:25:37
[2016-04-15T01:25Z] INFO  18:25:37,857 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:25Z] INFO  18:25:37,858 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:25Z] WARN  18:25:37,884 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T01:25Z] WARN  18:25:37,887 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/18/tx/tmpuaZLik/R14-18102_kapa-NGv3-PE100-NGv3-18_0_18531348.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T01:25Z] INFO  18:25:38,084 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:25Z] INFO  18:25:38,102 IntervalUtils - Processing 160149 bp from intervals
[2016-04-15T01:25Z] WARN  18:25:38,107 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:25Z] INFO  18:25:38,276 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:25Z] INFO  18:25:38,291 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T01:25Z] INFO  18:25:38,300 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:25Z] INFO  18:25:38,365 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:25Z] INFO  18:25:38,365 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:25Z] INFO  18:25:38,366 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T01:25Z] INFO  18:25:38,366 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T01:25Z] INFO  18:25:38,383 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T01:25Z] INFO  18:25:38,397 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T01:25Z] INFO  18:25:38,592 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.29
[2016-04-15T01:25Z] INFO  18:25:38,613 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T01:25Z] INFO  18:25:38,629 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T01:25Z] INFO  18:25:38,852 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:25Z] INFO  18:25:38,856 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:25Z] INFO  18:25:38,856 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:25Z] INFO  18:25:38,857 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:25Z] INFO  18:25:38,862 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/18/R14-18102_kapa-NGv3-PE100-NGv3-sort-18_18533538_34081962-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/18/R14-18102_kapa-NGv3-PE100-NGv3-18_18533538_34081962-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/18/tx/tmpeI7K5k/R14-18102_kapa-NGv3-PE100-NGv3-18_18533538_34081962.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:25Z] INFO  18:25:38,872 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:25Z] INFO  18:25:38,873 HelpFormatter - Date/Time: 2016/04/14 18:25:38
[2016-04-15T01:25Z] INFO  18:25:38,873 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:25Z] INFO  18:25:38,874 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:25Z] WARN  18:25:38,896 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T01:25Z] WARN  18:25:38,899 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/18/tx/tmpeI7K5k/R14-18102_kapa-NGv3-PE100-NGv3-18_18533538_34081962.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T01:25Z] INFO  18:25:39,009 IntervalUtils - Processing 162632 bp from intervals
[2016-04-15T01:25Z] WARN  18:25:39,025 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:25Z] INFO  18:25:39,070 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:25Z] INFO  18:25:39,129 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:25Z] INFO  18:25:39,259 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:25Z] INFO  18:25:39,259 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:25Z] INFO  18:25:39,260 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T01:25Z] INFO  18:25:39,260 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T01:25Z] INFO  18:25:39,272 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T01:25Z] INFO  18:25:39,273 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T01:25Z] INFO  18:25:39,294 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T01:25Z] INFO  18:25:39,303 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:25Z] INFO  18:25:39,411 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.11
[2016-04-15T01:25Z] INFO  18:25:39,428 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T01:25Z] INFO  18:25:39,429 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T01:25Z] INFO  18:25:39,525 ProgressMeter -     15:80743221     1.46109349E8    60.0 s            0.0 s       87.3%    68.0 s       8.0 s
[2016-04-15T01:25Z] INFO  18:25:39,863 IntervalUtils - Processing 148606 bp from intervals
[2016-04-15T01:25Z] WARN  18:25:39,869 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:25Z] INFO  18:25:39,960 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:25Z] INFO  18:25:40,104 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:25Z] INFO  18:25:40,105 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:25Z] INFO  18:25:40,106 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T01:25Z] INFO  18:25:40,107 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T01:25Z] INFO  18:25:40,119 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T01:25Z] INFO  18:25:40,119 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T01:25Z] INFO  18:25:40,464 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T01:25Z] INFO  18:25:40,591 ProgressMeter -     16:68109280      2.4054373E7    30.0 s            1.0 s       35.4%    84.0 s      54.0 s
[2016-04-15T01:25Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T01:25Z] INFO  18:25:41,592 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T01:25Z] INFO  18:25:41,604 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T01:25Z] WARN  18:25:41,893 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T01:25Z] WARN  18:25:41,894 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T01:25Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T01:25Z] INFO  18:25:44,286 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T01:25Z] INFO  18:25:44,287 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T01:25Z] WARN  18:25:44,637 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T01:25Z] WARN  18:25:44,638 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T01:25Z] INFO  18:25:46,837 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.019946654
[2016-04-15T01:25Z] INFO  18:25:46,838 PairHMM - Total compute time in PairHMM computeLikelihoods() : 0.923318348
[2016-04-15T01:25Z] INFO  18:25:46,838 HaplotypeCaller - Ran local assembly on 2144 active regions
[2016-04-15T01:25Z] INFO  18:25:46,908 ProgressMeter -            done     2.01008217E8    67.0 s            0.0 s      100.0%    67.0 s       0.0 s
[2016-04-15T01:25Z] INFO  18:25:46,909 ProgressMeter - Total runtime 67.44 secs, 1.12 min, 0.02 hours
[2016-04-15T01:25Z] INFO  18:25:46,909 MicroScheduler - 95476 reads were filtered out during the traversal out of approximately 494318 total reads (19.31%)
[2016-04-15T01:25Z] INFO  18:25:46,910 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:25Z] INFO  18:25:46,911 MicroScheduler -   -> 35540 reads (7.19% of total) failing DuplicateReadFilter
[2016-04-15T01:25Z] INFO  18:25:46,911 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:25Z] INFO  18:25:46,912 MicroScheduler -   -> 59936 reads (12.12% of total) failing HCMappingQualityFilter
[2016-04-15T01:25Z] INFO  18:25:46,912 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:25Z] INFO  18:25:46,913 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:25Z] INFO  18:25:46,914 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:25Z] INFO  18:25:46,914 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T01:25Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T01:25Z] INFO  18:25:46,979 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T01:25Z] INFO  18:25:46,990 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T01:25Z] INFO  18:25:47,227 ProgressMeter -     16:84691407        9808860.0    30.0 s            3.0 s       30.6%    98.0 s      68.0 s
[2016-04-15T01:25Z] WARN  18:25:47,334 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T01:25Z] WARN  18:25:47,335 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T01:25Z] INFO  18:25:47,990 ProgressMeter -      17:2267353      1.0592604E7    30.0 s            2.0 s       14.7%     3.4 m       2.9 m
[2016-04-15T01:25Z] INFO  18:25:48,401 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:25Z] GATK: HaplotypeCaller
[2016-04-15T01:25Z] INFO  18:25:48,724 ProgressMeter -      16:2577817      7.7524695E7    60.0 s            0.0 s       48.2%     2.1 m      64.0 s
[2016-04-15T01:25Z] INFO  18:25:49,704 ProgressMeter -     17:18285827      2.0620287E7    30.0 s            1.0 s       30.6%    98.0 s      68.0 s
[2016-04-15T01:25Z] INFO  18:25:52,017 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:25Z] INFO  18:25:52,020 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:25Z] INFO  18:25:52,020 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:25Z] INFO  18:25:52,020 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:25Z] INFO  18:25:52,035 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/18/R14-18102_kapa-NGv3-PE100-NGv3-sort-18_34092400_49867248-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/18/R14-18102_kapa-NGv3-PE100-NGv3-18_34092400_49867248-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/18/tx/tmpAcXOKr/R14-18102_kapa-NGv3-PE100-NGv3-18_34092400_49867248.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:25Z] INFO  18:25:52,047 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:25Z] INFO  18:25:52,072 HelpFormatter - Date/Time: 2016/04/14 18:25:52
[2016-04-15T01:25Z] INFO  18:25:52,073 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:25Z] INFO  18:25:52,074 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:25Z] WARN  18:25:52,107 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T01:25Z] WARN  18:25:52,110 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/18/tx/tmpAcXOKr/R14-18102_kapa-NGv3-PE100-NGv3-18_34092400_49867248.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T01:25Z] INFO  18:25:52,273 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:25Z] INFO  18:25:52,511 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T01:25Z] INFO  18:25:52,521 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:25Z] INFO  18:25:52,586 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-15T01:25Z] INFO  18:25:52,630 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T01:25Z] INFO  18:25:53,042 IntervalUtils - Processing 116317 bp from intervals
[2016-04-15T01:25Z] WARN  18:25:53,052 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:25Z] INFO  18:25:53,147 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:25Z] INFO  18:25:53,234 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:25Z] INFO  18:25:53,235 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:25Z] INFO  18:25:53,235 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T01:25Z] INFO  18:25:53,236 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T01:25Z] INFO  18:25:53,247 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T01:25Z] INFO  18:25:53,248 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T01:25Z] INFO  18:25:53,456 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T01:25Z] INFO  18:25:55,349 ProgressMeter -     16:28354336     1.35177477E8    60.0 s            0.0 s       59.5%   100.0 s      40.0 s
[2016-04-15T01:25Z] INFO  18:25:55,949 ProgressMeter -      11:6452871      9.8928834E7     3.5 m            2.0 s       58.3%     6.0 m       2.5 m
[2016-04-15T01:25Z] INFO  18:25:56,338 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.018530225
[2016-04-15T01:25Z] INFO  18:25:56,339 PairHMM - Total compute time in PairHMM computeLikelihoods() : 0.67601038
[2016-04-15T01:25Z] INFO  18:25:56,350 HaplotypeCaller - Ran local assembly on 2701 active regions
[2016-04-15T01:25Z] INFO  18:25:56,389 ProgressMeter -            done     3.66240357E8    85.0 s            0.0 s      100.0%    85.0 s       0.0 s
[2016-04-15T01:25Z] INFO  18:25:56,389 ProgressMeter - Total runtime 85.84 secs, 1.43 min, 0.02 hours
[2016-04-15T01:25Z] INFO  18:25:56,390 MicroScheduler - 66162 reads were filtered out during the traversal out of approximately 563537 total reads (11.74%)
[2016-04-15T01:25Z] INFO  18:25:56,390 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:25Z] INFO  18:25:56,390 MicroScheduler -   -> 43350 reads (7.69% of total) failing DuplicateReadFilter
[2016-04-15T01:25Z] INFO  18:25:56,390 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:25Z] INFO  18:25:56,391 MicroScheduler -   -> 22812 reads (4.05% of total) failing HCMappingQualityFilter
[2016-04-15T01:25Z] INFO  18:25:56,391 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:25Z] INFO  18:25:56,391 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:25Z] INFO  18:25:56,391 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:25Z] INFO  18:25:56,392 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T01:25Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T01:25Z] INFO  18:25:56,795 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T01:25Z] INFO  18:25:56,796 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T01:25Z] WARN  18:25:57,100 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T01:25Z] WARN  18:25:57,101 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T01:25Z] INFO  18:25:57,758 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:25Z] GATK: HaplotypeCaller
[2016-04-15T01:26Z] INFO  18:26:00,542 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:26Z] INFO  18:26:00,545 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:26Z] INFO  18:26:00,546 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:26Z] INFO  18:26:00,546 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:26Z] INFO  18:26:00,551 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/18/R14-18102_kapa-NGv3-PE100-NGv3-sort-18_50278423_66344430-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/18/R14-18102_kapa-NGv3-PE100-NGv3-18_50278423_66344430-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/18/tx/tmpcZ03kJ/R14-18102_kapa-NGv3-PE100-NGv3-18_50278423_66344430.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:26Z] INFO  18:26:00,570 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:26Z] INFO  18:26:00,570 HelpFormatter - Date/Time: 2016/04/14 18:26:00
[2016-04-15T01:26Z] INFO  18:26:00,571 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:26Z] INFO  18:26:00,571 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:26Z] WARN  18:26:00,605 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T01:26Z] WARN  18:26:00,608 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/18/tx/tmpcZ03kJ/R14-18102_kapa-NGv3-PE100-NGv3-18_50278423_66344430.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T01:26Z] INFO  18:26:00,809 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:26Z] INFO  18:26:00,894 ProgressMeter -     17:36080939      2.8766276E7    30.0 s            1.0 s       18.5%     2.7 m       2.2 m
[2016-04-15T01:26Z] INFO  18:26:01,026 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T01:26Z] INFO  18:26:01,034 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:26Z] INFO  18:26:01,106 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-15T01:26Z] INFO  18:26:01,140 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T01:26Z] INFO  18:26:01,457 IntervalUtils - Processing 111880 bp from intervals
[2016-04-15T01:26Z] WARN  18:26:01,462 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:26Z] INFO  18:26:01,509 ProgressMeter -     17:49713216      2.4823513E7    30.0 s            1.0 s       33.8%    88.0 s      58.0 s
[2016-04-15T01:26Z] INFO  18:26:01,546 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:26Z] INFO  18:26:01,640 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:26Z] INFO  18:26:01,641 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:26Z] INFO  18:26:01,641 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T01:26Z] INFO  18:26:01,641 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T01:26Z] INFO  18:26:01,647 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T01:26Z] INFO  18:26:01,648 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T01:26Z] INFO  18:26:01,796 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T01:26Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T01:26Z] INFO  18:26:04,118 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T01:26Z] INFO  18:26:04,119 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T01:26Z] INFO  18:26:04,161 ProgressMeter -     17:71197248      3.4212299E7    30.0 s            0.0 s       32.4%    92.0 s      62.0 s
[2016-04-15T01:26Z] WARN  18:26:04,377 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T01:26Z] WARN  18:26:04,378 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T01:26Z] INFO  18:26:06,174 ProgressMeter -     16:62055506     1.23843491E8    60.0 s            0.0 s       98.7%    60.0 s       0.0 s
[2016-04-15T01:26Z] INFO  18:26:07,168 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.015740729000000002
[2016-04-15T01:26Z] INFO  18:26:07,168 PairHMM - Total compute time in PairHMM computeLikelihoods() : 1.8775455410000002
[2016-04-15T01:26Z] INFO  18:26:07,169 HaplotypeCaller - Ran local assembly on 1722 active regions
[2016-04-15T01:26Z] INFO  18:26:07,229 ProgressMeter -            done     1.24288875E8    61.0 s            0.0 s      100.0%    61.0 s       0.0 s
[2016-04-15T01:26Z] INFO  18:26:07,229 ProgressMeter - Total runtime 61.09 secs, 1.02 min, 0.02 hours
[2016-04-15T01:26Z] INFO  18:26:07,230 MicroScheduler - 29355 reads were filtered out during the traversal out of approximately 343664 total reads (8.54%)
[2016-04-15T01:26Z] INFO  18:26:07,230 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:26Z] INFO  18:26:07,230 MicroScheduler -   -> 27892 reads (8.12% of total) failing DuplicateReadFilter
[2016-04-15T01:26Z] INFO  18:26:07,231 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:26Z] INFO  18:26:07,231 MicroScheduler -   -> 1463 reads (0.43% of total) failing HCMappingQualityFilter
[2016-04-15T01:26Z] INFO  18:26:07,231 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:26Z] INFO  18:26:07,231 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:26Z] INFO  18:26:07,232 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:26Z] INFO  18:26:07,232 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T01:26Z] INFO  18:26:08,395 ProgressMeter -     17:79637255      1.5323478E7    30.0 s            1.0 s       50.8%    59.0 s      29.0 s
[2016-04-15T01:26Z] INFO  18:26:08,685 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:26Z] GATK: HaplotypeCaller
[2016-04-15T01:26Z] INFO  18:26:09,280 ProgressMeter -      18:9887498      2.2559501E7    30.0 s            1.0 s       59.9%    50.0 s      20.0 s
[2016-04-15T01:26Z] INFO  18:26:10,121 ProgressMeter -     18:29848535      2.8325155E7    30.0 s            1.0 s       69.5%    43.0 s      13.0 s
[2016-04-15T01:26Z] INFO  18:26:10,592 ProgressMeter -     16:72205107     1.63174575E8    60.0 s            0.0 s       78.5%    76.0 s      16.0 s
[2016-04-15T01:26Z] INFO  18:26:11,950 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:26Z] INFO  18:26:11,953 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:26Z] INFO  18:26:11,954 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:26Z] INFO  18:26:11,954 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:26Z] INFO  18:26:11,959 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/18/R14-18102_kapa-NGv3-PE100-NGv3-sort-18_66346699_78077248-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/18/R14-18102_kapa-NGv3-PE100-NGv3-18_66346699_78077248-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/18/tx/tmpbZgKN4/R14-18102_kapa-NGv3-PE100-NGv3-18_66346699_78077248.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:26Z] INFO  18:26:11,969 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:26Z] INFO  18:26:11,970 HelpFormatter - Date/Time: 2016/04/14 18:26:11
[2016-04-15T01:26Z] INFO  18:26:11,970 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:26Z] INFO  18:26:11,971 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:26Z] WARN  18:26:11,995 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T01:26Z] WARN  18:26:11,998 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/18/tx/tmpbZgKN4/R14-18102_kapa-NGv3-PE100-NGv3-18_66346699_78077248.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T01:26Z] INFO  18:26:12,206 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:26Z] INFO  18:26:12,456 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T01:26Z] INFO  18:26:12,466 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:26Z] INFO  18:26:12,529 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-15T01:26Z] INFO  18:26:12,564 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T01:26Z] INFO  18:26:12,829 IntervalUtils - Processing 87308 bp from intervals
[2016-04-15T01:26Z] WARN  18:26:12,835 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:26Z] INFO  18:26:12,956 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:26Z] INFO  18:26:13,043 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:26Z] INFO  18:26:13,044 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:26Z] INFO  18:26:13,045 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T01:26Z] INFO  18:26:13,045 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T01:26Z] INFO  18:26:13,046 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T01:26Z] INFO  18:26:13,046 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T01:26Z] INFO  18:26:13,224 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T01:26Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T01:26Z] INFO  18:26:15,751 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T01:26Z] INFO  18:26:15,754 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T01:26Z] WARN  18:26:16,082 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T01:26Z] WARN  18:26:16,082 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T01:26Z] INFO  18:26:17,237 ProgressMeter -     16:89650179        5.57522E7    60.0 s            1.0 s       84.3%    71.0 s      11.0 s
[2016-04-15T01:26Z] INFO  18:26:17,991 ProgressMeter -      17:5073948      8.9823999E7    60.0 s            0.0 s       40.7%     2.5 m      87.0 s
[2016-04-15T01:26Z] INFO  18:26:18,726 ProgressMeter -      16:8622089     2.39875235E8    90.0 s            0.0 s       80.7%   111.0 s      21.0 s
[2016-04-15T01:26Z] INFO  18:26:18,938 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.029347349000000002
[2016-04-15T01:26Z] INFO  18:26:18,939 PairHMM - Total compute time in PairHMM computeLikelihoods() : 0.350758793
[2016-04-15T01:26Z] INFO  18:26:18,940 HaplotypeCaller - Ran local assembly on 1056 active regions
[2016-04-15T01:26Z] INFO  18:26:18,966 ProgressMeter -            done      5.2114591E7    38.0 s            0.0 s      100.0%    38.0 s       0.0 s
[2016-04-15T01:26Z] INFO  18:26:18,967 ProgressMeter - Total runtime 38.86 secs, 0.65 min, 0.01 hours
[2016-04-15T01:26Z] INFO  18:26:18,968 MicroScheduler - 16123 reads were filtered out during the traversal out of approximately 194325 total reads (8.30%)
[2016-04-15T01:26Z] INFO  18:26:18,968 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:26Z] INFO  18:26:18,969 MicroScheduler -   -> 15687 reads (8.07% of total) failing DuplicateReadFilter
[2016-04-15T01:26Z] INFO  18:26:18,970 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:26Z] INFO  18:26:18,971 MicroScheduler -   -> 436 reads (0.22% of total) failing HCMappingQualityFilter
[2016-04-15T01:26Z] INFO  18:26:18,971 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:26Z] INFO  18:26:18,972 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:26Z] INFO  18:26:18,973 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:26Z] INFO  18:26:18,974 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T01:26Z] INFO  18:26:19,714 ProgressMeter -     17:21432326      5.8273117E7    60.0 s            1.0 s       48.5%     2.1 m      63.0 s
[2016-04-15T01:26Z] INFO  18:26:20,788 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:26Z] GATK: HaplotypeCaller
[2016-04-15T01:26Z] INFO  18:26:23,250 ProgressMeter -     18:47788360      2.4111844E7    30.0 s            1.0 s       86.6%    34.0 s       4.0 s
[2016-04-15T01:26Z] INFO  18:26:24,067 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:26Z] INFO  18:26:24,071 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:26Z] INFO  18:26:24,072 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:26Z] INFO  18:26:24,072 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:26Z] INFO  18:26:24,079 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/19/R14-18102_kapa-NGv3-PE100-NGv3-sort-19_0_15509577-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/19/R14-18102_kapa-NGv3-PE100-NGv3-19_0_15509577-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/19/tx/tmpBFJpd6/R14-18102_kapa-NGv3-PE100-NGv3-19_0_15509577.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:26Z] INFO  18:26:24,098 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:26Z] INFO  18:26:24,100 HelpFormatter - Date/Time: 2016/04/14 18:26:24
[2016-04-15T01:26Z] INFO  18:26:24,100 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:26Z] INFO  18:26:24,101 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:26Z] WARN  18:26:24,155 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T01:26Z] WARN  18:26:24,157 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/19/tx/tmpBFJpd6/R14-18102_kapa-NGv3-PE100-NGv3-19_0_15509577.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T01:26Z] INFO  18:26:24,217 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.036907232000000005
[2016-04-15T01:26Z] INFO  18:26:24,218 PairHMM - Total compute time in PairHMM computeLikelihoods() : 3.297736221
[2016-04-15T01:26Z] INFO  18:26:24,219 HaplotypeCaller - Ran local assembly on 1587 active regions
[2016-04-15T01:26Z] INFO  18:26:24,278 ProgressMeter -            done      8.7428536E7    67.0 s            0.0 s      100.0%    67.0 s       0.0 s
[2016-04-15T01:26Z] INFO  18:26:24,278 ProgressMeter - Total runtime 67.10 secs, 1.12 min, 0.02 hours
[2016-04-15T01:26Z] INFO  18:26:24,279 MicroScheduler - 31409 reads were filtered out during the traversal out of approximately 347537 total reads (9.04%)
[2016-04-15T01:26Z] INFO  18:26:24,279 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:26Z] INFO  18:26:24,280 MicroScheduler -   -> 28393 reads (8.17% of total) failing DuplicateReadFilter
[2016-04-15T01:26Z] INFO  18:26:24,280 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:26Z] INFO  18:26:24,280 MicroScheduler -   -> 3016 reads (0.87% of total) failing HCMappingQualityFilter
[2016-04-15T01:26Z] INFO  18:26:24,281 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:26Z] INFO  18:26:24,281 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:26Z] INFO  18:26:24,281 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:26Z] INFO  18:26:24,281 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T01:26Z] INFO  18:26:24,410 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:26Z] INFO  18:26:24,596 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T01:26Z] INFO  18:26:24,607 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:26Z] INFO  18:26:24,682 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-15T01:26Z] INFO  18:26:24,699 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T01:26Z] INFO  18:26:25,134 IntervalUtils - Processing 793280 bp from intervals
[2016-04-15T01:26Z] WARN  18:26:25,140 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:26Z] INFO  18:26:25,214 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:26Z] INFO  18:26:25,350 ProgressMeter -     16:30779215     2.58897306E8    90.0 s            0.0 s       92.5%    97.0 s       7.0 s
[2016-04-15T01:26Z] INFO  18:26:25,369 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:26Z] INFO  18:26:25,370 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:26Z] INFO  18:26:25,371 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T01:26Z] INFO  18:26:25,372 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T01:26Z] INFO  18:26:25,372 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T01:26Z] INFO  18:26:25,373 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T01:26Z] INFO  18:26:25,543 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T01:26Z] INFO  18:26:25,570 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:26Z] GATK: HaplotypeCaller
[2016-04-15T01:26Z] INFO  18:26:25,950 ProgressMeter -     11:10819428     2.75609554E8     4.0 m            0.0 s       89.0%     4.5 m      29.0 s
[2016-04-15T01:26Z] INFO  18:26:26,481 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.008019338
[2016-04-15T01:26Z] INFO  18:26:26,483 PairHMM - Total compute time in PairHMM computeLikelihoods() : 0.45761158500000004
[2016-04-15T01:26Z] INFO  18:26:26,483 HaplotypeCaller - Ran local assembly on 808 active regions
[2016-04-15T01:26Z] INFO  18:26:26,528 ProgressMeter -            done      3.1603936E7    33.0 s            1.0 s      100.0%    33.0 s       0.0 s
[2016-04-15T01:26Z] INFO  18:26:26,529 ProgressMeter - Total runtime 33.29 secs, 0.55 min, 0.01 hours
[2016-04-15T01:26Z] INFO  18:26:26,529 MicroScheduler - 87958 reads were filtered out during the traversal out of approximately 243797 total reads (36.08%)
[2016-04-15T01:26Z] INFO  18:26:26,530 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:26Z] INFO  18:26:26,530 MicroScheduler -   -> 14601 reads (5.99% of total) failing DuplicateReadFilter
[2016-04-15T01:26Z] INFO  18:26:26,530 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:26Z] INFO  18:26:26,531 MicroScheduler -   -> 73357 reads (30.09% of total) failing HCMappingQualityFilter
[2016-04-15T01:26Z] INFO  18:26:26,531 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:26Z] INFO  18:26:26,531 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:26Z] INFO  18:26:26,531 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:26Z] INFO  18:26:26,532 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T01:26Z] INFO  18:26:27,763 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.016466391
[2016-04-15T01:26Z] INFO  18:26:27,764 PairHMM - Total compute time in PairHMM computeLikelihoods() : 1.6682412850000001
[2016-04-15T01:26Z] INFO  18:26:27,765 HaplotypeCaller - Ran local assembly on 1255 active regions
[2016-04-15T01:26Z] INFO  18:26:27,792 ProgressMeter -            done      5.7809529E7    49.0 s            0.0 s      100.0%    49.0 s       0.0 s
[2016-04-15T01:26Z] INFO  18:26:27,793 ProgressMeter - Total runtime 49.43 secs, 0.82 min, 0.01 hours
[2016-04-15T01:26Z] INFO  18:26:27,794 MicroScheduler - 24117 reads were filtered out during the traversal out of approximately 283390 total reads (8.51%)
[2016-04-15T01:26Z] INFO  18:26:27,795 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:26Z] INFO  18:26:27,795 MicroScheduler -   -> 23188 reads (8.18% of total) failing DuplicateReadFilter
[2016-04-15T01:26Z] INFO  18:26:27,796 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:26Z] INFO  18:26:27,796 MicroScheduler -   -> 929 reads (0.33% of total) failing HCMappingQualityFilter
[2016-04-15T01:26Z] INFO  18:26:27,797 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:26Z] INFO  18:26:27,798 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:26Z] INFO  18:26:27,798 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:26Z] INFO  18:26:27,799 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T01:26Z] INFO  18:26:27,972 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:26Z] GATK: HaplotypeCaller
[2016-04-15T01:26Z] INFO  18:26:28,611 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:26Z] INFO  18:26:28,621 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:26Z] INFO  18:26:28,621 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:26Z] INFO  18:26:28,621 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:26Z] INFO  18:26:28,625 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/19/R14-18102_kapa-NGv3-PE100-NGv3-sort-19_15510112_31025906-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/19/R14-18102_kapa-NGv3-PE100-NGv3-19_15510112_31025906-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/19/tx/tmpsPYOe3/R14-18102_kapa-NGv3-PE100-NGv3-19_15510112_31025906.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:26Z] INFO  18:26:28,635 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:26Z] INFO  18:26:28,639 HelpFormatter - Date/Time: 2016/04/14 18:26:28
[2016-04-15T01:26Z] INFO  18:26:28,640 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:26Z] INFO  18:26:28,640 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:26Z] WARN  18:26:28,686 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T01:26Z] WARN  18:26:28,689 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/19/tx/tmpsPYOe3/R14-18102_kapa-NGv3-PE100-NGv3-19_15510112_31025906.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T01:26Z] INFO  18:26:28,900 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:26Z] INFO  18:26:29,052 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:26Z] INFO  18:26:29,156 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T01:26Z] INFO  18:26:29,166 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:26Z] INFO  18:26:29,231 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-15T01:26Z] INFO  18:26:29,271 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T01:26Z] GATK: HaplotypeCaller
[2016-04-15T01:26Z] INFO  18:26:29,768 IntervalUtils - Processing 296880 bp from intervals
[2016-04-15T01:26Z] WARN  18:26:29,774 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:26Z] INFO  18:26:29,912 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:26Z] INFO  18:26:29,988 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:26Z] INFO  18:26:29,989 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:26Z] INFO  18:26:29,990 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T01:26Z] INFO  18:26:29,991 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T01:26Z] INFO  18:26:29,991 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T01:26Z] INFO  18:26:29,992 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T01:26Z] INFO  18:26:30,174 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T01:26Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T01:26Z] INFO  18:26:30,287 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T01:26Z] INFO  18:26:30,288 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T01:26Z] WARN  18:26:30,591 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T01:26Z] WARN  18:26:30,592 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T01:26Z] INFO  18:26:30,898 ProgressMeter -     17:39383307     1.33765423E8    60.0 s            0.0 s       44.0%     2.3 m      76.0 s
[2016-04-15T01:26Z] INFO  18:26:31,121 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:26Z] INFO  18:26:31,136 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:26Z] INFO  18:26:31,136 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:26Z] INFO  18:26:31,137 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:26Z] INFO  18:26:31,141 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/19/R14-18102_kapa-NGv3-PE100-NGv3-sort-19_31038849_46627578-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/19/R14-18102_kapa-NGv3-PE100-NGv3-19_31038849_46627578-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/19/tx/tmppZ4rwX/R14-18102_kapa-NGv3-PE100-NGv3-19_31038849_46627578.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:26Z] INFO  18:26:31,163 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:26Z] INFO  18:26:31,164 HelpFormatter - Date/Time: 2016/04/14 18:26:31
[2016-04-15T01:26Z] INFO  18:26:31,165 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:26Z] INFO  18:26:31,166 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:26Z] WARN  18:26:31,213 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T01:26Z] WARN  18:26:31,224 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/19/tx/tmppZ4rwX/R14-18102_kapa-NGv3-PE100-NGv3-19_31038849_46627578.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T01:26Z] INFO  18:26:31,457 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:26Z] INFO  18:26:31,486 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.023843177
[2016-04-15T01:26Z] INFO  18:26:31,487 PairHMM - Total compute time in PairHMM computeLikelihoods() : 2.2657997890000003
[2016-04-15T01:26Z] INFO  18:26:31,488 HaplotypeCaller - Ran local assembly on 2805 active regions
[2016-04-15T01:26Z] INFO  18:26:31,510 ProgressMeter -     17:61511763     1.67161488E8    60.0 s            0.0 s       86.4%    69.0 s       9.0 s
[2016-04-15T01:26Z] INFO  18:26:31,545 ProgressMeter -            done     2.83439102E8    96.0 s            0.0 s      100.0%    96.0 s       0.0 s
[2016-04-15T01:26Z] INFO  18:26:31,545 ProgressMeter - Total runtime 96.23 secs, 1.60 min, 0.03 hours
[2016-04-15T01:26Z] INFO  18:26:31,546 MicroScheduler - 305116 reads were filtered out during the traversal out of approximately 858298 total reads (35.55%)
[2016-04-15T01:26Z] INFO  18:26:31,546 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:26Z] INFO  18:26:31,546 MicroScheduler -   -> 49486 reads (5.77% of total) failing DuplicateReadFilter
[2016-04-15T01:26Z] INFO  18:26:31,547 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:26Z] INFO  18:26:31,547 MicroScheduler -   -> 255630 reads (29.78% of total) failing HCMappingQualityFilter
[2016-04-15T01:26Z] INFO  18:26:31,547 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:26Z] INFO  18:26:31,548 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:26Z] INFO  18:26:31,548 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:26Z] INFO  18:26:31,549 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T01:26Z] INFO  18:26:31,661 ProgressMeter -     18:61310395      2.2505073E7    30.0 s            1.0 s       85.2%    35.0 s       5.0 s
[2016-04-15T01:26Z] INFO  18:26:31,719 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T01:26Z] INFO  18:26:31,729 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:26Z] INFO  18:26:31,785 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-15T01:26Z] INFO  18:26:31,815 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T01:26Z] INFO  18:26:32,321 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.028906794000000003
[2016-04-15T01:26Z] INFO  18:26:32,332 PairHMM - Total compute time in PairHMM computeLikelihoods() : 2.649585071
[2016-04-15T01:26Z] INFO  18:26:32,334 HaplotypeCaller - Ran local assembly on 2395 active regions
[2016-04-15T01:26Z] INFO  18:26:32,381 ProgressMeter -            done     2.54086229E8    81.0 s            0.0 s      100.0%    81.0 s       0.0 s
[2016-04-15T01:26Z] INFO  18:26:32,382 ProgressMeter - Total runtime 81.81 secs, 1.36 min, 0.02 hours
[2016-04-15T01:26Z] INFO  18:26:32,382 MicroScheduler - 87664 reads were filtered out during the traversal out of approximately 599561 total reads (14.62%)
[2016-04-15T01:26Z] INFO  18:26:32,382 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:26Z] INFO  18:26:32,383 MicroScheduler -   -> 45708 reads (7.62% of total) failing DuplicateReadFilter
[2016-04-15T01:26Z] INFO  18:26:32,383 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:26Z] INFO  18:26:32,383 MicroScheduler -   -> 41956 reads (7.00% of total) failing HCMappingQualityFilter
[2016-04-15T01:26Z] INFO  18:26:32,383 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:26Z] INFO  18:26:32,384 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:26Z] INFO  18:26:32,384 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:26Z] INFO  18:26:32,384 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T01:26Z] INFO  18:26:32,474 IntervalUtils - Processing 631764 bp from intervals
[2016-04-15T01:26Z] WARN  18:26:32,486 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:26Z] INFO  18:26:32,636 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:26Z] INFO  18:26:32,871 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:26Z] INFO  18:26:32,883 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:26Z] INFO  18:26:32,884 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T01:26Z] INFO  18:26:32,884 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T01:26Z] INFO  18:26:32,899 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T01:26Z] INFO  18:26:32,900 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T01:26Z] INFO  18:26:33,078 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:26Z] INFO  18:26:33,081 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:26Z] INFO  18:26:33,082 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:26Z] INFO  18:26:33,083 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:26Z] INFO  18:26:33,087 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/19/R14-18102_kapa-NGv3-PE100-NGv3-sort-19_46627881_59128983-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/19/R14-18102_kapa-NGv3-PE100-NGv3-19_46627881_59128983-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/19/tx/tmp9O7nh_/R14-18102_kapa-NGv3-PE100-NGv3-19_46627881_59128983.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:26Z] INFO  18:26:33,117 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:26Z] INFO  18:26:33,118 HelpFormatter - Date/Time: 2016/04/14 18:26:33
[2016-04-15T01:26Z] INFO  18:26:33,119 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:26Z] INFO  18:26:33,120 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:26Z] WARN  18:26:33,145 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T01:26Z] WARN  18:26:33,148 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/19/tx/tmp9O7nh_/R14-18102_kapa-NGv3-PE100-NGv3-19_46627881_59128983.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T01:26Z] INFO  18:26:33,151 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T01:26Z] INFO  18:26:33,165 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:26Z] INFO  18:26:33,405 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:26Z] GATK: HaplotypeCaller
[2016-04-15T01:26Z] INFO  18:26:33,647 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T01:26Z] INFO  18:26:33,657 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:26Z] INFO  18:26:33,740 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-15T01:26Z] INFO  18:26:33,765 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T01:26Z] INFO  18:26:33,941 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:26Z] INFO  18:26:34,162 ProgressMeter -     17:74276368     1.49092185E8    60.0 s            0.0 s       74.0%    81.0 s      21.0 s
[2016-04-15T01:26Z] INFO  18:26:34,251 IntervalUtils - Processing 711484 bp from intervals
[2016-04-15T01:26Z] GATK: HaplotypeCaller
[2016-04-15T01:26Z] WARN  18:26:34,257 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:26Z] INFO  18:26:34,340 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:26Z] INFO  18:26:34,528 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:26Z] INFO  18:26:34,540 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:26Z] INFO  18:26:34,541 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T01:26Z] INFO  18:26:34,542 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T01:26Z] INFO  18:26:34,556 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T01:26Z] INFO  18:26:34,557 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T01:26Z] INFO  18:26:34,806 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T01:26Z] INFO  18:26:34,940 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.014188864
[2016-04-15T01:26Z] INFO  18:26:34,940 PairHMM - Total compute time in PairHMM computeLikelihoods() : 7.344143302000001
[2016-04-15T01:26Z] INFO  18:26:34,940 HaplotypeCaller - Ran local assembly on 1221 active regions
[2016-04-15T01:26Z] INFO  18:26:34,988 ProgressMeter -            done      6.3174533E7    55.0 s            0.0 s      100.0%    55.0 s       0.0 s
[2016-04-15T01:26Z] INFO  18:26:34,989 ProgressMeter - Total runtime 55.73 secs, 0.93 min, 0.02 hours
[2016-04-15T01:26Z] INFO  18:26:34,989 MicroScheduler - 21220 reads were filtered out during the traversal out of approximately 222249 total reads (9.55%)
[2016-04-15T01:26Z] INFO  18:26:34,989 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:26Z] INFO  18:26:34,990 MicroScheduler -   -> 17813 reads (8.01% of total) failing DuplicateReadFilter
[2016-04-15T01:26Z] INFO  18:26:34,990 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:26Z] INFO  18:26:34,990 MicroScheduler -   -> 3407 reads (1.53% of total) failing HCMappingQualityFilter
[2016-04-15T01:26Z] INFO  18:26:34,990 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:26Z] INFO  18:26:34,991 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:26Z] INFO  18:26:34,991 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:26Z] INFO  18:26:34,991 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T01:26Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T01:26Z] INFO  18:26:35,711 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T01:26Z] INFO  18:26:35,722 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T01:26Z] WARN  18:26:36,027 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T01:26Z] WARN  18:26:36,028 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T01:26Z] INFO  18:26:36,489 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.024786985
[2016-04-15T01:26Z] INFO  18:26:36,490 PairHMM - Total compute time in PairHMM computeLikelihoods() : 0.6834380330000001
[2016-04-15T01:26Z] INFO  18:26:36,491 HaplotypeCaller - Ran local assembly on 844 active regions
[2016-04-15T01:26Z] INFO  18:26:36,538 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:26Z] INFO  18:26:36,544 ProgressMeter -            done      2.9530103E7    34.0 s            1.0 s      100.0%    34.0 s       0.0 s
[2016-04-15T01:26Z] INFO  18:26:36,544 ProgressMeter - Total runtime 34.90 secs, 0.58 min, 0.01 hours
[2016-04-15T01:26Z] INFO  18:26:36,544 MicroScheduler - 11906 reads were filtered out during the traversal out of approximately 145217 total reads (8.20%)
[2016-04-15T01:26Z] INFO  18:26:36,545 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:26Z] INFO  18:26:36,545 MicroScheduler -   -> 11572 reads (7.97% of total) failing DuplicateReadFilter
[2016-04-15T01:26Z] INFO  18:26:36,545 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:26Z] INFO  18:26:36,545 MicroScheduler -   -> 334 reads (0.23% of total) failing HCMappingQualityFilter
[2016-04-15T01:26Z] INFO  18:26:36,546 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:26Z] INFO  18:26:36,546 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:26Z] INFO  18:26:36,546 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:26Z] INFO  18:26:36,546 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T01:26Z] INFO  18:26:36,714 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:26Z] INFO  18:26:36,718 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:26Z] INFO  18:26:36,718 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:26Z] INFO  18:26:36,719 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:26Z] INFO  18:26:36,723 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/20/R14-18102_kapa-NGv3-PE100-NGv3-sort-20_0_15843471-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/20/R14-18102_kapa-NGv3-PE100-NGv3-20_0_15843471-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/20/tx/tmp5943Yx/R14-18102_kapa-NGv3-PE100-NGv3-20_0_15843471.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:26Z] INFO  18:26:36,732 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:26Z] INFO  18:26:36,732 HelpFormatter - Date/Time: 2016/04/14 18:26:36
[2016-04-15T01:26Z] INFO  18:26:36,732 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:26Z] INFO  18:26:36,733 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:26Z] WARN  18:26:36,777 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T01:26Z] WARN  18:26:36,780 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/20/tx/tmp5943Yx/R14-18102_kapa-NGv3-PE100-NGv3-20_0_15843471.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T01:26Z] GATK: HaplotypeCaller
[2016-04-15T01:26Z] INFO  18:26:37,014 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:26Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T01:26Z] INFO  18:26:37,126 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T01:26Z] INFO  18:26:37,127 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T01:26Z] INFO  18:26:37,155 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:26Z] INFO  18:26:37,158 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:26Z] INFO  18:26:37,158 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:26Z] INFO  18:26:37,159 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:26Z] INFO  18:26:37,163 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/20/R14-18102_kapa-NGv3-PE100-NGv3-sort-20_15866408_31376818-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/20/R14-18102_kapa-NGv3-PE100-NGv3-20_15866408_31376818-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/20/tx/tmpCfCk_5/R14-18102_kapa-NGv3-PE100-NGv3-20_15866408_31376818.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:26Z] INFO  18:26:37,174 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:26Z] INFO  18:26:37,175 HelpFormatter - Date/Time: 2016/04/14 18:26:37
[2016-04-15T01:26Z] INFO  18:26:37,175 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:26Z] INFO  18:26:37,186 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:26Z] WARN  18:26:37,220 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T01:26Z] WARN  18:26:37,223 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/20/tx/tmpCfCk_5/R14-18102_kapa-NGv3-PE100-NGv3-20_15866408_31376818.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T01:26Z] INFO  18:26:37,223 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T01:26Z] INFO  18:26:37,247 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:26Z] INFO  18:26:37,329 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-15T01:26Z] INFO  18:26:37,376 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T01:26Z] INFO  18:26:37,449 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:26Z] INFO  18:26:37,629 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T01:26Z] INFO  18:26:37,639 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:26Z] INFO  18:26:37,706 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-15T01:26Z] INFO  18:26:37,740 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T01:26Z] WARN  18:26:37,811 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T01:26Z] WARN  18:26:37,823 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T01:26Z] INFO  18:26:37,910 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.111826095
[2016-04-15T01:26Z] INFO  18:26:37,911 PairHMM - Total compute time in PairHMM computeLikelihoods() : 93.115596462
[2016-04-15T01:26Z] INFO  18:26:37,912 HaplotypeCaller - Ran local assembly on 3203 active regions
[2016-04-15T01:26Z] INFO  18:26:37,954 IntervalUtils - Processing 179899 bp from intervals
[2016-04-15T01:26Z] WARN  18:26:37,959 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:26Z] INFO  18:26:37,964 ProgressMeter -            done     3.81945604E8     4.2 m            0.0 s      100.0%     4.2 m       0.0 s
[2016-04-15T01:26Z] INFO  18:26:37,964 ProgressMeter - Total runtime 252.08 secs, 4.20 min, 0.07 hours
[2016-04-15T01:26Z] INFO  18:26:37,965 MicroScheduler - 98838 reads were filtered out during the traversal out of approximately 781100 total reads (12.65%)
[2016-04-15T01:26Z] INFO  18:26:37,965 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:26Z] INFO  18:26:37,966 MicroScheduler -   -> 64432 reads (8.25% of total) failing DuplicateReadFilter
[2016-04-15T01:26Z] INFO  18:26:37,966 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:26Z] INFO  18:26:37,966 MicroScheduler -   -> 34406 reads (4.40% of total) failing HCMappingQualityFilter
[2016-04-15T01:26Z] INFO  18:26:37,967 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:26Z] INFO  18:26:37,967 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:26Z] INFO  18:26:37,968 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:26Z] INFO  18:26:37,968 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T01:26Z] INFO  18:26:37,973 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:26Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T01:26Z] INFO  18:26:38,016 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T01:26Z] INFO  18:26:38,018 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T01:26Z] INFO  18:26:38,130 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:26Z] INFO  18:26:38,197 IntervalUtils - Processing 150913 bp from intervals
[2016-04-15T01:26Z] WARN  18:26:38,212 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:26Z] INFO  18:26:38,227 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:26Z] INFO  18:26:38,228 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:26Z] INFO  18:26:38,228 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T01:26Z] INFO  18:26:38,229 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T01:26Z] INFO  18:26:38,230 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T01:26Z] INFO  18:26:38,230 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T01:26Z] INFO  18:26:38,304 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:26Z] WARN  18:26:38,365 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T01:26Z] WARN  18:26:38,366 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T01:26Z] GATK: HaplotypeCaller
[2016-04-15T01:26Z] INFO  18:26:38,402 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:26Z] INFO  18:26:38,403 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:26Z] INFO  18:26:38,404 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T01:26Z] INFO  18:26:38,405 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T01:26Z] INFO  18:26:38,405 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T01:26Z] INFO  18:26:38,406 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T01:26Z] INFO  18:26:38,469 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T01:26Z] INFO  18:26:38,573 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T01:26Z] INFO  18:26:39,074 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.012368971000000001
[2016-04-15T01:26Z] INFO  18:26:39,075 PairHMM - Total compute time in PairHMM computeLikelihoods() : 1.019453551
[2016-04-15T01:26Z] INFO  18:26:39,075 HaplotypeCaller - Ran local assembly on 2175 active regions
[2016-04-15T01:26Z] INFO  18:26:39,134 ProgressMeter -            done     2.16274885E8    67.0 s            0.0 s      100.0%    67.0 s       0.0 s
[2016-04-15T01:26Z] INFO  18:26:39,134 ProgressMeter - Total runtime 67.63 secs, 1.13 min, 0.02 hours
[2016-04-15T01:26Z] INFO  18:26:39,134 MicroScheduler - 42098 reads were filtered out during the traversal out of approximately 462755 total reads (9.10%)
[2016-04-15T01:26Z] INFO  18:26:39,135 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:26Z] INFO  18:26:39,135 MicroScheduler -   -> 36989 reads (7.99% of total) failing DuplicateReadFilter
[2016-04-15T01:26Z] INFO  18:26:39,136 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:26Z] INFO  18:26:39,136 MicroScheduler -   -> 5109 reads (1.10% of total) failing HCMappingQualityFilter
[2016-04-15T01:26Z] INFO  18:26:39,136 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:26Z] INFO  18:26:39,136 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:26Z] INFO  18:26:39,137 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:26Z] INFO  18:26:39,137 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T01:26Z] INFO  18:26:39,563 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:26Z] GATK: HaplotypeCaller
[2016-04-15T01:26Z] INFO  18:26:40,144 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:26Z] INFO  18:26:40,147 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:26Z] INFO  18:26:40,148 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:26Z] INFO  18:26:40,148 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:26Z] INFO  18:26:40,175 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/20/R14-18102_kapa-NGv3-PE100-NGv3-sort-20_31379406_47242465-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/20/R14-18102_kapa-NGv3-PE100-NGv3-20_31379406_47242465-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/20/tx/tmpTe164m/R14-18102_kapa-NGv3-PE100-NGv3-20_31379406_47242465.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:26Z] INFO  18:26:40,214 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:26Z] INFO  18:26:40,215 HelpFormatter - Date/Time: 2016/04/14 18:26:40
[2016-04-15T01:26Z] INFO  18:26:40,216 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:26Z] INFO  18:26:40,221 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:26Z] WARN  18:26:40,301 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T01:26Z] WARN  18:26:40,304 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/20/tx/tmpTe164m/R14-18102_kapa-NGv3-PE100-NGv3-20_31379406_47242465.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T01:26Z] INFO  18:26:40,531 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:26Z] INFO  18:26:40,623 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:26Z] GATK: HaplotypeCaller
[2016-04-15T01:26Z] INFO  18:26:40,883 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T01:26Z] INFO  18:26:40,903 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:26Z] INFO  18:26:40,983 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-15T01:26Z] INFO  18:26:41,023 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T01:26Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T01:26Z] INFO  18:26:41,234 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T01:26Z] INFO  18:26:41,235 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T01:26Z] INFO  18:26:41,411 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:26Z] INFO  18:26:41,426 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:26Z] INFO  18:26:41,427 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:26Z] INFO  18:26:41,428 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:26Z] INFO  18:26:41,432 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/20/R14-18102_kapa-NGv3-PE100-NGv3-sort-20_47244085_62830269-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/20/R14-18102_kapa-NGv3-PE100-NGv3-20_47244085_62830269-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/20/tx/tmplbD629/R14-18102_kapa-NGv3-PE100-NGv3-20_47244085_62830269.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:26Z] INFO  18:26:41,463 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:26Z] INFO  18:26:41,464 HelpFormatter - Date/Time: 2016/04/14 18:26:41
[2016-04-15T01:26Z] INFO  18:26:41,464 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:26Z] INFO  18:26:41,465 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:26Z] WARN  18:26:41,509 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T01:26Z] WARN  18:26:41,512 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/20/tx/tmplbD629/R14-18102_kapa-NGv3-PE100-NGv3-20_47244085_62830269.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T01:26Z] WARN  18:26:41,578 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T01:26Z] WARN  18:26:41,580 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T01:26Z] INFO  18:26:41,619 IntervalUtils - Processing 321885 bp from intervals
[2016-04-15T01:26Z] WARN  18:26:41,625 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:26Z] INFO  18:26:41,716 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:26Z] INFO  18:26:41,724 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:26Z] INFO  18:26:41,778 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.037871687
[2016-04-15T01:26Z] INFO  18:26:41,779 PairHMM - Total compute time in PairHMM computeLikelihoods() : 5.197318774
[2016-04-15T01:26Z] INFO  18:26:41,780 HaplotypeCaller - Ran local assembly on 3321 active regions
[2016-04-15T01:26Z] INFO  18:26:41,831 ProgressMeter -            done     4.23621461E8   113.0 s            0.0 s      100.0%   113.0 s       0.0 s
[2016-04-15T01:26Z] INFO  18:26:41,831 ProgressMeter - Total runtime 113.13 secs, 1.89 min, 0.03 hours
[2016-04-15T01:26Z] INFO  18:26:41,831 MicroScheduler - 124572 reads were filtered out during the traversal out of approximately 815949 total reads (15.27%)
[2016-04-15T01:26Z] INFO  18:26:41,832 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:26Z] INFO  18:26:41,832 MicroScheduler -   -> 62076 reads (7.61% of total) failing DuplicateReadFilter
[2016-04-15T01:26Z] INFO  18:26:41,832 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:26Z] INFO  18:26:41,833 MicroScheduler -   -> 62496 reads (7.66% of total) failing HCMappingQualityFilter
[2016-04-15T01:26Z] INFO  18:26:41,833 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:26Z] INFO  18:26:41,833 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:26Z] INFO  18:26:41,833 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:26Z] INFO  18:26:41,834 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T01:26Z] INFO  18:26:41,877 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:26Z] INFO  18:26:41,878 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:26Z] INFO  18:26:41,879 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T01:26Z] INFO  18:26:41,880 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T01:26Z] INFO  18:26:41,888 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T01:26Z] INFO  18:26:41,888 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T01:26Z] INFO  18:26:41,904 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T01:26Z] INFO  18:26:41,950 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:26Z] INFO  18:26:42,046 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.10
[2016-04-15T01:26Z] INFO  18:26:42,072 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T01:26Z] INFO  18:26:42,134 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T01:26Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T01:26Z] INFO  18:26:42,530 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T01:26Z] INFO  18:26:42,531 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T01:26Z] INFO  18:26:42,560 IntervalUtils - Processing 269605 bp from intervals
[2016-04-15T01:26Z] WARN  18:26:42,585 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:26Z] INFO  18:26:42,691 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:26Z] WARN  18:26:42,727 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T01:26Z] WARN  18:26:42,728 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T01:26Z] INFO  18:26:42,797 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:26Z] INFO  18:26:42,798 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:26Z] INFO  18:26:42,799 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T01:26Z] INFO  18:26:42,800 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T01:26Z] INFO  18:26:42,800 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T01:26Z] INFO  18:26:42,800 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T01:26Z] INFO  18:26:43,065 ProgressMeter -     18:77894332      1.2464143E7    30.0 s            2.0 s       96.0%    31.0 s       1.0 s
[2016-04-15T01:26Z] INFO  18:26:43,092 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T01:26Z] INFO  18:26:43,343 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:26Z] INFO  18:26:43,352 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:26Z] INFO  18:26:43,363 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:26Z] INFO  18:26:43,364 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:26Z] INFO  18:26:43,369 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/20/R14-18102_kapa-NGv3-PE100-NGv3-sort-20_62831244_63025520-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/20/R14-18102_kapa-NGv3-PE100-NGv3-20_62831244_63025520-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/20/tx/tmp2PuLzQ/R14-18102_kapa-NGv3-PE100-NGv3-20_62831244_63025520.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:26Z] INFO  18:26:43,386 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:26Z] INFO  18:26:43,387 HelpFormatter - Date/Time: 2016/04/14 18:26:43
[2016-04-15T01:26Z] INFO  18:26:43,387 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:26Z] INFO  18:26:43,388 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:26Z] WARN  18:26:43,436 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T01:26Z] INFO  18:26:43,441 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:26Z] WARN  18:26:43,442 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/20/tx/tmp2PuLzQ/R14-18102_kapa-NGv3-PE100-NGv3-20_62831244_63025520.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T01:26Z] INFO  18:26:43,740 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:26Z] GATK: HaplotypeCaller
[2016-04-15T01:26Z] INFO  18:26:43,827 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:26Z] INFO  18:26:43,830 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:26Z] INFO  18:26:43,830 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:26Z] INFO  18:26:43,831 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:26Z] INFO  18:26:43,833 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.029670101
[2016-04-15T01:26Z] INFO  18:26:43,834 PairHMM - Total compute time in PairHMM computeLikelihoods() : 0.660164688
[2016-04-15T01:26Z] INFO  18:26:43,834 HaplotypeCaller - Ran local assembly on 597 active regions
[2016-04-15T01:26Z] INFO  18:26:43,836 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/21/R14-18102_kapa-NGv3-PE100-NGv3-sort-21_0_15517120-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/21/R14-18102_kapa-NGv3-PE100-NGv3-21_0_15517120-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/21/tx/tmpMoKxjm/R14-18102_kapa-NGv3-PE100-NGv3-21_0_15517120.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:26Z] INFO  18:26:43,868 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:26Z] INFO  18:26:43,876 HelpFormatter - Date/Time: 2016/04/14 18:26:43
[2016-04-15T01:26Z] INFO  18:26:43,877 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:26Z] INFO  18:26:43,878 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:26Z] INFO  18:26:43,909 ProgressMeter -            done      1.2811877E7    30.0 s            2.0 s      100.0%    30.0 s       0.0 s
[2016-04-15T01:26Z] INFO  18:26:43,909 ProgressMeter - Total runtime 30.87 secs, 0.51 min, 0.01 hours
[2016-04-15T01:26Z] INFO  18:26:43,910 MicroScheduler - 11429 reads were filtered out during the traversal out of approximately 126151 total reads (9.06%)
[2016-04-15T01:26Z] INFO  18:26:43,910 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:26Z] INFO  18:26:43,910 MicroScheduler -   -> 10312 reads (8.17% of total) failing DuplicateReadFilter
[2016-04-15T01:26Z] INFO  18:26:43,910 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:26Z] INFO  18:26:43,911 MicroScheduler -   -> 1117 reads (0.89% of total) failing HCMappingQualityFilter
[2016-04-15T01:26Z] INFO  18:26:43,911 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:26Z] INFO  18:26:43,911 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:26Z] INFO  18:26:43,911 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:26Z] INFO  18:26:43,912 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T01:26Z] WARN  18:26:43,948 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T01:26Z] WARN  18:26:43,951 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/21/tx/tmpMoKxjm/R14-18102_kapa-NGv3-PE100-NGv3-21_0_15517120.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T01:26Z] INFO  18:26:43,959 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T01:26Z] INFO  18:26:43,969 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:26Z] INFO  18:26:44,036 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-15T01:26Z] INFO  18:26:44,076 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T01:26Z] INFO  18:26:44,167 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:26Z] INFO  18:26:44,356 IntervalUtils - Processing 4397 bp from intervals
[2016-04-15T01:26Z] WARN  18:26:44,362 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:26Z] INFO  18:26:44,391 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T01:26Z] INFO  18:26:44,400 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:26Z] INFO  18:26:44,474 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-15T01:26Z] INFO  18:26:44,497 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T01:26Z] INFO  18:26:44,505 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:26Z] INFO  18:26:44,565 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:26Z] INFO  18:26:44,566 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:26Z] INFO  18:26:44,567 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T01:26Z] INFO  18:26:44,568 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T01:26Z] INFO  18:26:44,579 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T01:26Z] INFO  18:26:44,580 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T01:26Z] INFO  18:26:44,810 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T01:26Z] INFO  18:26:44,916 IntervalUtils - Processing 4504 bp from intervals
[2016-04-15T01:26Z] WARN  18:26:44,921 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:26Z] INFO  18:26:45,008 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:26Z] INFO  18:26:45,054 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:26Z] INFO  18:26:45,055 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:26Z] INFO  18:26:45,055 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T01:26Z] INFO  18:26:45,056 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T01:26Z] INFO  18:26:45,063 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T01:26Z] INFO  18:26:45,064 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T01:26Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T01:26Z] INFO  18:26:45,122 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T01:26Z] INFO  18:26:45,123 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T01:26Z] INFO  18:26:45,317 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T01:26Z] WARN  18:26:45,518 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T01:26Z] WARN  18:26:45,519 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T01:26Z] INFO  18:26:45,549 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:26Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T01:26Z] INFO  18:26:45,747 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T01:26Z] INFO  18:26:45,748 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T01:26Z] GATK: HaplotypeCaller
[2016-04-15T01:26Z] WARN  18:26:46,324 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T01:26Z] WARN  18:26:46,325 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T01:26Z] INFO  18:26:47,740 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:26Z] INFO  18:26:47,744 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:26Z] INFO  18:26:47,744 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:26Z] INFO  18:26:47,745 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:26Z] INFO  18:26:47,749 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/21/R14-18102_kapa-NGv3-PE100-NGv3-sort-21_15524893_31045484-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/21/R14-18102_kapa-NGv3-PE100-NGv3-21_15524893_31045484-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/21/tx/tmp1FLjAz/R14-18102_kapa-NGv3-PE100-NGv3-21_15524893_31045484.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:26Z] INFO  18:26:47,782 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:26Z] INFO  18:26:47,782 HelpFormatter - Date/Time: 2016/04/14 18:26:47
[2016-04-15T01:26Z] INFO  18:26:47,782 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:26Z] INFO  18:26:47,783 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:26Z] WARN  18:26:47,824 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T01:26Z] WARN  18:26:47,827 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/21/tx/tmp1FLjAz/R14-18102_kapa-NGv3-PE100-NGv3-21_15524893_31045484.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T01:26Z] INFO  18:26:47,992 ProgressMeter -      17:7636405     2.04201601E8    90.0 s            0.0 s       64.9%     2.3 m      48.0 s
[2016-04-15T01:26Z] INFO  18:26:48,079 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:26Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T01:26Z] INFO  18:26:48,127 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T01:26Z] INFO  18:26:48,127 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T01:26Z] INFO  18:26:48,318 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T01:26Z] INFO  18:26:48,328 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:26Z] INFO  18:26:48,419 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.09
[2016-04-15T01:26Z] INFO  18:26:48,449 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T01:26Z] WARN  18:26:48,697 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T01:26Z] WARN  18:26:48,698 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T01:26Z] INFO  18:26:48,918 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:26Z] INFO  18:26:48,920 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:26Z] INFO  18:26:48,920 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:26Z] INFO  18:26:48,921 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:26Z] INFO  18:26:48,925 IntervalUtils - Processing 58639 bp from intervals
[2016-04-15T01:26Z] WARN  18:26:48,930 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:26Z] INFO  18:26:48,936 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/21/R14-18102_kapa-NGv3-PE100-NGv3-sort-21_31062047_46591599-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/21/R14-18102_kapa-NGv3-PE100-NGv3-21_31062047_46591599-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/21/tx/tmpSQcKiB/R14-18102_kapa-NGv3-PE100-NGv3-21_31062047_46591599.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:26Z] INFO  18:26:48,951 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:26Z] INFO  18:26:48,952 HelpFormatter - Date/Time: 2016/04/14 18:26:48
[2016-04-15T01:26Z] INFO  18:26:48,953 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:26Z] INFO  18:26:48,953 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:26Z] WARN  18:26:49,007 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T01:26Z] WARN  18:26:49,010 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/21/tx/tmpSQcKiB/R14-18102_kapa-NGv3-PE100-NGv3-21_31062047_46591599.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T01:26Z] INFO  18:26:49,090 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:26Z] INFO  18:26:49,165 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:26Z] INFO  18:26:49,166 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:26Z] INFO  18:26:49,167 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T01:26Z] INFO  18:26:49,168 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T01:26Z] INFO  18:26:49,168 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T01:26Z] INFO  18:26:49,169 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T01:26Z] INFO  18:26:49,310 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:26Z] INFO  18:26:49,405 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T01:26Z] INFO  18:26:49,593 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T01:26Z] INFO  18:26:49,602 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:26Z] INFO  18:26:49,697 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.09
[2016-04-15T01:26Z] INFO  18:26:49,715 ProgressMeter -     17:29528141     1.91356395E8    90.0 s            0.0 s       90.1%    99.0 s       9.0 s
[2016-04-15T01:26Z] INFO  18:26:49,721 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T01:26Z] INFO  18:26:50,323 IntervalUtils - Processing 282111 bp from intervals
[2016-04-15T01:26Z] WARN  18:26:50,339 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:26Z] INFO  18:26:50,452 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:26Z] INFO  18:26:50,588 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:26Z] INFO  18:26:50,589 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:26Z] INFO  18:26:50,590 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T01:26Z] INFO  18:26:50,590 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T01:26Z] INFO  18:26:50,610 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T01:26Z] INFO  18:26:50,620 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T01:26Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T01:26Z] INFO  18:26:50,648 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T01:26Z] INFO  18:26:50,664 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T01:26Z] INFO  18:26:50,889 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T01:26Z] WARN  18:26:51,042 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T01:26Z] WARN  18:26:51,043 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T01:26Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T01:26Z] INFO  18:26:51,551 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T01:26Z] INFO  18:26:51,561 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T01:26Z] WARN  18:26:51,775 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T01:26Z] WARN  18:26:51,776 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T01:26Z] INFO  18:26:52,179 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.007458882000000001
[2016-04-15T01:26Z] INFO  18:26:52,180 PairHMM - Total compute time in PairHMM computeLikelihoods() : 0.011333558
[2016-04-15T01:26Z] INFO  18:26:52,181 HaplotypeCaller - Ran local assembly on 32 active regions
[2016-04-15T01:26Z] INFO  18:26:52,247 ProgressMeter -            done          56928.0     7.0 s            2.2 m      100.0%     7.0 s       0.0 s
[2016-04-15T01:26Z] INFO  18:26:52,247 ProgressMeter - Total runtime 7.68 secs, 0.13 min, 0.00 hours
[2016-04-15T01:26Z] INFO  18:26:52,248 MicroScheduler - 550 reads were filtered out during the traversal out of approximately 7230 total reads (7.61%)
[2016-04-15T01:26Z] INFO  18:26:52,249 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:26Z] INFO  18:26:52,250 MicroScheduler -   -> 538 reads (7.44% of total) failing DuplicateReadFilter
[2016-04-15T01:26Z] INFO  18:26:52,251 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:26Z] INFO  18:26:52,252 MicroScheduler -   -> 12 reads (0.17% of total) failing HCMappingQualityFilter
[2016-04-15T01:26Z] INFO  18:26:52,253 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:26Z] INFO  18:26:52,253 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:26Z] INFO  18:26:52,254 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:26Z] INFO  18:26:52,254 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T01:26Z] INFO  18:26:53,824 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:26Z] GATK: HaplotypeCaller
[2016-04-15T01:26Z] INFO  18:26:55,391 ProgressMeter -      19:1225548        9660631.0    30.0 s            3.0 s        8.6%     5.8 m       5.3 m
[2016-04-15T01:26Z] INFO  18:26:56,159 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.035323647
[2016-04-15T01:26Z] INFO  18:26:56,160 PairHMM - Total compute time in PairHMM computeLikelihoods() : 9.713706613000001
[2016-04-15T01:26Z] INFO  18:26:56,161 HaplotypeCaller - Ran local assembly on 2304 active regions
[2016-04-15T01:26Z] INFO  18:26:56,208 ProgressMeter -            done     2.48819629E8    96.0 s            0.0 s      100.0%    96.0 s       0.0 s
[2016-04-15T01:26Z] INFO  18:26:56,208 ProgressMeter - Total runtime 96.52 secs, 1.61 min, 0.03 hours
[2016-04-15T01:26Z] INFO  18:26:56,209 MicroScheduler - 60870 reads were filtered out during the traversal out of approximately 539418 total reads (11.28%)
[2016-04-15T01:26Z] INFO  18:26:56,209 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:26Z] INFO  18:26:56,210 MicroScheduler -   -> 42494 reads (7.88% of total) failing DuplicateReadFilter
[2016-04-15T01:26Z] INFO  18:26:56,210 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:26Z] INFO  18:26:56,210 MicroScheduler -   -> 18376 reads (3.41% of total) failing HCMappingQualityFilter
[2016-04-15T01:26Z] INFO  18:26:56,210 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:26Z] INFO  18:26:56,211 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:26Z] INFO  18:26:56,211 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:26Z] INFO  18:26:56,211 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T01:26Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T01:26Z] INFO  18:26:57,061 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T01:26Z] INFO  18:26:57,061 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T01:26Z] WARN  18:26:57,484 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T01:26Z] WARN  18:26:57,485 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T01:26Z] INFO  18:26:57,660 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:26Z] INFO  18:26:57,663 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:26Z] INFO  18:26:57,664 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:26Z] INFO  18:26:57,664 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:26Z] INFO  18:26:57,669 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/21/R14-18102_kapa-NGv3-PE100-NGv3-sort-21_46595644_48129895-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/21/R14-18102_kapa-NGv3-PE100-NGv3-21_46595644_48129895-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/21/tx/tmpQKgrYY/R14-18102_kapa-NGv3-PE100-NGv3-21_46595644_48129895.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:26Z] INFO  18:26:57,700 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:26Z] INFO  18:26:57,708 HelpFormatter - Date/Time: 2016/04/14 18:26:57
[2016-04-15T01:26Z] INFO  18:26:57,709 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:26Z] INFO  18:26:57,709 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:26Z] WARN  18:26:57,754 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T01:26Z] WARN  18:26:57,756 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/21/tx/tmpQKgrYY/R14-18102_kapa-NGv3-PE100-NGv3-21_46595644_48129895.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T01:26Z] INFO  18:26:57,898 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:26Z] INFO  18:26:58,017 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:26Z] GATK: HaplotypeCaller
[2016-04-15T01:26Z] INFO  18:26:58,274 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T01:26Z] INFO  18:26:58,284 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:26Z] INFO  18:26:58,348 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-15T01:26Z] INFO  18:26:58,366 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T01:26Z] INFO  18:26:58,858 IntervalUtils - Processing 63011 bp from intervals
[2016-04-15T01:26Z] WARN  18:26:58,863 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:26Z] INFO  18:26:59,009 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:26Z] INFO  18:26:59,084 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:26Z] INFO  18:26:59,085 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:26Z] INFO  18:26:59,085 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T01:26Z] INFO  18:26:59,086 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T01:26Z] INFO  18:26:59,098 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T01:26Z] INFO  18:26:59,098 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T01:26Z] INFO  18:26:59,367 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T01:27Z] INFO  18:27:00,010 ProgressMeter -     19:17396499      1.5615141E7    30.0 s            1.0 s       26.8%   111.0 s      81.0 s
[2016-04-15T01:27Z] INFO  18:27:00,206 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.007123844000000001
[2016-04-15T01:27Z] INFO  18:27:00,208 PairHMM - Total compute time in PairHMM computeLikelihoods() : 1.672263767
[2016-04-15T01:27Z] INFO  18:27:00,209 HaplotypeCaller - Ran local assembly on 54 active regions
[2016-04-15T01:27Z] INFO  18:27:00,239 ProgressMeter -            done          75867.0    15.0 s            3.3 m      100.0%    15.0 s       0.0 s
[2016-04-15T01:27Z] INFO  18:27:00,240 ProgressMeter - Total runtime 15.19 secs, 0.25 min, 0.00 hours
[2016-04-15T01:27Z] INFO  18:27:00,241 MicroScheduler - 6188 reads were filtered out during the traversal out of approximately 19958 total reads (31.01%)
[2016-04-15T01:27Z] INFO  18:27:00,241 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:27Z] INFO  18:27:00,242 MicroScheduler -   -> 1305 reads (6.54% of total) failing DuplicateReadFilter
[2016-04-15T01:27Z] INFO  18:27:00,243 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:27Z] INFO  18:27:00,243 MicroScheduler -   -> 4883 reads (24.47% of total) failing HCMappingQualityFilter
[2016-04-15T01:27Z] INFO  18:27:00,244 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:27Z] INFO  18:27:00,245 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:27Z] INFO  18:27:00,245 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:27Z] INFO  18:27:00,246 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T01:27Z] INFO  18:27:00,899 ProgressMeter -     17:40970562     2.68846093E8    90.0 s            0.0 s       63.9%     2.3 m      50.0 s
[2016-04-15T01:27Z] WARN  18:27:01,011 ExactAFCalculator - this tool is currently set to genotype at most 6 alternate alleles in a given context, but the context at 19:17397501 has 10 alternate alleles so only the top alleles will be used; see the --max_alternate_alleles argument
[2016-04-15T01:27Z] INFO  18:27:01,541 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:27Z] INFO  18:27:01,544 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:27Z] INFO  18:27:01,545 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:27Z] INFO  18:27:01,546 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:27Z] INFO  18:27:01,550 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/22/R14-18102_kapa-NGv3-PE100-NGv3-sort-22_0_16258303-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/22/R14-18102_kapa-NGv3-PE100-NGv3-22_0_16258303-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/22/tx/tmpvOtwmn/R14-18102_kapa-NGv3-PE100-NGv3-22_0_16258303.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:27Z] INFO  18:27:01,579 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:27Z] INFO  18:27:01,580 HelpFormatter - Date/Time: 2016/04/14 18:27:01
[2016-04-15T01:27Z] INFO  18:27:01,580 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:27Z] INFO  18:27:01,580 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:27Z] WARN  18:27:01,647 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T01:27Z] WARN  18:27:01,649 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/22/tx/tmpvOtwmn/R14-18102_kapa-NGv3-PE100-NGv3-22_0_16258303.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T01:27Z] INFO  18:27:01,869 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:27Z] INFO  18:27:01,932 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:27Z] INFO  18:27:02,128 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T01:27Z] INFO  18:27:02,151 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:27Z] GATK: HaplotypeCaller
[2016-04-15T01:27Z] INFO  18:27:02,221 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-15T01:27Z] INFO  18:27:02,238 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T01:27Z] INFO  18:27:02,529 IntervalUtils - Processing 118 bp from intervals
[2016-04-15T01:27Z] WARN  18:27:02,533 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:27Z] INFO  18:27:02,667 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:27Z] INFO  18:27:02,708 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:27Z] INFO  18:27:02,709 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:27Z] INFO  18:27:02,710 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T01:27Z] INFO  18:27:02,711 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T01:27Z] INFO  18:27:02,711 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T01:27Z] INFO  18:27:02,711 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T01:27Z] INFO  18:27:02,902 ProgressMeter -     19:35617174      1.1893791E7    30.0 s            2.0 s       11.9%     4.2 m       3.7 m
[2016-04-15T01:27Z] INFO  18:27:02,928 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T01:27Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T01:27Z] INFO  18:27:04,009 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T01:27Z] INFO  18:27:04,010 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T01:27Z] INFO  18:27:04,016 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.0
[2016-04-15T01:27Z] INFO  18:27:04,017 PairHMM - Total compute time in PairHMM computeLikelihoods() : 0.0
[2016-04-15T01:27Z] INFO  18:27:04,017 HaplotypeCaller - Ran local assembly on 1 active regions
[2016-04-15T01:27Z] INFO  18:27:04,064 ProgressMeter -            done            118.0     1.0 s            3.2 h       99.2%     1.0 s       0.0 s
[2016-04-15T01:27Z] INFO  18:27:04,065 ProgressMeter - Total runtime 1.36 secs, 0.02 min, 0.00 hours
[2016-04-15T01:27Z] INFO  18:27:04,066 MicroScheduler - 164 reads were filtered out during the traversal out of approximately 166 total reads (98.80%)
[2016-04-15T01:27Z] INFO  18:27:04,067 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:27Z] INFO  18:27:04,067 MicroScheduler -   -> 0 reads (0.00% of total) failing DuplicateReadFilter
[2016-04-15T01:27Z] INFO  18:27:04,068 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:27Z] INFO  18:27:04,069 MicroScheduler -   -> 164 reads (98.80% of total) failing HCMappingQualityFilter
[2016-04-15T01:27Z] INFO  18:27:04,069 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:27Z] INFO  18:27:04,070 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:27Z] INFO  18:27:04,071 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:27Z] INFO  18:27:04,071 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T01:27Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T01:27Z] INFO  18:27:04,169 ProgressMeter -     17:77111797      2.6654911E8    90.0 s            0.0 s       99.9%    90.0 s       0.0 s
[2016-04-15T01:27Z] INFO  18:27:04,176 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T01:27Z] INFO  18:27:04,177 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T01:27Z] INFO  18:27:04,311 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.048250615000000004
[2016-04-15T01:27Z] INFO  18:27:04,311 PairHMM - Total compute time in PairHMM computeLikelihoods() : 5.569622479
[2016-04-15T01:27Z] INFO  18:27:04,311 HaplotypeCaller - Ran local assembly on 2583 active regions
[2016-04-15T01:27Z] INFO  18:27:04,356 ProgressMeter -            done     2.67239453E8    90.0 s            0.0 s      100.0%    90.0 s       0.0 s
[2016-04-15T01:27Z] INFO  18:27:04,357 ProgressMeter - Total runtime 90.22 secs, 1.50 min, 0.03 hours
[2016-04-15T01:27Z] INFO  18:27:04,357 MicroScheduler - 49789 reads were filtered out during the traversal out of approximately 570457 total reads (8.73%)
[2016-04-15T01:27Z] INFO  18:27:04,358 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:27Z] INFO  18:27:04,358 MicroScheduler -   -> 46268 reads (8.11% of total) failing DuplicateReadFilter
[2016-04-15T01:27Z] INFO  18:27:04,359 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:27Z] INFO  18:27:04,359 MicroScheduler -   -> 3521 reads (0.62% of total) failing HCMappingQualityFilter
[2016-04-15T01:27Z] INFO  18:27:04,359 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:27Z] INFO  18:27:04,360 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:27Z] INFO  18:27:04,360 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:27Z] INFO  18:27:04,360 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T01:27Z] WARN  18:27:04,466 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T01:27Z] WARN  18:27:04,467 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T01:27Z] INFO  18:27:04,559 ProgressMeter -     19:48305908        9110148.0    30.0 s            3.0 s       10.0%     5.0 m       4.5 m
[2016-04-15T01:27Z] INFO  18:27:05,073 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:27Z] INFO  18:27:05,076 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:27Z] INFO  18:27:05,077 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:27Z] INFO  18:27:05,078 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:27Z] INFO  18:27:05,082 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/22/R14-18102_kapa-NGv3-PE100-NGv3-sort-22_16266928_31795711-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/22/R14-18102_kapa-NGv3-PE100-NGv3-22_16266928_31795711-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/22/tx/tmpMVgbqP/R14-18102_kapa-NGv3-PE100-NGv3-22_16266928_31795711.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:27Z] INFO  18:27:05,103 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:27Z] INFO  18:27:05,104 HelpFormatter - Date/Time: 2016/04/14 18:27:05
[2016-04-15T01:27Z] INFO  18:27:05,104 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:27Z] INFO  18:27:05,104 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:27Z] WARN  18:27:05,139 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T01:27Z] WARN  18:27:05,142 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/22/tx/tmpMVgbqP/R14-18102_kapa-NGv3-PE100-NGv3-22_16266928_31795711.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T01:27Z] INFO  18:27:05,369 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:27Z] INFO  18:27:05,429 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:27Z] INFO  18:27:05,615 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T01:27Z] INFO  18:27:05,624 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:27Z] GATK: HaplotypeCaller
[2016-04-15T01:27Z] INFO  18:27:05,694 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:27Z] INFO  18:27:05,707 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-15T01:27Z] INFO  18:27:05,734 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T01:27Z] GATK: HaplotypeCaller
[2016-04-15T01:27Z] INFO  18:27:06,295 IntervalUtils - Processing 372769 bp from intervals
[2016-04-15T01:27Z] WARN  18:27:06,300 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:27Z] INFO  18:27:06,399 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:27Z] INFO  18:27:06,558 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:27Z] INFO  18:27:06,558 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:27Z] INFO  18:27:06,559 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T01:27Z] INFO  18:27:06,559 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T01:27Z] INFO  18:27:06,579 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T01:27Z] INFO  18:27:06,579 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T01:27Z] INFO  18:27:06,818 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T01:27Z] INFO  18:27:08,254 ProgressMeter -      20:2464551        4919436.0    30.0 s            6.0 s       26.2%   114.0 s      84.0 s
[2016-04-15T01:27Z] INFO  18:27:08,433 ProgressMeter -     20:23584026        1.52642E7    30.0 s            1.0 s       53.0%    56.0 s      26.0 s
[2016-04-15T01:27Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T01:27Z] INFO  18:27:09,094 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T01:27Z] INFO  18:27:09,105 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T01:27Z] INFO  18:27:09,224 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:27Z] INFO  18:27:09,226 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:27Z] INFO  18:27:09,226 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:27Z] INFO  18:27:09,227 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:27Z] INFO  18:27:09,231 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/22/R14-18102_kapa-NGv3-PE100-NGv3-sort-22_31796605_47308085-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/22/R14-18102_kapa-NGv3-PE100-NGv3-22_31796605_47308085-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/22/tx/tmpfPZsqg/R14-18102_kapa-NGv3-PE100-NGv3-22_31796605_47308085.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:27Z] INFO  18:27:09,240 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:27Z] INFO  18:27:09,240 HelpFormatter - Date/Time: 2016/04/14 18:27:09
[2016-04-15T01:27Z] INFO  18:27:09,241 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:27Z] INFO  18:27:09,241 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:27Z] WARN  18:27:09,262 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T01:27Z] WARN  18:27:09,263 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T01:27Z] WARN  18:27:09,297 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T01:27Z] WARN  18:27:09,299 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/22/tx/tmpfPZsqg/R14-18102_kapa-NGv3-PE100-NGv3-22_31796605_47308085.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T01:27Z] INFO  18:27:09,321 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:27Z] INFO  18:27:09,324 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:27Z] INFO  18:27:09,325 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:27Z] INFO  18:27:09,325 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:27Z] INFO  18:27:09,330 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/22/R14-18102_kapa-NGv3-PE100-NGv3-sort-22_47309229_51304566-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/22/R14-18102_kapa-NGv3-PE100-NGv3-22_47309229_51304566-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/22/tx/tmpN9IjPT/R14-18102_kapa-NGv3-PE100-NGv3-22_47309229_51304566.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:27Z] INFO  18:27:09,360 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:27Z] INFO  18:27:09,360 HelpFormatter - Date/Time: 2016/04/14 18:27:09
[2016-04-15T01:27Z] INFO  18:27:09,360 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:27Z] INFO  18:27:09,360 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:27Z] WARN  18:27:09,408 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T01:27Z] WARN  18:27:09,416 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/22/tx/tmpN9IjPT/R14-18102_kapa-NGv3-PE100-NGv3-22_47309229_51304566.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T01:27Z] INFO  18:27:09,513 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:27Z] INFO  18:27:09,656 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:27Z] INFO  18:27:09,850 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T01:27Z] INFO  18:27:09,867 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:27Z] INFO  18:27:09,942 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T01:27Z] INFO  18:27:09,959 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-15T01:27Z] INFO  18:27:09,967 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:27Z] INFO  18:27:09,985 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T01:27Z] INFO  18:27:10,057 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.09
[2016-04-15T01:27Z] INFO  18:27:10,095 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T01:27Z] INFO  18:27:10,548 IntervalUtils - Processing 366557 bp from intervals
[2016-04-15T01:27Z] WARN  18:27:10,554 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:27Z] INFO  18:27:10,582 IntervalUtils - Processing 81362 bp from intervals
[2016-04-15T01:27Z] WARN  18:27:10,587 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:27Z] INFO  18:27:10,661 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:27Z] INFO  18:27:10,718 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:27Z] INFO  18:27:10,795 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:27Z] INFO  18:27:10,796 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:27Z] INFO  18:27:10,796 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T01:27Z] INFO  18:27:10,797 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T01:27Z] INFO  18:27:10,808 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T01:27Z] INFO  18:27:10,809 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T01:27Z] INFO  18:27:10,828 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:27Z] INFO  18:27:10,832 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:27Z] INFO  18:27:10,833 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T01:27Z] INFO  18:27:10,834 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T01:27Z] INFO  18:27:10,834 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T01:27Z] INFO  18:27:10,835 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T01:27Z] INFO  18:27:11,050 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T01:27Z] INFO  18:27:11,072 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T01:27Z] INFO  18:27:11,912 ProgressMeter -     20:34765874       2.421956E7    30.0 s            1.0 s       30.8%    97.0 s      67.0 s
[2016-04-15T01:27Z] INFO  18:27:12,819 ProgressMeter -     20:55758964      1.6668605E7    30.0 s            1.0 s       33.9%    88.0 s      58.0 s
[2016-04-15T01:27Z] INFO  18:27:13,145 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.005571268000000001
[2016-04-15T01:27Z] INFO  18:27:13,146 PairHMM - Total compute time in PairHMM computeLikelihoods() : 0.21489158000000003
[2016-04-15T01:27Z] INFO  18:27:13,147 HaplotypeCaller - Ran local assembly on 444 active regions
[2016-04-15T01:27Z] INFO  18:27:13,188 ProgressMeter -            done        8975092.0    24.0 s            2.0 s      100.0%    24.0 s       0.0 s
[2016-04-15T01:27Z] INFO  18:27:13,189 ProgressMeter - Total runtime 24.02 secs, 0.40 min, 0.01 hours
[2016-04-15T01:27Z] INFO  18:27:13,190 MicroScheduler - 5799 reads were filtered out during the traversal out of approximately 67611 total reads (8.58%)
[2016-04-15T01:27Z] INFO  18:27:13,191 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:27Z] INFO  18:27:13,191 MicroScheduler -   -> 5507 reads (8.15% of total) failing DuplicateReadFilter
[2016-04-15T01:27Z] INFO  18:27:13,192 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:27Z] INFO  18:27:13,192 MicroScheduler -   -> 292 reads (0.43% of total) failing HCMappingQualityFilter
[2016-04-15T01:27Z] INFO  18:27:13,193 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:27Z] INFO  18:27:13,194 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:27Z] INFO  18:27:13,194 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:27Z] INFO  18:27:13,195 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T01:27Z] INFO  18:27:14,775 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:27Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T01:27Z] INFO  18:27:15,096 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T01:27Z] INFO  18:27:15,097 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T01:27Z] GATK: HaplotypeCaller
[2016-04-15T01:27Z] WARN  18:27:15,482 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T01:27Z] WARN  18:27:15,483 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T01:27Z] INFO  18:27:17,993 ProgressMeter -     17:11711049     4.42408515E8   120.0 s            0.0 s       94.2%     2.1 m       7.0 s
[2016-04-15T01:27Z] INFO  18:27:18,062 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:27Z] INFO  18:27:18,075 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:27Z] INFO  18:27:18,075 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:27Z] INFO  18:27:18,076 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:27Z] INFO  18:27:18,080 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/X/R14-18102_kapa-NGv3-PE100-NGv3-sort-X_0_15509380-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/X/R14-18102_kapa-NGv3-PE100-NGv3-X_0_15509380-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/X/tx/tmpxD5y1Z/R14-18102_kapa-NGv3-PE100-NGv3-X_0_15509380.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:27Z] INFO  18:27:18,099 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:27Z] INFO  18:27:18,099 HelpFormatter - Date/Time: 2016/04/14 18:27:18
[2016-04-15T01:27Z] INFO  18:27:18,099 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:27Z] INFO  18:27:18,100 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:27Z] WARN  18:27:18,139 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T01:27Z] WARN  18:27:18,141 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/X/tx/tmpxD5y1Z/R14-18102_kapa-NGv3-PE100-NGv3-X_0_15509380.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T01:27Z] INFO  18:27:18,400 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:27Z] INFO  18:27:18,599 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T01:27Z] INFO  18:27:18,609 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:27Z] INFO  18:27:18,673 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-15T01:27Z] INFO  18:27:18,720 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T01:27Z] INFO  18:27:19,152 IntervalUtils - Processing 114122 bp from intervals
[2016-04-15T01:27Z] WARN  18:27:19,157 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:27Z] INFO  18:27:19,238 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:27Z] INFO  18:27:19,285 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:27Z] INFO  18:27:19,286 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:27Z] INFO  18:27:19,286 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T01:27Z] INFO  18:27:19,287 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T01:27Z] INFO  18:27:19,288 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T01:27Z] INFO  18:27:19,288 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T01:27Z] INFO  18:27:19,447 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T01:27Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T01:27Z] INFO  18:27:20,031 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T01:27Z] INFO  18:27:20,032 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T01:27Z] WARN  18:27:20,476 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T01:27Z] WARN  18:27:20,484 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T01:27Z] INFO  18:27:20,613 ProgressMeter -     21:36206898      1.6943494E7    30.0 s            1.0 s       33.7%    89.0 s      59.0 s
[2016-04-15T01:27Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T01:27Z] INFO  18:27:21,383 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T01:27Z] INFO  18:27:21,384 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T01:27Z] WARN  18:27:21,691 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T01:27Z] WARN  18:27:21,692 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T01:27Z] INFO  18:27:24,602 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.009147193000000001
[2016-04-15T01:27Z] INFO  18:27:24,603 PairHMM - Total compute time in PairHMM computeLikelihoods() : 0.6029071730000001
[2016-04-15T01:27Z] INFO  18:27:24,604 HaplotypeCaller - Ran local assembly on 494 active regions
[2016-04-15T01:27Z] INFO  18:27:24,658 ProgressMeter -            done        9449583.0    25.0 s            2.0 s      100.0%    25.0 s       0.0 s
[2016-04-15T01:27Z] INFO  18:27:24,658 ProgressMeter - Total runtime 25.57 secs, 0.43 min, 0.01 hours
[2016-04-15T01:27Z] INFO  18:27:24,658 MicroScheduler - 8881 reads were filtered out during the traversal out of approximately 106888 total reads (8.31%)
[2016-04-15T01:27Z] INFO  18:27:24,659 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:27Z] INFO  18:27:24,659 MicroScheduler -   -> 8699 reads (8.14% of total) failing DuplicateReadFilter
[2016-04-15T01:27Z] INFO  18:27:24,659 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:27Z] INFO  18:27:24,659 MicroScheduler -   -> 182 reads (0.17% of total) failing HCMappingQualityFilter
[2016-04-15T01:27Z] INFO  18:27:24,660 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:27Z] INFO  18:27:24,660 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:27Z] INFO  18:27:24,661 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:27Z] INFO  18:27:24,661 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T01:27Z] INFO  18:27:24,955 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.02940985
[2016-04-15T01:27Z] INFO  18:27:24,956 PairHMM - Total compute time in PairHMM computeLikelihoods() : 1.681778218
[2016-04-15T01:27Z] INFO  18:27:24,956 HaplotypeCaller - Ran local assembly on 1134 active regions
[2016-04-15T01:27Z] INFO  18:27:24,993 ProgressMeter -            done      5.5115211E7    46.0 s            0.0 s      100.0%    46.0 s       0.0 s
[2016-04-15T01:27Z] INFO  18:27:24,994 ProgressMeter - Total runtime 46.59 secs, 0.78 min, 0.01 hours
[2016-04-15T01:27Z] INFO  18:27:24,995 MicroScheduler - 19602 reads were filtered out during the traversal out of approximately 230286 total reads (8.51%)
[2016-04-15T01:27Z] INFO  18:27:25,006 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:27Z] INFO  18:27:25,007 MicroScheduler -   -> 18658 reads (8.10% of total) failing DuplicateReadFilter
[2016-04-15T01:27Z] INFO  18:27:25,008 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:27Z] INFO  18:27:25,008 MicroScheduler -   -> 944 reads (0.41% of total) failing HCMappingQualityFilter
[2016-04-15T01:27Z] INFO  18:27:25,008 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:27Z] INFO  18:27:25,009 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:27Z] INFO  18:27:25,009 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:27Z] INFO  18:27:25,009 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T01:27Z] INFO  18:27:25,196 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.07413441800000001
[2016-04-15T01:27Z] INFO  18:27:25,198 PairHMM - Total compute time in PairHMM computeLikelihoods() : 5.3536066380000005
[2016-04-15T01:27Z] INFO  18:27:25,198 HaplotypeCaller - Ran local assembly on 3842 active regions
[2016-04-15T01:27Z] INFO  18:27:25,262 ProgressMeter -            done      5.1376592E8     2.1 m            0.0 s      100.0%     2.1 m       0.0 s
[2016-04-15T01:27Z] INFO  18:27:25,262 ProgressMeter - Total runtime 127.29 secs, 2.12 min, 0.04 hours
[2016-04-15T01:27Z] INFO  18:27:25,262 MicroScheduler - 79539 reads were filtered out during the traversal out of approximately 865847 total reads (9.19%)
[2016-04-15T01:27Z] INFO  18:27:25,263 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:27Z] INFO  18:27:25,263 MicroScheduler -   -> 69772 reads (8.06% of total) failing DuplicateReadFilter
[2016-04-15T01:27Z] INFO  18:27:25,263 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:27Z] INFO  18:27:25,263 MicroScheduler -   -> 9767 reads (1.13% of total) failing HCMappingQualityFilter
[2016-04-15T01:27Z] INFO  18:27:25,264 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:27Z] INFO  18:27:25,264 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:27Z] INFO  18:27:25,264 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:27Z] INFO  18:27:25,264 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T01:27Z] INFO  18:27:25,392 ProgressMeter -      19:3637133      8.0880761E7    60.0 s            0.0 s       25.7%     3.9 m       2.9 m
[2016-04-15T01:27Z] INFO  18:27:26,069 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:27Z] INFO  18:27:26,299 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:27Z] GATK: HaplotypeCaller
[2016-04-15T01:27Z] GATK: HaplotypeCaller
[2016-04-15T01:27Z] INFO  18:27:26,672 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:27Z] GATK: HaplotypeCaller
[2016-04-15T01:27Z] INFO  18:27:29,564 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:27Z] INFO  18:27:29,568 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:27Z] INFO  18:27:29,568 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:27Z] INFO  18:27:29,569 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:27Z] INFO  18:27:29,573 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/X/R14-18102_kapa-NGv3-PE100-NGv3-sort-X_15518899_31090070-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/X/R14-18102_kapa-NGv3-PE100-NGv3-X_15518899_31090070-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/X/tx/tmpkjI0Op/R14-18102_kapa-NGv3-PE100-NGv3-X_15518899_31090070.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:27Z] INFO  18:27:29,583 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:27Z] INFO  18:27:29,590 HelpFormatter - Date/Time: 2016/04/14 18:27:29
[2016-04-15T01:27Z] INFO  18:27:29,590 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:27Z] INFO  18:27:29,590 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:27Z] WARN  18:27:29,613 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T01:27Z] WARN  18:27:29,620 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/X/tx/tmpkjI0Op/R14-18102_kapa-NGv3-PE100-NGv3-X_15518899_31090070.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T01:27Z] INFO  18:27:29,675 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:27Z] INFO  18:27:29,678 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:27Z] INFO  18:27:29,679 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:27Z] INFO  18:27:29,679 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:27Z] INFO  18:27:29,684 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/X/R14-18102_kapa-NGv3-PE100-NGv3-sort-X_31139949_46696637-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/X/R14-18102_kapa-NGv3-PE100-NGv3-X_31139949_46696637-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/X/tx/tmpaFz5l7/R14-18102_kapa-NGv3-PE100-NGv3-X_31139949_46696637.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:27Z] INFO  18:27:29,693 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:27Z] INFO  18:27:29,704 HelpFormatter - Date/Time: 2016/04/14 18:27:29
[2016-04-15T01:27Z] INFO  18:27:29,705 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:27Z] INFO  18:27:29,706 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:27Z] WARN  18:27:29,743 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T01:27Z] WARN  18:27:29,746 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/X/tx/tmpaFz5l7/R14-18102_kapa-NGv3-PE100-NGv3-X_31139949_46696637.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T01:27Z] INFO  18:27:29,782 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:27Z] INFO  18:27:29,956 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:27Z] INFO  18:27:30,005 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T01:27Z] INFO  18:27:30,011 ProgressMeter -     19:19746224     1.01315297E8    60.0 s            0.0 s       70.2%    85.0 s      25.0 s
[2016-04-15T01:27Z] INFO  18:27:30,014 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:27Z] INFO  18:27:30,052 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:27Z] INFO  18:27:30,056 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:27Z] INFO  18:27:30,056 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:27Z] INFO  18:27:30,057 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:27Z] INFO  18:27:30,062 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/X/R14-18102_kapa-NGv3-PE100-NGv3-sort-X_46712910_62570698-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/X/R14-18102_kapa-NGv3-PE100-NGv3-X_46712910_62570698-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/X/tx/tmpj4X5ig/R14-18102_kapa-NGv3-PE100-NGv3-X_46712910_62570698.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:27Z] INFO  18:27:30,071 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:27Z] INFO  18:27:30,071 HelpFormatter - Date/Time: 2016/04/14 18:27:30
[2016-04-15T01:27Z] INFO  18:27:30,071 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:27Z] INFO  18:27:30,072 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:27Z] INFO  18:27:30,092 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-15T01:27Z] INFO  18:27:30,110 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T01:27Z] WARN  18:27:30,127 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T01:27Z] WARN  18:27:30,129 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/X/tx/tmpj4X5ig/R14-18102_kapa-NGv3-PE100-NGv3-X_46712910_62570698.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T01:27Z] INFO  18:27:30,140 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T01:27Z] INFO  18:27:30,149 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:27Z] INFO  18:27:30,230 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-15T01:27Z] INFO  18:27:30,250 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T01:27Z] INFO  18:27:30,341 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:27Z] INFO  18:27:30,450 IntervalUtils - Processing 133046 bp from intervals
[2016-04-15T01:27Z] WARN  18:27:30,455 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:27Z] INFO  18:27:30,513 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T01:27Z] INFO  18:27:30,528 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:27Z] INFO  18:27:30,572 IntervalUtils - Processing 99894 bp from intervals
[2016-04-15T01:27Z] WARN  18:27:30,576 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:27Z] INFO  18:27:30,581 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:27Z] INFO  18:27:30,625 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.10
[2016-04-15T01:27Z] INFO  18:27:30,650 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T01:27Z] INFO  18:27:30,657 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:27Z] INFO  18:27:30,657 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:27Z] INFO  18:27:30,658 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T01:27Z] INFO  18:27:30,658 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T01:27Z] INFO  18:27:30,658 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T01:27Z] INFO  18:27:30,659 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T01:27Z] INFO  18:27:30,677 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:27Z] INFO  18:27:30,742 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:27Z] INFO  18:27:30,743 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:27Z] INFO  18:27:30,744 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T01:27Z] INFO  18:27:30,745 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T01:27Z] INFO  18:27:30,745 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T01:27Z] INFO  18:27:30,746 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T01:27Z] INFO  18:27:30,876 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T01:27Z] INFO  18:27:30,900 ProgressMeter -     17:44631076     5.07793472E8   120.0 s            0.0 s       90.2%     2.2 m      13.0 s
[2016-04-15T01:27Z] INFO  18:27:30,926 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T01:27Z] INFO  18:27:31,017 IntervalUtils - Processing 228299 bp from intervals
[2016-04-15T01:27Z] WARN  18:27:31,023 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:27Z] INFO  18:27:31,106 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:27Z] INFO  18:27:31,201 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:27Z] INFO  18:27:31,202 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:27Z] INFO  18:27:31,203 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T01:27Z] INFO  18:27:31,203 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T01:27Z] INFO  18:27:31,210 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T01:27Z] INFO  18:27:31,211 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T01:27Z] INFO  18:27:31,460 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T01:27Z] INFO  18:27:32,903 ProgressMeter -     19:38384784      6.9823147E7    60.0 s            0.0 s       34.4%     2.9 m     114.0 s
[2016-04-15T01:27Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T01:27Z] INFO  18:27:33,949 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T01:27Z] INFO  18:27:33,950 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T01:27Z] WARN  18:27:34,201 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T01:27Z] WARN  18:27:34,202 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T01:27Z] INFO  18:27:34,560 ProgressMeter -     19:49956589      6.8296457E7    60.0 s            0.0 s       25.1%     4.0 m       3.0 m
[2016-04-15T01:27Z] INFO  18:27:36,581 ProgressMeter -     22:20102554      1.7939277E7    30.0 s            1.0 s       24.4%     2.1 m      93.0 s
[2016-04-15T01:27Z] INFO  18:27:37,078 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.015562698000000002
[2016-04-15T01:27Z] INFO  18:27:37,079 PairHMM - Total compute time in PairHMM computeLikelihoods() : 4.245125558000001
[2016-04-15T01:27Z] INFO  18:27:37,080 HaplotypeCaller - Ran local assembly on 1366 active regions
[2016-04-15T01:27Z] INFO  18:27:37,125 ProgressMeter -            done      8.3134367E7    58.0 s            0.0 s      100.0%    58.0 s       0.0 s
[2016-04-15T01:27Z] INFO  18:27:37,126 ProgressMeter - Total runtime 58.90 secs, 0.98 min, 0.02 hours
[2016-04-15T01:27Z] INFO  18:27:37,141 MicroScheduler - 24335 reads were filtered out during the traversal out of approximately 285686 total reads (8.52%)
[2016-04-15T01:27Z] INFO  18:27:37,142 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:27Z] INFO  18:27:37,142 MicroScheduler -   -> 23164 reads (8.11% of total) failing DuplicateReadFilter
[2016-04-15T01:27Z] INFO  18:27:37,142 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:27Z] INFO  18:27:37,143 MicroScheduler -   -> 1171 reads (0.41% of total) failing HCMappingQualityFilter
[2016-04-15T01:27Z] INFO  18:27:37,143 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:27Z] INFO  18:27:37,143 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:27Z] INFO  18:27:37,143 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:27Z] INFO  18:27:37,143 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T01:27Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T01:27Z] INFO  18:27:38,108 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T01:27Z] INFO  18:27:38,110 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T01:27Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T01:27Z] INFO  18:27:38,172 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T01:27Z] INFO  18:27:38,173 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T01:27Z] WARN  18:27:38,315 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T01:27Z] WARN  18:27:38,316 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T01:27Z] WARN  18:27:38,447 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T01:27Z] WARN  18:27:38,448 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T01:27Z] INFO  18:27:38,589 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:27Z] GATK: HaplotypeCaller
[2016-04-15T01:27Z] INFO  18:27:40,032 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.008074716000000001
[2016-04-15T01:27Z] INFO  18:27:40,033 PairHMM - Total compute time in PairHMM computeLikelihoods() : 0.38246300400000005
[2016-04-15T01:27Z] INFO  18:27:40,033 HaplotypeCaller - Ran local assembly on 635 active regions
[2016-04-15T01:27Z] INFO  18:27:40,118 ProgressMeter -            done      1.1546648E7    29.0 s            2.0 s      100.0%    29.0 s       0.0 s
[2016-04-15T01:27Z] INFO  18:27:40,119 ProgressMeter - Total runtime 29.32 secs, 0.49 min, 0.01 hours
[2016-04-15T01:27Z] INFO  18:27:40,119 MicroScheduler - 13234 reads were filtered out during the traversal out of approximately 146865 total reads (9.01%)
[2016-04-15T01:27Z] INFO  18:27:40,119 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:27Z] INFO  18:27:40,120 MicroScheduler -   -> 11950 reads (8.14% of total) failing DuplicateReadFilter
[2016-04-15T01:27Z] INFO  18:27:40,120 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:27Z] INFO  18:27:40,120 MicroScheduler -   -> 1284 reads (0.87% of total) failing HCMappingQualityFilter
[2016-04-15T01:27Z] INFO  18:27:40,120 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:27Z] INFO  18:27:40,121 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:27Z] INFO  18:27:40,121 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:27Z] INFO  18:27:40,121 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T01:27Z] INFO  18:27:40,861 ProgressMeter -     22:37887850      2.3623584E7    30.0 s            1.0 s       26.3%   114.0 s      84.0 s
[2016-04-15T01:27Z] INFO  18:27:41,725 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:27Z] INFO  18:27:41,913 ProgressMeter -     20:43996467      1.5347749E8    60.0 s            0.0 s       77.8%    77.0 s      17.0 s
[2016-04-15T01:27Z] INFO  18:27:41,922 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:27Z] INFO  18:27:41,934 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:27Z] INFO  18:27:41,934 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:27Z] INFO  18:27:41,935 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:27Z] INFO  18:27:41,939 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/X/R14-18102_kapa-NGv3-PE100-NGv3-sort-X_62857907_78427545-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/X/R14-18102_kapa-NGv3-PE100-NGv3-X_62857907_78427545-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/X/tx/tmp1WK9oM/R14-18102_kapa-NGv3-PE100-NGv3-X_62857907_78427545.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:27Z] INFO  18:27:41,973 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:27Z] INFO  18:27:41,973 HelpFormatter - Date/Time: 2016/04/14 18:27:41
[2016-04-15T01:27Z] INFO  18:27:41,973 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:27Z] INFO  18:27:41,973 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:27Z] WARN  18:27:42,002 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T01:27Z] WARN  18:27:42,004 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/X/tx/tmp1WK9oM/R14-18102_kapa-NGv3-PE100-NGv3-X_62857907_78427545.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T01:27Z] GATK: HaplotypeCaller
[2016-04-15T01:27Z] INFO  18:27:42,207 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:27Z] INFO  18:27:42,335 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T01:27Z] INFO  18:27:42,344 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:27Z] INFO  18:27:42,416 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.07
[2016-04-15T01:27Z] INFO  18:27:42,446 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T01:27Z] INFO  18:27:42,820 ProgressMeter -     20:61959479       9.896972E7    60.0 s            0.0 s       79.7%    75.0 s      15.0 s
[2016-04-15T01:27Z] INFO  18:27:42,849 IntervalUtils - Processing 175038 bp from intervals
[2016-04-15T01:27Z] WARN  18:27:42,865 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:27Z] INFO  18:27:42,985 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:27Z] INFO  18:27:43,062 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:27Z] INFO  18:27:43,063 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:27Z] INFO  18:27:43,064 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T01:27Z] INFO  18:27:43,065 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T01:27Z] INFO  18:27:43,066 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T01:27Z] INFO  18:27:43,066 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T01:27Z] INFO  18:27:43,230 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T01:27Z] INFO  18:27:45,199 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.053813576
[2016-04-15T01:27Z] INFO  18:27:45,200 PairHMM - Total compute time in PairHMM computeLikelihoods() : 7.323612453000001
[2016-04-15T01:27Z] INFO  18:27:45,201 HaplotypeCaller - Ran local assembly on 4001 active regions
[2016-04-15T01:27Z] INFO  18:27:45,254 ProgressMeter -            done     6.43955503E8     2.2 m            0.0 s      100.0%     2.2 m       0.0 s
[2016-04-15T01:27Z] INFO  18:27:45,254 ProgressMeter - Total runtime 134.40 secs, 2.24 min, 0.04 hours
[2016-04-15T01:27Z] INFO  18:27:45,255 MicroScheduler - 233886 reads were filtered out during the traversal out of approximately 1061994 total reads (22.02%)
[2016-04-15T01:27Z] INFO  18:27:45,255 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:27Z] INFO  18:27:45,255 MicroScheduler -   -> 74838 reads (7.05% of total) failing DuplicateReadFilter
[2016-04-15T01:27Z] INFO  18:27:45,256 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:27Z] INFO  18:27:45,256 MicroScheduler -   -> 159048 reads (14.98% of total) failing HCMappingQualityFilter
[2016-04-15T01:27Z] INFO  18:27:45,256 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:27Z] INFO  18:27:45,256 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:27Z] INFO  18:27:45,257 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:27Z] INFO  18:27:45,257 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T01:27Z] INFO  18:27:45,492 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:27Z] INFO  18:27:45,495 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:27Z] INFO  18:27:45,496 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:27Z] INFO  18:27:45,496 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:27Z] INFO  18:27:45,500 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/X/R14-18102_kapa-NGv3-PE100-NGv3-sort-X_78616585_95940189-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/X/R14-18102_kapa-NGv3-PE100-NGv3-X_78616585_95940189-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/X/tx/tmpt8tPwz/R14-18102_kapa-NGv3-PE100-NGv3-X_78616585_95940189.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:27Z] INFO  18:27:45,516 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:27Z] INFO  18:27:45,517 HelpFormatter - Date/Time: 2016/04/14 18:27:45
[2016-04-15T01:27Z] INFO  18:27:45,517 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:27Z] INFO  18:27:45,518 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:27Z] WARN  18:27:45,541 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T01:27Z] WARN  18:27:45,544 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/X/tx/tmpt8tPwz/R14-18102_kapa-NGv3-PE100-NGv3-X_78616585_95940189.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T01:27Z] INFO  18:27:45,746 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:27Z] INFO  18:27:45,935 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T01:27Z] INFO  18:27:45,956 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:27Z] INFO  18:27:46,048 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.09
[2016-04-15T01:27Z] INFO  18:27:46,071 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T01:27Z] INFO  18:27:46,433 IntervalUtils - Processing 45787 bp from intervals
[2016-04-15T01:27Z] WARN  18:27:46,438 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:27Z] INFO  18:27:46,556 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:27Z] INFO  18:27:46,588 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:27Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T01:27Z] INFO  18:27:46,605 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T01:27Z] INFO  18:27:46,606 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T01:27Z] INFO  18:27:46,619 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:27Z] INFO  18:27:46,621 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:27Z] INFO  18:27:46,621 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T01:27Z] INFO  18:27:46,622 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T01:27Z] INFO  18:27:46,623 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T01:27Z] INFO  18:27:46,623 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T01:27Z] INFO  18:27:46,808 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T01:27Z] GATK: HaplotypeCaller
[2016-04-15T01:27Z] WARN  18:27:46,971 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T01:27Z] WARN  18:27:46,972 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T01:27Z] INFO  18:27:49,307 ProgressMeter -      X:13337386      1.5123124E7    30.0 s            1.0 s       77.3%    38.0 s       8.0 s
[2016-04-15T01:27Z] INFO  18:27:50,240 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:27Z] INFO  18:27:50,244 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:27Z] INFO  18:27:50,244 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:27Z] INFO  18:27:50,244 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:27Z] INFO  18:27:50,249 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/X/R14-18102_kapa-NGv3-PE100-NGv3-sort-X_95990756_111698889-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/X/R14-18102_kapa-NGv3-PE100-NGv3-X_95990756_111698889-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/X/tx/tmpv10TtP/R14-18102_kapa-NGv3-PE100-NGv3-X_95990756_111698889.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:27Z] INFO  18:27:50,260 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:27Z] INFO  18:27:50,261 HelpFormatter - Date/Time: 2016/04/14 18:27:50
[2016-04-15T01:27Z] INFO  18:27:50,261 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:27Z] INFO  18:27:50,261 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:27Z] WARN  18:27:50,321 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T01:27Z] WARN  18:27:50,324 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/X/tx/tmpv10TtP/R14-18102_kapa-NGv3-PE100-NGv3-X_95990756_111698889.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T01:27Z] INFO  18:27:50,621 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:27Z] INFO  18:27:50,617 ProgressMeter -     21:44448907       1.138075E8    60.0 s            0.0 s       77.6%    77.0 s      17.0 s
[2016-04-15T01:27Z] INFO  18:27:50,858 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T01:27Z] INFO  18:27:50,868 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:27Z] INFO  18:27:50,961 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.09
[2016-04-15T01:27Z] INFO  18:27:50,985 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T01:27Z] INFO  18:27:51,415 IntervalUtils - Processing 181656 bp from intervals
[2016-04-15T01:27Z] WARN  18:27:51,420 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:27Z] INFO  18:27:51,538 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:27Z] INFO  18:27:51,663 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:27Z] INFO  18:27:51,677 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:27Z] INFO  18:27:51,678 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T01:27Z] INFO  18:27:51,679 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T01:27Z] INFO  18:27:51,685 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T01:27Z] INFO  18:27:51,686 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T01:27Z] INFO  18:27:51,910 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T01:27Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T01:27Z] INFO  18:27:52,104 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T01:27Z] INFO  18:27:52,105 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T01:27Z] INFO  18:27:52,269 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.025725352
[2016-04-15T01:27Z] INFO  18:27:52,270 PairHMM - Total compute time in PairHMM computeLikelihoods() : 2.284910161
[2016-04-15T01:27Z] INFO  18:27:52,270 HaplotypeCaller - Ran local assembly on 2185 active regions
[2016-04-15T01:27Z] INFO  18:27:52,322 ProgressMeter -            done     1.55945449E8    82.0 s            0.0 s      100.0%    82.0 s       0.0 s
[2016-04-15T01:27Z] INFO  18:27:52,323 ProgressMeter - Total runtime 82.33 secs, 1.37 min, 0.02 hours
[2016-04-15T01:27Z] INFO  18:27:52,323 MicroScheduler - 50023 reads were filtered out during the traversal out of approximately 532085 total reads (9.40%)
[2016-04-15T01:27Z] INFO  18:27:52,323 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:27Z] INFO  18:27:52,323 MicroScheduler -   -> 43217 reads (8.12% of total) failing DuplicateReadFilter
[2016-04-15T01:27Z] INFO  18:27:52,324 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:27Z] INFO  18:27:52,324 MicroScheduler -   -> 6806 reads (1.28% of total) failing HCMappingQualityFilter
[2016-04-15T01:27Z] INFO  18:27:52,324 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:27Z] INFO  18:27:52,324 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:27Z] INFO  18:27:52,325 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:27Z] INFO  18:27:52,325 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T01:27Z] WARN  18:27:52,468 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T01:27Z] WARN  18:27:52,469 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T01:27Z] INFO  18:27:53,933 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:27Z] GATK: HaplotypeCaller
[2016-04-15T01:27Z] INFO  18:27:54,718 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.00880914
[2016-04-15T01:27Z] INFO  18:27:54,719 PairHMM - Total compute time in PairHMM computeLikelihoods() : 0.573920294
[2016-04-15T01:27Z] INFO  18:27:54,719 HaplotypeCaller - Ran local assembly on 790 active regions
[2016-04-15T01:27Z] INFO  18:27:54,780 ProgressMeter -            done      2.7892284E7    35.0 s            1.0 s      100.0%    35.0 s       0.0 s
[2016-04-15T01:27Z] INFO  18:27:54,781 ProgressMeter - Total runtime 35.50 secs, 0.59 min, 0.01 hours
[2016-04-15T01:27Z] INFO  18:27:54,781 MicroScheduler - 24368 reads were filtered out during the traversal out of approximately 182210 total reads (13.37%)
[2016-04-15T01:27Z] INFO  18:27:54,781 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:27Z] INFO  18:27:54,782 MicroScheduler -   -> 14192 reads (7.79% of total) failing DuplicateReadFilter
[2016-04-15T01:27Z] INFO  18:27:54,782 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:27Z] INFO  18:27:54,783 MicroScheduler -   -> 10176 reads (5.58% of total) failing HCMappingQualityFilter
[2016-04-15T01:27Z] INFO  18:27:54,783 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:27Z] INFO  18:27:54,783 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:27Z] INFO  18:27:54,784 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:27Z] INFO  18:27:54,784 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T01:27Z] INFO  18:27:55,196 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.039884211
[2016-04-15T01:27Z] INFO  18:27:55,197 PairHMM - Total compute time in PairHMM computeLikelihoods() : 1.9041394900000002
[2016-04-15T01:27Z] INFO  18:27:55,198 HaplotypeCaller - Ran local assembly on 1985 active regions
[2016-04-15T01:27Z] INFO  18:27:55,230 ProgressMeter -            done      1.4684951E8    72.0 s            0.0 s      100.0%    72.0 s       0.0 s
[2016-04-15T01:27Z] INFO  18:27:55,231 ProgressMeter - Total runtime 72.43 secs, 1.21 min, 0.02 hours
[2016-04-15T01:27Z] INFO  18:27:55,231 MicroScheduler - 37386 reads were filtered out during the traversal out of approximately 441163 total reads (8.47%)
[2016-04-15T01:27Z] INFO  18:27:55,232 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:27Z] INFO  18:27:55,233 MicroScheduler -   -> 36259 reads (8.22% of total) failing DuplicateReadFilter
[2016-04-15T01:27Z] INFO  18:27:55,233 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:27Z] INFO  18:27:55,234 MicroScheduler -   -> 1127 reads (0.26% of total) failing HCMappingQualityFilter
[2016-04-15T01:27Z] INFO  18:27:55,234 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:27Z] INFO  18:27:55,235 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:27Z] INFO  18:27:55,236 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:27Z] INFO  18:27:55,236 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T01:27Z] INFO  18:27:55,393 ProgressMeter -      19:6217965     2.18580266E8    90.0 s            0.0 s       39.6%     3.8 m       2.3 m
[2016-04-15T01:27Z] INFO  18:27:56,330 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:27Z] INFO  18:27:56,587 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:27Z] GATK: HaplotypeCaller
[2016-04-15T01:27Z] INFO  18:27:56,674 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.004914866
[2016-04-15T01:27Z] INFO  18:27:56,675 PairHMM - Total compute time in PairHMM computeLikelihoods() : 0.09620442800000001
[2016-04-15T01:27Z] INFO  18:27:56,676 HaplotypeCaller - Ran local assembly on 654 active regions
[2016-04-15T01:27Z] INFO  18:27:56,744 ProgressMeter -            done      2.4524947E7    25.0 s            1.0 s      100.0%    25.0 s       0.0 s
[2016-04-15T01:27Z] INFO  18:27:56,744 ProgressMeter - Total runtime 26.00 secs, 0.43 min, 0.01 hours
[2016-04-15T01:27Z] INFO  18:27:56,745 MicroScheduler - 11856 reads were filtered out during the traversal out of approximately 139128 total reads (8.52%)
[2016-04-15T01:27Z] INFO  18:27:56,745 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:27Z] INFO  18:27:56,745 MicroScheduler -   -> 11119 reads (7.99% of total) failing DuplicateReadFilter
[2016-04-15T01:27Z] INFO  18:27:56,745 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:27Z] INFO  18:27:56,746 MicroScheduler -   -> 737 reads (0.53% of total) failing HCMappingQualityFilter
[2016-04-15T01:27Z] INFO  18:27:56,746 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:27Z] INFO  18:27:56,746 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:27Z] INFO  18:27:56,746 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:27Z] INFO  18:27:56,747 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T01:27Z] GATK: HaplotypeCaller
[2016-04-15T01:27Z] INFO  18:27:57,022 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:27Z] INFO  18:27:57,025 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:27Z] INFO  18:27:57,026 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:27Z] INFO  18:27:57,026 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:27Z] INFO  18:27:57,031 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/X/R14-18102_kapa-NGv3-PE100-NGv3-sort-X_111874647_128581278-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/X/R14-18102_kapa-NGv3-PE100-NGv3-X_111874647_128581278-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/X/tx/tmp3EsWxK/R14-18102_kapa-NGv3-PE100-NGv3-X_111874647_128581278.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:27Z] INFO  18:27:57,047 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:27Z] INFO  18:27:57,048 HelpFormatter - Date/Time: 2016/04/14 18:27:57
[2016-04-15T01:27Z] INFO  18:27:57,048 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:27Z] INFO  18:27:57,049 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:27Z] WARN  18:27:57,085 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T01:27Z] WARN  18:27:57,088 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/X/tx/tmp3EsWxK/R14-18102_kapa-NGv3-PE100-NGv3-X_111874647_128581278.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T01:27Z] INFO  18:27:57,300 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:27Z] INFO  18:27:57,552 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T01:27Z] INFO  18:27:57,561 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:27Z] INFO  18:27:57,642 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-15T01:27Z] INFO  18:27:57,676 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T01:27Z] INFO  18:27:58,102 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:27Z] INFO  18:27:58,111 IntervalUtils - Processing 115535 bp from intervals
[2016-04-15T01:27Z] WARN  18:27:58,127 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:27Z] INFO  18:27:58,256 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:27Z] INFO  18:27:58,329 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:27Z] INFO  18:27:58,330 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:27Z] INFO  18:27:58,331 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T01:27Z] INFO  18:27:58,332 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T01:27Z] GATK: HaplotypeCaller
[2016-04-15T01:27Z] INFO  18:27:58,342 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T01:27Z] INFO  18:27:58,342 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T01:27Z] INFO  18:27:58,373 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.016903726
[2016-04-15T01:27Z] INFO  18:27:58,374 PairHMM - Total compute time in PairHMM computeLikelihoods() : 1.0517773350000001
[2016-04-15T01:27Z] INFO  18:27:58,375 HaplotypeCaller - Ran local assembly on 2350 active regions
[2016-04-15T01:27Z] INFO  18:27:58,456 ProgressMeter -            done     2.49280923E8    76.0 s            0.0 s      100.0%    76.0 s       0.0 s
[2016-04-15T01:27Z] INFO  18:27:58,456 ProgressMeter - Total runtime 76.58 secs, 1.28 min, 0.02 hours
[2016-04-15T01:27Z] INFO  18:27:58,457 MicroScheduler - 44263 reads were filtered out during the traversal out of approximately 542385 total reads (8.16%)
[2016-04-15T01:27Z] INFO  18:27:58,457 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:27Z] INFO  18:27:58,457 MicroScheduler -   -> 43602 reads (8.04% of total) failing DuplicateReadFilter
[2016-04-15T01:27Z] INFO  18:27:58,457 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:27Z] INFO  18:27:58,458 MicroScheduler -   -> 661 reads (0.12% of total) failing HCMappingQualityFilter
[2016-04-15T01:27Z] INFO  18:27:58,458 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:27Z] INFO  18:27:58,458 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:27Z] INFO  18:27:58,458 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:27Z] INFO  18:27:58,459 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T01:27Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T01:27Z] INFO  18:27:58,477 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T01:27Z] INFO  18:27:58,477 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T01:27Z] INFO  18:27:58,511 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T01:27Z] WARN  18:27:58,722 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T01:27Z] WARN  18:27:58,723 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T01:27Z] INFO  18:27:59,254 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:27Z] INFO  18:27:59,257 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:27Z] INFO  18:27:59,257 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:27Z] INFO  18:27:59,258 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:27Z] INFO  18:27:59,262 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/X/R14-18102_kapa-NGv3-PE100-NGv3-sort-X_128582278_144329181-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/X/R14-18102_kapa-NGv3-PE100-NGv3-X_128582278_144329181-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/X/tx/tmp6s8z7i/R14-18102_kapa-NGv3-PE100-NGv3-X_128582278_144329181.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:27Z] INFO  18:27:59,289 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:27Z] INFO  18:27:59,290 HelpFormatter - Date/Time: 2016/04/14 18:27:59
[2016-04-15T01:27Z] INFO  18:27:59,290 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:27Z] INFO  18:27:59,295 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:27Z] WARN  18:27:59,332 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T01:27Z] WARN  18:27:59,342 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/X/tx/tmp6s8z7i/R14-18102_kapa-NGv3-PE100-NGv3-X_128582278_144329181.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T01:27Z] INFO  18:27:59,584 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:27Z] INFO  18:27:59,821 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T01:27Z] INFO  18:27:59,830 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:27Z] INFO  18:27:59,891 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-15T01:27Z] INFO  18:27:59,909 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:27Z] INFO  18:27:59,917 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T01:28Z] INFO  18:28:00,157 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:28Z] INFO  18:28:00,160 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:28Z] INFO  18:28:00,161 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:28Z] INFO  18:28:00,161 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:28Z] INFO  18:28:00,166 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/X/R14-18102_kapa-NGv3-PE100-NGv3-sort-X_144337190_155270560-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/X/R14-18102_kapa-NGv3-PE100-NGv3-X_144337190_155270560-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/X/tx/tmpTPMUM_/R14-18102_kapa-NGv3-PE100-NGv3-X_144337190_155270560.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 2 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:28Z] INFO  18:28:00,196 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:28Z] INFO  18:28:00,197 HelpFormatter - Date/Time: 2016/04/14 18:28:00
[2016-04-15T01:28Z] INFO  18:28:00,197 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:28Z] INFO  18:28:00,198 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:28Z] GATK: HaplotypeCaller
[2016-04-15T01:28Z] WARN  18:28:00,264 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T01:28Z] WARN  18:28:00,277 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/X/tx/tmpTPMUM_/R14-18102_kapa-NGv3-PE100-NGv3-X_144337190_155270560.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T01:28Z] INFO  18:28:00,299 IntervalUtils - Processing 143302 bp from intervals
[2016-04-15T01:28Z] WARN  18:28:00,304 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:28Z] INFO  18:28:00,416 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:28Z] INFO  18:28:00,469 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:28Z] INFO  18:28:00,495 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:28Z] INFO  18:28:00,496 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:28Z] INFO  18:28:00,497 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T01:28Z] INFO  18:28:00,498 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T01:28Z] INFO  18:28:00,498 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T01:28Z] INFO  18:28:00,499 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T01:28Z] INFO  18:28:00,672 ProgressMeter -      X:29417425      3.6674567E7    30.0 s            0.0 s       90.8%    33.0 s       3.0 s
[2016-04-15T01:28Z] INFO  18:28:00,708 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T01:28Z] INFO  18:28:00,728 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T01:28Z] INFO  18:28:00,730 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:28Z] INFO  18:28:00,809 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-15T01:28Z] INFO  18:28:00,848 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T01:28Z] INFO  18:28:01,209 IntervalUtils - Processing 184337 bp from intervals
[2016-04-15T01:28Z] WARN  18:28:01,215 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:28Z] INFO  18:28:01,231 ProgressMeter -      X:49180342      2.0489905E7    30.0 s            1.0 s       43.4%    69.0 s      39.0 s
[2016-04-15T01:28Z] INFO  18:28:01,243 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:28Z] INFO  18:28:01,246 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:28Z] INFO  18:28:01,247 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:28Z] INFO  18:28:01,247 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:28Z] INFO  18:28:01,252 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/Y/R14-18102_kapa-NGv3-PE100-NGv3-sort-Y_0_15522993-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/Y/R14-18102_kapa-NGv3-PE100-NGv3-Y_0_15522993-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/Y/tx/tmpFPxpP1/R14-18102_kapa-NGv3-PE100-NGv3-Y_0_15522993.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 1 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:28Z] INFO  18:28:01,282 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:28Z] INFO  18:28:01,283 HelpFormatter - Date/Time: 2016/04/14 18:28:01
[2016-04-15T01:28Z] INFO  18:28:01,284 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:28Z] INFO  18:28:01,284 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:28Z] INFO  18:28:01,293 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:28Z] WARN  18:28:01,311 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T01:28Z] WARN  18:28:01,314 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/Y/tx/tmpFPxpP1/R14-18102_kapa-NGv3-PE100-NGv3-Y_0_15522993.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T01:28Z] INFO  18:28:01,408 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:28Z] INFO  18:28:01,409 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:28Z] INFO  18:28:01,410 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T01:28Z] INFO  18:28:01,411 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T01:28Z] INFO  18:28:01,412 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T01:28Z] INFO  18:28:01,412 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T01:28Z] INFO  18:28:01,521 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:28Z] INFO  18:28:01,600 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T01:28Z] INFO  18:28:01,735 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T01:28Z] INFO  18:28:01,756 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:28Z] INFO  18:28:01,856 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.10
[2016-04-15T01:28Z] INFO  18:28:01,881 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T01:28Z] INFO  18:28:02,200 IntervalUtils - Processing 52192 bp from intervals
[2016-04-15T01:28Z] WARN  18:28:02,205 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:28Z] INFO  18:28:02,338 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:28Z] INFO  18:28:02,433 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:28Z] INFO  18:28:02,434 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:28Z] INFO  18:28:02,434 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T01:28Z] INFO  18:28:02,434 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T01:28Z] INFO  18:28:02,457 HaplotypeCaller - Currently, physical phasing is not available when ploidy is different than 2; therefore it won't be performed
[2016-04-15T01:28Z] INFO  18:28:02,458 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T01:28Z] INFO  18:28:02,458 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T01:28Z] INFO  18:28:02,763 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T01:28Z] INFO  18:28:02,904 ProgressMeter -     19:40395804     1.97655217E8    90.0 s            0.0 s       51.1%     2.9 m      86.0 s
[2016-04-15T01:28Z] INFO  18:28:03,263 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:28Z] INFO  18:28:03,267 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:28Z] INFO  18:28:03,267 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:28Z] INFO  18:28:03,268 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:28Z] INFO  18:28:03,272 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/Y/R14-18102_kapa-NGv3-PE100-NGv3-sort-Y_15526614_59222281-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/Y/R14-18102_kapa-NGv3-PE100-NGv3-Y_15526614_59222281-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/Y/tx/tmpAO6h1t/R14-18102_kapa-NGv3-PE100-NGv3-Y_15526614_59222281.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 1 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:28Z] INFO  18:28:03,294 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:28Z] INFO  18:28:03,305 HelpFormatter - Date/Time: 2016/04/14 18:28:03
[2016-04-15T01:28Z] INFO  18:28:03,306 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:28Z] INFO  18:28:03,307 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:28Z] WARN  18:28:03,329 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T01:28Z] WARN  18:28:03,332 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/Y/tx/tmpAO6h1t/R14-18102_kapa-NGv3-PE100-NGv3-Y_15526614_59222281.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T01:28Z] INFO  18:28:03,561 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:28Z] INFO  18:28:03,791 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.026129336000000003
[2016-04-15T01:28Z] INFO  18:28:03,792 PairHMM - Total compute time in PairHMM computeLikelihoods() : 0.264305628
[2016-04-15T01:28Z] INFO  18:28:03,793 HaplotypeCaller - Ran local assembly on 912 active regions
[2016-04-15T01:28Z] INFO  18:28:03,815 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T01:28Z] INFO  18:28:03,824 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:28Z] INFO  18:28:03,848 ProgressMeter -            done      4.2176641E7    33.0 s            0.0 s      100.0%    33.0 s       0.0 s
[2016-04-15T01:28Z] INFO  18:28:03,849 ProgressMeter - Total runtime 33.19 secs, 0.55 min, 0.01 hours
[2016-04-15T01:28Z] INFO  18:28:03,849 MicroScheduler - 15594 reads were filtered out during the traversal out of approximately 183616 total reads (8.49%)
[2016-04-15T01:28Z] INFO  18:28:03,849 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:28Z] INFO  18:28:03,849 MicroScheduler -   -> 14789 reads (8.05% of total) failing DuplicateReadFilter
[2016-04-15T01:28Z] INFO  18:28:03,850 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:28Z] INFO  18:28:03,850 MicroScheduler -   -> 805 reads (0.44% of total) failing HCMappingQualityFilter
[2016-04-15T01:28Z] INFO  18:28:03,850 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:28Z] INFO  18:28:03,851 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:28Z] INFO  18:28:03,851 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:28Z] INFO  18:28:03,851 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T01:28Z] INFO  18:28:03,889 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.06
[2016-04-15T01:28Z] INFO  18:28:03,929 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T01:28Z] INFO  18:28:04,450 IntervalUtils - Processing 44713 bp from intervals
[2016-04-15T01:28Z] WARN  18:28:04,456 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:28Z] INFO  18:28:04,552 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:28Z] INFO  18:28:04,563 ProgressMeter -     19:51918822     1.93143623E8    90.0 s            0.0 s       42.4%     3.5 m       2.0 m
[2016-04-15T01:28Z] INFO  18:28:04,588 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:28Z] INFO  18:28:04,589 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:28Z] INFO  18:28:04,590 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T01:28Z] INFO  18:28:04,591 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T01:28Z] INFO  18:28:04,592 HaplotypeCaller - Currently, physical phasing is not available when ploidy is different than 2; therefore it won't be performed
[2016-04-15T01:28Z] INFO  18:28:04,592 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T01:28Z] INFO  18:28:04,592 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T01:28Z] INFO  18:28:04,783 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T01:28Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T01:28Z] INFO  18:28:04,976 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T01:28Z] INFO  18:28:04,987 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T01:28Z] WARN  18:28:05,351 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T01:28Z] WARN  18:28:05,354 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T01:28Z] INFO  18:28:05,429 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:28Z] INFO  18:28:05,591 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.002558407
[2016-04-15T01:28Z] INFO  18:28:05,591 PairHMM - Total compute time in PairHMM computeLikelihoods() : 0.08177374800000001
[2016-04-15T01:28Z] INFO  18:28:05,591 HaplotypeCaller - Ran local assembly on 299 active regions
[2016-04-15T01:28Z] INFO  18:28:05,688 ProgressMeter -            done        3554725.0    19.0 s            5.0 s      100.0%    19.0 s       0.0 s
[2016-04-15T01:28Z] INFO  18:28:05,689 ProgressMeter - Total runtime 19.07 secs, 0.32 min, 0.01 hours
[2016-04-15T01:28Z] INFO  18:28:05,689 MicroScheduler - 5930 reads were filtered out during the traversal out of approximately 55401 total reads (10.70%)
[2016-04-15T01:28Z] INFO  18:28:05,690 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:28Z] INFO  18:28:05,690 MicroScheduler -   -> 4491 reads (8.11% of total) failing DuplicateReadFilter
[2016-04-15T01:28Z] INFO  18:28:05,690 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:28Z] INFO  18:28:05,690 MicroScheduler -   -> 1439 reads (2.60% of total) failing HCMappingQualityFilter
[2016-04-15T01:28Z] INFO  18:28:05,691 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:28Z] INFO  18:28:05,691 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:28Z] INFO  18:28:05,691 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:28Z] INFO  18:28:05,691 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T01:28Z] GATK: HaplotypeCaller
[2016-04-15T01:28Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T01:28Z] INFO  18:28:06,409 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T01:28Z] INFO  18:28:06,410 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T01:28Z] INFO  18:28:06,591 ProgressMeter -     22:24579463      8.7017552E7    60.0 s            0.0 s       56.6%   106.0 s      46.0 s
[2016-04-15T01:28Z] WARN  18:28:06,779 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T01:28Z] WARN  18:28:06,780 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T01:28Z] INFO  18:28:07,234 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:28Z] platypus variant calling
[2016-04-15T01:28Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T01:28Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T01:28Z] INFO  18:28:07,792 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T01:28Z] INFO  18:28:07,792 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T01:28Z] INFO  18:28:07,800 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T01:28Z] INFO  18:28:07,801 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T01:28Z] WARN  18:28:08,011 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T01:28Z] WARN  18:28:08,012 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T01:28Z] INFO  18:28:08,994 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:28Z] INFO  18:28:08,997 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:28Z] INFO  18:28:08,997 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:28Z] INFO  18:28:08,997 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:28Z] INFO  18:28:09,001 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --annotation BaseQualityRankSumTest --annotation FisherStrand --annotation GCContent --annotation HaplotypeScore --annotation HomopolymerRun --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation DepthPerAlleleBySample --annotation Coverage -I /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/bamprep/R14-18102_kapa-NGv3-PE100-NGv3/Y/R14-18102_kapa-NGv3-PE100-NGv3-sort-Y_59228291_59373566-prep.bam --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -L /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/Y/R14-18102_kapa-NGv3-PE100-NGv3-Y_59228291_59373566-regions.bed --interval_set_rule INTERSECTION -T HaplotypeCaller -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/Y/tx/tmpdpCl7p/R14-18102_kapa-NGv3-PE100-NGv3-Y_59228291_59373566.vcf.gz --annotation ClippingRankSumTest --annotation DepthPerSampleHC --pair_hmm_implementation VECTOR_LOGLESS_CACHING -ploidy 1 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:28Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T01:28Z] INFO  18:28:09,011 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:28Z] INFO  18:28:09,017 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T01:28Z] INFO  18:28:09,018 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T01:28Z] INFO  18:28:09,022 HelpFormatter - Date/Time: 2016/04/14 18:28:08
[2016-04-15T01:28Z] INFO  18:28:09,023 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:28Z] INFO  18:28:09,024 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:28Z] WARN  18:28:09,051 GATKVCFUtils - Naming your output file using the .g.vcf extension will automatically set the appropriate values  for --variant_index_type and --variant_index_parameter
[2016-04-15T01:28Z] WARN  18:28:09,054 GATKVCFUtils - Creating Tabix index for /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/Y/tx/tmpdpCl7p/R14-18102_kapa-NGv3-PE100-NGv3-Y_59228291_59373566.vcf.gz, ignoring user-specified index type and parameter
[2016-04-15T01:28Z] INFO  18:28:09,215 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:28Z] WARN  18:28:09,262 HaplotypeScore - Annotation will not be calculated, must be called from UnifiedGenotyper
[2016-04-15T01:28Z] WARN  18:28:09,262 InbreedingCoeff - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
[2016-04-15T01:28Z] INFO  18:28:09,486 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
[2016-04-15T01:28Z] INFO  18:28:09,496 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
[2016-04-15T01:28Z] INFO  18:28:09,579 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
[2016-04-15T01:28Z] INFO  18:28:09,619 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
[2016-04-15T01:28Z] INFO  18:28:10,059 IntervalUtils - Processing 2412 bp from intervals
[2016-04-15T01:28Z] WARN  18:28:10,065 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:28Z] INFO  18:28:10,188 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
[2016-04-15T01:28Z] INFO  18:28:10,232 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:28Z] INFO  18:28:10,233 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:28Z] INFO  18:28:10,234 ProgressMeter -                 |      processed |    time |         per 1M |           |   total | remaining
[2016-04-15T01:28Z] INFO  18:28:10,235 ProgressMeter -        Location | active regions | elapsed | active regions | completed | runtime |   runtime
[2016-04-15T01:28Z] INFO  18:28:10,236 HaplotypeCaller - Currently, physical phasing is not available when ploidy is different than 2; therefore it won't be performed
[2016-04-15T01:28Z] INFO  18:28:10,236 HaplotypeCaller - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
[2016-04-15T01:28Z] INFO  18:28:10,236 HaplotypeCaller - All sites annotated with PLs forced to true for reference-model confidence output
[2016-04-15T01:28Z] INFO  18:28:10,513 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
[2016-04-15T01:28Z] INFO  18:28:10,862 ProgressMeter -     22:41623093     1.20353834E8    60.0 s            0.0 s       61.5%    97.0 s      37.0 s
[2016-04-15T01:28Z] Using AVX accelerated implementation of PairHMM
[2016-04-15T01:28Z] INFO  18:28:11,862 VectorLoglessPairHMM - libVectorLoglessPairHMM unpacked successfully from GATK jar file
[2016-04-15T01:28Z] INFO  18:28:11,862 VectorLoglessPairHMM - Using vectorized implementation of PairHMM
[2016-04-15T01:28Z] INFO  18:28:11,863 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.0
[2016-04-15T01:28Z] INFO  18:28:11,863 PairHMM - Total compute time in PairHMM computeLikelihoods() : 0.0
[2016-04-15T01:28Z] INFO  18:28:11,864 HaplotypeCaller - Ran local assembly on 17 active regions
[2016-04-15T01:28Z] INFO  18:28:11,920 ProgressMeter -            done          14930.0     1.0 s          112.0 s      100.0%     1.0 s       0.0 s
[2016-04-15T01:28Z] INFO  18:28:11,920 ProgressMeter - Total runtime 1.69 secs, 0.03 min, 0.00 hours
[2016-04-15T01:28Z] INFO  18:28:11,987 VectorLoglessPairHMM - Time spent in setup for JNI call : 7.6718E-5
[2016-04-15T01:28Z] INFO  18:28:11,988 PairHMM - Total compute time in PairHMM computeLikelihoods() : 8.397740000000001E-4
[2016-04-15T01:28Z] INFO  18:28:11,989 HaplotypeCaller - Ran local assembly on 341 active regions
[2016-04-15T01:28Z] INFO  18:28:12,040 ProgressMeter -            done        6359922.0     9.0 s            1.0 s      100.0%     9.0 s       0.0 s
[2016-04-15T01:28Z] INFO  18:28:12,041 ProgressMeter - Total runtime 9.61 secs, 0.16 min, 0.00 hours
[2016-04-15T01:28Z] INFO  18:28:12,041 MicroScheduler - 1466 reads were filtered out during the traversal out of approximately 1594 total reads (91.97%)
[2016-04-15T01:28Z] INFO  18:28:12,042 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:28Z] INFO  18:28:12,042 MicroScheduler -   -> 0 reads (0.00% of total) failing DuplicateReadFilter
[2016-04-15T01:28Z] INFO  18:28:12,042 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:28Z] INFO  18:28:12,042 MicroScheduler -   -> 1466 reads (91.97% of total) failing HCMappingQualityFilter
[2016-04-15T01:28Z] INFO  18:28:12,043 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:28Z] INFO  18:28:12,043 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:28Z] INFO  18:28:12,043 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:28Z] INFO  18:28:12,043 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T01:28Z] INFO  18:28:12,870 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.0010180430000000002
[2016-04-15T01:28Z] INFO  18:28:12,871 PairHMM - Total compute time in PairHMM computeLikelihoods() : 0.13921656300000002
[2016-04-15T01:28Z] INFO  18:28:12,871 HaplotypeCaller - Ran local assembly on 340 active regions
[2016-04-15T01:28Z] INFO  18:28:12,947 ProgressMeter -            done        6560827.0     8.0 s            1.0 s      100.0%     8.0 s       0.0 s
[2016-04-15T01:28Z] INFO  18:28:12,947 ProgressMeter - Total runtime 8.36 secs, 0.14 min, 0.00 hours
[2016-04-15T01:28Z] INFO  18:28:12,949 MicroScheduler - 1086 reads were filtered out during the traversal out of approximately 1476 total reads (73.58%)
[2016-04-15T01:28Z] INFO  18:28:12,949 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:28Z] INFO  18:28:12,949 MicroScheduler -   -> 47 reads (3.18% of total) failing DuplicateReadFilter
[2016-04-15T01:28Z] INFO  18:28:12,950 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:28Z] INFO  18:28:12,950 MicroScheduler -   -> 1039 reads (70.39% of total) failing HCMappingQualityFilter
[2016-04-15T01:28Z] INFO  18:28:12,950 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:28Z] INFO  18:28:12,951 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:28Z] INFO  18:28:12,951 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:28Z] INFO  18:28:12,951 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T01:28Z] INFO  18:28:13,085 ProgressMeter -      X:70516701      1.8235528E7    30.0 s            1.0 s       49.7%    60.0 s      30.0 s
[2016-04-15T01:28Z] INFO  18:28:13,409 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:28Z] INFO  18:28:13,588 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:28Z] platypus variant calling
[2016-04-15T01:28Z] platypus variant calling
[2016-04-15T01:28Z] INFO  18:28:14,263 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:28Z] platypus variant calling
[2016-04-15T01:28Z] INFO  18:28:14,915 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.025121727
[2016-04-15T01:28Z] INFO  18:28:14,916 PairHMM - Total compute time in PairHMM computeLikelihoods() : 4.817328527
[2016-04-15T01:28Z] INFO  18:28:14,917 HaplotypeCaller - Ran local assembly on 2024 active regions
[2016-04-15T01:28Z] INFO  18:28:14,962 ProgressMeter -            done     1.91312624E8    84.0 s            0.0 s      100.0%    84.0 s       0.0 s
[2016-04-15T01:28Z] INFO  18:28:14,963 ProgressMeter - Total runtime 84.37 secs, 1.41 min, 0.02 hours
[2016-04-15T01:28Z] INFO  18:28:14,963 MicroScheduler - 41791 reads were filtered out during the traversal out of approximately 446472 total reads (9.36%)
[2016-04-15T01:28Z] INFO  18:28:14,963 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:28Z] INFO  18:28:14,964 MicroScheduler -   -> 36735 reads (8.23% of total) failing DuplicateReadFilter
[2016-04-15T01:28Z] INFO  18:28:14,964 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:28Z] INFO  18:28:14,964 MicroScheduler -   -> 5056 reads (1.13% of total) failing HCMappingQualityFilter
[2016-04-15T01:28Z] INFO  18:28:14,964 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:28Z] INFO  18:28:14,965 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:28Z] INFO  18:28:14,965 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:28Z] INFO  18:28:14,965 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T01:28Z] INFO  18:28:16,345 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:28Z] platypus variant calling
[2016-04-15T01:28Z] INFO  18:28:21,699 ProgressMeter -     X:106359092      2.5053022E7    30.0 s            1.0 s       64.9%    46.0 s      16.0 s
[2016-04-15T01:28Z] tabix index R14-18102_kapa-NGv3-PE100-NGv3-1_62231950_77749296.vcf.gz
[2016-04-15T01:28Z] platypus variant calling
[2016-04-15T01:28Z] tabix index R14-18102_kapa-NGv3-PE100-NGv3-1_46715671_62228851.vcf.gz
[2016-04-15T01:28Z] platypus variant calling
[2016-04-15T01:28Z] INFO  18:28:25,395 ProgressMeter -      19:9003293     4.24606495E8   120.0 s            0.0 s       55.2%     3.6 m      97.0 s
[2016-04-15T01:28Z] tabix index R14-18102_kapa-NGv3-PE100-NGv3-1_77752625_93297674.vcf.gz
[2016-04-15T01:28Z] INFO  18:28:27,295 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.0066786580000000005
[2016-04-15T01:28Z] INFO  18:28:27,296 PairHMM - Total compute time in PairHMM computeLikelihoods() : 3.14629949
[2016-04-15T01:28Z] INFO  18:28:27,296 HaplotypeCaller - Ran local assembly on 1119 active regions
[2016-04-15T01:28Z] INFO  18:28:27,367 ProgressMeter -            done      6.1608288E7    44.0 s            0.0 s      100.0%    44.0 s       0.0 s
[2016-04-15T01:28Z] INFO  18:28:27,367 ProgressMeter - Total runtime 44.30 secs, 0.74 min, 0.01 hours
[2016-04-15T01:28Z] INFO  18:28:27,368 MicroScheduler - 42081 reads were filtered out during the traversal out of approximately 284602 total reads (14.79%)
[2016-04-15T01:28Z] INFO  18:28:27,368 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:28Z] INFO  18:28:27,368 MicroScheduler -   -> 21556 reads (7.57% of total) failing DuplicateReadFilter
[2016-04-15T01:28Z] INFO  18:28:27,369 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:28Z] INFO  18:28:27,369 MicroScheduler -   -> 20525 reads (7.21% of total) failing HCMappingQualityFilter
[2016-04-15T01:28Z] INFO  18:28:27,369 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:28Z] INFO  18:28:27,370 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:28Z] INFO  18:28:27,370 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:28Z] INFO  18:28:27,370 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T01:28Z] platypus variant calling
[2016-04-15T01:28Z] tabix index R14-18102_kapa-NGv3-PE100-NGv3-1_93298945_108993401.vcf.gz
[2016-04-15T01:28Z] INFO  18:28:28,066 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.009993577
[2016-04-15T01:28Z] INFO  18:28:28,067 PairHMM - Total compute time in PairHMM computeLikelihoods() : 1.2826136060000002
[2016-04-15T01:28Z] INFO  18:28:28,068 HaplotypeCaller - Ran local assembly on 1552 active regions
[2016-04-15T01:28Z] INFO  18:28:28,105 ProgressMeter -            done     1.04022591E8    56.0 s            0.0 s      100.0%    56.0 s       0.0 s
[2016-04-15T01:28Z] INFO  18:28:28,106 ProgressMeter - Total runtime 56.90 secs, 0.95 min, 0.02 hours
[2016-04-15T01:28Z] INFO  18:28:28,107 MicroScheduler - 166019 reads were filtered out during the traversal out of approximately 504881 total reads (32.88%)
[2016-04-15T01:28Z] INFO  18:28:28,108 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:28Z] INFO  18:28:28,109 MicroScheduler -   -> 30573 reads (6.06% of total) failing DuplicateReadFilter
[2016-04-15T01:28Z] INFO  18:28:28,119 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:28Z] INFO  18:28:28,121 MicroScheduler -   -> 135446 reads (26.83% of total) failing HCMappingQualityFilter
[2016-04-15T01:28Z] INFO  18:28:28,121 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:28Z] INFO  18:28:28,122 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:28Z] INFO  18:28:28,123 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:28Z] INFO  18:28:28,124 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T01:28Z] platypus variant calling
[2016-04-15T01:28Z] INFO  18:28:28,345 ProgressMeter -     X:122613932      1.6066698E7    30.0 s            1.0 s       78.2%    38.0 s       8.0 s
[2016-04-15T01:28Z] INFO  18:28:28,921 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:28Z] platypus variant calling
[2016-04-15T01:28Z] INFO  18:28:29,419 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:28Z] tabix index R14-18102_kapa-NGv3-PE100-NGv3-1_0_15541927.vcf.gz
[2016-04-15T01:28Z] platypus variant calling
[2016-04-15T01:28Z] platypus variant calling
[2016-04-15T01:28Z] INFO  18:28:30,518 ProgressMeter -     X:138644102       2.986268E7    30.0 s            1.0 s       81.8%    36.0 s       6.0 s
[2016-04-15T01:28Z] INFO  18:28:31,450 ProgressMeter -     X:153209032      2.3359374E7    30.0 s            1.0 s       59.2%    50.0 s      20.0 s
[2016-04-15T01:28Z] INFO  18:28:32,907 ProgressMeter -     19:42933036     4.09433157E8   120.0 s            0.0 s       73.3%     2.7 m      43.0 s
[2016-04-15T01:28Z] INFO  18:28:33,609 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.019344036000000002
[2016-04-15T01:28Z] INFO  18:28:33,610 PairHMM - Total compute time in PairHMM computeLikelihoods() : 1.0279592370000001
[2016-04-15T01:28Z] INFO  18:28:33,610 HaplotypeCaller - Ran local assembly on 763 active regions
[2016-04-15T01:28Z] INFO  18:28:33,673 ProgressMeter -            done      2.7516501E7    35.0 s            1.0 s      100.0%    35.0 s       0.0 s
[2016-04-15T01:28Z] INFO  18:28:33,673 ProgressMeter - Total runtime 35.34 secs, 0.59 min, 0.01 hours
[2016-04-15T01:28Z] INFO  18:28:33,673 MicroScheduler - 45928 reads were filtered out during the traversal out of approximately 183923 total reads (24.97%)
[2016-04-15T01:28Z] INFO  18:28:33,674 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:28Z] INFO  18:28:33,674 MicroScheduler -   -> 12300 reads (6.69% of total) failing DuplicateReadFilter
[2016-04-15T01:28Z] INFO  18:28:33,674 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:28Z] INFO  18:28:33,675 MicroScheduler -   -> 33628 reads (18.28% of total) failing HCMappingQualityFilter
[2016-04-15T01:28Z] INFO  18:28:33,675 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:28Z] INFO  18:28:33,675 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:28Z] INFO  18:28:33,675 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:28Z] INFO  18:28:33,676 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T01:28Z] INFO  18:28:34,154 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.007712404000000001
[2016-04-15T01:28Z] INFO  18:28:34,155 PairHMM - Total compute time in PairHMM computeLikelihoods() : 1.598928469
[2016-04-15T01:28Z] INFO  18:28:34,155 HaplotypeCaller - Ran local assembly on 1191 active regions
[2016-04-15T01:28Z] INFO  18:28:34,218 ProgressMeter -            done      7.0564604E7    42.0 s            0.0 s      100.0%    42.0 s       0.0 s
[2016-04-15T01:28Z] INFO  18:28:34,218 ProgressMeter - Total runtime 42.54 secs, 0.71 min, 0.01 hours
[2016-04-15T01:28Z] INFO  18:28:34,219 MicroScheduler - 46964 reads were filtered out during the traversal out of approximately 279567 total reads (16.80%)
[2016-04-15T01:28Z] INFO  18:28:34,219 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:28Z] INFO  18:28:34,219 MicroScheduler -   -> 20256 reads (7.25% of total) failing DuplicateReadFilter
[2016-04-15T01:28Z] INFO  18:28:34,220 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:28Z] INFO  18:28:34,220 MicroScheduler -   -> 26708 reads (9.55% of total) failing HCMappingQualityFilter
[2016-04-15T01:28Z] INFO  18:28:34,220 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:28Z] INFO  18:28:34,220 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:28Z] INFO  18:28:34,221 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:28Z] INFO  18:28:34,221 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T01:28Z] tabix index R14-18102_kapa-NGv3-PE100-NGv3-1_15545821_31186478.vcf.gz
[2016-04-15T01:28Z] INFO  18:28:34,564 ProgressMeter -     19:54701194      3.1092905E8   120.0 s            0.0 s       59.8%     3.3 m      80.0 s
[2016-04-15T01:28Z] platypus variant calling
[2016-04-15T01:28Z] INFO  18:28:35,025 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:28Z] platypus variant calling
[2016-04-15T01:28Z] INFO  18:28:35,499 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:28Z] platypus variant calling
[2016-04-15T01:28Z] INFO  18:28:35,877 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.008660087
[2016-04-15T01:28Z] INFO  18:28:35,879 PairHMM - Total compute time in PairHMM computeLikelihoods() : 0.58308764
[2016-04-15T01:28Z] INFO  18:28:35,880 HaplotypeCaller - Ran local assembly on 964 active regions
[2016-04-15T01:28Z] INFO  18:28:35,948 ProgressMeter -            done      4.2570099E7    35.0 s            0.0 s      100.0%    35.0 s       0.0 s
[2016-04-15T01:28Z] INFO  18:28:35,950 ProgressMeter - Total runtime 35.45 secs, 0.59 min, 0.01 hours
[2016-04-15T01:28Z] INFO  18:28:35,951 MicroScheduler - 49166 reads were filtered out during the traversal out of approximately 225877 total reads (21.77%)
[2016-04-15T01:28Z] INFO  18:28:35,951 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:28Z] INFO  18:28:35,952 MicroScheduler -   -> 15538 reads (6.88% of total) failing DuplicateReadFilter
[2016-04-15T01:28Z] INFO  18:28:35,953 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:28Z] INFO  18:28:35,954 MicroScheduler -   -> 33628 reads (14.89% of total) failing HCMappingQualityFilter
[2016-04-15T01:28Z] INFO  18:28:35,955 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:28Z] INFO  18:28:35,955 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:28Z] INFO  18:28:35,956 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:28Z] INFO  18:28:35,957 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T01:28Z] tabix index R14-18102_kapa-NGv3-PE100-NGv3-1_31187093_46714270.vcf.gz
[2016-04-15T01:28Z] platypus variant calling
[2016-04-15T01:28Z] INFO  18:28:36,592 ProgressMeter -     22:31685301     2.99784368E8    90.0 s            0.0 s       98.9%    91.0 s       1.0 s
[2016-04-15T01:28Z] tabix index R14-18102_kapa-NGv3-PE100-NGv3-1_175048468_192127886.vcf.gz
[2016-04-15T01:28Z] INFO  18:28:37,239 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.026248331000000003
[2016-04-15T01:28Z] INFO  18:28:37,239 PairHMM - Total compute time in PairHMM computeLikelihoods() : 3.851679539
[2016-04-15T01:28Z] INFO  18:28:37,239 HaplotypeCaller - Ran local assembly on 2671 active regions
[2016-04-15T01:28Z] platypus variant calling
[2016-04-15T01:28Z] INFO  18:28:37,276 ProgressMeter -            done     3.03489097E8    90.0 s            0.0 s      100.0%    90.0 s       0.0 s
[2016-04-15T01:28Z] INFO  18:28:37,277 ProgressMeter - Total runtime 90.72 secs, 1.51 min, 0.03 hours
[2016-04-15T01:28Z] INFO  18:28:37,277 MicroScheduler - 109308 reads were filtered out during the traversal out of approximately 661827 total reads (16.52%)
[2016-04-15T01:28Z] INFO  18:28:37,278 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:28Z] INFO  18:28:37,278 MicroScheduler -   -> 49859 reads (7.53% of total) failing DuplicateReadFilter
[2016-04-15T01:28Z] INFO  18:28:37,278 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:28Z] INFO  18:28:37,279 MicroScheduler -   -> 59449 reads (8.98% of total) failing HCMappingQualityFilter
[2016-04-15T01:28Z] INFO  18:28:37,279 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:28Z] INFO  18:28:37,279 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:28Z] INFO  18:28:37,279 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:28Z] INFO  18:28:37,280 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T01:28Z] INFO  18:28:37,307 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:28Z] platypus variant calling
[2016-04-15T01:28Z] INFO  18:28:38,408 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.025090825
[2016-04-15T01:28Z] INFO  18:28:38,410 PairHMM - Total compute time in PairHMM computeLikelihoods() : 2.939451924
[2016-04-15T01:28Z] INFO  18:28:38,410 HaplotypeCaller - Ran local assembly on 2712 active regions
[2016-04-15T01:28Z] INFO  18:28:38,436 ProgressMeter -            done      3.3533286E8    87.0 s            0.0 s      100.0%    87.0 s       0.0 s
[2016-04-15T01:28Z] INFO  18:28:38,444 ProgressMeter - Total runtime 87.61 secs, 1.46 min, 0.02 hours
[2016-04-15T01:28Z] INFO  18:28:38,445 MicroScheduler - 56605 reads were filtered out during the traversal out of approximately 625390 total reads (9.05%)
[2016-04-15T01:28Z] INFO  18:28:38,446 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:28Z] INFO  18:28:38,447 MicroScheduler -   -> 50649 reads (8.10% of total) failing DuplicateReadFilter
[2016-04-15T01:28Z] INFO  18:28:38,448 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:28Z] INFO  18:28:38,449 MicroScheduler -   -> 5956 reads (0.95% of total) failing HCMappingQualityFilter
[2016-04-15T01:28Z] INFO  18:28:38,449 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:28Z] INFO  18:28:38,450 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:28Z] INFO  18:28:38,451 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:28Z] INFO  18:28:38,451 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T01:28Z] INFO  18:28:38,682 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:28Z] tabix index R14-18102_kapa-NGv3-PE100-NGv3-1_108994811_143767848.vcf.gz
[2016-04-15T01:28Z] platypus variant calling
[2016-04-15T01:28Z] platypus variant calling
[2016-04-15T01:28Z] tabix index R14-18102_kapa-NGv3-PE100-NGv3-1_159504867_175046963.vcf.gz
[2016-04-15T01:28Z] INFO  18:28:39,784 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:28Z] platypus variant calling
[2016-04-15T01:28Z] platypus variant calling
[2016-04-15T01:28Z] tabix index R14-18102_kapa-NGv3-PE100-NGv3-1_240255409_249250621.vcf.gz
[2016-04-15T01:28Z] platypus variant calling
[2016-04-15T01:28Z] tabix index R14-18102_kapa-NGv3-PE100-NGv3-2_0_15514844.vcf.gz
[2016-04-15T01:28Z] platypus variant calling
[2016-04-15T01:28Z] tabix index R14-18102_kapa-NGv3-PE100-NGv3-1_207641871_223156451.vcf.gz
[2016-04-15T01:28Z] platypus variant calling
[2016-04-15T01:28Z] tabix index R14-18102_kapa-NGv3-PE100-NGv3-1_192128349_207640257.vcf.gz
[2016-04-15T01:28Z] INFO  18:28:41,912 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.008277384
[2016-04-15T01:28Z] INFO  18:28:41,913 PairHMM - Total compute time in PairHMM computeLikelihoods() : 0.321391136
[2016-04-15T01:28Z] INFO  18:28:41,914 HaplotypeCaller - Ran local assembly on 1260 active regions
[2016-04-15T01:28Z] INFO  18:28:41,958 ProgressMeter -            done      6.5416759E7    40.0 s            0.0 s      100.0%    40.0 s       0.0 s
[2016-04-15T01:28Z] INFO  18:28:41,959 ProgressMeter - Total runtime 40.55 secs, 0.68 min, 0.01 hours
[2016-04-15T01:28Z] INFO  18:28:41,959 MicroScheduler - 67020 reads were filtered out during the traversal out of approximately 332447 total reads (20.16%)
[2016-04-15T01:28Z] INFO  18:28:41,960 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:28Z] INFO  18:28:41,960 MicroScheduler -   -> 24047 reads (7.23% of total) failing DuplicateReadFilter
[2016-04-15T01:28Z] INFO  18:28:41,960 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:28Z] INFO  18:28:41,961 MicroScheduler -   -> 42973 reads (12.93% of total) failing HCMappingQualityFilter
[2016-04-15T01:28Z] INFO  18:28:41,961 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:28Z] INFO  18:28:41,961 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:28Z] INFO  18:28:41,962 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:28Z] INFO  18:28:41,962 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T01:28Z] platypus variant calling
[2016-04-15T01:28Z] INFO  18:28:43,334 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:28Z] platypus variant calling
[2016-04-15T01:28Z] tabix index R14-18102_kapa-NGv3-PE100-NGv3-2_31135088_46706841.vcf.gz
[2016-04-15T01:28Z] tabix index R14-18102_kapa-NGv3-PE100-NGv3-2_46707543_62228117.vcf.gz
[2016-04-15T01:28Z] platypus variant calling
[2016-04-15T01:28Z] platypus variant calling
[2016-04-15T01:28Z] tabix index R14-18102_kapa-NGv3-PE100-NGv3-2_79253838_95537822.vcf.gz
[2016-04-15T01:28Z] platypus variant calling
[2016-04-15T01:28Z] tabix index R14-18102_kapa-NGv3-PE100-NGv3-2_143676177_159195597.vcf.gz
[2016-04-15T01:28Z] tabix index R14-18102_kapa-NGv3-PE100-NGv3-2_111281072_127413888.vcf.gz
[2016-04-15T01:28Z] platypus variant calling
[2016-04-15T01:28Z] platypus variant calling
[2016-04-15T01:28Z] tabix index R14-18102_kapa-NGv3-PE100-NGv3-1_223162737_240072524.vcf.gz
[2016-04-15T01:28Z] platypus variant calling
[2016-04-15T01:28Z] tabix index R14-18102_kapa-NGv3-PE100-NGv3-2_62362965_79253295.vcf.gz
[2016-04-15T01:28Z] tabix index R14-18102_kapa-NGv3-PE100-NGv3-2_127433207_143643105.vcf.gz
[2016-04-15T01:28Z] tabix index R14-18102_kapa-NGv3-PE100-NGv3-2_15519725_31133925.vcf.gz
[2016-04-15T01:28Z] platypus variant calling
[2016-04-15T01:28Z] platypus variant calling
[2016-04-15T01:28Z] platypus variant calling
[2016-04-15T01:28Z] tabix index R14-18102_kapa-NGv3-PE100-NGv3-3_15515506_31574805.vcf.gz
[2016-04-15T01:28Z] tabix index R14-18102_kapa-NGv3-PE100-NGv3-2_159196753_174774985.vcf.gz
[2016-04-15T01:28Z] platypus variant calling
[2016-04-15T01:28Z] platypus variant calling
[2016-04-15T01:28Z] tabix index R14-18102_kapa-NGv3-PE100-NGv3-2_190313104_205830046.vcf.gz
[2016-04-15T01:28Z] platypus variant calling
[2016-04-15T01:28Z] tabix index R14-18102_kapa-NGv3-PE100-NGv3-3_78649262_96533852.vcf.gz
[2016-04-15T01:28Z] tabix index R14-18102_kapa-NGv3-PE100-NGv3-2_237995374_243199373.vcf.gz
[2016-04-15T01:28Z] platypus variant calling
[2016-04-15T01:28Z] platypus variant calling
[2016-04-15T01:28Z] tabix index R14-18102_kapa-NGv3-PE100-NGv3-3_62739115_78648077.vcf.gz
[2016-04-15T01:28Z] platypus variant calling
[2016-04-15T01:28Z] tabix index R14-18102_kapa-NGv3-PE100-NGv3-2_222291154_237994685.vcf.gz
[2016-04-15T01:28Z] tabix index R14-18102_kapa-NGv3-PE100-NGv3-2_95538561_111273222.vcf.gz
[2016-04-15T01:28Z] platypus variant calling
[2016-04-15T01:28Z] platypus variant calling
[2016-04-15T01:28Z] tabix index R14-18102_kapa-NGv3-PE100-NGv3-3_0_15512123.vcf.gz
[2016-04-15T01:28Z] platypus variant calling
[2016-04-15T01:28Z] tabix index R14-18102_kapa-NGv3-PE100-NGv3-3_96585668_112185230.vcf.gz
[2016-04-15T01:28Z] platypus variant calling
[2016-04-15T01:28Z] INFO  18:28:55,396 ProgressMeter -     19:11512693     7.25658619E8     2.5 m            0.0 s       75.9%     3.3 m      47.0 s
[2016-04-15T01:28Z] tabix index R14-18102_kapa-NGv3-PE100-NGv3-3_158970515_174577240.vcf.gz
[2016-04-15T01:28Z] tabix index R14-18102_kapa-NGv3-PE100-NGv3-2_205912303_222290862.vcf.gz
[2016-04-15T01:28Z] tabix index R14-18102_kapa-NGv3-PE100-NGv3-2_174777797_190306304.vcf.gz
[2016-04-15T01:28Z] platypus variant calling
[2016-04-15T01:28Z] platypus variant calling
[2016-04-15T01:28Z] platypus variant calling
[2016-04-15T01:28Z] tabix index R14-18102_kapa-NGv3-PE100-NGv3-3_143297426_158963696.vcf.gz
[2016-04-15T01:28Z] tabix index R14-18102_kapa-NGv3-PE100-NGv3-1_143897546_159410511.vcf.gz
[2016-04-15T01:28Z] platypus variant calling
[2016-04-15T01:28Z] platypus variant calling
[2016-04-15T01:28Z] tabix index R14-18102_kapa-NGv3-PE100-NGv3-4_15512869_31144471.vcf.gz
[2016-04-15T01:28Z] platypus variant calling
[2016-04-15T01:28Z] tabix index R14-18102_kapa-NGv3-PE100-NGv3-4_52709749_68338393.vcf.gz
[2016-04-15T01:28Z] platypus variant calling
[2016-04-15T01:29Z] tabix index R14-18102_kapa-NGv3-PE100-NGv3-3_112188604_127703121.vcf.gz
[2016-04-15T01:29Z] platypus variant calling
[2016-04-15T01:29Z] tabix index R14-18102_kapa-NGv3-PE100-NGv3-4_36069528_52709433.vcf.gz
[2016-04-15T01:29Z] tabix index R14-18102_kapa-NGv3-PE100-NGv3-3_127770401_143293035.vcf.gz
[2016-04-15T01:29Z] platypus variant calling
[2016-04-15T01:29Z] tabix index R14-18102_kapa-NGv3-PE100-NGv3-3_31617887_47127804.vcf.gz
[2016-04-15T01:29Z] platypus variant calling
[2016-04-15T01:29Z] platypus variant calling
[2016-04-15T01:29Z] tabix index R14-18102_kapa-NGv3-PE100-NGv3-3_174814579_190326970.vcf.gz
[2016-04-15T01:29Z] platypus variant calling
[2016-04-15T01:29Z] tabix index R14-18102_kapa-NGv3-PE100-NGv3-4_83857133_99393738.vcf.gz
[2016-04-15T01:29Z] tabix index R14-18102_kapa-NGv3-PE100-NGv3-4_99397339_115544957.vcf.gz
[2016-04-15T01:29Z] tabix index R14-18102_kapa-NGv3-PE100-NGv3-3_190333063_198022430.vcf.gz
[2016-04-15T01:29Z] platypus variant calling
[2016-04-15T01:29Z] platypus variant calling
[2016-04-15T01:29Z] platypus variant calling
[2016-04-15T01:29Z] tabix index R14-18102_kapa-NGv3-PE100-NGv3-4_68340604_83852298.vcf.gz
[2016-04-15T01:29Z] INFO  18:29:02,908 ProgressMeter -     19:46145430     6.87950477E8     2.5 m            0.0 s       95.6%     2.6 m       6.0 s
[2016-04-15T01:29Z] platypus variant calling
[2016-04-15T01:29Z] tabix index R14-18102_kapa-NGv3-PE100-NGv3-5_15616091_31267808.vcf.gz
[2016-04-15T01:29Z] tabix index R14-18102_kapa-NGv3-PE100-NGv3-4_134075461_150351181.vcf.gz
[2016-04-15T01:29Z] platypus variant calling
[2016-04-15T01:29Z] tabix index R14-18102_kapa-NGv3-PE100-NGv3-4_165889318_183245405.vcf.gz
[2016-04-15T01:29Z] platypus variant calling
[2016-04-15T01:29Z] platypus variant calling
[2016-04-15T01:29Z] tabix index R14-18102_kapa-NGv3-PE100-NGv3-4_115584857_134074404.vcf.gz
[2016-04-15T01:29Z] platypus variant calling
[2016-04-15T01:29Z] INFO  18:29:04,566 ProgressMeter -     19:56128115     4.94349957E8     2.5 m            0.0 s       74.8%     3.3 m      50.0 s
[2016-04-15T01:29Z] tabix index R14-18102_kapa-NGv3-PE100-NGv3-4_150354547_165878648.vcf.gz
[2016-04-15T01:29Z] platypus variant calling
[2016-04-15T01:29Z] tabix index R14-18102_kapa-NGv3-PE100-NGv3-4_183267803_191154276.vcf.gz
[2016-04-15T01:29Z] tabix index R14-18102_kapa-NGv3-PE100-NGv3-5_96432513_112043579.vcf.gz
[2016-04-15T01:29Z] platypus variant calling
[2016-04-15T01:29Z] platypus variant calling
[2016-04-15T01:29Z] tabix index R14-18102_kapa-NGv3-PE100-NGv3-5_49695692_65288736.vcf.gz
[2016-04-15T01:29Z] tabix index R14-18102_kapa-NGv3-PE100-NGv3-4_0_15511864.vcf.gz
[2016-04-15T01:29Z] platypus variant calling
[2016-04-15T01:29Z] platypus variant calling
[2016-04-15T01:29Z] tabix index R14-18102_kapa-NGv3-PE100-NGv3-5_80911291_96430739.vcf.gz
[2016-04-15T01:29Z] tabix index R14-18102_kapa-NGv3-PE100-NGv3-5_112073555_127595521.vcf.gz
[2016-04-15T01:29Z] platypus variant calling
[2016-04-15T01:29Z] tabix index R14-18102_kapa-NGv3-PE100-NGv3-5_0_15580921.vcf.gz
[2016-04-15T01:29Z] platypus variant calling
[2016-04-15T01:29Z] platypus variant calling
[2016-04-15T01:29Z] INFO  18:29:08,306 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.058200850000000005
[2016-04-15T01:29Z] INFO  18:29:08,307 PairHMM - Total compute time in PairHMM computeLikelihoods() : 5.825312249
[2016-04-15T01:29Z] INFO  18:29:08,307 HaplotypeCaller - Ran local assembly on 4566 active regions
[2016-04-15T01:29Z] INFO  18:29:08,368 ProgressMeter -            done     7.46649334E8     2.6 m            0.0 s      100.0%     2.6 m       0.0 s
[2016-04-15T01:29Z] INFO  18:29:08,368 ProgressMeter - Total runtime 155.49 secs, 2.59 min, 0.04 hours
[2016-04-15T01:29Z] INFO  18:29:08,369 MicroScheduler - 121144 reads were filtered out during the traversal out of approximately 1140758 total reads (10.62%)
[2016-04-15T01:29Z] INFO  18:29:08,369 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:29Z] INFO  18:29:08,369 MicroScheduler -   -> 90971 reads (7.97% of total) failing DuplicateReadFilter
[2016-04-15T01:29Z] INFO  18:29:08,370 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:29Z] INFO  18:29:08,370 MicroScheduler -   -> 30173 reads (2.64% of total) failing HCMappingQualityFilter
[2016-04-15T01:29Z] INFO  18:29:08,370 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:29Z] INFO  18:29:08,371 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:29Z] INFO  18:29:08,371 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:29Z] INFO  18:29:08,371 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T01:29Z] tabix index R14-18102_kapa-NGv3-PE100-NGv3-5_31294068_49695124.vcf.gz
[2016-04-15T01:29Z] platypus variant calling
[2016-04-15T01:29Z] tabix index R14-18102_kapa-NGv3-PE100-NGv3-5_158711911_174870102.vcf.gz
[2016-04-15T01:29Z] tabix index R14-18102_kapa-NGv3-PE100-NGv3-5_65290574_80809536.vcf.gz
[2016-04-15T01:29Z] platypus variant calling
[2016-04-15T01:29Z] platypus variant calling
[2016-04-15T01:29Z] INFO  18:29:10,088 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:29Z] platypus variant calling
[2016-04-15T01:29Z] tabix index R14-18102_kapa-NGv3-PE100-NGv3-6_0_15509601.vcf.gz
[2016-04-15T01:29Z] platypus variant calling
[2016-04-15T01:29Z] tabix index R14-18102_kapa-NGv3-PE100-NGv3-6_62390867_78173120.vcf.gz
[2016-04-15T01:29Z] platypus variant calling
[2016-04-15T01:29Z] tabix index R14-18102_kapa-NGv3-PE100-NGv3-6_93955015_109466584.vcf.gz
[2016-04-15T01:29Z] platypus variant calling
[2016-04-15T01:29Z] tabix index R14-18102_kapa-NGv3-PE100-NGv3-5_143200044_158710347.vcf.gz
[2016-04-15T01:29Z] platypus variant calling
[2016-04-15T01:29Z] tabix index R14-18102_kapa-NGv3-PE100-NGv3-6_78400388_93953258.vcf.gz
[2016-04-15T01:29Z] platypus variant calling
[2016-04-15T01:29Z] tabix index R14-18102_kapa-NGv3-PE100-NGv3-6_46598699_62284307.vcf.gz
[2016-04-15T01:29Z] platypus variant calling
[2016-04-15T01:29Z] tabix index R14-18102_kapa-NGv3-PE100-NGv3-5_174919106_180915260.vcf.gz
[2016-04-15T01:29Z] platypus variant calling
[2016-04-15T01:29Z] tabix index R14-18102_kapa-NGv3-PE100-NGv3-3_47129602_62648069.vcf.gz
[2016-04-15T01:29Z] tabix index R14-18102_kapa-NGv3-PE100-NGv3-6_109467960_124979532.vcf.gz
[2016-04-15T01:29Z] platypus variant calling
[2016-04-15T01:29Z] platypus variant calling
[2016-04-15T01:29Z] tabix index R14-18102_kapa-NGv3-PE100-NGv3-6_125112484_142397186.vcf.gz
[2016-04-15T01:29Z] platypus variant calling
[2016-04-15T01:29Z] tabix index R14-18102_kapa-NGv3-PE100-NGv3-7_47319761_63093154.vcf.gz
[2016-04-15T01:29Z] platypus variant calling
[2016-04-15T01:29Z] tabix index R14-18102_kapa-NGv3-PE100-NGv3-6_142399691_157963777.vcf.gz
[2016-04-15T01:29Z] platypus variant calling
[2016-04-15T01:29Z] tabix index R14-18102_kapa-NGv3-PE100-NGv3-6_15511526_31080332.vcf.gz
[2016-04-15T01:29Z] platypus variant calling
[2016-04-15T01:29Z] tabix index R14-18102_kapa-NGv3-PE100-NGv3-7_15599765_31117713.vcf.gz
[2016-04-15T01:29Z] platypus variant calling
[2016-04-15T01:29Z] tabix index R14-18102_kapa-NGv3-PE100-NGv3-6_158013810_171115067.vcf.gz
[2016-04-15T01:29Z] tabix index R14-18102_kapa-NGv3-PE100-NGv3-7_157155854_159138663.vcf.gz
[2016-04-15T01:29Z] tabix index R14-18102_kapa-NGv3-PE100-NGv3-7_110526648_126079222.vcf.gz
[2016-04-15T01:29Z] platypus variant calling
[2016-04-15T01:29Z] platypus variant calling
[2016-04-15T01:29Z] platypus variant calling
[2016-04-15T01:29Z] tabix index R14-18102_kapa-NGv3-PE100-NGv3-7_31120227_47317818.vcf.gz
[2016-04-15T01:29Z] tabix index R14-18102_kapa-NGv3-PE100-NGv3-7_79082334_94740703.vcf.gz
[2016-04-15T01:29Z] platypus variant calling
[2016-04-15T01:29Z] platypus variant calling
[2016-04-15T01:29Z] tabix index R14-18102_kapa-NGv3-PE100-NGv3-7_0_15584548.vcf.gz
[2016-04-15T01:29Z] tabix index R14-18102_kapa-NGv3-PE100-NGv3-7_63095909_78636522.vcf.gz
[2016-04-15T01:29Z] platypus variant calling
[2016-04-15T01:29Z] platypus variant calling
[2016-04-15T01:29Z] tabix index R14-18102_kapa-NGv3-PE100-NGv3-8_79513976_95140568.vcf.gz
[2016-04-15T01:29Z] tabix index R14-18102_kapa-NGv3-PE100-NGv3-8_48003022_63659688.vcf.gz
[2016-04-15T01:29Z] tabix index R14-18102_kapa-NGv3-PE100-NGv3-5_127597427_143191869.vcf.gz
[2016-04-15T01:29Z] tabix index R14-18102_kapa-NGv3-PE100-NGv3-8_0_15517156.vcf.gz
[2016-04-15T01:29Z] platypus variant calling
[2016-04-15T01:29Z] platypus variant calling
[2016-04-15T01:29Z] platypus variant calling
[2016-04-15T01:29Z] platypus variant calling
[2016-04-15T01:29Z] tabix index R14-18102_kapa-NGv3-PE100-NGv3-8_63775819_79510770.vcf.gz
[2016-04-15T01:29Z] platypus variant calling
[2016-04-15T01:29Z] tabix index R14-18102_kapa-NGv3-PE100-NGv3-8_31496910_48001429.vcf.gz
[2016-04-15T01:29Z] platypus variant calling
[2016-04-15T01:29Z] tabix index R14-18102_kapa-NGv3-PE100-NGv3-8_126369460_141889736.vcf.gz
[2016-04-15T01:29Z] tabix index R14-18102_kapa-NGv3-PE100-NGv3-7_126086124_141619620.vcf.gz
[2016-04-15T01:29Z] platypus variant calling
[2016-04-15T01:29Z] platypus variant calling
[2016-04-15T01:29Z] tabix index R14-18102_kapa-NGv3-PE100-NGv3-8_110656864_126194498.vcf.gz
[2016-04-15T01:29Z] platypus variant calling
[2016-04-15T01:29Z] tabix index R14-18102_kapa-NGv3-PE100-NGv3-8_95142853_110655419.vcf.gz
[2016-04-15T01:29Z] platypus variant calling
[2016-04-15T01:29Z] tabix index R14-18102_kapa-NGv3-PE100-NGv3-9_15564086_32405601.vcf.gz
[2016-04-15T01:29Z] INFO  18:29:25,397 ProgressMeter -     19:15122039    1.157101998E9     3.0 m            0.0 s       97.3%     3.1 m       5.0 s
[2016-04-15T01:29Z] platypus variant calling
[2016-04-15T01:29Z] tabix index R14-18102_kapa-NGv3-PE100-NGv3-9_0_15510186.vcf.gz
[2016-04-15T01:29Z] platypus variant calling
[2016-04-15T01:29Z] tabix index R14-18102_kapa-NGv3-PE100-NGv3-8_15519664_31030618.vcf.gz
[2016-04-15T01:29Z] tabix index R14-18102_kapa-NGv3-PE100-NGv3-9_65507205_82187750.vcf.gz
[2016-04-15T01:29Z] platypus variant calling
[2016-04-15T01:29Z] platypus variant calling
[2016-04-15T01:29Z] tabix index R14-18102_kapa-NGv3-PE100-NGv3-7_141629903_157151331.vcf.gz
[2016-04-15T01:29Z] platypus variant calling
[2016-04-15T01:29Z] tabix index R14-18102_kapa-NGv3-PE100-NGv3-9_82188172_97717561.vcf.gz
[2016-04-15T01:29Z] INFO  18:29:29,870 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.083587268
[2016-04-15T01:29Z] INFO  18:29:29,871 PairHMM - Total compute time in PairHMM computeLikelihoods() : 10.099972399
[2016-04-15T01:29Z] INFO  18:29:29,872 HaplotypeCaller - Ran local assembly on 6005 active regions
[2016-04-15T01:29Z] INFO  18:29:29,906 ProgressMeter -            done    1.217430493E9     3.1 m            0.0 s      100.0%     3.1 m       0.0 s
[2016-04-15T01:29Z] INFO  18:29:29,907 ProgressMeter - Total runtime 184.54 secs, 3.08 min, 0.05 hours
[2016-04-15T01:29Z] INFO  18:29:29,908 MicroScheduler - 128245 reads were filtered out during the traversal out of approximately 1423209 total reads (9.01%)
[2016-04-15T01:29Z] INFO  18:29:29,908 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:29Z] INFO  18:29:29,909 MicroScheduler -   -> 115341 reads (8.10% of total) failing DuplicateReadFilter
[2016-04-15T01:29Z] INFO  18:29:29,910 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:29Z] INFO  18:29:29,911 MicroScheduler -   -> 12904 reads (0.91% of total) failing HCMappingQualityFilter
[2016-04-15T01:29Z] INFO  18:29:29,911 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:29Z] INFO  18:29:29,912 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:29Z] INFO  18:29:29,913 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:29Z] INFO  18:29:29,913 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T01:29Z] platypus variant calling
[2016-04-15T01:29Z] tabix index R14-18102_kapa-NGv3-PE100-NGv3-10_31137459_46960129.vcf.gz
[2016-04-15T01:29Z] tabix index R14-18102_kapa-NGv3-PE100-NGv3-10_15561288_31134502.vcf.gz
[2016-04-15T01:29Z] tabix index R14-18102_kapa-NGv3-PE100-NGv3-9_97718189_113228306.vcf.gz
[2016-04-15T01:29Z] tabix index R14-18102_kapa-NGv3-PE100-NGv3-10_0_15559243.vcf.gz
[2016-04-15T01:29Z] INFO  18:29:31,400 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:29Z] platypus variant calling
[2016-04-15T01:29Z] platypus variant calling
[2016-04-15T01:29Z] platypus variant calling
[2016-04-15T01:29Z] platypus variant calling
[2016-04-15T01:29Z] platypus variant calling
[2016-04-15T01:29Z] tabix index R14-18102_kapa-NGv3-PE100-NGv3-9_113231219_129089575.vcf.gz
[2016-04-15T01:29Z] platypus variant calling
[2016-04-15T01:29Z] tabix index R14-18102_kapa-NGv3-PE100-NGv3-9_32407258_65506776.vcf.gz
[2016-04-15T01:29Z] platypus variant calling
[2016-04-15T01:29Z] tabix index R14-18102_kapa-NGv3-PE100-NGv3-10_46960410_62493077.vcf.gz
[2016-04-15T01:29Z] platypus variant calling
[2016-04-15T01:29Z] INFO  18:29:34,568 ProgressMeter -     19:58477943     6.87489433E8     3.0 m            0.0 s       93.5%     3.2 m      12.0 s
[2016-04-15T01:29Z] tabix index R14-18102_kapa-NGv3-PE100-NGv3-8_141900641_146364022.vcf.gz
[2016-04-15T01:29Z] platypus variant calling
[2016-04-15T01:29Z] tabix index R14-18102_kapa-NGv3-PE100-NGv3-6_31083801_46593245.vcf.gz
[2016-04-15T01:29Z] tabix index R14-18102_kapa-NGv3-PE100-NGv3-10_78316966_93841258.vcf.gz
[2016-04-15T01:29Z] platypus variant calling
[2016-04-15T01:29Z] platypus variant calling
[2016-04-15T01:29Z] tabix index R14-18102_kapa-NGv3-PE100-NGv3-10_127328721_135534747.vcf.gz
[2016-04-15T01:29Z] platypus variant calling
[2016-04-15T01:29Z] tabix index R14-18102_kapa-NGv3-PE100-NGv3-10_62539923_78084243.vcf.gz
[2016-04-15T01:29Z] platypus variant calling
[2016-04-15T01:29Z] tabix index R14-18102_kapa-NGv3-PE100-NGv3-11_16007749_31531554.vcf.gz
[2016-04-15T01:29Z] tabix index R14-18102_kapa-NGv3-PE100-NGv3-7_94750023_110303777.vcf.gz
[2016-04-15T01:29Z] platypus variant calling
[2016-04-15T01:29Z] platypus variant calling
[2016-04-15T01:29Z] tabix index R14-18102_kapa-NGv3-PE100-NGv3-11_31541602_47074069.vcf.gz
[2016-04-15T01:29Z] tabix index R14-18102_kapa-NGv3-PE100-NGv3-11_78277177_93796886.vcf.gz
[2016-04-15T01:29Z] platypus variant calling
[2016-04-15T01:29Z] platypus variant calling
[2016-04-15T01:29Z] tabix index R14-18102_kapa-NGv3-PE100-NGv3-10_111628371_127265443.vcf.gz
[2016-04-15T01:29Z] platypus variant calling
[2016-04-15T01:29Z] tabix index R14-18102_kapa-NGv3-PE100-NGv3-11_93797496_109964158.vcf.gz
[2016-04-15T01:29Z] platypus variant calling
[2016-04-15T01:29Z] tabix index R14-18102_kapa-NGv3-PE100-NGv3-11_125523640_135006516.vcf.gz
[2016-04-15T01:29Z] platypus variant calling
[2016-04-15T01:29Z] tabix index R14-18102_kapa-NGv3-PE100-NGv3-12_78334098_93863131.vcf.gz
[2016-04-15T01:29Z] platypus variant calling
[2016-04-15T01:29Z] tabix index R14-18102_kapa-NGv3-PE100-NGv3-12_15650178_31231471.vcf.gz
[2016-04-15T01:29Z] tabix index R14-18102_kapa-NGv3-PE100-NGv3-13_0_19748299.vcf.gz
[2016-04-15T01:29Z] platypus variant calling
[2016-04-15T01:29Z] platypus variant calling
[2016-04-15T01:29Z] tabix index R14-18102_kapa-NGv3-PE100-NGv3-12_62687959_78225484.vcf.gz
[2016-04-15T01:29Z] platypus variant calling
[2016-04-15T01:29Z] tabix index R14-18102_kapa-NGv3-PE100-NGv3-10_93851586_111625070.vcf.gz
[2016-04-15T01:29Z] platypus variant calling
[2016-04-15T01:29Z] INFO  18:29:45,888 VectorLoglessPairHMM - Time spent in setup for JNI call : 0.112453432
[2016-04-15T01:29Z] INFO  18:29:45,889 PairHMM - Total compute time in PairHMM computeLikelihoods() : 12.524028828
[2016-04-15T01:29Z] INFO  18:29:45,890 HaplotypeCaller - Ran local assembly on 4940 active regions
[2016-04-15T01:29Z] INFO  18:29:45,931 ProgressMeter -            done      7.6177958E8     3.2 m            0.0 s      100.0%     3.2 m       0.0 s
[2016-04-15T01:29Z] INFO  18:29:45,931 ProgressMeter - Total runtime 191.39 secs, 3.19 min, 0.05 hours
[2016-04-15T01:29Z] INFO  18:29:45,931 MicroScheduler - 143801 reads were filtered out during the traversal out of approximately 1254161 total reads (11.47%)
[2016-04-15T01:29Z] INFO  18:29:45,932 MicroScheduler -   -> 0 reads (0.00% of total) failing BadCigarFilter
[2016-04-15T01:29Z] INFO  18:29:45,932 MicroScheduler -   -> 99551 reads (7.94% of total) failing DuplicateReadFilter
[2016-04-15T01:29Z] INFO  18:29:45,932 MicroScheduler -   -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
[2016-04-15T01:29Z] INFO  18:29:45,932 MicroScheduler -   -> 44250 reads (3.53% of total) failing HCMappingQualityFilter
[2016-04-15T01:29Z] INFO  18:29:45,933 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter
[2016-04-15T01:29Z] INFO  18:29:45,933 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
[2016-04-15T01:29Z] INFO  18:29:45,933 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter
[2016-04-15T01:29Z] INFO  18:29:45,933 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter
[2016-04-15T01:29Z] tabix index R14-18102_kapa-NGv3-PE100-NGv3-13_51396767_67205543.vcf.gz
[2016-04-15T01:29Z] platypus variant calling
[2016-04-15T01:29Z] INFO  18:29:47,256 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:29Z] tabix index R14-18102_kapa-NGv3-PE100-NGv3-12_93870729_109490566.vcf.gz
[2016-04-15T01:29Z] tabix index R14-18102_kapa-NGv3-PE100-NGv3-13_67477635_84455642.vcf.gz
[2016-04-15T01:29Z] platypus variant calling
[2016-04-15T01:29Z] platypus variant calling
[2016-04-15T01:29Z] tabix index R14-18102_kapa-NGv3-PE100-NGv3-11_47158866_62678572.vcf.gz
[2016-04-15T01:29Z] tabix index R14-18102_kapa-NGv3-PE100-NGv3-12_125267228_133851895.vcf.gz
[2016-04-15T01:29Z] platypus variant calling
[2016-04-15T01:29Z] tabix index R14-18102_kapa-NGv3-PE100-NGv3-12_31236746_46754992.vcf.gz
[2016-04-15T01:29Z] tabix index R14-18102_kapa-NGv3-PE100-NGv3-14_0_19378574.vcf.gz
[2016-04-15T01:29Z] platypus variant calling
[2016-04-15T01:29Z] platypus variant calling
[2016-04-15T01:29Z] platypus variant calling
[2016-04-15T01:29Z] platypus variant calling
[2016-04-15T01:29Z] tabix index R14-18102_kapa-NGv3-PE100-NGv3-13_35615069_51287376.vcf.gz
[2016-04-15T01:29Z] tabix index R14-18102_kapa-NGv3-PE100-NGv3-13_19751066_35517251.vcf.gz
[2016-04-15T01:29Z] platypus variant calling
[2016-04-15T01:29Z] platypus variant calling
[2016-04-15T01:29Z] tabix index R14-18102_kapa-NGv3-PE100-NGv3-13_86368117_101881935.vcf.gz
[2016-04-15T01:29Z] platypus variant calling
[2016-04-15T01:29Z] tabix index R14-18102_kapa-NGv3-PE100-NGv3-11_110001730_125514538.vcf.gz
[2016-04-15T01:29Z] tabix index R14-18102_kapa-NGv3-PE100-NGv3-15_0_20740485.vcf.gz
[2016-04-15T01:29Z] tabix index R14-18102_kapa-NGv3-PE100-NGv3-9_129097484_141213431.vcf.gz
[2016-04-15T01:29Z] platypus variant calling
[2016-04-15T01:29Z] platypus variant calling
[2016-04-15T01:29Z] platypus variant calling
[2016-04-15T01:29Z] tabix index R14-18102_kapa-NGv3-PE100-NGv3-14_35072553_50583270.vcf.gz
[2016-04-15T01:29Z] platypus variant calling
[2016-04-15T01:29Z] tabix index R14-18102_kapa-NGv3-PE100-NGv3-12_0_15637181.vcf.gz
[2016-04-15T01:29Z] platypus variant calling
[2016-04-15T01:29Z] tabix index R14-18102_kapa-NGv3-PE100-NGv3-13_101890105_115169878.vcf.gz
[2016-04-15T01:29Z] platypus variant calling
[2016-04-15T01:29Z] tabix index R14-18102_kapa-NGv3-PE100-NGv3-15_98984299_102531392.vcf.gz
[2016-04-15T01:29Z] tabix index R14-18102_kapa-NGv3-PE100-NGv3-14_81651874_97299968.vcf.gz
[2016-04-15T01:29Z] platypus variant calling
[2016-04-15T01:29Z] platypus variant calling
[2016-04-15T01:29Z] tabix index R14-18102_kapa-NGv3-PE100-NGv3-14_50585061_66096324.vcf.gz
[2016-04-15T01:29Z] platypus variant calling
[2016-04-15T01:29Z] tabix index R14-18102_kapa-NGv3-PE100-NGv3-12_109494486_125263132.vcf.gz
[2016-04-15T01:29Z] platypus variant calling
[2016-04-15T01:29Z] tabix index R14-18102_kapa-NGv3-PE100-NGv3-16_31120544_46629582.vcf.gz
[2016-04-15T01:29Z] tabix index R14-18102_kapa-NGv3-PE100-NGv3-14_66135960_81646674.vcf.gz
[2016-04-15T01:29Z] platypus variant calling
[2016-04-15T01:29Z] platypus variant calling
[2016-04-15T01:29Z] tabix index R14-18102_kapa-NGv3-PE100-NGv3-15_20741621_36872162.vcf.gz
[2016-04-15T01:29Z] platypus variant calling
[2016-04-15T01:29Z] tabix index R14-18102_kapa-NGv3-PE100-NGv3-14_97304098_107349540.vcf.gz
[2016-04-15T01:29Z] tabix index R14-18102_kapa-NGv3-PE100-NGv3-15_52404364_67923265.vcf.gz
[2016-04-15T01:29Z] tabix index R14-18102_kapa-NGv3-PE100-NGv3-15_83448996_98982979.vcf.gz
[2016-04-15T01:29Z] platypus variant calling
[2016-04-15T01:29Z] platypus variant calling
[2016-04-15T01:30Z] platypus variant calling
[2016-04-15T01:30Z] tabix index R14-18102_kapa-NGv3-PE100-NGv3-11_0_15994658.vcf.gz
[2016-04-15T01:30Z] platypus variant calling
[2016-04-15T01:30Z] tabix index R14-18102_kapa-NGv3-PE100-NGv3-11_62744265_78270665.vcf.gz
[2016-04-15T01:30Z] platypus variant calling
[2016-04-15T01:30Z] tabix index R14-18102_kapa-NGv3-PE100-NGv3-14_19553416_35066851.vcf.gz
[2016-04-15T01:30Z] tabix index R14-18102_kapa-NGv3-PE100-NGv3-15_67932890_83447639.vcf.gz
[2016-04-15T01:30Z] platypus variant calling
[2016-04-15T01:30Z] platypus variant calling
[2016-04-15T01:30Z] tabix index R14-18102_kapa-NGv3-PE100-NGv3-12_46756066_62654284.vcf.gz
[2016-04-15T01:30Z] tabix index R14-18102_kapa-NGv3-PE100-NGv3-16_46633742_64982002.vcf.gz
[2016-04-15T01:30Z] platypus variant calling
[2016-04-15T01:30Z] platypus variant calling
[2016-04-15T01:30Z] tabix index R14-18102_kapa-NGv3-PE100-NGv3-18_0_18531348.vcf.gz
[2016-04-15T01:30Z] platypus variant calling
[2016-04-15T01:30Z] tabix index R14-18102_kapa-NGv3-PE100-NGv3-15_36887086_52402170.vcf.gz
[2016-04-15T01:30Z] tabix index R14-18102_kapa-NGv3-PE100-NGv3-16_80575258_90354753.vcf.gz
[2016-04-15T01:30Z] platypus variant calling
[2016-04-15T01:30Z] platypus variant calling
[2016-04-15T01:30Z] tabix index R14-18102_kapa-NGv3-PE100-NGv3-18_18533538_34081962.vcf.gz
[2016-04-15T01:30Z] tabix index R14-18102_kapa-NGv3-PE100-NGv3-18_34092400_49867248.vcf.gz
[2016-04-15T01:30Z] platypus variant calling
[2016-04-15T01:30Z] platypus variant calling
[2016-04-15T01:30Z] tabix index R14-18102_kapa-NGv3-PE100-NGv3-17_77707305_81195210.vcf.gz
[2016-04-15T01:30Z] platypus variant calling
[2016-04-15T01:30Z] tabix index R14-18102_kapa-NGv3-PE100-NGv3-18_50278423_66344430.vcf.gz
[2016-04-15T01:30Z] tabix index R14-18102_kapa-NGv3-PE100-NGv3-18_66346699_78077248.vcf.gz
[2016-04-15T01:30Z] platypus variant calling
[2016-04-15T01:30Z] platypus variant calling
[2016-04-15T01:30Z] tabix index R14-18102_kapa-NGv3-PE100-NGv3-17_46607689_62121560.vcf.gz
[2016-04-15T01:30Z] tabix index R14-18102_kapa-NGv3-PE100-NGv3-16_64982511_80574976.vcf.gz
[2016-04-15T01:30Z] platypus variant calling
[2016-04-15T01:30Z] platypus variant calling
[2016-04-15T01:30Z] tabix index R14-18102_kapa-NGv3-PE100-NGv3-20_62831244_63025520.vcf.gz
[2016-04-15T01:30Z] platypus variant calling
[2016-04-15T01:30Z] tabix index R14-18102_kapa-NGv3-PE100-NGv3-21_0_15517120.vcf.gz
[2016-04-15T01:30Z] platypus variant calling
[2016-04-15T01:30Z] tabix index R14-18102_kapa-NGv3-PE100-NGv3-17_15515955_31039213.vcf.gz
[2016-04-15T01:30Z] tabix index R14-18102_kapa-NGv3-PE100-NGv3-16_15596122_31106473.vcf.gz
[2016-04-15T01:30Z] platypus variant calling
[2016-04-15T01:30Z] platypus variant calling
[2016-04-15T01:30Z] tabix index R14-18102_kapa-NGv3-PE100-NGv3-22_0_16258303.vcf.gz
[2016-04-15T01:30Z] tabix index R14-18102_kapa-NGv3-PE100-NGv3-20_15866408_31376818.vcf.gz
[2016-04-15T01:30Z] tabix index R14-18102_kapa-NGv3-PE100-NGv3-21_15524893_31045484.vcf.gz
[2016-04-15T01:30Z] platypus variant calling
[2016-04-15T01:30Z] platypus variant calling
[2016-04-15T01:30Z] platypus variant calling
[2016-04-15T01:30Z] tabix index R14-18102_kapa-NGv3-PE100-NGv3-20_0_15843471.vcf.gz
[2016-04-15T01:30Z] platypus variant calling
[2016-04-15T01:30Z] tabix index R14-18102_kapa-NGv3-PE100-NGv3-17_62122219_77705154.vcf.gz
[2016-04-15T01:30Z] platypus variant calling
[2016-04-15T01:30Z] tabix index R14-18102_kapa-NGv3-PE100-NGv3-21_46595644_48129895.vcf.gz
[2016-04-15T01:30Z] platypus variant calling
[2016-04-15T01:30Z] tabix index R14-18102_kapa-NGv3-PE100-NGv3-16_0_15528616.vcf.gz
[2016-04-15T01:30Z] platypus variant calling
[2016-04-15T01:30Z] tabix index R14-18102_kapa-NGv3-PE100-NGv3-X_0_15509380.vcf.gz
[2016-04-15T01:30Z] platypus variant calling
[2016-04-15T01:30Z] tabix index R14-18102_kapa-NGv3-PE100-NGv3-22_47309229_51304566.vcf.gz
[2016-04-15T01:30Z] platypus variant calling
[2016-04-15T01:30Z] tabix index R14-18102_kapa-NGv3-PE100-NGv3-X_31139949_46696637.vcf.gz
[2016-04-15T01:30Z] platypus variant calling
[2016-04-15T01:30Z] tabix index R14-18102_kapa-NGv3-PE100-NGv3-19_15510112_31025906.vcf.gz
[2016-04-15T01:30Z] tabix index R14-18102_kapa-NGv3-PE100-NGv3-X_15518899_31090070.vcf.gz
[2016-04-15T01:30Z] platypus variant calling
[2016-04-15T01:30Z] platypus variant calling
[2016-04-15T01:30Z] tabix index R14-18102_kapa-NGv3-PE100-NGv3-X_78616585_95940189.vcf.gz
[2016-04-15T01:30Z] tabix index R14-18102_kapa-NGv3-PE100-NGv3-20_47244085_62830269.vcf.gz
[2016-04-15T01:30Z] platypus variant calling
[2016-04-15T01:30Z] platypus variant calling
[2016-04-15T01:30Z] tabix index R14-18102_kapa-NGv3-PE100-NGv3-20_31379406_47242465.vcf.gz
[2016-04-15T01:30Z] tabix index R14-18102_kapa-NGv3-PE100-NGv3-Y_0_15522993.vcf.gz
[2016-04-15T01:30Z] platypus variant calling
[2016-04-15T01:30Z] platypus variant calling
[2016-04-15T01:30Z] tabix index R14-18102_kapa-NGv3-PE100-NGv3-17_0_15511002.vcf.gz
[2016-04-15T01:30Z] tabix index R14-18102_kapa-NGv3-PE100-NGv3-Y_59228291_59373566.vcf.gz
[2016-04-15T01:30Z] tabix index R14-18102_kapa-NGv3-PE100-NGv3-Y_15526614_59222281.vcf.gz
[2016-04-15T01:30Z] tabix index R14-18102_kapa-NGv3-PE100-NGv3-17_31048040_46607237.vcf.gz
[2016-04-15T01:30Z] tabix index R14-18102_kapa-NGv3-PE100-NGv3-21_31062047_46591599.vcf.gz
[2016-04-15T01:30Z] tabix index R14-18102_kapa-NGv3-PE100-NGv3-X_111874647_128581278.vcf.gz
[2016-04-15T01:30Z] tabix index R14-18102_kapa-NGv3-PE100-NGv3-X_62857907_78427545.vcf.gz
[2016-04-15T01:30Z] tabix index R14-18102_kapa-NGv3-PE100-NGv3-X_128582278_144329181.vcf.gz
[2016-04-15T01:30Z] tabix index R14-18102_kapa-NGv3-PE100-NGv3-X_95990756_111698889.vcf.gz
[2016-04-15T01:30Z] tabix index R14-18102_kapa-NGv3-PE100-NGv3-X_46712910_62570698.vcf.gz
[2016-04-15T01:30Z] tabix index R14-18102_kapa-NGv3-PE100-NGv3-22_31796605_47308085.vcf.gz
[2016-04-15T01:30Z] tabix index R14-18102_kapa-NGv3-PE100-NGv3-22_16266928_31795711.vcf.gz
[2016-04-15T01:30Z] tabix index R14-18102_kapa-NGv3-PE100-NGv3-X_144337190_155270560.vcf.gz
[2016-04-15T01:30Z] tabix index R14-18102_kapa-NGv3-PE100-NGv3-19_31038849_46627578.vcf.gz
[2016-04-15T01:30Z] tabix index R14-18102_kapa-NGv3-PE100-NGv3-19_46627881_59128983.vcf.gz
[2016-04-15T01:30Z] tabix index R14-18102_kapa-NGv3-PE100-NGv3-19_0_15509577.vcf.gz
[2016-04-15T01:30Z] multiprocessing: concat_variant_files
[2016-04-15T01:30Z] Resource requests: ; memory: 1.00; cores: 1
[2016-04-15T01:30Z] Configuring 1 jobs to run, using 1 cores each with 1.00g of memory reserved for each job
[2016-04-15T01:30Z] Resource requests: ; memory: 1.00; cores: 1
[2016-04-15T01:30Z] Resource requests: ; memory: 1.00; cores: 1
[2016-04-15T01:30Z] Configuring 1 jobs to run, using 1 cores each with 1.00g of memory reserved for each job
[2016-04-15T01:30Z] Configuring 1 jobs to run, using 1 cores each with 1.00g of memory reserved for each job
[2016-04-15T01:30Z] Resource requests: ; memory: 1.00; cores: 1
[2016-04-15T01:30Z] Configuring 1 jobs to run, using 1 cores each with 1.00g of memory reserved for each job
[2016-04-15T01:30Z] Resource requests: ; memory: 1.00; cores: 1
[2016-04-15T01:30Z] Configuring 1 jobs to run, using 1 cores each with 1.00g of memory reserved for each job
[2016-04-15T01:30Z] Resource requests: ; memory: 1.00; cores: 1
[2016-04-15T01:30Z] Configuring 1 jobs to run, using 1 cores each with 1.00g of memory reserved for each job
[2016-04-15T01:30Z] Resource requests: ; memory: 1.00; cores: 1
[2016-04-15T01:30Z] Resource requests: ; memory: 1.00; cores: 1
[2016-04-15T01:30Z] Resource requests: ; memory: 1.00; cores: 1
[2016-04-15T01:30Z] Configuring 1 jobs to run, using 1 cores each with 1.00g of memory reserved for each job
[2016-04-15T01:30Z] Configuring 1 jobs to run, using 1 cores each with 1.00g of memory reserved for each job
[2016-04-15T01:30Z] Configuring 1 jobs to run, using 1 cores each with 1.00g of memory reserved for each job
[2016-04-15T01:30Z] Concat variant files
[2016-04-15T01:30Z] Concat variant files
[2016-04-15T01:30Z] Concat variant files
[2016-04-15T01:30Z] Concat variant files
[2016-04-15T01:30Z] Concat variant files
[2016-04-15T01:30Z] Concat variant files
[2016-04-15T01:30Z] Concat variant files
[2016-04-15T01:30Z] Concat variant files
[2016-04-15T01:30Z] Concat variant files
[2016-04-15T01:30Z] INFO  18:30:49,806 HelpFormatter - -------------------------------------------------------
[2016-04-15T01:30Z] INFO  18:30:49,809 HelpFormatter - Program Name: org.broadinstitute.gatk.tools.CatVariants
[2016-04-15T01:30Z] INFO  18:30:49,814 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -V /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/R14-18105_kapa-NGv3-PE100-NGv3-files.list -out /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/tx/tmprqjq9y/R14-18105_kapa-NGv3-PE100-NGv3.vcf.gz -assumeSorted
[2016-04-15T01:30Z] INFO  18:30:49,829 HelpFormatter - -------------------------------------------------------
[2016-04-15T01:30Z] INFO  18:30:49,834 HelpFormatter - Program Name: org.broadinstitute.gatk.tools.CatVariants
[2016-04-15T01:30Z] INFO  18:30:49,842 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -V /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18105_kapa-NGv3-PE100-NGv3-files.list -out /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/tx/tmpTZMlh6/R14-18105_kapa-NGv3-PE100-NGv3.vcf.gz -assumeSorted
[2016-04-15T01:30Z] INFO  18:30:49,848 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:30Z] INFO  18:30:49,850 HelpFormatter - Date/Time: 2016/04/14 18:30:49
[2016-04-15T01:30Z] INFO  18:30:49,851 HelpFormatter - -------------------------------------------------------
[2016-04-15T01:30Z] INFO  18:30:49,852 HelpFormatter - -------------------------------------------------------
[2016-04-15T01:30Z] INFO  18:30:49,854 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:30Z] INFO  18:30:49,856 HelpFormatter - Date/Time: 2016/04/14 18:30:49
[2016-04-15T01:30Z] INFO  18:30:49,857 HelpFormatter - -------------------------------------------------------
[2016-04-15T01:30Z] INFO  18:30:49,857 HelpFormatter - -------------------------------------------------------
[2016-04-15T01:30Z] INFO  18:30:49,862 HelpFormatter - -------------------------------------------------------
[2016-04-15T01:30Z] INFO  18:30:49,866 HelpFormatter - Program Name: org.broadinstitute.gatk.tools.CatVariants
[2016-04-15T01:30Z] INFO  18:30:49,865 HelpFormatter - -------------------------------------------------------
[2016-04-15T01:30Z] INFO  18:30:49,870 HelpFormatter - Program Name: org.broadinstitute.gatk.tools.CatVariants
[2016-04-15T01:30Z] INFO  18:30:49,878 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -V /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18102_kapa-NGv3-PE100-NGv3-files.list -out /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/tx/tmpLE_Fk3/R14-18102_kapa-NGv3-PE100-NGv3.vcf.gz -assumeSorted
[2016-04-15T01:30Z] INFO  18:30:49,885 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -V /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/R14-18106_kapa-NGv3-PE100-NGv3-files.list -out /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/tx/tmpyiuGv7/R14-18106_kapa-NGv3-PE100-NGv3.vcf.gz -assumeSorted
[2016-04-15T01:30Z] INFO  18:30:49,897 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:30Z] INFO  18:30:49,895 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:30Z] INFO  18:30:49,897 HelpFormatter - Date/Time: 2016/04/14 18:30:49
[2016-04-15T01:30Z] INFO  18:30:49,897 HelpFormatter - -------------------------------------------------------
[2016-04-15T01:30Z] INFO  18:30:49,901 HelpFormatter - -------------------------------------------------------
[2016-04-15T01:30Z] INFO  18:30:49,903 HelpFormatter - Date/Time: 2016/04/14 18:30:49
[2016-04-15T01:30Z] INFO  18:30:49,905 HelpFormatter - -------------------------------------------------------
[2016-04-15T01:30Z] INFO  18:30:49,906 HelpFormatter - -------------------------------------------------------
[2016-04-15T01:30Z] INFO  18:30:49,953 HelpFormatter - -------------------------------------------------------
[2016-04-15T01:30Z] INFO  18:30:49,958 HelpFormatter - Program Name: org.broadinstitute.gatk.tools.CatVariants
[2016-04-15T01:30Z] INFO  18:30:49,963 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -V /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/platypus/R14-18105_kapa-NGv3-PE100-NGv3-files.list -out /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/platypus/tx/tmpUPw2Ho/R14-18105_kapa-NGv3-PE100-NGv3.vcf.gz -assumeSorted
[2016-04-15T01:30Z] INFO  18:30:49,976 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:30Z] INFO  18:30:49,977 HelpFormatter - Date/Time: 2016/04/14 18:30:49
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[2016-04-15T01:30Z] INFO  18:30:50,234 HelpFormatter - -------------------------------------------------------
[2016-04-15T01:30Z] INFO  18:30:50,238 HelpFormatter - Program Name: org.broadinstitute.gatk.tools.CatVariants
[2016-04-15T01:30Z] INFO  18:30:50,244 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -V /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/platypus/R14-18102_kapa-NGv3-PE100-NGv3-files.list -out /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/platypus/tx/tmpeuChmy/R14-18102_kapa-NGv3-PE100-NGv3.vcf.gz -assumeSorted
[2016-04-15T01:30Z] INFO  18:30:50,257 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:30Z] INFO  18:30:50,258 HelpFormatter - Date/Time: 2016/04/14 18:30:50
[2016-04-15T01:30Z] INFO  18:30:50,259 HelpFormatter - -------------------------------------------------------
[2016-04-15T01:30Z] INFO  18:30:50,266 HelpFormatter - -------------------------------------------------------
[2016-04-15T01:30Z] INFO  18:30:50,299 HelpFormatter - -------------------------------------------------------
[2016-04-15T01:30Z] INFO  18:30:50,304 HelpFormatter - Program Name: org.broadinstitute.gatk.tools.CatVariants
[2016-04-15T01:30Z] INFO  18:30:50,314 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -V /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18106_kapa-NGv3-PE100-NGv3-files.list -out /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/tx/tmp7n0aj5/R14-18106_kapa-NGv3-PE100-NGv3.vcf.gz -assumeSorted
[2016-04-15T01:30Z] INFO  18:30:50,327 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:30Z] INFO  18:30:50,328 HelpFormatter - Date/Time: 2016/04/14 18:30:50
[2016-04-15T01:30Z] INFO  18:30:50,328 HelpFormatter - -------------------------------------------------------
[2016-04-15T01:30Z] INFO  18:30:50,329 HelpFormatter - -------------------------------------------------------
[2016-04-15T01:30Z] INFO  18:30:50,337 HelpFormatter - -------------------------------------------------------
[2016-04-15T01:30Z] INFO  18:30:50,342 HelpFormatter - Program Name: org.broadinstitute.gatk.tools.CatVariants
[2016-04-15T01:30Z] INFO  18:30:50,349 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -V /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/platypus/R14-18106_kapa-NGv3-PE100-NGv3-files.list -out /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/platypus/tx/tmpS4Mq6V/R14-18106_kapa-NGv3-PE100-NGv3.vcf.gz -assumeSorted
[2016-04-15T01:30Z] INFO  18:30:50,365 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:30Z] INFO  18:30:50,366 HelpFormatter - Date/Time: 2016/04/14 18:30:50
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[2016-04-15T01:30Z] INFO  18:30:51,535 HelpFormatter - -------------------------------------------------------
[2016-04-15T01:30Z] INFO  18:30:51,539 HelpFormatter - Program Name: org.broadinstitute.gatk.tools.CatVariants
[2016-04-15T01:30Z] INFO  18:30:51,558 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -V /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/R14-18102_kapa-NGv3-PE100-NGv3-files.list -out /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk/tx/tmphXXJz8/R14-18102_kapa-NGv3-PE100-NGv3.vcf.gz -assumeSorted
[2016-04-15T01:30Z] INFO  18:30:51,586 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:30Z] INFO  18:30:51,588 HelpFormatter - Date/Time: 2016/04/14 18:30:51
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[2016-04-15T01:31Z] Resource requests: bamtools, bcbio-variation-recall, bcbio_variation, fastqc, gatk, gemini, qsignature, samtools, snpeff; memory: 2.00, 2.00, 2.50, 2.00, 3.50, 2.00, 0.12, 2.00, 6.00; cores: 16, 16, 1, 16, 1, 16, 1, 16, 1
[2016-04-15T01:31Z] Configuring 1 jobs to run, using 16 cores each with 96.1g of memory reserved for each job
[2016-04-15T01:31Z] Timing: joint squaring off/backfilling
[2016-04-15T01:31Z] multiprocessing: square_batch_region
[2016-04-15T01:31Z] GATK: GenotypeGVCFs
[2016-04-15T01:31Z] INFO  18:31:13,158 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:31Z] INFO  18:31:13,160 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:31Z] INFO  18:31:13,160 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:31Z] INFO  18:31:13,160 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:31Z] INFO  18:31:13,164 HelpFormatter - Program Args: -T GenotypeGVCFs -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/gatk-haplotype-joint/Batch1/1/tx/tmpuDAQg2/Batch1-1_0_15541927.vcf.gz -L 1:1-15541927 --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18106_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18105_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18102_kapa-NGv3-PE100-NGv3.vcf.gz --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -nt 16 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:31Z] INFO  18:31:13,174 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:31Z] INFO  18:31:13,174 HelpFormatter - Date/Time: 2016/04/14 18:31:13
[2016-04-15T01:31Z] INFO  18:31:13,174 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:31Z] INFO  18:31:13,174 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:31Z] INFO  18:31:13,338 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:31Z] INFO  18:31:13,443 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T01:31Z] INFO  18:31:14,202 IntervalUtils - Processing 15541927 bp from intervals
[2016-04-15T01:31Z] WARN  18:31:14,203 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:31Z] WARN  18:31:14,204 IndexDictionaryUtils - Track variant2 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:31Z] WARN  18:31:14,204 IndexDictionaryUtils - Track variant3 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:31Z] WARN  18:31:14,205 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:31Z] INFO  18:31:14,222 MicroScheduler - Running the GATK in parallel mode with 16 total threads, 1 CPU thread(s) for each of 16 data thread(s), of 16 processors available on this machine
[2016-04-15T01:31Z] INFO  18:31:14,367 GenomeAnalysisEngine - Preparing for traversal
[2016-04-15T01:31Z] INFO  18:31:14,369 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:31Z] INFO  18:31:14,370 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:31Z] INFO  18:31:14,371 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T01:31Z] INFO  18:31:14,371 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T01:31Z] INFO  18:31:14,627 GenotypeGVCFs - Notice that the -ploidy parameter is ignored in GenotypeGVCFs tool as this is automatically determined by the input variant files
[2016-04-15T01:31Z] INFO  18:31:23,049 ProgressMeter -            done    765340.0     8.0 s      11.0 s      100.0%     8.0 s       0.0 s
[2016-04-15T01:31Z] INFO  18:31:23,050 ProgressMeter - Total runtime 8.68 secs, 0.14 min, 0.00 hours
[2016-04-15T01:31Z] INFO  18:31:25,170 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:31Z] GATK: GenotypeGVCFs
[2016-04-15T01:31Z] INFO  18:31:27,245 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:31Z] INFO  18:31:27,247 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:31Z] INFO  18:31:27,247 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:31Z] INFO  18:31:27,247 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:31Z] INFO  18:31:27,251 HelpFormatter - Program Args: -T GenotypeGVCFs -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/gatk-haplotype-joint/Batch1/1/tx/tmpyJ4Diu/Batch1-1_15545821_31186478.vcf.gz -L 1:15545822-31186478 --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18106_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18105_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18102_kapa-NGv3-PE100-NGv3.vcf.gz --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -nt 16 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:31Z] INFO  18:31:27,259 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:31Z] INFO  18:31:27,259 HelpFormatter - Date/Time: 2016/04/14 18:31:27
[2016-04-15T01:31Z] INFO  18:31:27,259 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:31Z] INFO  18:31:27,259 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:31Z] INFO  18:31:27,331 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:31Z] INFO  18:31:27,428 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T01:31Z] INFO  18:31:27,838 IntervalUtils - Processing 15640657 bp from intervals
[2016-04-15T01:31Z] WARN  18:31:27,838 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:31Z] WARN  18:31:27,838 IndexDictionaryUtils - Track variant2 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:31Z] WARN  18:31:27,839 IndexDictionaryUtils - Track variant3 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:31Z] WARN  18:31:27,839 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:31Z] INFO  18:31:27,847 MicroScheduler - Running the GATK in parallel mode with 16 total threads, 1 CPU thread(s) for each of 16 data thread(s), of 16 processors available on this machine
[2016-04-15T01:31Z] INFO  18:31:27,896 GenomeAnalysisEngine - Preparing for traversal
[2016-04-15T01:31Z] INFO  18:31:27,897 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:31Z] INFO  18:31:27,898 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:31Z] INFO  18:31:27,898 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T01:31Z] INFO  18:31:27,899 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T01:31Z] INFO  18:31:28,021 GenotypeGVCFs - Notice that the -ploidy parameter is ignored in GenotypeGVCFs tool as this is automatically determined by the input variant files
[2016-04-15T01:31Z] INFO  18:31:38,903 ProgressMeter -            done    750010.0    11.0 s      14.0 s      100.0%    11.0 s       0.0 s
[2016-04-15T01:31Z] INFO  18:31:38,903 ProgressMeter - Total runtime 11.01 secs, 0.18 min, 0.00 hours
[2016-04-15T01:31Z] INFO  18:31:41,440 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:31Z] GATK: GenotypeGVCFs
[2016-04-15T01:31Z] INFO  18:31:43,614 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:31Z] INFO  18:31:43,616 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:31Z] INFO  18:31:43,616 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:31Z] INFO  18:31:43,617 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:31Z] INFO  18:31:43,620 HelpFormatter - Program Args: -T GenotypeGVCFs -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/gatk-haplotype-joint/Batch1/1/tx/tmp2Zcx1I/Batch1-1_31187093_46714270.vcf.gz -L 1:31187094-46714270 --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18106_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18105_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18102_kapa-NGv3-PE100-NGv3.vcf.gz --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -nt 16 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:31Z] INFO  18:31:43,628 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:31Z] INFO  18:31:43,628 HelpFormatter - Date/Time: 2016/04/14 18:31:43
[2016-04-15T01:31Z] INFO  18:31:43,628 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:31Z] INFO  18:31:43,629 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:31Z] INFO  18:31:43,700 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:31Z] INFO  18:31:43,797 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T01:31Z] INFO  18:31:44,213 IntervalUtils - Processing 15527177 bp from intervals
[2016-04-15T01:31Z] WARN  18:31:44,214 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:31Z] WARN  18:31:44,214 IndexDictionaryUtils - Track variant2 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:31Z] WARN  18:31:44,214 IndexDictionaryUtils - Track variant3 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:31Z] WARN  18:31:44,215 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:31Z] INFO  18:31:44,223 MicroScheduler - Running the GATK in parallel mode with 16 total threads, 1 CPU thread(s) for each of 16 data thread(s), of 16 processors available on this machine
[2016-04-15T01:31Z] INFO  18:31:44,273 GenomeAnalysisEngine - Preparing for traversal
[2016-04-15T01:31Z] INFO  18:31:44,274 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:31Z] INFO  18:31:44,275 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:31Z] INFO  18:31:44,275 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T01:31Z] INFO  18:31:44,276 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T01:31Z] INFO  18:31:44,398 GenotypeGVCFs - Notice that the -ploidy parameter is ignored in GenotypeGVCFs tool as this is automatically determined by the input variant files
[2016-04-15T01:31Z] INFO  18:31:54,144 ProgressMeter -            done    775307.0     9.0 s      12.0 s      100.0%     9.0 s       0.0 s
[2016-04-15T01:31Z] INFO  18:31:54,145 ProgressMeter - Total runtime 9.87 secs, 0.16 min, 0.00 hours
[2016-04-15T01:31Z] INFO  18:31:56,454 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:31Z] GATK: GenotypeGVCFs
[2016-04-15T01:31Z] INFO  18:31:58,287 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:31Z] INFO  18:31:58,291 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:31Z] INFO  18:31:58,292 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:31Z] INFO  18:31:58,292 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:31Z] INFO  18:31:58,301 HelpFormatter - Program Args: -T GenotypeGVCFs -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/gatk-haplotype-joint/Batch1/1/tx/tmpQ5TvFd/Batch1-1_46715671_62228851.vcf.gz -L 1:46715672-62228851 --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18106_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18105_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18102_kapa-NGv3-PE100-NGv3.vcf.gz --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -nt 16 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:31Z] INFO  18:31:58,318 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:31Z] INFO  18:31:58,319 HelpFormatter - Date/Time: 2016/04/14 18:31:58
[2016-04-15T01:31Z] INFO  18:31:58,319 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:31Z] INFO  18:31:58,320 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:31Z] INFO  18:31:58,474 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:31Z] INFO  18:31:58,572 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T01:31Z] INFO  18:31:58,989 IntervalUtils - Processing 15513180 bp from intervals
[2016-04-15T01:31Z] WARN  18:31:58,990 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:31Z] WARN  18:31:58,990 IndexDictionaryUtils - Track variant2 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:31Z] WARN  18:31:58,990 IndexDictionaryUtils - Track variant3 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:31Z] WARN  18:31:58,990 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:31Z] INFO  18:31:58,999 MicroScheduler - Running the GATK in parallel mode with 16 total threads, 1 CPU thread(s) for each of 16 data thread(s), of 16 processors available on this machine
[2016-04-15T01:31Z] INFO  18:31:59,048 GenomeAnalysisEngine - Preparing for traversal
[2016-04-15T01:31Z] INFO  18:31:59,049 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:31Z] INFO  18:31:59,050 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:31Z] INFO  18:31:59,050 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T01:31Z] INFO  18:31:59,050 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T01:31Z] INFO  18:31:59,173 GenotypeGVCFs - Notice that the -ploidy parameter is ignored in GenotypeGVCFs tool as this is automatically determined by the input variant files
[2016-04-15T01:32Z] INFO  18:32:08,628 ProgressMeter -            done    513338.0     9.0 s      18.0 s      100.0%     9.0 s       0.0 s
[2016-04-15T01:32Z] INFO  18:32:08,629 ProgressMeter - Total runtime 9.58 secs, 0.16 min, 0.00 hours
[2016-04-15T01:32Z] INFO  18:32:11,147 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:32Z] GATK: GenotypeGVCFs
[2016-04-15T01:32Z] INFO  18:32:13,253 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:32Z] INFO  18:32:13,255 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:32Z] INFO  18:32:13,255 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:32Z] INFO  18:32:13,255 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:32Z] INFO  18:32:13,259 HelpFormatter - Program Args: -T GenotypeGVCFs -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/gatk-haplotype-joint/Batch1/1/tx/tmpIEbtOs/Batch1-1_62231950_77749296.vcf.gz -L 1:62231951-77749296 --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18106_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18105_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18102_kapa-NGv3-PE100-NGv3.vcf.gz --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -nt 16 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:32Z] INFO  18:32:13,267 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:32Z] INFO  18:32:13,267 HelpFormatter - Date/Time: 2016/04/14 18:32:13
[2016-04-15T01:32Z] INFO  18:32:13,267 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:32Z] INFO  18:32:13,268 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:32Z] INFO  18:32:13,340 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:32Z] INFO  18:32:13,442 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T01:32Z] INFO  18:32:14,155 IntervalUtils - Processing 15517346 bp from intervals
[2016-04-15T01:32Z] WARN  18:32:14,156 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:32Z] WARN  18:32:14,157 IndexDictionaryUtils - Track variant2 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:32Z] WARN  18:32:14,157 IndexDictionaryUtils - Track variant3 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:32Z] WARN  18:32:14,158 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:32Z] INFO  18:32:14,175 MicroScheduler - Running the GATK in parallel mode with 16 total threads, 1 CPU thread(s) for each of 16 data thread(s), of 16 processors available on this machine
[2016-04-15T01:32Z] INFO  18:32:14,280 GenomeAnalysisEngine - Preparing for traversal
[2016-04-15T01:32Z] INFO  18:32:14,282 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:32Z] INFO  18:32:14,283 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:32Z] INFO  18:32:14,284 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T01:32Z] INFO  18:32:14,285 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T01:32Z] INFO  18:32:14,530 GenotypeGVCFs - Notice that the -ploidy parameter is ignored in GenotypeGVCFs tool as this is automatically determined by the input variant files
[2016-04-15T01:32Z] INFO  18:32:23,525 ProgressMeter -            done    482453.0     9.0 s      19.0 s      100.0%     9.0 s       0.0 s
[2016-04-15T01:32Z] INFO  18:32:23,526 ProgressMeter - Total runtime 9.24 secs, 0.15 min, 0.00 hours
[2016-04-15T01:32Z] INFO  18:32:26,064 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:32Z] GATK: GenotypeGVCFs
[2016-04-15T01:32Z] INFO  18:32:28,506 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:32Z] INFO  18:32:28,510 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:32Z] INFO  18:32:28,511 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:32Z] INFO  18:32:28,511 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:32Z] INFO  18:32:28,519 HelpFormatter - Program Args: -T GenotypeGVCFs -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/gatk-haplotype-joint/Batch1/1/tx/tmpfGU5kQ/Batch1-1_77752625_93297674.vcf.gz -L 1:77752626-93297674 --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18106_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18105_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18102_kapa-NGv3-PE100-NGv3.vcf.gz --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -nt 16 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:32Z] INFO  18:32:28,534 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:32Z] INFO  18:32:28,534 HelpFormatter - Date/Time: 2016/04/14 18:32:28
[2016-04-15T01:32Z] INFO  18:32:28,535 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:32Z] INFO  18:32:28,535 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:32Z] INFO  18:32:28,684 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:32Z] INFO  18:32:28,881 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T01:32Z] INFO  18:32:29,332 IntervalUtils - Processing 15545049 bp from intervals
[2016-04-15T01:32Z] WARN  18:32:29,333 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:32Z] WARN  18:32:29,333 IndexDictionaryUtils - Track variant2 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:32Z] WARN  18:32:29,333 IndexDictionaryUtils - Track variant3 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:32Z] WARN  18:32:29,333 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:32Z] INFO  18:32:29,342 MicroScheduler - Running the GATK in parallel mode with 16 total threads, 1 CPU thread(s) for each of 16 data thread(s), of 16 processors available on this machine
[2016-04-15T01:32Z] INFO  18:32:29,391 GenomeAnalysisEngine - Preparing for traversal
[2016-04-15T01:32Z] INFO  18:32:29,392 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:32Z] INFO  18:32:29,392 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:32Z] INFO  18:32:29,392 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T01:32Z] INFO  18:32:29,393 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T01:32Z] INFO  18:32:29,516 GenotypeGVCFs - Notice that the -ploidy parameter is ignored in GenotypeGVCFs tool as this is automatically determined by the input variant files
[2016-04-15T01:32Z] INFO  18:32:38,464 ProgressMeter -            done    486351.0     9.0 s      18.0 s      100.0%     9.0 s       0.0 s
[2016-04-15T01:32Z] INFO  18:32:38,465 ProgressMeter - Total runtime 9.07 secs, 0.15 min, 0.00 hours
[2016-04-15T01:32Z] INFO  18:32:40,739 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:32Z] GATK: GenotypeGVCFs
[2016-04-15T01:32Z] INFO  18:32:42,791 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:32Z] INFO  18:32:42,793 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:32Z] INFO  18:32:42,794 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:32Z] INFO  18:32:42,794 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:32Z] INFO  18:32:42,797 HelpFormatter - Program Args: -T GenotypeGVCFs -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/gatk-haplotype-joint/Batch1/1/tx/tmpnNosSb/Batch1-1_93298945_108993401.vcf.gz -L 1:93298946-108993401 --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18106_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18105_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18102_kapa-NGv3-PE100-NGv3.vcf.gz --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -nt 16 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:32Z] INFO  18:32:42,805 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:32Z] INFO  18:32:42,805 HelpFormatter - Date/Time: 2016/04/14 18:32:42
[2016-04-15T01:32Z] INFO  18:32:42,806 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:32Z] INFO  18:32:42,806 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:32Z] INFO  18:32:42,880 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:32Z] INFO  18:32:43,008 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T01:32Z] INFO  18:32:43,682 IntervalUtils - Processing 15694456 bp from intervals
[2016-04-15T01:32Z] WARN  18:32:43,683 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:32Z] WARN  18:32:43,684 IndexDictionaryUtils - Track variant2 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:32Z] WARN  18:32:43,684 IndexDictionaryUtils - Track variant3 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:32Z] WARN  18:32:43,685 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:32Z] INFO  18:32:43,702 MicroScheduler - Running the GATK in parallel mode with 16 total threads, 1 CPU thread(s) for each of 16 data thread(s), of 16 processors available on this machine
[2016-04-15T01:32Z] INFO  18:32:43,806 GenomeAnalysisEngine - Preparing for traversal
[2016-04-15T01:32Z] INFO  18:32:43,808 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:32Z] INFO  18:32:43,809 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:32Z] INFO  18:32:43,809 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T01:32Z] INFO  18:32:43,810 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T01:32Z] INFO  18:32:44,066 GenotypeGVCFs - Notice that the -ploidy parameter is ignored in GenotypeGVCFs tool as this is automatically determined by the input variant files
[2016-04-15T01:32Z] INFO  18:32:55,226 ProgressMeter -            done    455652.0    11.0 s      25.0 s      100.0%    11.0 s       0.0 s
[2016-04-15T01:32Z] INFO  18:32:55,227 ProgressMeter - Total runtime 11.42 secs, 0.19 min, 0.00 hours
[2016-04-15T01:32Z] INFO  18:32:57,521 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:32Z] GATK: GenotypeGVCFs
[2016-04-15T01:32Z] INFO  18:32:59,713 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:32Z] INFO  18:32:59,715 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:32Z] INFO  18:32:59,715 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:32Z] INFO  18:32:59,716 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:32Z] INFO  18:32:59,719 HelpFormatter - Program Args: -T GenotypeGVCFs -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/gatk-haplotype-joint/Batch1/1/tx/tmpiHXXr8/Batch1-1_108994811_143767848.vcf.gz -L 1:108994812-143767848 --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18106_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18105_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18102_kapa-NGv3-PE100-NGv3.vcf.gz --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -nt 16 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:32Z] INFO  18:32:59,728 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:32Z] INFO  18:32:59,728 HelpFormatter - Date/Time: 2016/04/14 18:32:59
[2016-04-15T01:32Z] INFO  18:32:59,728 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:32Z] INFO  18:32:59,728 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:32Z] INFO  18:32:59,802 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:32Z] INFO  18:32:59,900 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T01:33Z] INFO  18:33:00,332 IntervalUtils - Processing 34773037 bp from intervals
[2016-04-15T01:33Z] WARN  18:33:00,333 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:33Z] WARN  18:33:00,333 IndexDictionaryUtils - Track variant2 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:33Z] WARN  18:33:00,333 IndexDictionaryUtils - Track variant3 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:33Z] WARN  18:33:00,334 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:33Z] INFO  18:33:00,342 MicroScheduler - Running the GATK in parallel mode with 16 total threads, 1 CPU thread(s) for each of 16 data thread(s), of 16 processors available on this machine
[2016-04-15T01:33Z] INFO  18:33:00,393 GenomeAnalysisEngine - Preparing for traversal
[2016-04-15T01:33Z] INFO  18:33:00,395 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:33Z] INFO  18:33:00,395 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:33Z] INFO  18:33:00,395 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T01:33Z] INFO  18:33:00,396 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T01:33Z] INFO  18:33:00,522 GenotypeGVCFs - Notice that the -ploidy parameter is ignored in GenotypeGVCFs tool as this is automatically determined by the input variant files
[2016-04-15T01:33Z] WARN  18:33:07,797 ExactAFCalculator - this tool is currently set to genotype at most 6 alternate alleles in a given context, but the context at 1:120612040 has 10 alternate alleles so only the top alleles will be used; see the --max_alternate_alleles argument
[2016-04-15T01:33Z] INFO  18:33:10,025 ProgressMeter -            done    569419.0     9.0 s      16.0 s      100.0%     9.0 s       0.0 s
[2016-04-15T01:33Z] INFO  18:33:10,025 ProgressMeter - Total runtime 9.63 secs, 0.16 min, 0.00 hours
[2016-04-15T01:33Z] INFO  18:33:11,939 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:33Z] GATK: GenotypeGVCFs
[2016-04-15T01:33Z] INFO  18:33:14,112 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:33Z] INFO  18:33:14,114 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:33Z] INFO  18:33:14,114 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:33Z] INFO  18:33:14,114 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:33Z] INFO  18:33:14,118 HelpFormatter - Program Args: -T GenotypeGVCFs -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/gatk-haplotype-joint/Batch1/1/tx/tmp7Piv3b/Batch1-1_143897546_159410511.vcf.gz -L 1:143897547-159410511 --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18106_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18105_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18102_kapa-NGv3-PE100-NGv3.vcf.gz --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -nt 16 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:33Z] INFO  18:33:14,127 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:33Z] INFO  18:33:14,127 HelpFormatter - Date/Time: 2016/04/14 18:33:14
[2016-04-15T01:33Z] INFO  18:33:14,127 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:33Z] INFO  18:33:14,127 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:33Z] INFO  18:33:14,201 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:33Z] INFO  18:33:14,298 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T01:33Z] INFO  18:33:14,715 IntervalUtils - Processing 15512965 bp from intervals
[2016-04-15T01:33Z] WARN  18:33:14,716 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:33Z] WARN  18:33:14,716 IndexDictionaryUtils - Track variant2 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:33Z] WARN  18:33:14,716 IndexDictionaryUtils - Track variant3 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:33Z] WARN  18:33:14,716 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:33Z] INFO  18:33:14,725 MicroScheduler - Running the GATK in parallel mode with 16 total threads, 1 CPU thread(s) for each of 16 data thread(s), of 16 processors available on this machine
[2016-04-15T01:33Z] INFO  18:33:14,775 GenomeAnalysisEngine - Preparing for traversal
[2016-04-15T01:33Z] INFO  18:33:14,776 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:33Z] INFO  18:33:14,777 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:33Z] INFO  18:33:14,777 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T01:33Z] INFO  18:33:14,777 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T01:33Z] INFO  18:33:14,903 GenotypeGVCFs - Notice that the -ploidy parameter is ignored in GenotypeGVCFs tool as this is automatically determined by the input variant files
[2016-04-15T01:33Z] INFO  18:33:24,005 ProgressMeter -            done    803345.0     9.0 s      11.0 s      100.0%     9.0 s       0.0 s
[2016-04-15T01:33Z] INFO  18:33:24,005 ProgressMeter - Total runtime 9.23 secs, 0.15 min, 0.00 hours
[2016-04-15T01:33Z] INFO  18:33:27,083 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:33Z] GATK: GenotypeGVCFs
[2016-04-15T01:33Z] INFO  18:33:29,219 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:33Z] INFO  18:33:29,221 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:33Z] INFO  18:33:29,221 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:33Z] INFO  18:33:29,222 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:33Z] INFO  18:33:29,225 HelpFormatter - Program Args: -T GenotypeGVCFs -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/gatk-haplotype-joint/Batch1/1/tx/tmpwrIxyB/Batch1-1_159504867_175046963.vcf.gz -L 1:159504868-175046963 --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18106_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18105_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18102_kapa-NGv3-PE100-NGv3.vcf.gz --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -nt 16 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:33Z] INFO  18:33:29,234 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:33Z] INFO  18:33:29,234 HelpFormatter - Date/Time: 2016/04/14 18:33:29
[2016-04-15T01:33Z] INFO  18:33:29,234 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:33Z] INFO  18:33:29,234 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:33Z] INFO  18:33:29,307 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:33Z] INFO  18:33:29,406 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T01:33Z] INFO  18:33:29,758 IntervalUtils - Processing 15542096 bp from intervals
[2016-04-15T01:33Z] WARN  18:33:29,759 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:33Z] WARN  18:33:29,759 IndexDictionaryUtils - Track variant2 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:33Z] WARN  18:33:29,759 IndexDictionaryUtils - Track variant3 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:33Z] WARN  18:33:29,759 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:33Z] INFO  18:33:29,768 MicroScheduler - Running the GATK in parallel mode with 16 total threads, 1 CPU thread(s) for each of 16 data thread(s), of 16 processors available on this machine
[2016-04-15T01:33Z] INFO  18:33:29,819 GenomeAnalysisEngine - Preparing for traversal
[2016-04-15T01:33Z] INFO  18:33:29,820 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:33Z] INFO  18:33:29,820 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:33Z] INFO  18:33:29,821 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T01:33Z] INFO  18:33:29,821 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T01:33Z] INFO  18:33:29,947 GenotypeGVCFs - Notice that the -ploidy parameter is ignored in GenotypeGVCFs tool as this is automatically determined by the input variant files
[2016-04-15T01:33Z] WARN  18:33:37,720 ExactAFCalculator - this tool is currently set to genotype at most 6 alternate alleles in a given context, but the context at 1:174769068 has 7 alternate alleles so only the top alleles will be used; see the --max_alternate_alleles argument
[2016-04-15T01:33Z] INFO  18:33:39,998 ProgressMeter -            done    606498.0    10.0 s      16.0 s      100.0%    10.0 s       0.0 s
[2016-04-15T01:33Z] INFO  18:33:39,999 ProgressMeter - Total runtime 10.18 secs, 0.17 min, 0.00 hours
[2016-04-15T01:33Z] INFO  18:33:42,258 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:33Z] GATK: GenotypeGVCFs
[2016-04-15T01:33Z] INFO  18:33:44,274 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:33Z] INFO  18:33:44,276 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:33Z] INFO  18:33:44,276 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:33Z] INFO  18:33:44,276 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:33Z] INFO  18:33:44,280 HelpFormatter - Program Args: -T GenotypeGVCFs -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/gatk-haplotype-joint/Batch1/1/tx/tmpZ1Ro4C/Batch1-1_175048468_192127886.vcf.gz -L 1:175048469-192127886 --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18106_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18105_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18102_kapa-NGv3-PE100-NGv3.vcf.gz --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -nt 16 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:33Z] INFO  18:33:44,289 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:33Z] INFO  18:33:44,289 HelpFormatter - Date/Time: 2016/04/14 18:33:44
[2016-04-15T01:33Z] INFO  18:33:44,290 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:33Z] INFO  18:33:44,290 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:33Z] INFO  18:33:44,365 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:33Z] INFO  18:33:44,468 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T01:33Z] INFO  18:33:44,946 IntervalUtils - Processing 17079418 bp from intervals
[2016-04-15T01:33Z] WARN  18:33:44,947 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:33Z] WARN  18:33:44,947 IndexDictionaryUtils - Track variant2 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:33Z] WARN  18:33:44,948 IndexDictionaryUtils - Track variant3 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:33Z] WARN  18:33:44,948 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:33Z] INFO  18:33:44,957 MicroScheduler - Running the GATK in parallel mode with 16 total threads, 1 CPU thread(s) for each of 16 data thread(s), of 16 processors available on this machine
[2016-04-15T01:33Z] INFO  18:33:45,008 GenomeAnalysisEngine - Preparing for traversal
[2016-04-15T01:33Z] INFO  18:33:45,009 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:33Z] INFO  18:33:45,009 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:33Z] INFO  18:33:45,010 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T01:33Z] INFO  18:33:45,010 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T01:33Z] INFO  18:33:45,138 GenotypeGVCFs - Notice that the -ploidy parameter is ignored in GenotypeGVCFs tool as this is automatically determined by the input variant files
[2016-04-15T01:33Z] INFO  18:33:55,773 ProgressMeter -            done    566350.0    10.0 s      19.0 s      100.0%    10.0 s       0.0 s
[2016-04-15T01:33Z] INFO  18:33:55,773 ProgressMeter - Total runtime 10.76 secs, 0.18 min, 0.00 hours
[2016-04-15T01:33Z] INFO  18:33:58,104 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:33Z] GATK: GenotypeGVCFs
[2016-04-15T01:34Z] INFO  18:34:00,223 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:34Z] INFO  18:34:00,225 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:34Z] INFO  18:34:00,225 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:34Z] INFO  18:34:00,225 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:34Z] INFO  18:34:00,229 HelpFormatter - Program Args: -T GenotypeGVCFs -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/gatk-haplotype-joint/Batch1/1/tx/tmptebyOL/Batch1-1_192128349_207640257.vcf.gz -L 1:192128350-207640257 --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18106_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18105_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18102_kapa-NGv3-PE100-NGv3.vcf.gz --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -nt 16 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:34Z] INFO  18:34:00,238 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:34Z] INFO  18:34:00,238 HelpFormatter - Date/Time: 2016/04/14 18:34:00
[2016-04-15T01:34Z] INFO  18:34:00,238 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:34Z] INFO  18:34:00,239 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:34Z] INFO  18:34:00,315 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:34Z] INFO  18:34:00,419 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T01:34Z] INFO  18:34:00,907 IntervalUtils - Processing 15511908 bp from intervals
[2016-04-15T01:34Z] WARN  18:34:00,908 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:34Z] WARN  18:34:00,908 IndexDictionaryUtils - Track variant2 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:34Z] WARN  18:34:00,909 IndexDictionaryUtils - Track variant3 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:34Z] WARN  18:34:00,909 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:34Z] INFO  18:34:00,918 MicroScheduler - Running the GATK in parallel mode with 16 total threads, 1 CPU thread(s) for each of 16 data thread(s), of 16 processors available on this machine
[2016-04-15T01:34Z] INFO  18:34:00,971 GenomeAnalysisEngine - Preparing for traversal
[2016-04-15T01:34Z] INFO  18:34:00,972 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:34Z] INFO  18:34:00,973 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:34Z] INFO  18:34:00,973 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T01:34Z] INFO  18:34:00,974 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T01:34Z] INFO  18:34:01,163 GenotypeGVCFs - Notice that the -ploidy parameter is ignored in GenotypeGVCFs tool as this is automatically determined by the input variant files
[2016-04-15T01:34Z] INFO  18:34:12,582 ProgressMeter -            done    635788.0    11.0 s      18.0 s      100.0%    11.0 s       0.0 s
[2016-04-15T01:34Z] INFO  18:34:12,583 ProgressMeter - Total runtime 11.61 secs, 0.19 min, 0.00 hours
[2016-04-15T01:34Z] INFO  18:34:14,544 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:34Z] GATK: GenotypeGVCFs
[2016-04-15T01:34Z] INFO  18:34:16,690 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:34Z] INFO  18:34:16,692 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:34Z] INFO  18:34:16,692 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:34Z] INFO  18:34:16,692 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:34Z] INFO  18:34:16,696 HelpFormatter - Program Args: -T GenotypeGVCFs -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/gatk-haplotype-joint/Batch1/1/tx/tmpM83yw9/Batch1-1_207641871_223156451.vcf.gz -L 1:207641872-223156451 --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18106_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18105_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18102_kapa-NGv3-PE100-NGv3.vcf.gz --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -nt 16 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:34Z] INFO  18:34:16,704 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:34Z] INFO  18:34:16,704 HelpFormatter - Date/Time: 2016/04/14 18:34:16
[2016-04-15T01:34Z] INFO  18:34:16,705 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:34Z] INFO  18:34:16,705 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:34Z] INFO  18:34:16,778 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:34Z] INFO  18:34:16,877 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T01:34Z] INFO  18:34:17,574 IntervalUtils - Processing 15514580 bp from intervals
[2016-04-15T01:34Z] WARN  18:34:17,575 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:34Z] WARN  18:34:17,576 IndexDictionaryUtils - Track variant2 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:34Z] WARN  18:34:17,576 IndexDictionaryUtils - Track variant3 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:34Z] WARN  18:34:17,577 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:34Z] INFO  18:34:17,597 MicroScheduler - Running the GATK in parallel mode with 16 total threads, 1 CPU thread(s) for each of 16 data thread(s), of 16 processors available on this machine
[2016-04-15T01:34Z] INFO  18:34:17,721 GenomeAnalysisEngine - Preparing for traversal
[2016-04-15T01:34Z] INFO  18:34:17,723 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:34Z] INFO  18:34:17,724 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:34Z] INFO  18:34:17,725 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T01:34Z] INFO  18:34:17,726 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T01:34Z] INFO  18:34:17,992 GenotypeGVCFs - Notice that the -ploidy parameter is ignored in GenotypeGVCFs tool as this is automatically determined by the input variant files
[2016-04-15T01:34Z] INFO  18:34:28,353 ProgressMeter -            done    534193.0    10.0 s      19.0 s      100.0%    10.0 s       0.0 s
[2016-04-15T01:34Z] INFO  18:34:28,354 ProgressMeter - Total runtime 10.63 secs, 0.18 min, 0.00 hours
[2016-04-15T01:34Z] INFO  18:34:30,419 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:34Z] GATK: GenotypeGVCFs
[2016-04-15T01:34Z] INFO  18:34:32,578 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:34Z] INFO  18:34:32,580 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:34Z] INFO  18:34:32,580 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:34Z] INFO  18:34:32,580 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:34Z] INFO  18:34:32,584 HelpFormatter - Program Args: -T GenotypeGVCFs -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/gatk-haplotype-joint/Batch1/1/tx/tmpcWrM2T/Batch1-1_223162737_240072524.vcf.gz -L 1:223162738-240072524 --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18106_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18105_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18102_kapa-NGv3-PE100-NGv3.vcf.gz --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -nt 16 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:34Z] INFO  18:34:32,592 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:34Z] INFO  18:34:32,592 HelpFormatter - Date/Time: 2016/04/14 18:34:32
[2016-04-15T01:34Z] INFO  18:34:32,593 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:34Z] INFO  18:34:32,593 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:34Z] INFO  18:34:32,666 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:34Z] INFO  18:34:32,765 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T01:34Z] INFO  18:34:33,182 IntervalUtils - Processing 16909787 bp from intervals
[2016-04-15T01:34Z] WARN  18:34:33,182 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:34Z] WARN  18:34:33,183 IndexDictionaryUtils - Track variant2 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:34Z] WARN  18:34:33,183 IndexDictionaryUtils - Track variant3 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:34Z] WARN  18:34:33,183 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:34Z] INFO  18:34:33,192 MicroScheduler - Running the GATK in parallel mode with 16 total threads, 1 CPU thread(s) for each of 16 data thread(s), of 16 processors available on this machine
[2016-04-15T01:34Z] INFO  18:34:33,242 GenomeAnalysisEngine - Preparing for traversal
[2016-04-15T01:34Z] INFO  18:34:33,243 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:34Z] INFO  18:34:33,243 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:34Z] INFO  18:34:33,243 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T01:34Z] INFO  18:34:33,244 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T01:34Z] INFO  18:34:33,372 GenotypeGVCFs - Notice that the -ploidy parameter is ignored in GenotypeGVCFs tool as this is automatically determined by the input variant files
[2016-04-15T01:34Z] INFO  18:34:42,954 ProgressMeter -            done    686327.0     9.0 s      14.0 s      100.0%     9.0 s       0.0 s
[2016-04-15T01:34Z] INFO  18:34:42,954 ProgressMeter - Total runtime 9.71 secs, 0.16 min, 0.00 hours
[2016-04-15T01:34Z] INFO  18:34:45,120 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:34Z] GATK: GenotypeGVCFs
[2016-04-15T01:34Z] INFO  18:34:47,231 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:34Z] INFO  18:34:47,233 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:34Z] INFO  18:34:47,233 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:34Z] INFO  18:34:47,233 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:34Z] INFO  18:34:47,237 HelpFormatter - Program Args: -T GenotypeGVCFs -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/gatk-haplotype-joint/Batch1/1/tx/tmpoF6RqR/Batch1-1_240255409_249250621.vcf.gz -L 1:240255410-249250621 --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18106_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18105_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18102_kapa-NGv3-PE100-NGv3.vcf.gz --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -nt 16 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:34Z] INFO  18:34:47,245 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:34Z] INFO  18:34:47,246 HelpFormatter - Date/Time: 2016/04/14 18:34:47
[2016-04-15T01:34Z] INFO  18:34:47,246 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:34Z] INFO  18:34:47,246 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:34Z] INFO  18:34:47,318 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:34Z] INFO  18:34:47,416 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T01:34Z] INFO  18:34:47,832 IntervalUtils - Processing 8995212 bp from intervals
[2016-04-15T01:34Z] WARN  18:34:47,833 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:34Z] WARN  18:34:47,833 IndexDictionaryUtils - Track variant2 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:34Z] WARN  18:34:47,833 IndexDictionaryUtils - Track variant3 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:34Z] WARN  18:34:47,833 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:34Z] INFO  18:34:47,842 MicroScheduler - Running the GATK in parallel mode with 16 total threads, 1 CPU thread(s) for each of 16 data thread(s), of 16 processors available on this machine
[2016-04-15T01:34Z] INFO  18:34:47,892 GenomeAnalysisEngine - Preparing for traversal
[2016-04-15T01:34Z] INFO  18:34:47,893 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:34Z] INFO  18:34:47,893 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:34Z] INFO  18:34:47,894 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T01:34Z] INFO  18:34:47,894 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T01:34Z] INFO  18:34:48,018 GenotypeGVCFs - Notice that the -ploidy parameter is ignored in GenotypeGVCFs tool as this is automatically determined by the input variant files
[2016-04-15T01:34Z] INFO  18:34:53,202 ProgressMeter -            done    361050.0     5.0 s      14.0 s       99.9%     5.0 s       0.0 s
[2016-04-15T01:34Z] INFO  18:34:53,203 ProgressMeter - Total runtime 5.31 secs, 0.09 min, 0.00 hours
[2016-04-15T01:34Z] INFO  18:34:55,306 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:34Z] GATK: GenotypeGVCFs
[2016-04-15T01:34Z] INFO  18:34:57,343 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:34Z] INFO  18:34:57,346 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:34Z] INFO  18:34:57,346 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:34Z] INFO  18:34:57,346 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:34Z] INFO  18:34:57,350 HelpFormatter - Program Args: -T GenotypeGVCFs -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/gatk-haplotype-joint/Batch1/2/tx/tmpBmqlvQ/Batch1-2_0_15514844.vcf.gz -L 2:1-15514844 --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18106_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18105_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18102_kapa-NGv3-PE100-NGv3.vcf.gz --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -nt 16 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:34Z] INFO  18:34:57,359 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:34Z] INFO  18:34:57,359 HelpFormatter - Date/Time: 2016/04/14 18:34:57
[2016-04-15T01:34Z] INFO  18:34:57,360 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:34Z] INFO  18:34:57,360 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:34Z] INFO  18:34:57,441 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:34Z] INFO  18:34:57,541 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T01:34Z] INFO  18:34:57,895 IntervalUtils - Processing 15514844 bp from intervals
[2016-04-15T01:34Z] WARN  18:34:57,896 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:34Z] WARN  18:34:57,896 IndexDictionaryUtils - Track variant2 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:34Z] WARN  18:34:57,897 IndexDictionaryUtils - Track variant3 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:34Z] WARN  18:34:57,897 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:34Z] INFO  18:34:57,905 MicroScheduler - Running the GATK in parallel mode with 16 total threads, 1 CPU thread(s) for each of 16 data thread(s), of 16 processors available on this machine
[2016-04-15T01:34Z] INFO  18:34:57,956 GenomeAnalysisEngine - Preparing for traversal
[2016-04-15T01:34Z] INFO  18:34:57,956 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:34Z] INFO  18:34:57,957 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:34Z] INFO  18:34:57,957 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T01:34Z] INFO  18:34:57,958 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T01:34Z] INFO  18:34:58,084 GenotypeGVCFs - Notice that the -ploidy parameter is ignored in GenotypeGVCFs tool as this is automatically determined by the input variant files
[2016-04-15T01:35Z] INFO  18:35:07,835 ProgressMeter -            done    500312.0     9.0 s      19.0 s      100.0%     9.0 s       0.0 s
[2016-04-15T01:35Z] INFO  18:35:07,835 ProgressMeter - Total runtime 9.88 secs, 0.16 min, 0.00 hours
[2016-04-15T01:35Z] INFO  18:35:10,375 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:35Z] GATK: GenotypeGVCFs
[2016-04-15T01:35Z] INFO  18:35:12,344 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:35Z] INFO  18:35:12,346 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:35Z] INFO  18:35:12,346 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:35Z] INFO  18:35:12,346 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:35Z] INFO  18:35:12,350 HelpFormatter - Program Args: -T GenotypeGVCFs -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/gatk-haplotype-joint/Batch1/2/tx/tmpbtfsnC/Batch1-2_15519725_31133925.vcf.gz -L 2:15519726-31133925 --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18106_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18105_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18102_kapa-NGv3-PE100-NGv3.vcf.gz --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -nt 16 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:35Z] INFO  18:35:12,358 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:35Z] INFO  18:35:12,359 HelpFormatter - Date/Time: 2016/04/14 18:35:12
[2016-04-15T01:35Z] INFO  18:35:12,359 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:35Z] INFO  18:35:12,359 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:35Z] INFO  18:35:12,431 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:35Z] INFO  18:35:12,529 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T01:35Z] INFO  18:35:12,946 IntervalUtils - Processing 15614200 bp from intervals
[2016-04-15T01:35Z] WARN  18:35:12,946 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:35Z] WARN  18:35:12,947 IndexDictionaryUtils - Track variant2 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:35Z] WARN  18:35:12,947 IndexDictionaryUtils - Track variant3 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:35Z] WARN  18:35:12,947 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:35Z] INFO  18:35:12,955 MicroScheduler - Running the GATK in parallel mode with 16 total threads, 1 CPU thread(s) for each of 16 data thread(s), of 16 processors available on this machine
[2016-04-15T01:35Z] INFO  18:35:13,006 GenomeAnalysisEngine - Preparing for traversal
[2016-04-15T01:35Z] INFO  18:35:13,007 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:35Z] INFO  18:35:13,008 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:35Z] INFO  18:35:13,008 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T01:35Z] INFO  18:35:13,008 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T01:35Z] INFO  18:35:13,132 GenotypeGVCFs - Notice that the -ploidy parameter is ignored in GenotypeGVCFs tool as this is automatically determined by the input variant files
[2016-04-15T01:35Z] INFO  18:35:22,585 ProgressMeter -            done    576027.0     9.0 s      16.0 s      100.0%     9.0 s       0.0 s
[2016-04-15T01:35Z] INFO  18:35:22,585 ProgressMeter - Total runtime 9.58 secs, 0.16 min, 0.00 hours
[2016-04-15T01:35Z] INFO  18:35:24,742 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:35Z] GATK: GenotypeGVCFs
[2016-04-15T01:35Z] INFO  18:35:26,513 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:35Z] INFO  18:35:26,515 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:35Z] INFO  18:35:26,516 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:35Z] INFO  18:35:26,516 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:35Z] INFO  18:35:26,519 HelpFormatter - Program Args: -T GenotypeGVCFs -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/gatk-haplotype-joint/Batch1/2/tx/tmp7qhvoN/Batch1-2_31135088_46706841.vcf.gz -L 2:31135089-46706841 --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18106_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18105_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18102_kapa-NGv3-PE100-NGv3.vcf.gz --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -nt 16 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:35Z] INFO  18:35:26,527 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:35Z] INFO  18:35:26,528 HelpFormatter - Date/Time: 2016/04/14 18:35:26
[2016-04-15T01:35Z] INFO  18:35:26,528 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:35Z] INFO  18:35:26,528 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:35Z] INFO  18:35:26,600 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:35Z] INFO  18:35:26,700 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T01:35Z] INFO  18:35:27,115 IntervalUtils - Processing 15571753 bp from intervals
[2016-04-15T01:35Z] WARN  18:35:27,116 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:35Z] WARN  18:35:27,116 IndexDictionaryUtils - Track variant2 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:35Z] WARN  18:35:27,116 IndexDictionaryUtils - Track variant3 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:35Z] WARN  18:35:27,117 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:35Z] INFO  18:35:27,125 MicroScheduler - Running the GATK in parallel mode with 16 total threads, 1 CPU thread(s) for each of 16 data thread(s), of 16 processors available on this machine
[2016-04-15T01:35Z] INFO  18:35:27,176 GenomeAnalysisEngine - Preparing for traversal
[2016-04-15T01:35Z] INFO  18:35:27,177 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:35Z] INFO  18:35:27,177 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:35Z] INFO  18:35:27,177 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T01:35Z] INFO  18:35:27,178 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T01:35Z] INFO  18:35:27,302 GenotypeGVCFs - Notice that the -ploidy parameter is ignored in GenotypeGVCFs tool as this is automatically determined by the input variant files
[2016-04-15T01:35Z] INFO  18:35:37,842 ProgressMeter -            done    569175.0    10.0 s      18.0 s      100.0%    10.0 s       0.0 s
[2016-04-15T01:35Z] INFO  18:35:37,843 ProgressMeter - Total runtime 10.67 secs, 0.18 min, 0.00 hours
[2016-04-15T01:35Z] INFO  18:35:40,436 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:35Z] GATK: GenotypeGVCFs
[2016-04-15T01:35Z] INFO  18:35:42,666 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:35Z] INFO  18:35:42,668 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:35Z] INFO  18:35:42,668 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:35Z] INFO  18:35:42,669 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:35Z] INFO  18:35:42,672 HelpFormatter - Program Args: -T GenotypeGVCFs -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/gatk-haplotype-joint/Batch1/2/tx/tmp7rgeoQ/Batch1-2_46707543_62228117.vcf.gz -L 2:46707544-62228117 --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18106_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18105_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18102_kapa-NGv3-PE100-NGv3.vcf.gz --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -nt 16 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:35Z] INFO  18:35:42,681 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:35Z] INFO  18:35:42,681 HelpFormatter - Date/Time: 2016/04/14 18:35:42
[2016-04-15T01:35Z] INFO  18:35:42,681 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:35Z] INFO  18:35:42,682 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:35Z] INFO  18:35:42,753 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:35Z] INFO  18:35:42,852 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T01:35Z] INFO  18:35:43,272 IntervalUtils - Processing 15520574 bp from intervals
[2016-04-15T01:35Z] WARN  18:35:43,273 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:35Z] WARN  18:35:43,273 IndexDictionaryUtils - Track variant2 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:35Z] WARN  18:35:43,273 IndexDictionaryUtils - Track variant3 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:35Z] WARN  18:35:43,273 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:35Z] INFO  18:35:43,282 MicroScheduler - Running the GATK in parallel mode with 16 total threads, 1 CPU thread(s) for each of 16 data thread(s), of 16 processors available on this machine
[2016-04-15T01:35Z] INFO  18:35:43,332 GenomeAnalysisEngine - Preparing for traversal
[2016-04-15T01:35Z] INFO  18:35:43,333 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:35Z] INFO  18:35:43,333 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:35Z] INFO  18:35:43,334 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T01:35Z] INFO  18:35:43,334 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T01:35Z] INFO  18:35:43,458 GenotypeGVCFs - Notice that the -ploidy parameter is ignored in GenotypeGVCFs tool as this is automatically determined by the input variant files
[2016-04-15T01:35Z] INFO  18:35:52,183 ProgressMeter -            done    519835.0     8.0 s      17.0 s      100.0%     8.0 s       0.0 s
[2016-04-15T01:35Z] INFO  18:35:52,184 ProgressMeter - Total runtime 8.85 secs, 0.15 min, 0.00 hours
[2016-04-15T01:35Z] INFO  18:35:54,457 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:35Z] GATK: GenotypeGVCFs
[2016-04-15T01:35Z] INFO  18:35:56,608 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:35Z] INFO  18:35:56,610 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:35Z] INFO  18:35:56,610 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:35Z] INFO  18:35:56,610 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:35Z] INFO  18:35:56,614 HelpFormatter - Program Args: -T GenotypeGVCFs -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/gatk-haplotype-joint/Batch1/2/tx/tmposvmRl/Batch1-2_62362965_79253295.vcf.gz -L 2:62362966-79253295 --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18106_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18105_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18102_kapa-NGv3-PE100-NGv3.vcf.gz --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -nt 16 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:35Z] INFO  18:35:56,622 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:35Z] INFO  18:35:56,622 HelpFormatter - Date/Time: 2016/04/14 18:35:56
[2016-04-15T01:35Z] INFO  18:35:56,623 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:35Z] INFO  18:35:56,623 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:35Z] INFO  18:35:56,694 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:35Z] INFO  18:35:56,793 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T01:35Z] INFO  18:35:57,203 IntervalUtils - Processing 16890330 bp from intervals
[2016-04-15T01:35Z] WARN  18:35:57,204 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:35Z] WARN  18:35:57,204 IndexDictionaryUtils - Track variant2 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:35Z] WARN  18:35:57,204 IndexDictionaryUtils - Track variant3 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:35Z] WARN  18:35:57,205 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:35Z] INFO  18:35:57,213 MicroScheduler - Running the GATK in parallel mode with 16 total threads, 1 CPU thread(s) for each of 16 data thread(s), of 16 processors available on this machine
[2016-04-15T01:35Z] INFO  18:35:57,263 GenomeAnalysisEngine - Preparing for traversal
[2016-04-15T01:35Z] INFO  18:35:57,264 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:35Z] INFO  18:35:57,264 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:35Z] INFO  18:35:57,264 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T01:35Z] INFO  18:35:57,265 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T01:35Z] INFO  18:35:57,389 GenotypeGVCFs - Notice that the -ploidy parameter is ignored in GenotypeGVCFs tool as this is automatically determined by the input variant files
[2016-04-15T01:36Z] INFO  18:36:06,421 ProgressMeter -            done    604102.0     9.0 s      15.0 s      100.0%     9.0 s       0.0 s
[2016-04-15T01:36Z] INFO  18:36:06,421 ProgressMeter - Total runtime 9.16 secs, 0.15 min, 0.00 hours
[2016-04-15T01:36Z] INFO  18:36:08,475 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:36Z] GATK: GenotypeGVCFs
[2016-04-15T01:36Z] INFO  18:36:10,661 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:36Z] INFO  18:36:10,662 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:36Z] INFO  18:36:10,663 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:36Z] INFO  18:36:10,663 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:36Z] INFO  18:36:10,667 HelpFormatter - Program Args: -T GenotypeGVCFs -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/gatk-haplotype-joint/Batch1/2/tx/tmpQ_LAvY/Batch1-2_79253838_95537822.vcf.gz -L 2:79253839-95537822 --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18106_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18105_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18102_kapa-NGv3-PE100-NGv3.vcf.gz --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -nt 16 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:36Z] INFO  18:36:10,675 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:36Z] INFO  18:36:10,675 HelpFormatter - Date/Time: 2016/04/14 18:36:10
[2016-04-15T01:36Z] INFO  18:36:10,675 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:36Z] INFO  18:36:10,676 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:36Z] INFO  18:36:10,747 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:36Z] INFO  18:36:10,845 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T01:36Z] INFO  18:36:11,254 IntervalUtils - Processing 16283984 bp from intervals
[2016-04-15T01:36Z] WARN  18:36:11,255 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:36Z] WARN  18:36:11,255 IndexDictionaryUtils - Track variant2 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:36Z] WARN  18:36:11,255 IndexDictionaryUtils - Track variant3 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:36Z] WARN  18:36:11,255 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:36Z] INFO  18:36:11,264 MicroScheduler - Running the GATK in parallel mode with 16 total threads, 1 CPU thread(s) for each of 16 data thread(s), of 16 processors available on this machine
[2016-04-15T01:36Z] INFO  18:36:11,315 GenomeAnalysisEngine - Preparing for traversal
[2016-04-15T01:36Z] INFO  18:36:11,316 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:36Z] INFO  18:36:11,316 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:36Z] INFO  18:36:11,316 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T01:36Z] INFO  18:36:11,317 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T01:36Z] INFO  18:36:11,442 GenotypeGVCFs - Notice that the -ploidy parameter is ignored in GenotypeGVCFs tool as this is automatically determined by the input variant files
[2016-04-15T01:36Z] INFO  18:36:21,327 ProgressMeter -            done    379060.0    10.0 s      26.0 s      100.0%    10.0 s       0.0 s
[2016-04-15T01:36Z] INFO  18:36:21,328 ProgressMeter - Total runtime 10.01 secs, 0.17 min, 0.00 hours
[2016-04-15T01:36Z] INFO  18:36:24,064 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:36Z] GATK: GenotypeGVCFs
[2016-04-15T01:36Z] INFO  18:36:26,192 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:36Z] INFO  18:36:26,194 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:36Z] INFO  18:36:26,194 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:36Z] INFO  18:36:26,194 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:36Z] INFO  18:36:26,198 HelpFormatter - Program Args: -T GenotypeGVCFs -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/gatk-haplotype-joint/Batch1/2/tx/tmpe_Tsam/Batch1-2_95538561_111273222.vcf.gz -L 2:95538562-111273222 --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18106_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18105_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18102_kapa-NGv3-PE100-NGv3.vcf.gz --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -nt 16 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:36Z] INFO  18:36:26,207 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:36Z] INFO  18:36:26,207 HelpFormatter - Date/Time: 2016/04/14 18:36:26
[2016-04-15T01:36Z] INFO  18:36:26,208 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:36Z] INFO  18:36:26,208 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:36Z] INFO  18:36:26,283 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:36Z] INFO  18:36:26,388 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T01:36Z] INFO  18:36:26,885 IntervalUtils - Processing 15734661 bp from intervals
[2016-04-15T01:36Z] WARN  18:36:26,886 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:36Z] WARN  18:36:26,886 IndexDictionaryUtils - Track variant2 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:36Z] WARN  18:36:26,886 IndexDictionaryUtils - Track variant3 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:36Z] WARN  18:36:26,887 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:36Z] INFO  18:36:26,895 MicroScheduler - Running the GATK in parallel mode with 16 total threads, 1 CPU thread(s) for each of 16 data thread(s), of 16 processors available on this machine
[2016-04-15T01:36Z] INFO  18:36:26,947 GenomeAnalysisEngine - Preparing for traversal
[2016-04-15T01:36Z] INFO  18:36:26,948 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:36Z] INFO  18:36:26,948 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:36Z] INFO  18:36:26,949 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T01:36Z] INFO  18:36:26,949 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T01:36Z] INFO  18:36:27,076 GenotypeGVCFs - Notice that the -ploidy parameter is ignored in GenotypeGVCFs tool as this is automatically determined by the input variant files
[2016-04-15T01:36Z] INFO  18:36:36,860 ProgressMeter -            done    568254.0     9.0 s      17.0 s      100.0%     9.0 s       0.0 s
[2016-04-15T01:36Z] INFO  18:36:36,860 ProgressMeter - Total runtime 9.91 secs, 0.17 min, 0.00 hours
[2016-04-15T01:36Z] INFO  18:36:38,973 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:36Z] GATK: GenotypeGVCFs
[2016-04-15T01:36Z] INFO  18:36:41,141 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:36Z] INFO  18:36:41,143 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:36Z] INFO  18:36:41,143 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:36Z] INFO  18:36:41,143 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:36Z] INFO  18:36:41,147 HelpFormatter - Program Args: -T GenotypeGVCFs -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/gatk-haplotype-joint/Batch1/2/tx/tmp9rlyze/Batch1-2_111281072_127413888.vcf.gz -L 2:111281073-127413888 --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18106_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18105_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18102_kapa-NGv3-PE100-NGv3.vcf.gz --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -nt 16 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:36Z] INFO  18:36:41,155 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:36Z] INFO  18:36:41,155 HelpFormatter - Date/Time: 2016/04/14 18:36:41
[2016-04-15T01:36Z] INFO  18:36:41,155 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:36Z] INFO  18:36:41,156 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:36Z] INFO  18:36:41,228 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:36Z] INFO  18:36:41,328 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T01:36Z] INFO  18:36:41,742 IntervalUtils - Processing 16132816 bp from intervals
[2016-04-15T01:36Z] WARN  18:36:41,743 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:36Z] WARN  18:36:41,743 IndexDictionaryUtils - Track variant2 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:36Z] WARN  18:36:41,743 IndexDictionaryUtils - Track variant3 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:36Z] WARN  18:36:41,744 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:36Z] INFO  18:36:41,752 MicroScheduler - Running the GATK in parallel mode with 16 total threads, 1 CPU thread(s) for each of 16 data thread(s), of 16 processors available on this machine
[2016-04-15T01:36Z] INFO  18:36:41,803 GenomeAnalysisEngine - Preparing for traversal
[2016-04-15T01:36Z] INFO  18:36:41,804 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:36Z] INFO  18:36:41,804 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:36Z] INFO  18:36:41,805 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T01:36Z] INFO  18:36:41,805 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T01:36Z] INFO  18:36:41,929 GenotypeGVCFs - Notice that the -ploidy parameter is ignored in GenotypeGVCFs tool as this is automatically determined by the input variant files
[2016-04-15T01:36Z] INFO  18:36:51,219 ProgressMeter -            done    482820.0     9.0 s      19.0 s      100.0%     9.0 s       0.0 s
[2016-04-15T01:36Z] INFO  18:36:51,219 ProgressMeter - Total runtime 9.41 secs, 0.16 min, 0.00 hours
[2016-04-15T01:36Z] INFO  18:36:53,237 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:36Z] GATK: GenotypeGVCFs
[2016-04-15T01:36Z] INFO  18:36:55,650 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:36Z] INFO  18:36:55,652 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:36Z] INFO  18:36:55,652 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:36Z] INFO  18:36:55,652 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:36Z] INFO  18:36:55,656 HelpFormatter - Program Args: -T GenotypeGVCFs -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/gatk-haplotype-joint/Batch1/2/tx/tmpJkhHH7/Batch1-2_127433207_143643105.vcf.gz -L 2:127433208-143643105 --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18106_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18105_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18102_kapa-NGv3-PE100-NGv3.vcf.gz --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -nt 16 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:36Z] INFO  18:36:55,665 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:36Z] INFO  18:36:55,666 HelpFormatter - Date/Time: 2016/04/14 18:36:55
[2016-04-15T01:36Z] INFO  18:36:55,666 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:36Z] INFO  18:36:55,666 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:36Z] INFO  18:36:55,740 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:36Z] INFO  18:36:55,845 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T01:36Z] INFO  18:36:56,359 IntervalUtils - Processing 16209898 bp from intervals
[2016-04-15T01:36Z] WARN  18:36:56,359 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:36Z] WARN  18:36:56,360 IndexDictionaryUtils - Track variant2 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:36Z] WARN  18:36:56,360 IndexDictionaryUtils - Track variant3 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:36Z] WARN  18:36:56,360 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:36Z] INFO  18:36:56,369 MicroScheduler - Running the GATK in parallel mode with 16 total threads, 1 CPU thread(s) for each of 16 data thread(s), of 16 processors available on this machine
[2016-04-15T01:36Z] INFO  18:36:56,421 GenomeAnalysisEngine - Preparing for traversal
[2016-04-15T01:36Z] INFO  18:36:56,422 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:36Z] INFO  18:36:56,422 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:36Z] INFO  18:36:56,423 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T01:36Z] INFO  18:36:56,423 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T01:36Z] INFO  18:36:56,552 GenotypeGVCFs - Notice that the -ploidy parameter is ignored in GenotypeGVCFs tool as this is automatically determined by the input variant files
[2016-04-15T01:37Z] INFO  18:37:06,980 ProgressMeter -            done    567921.0    10.0 s      18.0 s      100.0%    10.0 s       0.0 s
[2016-04-15T01:37Z] INFO  18:37:06,980 ProgressMeter - Total runtime 10.56 secs, 0.18 min, 0.00 hours
[2016-04-15T01:37Z] INFO  18:37:08,871 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:37Z] GATK: GenotypeGVCFs
[2016-04-15T01:37Z] INFO  18:37:10,825 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:37Z] INFO  18:37:10,827 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:37Z] INFO  18:37:10,827 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:37Z] INFO  18:37:10,827 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:37Z] INFO  18:37:10,831 HelpFormatter - Program Args: -T GenotypeGVCFs -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/gatk-haplotype-joint/Batch1/2/tx/tmpxXC_Cr/Batch1-2_143676177_159195597.vcf.gz -L 2:143676178-159195597 --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18106_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18105_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18102_kapa-NGv3-PE100-NGv3.vcf.gz --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -nt 16 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:37Z] INFO  18:37:10,839 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:37Z] INFO  18:37:10,839 HelpFormatter - Date/Time: 2016/04/14 18:37:10
[2016-04-15T01:37Z] INFO  18:37:10,839 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:37Z] INFO  18:37:10,840 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:37Z] INFO  18:37:10,912 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:37Z] INFO  18:37:11,011 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T01:37Z] INFO  18:37:11,427 IntervalUtils - Processing 15519420 bp from intervals
[2016-04-15T01:37Z] WARN  18:37:11,428 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:37Z] WARN  18:37:11,428 IndexDictionaryUtils - Track variant2 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:37Z] WARN  18:37:11,428 IndexDictionaryUtils - Track variant3 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:37Z] WARN  18:37:11,429 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:37Z] INFO  18:37:11,437 MicroScheduler - Running the GATK in parallel mode with 16 total threads, 1 CPU thread(s) for each of 16 data thread(s), of 16 processors available on this machine
[2016-04-15T01:37Z] INFO  18:37:11,488 GenomeAnalysisEngine - Preparing for traversal
[2016-04-15T01:37Z] INFO  18:37:11,489 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:37Z] INFO  18:37:11,489 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:37Z] INFO  18:37:11,489 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T01:37Z] INFO  18:37:11,490 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T01:37Z] INFO  18:37:11,619 GenotypeGVCFs - Notice that the -ploidy parameter is ignored in GenotypeGVCFs tool as this is automatically determined by the input variant files
[2016-04-15T01:37Z] INFO  18:37:21,249 ProgressMeter -            done    411445.0     9.0 s      23.0 s      100.0%     9.0 s       0.0 s
[2016-04-15T01:37Z] INFO  18:37:21,250 ProgressMeter - Total runtime 9.76 secs, 0.16 min, 0.00 hours
[2016-04-15T01:37Z] INFO  18:37:23,695 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:37Z] GATK: GenotypeGVCFs
[2016-04-15T01:37Z] INFO  18:37:25,756 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:37Z] INFO  18:37:25,758 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:37Z] INFO  18:37:25,758 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:37Z] INFO  18:37:25,758 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:37Z] INFO  18:37:25,762 HelpFormatter - Program Args: -T GenotypeGVCFs -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/gatk-haplotype-joint/Batch1/2/tx/tmpiA_pOm/Batch1-2_159196753_174774985.vcf.gz -L 2:159196754-174774985 --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18106_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18105_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18102_kapa-NGv3-PE100-NGv3.vcf.gz --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -nt 16 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:37Z] INFO  18:37:25,771 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:37Z] INFO  18:37:25,771 HelpFormatter - Date/Time: 2016/04/14 18:37:25
[2016-04-15T01:37Z] INFO  18:37:25,771 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:37Z] INFO  18:37:25,771 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:37Z] INFO  18:37:25,844 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:37Z] INFO  18:37:25,942 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T01:37Z] INFO  18:37:26,356 IntervalUtils - Processing 15578232 bp from intervals
[2016-04-15T01:37Z] WARN  18:37:26,357 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:37Z] WARN  18:37:26,357 IndexDictionaryUtils - Track variant2 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:37Z] WARN  18:37:26,357 IndexDictionaryUtils - Track variant3 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:37Z] WARN  18:37:26,358 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:37Z] INFO  18:37:26,366 MicroScheduler - Running the GATK in parallel mode with 16 total threads, 1 CPU thread(s) for each of 16 data thread(s), of 16 processors available on this machine
[2016-04-15T01:37Z] INFO  18:37:26,417 GenomeAnalysisEngine - Preparing for traversal
[2016-04-15T01:37Z] INFO  18:37:26,418 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:37Z] INFO  18:37:26,418 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:37Z] INFO  18:37:26,419 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T01:37Z] INFO  18:37:26,419 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T01:37Z] INFO  18:37:26,543 GenotypeGVCFs - Notice that the -ploidy parameter is ignored in GenotypeGVCFs tool as this is automatically determined by the input variant files
[2016-04-15T01:37Z] INFO  18:37:36,543 ProgressMeter -            done    556245.0    10.0 s      18.0 s      100.0%    10.0 s       0.0 s
[2016-04-15T01:37Z] INFO  18:37:36,543 ProgressMeter - Total runtime 10.12 secs, 0.17 min, 0.00 hours
[2016-04-15T01:37Z] INFO  18:37:38,573 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:37Z] GATK: GenotypeGVCFs
[2016-04-15T01:37Z] INFO  18:37:40,693 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:37Z] INFO  18:37:40,694 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:37Z] INFO  18:37:40,695 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:37Z] INFO  18:37:40,695 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:37Z] INFO  18:37:40,699 HelpFormatter - Program Args: -T GenotypeGVCFs -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/gatk-haplotype-joint/Batch1/2/tx/tmpKl1jBr/Batch1-2_174777797_190306304.vcf.gz -L 2:174777798-190306304 --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18106_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18105_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18102_kapa-NGv3-PE100-NGv3.vcf.gz --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -nt 16 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:37Z] INFO  18:37:40,707 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:37Z] INFO  18:37:40,707 HelpFormatter - Date/Time: 2016/04/14 18:37:40
[2016-04-15T01:37Z] INFO  18:37:40,707 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:37Z] INFO  18:37:40,707 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:37Z] INFO  18:37:40,780 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:37Z] INFO  18:37:40,880 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T01:37Z] INFO  18:37:41,293 IntervalUtils - Processing 15528507 bp from intervals
[2016-04-15T01:37Z] WARN  18:37:41,293 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:37Z] WARN  18:37:41,293 IndexDictionaryUtils - Track variant2 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:37Z] WARN  18:37:41,294 IndexDictionaryUtils - Track variant3 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:37Z] WARN  18:37:41,294 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:37Z] INFO  18:37:41,302 MicroScheduler - Running the GATK in parallel mode with 16 total threads, 1 CPU thread(s) for each of 16 data thread(s), of 16 processors available on this machine
[2016-04-15T01:37Z] INFO  18:37:41,354 GenomeAnalysisEngine - Preparing for traversal
[2016-04-15T01:37Z] INFO  18:37:41,354 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:37Z] INFO  18:37:41,355 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:37Z] INFO  18:37:41,355 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T01:37Z] INFO  18:37:41,356 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T01:37Z] INFO  18:37:41,480 GenotypeGVCFs - Notice that the -ploidy parameter is ignored in GenotypeGVCFs tool as this is automatically determined by the input variant files
[2016-04-15T01:37Z] INFO  18:37:51,354 ProgressMeter -            done    583366.0     9.0 s      17.0 s      100.0%     9.0 s       0.0 s
[2016-04-15T01:37Z] INFO  18:37:51,355 ProgressMeter - Total runtime 10.00 secs, 0.17 min, 0.00 hours
[2016-04-15T01:37Z] INFO  18:37:54,019 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:37Z] GATK: GenotypeGVCFs
[2016-04-15T01:37Z] INFO  18:37:56,186 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:37Z] INFO  18:37:56,188 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:37Z] INFO  18:37:56,189 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:37Z] INFO  18:37:56,189 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:37Z] INFO  18:37:56,192 HelpFormatter - Program Args: -T GenotypeGVCFs -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/gatk-haplotype-joint/Batch1/2/tx/tmpirnhbH/Batch1-2_190313104_205830046.vcf.gz -L 2:190313105-205830046 --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18106_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18105_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18102_kapa-NGv3-PE100-NGv3.vcf.gz --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -nt 16 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:37Z] INFO  18:37:56,202 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:37Z] INFO  18:37:56,202 HelpFormatter - Date/Time: 2016/04/14 18:37:56
[2016-04-15T01:37Z] INFO  18:37:56,203 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:37Z] INFO  18:37:56,203 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:37Z] INFO  18:37:56,278 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:37Z] INFO  18:37:56,375 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T01:37Z] INFO  18:37:57,260 IntervalUtils - Processing 15516942 bp from intervals
[2016-04-15T01:37Z] WARN  18:37:57,262 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:37Z] WARN  18:37:57,262 IndexDictionaryUtils - Track variant2 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:37Z] WARN  18:37:57,262 IndexDictionaryUtils - Track variant3 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:37Z] WARN  18:37:57,263 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:37Z] INFO  18:37:57,283 MicroScheduler - Running the GATK in parallel mode with 16 total threads, 1 CPU thread(s) for each of 16 data thread(s), of 16 processors available on this machine
[2016-04-15T01:37Z] INFO  18:37:57,404 GenomeAnalysisEngine - Preparing for traversal
[2016-04-15T01:37Z] INFO  18:37:57,406 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:37Z] INFO  18:37:57,407 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:37Z] INFO  18:37:57,408 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T01:37Z] INFO  18:37:57,409 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T01:37Z] INFO  18:37:57,558 GenotypeGVCFs - Notice that the -ploidy parameter is ignored in GenotypeGVCFs tool as this is automatically determined by the input variant files
[2016-04-15T01:38Z] INFO  18:38:06,804 ProgressMeter -            done    520620.0     9.0 s      18.0 s      100.0%     9.0 s       0.0 s
[2016-04-15T01:38Z] INFO  18:38:06,805 ProgressMeter - Total runtime 9.40 secs, 0.16 min, 0.00 hours
[2016-04-15T01:38Z] INFO  18:38:09,006 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:38Z] GATK: GenotypeGVCFs
[2016-04-15T01:38Z] INFO  18:38:11,198 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:38Z] INFO  18:38:11,200 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:38Z] INFO  18:38:11,200 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:38Z] INFO  18:38:11,201 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:38Z] INFO  18:38:11,204 HelpFormatter - Program Args: -T GenotypeGVCFs -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/gatk-haplotype-joint/Batch1/2/tx/tmpmidS8Y/Batch1-2_205912303_222290862.vcf.gz -L 2:205912304-222290862 --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18106_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18105_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18102_kapa-NGv3-PE100-NGv3.vcf.gz --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -nt 16 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:38Z] INFO  18:38:11,213 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:38Z] INFO  18:38:11,213 HelpFormatter - Date/Time: 2016/04/14 18:38:11
[2016-04-15T01:38Z] INFO  18:38:11,213 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:38Z] INFO  18:38:11,213 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:38Z] INFO  18:38:11,286 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:38Z] INFO  18:38:11,385 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T01:38Z] INFO  18:38:11,805 IntervalUtils - Processing 16378559 bp from intervals
[2016-04-15T01:38Z] WARN  18:38:11,805 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:38Z] WARN  18:38:11,806 IndexDictionaryUtils - Track variant2 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:38Z] WARN  18:38:11,806 IndexDictionaryUtils - Track variant3 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:38Z] WARN  18:38:11,806 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:38Z] INFO  18:38:11,815 MicroScheduler - Running the GATK in parallel mode with 16 total threads, 1 CPU thread(s) for each of 16 data thread(s), of 16 processors available on this machine
[2016-04-15T01:38Z] INFO  18:38:11,865 GenomeAnalysisEngine - Preparing for traversal
[2016-04-15T01:38Z] INFO  18:38:11,866 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:38Z] INFO  18:38:11,867 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:38Z] INFO  18:38:11,867 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T01:38Z] INFO  18:38:11,868 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T01:38Z] INFO  18:38:11,993 GenotypeGVCFs - Notice that the -ploidy parameter is ignored in GenotypeGVCFs tool as this is automatically determined by the input variant files
[2016-04-15T01:38Z] INFO  18:38:22,161 ProgressMeter -            done    616472.0    10.0 s      16.0 s      100.0%    10.0 s       0.0 s
[2016-04-15T01:38Z] INFO  18:38:22,161 ProgressMeter - Total runtime 10.29 secs, 0.17 min, 0.00 hours
[2016-04-15T01:38Z] INFO  18:38:24,516 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:38Z] GATK: GenotypeGVCFs
[2016-04-15T01:38Z] INFO  18:38:26,703 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:38Z] INFO  18:38:26,705 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:38Z] INFO  18:38:26,705 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:38Z] INFO  18:38:26,705 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:38Z] INFO  18:38:26,709 HelpFormatter - Program Args: -T GenotypeGVCFs -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/gatk-haplotype-joint/Batch1/2/tx/tmpW0FzUA/Batch1-2_222291154_237994685.vcf.gz -L 2:222291155-237994685 --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18106_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18105_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18102_kapa-NGv3-PE100-NGv3.vcf.gz --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -nt 16 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:38Z] INFO  18:38:26,718 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:38Z] INFO  18:38:26,718 HelpFormatter - Date/Time: 2016/04/14 18:38:26
[2016-04-15T01:38Z] INFO  18:38:26,718 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:38Z] INFO  18:38:26,718 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:38Z] INFO  18:38:26,795 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:38Z] INFO  18:38:26,899 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T01:38Z] INFO  18:38:27,549 IntervalUtils - Processing 15703531 bp from intervals
[2016-04-15T01:38Z] WARN  18:38:27,550 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:38Z] WARN  18:38:27,551 IndexDictionaryUtils - Track variant2 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:38Z] WARN  18:38:27,551 IndexDictionaryUtils - Track variant3 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:38Z] WARN  18:38:27,552 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:38Z] INFO  18:38:27,572 MicroScheduler - Running the GATK in parallel mode with 16 total threads, 1 CPU thread(s) for each of 16 data thread(s), of 16 processors available on this machine
[2016-04-15T01:38Z] INFO  18:38:27,693 GenomeAnalysisEngine - Preparing for traversal
[2016-04-15T01:38Z] INFO  18:38:27,696 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:38Z] INFO  18:38:27,697 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:38Z] INFO  18:38:27,698 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T01:38Z] INFO  18:38:27,698 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T01:38Z] INFO  18:38:27,974 GenotypeGVCFs - Notice that the -ploidy parameter is ignored in GenotypeGVCFs tool as this is automatically determined by the input variant files
[2016-04-15T01:38Z] INFO  18:38:38,329 ProgressMeter -            done    561696.0    10.0 s      18.0 s      100.0%    10.0 s       0.0 s
[2016-04-15T01:38Z] INFO  18:38:38,329 ProgressMeter - Total runtime 10.63 secs, 0.18 min, 0.00 hours
[2016-04-15T01:38Z] INFO  18:38:40,405 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:38Z] GATK: GenotypeGVCFs
[2016-04-15T01:38Z] INFO  18:38:42,580 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:38Z] INFO  18:38:42,582 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:38Z] INFO  18:38:42,582 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:38Z] INFO  18:38:42,582 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:38Z] INFO  18:38:42,586 HelpFormatter - Program Args: -T GenotypeGVCFs -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/gatk-haplotype-joint/Batch1/2/tx/tmpDpfi5S/Batch1-2_237995374_243199373.vcf.gz -L 2:237995375-243199373 --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18106_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18105_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18102_kapa-NGv3-PE100-NGv3.vcf.gz --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -nt 16 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:38Z] INFO  18:38:42,594 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:38Z] INFO  18:38:42,594 HelpFormatter - Date/Time: 2016/04/14 18:38:42
[2016-04-15T01:38Z] INFO  18:38:42,595 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:38Z] INFO  18:38:42,595 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:38Z] INFO  18:38:42,667 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:38Z] INFO  18:38:42,765 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T01:38Z] INFO  18:38:43,184 IntervalUtils - Processing 5203999 bp from intervals
[2016-04-15T01:38Z] WARN  18:38:43,184 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:38Z] WARN  18:38:43,185 IndexDictionaryUtils - Track variant2 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:38Z] WARN  18:38:43,185 IndexDictionaryUtils - Track variant3 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:38Z] WARN  18:38:43,185 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:38Z] INFO  18:38:43,194 MicroScheduler - Running the GATK in parallel mode with 16 total threads, 1 CPU thread(s) for each of 16 data thread(s), of 16 processors available on this machine
[2016-04-15T01:38Z] INFO  18:38:43,244 GenomeAnalysisEngine - Preparing for traversal
[2016-04-15T01:38Z] INFO  18:38:43,245 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:38Z] INFO  18:38:43,245 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:38Z] INFO  18:38:43,245 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T01:38Z] INFO  18:38:43,246 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T01:38Z] INFO  18:38:43,370 GenotypeGVCFs - Notice that the -ploidy parameter is ignored in GenotypeGVCFs tool as this is automatically determined by the input variant files
[2016-04-15T01:38Z] INFO  18:38:48,125 ProgressMeter -            done    270453.0     4.0 s      18.0 s       99.7%     4.0 s       0.0 s
[2016-04-15T01:38Z] INFO  18:38:48,125 ProgressMeter - Total runtime 4.88 secs, 0.08 min, 0.00 hours
[2016-04-15T01:38Z] INFO  18:38:49,788 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:38Z] GATK: GenotypeGVCFs
[2016-04-15T01:38Z] INFO  18:38:51,790 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:38Z] INFO  18:38:51,792 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:38Z] INFO  18:38:51,793 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:38Z] INFO  18:38:51,793 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:38Z] INFO  18:38:51,796 HelpFormatter - Program Args: -T GenotypeGVCFs -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/gatk-haplotype-joint/Batch1/3/tx/tmpdeZE0s/Batch1-3_0_15512123.vcf.gz -L 3:1-15512123 --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18106_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18105_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18102_kapa-NGv3-PE100-NGv3.vcf.gz --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -nt 16 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:38Z] INFO  18:38:51,805 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:38Z] INFO  18:38:51,805 HelpFormatter - Date/Time: 2016/04/14 18:38:51
[2016-04-15T01:38Z] INFO  18:38:51,805 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:38Z] INFO  18:38:51,805 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:38Z] INFO  18:38:51,878 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:38Z] INFO  18:38:51,978 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T01:38Z] INFO  18:38:52,387 IntervalUtils - Processing 15512123 bp from intervals
[2016-04-15T01:38Z] WARN  18:38:52,387 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:38Z] WARN  18:38:52,387 IndexDictionaryUtils - Track variant2 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:38Z] WARN  18:38:52,388 IndexDictionaryUtils - Track variant3 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:38Z] WARN  18:38:52,388 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:38Z] INFO  18:38:52,396 MicroScheduler - Running the GATK in parallel mode with 16 total threads, 1 CPU thread(s) for each of 16 data thread(s), of 16 processors available on this machine
[2016-04-15T01:38Z] INFO  18:38:52,447 GenomeAnalysisEngine - Preparing for traversal
[2016-04-15T01:38Z] INFO  18:38:52,448 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:38Z] INFO  18:38:52,448 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:38Z] INFO  18:38:52,449 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T01:38Z] INFO  18:38:52,449 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T01:38Z] INFO  18:38:52,571 GenotypeGVCFs - Notice that the -ploidy parameter is ignored in GenotypeGVCFs tool as this is automatically determined by the input variant files
[2016-04-15T01:39Z] INFO  18:39:02,228 ProgressMeter -            done    601278.0     9.0 s      16.0 s      100.0%     9.0 s       0.0 s
[2016-04-15T01:39Z] INFO  18:39:02,228 ProgressMeter - Total runtime 9.78 secs, 0.16 min, 0.00 hours
[2016-04-15T01:39Z] INFO  18:39:04,443 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:39Z] GATK: GenotypeGVCFs
[2016-04-15T01:39Z] INFO  18:39:06,614 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:39Z] INFO  18:39:06,616 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:39Z] INFO  18:39:06,617 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:39Z] INFO  18:39:06,617 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:39Z] INFO  18:39:06,620 HelpFormatter - Program Args: -T GenotypeGVCFs -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/gatk-haplotype-joint/Batch1/3/tx/tmpFN8jhN/Batch1-3_15515506_31574805.vcf.gz -L 3:15515507-31574805 --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18106_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18105_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18102_kapa-NGv3-PE100-NGv3.vcf.gz --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -nt 16 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:39Z] INFO  18:39:06,629 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:39Z] INFO  18:39:06,630 HelpFormatter - Date/Time: 2016/04/14 18:39:06
[2016-04-15T01:39Z] INFO  18:39:06,630 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:39Z] INFO  18:39:06,630 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:39Z] INFO  18:39:06,704 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:39Z] INFO  18:39:06,801 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T01:39Z] INFO  18:39:07,429 IntervalUtils - Processing 16059299 bp from intervals
[2016-04-15T01:39Z] WARN  18:39:07,430 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:39Z] WARN  18:39:07,431 IndexDictionaryUtils - Track variant2 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:39Z] WARN  18:39:07,431 IndexDictionaryUtils - Track variant3 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:39Z] WARN  18:39:07,432 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:39Z] INFO  18:39:07,452 MicroScheduler - Running the GATK in parallel mode with 16 total threads, 1 CPU thread(s) for each of 16 data thread(s), of 16 processors available on this machine
[2016-04-15T01:39Z] INFO  18:39:07,572 GenomeAnalysisEngine - Preparing for traversal
[2016-04-15T01:39Z] INFO  18:39:07,574 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:39Z] INFO  18:39:07,575 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:39Z] INFO  18:39:07,576 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T01:39Z] INFO  18:39:07,577 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T01:39Z] INFO  18:39:07,876 GenotypeGVCFs - Notice that the -ploidy parameter is ignored in GenotypeGVCFs tool as this is automatically determined by the input variant files
[2016-04-15T01:39Z] INFO  18:39:16,669 ProgressMeter -            done    467582.0     9.0 s      19.0 s      100.0%     9.0 s       0.0 s
[2016-04-15T01:39Z] INFO  18:39:16,670 ProgressMeter - Total runtime 9.10 secs, 0.15 min, 0.00 hours
[2016-04-15T01:39Z] INFO  18:39:18,896 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:39Z] GATK: GenotypeGVCFs
[2016-04-15T01:39Z] INFO  18:39:20,829 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:39Z] INFO  18:39:20,831 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:39Z] INFO  18:39:20,831 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:39Z] INFO  18:39:20,832 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:39Z] INFO  18:39:20,835 HelpFormatter - Program Args: -T GenotypeGVCFs -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/gatk-haplotype-joint/Batch1/3/tx/tmpuv6YcU/Batch1-3_31617887_47127804.vcf.gz -L 3:31617888-47127804 --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18106_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18105_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18102_kapa-NGv3-PE100-NGv3.vcf.gz --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -nt 16 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:39Z] INFO  18:39:20,844 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:39Z] INFO  18:39:20,845 HelpFormatter - Date/Time: 2016/04/14 18:39:20
[2016-04-15T01:39Z] INFO  18:39:20,845 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:39Z] INFO  18:39:20,845 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:39Z] INFO  18:39:20,920 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:39Z] INFO  18:39:21,025 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T01:39Z] INFO  18:39:21,394 IntervalUtils - Processing 15509917 bp from intervals
[2016-04-15T01:39Z] WARN  18:39:21,395 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:39Z] WARN  18:39:21,395 IndexDictionaryUtils - Track variant2 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:39Z] WARN  18:39:21,395 IndexDictionaryUtils - Track variant3 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:39Z] WARN  18:39:21,395 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:39Z] INFO  18:39:21,404 MicroScheduler - Running the GATK in parallel mode with 16 total threads, 1 CPU thread(s) for each of 16 data thread(s), of 16 processors available on this machine
[2016-04-15T01:39Z] INFO  18:39:21,455 GenomeAnalysisEngine - Preparing for traversal
[2016-04-15T01:39Z] INFO  18:39:21,456 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:39Z] INFO  18:39:21,457 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:39Z] INFO  18:39:21,457 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T01:39Z] INFO  18:39:21,457 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T01:39Z] INFO  18:39:21,590 GenotypeGVCFs - Notice that the -ploidy parameter is ignored in GenotypeGVCFs tool as this is automatically determined by the input variant files
[2016-04-15T01:39Z] INFO  18:39:31,520 ProgressMeter -            done    646737.0    10.0 s      15.0 s      100.0%    10.0 s       0.0 s
[2016-04-15T01:39Z] INFO  18:39:31,521 ProgressMeter - Total runtime 10.06 secs, 0.17 min, 0.00 hours
[2016-04-15T01:39Z] INFO  18:39:33,953 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:39Z] GATK: GenotypeGVCFs
[2016-04-15T01:39Z] INFO  18:39:36,172 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:39Z] INFO  18:39:36,174 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:39Z] INFO  18:39:36,175 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:39Z] INFO  18:39:36,175 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:39Z] INFO  18:39:36,178 HelpFormatter - Program Args: -T GenotypeGVCFs -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/gatk-haplotype-joint/Batch1/3/tx/tmpkYDPsO/Batch1-3_47129602_62648069.vcf.gz -L 3:47129603-62648069 --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18106_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18105_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18102_kapa-NGv3-PE100-NGv3.vcf.gz --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -nt 16 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:39Z] INFO  18:39:36,187 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:39Z] INFO  18:39:36,187 HelpFormatter - Date/Time: 2016/04/14 18:39:36
[2016-04-15T01:39Z] INFO  18:39:36,187 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:39Z] INFO  18:39:36,188 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:39Z] INFO  18:39:36,260 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:39Z] INFO  18:39:36,360 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T01:39Z] INFO  18:39:36,779 IntervalUtils - Processing 15518467 bp from intervals
[2016-04-15T01:39Z] WARN  18:39:36,780 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:39Z] WARN  18:39:36,780 IndexDictionaryUtils - Track variant2 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:39Z] WARN  18:39:36,780 IndexDictionaryUtils - Track variant3 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:39Z] WARN  18:39:36,780 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:39Z] INFO  18:39:36,789 MicroScheduler - Running the GATK in parallel mode with 16 total threads, 1 CPU thread(s) for each of 16 data thread(s), of 16 processors available on this machine
[2016-04-15T01:39Z] INFO  18:39:36,841 GenomeAnalysisEngine - Preparing for traversal
[2016-04-15T01:39Z] INFO  18:39:36,842 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:39Z] INFO  18:39:36,842 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:39Z] INFO  18:39:36,842 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T01:39Z] INFO  18:39:36,843 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T01:39Z] INFO  18:39:36,971 GenotypeGVCFs - Notice that the -ploidy parameter is ignored in GenotypeGVCFs tool as this is automatically determined by the input variant files
[2016-04-15T01:39Z] INFO  18:39:45,637 ProgressMeter -            done    768965.0     8.0 s      11.0 s      100.0%     8.0 s       0.0 s
[2016-04-15T01:39Z] INFO  18:39:45,638 ProgressMeter - Total runtime 8.80 secs, 0.15 min, 0.00 hours
[2016-04-15T01:39Z] INFO  18:39:47,698 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:39Z] GATK: GenotypeGVCFs
[2016-04-15T01:39Z] INFO  18:39:49,789 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:39Z] INFO  18:39:49,791 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:39Z] INFO  18:39:49,791 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:39Z] INFO  18:39:49,791 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:39Z] INFO  18:39:49,795 HelpFormatter - Program Args: -T GenotypeGVCFs -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/gatk-haplotype-joint/Batch1/3/tx/tmpCrWadq/Batch1-3_62739115_78648077.vcf.gz -L 3:62739116-78648077 --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18106_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18105_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18102_kapa-NGv3-PE100-NGv3.vcf.gz --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -nt 16 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:39Z] INFO  18:39:49,804 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:39Z] INFO  18:39:49,804 HelpFormatter - Date/Time: 2016/04/14 18:39:49
[2016-04-15T01:39Z] INFO  18:39:49,804 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:39Z] INFO  18:39:49,804 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:39Z] INFO  18:39:49,879 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:39Z] INFO  18:39:49,991 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T01:39Z] INFO  18:39:50,605 IntervalUtils - Processing 15908962 bp from intervals
[2016-04-15T01:39Z] WARN  18:39:50,606 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:39Z] WARN  18:39:50,606 IndexDictionaryUtils - Track variant2 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:39Z] WARN  18:39:50,606 IndexDictionaryUtils - Track variant3 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:39Z] WARN  18:39:50,606 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:39Z] INFO  18:39:50,615 MicroScheduler - Running the GATK in parallel mode with 16 total threads, 1 CPU thread(s) for each of 16 data thread(s), of 16 processors available on this machine
[2016-04-15T01:39Z] INFO  18:39:50,666 GenomeAnalysisEngine - Preparing for traversal
[2016-04-15T01:39Z] INFO  18:39:50,666 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:39Z] INFO  18:39:50,667 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:39Z] INFO  18:39:50,667 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T01:39Z] INFO  18:39:50,668 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T01:39Z] INFO  18:39:50,795 GenotypeGVCFs - Notice that the -ploidy parameter is ignored in GenotypeGVCFs tool as this is automatically determined by the input variant files
[2016-04-15T01:40Z] INFO  18:40:00,111 ProgressMeter -            done    475700.0     9.0 s      19.0 s      100.0%     9.0 s       0.0 s
[2016-04-15T01:40Z] INFO  18:40:00,111 ProgressMeter - Total runtime 9.44 secs, 0.16 min, 0.00 hours
[2016-04-15T01:40Z] INFO  18:40:02,680 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:40Z] GATK: GenotypeGVCFs
[2016-04-15T01:40Z] INFO  18:40:04,736 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:40Z] INFO  18:40:04,738 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:40Z] INFO  18:40:04,738 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:40Z] INFO  18:40:04,739 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:40Z] INFO  18:40:04,742 HelpFormatter - Program Args: -T GenotypeGVCFs -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/gatk-haplotype-joint/Batch1/3/tx/tmprb7U6a/Batch1-3_78649262_96533852.vcf.gz -L 3:78649263-96533852 --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18106_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18105_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18102_kapa-NGv3-PE100-NGv3.vcf.gz --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -nt 16 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:40Z] INFO  18:40:04,750 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:40Z] INFO  18:40:04,750 HelpFormatter - Date/Time: 2016/04/14 18:40:04
[2016-04-15T01:40Z] INFO  18:40:04,751 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:40Z] INFO  18:40:04,751 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:40Z] INFO  18:40:04,825 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:40Z] INFO  18:40:04,929 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T01:40Z] INFO  18:40:05,417 IntervalUtils - Processing 17884590 bp from intervals
[2016-04-15T01:40Z] WARN  18:40:05,418 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:40Z] WARN  18:40:05,418 IndexDictionaryUtils - Track variant2 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:40Z] WARN  18:40:05,419 IndexDictionaryUtils - Track variant3 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:40Z] WARN  18:40:05,419 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:40Z] INFO  18:40:05,429 MicroScheduler - Running the GATK in parallel mode with 16 total threads, 1 CPU thread(s) for each of 16 data thread(s), of 16 processors available on this machine
[2016-04-15T01:40Z] INFO  18:40:05,483 GenomeAnalysisEngine - Preparing for traversal
[2016-04-15T01:40Z] INFO  18:40:05,484 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:40Z] INFO  18:40:05,485 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:40Z] INFO  18:40:05,485 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T01:40Z] INFO  18:40:05,485 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T01:40Z] INFO  18:40:05,614 GenotypeGVCFs - Notice that the -ploidy parameter is ignored in GenotypeGVCFs tool as this is automatically determined by the input variant files
[2016-04-15T01:40Z] INFO  18:40:14,771 ProgressMeter -            done    376190.0     9.0 s      24.0 s      100.0%     9.0 s       0.0 s
[2016-04-15T01:40Z] INFO  18:40:14,772 ProgressMeter - Total runtime 9.29 secs, 0.15 min, 0.00 hours
[2016-04-15T01:40Z] INFO  18:40:16,935 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:40Z] GATK: GenotypeGVCFs
[2016-04-15T01:40Z] INFO  18:40:19,111 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:40Z] INFO  18:40:19,112 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:40Z] INFO  18:40:19,113 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:40Z] INFO  18:40:19,113 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:40Z] INFO  18:40:19,116 HelpFormatter - Program Args: -T GenotypeGVCFs -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/gatk-haplotype-joint/Batch1/3/tx/tmpSZkXHO/Batch1-3_96585668_112185230.vcf.gz -L 3:96585669-112185230 --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18106_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18105_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18102_kapa-NGv3-PE100-NGv3.vcf.gz --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -nt 16 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:40Z] INFO  18:40:19,125 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:40Z] INFO  18:40:19,125 HelpFormatter - Date/Time: 2016/04/14 18:40:19
[2016-04-15T01:40Z] INFO  18:40:19,125 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:40Z] INFO  18:40:19,125 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:40Z] INFO  18:40:19,197 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:40Z] INFO  18:40:19,295 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T01:40Z] INFO  18:40:19,703 IntervalUtils - Processing 15599562 bp from intervals
[2016-04-15T01:40Z] WARN  18:40:19,704 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:40Z] WARN  18:40:19,704 IndexDictionaryUtils - Track variant2 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:40Z] WARN  18:40:19,704 IndexDictionaryUtils - Track variant3 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:40Z] WARN  18:40:19,704 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:40Z] INFO  18:40:19,713 MicroScheduler - Running the GATK in parallel mode with 16 total threads, 1 CPU thread(s) for each of 16 data thread(s), of 16 processors available on this machine
[2016-04-15T01:40Z] INFO  18:40:19,762 GenomeAnalysisEngine - Preparing for traversal
[2016-04-15T01:40Z] INFO  18:40:19,763 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:40Z] INFO  18:40:19,764 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:40Z] INFO  18:40:19,764 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T01:40Z] INFO  18:40:19,765 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T01:40Z] INFO  18:40:19,887 GenotypeGVCFs - Notice that the -ploidy parameter is ignored in GenotypeGVCFs tool as this is automatically determined by the input variant files
[2016-04-15T01:40Z] INFO  18:40:28,285 ProgressMeter -            done    489224.0     8.0 s      17.0 s      100.0%     8.0 s       0.0 s
[2016-04-15T01:40Z] INFO  18:40:28,286 ProgressMeter - Total runtime 8.52 secs, 0.14 min, 0.00 hours
[2016-04-15T01:40Z] INFO  18:40:30,471 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:40Z] GATK: GenotypeGVCFs
[2016-04-15T01:40Z] INFO  18:40:32,644 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:40Z] INFO  18:40:32,645 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:40Z] INFO  18:40:32,646 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:40Z] INFO  18:40:32,646 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:40Z] INFO  18:40:32,650 HelpFormatter - Program Args: -T GenotypeGVCFs -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/gatk-haplotype-joint/Batch1/3/tx/tmpSh9ZH_/Batch1-3_112188604_127703121.vcf.gz -L 3:112188605-127703121 --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18106_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18105_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18102_kapa-NGv3-PE100-NGv3.vcf.gz --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -nt 16 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:40Z] INFO  18:40:32,658 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:40Z] INFO  18:40:32,659 HelpFormatter - Date/Time: 2016/04/14 18:40:32
[2016-04-15T01:40Z] INFO  18:40:32,659 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:40Z] INFO  18:40:32,659 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:40Z] INFO  18:40:32,735 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:40Z] INFO  18:40:32,839 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T01:40Z] INFO  18:40:33,415 IntervalUtils - Processing 15514517 bp from intervals
[2016-04-15T01:40Z] WARN  18:40:33,417 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:40Z] WARN  18:40:33,417 IndexDictionaryUtils - Track variant2 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:40Z] WARN  18:40:33,418 IndexDictionaryUtils - Track variant3 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:40Z] WARN  18:40:33,418 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:40Z] INFO  18:40:33,438 MicroScheduler - Running the GATK in parallel mode with 16 total threads, 1 CPU thread(s) for each of 16 data thread(s), of 16 processors available on this machine
[2016-04-15T01:40Z] INFO  18:40:33,559 GenomeAnalysisEngine - Preparing for traversal
[2016-04-15T01:40Z] INFO  18:40:33,561 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:40Z] INFO  18:40:33,562 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:40Z] INFO  18:40:33,563 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T01:40Z] INFO  18:40:33,564 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T01:40Z] INFO  18:40:33,864 GenotypeGVCFs - Notice that the -ploidy parameter is ignored in GenotypeGVCFs tool as this is automatically determined by the input variant files
[2016-04-15T01:40Z] INFO  18:40:42,578 ProgressMeter -            done    592173.0     9.0 s      15.0 s      100.0%     9.0 s       0.0 s
[2016-04-15T01:40Z] INFO  18:40:42,578 ProgressMeter - Total runtime 9.02 secs, 0.15 min, 0.00 hours
[2016-04-15T01:40Z] INFO  18:40:44,542 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:40Z] GATK: GenotypeGVCFs
[2016-04-15T01:40Z] INFO  18:40:46,670 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:40Z] INFO  18:40:46,672 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:40Z] INFO  18:40:46,672 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:40Z] INFO  18:40:46,672 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:40Z] INFO  18:40:46,676 HelpFormatter - Program Args: -T GenotypeGVCFs -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/gatk-haplotype-joint/Batch1/3/tx/tmpzz227r/Batch1-3_127770401_143293035.vcf.gz -L 3:127770402-143293035 --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18106_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18105_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18102_kapa-NGv3-PE100-NGv3.vcf.gz --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -nt 16 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:40Z] INFO  18:40:46,685 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:40Z] INFO  18:40:46,685 HelpFormatter - Date/Time: 2016/04/14 18:40:46
[2016-04-15T01:40Z] INFO  18:40:46,685 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:40Z] INFO  18:40:46,685 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:40Z] INFO  18:40:46,761 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:40Z] INFO  18:40:46,863 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T01:40Z] INFO  18:40:47,511 IntervalUtils - Processing 15522634 bp from intervals
[2016-04-15T01:40Z] WARN  18:40:47,512 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:40Z] WARN  18:40:47,513 IndexDictionaryUtils - Track variant2 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:40Z] WARN  18:40:47,513 IndexDictionaryUtils - Track variant3 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:40Z] WARN  18:40:47,513 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:40Z] INFO  18:40:47,533 MicroScheduler - Running the GATK in parallel mode with 16 total threads, 1 CPU thread(s) for each of 16 data thread(s), of 16 processors available on this machine
[2016-04-15T01:40Z] INFO  18:40:47,654 GenomeAnalysisEngine - Preparing for traversal
[2016-04-15T01:40Z] INFO  18:40:47,656 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:40Z] INFO  18:40:47,657 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:40Z] INFO  18:40:47,658 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T01:40Z] INFO  18:40:47,658 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T01:40Z] INFO  18:40:47,954 GenotypeGVCFs - Notice that the -ploidy parameter is ignored in GenotypeGVCFs tool as this is automatically determined by the input variant files
[2016-04-15T01:40Z] INFO  18:40:57,716 ProgressMeter -            done    581296.0    10.0 s      17.0 s      100.0%    10.0 s       0.0 s
[2016-04-15T01:40Z] INFO  18:40:57,717 ProgressMeter - Total runtime 10.06 secs, 0.17 min, 0.00 hours
[2016-04-15T01:41Z] INFO  18:41:00,040 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:41Z] GATK: GenotypeGVCFs
[2016-04-15T01:41Z] INFO  18:41:02,201 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:41Z] INFO  18:41:02,203 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:41Z] INFO  18:41:02,203 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:41Z] INFO  18:41:02,203 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:41Z] INFO  18:41:02,207 HelpFormatter - Program Args: -T GenotypeGVCFs -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/gatk-haplotype-joint/Batch1/3/tx/tmpVb86jV/Batch1-3_143297426_158963696.vcf.gz -L 3:143297427-158963696 --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18106_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18105_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18102_kapa-NGv3-PE100-NGv3.vcf.gz --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -nt 16 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:41Z] INFO  18:41:02,215 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:41Z] INFO  18:41:02,215 HelpFormatter - Date/Time: 2016/04/14 18:41:02
[2016-04-15T01:41Z] INFO  18:41:02,215 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:41Z] INFO  18:41:02,215 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:41Z] INFO  18:41:02,287 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:41Z] INFO  18:41:02,384 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T01:41Z] INFO  18:41:02,803 IntervalUtils - Processing 15666270 bp from intervals
[2016-04-15T01:41Z] WARN  18:41:02,804 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:41Z] WARN  18:41:02,804 IndexDictionaryUtils - Track variant2 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:41Z] WARN  18:41:02,804 IndexDictionaryUtils - Track variant3 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:41Z] WARN  18:41:02,804 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:41Z] INFO  18:41:02,813 MicroScheduler - Running the GATK in parallel mode with 16 total threads, 1 CPU thread(s) for each of 16 data thread(s), of 16 processors available on this machine
[2016-04-15T01:41Z] INFO  18:41:02,863 GenomeAnalysisEngine - Preparing for traversal
[2016-04-15T01:41Z] INFO  18:41:02,863 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:41Z] INFO  18:41:02,864 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:41Z] INFO  18:41:02,864 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T01:41Z] INFO  18:41:02,865 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T01:41Z] INFO  18:41:02,987 GenotypeGVCFs - Notice that the -ploidy parameter is ignored in GenotypeGVCFs tool as this is automatically determined by the input variant files
[2016-04-15T01:41Z] INFO  18:41:12,939 ProgressMeter -            done    473825.0    10.0 s      21.0 s      100.0%    10.0 s       0.0 s
[2016-04-15T01:41Z] INFO  18:41:12,939 ProgressMeter - Total runtime 10.08 secs, 0.17 min, 0.00 hours
[2016-04-15T01:41Z] INFO  18:41:15,227 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:41Z] GATK: GenotypeGVCFs
[2016-04-15T01:41Z] INFO  18:41:17,257 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:41Z] INFO  18:41:17,259 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:41Z] INFO  18:41:17,259 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:41Z] INFO  18:41:17,259 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:41Z] INFO  18:41:17,263 HelpFormatter - Program Args: -T GenotypeGVCFs -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/gatk-haplotype-joint/Batch1/3/tx/tmpjGVHg2/Batch1-3_158970515_174577240.vcf.gz -L 3:158970516-174577240 --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18106_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18105_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18102_kapa-NGv3-PE100-NGv3.vcf.gz --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -nt 16 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:41Z] INFO  18:41:17,270 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:41Z] INFO  18:41:17,271 HelpFormatter - Date/Time: 2016/04/14 18:41:17
[2016-04-15T01:41Z] INFO  18:41:17,271 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:41Z] INFO  18:41:17,271 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:41Z] INFO  18:41:17,342 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:41Z] INFO  18:41:17,439 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T01:41Z] INFO  18:41:17,844 IntervalUtils - Processing 15606725 bp from intervals
[2016-04-15T01:41Z] WARN  18:41:17,845 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:41Z] WARN  18:41:17,845 IndexDictionaryUtils - Track variant2 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:41Z] WARN  18:41:17,845 IndexDictionaryUtils - Track variant3 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:41Z] WARN  18:41:17,845 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:41Z] INFO  18:41:17,854 MicroScheduler - Running the GATK in parallel mode with 16 total threads, 1 CPU thread(s) for each of 16 data thread(s), of 16 processors available on this machine
[2016-04-15T01:41Z] INFO  18:41:17,903 GenomeAnalysisEngine - Preparing for traversal
[2016-04-15T01:41Z] INFO  18:41:17,904 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:41Z] INFO  18:41:17,904 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:41Z] INFO  18:41:17,904 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T01:41Z] INFO  18:41:17,905 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T01:41Z] INFO  18:41:18,026 GenotypeGVCFs - Notice that the -ploidy parameter is ignored in GenotypeGVCFs tool as this is automatically determined by the input variant files
[2016-04-15T01:41Z] INFO  18:41:27,182 ProgressMeter -            done    451695.0     9.0 s      20.0 s      100.0%     9.0 s       0.0 s
[2016-04-15T01:41Z] INFO  18:41:27,182 ProgressMeter - Total runtime 9.28 secs, 0.15 min, 0.00 hours
[2016-04-15T01:41Z] INFO  18:41:29,418 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:41Z] GATK: GenotypeGVCFs
[2016-04-15T01:41Z] INFO  18:41:31,604 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:41Z] INFO  18:41:31,606 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:41Z] INFO  18:41:31,606 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:41Z] INFO  18:41:31,607 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:41Z] INFO  18:41:31,610 HelpFormatter - Program Args: -T GenotypeGVCFs -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/gatk-haplotype-joint/Batch1/3/tx/tmpZMHZwV/Batch1-3_174814579_190326970.vcf.gz -L 3:174814580-190326970 --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18106_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18105_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18102_kapa-NGv3-PE100-NGv3.vcf.gz --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -nt 16 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:41Z] INFO  18:41:31,619 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:41Z] INFO  18:41:31,620 HelpFormatter - Date/Time: 2016/04/14 18:41:31
[2016-04-15T01:41Z] INFO  18:41:31,620 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:41Z] INFO  18:41:31,620 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:41Z] INFO  18:41:31,696 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:41Z] INFO  18:41:31,801 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T01:41Z] INFO  18:41:32,352 IntervalUtils - Processing 15512391 bp from intervals
[2016-04-15T01:41Z] WARN  18:41:32,354 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:41Z] WARN  18:41:32,354 IndexDictionaryUtils - Track variant2 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:41Z] WARN  18:41:32,355 IndexDictionaryUtils - Track variant3 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:41Z] WARN  18:41:32,355 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:41Z] INFO  18:41:32,375 MicroScheduler - Running the GATK in parallel mode with 16 total threads, 1 CPU thread(s) for each of 16 data thread(s), of 16 processors available on this machine
[2016-04-15T01:41Z] INFO  18:41:32,496 GenomeAnalysisEngine - Preparing for traversal
[2016-04-15T01:41Z] INFO  18:41:32,498 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:41Z] INFO  18:41:32,499 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:41Z] INFO  18:41:32,500 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T01:41Z] INFO  18:41:32,501 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T01:41Z] INFO  18:41:32,799 GenotypeGVCFs - Notice that the -ploidy parameter is ignored in GenotypeGVCFs tool as this is automatically determined by the input variant files
[2016-04-15T01:41Z] INFO  18:41:42,579 ProgressMeter -            done    541116.0    10.0 s      18.0 s      100.0%    10.0 s       0.0 s
[2016-04-15T01:41Z] INFO  18:41:42,580 ProgressMeter - Total runtime 10.08 secs, 0.17 min, 0.00 hours
[2016-04-15T01:41Z] INFO  18:41:45,148 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:41Z] GATK: GenotypeGVCFs
[2016-04-15T01:41Z] INFO  18:41:47,266 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:41Z] INFO  18:41:47,268 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:41Z] INFO  18:41:47,268 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:41Z] INFO  18:41:47,268 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:41Z] INFO  18:41:47,272 HelpFormatter - Program Args: -T GenotypeGVCFs -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/gatk-haplotype-joint/Batch1/3/tx/tmpypNZF6/Batch1-3_190333063_198022430.vcf.gz -L 3:190333064-198022430 --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18106_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18105_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18102_kapa-NGv3-PE100-NGv3.vcf.gz --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -nt 16 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:41Z] INFO  18:41:47,280 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:41Z] INFO  18:41:47,281 HelpFormatter - Date/Time: 2016/04/14 18:41:47
[2016-04-15T01:41Z] INFO  18:41:47,281 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:41Z] INFO  18:41:47,281 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:41Z] INFO  18:41:47,357 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:41Z] INFO  18:41:47,500 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T01:41Z] INFO  18:41:47,988 IntervalUtils - Processing 7689367 bp from intervals
[2016-04-15T01:41Z] WARN  18:41:47,989 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:41Z] WARN  18:41:47,989 IndexDictionaryUtils - Track variant2 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:41Z] WARN  18:41:47,989 IndexDictionaryUtils - Track variant3 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:41Z] WARN  18:41:47,990 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:41Z] INFO  18:41:47,998 MicroScheduler - Running the GATK in parallel mode with 16 total threads, 1 CPU thread(s) for each of 16 data thread(s), of 16 processors available on this machine
[2016-04-15T01:41Z] INFO  18:41:48,050 GenomeAnalysisEngine - Preparing for traversal
[2016-04-15T01:41Z] INFO  18:41:48,051 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:41Z] INFO  18:41:48,051 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:41Z] INFO  18:41:48,052 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T01:41Z] INFO  18:41:48,052 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T01:41Z] INFO  18:41:48,182 GenotypeGVCFs - Notice that the -ploidy parameter is ignored in GenotypeGVCFs tool as this is automatically determined by the input variant files
[2016-04-15T01:41Z] INFO  18:41:55,104 ProgressMeter -            done    325176.0     7.0 s      21.0 s       98.8%     7.0 s       0.0 s
[2016-04-15T01:41Z] INFO  18:41:55,104 ProgressMeter - Total runtime 7.05 secs, 0.12 min, 0.00 hours
[2016-04-15T01:41Z] INFO  18:41:57,039 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:41Z] GATK: GenotypeGVCFs
[2016-04-15T01:41Z] INFO  18:41:59,170 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:41Z] INFO  18:41:59,172 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:41Z] INFO  18:41:59,173 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:41Z] INFO  18:41:59,173 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:41Z] INFO  18:41:59,176 HelpFormatter - Program Args: -T GenotypeGVCFs -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/gatk-haplotype-joint/Batch1/4/tx/tmpgg8D7W/Batch1-4_0_15511864.vcf.gz -L 4:1-15511864 --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18106_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18105_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18102_kapa-NGv3-PE100-NGv3.vcf.gz --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -nt 16 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:41Z] INFO  18:41:59,185 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:41Z] INFO  18:41:59,185 HelpFormatter - Date/Time: 2016/04/14 18:41:59
[2016-04-15T01:41Z] INFO  18:41:59,185 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:41Z] INFO  18:41:59,185 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:41Z] INFO  18:41:59,257 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:41Z] INFO  18:41:59,354 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T01:41Z] INFO  18:41:59,766 IntervalUtils - Processing 15511864 bp from intervals
[2016-04-15T01:41Z] WARN  18:41:59,767 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:41Z] WARN  18:41:59,767 IndexDictionaryUtils - Track variant2 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:41Z] WARN  18:41:59,767 IndexDictionaryUtils - Track variant3 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:41Z] WARN  18:41:59,767 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:41Z] INFO  18:41:59,775 MicroScheduler - Running the GATK in parallel mode with 16 total threads, 1 CPU thread(s) for each of 16 data thread(s), of 16 processors available on this machine
[2016-04-15T01:41Z] INFO  18:41:59,825 GenomeAnalysisEngine - Preparing for traversal
[2016-04-15T01:41Z] INFO  18:41:59,826 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:41Z] INFO  18:41:59,826 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:41Z] INFO  18:41:59,826 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T01:41Z] INFO  18:41:59,827 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T01:41Z] INFO  18:41:59,948 GenotypeGVCFs - Notice that the -ploidy parameter is ignored in GenotypeGVCFs tool as this is automatically determined by the input variant files
[2016-04-15T01:42Z] INFO  18:42:10,643 ProgressMeter -            done    700222.0    10.0 s      15.0 s      100.0%    10.0 s       0.0 s
[2016-04-15T01:42Z] INFO  18:42:10,643 ProgressMeter - Total runtime 10.82 secs, 0.18 min, 0.00 hours
[2016-04-15T01:42Z] INFO  18:42:13,708 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:42Z] GATK: GenotypeGVCFs
[2016-04-15T01:42Z] INFO  18:42:15,752 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:42Z] INFO  18:42:15,754 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:42Z] INFO  18:42:15,754 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:42Z] INFO  18:42:15,755 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:42Z] INFO  18:42:15,758 HelpFormatter - Program Args: -T GenotypeGVCFs -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/gatk-haplotype-joint/Batch1/4/tx/tmp0Wmzoe/Batch1-4_15512869_31144471.vcf.gz -L 4:15512870-31144471 --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18106_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18105_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18102_kapa-NGv3-PE100-NGv3.vcf.gz --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -nt 16 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:42Z] INFO  18:42:15,767 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:42Z] INFO  18:42:15,767 HelpFormatter - Date/Time: 2016/04/14 18:42:15
[2016-04-15T01:42Z] INFO  18:42:15,767 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:42Z] INFO  18:42:15,768 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:42Z] INFO  18:42:15,843 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:42Z] INFO  18:42:15,945 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T01:42Z] INFO  18:42:16,431 IntervalUtils - Processing 15631602 bp from intervals
[2016-04-15T01:42Z] WARN  18:42:16,431 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:42Z] WARN  18:42:16,432 IndexDictionaryUtils - Track variant2 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:42Z] WARN  18:42:16,432 IndexDictionaryUtils - Track variant3 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:42Z] WARN  18:42:16,432 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:42Z] INFO  18:42:16,441 MicroScheduler - Running the GATK in parallel mode with 16 total threads, 1 CPU thread(s) for each of 16 data thread(s), of 16 processors available on this machine
[2016-04-15T01:42Z] INFO  18:42:16,494 GenomeAnalysisEngine - Preparing for traversal
[2016-04-15T01:42Z] INFO  18:42:16,495 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:42Z] INFO  18:42:16,495 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:42Z] INFO  18:42:16,496 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T01:42Z] INFO  18:42:16,496 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T01:42Z] INFO  18:42:16,629 GenotypeGVCFs - Notice that the -ploidy parameter is ignored in GenotypeGVCFs tool as this is automatically determined by the input variant files
[2016-04-15T01:42Z] INFO  18:42:26,634 ProgressMeter -            done    458965.0    10.0 s      22.0 s      100.0%    10.0 s       0.0 s
[2016-04-15T01:42Z] INFO  18:42:26,634 ProgressMeter - Total runtime 10.14 secs, 0.17 min, 0.00 hours
[2016-04-15T01:42Z] INFO  18:42:29,003 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:42Z] GATK: GenotypeGVCFs
[2016-04-15T01:42Z] INFO  18:42:31,167 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:42Z] INFO  18:42:31,169 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:42Z] INFO  18:42:31,169 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:42Z] INFO  18:42:31,169 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:42Z] INFO  18:42:31,173 HelpFormatter - Program Args: -T GenotypeGVCFs -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/gatk-haplotype-joint/Batch1/4/tx/tmpxsaN2G/Batch1-4_36069528_52709433.vcf.gz -L 4:36069529-52709433 --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18106_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18105_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18102_kapa-NGv3-PE100-NGv3.vcf.gz --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -nt 16 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:42Z] INFO  18:42:31,181 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:42Z] INFO  18:42:31,181 HelpFormatter - Date/Time: 2016/04/14 18:42:31
[2016-04-15T01:42Z] INFO  18:42:31,181 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:42Z] INFO  18:42:31,181 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:42Z] INFO  18:42:31,253 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:42Z] INFO  18:42:31,351 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T01:42Z] INFO  18:42:31,766 IntervalUtils - Processing 16639905 bp from intervals
[2016-04-15T01:42Z] WARN  18:42:31,766 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:42Z] WARN  18:42:31,767 IndexDictionaryUtils - Track variant2 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:42Z] WARN  18:42:31,767 IndexDictionaryUtils - Track variant3 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:42Z] WARN  18:42:31,767 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:42Z] INFO  18:42:31,775 MicroScheduler - Running the GATK in parallel mode with 16 total threads, 1 CPU thread(s) for each of 16 data thread(s), of 16 processors available on this machine
[2016-04-15T01:42Z] INFO  18:42:31,826 GenomeAnalysisEngine - Preparing for traversal
[2016-04-15T01:42Z] INFO  18:42:31,827 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:42Z] INFO  18:42:31,827 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:42Z] INFO  18:42:31,828 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T01:42Z] INFO  18:42:31,828 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T01:42Z] INFO  18:42:31,954 GenotypeGVCFs - Notice that the -ploidy parameter is ignored in GenotypeGVCFs tool as this is automatically determined by the input variant files
[2016-04-15T01:42Z] INFO  18:42:41,514 ProgressMeter -            done    489815.0     9.0 s      19.0 s      100.0%     9.0 s       0.0 s
[2016-04-15T01:42Z] INFO  18:42:41,515 ProgressMeter - Total runtime 9.69 secs, 0.16 min, 0.00 hours
[2016-04-15T01:42Z] INFO  18:42:43,934 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:42Z] GATK: GenotypeGVCFs
[2016-04-15T01:42Z] INFO  18:42:46,128 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:42Z] INFO  18:42:46,130 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:42Z] INFO  18:42:46,130 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:42Z] INFO  18:42:46,131 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:42Z] INFO  18:42:46,134 HelpFormatter - Program Args: -T GenotypeGVCFs -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/gatk-haplotype-joint/Batch1/4/tx/tmp2CzoK7/Batch1-4_52709749_68338393.vcf.gz -L 4:52709750-68338393 --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18106_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18105_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18102_kapa-NGv3-PE100-NGv3.vcf.gz --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -nt 16 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:42Z] INFO  18:42:46,143 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:42Z] INFO  18:42:46,144 HelpFormatter - Date/Time: 2016/04/14 18:42:46
[2016-04-15T01:42Z] INFO  18:42:46,144 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:42Z] INFO  18:42:46,144 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:42Z] INFO  18:42:46,221 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:42Z] INFO  18:42:46,326 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T01:42Z] INFO  18:42:46,886 IntervalUtils - Processing 15628644 bp from intervals
[2016-04-15T01:42Z] WARN  18:42:46,887 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:42Z] WARN  18:42:46,887 IndexDictionaryUtils - Track variant2 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:42Z] WARN  18:42:46,887 IndexDictionaryUtils - Track variant3 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:42Z] WARN  18:42:46,887 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:42Z] INFO  18:42:46,896 MicroScheduler - Running the GATK in parallel mode with 16 total threads, 1 CPU thread(s) for each of 16 data thread(s), of 16 processors available on this machine
[2016-04-15T01:42Z] INFO  18:42:46,949 GenomeAnalysisEngine - Preparing for traversal
[2016-04-15T01:42Z] INFO  18:42:46,950 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:42Z] INFO  18:42:46,951 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:42Z] INFO  18:42:46,951 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T01:42Z] INFO  18:42:46,951 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T01:42Z] INFO  18:42:47,123 GenotypeGVCFs - Notice that the -ploidy parameter is ignored in GenotypeGVCFs tool as this is automatically determined by the input variant files
[2016-04-15T01:42Z] INFO  18:42:57,441 ProgressMeter -            done    466027.0    10.0 s      22.0 s      100.0%    10.0 s       0.0 s
[2016-04-15T01:42Z] INFO  18:42:57,442 ProgressMeter - Total runtime 10.49 secs, 0.17 min, 0.00 hours
[2016-04-15T01:42Z] INFO  18:42:59,388 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:42Z] GATK: GenotypeGVCFs
[2016-04-15T01:43Z] INFO  18:43:01,805 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:43Z] INFO  18:43:01,810 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:43Z] INFO  18:43:01,810 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:43Z] INFO  18:43:01,811 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:43Z] INFO  18:43:01,819 HelpFormatter - Program Args: -T GenotypeGVCFs -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/gatk-haplotype-joint/Batch1/4/tx/tmpwN7csC/Batch1-4_68340604_83852298.vcf.gz -L 4:68340605-83852298 --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18106_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18105_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18102_kapa-NGv3-PE100-NGv3.vcf.gz --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -nt 16 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:43Z] INFO  18:43:01,837 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:43Z] INFO  18:43:01,837 HelpFormatter - Date/Time: 2016/04/14 18:43:01
[2016-04-15T01:43Z] INFO  18:43:01,838 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:43Z] INFO  18:43:01,838 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:43Z] INFO  18:43:01,977 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:43Z] INFO  18:43:02,075 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T01:43Z] INFO  18:43:02,496 IntervalUtils - Processing 15511694 bp from intervals
[2016-04-15T01:43Z] WARN  18:43:02,496 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:43Z] WARN  18:43:02,496 IndexDictionaryUtils - Track variant2 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:43Z] WARN  18:43:02,497 IndexDictionaryUtils - Track variant3 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:43Z] WARN  18:43:02,497 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:43Z] INFO  18:43:02,505 MicroScheduler - Running the GATK in parallel mode with 16 total threads, 1 CPU thread(s) for each of 16 data thread(s), of 16 processors available on this machine
[2016-04-15T01:43Z] INFO  18:43:02,555 GenomeAnalysisEngine - Preparing for traversal
[2016-04-15T01:43Z] INFO  18:43:02,556 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:43Z] INFO  18:43:02,557 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:43Z] INFO  18:43:02,557 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T01:43Z] INFO  18:43:02,557 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T01:43Z] INFO  18:43:02,681 GenotypeGVCFs - Notice that the -ploidy parameter is ignored in GenotypeGVCFs tool as this is automatically determined by the input variant files
[2016-04-15T01:43Z] INFO  18:43:14,557 ProgressMeter -            done    550340.0    12.0 s      21.0 s      100.0%    12.0 s       0.0 s
[2016-04-15T01:43Z] INFO  18:43:14,558 ProgressMeter - Total runtime 12.00 secs, 0.20 min, 0.00 hours
[2016-04-15T01:43Z] INFO  18:43:17,276 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:43Z] GATK: GenotypeGVCFs
[2016-04-15T01:43Z] INFO  18:43:19,456 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:43Z] INFO  18:43:19,458 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:43Z] INFO  18:43:19,458 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:43Z] INFO  18:43:19,458 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:43Z] INFO  18:43:19,462 HelpFormatter - Program Args: -T GenotypeGVCFs -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/gatk-haplotype-joint/Batch1/4/tx/tmpO6i8Tr/Batch1-4_83857133_99393738.vcf.gz -L 4:83857134-99393738 --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18106_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18105_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18102_kapa-NGv3-PE100-NGv3.vcf.gz --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -nt 16 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:43Z] INFO  18:43:19,471 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:43Z] INFO  18:43:19,471 HelpFormatter - Date/Time: 2016/04/14 18:43:19
[2016-04-15T01:43Z] INFO  18:43:19,471 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:43Z] INFO  18:43:19,471 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:43Z] INFO  18:43:19,545 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:43Z] INFO  18:43:19,686 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T01:43Z] INFO  18:43:20,126 IntervalUtils - Processing 15536605 bp from intervals
[2016-04-15T01:43Z] WARN  18:43:20,126 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:43Z] WARN  18:43:20,127 IndexDictionaryUtils - Track variant2 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:43Z] WARN  18:43:20,127 IndexDictionaryUtils - Track variant3 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:43Z] WARN  18:43:20,127 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:43Z] INFO  18:43:20,136 MicroScheduler - Running the GATK in parallel mode with 16 total threads, 1 CPU thread(s) for each of 16 data thread(s), of 16 processors available on this machine
[2016-04-15T01:43Z] INFO  18:43:20,185 GenomeAnalysisEngine - Preparing for traversal
[2016-04-15T01:43Z] INFO  18:43:20,186 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:43Z] INFO  18:43:20,187 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:43Z] INFO  18:43:20,187 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T01:43Z] INFO  18:43:20,188 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T01:43Z] INFO  18:43:20,311 GenotypeGVCFs - Notice that the -ploidy parameter is ignored in GenotypeGVCFs tool as this is automatically determined by the input variant files
[2016-04-15T01:43Z] INFO  18:43:30,132 ProgressMeter -            done    462080.0     9.0 s      21.0 s      100.0%     9.0 s       0.0 s
[2016-04-15T01:43Z] INFO  18:43:30,132 ProgressMeter - Total runtime 9.95 secs, 0.17 min, 0.00 hours
[2016-04-15T01:43Z] INFO  18:43:32,729 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:43Z] GATK: GenotypeGVCFs
[2016-04-15T01:43Z] INFO  18:43:34,763 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:43Z] INFO  18:43:34,765 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:43Z] INFO  18:43:34,765 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:43Z] INFO  18:43:34,765 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:43Z] INFO  18:43:34,769 HelpFormatter - Program Args: -T GenotypeGVCFs -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/gatk-haplotype-joint/Batch1/4/tx/tmpVGn6q3/Batch1-4_99397339_115544957.vcf.gz -L 4:99397340-115544957 --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18106_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18105_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18102_kapa-NGv3-PE100-NGv3.vcf.gz --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -nt 16 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:43Z] INFO  18:43:34,777 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:43Z] INFO  18:43:34,778 HelpFormatter - Date/Time: 2016/04/14 18:43:34
[2016-04-15T01:43Z] INFO  18:43:34,778 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:43Z] INFO  18:43:34,778 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:43Z] INFO  18:43:34,849 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:43Z] INFO  18:43:34,949 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T01:43Z] INFO  18:43:35,301 IntervalUtils - Processing 16147618 bp from intervals
[2016-04-15T01:43Z] WARN  18:43:35,302 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:43Z] WARN  18:43:35,302 IndexDictionaryUtils - Track variant2 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:43Z] WARN  18:43:35,302 IndexDictionaryUtils - Track variant3 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:43Z] WARN  18:43:35,303 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:43Z] INFO  18:43:35,311 MicroScheduler - Running the GATK in parallel mode with 16 total threads, 1 CPU thread(s) for each of 16 data thread(s), of 16 processors available on this machine
[2016-04-15T01:43Z] INFO  18:43:35,362 GenomeAnalysisEngine - Preparing for traversal
[2016-04-15T01:43Z] INFO  18:43:35,363 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:43Z] INFO  18:43:35,363 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:43Z] INFO  18:43:35,363 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T01:43Z] INFO  18:43:35,364 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T01:43Z] INFO  18:43:35,491 GenotypeGVCFs - Notice that the -ploidy parameter is ignored in GenotypeGVCFs tool as this is automatically determined by the input variant files
[2016-04-15T01:43Z] INFO  18:43:43,873 ProgressMeter -            done    498464.0     8.0 s      17.0 s      100.0%     8.0 s       0.0 s
[2016-04-15T01:43Z] INFO  18:43:43,874 ProgressMeter - Total runtime 8.51 secs, 0.14 min, 0.00 hours
[2016-04-15T01:43Z] INFO  18:43:46,399 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:43Z] GATK: GenotypeGVCFs
[2016-04-15T01:43Z] INFO  18:43:48,625 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:43Z] INFO  18:43:48,627 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:43Z] INFO  18:43:48,627 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:43Z] INFO  18:43:48,628 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:43Z] INFO  18:43:48,631 HelpFormatter - Program Args: -T GenotypeGVCFs -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/gatk-haplotype-joint/Batch1/4/tx/tmp1XQ2Qo/Batch1-4_115584857_134074404.vcf.gz -L 4:115584858-134074404 --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18106_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18105_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18102_kapa-NGv3-PE100-NGv3.vcf.gz --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -nt 16 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:43Z] INFO  18:43:48,639 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:43Z] INFO  18:43:48,639 HelpFormatter - Date/Time: 2016/04/14 18:43:48
[2016-04-15T01:43Z] INFO  18:43:48,639 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:43Z] INFO  18:43:48,640 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:43Z] INFO  18:43:48,712 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:43Z] INFO  18:43:48,812 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T01:43Z] INFO  18:43:49,229 IntervalUtils - Processing 18489547 bp from intervals
[2016-04-15T01:43Z] WARN  18:43:49,230 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:43Z] WARN  18:43:49,230 IndexDictionaryUtils - Track variant2 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:43Z] WARN  18:43:49,231 IndexDictionaryUtils - Track variant3 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:43Z] WARN  18:43:49,231 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:43Z] INFO  18:43:49,239 MicroScheduler - Running the GATK in parallel mode with 16 total threads, 1 CPU thread(s) for each of 16 data thread(s), of 16 processors available on this machine
[2016-04-15T01:43Z] INFO  18:43:49,289 GenomeAnalysisEngine - Preparing for traversal
[2016-04-15T01:43Z] INFO  18:43:49,290 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:43Z] INFO  18:43:49,290 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:43Z] INFO  18:43:49,291 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T01:43Z] INFO  18:43:49,291 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T01:43Z] INFO  18:43:49,416 GenotypeGVCFs - Notice that the -ploidy parameter is ignored in GenotypeGVCFs tool as this is automatically determined by the input variant files
[2016-04-15T01:43Z] INFO  18:43:59,644 ProgressMeter -            done    570612.0    10.0 s      18.0 s      100.0%    10.0 s       0.0 s
[2016-04-15T01:43Z] INFO  18:43:59,645 ProgressMeter - Total runtime 10.35 secs, 0.17 min, 0.00 hours
[2016-04-15T01:44Z] INFO  18:44:01,896 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:44Z] GATK: GenotypeGVCFs
[2016-04-15T01:44Z] INFO  18:44:03,822 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:44Z] INFO  18:44:03,824 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:44Z] INFO  18:44:03,825 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:44Z] INFO  18:44:03,825 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:44Z] INFO  18:44:03,828 HelpFormatter - Program Args: -T GenotypeGVCFs -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/gatk-haplotype-joint/Batch1/4/tx/tmp0EXmWs/Batch1-4_134075461_150351181.vcf.gz -L 4:134075462-150351181 --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18106_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18105_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18102_kapa-NGv3-PE100-NGv3.vcf.gz --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -nt 16 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:44Z] INFO  18:44:03,837 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:44Z] INFO  18:44:03,837 HelpFormatter - Date/Time: 2016/04/14 18:44:03
[2016-04-15T01:44Z] INFO  18:44:03,837 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:44Z] INFO  18:44:03,837 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:44Z] INFO  18:44:03,909 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:44Z] INFO  18:44:04,006 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T01:44Z] INFO  18:44:04,413 IntervalUtils - Processing 16275720 bp from intervals
[2016-04-15T01:44Z] WARN  18:44:04,414 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:44Z] WARN  18:44:04,414 IndexDictionaryUtils - Track variant2 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:44Z] WARN  18:44:04,414 IndexDictionaryUtils - Track variant3 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:44Z] WARN  18:44:04,414 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:44Z] INFO  18:44:04,423 MicroScheduler - Running the GATK in parallel mode with 16 total threads, 1 CPU thread(s) for each of 16 data thread(s), of 16 processors available on this machine
[2016-04-15T01:44Z] INFO  18:44:04,472 GenomeAnalysisEngine - Preparing for traversal
[2016-04-15T01:44Z] INFO  18:44:04,473 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:44Z] INFO  18:44:04,473 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:44Z] INFO  18:44:04,474 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T01:44Z] INFO  18:44:04,474 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T01:44Z] INFO  18:44:04,596 GenotypeGVCFs - Notice that the -ploidy parameter is ignored in GenotypeGVCFs tool as this is automatically determined by the input variant files
[2016-04-15T01:44Z] INFO  18:44:13,696 ProgressMeter -            done    445573.0     9.0 s      20.0 s      100.0%     9.0 s       0.0 s
[2016-04-15T01:44Z] INFO  18:44:13,697 ProgressMeter - Total runtime 9.22 secs, 0.15 min, 0.00 hours
[2016-04-15T01:44Z] INFO  18:44:16,126 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:44Z] GATK: GenotypeGVCFs
[2016-04-15T01:44Z] INFO  18:44:17,812 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:44Z] INFO  18:44:17,814 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:44Z] INFO  18:44:17,814 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:44Z] INFO  18:44:17,814 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:44Z] INFO  18:44:17,818 HelpFormatter - Program Args: -T GenotypeGVCFs -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/gatk-haplotype-joint/Batch1/4/tx/tmpRWRNkm/Batch1-4_150354547_165878648.vcf.gz -L 4:150354548-165878648 --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18106_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18105_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18102_kapa-NGv3-PE100-NGv3.vcf.gz --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -nt 16 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:44Z] INFO  18:44:17,827 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:44Z] INFO  18:44:17,827 HelpFormatter - Date/Time: 2016/04/14 18:44:17
[2016-04-15T01:44Z] INFO  18:44:17,827 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:44Z] INFO  18:44:17,828 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:44Z] INFO  18:44:17,900 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:44Z] INFO  18:44:18,057 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T01:44Z] INFO  18:44:18,562 IntervalUtils - Processing 15524101 bp from intervals
[2016-04-15T01:44Z] WARN  18:44:18,563 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:44Z] WARN  18:44:18,563 IndexDictionaryUtils - Track variant2 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:44Z] WARN  18:44:18,563 IndexDictionaryUtils - Track variant3 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:44Z] WARN  18:44:18,563 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:44Z] INFO  18:44:18,572 MicroScheduler - Running the GATK in parallel mode with 16 total threads, 1 CPU thread(s) for each of 16 data thread(s), of 16 processors available on this machine
[2016-04-15T01:44Z] INFO  18:44:18,625 GenomeAnalysisEngine - Preparing for traversal
[2016-04-15T01:44Z] INFO  18:44:18,626 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:44Z] INFO  18:44:18,626 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:44Z] INFO  18:44:18,626 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T01:44Z] INFO  18:44:18,627 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T01:44Z] INFO  18:44:18,754 GenotypeGVCFs - Notice that the -ploidy parameter is ignored in GenotypeGVCFs tool as this is automatically determined by the input variant files
[2016-04-15T01:44Z] INFO  18:44:27,962 ProgressMeter -            done    470278.0     9.0 s      19.0 s      100.0%     9.0 s       0.0 s
[2016-04-15T01:44Z] INFO  18:44:27,963 ProgressMeter - Total runtime 9.34 secs, 0.16 min, 0.00 hours
[2016-04-15T01:44Z] INFO  18:44:30,281 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:44Z] GATK: GenotypeGVCFs
[2016-04-15T01:44Z] INFO  18:44:32,199 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:44Z] INFO  18:44:32,201 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:44Z] INFO  18:44:32,201 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:44Z] INFO  18:44:32,201 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:44Z] INFO  18:44:32,205 HelpFormatter - Program Args: -T GenotypeGVCFs -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/gatk-haplotype-joint/Batch1/4/tx/tmpyMAnI1/Batch1-4_165889318_183245405.vcf.gz -L 4:165889319-183245405 --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18106_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18105_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18102_kapa-NGv3-PE100-NGv3.vcf.gz --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -nt 16 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:44Z] INFO  18:44:32,213 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:44Z] INFO  18:44:32,213 HelpFormatter - Date/Time: 2016/04/14 18:44:32
[2016-04-15T01:44Z] INFO  18:44:32,213 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:44Z] INFO  18:44:32,214 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:44Z] INFO  18:44:32,285 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:44Z] INFO  18:44:32,383 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T01:44Z] INFO  18:44:32,792 IntervalUtils - Processing 17356087 bp from intervals
[2016-04-15T01:44Z] WARN  18:44:32,793 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:44Z] WARN  18:44:32,793 IndexDictionaryUtils - Track variant2 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:44Z] WARN  18:44:32,793 IndexDictionaryUtils - Track variant3 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:44Z] WARN  18:44:32,793 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:44Z] INFO  18:44:32,802 MicroScheduler - Running the GATK in parallel mode with 16 total threads, 1 CPU thread(s) for each of 16 data thread(s), of 16 processors available on this machine
[2016-04-15T01:44Z] INFO  18:44:32,851 GenomeAnalysisEngine - Preparing for traversal
[2016-04-15T01:44Z] INFO  18:44:32,852 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:44Z] INFO  18:44:32,853 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:44Z] INFO  18:44:32,853 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T01:44Z] INFO  18:44:32,853 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T01:44Z] INFO  18:44:32,977 GenotypeGVCFs - Notice that the -ploidy parameter is ignored in GenotypeGVCFs tool as this is automatically determined by the input variant files
[2016-04-15T01:44Z] INFO  18:44:43,018 ProgressMeter -            done    488190.0    10.0 s      20.0 s      100.0%    10.0 s       0.0 s
[2016-04-15T01:44Z] INFO  18:44:43,019 ProgressMeter - Total runtime 10.17 secs, 0.17 min, 0.00 hours
[2016-04-15T01:44Z] INFO  18:44:45,704 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:44Z] GATK: GenotypeGVCFs
[2016-04-15T01:44Z] INFO  18:44:47,761 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:44Z] INFO  18:44:47,763 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:44Z] INFO  18:44:47,763 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:44Z] INFO  18:44:47,763 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:44Z] INFO  18:44:47,767 HelpFormatter - Program Args: -T GenotypeGVCFs -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/gatk-haplotype-joint/Batch1/4/tx/tmph78Buu/Batch1-4_183267803_191154276.vcf.gz -L 4:183267804-191154276 --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18106_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18105_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18102_kapa-NGv3-PE100-NGv3.vcf.gz --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -nt 16 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:44Z] INFO  18:44:47,776 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:44Z] INFO  18:44:47,777 HelpFormatter - Date/Time: 2016/04/14 18:44:47
[2016-04-15T01:44Z] INFO  18:44:47,777 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:44Z] INFO  18:44:47,777 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:44Z] INFO  18:44:47,853 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:44Z] INFO  18:44:47,969 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T01:44Z] INFO  18:44:48,720 IntervalUtils - Processing 7886473 bp from intervals
[2016-04-15T01:44Z] WARN  18:44:48,720 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:44Z] WARN  18:44:48,721 IndexDictionaryUtils - Track variant2 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:44Z] WARN  18:44:48,721 IndexDictionaryUtils - Track variant3 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:44Z] WARN  18:44:48,721 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:44Z] INFO  18:44:48,730 MicroScheduler - Running the GATK in parallel mode with 16 total threads, 1 CPU thread(s) for each of 16 data thread(s), of 16 processors available on this machine
[2016-04-15T01:44Z] INFO  18:44:48,781 GenomeAnalysisEngine - Preparing for traversal
[2016-04-15T01:44Z] INFO  18:44:48,782 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:44Z] INFO  18:44:48,782 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:44Z] INFO  18:44:48,783 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T01:44Z] INFO  18:44:48,783 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T01:44Z] INFO  18:44:48,910 GenotypeGVCFs - Notice that the -ploidy parameter is ignored in GenotypeGVCFs tool as this is automatically determined by the input variant files
[2016-04-15T01:44Z] INFO  18:44:53,804 ProgressMeter -            done    338699.0     5.0 s      14.0 s       98.6%     5.0 s       0.0 s
[2016-04-15T01:44Z] INFO  18:44:53,804 ProgressMeter - Total runtime 5.02 secs, 0.08 min, 0.00 hours
[2016-04-15T01:44Z] INFO  18:44:55,423 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:44Z] GATK: GenotypeGVCFs
[2016-04-15T01:44Z] INFO  18:44:57,203 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:44Z] INFO  18:44:57,205 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:44Z] INFO  18:44:57,205 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:44Z] INFO  18:44:57,205 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:44Z] INFO  18:44:57,209 HelpFormatter - Program Args: -T GenotypeGVCFs -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/gatk-haplotype-joint/Batch1/5/tx/tmpBsFo3R/Batch1-5_0_15580921.vcf.gz -L 5:1-15580921 --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18106_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18105_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18102_kapa-NGv3-PE100-NGv3.vcf.gz --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -nt 16 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:44Z] INFO  18:44:57,217 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:44Z] INFO  18:44:57,217 HelpFormatter - Date/Time: 2016/04/14 18:44:57
[2016-04-15T01:44Z] INFO  18:44:57,217 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:44Z] INFO  18:44:57,218 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:44Z] INFO  18:44:57,290 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:44Z] INFO  18:44:57,386 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T01:44Z] INFO  18:44:57,799 IntervalUtils - Processing 15580921 bp from intervals
[2016-04-15T01:44Z] WARN  18:44:57,799 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:44Z] WARN  18:44:57,799 IndexDictionaryUtils - Track variant2 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:44Z] WARN  18:44:57,800 IndexDictionaryUtils - Track variant3 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:44Z] WARN  18:44:57,800 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:44Z] INFO  18:44:57,808 MicroScheduler - Running the GATK in parallel mode with 16 total threads, 1 CPU thread(s) for each of 16 data thread(s), of 16 processors available on this machine
[2016-04-15T01:44Z] INFO  18:44:57,858 GenomeAnalysisEngine - Preparing for traversal
[2016-04-15T01:44Z] INFO  18:44:57,859 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:44Z] INFO  18:44:57,859 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:44Z] INFO  18:44:57,859 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T01:44Z] INFO  18:44:57,860 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T01:44Z] INFO  18:44:57,982 GenotypeGVCFs - Notice that the -ploidy parameter is ignored in GenotypeGVCFs tool as this is automatically determined by the input variant files
[2016-04-15T01:45Z] INFO  18:45:06,849 ProgressMeter -            done    542563.0     8.0 s      16.0 s      100.0%     8.0 s       0.0 s
[2016-04-15T01:45Z] INFO  18:45:06,849 ProgressMeter - Total runtime 8.99 secs, 0.15 min, 0.00 hours
[2016-04-15T01:45Z] INFO  18:45:09,316 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:45Z] GATK: GenotypeGVCFs
[2016-04-15T01:45Z] INFO  18:45:11,309 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:45Z] INFO  18:45:11,311 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:45Z] INFO  18:45:11,312 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:45Z] INFO  18:45:11,312 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:45Z] INFO  18:45:11,315 HelpFormatter - Program Args: -T GenotypeGVCFs -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/gatk-haplotype-joint/Batch1/5/tx/tmpCcvwuD/Batch1-5_15616091_31267808.vcf.gz -L 5:15616092-31267808 --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18106_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18105_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18102_kapa-NGv3-PE100-NGv3.vcf.gz --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -nt 16 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:45Z] INFO  18:45:11,324 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:45Z] INFO  18:45:11,324 HelpFormatter - Date/Time: 2016/04/14 18:45:11
[2016-04-15T01:45Z] INFO  18:45:11,324 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:45Z] INFO  18:45:11,324 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:45Z] INFO  18:45:11,397 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:45Z] INFO  18:45:11,495 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T01:45Z] INFO  18:45:11,911 IntervalUtils - Processing 15651717 bp from intervals
[2016-04-15T01:45Z] WARN  18:45:11,911 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:45Z] WARN  18:45:11,911 IndexDictionaryUtils - Track variant2 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:45Z] WARN  18:45:11,912 IndexDictionaryUtils - Track variant3 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:45Z] WARN  18:45:11,912 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:45Z] INFO  18:45:11,920 MicroScheduler - Running the GATK in parallel mode with 16 total threads, 1 CPU thread(s) for each of 16 data thread(s), of 16 processors available on this machine
[2016-04-15T01:45Z] INFO  18:45:11,971 GenomeAnalysisEngine - Preparing for traversal
[2016-04-15T01:45Z] INFO  18:45:11,971 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:45Z] INFO  18:45:11,972 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:45Z] INFO  18:45:11,972 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T01:45Z] INFO  18:45:11,973 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T01:45Z] INFO  18:45:12,097 GenotypeGVCFs - Notice that the -ploidy parameter is ignored in GenotypeGVCFs tool as this is automatically determined by the input variant files
[2016-04-15T01:45Z] INFO  18:45:20,399 ProgressMeter -            done    397137.0     8.0 s      21.0 s      100.0%     8.0 s       0.0 s
[2016-04-15T01:45Z] INFO  18:45:20,399 ProgressMeter - Total runtime 8.43 secs, 0.14 min, 0.00 hours
[2016-04-15T01:45Z] INFO  18:45:22,417 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:45Z] GATK: GenotypeGVCFs
[2016-04-15T01:45Z] INFO  18:45:24,575 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:45Z] INFO  18:45:24,577 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:45Z] INFO  18:45:24,577 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:45Z] INFO  18:45:24,577 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:45Z] INFO  18:45:24,581 HelpFormatter - Program Args: -T GenotypeGVCFs -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/gatk-haplotype-joint/Batch1/5/tx/tmp4TOIwd/Batch1-5_31294068_49695124.vcf.gz -L 5:31294069-49695124 --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18106_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18105_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18102_kapa-NGv3-PE100-NGv3.vcf.gz --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -nt 16 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:45Z] INFO  18:45:24,589 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:45Z] INFO  18:45:24,589 HelpFormatter - Date/Time: 2016/04/14 18:45:24
[2016-04-15T01:45Z] INFO  18:45:24,589 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:45Z] INFO  18:45:24,589 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:45Z] INFO  18:45:24,661 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:45Z] INFO  18:45:24,758 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T01:45Z] INFO  18:45:25,174 IntervalUtils - Processing 18401056 bp from intervals
[2016-04-15T01:45Z] WARN  18:45:25,175 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:45Z] WARN  18:45:25,175 IndexDictionaryUtils - Track variant2 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:45Z] WARN  18:45:25,175 IndexDictionaryUtils - Track variant3 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:45Z] WARN  18:45:25,176 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:45Z] INFO  18:45:25,184 MicroScheduler - Running the GATK in parallel mode with 16 total threads, 1 CPU thread(s) for each of 16 data thread(s), of 16 processors available on this machine
[2016-04-15T01:45Z] INFO  18:45:25,233 GenomeAnalysisEngine - Preparing for traversal
[2016-04-15T01:45Z] INFO  18:45:25,234 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:45Z] INFO  18:45:25,235 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:45Z] INFO  18:45:25,235 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T01:45Z] INFO  18:45:25,235 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T01:45Z] INFO  18:45:25,357 GenotypeGVCFs - Notice that the -ploidy parameter is ignored in GenotypeGVCFs tool as this is automatically determined by the input variant files
[2016-04-15T01:45Z] INFO  18:45:35,153 ProgressMeter -            done    561342.0     9.0 s      17.0 s      100.0%     9.0 s       0.0 s
[2016-04-15T01:45Z] INFO  18:45:35,153 ProgressMeter - Total runtime 9.92 secs, 0.17 min, 0.00 hours
[2016-04-15T01:45Z] INFO  18:45:37,706 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:45Z] GATK: GenotypeGVCFs
[2016-04-15T01:45Z] INFO  18:45:39,767 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:45Z] INFO  18:45:39,769 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:45Z] INFO  18:45:39,770 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:45Z] INFO  18:45:39,770 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:45Z] INFO  18:45:39,773 HelpFormatter - Program Args: -T GenotypeGVCFs -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/gatk-haplotype-joint/Batch1/5/tx/tmp08QI0O/Batch1-5_49695692_65288736.vcf.gz -L 5:49695693-65288736 --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18106_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18105_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18102_kapa-NGv3-PE100-NGv3.vcf.gz --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -nt 16 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:45Z] INFO  18:45:39,782 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:45Z] INFO  18:45:39,782 HelpFormatter - Date/Time: 2016/04/14 18:45:39
[2016-04-15T01:45Z] INFO  18:45:39,782 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:45Z] INFO  18:45:39,782 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:45Z] INFO  18:45:39,855 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:45Z] INFO  18:45:39,956 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T01:45Z] INFO  18:45:40,366 IntervalUtils - Processing 15593044 bp from intervals
[2016-04-15T01:45Z] WARN  18:45:40,367 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:45Z] WARN  18:45:40,367 IndexDictionaryUtils - Track variant2 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:45Z] WARN  18:45:40,367 IndexDictionaryUtils - Track variant3 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:45Z] WARN  18:45:40,368 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:45Z] INFO  18:45:40,376 MicroScheduler - Running the GATK in parallel mode with 16 total threads, 1 CPU thread(s) for each of 16 data thread(s), of 16 processors available on this machine
[2016-04-15T01:45Z] INFO  18:45:40,426 GenomeAnalysisEngine - Preparing for traversal
[2016-04-15T01:45Z] INFO  18:45:40,427 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:45Z] INFO  18:45:40,427 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:45Z] INFO  18:45:40,428 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T01:45Z] INFO  18:45:40,428 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T01:45Z] INFO  18:45:40,552 GenotypeGVCFs - Notice that the -ploidy parameter is ignored in GenotypeGVCFs tool as this is automatically determined by the input variant files
[2016-04-15T01:45Z] INFO  18:45:50,281 ProgressMeter -            done    448722.0     9.0 s      21.0 s      100.0%     9.0 s       0.0 s
[2016-04-15T01:45Z] INFO  18:45:50,282 ProgressMeter - Total runtime 9.85 secs, 0.16 min, 0.00 hours
[2016-04-15T01:45Z] INFO  18:45:52,615 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:45Z] GATK: GenotypeGVCFs
[2016-04-15T01:45Z] INFO  18:45:54,710 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:45Z] INFO  18:45:54,712 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:45Z] INFO  18:45:54,713 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:45Z] INFO  18:45:54,713 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:45Z] INFO  18:45:54,716 HelpFormatter - Program Args: -T GenotypeGVCFs -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/gatk-haplotype-joint/Batch1/5/tx/tmpCPYqy2/Batch1-5_65290574_80809536.vcf.gz -L 5:65290575-80809536 --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18106_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18105_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18102_kapa-NGv3-PE100-NGv3.vcf.gz --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -nt 16 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:45Z] INFO  18:45:54,725 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:45Z] INFO  18:45:54,726 HelpFormatter - Date/Time: 2016/04/14 18:45:54
[2016-04-15T01:45Z] INFO  18:45:54,726 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:45Z] INFO  18:45:54,726 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:45Z] INFO  18:45:54,798 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:45Z] INFO  18:45:54,897 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T01:45Z] INFO  18:45:55,306 IntervalUtils - Processing 15518962 bp from intervals
[2016-04-15T01:45Z] WARN  18:45:55,307 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:45Z] WARN  18:45:55,307 IndexDictionaryUtils - Track variant2 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:45Z] WARN  18:45:55,308 IndexDictionaryUtils - Track variant3 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:45Z] WARN  18:45:55,308 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:45Z] INFO  18:45:55,316 MicroScheduler - Running the GATK in parallel mode with 16 total threads, 1 CPU thread(s) for each of 16 data thread(s), of 16 processors available on this machine
[2016-04-15T01:45Z] INFO  18:45:55,366 GenomeAnalysisEngine - Preparing for traversal
[2016-04-15T01:45Z] INFO  18:45:55,367 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:45Z] INFO  18:45:55,367 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:45Z] INFO  18:45:55,368 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T01:45Z] INFO  18:45:55,368 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T01:45Z] INFO  18:45:55,495 GenotypeGVCFs - Notice that the -ploidy parameter is ignored in GenotypeGVCFs tool as this is automatically determined by the input variant files
[2016-04-15T01:46Z] INFO  18:46:05,244 ProgressMeter -            done    511509.0     9.0 s      19.0 s      100.0%     9.0 s       0.0 s
[2016-04-15T01:46Z] INFO  18:46:05,244 ProgressMeter - Total runtime 9.88 secs, 0.16 min, 0.00 hours
[2016-04-15T01:46Z] INFO  18:46:07,539 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:46Z] GATK: GenotypeGVCFs
[2016-04-15T01:46Z] INFO  18:46:09,674 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:46Z] INFO  18:46:09,676 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:46Z] INFO  18:46:09,676 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:46Z] INFO  18:46:09,677 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:46Z] INFO  18:46:09,680 HelpFormatter - Program Args: -T GenotypeGVCFs -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/gatk-haplotype-joint/Batch1/5/tx/tmpKcBdeJ/Batch1-5_80911291_96430739.vcf.gz -L 5:80911292-96430739 --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18106_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18105_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18102_kapa-NGv3-PE100-NGv3.vcf.gz --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -nt 16 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:46Z] INFO  18:46:09,689 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:46Z] INFO  18:46:09,689 HelpFormatter - Date/Time: 2016/04/14 18:46:09
[2016-04-15T01:46Z] INFO  18:46:09,689 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:46Z] INFO  18:46:09,689 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:46Z] INFO  18:46:09,761 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:46Z] INFO  18:46:09,860 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T01:46Z] INFO  18:46:10,275 IntervalUtils - Processing 15519448 bp from intervals
[2016-04-15T01:46Z] WARN  18:46:10,275 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:46Z] WARN  18:46:10,276 IndexDictionaryUtils - Track variant2 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:46Z] WARN  18:46:10,276 IndexDictionaryUtils - Track variant3 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:46Z] WARN  18:46:10,276 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:46Z] INFO  18:46:10,284 MicroScheduler - Running the GATK in parallel mode with 16 total threads, 1 CPU thread(s) for each of 16 data thread(s), of 16 processors available on this machine
[2016-04-15T01:46Z] INFO  18:46:10,334 GenomeAnalysisEngine - Preparing for traversal
[2016-04-15T01:46Z] INFO  18:46:10,335 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:46Z] INFO  18:46:10,335 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:46Z] INFO  18:46:10,335 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T01:46Z] INFO  18:46:10,336 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T01:46Z] INFO  18:46:10,459 GenotypeGVCFs - Notice that the -ploidy parameter is ignored in GenotypeGVCFs tool as this is automatically determined by the input variant files
[2016-04-15T01:46Z] INFO  18:46:20,579 ProgressMeter -            done    426988.0    10.0 s      23.0 s      100.0%    10.0 s       0.0 s
[2016-04-15T01:46Z] INFO  18:46:20,580 ProgressMeter - Total runtime 10.24 secs, 0.17 min, 0.00 hours
[2016-04-15T01:46Z] INFO  18:46:22,718 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:46Z] GATK: GenotypeGVCFs
[2016-04-15T01:46Z] INFO  18:46:24,759 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:46Z] INFO  18:46:24,761 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:46Z] INFO  18:46:24,761 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:46Z] INFO  18:46:24,762 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:46Z] INFO  18:46:24,765 HelpFormatter - Program Args: -T GenotypeGVCFs -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/gatk-haplotype-joint/Batch1/5/tx/tmpNmraAK/Batch1-5_96432513_112043579.vcf.gz -L 5:96432514-112043579 --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18106_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18105_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18102_kapa-NGv3-PE100-NGv3.vcf.gz --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -nt 16 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:46Z] INFO  18:46:24,773 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:46Z] INFO  18:46:24,773 HelpFormatter - Date/Time: 2016/04/14 18:46:24
[2016-04-15T01:46Z] INFO  18:46:24,774 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:46Z] INFO  18:46:24,774 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:46Z] INFO  18:46:24,845 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:46Z] INFO  18:46:24,943 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T01:46Z] INFO  18:46:25,354 IntervalUtils - Processing 15611066 bp from intervals
[2016-04-15T01:46Z] WARN  18:46:25,355 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:46Z] WARN  18:46:25,355 IndexDictionaryUtils - Track variant2 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:46Z] WARN  18:46:25,355 IndexDictionaryUtils - Track variant3 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:46Z] WARN  18:46:25,356 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:46Z] INFO  18:46:25,364 MicroScheduler - Running the GATK in parallel mode with 16 total threads, 1 CPU thread(s) for each of 16 data thread(s), of 16 processors available on this machine
[2016-04-15T01:46Z] INFO  18:46:25,413 GenomeAnalysisEngine - Preparing for traversal
[2016-04-15T01:46Z] INFO  18:46:25,414 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:46Z] INFO  18:46:25,415 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:46Z] INFO  18:46:25,415 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T01:46Z] INFO  18:46:25,415 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T01:46Z] INFO  18:46:25,537 GenotypeGVCFs - Notice that the -ploidy parameter is ignored in GenotypeGVCFs tool as this is automatically determined by the input variant files
[2016-04-15T01:46Z] INFO  18:46:34,447 ProgressMeter -            done    420804.0     9.0 s      21.0 s      100.0%     9.0 s       0.0 s
[2016-04-15T01:46Z] INFO  18:46:34,448 ProgressMeter - Total runtime 9.03 secs, 0.15 min, 0.00 hours
[2016-04-15T01:46Z] INFO  18:46:36,891 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:46Z] GATK: GenotypeGVCFs
[2016-04-15T01:46Z] INFO  18:46:38,822 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:46Z] INFO  18:46:38,824 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:46Z] INFO  18:46:38,824 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:46Z] INFO  18:46:38,825 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:46Z] INFO  18:46:38,828 HelpFormatter - Program Args: -T GenotypeGVCFs -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/gatk-haplotype-joint/Batch1/5/tx/tmpbxV2eQ/Batch1-5_112073555_127595521.vcf.gz -L 5:112073556-127595521 --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18106_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18105_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18102_kapa-NGv3-PE100-NGv3.vcf.gz --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -nt 16 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:46Z] INFO  18:46:38,836 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:46Z] INFO  18:46:38,837 HelpFormatter - Date/Time: 2016/04/14 18:46:38
[2016-04-15T01:46Z] INFO  18:46:38,837 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:46Z] INFO  18:46:38,837 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:46Z] INFO  18:46:38,908 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:46Z] INFO  18:46:39,006 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T01:46Z] INFO  18:46:39,414 IntervalUtils - Processing 15521966 bp from intervals
[2016-04-15T01:46Z] WARN  18:46:39,415 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:46Z] WARN  18:46:39,415 IndexDictionaryUtils - Track variant2 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:46Z] WARN  18:46:39,415 IndexDictionaryUtils - Track variant3 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:46Z] WARN  18:46:39,415 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:46Z] INFO  18:46:39,424 MicroScheduler - Running the GATK in parallel mode with 16 total threads, 1 CPU thread(s) for each of 16 data thread(s), of 16 processors available on this machine
[2016-04-15T01:46Z] INFO  18:46:39,474 GenomeAnalysisEngine - Preparing for traversal
[2016-04-15T01:46Z] INFO  18:46:39,475 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:46Z] INFO  18:46:39,475 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:46Z] INFO  18:46:39,476 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T01:46Z] INFO  18:46:39,476 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T01:46Z] INFO  18:46:39,599 GenotypeGVCFs - Notice that the -ploidy parameter is ignored in GenotypeGVCFs tool as this is automatically determined by the input variant files
[2016-04-15T01:46Z] INFO  18:46:49,482 ProgressMeter -            done    487876.0    10.0 s      20.0 s      100.0%    10.0 s       0.0 s
[2016-04-15T01:46Z] INFO  18:46:49,482 ProgressMeter - Total runtime 10.01 secs, 0.17 min, 0.00 hours
[2016-04-15T01:46Z] INFO  18:46:51,497 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:46Z] GATK: GenotypeGVCFs
[2016-04-15T01:46Z] INFO  18:46:53,677 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:46Z] INFO  18:46:53,679 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:46Z] INFO  18:46:53,679 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:46Z] INFO  18:46:53,679 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:46Z] INFO  18:46:53,683 HelpFormatter - Program Args: -T GenotypeGVCFs -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/gatk-haplotype-joint/Batch1/5/tx/tmpUmhUQ1/Batch1-5_127597427_143191869.vcf.gz -L 5:127597428-143191869 --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18106_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18105_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18102_kapa-NGv3-PE100-NGv3.vcf.gz --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -nt 16 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:46Z] INFO  18:46:53,692 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:46Z] INFO  18:46:53,692 HelpFormatter - Date/Time: 2016/04/14 18:46:53
[2016-04-15T01:46Z] INFO  18:46:53,693 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:46Z] INFO  18:46:53,693 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:46Z] INFO  18:46:53,768 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:46Z] INFO  18:46:53,868 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T01:46Z] INFO  18:46:54,569 IntervalUtils - Processing 15594442 bp from intervals
[2016-04-15T01:46Z] WARN  18:46:54,571 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:46Z] WARN  18:46:54,571 IndexDictionaryUtils - Track variant2 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:46Z] WARN  18:46:54,572 IndexDictionaryUtils - Track variant3 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:46Z] WARN  18:46:54,572 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:46Z] INFO  18:46:54,593 MicroScheduler - Running the GATK in parallel mode with 16 total threads, 1 CPU thread(s) for each of 16 data thread(s), of 16 processors available on this machine
[2016-04-15T01:46Z] INFO  18:46:54,714 GenomeAnalysisEngine - Preparing for traversal
[2016-04-15T01:46Z] INFO  18:46:54,716 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:46Z] INFO  18:46:54,717 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:46Z] INFO  18:46:54,718 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T01:46Z] INFO  18:46:54,719 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T01:46Z] INFO  18:46:54,977 GenotypeGVCFs - Notice that the -ploidy parameter is ignored in GenotypeGVCFs tool as this is automatically determined by the input variant files
[2016-04-15T01:47Z] INFO  18:47:04,221 ProgressMeter -            done    712581.0     9.0 s      13.0 s      100.0%     9.0 s       0.0 s
[2016-04-15T01:47Z] INFO  18:47:04,221 ProgressMeter - Total runtime 9.50 secs, 0.16 min, 0.00 hours
[2016-04-15T01:47Z] INFO  18:47:06,768 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:47Z] GATK: GenotypeGVCFs
[2016-04-15T01:47Z] INFO  18:47:08,767 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:47Z] INFO  18:47:08,769 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:47Z] INFO  18:47:08,769 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:47Z] INFO  18:47:08,770 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:47Z] INFO  18:47:08,773 HelpFormatter - Program Args: -T GenotypeGVCFs -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/gatk-haplotype-joint/Batch1/5/tx/tmpdVObbP/Batch1-5_143200044_158710347.vcf.gz -L 5:143200045-158710347 --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18106_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18105_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18102_kapa-NGv3-PE100-NGv3.vcf.gz --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -nt 16 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:47Z] INFO  18:47:08,781 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:47Z] INFO  18:47:08,781 HelpFormatter - Date/Time: 2016/04/14 18:47:08
[2016-04-15T01:47Z] INFO  18:47:08,782 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:47Z] INFO  18:47:08,782 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:47Z] INFO  18:47:08,853 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:47Z] INFO  18:47:08,952 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T01:47Z] INFO  18:47:09,363 IntervalUtils - Processing 15510303 bp from intervals
[2016-04-15T01:47Z] WARN  18:47:09,363 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:47Z] WARN  18:47:09,364 IndexDictionaryUtils - Track variant2 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:47Z] WARN  18:47:09,364 IndexDictionaryUtils - Track variant3 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:47Z] WARN  18:47:09,364 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:47Z] INFO  18:47:09,372 MicroScheduler - Running the GATK in parallel mode with 16 total threads, 1 CPU thread(s) for each of 16 data thread(s), of 16 processors available on this machine
[2016-04-15T01:47Z] INFO  18:47:09,422 GenomeAnalysisEngine - Preparing for traversal
[2016-04-15T01:47Z] INFO  18:47:09,423 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:47Z] INFO  18:47:09,423 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:47Z] INFO  18:47:09,423 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T01:47Z] INFO  18:47:09,424 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T01:47Z] INFO  18:47:09,546 GenotypeGVCFs - Notice that the -ploidy parameter is ignored in GenotypeGVCFs tool as this is automatically determined by the input variant files
[2016-04-15T01:47Z] INFO  18:47:19,500 ProgressMeter -            done    553190.0    10.0 s      18.0 s      100.0%    10.0 s       0.0 s
[2016-04-15T01:47Z] INFO  18:47:19,500 ProgressMeter - Total runtime 10.08 secs, 0.17 min, 0.00 hours
[2016-04-15T01:47Z] INFO  18:47:21,876 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:47Z] GATK: GenotypeGVCFs
[2016-04-15T01:47Z] INFO  18:47:23,839 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:47Z] INFO  18:47:23,841 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:47Z] INFO  18:47:23,841 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:47Z] INFO  18:47:23,841 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:47Z] INFO  18:47:23,845 HelpFormatter - Program Args: -T GenotypeGVCFs -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/gatk-haplotype-joint/Batch1/5/tx/tmpuFnvCv/Batch1-5_158711911_174870102.vcf.gz -L 5:158711912-174870102 --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18106_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18105_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18102_kapa-NGv3-PE100-NGv3.vcf.gz --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -nt 16 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:47Z] INFO  18:47:23,854 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:47Z] INFO  18:47:23,854 HelpFormatter - Date/Time: 2016/04/14 18:47:23
[2016-04-15T01:47Z] INFO  18:47:23,854 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:47Z] INFO  18:47:23,854 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:47Z] INFO  18:47:23,931 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:47Z] INFO  18:47:24,038 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T01:47Z] INFO  18:47:24,539 IntervalUtils - Processing 16158191 bp from intervals
[2016-04-15T01:47Z] WARN  18:47:24,539 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:47Z] WARN  18:47:24,540 IndexDictionaryUtils - Track variant2 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:47Z] WARN  18:47:24,540 IndexDictionaryUtils - Track variant3 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:47Z] WARN  18:47:24,540 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:47Z] INFO  18:47:24,549 MicroScheduler - Running the GATK in parallel mode with 16 total threads, 1 CPU thread(s) for each of 16 data thread(s), of 16 processors available on this machine
[2016-04-15T01:47Z] INFO  18:47:24,601 GenomeAnalysisEngine - Preparing for traversal
[2016-04-15T01:47Z] INFO  18:47:24,602 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:47Z] INFO  18:47:24,603 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:47Z] INFO  18:47:24,603 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T01:47Z] INFO  18:47:24,604 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T01:47Z] INFO  18:47:24,733 GenotypeGVCFs - Notice that the -ploidy parameter is ignored in GenotypeGVCFs tool as this is automatically determined by the input variant files
[2016-04-15T01:47Z] INFO  18:47:34,838 ProgressMeter -            done    481085.0    10.0 s      21.0 s      100.0%    10.0 s       0.0 s
[2016-04-15T01:47Z] INFO  18:47:34,839 ProgressMeter - Total runtime 10.24 secs, 0.17 min, 0.00 hours
[2016-04-15T01:47Z] INFO  18:47:36,834 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:47Z] GATK: GenotypeGVCFs
[2016-04-15T01:47Z] INFO  18:47:38,796 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:47Z] INFO  18:47:38,798 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:47Z] INFO  18:47:38,798 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:47Z] INFO  18:47:38,799 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:47Z] INFO  18:47:38,802 HelpFormatter - Program Args: -T GenotypeGVCFs -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/gatk-haplotype-joint/Batch1/5/tx/tmpYuUvjG/Batch1-5_174919106_180915260.vcf.gz -L 5:174919107-180915260 --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18106_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18105_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18102_kapa-NGv3-PE100-NGv3.vcf.gz --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -nt 16 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:47Z] INFO  18:47:38,810 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:47Z] INFO  18:47:38,810 HelpFormatter - Date/Time: 2016/04/14 18:47:38
[2016-04-15T01:47Z] INFO  18:47:38,811 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:47Z] INFO  18:47:38,811 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:47Z] INFO  18:47:38,882 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:47Z] INFO  18:47:38,979 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T01:47Z] INFO  18:47:39,389 IntervalUtils - Processing 5996154 bp from intervals
[2016-04-15T01:47Z] WARN  18:47:39,389 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:47Z] WARN  18:47:39,389 IndexDictionaryUtils - Track variant2 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:47Z] WARN  18:47:39,390 IndexDictionaryUtils - Track variant3 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:47Z] WARN  18:47:39,390 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:47Z] INFO  18:47:39,398 MicroScheduler - Running the GATK in parallel mode with 16 total threads, 1 CPU thread(s) for each of 16 data thread(s), of 16 processors available on this machine
[2016-04-15T01:47Z] INFO  18:47:39,448 GenomeAnalysisEngine - Preparing for traversal
[2016-04-15T01:47Z] INFO  18:47:39,449 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:47Z] INFO  18:47:39,449 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:47Z] INFO  18:47:39,449 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T01:47Z] INFO  18:47:39,450 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T01:47Z] INFO  18:47:39,576 GenotypeGVCFs - Notice that the -ploidy parameter is ignored in GenotypeGVCFs tool as this is automatically determined by the input variant files
[2016-04-15T01:47Z] INFO  18:47:43,862 ProgressMeter -            done    308335.0     4.0 s      14.0 s       99.8%     4.0 s       0.0 s
[2016-04-15T01:47Z] INFO  18:47:43,862 ProgressMeter - Total runtime 4.41 secs, 0.07 min, 0.00 hours
[2016-04-15T01:47Z] INFO  18:47:45,293 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:47Z] GATK: GenotypeGVCFs
[2016-04-15T01:47Z] INFO  18:47:47,292 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:47Z] INFO  18:47:47,294 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:47Z] INFO  18:47:47,294 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:47Z] INFO  18:47:47,294 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:47Z] INFO  18:47:47,298 HelpFormatter - Program Args: -T GenotypeGVCFs -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/gatk-haplotype-joint/Batch1/6/tx/tmp88iktB/Batch1-6_0_15509601.vcf.gz -L 6:1-15509601 --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18106_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18105_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18102_kapa-NGv3-PE100-NGv3.vcf.gz --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -nt 16 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:47Z] INFO  18:47:47,306 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:47Z] INFO  18:47:47,306 HelpFormatter - Date/Time: 2016/04/14 18:47:47
[2016-04-15T01:47Z] INFO  18:47:47,306 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:47Z] INFO  18:47:47,306 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:47Z] INFO  18:47:47,378 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:47Z] INFO  18:47:47,476 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T01:47Z] INFO  18:47:47,885 IntervalUtils - Processing 15509601 bp from intervals
[2016-04-15T01:47Z] WARN  18:47:47,886 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:47Z] WARN  18:47:47,886 IndexDictionaryUtils - Track variant2 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:47Z] WARN  18:47:47,886 IndexDictionaryUtils - Track variant3 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:47Z] WARN  18:47:47,886 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:47Z] INFO  18:47:47,894 MicroScheduler - Running the GATK in parallel mode with 16 total threads, 1 CPU thread(s) for each of 16 data thread(s), of 16 processors available on this machine
[2016-04-15T01:47Z] INFO  18:47:47,944 GenomeAnalysisEngine - Preparing for traversal
[2016-04-15T01:47Z] INFO  18:47:47,945 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:47Z] INFO  18:47:47,946 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:47Z] INFO  18:47:47,946 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T01:47Z] INFO  18:47:47,947 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T01:47Z] INFO  18:47:48,072 GenotypeGVCFs - Notice that the -ploidy parameter is ignored in GenotypeGVCFs tool as this is automatically determined by the input variant files
[2016-04-15T01:47Z] INFO  18:47:57,959 ProgressMeter -            done    574949.0    10.0 s      17.0 s      100.0%    10.0 s       0.0 s
[2016-04-15T01:47Z] INFO  18:47:57,959 ProgressMeter - Total runtime 10.01 secs, 0.17 min, 0.00 hours
[2016-04-15T01:48Z] INFO  18:48:00,453 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:48Z] GATK: GenotypeGVCFs
[2016-04-15T01:48Z] INFO  18:48:02,641 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:48Z] INFO  18:48:02,643 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:48Z] INFO  18:48:02,644 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:48Z] INFO  18:48:02,644 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:48Z] INFO  18:48:02,647 HelpFormatter - Program Args: -T GenotypeGVCFs -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/gatk-haplotype-joint/Batch1/6/tx/tmpRIXGcD/Batch1-6_15511526_31080332.vcf.gz -L 6:15511527-31080332 --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18106_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18105_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18102_kapa-NGv3-PE100-NGv3.vcf.gz --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -nt 16 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:48Z] INFO  18:48:02,655 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:48Z] INFO  18:48:02,656 HelpFormatter - Date/Time: 2016/04/14 18:48:02
[2016-04-15T01:48Z] INFO  18:48:02,656 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:48Z] INFO  18:48:02,656 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:48Z] INFO  18:48:02,728 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:48Z] INFO  18:48:02,826 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T01:48Z] INFO  18:48:03,238 IntervalUtils - Processing 15568806 bp from intervals
[2016-04-15T01:48Z] WARN  18:48:03,239 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:48Z] WARN  18:48:03,239 IndexDictionaryUtils - Track variant2 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:48Z] WARN  18:48:03,239 IndexDictionaryUtils - Track variant3 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:48Z] WARN  18:48:03,239 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:48Z] INFO  18:48:03,247 MicroScheduler - Running the GATK in parallel mode with 16 total threads, 1 CPU thread(s) for each of 16 data thread(s), of 16 processors available on this machine
[2016-04-15T01:48Z] INFO  18:48:03,297 GenomeAnalysisEngine - Preparing for traversal
[2016-04-15T01:48Z] INFO  18:48:03,298 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:48Z] INFO  18:48:03,299 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:48Z] INFO  18:48:03,299 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T01:48Z] INFO  18:48:03,299 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T01:48Z] INFO  18:48:03,421 GenotypeGVCFs - Notice that the -ploidy parameter is ignored in GenotypeGVCFs tool as this is automatically determined by the input variant files
[2016-04-15T01:48Z] INFO  18:48:13,352 ProgressMeter -            done    622315.0    10.0 s      16.0 s      100.0%    10.0 s       0.0 s
[2016-04-15T01:48Z] INFO  18:48:13,352 ProgressMeter - Total runtime 10.05 secs, 0.17 min, 0.00 hours
[2016-04-15T01:48Z] INFO  18:48:15,877 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:48Z] GATK: GenotypeGVCFs
[2016-04-15T01:48Z] INFO  18:48:17,515 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:48Z] INFO  18:48:17,516 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:48Z] INFO  18:48:17,517 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:48Z] INFO  18:48:17,517 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:48Z] INFO  18:48:17,520 HelpFormatter - Program Args: -T GenotypeGVCFs -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/gatk-haplotype-joint/Batch1/6/tx/tmpxZC4m4/Batch1-6_31083801_46593245.vcf.gz -L 6:31083802-46593245 --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18106_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18105_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18102_kapa-NGv3-PE100-NGv3.vcf.gz --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -nt 16 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:48Z] INFO  18:48:17,529 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:48Z] INFO  18:48:17,529 HelpFormatter - Date/Time: 2016/04/14 18:48:17
[2016-04-15T01:48Z] INFO  18:48:17,529 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:48Z] INFO  18:48:17,529 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:48Z] INFO  18:48:17,600 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:48Z] INFO  18:48:17,700 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T01:48Z] INFO  18:48:18,114 IntervalUtils - Processing 15509444 bp from intervals
[2016-04-15T01:48Z] WARN  18:48:18,115 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:48Z] WARN  18:48:18,115 IndexDictionaryUtils - Track variant2 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:48Z] WARN  18:48:18,115 IndexDictionaryUtils - Track variant3 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:48Z] WARN  18:48:18,116 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:48Z] INFO  18:48:18,124 MicroScheduler - Running the GATK in parallel mode with 16 total threads, 1 CPU thread(s) for each of 16 data thread(s), of 16 processors available on this machine
[2016-04-15T01:48Z] INFO  18:48:18,174 GenomeAnalysisEngine - Preparing for traversal
[2016-04-15T01:48Z] INFO  18:48:18,174 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:48Z] INFO  18:48:18,175 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:48Z] INFO  18:48:18,175 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T01:48Z] INFO  18:48:18,176 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T01:48Z] INFO  18:48:18,297 GenotypeGVCFs - Notice that the -ploidy parameter is ignored in GenotypeGVCFs tool as this is automatically determined by the input variant files
[2016-04-15T01:48Z] WARN  18:48:22,233 ExactAFCalculator - this tool is currently set to genotype at most 6 alternate alleles in a given context, but the context at 6:43238152 has 10 alternate alleles so only the top alleles will be used; see the --max_alternate_alleles argument
[2016-04-15T01:48Z] INFO  18:48:29,572 ProgressMeter -            done    904371.0    11.0 s      12.0 s      100.0%    11.0 s       0.0 s
[2016-04-15T01:48Z] INFO  18:48:29,572 ProgressMeter - Total runtime 11.40 secs, 0.19 min, 0.00 hours
[2016-04-15T01:48Z] INFO  18:48:32,034 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:48Z] GATK: GenotypeGVCFs
[2016-04-15T01:48Z] INFO  18:48:34,162 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:48Z] INFO  18:48:34,164 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:48Z] INFO  18:48:34,164 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:48Z] INFO  18:48:34,164 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:48Z] INFO  18:48:34,168 HelpFormatter - Program Args: -T GenotypeGVCFs -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/gatk-haplotype-joint/Batch1/6/tx/tmpDhQOt9/Batch1-6_46598699_62284307.vcf.gz -L 6:46598700-62284307 --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18106_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18105_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18102_kapa-NGv3-PE100-NGv3.vcf.gz --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -nt 16 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:48Z] INFO  18:48:34,176 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:48Z] INFO  18:48:34,176 HelpFormatter - Date/Time: 2016/04/14 18:48:34
[2016-04-15T01:48Z] INFO  18:48:34,177 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:48Z] INFO  18:48:34,177 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:48Z] INFO  18:48:34,248 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:48Z] INFO  18:48:34,345 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T01:48Z] INFO  18:48:34,761 IntervalUtils - Processing 15685608 bp from intervals
[2016-04-15T01:48Z] WARN  18:48:34,761 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:48Z] WARN  18:48:34,762 IndexDictionaryUtils - Track variant2 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:48Z] WARN  18:48:34,762 IndexDictionaryUtils - Track variant3 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:48Z] WARN  18:48:34,762 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:48Z] INFO  18:48:34,771 MicroScheduler - Running the GATK in parallel mode with 16 total threads, 1 CPU thread(s) for each of 16 data thread(s), of 16 processors available on this machine
[2016-04-15T01:48Z] INFO  18:48:34,820 GenomeAnalysisEngine - Preparing for traversal
[2016-04-15T01:48Z] INFO  18:48:34,821 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:48Z] INFO  18:48:34,822 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:48Z] INFO  18:48:34,822 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T01:48Z] INFO  18:48:34,822 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T01:48Z] INFO  18:48:34,946 GenotypeGVCFs - Notice that the -ploidy parameter is ignored in GenotypeGVCFs tool as this is automatically determined by the input variant files
[2016-04-15T01:48Z] INFO  18:48:44,473 ProgressMeter -            done    461987.0     9.0 s      20.0 s      100.0%     9.0 s       0.0 s
[2016-04-15T01:48Z] INFO  18:48:44,474 ProgressMeter - Total runtime 9.65 secs, 0.16 min, 0.00 hours
[2016-04-15T01:48Z] INFO  18:48:46,494 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:48Z] GATK: GenotypeGVCFs
[2016-04-15T01:48Z] INFO  18:48:48,151 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:48Z] INFO  18:48:48,153 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:48Z] INFO  18:48:48,153 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:48Z] INFO  18:48:48,153 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:48Z] INFO  18:48:48,157 HelpFormatter - Program Args: -T GenotypeGVCFs -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/gatk-haplotype-joint/Batch1/6/tx/tmpn8rRKy/Batch1-6_62390867_78173120.vcf.gz -L 6:62390868-78173120 --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18106_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18105_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18102_kapa-NGv3-PE100-NGv3.vcf.gz --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -nt 16 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:48Z] INFO  18:48:48,166 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:48Z] INFO  18:48:48,167 HelpFormatter - Date/Time: 2016/04/14 18:48:48
[2016-04-15T01:48Z] INFO  18:48:48,167 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:48Z] INFO  18:48:48,167 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:48Z] INFO  18:48:48,246 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:48Z] INFO  18:48:48,351 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T01:48Z] INFO  18:48:48,830 IntervalUtils - Processing 15782253 bp from intervals
[2016-04-15T01:48Z] WARN  18:48:48,831 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:48Z] WARN  18:48:48,831 IndexDictionaryUtils - Track variant2 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:48Z] WARN  18:48:48,831 IndexDictionaryUtils - Track variant3 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:48Z] WARN  18:48:48,832 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:48Z] INFO  18:48:48,841 MicroScheduler - Running the GATK in parallel mode with 16 total threads, 1 CPU thread(s) for each of 16 data thread(s), of 16 processors available on this machine
[2016-04-15T01:48Z] INFO  18:48:48,893 GenomeAnalysisEngine - Preparing for traversal
[2016-04-15T01:48Z] INFO  18:48:48,895 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:48Z] INFO  18:48:48,895 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:48Z] INFO  18:48:48,895 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T01:48Z] INFO  18:48:48,896 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T01:48Z] INFO  18:48:49,028 GenotypeGVCFs - Notice that the -ploidy parameter is ignored in GenotypeGVCFs tool as this is automatically determined by the input variant files
[2016-04-15T01:48Z] INFO  18:48:58,941 ProgressMeter -            done    473674.0    10.0 s      21.0 s      100.0%    10.0 s       0.0 s
[2016-04-15T01:48Z] INFO  18:48:58,942 ProgressMeter - Total runtime 10.05 secs, 0.17 min, 0.00 hours
[2016-04-15T01:49Z] INFO  18:49:01,013 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:49Z] GATK: GenotypeGVCFs
[2016-04-15T01:49Z] INFO  18:49:03,089 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:49Z] INFO  18:49:03,091 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:49Z] INFO  18:49:03,091 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:49Z] INFO  18:49:03,091 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:49Z] INFO  18:49:03,095 HelpFormatter - Program Args: -T GenotypeGVCFs -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/gatk-haplotype-joint/Batch1/6/tx/tmpTDljk3/Batch1-6_78400388_93953258.vcf.gz -L 6:78400389-93953258 --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18106_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18105_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18102_kapa-NGv3-PE100-NGv3.vcf.gz --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -nt 16 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:49Z] INFO  18:49:03,103 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:49Z] INFO  18:49:03,103 HelpFormatter - Date/Time: 2016/04/14 18:49:03
[2016-04-15T01:49Z] INFO  18:49:03,103 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:49Z] INFO  18:49:03,104 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:49Z] INFO  18:49:03,176 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:49Z] INFO  18:49:03,274 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T01:49Z] INFO  18:49:03,624 IntervalUtils - Processing 15552870 bp from intervals
[2016-04-15T01:49Z] WARN  18:49:03,625 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:49Z] WARN  18:49:03,625 IndexDictionaryUtils - Track variant2 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:49Z] WARN  18:49:03,625 IndexDictionaryUtils - Track variant3 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:49Z] WARN  18:49:03,625 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:49Z] INFO  18:49:03,634 MicroScheduler - Running the GATK in parallel mode with 16 total threads, 1 CPU thread(s) for each of 16 data thread(s), of 16 processors available on this machine
[2016-04-15T01:49Z] INFO  18:49:03,684 GenomeAnalysisEngine - Preparing for traversal
[2016-04-15T01:49Z] INFO  18:49:03,685 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:49Z] INFO  18:49:03,685 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:49Z] INFO  18:49:03,685 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T01:49Z] INFO  18:49:03,686 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T01:49Z] INFO  18:49:03,808 GenotypeGVCFs - Notice that the -ploidy parameter is ignored in GenotypeGVCFs tool as this is automatically determined by the input variant files
[2016-04-15T01:49Z] INFO  18:49:13,379 ProgressMeter -            done    489334.0     9.0 s      19.0 s      100.0%     9.0 s       0.0 s
[2016-04-15T01:49Z] INFO  18:49:13,379 ProgressMeter - Total runtime 9.69 secs, 0.16 min, 0.00 hours
[2016-04-15T01:49Z] INFO  18:49:15,678 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:49Z] GATK: GenotypeGVCFs
[2016-04-15T01:49Z] INFO  18:49:17,746 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:49Z] INFO  18:49:17,748 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:49Z] INFO  18:49:17,749 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:49Z] INFO  18:49:17,749 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:49Z] INFO  18:49:17,752 HelpFormatter - Program Args: -T GenotypeGVCFs -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/gatk-haplotype-joint/Batch1/6/tx/tmpNqeGuT/Batch1-6_93955015_109466584.vcf.gz -L 6:93955016-109466584 --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18106_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18105_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18102_kapa-NGv3-PE100-NGv3.vcf.gz --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -nt 16 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:49Z] INFO  18:49:17,760 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:49Z] INFO  18:49:17,761 HelpFormatter - Date/Time: 2016/04/14 18:49:17
[2016-04-15T01:49Z] INFO  18:49:17,761 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:49Z] INFO  18:49:17,761 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:49Z] INFO  18:49:17,832 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:49Z] INFO  18:49:17,930 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T01:49Z] INFO  18:49:18,349 IntervalUtils - Processing 15511569 bp from intervals
[2016-04-15T01:49Z] WARN  18:49:18,349 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:49Z] WARN  18:49:18,350 IndexDictionaryUtils - Track variant2 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:49Z] WARN  18:49:18,350 IndexDictionaryUtils - Track variant3 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:49Z] WARN  18:49:18,350 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:49Z] INFO  18:49:18,358 MicroScheduler - Running the GATK in parallel mode with 16 total threads, 1 CPU thread(s) for each of 16 data thread(s), of 16 processors available on this machine
[2016-04-15T01:49Z] INFO  18:49:18,408 GenomeAnalysisEngine - Preparing for traversal
[2016-04-15T01:49Z] INFO  18:49:18,409 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:49Z] INFO  18:49:18,409 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:49Z] INFO  18:49:18,409 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T01:49Z] INFO  18:49:18,410 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T01:49Z] INFO  18:49:18,532 GenotypeGVCFs - Notice that the -ploidy parameter is ignored in GenotypeGVCFs tool as this is automatically determined by the input variant files
[2016-04-15T01:49Z] INFO  18:49:27,677 ProgressMeter -            done    433354.0     9.0 s      21.0 s      100.0%     9.0 s       0.0 s
[2016-04-15T01:49Z] INFO  18:49:27,677 ProgressMeter - Total runtime 9.27 secs, 0.15 min, 0.00 hours
[2016-04-15T01:49Z] INFO  18:49:30,056 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:49Z] GATK: GenotypeGVCFs
[2016-04-15T01:49Z] INFO  18:49:32,181 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:49Z] INFO  18:49:32,183 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:49Z] INFO  18:49:32,183 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:49Z] INFO  18:49:32,184 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:49Z] INFO  18:49:32,187 HelpFormatter - Program Args: -T GenotypeGVCFs -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/gatk-haplotype-joint/Batch1/6/tx/tmpJbVg8p/Batch1-6_109467960_124979532.vcf.gz -L 6:109467961-124979532 --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18106_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18105_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18102_kapa-NGv3-PE100-NGv3.vcf.gz --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -nt 16 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:49Z] INFO  18:49:32,196 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:49Z] INFO  18:49:32,196 HelpFormatter - Date/Time: 2016/04/14 18:49:32
[2016-04-15T01:49Z] INFO  18:49:32,197 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:49Z] INFO  18:49:32,197 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:49Z] INFO  18:49:32,273 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:49Z] INFO  18:49:32,377 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T01:49Z] INFO  18:49:32,799 IntervalUtils - Processing 15511572 bp from intervals
[2016-04-15T01:49Z] WARN  18:49:32,800 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:49Z] WARN  18:49:32,801 IndexDictionaryUtils - Track variant2 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:49Z] WARN  18:49:32,801 IndexDictionaryUtils - Track variant3 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:49Z] WARN  18:49:32,801 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:49Z] INFO  18:49:32,810 MicroScheduler - Running the GATK in parallel mode with 16 total threads, 1 CPU thread(s) for each of 16 data thread(s), of 16 processors available on this machine
[2016-04-15T01:49Z] INFO  18:49:32,868 GenomeAnalysisEngine - Preparing for traversal
[2016-04-15T01:49Z] INFO  18:49:32,869 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:49Z] INFO  18:49:32,869 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:49Z] INFO  18:49:32,869 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T01:49Z] INFO  18:49:32,870 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T01:49Z] INFO  18:49:33,000 GenotypeGVCFs - Notice that the -ploidy parameter is ignored in GenotypeGVCFs tool as this is automatically determined by the input variant files
[2016-04-15T01:49Z] INFO  18:49:43,012 ProgressMeter -            done    485510.0    10.0 s      20.0 s      100.0%    10.0 s       0.0 s
[2016-04-15T01:49Z] INFO  18:49:43,012 ProgressMeter - Total runtime 10.14 secs, 0.17 min, 0.00 hours
[2016-04-15T01:49Z] INFO  18:49:45,001 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:49Z] GATK: GenotypeGVCFs
[2016-04-15T01:49Z] INFO  18:49:47,170 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:49Z] INFO  18:49:47,172 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:49Z] INFO  18:49:47,172 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:49Z] INFO  18:49:47,172 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:49Z] INFO  18:49:47,175 HelpFormatter - Program Args: -T GenotypeGVCFs -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/gatk-haplotype-joint/Batch1/6/tx/tmp99Fq8T/Batch1-6_125112484_142397186.vcf.gz -L 6:125112485-142397186 --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18106_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18105_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18102_kapa-NGv3-PE100-NGv3.vcf.gz --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -nt 16 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:49Z] INFO  18:49:47,184 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:49Z] INFO  18:49:47,184 HelpFormatter - Date/Time: 2016/04/14 18:49:47
[2016-04-15T01:49Z] INFO  18:49:47,184 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:49Z] INFO  18:49:47,184 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:49Z] INFO  18:49:47,256 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:49Z] INFO  18:49:47,354 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T01:49Z] INFO  18:49:47,769 IntervalUtils - Processing 17284702 bp from intervals
[2016-04-15T01:49Z] WARN  18:49:47,770 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:49Z] WARN  18:49:47,770 IndexDictionaryUtils - Track variant2 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:49Z] WARN  18:49:47,770 IndexDictionaryUtils - Track variant3 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:49Z] WARN  18:49:47,771 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:49Z] INFO  18:49:47,779 MicroScheduler - Running the GATK in parallel mode with 16 total threads, 1 CPU thread(s) for each of 16 data thread(s), of 16 processors available on this machine
[2016-04-15T01:49Z] INFO  18:49:47,829 GenomeAnalysisEngine - Preparing for traversal
[2016-04-15T01:49Z] INFO  18:49:47,830 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:49Z] INFO  18:49:47,830 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:49Z] INFO  18:49:47,831 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T01:49Z] INFO  18:49:47,831 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T01:49Z] INFO  18:49:47,954 GenotypeGVCFs - Notice that the -ploidy parameter is ignored in GenotypeGVCFs tool as this is automatically determined by the input variant files
[2016-04-15T01:49Z] INFO  18:49:57,104 ProgressMeter -            done    539295.0     9.0 s      17.0 s      100.0%     9.0 s       0.0 s
[2016-04-15T01:49Z] INFO  18:49:57,104 ProgressMeter - Total runtime 9.27 secs, 0.15 min, 0.00 hours
[2016-04-15T01:49Z] INFO  18:49:59,396 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:49Z] GATK: GenotypeGVCFs
[2016-04-15T01:50Z] INFO  18:50:01,608 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:50Z] INFO  18:50:01,610 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:50Z] INFO  18:50:01,610 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:50Z] INFO  18:50:01,610 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:50Z] INFO  18:50:01,614 HelpFormatter - Program Args: -T GenotypeGVCFs -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/gatk-haplotype-joint/Batch1/6/tx/tmpJwdLUb/Batch1-6_142399691_157963777.vcf.gz -L 6:142399692-157963777 --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18106_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18105_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18102_kapa-NGv3-PE100-NGv3.vcf.gz --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -nt 16 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:50Z] INFO  18:50:01,623 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:50Z] INFO  18:50:01,623 HelpFormatter - Date/Time: 2016/04/14 18:50:01
[2016-04-15T01:50Z] INFO  18:50:01,623 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:50Z] INFO  18:50:01,623 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:50Z] INFO  18:50:01,699 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:50Z] INFO  18:50:01,798 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T01:50Z] INFO  18:50:02,565 IntervalUtils - Processing 15564086 bp from intervals
[2016-04-15T01:50Z] WARN  18:50:02,566 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:50Z] WARN  18:50:02,567 IndexDictionaryUtils - Track variant2 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:50Z] WARN  18:50:02,567 IndexDictionaryUtils - Track variant3 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:50Z] WARN  18:50:02,568 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:50Z] INFO  18:50:02,588 MicroScheduler - Running the GATK in parallel mode with 16 total threads, 1 CPU thread(s) for each of 16 data thread(s), of 16 processors available on this machine
[2016-04-15T01:50Z] INFO  18:50:02,709 GenomeAnalysisEngine - Preparing for traversal
[2016-04-15T01:50Z] INFO  18:50:02,711 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:50Z] INFO  18:50:02,712 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:50Z] INFO  18:50:02,713 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T01:50Z] INFO  18:50:02,714 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T01:50Z] INFO  18:50:02,973 GenotypeGVCFs - Notice that the -ploidy parameter is ignored in GenotypeGVCFs tool as this is automatically determined by the input variant files
[2016-04-15T01:50Z] INFO  18:50:13,613 ProgressMeter -            done    544676.0    10.0 s      20.0 s      100.0%    10.0 s       0.0 s
[2016-04-15T01:50Z] INFO  18:50:13,613 ProgressMeter - Total runtime 10.90 secs, 0.18 min, 0.00 hours
[2016-04-15T01:50Z] INFO  18:50:15,943 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:50Z] GATK: GenotypeGVCFs
[2016-04-15T01:50Z] INFO  18:50:18,132 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:50Z] INFO  18:50:18,134 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:50Z] INFO  18:50:18,134 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:50Z] INFO  18:50:18,135 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:50Z] INFO  18:50:18,138 HelpFormatter - Program Args: -T GenotypeGVCFs -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/gatk-haplotype-joint/Batch1/6/tx/tmpoF1zrF/Batch1-6_158013810_171115067.vcf.gz -L 6:158013811-171115067 --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18106_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18105_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18102_kapa-NGv3-PE100-NGv3.vcf.gz --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -nt 16 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:50Z] INFO  18:50:18,147 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:50Z] INFO  18:50:18,147 HelpFormatter - Date/Time: 2016/04/14 18:50:18
[2016-04-15T01:50Z] INFO  18:50:18,147 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:50Z] INFO  18:50:18,147 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:50Z] INFO  18:50:18,219 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:50Z] INFO  18:50:18,320 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T01:50Z] INFO  18:50:18,735 IntervalUtils - Processing 13101257 bp from intervals
[2016-04-15T01:50Z] WARN  18:50:18,736 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:50Z] WARN  18:50:18,736 IndexDictionaryUtils - Track variant2 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:50Z] WARN  18:50:18,736 IndexDictionaryUtils - Track variant3 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:50Z] WARN  18:50:18,736 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:50Z] INFO  18:50:18,744 MicroScheduler - Running the GATK in parallel mode with 16 total threads, 1 CPU thread(s) for each of 16 data thread(s), of 16 processors available on this machine
[2016-04-15T01:50Z] INFO  18:50:18,794 GenomeAnalysisEngine - Preparing for traversal
[2016-04-15T01:50Z] INFO  18:50:18,795 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:50Z] INFO  18:50:18,795 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:50Z] INFO  18:50:18,796 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T01:50Z] INFO  18:50:18,796 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T01:50Z] INFO  18:50:18,922 GenotypeGVCFs - Notice that the -ploidy parameter is ignored in GenotypeGVCFs tool as this is automatically determined by the input variant files
[2016-04-15T01:50Z] WARN  18:50:26,985 ExactAFCalculator - this tool is currently set to genotype at most 6 alternate alleles in a given context, but the context at 6:168365294 has 7 alternate alleles so only the top alleles will be used; see the --max_alternate_alleles argument
[2016-04-15T01:50Z] INFO  18:50:28,328 ProgressMeter -            done    501274.0     9.0 s      19.0 s       99.5%     9.0 s       0.0 s
[2016-04-15T01:50Z] INFO  18:50:28,328 ProgressMeter - Total runtime 9.53 secs, 0.16 min, 0.00 hours
[2016-04-15T01:50Z] INFO  18:50:30,462 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:50Z] GATK: GenotypeGVCFs
[2016-04-15T01:50Z] INFO  18:50:32,673 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:50Z] INFO  18:50:32,674 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:50Z] INFO  18:50:32,675 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:50Z] INFO  18:50:32,675 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:50Z] INFO  18:50:32,679 HelpFormatter - Program Args: -T GenotypeGVCFs -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/gatk-haplotype-joint/Batch1/7/tx/tmphdxo7Z/Batch1-7_0_15584548.vcf.gz -L 7:1-15584548 --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18106_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18105_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18102_kapa-NGv3-PE100-NGv3.vcf.gz --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -nt 16 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:50Z] INFO  18:50:32,687 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:50Z] INFO  18:50:32,687 HelpFormatter - Date/Time: 2016/04/14 18:50:32
[2016-04-15T01:50Z] INFO  18:50:32,687 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:50Z] INFO  18:50:32,688 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:50Z] INFO  18:50:32,760 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:50Z] INFO  18:50:32,859 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T01:50Z] INFO  18:50:33,282 IntervalUtils - Processing 15584548 bp from intervals
[2016-04-15T01:50Z] WARN  18:50:33,282 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:50Z] WARN  18:50:33,283 IndexDictionaryUtils - Track variant2 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:50Z] WARN  18:50:33,283 IndexDictionaryUtils - Track variant3 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:50Z] WARN  18:50:33,283 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:50Z] INFO  18:50:33,292 MicroScheduler - Running the GATK in parallel mode with 16 total threads, 1 CPU thread(s) for each of 16 data thread(s), of 16 processors available on this machine
[2016-04-15T01:50Z] INFO  18:50:33,343 GenomeAnalysisEngine - Preparing for traversal
[2016-04-15T01:50Z] INFO  18:50:33,344 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:50Z] INFO  18:50:33,344 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:50Z] INFO  18:50:33,345 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T01:50Z] INFO  18:50:33,345 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T01:50Z] INFO  18:50:33,470 GenotypeGVCFs - Notice that the -ploidy parameter is ignored in GenotypeGVCFs tool as this is automatically determined by the input variant files
[2016-04-15T01:50Z] INFO  18:50:42,686 ProgressMeter -            done    648904.0     9.0 s      14.0 s      100.0%     9.0 s       0.0 s
[2016-04-15T01:50Z] INFO  18:50:42,687 ProgressMeter - Total runtime 9.34 secs, 0.16 min, 0.00 hours
[2016-04-15T01:50Z] INFO  18:50:44,868 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:50Z] GATK: GenotypeGVCFs
[2016-04-15T01:50Z] INFO  18:50:46,801 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:50Z] INFO  18:50:46,803 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:50Z] INFO  18:50:46,803 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:50Z] INFO  18:50:46,804 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:50Z] INFO  18:50:46,807 HelpFormatter - Program Args: -T GenotypeGVCFs -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/gatk-haplotype-joint/Batch1/7/tx/tmplIQQwk/Batch1-7_15599765_31117713.vcf.gz -L 7:15599766-31117713 --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18106_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18105_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18102_kapa-NGv3-PE100-NGv3.vcf.gz --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -nt 16 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:50Z] INFO  18:50:46,816 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:50Z] INFO  18:50:46,816 HelpFormatter - Date/Time: 2016/04/14 18:50:46
[2016-04-15T01:50Z] INFO  18:50:46,816 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:50Z] INFO  18:50:46,816 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:50Z] INFO  18:50:46,888 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:50Z] INFO  18:50:46,988 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T01:50Z] INFO  18:50:47,399 IntervalUtils - Processing 15517948 bp from intervals
[2016-04-15T01:50Z] WARN  18:50:47,399 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:50Z] WARN  18:50:47,400 IndexDictionaryUtils - Track variant2 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:50Z] WARN  18:50:47,400 IndexDictionaryUtils - Track variant3 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:50Z] WARN  18:50:47,400 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:50Z] INFO  18:50:47,409 MicroScheduler - Running the GATK in parallel mode with 16 total threads, 1 CPU thread(s) for each of 16 data thread(s), of 16 processors available on this machine
[2016-04-15T01:50Z] INFO  18:50:47,459 GenomeAnalysisEngine - Preparing for traversal
[2016-04-15T01:50Z] INFO  18:50:47,460 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:50Z] INFO  18:50:47,460 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:50Z] INFO  18:50:47,461 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T01:50Z] INFO  18:50:47,461 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T01:50Z] INFO  18:50:47,589 GenotypeGVCFs - Notice that the -ploidy parameter is ignored in GenotypeGVCFs tool as this is automatically determined by the input variant files
[2016-04-15T01:50Z] INFO  18:50:57,535 ProgressMeter -            done    522960.0    10.0 s      19.0 s      100.0%    10.0 s       0.0 s
[2016-04-15T01:50Z] INFO  18:50:57,535 ProgressMeter - Total runtime 10.07 secs, 0.17 min, 0.00 hours
[2016-04-15T01:51Z] INFO  18:51:00,138 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:51Z] GATK: GenotypeGVCFs
[2016-04-15T01:51Z] INFO  18:51:02,600 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:51Z] INFO  18:51:02,604 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:51Z] INFO  18:51:02,605 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:51Z] INFO  18:51:02,605 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:51Z] INFO  18:51:02,612 HelpFormatter - Program Args: -T GenotypeGVCFs -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/gatk-haplotype-joint/Batch1/7/tx/tmpWFUtI0/Batch1-7_31120227_47317818.vcf.gz -L 7:31120228-47317818 --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18106_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18105_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18102_kapa-NGv3-PE100-NGv3.vcf.gz --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -nt 16 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:51Z] INFO  18:51:02,628 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:51Z] INFO  18:51:02,628 HelpFormatter - Date/Time: 2016/04/14 18:51:02
[2016-04-15T01:51Z] INFO  18:51:02,629 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:51Z] INFO  18:51:02,629 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:51Z] INFO  18:51:02,778 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:51Z] INFO  18:51:02,982 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T01:51Z] INFO  18:51:03,652 IntervalUtils - Processing 16197591 bp from intervals
[2016-04-15T01:51Z] WARN  18:51:03,654 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:51Z] WARN  18:51:03,654 IndexDictionaryUtils - Track variant2 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:51Z] WARN  18:51:03,654 IndexDictionaryUtils - Track variant3 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:51Z] WARN  18:51:03,655 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:51Z] INFO  18:51:03,671 MicroScheduler - Running the GATK in parallel mode with 16 total threads, 1 CPU thread(s) for each of 16 data thread(s), of 16 processors available on this machine
[2016-04-15T01:51Z] INFO  18:51:03,768 GenomeAnalysisEngine - Preparing for traversal
[2016-04-15T01:51Z] INFO  18:51:03,770 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:51Z] INFO  18:51:03,771 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:51Z] INFO  18:51:03,771 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T01:51Z] INFO  18:51:03,772 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T01:51Z] INFO  18:51:04,035 GenotypeGVCFs - Notice that the -ploidy parameter is ignored in GenotypeGVCFs tool as this is automatically determined by the input variant files
[2016-04-15T01:51Z] INFO  18:51:13,560 ProgressMeter -            done    506213.0     9.0 s      19.0 s      100.0%     9.0 s       0.0 s
[2016-04-15T01:51Z] INFO  18:51:13,560 ProgressMeter - Total runtime 9.79 secs, 0.16 min, 0.00 hours
[2016-04-15T01:51Z] INFO  18:51:16,012 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:51Z] GATK: GenotypeGVCFs
[2016-04-15T01:51Z] INFO  18:51:18,189 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:51Z] INFO  18:51:18,191 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:51Z] INFO  18:51:18,192 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:51Z] INFO  18:51:18,192 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:51Z] INFO  18:51:18,195 HelpFormatter - Program Args: -T GenotypeGVCFs -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/gatk-haplotype-joint/Batch1/7/tx/tmpg2R5u7/Batch1-7_47319761_63093154.vcf.gz -L 7:47319762-63093154 --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18106_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18105_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18102_kapa-NGv3-PE100-NGv3.vcf.gz --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -nt 16 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:51Z] INFO  18:51:18,204 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:51Z] INFO  18:51:18,204 HelpFormatter - Date/Time: 2016/04/14 18:51:18
[2016-04-15T01:51Z] INFO  18:51:18,205 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:51Z] INFO  18:51:18,205 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:51Z] INFO  18:51:18,277 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:51Z] INFO  18:51:18,376 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T01:51Z] INFO  18:51:18,790 IntervalUtils - Processing 15773393 bp from intervals
[2016-04-15T01:51Z] WARN  18:51:18,790 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:51Z] WARN  18:51:18,791 IndexDictionaryUtils - Track variant2 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:51Z] WARN  18:51:18,791 IndexDictionaryUtils - Track variant3 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:51Z] WARN  18:51:18,791 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:51Z] INFO  18:51:18,800 MicroScheduler - Running the GATK in parallel mode with 16 total threads, 1 CPU thread(s) for each of 16 data thread(s), of 16 processors available on this machine
[2016-04-15T01:51Z] INFO  18:51:18,849 GenomeAnalysisEngine - Preparing for traversal
[2016-04-15T01:51Z] INFO  18:51:18,850 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:51Z] INFO  18:51:18,851 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:51Z] INFO  18:51:18,851 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T01:51Z] INFO  18:51:18,852 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T01:51Z] INFO  18:51:18,976 GenotypeGVCFs - Notice that the -ploidy parameter is ignored in GenotypeGVCFs tool as this is automatically determined by the input variant files
[2016-04-15T01:51Z] INFO  18:51:27,621 ProgressMeter -            done    423744.0     8.0 s      20.0 s      100.0%     8.0 s       0.0 s
[2016-04-15T01:51Z] INFO  18:51:27,622 ProgressMeter - Total runtime 8.77 secs, 0.15 min, 0.00 hours
[2016-04-15T01:51Z] INFO  18:51:30,367 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:51Z] GATK: GenotypeGVCFs
[2016-04-15T01:51Z] INFO  18:51:32,325 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:51Z] INFO  18:51:32,327 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:51Z] INFO  18:51:32,327 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:51Z] INFO  18:51:32,328 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:51Z] INFO  18:51:32,331 HelpFormatter - Program Args: -T GenotypeGVCFs -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/gatk-haplotype-joint/Batch1/7/tx/tmpHPEG8B/Batch1-7_63095909_78636522.vcf.gz -L 7:63095910-78636522 --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18106_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18105_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18102_kapa-NGv3-PE100-NGv3.vcf.gz --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -nt 16 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:51Z] INFO  18:51:32,339 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:51Z] INFO  18:51:32,340 HelpFormatter - Date/Time: 2016/04/14 18:51:32
[2016-04-15T01:51Z] INFO  18:51:32,340 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:51Z] INFO  18:51:32,340 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:51Z] INFO  18:51:32,413 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:51Z] INFO  18:51:32,511 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T01:51Z] INFO  18:51:32,925 IntervalUtils - Processing 15540613 bp from intervals
[2016-04-15T01:51Z] WARN  18:51:32,926 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:51Z] WARN  18:51:32,926 IndexDictionaryUtils - Track variant2 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:51Z] WARN  18:51:32,926 IndexDictionaryUtils - Track variant3 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:51Z] WARN  18:51:32,927 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:51Z] INFO  18:51:32,935 MicroScheduler - Running the GATK in parallel mode with 16 total threads, 1 CPU thread(s) for each of 16 data thread(s), of 16 processors available on this machine
[2016-04-15T01:51Z] INFO  18:51:32,985 GenomeAnalysisEngine - Preparing for traversal
[2016-04-15T01:51Z] INFO  18:51:32,986 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:51Z] INFO  18:51:32,987 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:51Z] INFO  18:51:32,987 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T01:51Z] INFO  18:51:32,987 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T01:51Z] INFO  18:51:33,111 GenotypeGVCFs - Notice that the -ploidy parameter is ignored in GenotypeGVCFs tool as this is automatically determined by the input variant files
[2016-04-15T01:51Z] INFO  18:51:42,427 ProgressMeter -            done    499266.0     9.0 s      18.0 s      100.0%     9.0 s       0.0 s
[2016-04-15T01:51Z] INFO  18:51:42,427 ProgressMeter - Total runtime 9.44 secs, 0.16 min, 0.00 hours
[2016-04-15T01:51Z] INFO  18:51:44,518 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:51Z] GATK: GenotypeGVCFs
[2016-04-15T01:51Z] INFO  18:51:46,668 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:51Z] INFO  18:51:46,670 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:51Z] INFO  18:51:46,670 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:51Z] INFO  18:51:46,671 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:51Z] INFO  18:51:46,674 HelpFormatter - Program Args: -T GenotypeGVCFs -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/gatk-haplotype-joint/Batch1/7/tx/tmpPekb8U/Batch1-7_79082334_94740703.vcf.gz -L 7:79082335-94740703 --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18106_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18105_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18102_kapa-NGv3-PE100-NGv3.vcf.gz --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -nt 16 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:51Z] INFO  18:51:46,683 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:51Z] INFO  18:51:46,683 HelpFormatter - Date/Time: 2016/04/14 18:51:46
[2016-04-15T01:51Z] INFO  18:51:46,683 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:51Z] INFO  18:51:46,683 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:51Z] INFO  18:51:46,754 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:51Z] INFO  18:51:46,853 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T01:51Z] INFO  18:51:47,266 IntervalUtils - Processing 15658369 bp from intervals
[2016-04-15T01:51Z] WARN  18:51:47,267 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:51Z] WARN  18:51:47,267 IndexDictionaryUtils - Track variant2 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:51Z] WARN  18:51:47,267 IndexDictionaryUtils - Track variant3 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:51Z] WARN  18:51:47,267 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:51Z] INFO  18:51:47,276 MicroScheduler - Running the GATK in parallel mode with 16 total threads, 1 CPU thread(s) for each of 16 data thread(s), of 16 processors available on this machine
[2016-04-15T01:51Z] INFO  18:51:47,325 GenomeAnalysisEngine - Preparing for traversal
[2016-04-15T01:51Z] INFO  18:51:47,326 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:51Z] INFO  18:51:47,327 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:51Z] INFO  18:51:47,327 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T01:51Z] INFO  18:51:47,328 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T01:51Z] INFO  18:51:47,450 GenotypeGVCFs - Notice that the -ploidy parameter is ignored in GenotypeGVCFs tool as this is automatically determined by the input variant files
[2016-04-15T01:51Z] INFO  18:51:57,528 ProgressMeter -            done    503655.0    10.0 s      20.0 s      100.0%    10.0 s       0.0 s
[2016-04-15T01:51Z] INFO  18:51:57,529 ProgressMeter - Total runtime 10.20 secs, 0.17 min, 0.00 hours
[2016-04-15T01:52Z] INFO  18:52:00,390 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:52Z] GATK: GenotypeGVCFs
[2016-04-15T01:52Z] INFO  18:52:02,330 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:52Z] INFO  18:52:02,332 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:52Z] INFO  18:52:02,332 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:52Z] INFO  18:52:02,332 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:52Z] INFO  18:52:02,335 HelpFormatter - Program Args: -T GenotypeGVCFs -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/gatk-haplotype-joint/Batch1/7/tx/tmpcW67BV/Batch1-7_94750023_110303777.vcf.gz -L 7:94750024-110303777 --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18106_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18105_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18102_kapa-NGv3-PE100-NGv3.vcf.gz --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -nt 16 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:52Z] INFO  18:52:02,344 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:52Z] INFO  18:52:02,344 HelpFormatter - Date/Time: 2016/04/14 18:52:02
[2016-04-15T01:52Z] INFO  18:52:02,344 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:52Z] INFO  18:52:02,345 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:52Z] INFO  18:52:02,421 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:52Z] INFO  18:52:02,528 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T01:52Z] INFO  18:52:02,888 IntervalUtils - Processing 15553754 bp from intervals
[2016-04-15T01:52Z] WARN  18:52:02,889 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:52Z] WARN  18:52:02,889 IndexDictionaryUtils - Track variant2 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:52Z] WARN  18:52:02,889 IndexDictionaryUtils - Track variant3 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:52Z] WARN  18:52:02,890 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:52Z] INFO  18:52:02,899 MicroScheduler - Running the GATK in parallel mode with 16 total threads, 1 CPU thread(s) for each of 16 data thread(s), of 16 processors available on this machine
[2016-04-15T01:52Z] INFO  18:52:02,951 GenomeAnalysisEngine - Preparing for traversal
[2016-04-15T01:52Z] INFO  18:52:02,952 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:52Z] INFO  18:52:02,952 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:52Z] INFO  18:52:02,953 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T01:52Z] INFO  18:52:02,953 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T01:52Z] INFO  18:52:03,082 GenotypeGVCFs - Notice that the -ploidy parameter is ignored in GenotypeGVCFs tool as this is automatically determined by the input variant files
[2016-04-15T01:52Z] INFO  18:52:11,839 ProgressMeter -            done    702414.0     8.0 s      12.0 s      100.0%     8.0 s       0.0 s
[2016-04-15T01:52Z] INFO  18:52:11,839 ProgressMeter - Total runtime 8.89 secs, 0.15 min, 0.00 hours
[2016-04-15T01:52Z] INFO  18:52:14,165 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:52Z] GATK: GenotypeGVCFs
[2016-04-15T01:52Z] INFO  18:52:16,219 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:52Z] INFO  18:52:16,221 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:52Z] INFO  18:52:16,221 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:52Z] INFO  18:52:16,221 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:52Z] INFO  18:52:16,225 HelpFormatter - Program Args: -T GenotypeGVCFs -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/gatk-haplotype-joint/Batch1/7/tx/tmpFyMCwl/Batch1-7_110526648_126079222.vcf.gz -L 7:110526649-126079222 --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18106_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18105_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18102_kapa-NGv3-PE100-NGv3.vcf.gz --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -nt 16 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:52Z] INFO  18:52:16,233 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:52Z] INFO  18:52:16,234 HelpFormatter - Date/Time: 2016/04/14 18:52:16
[2016-04-15T01:52Z] INFO  18:52:16,234 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:52Z] INFO  18:52:16,234 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:52Z] INFO  18:52:16,306 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:52Z] INFO  18:52:16,403 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T01:52Z] INFO  18:52:16,810 IntervalUtils - Processing 15552574 bp from intervals
[2016-04-15T01:52Z] WARN  18:52:16,811 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:52Z] WARN  18:52:16,811 IndexDictionaryUtils - Track variant2 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:52Z] WARN  18:52:16,811 IndexDictionaryUtils - Track variant3 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:52Z] WARN  18:52:16,811 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:52Z] INFO  18:52:16,820 MicroScheduler - Running the GATK in parallel mode with 16 total threads, 1 CPU thread(s) for each of 16 data thread(s), of 16 processors available on this machine
[2016-04-15T01:52Z] INFO  18:52:16,869 GenomeAnalysisEngine - Preparing for traversal
[2016-04-15T01:52Z] INFO  18:52:16,870 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:52Z] INFO  18:52:16,870 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:52Z] INFO  18:52:16,871 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T01:52Z] INFO  18:52:16,871 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T01:52Z] INFO  18:52:16,994 GenotypeGVCFs - Notice that the -ploidy parameter is ignored in GenotypeGVCFs tool as this is automatically determined by the input variant files
[2016-04-15T01:52Z] INFO  18:52:26,231 ProgressMeter -            done    417627.0     9.0 s      22.0 s      100.0%     9.0 s       0.0 s
[2016-04-15T01:52Z] INFO  18:52:26,232 ProgressMeter - Total runtime 9.36 secs, 0.16 min, 0.00 hours
[2016-04-15T01:52Z] INFO  18:52:28,824 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:52Z] GATK: GenotypeGVCFs
[2016-04-15T01:52Z] INFO  18:52:30,532 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:52Z] INFO  18:52:30,534 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:52Z] INFO  18:52:30,534 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:52Z] INFO  18:52:30,534 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:52Z] INFO  18:52:30,537 HelpFormatter - Program Args: -T GenotypeGVCFs -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/gatk-haplotype-joint/Batch1/7/tx/tmpch2xGj/Batch1-7_126086124_141619620.vcf.gz -L 7:126086125-141619620 --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18106_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18105_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18102_kapa-NGv3-PE100-NGv3.vcf.gz --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -nt 16 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:52Z] INFO  18:52:30,546 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:52Z] INFO  18:52:30,546 HelpFormatter - Date/Time: 2016/04/14 18:52:30
[2016-04-15T01:52Z] INFO  18:52:30,546 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:52Z] INFO  18:52:30,546 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:52Z] INFO  18:52:30,619 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:52Z] INFO  18:52:30,718 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T01:52Z] INFO  18:52:31,139 IntervalUtils - Processing 15533496 bp from intervals
[2016-04-15T01:52Z] WARN  18:52:31,140 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:52Z] WARN  18:52:31,140 IndexDictionaryUtils - Track variant2 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:52Z] WARN  18:52:31,140 IndexDictionaryUtils - Track variant3 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:52Z] WARN  18:52:31,141 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:52Z] INFO  18:52:31,149 MicroScheduler - Running the GATK in parallel mode with 16 total threads, 1 CPU thread(s) for each of 16 data thread(s), of 16 processors available on this machine
[2016-04-15T01:52Z] INFO  18:52:31,199 GenomeAnalysisEngine - Preparing for traversal
[2016-04-15T01:52Z] INFO  18:52:31,200 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:52Z] INFO  18:52:31,200 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:52Z] INFO  18:52:31,201 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T01:52Z] INFO  18:52:31,201 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T01:52Z] INFO  18:52:31,324 GenotypeGVCFs - Notice that the -ploidy parameter is ignored in GenotypeGVCFs tool as this is automatically determined by the input variant files
[2016-04-15T01:52Z] INFO  18:52:40,553 ProgressMeter -            done    560232.0     9.0 s      16.0 s      100.0%     9.0 s       0.0 s
[2016-04-15T01:52Z] INFO  18:52:40,554 ProgressMeter - Total runtime 9.35 secs, 0.16 min, 0.00 hours
[2016-04-15T01:52Z] INFO  18:52:43,062 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:52Z] GATK: GenotypeGVCFs
[2016-04-15T01:52Z] INFO  18:52:45,181 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:52Z] INFO  18:52:45,183 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:52Z] INFO  18:52:45,183 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:52Z] INFO  18:52:45,183 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:52Z] INFO  18:52:45,187 HelpFormatter - Program Args: -T GenotypeGVCFs -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/gatk-haplotype-joint/Batch1/7/tx/tmpqSYmZA/Batch1-7_141629903_157151331.vcf.gz -L 7:141629904-157151331 --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18106_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18105_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18102_kapa-NGv3-PE100-NGv3.vcf.gz --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -nt 16 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:52Z] INFO  18:52:45,195 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:52Z] INFO  18:52:45,195 HelpFormatter - Date/Time: 2016/04/14 18:52:45
[2016-04-15T01:52Z] INFO  18:52:45,196 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:52Z] INFO  18:52:45,196 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:52Z] INFO  18:52:45,267 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:52Z] INFO  18:52:45,364 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T01:52Z] INFO  18:52:45,771 IntervalUtils - Processing 15521428 bp from intervals
[2016-04-15T01:52Z] WARN  18:52:45,771 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:52Z] WARN  18:52:45,771 IndexDictionaryUtils - Track variant2 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:52Z] WARN  18:52:45,772 IndexDictionaryUtils - Track variant3 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:52Z] WARN  18:52:45,772 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:52Z] INFO  18:52:45,780 MicroScheduler - Running the GATK in parallel mode with 16 total threads, 1 CPU thread(s) for each of 16 data thread(s), of 16 processors available on this machine
[2016-04-15T01:52Z] INFO  18:52:45,830 GenomeAnalysisEngine - Preparing for traversal
[2016-04-15T01:52Z] INFO  18:52:45,831 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:52Z] INFO  18:52:45,831 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:52Z] INFO  18:52:45,832 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T01:52Z] INFO  18:52:45,832 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T01:52Z] INFO  18:52:45,955 GenotypeGVCFs - Notice that the -ploidy parameter is ignored in GenotypeGVCFs tool as this is automatically determined by the input variant files
[2016-04-15T01:52Z] INFO  18:52:55,060 ProgressMeter -            done    637176.0     9.0 s      14.0 s      100.0%     9.0 s       0.0 s
[2016-04-15T01:52Z] INFO  18:52:55,061 ProgressMeter - Total runtime 9.23 secs, 0.15 min, 0.00 hours
[2016-04-15T01:52Z] INFO  18:52:57,174 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:52Z] GATK: GenotypeGVCFs
[2016-04-15T01:52Z] INFO  18:52:59,114 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:52Z] INFO  18:52:59,116 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:52Z] INFO  18:52:59,116 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:52Z] INFO  18:52:59,116 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:52Z] INFO  18:52:59,120 HelpFormatter - Program Args: -T GenotypeGVCFs -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/gatk-haplotype-joint/Batch1/7/tx/tmpzyP5oM/Batch1-7_157155854_159138663.vcf.gz -L 7:157155855-159138663 --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18106_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18105_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18102_kapa-NGv3-PE100-NGv3.vcf.gz --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -nt 16 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:52Z] INFO  18:52:59,130 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:52Z] INFO  18:52:59,130 HelpFormatter - Date/Time: 2016/04/14 18:52:59
[2016-04-15T01:52Z] INFO  18:52:59,130 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:52Z] INFO  18:52:59,131 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:52Z] INFO  18:52:59,206 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:52Z] INFO  18:52:59,306 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T01:53Z] INFO  18:53:00,125 IntervalUtils - Processing 1982809 bp from intervals
[2016-04-15T01:53Z] WARN  18:53:00,127 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:53Z] WARN  18:53:00,127 IndexDictionaryUtils - Track variant2 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:53Z] WARN  18:53:00,127 IndexDictionaryUtils - Track variant3 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:53Z] WARN  18:53:00,128 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:53Z] INFO  18:53:00,148 MicroScheduler - Running the GATK in parallel mode with 16 total threads, 1 CPU thread(s) for each of 16 data thread(s), of 16 processors available on this machine
[2016-04-15T01:53Z] INFO  18:53:00,227 GenomeAnalysisEngine - Preparing for traversal
[2016-04-15T01:53Z] INFO  18:53:00,228 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:53Z] INFO  18:53:00,228 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:53Z] INFO  18:53:00,229 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T01:53Z] INFO  18:53:00,229 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T01:53Z] INFO  18:53:00,374 GenotypeGVCFs - Notice that the -ploidy parameter is ignored in GenotypeGVCFs tool as this is automatically determined by the input variant files
[2016-04-15T01:53Z] INFO  18:53:02,881 ProgressMeter -            done     95767.0     2.0 s      27.0 s       99.5%     2.0 s       0.0 s
[2016-04-15T01:53Z] INFO  18:53:02,881 ProgressMeter - Total runtime 2.65 secs, 0.04 min, 0.00 hours
[2016-04-15T01:53Z] INFO  18:53:04,050 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:53Z] GATK: GenotypeGVCFs
[2016-04-15T01:53Z] INFO  18:53:06,194 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:53Z] INFO  18:53:06,196 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:53Z] INFO  18:53:06,197 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:53Z] INFO  18:53:06,197 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:53Z] INFO  18:53:06,200 HelpFormatter - Program Args: -T GenotypeGVCFs -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/gatk-haplotype-joint/Batch1/8/tx/tmpxkUXSF/Batch1-8_0_15517156.vcf.gz -L 8:1-15517156 --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18106_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18105_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18102_kapa-NGv3-PE100-NGv3.vcf.gz --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -nt 16 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:53Z] INFO  18:53:06,209 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:53Z] INFO  18:53:06,209 HelpFormatter - Date/Time: 2016/04/14 18:53:06
[2016-04-15T01:53Z] INFO  18:53:06,209 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:53Z] INFO  18:53:06,209 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:53Z] INFO  18:53:06,282 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:53Z] INFO  18:53:06,381 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T01:53Z] INFO  18:53:06,799 IntervalUtils - Processing 15517156 bp from intervals
[2016-04-15T01:53Z] WARN  18:53:06,800 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:53Z] WARN  18:53:06,800 IndexDictionaryUtils - Track variant2 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:53Z] WARN  18:53:06,800 IndexDictionaryUtils - Track variant3 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:53Z] WARN  18:53:06,801 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:53Z] INFO  18:53:06,810 MicroScheduler - Running the GATK in parallel mode with 16 total threads, 1 CPU thread(s) for each of 16 data thread(s), of 16 processors available on this machine
[2016-04-15T01:53Z] INFO  18:53:06,867 GenomeAnalysisEngine - Preparing for traversal
[2016-04-15T01:53Z] INFO  18:53:06,868 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:53Z] INFO  18:53:06,869 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:53Z] INFO  18:53:06,869 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T01:53Z] INFO  18:53:06,870 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T01:53Z] INFO  18:53:07,004 GenotypeGVCFs - Notice that the -ploidy parameter is ignored in GenotypeGVCFs tool as this is automatically determined by the input variant files
[2016-04-15T01:53Z] INFO  18:53:16,752 ProgressMeter -            done    664906.0     9.0 s      14.0 s      100.0%     9.0 s       0.0 s
[2016-04-15T01:53Z] INFO  18:53:16,753 ProgressMeter - Total runtime 9.88 secs, 0.16 min, 0.00 hours
[2016-04-15T01:53Z] INFO  18:53:19,501 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:53Z] GATK: GenotypeGVCFs
[2016-04-15T01:53Z] INFO  18:53:21,386 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:53Z] INFO  18:53:21,388 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:53Z] INFO  18:53:21,388 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:53Z] INFO  18:53:21,388 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:53Z] INFO  18:53:21,392 HelpFormatter - Program Args: -T GenotypeGVCFs -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/gatk-haplotype-joint/Batch1/8/tx/tmpLbLOUy/Batch1-8_15519664_31030618.vcf.gz -L 8:15519665-31030618 --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18106_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18105_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18102_kapa-NGv3-PE100-NGv3.vcf.gz --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -nt 16 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:53Z] INFO  18:53:21,399 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:53Z] INFO  18:53:21,399 HelpFormatter - Date/Time: 2016/04/14 18:53:21
[2016-04-15T01:53Z] INFO  18:53:21,400 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:53Z] INFO  18:53:21,400 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:53Z] INFO  18:53:21,477 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:53Z] INFO  18:53:21,626 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T01:53Z] INFO  18:53:22,122 IntervalUtils - Processing 15510954 bp from intervals
[2016-04-15T01:53Z] WARN  18:53:22,123 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:53Z] WARN  18:53:22,123 IndexDictionaryUtils - Track variant2 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:53Z] WARN  18:53:22,123 IndexDictionaryUtils - Track variant3 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:53Z] WARN  18:53:22,123 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:53Z] INFO  18:53:22,132 MicroScheduler - Running the GATK in parallel mode with 16 total threads, 1 CPU thread(s) for each of 16 data thread(s), of 16 processors available on this machine
[2016-04-15T01:53Z] INFO  18:53:22,182 GenomeAnalysisEngine - Preparing for traversal
[2016-04-15T01:53Z] INFO  18:53:22,183 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:53Z] INFO  18:53:22,184 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:53Z] INFO  18:53:22,184 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T01:53Z] INFO  18:53:22,185 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T01:53Z] INFO  18:53:22,316 GenotypeGVCFs - Notice that the -ploidy parameter is ignored in GenotypeGVCFs tool as this is automatically determined by the input variant files
[2016-04-15T01:53Z] INFO  18:53:34,109 ProgressMeter -            done    642638.0    11.0 s      18.0 s      100.0%    11.0 s       0.0 s
[2016-04-15T01:53Z] INFO  18:53:34,110 ProgressMeter - Total runtime 11.93 secs, 0.20 min, 0.00 hours
[2016-04-15T01:53Z] INFO  18:53:36,816 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:53Z] GATK: GenotypeGVCFs
[2016-04-15T01:53Z] INFO  18:53:38,733 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:53Z] INFO  18:53:38,735 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:53Z] INFO  18:53:38,735 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:53Z] INFO  18:53:38,736 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:53Z] INFO  18:53:38,739 HelpFormatter - Program Args: -T GenotypeGVCFs -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/gatk-haplotype-joint/Batch1/8/tx/tmpxAZUes/Batch1-8_31496910_48001429.vcf.gz -L 8:31496911-48001429 --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18106_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18105_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18102_kapa-NGv3-PE100-NGv3.vcf.gz --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -nt 16 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:53Z] INFO  18:53:38,747 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:53Z] INFO  18:53:38,748 HelpFormatter - Date/Time: 2016/04/14 18:53:38
[2016-04-15T01:53Z] INFO  18:53:38,748 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:53Z] INFO  18:53:38,748 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:53Z] INFO  18:53:38,820 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:53Z] INFO  18:53:38,919 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T01:53Z] INFO  18:53:39,334 IntervalUtils - Processing 16504519 bp from intervals
[2016-04-15T01:53Z] WARN  18:53:39,335 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:53Z] WARN  18:53:39,335 IndexDictionaryUtils - Track variant2 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:53Z] WARN  18:53:39,335 IndexDictionaryUtils - Track variant3 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:53Z] WARN  18:53:39,336 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:53Z] INFO  18:53:39,344 MicroScheduler - Running the GATK in parallel mode with 16 total threads, 1 CPU thread(s) for each of 16 data thread(s), of 16 processors available on this machine
[2016-04-15T01:53Z] INFO  18:53:39,394 GenomeAnalysisEngine - Preparing for traversal
[2016-04-15T01:53Z] INFO  18:53:39,395 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:53Z] INFO  18:53:39,396 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:53Z] INFO  18:53:39,396 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T01:53Z] INFO  18:53:39,396 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T01:53Z] INFO  18:53:39,521 GenotypeGVCFs - Notice that the -ploidy parameter is ignored in GenotypeGVCFs tool as this is automatically determined by the input variant files
[2016-04-15T01:53Z] INFO  18:53:48,555 ProgressMeter -            done    449023.0     9.0 s      20.0 s      100.0%     9.0 s       0.0 s
[2016-04-15T01:53Z] INFO  18:53:48,555 ProgressMeter - Total runtime 9.16 secs, 0.15 min, 0.00 hours
[2016-04-15T01:53Z] INFO  18:53:50,982 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:53Z] GATK: GenotypeGVCFs
[2016-04-15T01:53Z] INFO  18:53:53,138 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:53Z] INFO  18:53:53,140 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:53Z] INFO  18:53:53,141 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:53Z] INFO  18:53:53,141 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:53Z] INFO  18:53:53,144 HelpFormatter - Program Args: -T GenotypeGVCFs -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/gatk-haplotype-joint/Batch1/8/tx/tmpTE4DtL/Batch1-8_48003022_63659688.vcf.gz -L 8:48003023-63659688 --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18106_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18105_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18102_kapa-NGv3-PE100-NGv3.vcf.gz --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -nt 16 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:53Z] INFO  18:53:53,152 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:53Z] INFO  18:53:53,153 HelpFormatter - Date/Time: 2016/04/14 18:53:53
[2016-04-15T01:53Z] INFO  18:53:53,153 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:53Z] INFO  18:53:53,153 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:53Z] INFO  18:53:53,225 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:53Z] INFO  18:53:53,323 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T01:53Z] INFO  18:53:53,737 IntervalUtils - Processing 15656666 bp from intervals
[2016-04-15T01:53Z] WARN  18:53:53,737 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:53Z] WARN  18:53:53,738 IndexDictionaryUtils - Track variant2 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:53Z] WARN  18:53:53,738 IndexDictionaryUtils - Track variant3 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:53Z] WARN  18:53:53,738 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:53Z] INFO  18:53:53,746 MicroScheduler - Running the GATK in parallel mode with 16 total threads, 1 CPU thread(s) for each of 16 data thread(s), of 16 processors available on this machine
[2016-04-15T01:53Z] INFO  18:53:53,796 GenomeAnalysisEngine - Preparing for traversal
[2016-04-15T01:53Z] INFO  18:53:53,797 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:53Z] INFO  18:53:53,798 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:53Z] INFO  18:53:53,798 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T01:53Z] INFO  18:53:53,799 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T01:53Z] INFO  18:53:53,922 GenotypeGVCFs - Notice that the -ploidy parameter is ignored in GenotypeGVCFs tool as this is automatically determined by the input variant files
[2016-04-15T01:54Z] INFO  18:54:02,954 ProgressMeter -            done    453943.0     9.0 s      20.0 s      100.0%     9.0 s       0.0 s
[2016-04-15T01:54Z] INFO  18:54:02,955 ProgressMeter - Total runtime 9.16 secs, 0.15 min, 0.00 hours
[2016-04-15T01:54Z] INFO  18:54:05,160 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:54Z] GATK: GenotypeGVCFs
[2016-04-15T01:54Z] INFO  18:54:07,031 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:54Z] INFO  18:54:07,033 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:54Z] INFO  18:54:07,033 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:54Z] INFO  18:54:07,033 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:54Z] INFO  18:54:07,037 HelpFormatter - Program Args: -T GenotypeGVCFs -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/gatk-haplotype-joint/Batch1/8/tx/tmpEsxjPl/Batch1-8_63775819_79510770.vcf.gz -L 8:63775820-79510770 --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18106_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18105_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18102_kapa-NGv3-PE100-NGv3.vcf.gz --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -nt 16 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:54Z] INFO  18:54:07,045 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:54Z] INFO  18:54:07,045 HelpFormatter - Date/Time: 2016/04/14 18:54:07
[2016-04-15T01:54Z] INFO  18:54:07,045 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:54Z] INFO  18:54:07,046 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:54Z] INFO  18:54:07,123 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:54Z] INFO  18:54:07,268 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T01:54Z] INFO  18:54:07,725 IntervalUtils - Processing 15734951 bp from intervals
[2016-04-15T01:54Z] WARN  18:54:07,726 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:54Z] WARN  18:54:07,726 IndexDictionaryUtils - Track variant2 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:54Z] WARN  18:54:07,726 IndexDictionaryUtils - Track variant3 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:54Z] WARN  18:54:07,727 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:54Z] INFO  18:54:07,735 MicroScheduler - Running the GATK in parallel mode with 16 total threads, 1 CPU thread(s) for each of 16 data thread(s), of 16 processors available on this machine
[2016-04-15T01:54Z] INFO  18:54:07,785 GenomeAnalysisEngine - Preparing for traversal
[2016-04-15T01:54Z] INFO  18:54:07,786 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:54Z] INFO  18:54:07,786 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:54Z] INFO  18:54:07,787 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T01:54Z] INFO  18:54:07,787 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T01:54Z] INFO  18:54:07,913 GenotypeGVCFs - Notice that the -ploidy parameter is ignored in GenotypeGVCFs tool as this is automatically determined by the input variant files
[2016-04-15T01:54Z] INFO  18:54:19,409 ProgressMeter -            done    456447.0    11.0 s      25.0 s      100.0%    11.0 s       0.0 s
[2016-04-15T01:54Z] INFO  18:54:19,409 ProgressMeter - Total runtime 11.62 secs, 0.19 min, 0.00 hours
[2016-04-15T01:54Z] INFO  18:54:21,456 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:54Z] GATK: GenotypeGVCFs
[2016-04-15T01:54Z] INFO  18:54:23,643 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:54Z] INFO  18:54:23,645 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:54Z] INFO  18:54:23,645 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:54Z] INFO  18:54:23,646 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:54Z] INFO  18:54:23,649 HelpFormatter - Program Args: -T GenotypeGVCFs -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/gatk-haplotype-joint/Batch1/8/tx/tmpTHL6jG/Batch1-8_79513976_95140568.vcf.gz -L 8:79513977-95140568 --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18106_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18105_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18102_kapa-NGv3-PE100-NGv3.vcf.gz --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -nt 16 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:54Z] INFO  18:54:23,657 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:54Z] INFO  18:54:23,658 HelpFormatter - Date/Time: 2016/04/14 18:54:23
[2016-04-15T01:54Z] INFO  18:54:23,658 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:54Z] INFO  18:54:23,658 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:54Z] INFO  18:54:23,731 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:54Z] INFO  18:54:23,832 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T01:54Z] INFO  18:54:24,256 IntervalUtils - Processing 15626592 bp from intervals
[2016-04-15T01:54Z] WARN  18:54:24,257 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:54Z] WARN  18:54:24,257 IndexDictionaryUtils - Track variant2 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:54Z] WARN  18:54:24,257 IndexDictionaryUtils - Track variant3 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:54Z] WARN  18:54:24,257 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:54Z] INFO  18:54:24,266 MicroScheduler - Running the GATK in parallel mode with 16 total threads, 1 CPU thread(s) for each of 16 data thread(s), of 16 processors available on this machine
[2016-04-15T01:54Z] INFO  18:54:24,317 GenomeAnalysisEngine - Preparing for traversal
[2016-04-15T01:54Z] INFO  18:54:24,318 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:54Z] INFO  18:54:24,318 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:54Z] INFO  18:54:24,318 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T01:54Z] INFO  18:54:24,319 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T01:54Z] INFO  18:54:24,444 GenotypeGVCFs - Notice that the -ploidy parameter is ignored in GenotypeGVCFs tool as this is automatically determined by the input variant files
[2016-04-15T01:54Z] INFO  18:54:34,393 ProgressMeter -            done    417380.0    10.0 s      24.0 s      100.0%    10.0 s       0.0 s
[2016-04-15T01:54Z] INFO  18:54:34,393 ProgressMeter - Total runtime 10.08 secs, 0.17 min, 0.00 hours
[2016-04-15T01:54Z] INFO  18:54:36,459 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:54Z] GATK: GenotypeGVCFs
[2016-04-15T01:54Z] INFO  18:54:38,466 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:54Z] INFO  18:54:38,468 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:54Z] INFO  18:54:38,468 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:54Z] INFO  18:54:38,468 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:54Z] INFO  18:54:38,472 HelpFormatter - Program Args: -T GenotypeGVCFs -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/gatk-haplotype-joint/Batch1/8/tx/tmpgT5rAN/Batch1-8_95142853_110655419.vcf.gz -L 8:95142854-110655419 --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18106_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18105_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18102_kapa-NGv3-PE100-NGv3.vcf.gz --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -nt 16 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:54Z] INFO  18:54:38,479 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:54Z] INFO  18:54:38,479 HelpFormatter - Date/Time: 2016/04/14 18:54:38
[2016-04-15T01:54Z] INFO  18:54:38,480 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:54Z] INFO  18:54:38,480 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:54Z] INFO  18:54:38,556 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:54Z] INFO  18:54:38,702 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T01:54Z] INFO  18:54:39,199 IntervalUtils - Processing 15512566 bp from intervals
[2016-04-15T01:54Z] WARN  18:54:39,200 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:54Z] WARN  18:54:39,200 IndexDictionaryUtils - Track variant2 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:54Z] WARN  18:54:39,200 IndexDictionaryUtils - Track variant3 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:54Z] WARN  18:54:39,201 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:54Z] INFO  18:54:39,209 MicroScheduler - Running the GATK in parallel mode with 16 total threads, 1 CPU thread(s) for each of 16 data thread(s), of 16 processors available on this machine
[2016-04-15T01:54Z] INFO  18:54:39,260 GenomeAnalysisEngine - Preparing for traversal
[2016-04-15T01:54Z] INFO  18:54:39,261 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:54Z] INFO  18:54:39,261 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:54Z] INFO  18:54:39,261 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T01:54Z] INFO  18:54:39,262 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T01:54Z] INFO  18:54:39,393 GenotypeGVCFs - Notice that the -ploidy parameter is ignored in GenotypeGVCFs tool as this is automatically determined by the input variant files
[2016-04-15T01:54Z] INFO  18:54:48,674 ProgressMeter -            done    495790.0     9.0 s      18.0 s      100.0%     9.0 s       0.0 s
[2016-04-15T01:54Z] INFO  18:54:48,675 ProgressMeter - Total runtime 9.41 secs, 0.16 min, 0.00 hours
[2016-04-15T01:54Z] INFO  18:54:51,315 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:54Z] GATK: GenotypeGVCFs
[2016-04-15T01:54Z] INFO  18:54:53,283 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:54Z] INFO  18:54:53,285 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:54Z] INFO  18:54:53,285 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:54Z] INFO  18:54:53,285 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:54Z] INFO  18:54:53,289 HelpFormatter - Program Args: -T GenotypeGVCFs -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/gatk-haplotype-joint/Batch1/8/tx/tmp57bSaa/Batch1-8_110656864_126194498.vcf.gz -L 8:110656865-126194498 --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18106_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18105_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18102_kapa-NGv3-PE100-NGv3.vcf.gz --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -nt 16 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:54Z] INFO  18:54:53,297 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:54Z] INFO  18:54:53,297 HelpFormatter - Date/Time: 2016/04/14 18:54:53
[2016-04-15T01:54Z] INFO  18:54:53,298 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:54Z] INFO  18:54:53,298 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:54Z] INFO  18:54:53,369 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:54Z] INFO  18:54:53,466 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T01:54Z] INFO  18:54:53,886 IntervalUtils - Processing 15537634 bp from intervals
[2016-04-15T01:54Z] WARN  18:54:53,887 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:54Z] WARN  18:54:53,887 IndexDictionaryUtils - Track variant2 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:54Z] WARN  18:54:53,887 IndexDictionaryUtils - Track variant3 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:54Z] WARN  18:54:53,887 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:54Z] INFO  18:54:53,896 MicroScheduler - Running the GATK in parallel mode with 16 total threads, 1 CPU thread(s) for each of 16 data thread(s), of 16 processors available on this machine
[2016-04-15T01:54Z] INFO  18:54:53,945 GenomeAnalysisEngine - Preparing for traversal
[2016-04-15T01:54Z] INFO  18:54:53,946 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:54Z] INFO  18:54:53,947 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:54Z] INFO  18:54:53,947 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T01:54Z] INFO  18:54:53,948 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T01:54Z] INFO  18:54:54,071 GenotypeGVCFs - Notice that the -ploidy parameter is ignored in GenotypeGVCFs tool as this is automatically determined by the input variant files
[2016-04-15T01:55Z] INFO  18:55:02,541 ProgressMeter -            done    442978.0     8.0 s      19.0 s      100.0%     8.0 s       0.0 s
[2016-04-15T01:55Z] INFO  18:55:02,542 ProgressMeter - Total runtime 8.59 secs, 0.14 min, 0.00 hours
[2016-04-15T01:55Z] INFO  18:55:04,937 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:55Z] GATK: GenotypeGVCFs
[2016-04-15T01:55Z] INFO  18:55:07,151 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:55Z] INFO  18:55:07,153 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:55Z] INFO  18:55:07,153 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:55Z] INFO  18:55:07,153 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:55Z] INFO  18:55:07,156 HelpFormatter - Program Args: -T GenotypeGVCFs -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/gatk-haplotype-joint/Batch1/8/tx/tmpvS8OBY/Batch1-8_126369460_141889736.vcf.gz -L 8:126369461-141889736 --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18106_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18105_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18102_kapa-NGv3-PE100-NGv3.vcf.gz --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -nt 16 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:55Z] INFO  18:55:07,165 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:55Z] INFO  18:55:07,166 HelpFormatter - Date/Time: 2016/04/14 18:55:07
[2016-04-15T01:55Z] INFO  18:55:07,166 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:55Z] INFO  18:55:07,166 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:55Z] INFO  18:55:07,242 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:55Z] INFO  18:55:07,345 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T01:55Z] INFO  18:55:07,774 IntervalUtils - Processing 15520276 bp from intervals
[2016-04-15T01:55Z] WARN  18:55:07,775 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:55Z] WARN  18:55:07,775 IndexDictionaryUtils - Track variant2 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:55Z] WARN  18:55:07,775 IndexDictionaryUtils - Track variant3 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:55Z] WARN  18:55:07,775 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:55Z] INFO  18:55:07,784 MicroScheduler - Running the GATK in parallel mode with 16 total threads, 1 CPU thread(s) for each of 16 data thread(s), of 16 processors available on this machine
[2016-04-15T01:55Z] INFO  18:55:07,836 GenomeAnalysisEngine - Preparing for traversal
[2016-04-15T01:55Z] INFO  18:55:07,837 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:55Z] INFO  18:55:07,837 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:55Z] INFO  18:55:07,837 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T01:55Z] INFO  18:55:07,838 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T01:55Z] INFO  18:55:07,967 GenotypeGVCFs - Notice that the -ploidy parameter is ignored in GenotypeGVCFs tool as this is automatically determined by the input variant files
[2016-04-15T01:55Z] INFO  18:55:17,519 ProgressMeter -            done    453230.0     9.0 s      21.0 s      100.0%     9.0 s       0.0 s
[2016-04-15T01:55Z] INFO  18:55:17,520 ProgressMeter - Total runtime 9.68 secs, 0.16 min, 0.00 hours
[2016-04-15T01:55Z] INFO  18:55:19,494 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:55Z] GATK: GenotypeGVCFs
[2016-04-15T01:55Z] INFO  18:55:21,652 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:55Z] INFO  18:55:21,654 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:55Z] INFO  18:55:21,654 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:55Z] INFO  18:55:21,655 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:55Z] INFO  18:55:21,658 HelpFormatter - Program Args: -T GenotypeGVCFs -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/gatk-haplotype-joint/Batch1/8/tx/tmpUOfVsK/Batch1-8_141900641_146364022.vcf.gz -L 8:141900642-146364022 --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18106_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18105_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18102_kapa-NGv3-PE100-NGv3.vcf.gz --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -nt 16 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:55Z] INFO  18:55:21,666 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:55Z] INFO  18:55:21,666 HelpFormatter - Date/Time: 2016/04/14 18:55:21
[2016-04-15T01:55Z] INFO  18:55:21,667 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:55Z] INFO  18:55:21,667 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:55Z] INFO  18:55:21,738 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:55Z] INFO  18:55:21,835 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T01:55Z] INFO  18:55:22,249 IntervalUtils - Processing 4463381 bp from intervals
[2016-04-15T01:55Z] WARN  18:55:22,250 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:55Z] WARN  18:55:22,250 IndexDictionaryUtils - Track variant2 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:55Z] WARN  18:55:22,250 IndexDictionaryUtils - Track variant3 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:55Z] WARN  18:55:22,251 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:55Z] INFO  18:55:22,259 MicroScheduler - Running the GATK in parallel mode with 16 total threads, 1 CPU thread(s) for each of 16 data thread(s), of 16 processors available on this machine
[2016-04-15T01:55Z] INFO  18:55:22,308 GenomeAnalysisEngine - Preparing for traversal
[2016-04-15T01:55Z] INFO  18:55:22,308 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:55Z] INFO  18:55:22,309 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:55Z] INFO  18:55:22,309 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T01:55Z] INFO  18:55:22,309 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T01:55Z] INFO  18:55:22,432 GenotypeGVCFs - Notice that the -ploidy parameter is ignored in GenotypeGVCFs tool as this is automatically determined by the input variant files
[2016-04-15T01:55Z] INFO  18:55:26,167 ProgressMeter -            done    320041.0     3.0 s      12.0 s       98.6%     3.0 s       0.0 s
[2016-04-15T01:55Z] INFO  18:55:26,168 ProgressMeter - Total runtime 3.86 secs, 0.06 min, 0.00 hours
[2016-04-15T01:55Z] INFO  18:55:27,611 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:55Z] GATK: GenotypeGVCFs
[2016-04-15T01:55Z] INFO  18:55:29,685 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:55Z] INFO  18:55:29,687 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:55Z] INFO  18:55:29,687 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:55Z] INFO  18:55:29,687 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:55Z] INFO  18:55:29,691 HelpFormatter - Program Args: -T GenotypeGVCFs -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/gatk-haplotype-joint/Batch1/9/tx/tmpBZ7bat/Batch1-9_0_15510186.vcf.gz -L 9:1-15510186 --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18106_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18105_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18102_kapa-NGv3-PE100-NGv3.vcf.gz --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -nt 16 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:55Z] INFO  18:55:29,699 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:55Z] INFO  18:55:29,699 HelpFormatter - Date/Time: 2016/04/14 18:55:29
[2016-04-15T01:55Z] INFO  18:55:29,699 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:55Z] INFO  18:55:29,699 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:55Z] INFO  18:55:29,770 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:55Z] INFO  18:55:29,868 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T01:55Z] INFO  18:55:30,289 IntervalUtils - Processing 15510186 bp from intervals
[2016-04-15T01:55Z] WARN  18:55:30,290 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:55Z] WARN  18:55:30,290 IndexDictionaryUtils - Track variant2 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:55Z] WARN  18:55:30,291 IndexDictionaryUtils - Track variant3 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:55Z] WARN  18:55:30,291 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:55Z] INFO  18:55:30,299 MicroScheduler - Running the GATK in parallel mode with 16 total threads, 1 CPU thread(s) for each of 16 data thread(s), of 16 processors available on this machine
[2016-04-15T01:55Z] INFO  18:55:30,348 GenomeAnalysisEngine - Preparing for traversal
[2016-04-15T01:55Z] INFO  18:55:30,349 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:55Z] INFO  18:55:30,349 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:55Z] INFO  18:55:30,350 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T01:55Z] INFO  18:55:30,350 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T01:55Z] INFO  18:55:30,471 GenotypeGVCFs - Notice that the -ploidy parameter is ignored in GenotypeGVCFs tool as this is automatically determined by the input variant files
[2016-04-15T01:55Z] INFO  18:55:40,386 ProgressMeter -            done    574856.0    10.0 s      17.0 s      100.0%    10.0 s       0.0 s
[2016-04-15T01:55Z] INFO  18:55:40,386 ProgressMeter - Total runtime 10.04 secs, 0.17 min, 0.00 hours
[2016-04-15T01:55Z] INFO  18:55:42,864 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:55Z] GATK: GenotypeGVCFs
[2016-04-15T01:55Z] INFO  18:55:44,800 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:55Z] INFO  18:55:44,802 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:55Z] INFO  18:55:44,802 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:55Z] INFO  18:55:44,802 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:55Z] INFO  18:55:44,805 HelpFormatter - Program Args: -T GenotypeGVCFs -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/gatk-haplotype-joint/Batch1/9/tx/tmpkzPgEM/Batch1-9_15564086_32405601.vcf.gz -L 9:15564087-32405601 --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18106_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18105_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18102_kapa-NGv3-PE100-NGv3.vcf.gz --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -nt 16 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:55Z] INFO  18:55:44,813 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:55Z] INFO  18:55:44,813 HelpFormatter - Date/Time: 2016/04/14 18:55:44
[2016-04-15T01:55Z] INFO  18:55:44,814 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:55Z] INFO  18:55:44,814 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:55Z] INFO  18:55:44,885 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:55Z] INFO  18:55:44,982 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T01:55Z] INFO  18:55:45,403 IntervalUtils - Processing 16841515 bp from intervals
[2016-04-15T01:55Z] WARN  18:55:45,404 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:55Z] WARN  18:55:45,404 IndexDictionaryUtils - Track variant2 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:55Z] WARN  18:55:45,404 IndexDictionaryUtils - Track variant3 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:55Z] WARN  18:55:45,404 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:55Z] INFO  18:55:45,413 MicroScheduler - Running the GATK in parallel mode with 16 total threads, 1 CPU thread(s) for each of 16 data thread(s), of 16 processors available on this machine
[2016-04-15T01:55Z] INFO  18:55:45,462 GenomeAnalysisEngine - Preparing for traversal
[2016-04-15T01:55Z] INFO  18:55:45,463 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:55Z] INFO  18:55:45,463 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:55Z] INFO  18:55:45,464 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T01:55Z] INFO  18:55:45,464 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T01:55Z] INFO  18:55:45,585 GenotypeGVCFs - Notice that the -ploidy parameter is ignored in GenotypeGVCFs tool as this is automatically determined by the input variant files
[2016-04-15T01:55Z] INFO  18:55:54,484 ProgressMeter -            done    531390.0     9.0 s      16.0 s      100.0%     9.0 s       0.0 s
[2016-04-15T01:55Z] INFO  18:55:54,484 ProgressMeter - Total runtime 9.02 secs, 0.15 min, 0.00 hours
[2016-04-15T01:55Z] INFO  18:55:57,024 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:55Z] GATK: GenotypeGVCFs
[2016-04-15T01:55Z] INFO  18:55:58,982 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:55Z] INFO  18:55:58,984 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:55Z] INFO  18:55:58,984 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:55Z] INFO  18:55:58,984 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:55Z] INFO  18:55:58,988 HelpFormatter - Program Args: -T GenotypeGVCFs -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/gatk-haplotype-joint/Batch1/9/tx/tmp7EvVrI/Batch1-9_32407258_65506776.vcf.gz -L 9:32407259-65506776 --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18106_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18105_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18102_kapa-NGv3-PE100-NGv3.vcf.gz --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -nt 16 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:55Z] INFO  18:55:58,996 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:55Z] INFO  18:55:58,996 HelpFormatter - Date/Time: 2016/04/14 18:55:58
[2016-04-15T01:55Z] INFO  18:55:58,997 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:55Z] INFO  18:55:58,997 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:55Z] INFO  18:55:59,075 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:55Z] INFO  18:55:59,219 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T01:55Z] INFO  18:55:59,703 IntervalUtils - Processing 33099518 bp from intervals
[2016-04-15T01:55Z] WARN  18:55:59,703 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:55Z] WARN  18:55:59,704 IndexDictionaryUtils - Track variant2 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:55Z] WARN  18:55:59,704 IndexDictionaryUtils - Track variant3 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:55Z] WARN  18:55:59,704 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:55Z] INFO  18:55:59,712 MicroScheduler - Running the GATK in parallel mode with 16 total threads, 1 CPU thread(s) for each of 16 data thread(s), of 16 processors available on this machine
[2016-04-15T01:55Z] INFO  18:55:59,762 GenomeAnalysisEngine - Preparing for traversal
[2016-04-15T01:55Z] INFO  18:55:59,763 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:55Z] INFO  18:55:59,763 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:55Z] INFO  18:55:59,764 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T01:55Z] INFO  18:55:59,764 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T01:55Z] INFO  18:55:59,890 GenotypeGVCFs - Notice that the -ploidy parameter is ignored in GenotypeGVCFs tool as this is automatically determined by the input variant files
[2016-04-15T01:56Z] INFO  18:56:10,379 ProgressMeter -            done    423013.0    10.0 s      25.0 s      100.0%    10.0 s       0.0 s
[2016-04-15T01:56Z] INFO  18:56:10,379 ProgressMeter - Total runtime 10.62 secs, 0.18 min, 0.00 hours
[2016-04-15T01:56Z] INFO  18:56:12,343 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:56Z] GATK: GenotypeGVCFs
[2016-04-15T01:56Z] INFO  18:56:14,305 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:56Z] INFO  18:56:14,306 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:56Z] INFO  18:56:14,307 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:56Z] INFO  18:56:14,307 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:56Z] INFO  18:56:14,310 HelpFormatter - Program Args: -T GenotypeGVCFs -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/gatk-haplotype-joint/Batch1/9/tx/tmpb5lnU0/Batch1-9_65507205_82187750.vcf.gz -L 9:65507206-82187750 --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18106_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18105_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18102_kapa-NGv3-PE100-NGv3.vcf.gz --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -nt 16 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:56Z] INFO  18:56:14,318 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:56Z] INFO  18:56:14,319 HelpFormatter - Date/Time: 2016/04/14 18:56:14
[2016-04-15T01:56Z] INFO  18:56:14,319 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:56Z] INFO  18:56:14,319 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:56Z] INFO  18:56:14,390 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:56Z] INFO  18:56:14,488 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T01:56Z] INFO  18:56:14,898 IntervalUtils - Processing 16680545 bp from intervals
[2016-04-15T01:56Z] WARN  18:56:14,899 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:56Z] WARN  18:56:14,899 IndexDictionaryUtils - Track variant2 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:56Z] WARN  18:56:14,899 IndexDictionaryUtils - Track variant3 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:56Z] WARN  18:56:14,899 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:56Z] INFO  18:56:14,908 MicroScheduler - Running the GATK in parallel mode with 16 total threads, 1 CPU thread(s) for each of 16 data thread(s), of 16 processors available on this machine
[2016-04-15T01:56Z] INFO  18:56:14,957 GenomeAnalysisEngine - Preparing for traversal
[2016-04-15T01:56Z] INFO  18:56:14,958 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:56Z] INFO  18:56:14,958 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:56Z] INFO  18:56:14,959 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T01:56Z] INFO  18:56:14,959 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T01:56Z] INFO  18:56:15,081 GenotypeGVCFs - Notice that the -ploidy parameter is ignored in GenotypeGVCFs tool as this is automatically determined by the input variant files
[2016-04-15T01:56Z] INFO  18:56:24,200 ProgressMeter -            done    451039.0     9.0 s      20.0 s      100.0%     9.0 s       0.0 s
[2016-04-15T01:56Z] INFO  18:56:24,201 ProgressMeter - Total runtime 9.24 secs, 0.15 min, 0.00 hours
[2016-04-15T01:56Z] INFO  18:56:26,638 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:56Z] GATK: GenotypeGVCFs
[2016-04-15T01:56Z] INFO  18:56:28,716 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:56Z] INFO  18:56:28,718 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:56Z] INFO  18:56:28,718 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:56Z] INFO  18:56:28,718 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:56Z] INFO  18:56:28,721 HelpFormatter - Program Args: -T GenotypeGVCFs -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/gatk-haplotype-joint/Batch1/9/tx/tmpanQK8i/Batch1-9_82188172_97717561.vcf.gz -L 9:82188173-97717561 --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18106_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18105_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18102_kapa-NGv3-PE100-NGv3.vcf.gz --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -nt 16 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:56Z] INFO  18:56:28,730 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:56Z] INFO  18:56:28,730 HelpFormatter - Date/Time: 2016/04/14 18:56:28
[2016-04-15T01:56Z] INFO  18:56:28,730 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:56Z] INFO  18:56:28,730 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:56Z] INFO  18:56:28,802 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:56Z] INFO  18:56:28,899 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T01:56Z] INFO  18:56:29,316 IntervalUtils - Processing 15529389 bp from intervals
[2016-04-15T01:56Z] WARN  18:56:29,316 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:56Z] WARN  18:56:29,317 IndexDictionaryUtils - Track variant2 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:56Z] WARN  18:56:29,317 IndexDictionaryUtils - Track variant3 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:56Z] WARN  18:56:29,317 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:56Z] INFO  18:56:29,325 MicroScheduler - Running the GATK in parallel mode with 16 total threads, 1 CPU thread(s) for each of 16 data thread(s), of 16 processors available on this machine
[2016-04-15T01:56Z] INFO  18:56:29,375 GenomeAnalysisEngine - Preparing for traversal
[2016-04-15T01:56Z] INFO  18:56:29,376 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:56Z] INFO  18:56:29,376 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:56Z] INFO  18:56:29,376 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T01:56Z] INFO  18:56:29,377 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T01:56Z] INFO  18:56:29,503 GenotypeGVCFs - Notice that the -ploidy parameter is ignored in GenotypeGVCFs tool as this is automatically determined by the input variant files
[2016-04-15T01:56Z] WARN  18:56:37,831 ExactAFCalculator - this tool is currently set to genotype at most 6 alternate alleles in a given context, but the context at 9:85861584 has 7 alternate alleles so only the top alleles will be used; see the --max_alternate_alleles argument
[2016-04-15T01:56Z] INFO  18:56:39,429 ProgressMeter -            done    532533.0    10.0 s      18.0 s      100.0%    10.0 s       0.0 s
[2016-04-15T01:56Z] INFO  18:56:39,430 ProgressMeter - Total runtime 10.05 secs, 0.17 min, 0.00 hours
[2016-04-15T01:56Z] INFO  18:56:41,858 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:56Z] GATK: GenotypeGVCFs
[2016-04-15T01:56Z] INFO  18:56:43,807 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:56Z] INFO  18:56:43,809 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:56Z] INFO  18:56:43,810 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:56Z] INFO  18:56:43,810 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:56Z] INFO  18:56:43,814 HelpFormatter - Program Args: -T GenotypeGVCFs -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/gatk-haplotype-joint/Batch1/9/tx/tmpbEa511/Batch1-9_97718189_113228306.vcf.gz -L 9:97718190-113228306 --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18106_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18105_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18102_kapa-NGv3-PE100-NGv3.vcf.gz --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -nt 16 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:56Z] INFO  18:56:43,822 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:56Z] INFO  18:56:43,822 HelpFormatter - Date/Time: 2016/04/14 18:56:43
[2016-04-15T01:56Z] INFO  18:56:43,822 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:56Z] INFO  18:56:43,823 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:56Z] INFO  18:56:43,896 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:56Z] INFO  18:56:44,073 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T01:56Z] INFO  18:56:44,587 IntervalUtils - Processing 15510117 bp from intervals
[2016-04-15T01:56Z] WARN  18:56:44,588 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:56Z] WARN  18:56:44,588 IndexDictionaryUtils - Track variant2 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:56Z] WARN  18:56:44,588 IndexDictionaryUtils - Track variant3 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:56Z] WARN  18:56:44,588 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:56Z] INFO  18:56:44,597 MicroScheduler - Running the GATK in parallel mode with 16 total threads, 1 CPU thread(s) for each of 16 data thread(s), of 16 processors available on this machine
[2016-04-15T01:56Z] INFO  18:56:44,648 GenomeAnalysisEngine - Preparing for traversal
[2016-04-15T01:56Z] INFO  18:56:44,649 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:56Z] INFO  18:56:44,649 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:56Z] INFO  18:56:44,649 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T01:56Z] INFO  18:56:44,650 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T01:56Z] INFO  18:56:44,773 GenotypeGVCFs - Notice that the -ploidy parameter is ignored in GenotypeGVCFs tool as this is automatically determined by the input variant files
[2016-04-15T01:56Z] INFO  18:56:55,177 ProgressMeter -            done    549190.0    10.0 s      19.0 s      100.0%    10.0 s       0.0 s
[2016-04-15T01:56Z] INFO  18:56:55,178 ProgressMeter - Total runtime 10.53 secs, 0.18 min, 0.00 hours
[2016-04-15T01:56Z] INFO  18:56:57,924 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:56Z] GATK: GenotypeGVCFs
[2016-04-15T01:57Z] INFO  18:57:00,130 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:57Z] INFO  18:57:00,132 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:57Z] INFO  18:57:00,132 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:57Z] INFO  18:57:00,132 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:57Z] INFO  18:57:00,136 HelpFormatter - Program Args: -T GenotypeGVCFs -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/gatk-haplotype-joint/Batch1/9/tx/tmp_nO2Qd/Batch1-9_113231219_129089575.vcf.gz -L 9:113231220-129089575 --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18106_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18105_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18102_kapa-NGv3-PE100-NGv3.vcf.gz --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -nt 16 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:57Z] INFO  18:57:00,144 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:57Z] INFO  18:57:00,144 HelpFormatter - Date/Time: 2016/04/14 18:57:00
[2016-04-15T01:57Z] INFO  18:57:00,145 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:57Z] INFO  18:57:00,145 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:57Z] INFO  18:57:00,219 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:57Z] INFO  18:57:00,320 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T01:57Z] INFO  18:57:00,671 IntervalUtils - Processing 15858356 bp from intervals
[2016-04-15T01:57Z] WARN  18:57:00,671 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:57Z] WARN  18:57:00,671 IndexDictionaryUtils - Track variant2 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:57Z] WARN  18:57:00,672 IndexDictionaryUtils - Track variant3 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:57Z] WARN  18:57:00,672 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:57Z] INFO  18:57:00,680 MicroScheduler - Running the GATK in parallel mode with 16 total threads, 1 CPU thread(s) for each of 16 data thread(s), of 16 processors available on this machine
[2016-04-15T01:57Z] INFO  18:57:00,730 GenomeAnalysisEngine - Preparing for traversal
[2016-04-15T01:57Z] INFO  18:57:00,731 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:57Z] INFO  18:57:00,732 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:57Z] INFO  18:57:00,732 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T01:57Z] INFO  18:57:00,732 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T01:57Z] INFO  18:57:00,856 GenotypeGVCFs - Notice that the -ploidy parameter is ignored in GenotypeGVCFs tool as this is automatically determined by the input variant files
[2016-04-15T01:57Z] INFO  18:57:10,078 ProgressMeter -            done    579997.0     9.0 s      16.0 s      100.0%     9.0 s       0.0 s
[2016-04-15T01:57Z] INFO  18:57:10,078 ProgressMeter - Total runtime 9.35 secs, 0.16 min, 0.00 hours
[2016-04-15T01:57Z] INFO  18:57:12,539 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:57Z] GATK: GenotypeGVCFs
[2016-04-15T01:57Z] INFO  18:57:14,701 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:57Z] INFO  18:57:14,703 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:57Z] INFO  18:57:14,703 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:57Z] INFO  18:57:14,703 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:57Z] INFO  18:57:14,707 HelpFormatter - Program Args: -T GenotypeGVCFs -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/gatk-haplotype-joint/Batch1/9/tx/tmpeqBE0s/Batch1-9_129097484_141213431.vcf.gz -L 9:129097485-141213431 --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18106_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18105_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18102_kapa-NGv3-PE100-NGv3.vcf.gz --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -nt 16 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:57Z] INFO  18:57:14,715 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:57Z] INFO  18:57:14,715 HelpFormatter - Date/Time: 2016/04/14 18:57:14
[2016-04-15T01:57Z] INFO  18:57:14,715 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:57Z] INFO  18:57:14,716 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:57Z] INFO  18:57:14,793 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:57Z] INFO  18:57:14,935 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T01:57Z] INFO  18:57:15,416 IntervalUtils - Processing 12115947 bp from intervals
[2016-04-15T01:57Z] WARN  18:57:15,417 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:57Z] WARN  18:57:15,417 IndexDictionaryUtils - Track variant2 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:57Z] WARN  18:57:15,418 IndexDictionaryUtils - Track variant3 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:57Z] WARN  18:57:15,418 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:57Z] INFO  18:57:15,426 MicroScheduler - Running the GATK in parallel mode with 16 total threads, 1 CPU thread(s) for each of 16 data thread(s), of 16 processors available on this machine
[2016-04-15T01:57Z] INFO  18:57:15,478 GenomeAnalysisEngine - Preparing for traversal
[2016-04-15T01:57Z] INFO  18:57:15,479 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:57Z] INFO  18:57:15,479 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:57Z] INFO  18:57:15,479 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T01:57Z] INFO  18:57:15,480 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T01:57Z] INFO  18:57:15,606 GenotypeGVCFs - Notice that the -ploidy parameter is ignored in GenotypeGVCFs tool as this is automatically determined by the input variant files
[2016-04-15T01:57Z] INFO  18:57:25,189 ProgressMeter -            done    764885.0     9.0 s      12.0 s       99.5%     9.0 s       0.0 s
[2016-04-15T01:57Z] INFO  18:57:25,190 ProgressMeter - Total runtime 9.71 secs, 0.16 min, 0.00 hours
[2016-04-15T01:57Z] INFO  18:57:27,354 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:57Z] GATK: GenotypeGVCFs
[2016-04-15T01:57Z] INFO  18:57:29,327 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:57Z] INFO  18:57:29,329 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:57Z] INFO  18:57:29,329 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:57Z] INFO  18:57:29,329 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:57Z] INFO  18:57:29,333 HelpFormatter - Program Args: -T GenotypeGVCFs -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/gatk-haplotype-joint/Batch1/10/tx/tmps9_RWS/Batch1-10_0_15559243.vcf.gz -L 10:1-15559243 --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18106_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18105_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18102_kapa-NGv3-PE100-NGv3.vcf.gz --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -nt 16 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:57Z] INFO  18:57:29,341 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:57Z] INFO  18:57:29,341 HelpFormatter - Date/Time: 2016/04/14 18:57:29
[2016-04-15T01:57Z] INFO  18:57:29,341 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:57Z] INFO  18:57:29,341 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:57Z] INFO  18:57:29,414 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:57Z] INFO  18:57:29,513 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T01:57Z] INFO  18:57:29,929 IntervalUtils - Processing 15559243 bp from intervals
[2016-04-15T01:57Z] WARN  18:57:29,930 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:57Z] WARN  18:57:29,930 IndexDictionaryUtils - Track variant2 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:57Z] WARN  18:57:29,930 IndexDictionaryUtils - Track variant3 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:57Z] WARN  18:57:29,931 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:57Z] INFO  18:57:29,939 MicroScheduler - Running the GATK in parallel mode with 16 total threads, 1 CPU thread(s) for each of 16 data thread(s), of 16 processors available on this machine
[2016-04-15T01:57Z] INFO  18:57:29,989 GenomeAnalysisEngine - Preparing for traversal
[2016-04-15T01:57Z] INFO  18:57:29,990 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:57Z] INFO  18:57:29,990 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:57Z] INFO  18:57:29,991 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T01:57Z] INFO  18:57:29,991 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T01:57Z] INFO  18:57:30,122 GenotypeGVCFs - Notice that the -ploidy parameter is ignored in GenotypeGVCFs tool as this is automatically determined by the input variant files
[2016-04-15T01:57Z] INFO  18:57:40,878 ProgressMeter -            done    581833.0    10.0 s      18.0 s      100.0%    10.0 s       0.0 s
[2016-04-15T01:57Z] INFO  18:57:40,879 ProgressMeter - Total runtime 10.89 secs, 0.18 min, 0.00 hours
[2016-04-15T01:57Z] INFO  18:57:43,327 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:57Z] GATK: GenotypeGVCFs
[2016-04-15T01:57Z] INFO  18:57:45,013 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:57Z] INFO  18:57:45,015 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:57Z] INFO  18:57:45,015 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:57Z] INFO  18:57:45,016 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:57Z] INFO  18:57:45,019 HelpFormatter - Program Args: -T GenotypeGVCFs -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/gatk-haplotype-joint/Batch1/10/tx/tmpjhkLxs/Batch1-10_15561288_31134502.vcf.gz -L 10:15561289-31134502 --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18106_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18105_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18102_kapa-NGv3-PE100-NGv3.vcf.gz --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -nt 16 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:57Z] INFO  18:57:45,028 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:57Z] INFO  18:57:45,028 HelpFormatter - Date/Time: 2016/04/14 18:57:45
[2016-04-15T01:57Z] INFO  18:57:45,028 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:57Z] INFO  18:57:45,029 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:57Z] INFO  18:57:45,100 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:57Z] INFO  18:57:45,198 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T01:57Z] INFO  18:57:45,613 IntervalUtils - Processing 15573214 bp from intervals
[2016-04-15T01:57Z] WARN  18:57:45,614 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:57Z] WARN  18:57:45,614 IndexDictionaryUtils - Track variant2 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:57Z] WARN  18:57:45,614 IndexDictionaryUtils - Track variant3 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:57Z] WARN  18:57:45,614 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:57Z] INFO  18:57:45,623 MicroScheduler - Running the GATK in parallel mode with 16 total threads, 1 CPU thread(s) for each of 16 data thread(s), of 16 processors available on this machine
[2016-04-15T01:57Z] INFO  18:57:45,674 GenomeAnalysisEngine - Preparing for traversal
[2016-04-15T01:57Z] INFO  18:57:45,674 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:57Z] INFO  18:57:45,675 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:57Z] INFO  18:57:45,675 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T01:57Z] INFO  18:57:45,676 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T01:57Z] INFO  18:57:45,797 GenotypeGVCFs - Notice that the -ploidy parameter is ignored in GenotypeGVCFs tool as this is automatically determined by the input variant files
[2016-04-15T01:57Z] INFO  18:57:56,499 ProgressMeter -            done    538381.0    10.0 s      20.0 s      100.0%    10.0 s       0.0 s
[2016-04-15T01:57Z] INFO  18:57:56,499 ProgressMeter - Total runtime 10.82 secs, 0.18 min, 0.00 hours
[2016-04-15T01:57Z] INFO  18:57:58,843 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:57Z] GATK: GenotypeGVCFs
[2016-04-15T01:58Z] INFO  18:58:00,821 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:58Z] INFO  18:58:00,823 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:58Z] INFO  18:58:00,824 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:58Z] INFO  18:58:00,824 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:58Z] INFO  18:58:00,827 HelpFormatter - Program Args: -T GenotypeGVCFs -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/gatk-haplotype-joint/Batch1/10/tx/tmpnoo8Zp/Batch1-10_31137459_46960129.vcf.gz -L 10:31137460-46960129 --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18106_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18105_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18102_kapa-NGv3-PE100-NGv3.vcf.gz --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -nt 16 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:58Z] INFO  18:58:00,835 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:58Z] INFO  18:58:00,835 HelpFormatter - Date/Time: 2016/04/14 18:58:00
[2016-04-15T01:58Z] INFO  18:58:00,836 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:58Z] INFO  18:58:00,836 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:58Z] INFO  18:58:00,908 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:58Z] INFO  18:58:01,006 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T01:58Z] INFO  18:58:01,423 IntervalUtils - Processing 15822670 bp from intervals
[2016-04-15T01:58Z] WARN  18:58:01,424 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:58Z] WARN  18:58:01,424 IndexDictionaryUtils - Track variant2 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:58Z] WARN  18:58:01,424 IndexDictionaryUtils - Track variant3 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:58Z] WARN  18:58:01,425 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:58Z] INFO  18:58:01,433 MicroScheduler - Running the GATK in parallel mode with 16 total threads, 1 CPU thread(s) for each of 16 data thread(s), of 16 processors available on this machine
[2016-04-15T01:58Z] INFO  18:58:01,482 GenomeAnalysisEngine - Preparing for traversal
[2016-04-15T01:58Z] INFO  18:58:01,483 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:58Z] INFO  18:58:01,484 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:58Z] INFO  18:58:01,484 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T01:58Z] INFO  18:58:01,484 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T01:58Z] INFO  18:58:01,607 GenotypeGVCFs - Notice that the -ploidy parameter is ignored in GenotypeGVCFs tool as this is automatically determined by the input variant files
[2016-04-15T01:58Z] WARN  18:58:07,335 ExactAFCalculator - this tool is currently set to genotype at most 6 alternate alleles in a given context, but the context at 10:43702839 has 7 alternate alleles so only the top alleles will be used; see the --max_alternate_alleles argument
[2016-04-15T01:58Z] INFO  18:58:11,009 ProgressMeter -            done    439404.0     9.0 s      21.0 s      100.0%     9.0 s       0.0 s
[2016-04-15T01:58Z] INFO  18:58:11,009 ProgressMeter - Total runtime 9.53 secs, 0.16 min, 0.00 hours
[2016-04-15T01:58Z] INFO  18:58:13,464 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:58Z] GATK: GenotypeGVCFs
[2016-04-15T01:58Z] INFO  18:58:15,617 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:58Z] INFO  18:58:15,618 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:58Z] INFO  18:58:15,619 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:58Z] INFO  18:58:15,619 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:58Z] INFO  18:58:15,623 HelpFormatter - Program Args: -T GenotypeGVCFs -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/gatk-haplotype-joint/Batch1/10/tx/tmpO3y2fB/Batch1-10_46960410_62493077.vcf.gz -L 10:46960411-62493077 --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18106_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18105_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18102_kapa-NGv3-PE100-NGv3.vcf.gz --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -nt 16 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:58Z] INFO  18:58:15,631 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:58Z] INFO  18:58:15,631 HelpFormatter - Date/Time: 2016/04/14 18:58:15
[2016-04-15T01:58Z] INFO  18:58:15,632 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:58Z] INFO  18:58:15,632 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:58Z] INFO  18:58:15,703 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:58Z] INFO  18:58:15,800 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T01:58Z] INFO  18:58:16,212 IntervalUtils - Processing 15532667 bp from intervals
[2016-04-15T01:58Z] WARN  18:58:16,213 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:58Z] WARN  18:58:16,213 IndexDictionaryUtils - Track variant2 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:58Z] WARN  18:58:16,213 IndexDictionaryUtils - Track variant3 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:58Z] WARN  18:58:16,213 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:58Z] INFO  18:58:16,222 MicroScheduler - Running the GATK in parallel mode with 16 total threads, 1 CPU thread(s) for each of 16 data thread(s), of 16 processors available on this machine
[2016-04-15T01:58Z] INFO  18:58:16,272 GenomeAnalysisEngine - Preparing for traversal
[2016-04-15T01:58Z] INFO  18:58:16,273 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:58Z] INFO  18:58:16,273 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:58Z] INFO  18:58:16,274 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T01:58Z] INFO  18:58:16,274 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T01:58Z] INFO  18:58:16,396 GenotypeGVCFs - Notice that the -ploidy parameter is ignored in GenotypeGVCFs tool as this is automatically determined by the input variant files
[2016-04-15T01:58Z] WARN  18:58:25,227 ExactAFCalculator - this tool is currently set to genotype at most 6 alternate alleles in a given context, but the context at 10:50534969 has 8 alternate alleles so only the top alleles will be used; see the --max_alternate_alleles argument
[2016-04-15T01:58Z] INFO  18:58:25,728 ProgressMeter -            done    458682.0     9.0 s      20.0 s      100.0%     9.0 s       0.0 s
[2016-04-15T01:58Z] INFO  18:58:25,729 ProgressMeter - Total runtime 9.46 secs, 0.16 min, 0.00 hours
[2016-04-15T01:58Z] INFO  18:58:28,318 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:58Z] GATK: GenotypeGVCFs
[2016-04-15T01:58Z] INFO  18:58:30,294 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:58Z] INFO  18:58:30,296 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:58Z] INFO  18:58:30,297 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:58Z] INFO  18:58:30,297 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:58Z] INFO  18:58:30,300 HelpFormatter - Program Args: -T GenotypeGVCFs -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/gatk-haplotype-joint/Batch1/10/tx/tmpdunKbt/Batch1-10_62539923_78084243.vcf.gz -L 10:62539924-78084243 --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18106_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18105_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18102_kapa-NGv3-PE100-NGv3.vcf.gz --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -nt 16 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:58Z] INFO  18:58:30,308 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:58Z] INFO  18:58:30,309 HelpFormatter - Date/Time: 2016/04/14 18:58:30
[2016-04-15T01:58Z] INFO  18:58:30,309 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:58Z] INFO  18:58:30,309 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:58Z] INFO  18:58:30,381 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:58Z] INFO  18:58:30,479 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T01:58Z] INFO  18:58:30,830 IntervalUtils - Processing 15544320 bp from intervals
[2016-04-15T01:58Z] WARN  18:58:30,831 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:58Z] WARN  18:58:30,831 IndexDictionaryUtils - Track variant2 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:58Z] WARN  18:58:30,831 IndexDictionaryUtils - Track variant3 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:58Z] WARN  18:58:30,832 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:58Z] INFO  18:58:30,840 MicroScheduler - Running the GATK in parallel mode with 16 total threads, 1 CPU thread(s) for each of 16 data thread(s), of 16 processors available on this machine
[2016-04-15T01:58Z] INFO  18:58:30,891 GenomeAnalysisEngine - Preparing for traversal
[2016-04-15T01:58Z] INFO  18:58:30,892 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:58Z] INFO  18:58:30,892 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:58Z] INFO  18:58:30,893 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T01:58Z] INFO  18:58:30,893 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T01:58Z] INFO  18:58:31,016 GenotypeGVCFs - Notice that the -ploidy parameter is ignored in GenotypeGVCFs tool as this is automatically determined by the input variant files
[2016-04-15T01:58Z] INFO  18:58:41,017 ProgressMeter -            done    579957.0    10.0 s      17.0 s      100.0%    10.0 s       0.0 s
[2016-04-15T01:58Z] INFO  18:58:41,017 ProgressMeter - Total runtime 10.12 secs, 0.17 min, 0.00 hours
[2016-04-15T01:58Z] INFO  18:58:43,076 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:58Z] GATK: GenotypeGVCFs
[2016-04-15T01:58Z] INFO  18:58:45,198 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:58Z] INFO  18:58:45,199 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:58Z] INFO  18:58:45,200 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:58Z] INFO  18:58:45,200 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:58Z] INFO  18:58:45,204 HelpFormatter - Program Args: -T GenotypeGVCFs -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/gatk-haplotype-joint/Batch1/10/tx/tmpRsoGDT/Batch1-10_78316966_93841258.vcf.gz -L 10:78316967-93841258 --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18106_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18105_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18102_kapa-NGv3-PE100-NGv3.vcf.gz --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -nt 16 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:58Z] INFO  18:58:45,212 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:58Z] INFO  18:58:45,212 HelpFormatter - Date/Time: 2016/04/14 18:58:45
[2016-04-15T01:58Z] INFO  18:58:45,212 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:58Z] INFO  18:58:45,212 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:58Z] INFO  18:58:45,284 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:58Z] INFO  18:58:45,381 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T01:58Z] INFO  18:58:45,795 IntervalUtils - Processing 15524292 bp from intervals
[2016-04-15T01:58Z] WARN  18:58:45,796 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:58Z] WARN  18:58:45,796 IndexDictionaryUtils - Track variant2 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:58Z] WARN  18:58:45,797 IndexDictionaryUtils - Track variant3 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:58Z] WARN  18:58:45,797 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:58Z] INFO  18:58:45,805 MicroScheduler - Running the GATK in parallel mode with 16 total threads, 1 CPU thread(s) for each of 16 data thread(s), of 16 processors available on this machine
[2016-04-15T01:58Z] INFO  18:58:45,856 GenomeAnalysisEngine - Preparing for traversal
[2016-04-15T01:58Z] INFO  18:58:45,857 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:58Z] INFO  18:58:45,857 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:58Z] INFO  18:58:45,857 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T01:58Z] INFO  18:58:45,858 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T01:58Z] INFO  18:58:45,982 GenotypeGVCFs - Notice that the -ploidy parameter is ignored in GenotypeGVCFs tool as this is automatically determined by the input variant files
[2016-04-15T01:58Z] INFO  18:58:55,479 ProgressMeter -            done    494616.0     9.0 s      19.0 s      100.0%     9.0 s       0.0 s
[2016-04-15T01:58Z] INFO  18:58:55,479 ProgressMeter - Total runtime 9.62 secs, 0.16 min, 0.00 hours
[2016-04-15T01:58Z] INFO  18:58:58,184 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:58Z] GATK: GenotypeGVCFs
[2016-04-15T01:59Z] INFO  18:59:00,238 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:59Z] INFO  18:59:00,240 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:59Z] INFO  18:59:00,240 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:59Z] INFO  18:59:00,240 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:59Z] INFO  18:59:00,244 HelpFormatter - Program Args: -T GenotypeGVCFs -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/gatk-haplotype-joint/Batch1/10/tx/tmprLYwu4/Batch1-10_93851586_111625070.vcf.gz -L 10:93851587-111625070 --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18106_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18105_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18102_kapa-NGv3-PE100-NGv3.vcf.gz --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -nt 16 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:59Z] INFO  18:59:00,253 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:59Z] INFO  18:59:00,253 HelpFormatter - Date/Time: 2016/04/14 18:59:00
[2016-04-15T01:59Z] INFO  18:59:00,253 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:59Z] INFO  18:59:00,253 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:59Z] INFO  18:59:00,328 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:59Z] INFO  18:59:00,426 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T01:59Z] INFO  18:59:01,122 IntervalUtils - Processing 17773484 bp from intervals
[2016-04-15T01:59Z] WARN  18:59:01,124 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:59Z] WARN  18:59:01,124 IndexDictionaryUtils - Track variant2 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:59Z] WARN  18:59:01,125 IndexDictionaryUtils - Track variant3 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:59Z] WARN  18:59:01,125 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:59Z] INFO  18:59:01,145 MicroScheduler - Running the GATK in parallel mode with 16 total threads, 1 CPU thread(s) for each of 16 data thread(s), of 16 processors available on this machine
[2016-04-15T01:59Z] INFO  18:59:01,267 GenomeAnalysisEngine - Preparing for traversal
[2016-04-15T01:59Z] INFO  18:59:01,269 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:59Z] INFO  18:59:01,270 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:59Z] INFO  18:59:01,271 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T01:59Z] INFO  18:59:01,272 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T01:59Z] INFO  18:59:01,542 GenotypeGVCFs - Notice that the -ploidy parameter is ignored in GenotypeGVCFs tool as this is automatically determined by the input variant files
[2016-04-15T01:59Z] INFO  18:59:10,510 ProgressMeter -            done    724292.0     9.0 s      12.0 s      100.0%     9.0 s       0.0 s
[2016-04-15T01:59Z] INFO  18:59:10,511 ProgressMeter - Total runtime 9.24 secs, 0.15 min, 0.00 hours
[2016-04-15T01:59Z] INFO  18:59:12,469 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:59Z] GATK: GenotypeGVCFs
[2016-04-15T01:59Z] INFO  18:59:14,472 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:59Z] INFO  18:59:14,474 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:59Z] INFO  18:59:14,475 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:59Z] INFO  18:59:14,475 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:59Z] INFO  18:59:14,478 HelpFormatter - Program Args: -T GenotypeGVCFs -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/gatk-haplotype-joint/Batch1/10/tx/tmpfFvAfI/Batch1-10_111628371_127265443.vcf.gz -L 10:111628372-127265443 --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18106_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18105_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18102_kapa-NGv3-PE100-NGv3.vcf.gz --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -nt 16 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:59Z] INFO  18:59:14,487 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:59Z] INFO  18:59:14,488 HelpFormatter - Date/Time: 2016/04/14 18:59:14
[2016-04-15T01:59Z] INFO  18:59:14,488 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:59Z] INFO  18:59:14,488 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:59Z] INFO  18:59:14,563 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:59Z] INFO  18:59:14,666 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T01:59Z] INFO  18:59:15,107 IntervalUtils - Processing 15637072 bp from intervals
[2016-04-15T01:59Z] WARN  18:59:15,107 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:59Z] WARN  18:59:15,108 IndexDictionaryUtils - Track variant2 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:59Z] WARN  18:59:15,108 IndexDictionaryUtils - Track variant3 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:59Z] WARN  18:59:15,108 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:59Z] INFO  18:59:15,117 MicroScheduler - Running the GATK in parallel mode with 16 total threads, 1 CPU thread(s) for each of 16 data thread(s), of 16 processors available on this machine
[2016-04-15T01:59Z] INFO  18:59:15,168 GenomeAnalysisEngine - Preparing for traversal
[2016-04-15T01:59Z] INFO  18:59:15,169 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:59Z] INFO  18:59:15,169 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:59Z] INFO  18:59:15,170 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T01:59Z] INFO  18:59:15,170 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T01:59Z] INFO  18:59:15,300 GenotypeGVCFs - Notice that the -ploidy parameter is ignored in GenotypeGVCFs tool as this is automatically determined by the input variant files
[2016-04-15T01:59Z] INFO  18:59:24,596 ProgressMeter -            done    573748.0     9.0 s      16.0 s      100.0%     9.0 s       0.0 s
[2016-04-15T01:59Z] INFO  18:59:24,596 ProgressMeter - Total runtime 9.43 secs, 0.16 min, 0.00 hours
[2016-04-15T01:59Z] INFO  18:59:26,823 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:59Z] GATK: GenotypeGVCFs
[2016-04-15T01:59Z] INFO  18:59:28,788 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:59Z] INFO  18:59:28,790 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:59Z] INFO  18:59:28,790 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:59Z] INFO  18:59:28,790 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:59Z] INFO  18:59:28,794 HelpFormatter - Program Args: -T GenotypeGVCFs -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/gatk-haplotype-joint/Batch1/10/tx/tmpQAG18c/Batch1-10_127328721_135534747.vcf.gz -L 10:127328722-135534747 --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18106_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18105_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18102_kapa-NGv3-PE100-NGv3.vcf.gz --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -nt 16 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:59Z] INFO  18:59:28,802 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:59Z] INFO  18:59:28,802 HelpFormatter - Date/Time: 2016/04/14 18:59:28
[2016-04-15T01:59Z] INFO  18:59:28,803 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:59Z] INFO  18:59:28,803 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:59Z] INFO  18:59:28,874 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:59Z] INFO  18:59:28,973 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T01:59Z] INFO  18:59:29,387 IntervalUtils - Processing 8206026 bp from intervals
[2016-04-15T01:59Z] WARN  18:59:29,387 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:59Z] WARN  18:59:29,387 IndexDictionaryUtils - Track variant2 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:59Z] WARN  18:59:29,388 IndexDictionaryUtils - Track variant3 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:59Z] WARN  18:59:29,388 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:59Z] INFO  18:59:29,397 MicroScheduler - Running the GATK in parallel mode with 16 total threads, 1 CPU thread(s) for each of 16 data thread(s), of 16 processors available on this machine
[2016-04-15T01:59Z] INFO  18:59:29,447 GenomeAnalysisEngine - Preparing for traversal
[2016-04-15T01:59Z] INFO  18:59:29,448 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:59Z] INFO  18:59:29,448 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:59Z] INFO  18:59:29,449 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T01:59Z] INFO  18:59:29,449 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T01:59Z] INFO  18:59:29,576 GenotypeGVCFs - Notice that the -ploidy parameter is ignored in GenotypeGVCFs tool as this is automatically determined by the input variant files
[2016-04-15T01:59Z] INFO  18:59:35,195 ProgressMeter -            done    333465.0     5.0 s      17.0 s       99.9%     5.0 s       0.0 s
[2016-04-15T01:59Z] INFO  18:59:35,195 ProgressMeter - Total runtime 5.75 secs, 0.10 min, 0.00 hours
[2016-04-15T01:59Z] INFO  18:59:37,266 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:59Z] GATK: GenotypeGVCFs
[2016-04-15T01:59Z] INFO  18:59:39,180 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:59Z] INFO  18:59:39,182 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:59Z] INFO  18:59:39,182 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:59Z] INFO  18:59:39,182 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:59Z] INFO  18:59:39,186 HelpFormatter - Program Args: -T GenotypeGVCFs -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/gatk-haplotype-joint/Batch1/11/tx/tmpaX7Kbe/Batch1-11_0_15994658.vcf.gz -L 11:1-15994658 --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18106_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18105_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18102_kapa-NGv3-PE100-NGv3.vcf.gz --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -nt 16 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:59Z] INFO  18:59:39,194 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:59Z] INFO  18:59:39,195 HelpFormatter - Date/Time: 2016/04/14 18:59:39
[2016-04-15T01:59Z] INFO  18:59:39,195 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:59Z] INFO  18:59:39,195 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:59Z] INFO  18:59:39,267 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:59Z] INFO  18:59:39,365 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T01:59Z] INFO  18:59:39,802 IntervalUtils - Processing 15994658 bp from intervals
[2016-04-15T01:59Z] WARN  18:59:39,803 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:59Z] WARN  18:59:39,803 IndexDictionaryUtils - Track variant2 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:59Z] WARN  18:59:39,803 IndexDictionaryUtils - Track variant3 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:59Z] WARN  18:59:39,803 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:59Z] INFO  18:59:39,812 MicroScheduler - Running the GATK in parallel mode with 16 total threads, 1 CPU thread(s) for each of 16 data thread(s), of 16 processors available on this machine
[2016-04-15T01:59Z] INFO  18:59:39,865 GenomeAnalysisEngine - Preparing for traversal
[2016-04-15T01:59Z] INFO  18:59:39,866 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:59Z] INFO  18:59:39,866 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:59Z] INFO  18:59:39,866 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T01:59Z] INFO  18:59:39,867 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T01:59Z] INFO  18:59:40,002 GenotypeGVCFs - Notice that the -ploidy parameter is ignored in GenotypeGVCFs tool as this is automatically determined by the input variant files
[2016-04-15T01:59Z] INFO  18:59:50,392 ProgressMeter -            done    836681.0    10.0 s      12.0 s      100.0%    10.0 s       0.0 s
[2016-04-15T01:59Z] INFO  18:59:50,393 ProgressMeter - Total runtime 10.53 secs, 0.18 min, 0.00 hours
[2016-04-15T01:59Z] INFO  18:59:52,560 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T01:59Z] GATK: GenotypeGVCFs
[2016-04-15T01:59Z] INFO  18:59:54,704 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:59Z] INFO  18:59:54,706 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T01:59Z] INFO  18:59:54,706 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T01:59Z] INFO  18:59:54,706 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T01:59Z] INFO  18:59:54,710 HelpFormatter - Program Args: -T GenotypeGVCFs -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/gatk-haplotype-joint/Batch1/11/tx/tmpWDAH4s/Batch1-11_16007749_31531554.vcf.gz -L 11:16007750-31531554 --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18106_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18105_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18102_kapa-NGv3-PE100-NGv3.vcf.gz --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -nt 16 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T01:59Z] INFO  18:59:54,718 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T01:59Z] INFO  18:59:54,719 HelpFormatter - Date/Time: 2016/04/14 18:59:54
[2016-04-15T01:59Z] INFO  18:59:54,719 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:59Z] INFO  18:59:54,719 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T01:59Z] INFO  18:59:54,795 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T01:59Z] INFO  18:59:54,900 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T01:59Z] INFO  18:59:55,769 IntervalUtils - Processing 15523805 bp from intervals
[2016-04-15T01:59Z] WARN  18:59:55,771 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:59Z] WARN  18:59:55,771 IndexDictionaryUtils - Track variant2 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:59Z] WARN  18:59:55,772 IndexDictionaryUtils - Track variant3 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:59Z] WARN  18:59:55,772 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T01:59Z] INFO  18:59:55,792 MicroScheduler - Running the GATK in parallel mode with 16 total threads, 1 CPU thread(s) for each of 16 data thread(s), of 16 processors available on this machine
[2016-04-15T01:59Z] INFO  18:59:55,914 GenomeAnalysisEngine - Preparing for traversal
[2016-04-15T01:59Z] INFO  18:59:55,917 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T01:59Z] INFO  18:59:55,918 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T01:59Z] INFO  18:59:55,919 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T01:59Z] INFO  18:59:55,920 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T01:59Z] INFO  18:59:56,222 GenotypeGVCFs - Notice that the -ploidy parameter is ignored in GenotypeGVCFs tool as this is automatically determined by the input variant files
[2016-04-15T02:00Z] INFO  19:00:05,642 ProgressMeter -            done    503267.0     9.0 s      19.0 s      100.0%     9.0 s       0.0 s
[2016-04-15T02:00Z] INFO  19:00:05,642 ProgressMeter - Total runtime 9.72 secs, 0.16 min, 0.00 hours
[2016-04-15T02:00Z] INFO  19:00:07,859 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T02:00Z] GATK: GenotypeGVCFs
[2016-04-15T02:00Z] INFO  19:00:09,819 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T02:00Z] INFO  19:00:09,821 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T02:00Z] INFO  19:00:09,821 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T02:00Z] INFO  19:00:09,821 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T02:00Z] INFO  19:00:09,824 HelpFormatter - Program Args: -T GenotypeGVCFs -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/gatk-haplotype-joint/Batch1/11/tx/tmprnsRVM/Batch1-11_31541602_47074069.vcf.gz -L 11:31541603-47074069 --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18106_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18105_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18102_kapa-NGv3-PE100-NGv3.vcf.gz --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -nt 16 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T02:00Z] INFO  19:00:09,833 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T02:00Z] INFO  19:00:09,833 HelpFormatter - Date/Time: 2016/04/14 19:00:09
[2016-04-15T02:00Z] INFO  19:00:09,833 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T02:00Z] INFO  19:00:09,833 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T02:00Z] INFO  19:00:09,905 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T02:00Z] INFO  19:00:10,004 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T02:00Z] INFO  19:00:10,359 IntervalUtils - Processing 15532467 bp from intervals
[2016-04-15T02:00Z] WARN  19:00:10,359 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T02:00Z] WARN  19:00:10,360 IndexDictionaryUtils - Track variant2 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T02:00Z] WARN  19:00:10,360 IndexDictionaryUtils - Track variant3 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T02:00Z] WARN  19:00:10,360 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T02:00Z] INFO  19:00:10,368 MicroScheduler - Running the GATK in parallel mode with 16 total threads, 1 CPU thread(s) for each of 16 data thread(s), of 16 processors available on this machine
[2016-04-15T02:00Z] INFO  19:00:10,418 GenomeAnalysisEngine - Preparing for traversal
[2016-04-15T02:00Z] INFO  19:00:10,419 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T02:00Z] INFO  19:00:10,419 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T02:00Z] INFO  19:00:10,420 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T02:00Z] INFO  19:00:10,420 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T02:00Z] INFO  19:00:10,547 GenotypeGVCFs - Notice that the -ploidy parameter is ignored in GenotypeGVCFs tool as this is automatically determined by the input variant files
[2016-04-15T02:00Z] INFO  19:00:20,601 ProgressMeter -            done    504286.0    10.0 s      20.0 s      100.0%    10.0 s       0.0 s
[2016-04-15T02:00Z] INFO  19:00:20,601 ProgressMeter - Total runtime 10.18 secs, 0.17 min, 0.00 hours
[2016-04-15T02:00Z] INFO  19:00:22,966 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T02:00Z] GATK: GenotypeGVCFs
[2016-04-15T02:00Z] INFO  19:00:25,131 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T02:00Z] INFO  19:00:25,133 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T02:00Z] INFO  19:00:25,134 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T02:00Z] INFO  19:00:25,134 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T02:00Z] INFO  19:00:25,137 HelpFormatter - Program Args: -T GenotypeGVCFs -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/gatk-haplotype-joint/Batch1/11/tx/tmpnesufR/Batch1-11_47158866_62678572.vcf.gz -L 11:47158867-62678572 --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18106_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18105_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18102_kapa-NGv3-PE100-NGv3.vcf.gz --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -nt 16 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T02:00Z] INFO  19:00:25,146 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T02:00Z] INFO  19:00:25,146 HelpFormatter - Date/Time: 2016/04/14 19:00:25
[2016-04-15T02:00Z] INFO  19:00:25,146 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T02:00Z] INFO  19:00:25,146 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T02:00Z] INFO  19:00:25,218 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T02:00Z] INFO  19:00:25,316 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T02:00Z] INFO  19:00:25,727 IntervalUtils - Processing 15519706 bp from intervals
[2016-04-15T02:00Z] WARN  19:00:25,728 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T02:00Z] WARN  19:00:25,728 IndexDictionaryUtils - Track variant2 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T02:00Z] WARN  19:00:25,728 IndexDictionaryUtils - Track variant3 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T02:00Z] WARN  19:00:25,729 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T02:00Z] INFO  19:00:25,737 MicroScheduler - Running the GATK in parallel mode with 16 total threads, 1 CPU thread(s) for each of 16 data thread(s), of 16 processors available on this machine
[2016-04-15T02:00Z] INFO  19:00:25,786 GenomeAnalysisEngine - Preparing for traversal
[2016-04-15T02:00Z] INFO  19:00:25,787 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T02:00Z] INFO  19:00:25,787 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T02:00Z] INFO  19:00:25,788 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T02:00Z] INFO  19:00:25,788 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T02:00Z] INFO  19:00:25,909 GenotypeGVCFs - Notice that the -ploidy parameter is ignored in GenotypeGVCFs tool as this is automatically determined by the input variant files
[2016-04-15T02:00Z] INFO  19:00:35,800 ProgressMeter -            done    659550.0    10.0 s      15.0 s      100.0%    10.0 s       0.0 s
[2016-04-15T02:00Z] INFO  19:00:35,801 ProgressMeter - Total runtime 10.01 secs, 0.17 min, 0.00 hours
[2016-04-15T02:00Z] INFO  19:00:38,217 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T02:00Z] GATK: GenotypeGVCFs
[2016-04-15T02:00Z] INFO  19:00:40,810 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T02:00Z] INFO  19:00:40,812 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T02:00Z] INFO  19:00:40,813 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T02:00Z] INFO  19:00:40,813 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T02:00Z] INFO  19:00:40,816 HelpFormatter - Program Args: -T GenotypeGVCFs -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/gatk-haplotype-joint/Batch1/11/tx/tmp4wHRfy/Batch1-11_62744265_78270665.vcf.gz -L 11:62744266-78270665 --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18106_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18105_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18102_kapa-NGv3-PE100-NGv3.vcf.gz --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -nt 16 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T02:00Z] INFO  19:00:40,825 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T02:00Z] INFO  19:00:40,825 HelpFormatter - Date/Time: 2016/04/14 19:00:40
[2016-04-15T02:00Z] INFO  19:00:40,825 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T02:00Z] INFO  19:00:40,825 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T02:00Z] INFO  19:00:40,897 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T02:00Z] INFO  19:00:40,994 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T02:00Z] INFO  19:00:41,410 IntervalUtils - Processing 15526400 bp from intervals
[2016-04-15T02:00Z] WARN  19:00:41,411 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T02:00Z] WARN  19:00:41,411 IndexDictionaryUtils - Track variant2 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T02:00Z] WARN  19:00:41,411 IndexDictionaryUtils - Track variant3 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T02:00Z] WARN  19:00:41,411 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T02:00Z] INFO  19:00:41,419 MicroScheduler - Running the GATK in parallel mode with 16 total threads, 1 CPU thread(s) for each of 16 data thread(s), of 16 processors available on this machine
[2016-04-15T02:00Z] INFO  19:00:41,468 GenomeAnalysisEngine - Preparing for traversal
[2016-04-15T02:00Z] INFO  19:00:41,469 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T02:00Z] INFO  19:00:41,470 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T02:00Z] INFO  19:00:41,470 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T02:00Z] INFO  19:00:41,470 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T02:00Z] INFO  19:00:41,591 GenotypeGVCFs - Notice that the -ploidy parameter is ignored in GenotypeGVCFs tool as this is automatically determined by the input variant files
[2016-04-15T02:00Z] INFO  19:00:52,078 ProgressMeter -            done    870255.0    10.0 s      12.0 s      100.0%    10.0 s       0.0 s
[2016-04-15T02:00Z] INFO  19:00:52,079 ProgressMeter - Total runtime 10.61 secs, 0.18 min, 0.00 hours
[2016-04-15T02:00Z] INFO  19:00:54,304 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T02:00Z] GATK: GenotypeGVCFs
[2016-04-15T02:00Z] INFO  19:00:56,296 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T02:00Z] INFO  19:00:56,298 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T02:00Z] INFO  19:00:56,298 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T02:00Z] INFO  19:00:56,298 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T02:00Z] INFO  19:00:56,302 HelpFormatter - Program Args: -T GenotypeGVCFs -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/gatk-haplotype-joint/Batch1/11/tx/tmpR5beVM/Batch1-11_78277177_93796886.vcf.gz -L 11:78277178-93796886 --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18106_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18105_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18102_kapa-NGv3-PE100-NGv3.vcf.gz --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -nt 16 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T02:00Z] INFO  19:00:56,310 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T02:00Z] INFO  19:00:56,310 HelpFormatter - Date/Time: 2016/04/14 19:00:56
[2016-04-15T02:00Z] INFO  19:00:56,310 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T02:00Z] INFO  19:00:56,310 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T02:00Z] INFO  19:00:56,381 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T02:00Z] INFO  19:00:56,480 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T02:00Z] INFO  19:00:56,895 IntervalUtils - Processing 15519709 bp from intervals
[2016-04-15T02:00Z] WARN  19:00:56,896 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T02:00Z] WARN  19:00:56,896 IndexDictionaryUtils - Track variant2 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T02:00Z] WARN  19:00:56,896 IndexDictionaryUtils - Track variant3 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T02:00Z] WARN  19:00:56,896 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T02:00Z] INFO  19:00:56,905 MicroScheduler - Running the GATK in parallel mode with 16 total threads, 1 CPU thread(s) for each of 16 data thread(s), of 16 processors available on this machine
[2016-04-15T02:00Z] INFO  19:00:56,954 GenomeAnalysisEngine - Preparing for traversal
[2016-04-15T02:00Z] INFO  19:00:56,955 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T02:00Z] INFO  19:00:56,955 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T02:00Z] INFO  19:00:56,956 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T02:00Z] INFO  19:00:56,956 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T02:00Z] INFO  19:00:57,083 GenotypeGVCFs - Notice that the -ploidy parameter is ignored in GenotypeGVCFs tool as this is automatically determined by the input variant files
[2016-04-15T02:01Z] INFO  19:01:06,656 ProgressMeter -            done    481500.0     9.0 s      20.0 s      100.0%     9.0 s       0.0 s
[2016-04-15T02:01Z] INFO  19:01:06,657 ProgressMeter - Total runtime 9.70 secs, 0.16 min, 0.00 hours
[2016-04-15T02:01Z] INFO  19:01:09,138 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T02:01Z] GATK: GenotypeGVCFs
[2016-04-15T02:01Z] INFO  19:01:11,255 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T02:01Z] INFO  19:01:11,257 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T02:01Z] INFO  19:01:11,257 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T02:01Z] INFO  19:01:11,257 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T02:01Z] INFO  19:01:11,260 HelpFormatter - Program Args: -T GenotypeGVCFs -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/gatk-haplotype-joint/Batch1/11/tx/tmpECen3j/Batch1-11_93797496_109964158.vcf.gz -L 11:93797497-109964158 --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18106_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18105_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18102_kapa-NGv3-PE100-NGv3.vcf.gz --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -nt 16 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T02:01Z] INFO  19:01:11,269 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T02:01Z] INFO  19:01:11,269 HelpFormatter - Date/Time: 2016/04/14 19:01:11
[2016-04-15T02:01Z] INFO  19:01:11,269 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T02:01Z] INFO  19:01:11,269 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T02:01Z] INFO  19:01:11,341 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T02:01Z] INFO  19:01:11,439 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T02:01Z] INFO  19:01:11,854 IntervalUtils - Processing 16166662 bp from intervals
[2016-04-15T02:01Z] WARN  19:01:11,855 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T02:01Z] WARN  19:01:11,855 IndexDictionaryUtils - Track variant2 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T02:01Z] WARN  19:01:11,855 IndexDictionaryUtils - Track variant3 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T02:01Z] WARN  19:01:11,855 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T02:01Z] INFO  19:01:11,864 MicroScheduler - Running the GATK in parallel mode with 16 total threads, 1 CPU thread(s) for each of 16 data thread(s), of 16 processors available on this machine
[2016-04-15T02:01Z] INFO  19:01:11,913 GenomeAnalysisEngine - Preparing for traversal
[2016-04-15T02:01Z] INFO  19:01:11,914 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T02:01Z] INFO  19:01:11,915 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T02:01Z] INFO  19:01:11,915 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T02:01Z] INFO  19:01:11,915 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T02:01Z] INFO  19:01:12,042 GenotypeGVCFs - Notice that the -ploidy parameter is ignored in GenotypeGVCFs tool as this is automatically determined by the input variant files
[2016-04-15T02:01Z] INFO  19:01:22,412 ProgressMeter -            done    522914.0    10.0 s      20.0 s      100.0%    10.0 s       0.0 s
[2016-04-15T02:01Z] INFO  19:01:22,413 ProgressMeter - Total runtime 10.50 secs, 0.17 min, 0.00 hours
[2016-04-15T02:01Z] INFO  19:01:24,602 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T02:01Z] GATK: GenotypeGVCFs
[2016-04-15T02:01Z] INFO  19:01:26,724 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T02:01Z] INFO  19:01:26,726 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T02:01Z] INFO  19:01:26,727 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T02:01Z] INFO  19:01:26,727 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T02:01Z] INFO  19:01:26,730 HelpFormatter - Program Args: -T GenotypeGVCFs -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/gatk-haplotype-joint/Batch1/11/tx/tmpqJ9OSW/Batch1-11_110001730_125514538.vcf.gz -L 11:110001731-125514538 --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18106_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18105_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18102_kapa-NGv3-PE100-NGv3.vcf.gz --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -nt 16 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T02:01Z] INFO  19:01:26,738 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T02:01Z] INFO  19:01:26,739 HelpFormatter - Date/Time: 2016/04/14 19:01:26
[2016-04-15T02:01Z] INFO  19:01:26,739 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T02:01Z] INFO  19:01:26,739 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T02:01Z] INFO  19:01:26,810 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T02:01Z] INFO  19:01:26,908 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T02:01Z] INFO  19:01:27,322 IntervalUtils - Processing 15512808 bp from intervals
[2016-04-15T02:01Z] WARN  19:01:27,323 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T02:01Z] WARN  19:01:27,323 IndexDictionaryUtils - Track variant2 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T02:01Z] WARN  19:01:27,323 IndexDictionaryUtils - Track variant3 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T02:01Z] WARN  19:01:27,323 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T02:01Z] INFO  19:01:27,332 MicroScheduler - Running the GATK in parallel mode with 16 total threads, 1 CPU thread(s) for each of 16 data thread(s), of 16 processors available on this machine
[2016-04-15T02:01Z] INFO  19:01:27,382 GenomeAnalysisEngine - Preparing for traversal
[2016-04-15T02:01Z] INFO  19:01:27,383 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T02:01Z] INFO  19:01:27,383 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T02:01Z] INFO  19:01:27,384 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T02:01Z] INFO  19:01:27,384 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T02:01Z] INFO  19:01:27,509 GenotypeGVCFs - Notice that the -ploidy parameter is ignored in GenotypeGVCFs tool as this is automatically determined by the input variant files
[2016-04-15T02:01Z] INFO  19:01:37,260 ProgressMeter -            done    671117.0     9.0 s      14.0 s      100.0%     9.0 s       0.0 s
[2016-04-15T02:01Z] INFO  19:01:37,261 ProgressMeter - Total runtime 9.88 secs, 0.16 min, 0.00 hours
[2016-04-15T02:01Z] INFO  19:01:39,484 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T02:01Z] GATK: GenotypeGVCFs
[2016-04-15T02:01Z] INFO  19:01:41,120 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T02:01Z] INFO  19:01:41,122 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T02:01Z] INFO  19:01:41,123 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T02:01Z] INFO  19:01:41,123 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T02:01Z] INFO  19:01:41,126 HelpFormatter - Program Args: -T GenotypeGVCFs -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/gatk-haplotype-joint/Batch1/11/tx/tmprIgu0U/Batch1-11_125523640_135006516.vcf.gz -L 11:125523641-135006516 --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18106_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18105_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18102_kapa-NGv3-PE100-NGv3.vcf.gz --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -nt 16 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T02:01Z] INFO  19:01:41,135 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T02:01Z] INFO  19:01:41,135 HelpFormatter - Date/Time: 2016/04/14 19:01:41
[2016-04-15T02:01Z] INFO  19:01:41,135 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T02:01Z] INFO  19:01:41,135 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T02:01Z] INFO  19:01:41,207 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T02:01Z] INFO  19:01:41,306 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T02:01Z] INFO  19:01:41,718 IntervalUtils - Processing 9482876 bp from intervals
[2016-04-15T02:01Z] WARN  19:01:41,719 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T02:01Z] WARN  19:01:41,719 IndexDictionaryUtils - Track variant2 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T02:01Z] WARN  19:01:41,720 IndexDictionaryUtils - Track variant3 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T02:01Z] WARN  19:01:41,720 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T02:01Z] INFO  19:01:41,728 MicroScheduler - Running the GATK in parallel mode with 16 total threads, 1 CPU thread(s) for each of 16 data thread(s), of 16 processors available on this machine
[2016-04-15T02:01Z] INFO  19:01:41,778 GenomeAnalysisEngine - Preparing for traversal
[2016-04-15T02:01Z] INFO  19:01:41,779 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T02:01Z] INFO  19:01:41,779 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T02:01Z] INFO  19:01:41,780 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T02:01Z] INFO  19:01:41,780 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T02:01Z] INFO  19:01:41,904 GenotypeGVCFs - Notice that the -ploidy parameter is ignored in GenotypeGVCFs tool as this is automatically determined by the input variant files
[2016-04-15T02:01Z] INFO  19:01:46,964 ProgressMeter -            done    337008.0     5.0 s      15.0 s       99.4%     5.0 s       0.0 s
[2016-04-15T02:01Z] INFO  19:01:46,965 ProgressMeter - Total runtime 5.19 secs, 0.09 min, 0.00 hours
[2016-04-15T02:01Z] INFO  19:01:49,077 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T02:01Z] GATK: GenotypeGVCFs
[2016-04-15T02:01Z] INFO  19:01:51,214 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T02:01Z] INFO  19:01:51,216 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T02:01Z] INFO  19:01:51,216 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T02:01Z] INFO  19:01:51,216 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T02:01Z] INFO  19:01:51,220 HelpFormatter - Program Args: -T GenotypeGVCFs -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/gatk-haplotype-joint/Batch1/12/tx/tmpflGlVS/Batch1-12_0_15637181.vcf.gz -L 12:1-15637181 --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18106_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18105_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18102_kapa-NGv3-PE100-NGv3.vcf.gz --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -nt 16 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T02:01Z] INFO  19:01:51,229 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T02:01Z] INFO  19:01:51,229 HelpFormatter - Date/Time: 2016/04/14 19:01:51
[2016-04-15T02:01Z] INFO  19:01:51,229 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T02:01Z] INFO  19:01:51,230 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T02:01Z] INFO  19:01:51,301 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T02:01Z] INFO  19:01:51,398 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T02:01Z] INFO  19:01:51,810 IntervalUtils - Processing 15637181 bp from intervals
[2016-04-15T02:01Z] WARN  19:01:51,811 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T02:01Z] WARN  19:01:51,811 IndexDictionaryUtils - Track variant2 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T02:01Z] WARN  19:01:51,811 IndexDictionaryUtils - Track variant3 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T02:01Z] WARN  19:01:51,811 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T02:01Z] INFO  19:01:51,820 MicroScheduler - Running the GATK in parallel mode with 16 total threads, 1 CPU thread(s) for each of 16 data thread(s), of 16 processors available on this machine
[2016-04-15T02:01Z] INFO  19:01:51,870 GenomeAnalysisEngine - Preparing for traversal
[2016-04-15T02:01Z] INFO  19:01:51,871 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T02:01Z] INFO  19:01:51,871 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T02:01Z] INFO  19:01:51,872 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T02:01Z] INFO  19:01:51,872 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T02:01Z] INFO  19:01:51,994 GenotypeGVCFs - Notice that the -ploidy parameter is ignored in GenotypeGVCFs tool as this is automatically determined by the input variant files
[2016-04-15T02:02Z] INFO  19:02:02,675 ProgressMeter -            done    720730.0    10.0 s      14.0 s      100.0%    10.0 s       0.0 s
[2016-04-15T02:02Z] INFO  19:02:02,675 ProgressMeter - Total runtime 10.80 secs, 0.18 min, 0.00 hours
[2016-04-15T02:02Z] INFO  19:02:04,939 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T02:02Z] GATK: GenotypeGVCFs
[2016-04-15T02:02Z] INFO  19:02:06,956 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T02:02Z] INFO  19:02:06,958 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T02:02Z] INFO  19:02:06,958 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T02:02Z] INFO  19:02:06,959 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T02:02Z] INFO  19:02:06,962 HelpFormatter - Program Args: -T GenotypeGVCFs -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/gatk-haplotype-joint/Batch1/12/tx/tmpmP_jYh/Batch1-12_15650178_31231471.vcf.gz -L 12:15650179-31231471 --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18106_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18105_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18102_kapa-NGv3-PE100-NGv3.vcf.gz --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -nt 16 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T02:02Z] INFO  19:02:06,970 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T02:02Z] INFO  19:02:06,970 HelpFormatter - Date/Time: 2016/04/14 19:02:06
[2016-04-15T02:02Z] INFO  19:02:06,971 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T02:02Z] INFO  19:02:06,971 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T02:02Z] INFO  19:02:07,048 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T02:02Z] INFO  19:02:07,189 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T02:02Z] INFO  19:02:07,684 IntervalUtils - Processing 15581293 bp from intervals
[2016-04-15T02:02Z] WARN  19:02:07,685 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T02:02Z] WARN  19:02:07,685 IndexDictionaryUtils - Track variant2 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T02:02Z] WARN  19:02:07,686 IndexDictionaryUtils - Track variant3 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T02:02Z] WARN  19:02:07,686 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T02:02Z] INFO  19:02:07,694 MicroScheduler - Running the GATK in parallel mode with 16 total threads, 1 CPU thread(s) for each of 16 data thread(s), of 16 processors available on this machine
[2016-04-15T02:02Z] INFO  19:02:07,745 GenomeAnalysisEngine - Preparing for traversal
[2016-04-15T02:02Z] INFO  19:02:07,746 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T02:02Z] INFO  19:02:07,746 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T02:02Z] INFO  19:02:07,747 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T02:02Z] INFO  19:02:07,747 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T02:02Z] INFO  19:02:07,879 GenotypeGVCFs - Notice that the -ploidy parameter is ignored in GenotypeGVCFs tool as this is automatically determined by the input variant files
[2016-04-15T02:02Z] WARN  19:02:14,460 ExactAFCalculator - this tool is currently set to genotype at most 6 alternate alleles in a given context, but the context at 12:27953284 has 7 alternate alleles so only the top alleles will be used; see the --max_alternate_alleles argument
[2016-04-15T02:02Z] INFO  19:02:17,850 ProgressMeter -            done    494856.0    10.0 s      20.0 s      100.0%    10.0 s       0.0 s
[2016-04-15T02:02Z] INFO  19:02:17,851 ProgressMeter - Total runtime 10.10 secs, 0.17 min, 0.00 hours
[2016-04-15T02:02Z] INFO  19:02:20,177 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T02:02Z] GATK: GenotypeGVCFs
[2016-04-15T02:02Z] INFO  19:02:22,058 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T02:02Z] INFO  19:02:22,060 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T02:02Z] INFO  19:02:22,060 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T02:02Z] INFO  19:02:22,060 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T02:02Z] INFO  19:02:22,064 HelpFormatter - Program Args: -T GenotypeGVCFs -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/gatk-haplotype-joint/Batch1/12/tx/tmpdPtTN7/Batch1-12_31236746_46754992.vcf.gz -L 12:31236747-46754992 --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18106_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18105_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18102_kapa-NGv3-PE100-NGv3.vcf.gz --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -nt 16 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T02:02Z] INFO  19:02:22,072 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T02:02Z] INFO  19:02:22,073 HelpFormatter - Date/Time: 2016/04/14 19:02:22
[2016-04-15T02:02Z] INFO  19:02:22,073 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T02:02Z] INFO  19:02:22,073 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T02:02Z] INFO  19:02:22,150 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T02:02Z] INFO  19:02:22,292 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T02:02Z] INFO  19:02:22,753 IntervalUtils - Processing 15518246 bp from intervals
[2016-04-15T02:02Z] WARN  19:02:22,754 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T02:02Z] WARN  19:02:22,754 IndexDictionaryUtils - Track variant2 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T02:02Z] WARN  19:02:22,754 IndexDictionaryUtils - Track variant3 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T02:02Z] WARN  19:02:22,754 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T02:02Z] INFO  19:02:22,763 MicroScheduler - Running the GATK in parallel mode with 16 total threads, 1 CPU thread(s) for each of 16 data thread(s), of 16 processors available on this machine
[2016-04-15T02:02Z] INFO  19:02:22,812 GenomeAnalysisEngine - Preparing for traversal
[2016-04-15T02:02Z] INFO  19:02:22,813 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T02:02Z] INFO  19:02:22,814 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T02:02Z] INFO  19:02:22,814 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T02:02Z] INFO  19:02:22,814 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T02:02Z] INFO  19:02:22,941 GenotypeGVCFs - Notice that the -ploidy parameter is ignored in GenotypeGVCFs tool as this is automatically determined by the input variant files
[2016-04-15T02:02Z] INFO  19:02:31,194 ProgressMeter -            done    464711.0     8.0 s      18.0 s      100.0%     8.0 s       0.0 s
[2016-04-15T02:02Z] INFO  19:02:31,195 ProgressMeter - Total runtime 8.38 secs, 0.14 min, 0.00 hours
[2016-04-15T02:02Z] INFO  19:02:33,306 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T02:02Z] GATK: GenotypeGVCFs
[2016-04-15T02:02Z] INFO  19:02:35,250 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T02:02Z] INFO  19:02:35,252 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T02:02Z] INFO  19:02:35,253 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T02:02Z] INFO  19:02:35,253 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T02:02Z] INFO  19:02:35,256 HelpFormatter - Program Args: -T GenotypeGVCFs -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/gatk-haplotype-joint/Batch1/12/tx/tmpr2kOI1/Batch1-12_46756066_62654284.vcf.gz -L 12:46756067-62654284 --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18106_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18105_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18102_kapa-NGv3-PE100-NGv3.vcf.gz --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -nt 16 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T02:02Z] INFO  19:02:35,265 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T02:02Z] INFO  19:02:35,265 HelpFormatter - Date/Time: 2016/04/14 19:02:35
[2016-04-15T02:02Z] INFO  19:02:35,265 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T02:02Z] INFO  19:02:35,265 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T02:02Z] INFO  19:02:35,337 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T02:02Z] INFO  19:02:35,435 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T02:02Z] INFO  19:02:35,899 IntervalUtils - Processing 15898218 bp from intervals
[2016-04-15T02:02Z] WARN  19:02:35,900 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T02:02Z] WARN  19:02:35,900 IndexDictionaryUtils - Track variant2 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T02:02Z] WARN  19:02:35,900 IndexDictionaryUtils - Track variant3 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T02:02Z] WARN  19:02:35,901 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T02:02Z] INFO  19:02:35,910 MicroScheduler - Running the GATK in parallel mode with 16 total threads, 1 CPU thread(s) for each of 16 data thread(s), of 16 processors available on this machine
[2016-04-15T02:02Z] INFO  19:02:35,964 GenomeAnalysisEngine - Preparing for traversal
[2016-04-15T02:02Z] INFO  19:02:35,965 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T02:02Z] INFO  19:02:35,966 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T02:02Z] INFO  19:02:35,966 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T02:02Z] INFO  19:02:35,966 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T02:02Z] INFO  19:02:36,094 GenotypeGVCFs - Notice that the -ploidy parameter is ignored in GenotypeGVCFs tool as this is automatically determined by the input variant files
[2016-04-15T02:02Z] INFO  19:02:46,223 ProgressMeter -            done    857581.0    10.0 s      11.0 s      100.0%    10.0 s       0.0 s
[2016-04-15T02:02Z] INFO  19:02:46,223 ProgressMeter - Total runtime 10.26 secs, 0.17 min, 0.00 hours
[2016-04-15T02:02Z] INFO  19:02:49,133 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T02:02Z] GATK: GenotypeGVCFs
[2016-04-15T02:02Z] INFO  19:02:51,241 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T02:02Z] INFO  19:02:51,243 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T02:02Z] INFO  19:02:51,243 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T02:02Z] INFO  19:02:51,243 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T02:02Z] INFO  19:02:51,247 HelpFormatter - Program Args: -T GenotypeGVCFs -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/gatk-haplotype-joint/Batch1/12/tx/tmpYhuy5Z/Batch1-12_62687959_78225484.vcf.gz -L 12:62687960-78225484 --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18106_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18105_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18102_kapa-NGv3-PE100-NGv3.vcf.gz --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -nt 16 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T02:02Z] INFO  19:02:51,256 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T02:02Z] INFO  19:02:51,256 HelpFormatter - Date/Time: 2016/04/14 19:02:51
[2016-04-15T02:02Z] INFO  19:02:51,256 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T02:02Z] INFO  19:02:51,256 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T02:02Z] INFO  19:02:51,333 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T02:02Z] INFO  19:02:51,437 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T02:02Z] INFO  19:02:51,918 IntervalUtils - Processing 15537525 bp from intervals
[2016-04-15T02:02Z] WARN  19:02:51,919 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T02:02Z] WARN  19:02:51,919 IndexDictionaryUtils - Track variant2 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T02:02Z] WARN  19:02:51,919 IndexDictionaryUtils - Track variant3 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T02:02Z] WARN  19:02:51,919 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T02:02Z] INFO  19:02:51,928 MicroScheduler - Running the GATK in parallel mode with 16 total threads, 1 CPU thread(s) for each of 16 data thread(s), of 16 processors available on this machine
[2016-04-15T02:02Z] INFO  19:02:51,979 GenomeAnalysisEngine - Preparing for traversal
[2016-04-15T02:02Z] INFO  19:02:51,980 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T02:02Z] INFO  19:02:51,981 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T02:02Z] INFO  19:02:51,981 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T02:02Z] INFO  19:02:51,981 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T02:02Z] INFO  19:02:52,109 GenotypeGVCFs - Notice that the -ploidy parameter is ignored in GenotypeGVCFs tool as this is automatically determined by the input variant files
[2016-04-15T02:03Z] INFO  19:03:01,982 ProgressMeter -            done    485268.0     9.0 s      20.0 s      100.0%     9.0 s       0.0 s
[2016-04-15T02:03Z] INFO  19:03:01,983 ProgressMeter - Total runtime 10.00 secs, 0.17 min, 0.00 hours
[2016-04-15T02:03Z] INFO  19:03:04,313 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T02:03Z] GATK: GenotypeGVCFs
[2016-04-15T02:03Z] INFO  19:03:06,258 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T02:03Z] INFO  19:03:06,260 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T02:03Z] INFO  19:03:06,260 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T02:03Z] INFO  19:03:06,260 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T02:03Z] INFO  19:03:06,264 HelpFormatter - Program Args: -T GenotypeGVCFs -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/gatk-haplotype-joint/Batch1/12/tx/tmpSxRRi2/Batch1-12_78334098_93863131.vcf.gz -L 12:78334099-93863131 --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18106_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18105_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18102_kapa-NGv3-PE100-NGv3.vcf.gz --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -nt 16 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T02:03Z] INFO  19:03:06,272 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T02:03Z] INFO  19:03:06,272 HelpFormatter - Date/Time: 2016/04/14 19:03:06
[2016-04-15T02:03Z] INFO  19:03:06,272 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T02:03Z] INFO  19:03:06,273 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T02:03Z] INFO  19:03:06,345 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T02:03Z] INFO  19:03:06,444 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T02:03Z] INFO  19:03:06,850 IntervalUtils - Processing 15529033 bp from intervals
[2016-04-15T02:03Z] WARN  19:03:06,851 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T02:03Z] WARN  19:03:06,851 IndexDictionaryUtils - Track variant2 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T02:03Z] WARN  19:03:06,851 IndexDictionaryUtils - Track variant3 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T02:03Z] WARN  19:03:06,852 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T02:03Z] INFO  19:03:06,860 MicroScheduler - Running the GATK in parallel mode with 16 total threads, 1 CPU thread(s) for each of 16 data thread(s), of 16 processors available on this machine
[2016-04-15T02:03Z] INFO  19:03:06,910 GenomeAnalysisEngine - Preparing for traversal
[2016-04-15T02:03Z] INFO  19:03:06,911 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T02:03Z] INFO  19:03:06,911 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T02:03Z] INFO  19:03:06,912 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T02:03Z] INFO  19:03:06,912 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T02:03Z] INFO  19:03:07,041 GenotypeGVCFs - Notice that the -ploidy parameter is ignored in GenotypeGVCFs tool as this is automatically determined by the input variant files
[2016-04-15T02:03Z] INFO  19:03:16,863 ProgressMeter -            done    422872.0     9.0 s      23.0 s      100.0%     9.0 s       0.0 s
[2016-04-15T02:03Z] INFO  19:03:16,863 ProgressMeter - Total runtime 9.95 secs, 0.17 min, 0.00 hours
[2016-04-15T02:03Z] INFO  19:03:20,931 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T02:03Z] GATK: GenotypeGVCFs
[2016-04-15T02:03Z] INFO  19:03:23,137 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T02:03Z] INFO  19:03:23,139 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T02:03Z] INFO  19:03:23,139 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T02:03Z] INFO  19:03:23,139 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T02:03Z] INFO  19:03:23,142 HelpFormatter - Program Args: -T GenotypeGVCFs -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/gatk-haplotype-joint/Batch1/12/tx/tmpdi1DMX/Batch1-12_93870729_109490566.vcf.gz -L 12:93870730-109490566 --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18106_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18105_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18102_kapa-NGv3-PE100-NGv3.vcf.gz --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -nt 16 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T02:03Z] INFO  19:03:23,151 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T02:03Z] INFO  19:03:23,152 HelpFormatter - Date/Time: 2016/04/14 19:03:23
[2016-04-15T02:03Z] INFO  19:03:23,152 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T02:03Z] INFO  19:03:23,152 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T02:03Z] INFO  19:03:23,228 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T02:03Z] INFO  19:03:23,331 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T02:03Z] INFO  19:03:23,818 IntervalUtils - Processing 15619837 bp from intervals
[2016-04-15T02:03Z] WARN  19:03:23,819 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T02:03Z] WARN  19:03:23,820 IndexDictionaryUtils - Track variant2 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T02:03Z] WARN  19:03:23,820 IndexDictionaryUtils - Track variant3 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T02:03Z] WARN  19:03:23,820 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T02:03Z] INFO  19:03:23,829 MicroScheduler - Running the GATK in parallel mode with 16 total threads, 1 CPU thread(s) for each of 16 data thread(s), of 16 processors available on this machine
[2016-04-15T02:03Z] INFO  19:03:23,882 GenomeAnalysisEngine - Preparing for traversal
[2016-04-15T02:03Z] INFO  19:03:23,883 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T02:03Z] INFO  19:03:23,883 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T02:03Z] INFO  19:03:23,884 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T02:03Z] INFO  19:03:23,884 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T02:03Z] INFO  19:03:24,017 GenotypeGVCFs - Notice that the -ploidy parameter is ignored in GenotypeGVCFs tool as this is automatically determined by the input variant files
[2016-04-15T02:03Z] INFO  19:03:32,887 ProgressMeter -            done    553666.0     9.0 s      16.0 s      100.0%     9.0 s       0.0 s
[2016-04-15T02:03Z] INFO  19:03:32,887 ProgressMeter - Total runtime 9.00 secs, 0.15 min, 0.00 hours
[2016-04-15T02:03Z] INFO  19:03:35,205 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T02:03Z] GATK: GenotypeGVCFs
[2016-04-15T02:03Z] INFO  19:03:37,576 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T02:03Z] INFO  19:03:37,578 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T02:03Z] INFO  19:03:37,578 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T02:03Z] INFO  19:03:37,578 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T02:03Z] INFO  19:03:37,582 HelpFormatter - Program Args: -T GenotypeGVCFs -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/gatk-haplotype-joint/Batch1/12/tx/tmprNGjak/Batch1-12_109494486_125263132.vcf.gz -L 12:109494487-125263132 --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18106_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18105_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18102_kapa-NGv3-PE100-NGv3.vcf.gz --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -nt 16 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T02:03Z] INFO  19:03:37,590 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T02:03Z] INFO  19:03:37,590 HelpFormatter - Date/Time: 2016/04/14 19:03:37
[2016-04-15T02:03Z] INFO  19:03:37,591 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T02:03Z] INFO  19:03:37,591 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T02:03Z] INFO  19:03:37,666 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T02:03Z] INFO  19:03:37,770 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T02:03Z] INFO  19:03:38,162 IntervalUtils - Processing 15768646 bp from intervals
[2016-04-15T02:03Z] WARN  19:03:38,163 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T02:03Z] WARN  19:03:38,163 IndexDictionaryUtils - Track variant2 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T02:03Z] WARN  19:03:38,163 IndexDictionaryUtils - Track variant3 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T02:03Z] WARN  19:03:38,163 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T02:03Z] INFO  19:03:38,172 MicroScheduler - Running the GATK in parallel mode with 16 total threads, 1 CPU thread(s) for each of 16 data thread(s), of 16 processors available on this machine
[2016-04-15T02:03Z] INFO  19:03:38,221 GenomeAnalysisEngine - Preparing for traversal
[2016-04-15T02:03Z] INFO  19:03:38,222 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T02:03Z] INFO  19:03:38,223 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T02:03Z] INFO  19:03:38,223 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T02:03Z] INFO  19:03:38,224 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T02:03Z] INFO  19:03:38,347 GenotypeGVCFs - Notice that the -ploidy parameter is ignored in GenotypeGVCFs tool as this is automatically determined by the input variant files
[2016-04-15T02:03Z] WARN  19:03:47,823 ExactAFCalculator - this tool is currently set to genotype at most 6 alternate alleles in a given context, but the context at 12:117646196 has 7 alternate alleles so only the top alleles will be used; see the --max_alternate_alleles argument
[2016-04-15T02:03Z] INFO  19:03:50,111 ProgressMeter -            done    725566.0    11.0 s      16.0 s      100.0%    11.0 s       0.0 s
[2016-04-15T02:03Z] INFO  19:03:50,111 ProgressMeter - Total runtime 11.89 secs, 0.20 min, 0.00 hours
[2016-04-15T02:03Z] INFO  19:03:52,314 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T02:03Z] GATK: GenotypeGVCFs
[2016-04-15T02:03Z] INFO  19:03:54,296 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T02:03Z] INFO  19:03:54,298 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T02:03Z] INFO  19:03:54,298 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T02:03Z] INFO  19:03:54,298 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T02:03Z] INFO  19:03:54,302 HelpFormatter - Program Args: -T GenotypeGVCFs -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/gatk-haplotype-joint/Batch1/12/tx/tmpgWQP5Q/Batch1-12_125267228_133851895.vcf.gz -L 12:125267229-133851895 --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18106_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18105_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18102_kapa-NGv3-PE100-NGv3.vcf.gz --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -nt 16 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T02:03Z] INFO  19:03:54,311 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T02:03Z] INFO  19:03:54,311 HelpFormatter - Date/Time: 2016/04/14 19:03:54
[2016-04-15T02:03Z] INFO  19:03:54,311 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T02:03Z] INFO  19:03:54,311 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T02:03Z] INFO  19:03:54,383 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T02:03Z] INFO  19:03:54,483 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T02:03Z] INFO  19:03:54,895 IntervalUtils - Processing 8584667 bp from intervals
[2016-04-15T02:03Z] WARN  19:03:54,896 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T02:03Z] WARN  19:03:54,896 IndexDictionaryUtils - Track variant2 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T02:03Z] WARN  19:03:54,896 IndexDictionaryUtils - Track variant3 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T02:03Z] WARN  19:03:54,896 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T02:03Z] INFO  19:03:54,905 MicroScheduler - Running the GATK in parallel mode with 16 total threads, 1 CPU thread(s) for each of 16 data thread(s), of 16 processors available on this machine
[2016-04-15T02:03Z] INFO  19:03:54,954 GenomeAnalysisEngine - Preparing for traversal
[2016-04-15T02:03Z] INFO  19:03:54,955 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T02:03Z] INFO  19:03:54,955 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T02:03Z] INFO  19:03:54,955 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T02:03Z] INFO  19:03:54,956 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T02:03Z] INFO  19:03:55,077 GenotypeGVCFs - Notice that the -ploidy parameter is ignored in GenotypeGVCFs tool as this is automatically determined by the input variant files
[2016-04-15T02:03Z] WARN  19:03:59,421 ExactAFCalculator - this tool is currently set to genotype at most 6 alternate alleles in a given context, but the context at 12:132547093 has 7 alternate alleles so only the top alleles will be used; see the --max_alternate_alleles argument
[2016-04-15T02:04Z] INFO  19:04:00,685 ProgressMeter -            done    352331.0     5.0 s      16.0 s       99.9%     5.0 s       0.0 s
[2016-04-15T02:04Z] INFO  19:04:00,686 ProgressMeter - Total runtime 5.73 secs, 0.10 min, 0.00 hours
[2016-04-15T02:04Z] INFO  19:04:02,578 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T02:04Z] GATK: GenotypeGVCFs
[2016-04-15T02:04Z] INFO  19:04:05,009 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T02:04Z] INFO  19:04:05,013 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T02:04Z] INFO  19:04:05,013 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T02:04Z] INFO  19:04:05,014 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T02:04Z] INFO  19:04:05,021 HelpFormatter - Program Args: -T GenotypeGVCFs -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/gatk-haplotype-joint/Batch1/13/tx/tmpAMoxpT/Batch1-13_0_19748299.vcf.gz -L 13:1-19748299 --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18106_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18105_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18102_kapa-NGv3-PE100-NGv3.vcf.gz --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -nt 16 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T02:04Z] INFO  19:04:05,036 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T02:04Z] INFO  19:04:05,036 HelpFormatter - Date/Time: 2016/04/14 19:04:05
[2016-04-15T02:04Z] INFO  19:04:05,037 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T02:04Z] INFO  19:04:05,037 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T02:04Z] INFO  19:04:05,186 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T02:04Z] INFO  19:04:05,382 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T02:04Z] INFO  19:04:05,770 IntervalUtils - Processing 19748299 bp from intervals
[2016-04-15T02:04Z] WARN  19:04:05,770 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T02:04Z] WARN  19:04:05,771 IndexDictionaryUtils - Track variant2 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T02:04Z] WARN  19:04:05,771 IndexDictionaryUtils - Track variant3 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T02:04Z] WARN  19:04:05,771 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T02:04Z] INFO  19:04:05,780 MicroScheduler - Running the GATK in parallel mode with 16 total threads, 1 CPU thread(s) for each of 16 data thread(s), of 16 processors available on this machine
[2016-04-15T02:04Z] INFO  19:04:05,829 GenomeAnalysisEngine - Preparing for traversal
[2016-04-15T02:04Z] INFO  19:04:05,830 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T02:04Z] INFO  19:04:05,831 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T02:04Z] INFO  19:04:05,831 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T02:04Z] INFO  19:04:05,831 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T02:04Z] INFO  19:04:05,957 GenotypeGVCFs - Notice that the -ploidy parameter is ignored in GenotypeGVCFs tool as this is automatically determined by the input variant files
[2016-04-15T02:04Z] INFO  19:04:08,122 ProgressMeter -            done     24179.0     2.0 s      94.0 s      100.0%     2.0 s       0.0 s
[2016-04-15T02:04Z] INFO  19:04:08,123 ProgressMeter - Total runtime 2.29 secs, 0.04 min, 0.00 hours
[2016-04-15T02:04Z] INFO  19:04:10,332 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T02:04Z] GATK: GenotypeGVCFs
[2016-04-15T02:04Z] INFO  19:04:12,331 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T02:04Z] INFO  19:04:12,333 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T02:04Z] INFO  19:04:12,333 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T02:04Z] INFO  19:04:12,334 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T02:04Z] INFO  19:04:12,337 HelpFormatter - Program Args: -T GenotypeGVCFs -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/gatk-haplotype-joint/Batch1/13/tx/tmprA4Tvo/Batch1-13_19751066_35517251.vcf.gz -L 13:19751067-35517251 --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18106_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18105_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18102_kapa-NGv3-PE100-NGv3.vcf.gz --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -nt 16 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T02:04Z] INFO  19:04:12,345 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T02:04Z] INFO  19:04:12,345 HelpFormatter - Date/Time: 2016/04/14 19:04:12
[2016-04-15T02:04Z] INFO  19:04:12,346 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T02:04Z] INFO  19:04:12,346 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T02:04Z] INFO  19:04:12,419 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T02:04Z] INFO  19:04:12,516 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T02:04Z] INFO  19:04:12,931 IntervalUtils - Processing 15766185 bp from intervals
[2016-04-15T02:04Z] WARN  19:04:12,931 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T02:04Z] WARN  19:04:12,932 IndexDictionaryUtils - Track variant2 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T02:04Z] WARN  19:04:12,932 IndexDictionaryUtils - Track variant3 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T02:04Z] WARN  19:04:12,932 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T02:04Z] INFO  19:04:12,941 MicroScheduler - Running the GATK in parallel mode with 16 total threads, 1 CPU thread(s) for each of 16 data thread(s), of 16 processors available on this machine
[2016-04-15T02:04Z] INFO  19:04:12,991 GenomeAnalysisEngine - Preparing for traversal
[2016-04-15T02:04Z] INFO  19:04:12,992 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T02:04Z] INFO  19:04:12,992 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T02:04Z] INFO  19:04:12,993 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T02:04Z] INFO  19:04:12,993 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T02:04Z] INFO  19:04:13,118 GenotypeGVCFs - Notice that the -ploidy parameter is ignored in GenotypeGVCFs tool as this is automatically determined by the input variant files
[2016-04-15T02:04Z] INFO  19:04:22,870 ProgressMeter -            done    595573.0     9.0 s      16.0 s      100.0%     9.0 s       0.0 s
[2016-04-15T02:04Z] INFO  19:04:22,871 ProgressMeter - Total runtime 9.88 secs, 0.16 min, 0.00 hours
[2016-04-15T02:04Z] INFO  19:04:25,201 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T02:04Z] GATK: GenotypeGVCFs
[2016-04-15T02:04Z] INFO  19:04:27,260 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T02:04Z] INFO  19:04:27,262 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T02:04Z] INFO  19:04:27,262 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T02:04Z] INFO  19:04:27,262 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T02:04Z] INFO  19:04:27,266 HelpFormatter - Program Args: -T GenotypeGVCFs -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/gatk-haplotype-joint/Batch1/13/tx/tmp6u4yOV/Batch1-13_35615069_51287376.vcf.gz -L 13:35615070-51287376 --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18106_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18105_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18102_kapa-NGv3-PE100-NGv3.vcf.gz --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -nt 16 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T02:04Z] INFO  19:04:27,274 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T02:04Z] INFO  19:04:27,274 HelpFormatter - Date/Time: 2016/04/14 19:04:27
[2016-04-15T02:04Z] INFO  19:04:27,274 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T02:04Z] INFO  19:04:27,274 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T02:04Z] INFO  19:04:27,346 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T02:04Z] INFO  19:04:27,444 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T02:04Z] INFO  19:04:27,853 IntervalUtils - Processing 15672307 bp from intervals
[2016-04-15T02:04Z] WARN  19:04:27,853 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T02:04Z] WARN  19:04:27,854 IndexDictionaryUtils - Track variant2 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T02:04Z] WARN  19:04:27,854 IndexDictionaryUtils - Track variant3 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T02:04Z] WARN  19:04:27,854 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T02:04Z] INFO  19:04:27,862 MicroScheduler - Running the GATK in parallel mode with 16 total threads, 1 CPU thread(s) for each of 16 data thread(s), of 16 processors available on this machine
[2016-04-15T02:04Z] INFO  19:04:27,912 GenomeAnalysisEngine - Preparing for traversal
[2016-04-15T02:04Z] INFO  19:04:27,913 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T02:04Z] INFO  19:04:27,914 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T02:04Z] INFO  19:04:27,914 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T02:04Z] INFO  19:04:27,914 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T02:04Z] INFO  19:04:28,041 GenotypeGVCFs - Notice that the -ploidy parameter is ignored in GenotypeGVCFs tool as this is automatically determined by the input variant files
[2016-04-15T02:04Z] INFO  19:04:38,416 ProgressMeter -            done    525964.0    10.0 s      19.0 s      100.0%    10.0 s       0.0 s
[2016-04-15T02:04Z] INFO  19:04:38,417 ProgressMeter - Total runtime 10.50 secs, 0.18 min, 0.00 hours
[2016-04-15T02:04Z] INFO  19:04:40,673 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T02:04Z] GATK: GenotypeGVCFs
[2016-04-15T02:04Z] INFO  19:04:42,773 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T02:04Z] INFO  19:04:42,775 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T02:04Z] INFO  19:04:42,776 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T02:04Z] INFO  19:04:42,776 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T02:04Z] INFO  19:04:42,779 HelpFormatter - Program Args: -T GenotypeGVCFs -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/gatk-haplotype-joint/Batch1/13/tx/tmp1burVs/Batch1-13_51396767_67205543.vcf.gz -L 13:51396768-67205543 --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18106_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18105_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18102_kapa-NGv3-PE100-NGv3.vcf.gz --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -nt 16 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T02:04Z] INFO  19:04:42,787 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T02:04Z] INFO  19:04:42,788 HelpFormatter - Date/Time: 2016/04/14 19:04:42
[2016-04-15T02:04Z] INFO  19:04:42,788 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T02:04Z] INFO  19:04:42,788 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T02:04Z] INFO  19:04:42,859 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T02:04Z] INFO  19:04:42,958 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T02:04Z] INFO  19:04:43,371 IntervalUtils - Processing 15808776 bp from intervals
[2016-04-15T02:04Z] WARN  19:04:43,372 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T02:04Z] WARN  19:04:43,372 IndexDictionaryUtils - Track variant2 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T02:04Z] WARN  19:04:43,372 IndexDictionaryUtils - Track variant3 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T02:04Z] WARN  19:04:43,373 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T02:04Z] INFO  19:04:43,381 MicroScheduler - Running the GATK in parallel mode with 16 total threads, 1 CPU thread(s) for each of 16 data thread(s), of 16 processors available on this machine
[2016-04-15T02:04Z] INFO  19:04:43,430 GenomeAnalysisEngine - Preparing for traversal
[2016-04-15T02:04Z] INFO  19:04:43,431 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T02:04Z] INFO  19:04:43,432 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T02:04Z] INFO  19:04:43,432 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T02:04Z] INFO  19:04:43,432 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T02:04Z] INFO  19:04:43,555 GenotypeGVCFs - Notice that the -ploidy parameter is ignored in GenotypeGVCFs tool as this is automatically determined by the input variant files
[2016-04-15T02:04Z] INFO  19:04:50,979 ProgressMeter -            done    405309.0     7.0 s      18.0 s      100.0%     7.0 s       0.0 s
[2016-04-15T02:04Z] INFO  19:04:50,979 ProgressMeter - Total runtime 7.55 secs, 0.13 min, 0.00 hours
[2016-04-15T02:04Z] INFO  19:04:53,219 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T02:04Z] GATK: GenotypeGVCFs
[2016-04-15T02:04Z] INFO  19:04:55,163 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T02:04Z] INFO  19:04:55,165 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T02:04Z] INFO  19:04:55,166 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T02:04Z] INFO  19:04:55,166 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T02:04Z] INFO  19:04:55,169 HelpFormatter - Program Args: -T GenotypeGVCFs -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/gatk-haplotype-joint/Batch1/13/tx/tmpbmaaOb/Batch1-13_67477635_84455642.vcf.gz -L 13:67477636-84455642 --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18106_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18105_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18102_kapa-NGv3-PE100-NGv3.vcf.gz --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -nt 16 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T02:04Z] INFO  19:04:55,178 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T02:04Z] INFO  19:04:55,178 HelpFormatter - Date/Time: 2016/04/14 19:04:55
[2016-04-15T02:04Z] INFO  19:04:55,178 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T02:04Z] INFO  19:04:55,178 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T02:04Z] INFO  19:04:55,251 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T02:04Z] INFO  19:04:55,348 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T02:04Z] INFO  19:04:55,756 IntervalUtils - Processing 16978007 bp from intervals
[2016-04-15T02:04Z] WARN  19:04:55,757 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T02:04Z] WARN  19:04:55,757 IndexDictionaryUtils - Track variant2 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T02:04Z] WARN  19:04:55,757 IndexDictionaryUtils - Track variant3 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T02:04Z] WARN  19:04:55,757 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T02:04Z] INFO  19:04:55,766 MicroScheduler - Running the GATK in parallel mode with 16 total threads, 1 CPU thread(s) for each of 16 data thread(s), of 16 processors available on this machine
[2016-04-15T02:04Z] INFO  19:04:55,817 GenomeAnalysisEngine - Preparing for traversal
[2016-04-15T02:04Z] INFO  19:04:55,818 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T02:04Z] INFO  19:04:55,818 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T02:04Z] INFO  19:04:55,818 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T02:04Z] INFO  19:04:55,819 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T02:04Z] INFO  19:04:55,944 GenotypeGVCFs - Notice that the -ploidy parameter is ignored in GenotypeGVCFs tool as this is automatically determined by the input variant files
[2016-04-15T02:05Z] INFO  19:05:04,758 ProgressMeter -            done    456238.0     8.0 s      19.0 s      100.0%     8.0 s       0.0 s
[2016-04-15T02:05Z] INFO  19:05:04,759 ProgressMeter - Total runtime 8.94 secs, 0.15 min, 0.00 hours
[2016-04-15T02:05Z] INFO  19:05:07,216 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T02:05Z] GATK: GenotypeGVCFs
[2016-04-15T02:05Z] INFO  19:05:09,121 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T02:05Z] INFO  19:05:09,123 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T02:05Z] INFO  19:05:09,123 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T02:05Z] INFO  19:05:09,123 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T02:05Z] INFO  19:05:09,127 HelpFormatter - Program Args: -T GenotypeGVCFs -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/gatk-haplotype-joint/Batch1/13/tx/tmpSXqPrr/Batch1-13_86368117_101881935.vcf.gz -L 13:86368118-101881935 --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18106_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18105_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18102_kapa-NGv3-PE100-NGv3.vcf.gz --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -nt 16 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T02:05Z] INFO  19:05:09,134 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T02:05Z] INFO  19:05:09,135 HelpFormatter - Date/Time: 2016/04/14 19:05:09
[2016-04-15T02:05Z] INFO  19:05:09,135 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T02:05Z] INFO  19:05:09,135 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T02:05Z] INFO  19:05:09,214 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T02:05Z] INFO  19:05:09,372 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T02:05Z] INFO  19:05:09,877 IntervalUtils - Processing 15513818 bp from intervals
[2016-04-15T02:05Z] WARN  19:05:09,878 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T02:05Z] WARN  19:05:09,878 IndexDictionaryUtils - Track variant2 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T02:05Z] WARN  19:05:09,879 IndexDictionaryUtils - Track variant3 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T02:05Z] WARN  19:05:09,879 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T02:05Z] INFO  19:05:09,887 MicroScheduler - Running the GATK in parallel mode with 16 total threads, 1 CPU thread(s) for each of 16 data thread(s), of 16 processors available on this machine
[2016-04-15T02:05Z] INFO  19:05:09,939 GenomeAnalysisEngine - Preparing for traversal
[2016-04-15T02:05Z] INFO  19:05:09,940 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T02:05Z] INFO  19:05:09,940 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T02:05Z] INFO  19:05:09,941 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T02:05Z] INFO  19:05:09,941 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T02:05Z] INFO  19:05:10,072 GenotypeGVCFs - Notice that the -ploidy parameter is ignored in GenotypeGVCFs tool as this is automatically determined by the input variant files
[2016-04-15T02:05Z] INFO  19:05:18,858 ProgressMeter -            done    437048.0     8.0 s      20.0 s      100.0%     8.0 s       0.0 s
[2016-04-15T02:05Z] INFO  19:05:18,859 ProgressMeter - Total runtime 8.92 secs, 0.15 min, 0.00 hours
[2016-04-15T02:05Z] INFO  19:05:21,246 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T02:05Z] GATK: GenotypeGVCFs
[2016-04-15T02:05Z] INFO  19:05:23,296 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T02:05Z] INFO  19:05:23,298 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T02:05Z] INFO  19:05:23,298 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T02:05Z] INFO  19:05:23,298 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T02:05Z] INFO  19:05:23,301 HelpFormatter - Program Args: -T GenotypeGVCFs -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/gatk-haplotype-joint/Batch1/13/tx/tmpDDxZLd/Batch1-13_101890105_115169878.vcf.gz -L 13:101890106-115169878 --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18106_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18105_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18102_kapa-NGv3-PE100-NGv3.vcf.gz --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -nt 16 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T02:05Z] INFO  19:05:23,310 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T02:05Z] INFO  19:05:23,310 HelpFormatter - Date/Time: 2016/04/14 19:05:23
[2016-04-15T02:05Z] INFO  19:05:23,310 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T02:05Z] INFO  19:05:23,310 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T02:05Z] INFO  19:05:23,381 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T02:05Z] INFO  19:05:23,479 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T02:05Z] INFO  19:05:23,885 IntervalUtils - Processing 13279773 bp from intervals
[2016-04-15T02:05Z] WARN  19:05:23,886 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T02:05Z] WARN  19:05:23,886 IndexDictionaryUtils - Track variant2 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T02:05Z] WARN  19:05:23,886 IndexDictionaryUtils - Track variant3 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T02:05Z] WARN  19:05:23,886 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T02:05Z] INFO  19:05:23,895 MicroScheduler - Running the GATK in parallel mode with 16 total threads, 1 CPU thread(s) for each of 16 data thread(s), of 16 processors available on this machine
[2016-04-15T02:05Z] INFO  19:05:23,944 GenomeAnalysisEngine - Preparing for traversal
[2016-04-15T02:05Z] INFO  19:05:23,945 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T02:05Z] INFO  19:05:23,946 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T02:05Z] INFO  19:05:23,946 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T02:05Z] INFO  19:05:23,946 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T02:05Z] INFO  19:05:24,073 GenotypeGVCFs - Notice that the -ploidy parameter is ignored in GenotypeGVCFs tool as this is automatically determined by the input variant files
[2016-04-15T02:05Z] INFO  19:05:33,346 ProgressMeter -            done    492860.0     9.0 s      19.0 s       99.5%     9.0 s       0.0 s
[2016-04-15T02:05Z] INFO  19:05:33,346 ProgressMeter - Total runtime 9.40 secs, 0.16 min, 0.00 hours
[2016-04-15T02:05Z] INFO  19:05:35,413 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T02:05Z] GATK: GenotypeGVCFs
[2016-04-15T02:05Z] INFO  19:05:37,592 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T02:05Z] INFO  19:05:37,594 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T02:05Z] INFO  19:05:37,594 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T02:05Z] INFO  19:05:37,594 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T02:05Z] INFO  19:05:37,598 HelpFormatter - Program Args: -T GenotypeGVCFs -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/gatk-haplotype-joint/Batch1/14/tx/tmpSW33Aw/Batch1-14_0_19378574.vcf.gz -L 14:1-19378574 --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18106_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18105_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18102_kapa-NGv3-PE100-NGv3.vcf.gz --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -nt 16 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T02:05Z] INFO  19:05:37,606 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T02:05Z] INFO  19:05:37,606 HelpFormatter - Date/Time: 2016/04/14 19:05:37
[2016-04-15T02:05Z] INFO  19:05:37,606 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T02:05Z] INFO  19:05:37,606 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T02:05Z] INFO  19:05:37,678 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T02:05Z] INFO  19:05:37,775 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T02:05Z] INFO  19:05:38,184 IntervalUtils - Processing 19378574 bp from intervals
[2016-04-15T02:05Z] WARN  19:05:38,184 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T02:05Z] WARN  19:05:38,185 IndexDictionaryUtils - Track variant2 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T02:05Z] WARN  19:05:38,185 IndexDictionaryUtils - Track variant3 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T02:05Z] WARN  19:05:38,185 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T02:05Z] INFO  19:05:38,194 MicroScheduler - Running the GATK in parallel mode with 16 total threads, 1 CPU thread(s) for each of 16 data thread(s), of 16 processors available on this machine
[2016-04-15T02:05Z] INFO  19:05:38,244 GenomeAnalysisEngine - Preparing for traversal
[2016-04-15T02:05Z] INFO  19:05:38,245 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T02:05Z] INFO  19:05:38,245 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T02:05Z] INFO  19:05:38,246 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T02:05Z] INFO  19:05:38,246 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T02:05Z] INFO  19:05:38,373 GenotypeGVCFs - Notice that the -ploidy parameter is ignored in GenotypeGVCFs tool as this is automatically determined by the input variant files
[2016-04-15T02:05Z] INFO  19:05:40,822 ProgressMeter -            done     10401.0     2.0 s       4.1 m      100.0%     2.0 s       0.0 s
[2016-04-15T02:05Z] INFO  19:05:40,823 ProgressMeter - Total runtime 2.58 secs, 0.04 min, 0.00 hours
[2016-04-15T02:05Z] INFO  19:05:42,509 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T02:05Z] GATK: GenotypeGVCFs
[2016-04-15T02:05Z] INFO  19:05:44,656 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T02:05Z] INFO  19:05:44,658 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T02:05Z] INFO  19:05:44,658 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T02:05Z] INFO  19:05:44,658 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T02:05Z] INFO  19:05:44,662 HelpFormatter - Program Args: -T GenotypeGVCFs -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/gatk-haplotype-joint/Batch1/14/tx/tmp6RWPQh/Batch1-14_19553416_35066851.vcf.gz -L 14:19553417-35066851 --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18106_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18105_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18102_kapa-NGv3-PE100-NGv3.vcf.gz --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -nt 16 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T02:05Z] INFO  19:05:44,670 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T02:05Z] INFO  19:05:44,670 HelpFormatter - Date/Time: 2016/04/14 19:05:44
[2016-04-15T02:05Z] INFO  19:05:44,670 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T02:05Z] INFO  19:05:44,671 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T02:05Z] INFO  19:05:44,742 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T02:05Z] INFO  19:05:44,841 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T02:05Z] INFO  19:05:45,249 IntervalUtils - Processing 15513435 bp from intervals
[2016-04-15T02:05Z] WARN  19:05:45,250 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T02:05Z] WARN  19:05:45,250 IndexDictionaryUtils - Track variant2 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T02:05Z] WARN  19:05:45,250 IndexDictionaryUtils - Track variant3 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T02:05Z] WARN  19:05:45,250 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T02:05Z] INFO  19:05:45,259 MicroScheduler - Running the GATK in parallel mode with 16 total threads, 1 CPU thread(s) for each of 16 data thread(s), of 16 processors available on this machine
[2016-04-15T02:05Z] INFO  19:05:45,309 GenomeAnalysisEngine - Preparing for traversal
[2016-04-15T02:05Z] INFO  19:05:45,310 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T02:05Z] INFO  19:05:45,310 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T02:05Z] INFO  19:05:45,311 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T02:05Z] INFO  19:05:45,311 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T02:05Z] INFO  19:05:45,434 GenotypeGVCFs - Notice that the -ploidy parameter is ignored in GenotypeGVCFs tool as this is automatically determined by the input variant files
[2016-04-15T02:05Z] INFO  19:05:55,442 ProgressMeter -            done    647245.0    10.0 s      15.0 s      100.0%    10.0 s       0.0 s
[2016-04-15T02:05Z] INFO  19:05:55,442 ProgressMeter - Total runtime 10.13 secs, 0.17 min, 0.00 hours
[2016-04-15T02:05Z] INFO  19:05:57,510 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T02:05Z] GATK: GenotypeGVCFs
[2016-04-15T02:05Z] INFO  19:05:59,284 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T02:05Z] INFO  19:05:59,286 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T02:05Z] INFO  19:05:59,286 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T02:05Z] INFO  19:05:59,286 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T02:05Z] INFO  19:05:59,290 HelpFormatter - Program Args: -T GenotypeGVCFs -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/gatk-haplotype-joint/Batch1/14/tx/tmpdM6L1i/Batch1-14_35072553_50583270.vcf.gz -L 14:35072554-50583270 --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18106_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18105_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18102_kapa-NGv3-PE100-NGv3.vcf.gz --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -nt 16 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T02:05Z] INFO  19:05:59,298 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T02:05Z] INFO  19:05:59,299 HelpFormatter - Date/Time: 2016/04/14 19:05:59
[2016-04-15T02:05Z] INFO  19:05:59,299 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T02:05Z] INFO  19:05:59,299 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T02:05Z] INFO  19:05:59,371 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T02:05Z] INFO  19:05:59,468 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T02:05Z] INFO  19:05:59,907 IntervalUtils - Processing 15510717 bp from intervals
[2016-04-15T02:05Z] WARN  19:05:59,907 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T02:05Z] WARN  19:05:59,907 IndexDictionaryUtils - Track variant2 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T02:05Z] WARN  19:05:59,908 IndexDictionaryUtils - Track variant3 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T02:05Z] WARN  19:05:59,908 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T02:05Z] INFO  19:05:59,916 MicroScheduler - Running the GATK in parallel mode with 16 total threads, 1 CPU thread(s) for each of 16 data thread(s), of 16 processors available on this machine
[2016-04-15T02:05Z] INFO  19:05:59,966 GenomeAnalysisEngine - Preparing for traversal
[2016-04-15T02:05Z] INFO  19:05:59,967 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T02:05Z] INFO  19:05:59,968 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T02:05Z] INFO  19:05:59,968 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T02:05Z] INFO  19:05:59,968 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T02:06Z] INFO  19:06:00,095 GenotypeGVCFs - Notice that the -ploidy parameter is ignored in GenotypeGVCFs tool as this is automatically determined by the input variant files
[2016-04-15T02:06Z] INFO  19:06:08,844 ProgressMeter -            done    464807.0     8.0 s      19.0 s      100.0%     8.0 s       0.0 s
[2016-04-15T02:06Z] INFO  19:06:08,844 ProgressMeter - Total runtime 8.88 secs, 0.15 min, 0.00 hours
[2016-04-15T02:06Z] INFO  19:06:10,927 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T02:06Z] GATK: GenotypeGVCFs
[2016-04-15T02:06Z] INFO  19:06:12,867 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T02:06Z] INFO  19:06:12,872 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T02:06Z] INFO  19:06:12,873 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T02:06Z] INFO  19:06:12,873 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T02:06Z] INFO  19:06:12,882 HelpFormatter - Program Args: -T GenotypeGVCFs -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/gatk-haplotype-joint/Batch1/14/tx/tmp_dMG1m/Batch1-14_50585061_66096324.vcf.gz -L 14:50585062-66096324 --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18106_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18105_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18102_kapa-NGv3-PE100-NGv3.vcf.gz --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -nt 16 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T02:06Z] INFO  19:06:12,896 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T02:06Z] INFO  19:06:12,897 HelpFormatter - Date/Time: 2016/04/14 19:06:12
[2016-04-15T02:06Z] INFO  19:06:12,897 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T02:06Z] INFO  19:06:12,898 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T02:06Z] INFO  19:06:13,019 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T02:06Z] INFO  19:06:13,117 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T02:06Z] INFO  19:06:13,480 IntervalUtils - Processing 15511263 bp from intervals
[2016-04-15T02:06Z] WARN  19:06:13,481 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T02:06Z] WARN  19:06:13,481 IndexDictionaryUtils - Track variant2 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T02:06Z] WARN  19:06:13,481 IndexDictionaryUtils - Track variant3 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T02:06Z] WARN  19:06:13,481 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T02:06Z] INFO  19:06:13,490 MicroScheduler - Running the GATK in parallel mode with 16 total threads, 1 CPU thread(s) for each of 16 data thread(s), of 16 processors available on this machine
[2016-04-15T02:06Z] INFO  19:06:13,539 GenomeAnalysisEngine - Preparing for traversal
[2016-04-15T02:06Z] INFO  19:06:13,540 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T02:06Z] INFO  19:06:13,541 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T02:06Z] INFO  19:06:13,541 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T02:06Z] INFO  19:06:13,542 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T02:06Z] INFO  19:06:13,666 GenotypeGVCFs - Notice that the -ploidy parameter is ignored in GenotypeGVCFs tool as this is automatically determined by the input variant files
[2016-04-15T02:06Z] INFO  19:06:22,617 ProgressMeter -            done    577141.0     9.0 s      15.0 s      100.0%     9.0 s       0.0 s
[2016-04-15T02:06Z] INFO  19:06:22,618 ProgressMeter - Total runtime 9.08 secs, 0.15 min, 0.00 hours
[2016-04-15T02:06Z] INFO  19:06:25,089 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T02:06Z] GATK: GenotypeGVCFs
[2016-04-15T02:06Z] INFO  19:06:27,226 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T02:06Z] INFO  19:06:27,228 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T02:06Z] INFO  19:06:27,228 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T02:06Z] INFO  19:06:27,228 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T02:06Z] INFO  19:06:27,231 HelpFormatter - Program Args: -T GenotypeGVCFs -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/gatk-haplotype-joint/Batch1/14/tx/tmpE2h5de/Batch1-14_66135960_81646674.vcf.gz -L 14:66135961-81646674 --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18106_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18105_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18102_kapa-NGv3-PE100-NGv3.vcf.gz --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -nt 16 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T02:06Z] INFO  19:06:27,240 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T02:06Z] INFO  19:06:27,240 HelpFormatter - Date/Time: 2016/04/14 19:06:27
[2016-04-15T02:06Z] INFO  19:06:27,240 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T02:06Z] INFO  19:06:27,240 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T02:06Z] INFO  19:06:27,312 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T02:06Z] INFO  19:06:27,410 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T02:06Z] INFO  19:06:27,818 IntervalUtils - Processing 15510714 bp from intervals
[2016-04-15T02:06Z] WARN  19:06:27,818 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T02:06Z] WARN  19:06:27,819 IndexDictionaryUtils - Track variant2 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T02:06Z] WARN  19:06:27,819 IndexDictionaryUtils - Track variant3 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T02:06Z] WARN  19:06:27,819 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T02:06Z] INFO  19:06:27,827 MicroScheduler - Running the GATK in parallel mode with 16 total threads, 1 CPU thread(s) for each of 16 data thread(s), of 16 processors available on this machine
[2016-04-15T02:06Z] INFO  19:06:27,877 GenomeAnalysisEngine - Preparing for traversal
[2016-04-15T02:06Z] INFO  19:06:27,878 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T02:06Z] INFO  19:06:27,878 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T02:06Z] INFO  19:06:27,879 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T02:06Z] INFO  19:06:27,879 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T02:06Z] INFO  19:06:28,002 GenotypeGVCFs - Notice that the -ploidy parameter is ignored in GenotypeGVCFs tool as this is automatically determined by the input variant files
[2016-04-15T02:06Z] INFO  19:06:38,119 ProgressMeter -            done    592233.0    10.0 s      17.0 s      100.0%    10.0 s       0.0 s
[2016-04-15T02:06Z] INFO  19:06:38,120 ProgressMeter - Total runtime 10.24 secs, 0.17 min, 0.00 hours
[2016-04-15T02:06Z] INFO  19:06:40,150 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T02:06Z] GATK: GenotypeGVCFs
[2016-04-15T02:06Z] INFO  19:06:42,543 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T02:06Z] INFO  19:06:42,546 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T02:06Z] INFO  19:06:42,546 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T02:06Z] INFO  19:06:42,546 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T02:06Z] INFO  19:06:42,550 HelpFormatter - Program Args: -T GenotypeGVCFs -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/gatk-haplotype-joint/Batch1/14/tx/tmpdgoCrZ/Batch1-14_81651874_97299968.vcf.gz -L 14:81651875-97299968 --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18106_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18105_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18102_kapa-NGv3-PE100-NGv3.vcf.gz --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -nt 16 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T02:06Z] INFO  19:06:42,560 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T02:06Z] INFO  19:06:42,560 HelpFormatter - Date/Time: 2016/04/14 19:06:42
[2016-04-15T02:06Z] INFO  19:06:42,560 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T02:06Z] INFO  19:06:42,560 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T02:06Z] INFO  19:06:42,635 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T02:06Z] INFO  19:06:42,742 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T02:06Z] INFO  19:06:43,254 IntervalUtils - Processing 15648094 bp from intervals
[2016-04-15T02:06Z] WARN  19:06:43,255 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T02:06Z] WARN  19:06:43,255 IndexDictionaryUtils - Track variant2 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T02:06Z] WARN  19:06:43,255 IndexDictionaryUtils - Track variant3 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T02:06Z] WARN  19:06:43,255 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T02:06Z] INFO  19:06:43,264 MicroScheduler - Running the GATK in parallel mode with 16 total threads, 1 CPU thread(s) for each of 16 data thread(s), of 16 processors available on this machine
[2016-04-15T02:06Z] INFO  19:06:43,316 GenomeAnalysisEngine - Preparing for traversal
[2016-04-15T02:06Z] INFO  19:06:43,317 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T02:06Z] INFO  19:06:43,318 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T02:06Z] INFO  19:06:43,318 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T02:06Z] INFO  19:06:43,319 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T02:06Z] INFO  19:06:43,451 GenotypeGVCFs - Notice that the -ploidy parameter is ignored in GenotypeGVCFs tool as this is automatically determined by the input variant files
[2016-04-15T02:06Z] INFO  19:06:53,329 ProgressMeter -            done    549166.0    10.0 s      18.0 s      100.0%    10.0 s       0.0 s
[2016-04-15T02:06Z] INFO  19:06:53,330 ProgressMeter - Total runtime 10.01 secs, 0.17 min, 0.00 hours
[2016-04-15T02:06Z] INFO  19:06:55,973 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T02:06Z] GATK: GenotypeGVCFs
[2016-04-15T02:06Z] INFO  19:06:58,140 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T02:06Z] INFO  19:06:58,142 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T02:06Z] INFO  19:06:58,142 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T02:06Z] INFO  19:06:58,142 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T02:06Z] INFO  19:06:58,145 HelpFormatter - Program Args: -T GenotypeGVCFs -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/gatk-haplotype-joint/Batch1/14/tx/tmpFPaPxX/Batch1-14_97304098_107349540.vcf.gz -L 14:97304099-107349540 --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18106_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18105_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18102_kapa-NGv3-PE100-NGv3.vcf.gz --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -nt 16 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T02:06Z] INFO  19:06:58,154 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T02:06Z] INFO  19:06:58,154 HelpFormatter - Date/Time: 2016/04/14 19:06:58
[2016-04-15T02:06Z] INFO  19:06:58,154 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T02:06Z] INFO  19:06:58,154 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T02:06Z] INFO  19:06:58,228 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T02:06Z] INFO  19:06:58,327 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T02:06Z] INFO  19:06:58,748 IntervalUtils - Processing 10045442 bp from intervals
[2016-04-15T02:06Z] WARN  19:06:58,749 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T02:06Z] WARN  19:06:58,749 IndexDictionaryUtils - Track variant2 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T02:06Z] WARN  19:06:58,749 IndexDictionaryUtils - Track variant3 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T02:06Z] WARN  19:06:58,750 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T02:06Z] INFO  19:06:58,758 MicroScheduler - Running the GATK in parallel mode with 16 total threads, 1 CPU thread(s) for each of 16 data thread(s), of 16 processors available on this machine
[2016-04-15T02:06Z] INFO  19:06:58,809 GenomeAnalysisEngine - Preparing for traversal
[2016-04-15T02:06Z] INFO  19:06:58,810 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T02:06Z] INFO  19:06:58,811 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T02:06Z] INFO  19:06:58,811 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T02:06Z] INFO  19:06:58,812 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T02:06Z] INFO  19:06:58,938 GenotypeGVCFs - Notice that the -ploidy parameter is ignored in GenotypeGVCFs tool as this is automatically determined by the input variant files
[2016-04-15T02:07Z] INFO  19:07:07,156 ProgressMeter -            done    449787.0     8.0 s      18.0 s       99.4%     8.0 s       0.0 s
[2016-04-15T02:07Z] INFO  19:07:07,156 ProgressMeter - Total runtime 8.35 secs, 0.14 min, 0.00 hours
[2016-04-15T02:07Z] INFO  19:07:09,250 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T02:07Z] GATK: GenotypeGVCFs
[2016-04-15T02:07Z] INFO  19:07:11,073 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T02:07Z] INFO  19:07:11,075 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T02:07Z] INFO  19:07:11,075 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T02:07Z] INFO  19:07:11,076 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T02:07Z] INFO  19:07:11,079 HelpFormatter - Program Args: -T GenotypeGVCFs -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/gatk-haplotype-joint/Batch1/15/tx/tmpbo8P2z/Batch1-15_0_20740485.vcf.gz -L 15:1-20740485 --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18106_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18105_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18102_kapa-NGv3-PE100-NGv3.vcf.gz --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -nt 16 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T02:07Z] INFO  19:07:11,087 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T02:07Z] INFO  19:07:11,087 HelpFormatter - Date/Time: 2016/04/14 19:07:11
[2016-04-15T02:07Z] INFO  19:07:11,087 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T02:07Z] INFO  19:07:11,087 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T02:07Z] INFO  19:07:11,159 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T02:07Z] INFO  19:07:11,258 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T02:07Z] INFO  19:07:11,670 IntervalUtils - Processing 20740485 bp from intervals
[2016-04-15T02:07Z] WARN  19:07:11,670 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T02:07Z] WARN  19:07:11,671 IndexDictionaryUtils - Track variant2 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T02:07Z] WARN  19:07:11,671 IndexDictionaryUtils - Track variant3 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T02:07Z] WARN  19:07:11,671 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T02:07Z] INFO  19:07:11,679 MicroScheduler - Running the GATK in parallel mode with 16 total threads, 1 CPU thread(s) for each of 16 data thread(s), of 16 processors available on this machine
[2016-04-15T02:07Z] INFO  19:07:11,730 GenomeAnalysisEngine - Preparing for traversal
[2016-04-15T02:07Z] INFO  19:07:11,731 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T02:07Z] INFO  19:07:11,731 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T02:07Z] INFO  19:07:11,731 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T02:07Z] INFO  19:07:11,732 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T02:07Z] INFO  19:07:11,855 GenotypeGVCFs - Notice that the -ploidy parameter is ignored in GenotypeGVCFs tool as this is automatically determined by the input variant files
[2016-04-15T02:07Z] INFO  19:07:14,288 ProgressMeter -            done     24821.0     2.0 s     102.0 s      100.0%     2.0 s       0.0 s
[2016-04-15T02:07Z] INFO  19:07:14,289 ProgressMeter - Total runtime 2.56 secs, 0.04 min, 0.00 hours
[2016-04-15T02:07Z] INFO  19:07:15,932 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T02:07Z] GATK: GenotypeGVCFs
[2016-04-15T02:07Z] INFO  19:07:18,102 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T02:07Z] INFO  19:07:18,104 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T02:07Z] INFO  19:07:18,104 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T02:07Z] INFO  19:07:18,104 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T02:07Z] INFO  19:07:18,108 HelpFormatter - Program Args: -T GenotypeGVCFs -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/gatk-haplotype-joint/Batch1/15/tx/tmpi9ZBY3/Batch1-15_20741621_36872162.vcf.gz -L 15:20741622-36872162 --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18106_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18105_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18102_kapa-NGv3-PE100-NGv3.vcf.gz --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -nt 16 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T02:07Z] INFO  19:07:18,120 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T02:07Z] INFO  19:07:18,120 HelpFormatter - Date/Time: 2016/04/14 19:07:18
[2016-04-15T02:07Z] INFO  19:07:18,120 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T02:07Z] INFO  19:07:18,121 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T02:07Z] INFO  19:07:18,195 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T02:07Z] INFO  19:07:18,299 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T02:07Z] INFO  19:07:18,717 IntervalUtils - Processing 16130541 bp from intervals
[2016-04-15T02:07Z] WARN  19:07:18,718 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T02:07Z] WARN  19:07:18,718 IndexDictionaryUtils - Track variant2 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T02:07Z] WARN  19:07:18,718 IndexDictionaryUtils - Track variant3 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T02:07Z] WARN  19:07:18,719 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T02:07Z] INFO  19:07:18,727 MicroScheduler - Running the GATK in parallel mode with 16 total threads, 1 CPU thread(s) for each of 16 data thread(s), of 16 processors available on this machine
[2016-04-15T02:07Z] INFO  19:07:18,776 GenomeAnalysisEngine - Preparing for traversal
[2016-04-15T02:07Z] INFO  19:07:18,777 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T02:07Z] INFO  19:07:18,778 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T02:07Z] INFO  19:07:18,778 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T02:07Z] INFO  19:07:18,778 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T02:07Z] INFO  19:07:18,901 GenotypeGVCFs - Notice that the -ploidy parameter is ignored in GenotypeGVCFs tool as this is automatically determined by the input variant files
[2016-04-15T02:07Z] INFO  19:07:27,866 ProgressMeter -            done    521549.0     9.0 s      17.0 s      100.0%     9.0 s       0.0 s
[2016-04-15T02:07Z] INFO  19:07:27,866 ProgressMeter - Total runtime 9.09 secs, 0.15 min, 0.00 hours
[2016-04-15T02:07Z] INFO  19:07:30,070 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T02:07Z] GATK: GenotypeGVCFs
[2016-04-15T02:07Z] INFO  19:07:31,985 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T02:07Z] INFO  19:07:31,987 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T02:07Z] INFO  19:07:31,987 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T02:07Z] INFO  19:07:31,987 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T02:07Z] INFO  19:07:31,991 HelpFormatter - Program Args: -T GenotypeGVCFs -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/gatk-haplotype-joint/Batch1/15/tx/tmpYpMYzm/Batch1-15_36887086_52402170.vcf.gz -L 15:36887087-52402170 --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18106_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18105_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18102_kapa-NGv3-PE100-NGv3.vcf.gz --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -nt 16 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T02:07Z] INFO  19:07:31,999 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T02:07Z] INFO  19:07:32,000 HelpFormatter - Date/Time: 2016/04/14 19:07:31
[2016-04-15T02:07Z] INFO  19:07:32,000 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T02:07Z] INFO  19:07:32,000 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T02:07Z] INFO  19:07:32,076 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T02:07Z] INFO  19:07:32,177 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T02:07Z] INFO  19:07:32,666 IntervalUtils - Processing 15515084 bp from intervals
[2016-04-15T02:07Z] WARN  19:07:32,666 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T02:07Z] WARN  19:07:32,667 IndexDictionaryUtils - Track variant2 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T02:07Z] WARN  19:07:32,667 IndexDictionaryUtils - Track variant3 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T02:07Z] WARN  19:07:32,667 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T02:07Z] INFO  19:07:32,675 MicroScheduler - Running the GATK in parallel mode with 16 total threads, 1 CPU thread(s) for each of 16 data thread(s), of 16 processors available on this machine
[2016-04-15T02:07Z] INFO  19:07:32,726 GenomeAnalysisEngine - Preparing for traversal
[2016-04-15T02:07Z] INFO  19:07:32,727 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T02:07Z] INFO  19:07:32,728 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T02:07Z] INFO  19:07:32,728 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T02:07Z] INFO  19:07:32,728 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T02:07Z] INFO  19:07:32,855 GenotypeGVCFs - Notice that the -ploidy parameter is ignored in GenotypeGVCFs tool as this is automatically determined by the input variant files
[2016-04-15T02:07Z] WARN  19:07:42,820 ExactAFCalculator - this tool is currently set to genotype at most 6 alternate alleles in a given context, but the context at 15:40846104 has 8 alternate alleles so only the top alleles will be used; see the --max_alternate_alleles argument
[2016-04-15T02:07Z] INFO  19:07:43,577 ProgressMeter -            done    710080.0    10.0 s      15.0 s      100.0%    10.0 s       0.0 s
[2016-04-15T02:07Z] INFO  19:07:43,577 ProgressMeter - Total runtime 10.85 secs, 0.18 min, 0.00 hours
[2016-04-15T02:07Z] INFO  19:07:45,608 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T02:07Z] GATK: GenotypeGVCFs
[2016-04-15T02:07Z] INFO  19:07:47,545 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T02:07Z] INFO  19:07:47,547 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T02:07Z] INFO  19:07:47,547 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T02:07Z] INFO  19:07:47,547 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T02:07Z] INFO  19:07:47,551 HelpFormatter - Program Args: -T GenotypeGVCFs -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/gatk-haplotype-joint/Batch1/15/tx/tmpFvDDfP/Batch1-15_52404364_67923265.vcf.gz -L 15:52404365-67923265 --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18106_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18105_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18102_kapa-NGv3-PE100-NGv3.vcf.gz --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -nt 16 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T02:07Z] INFO  19:07:47,559 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T02:07Z] INFO  19:07:47,560 HelpFormatter - Date/Time: 2016/04/14 19:07:47
[2016-04-15T02:07Z] INFO  19:07:47,560 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T02:07Z] INFO  19:07:47,560 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T02:07Z] INFO  19:07:47,632 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T02:07Z] INFO  19:07:47,730 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T02:07Z] INFO  19:07:48,087 IntervalUtils - Processing 15518901 bp from intervals
[2016-04-15T02:07Z] WARN  19:07:48,088 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T02:07Z] WARN  19:07:48,088 IndexDictionaryUtils - Track variant2 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T02:07Z] WARN  19:07:48,088 IndexDictionaryUtils - Track variant3 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T02:07Z] WARN  19:07:48,088 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T02:07Z] INFO  19:07:48,097 MicroScheduler - Running the GATK in parallel mode with 16 total threads, 1 CPU thread(s) for each of 16 data thread(s), of 16 processors available on this machine
[2016-04-15T02:07Z] INFO  19:07:48,149 GenomeAnalysisEngine - Preparing for traversal
[2016-04-15T02:07Z] INFO  19:07:48,150 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T02:07Z] INFO  19:07:48,151 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T02:07Z] INFO  19:07:48,151 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T02:07Z] INFO  19:07:48,151 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T02:07Z] INFO  19:07:48,278 GenotypeGVCFs - Notice that the -ploidy parameter is ignored in GenotypeGVCFs tool as this is automatically determined by the input variant files
[2016-04-15T02:07Z] INFO  19:07:58,091 ProgressMeter -            done    626991.0     9.0 s      15.0 s      100.0%     9.0 s       0.0 s
[2016-04-15T02:07Z] INFO  19:07:58,091 ProgressMeter - Total runtime 9.94 secs, 0.17 min, 0.00 hours
[2016-04-15T02:08Z] INFO  19:08:00,238 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T02:08Z] GATK: GenotypeGVCFs
[2016-04-15T02:08Z] INFO  19:08:02,288 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T02:08Z] INFO  19:08:02,290 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T02:08Z] INFO  19:08:02,290 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T02:08Z] INFO  19:08:02,290 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T02:08Z] INFO  19:08:02,294 HelpFormatter - Program Args: -T GenotypeGVCFs -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/gatk-haplotype-joint/Batch1/15/tx/tmprm8np_/Batch1-15_67932890_83447639.vcf.gz -L 15:67932891-83447639 --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18106_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18105_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18102_kapa-NGv3-PE100-NGv3.vcf.gz --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -nt 16 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T02:08Z] INFO  19:08:02,302 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T02:08Z] INFO  19:08:02,302 HelpFormatter - Date/Time: 2016/04/14 19:08:02
[2016-04-15T02:08Z] INFO  19:08:02,303 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T02:08Z] INFO  19:08:02,303 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T02:08Z] INFO  19:08:02,374 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T02:08Z] INFO  19:08:02,472 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T02:08Z] INFO  19:08:02,883 IntervalUtils - Processing 15514749 bp from intervals
[2016-04-15T02:08Z] WARN  19:08:02,884 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T02:08Z] WARN  19:08:02,884 IndexDictionaryUtils - Track variant2 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T02:08Z] WARN  19:08:02,884 IndexDictionaryUtils - Track variant3 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T02:08Z] WARN  19:08:02,884 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T02:08Z] INFO  19:08:02,893 MicroScheduler - Running the GATK in parallel mode with 16 total threads, 1 CPU thread(s) for each of 16 data thread(s), of 16 processors available on this machine
[2016-04-15T02:08Z] INFO  19:08:02,943 GenomeAnalysisEngine - Preparing for traversal
[2016-04-15T02:08Z] INFO  19:08:02,944 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T02:08Z] INFO  19:08:02,944 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T02:08Z] INFO  19:08:02,945 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T02:08Z] INFO  19:08:02,945 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T02:08Z] INFO  19:08:03,071 GenotypeGVCFs - Notice that the -ploidy parameter is ignored in GenotypeGVCFs tool as this is automatically determined by the input variant files
[2016-04-15T02:08Z] INFO  19:08:12,976 ProgressMeter -            done    618383.0    10.0 s      16.0 s      100.0%    10.0 s       0.0 s
[2016-04-15T02:08Z] INFO  19:08:12,977 ProgressMeter - Total runtime 10.03 secs, 0.17 min, 0.00 hours
[2016-04-15T02:08Z] INFO  19:08:15,221 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T02:08Z] GATK: GenotypeGVCFs
[2016-04-15T02:08Z] INFO  19:08:17,279 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T02:08Z] INFO  19:08:17,281 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T02:08Z] INFO  19:08:17,281 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T02:08Z] INFO  19:08:17,281 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T02:08Z] INFO  19:08:17,285 HelpFormatter - Program Args: -T GenotypeGVCFs -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/gatk-haplotype-joint/Batch1/15/tx/tmpKG6pPn/Batch1-15_83448996_98982979.vcf.gz -L 15:83448997-98982979 --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18106_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18105_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18102_kapa-NGv3-PE100-NGv3.vcf.gz --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -nt 16 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T02:08Z] INFO  19:08:17,293 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T02:08Z] INFO  19:08:17,294 HelpFormatter - Date/Time: 2016/04/14 19:08:17
[2016-04-15T02:08Z] INFO  19:08:17,294 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T02:08Z] INFO  19:08:17,294 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T02:08Z] INFO  19:08:17,365 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T02:08Z] INFO  19:08:17,464 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T02:08Z] INFO  19:08:17,815 IntervalUtils - Processing 15533983 bp from intervals
[2016-04-15T02:08Z] WARN  19:08:17,816 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T02:08Z] WARN  19:08:17,816 IndexDictionaryUtils - Track variant2 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T02:08Z] WARN  19:08:17,816 IndexDictionaryUtils - Track variant3 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T02:08Z] WARN  19:08:17,817 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T02:08Z] INFO  19:08:17,825 MicroScheduler - Running the GATK in parallel mode with 16 total threads, 1 CPU thread(s) for each of 16 data thread(s), of 16 processors available on this machine
[2016-04-15T02:08Z] INFO  19:08:17,875 GenomeAnalysisEngine - Preparing for traversal
[2016-04-15T02:08Z] INFO  19:08:17,876 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T02:08Z] INFO  19:08:17,876 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T02:08Z] INFO  19:08:17,877 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T02:08Z] INFO  19:08:17,877 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T02:08Z] INFO  19:08:18,001 GenotypeGVCFs - Notice that the -ploidy parameter is ignored in GenotypeGVCFs tool as this is automatically determined by the input variant files
[2016-04-15T02:08Z] INFO  19:08:27,735 ProgressMeter -            done    566669.0     9.0 s      17.0 s      100.0%     9.0 s       0.0 s
[2016-04-15T02:08Z] INFO  19:08:27,749 ProgressMeter - Total runtime 9.87 secs, 0.16 min, 0.00 hours
[2016-04-15T02:08Z] INFO  19:08:30,278 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T02:08Z] GATK: GenotypeGVCFs
[2016-04-15T02:08Z] INFO  19:08:32,295 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T02:08Z] INFO  19:08:32,297 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T02:08Z] INFO  19:08:32,297 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T02:08Z] INFO  19:08:32,297 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T02:08Z] INFO  19:08:32,301 HelpFormatter - Program Args: -T GenotypeGVCFs -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/gatk-haplotype-joint/Batch1/15/tx/tmpdL5uD9/Batch1-15_98984299_102531392.vcf.gz -L 15:98984300-102531392 --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18106_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18105_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18102_kapa-NGv3-PE100-NGv3.vcf.gz --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -nt 16 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T02:08Z] INFO  19:08:32,309 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T02:08Z] INFO  19:08:32,309 HelpFormatter - Date/Time: 2016/04/14 19:08:32
[2016-04-15T02:08Z] INFO  19:08:32,309 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T02:08Z] INFO  19:08:32,309 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T02:08Z] INFO  19:08:32,381 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T02:08Z] INFO  19:08:32,479 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T02:08Z] INFO  19:08:32,892 IntervalUtils - Processing 3547093 bp from intervals
[2016-04-15T02:08Z] WARN  19:08:32,893 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T02:08Z] WARN  19:08:32,893 IndexDictionaryUtils - Track variant2 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T02:08Z] WARN  19:08:32,893 IndexDictionaryUtils - Track variant3 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T02:08Z] WARN  19:08:32,893 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T02:08Z] INFO  19:08:32,902 MicroScheduler - Running the GATK in parallel mode with 16 total threads, 1 CPU thread(s) for each of 16 data thread(s), of 16 processors available on this machine
[2016-04-15T02:08Z] INFO  19:08:32,953 GenomeAnalysisEngine - Preparing for traversal
[2016-04-15T02:08Z] INFO  19:08:32,954 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T02:08Z] INFO  19:08:32,954 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T02:08Z] INFO  19:08:32,954 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T02:08Z] INFO  19:08:32,955 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T02:08Z] INFO  19:08:33,077 GenotypeGVCFs - Notice that the -ploidy parameter is ignored in GenotypeGVCFs tool as this is automatically determined by the input variant files
[2016-04-15T02:08Z] INFO  19:08:36,137 ProgressMeter -            done    145936.0     3.0 s      21.0 s       99.7%     3.0 s       0.0 s
[2016-04-15T02:08Z] INFO  19:08:36,137 ProgressMeter - Total runtime 3.18 secs, 0.05 min, 0.00 hours
[2016-04-15T02:08Z] INFO  19:08:37,832 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T02:08Z] GATK: GenotypeGVCFs
[2016-04-15T02:08Z] INFO  19:08:39,815 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T02:08Z] INFO  19:08:39,817 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T02:08Z] INFO  19:08:39,817 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T02:08Z] INFO  19:08:39,817 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T02:08Z] INFO  19:08:39,821 HelpFormatter - Program Args: -T GenotypeGVCFs -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/gatk-haplotype-joint/Batch1/16/tx/tmpq1QhDp/Batch1-16_0_15528616.vcf.gz -L 16:1-15528616 --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18106_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18105_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18102_kapa-NGv3-PE100-NGv3.vcf.gz --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -nt 16 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T02:08Z] INFO  19:08:39,829 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T02:08Z] INFO  19:08:39,829 HelpFormatter - Date/Time: 2016/04/14 19:08:39
[2016-04-15T02:08Z] INFO  19:08:39,829 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T02:08Z] INFO  19:08:39,829 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T02:08Z] INFO  19:08:39,900 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T02:08Z] INFO  19:08:39,997 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T02:08Z] INFO  19:08:40,407 IntervalUtils - Processing 15528616 bp from intervals
[2016-04-15T02:08Z] WARN  19:08:40,407 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T02:08Z] WARN  19:08:40,408 IndexDictionaryUtils - Track variant2 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T02:08Z] WARN  19:08:40,408 IndexDictionaryUtils - Track variant3 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T02:08Z] WARN  19:08:40,408 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T02:08Z] INFO  19:08:40,416 MicroScheduler - Running the GATK in parallel mode with 16 total threads, 1 CPU thread(s) for each of 16 data thread(s), of 16 processors available on this machine
[2016-04-15T02:08Z] INFO  19:08:40,465 GenomeAnalysisEngine - Preparing for traversal
[2016-04-15T02:08Z] INFO  19:08:40,466 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T02:08Z] INFO  19:08:40,467 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T02:08Z] INFO  19:08:40,467 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T02:08Z] INFO  19:08:40,467 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T02:08Z] INFO  19:08:40,590 GenotypeGVCFs - Notice that the -ploidy parameter is ignored in GenotypeGVCFs tool as this is automatically determined by the input variant files
[2016-04-15T02:08Z] WARN  19:08:48,852 ExactAFCalculator - this tool is currently set to genotype at most 6 alternate alleles in a given context, but the context at 16:4737579 has 7 alternate alleles so only the top alleles will be used; see the --max_alternate_alleles argument
[2016-04-15T02:08Z] INFO  19:08:50,371 ProgressMeter -            done    911980.0     9.0 s      10.0 s      100.0%     9.0 s       0.0 s
[2016-04-15T02:08Z] INFO  19:08:50,371 ProgressMeter - Total runtime 9.90 secs, 0.17 min, 0.00 hours
[2016-04-15T02:08Z] INFO  19:08:52,569 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T02:08Z] GATK: GenotypeGVCFs
[2016-04-15T02:08Z] INFO  19:08:54,943 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T02:08Z] INFO  19:08:54,945 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T02:08Z] INFO  19:08:54,945 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T02:08Z] INFO  19:08:54,945 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T02:08Z] INFO  19:08:54,949 HelpFormatter - Program Args: -T GenotypeGVCFs -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/gatk-haplotype-joint/Batch1/16/tx/tmpEk4QOg/Batch1-16_15596122_31106473.vcf.gz -L 16:15596123-31106473 --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18106_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18105_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18102_kapa-NGv3-PE100-NGv3.vcf.gz --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -nt 16 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T02:08Z] INFO  19:08:54,957 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T02:08Z] INFO  19:08:54,958 HelpFormatter - Date/Time: 2016/04/14 19:08:54
[2016-04-15T02:08Z] INFO  19:08:54,958 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T02:08Z] INFO  19:08:54,958 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T02:08Z] INFO  19:08:55,030 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T02:08Z] INFO  19:08:55,132 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T02:08Z] INFO  19:08:55,556 IntervalUtils - Processing 15510351 bp from intervals
[2016-04-15T02:08Z] WARN  19:08:55,557 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T02:08Z] WARN  19:08:55,557 IndexDictionaryUtils - Track variant2 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T02:08Z] WARN  19:08:55,558 IndexDictionaryUtils - Track variant3 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T02:08Z] WARN  19:08:55,558 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T02:08Z] INFO  19:08:55,566 MicroScheduler - Running the GATK in parallel mode with 16 total threads, 1 CPU thread(s) for each of 16 data thread(s), of 16 processors available on this machine
[2016-04-15T02:08Z] INFO  19:08:55,617 GenomeAnalysisEngine - Preparing for traversal
[2016-04-15T02:08Z] INFO  19:08:55,618 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T02:08Z] INFO  19:08:55,619 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T02:08Z] INFO  19:08:55,619 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T02:08Z] INFO  19:08:55,620 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T02:08Z] INFO  19:08:55,745 GenotypeGVCFs - Notice that the -ploidy parameter is ignored in GenotypeGVCFs tool as this is automatically determined by the input variant files
[2016-04-15T02:09Z] INFO  19:09:05,150 ProgressMeter -            done    723633.0     9.0 s      13.0 s      100.0%     9.0 s       0.0 s
[2016-04-15T02:09Z] INFO  19:09:05,150 ProgressMeter - Total runtime 9.53 secs, 0.16 min, 0.00 hours
[2016-04-15T02:09Z] INFO  19:09:07,301 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T02:09Z] GATK: GenotypeGVCFs
[2016-04-15T02:09Z] INFO  19:09:09,233 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T02:09Z] INFO  19:09:09,235 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T02:09Z] INFO  19:09:09,235 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T02:09Z] INFO  19:09:09,235 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T02:09Z] INFO  19:09:09,239 HelpFormatter - Program Args: -T GenotypeGVCFs -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/gatk-haplotype-joint/Batch1/16/tx/tmpQV05Hy/Batch1-16_31120544_46629582.vcf.gz -L 16:31120545-46629582 --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18106_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18105_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18102_kapa-NGv3-PE100-NGv3.vcf.gz --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -nt 16 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T02:09Z] INFO  19:09:09,247 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T02:09Z] INFO  19:09:09,247 HelpFormatter - Date/Time: 2016/04/14 19:09:09
[2016-04-15T02:09Z] INFO  19:09:09,247 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T02:09Z] INFO  19:09:09,247 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T02:09Z] INFO  19:09:09,320 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T02:09Z] INFO  19:09:09,419 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T02:09Z] INFO  19:09:09,839 IntervalUtils - Processing 15509038 bp from intervals
[2016-04-15T02:09Z] WARN  19:09:09,839 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T02:09Z] WARN  19:09:09,840 IndexDictionaryUtils - Track variant2 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T02:09Z] WARN  19:09:09,840 IndexDictionaryUtils - Track variant3 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T02:09Z] WARN  19:09:09,840 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T02:09Z] INFO  19:09:09,849 MicroScheduler - Running the GATK in parallel mode with 16 total threads, 1 CPU thread(s) for each of 16 data thread(s), of 16 processors available on this machine
[2016-04-15T02:09Z] INFO  19:09:09,900 GenomeAnalysisEngine - Preparing for traversal
[2016-04-15T02:09Z] INFO  19:09:09,901 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T02:09Z] INFO  19:09:09,901 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T02:09Z] INFO  19:09:09,901 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T02:09Z] INFO  19:09:09,902 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T02:09Z] INFO  19:09:10,028 GenotypeGVCFs - Notice that the -ploidy parameter is ignored in GenotypeGVCFs tool as this is automatically determined by the input variant files
[2016-04-15T02:09Z] INFO  19:09:16,076 ProgressMeter -            done    177729.0     6.0 s      34.0 s      100.0%     6.0 s       0.0 s
[2016-04-15T02:09Z] INFO  19:09:16,077 ProgressMeter - Total runtime 6.18 secs, 0.10 min, 0.00 hours
[2016-04-15T02:09Z] INFO  19:09:18,031 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T02:09Z] GATK: GenotypeGVCFs
[2016-04-15T02:09Z] INFO  19:09:20,202 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T02:09Z] INFO  19:09:20,204 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T02:09Z] INFO  19:09:20,204 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T02:09Z] INFO  19:09:20,204 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T02:09Z] INFO  19:09:20,208 HelpFormatter - Program Args: -T GenotypeGVCFs -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/gatk-haplotype-joint/Batch1/16/tx/tmp3x_G2M/Batch1-16_46633742_64982002.vcf.gz -L 16:46633743-64982002 --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18106_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18105_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18102_kapa-NGv3-PE100-NGv3.vcf.gz --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -nt 16 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T02:09Z] INFO  19:09:20,216 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T02:09Z] INFO  19:09:20,217 HelpFormatter - Date/Time: 2016/04/14 19:09:20
[2016-04-15T02:09Z] INFO  19:09:20,217 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T02:09Z] INFO  19:09:20,217 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T02:09Z] INFO  19:09:20,288 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T02:09Z] INFO  19:09:20,388 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T02:09Z] INFO  19:09:20,805 IntervalUtils - Processing 18348260 bp from intervals
[2016-04-15T02:09Z] WARN  19:09:20,805 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T02:09Z] WARN  19:09:20,806 IndexDictionaryUtils - Track variant2 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T02:09Z] WARN  19:09:20,806 IndexDictionaryUtils - Track variant3 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T02:09Z] WARN  19:09:20,806 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T02:09Z] INFO  19:09:20,814 MicroScheduler - Running the GATK in parallel mode with 16 total threads, 1 CPU thread(s) for each of 16 data thread(s), of 16 processors available on this machine
[2016-04-15T02:09Z] INFO  19:09:20,864 GenomeAnalysisEngine - Preparing for traversal
[2016-04-15T02:09Z] INFO  19:09:20,865 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T02:09Z] INFO  19:09:20,866 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T02:09Z] INFO  19:09:20,866 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T02:09Z] INFO  19:09:20,866 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T02:09Z] INFO  19:09:20,990 GenotypeGVCFs - Notice that the -ploidy parameter is ignored in GenotypeGVCFs tool as this is automatically determined by the input variant files
[2016-04-15T02:09Z] INFO  19:09:31,349 ProgressMeter -            done    640169.0    10.0 s      16.0 s      100.0%    10.0 s       0.0 s
[2016-04-15T02:09Z] INFO  19:09:31,350 ProgressMeter - Total runtime 10.48 secs, 0.17 min, 0.00 hours
[2016-04-15T02:09Z] INFO  19:09:33,589 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T02:09Z] GATK: GenotypeGVCFs
[2016-04-15T02:09Z] INFO  19:09:35,530 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T02:09Z] INFO  19:09:35,532 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T02:09Z] INFO  19:09:35,532 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T02:09Z] INFO  19:09:35,532 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T02:09Z] INFO  19:09:35,536 HelpFormatter - Program Args: -T GenotypeGVCFs -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/gatk-haplotype-joint/Batch1/16/tx/tmpVppOxT/Batch1-16_64982511_80574976.vcf.gz -L 16:64982512-80574976 --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18106_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18105_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18102_kapa-NGv3-PE100-NGv3.vcf.gz --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -nt 16 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T02:09Z] INFO  19:09:35,545 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T02:09Z] INFO  19:09:35,545 HelpFormatter - Date/Time: 2016/04/14 19:09:35
[2016-04-15T02:09Z] INFO  19:09:35,545 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T02:09Z] INFO  19:09:35,545 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T02:09Z] INFO  19:09:35,620 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T02:09Z] INFO  19:09:35,717 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T02:09Z] INFO  19:09:36,258 IntervalUtils - Processing 15592465 bp from intervals
[2016-04-15T02:09Z] WARN  19:09:36,259 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T02:09Z] WARN  19:09:36,260 IndexDictionaryUtils - Track variant2 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T02:09Z] WARN  19:09:36,260 IndexDictionaryUtils - Track variant3 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T02:09Z] WARN  19:09:36,261 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T02:09Z] INFO  19:09:36,281 MicroScheduler - Running the GATK in parallel mode with 16 total threads, 1 CPU thread(s) for each of 16 data thread(s), of 16 processors available on this machine
[2016-04-15T02:09Z] INFO  19:09:36,401 GenomeAnalysisEngine - Preparing for traversal
[2016-04-15T02:09Z] INFO  19:09:36,403 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T02:09Z] INFO  19:09:36,404 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T02:09Z] INFO  19:09:36,405 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T02:09Z] INFO  19:09:36,406 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T02:09Z] INFO  19:09:36,677 GenotypeGVCFs - Notice that the -ploidy parameter is ignored in GenotypeGVCFs tool as this is automatically determined by the input variant files
[2016-04-15T02:09Z] INFO  19:09:45,705 ProgressMeter -            done    745314.0     9.0 s      12.0 s      100.0%     9.0 s       0.0 s
[2016-04-15T02:09Z] INFO  19:09:45,706 ProgressMeter - Total runtime 9.30 secs, 0.16 min, 0.00 hours
[2016-04-15T02:09Z] INFO  19:09:48,065 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T02:09Z] GATK: GenotypeGVCFs
[2016-04-15T02:09Z] INFO  19:09:50,019 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T02:09Z] INFO  19:09:50,021 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T02:09Z] INFO  19:09:50,021 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T02:09Z] INFO  19:09:50,021 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T02:09Z] INFO  19:09:50,025 HelpFormatter - Program Args: -T GenotypeGVCFs -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/gatk-haplotype-joint/Batch1/16/tx/tmpuuvhyy/Batch1-16_80575258_90354753.vcf.gz -L 16:80575259-90354753 --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18106_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18105_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18102_kapa-NGv3-PE100-NGv3.vcf.gz --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -nt 16 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T02:09Z] INFO  19:09:50,033 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T02:09Z] INFO  19:09:50,033 HelpFormatter - Date/Time: 2016/04/14 19:09:50
[2016-04-15T02:09Z] INFO  19:09:50,034 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T02:09Z] INFO  19:09:50,034 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T02:09Z] INFO  19:09:50,105 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T02:09Z] INFO  19:09:50,202 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T02:09Z] INFO  19:09:50,617 IntervalUtils - Processing 9779495 bp from intervals
[2016-04-15T02:09Z] WARN  19:09:50,618 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T02:09Z] WARN  19:09:50,618 IndexDictionaryUtils - Track variant2 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T02:09Z] WARN  19:09:50,618 IndexDictionaryUtils - Track variant3 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T02:09Z] WARN  19:09:50,618 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T02:09Z] INFO  19:09:50,627 MicroScheduler - Running the GATK in parallel mode with 16 total threads, 1 CPU thread(s) for each of 16 data thread(s), of 16 processors available on this machine
[2016-04-15T02:09Z] INFO  19:09:50,677 GenomeAnalysisEngine - Preparing for traversal
[2016-04-15T02:09Z] INFO  19:09:50,678 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T02:09Z] INFO  19:09:50,678 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T02:09Z] INFO  19:09:50,678 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T02:09Z] INFO  19:09:50,679 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T02:09Z] INFO  19:09:50,802 GenotypeGVCFs - Notice that the -ploidy parameter is ignored in GenotypeGVCFs tool as this is automatically determined by the input variant files
[2016-04-15T02:09Z] INFO  19:09:56,428 ProgressMeter -            done    535214.0     5.0 s      10.0 s       99.3%     5.0 s       0.0 s
[2016-04-15T02:09Z] INFO  19:09:56,429 ProgressMeter - Total runtime 5.75 secs, 0.10 min, 0.00 hours
[2016-04-15T02:09Z] INFO  19:09:58,308 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T02:09Z] GATK: GenotypeGVCFs
[2016-04-15T02:10Z] INFO  19:10:00,320 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T02:10Z] INFO  19:10:00,322 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T02:10Z] INFO  19:10:00,322 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T02:10Z] INFO  19:10:00,322 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T02:10Z] INFO  19:10:00,326 HelpFormatter - Program Args: -T GenotypeGVCFs -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/gatk-haplotype-joint/Batch1/17/tx/tmpwEZ14X/Batch1-17_0_15511002.vcf.gz -L 17:1-15511002 --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18106_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18105_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18102_kapa-NGv3-PE100-NGv3.vcf.gz --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -nt 16 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T02:10Z] INFO  19:10:00,334 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T02:10Z] INFO  19:10:00,334 HelpFormatter - Date/Time: 2016/04/14 19:10:00
[2016-04-15T02:10Z] INFO  19:10:00,335 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T02:10Z] INFO  19:10:00,335 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T02:10Z] INFO  19:10:00,410 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T02:10Z] INFO  19:10:00,516 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T02:10Z] INFO  19:10:01,004 IntervalUtils - Processing 15511002 bp from intervals
[2016-04-15T02:10Z] WARN  19:10:01,005 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T02:10Z] WARN  19:10:01,005 IndexDictionaryUtils - Track variant2 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T02:10Z] WARN  19:10:01,005 IndexDictionaryUtils - Track variant3 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T02:10Z] WARN  19:10:01,006 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T02:10Z] INFO  19:10:01,014 MicroScheduler - Running the GATK in parallel mode with 16 total threads, 1 CPU thread(s) for each of 16 data thread(s), of 16 processors available on this machine
[2016-04-15T02:10Z] INFO  19:10:01,066 GenomeAnalysisEngine - Preparing for traversal
[2016-04-15T02:10Z] INFO  19:10:01,067 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T02:10Z] INFO  19:10:01,068 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T02:10Z] INFO  19:10:01,068 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T02:10Z] INFO  19:10:01,068 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T02:10Z] INFO  19:10:01,196 GenotypeGVCFs - Notice that the -ploidy parameter is ignored in GenotypeGVCFs tool as this is automatically determined by the input variant files
[2016-04-15T02:10Z] INFO  19:10:12,986 ProgressMeter -            done    919269.0    11.0 s      12.0 s      100.0%    11.0 s       0.0 s
[2016-04-15T02:10Z] INFO  19:10:12,987 ProgressMeter - Total runtime 11.92 secs, 0.20 min, 0.00 hours
[2016-04-15T02:10Z] INFO  19:10:15,349 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T02:10Z] GATK: GenotypeGVCFs
[2016-04-15T02:10Z] INFO  19:10:17,344 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T02:10Z] INFO  19:10:17,346 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T02:10Z] INFO  19:10:17,346 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T02:10Z] INFO  19:10:17,346 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T02:10Z] INFO  19:10:17,350 HelpFormatter - Program Args: -T GenotypeGVCFs -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/gatk-haplotype-joint/Batch1/17/tx/tmpu8sbwl/Batch1-17_15515955_31039213.vcf.gz -L 17:15515956-31039213 --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18106_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18105_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18102_kapa-NGv3-PE100-NGv3.vcf.gz --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -nt 16 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T02:10Z] INFO  19:10:17,358 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T02:10Z] INFO  19:10:17,359 HelpFormatter - Date/Time: 2016/04/14 19:10:17
[2016-04-15T02:10Z] INFO  19:10:17,359 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T02:10Z] INFO  19:10:17,359 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T02:10Z] INFO  19:10:17,432 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T02:10Z] INFO  19:10:17,530 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T02:10Z] INFO  19:10:17,945 IntervalUtils - Processing 15523258 bp from intervals
[2016-04-15T02:10Z] WARN  19:10:17,946 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T02:10Z] WARN  19:10:17,946 IndexDictionaryUtils - Track variant2 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T02:10Z] WARN  19:10:17,946 IndexDictionaryUtils - Track variant3 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T02:10Z] WARN  19:10:17,946 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T02:10Z] INFO  19:10:17,955 MicroScheduler - Running the GATK in parallel mode with 16 total threads, 1 CPU thread(s) for each of 16 data thread(s), of 16 processors available on this machine
[2016-04-15T02:10Z] INFO  19:10:18,005 GenomeAnalysisEngine - Preparing for traversal
[2016-04-15T02:10Z] INFO  19:10:18,006 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T02:10Z] INFO  19:10:18,006 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T02:10Z] INFO  19:10:18,007 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T02:10Z] INFO  19:10:18,007 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T02:10Z] INFO  19:10:18,134 GenotypeGVCFs - Notice that the -ploidy parameter is ignored in GenotypeGVCFs tool as this is automatically determined by the input variant files
[2016-04-15T02:10Z] INFO  19:10:28,450 ProgressMeter -            done    593431.0    10.0 s      17.0 s      100.0%    10.0 s       0.0 s
[2016-04-15T02:10Z] INFO  19:10:28,451 ProgressMeter - Total runtime 10.44 secs, 0.17 min, 0.00 hours
[2016-04-15T02:10Z] INFO  19:10:30,487 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T02:10Z] GATK: GenotypeGVCFs
[2016-04-15T02:10Z] INFO  19:10:32,659 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T02:10Z] INFO  19:10:32,661 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T02:10Z] INFO  19:10:32,662 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T02:10Z] INFO  19:10:32,662 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T02:10Z] INFO  19:10:32,665 HelpFormatter - Program Args: -T GenotypeGVCFs -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/gatk-haplotype-joint/Batch1/17/tx/tmp1pcDFq/Batch1-17_31048040_46607237.vcf.gz -L 17:31048041-46607237 --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18106_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18105_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18102_kapa-NGv3-PE100-NGv3.vcf.gz --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -nt 16 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T02:10Z] INFO  19:10:32,674 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T02:10Z] INFO  19:10:32,674 HelpFormatter - Date/Time: 2016/04/14 19:10:32
[2016-04-15T02:10Z] INFO  19:10:32,674 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T02:10Z] INFO  19:10:32,674 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T02:10Z] INFO  19:10:32,746 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T02:10Z] INFO  19:10:32,845 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T02:10Z] INFO  19:10:33,260 IntervalUtils - Processing 15559197 bp from intervals
[2016-04-15T02:10Z] WARN  19:10:33,261 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T02:10Z] WARN  19:10:33,261 IndexDictionaryUtils - Track variant2 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T02:10Z] WARN  19:10:33,261 IndexDictionaryUtils - Track variant3 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T02:10Z] WARN  19:10:33,261 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T02:10Z] INFO  19:10:33,270 MicroScheduler - Running the GATK in parallel mode with 16 total threads, 1 CPU thread(s) for each of 16 data thread(s), of 16 processors available on this machine
[2016-04-15T02:10Z] INFO  19:10:33,320 GenomeAnalysisEngine - Preparing for traversal
[2016-04-15T02:10Z] INFO  19:10:33,321 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T02:10Z] INFO  19:10:33,321 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T02:10Z] INFO  19:10:33,322 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T02:10Z] INFO  19:10:33,322 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T02:10Z] INFO  19:10:33,446 GenotypeGVCFs - Notice that the -ploidy parameter is ignored in GenotypeGVCFs tool as this is automatically determined by the input variant files
[2016-04-15T02:10Z] INFO  19:10:43,843 ProgressMeter -            done    868546.0    10.0 s      12.0 s      100.0%    10.0 s       0.0 s
[2016-04-15T02:10Z] INFO  19:10:43,843 ProgressMeter - Total runtime 10.52 secs, 0.18 min, 0.00 hours
[2016-04-15T02:10Z] INFO  19:10:46,035 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T02:10Z] GATK: GenotypeGVCFs
[2016-04-15T02:10Z] INFO  19:10:48,232 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T02:10Z] INFO  19:10:48,234 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T02:10Z] INFO  19:10:48,234 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T02:10Z] INFO  19:10:48,234 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T02:10Z] INFO  19:10:48,238 HelpFormatter - Program Args: -T GenotypeGVCFs -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/gatk-haplotype-joint/Batch1/17/tx/tmpCrWtDY/Batch1-17_46607689_62121560.vcf.gz -L 17:46607690-62121560 --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18106_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18105_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18102_kapa-NGv3-PE100-NGv3.vcf.gz --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -nt 16 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T02:10Z] INFO  19:10:48,246 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T02:10Z] INFO  19:10:48,246 HelpFormatter - Date/Time: 2016/04/14 19:10:48
[2016-04-15T02:10Z] INFO  19:10:48,246 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T02:10Z] INFO  19:10:48,247 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T02:10Z] INFO  19:10:48,318 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T02:10Z] INFO  19:10:48,417 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T02:10Z] INFO  19:10:48,844 IntervalUtils - Processing 15513871 bp from intervals
[2016-04-15T02:10Z] WARN  19:10:48,845 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T02:10Z] WARN  19:10:48,845 IndexDictionaryUtils - Track variant2 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T02:10Z] WARN  19:10:48,845 IndexDictionaryUtils - Track variant3 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T02:10Z] WARN  19:10:48,845 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T02:10Z] INFO  19:10:48,854 MicroScheduler - Running the GATK in parallel mode with 16 total threads, 1 CPU thread(s) for each of 16 data thread(s), of 16 processors available on this machine
[2016-04-15T02:10Z] INFO  19:10:48,905 GenomeAnalysisEngine - Preparing for traversal
[2016-04-15T02:10Z] INFO  19:10:48,906 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T02:10Z] INFO  19:10:48,906 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T02:10Z] INFO  19:10:48,906 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T02:10Z] INFO  19:10:48,907 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T02:10Z] INFO  19:10:49,033 GenotypeGVCFs - Notice that the -ploidy parameter is ignored in GenotypeGVCFs tool as this is automatically determined by the input variant files
[2016-04-15T02:10Z] INFO  19:10:58,450 ProgressMeter -            done    630672.0     9.0 s      15.0 s      100.0%     9.0 s       0.0 s
[2016-04-15T02:10Z] INFO  19:10:58,451 ProgressMeter - Total runtime 9.54 secs, 0.16 min, 0.00 hours
[2016-04-15T02:11Z] INFO  19:11:00,813 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T02:11Z] GATK: GenotypeGVCFs
[2016-04-15T02:11Z] INFO  19:11:02,848 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T02:11Z] INFO  19:11:02,850 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T02:11Z] INFO  19:11:02,850 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T02:11Z] INFO  19:11:02,850 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T02:11Z] INFO  19:11:02,854 HelpFormatter - Program Args: -T GenotypeGVCFs -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/gatk-haplotype-joint/Batch1/17/tx/tmp1HNbQp/Batch1-17_62122219_77705154.vcf.gz -L 17:62122220-77705154 --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18106_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18105_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18102_kapa-NGv3-PE100-NGv3.vcf.gz --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -nt 16 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T02:11Z] INFO  19:11:02,862 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T02:11Z] INFO  19:11:02,862 HelpFormatter - Date/Time: 2016/04/14 19:11:02
[2016-04-15T02:11Z] INFO  19:11:02,863 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T02:11Z] INFO  19:11:02,863 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T02:11Z] INFO  19:11:02,936 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T02:11Z] INFO  19:11:03,035 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T02:11Z] INFO  19:11:03,448 IntervalUtils - Processing 15582935 bp from intervals
[2016-04-15T02:11Z] WARN  19:11:03,449 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T02:11Z] WARN  19:11:03,449 IndexDictionaryUtils - Track variant2 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T02:11Z] WARN  19:11:03,450 IndexDictionaryUtils - Track variant3 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T02:11Z] WARN  19:11:03,450 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T02:11Z] INFO  19:11:03,458 MicroScheduler - Running the GATK in parallel mode with 16 total threads, 1 CPU thread(s) for each of 16 data thread(s), of 16 processors available on this machine
[2016-04-15T02:11Z] INFO  19:11:03,508 GenomeAnalysisEngine - Preparing for traversal
[2016-04-15T02:11Z] INFO  19:11:03,509 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T02:11Z] INFO  19:11:03,509 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T02:11Z] INFO  19:11:03,510 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T02:11Z] INFO  19:11:03,510 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T02:11Z] INFO  19:11:03,639 GenotypeGVCFs - Notice that the -ploidy parameter is ignored in GenotypeGVCFs tool as this is automatically determined by the input variant files
[2016-04-15T02:11Z] INFO  19:11:13,662 ProgressMeter -            done    727939.0    10.0 s      13.0 s      100.0%    10.0 s       0.0 s
[2016-04-15T02:11Z] INFO  19:11:13,662 ProgressMeter - Total runtime 10.15 secs, 0.17 min, 0.00 hours
[2016-04-15T02:11Z] INFO  19:11:15,739 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T02:11Z] GATK: GenotypeGVCFs
[2016-04-15T02:11Z] INFO  19:11:17,780 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T02:11Z] INFO  19:11:17,781 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T02:11Z] INFO  19:11:17,782 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T02:11Z] INFO  19:11:17,782 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T02:11Z] INFO  19:11:17,785 HelpFormatter - Program Args: -T GenotypeGVCFs -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/gatk-haplotype-joint/Batch1/17/tx/tmpbT1bgG/Batch1-17_77707305_81195210.vcf.gz -L 17:77707306-81195210 --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18106_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18105_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18102_kapa-NGv3-PE100-NGv3.vcf.gz --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -nt 16 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T02:11Z] INFO  19:11:17,793 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T02:11Z] INFO  19:11:17,793 HelpFormatter - Date/Time: 2016/04/14 19:11:17
[2016-04-15T02:11Z] INFO  19:11:17,794 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T02:11Z] INFO  19:11:17,794 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T02:11Z] INFO  19:11:17,865 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T02:11Z] INFO  19:11:17,962 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T02:11Z] INFO  19:11:18,374 IntervalUtils - Processing 3487905 bp from intervals
[2016-04-15T02:11Z] WARN  19:11:18,374 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T02:11Z] WARN  19:11:18,375 IndexDictionaryUtils - Track variant2 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T02:11Z] WARN  19:11:18,375 IndexDictionaryUtils - Track variant3 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T02:11Z] WARN  19:11:18,375 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T02:11Z] INFO  19:11:18,383 MicroScheduler - Running the GATK in parallel mode with 16 total threads, 1 CPU thread(s) for each of 16 data thread(s), of 16 processors available on this machine
[2016-04-15T02:11Z] INFO  19:11:18,433 GenomeAnalysisEngine - Preparing for traversal
[2016-04-15T02:11Z] INFO  19:11:18,433 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T02:11Z] INFO  19:11:18,434 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T02:11Z] INFO  19:11:18,434 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T02:11Z] INFO  19:11:18,435 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T02:11Z] INFO  19:11:18,557 GenotypeGVCFs - Notice that the -ploidy parameter is ignored in GenotypeGVCFs tool as this is automatically determined by the input variant files
[2016-04-15T02:11Z] INFO  19:11:21,775 ProgressMeter -            done    263012.0     3.0 s      12.0 s       99.7%     3.0 s       0.0 s
[2016-04-15T02:11Z] INFO  19:11:21,776 ProgressMeter - Total runtime 3.34 secs, 0.06 min, 0.00 hours
[2016-04-15T02:11Z] INFO  19:11:23,541 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T02:11Z] GATK: GenotypeGVCFs
[2016-04-15T02:11Z] INFO  19:11:25,428 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T02:11Z] INFO  19:11:25,430 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T02:11Z] INFO  19:11:25,430 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T02:11Z] INFO  19:11:25,430 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T02:11Z] INFO  19:11:25,434 HelpFormatter - Program Args: -T GenotypeGVCFs -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/gatk-haplotype-joint/Batch1/18/tx/tmp8lOazs/Batch1-18_0_18531348.vcf.gz -L 18:1-18531348 --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18106_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18105_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18102_kapa-NGv3-PE100-NGv3.vcf.gz --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -nt 16 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T02:11Z] INFO  19:11:25,447 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T02:11Z] INFO  19:11:25,447 HelpFormatter - Date/Time: 2016/04/14 19:11:25
[2016-04-15T02:11Z] INFO  19:11:25,448 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T02:11Z] INFO  19:11:25,448 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T02:11Z] INFO  19:11:25,590 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T02:11Z] INFO  19:11:25,741 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T02:11Z] INFO  19:11:26,238 IntervalUtils - Processing 18531348 bp from intervals
[2016-04-15T02:11Z] WARN  19:11:26,239 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T02:11Z] WARN  19:11:26,239 IndexDictionaryUtils - Track variant2 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T02:11Z] WARN  19:11:26,239 IndexDictionaryUtils - Track variant3 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T02:11Z] WARN  19:11:26,239 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T02:11Z] INFO  19:11:26,248 MicroScheduler - Running the GATK in parallel mode with 16 total threads, 1 CPU thread(s) for each of 16 data thread(s), of 16 processors available on this machine
[2016-04-15T02:11Z] INFO  19:11:26,299 GenomeAnalysisEngine - Preparing for traversal
[2016-04-15T02:11Z] INFO  19:11:26,300 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T02:11Z] INFO  19:11:26,300 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T02:11Z] INFO  19:11:26,301 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T02:11Z] INFO  19:11:26,301 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T02:11Z] INFO  19:11:26,429 GenotypeGVCFs - Notice that the -ploidy parameter is ignored in GenotypeGVCFs tool as this is automatically determined by the input variant files
[2016-04-15T02:11Z] INFO  19:11:38,451 ProgressMeter -            done    562896.0    12.0 s      21.0 s      100.0%    12.0 s       0.0 s
[2016-04-15T02:11Z] INFO  19:11:38,452 ProgressMeter - Total runtime 12.15 secs, 0.20 min, 0.00 hours
[2016-04-15T02:11Z] INFO  19:11:41,002 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T02:11Z] GATK: GenotypeGVCFs
[2016-04-15T02:11Z] INFO  19:11:43,191 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T02:11Z] INFO  19:11:43,193 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T02:11Z] INFO  19:11:43,193 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T02:11Z] INFO  19:11:43,193 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T02:11Z] INFO  19:11:43,197 HelpFormatter - Program Args: -T GenotypeGVCFs -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/gatk-haplotype-joint/Batch1/18/tx/tmpmNE1py/Batch1-18_18533538_34081962.vcf.gz -L 18:18533539-34081962 --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18106_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18105_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18102_kapa-NGv3-PE100-NGv3.vcf.gz --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -nt 16 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T02:11Z] INFO  19:11:43,205 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T02:11Z] INFO  19:11:43,205 HelpFormatter - Date/Time: 2016/04/14 19:11:43
[2016-04-15T02:11Z] INFO  19:11:43,205 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T02:11Z] INFO  19:11:43,205 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T02:11Z] INFO  19:11:43,277 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T02:11Z] INFO  19:11:43,374 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T02:11Z] INFO  19:11:43,788 IntervalUtils - Processing 15548424 bp from intervals
[2016-04-15T02:11Z] WARN  19:11:43,789 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T02:11Z] WARN  19:11:43,789 IndexDictionaryUtils - Track variant2 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T02:11Z] WARN  19:11:43,789 IndexDictionaryUtils - Track variant3 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T02:11Z] WARN  19:11:43,789 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T02:11Z] INFO  19:11:43,798 MicroScheduler - Running the GATK in parallel mode with 16 total threads, 1 CPU thread(s) for each of 16 data thread(s), of 16 processors available on this machine
[2016-04-15T02:11Z] INFO  19:11:43,847 GenomeAnalysisEngine - Preparing for traversal
[2016-04-15T02:11Z] INFO  19:11:43,848 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T02:11Z] INFO  19:11:43,848 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T02:11Z] INFO  19:11:43,849 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T02:11Z] INFO  19:11:43,849 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T02:11Z] INFO  19:11:43,971 GenotypeGVCFs - Notice that the -ploidy parameter is ignored in GenotypeGVCFs tool as this is automatically determined by the input variant files
[2016-04-15T02:11Z] INFO  19:11:53,811 ProgressMeter -            done    483416.0     9.0 s      20.0 s      100.0%     9.0 s       0.0 s
[2016-04-15T02:11Z] INFO  19:11:53,811 ProgressMeter - Total runtime 9.96 secs, 0.17 min, 0.00 hours
[2016-04-15T02:11Z] INFO  19:11:56,285 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T02:11Z] GATK: GenotypeGVCFs
[2016-04-15T02:11Z] INFO  19:11:58,312 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T02:11Z] INFO  19:11:58,314 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T02:11Z] INFO  19:11:58,314 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T02:11Z] INFO  19:11:58,315 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T02:11Z] INFO  19:11:58,318 HelpFormatter - Program Args: -T GenotypeGVCFs -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/gatk-haplotype-joint/Batch1/18/tx/tmpvxvJhX/Batch1-18_34092400_49867248.vcf.gz -L 18:34092401-49867248 --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18106_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18105_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18102_kapa-NGv3-PE100-NGv3.vcf.gz --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -nt 16 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T02:11Z] INFO  19:11:58,327 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T02:11Z] INFO  19:11:58,327 HelpFormatter - Date/Time: 2016/04/14 19:11:58
[2016-04-15T02:11Z] INFO  19:11:58,328 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T02:11Z] INFO  19:11:58,328 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T02:11Z] INFO  19:11:58,399 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T02:11Z] INFO  19:11:58,497 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T02:11Z] INFO  19:11:58,906 IntervalUtils - Processing 15774848 bp from intervals
[2016-04-15T02:11Z] WARN  19:11:58,906 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T02:11Z] WARN  19:11:58,907 IndexDictionaryUtils - Track variant2 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T02:11Z] WARN  19:11:58,907 IndexDictionaryUtils - Track variant3 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T02:11Z] WARN  19:11:58,907 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T02:11Z] INFO  19:11:58,915 MicroScheduler - Running the GATK in parallel mode with 16 total threads, 1 CPU thread(s) for each of 16 data thread(s), of 16 processors available on this machine
[2016-04-15T02:11Z] INFO  19:11:58,965 GenomeAnalysisEngine - Preparing for traversal
[2016-04-15T02:11Z] INFO  19:11:58,966 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T02:11Z] INFO  19:11:58,966 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T02:11Z] INFO  19:11:58,967 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T02:11Z] INFO  19:11:58,967 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T02:11Z] INFO  19:11:59,093 GenotypeGVCFs - Notice that the -ploidy parameter is ignored in GenotypeGVCFs tool as this is automatically determined by the input variant files
[2016-04-15T02:12Z] WARN  19:12:03,188 ExactAFCalculator - this tool is currently set to genotype at most 6 alternate alleles in a given context, but the context at 18:34374795 has 9 alternate alleles so only the top alleles will be used; see the --max_alternate_alleles argument
[2016-04-15T02:12Z] INFO  19:12:08,109 ProgressMeter -            done    467412.0     9.0 s      19.0 s      100.0%     9.0 s       0.0 s
[2016-04-15T02:12Z] INFO  19:12:08,110 ProgressMeter - Total runtime 9.14 secs, 0.15 min, 0.00 hours
[2016-04-15T02:12Z] INFO  19:12:10,414 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T02:12Z] GATK: GenotypeGVCFs
[2016-04-15T02:12Z] INFO  19:12:12,601 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T02:12Z] INFO  19:12:12,603 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T02:12Z] INFO  19:12:12,603 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T02:12Z] INFO  19:12:12,604 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T02:12Z] INFO  19:12:12,607 HelpFormatter - Program Args: -T GenotypeGVCFs -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/gatk-haplotype-joint/Batch1/18/tx/tmpLzDqWo/Batch1-18_50278423_66344430.vcf.gz -L 18:50278424-66344430 --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18106_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18105_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18102_kapa-NGv3-PE100-NGv3.vcf.gz --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -nt 16 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T02:12Z] INFO  19:12:12,615 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T02:12Z] INFO  19:12:12,616 HelpFormatter - Date/Time: 2016/04/14 19:12:12
[2016-04-15T02:12Z] INFO  19:12:12,616 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T02:12Z] INFO  19:12:12,616 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T02:12Z] INFO  19:12:12,687 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T02:12Z] INFO  19:12:12,786 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T02:12Z] INFO  19:12:13,140 IntervalUtils - Processing 16066007 bp from intervals
[2016-04-15T02:12Z] WARN  19:12:13,140 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T02:12Z] WARN  19:12:13,140 IndexDictionaryUtils - Track variant2 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T02:12Z] WARN  19:12:13,141 IndexDictionaryUtils - Track variant3 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T02:12Z] WARN  19:12:13,141 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T02:12Z] INFO  19:12:13,149 MicroScheduler - Running the GATK in parallel mode with 16 total threads, 1 CPU thread(s) for each of 16 data thread(s), of 16 processors available on this machine
[2016-04-15T02:12Z] INFO  19:12:13,200 GenomeAnalysisEngine - Preparing for traversal
[2016-04-15T02:12Z] INFO  19:12:13,201 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T02:12Z] INFO  19:12:13,202 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T02:12Z] INFO  19:12:13,202 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T02:12Z] INFO  19:12:13,202 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T02:12Z] INFO  19:12:13,324 GenotypeGVCFs - Notice that the -ploidy parameter is ignored in GenotypeGVCFs tool as this is automatically determined by the input variant files
[2016-04-15T02:12Z] INFO  19:12:22,719 ProgressMeter -            done    489259.0     9.0 s      19.0 s      100.0%     9.0 s       0.0 s
[2016-04-15T02:12Z] INFO  19:12:22,719 ProgressMeter - Total runtime 9.52 secs, 0.16 min, 0.00 hours
[2016-04-15T02:12Z] INFO  19:12:25,181 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T02:12Z] GATK: GenotypeGVCFs
[2016-04-15T02:12Z] INFO  19:12:27,250 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T02:12Z] INFO  19:12:27,252 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T02:12Z] INFO  19:12:27,252 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T02:12Z] INFO  19:12:27,252 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T02:12Z] INFO  19:12:27,255 HelpFormatter - Program Args: -T GenotypeGVCFs -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/gatk-haplotype-joint/Batch1/18/tx/tmp1WGpSm/Batch1-18_66346699_78077248.vcf.gz -L 18:66346700-78077248 --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18106_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18105_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18102_kapa-NGv3-PE100-NGv3.vcf.gz --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -nt 16 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T02:12Z] INFO  19:12:27,264 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T02:12Z] INFO  19:12:27,264 HelpFormatter - Date/Time: 2016/04/14 19:12:27
[2016-04-15T02:12Z] INFO  19:12:27,264 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T02:12Z] INFO  19:12:27,265 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T02:12Z] INFO  19:12:27,336 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T02:12Z] INFO  19:12:27,434 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T02:12Z] INFO  19:12:27,845 IntervalUtils - Processing 11730549 bp from intervals
[2016-04-15T02:12Z] WARN  19:12:27,846 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T02:12Z] WARN  19:12:27,846 IndexDictionaryUtils - Track variant2 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T02:12Z] WARN  19:12:27,847 IndexDictionaryUtils - Track variant3 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T02:12Z] WARN  19:12:27,847 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T02:12Z] INFO  19:12:27,855 MicroScheduler - Running the GATK in parallel mode with 16 total threads, 1 CPU thread(s) for each of 16 data thread(s), of 16 processors available on this machine
[2016-04-15T02:12Z] INFO  19:12:27,905 GenomeAnalysisEngine - Preparing for traversal
[2016-04-15T02:12Z] INFO  19:12:27,905 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T02:12Z] INFO  19:12:27,906 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T02:12Z] INFO  19:12:27,906 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T02:12Z] INFO  19:12:27,906 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T02:12Z] INFO  19:12:28,032 GenotypeGVCFs - Notice that the -ploidy parameter is ignored in GenotypeGVCFs tool as this is automatically determined by the input variant files
[2016-04-15T02:12Z] WARN  19:12:34,874 ExactAFCalculator - this tool is currently set to genotype at most 6 alternate alleles in a given context, but the context at 18:77136172 has 8 alternate alleles so only the top alleles will be used; see the --max_alternate_alleles argument
[2016-04-15T02:12Z] INFO  19:12:35,260 ProgressMeter -            done    399154.0     7.0 s      18.0 s       99.5%     7.0 s       0.0 s
[2016-04-15T02:12Z] INFO  19:12:35,261 ProgressMeter - Total runtime 7.36 secs, 0.12 min, 0.00 hours
[2016-04-15T02:12Z] INFO  19:12:37,198 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T02:12Z] GATK: GenotypeGVCFs
[2016-04-15T02:12Z] INFO  19:12:39,071 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T02:12Z] INFO  19:12:39,073 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T02:12Z] INFO  19:12:39,073 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T02:12Z] INFO  19:12:39,073 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T02:12Z] INFO  19:12:39,077 HelpFormatter - Program Args: -T GenotypeGVCFs -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/gatk-haplotype-joint/Batch1/19/tx/tmpsQH_Rc/Batch1-19_0_15509577.vcf.gz -L 19:1-15509577 --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18106_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18105_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18102_kapa-NGv3-PE100-NGv3.vcf.gz --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -nt 16 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T02:12Z] INFO  19:12:39,086 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T02:12Z] INFO  19:12:39,086 HelpFormatter - Date/Time: 2016/04/14 19:12:39
[2016-04-15T02:12Z] INFO  19:12:39,086 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T02:12Z] INFO  19:12:39,087 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T02:12Z] INFO  19:12:39,165 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T02:12Z] INFO  19:12:39,310 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T02:12Z] INFO  19:12:39,820 IntervalUtils - Processing 15509577 bp from intervals
[2016-04-15T02:12Z] WARN  19:12:39,820 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T02:12Z] WARN  19:12:39,820 IndexDictionaryUtils - Track variant2 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T02:12Z] WARN  19:12:39,821 IndexDictionaryUtils - Track variant3 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T02:12Z] WARN  19:12:39,821 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T02:12Z] INFO  19:12:39,829 MicroScheduler - Running the GATK in parallel mode with 16 total threads, 1 CPU thread(s) for each of 16 data thread(s), of 16 processors available on this machine
[2016-04-15T02:12Z] INFO  19:12:39,881 GenomeAnalysisEngine - Preparing for traversal
[2016-04-15T02:12Z] INFO  19:12:39,882 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T02:12Z] INFO  19:12:39,882 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T02:12Z] INFO  19:12:39,882 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T02:12Z] INFO  19:12:39,883 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T02:12Z] INFO  19:12:40,011 GenotypeGVCFs - Notice that the -ploidy parameter is ignored in GenotypeGVCFs tool as this is automatically determined by the input variant files
[2016-04-15T02:12Z] WARN  19:12:49,455 ExactAFCalculator - this tool is currently set to genotype at most 6 alternate alleles in a given context, but the context at 19:14492077 has 7 alternate alleles so only the top alleles will be used; see the --max_alternate_alleles argument
[2016-04-15T02:12Z] INFO  19:12:53,518 ProgressMeter -            done   1214886.0    13.0 s      11.0 s      100.0%    13.0 s       0.0 s
[2016-04-15T02:12Z] INFO  19:12:53,519 ProgressMeter - Total runtime 13.64 secs, 0.23 min, 0.00 hours
[2016-04-15T02:12Z] INFO  19:12:56,059 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T02:12Z] GATK: GenotypeGVCFs
[2016-04-15T02:12Z] INFO  19:12:58,196 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T02:12Z] INFO  19:12:58,198 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T02:12Z] INFO  19:12:58,198 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T02:12Z] INFO  19:12:58,198 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T02:12Z] INFO  19:12:58,202 HelpFormatter - Program Args: -T GenotypeGVCFs -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/gatk-haplotype-joint/Batch1/19/tx/tmpF4zkOL/Batch1-19_15510112_31025906.vcf.gz -L 19:15510113-31025906 --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18106_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18105_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18102_kapa-NGv3-PE100-NGv3.vcf.gz --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -nt 16 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T02:12Z] INFO  19:12:58,210 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T02:12Z] INFO  19:12:58,210 HelpFormatter - Date/Time: 2016/04/14 19:12:58
[2016-04-15T02:12Z] INFO  19:12:58,210 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T02:12Z] INFO  19:12:58,210 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T02:12Z] INFO  19:12:58,282 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T02:12Z] INFO  19:12:58,380 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T02:12Z] INFO  19:12:58,730 IntervalUtils - Processing 15515794 bp from intervals
[2016-04-15T02:12Z] WARN  19:12:58,730 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T02:12Z] WARN  19:12:58,731 IndexDictionaryUtils - Track variant2 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T02:12Z] WARN  19:12:58,731 IndexDictionaryUtils - Track variant3 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T02:12Z] WARN  19:12:58,731 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T02:12Z] INFO  19:12:58,739 MicroScheduler - Running the GATK in parallel mode with 16 total threads, 1 CPU thread(s) for each of 16 data thread(s), of 16 processors available on this machine
[2016-04-15T02:12Z] INFO  19:12:58,789 GenomeAnalysisEngine - Preparing for traversal
[2016-04-15T02:12Z] INFO  19:12:58,790 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T02:12Z] INFO  19:12:58,790 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T02:12Z] INFO  19:12:58,790 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T02:12Z] INFO  19:12:58,791 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T02:12Z] INFO  19:12:58,914 GenotypeGVCFs - Notice that the -ploidy parameter is ignored in GenotypeGVCFs tool as this is automatically determined by the input variant files
[2016-04-15T02:13Z] WARN  19:13:07,655 ExactAFCalculator - this tool is currently set to genotype at most 6 alternate alleles in a given context, but the context at 19:17397501 has 12 alternate alleles so only the top alleles will be used; see the --max_alternate_alleles argument
[2016-04-15T02:13Z] INFO  19:13:08,004 ProgressMeter -            done    637231.0     9.0 s      14.0 s      100.0%     9.0 s       0.0 s
[2016-04-15T02:13Z] INFO  19:13:08,005 ProgressMeter - Total runtime 9.21 secs, 0.15 min, 0.00 hours
[2016-04-15T02:13Z] INFO  19:13:09,940 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T02:13Z] GATK: GenotypeGVCFs
[2016-04-15T02:13Z] INFO  19:13:11,671 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T02:13Z] INFO  19:13:11,673 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T02:13Z] INFO  19:13:11,673 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T02:13Z] INFO  19:13:11,673 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T02:13Z] INFO  19:13:11,676 HelpFormatter - Program Args: -T GenotypeGVCFs -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/gatk-haplotype-joint/Batch1/19/tx/tmpkG1sxT/Batch1-19_31038849_46627578.vcf.gz -L 19:31038850-46627578 --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18106_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18105_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18102_kapa-NGv3-PE100-NGv3.vcf.gz --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -nt 16 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T02:13Z] INFO  19:13:11,685 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T02:13Z] INFO  19:13:11,685 HelpFormatter - Date/Time: 2016/04/14 19:13:11
[2016-04-15T02:13Z] INFO  19:13:11,685 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T02:13Z] INFO  19:13:11,685 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T02:13Z] INFO  19:13:11,759 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T02:13Z] INFO  19:13:11,862 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T02:13Z] INFO  19:13:12,424 IntervalUtils - Processing 15588729 bp from intervals
[2016-04-15T02:13Z] WARN  19:13:12,425 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T02:13Z] WARN  19:13:12,426 IndexDictionaryUtils - Track variant2 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T02:13Z] WARN  19:13:12,426 IndexDictionaryUtils - Track variant3 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T02:13Z] WARN  19:13:12,427 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T02:13Z] INFO  19:13:12,447 MicroScheduler - Running the GATK in parallel mode with 16 total threads, 1 CPU thread(s) for each of 16 data thread(s), of 16 processors available on this machine
[2016-04-15T02:13Z] INFO  19:13:12,527 GenomeAnalysisEngine - Preparing for traversal
[2016-04-15T02:13Z] INFO  19:13:12,528 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T02:13Z] INFO  19:13:12,528 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T02:13Z] INFO  19:13:12,529 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T02:13Z] INFO  19:13:12,529 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T02:13Z] INFO  19:13:12,658 GenotypeGVCFs - Notice that the -ploidy parameter is ignored in GenotypeGVCFs tool as this is automatically determined by the input variant files
[2016-04-15T02:13Z] INFO  19:13:23,092 ProgressMeter -            done    999068.0    10.0 s      10.0 s      100.0%    10.0 s       0.0 s
[2016-04-15T02:13Z] INFO  19:13:23,093 ProgressMeter - Total runtime 10.56 secs, 0.18 min, 0.00 hours
[2016-04-15T02:13Z] INFO  19:13:25,122 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T02:13Z] GATK: GenotypeGVCFs
[2016-04-15T02:13Z] INFO  19:13:27,068 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T02:13Z] INFO  19:13:27,070 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T02:13Z] INFO  19:13:27,070 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T02:13Z] INFO  19:13:27,070 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T02:13Z] INFO  19:13:27,074 HelpFormatter - Program Args: -T GenotypeGVCFs -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/gatk-haplotype-joint/Batch1/19/tx/tmpBiAfbt/Batch1-19_46627881_59128983.vcf.gz -L 19:46627882-59128983 --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18106_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18105_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18102_kapa-NGv3-PE100-NGv3.vcf.gz --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -nt 16 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T02:13Z] INFO  19:13:27,082 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T02:13Z] INFO  19:13:27,082 HelpFormatter - Date/Time: 2016/04/14 19:13:27
[2016-04-15T02:13Z] INFO  19:13:27,082 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T02:13Z] INFO  19:13:27,083 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T02:13Z] INFO  19:13:27,154 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T02:13Z] INFO  19:13:27,252 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T02:13Z] INFO  19:13:27,664 IntervalUtils - Processing 12501102 bp from intervals
[2016-04-15T02:13Z] WARN  19:13:27,665 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T02:13Z] WARN  19:13:27,665 IndexDictionaryUtils - Track variant2 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T02:13Z] WARN  19:13:27,665 IndexDictionaryUtils - Track variant3 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T02:13Z] WARN  19:13:27,665 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T02:13Z] INFO  19:13:27,674 MicroScheduler - Running the GATK in parallel mode with 16 total threads, 1 CPU thread(s) for each of 16 data thread(s), of 16 processors available on this machine
[2016-04-15T02:13Z] INFO  19:13:27,724 GenomeAnalysisEngine - Preparing for traversal
[2016-04-15T02:13Z] INFO  19:13:27,724 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T02:13Z] INFO  19:13:27,725 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T02:13Z] INFO  19:13:27,725 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T02:13Z] INFO  19:13:27,726 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T02:13Z] INFO  19:13:27,849 GenotypeGVCFs - Notice that the -ploidy parameter is ignored in GenotypeGVCFs tool as this is automatically determined by the input variant files
[2016-04-15T02:13Z] WARN  19:13:32,003 ExactAFCalculator - this tool is currently set to genotype at most 6 alternate alleles in a given context, but the context at 19:46815969 has 7 alternate alleles so only the top alleles will be used; see the --max_alternate_alleles argument
[2016-04-15T02:13Z] WARN  19:13:35,161 ExactAFCalculator - this tool is currently set to genotype at most 6 alternate alleles in a given context, but the context at 19:47278309 has 7 alternate alleles so only the top alleles will be used; see the --max_alternate_alleles argument
[2016-04-15T02:13Z] INFO  19:13:39,073 ProgressMeter -            done   1051523.0    11.0 s      10.0 s       99.9%    11.0 s       0.0 s
[2016-04-15T02:13Z] INFO  19:13:39,074 ProgressMeter - Total runtime 11.35 secs, 0.19 min, 0.00 hours
[2016-04-15T02:13Z] INFO  19:13:41,403 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T02:13Z] GATK: GenotypeGVCFs
[2016-04-15T02:13Z] INFO  19:13:43,061 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T02:13Z] INFO  19:13:43,063 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T02:13Z] INFO  19:13:43,063 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T02:13Z] INFO  19:13:43,063 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T02:13Z] INFO  19:13:43,066 HelpFormatter - Program Args: -T GenotypeGVCFs -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/gatk-haplotype-joint/Batch1/20/tx/tmpeCJ8ED/Batch1-20_0_15843471.vcf.gz -L 20:1-15843471 --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18106_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18105_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18102_kapa-NGv3-PE100-NGv3.vcf.gz --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -nt 16 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T02:13Z] INFO  19:13:43,075 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T02:13Z] INFO  19:13:43,075 HelpFormatter - Date/Time: 2016/04/14 19:13:43
[2016-04-15T02:13Z] INFO  19:13:43,075 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T02:13Z] INFO  19:13:43,075 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T02:13Z] INFO  19:13:43,146 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T02:13Z] INFO  19:13:43,244 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T02:13Z] INFO  19:13:43,661 IntervalUtils - Processing 15843471 bp from intervals
[2016-04-15T02:13Z] WARN  19:13:43,662 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T02:13Z] WARN  19:13:43,662 IndexDictionaryUtils - Track variant2 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T02:13Z] WARN  19:13:43,662 IndexDictionaryUtils - Track variant3 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T02:13Z] WARN  19:13:43,663 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T02:13Z] INFO  19:13:43,671 MicroScheduler - Running the GATK in parallel mode with 16 total threads, 1 CPU thread(s) for each of 16 data thread(s), of 16 processors available on this machine
[2016-04-15T02:13Z] INFO  19:13:43,721 GenomeAnalysisEngine - Preparing for traversal
[2016-04-15T02:13Z] INFO  19:13:43,722 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T02:13Z] INFO  19:13:43,722 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T02:13Z] INFO  19:13:43,723 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T02:13Z] INFO  19:13:43,723 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T02:13Z] INFO  19:13:43,846 GenotypeGVCFs - Notice that the -ploidy parameter is ignored in GenotypeGVCFs tool as this is automatically determined by the input variant files
[2016-04-15T02:13Z] INFO  19:13:54,585 ProgressMeter -            done    563808.0    10.0 s      19.0 s      100.0%    10.0 s       0.0 s
[2016-04-15T02:13Z] INFO  19:13:54,585 ProgressMeter - Total runtime 10.86 secs, 0.18 min, 0.00 hours
[2016-04-15T02:13Z] INFO  19:13:57,285 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T02:13Z] GATK: GenotypeGVCFs
[2016-04-15T02:13Z] INFO  19:13:59,315 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T02:13Z] INFO  19:13:59,317 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T02:13Z] INFO  19:13:59,317 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T02:13Z] INFO  19:13:59,317 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T02:13Z] INFO  19:13:59,320 HelpFormatter - Program Args: -T GenotypeGVCFs -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/gatk-haplotype-joint/Batch1/20/tx/tmpesHkGg/Batch1-20_15866408_31376818.vcf.gz -L 20:15866409-31376818 --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18106_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18105_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18102_kapa-NGv3-PE100-NGv3.vcf.gz --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -nt 16 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T02:13Z] INFO  19:13:59,329 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T02:13Z] INFO  19:13:59,329 HelpFormatter - Date/Time: 2016/04/14 19:13:59
[2016-04-15T02:13Z] INFO  19:13:59,329 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T02:13Z] INFO  19:13:59,330 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T02:13Z] INFO  19:13:59,401 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T02:13Z] INFO  19:13:59,499 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T02:13Z] INFO  19:13:59,914 IntervalUtils - Processing 15510410 bp from intervals
[2016-04-15T02:13Z] WARN  19:13:59,915 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T02:13Z] WARN  19:13:59,915 IndexDictionaryUtils - Track variant2 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T02:13Z] WARN  19:13:59,915 IndexDictionaryUtils - Track variant3 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T02:13Z] WARN  19:13:59,915 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T02:13Z] INFO  19:13:59,923 MicroScheduler - Running the GATK in parallel mode with 16 total threads, 1 CPU thread(s) for each of 16 data thread(s), of 16 processors available on this machine
[2016-04-15T02:13Z] INFO  19:13:59,973 GenomeAnalysisEngine - Preparing for traversal
[2016-04-15T02:13Z] INFO  19:13:59,975 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T02:13Z] INFO  19:13:59,975 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T02:13Z] INFO  19:13:59,975 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T02:13Z] INFO  19:13:59,976 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T02:14Z] INFO  19:14:00,100 GenotypeGVCFs - Notice that the -ploidy parameter is ignored in GenotypeGVCFs tool as this is automatically determined by the input variant files
[2016-04-15T02:14Z] INFO  19:14:09,229 ProgressMeter -            done    481689.0     9.0 s      19.0 s      100.0%     9.0 s       0.0 s
[2016-04-15T02:14Z] INFO  19:14:09,230 ProgressMeter - Total runtime 9.25 secs, 0.15 min, 0.00 hours
[2016-04-15T02:14Z] INFO  19:14:11,798 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T02:14Z] GATK: GenotypeGVCFs
[2016-04-15T02:14Z] INFO  19:14:14,032 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T02:14Z] INFO  19:14:14,034 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T02:14Z] INFO  19:14:14,034 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T02:14Z] INFO  19:14:14,034 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T02:14Z] INFO  19:14:14,038 HelpFormatter - Program Args: -T GenotypeGVCFs -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/gatk-haplotype-joint/Batch1/20/tx/tmpyu9Evw/Batch1-20_31379406_47242465.vcf.gz -L 20:31379407-47242465 --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18106_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18105_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18102_kapa-NGv3-PE100-NGv3.vcf.gz --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -nt 16 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T02:14Z] INFO  19:14:14,047 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T02:14Z] INFO  19:14:14,047 HelpFormatter - Date/Time: 2016/04/14 19:14:14
[2016-04-15T02:14Z] INFO  19:14:14,048 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T02:14Z] INFO  19:14:14,048 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T02:14Z] INFO  19:14:14,124 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T02:14Z] INFO  19:14:14,229 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T02:14Z] INFO  19:14:14,731 IntervalUtils - Processing 15863059 bp from intervals
[2016-04-15T02:14Z] WARN  19:14:14,732 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T02:14Z] WARN  19:14:14,732 IndexDictionaryUtils - Track variant2 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T02:14Z] WARN  19:14:14,732 IndexDictionaryUtils - Track variant3 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T02:14Z] WARN  19:14:14,732 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T02:14Z] INFO  19:14:14,741 MicroScheduler - Running the GATK in parallel mode with 16 total threads, 1 CPU thread(s) for each of 16 data thread(s), of 16 processors available on this machine
[2016-04-15T02:14Z] INFO  19:14:14,792 GenomeAnalysisEngine - Preparing for traversal
[2016-04-15T02:14Z] INFO  19:14:14,793 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T02:14Z] INFO  19:14:14,793 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T02:14Z] INFO  19:14:14,793 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T02:14Z] INFO  19:14:14,794 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T02:14Z] INFO  19:14:14,921 GenotypeGVCFs - Notice that the -ploidy parameter is ignored in GenotypeGVCFs tool as this is automatically determined by the input variant files
[2016-04-15T02:14Z] INFO  19:14:24,467 ProgressMeter -            done    696490.0     9.0 s      13.0 s      100.0%     9.0 s       0.0 s
[2016-04-15T02:14Z] INFO  19:14:24,468 ProgressMeter - Total runtime 9.67 secs, 0.16 min, 0.00 hours
[2016-04-15T02:14Z] INFO  19:14:26,575 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T02:14Z] GATK: GenotypeGVCFs
[2016-04-15T02:14Z] INFO  19:14:28,712 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T02:14Z] INFO  19:14:28,714 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T02:14Z] INFO  19:14:28,714 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T02:14Z] INFO  19:14:28,714 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T02:14Z] INFO  19:14:28,717 HelpFormatter - Program Args: -T GenotypeGVCFs -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/gatk-haplotype-joint/Batch1/20/tx/tmpdS6Ojm/Batch1-20_47244085_62830269.vcf.gz -L 20:47244086-62830269 --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18106_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18105_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18102_kapa-NGv3-PE100-NGv3.vcf.gz --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -nt 16 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T02:14Z] INFO  19:14:28,725 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T02:14Z] INFO  19:14:28,726 HelpFormatter - Date/Time: 2016/04/14 19:14:28
[2016-04-15T02:14Z] INFO  19:14:28,726 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T02:14Z] INFO  19:14:28,726 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T02:14Z] INFO  19:14:28,797 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T02:14Z] INFO  19:14:28,894 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T02:14Z] INFO  19:14:29,311 IntervalUtils - Processing 15586184 bp from intervals
[2016-04-15T02:14Z] WARN  19:14:29,311 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T02:14Z] WARN  19:14:29,312 IndexDictionaryUtils - Track variant2 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T02:14Z] WARN  19:14:29,312 IndexDictionaryUtils - Track variant3 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T02:14Z] WARN  19:14:29,312 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T02:14Z] INFO  19:14:29,320 MicroScheduler - Running the GATK in parallel mode with 16 total threads, 1 CPU thread(s) for each of 16 data thread(s), of 16 processors available on this machine
[2016-04-15T02:14Z] INFO  19:14:29,370 GenomeAnalysisEngine - Preparing for traversal
[2016-04-15T02:14Z] INFO  19:14:29,371 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T02:14Z] INFO  19:14:29,371 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T02:14Z] INFO  19:14:29,372 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T02:14Z] INFO  19:14:29,372 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T02:14Z] INFO  19:14:29,496 GenotypeGVCFs - Notice that the -ploidy parameter is ignored in GenotypeGVCFs tool as this is automatically determined by the input variant files
[2016-04-15T02:14Z] INFO  19:14:40,365 ProgressMeter -            done    687246.0    10.0 s      15.0 s      100.0%    10.0 s       0.0 s
[2016-04-15T02:14Z] INFO  19:14:40,366 ProgressMeter - Total runtime 10.99 secs, 0.18 min, 0.00 hours
[2016-04-15T02:14Z] INFO  19:14:42,634 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T02:14Z] GATK: GenotypeGVCFs
[2016-04-15T02:14Z] INFO  19:14:44,560 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T02:14Z] INFO  19:14:44,562 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T02:14Z] INFO  19:14:44,562 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T02:14Z] INFO  19:14:44,562 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T02:14Z] INFO  19:14:44,566 HelpFormatter - Program Args: -T GenotypeGVCFs -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/gatk-haplotype-joint/Batch1/20/tx/tmpBZr7kr/Batch1-20_62831244_63025520.vcf.gz -L 20:62831245-63025520 --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18106_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18105_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18102_kapa-NGv3-PE100-NGv3.vcf.gz --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -nt 16 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T02:14Z] INFO  19:14:44,574 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T02:14Z] INFO  19:14:44,574 HelpFormatter - Date/Time: 2016/04/14 19:14:44
[2016-04-15T02:14Z] INFO  19:14:44,574 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T02:14Z] INFO  19:14:44,575 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T02:14Z] INFO  19:14:44,656 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T02:14Z] INFO  19:14:44,772 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T02:14Z] INFO  19:14:45,265 IntervalUtils - Processing 194276 bp from intervals
[2016-04-15T02:14Z] WARN  19:14:45,266 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T02:14Z] WARN  19:14:45,266 IndexDictionaryUtils - Track variant2 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T02:14Z] WARN  19:14:45,267 IndexDictionaryUtils - Track variant3 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T02:14Z] WARN  19:14:45,267 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T02:14Z] INFO  19:14:45,275 MicroScheduler - Running the GATK in parallel mode with 16 total threads, 1 CPU thread(s) for each of 16 data thread(s), of 16 processors available on this machine
[2016-04-15T02:14Z] INFO  19:14:45,326 GenomeAnalysisEngine - Preparing for traversal
[2016-04-15T02:14Z] INFO  19:14:45,327 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T02:14Z] INFO  19:14:45,328 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T02:14Z] INFO  19:14:45,328 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T02:14Z] INFO  19:14:45,328 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T02:14Z] INFO  19:14:45,455 GenotypeGVCFs - Notice that the -ploidy parameter is ignored in GenotypeGVCFs tool as this is automatically determined by the input variant files
[2016-04-15T02:14Z] INFO  19:14:46,433 ProgressMeter -            done      7681.0     1.0 s       2.4 m       66.6%     1.0 s       0.0 s
[2016-04-15T02:14Z] INFO  19:14:46,434 ProgressMeter - Total runtime 1.11 secs, 0.02 min, 0.00 hours
[2016-04-15T02:14Z] INFO  19:14:48,043 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T02:14Z] GATK: GenotypeGVCFs
[2016-04-15T02:14Z] INFO  19:14:50,268 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T02:14Z] INFO  19:14:50,270 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T02:14Z] INFO  19:14:50,270 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T02:14Z] INFO  19:14:50,270 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T02:14Z] INFO  19:14:50,274 HelpFormatter - Program Args: -T GenotypeGVCFs -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/gatk-haplotype-joint/Batch1/21/tx/tmpkfGTXN/Batch1-21_0_15517120.vcf.gz -L 21:1-15517120 --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18106_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18105_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18102_kapa-NGv3-PE100-NGv3.vcf.gz --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -nt 16 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T02:14Z] INFO  19:14:50,281 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T02:14Z] INFO  19:14:50,282 HelpFormatter - Date/Time: 2016/04/14 19:14:50
[2016-04-15T02:14Z] INFO  19:14:50,282 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T02:14Z] INFO  19:14:50,282 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T02:14Z] INFO  19:14:50,358 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T02:14Z] INFO  19:14:50,499 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T02:14Z] INFO  19:14:50,996 IntervalUtils - Processing 15517120 bp from intervals
[2016-04-15T02:14Z] WARN  19:14:50,997 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T02:14Z] WARN  19:14:50,997 IndexDictionaryUtils - Track variant2 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T02:14Z] WARN  19:14:50,997 IndexDictionaryUtils - Track variant3 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T02:14Z] WARN  19:14:50,997 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T02:14Z] INFO  19:14:51,006 MicroScheduler - Running the GATK in parallel mode with 16 total threads, 1 CPU thread(s) for each of 16 data thread(s), of 16 processors available on this machine
[2016-04-15T02:14Z] INFO  19:14:51,059 GenomeAnalysisEngine - Preparing for traversal
[2016-04-15T02:14Z] INFO  19:14:51,060 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T02:14Z] INFO  19:14:51,060 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T02:14Z] INFO  19:14:51,060 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T02:14Z] INFO  19:14:51,061 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T02:14Z] INFO  19:14:51,190 GenotypeGVCFs - Notice that the -ploidy parameter is ignored in GenotypeGVCFs tool as this is automatically determined by the input variant files
[2016-04-15T02:14Z] INFO  19:14:58,807 ProgressMeter -            done    106921.0     7.0 s      72.0 s      100.0%     7.0 s       0.0 s
[2016-04-15T02:14Z] INFO  19:14:58,808 ProgressMeter - Total runtime 7.75 secs, 0.13 min, 0.00 hours
[2016-04-15T02:15Z] INFO  19:15:01,240 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T02:15Z] GATK: GenotypeGVCFs
[2016-04-15T02:15Z] INFO  19:15:03,286 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T02:15Z] INFO  19:15:03,288 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T02:15Z] INFO  19:15:03,288 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T02:15Z] INFO  19:15:03,288 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T02:15Z] INFO  19:15:03,292 HelpFormatter - Program Args: -T GenotypeGVCFs -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/gatk-haplotype-joint/Batch1/21/tx/tmpmo6LuR/Batch1-21_15524893_31045484.vcf.gz -L 21:15524894-31045484 --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18106_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18105_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18102_kapa-NGv3-PE100-NGv3.vcf.gz --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -nt 16 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T02:15Z] INFO  19:15:03,300 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T02:15Z] INFO  19:15:03,300 HelpFormatter - Date/Time: 2016/04/14 19:15:03
[2016-04-15T02:15Z] INFO  19:15:03,300 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T02:15Z] INFO  19:15:03,301 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T02:15Z] INFO  19:15:03,372 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T02:15Z] INFO  19:15:03,471 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T02:15Z] INFO  19:15:03,883 IntervalUtils - Processing 15520591 bp from intervals
[2016-04-15T02:15Z] WARN  19:15:03,884 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T02:15Z] WARN  19:15:03,884 IndexDictionaryUtils - Track variant2 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T02:15Z] WARN  19:15:03,884 IndexDictionaryUtils - Track variant3 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T02:15Z] WARN  19:15:03,884 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T02:15Z] INFO  19:15:03,893 MicroScheduler - Running the GATK in parallel mode with 16 total threads, 1 CPU thread(s) for each of 16 data thread(s), of 16 processors available on this machine
[2016-04-15T02:15Z] INFO  19:15:03,942 GenomeAnalysisEngine - Preparing for traversal
[2016-04-15T02:15Z] INFO  19:15:03,943 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T02:15Z] INFO  19:15:03,944 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T02:15Z] INFO  19:15:03,944 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T02:15Z] INFO  19:15:03,945 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T02:15Z] INFO  19:15:04,068 GenotypeGVCFs - Notice that the -ploidy parameter is ignored in GenotypeGVCFs tool as this is automatically determined by the input variant files
[2016-04-15T02:15Z] INFO  19:15:12,808 ProgressMeter -            done    457032.0     8.0 s      19.0 s      100.0%     8.0 s       0.0 s
[2016-04-15T02:15Z] INFO  19:15:12,809 ProgressMeter - Total runtime 8.87 secs, 0.15 min, 0.00 hours
[2016-04-15T02:15Z] INFO  19:15:14,866 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T02:15Z] GATK: GenotypeGVCFs
[2016-04-15T02:15Z] INFO  19:15:16,841 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T02:15Z] INFO  19:15:16,843 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T02:15Z] INFO  19:15:16,843 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T02:15Z] INFO  19:15:16,843 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T02:15Z] INFO  19:15:16,847 HelpFormatter - Program Args: -T GenotypeGVCFs -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/gatk-haplotype-joint/Batch1/21/tx/tmpBVCgrd/Batch1-21_31062047_46591599.vcf.gz -L 21:31062048-46591599 --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18106_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18105_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18102_kapa-NGv3-PE100-NGv3.vcf.gz --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -nt 16 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T02:15Z] INFO  19:15:16,855 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T02:15Z] INFO  19:15:16,855 HelpFormatter - Date/Time: 2016/04/14 19:15:16
[2016-04-15T02:15Z] INFO  19:15:16,855 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T02:15Z] INFO  19:15:16,855 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T02:15Z] INFO  19:15:16,926 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T02:15Z] INFO  19:15:17,024 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T02:15Z] INFO  19:15:17,437 IntervalUtils - Processing 15529552 bp from intervals
[2016-04-15T02:15Z] WARN  19:15:17,438 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T02:15Z] WARN  19:15:17,438 IndexDictionaryUtils - Track variant2 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T02:15Z] WARN  19:15:17,438 IndexDictionaryUtils - Track variant3 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T02:15Z] WARN  19:15:17,439 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T02:15Z] INFO  19:15:17,447 MicroScheduler - Running the GATK in parallel mode with 16 total threads, 1 CPU thread(s) for each of 16 data thread(s), of 16 processors available on this machine
[2016-04-15T02:15Z] INFO  19:15:17,497 GenomeAnalysisEngine - Preparing for traversal
[2016-04-15T02:15Z] INFO  19:15:17,498 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T02:15Z] INFO  19:15:17,499 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T02:15Z] INFO  19:15:17,499 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T02:15Z] INFO  19:15:17,499 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T02:15Z] INFO  19:15:17,630 GenotypeGVCFs - Notice that the -ploidy parameter is ignored in GenotypeGVCFs tool as this is automatically determined by the input variant files
[2016-04-15T02:15Z] INFO  19:15:26,869 ProgressMeter -            done    678357.0     9.0 s      13.0 s      100.0%     9.0 s       0.0 s
[2016-04-15T02:15Z] INFO  19:15:26,869 ProgressMeter - Total runtime 9.37 secs, 0.16 min, 0.00 hours
[2016-04-15T02:15Z] INFO  19:15:29,402 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T02:15Z] GATK: GenotypeGVCFs
[2016-04-15T02:15Z] INFO  19:15:31,362 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T02:15Z] INFO  19:15:31,364 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T02:15Z] INFO  19:15:31,365 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T02:15Z] INFO  19:15:31,365 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T02:15Z] INFO  19:15:31,369 HelpFormatter - Program Args: -T GenotypeGVCFs -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/gatk-haplotype-joint/Batch1/21/tx/tmp444_Ei/Batch1-21_46595644_48129895.vcf.gz -L 21:46595645-48129895 --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18106_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18105_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18102_kapa-NGv3-PE100-NGv3.vcf.gz --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -nt 16 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T02:15Z] INFO  19:15:31,377 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T02:15Z] INFO  19:15:31,378 HelpFormatter - Date/Time: 2016/04/14 19:15:31
[2016-04-15T02:15Z] INFO  19:15:31,378 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T02:15Z] INFO  19:15:31,378 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T02:15Z] INFO  19:15:31,454 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T02:15Z] INFO  19:15:31,561 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T02:15Z] INFO  19:15:31,927 IntervalUtils - Processing 1534251 bp from intervals
[2016-04-15T02:15Z] WARN  19:15:31,928 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T02:15Z] WARN  19:15:31,928 IndexDictionaryUtils - Track variant2 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T02:15Z] WARN  19:15:31,928 IndexDictionaryUtils - Track variant3 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T02:15Z] WARN  19:15:31,928 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T02:15Z] INFO  19:15:31,937 MicroScheduler - Running the GATK in parallel mode with 16 total threads, 1 CPU thread(s) for each of 16 data thread(s), of 16 processors available on this machine
[2016-04-15T02:15Z] INFO  19:15:31,989 GenomeAnalysisEngine - Preparing for traversal
[2016-04-15T02:15Z] INFO  19:15:31,990 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T02:15Z] INFO  19:15:31,990 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T02:15Z] INFO  19:15:31,991 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T02:15Z] INFO  19:15:31,991 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T02:15Z] INFO  19:15:32,120 GenotypeGVCFs - Notice that the -ploidy parameter is ignored in GenotypeGVCFs tool as this is automatically determined by the input variant files
[2016-04-15T02:15Z] INFO  19:15:34,204 ProgressMeter -            done    111336.0     2.0 s      19.0 s       99.3%     2.0 s       0.0 s
[2016-04-15T02:15Z] INFO  19:15:34,204 ProgressMeter - Total runtime 2.21 secs, 0.04 min, 0.00 hours
[2016-04-15T02:15Z] INFO  19:15:35,700 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T02:15Z] GATK: GenotypeGVCFs
[2016-04-15T02:15Z] INFO  19:15:37,775 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T02:15Z] INFO  19:15:37,777 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T02:15Z] INFO  19:15:37,777 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T02:15Z] INFO  19:15:37,777 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T02:15Z] INFO  19:15:37,781 HelpFormatter - Program Args: -T GenotypeGVCFs -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/gatk-haplotype-joint/Batch1/22/tx/tmpY9N56M/Batch1-22_0_16258303.vcf.gz -L 22:1-16258303 --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18106_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18105_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18102_kapa-NGv3-PE100-NGv3.vcf.gz --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -nt 16 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T02:15Z] INFO  19:15:37,789 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T02:15Z] INFO  19:15:37,789 HelpFormatter - Date/Time: 2016/04/14 19:15:37
[2016-04-15T02:15Z] INFO  19:15:37,789 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T02:15Z] INFO  19:15:37,790 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T02:15Z] INFO  19:15:37,861 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T02:15Z] INFO  19:15:37,959 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T02:15Z] INFO  19:15:38,374 IntervalUtils - Processing 16258303 bp from intervals
[2016-04-15T02:15Z] WARN  19:15:38,375 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T02:15Z] WARN  19:15:38,375 IndexDictionaryUtils - Track variant2 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T02:15Z] WARN  19:15:38,375 IndexDictionaryUtils - Track variant3 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T02:15Z] WARN  19:15:38,375 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T02:15Z] INFO  19:15:38,384 MicroScheduler - Running the GATK in parallel mode with 16 total threads, 1 CPU thread(s) for each of 16 data thread(s), of 16 processors available on this machine
[2016-04-15T02:15Z] INFO  19:15:38,433 GenomeAnalysisEngine - Preparing for traversal
[2016-04-15T02:15Z] INFO  19:15:38,434 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T02:15Z] INFO  19:15:38,434 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T02:15Z] INFO  19:15:38,435 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T02:15Z] INFO  19:15:38,435 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T02:15Z] INFO  19:15:38,557 GenotypeGVCFs - Notice that the -ploidy parameter is ignored in GenotypeGVCFs tool as this is automatically determined by the input variant files
[2016-04-15T02:15Z] INFO  19:15:39,611 ProgressMeter -            done      3132.0     1.0 s       6.3 m      100.0%     1.0 s       0.0 s
[2016-04-15T02:15Z] INFO  19:15:39,612 ProgressMeter - Total runtime 1.18 secs, 0.02 min, 0.00 hours
[2016-04-15T02:15Z] INFO  19:15:40,724 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T02:15Z] GATK: GenotypeGVCFs
[2016-04-15T02:15Z] INFO  19:15:42,771 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T02:15Z] INFO  19:15:42,773 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T02:15Z] INFO  19:15:42,773 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T02:15Z] INFO  19:15:42,774 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T02:15Z] INFO  19:15:42,777 HelpFormatter - Program Args: -T GenotypeGVCFs -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/gatk-haplotype-joint/Batch1/22/tx/tmpFK7qdZ/Batch1-22_16266928_31795711.vcf.gz -L 22:16266929-31795711 --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18106_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18105_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18102_kapa-NGv3-PE100-NGv3.vcf.gz --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -nt 16 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T02:15Z] INFO  19:15:42,785 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T02:15Z] INFO  19:15:42,786 HelpFormatter - Date/Time: 2016/04/14 19:15:42
[2016-04-15T02:15Z] INFO  19:15:42,786 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T02:15Z] INFO  19:15:42,786 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T02:15Z] INFO  19:15:42,858 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T02:15Z] INFO  19:15:42,956 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T02:15Z] INFO  19:15:43,309 IntervalUtils - Processing 15528783 bp from intervals
[2016-04-15T02:15Z] WARN  19:15:43,309 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T02:15Z] WARN  19:15:43,310 IndexDictionaryUtils - Track variant2 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T02:15Z] WARN  19:15:43,310 IndexDictionaryUtils - Track variant3 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T02:15Z] WARN  19:15:43,310 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T02:15Z] INFO  19:15:43,319 MicroScheduler - Running the GATK in parallel mode with 16 total threads, 1 CPU thread(s) for each of 16 data thread(s), of 16 processors available on this machine
[2016-04-15T02:15Z] INFO  19:15:43,368 GenomeAnalysisEngine - Preparing for traversal
[2016-04-15T02:15Z] INFO  19:15:43,369 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T02:15Z] INFO  19:15:43,369 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T02:15Z] INFO  19:15:43,370 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T02:15Z] INFO  19:15:43,370 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T02:15Z] INFO  19:15:43,496 GenotypeGVCFs - Notice that the -ploidy parameter is ignored in GenotypeGVCFs tool as this is automatically determined by the input variant files
[2016-04-15T02:15Z] INFO  19:15:53,338 ProgressMeter -            done    747700.0     9.0 s      13.0 s      100.0%     9.0 s       0.0 s
[2016-04-15T02:15Z] INFO  19:15:53,339 ProgressMeter - Total runtime 9.97 secs, 0.17 min, 0.00 hours
[2016-04-15T02:15Z] INFO  19:15:55,740 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T02:15Z] GATK: GenotypeGVCFs
[2016-04-15T02:15Z] INFO  19:15:57,373 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T02:15Z] INFO  19:15:57,375 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T02:15Z] INFO  19:15:57,375 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T02:15Z] INFO  19:15:57,375 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T02:15Z] INFO  19:15:57,379 HelpFormatter - Program Args: -T GenotypeGVCFs -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/gatk-haplotype-joint/Batch1/22/tx/tmp1n9ii3/Batch1-22_31796605_47308085.vcf.gz -L 22:31796606-47308085 --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18106_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18105_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18102_kapa-NGv3-PE100-NGv3.vcf.gz --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -nt 16 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T02:15Z] INFO  19:15:57,388 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T02:15Z] INFO  19:15:57,388 HelpFormatter - Date/Time: 2016/04/14 19:15:57
[2016-04-15T02:15Z] INFO  19:15:57,389 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T02:15Z] INFO  19:15:57,389 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T02:15Z] INFO  19:15:57,463 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T02:15Z] INFO  19:15:57,568 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T02:15Z] INFO  19:15:58,022 IntervalUtils - Processing 15511480 bp from intervals
[2016-04-15T02:15Z] WARN  19:15:58,022 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T02:15Z] WARN  19:15:58,023 IndexDictionaryUtils - Track variant2 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T02:15Z] WARN  19:15:58,023 IndexDictionaryUtils - Track variant3 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T02:15Z] WARN  19:15:58,023 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T02:15Z] INFO  19:15:58,032 MicroScheduler - Running the GATK in parallel mode with 16 total threads, 1 CPU thread(s) for each of 16 data thread(s), of 16 processors available on this machine
[2016-04-15T02:15Z] INFO  19:15:58,082 GenomeAnalysisEngine - Preparing for traversal
[2016-04-15T02:15Z] INFO  19:15:58,083 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T02:15Z] INFO  19:15:58,084 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T02:15Z] INFO  19:15:58,084 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T02:15Z] INFO  19:15:58,085 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T02:15Z] INFO  19:15:58,210 GenotypeGVCFs - Notice that the -ploidy parameter is ignored in GenotypeGVCFs tool as this is automatically determined by the input variant files
[2016-04-15T02:16Z] WARN  19:16:09,242 ExactAFCalculator - this tool is currently set to genotype at most 6 alternate alleles in a given context, but the context at 22:42390887 has 7 alternate alleles so only the top alleles will be used; see the --max_alternate_alleles argument
[2016-04-15T02:16Z] INFO  19:16:10,091 ProgressMeter -            done    761238.0    12.0 s      15.0 s      100.0%    12.0 s       0.0 s
[2016-04-15T02:16Z] INFO  19:16:10,091 ProgressMeter - Total runtime 12.01 secs, 0.20 min, 0.00 hours
[2016-04-15T02:16Z] INFO  19:16:12,366 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T02:16Z] GATK: GenotypeGVCFs
[2016-04-15T02:16Z] INFO  19:16:14,643 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T02:16Z] INFO  19:16:14,645 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T02:16Z] INFO  19:16:14,645 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T02:16Z] INFO  19:16:14,646 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T02:16Z] INFO  19:16:14,649 HelpFormatter - Program Args: -T GenotypeGVCFs -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/gatk-haplotype-joint/Batch1/22/tx/tmpYatz9B/Batch1-22_47309229_51304566.vcf.gz -L 22:47309230-51304566 --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18106_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18105_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18102_kapa-NGv3-PE100-NGv3.vcf.gz --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -nt 16 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T02:16Z] INFO  19:16:14,659 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T02:16Z] INFO  19:16:14,659 HelpFormatter - Date/Time: 2016/04/14 19:16:14
[2016-04-15T02:16Z] INFO  19:16:14,659 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T02:16Z] INFO  19:16:14,660 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T02:16Z] INFO  19:16:14,736 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T02:16Z] INFO  19:16:14,840 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T02:16Z] INFO  19:16:15,553 IntervalUtils - Processing 3995337 bp from intervals
[2016-04-15T02:16Z] WARN  19:16:15,554 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T02:16Z] WARN  19:16:15,555 IndexDictionaryUtils - Track variant2 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T02:16Z] WARN  19:16:15,555 IndexDictionaryUtils - Track variant3 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T02:16Z] WARN  19:16:15,556 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T02:16Z] INFO  19:16:15,576 MicroScheduler - Running the GATK in parallel mode with 16 total threads, 1 CPU thread(s) for each of 16 data thread(s), of 16 processors available on this machine
[2016-04-15T02:16Z] INFO  19:16:15,696 GenomeAnalysisEngine - Preparing for traversal
[2016-04-15T02:16Z] INFO  19:16:15,698 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T02:16Z] INFO  19:16:15,699 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T02:16Z] INFO  19:16:15,700 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T02:16Z] INFO  19:16:15,701 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T02:16Z] INFO  19:16:15,976 GenotypeGVCFs - Notice that the -ploidy parameter is ignored in GenotypeGVCFs tool as this is automatically determined by the input variant files
[2016-04-15T02:16Z] INFO  19:16:19,699 ProgressMeter -            done    211034.0     3.0 s      18.0 s       98.3%     3.0 s       0.0 s
[2016-04-15T02:16Z] INFO  19:16:19,700 ProgressMeter - Total runtime 4.00 secs, 0.07 min, 0.00 hours
[2016-04-15T02:16Z] INFO  19:16:21,485 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T02:16Z] GATK: GenotypeGVCFs
[2016-04-15T02:16Z] INFO  19:16:23,649 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T02:16Z] INFO  19:16:23,651 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T02:16Z] INFO  19:16:23,651 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T02:16Z] INFO  19:16:23,651 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T02:16Z] INFO  19:16:23,655 HelpFormatter - Program Args: -T GenotypeGVCFs -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/gatk-haplotype-joint/Batch1/X/tx/tmp9lAPvx/Batch1-X_0_15509380.vcf.gz -L X:1-15509380 --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18106_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18105_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18102_kapa-NGv3-PE100-NGv3.vcf.gz --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -nt 16 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T02:16Z] INFO  19:16:23,663 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T02:16Z] INFO  19:16:23,663 HelpFormatter - Date/Time: 2016/04/14 19:16:23
[2016-04-15T02:16Z] INFO  19:16:23,663 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T02:16Z] INFO  19:16:23,663 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T02:16Z] INFO  19:16:23,734 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T02:16Z] INFO  19:16:23,832 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T02:16Z] INFO  19:16:24,247 IntervalUtils - Processing 15509380 bp from intervals
[2016-04-15T02:16Z] WARN  19:16:24,248 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T02:16Z] WARN  19:16:24,248 IndexDictionaryUtils - Track variant2 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T02:16Z] WARN  19:16:24,248 IndexDictionaryUtils - Track variant3 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T02:16Z] WARN  19:16:24,248 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T02:16Z] INFO  19:16:24,257 MicroScheduler - Running the GATK in parallel mode with 16 total threads, 1 CPU thread(s) for each of 16 data thread(s), of 16 processors available on this machine
[2016-04-15T02:16Z] INFO  19:16:24,308 GenomeAnalysisEngine - Preparing for traversal
[2016-04-15T02:16Z] INFO  19:16:24,309 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T02:16Z] INFO  19:16:24,309 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T02:16Z] INFO  19:16:24,309 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T02:16Z] INFO  19:16:24,310 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T02:16Z] INFO  19:16:24,434 GenotypeGVCFs - Notice that the -ploidy parameter is ignored in GenotypeGVCFs tool as this is automatically determined by the input variant files
[2016-04-15T02:16Z] INFO  19:16:32,780 ProgressMeter -            done    345174.0     8.0 s      24.0 s      100.0%     8.0 s       0.0 s
[2016-04-15T02:16Z] INFO  19:16:32,780 ProgressMeter - Total runtime 8.47 secs, 0.14 min, 0.00 hours
[2016-04-15T02:16Z] INFO  19:16:35,087 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T02:16Z] GATK: GenotypeGVCFs
[2016-04-15T02:16Z] INFO  19:16:37,232 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T02:16Z] INFO  19:16:37,234 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T02:16Z] INFO  19:16:37,234 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T02:16Z] INFO  19:16:37,234 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T02:16Z] INFO  19:16:37,238 HelpFormatter - Program Args: -T GenotypeGVCFs -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/gatk-haplotype-joint/Batch1/X/tx/tmpYXhm1Z/Batch1-X_15518899_31090070.vcf.gz -L X:15518900-31090070 --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18106_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18105_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18102_kapa-NGv3-PE100-NGv3.vcf.gz --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -nt 16 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T02:16Z] INFO  19:16:37,247 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T02:16Z] INFO  19:16:37,247 HelpFormatter - Date/Time: 2016/04/14 19:16:37
[2016-04-15T02:16Z] INFO  19:16:37,247 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T02:16Z] INFO  19:16:37,248 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T02:16Z] INFO  19:16:37,324 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T02:16Z] INFO  19:16:37,487 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T02:16Z] INFO  19:16:37,982 IntervalUtils - Processing 15571171 bp from intervals
[2016-04-15T02:16Z] WARN  19:16:37,983 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T02:16Z] WARN  19:16:37,983 IndexDictionaryUtils - Track variant2 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T02:16Z] WARN  19:16:37,983 IndexDictionaryUtils - Track variant3 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T02:16Z] WARN  19:16:37,983 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T02:16Z] INFO  19:16:37,992 MicroScheduler - Running the GATK in parallel mode with 16 total threads, 1 CPU thread(s) for each of 16 data thread(s), of 16 processors available on this machine
[2016-04-15T02:16Z] INFO  19:16:38,042 GenomeAnalysisEngine - Preparing for traversal
[2016-04-15T02:16Z] INFO  19:16:38,043 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T02:16Z] INFO  19:16:38,044 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T02:16Z] INFO  19:16:38,044 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T02:16Z] INFO  19:16:38,044 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T02:16Z] INFO  19:16:38,172 GenotypeGVCFs - Notice that the -ploidy parameter is ignored in GenotypeGVCFs tool as this is automatically determined by the input variant files
[2016-04-15T02:16Z] INFO  19:16:47,373 ProgressMeter -            done    368987.0     9.0 s      25.0 s      100.0%     9.0 s       0.0 s
[2016-04-15T02:16Z] INFO  19:16:47,373 ProgressMeter - Total runtime 9.33 secs, 0.16 min, 0.00 hours
[2016-04-15T02:16Z] INFO  19:16:49,393 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T02:16Z] GATK: GenotypeGVCFs
[2016-04-15T02:16Z] INFO  19:16:51,350 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T02:16Z] INFO  19:16:51,352 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T02:16Z] INFO  19:16:51,352 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T02:16Z] INFO  19:16:51,352 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T02:16Z] INFO  19:16:51,356 HelpFormatter - Program Args: -T GenotypeGVCFs -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/gatk-haplotype-joint/Batch1/X/tx/tmp_RcKwx/Batch1-X_31139949_46696637.vcf.gz -L X:31139950-46696637 --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18106_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18105_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18102_kapa-NGv3-PE100-NGv3.vcf.gz --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -nt 16 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T02:16Z] INFO  19:16:51,364 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T02:16Z] INFO  19:16:51,364 HelpFormatter - Date/Time: 2016/04/14 19:16:51
[2016-04-15T02:16Z] INFO  19:16:51,364 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T02:16Z] INFO  19:16:51,364 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T02:16Z] INFO  19:16:51,435 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T02:16Z] INFO  19:16:51,532 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T02:16Z] INFO  19:16:51,940 IntervalUtils - Processing 15556688 bp from intervals
[2016-04-15T02:16Z] WARN  19:16:51,941 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T02:16Z] WARN  19:16:51,941 IndexDictionaryUtils - Track variant2 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T02:16Z] WARN  19:16:51,941 IndexDictionaryUtils - Track variant3 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T02:16Z] WARN  19:16:51,942 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T02:16Z] INFO  19:16:51,950 MicroScheduler - Running the GATK in parallel mode with 16 total threads, 1 CPU thread(s) for each of 16 data thread(s), of 16 processors available on this machine
[2016-04-15T02:16Z] INFO  19:16:51,999 GenomeAnalysisEngine - Preparing for traversal
[2016-04-15T02:16Z] INFO  19:16:52,000 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T02:16Z] INFO  19:16:52,001 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T02:16Z] INFO  19:16:52,001 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T02:16Z] INFO  19:16:52,001 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T02:16Z] INFO  19:16:52,123 GenotypeGVCFs - Notice that the -ploidy parameter is ignored in GenotypeGVCFs tool as this is automatically determined by the input variant files
[2016-04-15T02:17Z] INFO  19:17:01,476 ProgressMeter -            done    340393.0     9.0 s      27.0 s      100.0%     9.0 s       0.0 s
[2016-04-15T02:17Z] INFO  19:17:01,476 ProgressMeter - Total runtime 9.48 secs, 0.16 min, 0.00 hours
[2016-04-15T02:17Z] INFO  19:17:03,683 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T02:17Z] GATK: GenotypeGVCFs
[2016-04-15T02:17Z] INFO  19:17:05,759 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T02:17Z] INFO  19:17:05,761 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T02:17Z] INFO  19:17:05,761 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T02:17Z] INFO  19:17:05,761 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T02:17Z] INFO  19:17:05,765 HelpFormatter - Program Args: -T GenotypeGVCFs -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/gatk-haplotype-joint/Batch1/X/tx/tmpM1zxft/Batch1-X_46712910_62570698.vcf.gz -L X:46712911-62570698 --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18106_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18105_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18102_kapa-NGv3-PE100-NGv3.vcf.gz --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -nt 16 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T02:17Z] INFO  19:17:05,773 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T02:17Z] INFO  19:17:05,774 HelpFormatter - Date/Time: 2016/04/14 19:17:05
[2016-04-15T02:17Z] INFO  19:17:05,774 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T02:17Z] INFO  19:17:05,774 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T02:17Z] INFO  19:17:05,846 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T02:17Z] INFO  19:17:05,944 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T02:17Z] INFO  19:17:06,363 IntervalUtils - Processing 15857788 bp from intervals
[2016-04-15T02:17Z] WARN  19:17:06,363 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T02:17Z] WARN  19:17:06,363 IndexDictionaryUtils - Track variant2 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T02:17Z] WARN  19:17:06,364 IndexDictionaryUtils - Track variant3 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T02:17Z] WARN  19:17:06,364 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T02:17Z] INFO  19:17:06,372 MicroScheduler - Running the GATK in parallel mode with 16 total threads, 1 CPU thread(s) for each of 16 data thread(s), of 16 processors available on this machine
[2016-04-15T02:17Z] INFO  19:17:06,423 GenomeAnalysisEngine - Preparing for traversal
[2016-04-15T02:17Z] INFO  19:17:06,424 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T02:17Z] INFO  19:17:06,424 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T02:17Z] INFO  19:17:06,424 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T02:17Z] INFO  19:17:06,425 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T02:17Z] INFO  19:17:06,552 GenotypeGVCFs - Notice that the -ploidy parameter is ignored in GenotypeGVCFs tool as this is automatically determined by the input variant files
[2016-04-15T02:17Z] INFO  19:17:15,949 ProgressMeter -            done    426534.0     9.0 s      22.0 s      100.0%     9.0 s       0.0 s
[2016-04-15T02:17Z] INFO  19:17:15,950 ProgressMeter - Total runtime 9.53 secs, 0.16 min, 0.00 hours
[2016-04-15T02:17Z] INFO  19:17:17,812 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T02:17Z] GATK: GenotypeGVCFs
[2016-04-15T02:17Z] INFO  19:17:19,807 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T02:17Z] INFO  19:17:19,809 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T02:17Z] INFO  19:17:19,809 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T02:17Z] INFO  19:17:19,809 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T02:17Z] INFO  19:17:19,813 HelpFormatter - Program Args: -T GenotypeGVCFs -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/gatk-haplotype-joint/Batch1/X/tx/tmpVW_jZk/Batch1-X_62857907_78427545.vcf.gz -L X:62857908-78427545 --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18106_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18105_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18102_kapa-NGv3-PE100-NGv3.vcf.gz --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -nt 16 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T02:17Z] INFO  19:17:19,821 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T02:17Z] INFO  19:17:19,821 HelpFormatter - Date/Time: 2016/04/14 19:17:19
[2016-04-15T02:17Z] INFO  19:17:19,821 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T02:17Z] INFO  19:17:19,821 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T02:17Z] INFO  19:17:19,893 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T02:17Z] INFO  19:17:19,990 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T02:17Z] INFO  19:17:20,401 IntervalUtils - Processing 15569638 bp from intervals
[2016-04-15T02:17Z] WARN  19:17:20,401 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T02:17Z] WARN  19:17:20,402 IndexDictionaryUtils - Track variant2 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T02:17Z] WARN  19:17:20,402 IndexDictionaryUtils - Track variant3 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T02:17Z] WARN  19:17:20,402 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T02:17Z] INFO  19:17:20,410 MicroScheduler - Running the GATK in parallel mode with 16 total threads, 1 CPU thread(s) for each of 16 data thread(s), of 16 processors available on this machine
[2016-04-15T02:17Z] INFO  19:17:20,459 GenomeAnalysisEngine - Preparing for traversal
[2016-04-15T02:17Z] INFO  19:17:20,460 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T02:17Z] INFO  19:17:20,461 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T02:17Z] INFO  19:17:20,461 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T02:17Z] INFO  19:17:20,461 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T02:17Z] INFO  19:17:20,583 GenotypeGVCFs - Notice that the -ploidy parameter is ignored in GenotypeGVCFs tool as this is automatically determined by the input variant files
[2016-04-15T02:17Z] INFO  19:17:29,757 ProgressMeter -            done    423189.0     9.0 s      21.0 s      100.0%     9.0 s       0.0 s
[2016-04-15T02:17Z] INFO  19:17:29,758 ProgressMeter - Total runtime 9.30 secs, 0.15 min, 0.00 hours
[2016-04-15T02:17Z] INFO  19:17:31,888 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T02:17Z] GATK: GenotypeGVCFs
[2016-04-15T02:17Z] INFO  19:17:33,823 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T02:17Z] INFO  19:17:33,825 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T02:17Z] INFO  19:17:33,825 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T02:17Z] INFO  19:17:33,825 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T02:17Z] INFO  19:17:33,829 HelpFormatter - Program Args: -T GenotypeGVCFs -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/gatk-haplotype-joint/Batch1/X/tx/tmpALqISE/Batch1-X_78616585_95940189.vcf.gz -L X:78616586-95940189 --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18106_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18105_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18102_kapa-NGv3-PE100-NGv3.vcf.gz --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -nt 16 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T02:17Z] INFO  19:17:33,838 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T02:17Z] INFO  19:17:33,838 HelpFormatter - Date/Time: 2016/04/14 19:17:33
[2016-04-15T02:17Z] INFO  19:17:33,838 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T02:17Z] INFO  19:17:33,839 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T02:17Z] INFO  19:17:33,910 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T02:17Z] INFO  19:17:34,008 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T02:17Z] INFO  19:17:34,420 IntervalUtils - Processing 17323604 bp from intervals
[2016-04-15T02:17Z] WARN  19:17:34,420 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T02:17Z] WARN  19:17:34,421 IndexDictionaryUtils - Track variant2 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T02:17Z] WARN  19:17:34,421 IndexDictionaryUtils - Track variant3 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T02:17Z] WARN  19:17:34,421 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T02:17Z] INFO  19:17:34,429 MicroScheduler - Running the GATK in parallel mode with 16 total threads, 1 CPU thread(s) for each of 16 data thread(s), of 16 processors available on this machine
[2016-04-15T02:17Z] INFO  19:17:34,479 GenomeAnalysisEngine - Preparing for traversal
[2016-04-15T02:17Z] INFO  19:17:34,480 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T02:17Z] INFO  19:17:34,480 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T02:17Z] INFO  19:17:34,480 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T02:17Z] INFO  19:17:34,481 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T02:17Z] INFO  19:17:34,602 GenotypeGVCFs - Notice that the -ploidy parameter is ignored in GenotypeGVCFs tool as this is automatically determined by the input variant files
[2016-04-15T02:17Z] INFO  19:17:44,310 ProgressMeter -            done    350229.0     9.0 s      28.0 s      100.0%     9.0 s       0.0 s
[2016-04-15T02:17Z] INFO  19:17:44,311 ProgressMeter - Total runtime 9.83 secs, 0.16 min, 0.00 hours
[2016-04-15T02:17Z] INFO  19:17:46,465 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T02:17Z] GATK: GenotypeGVCFs
[2016-04-15T02:17Z] INFO  19:17:48,354 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T02:17Z] INFO  19:17:48,356 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T02:17Z] INFO  19:17:48,356 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T02:17Z] INFO  19:17:48,356 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T02:17Z] INFO  19:17:48,360 HelpFormatter - Program Args: -T GenotypeGVCFs -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/gatk-haplotype-joint/Batch1/X/tx/tmpSgOfWg/Batch1-X_95990756_111698889.vcf.gz -L X:95990757-111698889 --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18106_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18105_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18102_kapa-NGv3-PE100-NGv3.vcf.gz --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -nt 16 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T02:17Z] INFO  19:17:48,367 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T02:17Z] INFO  19:17:48,367 HelpFormatter - Date/Time: 2016/04/14 19:17:48
[2016-04-15T02:17Z] INFO  19:17:48,368 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T02:17Z] INFO  19:17:48,368 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T02:17Z] INFO  19:17:48,446 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T02:17Z] INFO  19:17:48,595 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T02:17Z] INFO  19:17:49,050 IntervalUtils - Processing 15708133 bp from intervals
[2016-04-15T02:17Z] WARN  19:17:49,050 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T02:17Z] WARN  19:17:49,051 IndexDictionaryUtils - Track variant2 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T02:17Z] WARN  19:17:49,051 IndexDictionaryUtils - Track variant3 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T02:17Z] WARN  19:17:49,051 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T02:17Z] INFO  19:17:49,059 MicroScheduler - Running the GATK in parallel mode with 16 total threads, 1 CPU thread(s) for each of 16 data thread(s), of 16 processors available on this machine
[2016-04-15T02:17Z] INFO  19:17:49,110 GenomeAnalysisEngine - Preparing for traversal
[2016-04-15T02:17Z] INFO  19:17:49,111 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T02:17Z] INFO  19:17:49,111 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T02:17Z] INFO  19:17:49,111 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T02:17Z] INFO  19:17:49,112 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T02:17Z] INFO  19:17:49,239 GenotypeGVCFs - Notice that the -ploidy parameter is ignored in GenotypeGVCFs tool as this is automatically determined by the input variant files
[2016-04-15T02:18Z] INFO  19:18:00,126 ProgressMeter -            done    403788.0    11.0 s      27.0 s      100.0%    11.0 s       0.0 s
[2016-04-15T02:18Z] INFO  19:18:00,126 ProgressMeter - Total runtime 11.02 secs, 0.18 min, 0.00 hours
[2016-04-15T02:18Z] INFO  19:18:02,045 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T02:18Z] GATK: GenotypeGVCFs
[2016-04-15T02:18Z] INFO  19:18:04,207 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T02:18Z] INFO  19:18:04,209 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T02:18Z] INFO  19:18:04,209 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T02:18Z] INFO  19:18:04,209 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T02:18Z] INFO  19:18:04,213 HelpFormatter - Program Args: -T GenotypeGVCFs -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/gatk-haplotype-joint/Batch1/X/tx/tmpAgbyJq/Batch1-X_111874647_128581278.vcf.gz -L X:111874648-128581278 --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18106_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18105_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18102_kapa-NGv3-PE100-NGv3.vcf.gz --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -nt 16 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T02:18Z] INFO  19:18:04,221 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T02:18Z] INFO  19:18:04,221 HelpFormatter - Date/Time: 2016/04/14 19:18:04
[2016-04-15T02:18Z] INFO  19:18:04,222 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T02:18Z] INFO  19:18:04,222 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T02:18Z] INFO  19:18:04,293 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T02:18Z] INFO  19:18:04,392 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T02:18Z] INFO  19:18:04,808 IntervalUtils - Processing 16706631 bp from intervals
[2016-04-15T02:18Z] WARN  19:18:04,808 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T02:18Z] WARN  19:18:04,808 IndexDictionaryUtils - Track variant2 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T02:18Z] WARN  19:18:04,809 IndexDictionaryUtils - Track variant3 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T02:18Z] WARN  19:18:04,809 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T02:18Z] INFO  19:18:04,817 MicroScheduler - Running the GATK in parallel mode with 16 total threads, 1 CPU thread(s) for each of 16 data thread(s), of 16 processors available on this machine
[2016-04-15T02:18Z] INFO  19:18:04,867 GenomeAnalysisEngine - Preparing for traversal
[2016-04-15T02:18Z] INFO  19:18:04,868 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T02:18Z] INFO  19:18:04,868 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T02:18Z] INFO  19:18:04,868 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T02:18Z] INFO  19:18:04,869 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T02:18Z] INFO  19:18:04,992 GenotypeGVCFs - Notice that the -ploidy parameter is ignored in GenotypeGVCFs tool as this is automatically determined by the input variant files
[2016-04-15T02:18Z] INFO  19:18:14,403 ProgressMeter -            done    386833.0     9.0 s      24.0 s      100.0%     9.0 s       0.0 s
[2016-04-15T02:18Z] INFO  19:18:14,403 ProgressMeter - Total runtime 9.54 secs, 0.16 min, 0.00 hours
[2016-04-15T02:18Z] INFO  19:18:16,750 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T02:18Z] GATK: GenotypeGVCFs
[2016-04-15T02:18Z] INFO  19:18:18,742 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T02:18Z] INFO  19:18:18,743 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T02:18Z] INFO  19:18:18,744 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T02:18Z] INFO  19:18:18,744 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T02:18Z] INFO  19:18:18,747 HelpFormatter - Program Args: -T GenotypeGVCFs -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/gatk-haplotype-joint/Batch1/X/tx/tmpvWfhVn/Batch1-X_128582278_144329181.vcf.gz -L X:128582279-144329181 --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18106_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18105_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18102_kapa-NGv3-PE100-NGv3.vcf.gz --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -nt 16 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T02:18Z] INFO  19:18:18,757 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T02:18Z] INFO  19:18:18,757 HelpFormatter - Date/Time: 2016/04/14 19:18:18
[2016-04-15T02:18Z] INFO  19:18:18,757 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T02:18Z] INFO  19:18:18,757 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T02:18Z] INFO  19:18:18,833 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T02:18Z] INFO  19:18:18,930 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T02:18Z] INFO  19:18:19,734 IntervalUtils - Processing 15746903 bp from intervals
[2016-04-15T02:18Z] WARN  19:18:19,735 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T02:18Z] WARN  19:18:19,735 IndexDictionaryUtils - Track variant2 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T02:18Z] WARN  19:18:19,736 IndexDictionaryUtils - Track variant3 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T02:18Z] WARN  19:18:19,736 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T02:18Z] INFO  19:18:19,753 MicroScheduler - Running the GATK in parallel mode with 16 total threads, 1 CPU thread(s) for each of 16 data thread(s), of 16 processors available on this machine
[2016-04-15T02:18Z] INFO  19:18:19,858 GenomeAnalysisEngine - Preparing for traversal
[2016-04-15T02:18Z] INFO  19:18:19,860 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T02:18Z] INFO  19:18:19,860 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T02:18Z] INFO  19:18:19,861 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T02:18Z] INFO  19:18:19,862 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T02:18Z] INFO  19:18:20,101 GenotypeGVCFs - Notice that the -ploidy parameter is ignored in GenotypeGVCFs tool as this is automatically determined by the input variant files
[2016-04-15T02:18Z] INFO  19:18:29,026 ProgressMeter -            done    378752.0     9.0 s      24.0 s      100.0%     9.0 s       0.0 s
[2016-04-15T02:18Z] INFO  19:18:29,027 ProgressMeter - Total runtime 9.17 secs, 0.15 min, 0.00 hours
[2016-04-15T02:18Z] INFO  19:18:31,456 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T02:18Z] GATK: GenotypeGVCFs
[2016-04-15T02:18Z] INFO  19:18:33,621 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T02:18Z] INFO  19:18:33,623 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T02:18Z] INFO  19:18:33,623 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T02:18Z] INFO  19:18:33,623 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T02:18Z] INFO  19:18:33,627 HelpFormatter - Program Args: -T GenotypeGVCFs -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/gatk-haplotype-joint/Batch1/X/tx/tmpG6lPGp/Batch1-X_144337190_155270560.vcf.gz -L X:144337191-155270560 --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18106_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18105_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18102_kapa-NGv3-PE100-NGv3.vcf.gz --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -nt 16 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T02:18Z] INFO  19:18:33,635 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T02:18Z] INFO  19:18:33,635 HelpFormatter - Date/Time: 2016/04/14 19:18:33
[2016-04-15T02:18Z] INFO  19:18:33,636 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T02:18Z] INFO  19:18:33,636 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T02:18Z] INFO  19:18:33,707 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T02:18Z] INFO  19:18:33,805 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T02:18Z] INFO  19:18:34,217 IntervalUtils - Processing 10933370 bp from intervals
[2016-04-15T02:18Z] WARN  19:18:34,218 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T02:18Z] WARN  19:18:34,218 IndexDictionaryUtils - Track variant2 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T02:18Z] WARN  19:18:34,218 IndexDictionaryUtils - Track variant3 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T02:18Z] WARN  19:18:34,218 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T02:18Z] INFO  19:18:34,226 MicroScheduler - Running the GATK in parallel mode with 16 total threads, 1 CPU thread(s) for each of 16 data thread(s), of 16 processors available on this machine
[2016-04-15T02:18Z] INFO  19:18:34,276 GenomeAnalysisEngine - Preparing for traversal
[2016-04-15T02:18Z] INFO  19:18:34,277 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T02:18Z] INFO  19:18:34,277 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T02:18Z] INFO  19:18:34,278 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T02:18Z] INFO  19:18:34,278 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T02:18Z] INFO  19:18:34,400 GenotypeGVCFs - Notice that the -ploidy parameter is ignored in GenotypeGVCFs tool as this is automatically determined by the input variant files
[2016-04-15T02:18Z] INFO  19:18:42,046 ProgressMeter -            done    344986.0     7.0 s      22.0 s       97.6%     7.0 s       0.0 s
[2016-04-15T02:18Z] INFO  19:18:42,047 ProgressMeter - Total runtime 7.77 secs, 0.13 min, 0.00 hours
[2016-04-15T02:18Z] INFO  19:18:44,080 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T02:18Z] GATK: GenotypeGVCFs
[2016-04-15T02:18Z] INFO  19:18:46,203 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T02:18Z] INFO  19:18:46,205 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T02:18Z] INFO  19:18:46,205 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T02:18Z] INFO  19:18:46,205 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T02:18Z] INFO  19:18:46,208 HelpFormatter - Program Args: -T GenotypeGVCFs -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/gatk-haplotype-joint/Batch1/Y/tx/tmpi1Rwdx/Batch1-Y_0_15522993.vcf.gz -L Y:1-15522993 --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18106_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18105_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18102_kapa-NGv3-PE100-NGv3.vcf.gz --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -nt 16 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T02:18Z] INFO  19:18:46,217 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T02:18Z] INFO  19:18:46,217 HelpFormatter - Date/Time: 2016/04/14 19:18:46
[2016-04-15T02:18Z] INFO  19:18:46,217 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T02:18Z] INFO  19:18:46,217 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T02:18Z] INFO  19:18:46,289 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T02:18Z] INFO  19:18:46,386 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T02:18Z] INFO  19:18:46,800 IntervalUtils - Processing 15522993 bp from intervals
[2016-04-15T02:18Z] WARN  19:18:46,801 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T02:18Z] WARN  19:18:46,801 IndexDictionaryUtils - Track variant2 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T02:18Z] WARN  19:18:46,801 IndexDictionaryUtils - Track variant3 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T02:18Z] WARN  19:18:46,801 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T02:18Z] INFO  19:18:46,810 MicroScheduler - Running the GATK in parallel mode with 16 total threads, 1 CPU thread(s) for each of 16 data thread(s), of 16 processors available on this machine
[2016-04-15T02:18Z] INFO  19:18:46,861 GenomeAnalysisEngine - Preparing for traversal
[2016-04-15T02:18Z] INFO  19:18:46,862 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T02:18Z] INFO  19:18:46,862 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T02:18Z] INFO  19:18:46,863 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T02:18Z] INFO  19:18:46,863 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T02:18Z] INFO  19:18:46,987 GenotypeGVCFs - Notice that the -ploidy parameter is ignored in GenotypeGVCFs tool as this is automatically determined by the input variant files
[2016-04-15T02:18Z] INFO  19:18:55,296 ProgressMeter -            done    244643.0     8.0 s      34.0 s      100.0%     8.0 s       0.0 s
[2016-04-15T02:18Z] INFO  19:18:55,297 ProgressMeter - Total runtime 8.43 secs, 0.14 min, 0.00 hours
[2016-04-15T02:18Z] INFO  19:18:57,611 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T02:18Z] GATK: GenotypeGVCFs
[2016-04-15T02:18Z] INFO  19:18:59,584 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T02:18Z] INFO  19:18:59,586 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T02:18Z] INFO  19:18:59,586 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T02:18Z] INFO  19:18:59,586 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T02:18Z] INFO  19:18:59,590 HelpFormatter - Program Args: -T GenotypeGVCFs -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/gatk-haplotype-joint/Batch1/Y/tx/tmppXNbq9/Batch1-Y_15526614_59222281.vcf.gz -L Y:15526615-59222281 --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18106_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18105_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18102_kapa-NGv3-PE100-NGv3.vcf.gz --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -nt 16 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T02:18Z] INFO  19:18:59,597 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T02:18Z] INFO  19:18:59,597 HelpFormatter - Date/Time: 2016/04/14 19:18:59
[2016-04-15T02:18Z] INFO  19:18:59,597 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T02:18Z] INFO  19:18:59,597 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T02:18Z] INFO  19:18:59,676 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T02:18Z] INFO  19:18:59,819 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T02:19Z] INFO  19:19:00,275 IntervalUtils - Processing 43695667 bp from intervals
[2016-04-15T02:19Z] WARN  19:19:00,276 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T02:19Z] WARN  19:19:00,276 IndexDictionaryUtils - Track variant2 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T02:19Z] WARN  19:19:00,276 IndexDictionaryUtils - Track variant3 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T02:19Z] WARN  19:19:00,276 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T02:19Z] INFO  19:19:00,285 MicroScheduler - Running the GATK in parallel mode with 16 total threads, 1 CPU thread(s) for each of 16 data thread(s), of 16 processors available on this machine
[2016-04-15T02:19Z] INFO  19:19:00,335 GenomeAnalysisEngine - Preparing for traversal
[2016-04-15T02:19Z] INFO  19:19:00,336 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T02:19Z] INFO  19:19:00,336 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T02:19Z] INFO  19:19:00,337 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T02:19Z] INFO  19:19:00,337 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T02:19Z] INFO  19:19:00,464 GenotypeGVCFs - Notice that the -ploidy parameter is ignored in GenotypeGVCFs tool as this is automatically determined by the input variant files
[2016-04-15T02:19Z] INFO  19:19:08,259 ProgressMeter -            done    101116.0     7.0 s      78.0 s      100.0%     7.0 s       0.0 s
[2016-04-15T02:19Z] INFO  19:19:08,259 ProgressMeter - Total runtime 7.92 secs, 0.13 min, 0.00 hours
[2016-04-15T02:19Z] INFO  19:19:10,645 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T02:19Z] GATK: GenotypeGVCFs
[2016-04-15T02:19Z] INFO  19:19:12,608 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T02:19Z] INFO  19:19:12,610 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12
[2016-04-15T02:19Z] INFO  19:19:12,610 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T02:19Z] INFO  19:19:12,610 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T02:19Z] INFO  19:19:12,613 HelpFormatter - Program Args: -T GenotypeGVCFs -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -o /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/gatk-haplotype-joint/Batch1/Y/tx/tmppMQrjn/Batch1-Y_59228291_59373566.vcf.gz -L Y:59228292-59373566 --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18106_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18105_kapa-NGv3-PE100-NGv3.vcf.gz --variant /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/gatk-haplotype/R14-18102_kapa-NGv3-PE100-NGv3.vcf.gz --dbsnp /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/variation/dbsnp_138.vcf.gz -nt 16 -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment
[2016-04-15T02:19Z] INFO  19:19:12,622 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T02:19Z] INFO  19:19:12,622 HelpFormatter - Date/Time: 2016/04/14 19:19:12
[2016-04-15T02:19Z] INFO  19:19:12,622 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T02:19Z] INFO  19:19:12,622 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T02:19Z] INFO  19:19:12,694 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T02:19Z] INFO  19:19:12,792 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T02:19Z] INFO  19:19:13,207 IntervalUtils - Processing 145275 bp from intervals
[2016-04-15T02:19Z] WARN  19:19:13,208 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T02:19Z] WARN  19:19:13,208 IndexDictionaryUtils - Track variant2 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T02:19Z] WARN  19:19:13,208 IndexDictionaryUtils - Track variant3 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T02:19Z] WARN  19:19:13,208 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T02:19Z] INFO  19:19:13,217 MicroScheduler - Running the GATK in parallel mode with 16 total threads, 1 CPU thread(s) for each of 16 data thread(s), of 16 processors available on this machine
[2016-04-15T02:19Z] INFO  19:19:13,266 GenomeAnalysisEngine - Preparing for traversal
[2016-04-15T02:19Z] INFO  19:19:13,267 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T02:19Z] INFO  19:19:13,267 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T02:19Z] INFO  19:19:13,268 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T02:19Z] INFO  19:19:13,268 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T02:19Z] INFO  19:19:13,391 GenotypeGVCFs - Notice that the -ploidy parameter is ignored in GenotypeGVCFs tool as this is automatically determined by the input variant files
[2016-04-15T02:19Z] INFO  19:19:13,958 ProgressMeter -            done      5263.0     0.0 s       2.2 m       89.4%     0.0 s       0.0 s
[2016-04-15T02:19Z] INFO  19:19:13,959 ProgressMeter - Total runtime 0.69 secs, 0.01 min, 0.00 hours
[2016-04-15T02:19Z] INFO  19:19:15,070 GATKRunReport - Uploaded run statistics report to AWS S3
[2016-04-15T02:19Z] ['bcbio-variation-recall', 'square', '-Xms750m', '-Xmx7280m', '-XX:+UseSerialGC', '-c', 16, '-r', u'1:1-15541927', '--caller', 'platypus', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/1/Batch1-1_0_15541927.vcf.gz', '/mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/1/Batch1-1_0_15541927.vcf-inputs.txt'] in region: 1:1-15541927
[2016-04-15T02:19Z] 2016-04-14 19:19:28 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:19:28,436 - WARNING - Could not retrieve variants from source file in region 1:12009744-12024425. Error was invalid region `1:12009745-12024425`
[2016-04-15T02:19Z] 2016-04-14 19:19:28 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:19:28,433 - WARNING - Could not retrieve variants from source file in region 1:14142792-14143193. Error was invalid region `1:14142793-14143193`
[2016-04-15T02:19Z] 2016-04-14 19:19:28 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:19:28,442 - WARNING - Could not retrieve variants from source file in region 1:13182860-13183701. Error was invalid region `1:13182861-13183701`
[2016-04-15T02:19Z] 2016-04-14 19:19:28 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:19:28,438 - WARNING - Could not retrieve variants from source file in region 1:1420255-1420656. Error was invalid region `1:1420256-1420656`
[2016-04-15T02:19Z] 2016-04-14 19:19:28 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:19:28,433 - WARNING - Could not retrieve variants from source file in region 1:15541396-15541797. Error was invalid region `1:15541397-15541797`
[2016-04-15T02:19Z] 2016-04-14 19:19:28 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:19:28,522 - WARNING - Could not retrieve variants from source file in region 1:978551-1007622. Error was invalid region `1:978552-1007622`
[2016-04-15T02:19Z] 2016-04-14 19:19:28 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:19:28,598 - WARNING - Could not retrieve variants from source file in region 1:1242496-1294708. Error was invalid region `1:1242497-1294708`
[2016-04-15T02:19Z] 2016-04-14 19:19:28 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:19:28,650 - WARNING - Could not retrieve variants from source file in region 1:69300-69701. Error was invalid region `1:69301-69701`
[2016-04-15T02:19Z] 2016-04-14 19:19:28 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:19:28,714 - WARNING - Could not retrieve variants from source file in region 1:6145670-6158752. Error was invalid region `1:6145671-6158752`
[2016-04-15T02:19Z] 2016-04-14 19:19:36 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:19:36,417 - WARNING - Could not retrieve variants from source file in region 1:14142792-14143193. Error was invalid region `1:14142793-14143193`
[2016-04-15T02:19Z] 2016-04-14 19:19:37 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:19:37,200 - WARNING - Could not retrieve variants from source file in region 1:2160179-2172173. Error was invalid region `1:2160180-2172173`
[2016-04-15T02:19Z] 2016-04-14 19:19:37 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:19:37,654 - WARNING - Could not retrieve variants from source file in region 1:12009744-12024425. Error was invalid region `1:12009745-12024425`
[2016-04-15T02:19Z] 2016-04-14 19:19:37 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:19:37,671 - WARNING - Could not retrieve variants from source file in region 1:2938054-2938887. Error was invalid region `1:2938055-2938887`
[2016-04-15T02:19Z] 2016-04-14 19:19:37 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:19:37,726 - WARNING - Could not retrieve variants from source file in region 1:2430406-2452759. Error was invalid region `1:2430407-2452759`
[2016-04-15T02:19Z] 2016-04-14 19:19:38 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:19:38,680 - WARNING - Could not retrieve variants from source file in region 1:6145670-6158752. Error was invalid region `1:6145671-6158752`
[2016-04-15T02:19Z] 2016-04-14 19:19:38 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:19:38,838 - WARNING - Could not retrieve variants from source file in region 1:8930422-8931653. Error was invalid region `1:8930423-8931653`
[2016-04-15T02:19Z] 2016-04-14 19:19:38 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:19:38,907 - WARNING - Could not retrieve variants from source file in region 1:69300-69701. Error was invalid region `1:69301-69701`
[2016-04-15T02:19Z] 2016-04-14 19:19:39 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:19:39,476 - WARNING - Could not retrieve variants from source file in region 1:15541396-15541797. Error was invalid region `1:15541397-15541797`
[2016-04-15T02:19Z] 2016-04-14 19:19:41 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:19:41,927 - WARNING - Could not retrieve variants from source file in region 1:14142792-14143193. Error was invalid region `1:14142793-14143193`
[2016-04-15T02:19Z] 2016-04-14 19:19:43 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:19:43,319 - WARNING - Could not retrieve variants from source file in region 1:1599601-1608419. Error was invalid region `1:1599602-1608419`
[2016-04-15T02:19Z] 2016-04-14 19:19:43 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:19:43,731 - WARNING - Could not retrieve variants from source file in region 1:2160179-2172173. Error was invalid region `1:2160180-2172173`
[2016-04-15T02:19Z] 2016-04-14 19:19:45 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:19:45,115 - WARNING - Could not retrieve variants from source file in region 1:12009744-12024425. Error was invalid region `1:12009745-12024425`
[2016-04-15T02:19Z] 2016-04-14 19:19:46 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:19:46,748 - WARNING - Could not retrieve variants from source file in region 1:6145670-6158752. Error was invalid region `1:6145671-6158752`
[2016-04-15T02:19Z] 2016-04-14 19:19:47 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:19:47,178 - WARNING - Could not retrieve variants from source file in region 1:69300-69701. Error was invalid region `1:69301-69701`
[2016-04-15T02:19Z] 2016-04-14 19:19:56 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:19:56,421 - WARNING - Could not retrieve variants from source file in region 1:15494899-15495300. Error was invalid region `1:15494900-15495300`
[2016-04-15T02:19Z] 2016-04-14 19:19:58 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:19:58,988 - WARNING - Could not retrieve variants from source file in region 1:1374623-1375024. Error was invalid region `1:1374624-1375024`
[2016-04-15T02:19Z] 2016-04-14 19:19:59 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:19:59,559 - WARNING - Could not retrieve variants from source file in region 1:1551038-1558982. Error was invalid region `1:1551039-1558982`
[2016-04-15T02:19Z] 2016-04-14 19:19:59 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:19:59,581 - WARNING - Could not retrieve variants from source file in region 1:2125928-2126329. Error was invalid region `1:2125929-2126329`
[2016-04-15T02:20Z] 2016-04-14 19:20:01 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:20:01,087 - WARNING - Could not retrieve variants from source file in region 1:11982162-11983396. Error was invalid region `1:11982163-11983396`
[2016-04-15T02:20Z] 2016-04-14 19:20:01 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:20:01,273 - WARNING - Could not retrieve variants from source file in region 1:2526535-2573389. Error was invalid region `1:2526536-2573389`
[2016-04-15T02:20Z] 2016-04-14 19:20:02 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:20:02,329 - WARNING - Could not retrieve variants from source file in region 1:5965170-5965571. Error was invalid region `1:5965171-5965571`
[2016-04-15T02:20Z] 2016-04-14 19:20:03 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:20:03,088 - WARNING - Could not retrieve variants from source file in region 1:14099363-14109304. Error was invalid region `1:14099364-14109304`
[2016-04-15T02:20Z] 2016-04-14 19:20:05 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:20:05,789 - WARNING - Could not retrieve variants from source file in region 1:1551038-1558982. Error was invalid region `1:1551039-1558982`
[2016-04-15T02:20Z] 2016-04-14 19:20:05 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:20:05,933 - WARNING - Could not retrieve variants from source file in region 1:2125928-2126329. Error was invalid region `1:2125929-2126329`
[2016-04-15T02:20Z] 2016-04-14 19:20:06 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:20:06,174 - WARNING - Could not retrieve variants from source file in region 1:11982162-11983396. Error was invalid region `1:11982163-11983396`
[2016-04-15T02:20Z] 2016-04-14 19:20:06 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:20:06,289 - WARNING - Could not retrieve variants from source file in region 1:2526535-2573389. Error was invalid region `1:2526536-2573389`
[2016-04-15T02:20Z] 2016-04-14 19:20:08 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:20:08,545 - WARNING - Could not retrieve variants from source file in region 1:1141674-1158821. Error was invalid region `1:1141675-1158821`
[2016-04-15T02:20Z] 2016-04-14 19:20:09 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:20:09,431 - WARNING - Could not retrieve variants from source file in region 1:2337804-2340390. Error was invalid region `1:2337805-2340390`
[2016-04-15T02:20Z] 2016-04-14 19:20:10 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:20:10,719 - WARNING - Could not retrieve variants from source file in region 1:1114999-1115403. Error was invalid region `1:1115000-1115403`
[2016-04-15T02:20Z] 2016-04-14 19:20:10 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:20:10,765 - WARNING - Could not retrieve variants from source file in region 1:1374623-1375024. Error was invalid region `1:1374624-1375024`
[2016-04-15T02:20Z] 2016-04-14 19:20:11 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:20:11,439 - WARNING - Could not retrieve variants from source file in region 1:2125928-2126329. Error was invalid region `1:2125929-2126329`
[2016-04-15T02:20Z] 2016-04-14 19:20:12 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:20:12,157 - WARNING - Could not retrieve variants from source file in region 1:13802114-13802627. Error was invalid region `1:13802115-13802627`
[2016-04-15T02:20Z] 2016-04-14 19:20:12 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:20:12,763 - WARNING - Could not retrieve variants from source file in region 1:13141350-13141751. Error was invalid region `1:13141351-13141751`
[2016-04-15T02:20Z] 2016-04-14 19:20:12 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:20:12,837 - WARNING - Could not retrieve variants from source file in region 1:11982162-11983396. Error was invalid region `1:11982163-11983396`
[2016-04-15T02:20Z] 2016-04-14 19:20:13 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:20:13,774 - WARNING - Could not retrieve variants from source file in region 1:2337804-2340390. Error was invalid region `1:2337805-2340390`
[2016-04-15T02:20Z] 2016-04-14 19:20:16 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:20:16,186 - WARNING - Could not retrieve variants from source file in region 1:1114999-1115403. Error was invalid region `1:1115000-1115403`
[2016-04-15T02:20Z] 2016-04-14 19:20:16 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:20:16,975 - WARNING - Could not retrieve variants from source file in region 1:8390173-8426090. Error was invalid region `1:8390174-8426090`
[2016-04-15T02:20Z] 2016-04-14 19:20:19 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:20:19,326 - WARNING - Could not retrieve variants from source file in region 1:13141350-13141751. Error was invalid region `1:13141351-13141751`
[2016-04-15T02:20Z] 2016-04-14 19:20:20 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:20:20,091 - WARNING - Could not retrieve variants from source file in region 1:10435113-10511779. Error was invalid region `1:10435114-10511779`
[2016-04-15T02:20Z] 2016-04-14 19:20:26 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:20:26,400 - WARNING - Could not retrieve variants from source file in region 1:2036052-2036453. Error was invalid region `1:2036053-2036453`
[2016-04-15T02:20Z] 2016-04-14 19:20:26 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:20:26,415 - WARNING - Could not retrieve variants from source file in region 1:15438779-15439180. Error was invalid region `1:15438780-15439180`
[2016-04-15T02:20Z] 2016-04-14 19:20:27 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:20:27,117 - WARNING - Could not retrieve variants from source file in region 1:2487942-2494520. Error was invalid region `1:2487943-2494520`
[2016-04-15T02:20Z] 2016-04-14 19:20:27 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:20:27,788 - WARNING - Could not retrieve variants from source file in region 1:5926296-5937517. Error was invalid region `1:5926297-5937517`
[2016-04-15T02:20Z] 2016-04-14 19:20:29 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:20:29,022 - WARNING - Could not retrieve variants from source file in region 1:2253313-2255220. Error was invalid region `1:2253314-2255220`
[2016-04-15T02:20Z] 2016-04-14 19:20:29 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:20:29,110 - WARNING - Could not retrieve variants from source file in region 1:11884344-11906258. Error was invalid region `1:11884345-11906258`
[2016-04-15T02:20Z] 2016-04-14 19:20:29 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:20:29,598 - WARNING - Could not retrieve variants from source file in region 1:10435113-10511779. Error was invalid region `1:10435114-10511779`
[2016-04-15T02:20Z] 2016-04-14 19:20:30 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:20:30,234 - WARNING - Could not retrieve variants from source file in region 1:11579293-11590101. Error was invalid region `1:11579294-11590101`
[2016-04-15T02:20Z] 2016-04-14 19:20:30 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:20:30,421 - WARNING - Could not retrieve variants from source file in region 1:6947993-6948394. Error was invalid region `1:6947994-6948394`
[2016-04-15T02:20Z] 2016-04-14 19:20:31 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:20:31,920 - WARNING - Could not retrieve variants from source file in region 1:2036052-2036453. Error was invalid region `1:2036053-2036453`
[2016-04-15T02:20Z] 2016-04-14 19:20:31 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:20:31,987 - WARNING - Could not retrieve variants from source file in region 1:15438779-15439180. Error was invalid region `1:15438780-15439180`
[2016-04-15T02:20Z] 2016-04-14 19:20:33 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:20:33,170 - WARNING - Could not retrieve variants from source file in region 1:13695605-13696006. Error was invalid region `1:13695606-13696006`
[2016-04-15T02:20Z] 2016-04-14 19:20:33 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:20:33,403 - WARNING - Could not retrieve variants from source file in region 1:2487942-2494520. Error was invalid region `1:2487943-2494520`
[2016-04-15T02:20Z] 2016-04-14 19:20:35 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:20:35,716 - WARNING - Could not retrieve variants from source file in region 1:11884344-11906258. Error was invalid region `1:11884345-11906258`
[2016-04-15T02:20Z] 2016-04-14 19:20:36 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:20:36,633 - WARNING - Could not retrieve variants from source file in region 1:6947993-6948394. Error was invalid region `1:6947994-6948394`
[2016-04-15T02:20Z] 2016-04-14 19:20:36 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:20:36,676 - WARNING - Could not retrieve variants from source file in region 1:11579293-11590101. Error was invalid region `1:11579294-11590101`
[2016-04-15T02:20Z] 2016-04-14 19:20:37 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:20:37,218 - WARNING - Could not retrieve variants from source file in region 1:7869837-7913620. Error was invalid region `1:7869838-7913620`
[2016-04-15T02:20Z] 2016-04-14 19:20:37 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:20:37,303 - WARNING - Could not retrieve variants from source file in region 1:2036052-2036453. Error was invalid region `1:2036053-2036453`
[2016-04-15T02:20Z] 2016-04-14 19:20:37 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:20:37,799 - WARNING - Could not retrieve variants from source file in region 1:13695605-13696006. Error was invalid region `1:13695606-13696006`
[2016-04-15T02:20Z] 2016-04-14 19:20:39 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:20:39,530 - WARNING - Could not retrieve variants from source file in region 1:1987782-1988183. Error was invalid region `1:1987783-1988183`
[2016-04-15T02:20Z] 2016-04-14 19:20:41 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:20:41,572 - WARNING - Could not retrieve variants from source file in region 1:13036376-13036844. Error was invalid region `1:13036377-13036844`
[2016-04-15T02:20Z] 2016-04-14 19:20:41 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:20:41,673 - WARNING - Could not retrieve variants from source file in region 1:11884344-11906258. Error was invalid region `1:11884345-11906258`
[2016-04-15T02:20Z] 2016-04-14 19:20:42 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:20:42,392 - WARNING - Could not retrieve variants from source file in region 1:11579293-11590101. Error was invalid region `1:11579294-11590101`
[2016-04-15T02:20Z] 2016-04-14 19:20:42 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:20:42,531 - WARNING - Could not retrieve variants from source file in region 1:6947993-6948394. Error was invalid region `1:6947994-6948394`
[2016-04-15T02:20Z] 2016-04-14 19:20:43 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:20:43,087 - WARNING - Could not retrieve variants from source file in region 1:13695605-13696006. Error was invalid region `1:13695606-13696006`
[2016-04-15T02:20Z] 2016-04-14 19:20:46 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:20:46,243 - WARNING - Could not retrieve variants from source file in region 1:15250591-15250992. Error was invalid region `1:15250592-15250992`
[2016-04-15T02:20Z] 2016-04-14 19:20:46 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:20:46,628 - WARNING - Could not retrieve variants from source file in region 1:10366276-10366677. Error was invalid region `1:10366277-10366677`
[2016-04-15T02:20Z] 2016-04-14 19:20:47 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:20:47,619 - WARNING - Could not retrieve variants from source file in region 1:13036376-13036844. Error was invalid region `1:13036377-13036844`
[2016-04-15T02:20Z] 2016-04-14 19:20:48 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:20:48,879 - WARNING - Could not retrieve variants from source file in region 1:6500833-6524878. Error was invalid region `1:6500834-6524878`
[2016-04-15T02:20Z] 2016-04-14 19:20:51 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:20:51,853 - WARNING - Could not retrieve variants from source file in region 1:14219975-14220376. Error was invalid region `1:14219976-14220376`
[2016-04-15T02:20Z] 2016-04-14 19:20:51 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:20:51,859 - WARNING - Could not retrieve variants from source file in region 1:10366276-10366677. Error was invalid region `1:10366277-10366677`
[2016-04-15T02:20Z] 2016-04-14 19:20:55 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:20:55,058 - WARNING - Could not retrieve variants from source file in region 1:13448072-13448541. Error was invalid region `1:13448073-13448541`
[2016-04-15T02:20Z] 2016-04-14 19:20:56 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:20:56,714 - WARNING - Could not retrieve variants from source file in region 1:1956826-1957227. Error was invalid region `1:1956827-1957227`
[2016-04-15T02:20Z] 2016-04-14 19:20:56 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:20:56,980 - WARNING - Could not retrieve variants from source file in region 1:14219975-14220376. Error was invalid region `1:14219976-14220376`
[2016-04-15T02:20Z] 2016-04-14 19:20:57 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:20:57,205 - WARNING - Could not retrieve variants from source file in region 1:10366276-10366677. Error was invalid region `1:10366277-10366677`
[2016-04-15T02:20Z] 2016-04-14 19:20:57 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:20:57,430 - WARNING - Could not retrieve variants from source file in region 1:11288547-11301904. Error was invalid region `1:11288548-11301904`
[2016-04-15T02:20Z] 2016-04-14 19:20:57 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:20:57,558 - WARNING - Could not retrieve variants from source file in region 1:11808426-11856568. Error was invalid region `1:11808427-11856568`
[2016-04-15T02:20Z] 2016-04-14 19:20:57 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:20:57,628 - WARNING - Could not retrieve variants from source file in region 1:6692886-6706064. Error was invalid region `1:6692887-6706064`
[2016-04-15T02:21Z] 2016-04-14 19:21:02 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:21:02,393 - WARNING - Could not retrieve variants from source file in region 1:1956826-1957227. Error was invalid region `1:1956827-1957227`
[2016-04-15T02:21Z] 2016-04-14 19:21:03 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:21:03,248 - WARNING - Could not retrieve variants from source file in region 1:11288547-11301904. Error was invalid region `1:11288548-11301904`
[2016-04-15T02:21Z] 2016-04-14 19:21:03 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:21:03,415 - WARNING - Could not retrieve variants from source file in region 1:7797292-7797693. Error was invalid region `1:7797293-7797693`
[2016-04-15T02:21Z] 2016-04-14 19:21:03 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:21:03,567 - WARNING - Could not retrieve variants from source file in region 1:4771842-4772907. Error was invalid region `1:4771843-4772907`
[2016-04-15T02:21Z] 2016-04-14 19:21:08 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:21:08,607 - WARNING - Could not retrieve variants from source file in region 1:11288547-11301904. Error was invalid region `1:11288548-11301904`
[2016-04-15T02:21Z] 2016-04-14 19:21:09 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:21:09,054 - WARNING - Could not retrieve variants from source file in region 1:12638753-12639154. Error was invalid region `1:12638754-12639154`
[2016-04-15T02:21Z] 2016-04-14 19:21:09 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:21:09,177 - WARNING - Could not retrieve variants from source file in region 1:9415940-9416536. Error was invalid region `1:9415941-9416536`
[2016-04-15T02:21Z] 2016-04-14 19:21:10 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:21:10,880 - WARNING - Could not retrieve variants from source file in region 1:10318441-10318842. Error was invalid region `1:10318442-10318842`
[2016-04-15T02:21Z] 2016-04-14 19:21:12 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:21:12,094 - WARNING - Could not retrieve variants from source file in region 1:6293483-6315012. Error was invalid region `1:6293484-6315012`
[2016-04-15T02:21Z] 2016-04-14 19:21:13 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:21:13,734 - WARNING - Could not retrieve variants from source file in region 1:12638753-12639154. Error was invalid region `1:12638754-12639154`
[2016-04-15T02:21Z] 2016-04-14 19:21:15 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:21:15,856 - WARNING - Could not retrieve variants from source file in region 1:10318441-10318842. Error was invalid region `1:10318442-10318842`
[2016-04-15T02:21Z] 2016-04-14 19:21:19 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:21:19,109 - WARNING - Could not retrieve variants from source file in region 1:12638753-12639154. Error was invalid region `1:12638754-12639154`
[2016-04-15T02:21Z] 2016-04-14 19:21:19 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:21:19,165 - WARNING - Could not retrieve variants from source file in region 1:9415940-9416536. Error was invalid region `1:9415941-9416536`
[2016-04-15T02:21Z] 2016-04-14 19:21:21 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:21:21,158 - WARNING - Could not retrieve variants from source file in region 1:10318441-10318842. Error was invalid region `1:10318442-10318842`
[2016-04-15T02:21Z] 2016-04-14 19:21:23 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:21:23,694 - WARNING - Could not retrieve variants from source file in region 1:11254797-11255198. Error was invalid region `1:11254798-11255198`
[2016-04-15T02:21Z] 2016-04-14 19:21:23 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:21:23,769 - WARNING - Could not retrieve variants from source file in region 1:7723746-7724147. Error was invalid region `1:7723747-7724147`
[2016-04-15T02:21Z] 2016-04-14 19:21:24 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:21:24,747 - WARNING - Could not retrieve variants from source file in region 1:3638463-3638864. Error was invalid region `1:3638464-3638864`
[2016-04-15T02:21Z] 2016-04-14 19:21:25 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:21:25,432 - WARNING - Could not retrieve variants from source file in region 1:12776133-12785684. Error was invalid region `1:12776134-12785684`
[2016-04-15T02:21Z] 2016-04-14 19:21:28 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:21:28,498 - WARNING - Could not retrieve variants from source file in region 1:6614180-6635496. Error was invalid region `1:6614181-6635496`
[2016-04-15T02:21Z] 2016-04-14 19:21:29 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:21:29,011 - WARNING - Could not retrieve variants from source file in region 1:7723746-7724147. Error was invalid region `1:7723747-7724147`
[2016-04-15T02:21Z] 2016-04-14 19:21:29 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:21:29,372 - WARNING - Could not retrieve variants from source file in region 1:11766213-11772178. Error was invalid region `1:11766214-11772178`
[2016-04-15T02:21Z] 2016-04-14 19:21:30 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:21:30,977 - WARNING - Could not retrieve variants from source file in region 1:3638463-3638864. Error was invalid region `1:3638464-3638864`
[2016-04-15T02:21Z] 2016-04-14 19:21:31 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:21:31,907 - WARNING - Could not retrieve variants from source file in region 1:12776133-12785684. Error was invalid region `1:12776134-12785684`
[2016-04-15T02:21Z] 2016-04-14 19:21:32 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:21:32,151 - WARNING - Could not retrieve variants from source file in region 1:9811330-9811731. Error was invalid region `1:9811331-9811731`
[2016-04-15T02:21Z] 2016-04-14 19:21:32 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:21:32,373 - WARNING - Could not retrieve variants from source file in region 1:12776133-12785684. Error was invalid region `1:12776134-12785684`
[2016-04-15T02:21Z] 2016-04-14 19:21:34 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:21:34,931 - WARNING - Could not retrieve variants from source file in region 1:7723746-7724147. Error was invalid region `1:7723747-7724147`
[2016-04-15T02:21Z] 2016-04-14 19:21:35 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:21:35,372 - WARNING - Could not retrieve variants from source file in region 1:12401657-12402058. Error was invalid region `1:12401658-12402058`
[2016-04-15T02:21Z] 2016-04-14 19:21:36 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:21:36,489 - WARNING - Could not retrieve variants from source file in region 1:9670623-9671024. Error was invalid region `1:9670624-9671024`
[2016-04-15T02:21Z] 2016-04-14 19:21:36 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:21:36,880 - WARNING - Could not retrieve variants from source file in region 1:3638463-3638864. Error was invalid region `1:3638464-3638864`
[2016-04-15T02:21Z] 2016-04-14 19:21:37 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:21:37,273 - WARNING - Could not retrieve variants from source file in region 1:6183881-6184282. Error was invalid region `1:6183882-6184282`
[2016-04-15T02:21Z] 2016-04-14 19:21:40 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:21:40,812 - WARNING - Could not retrieve variants from source file in region 1:12401657-12402058. Error was invalid region `1:12401658-12402058`
[2016-04-15T02:21Z] 2016-04-14 19:21:41 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:21:41,354 - WARNING - Could not retrieve variants from source file in region 1:9352804-9353312. Error was invalid region `1:9352805-9353312`
[2016-04-15T02:21Z] 2016-04-14 19:21:41 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:21:41,971 - WARNING - Could not retrieve variants from source file in region 1:9670623-9671024. Error was invalid region `1:9670624-9671024`
[2016-04-15T02:21Z] 2016-04-14 19:21:43 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:21:43,045 - WARNING - Could not retrieve variants from source file in region 1:3668990-3678123. Error was invalid region `1:3668991-3678123`
[2016-04-15T02:21Z] 2016-04-14 19:21:45 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:21:45,795 - WARNING - Could not retrieve variants from source file in region 1:12401657-12402058. Error was invalid region `1:12401658-12402058`
[2016-04-15T02:21Z] 2016-04-14 19:21:46 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:21:46,435 - WARNING - Could not retrieve variants from source file in region 1:10689731-10725777. Error was invalid region `1:10689732-10725777`
[2016-04-15T02:21Z] 2016-04-14 19:21:46 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:21:46,650 - WARNING - Could not retrieve variants from source file in region 1:9352804-9353312. Error was invalid region `1:9352805-9353312`
[2016-04-15T02:21Z] 2016-04-14 19:21:46 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:21:46,914 - WARNING - Could not retrieve variants from source file in region 1:9670623-9671024. Error was invalid region `1:9670624-9671024`
[2016-04-15T02:21Z] 2016-04-14 19:21:48 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:21:48,118 - WARNING - Could not retrieve variants from source file in region 1:10596130-10596531. Error was invalid region `1:10596131-10596531`
[2016-04-15T02:21Z] 2016-04-14 19:21:49 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:21:49,906 - WARNING - Could not retrieve variants from source file in region 1:12248731-12254849. Error was invalid region `1:12248732-12254849`
[2016-04-15T02:21Z] 2016-04-14 19:21:50 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:21:50,607 - WARNING - Could not retrieve variants from source file in region 1:9642213-9642614. Error was invalid region `1:9642214-9642614`
[2016-04-15T02:21Z] 2016-04-14 19:21:51 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:21:51,311 - WARNING - Could not retrieve variants from source file in region 1:12313616-12314017. Error was invalid region `1:12313617-12314017`
[2016-04-15T02:21Z] 2016-04-14 19:21:51 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:21:51,314 - WARNING - Could not retrieve variants from source file in region 1:3668990-3678123. Error was invalid region `1:3668991-3678123`
[2016-04-15T02:21Z] 2016-04-14 19:21:54 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:21:54,303 - WARNING - Could not retrieve variants from source file in region 1:3547925-3551982. Error was invalid region `1:3547926-3551982`
[2016-04-15T02:21Z] 2016-04-14 19:21:54 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:21:54,642 - WARNING - Could not retrieve variants from source file in region 1:9642213-9642614. Error was invalid region `1:9642214-9642614`
[2016-04-15T02:21Z] 2016-04-14 19:21:57 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:21:57,685 - WARNING - Could not retrieve variants from source file in region 1:9302731-9324860. Error was invalid region `1:9302732-9324860`
[2016-04-15T02:22Z] 2016-04-14 19:22:01 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:22:01,134 - WARNING - Could not retrieve variants from source file in region 1:3496268-3496669. Error was invalid region `1:3496269-3496669`
[2016-04-15T02:22Z] 2016-04-14 19:22:01 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:22:01,190 - WARNING - Could not retrieve variants from source file in region 1:3496268-3496669. Error was invalid region `1:3496269-3496669`
[2016-04-15T02:22Z] 2016-04-14 19:22:01 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:22:01,221 - WARNING - Could not retrieve variants from source file in region 1:3496268-3496669. Error was invalid region `1:3496269-3496669`
[2016-04-15T02:22Z] 2016-04-14 19:22:02 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:22:02,996 - WARNING - Could not retrieve variants from source file in region 1:12164226-12198487. Error was invalid region `1:12164227-12198487`
[2016-04-15T02:22Z] 2016-04-14 19:22:06 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:22:06,413 - WARNING - Could not retrieve variants from source file in region 1:12164226-12198487. Error was invalid region `1:12164227-12198487`
[2016-04-15T02:22Z] 2016-04-14 19:22:07 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:22:07,434 - WARNING - Could not retrieve variants from source file in region 1:12082123-12083116. Error was invalid region `1:12082124-12083116`
[2016-04-15T02:22Z] 2016-04-14 19:22:07 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:22:07,603 - WARNING - Could not retrieve variants from source file in region 1:9165474-9165875. Error was invalid region `1:9165475-9165875`
[2016-04-15T02:22Z] 2016-04-14 19:22:07 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:22:07,879 - WARNING - Could not retrieve variants from source file in region 1:3328147-3328548. Error was invalid region `1:3328148-3328548`
[2016-04-15T02:22Z] 2016-04-14 19:22:08 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:22:08,350 - WARNING - Could not retrieve variants from source file in region 1:9074650-9075051. Error was invalid region `1:9074651-9075051`
[2016-04-15T02:22Z] 2016-04-14 19:22:11 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:22:11,164 - WARNING - Could not retrieve variants from source file in region 1:3328147-3328548. Error was invalid region `1:3328148-3328548`
[2016-04-15T02:22Z] 2016-04-14 19:22:12 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:22:12,110 - WARNING - Could not retrieve variants from source file in region 1:3328147-3328548. Error was invalid region `1:3328148-3328548`
[2016-04-15T02:22Z] 2016-04-14 19:22:14 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:22:14,039 - WARNING - Could not retrieve variants from source file in region 1:9074650-9075051. Error was invalid region `1:9074651-9075051`
[2016-04-15T02:22Z] 2016-04-14 19:22:14 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:22:14,557 - WARNING - Could not retrieve variants from source file in region 1:3301510-3301911. Error was invalid region `1:3301511-3301911`
[2016-04-15T02:22Z] ['bcbio-variation-recall', 'square', '-Xms750m', '-Xmx7280m', '-XX:+UseSerialGC', '-c', 16, '-r', u'1:15545822-31186478', '--caller', 'platypus', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/1/Batch1-1_15545821_31186478.vcf.gz', '/mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/1/Batch1-1_15545821_31186478.vcf-inputs.txt'] in region: 1:15545822-31186478
[2016-04-15T02:22Z] 2016-04-14 19:22:33 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:22:33,803 - WARNING - Could not retrieve variants from source file in region 1:21616721-21617122. Error was invalid region `1:21616722-21617122`
[2016-04-15T02:22Z] 2016-04-14 19:22:34 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:22:34,336 - WARNING - Could not retrieve variants from source file in region 1:22835466-22852905. Error was invalid region `1:22835467-22852905`
[2016-04-15T02:22Z] 2016-04-14 19:22:34 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:22:34,506 - WARNING - Could not retrieve variants from source file in region 1:22054216-22054617. Error was invalid region `1:22054217-22054617`
[2016-04-15T02:22Z] 2016-04-14 19:22:34 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:22:34,648 - WARNING - Could not retrieve variants from source file in region 1:20490307-20501772. Error was invalid region `1:20490308-20501772`
[2016-04-15T02:22Z] 2016-04-14 19:22:34 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:22:34,854 - WARNING - Could not retrieve variants from source file in region 1:29185513-29189787. Error was invalid region `1:29185514-29189787`
[2016-04-15T02:22Z] 2016-04-14 19:22:35 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:22:35,537 - WARNING - Could not retrieve variants from source file in region 1:29138764-29139165. Error was invalid region `1:29138765-29139165`
[2016-04-15T02:22Z] 2016-04-14 19:22:35 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:22:35,564 - WARNING - Could not retrieve variants from source file in region 1:28969103-28969504. Error was invalid region `1:28969104-28969504`
[2016-04-15T02:22Z] 2016-04-14 19:22:35 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:22:35,716 - WARNING - Could not retrieve variants from source file in region 1:16641688-16642089. Error was invalid region `1:16641689-16642089`
[2016-04-15T02:22Z] 2016-04-14 19:22:40 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:22:40,680 - WARNING - Could not retrieve variants from source file in region 1:19018194-19027429. Error was invalid region `1:19018195-19027429`
[2016-04-15T02:22Z] 2016-04-14 19:22:41 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:22:41,652 - WARNING - Could not retrieve variants from source file in region 1:22835466-22852905. Error was invalid region `1:22835467-22852905`
[2016-04-15T02:22Z] 2016-04-14 19:22:41 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:22:41,653 - WARNING - Could not retrieve variants from source file in region 1:28157235-28157636. Error was invalid region `1:28157236-28157636`
[2016-04-15T02:22Z] 2016-04-14 19:22:42 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:22:42,795 - WARNING - Could not retrieve variants from source file in region 1:22054216-22054617. Error was invalid region `1:22054217-22054617`
[2016-04-15T02:22Z] 2016-04-14 19:22:42 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:22:42,854 - WARNING - Could not retrieve variants from source file in region 1:27210510-27224157. Error was invalid region `1:27210511-27224157`
[2016-04-15T02:22Z] 2016-04-14 19:22:43 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:22:43,188 - WARNING - Could not retrieve variants from source file in region 1:26218835-26219236. Error was invalid region `1:26218836-26219236`
[2016-04-15T02:22Z] 2016-04-14 19:22:43 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:22:43,334 - WARNING - Could not retrieve variants from source file in region 1:29396736-29397137. Error was invalid region `1:29396737-29397137`
[2016-04-15T02:22Z] 2016-04-14 19:22:43 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:22:43,844 - WARNING - Could not retrieve variants from source file in region 1:28969103-28969504. Error was invalid region `1:28969104-28969504`
[2016-04-15T02:22Z] 2016-04-14 19:22:43 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:22:43,941 - WARNING - Could not retrieve variants from source file in region 1:29138764-29139165. Error was invalid region `1:29138765-29139165`
[2016-04-15T02:22Z] 2016-04-14 19:22:44 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:22:44,132 - WARNING - Could not retrieve variants from source file in region 1:16641688-16642089. Error was invalid region `1:16641689-16642089`
[2016-04-15T02:22Z] 2016-04-14 19:22:44 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:22:44,160 - WARNING - Could not retrieve variants from source file in region 1:21616721-21617122. Error was invalid region `1:21616722-21617122`
[2016-04-15T02:22Z] 2016-04-14 19:22:46 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:22:46,446 - WARNING - Could not retrieve variants from source file in region 1:22835466-22852905. Error was invalid region `1:22835467-22852905`
[2016-04-15T02:22Z] 2016-04-14 19:22:47 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:22:47,222 - WARNING - Could not retrieve variants from source file in region 1:29185513-29189787. Error was invalid region `1:29185514-29189787`
[2016-04-15T02:22Z] 2016-04-14 19:22:50 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:22:50,412 - WARNING - Could not retrieve variants from source file in region 1:22054216-22054617. Error was invalid region `1:22054217-22054617`
[2016-04-15T02:22Z] 2016-04-14 19:22:50 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:22:50,656 - WARNING - Could not retrieve variants from source file in region 1:27210510-27224157. Error was invalid region `1:27210511-27224157`
[2016-04-15T02:22Z] 2016-04-14 19:22:50 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:22:50,726 - WARNING - Could not retrieve variants from source file in region 1:26218835-26219236. Error was invalid region `1:26218836-26219236`
[2016-04-15T02:22Z] 2016-04-14 19:22:51 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:22:51,004 - WARNING - Could not retrieve variants from source file in region 1:29396736-29397137. Error was invalid region `1:29396737-29397137`
[2016-04-15T02:22Z] 2016-04-14 19:22:51 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:22:51,138 - WARNING - Could not retrieve variants from source file in region 1:29138764-29139165. Error was invalid region `1:29138765-29139165`
[2016-04-15T02:22Z] 2016-04-14 19:22:51 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:22:51,166 - WARNING - Could not retrieve variants from source file in region 1:28969103-28969504. Error was invalid region `1:28969104-28969504`
[2016-04-15T02:23Z] 2016-04-14 19:23:00 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:23:00,881 - WARNING - Could not retrieve variants from source file in region 1:20915490-20915891. Error was invalid region `1:20915491-20915891`
[2016-04-15T02:23Z] 2016-04-14 19:23:02 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:23:02,746 - WARNING - Could not retrieve variants from source file in region 1:21573511-21573912. Error was invalid region `1:21573512-21573912`
[2016-04-15T02:23Z] 2016-04-14 19:23:03 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:23:03,578 - WARNING - Could not retrieve variants from source file in region 1:22307129-22336467. Error was invalid region `1:22307130-22336467`
[2016-04-15T02:23Z] 2016-04-14 19:23:05 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:23:05,492 - WARNING - Could not retrieve variants from source file in region 1:27875613-27876672. Error was invalid region `1:27875614-27876672`
[2016-04-15T02:23Z] 2016-04-14 19:23:06 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:23:06,718 - WARNING - Could not retrieve variants from source file in region 1:21938373-21940745. Error was invalid region `1:21938374-21940745`
[2016-04-15T02:23Z] 2016-04-14 19:23:06 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:23:06,897 - WARNING - Could not retrieve variants from source file in region 1:20441843-20442244. Error was invalid region `1:20441844-20442244`
[2016-04-15T02:23Z] 2016-04-14 19:23:08 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:23:08,094 - WARNING - Could not retrieve variants from source file in region 1:18807686-18810534. Error was invalid region `1:18807687-18810534`
[2016-04-15T02:23Z] 2016-04-14 19:23:08 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:23:08,821 - WARNING - Could not retrieve variants from source file in region 1:26189125-26189526. Error was invalid region `1:26189126-26189526`
[2016-04-15T02:23Z] 2016-04-14 19:23:09 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:23:09,619 - WARNING - Could not retrieve variants from source file in region 1:27153232-27153639. Error was invalid region `1:27153233-27153639`
[2016-04-15T02:23Z] 2016-04-14 19:23:09 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:23:09,668 - WARNING - Could not retrieve variants from source file in region 1:22307129-22336467. Error was invalid region `1:22307130-22336467`
[2016-04-15T02:23Z] 2016-04-14 19:23:10 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:23:10,594 - WARNING - Could not retrieve variants from source file in region 1:28861425-28861826. Error was invalid region `1:28861426-28861826`
[2016-04-15T02:23Z] 2016-04-14 19:23:10 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:23:10,690 - WARNING - Could not retrieve variants from source file in region 1:29228620-29229021. Error was invalid region `1:29228621-29229021`
[2016-04-15T02:23Z] 2016-04-14 19:23:11 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:23:11,144 - WARNING - Could not retrieve variants from source file in region 1:29529488-29549860. Error was invalid region `1:29529489-29549860`
[2016-04-15T02:23Z] 2016-04-14 19:23:11 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:23:11,382 - WARNING - Could not retrieve variants from source file in region 1:27875613-27876672. Error was invalid region `1:27875614-27876672`
[2016-04-15T02:23Z] 2016-04-14 19:23:11 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:23:11,466 - WARNING - Could not retrieve variants from source file in region 1:16532592-16534836. Error was invalid region `1:16532593-16534836`
[2016-04-15T02:23Z] 2016-04-14 19:23:11 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:23:11,600 - WARNING - Could not retrieve variants from source file in region 1:29475437-29475838. Error was invalid region `1:29475438-29475838`
[2016-04-15T02:23Z] 2016-04-14 19:23:11 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:23:11,723 - WARNING - Could not retrieve variants from source file in region 1:20915490-20915891. Error was invalid region `1:20915491-20915891`
[2016-04-15T02:23Z] 2016-04-14 19:23:12 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:23:12,012 - WARNING - Could not retrieve variants from source file in region 1:20441843-20442244. Error was invalid region `1:20441844-20442244`
[2016-04-15T02:23Z] 2016-04-14 19:23:12 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:23:12,787 - WARNING - Could not retrieve variants from source file in region 1:18807686-18810534. Error was invalid region `1:18807687-18810534`
[2016-04-15T02:23Z] 2016-04-14 19:23:16 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:23:16,199 - WARNING - Could not retrieve variants from source file in region 1:22307129-22336467. Error was invalid region `1:22307130-22336467`
[2016-04-15T02:23Z] 2016-04-14 19:23:17 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:23:17,516 - WARNING - Could not retrieve variants from source file in region 1:29529488-29549860. Error was invalid region `1:29529489-29549860`
[2016-04-15T02:23Z] 2016-04-14 19:23:18 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:23:18,200 - WARNING - Could not retrieve variants from source file in region 1:29228620-29229021. Error was invalid region `1:29228621-29229021`
[2016-04-15T02:23Z] 2016-04-14 19:23:18 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:23:18,353 - WARNING - Could not retrieve variants from source file in region 1:20827005-20827406. Error was invalid region `1:20827006-20827406`
[2016-04-15T02:23Z] 2016-04-14 19:23:19 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:23:19,463 - WARNING - Could not retrieve variants from source file in region 1:27875613-27876672. Error was invalid region `1:27875614-27876672`
[2016-04-15T02:23Z] 2016-04-14 19:23:19 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:23:19,949 - WARNING - Could not retrieve variants from source file in region 1:16532592-16534836. Error was invalid region `1:16532593-16534836`
[2016-04-15T02:23Z] 2016-04-14 19:23:20 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:23:20,039 - WARNING - Could not retrieve variants from source file in region 1:29475437-29475838. Error was invalid region `1:29475438-29475838`
[2016-04-15T02:23Z] 2016-04-14 19:23:20 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:23:20,477 - WARNING - Could not retrieve variants from source file in region 1:20441843-20442244. Error was invalid region `1:20441844-20442244`
[2016-04-15T02:23Z] 2016-04-14 19:23:20 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:23:20,557 - WARNING - Could not retrieve variants from source file in region 1:21938373-21940745. Error was invalid region `1:21938374-21940745`
[2016-04-15T02:23Z] 2016-04-14 19:23:20 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:23:20,612 - WARNING - Could not retrieve variants from source file in region 1:26189125-26189526. Error was invalid region `1:26189126-26189526`
[2016-04-15T02:23Z] 2016-04-14 19:23:22 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:23:22,131 - WARNING - Could not retrieve variants from source file in region 1:29529488-29549860. Error was invalid region `1:29529489-29549860`
[2016-04-15T02:23Z] 2016-04-14 19:23:22 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:23:22,319 - WARNING - Could not retrieve variants from source file in region 1:28861425-28861826. Error was invalid region `1:28861426-28861826`
[2016-04-15T02:23Z] 2016-04-14 19:23:23 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:23:23,586 - WARNING - Could not retrieve variants from source file in region 1:29228620-29229021. Error was invalid region `1:29228621-29229021`
[2016-04-15T02:23Z] 2016-04-14 19:23:26 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:23:26,507 - WARNING - Could not retrieve variants from source file in region 1:16532592-16534836. Error was invalid region `1:16532593-16534836`
[2016-04-15T02:23Z] 2016-04-14 19:23:27 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:23:27,386 - WARNING - Could not retrieve variants from source file in region 1:29475437-29475838. Error was invalid region `1:29475438-29475838`
[2016-04-15T02:23Z] 2016-04-14 19:23:29 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:23:29,875 - WARNING - Could not retrieve variants from source file in region 1:21167193-21167594. Error was invalid region `1:21167194-21167594`
[2016-04-15T02:23Z] 2016-04-14 19:23:30 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:23:30,569 - WARNING - Could not retrieve variants from source file in region 1:20671750-20680908. Error was invalid region `1:20671751-20680908`
[2016-04-15T02:23Z] 2016-04-14 19:23:31 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:23:31,803 - WARNING - Could not retrieve variants from source file in region 1:18152371-18152772. Error was invalid region `1:18152372-18152772`
[2016-04-15T02:23Z] 2016-04-14 19:23:33 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:23:33,684 - WARNING - Could not retrieve variants from source file in region 1:21167193-21167594. Error was invalid region `1:21167194-21167594`
[2016-04-15T02:23Z] 2016-04-14 19:23:35 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:23:35,291 - WARNING - Could not retrieve variants from source file in region 1:21167193-21167594. Error was invalid region `1:21167194-21167594`
[2016-04-15T02:23Z] 2016-04-14 19:23:35 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:23:35,492 - WARNING - Could not retrieve variants from source file in region 1:21889424-21889825. Error was invalid region `1:21889425-21889825`
[2016-04-15T02:23Z] 2016-04-14 19:23:36 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:23:36,275 - WARNING - Could not retrieve variants from source file in region 1:20671750-20680908. Error was invalid region `1:20671751-20680908`
[2016-04-15T02:23Z] 2016-04-14 19:23:37 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:23:37,859 - WARNING - Could not retrieve variants from source file in region 1:26856251-26887782. Error was invalid region `1:26856252-26887782`
[2016-04-15T02:23Z] 2016-04-14 19:23:38 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:23:38,783 - WARNING - Could not retrieve variants from source file in region 1:20396522-20411522. Error was invalid region `1:20396523-20411522`
[2016-04-15T02:23Z] 2016-04-14 19:23:38 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:23:38,835 - WARNING - Could not retrieve variants from source file in region 1:28800169-28800570. Error was invalid region `1:28800170-28800570`
[2016-04-15T02:23Z] 2016-04-14 19:23:40 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:23:40,188 - WARNING - Could not retrieve variants from source file in region 1:22140995-22217298. Error was invalid region `1:22140996-22217298`
[2016-04-15T02:23Z] 2016-04-14 19:23:40 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:23:40,220 - WARNING - Could not retrieve variants from source file in region 1:21889424-21889825. Error was invalid region `1:21889425-21889825`
[2016-04-15T02:23Z] 2016-04-14 19:23:44 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:23:44,183 - WARNING - Could not retrieve variants from source file in region 1:26786416-26786817. Error was invalid region `1:26786417-26786817`
[2016-04-15T02:23Z] 2016-04-14 19:23:44 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:23:44,243 - WARNING - Could not retrieve variants from source file in region 1:16451556-16475316. Error was invalid region `1:16451557-16475316`
[2016-04-15T02:23Z] 2016-04-14 19:23:44 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:23:44,731 - WARNING - Could not retrieve variants from source file in region 1:28562873-28564469. Error was invalid region `1:28562874-28564469`
[2016-04-15T02:23Z] 2016-04-14 19:23:44 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:23:44,814 - WARNING - Could not retrieve variants from source file in region 1:21889424-21889825. Error was invalid region `1:21889425-21889825`
[2016-04-15T02:23Z] 2016-04-14 19:23:46 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:23:46,050 - WARNING - Could not retrieve variants from source file in region 1:28800169-28800570. Error was invalid region `1:28800170-28800570`
[2016-04-15T02:23Z] 2016-04-14 19:23:46 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:23:46,192 - WARNING - Could not retrieve variants from source file in region 1:26856251-26887782. Error was invalid region `1:26856252-26887782`
[2016-04-15T02:23Z] 2016-04-14 19:23:49 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:23:49,622 - WARNING - Could not retrieve variants from source file in region 1:16042555-16056554. Error was invalid region `1:16042556-16056554`
[2016-04-15T02:23Z] 2016-04-14 19:23:53 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:23:53,224 - WARNING - Could not retrieve variants from source file in region 1:21795177-21795578. Error was invalid region `1:21795178-21795578`
[2016-04-15T02:23Z] 2016-04-14 19:23:56 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:23:56,324 - WARNING - Could not retrieve variants from source file in region 1:21795177-21795578. Error was invalid region `1:21795178-21795578`
[2016-04-15T02:23Z] 2016-04-14 19:23:56 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:23:56,418 - WARNING - Could not retrieve variants from source file in region 1:16451556-16475316. Error was invalid region `1:16451557-16475316`
[2016-04-15T02:23Z] 2016-04-14 19:23:58 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:23:58,093 - WARNING - Could not retrieve variants from source file in region 1:18023154-18023880. Error was invalid region `1:18023155-18023880`
[2016-04-15T02:23Z] 2016-04-14 19:23:59 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:23:59,183 - WARNING - Could not retrieve variants from source file in region 1:28562873-28564469. Error was invalid region `1:28562874-28564469`
[2016-04-15T02:23Z] 2016-04-14 19:23:59 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:23:59,397 - WARNING - Could not retrieve variants from source file in region 1:26349034-26372994. Error was invalid region `1:26349035-26372994`
[2016-04-15T02:24Z] 2016-04-14 19:24:04 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:24:04,733 - WARNING - Could not retrieve variants from source file in region 1:24134510-24134911. Error was invalid region `1:24134511-24134911`
[2016-04-15T02:24Z] 2016-04-14 19:24:04 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:24:04,842 - WARNING - Could not retrieve variants from source file in region 1:26510099-26528141. Error was invalid region `1:26510100-26528141`
[2016-04-15T02:24Z] 2016-04-14 19:24:05 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:24:05,149 - WARNING - Could not retrieve variants from source file in region 1:18023154-18023880. Error was invalid region `1:18023155-18023880`
[2016-04-15T02:24Z] 2016-04-14 19:24:05 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:24:05,471 - WARNING - Could not retrieve variants from source file in region 1:25944243-25944644. Error was invalid region `1:25944244-25944644`
[2016-04-15T02:24Z] 2016-04-14 19:24:06 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:24:06,077 - WARNING - Could not retrieve variants from source file in region 1:20304751-20305152. Error was invalid region `1:20304752-20305152`
[2016-04-15T02:24Z] 2016-04-14 19:24:06 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:24:06,512 - WARNING - Could not retrieve variants from source file in region 1:28240872-28241273. Error was invalid region `1:28240873-28241273`
[2016-04-15T02:24Z] 2016-04-14 19:24:07 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:24:07,481 - WARNING - Could not retrieve variants from source file in region 1:27480546-27480947. Error was invalid region `1:27480547-27480947`
[2016-04-15T02:24Z] 2016-04-14 19:24:10 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:24:10,413 - WARNING - Could not retrieve variants from source file in region 1:26349034-26372994. Error was invalid region `1:26349035-26372994`
[2016-04-15T02:24Z] 2016-04-14 19:24:11 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:24:11,392 - WARNING - Could not retrieve variants from source file in region 1:24134510-24134911. Error was invalid region `1:24134511-24134911`
[2016-04-15T02:24Z] 2016-04-14 19:24:12 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:24:12,176 - WARNING - Could not retrieve variants from source file in region 1:18023154-18023880. Error was invalid region `1:18023155-18023880`
[2016-04-15T02:24Z] 2016-04-14 19:24:12 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:24:12,468 - WARNING - Could not retrieve variants from source file in region 1:28240872-28241273. Error was invalid region `1:28240873-28241273`
[2016-04-15T02:24Z] 2016-04-14 19:24:12 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:24:12,474 - WARNING - Could not retrieve variants from source file in region 1:16342026-16389216. Error was invalid region `1:16342027-16389216`
[2016-04-15T02:24Z] 2016-04-14 19:24:13 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:24:13,590 - WARNING - Could not retrieve variants from source file in region 1:15986336-15986737. Error was invalid region `1:15986337-15986737`
[2016-04-15T02:24Z] 2016-04-14 19:24:16 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:24:16,411 - WARNING - Could not retrieve variants from source file in region 1:24134510-24134911. Error was invalid region `1:24134511-24134911`
[2016-04-15T02:24Z] 2016-04-14 19:24:18 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:24:18,579 - WARNING - Could not retrieve variants from source file in region 1:20304751-20305152. Error was invalid region `1:20304752-20305152`
[2016-04-15T02:24Z] 2016-04-14 19:24:18 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:24:18,771 - WARNING - Could not retrieve variants from source file in region 1:27480546-27480947. Error was invalid region `1:27480547-27480947`
[2016-04-15T02:24Z] 2016-04-14 19:24:19 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:24:19,282 - WARNING - Could not retrieve variants from source file in region 1:15986336-15986737. Error was invalid region `1:15986337-15986737`
[2016-04-15T02:24Z] 2016-04-14 19:24:19 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:24:19,733 - WARNING - Could not retrieve variants from source file in region 1:28281995-28283009. Error was invalid region `1:28281996-28283009`
[2016-04-15T02:24Z] 2016-04-14 19:24:19 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:24:19,737 - WARNING - Could not retrieve variants from source file in region 1:15959766-15960167. Error was invalid region `1:15959767-15960167`
[2016-04-15T02:24Z] 2016-04-14 19:24:21 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:24:21,151 - WARNING - Could not retrieve variants from source file in region 1:15708329-15724033. Error was invalid region `1:15708330-15724033`
[2016-04-15T02:24Z] 2016-04-14 19:24:25 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:24:25,731 - WARNING - Could not retrieve variants from source file in region 1:17600948-17609638. Error was invalid region `1:17600949-17609638`
[2016-04-15T02:24Z] 2016-04-14 19:24:26 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:24:26,011 - WARNING - Could not retrieve variants from source file in region 1:15986336-15986737. Error was invalid region `1:15986337-15986737`
[2016-04-15T02:24Z] 2016-04-14 19:24:26 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:24:26,301 - WARNING - Could not retrieve variants from source file in region 1:15959766-15960167. Error was invalid region `1:15959767-15960167`
[2016-04-15T02:24Z] 2016-04-14 19:24:26 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:24:26,625 - WARNING - Could not retrieve variants from source file in region 1:17714804-17739776. Error was invalid region `1:17714805-17739776`
[2016-04-15T02:24Z] 2016-04-14 19:24:26 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:24:26,725 - WARNING - Could not retrieve variants from source file in region 1:25569870-25570740. Error was invalid region `1:25569871-25570740`
[2016-04-15T02:24Z] 2016-04-14 19:24:27 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:24:27,111 - WARNING - Could not retrieve variants from source file in region 1:28209094-28209556. Error was invalid region `1:28209095-28209556`
[2016-04-15T02:24Z] 2016-04-14 19:24:33 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:24:33,254 - WARNING - Could not retrieve variants from source file in region 1:24083283-24083684. Error was invalid region `1:24083284-24083684`
[2016-04-15T02:24Z] 2016-04-14 19:24:33 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:24:33,271 - WARNING - Could not retrieve variants from source file in region 1:15959766-15960167. Error was invalid region `1:15959767-15960167`
[2016-04-15T02:24Z] 2016-04-14 19:24:35 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:24:35,802 - WARNING - Could not retrieve variants from source file in region 1:25569870-25570740. Error was invalid region `1:25569871-25570740`
[2016-04-15T02:24Z] 2016-04-14 19:24:36 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:24:36,234 - WARNING - Could not retrieve variants from source file in region 1:28209094-28209556. Error was invalid region `1:28209095-28209556`
[2016-04-15T02:24Z] 2016-04-14 19:24:36 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:24:36,993 - WARNING - Could not retrieve variants from source file in region 1:27426830-27427231. Error was invalid region `1:27426831-27427231`
[2016-04-15T02:24Z] 2016-04-14 19:24:37 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:24:37,134 - WARNING - Could not retrieve variants from source file in region 1:28209094-28209556. Error was invalid region `1:28209095-28209556`
[2016-04-15T02:24Z] 2016-04-14 19:24:37 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:24:37,266 - WARNING - Could not retrieve variants from source file in region 1:17600948-17609638. Error was invalid region `1:17600949-17609638`
[2016-04-15T02:24Z] 2016-04-14 19:24:43 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:24:43,012 - WARNING - Could not retrieve variants from source file in region 1:25569870-25570740. Error was invalid region `1:25569871-25570740`
[2016-04-15T02:24Z] 2016-04-14 19:24:44 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:24:44,079 - WARNING - Could not retrieve variants from source file in region 1:15892204-15911539. Error was invalid region `1:15892205-15911539`
[2016-04-15T02:24Z] 2016-04-14 19:24:44 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:24:44,517 - WARNING - Could not retrieve variants from source file in region 1:20232840-20233276. Error was invalid region `1:20232841-20233276`
[2016-04-15T02:24Z] 2016-04-14 19:24:44 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:24:44,754 - WARNING - Could not retrieve variants from source file in region 1:25889421-25890437. Error was invalid region `1:25889422-25890437`
[2016-04-15T02:24Z] 2016-04-14 19:24:45 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:24:45,391 - WARNING - Could not retrieve variants from source file in region 1:27426830-27427231. Error was invalid region `1:27426831-27427231`
[2016-04-15T02:24Z] 2016-04-14 19:24:45 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:24:45,636 - WARNING - Could not retrieve variants from source file in region 1:24083283-24083684. Error was invalid region `1:24083284-24083684`
[2016-04-15T02:24Z] 2016-04-14 19:24:45 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:24:45,701 - WARNING - Could not retrieve variants from source file in region 1:16255796-16272996. Error was invalid region `1:16255797-16272996`
[2016-04-15T02:24Z] 2016-04-14 19:24:51 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:24:51,278 - WARNING - Could not retrieve variants from source file in region 1:15545866-15546267. Error was invalid region `1:15545867-15546267`
[2016-04-15T02:24Z] 2016-04-14 19:24:51 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:24:51,376 - WARNING - Could not retrieve variants from source file in region 1:25889421-25890437. Error was invalid region `1:25889422-25890437`
[2016-04-15T02:24Z] 2016-04-14 19:24:52 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:24:52,152 - WARNING - Could not retrieve variants from source file in region 1:27426830-27427231. Error was invalid region `1:27426831-27427231`
[2016-04-15T02:24Z] 2016-04-14 19:24:55 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:24:55,877 - WARNING - Could not retrieve variants from source file in region 1:19810532-19811000. Error was invalid region `1:19810533-19811000`
[2016-04-15T02:24Z] 2016-04-14 19:24:57 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:24:57,790 - WARNING - Could not retrieve variants from source file in region 1:27320145-27320546. Error was invalid region `1:27320146-27320546`
[2016-04-15T02:25Z] 2016-04-14 19:25:00 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:25:00,846 - WARNING - Could not retrieve variants from source file in region 1:23885287-23885688. Error was invalid region `1:23885288-23885688`
[2016-04-15T02:25Z] 2016-04-14 19:25:01 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:25:01,270 - WARNING - Could not retrieve variants from source file in region 1:17531552-17557323. Error was invalid region `1:17531553-17557323`
[2016-04-15T02:25Z] 2016-04-14 19:25:02 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:25:02,500 - WARNING - Could not retrieve variants from source file in region 1:27320145-27320546. Error was invalid region `1:27320146-27320546`
[2016-04-15T02:25Z] 2016-04-14 19:25:02 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:25:02,748 - WARNING - Could not retrieve variants from source file in region 1:23760817-23767859. Error was invalid region `1:23760818-23767859`
[2016-04-15T02:25Z] 2016-04-14 19:25:02 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:25:02,910 - WARNING - Could not retrieve variants from source file in region 1:25290799-25291200. Error was invalid region `1:25290800-25291200`
[2016-04-15T02:25Z] 2016-04-14 19:25:05 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:25:05,713 - WARNING - Could not retrieve variants from source file in region 1:23885287-23885688. Error was invalid region `1:23885288-23885688`
[2016-04-15T02:25Z] 2016-04-14 19:25:06 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:25:06,373 - WARNING - Could not retrieve variants from source file in region 1:17657323-17674727. Error was invalid region `1:17657324-17674727`
[2016-04-15T02:25Z] 2016-04-14 19:25:07 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:25:07,511 - WARNING - Could not retrieve variants from source file in region 1:27320145-27320546. Error was invalid region `1:27320146-27320546`
[2016-04-15T02:25Z] 2016-04-14 19:25:08 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:25:08,293 - WARNING - Could not retrieve variants from source file in region 1:20141317-20141718. Error was invalid region `1:20141318-20141718`
[2016-04-15T02:25Z] 2016-04-14 19:25:08 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:25:08,436 - WARNING - Could not retrieve variants from source file in region 1:25290799-25291200. Error was invalid region `1:25290800-25291200`
[2016-04-15T02:25Z] 2016-04-14 19:25:08 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:25:08,730 - WARNING - Could not retrieve variants from source file in region 1:19775281-19776001. Error was invalid region `1:19775282-19776001`
[2016-04-15T02:25Z] 2016-04-14 19:25:08 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:25:08,814 - WARNING - Could not retrieve variants from source file in region 1:23280213-23299597. Error was invalid region `1:23280214-23299597`
[2016-04-15T02:25Z] 2016-04-14 19:25:11 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:25:11,007 - WARNING - Could not retrieve variants from source file in region 1:23885287-23885688. Error was invalid region `1:23885288-23885688`
[2016-04-15T02:25Z] 2016-04-14 19:25:12 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:25:12,420 - WARNING - Could not retrieve variants from source file in region 1:24998539-24998940. Error was invalid region `1:24998540-24998940`
[2016-04-15T02:25Z] 2016-04-14 19:25:12 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:25:12,635 - WARNING - Could not retrieve variants from source file in region 1:27277812-27278213. Error was invalid region `1:27277813-27278213`
[2016-04-15T02:25Z] 2016-04-14 19:25:12 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:25:12,683 - WARNING - Could not retrieve variants from source file in region 1:16199952-16200353. Error was invalid region `1:16199953-16200353`
[2016-04-15T02:25Z] 2016-04-14 19:25:12 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:25:12,821 - WARNING - Could not retrieve variants from source file in region 1:16096723-16097124. Error was invalid region `1:16096724-16097124`
[2016-04-15T02:25Z] 2016-04-14 19:25:14 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:25:14,094 - WARNING - Could not retrieve variants from source file in region 1:20141317-20141718. Error was invalid region `1:20141318-20141718`
[2016-04-15T02:25Z] 2016-04-14 19:25:14 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:25:14,108 - WARNING - Could not retrieve variants from source file in region 1:19775281-19776001. Error was invalid region `1:19775282-19776001`
[2016-04-15T02:25Z] 2016-04-14 19:25:18 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:25:18,679 - WARNING - Could not retrieve variants from source file in region 1:16096723-16097124. Error was invalid region `1:16096724-16097124`
[2016-04-15T02:25Z] 2016-04-14 19:25:19 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:25:19,491 - WARNING - Could not retrieve variants from source file in region 1:19775281-19776001. Error was invalid region `1:19775282-19776001`
[2016-04-15T02:25Z] 2016-04-14 19:25:23 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:25:23,225 - WARNING - Could not retrieve variants from source file in region 1:16199952-16200353. Error was invalid region `1:16199953-16200353`
[2016-04-15T02:25Z] 2016-04-14 19:25:23 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:25:23,800 - WARNING - Could not retrieve variants from source file in region 1:16096723-16097124. Error was invalid region `1:16096724-16097124`
[2016-04-15T02:25Z] 2016-04-14 19:25:25 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:25:25,125 - WARNING - Could not retrieve variants from source file in region 1:23847253-23847654. Error was invalid region `1:23847254-23847654`
[2016-04-15T02:25Z] 2016-04-14 19:25:25 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:25:25,700 - WARNING - Could not retrieve variants from source file in region 1:17380286-17419214. Error was invalid region `1:17380287-17419214`
[2016-04-15T02:25Z] 2016-04-14 19:25:26 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:25:26,538 - WARNING - Could not retrieve variants from source file in region 1:25256233-25256634. Error was invalid region `1:25256234-25256634`
[2016-04-15T02:25Z] 2016-04-14 19:25:28 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:25:28,080 - WARNING - Could not retrieve variants from source file in region 1:23688722-23710995. Error was invalid region `1:23688723-23710995`
[2016-04-15T02:25Z] 2016-04-14 19:25:28 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:25:28,684 - WARNING - Could not retrieve variants from source file in region 1:20097611-20098131. Error was invalid region `1:20097612-20098131`
[2016-04-15T02:25Z] 2016-04-14 19:25:30 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:25:30,410 - WARNING - Could not retrieve variants from source file in region 1:23417942-23420045. Error was invalid region `1:23417943-23420045`
[2016-04-15T02:25Z] 2016-04-14 19:25:30 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:25:30,947 - WARNING - Could not retrieve variants from source file in region 1:17380286-17419214. Error was invalid region `1:17380287-17419214`
[2016-04-15T02:25Z] 2016-04-14 19:25:30 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:25:30,991 - WARNING - Could not retrieve variants from source file in region 1:23847253-23847654. Error was invalid region `1:23847254-23847654`
[2016-04-15T02:25Z] 2016-04-14 19:25:31 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:25:31,891 - WARNING - Could not retrieve variants from source file in region 1:25256233-25256634. Error was invalid region `1:25256234-25256634`
[2016-04-15T02:25Z] 2016-04-14 19:25:33 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:25:33,046 - WARNING - Could not retrieve variants from source file in region 1:23688722-23710995. Error was invalid region `1:23688723-23710995`
[2016-04-15T02:25Z] 2016-04-14 19:25:33 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:25:33,449 - WARNING - Could not retrieve variants from source file in region 1:23208714-23219683. Error was invalid region `1:23208715-23219683`
[2016-04-15T02:25Z] 2016-04-14 19:25:33 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:25:33,555 - WARNING - Could not retrieve variants from source file in region 1:20097611-20098131. Error was invalid region `1:20097612-20098131`
[2016-04-15T02:25Z] 2016-04-14 19:25:35 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:25:35,207 - WARNING - Could not retrieve variants from source file in region 1:25633994-25634395. Error was invalid region `1:25633995-25634395`
[2016-04-15T02:25Z] 2016-04-14 19:25:35 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:25:35,513 - WARNING - Could not retrieve variants from source file in region 1:19410918-19448033. Error was invalid region `1:19410919-19448033`
[2016-04-15T02:25Z] 2016-04-14 19:25:35 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:25:35,825 - WARNING - Could not retrieve variants from source file in region 1:23417942-23420045. Error was invalid region `1:23417943-23420045`
[2016-04-15T02:25Z] 2016-04-14 19:25:36 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:25:36,559 - WARNING - Could not retrieve variants from source file in region 1:24859406-24861894. Error was invalid region `1:24859407-24861894`
[2016-04-15T02:25Z] 2016-04-14 19:25:37 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:25:37,103 - WARNING - Could not retrieve variants from source file in region 1:24785182-24792807. Error was invalid region `1:24785183-24792807`
[2016-04-15T02:25Z] 2016-04-14 19:25:40 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:25:40,190 - WARNING - Could not retrieve variants from source file in region 1:19410918-19448033. Error was invalid region `1:19410919-19448033`
[2016-04-15T02:25Z] 2016-04-14 19:25:40 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:25:40,274 - WARNING - Could not retrieve variants from source file in region 1:23417942-23420045. Error was invalid region `1:23417943-23420045`
[2016-04-15T02:25Z] 2016-04-14 19:25:41 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:25:41,744 - WARNING - Could not retrieve variants from source file in region 1:24859406-24861894. Error was invalid region `1:24859407-24861894`
[2016-04-15T02:25Z] 2016-04-14 19:25:45 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:25:45,339 - WARNING - Could not retrieve variants from source file in region 1:19410918-19448033. Error was invalid region `1:19410919-19448033`
[2016-04-15T02:25Z] 2016-04-14 19:25:46 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:25:46,813 - WARNING - Could not retrieve variants from source file in region 1:23346014-23346415. Error was invalid region `1:23346015-23346415`
[2016-04-15T02:25Z] 2016-04-14 19:25:50 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:25:50,785 - WARNING - Could not retrieve variants from source file in region 1:19499349-19499750. Error was invalid region `1:19499350-19499750`
[2016-04-15T02:25Z] 2016-04-14 19:25:51 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:25:51,542 - WARNING - Could not retrieve variants from source file in region 1:22965227-22970832. Error was invalid region `1:22965228-22970832`
[2016-04-15T02:25Z] 2016-04-14 19:25:53 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:25:53,230 - WARNING - Could not retrieve variants from source file in region 1:24717868-24718269. Error was invalid region `1:24717869-24718269`
[2016-04-15T02:25Z] 2016-04-14 19:25:54 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:25:54,294 - WARNING - Could not retrieve variants from source file in region 1:24717868-24718269. Error was invalid region `1:24717869-24718269`
[2016-04-15T02:25Z] 2016-04-14 19:25:56 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:25:56,527 - WARNING - Could not retrieve variants from source file in region 1:24717868-24718269. Error was invalid region `1:24717869-24718269`
[2016-04-15T02:25Z] 2016-04-14 19:25:56 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:25:56,878 - WARNING - Could not retrieve variants from source file in region 1:22965227-22970832. Error was invalid region `1:22965228-22970832`
[2016-04-15T02:26Z] ['bcbio-variation-recall', 'square', '-Xms750m', '-Xmx7280m', '-XX:+UseSerialGC', '-c', 16, '-r', u'1:31187094-46714270', '--caller', 'platypus', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/1/Batch1-1_31187093_46714270.vcf.gz', '/mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/1/Batch1-1_31187093_46714270.vcf-inputs.txt'] in region: 1:31187094-46714270
[2016-04-15T02:26Z] 2016-04-14 19:26:16 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:26:16,899 - WARNING - Could not retrieve variants from source file in region 1:43395424-43409156. Error was invalid region `1:43395425-43409156`
[2016-04-15T02:26Z] 2016-04-14 19:26:18 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:26:18,015 - WARNING - Could not retrieve variants from source file in region 1:44137046-44137447. Error was invalid region `1:44137047-44137447`
[2016-04-15T02:26Z] 2016-04-14 19:26:18 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:26:18,906 - WARNING - Could not retrieve variants from source file in region 1:46654947-46660485. Error was invalid region `1:46654948-46660485`
[2016-04-15T02:26Z] 2016-04-14 19:26:19 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:26:19,888 - WARNING - Could not retrieve variants from source file in region 1:36316360-36316761. Error was invalid region `1:36316361-36316761`
[2016-04-15T02:26Z] 2016-04-14 19:26:19 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:26:19,898 - WARNING - Could not retrieve variants from source file in region 1:42628380-42630554. Error was invalid region `1:42628381-42630554`
[2016-04-15T02:26Z] 2016-04-14 19:26:19 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:26:19,931 - WARNING - Could not retrieve variants from source file in region 1:40036636-40037037. Error was invalid region `1:40036637-40037037`
[2016-04-15T02:26Z] 2016-04-14 19:26:20 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:26:20,401 - WARNING - Could not retrieve variants from source file in region 1:40348920-40363244. Error was invalid region `1:40348921-40363244`
[2016-04-15T02:26Z] 2016-04-14 19:26:20 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:26:20,897 - WARNING - Could not retrieve variants from source file in region 1:42745764-42746165. Error was invalid region `1:42745765-42746165`
[2016-04-15T02:26Z] 2016-04-14 19:26:20 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:26:20,975 - WARNING - Could not retrieve variants from source file in region 1:33329831-33330233. Error was invalid region `1:33329832-33330233`
[2016-04-15T02:26Z] 2016-04-14 19:26:22 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:26:22,768 - WARNING - Could not retrieve variants from source file in region 1:44137046-44137447. Error was invalid region `1:44137047-44137447`
[2016-04-15T02:26Z] 2016-04-14 19:26:24 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:26:24,339 - WARNING - Could not retrieve variants from source file in region 1:46654947-46660485. Error was invalid region `1:46654948-46660485`
[2016-04-15T02:26Z] 2016-04-14 19:26:27 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:26:27,635 - WARNING - Could not retrieve variants from source file in region 1:36316360-36316761. Error was invalid region `1:36316361-36316761`
[2016-04-15T02:26Z] 2016-04-14 19:26:28 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:26:28,195 - WARNING - Could not retrieve variants from source file in region 1:40348920-40363244. Error was invalid region `1:40348921-40363244`
[2016-04-15T02:26Z] 2016-04-14 19:26:28 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:26:28,237 - WARNING - Could not retrieve variants from source file in region 1:41284876-41300880. Error was invalid region `1:41284877-41300880`
[2016-04-15T02:26Z] 2016-04-14 19:26:28 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:26:28,409 - WARNING - Could not retrieve variants from source file in region 1:44442719-44443649. Error was invalid region `1:44442720-44443649`
[2016-04-15T02:26Z] 2016-04-14 19:26:28 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:26:28,660 - WARNING - Could not retrieve variants from source file in region 1:44819164-44820509. Error was invalid region `1:44819165-44820509`
[2016-04-15T02:26Z] 2016-04-14 19:26:28 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:26:28,714 - WARNING - Could not retrieve variants from source file in region 1:42745764-42746165. Error was invalid region `1:42745765-42746165`
[2016-04-15T02:26Z] 2016-04-14 19:26:28 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:26:28,886 - WARNING - Could not retrieve variants from source file in region 1:44137046-44137447. Error was invalid region `1:44137047-44137447`
[2016-04-15T02:26Z] 2016-04-14 19:26:29 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:26:29,097 - WARNING - Could not retrieve variants from source file in region 1:33329831-33330233. Error was invalid region `1:33329832-33330233`
[2016-04-15T02:26Z] 2016-04-14 19:26:29 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:26:29,179 - WARNING - Could not retrieve variants from source file in region 1:37944295-37959660. Error was invalid region `1:37944296-37959660`
[2016-04-15T02:26Z] 2016-04-14 19:26:29 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:26:29,354 - WARNING - Could not retrieve variants from source file in region 1:46654947-46660485. Error was invalid region `1:46654948-46660485`
[2016-04-15T02:26Z] 2016-04-14 19:26:35 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:26:35,015 - WARNING - Could not retrieve variants from source file in region 1:36316360-36316761. Error was invalid region `1:36316361-36316761`
[2016-04-15T02:26Z] 2016-04-14 19:26:35 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:26:35,683 - WARNING - Could not retrieve variants from source file in region 1:40036636-40037037. Error was invalid region `1:40036637-40037037`
[2016-04-15T02:26Z] 2016-04-14 19:26:36 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:26:36,625 - WARNING - Could not retrieve variants from source file in region 1:40348920-40363244. Error was invalid region `1:40348921-40363244`
[2016-04-15T02:26Z] 2016-04-14 19:26:37 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:26:37,729 - WARNING - Could not retrieve variants from source file in region 1:35250950-35260959. Error was invalid region `1:35250951-35260959`
[2016-04-15T02:26Z] 2016-04-14 19:26:37 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:26:37,984 - WARNING - Could not retrieve variants from source file in region 1:41284876-41300880. Error was invalid region `1:41284877-41300880`
[2016-04-15T02:26Z] 2016-04-14 19:26:38 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:26:38,449 - WARNING - Could not retrieve variants from source file in region 1:42745764-42746165. Error was invalid region `1:42745765-42746165`
[2016-04-15T02:26Z] 2016-04-14 19:26:48 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:26:48,482 - WARNING - Could not retrieve variants from source file in region 1:44071010-44087021. Error was invalid region `1:44071011-44087021`
[2016-04-15T02:26Z] 2016-04-14 19:26:50 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:26:50,668 - WARNING - Could not retrieve variants from source file in region 1:42094287-42094688. Error was invalid region `1:42094288-42094688`
[2016-04-15T02:26Z] 2016-04-14 19:26:51 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:26:51,576 - WARNING - Could not retrieve variants from source file in region 1:36200179-36200580. Error was invalid region `1:36200180-36200580`
[2016-04-15T02:26Z] 2016-04-14 19:26:51 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:26:51,583 - WARNING - Could not retrieve variants from source file in region 1:46598062-46598463. Error was invalid region `1:46598063-46598463`
[2016-04-15T02:26Z] 2016-04-14 19:26:53 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:26:53,381 - WARNING - Could not retrieve variants from source file in region 1:44401173-44415605. Error was invalid region `1:44401174-44415605`
[2016-04-15T02:26Z] 2016-04-14 19:26:55 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:26:55,640 - WARNING - Could not retrieve variants from source file in region 1:40705515-40728720. Error was invalid region `1:40705516-40728720`
[2016-04-15T02:26Z] 2016-04-14 19:26:55 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:26:55,672 - WARNING - Could not retrieve variants from source file in region 1:41204358-41204759. Error was invalid region `1:41204359-41204759`
[2016-04-15T02:26Z] 2016-04-14 19:26:56 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:26:56,158 - WARNING - Could not retrieve variants from source file in region 1:39987873-39988274. Error was invalid region `1:39987874-39988274`
[2016-04-15T02:26Z] 2016-04-14 19:26:56 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:26:56,250 - WARNING - Could not retrieve variants from source file in region 1:42094287-42094688. Error was invalid region `1:42094288-42094688`
[2016-04-15T02:26Z] 2016-04-14 19:26:56 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:26:56,356 - WARNING - Could not retrieve variants from source file in region 1:44594836-44595616. Error was invalid region `1:44594837-44595616`
[2016-04-15T02:26Z] 2016-04-14 19:26:56 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:26:56,463 - WARNING - Could not retrieve variants from source file in region 1:42693386-42693787. Error was invalid region `1:42693387-42693787`
[2016-04-15T02:26Z] 2016-04-14 19:26:56 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:26:56,472 - WARNING - Could not retrieve variants from source file in region 1:36200179-36200580. Error was invalid region `1:36200180-36200580`
[2016-04-15T02:26Z] 2016-04-14 19:26:56 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:26:56,888 - WARNING - Could not retrieve variants from source file in region 1:46598062-46598463. Error was invalid region `1:46598063-46598463`
[2016-04-15T02:26Z] 2016-04-14 19:26:58 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:26:58,519 - WARNING - Could not retrieve variants from source file in region 1:44401173-44415605. Error was invalid region `1:44401174-44415605`
[2016-04-15T02:26Z] 2016-04-14 19:26:59 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:26:59,357 - WARNING - Could not retrieve variants from source file in region 1:35223134-35223535. Error was invalid region `1:35223135-35223535`
[2016-04-15T02:27Z] 2016-04-14 19:27:00 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:27:00,825 - WARNING - Could not retrieve variants from source file in region 1:33291978-33292379. Error was invalid region `1:33291979-33292379`
[2016-04-15T02:27Z] 2016-04-14 19:27:00 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:27:00,909 - WARNING - Could not retrieve variants from source file in region 1:45097428-45120556. Error was invalid region `1:45097429-45120556`
[2016-04-15T02:27Z] 2016-04-14 19:27:02 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:27:02,618 - WARNING - Could not retrieve variants from source file in region 1:41204358-41204759. Error was invalid region `1:41204359-41204759`
[2016-04-15T02:27Z] 2016-04-14 19:27:02 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:27:02,873 - WARNING - Could not retrieve variants from source file in region 1:40705515-40728720. Error was invalid region `1:40705516-40728720`
[2016-04-15T02:27Z] 2016-04-14 19:27:03 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:27:03,830 - WARNING - Could not retrieve variants from source file in region 1:46598062-46598463. Error was invalid region `1:46598063-46598463`
[2016-04-15T02:27Z] 2016-04-14 19:27:03 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:27:03,889 - WARNING - Could not retrieve variants from source file in region 1:42693386-42693787. Error was invalid region `1:42693387-42693787`
[2016-04-15T02:27Z] 2016-04-14 19:27:04 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:27:04,571 - WARNING - Could not retrieve variants from source file in region 1:36200179-36200580. Error was invalid region `1:36200180-36200580`
[2016-04-15T02:27Z] 2016-04-14 19:27:04 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:27:04,583 - WARNING - Could not retrieve variants from source file in region 1:42094287-42094688. Error was invalid region `1:42094288-42094688`
[2016-04-15T02:27Z] 2016-04-14 19:27:04 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:27:04,681 - WARNING - Could not retrieve variants from source file in region 1:44401173-44415605. Error was invalid region `1:44401174-44415605`
[2016-04-15T02:27Z] 2016-04-14 19:27:04 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:27:04,771 - WARNING - Could not retrieve variants from source file in region 1:35223134-35223535. Error was invalid region `1:35223135-35223535`
[2016-04-15T02:27Z] 2016-04-14 19:27:05 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:27:05,715 - WARNING - Could not retrieve variants from source file in region 1:33291978-33292379. Error was invalid region `1:33291979-33292379`
[2016-04-15T02:27Z] 2016-04-14 19:27:07 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:27:07,605 - WARNING - Could not retrieve variants from source file in region 1:41204358-41204759. Error was invalid region `1:41204359-41204759`
[2016-04-15T02:27Z] 2016-04-14 19:27:08 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:27:08,053 - WARNING - Could not retrieve variants from source file in region 1:37325266-37325788. Error was invalid region `1:37325267-37325788`
[2016-04-15T02:27Z] 2016-04-14 19:27:10 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:27:10,134 - WARNING - Could not retrieve variants from source file in region 1:42693386-42693787. Error was invalid region `1:42693387-42693787`
[2016-04-15T02:27Z] 2016-04-14 19:27:10 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:27:10,821 - WARNING - Could not retrieve variants from source file in region 1:44594836-44595616. Error was invalid region `1:44594837-44595616`
[2016-04-15T02:27Z] 2016-04-14 19:27:19 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:27:19,477 - WARNING - Could not retrieve variants from source file in region 1:40533055-40533537. Error was invalid region `1:40533056-40533537`
[2016-04-15T02:27Z] 2016-04-14 19:27:20 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:27:20,114 - WARNING - Could not retrieve variants from source file in region 1:43201005-43213059. Error was invalid region `1:43201006-43213059`
[2016-04-15T02:27Z] 2016-04-14 19:27:21 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:27:21,498 - WARNING - Could not retrieve variants from source file in region 1:34643239-34643640. Error was invalid region `1:34643240-34643640`
[2016-04-15T02:27Z] 2016-04-14 19:27:21 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:27:21,605 - WARNING - Could not retrieve variants from source file in region 1:40149431-40150346. Error was invalid region `1:40149432-40150346`
[2016-04-15T02:27Z] 2016-04-14 19:27:22 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:27:22,293 - WARNING - Could not retrieve variants from source file in region 1:39957702-39958103. Error was invalid region `1:39957703-39958103`
[2016-04-15T02:27Z] 2016-04-14 19:27:22 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:27:22,399 - WARNING - Could not retrieve variants from source file in region 1:41847849-41848486. Error was invalid region `1:41847850-41848486`
[2016-04-15T02:27Z] 2016-04-14 19:27:22 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:27:22,464 - WARNING - Could not retrieve variants from source file in region 1:36107039-36107440. Error was invalid region `1:36107040-36107440`
[2016-04-15T02:27Z] 2016-04-14 19:27:22 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:27:22,818 - WARNING - Could not retrieve variants from source file in region 1:34038003-34038404. Error was invalid region `1:34038004-34038404`
[2016-04-15T02:27Z] 2016-04-14 19:27:23 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:27:23,040 - WARNING - Could not retrieve variants from source file in region 1:33231169-33231593. Error was invalid region `1:33231170-33231593`
[2016-04-15T02:27Z] 2016-04-14 19:27:23 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:27:23,088 - WARNING - Could not retrieve variants from source file in region 1:44889298-44889699. Error was invalid region `1:44889299-44889699`
[2016-04-15T02:27Z] 2016-04-14 19:27:24 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:27:24,110 - WARNING - Could not retrieve variants from source file in region 1:36927522-36937255. Error was invalid region `1:36927523-36937255`
[2016-04-15T02:27Z] 2016-04-14 19:27:24 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:27:24,818 - WARNING - Could not retrieve variants from source file in region 1:40533055-40533537. Error was invalid region `1:40533056-40533537`
[2016-04-15T02:27Z] 2016-04-14 19:27:25 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:27:25,293 - WARNING - Could not retrieve variants from source file in region 1:43201005-43213059. Error was invalid region `1:43201006-43213059`
[2016-04-15T02:27Z] 2016-04-14 19:27:26 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:27:25,999 - WARNING - Could not retrieve variants from source file in region 1:42656985-42657386. Error was invalid region `1:42656986-42657386`
[2016-04-15T02:27Z] 2016-04-14 19:27:27 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:27:27,200 - WARNING - Could not retrieve variants from source file in region 1:32193436-32222103. Error was invalid region `1:32193437-32222103`
[2016-04-15T02:27Z] 2016-04-14 19:27:29 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:27:29,448 - WARNING - Could not retrieve variants from source file in region 1:41847849-41848486. Error was invalid region `1:41847850-41848486`
[2016-04-15T02:27Z] 2016-04-14 19:27:29 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:27:29,628 - WARNING - Could not retrieve variants from source file in region 1:39957702-39958103. Error was invalid region `1:39957703-39958103`
[2016-04-15T02:27Z] 2016-04-14 19:27:30 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:27:30,100 - WARNING - Could not retrieve variants from source file in region 1:36107039-36107440. Error was invalid region `1:36107040-36107440`
[2016-04-15T02:27Z] 2016-04-14 19:27:30 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:27:30,227 - WARNING - Could not retrieve variants from source file in region 1:34038003-34038404. Error was invalid region `1:34038004-34038404`
[2016-04-15T02:27Z] 2016-04-14 19:27:30 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:27:30,559 - WARNING - Could not retrieve variants from source file in region 1:41012452-41012853. Error was invalid region `1:41012453-41012853`
[2016-04-15T02:27Z] 2016-04-14 19:27:30 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:27:30,689 - WARNING - Could not retrieve variants from source file in region 1:33231169-33231593. Error was invalid region `1:33231170-33231593`
[2016-04-15T02:27Z] 2016-04-14 19:27:30 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:27:30,876 - WARNING - Could not retrieve variants from source file in region 1:44889298-44889699. Error was invalid region `1:44889299-44889699`
[2016-04-15T02:27Z] 2016-04-14 19:27:30 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:27:30,929 - WARNING - Could not retrieve variants from source file in region 1:40533055-40533537. Error was invalid region `1:40533056-40533537`
[2016-04-15T02:27Z] 2016-04-14 19:27:32 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:27:32,576 - WARNING - Could not retrieve variants from source file in region 1:34643239-34643640. Error was invalid region `1:34643240-34643640`
[2016-04-15T02:27Z] 2016-04-14 19:27:36 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:27:36,052 - WARNING - Could not retrieve variants from source file in region 1:39957702-39958103. Error was invalid region `1:39957703-39958103`
[2016-04-15T02:27Z] 2016-04-14 19:27:36 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:27:36,071 - WARNING - Could not retrieve variants from source file in region 1:41847849-41848486. Error was invalid region `1:41847850-41848486`
[2016-04-15T02:27Z] 2016-04-14 19:27:36 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:27:36,445 - WARNING - Could not retrieve variants from source file in region 1:36107039-36107440. Error was invalid region `1:36107040-36107440`
[2016-04-15T02:27Z] 2016-04-14 19:27:36 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:27:36,781 - WARNING - Could not retrieve variants from source file in region 1:41012452-41012853. Error was invalid region `1:41012453-41012853`
[2016-04-15T02:27Z] 2016-04-14 19:27:37 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:27:37,869 - WARNING - Could not retrieve variants from source file in region 1:44889298-44889699. Error was invalid region `1:44889299-44889699`
[2016-04-15T02:27Z] 2016-04-14 19:27:38 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:27:38,444 - WARNING - Could not retrieve variants from source file in region 1:33231169-33231593. Error was invalid region `1:33231170-33231593`
[2016-04-15T02:27Z] 2016-04-14 19:27:38 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:27:38,485 - WARNING - Could not retrieve variants from source file in region 1:34038003-34038404. Error was invalid region `1:34038004-34038404`
[2016-04-15T02:27Z] 2016-04-14 19:27:38 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:27:38,790 - WARNING - Could not retrieve variants from source file in region 1:32193436-32222103. Error was invalid region `1:32193437-32222103`
[2016-04-15T02:27Z] 2016-04-14 19:27:41 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:27:41,225 - WARNING - Could not retrieve variants from source file in region 1:43107977-43131843. Error was invalid region `1:43107978-43131843`
[2016-04-15T02:27Z] 2016-04-14 19:27:49 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:27:49,412 - WARNING - Could not retrieve variants from source file in region 1:43825433-43825834. Error was invalid region `1:43825434-43825834`
[2016-04-15T02:27Z] 2016-04-14 19:27:49 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:27:49,446 - WARNING - Could not retrieve variants from source file in region 1:46379307-46379708. Error was invalid region `1:46379308-46379708`
[2016-04-15T02:27Z] 2016-04-14 19:27:50 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:27:50,631 - WARNING - Could not retrieve variants from source file in region 1:39908295-39914553. Error was invalid region `1:39908296-39914553`
[2016-04-15T02:27Z] 2016-04-14 19:27:50 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:27:50,938 - WARNING - Could not retrieve variants from source file in region 1:34329686-34330257. Error was invalid region `1:34329687-34330257`
[2016-04-15T02:27Z] 2016-04-14 19:27:51 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:27:51,440 - WARNING - Could not retrieve variants from source file in region 1:41485691-41486092. Error was invalid region `1:41485692-41486092`
[2016-04-15T02:27Z] 2016-04-14 19:27:52 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:27:52,170 - WARNING - Could not retrieve variants from source file in region 1:43107977-43131843. Error was invalid region `1:43107978-43131843`
[2016-04-15T02:27Z] 2016-04-14 19:27:52 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:27:52,994 - WARNING - Could not retrieve variants from source file in region 1:40098117-40098814. Error was invalid region `1:40098118-40098814`
[2016-04-15T02:27Z] 2016-04-14 19:27:53 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:27:53,514 - WARNING - Could not retrieve variants from source file in region 1:36820716-36821117. Error was invalid region `1:36820717-36821117`
[2016-04-15T02:27Z] 2016-04-14 19:27:54 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:27:54,317 - WARNING - Could not retrieve variants from source file in region 1:46379307-46379708. Error was invalid region `1:46379308-46379708`
[2016-04-15T02:27Z] 2016-04-14 19:27:55 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:27:55,965 - WARNING - Could not retrieve variants from source file in region 1:34329686-34330257. Error was invalid region `1:34329687-34330257`
[2016-04-15T02:27Z] 2016-04-14 19:27:56 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:27:56,660 - WARNING - Could not retrieve variants from source file in region 1:41485691-41486092. Error was invalid region `1:41485692-41486092`
[2016-04-15T02:27Z] 2016-04-14 19:27:57 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:27:57,106 - WARNING - Could not retrieve variants from source file in region 1:35846821-35847222. Error was invalid region `1:35846822-35847222`
[2016-04-15T02:27Z] 2016-04-14 19:27:57 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:27:57,140 - WARNING - Could not retrieve variants from source file in region 1:40980348-40981446. Error was invalid region `1:40980349-40981446`
[2016-04-15T02:27Z] 2016-04-14 19:27:57 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:27:57,741 - WARNING - Could not retrieve variants from source file in region 1:40098117-40098814. Error was invalid region `1:40098118-40098814`
[2016-04-15T02:27Z] 2016-04-14 19:27:58 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:27:58,547 - WARNING - Could not retrieve variants from source file in region 1:36820716-36821117. Error was invalid region `1:36820717-36821117`
[2016-04-15T02:27Z] 2016-04-14 19:27:58 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:27:58,657 - WARNING - Could not retrieve variants from source file in region 1:43675256-43675689. Error was invalid region `1:43675257-43675689`
[2016-04-15T02:27Z] 2016-04-14 19:27:59 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:27:59,523 - WARNING - Could not retrieve variants from source file in region 1:46379307-46379708. Error was invalid region `1:46379308-46379708`
[2016-04-15T02:28Z] 2016-04-14 19:28:00 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:28:00,324 - WARNING - Could not retrieve variants from source file in region 1:43825433-43825834. Error was invalid region `1:43825434-43825834`
[2016-04-15T02:28Z] 2016-04-14 19:28:01 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:28:01,004 - WARNING - Could not retrieve variants from source file in region 1:39908295-39914553. Error was invalid region `1:39908296-39914553`
[2016-04-15T02:28Z] 2016-04-14 19:28:01 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:28:01,108 - WARNING - Could not retrieve variants from source file in region 1:34329686-34330257. Error was invalid region `1:34329687-34330257`
[2016-04-15T02:28Z] 2016-04-14 19:28:01 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:28:01,490 - WARNING - Could not retrieve variants from source file in region 1:41485691-41486092. Error was invalid region `1:41485692-41486092`
[2016-04-15T02:28Z] 2016-04-14 19:28:02 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:28:02,088 - WARNING - Could not retrieve variants from source file in region 1:35846821-35847222. Error was invalid region `1:35846822-35847222`
[2016-04-15T02:28Z] 2016-04-14 19:28:02 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:28:02,871 - WARNING - Could not retrieve variants from source file in region 1:36820716-36821117. Error was invalid region `1:36820717-36821117`
[2016-04-15T02:28Z] 2016-04-14 19:28:02 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:28:02,996 - WARNING - Could not retrieve variants from source file in region 1:43675256-43675689. Error was invalid region `1:43675257-43675689`
[2016-04-15T02:28Z] 2016-04-14 19:28:04 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:28:04,593 - WARNING - Could not retrieve variants from source file in region 1:33133757-33161802. Error was invalid region `1:33133758-33161802`
[2016-04-15T02:28Z] 2016-04-14 19:28:06 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:28:06,050 - WARNING - Could not retrieve variants from source file in region 1:43042492-43055226. Error was invalid region `1:43042493-43055226`
[2016-04-15T02:28Z] 2016-04-14 19:28:12 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:28:12,761 - WARNING - Could not retrieve variants from source file in region 1:34238072-34238473. Error was invalid region `1:34238073-34238473`
[2016-04-15T02:28Z] 2016-04-14 19:28:13 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:28:13,761 - WARNING - Could not retrieve variants from source file in region 1:46195164-46195565. Error was invalid region `1:46195165-46195565`
[2016-04-15T02:28Z] 2016-04-14 19:28:14 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:28:14,229 - WARNING - Could not retrieve variants from source file in region 1:43779353-43785146. Error was invalid region `1:43779354-43785146`
[2016-04-15T02:28Z] 2016-04-14 19:28:14 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:28:14,787 - WARNING - Could not retrieve variants from source file in region 1:34285131-34285571. Error was invalid region `1:34285132-34285571`
[2016-04-15T02:28Z] 2016-04-14 19:28:16 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:28:16,463 - WARNING - Could not retrieve variants from source file in region 1:43042492-43055226. Error was invalid region `1:43042493-43055226`
[2016-04-15T02:28Z] 2016-04-14 19:28:18 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:28:18,267 - WARNING - Could not retrieve variants from source file in region 1:40922808-40923209. Error was invalid region `1:40922809-40923209`
[2016-04-15T02:28Z] 2016-04-14 19:28:18 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:28:18,400 - WARNING - Could not retrieve variants from source file in region 1:35774404-35774805. Error was invalid region `1:35774405-35774805`
[2016-04-15T02:28Z] 2016-04-14 19:28:18 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:28:18,679 - WARNING - Could not retrieve variants from source file in region 1:43647129-43649698. Error was invalid region `1:43647130-43649698`
[2016-04-15T02:28Z] 2016-04-14 19:28:19 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:28:19,162 - WARNING - Could not retrieve variants from source file in region 1:36751941-36773595. Error was invalid region `1:36751942-36773595`
[2016-04-15T02:28Z] 2016-04-14 19:28:19 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:28:19,279 - WARNING - Could not retrieve variants from source file in region 1:46195164-46195565. Error was invalid region `1:46195165-46195565`
[2016-04-15T02:28Z] 2016-04-14 19:28:19 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:28:19,415 - WARNING - Could not retrieve variants from source file in region 1:33099426-33099827. Error was invalid region `1:33099427-33099827`
[2016-04-15T02:28Z] 2016-04-14 19:28:19 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:28:19,643 - WARNING - Could not retrieve variants from source file in region 1:34285131-34285571. Error was invalid region `1:34285132-34285571`
[2016-04-15T02:28Z] 2016-04-14 19:28:20 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:28:20,048 - WARNING - Could not retrieve variants from source file in region 1:32084693-32096455. Error was invalid region `1:32084694-32096455`
[2016-04-15T02:28Z] 2016-04-14 19:28:26 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:28:26,365 - WARNING - Could not retrieve variants from source file in region 1:40922808-40923209. Error was invalid region `1:40922809-40923209`
[2016-04-15T02:28Z] 2016-04-14 19:28:27 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:28:27,207 - WARNING - Could not retrieve variants from source file in region 1:36614502-36642610. Error was invalid region `1:36614503-36642610`
[2016-04-15T02:28Z] 2016-04-14 19:28:27 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:28:27,219 - WARNING - Could not retrieve variants from source file in region 1:42962589-42962990. Error was invalid region `1:42962590-42962990`
[2016-04-15T02:28Z] 2016-04-14 19:28:27 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:28:27,497 - WARNING - Could not retrieve variants from source file in region 1:46195164-46195565. Error was invalid region `1:46195165-46195565`
[2016-04-15T02:28Z] 2016-04-14 19:28:27 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:28:27,592 - WARNING - Could not retrieve variants from source file in region 1:36553462-36558267. Error was invalid region `1:36553463-36558267`
[2016-04-15T02:28Z] 2016-04-14 19:28:27 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:28:27,856 - WARNING - Could not retrieve variants from source file in region 1:34285131-34285571. Error was invalid region `1:34285132-34285571`
[2016-04-15T02:28Z] 2016-04-14 19:28:27 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:28:27,911 - WARNING - Could not retrieve variants from source file in region 1:43779353-43785146. Error was invalid region `1:43779354-43785146`
[2016-04-15T02:28Z] 2016-04-14 19:28:33 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:28:33,178 - WARNING - Could not retrieve variants from source file in region 1:35774404-35774805. Error was invalid region `1:35774405-35774805`
[2016-04-15T02:28Z] 2016-04-14 19:28:33 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:28:33,347 - WARNING - Could not retrieve variants from source file in region 1:40922808-40923209. Error was invalid region `1:40922809-40923209`
[2016-04-15T02:28Z] 2016-04-14 19:28:33 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:28:33,859 - WARNING - Could not retrieve variants from source file in region 1:43647129-43649698. Error was invalid region `1:43647130-43649698`
[2016-04-15T02:28Z] 2016-04-14 19:28:34 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:28:34,522 - WARNING - Could not retrieve variants from source file in region 1:42880305-42925878. Error was invalid region `1:42880306-42925878`
[2016-04-15T02:28Z] 2016-04-14 19:28:35 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:28:35,827 - WARNING - Could not retrieve variants from source file in region 1:42962589-42962990. Error was invalid region `1:42962590-42962990`
[2016-04-15T02:28Z] 2016-04-14 19:28:36 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:28:36,313 - WARNING - Could not retrieve variants from source file in region 1:33099426-33099827. Error was invalid region `1:33099427-33099827`
[2016-04-15T02:28Z] 2016-04-14 19:28:38 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:28:38,195 - WARNING - Could not retrieve variants from source file in region 1:36553462-36558267. Error was invalid region `1:36553463-36558267`
[2016-04-15T02:28Z] 2016-04-14 19:28:44 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:28:44,174 - WARNING - Could not retrieve variants from source file in region 1:34071314-34071715. Error was invalid region `1:34071315-34071715`
[2016-04-15T02:28Z] 2016-04-14 19:28:44 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:28:44,743 - WARNING - Could not retrieve variants from source file in region 1:42880305-42925878. Error was invalid region `1:42880306-42925878`
[2016-04-15T02:28Z] 2016-04-14 19:28:44 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:28:44,802 - WARNING - Could not retrieve variants from source file in region 1:46164635-46165036. Error was invalid region `1:46164636-46165036`
[2016-04-15T02:28Z] 2016-04-14 19:28:46 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:28:46,096 - WARNING - Could not retrieve variants from source file in region 1:39717355-39749111. Error was invalid region `1:39717356-39749111`
[2016-04-15T02:28Z] 2016-04-14 19:28:47 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:28:47,076 - WARNING - Could not retrieve variants from source file in region 1:40880830-40881231. Error was invalid region `1:40880831-40881231`
[2016-04-15T02:28Z] 2016-04-14 19:28:48 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:28:48,618 - WARNING - Could not retrieve variants from source file in region 1:40840142-40840543. Error was invalid region `1:40840143-40840543`
[2016-04-15T02:28Z] 2016-04-14 19:28:48 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:28:48,848 - WARNING - Could not retrieve variants from source file in region 1:33740607-33741008. Error was invalid region `1:33740608-33741008`
[2016-04-15T02:28Z] 2016-04-14 19:28:49 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:28:49,175 - WARNING - Could not retrieve variants from source file in region 1:34071314-34071715. Error was invalid region `1:34071315-34071715`
[2016-04-15T02:28Z] 2016-04-14 19:28:49 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:28:49,818 - WARNING - Could not retrieve variants from source file in region 1:40840142-40840543. Error was invalid region `1:40840143-40840543`
[2016-04-15T02:28Z] 2016-04-14 19:28:49 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:28:49,854 - WARNING - Could not retrieve variants from source file in region 1:46164635-46165036. Error was invalid region `1:46164636-46165036`
[2016-04-15T02:28Z] 2016-04-14 19:28:50 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:28:50,795 - WARNING - Could not retrieve variants from source file in region 1:33065736-33066137. Error was invalid region `1:33065737-33066137`
[2016-04-15T02:28Z] 2016-04-14 19:28:51 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:28:51,844 - WARNING - Could not retrieve variants from source file in region 1:40880830-40881231. Error was invalid region `1:40880831-40881231`
[2016-04-15T02:28Z] 2016-04-14 19:28:53 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:28:53,397 - WARNING - Could not retrieve variants from source file in region 1:40840142-40840543. Error was invalid region `1:40840143-40840543`
[2016-04-15T02:28Z] 2016-04-14 19:28:53 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:28:53,983 - WARNING - Could not retrieve variants from source file in region 1:33740607-33741008. Error was invalid region `1:33740608-33741008`
[2016-04-15T02:28Z] 2016-04-14 19:28:54 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:28:54,001 - WARNING - Could not retrieve variants from source file in region 1:35648615-35649021. Error was invalid region `1:35648616-35649021`
[2016-04-15T02:28Z] 2016-04-14 19:28:54 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:28:54,749 - WARNING - Could not retrieve variants from source file in region 1:34071314-34071715. Error was invalid region `1:34071315-34071715`
[2016-04-15T02:28Z] 2016-04-14 19:28:55 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:28:55,163 - WARNING - Could not retrieve variants from source file in region 1:40880830-40881231. Error was invalid region `1:40880831-40881231`
[2016-04-15T02:28Z] 2016-04-14 19:28:55 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:28:55,235 - WARNING - Could not retrieve variants from source file in region 1:35562754-35563155. Error was invalid region `1:35562755-35563155`
[2016-04-15T02:28Z] 2016-04-14 19:28:55 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:28:55,386 - WARNING - Could not retrieve variants from source file in region 1:46164635-46165036. Error was invalid region `1:46164636-46165036`
[2016-04-15T02:28Z] 2016-04-14 19:28:55 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:28:55,699 - WARNING - Could not retrieve variants from source file in region 1:33065736-33066137. Error was invalid region `1:33065737-33066137`
[2016-04-15T02:28Z] 2016-04-14 19:28:58 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:28:58,289 - WARNING - Could not retrieve variants from source file in region 1:33065736-33066137. Error was invalid region `1:33065737-33066137`
[2016-04-15T02:28Z] 2016-04-14 19:28:59 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:28:59,773 - WARNING - Could not retrieve variants from source file in region 1:33740607-33741008. Error was invalid region `1:33740608-33741008`
[2016-04-15T02:29Z] 2016-04-14 19:29:00 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:29:00,709 - WARNING - Could not retrieve variants from source file in region 1:35562754-35563155. Error was invalid region `1:35562755-35563155`
[2016-04-15T02:29Z] 2016-04-14 19:29:03 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:29:03,356 - WARNING - Could not retrieve variants from source file in region 1:33477038-33487197. Error was invalid region `1:33477039-33487197`
[2016-04-15T02:29Z] 2016-04-14 19:29:04 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:29:04,285 - WARNING - Could not retrieve variants from source file in region 1:32279418-32280977. Error was invalid region `1:32279419-32280977`
[2016-04-15T02:29Z] 2016-04-14 19:29:05 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:29:05,851 - WARNING - Could not retrieve variants from source file in region 1:46078643-46095462. Error was invalid region `1:46078644-46095462`
[2016-04-15T02:29Z] 2016-04-14 19:29:05 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:29:05,951 - WARNING - Could not retrieve variants from source file in region 1:35562754-35563155. Error was invalid region `1:35562755-35563155`
[2016-04-15T02:29Z] 2016-04-14 19:29:06 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:29:06,741 - WARNING - Could not retrieve variants from source file in region 1:31733715-31734116. Error was invalid region `1:31733716-31734116`
[2016-04-15T02:29Z] 2016-04-14 19:29:08 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:29:08,028 - WARNING - Could not retrieve variants from source file in region 1:33409482-33409883. Error was invalid region `1:33409483-33409883`
[2016-04-15T02:29Z] 2016-04-14 19:29:09 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:29:09,762 - WARNING - Could not retrieve variants from source file in region 1:39549772-39571401. Error was invalid region `1:39549773-39571401`
[2016-04-15T02:29Z] 2016-04-14 19:29:10 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:29:10,807 - WARNING - Could not retrieve variants from source file in region 1:31733715-31734116. Error was invalid region `1:31733716-31734116`
[2016-04-15T02:29Z] 2016-04-14 19:29:12 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:29:12,467 - WARNING - Could not retrieve variants from source file in region 1:33409482-33409883. Error was invalid region `1:33409483-33409883`
[2016-04-15T02:29Z] 2016-04-14 19:29:12 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:29:12,479 - WARNING - Could not retrieve variants from source file in region 1:33409482-33409883. Error was invalid region `1:33409483-33409883`
[2016-04-15T02:29Z] 2016-04-14 19:29:14 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:29:14,129 - WARNING - Could not retrieve variants from source file in region 1:46125669-46126369. Error was invalid region `1:46125670-46126369`
[2016-04-15T02:29Z] 2016-04-14 19:29:14 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:29:14,746 - WARNING - Could not retrieve variants from source file in region 1:39549772-39571401. Error was invalid region `1:39549773-39571401`
[2016-04-15T02:29Z] 2016-04-14 19:29:15 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:29:15,493 - WARNING - Could not retrieve variants from source file in region 1:31733715-31734116. Error was invalid region `1:31733716-31734116`
[2016-04-15T02:29Z] 2016-04-14 19:29:16 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:29:16,004 - WARNING - Could not retrieve variants from source file in region 1:31409423-31427005. Error was invalid region `1:31409424-31427005`
[2016-04-15T02:29Z] 2016-04-14 19:29:17 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:29:17,079 - WARNING - Could not retrieve variants from source file in region 1:33646739-33647140. Error was invalid region `1:33646740-33647140`
[2016-04-15T02:29Z] 2016-04-14 19:29:19 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:29:19,177 - WARNING - Could not retrieve variants from source file in region 1:31187878-31215554. Error was invalid region `1:31187879-31215554`
[2016-04-15T02:29Z] 2016-04-14 19:29:19 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:29:19,213 - WARNING - Could not retrieve variants from source file in region 1:46125669-46126369. Error was invalid region `1:46125670-46126369`
[2016-04-15T02:29Z] 2016-04-14 19:29:20 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:29:20,489 - WARNING - Could not retrieve variants from source file in region 1:38184259-38187637. Error was invalid region `1:38184260-38187637`
[2016-04-15T02:29Z] 2016-04-14 19:29:20 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:29:20,733 - WARNING - Could not retrieve variants from source file in region 1:39549772-39571401. Error was invalid region `1:39549773-39571401`
[2016-04-15T02:29Z] 2016-04-14 19:29:23 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:29:23,844 - WARNING - Could not retrieve variants from source file in region 1:31187878-31215554. Error was invalid region `1:31187879-31215554`
[2016-04-15T02:29Z] 2016-04-14 19:29:24 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:29:24,570 - WARNING - Could not retrieve variants from source file in region 1:46033500-46033901. Error was invalid region `1:46033501-46033901`
[2016-04-15T02:29Z] 2016-04-14 19:29:25 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:29:25,218 - WARNING - Could not retrieve variants from source file in region 1:45799945-45811055. Error was invalid region `1:45799946-45811055`
[2016-04-15T02:29Z] 2016-04-14 19:29:25 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:29:25,609 - WARNING - Could not retrieve variants from source file in region 1:38184259-38187637. Error was invalid region `1:38184260-38187637`
[2016-04-15T02:29Z] 2016-04-14 19:29:30 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:29:30,492 - WARNING - Could not retrieve variants from source file in region 1:31452705-31453106. Error was invalid region `1:31452706-31453106`
[2016-04-15T02:29Z] 2016-04-14 19:29:31 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:29:31,748 - WARNING - Could not retrieve variants from source file in region 1:45973717-45974118. Error was invalid region `1:45973718-45974118`
[2016-04-15T02:29Z] 2016-04-14 19:29:33 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:29:33,295 - WARNING - Could not retrieve variants from source file in region 1:38449699-38463694. Error was invalid region `1:38449700-38463694`
[2016-04-15T02:29Z] 2016-04-14 19:29:34 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:29:34,549 - WARNING - Could not retrieve variants from source file in region 1:38148554-38155889. Error was invalid region `1:38148555-38155889`
[2016-04-15T02:29Z] 2016-04-14 19:29:34 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:29:34,943 - WARNING - Could not retrieve variants from source file in region 1:45671755-45672156. Error was invalid region `1:45671756-45672156`
[2016-04-15T02:29Z] 2016-04-14 19:29:35 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:29:35,270 - WARNING - Could not retrieve variants from source file in region 1:45799945-45811055. Error was invalid region `1:45799946-45811055`
[2016-04-15T02:29Z] 2016-04-14 19:29:35 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:29:35,814 - WARNING - Could not retrieve variants from source file in region 1:38397158-38397559. Error was invalid region `1:38397159-38397559`
[2016-04-15T02:29Z] 2016-04-14 19:29:35 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:29:35,868 - WARNING - Could not retrieve variants from source file in region 1:38449699-38463694. Error was invalid region `1:38449700-38463694`
[2016-04-15T02:29Z] 2016-04-14 19:29:38 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:29:38,928 - WARNING - Could not retrieve variants from source file in region 1:45671755-45672156. Error was invalid region `1:45671756-45672156`
[2016-04-15T02:29Z] 2016-04-14 19:29:45 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:29:45,054 - WARNING - Could not retrieve variants from source file in region 1:45269813-45293942. Error was invalid region `1:45269814-45293942`
[2016-04-15T02:29Z] 2016-04-14 19:29:45 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:29:45,086 - WARNING - Could not retrieve variants from source file in region 1:45269813-45293942. Error was invalid region `1:45269814-45293942`
[2016-04-15T02:29Z] ['bcbio-variation-recall', 'square', '-Xms750m', '-Xmx7280m', '-XX:+UseSerialGC', '-c', 16, '-r', u'1:46715672-62228851', '--caller', 'platypus', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/1/Batch1-1_46715671_62228851.vcf.gz', '/mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/1/Batch1-1_46715671_62228851.vcf-inputs.txt'] in region: 1:46715672-62228851
[2016-04-15T02:30Z] 2016-04-14 19:30:00 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:30:00,174 - WARNING - Could not retrieve variants from source file in region 1:59041970-59042578. Error was invalid region `1:59041971-59042578`
[2016-04-15T02:30Z] 2016-04-14 19:30:00 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:30:00,604 - WARNING - Could not retrieve variants from source file in region 1:61869572-61869973. Error was invalid region `1:61869573-61869973`
[2016-04-15T02:30Z] 2016-04-14 19:30:01 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:30:01,543 - WARNING - Could not retrieve variants from source file in region 1:46870550-46872176. Error was invalid region `1:46870551-46872176`
[2016-04-15T02:30Z] 2016-04-14 19:30:01 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:30:01,703 - WARNING - Could not retrieve variants from source file in region 1:51443230-51443631. Error was invalid region `1:51443231-51443631`
[2016-04-15T02:30Z] 2016-04-14 19:30:02 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:30:02,122 - WARNING - Could not retrieve variants from source file in region 1:55637864-55638265. Error was invalid region `1:55637865-55638265`
[2016-04-15T02:30Z] 2016-04-14 19:30:02 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:30:02,841 - WARNING - Could not retrieve variants from source file in region 1:47767703-47768104. Error was invalid region `1:47767704-47768104`
[2016-04-15T02:30Z] 2016-04-14 19:30:02 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:30:02,845 - WARNING - Could not retrieve variants from source file in region 1:47560098-47572095. Error was invalid region `1:47560099-47572095`
[2016-04-15T02:30Z] 2016-04-14 19:30:02 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:30:02,863 - WARNING - Could not retrieve variants from source file in region 1:55451644-55457900. Error was invalid region `1:55451645-55457900`
[2016-04-15T02:30Z] 2016-04-14 19:30:02 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:30:02,899 - WARNING - Could not retrieve variants from source file in region 1:53387168-53387569. Error was invalid region `1:53387169-53387569`
[2016-04-15T02:30Z] 2016-04-14 19:30:03 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:30:03,576 - WARNING - Could not retrieve variants from source file in region 1:57257606-57258007. Error was invalid region `1:57257607-57258007`
[2016-04-15T02:30Z] 2016-04-14 19:30:03 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:30:03,584 - WARNING - Could not retrieve variants from source file in region 1:47078426-47080931. Error was invalid region `1:47078427-47080931`
[2016-04-15T02:30Z] 2016-04-14 19:30:05 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:30:05,098 - WARNING - Could not retrieve variants from source file in region 1:61869572-61869973. Error was invalid region `1:61869573-61869973`
[2016-04-15T02:30Z] 2016-04-14 19:30:05 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:30:05,912 - WARNING - Could not retrieve variants from source file in region 1:60466603-60467004. Error was invalid region `1:60466604-60467004`
[2016-04-15T02:30Z] 2016-04-14 19:30:08 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:30:08,288 - WARNING - Could not retrieve variants from source file in region 1:55637864-55638265. Error was invalid region `1:55637865-55638265`
[2016-04-15T02:30Z] 2016-04-14 19:30:09 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:30:09,459 - WARNING - Could not retrieve variants from source file in region 1:51913484-51913885. Error was invalid region `1:51913485-51913885`
[2016-04-15T02:30Z] 2016-04-14 19:30:09 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:30:09,922 - WARNING - Could not retrieve variants from source file in region 1:53387168-53387569. Error was invalid region `1:53387169-53387569`
[2016-04-15T02:30Z] 2016-04-14 19:30:10 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:30:10,261 - WARNING - Could not retrieve variants from source file in region 1:60164567-60165139. Error was invalid region `1:60164568-60165139`
[2016-04-15T02:30Z] 2016-04-14 19:30:11 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:30:11,255 - WARNING - Could not retrieve variants from source file in region 1:61869572-61869973. Error was invalid region `1:61869573-61869973`
[2016-04-15T02:30Z] 2016-04-14 19:30:11 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:30:11,291 - WARNING - Could not retrieve variants from source file in region 1:59787059-59787540. Error was invalid region `1:59787060-59787540`
[2016-04-15T02:30Z] 2016-04-14 19:30:11 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:30:11,561 - WARNING - Could not retrieve variants from source file in region 1:60466603-60467004. Error was invalid region `1:60466604-60467004`
[2016-04-15T02:30Z] 2016-04-14 19:30:12 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:30:12,217 - WARNING - Could not retrieve variants from source file in region 1:46870550-46872176. Error was invalid region `1:46870551-46872176`
[2016-04-15T02:30Z] 2016-04-14 19:30:13 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:30:13,597 - WARNING - Could not retrieve variants from source file in region 1:55637864-55638265. Error was invalid region `1:55637865-55638265`
[2016-04-15T02:30Z] 2016-04-14 19:30:14 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:30:14,746 - WARNING - Could not retrieve variants from source file in region 1:51443230-51443631. Error was invalid region `1:51443231-51443631`
[2016-04-15T02:30Z] 2016-04-14 19:30:15 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:30:15,302 - WARNING - Could not retrieve variants from source file in region 1:51913484-51913885. Error was invalid region `1:51913485-51913885`
[2016-04-15T02:30Z] 2016-04-14 19:30:16 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:30:16,115 - WARNING - Could not retrieve variants from source file in region 1:53387168-53387569. Error was invalid region `1:53387169-53387569`
[2016-04-15T02:30Z] 2016-04-14 19:30:16 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:30:16,752 - WARNING - Could not retrieve variants from source file in region 1:60164567-60165139. Error was invalid region `1:60164568-60165139`
[2016-04-15T02:30Z] 2016-04-14 19:30:17 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:30:17,551 - WARNING - Could not retrieve variants from source file in region 1:47767703-47768104. Error was invalid region `1:47767704-47768104`
[2016-04-15T02:30Z] 2016-04-14 19:30:18 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:30:18,482 - WARNING - Could not retrieve variants from source file in region 1:55451644-55457900. Error was invalid region `1:55451645-55457900`
[2016-04-15T02:30Z] 2016-04-14 19:30:19 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:30:19,156 - WARNING - Could not retrieve variants from source file in region 1:48697522-48708468. Error was invalid region `1:48697523-48708468`
[2016-04-15T02:30Z] 2016-04-14 19:30:19 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:30:19,858 - WARNING - Could not retrieve variants from source file in region 1:47078426-47080931. Error was invalid region `1:47078427-47080931`
[2016-04-15T02:30Z] 2016-04-14 19:30:28 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:30:28,651 - WARNING - Could not retrieve variants from source file in region 1:60503551-60503952. Error was invalid region `1:60503552-60503952`
[2016-04-15T02:30Z] 2016-04-14 19:30:28 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:30:28,717 - WARNING - Could not retrieve variants from source file in region 1:58934431-58934832. Error was invalid region `1:58934432-58934832`
[2016-04-15T02:30Z] 2016-04-14 19:30:29 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:30:29,786 - WARNING - Could not retrieve variants from source file in region 1:55505341-55562952. Error was invalid region `1:55505342-55562952`
[2016-04-15T02:30Z] 2016-04-14 19:30:30 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:30:30,066 - WARNING - Could not retrieve variants from source file in region 1:59126875-59148116. Error was invalid region `1:59126876-59148116`
[2016-04-15T02:30Z] 2016-04-14 19:30:31 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:30:31,192 - WARNING - Could not retrieve variants from source file in region 1:50661200-50666705. Error was invalid region `1:50661201-50666705`
[2016-04-15T02:30Z] 2016-04-14 19:30:32 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:30:32,593 - WARNING - Could not retrieve variants from source file in region 1:53320063-53320464. Error was invalid region `1:53320064-53320464`
[2016-04-15T02:30Z] 2016-04-14 19:30:33 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:30:33,040 - WARNING - Could not retrieve variants from source file in region 1:47716978-47726277. Error was invalid region `1:47716979-47726277`
[2016-04-15T02:30Z] 2016-04-14 19:30:33 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:30:33,157 - WARNING - Could not retrieve variants from source file in region 1:57139859-57140260. Error was invalid region `1:57139860-57140260`
[2016-04-15T02:30Z] 2016-04-14 19:30:33 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:30:33,611 - WARNING - Could not retrieve variants from source file in region 1:58934431-58934832. Error was invalid region `1:58934432-58934832`
[2016-04-15T02:30Z] 2016-04-14 19:30:36 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:30:36,022 - WARNING - Could not retrieve variants from source file in region 1:55307290-55320092. Error was invalid region `1:55307291-55320092`
[2016-04-15T02:30Z] 2016-04-14 19:30:36 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:30:36,390 - WARNING - Could not retrieve variants from source file in region 1:46976506-46976907. Error was invalid region `1:46976507-46976907`
[2016-04-15T02:30Z] 2016-04-14 19:30:36 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:30:36,495 - WARNING - Could not retrieve variants from source file in region 1:59126875-59148116. Error was invalid region `1:59126876-59148116`
[2016-04-15T02:30Z] 2016-04-14 19:30:37 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:30:37,994 - WARNING - Could not retrieve variants from source file in region 1:50661200-50666705. Error was invalid region `1:50661201-50666705`
[2016-04-15T02:30Z] 2016-04-14 19:30:38 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:30:38,054 - WARNING - Could not retrieve variants from source file in region 1:60392060-60392461. Error was invalid region `1:60392061-60392461`
[2016-04-15T02:30Z] 2016-04-14 19:30:38 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:30:38,556 - WARNING - Could not retrieve variants from source file in region 1:59844260-59844661. Error was invalid region `1:59844261-59844661`
[2016-04-15T02:30Z] 2016-04-14 19:30:39 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:30:39,069 - WARNING - Could not retrieve variants from source file in region 1:53320063-53320464. Error was invalid region `1:53320064-53320464`
[2016-04-15T02:30Z] 2016-04-14 19:30:39 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:30:39,160 - WARNING - Could not retrieve variants from source file in region 1:51873668-51874141. Error was invalid region `1:51873669-51874141`
[2016-04-15T02:30Z] 2016-04-14 19:30:39 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:30:39,203 - WARNING - Could not retrieve variants from source file in region 1:58934431-58934832. Error was invalid region `1:58934432-58934832`
[2016-04-15T02:30Z] 2016-04-14 19:30:39 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:30:39,325 - WARNING - Could not retrieve variants from source file in region 1:46806339-46827675. Error was invalid region `1:46806340-46827675`
[2016-04-15T02:30Z] 2016-04-14 19:30:40 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:30:40,729 - WARNING - Could not retrieve variants from source file in region 1:47395762-47400157. Error was invalid region `1:47395763-47400157`
[2016-04-15T02:30Z] 2016-04-14 19:30:41 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:30:41,942 - WARNING - Could not retrieve variants from source file in region 1:55307290-55320092. Error was invalid region `1:55307291-55320092`
[2016-04-15T02:30Z] 2016-04-14 19:30:42 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:30:42,411 - WARNING - Could not retrieve variants from source file in region 1:60503551-60503952. Error was invalid region `1:60503552-60503952`
[2016-04-15T02:30Z] 2016-04-14 19:30:44 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:30:44,091 - WARNING - Could not retrieve variants from source file in region 1:50661200-50666705. Error was invalid region `1:50661201-50666705`
[2016-04-15T02:30Z] 2016-04-14 19:30:44 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:30:44,940 - WARNING - Could not retrieve variants from source file in region 1:59844260-59844661. Error was invalid region `1:59844261-59844661`
[2016-04-15T02:30Z] 2016-04-14 19:30:45 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:30:45,458 - WARNING - Could not retrieve variants from source file in region 1:53320063-53320464. Error was invalid region `1:53320064-53320464`
[2016-04-15T02:30Z] 2016-04-14 19:30:46 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:30:46,159 - WARNING - Could not retrieve variants from source file in region 1:51873668-51874141. Error was invalid region `1:51873669-51874141`
[2016-04-15T02:30Z] 2016-04-14 19:30:46 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:30:46,228 - WARNING - Could not retrieve variants from source file in region 1:48459696-48462965. Error was invalid region `1:48459697-48462965`
[2016-04-15T02:30Z] 2016-04-14 19:30:46 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:30:46,384 - WARNING - Could not retrieve variants from source file in region 1:47716978-47726277. Error was invalid region `1:47716979-47726277`
[2016-04-15T02:30Z] 2016-04-14 19:30:47 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:30:47,311 - WARNING - Could not retrieve variants from source file in region 1:55307290-55320092. Error was invalid region `1:55307291-55320092`
[2016-04-15T02:30Z] 2016-04-14 19:30:56 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:30:56,758 - WARNING - Could not retrieve variants from source file in region 1:57422273-57422674. Error was invalid region `1:57422274-57422674`
[2016-04-15T02:30Z] 2016-04-14 19:30:58 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:30:58,603 - WARNING - Could not retrieve variants from source file in region 1:53067882-53072644. Error was invalid region `1:53067883-53072644`
[2016-04-15T02:30Z] 2016-04-14 19:30:59 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:30:59,655 - WARNING - Could not retrieve variants from source file in region 1:48764208-48764609. Error was invalid region `1:48764209-48764609`
[2016-04-15T02:31Z] 2016-04-14 19:31:00 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:31:00,301 - WARNING - Could not retrieve variants from source file in region 1:52498023-52498424. Error was invalid region `1:52498024-52498424`
[2016-04-15T02:31Z] 2016-04-14 19:31:00 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:31:00,351 - WARNING - Could not retrieve variants from source file in region 1:49224373-49224774. Error was invalid region `1:49224374-49224774`
[2016-04-15T02:31Z] 2016-04-14 19:31:01 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:31:01,391 - WARNING - Could not retrieve variants from source file in region 1:57340516-57340917. Error was invalid region `1:57340517-57340917`
[2016-04-15T02:31Z] 2016-04-14 19:31:01 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:31:01,990 - WARNING - Could not retrieve variants from source file in region 1:53250439-53250840. Error was invalid region `1:53250440-53250840`
[2016-04-15T02:31Z] 2016-04-14 19:31:02 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:31:02,166 - WARNING - Could not retrieve variants from source file in region 1:51796007-51796408. Error was invalid region `1:51796008-51796408`
[2016-04-15T02:31Z] 2016-04-14 19:31:02 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:31:02,419 - WARNING - Could not retrieve variants from source file in region 1:46743689-46746354. Error was invalid region `1:46743690-46746354`
[2016-04-15T02:31Z] 2016-04-14 19:31:02 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:31:02,454 - WARNING - Could not retrieve variants from source file in region 1:57422273-57422674. Error was invalid region `1:57422274-57422674`
[2016-04-15T02:31Z] 2016-04-14 19:31:03 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:31:03,241 - WARNING - Could not retrieve variants from source file in region 1:55251478-55277789. Error was invalid region `1:55251479-55277789`
[2016-04-15T02:31Z] 2016-04-14 19:31:03 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:31:03,831 - WARNING - Could not retrieve variants from source file in region 1:47278964-47279365. Error was invalid region `1:47278965-47279365`
[2016-04-15T02:31Z] 2016-04-14 19:31:04 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:31:04,269 - WARNING - Could not retrieve variants from source file in region 1:47685244-47685645. Error was invalid region `1:47685245-47685645`
[2016-04-15T02:31Z] 2016-04-14 19:31:05 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:31:05,032 - WARNING - Could not retrieve variants from source file in region 1:48764208-48764609. Error was invalid region `1:48764209-48764609`
[2016-04-15T02:31Z] 2016-04-14 19:31:06 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:31:06,182 - WARNING - Could not retrieve variants from source file in region 1:49224373-49224774. Error was invalid region `1:49224374-49224774`
[2016-04-15T02:31Z] 2016-04-14 19:31:07 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:31:07,216 - WARNING - Could not retrieve variants from source file in region 1:52263853-52306256. Error was invalid region `1:52263854-52306256`
[2016-04-15T02:31Z] 2016-04-14 19:31:07 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:31:07,409 - WARNING - Could not retrieve variants from source file in region 1:57340516-57340917. Error was invalid region `1:57340517-57340917`
[2016-04-15T02:31Z] 2016-04-14 19:31:07 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:31:07,418 - WARNING - Could not retrieve variants from source file in region 1:51826710-51827111. Error was invalid region `1:51826711-51827111`
[2016-04-15T02:31Z] 2016-04-14 19:31:08 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:31:08,358 - WARNING - Could not retrieve variants from source file in region 1:57422273-57422674. Error was invalid region `1:57422274-57422674`
[2016-04-15T02:31Z] 2016-04-14 19:31:09 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:31:09,897 - WARNING - Could not retrieve variants from source file in region 1:53067882-53072644. Error was invalid region `1:53067883-53072644`
[2016-04-15T02:31Z] 2016-04-14 19:31:10 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:31:10,816 - WARNING - Could not retrieve variants from source file in region 1:47882286-47905099. Error was invalid region `1:47882287-47905099`
[2016-04-15T02:31Z] 2016-04-14 19:31:10 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:31:10,841 - WARNING - Could not retrieve variants from source file in region 1:47685244-47685645. Error was invalid region `1:47685245-47685645`
[2016-04-15T02:31Z] 2016-04-14 19:31:10 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:31:10,884 - WARNING - Could not retrieve variants from source file in region 1:48764208-48764609. Error was invalid region `1:48764209-48764609`
[2016-04-15T02:31Z] 2016-04-14 19:31:11 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:31:11,410 - WARNING - Could not retrieve variants from source file in region 1:52498023-52498424. Error was invalid region `1:52498024-52498424`
[2016-04-15T02:31Z] 2016-04-14 19:31:11 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:31:11,564 - WARNING - Could not retrieve variants from source file in region 1:49224373-49224774. Error was invalid region `1:49224374-49224774`
[2016-04-15T02:31Z] 2016-04-14 19:31:13 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:31:13,122 - WARNING - Could not retrieve variants from source file in region 1:51826710-51827111. Error was invalid region `1:51826711-51827111`
[2016-04-15T02:31Z] 2016-04-14 19:31:13 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:31:13,355 - WARNING - Could not retrieve variants from source file in region 1:57340516-57340917. Error was invalid region `1:57340517-57340917`
[2016-04-15T02:31Z] 2016-04-14 19:31:15 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:31:15,417 - WARNING - Could not retrieve variants from source file in region 1:55251478-55277789. Error was invalid region `1:55251479-55277789`
[2016-04-15T02:31Z] 2016-04-14 19:31:16 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:31:16,226 - WARNING - Could not retrieve variants from source file in region 1:47685244-47685645. Error was invalid region `1:47685245-47685645`
[2016-04-15T02:31Z] 2016-04-14 19:31:22 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:31:22,046 - WARNING - Could not retrieve variants from source file in region 1:47882286-47905099. Error was invalid region `1:47882287-47905099`
[2016-04-15T02:31Z] 2016-04-14 19:31:26 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:31:26,697 - WARNING - Could not retrieve variants from source file in region 1:53153221-53153622. Error was invalid region `1:53153222-53153622`
[2016-04-15T02:31Z] 2016-04-14 19:31:27 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:31:27,022 - WARNING - Could not retrieve variants from source file in region 1:47133600-47139293. Error was invalid region `1:47133601-47139293`
[2016-04-15T02:31Z] 2016-04-14 19:31:27 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:31:27,652 - WARNING - Could not retrieve variants from source file in region 1:47799428-47824590. Error was invalid region `1:47799429-47824590`
[2016-04-15T02:31Z] 2016-04-14 19:31:27 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:31:27,912 - WARNING - Could not retrieve variants from source file in region 1:54359711-54360112. Error was invalid region `1:54359712-54360112`
[2016-04-15T02:31Z] 2016-04-14 19:31:28 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:31:28,325 - WARNING - Could not retrieve variants from source file in region 1:54059805-54066114. Error was invalid region `1:54059806-54066114`
[2016-04-15T02:31Z] 2016-04-14 19:31:28 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:31:28,414 - WARNING - Could not retrieve variants from source file in region 1:55013802-55014203. Error was invalid region `1:55013803-55014203`
[2016-04-15T02:31Z] 2016-04-14 19:31:31 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:31:31,694 - WARNING - Could not retrieve variants from source file in region 1:53153221-53153622. Error was invalid region `1:53153222-53153622`
[2016-04-15T02:31Z] 2016-04-14 19:31:32 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:31:32,326 - WARNING - Could not retrieve variants from source file in region 1:47133600-47139293. Error was invalid region `1:47133601-47139293`
[2016-04-15T02:31Z] 2016-04-14 19:31:32 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:31:32,797 - WARNING - Could not retrieve variants from source file in region 1:47799428-47824590. Error was invalid region `1:47799429-47824590`
[2016-04-15T02:31Z] 2016-04-14 19:31:33 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:31:33,922 - WARNING - Could not retrieve variants from source file in region 1:54431808-54432209. Error was invalid region `1:54431809-54432209`
[2016-04-15T02:31Z] 2016-04-14 19:31:34 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:31:34,078 - WARNING - Could not retrieve variants from source file in region 1:55166631-55182490. Error was invalid region `1:55166632-55182490`
[2016-04-15T02:31Z] 2016-04-14 19:31:34 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:31:34,324 - WARNING - Could not retrieve variants from source file in region 1:52821681-52839182. Error was invalid region `1:52821682-52839182`
[2016-04-15T02:31Z] 2016-04-14 19:31:36 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:31:36,371 - WARNING - Could not retrieve variants from source file in region 1:53153221-53153622. Error was invalid region `1:53153222-53153622`
[2016-04-15T02:31Z] 2016-04-14 19:31:36 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:31:36,824 - WARNING - Could not retrieve variants from source file in region 1:47133600-47139293. Error was invalid region `1:47133601-47139293`
[2016-04-15T02:31Z] 2016-04-14 19:31:38 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:31:38,827 - WARNING - Could not retrieve variants from source file in region 1:54359711-54360112. Error was invalid region `1:54359712-54360112`
[2016-04-15T02:31Z] 2016-04-14 19:31:39 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:31:39,244 - WARNING - Could not retrieve variants from source file in region 1:55013802-55014203. Error was invalid region `1:55013803-55014203`
[2016-04-15T02:31Z] 2016-04-14 19:31:39 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:31:39,853 - WARNING - Could not retrieve variants from source file in region 1:55166631-55182490. Error was invalid region `1:55166632-55182490`
[2016-04-15T02:31Z] 2016-04-14 19:31:39 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:31:39,859 - WARNING - Could not retrieve variants from source file in region 1:54059805-54066114. Error was invalid region `1:54059806-54066114`
[2016-04-15T02:31Z] 2016-04-14 19:31:48 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:31:48,942 - WARNING - Could not retrieve variants from source file in region 1:53712516-53742696. Error was invalid region `1:53712517-53742696`
[2016-04-15T02:31Z] 2016-04-14 19:31:49 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:31:49,338 - WARNING - Could not retrieve variants from source file in region 1:53792440-53793701. Error was invalid region `1:53792441-53793701`
[2016-04-15T02:31Z] 2016-04-14 19:31:49 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:31:49,338 - WARNING - Could not retrieve variants from source file in region 1:53792440-53793701. Error was invalid region `1:53792441-53793701`
[2016-04-15T02:31Z] 2016-04-14 19:31:49 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:31:49,522 - WARNING - Could not retrieve variants from source file in region 1:54199523-54199925. Error was invalid region `1:54199524-54199925`
[2016-04-15T02:31Z] 2016-04-14 19:31:50 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:31:50,450 - WARNING - Could not retrieve variants from source file in region 1:53535267-53558460. Error was invalid region `1:53535268-53558460`
[2016-04-15T02:31Z] 2016-04-14 19:31:50 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:31:50,733 - WARNING - Could not retrieve variants from source file in region 1:53676237-53681889. Error was invalid region `1:53676238-53681889`
[2016-04-15T02:31Z] 2016-04-14 19:31:51 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:31:51,113 - WARNING - Could not retrieve variants from source file in region 1:53792440-53793701. Error was invalid region `1:53792441-53793701`
[2016-04-15T02:31Z] 2016-04-14 19:31:53 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:31:53,152 - WARNING - Could not retrieve variants from source file in region 1:53535267-53558460. Error was invalid region `1:53535268-53558460`
[2016-04-15T02:31Z] 2016-04-14 19:31:53 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:31:53,498 - WARNING - Could not retrieve variants from source file in region 1:54199523-54199925. Error was invalid region `1:54199524-54199925`
[2016-04-15T02:31Z] 2016-04-14 19:31:54 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:31:54,637 - WARNING - Could not retrieve variants from source file in region 1:53676237-53681889. Error was invalid region `1:53676238-53681889`
[2016-04-15T02:31Z] ['bcbio-variation-recall', 'square', '-Xms750m', '-Xmx7280m', '-XX:+UseSerialGC', '-c', 16, '-r', u'1:62231951-77749296', '--caller', 'platypus', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/1/Batch1-1_62231950_77749296.vcf.gz', '/mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/1/Batch1-1_62231950_77749296.vcf-inputs.txt'] in region: 1:62231951-77749296
[2016-04-15T02:32Z] 2016-04-14 19:32:08 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:32:08,693 - WARNING - Could not retrieve variants from source file in region 1:77748453-77748976. Error was invalid region `1:77748454-77748976`
[2016-04-15T02:32Z] 2016-04-14 19:32:08 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:32:08,793 - WARNING - Could not retrieve variants from source file in region 1:62516472-62516873. Error was invalid region `1:62516473-62516873`
[2016-04-15T02:32Z] 2016-04-14 19:32:09 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:32:09,949 - WARNING - Could not retrieve variants from source file in region 1:62455803-62456204. Error was invalid region `1:62455804-62456204`
[2016-04-15T02:32Z] 2016-04-14 19:32:11 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:32:11,280 - WARNING - Could not retrieve variants from source file in region 1:62675408-62675809. Error was invalid region `1:62675409-62675809`
[2016-04-15T02:32Z] 2016-04-14 19:32:11 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:32:11,423 - WARNING - Could not retrieve variants from source file in region 1:64094900-64114491. Error was invalid region `1:64094901-64114491`
[2016-04-15T02:32Z] 2016-04-14 19:32:11 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:32:11,751 - WARNING - Could not retrieve variants from source file in region 1:67235886-67236287. Error was invalid region `1:67235887-67236287`
[2016-04-15T02:32Z] 2016-04-14 19:32:11 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:32:11,944 - WARNING - Could not retrieve variants from source file in region 1:76257681-76269650. Error was invalid region `1:76257682-76269650`
[2016-04-15T02:32Z] 2016-04-14 19:32:12 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:32:12,504 - WARNING - Could not retrieve variants from source file in region 1:74574971-74575372. Error was invalid region `1:74574972-74575372`
[2016-04-15T02:32Z] 2016-04-14 19:32:12 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:32:12,613 - WARNING - Could not retrieve variants from source file in region 1:62329869-62330270. Error was invalid region `1:62329870-62330270`
[2016-04-15T02:32Z] 2016-04-14 19:32:12 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:32:12,714 - WARNING - Could not retrieve variants from source file in region 1:67558528-67579576. Error was invalid region `1:67558529-67579576`
[2016-04-15T02:32Z] 2016-04-14 19:32:13 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:32:13,486 - WARNING - Could not retrieve variants from source file in region 1:62516472-62516873. Error was invalid region `1:62516473-62516873`
[2016-04-15T02:32Z] 2016-04-14 19:32:14 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:32:14,823 - WARNING - Could not retrieve variants from source file in region 1:62455803-62456204. Error was invalid region `1:62455804-62456204`
[2016-04-15T02:32Z] 2016-04-14 19:32:14 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:32:14,878 - WARNING - Could not retrieve variants from source file in region 1:63788740-63789141. Error was invalid region `1:63788741-63789141`
[2016-04-15T02:32Z] 2016-04-14 19:32:15 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:32:15,536 - WARNING - Could not retrieve variants from source file in region 1:76397761-76398162. Error was invalid region `1:76397762-76398162`
[2016-04-15T02:32Z] 2016-04-14 19:32:17 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:32:17,771 - WARNING - Could not retrieve variants from source file in region 1:68903731-68904132. Error was invalid region `1:68903732-68904132`
[2016-04-15T02:32Z] 2016-04-14 19:32:17 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:32:17,949 - WARNING - Could not retrieve variants from source file in region 1:62675408-62675809. Error was invalid region `1:62675409-62675809`
[2016-04-15T02:32Z] 2016-04-14 19:32:18 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:32:18,551 - WARNING - Could not retrieve variants from source file in region 1:67235886-67236287. Error was invalid region `1:67235887-67236287`
[2016-04-15T02:32Z] 2016-04-14 19:32:19 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:32:19,185 - WARNING - Could not retrieve variants from source file in region 1:75681300-75717115. Error was invalid region `1:75681301-75717115`
[2016-04-15T02:32Z] 2016-04-14 19:32:19 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:32:19,186 - WARNING - Could not retrieve variants from source file in region 1:63991056-64021286. Error was invalid region `1:63991057-64021286`
[2016-04-15T02:32Z] 2016-04-14 19:32:19 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:32:19,898 - WARNING - Could not retrieve variants from source file in region 1:62329869-62330270. Error was invalid region `1:62329870-62330270`
[2016-04-15T02:32Z] 2016-04-14 19:32:19 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:32:19,952 - WARNING - Could not retrieve variants from source file in region 1:62516472-62516873. Error was invalid region `1:62516473-62516873`
[2016-04-15T02:32Z] 2016-04-14 19:32:19 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:32:19,960 - WARNING - Could not retrieve variants from source file in region 1:67558528-67579576. Error was invalid region `1:67558529-67579576`
[2016-04-15T02:32Z] 2016-04-14 19:32:20 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:32:20,288 - WARNING - Could not retrieve variants from source file in region 1:74574971-74575372. Error was invalid region `1:74574972-74575372`
[2016-04-15T02:32Z] 2016-04-14 19:32:20 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:32:20,308 - WARNING - Could not retrieve variants from source file in region 1:77748453-77748976. Error was invalid region `1:77748454-77748976`
[2016-04-15T02:32Z] 2016-04-14 19:32:20 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:32:20,318 - WARNING - Could not retrieve variants from source file in region 1:62455803-62456204. Error was invalid region `1:62455804-62456204`
[2016-04-15T02:32Z] 2016-04-14 19:32:20 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:32:20,612 - WARNING - Could not retrieve variants from source file in region 1:76397761-76398162. Error was invalid region `1:76397762-76398162`
[2016-04-15T02:32Z] 2016-04-14 19:32:23 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:32:23,265 - WARNING - Could not retrieve variants from source file in region 1:68903731-68904132. Error was invalid region `1:68903732-68904132`
[2016-04-15T02:32Z] 2016-04-14 19:32:23 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:32:23,307 - WARNING - Could not retrieve variants from source file in region 1:62675408-62675809. Error was invalid region `1:62675409-62675809`
[2016-04-15T02:32Z] 2016-04-14 19:32:24 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:32:24,109 - WARNING - Could not retrieve variants from source file in region 1:67235886-67236287. Error was invalid region `1:67235887-67236287`
[2016-04-15T02:32Z] 2016-04-14 19:32:26 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:32:26,952 - WARNING - Could not retrieve variants from source file in region 1:62329869-62330270. Error was invalid region `1:62329870-62330270`
[2016-04-15T02:32Z] 2016-04-14 19:32:26 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:32:26,960 - WARNING - Could not retrieve variants from source file in region 1:67558528-67579576. Error was invalid region `1:67558529-67579576`
[2016-04-15T02:32Z] 2016-04-14 19:32:27 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:32:27,385 - WARNING - Could not retrieve variants from source file in region 1:74574971-74575372. Error was invalid region `1:74574972-74575372`
[2016-04-15T02:32Z] 2016-04-14 19:32:36 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:32:36,647 - WARNING - Could not retrieve variants from source file in region 1:62483388-62483789. Error was invalid region `1:62483389-62483789`
[2016-04-15T02:32Z] 2016-04-14 19:32:36 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:32:36,677 - WARNING - Could not retrieve variants from source file in region 1:77634737-77635138. Error was invalid region `1:77634738-77635138`
[2016-04-15T02:32Z] 2016-04-14 19:32:37 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:32:37,724 - WARNING - Could not retrieve variants from source file in region 1:63049608-63050009. Error was invalid region `1:63049609-63050009`
[2016-04-15T02:32Z] 2016-04-14 19:32:38 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:32:38,277 - WARNING - Could not retrieve variants from source file in region 1:62380059-62380488. Error was invalid region `1:62380060-62380488`
[2016-04-15T02:32Z] 2016-04-14 19:32:41 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:32:41,559 - WARNING - Could not retrieve variants from source file in region 1:68590893-68625068. Error was invalid region `1:68590894-68625068`
[2016-04-15T02:32Z] 2016-04-14 19:32:41 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:32:41,643 - WARNING - Could not retrieve variants from source file in region 1:66831159-66831560. Error was invalid region `1:66831160-66831560`
[2016-04-15T02:32Z] 2016-04-14 19:32:42 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:32:42,435 - WARNING - Could not retrieve variants from source file in region 1:75622405-75622806. Error was invalid region `1:75622406-75622806`
[2016-04-15T02:32Z] 2016-04-14 19:32:42 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:32:42,585 - WARNING - Could not retrieve variants from source file in region 1:62579612-62594783. Error was invalid region `1:62579613-62594783`
[2016-04-15T02:32Z] 2016-04-14 19:32:42 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:32:42,948 - WARNING - Could not retrieve variants from source file in region 1:62483388-62483789. Error was invalid region `1:62483389-62483789`
[2016-04-15T02:32Z] 2016-04-14 19:32:43 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:32:43,115 - WARNING - Could not retrieve variants from source file in region 1:77634737-77635138. Error was invalid region `1:77634738-77635138`
[2016-04-15T02:32Z] 2016-04-14 19:32:45 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:32:45,325 - WARNING - Could not retrieve variants from source file in region 1:64059433-64059834. Error was invalid region `1:64059434-64059834`
[2016-04-15T02:32Z] 2016-04-14 19:32:45 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:32:45,383 - WARNING - Could not retrieve variants from source file in region 1:76226811-76227212. Error was invalid region `1:76226812-76227212`
[2016-04-15T02:32Z] 2016-04-14 19:32:45 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:32:45,896 - WARNING - Could not retrieve variants from source file in region 1:76344494-76344901. Error was invalid region `1:76344495-76344901`
[2016-04-15T02:32Z] 2016-04-14 19:32:46 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:32:46,196 - WARNING - Could not retrieve variants from source file in region 1:65857934-65860877. Error was invalid region `1:65857935-65860877`
[2016-04-15T02:32Z] 2016-04-14 19:32:46 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:32:46,213 - WARNING - Could not retrieve variants from source file in region 1:74492318-74492719. Error was invalid region `1:74492319-74492719`
[2016-04-15T02:32Z] 2016-04-14 19:32:46 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:32:46,253 - WARNING - Could not retrieve variants from source file in region 1:62260957-62261358. Error was invalid region `1:62260958-62261358`
[2016-04-15T02:32Z] 2016-04-14 19:32:48 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:32:48,282 - WARNING - Could not retrieve variants from source file in region 1:66831159-66831560. Error was invalid region `1:66831160-66831560`
[2016-04-15T02:32Z] 2016-04-14 19:32:48 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:32:48,522 - WARNING - Could not retrieve variants from source file in region 1:75622405-75622806. Error was invalid region `1:75622406-75622806`
[2016-04-15T02:32Z] 2016-04-14 19:32:49 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:32:49,651 - WARNING - Could not retrieve variants from source file in region 1:77634737-77635138. Error was invalid region `1:77634738-77635138`
[2016-04-15T02:32Z] 2016-04-14 19:32:50 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:32:50,384 - WARNING - Could not retrieve variants from source file in region 1:63049608-63050009. Error was invalid region `1:63049609-63050009`
[2016-04-15T02:32Z] 2016-04-14 19:32:51 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:32:51,342 - WARNING - Could not retrieve variants from source file in region 1:64059433-64059834. Error was invalid region `1:64059434-64059834`
[2016-04-15T02:32Z] 2016-04-14 19:32:51 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:32:51,613 - WARNING - Could not retrieve variants from source file in region 1:62380059-62380488. Error was invalid region `1:62380060-62380488`
[2016-04-15T02:32Z] 2016-04-14 19:32:52 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:32:52,094 - WARNING - Could not retrieve variants from source file in region 1:76344494-76344901. Error was invalid region `1:76344495-76344901`
[2016-04-15T02:32Z] 2016-04-14 19:32:52 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:32:52,182 - WARNING - Could not retrieve variants from source file in region 1:76226811-76227212. Error was invalid region `1:76226812-76227212`
[2016-04-15T02:32Z] 2016-04-14 19:32:52 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:32:52,561 - WARNING - Could not retrieve variants from source file in region 1:62260957-62261358. Error was invalid region `1:62260958-62261358`
[2016-04-15T02:32Z] 2016-04-14 19:32:52 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:32:52,696 - WARNING - Could not retrieve variants from source file in region 1:65857934-65860877. Error was invalid region `1:65857935-65860877`
[2016-04-15T02:32Z] 2016-04-14 19:32:53 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:32:53,958 - WARNING - Could not retrieve variants from source file in region 1:68590893-68625068. Error was invalid region `1:68590894-68625068`
[2016-04-15T02:32Z] 2016-04-14 19:32:54 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:32:54,216 - WARNING - Could not retrieve variants from source file in region 1:75622405-75622806. Error was invalid region `1:75622406-75622806`
[2016-04-15T02:32Z] 2016-04-14 19:32:54 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:32:54,799 - WARNING - Could not retrieve variants from source file in region 1:62579612-62594783. Error was invalid region `1:62579613-62594783`
[2016-04-15T02:32Z] 2016-04-14 19:32:58 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:32:58,783 - WARNING - Could not retrieve variants from source file in region 1:76226811-76227212. Error was invalid region `1:76226812-76227212`
[2016-04-15T02:33Z] 2016-04-14 19:33:00 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:33:00,462 - WARNING - Could not retrieve variants from source file in region 1:65857934-65860877. Error was invalid region `1:65857935-65860877`
[2016-04-15T02:33Z] 2016-04-14 19:33:00 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:33:00,496 - WARNING - Could not retrieve variants from source file in region 1:62260957-62261358. Error was invalid region `1:62260958-62261358`
[2016-04-15T02:33Z] 2016-04-14 19:33:07 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:33:07,003 - WARNING - Could not retrieve variants from source file in region 1:62950647-62960291. Error was invalid region `1:62950648-62960291`
[2016-04-15T02:33Z] 2016-04-14 19:33:07 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:33:07,441 - WARNING - Could not retrieve variants from source file in region 1:62231820-62232320. Error was invalid region `1:62231821-62232320`
[2016-04-15T02:33Z] 2016-04-14 19:33:10 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:33:10,915 - WARNING - Could not retrieve variants from source file in region 1:68512230-68513089. Error was invalid region `1:68512231-68513089`
[2016-04-15T02:33Z] 2016-04-14 19:33:11 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:33:11,515 - WARNING - Could not retrieve variants from source file in region 1:75171790-75199342. Error was invalid region `1:75171791-75199342`
[2016-04-15T02:33Z] 2016-04-14 19:33:12 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:33:12,263 - WARNING - Could not retrieve variants from source file in region 1:62713013-62740639. Error was invalid region `1:62713014-62740639`
[2016-04-15T02:33Z] 2016-04-14 19:33:12 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:33:12,382 - WARNING - Could not retrieve variants from source file in region 1:62231820-62232320. Error was invalid region `1:62231821-62232320`
[2016-04-15T02:33Z] 2016-04-14 19:33:13 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:33:13,818 - WARNING - Could not retrieve variants from source file in region 1:72058341-72058742. Error was invalid region `1:72058342-72058742`
[2016-04-15T02:33Z] 2016-04-14 19:33:13 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:33:13,818 - WARNING - Could not retrieve variants from source file in region 1:71418241-71418642. Error was invalid region `1:71418242-71418642`
[2016-04-15T02:33Z] 2016-04-14 19:33:14 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:33:14,724 - WARNING - Could not retrieve variants from source file in region 1:65811150-65811552. Error was invalid region `1:65811151-65811552`
[2016-04-15T02:33Z] 2016-04-14 19:33:15 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:33:15,648 - WARNING - Could not retrieve variants from source file in region 1:65991615-65992016. Error was invalid region `1:65991616-65992016`
[2016-04-15T02:33Z] 2016-04-14 19:33:16 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:33:16,445 - WARNING - Could not retrieve variants from source file in region 1:75171790-75199342. Error was invalid region `1:75171791-75199342`
[2016-04-15T02:33Z] 2016-04-14 19:33:16 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:33:16,616 - WARNING - Could not retrieve variants from source file in region 1:62713013-62740639. Error was invalid region `1:62713014-62740639`
[2016-04-15T02:33Z] 2016-04-14 19:33:17 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:33:17,405 - WARNING - Could not retrieve variants from source file in region 1:62950647-62960291. Error was invalid region `1:62950648-62960291`
[2016-04-15T02:33Z] 2016-04-14 19:33:18 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:33:18,224 - WARNING - Could not retrieve variants from source file in region 1:67390205-67412451. Error was invalid region `1:67390206-67412451`
[2016-04-15T02:33Z] 2016-04-14 19:33:18 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:33:18,465 - WARNING - Could not retrieve variants from source file in region 1:75065230-75065631. Error was invalid region `1:75065231-75065631`
[2016-04-15T02:33Z] 2016-04-14 19:33:19 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:33:19,458 - WARNING - Could not retrieve variants from source file in region 1:72058341-72058742. Error was invalid region `1:72058342-72058742`
[2016-04-15T02:33Z] 2016-04-14 19:33:20 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:33:20,238 - WARNING - Could not retrieve variants from source file in region 1:65811150-65811552. Error was invalid region `1:65811151-65811552`
[2016-04-15T02:33Z] 2016-04-14 19:33:22 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:33:22,521 - WARNING - Could not retrieve variants from source file in region 1:62713013-62740639. Error was invalid region `1:62713014-62740639`
[2016-04-15T02:33Z] 2016-04-14 19:33:23 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:33:23,592 - WARNING - Could not retrieve variants from source file in region 1:67390205-67412451. Error was invalid region `1:67390206-67412451`
[2016-04-15T02:33Z] 2016-04-14 19:33:25 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:33:25,212 - WARNING - Could not retrieve variants from source file in region 1:72058341-72058742. Error was invalid region `1:72058342-72058742`
[2016-04-15T02:33Z] 2016-04-14 19:33:25 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:33:25,404 - WARNING - Could not retrieve variants from source file in region 1:65811150-65811552. Error was invalid region `1:65811151-65811552`
[2016-04-15T02:33Z] 2016-04-14 19:33:26 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:33:26,665 - WARNING - Could not retrieve variants from source file in region 1:65113357-65113758. Error was invalid region `1:65113358-65113758`
[2016-04-15T02:33Z] 2016-04-14 19:33:27 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:33:27,927 - WARNING - Could not retrieve variants from source file in region 1:77042420-77042825. Error was invalid region `1:77042421-77042825`
[2016-04-15T02:33Z] 2016-04-14 19:33:32 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:33:32,247 - WARNING - Could not retrieve variants from source file in region 1:65113357-65113758. Error was invalid region `1:65113358-65113758`
[2016-04-15T02:33Z] 2016-04-14 19:33:34 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:33:34,773 - WARNING - Could not retrieve variants from source file in region 1:68299080-68299481. Error was invalid region `1:68299081-68299481`
[2016-04-15T02:33Z] 2016-04-14 19:33:35 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:33:35,179 - WARNING - Could not retrieve variants from source file in region 1:75036601-75038418. Error was invalid region `1:75036602-75038418`
[2016-04-15T02:33Z] 2016-04-14 19:33:36 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:33:36,301 - WARNING - Could not retrieve variants from source file in region 1:75097215-75097616. Error was invalid region `1:75097216-75097616`
[2016-04-15T02:33Z] 2016-04-14 19:33:37 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:33:37,477 - WARNING - Could not retrieve variants from source file in region 1:65113357-65113758. Error was invalid region `1:65113358-65113758`
[2016-04-15T02:33Z] 2016-04-14 19:33:37 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:33:37,958 - WARNING - Could not retrieve variants from source file in region 1:67266545-67288235. Error was invalid region `1:67266546-67288235`
[2016-04-15T02:33Z] 2016-04-14 19:33:38 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:33:38,018 - WARNING - Could not retrieve variants from source file in region 1:64608118-64608519. Error was invalid region `1:64608119-64608519`
[2016-04-15T02:33Z] 2016-04-14 19:33:38 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:33:38,052 - WARNING - Could not retrieve variants from source file in region 1:75097215-75097616. Error was invalid region `1:75097216-75097616`
[2016-04-15T02:33Z] 2016-04-14 19:33:38 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:33:38,093 - WARNING - Could not retrieve variants from source file in region 1:64608118-64608519. Error was invalid region `1:64608119-64608519`
[2016-04-15T02:33Z] 2016-04-14 19:33:39 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:33:39,483 - WARNING - Could not retrieve variants from source file in region 1:65303448-65335252. Error was invalid region `1:65303449-65335252`
[2016-04-15T02:33Z] 2016-04-14 19:33:40 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:33:40,642 - WARNING - Could not retrieve variants from source file in region 1:75097215-75097616. Error was invalid region `1:75097216-75097616`
[2016-04-15T02:33Z] 2016-04-14 19:33:40 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:33:40,675 - WARNING - Could not retrieve variants from source file in region 1:64515168-64515569. Error was invalid region `1:64515169-64515569`
[2016-04-15T02:33Z] 2016-04-14 19:33:41 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:33:41,022 - WARNING - Could not retrieve variants from source file in region 1:71331219-71331688. Error was invalid region `1:71331220-71331688`
[2016-04-15T02:33Z] 2016-04-14 19:33:42 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:33:42,892 - WARNING - Could not retrieve variants from source file in region 1:64608118-64608519. Error was invalid region `1:64608119-64608519`
[2016-04-15T02:33Z] 2016-04-14 19:33:42 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:33:42,947 - WARNING - Could not retrieve variants from source file in region 1:67266545-67288235. Error was invalid region `1:67266546-67288235`
[2016-04-15T02:33Z] 2016-04-14 19:33:43 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:33:43,444 - WARNING - Could not retrieve variants from source file in region 1:71331219-71331688. Error was invalid region `1:71331220-71331688`
[2016-04-15T02:33Z] 2016-04-14 19:33:44 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:33:44,994 - WARNING - Could not retrieve variants from source file in region 1:70904589-70904990. Error was invalid region `1:70904590-70904990`
[2016-04-15T02:33Z] 2016-04-14 19:33:45 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:33:45,149 - WARNING - Could not retrieve variants from source file in region 1:75036601-75038418. Error was invalid region `1:75036602-75038418`
[2016-04-15T02:33Z] 2016-04-14 19:33:45 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:33:45,215 - WARNING - Could not retrieve variants from source file in region 1:64515168-64515569. Error was invalid region `1:64515169-64515569`
[2016-04-15T02:33Z] 2016-04-14 19:33:47 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:33:47,273 - WARNING - Could not retrieve variants from source file in region 1:67266545-67288235. Error was invalid region `1:67266546-67288235`
[2016-04-15T02:33Z] 2016-04-14 19:33:48 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:33:48,359 - WARNING - Could not retrieve variants from source file in region 1:65303448-65335252. Error was invalid region `1:65303449-65335252`
[2016-04-15T02:33Z] 2016-04-14 19:33:49 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:33:49,519 - WARNING - Could not retrieve variants from source file in region 1:64709680-64710081. Error was invalid region `1:64709681-64710081`
[2016-04-15T02:33Z] 2016-04-14 19:33:50 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:33:50,145 - WARNING - Could not retrieve variants from source file in region 1:74603977-74604378. Error was invalid region `1:74603978-74604378`
[2016-04-15T02:33Z] 2016-04-14 19:33:52 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:33:52,836 - WARNING - Could not retrieve variants from source file in region 1:70904589-70904990. Error was invalid region `1:70904590-70904990`
[2016-04-15T02:33Z] 2016-04-14 19:33:55 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:33:55,219 - WARNING - Could not retrieve variants from source file in region 1:68153240-68153641. Error was invalid region `1:68153241-68153641`
[2016-04-15T02:33Z] 2016-04-14 19:33:55 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:33:55,245 - WARNING - Could not retrieve variants from source file in region 1:68153240-68153641. Error was invalid region `1:68153241-68153641`
[2016-04-15T02:33Z] 2016-04-14 19:33:58 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:33:58,611 - WARNING - Could not retrieve variants from source file in region 1:67852124-67861710. Error was invalid region `1:67852125-67861710`
[2016-04-15T02:33Z] 2016-04-14 19:33:59 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:33:59,174 - WARNING - Could not retrieve variants from source file in region 1:70819797-70821070. Error was invalid region `1:70819798-70821070`
[2016-04-15T02:33Z] 2016-04-14 19:33:59 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:33:59,185 - WARNING - Could not retrieve variants from source file in region 1:67787075-67795509. Error was invalid region `1:67787076-67795509`
[2016-04-15T02:34Z] 2016-04-14 19:34:01 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:34:01,112 - WARNING - Could not retrieve variants from source file in region 1:67787075-67795509. Error was invalid region `1:67787076-67795509`
[2016-04-15T02:34Z] 2016-04-14 19:34:02 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:34:02,621 - WARNING - Could not retrieve variants from source file in region 1:67685176-67706148. Error was invalid region `1:67685177-67706148`
[2016-04-15T02:34Z] 2016-04-14 19:34:04 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:34:04,267 - WARNING - Could not retrieve variants from source file in region 1:67633601-67634002. Error was invalid region `1:67633602-67634002`
[2016-04-15T02:34Z] 2016-04-14 19:34:04 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:34:04,267 - WARNING - Could not retrieve variants from source file in region 1:67633601-67634002. Error was invalid region `1:67633602-67634002`
[2016-04-15T02:34Z] 2016-04-14 19:34:04 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:34:04,296 - WARNING - Could not retrieve variants from source file in region 1:67633601-67634002. Error was invalid region `1:67633602-67634002`
[2016-04-15T02:34Z] ['bcbio-variation-recall', 'square', '-Xms750m', '-Xmx7280m', '-XX:+UseSerialGC', '-c', 16, '-r', u'1:77752626-93297674', '--caller', 'platypus', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/1/Batch1-1_77752625_93297674.vcf.gz', '/mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/1/Batch1-1_77752625_93297674.vcf-inputs.txt'] in region: 1:77752626-93297674
[2016-04-15T02:34Z] 2016-04-14 19:34:20 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:34:20,123 - WARNING - Could not retrieve variants from source file in region 1:93160691-93161092. Error was invalid region `1:93160692-93161092`
[2016-04-15T02:34Z] 2016-04-14 19:34:22 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:34:22,008 - WARNING - Could not retrieve variants from source file in region 1:92262663-92263064. Error was invalid region `1:92262664-92263064`
[2016-04-15T02:34Z] 2016-04-14 19:34:22 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:34:22,221 - WARNING - Could not retrieve variants from source file in region 1:92174049-92185712. Error was invalid region `1:92174050-92185712`
[2016-04-15T02:34Z] 2016-04-14 19:34:22 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:34:22,233 - WARNING - Could not retrieve variants from source file in region 1:79357149-79357550. Error was invalid region `1:79357150-79357550`
[2016-04-15T02:34Z] 2016-04-14 19:34:22 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:34:22,299 - WARNING - Could not retrieve variants from source file in region 1:92946268-92948741. Error was invalid region `1:92946269-92948741`
[2016-04-15T02:34Z] 2016-04-14 19:34:23 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:34:23,109 - WARNING - Could not retrieve variants from source file in region 1:89322771-89323172. Error was invalid region `1:89322772-89323172`
[2016-04-15T02:34Z] 2016-04-14 19:34:23 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:34:23,504 - WARNING - Could not retrieve variants from source file in region 1:91727842-91728243. Error was invalid region `1:91727843-91728243`
[2016-04-15T02:34Z] 2016-04-14 19:34:23 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:34:23,620 - WARNING - Could not retrieve variants from source file in region 1:92645810-92647722. Error was invalid region `1:92645811-92647722`
[2016-04-15T02:34Z] 2016-04-14 19:34:23 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:34:23,656 - WARNING - Could not retrieve variants from source file in region 1:90178532-90179722. Error was invalid region `1:90178533-90179722`
[2016-04-15T02:34Z] 2016-04-14 19:34:24 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:34:24,096 - WARNING - Could not retrieve variants from source file in region 1:86818361-86852811. Error was invalid region `1:86818362-86852811`
[2016-04-15T02:34Z] 2016-04-14 19:34:26 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:34:26,376 - WARNING - Could not retrieve variants from source file in region 1:85009683-85040260. Error was invalid region `1:85009684-85040260`
[2016-04-15T02:34Z] 2016-04-14 19:34:27 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:34:27,376 - WARNING - Could not retrieve variants from source file in region 1:93160691-93161092. Error was invalid region `1:93160692-93161092`
[2016-04-15T02:34Z] 2016-04-14 19:34:29 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:34:29,022 - WARNING - Could not retrieve variants from source file in region 1:92262663-92263064. Error was invalid region `1:92262664-92263064`
[2016-04-15T02:34Z] 2016-04-14 19:34:29 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:34:29,301 - WARNING - Could not retrieve variants from source file in region 1:93073017-93090013. Error was invalid region `1:93073018-93090013`
[2016-04-15T02:34Z] 2016-04-14 19:34:29 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:34:29,422 - WARNING - Could not retrieve variants from source file in region 1:78584875-78601593. Error was invalid region `1:78584876-78601593`
[2016-04-15T02:34Z] 2016-04-14 19:34:30 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:34:30,561 - WARNING - Could not retrieve variants from source file in region 1:79357149-79357550. Error was invalid region `1:79357150-79357550`
[2016-04-15T02:34Z] 2016-04-14 19:34:31 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:34:31,369 - WARNING - Could not retrieve variants from source file in region 1:89322771-89323172. Error was invalid region `1:89322772-89323172`
[2016-04-15T02:34Z] 2016-04-14 19:34:31 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:34:31,976 - WARNING - Could not retrieve variants from source file in region 1:91727842-91728243. Error was invalid region `1:91727843-91728243`
[2016-04-15T02:34Z] 2016-04-14 19:34:32 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:34:32,290 - WARNING - Could not retrieve variants from source file in region 1:92645810-92647722. Error was invalid region `1:92645811-92647722`
[2016-04-15T02:34Z] 2016-04-14 19:34:32 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:34:32,540 - WARNING - Could not retrieve variants from source file in region 1:85930061-85930466. Error was invalid region `1:85930062-85930466`
[2016-04-15T02:34Z] 2016-04-14 19:34:32 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:34:32,845 - WARNING - Could not retrieve variants from source file in region 1:93160691-93161092. Error was invalid region `1:93160692-93161092`
[2016-04-15T02:34Z] 2016-04-14 19:34:32 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:34:32,882 - WARNING - Could not retrieve variants from source file in region 1:90178532-90179722. Error was invalid region `1:90178533-90179722`
[2016-04-15T02:34Z] 2016-04-14 19:34:34 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:34:34,091 - WARNING - Could not retrieve variants from source file in region 1:92262663-92263064. Error was invalid region `1:92262664-92263064`
[2016-04-15T02:34Z] 2016-04-14 19:34:34 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:34:34,715 - WARNING - Could not retrieve variants from source file in region 1:78584875-78601593. Error was invalid region `1:78584876-78601593`
[2016-04-15T02:34Z] 2016-04-14 19:34:35 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:34:35,707 - WARNING - Could not retrieve variants from source file in region 1:79357149-79357550. Error was invalid region `1:79357150-79357550`
[2016-04-15T02:34Z] 2016-04-14 19:34:38 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:34:38,000 - WARNING - Could not retrieve variants from source file in region 1:89322771-89323172. Error was invalid region `1:89322772-89323172`
[2016-04-15T02:34Z] 2016-04-14 19:34:38 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:34:38,838 - WARNING - Could not retrieve variants from source file in region 1:91727842-91728243. Error was invalid region `1:91727843-91728243`
[2016-04-15T02:34Z] 2016-04-14 19:34:38 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:34:38,858 - WARNING - Could not retrieve variants from source file in region 1:92645810-92647722. Error was invalid region `1:92645811-92647722`
[2016-04-15T02:34Z] 2016-04-14 19:34:39 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:34:39,134 - WARNING - Could not retrieve variants from source file in region 1:86818361-86852811. Error was invalid region `1:86818362-86852811`
[2016-04-15T02:34Z] 2016-04-14 19:34:39 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:34:39,628 - WARNING - Could not retrieve variants from source file in region 1:90178532-90179722. Error was invalid region `1:90178533-90179722`
[2016-04-15T02:34Z] 2016-04-14 19:34:49 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:34:49,836 - WARNING - Could not retrieve variants from source file in region 1:92979143-92979544. Error was invalid region `1:92979144-92979544`
[2016-04-15T02:34Z] 2016-04-14 19:34:51 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:34:51,282 - WARNING - Could not retrieve variants from source file in region 1:84944778-84945179. Error was invalid region `1:84944779-84945179`
[2016-04-15T02:34Z] 2016-04-14 19:34:53 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:34:53,684 - WARNING - Could not retrieve variants from source file in region 1:89271363-89271764. Error was invalid region `1:89271364-89271764`
[2016-04-15T02:34Z] 2016-04-14 19:34:54 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:34:54,711 - WARNING - Could not retrieve variants from source file in region 1:92979143-92979544. Error was invalid region `1:92979144-92979544`
[2016-04-15T02:34Z] 2016-04-14 19:34:56 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:34:56,082 - WARNING - Could not retrieve variants from source file in region 1:84944778-84945179. Error was invalid region `1:84944779-84945179`
[2016-04-15T02:34Z] 2016-04-14 19:34:56 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:34:56,527 - WARNING - Could not retrieve variants from source file in region 1:78392235-78392636. Error was invalid region `1:78392236-78392636`
[2016-04-15T02:34Z] 2016-04-14 19:34:56 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:34:56,558 - WARNING - Could not retrieve variants from source file in region 1:90470704-90493216. Error was invalid region `1:90470705-90493216`
[2016-04-15T02:34Z] 2016-04-14 19:34:56 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:34:56,660 - WARNING - Could not retrieve variants from source file in region 1:91980236-91989897. Error was invalid region `1:91980237-91989897`
[2016-04-15T02:34Z] 2016-04-14 19:34:56 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:34:56,950 - WARNING - Could not retrieve variants from source file in region 1:89522435-89522836. Error was invalid region `1:89522436-89522836`
[2016-04-15T02:34Z] 2016-04-14 19:34:57 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:34:57,130 - WARNING - Could not retrieve variants from source file in region 1:89847161-89849932. Error was invalid region `1:89847162-89849932`
[2016-04-15T02:34Z] 2016-04-14 19:34:57 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:34:57,190 - WARNING - Could not retrieve variants from source file in region 1:85845156-85845557. Error was invalid region `1:85845157-85845557`
[2016-04-15T02:34Z] 2016-04-14 19:34:57 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:34:57,859 - WARNING - Could not retrieve variants from source file in region 1:79128359-79129104. Error was invalid region `1:79128360-79129104`
[2016-04-15T02:34Z] 2016-04-14 19:34:58 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:34:58,098 - WARNING - Could not retrieve variants from source file in region 1:89271363-89271764. Error was invalid region `1:89271364-89271764`
[2016-04-15T02:34Z] 2016-04-14 19:34:59 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:34:59,411 - WARNING - Could not retrieve variants from source file in region 1:92979143-92979544. Error was invalid region `1:92979144-92979544`
[2016-04-15T02:35Z] 2016-04-14 19:35:00 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:35:00,057 - WARNING - Could not retrieve variants from source file in region 1:92428284-92458033. Error was invalid region `1:92428285-92458033`
[2016-04-15T02:35Z] 2016-04-14 19:35:00 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:35:00,476 - WARNING - Could not retrieve variants from source file in region 1:84944778-84945179. Error was invalid region `1:84944779-84945179`
[2016-04-15T02:35Z] 2016-04-14 19:35:01 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:35:01,079 - WARNING - Could not retrieve variants from source file in region 1:90470704-90493216. Error was invalid region `1:90470705-90493216`
[2016-04-15T02:35Z] 2016-04-14 19:35:01 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:35:01,832 - WARNING - Could not retrieve variants from source file in region 1:78392235-78392636. Error was invalid region `1:78392236-78392636`
[2016-04-15T02:35Z] 2016-04-14 19:35:01 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:35:01,836 - WARNING - Could not retrieve variants from source file in region 1:86590704-86592027. Error was invalid region `1:86590705-86592027`
[2016-04-15T02:35Z] 2016-04-14 19:35:02 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:35:02,306 - WARNING - Could not retrieve variants from source file in region 1:89522435-89522836. Error was invalid region `1:89522436-89522836`
[2016-04-15T02:35Z] 2016-04-14 19:35:02 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:35:02,379 - WARNING - Could not retrieve variants from source file in region 1:89847161-89849932. Error was invalid region `1:89847162-89849932`
[2016-04-15T02:35Z] 2016-04-14 19:35:02 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:35:02,468 - WARNING - Could not retrieve variants from source file in region 1:79128359-79129104. Error was invalid region `1:79128360-79129104`
[2016-04-15T02:35Z] 2016-04-14 19:35:02 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:35:02,557 - WARNING - Could not retrieve variants from source file in region 1:89271363-89271764. Error was invalid region `1:89271364-89271764`
[2016-04-15T02:35Z] 2016-04-14 19:35:04 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:35:04,278 - WARNING - Could not retrieve variants from source file in region 1:92428284-92458033. Error was invalid region `1:92428285-92458033`
[2016-04-15T02:35Z] 2016-04-14 19:35:05 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:35:05,439 - WARNING - Could not retrieve variants from source file in region 1:90470704-90493216. Error was invalid region `1:90470705-90493216`
[2016-04-15T02:35Z] 2016-04-14 19:35:07 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:35:07,412 - WARNING - Could not retrieve variants from source file in region 1:89522435-89522836. Error was invalid region `1:89522436-89522836`
[2016-04-15T02:35Z] 2016-04-14 19:35:07 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:35:07,606 - WARNING - Could not retrieve variants from source file in region 1:89847161-89849932. Error was invalid region `1:89847162-89849932`
[2016-04-15T02:35Z] 2016-04-14 19:35:07 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:35:07,634 - WARNING - Could not retrieve variants from source file in region 1:85845156-85845557. Error was invalid region `1:85845157-85845557`
[2016-04-15T02:35Z] 2016-04-14 19:35:13 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:35:13,771 - WARNING - Could not retrieve variants from source file in region 1:89732026-89732427. Error was invalid region `1:89732027-89732427`
[2016-04-15T02:35Z] 2016-04-14 19:35:16 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:35:16,010 - WARNING - Could not retrieve variants from source file in region 1:78024134-78024535. Error was invalid region `1:78024135-78024535`
[2016-04-15T02:35Z] 2016-04-14 19:35:16 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:35:16,859 - WARNING - Could not retrieve variants from source file in region 1:89225765-89226166. Error was invalid region `1:89225766-89226166`
[2016-04-15T02:35Z] 2016-04-14 19:35:18 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:35:18,354 - WARNING - Could not retrieve variants from source file in region 1:78024134-78024535. Error was invalid region `1:78024135-78024535`
[2016-04-15T02:35Z] 2016-04-14 19:35:18 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:35:18,370 - WARNING - Could not retrieve variants from source file in region 1:77763331-77763732. Error was invalid region `1:77763332-77763732`
[2016-04-15T02:35Z] 2016-04-14 19:35:18 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:35:18,758 - WARNING - Could not retrieve variants from source file in region 1:84670373-84671006. Error was invalid region `1:84670374-84671006`
[2016-04-15T02:35Z] 2016-04-14 19:35:19 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:35:19,962 - WARNING - Could not retrieve variants from source file in region 1:78024134-78024535. Error was invalid region `1:78024135-78024535`
[2016-04-15T02:35Z] 2016-04-14 19:35:20 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:35:20,466 - WARNING - Could not retrieve variants from source file in region 1:89426691-89427092. Error was invalid region `1:89426692-89427092`
[2016-04-15T02:35Z] 2016-04-14 19:35:21 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:35:21,512 - WARNING - Could not retrieve variants from source file in region 1:89225765-89226166. Error was invalid region `1:89225766-89226166`
[2016-04-15T02:35Z] 2016-04-14 19:35:22 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:35:22,427 - WARNING - Could not retrieve variants from source file in region 1:85815923-85816324. Error was invalid region `1:85815924-85816324`
[2016-04-15T02:35Z] 2016-04-14 19:35:23 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:35:23,650 - WARNING - Could not retrieve variants from source file in region 1:77763331-77763732. Error was invalid region `1:77763332-77763732`
[2016-04-15T02:35Z] 2016-04-14 19:35:24 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:35:24,261 - WARNING - Could not retrieve variants from source file in region 1:84670373-84671006. Error was invalid region `1:84670374-84671006`
[2016-04-15T02:35Z] 2016-04-14 19:35:24 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:35:24,643 - WARNING - Could not retrieve variants from source file in region 1:86557756-86558157. Error was invalid region `1:86557757-86558157`
[2016-04-15T02:35Z] 2016-04-14 19:35:24 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:35:24,999 - WARNING - Could not retrieve variants from source file in region 1:89426691-89427092. Error was invalid region `1:89426692-89427092`
[2016-04-15T02:35Z] 2016-04-14 19:35:25 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:35:25,934 - WARNING - Could not retrieve variants from source file in region 1:89225765-89226166. Error was invalid region `1:89225766-89226166`
[2016-04-15T02:35Z] 2016-04-14 19:35:28 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:35:28,145 - WARNING - Could not retrieve variants from source file in region 1:85724117-85742202. Error was invalid region `1:85724118-85742202`
[2016-04-15T02:35Z] 2016-04-14 19:35:28 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:35:28,146 - WARNING - Could not retrieve variants from source file in region 1:77763331-77763732. Error was invalid region `1:77763332-77763732`
[2016-04-15T02:35Z] 2016-04-14 19:35:29 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:35:29,167 - WARNING - Could not retrieve variants from source file in region 1:84670373-84671006. Error was invalid region `1:84670374-84671006`
[2016-04-15T02:35Z] 2016-04-14 19:35:29 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:35:29,705 - WARNING - Could not retrieve variants from source file in region 1:86557756-86558157. Error was invalid region `1:86557757-86558157`
[2016-04-15T02:35Z] 2016-04-14 19:35:31 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:35:31,299 - WARNING - Could not retrieve variants from source file in region 1:85815923-85816324. Error was invalid region `1:85815924-85816324`
[2016-04-15T02:35Z] 2016-04-14 19:35:31 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:35:31,889 - WARNING - Could not retrieve variants from source file in region 1:82421385-82421786. Error was invalid region `1:82421386-82421786`
[2016-04-15T02:35Z] 2016-04-14 19:35:33 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:35:33,623 - WARNING - Could not retrieve variants from source file in region 1:87563457-87564300. Error was invalid region `1:87563458-87564300`
[2016-04-15T02:35Z] 2016-04-14 19:35:35 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:35:35,788 - WARNING - Could not retrieve variants from source file in region 1:79392545-79392946. Error was invalid region `1:79392546-79392946`
[2016-04-15T02:35Z] 2016-04-14 19:35:36 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:35:36,230 - WARNING - Could not retrieve variants from source file in region 1:82421385-82421786. Error was invalid region `1:82421386-82421786`
[2016-04-15T02:35Z] 2016-04-14 19:35:36 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:35:36,663 - WARNING - Could not retrieve variants from source file in region 1:82421385-82421786. Error was invalid region `1:82421386-82421786`
[2016-04-15T02:35Z] 2016-04-14 19:35:37 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:35:37,757 - WARNING - Could not retrieve variants from source file in region 1:87563457-87564300. Error was invalid region `1:87563458-87564300`
[2016-04-15T02:35Z] 2016-04-14 19:35:37 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:35:37,829 - WARNING - Could not retrieve variants from source file in region 1:84352721-84353122. Error was invalid region `1:84352722-84353122`
[2016-04-15T02:35Z] 2016-04-14 19:35:38 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:35:38,618 - WARNING - Could not retrieve variants from source file in region 1:87045685-87046092. Error was invalid region `1:87045686-87046092`
[2016-04-15T02:35Z] 2016-04-14 19:35:38 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:35:38,680 - WARNING - Could not retrieve variants from source file in region 1:87563457-87564300. Error was invalid region `1:87563458-87564300`
[2016-04-15T02:35Z] 2016-04-14 19:35:40 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:35:40,584 - WARNING - Could not retrieve variants from source file in region 1:85487819-85488220. Error was invalid region `1:85487820-85488220`
[2016-04-15T02:35Z] 2016-04-14 19:35:40 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:35:40,626 - WARNING - Could not retrieve variants from source file in region 1:79392545-79392946. Error was invalid region `1:79392546-79392946`
[2016-04-15T02:35Z] 2016-04-14 19:35:40 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:35:40,629 - WARNING - Could not retrieve variants from source file in region 1:87368920-87369321. Error was invalid region `1:87368921-87369321`
[2016-04-15T02:35Z] 2016-04-14 19:35:41 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:35:41,686 - WARNING - Could not retrieve variants from source file in region 1:85648409-85667102. Error was invalid region `1:85648410-85667102`
[2016-04-15T02:35Z] 2016-04-14 19:35:42 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:35:42,277 - WARNING - Could not retrieve variants from source file in region 1:84352721-84353122. Error was invalid region `1:84352722-84353122`
[2016-04-15T02:35Z] 2016-04-14 19:35:43 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:35:43,109 - WARNING - Could not retrieve variants from source file in region 1:86488021-86488422. Error was invalid region `1:86488022-86488422`
[2016-04-15T02:35Z] 2016-04-14 19:35:43 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:35:43,131 - WARNING - Could not retrieve variants from source file in region 1:87045685-87046092. Error was invalid region `1:87045686-87046092`
[2016-04-15T02:35Z] 2016-04-14 19:35:45 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:35:45,127 - WARNING - Could not retrieve variants from source file in region 1:85487819-85488220. Error was invalid region `1:85487820-85488220`
[2016-04-15T02:35Z] 2016-04-14 19:35:45 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:35:45,263 - WARNING - Could not retrieve variants from source file in region 1:85112992-85121445. Error was invalid region `1:85112993-85121445`
[2016-04-15T02:35Z] 2016-04-14 19:35:45 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:35:45,845 - WARNING - Could not retrieve variants from source file in region 1:85648409-85667102. Error was invalid region `1:85648410-85667102`
[2016-04-15T02:35Z] 2016-04-14 19:35:47 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:35:47,259 - WARNING - Could not retrieve variants from source file in region 1:87045685-87046092. Error was invalid region `1:87045686-87046092`
[2016-04-15T02:35Z] 2016-04-14 19:35:47 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:35:47,440 - WARNING - Could not retrieve variants from source file in region 1:86488021-86488422. Error was invalid region `1:86488022-86488422`
[2016-04-15T02:35Z] 2016-04-14 19:35:48 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:35:48,726 - WARNING - Could not retrieve variants from source file in region 1:85487819-85488220. Error was invalid region `1:85487820-85488220`
[2016-04-15T02:35Z] 2016-04-14 19:35:48 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:35:48,938 - WARNING - Could not retrieve variants from source file in region 1:85112992-85121445. Error was invalid region `1:85112993-85121445`
[2016-04-15T02:35Z] 2016-04-14 19:35:50 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:35:50,741 - WARNING - Could not retrieve variants from source file in region 1:86488021-86488422. Error was invalid region `1:86488022-86488422`
[2016-04-15T02:35Z] 2016-04-14 19:35:51 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:35:51,720 - WARNING - Could not retrieve variants from source file in region 1:85112992-85121445. Error was invalid region `1:85112993-85121445`
[2016-04-15T02:35Z] 2016-04-14 19:35:52 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:35:52,923 - WARNING - Could not retrieve variants from source file in region 1:86375443-86375844. Error was invalid region `1:86375444-86375844`
[2016-04-15T02:35Z] 2016-04-14 19:35:52 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:35:52,936 - WARNING - Could not retrieve variants from source file in region 1:86375443-86375844. Error was invalid region `1:86375444-86375844`
[2016-04-15T02:35Z] 2016-04-14 19:35:52 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:35:52,946 - WARNING - Could not retrieve variants from source file in region 1:86375443-86375844. Error was invalid region `1:86375444-86375844`
[2016-04-15T02:35Z] 2016-04-14 19:35:55 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:35:55,065 - WARNING - Could not retrieve variants from source file in region 1:85987161-85987605. Error was invalid region `1:85987162-85987605`
[2016-04-15T02:35Z] 2016-04-14 19:35:56 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:35:56,571 - WARNING - Could not retrieve variants from source file in region 1:85987161-85987605. Error was invalid region `1:85987162-85987605`
[2016-04-15T02:35Z] 2016-04-14 19:35:56 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:35:56,580 - WARNING - Could not retrieve variants from source file in region 1:85987161-85987605. Error was invalid region `1:85987162-85987605`
[2016-04-15T02:36Z] ['bcbio-variation-recall', 'square', '-Xms750m', '-Xmx7280m', '-XX:+UseSerialGC', '-c', 16, '-r', u'1:93298946-108993401', '--caller', 'platypus', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/1/Batch1-1_93298945_108993401.vcf.gz', '/mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/1/Batch1-1_93298945_108993401.vcf-inputs.txt'] in region: 1:93298946-108993401
[2016-04-15T02:36Z] 2016-04-14 19:36:12 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:36:12,590 - WARNING - Could not retrieve variants from source file in region 1:94930134-94930535. Error was invalid region `1:94930135-94930535`
[2016-04-15T02:36Z] 2016-04-14 19:36:12 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:36:12,971 - WARNING - Could not retrieve variants from source file in region 1:97770709-97771110. Error was invalid region `1:97770710-97771110`
[2016-04-15T02:36Z] 2016-04-14 19:36:13 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:36:13,618 - WARNING - Could not retrieve variants from source file in region 1:108307516-108313448. Error was invalid region `1:108307517-108313448`
[2016-04-15T02:36Z] 2016-04-14 19:36:13 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:36:13,620 - WARNING - Could not retrieve variants from source file in region 1:101346279-101346680. Error was invalid region `1:101346280-101346680`
[2016-04-15T02:36Z] 2016-04-14 19:36:13 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:36:13,687 - WARNING - Could not retrieve variants from source file in region 1:94544023-94544424. Error was invalid region `1:94544024-94544424`
[2016-04-15T02:36Z] 2016-04-14 19:36:13 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:36:13,749 - WARNING - Could not retrieve variants from source file in region 1:93580370-93587552. Error was invalid region `1:93580371-93587552`
[2016-04-15T02:36Z] 2016-04-14 19:36:14 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:36:14,109 - WARNING - Could not retrieve variants from source file in region 1:95293878-95294279. Error was invalid region `1:95293879-95294279`
[2016-04-15T02:36Z] 2016-04-14 19:36:14 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:36:14,245 - WARNING - Could not retrieve variants from source file in region 1:97272245-97272646. Error was invalid region `1:97272246-97272646`
[2016-04-15T02:36Z] 2016-04-14 19:36:14 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:36:14,851 - WARNING - Could not retrieve variants from source file in region 1:94037118-94037519. Error was invalid region `1:94037119-94037519`
[2016-04-15T02:36Z] 2016-04-14 19:36:14 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:36:14,874 - WARNING - Could not retrieve variants from source file in region 1:95330161-95330562. Error was invalid region `1:95330162-95330562`
[2016-04-15T02:36Z] 2016-04-14 19:36:14 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:36:14,932 - WARNING - Could not retrieve variants from source file in region 1:95001389-95001790. Error was invalid region `1:95001390-95001790`
[2016-04-15T02:36Z] 2016-04-14 19:36:17 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:36:17,920 - WARNING - Could not retrieve variants from source file in region 1:94341056-94345327. Error was invalid region `1:94341057-94345327`
[2016-04-15T02:36Z] 2016-04-14 19:36:19 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:36:19,650 - WARNING - Could not retrieve variants from source file in region 1:99164223-99164624. Error was invalid region `1:99164224-99164624`
[2016-04-15T02:36Z] 2016-04-14 19:36:21 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:36:21,168 - WARNING - Could not retrieve variants from source file in region 1:97770709-97771110. Error was invalid region `1:97770710-97771110`
[2016-04-15T02:36Z] 2016-04-14 19:36:21 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:36:21,585 - WARNING - Could not retrieve variants from source file in region 1:101346279-101346680. Error was invalid region `1:101346280-101346680`
[2016-04-15T02:36Z] 2016-04-14 19:36:22 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:36:22,380 - WARNING - Could not retrieve variants from source file in region 1:93580370-93587552. Error was invalid region `1:93580371-93587552`
[2016-04-15T02:36Z] 2016-04-14 19:36:23 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:36:23,085 - WARNING - Could not retrieve variants from source file in region 1:93825967-93826368. Error was invalid region `1:93825968-93826368`
[2016-04-15T02:36Z] 2016-04-14 19:36:23 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:36:23,283 - WARNING - Could not retrieve variants from source file in region 1:95001389-95001790. Error was invalid region `1:95001390-95001790`
[2016-04-15T02:36Z] 2016-04-14 19:36:23 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:36:23,375 - WARNING - Could not retrieve variants from source file in region 1:95330161-95330562. Error was invalid region `1:95330162-95330562`
[2016-04-15T02:36Z] 2016-04-14 19:36:24 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:36:24,480 - WARNING - Could not retrieve variants from source file in region 1:99164223-99164624. Error was invalid region `1:99164224-99164624`
[2016-04-15T02:36Z] 2016-04-14 19:36:26 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:36:26,906 - WARNING - Could not retrieve variants from source file in region 1:97770709-97771110. Error was invalid region `1:97770710-97771110`
[2016-04-15T02:36Z] 2016-04-14 19:36:27 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:36:27,768 - WARNING - Could not retrieve variants from source file in region 1:101346279-101346680. Error was invalid region `1:101346280-101346680`
[2016-04-15T02:36Z] 2016-04-14 19:36:30 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:36:30,201 - WARNING - Could not retrieve variants from source file in region 1:97272245-97272646. Error was invalid region `1:97272246-97272646`
[2016-04-15T02:36Z] 2016-04-14 19:36:30 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:36:30,669 - WARNING - Could not retrieve variants from source file in region 1:93580370-93587552. Error was invalid region `1:93580371-93587552`
[2016-04-15T02:36Z] 2016-04-14 19:36:31 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:36:31,142 - WARNING - Could not retrieve variants from source file in region 1:94544023-94544424. Error was invalid region `1:94544024-94544424`
[2016-04-15T02:36Z] 2016-04-14 19:36:31 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:36:31,306 - WARNING - Could not retrieve variants from source file in region 1:93825967-93826368. Error was invalid region `1:93825968-93826368`
[2016-04-15T02:36Z] 2016-04-14 19:36:31 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:36:31,357 - WARNING - Could not retrieve variants from source file in region 1:95001389-95001790. Error was invalid region `1:95001390-95001790`
[2016-04-15T02:36Z] 2016-04-14 19:36:31 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:36:31,464 - WARNING - Could not retrieve variants from source file in region 1:95330161-95330562. Error was invalid region `1:95330162-95330562`
[2016-04-15T02:36Z] 2016-04-14 19:36:42 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:36:42,737 - WARNING - Could not retrieve variants from source file in region 1:99127181-99127582. Error was invalid region `1:99127182-99127582`
[2016-04-15T02:36Z] 2016-04-14 19:36:43 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:36:43,836 - WARNING - Could not retrieve variants from source file in region 1:94639236-94639637. Error was invalid region `1:94639237-94639637`
[2016-04-15T02:36Z] 2016-04-14 19:36:45 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:36:45,046 - WARNING - Could not retrieve variants from source file in region 1:94578337-94578738. Error was invalid region `1:94578338-94578738`
[2016-04-15T02:36Z] 2016-04-14 19:36:45 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:36:45,763 - WARNING - Could not retrieve variants from source file in region 1:95709610-95710129. Error was invalid region `1:95709611-95710129`
[2016-04-15T02:36Z] 2016-04-14 19:36:46 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:36:46,080 - WARNING - Could not retrieve variants from source file in region 1:94639236-94639637. Error was invalid region `1:94639237-94639637`
[2016-04-15T02:36Z] 2016-04-14 19:36:46 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:36:46,084 - WARNING - Could not retrieve variants from source file in region 1:94578337-94578738. Error was invalid region `1:94578338-94578738`
[2016-04-15T02:36Z] 2016-04-14 19:36:46 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:36:46,094 - WARNING - Could not retrieve variants from source file in region 1:95709610-95710129. Error was invalid region `1:95709611-95710129`
[2016-04-15T02:36Z] 2016-04-14 19:36:47 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:36:47,318 - WARNING - Could not retrieve variants from source file in region 1:99127181-99127582. Error was invalid region `1:99127182-99127582`
[2016-04-15T02:36Z] 2016-04-14 19:36:48 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:36:48,481 - WARNING - Could not retrieve variants from source file in region 1:94639236-94639637. Error was invalid region `1:94639237-94639637`
[2016-04-15T02:36Z] 2016-04-14 19:36:49 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:36:49,164 - WARNING - Could not retrieve variants from source file in region 1:108185090-108185499. Error was invalid region `1:108185091-108185499`
[2016-04-15T02:36Z] 2016-04-14 19:36:49 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:36:49,548 - WARNING - Could not retrieve variants from source file in region 1:94578337-94578738. Error was invalid region `1:94578338-94578738`
[2016-04-15T02:36Z] 2016-04-14 19:36:50 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:36:50,067 - WARNING - Could not retrieve variants from source file in region 1:93719859-93736745. Error was invalid region `1:93719860-93736745`
[2016-04-15T02:36Z] 2016-04-14 19:36:50 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:36:50,484 - WARNING - Could not retrieve variants from source file in region 1:100575722-100599057. Error was invalid region `1:100575723-100599057`
[2016-04-15T02:36Z] 2016-04-14 19:36:50 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:36:50,562 - WARNING - Could not retrieve variants from source file in region 1:95709610-95710129. Error was invalid region `1:95709611-95710129`
[2016-04-15T02:36Z] 2016-04-14 19:36:50 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:36:50,645 - WARNING - Could not retrieve variants from source file in region 1:99729879-99730280. Error was invalid region `1:99729880-99730280`
[2016-04-15T02:36Z] 2016-04-14 19:36:50 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:36:50,779 - WARNING - Could not retrieve variants from source file in region 1:101203487-101204017. Error was invalid region `1:101203488-101204017`
[2016-04-15T02:36Z] 2016-04-14 19:36:51 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:36:51,485 - WARNING - Could not retrieve variants from source file in region 1:99127181-99127582. Error was invalid region `1:99127182-99127582`
[2016-04-15T02:36Z] 2016-04-14 19:36:52 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:36:52,721 - WARNING - Could not retrieve variants from source file in region 1:93307697-93309043. Error was invalid region `1:93307698-93309043`
[2016-04-15T02:36Z] 2016-04-14 19:36:53 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:36:53,429 - WARNING - Could not retrieve variants from source file in region 1:108185090-108185499. Error was invalid region `1:108185091-108185499`
[2016-04-15T02:36Z] 2016-04-14 19:36:54 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:36:54,642 - WARNING - Could not retrieve variants from source file in region 1:100575722-100599057. Error was invalid region `1:100575723-100599057`
[2016-04-15T02:36Z] 2016-04-14 19:36:55 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:36:55,091 - WARNING - Could not retrieve variants from source file in region 1:101203487-101204017. Error was invalid region `1:101203488-101204017`
[2016-04-15T02:36Z] 2016-04-14 19:36:56 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:36:56,829 - WARNING - Could not retrieve variants from source file in region 1:99418436-99418837. Error was invalid region `1:99418437-99418837`
[2016-04-15T02:36Z] 2016-04-14 19:36:59 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:36:59,230 - WARNING - Could not retrieve variants from source file in region 1:100575722-100599057. Error was invalid region `1:100575723-100599057`
[2016-04-15T02:36Z] 2016-04-14 19:36:59 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:36:59,525 - WARNING - Could not retrieve variants from source file in region 1:93719859-93736745. Error was invalid region `1:93719860-93736745`
[2016-04-15T02:37Z] 2016-04-14 19:37:01 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:37:01,429 - WARNING - Could not retrieve variants from source file in region 1:99418436-99418837. Error was invalid region `1:99418437-99418837`
[2016-04-15T02:37Z] 2016-04-14 19:37:01 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:37:01,494 - WARNING - Could not retrieve variants from source file in region 1:104116202-104116603. Error was invalid region `1:104116203-104116603`
[2016-04-15T02:37Z] 2016-04-14 19:37:03 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:37:03,558 - WARNING - Could not retrieve variants from source file in region 1:98348674-98349075. Error was invalid region `1:98348675-98349075`
[2016-04-15T02:37Z] 2016-04-14 19:37:04 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:37:04,477 - WARNING - Could not retrieve variants from source file in region 1:100326815-100358293. Error was invalid region `1:100326816-100358293`
[2016-04-15T02:37Z] 2016-04-14 19:37:04 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:37:04,559 - WARNING - Could not retrieve variants from source file in region 1:100950222-100951109. Error was invalid region `1:100950223-100951109`
[2016-04-15T02:37Z] 2016-04-14 19:37:06 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:37:06,236 - WARNING - Could not retrieve variants from source file in region 1:99418436-99418837. Error was invalid region `1:99418437-99418837`
[2016-04-15T02:37Z] 2016-04-14 19:37:06 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:37:06,643 - WARNING - Could not retrieve variants from source file in region 1:98164880-98186419. Error was invalid region `1:98164881-98186419`
[2016-04-15T02:37Z] 2016-04-14 19:37:08 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:37:08,615 - WARNING - Could not retrieve variants from source file in region 1:98348674-98349075. Error was invalid region `1:98348675-98349075`
[2016-04-15T02:37Z] 2016-04-14 19:37:09 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:37:09,445 - WARNING - Could not retrieve variants from source file in region 1:99225416-99225817. Error was invalid region `1:99225417-99225817`
[2016-04-15T02:37Z] 2016-04-14 19:37:11 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:37:11,372 - WARNING - Could not retrieve variants from source file in region 1:108121112-108121513. Error was invalid region `1:108121113-108121513`
[2016-04-15T02:37Z] 2016-04-14 19:37:12 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:37:12,990 - WARNING - Could not retrieve variants from source file in region 1:107979185-107979586. Error was invalid region `1:107979186-107979586`
[2016-04-15T02:37Z] 2016-04-14 19:37:14 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:37:14,693 - WARNING - Could not retrieve variants from source file in region 1:99225416-99225817. Error was invalid region `1:99225417-99225817`
[2016-04-15T02:37Z] 2016-04-14 19:37:15 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:37:15,781 - WARNING - Could not retrieve variants from source file in region 1:99225416-99225817. Error was invalid region `1:99225417-99225817`
[2016-04-15T02:37Z] 2016-04-14 19:37:16 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:37:16,093 - WARNING - Could not retrieve variants from source file in region 1:100950222-100951109. Error was invalid region `1:100950223-100951109`
[2016-04-15T02:37Z] 2016-04-14 19:37:17 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:37:17,046 - WARNING - Could not retrieve variants from source file in region 1:101004879-101005280. Error was invalid region `1:101004880-101005280`
[2016-04-15T02:37Z] 2016-04-14 19:37:17 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:37:17,080 - WARNING - Could not retrieve variants from source file in region 1:100817967-100818654. Error was invalid region `1:100817968-100818654`
[2016-04-15T02:37Z] 2016-04-14 19:37:17 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:37:17,092 - WARNING - Could not retrieve variants from source file in region 1:103379707-103380108. Error was invalid region `1:103379708-103380108`
[2016-04-15T02:37Z] 2016-04-14 19:37:17 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:37:17,577 - WARNING - Could not retrieve variants from source file in region 1:100203437-100203883. Error was invalid region `1:100203438-100203883`
[2016-04-15T02:37Z] 2016-04-14 19:37:17 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:37:17,828 - WARNING - Could not retrieve variants from source file in region 1:107979185-107979586. Error was invalid region `1:107979186-107979586`
[2016-04-15T02:37Z] 2016-04-14 19:37:18 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:37:18,658 - WARNING - Could not retrieve variants from source file in region 1:103352240-103354618. Error was invalid region `1:103352241-103354618`
[2016-04-15T02:37Z] 2016-04-14 19:37:19 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:37:19,304 - WARNING - Could not retrieve variants from source file in region 1:100203437-100203883. Error was invalid region `1:100203438-100203883`
[2016-04-15T02:37Z] 2016-04-14 19:37:21 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:37:21,509 - WARNING - Could not retrieve variants from source file in region 1:97981184-97981585. Error was invalid region `1:97981185-97981585`
[2016-04-15T02:37Z] 2016-04-14 19:37:22 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:37:22,869 - WARNING - Could not retrieve variants from source file in region 1:101004879-101005280. Error was invalid region `1:101004880-101005280`
[2016-04-15T02:37Z] 2016-04-14 19:37:22 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:37:22,953 - WARNING - Could not retrieve variants from source file in region 1:100817967-100818654. Error was invalid region `1:100817968-100818654`
[2016-04-15T02:37Z] 2016-04-14 19:37:23 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:37:23,008 - WARNING - Could not retrieve variants from source file in region 1:103379707-103380108. Error was invalid region `1:103379708-103380108`
[2016-04-15T02:37Z] 2016-04-14 19:37:23 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:37:23,342 - WARNING - Could not retrieve variants from source file in region 1:107979185-107979586. Error was invalid region `1:107979186-107979586`
[2016-04-15T02:37Z] 2016-04-14 19:37:23 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:37:23,823 - WARNING - Could not retrieve variants from source file in region 1:102269712-102278505. Error was invalid region `1:102269713-102278505`
[2016-04-15T02:37Z] 2016-04-14 19:37:29 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:37:29,060 - WARNING - Could not retrieve variants from source file in region 1:97915413-97915814. Error was invalid region `1:97915414-97915814`
[2016-04-15T02:37Z] 2016-04-14 19:37:29 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:37:29,531 - WARNING - Could not retrieve variants from source file in region 1:97915413-97915814. Error was invalid region `1:97915414-97915814`
[2016-04-15T02:37Z] 2016-04-14 19:37:29 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:37:29,670 - WARNING - Could not retrieve variants from source file in region 1:103352240-103354618. Error was invalid region `1:103352241-103354618`
[2016-04-15T02:37Z] 2016-04-14 19:37:29 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:37:29,749 - WARNING - Could not retrieve variants from source file in region 1:100671849-100672250. Error was invalid region `1:100671850-100672250`
[2016-04-15T02:37Z] 2016-04-14 19:37:29 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:37:29,949 - WARNING - Could not retrieve variants from source file in region 1:104166285-104166686. Error was invalid region `1:104166286-104166686`
[2016-04-15T02:37Z] 2016-04-14 19:37:31 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:37:31,244 - WARNING - Could not retrieve variants from source file in region 1:104076251-104076657. Error was invalid region `1:104076252-104076657`
[2016-04-15T02:37Z] 2016-04-14 19:37:31 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:37:31,315 - WARNING - Could not retrieve variants from source file in region 1:100671849-100672250. Error was invalid region `1:100671850-100672250`
[2016-04-15T02:37Z] 2016-04-14 19:37:34 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:37:34,064 - WARNING - Could not retrieve variants from source file in region 1:100671849-100672250. Error was invalid region `1:100671850-100672250`
[2016-04-15T02:37Z] 2016-04-14 19:37:37 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:37:37,318 - WARNING - Could not retrieve variants from source file in region 1:103405681-103406082. Error was invalid region `1:103405682-103406082`
[2016-04-15T02:37Z] ['bcbio-variation-recall', 'square', '-Xms750m', '-Xmx7280m', '-XX:+UseSerialGC', '-c', 16, '-r', u'1:108994812-143767848', '--caller', 'platypus', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/1/Batch1-1_108994811_143767848.vcf.gz', '/mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/1/Batch1-1_108994811_143767848.vcf-inputs.txt'] in region: 1:108994812-143767848
[2016-04-15T02:37Z] 2016-04-14 19:37:53 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:37:53,013 - WARNING - Could not retrieve variants from source file in region 1:109440004-109486386. Error was invalid region `1:109440005-109486386`
[2016-04-15T02:37Z] 2016-04-14 19:37:53 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:37:53,946 - WARNING - Could not retrieve variants from source file in region 1:110998643-110999044. Error was invalid region `1:110998644-110999044`
[2016-04-15T02:37Z] 2016-04-14 19:37:54 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:37:54,218 - WARNING - Could not retrieve variants from source file in region 1:118420241-118420642. Error was invalid region `1:118420242-118420642`
[2016-04-15T02:37Z] 2016-04-14 19:37:54 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:37:54,560 - WARNING - Could not retrieve variants from source file in region 1:109656735-109657136. Error was invalid region `1:109656736-109657136`
[2016-04-15T02:37Z] 2016-04-14 19:37:54 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:37:54,896 - WARNING - Could not retrieve variants from source file in region 1:115829102-115829503. Error was invalid region `1:115829103-115829503`
[2016-04-15T02:37Z] 2016-04-14 19:37:54 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:37:54,969 - WARNING - Could not retrieve variants from source file in region 1:118565742-118583598. Error was invalid region `1:118565743-118583598`
[2016-04-15T02:37Z] 2016-04-14 19:37:55 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:37:55,180 - WARNING - Could not retrieve variants from source file in region 1:109704407-109704808. Error was invalid region `1:109704408-109704808`
[2016-04-15T02:37Z] 2016-04-14 19:37:55 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:37:55,413 - WARNING - Could not retrieve variants from source file in region 1:119624785-119625186. Error was invalid region `1:119624786-119625186`
[2016-04-15T02:37Z] 2016-04-14 19:37:55 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:37:55,546 - WARNING - Could not retrieve variants from source file in region 1:114377357-114377758. Error was invalid region `1:114377358-114377758`
[2016-04-15T02:37Z] 2016-04-14 19:37:55 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:37:55,577 - WARNING - Could not retrieve variants from source file in region 1:120925452-120925853. Error was invalid region `1:120925453-120925853`
[2016-04-15T02:38Z] 2016-04-14 19:38:02 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:38:02,122 - WARNING - Could not retrieve variants from source file in region 1:118420241-118420642. Error was invalid region `1:118420242-118420642`
[2016-04-15T02:38Z] 2016-04-14 19:38:02 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:38:02,290 - WARNING - Could not retrieve variants from source file in region 1:110148763-110171086. Error was invalid region `1:110148764-110171086`
[2016-04-15T02:38Z] 2016-04-14 19:38:03 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:38:03,095 - WARNING - Could not retrieve variants from source file in region 1:112298371-112309521. Error was invalid region `1:112298372-112309521`
[2016-04-15T02:38Z] 2016-04-14 19:38:03 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:38:03,739 - WARNING - Could not retrieve variants from source file in region 1:119575607-119576008. Error was invalid region `1:119575608-119576008`
[2016-04-15T02:38Z] 2016-04-14 19:38:03 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:38:03,813 - WARNING - Could not retrieve variants from source file in region 1:109656735-109657136. Error was invalid region `1:109656736-109657136`
[2016-04-15T02:38Z] 2016-04-14 19:38:03 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:38:03,915 - WARNING - Could not retrieve variants from source file in region 1:109704407-109704808. Error was invalid region `1:109704408-109704808`
[2016-04-15T02:38Z] 2016-04-14 19:38:04 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:38:04,312 - WARNING - Could not retrieve variants from source file in region 1:120925452-120925853. Error was invalid region `1:120925453-120925853`
[2016-04-15T02:38Z] 2016-04-14 19:38:04 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:38:04,525 - WARNING - Could not retrieve variants from source file in region 1:118565742-118583598. Error was invalid region `1:118565743-118583598`
[2016-04-15T02:38Z] 2016-04-14 19:38:04 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:38:04,846 - WARNING - Could not retrieve variants from source file in region 1:109440004-109486386. Error was invalid region `1:109440005-109486386`
[2016-04-15T02:38Z] 2016-04-14 19:38:05 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:38:05,061 - WARNING - Could not retrieve variants from source file in region 1:115829102-115829503. Error was invalid region `1:115829103-115829503`
[2016-04-15T02:38Z] 2016-04-14 19:38:05 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:38:05,124 - WARNING - Could not retrieve variants from source file in region 1:114377357-114377758. Error was invalid region `1:114377358-114377758`
[2016-04-15T02:38Z] 2016-04-14 19:38:05 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:38:05,167 - WARNING - Could not retrieve variants from source file in region 1:117529247-117561119. Error was invalid region `1:117529248-117561119`
[2016-04-15T02:38Z] 2016-04-14 19:38:08 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:38:08,175 - WARNING - Could not retrieve variants from source file in region 1:118420241-118420642. Error was invalid region `1:118420242-118420642`
[2016-04-15T02:38Z] 2016-04-14 19:38:08 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:38:08,318 - WARNING - Could not retrieve variants from source file in region 1:110148763-110171086. Error was invalid region `1:110148764-110171086`
[2016-04-15T02:38Z] 2016-04-14 19:38:11 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:38:11,034 - WARNING - Could not retrieve variants from source file in region 1:119575607-119576008. Error was invalid region `1:119575608-119576008`
[2016-04-15T02:38Z] 2016-04-14 19:38:11 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:38:11,665 - WARNING - Could not retrieve variants from source file in region 1:109656735-109657136. Error was invalid region `1:109656736-109657136`
[2016-04-15T02:38Z] 2016-04-14 19:38:11 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:38:11,800 - WARNING - Could not retrieve variants from source file in region 1:109704407-109704808. Error was invalid region `1:109704408-109704808`
[2016-04-15T02:38Z] 2016-04-14 19:38:12 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:38:12,289 - WARNING - Could not retrieve variants from source file in region 1:120925452-120925853. Error was invalid region `1:120925453-120925853`
[2016-04-15T02:38Z] 2016-04-14 19:38:12 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:38:12,517 - WARNING - Could not retrieve variants from source file in region 1:119624785-119625186. Error was invalid region `1:119624786-119625186`
[2016-04-15T02:38Z] 2016-04-14 19:38:12 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:38:12,651 - WARNING - Could not retrieve variants from source file in region 1:118565742-118583598. Error was invalid region `1:118565743-118583598`
[2016-04-15T02:38Z] 2016-04-14 19:38:12 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:38:12,781 - WARNING - Could not retrieve variants from source file in region 1:114377357-114377758. Error was invalid region `1:114377358-114377758`
[2016-04-15T02:38Z] 2016-04-14 19:38:12 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:38:12,840 - WARNING - Could not retrieve variants from source file in region 1:117529247-117561119. Error was invalid region `1:117529248-117561119`
[2016-04-15T02:38Z] 2016-04-14 19:38:12 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:38:12,874 - WARNING - Could not retrieve variants from source file in region 1:115829102-115829503. Error was invalid region `1:115829103-115829503`
[2016-04-15T02:38Z] 2016-04-14 19:38:24 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:38:24,862 - WARNING - Could not retrieve variants from source file in region 1:117655877-117659542. Error was invalid region `1:117655878-117659542`
[2016-04-15T02:38Z] 2016-04-14 19:38:27 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:38:27,380 - WARNING - Could not retrieve variants from source file in region 1:118644219-118644620. Error was invalid region `1:118644220-118644620`
[2016-04-15T02:38Z] 2016-04-14 19:38:27 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:38:27,883 - WARNING - Could not retrieve variants from source file in region 1:112269661-112270062. Error was invalid region `1:112269662-112270062`
[2016-04-15T02:38Z] 2016-04-14 19:38:28 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:38:28,244 - WARNING - Could not retrieve variants from source file in region 1:109935114-109940693. Error was invalid region `1:109935115-109940693`
[2016-04-15T02:38Z] 2016-04-14 19:38:28 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:38:28,571 - WARNING - Could not retrieve variants from source file in region 1:109264818-109273646. Error was invalid region `1:109264819-109273646`
[2016-04-15T02:38Z] 2016-04-14 19:38:28 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:38:28,581 - WARNING - Could not retrieve variants from source file in region 1:120345018-120345419. Error was invalid region `1:120345019-120345419`
[2016-04-15T02:38Z] 2016-04-14 19:38:28 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:38:28,822 - WARNING - Could not retrieve variants from source file in region 1:110950066-110950629. Error was invalid region `1:110950067-110950629`
[2016-04-15T02:38Z] 2016-04-14 19:38:29 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:38:29,482 - WARNING - Could not retrieve variants from source file in region 1:120854317-120854718. Error was invalid region `1:120854318-120854718`
[2016-04-15T02:38Z] 2016-04-14 19:38:29 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:38:29,802 - WARNING - Could not retrieve variants from source file in region 1:114225095-114225496. Error was invalid region `1:114225096-114225496`
[2016-04-15T02:38Z] 2016-04-14 19:38:30 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:38:30,402 - WARNING - Could not retrieve variants from source file in region 1:117484220-117487901. Error was invalid region `1:117484221-117487901`
[2016-04-15T02:38Z] 2016-04-14 19:38:30 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:38:30,897 - WARNING - Could not retrieve variants from source file in region 1:118693006-118693407. Error was invalid region `1:118693007-118693407`
[2016-04-15T02:38Z] 2016-04-14 19:38:32 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:38:32,773 - WARNING - Could not retrieve variants from source file in region 1:118644219-118644620. Error was invalid region `1:118644220-118644620`
[2016-04-15T02:38Z] 2016-04-14 19:38:33 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:38:33,170 - WARNING - Could not retrieve variants from source file in region 1:112269661-112270062. Error was invalid region `1:112269662-112270062`
[2016-04-15T02:38Z] 2016-04-14 19:38:34 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:38:34,717 - WARNING - Could not retrieve variants from source file in region 1:110950066-110950629. Error was invalid region `1:110950067-110950629`
[2016-04-15T02:38Z] 2016-04-14 19:38:35 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:38:35,369 - WARNING - Could not retrieve variants from source file in region 1:115604587-115604988. Error was invalid region `1:115604588-115604988`
[2016-04-15T02:38Z] 2016-04-14 19:38:35 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:38:35,452 - WARNING - Could not retrieve variants from source file in region 1:114225095-114225496. Error was invalid region `1:114225096-114225496`
[2016-04-15T02:38Z] 2016-04-14 19:38:35 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:38:35,648 - WARNING - Could not retrieve variants from source file in region 1:118693006-118693407. Error was invalid region `1:118693007-118693407`
[2016-04-15T02:38Z] 2016-04-14 19:38:37 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:38:37,273 - WARNING - Could not retrieve variants from source file in region 1:118644219-118644620. Error was invalid region `1:118644220-118644620`
[2016-04-15T02:38Z] 2016-04-14 19:38:38 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:38:38,048 - WARNING - Could not retrieve variants from source file in region 1:112269661-112270062. Error was invalid region `1:112269662-112270062`
[2016-04-15T02:38Z] 2016-04-14 19:38:38 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:38:38,599 - WARNING - Could not retrieve variants from source file in region 1:120345018-120345419. Error was invalid region `1:120345019-120345419`
[2016-04-15T02:38Z] 2016-04-14 19:38:40 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:38:40,490 - WARNING - Could not retrieve variants from source file in region 1:120854317-120854718. Error was invalid region `1:120854318-120854718`
[2016-04-15T02:38Z] 2016-04-14 19:38:41 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:38:41,079 - WARNING - Could not retrieve variants from source file in region 1:115604587-115604988. Error was invalid region `1:115604588-115604988`
[2016-04-15T02:38Z] 2016-04-14 19:38:41 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:38:41,110 - WARNING - Could not retrieve variants from source file in region 1:117484220-117487901. Error was invalid region `1:117484221-117487901`
[2016-04-15T02:38Z] 2016-04-14 19:38:41 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:38:41,322 - WARNING - Could not retrieve variants from source file in region 1:114225095-114225496. Error was invalid region `1:114225096-114225496`
[2016-04-15T02:38Z] 2016-04-14 19:38:50 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:38:50,141 - WARNING - Could not retrieve variants from source file in region 1:110924142-110924543. Error was invalid region `1:110924143-110924543`
[2016-04-15T02:38Z] 2016-04-14 19:38:51 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:38:51,350 - WARNING - Could not retrieve variants from source file in region 1:113240500-113255579. Error was invalid region `1:113240501-113255579`
[2016-04-15T02:38Z] 2016-04-14 19:38:51 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:38:51,411 - WARNING - Could not retrieve variants from source file in region 1:114196284-114196685. Error was invalid region `1:114196285-114196685`
[2016-04-15T02:38Z] 2016-04-14 19:38:52 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:38:52,180 - WARNING - Could not retrieve variants from source file in region 1:109884564-109897293. Error was invalid region `1:109884565-109897293`
[2016-04-15T02:38Z] 2016-04-14 19:38:52 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:38:52,825 - WARNING - Could not retrieve variants from source file in region 1:120285335-120285736. Error was invalid region `1:120285336-120285736`
[2016-04-15T02:38Z] 2016-04-14 19:38:53 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:38:53,498 - WARNING - Could not retrieve variants from source file in region 1:109735087-109759966. Error was invalid region `1:109735088-109759966`
[2016-04-15T02:38Z] 2016-04-14 19:38:54 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:38:54,890 - WARNING - Could not retrieve variants from source file in region 1:113656881-113657282. Error was invalid region `1:113656882-113657282`
[2016-04-15T02:38Z] 2016-04-14 19:38:55 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:38:55,057 - WARNING - Could not retrieve variants from source file in region 1:115575812-115576213. Error was invalid region `1:115575813-115576213`
[2016-04-15T02:38Z] 2016-04-14 19:38:55 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:38:55,422 - WARNING - Could not retrieve variants from source file in region 1:117297116-117297517. Error was invalid region `1:117297117-117297517`
[2016-04-15T02:38Z] 2016-04-14 19:38:56 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:38:56,234 - WARNING - Could not retrieve variants from source file in region 1:114196284-114196685. Error was invalid region `1:114196285-114196685`
[2016-04-15T02:38Z] 2016-04-14 19:38:56 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:38:56,964 - WARNING - Could not retrieve variants from source file in region 1:109884564-109897293. Error was invalid region `1:109884565-109897293`
[2016-04-15T02:38Z] 2016-04-14 19:38:57 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:38:57,952 - WARNING - Could not retrieve variants from source file in region 1:120285335-120285736. Error was invalid region `1:120285336-120285736`
[2016-04-15T02:39Z] 2016-04-14 19:39:00 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:39:00,359 - WARNING - Could not retrieve variants from source file in region 1:114680329-114680730. Error was invalid region `1:114680330-114680730`
[2016-04-15T02:39Z] 2016-04-14 19:39:01 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:39:01,375 - WARNING - Could not retrieve variants from source file in region 1:115575812-115576213. Error was invalid region `1:115575813-115576213`
[2016-04-15T02:39Z] 2016-04-14 19:39:01 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:39:01,919 - WARNING - Could not retrieve variants from source file in region 1:113656881-113657282. Error was invalid region `1:113656882-113657282`
[2016-04-15T02:39Z] 2016-04-14 19:39:02 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:39:02,059 - WARNING - Could not retrieve variants from source file in region 1:113240500-113255579. Error was invalid region `1:113240501-113255579`
[2016-04-15T02:39Z] 2016-04-14 19:39:02 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:39:02,347 - WARNING - Could not retrieve variants from source file in region 1:109884564-109897293. Error was invalid region `1:109884565-109897293`
[2016-04-15T02:39Z] 2016-04-14 19:39:02 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:39:02,612 - WARNING - Could not retrieve variants from source file in region 1:120285335-120285736. Error was invalid region `1:120285336-120285736`
[2016-04-15T02:39Z] 2016-04-14 19:39:05 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:39:05,168 - WARNING - Could not retrieve variants from source file in region 1:114680329-114680730. Error was invalid region `1:114680330-114680730`
[2016-04-15T02:39Z] 2016-04-14 19:39:07 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:39:07,279 - WARNING - Could not retrieve variants from source file in region 1:115575812-115576213. Error was invalid region `1:115575813-115576213`
[2016-04-15T02:39Z] 2016-04-14 19:39:08 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:39:08,944 - WARNING - Could not retrieve variants from source file in region 1:113656881-113657282. Error was invalid region `1:113656882-113657282`
[2016-04-15T02:39Z] 2016-04-14 19:39:15 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:39:15,605 - WARNING - Could not retrieve variants from source file in region 1:110882233-110884626. Error was invalid region `1:110882234-110884626`
[2016-04-15T02:39Z] 2016-04-14 19:39:17 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:39:17,500 - WARNING - Could not retrieve variants from source file in region 1:120056947-120057436. Error was invalid region `1:120056948-120057436`
[2016-04-15T02:39Z] 2016-04-14 19:39:19 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:39:19,073 - WARNING - Could not retrieve variants from source file in region 1:114515506-114515907. Error was invalid region `1:114515507-114515907`
[2016-04-15T02:39Z] 2016-04-14 19:39:19 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:39:19,535 - WARNING - Could not retrieve variants from source file in region 1:113456335-113456736. Error was invalid region `1:113456336-113456736`
[2016-04-15T02:39Z] 2016-04-14 19:39:19 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:39:19,926 - WARNING - Could not retrieve variants from source file in region 1:114424390-114439141. Error was invalid region `1:114424391-114439141`
[2016-04-15T02:39Z] 2016-04-14 19:39:20 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:39:20,148 - WARNING - Could not retrieve variants from source file in region 1:119923513-119928573. Error was invalid region `1:119923514-119928573`
[2016-04-15T02:39Z] 2016-04-14 19:39:21 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:39:21,946 - WARNING - Could not retrieve variants from source file in region 1:117122074-117122478. Error was invalid region `1:117122075-117122478`
[2016-04-15T02:39Z] 2016-04-14 19:39:22 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:39:22,797 - WARNING - Could not retrieve variants from source file in region 1:113456335-113456736. Error was invalid region `1:113456336-113456736`
[2016-04-15T02:39Z] 2016-04-14 19:39:23 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:39:23,113 - WARNING - Could not retrieve variants from source file in region 1:119923513-119928573. Error was invalid region `1:119923514-119928573`
[2016-04-15T02:39Z] 2016-04-14 19:39:23 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:39:23,575 - WARNING - Could not retrieve variants from source file in region 1:114948070-114973619. Error was invalid region `1:114948071-114973619`
[2016-04-15T02:39Z] 2016-04-14 19:39:25 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:39:25,149 - WARNING - Could not retrieve variants from source file in region 1:120436540-120478188. Error was invalid region `1:120436541-120478188`
[2016-04-15T02:39Z] 2016-04-14 19:39:25 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:39:25,372 - WARNING - Could not retrieve variants from source file in region 1:114515506-114515907. Error was invalid region `1:114515507-114515907`
[2016-04-15T02:39Z] 2016-04-14 19:39:25 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:39:25,759 - WARNING - Could not retrieve variants from source file in region 1:115399876-115400277. Error was invalid region `1:115399877-115400277`
[2016-04-15T02:39Z] 2016-04-14 19:39:25 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:39:25,951 - WARNING - Could not retrieve variants from source file in region 1:111956886-111992285. Error was invalid region `1:111956887-111992285`
[2016-04-15T02:39Z] 2016-04-14 19:39:28 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:39:28,085 - WARNING - Could not retrieve variants from source file in region 1:114424390-114439141. Error was invalid region `1:114424391-114439141`
[2016-04-15T02:39Z] 2016-04-14 19:39:30 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:39:30,157 - WARNING - Could not retrieve variants from source file in region 1:115231043-115236247. Error was invalid region `1:115231044-115236247`
[2016-04-15T02:39Z] 2016-04-14 19:39:30 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:39:30,405 - WARNING - Could not retrieve variants from source file in region 1:114515506-114515907. Error was invalid region `1:114515507-114515907`
[2016-04-15T02:39Z] 2016-04-14 19:39:30 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:39:30,853 - WARNING - Could not retrieve variants from source file in region 1:111956886-111992285. Error was invalid region `1:111956887-111992285`
[2016-04-15T02:39Z] 2016-04-14 19:39:34 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:39:34,885 - WARNING - Could not retrieve variants from source file in region 1:120436540-120478188. Error was invalid region `1:120436541-120478188`
[2016-04-15T02:39Z] 2016-04-14 19:39:35 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:39:35,342 - WARNING - Could not retrieve variants from source file in region 1:115231043-115236247. Error was invalid region `1:115231044-115236247`
[2016-04-15T02:39Z] 2016-04-14 19:39:37 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:39:37,760 - WARNING - Could not retrieve variants from source file in region 1:116310756-116311157. Error was invalid region `1:116310757-116311157`
[2016-04-15T02:39Z] 2016-04-14 19:39:38 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:39:38,053 - WARNING - Could not retrieve variants from source file in region 1:116569319-116569720. Error was invalid region `1:116569320-116569720`
[2016-04-15T02:39Z] 2016-04-14 19:39:41 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:39:41,209 - WARNING - Could not retrieve variants from source file in region 1:112991487-112999417. Error was invalid region `1:112991488-112999417`
[2016-04-15T02:39Z] 2016-04-14 19:39:42 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:39:42,455 - WARNING - Could not retrieve variants from source file in region 1:116243666-116244067. Error was invalid region `1:116243667-116244067`
[2016-04-15T02:39Z] 2016-04-14 19:39:43 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:39:43,612 - WARNING - Could not retrieve variants from source file in region 1:116569319-116569720. Error was invalid region `1:116569320-116569720`
[2016-04-15T02:39Z] 2016-04-14 19:39:43 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:39:43,628 - WARNING - Could not retrieve variants from source file in region 1:116310756-116311157. Error was invalid region `1:116310757-116311157`
[2016-04-15T02:39Z] 2016-04-14 19:39:43 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:39:43,698 - WARNING - Could not retrieve variants from source file in region 1:116916434-116916836. Error was invalid region `1:116916435-116916836`
[2016-04-15T02:39Z] 2016-04-14 19:39:44 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:39:44,528 - WARNING - Could not retrieve variants from source file in region 1:116916434-116916836. Error was invalid region `1:116916435-116916836`
[2016-04-15T02:39Z] 2016-04-14 19:39:44 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:39:44,625 - WARNING - Could not retrieve variants from source file in region 1:116916434-116916836. Error was invalid region `1:116916435-116916836`
[2016-04-15T02:39Z] 2016-04-14 19:39:44 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:39:44,712 - WARNING - Could not retrieve variants from source file in region 1:111890981-111891382. Error was invalid region `1:111890982-111891382`
[2016-04-15T02:39Z] 2016-04-14 19:39:45 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:39:45,194 - WARNING - Could not retrieve variants from source file in region 1:110766243-110766644. Error was invalid region `1:110766244-110766644`
[2016-04-15T02:39Z] 2016-04-14 19:39:45 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:39:45,453 - WARNING - Could not retrieve variants from source file in region 1:112991487-112999417. Error was invalid region `1:112991488-112999417`
[2016-04-15T02:39Z] 2016-04-14 19:39:46 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:39:46,913 - WARNING - Could not retrieve variants from source file in region 1:116243666-116244067. Error was invalid region `1:116243667-116244067`
[2016-04-15T02:39Z] 2016-04-14 19:39:48 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:39:48,664 - WARNING - Could not retrieve variants from source file in region 1:116569319-116569720. Error was invalid region `1:116569320-116569720`
[2016-04-15T02:39Z] 2016-04-14 19:39:49 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:39:49,977 - WARNING - Could not retrieve variants from source file in region 1:111890981-111891382. Error was invalid region `1:111890982-111891382`
[2016-04-15T02:39Z] 2016-04-14 19:39:51 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:39:51,042 - WARNING - Could not retrieve variants from source file in region 1:112991487-112999417. Error was invalid region `1:112991488-112999417`
[2016-04-15T02:39Z] 2016-04-14 19:39:51 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:39:51,230 - WARNING - Could not retrieve variants from source file in region 1:116243666-116244067. Error was invalid region `1:116243667-116244067`
[2016-04-15T02:39Z] 2016-04-14 19:39:53 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:39:53,262 - WARNING - Could not retrieve variants from source file in region 1:120378467-120387310. Error was invalid region `1:120378468-120387310`
[2016-04-15T02:39Z] 2016-04-14 19:39:54 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:39:54,923 - WARNING - Could not retrieve variants from source file in region 1:116534641-116535042. Error was invalid region `1:116534642-116535042`
[2016-04-15T02:39Z] 2016-04-14 19:39:55 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:39:55,725 - WARNING - Could not retrieve variants from source file in region 1:111890981-111891382. Error was invalid region `1:111890982-111891382`
[2016-04-15T02:39Z] 2016-04-14 19:39:57 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:39:57,823 - WARNING - Could not retrieve variants from source file in region 1:116534641-116535042. Error was invalid region `1:116534642-116535042`
[2016-04-15T02:39Z] 2016-04-14 19:39:58 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:39:58,319 - WARNING - Could not retrieve variants from source file in region 1:116206212-116206613. Error was invalid region `1:116206213-116206613`
[2016-04-15T02:39Z] 2016-04-14 19:39:59 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:39:59,243 - WARNING - Could not retrieve variants from source file in region 1:116534641-116535042. Error was invalid region `1:116534642-116535042`
[2016-04-15T02:40Z] 2016-04-14 19:40:03 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:40:03,403 - WARNING - Could not retrieve variants from source file in region 1:110738085-110738486. Error was invalid region `1:110738086-110738486`
[2016-04-15T02:40Z] 2016-04-14 19:40:04 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:40:04,398 - WARNING - Could not retrieve variants from source file in region 1:111778114-111784186. Error was invalid region `1:111778115-111784186`
[2016-04-15T02:40Z] 2016-04-14 19:40:04 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:40:04,857 - WARNING - Could not retrieve variants from source file in region 1:111060089-111061252. Error was invalid region `1:111060090-111061252`
[2016-04-15T02:40Z] 2016-04-14 19:40:05 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:40:05,210 - WARNING - Could not retrieve variants from source file in region 1:111778114-111784186. Error was invalid region `1:111778115-111784186`
[2016-04-15T02:40Z] 2016-04-14 19:40:09 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:40:09,051 - WARNING - Could not retrieve variants from source file in region 1:110466127-110466899. Error was invalid region `1:110466128-110466899`
[2016-04-15T02:40Z] 2016-04-14 19:40:12 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:40:12,527 - WARNING - Could not retrieve variants from source file in region 1:110709508-110709924. Error was invalid region `1:110709509-110709924`
[2016-04-15T02:40Z] 2016-04-14 19:40:12 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:40:12,907 - WARNING - Could not retrieve variants from source file in region 1:110709508-110709924. Error was invalid region `1:110709509-110709924`
[2016-04-15T02:40Z] 2016-04-14 19:40:13 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:40:13,091 - WARNING - Could not retrieve variants from source file in region 1:110257643-110258044. Error was invalid region `1:110257644-110258044`
[2016-04-15T02:40Z] 2016-04-14 19:40:13 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:40:13,120 - WARNING - Could not retrieve variants from source file in region 1:110709508-110709924. Error was invalid region `1:110709509-110709924`
[2016-04-15T02:40Z] 2016-04-14 19:40:13 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:40:13,405 - WARNING - Could not retrieve variants from source file in region 1:110257643-110258044. Error was invalid region `1:110257644-110258044`
[2016-04-15T02:40Z] 2016-04-14 19:40:13 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:40:13,464 - WARNING - Could not retrieve variants from source file in region 1:110201488-110201889. Error was invalid region `1:110201489-110201889`
[2016-04-15T02:40Z] 2016-04-14 19:40:16 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:40:16,482 - WARNING - Could not retrieve variants from source file in region 1:110201488-110201889. Error was invalid region `1:110201489-110201889`
[2016-04-15T02:40Z] 2016-04-14 19:40:16 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:40:16,486 - WARNING - Could not retrieve variants from source file in region 1:110201488-110201889. Error was invalid region `1:110201489-110201889`
[2016-04-15T02:40Z] ['bcbio-variation-recall', 'square', '-Xms750m', '-Xmx7280m', '-XX:+UseSerialGC', '-c', 16, '-r', u'1:143897547-159410511', '--caller', 'platypus', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/1/Batch1-1_143897546_159410511.vcf.gz', '/mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/1/Batch1-1_143897546_159410511.vcf-inputs.txt'] in region: 1:143897547-159410511
[2016-04-15T02:40Z] 2016-04-14 19:40:32 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:40:32,910 - WARNING - Could not retrieve variants from source file in region 1:158686952-158687414. Error was invalid region `1:158686953-158687414`
[2016-04-15T02:40Z] 2016-04-14 19:40:33 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:40:33,641 - WARNING - Could not retrieve variants from source file in region 1:154401468-154479861. Error was invalid region `1:154401469-154479861`
[2016-04-15T02:40Z] 2016-04-14 19:40:33 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:40:33,780 - WARNING - Could not retrieve variants from source file in region 1:155143735-155178972. Error was invalid region `1:155143736-155178972`
[2016-04-15T02:40Z] 2016-04-14 19:40:33 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:40:33,895 - WARNING - Could not retrieve variants from source file in region 1:155102936-155108477. Error was invalid region `1:155102937-155108477`
[2016-04-15T02:40Z] 2016-04-14 19:40:34 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:40:34,807 - WARNING - Could not retrieve variants from source file in region 1:150808678-150809079. Error was invalid region `1:150808679-150809079`
[2016-04-15T02:40Z] 2016-04-14 19:40:34 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:40:34,868 - WARNING - Could not retrieve variants from source file in region 1:150234446-150234847. Error was invalid region `1:150234447-150234847`
[2016-04-15T02:40Z] 2016-04-14 19:40:35 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:40:35,092 - WARNING - Could not retrieve variants from source file in region 1:159409523-159410074. Error was invalid region `1:159409524-159410074`
[2016-04-15T02:40Z] 2016-04-14 19:40:35 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:40:35,179 - WARNING - Could not retrieve variants from source file in region 1:156446692-156450930. Error was invalid region `1:156446693-156450930`
[2016-04-15T02:40Z] 2016-04-14 19:40:38 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:40:38,373 - WARNING - Could not retrieve variants from source file in region 1:157771669-157772156. Error was invalid region `1:157771670-157772156`
[2016-04-15T02:40Z] 2016-04-14 19:40:40 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:40:40,733 - WARNING - Could not retrieve variants from source file in region 1:158686952-158687414. Error was invalid region `1:158686953-158687414`
[2016-04-15T02:40Z] 2016-04-14 19:40:40 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:40:40,781 - WARNING - Could not retrieve variants from source file in region 1:158986266-159024858. Error was invalid region `1:158986267-159024858`
[2016-04-15T02:40Z] 2016-04-14 19:40:41 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:40:41,941 - WARNING - Could not retrieve variants from source file in region 1:154401468-154479861. Error was invalid region `1:154401469-154479861`
[2016-04-15T02:40Z] 2016-04-14 19:40:41 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:40:41,955 - WARNING - Could not retrieve variants from source file in region 1:153509681-153534217. Error was invalid region `1:153509682-153534217`
[2016-04-15T02:40Z] 2016-04-14 19:40:42 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:40:42,039 - WARNING - Could not retrieve variants from source file in region 1:155102936-155108477. Error was invalid region `1:155102937-155108477`
[2016-04-15T02:40Z] 2016-04-14 19:40:42 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:40:42,245 - WARNING - Could not retrieve variants from source file in region 1:155143735-155178972. Error was invalid region `1:155143736-155178972`
[2016-04-15T02:40Z] 2016-04-14 19:40:42 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:40:42,477 - WARNING - Could not retrieve variants from source file in region 1:150808678-150809079. Error was invalid region `1:150808679-150809079`
[2016-04-15T02:40Z] 2016-04-14 19:40:42 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:40:42,923 - WARNING - Could not retrieve variants from source file in region 1:149224165-149224600. Error was invalid region `1:149224166-149224600`
[2016-04-15T02:40Z] 2016-04-14 19:40:42 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:40:42,928 - WARNING - Could not retrieve variants from source file in region 1:156446692-156450930. Error was invalid region `1:156446693-156450930`
[2016-04-15T02:40Z] 2016-04-14 19:40:46 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:40:46,756 - WARNING - Could not retrieve variants from source file in region 1:158986266-159024858. Error was invalid region `1:158986267-159024858`
[2016-04-15T02:40Z] 2016-04-14 19:40:48 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:40:48,952 - WARNING - Could not retrieve variants from source file in region 1:155102936-155108477. Error was invalid region `1:155102937-155108477`
[2016-04-15T02:40Z] 2016-04-14 19:40:49 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:40:49,106 - WARNING - Could not retrieve variants from source file in region 1:153509681-153534217. Error was invalid region `1:153509682-153534217`
[2016-04-15T02:40Z] 2016-04-14 19:40:50 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:40:50,044 - WARNING - Could not retrieve variants from source file in region 1:154401468-154479861. Error was invalid region `1:154401469-154479861`
[2016-04-15T02:40Z] 2016-04-14 19:40:50 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:40:50,415 - WARNING - Could not retrieve variants from source file in region 1:155143735-155178972. Error was invalid region `1:155143736-155178972`
[2016-04-15T02:40Z] 2016-04-14 19:40:51 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:40:51,291 - WARNING - Could not retrieve variants from source file in region 1:150234446-150234847. Error was invalid region `1:150234447-150234847`
[2016-04-15T02:41Z] 2016-04-14 19:41:03 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:41:03,211 - WARNING - Could not retrieve variants from source file in region 1:154744596-154745042. Error was invalid region `1:154744597-154745042`
[2016-04-15T02:41Z] 2016-04-14 19:41:06 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:41:06,087 - WARNING - Could not retrieve variants from source file in region 1:154138954-154139355. Error was invalid region `1:154138955-154139355`
[2016-04-15T02:41Z] 2016-04-14 19:41:06 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:41:06,166 - WARNING - Could not retrieve variants from source file in region 1:153410611-153431596. Error was invalid region `1:153410612-153431596`
[2016-04-15T02:41Z] 2016-04-14 19:41:06 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:41:06,957 - WARNING - Could not retrieve variants from source file in region 1:156146007-156146830. Error was invalid region `1:156146008-156146830`
[2016-04-15T02:41Z] 2016-04-14 19:41:07 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:41:07,418 - WARNING - Could not retrieve variants from source file in region 1:150771492-150771893. Error was invalid region `1:150771493-150771893`
[2016-04-15T02:41Z] 2016-04-14 19:41:07 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:41:07,506 - WARNING - Could not retrieve variants from source file in region 1:156639542-156646858. Error was invalid region `1:156639543-156646858`
[2016-04-15T02:41Z] 2016-04-14 19:41:08 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:41:08,245 - WARNING - Could not retrieve variants from source file in region 1:158576898-158655226. Error was invalid region `1:158576899-158655226`
[2016-04-15T02:41Z] 2016-04-14 19:41:08 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:41:08,910 - WARNING - Could not retrieve variants from source file in region 1:154744596-154745042. Error was invalid region `1:154744597-154745042`
[2016-04-15T02:41Z] 2016-04-14 19:41:09 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:41:09,062 - WARNING - Could not retrieve variants from source file in region 1:157647578-157670480. Error was invalid region `1:157647579-157670480`
[2016-04-15T02:41Z] 2016-04-14 19:41:10 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:41:10,126 - WARNING - Could not retrieve variants from source file in region 1:156382259-156382660. Error was invalid region `1:156382260-156382660`
[2016-04-15T02:41Z] 2016-04-14 19:41:10 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:41:10,368 - WARNING - Could not retrieve variants from source file in region 1:158906605-158907006. Error was invalid region `1:158906606-158907006`
[2016-04-15T02:41Z] 2016-04-14 19:41:11 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:41:11,575 - WARNING - Could not retrieve variants from source file in region 1:154138954-154139355. Error was invalid region `1:154138955-154139355`
[2016-04-15T02:41Z] 2016-04-14 19:41:11 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:41:11,719 - WARNING - Could not retrieve variants from source file in region 1:153410611-153431596. Error was invalid region `1:153410612-153431596`
[2016-04-15T02:41Z] 2016-04-14 19:41:12 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:41:12,229 - WARNING - Could not retrieve variants from source file in region 1:154293464-154321132. Error was invalid region `1:154293465-154321132`
[2016-04-15T02:41Z] 2016-04-14 19:41:12 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:41:12,698 - WARNING - Could not retrieve variants from source file in region 1:154918141-154919270. Error was invalid region `1:154918142-154919270`
[2016-04-15T02:41Z] 2016-04-14 19:41:12 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:41:12,962 - WARNING - Could not retrieve variants from source file in region 1:150771492-150771893. Error was invalid region `1:150771493-150771893`
[2016-04-15T02:41Z] 2016-04-14 19:41:13 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:41:13,959 - WARNING - Could not retrieve variants from source file in region 1:150198828-150199313. Error was invalid region `1:150198829-150199313`
[2016-04-15T02:41Z] 2016-04-14 19:41:14 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:41:14,813 - WARNING - Could not retrieve variants from source file in region 1:159283283-159283936. Error was invalid region `1:159283284-159283936`
[2016-04-15T02:41Z] 2016-04-14 19:41:15 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:41:15,424 - WARNING - Could not retrieve variants from source file in region 1:154744596-154745042. Error was invalid region `1:154744597-154745042`
[2016-04-15T02:41Z] 2016-04-14 19:41:15 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:41:15,602 - WARNING - Could not retrieve variants from source file in region 1:148644197-148644598. Error was invalid region `1:148644198-148644598`
[2016-04-15T02:41Z] 2016-04-14 19:41:15 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:41:15,810 - WARNING - Could not retrieve variants from source file in region 1:157647578-157670480. Error was invalid region `1:157647579-157670480`
[2016-04-15T02:41Z] 2016-04-14 19:41:16 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:41:16,080 - WARNING - Could not retrieve variants from source file in region 1:158906605-158907006. Error was invalid region `1:158906606-158907006`
[2016-04-15T02:41Z] 2016-04-14 19:41:16 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:41:16,788 - WARNING - Could not retrieve variants from source file in region 1:154138954-154139355. Error was invalid region `1:154138955-154139355`
[2016-04-15T02:41Z] 2016-04-14 19:41:17 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:41:17,501 - WARNING - Could not retrieve variants from source file in region 1:153410611-153431596. Error was invalid region `1:153410612-153431596`
[2016-04-15T02:41Z] 2016-04-14 19:41:18 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:41:18,662 - WARNING - Could not retrieve variants from source file in region 1:154918141-154919270. Error was invalid region `1:154918142-154919270`
[2016-04-15T02:41Z] 2016-04-14 19:41:18 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:41:18,843 - WARNING - Could not retrieve variants from source file in region 1:150771492-150771893. Error was invalid region `1:150771493-150771893`
[2016-04-15T02:41Z] 2016-04-14 19:41:19 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:41:19,336 - WARNING - Could not retrieve variants from source file in region 1:156639542-156646858. Error was invalid region `1:156639543-156646858`
[2016-04-15T02:41Z] 2016-04-14 19:41:19 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:41:19,407 - WARNING - Could not retrieve variants from source file in region 1:150198828-150199313. Error was invalid region `1:150198829-150199313`
[2016-04-15T02:41Z] 2016-04-14 19:41:21 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:41:21,098 - WARNING - Could not retrieve variants from source file in region 1:148644197-148644598. Error was invalid region `1:148644198-148644598`
[2016-04-15T02:41Z] 2016-04-14 19:41:29 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:41:29,956 - WARNING - Could not retrieve variants from source file in region 1:154573756-154575230. Error was invalid region `1:154573757-154575230`
[2016-04-15T02:41Z] 2016-04-14 19:41:32 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:41:32,396 - WARNING - Could not retrieve variants from source file in region 1:157557490-157559312. Error was invalid region `1:157557491-157559312`
[2016-04-15T02:41Z] 2016-04-14 19:41:33 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:41:33,041 - WARNING - Could not retrieve variants from source file in region 1:158813608-158814009. Error was invalid region `1:158813609-158814009`
[2016-04-15T02:41Z] 2016-04-14 19:41:33 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:41:33,518 - WARNING - Could not retrieve variants from source file in region 1:154108176-154108577. Error was invalid region `1:154108177-154108577`
[2016-04-15T02:41Z] 2016-04-14 19:41:35 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:41:35,173 - WARNING - Could not retrieve variants from source file in region 1:154516266-154523405. Error was invalid region `1:154516267-154523405`
[2016-04-15T02:41Z] 2016-04-14 19:41:35 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:41:35,795 - WARNING - Could not retrieve variants from source file in region 1:150727328-150727729. Error was invalid region `1:150727329-150727729`
[2016-04-15T02:41Z] 2016-04-14 19:41:35 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:41:35,866 - WARNING - Could not retrieve variants from source file in region 1:158724600-158747037. Error was invalid region `1:158724601-158747037`
[2016-04-15T02:41Z] 2016-04-14 19:41:35 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:41:35,879 - WARNING - Could not retrieve variants from source file in region 1:156526176-156565239. Error was invalid region `1:156526177-156565239`
[2016-04-15T02:41Z] 2016-04-14 19:41:35 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:41:35,990 - WARNING - Could not retrieve variants from source file in region 1:154573756-154575230. Error was invalid region `1:154573757-154575230`
[2016-04-15T02:41Z] 2016-04-14 19:41:36 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:41:36,398 - WARNING - Could not retrieve variants from source file in region 1:159169430-159175544. Error was invalid region `1:159169431-159175544`
[2016-04-15T02:41Z] 2016-04-14 19:41:37 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:41:37,486 - WARNING - Could not retrieve variants from source file in region 1:148017367-148017768. Error was invalid region `1:148017368-148017768`
[2016-04-15T02:41Z] 2016-04-14 19:41:38 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:41:38,470 - WARNING - Could not retrieve variants from source file in region 1:158516931-158549701. Error was invalid region `1:158516932-158549701`
[2016-04-15T02:41Z] 2016-04-14 19:41:39 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:41:39,428 - WARNING - Could not retrieve variants from source file in region 1:154108176-154108577. Error was invalid region `1:154108177-154108577`
[2016-04-15T02:41Z] 2016-04-14 19:41:39 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:41:39,499 - WARNING - Could not retrieve variants from source file in region 1:154242904-154243305. Error was invalid region `1:154242905-154243305`
[2016-04-15T02:41Z] 2016-04-14 19:41:41 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:41:41,112 - WARNING - Could not retrieve variants from source file in region 1:156104817-156109284. Error was invalid region `1:156104818-156109284`
[2016-04-15T02:41Z] 2016-04-14 19:41:41 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:41:41,346 - WARNING - Could not retrieve variants from source file in region 1:150131460-150131861. Error was invalid region `1:150131461-150131861`
[2016-04-15T02:41Z] 2016-04-14 19:41:41 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:41:41,491 - WARNING - Could not retrieve variants from source file in region 1:154516266-154523405. Error was invalid region `1:154516267-154523405`
[2016-04-15T02:41Z] 2016-04-14 19:41:42 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:41:42,153 - WARNING - Could not retrieve variants from source file in region 1:150727328-150727729. Error was invalid region `1:150727329-150727729`
[2016-04-15T02:41Z] 2016-04-14 19:41:43 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:41:43,553 - WARNING - Could not retrieve variants from source file in region 1:154573756-154575230. Error was invalid region `1:154573757-154575230`
[2016-04-15T02:41Z] 2016-04-14 19:41:44 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:41:44,887 - WARNING - Could not retrieve variants from source file in region 1:156346920-156354557. Error was invalid region `1:156346921-156354557`
[2016-04-15T02:41Z] 2016-04-14 19:41:44 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:41:44,935 - WARNING - Could not retrieve variants from source file in region 1:154108176-154108577. Error was invalid region `1:154108177-154108577`
[2016-04-15T02:41Z] 2016-04-14 19:41:46 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:41:46,888 - WARNING - Could not retrieve variants from source file in region 1:154516266-154523405. Error was invalid region `1:154516267-154523405`
[2016-04-15T02:41Z] 2016-04-14 19:41:49 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:41:49,257 - WARNING - Could not retrieve variants from source file in region 1:156526176-156565239. Error was invalid region `1:156526177-156565239`
[2016-04-15T02:41Z] 2016-04-14 19:41:52 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:41:52,041 - WARNING - Could not retrieve variants from source file in region 1:156346920-156354557. Error was invalid region `1:156346921-156354557`
[2016-04-15T02:41Z] 2016-04-14 19:41:59 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:41:59,195 - WARNING - Could not retrieve variants from source file in region 1:157508671-157514287. Error was invalid region `1:157508672-157514287`
[2016-04-15T02:42Z] 2016-04-14 19:42:01 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:42:01,443 - WARNING - Could not retrieve variants from source file in region 1:153994436-153994837. Error was invalid region `1:153994437-153994837`
[2016-04-15T02:42Z] 2016-04-14 19:42:02 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:42:02,205 - WARNING - Could not retrieve variants from source file in region 1:158435717-158450572. Error was invalid region `1:158435718-158450572`
[2016-04-15T02:42Z] 2016-04-14 19:42:03 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:42:03,702 - WARNING - Could not retrieve variants from source file in region 1:153277212-153277613. Error was invalid region `1:153277213-153277613`
[2016-04-15T02:42Z] 2016-04-14 19:42:04 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:42:04,040 - WARNING - Could not retrieve variants from source file in region 1:150678822-150679223. Error was invalid region `1:150678823-150679223`
[2016-04-15T02:42Z] 2016-04-14 19:42:04 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:42:04,125 - WARNING - Could not retrieve variants from source file in region 1:156499758-156500159. Error was invalid region `1:156499759-156500159`
[2016-04-15T02:42Z] 2016-04-14 19:42:05 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:42:05,089 - WARNING - Could not retrieve variants from source file in region 1:158223848-158225209. Error was invalid region `1:158223849-158225209`
[2016-04-15T02:42Z] 2016-04-14 19:42:05 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:42:05,282 - WARNING - Could not retrieve variants from source file in region 1:150597050-150598080. Error was invalid region `1:150597051-150598080`
[2016-04-15T02:42Z] 2016-04-14 19:42:06 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:42:06,179 - WARNING - Could not retrieve variants from source file in region 1:153994436-153994837. Error was invalid region `1:153994437-153994837`
[2016-04-15T02:42Z] 2016-04-14 19:42:08 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:42:08,998 - WARNING - Could not retrieve variants from source file in region 1:149905956-149943347. Error was invalid region `1:149905957-149943347`
[2016-04-15T02:42Z] 2016-04-14 19:42:09 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:42:09,563 - WARNING - Could not retrieve variants from source file in region 1:150678822-150679223. Error was invalid region `1:150678823-150679223`
[2016-04-15T02:42Z] 2016-04-14 19:42:10 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:42:10,085 - WARNING - Could not retrieve variants from source file in region 1:157508671-157514287. Error was invalid region `1:157508672-157514287`
[2016-04-15T02:42Z] 2016-04-14 19:42:11 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:42:11,469 - WARNING - Could not retrieve variants from source file in region 1:153994436-153994837. Error was invalid region `1:153994437-153994837`
[2016-04-15T02:42Z] 2016-04-14 19:42:12 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:42:12,411 - WARNING - Could not retrieve variants from source file in region 1:156306707-156307108. Error was invalid region `1:156306708-156307108`
[2016-04-15T02:42Z] 2016-04-14 19:42:12 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:42:12,965 - WARNING - Could not retrieve variants from source file in region 1:158435717-158450572. Error was invalid region `1:158435718-158450572`
[2016-04-15T02:42Z] 2016-04-14 19:42:13 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:42:13,035 - WARNING - Could not retrieve variants from source file in region 1:147091478-147124500. Error was invalid region `1:147091479-147124500`
[2016-04-15T02:42Z] 2016-04-14 19:42:14 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:42:14,749 - WARNING - Could not retrieve variants from source file in region 1:150678822-150679223. Error was invalid region `1:150678823-150679223`
[2016-04-15T02:42Z] 2016-04-14 19:42:15 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:42:15,431 - WARNING - Could not retrieve variants from source file in region 1:158223848-158225209. Error was invalid region `1:158223849-158225209`
[2016-04-15T02:42Z] 2016-04-14 19:42:15 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:42:15,653 - WARNING - Could not retrieve variants from source file in region 1:150597050-150598080. Error was invalid region `1:150597051-150598080`
[2016-04-15T02:42Z] 2016-04-14 19:42:15 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:42:15,684 - WARNING - Could not retrieve variants from source file in region 1:156499758-156500159. Error was invalid region `1:156499759-156500159`
[2016-04-15T02:42Z] 2016-04-14 19:42:26 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:42:26,231 - WARNING - Could not retrieve variants from source file in region 1:153907067-153941704. Error was invalid region `1:153907068-153941704`
[2016-04-15T02:42Z] 2016-04-14 19:42:26 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:42:26,960 - WARNING - Could not retrieve variants from source file in region 1:158324214-158324615. Error was invalid region `1:158324215-158324615`
[2016-04-15T02:42Z] 2016-04-14 19:42:27 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:42:27,246 - WARNING - Could not retrieve variants from source file in region 1:155947664-155948120. Error was invalid region `1:155947665-155948120`
[2016-04-15T02:42Z] 2016-04-14 19:42:27 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:42:27,325 - WARNING - Could not retrieve variants from source file in region 1:153233299-153234181. Error was invalid region `1:153233300-153234181`
[2016-04-15T02:42Z] 2016-04-14 19:42:28 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:42:28,962 - WARNING - Could not retrieve variants from source file in region 1:150483144-150485177. Error was invalid region `1:150483145-150485177`
[2016-04-15T02:42Z] 2016-04-14 19:42:29 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:42:29,015 - WARNING - Could not retrieve variants from source file in region 1:157062485-157062886. Error was invalid region `1:157062486-157062886`
[2016-04-15T02:42Z] 2016-04-14 19:42:30 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:42:30,464 - WARNING - Could not retrieve variants from source file in region 1:158057422-158057823. Error was invalid region `1:158057423-158057823`
[2016-04-15T02:42Z] 2016-04-14 19:42:31 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:42:31,325 - WARNING - Could not retrieve variants from source file in region 1:146751571-146767339. Error was invalid region `1:146751572-146767339`
[2016-04-15T02:42Z] 2016-04-14 19:42:31 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:42:31,570 - WARNING - Could not retrieve variants from source file in region 1:155947664-155948120. Error was invalid region `1:155947665-155948120`
[2016-04-15T02:42Z] 2016-04-14 19:42:33 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:42:33,246 - WARNING - Could not retrieve variants from source file in region 1:150483144-150485177. Error was invalid region `1:150483145-150485177`
[2016-04-15T02:42Z] 2016-04-14 19:42:33 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:42:33,290 - WARNING - Could not retrieve variants from source file in region 1:157062485-157062886. Error was invalid region `1:157062486-157062886`
[2016-04-15T02:42Z] 2016-04-14 19:42:34 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:42:34,758 - WARNING - Could not retrieve variants from source file in region 1:158057422-158057823. Error was invalid region `1:158057423-158057823`
[2016-04-15T02:42Z] 2016-04-14 19:42:35 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:42:35,220 - WARNING - Could not retrieve variants from source file in region 1:152759739-152785360. Error was invalid region `1:152759740-152785360`
[2016-04-15T02:42Z] 2016-04-14 19:42:35 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:42:35,536 - WARNING - Could not retrieve variants from source file in region 1:153907067-153941704. Error was invalid region `1:153907068-153941704`
[2016-04-15T02:42Z] 2016-04-14 19:42:35 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:42:35,693 - WARNING - Could not retrieve variants from source file in region 1:158324214-158324615. Error was invalid region `1:158324215-158324615`
[2016-04-15T02:42Z] 2016-04-14 19:42:36 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:42:36,136 - WARNING - Could not retrieve variants from source file in region 1:155947664-155948120. Error was invalid region `1:155947665-155948120`
[2016-04-15T02:42Z] 2016-04-14 19:42:37 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:42:37,358 - WARNING - Could not retrieve variants from source file in region 1:149871694-149876855. Error was invalid region `1:149871695-149876855`
[2016-04-15T02:42Z] 2016-04-14 19:42:37 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:42:37,428 - WARNING - Could not retrieve variants from source file in region 1:150483144-150485177. Error was invalid region `1:150483145-150485177`
[2016-04-15T02:42Z] 2016-04-14 19:42:38 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:42:38,981 - WARNING - Could not retrieve variants from source file in region 1:158057422-158057823. Error was invalid region `1:158057423-158057823`
[2016-04-15T02:42Z] 2016-04-14 19:42:40 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:42:40,368 - WARNING - Could not retrieve variants from source file in region 1:146751571-146767339. Error was invalid region `1:146751572-146767339`
[2016-04-15T02:42Z] 2016-04-14 19:42:49 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:42:49,100 - WARNING - Could not retrieve variants from source file in region 1:155912275-155912676. Error was invalid region `1:155912276-155912676`
[2016-04-15T02:42Z] 2016-04-14 19:42:49 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:42:49,169 - WARNING - Could not retrieve variants from source file in region 1:150280410-150280811. Error was invalid region `1:150280411-150280811`
[2016-04-15T02:42Z] 2016-04-14 19:42:49 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:42:49,556 - WARNING - Could not retrieve variants from source file in region 1:153004637-153029327. Error was invalid region `1:153004638-153029327`
[2016-04-15T02:42Z] 2016-04-14 19:42:53 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:42:53,287 - WARNING - Could not retrieve variants from source file in region 1:156846022-156849185. Error was invalid region `1:156846023-156849185`
[2016-04-15T02:42Z] 2016-04-14 19:42:53 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:42:53,360 - WARNING - Could not retrieve variants from source file in region 1:155837654-155838457. Error was invalid region `1:155837655-155838457`
[2016-04-15T02:42Z] 2016-04-14 19:42:53 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:42:53,623 - WARNING - Could not retrieve variants from source file in region 1:152552074-152552475. Error was invalid region `1:152552075-152552475`
[2016-04-15T02:42Z] 2016-04-14 19:42:53 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:42:53,645 - WARNING - Could not retrieve variants from source file in region 1:152732225-152733491. Error was invalid region `1:152732226-152733491`
[2016-04-15T02:42Z] 2016-04-14 19:42:53 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:42:53,827 - WARNING - Could not retrieve variants from source file in region 1:146714181-146714617. Error was invalid region `1:146714182-146714617`
[2016-04-15T02:42Z] 2016-04-14 19:42:54 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:42:54,252 - WARNING - Could not retrieve variants from source file in region 1:152681469-152692778. Error was invalid region `1:152681470-152692778`
[2016-04-15T02:42Z] 2016-04-14 19:42:54 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:42:54,280 - WARNING - Could not retrieve variants from source file in region 1:155912275-155912676. Error was invalid region `1:155912276-155912676`
[2016-04-15T02:42Z] 2016-04-14 19:42:54 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:42:54,993 - WARNING - Could not retrieve variants from source file in region 1:149783675-149784076. Error was invalid region `1:149783676-149784076`
[2016-04-15T02:42Z] 2016-04-14 19:42:58 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:42:58,020 - WARNING - Could not retrieve variants from source file in region 1:152636632-152637033. Error was invalid region `1:152636633-152637033`
[2016-04-15T02:42Z] 2016-04-14 19:42:58 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:42:58,480 - WARNING - Could not retrieve variants from source file in region 1:156846022-156849185. Error was invalid region `1:156846023-156849185`
[2016-04-15T02:42Z] 2016-04-14 19:42:59 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:42:59,035 - WARNING - Could not retrieve variants from source file in region 1:152381909-152382310. Error was invalid region `1:152381910-152382310`
[2016-04-15T02:42Z] 2016-04-14 19:42:59 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:42:59,039 - WARNING - Could not retrieve variants from source file in region 1:155837654-155838457. Error was invalid region `1:155837655-155838457`
[2016-04-15T02:42Z] 2016-04-14 19:42:59 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:42:59,526 - WARNING - Could not retrieve variants from source file in region 1:152732225-152733491. Error was invalid region `1:152732226-152733491`
[2016-04-15T02:43Z] 2016-04-14 19:43:00 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:43:00,456 - WARNING - Could not retrieve variants from source file in region 1:149783675-149784076. Error was invalid region `1:149783676-149784076`
[2016-04-15T02:43Z] 2016-04-14 19:43:00 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:43:00,533 - WARNING - Could not retrieve variants from source file in region 1:155912275-155912676. Error was invalid region `1:155912276-155912676`
[2016-04-15T02:43Z] 2016-04-14 19:43:03 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:43:03,259 - WARNING - Could not retrieve variants from source file in region 1:156846022-156849185. Error was invalid region `1:156846023-156849185`
[2016-04-15T02:43Z] 2016-04-14 19:43:03 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:43:03,983 - WARNING - Could not retrieve variants from source file in region 1:155837654-155838457. Error was invalid region `1:155837655-155838457`
[2016-04-15T02:43Z] 2016-04-14 19:43:04 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:43:04,021 - WARNING - Could not retrieve variants from source file in region 1:152381909-152382310. Error was invalid region `1:152381910-152382310`
[2016-04-15T02:43Z] 2016-04-14 19:43:05 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:43:05,314 - WARNING - Could not retrieve variants from source file in region 1:152732225-152733491. Error was invalid region `1:152732226-152733491`
[2016-04-15T02:43Z] 2016-04-14 19:43:05 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:43:05,427 - WARNING - Could not retrieve variants from source file in region 1:146714181-146714617. Error was invalid region `1:146714182-146714617`
[2016-04-15T02:43Z] 2016-04-14 19:43:10 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:43:10,955 - WARNING - Could not retrieve variants from source file in region 1:156813816-156814217. Error was invalid region `1:156813817-156814217`
[2016-04-15T02:43Z] 2016-04-14 19:43:15 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:43:15,028 - WARNING - Could not retrieve variants from source file in region 1:155880362-155880763. Error was invalid region `1:155880363-155880763`
[2016-04-15T02:43Z] 2016-04-14 19:43:15 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:43:15,118 - WARNING - Could not retrieve variants from source file in region 1:149698330-149701193. Error was invalid region `1:149698331-149701193`
[2016-04-15T02:43Z] 2016-04-14 19:43:15 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:43:15,474 - WARNING - Could not retrieve variants from source file in region 1:155408424-155408825. Error was invalid region `1:155408425-155408825`
[2016-04-15T02:43Z] 2016-04-14 19:43:16 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:43:16,832 - WARNING - Could not retrieve variants from source file in region 1:152483918-152488253. Error was invalid region `1:152483919-152488253`
[2016-04-15T02:43Z] 2016-04-14 19:43:17 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:43:17,434 - WARNING - Could not retrieve variants from source file in region 1:152944383-152976131. Error was invalid region `1:152944384-152976131`
[2016-04-15T02:43Z] 2016-04-14 19:43:17 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:43:17,466 - WARNING - Could not retrieve variants from source file in region 1:145227046-145227447. Error was invalid region `1:145227047-145227447`
[2016-04-15T02:43Z] 2016-04-14 19:43:17 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:43:17,562 - WARNING - Could not retrieve variants from source file in region 1:155734801-155735202. Error was invalid region `1:155734802-155735202`
[2016-04-15T02:43Z] 2016-04-14 19:43:19 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:43:19,425 - WARNING - Could not retrieve variants from source file in region 1:146672695-146673096. Error was invalid region `1:146672696-146673096`
[2016-04-15T02:43Z] 2016-04-14 19:43:19 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:43:19,558 - WARNING - Could not retrieve variants from source file in region 1:155880362-155880763. Error was invalid region `1:155880363-155880763`
[2016-04-15T02:43Z] 2016-04-14 19:43:19 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:43:19,939 - WARNING - Could not retrieve variants from source file in region 1:155408424-155408825. Error was invalid region `1:155408425-155408825`
[2016-04-15T02:43Z] 2016-04-14 19:43:21 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:43:21,677 - WARNING - Could not retrieve variants from source file in region 1:152483918-152488253. Error was invalid region `1:152483919-152488253`
[2016-04-15T02:43Z] 2016-04-14 19:43:22 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:43:22,001 - WARNING - Could not retrieve variants from source file in region 1:152944383-152976131. Error was invalid region `1:152944384-152976131`
[2016-04-15T02:43Z] 2016-04-14 19:43:22 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:43:22,147 - WARNING - Could not retrieve variants from source file in region 1:145227046-145227447. Error was invalid region `1:145227047-145227447`
[2016-04-15T02:43Z] 2016-04-14 19:43:22 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:43:22,231 - WARNING - Could not retrieve variants from source file in region 1:155734801-155735202. Error was invalid region `1:155734802-155735202`
[2016-04-15T02:43Z] 2016-04-14 19:43:23 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:43:23,707 - WARNING - Could not retrieve variants from source file in region 1:146672695-146673096. Error was invalid region `1:146672696-146673096`
[2016-04-15T02:43Z] 2016-04-14 19:43:24 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:43:24,052 - WARNING - Could not retrieve variants from source file in region 1:155880362-155880763. Error was invalid region `1:155880363-155880763`
[2016-04-15T02:43Z] 2016-04-14 19:43:24 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:43:24,428 - WARNING - Could not retrieve variants from source file in region 1:155408424-155408825. Error was invalid region `1:155408425-155408825`
[2016-04-15T02:43Z] 2016-04-14 19:43:24 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:43:24,960 - WARNING - Could not retrieve variants from source file in region 1:152127244-152129284. Error was invalid region `1:152127245-152129284`
[2016-04-15T02:43Z] 2016-04-14 19:43:25 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:43:25,121 - WARNING - Could not retrieve variants from source file in region 1:149379026-149379915. Error was invalid region `1:149379027-149379915`
[2016-04-15T02:43Z] 2016-04-14 19:43:26 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:43:26,292 - WARNING - Could not retrieve variants from source file in region 1:152483918-152488253. Error was invalid region `1:152483919-152488253`
[2016-04-15T02:43Z] 2016-04-14 19:43:26 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:43:26,490 - WARNING - Could not retrieve variants from source file in region 1:145227046-145227447. Error was invalid region `1:145227047-145227447`
[2016-04-15T02:43Z] 2016-04-14 19:43:26 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:43:26,566 - WARNING - Could not retrieve variants from source file in region 1:152322921-152331430. Error was invalid region `1:152322922-152331430`
[2016-04-15T02:43Z] 2016-04-14 19:43:26 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:43:26,782 - WARNING - Could not retrieve variants from source file in region 1:155734801-155735202. Error was invalid region `1:155734802-155735202`
[2016-04-15T02:43Z] 2016-04-14 19:43:27 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:43:27,740 - WARNING - Could not retrieve variants from source file in region 1:146672695-146673096. Error was invalid region `1:146672696-146673096`
[2016-04-15T02:43Z] 2016-04-14 19:43:29 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:43:29,307 - WARNING - Could not retrieve variants from source file in region 1:152127244-152129284. Error was invalid region `1:152127245-152129284`
[2016-04-15T02:43Z] 2016-04-14 19:43:34 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:43:34,034 - WARNING - Could not retrieve variants from source file in region 1:155260172-155260573. Error was invalid region `1:155260173-155260573`
[2016-04-15T02:43Z] 2016-04-14 19:43:35 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:43:35,305 - WARNING - Could not retrieve variants from source file in region 1:155260172-155260573. Error was invalid region `1:155260173-155260573`
[2016-04-15T02:43Z] 2016-04-14 19:43:36 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:43:36,585 - WARNING - Could not retrieve variants from source file in region 1:155657874-155658531. Error was invalid region `1:155657875-155658531`
[2016-04-15T02:43Z] 2016-04-14 19:43:36 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:43:36,945 - WARNING - Could not retrieve variants from source file in region 1:151588068-151588469. Error was invalid region `1:151588069-151588469`
[2016-04-15T02:43Z] 2016-04-14 19:43:38 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:43:38,841 - WARNING - Could not retrieve variants from source file in region 1:155260172-155260573. Error was invalid region `1:155260173-155260573`
[2016-04-15T02:43Z] 2016-04-14 19:43:38 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:43:38,876 - WARNING - Could not retrieve variants from source file in region 1:155229920-155230321. Error was invalid region `1:155229921-155230321`
[2016-04-15T02:43Z] 2016-04-14 19:43:39 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:43:39,200 - WARNING - Could not retrieve variants from source file in region 1:155581100-155581501. Error was invalid region `1:155581101-155581501`
[2016-04-15T02:43Z] 2016-04-14 19:43:39 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:43:39,631 - WARNING - Could not retrieve variants from source file in region 1:151867349-151882075. Error was invalid region `1:151867350-151882075`
[2016-04-15T02:43Z] 2016-04-14 19:43:39 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:43:39,691 - WARNING - Could not retrieve variants from source file in region 1:145103736-145116000. Error was invalid region `1:145103737-145116000`
[2016-04-15T02:43Z] 2016-04-14 19:43:40 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:43:40,056 - WARNING - Could not retrieve variants from source file in region 1:144994447-144995051. Error was invalid region `1:144994448-144995051`
[2016-04-15T02:43Z] 2016-04-14 19:43:41 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:43:41,654 - WARNING - Could not retrieve variants from source file in region 1:151588068-151588469. Error was invalid region `1:151588069-151588469`
[2016-04-15T02:43Z] 2016-04-14 19:43:41 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:43:41,843 - WARNING - Could not retrieve variants from source file in region 1:155657874-155658531. Error was invalid region `1:155657875-155658531`
[2016-04-15T02:43Z] 2016-04-14 19:43:42 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:43:42,323 - WARNING - Could not retrieve variants from source file in region 1:152079778-152085695. Error was invalid region `1:152079779-152085695`
[2016-04-15T02:43Z] 2016-04-14 19:43:42 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:43:42,811 - WARNING - Could not retrieve variants from source file in region 1:155294063-155295595. Error was invalid region `1:155294064-155295595`
[2016-04-15T02:43Z] 2016-04-14 19:43:43 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:43:43,133 - WARNING - Could not retrieve variants from source file in region 1:155581100-155581501. Error was invalid region `1:155581101-155581501`
[2016-04-15T02:43Z] 2016-04-14 19:43:43 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:43:43,310 - WARNING - Could not retrieve variants from source file in region 1:155229920-155230321. Error was invalid region `1:155229921-155230321`
[2016-04-15T02:43Z] 2016-04-14 19:43:43 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:43:43,664 - WARNING - Could not retrieve variants from source file in region 1:155581100-155581501. Error was invalid region `1:155581101-155581501`
[2016-04-15T02:43Z] 2016-04-14 19:43:44 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:43:44,328 - WARNING - Could not retrieve variants from source file in region 1:151867349-151882075. Error was invalid region `1:151867350-151882075`
[2016-04-15T02:43Z] 2016-04-14 19:43:44 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:43:44,855 - WARNING - Could not retrieve variants from source file in region 1:144994447-144995051. Error was invalid region `1:144994448-144995051`
[2016-04-15T02:43Z] 2016-04-14 19:43:44 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:43:44,940 - WARNING - Could not retrieve variants from source file in region 1:151238840-151288581. Error was invalid region `1:151238841-151288581`
[2016-04-15T02:43Z] 2016-04-14 19:43:46 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:43:46,180 - WARNING - Could not retrieve variants from source file in region 1:151588068-151588469. Error was invalid region `1:151588069-151588469`
[2016-04-15T02:43Z] 2016-04-14 19:43:46 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:43:46,205 - WARNING - Could not retrieve variants from source file in region 1:155657874-155658531. Error was invalid region `1:155657875-155658531`
[2016-04-15T02:43Z] 2016-04-14 19:43:47 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:43:47,324 - WARNING - Could not retrieve variants from source file in region 1:155229920-155230321. Error was invalid region `1:155229921-155230321`
[2016-04-15T02:43Z] 2016-04-14 19:43:47 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:43:47,370 - WARNING - Could not retrieve variants from source file in region 1:155294063-155295595. Error was invalid region `1:155294064-155295595`
[2016-04-15T02:43Z] 2016-04-14 19:43:48 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:43:48,834 - WARNING - Could not retrieve variants from source file in region 1:145103736-145116000. Error was invalid region `1:145103737-145116000`
[2016-04-15T02:43Z] 2016-04-14 19:43:48 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:43:48,980 - WARNING - Could not retrieve variants from source file in region 1:151867349-151882075. Error was invalid region `1:151867350-151882075`
[2016-04-15T02:43Z] 2016-04-14 19:43:49 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:43:49,367 - WARNING - Could not retrieve variants from source file in region 1:144994447-144995051. Error was invalid region `1:144994448-144995051`
[2016-04-15T02:43Z] 2016-04-14 19:43:51 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:43:51,459 - WARNING - Could not retrieve variants from source file in region 1:152079778-152085695. Error was invalid region `1:152079779-152085695`
[2016-04-15T02:43Z] 2016-04-14 19:43:56 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:43:56,632 - WARNING - Could not retrieve variants from source file in region 1:145075472-145076044. Error was invalid region `1:145075473-145076044`
[2016-04-15T02:43Z] 2016-04-14 19:43:58 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:43:58,328 - WARNING - Could not retrieve variants from source file in region 1:151533931-151534332. Error was invalid region `1:151533932-151534332`
[2016-04-15T02:43Z] 2016-04-14 19:43:59 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:43:59,665 - WARNING - Could not retrieve variants from source file in region 1:151733124-151748160. Error was invalid region `1:151733125-151748160`
[2016-04-15T02:43Z] 2016-04-14 19:43:59 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:43:59,737 - WARNING - Could not retrieve variants from source file in region 1:151104739-151115207. Error was invalid region `1:151104740-151115207`
[2016-04-15T02:43Z] 2016-04-14 19:43:59 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:43:59,759 - WARNING - Could not retrieve variants from source file in region 1:151371927-151377438. Error was invalid region `1:151371928-151377438`
[2016-04-15T02:44Z] 2016-04-14 19:44:00 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:44:00,520 - WARNING - Could not retrieve variants from source file in region 1:151803238-151826181. Error was invalid region `1:151803239-151826181`
[2016-04-15T02:44Z] 2016-04-14 19:44:00 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:44:00,853 - WARNING - Could not retrieve variants from source file in region 1:145039655-145040056. Error was invalid region `1:145039656-145040056`
[2016-04-15T02:44Z] 2016-04-14 19:44:00 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:44:00,938 - WARNING - Could not retrieve variants from source file in region 1:151803238-151826181. Error was invalid region `1:151803239-151826181`
[2016-04-15T02:44Z] 2016-04-14 19:44:01 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:44:01,957 - WARNING - Could not retrieve variants from source file in region 1:151208852-151209253. Error was invalid region `1:151208853-151209253`
[2016-04-15T02:44Z] 2016-04-14 19:44:04 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:44:04,101 - WARNING - Could not retrieve variants from source file in region 1:151371927-151377438. Error was invalid region `1:151371928-151377438`
[2016-04-15T02:44Z] 2016-04-14 19:44:04 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:44:04,549 - WARNING - Could not retrieve variants from source file in region 1:151315076-151316351. Error was invalid region `1:151315077-151316351`
[2016-04-15T02:44Z] 2016-04-14 19:44:05 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:44:05,007 - WARNING - Could not retrieve variants from source file in region 1:151803238-151826181. Error was invalid region `1:151803239-151826181`
[2016-04-15T02:44Z] 2016-04-14 19:44:05 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:44:05,473 - WARNING - Could not retrieve variants from source file in region 1:145039655-145040056. Error was invalid region `1:145039656-145040056`
[2016-04-15T02:44Z] 2016-04-14 19:44:06 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:44:06,429 - WARNING - Could not retrieve variants from source file in region 1:151208852-151209253. Error was invalid region `1:151208853-151209253`
[2016-04-15T02:44Z] 2016-04-14 19:44:08 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:44:08,116 - WARNING - Could not retrieve variants from source file in region 1:151104739-151115207. Error was invalid region `1:151104740-151115207`
[2016-04-15T02:44Z] 2016-04-14 19:44:08 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:44:08,337 - WARNING - Could not retrieve variants from source file in region 1:151371927-151377438. Error was invalid region `1:151371928-151377438`
[2016-04-15T02:44Z] 2016-04-14 19:44:08 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:44:08,518 - WARNING - Could not retrieve variants from source file in region 1:151315076-151316351. Error was invalid region `1:151315077-151316351`
[2016-04-15T02:44Z] 2016-04-14 19:44:09 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:44:09,427 - WARNING - Could not retrieve variants from source file in region 1:145039655-145040056. Error was invalid region `1:145039656-145040056`
[2016-04-15T02:44Z] 2016-04-14 19:44:10 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:44:10,585 - WARNING - Could not retrieve variants from source file in region 1:151208852-151209253. Error was invalid region `1:151208853-151209253`
[2016-04-15T02:44Z] 2016-04-14 19:44:18 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:44:18,928 - WARNING - Could not retrieve variants from source file in region 1:144013840-144014258. Error was invalid region `1:144013841-144014258`
[2016-04-15T02:44Z] 2016-04-14 19:44:18 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:44:18,969 - WARNING - Could not retrieve variants from source file in region 1:144013840-144014258. Error was invalid region `1:144013841-144014258`
[2016-04-15T02:44Z] 2016-04-14 19:44:18 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:44:18,995 - WARNING - Could not retrieve variants from source file in region 1:144013840-144014258. Error was invalid region `1:144013841-144014258`
[2016-04-15T02:44Z] ['bcbio-variation-recall', 'square', '-Xms750m', '-Xmx7280m', '-XX:+UseSerialGC', '-c', 16, '-r', u'1:159504868-175046963', '--caller', 'platypus', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/1/Batch1-1_159504867_175046963.vcf.gz', '/mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/1/Batch1-1_159504867_175046963.vcf-inputs.txt'] in region: 1:159504868-175046963
[2016-04-15T02:44Z] 2016-04-14 19:44:35 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:44:35,092 - WARNING - Could not retrieve variants from source file in region 1:171939079-171939480. Error was invalid region `1:171939080-171939480`
[2016-04-15T02:44Z] 2016-04-14 19:44:35 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:44:35,099 - WARNING - Could not retrieve variants from source file in region 1:173516660-173517093. Error was invalid region `1:173516661-173517093`
[2016-04-15T02:44Z] 2016-04-14 19:44:35 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:44:35,689 - WARNING - Could not retrieve variants from source file in region 1:175046578-175046979. Error was invalid region `1:175046579-175046979`
[2016-04-15T02:44Z] 2016-04-14 19:44:36 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:44:36,572 - WARNING - Could not retrieve variants from source file in region 1:160393694-160395193. Error was invalid region `1:160393695-160395193`
[2016-04-15T02:44Z] 2016-04-14 19:44:37 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:44:37,582 - WARNING - Could not retrieve variants from source file in region 1:161565113-161569759. Error was invalid region `1:161565114-161569759`
[2016-04-15T02:44Z] 2016-04-14 19:44:38 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:44:38,838 - WARNING - Could not retrieve variants from source file in region 1:168059655-168060056. Error was invalid region `1:168059656-168060056`
[2016-04-15T02:44Z] 2016-04-14 19:44:38 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:44:38,878 - WARNING - Could not retrieve variants from source file in region 1:160851615-160852084. Error was invalid region `1:160851616-160852084`
[2016-04-15T02:44Z] 2016-04-14 19:44:38 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:44:38,897 - WARNING - Could not retrieve variants from source file in region 1:165648498-165652463. Error was invalid region `1:165648499-165652463`
[2016-04-15T02:44Z] 2016-04-14 19:44:40 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:44:40,752 - WARNING - Could not retrieve variants from source file in region 1:171939079-171939480. Error was invalid region `1:171939080-171939480`
[2016-04-15T02:44Z] 2016-04-14 19:44:42 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:44:42,045 - WARNING - Could not retrieve variants from source file in region 1:161275732-161276133. Error was invalid region `1:161275733-161276133`
[2016-04-15T02:44Z] 2016-04-14 19:44:45 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:44:45,049 - WARNING - Could not retrieve variants from source file in region 1:170501174-170521566. Error was invalid region `1:170501175-170521566`
[2016-04-15T02:44Z] 2016-04-14 19:44:45 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:44:45,134 - WARNING - Could not retrieve variants from source file in region 1:161642774-161643175. Error was invalid region `1:161642775-161643175`
[2016-04-15T02:44Z] 2016-04-14 19:44:45 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:44:45,696 - WARNING - Could not retrieve variants from source file in region 1:160851615-160852084. Error was invalid region `1:160851616-160852084`
[2016-04-15T02:44Z] 2016-04-14 19:44:45 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:44:45,727 - WARNING - Could not retrieve variants from source file in region 1:172410756-172437782. Error was invalid region `1:172410757-172437782`
[2016-04-15T02:44Z] 2016-04-14 19:44:45 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:44:45,819 - WARNING - Could not retrieve variants from source file in region 1:168059655-168060056. Error was invalid region `1:168059656-168060056`
[2016-04-15T02:44Z] 2016-04-14 19:44:46 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:44:46,419 - WARNING - Could not retrieve variants from source file in region 1:173516660-173517093. Error was invalid region `1:173516661-173517093`
[2016-04-15T02:44Z] 2016-04-14 19:44:46 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:44:46,567 - WARNING - Could not retrieve variants from source file in region 1:175046578-175046979. Error was invalid region `1:175046579-175046979`
[2016-04-15T02:44Z] 2016-04-14 19:44:46 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:44:46,799 - WARNING - Could not retrieve variants from source file in region 1:171939079-171939480. Error was invalid region `1:171939080-171939480`
[2016-04-15T02:44Z] 2016-04-14 19:44:51 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:44:51,995 - WARNING - Could not retrieve variants from source file in region 1:161642774-161643175. Error was invalid region `1:161642775-161643175`
[2016-04-15T02:44Z] 2016-04-14 19:44:53 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:44:53,925 - WARNING - Could not retrieve variants from source file in region 1:160851615-160852084. Error was invalid region `1:160851616-160852084`
[2016-04-15T02:44Z] 2016-04-14 19:44:54 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:44:54,237 - WARNING - Could not retrieve variants from source file in region 1:168059655-168060056. Error was invalid region `1:168059656-168060056`
[2016-04-15T02:45Z] 2016-04-14 19:45:04 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:45:04,743 - WARNING - Could not retrieve variants from source file in region 1:160303205-160323543. Error was invalid region `1:160303206-160323543`
[2016-04-15T02:45Z] 2016-04-14 19:45:05 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:45:05,544 - WARNING - Could not retrieve variants from source file in region 1:173474218-173474619. Error was invalid region `1:173474219-173474619`
[2016-04-15T02:45Z] 2016-04-14 19:45:06 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:45:06,357 - WARNING - Could not retrieve variants from source file in region 1:174958897-174959298. Error was invalid region `1:174958898-174959298`
[2016-04-15T02:45Z] 2016-04-14 19:45:06 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:45:06,735 - WARNING - Could not retrieve variants from source file in region 1:170135458-170135955. Error was invalid region `1:170135459-170135955`
[2016-04-15T02:45Z] 2016-04-14 19:45:07 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:45:07,030 - WARNING - Could not retrieve variants from source file in region 1:161599482-161601022. Error was invalid region `1:161599483-161601022`
[2016-04-15T02:45Z] 2016-04-14 19:45:10 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:45:10,890 - WARNING - Could not retrieve variants from source file in region 1:168013639-168014040. Error was invalid region `1:168013640-168014040`
[2016-04-15T02:45Z] 2016-04-14 19:45:10 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:45:10,928 - WARNING - Could not retrieve variants from source file in region 1:161967470-161976424. Error was invalid region `1:161967471-161976424`
[2016-04-15T02:45Z] 2016-04-14 19:45:11 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:45:11,040 - WARNING - Could not retrieve variants from source file in region 1:173474218-173474619. Error was invalid region `1:173474219-173474619`
[2016-04-15T02:45Z] 2016-04-14 19:45:11 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:45:11,052 - WARNING - Could not retrieve variants from source file in region 1:161049172-161069026. Error was invalid region `1:161049173-161069026`
[2016-04-15T02:45Z] 2016-04-14 19:45:12 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:45:12,129 - WARNING - Could not retrieve variants from source file in region 1:170135458-170135955. Error was invalid region `1:170135459-170135955`
[2016-04-15T02:45Z] 2016-04-14 19:45:12 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:45:12,303 - WARNING - Could not retrieve variants from source file in region 1:161599482-161601022. Error was invalid region `1:161599483-161601022`
[2016-04-15T02:45Z] 2016-04-14 19:45:13 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:45:13,568 - WARNING - Could not retrieve variants from source file in region 1:160766714-160794687. Error was invalid region `1:160766715-160794687`
[2016-04-15T02:45Z] 2016-04-14 19:45:14 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:45:14,271 - WARNING - Could not retrieve variants from source file in region 1:171750840-171763739. Error was invalid region `1:171750841-171763739`
[2016-04-15T02:45Z] 2016-04-14 19:45:15 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:45:15,230 - WARNING - Could not retrieve variants from source file in region 1:165532535-165533195. Error was invalid region `1:165532536-165533195`
[2016-04-15T02:45Z] 2016-04-14 19:45:15 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:45:15,591 - WARNING - Could not retrieve variants from source file in region 1:161967470-161976424. Error was invalid region `1:161967471-161976424`
[2016-04-15T02:45Z] 2016-04-14 19:45:15 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:45:15,756 - WARNING - Could not retrieve variants from source file in region 1:168013639-168014040. Error was invalid region `1:168013640-168014040`
[2016-04-15T02:45Z] 2016-04-14 19:45:17 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:45:17,156 - WARNING - Could not retrieve variants from source file in region 1:174958897-174959298. Error was invalid region `1:174958898-174959298`
[2016-04-15T02:45Z] 2016-04-14 19:45:17 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:45:17,289 - WARNING - Could not retrieve variants from source file in region 1:161130490-161136414. Error was invalid region `1:161130491-161136414`
[2016-04-15T02:45Z] 2016-04-14 19:45:17 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:45:17,389 - WARNING - Could not retrieve variants from source file in region 1:170135458-170135955. Error was invalid region `1:170135459-170135955`
[2016-04-15T02:45Z] 2016-04-14 19:45:17 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:45:17,449 - WARNING - Could not retrieve variants from source file in region 1:161599482-161601022. Error was invalid region `1:161599483-161601022`
[2016-04-15T02:45Z] 2016-04-14 19:45:20 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:45:20,424 - WARNING - Could not retrieve variants from source file in region 1:161928116-161928517. Error was invalid region `1:161928117-161928517`
[2016-04-15T02:45Z] 2016-04-14 19:45:20 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:45:20,787 - WARNING - Could not retrieve variants from source file in region 1:161967470-161976424. Error was invalid region `1:161967471-161976424`
[2016-04-15T02:45Z] 2016-04-14 19:45:20 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:45:20,929 - WARNING - Could not retrieve variants from source file in region 1:168013639-168014040. Error was invalid region `1:168013640-168014040`
[2016-04-15T02:45Z] 2016-04-14 19:45:21 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:45:21,333 - WARNING - Could not retrieve variants from source file in region 1:161049172-161069026. Error was invalid region `1:161049173-161069026`
[2016-04-15T02:45Z] 2016-04-14 19:45:25 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:45:25,641 - WARNING - Could not retrieve variants from source file in region 1:161928116-161928517. Error was invalid region `1:161928117-161928517`
[2016-04-15T02:45Z] 2016-04-14 19:45:28 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:45:28,953 - WARNING - Could not retrieve variants from source file in region 1:160268770-160269171. Error was invalid region `1:160268771-160269171`
[2016-04-15T02:45Z] 2016-04-14 19:45:31 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:45:31,968 - WARNING - Could not retrieve variants from source file in region 1:171303479-171303880. Error was invalid region `1:171303480-171303880`
[2016-04-15T02:45Z] 2016-04-14 19:45:32 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:45:32,106 - WARNING - Could not retrieve variants from source file in region 1:159897427-159923301. Error was invalid region `1:159897428-159923301`
[2016-04-15T02:45Z] 2016-04-14 19:45:32 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:45:32,397 - WARNING - Could not retrieve variants from source file in region 1:161928116-161928517. Error was invalid region `1:161928117-161928517`
[2016-04-15T02:45Z] 2016-04-14 19:45:32 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:45:32,435 - WARNING - Could not retrieve variants from source file in region 1:161747845-161761502. Error was invalid region `1:161747846-161761502`
[2016-04-15T02:45Z] 2016-04-14 19:45:32 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:45:32,792 - WARNING - Could not retrieve variants from source file in region 1:161017345-161019230. Error was invalid region `1:161017346-161019230`
[2016-04-15T02:45Z] 2016-04-14 19:45:32 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:45:32,991 - WARNING - Could not retrieve variants from source file in region 1:171621175-171621576. Error was invalid region `1:171621176-171621576`
[2016-04-15T02:45Z] 2016-04-14 19:45:33 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:45:33,181 - WARNING - Could not retrieve variants from source file in region 1:169951786-169952187. Error was invalid region `1:169951787-169952187`
[2016-04-15T02:45Z] 2016-04-14 19:45:35 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:45:35,606 - WARNING - Could not retrieve variants from source file in region 1:160920755-160921156. Error was invalid region `1:160920756-160921156`
[2016-04-15T02:45Z] 2016-04-14 19:45:37 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:45:37,089 - WARNING - Could not retrieve variants from source file in region 1:167973765-167974166. Error was invalid region `1:167973766-167974166`
[2016-04-15T02:45Z] 2016-04-14 19:45:39 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:45:39,779 - WARNING - Could not retrieve variants from source file in region 1:161017345-161019230. Error was invalid region `1:161017346-161019230`
[2016-04-15T02:45Z] 2016-04-14 19:45:40 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:45:40,685 - WARNING - Could not retrieve variants from source file in region 1:169951786-169952187. Error was invalid region `1:169951787-169952187`
[2016-04-15T02:45Z] 2016-04-14 19:45:41 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:45:41,054 - WARNING - Could not retrieve variants from source file in region 1:160920755-160921156. Error was invalid region `1:160920756-160921156`
[2016-04-15T02:45Z] 2016-04-14 19:45:41 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:45:41,318 - WARNING - Could not retrieve variants from source file in region 1:167973765-167974166. Error was invalid region `1:167973766-167974166`
[2016-04-15T02:45Z] 2016-04-14 19:45:44 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:45:44,186 - WARNING - Could not retrieve variants from source file in region 1:161747845-161761502. Error was invalid region `1:161747846-161761502`
[2016-04-15T02:45Z] 2016-04-14 19:45:44 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:45:44,421 - WARNING - Could not retrieve variants from source file in region 1:171303479-171303880. Error was invalid region `1:171303480-171303880`
[2016-04-15T02:45Z] 2016-04-14 19:45:46 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:45:46,160 - WARNING - Could not retrieve variants from source file in region 1:161017345-161019230. Error was invalid region `1:161017346-161019230`
[2016-04-15T02:45Z] 2016-04-14 19:45:46 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:45:46,324 - WARNING - Could not retrieve variants from source file in region 1:173854997-173879052. Error was invalid region `1:173854998-173879052`
[2016-04-15T02:45Z] 2016-04-14 19:45:47 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:45:47,437 - WARNING - Could not retrieve variants from source file in region 1:174516788-174517633. Error was invalid region `1:174516789-174517633`
[2016-04-15T02:45Z] 2016-04-14 19:45:47 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:45:47,842 - WARNING - Could not retrieve variants from source file in region 1:169951786-169952187. Error was invalid region `1:169951787-169952187`
[2016-04-15T02:45Z] 2016-04-14 19:45:47 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:45:47,867 - WARNING - Could not retrieve variants from source file in region 1:161681569-161696972. Error was invalid region `1:161681570-161696972`
[2016-04-15T02:45Z] 2016-04-14 19:45:47 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:45:47,883 - WARNING - Could not retrieve variants from source file in region 1:167973765-167974166. Error was invalid region `1:167973766-167974166`
[2016-04-15T02:45Z] 2016-04-14 19:45:48 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:45:48,029 - WARNING - Could not retrieve variants from source file in region 1:160920755-160921156. Error was invalid region `1:160920756-160921156`
[2016-04-15T02:45Z] 2016-04-14 19:45:54 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:45:54,255 - WARNING - Could not retrieve variants from source file in region 1:161681569-161696972. Error was invalid region `1:161681570-161696972`
[2016-04-15T02:45Z] 2016-04-14 19:45:56 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:45:56,297 - WARNING - Could not retrieve variants from source file in region 1:171555954-171558706. Error was invalid region `1:171555955-171558706`
[2016-04-15T02:45Z] 2016-04-14 19:45:57 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:45:57,625 - WARNING - Could not retrieve variants from source file in region 1:171555954-171558706. Error was invalid region `1:171555955-171558706`
[2016-04-15T02:46Z] 2016-04-14 19:46:00 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:46:00,376 - WARNING - Could not retrieve variants from source file in region 1:171509116-171514921. Error was invalid region `1:171509117-171514921`
[2016-04-15T02:46Z] 2016-04-14 19:46:00 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:46:00,812 - WARNING - Could not retrieve variants from source file in region 1:171555954-171558706. Error was invalid region `1:171555955-171558706`
[2016-04-15T02:46Z] 2016-04-14 19:46:01 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:46:01,321 - WARNING - Could not retrieve variants from source file in region 1:160603961-160604362. Error was invalid region `1:160603962-160604362`
[2016-04-15T02:46Z] 2016-04-14 19:46:01 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:46:01,925 - WARNING - Could not retrieve variants from source file in region 1:165218468-165218869. Error was invalid region `1:165218469-165218869`
[2016-04-15T02:46Z] 2016-04-14 19:46:04 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:46:04,194 - WARNING - Could not retrieve variants from source file in region 1:169823449-169823908. Error was invalid region `1:169823450-169823908`
[2016-04-15T02:46Z] 2016-04-14 19:46:04 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:46:04,969 - WARNING - Could not retrieve variants from source file in region 1:160458773-160459174. Error was invalid region `1:160458774-160459174`
[2016-04-15T02:46Z] 2016-04-14 19:46:05 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:46:05,580 - WARNING - Could not retrieve variants from source file in region 1:171509116-171514921. Error was invalid region `1:171509117-171514921`
[2016-04-15T02:46Z] 2016-04-14 19:46:06 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:46:06,297 - WARNING - Could not retrieve variants from source file in region 1:160603961-160604362. Error was invalid region `1:160603962-160604362`
[2016-04-15T02:46Z] 2016-04-14 19:46:06 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:46:06,695 - WARNING - Could not retrieve variants from source file in region 1:165218468-165218869. Error was invalid region `1:165218469-165218869`
[2016-04-15T02:46Z] 2016-04-14 19:46:07 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:46:07,468 - WARNING - Could not retrieve variants from source file in region 1:169676275-169697458. Error was invalid region `1:169676276-169697458`
[2016-04-15T02:46Z] 2016-04-14 19:46:09 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:46:09,701 - WARNING - Could not retrieve variants from source file in region 1:167817428-167849604. Error was invalid region `1:167817429-167849604`
[2016-04-15T02:46Z] 2016-04-14 19:46:10 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:46:10,213 - WARNING - Could not retrieve variants from source file in region 1:171239482-171252477. Error was invalid region `1:171239483-171252477`
[2016-04-15T02:46Z] 2016-04-14 19:46:10 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:46:10,947 - WARNING - Could not retrieve variants from source file in region 1:169823449-169823908. Error was invalid region `1:169823450-169823908`
[2016-04-15T02:46Z] 2016-04-14 19:46:11 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:46:11,165 - WARNING - Could not retrieve variants from source file in region 1:171509116-171514921. Error was invalid region `1:171509117-171514921`
[2016-04-15T02:46Z] 2016-04-14 19:46:11 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:46:11,194 - WARNING - Could not retrieve variants from source file in region 1:167893548-167906429. Error was invalid region `1:167893549-167906429`
[2016-04-15T02:46Z] 2016-04-14 19:46:11 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:46:11,733 - WARNING - Could not retrieve variants from source file in region 1:165218468-165218869. Error was invalid region `1:165218469-165218869`
[2016-04-15T02:46Z] 2016-04-14 19:46:11 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:46:11,818 - WARNING - Could not retrieve variants from source file in region 1:160603961-160604362. Error was invalid region `1:160603962-160604362`
[2016-04-15T02:46Z] 2016-04-14 19:46:14 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:46:14,443 - WARNING - Could not retrieve variants from source file in region 1:164815726-164817146. Error was invalid region `1:164815727-164817146`
[2016-04-15T02:46Z] 2016-04-14 19:46:15 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:46:15,883 - WARNING - Could not retrieve variants from source file in region 1:160458773-160459174. Error was invalid region `1:160458774-160459174`
[2016-04-15T02:46Z] 2016-04-14 19:46:15 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:46:15,940 - WARNING - Could not retrieve variants from source file in region 1:160057311-160062917. Error was invalid region `1:160057312-160062917`
[2016-04-15T02:46Z] 2016-04-14 19:46:16 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:46:16,558 - WARNING - Could not retrieve variants from source file in region 1:169823449-169823908. Error was invalid region `1:169823450-169823908`
[2016-04-15T02:46Z] 2016-04-14 19:46:19 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:46:19,418 - WARNING - Could not retrieve variants from source file in region 1:167817428-167849604. Error was invalid region `1:167817429-167849604`
[2016-04-15T02:46Z] 2016-04-14 19:46:23 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:46:23,896 - WARNING - Could not retrieve variants from source file in region 1:171168334-171168775. Error was invalid region `1:171168335-171168775`
[2016-04-15T02:46Z] 2016-04-14 19:46:25 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:46:25,622 - WARNING - Could not retrieve variants from source file in region 1:159751855-159752256. Error was invalid region `1:159751856-159752256`
[2016-04-15T02:46Z] 2016-04-14 19:46:27 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:46:27,409 - WARNING - Could not retrieve variants from source file in region 1:165173005-165173406. Error was invalid region `1:165173006-165173406`
[2016-04-15T02:46Z] 2016-04-14 19:46:27 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:46:27,456 - WARNING - Could not retrieve variants from source file in region 1:159751855-159752256. Error was invalid region `1:159751856-159752256`
[2016-04-15T02:46Z] 2016-04-14 19:46:29 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:46:29,469 - WARNING - Could not retrieve variants from source file in region 1:159558047-159558448. Error was invalid region `1:159558048-159558448`
[2016-04-15T02:46Z] 2016-04-14 19:46:30 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:46:30,471 - WARNING - Could not retrieve variants from source file in region 1:169764357-169768270. Error was invalid region `1:169764358-169768270`
[2016-04-15T02:46Z] 2016-04-14 19:46:30 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:46:30,802 - WARNING - Could not retrieve variants from source file in region 1:167042551-167042952. Error was invalid region `1:167042552-167042952`
[2016-04-15T02:46Z] 2016-04-14 19:46:32 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:46:32,499 - WARNING - Could not retrieve variants from source file in region 1:165173005-165173406. Error was invalid region `1:165173006-165173406`
[2016-04-15T02:46Z] 2016-04-14 19:46:32 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:46:32,557 - WARNING - Could not retrieve variants from source file in region 1:166958390-166958900. Error was invalid region `1:166958391-166958900`
[2016-04-15T02:46Z] 2016-04-14 19:46:33 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:46:33,152 - WARNING - Could not retrieve variants from source file in region 1:165173005-165173406. Error was invalid region `1:165173006-165173406`
[2016-04-15T02:46Z] 2016-04-14 19:46:33 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:46:33,204 - WARNING - Could not retrieve variants from source file in region 1:159504890-159505487. Error was invalid region `1:159504891-159505487`
[2016-04-15T02:46Z] 2016-04-14 19:46:33 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:46:33,665 - WARNING - Could not retrieve variants from source file in region 1:159558047-159558448. Error was invalid region `1:159558048-159558448`
[2016-04-15T02:46Z] 2016-04-14 19:46:35 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:46:35,022 - WARNING - Could not retrieve variants from source file in region 1:169764357-169768270. Error was invalid region `1:169764358-169768270`
[2016-04-15T02:46Z] 2016-04-14 19:46:36 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:46:36,201 - WARNING - Could not retrieve variants from source file in region 1:159558047-159558448. Error was invalid region `1:159558048-159558448`
[2016-04-15T02:46Z] 2016-04-14 19:46:36 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:46:36,218 - WARNING - Could not retrieve variants from source file in region 1:163309008-163309409. Error was invalid region `1:163309009-163309409`
[2016-04-15T02:46Z] 2016-04-14 19:46:38 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:46:38,206 - WARNING - Could not retrieve variants from source file in region 1:164528909-164529310. Error was invalid region `1:164528910-164529310`
[2016-04-15T02:46Z] 2016-04-14 19:46:39 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:46:39,529 - WARNING - Could not retrieve variants from source file in region 1:169764357-169768270. Error was invalid region `1:169764358-169768270`
[2016-04-15T02:46Z] 2016-04-14 19:46:40 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:46:40,460 - WARNING - Could not retrieve variants from source file in region 1:163309008-163309409. Error was invalid region `1:163309009-163309409`
[2016-04-15T02:46Z] 2016-04-14 19:46:41 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:46:41,815 - WARNING - Could not retrieve variants from source file in region 1:170928460-170928861. Error was invalid region `1:170928461-170928861`
[2016-04-15T02:46Z] 2016-04-14 19:46:44 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:46:44,660 - WARNING - Could not retrieve variants from source file in region 1:163309008-163309409. Error was invalid region `1:163309009-163309409`
[2016-04-15T02:46Z] 2016-04-14 19:46:45 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:46:45,858 - WARNING - Could not retrieve variants from source file in region 1:170928460-170928861. Error was invalid region `1:170928461-170928861`
[2016-04-15T02:46Z] 2016-04-14 19:46:46 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:46:46,373 - WARNING - Could not retrieve variants from source file in region 1:170928460-170928861. Error was invalid region `1:170928461-170928861`
[2016-04-15T02:46Z] 2016-04-14 19:46:46 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:46:46,573 - WARNING - Could not retrieve variants from source file in region 1:166818355-166818756. Error was invalid region `1:166818356-166818756`
[2016-04-15T02:46Z] 2016-04-14 19:46:50 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:46:50,105 - WARNING - Could not retrieve variants from source file in region 1:169390746-169391344. Error was invalid region `1:169390747-169391344`
[2016-04-15T02:46Z] 2016-04-14 19:46:50 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:46:50,141 - WARNING - Could not retrieve variants from source file in region 1:165865267-165865668. Error was invalid region `1:165865268-165865668`
[2016-04-15T02:46Z] 2016-04-14 19:46:50 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:46:50,751 - WARNING - Could not retrieve variants from source file in region 1:169293510-169293911. Error was invalid region `1:169293511-169293911`
[2016-04-15T02:46Z] 2016-04-14 19:46:51 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:46:51,318 - WARNING - Could not retrieve variants from source file in region 1:169390746-169391344. Error was invalid region `1:169390747-169391344`
[2016-04-15T02:46Z] 2016-04-14 19:46:53 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:46:53,163 - WARNING - Could not retrieve variants from source file in region 1:163038642-163039043. Error was invalid region `1:163038643-163039043`
[2016-04-15T02:46Z] 2016-04-14 19:46:53 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:46:53,582 - WARNING - Could not retrieve variants from source file in region 1:169293510-169293911. Error was invalid region `1:169293511-169293911`
[2016-04-15T02:46Z] 2016-04-14 19:46:53 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:46:53,587 - WARNING - Could not retrieve variants from source file in region 1:162775056-162775457. Error was invalid region `1:162775057-162775457`
[2016-04-15T02:46Z] 2016-04-14 19:46:53 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:46:53,840 - WARNING - Could not retrieve variants from source file in region 1:162775056-162775457. Error was invalid region `1:162775057-162775457`
[2016-04-15T02:46Z] 2016-04-14 19:46:54 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:46:54,367 - WARNING - Could not retrieve variants from source file in region 1:169293510-169293911. Error was invalid region `1:169293511-169293911`
[2016-04-15T02:46Z] 2016-04-14 19:46:55 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:46:55,048 - WARNING - Could not retrieve variants from source file in region 1:163038642-163039043. Error was invalid region `1:163038643-163039043`
[2016-04-15T02:46Z] 2016-04-14 19:46:56 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:46:56,315 - WARNING - Could not retrieve variants from source file in region 1:163038642-163039043. Error was invalid region `1:163038643-163039043`
[2016-04-15T02:46Z] 2016-04-14 19:46:57 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:46:57,120 - WARNING - Could not retrieve variants from source file in region 1:168105888-168106289. Error was invalid region `1:168105889-168106289`
[2016-04-15T02:46Z] 2016-04-14 19:46:57 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:46:57,368 - WARNING - Could not retrieve variants from source file in region 1:162775056-162775457. Error was invalid region `1:162775057-162775457`
[2016-04-15T02:46Z] 2016-04-14 19:46:59 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:46:59,098 - WARNING - Could not retrieve variants from source file in region 1:168105888-168106289. Error was invalid region `1:168105889-168106289`
[2016-04-15T02:47Z] ['bcbio-variation-recall', 'square', '-Xms750m', '-Xmx7280m', '-XX:+UseSerialGC', '-c', 16, '-r', u'1:175048469-192127886', '--caller', 'platypus', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/1/Batch1-1_175048468_192127886.vcf.gz', '/mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/1/Batch1-1_175048468_192127886.vcf-inputs.txt'] in region: 1:175048469-192127886
[2016-04-15T02:47Z] 2016-04-14 19:47:13 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:47:13,436 - WARNING - Could not retrieve variants from source file in region 1:179347621-179348022. Error was invalid region `1:179347622-179348022`
[2016-04-15T02:47Z] 2016-04-14 19:47:14 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:47:14,091 - WARNING - Could not retrieve variants from source file in region 1:190122984-190123385. Error was invalid region `1:190122985-190123385`
[2016-04-15T02:47Z] 2016-04-14 19:47:15 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:47:15,687 - WARNING - Could not retrieve variants from source file in region 1:186946701-186947102. Error was invalid region `1:186946702-186947102`
[2016-04-15T02:47Z] 2016-04-14 19:47:16 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:47:16,211 - WARNING - Could not retrieve variants from source file in region 1:183875971-183876372. Error was invalid region `1:183875972-183876372`
[2016-04-15T02:47Z] 2016-04-14 19:47:16 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:47:16,457 - WARNING - Could not retrieve variants from source file in region 1:182850272-182850917. Error was invalid region `1:182850273-182850917`
[2016-04-15T02:47Z] 2016-04-14 19:47:16 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:47:16,583 - WARNING - Could not retrieve variants from source file in region 1:185984306-185984707. Error was invalid region `1:185984307-185984707`
[2016-04-15T02:47Z] 2016-04-14 19:47:16 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:47:16,753 - WARNING - Could not retrieve variants from source file in region 1:183184479-183184880. Error was invalid region `1:183184480-183184880`
[2016-04-15T02:47Z] 2016-04-14 19:47:17 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:47:17,021 - WARNING - Could not retrieve variants from source file in region 1:183486648-183496002. Error was invalid region `1:183486649-183496002`
[2016-04-15T02:47Z] 2016-04-14 19:47:17 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:47:17,040 - WARNING - Could not retrieve variants from source file in region 1:185135534-185143911. Error was invalid region `1:185135535-185143911`
[2016-04-15T02:47Z] 2016-04-14 19:47:18 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:47:18,950 - WARNING - Could not retrieve variants from source file in region 1:179347621-179348022. Error was invalid region `1:179347622-179348022`
[2016-04-15T02:47Z] 2016-04-14 19:47:19 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:47:19,283 - WARNING - Could not retrieve variants from source file in region 1:190122984-190123385. Error was invalid region `1:190122985-190123385`
[2016-04-15T02:47Z] 2016-04-14 19:47:19 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:47:19,840 - WARNING - Could not retrieve variants from source file in region 1:186362908-186363309. Error was invalid region `1:186362909-186363309`
[2016-04-15T02:47Z] 2016-04-14 19:47:22 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:47:22,833 - WARNING - Could not retrieve variants from source file in region 1:186101328-186101729. Error was invalid region `1:186101329-186101729`
[2016-04-15T02:47Z] 2016-04-14 19:47:23 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:47:23,097 - WARNING - Could not retrieve variants from source file in region 1:186946701-186947102. Error was invalid region `1:186946702-186947102`
[2016-04-15T02:47Z] 2016-04-14 19:47:23 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:47:23,822 - WARNING - Could not retrieve variants from source file in region 1:184663326-184677654. Error was invalid region `1:184663327-184677654`
[2016-04-15T02:47Z] 2016-04-14 19:47:24 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:47:24,499 - WARNING - Could not retrieve variants from source file in region 1:183875971-183876372. Error was invalid region `1:183875972-183876372`
[2016-04-15T02:47Z] 2016-04-14 19:47:24 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:47:24,631 - WARNING - Could not retrieve variants from source file in region 1:184006338-184023719. Error was invalid region `1:184006339-184023719`
[2016-04-15T02:47Z] 2016-04-14 19:47:24 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:47:24,760 - WARNING - Could not retrieve variants from source file in region 1:179347621-179348022. Error was invalid region `1:179347622-179348022`
[2016-04-15T02:47Z] 2016-04-14 19:47:24 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:47:24,968 - WARNING - Could not retrieve variants from source file in region 1:182356188-182369423. Error was invalid region `1:182356189-182369423`
[2016-04-15T02:47Z] 2016-04-14 19:47:25 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:47:25,131 - WARNING - Could not retrieve variants from source file in region 1:190122984-190123385. Error was invalid region `1:190122985-190123385`
[2016-04-15T02:47Z] 2016-04-14 19:47:25 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:47:25,204 - WARNING - Could not retrieve variants from source file in region 1:185135534-185143911. Error was invalid region `1:185135535-185143911`
[2016-04-15T02:47Z] 2016-04-14 19:47:25 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:47:25,331 - WARNING - Could not retrieve variants from source file in region 1:186362908-186363309. Error was invalid region `1:186362909-186363309`
[2016-04-15T02:47Z] 2016-04-14 19:47:29 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:47:29,396 - WARNING - Could not retrieve variants from source file in region 1:186101328-186101729. Error was invalid region `1:186101329-186101729`
[2016-04-15T02:47Z] 2016-04-14 19:47:30 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:47:30,017 - WARNING - Could not retrieve variants from source file in region 1:186946701-186947102. Error was invalid region `1:186946702-186947102`
[2016-04-15T02:47Z] 2016-04-14 19:47:31 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:47:31,821 - WARNING - Could not retrieve variants from source file in region 1:182850272-182850917. Error was invalid region `1:182850273-182850917`
[2016-04-15T02:47Z] 2016-04-14 19:47:33 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:47:33,325 - WARNING - Could not retrieve variants from source file in region 1:183184479-183184880. Error was invalid region `1:183184480-183184880`
[2016-04-15T02:47Z] 2016-04-14 19:47:33 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:47:33,445 - WARNING - Could not retrieve variants from source file in region 1:185984306-185984707. Error was invalid region `1:185984307-185984707`
[2016-04-15T02:47Z] 2016-04-14 19:47:34 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:47:34,132 - WARNING - Could not retrieve variants from source file in region 1:185135534-185143911. Error was invalid region `1:185135535-185143911`
[2016-04-15T02:47Z] 2016-04-14 19:47:34 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:47:34,199 - WARNING - Could not retrieve variants from source file in region 1:183486648-183496002. Error was invalid region `1:183486649-183496002`
[2016-04-15T02:47Z] 2016-04-14 19:47:43 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:47:43,802 - WARNING - Could not retrieve variants from source file in region 1:179310228-179310629. Error was invalid region `1:179310229-179310629`
[2016-04-15T02:47Z] 2016-04-14 19:47:44 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:47:44,867 - WARNING - Could not retrieve variants from source file in region 1:186839650-186840051. Error was invalid region `1:186839651-186840051`
[2016-04-15T02:47Z] 2016-04-14 19:47:46 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:47:46,013 - WARNING - Could not retrieve variants from source file in region 1:179989531-179989932. Error was invalid region `1:179989532-179989932`
[2016-04-15T02:47Z] 2016-04-14 19:47:47 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:47:47,705 - WARNING - Could not retrieve variants from source file in region 1:186026263-186050607. Error was invalid region `1:186026264-186050607`
[2016-04-15T02:47Z] 2016-04-14 19:47:48 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:47:48,966 - WARNING - Could not retrieve variants from source file in region 1:183072379-183105895. Error was invalid region `1:183072380-183105895`
[2016-04-15T02:47Z] 2016-04-14 19:47:49 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:47:49,523 - WARNING - Could not retrieve variants from source file in region 1:179310228-179310629. Error was invalid region `1:179310229-179310629`
[2016-04-15T02:47Z] 2016-04-14 19:47:50 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:47:50,205 - WARNING - Could not retrieve variants from source file in region 1:186273783-186278179. Error was invalid region `1:186273784-186278179`
[2016-04-15T02:47Z] 2016-04-14 19:47:50 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:47:50,509 - WARNING - Could not retrieve variants from source file in region 1:184836809-184837210. Error was invalid region `1:184836810-184837210`
[2016-04-15T02:47Z] 2016-04-14 19:47:50 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:47:50,671 - WARNING - Could not retrieve variants from source file in region 1:179631031-179631432. Error was invalid region `1:179631032-179631432`
[2016-04-15T02:47Z] 2016-04-14 19:47:51 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:47:51,049 - WARNING - Could not retrieve variants from source file in region 1:179989531-179989932. Error was invalid region `1:179989532-179989932`
[2016-04-15T02:47Z] 2016-04-14 19:47:51 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:47:51,537 - WARNING - Could not retrieve variants from source file in region 1:179828273-179887315. Error was invalid region `1:179828274-179887315`
[2016-04-15T02:47Z] 2016-04-14 19:47:52 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:47:52,111 - WARNING - Could not retrieve variants from source file in region 1:185240263-185240664. Error was invalid region `1:185240264-185240664`
[2016-04-15T02:47Z] 2016-04-14 19:47:52 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:47:52,664 - WARNING - Could not retrieve variants from source file in region 1:186026263-186050607. Error was invalid region `1:186026264-186050607`
[2016-04-15T02:47Z] 2016-04-14 19:47:52 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:47:52,887 - WARNING - Could not retrieve variants from source file in region 1:183904862-183907860. Error was invalid region `1:183904863-183907860`
[2016-04-15T02:47Z] 2016-04-14 19:47:54 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:47:54,561 - WARNING - Could not retrieve variants from source file in region 1:179310228-179310629. Error was invalid region `1:179310229-179310629`
[2016-04-15T02:47Z] 2016-04-14 19:47:55 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:47:55,281 - WARNING - Could not retrieve variants from source file in region 1:186273783-186278179. Error was invalid region `1:186273784-186278179`
[2016-04-15T02:47Z] 2016-04-14 19:47:56 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:47:56,440 - WARNING - Could not retrieve variants from source file in region 1:184836809-184837210. Error was invalid region `1:184836810-184837210`
[2016-04-15T02:47Z] 2016-04-14 19:47:56 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:47:56,447 - WARNING - Could not retrieve variants from source file in region 1:179631031-179631432. Error was invalid region `1:179631032-179631432`
[2016-04-15T02:47Z] 2016-04-14 19:47:56 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:47:56,666 - WARNING - Could not retrieve variants from source file in region 1:179989531-179989932. Error was invalid region `1:179989532-179989932`
[2016-04-15T02:47Z] 2016-04-14 19:47:57 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:47:57,547 - WARNING - Could not retrieve variants from source file in region 1:181701588-181759847. Error was invalid region `1:181701589-181759847`
[2016-04-15T02:47Z] 2016-04-14 19:47:57 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:47:57,642 - WARNING - Could not retrieve variants from source file in region 1:185240263-185240664. Error was invalid region `1:185240264-185240664`
[2016-04-15T02:47Z] 2016-04-14 19:47:58 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:47:58,042 - WARNING - Could not retrieve variants from source file in region 1:186026263-186050607. Error was invalid region `1:186026264-186050607`
[2016-04-15T02:48Z] 2016-04-14 19:48:01 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:48:01,787 - WARNING - Could not retrieve variants from source file in region 1:184836809-184837210. Error was invalid region `1:184836810-184837210`
[2016-04-15T02:48Z] 2016-04-14 19:48:01 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:48:01,917 - WARNING - Could not retrieve variants from source file in region 1:179631031-179631432. Error was invalid region `1:179631032-179631432`
[2016-04-15T02:48Z] 2016-04-14 19:48:03 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:48:03,355 - WARNING - Could not retrieve variants from source file in region 1:185240263-185240664. Error was invalid region `1:185240264-185240664`
[2016-04-15T02:48Z] 2016-04-14 19:48:03 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:48:03,751 - WARNING - Could not retrieve variants from source file in region 1:181701588-181759847. Error was invalid region `1:181701589-181759847`
[2016-04-15T02:48Z] 2016-04-14 19:48:08 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:48:08,455 - WARNING - Could not retrieve variants from source file in region 1:182496618-182497019. Error was invalid region `1:182496619-182497019`
[2016-04-15T02:48Z] 2016-04-14 19:48:08 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:48:08,706 - WARNING - Could not retrieve variants from source file in region 1:179051089-179065315. Error was invalid region `1:179051090-179065315`
[2016-04-15T02:48Z] 2016-04-14 19:48:12 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:48:12,401 - WARNING - Could not retrieve variants from source file in region 1:185171658-185172059. Error was invalid region `1:185171659-185172059`
[2016-04-15T02:48Z] 2016-04-14 19:48:12 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:48:12,653 - WARNING - Could not retrieve variants from source file in region 1:185171658-185172059. Error was invalid region `1:185171659-185172059`
[2016-04-15T02:48Z] 2016-04-14 19:48:12 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:48:12,865 - WARNING - Could not retrieve variants from source file in region 1:182992814-182993215. Error was invalid region `1:182992815-182993215`
[2016-04-15T02:48Z] 2016-04-14 19:48:12 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:48:12,903 - WARNING - Could not retrieve variants from source file in region 1:181058432-181058833. Error was invalid region `1:181058433-181058833`
[2016-04-15T02:48Z] 2016-04-14 19:48:13 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:48:13,437 - WARNING - Could not retrieve variants from source file in region 1:184800854-184801255. Error was invalid region `1:184800855-184801255`
[2016-04-15T02:48Z] 2016-04-14 19:48:13 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:48:13,691 - WARNING - Could not retrieve variants from source file in region 1:182496618-182497019. Error was invalid region `1:182496619-182497019`
[2016-04-15T02:48Z] 2016-04-14 19:48:15 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:48:15,259 - WARNING - Could not retrieve variants from source file in region 1:179604653-179605054. Error was invalid region `1:179604654-179605054`
[2016-04-15T02:48Z] 2016-04-14 19:48:17 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:48:17,023 - WARNING - Could not retrieve variants from source file in region 1:182442803-182443652. Error was invalid region `1:182442804-182443652`
[2016-04-15T02:48Z] 2016-04-14 19:48:17 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:48:17,102 - WARNING - Could not retrieve variants from source file in region 1:179503814-179562930. Error was invalid region `1:179503815-179562930`
[2016-04-15T02:48Z] 2016-04-14 19:48:17 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:48:17,133 - WARNING - Could not retrieve variants from source file in region 1:181548130-181548531. Error was invalid region `1:181548131-181548531`
[2016-04-15T02:48Z] 2016-04-14 19:48:17 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:48:17,404 - WARNING - Could not retrieve variants from source file in region 1:185171658-185172059. Error was invalid region `1:185171659-185172059`
[2016-04-15T02:48Z] 2016-04-14 19:48:17 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:48:17,705 - WARNING - Could not retrieve variants from source file in region 1:181058432-181058833. Error was invalid region `1:181058433-181058833`
[2016-04-15T02:48Z] 2016-04-14 19:48:17 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:48:17,985 - WARNING - Could not retrieve variants from source file in region 1:184800854-184801255. Error was invalid region `1:184800855-184801255`
[2016-04-15T02:48Z] 2016-04-14 19:48:18 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:48:18,194 - WARNING - Could not retrieve variants from source file in region 1:184764470-184765262. Error was invalid region `1:184764471-184765262`
[2016-04-15T02:48Z] 2016-04-14 19:48:19 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:48:19,608 - WARNING - Could not retrieve variants from source file in region 1:179604653-179605054. Error was invalid region `1:179604654-179605054`
[2016-04-15T02:48Z] 2016-04-14 19:48:21 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:48:21,538 - WARNING - Could not retrieve variants from source file in region 1:181548130-181548531. Error was invalid region `1:181548131-181548531`
[2016-04-15T02:48Z] 2016-04-14 19:48:21 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:48:21,755 - WARNING - Could not retrieve variants from source file in region 1:179503814-179562930. Error was invalid region `1:179503815-179562930`
[2016-04-15T02:48Z] 2016-04-14 19:48:22 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:48:22,459 - WARNING - Could not retrieve variants from source file in region 1:176992342-176992866. Error was invalid region `1:176992343-176992866`
[2016-04-15T02:48Z] 2016-04-14 19:48:22 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:48:22,479 - WARNING - Could not retrieve variants from source file in region 1:181058432-181058833. Error was invalid region `1:181058433-181058833`
[2016-04-15T02:48Z] 2016-04-14 19:48:22 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:48:22,602 - WARNING - Could not retrieve variants from source file in region 1:184800854-184801255. Error was invalid region `1:184800855-184801255`
[2016-04-15T02:48Z] 2016-04-14 19:48:23 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:48:23,873 - WARNING - Could not retrieve variants from source file in region 1:179604653-179605054. Error was invalid region `1:179604654-179605054`
[2016-04-15T02:48Z] 2016-04-14 19:48:25 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:48:25,651 - WARNING - Could not retrieve variants from source file in region 1:181548130-181548531. Error was invalid region `1:181548131-181548531`
[2016-04-15T02:48Z] 2016-04-14 19:48:25 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:48:25,855 - WARNING - Could not retrieve variants from source file in region 1:179503814-179562930. Error was invalid region `1:179503815-179562930`
[2016-04-15T02:48Z] 2016-04-14 19:48:30 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:48:30,726 - WARNING - Could not retrieve variants from source file in region 1:176992342-176992866. Error was invalid region `1:176992343-176992866`
[2016-04-15T02:48Z] 2016-04-14 19:48:33 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:48:33,218 - WARNING - Could not retrieve variants from source file in region 1:176863625-176864057. Error was invalid region `1:176863626-176864057`
[2016-04-15T02:48Z] 2016-04-14 19:48:33 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:48:33,317 - WARNING - Could not retrieve variants from source file in region 1:176659252-176660437. Error was invalid region `1:176659253-176660437`
[2016-04-15T02:48Z] 2016-04-14 19:48:34 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:48:34,317 - WARNING - Could not retrieve variants from source file in region 1:178834642-178835043. Error was invalid region `1:178834643-178835043`
[2016-04-15T02:48Z] 2016-04-14 19:48:35 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:48:35,107 - WARNING - Could not retrieve variants from source file in region 1:180243313-180243714. Error was invalid region `1:180243314-180243714`
[2016-04-15T02:48Z] 2016-04-14 19:48:35 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:48:35,229 - WARNING - Could not retrieve variants from source file in region 1:179413894-179414295. Error was invalid region `1:179413895-179414295`
[2016-04-15T02:48Z] 2016-04-14 19:48:37 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:48:37,059 - WARNING - Could not retrieve variants from source file in region 1:176863625-176864057. Error was invalid region `1:176863626-176864057`
[2016-04-15T02:48Z] 2016-04-14 19:48:38 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:48:38,357 - WARNING - Could not retrieve variants from source file in region 1:178834642-178835043. Error was invalid region `1:178834643-178835043`
[2016-04-15T02:48Z] 2016-04-14 19:48:38 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:48:38,416 - WARNING - Could not retrieve variants from source file in region 1:178745736-178746137. Error was invalid region `1:178745737-178746137`
[2016-04-15T02:48Z] 2016-04-14 19:48:39 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:48:39,047 - WARNING - Could not retrieve variants from source file in region 1:180243313-180243714. Error was invalid region `1:180243314-180243714`
[2016-04-15T02:48Z] 2016-04-14 19:48:39 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:48:39,049 - WARNING - Could not retrieve variants from source file in region 1:180885219-180915156. Error was invalid region `1:180885220-180915156`
[2016-04-15T02:48Z] 2016-04-14 19:48:39 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:48:39,432 - WARNING - Could not retrieve variants from source file in region 1:180953642-180954043. Error was invalid region `1:180953643-180954043`
[2016-04-15T02:48Z] 2016-04-14 19:48:41 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:48:41,051 - WARNING - Could not retrieve variants from source file in region 1:176863625-176864057. Error was invalid region `1:176863626-176864057`
[2016-04-15T02:48Z] 2016-04-14 19:48:41 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:48:41,216 - WARNING - Could not retrieve variants from source file in region 1:176659252-176660437. Error was invalid region `1:176659253-176660437`
[2016-04-15T02:48Z] 2016-04-14 19:48:43 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:48:43,112 - WARNING - Could not retrieve variants from source file in region 1:180885219-180915156. Error was invalid region `1:180885220-180915156`
[2016-04-15T02:48Z] 2016-04-14 19:48:43 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:48:43,511 - WARNING - Could not retrieve variants from source file in region 1:180243313-180243714. Error was invalid region `1:180243314-180243714`
[2016-04-15T02:48Z] 2016-04-14 19:48:43 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:48:43,668 - WARNING - Could not retrieve variants from source file in region 1:180953642-180954043. Error was invalid region `1:180953643-180954043`
[2016-04-15T02:48Z] 2016-04-14 19:48:46 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:48:46,398 - WARNING - Could not retrieve variants from source file in region 1:178745736-178746137. Error was invalid region `1:178745737-178746137`
[2016-04-15T02:48Z] 2016-04-14 19:48:52 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:48:52,192 - WARNING - Could not retrieve variants from source file in region 1:175299090-175375992. Error was invalid region `1:175299091-175375992`
[2016-04-15T02:48Z] 2016-04-14 19:48:54 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:48:54,710 - WARNING - Could not retrieve variants from source file in region 1:175049168-175054738. Error was invalid region `1:175049169-175054738`
[2016-04-15T02:48Z] 2016-04-14 19:48:54 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:48:54,737 - WARNING - Could not retrieve variants from source file in region 1:177901444-177930177. Error was invalid region `1:177901445-177930177`
[2016-04-15T02:48Z] 2016-04-14 19:48:54 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:48:54,771 - WARNING - Could not retrieve variants from source file in region 1:177901444-177930177. Error was invalid region `1:177901445-177930177`
[2016-04-15T02:49Z] ['bcbio-variation-recall', 'square', '-Xms750m', '-Xmx7280m', '-XX:+UseSerialGC', '-c', 16, '-r', u'1:192128350-207640257', '--caller', 'platypus', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/1/Batch1-1_192128349_207640257.vcf.gz', '/mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/1/Batch1-1_192128349_207640257.vcf-inputs.txt'] in region: 1:192128350-207640257
[2016-04-15T02:49Z] 2016-04-14 19:49:12 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:49:12,471 - WARNING - Could not retrieve variants from source file in region 1:202431791-202432350. Error was invalid region `1:202431792-202432350`
[2016-04-15T02:49Z] 2016-04-14 19:49:12 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:49:12,510 - WARNING - Could not retrieve variants from source file in region 1:205130202-205130603. Error was invalid region `1:205130203-205130603`
[2016-04-15T02:49Z] 2016-04-14 19:49:13 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:49:13,166 - WARNING - Could not retrieve variants from source file in region 1:201112770-201123137. Error was invalid region `1:201112771-201123137`
[2016-04-15T02:49Z] 2016-04-14 19:49:13 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:49:13,277 - WARNING - Could not retrieve variants from source file in region 1:207195568-207195969. Error was invalid region `1:207195569-207195969`
[2016-04-15T02:49Z] 2016-04-14 19:49:13 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:49:13,858 - WARNING - Could not retrieve variants from source file in region 1:202977598-202977999. Error was invalid region `1:202977599-202977999`
[2016-04-15T02:49Z] 2016-04-14 19:49:14 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:49:14,027 - WARNING - Could not retrieve variants from source file in region 1:206904829-206905230. Error was invalid region `1:206904830-206905230`
[2016-04-15T02:49Z] 2016-04-14 19:49:19 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:49:19,075 - WARNING - Could not retrieve variants from source file in region 1:206730430-206730881. Error was invalid region `1:206730431-206730881`
[2016-04-15T02:49Z] 2016-04-14 19:49:19 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:49:19,370 - WARNING - Could not retrieve variants from source file in region 1:200956077-200959492. Error was invalid region `1:200956078-200959492`
[2016-04-15T02:49Z] 2016-04-14 19:49:20 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:49:20,645 - WARNING - Could not retrieve variants from source file in region 1:202431791-202432350. Error was invalid region `1:202431792-202432350`
[2016-04-15T02:49Z] 2016-04-14 19:49:21 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:49:21,667 - WARNING - Could not retrieve variants from source file in region 1:205130202-205130603. Error was invalid region `1:205130203-205130603`
[2016-04-15T02:49Z] 2016-04-14 19:49:22 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:49:22,196 - WARNING - Could not retrieve variants from source file in region 1:201112770-201123137. Error was invalid region `1:201112771-201123137`
[2016-04-15T02:49Z] 2016-04-14 19:49:22 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:49:22,630 - WARNING - Could not retrieve variants from source file in region 1:207195568-207195969. Error was invalid region `1:207195569-207195969`
[2016-04-15T02:49Z] 2016-04-14 19:49:23 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:49:23,209 - WARNING - Could not retrieve variants from source file in region 1:200776430-200776831. Error was invalid region `1:200776431-200776831`
[2016-04-15T02:49Z] 2016-04-14 19:49:24 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:49:24,575 - WARNING - Could not retrieve variants from source file in region 1:205767674-205814687. Error was invalid region `1:205767675-205814687`
[2016-04-15T02:49Z] 2016-04-14 19:49:26 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:49:26,763 - WARNING - Could not retrieve variants from source file in region 1:202431791-202432350. Error was invalid region `1:202431792-202432350`
[2016-04-15T02:49Z] 2016-04-14 19:49:29 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:49:29,006 - WARNING - Could not retrieve variants from source file in region 1:207195568-207195969. Error was invalid region `1:207195569-207195969`
[2016-04-15T02:49Z] 2016-04-14 19:49:29 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:49:29,128 - WARNING - Could not retrieve variants from source file in region 1:205130202-205130603. Error was invalid region `1:205130203-205130603`
[2016-04-15T02:49Z] 2016-04-14 19:49:30 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:49:30,394 - WARNING - Could not retrieve variants from source file in region 1:201112770-201123137. Error was invalid region `1:201112771-201123137`
[2016-04-15T02:49Z] 2016-04-14 19:49:31 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:49:31,336 - WARNING - Could not retrieve variants from source file in region 1:202977598-202977999. Error was invalid region `1:202977599-202977999`
[2016-04-15T02:49Z] 2016-04-14 19:49:41 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:49:41,120 - WARNING - Could not retrieve variants from source file in region 1:200880767-200881362. Error was invalid region `1:200880768-200881362`
[2016-04-15T02:49Z] 2016-04-14 19:49:43 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:49:43,633 - WARNING - Could not retrieve variants from source file in region 1:202276283-202305058. Error was invalid region `1:202276284-202305058`
[2016-04-15T02:49Z] 2016-04-14 19:49:45 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:49:45,582 - WARNING - Could not retrieve variants from source file in region 1:207007430-207016147. Error was invalid region `1:207007431-207016147`
[2016-04-15T02:49Z] 2016-04-14 19:49:45 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:49:45,752 - WARNING - Could not retrieve variants from source file in region 1:207074694-207134294. Error was invalid region `1:207074695-207134294`
[2016-04-15T02:49Z] 2016-04-14 19:49:45 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:49:45,759 - WARNING - Could not retrieve variants from source file in region 1:206773448-206773849. Error was invalid region `1:206773449-206773849`
[2016-04-15T02:49Z] 2016-04-14 19:49:46 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:49:46,386 - WARNING - Could not retrieve variants from source file in region 1:200880767-200881362. Error was invalid region `1:200880768-200881362`
[2016-04-15T02:49Z] 2016-04-14 19:49:47 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:49:47,309 - WARNING - Could not retrieve variants from source file in region 1:205027526-205053409. Error was invalid region `1:205027527-205053409`
[2016-04-15T02:49Z] 2016-04-14 19:49:47 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:49:47,809 - WARNING - Could not retrieve variants from source file in region 1:205686312-205686815. Error was invalid region `1:205686313-205686815`
[2016-04-15T02:49Z] 2016-04-14 19:49:48 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:49:48,438 - WARNING - Could not retrieve variants from source file in region 1:201079133-201084076. Error was invalid region `1:201079134-201084076`
[2016-04-15T02:49Z] 2016-04-14 19:49:49 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:49:49,057 - WARNING - Could not retrieve variants from source file in region 1:202705244-202733428. Error was invalid region `1:202705245-202733428`
[2016-04-15T02:49Z] 2016-04-14 19:49:49 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:49:49,251 - WARNING - Could not retrieve variants from source file in region 1:200618027-200618428. Error was invalid region `1:200618028-200618428`
[2016-04-15T02:49Z] 2016-04-14 19:49:49 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:49:49,377 - WARNING - Could not retrieve variants from source file in region 1:201860415-201860816. Error was invalid region `1:201860416-201860816`
[2016-04-15T02:49Z] 2016-04-14 19:49:50 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:49:50,535 - WARNING - Could not retrieve variants from source file in region 1:206773448-206773849. Error was invalid region `1:206773449-206773849`
[2016-04-15T02:49Z] 2016-04-14 19:49:51 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:49:51,098 - WARNING - Could not retrieve variants from source file in region 1:207007430-207016147. Error was invalid region `1:207007431-207016147`
[2016-04-15T02:49Z] 2016-04-14 19:49:51 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:49:51,988 - WARNING - Could not retrieve variants from source file in region 1:205027526-205053409. Error was invalid region `1:205027527-205053409`
[2016-04-15T02:49Z] 2016-04-14 19:49:52 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:49:52,939 - WARNING - Could not retrieve variants from source file in region 1:206647531-206681339. Error was invalid region `1:206647532-206681339`
[2016-04-15T02:49Z] 2016-04-14 19:49:54 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:49:54,091 - WARNING - Could not retrieve variants from source file in region 1:200618027-200618428. Error was invalid region `1:200618028-200618428`
[2016-04-15T02:49Z] 2016-04-14 19:49:54 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:49:54,278 - WARNING - Could not retrieve variants from source file in region 1:201860415-201860816. Error was invalid region `1:201860416-201860816`
[2016-04-15T02:49Z] 2016-04-14 19:49:55 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:49:55,677 - WARNING - Could not retrieve variants from source file in region 1:207007430-207016147. Error was invalid region `1:207007431-207016147`
[2016-04-15T02:49Z] 2016-04-14 19:49:55 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:49:55,929 - WARNING - Could not retrieve variants from source file in region 1:206773448-206773849. Error was invalid region `1:206773449-206773849`
[2016-04-15T02:49Z] 2016-04-14 19:49:58 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:49:58,538 - WARNING - Could not retrieve variants from source file in region 1:202705244-202733428. Error was invalid region `1:202705245-202733428`
[2016-04-15T02:49Z] 2016-04-14 19:49:58 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:49:58,969 - WARNING - Could not retrieve variants from source file in region 1:201860415-201860816. Error was invalid region `1:201860416-201860816`
[2016-04-15T02:49Z] 2016-04-14 19:49:59 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:49:59,531 - WARNING - Could not retrieve variants from source file in region 1:200618027-200618428. Error was invalid region `1:200618028-200618428`
[2016-04-15T02:50Z] 2016-04-14 19:50:01 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:50:01,904 - WARNING - Could not retrieve variants from source file in region 1:205883851-205901190. Error was invalid region `1:205883852-205901190`
[2016-04-15T02:50Z] 2016-04-14 19:50:05 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:50:05,701 - WARNING - Could not retrieve variants from source file in region 1:205883851-205901190. Error was invalid region `1:205883852-205901190`
[2016-04-15T02:50Z] 2016-04-14 19:50:09 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:50:09,327 - WARNING - Could not retrieve variants from source file in region 1:202183097-202183498. Error was invalid region `1:202183098-202183498`
[2016-04-15T02:50Z] 2016-04-14 19:50:10 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:50:10,662 - WARNING - Could not retrieve variants from source file in region 1:205631556-205631957. Error was invalid region `1:205631557-205631957`
[2016-04-15T02:50Z] 2016-04-14 19:50:11 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:50:11,171 - WARNING - Could not retrieve variants from source file in region 1:197390157-197390558. Error was invalid region `1:197390158-197390558`
[2016-04-15T02:50Z] 2016-04-14 19:50:11 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:50:11,603 - WARNING - Could not retrieve variants from source file in region 1:202565737-202574974. Error was invalid region `1:202565738-202574974`
[2016-04-15T02:50Z] 2016-04-14 19:50:12 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:50:12,631 - WARNING - Could not retrieve variants from source file in region 1:200586554-200586955. Error was invalid region `1:200586555-200586955`
[2016-04-15T02:50Z] 2016-04-14 19:50:13 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:50:13,221 - WARNING - Could not retrieve variants from source file in region 1:202129615-202130356. Error was invalid region `1:202129616-202130356`
[2016-04-15T02:50Z] 2016-04-14 19:50:14 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:50:14,706 - WARNING - Could not retrieve variants from source file in region 1:202605358-202609142. Error was invalid region `1:202605359-202609142`
[2016-04-15T02:50Z] 2016-04-14 19:50:16 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:50:16,480 - WARNING - Could not retrieve variants from source file in region 1:202605358-202609142. Error was invalid region `1:202605359-202609142`
[2016-04-15T02:50Z] 2016-04-14 19:50:16 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:50:16,683 - WARNING - Could not retrieve variants from source file in region 1:197390157-197390558. Error was invalid region `1:197390158-197390558`
[2016-04-15T02:50Z] 2016-04-14 19:50:19 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:50:19,826 - WARNING - Could not retrieve variants from source file in region 1:202129615-202130356. Error was invalid region `1:202129616-202130356`
[2016-04-15T02:50Z] 2016-04-14 19:50:19 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:50:19,874 - WARNING - Could not retrieve variants from source file in region 1:202092149-202092770. Error was invalid region `1:202092150-202092770`
[2016-04-15T02:50Z] 2016-04-14 19:50:20 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:50:20,134 - WARNING - Could not retrieve variants from source file in region 1:202183097-202183498. Error was invalid region `1:202183098-202183498`
[2016-04-15T02:50Z] 2016-04-14 19:50:20 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:50:20,366 - WARNING - Could not retrieve variants from source file in region 1:205389381-205389782. Error was invalid region `1:205389382-205389782`
[2016-04-15T02:50Z] 2016-04-14 19:50:20 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:50:20,430 - WARNING - Could not retrieve variants from source file in region 1:196797027-196801268. Error was invalid region `1:196797028-196801268`
[2016-04-15T02:50Z] 2016-04-14 19:50:21 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:50:21,888 - WARNING - Could not retrieve variants from source file in region 1:197390157-197390558. Error was invalid region `1:197390158-197390558`
[2016-04-15T02:50Z] 2016-04-14 19:50:25 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:50:25,827 - WARNING - Could not retrieve variants from source file in region 1:202092149-202092770. Error was invalid region `1:202092150-202092770`
[2016-04-15T02:50Z] 2016-04-14 19:50:26 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:50:26,238 - WARNING - Could not retrieve variants from source file in region 1:205553874-205554285. Error was invalid region `1:205553875-205554285`
[2016-04-15T02:50Z] 2016-04-14 19:50:28 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:50:28,598 - WARNING - Could not retrieve variants from source file in region 1:204369664-204379807. Error was invalid region `1:204369665-204379807`
[2016-04-15T02:50Z] 2016-04-14 19:50:29 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:50:29,553 - WARNING - Could not retrieve variants from source file in region 1:205492545-205492946. Error was invalid region `1:205492546-205492946`
[2016-04-15T02:50Z] 2016-04-14 19:50:30 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:50:30,342 - WARNING - Could not retrieve variants from source file in region 1:202092149-202092770. Error was invalid region `1:202092150-202092770`
[2016-04-15T02:50Z] 2016-04-14 19:50:31 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:50:31,950 - WARNING - Could not retrieve variants from source file in region 1:202471104-202471505. Error was invalid region `1:202471105-202471505`
[2016-04-15T02:50Z] 2016-04-14 19:50:34 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:50:34,011 - WARNING - Could not retrieve variants from source file in region 1:202471104-202471505. Error was invalid region `1:202471105-202471505`
[2016-04-15T02:50Z] 2016-04-14 19:50:35 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:50:35,312 - WARNING - Could not retrieve variants from source file in region 1:205492545-205492946. Error was invalid region `1:205492546-205492946`
[2016-04-15T02:50Z] 2016-04-14 19:50:35 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:50:35,345 - WARNING - Could not retrieve variants from source file in region 1:203455691-203456092. Error was invalid region `1:203455692-203456092`
[2016-04-15T02:50Z] 2016-04-14 19:50:36 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:50:36,421 - WARNING - Could not retrieve variants from source file in region 1:202471104-202471505. Error was invalid region `1:202471105-202471505`
[2016-04-15T02:50Z] 2016-04-14 19:50:38 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:50:38,643 - WARNING - Could not retrieve variants from source file in region 1:200522355-200558553. Error was invalid region `1:200522356-200558553`
[2016-04-15T02:50Z] 2016-04-14 19:50:38 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:50:38,740 - WARNING - Could not retrieve variants from source file in region 1:204438123-204438833. Error was invalid region `1:204438124-204438833`
[2016-04-15T02:50Z] 2016-04-14 19:50:40 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:50:40,207 - WARNING - Could not retrieve variants from source file in region 1:205492545-205492946. Error was invalid region `1:205492546-205492946`
[2016-04-15T02:50Z] 2016-04-14 19:50:40 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:50:40,806 - WARNING - Could not retrieve variants from source file in region 1:203455691-203456092. Error was invalid region `1:203455692-203456092`
[2016-04-15T02:50Z] 2016-04-14 19:50:43 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:50:43,739 - WARNING - Could not retrieve variants from source file in region 1:204438123-204438833. Error was invalid region `1:204438124-204438833`
[2016-04-15T02:50Z] 2016-04-14 19:50:43 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:50:43,913 - WARNING - Could not retrieve variants from source file in region 1:204120741-204131376. Error was invalid region `1:204120742-204131376`
[2016-04-15T02:50Z] 2016-04-14 19:50:44 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:50:44,916 - WARNING - Could not retrieve variants from source file in region 1:203098064-203098465. Error was invalid region `1:203098065-203098465`
[2016-04-15T02:50Z] 2016-04-14 19:50:45 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:50:45,016 - WARNING - Could not retrieve variants from source file in region 1:204278017-204289807. Error was invalid region `1:204278018-204289807`
[2016-04-15T02:50Z] 2016-04-14 19:50:45 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:50:45,404 - WARNING - Could not retrieve variants from source file in region 1:204438123-204438833. Error was invalid region `1:204438124-204438833`
[2016-04-15T02:50Z] 2016-04-14 19:50:49 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:50:49,098 - WARNING - Could not retrieve variants from source file in region 1:200522355-200558553. Error was invalid region `1:200522356-200558553`
[2016-04-15T02:50Z] 2016-04-14 19:50:50 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:50:50,728 - WARNING - Could not retrieve variants from source file in region 1:203053576-203053977. Error was invalid region `1:203053577-203053977`
[2016-04-15T02:50Z] 2016-04-14 19:50:50 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:50:50,815 - WARNING - Could not retrieve variants from source file in region 1:204328530-204328931. Error was invalid region `1:204328531-204328931`
[2016-04-15T02:50Z] 2016-04-14 19:50:51 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:50:51,081 - WARNING - Could not retrieve variants from source file in region 1:200143070-200143471. Error was invalid region `1:200143071-200143471`
[2016-04-15T02:50Z] 2016-04-14 19:50:51 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:50:51,520 - WARNING - Could not retrieve variants from source file in region 1:205272715-205275611. Error was invalid region `1:205272716-205275611`
[2016-04-15T02:50Z] 2016-04-14 19:50:51 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:50:51,654 - WARNING - Could not retrieve variants from source file in region 1:204278017-204289807. Error was invalid region `1:204278018-204289807`
[2016-04-15T02:50Z] 2016-04-14 19:50:55 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:50:55,374 - WARNING - Could not retrieve variants from source file in region 1:204328530-204328931. Error was invalid region `1:204328531-204328931`
[2016-04-15T02:50Z] 2016-04-14 19:50:55 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:50:55,395 - WARNING - Could not retrieve variants from source file in region 1:203098064-203098465. Error was invalid region `1:203098065-203098465`
[2016-04-15T02:50Z] 2016-04-14 19:50:55 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:50:55,918 - WARNING - Could not retrieve variants from source file in region 1:203316951-203317352. Error was invalid region `1:203316952-203317352`
[2016-04-15T02:50Z] 2016-04-14 19:50:56 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:50:56,350 - WARNING - Could not retrieve variants from source file in region 1:204328530-204328931. Error was invalid region `1:204328531-204328931`
[2016-04-15T02:50Z] 2016-04-14 19:50:56 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:50:56,946 - WARNING - Could not retrieve variants from source file in region 1:204278017-204289807. Error was invalid region `1:204278018-204289807`
[2016-04-15T02:51Z] 2016-04-14 19:51:00 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:51:00,351 - WARNING - Could not retrieve variants from source file in region 1:203053576-203053977. Error was invalid region `1:203053577-203053977`
[2016-04-15T02:51Z] 2016-04-14 19:51:01 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:51:01,427 - WARNING - Could not retrieve variants from source file in region 1:200143070-200143471. Error was invalid region `1:200143071-200143471`
[2016-04-15T02:51Z] 2016-04-14 19:51:01 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:51:01,521 - WARNING - Could not retrieve variants from source file in region 1:203316951-203317352. Error was invalid region `1:203316952-203317352`
[2016-04-15T02:51Z] 2016-04-14 19:51:02 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:51:02,151 - WARNING - Could not retrieve variants from source file in region 1:205272715-205275611. Error was invalid region `1:205272716-205275611`
[2016-04-15T02:51Z] 2016-04-14 19:51:02 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:51:02,895 - WARNING - Could not retrieve variants from source file in region 1:200376397-200376798. Error was invalid region `1:200376398-200376798`
[2016-04-15T02:51Z] 2016-04-14 19:51:06 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:51:06,413 - WARNING - Could not retrieve variants from source file in region 1:203316951-203317352. Error was invalid region `1:203316952-203317352`
[2016-04-15T02:51Z] 2016-04-14 19:51:07 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:51:07,124 - WARNING - Could not retrieve variants from source file in region 1:203818762-203821504. Error was invalid region `1:203818763-203821504`
[2016-04-15T02:51Z] 2016-04-14 19:51:07 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:51:07,409 - WARNING - Could not retrieve variants from source file in region 1:197009587-197031211. Error was invalid region `1:197009588-197031211`
[2016-04-15T02:51Z] 2016-04-14 19:51:10 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:51:10,925 - WARNING - Could not retrieve variants from source file in region 1:204197998-204199804. Error was invalid region `1:204197999-204199804`
[2016-04-15T02:51Z] 2016-04-14 19:51:12 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:51:12,102 - WARNING - Could not retrieve variants from source file in region 1:197009587-197031211. Error was invalid region `1:197009588-197031211`
[2016-04-15T02:51Z] 2016-04-14 19:51:12 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:51:12,486 - WARNING - Could not retrieve variants from source file in region 1:200376397-200376798. Error was invalid region `1:200376398-200376798`
[2016-04-15T02:51Z] 2016-04-14 19:51:14 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:51:14,608 - WARNING - Could not retrieve variants from source file in region 1:196642022-196712776. Error was invalid region `1:196642023-196712776`
[2016-04-15T02:51Z] 2016-04-14 19:51:14 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:51:14,636 - WARNING - Could not retrieve variants from source file in region 1:204237205-204245076. Error was invalid region `1:204237206-204245076`
[2016-04-15T02:51Z] 2016-04-14 19:51:15 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:51:15,307 - WARNING - Could not retrieve variants from source file in region 1:204197998-204199804. Error was invalid region `1:204197999-204199804`
[2016-04-15T02:51Z] 2016-04-14 19:51:19 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:51:19,175 - WARNING - Could not retrieve variants from source file in region 1:198665706-198666107. Error was invalid region `1:198665707-198666107`
[2016-04-15T02:51Z] 2016-04-14 19:51:19 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:51:19,545 - WARNING - Could not retrieve variants from source file in region 1:203148422-203152991. Error was invalid region `1:203148423-203152991`
[2016-04-15T02:51Z] 2016-04-14 19:51:19 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:51:19,825 - WARNING - Could not retrieve variants from source file in region 1:204197998-204199804. Error was invalid region `1:204197999-204199804`
[2016-04-15T02:51Z] 2016-04-14 19:51:19 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:51:19,859 - WARNING - Could not retrieve variants from source file in region 1:205225246-205240441. Error was invalid region `1:205225247-205240441`
[2016-04-15T02:51Z] 2016-04-14 19:51:19 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:51:19,921 - WARNING - Could not retrieve variants from source file in region 1:205198931-205199390. Error was invalid region `1:205198932-205199390`
[2016-04-15T02:51Z] 2016-04-14 19:51:24 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:51:24,127 - WARNING - Could not retrieve variants from source file in region 1:203148422-203152991. Error was invalid region `1:203148423-203152991`
[2016-04-15T02:51Z] 2016-04-14 19:51:24 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:51:24,705 - WARNING - Could not retrieve variants from source file in region 1:205198931-205199390. Error was invalid region `1:205198932-205199390`
[2016-04-15T02:51Z] 2016-04-14 19:51:24 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:51:24,716 - WARNING - Could not retrieve variants from source file in region 1:205225246-205240441. Error was invalid region `1:205225247-205240441`
[2016-04-15T02:51Z] 2016-04-14 19:51:26 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:51:26,262 - WARNING - Could not retrieve variants from source file in region 1:203766616-203787890. Error was invalid region `1:203766617-203787890`
[2016-04-15T02:51Z] 2016-04-14 19:51:26 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:51:26,383 - WARNING - Could not retrieve variants from source file in region 1:196874145-196884448. Error was invalid region `1:196874146-196884448`
[2016-04-15T02:51Z] 2016-04-14 19:51:26 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:51:26,670 - WARNING - Could not retrieve variants from source file in region 1:197703684-197704085. Error was invalid region `1:197703685-197704085`
[2016-04-15T02:51Z] 2016-04-14 19:51:28 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:51:28,784 - WARNING - Could not retrieve variants from source file in region 1:203148422-203152991. Error was invalid region `1:203148423-203152991`
[2016-04-15T02:51Z] 2016-04-14 19:51:28 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:51:28,998 - WARNING - Could not retrieve variants from source file in region 1:203652233-203667599. Error was invalid region `1:203652234-203667599`
[2016-04-15T02:51Z] 2016-04-14 19:51:31 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:51:31,031 - WARNING - Could not retrieve variants from source file in region 1:196874145-196884448. Error was invalid region `1:196874146-196884448`
[2016-04-15T02:51Z] 2016-04-14 19:51:34 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:51:34,112 - WARNING - Could not retrieve variants from source file in region 1:203652233-203667599. Error was invalid region `1:203652234-203667599`
[2016-04-15T02:51Z] 2016-04-14 19:51:34 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:51:34,272 - WARNING - Could not retrieve variants from source file in region 1:203652233-203667599. Error was invalid region `1:203652234-203667599`
[2016-04-15T02:51Z] 2016-04-14 19:51:34 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:51:34,509 - WARNING - Could not retrieve variants from source file in region 1:197521666-197522067. Error was invalid region `1:197521667-197522067`
[2016-04-15T02:51Z] 2016-04-14 19:51:34 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:51:34,559 - WARNING - Could not retrieve variants from source file in region 1:197703684-197704085. Error was invalid region `1:197703685-197704085`
[2016-04-15T02:51Z] 2016-04-14 19:51:36 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:51:36,731 - WARNING - Could not retrieve variants from source file in region 1:196226678-196227716. Error was invalid region `1:196226679-196227716`
[2016-04-15T02:51Z] 2016-04-14 19:51:37 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:51:37,207 - WARNING - Could not retrieve variants from source file in region 1:196311042-196311443. Error was invalid region `1:196311043-196311443`
[2016-04-15T02:51Z] 2016-04-14 19:51:37 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:51:37,637 - WARNING - Could not retrieve variants from source file in region 1:197521666-197522067. Error was invalid region `1:197521667-197522067`
[2016-04-15T02:51Z] 2016-04-14 19:51:38 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:51:38,447 - WARNING - Could not retrieve variants from source file in region 1:197521666-197522067. Error was invalid region `1:197521667-197522067`
[2016-04-15T02:51Z] 2016-04-14 19:51:40 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:51:40,716 - WARNING - Could not retrieve variants from source file in region 1:196226678-196227716. Error was invalid region `1:196226679-196227716`
[2016-04-15T02:51Z] 2016-04-14 19:51:41 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:51:41,882 - WARNING - Could not retrieve variants from source file in region 1:193053943-193075308. Error was invalid region `1:193053944-193075308`
[2016-04-15T02:51Z] 2016-04-14 19:51:42 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:51:42,421 - WARNING - Could not retrieve variants from source file in region 1:196226678-196227716. Error was invalid region `1:196226679-196227716`
[2016-04-15T02:51Z] ['bcbio-variation-recall', 'square', '-Xms750m', '-Xmx7280m', '-XX:+UseSerialGC', '-c', 16, '-r', u'1:207641872-223156451', '--caller', 'platypus', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/1/Batch1-1_207641871_223156451.vcf.gz', '/mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/1/Batch1-1_207641871_223156451.vcf-inputs.txt'] in region: 1:207641872-223156451
[2016-04-15T02:51Z] 2016-04-14 19:51:57 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:51:57,709 - WARNING - Could not retrieve variants from source file in region 1:215740842-215741243. Error was invalid region `1:215740843-215741243`
[2016-04-15T02:51Z] 2016-04-14 19:51:57 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:51:57,794 - WARNING - Could not retrieve variants from source file in region 1:208252566-208252967. Error was invalid region `1:208252567-208252967`
[2016-04-15T02:51Z] 2016-04-14 19:51:58 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:51:58,844 - WARNING - Could not retrieve variants from source file in region 1:215959956-215960357. Error was invalid region `1:215959957-215960357`
[2016-04-15T02:51Z] 2016-04-14 19:51:59 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:51:59,362 - WARNING - Could not retrieve variants from source file in region 1:212273428-212274603. Error was invalid region `1:212273429-212274603`
[2016-04-15T02:51Z] 2016-04-14 19:51:59 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:51:59,921 - WARNING - Could not retrieve variants from source file in region 1:223116261-223116664. Error was invalid region `1:223116262-223116664`
[2016-04-15T02:51Z] 2016-04-14 19:51:59 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:51:59,947 - WARNING - Could not retrieve variants from source file in region 1:210333870-210334271. Error was invalid region `1:210333871-210334271`
[2016-04-15T02:52Z] 2016-04-14 19:52:00 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:52:00,188 - WARNING - Could not retrieve variants from source file in region 1:212619128-212619529. Error was invalid region `1:212619129-212619529`
[2016-04-15T02:52Z] 2016-04-14 19:52:00 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:52:00,630 - WARNING - Could not retrieve variants from source file in region 1:207782705-207795510. Error was invalid region `1:207782706-207795510`
[2016-04-15T02:52Z] 2016-04-14 19:52:01 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:52:01,020 - WARNING - Could not retrieve variants from source file in region 1:220969817-220972533. Error was invalid region `1:220969818-220972533`
[2016-04-15T02:52Z] 2016-04-14 19:52:03 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:52:03,303 - WARNING - Could not retrieve variants from source file in region 1:215740842-215741243. Error was invalid region `1:215740843-215741243`
[2016-04-15T02:52Z] 2016-04-14 19:52:03 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:52:03,822 - WARNING - Could not retrieve variants from source file in region 1:217604443-217604844. Error was invalid region `1:217604444-217604844`
[2016-04-15T02:52Z] 2016-04-14 19:52:04 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:52:04,602 - WARNING - Could not retrieve variants from source file in region 1:215959956-215960357. Error was invalid region `1:215959957-215960357`
[2016-04-15T02:52Z] 2016-04-14 19:52:05 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:52:05,149 - WARNING - Could not retrieve variants from source file in region 1:212273428-212274603. Error was invalid region `1:212273429-212274603`
[2016-04-15T02:52Z] 2016-04-14 19:52:06 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:52:06,782 - WARNING - Could not retrieve variants from source file in region 1:212964884-212965474. Error was invalid region `1:212964885-212965474`
[2016-04-15T02:52Z] 2016-04-14 19:52:07 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:52:07,175 - WARNING - Could not retrieve variants from source file in region 1:211835981-211847066. Error was invalid region `1:211835982-211847066`
[2016-04-15T02:52Z] 2016-04-14 19:52:07 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:52:07,859 - WARNING - Could not retrieve variants from source file in region 1:213061097-213068785. Error was invalid region `1:213061098-213068785`
[2016-04-15T02:52Z] 2016-04-14 19:52:08 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:52:08,366 - WARNING - Could not retrieve variants from source file in region 1:213140458-213147134. Error was invalid region `1:213140459-213147134`
[2016-04-15T02:52Z] 2016-04-14 19:52:08 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:52:08,410 - WARNING - Could not retrieve variants from source file in region 1:223116261-223116664. Error was invalid region `1:223116262-223116664`
[2016-04-15T02:52Z] 2016-04-14 19:52:08 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:52:08,422 - WARNING - Could not retrieve variants from source file in region 1:212619128-212619529. Error was invalid region `1:212619129-212619529`
[2016-04-15T02:52Z] 2016-04-14 19:52:08 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:52:08,881 - WARNING - Could not retrieve variants from source file in region 1:216347241-216348954. Error was invalid region `1:216347242-216348954`
[2016-04-15T02:52Z] 2016-04-14 19:52:09 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:52:09,098 - WARNING - Could not retrieve variants from source file in region 1:215740842-215741243. Error was invalid region `1:215740843-215741243`
[2016-04-15T02:52Z] 2016-04-14 19:52:09 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:52:09,285 - WARNING - Could not retrieve variants from source file in region 1:208252566-208252967. Error was invalid region `1:208252567-208252967`
[2016-04-15T02:52Z] 2016-04-14 19:52:09 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:52:09,548 - WARNING - Could not retrieve variants from source file in region 1:212273428-212274603. Error was invalid region `1:212273429-212274603`
[2016-04-15T02:52Z] 2016-04-14 19:52:12 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:52:12,302 - WARNING - Could not retrieve variants from source file in region 1:212964884-212965474. Error was invalid region `1:212964885-212965474`
[2016-04-15T02:52Z] 2016-04-14 19:52:17 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:52:17,021 - WARNING - Could not retrieve variants from source file in region 1:220969817-220972533. Error was invalid region `1:220969818-220972533`
[2016-04-15T02:52Z] 2016-04-14 19:52:18 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:52:18,082 - WARNING - Could not retrieve variants from source file in region 1:207782705-207795510. Error was invalid region `1:207782706-207795510`
[2016-04-15T02:52Z] 2016-04-14 19:52:26 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:52:26,688 - WARNING - Could not retrieve variants from source file in region 1:216692458-216692859. Error was invalid region `1:216692459-216692859`
[2016-04-15T02:52Z] 2016-04-14 19:52:27 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:52:27,410 - WARNING - Could not retrieve variants from source file in region 1:214786919-214837300. Error was invalid region `1:214786920-214837300`
[2016-04-15T02:52Z] 2016-04-14 19:52:29 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:52:29,802 - WARNING - Could not retrieve variants from source file in region 1:210267682-210268086. Error was invalid region `1:210267683-210268086`
[2016-04-15T02:52Z] 2016-04-14 19:52:31 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:52:31,298 - WARNING - Could not retrieve variants from source file in region 1:222919684-222924029. Error was invalid region `1:222919685-222924029`
[2016-04-15T02:52Z] 2016-04-14 19:52:31 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:52:31,398 - WARNING - Could not retrieve variants from source file in region 1:216692458-216692859. Error was invalid region `1:216692459-216692859`
[2016-04-15T02:52Z] 2016-04-14 19:52:32 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:52:32,990 - WARNING - Could not retrieve variants from source file in region 1:212560116-212560517. Error was invalid region `1:212560117-212560517`
[2016-04-15T02:52Z] 2016-04-14 19:52:33 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:52:33,858 - WARNING - Could not retrieve variants from source file in region 1:211451256-211451657. Error was invalid region `1:211451257-211451657`
[2016-04-15T02:52Z] 2016-04-14 19:52:34 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:52:34,114 - WARNING - Could not retrieve variants from source file in region 1:220344242-220344643. Error was invalid region `1:220344243-220344643`
[2016-04-15T02:52Z] 2016-04-14 19:52:34 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:52:34,897 - WARNING - Could not retrieve variants from source file in region 1:216219570-216219971. Error was invalid region `1:216219571-216219971`
[2016-04-15T02:52Z] 2016-04-14 19:52:35 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:52:35,005 - WARNING - Could not retrieve variants from source file in region 1:213009258-213032138. Error was invalid region `1:213009259-213032138`
[2016-04-15T02:52Z] 2016-04-14 19:52:35 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:52:35,207 - WARNING - Could not retrieve variants from source file in region 1:207753410-207753811. Error was invalid region `1:207753411-207753811`
[2016-04-15T02:52Z] 2016-04-14 19:52:35 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:52:35,318 - WARNING - Could not retrieve variants from source file in region 1:215847851-215848831. Error was invalid region `1:215847852-215848831`
[2016-04-15T02:52Z] 2016-04-14 19:52:35 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:52:35,697 - WARNING - Could not retrieve variants from source file in region 1:222919684-222924029. Error was invalid region `1:222919685-222924029`
[2016-04-15T02:52Z] 2016-04-14 19:52:36 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:52:36,024 - WARNING - Could not retrieve variants from source file in region 1:216692458-216692859. Error was invalid region `1:216692459-216692859`
[2016-04-15T02:52Z] 2016-04-14 19:52:37 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:52:37,644 - WARNING - Could not retrieve variants from source file in region 1:212560116-212560517. Error was invalid region `1:212560117-212560517`
[2016-04-15T02:52Z] 2016-04-14 19:52:39 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:52:39,571 - WARNING - Could not retrieve variants from source file in region 1:211451256-211451657. Error was invalid region `1:211451257-211451657`
[2016-04-15T02:52Z] 2016-04-14 19:52:43 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:52:43,317 - WARNING - Could not retrieve variants from source file in region 1:213009258-213032138. Error was invalid region `1:213009259-213032138`
[2016-04-15T02:52Z] 2016-04-14 19:52:43 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:52:43,370 - WARNING - Could not retrieve variants from source file in region 1:222919684-222924029. Error was invalid region `1:222919685-222924029`
[2016-04-15T02:52Z] 2016-04-14 19:52:43 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:52:43,424 - WARNING - Could not retrieve variants from source file in region 1:212560116-212560517. Error was invalid region `1:212560117-212560517`
[2016-04-15T02:52Z] 2016-04-14 19:52:47 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:52:47,918 - WARNING - Could not retrieve variants from source file in region 1:216219570-216219971. Error was invalid region `1:216219571-216219971`
[2016-04-15T02:52Z] 2016-04-14 19:52:48 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:52:48,949 - WARNING - Could not retrieve variants from source file in region 1:207753410-207753811. Error was invalid region `1:207753411-207753811`
[2016-04-15T02:52Z] 2016-04-14 19:52:49 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:52:49,375 - WARNING - Could not retrieve variants from source file in region 1:215847851-215848831. Error was invalid region `1:215847852-215848831`
[2016-04-15T02:52Z] 2016-04-14 19:52:49 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:52:49,815 - WARNING - Could not retrieve variants from source file in region 1:208062856-208063695. Error was invalid region `1:208062857-208063695`
[2016-04-15T02:52Z] 2016-04-14 19:52:51 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:52:51,218 - WARNING - Could not retrieve variants from source file in region 1:216591792-216595496. Error was invalid region `1:216591793-216595496`
[2016-04-15T02:52Z] 2016-04-14 19:52:55 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:52:55,438 - WARNING - Could not retrieve variants from source file in region 1:210857246-210857647. Error was invalid region `1:210857247-210857647`
[2016-04-15T02:52Z] 2016-04-14 19:52:56 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:52:56,519 - WARNING - Could not retrieve variants from source file in region 1:212872863-212873286. Error was invalid region `1:212872864-212873286`
[2016-04-15T02:52Z] 2016-04-14 19:52:56 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:52:56,930 - WARNING - Could not retrieve variants from source file in region 1:216591792-216595496. Error was invalid region `1:216591793-216595496`
[2016-04-15T02:52Z] 2016-04-14 19:52:58 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:52:58,257 - WARNING - Could not retrieve variants from source file in region 1:210190031-210190432. Error was invalid region `1:210190032-210190432`
[2016-04-15T02:53Z] 2016-04-14 19:53:00 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:53:00,406 - WARNING - Could not retrieve variants from source file in region 1:222885908-222886309. Error was invalid region `1:222885909-222886309`
[2016-04-15T02:53Z] 2016-04-14 19:53:01 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:53:01,146 - WARNING - Could not retrieve variants from source file in region 1:210577620-210578091. Error was invalid region `1:210577621-210578091`
[2016-04-15T02:53Z] 2016-04-14 19:53:01 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:53:01,582 - WARNING - Could not retrieve variants from source file in region 1:210857246-210857647. Error was invalid region `1:210857247-210857647`
[2016-04-15T02:53Z] 2016-04-14 19:53:01 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:53:01,844 - WARNING - Could not retrieve variants from source file in region 1:216172169-216172570. Error was invalid region `1:216172170-216172570`
[2016-04-15T02:53Z] 2016-04-14 19:53:01 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:53:01,941 - WARNING - Could not retrieve variants from source file in region 1:212872863-212873286. Error was invalid region `1:212872864-212873286`
[2016-04-15T02:53Z] 2016-04-14 19:53:02 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:53:02,179 - WARNING - Could not retrieve variants from source file in region 1:216591792-216595496. Error was invalid region `1:216591793-216595496`
[2016-04-15T02:53Z] 2016-04-14 19:53:02 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:53:02,276 - WARNING - Could not retrieve variants from source file in region 1:214542608-214576431. Error was invalid region `1:214542609-214576431`
[2016-04-15T02:53Z] 2016-04-14 19:53:03 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:53:03,035 - WARNING - Could not retrieve variants from source file in region 1:207679096-207679497. Error was invalid region `1:207679097-207679497`
[2016-04-15T02:53Z] 2016-04-14 19:53:04 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:53:04,842 - WARNING - Could not retrieve variants from source file in region 1:222885908-222886309. Error was invalid region `1:222885909-222886309`
[2016-04-15T02:53Z] 2016-04-14 19:53:05 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:53:05,750 - WARNING - Could not retrieve variants from source file in region 1:212798766-212800139. Error was invalid region `1:212798767-212800139`
[2016-04-15T02:53Z] 2016-04-14 19:53:07 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:53:07,186 - WARNING - Could not retrieve variants from source file in region 1:216172169-216172570. Error was invalid region `1:216172170-216172570`
[2016-04-15T02:53Z] 2016-04-14 19:53:07 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:53:07,202 - WARNING - Could not retrieve variants from source file in region 1:210857246-210857647. Error was invalid region `1:210857247-210857647`
[2016-04-15T02:53Z] 2016-04-14 19:53:07 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:53:07,223 - WARNING - Could not retrieve variants from source file in region 1:212872863-212873286. Error was invalid region `1:212872864-212873286`
[2016-04-15T02:53Z] 2016-04-14 19:53:07 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:53:07,444 - WARNING - Could not retrieve variants from source file in region 1:214542608-214576431. Error was invalid region `1:214542609-214576431`
[2016-04-15T02:53Z] 2016-04-14 19:53:09 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:53:09,516 - WARNING - Could not retrieve variants from source file in region 1:222885908-222886309. Error was invalid region `1:222885909-222886309`
[2016-04-15T02:53Z] 2016-04-14 19:53:10 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:53:10,068 - WARNING - Could not retrieve variants from source file in region 1:212798766-212800139. Error was invalid region `1:212798767-212800139`
[2016-04-15T02:53Z] 2016-04-14 19:53:11 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:53:11,933 - WARNING - Could not retrieve variants from source file in region 1:210577620-210578091. Error was invalid region `1:210577621-210578091`
[2016-04-15T02:53Z] 2016-04-14 19:53:13 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:53:12,997 - WARNING - Could not retrieve variants from source file in region 1:216172169-216172570. Error was invalid region `1:216172170-216172570`
[2016-04-15T02:53Z] 2016-04-14 19:53:13 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:53:13,206 - WARNING - Could not retrieve variants from source file in region 1:207679096-207679497. Error was invalid region `1:207679097-207679497`
[2016-04-15T02:53Z] 2016-04-14 19:53:20 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:53:20,205 - WARNING - Could not retrieve variants from source file in region 1:216143838-216144239. Error was invalid region `1:216143839-216144239`
[2016-04-15T02:53Z] 2016-04-14 19:53:20 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:53:20,843 - WARNING - Could not retrieve variants from source file in region 1:216496721-216497137. Error was invalid region `1:216496722-216497137`
[2016-04-15T02:53Z] 2016-04-14 19:53:22 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:53:22,047 - WARNING - Could not retrieve variants from source file in region 1:214492075-214492476. Error was invalid region `1:214492076-214492476`
[2016-04-15T02:53Z] 2016-04-14 19:53:22 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:53:22,351 - WARNING - Could not retrieve variants from source file in region 1:214492075-214492476. Error was invalid region `1:214492076-214492476`
[2016-04-15T02:53Z] 2016-04-14 19:53:23 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:53:23,067 - WARNING - Could not retrieve variants from source file in region 1:210003988-210006793. Error was invalid region `1:210003989-210006793`
[2016-04-15T02:53Z] 2016-04-14 19:53:23 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:53:23,075 - WARNING - Could not retrieve variants from source file in region 1:209933329-209968874. Error was invalid region `1:209933330-209968874`
[2016-04-15T02:53Z] 2016-04-14 19:53:23 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:53:23,110 - WARNING - Could not retrieve variants from source file in region 1:222801795-222833791. Error was invalid region `1:222801796-222833791`
[2016-04-15T02:53Z] 2016-04-14 19:53:26 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:53:26,130 - WARNING - Could not retrieve variants from source file in region 1:221910077-221912998. Error was invalid region `1:221910078-221912998`
[2016-04-15T02:53Z] 2016-04-14 19:53:26 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:53:26,708 - WARNING - Could not retrieve variants from source file in region 1:214492075-214492476. Error was invalid region `1:214492076-214492476`
[2016-04-15T02:53Z] 2016-04-14 19:53:26 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:53:26,738 - WARNING - Could not retrieve variants from source file in region 1:220197414-220197815. Error was invalid region `1:220197415-220197815`
[2016-04-15T02:53Z] 2016-04-14 19:53:29 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:53:29,221 - WARNING - Could not retrieve variants from source file in region 1:220197414-220197815. Error was invalid region `1:220197415-220197815`
[2016-04-15T02:53Z] 2016-04-14 19:53:29 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:53:29,576 - WARNING - Could not retrieve variants from source file in region 1:220154557-220154958. Error was invalid region `1:220154558-220154958`
[2016-04-15T02:53Z] 2016-04-14 19:53:31 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:53:31,484 - WARNING - Could not retrieve variants from source file in region 1:220197414-220197815. Error was invalid region `1:220197415-220197815`
[2016-04-15T02:53Z] 2016-04-14 19:53:32 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:53:32,597 - WARNING - Could not retrieve variants from source file in region 1:210003988-210006793. Error was invalid region `1:210003989-210006793`
[2016-04-15T02:53Z] 2016-04-14 19:53:33 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:53:33,106 - WARNING - Could not retrieve variants from source file in region 1:209933329-209968874. Error was invalid region `1:209933330-209968874`
[2016-04-15T02:53Z] 2016-04-14 19:53:33 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:53:33,196 - WARNING - Could not retrieve variants from source file in region 1:222801795-222833791. Error was invalid region `1:222801796-222833791`
[2016-04-15T02:53Z] 2016-04-14 19:53:33 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:53:33,547 - WARNING - Could not retrieve variants from source file in region 1:221053334-221057929. Error was invalid region `1:221053335-221057929`
[2016-04-15T02:53Z] 2016-04-14 19:53:34 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:53:34,390 - WARNING - Could not retrieve variants from source file in region 1:209605425-209605838. Error was invalid region `1:209605426-209605838`
[2016-04-15T02:53Z] 2016-04-14 19:53:39 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:53:39,022 - WARNING - Could not retrieve variants from source file in region 1:220154557-220154958. Error was invalid region `1:220154558-220154958`
[2016-04-15T02:53Z] 2016-04-14 19:53:40 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:53:40,692 - WARNING - Could not retrieve variants from source file in region 1:217947527-217947928. Error was invalid region `1:217947528-217947928`
[2016-04-15T02:53Z] 2016-04-14 19:53:40 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:53:40,734 - WARNING - Could not retrieve variants from source file in region 1:217947527-217947928. Error was invalid region `1:217947528-217947928`
[2016-04-15T02:53Z] 2016-04-14 19:53:43 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:53:43,222 - WARNING - Could not retrieve variants from source file in region 1:222713292-222742866. Error was invalid region `1:222713293-222742866`
[2016-04-15T02:53Z] 2016-04-14 19:53:45 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:53:45,457 - WARNING - Could not retrieve variants from source file in region 1:219383656-219384095. Error was invalid region `1:219383657-219384095`
[2016-04-15T02:53Z] 2016-04-14 19:53:45 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:53:45,477 - WARNING - Could not retrieve variants from source file in region 1:219383656-219384095. Error was invalid region `1:219383657-219384095`
[2016-04-15T02:53Z] 2016-04-14 19:53:46 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:53:46,654 - WARNING - Could not retrieve variants from source file in region 1:219383656-219384095. Error was invalid region `1:219383657-219384095`
[2016-04-15T02:53Z] 2016-04-14 19:53:46 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:53:46,695 - WARNING - Could not retrieve variants from source file in region 1:217782062-217804515. Error was invalid region `1:217782063-217804515`
[2016-04-15T02:53Z] ['bcbio-variation-recall', 'square', '-Xms750m', '-Xmx7280m', '-XX:+UseSerialGC', '-c', 16, '-r', u'1:223162738-240072524', '--caller', 'platypus', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/1/Batch1-1_223162737_240072524.vcf.gz', '/mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/1/Batch1-1_223162737_240072524.vcf-inputs.txt'] in region: 1:223162738-240072524
[2016-04-15T02:54Z] 2016-04-14 19:54:02 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:54:02,307 - WARNING - Could not retrieve variants from source file in region 1:236413019-236413420. Error was invalid region `1:236413020-236413420`
[2016-04-15T02:54Z] 2016-04-14 19:54:03 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:54:03,127 - WARNING - Could not retrieve variants from source file in region 1:236882092-236926034. Error was invalid region `1:236882093-236926034`
[2016-04-15T02:54Z] 2016-04-14 19:54:03 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:54:03,832 - WARNING - Could not retrieve variants from source file in region 1:235382977-235392736. Error was invalid region `1:235382978-235392736`
[2016-04-15T02:54Z] 2016-04-14 19:54:04 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:54:04,269 - WARNING - Could not retrieve variants from source file in region 1:231042521-231057437. Error was invalid region `1:231042522-231057437`
[2016-04-15T02:54Z] 2016-04-14 19:54:04 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:54:04,287 - WARNING - Could not retrieve variants from source file in region 1:226923053-226925074. Error was invalid region `1:226923054-226925074`
[2016-04-15T02:54Z] 2016-04-14 19:54:04 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:54:04,468 - WARNING - Could not retrieve variants from source file in region 1:231858970-231859371. Error was invalid region `1:231858971-231859371`
[2016-04-15T02:54Z] 2016-04-14 19:54:04 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:54:04,889 - WARNING - Could not retrieve variants from source file in region 1:236557560-236557961. Error was invalid region `1:236557561-236557961`
[2016-04-15T02:54Z] 2016-04-14 19:54:05 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:54:05,259 - WARNING - Could not retrieve variants from source file in region 1:225211473-225230798. Error was invalid region `1:225211474-225230798`
[2016-04-15T02:54Z] 2016-04-14 19:54:05 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:54:05,431 - WARNING - Could not retrieve variants from source file in region 1:237841179-237890627. Error was invalid region `1:237841180-237890627`
[2016-04-15T02:54Z] 2016-04-14 19:54:05 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:54:05,524 - WARNING - Could not retrieve variants from source file in region 1:234041211-234041612. Error was invalid region `1:234041212-234041612`
[2016-04-15T02:54Z] 2016-04-14 19:54:08 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:54:08,596 - WARNING - Could not retrieve variants from source file in region 1:228871482-228871883. Error was invalid region `1:228871483-228871883`
[2016-04-15T02:54Z] 2016-04-14 19:54:10 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:54:10,754 - WARNING - Could not retrieve variants from source file in region 1:235382977-235392736. Error was invalid region `1:235382978-235392736`
[2016-04-15T02:54Z] 2016-04-14 19:54:11 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:54:11,859 - WARNING - Could not retrieve variants from source file in region 1:230384759-230385160. Error was invalid region `1:230384760-230385160`
[2016-04-15T02:54Z] 2016-04-14 19:54:12 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:54:12,634 - WARNING - Could not retrieve variants from source file in region 1:228247140-228248112. Error was invalid region `1:228247141-228248112`
[2016-04-15T02:54Z] 2016-04-14 19:54:13 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:54:13,118 - WARNING - Could not retrieve variants from source file in region 1:235875672-235975672. Error was invalid region `1:235875673-235975672`
[2016-04-15T02:54Z] 2016-04-14 19:54:13 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:54:13,130 - WARNING - Could not retrieve variants from source file in region 1:235975672-235991207. Error was invalid region `1:235975673-235991207`
[2016-04-15T02:54Z] 2016-04-14 19:54:14 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:54:14,196 - WARNING - Could not retrieve variants from source file in region 1:236557560-236557961. Error was invalid region `1:236557561-236557961`
[2016-04-15T02:54Z] 2016-04-14 19:54:14 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:54:14,260 - WARNING - Could not retrieve variants from source file in region 1:234041211-234041612. Error was invalid region `1:234041212-234041612`
[2016-04-15T02:54Z] 2016-04-14 19:54:14 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:54:14,340 - WARNING - Could not retrieve variants from source file in region 1:236208562-236208963. Error was invalid region `1:236208563-236208963`
[2016-04-15T02:54Z] 2016-04-14 19:54:14 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:54:14,354 - WARNING - Could not retrieve variants from source file in region 1:228871482-228871883. Error was invalid region `1:228871483-228871883`
[2016-04-15T02:54Z] 2016-04-14 19:54:14 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:54:14,424 - WARNING - Could not retrieve variants from source file in region 1:225211473-225230798. Error was invalid region `1:225211474-225230798`
[2016-04-15T02:54Z] 2016-04-14 19:54:14 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:54:14,463 - WARNING - Could not retrieve variants from source file in region 1:226019442-226074753. Error was invalid region `1:226019443-226074753`
[2016-04-15T02:54Z] 2016-04-14 19:54:14 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:54:14,692 - WARNING - Could not retrieve variants from source file in region 1:237841179-237890627. Error was invalid region `1:237841180-237890627`
[2016-04-15T02:54Z] 2016-04-14 19:54:14 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:54:14,899 - WARNING - Could not retrieve variants from source file in region 1:236882092-236926034. Error was invalid region `1:236882093-236926034`
[2016-04-15T02:54Z] 2016-04-14 19:54:16 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:54:16,133 - WARNING - Could not retrieve variants from source file in region 1:235382977-235392736. Error was invalid region `1:235382978-235392736`
[2016-04-15T02:54Z] 2016-04-14 19:54:20 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:54:20,498 - WARNING - Could not retrieve variants from source file in region 1:231858970-231859371. Error was invalid region `1:231858971-231859371`
[2016-04-15T02:54Z] 2016-04-14 19:54:22 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:54:22,894 - WARNING - Could not retrieve variants from source file in region 1:234041211-234041612. Error was invalid region `1:234041212-234041612`
[2016-04-15T02:54Z] 2016-04-14 19:54:23 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:54:23,191 - WARNING - Could not retrieve variants from source file in region 1:236557560-236557961. Error was invalid region `1:236557561-236557961`
[2016-04-15T02:54Z] 2016-04-14 19:54:23 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:54:23,676 - WARNING - Could not retrieve variants from source file in region 1:225211473-225230798. Error was invalid region `1:225211474-225230798`
[2016-04-15T02:54Z] 2016-04-14 19:54:31 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:54:31,697 - WARNING - Could not retrieve variants from source file in region 1:236371544-236382015. Error was invalid region `1:236371545-236382015`
[2016-04-15T02:54Z] 2016-04-14 19:54:35 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:54:35,248 - WARNING - Could not retrieve variants from source file in region 1:229772482-229790238. Error was invalid region `1:229772483-229790238`
[2016-04-15T02:54Z] 2016-04-14 19:54:36 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:54:36,492 - WARNING - Could not retrieve variants from source file in region 1:236700596-236767520. Error was invalid region `1:236700597-236767520`
[2016-04-15T02:54Z] 2016-04-14 19:54:36 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:54:36,725 - WARNING - Could not retrieve variants from source file in region 1:228156495-228156896. Error was invalid region `1:228156496-228156896`
[2016-04-15T02:54Z] 2016-04-14 19:54:36 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:54:36,750 - WARNING - Could not retrieve variants from source file in region 1:231830084-231830485. Error was invalid region `1:231830085-231830485`
[2016-04-15T02:54Z] 2016-04-14 19:54:37 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:54:37,517 - WARNING - Could not retrieve variants from source file in region 1:236371544-236382015. Error was invalid region `1:236371545-236382015`
[2016-04-15T02:54Z] 2016-04-14 19:54:37 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:54:37,644 - WARNING - Could not retrieve variants from source file in region 1:228674307-228699667. Error was invalid region `1:228674308-228699667`
[2016-04-15T02:54Z] 2016-04-14 19:54:38 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:54:38,336 - WARNING - Could not retrieve variants from source file in region 1:235324087-235324488. Error was invalid region `1:235324088-235324488`
[2016-04-15T02:54Z] 2016-04-14 19:54:38 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:54:38,378 - WARNING - Could not retrieve variants from source file in region 1:236175116-236175529. Error was invalid region `1:236175117-236175529`
[2016-04-15T02:54Z] 2016-04-14 19:54:40 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:54:40,297 - WARNING - Could not retrieve variants from source file in region 1:237801559-237814973. Error was invalid region `1:237801560-237814973`
[2016-04-15T02:54Z] 2016-04-14 19:54:40 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:54:40,971 - WARNING - Could not retrieve variants from source file in region 1:233514723-233515292. Error was invalid region `1:233514724-233515292`
[2016-04-15T02:54Z] 2016-04-14 19:54:42 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:54:42,070 - WARNING - Could not retrieve variants from source file in region 1:229772482-229790238. Error was invalid region `1:229772483-229790238`
[2016-04-15T02:54Z] 2016-04-14 19:54:43 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:54:43,463 - WARNING - Could not retrieve variants from source file in region 1:236700596-236767520. Error was invalid region `1:236700597-236767520`
[2016-04-15T02:54Z] 2016-04-14 19:54:43 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:54:43,558 - WARNING - Could not retrieve variants from source file in region 1:228156495-228156896. Error was invalid region `1:228156496-228156896`
[2016-04-15T02:54Z] 2016-04-14 19:54:45 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:54:45,228 - WARNING - Could not retrieve variants from source file in region 1:226555091-226590148. Error was invalid region `1:226555092-226590148`
[2016-04-15T02:54Z] 2016-04-14 19:54:45 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:54:45,317 - WARNING - Could not retrieve variants from source file in region 1:235715312-235715713. Error was invalid region `1:235715313-235715713`
[2016-04-15T02:54Z] 2016-04-14 19:54:45 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:54:45,334 - WARNING - Could not retrieve variants from source file in region 1:235324087-235324488. Error was invalid region `1:235324088-235324488`
[2016-04-15T02:54Z] 2016-04-14 19:54:45 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:54:45,771 - WARNING - Could not retrieve variants from source file in region 1:225706732-225712566. Error was invalid region `1:225706733-225712566`
[2016-04-15T02:54Z] 2016-04-14 19:54:46 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:54:46,243 - WARNING - Could not retrieve variants from source file in region 1:233514723-233515292. Error was invalid region `1:233514724-233515292`
[2016-04-15T02:54Z] 2016-04-14 19:54:46 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:54:46,325 - WARNING - Could not retrieve variants from source file in region 1:224621723-224622124. Error was invalid region `1:224621724-224622124`
[2016-04-15T02:54Z] 2016-04-14 19:54:46 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:54:46,705 - WARNING - Could not retrieve variants from source file in region 1:229772482-229790238. Error was invalid region `1:229772483-229790238`
[2016-04-15T02:54Z] 2016-04-14 19:54:47 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:54:47,656 - WARNING - Could not retrieve variants from source file in region 1:231830084-231830485. Error was invalid region `1:231830085-231830485`
[2016-04-15T02:54Z] 2016-04-14 19:54:47 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:54:47,669 - WARNING - Could not retrieve variants from source file in region 1:236175116-236175529. Error was invalid region `1:236175117-236175529`
[2016-04-15T02:54Z] 2016-04-14 19:54:48 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:54:48,194 - WARNING - Could not retrieve variants from source file in region 1:236700596-236767520. Error was invalid region `1:236700597-236767520`
[2016-04-15T02:54Z] 2016-04-14 19:54:48 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:54:48,574 - WARNING - Could not retrieve variants from source file in region 1:228156495-228156896. Error was invalid region `1:228156496-228156896`
[2016-04-15T02:54Z] 2016-04-14 19:54:50 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:54:50,755 - WARNING - Could not retrieve variants from source file in region 1:228674307-228699667. Error was invalid region `1:228674308-228699667`
[2016-04-15T02:54Z] 2016-04-14 19:54:52 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:54:52,252 - WARNING - Could not retrieve variants from source file in region 1:235715312-235715713. Error was invalid region `1:235715313-235715713`
[2016-04-15T02:54Z] 2016-04-14 19:54:52 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:54:52,690 - WARNING - Could not retrieve variants from source file in region 1:233514723-233515292. Error was invalid region `1:233514724-233515292`
[2016-04-15T02:54Z] 2016-04-14 19:54:52 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:54:52,848 - WARNING - Could not retrieve variants from source file in region 1:225494957-225495358. Error was invalid region `1:225494958-225495358`
[2016-04-15T02:54Z] 2016-04-14 19:54:52 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:54:52,860 - WARNING - Could not retrieve variants from source file in region 1:225706732-225712566. Error was invalid region `1:225706733-225712566`
[2016-04-15T02:55Z] 2016-04-14 19:55:01 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:55:01,295 - WARNING - Could not retrieve variants from source file in region 1:225494957-225495358. Error was invalid region `1:225494958-225495358`
[2016-04-15T02:55Z] 2016-04-14 19:55:02 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:55:02,718 - WARNING - Could not retrieve variants from source file in region 1:229730241-229743163. Error was invalid region `1:229730242-229743163`
[2016-04-15T02:55Z] 2016-04-14 19:55:04 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:55:04,827 - WARNING - Could not retrieve variants from source file in region 1:235628697-235652703. Error was invalid region `1:235628698-235652703`
[2016-04-15T02:55Z] 2016-04-14 19:55:07 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:55:07,158 - WARNING - Could not retrieve variants from source file in region 1:231344660-231345061. Error was invalid region `1:231344661-231345061`
[2016-04-15T02:55Z] 2016-04-14 19:55:07 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:55:07,794 - WARNING - Could not retrieve variants from source file in region 1:225494957-225495358. Error was invalid region `1:225494958-225495358`
[2016-04-15T02:55Z] 2016-04-14 19:55:07 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:55:07,911 - WARNING - Could not retrieve variants from source file in region 1:235291800-235292201. Error was invalid region `1:235291801-235292201`
[2016-04-15T02:55Z] 2016-04-14 19:55:08 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:55:08,421 - WARNING - Could not retrieve variants from source file in region 1:226473921-226474322. Error was invalid region `1:226473922-226474322`
[2016-04-15T02:55Z] 2016-04-14 19:55:08 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:55:08,613 - WARNING - Could not retrieve variants from source file in region 1:237711586-237711987. Error was invalid region `1:237711587-237711987`
[2016-04-15T02:55Z] 2016-04-14 19:55:10 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:55:10,534 - WARNING - Could not retrieve variants from source file in region 1:231472624-231490295. Error was invalid region `1:231472625-231490295`
[2016-04-15T02:55Z] 2016-04-14 19:55:10 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:55:10,571 - WARNING - Could not retrieve variants from source file in region 1:233222612-233223013. Error was invalid region `1:233222613-233223013`
[2016-04-15T02:55Z] 2016-04-14 19:55:13 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:55:13,179 - WARNING - Could not retrieve variants from source file in region 1:228109260-228113353. Error was invalid region `1:228109261-228113353`
[2016-04-15T02:55Z] 2016-04-14 19:55:13 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:55:13,881 - WARNING - Could not retrieve variants from source file in region 1:235291800-235292201. Error was invalid region `1:235291801-235292201`
[2016-04-15T02:55Z] 2016-04-14 19:55:14 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:55:14,933 - WARNING - Could not retrieve variants from source file in region 1:237711586-237711987. Error was invalid region `1:237711587-237711987`
[2016-04-15T02:55Z] 2016-04-14 19:55:15 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:55:15,077 - WARNING - Could not retrieve variants from source file in region 1:230841476-230846167. Error was invalid region `1:230841477-230846167`
[2016-04-15T02:55Z] 2016-04-14 19:55:15 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:55:15,117 - WARNING - Could not retrieve variants from source file in region 1:226473921-226474322. Error was invalid region `1:226473922-226474322`
[2016-04-15T02:55Z] 2016-04-14 19:55:15 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:55:15,178 - WARNING - Could not retrieve variants from source file in region 1:224544448-224564682. Error was invalid region `1:224544449-224564682`
[2016-04-15T02:55Z] 2016-04-14 19:55:15 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:55:15,601 - WARNING - Could not retrieve variants from source file in region 1:235628697-235652703. Error was invalid region `1:235628698-235652703`
[2016-04-15T02:55Z] 2016-04-14 19:55:17 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:55:17,874 - WARNING - Could not retrieve variants from source file in region 1:228109260-228113353. Error was invalid region `1:228109261-228113353`
[2016-04-15T02:55Z] 2016-04-14 19:55:21 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:55:21,423 - WARNING - Could not retrieve variants from source file in region 1:226473921-226474322. Error was invalid region `1:226473922-226474322`
[2016-04-15T02:55Z] 2016-04-14 19:55:21 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:55:21,490 - WARNING - Could not retrieve variants from source file in region 1:237711586-237711987. Error was invalid region `1:237711587-237711987`
[2016-04-15T02:55Z] 2016-04-14 19:55:23 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:55:23,076 - WARNING - Could not retrieve variants from source file in region 1:233222612-233223013. Error was invalid region `1:233222613-233223013`
[2016-04-15T02:55Z] 2016-04-14 19:55:23 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:55:23,179 - WARNING - Could not retrieve variants from source file in region 1:225372861-225373262. Error was invalid region `1:225372862-225373262`
[2016-04-15T02:55Z] 2016-04-14 19:55:29 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:55:29,445 - WARNING - Could not retrieve variants from source file in region 1:229683053-229683454. Error was invalid region `1:229683054-229683454`
[2016-04-15T02:55Z] 2016-04-14 19:55:31 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:55:31,503 - WARNING - Could not retrieve variants from source file in region 1:234582440-234607188. Error was invalid region `1:234582441-234607188`
[2016-04-15T02:55Z] 2016-04-14 19:55:33 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:55:33,094 - WARNING - Could not retrieve variants from source file in region 1:228032986-228033387. Error was invalid region `1:228032987-228033387`
[2016-04-15T02:55Z] 2016-04-14 19:55:35 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:55:35,739 - WARNING - Could not retrieve variants from source file in region 1:227964188-227965000. Error was invalid region `1:227964189-227965000`
[2016-04-15T02:55Z] 2016-04-14 19:55:35 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:55:35,908 - WARNING - Could not retrieve variants from source file in region 1:230813872-230814273. Error was invalid region `1:230813873-230814273`
[2016-04-15T02:55Z] 2016-04-14 19:55:35 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:55:35,921 - WARNING - Could not retrieve variants from source file in region 1:226352287-226352688. Error was invalid region `1:226352288-226352688`
[2016-04-15T02:55Z] 2016-04-14 19:55:36 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:55:36,490 - WARNING - Could not retrieve variants from source file in region 1:224492535-224496042. Error was invalid region `1:224492536-224496042`
[2016-04-15T02:55Z] 2016-04-14 19:55:36 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:55:36,615 - WARNING - Could not retrieve variants from source file in region 1:237617546-237617947. Error was invalid region `1:237617547-237617947`
[2016-04-15T02:55Z] 2016-04-14 19:55:37 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:55:37,541 - WARNING - Could not retrieve variants from source file in region 1:225266755-225273438. Error was invalid region `1:225266756-225273438`
[2016-04-15T02:55Z] 2016-04-14 19:55:37 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:55:37,947 - WARNING - Could not retrieve variants from source file in region 1:233121916-233193990. Error was invalid region `1:233121917-233193990`
[2016-04-15T02:55Z] 2016-04-14 19:55:37 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:55:37,974 - WARNING - Could not retrieve variants from source file in region 1:231114209-231114655. Error was invalid region `1:231114210-231114655`
[2016-04-15T02:55Z] 2016-04-14 19:55:38 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:55:38,169 - WARNING - Could not retrieve variants from source file in region 1:228032986-228033387. Error was invalid region `1:228032987-228033387`
[2016-04-15T02:55Z] 2016-04-14 19:55:38 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:55:38,848 - WARNING - Could not retrieve variants from source file in region 1:229683053-229683454. Error was invalid region `1:229683054-229683454`
[2016-04-15T02:55Z] 2016-04-14 19:55:41 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:55:41,434 - WARNING - Could not retrieve variants from source file in region 1:230813872-230814273. Error was invalid region `1:230813873-230814273`
[2016-04-15T02:55Z] 2016-04-14 19:55:41 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:55:41,623 - WARNING - Could not retrieve variants from source file in region 1:224492535-224496042. Error was invalid region `1:224492536-224496042`
[2016-04-15T02:55Z] 2016-04-14 19:55:41 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:55:41,665 - WARNING - Could not retrieve variants from source file in region 1:226352287-226352688. Error was invalid region `1:226352288-226352688`
[2016-04-15T02:55Z] 2016-04-14 19:55:42 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:55:42,130 - WARNING - Could not retrieve variants from source file in region 1:225266755-225273438. Error was invalid region `1:225266756-225273438`
[2016-04-15T02:55Z] 2016-04-14 19:55:43 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:55:43,404 - WARNING - Could not retrieve variants from source file in region 1:225266755-225273438. Error was invalid region `1:225266756-225273438`
[2016-04-15T02:55Z] 2016-04-14 19:55:43 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:55:43,463 - WARNING - Could not retrieve variants from source file in region 1:228032986-228033387. Error was invalid region `1:228032987-228033387`
[2016-04-15T02:55Z] 2016-04-14 19:55:46 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:55:46,221 - WARNING - Could not retrieve variants from source file in region 1:230813872-230814273. Error was invalid region `1:230813873-230814273`
[2016-04-15T02:55Z] 2016-04-14 19:55:46 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:55:46,807 - WARNING - Could not retrieve variants from source file in region 1:224492535-224496042. Error was invalid region `1:224492536-224496042`
[2016-04-15T02:55Z] 2016-04-14 19:55:46 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:55:46,973 - WARNING - Could not retrieve variants from source file in region 1:237617546-237617947. Error was invalid region `1:237617547-237617947`
[2016-04-15T02:55Z] 2016-04-14 19:55:47 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:55:47,289 - WARNING - Could not retrieve variants from source file in region 1:226352287-226352688. Error was invalid region `1:226352288-226352688`
[2016-04-15T02:55Z] 2016-04-14 19:55:52 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:55:52,665 - WARNING - Could not retrieve variants from source file in region 1:229599203-229635711. Error was invalid region `1:229599204-229635711`
[2016-04-15T02:55Z] 2016-04-14 19:55:57 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:55:57,100 - WARNING - Could not retrieve variants from source file in region 1:230561178-230561817. Error was invalid region `1:230561179-230561817`
[2016-04-15T02:55Z] 2016-04-14 19:55:57 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:55:57,115 - WARNING - Could not retrieve variants from source file in region 1:226107989-226108390. Error was invalid region `1:226107990-226108390`
[2016-04-15T02:55Z] 2016-04-14 19:55:57 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:55:57,580 - WARNING - Could not retrieve variants from source file in region 1:228004755-228005156. Error was invalid region `1:228004756-228005156`
[2016-04-15T02:55Z] 2016-04-14 19:55:58 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:55:58,424 - WARNING - Could not retrieve variants from source file in region 1:234509048-234546435. Error was invalid region `1:234509049-234546435`
[2016-04-15T02:55Z] 2016-04-14 19:55:58 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:55:58,450 - WARNING - Could not retrieve variants from source file in region 1:230460868-230461269. Error was invalid region `1:230460869-230461269`
[2016-04-15T02:55Z] 2016-04-14 19:55:58 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:55:58,539 - WARNING - Could not retrieve variants from source file in region 1:227922663-227935634. Error was invalid region `1:227922664-227935634`
[2016-04-15T02:56Z] 2016-04-14 19:56:02 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:56:02,107 - WARNING - Could not retrieve variants from source file in region 1:233086245-233086646. Error was invalid region `1:233086246-233086646`
[2016-04-15T02:56Z] 2016-04-14 19:56:02 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:56:02,437 - WARNING - Could not retrieve variants from source file in region 1:232940742-232941544. Error was invalid region `1:232940743-232941544`
[2016-04-15T02:56Z] 2016-04-14 19:56:02 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:56:02,829 - WARNING - Could not retrieve variants from source file in region 1:229599203-229635711. Error was invalid region `1:229599204-229635711`
[2016-04-15T02:56Z] 2016-04-14 19:56:02 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:56:02,913 - WARNING - Could not retrieve variants from source file in region 1:234509048-234546435. Error was invalid region `1:234509049-234546435`
[2016-04-15T02:56Z] 2016-04-14 19:56:03 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:56:03,697 - WARNING - Could not retrieve variants from source file in region 1:224218218-224218619. Error was invalid region `1:224218219-224218619`
[2016-04-15T02:56Z] 2016-04-14 19:56:06 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:56:06,048 - WARNING - Could not retrieve variants from source file in region 1:228004755-228005156. Error was invalid region `1:228004756-228005156`
[2016-04-15T02:56Z] 2016-04-14 19:56:06 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:56:06,209 - WARNING - Could not retrieve variants from source file in region 1:233086245-233086646. Error was invalid region `1:233086246-233086646`
[2016-04-15T02:56Z] 2016-04-14 19:56:07 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:56:07,642 - WARNING - Could not retrieve variants from source file in region 1:230460868-230461269. Error was invalid region `1:230460869-230461269`
[2016-04-15T02:56Z] 2016-04-14 19:56:13 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:56:13,143 - WARNING - Could not retrieve variants from source file in region 1:223983339-223983740. Error was invalid region `1:223983340-223983740`
[2016-04-15T02:56Z] 2016-04-14 19:56:15 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:56:15,435 - WARNING - Could not retrieve variants from source file in region 1:223813375-223813776. Error was invalid region `1:223813376-223813776`
[2016-04-15T02:56Z] 2016-04-14 19:56:15 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:56:15,967 - WARNING - Could not retrieve variants from source file in region 1:227504583-227504984. Error was invalid region `1:227504584-227504984`
[2016-04-15T02:56Z] 2016-04-14 19:56:19 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:56:19,236 - WARNING - Could not retrieve variants from source file in region 1:232650539-232651057. Error was invalid region `1:232650540-232651057`
[2016-04-15T02:56Z] 2016-04-14 19:56:20 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:56:20,618 - WARNING - Could not retrieve variants from source file in region 1:223283699-223284789. Error was invalid region `1:223283700-223284789`
[2016-04-15T02:56Z] 2016-04-14 19:56:21 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:56:21,055 - WARNING - Could not retrieve variants from source file in region 1:227216451-227216965. Error was invalid region `1:227216452-227216965`
[2016-04-15T02:56Z] 2016-04-14 19:56:23 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:56:23,418 - WARNING - Could not retrieve variants from source file in region 1:232650539-232651057. Error was invalid region `1:232650540-232651057`
[2016-04-15T02:56Z] 2016-04-14 19:56:24 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:56:24,279 - WARNING - Could not retrieve variants from source file in region 1:223934509-223954270. Error was invalid region `1:223934510-223954270`
[2016-04-15T02:56Z] 2016-04-14 19:56:24 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:56:24,770 - WARNING - Could not retrieve variants from source file in region 1:227148992-227182765. Error was invalid region `1:227148993-227182765`
[2016-04-15T02:56Z] 2016-04-14 19:56:25 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:56:25,030 - WARNING - Could not retrieve variants from source file in region 1:223162538-223178751. Error was invalid region `1:223162539-223178751`
[2016-04-15T02:56Z] 2016-04-14 19:56:25 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:56:25,247 - WARNING - Could not retrieve variants from source file in region 1:232650539-232651057. Error was invalid region `1:232650540-232651057`
[2016-04-15T02:56Z] 2016-04-14 19:56:27 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:56:27,871 - WARNING - Could not retrieve variants from source file in region 1:223934509-223954270. Error was invalid region `1:223934510-223954270`
[2016-04-15T02:56Z] 2016-04-14 19:56:28 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:56:28,512 - WARNING - Could not retrieve variants from source file in region 1:227148992-227182765. Error was invalid region `1:227148993-227182765`
[2016-04-15T02:56Z] 2016-04-14 19:56:29 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:56:29,138 - WARNING - Could not retrieve variants from source file in region 1:223900197-223905722. Error was invalid region `1:223900198-223905722`
[2016-04-15T02:56Z] 2016-04-14 19:56:29 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:56:29,159 - WARNING - Could not retrieve variants from source file in region 1:223162538-223178751. Error was invalid region `1:223162539-223178751`
[2016-04-15T02:56Z] 2016-04-14 19:56:31 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:56:31,865 - WARNING - Could not retrieve variants from source file in region 1:227148992-227182765. Error was invalid region `1:227148993-227182765`
[2016-04-15T02:56Z] 2016-04-14 19:56:32 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:56:32,318 - WARNING - Could not retrieve variants from source file in region 1:227069466-227071715. Error was invalid region `1:227069467-227071715`
[2016-04-15T02:56Z] 2016-04-14 19:56:32 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:56:32,673 - WARNING - Could not retrieve variants from source file in region 1:223900197-223905722. Error was invalid region `1:223900198-223905722`
[2016-04-15T02:56Z] 2016-04-14 19:56:34 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:56:34,411 - WARNING - Could not retrieve variants from source file in region 1:223900197-223905722. Error was invalid region `1:223900198-223905722`
[2016-04-15T02:56Z] 2016-04-14 19:56:35 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:56:35,419 - WARNING - Could not retrieve variants from source file in region 1:232144387-232145077. Error was invalid region `1:232144388-232145077`
[2016-04-15T02:56Z] 2016-04-14 19:56:35 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:56:35,697 - WARNING - Could not retrieve variants from source file in region 1:231953890-231954799. Error was invalid region `1:231953891-231954799`
[2016-04-15T02:56Z] 2016-04-14 19:56:38 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:56:38,843 - WARNING - Could not retrieve variants from source file in region 1:231953890-231954799. Error was invalid region `1:231953891-231954799`
[2016-04-15T02:56Z] ['bcbio-variation-recall', 'square', '-Xms750m', '-Xmx7280m', '-XX:+UseSerialGC', '-c', 16, '-r', u'1:240255410-249250621', '--caller', 'platypus', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/1/Batch1-1_240255409_249250621.vcf.gz', '/mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/1/Batch1-1_240255409_249250621.vcf-inputs.txt'] in region: 1:240255410-249250621
[2016-04-15T02:56Z] 2016-04-14 19:56:54 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:56:54,727 - WARNING - Could not retrieve variants from source file in region 1:248737048-248737449. Error was invalid region `1:248737049-248737449`
[2016-04-15T02:56Z] 2016-04-14 19:56:56 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:56:56,097 - WARNING - Could not retrieve variants from source file in region 1:247977924-247979186. Error was invalid region `1:247977925-247979186`
[2016-04-15T02:56Z] 2016-04-14 19:56:56 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:56:56,634 - WARNING - Could not retrieve variants from source file in region 1:242159403-242159804. Error was invalid region `1:242159404-242159804`
[2016-04-15T02:56Z] 2016-04-14 19:56:57 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:56:57,103 - WARNING - Could not retrieve variants from source file in region 1:246670270-246670671. Error was invalid region `1:246670271-246670671`
[2016-04-15T02:56Z] 2016-04-14 19:56:57 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:56:57,809 - WARNING - Could not retrieve variants from source file in region 1:248224535-248224936. Error was invalid region `1:248224536-248224936`
[2016-04-15T02:56Z] 2016-04-14 19:56:57 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:56:57,826 - WARNING - Could not retrieve variants from source file in region 1:248487089-248569559. Error was invalid region `1:248487090-248569559`
[2016-04-15T02:56Z] 2016-04-14 19:56:59 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:56:59,496 - WARNING - Could not retrieve variants from source file in region 1:248737048-248737449. Error was invalid region `1:248737049-248737449`
[2016-04-15T02:57Z] 2016-04-14 19:57:03 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:57:03,108 - WARNING - Could not retrieve variants from source file in region 1:249106137-249106538. Error was invalid region `1:249106138-249106538`
[2016-04-15T02:57Z] 2016-04-14 19:57:04 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:57:04,076 - WARNING - Could not retrieve variants from source file in region 1:241711923-241712324. Error was invalid region `1:241711924-241712324`
[2016-04-15T02:57Z] 2016-04-14 19:57:04 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:57:04,262 - WARNING - Could not retrieve variants from source file in region 1:246670270-246670671. Error was invalid region `1:246670271-246670671`
[2016-04-15T02:57Z] 2016-04-14 19:57:05 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:57:05,743 - WARNING - Could not retrieve variants from source file in region 1:248685042-248685909. Error was invalid region `1:248685043-248685909`
[2016-04-15T02:57Z] 2016-04-14 19:57:05 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:57:05,798 - WARNING - Could not retrieve variants from source file in region 1:248616457-248616858. Error was invalid region `1:248616458-248616858`
[2016-04-15T02:57Z] 2016-04-14 19:57:06 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:57:06,526 - WARNING - Could not retrieve variants from source file in region 1:248112416-248129430. Error was invalid region `1:248112417-248129430`
[2016-04-15T02:57Z] 2016-04-14 19:57:06 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:57:06,697 - WARNING - Could not retrieve variants from source file in region 1:242159403-242159804. Error was invalid region `1:242159404-242159804`
[2016-04-15T02:57Z] 2016-04-14 19:57:06 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:57:06,705 - WARNING - Could not retrieve variants from source file in region 1:248343332-248366982. Error was invalid region `1:248343333-248366982`
[2016-04-15T02:57Z] 2016-04-14 19:57:06 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:57:06,874 - WARNING - Could not retrieve variants from source file in region 1:248737048-248737449. Error was invalid region `1:248737049-248737449`
[2016-04-15T02:57Z] 2016-04-14 19:57:07 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:57:07,107 - WARNING - Could not retrieve variants from source file in region 1:247148416-247162848. Error was invalid region `1:247148417-247162848`
[2016-04-15T02:57Z] 2016-04-14 19:57:07 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:57:07,551 - WARNING - Could not retrieve variants from source file in region 1:249106137-249106538. Error was invalid region `1:249106138-249106538`
[2016-04-15T02:57Z] 2016-04-14 19:57:09 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:57:09,189 - WARNING - Could not retrieve variants from source file in region 1:241711923-241712324. Error was invalid region `1:241711924-241712324`
[2016-04-15T02:57Z] 2016-04-14 19:57:09 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:57:09,709 - WARNING - Could not retrieve variants from source file in region 1:246670270-246670671. Error was invalid region `1:246670271-246670671`
[2016-04-15T02:57Z] 2016-04-14 19:57:14 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:57:14,326 - WARNING - Could not retrieve variants from source file in region 1:248224535-248224936. Error was invalid region `1:248224536-248224936`
[2016-04-15T02:57Z] 2016-04-14 19:57:14 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:57:14,527 - WARNING - Could not retrieve variants from source file in region 1:248112416-248129430. Error was invalid region `1:248112417-248129430`
[2016-04-15T02:57Z] 2016-04-14 19:57:14 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:57:14,578 - WARNING - Could not retrieve variants from source file in region 1:248487089-248569559. Error was invalid region `1:248487090-248569559`
[2016-04-15T02:57Z] 2016-04-14 19:57:24 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:57:24,577 - WARNING - Could not retrieve variants from source file in region 1:248902996-248903397. Error was invalid region `1:248902997-248903397`
[2016-04-15T02:57Z] 2016-04-14 19:57:25 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:57:25,298 - WARNING - Could not retrieve variants from source file in region 1:247048623-247049024. Error was invalid region `1:247048624-247049024`
[2016-04-15T02:57Z] 2016-04-14 19:57:26 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:57:26,692 - WARNING - Could not retrieve variants from source file in region 1:241669187-241669588. Error was invalid region `1:241669188-241669588`
[2016-04-15T02:57Z] 2016-04-14 19:57:27 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:57:27,585 - WARNING - Could not retrieve variants from source file in region 1:248402547-248402948. Error was invalid region `1:248402548-248402948`
[2016-04-15T02:57Z] 2016-04-14 19:57:29 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:57:29,030 - WARNING - Could not retrieve variants from source file in region 1:246119035-246119436. Error was invalid region `1:246119036-246119436`
[2016-04-15T02:57Z] 2016-04-14 19:57:29 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:57:29,585 - WARNING - Could not retrieve variants from source file in region 1:245245191-245251330. Error was invalid region `1:245245192-245251330`
[2016-04-15T02:57Z] 2016-04-14 19:57:30 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:57:30,636 - WARNING - Could not retrieve variants from source file in region 1:246021730-246022131. Error was invalid region `1:246021731-246022131`
[2016-04-15T02:57Z] 2016-04-14 19:57:30 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:57:30,776 - WARNING - Could not retrieve variants from source file in region 1:247048623-247049024. Error was invalid region `1:247048624-247049024`
[2016-04-15T02:57Z] 2016-04-14 19:57:31 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:57:31,478 - WARNING - Could not retrieve variants from source file in region 1:247654287-247655465. Error was invalid region `1:247654288-247655465`
[2016-04-15T02:57Z] 2016-04-14 19:57:33 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:57:33,129 - WARNING - Could not retrieve variants from source file in region 1:247920889-247921602. Error was invalid region `1:247920890-247921602`
[2016-04-15T02:57Z] 2016-04-14 19:57:33 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:57:33,230 - WARNING - Could not retrieve variants from source file in region 1:248402547-248402948. Error was invalid region `1:248402548-248402948`
[2016-04-15T02:57Z] 2016-04-14 19:57:34 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:57:34,086 - WARNING - Could not retrieve variants from source file in region 1:240492523-240492924. Error was invalid region `1:240492524-240492924`
[2016-04-15T02:57Z] 2016-04-14 19:57:34 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:57:34,552 - WARNING - Could not retrieve variants from source file in region 1:246119035-246119436. Error was invalid region `1:246119036-246119436`
[2016-04-15T02:57Z] 2016-04-14 19:57:34 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:57:34,875 - WARNING - Could not retrieve variants from source file in region 1:247835568-247836140. Error was invalid region `1:247835569-247836140`
[2016-04-15T02:57Z] 2016-04-14 19:57:35 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:57:35,993 - WARNING - Could not retrieve variants from source file in region 1:245245191-245251330. Error was invalid region `1:245245192-245251330`
[2016-04-15T02:57Z] 2016-04-14 19:57:36 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:57:36,095 - WARNING - Could not retrieve variants from source file in region 1:246021730-246022131. Error was invalid region `1:246021731-246022131`
[2016-04-15T02:57Z] 2016-04-14 19:57:36 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:57:36,912 - WARNING - Could not retrieve variants from source file in region 1:247048623-247049024. Error was invalid region `1:247048624-247049024`
[2016-04-15T02:57Z] 2016-04-14 19:57:38 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:57:38,600 - WARNING - Could not retrieve variants from source file in region 1:241798420-241798821. Error was invalid region `1:241798421-241798821`
[2016-04-15T02:57Z] 2016-04-14 19:57:38 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:57:38,711 - WARNING - Could not retrieve variants from source file in region 1:242120800-242121986. Error was invalid region `1:242120801-242121986`
[2016-04-15T02:57Z] 2016-04-14 19:57:39 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:57:39,182 - WARNING - Could not retrieve variants from source file in region 1:241907606-241951519. Error was invalid region `1:241907607-241951519`
[2016-04-15T02:57Z] 2016-04-14 19:57:39 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:57:39,328 - WARNING - Could not retrieve variants from source file in region 1:248402547-248402948. Error was invalid region `1:248402548-248402948`
[2016-04-15T02:57Z] 2016-04-14 19:57:39 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:57:39,807 - WARNING - Could not retrieve variants from source file in region 1:246119035-246119436. Error was invalid region `1:246119036-246119436`
[2016-04-15T02:57Z] 2016-04-14 19:57:40 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:57:40,953 - WARNING - Could not retrieve variants from source file in region 1:245245191-245251330. Error was invalid region `1:245245192-245251330`
[2016-04-15T02:57Z] 2016-04-14 19:57:41 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:57:41,057 - WARNING - Could not retrieve variants from source file in region 1:246021730-246022131. Error was invalid region `1:246021731-246022131`
[2016-04-15T02:57Z] 2016-04-14 19:57:44 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:57:44,646 - WARNING - Could not retrieve variants from source file in region 1:241798420-241798821. Error was invalid region `1:241798421-241798821`
[2016-04-15T02:57Z] 2016-04-14 19:57:44 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:57:44,969 - WARNING - Could not retrieve variants from source file in region 1:242120800-242121986. Error was invalid region `1:242120801-242121986`
[2016-04-15T02:57Z] 2016-04-14 19:57:51 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:57:51,240 - WARNING - Could not retrieve variants from source file in region 1:247005840-247021275. Error was invalid region `1:247005841-247021275`
[2016-04-15T02:57Z] 2016-04-14 19:57:52 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:57:52,695 - WARNING - Could not retrieve variants from source file in region 1:241031688-241032089. Error was invalid region `1:241031689-241032089`
[2016-04-15T02:57Z] 2016-04-14 19:57:56 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:57:56,307 - WARNING - Could not retrieve variants from source file in region 1:247470492-247471311. Error was invalid region `1:247470493-247471311`
[2016-04-15T02:57Z] 2016-04-14 19:57:56 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:57:56,744 - WARNING - Could not retrieve variants from source file in region 1:247694738-247695946. Error was invalid region `1:247694739-247695946`
[2016-04-15T02:58Z] 2016-04-14 19:58:00 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:58:00,103 - WARNING - Could not retrieve variants from source file in region 1:241755137-241755538. Error was invalid region `1:241755138-241755538`
[2016-04-15T02:58Z] 2016-04-14 19:58:00 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:58:00,775 - WARNING - Could not retrieve variants from source file in region 1:243578901-243579302. Error was invalid region `1:243578902-243579302`
[2016-04-15T02:58Z] 2016-04-14 19:58:01 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:58:01,015 - WARNING - Could not retrieve variants from source file in region 1:247875103-247875879. Error was invalid region `1:247875104-247875879`
[2016-04-15T02:58Z] 2016-04-14 19:58:01 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:58:01,773 - WARNING - Could not retrieve variants from source file in region 1:247751520-247769942. Error was invalid region `1:247751521-247769942`
[2016-04-15T02:58Z] 2016-04-14 19:58:02 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:58:02,530 - WARNING - Could not retrieve variants from source file in region 1:247614175-247615086. Error was invalid region `1:247614176-247615086`
[2016-04-15T02:58Z] 2016-04-14 19:58:04 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:58:04,347 - WARNING - Could not retrieve variants from source file in region 1:241846617-241847018. Error was invalid region `1:241846618-241847018`
[2016-04-15T02:58Z] 2016-04-14 19:58:05 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:58:05,146 - WARNING - Could not retrieve variants from source file in region 1:243578901-243579302. Error was invalid region `1:243578902-243579302`
[2016-04-15T02:58Z] 2016-04-14 19:58:06 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:58:06,174 - WARNING - Could not retrieve variants from source file in region 1:247470492-247471311. Error was invalid region `1:247470493-247471311`
[2016-04-15T02:58Z] 2016-04-14 19:58:08 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:58:08,068 - WARNING - Could not retrieve variants from source file in region 1:242023687-242048864. Error was invalid region `1:242023688-242048864`
[2016-04-15T02:58Z] 2016-04-14 19:58:08 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:58:08,148 - WARNING - Could not retrieve variants from source file in region 1:247694738-247695946. Error was invalid region `1:247694739-247695946`
[2016-04-15T02:58Z] 2016-04-14 19:58:08 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:58:08,633 - WARNING - Could not retrieve variants from source file in region 1:241846617-241847018. Error was invalid region `1:241846618-241847018`
[2016-04-15T02:58Z] 2016-04-14 19:58:17 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:58:17,266 - WARNING - Could not retrieve variants from source file in region 1:240341057-240341458. Error was invalid region `1:240341058-240341458`
[2016-04-15T02:58Z] 2016-04-14 19:58:17 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:58:17,993 - WARNING - Could not retrieve variants from source file in region 1:246939302-246949488. Error was invalid region `1:246939303-246949488`
[2016-04-15T02:58Z] 2016-04-14 19:58:18 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:58:18,497 - WARNING - Could not retrieve variants from source file in region 1:247419298-247420611. Error was invalid region `1:247419299-247420611`
[2016-04-15T02:58Z] 2016-04-14 19:58:20 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:58:20,366 - WARNING - Could not retrieve variants from source file in region 1:240341057-240341458. Error was invalid region `1:240341058-240341458`
[2016-04-15T02:58Z] 2016-04-14 19:58:21 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:58:21,031 - WARNING - Could not retrieve variants from source file in region 1:240255357-240257012. Error was invalid region `1:240255358-240257012`
[2016-04-15T02:58Z] 2016-04-14 19:58:21 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:58:21,691 - WARNING - Could not retrieve variants from source file in region 1:246754913-246755314. Error was invalid region `1:246754914-246755314`
[2016-04-15T02:58Z] 2016-04-14 19:58:22 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:58:22,145 - WARNING - Could not retrieve variants from source file in region 1:246707647-246720988. Error was invalid region `1:246707648-246720988`
[2016-04-15T02:58Z] 2016-04-14 19:58:22 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:58:22,456 - WARNING - Could not retrieve variants from source file in region 1:247419298-247420611. Error was invalid region `1:247419299-247420611`
[2016-04-15T02:58Z] 2016-04-14 19:58:22 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:58:22,461 - WARNING - Could not retrieve variants from source file in region 1:246754913-246755314. Error was invalid region `1:246754914-246755314`
[2016-04-15T02:58Z] 2016-04-14 19:58:22 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:58:22,682 - WARNING - Could not retrieve variants from source file in region 1:247419298-247420611. Error was invalid region `1:247419299-247420611`
[2016-04-15T02:58Z] 2016-04-14 19:58:24 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:58:24,292 - WARNING - Could not retrieve variants from source file in region 1:246754913-246755314. Error was invalid region `1:246754914-246755314`
[2016-04-15T02:58Z] 2016-04-14 19:58:24 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:58:24,940 - WARNING - Could not retrieve variants from source file in region 1:247267063-247275408. Error was invalid region `1:247267064-247275408`
[2016-04-15T02:58Z] 2016-04-14 19:58:26 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:58:26,670 - WARNING - Could not retrieve variants from source file in region 1:246707647-246720988. Error was invalid region `1:246707648-246720988`
[2016-04-15T02:58Z] 2016-04-14 19:58:29 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:58:29,922 - WARNING - Could not retrieve variants from source file in region 1:247201401-247201802. Error was invalid region `1:247201402-247201802`
[2016-04-15T02:58Z] 2016-04-14 19:58:30 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:58:30,006 - WARNING - Could not retrieve variants from source file in region 1:247201401-247201802. Error was invalid region `1:247201402-247201802`
[2016-04-15T02:58Z] ['bcbio-variation-recall', 'square', '-Xms750m', '-Xmx7280m', '-XX:+UseSerialGC', '-c', 16, '-r', u'2:1-15514844', '--caller', 'platypus', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/2/Batch1-2_0_15514844.vcf.gz', '/mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/2/Batch1-2_0_15514844.vcf-inputs.txt'] in region: 2:1-15514844
[2016-04-15T02:58Z] 2016-04-14 19:58:44 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:58:44,934 - WARNING - Could not retrieve variants from source file in region 2:11300658-11301059. Error was invalid region `2:11300659-11301059`
[2016-04-15T02:58Z] 2016-04-14 19:58:47 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:58:47,451 - WARNING - Could not retrieve variants from source file in region 2:11484251-11484652. Error was invalid region `2:11484252-11484652`
[2016-04-15T02:58Z] 2016-04-14 19:58:47 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:58:47,650 - WARNING - Could not retrieve variants from source file in region 2:1319932-1320333. Error was invalid region `2:1319933-1320333`
[2016-04-15T02:58Z] 2016-04-14 19:58:47 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:58:47,789 - WARNING - Could not retrieve variants from source file in region 2:1161084-1161485. Error was invalid region `2:1161085-1161485`
[2016-04-15T02:58Z] 2016-04-14 19:58:47 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:58:47,859 - WARNING - Could not retrieve variants from source file in region 2:11911550-11911951. Error was invalid region `2:11911551-11911951`
[2016-04-15T02:58Z] 2016-04-14 19:58:48 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:58:48,301 - WARNING - Could not retrieve variants from source file in region 2:1417981-1418382. Error was invalid region `2:1417982-1418382`
[2016-04-15T02:58Z] 2016-04-14 19:58:49 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:58:49,380 - WARNING - Could not retrieve variants from source file in region 2:11300658-11301059. Error was invalid region `2:11300659-11301059`
[2016-04-15T02:58Z] 2016-04-14 19:58:52 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:58:52,513 - WARNING - Could not retrieve variants from source file in region 2:7136856-7182367. Error was invalid region `2:7136857-7182367`
[2016-04-15T02:58Z] 2016-04-14 19:58:53 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:58:53,725 - WARNING - Could not retrieve variants from source file in region 2:1646960-1664844. Error was invalid region `2:1646961-1664844`
[2016-04-15T02:58Z] 2016-04-14 19:58:54 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:58:54,562 - WARNING - Could not retrieve variants from source file in region 2:11484251-11484652. Error was invalid region `2:11484252-11484652`
[2016-04-15T02:58Z] 2016-04-14 19:58:54 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:58:54,648 - WARNING - Could not retrieve variants from source file in region 2:3673437-3673838. Error was invalid region `2:3673438-3673838`
[2016-04-15T02:58Z] 2016-04-14 19:58:55 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:58:55,492 - WARNING - Could not retrieve variants from source file in region 2:1319932-1320333. Error was invalid region `2:1319933-1320333`
[2016-04-15T02:58Z] 2016-04-14 19:58:56 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:58:56,407 - WARNING - Could not retrieve variants from source file in region 2:1842757-1843158. Error was invalid region `2:1842758-1843158`
[2016-04-15T02:58Z] 2016-04-14 19:58:57 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:58:57,139 - WARNING - Could not retrieve variants from source file in region 2:3748940-3749344. Error was invalid region `2:3748941-3749344`
[2016-04-15T02:58Z] 2016-04-14 19:58:57 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:58:57,712 - WARNING - Could not retrieve variants from source file in region 2:11300658-11301059. Error was invalid region `2:11300659-11301059`
[2016-04-15T02:58Z] 2016-04-14 19:58:57 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:58:57,814 - WARNING - Could not retrieve variants from source file in region 2:1417981-1418382. Error was invalid region `2:1417982-1418382`
[2016-04-15T02:58Z] 2016-04-14 19:58:57 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:58:57,815 - WARNING - Could not retrieve variants from source file in region 2:6988458-7006829. Error was invalid region `2:6988459-7006829`
[2016-04-15T02:58Z] 2016-04-14 19:58:57 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:58:57,816 - WARNING - Could not retrieve variants from source file in region 2:10717595-10717996. Error was invalid region `2:10717596-10717996`
[2016-04-15T02:58Z] 2016-04-14 19:58:57 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:58:57,833 - WARNING - Could not retrieve variants from source file in region 2:3469252-3520874. Error was invalid region `2:3469253-3520874`
[2016-04-15T02:58Z] 2016-04-14 19:58:58 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:58:58,575 - WARNING - Could not retrieve variants from source file in region 2:1646960-1664844. Error was invalid region `2:1646961-1664844`
[2016-04-15T02:58Z] 2016-04-14 19:58:59 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:58:59,300 - WARNING - Could not retrieve variants from source file in region 2:11484251-11484652. Error was invalid region `2:11484252-11484652`
[2016-04-15T02:59Z] 2016-04-14 19:59:00 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:59:00,003 - WARNING - Could not retrieve variants from source file in region 2:3673437-3673838. Error was invalid region `2:3673438-3673838`
[2016-04-15T02:59Z] 2016-04-14 19:59:00 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:59:00,791 - WARNING - Could not retrieve variants from source file in region 2:1319932-1320333. Error was invalid region `2:1319933-1320333`
[2016-04-15T02:59Z] 2016-04-14 19:59:01 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:59:01,219 - WARNING - Could not retrieve variants from source file in region 2:1161084-1161485. Error was invalid region `2:1161085-1161485`
[2016-04-15T02:59Z] 2016-04-14 19:59:02 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:59:02,729 - WARNING - Could not retrieve variants from source file in region 2:1842757-1843158. Error was invalid region `2:1842758-1843158`
[2016-04-15T02:59Z] 2016-04-14 19:59:04 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:59:04,325 - WARNING - Could not retrieve variants from source file in region 2:3469252-3520874. Error was invalid region `2:3469253-3520874`
[2016-04-15T02:59Z] 2016-04-14 19:59:04 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:59:04,599 - WARNING - Could not retrieve variants from source file in region 2:10717595-10717996. Error was invalid region `2:10717596-10717996`
[2016-04-15T02:59Z] 2016-04-14 19:59:04 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:59:04,712 - WARNING - Could not retrieve variants from source file in region 2:1417981-1418382. Error was invalid region `2:1417982-1418382`
[2016-04-15T02:59Z] 2016-04-14 19:59:12 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:59:12,111 - WARNING - Could not retrieve variants from source file in region 2:11052809-11053930. Error was invalid region `2:11052810-11053930`
[2016-04-15T02:59Z] 2016-04-14 19:59:14 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:59:14,394 - WARNING - Could not retrieve variants from source file in region 2:11358909-11359310. Error was invalid region `2:11358910-11359310`
[2016-04-15T02:59Z] 2016-04-14 19:59:17 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:59:17,037 - WARNING - Could not retrieve variants from source file in region 2:1079109-1079510. Error was invalid region `2:1079110-1079510`
[2016-04-15T02:59Z] 2016-04-14 19:59:17 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:59:17,112 - WARNING - Could not retrieve variants from source file in region 2:11358909-11359310. Error was invalid region `2:11358910-11359310`
[2016-04-15T02:59Z] 2016-04-14 19:59:17 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:59:17,152 - WARNING - Could not retrieve variants from source file in region 2:10908682-10959665. Error was invalid region `2:10908683-10959665`
[2016-04-15T02:59Z] 2016-04-14 19:59:17 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:59:17,523 - WARNING - Could not retrieve variants from source file in region 2:11052809-11053930. Error was invalid region `2:11052810-11053930`
[2016-04-15T02:59Z] 2016-04-14 19:59:18 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:59:18,762 - WARNING - Could not retrieve variants from source file in region 2:9983475-9983876. Error was invalid region `2:9983476-9983876`
[2016-04-15T02:59Z] 2016-04-14 19:59:18 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:59:18,975 - WARNING - Could not retrieve variants from source file in region 2:11358909-11359310. Error was invalid region `2:11358910-11359310`
[2016-04-15T02:59Z] 2016-04-14 19:59:19 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:59:19,760 - WARNING - Could not retrieve variants from source file in region 2:10262648-10263110. Error was invalid region `2:10262649-10263110`
[2016-04-15T02:59Z] 2016-04-14 19:59:20 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:59:20,367 - WARNING - Could not retrieve variants from source file in region 2:9563096-9564386. Error was invalid region `2:9563097-9564386`
[2016-04-15T02:59Z] 2016-04-14 19:59:21 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:59:21,902 - WARNING - Could not retrieve variants from source file in region 2:675620-676367. Error was invalid region `2:675621-676367`
[2016-04-15T02:59Z] 2016-04-14 19:59:22 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:59:22,277 - WARNING - Could not retrieve variants from source file in region 2:1079109-1079510. Error was invalid region `2:1079110-1079510`
[2016-04-15T02:59Z] 2016-04-14 19:59:22 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:59:22,557 - WARNING - Could not retrieve variants from source file in region 2:11052809-11053930. Error was invalid region `2:11052810-11053930`
[2016-04-15T02:59Z] 2016-04-14 19:59:22 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:59:22,571 - WARNING - Could not retrieve variants from source file in region 2:11853702-11854103. Error was invalid region `2:11853703-11854103`
[2016-04-15T02:59Z] 2016-04-14 19:59:23 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:59:23,753 - WARNING - Could not retrieve variants from source file in region 2:3391615-3392485. Error was invalid region `2:3391616-3392485`
[2016-04-15T02:59Z] 2016-04-14 19:59:23 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:59:23,873 - WARNING - Could not retrieve variants from source file in region 2:9983475-9983876. Error was invalid region `2:9983476-9983876`
[2016-04-15T02:59Z] 2016-04-14 19:59:25 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:59:25,182 - WARNING - Could not retrieve variants from source file in region 2:9563096-9564386. Error was invalid region `2:9563097-9564386`
[2016-04-15T02:59Z] 2016-04-14 19:59:25 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:59:25,318 - WARNING - Could not retrieve variants from source file in region 2:1926226-1947104. Error was invalid region `2:1926227-1947104`
[2016-04-15T02:59Z] 2016-04-14 19:59:26 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:59:26,855 - WARNING - Could not retrieve variants from source file in region 2:675620-676367. Error was invalid region `2:675621-676367`
[2016-04-15T02:59Z] 2016-04-14 19:59:26 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:59:26,909 - WARNING - Could not retrieve variants from source file in region 2:1079109-1079510. Error was invalid region `2:1079110-1079510`
[2016-04-15T02:59Z] 2016-04-14 19:59:27 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:59:27,336 - WARNING - Could not retrieve variants from source file in region 2:11853702-11854103. Error was invalid region `2:11853703-11854103`
[2016-04-15T02:59Z] 2016-04-14 19:59:28 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:59:28,468 - WARNING - Could not retrieve variants from source file in region 2:3391615-3392485. Error was invalid region `2:3391616-3392485`
[2016-04-15T02:59Z] 2016-04-14 19:59:28 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:59:28,472 - WARNING - Could not retrieve variants from source file in region 2:9634645-9635046. Error was invalid region `2:9634646-9635046`
[2016-04-15T02:59Z] 2016-04-14 19:59:28 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:59:28,593 - WARNING - Could not retrieve variants from source file in region 2:9983475-9983876. Error was invalid region `2:9983476-9983876`
[2016-04-15T02:59Z] 2016-04-14 19:59:29 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:59:29,260 - WARNING - Could not retrieve variants from source file in region 2:9563096-9564386. Error was invalid region `2:9563097-9564386`
[2016-04-15T02:59Z] 2016-04-14 19:59:29 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:59:29,663 - WARNING - Could not retrieve variants from source file in region 2:1926226-1947104. Error was invalid region `2:1926227-1947104`
[2016-04-15T02:59Z] 2016-04-14 19:59:32 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:59:32,491 - WARNING - Could not retrieve variants from source file in region 2:9634645-9635046. Error was invalid region `2:9634646-9635046`
[2016-04-15T02:59Z] 2016-04-14 19:59:36 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:59:36,087 - WARNING - Could not retrieve variants from source file in region 2:9634645-9635046. Error was invalid region `2:9634646-9635046`
[2016-04-15T02:59Z] 2016-04-14 19:59:37 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:59:37,719 - WARNING - Could not retrieve variants from source file in region 2:283020-283421. Error was invalid region `2:283021-283421`
[2016-04-15T02:59Z] 2016-04-14 19:59:37 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:59:37,748 - WARNING - Could not retrieve variants from source file in region 2:11809884-11818002. Error was invalid region `2:11809885-11818002`
[2016-04-15T02:59Z] 2016-04-14 19:59:37 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:59:37,984 - WARNING - Could not retrieve variants from source file in region 2:45684-46085. Error was invalid region `2:45685-46085`
[2016-04-15T02:59Z] 2016-04-14 19:59:39 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:59:39,573 - WARNING - Could not retrieve variants from source file in region 2:9490806-9528726. Error was invalid region `2:9490807-9528726`
[2016-04-15T02:59Z] 2016-04-14 19:59:40 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:59:40,389 - WARNING - Could not retrieve variants from source file in region 2:10044803-10059960. Error was invalid region `2:10044804-10059960`
[2016-04-15T02:59Z] 2016-04-14 19:59:40 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:59:40,597 - WARNING - Could not retrieve variants from source file in region 2:10183759-10188839. Error was invalid region `2:10183760-10188839`
[2016-04-15T02:59Z] 2016-04-14 19:59:41 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:59:41,295 - WARNING - Could not retrieve variants from source file in region 2:283020-283421. Error was invalid region `2:283021-283421`
[2016-04-15T02:59Z] 2016-04-14 19:59:41 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:59:41,588 - WARNING - Could not retrieve variants from source file in region 2:11809884-11818002. Error was invalid region `2:11809885-11818002`
[2016-04-15T02:59Z] 2016-04-14 19:59:42 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:59:42,088 - WARNING - Could not retrieve variants from source file in region 2:45684-46085. Error was invalid region `2:45685-46085`
[2016-04-15T02:59Z] 2016-04-14 19:59:43 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:59:43,057 - WARNING - Could not retrieve variants from source file in region 2:283020-283421. Error was invalid region `2:283021-283421`
[2016-04-15T02:59Z] 2016-04-14 19:59:43 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:59:43,313 - WARNING - Could not retrieve variants from source file in region 2:9490806-9528726. Error was invalid region `2:9490807-9528726`
[2016-04-15T02:59Z] 2016-04-14 19:59:44 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:59:44,360 - WARNING - Could not retrieve variants from source file in region 2:10094974-10126520. Error was invalid region `2:10094975-10126520`
[2016-04-15T02:59Z] 2016-04-14 19:59:44 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:59:44,364 - WARNING - Could not retrieve variants from source file in region 2:8870603-8877232. Error was invalid region `2:8870604-8877232`
[2016-04-15T02:59Z] 2016-04-14 19:59:44 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:59:44,437 - WARNING - Could not retrieve variants from source file in region 2:10044803-10059960. Error was invalid region `2:10044804-10059960`
[2016-04-15T02:59Z] 2016-04-14 19:59:45 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:59:45,530 - WARNING - Could not retrieve variants from source file in region 2:11809884-11818002. Error was invalid region `2:11809885-11818002`
[2016-04-15T02:59Z] 2016-04-14 19:59:45 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:59:45,829 - WARNING - Could not retrieve variants from source file in region 2:45684-46085. Error was invalid region `2:45685-46085`
[2016-04-15T02:59Z] 2016-04-14 19:59:46 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:59:46,899 - WARNING - Could not retrieve variants from source file in region 2:10094974-10126520. Error was invalid region `2:10094975-10126520`
[2016-04-15T02:59Z] 2016-04-14 19:59:48 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:59:48,039 - WARNING - Could not retrieve variants from source file in region 2:8870603-8877232. Error was invalid region `2:8870604-8877232`
[2016-04-15T02:59Z] 2016-04-14 19:59:48 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 19:59:48,269 - WARNING - Could not retrieve variants from source file in region 2:10044803-10059960. Error was invalid region `2:10044804-10059960`
[2016-04-15T02:59Z] ['bcbio-variation-recall', 'square', '-Xms750m', '-Xmx7280m', '-XX:+UseSerialGC', '-c', 16, '-r', u'2:15519726-31133925', '--caller', 'platypus', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/2/Batch1-2_15519725_31133925.vcf.gz', '/mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/2/Batch1-2_15519725_31133925.vcf-inputs.txt'] in region: 2:15519726-31133925
[2016-04-15T03:00Z] 2016-04-14 20:00:04 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:00:04,788 - WARNING - Could not retrieve variants from source file in region 2:26739212-26742151. Error was invalid region `2:26739213-26742151`
[2016-04-15T03:00Z] 2016-04-14 20:00:05 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:00:05,209 - WARNING - Could not retrieve variants from source file in region 2:23919164-23926849. Error was invalid region `2:23919165-23926849`
[2016-04-15T03:00Z] 2016-04-14 20:00:05 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:00:05,371 - WARNING - Could not retrieve variants from source file in region 2:30143288-30143689. Error was invalid region `2:30143289-30143689`
[2016-04-15T03:00Z] 2016-04-14 20:00:05 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:00:05,466 - WARNING - Could not retrieve variants from source file in region 2:26800211-26804437. Error was invalid region `2:26800212-26804437`
[2016-04-15T03:00Z] 2016-04-14 20:00:05 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:00:05,769 - WARNING - Could not retrieve variants from source file in region 2:26947159-26947560. Error was invalid region `2:26947160-26947560`
[2016-04-15T03:00Z] 2016-04-14 20:00:05 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:00:05,869 - WARNING - Could not retrieve variants from source file in region 2:26174533-26177388. Error was invalid region `2:26174534-26177388`
[2016-04-15T03:00Z] 2016-04-14 20:00:05 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:00:05,984 - WARNING - Could not retrieve variants from source file in region 2:27730729-27731130. Error was invalid region `2:27730730-27731130`
[2016-04-15T03:00Z] 2016-04-14 20:00:06 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:00:06,023 - WARNING - Could not retrieve variants from source file in region 2:29225291-29297258. Error was invalid region `2:29225292-29297258`
[2016-04-15T03:00Z] 2016-04-14 20:00:06 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:00:06,414 - WARNING - Could not retrieve variants from source file in region 2:29063299-29063700. Error was invalid region `2:29063300-29063700`
[2016-04-15T03:00Z] 2016-04-14 20:00:06 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:00:06,456 - WARNING - Could not retrieve variants from source file in region 2:31010001-31010402. Error was invalid region `2:31010002-31010402`
[2016-04-15T03:00Z] 2016-04-14 20:00:07 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:00:07,014 - WARNING - Could not retrieve variants from source file in region 2:29356356-29356859. Error was invalid region `2:29356357-29356859`
[2016-04-15T03:00Z] 2016-04-14 20:00:07 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:00:07,033 - WARNING - Could not retrieve variants from source file in region 2:29129207-29169802. Error was invalid region `2:29129208-29169802`
[2016-04-15T03:00Z] 2016-04-14 20:00:08 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:00:08,581 - WARNING - Could not retrieve variants from source file in region 2:28813822-28824983. Error was invalid region `2:28813823-28824983`
[2016-04-15T03:00Z] 2016-04-14 20:00:11 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:00:11,063 - WARNING - Could not retrieve variants from source file in region 2:30862881-30863298. Error was invalid region `2:30862882-30863298`
[2016-04-15T03:00Z] 2016-04-14 20:00:12 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:00:12,490 - WARNING - Could not retrieve variants from source file in region 2:30143288-30143689. Error was invalid region `2:30143289-30143689`
[2016-04-15T03:00Z] 2016-04-14 20:00:12 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:00:12,523 - WARNING - Could not retrieve variants from source file in region 2:23919164-23926849. Error was invalid region `2:23919165-23926849`
[2016-04-15T03:00Z] 2016-04-14 20:00:12 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:00:12,988 - WARNING - Could not retrieve variants from source file in region 2:26800211-26804437. Error was invalid region `2:26800212-26804437`
[2016-04-15T03:00Z] 2016-04-14 20:00:13 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:00:13,317 - WARNING - Could not retrieve variants from source file in region 2:26947159-26947560. Error was invalid region `2:26947160-26947560`
[2016-04-15T03:00Z] 2016-04-14 20:00:13 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:00:13,909 - WARNING - Could not retrieve variants from source file in region 2:31010001-31010402. Error was invalid region `2:31010002-31010402`
[2016-04-15T03:00Z] 2016-04-14 20:00:14 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:00:14,352 - WARNING - Could not retrieve variants from source file in region 2:27730729-27731130. Error was invalid region `2:27730730-27731130`
[2016-04-15T03:00Z] 2016-04-14 20:00:15 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:00:15,395 - WARNING - Could not retrieve variants from source file in region 2:26532232-26536917. Error was invalid region `2:26532233-26536917`
[2016-04-15T03:00Z] 2016-04-14 20:00:16 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:00:16,036 - WARNING - Could not retrieve variants from source file in region 2:30862881-30863298. Error was invalid region `2:30862882-30863298`
[2016-04-15T03:00Z] 2016-04-14 20:00:17 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:00:17,829 - WARNING - Could not retrieve variants from source file in region 2:30143288-30143689. Error was invalid region `2:30143289-30143689`
[2016-04-15T03:00Z] 2016-04-14 20:00:17 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:00:17,850 - WARNING - Could not retrieve variants from source file in region 2:23919164-23926849. Error was invalid region `2:23919165-23926849`
[2016-04-15T03:00Z] 2016-04-14 20:00:18 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:00:18,212 - WARNING - Could not retrieve variants from source file in region 2:26800211-26804437. Error was invalid region `2:26800212-26804437`
[2016-04-15T03:00Z] 2016-04-14 20:00:18 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:00:18,740 - WARNING - Could not retrieve variants from source file in region 2:26947159-26947560. Error was invalid region `2:26947160-26947560`
[2016-04-15T03:00Z] 2016-04-14 20:00:20 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:00:20,417 - WARNING - Could not retrieve variants from source file in region 2:31010001-31010402. Error was invalid region `2:31010002-31010402`
[2016-04-15T03:00Z] 2016-04-14 20:00:21 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:00:21,286 - WARNING - Could not retrieve variants from source file in region 2:29063299-29063700. Error was invalid region `2:29063300-29063700`
[2016-04-15T03:00Z] 2016-04-14 20:00:21 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:00:21,339 - WARNING - Could not retrieve variants from source file in region 2:27730729-27731130. Error was invalid region `2:27730730-27731130`
[2016-04-15T03:00Z] 2016-04-14 20:00:22 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:00:22,624 - WARNING - Could not retrieve variants from source file in region 2:26532232-26536917. Error was invalid region `2:26532233-26536917`
[2016-04-15T03:00Z] 2016-04-14 20:00:32 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:00:32,256 - WARNING - Could not retrieve variants from source file in region 2:27837847-27852108. Error was invalid region `2:27837848-27852108`
[2016-04-15T03:00Z] 2016-04-14 20:00:33 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:00:33,210 - WARNING - Could not retrieve variants from source file in region 2:30381294-30381695. Error was invalid region `2:30381295-30381695`
[2016-04-15T03:00Z] 2016-04-14 20:00:33 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:00:33,233 - WARNING - Could not retrieve variants from source file in region 2:26589873-26608182. Error was invalid region `2:26589874-26608182`
[2016-04-15T03:00Z] 2016-04-14 20:00:33 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:00:33,961 - WARNING - Could not retrieve variants from source file in region 2:29940318-29940719. Error was invalid region `2:29940319-29940719`
[2016-04-15T03:00Z] 2016-04-14 20:00:34 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:00:34,012 - WARNING - Could not retrieve variants from source file in region 2:23865049-23865450. Error was invalid region `2:23865050-23865450`
[2016-04-15T03:00Z] 2016-04-14 20:00:34 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:00:34,877 - WARNING - Could not retrieve variants from source file in region 2:26589873-26608182. Error was invalid region `2:26589874-26608182`
[2016-04-15T03:00Z] 2016-04-14 20:00:35 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:00:35,248 - WARNING - Could not retrieve variants from source file in region 2:29543452-29543853. Error was invalid region `2:29543453-29543853`
[2016-04-15T03:00Z] 2016-04-14 20:00:36 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:00:36,177 - WARNING - Could not retrieve variants from source file in region 2:29001480-29001881. Error was invalid region `2:29001481-29001881`
[2016-04-15T03:00Z] 2016-04-14 20:00:36 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:00:36,365 - WARNING - Could not retrieve variants from source file in region 2:27694997-27695398. Error was invalid region `2:27694998-27695398`
[2016-04-15T03:00Z] 2016-04-14 20:00:38 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:00:38,722 - WARNING - Could not retrieve variants from source file in region 2:26589873-26608182. Error was invalid region `2:26589874-26608182`
[2016-04-15T03:00Z] 2016-04-14 20:00:38 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:00:38,779 - WARNING - Could not retrieve variants from source file in region 2:30381294-30381695. Error was invalid region `2:30381295-30381695`
[2016-04-15T03:00Z] 2016-04-14 20:00:38 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:00:38,812 - WARNING - Could not retrieve variants from source file in region 2:26022066-26022467. Error was invalid region `2:26022067-26022467`
[2016-04-15T03:00Z] 2016-04-14 20:00:39 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:00:39,180 - WARNING - Could not retrieve variants from source file in region 2:29940318-29940719. Error was invalid region `2:29940319-29940719`
[2016-04-15T03:00Z] 2016-04-14 20:00:39 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:00:39,347 - WARNING - Could not retrieve variants from source file in region 2:23865049-23865450. Error was invalid region `2:23865050-23865450`
[2016-04-15T03:00Z] 2016-04-14 20:00:39 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:00:39,916 - WARNING - Could not retrieve variants from source file in region 2:29092468-29093040. Error was invalid region `2:29092469-29093040`
[2016-04-15T03:00Z] 2016-04-14 20:00:40 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:00:40,297 - WARNING - Could not retrieve variants from source file in region 2:29543452-29543853. Error was invalid region `2:29543453-29543853`
[2016-04-15T03:00Z] 2016-04-14 20:00:40 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:00:40,386 - WARNING - Could not retrieve variants from source file in region 2:26502664-26503065. Error was invalid region `2:26502665-26503065`
[2016-04-15T03:00Z] 2016-04-14 20:00:40 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:00:40,439 - WARNING - Could not retrieve variants from source file in region 2:27351737-27352138. Error was invalid region `2:27351738-27352138`
[2016-04-15T03:00Z] 2016-04-14 20:00:41 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:00:41,496 - WARNING - Could not retrieve variants from source file in region 2:30964421-30981130. Error was invalid region `2:30964422-30981130`
[2016-04-15T03:00Z] 2016-04-14 20:00:43 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:00:43,449 - WARNING - Could not retrieve variants from source file in region 2:30381294-30381695. Error was invalid region `2:30381295-30381695`
[2016-04-15T03:00Z] 2016-04-14 20:00:44 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:00:44,042 - WARNING - Could not retrieve variants from source file in region 2:29940318-29940719. Error was invalid region `2:29940319-29940719`
[2016-04-15T03:00Z] 2016-04-14 20:00:44 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:00:44,280 - WARNING - Could not retrieve variants from source file in region 2:23865049-23865450. Error was invalid region `2:23865050-23865450`
[2016-04-15T03:00Z] 2016-04-14 20:00:44 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:00:44,740 - WARNING - Could not retrieve variants from source file in region 2:29092468-29093040. Error was invalid region `2:29092469-29093040`
[2016-04-15T03:00Z] 2016-04-14 20:00:45 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:00:45,043 - WARNING - Could not retrieve variants from source file in region 2:29543452-29543853. Error was invalid region `2:29543453-29543853`
[2016-04-15T03:00Z] 2016-04-14 20:00:45 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:00:45,508 - WARNING - Could not retrieve variants from source file in region 2:27351737-27352138. Error was invalid region `2:27351738-27352138`
[2016-04-15T03:00Z] 2016-04-14 20:00:46 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:00:46,124 - WARNING - Could not retrieve variants from source file in region 2:27694997-27695398. Error was invalid region `2:27694998-27695398`
[2016-04-15T03:00Z] 2016-04-14 20:00:47 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:00:47,427 - WARNING - Could not retrieve variants from source file in region 2:29092468-29093040. Error was invalid region `2:29092469-29093040`
[2016-04-15T03:00Z] 2016-04-14 20:00:50 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:00:50,571 - WARNING - Could not retrieve variants from source file in region 2:27351737-27352138. Error was invalid region `2:27351738-27352138`
[2016-04-15T03:00Z] 2016-04-14 20:00:52 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:00:52,506 - WARNING - Could not retrieve variants from source file in region 2:26454916-26477315. Error was invalid region `2:26454917-26477315`
[2016-04-15T03:00Z] 2016-04-14 20:00:54 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:00:54,805 - WARNING - Could not retrieve variants from source file in region 2:27801192-27804622. Error was invalid region `2:27801193-27804622`
[2016-04-15T03:00Z] 2016-04-14 20:00:59 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:00:59,032 - WARNING - Could not retrieve variants from source file in region 2:29404230-29416762. Error was invalid region `2:29404231-29416762`
[2016-04-15T03:00Z] 2016-04-14 20:00:59 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:00:59,993 - WARNING - Could not retrieve variants from source file in region 2:27528293-27528694. Error was invalid region `2:27528294-27528694`
[2016-04-15T03:01Z] 2016-04-14 20:01:00 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:01:00,883 - WARNING - Could not retrieve variants from source file in region 2:26399003-26408254. Error was invalid region `2:26399004-26408254`
[2016-04-15T03:01Z] 2016-04-14 20:01:01 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:01:01,238 - WARNING - Could not retrieve variants from source file in region 2:29449608-29455457. Error was invalid region `2:29449609-29455457`
[2016-04-15T03:01Z] 2016-04-14 20:01:01 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:01:01,649 - WARNING - Could not retrieve variants from source file in region 2:25972849-25973250. Error was invalid region `2:25972850-25973250`
[2016-04-15T03:01Z] 2016-04-14 20:01:01 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:01:01,659 - WARNING - Could not retrieve variants from source file in region 2:27246074-27260659. Error was invalid region `2:27246075-27260659`
[2016-04-15T03:01Z] 2016-04-14 20:01:04 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:01:04,907 - WARNING - Could not retrieve variants from source file in region 2:29449608-29455457. Error was invalid region `2:29449609-29455457`
[2016-04-15T03:01Z] 2016-04-14 20:01:06 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:01:06,397 - WARNING - Could not retrieve variants from source file in region 2:21225070-21266973. Error was invalid region `2:21225071-21266973`
[2016-04-15T03:01Z] 2016-04-14 20:01:06 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:01:06,757 - WARNING - Could not retrieve variants from source file in region 2:29404230-29416762. Error was invalid region `2:29404231-29416762`
[2016-04-15T03:01Z] 2016-04-14 20:01:06 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:01:06,962 - WARNING - Could not retrieve variants from source file in region 2:26399003-26408254. Error was invalid region `2:26399004-26408254`
[2016-04-15T03:01Z] 2016-04-14 20:01:07 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:01:07,386 - WARNING - Could not retrieve variants from source file in region 2:27528293-27528694. Error was invalid region `2:27528294-27528694`
[2016-04-15T03:01Z] 2016-04-14 20:01:08 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:01:08,605 - WARNING - Could not retrieve variants from source file in region 2:26203467-26203868. Error was invalid region `2:26203468-26203868`
[2016-04-15T03:01Z] 2016-04-14 20:01:11 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:01:11,259 - WARNING - Could not retrieve variants from source file in region 2:27169631-27170032. Error was invalid region `2:27169632-27170032`
[2016-04-15T03:01Z] 2016-04-14 20:01:11 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:01:11,710 - WARNING - Could not retrieve variants from source file in region 2:27291450-27326027. Error was invalid region `2:27291451-27326027`
[2016-04-15T03:01Z] 2016-04-14 20:01:12 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:01:12,927 - WARNING - Could not retrieve variants from source file in region 2:26203467-26203868. Error was invalid region `2:26203468-26203868`
[2016-04-15T03:01Z] 2016-04-14 20:01:15 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:01:15,277 - WARNING - Could not retrieve variants from source file in region 2:26203467-26203868. Error was invalid region `2:26203468-26203868`
[2016-04-15T03:01Z] 2016-04-14 20:01:16 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:01:16,925 - WARNING - Could not retrieve variants from source file in region 2:26987600-26988001. Error was invalid region `2:26987601-26988001`
[2016-04-15T03:01Z] 2016-04-14 20:01:18 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:01:18,440 - WARNING - Could not retrieve variants from source file in region 2:20870368-20870769. Error was invalid region `2:20870369-20870769`
[2016-04-15T03:01Z] 2016-04-14 20:01:18 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:01:18,594 - WARNING - Could not retrieve variants from source file in region 2:20135072-20135473. Error was invalid region `2:20135073-20135473`
[2016-04-15T03:01Z] 2016-04-14 20:01:20 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:01:20,513 - WARNING - Could not retrieve variants from source file in region 2:26987600-26988001. Error was invalid region `2:26987601-26988001`
[2016-04-15T03:01Z] 2016-04-14 20:01:22 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:01:22,088 - WARNING - Could not retrieve variants from source file in region 2:20870368-20870769. Error was invalid region `2:20870369-20870769`
[2016-04-15T03:01Z] 2016-04-14 20:01:22 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:01:22,864 - WARNING - Could not retrieve variants from source file in region 2:26987600-26988001. Error was invalid region `2:26987601-26988001`
[2016-04-15T03:01Z] 2016-04-14 20:01:22 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:01:22,883 - WARNING - Could not retrieve variants from source file in region 2:20870368-20870769. Error was invalid region `2:20870369-20870769`
[2016-04-15T03:01Z] 2016-04-14 20:01:22 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:01:22,914 - WARNING - Could not retrieve variants from source file in region 2:20135072-20135473. Error was invalid region `2:20135073-20135473`
[2016-04-15T03:01Z] 2016-04-14 20:01:23 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:01:23,953 - WARNING - Could not retrieve variants from source file in region 2:17884284-17897678. Error was invalid region `2:17884285-17897678`
[2016-04-15T03:01Z] 2016-04-14 20:01:24 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:01:24,683 - WARNING - Could not retrieve variants from source file in region 2:25872871-25873272. Error was invalid region `2:25872872-25873272`
[2016-04-15T03:01Z] 2016-04-14 20:01:26 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:01:26,556 - WARNING - Could not retrieve variants from source file in region 2:25655561-25655962. Error was invalid region `2:25655562-25655962`
[2016-04-15T03:01Z] 2016-04-14 20:01:26 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:01:26,604 - WARNING - Could not retrieve variants from source file in region 2:18112262-18113813. Error was invalid region `2:18112263-18113813`
[2016-04-15T03:01Z] 2016-04-14 20:01:26 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:01:26,710 - WARNING - Could not retrieve variants from source file in region 2:20818243-20824749. Error was invalid region `2:20818244-20824749`
[2016-04-15T03:01Z] 2016-04-14 20:01:27 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:01:27,524 - WARNING - Could not retrieve variants from source file in region 2:20135072-20135473. Error was invalid region `2:20135073-20135473`
[2016-04-15T03:01Z] 2016-04-14 20:01:27 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:01:27,579 - WARNING - Could not retrieve variants from source file in region 2:25872871-25873272. Error was invalid region `2:25872872-25873272`
[2016-04-15T03:01Z] 2016-04-14 20:01:27 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:01:27,657 - WARNING - Could not retrieve variants from source file in region 2:17997814-17998521. Error was invalid region `2:17997815-17998521`
[2016-04-15T03:01Z] 2016-04-14 20:01:27 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:01:27,705 - WARNING - Could not retrieve variants from source file in region 2:25043399-25064383. Error was invalid region `2:25043400-25064383`
[2016-04-15T03:01Z] 2016-04-14 20:01:27 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:01:27,878 - WARNING - Could not retrieve variants from source file in region 2:17884284-17897678. Error was invalid region `2:17884285-17897678`
[2016-04-15T03:01Z] 2016-04-14 20:01:30 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:01:30,964 - WARNING - Could not retrieve variants from source file in region 2:25655561-25655962. Error was invalid region `2:25655562-25655962`
[2016-04-15T03:01Z] 2016-04-14 20:01:31 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:01:31,046 - WARNING - Could not retrieve variants from source file in region 2:18112262-18113813. Error was invalid region `2:18112263-18113813`
[2016-04-15T03:01Z] 2016-04-14 20:01:31 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:01:31,066 - WARNING - Could not retrieve variants from source file in region 2:17942564-17962708. Error was invalid region `2:17942565-17962708`
[2016-04-15T03:01Z] 2016-04-14 20:01:31 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:01:31,118 - WARNING - Could not retrieve variants from source file in region 2:18112262-18113813. Error was invalid region `2:18112263-18113813`
[2016-04-15T03:01Z] 2016-04-14 20:01:33 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:01:33,232 - WARNING - Could not retrieve variants from source file in region 2:17884284-17897678. Error was invalid region `2:17884285-17897678`
[2016-04-15T03:01Z] 2016-04-14 20:01:33 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:01:33,332 - WARNING - Could not retrieve variants from source file in region 2:17997814-17998521. Error was invalid region `2:17997815-17998521`
[2016-04-15T03:01Z] 2016-04-14 20:01:35 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:01:35,985 - WARNING - Could not retrieve variants from source file in region 2:20403583-20404139. Error was invalid region `2:20403584-20404139`
[2016-04-15T03:01Z] 2016-04-14 20:01:36 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:01:36,056 - WARNING - Could not retrieve variants from source file in region 2:18757290-18769040. Error was invalid region `2:18757291-18769040`
[2016-04-15T03:01Z] 2016-04-14 20:01:36 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:01:36,113 - WARNING - Could not retrieve variants from source file in region 2:25655561-25655962. Error was invalid region `2:25655562-25655962`
[2016-04-15T03:01Z] 2016-04-14 20:01:36 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:01:36,352 - WARNING - Could not retrieve variants from source file in region 2:17942564-17962708. Error was invalid region `2:17942565-17962708`
[2016-04-15T03:01Z] 2016-04-14 20:01:37 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:01:37,738 - WARNING - Could not retrieve variants from source file in region 2:17997814-17998521. Error was invalid region `2:17997815-17998521`
[2016-04-15T03:01Z] 2016-04-14 20:01:39 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:01:39,980 - WARNING - Could not retrieve variants from source file in region 2:20240457-20240858. Error was invalid region `2:20240458-20240858`
[2016-04-15T03:01Z] 2016-04-14 20:01:40 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:01:40,733 - WARNING - Could not retrieve variants from source file in region 2:25372363-25377366. Error was invalid region `2:25372364-25377366`
[2016-04-15T03:01Z] 2016-04-14 20:01:40 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:01:40,987 - WARNING - Could not retrieve variants from source file in region 2:25469291-25469692. Error was invalid region `2:25469292-25469692`
[2016-04-15T03:01Z] 2016-04-14 20:01:44 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:01:44,058 - WARNING - Could not retrieve variants from source file in region 2:20240457-20240858. Error was invalid region `2:20240458-20240858`
[2016-04-15T03:01Z] 2016-04-14 20:01:45 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:01:45,199 - WARNING - Could not retrieve variants from source file in region 2:15735437-15747583. Error was invalid region `2:15735438-15747583`
[2016-04-15T03:01Z] 2016-04-14 20:01:45 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:01:45,206 - WARNING - Could not retrieve variants from source file in region 2:25372363-25377366. Error was invalid region `2:25372364-25377366`
[2016-04-15T03:01Z] 2016-04-14 20:01:45 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:01:45,800 - WARNING - Could not retrieve variants from source file in region 2:20202718-20206038. Error was invalid region `2:20202719-20206038`
[2016-04-15T03:01Z] 2016-04-14 20:01:46 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:01:46,130 - WARNING - Could not retrieve variants from source file in region 2:17696362-17698868. Error was invalid region `2:17696363-17698868`
[2016-04-15T03:01Z] 2016-04-14 20:01:46 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:01:46,250 - WARNING - Could not retrieve variants from source file in region 2:25016139-25016540. Error was invalid region `2:25016140-25016540`
[2016-04-15T03:01Z] 2016-04-14 20:01:50 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:01:50,366 - WARNING - Could not retrieve variants from source file in region 2:15674475-15674876. Error was invalid region `2:15674476-15674876`
[2016-04-15T03:01Z] 2016-04-14 20:01:50 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:01:50,875 - WARNING - Could not retrieve variants from source file in region 2:20202718-20206038. Error was invalid region `2:20202719-20206038`
[2016-04-15T03:01Z] 2016-04-14 20:01:50 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:01:50,877 - WARNING - Could not retrieve variants from source file in region 2:24524747-24525148. Error was invalid region `2:24524748-24525148`
[2016-04-15T03:01Z] 2016-04-14 20:01:51 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:01:51,172 - WARNING - Could not retrieve variants from source file in region 2:17696362-17698868. Error was invalid region `2:17696363-17698868`
[2016-04-15T03:01Z] 2016-04-14 20:01:54 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:01:54,180 - WARNING - Could not retrieve variants from source file in region 2:25194530-25194931. Error was invalid region `2:25194531-25194931`
[2016-04-15T03:01Z] 2016-04-14 20:01:54 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:01:54,767 - WARNING - Could not retrieve variants from source file in region 2:20202718-20206038. Error was invalid region `2:20202719-20206038`
[2016-04-15T03:01Z] 2016-04-14 20:01:55 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:01:55,027 - WARNING - Could not retrieve variants from source file in region 2:25016139-25016540. Error was invalid region `2:25016140-25016540`
[2016-04-15T03:01Z] 2016-04-14 20:01:55 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:01:55,176 - WARNING - Could not retrieve variants from source file in region 2:20175101-20175502. Error was invalid region `2:20175102-20175502`
[2016-04-15T03:01Z] 2016-04-14 20:01:55 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:01:55,339 - WARNING - Could not retrieve variants from source file in region 2:15674475-15674876. Error was invalid region `2:15674476-15674876`
[2016-04-15T03:01Z] 2016-04-14 20:01:55 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:01:55,676 - WARNING - Could not retrieve variants from source file in region 2:25194530-25194931. Error was invalid region `2:25194531-25194931`
[2016-04-15T03:01Z] 2016-04-14 20:01:56 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:01:56,955 - WARNING - Could not retrieve variants from source file in region 2:25141327-25141728. Error was invalid region `2:25141328-25141728`
[2016-04-15T03:01Z] 2016-04-14 20:01:57 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:01:57,887 - WARNING - Could not retrieve variants from source file in region 2:25194530-25194931. Error was invalid region `2:25194531-25194931`
[2016-04-15T03:01Z] 2016-04-14 20:01:58 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:01:58,829 - WARNING - Could not retrieve variants from source file in region 2:24524747-24525148. Error was invalid region `2:24524748-24525148`
[2016-04-15T03:01Z] 2016-04-14 20:01:59 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:01:59,141 - WARNING - Could not retrieve variants from source file in region 2:15674475-15674876. Error was invalid region `2:15674476-15674876`
[2016-04-15T03:02Z] 2016-04-14 20:02:00 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:02:00,339 - WARNING - Could not retrieve variants from source file in region 2:25141327-25141728. Error was invalid region `2:25141328-25141728`
[2016-04-15T03:02Z] 2016-04-14 20:02:00 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:02:00,481 - WARNING - Could not retrieve variants from source file in region 2:15601230-15616100. Error was invalid region `2:15601231-15616100`
[2016-04-15T03:02Z] 2016-04-14 20:02:01 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:02:01,429 - WARNING - Could not retrieve variants from source file in region 2:20175101-20175502. Error was invalid region `2:20175102-20175502`
[2016-04-15T03:02Z] 2016-04-14 20:02:03 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:02:03,604 - WARNING - Could not retrieve variants from source file in region 2:25141327-25141728. Error was invalid region `2:25141328-25141728`
[2016-04-15T03:02Z] 2016-04-14 20:02:03 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:02:03,764 - WARNING - Could not retrieve variants from source file in region 2:15601230-15616100. Error was invalid region `2:15601231-15616100`
[2016-04-15T03:02Z] 2016-04-14 20:02:04 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:02:04,332 - WARNING - Could not retrieve variants from source file in region 2:24300352-24300753. Error was invalid region `2:24300353-24300753`
[2016-04-15T03:02Z] 2016-04-14 20:02:04 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:02:04,619 - WARNING - Could not retrieve variants from source file in region 2:24974734-24975135. Error was invalid region `2:24974735-24975135`
[2016-04-15T03:02Z] 2016-04-14 20:02:05 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:02:05,267 - WARNING - Could not retrieve variants from source file in region 2:15601230-15616100. Error was invalid region `2:15601231-15616100`
[2016-04-15T03:02Z] 2016-04-14 20:02:07 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:02:07,523 - WARNING - Could not retrieve variants from source file in region 2:24300352-24300753. Error was invalid region `2:24300353-24300753`
[2016-04-15T03:02Z] 2016-04-14 20:02:07 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:02:07,804 - WARNING - Could not retrieve variants from source file in region 2:24974734-24975135. Error was invalid region `2:24974735-24975135`
[2016-04-15T03:02Z] 2016-04-14 20:02:08 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:02:08,362 - WARNING - Could not retrieve variants from source file in region 2:24342294-24442294. Error was invalid region `2:24342295-24442294`
[2016-04-15T03:02Z] 2016-04-14 20:02:08 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:02:08,367 - WARNING - Could not retrieve variants from source file in region 2:24442294-24443520. Error was invalid region `2:24442295-24443520`
[2016-04-15T03:02Z] 2016-04-14 20:02:09 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:02:09,963 - WARNING - Could not retrieve variants from source file in region 2:24974734-24975135. Error was invalid region `2:24974735-24975135`
[2016-04-15T03:02Z] 2016-04-14 20:02:10 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:02:10,893 - WARNING - Could not retrieve variants from source file in region 2:24261849-24262250. Error was invalid region `2:24261850-24262250`
[2016-04-15T03:02Z] 2016-04-14 20:02:11 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:02:11,033 - WARNING - Could not retrieve variants from source file in region 2:24108441-24108842. Error was invalid region `2:24108442-24108842`
[2016-04-15T03:02Z] 2016-04-14 20:02:11 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:02:11,887 - WARNING - Could not retrieve variants from source file in region 2:24342294-24442294. Error was invalid region `2:24342295-24442294`
[2016-04-15T03:02Z] 2016-04-14 20:02:11 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:02:11,891 - WARNING - Could not retrieve variants from source file in region 2:24442294-24443520. Error was invalid region `2:24442295-24443520`
[2016-04-15T03:02Z] 2016-04-14 20:02:11 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:02:11,924 - WARNING - Could not retrieve variants from source file in region 2:24261849-24262250. Error was invalid region `2:24261850-24262250`
[2016-04-15T03:02Z] 2016-04-14 20:02:11 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:02:11,926 - WARNING - Could not retrieve variants from source file in region 2:24108441-24108842. Error was invalid region `2:24108442-24108842`
[2016-04-15T03:02Z] 2016-04-14 20:02:11 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:02:11,939 - WARNING - Could not retrieve variants from source file in region 2:24108441-24108842. Error was invalid region `2:24108442-24108842`
[2016-04-15T03:02Z] 2016-04-14 20:02:13 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:02:13,778 - WARNING - Could not retrieve variants from source file in region 2:24905716-24906117. Error was invalid region `2:24905717-24906117`
[2016-04-15T03:02Z] 2016-04-14 20:02:13 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:02:13,778 - WARNING - Could not retrieve variants from source file in region 2:24905716-24906117. Error was invalid region `2:24905717-24906117`
[2016-04-15T03:02Z] 2016-04-14 20:02:13 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:02:13,997 - WARNING - Could not retrieve variants from source file in region 2:24905716-24906117. Error was invalid region `2:24905717-24906117`
[2016-04-15T03:02Z] ['bcbio-variation-recall', 'square', '-Xms750m', '-Xmx7280m', '-XX:+UseSerialGC', '-c', 16, '-r', u'2:31135089-46706841', '--caller', 'platypus', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/2/Batch1-2_31135088_46706841.vcf.gz', '/mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/2/Batch1-2_31135088_46706841.vcf-inputs.txt'] in region: 2:31135089-46706841
[2016-04-15T03:02Z] 2016-04-14 20:02:30 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:02:30,558 - WARNING - Could not retrieve variants from source file in region 2:33488208-33488609. Error was invalid region `2:33488209-33488609`
[2016-04-15T03:02Z] 2016-04-14 20:02:31 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:02:31,337 - WARNING - Could not retrieve variants from source file in region 2:39082133-39082534. Error was invalid region `2:39082134-39082534`
[2016-04-15T03:02Z] 2016-04-14 20:02:31 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:02:31,350 - WARNING - Could not retrieve variants from source file in region 2:44209266-44209667. Error was invalid region `2:44209267-44209667`
[2016-04-15T03:02Z] 2016-04-14 20:02:32 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:02:32,489 - WARNING - Could not retrieve variants from source file in region 2:39583235-39583636. Error was invalid region `2:39583236-39583636`
[2016-04-15T03:02Z] 2016-04-14 20:02:32 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:02:32,570 - WARNING - Could not retrieve variants from source file in region 2:45773183-45773584. Error was invalid region `2:45773184-45773584`
[2016-04-15T03:02Z] 2016-04-14 20:02:32 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:02:32,696 - WARNING - Could not retrieve variants from source file in region 2:36986338-36986739. Error was invalid region `2:36986339-36986739`
[2016-04-15T03:02Z] 2016-04-14 20:02:32 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:02:32,710 - WARNING - Could not retrieve variants from source file in region 2:38604140-38604541. Error was invalid region `2:38604141-38604541`
[2016-04-15T03:02Z] 2016-04-14 20:02:33 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:02:33,668 - WARNING - Could not retrieve variants from source file in region 2:31178607-31179008. Error was invalid region `2:31178608-31179008`
[2016-04-15T03:02Z] 2016-04-14 20:02:33 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:02:33,911 - WARNING - Could not retrieve variants from source file in region 2:44932361-44932762. Error was invalid region `2:44932362-44932762`
[2016-04-15T03:02Z] 2016-04-14 20:02:33 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:02:33,934 - WARNING - Could not retrieve variants from source file in region 2:31571575-31593455. Error was invalid region `2:31571576-31593455`
[2016-04-15T03:02Z] 2016-04-14 20:02:34 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:02:34,009 - WARNING - Could not retrieve variants from source file in region 2:39186979-39187709. Error was invalid region `2:39186980-39187709`
[2016-04-15T03:02Z] 2016-04-14 20:02:34 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:02:34,085 - WARNING - Could not retrieve variants from source file in region 2:45171631-45172032. Error was invalid region `2:45171632-45172032`
[2016-04-15T03:02Z] 2016-04-14 20:02:37 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:02:37,165 - WARNING - Could not retrieve variants from source file in region 2:33488208-33488609. Error was invalid region `2:33488209-33488609`
[2016-04-15T03:02Z] 2016-04-14 20:02:37 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:02:37,959 - WARNING - Could not retrieve variants from source file in region 2:39082133-39082534. Error was invalid region `2:39082134-39082534`
[2016-04-15T03:02Z] 2016-04-14 20:02:39 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:02:39,042 - WARNING - Could not retrieve variants from source file in region 2:32666200-32667372. Error was invalid region `2:32666201-32667372`
[2016-04-15T03:02Z] 2016-04-14 20:02:39 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:02:39,084 - WARNING - Could not retrieve variants from source file in region 2:44209266-44209667. Error was invalid region `2:44209267-44209667`
[2016-04-15T03:02Z] 2016-04-14 20:02:40 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:02:40,758 - WARNING - Could not retrieve variants from source file in region 2:39583235-39583636. Error was invalid region `2:39583236-39583636`
[2016-04-15T03:02Z] 2016-04-14 20:02:41 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:02:41,611 - WARNING - Could not retrieve variants from source file in region 2:36986338-36986739. Error was invalid region `2:36986339-36986739`
[2016-04-15T03:02Z] 2016-04-14 20:02:42 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:02:42,048 - WARNING - Could not retrieve variants from source file in region 2:45773183-45773584. Error was invalid region `2:45773184-45773584`
[2016-04-15T03:02Z] 2016-04-14 20:02:42 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:02:42,369 - WARNING - Could not retrieve variants from source file in region 2:39008738-39050331. Error was invalid region `2:39008739-39050331`
[2016-04-15T03:02Z] 2016-04-14 20:02:42 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:02:42,625 - WARNING - Could not retrieve variants from source file in region 2:39186979-39187709. Error was invalid region `2:39186980-39187709`
[2016-04-15T03:02Z] 2016-04-14 20:02:42 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:02:42,881 - WARNING - Could not retrieve variants from source file in region 2:45171631-45172032. Error was invalid region `2:45171632-45172032`
[2016-04-15T03:02Z] 2016-04-14 20:02:42 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:02:42,993 - WARNING - Could not retrieve variants from source file in region 2:33488208-33488609. Error was invalid region `2:33488209-33488609`
[2016-04-15T03:02Z] 2016-04-14 20:02:43 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:02:43,093 - WARNING - Could not retrieve variants from source file in region 2:39082133-39082534. Error was invalid region `2:39082134-39082534`
[2016-04-15T03:02Z] 2016-04-14 20:02:44 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:02:44,016 - WARNING - Could not retrieve variants from source file in region 2:32666200-32667372. Error was invalid region `2:32666201-32667372`
[2016-04-15T03:02Z] 2016-04-14 20:02:44 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:02:44,029 - WARNING - Could not retrieve variants from source file in region 2:44209266-44209667. Error was invalid region `2:44209267-44209667`
[2016-04-15T03:02Z] 2016-04-14 20:02:47 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:02:47,180 - WARNING - Could not retrieve variants from source file in region 2:39583235-39583636. Error was invalid region `2:39583236-39583636`
[2016-04-15T03:02Z] 2016-04-14 20:02:48 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:02:48,253 - WARNING - Could not retrieve variants from source file in region 2:36986338-36986739. Error was invalid region `2:36986339-36986739`
[2016-04-15T03:02Z] 2016-04-14 20:02:49 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:02:49,189 - WARNING - Could not retrieve variants from source file in region 2:45773183-45773584. Error was invalid region `2:45773184-45773584`
[2016-04-15T03:02Z] 2016-04-14 20:02:49 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:02:49,857 - WARNING - Could not retrieve variants from source file in region 2:38604140-38604541. Error was invalid region `2:38604141-38604541`
[2016-04-15T03:02Z] 2016-04-14 20:02:50 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:02:50,847 - WARNING - Could not retrieve variants from source file in region 2:44932361-44932762. Error was invalid region `2:44932362-44932762`
[2016-04-15T03:02Z] 2016-04-14 20:02:51 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:02:51,010 - WARNING - Could not retrieve variants from source file in region 2:39008738-39050331. Error was invalid region `2:39008739-39050331`
[2016-04-15T03:02Z] 2016-04-14 20:02:51 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:02:51,701 - WARNING - Could not retrieve variants from source file in region 2:45171631-45172032. Error was invalid region `2:45171632-45172032`
[2016-04-15T03:02Z] 2016-04-14 20:02:51 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:02:51,983 - WARNING - Could not retrieve variants from source file in region 2:39186979-39187709. Error was invalid region `2:39186980-39187709`
[2016-04-15T03:03Z] 2016-04-14 20:03:01 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:03:01,997 - WARNING - Could not retrieve variants from source file in region 2:33446991-33447392. Error was invalid region `2:33446992-33447392`
[2016-04-15T03:03Z] 2016-04-14 20:03:03 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:03:03,080 - WARNING - Could not retrieve variants from source file in region 2:43972888-44040591. Error was invalid region `2:43972889-44040591`
[2016-04-15T03:03Z] 2016-04-14 20:03:04 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:03:04,283 - WARNING - Could not retrieve variants from source file in region 2:36810375-36825360. Error was invalid region `2:36810376-36825360`
[2016-04-15T03:03Z] 2016-04-14 20:03:04 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:03:04,425 - WARNING - Could not retrieve variants from source file in region 2:39507206-39507607. Error was invalid region `2:39507207-39507607`
[2016-04-15T03:03Z] 2016-04-14 20:03:05 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:03:05,004 - WARNING - Could not retrieve variants from source file in region 2:44993441-44993842. Error was invalid region `2:44993442-44993842`
[2016-04-15T03:03Z] 2016-04-14 20:03:05 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:03:05,045 - WARNING - Could not retrieve variants from source file in region 2:44099222-44105115. Error was invalid region `2:44099223-44105115`
[2016-04-15T03:03Z] 2016-04-14 20:03:05 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:03:05,811 - WARNING - Could not retrieve variants from source file in region 2:31134973-31135374. Error was invalid region `2:31134974-31135374`
[2016-04-15T03:03Z] 2016-04-14 20:03:06 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:03:06,783 - WARNING - Could not retrieve variants from source file in region 2:38916759-38917160. Error was invalid region `2:38916760-38917160`
[2016-04-15T03:03Z] 2016-04-14 20:03:07 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:03:07,610 - WARNING - Could not retrieve variants from source file in region 2:33446991-33447392. Error was invalid region `2:33446992-33447392`
[2016-04-15T03:03Z] 2016-04-14 20:03:08 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:03:08,177 - WARNING - Could not retrieve variants from source file in region 2:44547363-44547764. Error was invalid region `2:44547364-44547764`
[2016-04-15T03:03Z] 2016-04-14 20:03:09 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:03:09,304 - WARNING - Could not retrieve variants from source file in region 2:31399777-31420333. Error was invalid region `2:31399778-31420333`
[2016-04-15T03:03Z] 2016-04-14 20:03:09 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:03:09,914 - WARNING - Could not retrieve variants from source file in region 2:39507206-39507607. Error was invalid region `2:39507207-39507607`
[2016-04-15T03:03Z] 2016-04-14 20:03:13 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:03:13,039 - WARNING - Could not retrieve variants from source file in region 2:38916759-38917160. Error was invalid region `2:38916760-38917160`
[2016-04-15T03:03Z] 2016-04-14 20:03:13 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:03:13,078 - WARNING - Could not retrieve variants from source file in region 2:32530588-32531136. Error was invalid region `2:32530589-32531136`
[2016-04-15T03:03Z] 2016-04-14 20:03:13 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:03:13,643 - WARNING - Could not retrieve variants from source file in region 2:43451746-43452373. Error was invalid region `2:43451747-43452373`
[2016-04-15T03:03Z] 2016-04-14 20:03:13 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:03:13,721 - WARNING - Could not retrieve variants from source file in region 2:33446991-33447392. Error was invalid region `2:33446992-33447392`
[2016-04-15T03:03Z] 2016-04-14 20:03:14 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:03:14,169 - WARNING - Could not retrieve variants from source file in region 2:38178195-38179324. Error was invalid region `2:38178196-38179324`
[2016-04-15T03:03Z] 2016-04-14 20:03:15 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:03:15,553 - WARNING - Could not retrieve variants from source file in region 2:39507206-39507607. Error was invalid region `2:39507207-39507607`
[2016-04-15T03:03Z] 2016-04-14 20:03:15 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:03:15,725 - WARNING - Could not retrieve variants from source file in region 2:36810375-36825360. Error was invalid region `2:36810376-36825360`
[2016-04-15T03:03Z] 2016-04-14 20:03:16 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:03:16,040 - WARNING - Could not retrieve variants from source file in region 2:44993441-44993842. Error was invalid region `2:44993442-44993842`
[2016-04-15T03:03Z] 2016-04-14 20:03:17 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:03:16,999 - WARNING - Could not retrieve variants from source file in region 2:31134973-31135374. Error was invalid region `2:31134974-31135374`
[2016-04-15T03:03Z] 2016-04-14 20:03:18 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:03:18,700 - WARNING - Could not retrieve variants from source file in region 2:38916759-38917160. Error was invalid region `2:38916760-38917160`
[2016-04-15T03:03Z] 2016-04-14 20:03:19 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:03:19,222 - WARNING - Could not retrieve variants from source file in region 2:43451746-43452373. Error was invalid region `2:43451747-43452373`
[2016-04-15T03:03Z] 2016-04-14 20:03:19 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:03:19,971 - WARNING - Could not retrieve variants from source file in region 2:44547363-44547764. Error was invalid region `2:44547364-44547764`
[2016-04-15T03:03Z] 2016-04-14 20:03:20 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:03:20,126 - WARNING - Could not retrieve variants from source file in region 2:38178195-38179324. Error was invalid region `2:38178196-38179324`
[2016-04-15T03:03Z] 2016-04-14 20:03:27 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:03:27,823 - WARNING - Could not retrieve variants from source file in region 2:32474898-32476580. Error was invalid region `2:32474899-32476580`
[2016-04-15T03:03Z] 2016-04-14 20:03:28 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:03:28,074 - WARNING - Could not retrieve variants from source file in region 2:33411866-33412267. Error was invalid region `2:33411867-33412267`
[2016-04-15T03:03Z] 2016-04-14 20:03:30 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:03:30,704 - WARNING - Could not retrieve variants from source file in region 2:36782675-36783076. Error was invalid region `2:36782676-36783076`
[2016-04-15T03:03Z] 2016-04-14 20:03:31 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:03:31,110 - WARNING - Could not retrieve variants from source file in region 2:43902855-43939269. Error was invalid region `2:43902856-43939269`
[2016-04-15T03:03Z] 2016-04-14 20:03:32 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:03:32,138 - WARNING - Could not retrieve variants from source file in region 2:43732612-43733013. Error was invalid region `2:43732613-43733013`
[2016-04-15T03:03Z] 2016-04-14 20:03:32 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:03:32,185 - WARNING - Could not retrieve variants from source file in region 2:42936208-42936609. Error was invalid region `2:42936209-42936609`
[2016-04-15T03:03Z] 2016-04-14 20:03:32 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:03:32,273 - WARNING - Could not retrieve variants from source file in region 2:44071532-44071933. Error was invalid region `2:44071533-44071933`
[2016-04-15T03:03Z] 2016-04-14 20:03:32 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:03:32,637 - WARNING - Could not retrieve variants from source file in region 2:44502577-44502978. Error was invalid region `2:44502578-44502978`
[2016-04-15T03:03Z] 2016-04-14 20:03:32 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:03:32,754 - WARNING - Could not retrieve variants from source file in region 2:44460059-44471599. Error was invalid region `2:44460060-44471599`
[2016-04-15T03:03Z] 2016-04-14 20:03:33 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:03:33,115 - WARNING - Could not retrieve variants from source file in region 2:32474898-32476580. Error was invalid region `2:32474899-32476580`
[2016-04-15T03:03Z] 2016-04-14 20:03:33 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:03:33,129 - WARNING - Could not retrieve variants from source file in region 2:33411866-33412267. Error was invalid region `2:33411867-33412267`
[2016-04-15T03:03Z] 2016-04-14 20:03:33 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:03:33,912 - WARNING - Could not retrieve variants from source file in region 2:32983315-32983716. Error was invalid region `2:32983316-32983716`
[2016-04-15T03:03Z] 2016-04-14 20:03:34 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:03:34,032 - WARNING - Could not retrieve variants from source file in region 2:42981028-43015909. Error was invalid region `2:42981029-43015909`
[2016-04-15T03:03Z] 2016-04-14 20:03:34 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:03:34,469 - WARNING - Could not retrieve variants from source file in region 2:43902855-43939269. Error was invalid region `2:43902856-43939269`
[2016-04-15T03:03Z] 2016-04-14 20:03:35 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:03:35,224 - WARNING - Could not retrieve variants from source file in region 2:36782675-36783076. Error was invalid region `2:36782676-36783076`
[2016-04-15T03:03Z] 2016-04-14 20:03:36 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:03:36,668 - WARNING - Could not retrieve variants from source file in region 2:43732612-43733013. Error was invalid region `2:43732613-43733013`
[2016-04-15T03:03Z] 2016-04-14 20:03:36 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:03:36,983 - WARNING - Could not retrieve variants from source file in region 2:42936208-42936609. Error was invalid region `2:42936209-42936609`
[2016-04-15T03:03Z] 2016-04-14 20:03:38 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:03:38,005 - WARNING - Could not retrieve variants from source file in region 2:44460059-44471599. Error was invalid region `2:44460060-44471599`
[2016-04-15T03:03Z] 2016-04-14 20:03:38 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:03:38,022 - WARNING - Could not retrieve variants from source file in region 2:44502577-44502978. Error was invalid region `2:44502578-44502978`
[2016-04-15T03:03Z] 2016-04-14 20:03:38 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:03:38,135 - WARNING - Could not retrieve variants from source file in region 2:33411866-33412267. Error was invalid region `2:33411867-33412267`
[2016-04-15T03:03Z] 2016-04-14 20:03:38 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:03:38,210 - WARNING - Could not retrieve variants from source file in region 2:32474898-32476580. Error was invalid region `2:32474899-32476580`
[2016-04-15T03:03Z] 2016-04-14 20:03:38 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:03:38,847 - WARNING - Could not retrieve variants from source file in region 2:32983315-32983716. Error was invalid region `2:32983316-32983716`
[2016-04-15T03:03Z] 2016-04-14 20:03:39 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:03:39,174 - WARNING - Could not retrieve variants from source file in region 2:44502577-44502978. Error was invalid region `2:44502578-44502978`
[2016-04-15T03:03Z] 2016-04-14 20:03:39 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:03:39,771 - WARNING - Could not retrieve variants from source file in region 2:37543333-37544509. Error was invalid region `2:37543334-37544509`
[2016-04-15T03:03Z] 2016-04-14 20:03:39 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:03:39,811 - WARNING - Could not retrieve variants from source file in region 2:36782675-36783076. Error was invalid region `2:36782676-36783076`
[2016-04-15T03:03Z] 2016-04-14 20:03:41 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:03:41,731 - WARNING - Could not retrieve variants from source file in region 2:44071532-44071933. Error was invalid region `2:44071533-44071933`
[2016-04-15T03:03Z] 2016-04-14 20:03:42 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:03:42,301 - WARNING - Could not retrieve variants from source file in region 2:44460059-44471599. Error was invalid region `2:44460060-44471599`
[2016-04-15T03:03Z] 2016-04-14 20:03:43 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:03:43,158 - WARNING - Could not retrieve variants from source file in region 2:32983315-32983716. Error was invalid region `2:32983316-32983716`
[2016-04-15T03:03Z] 2016-04-14 20:03:49 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:03:49,923 - WARNING - Could not retrieve variants from source file in region 2:40342437-40342838. Error was invalid region `2:40342438-40342838`
[2016-04-15T03:03Z] 2016-04-14 20:03:50 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:03:50,024 - WARNING - Could not retrieve variants from source file in region 2:42509807-42515578. Error was invalid region `2:42509808-42515578`
[2016-04-15T03:03Z] 2016-04-14 20:03:50 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:03:50,034 - WARNING - Could not retrieve variants from source file in region 2:36703933-36704334. Error was invalid region `2:36703934-36704334`
[2016-04-15T03:03Z] 2016-04-14 20:03:50 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:03:50,678 - WARNING - Could not retrieve variants from source file in region 2:42509807-42515578. Error was invalid region `2:42509808-42515578`
[2016-04-15T03:03Z] 2016-04-14 20:03:51 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:03:51,984 - WARNING - Could not retrieve variants from source file in region 2:31805495-31806070. Error was invalid region `2:31805496-31806070`
[2016-04-15T03:03Z] 2016-04-14 20:03:52 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:03:52,008 - WARNING - Could not retrieve variants from source file in region 2:32822746-32823147. Error was invalid region `2:32822747-32823147`
[2016-04-15T03:03Z] 2016-04-14 20:03:52 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:03:52,804 - WARNING - Could not retrieve variants from source file in region 2:31805495-31806070. Error was invalid region `2:31805496-31806070`
[2016-04-15T03:03Z] 2016-04-14 20:03:53 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:03:53,425 - WARNING - Could not retrieve variants from source file in region 2:33572344-33585986. Error was invalid region `2:33572345-33585986`
[2016-04-15T03:03Z] 2016-04-14 20:03:53 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:03:53,435 - WARNING - Could not retrieve variants from source file in region 2:42275453-42276009. Error was invalid region `2:42275454-42276009`
[2016-04-15T03:03Z] 2016-04-14 20:03:54 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:03:54,601 - WARNING - Could not retrieve variants from source file in region 2:32855404-32855805. Error was invalid region `2:32855405-32855805`
[2016-04-15T03:03Z] 2016-04-14 20:03:55 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:03:55,094 - WARNING - Could not retrieve variants from source file in region 2:42509807-42515578. Error was invalid region `2:42509808-42515578`
[2016-04-15T03:03Z] 2016-04-14 20:03:55 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:03:55,131 - WARNING - Could not retrieve variants from source file in region 2:36703933-36704334. Error was invalid region `2:36703934-36704334`
[2016-04-15T03:03Z] 2016-04-14 20:03:55 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:03:55,174 - WARNING - Could not retrieve variants from source file in region 2:40342437-40342838. Error was invalid region `2:40342438-40342838`
[2016-04-15T03:03Z] 2016-04-14 20:03:55 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:03:55,770 - WARNING - Could not retrieve variants from source file in region 2:32713495-32713896. Error was invalid region `2:32713496-32713896`
[2016-04-15T03:03Z] 2016-04-14 20:03:56 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:03:56,507 - WARNING - Could not retrieve variants from source file in region 2:31805495-31806070. Error was invalid region `2:31805496-31806070`
[2016-04-15T03:03Z] 2016-04-14 20:03:58 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:03:58,689 - WARNING - Could not retrieve variants from source file in region 2:32855404-32855805. Error was invalid region `2:32855405-32855805`
[2016-04-15T03:03Z] 2016-04-14 20:03:59 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:03:59,255 - WARNING - Could not retrieve variants from source file in region 2:36703933-36704334. Error was invalid region `2:36703934-36704334`
[2016-04-15T03:03Z] 2016-04-14 20:03:59 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:03:59,488 - WARNING - Could not retrieve variants from source file in region 2:32713495-32713896. Error was invalid region `2:32713496-32713896`
[2016-04-15T03:04Z] 2016-04-14 20:04:00 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:04:00,135 - WARNING - Could not retrieve variants from source file in region 2:32822746-32823147. Error was invalid region `2:32822747-32823147`
[2016-04-15T03:04Z] 2016-04-14 20:04:03 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:04:03,506 - WARNING - Could not retrieve variants from source file in region 2:32855404-32855805. Error was invalid region `2:32855405-32855805`
[2016-04-15T03:04Z] 2016-04-14 20:04:03 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:04:03,510 - WARNING - Could not retrieve variants from source file in region 2:32713495-32713896. Error was invalid region `2:32713496-32713896`
[2016-04-15T03:04Z] 2016-04-14 20:04:04 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:04:04,380 - WARNING - Could not retrieve variants from source file in region 2:33540037-33540438. Error was invalid region `2:33540038-33540438`
[2016-04-15T03:04Z] 2016-04-14 20:04:05 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:04:05,453 - WARNING - Could not retrieve variants from source file in region 2:33759184-33759585. Error was invalid region `2:33759185-33759585`
[2016-04-15T03:04Z] 2016-04-14 20:04:07 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:04:07,840 - WARNING - Could not retrieve variants from source file in region 2:33759184-33759585. Error was invalid region `2:33759185-33759585`
[2016-04-15T03:04Z] 2016-04-14 20:04:08 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:04:08,642 - WARNING - Could not retrieve variants from source file in region 2:33540037-33540438. Error was invalid region `2:33540038-33540438`
[2016-04-15T03:04Z] 2016-04-14 20:04:09 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:04:09,415 - WARNING - Could not retrieve variants from source file in region 2:33540037-33540438. Error was invalid region `2:33540038-33540438`
[2016-04-15T03:04Z] 2016-04-14 20:04:11 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:04:11,484 - WARNING - Could not retrieve variants from source file in region 2:37306129-37319346. Error was invalid region `2:37306130-37319346`
[2016-04-15T03:04Z] 2016-04-14 20:04:11 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:04:11,494 - WARNING - Could not retrieve variants from source file in region 2:37406433-37429119. Error was invalid region `2:37406434-37429119`
[2016-04-15T03:04Z] ['bcbio-variation-recall', 'square', '-Xms750m', '-Xmx7280m', '-XX:+UseSerialGC', '-c', 16, '-r', u'2:46707544-62228117', '--caller', 'platypus', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/2/Batch1-2_46707543_62228117.vcf.gz', '/mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/2/Batch1-2_46707543_62228117.vcf-inputs.txt'] in region: 2:46707544-62228117
[2016-04-15T03:04Z] 2016-04-14 20:04:27 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:04:27,695 - WARNING - Could not retrieve variants from source file in region 2:55469904-55491009. Error was invalid region `2:55469905-55491009`
[2016-04-15T03:04Z] 2016-04-14 20:04:27 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:04:27,855 - WARNING - Could not retrieve variants from source file in region 2:55436723-55437124. Error was invalid region `2:55436724-55437124`
[2016-04-15T03:04Z] 2016-04-14 20:04:27 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:04:27,904 - WARNING - Could not retrieve variants from source file in region 2:56410733-56412007. Error was invalid region `2:56410734-56412007`
[2016-04-15T03:04Z] 2016-04-14 20:04:27 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:04:27,920 - WARNING - Could not retrieve variants from source file in region 2:58316603-58317004. Error was invalid region `2:58316604-58317004`
[2016-04-15T03:04Z] 2016-04-14 20:04:28 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:04:28,391 - WARNING - Could not retrieve variants from source file in region 2:55883106-55883507. Error was invalid region `2:55883107-55883507`
[2016-04-15T03:04Z] 2016-04-14 20:04:28 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:04:28,475 - WARNING - Could not retrieve variants from source file in region 2:55770950-55771351. Error was invalid region `2:55770951-55771351`
[2016-04-15T03:04Z] 2016-04-14 20:04:28 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:04:28,690 - WARNING - Could not retrieve variants from source file in region 2:56144719-56151075. Error was invalid region `2:56144720-56151075`
[2016-04-15T03:04Z] 2016-04-14 20:04:28 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:04:28,786 - WARNING - Could not retrieve variants from source file in region 2:47739340-47748482. Error was invalid region `2:47739341-47748482`
[2016-04-15T03:04Z] 2016-04-14 20:04:29 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:04:29,285 - WARNING - Could not retrieve variants from source file in region 2:55177611-55186584. Error was invalid region `2:55177612-55186584`
[2016-04-15T03:04Z] 2016-04-14 20:04:29 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:04:29,290 - WARNING - Could not retrieve variants from source file in region 2:55911909-55912310. Error was invalid region `2:55911910-55912310`
[2016-04-15T03:04Z] 2016-04-14 20:04:33 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:04:33,393 - WARNING - Could not retrieve variants from source file in region 2:48713566-48713967. Error was invalid region `2:48713567-48713967`
[2016-04-15T03:04Z] 2016-04-14 20:04:34 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:04:34,480 - WARNING - Could not retrieve variants from source file in region 2:55469904-55491009. Error was invalid region `2:55469905-55491009`
[2016-04-15T03:04Z] 2016-04-14 20:04:34 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:04:34,784 - WARNING - Could not retrieve variants from source file in region 2:62227802-62228203. Error was invalid region `2:62227803-62228203`
[2016-04-15T03:04Z] 2016-04-14 20:04:35 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:04:35,729 - WARNING - Could not retrieve variants from source file in region 2:58316603-58317004. Error was invalid region `2:58316604-58317004`
[2016-04-15T03:04Z] 2016-04-14 20:04:35 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:04:35,924 - WARNING - Could not retrieve variants from source file in region 2:56410733-56412007. Error was invalid region `2:56410734-56412007`
[2016-04-15T03:04Z] 2016-04-14 20:04:36 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:04:36,561 - WARNING - Could not retrieve variants from source file in region 2:58387047-58388886. Error was invalid region `2:58387048-58388886`
[2016-04-15T03:04Z] 2016-04-14 20:04:37 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:04:37,154 - WARNING - Could not retrieve variants from source file in region 2:54482342-54483462. Error was invalid region `2:54482343-54483462`
[2016-04-15T03:04Z] 2016-04-14 20:04:37 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:04:37,339 - WARNING - Could not retrieve variants from source file in region 2:55911909-55912310. Error was invalid region `2:55911910-55912310`
[2016-04-15T03:04Z] 2016-04-14 20:04:38 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:04:38,330 - WARNING - Could not retrieve variants from source file in region 2:48982544-48982945. Error was invalid region `2:48982545-48982945`
[2016-04-15T03:04Z] 2016-04-14 20:04:38 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:04:38,330 - WARNING - Could not retrieve variants from source file in region 2:55177611-55186584. Error was invalid region `2:55177612-55186584`
[2016-04-15T03:04Z] 2016-04-14 20:04:38 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:04:38,363 - WARNING - Could not retrieve variants from source file in region 2:61468550-61493415. Error was invalid region `2:61468551-61493415`
[2016-04-15T03:04Z] 2016-04-14 20:04:38 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:04:38,573 - WARNING - Could not retrieve variants from source file in region 2:55883106-55883507. Error was invalid region `2:55883107-55883507`
[2016-04-15T03:04Z] 2016-04-14 20:04:38 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:04:38,620 - WARNING - Could not retrieve variants from source file in region 2:55770950-55771351. Error was invalid region `2:55770951-55771351`
[2016-04-15T03:04Z] 2016-04-14 20:04:39 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:04:39,542 - WARNING - Could not retrieve variants from source file in region 2:55469904-55491009. Error was invalid region `2:55469905-55491009`
[2016-04-15T03:04Z] 2016-04-14 20:04:41 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:04:41,203 - WARNING - Could not retrieve variants from source file in region 2:56410733-56412007. Error was invalid region `2:56410734-56412007`
[2016-04-15T03:04Z] 2016-04-14 20:04:41 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:04:41,214 - WARNING - Could not retrieve variants from source file in region 2:58316603-58317004. Error was invalid region `2:58316604-58317004`
[2016-04-15T03:04Z] 2016-04-14 20:04:41 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:04:41,706 - WARNING - Could not retrieve variants from source file in region 2:58387047-58388886. Error was invalid region `2:58387048-58388886`
[2016-04-15T03:04Z] 2016-04-14 20:04:43 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:04:43,812 - WARNING - Could not retrieve variants from source file in region 2:55911909-55912310. Error was invalid region `2:55911910-55912310`
[2016-04-15T03:04Z] 2016-04-14 20:04:45 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:04:45,209 - WARNING - Could not retrieve variants from source file in region 2:55177611-55186584. Error was invalid region `2:55177612-55186584`
[2016-04-15T03:04Z] 2016-04-14 20:04:45 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:04:45,431 - WARNING - Could not retrieve variants from source file in region 2:55770950-55771351. Error was invalid region `2:55770951-55771351`
[2016-04-15T03:04Z] 2016-04-14 20:04:45 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:04:45,916 - WARNING - Could not retrieve variants from source file in region 2:47739340-47748482. Error was invalid region `2:47739341-47748482`
[2016-04-15T03:04Z] 2016-04-14 20:04:46 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:04:46,049 - WARNING - Could not retrieve variants from source file in region 2:55883106-55883507. Error was invalid region `2:55883107-55883507`
[2016-04-15T03:04Z] 2016-04-14 20:04:53 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:04:53,578 - WARNING - Could not retrieve variants from source file in region 2:48601975-48602442. Error was invalid region `2:48601976-48602442`
[2016-04-15T03:04Z] 2016-04-14 20:04:55 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:04:55,758 - WARNING - Could not retrieve variants from source file in region 2:55404583-55407944. Error was invalid region `2:55404584-55407944`
[2016-04-15T03:04Z] 2016-04-14 20:04:56 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:04:56,785 - WARNING - Could not retrieve variants from source file in region 2:61304060-61304461. Error was invalid region `2:61304061-61304461`
[2016-04-15T03:04Z] 2016-04-14 20:04:58 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:04:58,047 - WARNING - Could not retrieve variants from source file in region 2:48601975-48602442. Error was invalid region `2:48601976-48602442`
[2016-04-15T03:04Z] 2016-04-14 20:04:58 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:04:58,473 - WARNING - Could not retrieve variants from source file in region 2:55522211-55522612. Error was invalid region `2:55522212-55522612`
[2016-04-15T03:04Z] 2016-04-14 20:04:59 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:04:59,771 - WARNING - Could not retrieve variants from source file in region 2:55040215-55040616. Error was invalid region `2:55040216-55040616`
[2016-04-15T03:05Z] 2016-04-14 20:05:00 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:05:00,385 - WARNING - Could not retrieve variants from source file in region 2:55404583-55407944. Error was invalid region `2:55404584-55407944`
[2016-04-15T03:05Z] 2016-04-14 20:05:00 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:05:00,854 - WARNING - Could not retrieve variants from source file in region 2:47600895-47601296. Error was invalid region `2:47600896-47601296`
[2016-04-15T03:05Z] 2016-04-14 20:05:01 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:05:01,179 - WARNING - Could not retrieve variants from source file in region 2:62066716-62103541. Error was invalid region `2:62066717-62103541`
[2016-04-15T03:05Z] 2016-04-14 20:05:01 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:05:01,661 - WARNING - Could not retrieve variants from source file in region 2:54120609-54127231. Error was invalid region `2:54120610-54127231`
[2016-04-15T03:05Z] 2016-04-14 20:05:01 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:05:01,664 - WARNING - Could not retrieve variants from source file in region 2:61304060-61304461. Error was invalid region `2:61304061-61304461`
[2016-04-15T03:05Z] 2016-04-14 20:05:01 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:05:01,833 - WARNING - Could not retrieve variants from source file in region 2:61389526-61415682. Error was invalid region `2:61389527-61415682`
[2016-04-15T03:05Z] 2016-04-14 20:05:02 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:05:02,429 - WARNING - Could not retrieve variants from source file in region 2:48601975-48602442. Error was invalid region `2:48601976-48602442`
[2016-04-15T03:05Z] 2016-04-14 20:05:02 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:05:02,739 - WARNING - Could not retrieve variants from source file in region 2:55522211-55522612. Error was invalid region `2:55522212-55522612`
[2016-04-15T03:05Z] 2016-04-14 20:05:04 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:05:04,359 - WARNING - Could not retrieve variants from source file in region 2:55040215-55040616. Error was invalid region `2:55040216-55040616`
[2016-04-15T03:05Z] 2016-04-14 20:05:04 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:05:04,374 - WARNING - Could not retrieve variants from source file in region 2:61349235-61350327. Error was invalid region `2:61349236-61350327`
[2016-04-15T03:05Z] 2016-04-14 20:05:04 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:05:04,660 - WARNING - Could not retrieve variants from source file in region 2:55404583-55407944. Error was invalid region `2:55404584-55407944`
[2016-04-15T03:05Z] 2016-04-14 20:05:05 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:05:05,356 - WARNING - Could not retrieve variants from source file in region 2:47600895-47601296. Error was invalid region `2:47600896-47601296`
[2016-04-15T03:05Z] 2016-04-14 20:05:05 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:05:05,830 - WARNING - Could not retrieve variants from source file in region 2:61304060-61304461. Error was invalid region `2:61304061-61304461`
[2016-04-15T03:05Z] 2016-04-14 20:05:06 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:05:06,961 - WARNING - Could not retrieve variants from source file in region 2:55522211-55522612. Error was invalid region `2:55522212-55522612`
[2016-04-15T03:05Z] 2016-04-14 20:05:08 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:05:08,777 - WARNING - Could not retrieve variants from source file in region 2:55040215-55040616. Error was invalid region `2:55040216-55040616`
[2016-04-15T03:05Z] 2016-04-14 20:05:10 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:05:10,537 - WARNING - Could not retrieve variants from source file in region 2:47600895-47601296. Error was invalid region `2:47600896-47601296`
[2016-04-15T03:05Z] 2016-04-14 20:05:17 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:05:17,570 - WARNING - Could not retrieve variants from source file in region 2:61175101-61175502. Error was invalid region `2:61175102-61175502`
[2016-04-15T03:05Z] 2016-04-14 20:05:18 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:05:18,651 - WARNING - Could not retrieve variants from source file in region 2:61647690-61648091. Error was invalid region `2:61647691-61648091`
[2016-04-15T03:05Z] 2016-04-14 20:05:19 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:05:19,754 - WARNING - Could not retrieve variants from source file in region 2:48807585-48822571. Error was invalid region `2:48807586-48822571`
[2016-04-15T03:05Z] 2016-04-14 20:05:20 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:05:20,412 - WARNING - Could not retrieve variants from source file in region 2:47142739-47143420. Error was invalid region `2:47142740-47143420`
[2016-04-15T03:05Z] 2016-04-14 20:05:20 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:05:20,857 - WARNING - Could not retrieve variants from source file in region 2:61521912-61522313. Error was invalid region `2:61521913-61522313`
[2016-04-15T03:05Z] 2016-04-14 20:05:22 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:05:22,254 - WARNING - Could not retrieve variants from source file in region 2:61175101-61175502. Error was invalid region `2:61175102-61175502`
[2016-04-15T03:05Z] 2016-04-14 20:05:22 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:05:22,279 - WARNING - Could not retrieve variants from source file in region 2:49224219-49224620. Error was invalid region `2:49224220-49224620`
[2016-04-15T03:05Z] 2016-04-14 20:05:24 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:05:24,311 - WARNING - Could not retrieve variants from source file in region 2:54093745-54094146. Error was invalid region `2:54093746-54094146`
[2016-04-15T03:05Z] 2016-04-14 20:05:25 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:05:25,401 - WARNING - Could not retrieve variants from source file in region 2:54886136-54889580. Error was invalid region `2:54886137-54889580`
[2016-04-15T03:05Z] 2016-04-14 20:05:25 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:05:25,909 - WARNING - Could not retrieve variants from source file in region 2:47382131-47382532. Error was invalid region `2:47382132-47382532`
[2016-04-15T03:05Z] 2016-04-14 20:05:26 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:05:26,517 - WARNING - Could not retrieve variants from source file in region 2:61566325-61577625. Error was invalid region `2:61566326-61577625`
[2016-04-15T03:05Z] 2016-04-14 20:05:26 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:05:26,622 - WARNING - Could not retrieve variants from source file in region 2:61521912-61522313. Error was invalid region `2:61521913-61522313`
[2016-04-15T03:05Z] 2016-04-14 20:05:26 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:05:26,870 - WARNING - Could not retrieve variants from source file in region 2:54858300-54858701. Error was invalid region `2:54858301-54858701`
[2016-04-15T03:05Z] 2016-04-14 20:05:27 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:05:27,015 - WARNING - Could not retrieve variants from source file in region 2:49224219-49224620. Error was invalid region `2:49224220-49224620`
[2016-04-15T03:05Z] 2016-04-14 20:05:27 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:05:27,021 - WARNING - Could not retrieve variants from source file in region 2:61175101-61175502. Error was invalid region `2:61175102-61175502`
[2016-04-15T03:05Z] 2016-04-14 20:05:27 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:05:27,584 - WARNING - Could not retrieve variants from source file in region 2:50573797-50574675. Error was invalid region `2:50573798-50574675`
[2016-04-15T03:05Z] 2016-04-14 20:05:28 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:05:28,020 - WARNING - Could not retrieve variants from source file in region 2:61647690-61648091. Error was invalid region `2:61647691-61648091`
[2016-04-15T03:05Z] 2016-04-14 20:05:30 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:05:30,538 - WARNING - Could not retrieve variants from source file in region 2:54886136-54889580. Error was invalid region `2:54886137-54889580`
[2016-04-15T03:05Z] 2016-04-14 20:05:31 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:05:31,434 - WARNING - Could not retrieve variants from source file in region 2:47382131-47382532. Error was invalid region `2:47382132-47382532`
[2016-04-15T03:05Z] 2016-04-14 20:05:31 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:05:31,596 - WARNING - Could not retrieve variants from source file in region 2:47142739-47143420. Error was invalid region `2:47142740-47143420`
[2016-04-15T03:05Z] 2016-04-14 20:05:32 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:05:32,053 - WARNING - Could not retrieve variants from source file in region 2:61521912-61522313. Error was invalid region `2:61521913-61522313`
[2016-04-15T03:05Z] 2016-04-14 20:05:32 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:05:32,692 - WARNING - Could not retrieve variants from source file in region 2:49224219-49224620. Error was invalid region `2:49224220-49224620`
[2016-04-15T03:05Z] 2016-04-14 20:05:42 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:05:42,031 - WARNING - Could not retrieve variants from source file in region 2:49189710-49191231. Error was invalid region `2:49189711-49191231`
[2016-04-15T03:05Z] 2016-04-14 20:05:42 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:05:42,036 - WARNING - Could not retrieve variants from source file in region 2:49189710-49191231. Error was invalid region `2:49189711-49191231`
[2016-04-15T03:05Z] 2016-04-14 20:05:45 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:05:45,627 - WARNING - Could not retrieve variants from source file in region 2:49189710-49191231. Error was invalid region `2:49189711-49191231`
[2016-04-15T03:05Z] ['bcbio-variation-recall', 'square', '-Xms750m', '-Xmx7280m', '-XX:+UseSerialGC', '-c', 16, '-r', u'2:62362966-79253295', '--caller', 'platypus', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/2/Batch1-2_62362965_79253295.vcf.gz', '/mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/2/Batch1-2_62362965_79253295.vcf-inputs.txt'] in region: 2:62362966-79253295
[2016-04-15T03:06Z] 2016-04-14 20:06:00 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:06:00,742 - WARNING - Could not retrieve variants from source file in region 2:74035669-74036070. Error was invalid region `2:74035670-74036070`
[2016-04-15T03:06Z] 2016-04-14 20:06:01 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:06:01,625 - WARNING - Could not retrieve variants from source file in region 2:74449847-74466784. Error was invalid region `2:74449848-74466784`
[2016-04-15T03:06Z] 2016-04-14 20:06:01 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:06:01,935 - WARNING - Could not retrieve variants from source file in region 2:75113446-75115298. Error was invalid region `2:75113447-75115298`
[2016-04-15T03:06Z] 2016-04-14 20:06:02 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:06:02,378 - WARNING - Could not retrieve variants from source file in region 2:71558713-71559114. Error was invalid region `2:71558714-71559114`
[2016-04-15T03:06Z] 2016-04-14 20:06:02 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:06:02,894 - WARNING - Could not retrieve variants from source file in region 2:70188465-70188866. Error was invalid region `2:70188466-70188866`
[2016-04-15T03:06Z] 2016-04-14 20:06:02 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:06:02,917 - WARNING - Could not retrieve variants from source file in region 2:74300506-74300907. Error was invalid region `2:74300507-74300907`
[2016-04-15T03:06Z] 2016-04-14 20:06:03 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:06:03,103 - WARNING - Could not retrieve variants from source file in region 2:75425517-75425918. Error was invalid region `2:75425518-75425918`
[2016-04-15T03:06Z] 2016-04-14 20:06:03 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:06:03,119 - WARNING - Could not retrieve variants from source file in region 2:70408595-70408996. Error was invalid region `2:70408596-70408996`
[2016-04-15T03:06Z] 2016-04-14 20:06:03 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:06:03,785 - WARNING - Could not retrieve variants from source file in region 2:73828327-73829562. Error was invalid region `2:73828328-73829562`
[2016-04-15T03:06Z] 2016-04-14 20:06:05 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:06:05,258 - WARNING - Could not retrieve variants from source file in region 2:69040289-69050131. Error was invalid region `2:69040290-69050131`
[2016-04-15T03:06Z] 2016-04-14 20:06:06 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:06:06,200 - WARNING - Could not retrieve variants from source file in region 2:74035669-74036070. Error was invalid region `2:74035670-74036070`
[2016-04-15T03:06Z] 2016-04-14 20:06:08 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:06:08,583 - WARNING - Could not retrieve variants from source file in region 2:77745044-77745447. Error was invalid region `2:77745045-77745447`
[2016-04-15T03:06Z] 2016-04-14 20:06:09 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:06:09,396 - WARNING - Could not retrieve variants from source file in region 2:73152626-73153027. Error was invalid region `2:73152627-73153027`
[2016-04-15T03:06Z] 2016-04-14 20:06:09 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:06:09,949 - WARNING - Could not retrieve variants from source file in region 2:71558713-71559114. Error was invalid region `2:71558714-71559114`
[2016-04-15T03:06Z] 2016-04-14 20:06:09 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:06:09,982 - WARNING - Could not retrieve variants from source file in region 2:70188465-70188866. Error was invalid region `2:70188466-70188866`
[2016-04-15T03:06Z] 2016-04-14 20:06:10 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:06:10,699 - WARNING - Could not retrieve variants from source file in region 2:70315143-70315544. Error was invalid region `2:70315144-70315544`
[2016-04-15T03:06Z] 2016-04-14 20:06:10 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:06:10,812 - WARNING - Could not retrieve variants from source file in region 2:73828327-73829562. Error was invalid region `2:73828328-73829562`
[2016-04-15T03:06Z] 2016-04-14 20:06:11 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:06:11,000 - WARNING - Could not retrieve variants from source file in region 2:74035669-74036070. Error was invalid region `2:74035670-74036070`
[2016-04-15T03:06Z] 2016-04-14 20:06:12 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:06:12,580 - WARNING - Could not retrieve variants from source file in region 2:74449847-74466784. Error was invalid region `2:74449848-74466784`
[2016-04-15T03:06Z] 2016-04-14 20:06:15 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:06:15,791 - WARNING - Could not retrieve variants from source file in region 2:70188465-70188866. Error was invalid region `2:70188466-70188866`
[2016-04-15T03:06Z] 2016-04-14 20:06:16 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:06:16,536 - WARNING - Could not retrieve variants from source file in region 2:71558713-71559114. Error was invalid region `2:71558714-71559114`
[2016-04-15T03:06Z] 2016-04-14 20:06:17 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:06:17,376 - WARNING - Could not retrieve variants from source file in region 2:74300506-74300907. Error was invalid region `2:74300507-74300907`
[2016-04-15T03:06Z] 2016-04-14 20:06:18 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:06:18,605 - WARNING - Could not retrieve variants from source file in region 2:70408595-70408996. Error was invalid region `2:70408596-70408996`
[2016-04-15T03:06Z] 2016-04-14 20:06:27 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:06:27,380 - WARNING - Could not retrieve variants from source file in region 2:74006925-74007326. Error was invalid region `2:74006926-74007326`
[2016-04-15T03:06Z] 2016-04-14 20:06:29 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:06:29,176 - WARNING - Could not retrieve variants from source file in region 2:69002070-69002471. Error was invalid region `2:69002071-69002471`
[2016-04-15T03:06Z] 2016-04-14 20:06:29 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:06:29,279 - WARNING - Could not retrieve variants from source file in region 2:70162323-70162724. Error was invalid region `2:70162324-70162724`
[2016-04-15T03:06Z] 2016-04-14 20:06:30 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:06:30,268 - WARNING - Could not retrieve variants from source file in region 2:73746712-73747113. Error was invalid region `2:73746713-73747113`
[2016-04-15T03:06Z] 2016-04-14 20:06:31 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:06:31,256 - WARNING - Could not retrieve variants from source file in region 2:74900377-74900778. Error was invalid region `2:74900378-74900778`
[2016-04-15T03:06Z] 2016-04-14 20:06:31 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:06:31,589 - WARNING - Could not retrieve variants from source file in region 2:70096651-70097052. Error was invalid region `2:70096652-70097052`
[2016-04-15T03:06Z] 2016-04-14 20:06:31 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:06:31,667 - WARNING - Could not retrieve variants from source file in region 2:72742609-72743010. Error was invalid region `2:72742610-72743010`
[2016-04-15T03:06Z] 2016-04-14 20:06:32 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:06:32,023 - WARNING - Could not retrieve variants from source file in region 2:71416854-71417255. Error was invalid region `2:71416855-71417255`
[2016-04-15T03:06Z] 2016-04-14 20:06:32 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:06:32,751 - WARNING - Could not retrieve variants from source file in region 2:74006925-74007326. Error was invalid region `2:74006926-74007326`
[2016-04-15T03:06Z] 2016-04-14 20:06:33 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:06:33,420 - WARNING - Could not retrieve variants from source file in region 2:68269857-68270258. Error was invalid region `2:68269858-68270258`
[2016-04-15T03:06Z] 2016-04-14 20:06:34 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:06:34,755 - WARNING - Could not retrieve variants from source file in region 2:69002070-69002471. Error was invalid region `2:69002071-69002471`
[2016-04-15T03:06Z] 2016-04-14 20:06:34 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:06:34,960 - WARNING - Could not retrieve variants from source file in region 2:74327407-74327808. Error was invalid region `2:74327408-74327808`
[2016-04-15T03:06Z] 2016-04-14 20:06:35 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:06:35,248 - WARNING - Could not retrieve variants from source file in region 2:75185645-75186046. Error was invalid region `2:75185646-75186046`
[2016-04-15T03:06Z] 2016-04-14 20:06:35 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:06:35,707 - WARNING - Could not retrieve variants from source file in region 2:73746712-73747113. Error was invalid region `2:73746713-73747113`
[2016-04-15T03:06Z] 2016-04-14 20:06:36 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:06:36,754 - WARNING - Could not retrieve variants from source file in region 2:75720453-75720854. Error was invalid region `2:75720454-75720854`
[2016-04-15T03:06Z] 2016-04-14 20:06:36 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:06:36,887 - WARNING - Could not retrieve variants from source file in region 2:72742609-72743010. Error was invalid region `2:72742610-72743010`
[2016-04-15T03:06Z] 2016-04-14 20:06:37 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:06:37,411 - WARNING - Could not retrieve variants from source file in region 2:71416854-71417255. Error was invalid region `2:71416855-71417255`
[2016-04-15T03:06Z] 2016-04-14 20:06:38 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:06:38,004 - WARNING - Could not retrieve variants from source file in region 2:74006925-74007326. Error was invalid region `2:74006926-74007326`
[2016-04-15T03:06Z] 2016-04-14 20:06:41 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:06:41,392 - WARNING - Could not retrieve variants from source file in region 2:74327407-74327808. Error was invalid region `2:74327408-74327808`
[2016-04-15T03:06Z] 2016-04-14 20:06:41 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:06:41,430 - WARNING - Could not retrieve variants from source file in region 2:70162323-70162724. Error was invalid region `2:70162324-70162724`
[2016-04-15T03:06Z] 2016-04-14 20:06:41 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:06:41,437 - WARNING - Could not retrieve variants from source file in region 2:74135687-74159924. Error was invalid region `2:74135688-74159924`
[2016-04-15T03:06Z] 2016-04-14 20:06:41 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:06:41,463 - WARNING - Could not retrieve variants from source file in region 2:74900377-74900778. Error was invalid region `2:74900378-74900778`
[2016-04-15T03:06Z] 2016-04-14 20:06:41 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:06:41,549 - WARNING - Could not retrieve variants from source file in region 2:73746712-73747113. Error was invalid region `2:73746713-73747113`
[2016-04-15T03:06Z] 2016-04-14 20:06:41 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:06:41,864 - WARNING - Could not retrieve variants from source file in region 2:70096651-70097052. Error was invalid region `2:70096652-70097052`
[2016-04-15T03:06Z] 2016-04-14 20:06:41 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:06:41,949 - WARNING - Could not retrieve variants from source file in region 2:75720453-75720854. Error was invalid region `2:75720454-75720854`
[2016-04-15T03:06Z] 2016-04-14 20:06:42 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:06:42,077 - WARNING - Could not retrieve variants from source file in region 2:72742609-72743010. Error was invalid region `2:72742610-72743010`
[2016-04-15T03:06Z] 2016-04-14 20:06:42 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:06:42,253 - WARNING - Could not retrieve variants from source file in region 2:71416854-71417255. Error was invalid region `2:71416855-71417255`
[2016-04-15T03:06Z] 2016-04-14 20:06:43 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:06:43,723 - WARNING - Could not retrieve variants from source file in region 2:68269857-68270258. Error was invalid region `2:68269858-68270258`
[2016-04-15T03:06Z] 2016-04-14 20:06:46 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:06:46,500 - WARNING - Could not retrieve variants from source file in region 2:75185645-75186046. Error was invalid region `2:75185646-75186046`
[2016-04-15T03:06Z] 2016-04-14 20:06:48 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:06:48,352 - WARNING - Could not retrieve variants from source file in region 2:74135687-74159924. Error was invalid region `2:74135688-74159924`
[2016-04-15T03:06Z] 2016-04-14 20:06:54 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:06:54,665 - WARNING - Could not retrieve variants from source file in region 2:73956913-73957314. Error was invalid region `2:73956914-73957314`
[2016-04-15T03:06Z] 2016-04-14 20:06:55 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:06:55,263 - WARNING - Could not retrieve variants from source file in region 2:68764923-68765327. Error was invalid region `2:68764924-68765327`
[2016-04-15T03:06Z] 2016-04-14 20:06:59 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:06:59,300 - WARNING - Could not retrieve variants from source file in region 2:73716599-73717846. Error was invalid region `2:73716600-73717846`
[2016-04-15T03:06Z] 2016-04-14 20:06:59 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:06:59,472 - WARNING - Could not retrieve variants from source file in region 2:74087499-74087900. Error was invalid region `2:74087500-74087900`
[2016-04-15T03:07Z] 2016-04-14 20:07:00 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:07:00,025 - WARNING - Could not retrieve variants from source file in region 2:73956913-73957314. Error was invalid region `2:73956914-73957314`
[2016-04-15T03:07Z] 2016-04-14 20:07:00 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:07:00,125 - WARNING - Could not retrieve variants from source file in region 2:72707663-72708064. Error was invalid region `2:72707664-72708064`
[2016-04-15T03:07Z] 2016-04-14 20:07:00 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:07:00,157 - WARNING - Could not retrieve variants from source file in region 2:67630769-67632315. Error was invalid region `2:67630770-67632315`
[2016-04-15T03:07Z] 2016-04-14 20:07:00 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:07:00,249 - WARNING - Could not retrieve variants from source file in region 2:69658915-69659316. Error was invalid region `2:69658916-69659316`
[2016-04-15T03:07Z] 2016-04-14 20:07:01 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:07:01,434 - WARNING - Could not retrieve variants from source file in region 2:69204418-69204861. Error was invalid region `2:69204419-69204861`
[2016-04-15T03:07Z] 2016-04-14 20:07:01 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:07:01,925 - WARNING - Could not retrieve variants from source file in region 2:70901685-70903509. Error was invalid region `2:70901686-70903509`
[2016-04-15T03:07Z] 2016-04-14 20:07:04 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:07:04,189 - WARNING - Could not retrieve variants from source file in region 2:71351192-71360472. Error was invalid region `2:71351193-71360472`
[2016-04-15T03:07Z] 2016-04-14 20:07:05 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:07:05,878 - WARNING - Could not retrieve variants from source file in region 2:74652029-74652430. Error was invalid region `2:74652030-74652430`
[2016-04-15T03:07Z] 2016-04-14 20:07:05 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:07:05,886 - WARNING - Could not retrieve variants from source file in region 2:73956913-73957314. Error was invalid region `2:73956914-73957314`
[2016-04-15T03:07Z] 2016-04-14 20:07:06 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:07:06,263 - WARNING - Could not retrieve variants from source file in region 2:69658915-69659316. Error was invalid region `2:69658916-69659316`
[2016-04-15T03:07Z] 2016-04-14 20:07:06 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:07:06,628 - WARNING - Could not retrieve variants from source file in region 2:68764923-68765327. Error was invalid region `2:68764924-68765327`
[2016-04-15T03:07Z] 2016-04-14 20:07:06 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:07:06,672 - WARNING - Could not retrieve variants from source file in region 2:69204418-69204861. Error was invalid region `2:69204419-69204861`
[2016-04-15T03:07Z] 2016-04-14 20:07:06 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:07:06,712 - WARNING - Could not retrieve variants from source file in region 2:73478250-73492804. Error was invalid region `2:73478251-73492804`
[2016-04-15T03:07Z] 2016-04-14 20:07:07 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:07:07,809 - WARNING - Could not retrieve variants from source file in region 2:70901685-70903509. Error was invalid region `2:70901686-70903509`
[2016-04-15T03:07Z] 2016-04-14 20:07:07 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:07:07,905 - WARNING - Could not retrieve variants from source file in region 2:70677783-70678184. Error was invalid region `2:70677784-70678184`
[2016-04-15T03:07Z] 2016-04-14 20:07:08 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:07:08,601 - WARNING - Could not retrieve variants from source file in region 2:74719791-74756738. Error was invalid region `2:74719792-74756738`
[2016-04-15T03:07Z] 2016-04-14 20:07:08 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:07:08,630 - WARNING - Could not retrieve variants from source file in region 2:71351192-71360472. Error was invalid region `2:71351193-71360472`
[2016-04-15T03:07Z] 2016-04-14 20:07:12 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:07:12,278 - WARNING - Could not retrieve variants from source file in region 2:67630769-67632315. Error was invalid region `2:67630770-67632315`
[2016-04-15T03:07Z] 2016-04-14 20:07:13 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:07:13,209 - WARNING - Could not retrieve variants from source file in region 2:70677783-70678184. Error was invalid region `2:70677784-70678184`
[2016-04-15T03:07Z] 2016-04-14 20:07:16 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:07:16,694 - WARNING - Could not retrieve variants from source file in region 2:73339497-73339898. Error was invalid region `2:73339498-73339898`
[2016-04-15T03:07Z] 2016-04-14 20:07:17 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:07:17,068 - WARNING - Could not retrieve variants from source file in region 2:73927720-73928556. Error was invalid region `2:73927721-73928556`
[2016-04-15T03:07Z] 2016-04-14 20:07:19 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:07:19,558 - WARNING - Could not retrieve variants from source file in region 2:73868117-73868518. Error was invalid region `2:73868118-73868518`
[2016-04-15T03:07Z] 2016-04-14 20:07:21 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:07:21,869 - WARNING - Could not retrieve variants from source file in region 2:73339497-73339898. Error was invalid region `2:73339498-73339898`
[2016-04-15T03:07Z] 2016-04-14 20:07:22 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:07:22,744 - WARNING - Could not retrieve variants from source file in region 2:70488259-70488660. Error was invalid region `2:70488260-70488660`
[2016-04-15T03:07Z] 2016-04-14 20:07:23 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:07:23,374 - WARNING - Could not retrieve variants from source file in region 2:71297484-71305646. Error was invalid region `2:71297485-71305646`
[2016-04-15T03:07Z] 2016-04-14 20:07:23 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:07:23,389 - WARNING - Could not retrieve variants from source file in region 2:70488259-70488660. Error was invalid region `2:70488260-70488660`
[2016-04-15T03:07Z] 2016-04-14 20:07:24 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:07:24,228 - WARNING - Could not retrieve variants from source file in region 2:69177058-69177459. Error was invalid region `2:69177059-69177459`
[2016-04-15T03:07Z] 2016-04-14 20:07:24 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:07:24,472 - WARNING - Could not retrieve variants from source file in region 2:73868117-73868518. Error was invalid region `2:73868118-73868518`
[2016-04-15T03:07Z] 2016-04-14 20:07:26 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:07:26,474 - WARNING - Could not retrieve variants from source file in region 2:72361749-72362150. Error was invalid region `2:72361750-72362150`
[2016-04-15T03:07Z] 2016-04-14 20:07:26 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:07:26,900 - WARNING - Could not retrieve variants from source file in region 2:68729728-68730129. Error was invalid region `2:68729729-68730129`
[2016-04-15T03:07Z] 2016-04-14 20:07:26 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:07:26,937 - WARNING - Could not retrieve variants from source file in region 2:73339497-73339898. Error was invalid region `2:73339498-73339898`
[2016-04-15T03:07Z] 2016-04-14 20:07:27 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:07:27,362 - WARNING - Could not retrieve variants from source file in region 2:70488259-70488660. Error was invalid region `2:70488260-70488660`
[2016-04-15T03:07Z] 2016-04-14 20:07:28 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:07:28,527 - WARNING - Could not retrieve variants from source file in region 2:69177058-69177459. Error was invalid region `2:69177059-69177459`
[2016-04-15T03:07Z] 2016-04-14 20:07:28 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:07:28,819 - WARNING - Could not retrieve variants from source file in region 2:73868117-73868518. Error was invalid region `2:73868118-73868518`
[2016-04-15T03:07Z] 2016-04-14 20:07:31 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:07:31,421 - WARNING - Could not retrieve variants from source file in region 2:65538277-65541095. Error was invalid region `2:65538278-65541095`
[2016-04-15T03:07Z] 2016-04-14 20:07:32 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:07:32,444 - WARNING - Could not retrieve variants from source file in region 2:74517538-74517941. Error was invalid region `2:74517539-74517941`
[2016-04-15T03:07Z] 2016-04-14 20:07:34 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:07:34,906 - WARNING - Could not retrieve variants from source file in region 2:72361749-72362150. Error was invalid region `2:72361750-72362150`
[2016-04-15T03:07Z] 2016-04-14 20:07:36 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:07:36,054 - WARNING - Could not retrieve variants from source file in region 2:73429597-73441787. Error was invalid region `2:73429598-73441787`
[2016-04-15T03:07Z] 2016-04-14 20:07:40 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:07:40,495 - WARNING - Could not retrieve variants from source file in region 2:71838386-71838787. Error was invalid region `2:71838387-71838787`
[2016-04-15T03:07Z] 2016-04-14 20:07:41 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:07:41,653 - WARNING - Could not retrieve variants from source file in region 2:73225879-73226280. Error was invalid region `2:73225880-73226280`
[2016-04-15T03:07Z] 2016-04-14 20:07:41 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:07:41,734 - WARNING - Could not retrieve variants from source file in region 2:68511373-68511774. Error was invalid region `2:68511374-68511774`
[2016-04-15T03:07Z] 2016-04-14 20:07:43 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:07:43,399 - WARNING - Could not retrieve variants from source file in region 2:71906067-71906468. Error was invalid region `2:71906068-71906468`
[2016-04-15T03:07Z] 2016-04-14 20:07:45 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:07:45,273 - WARNING - Could not retrieve variants from source file in region 2:71838386-71838787. Error was invalid region `2:71838387-71838787`
[2016-04-15T03:07Z] 2016-04-14 20:07:45 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:07:45,864 - WARNING - Could not retrieve variants from source file in region 2:68607736-68623104. Error was invalid region `2:68607737-68623104`
[2016-04-15T03:07Z] 2016-04-14 20:07:46 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:07:46,842 - WARNING - Could not retrieve variants from source file in region 2:73307359-73308492. Error was invalid region `2:73307360-73308492`
[2016-04-15T03:07Z] 2016-04-14 20:07:47 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:07:47,197 - WARNING - Could not retrieve variants from source file in region 2:73225879-73226280. Error was invalid region `2:73225880-73226280`
[2016-04-15T03:07Z] 2016-04-14 20:07:47 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:07:47,284 - WARNING - Could not retrieve variants from source file in region 2:71906067-71906468. Error was invalid region `2:71906068-71906468`
[2016-04-15T03:07Z] 2016-04-14 20:07:48 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:07:48,804 - WARNING - Could not retrieve variants from source file in region 2:68546163-68546639. Error was invalid region `2:68546164-68546639`
[2016-04-15T03:07Z] 2016-04-14 20:07:51 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:07:51,189 - WARNING - Could not retrieve variants from source file in region 2:71693634-71694133. Error was invalid region `2:71693635-71694133`
[2016-04-15T03:07Z] 2016-04-14 20:07:51 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:07:51,316 - WARNING - Could not retrieve variants from source file in region 2:68546163-68546639. Error was invalid region `2:68546164-68546639`
[2016-04-15T03:07Z] 2016-04-14 20:07:53 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:07:53,895 - WARNING - Could not retrieve variants from source file in region 2:65298628-65299956. Error was invalid region `2:65298629-65299956`
[2016-04-15T03:07Z] 2016-04-14 20:07:58 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:07:58,248 - WARNING - Could not retrieve variants from source file in region 2:71780004-71795650. Error was invalid region `2:71780005-71795650`
[2016-04-15T03:07Z] 2016-04-14 20:07:59 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:07:59,076 - WARNING - Could not retrieve variants from source file in region 2:64069521-64069922. Error was invalid region `2:64069522-64069922`
[2016-04-15T03:07Z] 2016-04-14 20:07:59 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:07:59,231 - WARNING - Could not retrieve variants from source file in region 2:71633064-71633579. Error was invalid region `2:71633065-71633579`
[2016-04-15T03:08Z] 2016-04-14 20:08:01 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:08:01,361 - WARNING - Could not retrieve variants from source file in region 2:65216878-65217279. Error was invalid region `2:65216879-65217279`
[2016-04-15T03:08Z] 2016-04-14 20:08:01 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:08:01,666 - WARNING - Could not retrieve variants from source file in region 2:68479365-68479766. Error was invalid region `2:68479366-68479766`
[2016-04-15T03:08Z] 2016-04-14 20:08:02 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:08:02,277 - WARNING - Could not retrieve variants from source file in region 2:71633064-71633579. Error was invalid region `2:71633065-71633579`
[2016-04-15T03:08Z] 2016-04-14 20:08:02 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:08:02,380 - WARNING - Could not retrieve variants from source file in region 2:64069521-64069922. Error was invalid region `2:64069522-64069922`
[2016-04-15T03:08Z] 2016-04-14 20:08:02 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:08:02,475 - WARNING - Could not retrieve variants from source file in region 2:71633064-71633579. Error was invalid region `2:71633065-71633579`
[2016-04-15T03:08Z] 2016-04-14 20:08:04 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:08:04,580 - WARNING - Could not retrieve variants from source file in region 2:65216878-65217279. Error was invalid region `2:65216879-65217279`
[2016-04-15T03:08Z] 2016-04-14 20:08:04 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:08:04,768 - WARNING - Could not retrieve variants from source file in region 2:71780004-71795650. Error was invalid region `2:71780005-71795650`
[2016-04-15T03:08Z] 2016-04-14 20:08:04 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:08:04,936 - WARNING - Could not retrieve variants from source file in region 2:68415556-68415957. Error was invalid region `2:68415557-68415957`
[2016-04-15T03:08Z] 2016-04-14 20:08:05 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:08:05,627 - WARNING - Could not retrieve variants from source file in region 2:64069521-64069922. Error was invalid region `2:64069522-64069922`
[2016-04-15T03:08Z] 2016-04-14 20:08:07 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:08:07,008 - WARNING - Could not retrieve variants from source file in region 2:64327333-64327782. Error was invalid region `2:64327334-64327782`
[2016-04-15T03:08Z] 2016-04-14 20:08:10 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:08:10,431 - WARNING - Could not retrieve variants from source file in region 2:64327333-64327782. Error was invalid region `2:64327334-64327782`
[2016-04-15T03:08Z] 2016-04-14 20:08:12 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:08:12,116 - WARNING - Could not retrieve variants from source file in region 2:62362784-62363185. Error was invalid region `2:62362785-62363185`
[2016-04-15T03:08Z] 2016-04-14 20:08:12 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:08:12,125 - WARNING - Could not retrieve variants from source file in region 2:62729463-62733443. Error was invalid region `2:62729464-62733443`
[2016-04-15T03:08Z] ['bcbio-variation-recall', 'square', '-Xms750m', '-Xmx7280m', '-XX:+UseSerialGC', '-c', 16, '-r', u'2:79253839-95537822', '--caller', 'platypus', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/2/Batch1-2_79253838_95537822.vcf.gz', '/mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/2/Batch1-2_79253838_95537822.vcf-inputs.txt'] in region: 2:79253839-95537822
[2016-04-15T03:08Z] 2016-04-14 20:08:27 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:08:27,686 - WARNING - Could not retrieve variants from source file in region 2:85808526-85826911. Error was invalid region `2:85808527-85826911`
[2016-04-15T03:08Z] 2016-04-14 20:08:29 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:08:29,628 - WARNING - Could not retrieve variants from source file in region 2:85360617-85361021. Error was invalid region `2:85360618-85361021`
[2016-04-15T03:08Z] 2016-04-14 20:08:29 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:08:29,654 - WARNING - Could not retrieve variants from source file in region 2:85769500-85781508. Error was invalid region `2:85769501-85781508`
[2016-04-15T03:08Z] 2016-04-14 20:08:30 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:08:30,649 - WARNING - Could not retrieve variants from source file in region 2:86371672-86372073. Error was invalid region `2:86371673-86372073`
[2016-04-15T03:08Z] 2016-04-14 20:08:30 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:08:30,677 - WARNING - Could not retrieve variants from source file in region 2:86841668-86850212. Error was invalid region `2:86841669-86850212`
[2016-04-15T03:08Z] 2016-04-14 20:08:30 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:08:30,764 - WARNING - Could not retrieve variants from source file in region 2:85661806-85662207. Error was invalid region `2:85661807-85662207`
[2016-04-15T03:08Z] 2016-04-14 20:08:31 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:08:31,275 - WARNING - Could not retrieve variants from source file in region 2:86481624-86482025. Error was invalid region `2:86481625-86482025`
[2016-04-15T03:08Z] 2016-04-14 20:08:31 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:08:31,354 - WARNING - Could not retrieve variants from source file in region 2:86683431-86691440. Error was invalid region `2:86683432-86691440`
[2016-04-15T03:08Z] 2016-04-14 20:08:34 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:08:34,147 - WARNING - Could not retrieve variants from source file in region 2:88423855-88424256. Error was invalid region `2:88423856-88424256`
[2016-04-15T03:08Z] 2016-04-14 20:08:34 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:08:34,331 - WARNING - Could not retrieve variants from source file in region 2:88125001-88125402. Error was invalid region `2:88125002-88125402`
[2016-04-15T03:08Z] 2016-04-14 20:08:36 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:08:36,903 - WARNING - Could not retrieve variants from source file in region 2:85360617-85361021. Error was invalid region `2:85360618-85361021`
[2016-04-15T03:08Z] 2016-04-14 20:08:37 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:08:37,579 - WARNING - Could not retrieve variants from source file in region 2:87042614-87043015. Error was invalid region `2:87042615-87043015`
[2016-04-15T03:08Z] 2016-04-14 20:08:37 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:08:37,980 - WARNING - Could not retrieve variants from source file in region 2:85661806-85662207. Error was invalid region `2:85661807-85662207`
[2016-04-15T03:08Z] 2016-04-14 20:08:38 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:08:38,329 - WARNING - Could not retrieve variants from source file in region 2:84972112-84972513. Error was invalid region `2:84972113-84972513`
[2016-04-15T03:08Z] 2016-04-14 20:08:39 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:08:39,186 - WARNING - Could not retrieve variants from source file in region 2:86683431-86691440. Error was invalid region `2:86683432-86691440`
[2016-04-15T03:08Z] 2016-04-14 20:08:39 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:08:39,239 - WARNING - Could not retrieve variants from source file in region 2:95537394-95537795. Error was invalid region `2:95537395-95537795`
[2016-04-15T03:08Z] 2016-04-14 20:08:39 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:08:39,438 - WARNING - Could not retrieve variants from source file in region 2:86481624-86482025. Error was invalid region `2:86481625-86482025`
[2016-04-15T03:08Z] 2016-04-14 20:08:40 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:08:40,097 - WARNING - Could not retrieve variants from source file in region 2:86841668-86850212. Error was invalid region `2:86841669-86850212`
[2016-04-15T03:08Z] 2016-04-14 20:08:40 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:08:40,208 - WARNING - Could not retrieve variants from source file in region 2:84800394-84816205. Error was invalid region `2:84800395-84816205`
[2016-04-15T03:08Z] 2016-04-14 20:08:40 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:08:40,282 - WARNING - Could not retrieve variants from source file in region 2:86433029-86440626. Error was invalid region `2:86433030-86440626`
[2016-04-15T03:08Z] 2016-04-14 20:08:42 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:08:42,296 - WARNING - Could not retrieve variants from source file in region 2:85360617-85361021. Error was invalid region `2:85360618-85361021`
[2016-04-15T03:08Z] 2016-04-14 20:08:42 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:08:42,925 - WARNING - Could not retrieve variants from source file in region 2:85661806-85662207. Error was invalid region `2:85661807-85662207`
[2016-04-15T03:08Z] 2016-04-14 20:08:44 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:08:44,761 - WARNING - Could not retrieve variants from source file in region 2:86259232-86260975. Error was invalid region `2:86259233-86260975`
[2016-04-15T03:08Z] 2016-04-14 20:08:46 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:08:46,004 - WARNING - Could not retrieve variants from source file in region 2:86683431-86691440. Error was invalid region `2:86683432-86691440`
[2016-04-15T03:08Z] 2016-04-14 20:08:46 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:08:46,457 - WARNING - Could not retrieve variants from source file in region 2:86371672-86372073. Error was invalid region `2:86371673-86372073`
[2016-04-15T03:08Z] 2016-04-14 20:08:46 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:08:46,852 - WARNING - Could not retrieve variants from source file in region 2:86841668-86850212. Error was invalid region `2:86841669-86850212`
[2016-04-15T03:08Z] 2016-04-14 20:08:47 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:08:47,082 - WARNING - Could not retrieve variants from source file in region 2:84800394-84816205. Error was invalid region `2:84800395-84816205`
[2016-04-15T03:08Z] 2016-04-14 20:08:56 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:08:56,375 - WARNING - Could not retrieve variants from source file in region 2:88387192-88396364. Error was invalid region `2:88387193-88396364`
[2016-04-15T03:08Z] 2016-04-14 20:08:58 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:08:58,183 - WARNING - Could not retrieve variants from source file in region 2:85621848-85625412. Error was invalid region `2:85621849-85625412`
[2016-04-15T03:09Z] 2016-04-14 20:09:01 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:09:01,064 - WARNING - Could not retrieve variants from source file in region 2:86978882-86979283. Error was invalid region `2:86978883-86979283`
[2016-04-15T03:09Z] 2016-04-14 20:09:01 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:09:01,368 - WARNING - Could not retrieve variants from source file in region 2:86074301-86088501. Error was invalid region `2:86074302-86088501`
[2016-04-15T03:09Z] 2016-04-14 20:09:01 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:09:01,868 - WARNING - Could not retrieve variants from source file in region 2:80529745-80540790. Error was invalid region `2:80529746-80540790`
[2016-04-15T03:09Z] 2016-04-14 20:09:02 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:09:02,208 - WARNING - Could not retrieve variants from source file in region 2:86400613-86401014. Error was invalid region `2:86400614-86401014`
[2016-04-15T03:09Z] 2016-04-14 20:09:02 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:09:02,376 - WARNING - Could not retrieve variants from source file in region 2:84755838-84771757. Error was invalid region `2:84755839-84771757`
[2016-04-15T03:09Z] 2016-04-14 20:09:02 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:09:02,704 - WARNING - Could not retrieve variants from source file in region 2:87169206-87169607. Error was invalid region `2:87169207-87169607`
[2016-04-15T03:09Z] 2016-04-14 20:09:03 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:09:03,678 - WARNING - Could not retrieve variants from source file in region 2:85621848-85625412. Error was invalid region `2:85621849-85625412`
[2016-04-15T03:09Z] 2016-04-14 20:09:05 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:09:05,850 - WARNING - Could not retrieve variants from source file in region 2:84924612-84932910. Error was invalid region `2:84924613-84932910`
[2016-04-15T03:09Z] 2016-04-14 20:09:06 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:09:06,721 - WARNING - Could not retrieve variants from source file in region 2:86978882-86979283. Error was invalid region `2:86978883-86979283`
[2016-04-15T03:09Z] 2016-04-14 20:09:07 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:09:07,447 - WARNING - Could not retrieve variants from source file in region 2:84846719-84897707. Error was invalid region `2:84846720-84897707`
[2016-04-15T03:09Z] 2016-04-14 20:09:08 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:09:08,195 - WARNING - Could not retrieve variants from source file in region 2:84755838-84771757. Error was invalid region `2:84755839-84771757`
[2016-04-15T03:09Z] 2016-04-14 20:09:08 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:09:08,345 - WARNING - Could not retrieve variants from source file in region 2:86344026-86344427. Error was invalid region `2:86344027-86344427`
[2016-04-15T03:09Z] 2016-04-14 20:09:08 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:09:08,541 - WARNING - Could not retrieve variants from source file in region 2:87169206-87169607. Error was invalid region `2:87169207-87169607`
[2016-04-15T03:09Z] 2016-04-14 20:09:08 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:09:08,924 - WARNING - Could not retrieve variants from source file in region 2:91635754-91636178. Error was invalid region `2:91635755-91636178`
[2016-04-15T03:09Z] 2016-04-14 20:09:11 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:09:11,902 - WARNING - Could not retrieve variants from source file in region 2:86978882-86979283. Error was invalid region `2:86978883-86979283`
[2016-04-15T03:09Z] 2016-04-14 20:09:13 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:09:13,380 - WARNING - Could not retrieve variants from source file in region 2:80801135-80801536. Error was invalid region `2:80801136-80801536`
[2016-04-15T03:09Z] 2016-04-14 20:09:13 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:09:13,761 - WARNING - Could not retrieve variants from source file in region 2:85024520-85059417. Error was invalid region `2:85024521-85059417`
[2016-04-15T03:09Z] 2016-04-14 20:09:14 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:09:14,029 - WARNING - Could not retrieve variants from source file in region 2:86344026-86344427. Error was invalid region `2:86344027-86344427`
[2016-04-15T03:09Z] 2016-04-14 20:09:14 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:09:14,555 - WARNING - Could not retrieve variants from source file in region 2:80529745-80540790. Error was invalid region `2:80529746-80540790`
[2016-04-15T03:09Z] 2016-04-14 20:09:14 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:09:14,705 - WARNING - Could not retrieve variants from source file in region 2:86074301-86088501. Error was invalid region `2:86074302-86088501`
[2016-04-15T03:09Z] 2016-04-14 20:09:15 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:09:15,059 - WARNING - Could not retrieve variants from source file in region 2:84755838-84771757. Error was invalid region `2:84755839-84771757`
[2016-04-15T03:09Z] 2016-04-14 20:09:18 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:09:18,376 - WARNING - Could not retrieve variants from source file in region 2:80801135-80801536. Error was invalid region `2:80801136-80801536`
[2016-04-15T03:09Z] 2016-04-14 20:09:23 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:09:23,370 - WARNING - Could not retrieve variants from source file in region 2:80801135-80801536. Error was invalid region `2:80801136-80801536`
[2016-04-15T03:09Z] 2016-04-14 20:09:24 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:09:24,104 - WARNING - Could not retrieve variants from source file in region 2:86315530-86317227. Error was invalid region `2:86315531-86317227`
[2016-04-15T03:09Z] 2016-04-14 20:09:24 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:09:24,314 - WARNING - Could not retrieve variants from source file in region 2:86315530-86317227. Error was invalid region `2:86315531-86317227`
[2016-04-15T03:09Z] 2016-04-14 20:09:28 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:09:28,021 - WARNING - Could not retrieve variants from source file in region 2:86315530-86317227. Error was invalid region `2:86315531-86317227`
[2016-04-15T03:09Z] 2016-04-14 20:09:28 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:09:28,029 - WARNING - Could not retrieve variants from source file in region 2:88751540-88751941. Error was invalid region `2:88751541-88751941`
[2016-04-15T03:09Z] 2016-04-14 20:09:29 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:09:29,084 - WARNING - Could not retrieve variants from source file in region 2:88874680-88926925. Error was invalid region `2:88874681-88926925`
[2016-04-15T03:09Z] 2016-04-14 20:09:30 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:09:30,793 - WARNING - Could not retrieve variants from source file in region 2:80101110-80101511. Error was invalid region `2:80101111-80101511`
[2016-04-15T03:09Z] 2016-04-14 20:09:31 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:09:31,790 - WARNING - Could not retrieve variants from source file in region 2:85921781-85926038. Error was invalid region `2:85921782-85926038`
[2016-04-15T03:09Z] 2016-04-14 20:09:32 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:09:32,264 - WARNING - Could not retrieve variants from source file in region 2:88751540-88751941. Error was invalid region `2:88751541-88751941`
[2016-04-15T03:09Z] 2016-04-14 20:09:34 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:09:34,480 - WARNING - Could not retrieve variants from source file in region 2:79254050-79254451. Error was invalid region `2:79254051-79254451`
[2016-04-15T03:09Z] 2016-04-14 20:09:35 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:09:35,793 - WARNING - Could not retrieve variants from source file in region 2:85921781-85926038. Error was invalid region `2:85921782-85926038`
[2016-04-15T03:09Z] 2016-04-14 20:09:36 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:09:36,351 - WARNING - Could not retrieve variants from source file in region 2:79254050-79254451. Error was invalid region `2:79254051-79254451`
[2016-04-15T03:09Z] 2016-04-14 20:09:36 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:09:36,354 - WARNING - Could not retrieve variants from source file in region 2:88751540-88751941. Error was invalid region `2:88751541-88751941`
[2016-04-15T03:09Z] 2016-04-14 20:09:36 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:09:36,354 - WARNING - Could not retrieve variants from source file in region 2:88472580-88474404. Error was invalid region `2:88472581-88474404`
[2016-04-15T03:09Z] 2016-04-14 20:09:36 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:09:36,454 - WARNING - Could not retrieve variants from source file in region 2:79254050-79254451. Error was invalid region `2:79254051-79254451`
[2016-04-15T03:09Z] ['bcbio-variation-recall', 'square', '-Xms750m', '-Xmx7280m', '-XX:+UseSerialGC', '-c', 16, '-r', u'2:95538562-111273222', '--caller', 'platypus', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/2/Batch1-2_95538561_111273222.vcf.gz', '/mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/2/Batch1-2_95538561_111273222.vcf-inputs.txt'] in region: 2:95538562-111273222
[2016-04-15T03:09Z] 2016-04-14 20:09:52 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:09:52,621 - WARNING - Could not retrieve variants from source file in region 2:106754523-106754924. Error was invalid region `2:106754524-106754924`
[2016-04-15T03:09Z] 2016-04-14 20:09:52 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:09:52,784 - WARNING - Could not retrieve variants from source file in region 2:101898201-101898602. Error was invalid region `2:101898202-101898602`
[2016-04-15T03:09Z] 2016-04-14 20:09:53 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:09:53,885 - WARNING - Could not retrieve variants from source file in region 2:107422977-107423585. Error was invalid region `2:107422978-107423585`
[2016-04-15T03:09Z] 2016-04-14 20:09:53 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:09:53,891 - WARNING - Could not retrieve variants from source file in region 2:108921825-108922226. Error was invalid region `2:108921826-108922226`
[2016-04-15T03:09Z] 2016-04-14 20:09:54 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:09:54,554 - WARNING - Could not retrieve variants from source file in region 2:102851626-102852027. Error was invalid region `2:102851627-102852027`
[2016-04-15T03:09Z] 2016-04-14 20:09:54 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:09:54,588 - WARNING - Could not retrieve variants from source file in region 2:102781438-102781839. Error was invalid region `2:102781439-102781839`
[2016-04-15T03:09Z] 2016-04-14 20:09:55 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:09:55,258 - WARNING - Could not retrieve variants from source file in region 2:109513443-109527159. Error was invalid region `2:109513444-109527159`
[2016-04-15T03:09Z] 2016-04-14 20:09:58 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:09:58,672 - WARNING - Could not retrieve variants from source file in region 2:106012936-106013337. Error was invalid region `2:106012937-106013337`
[2016-04-15T03:09Z] 2016-04-14 20:09:59 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:09:59,152 - WARNING - Could not retrieve variants from source file in region 2:101898201-101898602. Error was invalid region `2:101898202-101898602`
[2016-04-15T03:10Z] 2016-04-14 20:10:00 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:10:00,439 - WARNING - Could not retrieve variants from source file in region 2:105885750-105924700. Error was invalid region `2:105885751-105924700`
[2016-04-15T03:10Z] 2016-04-14 20:10:02 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:10:02,595 - WARNING - Could not retrieve variants from source file in region 2:110958815-110959216. Error was invalid region `2:110958816-110959216`
[2016-04-15T03:10Z] 2016-04-14 20:10:02 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:10:02,870 - WARNING - Could not retrieve variants from source file in region 2:101185877-101186278. Error was invalid region `2:101185878-101186278`
[2016-04-15T03:10Z] 2016-04-14 20:10:03 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:10:03,370 - WARNING - Could not retrieve variants from source file in region 2:109513443-109527159. Error was invalid region `2:109513444-109527159`
[2016-04-15T03:10Z] 2016-04-14 20:10:03 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:10:03,475 - WARNING - Could not retrieve variants from source file in region 2:102472248-102472649. Error was invalid region `2:102472249-102472649`
[2016-04-15T03:10Z] 2016-04-14 20:10:03 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:10:03,498 - WARNING - Could not retrieve variants from source file in region 2:98354300-98354701. Error was invalid region `2:98354301-98354701`
[2016-04-15T03:10Z] 2016-04-14 20:10:03 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:10:03,785 - WARNING - Could not retrieve variants from source file in region 2:108475747-108496625. Error was invalid region `2:108475748-108496625`
[2016-04-15T03:10Z] 2016-04-14 20:10:03 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:10:03,887 - WARNING - Could not retrieve variants from source file in region 2:106012936-106013337. Error was invalid region `2:106012937-106013337`
[2016-04-15T03:10Z] 2016-04-14 20:10:04 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:10:04,591 - WARNING - Could not retrieve variants from source file in region 2:101898201-101898602. Error was invalid region `2:101898202-101898602`
[2016-04-15T03:10Z] 2016-04-14 20:10:07 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:10:07,060 - WARNING - Could not retrieve variants from source file in region 2:107422977-107423585. Error was invalid region `2:107422978-107423585`
[2016-04-15T03:10Z] 2016-04-14 20:10:09 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:10:09,478 - WARNING - Could not retrieve variants from source file in region 2:110958815-110959216. Error was invalid region `2:110958816-110959216`
[2016-04-15T03:10Z] 2016-04-14 20:10:09 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:10:09,726 - WARNING - Could not retrieve variants from source file in region 2:108921825-108922226. Error was invalid region `2:108921826-108922226`
[2016-04-15T03:10Z] 2016-04-14 20:10:10 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:10:10,170 - WARNING - Could not retrieve variants from source file in region 2:102781438-102781839. Error was invalid region `2:102781439-102781839`
[2016-04-15T03:10Z] 2016-04-14 20:10:11 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:10:11,058 - WARNING - Could not retrieve variants from source file in region 2:102851626-102852027. Error was invalid region `2:102851627-102852027`
[2016-04-15T03:10Z] 2016-04-14 20:10:11 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:10:11,489 - WARNING - Could not retrieve variants from source file in region 2:101185877-101186278. Error was invalid region `2:101185878-101186278`
[2016-04-15T03:10Z] 2016-04-14 20:10:12 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:10:12,045 - WARNING - Could not retrieve variants from source file in region 2:109513443-109527159. Error was invalid region `2:109513444-109527159`
[2016-04-15T03:10Z] 2016-04-14 20:10:12 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:10:12,956 - WARNING - Could not retrieve variants from source file in region 2:105471844-105472263. Error was invalid region `2:105471845-105472263`
[2016-04-15T03:10Z] 2016-04-14 20:10:12 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:10:12,958 - WARNING - Could not retrieve variants from source file in region 2:102472248-102472649. Error was invalid region `2:102472249-102472649`
[2016-04-15T03:10Z] 2016-04-14 20:10:13 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:10:13,271 - WARNING - Could not retrieve variants from source file in region 2:98354300-98354701. Error was invalid region `2:98354301-98354701`
[2016-04-15T03:10Z] 2016-04-14 20:10:22 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:10:22,807 - WARNING - Could not retrieve variants from source file in region 2:101869377-101869778. Error was invalid region `2:101869378-101869778`
[2016-04-15T03:10Z] 2016-04-14 20:10:23 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:10:23,962 - WARNING - Could not retrieve variants from source file in region 2:105705296-105713887. Error was invalid region `2:105705297-105713887`
[2016-04-15T03:10Z] 2016-04-14 20:10:24 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:10:24,484 - WARNING - Could not retrieve variants from source file in region 2:105953727-105954128. Error was invalid region `2:105953728-105954128`
[2016-04-15T03:10Z] 2016-04-14 20:10:25 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:10:25,286 - WARNING - Could not retrieve variants from source file in region 2:108863439-108875434. Error was invalid region `2:108863440-108875434`
[2016-04-15T03:10Z] 2016-04-14 20:10:25 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:10:25,383 - WARNING - Could not retrieve variants from source file in region 2:110922492-110922893. Error was invalid region `2:110922493-110922893`
[2016-04-15T03:10Z] 2016-04-14 20:10:25 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:10:25,429 - WARNING - Could not retrieve variants from source file in region 2:102066872-102067273. Error was invalid region `2:102066873-102067273`
[2016-04-15T03:10Z] 2016-04-14 20:10:26 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:10:26,977 - WARNING - Could not retrieve variants from source file in region 2:106509290-106509691. Error was invalid region `2:106509291-106509691`
[2016-04-15T03:10Z] 2016-04-14 20:10:28 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:10:28,388 - WARNING - Could not retrieve variants from source file in region 2:103431193-103433814. Error was invalid region `2:103431194-103433814`
[2016-04-15T03:10Z] 2016-04-14 20:10:29 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:10:29,489 - WARNING - Could not retrieve variants from source file in region 2:105953727-105954128. Error was invalid region `2:105953728-105954128`
[2016-04-15T03:10Z] 2016-04-14 20:10:30 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:10:30,594 - WARNING - Could not retrieve variants from source file in region 2:108863439-108875434. Error was invalid region `2:108863440-108875434`
[2016-04-15T03:10Z] 2016-04-14 20:10:30 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:10:30,872 - WARNING - Could not retrieve variants from source file in region 2:102066872-102067273. Error was invalid region `2:102066873-102067273`
[2016-04-15T03:10Z] 2016-04-14 20:10:31 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:10:31,287 - WARNING - Could not retrieve variants from source file in region 2:101086755-101097150. Error was invalid region `2:101086756-101097150`
[2016-04-15T03:10Z] 2016-04-14 20:10:31 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:10:31,832 - WARNING - Could not retrieve variants from source file in region 2:106509290-106509691. Error was invalid region `2:106509291-106509691`
[2016-04-15T03:10Z] 2016-04-14 20:10:32 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:10:32,515 - WARNING - Could not retrieve variants from source file in region 2:101869377-101869778. Error was invalid region `2:101869378-101869778`
[2016-04-15T03:10Z] 2016-04-14 20:10:33 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:10:33,278 - WARNING - Could not retrieve variants from source file in region 2:102018697-102039039. Error was invalid region `2:102018698-102039039`
[2016-04-15T03:10Z] 2016-04-14 20:10:34 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:10:34,085 - WARNING - Could not retrieve variants from source file in region 2:103431193-103433814. Error was invalid region `2:103431194-103433814`
[2016-04-15T03:10Z] 2016-04-14 20:10:34 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:10:34,644 - WARNING - Could not retrieve variants from source file in region 2:108443300-108443701. Error was invalid region `2:108443301-108443701`
[2016-04-15T03:10Z] 2016-04-14 20:10:35 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:10:35,247 - WARNING - Could not retrieve variants from source file in region 2:105953727-105954128. Error was invalid region `2:105953728-105954128`
[2016-04-15T03:10Z] 2016-04-14 20:10:35 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:10:35,828 - WARNING - Could not retrieve variants from source file in region 2:102066872-102067273. Error was invalid region `2:102066873-102067273`
[2016-04-15T03:10Z] 2016-04-14 20:10:36 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:10:36,467 - WARNING - Could not retrieve variants from source file in region 2:101086755-101097150. Error was invalid region `2:101086756-101097150`
[2016-04-15T03:10Z] 2016-04-14 20:10:40 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:10:40,799 - WARNING - Could not retrieve variants from source file in region 2:109374741-109429336. Error was invalid region `2:109374742-109429336`
[2016-04-15T03:10Z] 2016-04-14 20:10:46 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:10:46,851 - WARNING - Could not retrieve variants from source file in region 2:101726216-101726617. Error was invalid region `2:101726217-101726617`
[2016-04-15T03:10Z] 2016-04-14 20:10:47 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:10:47,500 - WARNING - Could not retrieve variants from source file in region 2:109297673-109298074. Error was invalid region `2:109297674-109298074`
[2016-04-15T03:10Z] 2016-04-14 20:10:48 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:10:48,088 - WARNING - Could not retrieve variants from source file in region 2:105665597-105665998. Error was invalid region `2:105665598-105665998`
[2016-04-15T03:10Z] 2016-04-14 20:10:51 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:10:51,397 - WARNING - Could not retrieve variants from source file in region 2:101009871-101031751. Error was invalid region `2:101009872-101031751`
[2016-04-15T03:10Z] 2016-04-14 20:10:52 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:10:52,133 - WARNING - Could not retrieve variants from source file in region 2:101726216-101726617. Error was invalid region `2:101726217-101726617`
[2016-04-15T03:10Z] 2016-04-14 20:10:52 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:10:52,419 - WARNING - Could not retrieve variants from source file in region 2:103148889-103149290. Error was invalid region `2:103148890-103149290`
[2016-04-15T03:10Z] 2016-04-14 20:10:52 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:10:52,890 - WARNING - Could not retrieve variants from source file in region 2:109297673-109298074. Error was invalid region `2:109297674-109298074`
[2016-04-15T03:10Z] 2016-04-14 20:10:53 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:10:53,007 - WARNING - Could not retrieve variants from source file in region 2:110371282-110373387. Error was invalid region `2:110371283-110373387`
[2016-04-15T03:10Z] 2016-04-14 20:10:53 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:10:53,763 - WARNING - Could not retrieve variants from source file in region 2:103095087-103095721. Error was invalid region `2:103095088-103095721`
[2016-04-15T03:10Z] 2016-04-14 20:10:54 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:10:54,485 - WARNING - Could not retrieve variants from source file in region 2:109099361-109106571. Error was invalid region `2:109099362-109106571`
[2016-04-15T03:10Z] 2016-04-14 20:10:55 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:10:55,034 - WARNING - Could not retrieve variants from source file in region 2:110302253-110303502. Error was invalid region `2:110302254-110303502`
[2016-04-15T03:10Z] 2016-04-14 20:10:56 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:10:56,908 - WARNING - Could not retrieve variants from source file in region 2:101726216-101726617. Error was invalid region `2:101726217-101726617`
[2016-04-15T03:10Z] 2016-04-14 20:10:57 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:10:57,710 - WARNING - Could not retrieve variants from source file in region 2:103148889-103149290. Error was invalid region `2:103148890-103149290`
[2016-04-15T03:10Z] 2016-04-14 20:10:57 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:10:57,796 - WARNING - Could not retrieve variants from source file in region 2:109745828-109746229. Error was invalid region `2:109745829-109746229`
[2016-04-15T03:10Z] 2016-04-14 20:10:57 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:10:57,850 - WARNING - Could not retrieve variants from source file in region 2:110371282-110373387. Error was invalid region `2:110371283-110373387`
[2016-04-15T03:10Z] 2016-04-14 20:10:57 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:10:57,939 - WARNING - Could not retrieve variants from source file in region 2:109297673-109298074. Error was invalid region `2:109297674-109298074`
[2016-04-15T03:10Z] 2016-04-14 20:10:59 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:10:59,279 - WARNING - Could not retrieve variants from source file in region 2:109099361-109106571. Error was invalid region `2:109099362-109106571`
[2016-04-15T03:11Z] 2016-04-14 20:11:00 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:11:00,393 - WARNING - Could not retrieve variants from source file in region 2:101009871-101031751. Error was invalid region `2:101009872-101031751`
[2016-04-15T03:11Z] 2016-04-14 20:11:02 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:11:02,562 - WARNING - Could not retrieve variants from source file in region 2:103148889-103149290. Error was invalid region `2:103148890-103149290`
[2016-04-15T03:11Z] 2016-04-14 20:11:03 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:11:03,791 - WARNING - Could not retrieve variants from source file in region 2:109099361-109106571. Error was invalid region `2:109099362-109106571`
[2016-04-15T03:11Z] 2016-04-14 20:11:09 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:11:09,537 - WARNING - Could not retrieve variants from source file in region 2:101494269-101494670. Error was invalid region `2:101494270-101494670`
[2016-04-15T03:11Z] 2016-04-14 20:11:09 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:11:09,784 - WARNING - Could not retrieve variants from source file in region 2:101494269-101494670. Error was invalid region `2:101494270-101494670`
[2016-04-15T03:11Z] 2016-04-14 20:11:10 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:11:10,283 - WARNING - Could not retrieve variants from source file in region 2:108994597-108994998. Error was invalid region `2:108994598-108994998`
[2016-04-15T03:11Z] 2016-04-14 20:11:10 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:11:10,350 - WARNING - Could not retrieve variants from source file in region 2:99778774-99779321. Error was invalid region `2:99778775-99779321`
[2016-04-15T03:11Z] 2016-04-14 20:11:11 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:11:11,588 - WARNING - Could not retrieve variants from source file in region 2:108994597-108994998. Error was invalid region `2:108994598-108994998`
[2016-04-15T03:11Z] 2016-04-14 20:11:12 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:11:12,666 - WARNING - Could not retrieve variants from source file in region 2:100915561-100938671. Error was invalid region `2:100915562-100938671`
[2016-04-15T03:11Z] 2016-04-14 20:11:13 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:11:13,384 - WARNING - Could not retrieve variants from source file in region 2:101494269-101494670. Error was invalid region `2:101494270-101494670`
[2016-04-15T03:11Z] 2016-04-14 20:11:13 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:11:13,983 - WARNING - Could not retrieve variants from source file in region 2:108994597-108994998. Error was invalid region `2:108994598-108994998`
[2016-04-15T03:11Z] 2016-04-14 20:11:14 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:11:14,134 - WARNING - Could not retrieve variants from source file in region 2:99778774-99779321. Error was invalid region `2:99778775-99779321`
[2016-04-15T03:11Z] 2016-04-14 20:11:14 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:11:14,644 - WARNING - Could not retrieve variants from source file in region 2:98844463-98853363. Error was invalid region `2:98844464-98853363`
[2016-04-15T03:11Z] 2016-04-14 20:11:15 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:11:15,825 - WARNING - Could not retrieve variants from source file in region 2:100915561-100938671. Error was invalid region `2:100915562-100938671`
[2016-04-15T03:11Z] 2016-04-14 20:11:17 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:11:17,385 - WARNING - Could not retrieve variants from source file in region 2:99778774-99779321. Error was invalid region `2:99778775-99779321`
[2016-04-15T03:11Z] 2016-04-14 20:11:19 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:11:19,332 - WARNING - Could not retrieve variants from source file in region 2:100915561-100938671. Error was invalid region `2:100915562-100938671`
[2016-04-15T03:11Z] 2016-04-14 20:11:21 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:11:21,938 - WARNING - Could not retrieve variants from source file in region 2:98844463-98853363. Error was invalid region `2:98844464-98853363`
[2016-04-15T03:11Z] 2016-04-14 20:11:23 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:11:23,351 - WARNING - Could not retrieve variants from source file in region 2:98129496-98130007. Error was invalid region `2:98129497-98130007`
[2016-04-15T03:11Z] 2016-04-14 20:11:23 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:11:23,737 - WARNING - Could not retrieve variants from source file in region 2:100055295-100068032. Error was invalid region `2:100055296-100068032`
[2016-04-15T03:11Z] 2016-04-14 20:11:24 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:11:24,702 - WARNING - Could not retrieve variants from source file in region 2:100722697-100723835. Error was invalid region `2:100722698-100723835`
[2016-04-15T03:11Z] 2016-04-14 20:11:24 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:11:24,785 - WARNING - Could not retrieve variants from source file in region 2:99734841-99735242. Error was invalid region `2:99734842-99735242`
[2016-04-15T03:11Z] 2016-04-14 20:11:24 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:11:24,829 - WARNING - Could not retrieve variants from source file in region 2:97019838-97030437. Error was invalid region `2:97019839-97030437`
[2016-04-15T03:11Z] 2016-04-14 20:11:28 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:11:28,120 - WARNING - Could not retrieve variants from source file in region 2:100722697-100723835. Error was invalid region `2:100722698-100723835`
[2016-04-15T03:11Z] 2016-04-14 20:11:28 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:11:28,230 - WARNING - Could not retrieve variants from source file in region 2:99734841-99735242. Error was invalid region `2:99734842-99735242`
[2016-04-15T03:11Z] 2016-04-14 20:11:28 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:11:28,364 - WARNING - Could not retrieve variants from source file in region 2:99992611-100019686. Error was invalid region `2:99992612-100019686`
[2016-04-15T03:11Z] 2016-04-14 20:11:29 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:11:29,529 - WARNING - Could not retrieve variants from source file in region 2:99734841-99735242. Error was invalid region `2:99734842-99735242`
[2016-04-15T03:11Z] 2016-04-14 20:11:34 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:11:34,132 - WARNING - Could not retrieve variants from source file in region 2:98736014-98736415. Error was invalid region `2:98736015-98736415`
[2016-04-15T03:11Z] 2016-04-14 20:11:34 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:11:34,576 - WARNING - Could not retrieve variants from source file in region 2:97019838-97030437. Error was invalid region `2:97019839-97030437`
[2016-04-15T03:11Z] 2016-04-14 20:11:36 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:11:36,417 - WARNING - Could not retrieve variants from source file in region 2:98709473-98709874. Error was invalid region `2:98709474-98709874`
[2016-04-15T03:11Z] 2016-04-14 20:11:37 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:11:37,019 - WARNING - Could not retrieve variants from source file in region 2:99149735-99193686. Error was invalid region `2:99149736-99193686`
[2016-04-15T03:11Z] 2016-04-14 20:11:37 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:11:37,897 - WARNING - Could not retrieve variants from source file in region 2:100209863-100210832. Error was invalid region `2:100209864-100210832`
[2016-04-15T03:11Z] 2016-04-14 20:11:40 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:11:40,885 - WARNING - Could not retrieve variants from source file in region 2:95946874-95947275. Error was invalid region `2:95946875-95947275`
[2016-04-15T03:11Z] 2016-04-14 20:11:40 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:11:40,985 - WARNING - Could not retrieve variants from source file in region 2:98709473-98709874. Error was invalid region `2:98709474-98709874`
[2016-04-15T03:11Z] 2016-04-14 20:11:41 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:11:41,432 - WARNING - Could not retrieve variants from source file in region 2:99804431-99812260. Error was invalid region `2:99804432-99812260`
[2016-04-15T03:11Z] 2016-04-14 20:11:42 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:11:42,657 - WARNING - Could not retrieve variants from source file in region 2:100209863-100210832. Error was invalid region `2:100209864-100210832`
[2016-04-15T03:11Z] 2016-04-14 20:11:43 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:11:43,742 - WARNING - Could not retrieve variants from source file in region 2:98736014-98736415. Error was invalid region `2:98736015-98736415`
[2016-04-15T03:11Z] 2016-04-14 20:11:45 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:11:45,647 - WARNING - Could not retrieve variants from source file in region 2:95946874-95947275. Error was invalid region `2:95946875-95947275`
[2016-04-15T03:11Z] 2016-04-14 20:11:46 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:11:46,218 - WARNING - Could not retrieve variants from source file in region 2:99804431-99812260. Error was invalid region `2:99804432-99812260`
[2016-04-15T03:11Z] 2016-04-14 20:11:46 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:11:46,253 - WARNING - Could not retrieve variants from source file in region 2:99804431-99812260. Error was invalid region `2:99804432-99812260`
[2016-04-15T03:11Z] 2016-04-14 20:11:47 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:11:47,321 - WARNING - Could not retrieve variants from source file in region 2:98916357-98928684. Error was invalid region `2:98916358-98928684`
[2016-04-15T03:11Z] 2016-04-14 20:11:47 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:11:47,694 - WARNING - Could not retrieve variants from source file in region 2:96993546-96994074. Error was invalid region `2:96993547-96994074`
[2016-04-15T03:11Z] 2016-04-14 20:11:50 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:11:50,809 - WARNING - Could not retrieve variants from source file in region 2:95946874-95947275. Error was invalid region `2:95946875-95947275`
[2016-04-15T03:11Z] 2016-04-14 20:11:51 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:11:51,585 - WARNING - Could not retrieve variants from source file in region 2:98916357-98928684. Error was invalid region `2:98916358-98928684`
[2016-04-15T03:11Z] 2016-04-14 20:11:52 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:11:52,881 - WARNING - Could not retrieve variants from source file in region 2:98611783-98612184. Error was invalid region `2:98611784-98612184`
[2016-04-15T03:11Z] 2016-04-14 20:11:55 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:11:55,036 - WARNING - Could not retrieve variants from source file in region 2:97613405-97638228. Error was invalid region `2:97613406-97638228`
[2016-04-15T03:11Z] 2016-04-14 20:11:56 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:11:56,337 - WARNING - Could not retrieve variants from source file in region 2:96993546-96994074. Error was invalid region `2:96993547-96994074`
[2016-04-15T03:11Z] 2016-04-14 20:11:57 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:11:57,095 - WARNING - Could not retrieve variants from source file in region 2:98611783-98612184. Error was invalid region `2:98611784-98612184`
[2016-04-15T03:12Z] 2016-04-14 20:12:00 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:12:00,192 - WARNING - Could not retrieve variants from source file in region 2:98408835-98409236. Error was invalid region `2:98408836-98409236`
[2016-04-15T03:12Z] 2016-04-14 20:12:01 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:12:01,398 - WARNING - Could not retrieve variants from source file in region 2:98611783-98612184. Error was invalid region `2:98611784-98612184`
[2016-04-15T03:12Z] 2016-04-14 20:12:01 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:12:01,901 - WARNING - Could not retrieve variants from source file in region 2:97351629-97352030. Error was invalid region `2:97351630-97352030`
[2016-04-15T03:12Z] 2016-04-14 20:12:03 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:12:03,081 - WARNING - Could not retrieve variants from source file in region 2:97526927-97563935. Error was invalid region `2:97526928-97563935`
[2016-04-15T03:12Z] 2016-04-14 20:12:03 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:12:03,568 - WARNING - Could not retrieve variants from source file in region 2:97613405-97638228. Error was invalid region `2:97613406-97638228`
[2016-04-15T03:12Z] 2016-04-14 20:12:03 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:12:03,888 - WARNING - Could not retrieve variants from source file in region 2:97165993-97166394. Error was invalid region `2:97165994-97166394`
[2016-04-15T03:12Z] 2016-04-14 20:12:04 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:12:04,147 - WARNING - Could not retrieve variants from source file in region 2:97267049-97267483. Error was invalid region `2:97267050-97267483`
[2016-04-15T03:12Z] 2016-04-14 20:12:04 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:12:04,448 - WARNING - Could not retrieve variants from source file in region 2:98408835-98409236. Error was invalid region `2:98408836-98409236`
[2016-04-15T03:12Z] 2016-04-14 20:12:06 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:12:06,448 - WARNING - Could not retrieve variants from source file in region 2:97351629-97352030. Error was invalid region `2:97351630-97352030`
[2016-04-15T03:12Z] 2016-04-14 20:12:07 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:12:07,646 - WARNING - Could not retrieve variants from source file in region 2:95824413-95847233. Error was invalid region `2:95824414-95847233`
[2016-04-15T03:12Z] 2016-04-14 20:12:07 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:12:07,760 - WARNING - Could not retrieve variants from source file in region 2:96779911-96796047. Error was invalid region `2:96779912-96796047`
[2016-04-15T03:12Z] 2016-04-14 20:12:08 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:12:08,136 - WARNING - Could not retrieve variants from source file in region 2:97165993-97166394. Error was invalid region `2:97165994-97166394`
[2016-04-15T03:12Z] 2016-04-14 20:12:08 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:12:08,793 - WARNING - Could not retrieve variants from source file in region 2:96688718-96689368. Error was invalid region `2:96688719-96689368`
[2016-04-15T03:12Z] 2016-04-14 20:12:11 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:12:11,933 - WARNING - Could not retrieve variants from source file in region 2:97267049-97267483. Error was invalid region `2:97267050-97267483`
[2016-04-15T03:12Z] 2016-04-14 20:12:12 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:12:12,109 - WARNING - Could not retrieve variants from source file in region 2:97165993-97166394. Error was invalid region `2:97165994-97166394`
[2016-04-15T03:12Z] 2016-04-14 20:12:15 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:12:15,105 - WARNING - Could not retrieve variants from source file in region 2:95775550-95775951. Error was invalid region `2:95775551-95775951`
[2016-04-15T03:12Z] 2016-04-14 20:12:15 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:12:15,105 - WARNING - Could not retrieve variants from source file in region 2:95775550-95775951. Error was invalid region `2:95775551-95775951`
[2016-04-15T03:12Z] ['bcbio-variation-recall', 'square', '-Xms750m', '-Xmx7280m', '-XX:+UseSerialGC', '-c', 16, '-r', u'2:111281073-127413888', '--caller', 'platypus', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/2/Batch1-2_111281072_127413888.vcf.gz', '/mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/2/Batch1-2_111281072_127413888.vcf-inputs.txt'] in region: 2:111281073-127413888
[2016-04-15T03:12Z] 2016-04-14 20:12:31 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:12:31,004 - WARNING - Could not retrieve variants from source file in region 2:116447066-116447467. Error was invalid region `2:116447067-116447467`
[2016-04-15T03:12Z] 2016-04-14 20:12:31 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:12:31,723 - WARNING - Could not retrieve variants from source file in region 2:114395617-114396362. Error was invalid region `2:114395618-114396362`
[2016-04-15T03:12Z] 2016-04-14 20:12:31 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:12:31,901 - WARNING - Could not retrieve variants from source file in region 2:113404497-113404898. Error was invalid region `2:113404498-113404898`
[2016-04-15T03:12Z] 2016-04-14 20:12:32 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:12:32,075 - WARNING - Could not retrieve variants from source file in region 2:112536053-112536454. Error was invalid region `2:112536054-112536454`
[2016-04-15T03:12Z] 2016-04-14 20:12:32 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:12:32,920 - WARNING - Could not retrieve variants from source file in region 2:113819909-113832523. Error was invalid region `2:113819910-113832523`
[2016-04-15T03:12Z] 2016-04-14 20:12:33 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:12:33,116 - WARNING - Could not retrieve variants from source file in region 2:118575004-118594582. Error was invalid region `2:118575005-118594582`
[2016-04-15T03:12Z] 2016-04-14 20:12:33 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:12:33,230 - WARNING - Could not retrieve variants from source file in region 2:113067411-113090237. Error was invalid region `2:113067412-113090237`
[2016-04-15T03:12Z] 2016-04-14 20:12:37 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:12:37,762 - WARNING - Could not retrieve variants from source file in region 2:116447066-116447467. Error was invalid region `2:116447067-116447467`
[2016-04-15T03:12Z] 2016-04-14 20:12:40 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:12:40,395 - WARNING - Could not retrieve variants from source file in region 2:113404497-113404898. Error was invalid region `2:113404498-113404898`
[2016-04-15T03:12Z] 2016-04-14 20:12:40 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:12:40,405 - WARNING - Could not retrieve variants from source file in region 2:121010232-121036523. Error was invalid region `2:121010233-121036523`
[2016-04-15T03:12Z] 2016-04-14 20:12:41 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:12:41,641 - WARNING - Could not retrieve variants from source file in region 2:112536053-112536454. Error was invalid region `2:112536054-112536454`
[2016-04-15T03:12Z] 2016-04-14 20:12:41 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:12:41,809 - WARNING - Could not retrieve variants from source file in region 2:113590179-113590580. Error was invalid region `2:113590180-113590580`
[2016-04-15T03:12Z] 2016-04-14 20:12:41 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:12:41,881 - WARNING - Could not retrieve variants from source file in region 2:112751717-112786713. Error was invalid region `2:112751718-112786713`
[2016-04-15T03:12Z] 2016-04-14 20:12:42 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:12:42,382 - WARNING - Could not retrieve variants from source file in region 2:112686777-112687178. Error was invalid region `2:112686778-112687178`
[2016-04-15T03:12Z] 2016-04-14 20:12:42 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:12:42,533 - WARNING - Could not retrieve variants from source file in region 2:113146948-113147349. Error was invalid region `2:113146949-113147349`
[2016-04-15T03:12Z] 2016-04-14 20:12:42 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:12:42,543 - WARNING - Could not retrieve variants from source file in region 2:120124818-120125219. Error was invalid region `2:120124819-120125219`
[2016-04-15T03:12Z] 2016-04-14 20:12:42 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:12:42,907 - WARNING - Could not retrieve variants from source file in region 2:113308305-113309663. Error was invalid region `2:113308306-113309663`
[2016-04-15T03:12Z] 2016-04-14 20:12:42 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:12:42,989 - WARNING - Could not retrieve variants from source file in region 2:118575004-118594582. Error was invalid region `2:118575005-118594582`
[2016-04-15T03:12Z] 2016-04-14 20:12:43 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:12:43,094 - WARNING - Could not retrieve variants from source file in region 2:116447066-116447467. Error was invalid region `2:116447067-116447467`
[2016-04-15T03:12Z] 2016-04-14 20:12:45 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:12:45,542 - WARNING - Could not retrieve variants from source file in region 2:121010232-121036523. Error was invalid region `2:121010233-121036523`
[2016-04-15T03:12Z] 2016-04-14 20:12:45 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:12:45,586 - WARNING - Could not retrieve variants from source file in region 2:113404497-113404898. Error was invalid region `2:113404498-113404898`
[2016-04-15T03:12Z] 2016-04-14 20:12:47 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:12:47,937 - WARNING - Could not retrieve variants from source file in region 2:112536053-112536454. Error was invalid region `2:112536054-112536454`
[2016-04-15T03:12Z] 2016-04-14 20:12:50 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:12:50,100 - WARNING - Could not retrieve variants from source file in region 2:113819909-113832523. Error was invalid region `2:113819910-113832523`
[2016-04-15T03:12Z] 2016-04-14 20:12:50 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:12:50,106 - WARNING - Could not retrieve variants from source file in region 2:112686777-112687178. Error was invalid region `2:112686778-112687178`
[2016-04-15T03:12Z] 2016-04-14 20:12:50 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:12:50,512 - WARNING - Could not retrieve variants from source file in region 2:113308305-113309663. Error was invalid region `2:113308306-113309663`
[2016-04-15T03:12Z] 2016-04-14 20:12:50 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:12:50,656 - WARNING - Could not retrieve variants from source file in region 2:120124818-120125219. Error was invalid region `2:120124819-120125219`
[2016-04-15T03:12Z] 2016-04-14 20:12:50 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:12:50,730 - WARNING - Could not retrieve variants from source file in region 2:113067411-113090237. Error was invalid region `2:113067412-113090237`
[2016-04-15T03:13Z] 2016-04-14 20:13:00 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:13:00,839 - WARNING - Could not retrieve variants from source file in region 2:125191857-125192258. Error was invalid region `2:125191858-125192258`
[2016-04-15T03:13Z] 2016-04-14 20:13:02 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:13:02,409 - WARNING - Could not retrieve variants from source file in region 2:115822075-115822476. Error was invalid region `2:115822076-115822476`
[2016-04-15T03:13Z] 2016-04-14 20:13:03 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:13:03,383 - WARNING - Could not retrieve variants from source file in region 2:113343618-113344019. Error was invalid region `2:113343619-113344019`
[2016-04-15T03:13Z] 2016-04-14 20:13:04 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:13:04,673 - WARNING - Could not retrieve variants from source file in region 2:111880073-111907881. Error was invalid region `2:111880074-111907881`
[2016-04-15T03:13Z] 2016-04-14 20:13:05 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:13:05,251 - WARNING - Could not retrieve variants from source file in region 2:125191857-125192258. Error was invalid region `2:125191858-125192258`
[2016-04-15T03:13Z] 2016-04-14 20:13:06 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:13:06,953 - WARNING - Could not retrieve variants from source file in region 2:113763364-113785392. Error was invalid region `2:113763365-113785392`
[2016-04-15T03:13Z] 2016-04-14 20:13:07 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:13:07,856 - WARNING - Could not retrieve variants from source file in region 2:115822075-115822476. Error was invalid region `2:115822076-115822476`
[2016-04-15T03:13Z] 2016-04-14 20:13:08 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:13:08,297 - WARNING - Could not retrieve variants from source file in region 2:116503460-116526150. Error was invalid region `2:116503461-116526150`
[2016-04-15T03:13Z] 2016-04-14 20:13:08 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:13:08,330 - WARNING - Could not retrieve variants from source file in region 2:120980217-120980618. Error was invalid region `2:120980218-120980618`
[2016-04-15T03:13Z] 2016-04-14 20:13:08 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:13:08,397 - WARNING - Could not retrieve variants from source file in region 2:112832324-112832728. Error was invalid region `2:112832325-112832728`
[2016-04-15T03:13Z] 2016-04-14 20:13:08 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:13:08,561 - WARNING - Could not retrieve variants from source file in region 2:114257108-114257509. Error was invalid region `2:114257109-114257509`
[2016-04-15T03:13Z] 2016-04-14 20:13:08 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:13:08,648 - WARNING - Could not retrieve variants from source file in region 2:113258705-113279054. Error was invalid region `2:113258706-113279054`
[2016-04-15T03:13Z] 2016-04-14 20:13:09 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:13:09,769 - WARNING - Could not retrieve variants from source file in region 2:125191857-125192258. Error was invalid region `2:125191858-125192258`
[2016-04-15T03:13Z] 2016-04-14 20:13:11 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:13:11,381 - WARNING - Could not retrieve variants from source file in region 2:113763364-113785392. Error was invalid region `2:113763365-113785392`
[2016-04-15T03:13Z] 2016-04-14 20:13:12 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:13:12,567 - WARNING - Could not retrieve variants from source file in region 2:113343618-113344019. Error was invalid region `2:113343619-113344019`
[2016-04-15T03:13Z] 2016-04-14 20:13:13 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:13:13,109 - WARNING - Could not retrieve variants from source file in region 2:112832324-112832728. Error was invalid region `2:112832325-112832728`
[2016-04-15T03:13Z] 2016-04-14 20:13:14 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:13:14,148 - WARNING - Could not retrieve variants from source file in region 2:120078567-120078968. Error was invalid region `2:120078568-120078968`
[2016-04-15T03:13Z] 2016-04-14 20:13:14 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:13:14,533 - WARNING - Could not retrieve variants from source file in region 2:111880073-111907881. Error was invalid region `2:111880074-111907881`
[2016-04-15T03:13Z] 2016-04-14 20:13:15 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:13:15,731 - WARNING - Could not retrieve variants from source file in region 2:113763364-113785392. Error was invalid region `2:113763365-113785392`
[2016-04-15T03:13Z] 2016-04-14 20:13:17 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:13:17,632 - WARNING - Could not retrieve variants from source file in region 2:112832324-112832728. Error was invalid region `2:112832325-112832728`
[2016-04-15T03:13Z] 2016-04-14 20:13:19 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:13:19,773 - WARNING - Could not retrieve variants from source file in region 2:120078567-120078968. Error was invalid region `2:120078568-120078968`
[2016-04-15T03:13Z] 2016-04-14 20:13:23 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:13:23,650 - WARNING - Could not retrieve variants from source file in region 2:122216208-122216609. Error was invalid region `2:122216209-122216609`
[2016-04-15T03:13Z] 2016-04-14 20:13:26 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:13:26,208 - WARNING - Could not retrieve variants from source file in region 2:113671167-113671600. Error was invalid region `2:113671168-113671600`
[2016-04-15T03:13Z] 2016-04-14 20:13:27 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:13:27,069 - WARNING - Could not retrieve variants from source file in region 2:114036225-114036626. Error was invalid region `2:114036226-114036626`
[2016-04-15T03:13Z] 2016-04-14 20:13:27 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:13:27,588 - WARNING - Could not retrieve variants from source file in region 2:113671167-113671600. Error was invalid region `2:113671168-113671600`
[2016-04-15T03:13Z] 2016-04-14 20:13:28 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:13:28,115 - WARNING - Could not retrieve variants from source file in region 2:113671167-113671600. Error was invalid region `2:113671168-113671600`
[2016-04-15T03:13Z] 2016-04-14 20:13:28 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:13:28,838 - WARNING - Could not retrieve variants from source file in region 2:122216208-122216609. Error was invalid region `2:122216209-122216609`
[2016-04-15T03:13Z] 2016-04-14 20:13:29 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:13:29,113 - WARNING - Could not retrieve variants from source file in region 2:120438312-120439420. Error was invalid region `2:120438313-120439420`
[2016-04-15T03:13Z] 2016-04-14 20:13:29 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:13:29,189 - WARNING - Could not retrieve variants from source file in region 2:111850304-111850705. Error was invalid region `2:111850305-111850705`
[2016-04-15T03:13Z] 2016-04-14 20:13:29 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:13:29,228 - WARNING - Could not retrieve variants from source file in region 2:119915038-119915439. Error was invalid region `2:119915039-119915439`
[2016-04-15T03:13Z] 2016-04-14 20:13:30 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:13:30,317 - WARNING - Could not retrieve variants from source file in region 2:115219317-115219718. Error was invalid region `2:115219318-115219718`
[2016-04-15T03:13Z] 2016-04-14 20:13:30 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:13:30,891 - WARNING - Could not retrieve variants from source file in region 2:120862242-120885500. Error was invalid region `2:120862243-120885500`
[2016-04-15T03:13Z] 2016-04-14 20:13:31 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:13:31,966 - WARNING - Could not retrieve variants from source file in region 2:114036225-114036626. Error was invalid region `2:114036226-114036626`
[2016-04-15T03:13Z] 2016-04-14 20:13:32 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:13:32,218 - WARNING - Could not retrieve variants from source file in region 2:119738852-119739253. Error was invalid region `2:119738853-119739253`
[2016-04-15T03:13Z] 2016-04-14 20:13:33 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:13:33,868 - WARNING - Could not retrieve variants from source file in region 2:114513576-114514288. Error was invalid region `2:114513577-114514288`
[2016-04-15T03:13Z] 2016-04-14 20:13:34 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:13:34,813 - WARNING - Could not retrieve variants from source file in region 2:122216208-122216609. Error was invalid region `2:122216209-122216609`
[2016-04-15T03:13Z] 2016-04-14 20:13:35 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:13:35,053 - WARNING - Could not retrieve variants from source file in region 2:120438312-120439420. Error was invalid region `2:120438313-120439420`
[2016-04-15T03:13Z] 2016-04-14 20:13:35 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:13:35,354 - WARNING - Could not retrieve variants from source file in region 2:113190799-113191200. Error was invalid region `2:113190800-113191200`
[2016-04-15T03:13Z] 2016-04-14 20:13:35 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:13:35,831 - WARNING - Could not retrieve variants from source file in region 2:119915038-119915439. Error was invalid region `2:119915039-119915439`
[2016-04-15T03:13Z] 2016-04-14 20:13:35 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:13:35,842 - WARNING - Could not retrieve variants from source file in region 2:115219317-115219718. Error was invalid region `2:115219318-115219718`
[2016-04-15T03:13Z] 2016-04-14 20:13:35 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:13:35,899 - WARNING - Could not retrieve variants from source file in region 2:111559020-111559421. Error was invalid region `2:111559021-111559421`
[2016-04-15T03:13Z] 2016-04-14 20:13:36 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:13:36,066 - WARNING - Could not retrieve variants from source file in region 2:120862242-120885500. Error was invalid region `2:120862243-120885500`
[2016-04-15T03:13Z] 2016-04-14 20:13:36 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:13:36,802 - WARNING - Could not retrieve variants from source file in region 2:114036225-114036626. Error was invalid region `2:114036226-114036626`
[2016-04-15T03:13Z] 2016-04-14 20:13:36 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:13:36,912 - WARNING - Could not retrieve variants from source file in region 2:119738852-119739253. Error was invalid region `2:119738853-119739253`
[2016-04-15T03:13Z] 2016-04-14 20:13:37 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:13:37,713 - WARNING - Could not retrieve variants from source file in region 2:111850304-111850705. Error was invalid region `2:111850305-111850705`
[2016-04-15T03:13Z] 2016-04-14 20:13:37 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:13:37,763 - WARNING - Could not retrieve variants from source file in region 2:120005101-120015387. Error was invalid region `2:120005102-120015387`
[2016-04-15T03:13Z] 2016-04-14 20:13:39 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:13:39,702 - WARNING - Could not retrieve variants from source file in region 2:111559020-111559421. Error was invalid region `2:111559021-111559421`
[2016-04-15T03:13Z] 2016-04-14 20:13:41 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:13:41,410 - WARNING - Could not retrieve variants from source file in region 2:120438312-120439420. Error was invalid region `2:120438313-120439420`
[2016-04-15T03:13Z] 2016-04-14 20:13:41 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:13:41,750 - WARNING - Could not retrieve variants from source file in region 2:119915038-119915439. Error was invalid region `2:119915039-119915439`
[2016-04-15T03:13Z] 2016-04-14 20:13:49 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:13:49,067 - WARNING - Could not retrieve variants from source file in region 2:118771355-118771878. Error was invalid region `2:118771356-118771878`
[2016-04-15T03:13Z] 2016-04-14 20:13:49 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:13:49,532 - WARNING - Could not retrieve variants from source file in region 2:113983822-113984493. Error was invalid region `2:113983823-113984493`
[2016-04-15T03:13Z] 2016-04-14 20:13:49 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:13:49,811 - WARNING - Could not retrieve variants from source file in region 2:121981739-122005975. Error was invalid region `2:121981740-122005975`
[2016-04-15T03:13Z] 2016-04-14 20:13:51 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:13:51,476 - WARNING - Could not retrieve variants from source file in region 2:120358593-120388602. Error was invalid region `2:120358594-120388602`
[2016-04-15T03:13Z] 2016-04-14 20:13:52 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:13:52,496 - WARNING - Could not retrieve variants from source file in region 2:120194440-120199330. Error was invalid region `2:120194441-120199330`
[2016-04-15T03:13Z] 2016-04-14 20:13:53 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:13:53,245 - WARNING - Could not retrieve variants from source file in region 2:121726236-121747619. Error was invalid region `2:121726237-121747619`
[2016-04-15T03:13Z] 2016-04-14 20:13:54 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:13:54,867 - WARNING - Could not retrieve variants from source file in region 2:113940470-113956561. Error was invalid region `2:113940471-113956561`
[2016-04-15T03:13Z] 2016-04-14 20:13:55 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:13:55,221 - WARNING - Could not retrieve variants from source file in region 2:120303609-120304010. Error was invalid region `2:120303610-120304010`
[2016-04-15T03:13Z] 2016-04-14 20:13:56 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:13:56,288 - WARNING - Could not retrieve variants from source file in region 2:120194440-120199330. Error was invalid region `2:120194441-120199330`
[2016-04-15T03:13Z] 2016-04-14 20:13:57 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:13:57,430 - WARNING - Could not retrieve variants from source file in region 2:120303609-120304010. Error was invalid region `2:120303610-120304010`
[2016-04-15T03:13Z] 2016-04-14 20:13:57 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:13:57,439 - WARNING - Could not retrieve variants from source file in region 2:113940470-113956561. Error was invalid region `2:113940471-113956561`
[2016-04-15T03:13Z] 2016-04-14 20:13:57 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:13:57,812 - WARNING - Could not retrieve variants from source file in region 2:113983822-113984493. Error was invalid region `2:113983823-113984493`
[2016-04-15T03:13Z] 2016-04-14 20:13:59 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:13:59,143 - WARNING - Could not retrieve variants from source file in region 2:120358593-120388602. Error was invalid region `2:120358594-120388602`
[2016-04-15T03:14Z] 2016-04-14 20:14:00 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:14:00,067 - WARNING - Could not retrieve variants from source file in region 2:121726236-121747619. Error was invalid region `2:121726237-121747619`
[2016-04-15T03:14Z] ['bcbio-variation-recall', 'square', '-Xms750m', '-Xmx7280m', '-XX:+UseSerialGC', '-c', 16, '-r', u'2:127433208-143643105', '--caller', 'platypus', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/2/Batch1-2_127433207_143643105.vcf.gz', '/mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/2/Batch1-2_127433207_143643105.vcf-inputs.txt'] in region: 2:127433208-143643105
[2016-04-15T03:14Z] 2016-04-14 20:14:17 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:14:17,306 - WARNING - Could not retrieve variants from source file in region 2:136407268-136409764. Error was invalid region `2:136407269-136409764`
[2016-04-15T03:14Z] 2016-04-14 20:14:18 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:14:18,127 - WARNING - Could not retrieve variants from source file in region 2:128175829-128184960. Error was invalid region `2:128175830-128184960`
[2016-04-15T03:14Z] 2016-04-14 20:14:18 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:14:18,216 - WARNING - Could not retrieve variants from source file in region 2:141259072-141274766. Error was invalid region `2:141259073-141274766`
[2016-04-15T03:14Z] 2016-04-14 20:14:18 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:14:18,584 - WARNING - Could not retrieve variants from source file in region 2:131519967-131520853. Error was invalid region `2:131519968-131520853`
[2016-04-15T03:14Z] 2016-04-14 20:14:18 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:14:18,881 - WARNING - Could not retrieve variants from source file in region 2:127816421-127826723. Error was invalid region `2:127816422-127826723`
[2016-04-15T03:14Z] 2016-04-14 20:14:18 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:14:18,891 - WARNING - Could not retrieve variants from source file in region 2:135700770-135711847. Error was invalid region `2:135700771-135711847`
[2016-04-15T03:14Z] 2016-04-14 20:14:19 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:14:19,017 - WARNING - Could not retrieve variants from source file in region 2:128459003-128464306. Error was invalid region `2:128459004-128464306`
[2016-04-15T03:14Z] 2016-04-14 20:14:19 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:14:19,483 - WARNING - Could not retrieve variants from source file in region 2:141816410-141816811. Error was invalid region `2:141816411-141816811`
[2016-04-15T03:14Z] 2016-04-14 20:14:19 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:14:19,647 - WARNING - Could not retrieve variants from source file in region 2:128079595-128079996. Error was invalid region `2:128079596-128079996`
[2016-04-15T03:14Z] 2016-04-14 20:14:19 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:14:19,697 - WARNING - Could not retrieve variants from source file in region 2:128757784-128758185. Error was invalid region `2:128757785-128758185`
[2016-04-15T03:14Z] 2016-04-14 20:14:25 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:14:25,518 - WARNING - Could not retrieve variants from source file in region 2:128175829-128184960. Error was invalid region `2:128175830-128184960`
[2016-04-15T03:14Z] 2016-04-14 20:14:27 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:14:27,414 - WARNING - Could not retrieve variants from source file in region 2:137917711-137918112. Error was invalid region `2:137917712-137918112`
[2016-04-15T03:14Z] 2016-04-14 20:14:27 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:14:27,510 - WARNING - Could not retrieve variants from source file in region 2:139428857-139429258. Error was invalid region `2:139428858-139429258`
[2016-04-15T03:14Z] 2016-04-14 20:14:28 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:14:28,046 - WARNING - Could not retrieve variants from source file in region 2:128262988-128263389. Error was invalid region `2:128262989-128263389`
[2016-04-15T03:14Z] 2016-04-14 20:14:28 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:14:28,100 - WARNING - Could not retrieve variants from source file in region 2:141816410-141816811. Error was invalid region `2:141816411-141816811`
[2016-04-15T03:14Z] 2016-04-14 20:14:28 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:14:28,595 - WARNING - Could not retrieve variants from source file in region 2:128079595-128079996. Error was invalid region `2:128079596-128079996`
[2016-04-15T03:14Z] 2016-04-14 20:14:28 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:14:28,788 - WARNING - Could not retrieve variants from source file in region 2:141457774-141458175. Error was invalid region `2:141457775-141458175`
[2016-04-15T03:14Z] 2016-04-14 20:14:30 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:14:30,585 - WARNING - Could not retrieve variants from source file in region 2:128175829-128184960. Error was invalid region `2:128175830-128184960`
[2016-04-15T03:14Z] 2016-04-14 20:14:31 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:14:31,060 - WARNING - Could not retrieve variants from source file in region 2:141259072-141274766. Error was invalid region `2:141259073-141274766`
[2016-04-15T03:14Z] 2016-04-14 20:14:32 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:14:32,883 - WARNING - Could not retrieve variants from source file in region 2:137917711-137918112. Error was invalid region `2:137917712-137918112`
[2016-04-15T03:14Z] 2016-04-14 20:14:34 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:14:34,119 - WARNING - Could not retrieve variants from source file in region 2:139428857-139429258. Error was invalid region `2:139428858-139429258`
[2016-04-15T03:14Z] 2016-04-14 20:14:34 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:14:34,334 - WARNING - Could not retrieve variants from source file in region 2:128459003-128464306. Error was invalid region `2:128459004-128464306`
[2016-04-15T03:14Z] 2016-04-14 20:14:35 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:14:35,550 - WARNING - Could not retrieve variants from source file in region 2:128262988-128263389. Error was invalid region `2:128262989-128263389`
[2016-04-15T03:14Z] 2016-04-14 20:14:35 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:14:35,591 - WARNING - Could not retrieve variants from source file in region 2:128079595-128079996. Error was invalid region `2:128079596-128079996`
[2016-04-15T03:14Z] 2016-04-14 20:14:35 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:14:35,876 - WARNING - Could not retrieve variants from source file in region 2:141457774-141458175. Error was invalid region `2:141457775-141458175`
[2016-04-15T03:14Z] 2016-04-14 20:14:36 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:14:36,102 - WARNING - Could not retrieve variants from source file in region 2:141816410-141816811. Error was invalid region `2:141816411-141816811`
[2016-04-15T03:14Z] 2016-04-14 20:14:36 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:14:36,107 - WARNING - Could not retrieve variants from source file in region 2:127443381-127453854. Error was invalid region `2:127443382-127453854`
[2016-04-15T03:14Z] 2016-04-14 20:14:46 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:14:46,435 - WARNING - Could not retrieve variants from source file in region 2:135893161-135911612. Error was invalid region `2:135893162-135911612`
[2016-04-15T03:14Z] 2016-04-14 20:14:48 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:14:48,041 - WARNING - Could not retrieve variants from source file in region 2:141031877-141032278. Error was invalid region `2:141031878-141032278`
[2016-04-15T03:14Z] 2016-04-14 20:14:48 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:14:48,143 - WARNING - Could not retrieve variants from source file in region 2:128145261-128146652. Error was invalid region `2:128145262-128146652`
[2016-04-15T03:14Z] 2016-04-14 20:14:48 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:14:48,971 - WARNING - Could not retrieve variants from source file in region 2:132794849-132796410. Error was invalid region `2:132794850-132796410`
[2016-04-15T03:14Z] 2016-04-14 20:14:49 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:14:49,735 - WARNING - Could not retrieve variants from source file in region 2:131487462-131487863. Error was invalid region `2:131487463-131487863`
[2016-04-15T03:14Z] 2016-04-14 20:14:51 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:14:51,579 - WARNING - Could not retrieve variants from source file in region 2:133539355-133554478. Error was invalid region `2:133539356-133554478`
[2016-04-15T03:14Z] 2016-04-14 20:14:53 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:14:53,595 - WARNING - Could not retrieve variants from source file in region 2:127952843-127957181. Error was invalid region `2:127952844-127957181`
[2016-04-15T03:14Z] 2016-04-14 20:14:53 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:14:53,632 - WARNING - Could not retrieve variants from source file in region 2:141031877-141032278. Error was invalid region `2:141031878-141032278`
[2016-04-15T03:14Z] 2016-04-14 20:14:54 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:14:54,418 - WARNING - Could not retrieve variants from source file in region 2:141707657-141708058. Error was invalid region `2:141707658-141708058`
[2016-04-15T03:14Z] 2016-04-14 20:14:56 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:14:56,029 - WARNING - Could not retrieve variants from source file in region 2:132794849-132796410. Error was invalid region `2:132794850-132796410`
[2016-04-15T03:14Z] 2016-04-14 20:14:56 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:14:56,552 - WARNING - Could not retrieve variants from source file in region 2:131487462-131487863. Error was invalid region `2:131487463-131487863`
[2016-04-15T03:14Z] 2016-04-14 20:14:57 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:14:57,132 - WARNING - Could not retrieve variants from source file in region 2:138759438-138759839. Error was invalid region `2:138759439-138759839`
[2016-04-15T03:14Z] 2016-04-14 20:14:57 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:14:57,326 - WARNING - Could not retrieve variants from source file in region 2:137814266-137814667. Error was invalid region `2:137814267-137814667`
[2016-04-15T03:14Z] 2016-04-14 20:14:57 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:14:57,528 - WARNING - Could not retrieve variants from source file in region 2:133539355-133554478. Error was invalid region `2:133539356-133554478`
[2016-04-15T03:14Z] 2016-04-14 20:14:59 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:14:59,260 - WARNING - Could not retrieve variants from source file in region 2:141707657-141708058. Error was invalid region `2:141707658-141708058`
[2016-04-15T03:14Z] 2016-04-14 20:14:59 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:14:59,298 - WARNING - Could not retrieve variants from source file in region 2:141571118-141571519. Error was invalid region `2:141571119-141571519`
[2016-04-15T03:14Z] 2016-04-14 20:14:59 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:14:59,774 - WARNING - Could not retrieve variants from source file in region 2:128519932-128520737. Error was invalid region `2:128519933-128520737`
[2016-04-15T03:15Z] 2016-04-14 20:15:01 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:15:01,266 - WARNING - Could not retrieve variants from source file in region 2:132794849-132796410. Error was invalid region `2:132794850-132796410`
[2016-04-15T03:15Z] 2016-04-14 20:15:02 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:15:02,360 - WARNING - Could not retrieve variants from source file in region 2:138759438-138759839. Error was invalid region `2:138759439-138759839`
[2016-04-15T03:15Z] 2016-04-14 20:15:02 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:15:02,825 - WARNING - Could not retrieve variants from source file in region 2:131487462-131487863. Error was invalid region `2:131487463-131487863`
[2016-04-15T03:15Z] 2016-04-14 20:15:03 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:15:03,292 - WARNING - Could not retrieve variants from source file in region 2:137814266-137814667. Error was invalid region `2:137814267-137814667`
[2016-04-15T03:15Z] 2016-04-14 20:15:03 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:15:03,308 - WARNING - Could not retrieve variants from source file in region 2:133539355-133554478. Error was invalid region `2:133539356-133554478`
[2016-04-15T03:15Z] 2016-04-14 20:15:04 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:15:04,736 - WARNING - Could not retrieve variants from source file in region 2:135745181-135745912. Error was invalid region `2:135745182-135745912`
[2016-04-15T03:15Z] 2016-04-14 20:15:04 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:15:04,770 - WARNING - Could not retrieve variants from source file in region 2:141571118-141571519. Error was invalid region `2:141571119-141571519`
[2016-04-15T03:15Z] 2016-04-14 20:15:05 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:15:05,911 - WARNING - Could not retrieve variants from source file in region 2:135745181-135745912. Error was invalid region `2:135745182-135745912`
[2016-04-15T03:15Z] 2016-04-14 20:15:11 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:15:11,213 - WARNING - Could not retrieve variants from source file in region 2:128519932-128520737. Error was invalid region `2:128519933-128520737`
[2016-04-15T03:15Z] 2016-04-14 20:15:13 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:15:13,507 - WARNING - Could not retrieve variants from source file in region 2:133489190-133489591. Error was invalid region `2:133489191-133489591`
[2016-04-15T03:15Z] 2016-04-14 20:15:13 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:15:13,786 - WARNING - Could not retrieve variants from source file in region 2:133174553-133175189. Error was invalid region `2:133174554-133175189`
[2016-04-15T03:15Z] 2016-04-14 20:15:14 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:15:14,353 - WARNING - Could not retrieve variants from source file in region 2:138420785-138421186. Error was invalid region `2:138420786-138421186`
[2016-04-15T03:15Z] 2016-04-14 20:15:14 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:15:14,657 - WARNING - Could not retrieve variants from source file in region 2:136873338-136873739. Error was invalid region `2:136873339-136873739`
[2016-04-15T03:15Z] 2016-04-14 20:15:16 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:15:16,416 - WARNING - Could not retrieve variants from source file in region 2:136545899-136594348. Error was invalid region `2:136545900-136594348`
[2016-04-15T03:15Z] 2016-04-14 20:15:17 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:15:17,230 - WARNING - Could not retrieve variants from source file in region 2:128366881-128367282. Error was invalid region `2:128366882-128367282`
[2016-04-15T03:15Z] 2016-04-14 20:15:18 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:15:18,019 - WARNING - Could not retrieve variants from source file in region 2:138420785-138421186. Error was invalid region `2:138420786-138421186`
[2016-04-15T03:15Z] 2016-04-14 20:15:19 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:15:19,023 - WARNING - Could not retrieve variants from source file in region 2:133489190-133489591. Error was invalid region `2:133489191-133489591`
[2016-04-15T03:15Z] 2016-04-14 20:15:19 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:15:19,024 - WARNING - Could not retrieve variants from source file in region 2:133174553-133175189. Error was invalid region `2:133174554-133175189`
[2016-04-15T03:15Z] 2016-04-14 20:15:20 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:15:20,448 - WARNING - Could not retrieve variants from source file in region 2:131413965-131414544. Error was invalid region `2:131413966-131414544`
[2016-04-15T03:15Z] 2016-04-14 20:15:23 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:15:23,225 - WARNING - Could not retrieve variants from source file in region 2:136873338-136873739. Error was invalid region `2:136873339-136873739`
[2016-04-15T03:15Z] 2016-04-14 20:15:23 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:15:23,843 - WARNING - Could not retrieve variants from source file in region 2:128321559-128321960. Error was invalid region `2:128321560-128321960`
[2016-04-15T03:15Z] 2016-04-14 20:15:23 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:15:23,896 - WARNING - Could not retrieve variants from source file in region 2:131100523-131100924. Error was invalid region `2:131100524-131100924`
[2016-04-15T03:15Z] 2016-04-14 20:15:26 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:15:26,199 - WARNING - Could not retrieve variants from source file in region 2:131266319-131266936. Error was invalid region `2:131266320-131266936`
[2016-04-15T03:15Z] 2016-04-14 20:15:26 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:15:26,811 - WARNING - Could not retrieve variants from source file in region 2:128321559-128321960. Error was invalid region `2:128321560-128321960`
[2016-04-15T03:15Z] 2016-04-14 20:15:28 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:15:28,013 - WARNING - Could not retrieve variants from source file in region 2:128321559-128321960. Error was invalid region `2:128321560-128321960`
[2016-04-15T03:15Z] 2016-04-14 20:15:28 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:15:28,824 - WARNING - Could not retrieve variants from source file in region 2:131100523-131100924. Error was invalid region `2:131100524-131100924`
[2016-04-15T03:15Z] 2016-04-14 20:15:29 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:15:29,467 - WARNING - Could not retrieve variants from source file in region 2:130737952-130738353. Error was invalid region `2:130737953-130738353`
[2016-04-15T03:15Z] 2016-04-14 20:15:31 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:15:31,102 - WARNING - Could not retrieve variants from source file in region 2:130877541-130952139. Error was invalid region `2:130877542-130952139`
[2016-04-15T03:15Z] 2016-04-14 20:15:31 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:15:31,384 - WARNING - Could not retrieve variants from source file in region 2:132229509-132250283. Error was invalid region `2:132229510-132250283`
[2016-04-15T03:15Z] 2016-04-14 20:15:32 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:15:32,275 - WARNING - Could not retrieve variants from source file in region 2:131100523-131100924. Error was invalid region `2:131100524-131100924`
[2016-04-15T03:15Z] 2016-04-14 20:15:33 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:15:33,867 - WARNING - Could not retrieve variants from source file in region 2:130737952-130738353. Error was invalid region `2:130737953-130738353`
[2016-04-15T03:15Z] 2016-04-14 20:15:37 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:15:37,039 - WARNING - Could not retrieve variants from source file in region 2:128934189-128940007. Error was invalid region `2:128934190-128940007`
[2016-04-15T03:15Z] 2016-04-14 20:15:37 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:15:37,420 - WARNING - Could not retrieve variants from source file in region 2:131220959-131221360. Error was invalid region `2:131220960-131221360`
[2016-04-15T03:15Z] 2016-04-14 20:15:37 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:15:37,991 - WARNING - Could not retrieve variants from source file in region 2:130737952-130738353. Error was invalid region `2:130737953-130738353`
[2016-04-15T03:15Z] 2016-04-14 20:15:38 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:15:38,872 - WARNING - Could not retrieve variants from source file in region 2:131797097-131809387. Error was invalid region `2:131797098-131809387`
[2016-04-15T03:15Z] 2016-04-14 20:15:40 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:15:40,091 - WARNING - Could not retrieve variants from source file in region 2:128848903-128878204. Error was invalid region `2:128848904-128878204`
[2016-04-15T03:15Z] 2016-04-14 20:15:40 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:15:40,727 - WARNING - Could not retrieve variants from source file in region 2:130832081-130832721. Error was invalid region `2:130832082-130832721`
[2016-04-15T03:15Z] 2016-04-14 20:15:41 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:15:41,675 - WARNING - Could not retrieve variants from source file in region 2:131671890-131688973. Error was invalid region `2:131671891-131688973`
[2016-04-15T03:15Z] 2016-04-14 20:15:41 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:15:41,907 - WARNING - Could not retrieve variants from source file in region 2:128934189-128940007. Error was invalid region `2:128934190-128940007`
[2016-04-15T03:15Z] 2016-04-14 20:15:41 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:15:41,936 - WARNING - Could not retrieve variants from source file in region 2:131220959-131221360. Error was invalid region `2:131220960-131221360`
[2016-04-15T03:15Z] 2016-04-14 20:15:42 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:15:42,105 - WARNING - Could not retrieve variants from source file in region 2:130832081-130832721. Error was invalid region `2:130832082-130832721`
[2016-04-15T03:15Z] 2016-04-14 20:15:44 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:15:44,549 - WARNING - Could not retrieve variants from source file in region 2:128848903-128878204. Error was invalid region `2:128848904-128878204`
[2016-04-15T03:15Z] 2016-04-14 20:15:45 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:15:45,715 - WARNING - Could not retrieve variants from source file in region 2:131671890-131688973. Error was invalid region `2:131671891-131688973`
[2016-04-15T03:15Z] 2016-04-14 20:15:46 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:15:46,186 - WARNING - Could not retrieve variants from source file in region 2:131220959-131221360. Error was invalid region `2:131220960-131221360`
[2016-04-15T03:15Z] 2016-04-14 20:15:46 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:15:46,287 - WARNING - Could not retrieve variants from source file in region 2:128848903-128878204. Error was invalid region `2:128848904-128878204`
[2016-04-15T03:15Z] 2016-04-14 20:15:46 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:15:46,598 - WARNING - Could not retrieve variants from source file in region 2:129075666-129076151. Error was invalid region `2:129075667-129076151`
[2016-04-15T03:15Z] 2016-04-14 20:15:49 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:15:49,879 - WARNING - Could not retrieve variants from source file in region 2:129075666-129076151. Error was invalid region `2:129075667-129076151`
[2016-04-15T03:15Z] 2016-04-14 20:15:51 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:15:51,253 - WARNING - Could not retrieve variants from source file in region 2:131976061-131976462. Error was invalid region `2:131976062-131976462`
[2016-04-15T03:15Z] 2016-04-14 20:15:52 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:15:52,886 - WARNING - Could not retrieve variants from source file in region 2:131976061-131976462. Error was invalid region `2:131976062-131976462`
[2016-04-15T03:15Z] ['bcbio-variation-recall', 'square', '-Xms750m', '-Xmx7280m', '-XX:+UseSerialGC', '-c', 16, '-r', u'2:143676178-159195597', '--caller', 'platypus', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/2/Batch1-2_143676177_159195597.vcf.gz', '/mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/2/Batch1-2_143676177_159195597.vcf-inputs.txt'] in region: 2:143676178-159195597
[2016-04-15T03:16Z] 2016-04-14 20:16:06 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:16:06,353 - WARNING - Could not retrieve variants from source file in region 2:145270381-145270782. Error was invalid region `2:145270382-145270782`
[2016-04-15T03:16Z] 2016-04-14 20:16:07 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:16:07,423 - WARNING - Could not retrieve variants from source file in region 2:153378248-153378649. Error was invalid region `2:153378249-153378649`
[2016-04-15T03:16Z] 2016-04-14 20:16:07 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:16:07,532 - WARNING - Could not retrieve variants from source file in region 2:153475855-153476256. Error was invalid region `2:153475856-153476256`
[2016-04-15T03:16Z] 2016-04-14 20:16:08 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:16:08,948 - WARNING - Could not retrieve variants from source file in region 2:152573770-152574171. Error was invalid region `2:152573771-152574171`
[2016-04-15T03:16Z] 2016-04-14 20:16:09 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:16:09,195 - WARNING - Could not retrieve variants from source file in region 2:150432765-150433166. Error was invalid region `2:150432766-150433166`
[2016-04-15T03:16Z] 2016-04-14 20:16:09 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:16:09,392 - WARNING - Could not retrieve variants from source file in region 2:158443678-158444079. Error was invalid region `2:158443679-158444079`
[2016-04-15T03:16Z] 2016-04-14 20:16:09 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:16:09,441 - WARNING - Could not retrieve variants from source file in region 2:158626769-158637100. Error was invalid region `2:158626770-158637100`
[2016-04-15T03:16Z] 2016-04-14 20:16:09 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:16:09,459 - WARNING - Could not retrieve variants from source file in region 2:159165858-159166259. Error was invalid region `2:159165859-159166259`
[2016-04-15T03:16Z] 2016-04-14 20:16:10 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:16:10,104 - WARNING - Could not retrieve variants from source file in region 2:144194354-144194755. Error was invalid region `2:144194355-144194755`
[2016-04-15T03:16Z] 2016-04-14 20:16:10 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:16:10,418 - WARNING - Could not retrieve variants from source file in region 2:153405383-153405784. Error was invalid region `2:153405384-153405784`
[2016-04-15T03:16Z] 2016-04-14 20:16:10 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:16:10,476 - WARNING - Could not retrieve variants from source file in region 2:152387342-152387743. Error was invalid region `2:152387343-152387743`
[2016-04-15T03:16Z] 2016-04-14 20:16:10 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:16:10,609 - WARNING - Could not retrieve variants from source file in region 2:157406038-157406439. Error was invalid region `2:157406039-157406439`
[2016-04-15T03:16Z] 2016-04-14 20:16:10 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:16:10,626 - WARNING - Could not retrieve variants from source file in region 2:159195351-159195752. Error was invalid region `2:159195352-159195752`
[2016-04-15T03:16Z] 2016-04-14 20:16:10 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:16:10,685 - WARNING - Could not retrieve variants from source file in region 2:144899348-144899749. Error was invalid region `2:144899349-144899749`
[2016-04-15T03:16Z] 2016-04-14 20:16:10 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:16:10,775 - WARNING - Could not retrieve variants from source file in region 2:152475817-152536688. Error was invalid region `2:152475818-152536688`
[2016-04-15T03:16Z] 2016-04-14 20:16:10 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:16:10,846 - WARNING - Could not retrieve variants from source file in region 2:155711146-155711547. Error was invalid region `2:155711147-155711547`
[2016-04-15T03:16Z] 2016-04-14 20:16:11 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:16:11,157 - WARNING - Could not retrieve variants from source file in region 2:145270381-145270782. Error was invalid region `2:145270382-145270782`
[2016-04-15T03:16Z] 2016-04-14 20:16:13 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:16:13,105 - WARNING - Could not retrieve variants from source file in region 2:153378248-153378649. Error was invalid region `2:153378249-153378649`
[2016-04-15T03:16Z] 2016-04-14 20:16:13 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:16:13,126 - WARNING - Could not retrieve variants from source file in region 2:153475855-153476256. Error was invalid region `2:153475856-153476256`
[2016-04-15T03:16Z] 2016-04-14 20:16:14 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:16:14,264 - WARNING - Could not retrieve variants from source file in region 2:152573770-152574171. Error was invalid region `2:152573771-152574171`
[2016-04-15T03:16Z] 2016-04-14 20:16:14 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:16:14,905 - WARNING - Could not retrieve variants from source file in region 2:150432765-150433166. Error was invalid region `2:150432766-150433166`
[2016-04-15T03:16Z] 2016-04-14 20:16:16 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:16:16,507 - WARNING - Could not retrieve variants from source file in region 2:158626769-158637100. Error was invalid region `2:158626770-158637100`
[2016-04-15T03:16Z] 2016-04-14 20:16:17 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:16:17,416 - WARNING - Could not retrieve variants from source file in region 2:144194354-144194755. Error was invalid region `2:144194355-144194755`
[2016-04-15T03:16Z] 2016-04-14 20:16:17 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:16:17,428 - WARNING - Could not retrieve variants from source file in region 2:158443678-158444079. Error was invalid region `2:158443679-158444079`
[2016-04-15T03:16Z] 2016-04-14 20:16:17 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:16:17,971 - WARNING - Could not retrieve variants from source file in region 2:159165858-159166259. Error was invalid region `2:159165859-159166259`
[2016-04-15T03:16Z] 2016-04-14 20:16:18 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:16:18,269 - WARNING - Could not retrieve variants from source file in region 2:152387342-152387743. Error was invalid region `2:152387343-152387743`
[2016-04-15T03:16Z] 2016-04-14 20:16:18 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:16:18,356 - WARNING - Could not retrieve variants from source file in region 2:155711146-155711547. Error was invalid region `2:155711147-155711547`
[2016-04-15T03:16Z] 2016-04-14 20:16:18 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:16:18,486 - WARNING - Could not retrieve variants from source file in region 2:145270381-145270782. Error was invalid region `2:145270382-145270782`
[2016-04-15T03:16Z] 2016-04-14 20:16:18 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:16:18,639 - WARNING - Could not retrieve variants from source file in region 2:153378248-153378649. Error was invalid region `2:153378249-153378649`
[2016-04-15T03:16Z] 2016-04-14 20:16:18 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:16:18,640 - WARNING - Could not retrieve variants from source file in region 2:153475855-153476256. Error was invalid region `2:153475856-153476256`
[2016-04-15T03:16Z] 2016-04-14 20:16:19 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:16:19,100 - WARNING - Could not retrieve variants from source file in region 2:152573770-152574171. Error was invalid region `2:152573771-152574171`
[2016-04-15T03:16Z] 2016-04-14 20:16:19 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:16:19,848 - WARNING - Could not retrieve variants from source file in region 2:150432765-150433166. Error was invalid region `2:150432766-150433166`
[2016-04-15T03:16Z] 2016-04-14 20:16:23 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:16:23,208 - WARNING - Could not retrieve variants from source file in region 2:158626769-158637100. Error was invalid region `2:158626770-158637100`
[2016-04-15T03:16Z] 2016-04-14 20:16:24 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:16:24,977 - WARNING - Could not retrieve variants from source file in region 2:158443678-158444079. Error was invalid region `2:158443679-158444079`
[2016-04-15T03:16Z] 2016-04-14 20:16:25 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:16:25,386 - WARNING - Could not retrieve variants from source file in region 2:144194354-144194755. Error was invalid region `2:144194355-144194755`
[2016-04-15T03:16Z] 2016-04-14 20:16:26 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:16:26,538 - WARNING - Could not retrieve variants from source file in region 2:153405383-153405784. Error was invalid region `2:153405384-153405784`
[2016-04-15T03:16Z] 2016-04-14 20:16:26 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:16:26,761 - WARNING - Could not retrieve variants from source file in region 2:144899348-144899749. Error was invalid region `2:144899349-144899749`
[2016-04-15T03:16Z] 2016-04-14 20:16:26 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:16:26,891 - WARNING - Could not retrieve variants from source file in region 2:157406038-157406439. Error was invalid region `2:157406039-157406439`
[2016-04-15T03:16Z] 2016-04-14 20:16:27 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:16:27,128 - WARNING - Could not retrieve variants from source file in region 2:155711146-155711547. Error was invalid region `2:155711147-155711547`
[2016-04-15T03:16Z] 2016-04-14 20:16:27 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:16:27,145 - WARNING - Could not retrieve variants from source file in region 2:152387342-152387743. Error was invalid region `2:152387343-152387743`
[2016-04-15T03:16Z] 2016-04-14 20:16:27 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:16:27,273 - WARNING - Could not retrieve variants from source file in region 2:159165858-159166259. Error was invalid region `2:159165859-159166259`
[2016-04-15T03:16Z] 2016-04-14 20:16:40 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:16:40,098 - WARNING - Could not retrieve variants from source file in region 2:148716217-148716618. Error was invalid region `2:148716218-148716618`
[2016-04-15T03:16Z] 2016-04-14 20:16:41 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:16:41,459 - WARNING - Could not retrieve variants from source file in region 2:158157150-158157551. Error was invalid region `2:158157151-158157551`
[2016-04-15T03:16Z] 2016-04-14 20:16:44 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:16:44,607 - WARNING - Could not retrieve variants from source file in region 2:148716217-148716618. Error was invalid region `2:148716218-148716618`
[2016-04-15T03:16Z] 2016-04-14 20:16:45 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:16:45,051 - WARNING - Could not retrieve variants from source file in region 2:157188800-157189201. Error was invalid region `2:157188801-157189201`
[2016-04-15T03:16Z] 2016-04-14 20:16:45 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:16:45,329 - WARNING - Could not retrieve variants from source file in region 2:148656906-148657307. Error was invalid region `2:148656907-148657307`
[2016-04-15T03:16Z] 2016-04-14 20:16:45 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:16:45,684 - WARNING - Could not retrieve variants from source file in region 2:153435223-153435624. Error was invalid region `2:153435224-153435624`
[2016-04-15T03:16Z] 2016-04-14 20:16:46 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:16:46,168 - WARNING - Could not retrieve variants from source file in region 2:158157150-158157551. Error was invalid region `2:158157151-158157551`
[2016-04-15T03:16Z] 2016-04-14 20:16:46 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:16:46,500 - WARNING - Could not retrieve variants from source file in region 2:143797978-143798379. Error was invalid region `2:143797979-143798379`
[2016-04-15T03:16Z] 2016-04-14 20:16:46 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:16:46,951 - WARNING - Could not retrieve variants from source file in region 2:152311359-152353033. Error was invalid region `2:152311360-152353033`
[2016-04-15T03:16Z] 2016-04-14 20:16:47 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:16:47,893 - WARNING - Could not retrieve variants from source file in region 2:155555667-155556068. Error was invalid region `2:155555668-155556068`
[2016-04-15T03:16Z] 2016-04-14 20:16:49 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:16:49,479 - WARNING - Could not retrieve variants from source file in region 2:153533049-153533450. Error was invalid region `2:153533050-153533450`
[2016-04-15T03:16Z] 2016-04-14 20:16:49 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:16:49,538 - WARNING - Could not retrieve variants from source file in region 2:157188800-157189201. Error was invalid region `2:157188801-157189201`
[2016-04-15T03:16Z] 2016-04-14 20:16:49 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:16:49,784 - WARNING - Could not retrieve variants from source file in region 2:148656906-148657307. Error was invalid region `2:148656907-148657307`
[2016-04-15T03:16Z] 2016-04-14 20:16:50 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:16:50,424 - WARNING - Could not retrieve variants from source file in region 2:152235834-152236237. Error was invalid region `2:152235835-152236237`
[2016-04-15T03:16Z] 2016-04-14 20:16:50 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:16:50,869 - WARNING - Could not retrieve variants from source file in region 2:143797978-143798379. Error was invalid region `2:143797979-143798379`
[2016-04-15T03:16Z] 2016-04-14 20:16:51 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:16:51,926 - WARNING - Could not retrieve variants from source file in region 2:155555667-155556068. Error was invalid region `2:155555668-155556068`
[2016-04-15T03:16Z] 2016-04-14 20:16:53 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:16:53,804 - WARNING - Could not retrieve variants from source file in region 2:157188800-157189201. Error was invalid region `2:157188801-157189201`
[2016-04-15T03:16Z] 2016-04-14 20:16:53 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:16:53,910 - WARNING - Could not retrieve variants from source file in region 2:153533049-153533450. Error was invalid region `2:153533050-153533450`
[2016-04-15T03:17Z] ['bcbio-variation-recall', 'square', '-Xms750m', '-Xmx7280m', '-XX:+UseSerialGC', '-c', 16, '-r', u'2:159196754-174774985', '--caller', 'platypus', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/2/Batch1-2_159196753_174774985.vcf.gz', '/mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/2/Batch1-2_159196753_174774985.vcf-inputs.txt'] in region: 2:159196754-174774985
[2016-04-15T03:17Z] 2016-04-14 20:17:10 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:17:10,638 - WARNING - Could not retrieve variants from source file in region 2:173940409-173940810. Error was invalid region `2:173940410-173940810`
[2016-04-15T03:17Z] 2016-04-14 20:17:11 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:17:11,137 - WARNING - Could not retrieve variants from source file in region 2:167144763-167168283. Error was invalid region `2:167144764-167168283`
[2016-04-15T03:17Z] 2016-04-14 20:17:12 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:17:12,659 - WARNING - Could not retrieve variants from source file in region 2:169830117-169830518. Error was invalid region `2:169830118-169830518`
[2016-04-15T03:17Z] 2016-04-14 20:17:13 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:17:13,113 - WARNING - Could not retrieve variants from source file in region 2:171354987-171356464. Error was invalid region `2:171354988-171356464`
[2016-04-15T03:17Z] 2016-04-14 20:17:13 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:17:13,269 - WARNING - Could not retrieve variants from source file in region 2:166769909-166797836. Error was invalid region `2:166769910-166797836`
[2016-04-15T03:17Z] 2016-04-14 20:17:13 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:17:13,321 - WARNING - Could not retrieve variants from source file in region 2:173883312-173883713. Error was invalid region `2:173883313-173883713`
[2016-04-15T03:17Z] 2016-04-14 20:17:13 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:17:13,695 - WARNING - Could not retrieve variants from source file in region 2:162069023-162069424. Error was invalid region `2:162069024-162069424`
[2016-04-15T03:17Z] 2016-04-14 20:17:13 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:17:13,841 - WARNING - Could not retrieve variants from source file in region 2:164473542-164473943. Error was invalid region `2:164473543-164473943`
[2016-04-15T03:17Z] 2016-04-14 20:17:13 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:17:13,850 - WARNING - Could not retrieve variants from source file in region 2:173724710-173725112. Error was invalid region `2:173724711-173725112`
[2016-04-15T03:17Z] 2016-04-14 20:17:15 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:17:15,633 - WARNING - Could not retrieve variants from source file in region 2:173940409-173940810. Error was invalid region `2:173940410-173940810`
[2016-04-15T03:17Z] 2016-04-14 20:17:17 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:17:17,044 - WARNING - Could not retrieve variants from source file in region 2:167144763-167168283. Error was invalid region `2:167144764-167168283`
[2016-04-15T03:17Z] 2016-04-14 20:17:18 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:17:18,169 - WARNING - Could not retrieve variants from source file in region 2:171910102-171916685. Error was invalid region `2:171910103-171916685`
[2016-04-15T03:17Z] 2016-04-14 20:17:18 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:17:18,611 - WARNING - Could not retrieve variants from source file in region 2:170493652-170494053. Error was invalid region `2:170493653-170494053`
[2016-04-15T03:17Z] 2016-04-14 20:17:19 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:17:19,245 - WARNING - Could not retrieve variants from source file in region 2:170366888-170367289. Error was invalid region `2:170366889-170367289`
[2016-04-15T03:17Z] 2016-04-14 20:17:20 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:17:20,696 - WARNING - Could not retrieve variants from source file in region 2:170684013-170684414. Error was invalid region `2:170684014-170684414`
[2016-04-15T03:17Z] 2016-04-14 20:17:20 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:17:20,738 - WARNING - Could not retrieve variants from source file in region 2:160639759-160676635. Error was invalid region `2:160639760-160676635`
[2016-04-15T03:17Z] 2016-04-14 20:17:21 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:17:21,286 - WARNING - Could not retrieve variants from source file in region 2:171354987-171356464. Error was invalid region `2:171354988-171356464`
[2016-04-15T03:17Z] 2016-04-14 20:17:21 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:17:21,383 - WARNING - Could not retrieve variants from source file in region 2:174128302-174128703. Error was invalid region `2:174128303-174128703`
[2016-04-15T03:17Z] 2016-04-14 20:17:21 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:17:21,421 - WARNING - Could not retrieve variants from source file in region 2:173292168-173292569. Error was invalid region `2:173292169-173292569`
[2016-04-15T03:17Z] 2016-04-14 20:17:21 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:17:21,862 - WARNING - Could not retrieve variants from source file in region 2:162069023-162069424. Error was invalid region `2:162069024-162069424`
[2016-04-15T03:17Z] 2016-04-14 20:17:21 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:17:21,936 - WARNING - Could not retrieve variants from source file in region 2:173724710-173725112. Error was invalid region `2:173724711-173725112`
[2016-04-15T03:17Z] 2016-04-14 20:17:21 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:17:21,972 - WARNING - Could not retrieve variants from source file in region 2:173940409-173940810. Error was invalid region `2:173940410-173940810`
[2016-04-15T03:17Z] 2016-04-14 20:17:22 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:17:22,143 - WARNING - Could not retrieve variants from source file in region 2:167144763-167168283. Error was invalid region `2:167144764-167168283`
[2016-04-15T03:17Z] 2016-04-14 20:17:27 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:17:27,719 - WARNING - Could not retrieve variants from source file in region 2:170684013-170684414. Error was invalid region `2:170684014-170684414`
[2016-04-15T03:17Z] 2016-04-14 20:17:28 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:17:28,816 - WARNING - Could not retrieve variants from source file in region 2:169830117-169830518. Error was invalid region `2:169830118-169830518`
[2016-04-15T03:17Z] 2016-04-14 20:17:29 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:17:29,278 - WARNING - Could not retrieve variants from source file in region 2:171354987-171356464. Error was invalid region `2:171354988-171356464`
[2016-04-15T03:17Z] 2016-04-14 20:17:29 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:17:29,385 - WARNING - Could not retrieve variants from source file in region 2:173883312-173883713. Error was invalid region `2:173883313-173883713`
[2016-04-15T03:17Z] 2016-04-14 20:17:29 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:17:29,995 - WARNING - Could not retrieve variants from source file in region 2:164473542-164473943. Error was invalid region `2:164473543-164473943`
[2016-04-15T03:17Z] 2016-04-14 20:17:30 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:17:30,188 - WARNING - Could not retrieve variants from source file in region 2:162069023-162069424. Error was invalid region `2:162069024-162069424`
[2016-04-15T03:17Z] 2016-04-14 20:17:30 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:17:30,220 - WARNING - Could not retrieve variants from source file in region 2:174128302-174128703. Error was invalid region `2:174128303-174128703`
[2016-04-15T03:17Z] 2016-04-14 20:17:30 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:17:30,312 - WARNING - Could not retrieve variants from source file in region 2:173292168-173292569. Error was invalid region `2:173292169-173292569`
[2016-04-15T03:17Z] 2016-04-14 20:17:30 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:17:30,445 - WARNING - Could not retrieve variants from source file in region 2:173724710-173725112. Error was invalid region `2:173724711-173725112`
[2016-04-15T03:17Z] 2016-04-14 20:17:43 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:17:43,045 - WARNING - Could not retrieve variants from source file in region 2:170402819-170411883. Error was invalid region `2:170402820-170411883`
[2016-04-15T03:17Z] 2016-04-14 20:17:43 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:17:43,304 - WARNING - Could not retrieve variants from source file in region 2:170218636-170219037. Error was invalid region `2:170218637-170219037`
[2016-04-15T03:17Z] 2016-04-14 20:17:43 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:17:43,379 - WARNING - Could not retrieve variants from source file in region 2:171822255-171822656. Error was invalid region `2:171822256-171822656`
[2016-04-15T03:17Z] 2016-04-14 20:17:43 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:17:43,417 - WARNING - Could not retrieve variants from source file in region 2:167098947-167099348. Error was invalid region `2:167098948-167099348`
[2016-04-15T03:17Z] 2016-04-14 20:17:44 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:17:44,325 - WARNING - Could not retrieve variants from source file in region 2:170605770-170606171. Error was invalid region `2:170605771-170606171`
[2016-04-15T03:17Z] 2016-04-14 20:17:47 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:17:47,439 - WARNING - Could not retrieve variants from source file in region 2:171070701-171074077. Error was invalid region `2:171070702-171074077`
[2016-04-15T03:17Z] 2016-04-14 20:17:48 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:17:48,337 - WARNING - Could not retrieve variants from source file in region 2:160901306-160919174. Error was invalid region `2:160901307-160919174`
[2016-04-15T03:17Z] 2016-04-14 20:17:49 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:17:49,879 - WARNING - Could not retrieve variants from source file in region 2:170402819-170411883. Error was invalid region `2:170402820-170411883`
[2016-04-15T03:17Z] 2016-04-14 20:17:50 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:17:50,147 - WARNING - Could not retrieve variants from source file in region 2:166535672-166536073. Error was invalid region `2:166535673-166536073`
[2016-04-15T03:17Z] 2016-04-14 20:17:50 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:17:50,588 - WARNING - Could not retrieve variants from source file in region 2:170218636-170219037. Error was invalid region `2:170218637-170219037`
[2016-04-15T03:17Z] 2016-04-14 20:17:50 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:17:50,733 - WARNING - Could not retrieve variants from source file in region 2:171822255-171822656. Error was invalid region `2:171822256-171822656`
[2016-04-15T03:17Z] 2016-04-14 20:17:50 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:17:50,793 - WARNING - Could not retrieve variants from source file in region 2:172966039-172966440. Error was invalid region `2:172966040-172966440`
[2016-04-15T03:17Z] 2016-04-14 20:17:50 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:17:50,962 - WARNING - Could not retrieve variants from source file in region 2:167098947-167099348. Error was invalid region `2:167098948-167099348`
[2016-04-15T03:17Z] 2016-04-14 20:17:51 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:17:51,018 - WARNING - Could not retrieve variants from source file in region 2:170605770-170606171. Error was invalid region `2:170605771-170606171`
[2016-04-15T03:17Z] 2016-04-14 20:17:51 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:17:51,361 - WARNING - Could not retrieve variants from source file in region 2:169747005-169789206. Error was invalid region `2:169747006-169789206`
[2016-04-15T03:17Z] 2016-04-14 20:17:51 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:17:51,558 - WARNING - Could not retrieve variants from source file in region 2:171225630-171261010. Error was invalid region `2:171225631-171261010`
[2016-04-15T03:17Z] 2016-04-14 20:17:51 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:17:51,947 - WARNING - Could not retrieve variants from source file in region 2:163217601-163218002. Error was invalid region `2:163217602-163218002`
[2016-04-15T03:17Z] 2016-04-14 20:17:52 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:17:52,200 - WARNING - Could not retrieve variants from source file in region 2:163123840-163136695. Error was invalid region `2:163123841-163136695`
[2016-04-15T03:17Z] 2016-04-14 20:17:52 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:17:52,536 - WARNING - Could not retrieve variants from source file in region 2:171070701-171074077. Error was invalid region `2:171070702-171074077`
[2016-04-15T03:17Z] 2016-04-14 20:17:57 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:17:57,267 - WARNING - Could not retrieve variants from source file in region 2:170402819-170411883. Error was invalid region `2:170402820-170411883`
[2016-04-15T03:17Z] 2016-04-14 20:17:57 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:17:57,464 - WARNING - Could not retrieve variants from source file in region 2:173686452-173686853. Error was invalid region `2:173686453-173686853`
[2016-04-15T03:17Z] 2016-04-14 20:17:57 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:17:57,585 - WARNING - Could not retrieve variants from source file in region 2:166535672-166536073. Error was invalid region `2:166535673-166536073`
[2016-04-15T03:17Z] 2016-04-14 20:17:58 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:17:58,395 - WARNING - Could not retrieve variants from source file in region 2:170218636-170219037. Error was invalid region `2:170218637-170219037`
[2016-04-15T03:17Z] 2016-04-14 20:17:58 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:17:58,409 - WARNING - Could not retrieve variants from source file in region 2:171822255-171822656. Error was invalid region `2:171822256-171822656`
[2016-04-15T03:17Z] 2016-04-14 20:17:58 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:17:58,791 - WARNING - Could not retrieve variants from source file in region 2:170605770-170606171. Error was invalid region `2:170605771-170606171`
[2016-04-15T03:17Z] 2016-04-14 20:17:58 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:17:58,792 - WARNING - Could not retrieve variants from source file in region 2:167098947-167099348. Error was invalid region `2:167098948-167099348`
[2016-04-15T03:17Z] 2016-04-14 20:17:59 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:17:59,459 - WARNING - Could not retrieve variants from source file in region 2:172966039-172966440. Error was invalid region `2:172966040-172966440`
[2016-04-15T03:17Z] 2016-04-14 20:17:59 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:17:59,802 - WARNING - Could not retrieve variants from source file in region 2:171070701-171074077. Error was invalid region `2:171070702-171074077`
[2016-04-15T03:18Z] 2016-04-14 20:18:03 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:18:03,405 - WARNING - Could not retrieve variants from source file in region 2:173686452-173686853. Error was invalid region `2:173686453-173686853`
[2016-04-15T03:18Z] 2016-04-14 20:18:06 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:18:06,652 - WARNING - Could not retrieve variants from source file in region 2:172966039-172966440. Error was invalid region `2:172966040-172966440`
[2016-04-15T03:18Z] 2016-04-14 20:18:14 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:18:14,875 - WARNING - Could not retrieve variants from source file in region 2:171678414-171678815. Error was invalid region `2:171678415-171678815`
[2016-04-15T03:18Z] 2016-04-14 20:18:15 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:18:15,932 - WARNING - Could not retrieve variants from source file in region 2:162929768-162930915. Error was invalid region `2:162929769-162930915`
[2016-04-15T03:18Z] 2016-04-14 20:18:16 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:18:16,744 - WARNING - Could not retrieve variants from source file in region 2:170917437-170917838. Error was invalid region `2:170917438-170917838`
[2016-04-15T03:18Z] 2016-04-14 20:18:16 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:18:16,878 - WARNING - Could not retrieve variants from source file in region 2:169996840-170053695. Error was invalid region `2:169996841-170053695`
[2016-04-15T03:18Z] 2016-04-14 20:18:17 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:18:17,954 - WARNING - Could not retrieve variants from source file in region 2:166892577-166903635. Error was invalid region `2:166892578-166903635`
[2016-04-15T03:18Z] 2016-04-14 20:18:18 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:18:18,097 - WARNING - Could not retrieve variants from source file in region 2:160802433-160808265. Error was invalid region `2:160802434-160808265`
[2016-04-15T03:18Z] 2016-04-14 20:18:18 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:18:18,162 - WARNING - Could not retrieve variants from source file in region 2:160182091-160182492. Error was invalid region `2:160182092-160182492`
[2016-04-15T03:18Z] 2016-04-14 20:18:18 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:18:18,715 - WARNING - Could not retrieve variants from source file in region 2:169707217-169721571. Error was invalid region `2:169707218-169721571`
[2016-04-15T03:18Z] 2016-04-14 20:18:19 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:18:19,078 - WARNING - Could not retrieve variants from source file in region 2:169019955-169020369. Error was invalid region `2:169019956-169020369`
[2016-04-15T03:18Z] 2016-04-14 20:18:19 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:18:19,426 - WARNING - Could not retrieve variants from source file in region 2:165987561-166003669. Error was invalid region `2:165987562-166003669`
[2016-04-15T03:18Z] 2016-04-14 20:18:19 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:18:19,426 - WARNING - Could not retrieve variants from source file in region 2:170762355-170762756. Error was invalid region `2:170762356-170762756`
[2016-04-15T03:18Z] 2016-04-14 20:18:20 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:18:20,017 - WARNING - Could not retrieve variants from source file in region 2:171678414-171678815. Error was invalid region `2:171678415-171678815`
[2016-04-15T03:18Z] 2016-04-14 20:18:21 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:18:21,848 - WARNING - Could not retrieve variants from source file in region 2:172725090-172725491. Error was invalid region `2:172725091-172725491`
[2016-04-15T03:18Z] 2016-04-14 20:18:23 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:18:23,190 - WARNING - Could not retrieve variants from source file in region 2:169996840-170053695. Error was invalid region `2:169996841-170053695`
[2016-04-15T03:18Z] 2016-04-14 20:18:25 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:18:25,951 - WARNING - Could not retrieve variants from source file in region 2:173450863-173451264. Error was invalid region `2:173450864-173451264`
[2016-04-15T03:18Z] 2016-04-14 20:18:26 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:18:26,133 - WARNING - Could not retrieve variants from source file in region 2:171678414-171678815. Error was invalid region `2:171678415-171678815`
[2016-04-15T03:18Z] 2016-04-14 20:18:26 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:18:26,453 - WARNING - Could not retrieve variants from source file in region 2:162929768-162930915. Error was invalid region `2:162929769-162930915`
[2016-04-15T03:18Z] 2016-04-14 20:18:27 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:18:27,053 - WARNING - Could not retrieve variants from source file in region 2:172725090-172725491. Error was invalid region `2:172725091-172725491`
[2016-04-15T03:18Z] 2016-04-14 20:18:27 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:18:27,128 - WARNING - Could not retrieve variants from source file in region 2:170917437-170917838. Error was invalid region `2:170917438-170917838`
[2016-04-15T03:18Z] 2016-04-14 20:18:27 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:18:27,880 - WARNING - Could not retrieve variants from source file in region 2:169996840-170053695. Error was invalid region `2:169996841-170053695`
[2016-04-15T03:18Z] 2016-04-14 20:18:28 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:18:28,589 - WARNING - Could not retrieve variants from source file in region 2:160802433-160808265. Error was invalid region `2:160802434-160808265`
[2016-04-15T03:18Z] 2016-04-14 20:18:30 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:18:30,725 - WARNING - Could not retrieve variants from source file in region 2:160182091-160182492. Error was invalid region `2:160182092-160182492`
[2016-04-15T03:18Z] 2016-04-14 20:18:31 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:18:31,062 - WARNING - Could not retrieve variants from source file in region 2:170762355-170762756. Error was invalid region `2:170762356-170762756`
[2016-04-15T03:18Z] 2016-04-14 20:18:31 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:18:31,899 - WARNING - Could not retrieve variants from source file in region 2:169707217-169721571. Error was invalid region `2:169707218-169721571`
[2016-04-15T03:18Z] 2016-04-14 20:18:31 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:18:31,966 - WARNING - Could not retrieve variants from source file in region 2:173450863-173451264. Error was invalid region `2:173450864-173451264`
[2016-04-15T03:18Z] 2016-04-14 20:18:33 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:18:33,068 - WARNING - Could not retrieve variants from source file in region 2:172725090-172725491. Error was invalid region `2:172725091-172725491`
[2016-04-15T03:18Z] 2016-04-14 20:18:41 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:18:41,553 - WARNING - Could not retrieve variants from source file in region 2:160742829-160743230. Error was invalid region `2:160742830-160743230`
[2016-04-15T03:18Z] 2016-04-14 20:18:41 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:18:41,826 - WARNING - Could not retrieve variants from source file in region 2:171572081-171573375. Error was invalid region `2:171572082-171573375`
[2016-04-15T03:18Z] 2016-04-14 20:18:43 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:18:43,481 - WARNING - Could not retrieve variants from source file in region 2:160710711-160711235. Error was invalid region `2:160710712-160711235`
[2016-04-15T03:18Z] 2016-04-14 20:18:45 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:18:45,722 - WARNING - Could not retrieve variants from source file in region 2:160084262-160086921. Error was invalid region `2:160084263-160086921`
[2016-04-15T03:18Z] 2016-04-14 20:18:45 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:18:45,735 - WARNING - Could not retrieve variants from source file in region 2:168931425-168931826. Error was invalid region `2:168931426-168931826`
[2016-04-15T03:18Z] 2016-04-14 20:18:46 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:18:46,419 - WARNING - Could not retrieve variants from source file in region 2:169680940-169681341. Error was invalid region `2:169680941-169681341`
[2016-04-15T03:18Z] 2016-04-14 20:18:46 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:18:46,492 - WARNING - Could not retrieve variants from source file in region 2:165476042-165476443. Error was invalid region `2:165476043-165476443`
[2016-04-15T03:18Z] 2016-04-14 20:18:47 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:18:47,242 - WARNING - Could not retrieve variants from source file in region 2:169951962-169952423. Error was invalid region `2:169951963-169952423`
[2016-04-15T03:18Z] 2016-04-14 20:18:47 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:18:47,442 - WARNING - Could not retrieve variants from source file in region 2:172411062-172411463. Error was invalid region `2:172411063-172411463`
[2016-04-15T03:18Z] 2016-04-14 20:18:47 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:18:47,998 - WARNING - Could not retrieve variants from source file in region 2:166848156-166848557. Error was invalid region `2:166848157-166848557`
[2016-04-15T03:18Z] 2016-04-14 20:18:50 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:18:50,092 - WARNING - Could not retrieve variants from source file in region 2:160112670-160136527. Error was invalid region `2:160112671-160136527`
[2016-04-15T03:18Z] 2016-04-14 20:18:50 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:18:50,810 - WARNING - Could not retrieve variants from source file in region 2:172378678-172379083. Error was invalid region `2:172378679-172379083`
[2016-04-15T03:18Z] 2016-04-14 20:18:51 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:18:51,545 - WARNING - Could not retrieve variants from source file in region 2:165476042-165476443. Error was invalid region `2:165476043-165476443`
[2016-04-15T03:18Z] 2016-04-14 20:18:53 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:18:53,059 - WARNING - Could not retrieve variants from source file in region 2:166848156-166848557. Error was invalid region `2:166848157-166848557`
[2016-04-15T03:18Z] 2016-04-14 20:18:55 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:18:55,586 - WARNING - Could not retrieve variants from source file in region 2:172378678-172379083. Error was invalid region `2:172378679-172379083`
[2016-04-15T03:18Z] 2016-04-14 20:18:55 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:18:55,772 - WARNING - Could not retrieve variants from source file in region 2:169680940-169681341. Error was invalid region `2:169680941-169681341`
[2016-04-15T03:18Z] 2016-04-14 20:18:56 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:18:56,171 - WARNING - Could not retrieve variants from source file in region 2:165476042-165476443. Error was invalid region `2:165476043-165476443`
[2016-04-15T03:18Z] 2016-04-14 20:18:57 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:18:57,799 - WARNING - Could not retrieve variants from source file in region 2:172411062-172411463. Error was invalid region `2:172411063-172411463`
[2016-04-15T03:19Z] 2016-04-14 20:19:05 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:19:05,118 - WARNING - Could not retrieve variants from source file in region 2:168099460-168099861. Error was invalid region `2:168099461-168099861`
[2016-04-15T03:19Z] 2016-04-14 20:19:06 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:19:06,426 - WARNING - Could not retrieve variants from source file in region 2:167313240-167334275. Error was invalid region `2:167313241-167334275`
[2016-04-15T03:19Z] 2016-04-14 20:19:06 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:19:06,653 - WARNING - Could not retrieve variants from source file in region 2:172330182-172330583. Error was invalid region `2:172330183-172330583`
[2016-04-15T03:19Z] 2016-04-14 20:19:07 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:19:07,545 - WARNING - Could not retrieve variants from source file in region 2:165424626-165425027. Error was invalid region `2:165424627-165425027`
[2016-04-15T03:19Z] 2016-04-14 20:19:07 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:19:07,786 - WARNING - Could not retrieve variants from source file in region 2:160019652-160035397. Error was invalid region `2:160019653-160035397`
[2016-04-15T03:19Z] 2016-04-14 20:19:07 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:19:07,821 - WARNING - Could not retrieve variants from source file in region 2:172216758-172217159. Error was invalid region `2:172216759-172217159`
[2016-04-15T03:19Z] 2016-04-14 20:19:10 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:19:10,494 - WARNING - Could not retrieve variants from source file in region 2:159517660-159518061. Error was invalid region `2:159517661-159518061`
[2016-04-15T03:19Z] 2016-04-14 20:19:10 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:19:10,684 - WARNING - Could not retrieve variants from source file in region 2:172291405-172291806. Error was invalid region `2:172291406-172291806`
[2016-04-15T03:19Z] 2016-04-14 20:19:11 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:19:11,307 - WARNING - Could not retrieve variants from source file in region 2:165424626-165425027. Error was invalid region `2:165424627-165425027`
[2016-04-15T03:19Z] 2016-04-14 20:19:11 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:19:11,758 - WARNING - Could not retrieve variants from source file in region 2:160019652-160035397. Error was invalid region `2:160019653-160035397`
[2016-04-15T03:19Z] 2016-04-14 20:19:14 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:19:14,961 - WARNING - Could not retrieve variants from source file in region 2:165424626-165425027. Error was invalid region `2:165424627-165425027`
[2016-04-15T03:19Z] 2016-04-14 20:19:15 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:19:15,337 - WARNING - Could not retrieve variants from source file in region 2:172216758-172217159. Error was invalid region `2:172216759-172217159`
[2016-04-15T03:19Z] 2016-04-14 20:19:15 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:19:15,350 - WARNING - Could not retrieve variants from source file in region 2:160019652-160035397. Error was invalid region `2:160019653-160035397`
[2016-04-15T03:19Z] 2016-04-14 20:19:17 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:19:17,275 - WARNING - Could not retrieve variants from source file in region 2:159517660-159518061. Error was invalid region `2:159517661-159518061`
[2016-04-15T03:19Z] 2016-04-14 20:19:20 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:19:20,228 - WARNING - Could not retrieve variants from source file in region 2:172180560-172188558. Error was invalid region `2:172180561-172188558`
[2016-04-15T03:19Z] 2016-04-14 20:19:21 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:19:21,798 - WARNING - Could not retrieve variants from source file in region 2:172180560-172188558. Error was invalid region `2:172180561-172188558`
[2016-04-15T03:19Z] 2016-04-14 20:19:23 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:19:23,792 - WARNING - Could not retrieve variants from source file in region 2:159477656-159478057. Error was invalid region `2:159477657-159478057`
[2016-04-15T03:19Z] ['bcbio-variation-recall', 'square', '-Xms750m', '-Xmx7280m', '-XX:+UseSerialGC', '-c', 16, '-r', u'2:174777798-190306304', '--caller', 'platypus', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/2/Batch1-2_174777797_190306304.vcf.gz', '/mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/2/Batch1-2_174777797_190306304.vcf-inputs.txt'] in region: 2:174777798-190306304
[2016-04-15T03:19Z] 2016-04-14 20:19:39 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:19:39,446 - WARNING - Could not retrieve variants from source file in region 2:188250090-188250491. Error was invalid region `2:188250091-188250491`
[2016-04-15T03:19Z] 2016-04-14 20:19:39 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:19:39,880 - WARNING - Could not retrieve variants from source file in region 2:187558749-187559237. Error was invalid region `2:187558750-187559237`
[2016-04-15T03:19Z] 2016-04-14 20:19:40 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:19:40,946 - WARNING - Could not retrieve variants from source file in region 2:178753196-178753597. Error was invalid region `2:178753197-178753597`
[2016-04-15T03:19Z] 2016-04-14 20:19:41 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:19:41,373 - WARNING - Could not retrieve variants from source file in region 2:178096195-178096596. Error was invalid region `2:178096196-178096596`
[2016-04-15T03:19Z] 2016-04-14 20:19:41 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:19:41,526 - WARNING - Could not retrieve variants from source file in region 2:189974747-189975148. Error was invalid region `2:189974748-189975148`
[2016-04-15T03:19Z] 2016-04-14 20:19:41 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:19:41,962 - WARNING - Could not retrieve variants from source file in region 2:175711731-175712132. Error was invalid region `2:175711732-175712132`
[2016-04-15T03:19Z] 2016-04-14 20:19:42 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:19:42,111 - WARNING - Could not retrieve variants from source file in region 2:180809969-180810454. Error was invalid region `2:180809970-180810454`
[2016-04-15T03:19Z] 2016-04-14 20:19:42 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:19:42,119 - WARNING - Could not retrieve variants from source file in region 2:182521367-182543645. Error was invalid region `2:182521368-182543645`
[2016-04-15T03:19Z] 2016-04-14 20:19:42 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:19:42,658 - WARNING - Could not retrieve variants from source file in region 2:179979719-179980120. Error was invalid region `2:179979720-179980120`
[2016-04-15T03:19Z] 2016-04-14 20:19:42 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:19:42,709 - WARNING - Could not retrieve variants from source file in region 2:178481607-178494363. Error was invalid region `2:178481608-178494363`
[2016-04-15T03:19Z] 2016-04-14 20:19:42 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:19:42,735 - WARNING - Could not retrieve variants from source file in region 2:182363402-182404041. Error was invalid region `2:182363403-182404041`
[2016-04-15T03:19Z] 2016-04-14 20:19:42 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:19:42,772 - WARNING - Could not retrieve variants from source file in region 2:186625559-186628133. Error was invalid region `2:186625560-186628133`
[2016-04-15T03:19Z] 2016-04-14 20:19:44 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:19:44,688 - WARNING - Could not retrieve variants from source file in region 2:188250090-188250491. Error was invalid region `2:188250091-188250491`
[2016-04-15T03:19Z] 2016-04-14 20:19:48 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:19:48,866 - WARNING - Could not retrieve variants from source file in region 2:188343286-188343687. Error was invalid region `2:188343287-188343687`
[2016-04-15T03:19Z] 2016-04-14 20:19:50 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:19:50,323 - WARNING - Could not retrieve variants from source file in region 2:180809969-180810454. Error was invalid region `2:180809970-180810454`
[2016-04-15T03:19Z] 2016-04-14 20:19:50 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:19:50,359 - WARNING - Could not retrieve variants from source file in region 2:189974747-189975148. Error was invalid region `2:189974748-189975148`
[2016-04-15T03:19Z] 2016-04-14 20:19:50 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:19:50,865 - WARNING - Could not retrieve variants from source file in region 2:183584544-183627694. Error was invalid region `2:183584545-183627694`
[2016-04-15T03:19Z] 2016-04-14 20:19:50 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:19:50,981 - WARNING - Could not retrieve variants from source file in region 2:178481607-178494363. Error was invalid region `2:178481608-178494363`
[2016-04-15T03:19Z] 2016-04-14 20:19:51 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:19:51,568 - WARNING - Could not retrieve variants from source file in region 2:182363402-182404041. Error was invalid region `2:182363403-182404041`
[2016-04-15T03:19Z] 2016-04-14 20:19:51 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:19:51,869 - WARNING - Could not retrieve variants from source file in region 2:187558749-187559237. Error was invalid region `2:187558750-187559237`
[2016-04-15T03:19Z] 2016-04-14 20:19:52 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:19:52,091 - WARNING - Could not retrieve variants from source file in region 2:175711731-175712132. Error was invalid region `2:175711732-175712132`
[2016-04-15T03:19Z] 2016-04-14 20:19:52 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:19:52,315 - WARNING - Could not retrieve variants from source file in region 2:186625559-186628133. Error was invalid region `2:186625560-186628133`
[2016-04-15T03:19Z] 2016-04-14 20:19:52 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:19:52,590 - WARNING - Could not retrieve variants from source file in region 2:179979719-179980120. Error was invalid region `2:179979720-179980120`
[2016-04-15T03:19Z] 2016-04-14 20:19:52 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:19:52,711 - WARNING - Could not retrieve variants from source file in region 2:188250090-188250491. Error was invalid region `2:188250091-188250491`
[2016-04-15T03:19Z] 2016-04-14 20:19:54 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:19:54,576 - WARNING - Could not retrieve variants from source file in region 2:178753196-178753597. Error was invalid region `2:178753197-178753597`
[2016-04-15T03:19Z] 2016-04-14 20:19:54 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:19:54,741 - WARNING - Could not retrieve variants from source file in region 2:188343286-188343687. Error was invalid region `2:188343287-188343687`
[2016-04-15T03:19Z] 2016-04-14 20:19:55 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:19:55,301 - WARNING - Could not retrieve variants from source file in region 2:178096195-178096596. Error was invalid region `2:178096196-178096596`
[2016-04-15T03:19Z] 2016-04-14 20:19:56 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:19:56,552 - WARNING - Could not retrieve variants from source file in region 2:189974747-189975148. Error was invalid region `2:189974748-189975148`
[2016-04-15T03:19Z] 2016-04-14 20:19:56 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:19:56,563 - WARNING - Could not retrieve variants from source file in region 2:180809969-180810454. Error was invalid region `2:180809970-180810454`
[2016-04-15T03:19Z] 2016-04-14 20:19:57 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:19:57,472 - WARNING - Could not retrieve variants from source file in region 2:182363402-182404041. Error was invalid region `2:182363403-182404041`
[2016-04-15T03:19Z] 2016-04-14 20:19:58 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:19:58,398 - WARNING - Could not retrieve variants from source file in region 2:178481607-178494363. Error was invalid region `2:178481608-178494363`
[2016-04-15T03:19Z] 2016-04-14 20:19:58 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:19:58,460 - WARNING - Could not retrieve variants from source file in region 2:183584544-183627694. Error was invalid region `2:183584545-183627694`
[2016-04-15T03:19Z] 2016-04-14 20:19:59 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:19:59,015 - WARNING - Could not retrieve variants from source file in region 2:175711731-175712132. Error was invalid region `2:175711732-175712132`
[2016-04-15T03:19Z] 2016-04-14 20:19:59 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:19:59,143 - WARNING - Could not retrieve variants from source file in region 2:179979719-179980120. Error was invalid region `2:179979720-179980120`
[2016-04-15T03:19Z] 2016-04-14 20:19:59 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:19:59,242 - WARNING - Could not retrieve variants from source file in region 2:186625559-186628133. Error was invalid region `2:186625560-186628133`
[2016-04-15T03:19Z] 2016-04-14 20:19:59 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:19:59,955 - WARNING - Could not retrieve variants from source file in region 2:182521367-182543645. Error was invalid region `2:182521368-182543645`
[2016-04-15T03:20Z] 2016-04-14 20:20:06 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:20:06,747 - WARNING - Could not retrieve variants from source file in region 2:187532206-187532607. Error was invalid region `2:187532207-187532607`
[2016-04-15T03:20Z] 2016-04-14 20:20:09 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:20:09,961 - WARNING - Could not retrieve variants from source file in region 2:187698540-187698941. Error was invalid region `2:187698541-187698941`
[2016-04-15T03:20Z] 2016-04-14 20:20:10 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:20:10,979 - WARNING - Could not retrieve variants from source file in region 2:178682392-178682793. Error was invalid region `2:178682393-178682793`
[2016-04-15T03:20Z] 2016-04-14 20:20:11 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:20:11,938 - WARNING - Could not retrieve variants from source file in region 2:180427079-180427480. Error was invalid region `2:180427080-180427480`
[2016-04-15T03:20Z] 2016-04-14 20:20:12 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:20:12,545 - WARNING - Could not retrieve variants from source file in region 2:187532206-187532607. Error was invalid region `2:187532207-187532607`
[2016-04-15T03:20Z] 2016-04-14 20:20:12 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:20:12,671 - WARNING - Could not retrieve variants from source file in region 2:189907726-189933021. Error was invalid region `2:189907727-189933021`
[2016-04-15T03:20Z] 2016-04-14 20:20:13 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:20:13,327 - WARNING - Could not retrieve variants from source file in region 2:180835581-180835982. Error was invalid region `2:180835582-180835982`
[2016-04-15T03:20Z] 2016-04-14 20:20:13 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:20:13,847 - WARNING - Could not retrieve variants from source file in region 2:178416931-178417415. Error was invalid region `2:178416932-178417415`
[2016-04-15T03:20Z] 2016-04-14 20:20:14 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:20:14,347 - WARNING - Could not retrieve variants from source file in region 2:187698540-187698941. Error was invalid region `2:187698541-187698941`
[2016-04-15T03:20Z] 2016-04-14 20:20:14 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:20:14,616 - WARNING - Could not retrieve variants from source file in region 2:183106547-183106948. Error was invalid region `2:183106548-183106948`
[2016-04-15T03:20Z] 2016-04-14 20:20:14 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:20:14,766 - WARNING - Could not retrieve variants from source file in region 2:175436729-175437130. Error was invalid region `2:175436730-175437130`
[2016-04-15T03:20Z] 2016-04-14 20:20:16 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:20:16,491 - WARNING - Could not retrieve variants from source file in region 2:185800694-185803554. Error was invalid region `2:185800695-185803554`
[2016-04-15T03:20Z] 2016-04-14 20:20:17 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:20:17,286 - WARNING - Could not retrieve variants from source file in region 2:179702057-179721222. Error was invalid region `2:179702058-179721222`
[2016-04-15T03:20Z] 2016-04-14 20:20:17 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:20:17,339 - WARNING - Could not retrieve variants from source file in region 2:177036543-177053944. Error was invalid region `2:177036544-177053944`
[2016-04-15T03:20Z] 2016-04-14 20:20:17 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:20:17,696 - WARNING - Could not retrieve variants from source file in region 2:187532206-187532607. Error was invalid region `2:187532207-187532607`
[2016-04-15T03:20Z] 2016-04-14 20:20:17 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:20:17,773 - WARNING - Could not retrieve variants from source file in region 2:189907726-189933021. Error was invalid region `2:189907727-189933021`
[2016-04-15T03:20Z] 2016-04-14 20:20:18 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:20:18,129 - WARNING - Could not retrieve variants from source file in region 2:180835581-180835982. Error was invalid region `2:180835582-180835982`
[2016-04-15T03:20Z] 2016-04-14 20:20:18 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:20:18,738 - WARNING - Could not retrieve variants from source file in region 2:179496922-179497323. Error was invalid region `2:179496923-179497323`
[2016-04-15T03:20Z] 2016-04-14 20:20:18 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:20:18,741 - WARNING - Could not retrieve variants from source file in region 2:178416931-178417415. Error was invalid region `2:178416932-178417415`
[2016-04-15T03:20Z] 2016-04-14 20:20:19 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:20:19,189 - WARNING - Could not retrieve variants from source file in region 2:187698540-187698941. Error was invalid region `2:187698541-187698941`
[2016-04-15T03:20Z] 2016-04-14 20:20:19 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:20:19,243 - WARNING - Could not retrieve variants from source file in region 2:183106547-183106948. Error was invalid region `2:183106548-183106948`
[2016-04-15T03:20Z] 2016-04-14 20:20:19 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:20:19,518 - WARNING - Could not retrieve variants from source file in region 2:175436729-175437130. Error was invalid region `2:175436730-175437130`
[2016-04-15T03:20Z] 2016-04-14 20:20:20 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:20:20,148 - WARNING - Could not retrieve variants from source file in region 2:178682392-178682793. Error was invalid region `2:178682393-178682793`
[2016-04-15T03:20Z] 2016-04-14 20:20:20 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:20:20,790 - WARNING - Could not retrieve variants from source file in region 2:185800694-185803554. Error was invalid region `2:185800695-185803554`
[2016-04-15T03:20Z] 2016-04-14 20:20:22 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:20:22,174 - WARNING - Could not retrieve variants from source file in region 2:180427079-180427480. Error was invalid region `2:180427080-180427480`
[2016-04-15T03:20Z] 2016-04-14 20:20:23 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:20:23,013 - WARNING - Could not retrieve variants from source file in region 2:189907726-189933021. Error was invalid region `2:189907727-189933021`
[2016-04-15T03:20Z] 2016-04-14 20:20:23 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:20:23,377 - WARNING - Could not retrieve variants from source file in region 2:180835581-180835982. Error was invalid region `2:180835582-180835982`
[2016-04-15T03:20Z] 2016-04-14 20:20:24 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:20:24,021 - WARNING - Could not retrieve variants from source file in region 2:179496922-179497323. Error was invalid region `2:179496923-179497323`
[2016-04-15T03:20Z] 2016-04-14 20:20:24 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:20:24,181 - WARNING - Could not retrieve variants from source file in region 2:178416931-178417415. Error was invalid region `2:178416932-178417415`
[2016-04-15T03:20Z] 2016-04-14 20:20:24 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:20:24,375 - WARNING - Could not retrieve variants from source file in region 2:183106547-183106948. Error was invalid region `2:183106548-183106948`
[2016-04-15T03:20Z] 2016-04-14 20:20:24 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:20:24,422 - WARNING - Could not retrieve variants from source file in region 2:175436729-175437130. Error was invalid region `2:175436730-175437130`
[2016-04-15T03:20Z] 2016-04-14 20:20:25 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:20:25,381 - WARNING - Could not retrieve variants from source file in region 2:185800694-185803554. Error was invalid region `2:185800695-185803554`
[2016-04-15T03:20Z] 2016-04-14 20:20:33 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:20:33,107 - WARNING - Could not retrieve variants from source file in region 2:183799347-183799748. Error was invalid region `2:183799348-183799748`
[2016-04-15T03:20Z] 2016-04-14 20:20:35 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:20:35,165 - WARNING - Could not retrieve variants from source file in region 2:183799347-183799748. Error was invalid region `2:183799348-183799748`
[2016-04-15T03:20Z] 2016-04-14 20:20:35 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:20:35,324 - WARNING - Could not retrieve variants from source file in region 2:178565702-178566103. Error was invalid region `2:178565703-178566103`
[2016-04-15T03:20Z] 2016-04-14 20:20:35 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:20:35,993 - WARNING - Could not retrieve variants from source file in region 2:180047697-180048098. Error was invalid region `2:180047698-180048098`
[2016-04-15T03:20Z] 2016-04-14 20:20:37 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:20:37,396 - WARNING - Could not retrieve variants from source file in region 2:176944801-176988480. Error was invalid region `2:176944802-176988480`
[2016-04-15T03:20Z] 2016-04-14 20:20:37 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:20:37,617 - WARNING - Could not retrieve variants from source file in region 2:176794177-176794578. Error was invalid region `2:176794178-176794578`
[2016-04-15T03:20Z] 2016-04-14 20:20:39 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:20:39,392 - WARNING - Could not retrieve variants from source file in region 2:183799347-183799748. Error was invalid region `2:183799348-183799748`
[2016-04-15T03:20Z] 2016-04-14 20:20:40 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:20:40,711 - WARNING - Could not retrieve variants from source file in region 2:182780096-182793174. Error was invalid region `2:182780097-182793174`
[2016-04-15T03:20Z] 2016-04-14 20:20:40 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:20:40,727 - WARNING - Could not retrieve variants from source file in region 2:189861886-189875611. Error was invalid region `2:189861887-189875611`
[2016-04-15T03:20Z] 2016-04-14 20:20:41 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:20:41,143 - WARNING - Could not retrieve variants from source file in region 2:175289048-175301187. Error was invalid region `2:175289049-175301187`
[2016-04-15T03:20Z] 2016-04-14 20:20:41 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:20:41,172 - WARNING - Could not retrieve variants from source file in region 2:178332947-178333348. Error was invalid region `2:178332948-178333348`
[2016-04-15T03:20Z] 2016-04-14 20:20:42 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:20:42,209 - WARNING - Could not retrieve variants from source file in region 2:180047697-180048098. Error was invalid region `2:180047698-180048098`
[2016-04-15T03:20Z] 2016-04-14 20:20:43 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:20:43,436 - WARNING - Could not retrieve variants from source file in region 2:180047697-180048098. Error was invalid region `2:180047698-180048098`
[2016-04-15T03:20Z] 2016-04-14 20:20:43 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:20:43,794 - WARNING - Could not retrieve variants from source file in region 2:179358454-179358855. Error was invalid region `2:179358455-179358855`
[2016-04-15T03:20Z] 2016-04-14 20:20:46 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:20:46,479 - WARNING - Could not retrieve variants from source file in region 2:178565702-178566103. Error was invalid region `2:178565703-178566103`
[2016-04-15T03:20Z] 2016-04-14 20:20:48 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:20:48,790 - WARNING - Could not retrieve variants from source file in region 2:178332947-178333348. Error was invalid region `2:178332948-178333348`
[2016-04-15T03:20Z] 2016-04-14 20:20:48 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:20:48,791 - WARNING - Could not retrieve variants from source file in region 2:182780096-182793174. Error was invalid region `2:182780097-182793174`
[2016-04-15T03:20Z] 2016-04-14 20:20:49 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:20:49,161 - WARNING - Could not retrieve variants from source file in region 2:176944801-176988480. Error was invalid region `2:176944802-176988480`
[2016-04-15T03:20Z] 2016-04-14 20:20:53 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:20:53,501 - WARNING - Could not retrieve variants from source file in region 2:179203586-179203987. Error was invalid region `2:179203587-179203987`
[2016-04-15T03:20Z] 2016-04-14 20:20:54 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:20:54,409 - WARNING - Could not retrieve variants from source file in region 2:179203586-179203987. Error was invalid region `2:179203587-179203987`
[2016-04-15T03:20Z] 2016-04-14 20:20:54 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:20:54,492 - WARNING - Could not retrieve variants from source file in region 2:179203586-179203987. Error was invalid region `2:179203587-179203987`
[2016-04-15T03:20Z] 2016-04-14 20:20:58 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:20:58,364 - WARNING - Could not retrieve variants from source file in region 2:176042886-176043287. Error was invalid region `2:176042887-176043287`
[2016-04-15T03:20Z] 2016-04-14 20:20:58 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:20:58,400 - WARNING - Could not retrieve variants from source file in region 2:178936162-178936804. Error was invalid region `2:178936163-178936804`
[2016-04-15T03:20Z] 2016-04-14 20:20:58 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:20:58,698 - WARNING - Could not retrieve variants from source file in region 2:175869465-175869866. Error was invalid region `2:175869466-175869866`
[2016-04-15T03:20Z] 2016-04-14 20:20:58 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:20:58,703 - WARNING - Could not retrieve variants from source file in region 2:176042886-176043287. Error was invalid region `2:176042887-176043287`
[2016-04-15T03:20Z] 2016-04-14 20:20:59 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:20:59,422 - WARNING - Could not retrieve variants from source file in region 2:178936162-178936804. Error was invalid region `2:178936163-178936804`
[2016-04-15T03:20Z] 2016-04-14 20:20:59 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:20:59,571 - WARNING - Could not retrieve variants from source file in region 2:178936162-178936804. Error was invalid region `2:178936163-178936804`
[2016-04-15T03:20Z] 2016-04-14 20:20:59 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:20:59,791 - WARNING - Could not retrieve variants from source file in region 2:175869465-175869866. Error was invalid region `2:175869466-175869866`
[2016-04-15T03:21Z] 2016-04-14 20:21:02 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:21:02,632 - WARNING - Could not retrieve variants from source file in region 2:175201088-175201489. Error was invalid region `2:175201089-175201489`
[2016-04-15T03:21Z] 2016-04-14 20:21:03 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:21:03,003 - WARNING - Could not retrieve variants from source file in region 2:175201088-175201489. Error was invalid region `2:175201089-175201489`
[2016-04-15T03:21Z] 2016-04-14 20:21:03 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:21:03,147 - WARNING - Could not retrieve variants from source file in region 2:174946549-174946950. Error was invalid region `2:174946550-174946950`
[2016-04-15T03:21Z] 2016-04-14 20:21:03 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:21:03,444 - WARNING - Could not retrieve variants from source file in region 2:175201088-175201489. Error was invalid region `2:175201089-175201489`
[2016-04-15T03:21Z] ['bcbio-variation-recall', 'square', '-Xms750m', '-Xmx7280m', '-XX:+UseSerialGC', '-c', 16, '-r', u'2:190313105-205830046', '--caller', 'platypus', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/2/Batch1-2_190313104_205830046.vcf.gz', '/mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/2/Batch1-2_190313104_205830046.vcf-inputs.txt'] in region: 2:190313105-205830046
[2016-04-15T03:21Z] 2016-04-14 20:21:19 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:21:19,441 - WARNING - Could not retrieve variants from source file in region 2:203139633-203156126. Error was invalid region `2:203139634-203156126`
[2016-04-15T03:21Z] 2016-04-14 20:21:20 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:21:20,092 - WARNING - Could not retrieve variants from source file in region 2:191301157-191301558. Error was invalid region `2:191301158-191301558`
[2016-04-15T03:21Z] 2016-04-14 20:21:20 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:21:20,688 - WARNING - Could not retrieve variants from source file in region 2:197184110-197196202. Error was invalid region `2:197184111-197196202`
[2016-04-15T03:21Z] 2016-04-14 20:21:20 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:21:20,749 - WARNING - Could not retrieve variants from source file in region 2:192814418-192814819. Error was invalid region `2:192814419-192814819`
[2016-04-15T03:21Z] 2016-04-14 20:21:20 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:21:20,882 - WARNING - Could not retrieve variants from source file in region 2:202741045-202741459. Error was invalid region `2:202741046-202741459`
[2016-04-15T03:21Z] 2016-04-14 20:21:21 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:21:21,359 - WARNING - Could not retrieve variants from source file in region 2:204154341-204154742. Error was invalid region `2:204154342-204154742`
[2016-04-15T03:21Z] 2016-04-14 20:21:21 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:21:21,710 - WARNING - Could not retrieve variants from source file in region 2:202215281-202215682. Error was invalid region `2:202215282-202215682`
[2016-04-15T03:21Z] 2016-04-14 20:21:21 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:21:21,948 - WARNING - Could not retrieve variants from source file in region 2:196791065-196791466. Error was invalid region `2:196791066-196791466`
[2016-04-15T03:21Z] 2016-04-14 20:21:22 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:21:22,006 - WARNING - Could not retrieve variants from source file in region 2:205829780-205830181. Error was invalid region `2:205829781-205830181`
[2016-04-15T03:21Z] 2016-04-14 20:21:22 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:21:22,062 - WARNING - Could not retrieve variants from source file in region 2:204061850-204073625. Error was invalid region `2:204061851-204073625`
[2016-04-15T03:21Z] 2016-04-14 20:21:27 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:21:27,745 - WARNING - Could not retrieve variants from source file in region 2:203846606-203847007. Error was invalid region `2:203846607-203847007`
[2016-04-15T03:21Z] 2016-04-14 20:21:27 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:21:27,753 - WARNING - Could not retrieve variants from source file in region 2:191301157-191301558. Error was invalid region `2:191301158-191301558`
[2016-04-15T03:21Z] 2016-04-14 20:21:28 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:21:28,472 - WARNING - Could not retrieve variants from source file in region 2:202700188-202700589. Error was invalid region `2:202700189-202700589`
[2016-04-15T03:21Z] 2016-04-14 20:21:29 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:21:29,579 - WARNING - Could not retrieve variants from source file in region 2:197184110-197196202. Error was invalid region `2:197184111-197196202`
[2016-04-15T03:21Z] 2016-04-14 20:21:29 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:21:29,887 - WARNING - Could not retrieve variants from source file in region 2:201437117-201437524. Error was invalid region `2:201437118-201437524`
[2016-04-15T03:21Z] 2016-04-14 20:21:30 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:21:30,447 - WARNING - Could not retrieve variants from source file in region 2:202741045-202741459. Error was invalid region `2:202741046-202741459`
[2016-04-15T03:21Z] 2016-04-14 20:21:30 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:21:30,457 - WARNING - Could not retrieve variants from source file in region 2:203990578-203990979. Error was invalid region `2:203990579-203990979`
[2016-04-15T03:21Z] 2016-04-14 20:21:30 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:21:30,540 - WARNING - Could not retrieve variants from source file in region 2:192814418-192814819. Error was invalid region `2:192814419-192814819`
[2016-04-15T03:21Z] 2016-04-14 20:21:30 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:21:30,586 - WARNING - Could not retrieve variants from source file in region 2:204154341-204154742. Error was invalid region `2:204154342-204154742`
[2016-04-15T03:21Z] 2016-04-14 20:21:31 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:21:31,093 - WARNING - Could not retrieve variants from source file in region 2:198949818-198950430. Error was invalid region `2:198949819-198950430`
[2016-04-15T03:21Z] 2016-04-14 20:21:31 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:21:31,204 - WARNING - Could not retrieve variants from source file in region 2:196791065-196791466. Error was invalid region `2:196791066-196791466`
[2016-04-15T03:21Z] 2016-04-14 20:21:31 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:21:31,428 - WARNING - Could not retrieve variants from source file in region 2:202215281-202215682. Error was invalid region `2:202215282-202215682`
[2016-04-15T03:21Z] 2016-04-14 20:21:31 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:21:31,524 - WARNING - Could not retrieve variants from source file in region 2:205829780-205830181. Error was invalid region `2:205829781-205830181`
[2016-04-15T03:21Z] 2016-04-14 20:21:31 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:21:31,885 - WARNING - Could not retrieve variants from source file in region 2:203139633-203156126. Error was invalid region `2:203139634-203156126`
[2016-04-15T03:21Z] 2016-04-14 20:21:32 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:21:32,256 - WARNING - Could not retrieve variants from source file in region 2:203846606-203847007. Error was invalid region `2:203846607-203847007`
[2016-04-15T03:21Z] 2016-04-14 20:21:36 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:21:36,287 - WARNING - Could not retrieve variants from source file in region 2:201437117-201437524. Error was invalid region `2:201437118-201437524`
[2016-04-15T03:21Z] 2016-04-14 20:21:36 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:21:36,683 - WARNING - Could not retrieve variants from source file in region 2:197184110-197196202. Error was invalid region `2:197184111-197196202`
[2016-04-15T03:21Z] 2016-04-14 20:21:37 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:21:37,599 - WARNING - Could not retrieve variants from source file in region 2:202741045-202741459. Error was invalid region `2:202741046-202741459`
[2016-04-15T03:21Z] 2016-04-14 20:21:38 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:21:38,484 - WARNING - Could not retrieve variants from source file in region 2:192814418-192814819. Error was invalid region `2:192814419-192814819`
[2016-04-15T03:21Z] 2016-04-14 20:21:39 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:21:39,103 - WARNING - Could not retrieve variants from source file in region 2:204154341-204154742. Error was invalid region `2:204154342-204154742`
[2016-04-15T03:21Z] 2016-04-14 20:21:39 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:21:39,220 - WARNING - Could not retrieve variants from source file in region 2:196791065-196791466. Error was invalid region `2:196791066-196791466`
[2016-04-15T03:21Z] 2016-04-14 20:21:39 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:21:39,465 - WARNING - Could not retrieve variants from source file in region 2:203990578-203990979. Error was invalid region `2:203990579-203990979`
[2016-04-15T03:21Z] 2016-04-14 20:21:39 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:21:39,524 - WARNING - Could not retrieve variants from source file in region 2:202215281-202215682. Error was invalid region `2:202215282-202215682`
[2016-04-15T03:21Z] 2016-04-14 20:21:39 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:21:39,603 - WARNING - Could not retrieve variants from source file in region 2:205829780-205830181. Error was invalid region `2:205829781-205830181`
[2016-04-15T03:21Z] 2016-04-14 20:21:51 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:21:51,587 - WARNING - Could not retrieve variants from source file in region 2:202625404-202625805. Error was invalid region `2:202625405-202625805`
[2016-04-15T03:21Z] 2016-04-14 20:21:51 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:21:51,640 - WARNING - Could not retrieve variants from source file in region 2:191224770-191236091. Error was invalid region `2:191224771-191236091`
[2016-04-15T03:21Z] 2016-04-14 20:21:53 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:21:53,605 - WARNING - Could not retrieve variants from source file in region 2:197118518-197118919. Error was invalid region `2:197118519-197118919`
[2016-04-15T03:21Z] 2016-04-14 20:21:56 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:21:56,126 - WARNING - Could not retrieve variants from source file in region 2:203052736-203053137. Error was invalid region `2:203052737-203053137`
[2016-04-15T03:21Z] 2016-04-14 20:21:57 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:21:57,491 - WARNING - Could not retrieve variants from source file in region 2:203765545-203765946. Error was invalid region `2:203765546-203765946`
[2016-04-15T03:21Z] 2016-04-14 20:21:58 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:21:58,429 - WARNING - Could not retrieve variants from source file in region 2:202625404-202625805. Error was invalid region `2:202625405-202625805`
[2016-04-15T03:21Z] 2016-04-14 20:21:58 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:21:58,430 - WARNING - Could not retrieve variants from source file in region 2:204116479-204116880. Error was invalid region `2:204116480-204116880`
[2016-04-15T03:21Z] 2016-04-14 20:21:58 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:21:58,464 - WARNING - Could not retrieve variants from source file in region 2:190924866-190925267. Error was invalid region `2:190924867-190925267`
[2016-04-15T03:21Z] 2016-04-14 20:21:59 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:21:59,229 - WARNING - Could not retrieve variants from source file in region 2:202122784-202123185. Error was invalid region `2:202122785-202123185`
[2016-04-15T03:21Z] 2016-04-14 20:21:59 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:21:59,719 - WARNING - Could not retrieve variants from source file in region 2:204732503-204732904. Error was invalid region `2:204732504-204732904`
[2016-04-15T03:21Z] 2016-04-14 20:21:59 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:21:59,808 - WARNING - Could not retrieve variants from source file in region 2:198327103-198327504. Error was invalid region `2:198327104-198327504`
[2016-04-15T03:21Z] 2016-04-14 20:21:59 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:21:59,859 - WARNING - Could not retrieve variants from source file in region 2:197118518-197118919. Error was invalid region `2:197118519-197118919`
[2016-04-15T03:21Z] 2016-04-14 20:21:59 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:21:59,882 - WARNING - Could not retrieve variants from source file in region 2:197004228-197021562. Error was invalid region `2:197004229-197021562`
[2016-04-15T03:22Z] 2016-04-14 20:22:03 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:22:03,918 - WARNING - Could not retrieve variants from source file in region 2:203765545-203765946. Error was invalid region `2:203765546-203765946`
[2016-04-15T03:22Z] 2016-04-14 20:22:04 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:22:04,365 - WARNING - Could not retrieve variants from source file in region 2:196738154-196749694. Error was invalid region `2:196738155-196749694`
[2016-04-15T03:22Z] 2016-04-14 20:22:04 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:22:04,799 - WARNING - Could not retrieve variants from source file in region 2:198649694-198670061. Error was invalid region `2:198649695-198670061`
[2016-04-15T03:22Z] 2016-04-14 20:22:06 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:22:06,968 - WARNING - Could not retrieve variants from source file in region 2:191224770-191236091. Error was invalid region `2:191224771-191236091`
[2016-04-15T03:22Z] 2016-04-14 20:22:07 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:22:07,487 - WARNING - Could not retrieve variants from source file in region 2:201354724-201355296. Error was invalid region `2:201354725-201355296`
[2016-04-15T03:22Z] 2016-04-14 20:22:07 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:22:07,649 - WARNING - Could not retrieve variants from source file in region 2:204116479-204116880. Error was invalid region `2:204116480-204116880`
[2016-04-15T03:22Z] 2016-04-14 20:22:07 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:22:07,670 - WARNING - Could not retrieve variants from source file in region 2:202625404-202625805. Error was invalid region `2:202625405-202625805`
[2016-04-15T03:22Z] 2016-04-14 20:22:07 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:22:07,987 - WARNING - Could not retrieve variants from source file in region 2:202122784-202123185. Error was invalid region `2:202122785-202123185`
[2016-04-15T03:22Z] 2016-04-14 20:22:08 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:22:08,167 - WARNING - Could not retrieve variants from source file in region 2:197004228-197021562. Error was invalid region `2:197004229-197021562`
[2016-04-15T03:22Z] 2016-04-14 20:22:08 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:22:08,253 - WARNING - Could not retrieve variants from source file in region 2:197118518-197118919. Error was invalid region `2:197118519-197118919`
[2016-04-15T03:22Z] 2016-04-14 20:22:14 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:22:14,471 - WARNING - Could not retrieve variants from source file in region 2:190924866-190925267. Error was invalid region `2:190924867-190925267`
[2016-04-15T03:22Z] 2016-04-14 20:22:16 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:22:16,085 - WARNING - Could not retrieve variants from source file in region 2:204116479-204116880. Error was invalid region `2:204116480-204116880`
[2016-04-15T03:22Z] 2016-04-14 20:22:17 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:22:17,750 - WARNING - Could not retrieve variants from source file in region 2:197004228-197021562. Error was invalid region `2:197004229-197021562`
[2016-04-15T03:22Z] 2016-04-14 20:22:17 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:22:17,789 - WARNING - Could not retrieve variants from source file in region 2:202122784-202123185. Error was invalid region `2:202122785-202123185`
[2016-04-15T03:22Z] 2016-04-14 20:22:18 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:22:18,909 - WARNING - Could not retrieve variants from source file in region 2:204591302-204591703. Error was invalid region `2:204591303-204591703`
[2016-04-15T03:22Z] 2016-04-14 20:22:21 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:22:21,714 - WARNING - Could not retrieve variants from source file in region 2:203690176-203690577. Error was invalid region `2:203690177-203690577`
[2016-04-15T03:22Z] 2016-04-14 20:22:25 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:22:25,476 - WARNING - Could not retrieve variants from source file in region 2:201170803-201171661. Error was invalid region `2:201170804-201171661`
[2016-04-15T03:22Z] 2016-04-14 20:22:25 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:22:25,506 - WARNING - Could not retrieve variants from source file in region 2:198257584-198283495. Error was invalid region `2:198257585-198283495`
[2016-04-15T03:22Z] 2016-04-14 20:22:27 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:22:27,289 - WARNING - Could not retrieve variants from source file in region 2:203690176-203690577. Error was invalid region `2:203690177-203690577`
[2016-04-15T03:22Z] 2016-04-14 20:22:28 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:22:28,628 - WARNING - Could not retrieve variants from source file in region 2:196673322-196673723. Error was invalid region `2:196673323-196673723`
[2016-04-15T03:22Z] 2016-04-14 20:22:29 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:22:29,509 - WARNING - Could not retrieve variants from source file in region 2:196825191-196866610. Error was invalid region `2:196825192-196866610`
[2016-04-15T03:22Z] 2016-04-14 20:22:30 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:22:30,104 - WARNING - Could not retrieve variants from source file in region 2:198508740-198509141. Error was invalid region `2:198508741-198509141`
[2016-04-15T03:22Z] 2016-04-14 20:22:30 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:22:30,127 - WARNING - Could not retrieve variants from source file in region 2:192279116-192279517. Error was invalid region `2:192279117-192279517`
[2016-04-15T03:22Z] 2016-04-14 20:22:30 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:22:30,264 - WARNING - Could not retrieve variants from source file in region 2:190595047-190628066. Error was invalid region `2:190595048-190628066`
[2016-04-15T03:22Z] 2016-04-14 20:22:31 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:22:31,091 - WARNING - Could not retrieve variants from source file in region 2:191161411-191184714. Error was invalid region `2:191161412-191184714`
[2016-04-15T03:22Z] 2016-04-14 20:22:31 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:22:31,131 - WARNING - Could not retrieve variants from source file in region 2:204591302-204591703. Error was invalid region `2:204591303-204591703`
[2016-04-15T03:22Z] 2016-04-14 20:22:31 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:22:31,427 - WARNING - Could not retrieve variants from source file in region 2:201170803-201171661. Error was invalid region `2:201170804-201171661`
[2016-04-15T03:22Z] 2016-04-14 20:22:31 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:22:31,671 - WARNING - Could not retrieve variants from source file in region 2:198257584-198283495. Error was invalid region `2:198257585-198283495`
[2016-04-15T03:22Z] 2016-04-14 20:22:32 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:22:32,208 - WARNING - Could not retrieve variants from source file in region 2:203690176-203690577. Error was invalid region `2:203690177-203690577`
[2016-04-15T03:22Z] 2016-04-14 20:22:34 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:22:34,595 - WARNING - Could not retrieve variants from source file in region 2:196673322-196673723. Error was invalid region `2:196673323-196673723`
[2016-04-15T03:22Z] 2016-04-14 20:22:36 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:22:36,088 - WARNING - Could not retrieve variants from source file in region 2:198508740-198509141. Error was invalid region `2:198508741-198509141`
[2016-04-15T03:22Z] 2016-04-14 20:22:37 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:22:37,494 - WARNING - Could not retrieve variants from source file in region 2:190595047-190628066. Error was invalid region `2:190595048-190628066`
[2016-04-15T03:22Z] 2016-04-14 20:22:37 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:22:37,509 - WARNING - Could not retrieve variants from source file in region 2:192279116-192279517. Error was invalid region `2:192279117-192279517`
[2016-04-15T03:22Z] 2016-04-14 20:22:37 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:22:37,583 - WARNING - Could not retrieve variants from source file in region 2:191161411-191184714. Error was invalid region `2:191161412-191184714`
[2016-04-15T03:22Z] 2016-04-14 20:22:38 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:22:38,203 - WARNING - Could not retrieve variants from source file in region 2:201170803-201171661. Error was invalid region `2:201170804-201171661`
[2016-04-15T03:22Z] 2016-04-14 20:22:38 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:22:38,519 - WARNING - Could not retrieve variants from source file in region 2:198257584-198283495. Error was invalid region `2:198257585-198283495`
[2016-04-15T03:22Z] 2016-04-14 20:22:39 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:22:39,778 - WARNING - Could not retrieve variants from source file in region 2:200776142-200776543. Error was invalid region `2:200776143-200776543`
[2016-04-15T03:22Z] 2016-04-14 20:22:39 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:22:39,993 - WARNING - Could not retrieve variants from source file in region 2:204304003-204322488. Error was invalid region `2:204304004-204322488`
[2016-04-15T03:22Z] 2016-04-14 20:22:40 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:22:40,330 - WARNING - Could not retrieve variants from source file in region 2:196673322-196673723. Error was invalid region `2:196673323-196673723`
[2016-04-15T03:22Z] 2016-04-14 20:22:40 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:22:40,490 - WARNING - Could not retrieve variants from source file in region 2:202072947-202073348. Error was invalid region `2:202072948-202073348`
[2016-04-15T03:22Z] 2016-04-14 20:22:41 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:22:41,091 - WARNING - Could not retrieve variants from source file in region 2:198508740-198509141. Error was invalid region `2:198508741-198509141`
[2016-04-15T03:22Z] 2016-04-14 20:22:41 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:22:41,611 - WARNING - Could not retrieve variants from source file in region 2:204304003-204322488. Error was invalid region `2:204304004-204322488`
[2016-04-15T03:22Z] 2016-04-14 20:22:42 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:22:42,467 - WARNING - Could not retrieve variants from source file in region 2:192279116-192279517. Error was invalid region `2:192279117-192279517`
[2016-04-15T03:22Z] 2016-04-14 20:22:42 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:22:42,489 - WARNING - Could not retrieve variants from source file in region 2:190595047-190628066. Error was invalid region `2:190595048-190628066`
[2016-04-15T03:22Z] 2016-04-14 20:22:46 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:22:46,925 - WARNING - Could not retrieve variants from source file in region 2:200776142-200776543. Error was invalid region `2:200776143-200776543`
[2016-04-15T03:22Z] 2016-04-14 20:22:48 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:22:48,988 - WARNING - Could not retrieve variants from source file in region 2:202469150-202469551. Error was invalid region `2:202469151-202469551`
[2016-04-15T03:22Z] 2016-04-14 20:22:49 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:22:49,171 - WARNING - Could not retrieve variants from source file in region 2:203420988-203421389. Error was invalid region `2:203420989-203421389`
[2016-04-15T03:22Z] 2016-04-14 20:22:49 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:22:49,244 - WARNING - Could not retrieve variants from source file in region 2:196522075-196522476. Error was invalid region `2:196522076-196522476`
[2016-04-15T03:22Z] 2016-04-14 20:22:52 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:22:52,093 - WARNING - Could not retrieve variants from source file in region 2:196522075-196522476. Error was invalid region `2:196522076-196522476`
[2016-04-15T03:22Z] 2016-04-14 20:22:52 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:22:52,112 - WARNING - Could not retrieve variants from source file in region 2:191064542-191064943. Error was invalid region `2:191064543-191064943`
[2016-04-15T03:22Z] 2016-04-14 20:22:54 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:22:54,855 - WARNING - Could not retrieve variants from source file in region 2:203420988-203421389. Error was invalid region `2:203420989-203421389`
[2016-04-15T03:22Z] 2016-04-14 20:22:55 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:22:55,004 - WARNING - Could not retrieve variants from source file in region 2:202469150-202469551. Error was invalid region `2:202469151-202469551`
[2016-04-15T03:22Z] 2016-04-14 20:22:55 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:22:55,004 - WARNING - Could not retrieve variants from source file in region 2:196522075-196522476. Error was invalid region `2:196522076-196522476`
[2016-04-15T03:22Z] 2016-04-14 20:22:55 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:22:55,025 - WARNING - Could not retrieve variants from source file in region 2:202516474-202516965. Error was invalid region `2:202516475-202516965`
[2016-04-15T03:22Z] 2016-04-14 20:22:56 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:22:56,206 - WARNING - Could not retrieve variants from source file in region 2:202337519-202358139. Error was invalid region `2:202337520-202358139`
[2016-04-15T03:22Z] 2016-04-14 20:22:57 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:22:57,942 - WARNING - Could not retrieve variants from source file in region 2:190531215-190531616. Error was invalid region `2:190531216-190531616`
[2016-04-15T03:22Z] 2016-04-14 20:22:58 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:22:58,239 - WARNING - Could not retrieve variants from source file in region 2:191064542-191064943. Error was invalid region `2:191064543-191064943`
[2016-04-15T03:22Z] 2016-04-14 20:22:58 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:22:58,300 - WARNING - Could not retrieve variants from source file in region 2:192250515-192250916. Error was invalid region `2:192250516-192250916`
[2016-04-15T03:22Z] 2016-04-14 20:22:59 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:22:59,961 - WARNING - Could not retrieve variants from source file in region 2:202469150-202469551. Error was invalid region `2:202469151-202469551`
[2016-04-15T03:23Z] 2016-04-14 20:23:00 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:23:00,905 - WARNING - Could not retrieve variants from source file in region 2:202337519-202358139. Error was invalid region `2:202337520-202358139`
[2016-04-15T03:23Z] 2016-04-14 20:23:01 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:23:01,563 - WARNING - Could not retrieve variants from source file in region 2:198361807-198363694. Error was invalid region `2:198361808-198363694`
[2016-04-15T03:23Z] 2016-04-14 20:23:01 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:23:01,886 - WARNING - Could not retrieve variants from source file in region 2:202399293-202410490. Error was invalid region `2:202399294-202410490`
[2016-04-15T03:23Z] 2016-04-14 20:23:01 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:23:01,905 - WARNING - Could not retrieve variants from source file in region 2:190429966-190445685. Error was invalid region `2:190429967-190445685`
[2016-04-15T03:23Z] 2016-04-14 20:23:02 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:23:02,659 - WARNING - Could not retrieve variants from source file in region 2:190531215-190531616. Error was invalid region `2:190531216-190531616`
[2016-04-15T03:23Z] 2016-04-14 20:23:03 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:23:03,548 - WARNING - Could not retrieve variants from source file in region 2:192250515-192250916. Error was invalid region `2:192250516-192250916`
[2016-04-15T03:23Z] 2016-04-14 20:23:03 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:23:03,844 - WARNING - Could not retrieve variants from source file in region 2:202516474-202516965. Error was invalid region `2:202516475-202516965`
[2016-04-15T03:23Z] 2016-04-14 20:23:04 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:23:04,692 - WARNING - Could not retrieve variants from source file in region 2:202399293-202410490. Error was invalid region `2:202399294-202410490`
[2016-04-15T03:23Z] 2016-04-14 20:23:05 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:23:05,502 - WARNING - Could not retrieve variants from source file in region 2:202337519-202358139. Error was invalid region `2:202337520-202358139`
[2016-04-15T03:23Z] 2016-04-14 20:23:06 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:23:06,517 - WARNING - Could not retrieve variants from source file in region 2:202399293-202410490. Error was invalid region `2:202399294-202410490`
[2016-04-15T03:23Z] 2016-04-14 20:23:07 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:23:07,716 - WARNING - Could not retrieve variants from source file in region 2:190531215-190531616. Error was invalid region `2:190531216-190531616`
[2016-04-15T03:23Z] 2016-04-14 20:23:08 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:23:08,134 - WARNING - Could not retrieve variants from source file in region 2:190314594-190323720. Error was invalid region `2:190314595-190323720`
[2016-04-15T03:23Z] 2016-04-14 20:23:08 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:23:08,417 - WARNING - Could not retrieve variants from source file in region 2:192250515-192250916. Error was invalid region `2:192250516-192250916`
[2016-04-15T03:23Z] 2016-04-14 20:23:09 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:23:09,372 - WARNING - Could not retrieve variants from source file in region 2:192160628-192161065. Error was invalid region `2:192160629-192161065`
[2016-04-15T03:23Z] 2016-04-14 20:23:11 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:23:11,025 - WARNING - Could not retrieve variants from source file in region 2:190429966-190445685. Error was invalid region `2:190429967-190445685`
[2016-04-15T03:23Z] 2016-04-14 20:23:13 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:23:13,514 - WARNING - Could not retrieve variants from source file in region 2:192160628-192161065. Error was invalid region `2:192160629-192161065`
[2016-04-15T03:23Z] 2016-04-14 20:23:16 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:23:16,180 - WARNING - Could not retrieve variants from source file in region 2:192160628-192161065. Error was invalid region `2:192160629-192161065`
[2016-04-15T03:23Z] 2016-04-14 20:23:16 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:23:16,498 - WARNING - Could not retrieve variants from source file in region 2:191840141-191840543. Error was invalid region `2:191840142-191840543`
[2016-04-15T03:23Z] 2016-04-14 20:23:18 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:23:18,102 - WARNING - Could not retrieve variants from source file in region 2:191874456-191874857. Error was invalid region `2:191874457-191874857`
[2016-04-15T03:23Z] 2016-04-14 20:23:21 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:23:21,387 - WARNING - Could not retrieve variants from source file in region 2:191874456-191874857. Error was invalid region `2:191874457-191874857`
[2016-04-15T03:23Z] ['bcbio-variation-recall', 'square', '-Xms750m', '-Xmx7280m', '-XX:+UseSerialGC', '-c', 16, '-r', u'2:205912304-222290862', '--caller', 'platypus', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/2/Batch1-2_205912303_222290862.vcf.gz', '/mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/2/Batch1-2_205912303_222290862.vcf-inputs.txt'] in region: 2:205912304-222290862
[2016-04-15T03:23Z] 2016-04-14 20:23:38 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:23:38,604 - WARNING - Could not retrieve variants from source file in region 2:220462429-220505455. Error was invalid region `2:220462430-220505455`
[2016-04-15T03:23Z] 2016-04-14 20:23:38 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:23:38,918 - WARNING - Could not retrieve variants from source file in region 2:208810886-208811287. Error was invalid region `2:208810887-208811287`
[2016-04-15T03:23Z] 2016-04-14 20:23:39 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:23:39,004 - WARNING - Could not retrieve variants from source file in region 2:210654085-210654486. Error was invalid region `2:210654086-210654486`
[2016-04-15T03:23Z] 2016-04-14 20:23:39 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:23:39,390 - WARNING - Could not retrieve variants from source file in region 2:207006465-207008953. Error was invalid region `2:207006466-207008953`
[2016-04-15T03:23Z] 2016-04-14 20:23:39 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:23:39,953 - WARNING - Could not retrieve variants from source file in region 2:209357816-209358217. Error was invalid region `2:209357817-209358217`
[2016-04-15T03:23Z] 2016-04-14 20:23:40 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:23:40,541 - WARNING - Could not retrieve variants from source file in region 2:209184769-209215776. Error was invalid region `2:209184770-209215776`
[2016-04-15T03:23Z] 2016-04-14 20:23:41 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:23:41,127 - WARNING - Could not retrieve variants from source file in region 2:209036501-209036968. Error was invalid region `2:209036502-209036968`
[2016-04-15T03:23Z] 2016-04-14 20:23:41 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:23:41,177 - WARNING - Could not retrieve variants from source file in region 2:220197110-220197614. Error was invalid region `2:220197111-220197614`
[2016-04-15T03:23Z] 2016-04-14 20:23:41 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:23:41,183 - WARNING - Could not retrieve variants from source file in region 2:211540296-211540697. Error was invalid region `2:211540297-211540697`
[2016-04-15T03:23Z] 2016-04-14 20:23:41 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:23:41,573 - WARNING - Could not retrieve variants from source file in region 2:208986426-209010748. Error was invalid region `2:208986427-209010748`
[2016-04-15T03:23Z] 2016-04-14 20:23:45 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:23:45,984 - WARNING - Could not retrieve variants from source file in region 2:220462429-220505455. Error was invalid region `2:220462430-220505455`
[2016-04-15T03:23Z] 2016-04-14 20:23:47 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:23:47,067 - WARNING - Could not retrieve variants from source file in region 2:208810886-208811287. Error was invalid region `2:208810887-208811287`
[2016-04-15T03:23Z] 2016-04-14 20:23:48 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:23:48,331 - WARNING - Could not retrieve variants from source file in region 2:217315576-217315977. Error was invalid region `2:217315577-217315977`
[2016-04-15T03:23Z] 2016-04-14 20:23:48 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:23:48,995 - WARNING - Could not retrieve variants from source file in region 2:209357816-209358217. Error was invalid region `2:209357817-209358217`
[2016-04-15T03:23Z] 2016-04-14 20:23:49 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:23:49,057 - WARNING - Could not retrieve variants from source file in region 2:218745474-218751007. Error was invalid region `2:218745475-218751007`
[2016-04-15T03:23Z] 2016-04-14 20:23:49 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:23:49,614 - WARNING - Could not retrieve variants from source file in region 2:208986426-209010748. Error was invalid region `2:208986427-209010748`
[2016-04-15T03:23Z] 2016-04-14 20:23:50 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:23:50,073 - WARNING - Could not retrieve variants from source file in region 2:209036501-209036968. Error was invalid region `2:209036502-209036968`
[2016-04-15T03:23Z] 2016-04-14 20:23:50 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:23:50,392 - WARNING - Could not retrieve variants from source file in region 2:220283048-220286332. Error was invalid region `2:220283049-220286332`
[2016-04-15T03:23Z] 2016-04-14 20:23:50 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:23:50,442 - WARNING - Could not retrieve variants from source file in region 2:220197110-220197614. Error was invalid region `2:220197111-220197614`
[2016-04-15T03:23Z] 2016-04-14 20:23:50 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:23:50,556 - WARNING - Could not retrieve variants from source file in region 2:209184769-209215776. Error was invalid region `2:209184770-209215776`
[2016-04-15T03:23Z] 2016-04-14 20:23:51 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:23:51,146 - WARNING - Could not retrieve variants from source file in region 2:220462429-220505455. Error was invalid region `2:220462430-220505455`
[2016-04-15T03:23Z] 2016-04-14 20:23:52 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:23:52,172 - WARNING - Could not retrieve variants from source file in region 2:208810886-208811287. Error was invalid region `2:208810887-208811287`
[2016-04-15T03:23Z] 2016-04-14 20:23:52 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:23:52,759 - WARNING - Could not retrieve variants from source file in region 2:210654085-210654486. Error was invalid region `2:210654086-210654486`
[2016-04-15T03:23Z] 2016-04-14 20:23:54 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:23:54,754 - WARNING - Could not retrieve variants from source file in region 2:209357816-209358217. Error was invalid region `2:209357817-209358217`
[2016-04-15T03:23Z] 2016-04-14 20:23:57 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:23:57,536 - WARNING - Could not retrieve variants from source file in region 2:209036501-209036968. Error was invalid region `2:209036502-209036968`
[2016-04-15T03:23Z] 2016-04-14 20:23:58 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:23:58,234 - WARNING - Could not retrieve variants from source file in region 2:220197110-220197614. Error was invalid region `2:220197111-220197614`
[2016-04-15T03:23Z] 2016-04-14 20:23:58 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:23:58,262 - WARNING - Could not retrieve variants from source file in region 2:208986426-209010748. Error was invalid region `2:208986427-209010748`
[2016-04-15T03:23Z] 2016-04-14 20:23:58 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:23:58,266 - WARNING - Could not retrieve variants from source file in region 2:209184769-209215776. Error was invalid region `2:209184770-209215776`
[2016-04-15T03:24Z] 2016-04-14 20:24:08 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:24:08,817 - WARNING - Could not retrieve variants from source file in region 2:217148206-217148607. Error was invalid region `2:217148207-217148607`
[2016-04-15T03:24Z] 2016-04-14 20:24:11 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:24:11,936 - WARNING - Could not retrieve variants from source file in region 2:206911017-206921641. Error was invalid region `2:206911018-206921641`
[2016-04-15T03:24Z] 2016-04-14 20:24:11 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:24:11,940 - WARNING - Could not retrieve variants from source file in region 2:218674486-218715482. Error was invalid region `2:218674487-218715482`
[2016-04-15T03:24Z] 2016-04-14 20:24:12 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:24:12,071 - WARNING - Could not retrieve variants from source file in region 2:219602288-219610623. Error was invalid region `2:219602289-219610623`
[2016-04-15T03:24Z] 2016-04-14 20:24:13 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:24:13,125 - WARNING - Could not retrieve variants from source file in region 2:208632606-208633603. Error was invalid region `2:208632607-208633603`
[2016-04-15T03:24Z] 2016-04-14 20:24:13 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:24:13,500 - WARNING - Could not retrieve variants from source file in region 2:217148206-217148607. Error was invalid region `2:217148207-217148607`
[2016-04-15T03:24Z] 2016-04-14 20:24:15 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:24:15,055 - WARNING - Could not retrieve variants from source file in region 2:220249936-220252852. Error was invalid region `2:220249937-220252852`
[2016-04-15T03:24Z] 2016-04-14 20:24:15 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:24:15,570 - WARNING - Could not retrieve variants from source file in region 2:211456426-211481447. Error was invalid region `2:211456427-211481447`
[2016-04-15T03:24Z] 2016-04-14 20:24:15 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:24:15,728 - WARNING - Could not retrieve variants from source file in region 2:206480182-206480583. Error was invalid region `2:206480183-206480583`
[2016-04-15T03:24Z] 2016-04-14 20:24:17 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:24:17,350 - WARNING - Could not retrieve variants from source file in region 2:209306893-209307294. Error was invalid region `2:209306894-209307294`
[2016-04-15T03:24Z] 2016-04-14 20:24:17 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:24:17,520 - WARNING - Could not retrieve variants from source file in region 2:210557923-210558324. Error was invalid region `2:210557924-210558324`
[2016-04-15T03:24Z] 2016-04-14 20:24:18 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:24:18,186 - WARNING - Could not retrieve variants from source file in region 2:206911017-206921641. Error was invalid region `2:206911018-206921641`
[2016-04-15T03:24Z] 2016-04-14 20:24:18 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:24:18,190 - WARNING - Could not retrieve variants from source file in region 2:219602288-219610623. Error was invalid region `2:219602289-219610623`
[2016-04-15T03:24Z] 2016-04-14 20:24:18 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:24:18,290 - WARNING - Could not retrieve variants from source file in region 2:215864338-215876356. Error was invalid region `2:215864339-215876356`
[2016-04-15T03:24Z] 2016-04-14 20:24:18 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:24:18,811 - WARNING - Could not retrieve variants from source file in region 2:208632606-208633603. Error was invalid region `2:208632607-208633603`
[2016-04-15T03:24Z] 2016-04-14 20:24:18 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:24:18,885 - WARNING - Could not retrieve variants from source file in region 2:217148206-217148607. Error was invalid region `2:217148207-217148607`
[2016-04-15T03:24Z] 2016-04-14 20:24:19 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:24:19,047 - WARNING - Could not retrieve variants from source file in region 2:208841753-208866539. Error was invalid region `2:208841754-208866539`
[2016-04-15T03:24Z] 2016-04-14 20:24:19 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:24:19,988 - WARNING - Could not retrieve variants from source file in region 2:220249936-220252852. Error was invalid region `2:220249937-220252852`
[2016-04-15T03:24Z] 2016-04-14 20:24:21 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:24:21,179 - WARNING - Could not retrieve variants from source file in region 2:209108090-209108491. Error was invalid region `2:209108091-209108491`
[2016-04-15T03:24Z] 2016-04-14 20:24:23 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:24:23,462 - WARNING - Could not retrieve variants from source file in region 2:209306893-209307294. Error was invalid region `2:209306894-209307294`
[2016-04-15T03:24Z] 2016-04-14 20:24:24 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:24:24,223 - WARNING - Could not retrieve variants from source file in region 2:206911017-206921641. Error was invalid region `2:206911018-206921641`
[2016-04-15T03:24Z] 2016-04-14 20:24:24 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:24:24,462 - WARNING - Could not retrieve variants from source file in region 2:219602288-219610623. Error was invalid region `2:219602289-219610623`
[2016-04-15T03:24Z] 2016-04-14 20:24:25 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:24:25,981 - WARNING - Could not retrieve variants from source file in region 2:220249936-220252852. Error was invalid region `2:220249937-220252852`
[2016-04-15T03:24Z] 2016-04-14 20:24:26 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:24:26,043 - WARNING - Could not retrieve variants from source file in region 2:215864338-215876356. Error was invalid region `2:215864339-215876356`
[2016-04-15T03:24Z] 2016-04-14 20:24:26 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:24:26,296 - WARNING - Could not retrieve variants from source file in region 2:211456426-211481447. Error was invalid region `2:211456427-211481447`
[2016-04-15T03:24Z] 2016-04-14 20:24:34 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:24:34,954 - WARNING - Could not retrieve variants from source file in region 2:208477641-208478245. Error was invalid region `2:208477642-208478245`
[2016-04-15T03:24Z] 2016-04-14 20:24:35 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:24:35,206 - WARNING - Could not retrieve variants from source file in region 2:217012690-217013091. Error was invalid region `2:217012691-217013091`
[2016-04-15T03:24Z] 2016-04-14 20:24:36 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:24:36,256 - WARNING - Could not retrieve variants from source file in region 2:206364526-206364927. Error was invalid region `2:206364527-206364927`
[2016-04-15T03:24Z] 2016-04-14 20:24:38 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:24:38,492 - WARNING - Could not retrieve variants from source file in region 2:206874128-206874529. Error was invalid region `2:206874129-206874529`
[2016-04-15T03:24Z] 2016-04-14 20:24:40 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:24:40,118 - WARNING - Could not retrieve variants from source file in region 2:208477641-208478245. Error was invalid region `2:208477642-208478245`
[2016-04-15T03:24Z] 2016-04-14 20:24:40 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:24:40,399 - WARNING - Could not retrieve variants from source file in region 2:219555051-219562865. Error was invalid region `2:219555052-219562865`
[2016-04-15T03:24Z] 2016-04-14 20:24:41 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:24:41,034 - WARNING - Could not retrieve variants from source file in region 2:217012690-217013091. Error was invalid region `2:217012691-217013091`
[2016-04-15T03:24Z] 2016-04-14 20:24:43 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:24:43,122 - WARNING - Could not retrieve variants from source file in region 2:217541371-217541772. Error was invalid region `2:217541372-217541772`
[2016-04-15T03:24Z] 2016-04-14 20:24:43 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:24:43,253 - WARNING - Could not retrieve variants from source file in region 2:215819802-215820203. Error was invalid region `2:215819803-215820203`
[2016-04-15T03:24Z] 2016-04-14 20:24:43 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:24:43,629 - WARNING - Could not retrieve variants from source file in region 2:219296626-219319847. Error was invalid region `2:219296627-219319847`
[2016-04-15T03:24Z] 2016-04-14 20:24:43 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:24:43,794 - WARNING - Could not retrieve variants from source file in region 2:206641030-206641436. Error was invalid region `2:206641031-206641436`
[2016-04-15T03:24Z] 2016-04-14 20:24:43 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:24:43,920 - WARNING - Could not retrieve variants from source file in region 2:216877797-216878198. Error was invalid region `2:216877798-216878198`
[2016-04-15T03:24Z] 2016-04-14 20:24:44 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:24:44,075 - WARNING - Could not retrieve variants from source file in region 2:206874128-206874529. Error was invalid region `2:206874129-206874529`
[2016-04-15T03:24Z] 2016-04-14 20:24:44 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:24:44,711 - WARNING - Could not retrieve variants from source file in region 2:208477641-208478245. Error was invalid region `2:208477642-208478245`
[2016-04-15T03:24Z] 2016-04-14 20:24:44 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:24:44,841 - WARNING - Could not retrieve variants from source file in region 2:219555051-219562865. Error was invalid region `2:219555052-219562865`
[2016-04-15T03:24Z] 2016-04-14 20:24:46 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:24:46,437 - WARNING - Could not retrieve variants from source file in region 2:217012690-217013091. Error was invalid region `2:217012691-217013091`
[2016-04-15T03:24Z] 2016-04-14 20:24:48 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:24:48,611 - WARNING - Could not retrieve variants from source file in region 2:219492713-219513972. Error was invalid region `2:219492714-219513972`
[2016-04-15T03:24Z] 2016-04-14 20:24:49 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:24:49,445 - WARNING - Could not retrieve variants from source file in region 2:206364526-206364927. Error was invalid region `2:206364527-206364927`
[2016-04-15T03:24Z] 2016-04-14 20:24:50 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:24:50,431 - WARNING - Could not retrieve variants from source file in region 2:211421241-211421642. Error was invalid region `2:211421242-211421642`
[2016-04-15T03:24Z] 2016-04-14 20:24:50 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:24:50,492 - WARNING - Could not retrieve variants from source file in region 2:211059839-211060240. Error was invalid region `2:211059840-211060240`
[2016-04-15T03:24Z] 2016-04-14 20:24:51 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:24:51,105 - WARNING - Could not retrieve variants from source file in region 2:215819802-215820203. Error was invalid region `2:215819803-215820203`
[2016-04-15T03:24Z] 2016-04-14 20:24:51 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:24:51,133 - WARNING - Could not retrieve variants from source file in region 2:217541371-217541772. Error was invalid region `2:217541372-217541772`
[2016-04-15T03:24Z] 2016-04-14 20:24:51 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:24:51,737 - WARNING - Could not retrieve variants from source file in region 2:206874128-206874529. Error was invalid region `2:206874129-206874529`
[2016-04-15T03:24Z] 2016-04-14 20:24:51 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:24:51,800 - WARNING - Could not retrieve variants from source file in region 2:219555051-219562865. Error was invalid region `2:219555052-219562865`
[2016-04-15T03:24Z] 2016-04-14 20:24:57 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:24:57,341 - WARNING - Could not retrieve variants from source file in region 2:211421241-211421642. Error was invalid region `2:211421242-211421642`
[2016-04-15T03:24Z] 2016-04-14 20:24:58 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:24:58,594 - WARNING - Could not retrieve variants from source file in region 2:215819802-215820203. Error was invalid region `2:215819803-215820203`
[2016-04-15T03:24Z] 2016-04-14 20:24:59 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:24:59,111 - WARNING - Could not retrieve variants from source file in region 2:217541371-217541772. Error was invalid region `2:217541372-217541772`
[2016-04-15T03:24Z] 2016-04-14 20:24:59 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:24:59,228 - WARNING - Could not retrieve variants from source file in region 2:216877797-216878198. Error was invalid region `2:216877798-216878198`
[2016-04-15T03:24Z] 2016-04-14 20:24:59 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:24:59,500 - WARNING - Could not retrieve variants from source file in region 2:206641030-206641436. Error was invalid region `2:206641031-206641436`
[2016-04-15T03:24Z] 2016-04-14 20:24:59 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:24:59,597 - WARNING - Could not retrieve variants from source file in region 2:219892022-219920755. Error was invalid region `2:219892023-219920755`
[2016-04-15T03:25Z] 2016-04-14 20:25:02 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:25:02,857 - WARNING - Could not retrieve variants from source file in region 2:207988402-207988803. Error was invalid region `2:207988403-207988803`
[2016-04-15T03:25Z] 2016-04-14 20:25:08 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:25:08,205 - WARNING - Could not retrieve variants from source file in region 2:207988402-207988803. Error was invalid region `2:207988403-207988803`
[2016-04-15T03:25Z] 2016-04-14 20:25:11 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:25:11,257 - WARNING - Could not retrieve variants from source file in region 2:205969009-205990543. Error was invalid region `2:205969010-205990543`
[2016-04-15T03:25Z] 2016-04-14 20:25:12 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:25:12,197 - WARNING - Could not retrieve variants from source file in region 2:211341138-211341539. Error was invalid region `2:211341139-211341539`
[2016-04-15T03:25Z] 2016-04-14 20:25:12 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:25:12,983 - WARNING - Could not retrieve variants from source file in region 2:215674013-215674414. Error was invalid region `2:215674014-215674414`
[2016-04-15T03:25Z] 2016-04-14 20:25:13 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:25:13,016 - WARNING - Could not retrieve variants from source file in region 2:207988402-207988803. Error was invalid region `2:207988403-207988803`
[2016-04-15T03:25Z] 2016-04-14 20:25:14 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:25:14,990 - WARNING - Could not retrieve variants from source file in region 2:205912192-205912593. Error was invalid region `2:205912193-205912593`
[2016-04-15T03:25Z] 2016-04-14 20:25:15 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:25:15,500 - WARNING - Could not retrieve variants from source file in region 2:219000099-219000500. Error was invalid region `2:219000100-219000500`
[2016-04-15T03:25Z] 2016-04-14 20:25:15 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:25:15,919 - WARNING - Could not retrieve variants from source file in region 2:214727010-214727411. Error was invalid region `2:214727011-214727411`
[2016-04-15T03:25Z] 2016-04-14 20:25:16 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:25:16,751 - WARNING - Could not retrieve variants from source file in region 2:219187690-219188091. Error was invalid region `2:219187691-219188091`
[2016-04-15T03:25Z] 2016-04-14 20:25:16 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:25:16,792 - WARNING - Could not retrieve variants from source file in region 2:214161562-214182518. Error was invalid region `2:214161563-214182518`
[2016-04-15T03:25Z] 2016-04-14 20:25:17 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:25:17,006 - WARNING - Could not retrieve variants from source file in region 2:211341138-211341539. Error was invalid region `2:211341139-211341539`
[2016-04-15T03:25Z] 2016-04-14 20:25:17 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:25:17,032 - WARNING - Could not retrieve variants from source file in region 2:210961299-210961700. Error was invalid region `2:210961300-210961700`
[2016-04-15T03:25Z] 2016-04-14 20:25:18 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:25:18,790 - WARNING - Could not retrieve variants from source file in region 2:219187690-219188091. Error was invalid region `2:219187691-219188091`
[2016-04-15T03:25Z] 2016-04-14 20:25:19 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:25:19,398 - WARNING - Could not retrieve variants from source file in region 2:205912192-205912593. Error was invalid region `2:205912193-205912593`
[2016-04-15T03:25Z] 2016-04-14 20:25:20 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:25:20,228 - WARNING - Could not retrieve variants from source file in region 2:219000099-219000500. Error was invalid region `2:219000100-219000500`
[2016-04-15T03:25Z] 2016-04-14 20:25:20 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:25:20,740 - WARNING - Could not retrieve variants from source file in region 2:214727010-214727411. Error was invalid region `2:214727011-214727411`
[2016-04-15T03:25Z] 2016-04-14 20:25:22 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:25:22,228 - WARNING - Could not retrieve variants from source file in region 2:211341138-211341539. Error was invalid region `2:211341139-211341539`
[2016-04-15T03:25Z] 2016-04-14 20:25:24 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:25:24,011 - WARNING - Could not retrieve variants from source file in region 2:219140077-219146993. Error was invalid region `2:219140078-219146993`
[2016-04-15T03:25Z] 2016-04-14 20:25:24 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:25:24,107 - WARNING - Could not retrieve variants from source file in region 2:205912192-205912593. Error was invalid region `2:205912193-205912593`
[2016-04-15T03:25Z] 2016-04-14 20:25:24 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:25:24,868 - WARNING - Could not retrieve variants from source file in region 2:219000099-219000500. Error was invalid region `2:219000100-219000500`
[2016-04-15T03:25Z] 2016-04-14 20:25:25 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:25:25,349 - WARNING - Could not retrieve variants from source file in region 2:214727010-214727411. Error was invalid region `2:214727011-214727411`
[2016-04-15T03:25Z] 2016-04-14 20:25:28 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:25:28,602 - WARNING - Could not retrieve variants from source file in region 2:207527629-207528030. Error was invalid region `2:207527630-207528030`
[2016-04-15T03:25Z] 2016-04-14 20:25:30 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:25:30,752 - WARNING - Could not retrieve variants from source file in region 2:207820065-207834173. Error was invalid region `2:207820066-207834173`
[2016-04-15T03:25Z] 2016-04-14 20:25:33 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:25:33,211 - WARNING - Could not retrieve variants from source file in region 2:207820065-207834173. Error was invalid region `2:207820066-207834173`
[2016-04-15T03:25Z] 2016-04-14 20:25:34 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:25:34,627 - WARNING - Could not retrieve variants from source file in region 2:210810388-210843573. Error was invalid region `2:210810389-210843573`
[2016-04-15T03:25Z] 2016-04-14 20:25:34 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:25:34,857 - WARNING - Could not retrieve variants from source file in region 2:214012297-214012698. Error was invalid region `2:214012298-214012698`
[2016-04-15T03:25Z] 2016-04-14 20:25:35 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:25:35,694 - WARNING - Could not retrieve variants from source file in region 2:210705137-210705538. Error was invalid region `2:210705138-210705538`
[2016-04-15T03:25Z] 2016-04-14 20:25:36 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:25:36,163 - WARNING - Could not retrieve variants from source file in region 2:212251653-212252054. Error was invalid region `2:212251654-212252054`
[2016-04-15T03:25Z] 2016-04-14 20:25:36 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:25:36,660 - WARNING - Could not retrieve variants from source file in region 2:207603023-207621949. Error was invalid region `2:207603024-207621949`
[2016-04-15T03:25Z] 2016-04-14 20:25:36 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:25:36,781 - WARNING - Could not retrieve variants from source file in region 2:207040842-207042123. Error was invalid region `2:207040843-207042123`
[2016-04-15T03:25Z] 2016-04-14 20:25:39 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:25:39,524 - WARNING - Could not retrieve variants from source file in region 2:210705137-210705538. Error was invalid region `2:210705138-210705538`
[2016-04-15T03:25Z] 2016-04-14 20:25:40 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:25:40,591 - WARNING - Could not retrieve variants from source file in region 2:207169520-207174506. Error was invalid region `2:207169521-207174506`
[2016-04-15T03:25Z] 2016-04-14 20:25:40 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:25:40,931 - WARNING - Could not retrieve variants from source file in region 2:207603023-207621949. Error was invalid region `2:207603024-207621949`
[2016-04-15T03:25Z] 2016-04-14 20:25:42 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:25:42,430 - WARNING - Could not retrieve variants from source file in region 2:212251653-212252054. Error was invalid region `2:212251654-212252054`
[2016-04-15T03:25Z] 2016-04-14 20:25:42 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:25:42,551 - WARNING - Could not retrieve variants from source file in region 2:214012297-214012698. Error was invalid region `2:214012298-214012698`
[2016-04-15T03:25Z] ['bcbio-variation-recall', 'square', '-Xms750m', '-Xmx7280m', '-XX:+UseSerialGC', '-c', 16, '-r', u'2:222291155-237994685', '--caller', 'platypus', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/2/Batch1-2_222291154_237994685.vcf.gz', '/mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/2/Batch1-2_222291154_237994685.vcf-inputs.txt'] in region: 2:222291155-237994685
[2016-04-15T03:25Z] 2016-04-14 20:25:58 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:25:58,887 - WARNING - Could not retrieve variants from source file in region 2:228565445-228582936. Error was invalid region `2:228565446-228582936`
[2016-04-15T03:25Z] 2016-04-14 20:25:59 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:25:59,804 - WARNING - Could not retrieve variants from source file in region 2:237149730-237150131. Error was invalid region `2:237149731-237150131`
[2016-04-15T03:26Z] 2016-04-14 20:26:00 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:26:00,283 - WARNING - Could not retrieve variants from source file in region 2:231406469-231406870. Error was invalid region `2:231406470-231406870`
[2016-04-15T03:26Z] 2016-04-14 20:26:00 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:26:00,629 - WARNING - Could not retrieve variants from source file in region 2:230451270-230451672. Error was invalid region `2:230451271-230451672`
[2016-04-15T03:26Z] 2016-04-14 20:26:01 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:26:01,417 - WARNING - Could not retrieve variants from source file in region 2:228476042-228476443. Error was invalid region `2:228476043-228476443`
[2016-04-15T03:26Z] 2016-04-14 20:26:01 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:26:01,525 - WARNING - Could not retrieve variants from source file in region 2:233432422-233433073. Error was invalid region `2:233432423-233433073`
[2016-04-15T03:26Z] 2016-04-14 20:26:01 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:26:01,600 - WARNING - Could not retrieve variants from source file in region 2:233749863-233757887. Error was invalid region `2:233749864-233757887`
[2016-04-15T03:26Z] 2016-04-14 20:26:01 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:26:01,720 - WARNING - Could not retrieve variants from source file in region 2:228416501-228416902. Error was invalid region `2:228416502-228416902`
[2016-04-15T03:26Z] 2016-04-14 20:26:01 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:26:01,765 - WARNING - Could not retrieve variants from source file in region 2:228243694-228244095. Error was invalid region `2:228243695-228244095`
[2016-04-15T03:26Z] 2016-04-14 20:26:05 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:26:05,739 - WARNING - Could not retrieve variants from source file in region 2:228565445-228582936. Error was invalid region `2:228565446-228582936`
[2016-04-15T03:26Z] 2016-04-14 20:26:07 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:26:07,036 - WARNING - Could not retrieve variants from source file in region 2:237149730-237150131. Error was invalid region `2:237149731-237150131`
[2016-04-15T03:26Z] 2016-04-14 20:26:08 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:26:08,679 - WARNING - Could not retrieve variants from source file in region 2:231406469-231406870. Error was invalid region `2:231406470-231406870`
[2016-04-15T03:26Z] 2016-04-14 20:26:09 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:26:09,039 - WARNING - Could not retrieve variants from source file in region 2:232952075-232952476. Error was invalid region `2:232952076-232952476`
[2016-04-15T03:26Z] 2016-04-14 20:26:09 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:26:09,043 - WARNING - Could not retrieve variants from source file in region 2:236761185-236761604. Error was invalid region `2:236761186-236761604`
[2016-04-15T03:26Z] 2016-04-14 20:26:09 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:26:09,070 - WARNING - Could not retrieve variants from source file in region 2:231110371-231110772. Error was invalid region `2:231110372-231110772`
[2016-04-15T03:26Z] 2016-04-14 20:26:09 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:26:09,281 - WARNING - Could not retrieve variants from source file in region 2:230451270-230451672. Error was invalid region `2:230451271-230451672`
[2016-04-15T03:26Z] 2016-04-14 20:26:09 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:26:09,314 - WARNING - Could not retrieve variants from source file in region 2:237123173-237123574. Error was invalid region `2:237123174-237123574`
[2016-04-15T03:26Z] 2016-04-14 20:26:09 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:26:09,947 - WARNING - Could not retrieve variants from source file in region 2:228476042-228476443. Error was invalid region `2:228476043-228476443`
[2016-04-15T03:26Z] 2016-04-14 20:26:10 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:26:10,019 - WARNING - Could not retrieve variants from source file in region 2:233432422-233433073. Error was invalid region `2:233432423-233433073`
[2016-04-15T03:26Z] 2016-04-14 20:26:10 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:26:10,274 - WARNING - Could not retrieve variants from source file in region 2:237489086-237490094. Error was invalid region `2:237489087-237490094`
[2016-04-15T03:26Z] 2016-04-14 20:26:10 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:26:10,345 - WARNING - Could not retrieve variants from source file in region 2:228416501-228416902. Error was invalid region `2:228416502-228416902`
[2016-04-15T03:26Z] 2016-04-14 20:26:10 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:26:10,771 - WARNING - Could not retrieve variants from source file in region 2:228565445-228582936. Error was invalid region `2:228565446-228582936`
[2016-04-15T03:26Z] 2016-04-14 20:26:11 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:26:11,649 - WARNING - Could not retrieve variants from source file in region 2:237149730-237150131. Error was invalid region `2:237149731-237150131`
[2016-04-15T03:26Z] 2016-04-14 20:26:13 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:26:13,234 - WARNING - Could not retrieve variants from source file in region 2:231406469-231406870. Error was invalid region `2:231406470-231406870`
[2016-04-15T03:26Z] 2016-04-14 20:26:14 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:26:14,909 - WARNING - Could not retrieve variants from source file in region 2:231110371-231110772. Error was invalid region `2:231110372-231110772`
[2016-04-15T03:26Z] 2016-04-14 20:26:17 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:26:17,604 - WARNING - Could not retrieve variants from source file in region 2:228416501-228416902. Error was invalid region `2:228416502-228416902`
[2016-04-15T03:26Z] 2016-04-14 20:26:17 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:26:17,879 - WARNING - Could not retrieve variants from source file in region 2:228476042-228476443. Error was invalid region `2:228476043-228476443`
[2016-04-15T03:26Z] 2016-04-14 20:26:17 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:26:17,935 - WARNING - Could not retrieve variants from source file in region 2:237123173-237123574. Error was invalid region `2:237123174-237123574`
[2016-04-15T03:26Z] 2016-04-14 20:26:17 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:26:17,991 - WARNING - Could not retrieve variants from source file in region 2:230451270-230451672. Error was invalid region `2:230451271-230451672`
[2016-04-15T03:26Z] 2016-04-14 20:26:28 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:26:28,264 - WARNING - Could not retrieve variants from source file in region 2:227954388-227954789. Error was invalid region `2:227954389-227954789`
[2016-04-15T03:26Z] 2016-04-14 20:26:29 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:26:29,742 - WARNING - Could not retrieve variants from source file in region 2:231380524-231380925. Error was invalid region `2:231380525-231380925`
[2016-04-15T03:26Z] 2016-04-14 20:26:31 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:26:31,165 - WARNING - Could not retrieve variants from source file in region 2:236403251-236403652. Error was invalid region `2:236403252-236403652`
[2016-04-15T03:26Z] 2016-04-14 20:26:31 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:26:31,393 - WARNING - Could not retrieve variants from source file in region 2:231036649-231077915. Error was invalid region `2:231036650-231077915`
[2016-04-15T03:26Z] 2016-04-14 20:26:31 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:26:31,740 - WARNING - Could not retrieve variants from source file in region 2:232458232-232458633. Error was invalid region `2:232458233-232458633`
[2016-04-15T03:26Z] 2016-04-14 20:26:33 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:26:33,998 - WARNING - Could not retrieve variants from source file in region 2:227954388-227954789. Error was invalid region `2:227954389-227954789`
[2016-04-15T03:26Z] 2016-04-14 20:26:34 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:26:34,551 - WARNING - Could not retrieve variants from source file in region 2:233385185-233391127. Error was invalid region `2:233385186-233391127`
[2016-04-15T03:26Z] 2016-04-14 20:26:34 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:26:34,701 - WARNING - Could not retrieve variants from source file in region 2:231380524-231380925. Error was invalid region `2:231380525-231380925`
[2016-04-15T03:26Z] 2016-04-14 20:26:34 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:26:34,969 - WARNING - Could not retrieve variants from source file in region 2:233708595-233712438. Error was invalid region `2:233708596-233712438`
[2016-04-15T03:26Z] 2016-04-14 20:26:35 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:26:35,426 - WARNING - Could not retrieve variants from source file in region 2:237374098-237374499. Error was invalid region `2:237374099-237374499`
[2016-04-15T03:26Z] 2016-04-14 20:26:35 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:26:35,489 - WARNING - Could not retrieve variants from source file in region 2:233349377-233349778. Error was invalid region `2:233349378-233349778`
[2016-04-15T03:26Z] 2016-04-14 20:26:36 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:26:36,636 - WARNING - Could not retrieve variants from source file in region 2:229046403-229046804. Error was invalid region `2:229046404-229046804`
[2016-04-15T03:26Z] 2016-04-14 20:26:36 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:26:36,741 - WARNING - Could not retrieve variants from source file in region 2:232458232-232458633. Error was invalid region `2:232458233-232458633`
[2016-04-15T03:26Z] 2016-04-14 20:26:37 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:26:37,946 - WARNING - Could not retrieve variants from source file in region 2:228194269-228194671. Error was invalid region `2:228194270-228194671`
[2016-04-15T03:26Z] 2016-04-14 20:26:39 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:26:39,039 - WARNING - Could not retrieve variants from source file in region 2:227954388-227954789. Error was invalid region `2:227954389-227954789`
[2016-04-15T03:26Z] 2016-04-14 20:26:39 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:26:39,771 - WARNING - Could not retrieve variants from source file in region 2:231380524-231380925. Error was invalid region `2:231380525-231380925`
[2016-04-15T03:26Z] 2016-04-14 20:26:41 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:26:41,066 - WARNING - Could not retrieve variants from source file in region 2:233349377-233349778. Error was invalid region `2:233349378-233349778`
[2016-04-15T03:26Z] 2016-04-14 20:26:42 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:26:42,327 - WARNING - Could not retrieve variants from source file in region 2:236403251-236403652. Error was invalid region `2:236403252-236403652`
[2016-04-15T03:26Z] 2016-04-14 20:26:42 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:26:42,329 - WARNING - Could not retrieve variants from source file in region 2:232458232-232458633. Error was invalid region `2:232458233-232458633`
[2016-04-15T03:26Z] 2016-04-14 20:26:42 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:26:42,347 - WARNING - Could not retrieve variants from source file in region 2:228882818-228892925. Error was invalid region `2:228882819-228892925`
[2016-04-15T03:26Z] 2016-04-14 20:26:43 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:26:43,003 - WARNING - Could not retrieve variants from source file in region 2:228194269-228194671. Error was invalid region `2:228194270-228194671`
[2016-04-15T03:26Z] 2016-04-14 20:26:46 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:26:46,318 - WARNING - Could not retrieve variants from source file in region 2:237374098-237374499. Error was invalid region `2:237374099-237374499`
[2016-04-15T03:26Z] 2016-04-14 20:26:46 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:26:46,801 - WARNING - Could not retrieve variants from source file in region 2:233349377-233349778. Error was invalid region `2:233349378-233349778`
[2016-04-15T03:26Z] 2016-04-14 20:26:47 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:26:47,733 - WARNING - Could not retrieve variants from source file in region 2:229046403-229046804. Error was invalid region `2:229046404-229046804`
[2016-04-15T03:26Z] 2016-04-14 20:26:48 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:26:48,749 - WARNING - Could not retrieve variants from source file in region 2:228882818-228892925. Error was invalid region `2:228882819-228892925`
[2016-04-15T03:26Z] 2016-04-14 20:26:57 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:26:57,282 - WARNING - Could not retrieve variants from source file in region 2:230861308-230861709. Error was invalid region `2:230861309-230861709`
[2016-04-15T03:26Z] 2016-04-14 20:26:57 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:26:57,756 - WARNING - Could not retrieve variants from source file in region 2:232326206-232326607. Error was invalid region `2:232326207-232326607`
[2016-04-15T03:26Z] 2016-04-14 20:26:58 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:26:58,613 - WARNING - Could not retrieve variants from source file in region 2:234967328-234967729. Error was invalid region `2:234967329-234967729`
[2016-04-15T03:27Z] 2016-04-14 20:27:00 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:27:00,116 - WARNING - Could not retrieve variants from source file in region 2:234526660-234527373. Error was invalid region `2:234526661-234527373`
[2016-04-15T03:27Z] 2016-04-14 20:27:00 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:27:00,508 - WARNING - Could not retrieve variants from source file in region 2:227871971-227920938. Error was invalid region `2:227871972-227920938`
[2016-04-15T03:27Z] 2016-04-14 20:27:01 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:27:01,077 - WARNING - Could not retrieve variants from source file in region 2:231331685-231335349. Error was invalid region `2:231331686-231335349`
[2016-04-15T03:27Z] 2016-04-14 20:27:01 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:27:01,824 - WARNING - Could not retrieve variants from source file in region 2:233536914-233537315. Error was invalid region `2:233536915-233537315`
[2016-04-15T03:27Z] 2016-04-14 20:27:02 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:27:02,049 - WARNING - Could not retrieve variants from source file in region 2:233244375-233245331. Error was invalid region `2:233244376-233245331`
[2016-04-15T03:27Z] 2016-04-14 20:27:04 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:27:04,386 - WARNING - Could not retrieve variants from source file in region 2:228846552-228856056. Error was invalid region `2:228846553-228856056`
[2016-04-15T03:27Z] 2016-04-14 20:27:04 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:27:04,389 - WARNING - Could not retrieve variants from source file in region 2:234967328-234967729. Error was invalid region `2:234967329-234967729`
[2016-04-15T03:27Z] 2016-04-14 20:27:04 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:27:04,391 - WARNING - Could not retrieve variants from source file in region 2:230723566-230723967. Error was invalid region `2:230723567-230723967`
[2016-04-15T03:27Z] 2016-04-14 20:27:05 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:27:05,271 - WARNING - Could not retrieve variants from source file in region 2:233660635-233661036. Error was invalid region `2:233660636-233661036`
[2016-04-15T03:27Z] 2016-04-14 20:27:08 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:27:08,270 - WARNING - Could not retrieve variants from source file in region 2:234904867-234905268. Error was invalid region `2:234904868-234905268`
[2016-04-15T03:27Z] 2016-04-14 20:27:09 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:27:09,645 - WARNING - Could not retrieve variants from source file in region 2:232326206-232326607. Error was invalid region `2:232326207-232326607`
[2016-04-15T03:27Z] 2016-04-14 20:27:10 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:27:10,458 - WARNING - Could not retrieve variants from source file in region 2:230723566-230723967. Error was invalid region `2:230723567-230723967`
[2016-04-15T03:27Z] 2016-04-14 20:27:10 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:27:10,469 - WARNING - Could not retrieve variants from source file in region 2:234967328-234967729. Error was invalid region `2:234967329-234967729`
[2016-04-15T03:27Z] 2016-04-14 20:27:10 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:27:10,843 - WARNING - Could not retrieve variants from source file in region 2:228758343-228777186. Error was invalid region `2:228758344-228777186`
[2016-04-15T03:27Z] 2016-04-14 20:27:14 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:27:14,147 - WARNING - Could not retrieve variants from source file in region 2:233271880-233274335. Error was invalid region `2:233271881-233274335`
[2016-04-15T03:27Z] 2016-04-14 20:27:14 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:27:14,419 - WARNING - Could not retrieve variants from source file in region 2:233244375-233245331. Error was invalid region `2:233244376-233245331`
[2016-04-15T03:27Z] 2016-04-14 20:27:14 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:27:14,490 - WARNING - Could not retrieve variants from source file in region 2:233536914-233537315. Error was invalid region `2:233536915-233537315`
[2016-04-15T03:27Z] 2016-04-14 20:27:16 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:27:16,305 - WARNING - Could not retrieve variants from source file in region 2:228758343-228777186. Error was invalid region `2:228758344-228777186`
[2016-04-15T03:27Z] 2016-04-14 20:27:22 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:27:22,623 - WARNING - Could not retrieve variants from source file in region 2:230668647-230669048. Error was invalid region `2:230668648-230669048`
[2016-04-15T03:27Z] 2016-04-14 20:27:22 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:27:22,890 - WARNING - Could not retrieve variants from source file in region 2:231148897-231149298. Error was invalid region `2:231148898-231149298`
[2016-04-15T03:27Z] 2016-04-14 20:27:23 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:27:23,509 - WARNING - Could not retrieve variants from source file in region 2:231148897-231149298. Error was invalid region `2:231148898-231149298`
[2016-04-15T03:27Z] 2016-04-14 20:27:24 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:27:24,389 - WARNING - Could not retrieve variants from source file in region 2:231148897-231149298. Error was invalid region `2:231148898-231149298`
[2016-04-15T03:27Z] 2016-04-14 20:27:24 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:27:24,450 - WARNING - Could not retrieve variants from source file in region 2:232262916-232263317. Error was invalid region `2:232262917-232263317`
[2016-04-15T03:27Z] 2016-04-14 20:27:26 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:27:26,480 - WARNING - Could not retrieve variants from source file in region 2:234429528-234449506. Error was invalid region `2:234429529-234449506`
[2016-04-15T03:27Z] 2016-04-14 20:27:27 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:27:27,437 - WARNING - Could not retrieve variants from source file in region 2:227732086-227732487. Error was invalid region `2:227732087-227732487`
[2016-04-15T03:27Z] 2016-04-14 20:27:27 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:27:27,885 - WARNING - Could not retrieve variants from source file in region 2:232196353-232196787. Error was invalid region `2:232196354-232196787`
[2016-04-15T03:27Z] 2016-04-14 20:27:27 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:27:27,991 - WARNING - Could not retrieve variants from source file in region 2:234255336-234255737. Error was invalid region `2:234255337-234255737`
[2016-04-15T03:27Z] 2016-04-14 20:27:28 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:27:28,393 - WARNING - Could not retrieve variants from source file in region 2:231864933-231865334. Error was invalid region `2:231864934-231865334`
[2016-04-15T03:27Z] 2016-04-14 20:27:29 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:27:29,462 - WARNING - Could not retrieve variants from source file in region 2:232262916-232263317. Error was invalid region `2:232262917-232263317`
[2016-04-15T03:27Z] 2016-04-14 20:27:29 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:27:29,627 - WARNING - Could not retrieve variants from source file in region 2:233498052-233498453. Error was invalid region `2:233498053-233498453`
[2016-04-15T03:27Z] 2016-04-14 20:27:30 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:27:30,055 - WARNING - Could not retrieve variants from source file in region 2:232225324-232225725. Error was invalid region `2:232225325-232225725`
[2016-04-15T03:27Z] 2016-04-14 20:27:30 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:27:30,230 - WARNING - Could not retrieve variants from source file in region 2:232087263-232087665. Error was invalid region `2:232087264-232087665`
[2016-04-15T03:27Z] 2016-04-14 20:27:31 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:27:31,112 - WARNING - Could not retrieve variants from source file in region 2:234429528-234449506. Error was invalid region `2:234429529-234449506`
[2016-04-15T03:27Z] 2016-04-14 20:27:31 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:27:31,871 - WARNING - Could not retrieve variants from source file in region 2:230668647-230669048. Error was invalid region `2:230668648-230669048`
[2016-04-15T03:27Z] 2016-04-14 20:27:32 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:27:32,652 - WARNING - Could not retrieve variants from source file in region 2:232196353-232196787. Error was invalid region `2:232196354-232196787`
[2016-04-15T03:27Z] 2016-04-14 20:27:32 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:27:32,655 - WARNING - Could not retrieve variants from source file in region 2:234255336-234255737. Error was invalid region `2:234255337-234255737`
[2016-04-15T03:27Z] 2016-04-14 20:27:33 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:27:33,786 - WARNING - Could not retrieve variants from source file in region 2:231864933-231865334. Error was invalid region `2:231864934-231865334`
[2016-04-15T03:27Z] 2016-04-14 20:27:33 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:27:33,816 - WARNING - Could not retrieve variants from source file in region 2:225434234-225434635. Error was invalid region `2:225434235-225434635`
[2016-04-15T03:27Z] 2016-04-14 20:27:34 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:27:34,986 - WARNING - Could not retrieve variants from source file in region 2:232225324-232225725. Error was invalid region `2:232225325-232225725`
[2016-04-15T03:27Z] 2016-04-14 20:27:35 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:27:35,236 - WARNING - Could not retrieve variants from source file in region 2:232087263-232087665. Error was invalid region `2:232087264-232087665`
[2016-04-15T03:27Z] 2016-04-14 20:27:37 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:27:37,513 - WARNING - Could not retrieve variants from source file in region 2:226447524-226447925. Error was invalid region `2:226447525-226447925`
[2016-04-15T03:27Z] 2016-04-14 20:27:37 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:27:37,896 - WARNING - Could not retrieve variants from source file in region 2:234255336-234255737. Error was invalid region `2:234255337-234255737`
[2016-04-15T03:27Z] 2016-04-14 20:27:38 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:27:38,501 - WARNING - Could not retrieve variants from source file in region 2:225434234-225434635. Error was invalid region `2:225434235-225434635`
[2016-04-15T03:27Z] 2016-04-14 20:27:38 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:27:38,984 - WARNING - Could not retrieve variants from source file in region 2:234385923-234394759. Error was invalid region `2:234385924-234394759`
[2016-04-15T03:27Z] 2016-04-14 20:27:39 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:27:39,499 - WARNING - Could not retrieve variants from source file in region 2:234385923-234394759. Error was invalid region `2:234385924-234394759`
[2016-04-15T03:27Z] 2016-04-14 20:27:40 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:27:40,439 - WARNING - Could not retrieve variants from source file in region 2:232087263-232087665. Error was invalid region `2:232087264-232087665`
[2016-04-15T03:27Z] 2016-04-14 20:27:40 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:27:40,463 - WARNING - Could not retrieve variants from source file in region 2:232225324-232225725. Error was invalid region `2:232225325-232225725`
[2016-04-15T03:27Z] 2016-04-14 20:27:42 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:27:42,197 - WARNING - Could not retrieve variants from source file in region 2:226447524-226447925. Error was invalid region `2:226447525-226447925`
[2016-04-15T03:27Z] 2016-04-14 20:27:43 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:27:43,813 - WARNING - Could not retrieve variants from source file in region 2:225434234-225434635. Error was invalid region `2:225434235-225434635`
[2016-04-15T03:27Z] 2016-04-14 20:27:45 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:27:45,047 - WARNING - Could not retrieve variants from source file in region 2:226491559-226491960. Error was invalid region `2:226491560-226491960`
[2016-04-15T03:27Z] 2016-04-14 20:27:46 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:27:46,994 - WARNING - Could not retrieve variants from source file in region 2:226447524-226447925. Error was invalid region `2:226447525-226447925`
[2016-04-15T03:27Z] 2016-04-14 20:27:48 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:27:48,956 - WARNING - Could not retrieve variants from source file in region 2:226273478-226273879. Error was invalid region `2:226273479-226273879`
[2016-04-15T03:27Z] 2016-04-14 20:27:49 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:27:49,005 - WARNING - Could not retrieve variants from source file in region 2:226273478-226273879. Error was invalid region `2:226273479-226273879`
[2016-04-15T03:27Z] 2016-04-14 20:27:49 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:27:49,276 - WARNING - Could not retrieve variants from source file in region 2:226491559-226491960. Error was invalid region `2:226491560-226491960`
[2016-04-15T03:27Z] 2016-04-14 20:27:49 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:27:49,634 - WARNING - Could not retrieve variants from source file in region 2:225811370-225811782. Error was invalid region `2:225811371-225811782`
[2016-04-15T03:27Z] 2016-04-14 20:27:49 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:27:49,894 - WARNING - Could not retrieve variants from source file in region 2:226491559-226491960. Error was invalid region `2:226491560-226491960`
[2016-04-15T03:27Z] 2016-04-14 20:27:50 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:27:50,342 - WARNING - Could not retrieve variants from source file in region 2:234183157-234183558. Error was invalid region `2:234183158-234183558`
[2016-04-15T03:27Z] 2016-04-14 20:27:52 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:27:52,976 - WARNING - Could not retrieve variants from source file in region 2:233898915-233899316. Error was invalid region `2:233898916-233899316`
[2016-04-15T03:27Z] 2016-04-14 20:27:53 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:27:53,651 - WARNING - Could not retrieve variants from source file in region 2:231729591-231729992. Error was invalid region `2:231729592-231729992`
[2016-04-15T03:27Z] 2016-04-14 20:27:53 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:27:53,775 - WARNING - Could not retrieve variants from source file in region 2:225811370-225811782. Error was invalid region `2:225811371-225811782`
[2016-04-15T03:27Z] 2016-04-14 20:27:54 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:27:54,785 - WARNING - Could not retrieve variants from source file in region 2:234183157-234183558. Error was invalid region `2:234183158-234183558`
[2016-04-15T03:27Z] 2016-04-14 20:27:56 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:27:56,218 - WARNING - Could not retrieve variants from source file in region 2:231774633-231775487. Error was invalid region `2:231774634-231775487`
[2016-04-15T03:27Z] 2016-04-14 20:27:56 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:27:56,258 - WARNING - Could not retrieve variants from source file in region 2:224895766-224896168. Error was invalid region `2:224895767-224896168`
[2016-04-15T03:27Z] 2016-04-14 20:27:56 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:27:56,264 - WARNING - Could not retrieve variants from source file in region 2:225709715-225751051. Error was invalid region `2:225709716-225751051`
[2016-04-15T03:27Z] 2016-04-14 20:27:57 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:27:57,187 - WARNING - Could not retrieve variants from source file in region 2:233898915-233899316. Error was invalid region `2:233898916-233899316`
[2016-04-15T03:27Z] 2016-04-14 20:27:57 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:27:57,758 - WARNING - Could not retrieve variants from source file in region 2:231729591-231729992. Error was invalid region `2:231729592-231729992`
[2016-04-15T03:27Z] 2016-04-14 20:27:58 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:27:58,823 - WARNING - Could not retrieve variants from source file in region 2:234183157-234183558. Error was invalid region `2:234183158-234183558`
[2016-04-15T03:28Z] 2016-04-14 20:28:00 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:28:00,010 - WARNING - Could not retrieve variants from source file in region 2:224895766-224896168. Error was invalid region `2:224895767-224896168`
[2016-04-15T03:28Z] 2016-04-14 20:28:00 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:28:00,083 - WARNING - Could not retrieve variants from source file in region 2:231774633-231775487. Error was invalid region `2:231774634-231775487`
[2016-04-15T03:28Z] 2016-04-14 20:28:00 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:28:00,752 - WARNING - Could not retrieve variants from source file in region 2:233898915-233899316. Error was invalid region `2:233898916-233899316`
[2016-04-15T03:28Z] 2016-04-14 20:28:01 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:28:01,830 - WARNING - Could not retrieve variants from source file in region 2:225670690-225684356. Error was invalid region `2:225670691-225684356`
[2016-04-15T03:28Z] 2016-04-14 20:28:03 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:28:03,316 - WARNING - Could not retrieve variants from source file in region 2:225670690-225684356. Error was invalid region `2:225670691-225684356`
[2016-04-15T03:28Z] 2016-04-14 20:28:03 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:28:03,565 - WARNING - Could not retrieve variants from source file in region 2:224895766-224896168. Error was invalid region `2:224895767-224896168`
[2016-04-15T03:28Z] 2016-04-14 20:28:04 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:28:04,623 - WARNING - Could not retrieve variants from source file in region 2:223783630-223784031. Error was invalid region `2:223783631-223784031`
[2016-04-15T03:28Z] 2016-04-14 20:28:04 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:28:04,645 - WARNING - Could not retrieve variants from source file in region 2:233834764-233835165. Error was invalid region `2:233834765-233835165`
[2016-04-15T03:28Z] 2016-04-14 20:28:07 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:28:07,287 - WARNING - Could not retrieve variants from source file in region 2:233834764-233835165. Error was invalid region `2:233834765-233835165`
[2016-04-15T03:28Z] 2016-04-14 20:28:08 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:28:08,225 - WARNING - Could not retrieve variants from source file in region 2:223783630-223784031. Error was invalid region `2:223783631-223784031`
[2016-04-15T03:28Z] 2016-04-14 20:28:08 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:28:08,225 - WARNING - Could not retrieve variants from source file in region 2:233834764-233835165. Error was invalid region `2:233834765-233835165`
[2016-04-15T03:28Z] 2016-04-14 20:28:10 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:28:10,555 - WARNING - Could not retrieve variants from source file in region 2:224856439-224863032. Error was invalid region `2:224856440-224863032`
[2016-04-15T03:28Z] 2016-04-14 20:28:10 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:28:10,989 - WARNING - Could not retrieve variants from source file in region 2:223423151-223436797. Error was invalid region `2:223423152-223436797`
[2016-04-15T03:28Z] 2016-04-14 20:28:11 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:28:11,012 - WARNING - Could not retrieve variants from source file in region 2:223917418-223918173. Error was invalid region `2:223917419-223918173`
[2016-04-15T03:28Z] 2016-04-14 20:28:11 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:28:11,052 - WARNING - Could not retrieve variants from source file in region 2:233784804-233785205. Error was invalid region `2:233784805-233785205`
[2016-04-15T03:28Z] 2016-04-14 20:28:11 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:28:11,561 - WARNING - Could not retrieve variants from source file in region 2:224856439-224863032. Error was invalid region `2:224856440-224863032`
[2016-04-15T03:28Z] 2016-04-14 20:28:14 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:28:14,456 - WARNING - Could not retrieve variants from source file in region 2:223158441-223162079. Error was invalid region `2:223158442-223162079`
[2016-04-15T03:28Z] 2016-04-14 20:28:14 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:28:14,845 - WARNING - Could not retrieve variants from source file in region 2:223917418-223918173. Error was invalid region `2:223917419-223918173`
[2016-04-15T03:28Z] 2016-04-14 20:28:15 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:28:15,293 - WARNING - Could not retrieve variants from source file in region 2:223423151-223436797. Error was invalid region `2:223423152-223436797`
[2016-04-15T03:28Z] 2016-04-14 20:28:15 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:28:15,322 - WARNING - Could not retrieve variants from source file in region 2:233784804-233785205. Error was invalid region `2:233784805-233785205`
[2016-04-15T03:28Z] 2016-04-14 20:28:15 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:28:15,470 - WARNING - Could not retrieve variants from source file in region 2:224622649-224642683. Error was invalid region `2:224622650-224642683`
[2016-04-15T03:28Z] 2016-04-14 20:28:15 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:28:15,782 - WARNING - Could not retrieve variants from source file in region 2:223558878-223559279. Error was invalid region `2:223558879-223559279`
[2016-04-15T03:28Z] 2016-04-14 20:28:16 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:28:16,181 - WARNING - Could not retrieve variants from source file in region 2:233784804-233785205. Error was invalid region `2:233784805-233785205`
[2016-04-15T03:28Z] 2016-04-14 20:28:18 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:28:18,219 - WARNING - Could not retrieve variants from source file in region 2:223558878-223559279. Error was invalid region `2:223558879-223559279`
[2016-04-15T03:28Z] 2016-04-14 20:28:18 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:28:18,412 - WARNING - Could not retrieve variants from source file in region 2:223158441-223162079. Error was invalid region `2:223158442-223162079`
[2016-04-15T03:28Z] 2016-04-14 20:28:18 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:28:18,824 - WARNING - Could not retrieve variants from source file in region 2:223917418-223918173. Error was invalid region `2:223917419-223918173`
[2016-04-15T03:28Z] 2016-04-14 20:28:19 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:28:19,701 - WARNING - Could not retrieve variants from source file in region 2:223423151-223436797. Error was invalid region `2:223423152-223436797`
[2016-04-15T03:28Z] 2016-04-14 20:28:19 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:28:19,739 - WARNING - Could not retrieve variants from source file in region 2:223158441-223162079. Error was invalid region `2:223158442-223162079`
[2016-04-15T03:28Z] ['bcbio-variation-recall', 'square', '-Xms750m', '-Xmx7280m', '-XX:+UseSerialGC', '-c', 16, '-r', u'2:237995375-243199373', '--caller', 'platypus', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/2/Batch1-2_237995374_243199373.vcf.gz', '/mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/2/Batch1-2_237995374_243199373.vcf-inputs.txt'] in region: 2:237995375-243199373
[2016-04-15T03:28Z] 2016-04-14 20:28:37 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:28:37,226 - WARNING - Could not retrieve variants from source file in region 2:238732805-238733206. Error was invalid region `2:238732806-238733206`
[2016-04-15T03:28Z] 2016-04-14 20:28:37 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:28:37,921 - WARNING - Could not retrieve variants from source file in region 2:242610527-242618240. Error was invalid region `2:242610528-242618240`
[2016-04-15T03:28Z] 2016-04-14 20:28:38 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:28:38,271 - WARNING - Could not retrieve variants from source file in region 2:242572635-242573401. Error was invalid region `2:242572636-242573401`
[2016-04-15T03:28Z] 2016-04-14 20:28:38 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:28:38,857 - WARNING - Could not retrieve variants from source file in region 2:239229161-239229562. Error was invalid region `2:239229162-239229562`
[2016-04-15T03:28Z] 2016-04-14 20:28:39 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:28:39,643 - WARNING - Could not retrieve variants from source file in region 2:241451140-241463785. Error was invalid region `2:241451141-241463785`
[2016-04-15T03:28Z] 2016-04-14 20:28:39 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:28:39,686 - WARNING - Could not retrieve variants from source file in region 2:242312361-242312762. Error was invalid region `2:242312362-242312762`
[2016-04-15T03:28Z] 2016-04-14 20:28:39 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:28:39,776 - WARNING - Could not retrieve variants from source file in region 2:242793062-242839553. Error was invalid region `2:242793063-242839553`
[2016-04-15T03:28Z] 2016-04-14 20:28:40 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:28:40,197 - WARNING - Could not retrieve variants from source file in region 2:242447751-242448152. Error was invalid region `2:242447752-242448152`
[2016-04-15T03:28Z] 2016-04-14 20:28:40 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:28:40,383 - WARNING - Could not retrieve variants from source file in region 2:241929017-241929418. Error was invalid region `2:241929018-241929418`
[2016-04-15T03:28Z] 2016-04-14 20:28:40 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:28:40,724 - WARNING - Could not retrieve variants from source file in region 2:241066069-241066515. Error was invalid region `2:241066070-241066515`
[2016-04-15T03:28Z] 2016-04-14 20:28:42 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:28:42,468 - WARNING - Could not retrieve variants from source file in region 2:238732805-238733206. Error was invalid region `2:238732806-238733206`
[2016-04-15T03:28Z] 2016-04-14 20:28:46 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:28:46,527 - WARNING - Could not retrieve variants from source file in region 2:242793062-242839553. Error was invalid region `2:242793063-242839553`
[2016-04-15T03:28Z] 2016-04-14 20:28:48 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:28:48,530 - WARNING - Could not retrieve variants from source file in region 2:242370890-242371291. Error was invalid region `2:242370891-242371291`
[2016-04-15T03:28Z] 2016-04-14 20:28:48 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:28:48,592 - WARNING - Could not retrieve variants from source file in region 2:241929017-241929418. Error was invalid region `2:241929018-241929418`
[2016-04-15T03:28Z] 2016-04-14 20:28:48 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:28:48,959 - WARNING - Could not retrieve variants from source file in region 2:242572635-242573401. Error was invalid region `2:242572636-242573401`
[2016-04-15T03:28Z] 2016-04-14 20:28:51 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:28:51,009 - WARNING - Could not retrieve variants from source file in region 2:239229161-239229562. Error was invalid region `2:239229162-239229562`
[2016-04-15T03:28Z] 2016-04-14 20:28:52 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:28:52,231 - WARNING - Could not retrieve variants from source file in region 2:242793062-242839553. Error was invalid region `2:242793063-242839553`
[2016-04-15T03:28Z] 2016-04-14 20:28:53 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:28:53,750 - WARNING - Could not retrieve variants from source file in region 2:241451140-241463785. Error was invalid region `2:241451141-241463785`
[2016-04-15T03:28Z] 2016-04-14 20:28:55 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:28:55,835 - WARNING - Could not retrieve variants from source file in region 2:241564769-241570439. Error was invalid region `2:241564770-241570439`
[2016-04-15T03:28Z] 2016-04-14 20:28:57 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:28:57,368 - WARNING - Could not retrieve variants from source file in region 2:241929017-241929418. Error was invalid region `2:241929018-241929418`
[2016-04-15T03:29Z] 2016-04-14 20:29:07 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:29:07,185 - WARNING - Could not retrieve variants from source file in region 2:241808103-241835733. Error was invalid region `2:241808104-241835733`
[2016-04-15T03:29Z] 2016-04-14 20:29:08 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:29:08,040 - WARNING - Could not retrieve variants from source file in region 2:238786513-238786914. Error was invalid region `2:238786514-238786914`
[2016-04-15T03:29Z] 2016-04-14 20:29:09 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:29:09,349 - WARNING - Could not retrieve variants from source file in region 2:241404106-241405718. Error was invalid region `2:241404107-241405718`
[2016-04-15T03:29Z] 2016-04-14 20:29:10 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:29:10,565 - WARNING - Could not retrieve variants from source file in region 2:238668591-238674745. Error was invalid region `2:238668592-238674745`
[2016-04-15T03:29Z] 2016-04-14 20:29:12 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:29:12,444 - WARNING - Could not retrieve variants from source file in region 2:241872511-241872912. Error was invalid region `2:241872512-241872912`
[2016-04-15T03:29Z] 2016-04-14 20:29:14 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:29:14,367 - WARNING - Could not retrieve variants from source file in region 2:241696629-241721726. Error was invalid region `2:241696630-241721726`
[2016-04-15T03:29Z] 2016-04-14 20:29:19 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:29:19,131 - WARNING - Could not retrieve variants from source file in region 2:241515883-241538264. Error was invalid region `2:241515884-241538264`
[2016-04-15T03:29Z] 2016-04-14 20:29:19 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:29:19,133 - WARNING - Could not retrieve variants from source file in region 2:241808103-241835733. Error was invalid region `2:241808104-241835733`
[2016-04-15T03:29Z] 2016-04-14 20:29:19 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:29:19,941 - WARNING - Could not retrieve variants from source file in region 2:238483460-238494871. Error was invalid region `2:238483461-238494871`
[2016-04-15T03:29Z] 2016-04-14 20:29:20 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:29:20,830 - WARNING - Could not retrieve variants from source file in region 2:241979339-242005056. Error was invalid region `2:241979340-242005056`
[2016-04-15T03:29Z] 2016-04-14 20:29:22 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:29:22,289 - WARNING - Could not retrieve variants from source file in region 2:241872511-241872912. Error was invalid region `2:241872512-241872912`
[2016-04-15T03:29Z] 2016-04-14 20:29:24 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:29:24,982 - WARNING - Could not retrieve variants from source file in region 2:241515883-241538264. Error was invalid region `2:241515884-241538264`
[2016-04-15T03:29Z] 2016-04-14 20:29:25 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:29:25,666 - WARNING - Could not retrieve variants from source file in region 2:242053402-242089763. Error was invalid region `2:242053403-242089763`
[2016-04-15T03:29Z] 2016-04-14 20:29:25 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:29:25,839 - WARNING - Could not retrieve variants from source file in region 2:241696629-241721726. Error was invalid region `2:241696630-241721726`
[2016-04-15T03:29Z] 2016-04-14 20:29:31 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:29:31,594 - WARNING - Could not retrieve variants from source file in region 2:241979339-242005056. Error was invalid region `2:241979340-242005056`
[2016-04-15T03:29Z] 2016-04-14 20:29:32 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:29:32,247 - WARNING - Could not retrieve variants from source file in region 2:242716169-242716570. Error was invalid region `2:242716170-242716570`
[2016-04-15T03:29Z] 2016-04-14 20:29:33 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:29:33,706 - WARNING - Could not retrieve variants from source file in region 2:238426983-238454396. Error was invalid region `2:238426984-238454396`
[2016-04-15T03:29Z] 2016-04-14 20:29:33 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:29:33,707 - WARNING - Could not retrieve variants from source file in region 2:241621658-241632029. Error was invalid region `2:241621659-241632029`
[2016-04-15T03:29Z] 2016-04-14 20:29:35 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:29:35,224 - WARNING - Could not retrieve variants from source file in region 2:238234074-238259004. Error was invalid region `2:238234075-238259004`
[2016-04-15T03:29Z] 2016-04-14 20:29:36 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:29:36,032 - WARNING - Could not retrieve variants from source file in region 2:242716169-242716570. Error was invalid region `2:242716170-242716570`
[2016-04-15T03:29Z] 2016-04-14 20:29:38 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:29:38,748 - WARNING - Could not retrieve variants from source file in region 2:242716169-242716570. Error was invalid region `2:242716170-242716570`
[2016-04-15T03:29Z] 2016-04-14 20:29:38 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:29:38,759 - WARNING - Could not retrieve variants from source file in region 2:238234074-238259004. Error was invalid region `2:238234075-238259004`
[2016-04-15T03:29Z] ['bcbio-variation-recall', 'square', '-Xms750m', '-Xmx7280m', '-XX:+UseSerialGC', '-c', 16, '-r', u'3:1-15512123', '--caller', 'platypus', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/3/Batch1-3_0_15512123.vcf.gz', '/mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/3/Batch1-3_0_15512123.vcf-inputs.txt'] in region: 3:1-15512123
[2016-04-15T03:29Z] 2016-04-14 20:29:55 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:29:55,304 - WARNING - Could not retrieve variants from source file in region 3:14551233-14563427. Error was invalid region `3:14551234-14563427`
[2016-04-15T03:29Z] 2016-04-14 20:29:56 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:29:56,155 - WARNING - Could not retrieve variants from source file in region 3:12228804-12232398. Error was invalid region `3:12228805-12232398`
[2016-04-15T03:29Z] 2016-04-14 20:29:57 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:29:57,056 - WARNING - Could not retrieve variants from source file in region 3:5241098-5241499. Error was invalid region `3:5241099-5241499`
[2016-04-15T03:29Z] 2016-04-14 20:29:57 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:29:57,210 - WARNING - Could not retrieve variants from source file in region 3:14939268-14939669. Error was invalid region `3:14939269-14939669`
[2016-04-15T03:29Z] 2016-04-14 20:29:57 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:29:57,306 - WARNING - Could not retrieve variants from source file in region 3:12475346-12475747. Error was invalid region `3:12475347-12475747`
[2016-04-15T03:29Z] 2016-04-14 20:29:58 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:29:58,099 - WARNING - Could not retrieve variants from source file in region 3:14861910-14862311. Error was invalid region `3:14861911-14862311`
[2016-04-15T03:29Z] 2016-04-14 20:29:59 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:29:59,411 - WARNING - Could not retrieve variants from source file in region 3:11063880-11064281. Error was invalid region `3:11063881-11064281`
[2016-04-15T03:30Z] 2016-04-14 20:30:01 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:30:01,370 - WARNING - Could not retrieve variants from source file in region 3:12228804-12232398. Error was invalid region `3:12228805-12232398`
[2016-04-15T03:30Z] 2016-04-14 20:30:02 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:30:02,292 - WARNING - Could not retrieve variants from source file in region 3:10413315-10420277. Error was invalid region `3:10413316-10420277`
[2016-04-15T03:30Z] 2016-04-14 20:30:04 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:30:04,031 - WARNING - Could not retrieve variants from source file in region 3:10967528-10967929. Error was invalid region `3:10967529-10967929`
[2016-04-15T03:30Z] 2016-04-14 20:30:04 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:30:04,057 - WARNING - Could not retrieve variants from source file in region 3:12475346-12475747. Error was invalid region `3:12475347-12475747`
[2016-04-15T03:30Z] 2016-04-14 20:30:04 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:30:04,426 - WARNING - Could not retrieve variants from source file in region 3:5241098-5241499. Error was invalid region `3:5241099-5241499`
[2016-04-15T03:30Z] 2016-04-14 20:30:04 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:30:04,873 - WARNING - Could not retrieve variants from source file in region 3:12848611-12875633. Error was invalid region `3:12848612-12875633`
[2016-04-15T03:30Z] 2016-04-14 20:30:05 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:30:05,419 - WARNING - Could not retrieve variants from source file in region 3:14939268-14939669. Error was invalid region `3:14939269-14939669`
[2016-04-15T03:30Z] 2016-04-14 20:30:05 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:30:05,771 - WARNING - Could not retrieve variants from source file in region 3:10860997-10886110. Error was invalid region `3:10860998-10886110`
[2016-04-15T03:30Z] 2016-04-14 20:30:05 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:30:05,799 - WARNING - Could not retrieve variants from source file in region 3:11871004-11871405. Error was invalid region `3:11871005-11871405`
[2016-04-15T03:30Z] 2016-04-14 20:30:06 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:30:06,161 - WARNING - Could not retrieve variants from source file in region 3:12228804-12232398. Error was invalid region `3:12228805-12232398`
[2016-04-15T03:30Z] 2016-04-14 20:30:11 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:30:11,165 - WARNING - Could not retrieve variants from source file in region 3:5241098-5241499. Error was invalid region `3:5241099-5241499`
[2016-04-15T03:30Z] 2016-04-14 20:30:13 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:30:13,835 - WARNING - Could not retrieve variants from source file in region 3:14939268-14939669. Error was invalid region `3:14939269-14939669`
[2016-04-15T03:30Z] 2016-04-14 20:30:14 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:30:14,068 - WARNING - Could not retrieve variants from source file in region 3:10860997-10886110. Error was invalid region `3:10860998-10886110`
[2016-04-15T03:30Z] 2016-04-14 20:30:25 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:30:25,390 - WARNING - Could not retrieve variants from source file in region 3:14489159-14489560. Error was invalid region `3:14489160-14489560`
[2016-04-15T03:30Z] 2016-04-14 20:30:25 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:30:25,674 - WARNING - Could not retrieve variants from source file in region 3:3170581-3189469. Error was invalid region `3:3170582-3189469`
[2016-04-15T03:30Z] 2016-04-14 20:30:26 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:30:26,625 - WARNING - Could not retrieve variants from source file in region 3:12392914-12393315. Error was invalid region `3:12392915-12393315`
[2016-04-15T03:30Z] 2016-04-14 20:30:27 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:30:27,160 - WARNING - Could not retrieve variants from source file in region 3:12392914-12393315. Error was invalid region `3:12392915-12393315`
[2016-04-15T03:30Z] 2016-04-14 20:30:27 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:30:27,204 - WARNING - Could not retrieve variants from source file in region 3:4816846-4856424. Error was invalid region `3:4816847-4856424`
[2016-04-15T03:30Z] 2016-04-14 20:30:29 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:30:29,530 - WARNING - Could not retrieve variants from source file in region 3:14745646-14755807. Error was invalid region `3:14745647-14755807`
[2016-04-15T03:30Z] 2016-04-14 20:30:29 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:30:29,941 - WARNING - Could not retrieve variants from source file in region 3:12613655-12614056. Error was invalid region `3:12613656-12614056`
[2016-04-15T03:30Z] 2016-04-14 20:30:30 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:30:30,498 - WARNING - Could not retrieve variants from source file in region 3:11925278-11925679. Error was invalid region `3:11925279-11925679`
[2016-04-15T03:30Z] 2016-04-14 20:30:30 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:30:30,597 - WARNING - Could not retrieve variants from source file in region 3:14489159-14489560. Error was invalid region `3:14489160-14489560`
[2016-04-15T03:30Z] 2016-04-14 20:30:30 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:30:30,602 - WARNING - Could not retrieve variants from source file in region 3:11643254-11646200. Error was invalid region `3:11643255-11646200`
[2016-04-15T03:30Z] 2016-04-14 20:30:31 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:30:31,315 - WARNING - Could not retrieve variants from source file in region 3:3170581-3189469. Error was invalid region `3:3170582-3189469`
[2016-04-15T03:30Z] 2016-04-14 20:30:31 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:30:31,321 - WARNING - Could not retrieve variants from source file in region 3:9406625-9426101. Error was invalid region `3:9406626-9426101`
[2016-04-15T03:30Z] 2016-04-14 20:30:31 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:30:31,588 - WARNING - Could not retrieve variants from source file in region 3:15311114-15315002. Error was invalid region `3:15311115-15315002`
[2016-04-15T03:30Z] 2016-04-14 20:30:32 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:30:32,113 - WARNING - Could not retrieve variants from source file in region 3:11925278-11925679. Error was invalid region `3:11925279-11925679`
[2016-04-15T03:30Z] 2016-04-14 20:30:32 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:30:32,733 - WARNING - Could not retrieve variants from source file in region 3:10301961-10302362. Error was invalid region `3:10301962-10302362`
[2016-04-15T03:30Z] 2016-04-14 20:30:32 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:30:32,769 - WARNING - Could not retrieve variants from source file in region 3:4816846-4856424. Error was invalid region `3:4816847-4856424`
[2016-04-15T03:30Z] 2016-04-14 20:30:33 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:30:33,993 - WARNING - Could not retrieve variants from source file in region 3:14745646-14755807. Error was invalid region `3:14745647-14755807`
[2016-04-15T03:30Z] 2016-04-14 20:30:34 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:30:34,703 - WARNING - Could not retrieve variants from source file in region 3:12613655-12614056. Error was invalid region `3:12613656-12614056`
[2016-04-15T03:30Z] 2016-04-14 20:30:35 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:30:35,580 - WARNING - Could not retrieve variants from source file in region 3:11643254-11646200. Error was invalid region `3:11643255-11646200`
[2016-04-15T03:30Z] 2016-04-14 20:30:35 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:30:35,691 - WARNING - Could not retrieve variants from source file in region 3:14489159-14489560. Error was invalid region `3:14489160-14489560`
[2016-04-15T03:30Z] 2016-04-14 20:30:35 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:30:35,853 - WARNING - Could not retrieve variants from source file in region 3:3170581-3189469. Error was invalid region `3:3170582-3189469`
[2016-04-15T03:30Z] 2016-04-14 20:30:36 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:30:36,131 - WARNING - Could not retrieve variants from source file in region 3:9406625-9426101. Error was invalid region `3:9406626-9426101`
[2016-04-15T03:30Z] 2016-04-14 20:30:37 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:30:37,128 - WARNING - Could not retrieve variants from source file in region 3:12571209-12572374. Error was invalid region `3:12571210-12572374`
[2016-04-15T03:30Z] 2016-04-14 20:30:37 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:30:37,948 - WARNING - Could not retrieve variants from source file in region 3:10301961-10302362. Error was invalid region `3:10301962-10302362`
[2016-04-15T03:30Z] 2016-04-14 20:30:37 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:30:37,967 - WARNING - Could not retrieve variants from source file in region 3:4816846-4856424. Error was invalid region `3:4816847-4856424`
[2016-04-15T03:30Z] 2016-04-14 20:30:38 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:30:38,933 - WARNING - Could not retrieve variants from source file in region 3:12613655-12614056. Error was invalid region `3:12613656-12614056`
[2016-04-15T03:30Z] 2016-04-14 20:30:39 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:30:39,714 - WARNING - Could not retrieve variants from source file in region 3:11643254-11646200. Error was invalid region `3:11643255-11646200`
[2016-04-15T03:30Z] 2016-04-14 20:30:40 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:30:40,388 - WARNING - Could not retrieve variants from source file in region 3:9406625-9426101. Error was invalid region `3:9406626-9426101`
[2016-04-15T03:30Z] 2016-04-14 20:30:42 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:30:42,148 - WARNING - Could not retrieve variants from source file in region 3:10301961-10302362. Error was invalid region `3:10301962-10302362`
[2016-04-15T03:30Z] 2016-04-14 20:30:45 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:30:45,434 - WARNING - Could not retrieve variants from source file in region 3:9969785-9991578. Error was invalid region `3:9969786-9991578`
[2016-04-15T03:30Z] 2016-04-14 20:30:45 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:30:45,642 - WARNING - Could not retrieve variants from source file in region 3:11596091-11596492. Error was invalid region `3:11596092-11596492`
[2016-04-15T03:30Z] 2016-04-14 20:30:46 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:30:46,126 - WARNING - Could not retrieve variants from source file in region 3:1262263-1262664. Error was invalid region `3:1262264-1262664`
[2016-04-15T03:30Z] 2016-04-14 20:30:46 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:30:46,496 - WARNING - Could not retrieve variants from source file in region 3:10254791-10276353. Error was invalid region `3:10254792-10276353`
[2016-04-15T03:30Z] 2016-04-14 20:30:48 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:30:48,038 - WARNING - Could not retrieve variants from source file in region 3:14174216-14198177. Error was invalid region `3:14174217-14198177`
[2016-04-15T03:30Z] 2016-04-14 20:30:48 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:30:48,829 - WARNING - Could not retrieve variants from source file in region 3:11596091-11596492. Error was invalid region `3:11596092-11596492`
[2016-04-15T03:30Z] 2016-04-14 20:30:48 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:30:48,903 - WARNING - Could not retrieve variants from source file in region 3:3133580-3134086. Error was invalid region `3:3133581-3134086`
[2016-04-15T03:30Z] 2016-04-14 20:30:51 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:30:51,041 - WARNING - Could not retrieve variants from source file in region 3:11596091-11596492. Error was invalid region `3:11596092-11596492`
[2016-04-15T03:30Z] 2016-04-14 20:30:51 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:30:51,618 - WARNING - Could not retrieve variants from source file in region 3:3067639-3082015. Error was invalid region `3:3067640-3082015`
[2016-04-15T03:30Z] 2016-04-14 20:30:52 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:30:52,187 - WARNING - Could not retrieve variants from source file in region 3:13610049-13613126. Error was invalid region `3:13610050-13613126`
[2016-04-15T03:30Z] 2016-04-14 20:30:52 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:30:52,608 - WARNING - Could not retrieve variants from source file in region 3:11518544-11518945. Error was invalid region `3:11518545-11518945`
[2016-04-15T03:30Z] 2016-04-14 20:30:53 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:30:53,138 - WARNING - Could not retrieve variants from source file in region 3:10254791-10276353. Error was invalid region `3:10254792-10276353`
[2016-04-15T03:30Z] 2016-04-14 20:30:53 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:30:53,280 - WARNING - Could not retrieve variants from source file in region 3:4767051-4767452. Error was invalid region `3:4767052-4767452`
[2016-04-15T03:30Z] 2016-04-14 20:30:53 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:30:53,946 - WARNING - Could not retrieve variants from source file in region 3:8955178-8955579. Error was invalid region `3:8955179-8955579`
[2016-04-15T03:30Z] 2016-04-14 20:30:55 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:30:55,060 - WARNING - Could not retrieve variants from source file in region 3:12544618-12545019. Error was invalid region `3:12544619-12545019`
[2016-04-15T03:30Z] 2016-04-14 20:30:55 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:30:55,088 - WARNING - Could not retrieve variants from source file in region 3:9969785-9991578. Error was invalid region `3:9969786-9991578`
[2016-04-15T03:30Z] 2016-04-14 20:30:57 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:30:57,388 - WARNING - Could not retrieve variants from source file in region 3:10191732-10192133. Error was invalid region `3:10191733-10192133`
[2016-04-15T03:30Z] 2016-04-14 20:30:57 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:30:57,866 - WARNING - Could not retrieve variants from source file in region 3:11518544-11518945. Error was invalid region `3:11518545-11518945`
[2016-04-15T03:30Z] 2016-04-14 20:30:58 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:30:58,283 - WARNING - Could not retrieve variants from source file in region 3:4508531-4508932. Error was invalid region `3:4508532-4508932`
[2016-04-15T03:30Z] 2016-04-14 20:30:58 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:30:58,432 - WARNING - Could not retrieve variants from source file in region 3:4767051-4767452. Error was invalid region `3:4767052-4767452`
[2016-04-15T03:30Z] 2016-04-14 20:30:59 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:30:59,418 - WARNING - Could not retrieve variants from source file in region 3:8955178-8955579. Error was invalid region `3:8955179-8955579`
[2016-04-15T03:30Z] 2016-04-14 20:30:59 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:30:59,572 - WARNING - Could not retrieve variants from source file in region 3:14174216-14198177. Error was invalid region `3:14174217-14198177`
[2016-04-15T03:31Z] 2016-04-14 20:31:00 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:31:00,023 - WARNING - Could not retrieve variants from source file in region 3:11518544-11518945. Error was invalid region `3:11518545-11518945`
[2016-04-15T03:31Z] 2016-04-14 20:31:02 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:31:02,356 - WARNING - Could not retrieve variants from source file in region 3:3067639-3082015. Error was invalid region `3:3067640-3082015`
[2016-04-15T03:31Z] 2016-04-14 20:31:02 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:31:02,434 - WARNING - Could not retrieve variants from source file in region 3:10191732-10192133. Error was invalid region `3:10191733-10192133`
[2016-04-15T03:31Z] 2016-04-14 20:31:02 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:31:02,465 - WARNING - Could not retrieve variants from source file in region 3:13610049-13613126. Error was invalid region `3:13610050-13613126`
[2016-04-15T03:31Z] 2016-04-14 20:31:03 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:31:03,716 - WARNING - Could not retrieve variants from source file in region 3:4767051-4767452. Error was invalid region `3:4767052-4767452`
[2016-04-15T03:31Z] 2016-04-14 20:31:04 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:31:04,732 - WARNING - Could not retrieve variants from source file in region 3:8955178-8955579. Error was invalid region `3:8955179-8955579`
[2016-04-15T03:31Z] 2016-04-14 20:31:07 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:31:07,160 - WARNING - Could not retrieve variants from source file in region 3:439752-440218. Error was invalid region `3:439753-440218`
[2016-04-15T03:31Z] 2016-04-14 20:31:07 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:31:07,264 - WARNING - Could not retrieve variants from source file in region 3:10191732-10192133. Error was invalid region `3:10191733-10192133`
[2016-04-15T03:31Z] 2016-04-14 20:31:11 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:31:11,890 - WARNING - Could not retrieve variants from source file in region 3:439752-440218. Error was invalid region `3:439753-440218`
[2016-04-15T03:31Z] 2016-04-14 20:31:12 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:31:12,447 - WARNING - Could not retrieve variants from source file in region 3:9908724-9934795. Error was invalid region `3:9908725-9934795`
[2016-04-15T03:31Z] 2016-04-14 20:31:13 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:31:13,886 - WARNING - Could not retrieve variants from source file in region 3:13056933-13064011. Error was invalid region `3:13056934-13064011`
[2016-04-15T03:31Z] 2016-04-14 20:31:13 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:31:13,990 - WARNING - Could not retrieve variants from source file in region 3:1424639-1425040. Error was invalid region `3:1424640-1425040`
[2016-04-15T03:31Z] 2016-04-14 20:31:13 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:31:13,991 - WARNING - Could not retrieve variants from source file in region 3:4354486-4354887. Error was invalid region `3:4354487-4354887`
[2016-04-15T03:31Z] 2016-04-14 20:31:14 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:31:14,027 - WARNING - Could not retrieve variants from source file in region 3:13670270-13679525. Error was invalid region `3:13670271-13679525`
[2016-04-15T03:31Z] 2016-04-14 20:31:14 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:31:14,305 - WARNING - Could not retrieve variants from source file in region 3:4403626-4404027. Error was invalid region `3:4403627-4404027`
[2016-04-15T03:31Z] 2016-04-14 20:31:15 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:31:15,828 - WARNING - Could not retrieve variants from source file in region 3:13361076-13421340. Error was invalid region `3:13361077-13421340`
[2016-04-15T03:31Z] 2016-04-14 20:31:16 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:31:16,416 - WARNING - Could not retrieve variants from source file in region 3:439752-440218. Error was invalid region `3:439753-440218`
[2016-04-15T03:31Z] 2016-04-14 20:31:18 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:31:18,729 - WARNING - Could not retrieve variants from source file in region 3:1424639-1425040. Error was invalid region `3:1424640-1425040`
[2016-04-15T03:31Z] 2016-04-14 20:31:18 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:31:18,896 - WARNING - Could not retrieve variants from source file in region 3:13670270-13679525. Error was invalid region `3:13670271-13679525`
[2016-04-15T03:31Z] 2016-04-14 20:31:19 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:31:19,329 - WARNING - Could not retrieve variants from source file in region 3:4403626-4404027. Error was invalid region `3:4403627-4404027`
[2016-04-15T03:31Z] 2016-04-14 20:31:20 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:31:20,177 - WARNING - Could not retrieve variants from source file in region 3:13361076-13421340. Error was invalid region `3:13361077-13421340`
[2016-04-15T03:31Z] 2016-04-14 20:31:22 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:31:22,036 - WARNING - Could not retrieve variants from source file in region 3:4712202-4717001. Error was invalid region `3:4712203-4717001`
[2016-04-15T03:31Z] 2016-04-14 20:31:22 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:31:22,207 - WARNING - Could not retrieve variants from source file in region 3:8775450-8809893. Error was invalid region `3:8775451-8809893`
[2016-04-15T03:31Z] 2016-04-14 20:31:22 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:31:22,529 - WARNING - Could not retrieve variants from source file in region 3:13056933-13064011. Error was invalid region `3:13056934-13064011`
[2016-04-15T03:31Z] 2016-04-14 20:31:23 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:31:23,095 - WARNING - Could not retrieve variants from source file in region 3:1424639-1425040. Error was invalid region `3:1424640-1425040`
[2016-04-15T03:31Z] 2016-04-14 20:31:23 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:31:23,298 - WARNING - Could not retrieve variants from source file in region 3:4354486-4354887. Error was invalid region `3:4354487-4354887`
[2016-04-15T03:31Z] 2016-04-14 20:31:23 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:31:23,500 - WARNING - Could not retrieve variants from source file in region 3:13670270-13679525. Error was invalid region `3:13670271-13679525`
[2016-04-15T03:31Z] 2016-04-14 20:31:24 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:31:24,253 - WARNING - Could not retrieve variants from source file in region 3:4403626-4404027. Error was invalid region `3:4403627-4404027`
[2016-04-15T03:31Z] 2016-04-14 20:31:24 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:31:24,644 - WARNING - Could not retrieve variants from source file in region 3:13361076-13421340. Error was invalid region `3:13361077-13421340`
[2016-04-15T03:31Z] 2016-04-14 20:31:28 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:31:28,299 - WARNING - Could not retrieve variants from source file in region 3:390889-391290. Error was invalid region `3:390890-391290`
[2016-04-15T03:31Z] 2016-04-14 20:31:31 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:31:31,554 - WARNING - Could not retrieve variants from source file in region 3:9798562-9798963. Error was invalid region `3:9798563-9798963`
[2016-04-15T03:31Z] 2016-04-14 20:31:31 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:31:31,562 - WARNING - Could not retrieve variants from source file in region 3:9798562-9798963. Error was invalid region `3:9798563-9798963`
[2016-04-15T03:31Z] 2016-04-14 20:31:32 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:31:32,840 - WARNING - Could not retrieve variants from source file in region 3:390889-391290. Error was invalid region `3:390890-391290`
[2016-04-15T03:31Z] 2016-04-14 20:31:34 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:31:34,679 - WARNING - Could not retrieve variants from source file in region 3:3886369-3888066. Error was invalid region `3:3886370-3888066`
[2016-04-15T03:31Z] 2016-04-14 20:31:34 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:31:34,915 - WARNING - Could not retrieve variants from source file in region 3:8591906-8592307. Error was invalid region `3:8591907-8592307`
[2016-04-15T03:31Z] 2016-04-14 20:31:35 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:31:35,183 - WARNING - Could not retrieve variants from source file in region 3:7494206-7494607. Error was invalid region `3:7494207-7494607`
[2016-04-15T03:31Z] 2016-04-14 20:31:35 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:31:35,230 - WARNING - Could not retrieve variants from source file in region 3:3886369-3888066. Error was invalid region `3:3886370-3888066`
[2016-04-15T03:31Z] 2016-04-14 20:31:36 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:31:36,206 - WARNING - Could not retrieve variants from source file in region 3:390889-391290. Error was invalid region `3:390890-391290`
[2016-04-15T03:31Z] 2016-04-14 20:31:37 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:31:37,633 - WARNING - Could not retrieve variants from source file in region 3:8675328-8676394. Error was invalid region `3:8675329-8676394`
[2016-04-15T03:31Z] 2016-04-14 20:31:38 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:31:38,474 - WARNING - Could not retrieve variants from source file in region 3:3886369-3888066. Error was invalid region `3:3886370-3888066`
[2016-04-15T03:31Z] 2016-04-14 20:31:38 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:31:38,738 - WARNING - Could not retrieve variants from source file in region 3:8591906-8592307. Error was invalid region `3:8591907-8592307`
[2016-04-15T03:31Z] 2016-04-14 20:31:38 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:31:38,885 - WARNING - Could not retrieve variants from source file in region 3:7494206-7494607. Error was invalid region `3:7494207-7494607`
[2016-04-15T03:31Z] 2016-04-14 20:31:39 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:31:39,684 - WARNING - Could not retrieve variants from source file in region 3:7619957-7621018. Error was invalid region `3:7619958-7621018`
[2016-04-15T03:31Z] 2016-04-14 20:31:42 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:31:42,246 - WARNING - Could not retrieve variants from source file in region 3:6903086-6903487. Error was invalid region `3:6903087-6903487`
[2016-04-15T03:31Z] 2016-04-14 20:31:42 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:31:42,454 - WARNING - Could not retrieve variants from source file in region 3:8591906-8592307. Error was invalid region `3:8591907-8592307`
[2016-04-15T03:31Z] 2016-04-14 20:31:42 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:31:42,496 - WARNING - Could not retrieve variants from source file in region 3:7619957-7621018. Error was invalid region `3:7619958-7621018`
[2016-04-15T03:31Z] 2016-04-14 20:31:42 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:31:42,579 - WARNING - Could not retrieve variants from source file in region 3:6903086-6903487. Error was invalid region `3:6903087-6903487`
[2016-04-15T03:31Z] 2016-04-14 20:31:43 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:31:43,733 - WARNING - Could not retrieve variants from source file in region 3:6903086-6903487. Error was invalid region `3:6903087-6903487`
[2016-04-15T03:31Z] ['bcbio-variation-recall', 'square', '-Xms750m', '-Xmx7280m', '-XX:+UseSerialGC', '-c', 16, '-r', u'3:15515507-31574805', '--caller', 'platypus', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/3/Batch1-3_15515506_31574805.vcf.gz', '/mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/3/Batch1-3_15515506_31574805.vcf-inputs.txt'] in region: 3:15515507-31574805
[2016-04-15T03:31Z] 2016-04-14 20:31:59 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:31:59,786 - WARNING - Could not retrieve variants from source file in region 3:17208056-17208457. Error was invalid region `3:17208057-17208457`
[2016-04-15T03:31Z] 2016-04-14 20:31:59 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:31:59,787 - WARNING - Could not retrieve variants from source file in region 3:18392608-18393009. Error was invalid region `3:18392609-18393009`
[2016-04-15T03:32Z] 2016-04-14 20:32:00 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:32:00,701 - WARNING - Could not retrieve variants from source file in region 3:16645936-16646384. Error was invalid region `3:16645937-16646384`
[2016-04-15T03:32Z] 2016-04-14 20:32:00 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:32:00,763 - WARNING - Could not retrieve variants from source file in region 3:26751282-26751683. Error was invalid region `3:26751283-26751683`
[2016-04-15T03:32Z] 2016-04-14 20:32:00 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:32:00,772 - WARNING - Could not retrieve variants from source file in region 3:25679527-25679928. Error was invalid region `3:25679528-25679928`
[2016-04-15T03:32Z] 2016-04-14 20:32:01 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:32:01,113 - WARNING - Could not retrieve variants from source file in region 3:27242834-27243235. Error was invalid region `3:27242835-27243235`
[2016-04-15T03:32Z] 2016-04-14 20:32:01 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:32:01,153 - WARNING - Could not retrieve variants from source file in region 3:24006266-24006667. Error was invalid region `3:24006267-24006667`
[2016-04-15T03:32Z] 2016-04-14 20:32:01 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:32:01,598 - WARNING - Could not retrieve variants from source file in region 3:15642832-15643233. Error was invalid region `3:15642833-15643233`
[2016-04-15T03:32Z] 2016-04-14 20:32:01 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:32:01,906 - WARNING - Could not retrieve variants from source file in region 3:15737478-15737888. Error was invalid region `3:15737479-15737888`
[2016-04-15T03:32Z] 2016-04-14 20:32:01 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:32:01,987 - WARNING - Could not retrieve variants from source file in region 3:21792391-21792792. Error was invalid region `3:21792392-21792792`
[2016-04-15T03:32Z] 2016-04-14 20:32:02 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:32:02,026 - WARNING - Could not retrieve variants from source file in region 3:25776070-25776541. Error was invalid region `3:25776071-25776541`
[2016-04-15T03:32Z] 2016-04-14 20:32:06 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:32:06,033 - WARNING - Could not retrieve variants from source file in region 3:18392608-18393009. Error was invalid region `3:18392609-18393009`
[2016-04-15T03:32Z] 2016-04-14 20:32:06 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:32:06,815 - WARNING - Could not retrieve variants from source file in region 3:27424507-27490384. Error was invalid region `3:27424508-27490384`
[2016-04-15T03:32Z] 2016-04-14 20:32:10 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:32:10,369 - WARNING - Could not retrieve variants from source file in region 3:15737478-15737888. Error was invalid region `3:15737479-15737888`
[2016-04-15T03:32Z] 2016-04-14 20:32:10 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:32:10,640 - WARNING - Could not retrieve variants from source file in region 3:24006266-24006667. Error was invalid region `3:24006267-24006667`
[2016-04-15T03:32Z] 2016-04-14 20:32:10 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:32:10,652 - WARNING - Could not retrieve variants from source file in region 3:25776070-25776541. Error was invalid region `3:25776071-25776541`
[2016-04-15T03:32Z] 2016-04-14 20:32:10 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:32:10,710 - WARNING - Could not retrieve variants from source file in region 3:15642832-15643233. Error was invalid region `3:15642833-15643233`
[2016-04-15T03:32Z] 2016-04-14 20:32:10 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:32:10,769 - WARNING - Could not retrieve variants from source file in region 3:21792391-21792792. Error was invalid region `3:21792392-21792792`
[2016-04-15T03:32Z] 2016-04-14 20:32:10 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:32:10,779 - WARNING - Could not retrieve variants from source file in region 3:19575170-19575571. Error was invalid region `3:19575171-19575571`
[2016-04-15T03:32Z] 2016-04-14 20:32:12 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:32:12,750 - WARNING - Could not retrieve variants from source file in region 3:27242834-27243235. Error was invalid region `3:27242835-27243235`
[2016-04-15T03:32Z] 2016-04-14 20:32:18 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:32:18,060 - WARNING - Could not retrieve variants from source file in region 3:26751282-26751683. Error was invalid region `3:26751283-26751683`
[2016-04-15T03:32Z] 2016-04-14 20:32:18 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:32:18,064 - WARNING - Could not retrieve variants from source file in region 3:27297605-27333010. Error was invalid region `3:27297606-27333010`
[2016-04-15T03:32Z] 2016-04-14 20:32:18 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:32:18,695 - WARNING - Could not retrieve variants from source file in region 3:24006266-24006667. Error was invalid region `3:24006267-24006667`
[2016-04-15T03:32Z] 2016-04-14 20:32:18 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:32:18,716 - WARNING - Could not retrieve variants from source file in region 3:15737478-15737888. Error was invalid region `3:15737479-15737888`
[2016-04-15T03:32Z] 2016-04-14 20:32:19 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:32:19,085 - WARNING - Could not retrieve variants from source file in region 3:15642832-15643233. Error was invalid region `3:15642833-15643233`
[2016-04-15T03:32Z] 2016-04-14 20:32:19 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:32:19,643 - WARNING - Could not retrieve variants from source file in region 3:21792391-21792792. Error was invalid region `3:21792392-21792792`
[2016-04-15T03:32Z] 2016-04-14 20:32:19 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:32:19,654 - WARNING - Could not retrieve variants from source file in region 3:25776070-25776541. Error was invalid region `3:25776071-25776541`
[2016-04-15T03:32Z] 2016-04-14 20:32:20 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:32:20,140 - WARNING - Could not retrieve variants from source file in region 3:27763216-27764318. Error was invalid region `3:27763217-27764318`
[2016-04-15T03:32Z] 2016-04-14 20:32:29 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:32:29,700 - WARNING - Could not retrieve variants from source file in region 3:17051117-17053689. Error was invalid region `3:17051118-17053689`
[2016-04-15T03:32Z] 2016-04-14 20:32:30 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:32:30,303 - WARNING - Could not retrieve variants from source file in region 3:18055020-18055421. Error was invalid region `3:18055021-18055421`
[2016-04-15T03:32Z] 2016-04-14 20:32:31 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:32:31,322 - WARNING - Could not retrieve variants from source file in region 3:25300339-25300740. Error was invalid region `3:25300340-25300740`
[2016-04-15T03:32Z] 2016-04-14 20:32:31 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:32:31,648 - WARNING - Could not retrieve variants from source file in region 3:16358373-16365144. Error was invalid region `3:16358374-16365144`
[2016-04-15T03:32Z] 2016-04-14 20:32:32 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:32:32,168 - WARNING - Could not retrieve variants from source file in region 3:25705860-25706467. Error was invalid region `3:25705861-25706467`
[2016-04-15T03:32Z] 2016-04-14 20:32:32 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:32:32,176 - WARNING - Could not retrieve variants from source file in region 3:20042623-20043721. Error was invalid region `3:20042624-20043721`
[2016-04-15T03:32Z] 2016-04-14 20:32:32 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:32:32,827 - WARNING - Could not retrieve variants from source file in region 3:16305463-16328045. Error was invalid region `3:16305464-16328045`
[2016-04-15T03:32Z] 2016-04-14 20:32:34 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:32:34,106 - WARNING - Could not retrieve variants from source file in region 3:17051117-17053689. Error was invalid region `3:17051118-17053689`
[2016-04-15T03:32Z] 2016-04-14 20:32:35 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:32:35,050 - WARNING - Could not retrieve variants from source file in region 3:21462543-21484952. Error was invalid region `3:21462544-21484952`
[2016-04-15T03:32Z] 2016-04-14 20:32:36 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:32:36,183 - WARNING - Could not retrieve variants from source file in region 3:20042623-20043721. Error was invalid region `3:20042624-20043721`
[2016-04-15T03:32Z] 2016-04-14 20:32:36 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:32:36,692 - WARNING - Could not retrieve variants from source file in region 3:15609859-15610260. Error was invalid region `3:15609860-15610260`
[2016-04-15T03:32Z] 2016-04-14 20:32:36 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:32:36,709 - WARNING - Could not retrieve variants from source file in region 3:22210252-22210653. Error was invalid region `3:22210253-22210653`
[2016-04-15T03:32Z] 2016-04-14 20:32:36 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:32:36,946 - WARNING - Could not retrieve variants from source file in region 3:16305463-16328045. Error was invalid region `3:16305464-16328045`
[2016-04-15T03:32Z] 2016-04-14 20:32:38 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:32:38,087 - WARNING - Could not retrieve variants from source file in region 3:17051117-17053689. Error was invalid region `3:17051118-17053689`
[2016-04-15T03:32Z] 2016-04-14 20:32:38 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:32:38,201 - WARNING - Could not retrieve variants from source file in region 3:18055020-18055421. Error was invalid region `3:18055021-18055421`
[2016-04-15T03:32Z] 2016-04-14 20:32:38 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:32:38,653 - WARNING - Could not retrieve variants from source file in region 3:19190030-19190431. Error was invalid region `3:19190031-19190431`
[2016-04-15T03:32Z] 2016-04-14 20:32:38 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:32:38,938 - WARNING - Could not retrieve variants from source file in region 3:25300339-25300740. Error was invalid region `3:25300340-25300740`
[2016-04-15T03:32Z] 2016-04-14 20:32:40 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:32:40,235 - WARNING - Could not retrieve variants from source file in region 3:20042623-20043721. Error was invalid region `3:20042624-20043721`
[2016-04-15T03:32Z] 2016-04-14 20:32:40 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:32:40,687 - WARNING - Could not retrieve variants from source file in region 3:22210252-22210653. Error was invalid region `3:22210253-22210653`
[2016-04-15T03:32Z] 2016-04-14 20:32:41 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:32:41,070 - WARNING - Could not retrieve variants from source file in region 3:16305463-16328045. Error was invalid region `3:16305464-16328045`
[2016-04-15T03:32Z] 2016-04-14 20:32:41 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:32:41,098 - WARNING - Could not retrieve variants from source file in region 3:15609859-15610260. Error was invalid region `3:15609860-15610260`
[2016-04-15T03:32Z] 2016-04-14 20:32:42 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:32:42,975 - WARNING - Could not retrieve variants from source file in region 3:19190030-19190431. Error was invalid region `3:19190031-19190431`
[2016-04-15T03:32Z] 2016-04-14 20:32:48 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:32:48,907 - WARNING - Could not retrieve variants from source file in region 3:18427713-18428114. Error was invalid region `3:18427714-18428114`
[2016-04-15T03:32Z] 2016-04-14 20:32:48 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:32:48,907 - WARNING - Could not retrieve variants from source file in region 3:18427713-18428114. Error was invalid region `3:18427714-18428114`
[2016-04-15T03:32Z] 2016-04-14 20:32:48 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:32:48,933 - WARNING - Could not retrieve variants from source file in region 3:18427713-18428114. Error was invalid region `3:18427714-18428114`
[2016-04-15T03:32Z] 2016-04-14 20:32:49 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:32:49,371 - WARNING - Could not retrieve variants from source file in region 3:19959545-19992622. Error was invalid region `3:19959546-19992622`
[2016-04-15T03:32Z] 2016-04-14 20:32:49 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:32:49,379 - WARNING - Could not retrieve variants from source file in region 3:19959545-19992622. Error was invalid region `3:19959546-19992622`
[2016-04-15T03:32Z] ['bcbio-variation-recall', 'square', '-Xms750m', '-Xmx7280m', '-XX:+UseSerialGC', '-c', 16, '-r', u'3:31617888-47127804', '--caller', 'platypus', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/3/Batch1-3_31617887_47127804.vcf.gz', '/mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/3/Batch1-3_31617887_47127804.vcf-inputs.txt'] in region: 3:31617888-47127804
[2016-04-15T03:33Z] 2016-04-14 20:33:04 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:33:04,924 - WARNING - Could not retrieve variants from source file in region 3:33434620-33458456. Error was invalid region `3:33434621-33458456`
[2016-04-15T03:33Z] 2016-04-14 20:33:07 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:33:07,727 - WARNING - Could not retrieve variants from source file in region 3:46620403-46622819. Error was invalid region `3:46620404-46622819`
[2016-04-15T03:33Z] 2016-04-14 20:33:07 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:33:07,814 - WARNING - Could not retrieve variants from source file in region 3:45527007-45565744. Error was invalid region `3:45527008-45565744`
[2016-04-15T03:33Z] 2016-04-14 20:33:08 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:33:08,236 - WARNING - Could not retrieve variants from source file in region 3:46658526-46658927. Error was invalid region `3:46658527-46658927`
[2016-04-15T03:33Z] 2016-04-14 20:33:08 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:33:08,449 - WARNING - Could not retrieve variants from source file in region 3:44762181-44776152. Error was invalid region `3:44762182-44776152`
[2016-04-15T03:33Z] 2016-04-14 20:33:08 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:33:08,603 - WARNING - Could not retrieve variants from source file in region 3:38674501-38674902. Error was invalid region `3:38674502-38674902`
[2016-04-15T03:33Z] 2016-04-14 20:33:08 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:33:08,907 - WARNING - Could not retrieve variants from source file in region 3:39225916-39230090. Error was invalid region `3:39225917-39230090`
[2016-04-15T03:33Z] 2016-04-14 20:33:09 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:33:09,058 - WARNING - Could not retrieve variants from source file in region 3:47125174-47125575. Error was invalid region `3:47125175-47125575`
[2016-04-15T03:33Z] 2016-04-14 20:33:09 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:33:09,186 - WARNING - Could not retrieve variants from source file in region 3:38519213-38539287. Error was invalid region `3:38519214-38539287`
[2016-04-15T03:33Z] 2016-04-14 20:33:11 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:33:11,514 - WARNING - Could not retrieve variants from source file in region 3:45754474-45779326. Error was invalid region `3:45754475-45779326`
[2016-04-15T03:33Z] 2016-04-14 20:33:11 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:33:11,991 - WARNING - Could not retrieve variants from source file in region 3:46063118-46063519. Error was invalid region `3:46063119-46063519`
[2016-04-15T03:33Z] 2016-04-14 20:33:12 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:33:12,958 - WARNING - Could not retrieve variants from source file in region 3:46620403-46622819. Error was invalid region `3:46620404-46622819`
[2016-04-15T03:33Z] 2016-04-14 20:33:14 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:33:14,371 - WARNING - Could not retrieve variants from source file in region 3:45527007-45565744. Error was invalid region `3:45527008-45565744`
[2016-04-15T03:33Z] 2016-04-14 20:33:14 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:33:14,579 - WARNING - Could not retrieve variants from source file in region 3:37459123-37459524. Error was invalid region `3:37459124-37459524`
[2016-04-15T03:33Z] 2016-04-14 20:33:15 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:33:15,070 - WARNING - Could not retrieve variants from source file in region 3:46658526-46658927. Error was invalid region `3:46658527-46658927`
[2016-04-15T03:33Z] 2016-04-14 20:33:15 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:33:15,777 - WARNING - Could not retrieve variants from source file in region 3:38051350-38081221. Error was invalid region `3:38051351-38081221`
[2016-04-15T03:33Z] 2016-04-14 20:33:15 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:33:15,926 - WARNING - Could not retrieve variants from source file in region 3:40498722-40503710. Error was invalid region `3:40498723-40503710`
[2016-04-15T03:33Z] 2016-04-14 20:33:16 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:33:16,200 - WARNING - Could not retrieve variants from source file in region 3:38674501-38674902. Error was invalid region `3:38674502-38674902`
[2016-04-15T03:33Z] 2016-04-14 20:33:16 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:33:16,580 - WARNING - Could not retrieve variants from source file in region 3:47125174-47125575. Error was invalid region `3:47125175-47125575`
[2016-04-15T03:33Z] 2016-04-14 20:33:16 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:33:16,743 - WARNING - Could not retrieve variants from source file in region 3:33434620-33458456. Error was invalid region `3:33434621-33458456`
[2016-04-15T03:33Z] 2016-04-14 20:33:16 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:33:16,939 - WARNING - Could not retrieve variants from source file in region 3:38271670-38272071. Error was invalid region `3:38271671-38272071`
[2016-04-15T03:33Z] 2016-04-14 20:33:17 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:33:17,104 - WARNING - Could not retrieve variants from source file in region 3:45754474-45779326. Error was invalid region `3:45754475-45779326`
[2016-04-15T03:33Z] 2016-04-14 20:33:17 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:33:17,359 - WARNING - Could not retrieve variants from source file in region 3:46063118-46063519. Error was invalid region `3:46063119-46063519`
[2016-04-15T03:33Z] 2016-04-14 20:33:17 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:33:17,590 - WARNING - Could not retrieve variants from source file in region 3:46620403-46622819. Error was invalid region `3:46620404-46622819`
[2016-04-15T03:33Z] 2016-04-14 20:33:19 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:33:19,417 - WARNING - Could not retrieve variants from source file in region 3:45527007-45565744. Error was invalid region `3:45527008-45565744`
[2016-04-15T03:33Z] 2016-04-14 20:33:20 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:33:20,551 - WARNING - Could not retrieve variants from source file in region 3:37459123-37459524. Error was invalid region `3:37459124-37459524`
[2016-04-15T03:33Z] 2016-04-14 20:33:22 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:33:22,446 - WARNING - Could not retrieve variants from source file in region 3:46658526-46658927. Error was invalid region `3:46658527-46658927`
[2016-04-15T03:33Z] 2016-04-14 20:33:23 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:33:23,423 - WARNING - Could not retrieve variants from source file in region 3:38674501-38674902. Error was invalid region `3:38674502-38674902`
[2016-04-15T03:33Z] 2016-04-14 20:33:23 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:33:23,900 - WARNING - Could not retrieve variants from source file in region 3:47125174-47125575. Error was invalid region `3:47125175-47125575`
[2016-04-15T03:33Z] 2016-04-14 20:33:23 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:33:23,967 - WARNING - Could not retrieve variants from source file in region 3:46480590-46501474. Error was invalid region `3:46480591-46501474`
[2016-04-15T03:33Z] 2016-04-14 20:33:24 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:33:24,010 - WARNING - Could not retrieve variants from source file in region 3:39225916-39230090. Error was invalid region `3:39225917-39230090`
[2016-04-15T03:33Z] 2016-04-14 20:33:35 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:33:35,433 - WARNING - Could not retrieve variants from source file in region 3:33255381-33255782. Error was invalid region `3:33255382-33255782`
[2016-04-15T03:33Z] 2016-04-14 20:33:36 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:33:36,767 - WARNING - Could not retrieve variants from source file in region 3:45677187-45677588. Error was invalid region `3:45677188-45677588`
[2016-04-15T03:33Z] 2016-04-14 20:33:37 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:33:37,716 - WARNING - Could not retrieve variants from source file in region 3:46580380-46580781. Error was invalid region `3:46580381-46580781`
[2016-04-15T03:33Z] 2016-04-14 20:33:38 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:33:38,511 - WARNING - Could not retrieve variants from source file in region 3:37396467-37396868. Error was invalid region `3:37396468-37396868`
[2016-04-15T03:33Z] 2016-04-14 20:33:39 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:33:39,217 - WARNING - Could not retrieve variants from source file in region 3:44687089-44687490. Error was invalid region `3:44687090-44687490`
[2016-04-15T03:33Z] 2016-04-14 20:33:40 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:33:40,018 - WARNING - Could not retrieve variants from source file in region 3:40231672-40251582. Error was invalid region `3:40231673-40251582`
[2016-04-15T03:33Z] 2016-04-14 20:33:40 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:33:40,840 - WARNING - Could not retrieve variants from source file in region 3:33255381-33255782. Error was invalid region `3:33255382-33255782`
[2016-04-15T03:33Z] 2016-04-14 20:33:42 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:33:42,123 - WARNING - Could not retrieve variants from source file in region 3:38622256-38622657. Error was invalid region `3:38622257-38622657`
[2016-04-15T03:33Z] 2016-04-14 20:33:42 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:33:42,157 - WARNING - Could not retrieve variants from source file in region 3:47017704-47045929. Error was invalid region `3:47017705-47045929`
[2016-04-15T03:33Z] 2016-04-14 20:33:42 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:33:42,747 - WARNING - Could not retrieve variants from source file in region 3:45677187-45677588. Error was invalid region `3:45677188-45677588`
[2016-04-15T03:33Z] 2016-04-14 20:33:42 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:33:42,782 - WARNING - Could not retrieve variants from source file in region 3:46449767-46450260. Error was invalid region `3:46449768-46450260`
[2016-04-15T03:33Z] 2016-04-14 20:33:43 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:33:43,879 - WARNING - Could not retrieve variants from source file in region 3:38401628-38408551. Error was invalid region `3:38401629-38408551`
[2016-04-15T03:33Z] 2016-04-14 20:33:44 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:33:44,016 - WARNING - Could not retrieve variants from source file in region 3:46580380-46580781. Error was invalid region `3:46580381-46580781`
[2016-04-15T03:33Z] 2016-04-14 20:33:44 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:33:44,619 - WARNING - Could not retrieve variants from source file in region 3:45266847-45267511. Error was invalid region `3:45266848-45267511`
[2016-04-15T03:33Z] 2016-04-14 20:33:44 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:33:44,910 - WARNING - Could not retrieve variants from source file in region 3:44687089-44687490. Error was invalid region `3:44687090-44687490`
[2016-04-15T03:33Z] 2016-04-14 20:33:45 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:33:45,179 - WARNING - Could not retrieve variants from source file in region 3:40231672-40251582. Error was invalid region `3:40231673-40251582`
[2016-04-15T03:33Z] 2016-04-14 20:33:46 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:33:46,059 - WARNING - Could not retrieve variants from source file in region 3:33255381-33255782. Error was invalid region `3:33255382-33255782`
[2016-04-15T03:33Z] 2016-04-14 20:33:47 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:33:47,341 - WARNING - Could not retrieve variants from source file in region 3:37574740-37575141. Error was invalid region `3:37574741-37575141`
[2016-04-15T03:33Z] 2016-04-14 20:33:47 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:33:47,653 - WARNING - Could not retrieve variants from source file in region 3:47017704-47045929. Error was invalid region `3:47017705-47045929`
[2016-04-15T03:33Z] 2016-04-14 20:33:47 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:33:47,667 - WARNING - Could not retrieve variants from source file in region 3:38622256-38622657. Error was invalid region `3:38622257-38622657`
[2016-04-15T03:33Z] 2016-04-14 20:33:48 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:33:48,421 - WARNING - Could not retrieve variants from source file in region 3:45677187-45677588. Error was invalid region `3:45677188-45677588`
[2016-04-15T03:33Z] 2016-04-14 20:33:48 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:33:48,505 - WARNING - Could not retrieve variants from source file in region 3:46449767-46450260. Error was invalid region `3:46449768-46450260`
[2016-04-15T03:33Z] 2016-04-14 20:33:49 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:33:49,500 - WARNING - Could not retrieve variants from source file in region 3:46580380-46580781. Error was invalid region `3:46580381-46580781`
[2016-04-15T03:33Z] 2016-04-14 20:33:50 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:33:50,266 - WARNING - Could not retrieve variants from source file in region 3:38401628-38408551. Error was invalid region `3:38401629-38408551`
[2016-04-15T03:33Z] 2016-04-14 20:33:50 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:33:50,859 - WARNING - Could not retrieve variants from source file in region 3:44687089-44687490. Error was invalid region `3:44687090-44687490`
[2016-04-15T03:33Z] 2016-04-14 20:33:50 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:33:50,943 - WARNING - Could not retrieve variants from source file in region 3:39152134-39188372. Error was invalid region `3:39152135-39188372`
[2016-04-15T03:33Z] 2016-04-14 20:33:51 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:33:51,074 - WARNING - Could not retrieve variants from source file in region 3:40231672-40251582. Error was invalid region `3:40231673-40251582`
[2016-04-15T03:33Z] 2016-04-14 20:33:52 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:33:52,706 - WARNING - Could not retrieve variants from source file in region 3:37574740-37575141. Error was invalid region `3:37574741-37575141`
[2016-04-15T03:33Z] 2016-04-14 20:33:53 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:33:53,227 - WARNING - Could not retrieve variants from source file in region 3:38622256-38622657. Error was invalid region `3:38622257-38622657`
[2016-04-15T03:33Z] 2016-04-14 20:33:53 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:33:53,407 - WARNING - Could not retrieve variants from source file in region 3:46449767-46450260. Error was invalid region `3:46449768-46450260`
[2016-04-15T03:33Z] 2016-04-14 20:33:56 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:33:56,480 - WARNING - Could not retrieve variants from source file in region 3:38401628-38408551. Error was invalid region `3:38401629-38408551`
[2016-04-15T03:33Z] 2016-04-14 20:33:59 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:33:59,970 - WARNING - Could not retrieve variants from source file in region 3:45817207-45817608. Error was invalid region `3:45817208-45817608`
[2016-04-15T03:34Z] 2016-04-14 20:34:02 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:34:02,091 - WARNING - Could not retrieve variants from source file in region 3:33173945-33195180. Error was invalid region `3:33173946-33195180`
[2016-04-15T03:34Z] 2016-04-14 20:34:03 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:34:03,141 - WARNING - Could not retrieve variants from source file in region 3:45637042-45637629. Error was invalid region `3:45637043-45637629`
[2016-04-15T03:34Z] 2016-04-14 20:34:04 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:34:04,266 - WARNING - Could not retrieve variants from source file in region 3:46399587-46399988. Error was invalid region `3:46399588-46399988`
[2016-04-15T03:34Z] 2016-04-14 20:34:05 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:34:05,069 - WARNING - Could not retrieve variants from source file in region 3:38125494-38125895. Error was invalid region `3:38125495-38125895`
[2016-04-15T03:34Z] 2016-04-14 20:34:05 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:34:05,075 - WARNING - Could not retrieve variants from source file in region 3:45817207-45817608. Error was invalid region `3:45817208-45817608`
[2016-04-15T03:34Z] 2016-04-14 20:34:05 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:34:05,472 - WARNING - Could not retrieve variants from source file in region 3:45127304-45153898. Error was invalid region `3:45127305-45153898`
[2016-04-15T03:34Z] 2016-04-14 20:34:05 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:34:05,912 - WARNING - Could not retrieve variants from source file in region 3:44606802-44613204. Error was invalid region `3:44606803-44613204`
[2016-04-15T03:34Z] 2016-04-14 20:34:06 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:34:06,425 - WARNING - Could not retrieve variants from source file in region 3:39430870-39431271. Error was invalid region `3:39430871-39431271`
[2016-04-15T03:34Z] 2016-04-14 20:34:08 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:34:08,083 - WARNING - Could not retrieve variants from source file in region 3:38566024-38567961. Error was invalid region `3:38566025-38567961`
[2016-04-15T03:34Z] 2016-04-14 20:34:08 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:34:08,185 - WARNING - Could not retrieve variants from source file in region 3:45637042-45637629. Error was invalid region `3:45637043-45637629`
[2016-04-15T03:34Z] 2016-04-14 20:34:10 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:34:10,033 - WARNING - Could not retrieve variants from source file in region 3:45817207-45817608. Error was invalid region `3:45817208-45817608`
[2016-04-15T03:34Z] 2016-04-14 20:34:10 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:34:10,322 - WARNING - Could not retrieve variants from source file in region 3:38125494-38125895. Error was invalid region `3:38125495-38125895`
[2016-04-15T03:34Z] 2016-04-14 20:34:10 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:34:10,596 - WARNING - Could not retrieve variants from source file in region 3:45127304-45153898. Error was invalid region `3:45127305-45153898`
[2016-04-15T03:34Z] 2016-04-14 20:34:11 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:34:11,128 - WARNING - Could not retrieve variants from source file in region 3:44606802-44613204. Error was invalid region `3:44606803-44613204`
[2016-04-15T03:34Z] 2016-04-14 20:34:11 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:34:11,947 - WARNING - Could not retrieve variants from source file in region 3:39430870-39431271. Error was invalid region `3:39430871-39431271`
[2016-04-15T03:34Z] 2016-04-14 20:34:12 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:34:12,663 - WARNING - Could not retrieve variants from source file in region 3:37366248-37368945. Error was invalid region `3:37366249-37368945`
[2016-04-15T03:34Z] 2016-04-14 20:34:12 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:34:12,691 - WARNING - Could not retrieve variants from source file in region 3:37535845-37536246. Error was invalid region `3:37535846-37536246`
[2016-04-15T03:34Z] 2016-04-14 20:34:13 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:34:13,459 - WARNING - Could not retrieve variants from source file in region 3:46982292-46982693. Error was invalid region `3:46982293-46982693`
[2016-04-15T03:34Z] 2016-04-14 20:34:13 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:34:13,538 - WARNING - Could not retrieve variants from source file in region 3:45637042-45637629. Error was invalid region `3:45637043-45637629`
[2016-04-15T03:34Z] 2016-04-14 20:34:13 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:34:13,879 - WARNING - Could not retrieve variants from source file in region 3:46399587-46399988. Error was invalid region `3:46399588-46399988`
[2016-04-15T03:34Z] 2016-04-14 20:34:14 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:34:14,485 - WARNING - Could not retrieve variants from source file in region 3:38125494-38125895. Error was invalid region `3:38125495-38125895`
[2016-04-15T03:34Z] 2016-04-14 20:34:15 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:34:15,471 - WARNING - Could not retrieve variants from source file in region 3:45127304-45153898. Error was invalid region `3:45127305-45153898`
[2016-04-15T03:34Z] 2016-04-14 20:34:15 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:34:15,840 - WARNING - Could not retrieve variants from source file in region 3:44606802-44613204. Error was invalid region `3:44606803-44613204`
[2016-04-15T03:34Z] 2016-04-14 20:34:17 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:34:17,235 - WARNING - Could not retrieve variants from source file in region 3:39110929-39111330. Error was invalid region `3:39110930-39111330`
[2016-04-15T03:34Z] 2016-04-14 20:34:17 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:34:17,421 - WARNING - Could not retrieve variants from source file in region 3:38347422-38358151. Error was invalid region `3:38347423-38358151`
[2016-04-15T03:34Z] 2016-04-14 20:34:17 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:34:17,670 - WARNING - Could not retrieve variants from source file in region 3:39430870-39431271. Error was invalid region `3:39430871-39431271`
[2016-04-15T03:34Z] 2016-04-14 20:34:18 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:34:18,672 - WARNING - Could not retrieve variants from source file in region 3:37366248-37368945. Error was invalid region `3:37366249-37368945`
[2016-04-15T03:34Z] 2016-04-14 20:34:18 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:34:18,716 - WARNING - Could not retrieve variants from source file in region 3:37535845-37536246. Error was invalid region `3:37535846-37536246`
[2016-04-15T03:34Z] 2016-04-14 20:34:28 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:34:28,817 - WARNING - Could not retrieve variants from source file in region 3:32200022-32200512. Error was invalid region `3:32200023-32200512`
[2016-04-15T03:34Z] 2016-04-14 20:34:29 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:34:29,097 - WARNING - Could not retrieve variants from source file in region 3:45046586-45052965. Error was invalid region `3:45046587-45052965`
[2016-04-15T03:34Z] 2016-04-14 20:34:29 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:34:29,346 - WARNING - Could not retrieve variants from source file in region 3:32995717-32996118. Error was invalid region `3:32995718-32996118`
[2016-04-15T03:34Z] 2016-04-14 20:34:29 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:34:29,705 - WARNING - Could not retrieve variants from source file in region 3:44540580-44540983. Error was invalid region `3:44540581-44540983`
[2016-04-15T03:34Z] 2016-04-14 20:34:31 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:34:31,915 - WARNING - Could not retrieve variants from source file in region 3:39373691-39374092. Error was invalid region `3:39373692-39374092`
[2016-04-15T03:34Z] 2016-04-14 20:34:32 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:34:32,499 - WARNING - Could not retrieve variants from source file in region 3:46934081-46944464. Error was invalid region `3:46934082-46944464`
[2016-04-15T03:34Z] 2016-04-14 20:34:32 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:34:32,959 - WARNING - Could not retrieve variants from source file in region 3:38935923-38945750. Error was invalid region `3:38935924-38945750`
[2016-04-15T03:34Z] 2016-04-14 20:34:34 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:34:34,178 - WARNING - Could not retrieve variants from source file in region 3:32927298-32927699. Error was invalid region `3:32927299-32927699`
[2016-04-15T03:34Z] 2016-04-14 20:34:35 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:34:35,159 - WARNING - Could not retrieve variants from source file in region 3:45046586-45052965. Error was invalid region `3:45046587-45052965`
[2016-04-15T03:34Z] 2016-04-14 20:34:35 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:34:35,313 - WARNING - Could not retrieve variants from source file in region 3:32200022-32200512. Error was invalid region `3:32200023-32200512`
[2016-04-15T03:34Z] 2016-04-14 20:34:35 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:34:35,393 - WARNING - Could not retrieve variants from source file in region 3:44540580-44540983. Error was invalid region `3:44540581-44540983`
[2016-04-15T03:34Z] 2016-04-14 20:34:36 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:34:36,873 - WARNING - Could not retrieve variants from source file in region 3:46934081-46944464. Error was invalid region `3:46934082-46944464`
[2016-04-15T03:34Z] 2016-04-14 20:34:40 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:34:40,143 - WARNING - Could not retrieve variants from source file in region 3:37032085-37046118. Error was invalid region `3:37032086-37046118`
[2016-04-15T03:34Z] 2016-04-14 20:34:41 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:34:41,092 - WARNING - Could not retrieve variants from source file in region 3:46934081-46944464. Error was invalid region `3:46934082-46944464`
[2016-04-15T03:34Z] 2016-04-14 20:34:41 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:34:41,092 - WARNING - Could not retrieve variants from source file in region 3:33131933-33138739. Error was invalid region `3:33131934-33138739`
[2016-04-15T03:34Z] 2016-04-14 20:34:41 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:34:41,108 - WARNING - Could not retrieve variants from source file in region 3:32927298-32927699. Error was invalid region `3:32927299-32927699`
[2016-04-15T03:34Z] 2016-04-14 20:34:41 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:34:41,492 - WARNING - Could not retrieve variants from source file in region 3:44540580-44540983. Error was invalid region `3:44540581-44540983`
[2016-04-15T03:34Z] 2016-04-14 20:34:41 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:34:41,495 - WARNING - Could not retrieve variants from source file in region 3:32200022-32200512. Error was invalid region `3:32200023-32200512`
[2016-04-15T03:34Z] 2016-04-14 20:34:41 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:34:41,862 - WARNING - Could not retrieve variants from source file in region 3:42781065-42799955. Error was invalid region `3:42781066-42799955`
[2016-04-15T03:34Z] 2016-04-14 20:34:41 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:34:41,969 - WARNING - Could not retrieve variants from source file in region 3:32995717-32996118. Error was invalid region `3:32995718-32996118`
[2016-04-15T03:34Z] 2016-04-14 20:34:42 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:34:42,011 - WARNING - Could not retrieve variants from source file in region 3:38887982-38888383. Error was invalid region `3:38887983-38888383`
[2016-04-15T03:34Z] 2016-04-14 20:34:46 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:34:46,527 - WARNING - Could not retrieve variants from source file in region 3:32927298-32927699. Error was invalid region `3:32927299-32927699`
[2016-04-15T03:34Z] 2016-04-14 20:34:47 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:34:47,692 - WARNING - Could not retrieve variants from source file in region 3:42781065-42799955. Error was invalid region `3:42781066-42799955`
[2016-04-15T03:34Z] 2016-04-14 20:34:48 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:34:48,278 - WARNING - Could not retrieve variants from source file in region 3:38887982-38888383. Error was invalid region `3:38887983-38888383`
[2016-04-15T03:34Z] 2016-04-14 20:34:51 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:34:51,140 - WARNING - Could not retrieve variants from source file in region 3:36779496-36779897. Error was invalid region `3:36779497-36779897`
[2016-04-15T03:34Z] 2016-04-14 20:34:52 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:34:52,228 - WARNING - Could not retrieve variants from source file in region 3:38739363-38768524. Error was invalid region `3:38739364-38768524`
[2016-04-15T03:34Z] 2016-04-14 20:34:54 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:34:54,958 - WARNING - Could not retrieve variants from source file in region 3:33086846-33087247. Error was invalid region `3:33086847-33087247`
[2016-04-15T03:34Z] 2016-04-14 20:34:55 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:34:55,592 - WARNING - Could not retrieve variants from source file in region 3:36779496-36779897. Error was invalid region `3:36779497-36779897`
[2016-04-15T03:34Z] 2016-04-14 20:34:56 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:34:56,447 - WARNING - Could not retrieve variants from source file in region 3:39307045-39323353. Error was invalid region `3:39307046-39323353`
[2016-04-15T03:34Z] 2016-04-14 20:34:56 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:34:56,692 - WARNING - Could not retrieve variants from source file in region 3:32030813-32032587. Error was invalid region `3:32030814-32032587`
[2016-04-15T03:34Z] 2016-04-14 20:34:57 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:34:57,019 - WARNING - Could not retrieve variants from source file in region 3:44408927-44409328. Error was invalid region `3:44408928-44409328`
[2016-04-15T03:34Z] 2016-04-14 20:34:57 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:34:57,078 - WARNING - Could not retrieve variants from source file in region 3:32493471-32493872. Error was invalid region `3:32493472-32493872`
[2016-04-15T03:34Z] 2016-04-14 20:34:58 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:34:58,767 - WARNING - Could not retrieve variants from source file in region 3:36931186-36931587. Error was invalid region `3:36931187-36931587`
[2016-04-15T03:34Z] 2016-04-14 20:34:59 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:34:59,242 - WARNING - Could not retrieve variants from source file in region 3:33086846-33087247. Error was invalid region `3:33086847-33087247`
[2016-04-15T03:34Z] 2016-04-14 20:34:59 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:34:59,708 - WARNING - Could not retrieve variants from source file in region 3:36779496-36779897. Error was invalid region `3:36779497-36779897`
[2016-04-15T03:35Z] 2016-04-14 20:35:00 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:35:00,452 - WARNING - Could not retrieve variants from source file in region 3:39307045-39323353. Error was invalid region `3:39307046-39323353`
[2016-04-15T03:35Z] 2016-04-14 20:35:01 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:35:01,171 - WARNING - Could not retrieve variants from source file in region 3:42727933-42735464. Error was invalid region `3:42727934-42735464`
[2016-04-15T03:35Z] 2016-04-14 20:35:01 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:35:01,313 - WARNING - Could not retrieve variants from source file in region 3:32493471-32493872. Error was invalid region `3:32493472-32493872`
[2016-04-15T03:35Z] 2016-04-14 20:35:03 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:35:03,449 - WARNING - Could not retrieve variants from source file in region 3:33086846-33087247. Error was invalid region `3:33086847-33087247`
[2016-04-15T03:35Z] 2016-04-14 20:35:04 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:35:04,585 - WARNING - Could not retrieve variants from source file in region 3:39307045-39323353. Error was invalid region `3:39307046-39323353`
[2016-04-15T03:35Z] 2016-04-14 20:35:05 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:35:05,891 - WARNING - Could not retrieve variants from source file in region 3:42727933-42735464. Error was invalid region `3:42727934-42735464`
[2016-04-15T03:35Z] 2016-04-14 20:35:06 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:35:06,337 - WARNING - Could not retrieve variants from source file in region 3:33055510-33060171. Error was invalid region `3:33055511-33060171`
[2016-04-15T03:35Z] 2016-04-14 20:35:06 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:35:06,513 - WARNING - Could not retrieve variants from source file in region 3:44283461-44283998. Error was invalid region `3:44283462-44283998`
[2016-04-15T03:35Z] 2016-04-14 20:35:06 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:35:06,632 - WARNING - Could not retrieve variants from source file in region 3:43732312-43732713. Error was invalid region `3:43732313-43732713`
[2016-04-15T03:35Z] 2016-04-14 20:35:07 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:35:07,118 - WARNING - Could not retrieve variants from source file in region 3:32493471-32493872. Error was invalid region `3:32493472-32493872`
[2016-04-15T03:35Z] 2016-04-14 20:35:07 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:35:07,244 - WARNING - Could not retrieve variants from source file in region 3:36931186-36931587. Error was invalid region `3:36931187-36931587`
[2016-04-15T03:35Z] 2016-04-14 20:35:12 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:35:12,374 - WARNING - Could not retrieve variants from source file in region 3:44283461-44283998. Error was invalid region `3:44283462-44283998`
[2016-04-15T03:35Z] 2016-04-14 20:35:12 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:35:12,379 - WARNING - Could not retrieve variants from source file in region 3:42727933-42735464. Error was invalid region `3:42727934-42735464`
[2016-04-15T03:35Z] 2016-04-14 20:35:15 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:35:15,467 - WARNING - Could not retrieve variants from source file in region 3:44283461-44283998. Error was invalid region `3:44283462-44283998`
[2016-04-15T03:35Z] 2016-04-14 20:35:16 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:35:16,413 - WARNING - Could not retrieve variants from source file in region 3:36892375-36898571. Error was invalid region `3:36892376-36898571`
[2016-04-15T03:35Z] 2016-04-14 20:35:17 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:35:17,463 - WARNING - Could not retrieve variants from source file in region 3:36421936-36422337. Error was invalid region `3:36421937-36422337`
[2016-04-15T03:35Z] 2016-04-14 20:35:18 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:35:18,011 - WARNING - Could not retrieve variants from source file in region 3:39255519-39256061. Error was invalid region `3:39255520-39256061`
[2016-04-15T03:35Z] 2016-04-14 20:35:20 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:35:20,376 - WARNING - Could not retrieve variants from source file in region 3:41830992-41841906. Error was invalid region `3:41830993-41841906`
[2016-04-15T03:35Z] 2016-04-14 20:35:20 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:35:20,742 - WARNING - Could not retrieve variants from source file in region 3:31705069-31750710. Error was invalid region `3:31705070-31750710`
[2016-04-15T03:35Z] 2016-04-14 20:35:22 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:35:22,039 - WARNING - Could not retrieve variants from source file in region 3:36421936-36422337. Error was invalid region `3:36421937-36422337`
[2016-04-15T03:35Z] 2016-04-14 20:35:25 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:35:25,360 - WARNING - Could not retrieve variants from source file in region 3:35725039-35727415. Error was invalid region `3:35725040-35727415`
[2016-04-15T03:35Z] 2016-04-14 20:35:25 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:35:25,438 - WARNING - Could not retrieve variants from source file in region 3:42700245-42700820. Error was invalid region `3:42700246-42700820`
[2016-04-15T03:35Z] 2016-04-14 20:35:29 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:35:29,201 - WARNING - Could not retrieve variants from source file in region 3:35778562-35779940. Error was invalid region `3:35778563-35779940`
[2016-04-15T03:35Z] 2016-04-14 20:35:29 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:35:29,507 - WARNING - Could not retrieve variants from source file in region 3:41830992-41841906. Error was invalid region `3:41830993-41841906`
[2016-04-15T03:35Z] 2016-04-14 20:35:30 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:35:30,123 - WARNING - Could not retrieve variants from source file in region 3:43414107-43414508. Error was invalid region `3:43414108-43414508`
[2016-04-15T03:35Z] 2016-04-14 20:35:33 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:35:33,123 - WARNING - Could not retrieve variants from source file in region 3:41925187-41925613. Error was invalid region `3:41925188-41925613`
[2016-04-15T03:35Z] 2016-04-14 20:35:33 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:35:33,997 - WARNING - Could not retrieve variants from source file in region 3:43073550-43121749. Error was invalid region `3:43073551-43121749`
[2016-04-15T03:35Z] 2016-04-14 20:35:34 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:35:34,415 - WARNING - Could not retrieve variants from source file in region 3:42700245-42700820. Error was invalid region `3:42700246-42700820`
[2016-04-15T03:35Z] 2016-04-14 20:35:34 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:35:34,784 - WARNING - Could not retrieve variants from source file in region 3:41877203-41877604. Error was invalid region `3:41877204-41877604`
[2016-04-15T03:35Z] 2016-04-14 20:35:34 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:35:34,809 - WARNING - Could not retrieve variants from source file in region 3:43414107-43414508. Error was invalid region `3:43414108-43414508`
[2016-04-15T03:35Z] 2016-04-14 20:35:37 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:35:37,220 - WARNING - Could not retrieve variants from source file in region 3:41925187-41925613. Error was invalid region `3:41925188-41925613`
[2016-04-15T03:35Z] 2016-04-14 20:35:40 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:35:40,258 - WARNING - Could not retrieve variants from source file in region 3:43414107-43414508. Error was invalid region `3:43414108-43414508`
[2016-04-15T03:35Z] 2016-04-14 20:35:40 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:35:40,277 - WARNING - Could not retrieve variants from source file in region 3:41877203-41877604. Error was invalid region `3:41877204-41877604`
[2016-04-15T03:35Z] 2016-04-14 20:35:42 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:35:42,555 - WARNING - Could not retrieve variants from source file in region 3:41756754-41757176. Error was invalid region `3:41756755-41757176`
[2016-04-15T03:35Z] 2016-04-14 20:35:44 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:35:44,432 - WARNING - Could not retrieve variants from source file in region 3:33728399-33728800. Error was invalid region `3:33728400-33728800`
[2016-04-15T03:35Z] 2016-04-14 20:35:45 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:35:45,729 - WARNING - Could not retrieve variants from source file in region 3:42956062-42956463. Error was invalid region `3:42956063-42956463`
[2016-04-15T03:35Z] 2016-04-14 20:35:48 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:35:48,098 - WARNING - Could not retrieve variants from source file in region 3:42956062-42956463. Error was invalid region `3:42956063-42956463`
[2016-04-15T03:35Z] 2016-04-14 20:35:49 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:35:49,653 - WARNING - Could not retrieve variants from source file in region 3:42956062-42956463. Error was invalid region `3:42956063-42956463`
[2016-04-15T03:35Z] 2016-04-14 20:35:50 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:35:50,019 - WARNING - Could not retrieve variants from source file in region 3:41756754-41757176. Error was invalid region `3:41756755-41757176`
[2016-04-15T03:35Z] 2016-04-14 20:35:51 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:35:51,350 - WARNING - Could not retrieve variants from source file in region 3:42916836-42917237. Error was invalid region `3:42916837-42917237`
[2016-04-15T03:35Z] 2016-04-14 20:35:52 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:35:52,975 - WARNING - Could not retrieve variants from source file in region 3:40573663-40574064. Error was invalid region `3:40573664-40574064`
[2016-04-15T03:35Z] 2016-04-14 20:35:54 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:35:54,592 - WARNING - Could not retrieve variants from source file in region 3:42916836-42917237. Error was invalid region `3:42916837-42917237`
[2016-04-15T03:35Z] 2016-04-14 20:35:55 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:35:55,266 - WARNING - Could not retrieve variants from source file in region 3:42916836-42917237. Error was invalid region `3:42916837-42917237`
[2016-04-15T03:36Z] ['bcbio-variation-recall', 'square', '-Xms750m', '-Xmx7280m', '-XX:+UseSerialGC', '-c', 16, '-r', u'3:47129603-62648069', '--caller', 'platypus', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/3/Batch1-3_47129602_62648069.vcf.gz', '/mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/3/Batch1-3_47129602_62648069.vcf-inputs.txt'] in region: 3:47129603-62648069
[2016-04-15T03:36Z] 2016-04-14 20:36:09 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:36:09,772 - WARNING - Could not retrieve variants from source file in region 3:62229342-62229743. Error was invalid region `3:62229343-62229743`
[2016-04-15T03:36Z] 2016-04-14 20:36:10 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:36:10,309 - WARNING - Could not retrieve variants from source file in region 3:49342964-49362559. Error was invalid region `3:49342965-49362559`
[2016-04-15T03:36Z] 2016-04-14 20:36:11 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:36:11,406 - WARNING - Could not retrieve variants from source file in region 3:58154116-58154517. Error was invalid region `3:58154117-58154517`
[2016-04-15T03:36Z] 2016-04-14 20:36:11 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:36:11,744 - WARNING - Could not retrieve variants from source file in region 3:48625055-48628204. Error was invalid region `3:48625056-48628204`
[2016-04-15T03:36Z] 2016-04-14 20:36:11 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:36:11,775 - WARNING - Could not retrieve variants from source file in region 3:49881128-49881529. Error was invalid region `3:49881129-49881529`
[2016-04-15T03:36Z] 2016-04-14 20:36:12 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:36:12,060 - WARNING - Could not retrieve variants from source file in region 3:48413986-48420087. Error was invalid region `3:48413987-48420087`
[2016-04-15T03:36Z] 2016-04-14 20:36:12 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:36:12,114 - WARNING - Could not retrieve variants from source file in region 3:48540971-48541372. Error was invalid region `3:48540972-48541372`
[2016-04-15T03:36Z] 2016-04-14 20:36:12 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:36:12,612 - WARNING - Could not retrieve variants from source file in region 3:48476220-48476621. Error was invalid region `3:48476221-48476621`
[2016-04-15T03:36Z] 2016-04-14 20:36:12 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:36:12,665 - WARNING - Could not retrieve variants from source file in region 3:56809417-56809818. Error was invalid region `3:56809418-56809818`
[2016-04-15T03:36Z] 2016-04-14 20:36:12 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:36:12,843 - WARNING - Could not retrieve variants from source file in region 3:52237759-52294049. Error was invalid region `3:52237760-52294049`
[2016-04-15T03:36Z] 2016-04-14 20:36:14 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:36:14,991 - WARNING - Could not retrieve variants from source file in region 3:62229342-62229743. Error was invalid region `3:62229343-62229743`
[2016-04-15T03:36Z] 2016-04-14 20:36:16 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:36:16,407 - WARNING - Could not retrieve variants from source file in region 3:49342964-49362559. Error was invalid region `3:49342965-49362559`
[2016-04-15T03:36Z] 2016-04-14 20:36:16 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:36:16,418 - WARNING - Could not retrieve variants from source file in region 3:47448847-47462390. Error was invalid region `3:47448848-47462390`
[2016-04-15T03:36Z] 2016-04-14 20:36:17 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:36:17,412 - WARNING - Could not retrieve variants from source file in region 3:48309617-48310018. Error was invalid region `3:48309618-48310018`
[2016-04-15T03:36Z] 2016-04-14 20:36:17 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:36:17,507 - WARNING - Could not retrieve variants from source file in region 3:58154116-58154517. Error was invalid region `3:58154117-58154517`
[2016-04-15T03:36Z] 2016-04-14 20:36:19 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:36:19,585 - WARNING - Could not retrieve variants from source file in region 3:48413986-48420087. Error was invalid region `3:48413987-48420087`
[2016-04-15T03:36Z] 2016-04-14 20:36:20 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:36:20,623 - WARNING - Could not retrieve variants from source file in region 3:47711991-47712392. Error was invalid region `3:47711992-47712392`
[2016-04-15T03:36Z] 2016-04-14 20:36:21 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:36:21,198 - WARNING - Could not retrieve variants from source file in region 3:50222715-50225343. Error was invalid region `3:50222716-50225343`
[2016-04-15T03:36Z] 2016-04-14 20:36:21 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:36:21,320 - WARNING - Could not retrieve variants from source file in region 3:48476220-48476621. Error was invalid region `3:48476221-48476621`
[2016-04-15T03:36Z] 2016-04-14 20:36:21 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:36:21,579 - WARNING - Could not retrieve variants from source file in region 3:62229342-62229743. Error was invalid region `3:62229343-62229743`
[2016-04-15T03:36Z] 2016-04-14 20:36:21 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:36:21,871 - WARNING - Could not retrieve variants from source file in region 3:49342964-49362559. Error was invalid region `3:49342965-49362559`
[2016-04-15T03:36Z] 2016-04-14 20:36:22 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:36:22,317 - WARNING - Could not retrieve variants from source file in region 3:48309617-48310018. Error was invalid region `3:48309618-48310018`
[2016-04-15T03:36Z] 2016-04-14 20:36:22 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:36:22,386 - WARNING - Could not retrieve variants from source file in region 3:58154116-58154517. Error was invalid region `3:58154117-58154517`
[2016-04-15T03:36Z] 2016-04-14 20:36:23 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:36:23,704 - WARNING - Could not retrieve variants from source file in region 3:48625055-48628204. Error was invalid region `3:48625056-48628204`
[2016-04-15T03:36Z] 2016-04-14 20:36:25 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:36:25,742 - WARNING - Could not retrieve variants from source file in region 3:48413986-48420087. Error was invalid region `3:48413987-48420087`
[2016-04-15T03:36Z] 2016-04-14 20:36:27 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:36:27,242 - WARNING - Could not retrieve variants from source file in region 3:47711991-47712392. Error was invalid region `3:47711992-47712392`
[2016-04-15T03:36Z] 2016-04-14 20:36:28 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:36:28,125 - WARNING - Could not retrieve variants from source file in region 3:56809417-56809818. Error was invalid region `3:56809418-56809818`
[2016-04-15T03:36Z] 2016-04-14 20:36:28 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:36:28,239 - WARNING - Could not retrieve variants from source file in region 3:48476220-48476621. Error was invalid region `3:48476221-48476621`
[2016-04-15T03:36Z] 2016-04-14 20:36:39 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:36:39,479 - WARNING - Could not retrieve variants from source file in region 3:58108951-58118745. Error was invalid region `3:58108952-58118745`
[2016-04-15T03:36Z] 2016-04-14 20:36:39 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:36:39,704 - WARNING - Could not retrieve variants from source file in region 3:49273785-49314168. Error was invalid region `3:49273786-49314168`
[2016-04-15T03:36Z] 2016-04-14 20:36:40 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:36:40,610 - WARNING - Could not retrieve variants from source file in region 3:47281022-47282493. Error was invalid region `3:47281023-47282493`
[2016-04-15T03:36Z] 2016-04-14 20:36:42 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:36:42,216 - WARNING - Could not retrieve variants from source file in region 3:53769268-53769669. Error was invalid region `3:53769269-53769669`
[2016-04-15T03:36Z] 2016-04-14 20:36:42 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:36:42,318 - WARNING - Could not retrieve variants from source file in region 3:47618742-47619143. Error was invalid region `3:47618743-47619143`
[2016-04-15T03:36Z] 2016-04-14 20:36:42 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:36:42,438 - WARNING - Could not retrieve variants from source file in region 3:50103706-50114705. Error was invalid region `3:50103707-50114705`
[2016-04-15T03:36Z] 2016-04-14 20:36:42 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:36:42,852 - WARNING - Could not retrieve variants from source file in region 3:52055776-52056177. Error was invalid region `3:52055777-52056177`
[2016-04-15T03:36Z] 2016-04-14 20:36:44 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:36:44,071 - WARNING - Could not retrieve variants from source file in region 3:61975171-61975572. Error was invalid region `3:61975172-61975572`
[2016-04-15T03:36Z] 2016-04-14 20:36:44 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:36:44,545 - WARNING - Could not retrieve variants from source file in region 3:50196886-50197287. Error was invalid region `3:50196887-50197287`
[2016-04-15T03:36Z] 2016-04-14 20:36:45 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:36:45,577 - WARNING - Could not retrieve variants from source file in region 3:57385937-57386338. Error was invalid region `3:57385938-57386338`
[2016-04-15T03:36Z] 2016-04-14 20:36:47 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:36:47,218 - WARNING - Could not retrieve variants from source file in region 3:48282484-48282885. Error was invalid region `3:48282485-48282885`
[2016-04-15T03:36Z] 2016-04-14 20:36:47 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:36:47,557 - WARNING - Could not retrieve variants from source file in region 3:47618742-47619143. Error was invalid region `3:47618743-47619143`
[2016-04-15T03:36Z] 2016-04-14 20:36:48 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:36:48,044 - WARNING - Could not retrieve variants from source file in region 3:50103706-50114705. Error was invalid region `3:50103707-50114705`
[2016-04-15T03:36Z] 2016-04-14 20:36:49 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:36:49,545 - WARNING - Could not retrieve variants from source file in region 3:50196886-50197287. Error was invalid region `3:50196887-50197287`
[2016-04-15T03:36Z] 2016-04-14 20:36:50 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:36:50,912 - WARNING - Could not retrieve variants from source file in region 3:58108951-58118745. Error was invalid region `3:58108952-58118745`
[2016-04-15T03:36Z] 2016-04-14 20:36:50 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:36:50,961 - WARNING - Could not retrieve variants from source file in region 3:57385937-57386338. Error was invalid region `3:57385938-57386338`
[2016-04-15T03:36Z] 2016-04-14 20:36:51 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:36:51,480 - WARNING - Could not retrieve variants from source file in region 3:49829821-49832978. Error was invalid region `3:49829822-49832978`
[2016-04-15T03:36Z] 2016-04-14 20:36:52 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:36:52,458 - WARNING - Could not retrieve variants from source file in region 3:48282484-48282885. Error was invalid region `3:48282485-48282885`
[2016-04-15T03:36Z] 2016-04-14 20:36:52 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:36:52,970 - WARNING - Could not retrieve variants from source file in region 3:52055776-52056177. Error was invalid region `3:52055777-52056177`
[2016-04-15T03:36Z] 2016-04-14 20:36:52 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:36:52,973 - WARNING - Could not retrieve variants from source file in region 3:47618742-47619143. Error was invalid region `3:47618743-47619143`
[2016-04-15T03:36Z] 2016-04-14 20:36:53 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:36:53,187 - WARNING - Could not retrieve variants from source file in region 3:53769268-53769669. Error was invalid region `3:53769269-53769669`
[2016-04-15T03:36Z] 2016-04-14 20:36:53 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:36:53,314 - WARNING - Could not retrieve variants from source file in region 3:50103706-50114705. Error was invalid region `3:50103707-50114705`
[2016-04-15T03:36Z] 2016-04-14 20:36:53 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:36:53,981 - WARNING - Could not retrieve variants from source file in region 3:56763105-56771441. Error was invalid region `3:56763106-56771441`
[2016-04-15T03:36Z] 2016-04-14 20:36:54 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:36:54,338 - WARNING - Could not retrieve variants from source file in region 3:50196886-50197287. Error was invalid region `3:50196887-50197287`
[2016-04-15T03:37Z] 2016-04-14 20:37:02 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:37:02,846 - WARNING - Could not retrieve variants from source file in region 3:61644817-61645218. Error was invalid region `3:61644818-61645218`
[2016-04-15T03:37Z] 2016-04-14 20:37:04 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:37:04,518 - WARNING - Could not retrieve variants from source file in region 3:58081677-58082078. Error was invalid region `3:58081678-58082078`
[2016-04-15T03:37Z] 2016-04-14 20:37:05 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:37:05,118 - WARNING - Could not retrieve variants from source file in region 3:49200416-49216156. Error was invalid region `3:49200417-49216156`
[2016-04-15T03:37Z] 2016-04-14 20:37:07 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:37:07,057 - WARNING - Could not retrieve variants from source file in region 3:57882390-57882791. Error was invalid region `3:57882391-57882791`
[2016-04-15T03:37Z] 2016-04-14 20:37:07 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:37:07,765 - WARNING - Could not retrieve variants from source file in region 3:48015961-48016362. Error was invalid region `3:48015962-48016362`
[2016-04-15T03:37Z] 2016-04-14 20:37:07 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:37:07,924 - WARNING - Could not retrieve variants from source file in region 3:47162450-47162851. Error was invalid region `3:47162451-47162851`
[2016-04-15T03:37Z] 2016-04-14 20:37:08 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:37:08,297 - WARNING - Could not retrieve variants from source file in region 3:49928480-49928881. Error was invalid region `3:49928481-49928881`
[2016-04-15T03:37Z] 2016-04-14 20:37:08 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:37:08,364 - WARNING - Could not retrieve variants from source file in region 3:61644817-61645218. Error was invalid region `3:61644818-61645218`
[2016-04-15T03:37Z] 2016-04-14 20:37:09 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:37:09,040 - WARNING - Could not retrieve variants from source file in region 3:51978009-51990505. Error was invalid region `3:51978010-51990505`
[2016-04-15T03:37Z] 2016-04-14 20:37:09 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:37:09,144 - WARNING - Could not retrieve variants from source file in region 3:50144740-50153546. Error was invalid region `3:50144741-50153546`
[2016-04-15T03:37Z] 2016-04-14 20:37:13 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:37:13,211 - WARNING - Could not retrieve variants from source file in region 3:57882390-57882791. Error was invalid region `3:57882391-57882791`
[2016-04-15T03:37Z] 2016-04-14 20:37:13 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:37:13,315 - WARNING - Could not retrieve variants from source file in region 3:58625664-58626065. Error was invalid region `3:58625665-58626065`
[2016-04-15T03:37Z] 2016-04-14 20:37:13 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:37:13,450 - WARNING - Could not retrieve variants from source file in region 3:50005705-50006106. Error was invalid region `3:50005706-50006106`
[2016-04-15T03:37Z] 2016-04-14 20:37:14 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:37:14,074 - WARNING - Could not retrieve variants from source file in region 3:57335665-57336066. Error was invalid region `3:57335666-57336066`
[2016-04-15T03:37Z] 2016-04-14 20:37:14 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:37:14,554 - WARNING - Could not retrieve variants from source file in region 3:48015961-48016362. Error was invalid region `3:48015962-48016362`
[2016-04-15T03:37Z] 2016-04-14 20:37:15 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:37:15,481 - WARNING - Could not retrieve variants from source file in region 3:47162450-47162851. Error was invalid region `3:47162451-47162851`
[2016-04-15T03:37Z] 2016-04-14 20:37:15 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:37:15,789 - WARNING - Could not retrieve variants from source file in region 3:49928480-49928881. Error was invalid region `3:49928481-49928881`
[2016-04-15T03:37Z] 2016-04-14 20:37:16 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:37:16,218 - WARNING - Could not retrieve variants from source file in region 3:53321420-53325015. Error was invalid region `3:53321421-53325015`
[2016-04-15T03:37Z] 2016-04-14 20:37:16 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:37:16,562 - WARNING - Could not retrieve variants from source file in region 3:61644817-61645218. Error was invalid region `3:61644818-61645218`
[2016-04-15T03:37Z] 2016-04-14 20:37:16 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:37:16,720 - WARNING - Could not retrieve variants from source file in region 3:58081677-58082078. Error was invalid region `3:58081678-58082078`
[2016-04-15T03:37Z] 2016-04-14 20:37:17 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:37:17,366 - WARNING - Could not retrieve variants from source file in region 3:51978009-51990505. Error was invalid region `3:51978010-51990505`
[2016-04-15T03:37Z] 2016-04-14 20:37:17 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:37:17,379 - WARNING - Could not retrieve variants from source file in region 3:50144740-50153546. Error was invalid region `3:50144741-50153546`
[2016-04-15T03:37Z] 2016-04-14 20:37:18 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:37:18,205 - WARNING - Could not retrieve variants from source file in region 3:58625664-58626065. Error was invalid region `3:58625665-58626065`
[2016-04-15T03:37Z] 2016-04-14 20:37:18 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:37:18,492 - WARNING - Could not retrieve variants from source file in region 3:57882390-57882791. Error was invalid region `3:57882391-57882791`
[2016-04-15T03:37Z] 2016-04-14 20:37:18 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:37:18,952 - WARNING - Could not retrieve variants from source file in region 3:57335665-57336066. Error was invalid region `3:57335666-57336066`
[2016-04-15T03:37Z] 2016-04-14 20:37:19 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:37:19,689 - WARNING - Could not retrieve variants from source file in region 3:48015961-48016362. Error was invalid region `3:48015962-48016362`
[2016-04-15T03:37Z] 2016-04-14 20:37:20 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:37:20,266 - WARNING - Could not retrieve variants from source file in region 3:47162450-47162851. Error was invalid region `3:47162451-47162851`
[2016-04-15T03:37Z] 2016-04-14 20:37:21 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:37:21,788 - WARNING - Could not retrieve variants from source file in region 3:49928480-49928881. Error was invalid region `3:49928481-49928881`
[2016-04-15T03:37Z] 2016-04-14 20:37:23 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:37:23,922 - WARNING - Could not retrieve variants from source file in region 3:56697646-56717112. Error was invalid region `3:56697647-56717112`
[2016-04-15T03:37Z] 2016-04-14 20:37:24 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:37:24,381 - WARNING - Could not retrieve variants from source file in region 3:50144740-50153546. Error was invalid region `3:50144741-50153546`
[2016-04-15T03:37Z] 2016-04-14 20:37:26 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:37:26,366 - WARNING - Could not retrieve variants from source file in region 3:51978009-51990505. Error was invalid region `3:51978010-51990505`
[2016-04-15T03:37Z] 2016-04-14 20:37:35 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:37:35,269 - WARNING - Could not retrieve variants from source file in region 3:57176294-57176695. Error was invalid region `3:57176295-57176695`
[2016-04-15T03:37Z] 2016-04-14 20:37:35 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:37:35,386 - WARNING - Could not retrieve variants from source file in region 3:57475140-57494328. Error was invalid region `3:57475141-57494328`
[2016-04-15T03:37Z] 2016-04-14 20:37:35 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:37:35,445 - WARNING - Could not retrieve variants from source file in region 3:58552118-58563341. Error was invalid region `3:58552119-58563341`
[2016-04-15T03:37Z] 2016-04-14 20:37:37 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:37:37,180 - WARNING - Could not retrieve variants from source file in region 3:51928972-51931040. Error was invalid region `3:51928973-51931040`
[2016-04-15T03:37Z] 2016-04-14 20:37:37 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:37:37,320 - WARNING - Could not retrieve variants from source file in region 3:49547797-49570390. Error was invalid region `3:49547798-49570390`
[2016-04-15T03:37Z] 2016-04-14 20:37:38 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:37:38,225 - WARNING - Could not retrieve variants from source file in region 3:51671979-51672380. Error was invalid region `3:51671980-51672380`
[2016-04-15T03:37Z] 2016-04-14 20:37:38 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:37:38,841 - WARNING - Could not retrieve variants from source file in region 3:58834613-58852488. Error was invalid region `3:58834614-58852488`
[2016-04-15T03:37Z] 2016-04-14 20:37:41 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:37:41,813 - WARNING - Could not retrieve variants from source file in region 3:51747077-51747478. Error was invalid region `3:51747078-51747478`
[2016-04-15T03:37Z] 2016-04-14 20:37:42 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:37:42,710 - WARNING - Could not retrieve variants from source file in region 3:49547797-49570390. Error was invalid region `3:49547798-49570390`
[2016-04-15T03:37Z] 2016-04-14 20:37:44 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:37:44,088 - WARNING - Could not retrieve variants from source file in region 3:49455119-49462600. Error was invalid region `3:49455120-49462600`
[2016-04-15T03:37Z] 2016-04-14 20:37:44 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:37:44,950 - WARNING - Could not retrieve variants from source file in region 3:53259639-53269353. Error was invalid region `3:53259640-53269353`
[2016-04-15T03:37Z] 2016-04-14 20:37:45 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:37:45,249 - WARNING - Could not retrieve variants from source file in region 3:57176294-57176695. Error was invalid region `3:57176295-57176695`
[2016-04-15T03:37Z] 2016-04-14 20:37:47 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:37:47,551 - WARNING - Could not retrieve variants from source file in region 3:49547797-49570390. Error was invalid region `3:49547798-49570390`
[2016-04-15T03:37Z] 2016-04-14 20:37:51 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:37:51,097 - WARNING - Could not retrieve variants from source file in region 3:51671979-51672380. Error was invalid region `3:51671980-51672380`
[2016-04-15T03:37Z] 2016-04-14 20:37:51 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:37:51,897 - WARNING - Could not retrieve variants from source file in region 3:51747077-51747478. Error was invalid region `3:51747078-51747478`
[2016-04-15T03:37Z] 2016-04-14 20:37:54 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:37:54,159 - WARNING - Could not retrieve variants from source file in region 3:49394623-49395869. Error was invalid region `3:49394624-49395869`
[2016-04-15T03:37Z] 2016-04-14 20:37:59 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:37:59,581 - WARNING - Could not retrieve variants from source file in region 3:57131989-57140162. Error was invalid region `3:57131990-57140162`
[2016-04-15T03:38Z] 2016-04-14 20:38:00 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:38:00,492 - WARNING - Could not retrieve variants from source file in region 3:47894169-47894570. Error was invalid region `3:47894170-47894570`
[2016-04-15T03:38Z] 2016-04-14 20:38:00 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:38:00,678 - WARNING - Could not retrieve variants from source file in region 3:58520095-58520496. Error was invalid region `3:58520096-58520496`
[2016-04-15T03:38Z] 2016-04-14 20:38:00 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:38:00,863 - WARNING - Could not retrieve variants from source file in region 3:56835550-56835951. Error was invalid region `3:56835551-56835951`
[2016-04-15T03:38Z] 2016-04-14 20:38:01 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:38:01,095 - WARNING - Could not retrieve variants from source file in region 3:56835550-56835951. Error was invalid region `3:56835551-56835951`
[2016-04-15T03:38Z] 2016-04-14 20:38:02 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:38:02,327 - WARNING - Could not retrieve variants from source file in region 3:47857364-47858598. Error was invalid region `3:47857365-47858598`
[2016-04-15T03:38Z] 2016-04-14 20:38:02 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:38:02,866 - WARNING - Could not retrieve variants from source file in region 3:49039773-49068094. Error was invalid region `3:49039774-49068094`
[2016-04-15T03:38Z] 2016-04-14 20:38:04 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:38:04,451 - WARNING - Could not retrieve variants from source file in region 3:51315619-51316020. Error was invalid region `3:51315620-51316020`
[2016-04-15T03:38Z] 2016-04-14 20:38:05 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:38:05,716 - WARNING - Could not retrieve variants from source file in region 3:56591067-56598144. Error was invalid region `3:56591068-56598144`
[2016-04-15T03:38Z] 2016-04-14 20:38:05 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:38:05,783 - WARNING - Could not retrieve variants from source file in region 3:50596881-50609814. Error was invalid region `3:50596882-50609814`
[2016-04-15T03:38Z] 2016-04-14 20:38:06 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:38:06,019 - WARNING - Could not retrieve variants from source file in region 3:58727733-58728134. Error was invalid region `3:58727734-58728134`
[2016-04-15T03:38Z] 2016-04-14 20:38:06 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:38:06,105 - WARNING - Could not retrieve variants from source file in region 3:58520095-58520496. Error was invalid region `3:58520096-58520496`
[2016-04-15T03:38Z] 2016-04-14 20:38:07 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:38:07,806 - WARNING - Could not retrieve variants from source file in region 3:47857364-47858598. Error was invalid region `3:47857365-47858598`
[2016-04-15T03:38Z] 2016-04-14 20:38:07 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:38:07,892 - WARNING - Could not retrieve variants from source file in region 3:57131989-57140162. Error was invalid region `3:57131990-57140162`
[2016-04-15T03:38Z] 2016-04-14 20:38:08 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:38:08,787 - WARNING - Could not retrieve variants from source file in region 3:51315619-51316020. Error was invalid region `3:51315620-51316020`
[2016-04-15T03:38Z] 2016-04-14 20:38:09 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:38:09,212 - WARNING - Could not retrieve variants from source file in region 3:53213446-53224192. Error was invalid region `3:53213447-53224192`
[2016-04-15T03:38Z] 2016-04-14 20:38:10 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:38:10,827 - WARNING - Could not retrieve variants from source file in region 3:50596881-50609814. Error was invalid region `3:50596882-50609814`
[2016-04-15T03:38Z] 2016-04-14 20:38:10 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:38:10,839 - WARNING - Could not retrieve variants from source file in region 3:56591067-56598144. Error was invalid region `3:56591068-56598144`
[2016-04-15T03:38Z] 2016-04-14 20:38:10 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:38:10,864 - WARNING - Could not retrieve variants from source file in region 3:47894169-47894570. Error was invalid region `3:47894170-47894570`
[2016-04-15T03:38Z] 2016-04-14 20:38:11 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:38:11,718 - WARNING - Could not retrieve variants from source file in region 3:58520095-58520496. Error was invalid region `3:58520096-58520496`
[2016-04-15T03:38Z] 2016-04-14 20:38:12 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:38:12,547 - WARNING - Could not retrieve variants from source file in region 3:48972140-48972541. Error was invalid region `3:48972141-48972541`
[2016-04-15T03:38Z] 2016-04-14 20:38:14 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:38:14,542 - WARNING - Could not retrieve variants from source file in region 3:51315619-51316020. Error was invalid region `3:51315620-51316020`
[2016-04-15T03:38Z] 2016-04-14 20:38:15 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:38:15,986 - WARNING - Could not retrieve variants from source file in region 3:56591067-56598144. Error was invalid region `3:56591068-56598144`
[2016-04-15T03:38Z] 2016-04-14 20:38:16 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:38:16,246 - WARNING - Could not retrieve variants from source file in region 3:50596881-50609814. Error was invalid region `3:50596882-50609814`
[2016-04-15T03:38Z] 2016-04-14 20:38:18 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:38:18,066 - WARNING - Could not retrieve variants from source file in region 3:48972140-48972541. Error was invalid region `3:48972141-48972541`
[2016-04-15T03:38Z] 2016-04-14 20:38:18 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:38:18,085 - WARNING - Could not retrieve variants from source file in region 3:52610440-52610841. Error was invalid region `3:52610441-52610841`
[2016-04-15T03:38Z] 2016-04-14 20:38:19 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:38:19,064 - WARNING - Could not retrieve variants from source file in region 3:53098664-53099128. Error was invalid region `3:53098665-53099128`
[2016-04-15T03:38Z] 2016-04-14 20:38:22 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:38:22,833 - WARNING - Could not retrieve variants from source file in region 3:58487046-58487447. Error was invalid region `3:58487047-58487447`
[2016-04-15T03:38Z] 2016-04-14 20:38:23 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:38:23,078 - WARNING - Could not retrieve variants from source file in region 3:53002968-53003369. Error was invalid region `3:53002969-53003369`
[2016-04-15T03:38Z] 2016-04-14 20:38:23 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:38:23,827 - WARNING - Could not retrieve variants from source file in region 3:52610440-52610841. Error was invalid region `3:52610441-52610841`
[2016-04-15T03:38Z] 2016-04-14 20:38:23 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:38:23,837 - WARNING - Could not retrieve variants from source file in region 3:48972140-48972541. Error was invalid region `3:48972141-48972541`
[2016-04-15T03:38Z] 2016-04-14 20:38:24 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:38:24,083 - WARNING - Could not retrieve variants from source file in region 3:53098664-53099128. Error was invalid region `3:53098665-53099128`
[2016-04-15T03:38Z] 2016-04-14 20:38:25 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:38:25,260 - WARNING - Could not retrieve variants from source file in region 3:52721094-52740372. Error was invalid region `3:52721095-52740372`
[2016-04-15T03:38Z] 2016-04-14 20:38:25 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:38:25,591 - WARNING - Could not retrieve variants from source file in region 3:52391524-52491524. Error was invalid region `3:52391525-52491524`
[2016-04-15T03:38Z] 2016-04-14 20:38:25 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:38:25,695 - WARNING - Could not retrieve variants from source file in region 3:52491524-52584977. Error was invalid region `3:52491525-52584977`
[2016-04-15T03:38Z] 2016-04-14 20:38:28 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:38:28,862 - WARNING - Could not retrieve variants from source file in region 3:52610440-52610841. Error was invalid region `3:52610441-52610841`
[2016-04-15T03:38Z] 2016-04-14 20:38:29 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:38:29,349 - WARNING - Could not retrieve variants from source file in region 3:50648349-50655380. Error was invalid region `3:50648350-50655380`
[2016-04-15T03:38Z] 2016-04-14 20:38:29 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:38:29,931 - WARNING - Could not retrieve variants from source file in region 3:52721094-52740372. Error was invalid region `3:52721095-52740372`
[2016-04-15T03:38Z] 2016-04-14 20:38:31 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:38:31,135 - WARNING - Could not retrieve variants from source file in region 3:58382635-58416728. Error was invalid region `3:58382636-58416728`
[2016-04-15T03:38Z] 2016-04-14 20:38:31 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:38:31,310 - WARNING - Could not retrieve variants from source file in region 3:50251622-50252023. Error was invalid region `3:50251623-50252023`
[2016-04-15T03:38Z] 2016-04-14 20:38:34 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:38:34,327 - WARNING - Could not retrieve variants from source file in region 3:50648349-50655380. Error was invalid region `3:50648350-50655380`
[2016-04-15T03:38Z] 2016-04-14 20:38:34 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:38:34,391 - WARNING - Could not retrieve variants from source file in region 3:52721094-52740372. Error was invalid region `3:52721095-52740372`
[2016-04-15T03:38Z] 2016-04-14 20:38:34 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:38:34,888 - WARNING - Could not retrieve variants from source file in region 3:54919140-54930984. Error was invalid region `3:54919141-54930984`
[2016-04-15T03:38Z] 2016-04-14 20:38:35 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:38:35,674 - WARNING - Could not retrieve variants from source file in region 3:58382635-58416728. Error was invalid region `3:58382636-58416728`
[2016-04-15T03:38Z] 2016-04-14 20:38:35 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:38:35,817 - WARNING - Could not retrieve variants from source file in region 3:50251622-50252023. Error was invalid region `3:50251623-50252023`
[2016-04-15T03:38Z] 2016-04-14 20:38:38 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:38:38,654 - WARNING - Could not retrieve variants from source file in region 3:52643474-52661541. Error was invalid region `3:52643475-52661541`
[2016-04-15T03:38Z] 2016-04-14 20:38:40 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:38:40,251 - WARNING - Could not retrieve variants from source file in region 3:50251622-50252023. Error was invalid region `3:50251623-50252023`
[2016-04-15T03:38Z] 2016-04-14 20:38:40 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:38:40,931 - WARNING - Could not retrieve variants from source file in region 3:58191055-58191456. Error was invalid region `3:58191056-58191456`
[2016-04-15T03:38Z] 2016-04-14 20:38:41 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:38:41,038 - WARNING - Could not retrieve variants from source file in region 3:58191055-58191456. Error was invalid region `3:58191056-58191456`
[2016-04-15T03:38Z] 2016-04-14 20:38:42 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:38:42,060 - WARNING - Could not retrieve variants from source file in region 3:52324828-52325229. Error was invalid region `3:52324829-52325229`
[2016-04-15T03:38Z] 2016-04-14 20:38:44 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:38:44,614 - WARNING - Could not retrieve variants from source file in region 3:52324828-52325229. Error was invalid region `3:52324829-52325229`
[2016-04-15T03:38Z] 2016-04-14 20:38:49 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:38:49,974 - WARNING - Could not retrieve variants from source file in region 3:54880250-54880651. Error was invalid region `3:54880251-54880651`
[2016-04-15T03:38Z] 2016-04-14 20:38:50 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:38:50,005 - WARNING - Could not retrieve variants from source file in region 3:54880250-54880651. Error was invalid region `3:54880251-54880651`
[2016-04-15T03:38Z] 2016-04-14 20:38:51 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:38:51,872 - WARNING - Could not retrieve variants from source file in region 3:53804278-53804679. Error was invalid region `3:53804279-53804679`
[2016-04-15T03:38Z] 2016-04-14 20:38:51 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:38:51,948 - WARNING - Could not retrieve variants from source file in region 3:53883511-53916320. Error was invalid region `3:53883512-53916320`
[2016-04-15T03:38Z] 2016-04-14 20:38:52 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:38:52,006 - WARNING - Could not retrieve variants from source file in region 3:53804278-53804679. Error was invalid region `3:53804279-53804679`
[2016-04-15T03:38Z] 2016-04-14 20:38:52 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:38:52,031 - WARNING - Could not retrieve variants from source file in region 3:54880250-54880651. Error was invalid region `3:54880251-54880651`
[2016-04-15T03:38Z] 2016-04-14 20:38:52 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:38:52,394 - WARNING - Could not retrieve variants from source file in region 3:53883511-53916320. Error was invalid region `3:53883512-53916320`
[2016-04-15T03:38Z] 2016-04-14 20:38:52 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:38:52,561 - WARNING - Could not retrieve variants from source file in region 3:54354299-54354700. Error was invalid region `3:54354300-54354700`
[2016-04-15T03:38Z] 2016-04-14 20:38:52 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:38:52,562 - WARNING - Could not retrieve variants from source file in region 3:54798047-54798448. Error was invalid region `3:54798048-54798448`
[2016-04-15T03:38Z] 2016-04-14 20:38:54 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:38:54,307 - WARNING - Could not retrieve variants from source file in region 3:54354299-54354700. Error was invalid region `3:54354300-54354700`
[2016-04-15T03:38Z] 2016-04-14 20:38:56 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:38:56,888 - WARNING - Could not retrieve variants from source file in region 3:54354299-54354700. Error was invalid region `3:54354300-54354700`
[2016-04-15T03:39Z] ['bcbio-variation-recall', 'square', '-Xms750m', '-Xmx7280m', '-XX:+UseSerialGC', '-c', 16, '-r', u'3:62739116-78648077', '--caller', 'platypus', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/3/Batch1-3_62739115_78648077.vcf.gz', '/mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/3/Batch1-3_62739115_78648077.vcf-inputs.txt'] in region: 3:62739116-78648077
[2016-04-15T03:39Z] 2016-04-14 20:39:12 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:39:12,348 - WARNING - Could not retrieve variants from source file in region 3:64210891-64211292. Error was invalid region `3:64210892-64211292`
[2016-04-15T03:39Z] 2016-04-14 20:39:13 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:39:13,668 - WARNING - Could not retrieve variants from source file in region 3:74344145-74351085. Error was invalid region `3:74344146-74351085`
[2016-04-15T03:39Z] 2016-04-14 20:39:14 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:39:14,594 - WARNING - Could not retrieve variants from source file in region 3:77089184-77089889. Error was invalid region `3:77089185-77089889`
[2016-04-15T03:39Z] 2016-04-14 20:39:14 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:39:14,604 - WARNING - Could not retrieve variants from source file in region 3:63898149-63898550. Error was invalid region `3:63898150-63898550`
[2016-04-15T03:39Z] 2016-04-14 20:39:14 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:39:14,627 - WARNING - Could not retrieve variants from source file in region 3:66419731-66444805. Error was invalid region `3:66419732-66444805`
[2016-04-15T03:39Z] 2016-04-14 20:39:14 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:39:14,700 - WARNING - Could not retrieve variants from source file in region 3:64587607-64588008. Error was invalid region `3:64587608-64588008`
[2016-04-15T03:39Z] 2016-04-14 20:39:14 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:39:14,754 - WARNING - Could not retrieve variants from source file in region 3:67425042-67427101. Error was invalid region `3:67425043-67427101`
[2016-04-15T03:39Z] 2016-04-14 20:39:15 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:39:15,736 - WARNING - Could not retrieve variants from source file in region 3:75986452-75986909. Error was invalid region `3:75986453-75986909`
[2016-04-15T03:39Z] 2016-04-14 20:39:15 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:39:15,783 - WARNING - Could not retrieve variants from source file in region 3:65344817-65345218. Error was invalid region `3:65344818-65345218`
[2016-04-15T03:39Z] 2016-04-14 20:39:15 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:39:15,854 - WARNING - Could not retrieve variants from source file in region 3:74413465-74413866. Error was invalid region `3:74413466-74413866`
[2016-04-15T03:39Z] 2016-04-14 20:39:20 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:39:20,259 - WARNING - Could not retrieve variants from source file in region 3:69299022-69299423. Error was invalid region `3:69299023-69299423`
[2016-04-15T03:39Z] 2016-04-14 20:39:21 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:39:21,848 - WARNING - Could not retrieve variants from source file in region 3:65425349-65425750. Error was invalid region `3:65425350-65425750`
[2016-04-15T03:39Z] 2016-04-14 20:39:23 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:39:23,798 - WARNING - Could not retrieve variants from source file in region 3:73111157-73112188. Error was invalid region `3:73111158-73112188`
[2016-04-15T03:39Z] 2016-04-14 20:39:24 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:39:24,003 - WARNING - Could not retrieve variants from source file in region 3:63898149-63898550. Error was invalid region `3:63898150-63898550`
[2016-04-15T03:39Z] 2016-04-14 20:39:24 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:39:24,571 - WARNING - Could not retrieve variants from source file in region 3:75986452-75986909. Error was invalid region `3:75986453-75986909`
[2016-04-15T03:39Z] 2016-04-14 20:39:24 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:39:24,729 - WARNING - Could not retrieve variants from source file in region 3:74413465-74413866. Error was invalid region `3:74413466-74413866`
[2016-04-15T03:39Z] 2016-04-14 20:39:25 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:39:25,123 - WARNING - Could not retrieve variants from source file in region 3:69299022-69299423. Error was invalid region `3:69299023-69299423`
[2016-04-15T03:39Z] 2016-04-14 20:39:26 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:39:26,534 - WARNING - Could not retrieve variants from source file in region 3:65425349-65425750. Error was invalid region `3:65425350-65425750`
[2016-04-15T03:39Z] 2016-04-14 20:39:28 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:39:28,040 - WARNING - Could not retrieve variants from source file in region 3:77089184-77089889. Error was invalid region `3:77089185-77089889`
[2016-04-15T03:39Z] 2016-04-14 20:39:29 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:39:29,409 - WARNING - Could not retrieve variants from source file in region 3:67425042-67427101. Error was invalid region `3:67425043-67427101`
[2016-04-15T03:39Z] 2016-04-14 20:39:30 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:39:30,070 - WARNING - Could not retrieve variants from source file in region 3:66419731-66444805. Error was invalid region `3:66419732-66444805`
[2016-04-15T03:39Z] 2016-04-14 20:39:31 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:39:31,907 - WARNING - Could not retrieve variants from source file in region 3:64009297-64009698. Error was invalid region `3:64009298-64009698`
[2016-04-15T03:39Z] 2016-04-14 20:39:31 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:39:31,943 - WARNING - Could not retrieve variants from source file in region 3:73111157-73112188. Error was invalid region `3:73111158-73112188`
[2016-04-15T03:39Z] 2016-04-14 20:39:32 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:39:32,591 - WARNING - Could not retrieve variants from source file in region 3:75986452-75986909. Error was invalid region `3:75986453-75986909`
[2016-04-15T03:39Z] 2016-04-14 20:39:32 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:39:32,642 - WARNING - Could not retrieve variants from source file in region 3:69037877-69054531. Error was invalid region `3:69037878-69054531`
[2016-04-15T03:39Z] 2016-04-14 20:39:32 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:39:32,788 - WARNING - Could not retrieve variants from source file in region 3:74413465-74413866. Error was invalid region `3:74413466-74413866`
[2016-04-15T03:39Z] 2016-04-14 20:39:43 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:39:43,594 - WARNING - Could not retrieve variants from source file in region 3:65387293-65387704. Error was invalid region `3:65387294-65387704`
[2016-04-15T03:39Z] 2016-04-14 20:39:44 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:39:44,642 - WARNING - Could not retrieve variants from source file in region 3:73673367-73673768. Error was invalid region `3:73673368-73673768`
[2016-04-15T03:39Z] 2016-04-14 20:39:44 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:39:44,778 - WARNING - Could not retrieve variants from source file in region 3:64132971-64143049. Error was invalid region `3:64132972-64143049`
[2016-04-15T03:39Z] 2016-04-14 20:39:45 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:39:45,373 - WARNING - Could not retrieve variants from source file in region 3:73673367-73673768. Error was invalid region `3:73673368-73673768`
[2016-04-15T03:39Z] 2016-04-14 20:39:45 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:39:45,572 - WARNING - Could not retrieve variants from source file in region 3:64132971-64143049. Error was invalid region `3:64132972-64143049`
[2016-04-15T03:39Z] 2016-04-14 20:39:45 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:39:45,840 - WARNING - Could not retrieve variants from source file in region 3:66550545-66550952. Error was invalid region `3:66550546-66550952`
[2016-04-15T03:39Z] 2016-04-14 20:39:45 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:39:45,844 - WARNING - Could not retrieve variants from source file in region 3:66286845-66287246. Error was invalid region `3:66286846-66287246`
[2016-04-15T03:39Z] 2016-04-14 20:39:46 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:39:46,468 - WARNING - Could not retrieve variants from source file in region 3:63967689-63984066. Error was invalid region `3:63967690-63984066`
[2016-04-15T03:39Z] 2016-04-14 20:39:48 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:39:48,472 - WARNING - Could not retrieve variants from source file in region 3:65387293-65387704. Error was invalid region `3:65387294-65387704`
[2016-04-15T03:39Z] 2016-04-14 20:39:49 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:39:49,900 - WARNING - Could not retrieve variants from source file in region 3:73618368-73618769. Error was invalid region `3:73618369-73618769`
[2016-04-15T03:39Z] 2016-04-14 20:39:50 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:39:50,491 - WARNING - Could not retrieve variants from source file in region 3:63600694-63601095. Error was invalid region `3:63600695-63601095`
[2016-04-15T03:39Z] 2016-04-14 20:39:50 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:39:50,507 - WARNING - Could not retrieve variants from source file in region 3:67458808-67459240. Error was invalid region `3:67458809-67459240`
[2016-04-15T03:39Z] 2016-04-14 20:39:50 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:39:50,524 - WARNING - Could not retrieve variants from source file in region 3:73673367-73673768. Error was invalid region `3:73673368-73673768`
[2016-04-15T03:39Z] 2016-04-14 20:39:51 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:39:51,137 - WARNING - Could not retrieve variants from source file in region 3:66550545-66550952. Error was invalid region `3:66550546-66550952`
[2016-04-15T03:39Z] 2016-04-14 20:39:51 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:39:51,768 - WARNING - Could not retrieve variants from source file in region 3:63967689-63984066. Error was invalid region `3:63967690-63984066`
[2016-04-15T03:39Z] 2016-04-14 20:39:51 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:39:51,953 - WARNING - Could not retrieve variants from source file in region 3:69229850-69271222. Error was invalid region `3:69229851-69271222`
[2016-04-15T03:39Z] 2016-04-14 20:39:52 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:39:52,106 - WARNING - Could not retrieve variants from source file in region 3:71632785-71633186. Error was invalid region `3:71632786-71633186`
[2016-04-15T03:39Z] 2016-04-14 20:39:52 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:39:52,798 - WARNING - Could not retrieve variants from source file in region 3:69987496-69987897. Error was invalid region `3:69987497-69987897`
[2016-04-15T03:39Z] 2016-04-14 20:39:52 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:39:52,882 - WARNING - Could not retrieve variants from source file in region 3:65387293-65387704. Error was invalid region `3:65387294-65387704`
[2016-04-15T03:39Z] 2016-04-14 20:39:55 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:39:55,320 - WARNING - Could not retrieve variants from source file in region 3:63600694-63601095. Error was invalid region `3:63600695-63601095`
[2016-04-15T03:39Z] 2016-04-14 20:39:56 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:39:56,525 - WARNING - Could not retrieve variants from source file in region 3:66550545-66550952. Error was invalid region `3:66550546-66550952`
[2016-04-15T03:39Z] 2016-04-14 20:39:56 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:39:56,808 - WARNING - Could not retrieve variants from source file in region 3:66286845-66287246. Error was invalid region `3:66286846-66287246`
[2016-04-15T03:39Z] 2016-04-14 20:39:56 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:39:56,921 - WARNING - Could not retrieve variants from source file in region 3:71632785-71633186. Error was invalid region `3:71632786-71633186`
[2016-04-15T03:39Z] 2016-04-14 20:39:58 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:39:58,631 - WARNING - Could not retrieve variants from source file in region 3:73618368-73618769. Error was invalid region `3:73618369-73618769`
[2016-04-15T03:40Z] 2016-04-14 20:40:00 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:40:00,788 - WARNING - Could not retrieve variants from source file in region 3:69168536-69168937. Error was invalid region `3:69168537-69168937`
[2016-04-15T03:40Z] 2016-04-14 20:40:01 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:40:01,123 - WARNING - Could not retrieve variants from source file in region 3:69168536-69168937. Error was invalid region `3:69168537-69168937`
[2016-04-15T03:40Z] 2016-04-14 20:40:01 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:40:01,220 - WARNING - Could not retrieve variants from source file in region 3:67458808-67459240. Error was invalid region `3:67458809-67459240`
[2016-04-15T03:40Z] 2016-04-14 20:40:04 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:40:04,817 - WARNING - Could not retrieve variants from source file in region 3:73433158-73453515. Error was invalid region `3:73433159-73453515`
[2016-04-15T03:40Z] 2016-04-14 20:40:05 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:40:05,660 - WARNING - Could not retrieve variants from source file in region 3:69082497-69096804. Error was invalid region `3:69082498-69096804`
[2016-04-15T03:40Z] 2016-04-14 20:40:05 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:40:05,731 - WARNING - Could not retrieve variants from source file in region 3:69082497-69096804. Error was invalid region `3:69082498-69096804`
[2016-04-15T03:40Z] 2016-04-14 20:40:06 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:40:06,018 - WARNING - Could not retrieve variants from source file in region 3:69402590-69402991. Error was invalid region `3:69402591-69402991`
[2016-04-15T03:40Z] 2016-04-14 20:40:06 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:40:06,066 - WARNING - Could not retrieve variants from source file in region 3:69402590-69402991. Error was invalid region `3:69402591-69402991`
[2016-04-15T03:40Z] 2016-04-14 20:40:06 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:40:06,068 - WARNING - Could not retrieve variants from source file in region 3:69402590-69402991. Error was invalid region `3:69402591-69402991`
[2016-04-15T03:40Z] ['bcbio-variation-recall', 'square', '-Xms750m', '-Xmx7280m', '-XX:+UseSerialGC', '-c', 16, '-r', u'3:78649263-96533852', '--caller', 'platypus', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/3/Batch1-3_78649262_96533852.vcf.gz', '/mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/3/Batch1-3_78649262_96533852.vcf-inputs.txt'] in region: 3:78649263-96533852
[2016-04-15T03:40Z] 2016-04-14 20:40:20 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:40:20,199 - WARNING - Could not retrieve variants from source file in region 3:93768057-93780050. Error was invalid region `3:93768058-93780050`
[2016-04-15T03:40Z] 2016-04-14 20:40:20 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:40:20,595 - WARNING - Could not retrieve variants from source file in region 3:87294838-87295239. Error was invalid region `3:87294839-87295239`
[2016-04-15T03:40Z] 2016-04-14 20:40:20 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:40:20,627 - WARNING - Could not retrieve variants from source file in region 3:87294838-87295239. Error was invalid region `3:87294839-87295239`
[2016-04-15T03:40Z] 2016-04-14 20:40:20 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:40:20,692 - WARNING - Could not retrieve variants from source file in region 3:87294838-87295239. Error was invalid region `3:87294839-87295239`
[2016-04-15T03:40Z] 2016-04-14 20:40:20 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:40:20,716 - WARNING - Could not retrieve variants from source file in region 3:93592908-93593309. Error was invalid region `3:93592909-93593309`
[2016-04-15T03:40Z] 2016-04-14 20:40:20 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:40:20,865 - WARNING - Could not retrieve variants from source file in region 3:93619466-93619867. Error was invalid region `3:93619467-93619867`
[2016-04-15T03:40Z] 2016-04-14 20:40:20 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:40:20,967 - WARNING - Could not retrieve variants from source file in region 3:79067754-79068155. Error was invalid region `3:79067755-79068155`
[2016-04-15T03:40Z] 2016-04-14 20:40:21 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:40:21,155 - WARNING - Could not retrieve variants from source file in region 3:81642956-81643357. Error was invalid region `3:81642957-81643357`
[2016-04-15T03:40Z] 2016-04-14 20:40:21 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:40:21,503 - WARNING - Could not retrieve variants from source file in region 3:89498217-89521883. Error was invalid region `3:89498218-89521883`
[2016-04-15T03:40Z] 2016-04-14 20:40:21 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:40:21,612 - WARNING - Could not retrieve variants from source file in region 3:88514555-88515990. Error was invalid region `3:88514556-88515990`
[2016-04-15T03:40Z] 2016-04-14 20:40:21 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:40:21,864 - WARNING - Could not retrieve variants from source file in region 3:81697919-81698320. Error was invalid region `3:81697920-81698320`
[2016-04-15T03:40Z] 2016-04-14 20:40:22 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:40:22,044 - WARNING - Could not retrieve variants from source file in region 3:78700690-78717533. Error was invalid region `3:78700691-78717533`
[2016-04-15T03:40Z] 2016-04-14 20:40:22 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:40:22,056 - WARNING - Could not retrieve variants from source file in region 3:88188209-88199488. Error was invalid region `3:88188210-88199488`
[2016-04-15T03:40Z] 2016-04-14 20:40:27 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:40:27,614 - WARNING - Could not retrieve variants from source file in region 3:81642956-81643357. Error was invalid region `3:81642957-81643357`
[2016-04-15T03:40Z] 2016-04-14 20:40:29 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:40:29,645 - WARNING - Could not retrieve variants from source file in region 3:93592908-93593309. Error was invalid region `3:93592909-93593309`
[2016-04-15T03:40Z] 2016-04-14 20:40:30 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:40:30,254 - WARNING - Could not retrieve variants from source file in region 3:78766781-78767182. Error was invalid region `3:78766782-78767182`
[2016-04-15T03:40Z] 2016-04-14 20:40:30 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:40:30,538 - WARNING - Could not retrieve variants from source file in region 3:79067754-79068155. Error was invalid region `3:79067755-79068155`
[2016-04-15T03:40Z] 2016-04-14 20:40:30 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:40:30,662 - WARNING - Could not retrieve variants from source file in region 3:81642956-81643357. Error was invalid region `3:81642957-81643357`
[2016-04-15T03:40Z] 2016-04-14 20:40:31 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:40:31,191 - WARNING - Could not retrieve variants from source file in region 3:88188209-88199488. Error was invalid region `3:88188210-88199488`
[2016-04-15T03:40Z] 2016-04-14 20:40:31 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:40:31,192 - WARNING - Could not retrieve variants from source file in region 3:78700690-78717533. Error was invalid region `3:78700691-78717533`
[2016-04-15T03:40Z] 2016-04-14 20:40:36 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:40:36,014 - WARNING - Could not retrieve variants from source file in region 3:88188209-88199488. Error was invalid region `3:88188210-88199488`
[2016-04-15T03:40Z] 2016-04-14 20:40:36 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:40:36,171 - WARNING - Could not retrieve variants from source file in region 3:79067754-79068155. Error was invalid region `3:79067755-79068155`
[2016-04-15T03:40Z] ['bcbio-variation-recall', 'square', '-Xms750m', '-Xmx7280m', '-XX:+UseSerialGC', '-c', 16, '-r', u'3:96585669-112185230', '--caller', 'platypus', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/3/Batch1-3_96585668_112185230.vcf.gz', '/mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/3/Batch1-3_96585668_112185230.vcf-inputs.txt'] in region: 3:96585669-112185230
[2016-04-15T03:40Z] 2016-04-14 20:40:52 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:40:52,640 - WARNING - Could not retrieve variants from source file in region 3:111577834-111578485. Error was invalid region `3:111577835-111578485`
[2016-04-15T03:40Z] 2016-04-14 20:40:53 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:40:53,834 - WARNING - Could not retrieve variants from source file in region 3:112184814-112185215. Error was invalid region `3:112184815-112185215`
[2016-04-15T03:40Z] 2016-04-14 20:40:53 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:40:53,949 - WARNING - Could not retrieve variants from source file in region 3:105422633-105439216. Error was invalid region `3:105422634-105439216`
[2016-04-15T03:40Z] 2016-04-14 20:40:55 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:40:55,469 - WARNING - Could not retrieve variants from source file in region 3:110790902-110791303. Error was invalid region `3:110790903-110791303`
[2016-04-15T03:40Z] 2016-04-14 20:40:55 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:40:55,596 - WARNING - Could not retrieve variants from source file in region 3:111355872-111356273. Error was invalid region `3:111355873-111356273`
[2016-04-15T03:40Z] 2016-04-14 20:40:56 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:40:56,024 - WARNING - Could not retrieve variants from source file in region 3:107937197-107937598. Error was invalid region `3:107937198-107937598`
[2016-04-15T03:40Z] 2016-04-14 20:40:56 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:40:56,119 - WARNING - Could not retrieve variants from source file in region 3:108188782-108189183. Error was invalid region `3:108188783-108189183`
[2016-04-15T03:40Z] 2016-04-14 20:40:56 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:40:56,157 - WARNING - Could not retrieve variants from source file in region 3:109178547-109178948. Error was invalid region `3:109178548-109178948`
[2016-04-15T03:40Z] 2016-04-14 20:40:59 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:40:59,330 - WARNING - Could not retrieve variants from source file in region 3:112184814-112185215. Error was invalid region `3:112184815-112185215`
[2016-04-15T03:41Z] 2016-04-14 20:41:00 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:41:00,624 - WARNING - Could not retrieve variants from source file in region 3:105422633-105439216. Error was invalid region `3:105422634-105439216`
[2016-04-15T03:41Z] 2016-04-14 20:41:02 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:41:02,853 - WARNING - Could not retrieve variants from source file in region 3:100170417-100174912. Error was invalid region `3:100170418-100174912`
[2016-04-15T03:41Z] 2016-04-14 20:41:03 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:41:03,842 - WARNING - Could not retrieve variants from source file in region 3:109052521-109052922. Error was invalid region `3:109052522-109052922`
[2016-04-15T03:41Z] 2016-04-14 20:41:04 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:41:04,120 - WARNING - Could not retrieve variants from source file in region 3:111962640-111996744. Error was invalid region `3:111962641-111996744`
[2016-04-15T03:41Z] 2016-04-14 20:41:04 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:41:04,292 - WARNING - Could not retrieve variants from source file in region 3:111355872-111356273. Error was invalid region `3:111355873-111356273`
[2016-04-15T03:41Z] 2016-04-14 20:41:04 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:41:04,456 - WARNING - Could not retrieve variants from source file in region 3:110790902-110791303. Error was invalid region `3:110790903-110791303`
[2016-04-15T03:41Z] 2016-04-14 20:41:04 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:41:04,564 - WARNING - Could not retrieve variants from source file in region 3:108188782-108189183. Error was invalid region `3:108188783-108189183`
[2016-04-15T03:41Z] 2016-04-14 20:41:04 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:41:04,923 - WARNING - Could not retrieve variants from source file in region 3:111918004-111923313. Error was invalid region `3:111918005-111923313`
[2016-04-15T03:41Z] 2016-04-14 20:41:04 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:41:04,974 - WARNING - Could not retrieve variants from source file in region 3:109178547-109178948. Error was invalid region `3:109178548-109178948`
[2016-04-15T03:41Z] 2016-04-14 20:41:05 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:41:05,045 - WARNING - Could not retrieve variants from source file in region 3:112051892-112064040. Error was invalid region `3:112051893-112064040`
[2016-04-15T03:41Z] 2016-04-14 20:41:05 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:41:05,121 - WARNING - Could not retrieve variants from source file in region 3:112184814-112185215. Error was invalid region `3:112184815-112185215`
[2016-04-15T03:41Z] 2016-04-14 20:41:08 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:41:08,523 - WARNING - Could not retrieve variants from source file in region 3:100170417-100174912. Error was invalid region `3:100170418-100174912`
[2016-04-15T03:41Z] 2016-04-14 20:41:11 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:41:11,499 - WARNING - Could not retrieve variants from source file in region 3:107937197-107937598. Error was invalid region `3:107937198-107937598`
[2016-04-15T03:41Z] 2016-04-14 20:41:11 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:41:11,829 - WARNING - Could not retrieve variants from source file in region 3:111355872-111356273. Error was invalid region `3:111355873-111356273`
[2016-04-15T03:41Z] 2016-04-14 20:41:11 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:41:11,987 - WARNING - Could not retrieve variants from source file in region 3:110790902-110791303. Error was invalid region `3:110790903-110791303`
[2016-04-15T03:41Z] 2016-04-14 20:41:12 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:41:12,108 - WARNING - Could not retrieve variants from source file in region 3:111918004-111923313. Error was invalid region `3:111918005-111923313`
[2016-04-15T03:41Z] 2016-04-14 20:41:12 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:41:12,303 - WARNING - Could not retrieve variants from source file in region 3:109178547-109178948. Error was invalid region `3:109178548-109178948`
[2016-04-15T03:41Z] 2016-04-14 20:41:22 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:41:22,502 - WARNING - Could not retrieve variants from source file in region 3:105388942-105389343. Error was invalid region `3:105388943-105389343`
[2016-04-15T03:41Z] 2016-04-14 20:41:24 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:41:24,331 - WARNING - Could not retrieve variants from source file in region 3:100949631-100963344. Error was invalid region `3:100949632-100963344`
[2016-04-15T03:41Z] 2016-04-14 20:41:25 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:41:25,494 - WARNING - Could not retrieve variants from source file in region 3:108754003-108754450. Error was invalid region `3:108754004-108754450`
[2016-04-15T03:41Z] 2016-04-14 20:41:26 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:41:26,563 - WARNING - Could not retrieve variants from source file in region 3:107096336-107096737. Error was invalid region `3:107096337-107096737`
[2016-04-15T03:41Z] 2016-04-14 20:41:26 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:41:26,664 - WARNING - Could not retrieve variants from source file in region 3:108639173-108639613. Error was invalid region `3:108639174-108639613`
[2016-04-15T03:41Z] 2016-04-14 20:41:26 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:41:26,996 - WARNING - Could not retrieve variants from source file in region 3:105388942-105389343. Error was invalid region `3:105388943-105389343`
[2016-04-15T03:41Z] 2016-04-14 20:41:28 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:41:28,333 - WARNING - Could not retrieve variants from source file in region 3:105587536-105587937. Error was invalid region `3:105587537-105587937`
[2016-04-15T03:41Z] 2016-04-14 20:41:28 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:41:28,438 - WARNING - Could not retrieve variants from source file in region 3:108072087-108072714. Error was invalid region `3:108072088-108072714`
[2016-04-15T03:41Z] 2016-04-14 20:41:28 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:41:28,812 - WARNING - Could not retrieve variants from source file in region 3:100949631-100963344. Error was invalid region `3:100949632-100963344`
[2016-04-15T03:41Z] 2016-04-14 20:41:30 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:41:30,511 - WARNING - Could not retrieve variants from source file in region 3:107096336-107096737. Error was invalid region `3:107096337-107096737`
[2016-04-15T03:41Z] 2016-04-14 20:41:30 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:41:30,887 - WARNING - Could not retrieve variants from source file in region 3:108639173-108639613. Error was invalid region `3:108639174-108639613`
[2016-04-15T03:41Z] 2016-04-14 20:41:31 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:41:31,165 - WARNING - Could not retrieve variants from source file in region 3:105388942-105389343. Error was invalid region `3:105388943-105389343`
[2016-04-15T03:41Z] 2016-04-14 20:41:32 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:41:32,735 - WARNING - Could not retrieve variants from source file in region 3:111672614-111673015. Error was invalid region `3:111672615-111673015`
[2016-04-15T03:41Z] 2016-04-14 20:41:33 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:41:33,965 - WARNING - Could not retrieve variants from source file in region 3:108754003-108754450. Error was invalid region `3:108754004-108754450`
[2016-04-15T03:41Z] 2016-04-14 20:41:33 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:41:33,968 - WARNING - Could not retrieve variants from source file in region 3:111672614-111673015. Error was invalid region `3:111672615-111673015`
[2016-04-15T03:41Z] 2016-04-14 20:41:34 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:41:34,886 - WARNING - Could not retrieve variants from source file in region 3:108639173-108639613. Error was invalid region `3:108639174-108639613`
[2016-04-15T03:41Z] 2016-04-14 20:41:40 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:41:40,252 - WARNING - Could not retrieve variants from source file in region 3:108475763-108476164. Error was invalid region `3:108475764-108476164`
[2016-04-15T03:41Z] 2016-04-14 20:41:42 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:41:42,740 - WARNING - Could not retrieve variants from source file in region 3:108475763-108476164. Error was invalid region `3:108475764-108476164`
[2016-04-15T03:41Z] 2016-04-14 20:41:43 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:41:43,293 - WARNING - Could not retrieve variants from source file in region 3:108402875-108403276. Error was invalid region `3:108402876-108403276`
[2016-04-15T03:41Z] 2016-04-14 20:41:44 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:41:44,675 - WARNING - Could not retrieve variants from source file in region 3:108475763-108476164. Error was invalid region `3:108475764-108476164`
[2016-04-15T03:41Z] 2016-04-14 20:41:46 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:41:46,741 - WARNING - Could not retrieve variants from source file in region 3:108572384-108572785. Error was invalid region `3:108572385-108572785`
[2016-04-15T03:41Z] 2016-04-14 20:41:47 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:41:47,207 - WARNING - Could not retrieve variants from source file in region 3:101575964-101576952. Error was invalid region `3:101575965-101576952`
[2016-04-15T03:41Z] 2016-04-14 20:41:48 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:41:48,215 - WARNING - Could not retrieve variants from source file in region 3:108402875-108403276. Error was invalid region `3:108402876-108403276`
[2016-04-15T03:41Z] 2016-04-14 20:41:49 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:41:49,649 - WARNING - Could not retrieve variants from source file in region 3:101575964-101576952. Error was invalid region `3:101575965-101576952`
[2016-04-15T03:41Z] 2016-04-14 20:41:50 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:41:50,318 - WARNING - Could not retrieve variants from source file in region 3:97983046-97984171. Error was invalid region `3:97983047-97984171`
[2016-04-15T03:41Z] 2016-04-14 20:41:50 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:41:50,342 - WARNING - Could not retrieve variants from source file in region 3:101484124-101484525. Error was invalid region `3:101484125-101484525`
[2016-04-15T03:41Z] 2016-04-14 20:41:51 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:41:51,471 - WARNING - Could not retrieve variants from source file in region 3:100466807-100473695. Error was invalid region `3:100466808-100473695`
[2016-04-15T03:41Z] 2016-04-14 20:41:52 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:41:52,740 - WARNING - Could not retrieve variants from source file in region 3:101575964-101576952. Error was invalid region `3:101575965-101576952`
[2016-04-15T03:41Z] 2016-04-14 20:41:52 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:41:52,794 - WARNING - Could not retrieve variants from source file in region 3:97726536-97726937. Error was invalid region `3:97726537-97726937`
[2016-04-15T03:41Z] 2016-04-14 20:41:53 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:41:53,337 - WARNING - Could not retrieve variants from source file in region 3:98451976-98452377. Error was invalid region `3:98451977-98452377`
[2016-04-15T03:41Z] 2016-04-14 20:41:53 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:41:53,418 - WARNING - Could not retrieve variants from source file in region 3:108402875-108403276. Error was invalid region `3:108402876-108403276`
[2016-04-15T03:41Z] 2016-04-14 20:41:55 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:41:55,376 - WARNING - Could not retrieve variants from source file in region 3:97983046-97984171. Error was invalid region `3:97983047-97984171`
[2016-04-15T03:41Z] 2016-04-14 20:41:55 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:41:55,389 - WARNING - Could not retrieve variants from source file in region 3:108372811-108373212. Error was invalid region `3:108372812-108373212`
[2016-04-15T03:41Z] 2016-04-14 20:41:55 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:41:55,485 - WARNING - Could not retrieve variants from source file in region 3:101484124-101484525. Error was invalid region `3:101484125-101484525`
[2016-04-15T03:41Z] 2016-04-14 20:41:55 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:41:55,994 - WARNING - Could not retrieve variants from source file in region 3:100466807-100473695. Error was invalid region `3:100466808-100473695`
[2016-04-15T03:41Z] 2016-04-14 20:41:57 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:41:57,500 - WARNING - Could not retrieve variants from source file in region 3:100287553-100287954. Error was invalid region `3:100287554-100287954`
[2016-04-15T03:41Z] 2016-04-14 20:41:57 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:41:57,786 - WARNING - Could not retrieve variants from source file in region 3:97726536-97726937. Error was invalid region `3:97726537-97726937`
[2016-04-15T03:41Z] 2016-04-14 20:41:59 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:41:59,703 - WARNING - Could not retrieve variants from source file in region 3:97983046-97984171. Error was invalid region `3:97983047-97984171`
[2016-04-15T03:42Z] 2016-04-14 20:42:00 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:42:00,667 - WARNING - Could not retrieve variants from source file in region 3:101484124-101484525. Error was invalid region `3:101484125-101484525`
[2016-04-15T03:42Z] 2016-04-14 20:42:00 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:42:00,711 - WARNING - Could not retrieve variants from source file in region 3:100466807-100473695. Error was invalid region `3:100466808-100473695`
[2016-04-15T03:42Z] 2016-04-14 20:42:00 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:42:00,863 - WARNING - Could not retrieve variants from source file in region 3:100287553-100287954. Error was invalid region `3:100287554-100287954`
[2016-04-15T03:42Z] 2016-04-14 20:42:02 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:42:02,153 - WARNING - Could not retrieve variants from source file in region 3:97851787-97888628. Error was invalid region `3:97851788-97888628`
[2016-04-15T03:42Z] 2016-04-14 20:42:02 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:42:02,355 - WARNING - Could not retrieve variants from source file in region 3:97726536-97726937. Error was invalid region `3:97726537-97726937`
[2016-04-15T03:42Z] 2016-04-14 20:42:05 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:42:05,444 - WARNING - Could not retrieve variants from source file in region 3:101283581-101283982. Error was invalid region `3:101283582-101283982`
[2016-04-15T03:42Z] 2016-04-14 20:42:08 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:42:08,703 - WARNING - Could not retrieve variants from source file in region 3:101283581-101283982. Error was invalid region `3:101283582-101283982`
[2016-04-15T03:42Z] 2016-04-14 20:42:11 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:42:11,238 - WARNING - Could not retrieve variants from source file in region 3:97806405-97806806. Error was invalid region `3:97806406-97806806`
[2016-04-15T03:42Z] 2016-04-14 20:42:11 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:42:11,638 - WARNING - Could not retrieve variants from source file in region 3:97364827-97367420. Error was invalid region `3:97364828-97367420`
[2016-04-15T03:42Z] 2016-04-14 20:42:12 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:42:12,897 - WARNING - Could not retrieve variants from source file in region 3:98298389-98304657. Error was invalid region `3:98298390-98304657`
[2016-04-15T03:42Z] 2016-04-14 20:42:14 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:42:14,140 - WARNING - Could not retrieve variants from source file in region 3:98298389-98304657. Error was invalid region `3:98298390-98304657`
[2016-04-15T03:42Z] 2016-04-14 20:42:15 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:42:15,601 - WARNING - Could not retrieve variants from source file in region 3:97806405-97806806. Error was invalid region `3:97806406-97806806`
[2016-04-15T03:42Z] 2016-04-14 20:42:15 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:42:15,865 - WARNING - Could not retrieve variants from source file in region 3:97806405-97806806. Error was invalid region `3:97806406-97806806`
[2016-04-15T03:42Z] 2016-04-14 20:42:16 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:42:16,720 - WARNING - Could not retrieve variants from source file in region 3:98073102-98073782. Error was invalid region `3:98073103-98073782`
[2016-04-15T03:42Z] 2016-04-14 20:42:16 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:42:16,965 - WARNING - Could not retrieve variants from source file in region 3:97659873-97686209. Error was invalid region `3:97659874-97686209`
[2016-04-15T03:42Z] 2016-04-14 20:42:17 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:42:17,352 - WARNING - Could not retrieve variants from source file in region 3:97590942-97607480. Error was invalid region `3:97590943-97607480`
[2016-04-15T03:42Z] ['bcbio-variation-recall', 'square', '-Xms750m', '-Xmx7280m', '-XX:+UseSerialGC', '-c', 16, '-r', u'3:112188605-127703121', '--caller', 'platypus', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/3/Batch1-3_112188604_127703121.vcf.gz', '/mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/3/Batch1-3_112188604_127703121.vcf-inputs.txt'] in region: 3:112188605-127703121
[2016-04-15T03:42Z] 2016-04-14 20:42:34 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:42:34,553 - WARNING - Could not retrieve variants from source file in region 3:122864225-122880381. Error was invalid region `3:122864226-122880381`
[2016-04-15T03:42Z] 2016-04-14 20:42:34 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:42:34,900 - WARNING - Could not retrieve variants from source file in region 3:113084932-113085333. Error was invalid region `3:113084933-113085333`
[2016-04-15T03:42Z] 2016-04-14 20:42:35 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:42:35,374 - WARNING - Could not retrieve variants from source file in region 3:125725837-125726238. Error was invalid region `3:125725838-125726238`
[2016-04-15T03:42Z] 2016-04-14 20:42:35 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:42:35,391 - WARNING - Could not retrieve variants from source file in region 3:112189926-112190327. Error was invalid region `3:112189927-112190327`
[2016-04-15T03:42Z] 2016-04-14 20:42:35 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:42:35,415 - WARNING - Could not retrieve variants from source file in region 3:119367179-119379376. Error was invalid region `3:119367180-119379376`
[2016-04-15T03:42Z] 2016-04-14 20:42:35 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:42:35,853 - WARNING - Could not retrieve variants from source file in region 3:112642357-112648412. Error was invalid region `3:112642358-112648412`
[2016-04-15T03:42Z] 2016-04-14 20:42:35 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:42:35,862 - WARNING - Could not retrieve variants from source file in region 3:124351105-124380007. Error was invalid region `3:124351106-124380007`
[2016-04-15T03:42Z] 2016-04-14 20:42:36 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:42:36,300 - WARNING - Could not retrieve variants from source file in region 3:112251564-112253248. Error was invalid region `3:112251565-112253248`
[2016-04-15T03:42Z] 2016-04-14 20:42:36 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:42:36,322 - WARNING - Could not retrieve variants from source file in region 3:118908948-118909349. Error was invalid region `3:118908949-118909349`
[2016-04-15T03:42Z] 2016-04-14 20:42:36 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:42:36,382 - WARNING - Could not retrieve variants from source file in region 3:120495145-120495546. Error was invalid region `3:120495146-120495546`
[2016-04-15T03:42Z] 2016-04-14 20:42:38 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:42:38,497 - WARNING - Could not retrieve variants from source file in region 3:112991101-113046830. Error was invalid region `3:112991102-113046830`
[2016-04-15T03:42Z] 2016-04-14 20:42:40 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:42:40,979 - WARNING - Could not retrieve variants from source file in region 3:122864225-122880381. Error was invalid region `3:122864226-122880381`
[2016-04-15T03:42Z] 2016-04-14 20:42:42 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:42:42,109 - WARNING - Could not retrieve variants from source file in region 3:121711840-121713233. Error was invalid region `3:121711841-121713233`
[2016-04-15T03:42Z] 2016-04-14 20:42:42 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:42:42,970 - WARNING - Could not retrieve variants from source file in region 3:127641757-127643004. Error was invalid region `3:127641758-127643004`
[2016-04-15T03:42Z] 2016-04-14 20:42:43 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:42:43,520 - WARNING - Could not retrieve variants from source file in region 3:112189926-112190327. Error was invalid region `3:112189927-112190327`
[2016-04-15T03:42Z] 2016-04-14 20:42:43 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:42:43,522 - WARNING - Could not retrieve variants from source file in region 3:118908948-118909349. Error was invalid region `3:118908949-118909349`
[2016-04-15T03:42Z] 2016-04-14 20:42:43 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:42:43,890 - WARNING - Could not retrieve variants from source file in region 3:112251564-112253248. Error was invalid region `3:112251565-112253248`
[2016-04-15T03:42Z] 2016-04-14 20:42:44 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:42:44,004 - WARNING - Could not retrieve variants from source file in region 3:119367179-119379376. Error was invalid region `3:119367180-119379376`
[2016-04-15T03:42Z] 2016-04-14 20:42:44 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:42:44,421 - WARNING - Could not retrieve variants from source file in region 3:112642357-112648412. Error was invalid region `3:112642358-112648412`
[2016-04-15T03:42Z] 2016-04-14 20:42:46 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:42:46,784 - WARNING - Could not retrieve variants from source file in region 3:122864225-122880381. Error was invalid region `3:122864226-122880381`
[2016-04-15T03:42Z] 2016-04-14 20:42:48 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:42:48,205 - WARNING - Could not retrieve variants from source file in region 3:113084932-113085333. Error was invalid region `3:113084933-113085333`
[2016-04-15T03:42Z] 2016-04-14 20:42:49 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:42:49,985 - WARNING - Could not retrieve variants from source file in region 3:125725837-125726238. Error was invalid region `3:125725838-125726238`
[2016-04-15T03:42Z] 2016-04-14 20:42:50 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:42:50,771 - WARNING - Could not retrieve variants from source file in region 3:127641757-127643004. Error was invalid region `3:127641758-127643004`
[2016-04-15T03:42Z] 2016-04-14 20:42:51 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:42:51,138 - WARNING - Could not retrieve variants from source file in region 3:118908948-118909349. Error was invalid region `3:118908949-118909349`
[2016-04-15T03:42Z] 2016-04-14 20:42:51 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:42:51,364 - WARNING - Could not retrieve variants from source file in region 3:112189926-112190327. Error was invalid region `3:112189927-112190327`
[2016-04-15T03:42Z] 2016-04-14 20:42:51 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:42:51,454 - WARNING - Could not retrieve variants from source file in region 3:120495145-120495546. Error was invalid region `3:120495146-120495546`
[2016-04-15T03:42Z] 2016-04-14 20:42:51 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:42:51,526 - WARNING - Could not retrieve variants from source file in region 3:124351105-124380007. Error was invalid region `3:124351106-124380007`
[2016-04-15T03:42Z] 2016-04-14 20:42:51 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:42:51,964 - WARNING - Could not retrieve variants from source file in region 3:119367179-119379376. Error was invalid region `3:119367180-119379376`
[2016-04-15T03:43Z] 2016-04-14 20:43:02 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:43:02,661 - WARNING - Could not retrieve variants from source file in region 3:122679930-122695120. Error was invalid region `3:122679931-122695120`
[2016-04-15T03:43Z] 2016-04-14 20:43:04 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:43:04,073 - WARNING - Could not retrieve variants from source file in region 3:124692478-124692879. Error was invalid region `3:124692479-124692879`
[2016-04-15T03:43Z] 2016-04-14 20:43:04 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:43:04,139 - WARNING - Could not retrieve variants from source file in region 3:112726973-112727374. Error was invalid region `3:112726974-112727374`
[2016-04-15T03:43Z] 2016-04-14 20:43:05 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:43:05,231 - WARNING - Could not retrieve variants from source file in region 3:121641482-121648358. Error was invalid region `3:121641483-121648358`
[2016-04-15T03:43Z] 2016-04-14 20:43:06 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:43:06,210 - WARNING - Could not retrieve variants from source file in region 3:125648145-125653481. Error was invalid region `3:125648146-125653481`
[2016-04-15T03:43Z] 2016-04-14 20:43:07 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:43:07,081 - WARNING - Could not retrieve variants from source file in region 3:121304936-121305337. Error was invalid region `3:121304937-121305337`
[2016-04-15T03:43Z] 2016-04-14 20:43:08 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:43:08,607 - WARNING - Could not retrieve variants from source file in region 3:122185977-122186378. Error was invalid region `3:122185978-122186378`
[2016-04-15T03:43Z] 2016-04-14 20:43:08 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:43:08,763 - WARNING - Could not retrieve variants from source file in region 3:127454820-127455276. Error was invalid region `3:127454821-127455276`
[2016-04-15T03:43Z] 2016-04-14 20:43:09 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:43:09,308 - WARNING - Could not retrieve variants from source file in region 3:124209492-124209893. Error was invalid region `3:124209493-124209893`
[2016-04-15T03:43Z] 2016-04-14 20:43:09 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:43:09,308 - WARNING - Could not retrieve variants from source file in region 3:112545699-112546663. Error was invalid region `3:112545700-112546663`
[2016-04-15T03:43Z] 2016-04-14 20:43:09 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:43:09,414 - WARNING - Could not retrieve variants from source file in region 3:124692478-124692879. Error was invalid region `3:124692479-124692879`
[2016-04-15T03:43Z] 2016-04-14 20:43:09 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:43:09,723 - WARNING - Could not retrieve variants from source file in region 3:120389105-120389506. Error was invalid region `3:120389106-120389506`
[2016-04-15T03:43Z] 2016-04-14 20:43:09 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:43:09,811 - WARNING - Could not retrieve variants from source file in region 3:112726973-112727374. Error was invalid region `3:112726974-112727374`
[2016-04-15T03:43Z] 2016-04-14 20:43:09 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:43:09,831 - WARNING - Could not retrieve variants from source file in region 3:119305168-119305569. Error was invalid region `3:119305169-119305569`
[2016-04-15T03:43Z] 2016-04-14 20:43:09 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:43:09,995 - WARNING - Could not retrieve variants from source file in region 3:123665691-123666092. Error was invalid region `3:123665692-123666092`
[2016-04-15T03:43Z] 2016-04-14 20:43:10 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:43:10,304 - WARNING - Could not retrieve variants from source file in region 3:121641482-121648358. Error was invalid region `3:121641483-121648358`
[2016-04-15T03:43Z] 2016-04-14 20:43:10 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:43:10,346 - WARNING - Could not retrieve variants from source file in region 3:113286194-113286595. Error was invalid region `3:113286195-113286595`
[2016-04-15T03:43Z] 2016-04-14 20:43:14 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:43:14,897 - WARNING - Could not retrieve variants from source file in region 3:122185977-122186378. Error was invalid region `3:122185978-122186378`
[2016-04-15T03:43Z] 2016-04-14 20:43:15 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:43:15,297 - WARNING - Could not retrieve variants from source file in region 3:122679930-122695120. Error was invalid region `3:122679931-122695120`
[2016-04-15T03:43Z] 2016-04-14 20:43:15 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:43:15,404 - WARNING - Could not retrieve variants from source file in region 3:127454820-127455276. Error was invalid region `3:127454821-127455276`
[2016-04-15T03:43Z] 2016-04-14 20:43:17 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:43:17,059 - WARNING - Could not retrieve variants from source file in region 3:112545699-112546663. Error was invalid region `3:112545700-112546663`
[2016-04-15T03:43Z] 2016-04-14 20:43:17 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:43:17,062 - WARNING - Could not retrieve variants from source file in region 3:112726973-112727374. Error was invalid region `3:112726974-112727374`
[2016-04-15T03:43Z] 2016-04-14 20:43:17 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:43:17,536 - WARNING - Could not retrieve variants from source file in region 3:120389105-120389506. Error was invalid region `3:120389106-120389506`
[2016-04-15T03:43Z] 2016-04-14 20:43:17 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:43:17,660 - WARNING - Could not retrieve variants from source file in region 3:113286194-113286595. Error was invalid region `3:113286195-113286595`
[2016-04-15T03:43Z] 2016-04-14 20:43:17 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:43:17,684 - WARNING - Could not retrieve variants from source file in region 3:123665691-123666092. Error was invalid region `3:123665692-123666092`
[2016-04-15T03:43Z] 2016-04-14 20:43:18 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:43:18,088 - WARNING - Could not retrieve variants from source file in region 3:124692478-124692879. Error was invalid region `3:124692479-124692879`
[2016-04-15T03:43Z] 2016-04-14 20:43:18 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:43:18,103 - WARNING - Could not retrieve variants from source file in region 3:121641482-121648358. Error was invalid region `3:121641483-121648358`
[2016-04-15T03:43Z] 2016-04-14 20:43:18 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:43:18,346 - WARNING - Could not retrieve variants from source file in region 3:125648145-125653481. Error was invalid region `3:125648146-125653481`
[2016-04-15T03:43Z] 2016-04-14 20:43:19 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:43:19,896 - WARNING - Could not retrieve variants from source file in region 3:122185977-122186378. Error was invalid region `3:122185978-122186378`
[2016-04-15T03:43Z] 2016-04-14 20:43:23 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:43:23,707 - WARNING - Could not retrieve variants from source file in region 3:113286194-113286595. Error was invalid region `3:113286195-113286595`
[2016-04-15T03:43Z] 2016-04-14 20:43:24 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:43:24,165 - WARNING - Could not retrieve variants from source file in region 3:123665691-123666092. Error was invalid region `3:123665692-123666092`
[2016-04-15T03:43Z] 2016-04-14 20:43:24 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:43:24,219 - WARNING - Could not retrieve variants from source file in region 3:120389105-120389506. Error was invalid region `3:120389106-120389506`
[2016-04-15T03:43Z] 2016-04-14 20:43:24 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:43:24,633 - WARNING - Could not retrieve variants from source file in region 3:119305168-119305569. Error was invalid region `3:119305169-119305569`
[2016-04-15T03:43Z] 2016-04-14 20:43:30 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:43:30,395 - WARNING - Could not retrieve variants from source file in region 3:122630112-122642780. Error was invalid region `3:122630113-122642780`
[2016-04-15T03:43Z] 2016-04-14 20:43:32 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:43:32,171 - WARNING - Could not retrieve variants from source file in region 3:123451562-123458083. Error was invalid region `3:123451563-123458083`
[2016-04-15T03:43Z] 2016-04-14 20:43:33 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:43:33,225 - WARNING - Could not retrieve variants from source file in region 3:121238538-121263910. Error was invalid region `3:121238539-121263910`
[2016-04-15T03:43Z] 2016-04-14 20:43:36 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:43:36,511 - WARNING - Could not retrieve variants from source file in region 3:124951610-124952011. Error was invalid region `3:124951611-124952011`
[2016-04-15T03:43Z] 2016-04-14 20:43:37 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:43:37,833 - WARNING - Could not retrieve variants from source file in region 3:124181243-124181644. Error was invalid region `3:124181244-124181644`
[2016-04-15T03:43Z] 2016-04-14 20:43:38 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:43:38,114 - WARNING - Could not retrieve variants from source file in region 3:123451562-123458083. Error was invalid region `3:123451563-123458083`
[2016-04-15T03:43Z] 2016-04-14 20:43:38 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:43:38,154 - WARNING - Could not retrieve variants from source file in region 3:126329699-126330100. Error was invalid region `3:126329700-126330100`
[2016-04-15T03:43Z] 2016-04-14 20:43:38 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:43:38,762 - WARNING - Could not retrieve variants from source file in region 3:121238538-121263910. Error was invalid region `3:121238539-121263910`
[2016-04-15T03:43Z] 2016-04-14 20:43:38 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:43:38,865 - WARNING - Could not retrieve variants from source file in region 3:118753331-118753732. Error was invalid region `3:118753332-118753732`
[2016-04-15T03:43Z] 2016-04-14 20:43:39 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:43:39,215 - WARNING - Could not retrieve variants from source file in region 3:123616246-123634236. Error was invalid region `3:123616247-123634236`
[2016-04-15T03:43Z] 2016-04-14 20:43:39 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:43:39,222 - WARNING - Could not retrieve variants from source file in region 3:121615063-121615464. Error was invalid region `3:121615064-121615464`
[2016-04-15T03:43Z] 2016-04-14 20:43:40 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:43:40,176 - WARNING - Could not retrieve variants from source file in region 3:119263469-119263870. Error was invalid region `3:119263470-119263870`
[2016-04-15T03:43Z] 2016-04-14 20:43:41 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:43:41,299 - WARNING - Could not retrieve variants from source file in region 3:120320546-120320947. Error was invalid region `3:120320547-120320947`
[2016-04-15T03:43Z] 2016-04-14 20:43:41 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:43:41,696 - WARNING - Could not retrieve variants from source file in region 3:122133619-122134020. Error was invalid region `3:122133620-122134020`
[2016-04-15T03:43Z] 2016-04-14 20:43:42 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:43:42,892 - WARNING - Could not retrieve variants from source file in region 3:124951610-124952011. Error was invalid region `3:124951611-124952011`
[2016-04-15T03:43Z] 2016-04-14 20:43:44 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:43:44,080 - WARNING - Could not retrieve variants from source file in region 3:122630112-122642780. Error was invalid region `3:122630113-122642780`
[2016-04-15T03:43Z] 2016-04-14 20:43:45 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:43:45,043 - WARNING - Could not retrieve variants from source file in region 3:124181243-124181644. Error was invalid region `3:124181244-124181644`
[2016-04-15T03:43Z] 2016-04-14 20:43:45 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:43:45,778 - WARNING - Could not retrieve variants from source file in region 3:123451562-123458083. Error was invalid region `3:123451563-123458083`
[2016-04-15T03:43Z] 2016-04-14 20:43:45 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:43:45,898 - WARNING - Could not retrieve variants from source file in region 3:113221825-113222226. Error was invalid region `3:113221826-113222226`
[2016-04-15T03:43Z] 2016-04-14 20:43:46 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:43:46,909 - WARNING - Could not retrieve variants from source file in region 3:119263469-119263870. Error was invalid region `3:119263470-119263870`
[2016-04-15T03:43Z] 2016-04-14 20:43:47 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:43:47,004 - WARNING - Could not retrieve variants from source file in region 3:119198662-119222646. Error was invalid region `3:119198663-119222646`
[2016-04-15T03:43Z] 2016-04-14 20:43:47 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:43:47,030 - WARNING - Could not retrieve variants from source file in region 3:126329699-126330100. Error was invalid region `3:126329700-126330100`
[2016-04-15T03:43Z] 2016-04-14 20:43:47 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:43:47,157 - WARNING - Could not retrieve variants from source file in region 3:120320546-120320947. Error was invalid region `3:120320547-120320947`
[2016-04-15T03:43Z] 2016-04-14 20:43:47 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:43:47,304 - WARNING - Could not retrieve variants from source file in region 3:122133619-122134020. Error was invalid region `3:122133620-122134020`
[2016-04-15T03:43Z] 2016-04-14 20:43:47 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:43:47,908 - WARNING - Could not retrieve variants from source file in region 3:124951610-124952011. Error was invalid region `3:124951611-124952011`
[2016-04-15T03:43Z] 2016-04-14 20:43:49 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:43:49,978 - WARNING - Could not retrieve variants from source file in region 3:124181243-124181644. Error was invalid region `3:124181244-124181644`
[2016-04-15T03:43Z] 2016-04-14 20:43:54 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:43:54,452 - WARNING - Could not retrieve variants from source file in region 3:119198662-119222646. Error was invalid region `3:119198663-119222646`
[2016-04-15T03:43Z] 2016-04-14 20:43:54 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:43:54,461 - WARNING - Could not retrieve variants from source file in region 3:119263469-119263870. Error was invalid region `3:119263470-119263870`
[2016-04-15T03:43Z] 2016-04-14 20:43:54 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:43:54,569 - WARNING - Could not retrieve variants from source file in region 3:120320546-120320947. Error was invalid region `3:120320547-120320947`
[2016-04-15T03:43Z] 2016-04-14 20:43:54 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:43:54,952 - WARNING - Could not retrieve variants from source file in region 3:123616246-123634236. Error was invalid region `3:123616247-123634236`
[2016-04-15T03:43Z] 2016-04-14 20:43:55 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:43:55,215 - WARNING - Could not retrieve variants from source file in region 3:126329699-126330100. Error was invalid region `3:126329700-126330100`
[2016-04-15T03:43Z] 2016-04-14 20:43:55 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:43:55,935 - WARNING - Could not retrieve variants from source file in region 3:121207965-121209077. Error was invalid region `3:121207966-121209077`
[2016-04-15T03:44Z] 2016-04-14 20:44:02 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:44:02,486 - WARNING - Could not retrieve variants from source file in region 3:123411378-123419103. Error was invalid region `3:123411379-123419103`
[2016-04-15T03:44Z] 2016-04-14 20:44:03 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:44:03,340 - WARNING - Could not retrieve variants from source file in region 3:121563144-121563545. Error was invalid region `3:121563145-121563545`
[2016-04-15T03:44Z] 2016-04-14 20:44:04 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:44:04,551 - WARNING - Could not retrieve variants from source file in region 3:122102909-122103310. Error was invalid region `3:122102910-122103310`
[2016-04-15T03:44Z] 2016-04-14 20:44:04 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:44:04,959 - WARNING - Could not retrieve variants from source file in region 3:124515097-124515699. Error was invalid region `3:124515098-124515699`
[2016-04-15T03:44Z] 2016-04-14 20:44:06 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:44:06,721 - WARNING - Could not retrieve variants from source file in region 3:122418539-122473621. Error was invalid region `3:122418540-122473621`
[2016-04-15T03:44Z] 2016-04-14 20:44:07 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:44:07,302 - WARNING - Could not retrieve variants from source file in region 3:124044738-124045139. Error was invalid region `3:124044739-124045139`
[2016-04-15T03:44Z] 2016-04-14 20:44:07 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:44:07,764 - WARNING - Could not retrieve variants from source file in region 3:127323619-127324020. Error was invalid region `3:127323620-127324020`
[2016-04-15T03:44Z] 2016-04-14 20:44:09 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:44:09,484 - WARNING - Could not retrieve variants from source file in region 3:118648849-118649250. Error was invalid region `3:118648850-118649250`
[2016-04-15T03:44Z] 2016-04-14 20:44:10 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:44:10,082 - WARNING - Could not retrieve variants from source file in region 3:119886337-119886966. Error was invalid region `3:119886338-119886966`
[2016-04-15T03:44Z] 2016-04-14 20:44:13 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:44:13,721 - WARNING - Could not retrieve variants from source file in region 3:124044738-124045139. Error was invalid region `3:124044739-124045139`
[2016-04-15T03:44Z] 2016-04-14 20:44:13 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:44:13,729 - WARNING - Could not retrieve variants from source file in region 3:124837473-124844947. Error was invalid region `3:124837474-124844947`
[2016-04-15T03:44Z] 2016-04-14 20:44:13 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:44:13,849 - WARNING - Could not retrieve variants from source file in region 3:126291087-126291488. Error was invalid region `3:126291088-126291488`
[2016-04-15T03:44Z] 2016-04-14 20:44:14 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:44:14,225 - WARNING - Could not retrieve variants from source file in region 3:127323619-127324020. Error was invalid region `3:127323620-127324020`
[2016-04-15T03:44Z] 2016-04-14 20:44:14 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:44:14,428 - WARNING - Could not retrieve variants from source file in region 3:113175773-113176312. Error was invalid region `3:113175774-113176312`
[2016-04-15T03:44Z] 2016-04-14 20:44:14 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:44:14,633 - WARNING - Could not retrieve variants from source file in region 3:118648849-118649250. Error was invalid region `3:118648850-118649250`
[2016-04-15T03:44Z] 2016-04-14 20:44:14 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:44:14,638 - WARNING - Could not retrieve variants from source file in region 3:123411378-123419103. Error was invalid region `3:123411379-123419103`
[2016-04-15T03:44Z] 2016-04-14 20:44:14 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:44:14,817 - WARNING - Could not retrieve variants from source file in region 3:119886337-119886966. Error was invalid region `3:119886338-119886966`
[2016-04-15T03:44Z] 2016-04-14 20:44:14 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:44:14,947 - WARNING - Could not retrieve variants from source file in region 3:124515097-124515699. Error was invalid region `3:124515098-124515699`
[2016-04-15T03:44Z] 2016-04-14 20:44:15 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:44:15,256 - WARNING - Could not retrieve variants from source file in region 3:122102909-122103310. Error was invalid region `3:122102910-122103310`
[2016-04-15T03:44Z] 2016-04-14 20:44:22 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:44:22,863 - WARNING - Could not retrieve variants from source file in region 3:124044738-124045139. Error was invalid region `3:124044739-124045139`
[2016-04-15T03:44Z] 2016-04-14 20:44:22 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:44:22,983 - WARNING - Could not retrieve variants from source file in region 3:127323619-127324020. Error was invalid region `3:127323620-127324020`
[2016-04-15T03:44Z] 2016-04-14 20:44:23 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:44:23,428 - WARNING - Could not retrieve variants from source file in region 3:118945585-118945986. Error was invalid region `3:118945586-118945986`
[2016-04-15T03:44Z] 2016-04-14 20:44:23 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:44:23,563 - WARNING - Could not retrieve variants from source file in region 3:119886337-119886966. Error was invalid region `3:119886338-119886966`
[2016-04-15T03:44Z] 2016-04-14 20:44:23 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:44:23,718 - WARNING - Could not retrieve variants from source file in region 3:123512416-123512817. Error was invalid region `3:123512417-123512817`
[2016-04-15T03:44Z] 2016-04-14 20:44:23 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:44:23,843 - WARNING - Could not retrieve variants from source file in region 3:118648849-118649250. Error was invalid region `3:118648850-118649250`
[2016-04-15T03:44Z] 2016-04-14 20:44:25 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:44:25,644 - WARNING - Could not retrieve variants from source file in region 3:121154763-121155164. Error was invalid region `3:121154764-121155164`
[2016-04-15T03:44Z] 2016-04-14 20:44:30 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:44:30,864 - WARNING - Could not retrieve variants from source file in region 3:122345659-122354906. Error was invalid region `3:122345660-122354906`
[2016-04-15T03:44Z] 2016-04-14 20:44:31 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:44:31,406 - WARNING - Could not retrieve variants from source file in region 3:123512416-123512817. Error was invalid region `3:123512417-123512817`
[2016-04-15T03:44Z] 2016-04-14 20:44:31 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:44:31,721 - WARNING - Could not retrieve variants from source file in region 3:121154763-121155164. Error was invalid region `3:121154764-121155164`
[2016-04-15T03:44Z] 2016-04-14 20:44:32 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:44:32,463 - WARNING - Could not retrieve variants from source file in region 3:123166831-123167439. Error was invalid region `3:123166832-123167439`
[2016-04-15T03:44Z] 2016-04-14 20:44:33 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:44:33,486 - WARNING - Could not retrieve variants from source file in region 3:122056221-122056622. Error was invalid region `3:122056222-122056622`
[2016-04-15T03:44Z] 2016-04-14 20:44:33 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:44:33,783 - WARNING - Could not retrieve variants from source file in region 3:124456531-124462998. Error was invalid region `3:124456532-124462998`
[2016-04-15T03:44Z] 2016-04-14 20:44:37 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:44:37,931 - WARNING - Could not retrieve variants from source file in region 3:121154763-121155164. Error was invalid region `3:121154764-121155164`
[2016-04-15T03:44Z] 2016-04-14 20:44:39 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:44:39,062 - WARNING - Could not retrieve variants from source file in region 3:123987828-123988229. Error was invalid region `3:123987829-123988229`
[2016-04-15T03:44Z] 2016-04-14 20:44:39 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:44:39,520 - WARNING - Could not retrieve variants from source file in region 3:121525993-121526394. Error was invalid region `3:121525994-121526394`
[2016-04-15T03:44Z] 2016-04-14 20:44:39 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:44:39,718 - WARNING - Could not retrieve variants from source file in region 3:122056221-122056622. Error was invalid region `3:122056222-122056622`
[2016-04-15T03:44Z] 2016-04-14 20:44:40 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:44:40,047 - WARNING - Could not retrieve variants from source file in region 3:113144795-113146320. Error was invalid region `3:113144796-113146320`
[2016-04-15T03:44Z] 2016-04-14 20:44:40 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:44:40,078 - WARNING - Could not retrieve variants from source file in region 3:124802670-124803078. Error was invalid region `3:124802671-124803078`
[2016-04-15T03:44Z] 2016-04-14 20:44:40 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:44:40,344 - WARNING - Could not retrieve variants from source file in region 3:119533699-119537116. Error was invalid region `3:119533700-119537116`
[2016-04-15T03:44Z] 2016-04-14 20:44:40 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:44:40,631 - WARNING - Could not retrieve variants from source file in region 3:118621453-118621854. Error was invalid region `3:118621454-118621854`
[2016-04-15T03:44Z] 2016-04-14 20:44:41 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:44:41,954 - WARNING - Could not retrieve variants from source file in region 3:123166831-123167439. Error was invalid region `3:123166832-123167439`
[2016-04-15T03:44Z] 2016-04-14 20:44:44 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:44:44,029 - WARNING - Could not retrieve variants from source file in region 3:123987828-123988229. Error was invalid region `3:123987829-123988229`
[2016-04-15T03:44Z] 2016-04-14 20:44:46 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:44:46,070 - WARNING - Could not retrieve variants from source file in region 3:121525993-121526394. Error was invalid region `3:121525994-121526394`
[2016-04-15T03:44Z] 2016-04-14 20:44:46 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:44:46,390 - WARNING - Could not retrieve variants from source file in region 3:124456531-124462998. Error was invalid region `3:124456532-124462998`
[2016-04-15T03:44Z] 2016-04-14 20:44:46 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:44:46,801 - WARNING - Could not retrieve variants from source file in region 3:122056221-122056622. Error was invalid region `3:122056222-122056622`
[2016-04-15T03:44Z] 2016-04-14 20:44:46 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:44:46,818 - WARNING - Could not retrieve variants from source file in region 3:113144795-113146320. Error was invalid region `3:113144796-113146320`
[2016-04-15T03:44Z] 2016-04-14 20:44:46 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:44:46,866 - WARNING - Could not retrieve variants from source file in region 3:119533699-119537116. Error was invalid region `3:119533700-119537116`
[2016-04-15T03:44Z] 2016-04-14 20:44:46 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:44:46,871 - WARNING - Could not retrieve variants from source file in region 3:124802670-124803078. Error was invalid region `3:124802671-124803078`
[2016-04-15T03:44Z] 2016-04-14 20:44:47 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:44:47,178 - WARNING - Could not retrieve variants from source file in region 3:121824986-121838509. Error was invalid region `3:121824987-121838509`
[2016-04-15T03:44Z] 2016-04-14 20:44:48 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:44:48,640 - WARNING - Could not retrieve variants from source file in region 3:123987828-123988229. Error was invalid region `3:123987829-123988229`
[2016-04-15T03:44Z] 2016-04-14 20:44:54 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:44:54,952 - WARNING - Could not retrieve variants from source file in region 3:119533699-119537116. Error was invalid region `3:119533700-119537116`
[2016-04-15T03:44Z] 2016-04-14 20:44:55 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:44:55,194 - WARNING - Could not retrieve variants from source file in region 3:124802670-124803078. Error was invalid region `3:124802671-124803078`
[2016-04-15T03:44Z] 2016-04-14 20:44:55 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:44:55,203 - WARNING - Could not retrieve variants from source file in region 3:113144795-113146320. Error was invalid region `3:113144796-113146320`
[2016-04-15T03:44Z] 2016-04-14 20:44:55 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:44:55,767 - WARNING - Could not retrieve variants from source file in region 3:123882472-123882873. Error was invalid region `3:123882473-123882873`
[2016-04-15T03:44Z] 2016-04-14 20:44:58 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:44:58,150 - WARNING - Could not retrieve variants from source file in region 3:121796557-121796958. Error was invalid region `3:121796558-121796958`
[2016-04-15T03:44Z] 2016-04-14 20:44:58 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:44:58,898 - WARNING - Could not retrieve variants from source file in region 3:121100072-121100473. Error was invalid region `3:121100073-121100473`
[2016-04-15T03:45Z] 2016-04-14 20:45:01 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:45:01,280 - WARNING - Could not retrieve variants from source file in region 3:123882472-123882873. Error was invalid region `3:123882473-123882873`
[2016-04-15T03:45Z] 2016-04-14 20:45:03 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:45:03,182 - WARNING - Could not retrieve variants from source file in region 3:121824986-121838509. Error was invalid region `3:121824987-121838509`
[2016-04-15T03:45Z] 2016-04-14 20:45:04 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:45:04,728 - WARNING - Could not retrieve variants from source file in region 3:119421752-119434717. Error was invalid region `3:119421753-119434717`
[2016-04-15T03:45Z] 2016-04-14 20:45:04 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:45:04,870 - WARNING - Could not retrieve variants from source file in region 3:121980863-122004022. Error was invalid region `3:121980864-122004022`
[2016-04-15T03:45Z] 2016-04-14 20:45:09 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:45:09,888 - WARNING - Could not retrieve variants from source file in region 3:121796557-121796958. Error was invalid region `3:121796558-121796958`
[2016-04-15T03:45Z] 2016-04-14 20:45:12 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:45:12,239 - WARNING - Could not retrieve variants from source file in region 3:121413850-121435814. Error was invalid region `3:121413851-121435814`
[2016-04-15T03:45Z] 2016-04-14 20:45:12 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:45:12,566 - WARNING - Could not retrieve variants from source file in region 3:125872082-125872483. Error was invalid region `3:125872083-125872483`
[2016-04-15T03:45Z] 2016-04-14 20:45:12 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:45:12,915 - WARNING - Could not retrieve variants from source file in region 3:126373780-126374184. Error was invalid region `3:126373781-126374184`
[2016-04-15T03:45Z] 2016-04-14 20:45:13 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:45:13,073 - WARNING - Could not retrieve variants from source file in region 3:124774454-124774855. Error was invalid region `3:124774455-124774855`
[2016-04-15T03:45Z] 2016-04-14 20:45:14 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:45:14,377 - WARNING - Could not retrieve variants from source file in region 3:124418635-124419069. Error was invalid region `3:124418636-124419069`
[2016-04-15T03:45Z] 2016-04-14 20:45:15 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:45:15,523 - WARNING - Could not retrieve variants from source file in region 3:113954953-113956010. Error was invalid region `3:113954954-113956010`
[2016-04-15T03:45Z] 2016-04-14 20:45:15 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:45:15,558 - WARNING - Could not retrieve variants from source file in region 3:115571153-115571554. Error was invalid region `3:115571154-115571554`
[2016-04-15T03:45Z] 2016-04-14 20:45:15 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:45:15,989 - WARNING - Could not retrieve variants from source file in region 3:121980863-122004022. Error was invalid region `3:121980864-122004022`
[2016-04-15T03:45Z] 2016-04-14 20:45:16 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:45:16,031 - WARNING - Could not retrieve variants from source file in region 3:113115332-113115733. Error was invalid region `3:113115333-113115733`
[2016-04-15T03:45Z] 2016-04-14 20:45:18 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:45:18,218 - WARNING - Could not retrieve variants from source file in region 3:125872082-125872483. Error was invalid region `3:125872083-125872483`
[2016-04-15T03:45Z] 2016-04-14 20:45:22 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:45:22,834 - WARNING - Could not retrieve variants from source file in region 3:124774454-124774855. Error was invalid region `3:124774455-124774855`
[2016-04-15T03:45Z] 2016-04-14 20:45:24 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:45:24,208 - WARNING - Could not retrieve variants from source file in region 3:113654996-113679240. Error was invalid region `3:113654997-113679240`
[2016-04-15T03:45Z] 2016-04-14 20:45:24 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:45:24,926 - WARNING - Could not retrieve variants from source file in region 3:125844268-125844669. Error was invalid region `3:125844269-125844669`
[2016-04-15T03:45Z] 2016-04-14 20:45:26 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:45:26,870 - WARNING - Could not retrieve variants from source file in region 3:113858139-113858540. Error was invalid region `3:113858140-113858540`
[2016-04-15T03:45Z] 2016-04-14 20:45:27 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:45:27,449 - WARNING - Could not retrieve variants from source file in region 3:113858139-113858540. Error was invalid region `3:113858140-113858540`
[2016-04-15T03:45Z] 2016-04-14 20:45:27 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:45:27,561 - WARNING - Could not retrieve variants from source file in region 3:113594166-113594567. Error was invalid region `3:113594167-113594567`
[2016-04-15T03:45Z] 2016-04-14 20:45:29 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:45:29,271 - WARNING - Could not retrieve variants from source file in region 3:113654996-113679240. Error was invalid region `3:113654997-113679240`
[2016-04-15T03:45Z] 2016-04-14 20:45:30 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:45:30,787 - WARNING - Could not retrieve variants from source file in region 3:125844268-125844669. Error was invalid region `3:125844269-125844669`
[2016-04-15T03:45Z] 2016-04-14 20:45:30 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:45:30,996 - WARNING - Could not retrieve variants from source file in region 3:113890578-113891005. Error was invalid region `3:113890579-113891005`
[2016-04-15T03:45Z] 2016-04-14 20:45:31 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:45:31,504 - WARNING - Could not retrieve variants from source file in region 3:125769546-125787069. Error was invalid region `3:125769547-125787069`
[2016-04-15T03:45Z] 2016-04-14 20:45:31 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:45:31,706 - WARNING - Could not retrieve variants from source file in region 3:113858139-113858540. Error was invalid region `3:113858140-113858540`
[2016-04-15T03:45Z] 2016-04-14 20:45:33 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:45:33,861 - WARNING - Could not retrieve variants from source file in region 3:113594166-113594567. Error was invalid region `3:113594167-113594567`
[2016-04-15T03:45Z] 2016-04-14 20:45:34 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:45:34,017 - WARNING - Could not retrieve variants from source file in region 3:125769546-125787069. Error was invalid region `3:125769547-125787069`
[2016-04-15T03:45Z] 2016-04-14 20:45:34 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:45:34,608 - WARNING - Could not retrieve variants from source file in region 3:113890578-113891005. Error was invalid region `3:113890579-113891005`
[2016-04-15T03:45Z] ['bcbio-variation-recall', 'square', '-Xms750m', '-Xmx7280m', '-XX:+UseSerialGC', '-c', 16, '-r', u'3:127770402-143293035', '--caller', 'platypus', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/3/Batch1-3_127770401_143293035.vcf.gz', '/mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/3/Batch1-3_127770401_143293035.vcf-inputs.txt'] in region: 3:127770402-143293035
[2016-04-15T03:45Z] 2016-04-14 20:45:48 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:45:48,806 - WARNING - Could not retrieve variants from source file in region 3:130449011-130449412. Error was invalid region `3:130449012-130449412`
[2016-04-15T03:45Z] 2016-04-14 20:45:51 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:45:51,245 - WARNING - Could not retrieve variants from source file in region 3:138244189-138249827. Error was invalid region `3:138244190-138249827`
[2016-04-15T03:45Z] 2016-04-14 20:45:51 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:45:51,435 - WARNING - Could not retrieve variants from source file in region 3:136087827-136088228. Error was invalid region `3:136087828-136088228`
[2016-04-15T03:45Z] 2016-04-14 20:45:51 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:45:51,505 - WARNING - Could not retrieve variants from source file in region 3:132360672-132361073. Error was invalid region `3:132360673-132361073`
[2016-04-15T03:45Z] 2016-04-14 20:45:51 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:45:51,773 - WARNING - Could not retrieve variants from source file in region 3:137786231-137807449. Error was invalid region `3:137786232-137807449`
[2016-04-15T03:45Z] 2016-04-14 20:45:52 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:45:52,904 - WARNING - Could not retrieve variants from source file in region 3:140167325-140178675. Error was invalid region `3:140167326-140178675`
[2016-04-15T03:45Z] 2016-04-14 20:45:53 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:45:53,547 - WARNING - Could not retrieve variants from source file in region 3:130449011-130449412. Error was invalid region `3:130449012-130449412`
[2016-04-15T03:45Z] 2016-04-14 20:45:54 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:45:54,008 - WARNING - Could not retrieve variants from source file in region 3:138329651-138330052. Error was invalid region `3:138329652-138330052`
[2016-04-15T03:45Z] 2016-04-14 20:45:56 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:45:56,629 - WARNING - Could not retrieve variants from source file in region 3:137880532-137892619. Error was invalid region `3:137880533-137892619`
[2016-04-15T03:45Z] 2016-04-14 20:45:57 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:45:57,165 - WARNING - Could not retrieve variants from source file in region 3:138244189-138249827. Error was invalid region `3:138244190-138249827`
[2016-04-15T03:45Z] 2016-04-14 20:45:59 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:45:59,354 - WARNING - Could not retrieve variants from source file in region 3:132360672-132361073. Error was invalid region `3:132360673-132361073`
[2016-04-15T03:46Z] 2016-04-14 20:46:00 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:46:00,127 - WARNING - Could not retrieve variants from source file in region 3:141150779-141151180. Error was invalid region `3:141150780-141151180`
[2016-04-15T03:46Z] 2016-04-14 20:46:00 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:46:00,173 - WARNING - Could not retrieve variants from source file in region 3:137786231-137807449. Error was invalid region `3:137786232-137807449`
[2016-04-15T03:46Z] 2016-04-14 20:46:00 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:46:00,638 - WARNING - Could not retrieve variants from source file in region 3:129206980-129214492. Error was invalid region `3:129206981-129214492`
[2016-04-15T03:46Z] 2016-04-14 20:46:00 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:46:00,901 - WARNING - Could not retrieve variants from source file in region 3:143292801-143293202. Error was invalid region `3:143292802-143293202`
[2016-04-15T03:46Z] 2016-04-14 20:46:01 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:46:01,387 - WARNING - Could not retrieve variants from source file in region 3:140686951-140687352. Error was invalid region `3:140686952-140687352`
[2016-04-15T03:46Z] 2016-04-14 20:46:01 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:46:01,544 - WARNING - Could not retrieve variants from source file in region 3:130449011-130449412. Error was invalid region `3:130449012-130449412`
[2016-04-15T03:46Z] 2016-04-14 20:46:01 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:46:01,576 - WARNING - Could not retrieve variants from source file in region 3:138289010-138289411. Error was invalid region `3:138289011-138289411`
[2016-04-15T03:46Z] 2016-04-14 20:46:01 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:46:01,585 - WARNING - Could not retrieve variants from source file in region 3:133368151-133371661. Error was invalid region `3:133368152-133371661`
[2016-04-15T03:46Z] 2016-04-14 20:46:01 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:46:01,791 - WARNING - Could not retrieve variants from source file in region 3:137880532-137892619. Error was invalid region `3:137880533-137892619`
[2016-04-15T03:46Z] 2016-04-14 20:46:01 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:46:01,937 - WARNING - Could not retrieve variants from source file in region 3:138244189-138249827. Error was invalid region `3:138244190-138249827`
[2016-04-15T03:46Z] 2016-04-14 20:46:06 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:46:06,262 - WARNING - Could not retrieve variants from source file in region 3:132360672-132361073. Error was invalid region `3:132360673-132361073`
[2016-04-15T03:46Z] 2016-04-14 20:46:07 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:46:07,490 - WARNING - Could not retrieve variants from source file in region 3:137786231-137807449. Error was invalid region `3:137786232-137807449`
[2016-04-15T03:46Z] 2016-04-14 20:46:09 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:46:09,762 - WARNING - Could not retrieve variants from source file in region 3:143292801-143293202. Error was invalid region `3:143292802-143293202`
[2016-04-15T03:46Z] 2016-04-14 20:46:10 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:46:10,113 - WARNING - Could not retrieve variants from source file in region 3:141535347-141535798. Error was invalid region `3:141535348-141535798`
[2016-04-15T03:46Z] 2016-04-14 20:46:10 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:46:10,114 - WARNING - Could not retrieve variants from source file in region 3:133368151-133371661. Error was invalid region `3:133368152-133371661`
[2016-04-15T03:46Z] 2016-04-14 20:46:20 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:46:20,650 - WARNING - Could not retrieve variants from source file in region 3:137842895-137850193. Error was invalid region `3:137842896-137850193`
[2016-04-15T03:46Z] 2016-04-14 20:46:23 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:46:23,182 - WARNING - Could not retrieve variants from source file in region 3:135914265-135914666. Error was invalid region `3:135914266-135914666`
[2016-04-15T03:46Z] 2016-04-14 20:46:24 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:46:24,634 - WARNING - Could not retrieve variants from source file in region 3:132217864-132218813. Error was invalid region `3:132217865-132218813`
[2016-04-15T03:46Z] 2016-04-14 20:46:24 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:46:24,941 - WARNING - Could not retrieve variants from source file in region 3:136664526-136664927. Error was invalid region `3:136664527-136664927`
[2016-04-15T03:46Z] 2016-04-14 20:46:25 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:46:25,967 - WARNING - Could not retrieve variants from source file in region 3:137842895-137850193. Error was invalid region `3:137842896-137850193`
[2016-04-15T03:46Z] 2016-04-14 20:46:27 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:46:27,011 - WARNING - Could not retrieve variants from source file in region 3:138724546-138724947. Error was invalid region `3:138724547-138724947`
[2016-04-15T03:46Z] 2016-04-14 20:46:27 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:46:27,562 - WARNING - Could not retrieve variants from source file in region 3:134322531-134326874. Error was invalid region `3:134322532-134326874`
[2016-04-15T03:46Z] 2016-04-14 20:46:28 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:46:28,830 - WARNING - Could not retrieve variants from source file in region 3:138032970-138033371. Error was invalid region `3:138032971-138033371`
[2016-04-15T03:46Z] 2016-04-14 20:46:29 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:46:29,575 - WARNING - Could not retrieve variants from source file in region 3:142682013-142682414. Error was invalid region `3:142682014-142682414`
[2016-04-15T03:46Z] 2016-04-14 20:46:29 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:46:29,833 - WARNING - Could not retrieve variants from source file in region 3:140401482-140407450. Error was invalid region `3:140401483-140407450`
[2016-04-15T03:46Z] 2016-04-14 20:46:30 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:46:30,048 - WARNING - Could not retrieve variants from source file in region 3:135914265-135914666. Error was invalid region `3:135914266-135914666`
[2016-04-15T03:46Z] 2016-04-14 20:46:30 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:46:30,126 - WARNING - Could not retrieve variants from source file in region 3:141497501-141497903. Error was invalid region `3:141497502-141497903`
[2016-04-15T03:46Z] 2016-04-14 20:46:30 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:46:30,754 - WARNING - Could not retrieve variants from source file in region 3:129100017-129155860. Error was invalid region `3:129100018-129155860`
[2016-04-15T03:46Z] 2016-04-14 20:46:30 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:46:30,786 - WARNING - Could not retrieve variants from source file in region 3:137842895-137850193. Error was invalid region `3:137842896-137850193`
[2016-04-15T03:46Z] 2016-04-14 20:46:31 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:46:31,618 - WARNING - Could not retrieve variants from source file in region 3:138724546-138724947. Error was invalid region `3:138724547-138724947`
[2016-04-15T03:46Z] 2016-04-14 20:46:33 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:46:33,760 - WARNING - Could not retrieve variants from source file in region 3:134322531-134326874. Error was invalid region `3:134322532-134326874`
[2016-04-15T03:46Z] 2016-04-14 20:46:35 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:46:35,454 - WARNING - Could not retrieve variants from source file in region 3:138032970-138033371. Error was invalid region `3:138032971-138033371`
[2016-04-15T03:46Z] 2016-04-14 20:46:38 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:46:38,227 - WARNING - Could not retrieve variants from source file in region 3:135914265-135914666. Error was invalid region `3:135914266-135914666`
[2016-04-15T03:46Z] 2016-04-14 20:46:38 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:46:38,889 - WARNING - Could not retrieve variants from source file in region 3:136664526-136664927. Error was invalid region `3:136664527-136664927`
[2016-04-15T03:46Z] 2016-04-14 20:46:39 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:46:39,474 - WARNING - Could not retrieve variants from source file in region 3:138724546-138724947. Error was invalid region `3:138724547-138724947`
[2016-04-15T03:46Z] 2016-04-14 20:46:40 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:46:40,555 - WARNING - Could not retrieve variants from source file in region 3:138032970-138033371. Error was invalid region `3:138032971-138033371`
[2016-04-15T03:46Z] 2016-04-14 20:46:41 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:46:41,738 - WARNING - Could not retrieve variants from source file in region 3:140401482-140407450. Error was invalid region `3:140401483-140407450`
[2016-04-15T03:46Z] 2016-04-14 20:46:49 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:46:49,885 - WARNING - Could not retrieve variants from source file in region 3:136573229-136574691. Error was invalid region `3:136573230-136574691`
[2016-04-15T03:46Z] 2016-04-14 20:46:50 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:46:50,694 - WARNING - Could not retrieve variants from source file in region 3:130284073-130300840. Error was invalid region `3:130284074-130300840`
[2016-04-15T03:46Z] 2016-04-14 20:46:50 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:46:50,795 - WARNING - Could not retrieve variants from source file in region 3:136573229-136574691. Error was invalid region `3:136573230-136574691`
[2016-04-15T03:46Z] 2016-04-14 20:46:53 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:46:53,506 - WARNING - Could not retrieve variants from source file in region 3:134898531-134898932. Error was invalid region `3:134898532-134898932`
[2016-04-15T03:46Z] 2016-04-14 20:46:55 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:46:55,637 - WARNING - Could not retrieve variants from source file in region 3:140281512-140283051. Error was invalid region `3:140281513-140283051`
[2016-04-15T03:46Z] 2016-04-14 20:46:55 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:46:55,726 - WARNING - Could not retrieve variants from source file in region 3:136573229-136574691. Error was invalid region `3:136573230-136574691`
[2016-04-15T03:46Z] 2016-04-14 20:46:56 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:46:56,183 - WARNING - Could not retrieve variants from source file in region 3:130284073-130300840. Error was invalid region `3:130284074-130300840`
[2016-04-15T03:46Z] 2016-04-14 20:46:56 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:46:56,210 - WARNING - Could not retrieve variants from source file in region 3:128890139-128890540. Error was invalid region `3:128890140-128890540`
[2016-04-15T03:46Z] 2016-04-14 20:46:57 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:46:57,573 - WARNING - Could not retrieve variants from source file in region 3:138664496-138664897. Error was invalid region `3:138664497-138664897`
[2016-04-15T03:46Z] 2016-04-14 20:46:58 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:46:58,127 - WARNING - Could not retrieve variants from source file in region 3:142408395-142408796. Error was invalid region `3:142408396-142408796`
[2016-04-15T03:46Z] 2016-04-14 20:46:58 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:46:58,219 - WARNING - Could not retrieve variants from source file in region 3:133167152-133167553. Error was invalid region `3:133167153-133167553`
[2016-04-15T03:46Z] 2016-04-14 20:46:58 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:46:58,291 - WARNING - Could not retrieve variants from source file in region 3:134670313-134670714. Error was invalid region `3:134670314-134670714`
[2016-04-15T03:46Z] 2016-04-14 20:46:58 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:46:58,350 - WARNING - Could not retrieve variants from source file in region 3:134898531-134898932. Error was invalid region `3:134898532-134898932`
[2016-04-15T03:46Z] 2016-04-14 20:46:58 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:46:58,362 - WARNING - Could not retrieve variants from source file in region 3:142443230-142443631. Error was invalid region `3:142443231-142443631`
[2016-04-15T03:47Z] 2016-04-14 20:47:00 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:47:00,365 - WARNING - Could not retrieve variants from source file in region 3:140281512-140283051. Error was invalid region `3:140281513-140283051`
[2016-04-15T03:47Z] 2016-04-14 20:47:01 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:47:01,188 - WARNING - Could not retrieve variants from source file in region 3:128890139-128890540. Error was invalid region `3:128890140-128890540`
[2016-04-15T03:47Z] 2016-04-14 20:47:01 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:47:01,238 - WARNING - Could not retrieve variants from source file in region 3:130284073-130300840. Error was invalid region `3:130284074-130300840`
[2016-04-15T03:47Z] 2016-04-14 20:47:02 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:47:02,320 - WARNING - Could not retrieve variants from source file in region 3:134278059-134283369. Error was invalid region `3:134278060-134283369`
[2016-04-15T03:47Z] 2016-04-14 20:47:03 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:47:03,577 - WARNING - Could not retrieve variants from source file in region 3:142408395-142408796. Error was invalid region `3:142408396-142408796`
[2016-04-15T03:47Z] 2016-04-14 20:47:03 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:47:03,899 - WARNING - Could not retrieve variants from source file in region 3:133167152-133167553. Error was invalid region `3:133167153-133167553`
[2016-04-15T03:47Z] 2016-04-14 20:47:04 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:47:04,297 - WARNING - Could not retrieve variants from source file in region 3:134670313-134670714. Error was invalid region `3:134670314-134670714`
[2016-04-15T03:47Z] 2016-04-14 20:47:04 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:47:04,503 - WARNING - Could not retrieve variants from source file in region 3:142503394-142548750. Error was invalid region `3:142503395-142548750`
[2016-04-15T03:47Z] 2016-04-14 20:47:05 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:47:05,077 - WARNING - Could not retrieve variants from source file in region 3:140281512-140283051. Error was invalid region `3:140281513-140283051`
[2016-04-15T03:47Z] 2016-04-14 20:47:05 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:47:05,912 - WARNING - Could not retrieve variants from source file in region 3:128890139-128890540. Error was invalid region `3:128890140-128890540`
[2016-04-15T03:47Z] 2016-04-14 20:47:07 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:47:07,145 - WARNING - Could not retrieve variants from source file in region 3:141457026-141457427. Error was invalid region `3:141457027-141457427`
[2016-04-15T03:47Z] 2016-04-14 20:47:09 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:47:09,026 - WARNING - Could not retrieve variants from source file in region 3:142408395-142408796. Error was invalid region `3:142408396-142408796`
[2016-04-15T03:47Z] 2016-04-14 20:47:09 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:47:09,035 - WARNING - Could not retrieve variants from source file in region 3:142443230-142443631. Error was invalid region `3:142443231-142443631`
[2016-04-15T03:47Z] 2016-04-14 20:47:09 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:47:09,128 - WARNING - Could not retrieve variants from source file in region 3:133167152-133167553. Error was invalid region `3:133167153-133167553`
[2016-04-15T03:47Z] 2016-04-14 20:47:09 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:47:09,466 - WARNING - Could not retrieve variants from source file in region 3:134670313-134670714. Error was invalid region `3:134670314-134670714`
[2016-04-15T03:47Z] 2016-04-14 20:47:15 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:47:15,094 - WARNING - Could not retrieve variants from source file in region 3:130162184-130190911. Error was invalid region `3:130162185-130190911`
[2016-04-15T03:47Z] 2016-04-14 20:47:20 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:47:20,362 - WARNING - Could not retrieve variants from source file in region 3:128755742-128756143. Error was invalid region `3:128755743-128756143`
[2016-04-15T03:47Z] 2016-04-14 20:47:21 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:47:21,259 - WARNING - Could not retrieve variants from source file in region 3:130162184-130190911. Error was invalid region `3:130162185-130190911`
[2016-04-15T03:47Z] 2016-04-14 20:47:21 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:47:21,743 - WARNING - Could not retrieve variants from source file in region 3:131753312-131753878. Error was invalid region `3:131753313-131753878`
[2016-04-15T03:47Z] 2016-04-14 20:47:22 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:47:22,443 - WARNING - Could not retrieve variants from source file in region 3:134204860-134205421. Error was invalid region `3:134204861-134205421`
[2016-04-15T03:47Z] 2016-04-14 20:47:22 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:47:22,741 - WARNING - Could not retrieve variants from source file in region 3:130947224-130947625. Error was invalid region `3:130947225-130947625`
[2016-04-15T03:47Z] 2016-04-14 20:47:23 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:47:23,235 - WARNING - Could not retrieve variants from source file in region 3:142277325-142281802. Error was invalid region `3:142277326-142281802`
[2016-04-15T03:47Z] 2016-04-14 20:47:23 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:47:23,885 - WARNING - Could not retrieve variants from source file in region 3:142222073-142222474. Error was invalid region `3:142222074-142222474`
[2016-04-15T03:47Z] 2016-04-14 20:47:24 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:47:24,266 - WARNING - Could not retrieve variants from source file in region 3:132401389-132401790. Error was invalid region `3:132401390-132401790`
[2016-04-15T03:47Z] 2016-04-14 20:47:25 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:47:25,704 - WARNING - Could not retrieve variants from source file in region 3:141327263-141327664. Error was invalid region `3:141327264-141327664`
[2016-04-15T03:47Z] 2016-04-14 20:47:27 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:47:27,275 - WARNING - Could not retrieve variants from source file in region 3:141381840-141385880. Error was invalid region `3:141381841-141385880`
[2016-04-15T03:47Z] 2016-04-14 20:47:27 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:47:27,350 - WARNING - Could not retrieve variants from source file in region 3:130162184-130190911. Error was invalid region `3:130162185-130190911`
[2016-04-15T03:47Z] 2016-04-14 20:47:28 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:47:28,335 - WARNING - Could not retrieve variants from source file in region 3:128344575-128357042. Error was invalid region `3:128344576-128357042`
[2016-04-15T03:47Z] 2016-04-14 20:47:28 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:47:28,378 - WARNING - Could not retrieve variants from source file in region 3:131753312-131753878. Error was invalid region `3:131753313-131753878`
[2016-04-15T03:47Z] 2016-04-14 20:47:29 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:47:29,441 - WARNING - Could not retrieve variants from source file in region 3:134204860-134205421. Error was invalid region `3:134204861-134205421`
[2016-04-15T03:47Z] 2016-04-14 20:47:30 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:47:30,087 - WARNING - Could not retrieve variants from source file in region 3:138426217-138426618. Error was invalid region `3:138426218-138426618`
[2016-04-15T03:47Z] 2016-04-14 20:47:30 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:47:30,250 - WARNING - Could not retrieve variants from source file in region 3:130947224-130947625. Error was invalid region `3:130947225-130947625`
[2016-04-15T03:47Z] 2016-04-14 20:47:30 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:47:30,648 - WARNING - Could not retrieve variants from source file in region 3:142277325-142281802. Error was invalid region `3:142277326-142281802`
[2016-04-15T03:47Z] 2016-04-14 20:47:31 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:47:31,135 - WARNING - Could not retrieve variants from source file in region 3:142222073-142222474. Error was invalid region `3:142222074-142222474`
[2016-04-15T03:47Z] 2016-04-14 20:47:31 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:47:31,163 - WARNING - Could not retrieve variants from source file in region 3:132401389-132401790. Error was invalid region `3:132401390-132401790`
[2016-04-15T03:47Z] 2016-04-14 20:47:31 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:47:31,759 - WARNING - Could not retrieve variants from source file in region 3:141381840-141385880. Error was invalid region `3:141381841-141385880`
[2016-04-15T03:47Z] 2016-04-14 20:47:32 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:47:32,064 - WARNING - Could not retrieve variants from source file in region 3:128755742-128756143. Error was invalid region `3:128755743-128756143`
[2016-04-15T03:47Z] 2016-04-14 20:47:32 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:47:32,104 - WARNING - Could not retrieve variants from source file in region 3:141327263-141327664. Error was invalid region `3:141327264-141327664`
[2016-04-15T03:47Z] 2016-04-14 20:47:32 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:47:32,113 - WARNING - Could not retrieve variants from source file in region 3:134077259-134093933. Error was invalid region `3:134077260-134093933`
[2016-04-15T03:47Z] 2016-04-14 20:47:33 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:47:33,041 - WARNING - Could not retrieve variants from source file in region 3:128344575-128357042. Error was invalid region `3:128344576-128357042`
[2016-04-15T03:47Z] 2016-04-14 20:47:33 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:47:33,167 - WARNING - Could not retrieve variants from source file in region 3:131753312-131753878. Error was invalid region `3:131753313-131753878`
[2016-04-15T03:47Z] 2016-04-14 20:47:34 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:47:34,078 - WARNING - Could not retrieve variants from source file in region 3:134204860-134205421. Error was invalid region `3:134204861-134205421`
[2016-04-15T03:47Z] 2016-04-14 20:47:35 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:47:35,095 - WARNING - Could not retrieve variants from source file in region 3:138426217-138426618. Error was invalid region `3:138426218-138426618`
[2016-04-15T03:47Z] 2016-04-14 20:47:36 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:47:36,796 - WARNING - Could not retrieve variants from source file in region 3:142277325-142281802. Error was invalid region `3:142277326-142281802`
[2016-04-15T03:47Z] 2016-04-14 20:47:37 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:47:37,516 - WARNING - Could not retrieve variants from source file in region 3:142222073-142222474. Error was invalid region `3:142222074-142222474`
[2016-04-15T03:47Z] 2016-04-14 20:47:38 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:47:38,574 - WARNING - Could not retrieve variants from source file in region 3:134077259-134093933. Error was invalid region `3:134077260-134093933`
[2016-04-15T03:47Z] 2016-04-14 20:47:42 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:47:42,657 - WARNING - Could not retrieve variants from source file in region 3:130098138-130134682. Error was invalid region `3:130098139-130134682`
[2016-04-15T03:47Z] 2016-04-14 20:47:47 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:47:47,604 - WARNING - Could not retrieve variants from source file in region 3:128292002-128292403. Error was invalid region `3:128292003-128292403`
[2016-04-15T03:47Z] 2016-04-14 20:47:47 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:47:47,776 - WARNING - Could not retrieve variants from source file in region 3:128720276-128720677. Error was invalid region `3:128720277-128720677`
[2016-04-15T03:47Z] 2016-04-14 20:47:47 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:47:47,942 - WARNING - Could not retrieve variants from source file in region 3:127983284-127983685. Error was invalid region `3:127983285-127983685`
[2016-04-15T03:47Z] 2016-04-14 20:47:48 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:47:48,265 - WARNING - Could not retrieve variants from source file in region 3:127983284-127983685. Error was invalid region `3:127983285-127983685`
[2016-04-15T03:47Z] 2016-04-14 20:47:48 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:47:48,462 - WARNING - Could not retrieve variants from source file in region 3:142168120-142168521. Error was invalid region `3:142168121-142168521`
[2016-04-15T03:47Z] 2016-04-14 20:47:50 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:47:50,101 - WARNING - Could not retrieve variants from source file in region 3:133969226-133969677. Error was invalid region `3:133969227-133969677`
[2016-04-15T03:47Z] 2016-04-14 20:47:50 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:47:50,326 - WARNING - Could not retrieve variants from source file in region 3:129809917-129815125. Error was invalid region `3:129809918-129815125`
[2016-04-15T03:47Z] 2016-04-14 20:47:51 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:47:51,322 - WARNING - Could not retrieve variants from source file in region 3:133524506-133547882. Error was invalid region `3:133524507-133547882`
[2016-04-15T03:47Z] 2016-04-14 20:47:51 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:47:51,544 - WARNING - Could not retrieve variants from source file in region 3:129546518-129546919. Error was invalid region `3:129546519-129546919`
[2016-04-15T03:47Z] 2016-04-14 20:47:52 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:47:52,086 - WARNING - Could not retrieve variants from source file in region 3:128292002-128292403. Error was invalid region `3:128292003-128292403`
[2016-04-15T03:47Z] 2016-04-14 20:47:52 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:47:52,721 - WARNING - Could not retrieve variants from source file in region 3:130098138-130134682. Error was invalid region `3:130098139-130134682`
[2016-04-15T03:47Z] 2016-04-14 20:47:52 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:47:52,895 - WARNING - Could not retrieve variants from source file in region 3:127983284-127983685. Error was invalid region `3:127983285-127983685`
[2016-04-15T03:47Z] 2016-04-14 20:47:53 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:47:53,018 - WARNING - Could not retrieve variants from source file in region 3:142168120-142168521. Error was invalid region `3:142168121-142168521`
[2016-04-15T03:47Z] 2016-04-14 20:47:53 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:47:53,169 - WARNING - Could not retrieve variants from source file in region 3:133665998-133670263. Error was invalid region `3:133665999-133670263`
[2016-04-15T03:47Z] 2016-04-14 20:47:54 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:47:54,428 - WARNING - Could not retrieve variants from source file in region 3:127872295-127872792. Error was invalid region `3:127872296-127872792`
[2016-04-15T03:47Z] 2016-04-14 20:47:54 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:47:54,443 - WARNING - Could not retrieve variants from source file in region 3:133969226-133969677. Error was invalid region `3:133969227-133969677`
[2016-04-15T03:47Z] 2016-04-14 20:47:55 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:47:55,426 - WARNING - Could not retrieve variants from source file in region 3:141903694-141904664. Error was invalid region `3:141903695-141904664`
[2016-04-15T03:47Z] 2016-04-14 20:47:55 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:47:55,900 - WARNING - Could not retrieve variants from source file in region 3:133524506-133547882. Error was invalid region `3:133524507-133547882`
[2016-04-15T03:47Z] 2016-04-14 20:47:56 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:47:56,129 - WARNING - Could not retrieve variants from source file in region 3:129546518-129546919. Error was invalid region `3:129546519-129546919`
[2016-04-15T03:47Z] 2016-04-14 20:47:56 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:47:56,588 - WARNING - Could not retrieve variants from source file in region 3:128292002-128292403. Error was invalid region `3:128292003-128292403`
[2016-04-15T03:47Z] 2016-04-14 20:47:57 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:47:57,126 - WARNING - Could not retrieve variants from source file in region 3:128720276-128720677. Error was invalid region `3:128720277-128720677`
[2016-04-15T03:47Z] 2016-04-14 20:47:57 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:47:57,623 - WARNING - Could not retrieve variants from source file in region 3:142168120-142168521. Error was invalid region `3:142168121-142168521`
[2016-04-15T03:47Z] 2016-04-14 20:47:57 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:47:57,998 - WARNING - Could not retrieve variants from source file in region 3:133665998-133670263. Error was invalid region `3:133665999-133670263`
[2016-04-15T03:48Z] 2016-04-14 20:48:00 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:48:00,006 - WARNING - Could not retrieve variants from source file in region 3:133524506-133547882. Error was invalid region `3:133524507-133547882`
[2016-04-15T03:48Z] 2016-04-14 20:48:00 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:48:00,037 - WARNING - Could not retrieve variants from source file in region 3:141903694-141904664. Error was invalid region `3:141903695-141904664`
[2016-04-15T03:48Z] 2016-04-14 20:48:00 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:48:00,437 - WARNING - Could not retrieve variants from source file in region 3:129546518-129546919. Error was invalid region `3:129546519-129546919`
[2016-04-15T03:48Z] 2016-04-14 20:48:06 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:48:06,498 - WARNING - Could not retrieve variants from source file in region 3:129695503-129696231. Error was invalid region `3:129695504-129696231`
[2016-04-15T03:48Z] 2016-04-14 20:48:08 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:48:08,211 - WARNING - Could not retrieve variants from source file in region 3:129323982-129324383. Error was invalid region `3:129323983-129324383`
[2016-04-15T03:48Z] 2016-04-14 20:48:08 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:48:08,221 - WARNING - Could not retrieve variants from source file in region 3:129323982-129324383. Error was invalid region `3:129323983-129324383`
[2016-04-15T03:48Z] 2016-04-14 20:48:08 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:48:08,225 - WARNING - Could not retrieve variants from source file in region 3:129323982-129324383. Error was invalid region `3:129323983-129324383`
[2016-04-15T03:48Z] 2016-04-14 20:48:09 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:48:09,983 - WARNING - Could not retrieve variants from source file in region 3:129267048-129297413. Error was invalid region `3:129267049-129297413`
[2016-04-15T03:48Z] 2016-04-14 20:48:10 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:48:10,031 - WARNING - Could not retrieve variants from source file in region 3:133474117-133494544. Error was invalid region `3:133474118-133494544`
[2016-04-15T03:48Z] 2016-04-14 20:48:10 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:48:10,044 - WARNING - Could not retrieve variants from source file in region 3:133474117-133494544. Error was invalid region `3:133474118-133494544`
[2016-04-15T03:48Z] ['bcbio-variation-recall', 'square', '-Xms750m', '-Xmx7280m', '-XX:+UseSerialGC', '-c', 16, '-r', u'3:143297427-158963696', '--caller', 'platypus', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/3/Batch1-3_143297426_158963696.vcf.gz', '/mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/3/Batch1-3_143297426_158963696.vcf-inputs.txt'] in region: 3:143297427-158963696
[2016-04-15T03:48Z] 2016-04-14 20:48:27 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:48:27,804 - WARNING - Could not retrieve variants from source file in region 3:154146711-154147112. Error was invalid region `3:154146712-154147112`
[2016-04-15T03:48Z] 2016-04-14 20:48:27 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:48:27,889 - WARNING - Could not retrieve variants from source file in region 3:153839655-153840150. Error was invalid region `3:153839656-153840150`
[2016-04-15T03:48Z] 2016-04-14 20:48:27 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:48:27,955 - WARNING - Could not retrieve variants from source file in region 3:149093027-149093428. Error was invalid region `3:149093028-149093428`
[2016-04-15T03:48Z] 2016-04-14 20:48:28 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:48:28,163 - WARNING - Could not retrieve variants from source file in region 3:151463210-151463611. Error was invalid region `3:151463211-151463611`
[2016-04-15T03:48Z] 2016-04-14 20:48:28 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:48:28,272 - WARNING - Could not retrieve variants from source file in region 3:156570492-156570893. Error was invalid region `3:156570493-156570893`
[2016-04-15T03:48Z] 2016-04-14 20:48:28 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:48:28,415 - WARNING - Could not retrieve variants from source file in region 3:158320386-158320893. Error was invalid region `3:158320387-158320893`
[2016-04-15T03:48Z] 2016-04-14 20:48:28 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:48:28,617 - WARNING - Could not retrieve variants from source file in region 3:156868239-156871006. Error was invalid region `3:156868240-156871006`
[2016-04-15T03:48Z] 2016-04-14 20:48:28 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:48:28,884 - WARNING - Could not retrieve variants from source file in region 3:153905285-153905686. Error was invalid region `3:153905286-153905686`
[2016-04-15T03:48Z] 2016-04-14 20:48:28 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:48:28,892 - WARNING - Could not retrieve variants from source file in region 3:157081113-157081514. Error was invalid region `3:157081114-157081514`
[2016-04-15T03:48Z] 2016-04-14 20:48:31 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:48:31,700 - WARNING - Could not retrieve variants from source file in region 3:157287131-157287532. Error was invalid region `3:157287132-157287532`
[2016-04-15T03:48Z] 2016-04-14 20:48:31 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:48:31,891 - WARNING - Could not retrieve variants from source file in region 3:158537232-158538246. Error was invalid region `3:158537233-158538246`
[2016-04-15T03:48Z] 2016-04-14 20:48:32 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:48:32,189 - WARNING - Could not retrieve variants from source file in region 3:157823370-157823797. Error was invalid region `3:157823371-157823797`
[2016-04-15T03:48Z] 2016-04-14 20:48:35 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:48:35,178 - WARNING - Could not retrieve variants from source file in region 3:153839655-153840150. Error was invalid region `3:153839656-153840150`
[2016-04-15T03:48Z] 2016-04-14 20:48:36 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:48:36,210 - WARNING - Could not retrieve variants from source file in region 3:151463210-151463611. Error was invalid region `3:151463211-151463611`
[2016-04-15T03:48Z] 2016-04-14 20:48:36 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:48:36,420 - WARNING - Could not retrieve variants from source file in region 3:158320386-158320893. Error was invalid region `3:158320387-158320893`
[2016-04-15T03:48Z] 2016-04-14 20:48:36 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:48:36,765 - WARNING - Could not retrieve variants from source file in region 3:153973197-153974116. Error was invalid region `3:153973198-153974116`
[2016-04-15T03:48Z] 2016-04-14 20:48:36 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:48:36,849 - WARNING - Could not retrieve variants from source file in region 3:154018676-154033256. Error was invalid region `3:154018677-154033256`
[2016-04-15T03:48Z] 2016-04-14 20:48:36 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:48:36,856 - WARNING - Could not retrieve variants from source file in region 3:156868239-156871006. Error was invalid region `3:156868240-156871006`
[2016-04-15T03:48Z] 2016-04-14 20:48:38 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:48:38,007 - WARNING - Could not retrieve variants from source file in region 3:153943559-153943960. Error was invalid region `3:153943560-153943960`
[2016-04-15T03:48Z] 2016-04-14 20:48:38 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:48:38,023 - WARNING - Could not retrieve variants from source file in region 3:149093027-149093428. Error was invalid region `3:149093028-149093428`
[2016-04-15T03:48Z] 2016-04-14 20:48:38 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:48:38,071 - WARNING - Could not retrieve variants from source file in region 3:158537232-158538246. Error was invalid region `3:158537233-158538246`
[2016-04-15T03:48Z] 2016-04-14 20:48:38 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:48:38,155 - WARNING - Could not retrieve variants from source file in region 3:157287131-157287532. Error was invalid region `3:157287132-157287532`
[2016-04-15T03:48Z] 2016-04-14 20:48:38 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:48:38,157 - WARNING - Could not retrieve variants from source file in region 3:157081113-157081514. Error was invalid region `3:157081114-157081514`
[2016-04-15T03:48Z] 2016-04-14 20:48:40 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:48:40,876 - WARNING - Could not retrieve variants from source file in region 3:154146711-154147112. Error was invalid region `3:154146712-154147112`
[2016-04-15T03:48Z] 2016-04-14 20:48:41 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:48:41,555 - WARNING - Could not retrieve variants from source file in region 3:153839655-153840150. Error was invalid region `3:153839656-153840150`
[2016-04-15T03:48Z] 2016-04-14 20:48:43 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:48:43,723 - WARNING - Could not retrieve variants from source file in region 3:151463210-151463611. Error was invalid region `3:151463211-151463611`
[2016-04-15T03:48Z] 2016-04-14 20:48:44 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:48:44,123 - WARNING - Could not retrieve variants from source file in region 3:158320386-158320893. Error was invalid region `3:158320387-158320893`
[2016-04-15T03:48Z] 2016-04-14 20:48:44 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:48:44,841 - WARNING - Could not retrieve variants from source file in region 3:154018676-154033256. Error was invalid region `3:154018677-154033256`
[2016-04-15T03:48Z] 2016-04-14 20:48:45 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:48:45,216 - WARNING - Could not retrieve variants from source file in region 3:153973197-153974116. Error was invalid region `3:153973198-153974116`
[2016-04-15T03:48Z] 2016-04-14 20:48:45 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:48:45,533 - WARNING - Could not retrieve variants from source file in region 3:156868239-156871006. Error was invalid region `3:156868240-156871006`
[2016-04-15T03:48Z] 2016-04-14 20:48:46 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:48:46,010 - WARNING - Could not retrieve variants from source file in region 3:153905285-153905686. Error was invalid region `3:153905286-153905686`
[2016-04-15T03:48Z] 2016-04-14 20:48:46 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:48:46,311 - WARNING - Could not retrieve variants from source file in region 3:149093027-149093428. Error was invalid region `3:149093028-149093428`
[2016-04-15T03:48Z] 2016-04-14 20:48:46 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:48:46,629 - WARNING - Could not retrieve variants from source file in region 3:157081113-157081514. Error was invalid region `3:157081114-157081514`
[2016-04-15T03:48Z] 2016-04-14 20:48:56 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:48:56,651 - WARNING - Could not retrieve variants from source file in region 3:158362230-158388970. Error was invalid region `3:158362231-158388970`
[2016-04-15T03:48Z] 2016-04-14 20:48:57 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:48:57,241 - WARNING - Could not retrieve variants from source file in region 3:157318046-157318933. Error was invalid region `3:157318047-157318933`
[2016-04-15T03:48Z] 2016-04-14 20:48:57 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:48:57,282 - WARNING - Could not retrieve variants from source file in region 3:158362230-158388970. Error was invalid region `3:158362231-158388970`
[2016-04-15T03:48Z] 2016-04-14 20:48:57 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:48:57,573 - WARNING - Could not retrieve variants from source file in region 3:151531778-151545791. Error was invalid region `3:151531779-151545791`
[2016-04-15T03:48Z] 2016-04-14 20:48:58 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:48:58,728 - WARNING - Could not retrieve variants from source file in region 3:156174898-156175299. Error was invalid region `3:156174899-156175299`
[2016-04-15T03:48Z] 2016-04-14 20:48:59 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:48:59,479 - WARNING - Could not retrieve variants from source file in region 3:157127375-157127776. Error was invalid region `3:157127376-157127776`
[2016-04-15T03:49Z] 2016-04-14 20:49:01 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:49:01,136 - WARNING - Could not retrieve variants from source file in region 3:157155103-157155504. Error was invalid region `3:157155104-157155504`
[2016-04-15T03:49Z] 2016-04-14 20:49:01 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:49:01,446 - WARNING - Could not retrieve variants from source file in region 3:158362230-158388970. Error was invalid region `3:158362231-158388970`
[2016-04-15T03:49Z] 2016-04-14 20:49:02 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:49:02,415 - WARNING - Could not retrieve variants from source file in region 3:156696844-156697245. Error was invalid region `3:156696845-156697245`
[2016-04-15T03:49Z] 2016-04-14 20:49:02 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:49:02,444 - WARNING - Could not retrieve variants from source file in region 3:151531778-151545791. Error was invalid region `3:151531779-151545791`
[2016-04-15T03:49Z] 2016-04-14 20:49:02 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:49:02,472 - WARNING - Could not retrieve variants from source file in region 3:157318046-157318933. Error was invalid region `3:157318047-157318933`
[2016-04-15T03:49Z] 2016-04-14 20:49:02 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:49:02,726 - WARNING - Could not retrieve variants from source file in region 3:156983203-156983604. Error was invalid region `3:156983204-156983604`
[2016-04-15T03:49Z] 2016-04-14 20:49:03 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:49:03,103 - WARNING - Could not retrieve variants from source file in region 3:148916024-148916425. Error was invalid region `3:148916025-148916425`
[2016-04-15T03:49Z] 2016-04-14 20:49:03 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:49:03,176 - WARNING - Could not retrieve variants from source file in region 3:156174898-156175299. Error was invalid region `3:156174899-156175299`
[2016-04-15T03:49Z] 2016-04-14 20:49:03 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:49:03,848 - WARNING - Could not retrieve variants from source file in region 3:157127375-157127776. Error was invalid region `3:157127376-157127776`
[2016-04-15T03:49Z] 2016-04-14 20:49:04 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:49:04,166 - WARNING - Could not retrieve variants from source file in region 3:155481398-155485492. Error was invalid region `3:155481399-155485492`
[2016-04-15T03:49Z] 2016-04-14 20:49:05 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:49:05,255 - WARNING - Could not retrieve variants from source file in region 3:157155103-157155504. Error was invalid region `3:157155104-157155504`
[2016-04-15T03:49Z] 2016-04-14 20:49:07 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:49:07,184 - WARNING - Could not retrieve variants from source file in region 3:157318046-157318933. Error was invalid region `3:157318047-157318933`
[2016-04-15T03:49Z] 2016-04-14 20:49:07 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:49:07,225 - WARNING - Could not retrieve variants from source file in region 3:156983203-156983604. Error was invalid region `3:156983204-156983604`
[2016-04-15T03:49Z] 2016-04-14 20:49:07 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:49:07,469 - WARNING - Could not retrieve variants from source file in region 3:148916024-148916425. Error was invalid region `3:148916025-148916425`
[2016-04-15T03:49Z] 2016-04-14 20:49:07 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:49:07,704 - WARNING - Could not retrieve variants from source file in region 3:156174898-156175299. Error was invalid region `3:156174899-156175299`
[2016-04-15T03:49Z] 2016-04-14 20:49:08 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:49:08,094 - WARNING - Could not retrieve variants from source file in region 3:157127375-157127776. Error was invalid region `3:157127376-157127776`
[2016-04-15T03:49Z] 2016-04-14 20:49:11 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:49:11,372 - WARNING - Could not retrieve variants from source file in region 3:150391599-150392000. Error was invalid region `3:150391600-150392000`
[2016-04-15T03:49Z] 2016-04-14 20:49:11 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:49:11,932 - WARNING - Could not retrieve variants from source file in region 3:156983203-156983604. Error was invalid region `3:156983204-156983604`
[2016-04-15T03:49Z] 2016-04-14 20:49:12 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:49:12,143 - WARNING - Could not retrieve variants from source file in region 3:148916024-148916425. Error was invalid region `3:148916025-148916425`
[2016-04-15T03:49Z] 2016-04-14 20:49:13 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:49:13,863 - WARNING - Could not retrieve variants from source file in region 3:151011758-151012687. Error was invalid region `3:151011759-151012687`
[2016-04-15T03:49Z] 2016-04-14 20:49:16 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:49:16,182 - WARNING - Could not retrieve variants from source file in region 3:156009403-156009804. Error was invalid region `3:156009404-156009804`
[2016-04-15T03:49Z] 2016-04-14 20:49:16 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:49:16,558 - WARNING - Could not retrieve variants from source file in region 3:151046097-151056806. Error was invalid region `3:151046098-151056806`
[2016-04-15T03:49Z] 2016-04-14 20:49:16 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:49:16,572 - WARNING - Could not retrieve variants from source file in region 3:156009403-156009804. Error was invalid region `3:156009404-156009804`
[2016-04-15T03:49Z] 2016-04-14 20:49:17 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:49:17,009 - WARNING - Could not retrieve variants from source file in region 3:151046097-151056806. Error was invalid region `3:151046098-151056806`
[2016-04-15T03:49Z] 2016-04-14 20:49:18 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:49:18,282 - WARNING - Could not retrieve variants from source file in region 3:151011758-151012687. Error was invalid region `3:151011759-151012687`
[2016-04-15T03:49Z] 2016-04-14 20:49:20 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:49:20,971 - WARNING - Could not retrieve variants from source file in region 3:155301053-155314224. Error was invalid region `3:155301054-155314224`
[2016-04-15T03:49Z] 2016-04-14 20:49:21 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:49:21,024 - WARNING - Could not retrieve variants from source file in region 3:156009403-156009804. Error was invalid region `3:156009404-156009804`
[2016-04-15T03:49Z] 2016-04-14 20:49:21 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:49:21,540 - WARNING - Could not retrieve variants from source file in region 3:151011758-151012687. Error was invalid region `3:151011759-151012687`
[2016-04-15T03:49Z] 2016-04-14 20:49:22 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:49:22,021 - WARNING - Could not retrieve variants from source file in region 3:148457431-148457832. Error was invalid region `3:148457432-148457832`
[2016-04-15T03:49Z] 2016-04-14 20:49:22 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:49:22,148 - WARNING - Could not retrieve variants from source file in region 3:155241529-155241930. Error was invalid region `3:155241530-155241930`
[2016-04-15T03:49Z] 2016-04-14 20:49:23 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:49:23,626 - WARNING - Could not retrieve variants from source file in region 3:150663123-150663640. Error was invalid region `3:150663124-150663640`
[2016-04-15T03:49Z] 2016-04-14 20:49:25 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:49:25,008 - WARNING - Could not retrieve variants from source file in region 3:148785897-148786298. Error was invalid region `3:148785898-148786298`
[2016-04-15T03:49Z] 2016-04-14 20:49:26 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:49:26,388 - WARNING - Could not retrieve variants from source file in region 3:148457431-148457832. Error was invalid region `3:148457432-148457832`
[2016-04-15T03:49Z] 2016-04-14 20:49:26 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:49:26,849 - WARNING - Could not retrieve variants from source file in region 3:155241529-155241930. Error was invalid region `3:155241530-155241930`
[2016-04-15T03:49Z] 2016-04-14 20:49:27 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:49:27,935 - WARNING - Could not retrieve variants from source file in region 3:150663123-150663640. Error was invalid region `3:150663124-150663640`
[2016-04-15T03:49Z] 2016-04-14 20:49:29 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:49:29,773 - WARNING - Could not retrieve variants from source file in region 3:150421208-150421609. Error was invalid region `3:150421209-150421609`
[2016-04-15T03:49Z] 2016-04-14 20:49:29 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:49:29,872 - WARNING - Could not retrieve variants from source file in region 3:150663123-150663640. Error was invalid region `3:150663124-150663640`
[2016-04-15T03:49Z] 2016-04-14 20:49:29 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:49:29,946 - WARNING - Could not retrieve variants from source file in region 3:155301053-155314224. Error was invalid region `3:155301054-155314224`
[2016-04-15T03:49Z] 2016-04-14 20:49:30 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:49:30,004 - WARNING - Could not retrieve variants from source file in region 3:150421208-150421609. Error was invalid region `3:150421209-150421609`
[2016-04-15T03:49Z] 2016-04-14 20:49:31 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:49:31,303 - WARNING - Could not retrieve variants from source file in region 3:155241529-155241930. Error was invalid region `3:155241530-155241930`
[2016-04-15T03:49Z] 2016-04-14 20:49:33 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:49:33,672 - WARNING - Could not retrieve variants from source file in region 3:150421208-150421609. Error was invalid region `3:150421209-150421609`
[2016-04-15T03:49Z] 2016-04-14 20:49:33 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:49:33,813 - WARNING - Could not retrieve variants from source file in region 3:148785897-148786298. Error was invalid region `3:148785898-148786298`
[2016-04-15T03:49Z] 2016-04-14 20:49:37 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:49:37,543 - WARNING - Could not retrieve variants from source file in region 3:148726922-148727323. Error was invalid region `3:148726923-148727323`
[2016-04-15T03:49Z] 2016-04-14 20:49:37 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:49:37,938 - WARNING - Could not retrieve variants from source file in region 3:148597401-148597802. Error was invalid region `3:148597402-148597802`
[2016-04-15T03:49Z] 2016-04-14 20:49:38 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:49:38,227 - WARNING - Could not retrieve variants from source file in region 3:150285309-150285710. Error was invalid region `3:150285310-150285710`
[2016-04-15T03:49Z] 2016-04-14 20:49:41 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:49:41,825 - WARNING - Could not retrieve variants from source file in region 3:150285309-150285710. Error was invalid region `3:150285310-150285710`
[2016-04-15T03:49Z] 2016-04-14 20:49:41 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:49:41,826 - WARNING - Could not retrieve variants from source file in region 3:148759114-148759515. Error was invalid region `3:148759115-148759515`
[2016-04-15T03:49Z] 2016-04-14 20:49:42 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:49:42,238 - WARNING - Could not retrieve variants from source file in region 3:148597401-148597802. Error was invalid region `3:148597402-148597802`
[2016-04-15T03:49Z] 2016-04-14 20:49:42 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:49:42,782 - WARNING - Could not retrieve variants from source file in region 3:149238384-149238785. Error was invalid region `3:149238385-149238785`
[2016-04-15T03:49Z] 2016-04-14 20:49:43 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:49:43,234 - WARNING - Could not retrieve variants from source file in region 3:145917550-145938809. Error was invalid region `3:145917551-145938809`
[2016-04-15T03:49Z] 2016-04-14 20:49:43 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:49:43,236 - WARNING - Could not retrieve variants from source file in region 3:143566996-143567397. Error was invalid region `3:143566997-143567397`
[2016-04-15T03:49Z] 2016-04-14 20:49:45 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:49:45,594 - WARNING - Could not retrieve variants from source file in region 3:150127943-150129184. Error was invalid region `3:150127944-150129184`
[2016-04-15T03:49Z] 2016-04-14 20:49:46 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:49:46,356 - WARNING - Could not retrieve variants from source file in region 3:148726922-148727323. Error was invalid region `3:148726923-148727323`
[2016-04-15T03:49Z] 2016-04-14 20:49:46 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:49:46,383 - WARNING - Could not retrieve variants from source file in region 3:148759114-148759515. Error was invalid region `3:148759115-148759515`
[2016-04-15T03:49Z] 2016-04-14 20:49:47 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:49:47,026 - WARNING - Could not retrieve variants from source file in region 3:148597401-148597802. Error was invalid region `3:148597402-148597802`
[2016-04-15T03:49Z] 2016-04-14 20:49:47 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:49:47,050 - WARNING - Could not retrieve variants from source file in region 3:149238384-149238785. Error was invalid region `3:149238385-149238785`
[2016-04-15T03:49Z] 2016-04-14 20:49:47 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:49:47,817 - WARNING - Could not retrieve variants from source file in region 3:143566996-143567397. Error was invalid region `3:143566997-143567397`
[2016-04-15T03:49Z] 2016-04-14 20:49:49 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:49:49,632 - WARNING - Could not retrieve variants from source file in region 3:150127943-150129184. Error was invalid region `3:150127944-150129184`
[2016-04-15T03:49Z] 2016-04-14 20:49:50 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:49:50,230 - WARNING - Could not retrieve variants from source file in region 3:150127943-150129184. Error was invalid region `3:150127944-150129184`
[2016-04-15T03:49Z] 2016-04-14 20:49:51 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:49:51,431 - WARNING - Could not retrieve variants from source file in region 3:149238384-149238785. Error was invalid region `3:149238385-149238785`
[2016-04-15T03:49Z] 2016-04-14 20:49:51 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:49:51,847 - WARNING - Could not retrieve variants from source file in region 3:145917550-145938809. Error was invalid region `3:145917551-145938809`
[2016-04-15T03:49Z] 2016-04-14 20:49:51 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:49:51,994 - WARNING - Could not retrieve variants from source file in region 3:149459130-149488632. Error was invalid region `3:149459131-149488632`
[2016-04-15T03:49Z] 2016-04-14 20:49:52 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:49:52,165 - WARNING - Could not retrieve variants from source file in region 3:143566996-143567397. Error was invalid region `3:143566997-143567397`
[2016-04-15T03:49Z] 2016-04-14 20:49:54 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:49:54,278 - WARNING - Could not retrieve variants from source file in region 3:149192465-149193874. Error was invalid region `3:149192466-149193874`
[2016-04-15T03:49Z] 2016-04-14 20:49:55 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:49:55,155 - WARNING - Could not retrieve variants from source file in region 3:146177604-146178005. Error was invalid region `3:146177605-146178005`
[2016-04-15T03:49Z] 2016-04-14 20:49:55 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:49:55,188 - WARNING - Could not retrieve variants from source file in region 3:146177604-146178005. Error was invalid region `3:146177605-146178005`
[2016-04-15T03:49Z] 2016-04-14 20:49:58 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:49:58,272 - WARNING - Could not retrieve variants from source file in region 3:143370990-143371391. Error was invalid region `3:143370991-143371391`
[2016-04-15T03:49Z] 2016-04-14 20:49:58 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:49:58,871 - WARNING - Could not retrieve variants from source file in region 3:145794565-145794970. Error was invalid region `3:145794566-145794970`
[2016-04-15T03:50Z] 2016-04-14 20:50:01 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:50:01,459 - WARNING - Could not retrieve variants from source file in region 3:145794565-145794970. Error was invalid region `3:145794566-145794970`
[2016-04-15T03:50Z] ['bcbio-variation-recall', 'square', '-Xms750m', '-Xmx7280m', '-XX:+UseSerialGC', '-c', 16, '-r', u'3:158970516-174577240', '--caller', 'platypus', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/3/Batch1-3_158970515_174577240.vcf.gz', '/mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/3/Batch1-3_158970515_174577240.vcf-inputs.txt'] in region: 3:158970516-174577240
[2016-04-15T03:50Z] 2016-04-14 20:50:17 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:50:17,497 - WARNING - Could not retrieve variants from source file in region 3:172766611-172767012. Error was invalid region `3:172766612-172767012`
[2016-04-15T03:50Z] 2016-04-14 20:50:17 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:50:17,645 - WARNING - Could not retrieve variants from source file in region 3:170892859-170893260. Error was invalid region `3:170892860-170893260`
[2016-04-15T03:50Z] 2016-04-14 20:50:18 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:50:18,533 - WARNING - Could not retrieve variants from source file in region 3:167166975-167185068. Error was invalid region `3:167166976-167185068`
[2016-04-15T03:50Z] 2016-04-14 20:50:18 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:50:18,541 - WARNING - Could not retrieve variants from source file in region 3:169539601-169571335. Error was invalid region `3:169539602-169571335`
[2016-04-15T03:50Z] 2016-04-14 20:50:19 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:50:19,397 - WARNING - Could not retrieve variants from source file in region 3:165491069-165491470. Error was invalid region `3:165491070-165491470`
[2016-04-15T03:50Z] 2016-04-14 20:50:19 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:50:19,611 - WARNING - Could not retrieve variants from source file in region 3:164714321-164714722. Error was invalid region `3:164714322-164714722`
[2016-04-15T03:50Z] 2016-04-14 20:50:19 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:50:19,709 - WARNING - Could not retrieve variants from source file in region 3:172165516-172166223. Error was invalid region `3:172165517-172166223`
[2016-04-15T03:50Z] 2016-04-14 20:50:20 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:50:20,671 - WARNING - Could not retrieve variants from source file in region 3:172365621-172366022. Error was invalid region `3:172365622-172366022`
[2016-04-15T03:50Z] 2016-04-14 20:50:20 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:50:20,703 - WARNING - Could not retrieve variants from source file in region 3:171455490-171455891. Error was invalid region `3:171455491-171455891`
[2016-04-15T03:50Z] 2016-04-14 20:50:23 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:50:23,213 - WARNING - Could not retrieve variants from source file in region 3:172766611-172767012. Error was invalid region `3:172766612-172767012`
[2016-04-15T03:50Z] 2016-04-14 20:50:26 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:50:26,244 - WARNING - Could not retrieve variants from source file in region 3:160227395-160227796. Error was invalid region `3:160227396-160227796`
[2016-04-15T03:50Z] 2016-04-14 20:50:27 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:50:27,410 - WARNING - Could not retrieve variants from source file in region 3:169638839-169639240. Error was invalid region `3:169638840-169639240`
[2016-04-15T03:50Z] 2016-04-14 20:50:27 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:50:27,562 - WARNING - Could not retrieve variants from source file in region 3:164714321-164714722. Error was invalid region `3:164714322-164714722`
[2016-04-15T03:50Z] 2016-04-14 20:50:28 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:50:28,306 - WARNING - Could not retrieve variants from source file in region 3:172834914-172835315. Error was invalid region `3:172834915-172835315`
[2016-04-15T03:50Z] 2016-04-14 20:50:28 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:50:28,526 - WARNING - Could not retrieve variants from source file in region 3:168810663-168811064. Error was invalid region `3:168810664-168811064`
[2016-04-15T03:50Z] 2016-04-14 20:50:29 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:50:29,567 - WARNING - Could not retrieve variants from source file in region 3:173998744-173999145. Error was invalid region `3:173998745-173999145`
[2016-04-15T03:50Z] 2016-04-14 20:50:29 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:50:29,720 - WARNING - Could not retrieve variants from source file in region 3:172766611-172767012. Error was invalid region `3:172766612-172767012`
[2016-04-15T03:50Z] 2016-04-14 20:50:29 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:50:29,741 - WARNING - Could not retrieve variants from source file in region 3:169988075-169988476. Error was invalid region `3:169988076-169988476`
[2016-04-15T03:50Z] 2016-04-14 20:50:30 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:50:30,104 - WARNING - Could not retrieve variants from source file in region 3:167166975-167185068. Error was invalid region `3:167166976-167185068`
[2016-04-15T03:50Z] 2016-04-14 20:50:30 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:50:30,316 - WARNING - Could not retrieve variants from source file in region 3:169539601-169571335. Error was invalid region `3:169539602-169571335`
[2016-04-15T03:50Z] 2016-04-14 20:50:31 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:50:31,869 - WARNING - Could not retrieve variants from source file in region 3:165491069-165491470. Error was invalid region `3:165491070-165491470`
[2016-04-15T03:50Z] 2016-04-14 20:50:33 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:50:33,070 - WARNING - Could not retrieve variants from source file in region 3:164714321-164714722. Error was invalid region `3:164714322-164714722`
[2016-04-15T03:50Z] 2016-04-14 20:50:34 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:50:34,765 - WARNING - Could not retrieve variants from source file in region 3:172834914-172835315. Error was invalid region `3:172834915-172835315`
[2016-04-15T03:50Z] 2016-04-14 20:50:35 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:50:35,617 - WARNING - Could not retrieve variants from source file in region 3:168810663-168811064. Error was invalid region `3:168810664-168811064`
[2016-04-15T03:50Z] 2016-04-14 20:50:36 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:50:36,375 - WARNING - Could not retrieve variants from source file in region 3:172365621-172366022. Error was invalid region `3:172365622-172366022`
[2016-04-15T03:50Z] 2016-04-14 20:50:37 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:50:37,239 - WARNING - Could not retrieve variants from source file in region 3:169988075-169988476. Error was invalid region `3:169988076-169988476`
[2016-04-15T03:50Z] 2016-04-14 20:50:46 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:50:46,353 - WARNING - Could not retrieve variants from source file in region 3:170802699-170843972. Error was invalid region `3:170802700-170843972`
[2016-04-15T03:50Z] 2016-04-14 20:50:49 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:50:49,603 - WARNING - Could not retrieve variants from source file in region 3:172428571-172428972. Error was invalid region `3:172428572-172428972`
[2016-04-15T03:50Z] 2016-04-14 20:50:50 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:50:50,644 - WARNING - Could not retrieve variants from source file in region 3:160130303-160154937. Error was invalid region `3:160130304-160154937`
[2016-04-15T03:50Z] 2016-04-14 20:50:50 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:50:50,684 - WARNING - Could not retrieve variants from source file in region 3:168864339-168865711. Error was invalid region `3:168864340-168865711`
[2016-04-15T03:50Z] 2016-04-14 20:50:51 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:50:51,093 - WARNING - Could not retrieve variants from source file in region 3:161221494-161221895. Error was invalid region `3:161221495-161221895`
[2016-04-15T03:50Z] 2016-04-14 20:50:51 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:50:51,204 - WARNING - Could not retrieve variants from source file in region 3:172428571-172428972. Error was invalid region `3:172428572-172428972`
[2016-04-15T03:50Z] 2016-04-14 20:50:51 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:50:51,403 - WARNING - Could not retrieve variants from source file in region 3:165554914-165555315. Error was invalid region `3:165554915-165555315`
[2016-04-15T03:50Z] 2016-04-14 20:50:52 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:50:52,008 - WARNING - Could not retrieve variants from source file in region 3:171320696-171338427. Error was invalid region `3:171320697-171338427`
[2016-04-15T03:50Z] 2016-04-14 20:50:52 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:50:52,321 - WARNING - Could not retrieve variants from source file in region 3:172224092-172235468. Error was invalid region `3:172224093-172235468`
[2016-04-15T03:50Z] 2016-04-14 20:50:54 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:50:54,449 - WARNING - Could not retrieve variants from source file in region 3:172046650-172047051. Error was invalid region `3:172046651-172047051`
[2016-04-15T03:50Z] 2016-04-14 20:50:55 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:50:55,622 - WARNING - Could not retrieve variants from source file in region 3:172428571-172428972. Error was invalid region `3:172428572-172428972`
[2016-04-15T03:50Z] 2016-04-14 20:50:57 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:50:57,015 - WARNING - Could not retrieve variants from source file in region 3:171395257-171395658. Error was invalid region `3:171395258-171395658`
[2016-04-15T03:50Z] 2016-04-14 20:50:57 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:50:57,931 - WARNING - Could not retrieve variants from source file in region 3:161221494-161221895. Error was invalid region `3:161221495-161221895`
[2016-04-15T03:50Z] 2016-04-14 20:50:58 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:50:58,175 - WARNING - Could not retrieve variants from source file in region 3:170715619-170732490. Error was invalid region `3:170715620-170732490`
[2016-04-15T03:50Z] 2016-04-14 20:50:58 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:50:58,237 - WARNING - Could not retrieve variants from source file in region 3:165554914-165555315. Error was invalid region `3:165554915-165555315`
[2016-04-15T03:50Z] 2016-04-14 20:50:58 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:50:58,902 - WARNING - Could not retrieve variants from source file in region 3:167506726-167510662. Error was invalid region `3:167506727-167510662`
[2016-04-15T03:50Z] 2016-04-14 20:50:59 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:50:59,470 - WARNING - Could not retrieve variants from source file in region 3:172224092-172235468. Error was invalid region `3:172224093-172235468`
[2016-04-15T03:51Z] 2016-04-14 20:51:00 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:51:00,169 - WARNING - Could not retrieve variants from source file in region 3:164764508-164793948. Error was invalid region `3:164764509-164793948`
[2016-04-15T03:51Z] 2016-04-14 20:51:02 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:51:02,543 - WARNING - Could not retrieve variants from source file in region 3:161221494-161221895. Error was invalid region `3:161221495-161221895`
[2016-04-15T03:51Z] 2016-04-14 20:51:03 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:51:03,319 - WARNING - Could not retrieve variants from source file in region 3:167506726-167510662. Error was invalid region `3:167506727-167510662`
[2016-04-15T03:51Z] 2016-04-14 20:51:04 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:51:04,307 - WARNING - Could not retrieve variants from source file in region 3:172224092-172235468. Error was invalid region `3:172224093-172235468`
[2016-04-15T03:51Z] 2016-04-14 20:51:04 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:51:04,770 - WARNING - Could not retrieve variants from source file in region 3:172046650-172047051. Error was invalid region `3:172046651-172047051`
[2016-04-15T03:51Z] 2016-04-14 20:51:08 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:51:08,521 - WARNING - Could not retrieve variants from source file in region 3:171968866-171969267. Error was invalid region `3:171968867-171969267`
[2016-04-15T03:51Z] 2016-04-14 20:51:12 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:51:12,911 - WARNING - Could not retrieve variants from source file in region 3:159996850-159997251. Error was invalid region `3:159996851-159997251`
[2016-04-15T03:51Z] 2016-04-14 20:51:12 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:51:12,988 - WARNING - Could not retrieve variants from source file in region 3:171968866-171969267. Error was invalid region `3:171968867-171969267`
[2016-04-15T03:51Z] 2016-04-14 20:51:13 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:51:13,136 - WARNING - Could not retrieve variants from source file in region 3:170198687-170199088. Error was invalid region `3:170198688-170199088`
[2016-04-15T03:51Z] 2016-04-14 20:51:13 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:51:13,292 - WARNING - Could not retrieve variants from source file in region 3:161077419-161077820. Error was invalid region `3:161077420-161077820`
[2016-04-15T03:51Z] 2016-04-14 20:51:13 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:51:13,980 - WARNING - Could not retrieve variants from source file in region 3:170198687-170199088. Error was invalid region `3:170198688-170199088`
[2016-04-15T03:51Z] 2016-04-14 20:51:14 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:51:14,807 - WARNING - Could not retrieve variants from source file in region 3:159557742-159558143. Error was invalid region `3:159557743-159558143`
[2016-04-15T03:51Z] 2016-04-14 20:51:15 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:51:15,744 - WARNING - Could not retrieve variants from source file in region 3:170078021-170078422. Error was invalid region `3:170078022-170078422`
[2016-04-15T03:51Z] 2016-04-14 20:51:16 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:51:16,026 - WARNING - Could not retrieve variants from source file in region 3:171087258-171087659. Error was invalid region `3:171087259-171087659`
[2016-04-15T03:51Z] 2016-04-14 20:51:16 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:51:16,398 - WARNING - Could not retrieve variants from source file in region 3:161077419-161077820. Error was invalid region `3:161077420-161077820`
[2016-04-15T03:51Z] 2016-04-14 20:51:16 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:51:16,662 - WARNING - Could not retrieve variants from source file in region 3:161077419-161077820. Error was invalid region `3:161077420-161077820`
[2016-04-15T03:51Z] 2016-04-14 20:51:19 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:51:19,149 - WARNING - Could not retrieve variants from source file in region 3:170078021-170078422. Error was invalid region `3:170078022-170078422`
[2016-04-15T03:51Z] 2016-04-14 20:51:19 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:51:19,389 - WARNING - Could not retrieve variants from source file in region 3:171087258-171087659. Error was invalid region `3:171087259-171087659`
[2016-04-15T03:51Z] 2016-04-14 20:51:19 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:51:19,732 - WARNING - Could not retrieve variants from source file in region 3:171087258-171087659. Error was invalid region `3:171087259-171087659`
[2016-04-15T03:51Z] 2016-04-14 20:51:19 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:51:19,751 - WARNING - Could not retrieve variants from source file in region 3:170078021-170078422. Error was invalid region `3:170078022-170078422`
[2016-04-15T03:51Z] 2016-04-14 20:51:20 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:51:20,629 - WARNING - Could not retrieve variants from source file in region 3:158980534-158992693. Error was invalid region `3:158980535-158992693`
[2016-04-15T03:51Z] 2016-04-14 20:51:23 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:51:23,129 - WARNING - Could not retrieve variants from source file in region 3:158980534-158992693. Error was invalid region `3:158980535-158992693`
[2016-04-15T03:51Z] 2016-04-14 20:51:23 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:51:23,317 - WARNING - Could not retrieve variants from source file in region 3:158980534-158992693. Error was invalid region `3:158980535-158992693`
[2016-04-15T03:51Z] ['bcbio-variation-recall', 'square', '-Xms750m', '-Xmx7280m', '-XX:+UseSerialGC', '-c', 16, '-r', u'3:174814580-190326970', '--caller', 'platypus', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/3/Batch1-3_174814579_190326970.vcf.gz', '/mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/3/Batch1-3_174814579_190326970.vcf-inputs.txt'] in region: 3:174814580-190326970
[2016-04-15T03:51Z] 2016-04-14 20:51:39 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:51:39,000 - WARNING - Could not retrieve variants from source file in region 3:184428692-184429604. Error was invalid region `3:184428693-184429604`
[2016-04-15T03:51Z] 2016-04-14 20:51:40 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:51:40,280 - WARNING - Could not retrieve variants from source file in region 3:189507307-189507708. Error was invalid region `3:189507308-189507708`
[2016-04-15T03:51Z] 2016-04-14 20:51:40 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:51:40,492 - WARNING - Could not retrieve variants from source file in region 3:182681529-182681930. Error was invalid region `3:182681530-182681930`
[2016-04-15T03:51Z] 2016-04-14 20:51:40 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:51:40,885 - WARNING - Could not retrieve variants from source file in region 3:183432772-183433173. Error was invalid region `3:183432773-183433173`
[2016-04-15T03:51Z] 2016-04-14 20:51:40 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:51:40,920 - WARNING - Could not retrieve variants from source file in region 3:189349036-189349437. Error was invalid region `3:189349037-189349437`
[2016-04-15T03:51Z] 2016-04-14 20:51:41 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:51:41,156 - WARNING - Could not retrieve variants from source file in region 3:184700145-184700616. Error was invalid region `3:184700146-184700616`
[2016-04-15T03:51Z] 2016-04-14 20:51:41 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:51:41,230 - WARNING - Could not retrieve variants from source file in region 3:186301492-186301893. Error was invalid region `3:186301493-186301893`
[2016-04-15T03:51Z] 2016-04-14 20:51:41 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:51:41,516 - WARNING - Could not retrieve variants from source file in region 3:185009480-185009882. Error was invalid region `3:185009481-185009882`
[2016-04-15T03:51Z] 2016-04-14 20:51:41 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:51:41,713 - WARNING - Could not retrieve variants from source file in region 3:184633036-184647603. Error was invalid region `3:184633037-184647603`
[2016-04-15T03:51Z] 2016-04-14 20:51:41 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:51:41,874 - WARNING - Could not retrieve variants from source file in region 3:190105862-190106264. Error was invalid region `3:190105863-190106264`
[2016-04-15T03:51Z] 2016-04-14 20:51:41 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:51:41,875 - WARNING - Could not retrieve variants from source file in region 3:188590235-188590636. Error was invalid region `3:188590236-188590636`
[2016-04-15T03:51Z] 2016-04-14 20:51:41 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:51:41,910 - WARNING - Could not retrieve variants from source file in region 3:187443103-187447222. Error was invalid region `3:187443104-187447222`
[2016-04-15T03:51Z] 2016-04-14 20:51:45 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:51:45,075 - WARNING - Could not retrieve variants from source file in region 3:184428692-184429604. Error was invalid region `3:184428693-184429604`
[2016-04-15T03:51Z] 2016-04-14 20:51:46 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:51:46,943 - WARNING - Could not retrieve variants from source file in region 3:189507307-189507708. Error was invalid region `3:189507308-189507708`
[2016-04-15T03:51Z] 2016-04-14 20:51:47 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:51:47,434 - WARNING - Could not retrieve variants from source file in region 3:189598759-189599160. Error was invalid region `3:189598760-189599160`
[2016-04-15T03:51Z] 2016-04-14 20:51:48 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:51:48,375 - WARNING - Could not retrieve variants from source file in region 3:182681529-182681930. Error was invalid region `3:182681530-182681930`
[2016-04-15T03:51Z] 2016-04-14 20:51:48 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:51:48,923 - WARNING - Could not retrieve variants from source file in region 3:185229253-185229654. Error was invalid region `3:185229254-185229654`
[2016-04-15T03:51Z] 2016-04-14 20:51:49 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:51:49,301 - WARNING - Could not retrieve variants from source file in region 3:183432772-183433173. Error was invalid region `3:183432773-183433173`
[2016-04-15T03:51Z] 2016-04-14 20:51:49 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:51:49,931 - WARNING - Could not retrieve variants from source file in region 3:189349036-189349437. Error was invalid region `3:189349037-189349437`
[2016-04-15T03:51Z] 2016-04-14 20:51:50 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:51:50,238 - WARNING - Could not retrieve variants from source file in region 3:184633036-184647603. Error was invalid region `3:184633037-184647603`
[2016-04-15T03:51Z] 2016-04-14 20:51:50 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:51:50,383 - WARNING - Could not retrieve variants from source file in region 3:188590235-188590636. Error was invalid region `3:188590236-188590636`
[2016-04-15T03:51Z] 2016-04-14 20:51:50 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:51:50,760 - WARNING - Could not retrieve variants from source file in region 3:184428692-184429604. Error was invalid region `3:184428693-184429604`
[2016-04-15T03:51Z] 2016-04-14 20:51:50 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:51:50,837 - WARNING - Could not retrieve variants from source file in region 3:184037322-184099568. Error was invalid region `3:184037323-184099568`
[2016-04-15T03:51Z] 2016-04-14 20:51:51 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:51:51,871 - WARNING - Could not retrieve variants from source file in region 3:189507307-189507708. Error was invalid region `3:189507308-189507708`
[2016-04-15T03:51Z] 2016-04-14 20:51:53 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:51:53,369 - WARNING - Could not retrieve variants from source file in region 3:189598759-189599160. Error was invalid region `3:189598760-189599160`
[2016-04-15T03:51Z] 2016-04-14 20:51:54 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:51:54,552 - WARNING - Could not retrieve variants from source file in region 3:182681529-182681930. Error was invalid region `3:182681530-182681930`
[2016-04-15T03:51Z] 2016-04-14 20:51:56 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:51:56,387 - WARNING - Could not retrieve variants from source file in region 3:185009480-185009882. Error was invalid region `3:185009481-185009882`
[2016-04-15T03:51Z] 2016-04-14 20:51:57 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:51:57,741 - WARNING - Could not retrieve variants from source file in region 3:190105862-190106264. Error was invalid region `3:190105863-190106264`
[2016-04-15T03:51Z] 2016-04-14 20:51:57 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:51:57,952 - WARNING - Could not retrieve variants from source file in region 3:184633036-184647603. Error was invalid region `3:184633037-184647603`
[2016-04-15T03:51Z] 2016-04-14 20:51:58 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:51:58,680 - WARNING - Could not retrieve variants from source file in region 3:184700145-184700616. Error was invalid region `3:184700146-184700616`
[2016-04-15T03:51Z] 2016-04-14 20:51:58 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:51:58,727 - WARNING - Could not retrieve variants from source file in region 3:188590235-188590636. Error was invalid region `3:188590236-188590636`
[2016-04-15T03:51Z] 2016-04-14 20:51:58 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:51:58,738 - WARNING - Could not retrieve variants from source file in region 3:189349036-189349437. Error was invalid region `3:189349037-189349437`
[2016-04-15T03:52Z] 2016-04-14 20:52:09 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:52:09,770 - WARNING - Could not retrieve variants from source file in region 3:185795644-185796045. Error was invalid region `3:185795645-185796045`
[2016-04-15T03:52Z] 2016-04-14 20:52:10 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:52:10,179 - WARNING - Could not retrieve variants from source file in region 3:182631581-182635535. Error was invalid region `3:182631582-182635535`
[2016-04-15T03:52Z] 2016-04-14 20:52:11 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:52:11,130 - WARNING - Could not retrieve variants from source file in region 3:184293558-184299357. Error was invalid region `3:184293559-184299357`
[2016-04-15T03:52Z] 2016-04-14 20:52:11 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:52:11,713 - WARNING - Could not retrieve variants from source file in region 3:184293558-184299357. Error was invalid region `3:184293559-184299357`
[2016-04-15T03:52Z] 2016-04-14 20:52:11 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:52:11,893 - WARNING - Could not retrieve variants from source file in region 3:185080677-185081078. Error was invalid region `3:185080678-185081078`
[2016-04-15T03:52Z] 2016-04-14 20:52:12 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:52:12,661 - WARNING - Could not retrieve variants from source file in region 3:183368005-183369081. Error was invalid region `3:183368006-183369081`
[2016-04-15T03:52Z] 2016-04-14 20:52:12 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:52:12,740 - WARNING - Could not retrieve variants from source file in region 3:184909922-184911341. Error was invalid region `3:184909923-184911341`
[2016-04-15T03:52Z] 2016-04-14 20:52:12 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:52:12,783 - WARNING - Could not retrieve variants from source file in region 3:186256982-186257383. Error was invalid region `3:186256983-186257383`
[2016-04-15T03:52Z] 2016-04-14 20:52:13 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:52:13,676 - WARNING - Could not retrieve variants from source file in region 3:182925193-182925594. Error was invalid region `3:182925194-182925594`
[2016-04-15T03:52Z] 2016-04-14 20:52:15 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:52:15,386 - WARNING - Could not retrieve variants from source file in region 3:179096297-179096698. Error was invalid region `3:179096298-179096698`
[2016-04-15T03:52Z] 2016-04-14 20:52:16 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:52:16,128 - WARNING - Could not retrieve variants from source file in region 3:190030469-190030870. Error was invalid region `3:190030470-190030870`
[2016-04-15T03:52Z] 2016-04-14 20:52:17 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:52:17,221 - WARNING - Could not retrieve variants from source file in region 3:187416423-187416909. Error was invalid region `3:187416424-187416909`
[2016-04-15T03:52Z] 2016-04-14 20:52:17 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:52:17,301 - WARNING - Could not retrieve variants from source file in region 3:185080677-185081078. Error was invalid region `3:185080678-185081078`
[2016-04-15T03:52Z] 2016-04-14 20:52:17 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:52:17,746 - WARNING - Could not retrieve variants from source file in region 3:185080677-185081078. Error was invalid region `3:185080678-185081078`
[2016-04-15T03:52Z] 2016-04-14 20:52:18 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:52:18,299 - WARNING - Could not retrieve variants from source file in region 3:183368005-183369081. Error was invalid region `3:183368006-183369081`
[2016-04-15T03:52Z] 2016-04-14 20:52:18 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:52:18,633 - WARNING - Could not retrieve variants from source file in region 3:182925193-182925594. Error was invalid region `3:182925194-182925594`
[2016-04-15T03:52Z] 2016-04-14 20:52:19 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:52:19,624 - WARNING - Could not retrieve variants from source file in region 3:185795644-185796045. Error was invalid region `3:185795645-185796045`
[2016-04-15T03:52Z] 2016-04-14 20:52:20 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:52:20,128 - WARNING - Could not retrieve variants from source file in region 3:182631581-182635535. Error was invalid region `3:182631582-182635535`
[2016-04-15T03:52Z] 2016-04-14 20:52:20 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:52:20,441 - WARNING - Could not retrieve variants from source file in region 3:179096297-179096698. Error was invalid region `3:179096298-179096698`
[2016-04-15T03:52Z] 2016-04-14 20:52:21 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:52:21,250 - WARNING - Could not retrieve variants from source file in region 3:190030469-190030870. Error was invalid region `3:190030470-190030870`
[2016-04-15T03:52Z] 2016-04-14 20:52:21 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:52:21,309 - WARNING - Could not retrieve variants from source file in region 3:188327250-188327651. Error was invalid region `3:188327251-188327651`
[2016-04-15T03:52Z] 2016-04-14 20:52:21 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:52:21,879 - WARNING - Could not retrieve variants from source file in region 3:190030469-190030870. Error was invalid region `3:190030470-190030870`
[2016-04-15T03:52Z] 2016-04-14 20:52:23 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:52:23,189 - WARNING - Could not retrieve variants from source file in region 3:187416423-187416909. Error was invalid region `3:187416424-187416909`
[2016-04-15T03:52Z] 2016-04-14 20:52:23 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:52:23,965 - WARNING - Could not retrieve variants from source file in region 3:184909922-184911341. Error was invalid region `3:184909923-184911341`
[2016-04-15T03:52Z] 2016-04-14 20:52:24 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:52:24,593 - WARNING - Could not retrieve variants from source file in region 3:182925193-182925594. Error was invalid region `3:182925194-182925594`
[2016-04-15T03:52Z] 2016-04-14 20:52:25 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:52:25,589 - WARNING - Could not retrieve variants from source file in region 3:179096297-179096698. Error was invalid region `3:179096298-179096698`
[2016-04-15T03:52Z] 2016-04-14 20:52:26 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:52:26,305 - WARNING - Could not retrieve variants from source file in region 3:178545815-178560771. Error was invalid region `3:178545816-178560771`
[2016-04-15T03:52Z] 2016-04-14 20:52:28 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:52:28,473 - WARNING - Could not retrieve variants from source file in region 3:187416423-187416909. Error was invalid region `3:187416424-187416909`
[2016-04-15T03:52Z] 2016-04-14 20:52:31 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:52:31,395 - WARNING - Could not retrieve variants from source file in region 3:178545815-178560771. Error was invalid region `3:178545816-178560771`
[2016-04-15T03:52Z] 2016-04-14 20:52:33 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:52:33,133 - WARNING - Could not retrieve variants from source file in region 3:185989885-186006808. Error was invalid region `3:185989886-186006808`
[2016-04-15T03:52Z] 2016-04-14 20:52:34 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:52:34,874 - WARNING - Could not retrieve variants from source file in region 3:185989885-186006808. Error was invalid region `3:185989886-186006808`
[2016-04-15T03:52Z] 2016-04-14 20:52:36 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:52:36,880 - WARNING - Could not retrieve variants from source file in region 3:178545815-178560771. Error was invalid region `3:178545816-178560771`
[2016-04-15T03:52Z] 2016-04-14 20:52:36 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:52:36,946 - WARNING - Could not retrieve variants from source file in region 3:183752753-183778200. Error was invalid region `3:183752754-183778200`
[2016-04-15T03:52Z] 2016-04-14 20:52:39 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:52:39,018 - WARNING - Could not retrieve variants from source file in region 3:183211695-183226304. Error was invalid region `3:183211696-183226304`
[2016-04-15T03:52Z] 2016-04-14 20:52:42 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:52:42,291 - WARNING - Could not retrieve variants from source file in region 3:186917540-186917941. Error was invalid region `3:186917541-186917941`
[2016-04-15T03:52Z] 2016-04-14 20:52:42 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:52:42,541 - WARNING - Could not retrieve variants from source file in region 3:180365745-180366146. Error was invalid region `3:180365746-180366146`
[2016-04-15T03:52Z] 2016-04-14 20:52:42 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:52:42,776 - WARNING - Could not retrieve variants from source file in region 3:182790038-182790439. Error was invalid region `3:182790039-182790439`
[2016-04-15T03:52Z] 2016-04-14 20:52:43 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:52:43,552 - WARNING - Could not retrieve variants from source file in region 3:183752753-183778200. Error was invalid region `3:183752754-183778200`
[2016-04-15T03:52Z] 2016-04-14 20:52:43 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:52:43,586 - WARNING - Could not retrieve variants from source file in region 3:183881903-183904239. Error was invalid region `3:183881904-183904239`
[2016-04-15T03:52Z] 2016-04-14 20:52:44 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:52:44,321 - WARNING - Could not retrieve variants from source file in region 3:183818205-183823766. Error was invalid region `3:183818206-183823766`
[2016-04-15T03:52Z] 2016-04-14 20:52:45 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:52:45,051 - WARNING - Could not retrieve variants from source file in region 3:182849528-182872152. Error was invalid region `3:182849529-182872152`
[2016-04-15T03:52Z] 2016-04-14 20:52:45 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:52:45,170 - WARNING - Could not retrieve variants from source file in region 3:178968423-178984765. Error was invalid region `3:178968424-178984765`
[2016-04-15T03:52Z] 2016-04-14 20:52:49 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:52:49,043 - WARNING - Could not retrieve variants from source file in region 3:179690883-179692166. Error was invalid region `3:179690884-179692166`
[2016-04-15T03:52Z] 2016-04-14 20:52:49 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:52:49,266 - WARNING - Could not retrieve variants from source file in region 3:186917540-186917941. Error was invalid region `3:186917541-186917941`
[2016-04-15T03:52Z] 2016-04-14 20:52:50 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:52:50,010 - WARNING - Could not retrieve variants from source file in region 3:182790038-182790439. Error was invalid region `3:182790039-182790439`
[2016-04-15T03:52Z] 2016-04-14 20:52:50 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:52:50,915 - WARNING - Could not retrieve variants from source file in region 3:187088445-187089221. Error was invalid region `3:187088446-187089221`
[2016-04-15T03:52Z] 2016-04-14 20:52:50 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:52:50,989 - WARNING - Could not retrieve variants from source file in region 3:183818205-183823766. Error was invalid region `3:183818206-183823766`
[2016-04-15T03:52Z] 2016-04-14 20:52:51 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:52:51,324 - WARNING - Could not retrieve variants from source file in region 3:183881903-183904239. Error was invalid region `3:183881904-183904239`
[2016-04-15T03:52Z] 2016-04-14 20:52:51 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:52:51,389 - WARNING - Could not retrieve variants from source file in region 3:183211695-183226304. Error was invalid region `3:183211696-183226304`
[2016-04-15T03:52Z] 2016-04-14 20:52:52 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:52:52,293 - WARNING - Could not retrieve variants from source file in region 3:175472836-175473237. Error was invalid region `3:175472837-175473237`
[2016-04-15T03:52Z] 2016-04-14 20:52:56 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:52:56,378 - WARNING - Could not retrieve variants from source file in region 3:182790038-182790439. Error was invalid region `3:182790039-182790439`
[2016-04-15T03:52Z] 2016-04-14 20:52:58 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:52:58,350 - WARNING - Could not retrieve variants from source file in region 3:175472836-175473237. Error was invalid region `3:175472837-175473237`
[2016-04-15T03:52Z] 2016-04-14 20:52:58 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:52:58,417 - WARNING - Could not retrieve variants from source file in region 3:178968423-178984765. Error was invalid region `3:178968424-178984765`
[2016-04-15T03:53Z] 2016-04-14 20:53:00 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:53:00,088 - WARNING - Could not retrieve variants from source file in region 3:183685323-183702465. Error was invalid region `3:183685324-183702465`
[2016-04-15T03:53Z] 2016-04-14 20:53:01 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:53:01,375 - WARNING - Could not retrieve variants from source file in region 3:179298788-179299189. Error was invalid region `3:179298789-179299189`
[2016-04-15T03:53Z] 2016-04-14 20:53:02 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:53:02,105 - WARNING - Could not retrieve variants from source file in region 3:185330954-185331355. Error was invalid region `3:185330955-185331355`
[2016-04-15T03:53Z] 2016-04-14 20:53:04 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:53:04,645 - WARNING - Could not retrieve variants from source file in region 3:175472836-175473237. Error was invalid region `3:175472837-175473237`
[2016-04-15T03:53Z] 2016-04-14 20:53:05 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:53:05,868 - WARNING - Could not retrieve variants from source file in region 3:183685323-183702465. Error was invalid region `3:183685324-183702465`
[2016-04-15T03:53Z] 2016-04-14 20:53:06 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:53:06,216 - WARNING - Could not retrieve variants from source file in region 3:185303807-185304208. Error was invalid region `3:185303808-185304208`
[2016-04-15T03:53Z] 2016-04-14 20:53:06 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:53:06,836 - WARNING - Could not retrieve variants from source file in region 3:179298788-179299189. Error was invalid region `3:179298789-179299189`
[2016-04-15T03:53Z] 2016-04-14 20:53:07 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:53:07,613 - WARNING - Could not retrieve variants from source file in region 3:183027331-183027732. Error was invalid region `3:183027332-183027732`
[2016-04-15T03:53Z] 2016-04-14 20:53:08 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:53:08,079 - WARNING - Could not retrieve variants from source file in region 3:182754998-182755399. Error was invalid region `3:182754999-182755399`
[2016-04-15T03:53Z] 2016-04-14 20:53:09 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:53:09,201 - WARNING - Could not retrieve variants from source file in region 3:178785338-178785739. Error was invalid region `3:178785339-178785739`
[2016-04-15T03:53Z] 2016-04-14 20:53:09 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:53:09,239 - WARNING - Could not retrieve variants from source file in region 3:183597260-183601688. Error was invalid region `3:183597261-183601688`
[2016-04-15T03:53Z] 2016-04-14 20:53:10 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:53:10,160 - WARNING - Could not retrieve variants from source file in region 3:186507546-186509707. Error was invalid region `3:186507547-186509707`
[2016-04-15T03:53Z] 2016-04-14 20:53:10 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:53:10,858 - WARNING - Could not retrieve variants from source file in region 3:180334412-180334813. Error was invalid region `3:180334413-180334813`
[2016-04-15T03:53Z] 2016-04-14 20:53:10 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:53:10,911 - WARNING - Could not retrieve variants from source file in region 3:183685323-183702465. Error was invalid region `3:183685324-183702465`
[2016-04-15T03:53Z] 2016-04-14 20:53:11 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:53:11,880 - WARNING - Could not retrieve variants from source file in region 3:179298788-179299189. Error was invalid region `3:179298789-179299189`
[2016-04-15T03:53Z] 2016-04-14 20:53:13 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:53:13,015 - WARNING - Could not retrieve variants from source file in region 3:182754998-182755399. Error was invalid region `3:182754999-182755399`
[2016-04-15T03:53Z] 2016-04-14 20:53:13 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:53:13,932 - WARNING - Could not retrieve variants from source file in region 3:178785338-178785739. Error was invalid region `3:178785339-178785739`
[2016-04-15T03:53Z] 2016-04-14 20:53:14 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:53:14,178 - WARNING - Could not retrieve variants from source file in region 3:183597260-183601688. Error was invalid region `3:183597261-183601688`
[2016-04-15T03:53Z] 2016-04-14 20:53:16 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:53:16,885 - WARNING - Could not retrieve variants from source file in region 3:183027331-183027732. Error was invalid region `3:183027332-183027732`
[2016-04-15T03:53Z] 2016-04-14 20:53:18 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:53:18,281 - WARNING - Could not retrieve variants from source file in region 3:175344932-175345333. Error was invalid region `3:175344933-175345333`
[2016-04-15T03:53Z] 2016-04-14 20:53:18 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:53:18,876 - WARNING - Could not retrieve variants from source file in region 3:178785338-178785739. Error was invalid region `3:178785339-178785739`
[2016-04-15T03:53Z] 2016-04-14 20:53:19 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:53:19,206 - WARNING - Could not retrieve variants from source file in region 3:183597260-183601688. Error was invalid region `3:183597261-183601688`
[2016-04-15T03:53Z] 2016-04-14 20:53:23 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:53:23,004 - WARNING - Could not retrieve variants from source file in region 3:175344932-175345333. Error was invalid region `3:175344933-175345333`
[2016-04-15T03:53Z] 2016-04-14 20:53:24 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:53:24,021 - WARNING - Could not retrieve variants from source file in region 3:179137062-179144131. Error was invalid region `3:179137063-179144131`
[2016-04-15T03:53Z] 2016-04-14 20:53:27 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:53:27,568 - WARNING - Could not retrieve variants from source file in region 3:175344932-175345333. Error was invalid region `3:175344933-175345333`
[2016-04-15T03:53Z] 2016-04-14 20:53:29 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:53:29,972 - WARNING - Could not retrieve variants from source file in region 3:175164868-175189637. Error was invalid region `3:175164869-175189637`
[2016-04-15T03:53Z] 2016-04-14 20:53:30 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:53:30,105 - WARNING - Could not retrieve variants from source file in region 3:186337502-186395762. Error was invalid region `3:186337503-186395762`
[2016-04-15T03:53Z] 2016-04-14 20:53:33 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:53:33,758 - WARNING - Could not retrieve variants from source file in region 3:175164868-175189637. Error was invalid region `3:175164869-175189637`
[2016-04-15T03:53Z] 2016-04-14 20:53:34 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:53:34,022 - WARNING - Could not retrieve variants from source file in region 3:175164868-175189637. Error was invalid region `3:175164869-175189637`
[2016-04-15T03:53Z] 2016-04-14 20:53:35 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:53:35,899 - WARNING - Could not retrieve variants from source file in region 3:174951545-174951946. Error was invalid region `3:174951546-174951946`
[2016-04-15T03:53Z] 2016-04-14 20:53:35 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:53:35,908 - WARNING - Could not retrieve variants from source file in region 3:174951545-174951946. Error was invalid region `3:174951546-174951946`
[2016-04-15T03:53Z] 2016-04-14 20:53:35 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:53:35,913 - WARNING - Could not retrieve variants from source file in region 3:174951545-174951946. Error was invalid region `3:174951546-174951946`
[2016-04-15T03:53Z] ['bcbio-variation-recall', 'square', '-Xms750m', '-Xmx7280m', '-XX:+UseSerialGC', '-c', 16, '-r', u'3:190333064-198022430', '--caller', 'platypus', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/3/Batch1-3_190333063_198022430.vcf.gz', '/mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/3/Batch1-3_190333063_198022430.vcf-inputs.txt'] in region: 3:190333064-198022430
[2016-04-15T03:53Z] 2016-04-14 20:53:50 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:53:50,547 - WARNING - Could not retrieve variants from source file in region 3:197879919-197880329. Error was invalid region `3:197879920-197880329`
[2016-04-15T03:53Z] 2016-04-14 20:53:52 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:53:52,933 - WARNING - Could not retrieve variants from source file in region 3:196280997-196281398. Error was invalid region `3:196280998-196281398`
[2016-04-15T03:53Z] 2016-04-14 20:53:53 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:53:53,156 - WARNING - Could not retrieve variants from source file in region 3:194118663-194119064. Error was invalid region `3:194118664-194119064`
[2016-04-15T03:53Z] 2016-04-14 20:53:53 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:53:53,184 - WARNING - Could not retrieve variants from source file in region 3:193334780-193335181. Error was invalid region `3:193334781-193335181`
[2016-04-15T03:53Z] 2016-04-14 20:53:53 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:53:53,230 - WARNING - Could not retrieve variants from source file in region 3:191178982-191179383. Error was invalid region `3:191178983-191179383`
[2016-04-15T03:53Z] 2016-04-14 20:53:53 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:53:53,231 - WARNING - Could not retrieve variants from source file in region 3:190999706-191000107. Error was invalid region `3:190999707-191000107`
[2016-04-15T03:53Z] 2016-04-14 20:53:53 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:53:53,833 - WARNING - Could not retrieve variants from source file in region 3:197427346-197432226. Error was invalid region `3:197427347-197432226`
[2016-04-15T03:53Z] 2016-04-14 20:53:54 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:53:54,128 - WARNING - Could not retrieve variants from source file in region 3:196159126-196159528. Error was invalid region `3:196159127-196159528`
[2016-04-15T03:53Z] 2016-04-14 20:53:57 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:53:57,959 - WARNING - Could not retrieve variants from source file in region 3:195800600-195801001. Error was invalid region `3:195800601-195801001`
[2016-04-15T03:53Z] 2016-04-14 20:53:58 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:53:58,379 - WARNING - Could not retrieve variants from source file in region 3:196555053-196555454. Error was invalid region `3:196555054-196555454`
[2016-04-15T03:53Z] 2016-04-14 20:53:59 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:53:59,724 - WARNING - Could not retrieve variants from source file in region 3:196280997-196281398. Error was invalid region `3:196280998-196281398`
[2016-04-15T03:54Z] 2016-04-14 20:54:00 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:54:00,153 - WARNING - Could not retrieve variants from source file in region 3:196118491-196118892. Error was invalid region `3:196118492-196118892`
[2016-04-15T03:54Z] 2016-04-14 20:54:00 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:54:00,340 - WARNING - Could not retrieve variants from source file in region 3:191178982-191179383. Error was invalid region `3:191178983-191179383`
[2016-04-15T03:54Z] 2016-04-14 20:54:00 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:54:00,954 - WARNING - Could not retrieve variants from source file in region 3:190999706-191000107. Error was invalid region `3:190999707-191000107`
[2016-04-15T03:54Z] 2016-04-14 20:54:01 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:54:01,945 - WARNING - Could not retrieve variants from source file in region 3:194118663-194119064. Error was invalid region `3:194118664-194119064`
[2016-04-15T03:54Z] 2016-04-14 20:54:02 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:54:02,004 - WARNING - Could not retrieve variants from source file in region 3:194900928-194901329. Error was invalid region `3:194900929-194901329`
[2016-04-15T03:54Z] 2016-04-14 20:54:08 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:54:08,341 - WARNING - Could not retrieve variants from source file in region 3:197427346-197432226. Error was invalid region `3:197427347-197432226`
[2016-04-15T03:54Z] 2016-04-14 20:54:08 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:54:08,958 - WARNING - Could not retrieve variants from source file in region 3:196159126-196159528. Error was invalid region `3:196159127-196159528`
[2016-04-15T03:54Z] 2016-04-14 20:54:09 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:54:09,093 - WARNING - Could not retrieve variants from source file in region 3:194900928-194901329. Error was invalid region `3:194900929-194901329`
[2016-04-15T03:54Z] 2016-04-14 20:54:09 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:54:09,140 - WARNING - Could not retrieve variants from source file in region 3:194118663-194119064. Error was invalid region `3:194118664-194119064`
[2016-04-15T03:54Z] 2016-04-14 20:54:09 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:54:09,270 - WARNING - Could not retrieve variants from source file in region 3:195594739-195622488. Error was invalid region `3:195594740-195622488`
[2016-04-15T03:54Z] 2016-04-14 20:54:09 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:54:09,373 - WARNING - Could not retrieve variants from source file in region 3:191075691-191100751. Error was invalid region `3:191075692-191100751`
[2016-04-15T03:54Z] 2016-04-14 20:54:22 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:54:22,501 - WARNING - Could not retrieve variants from source file in region 3:196674307-196675163. Error was invalid region `3:196674308-196675163`
[2016-04-15T03:54Z] 2016-04-14 20:54:22 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:54:22,565 - WARNING - Could not retrieve variants from source file in region 3:196198993-196199394. Error was invalid region `3:196198994-196199394`
[2016-04-15T03:54Z] 2016-04-14 20:54:22 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:54:22,995 - WARNING - Could not retrieve variants from source file in region 3:196050517-196054629. Error was invalid region `3:196050518-196054629`
[2016-04-15T03:54Z] 2016-04-14 20:54:23 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:54:23,680 - WARNING - Could not retrieve variants from source file in region 3:197607752-197608157. Error was invalid region `3:197607753-197608157`
[2016-04-15T03:54Z] 2016-04-14 20:54:24 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:54:24,055 - WARNING - Could not retrieve variants from source file in region 3:190578355-190578756. Error was invalid region `3:190578356-190578756`
[2016-04-15T03:54Z] 2016-04-14 20:54:24 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:54:24,587 - WARNING - Could not retrieve variants from source file in region 3:197401741-197402142. Error was invalid region `3:197401742-197402142`
[2016-04-15T03:54Z] 2016-04-14 20:54:26 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:54:26,295 - WARNING - Could not retrieve variants from source file in region 3:193180381-193210958. Error was invalid region `3:193180382-193210958`
[2016-04-15T03:54Z] 2016-04-14 20:54:27 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:54:27,880 - WARNING - Could not retrieve variants from source file in region 3:196674307-196675163. Error was invalid region `3:196674308-196675163`
[2016-04-15T03:54Z] 2016-04-14 20:54:27 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:54:27,949 - WARNING - Could not retrieve variants from source file in region 3:196386753-196387154. Error was invalid region `3:196386754-196387154`
[2016-04-15T03:54Z] 2016-04-14 20:54:28 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:54:28,189 - WARNING - Could not retrieve variants from source file in region 3:196198993-196199394. Error was invalid region `3:196198994-196199394`
[2016-04-15T03:54Z] 2016-04-14 20:54:32 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:54:32,779 - WARNING - Could not retrieve variants from source file in region 3:194061695-194081825. Error was invalid region `3:194061696-194081825`
[2016-04-15T03:54Z] 2016-04-14 20:54:32 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:54:32,804 - WARNING - Could not retrieve variants from source file in region 3:196386753-196387154. Error was invalid region `3:196386754-196387154`
[2016-04-15T03:54Z] 2016-04-14 20:54:32 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:54:32,865 - WARNING - Could not retrieve variants from source file in region 3:196674307-196675163. Error was invalid region `3:196674308-196675163`
[2016-04-15T03:54Z] 2016-04-14 20:54:33 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:54:33,121 - WARNING - Could not retrieve variants from source file in region 3:196198993-196199394. Error was invalid region `3:196198994-196199394`
[2016-04-15T03:54Z] 2016-04-14 20:54:34 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:54:34,069 - WARNING - Could not retrieve variants from source file in region 3:194337690-194409011. Error was invalid region `3:194337691-194409011`
[2016-04-15T03:54Z] 2016-04-14 20:54:34 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:54:34,194 - WARNING - Could not retrieve variants from source file in region 3:197401741-197402142. Error was invalid region `3:197401742-197402142`
[2016-04-15T03:54Z] 2016-04-14 20:54:34 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:54:34,435 - WARNING - Could not retrieve variants from source file in region 3:196050517-196054629. Error was invalid region `3:196050518-196054629`
[2016-04-15T03:54Z] 2016-04-14 20:54:35 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:54:35,356 - WARNING - Could not retrieve variants from source file in region 3:193180381-193210958. Error was invalid region `3:193180382-193210958`
[2016-04-15T03:54Z] 2016-04-14 20:54:37 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:54:37,429 - WARNING - Could not retrieve variants from source file in region 3:196386753-196387154. Error was invalid region `3:196386754-196387154`
[2016-04-15T03:54Z] 2016-04-14 20:54:39 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:54:39,196 - WARNING - Could not retrieve variants from source file in region 3:194337690-194409011. Error was invalid region `3:194337691-194409011`
[2016-04-15T03:54Z] 2016-04-14 20:54:43 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:54:43,687 - WARNING - Could not retrieve variants from source file in region 3:197566043-197566444. Error was invalid region `3:197566044-197566444`
[2016-04-15T03:54Z] 2016-04-14 20:54:43 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:54:43,863 - WARNING - Could not retrieve variants from source file in region 3:197269769-197270170. Error was invalid region `3:197269770-197270170`
[2016-04-15T03:54Z] 2016-04-14 20:54:43 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:54:43,940 - WARNING - Could not retrieve variants from source file in region 3:197269769-197270170. Error was invalid region `3:197269770-197270170`
[2016-04-15T03:54Z] 2016-04-14 20:54:44 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:54:44,227 - WARNING - Could not retrieve variants from source file in region 3:197495123-197495524. Error was invalid region `3:197495124-197495524`
[2016-04-15T03:54Z] 2016-04-14 20:54:47 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:54:47,074 - WARNING - Could not retrieve variants from source file in region 3:197566043-197566444. Error was invalid region `3:197566044-197566444`
[2016-04-15T03:54Z] 2016-04-14 20:54:47 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:54:47,485 - WARNING - Could not retrieve variants from source file in region 3:197269769-197270170. Error was invalid region `3:197269770-197270170`
[2016-04-15T03:54Z] 2016-04-14 20:54:47 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:54:47,489 - WARNING - Could not retrieve variants from source file in region 3:197495123-197495524. Error was invalid region `3:197495124-197495524`
[2016-04-15T03:54Z] 2016-04-14 20:54:47 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:54:47,552 - WARNING - Could not retrieve variants from source file in region 3:197495123-197495524. Error was invalid region `3:197495124-197495524`
[2016-04-15T03:54Z] 2016-04-14 20:54:48 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:54:48,014 - WARNING - Could not retrieve variants from source file in region 3:197241075-197242793. Error was invalid region `3:197241076-197242793`
[2016-04-15T03:54Z] 2016-04-14 20:54:48 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:54:48,014 - WARNING - Could not retrieve variants from source file in region 3:197024470-197024871. Error was invalid region `3:197024471-197024871`
[2016-04-15T03:54Z] 2016-04-14 20:54:50 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:54:50,252 - WARNING - Could not retrieve variants from source file in region 3:193374753-193386728. Error was invalid region `3:193374754-193386728`
[2016-04-15T03:54Z] 2016-04-14 20:54:50 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:54:50,948 - WARNING - Could not retrieve variants from source file in region 3:193024717-193042966. Error was invalid region `3:193024718-193042966`
[2016-04-15T03:54Z] 2016-04-14 20:54:55 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:54:55,783 - WARNING - Could not retrieve variants from source file in region 3:193080203-193081312. Error was invalid region `3:193080204-193081312`
[2016-04-15T03:54Z] 2016-04-14 20:54:58 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:54:58,291 - WARNING - Could not retrieve variants from source file in region 3:192994332-192994733. Error was invalid region `3:192994333-192994733`
[2016-04-15T03:54Z] 2016-04-14 20:54:58 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:54:58,305 - WARNING - Could not retrieve variants from source file in region 3:192994332-192994733. Error was invalid region `3:192994333-192994733`
[2016-04-15T03:54Z] 2016-04-14 20:54:58 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:54:58,312 - WARNING - Could not retrieve variants from source file in region 3:192994332-192994733. Error was invalid region `3:192994333-192994733`
[2016-04-15T03:55Z] ['bcbio-variation-recall', 'square', '-Xms750m', '-Xmx7280m', '-XX:+UseSerialGC', '-c', 16, '-r', u'4:1-15511864', '--caller', 'platypus', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/4/Batch1-4_0_15511864.vcf.gz', '/mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/4/Batch1-4_0_15511864.vcf-inputs.txt'] in region: 4:1-15511864
[2016-04-15T03:55Z] 2016-04-14 20:55:15 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:55:15,299 - WARNING - Could not retrieve variants from source file in region 4:6422523-6422924. Error was invalid region `4:6422524-6422924`
[2016-04-15T03:55Z] 2016-04-14 20:55:15 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:55:15,311 - WARNING - Could not retrieve variants from source file in region 4:4861534-4861935. Error was invalid region `4:4861535-4861935`
[2016-04-15T03:55Z] 2016-04-14 20:55:15 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:55:15,607 - WARNING - Could not retrieve variants from source file in region 4:3769118-3769519. Error was invalid region `4:3769119-3769519`
[2016-04-15T03:55Z] 2016-04-14 20:55:16 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:55:16,044 - WARNING - Could not retrieve variants from source file in region 4:2209854-2210255. Error was invalid region `4:2209855-2210255`
[2016-04-15T03:55Z] 2016-04-14 20:55:16 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:55:16,498 - WARNING - Could not retrieve variants from source file in region 4:6698456-6698896. Error was invalid region `4:6698457-6698896`
[2016-04-15T03:55Z] 2016-04-14 20:55:16 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:55:16,551 - WARNING - Could not retrieve variants from source file in region 4:4275921-4276322. Error was invalid region `4:4275922-4276322`
[2016-04-15T03:55Z] 2016-04-14 20:55:20 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:55:20,468 - WARNING - Could not retrieve variants from source file in region 4:15004288-15005066. Error was invalid region `4:15004289-15005066`
[2016-04-15T03:55Z] 2016-04-14 20:55:22 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:55:22,627 - WARNING - Could not retrieve variants from source file in region 4:7044146-7044570. Error was invalid region `4:7044147-7044570`
[2016-04-15T03:55Z] 2016-04-14 20:55:24 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:55:24,514 - WARNING - Could not retrieve variants from source file in region 4:4861534-4861935. Error was invalid region `4:4861535-4861935`
[2016-04-15T03:55Z] 2016-04-14 20:55:25 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:55:25,205 - WARNING - Could not retrieve variants from source file in region 4:11400801-11401277. Error was invalid region `4:11400802-11401277`
[2016-04-15T03:55Z] 2016-04-14 20:55:25 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:55:25,213 - WARNING - Could not retrieve variants from source file in region 4:4275921-4276322. Error was invalid region `4:4275922-4276322`
[2016-04-15T03:55Z] 2016-04-14 20:55:25 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:55:25,322 - WARNING - Could not retrieve variants from source file in region 4:6698456-6698896. Error was invalid region `4:6698457-6698896`
[2016-04-15T03:55Z] 2016-04-14 20:55:25 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:55:25,821 - WARNING - Could not retrieve variants from source file in region 4:15004288-15005066. Error was invalid region `4:15004289-15005066`
[2016-04-15T03:55Z] 2016-04-14 20:55:28 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:55:28,563 - WARNING - Could not retrieve variants from source file in region 4:7044146-7044570. Error was invalid region `4:7044147-7044570`
[2016-04-15T03:55Z] 2016-04-14 20:55:30 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:55:30,722 - WARNING - Could not retrieve variants from source file in region 4:6422523-6422924. Error was invalid region `4:6422524-6422924`
[2016-04-15T03:55Z] 2016-04-14 20:55:32 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:55:32,533 - WARNING - Could not retrieve variants from source file in region 4:3769118-3769519. Error was invalid region `4:3769119-3769519`
[2016-04-15T03:55Z] 2016-04-14 20:55:32 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:55:32,843 - WARNING - Could not retrieve variants from source file in region 4:4861534-4861935. Error was invalid region `4:4861535-4861935`
[2016-04-15T03:55Z] 2016-04-14 20:55:32 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:55:32,883 - WARNING - Could not retrieve variants from source file in region 4:5785231-5795602. Error was invalid region `4:5785232-5795602`
[2016-04-15T03:55Z] 2016-04-14 20:55:32 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:55:32,959 - WARNING - Could not retrieve variants from source file in region 4:11400801-11401277. Error was invalid region `4:11400802-11401277`
[2016-04-15T03:55Z] 2016-04-14 20:55:33 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:55:33,130 - WARNING - Could not retrieve variants from source file in region 4:8108104-8129572. Error was invalid region `4:8108105-8129572`
[2016-04-15T03:55Z] 2016-04-14 20:55:33 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:55:33,130 - WARNING - Could not retrieve variants from source file in region 4:4275921-4276322. Error was invalid region `4:4275922-4276322`
[2016-04-15T03:55Z] 2016-04-14 20:55:33 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:55:33,323 - WARNING - Could not retrieve variants from source file in region 4:6698456-6698896. Error was invalid region `4:6698457-6698896`
[2016-04-15T03:55Z] 2016-04-14 20:55:47 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:55:47,221 - WARNING - Could not retrieve variants from source file in region 4:6383581-6386229. Error was invalid region `4:6383582-6386229`
[2016-04-15T03:55Z] 2016-04-14 20:55:48 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:55:48,328 - WARNING - Could not retrieve variants from source file in region 4:3038939-3039340. Error was invalid region `4:3038940-3039340`
[2016-04-15T03:55Z] 2016-04-14 20:55:50 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:55:50,208 - WARNING - Could not retrieve variants from source file in region 4:10446174-10447358. Error was invalid region `4:10446175-10447358`
[2016-04-15T03:55Z] 2016-04-14 20:55:50 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:55:50,913 - WARNING - Could not retrieve variants from source file in region 4:10586360-10586761. Error was invalid region `4:10586361-10586761`
[2016-04-15T03:55Z] 2016-04-14 20:55:51 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:55:51,451 - WARNING - Could not retrieve variants from source file in region 4:3189336-3257783. Error was invalid region `4:3189337-3257783`
[2016-04-15T03:55Z] 2016-04-14 20:55:51 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:55:51,994 - WARNING - Could not retrieve variants from source file in region 4:9880947-9882041. Error was invalid region `4:9880948-9882041`
[2016-04-15T03:55Z] 2016-04-14 20:55:52 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:55:52,261 - WARNING - Could not retrieve variants from source file in region 4:6383581-6386229. Error was invalid region `4:6383582-6386229`
[2016-04-15T03:55Z] 2016-04-14 20:55:53 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:55:53,266 - WARNING - Could not retrieve variants from source file in region 4:3038939-3039340. Error was invalid region `4:3038940-3039340`
[2016-04-15T03:55Z] 2016-04-14 20:55:53 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:55:53,557 - WARNING - Could not retrieve variants from source file in region 4:7194234-7194674. Error was invalid region `4:7194235-7194674`
[2016-04-15T03:55Z] 2016-04-14 20:55:55 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:55:55,589 - WARNING - Could not retrieve variants from source file in region 4:10446174-10447358. Error was invalid region `4:10446175-10447358`
[2016-04-15T03:55Z] 2016-04-14 20:55:56 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:55:56,685 - WARNING - Could not retrieve variants from source file in region 4:2061123-2082285. Error was invalid region `4:2061124-2082285`
[2016-04-15T03:55Z] 2016-04-14 20:55:56 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:55:56,787 - WARNING - Could not retrieve variants from source file in region 4:13583683-13606766. Error was invalid region `4:13583684-13606766`
[2016-04-15T03:55Z] 2016-04-14 20:55:58 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:55:58,106 - WARNING - Could not retrieve variants from source file in region 4:4304126-4304712. Error was invalid region `4:4304127-4304712`
[2016-04-15T03:55Z] 2016-04-14 20:55:58 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:55:58,285 - WARNING - Could not retrieve variants from source file in region 4:9880947-9882041. Error was invalid region `4:9880948-9882041`
[2016-04-15T03:55Z] 2016-04-14 20:55:59 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:55:59,092 - WARNING - Could not retrieve variants from source file in region 4:6383581-6386229. Error was invalid region `4:6383582-6386229`
[2016-04-15T03:55Z] 2016-04-14 20:55:59 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:55:59,437 - WARNING - Could not retrieve variants from source file in region 4:8009548-8031661. Error was invalid region `4:8009549-8031661`
[2016-04-15T03:56Z] 2016-04-14 20:56:01 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:56:01,153 - WARNING - Could not retrieve variants from source file in region 4:10586360-10586761. Error was invalid region `4:10586361-10586761`
[2016-04-15T03:56Z] 2016-04-14 20:56:04 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:56:04,601 - WARNING - Could not retrieve variants from source file in region 4:4304126-4304712. Error was invalid region `4:4304127-4304712`
[2016-04-15T03:56Z] 2016-04-14 20:56:05 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:56:05,352 - WARNING - Could not retrieve variants from source file in region 4:4249409-4250099. Error was invalid region `4:4249410-4250099`
[2016-04-15T03:56Z] 2016-04-14 20:56:05 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:56:05,397 - WARNING - Could not retrieve variants from source file in region 4:9880947-9882041. Error was invalid region `4:9880948-9882041`
[2016-04-15T03:56Z] 2016-04-14 20:56:06 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:56:06,504 - WARNING - Could not retrieve variants from source file in region 4:8009548-8031661. Error was invalid region `4:8009549-8031661`
[2016-04-15T03:56Z] 2016-04-14 20:56:08 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:56:08,979 - WARNING - Could not retrieve variants from source file in region 4:13545581-13545982. Error was invalid region `4:13545582-13545982`
[2016-04-15T03:56Z] 2016-04-14 20:56:11 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:56:11,740 - WARNING - Could not retrieve variants from source file in region 4:13461229-13461630. Error was invalid region `4:13461230-13461630`
[2016-04-15T03:56Z] 2016-04-14 20:56:13 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:56:13,814 - WARNING - Could not retrieve variants from source file in region 4:13545581-13545982. Error was invalid region `4:13545582-13545982`
[2016-04-15T03:56Z] 2016-04-14 20:56:14 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:56:14,338 - WARNING - Could not retrieve variants from source file in region 4:2990288-3006233. Error was invalid region `4:2990289-3006233`
[2016-04-15T03:56Z] 2016-04-14 20:56:15 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:56:15,449 - WARNING - Could not retrieve variants from source file in region 4:7844856-7857420. Error was invalid region `4:7844857-7857420`
[2016-04-15T03:56Z] 2016-04-14 20:56:15 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:56:15,515 - WARNING - Could not retrieve variants from source file in region 4:6350597-6352952. Error was invalid region `4:6350598-6352952`
[2016-04-15T03:56Z] 2016-04-14 20:56:16 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:56:16,042 - WARNING - Could not retrieve variants from source file in region 4:10502726-10515332. Error was invalid region `4:10502727-10515332`
[2016-04-15T03:56Z] 2016-04-14 20:56:17 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:56:17,116 - WARNING - Could not retrieve variants from source file in region 4:3318202-3319461. Error was invalid region `4:3318203-3319461`
[2016-04-15T03:56Z] 2016-04-14 20:56:18 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:56:18,578 - WARNING - Could not retrieve variants from source file in region 4:13545581-13545982. Error was invalid region `4:13545582-13545982`
[2016-04-15T03:56Z] 2016-04-14 20:56:21 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:56:21,249 - WARNING - Could not retrieve variants from source file in region 4:6350597-6352952. Error was invalid region `4:6350598-6352952`
[2016-04-15T03:56Z] 2016-04-14 20:56:22 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:56:22,315 - WARNING - Could not retrieve variants from source file in region 4:1986348-1986749. Error was invalid region `4:1986349-1986749`
[2016-04-15T03:56Z] 2016-04-14 20:56:22 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:56:22,497 - WARNING - Could not retrieve variants from source file in region 4:3161845-3162246. Error was invalid region `4:3161846-3162246`
[2016-04-15T03:56Z] 2016-04-14 20:56:22 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:56:22,900 - WARNING - Could not retrieve variants from source file in region 4:3116957-3117358. Error was invalid region `4:3116958-3117358`
[2016-04-15T03:56Z] 2016-04-14 20:56:23 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:56:23,191 - WARNING - Could not retrieve variants from source file in region 4:3318202-3319461. Error was invalid region `4:3318203-3319461`
[2016-04-15T03:56Z] 2016-04-14 20:56:23 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:56:23,274 - WARNING - Could not retrieve variants from source file in region 4:5690691-5691092. Error was invalid region `4:5690692-5691092`
[2016-04-15T03:56Z] 2016-04-14 20:56:23 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:56:23,277 - WARNING - Could not retrieve variants from source file in region 4:9784420-9784821. Error was invalid region `4:9784421-9784821`
[2016-04-15T03:56Z] 2016-04-14 20:56:24 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:56:24,932 - WARNING - Could not retrieve variants from source file in region 4:7844856-7857420. Error was invalid region `4:7844857-7857420`
[2016-04-15T03:56Z] 2016-04-14 20:56:26 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:56:26,696 - WARNING - Could not retrieve variants from source file in region 4:6350597-6352952. Error was invalid region `4:6350598-6352952`
[2016-04-15T03:56Z] 2016-04-14 20:56:28 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:56:28,150 - WARNING - Could not retrieve variants from source file in region 4:1986348-1986749. Error was invalid region `4:1986349-1986749`
[2016-04-15T03:56Z] 2016-04-14 20:56:30 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:56:30,099 - WARNING - Could not retrieve variants from source file in region 4:5690691-5691092. Error was invalid region `4:5690692-5691092`
[2016-04-15T03:56Z] 2016-04-14 20:56:30 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:56:30,142 - WARNING - Could not retrieve variants from source file in region 4:9784420-9784821. Error was invalid region `4:9784421-9784821`
[2016-04-15T03:56Z] 2016-04-14 20:56:35 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:56:35,523 - WARNING - Could not retrieve variants from source file in region 4:9784420-9784821. Error was invalid region `4:9784421-9784821`
[2016-04-15T03:56Z] 2016-04-14 20:56:35 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:56:35,537 - WARNING - Could not retrieve variants from source file in region 4:3161845-3162246. Error was invalid region `4:3161846-3162246`
[2016-04-15T03:56Z] 2016-04-14 20:56:37 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:56:37,064 - WARNING - Could not retrieve variants from source file in region 4:9982119-10023171. Error was invalid region `4:9982120-10023171`
[2016-04-15T03:56Z] 2016-04-14 20:56:38 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:56:38,506 - WARNING - Could not retrieve variants from source file in region 4:2943150-2951994. Error was invalid region `4:2943151-2951994`
[2016-04-15T03:56Z] 2016-04-14 20:56:38 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:56:38,669 - WARNING - Could not retrieve variants from source file in region 4:7714279-7735301. Error was invalid region `4:7714280-7735301`
[2016-04-15T03:56Z] 2016-04-14 20:56:39 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:56:39,854 - WARNING - Could not retrieve variants from source file in region 4:6293485-6325276. Error was invalid region `4:6293486-6325276`
[2016-04-15T03:56Z] 2016-04-14 20:56:40 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:56:40,397 - WARNING - Could not retrieve variants from source file in region 4:1954734-1955135. Error was invalid region `4:1954735-1955135`
[2016-04-15T03:56Z] 2016-04-14 20:56:41 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:56:41,909 - WARNING - Could not retrieve variants from source file in region 4:9982119-10023171. Error was invalid region `4:9982120-10023171`
[2016-04-15T03:56Z] 2016-04-14 20:56:41 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:56:41,937 - WARNING - Could not retrieve variants from source file in region 4:9982119-10023171. Error was invalid region `4:9982120-10023171`
[2016-04-15T03:56Z] 2016-04-14 20:56:42 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:56:42,406 - WARNING - Could not retrieve variants from source file in region 4:2943150-2951994. Error was invalid region `4:2943151-2951994`
[2016-04-15T03:56Z] 2016-04-14 20:56:45 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:56:45,584 - WARNING - Could not retrieve variants from source file in region 4:1954734-1955135. Error was invalid region `4:1954735-1955135`
[2016-04-15T03:56Z] 2016-04-14 20:56:46 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:56:46,802 - WARNING - Could not retrieve variants from source file in region 4:2943150-2951994. Error was invalid region `4:2943151-2951994`
[2016-04-15T03:56Z] 2016-04-14 20:56:48 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:56:48,300 - WARNING - Could not retrieve variants from source file in region 4:8951605-8952006. Error was invalid region `4:8951606-8952006`
[2016-04-15T03:56Z] 2016-04-14 20:56:48 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:56:48,554 - WARNING - Could not retrieve variants from source file in region 4:2743788-2744277. Error was invalid region `4:2743789-2744277`
[2016-04-15T03:56Z] 2016-04-14 20:56:49 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:56:49,510 - WARNING - Could not retrieve variants from source file in region 4:5624204-5642464. Error was invalid region `4:5624205-5642464`
[2016-04-15T03:56Z] 2016-04-14 20:56:49 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:56:49,753 - WARNING - Could not retrieve variants from source file in region 4:1954734-1955135. Error was invalid region `4:1954735-1955135`
[2016-04-15T03:56Z] 2016-04-14 20:56:50 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:56:50,462 - WARNING - Could not retrieve variants from source file in region 4:8951605-8952006. Error was invalid region `4:8951606-8952006`
[2016-04-15T03:56Z] 2016-04-14 20:56:51 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:56:51,216 - WARNING - Could not retrieve variants from source file in region 4:5966590-5991666. Error was invalid region `4:5966591-5991666`
[2016-04-15T03:56Z] 2016-04-14 20:56:53 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:56:53,475 - WARNING - Could not retrieve variants from source file in region 4:1207169-1207570. Error was invalid region `4:1207170-1207570`
[2016-04-15T03:56Z] 2016-04-14 20:56:53 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:56:53,569 - WARNING - Could not retrieve variants from source file in region 4:8951605-8952006. Error was invalid region `4:8951606-8952006`
[2016-04-15T03:56Z] 2016-04-14 20:56:54 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:56:54,023 - WARNING - Could not retrieve variants from source file in region 4:8869046-8870258. Error was invalid region `4:8869047-8870258`
[2016-04-15T03:56Z] 2016-04-14 20:56:54 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:56:54,143 - WARNING - Could not retrieve variants from source file in region 4:9400700-9401143. Error was invalid region `4:9400701-9401143`
[2016-04-15T03:56Z] 2016-04-14 20:56:54 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:56:54,522 - WARNING - Could not retrieve variants from source file in region 4:5624204-5642464. Error was invalid region `4:5624205-5642464`
[2016-04-15T03:56Z] 2016-04-14 20:56:54 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:56:54,607 - WARNING - Could not retrieve variants from source file in region 4:1807683-1843514. Error was invalid region `4:1807684-1843514`
[2016-04-15T03:56Z] 2016-04-14 20:56:54 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:56:54,941 - WARNING - Could not retrieve variants from source file in region 4:5888906-5894588. Error was invalid region `4:5888907-5894588`
[2016-04-15T03:56Z] 2016-04-14 20:56:59 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:56:59,204 - WARNING - Could not retrieve variants from source file in region 4:2743788-2744277. Error was invalid region `4:2743789-2744277`
[2016-04-15T03:57Z] 2016-04-14 20:57:00 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:57:00,306 - WARNING - Could not retrieve variants from source file in region 4:2906496-2916952. Error was invalid region `4:2906497-2916952`
[2016-04-15T03:57Z] 2016-04-14 20:57:02 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:57:02,670 - WARNING - Could not retrieve variants from source file in region 4:1207169-1207570. Error was invalid region `4:1207170-1207570`
[2016-04-15T03:57Z] 2016-04-14 20:57:03 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:57:03,376 - WARNING - Could not retrieve variants from source file in region 4:1902267-1902668. Error was invalid region `4:1902268-1902668`
[2016-04-15T03:57Z] 2016-04-14 20:57:06 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:57:06,203 - WARNING - Could not retrieve variants from source file in region 4:2822256-2831573. Error was invalid region `4:2822257-2831573`
[2016-04-15T03:57Z] 2016-04-14 20:57:09 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:57:09,083 - WARNING - Could not retrieve variants from source file in region 4:2906496-2916952. Error was invalid region `4:2906497-2916952`
[2016-04-15T03:57Z] 2016-04-14 20:57:10 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:57:10,621 - WARNING - Could not retrieve variants from source file in region 4:2822256-2831573. Error was invalid region `4:2822257-2831573`
[2016-04-15T03:57Z] 2016-04-14 20:57:12 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:57:12,251 - WARNING - Could not retrieve variants from source file in region 4:8375131-8394283. Error was invalid region `4:8375132-8394283`
[2016-04-15T03:57Z] 2016-04-14 20:57:12 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:57:12,427 - WARNING - Could not retrieve variants from source file in region 4:5020938-5021339. Error was invalid region `4:5020939-5021339`
[2016-04-15T03:57Z] 2016-04-14 20:57:12 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:57:12,552 - WARNING - Could not retrieve variants from source file in region 4:1902267-1902668. Error was invalid region `4:1902268-1902668`
[2016-04-15T03:57Z] 2016-04-14 20:57:14 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:57:14,690 - WARNING - Could not retrieve variants from source file in region 4:1164066-1165931. Error was invalid region `4:1164067-1165931`
[2016-04-15T03:57Z] 2016-04-14 20:57:17 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:57:17,002 - WARNING - Could not retrieve variants from source file in region 4:8297559-8297960. Error was invalid region `4:8297560-8297960`
[2016-04-15T03:57Z] 2016-04-14 20:57:17 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:57:17,036 - WARNING - Could not retrieve variants from source file in region 4:8454428-8454829. Error was invalid region `4:8454429-8454829`
[2016-04-15T03:57Z] 2016-04-14 20:57:17 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:57:17,038 - WARNING - Could not retrieve variants from source file in region 4:755650-782491. Error was invalid region `4:755651-782491`
[2016-04-15T03:57Z] 2016-04-14 20:57:18 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:57:18,918 - WARNING - Could not retrieve variants from source file in region 4:1164066-1165931. Error was invalid region `4:1164067-1165931`
[2016-04-15T03:57Z] 2016-04-14 20:57:21 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:57:21,148 - WARNING - Could not retrieve variants from source file in region 4:8454428-8454829. Error was invalid region `4:8454429-8454829`
[2016-04-15T03:57Z] 2016-04-14 20:57:21 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:57:21,484 - WARNING - Could not retrieve variants from source file in region 4:8375131-8394283. Error was invalid region `4:8375132-8394283`
[2016-04-15T03:57Z] 2016-04-14 20:57:22 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:57:22,961 - WARNING - Could not retrieve variants from source file in region 4:1164066-1165931. Error was invalid region `4:1164067-1165931`
[2016-04-15T03:57Z] 2016-04-14 20:57:23 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:57:23,005 - WARNING - Could not retrieve variants from source file in region 4:2332108-2366635. Error was invalid region `4:2332109-2366635`
[2016-04-15T03:57Z] 2016-04-14 20:57:26 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:57:26,765 - WARNING - Could not retrieve variants from source file in region 4:1303471-1303872. Error was invalid region `4:1303472-1303872`
[2016-04-15T03:57Z] 2016-04-14 20:57:27 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:57:27,152 - WARNING - Could not retrieve variants from source file in region 4:8297559-8297960. Error was invalid region `4:8297560-8297960`
[2016-04-15T03:57Z] 2016-04-14 20:57:27 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:57:27,399 - WARNING - Could not retrieve variants from source file in region 4:2275624-2276025. Error was invalid region `4:2275625-2276025`
[2016-04-15T03:57Z] 2016-04-14 20:57:27 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:57:27,665 - WARNING - Could not retrieve variants from source file in region 4:2305842-2306243. Error was invalid region `4:2305843-2306243`
[2016-04-15T03:57Z] 2016-04-14 20:57:31 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:57:31,863 - WARNING - Could not retrieve variants from source file in region 4:2444720-2464369. Error was invalid region `4:2444721-2464369`
[2016-04-15T03:57Z] 2016-04-14 20:57:32 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:57:32,020 - WARNING - Could not retrieve variants from source file in region 4:1303471-1303872. Error was invalid region `4:1303472-1303872`
[2016-04-15T03:57Z] 2016-04-14 20:57:32 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:57:32,537 - WARNING - Could not retrieve variants from source file in region 4:2275624-2276025. Error was invalid region `4:2275625-2276025`
[2016-04-15T03:57Z] 2016-04-14 20:57:33 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:57:33,285 - WARNING - Could not retrieve variants from source file in region 4:2305842-2306243. Error was invalid region `4:2305843-2306243`
[2016-04-15T03:57Z] 2016-04-14 20:57:33 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:57:33,471 - WARNING - Could not retrieve variants from source file in region 4:2332108-2366635. Error was invalid region `4:2332109-2366635`
[2016-04-15T03:57Z] 2016-04-14 20:57:33 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:57:33,724 - WARNING - Could not retrieve variants from source file in region 4:1235432-1239502. Error was invalid region `4:1235433-1239502`
[2016-04-15T03:57Z] 2016-04-14 20:57:36 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:57:36,483 - WARNING - Could not retrieve variants from source file in region 4:8206872-8242656. Error was invalid region `4:8206873-8242656`
[2016-04-15T03:57Z] 2016-04-14 20:57:36 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:57:36,504 - WARNING - Could not retrieve variants from source file in region 4:1303471-1303872. Error was invalid region `4:1303472-1303872`
[2016-04-15T03:57Z] 2016-04-14 20:57:37 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:57:37,133 - WARNING - Could not retrieve variants from source file in region 4:2275624-2276025. Error was invalid region `4:2275625-2276025`
[2016-04-15T03:57Z] 2016-04-14 20:57:37 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:57:37,894 - WARNING - Could not retrieve variants from source file in region 4:2305842-2306243. Error was invalid region `4:2305843-2306243`
[2016-04-15T03:57Z] 2016-04-14 20:57:40 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:57:40,932 - WARNING - Could not retrieve variants from source file in region 4:727484-728301. Error was invalid region `4:727485-728301`
[2016-04-15T03:57Z] 2016-04-14 20:57:44 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:57:44,220 - WARNING - Could not retrieve variants from source file in region 4:1645806-1657471. Error was invalid region `4:1645807-1657471`
[2016-04-15T03:57Z] 2016-04-14 20:57:45 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:57:45,374 - WARNING - Could not retrieve variants from source file in region 4:1645806-1657471. Error was invalid region `4:1645807-1657471`
[2016-04-15T03:57Z] 2016-04-14 20:57:47 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:57:47,519 - WARNING - Could not retrieve variants from source file in region 4:1050442-1052356. Error was invalid region `4:1050443-1052356`
[2016-04-15T03:57Z] 2016-04-14 20:57:48 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:57:48,010 - WARNING - Could not retrieve variants from source file in region 4:1050442-1052356. Error was invalid region `4:1050443-1052356`
[2016-04-15T03:57Z] 2016-04-14 20:57:48 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:57:48,013 - WARNING - Could not retrieve variants from source file in region 4:1050442-1052356. Error was invalid region `4:1050443-1052356`
[2016-04-15T03:57Z] 2016-04-14 20:57:48 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:57:48,023 - WARNING - Could not retrieve variants from source file in region 4:727484-728301. Error was invalid region `4:727485-728301`
[2016-04-15T03:57Z] 2016-04-14 20:57:49 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:57:49,107 - WARNING - Could not retrieve variants from source file in region 4:515278-533191. Error was invalid region `4:515279-533191`
[2016-04-15T03:57Z] 2016-04-14 20:57:49 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:57:49,296 - WARNING - Could not retrieve variants from source file in region 4:843484-882833. Error was invalid region `4:843485-882833`
[2016-04-15T03:57Z] 2016-04-14 20:57:49 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:57:49,338 - WARNING - Could not retrieve variants from source file in region 4:437620-438021. Error was invalid region `4:437621-438021`
[2016-04-15T03:57Z] 2016-04-14 20:57:49 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:57:49,611 - WARNING - Could not retrieve variants from source file in region 4:647720-678473. Error was invalid region `4:647721-678473`
[2016-04-15T03:57Z] 2016-04-14 20:57:51 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:57:51,834 - WARNING - Could not retrieve variants from source file in region 4:85784-87503. Error was invalid region `4:85785-87503`
[2016-04-15T03:57Z] 2016-04-14 20:57:52 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:57:52,235 - WARNING - Could not retrieve variants from source file in region 4:843484-882833. Error was invalid region `4:843485-882833`
[2016-04-15T03:57Z] 2016-04-14 20:57:52 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:57:52,833 - WARNING - Could not retrieve variants from source file in region 4:85784-87503. Error was invalid region `4:85785-87503`
[2016-04-15T03:57Z] 2016-04-14 20:57:52 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:57:52,851 - WARNING - Could not retrieve variants from source file in region 4:941921-1018895. Error was invalid region `4:941922-1018895`
[2016-04-15T03:57Z] 2016-04-14 20:57:53 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:57:53,835 - WARNING - Could not retrieve variants from source file in region 4:85784-87503. Error was invalid region `4:85785-87503`
[2016-04-15T03:57Z] 2016-04-14 20:57:56 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:57:56,402 - WARNING - Could not retrieve variants from source file in region 4:647720-678473. Error was invalid region `4:647721-678473`
[2016-04-15T03:57Z] 2016-04-14 20:57:56 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:57:56,501 - WARNING - Could not retrieve variants from source file in region 4:515278-533191. Error was invalid region `4:515279-533191`
[2016-04-15T03:57Z] 2016-04-14 20:57:56 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:57:56,534 - WARNING - Could not retrieve variants from source file in region 4:437620-438021. Error was invalid region `4:437621-438021`
[2016-04-15T03:58Z] ['bcbio-variation-recall', 'square', '-Xms750m', '-Xmx7280m', '-XX:+UseSerialGC', '-c', 16, '-r', u'4:15512870-31144471', '--caller', 'platypus', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/4/Batch1-4_15512869_31144471.vcf.gz', '/mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/4/Batch1-4_15512869_31144471.vcf-inputs.txt'] in region: 4:15512870-31144471
[2016-04-15T03:58Z] 2016-04-14 20:58:11 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:58:11,124 - WARNING - Could not retrieve variants from source file in region 4:24836408-24836809. Error was invalid region `4:24836409-24836809`
[2016-04-15T03:58Z] 2016-04-14 20:58:12 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:58:11,993 - WARNING - Could not retrieve variants from source file in region 4:27003800-27004201. Error was invalid region `4:27003801-27004201`
[2016-04-15T03:58Z] 2016-04-14 20:58:12 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:58:12,708 - WARNING - Could not retrieve variants from source file in region 4:23890371-23890772. Error was invalid region `4:23890372-23890772`
[2016-04-15T03:58Z] 2016-04-14 20:58:13 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:58:13,248 - WARNING - Could not retrieve variants from source file in region 4:26673576-26673977. Error was invalid region `4:26673577-26673977`
[2016-04-15T03:58Z] 2016-04-14 20:58:13 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:58:13,446 - WARNING - Could not retrieve variants from source file in region 4:26416925-26417326. Error was invalid region `4:26416926-26417326`
[2016-04-15T03:58Z] 2016-04-14 20:58:13 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:58:13,740 - WARNING - Could not retrieve variants from source file in region 4:17503171-17524760. Error was invalid region `4:17503172-17524760`
[2016-04-15T03:58Z] 2016-04-14 20:58:13 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:58:13,870 - WARNING - Could not retrieve variants from source file in region 4:20851955-20852434. Error was invalid region `4:20851956-20852434`
[2016-04-15T03:58Z] 2016-04-14 20:58:14 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:58:14,406 - WARNING - Could not retrieve variants from source file in region 4:22820293-22820694. Error was invalid region `4:22820294-22820694`
[2016-04-15T03:58Z] 2016-04-14 20:58:14 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:58:14,462 - WARNING - Could not retrieve variants from source file in region 4:22439703-22440104. Error was invalid region `4:22439704-22440104`
[2016-04-15T03:58Z] 2016-04-14 20:58:14 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:58:14,535 - WARNING - Could not retrieve variants from source file in region 4:17694732-17711266. Error was invalid region `4:17694733-17711266`
[2016-04-15T03:58Z] 2016-04-14 20:58:14 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:58:14,596 - WARNING - Could not retrieve variants from source file in region 4:26862543-26862972. Error was invalid region `4:26862544-26862972`
[2016-04-15T03:58Z] 2016-04-14 20:58:18 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:58:18,084 - WARNING - Could not retrieve variants from source file in region 4:27003800-27004201. Error was invalid region `4:27003801-27004201`
[2016-04-15T03:58Z] 2016-04-14 20:58:18 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:58:18,794 - WARNING - Could not retrieve variants from source file in region 4:23890371-23890772. Error was invalid region `4:23890372-23890772`
[2016-04-15T03:58Z] 2016-04-14 20:58:20 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:58:20,184 - WARNING - Could not retrieve variants from source file in region 4:26673576-26673977. Error was invalid region `4:26673577-26673977`
[2016-04-15T03:58Z] 2016-04-14 20:58:20 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:58:20,493 - WARNING - Could not retrieve variants from source file in region 4:26416925-26417326. Error was invalid region `4:26416926-26417326`
[2016-04-15T03:58Z] 2016-04-14 20:58:21 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:58:21,524 - WARNING - Could not retrieve variants from source file in region 4:25398081-25419473. Error was invalid region `4:25398082-25419473`
[2016-04-15T03:58Z] 2016-04-14 20:58:21 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:58:21,673 - WARNING - Could not retrieve variants from source file in region 4:30788169-30788570. Error was invalid region `4:30788170-30788570`
[2016-04-15T03:58Z] 2016-04-14 20:58:22 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:58:22,333 - WARNING - Could not retrieve variants from source file in region 4:17818674-17819075. Error was invalid region `4:17818675-17819075`
[2016-04-15T03:58Z] 2016-04-14 20:58:22 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:58:22,369 - WARNING - Could not retrieve variants from source file in region 4:22820293-22820694. Error was invalid region `4:22820294-22820694`
[2016-04-15T03:58Z] 2016-04-14 20:58:22 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:58:22,669 - WARNING - Could not retrieve variants from source file in region 4:17694732-17711266. Error was invalid region `4:17694733-17711266`
[2016-04-15T03:58Z] 2016-04-14 20:58:22 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:58:22,721 - WARNING - Could not retrieve variants from source file in region 4:22439703-22440104. Error was invalid region `4:22439704-22440104`
[2016-04-15T03:58Z] 2016-04-14 20:58:23 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:58:23,069 - WARNING - Could not retrieve variants from source file in region 4:27003800-27004201. Error was invalid region `4:27003801-27004201`
[2016-04-15T03:58Z] 2016-04-14 20:58:23 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:58:23,322 - WARNING - Could not retrieve variants from source file in region 4:23890371-23890772. Error was invalid region `4:23890372-23890772`
[2016-04-15T03:58Z] 2016-04-14 20:58:25 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:58:25,467 - WARNING - Could not retrieve variants from source file in region 4:26673576-26673977. Error was invalid region `4:26673577-26673977`
[2016-04-15T03:58Z] 2016-04-14 20:58:25 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:58:25,765 - WARNING - Could not retrieve variants from source file in region 4:26416925-26417326. Error was invalid region `4:26416926-26417326`
[2016-04-15T03:58Z] 2016-04-14 20:58:27 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:58:27,152 - WARNING - Could not retrieve variants from source file in region 4:17503171-17524760. Error was invalid region `4:17503172-17524760`
[2016-04-15T03:58Z] 2016-04-14 20:58:29 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:58:29,722 - WARNING - Could not retrieve variants from source file in region 4:26862543-26862972. Error was invalid region `4:26862544-26862972`
[2016-04-15T03:58Z] 2016-04-14 20:58:29 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:58:29,761 - WARNING - Could not retrieve variants from source file in region 4:20851955-20852434. Error was invalid region `4:20851956-20852434`
[2016-04-15T03:58Z] 2016-04-14 20:58:30 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:58:30,233 - WARNING - Could not retrieve variants from source file in region 4:22820293-22820694. Error was invalid region `4:22820294-22820694`
[2016-04-15T03:58Z] 2016-04-14 20:58:30 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:58:30,241 - WARNING - Could not retrieve variants from source file in region 4:17818674-17819075. Error was invalid region `4:17818675-17819075`
[2016-04-15T03:58Z] 2016-04-14 20:58:30 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:58:30,703 - WARNING - Could not retrieve variants from source file in region 4:22439703-22440104. Error was invalid region `4:22439704-22440104`
[2016-04-15T03:58Z] 2016-04-14 20:58:30 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:58:30,853 - WARNING - Could not retrieve variants from source file in region 4:17694732-17711266. Error was invalid region `4:17694733-17711266`
[2016-04-15T03:58Z] 2016-04-14 20:58:39 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:58:39,501 - WARNING - Could not retrieve variants from source file in region 4:24801104-24801544. Error was invalid region `4:24801105-24801544`
[2016-04-15T03:58Z] 2016-04-14 20:58:41 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:58:41,171 - WARNING - Could not retrieve variants from source file in region 4:26719358-26719759. Error was invalid region `4:26719359-26719759`
[2016-04-15T03:58Z] 2016-04-14 20:58:43 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:58:43,383 - WARNING - Could not retrieve variants from source file in region 4:26719358-26719759. Error was invalid region `4:26719359-26719759`
[2016-04-15T03:58Z] 2016-04-14 20:58:44 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:58:44,937 - WARNING - Could not retrieve variants from source file in region 4:16675687-16676088. Error was invalid region `4:16675688-16676088`
[2016-04-15T03:58Z] 2016-04-14 20:58:45 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:58:45,511 - WARNING - Could not retrieve variants from source file in region 4:20732838-20733500. Error was invalid region `4:20732839-20733500`
[2016-04-15T03:58Z] 2016-04-14 20:58:46 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:58:46,840 - WARNING - Could not retrieve variants from source file in region 4:21950048-21950449. Error was invalid region `4:21950049-21950449`
[2016-04-15T03:58Z] 2016-04-14 20:58:47 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:58:47,837 - WARNING - Could not retrieve variants from source file in region 4:15937520-15937921. Error was invalid region `4:15937521-15937921`
[2016-04-15T03:58Z] 2016-04-14 20:58:47 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:58:47,984 - WARNING - Could not retrieve variants from source file in region 4:17634002-17660272. Error was invalid region `4:17634003-17660272`
[2016-04-15T03:58Z] 2016-04-14 20:58:48 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:58:48,338 - WARNING - Could not retrieve variants from source file in region 4:17586492-17586893. Error was invalid region `4:17586493-17586893`
[2016-04-15T03:58Z] 2016-04-14 20:58:49 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:58:49,928 - WARNING - Could not retrieve variants from source file in region 4:16675687-16676088. Error was invalid region `4:16675688-16676088`
[2016-04-15T03:58Z] 2016-04-14 20:58:50 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:58:50,156 - WARNING - Could not retrieve variants from source file in region 4:26585670-26586071. Error was invalid region `4:26585671-26586071`
[2016-04-15T03:58Z] 2016-04-14 20:58:51 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:58:51,472 - WARNING - Could not retrieve variants from source file in region 4:21950048-21950449. Error was invalid region `4:21950049-21950449`
[2016-04-15T03:58Z] 2016-04-14 20:58:52 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:58:52,548 - WARNING - Could not retrieve variants from source file in region 4:15937520-15937921. Error was invalid region `4:15937521-15937921`
[2016-04-15T03:58Z] 2016-04-14 20:58:52 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:58:52,573 - WARNING - Could not retrieve variants from source file in region 4:26585670-26586071. Error was invalid region `4:26585671-26586071`
[2016-04-15T03:58Z] 2016-04-14 20:58:53 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:58:53,513 - WARNING - Could not retrieve variants from source file in region 4:25235664-25254185. Error was invalid region `4:25235665-25254185`
[2016-04-15T03:58Z] 2016-04-14 20:58:53 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:58:53,595 - WARNING - Could not retrieve variants from source file in region 4:15937520-15937921. Error was invalid region `4:15937521-15937921`
[2016-04-15T03:58Z] 2016-04-14 20:58:54 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:58:54,289 - WARNING - Could not retrieve variants from source file in region 4:15639957-15640358. Error was invalid region `4:15639958-15640358`
[2016-04-15T03:58Z] 2016-04-14 20:58:54 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:58:54,332 - WARNING - Could not retrieve variants from source file in region 4:20543973-20544374. Error was invalid region `4:20543974-20544374`
[2016-04-15T03:58Z] 2016-04-14 20:58:54 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:58:54,382 - WARNING - Could not retrieve variants from source file in region 4:17634002-17660272. Error was invalid region `4:17634003-17660272`
[2016-04-15T03:58Z] 2016-04-14 20:58:54 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:58:54,587 - WARNING - Could not retrieve variants from source file in region 4:17586492-17586893. Error was invalid region `4:17586493-17586893`
[2016-04-15T03:58Z] 2016-04-14 20:58:55 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:58:55,346 - WARNING - Could not retrieve variants from source file in region 4:16675687-16676088. Error was invalid region `4:16675688-16676088`
[2016-04-15T03:58Z] 2016-04-14 20:58:56 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:58:56,461 - WARNING - Could not retrieve variants from source file in region 4:21950048-21950449. Error was invalid region `4:21950049-21950449`
[2016-04-15T03:58Z] 2016-04-14 20:58:56 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:58:56,855 - WARNING - Could not retrieve variants from source file in region 4:15709041-15733644. Error was invalid region `4:15709042-15733644`
[2016-04-15T03:59Z] 2016-04-14 20:59:00 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:59:00,358 - WARNING - Could not retrieve variants from source file in region 4:20543973-20544374. Error was invalid region `4:20543974-20544374`
[2016-04-15T03:59Z] 2016-04-14 20:59:00 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:59:00,551 - WARNING - Could not retrieve variants from source file in region 4:17634002-17660272. Error was invalid region `4:17634003-17660272`
[2016-04-15T03:59Z] 2016-04-14 20:59:00 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:59:00,571 - WARNING - Could not retrieve variants from source file in region 4:17586492-17586893. Error was invalid region `4:17586493-17586893`
[2016-04-15T03:59Z] 2016-04-14 20:59:03 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:59:03,957 - WARNING - Could not retrieve variants from source file in region 4:15709041-15733644. Error was invalid region `4:15709042-15733644`
[2016-04-15T03:59Z] 2016-04-14 20:59:04 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:59:04,416 - WARNING - Could not retrieve variants from source file in region 4:16227383-16227784. Error was invalid region `4:16227384-16227784`
[2016-04-15T03:59Z] 2016-04-14 20:59:05 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:59:05,262 - WARNING - Could not retrieve variants from source file in region 4:15568807-15569208. Error was invalid region `4:15568808-15569208`
[2016-04-15T03:59Z] 2016-04-14 20:59:08 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:59:08,908 - WARNING - Could not retrieve variants from source file in region 4:16227383-16227784. Error was invalid region `4:16227384-16227784`
[2016-04-15T03:59Z] 2016-04-14 20:59:09 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:59:09,035 - WARNING - Could not retrieve variants from source file in region 4:25669319-25678389. Error was invalid region `4:25669320-25678389`
[2016-04-15T03:59Z] 2016-04-14 20:59:10 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:59:10,300 - WARNING - Could not retrieve variants from source file in region 4:15568807-15569208. Error was invalid region `4:15568808-15569208`
[2016-04-15T03:59Z] 2016-04-14 20:59:10 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:59:10,424 - WARNING - Could not retrieve variants from source file in region 4:25031924-25032325. Error was invalid region `4:25031925-25032325`
[2016-04-15T03:59Z] 2016-04-14 20:59:10 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:59:10,448 - WARNING - Could not retrieve variants from source file in region 4:25669319-25678389. Error was invalid region `4:25669320-25678389`
[2016-04-15T03:59Z] 2016-04-14 20:59:10 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:59:10,876 - WARNING - Could not retrieve variants from source file in region 4:15568807-15569208. Error was invalid region `4:15568808-15569208`
[2016-04-15T03:59Z] 2016-04-14 20:59:11 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:59:11,947 - WARNING - Could not retrieve variants from source file in region 4:25031924-25032325. Error was invalid region `4:25031925-25032325`
[2016-04-15T03:59Z] 2016-04-14 20:59:12 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:59:12,654 - WARNING - Could not retrieve variants from source file in region 4:15964274-15964763. Error was invalid region `4:15964275-15964763`
[2016-04-15T03:59Z] 2016-04-14 20:59:13 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:59:13,179 - WARNING - Could not retrieve variants from source file in region 4:16227383-16227784. Error was invalid region `4:16227384-16227784`
[2016-04-15T03:59Z] 2016-04-14 20:59:14 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:59:14,011 - WARNING - Could not retrieve variants from source file in region 4:15516178-15516579. Error was invalid region `4:15516179-15516579`
[2016-04-15T03:59Z] 2016-04-14 20:59:14 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:59:14,653 - WARNING - Could not retrieve variants from source file in region 4:25031924-25032325. Error was invalid region `4:25031925-25032325`
[2016-04-15T03:59Z] 2016-04-14 20:59:15 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:59:15,356 - WARNING - Could not retrieve variants from source file in region 4:25004982-25005383. Error was invalid region `4:25004983-25005383`
[2016-04-15T03:59Z] 2016-04-14 20:59:16 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:59:16,336 - WARNING - Could not retrieve variants from source file in region 4:15964274-15964763. Error was invalid region `4:15964275-15964763`
[2016-04-15T03:59Z] 2016-04-14 20:59:17 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:59:17,879 - WARNING - Could not retrieve variants from source file in region 4:15516178-15516579. Error was invalid region `4:15516179-15516579`
[2016-04-15T03:59Z] 2016-04-14 20:59:18 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:59:18,123 - WARNING - Could not retrieve variants from source file in region 4:25004982-25005383. Error was invalid region `4:25004983-25005383`
[2016-04-15T03:59Z] 2016-04-14 20:59:18 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:59:18,137 - WARNING - Could not retrieve variants from source file in region 4:25004982-25005383. Error was invalid region `4:25004983-25005383`
[2016-04-15T03:59Z] ['bcbio-variation-recall', 'square', '-Xms750m', '-Xmx7280m', '-XX:+UseSerialGC', '-c', 16, '-r', u'4:36069529-52709433', '--caller', 'platypus', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/4/Batch1-4_36069528_52709433.vcf.gz', '/mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/4/Batch1-4_36069528_52709433.vcf-inputs.txt'] in region: 4:36069529-52709433
[2016-04-15T03:59Z] 2016-04-14 20:59:33 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:59:33,153 - WARNING - Could not retrieve variants from source file in region 4:46995155-46995556. Error was invalid region `4:46995156-46995556`
[2016-04-15T03:59Z] 2016-04-14 20:59:33 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:59:33,464 - WARNING - Could not retrieve variants from source file in region 4:41015612-41016089. Error was invalid region `4:41015613-41016089`
[2016-04-15T03:59Z] 2016-04-14 20:59:34 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:59:34,107 - WARNING - Could not retrieve variants from source file in region 4:44626430-44652220. Error was invalid region `4:44626431-44652220`
[2016-04-15T03:59Z] 2016-04-14 20:59:34 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:59:34,172 - WARNING - Could not retrieve variants from source file in region 4:46314382-46314783. Error was invalid region `4:46314383-46314783`
[2016-04-15T03:59Z] 2016-04-14 20:59:34 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:59:34,525 - WARNING - Could not retrieve variants from source file in region 4:41983907-42022654. Error was invalid region `4:41983908-42022654`
[2016-04-15T03:59Z] 2016-04-14 20:59:34 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:59:34,937 - WARNING - Could not retrieve variants from source file in region 4:39921731-39922132. Error was invalid region `4:39921732-39922132`
[2016-04-15T03:59Z] 2016-04-14 20:59:35 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:59:35,326 - WARNING - Could not retrieve variants from source file in region 4:39046375-39064352. Error was invalid region `4:39046376-39064352`
[2016-04-15T03:59Z] 2016-04-14 20:59:35 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:59:35,750 - WARNING - Could not retrieve variants from source file in region 4:46390654-46392017. Error was invalid region `4:46390655-46392017`
[2016-04-15T03:59Z] 2016-04-14 20:59:36 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:59:36,000 - WARNING - Could not retrieve variants from source file in region 4:42399901-42400302. Error was invalid region `4:42399902-42400302`
[2016-04-15T03:59Z] 2016-04-14 20:59:36 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:59:36,036 - WARNING - Could not retrieve variants from source file in region 4:38937161-38945359. Error was invalid region `4:38937162-38945359`
[2016-04-15T03:59Z] 2016-04-14 20:59:39 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:59:39,972 - WARNING - Could not retrieve variants from source file in region 4:46995155-46995556. Error was invalid region `4:46995156-46995556`
[2016-04-15T03:59Z] 2016-04-14 20:59:42 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:59:42,173 - WARNING - Could not retrieve variants from source file in region 4:46314382-46314783. Error was invalid region `4:46314383-46314783`
[2016-04-15T03:59Z] 2016-04-14 20:59:43 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:59:43,183 - WARNING - Could not retrieve variants from source file in region 4:37841538-37841939. Error was invalid region `4:37841539-37841939`
[2016-04-15T03:59Z] 2016-04-14 20:59:43 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:59:43,595 - WARNING - Could not retrieve variants from source file in region 4:39921731-39922132. Error was invalid region `4:39921732-39922132`
[2016-04-15T03:59Z] 2016-04-14 20:59:44 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:59:44,080 - WARNING - Could not retrieve variants from source file in region 4:39207107-39216411. Error was invalid region `4:39207108-39216411`
[2016-04-15T03:59Z] 2016-04-14 20:59:44 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:59:44,348 - WARNING - Could not retrieve variants from source file in region 4:39046375-39064352. Error was invalid region `4:39046376-39064352`
[2016-04-15T03:59Z] 2016-04-14 20:59:44 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:59:44,716 - WARNING - Could not retrieve variants from source file in region 4:46995155-46995556. Error was invalid region `4:46995156-46995556`
[2016-04-15T03:59Z] 2016-04-14 20:59:47 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:59:47,232 - WARNING - Could not retrieve variants from source file in region 4:46314382-46314783. Error was invalid region `4:46314383-46314783`
[2016-04-15T03:59Z] 2016-04-14 20:59:49 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:59:49,477 - WARNING - Could not retrieve variants from source file in region 4:49063661-49064062. Error was invalid region `4:49063662-49064062`
[2016-04-15T03:59Z] 2016-04-14 20:59:50 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:59:50,665 - WARNING - Could not retrieve variants from source file in region 4:41648409-41691791. Error was invalid region `4:41648410-41691791`
[2016-04-15T03:59Z] 2016-04-14 20:59:51 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:59:51,663 - WARNING - Could not retrieve variants from source file in region 4:47408498-47409028. Error was invalid region `4:47408499-47409028`
[2016-04-15T03:59Z] 2016-04-14 20:59:51 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:59:51,870 - WARNING - Could not retrieve variants from source file in region 4:39921731-39922132. Error was invalid region `4:39921732-39922132`
[2016-04-15T03:59Z] 2016-04-14 20:59:52 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:59:52,028 - WARNING - Could not retrieve variants from source file in region 4:39207107-39216411. Error was invalid region `4:39207108-39216411`
[2016-04-15T03:59Z] 2016-04-14 20:59:52 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:59:52,410 - WARNING - Could not retrieve variants from source file in region 4:38937161-38945359. Error was invalid region `4:38937162-38945359`
[2016-04-15T03:59Z] 2016-04-14 20:59:52 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 20:59:52,711 - WARNING - Could not retrieve variants from source file in region 4:42895097-42895613. Error was invalid region `4:42895098-42895613`
[2016-04-15T04:00Z] 2016-04-14 21:00:02 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:00:02,202 - WARNING - Could not retrieve variants from source file in region 4:46085849-46086250. Error was invalid region `4:46085850-46086250`
[2016-04-15T04:00Z] 2016-04-14 21:00:02 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:00:02,990 - WARNING - Could not retrieve variants from source file in region 4:44176749-44177150. Error was invalid region `4:44176750-44177150`
[2016-04-15T04:00Z] 2016-04-14 21:00:06 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:00:06,747 - WARNING - Could not retrieve variants from source file in region 4:37591917-37592318. Error was invalid region `4:37591918-37592318`
[2016-04-15T04:00Z] 2016-04-14 21:00:06 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:00:06,778 - WARNING - Could not retrieve variants from source file in region 4:48988239-48988895. Error was invalid region `4:48988240-48988895`
[2016-04-15T04:00Z] 2016-04-14 21:00:07 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:00:07,190 - WARNING - Could not retrieve variants from source file in region 4:40858942-40859343. Error was invalid region `4:40858943-40859343`
[2016-04-15T04:00Z] 2016-04-14 21:00:07 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:00:07,739 - WARNING - Could not retrieve variants from source file in region 4:47321979-47322380. Error was invalid region `4:47321980-47322380`
[2016-04-15T04:00Z] 2016-04-14 21:00:08 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:00:08,488 - WARNING - Could not retrieve variants from source file in region 4:46085849-46086250. Error was invalid region `4:46085850-46086250`
[2016-04-15T04:00Z] 2016-04-14 21:00:09 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:00:09,263 - WARNING - Could not retrieve variants from source file in region 4:39510053-39515926. Error was invalid region `4:39510054-39515926`
[2016-04-15T04:00Z] 2016-04-14 21:00:09 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:00:09,498 - WARNING - Could not retrieve variants from source file in region 4:44176749-44177150. Error was invalid region `4:44176750-44177150`
[2016-04-15T04:00Z] 2016-04-14 21:00:09 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:00:09,548 - WARNING - Could not retrieve variants from source file in region 4:38879738-38880236. Error was invalid region `4:38879739-38880236`
[2016-04-15T04:00Z] 2016-04-14 21:00:10 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:00:10,277 - WARNING - Could not retrieve variants from source file in region 4:40427799-40441044. Error was invalid region `4:40427800-40441044`
[2016-04-15T04:00Z] 2016-04-14 21:00:10 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:00:10,311 - WARNING - Could not retrieve variants from source file in region 4:39116700-39117857. Error was invalid region `4:39116701-39117857`
[2016-04-15T04:00Z] 2016-04-14 21:00:10 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:00:10,313 - WARNING - Could not retrieve variants from source file in region 4:37961975-37962376. Error was invalid region `4:37961976-37962376`
[2016-04-15T04:00Z] 2016-04-14 21:00:10 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:00:10,760 - WARNING - Could not retrieve variants from source file in region 4:38995163-39000495. Error was invalid region `4:38995164-39000495`
[2016-04-15T04:00Z] 2016-04-14 21:00:10 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:00:10,776 - WARNING - Could not retrieve variants from source file in region 4:41614747-41615148. Error was invalid region `4:41614748-41615148`
[2016-04-15T04:00Z] 2016-04-14 21:00:11 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:00:11,163 - WARNING - Could not retrieve variants from source file in region 4:48988239-48988895. Error was invalid region `4:48988240-48988895`
[2016-04-15T04:00Z] 2016-04-14 21:00:11 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:00:11,354 - WARNING - Could not retrieve variants from source file in region 4:37591917-37592318. Error was invalid region `4:37591918-37592318`
[2016-04-15T04:00Z] 2016-04-14 21:00:12 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:00:12,611 - WARNING - Could not retrieve variants from source file in region 4:47321979-47322380. Error was invalid region `4:47321980-47322380`
[2016-04-15T04:00Z] 2016-04-14 21:00:13 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:00:13,648 - WARNING - Could not retrieve variants from source file in region 4:46085849-46086250. Error was invalid region `4:46085850-46086250`
[2016-04-15T04:00Z] 2016-04-14 21:00:15 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:00:15,922 - WARNING - Could not retrieve variants from source file in region 4:41747688-41748089. Error was invalid region `4:41747689-41748089`
[2016-04-15T04:00Z] 2016-04-14 21:00:16 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:00:16,079 - WARNING - Could not retrieve variants from source file in region 4:44176749-44177150. Error was invalid region `4:44176750-44177150`
[2016-04-15T04:00Z] 2016-04-14 21:00:16 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:00:16,701 - WARNING - Could not retrieve variants from source file in region 4:38879738-38880236. Error was invalid region `4:38879739-38880236`
[2016-04-15T04:00Z] 2016-04-14 21:00:17 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:00:17,124 - WARNING - Could not retrieve variants from source file in region 4:38113430-38113831. Error was invalid region `4:38113431-38113831`
[2016-04-15T04:00Z] 2016-04-14 21:00:18 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:00:18,052 - WARNING - Could not retrieve variants from source file in region 4:38828952-38830540. Error was invalid region `4:38828953-38830540`
[2016-04-15T04:00Z] 2016-04-14 21:00:18 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:00:18,802 - WARNING - Could not retrieve variants from source file in region 4:48988239-48988895. Error was invalid region `4:48988240-48988895`
[2016-04-15T04:00Z] 2016-04-14 21:00:19 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:00:19,274 - WARNING - Could not retrieve variants from source file in region 4:37591917-37592318. Error was invalid region `4:37591918-37592318`
[2016-04-15T04:00Z] 2016-04-14 21:00:19 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:00:19,476 - WARNING - Could not retrieve variants from source file in region 4:41614747-41615148. Error was invalid region `4:41614748-41615148`
[2016-04-15T04:00Z] 2016-04-14 21:00:19 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:00:19,566 - WARNING - Could not retrieve variants from source file in region 4:47321979-47322380. Error was invalid region `4:47321980-47322380`
[2016-04-15T04:00Z] 2016-04-14 21:00:19 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:00:19,978 - WARNING - Could not retrieve variants from source file in region 4:39510053-39515926. Error was invalid region `4:39510054-39515926`
[2016-04-15T04:00Z] 2016-04-14 21:00:21 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:00:21,353 - WARNING - Could not retrieve variants from source file in region 4:38879738-38880236. Error was invalid region `4:38879739-38880236`
[2016-04-15T04:00Z] 2016-04-14 21:00:22 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:00:22,403 - WARNING - Could not retrieve variants from source file in region 4:38113430-38113831. Error was invalid region `4:38113431-38113831`
[2016-04-15T04:00Z] 2016-04-14 21:00:22 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:00:22,438 - WARNING - Could not retrieve variants from source file in region 4:37961975-37962376. Error was invalid region `4:37961976-37962376`
[2016-04-15T04:00Z] 2016-04-14 21:00:24 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:00:24,837 - WARNING - Could not retrieve variants from source file in region 4:38828952-38830540. Error was invalid region `4:38828953-38830540`
[2016-04-15T04:00Z] 2016-04-14 21:00:26 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:00:26,095 - WARNING - Could not retrieve variants from source file in region 4:38995163-39000495. Error was invalid region `4:38995164-39000495`
[2016-04-15T04:00Z] 2016-04-14 21:00:28 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:00:28,167 - WARNING - Could not retrieve variants from source file in region 4:46060144-46060545. Error was invalid region `4:46060145-46060545`
[2016-04-15T04:00Z] 2016-04-14 21:00:33 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:00:33,251 - WARNING - Could not retrieve variants from source file in region 4:40810452-40810937. Error was invalid region `4:40810453-40810937`
[2016-04-15T04:00Z] 2016-04-14 21:00:35 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:00:35,011 - WARNING - Could not retrieve variants from source file in region 4:37445104-37445505. Error was invalid region `4:37445105-37445505`
[2016-04-15T04:00Z] 2016-04-14 21:00:35 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:00:35,830 - WARNING - Could not retrieve variants from source file in region 4:48115053-48115454. Error was invalid region `4:48115054-48115454`
[2016-04-15T04:00Z] 2016-04-14 21:00:36 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:00:36,791 - WARNING - Could not retrieve variants from source file in region 4:47839718-47840119. Error was invalid region `4:47839719-47840119`
[2016-04-15T04:00Z] 2016-04-14 21:00:37 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:00:37,305 - WARNING - Could not retrieve variants from source file in region 4:46060144-46060545. Error was invalid region `4:46060145-46060545`
[2016-04-15T04:00Z] 2016-04-14 21:00:37 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:00:37,875 - WARNING - Could not retrieve variants from source file in region 4:37903545-37904279. Error was invalid region `4:37903546-37904279`
[2016-04-15T04:00Z] 2016-04-14 21:00:38 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:00:38,023 - WARNING - Could not retrieve variants from source file in region 4:39448331-39458241. Error was invalid region `4:39448332-39458241`
[2016-04-15T04:00Z] 2016-04-14 21:00:38 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:00:38,117 - WARNING - Could not retrieve variants from source file in region 4:40810452-40810937. Error was invalid region `4:40810453-40810937`
[2016-04-15T04:00Z] 2016-04-14 21:00:40 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:00:40,511 - WARNING - Could not retrieve variants from source file in region 4:48115053-48115454. Error was invalid region `4:48115054-48115454`
[2016-04-15T04:00Z] 2016-04-14 21:00:41 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:00:41,470 - WARNING - Could not retrieve variants from source file in region 4:47839718-47840119. Error was invalid region `4:47839719-47840119`
[2016-04-15T04:00Z] 2016-04-14 21:00:42 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:00:42,722 - WARNING - Could not retrieve variants from source file in region 4:48655613-48656020. Error was invalid region `4:48655614-48656020`
[2016-04-15T04:00Z] 2016-04-14 21:00:43 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:00:43,344 - WARNING - Could not retrieve variants from source file in region 4:38016184-38029642. Error was invalid region `4:38016185-38029642`
[2016-04-15T04:00Z] 2016-04-14 21:00:43 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:00:43,370 - WARNING - Could not retrieve variants from source file in region 4:39448331-39458241. Error was invalid region `4:39448332-39458241`
[2016-04-15T04:00Z] 2016-04-14 21:00:45 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:00:45,642 - WARNING - Could not retrieve variants from source file in region 4:40337312-40356612. Error was invalid region `4:40337313-40356612`
[2016-04-15T04:00Z] 2016-04-14 21:00:46 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:00:46,010 - WARNING - Could not retrieve variants from source file in region 4:47839718-47840119. Error was invalid region `4:47839719-47840119`
[2016-04-15T04:00Z] 2016-04-14 21:00:47 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:00:47,178 - WARNING - Could not retrieve variants from source file in region 4:38775428-38800529. Error was invalid region `4:38775429-38800529`
[2016-04-15T04:00Z] 2016-04-14 21:00:48 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:00:48,590 - WARNING - Could not retrieve variants from source file in region 4:39448331-39458241. Error was invalid region `4:39448332-39458241`
[2016-04-15T04:00Z] 2016-04-14 21:00:50 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:00:50,521 - WARNING - Could not retrieve variants from source file in region 4:40337312-40356612. Error was invalid region `4:40337313-40356612`
[2016-04-15T04:00Z] 2016-04-14 21:00:51 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:00:51,537 - WARNING - Could not retrieve variants from source file in region 4:40777935-40778352. Error was invalid region `4:40777936-40778352`
[2016-04-15T04:00Z] 2016-04-14 21:00:56 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:00:56,248 - WARNING - Could not retrieve variants from source file in region 4:40777935-40778352. Error was invalid region `4:40777936-40778352`
[2016-04-15T04:00Z] 2016-04-14 21:00:57 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:00:57,080 - WARNING - Could not retrieve variants from source file in region 4:37327372-37327773. Error was invalid region `4:37327373-37327773`
[2016-04-15T04:01Z] 2016-04-14 21:01:00 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:01:00,919 - WARNING - Could not retrieve variants from source file in region 4:47514474-47514875. Error was invalid region `4:47514475-47514875`
[2016-04-15T04:01Z] 2016-04-14 21:01:00 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:01:00,948 - WARNING - Could not retrieve variants from source file in region 4:47666853-47682364. Error was invalid region `4:47666854-47682364`
[2016-04-15T04:01Z] 2016-04-14 21:01:00 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:01:00,982 - WARNING - Could not retrieve variants from source file in region 4:48069485-48069886. Error was invalid region `4:48069486-48069886`
[2016-04-15T04:01Z] 2016-04-14 21:01:01 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:01:01,001 - WARNING - Could not retrieve variants from source file in region 4:47514474-47514875. Error was invalid region `4:47514475-47514875`
[2016-04-15T04:01Z] 2016-04-14 21:01:01 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:01:01,683 - WARNING - Could not retrieve variants from source file in region 4:47887325-47888181. Error was invalid region `4:47887326-47888181`
[2016-04-15T04:01Z] 2016-04-14 21:01:01 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:01:01,714 - WARNING - Could not retrieve variants from source file in region 4:40777935-40778352. Error was invalid region `4:40777936-40778352`
[2016-04-15T04:01Z] 2016-04-14 21:01:01 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:01:01,797 - WARNING - Could not retrieve variants from source file in region 4:48037715-48038116. Error was invalid region `4:48037716-48038116`
[2016-04-15T04:01Z] 2016-04-14 21:01:01 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:01:01,890 - WARNING - Could not retrieve variants from source file in region 4:48492223-48493427. Error was invalid region `4:48492224-48493427`
[2016-04-15T04:01Z] 2016-04-14 21:01:02 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:01:02,291 - WARNING - Could not retrieve variants from source file in region 4:48582698-48588932. Error was invalid region `4:48582699-48588932`
[2016-04-15T04:01Z] 2016-04-14 21:01:02 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:01:02,422 - WARNING - Could not retrieve variants from source file in region 4:36317759-36318160. Error was invalid region `4:36317760-36318160`
[2016-04-15T04:01Z] 2016-04-14 21:01:02 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:01:02,505 - WARNING - Could not retrieve variants from source file in region 4:40245305-40245706. Error was invalid region `4:40245306-40245706`
[2016-04-15T04:01Z] 2016-04-14 21:01:02 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:01:02,585 - WARNING - Could not retrieve variants from source file in region 4:48147098-48147499. Error was invalid region `4:48147099-48147499`
[2016-04-15T04:01Z] 2016-04-14 21:01:07 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:01:07,699 - WARNING - Could not retrieve variants from source file in region 4:47666853-47682364. Error was invalid region `4:47666854-47682364`
[2016-04-15T04:01Z] 2016-04-14 21:01:07 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:01:07,711 - WARNING - Could not retrieve variants from source file in region 4:48492223-48493427. Error was invalid region `4:48492224-48493427`
[2016-04-15T04:01Z] 2016-04-14 21:01:08 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:01:08,535 - WARNING - Could not retrieve variants from source file in region 4:48069485-48069886. Error was invalid region `4:48069486-48069886`
[2016-04-15T04:01Z] 2016-04-14 21:01:08 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:01:08,863 - WARNING - Could not retrieve variants from source file in region 4:47887325-47888181. Error was invalid region `4:47887326-47888181`
[2016-04-15T04:01Z] 2016-04-14 21:01:09 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:01:09,162 - WARNING - Could not retrieve variants from source file in region 4:48037715-48038116. Error was invalid region `4:48037716-48038116`
[2016-04-15T04:01Z] 2016-04-14 21:01:09 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:01:09,516 - WARNING - Could not retrieve variants from source file in region 4:48492223-48493427. Error was invalid region `4:48492224-48493427`
[2016-04-15T04:01Z] 2016-04-14 21:01:10 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:01:10,126 - WARNING - Could not retrieve variants from source file in region 4:48147098-48147499. Error was invalid region `4:48147099-48147499`
[2016-04-15T04:01Z] 2016-04-14 21:01:12 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:01:12,320 - WARNING - Could not retrieve variants from source file in region 4:40245305-40245706. Error was invalid region `4:40245306-40245706`
[2016-04-15T04:01Z] 2016-04-14 21:01:14 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:01:14,900 - WARNING - Could not retrieve variants from source file in region 4:47887325-47888181. Error was invalid region `4:47887326-47888181`
[2016-04-15T04:01Z] 2016-04-14 21:01:15 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:01:15,720 - WARNING - Could not retrieve variants from source file in region 4:48147098-48147499. Error was invalid region `4:48147099-48147499`
[2016-04-15T04:01Z] 2016-04-14 21:01:16 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:01:16,740 - WARNING - Could not retrieve variants from source file in region 4:48037715-48038116. Error was invalid region `4:48037716-48038116`
[2016-04-15T04:01Z] 2016-04-14 21:01:17 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:01:17,883 - WARNING - Could not retrieve variants from source file in region 4:48553330-48553731. Error was invalid region `4:48553331-48553731`
[2016-04-15T04:01Z] 2016-04-14 21:01:23 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:01:23,750 - WARNING - Could not retrieve variants from source file in region 4:36283102-36292208. Error was invalid region `4:36283103-36292208`
[2016-04-15T04:01Z] 2016-04-14 21:01:24 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:01:24,009 - WARNING - Could not retrieve variants from source file in region 4:36069594-36082068. Error was invalid region `4:36069595-36082068`
[2016-04-15T04:01Z] 2016-04-14 21:01:24 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:01:24,050 - WARNING - Could not retrieve variants from source file in region 4:36152373-36152774. Error was invalid region `4:36152374-36152774`
[2016-04-15T04:01Z] 2016-04-14 21:01:24 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:01:24,992 - WARNING - Could not retrieve variants from source file in region 4:36152373-36152774. Error was invalid region `4:36152374-36152774`
[2016-04-15T04:01Z] ['bcbio-variation-recall', 'square', '-Xms750m', '-Xmx7280m', '-XX:+UseSerialGC', '-c', 16, '-r', u'4:52709750-68338393', '--caller', 'platypus', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/4/Batch1-4_52709749_68338393.vcf.gz', '/mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/4/Batch1-4_52709749_68338393.vcf-inputs.txt'] in region: 4:52709750-68338393
[2016-04-15T04:01Z] 2016-04-14 21:01:40 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:01:40,373 - WARNING - Could not retrieve variants from source file in region 4:66535073-66535474. Error was invalid region `4:66535074-66535474`
[2016-04-15T04:01Z] 2016-04-14 21:01:40 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:01:40,438 - WARNING - Could not retrieve variants from source file in region 4:62845177-62845680. Error was invalid region `4:62845178-62845680`
[2016-04-15T04:01Z] 2016-04-14 21:01:41 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:01:41,125 - WARNING - Could not retrieve variants from source file in region 4:55593253-55602955. Error was invalid region `4:55593254-55602955`
[2016-04-15T04:01Z] 2016-04-14 21:01:42 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:01:42,078 - WARNING - Could not retrieve variants from source file in region 4:62800517-62800918. Error was invalid region `4:62800518-62800918`
[2016-04-15T04:01Z] 2016-04-14 21:01:42 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:01:42,250 - WARNING - Could not retrieve variants from source file in region 4:57273629-57286226. Error was invalid region `4:57273630-57286226`
[2016-04-15T04:01Z] 2016-04-14 21:01:42 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:01:42,266 - WARNING - Could not retrieve variants from source file in region 4:65145261-65145663. Error was invalid region `4:65145262-65145663`
[2016-04-15T04:01Z] 2016-04-14 21:01:42 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:01:42,770 - WARNING - Could not retrieve variants from source file in region 4:56741994-56756721. Error was invalid region `4:56741995-56756721`
[2016-04-15T04:01Z] 2016-04-14 21:01:46 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:01:46,075 - WARNING - Could not retrieve variants from source file in region 4:62845177-62845680. Error was invalid region `4:62845178-62845680`
[2016-04-15T04:01Z] 2016-04-14 21:01:47 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:01:47,268 - WARNING - Could not retrieve variants from source file in region 4:55593253-55602955. Error was invalid region `4:55593254-55602955`
[2016-04-15T04:01Z] 2016-04-14 21:01:49 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:01:49,004 - WARNING - Could not retrieve variants from source file in region 4:62800517-62800918. Error was invalid region `4:62800518-62800918`
[2016-04-15T04:01Z] 2016-04-14 21:01:49 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:01:49,366 - WARNING - Could not retrieve variants from source file in region 4:57273629-57286226. Error was invalid region `4:57273630-57286226`
[2016-04-15T04:01Z] 2016-04-14 21:01:50 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:01:50,073 - WARNING - Could not retrieve variants from source file in region 4:65145261-65145663. Error was invalid region `4:65145262-65145663`
[2016-04-15T04:01Z] 2016-04-14 21:01:50 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:01:50,683 - WARNING - Could not retrieve variants from source file in region 4:56448111-56448512. Error was invalid region `4:56448112-56448512`
[2016-04-15T04:01Z] 2016-04-14 21:01:50 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:01:50,729 - WARNING - Could not retrieve variants from source file in region 4:56301464-56325555. Error was invalid region `4:56301465-56325555`
[2016-04-15T04:01Z] 2016-04-14 21:01:51 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:01:51,456 - WARNING - Could not retrieve variants from source file in region 4:57516638-57547992. Error was invalid region `4:57516639-57547992`
[2016-04-15T04:01Z] 2016-04-14 21:01:51 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:01:51,606 - WARNING - Could not retrieve variants from source file in region 4:56475127-56475528. Error was invalid region `4:56475128-56475528`
[2016-04-15T04:01Z] 2016-04-14 21:01:51 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:01:51,652 - WARNING - Could not retrieve variants from source file in region 4:65274726-65275127. Error was invalid region `4:65274727-65275127`
[2016-04-15T04:01Z] 2016-04-14 21:01:51 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:01:51,718 - WARNING - Could not retrieve variants from source file in region 4:62845177-62845680. Error was invalid region `4:62845178-62845680`
[2016-04-15T04:01Z] 2016-04-14 21:01:51 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:01:51,967 - WARNING - Could not retrieve variants from source file in region 4:56262163-56262564. Error was invalid region `4:56262164-56262564`
[2016-04-15T04:01Z] 2016-04-14 21:01:51 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:01:51,991 - WARNING - Could not retrieve variants from source file in region 4:66535073-66535474. Error was invalid region `4:66535074-66535474`
[2016-04-15T04:01Z] 2016-04-14 21:01:52 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:01:52,266 - WARNING - Could not retrieve variants from source file in region 4:55593253-55602955. Error was invalid region `4:55593254-55602955`
[2016-04-15T04:01Z] 2016-04-14 21:01:54 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:01:54,986 - WARNING - Could not retrieve variants from source file in region 4:62800517-62800918. Error was invalid region `4:62800518-62800918`
[2016-04-15T04:01Z] 2016-04-14 21:01:55 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:01:55,437 - WARNING - Could not retrieve variants from source file in region 4:57273629-57286226. Error was invalid region `4:57273630-57286226`
[2016-04-15T04:01Z] 2016-04-14 21:01:57 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:01:57,269 - WARNING - Could not retrieve variants from source file in region 4:65145261-65145663. Error was invalid region `4:65145262-65145663`
[2016-04-15T04:01Z] 2016-04-14 21:01:57 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:01:57,282 - WARNING - Could not retrieve variants from source file in region 4:56741994-56756721. Error was invalid region `4:56741995-56756721`
[2016-04-15T04:01Z] 2016-04-14 21:01:59 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:01:59,913 - WARNING - Could not retrieve variants from source file in region 4:62598337-62598879. Error was invalid region `4:62598338-62598879`
[2016-04-15T04:02Z] 2016-04-14 21:02:00 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:02:00,486 - WARNING - Could not retrieve variants from source file in region 4:65274726-65275127. Error was invalid region `4:65274727-65275127`
[2016-04-15T04:02Z] 2016-04-14 21:02:10 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:02:10,231 - WARNING - Could not retrieve variants from source file in region 4:57876744-57889867. Error was invalid region `4:57876745-57889867`
[2016-04-15T04:02Z] 2016-04-14 21:02:10 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:02:10,389 - WARNING - Could not retrieve variants from source file in region 4:57843109-57851651. Error was invalid region `4:57843110-57851651`
[2016-04-15T04:02Z] 2016-04-14 21:02:11 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:02:11,227 - WARNING - Could not retrieve variants from source file in region 4:66508874-66509275. Error was invalid region `4:66508875-66509275`
[2016-04-15T04:02Z] 2016-04-14 21:02:12 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:02:12,004 - WARNING - Could not retrieve variants from source file in region 4:57372032-57397386. Error was invalid region `4:57372033-57397386`
[2016-04-15T04:02Z] 2016-04-14 21:02:12 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:02:12,571 - WARNING - Could not retrieve variants from source file in region 4:57441516-57441917. Error was invalid region `4:57441517-57441917`
[2016-04-15T04:02Z] 2016-04-14 21:02:15 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:02:15,353 - WARNING - Could not retrieve variants from source file in region 4:57843109-57851651. Error was invalid region `4:57843110-57851651`
[2016-04-15T04:02Z] 2016-04-14 21:02:16 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:02:16,386 - WARNING - Could not retrieve variants from source file in region 4:57797203-57798379. Error was invalid region `4:57797204-57798379`
[2016-04-15T04:02Z] 2016-04-14 21:02:16 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:02:16,588 - WARNING - Could not retrieve variants from source file in region 4:54966456-54967109. Error was invalid region `4:54966457-54967109`
[2016-04-15T04:02Z] 2016-04-14 21:02:16 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:02:16,642 - WARNING - Could not retrieve variants from source file in region 4:55140844-55161581. Error was invalid region `4:55140845-55161581`
[2016-04-15T04:02Z] 2016-04-14 21:02:16 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:02:16,650 - WARNING - Could not retrieve variants from source file in region 4:57333611-57334012. Error was invalid region `4:57333612-57334012`
[2016-04-15T04:02Z] 2016-04-14 21:02:21 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:02:21,167 - WARNING - Could not retrieve variants from source file in region 4:54966456-54967109. Error was invalid region `4:54966457-54967109`
[2016-04-15T04:02Z] 2016-04-14 21:02:21 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:02:21,399 - WARNING - Could not retrieve variants from source file in region 4:57441516-57441917. Error was invalid region `4:57441517-57441917`
[2016-04-15T04:02Z] 2016-04-14 21:02:23 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:02:23,917 - WARNING - Could not retrieve variants from source file in region 4:54441631-54457827. Error was invalid region `4:54441632-54457827`
[2016-04-15T04:02Z] 2016-04-14 21:02:24 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:02:24,361 - WARNING - Could not retrieve variants from source file in region 4:66196411-66197994. Error was invalid region `4:66196412-66197994`
[2016-04-15T04:02Z] 2016-04-14 21:02:24 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:02:24,367 - WARNING - Could not retrieve variants from source file in region 4:54966456-54967109. Error was invalid region `4:54966457-54967109`
[2016-04-15T04:02Z] 2016-04-14 21:02:25 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:02:25,128 - WARNING - Could not retrieve variants from source file in region 4:57333611-57334012. Error was invalid region `4:57333612-57334012`
[2016-04-15T04:02Z] 2016-04-14 21:02:27 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:02:27,388 - WARNING - Could not retrieve variants from source file in region 4:54930336-54930737. Error was invalid region `4:54930337-54930737`
[2016-04-15T04:02Z] 2016-04-14 21:02:27 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:02:27,845 - WARNING - Could not retrieve variants from source file in region 4:52938032-52949452. Error was invalid region `4:52938033-52949452`
[2016-04-15T04:02Z] 2016-04-14 21:02:31 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:02:31,324 - WARNING - Could not retrieve variants from source file in region 4:54930336-54930737. Error was invalid region `4:54930337-54930737`
[2016-04-15T04:02Z] 2016-04-14 21:02:31 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:02:31,627 - WARNING - Could not retrieve variants from source file in region 4:52884028-52884429. Error was invalid region `4:52884029-52884429`
[2016-04-15T04:02Z] 2016-04-14 21:02:31 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:02:31,631 - WARNING - Could not retrieve variants from source file in region 4:52884028-52884429. Error was invalid region `4:52884029-52884429`
[2016-04-15T04:02Z] 2016-04-14 21:02:31 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:02:31,706 - WARNING - Could not retrieve variants from source file in region 4:52884028-52884429. Error was invalid region `4:52884029-52884429`
[2016-04-15T04:02Z] 2016-04-14 21:02:34 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:02:34,131 - WARNING - Could not retrieve variants from source file in region 4:54011315-54011716. Error was invalid region `4:54011316-54011716`
[2016-04-15T04:02Z] 2016-04-14 21:02:34 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:02:34,171 - WARNING - Could not retrieve variants from source file in region 4:54011315-54011716. Error was invalid region `4:54011316-54011716`
[2016-04-15T04:02Z] ['bcbio-variation-recall', 'square', '-Xms750m', '-Xmx7280m', '-XX:+UseSerialGC', '-c', 16, '-r', u'4:68340605-83852298', '--caller', 'platypus', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/4/Batch1-4_68340604_83852298.vcf.gz', '/mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/4/Batch1-4_68340604_83852298.vcf-inputs.txt'] in region: 4:68340605-83852298
[2016-04-15T04:02Z] 2016-04-14 21:02:50 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:02:50,175 - WARNING - Could not retrieve variants from source file in region 4:70461831-70462232. Error was invalid region `4:70461832-70462232`
[2016-04-15T04:02Z] 2016-04-14 21:02:50 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:02:50,985 - WARNING - Could not retrieve variants from source file in region 4:83838006-83839989. Error was invalid region `4:83838007-83839989`
[2016-04-15T04:02Z] 2016-04-14 21:02:51 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:02:51,222 - WARNING - Could not retrieve variants from source file in region 4:71808363-71808769. Error was invalid region `4:71808364-71808769`
[2016-04-15T04:02Z] 2016-04-14 21:02:51 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:02:51,241 - WARNING - Could not retrieve variants from source file in region 4:78079484-78079885. Error was invalid region `4:78079485-78079885`
[2016-04-15T04:02Z] 2016-04-14 21:02:51 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:02:51,728 - WARNING - Could not retrieve variants from source file in region 4:69795415-69796497. Error was invalid region `4:69795416-69796497`
[2016-04-15T04:02Z] 2016-04-14 21:02:52 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:02:52,322 - WARNING - Could not retrieve variants from source file in region 4:77192627-77201677. Error was invalid region `4:77192628-77201677`
[2016-04-15T04:02Z] 2016-04-14 21:02:52 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:02:52,403 - WARNING - Could not retrieve variants from source file in region 4:76452938-76455040. Error was invalid region `4:76452939-76455040`
[2016-04-15T04:02Z] 2016-04-14 21:02:57 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:02:57,701 - WARNING - Could not retrieve variants from source file in region 4:73956525-73956926. Error was invalid region `4:73956526-73956926`
[2016-04-15T04:02Z] 2016-04-14 21:02:58 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:02:58,001 - WARNING - Could not retrieve variants from source file in region 4:74735033-74735434. Error was invalid region `4:74735034-74735434`
[2016-04-15T04:02Z] 2016-04-14 21:02:58 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:02:58,826 - WARNING - Could not retrieve variants from source file in region 4:80993585-80993986. Error was invalid region `4:80993586-80993986`
[2016-04-15T04:02Z] 2016-04-14 21:02:59 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:02:59,189 - WARNING - Could not retrieve variants from source file in region 4:83838006-83839989. Error was invalid region `4:83838007-83839989`
[2016-04-15T04:03Z] 2016-04-14 21:03:00 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:03:00,511 - WARNING - Could not retrieve variants from source file in region 4:71808363-71808769. Error was invalid region `4:71808364-71808769`
[2016-04-15T04:03Z] 2016-04-14 21:03:00 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:03:00,637 - WARNING - Could not retrieve variants from source file in region 4:82125910-82126311. Error was invalid region `4:82125911-82126311`
[2016-04-15T04:03Z] 2016-04-14 21:03:01 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:03:01,612 - WARNING - Could not retrieve variants from source file in region 4:69203340-69203836. Error was invalid region `4:69203341-69203836`
[2016-04-15T04:03Z] 2016-04-14 21:03:02 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:03:02,553 - WARNING - Could not retrieve variants from source file in region 4:70461831-70462232. Error was invalid region `4:70461832-70462232`
[2016-04-15T04:03Z] 2016-04-14 21:03:03 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:03:03,109 - WARNING - Could not retrieve variants from source file in region 4:74735033-74735434. Error was invalid region `4:74735034-74735434`
[2016-04-15T04:03Z] 2016-04-14 21:03:03 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:03:03,503 - WARNING - Could not retrieve variants from source file in region 4:80993585-80993986. Error was invalid region `4:80993586-80993986`
[2016-04-15T04:03Z] 2016-04-14 21:03:04 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:03:04,207 - WARNING - Could not retrieve variants from source file in region 4:83838006-83839989. Error was invalid region `4:83838007-83839989`
[2016-04-15T04:03Z] 2016-04-14 21:03:06 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:03:06,405 - WARNING - Could not retrieve variants from source file in region 4:75485661-75486062. Error was invalid region `4:75485662-75486062`
[2016-04-15T04:03Z] 2016-04-14 21:03:07 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:03:07,062 - WARNING - Could not retrieve variants from source file in region 4:71808363-71808769. Error was invalid region `4:71808364-71808769`
[2016-04-15T04:03Z] 2016-04-14 21:03:07 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:03:07,980 - WARNING - Could not retrieve variants from source file in region 4:71388340-71397179. Error was invalid region `4:71388341-71397179`
[2016-04-15T04:03Z] 2016-04-14 21:03:08 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:03:08,211 - WARNING - Could not retrieve variants from source file in region 4:82125910-82126311. Error was invalid region `4:82125911-82126311`
[2016-04-15T04:03Z] 2016-04-14 21:03:08 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:03:08,373 - WARNING - Could not retrieve variants from source file in region 4:77192627-77201677. Error was invalid region `4:77192628-77201677`
[2016-04-15T04:03Z] 2016-04-14 21:03:08 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:03:08,495 - WARNING - Could not retrieve variants from source file in region 4:69795415-69796497. Error was invalid region `4:69795416-69796497`
[2016-04-15T04:03Z] 2016-04-14 21:03:20 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:03:20,029 - WARNING - Could not retrieve variants from source file in region 4:74485841-74486242. Error was invalid region `4:74485842-74486242`
[2016-04-15T04:03Z] 2016-04-14 21:03:20 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:03:20,350 - WARNING - Could not retrieve variants from source file in region 4:70391218-70391619. Error was invalid region `4:70391219-70391619`
[2016-04-15T04:03Z] 2016-04-14 21:03:22 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:03:22,125 - WARNING - Could not retrieve variants from source file in region 4:83788133-83795996. Error was invalid region `4:83788134-83795996`
[2016-04-15T04:03Z] 2016-04-14 21:03:23 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:03:23,206 - WARNING - Could not retrieve variants from source file in region 4:75248223-75248624. Error was invalid region `4:75248224-75248624`
[2016-04-15T04:03Z] 2016-04-14 21:03:23 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:03:23,206 - WARNING - Could not retrieve variants from source file in region 4:71704754-71705452. Error was invalid region `4:71704755-71705452`
[2016-04-15T04:03Z] 2016-04-14 21:03:24 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:03:24,217 - WARNING - Could not retrieve variants from source file in region 4:78986946-78987347. Error was invalid region `4:78986947-78987347`
[2016-04-15T04:03Z] 2016-04-14 21:03:24 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:03:24,664 - WARNING - Could not retrieve variants from source file in region 4:73930341-73930742. Error was invalid region `4:73930342-73930742`
[2016-04-15T04:03Z] 2016-04-14 21:03:25 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:03:25,206 - WARNING - Could not retrieve variants from source file in region 4:81966977-81967378. Error was invalid region `4:81966978-81967378`
[2016-04-15T04:03Z] 2016-04-14 21:03:25 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:03:25,441 - WARNING - Could not retrieve variants from source file in region 4:71346490-71346891. Error was invalid region `4:71346491-71346891`
[2016-04-15T04:03Z] 2016-04-14 21:03:25 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:03:25,845 - WARNING - Could not retrieve variants from source file in region 4:74485841-74486242. Error was invalid region `4:74485842-74486242`
[2016-04-15T04:03Z] 2016-04-14 21:03:26 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:03:26,267 - WARNING - Could not retrieve variants from source file in region 4:69681637-69688177. Error was invalid region `4:69681638-69688177`
[2016-04-15T04:03Z] 2016-04-14 21:03:26 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:03:26,680 - WARNING - Could not retrieve variants from source file in region 4:70391218-70391619. Error was invalid region `4:70391219-70391619`
[2016-04-15T04:03Z] 2016-04-14 21:03:26 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:03:26,691 - WARNING - Could not retrieve variants from source file in region 4:69094296-69095387. Error was invalid region `4:69094297-69095387`
[2016-04-15T04:03Z] 2016-04-14 21:03:28 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:03:28,410 - WARNING - Could not retrieve variants from source file in region 4:80898597-80906181. Error was invalid region `4:80898598-80906181`
[2016-04-15T04:03Z] 2016-04-14 21:03:28 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:03:28,463 - WARNING - Could not retrieve variants from source file in region 4:83788133-83795996. Error was invalid region `4:83788134-83795996`
[2016-04-15T04:03Z] 2016-04-14 21:03:29 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:03:29,898 - WARNING - Could not retrieve variants from source file in region 4:75248223-75248624. Error was invalid region `4:75248224-75248624`
[2016-04-15T04:03Z] 2016-04-14 21:03:30 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:03:30,284 - WARNING - Could not retrieve variants from source file in region 4:71704754-71705452. Error was invalid region `4:71704755-71705452`
[2016-04-15T04:03Z] 2016-04-14 21:03:31 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:03:31,813 - WARNING - Could not retrieve variants from source file in region 4:78986946-78987347. Error was invalid region `4:78986947-78987347`
[2016-04-15T04:03Z] 2016-04-14 21:03:32 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:03:32,276 - WARNING - Could not retrieve variants from source file in region 4:81966977-81967378. Error was invalid region `4:81966978-81967378`
[2016-04-15T04:03Z] 2016-04-14 21:03:32 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:03:32,508 - WARNING - Could not retrieve variants from source file in region 4:69681637-69688177. Error was invalid region `4:69681638-69688177`
[2016-04-15T04:03Z] 2016-04-14 21:03:32 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:03:32,973 - WARNING - Could not retrieve variants from source file in region 4:75937760-75938426. Error was invalid region `4:75937761-75938426`
[2016-04-15T04:03Z] 2016-04-14 21:03:33 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:03:33,018 - WARNING - Could not retrieve variants from source file in region 4:74485841-74486242. Error was invalid region `4:74485842-74486242`
[2016-04-15T04:03Z] 2016-04-14 21:03:33 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:03:33,305 - WARNING - Could not retrieve variants from source file in region 4:69094296-69095387. Error was invalid region `4:69094297-69095387`
[2016-04-15T04:03Z] 2016-04-14 21:03:33 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:03:33,386 - WARNING - Could not retrieve variants from source file in region 4:70391218-70391619. Error was invalid region `4:70391219-70391619`
[2016-04-15T04:03Z] 2016-04-14 21:03:33 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:03:33,789 - WARNING - Could not retrieve variants from source file in region 4:77026899-77065770. Error was invalid region `4:77026900-77065770`
[2016-04-15T04:03Z] 2016-04-14 21:03:34 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:03:34,344 - WARNING - Could not retrieve variants from source file in region 4:80898597-80906181. Error was invalid region `4:80898598-80906181`
[2016-04-15T04:03Z] 2016-04-14 21:03:34 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:03:34,365 - WARNING - Could not retrieve variants from source file in region 4:83788133-83795996. Error was invalid region `4:83788134-83795996`
[2016-04-15T04:03Z] 2016-04-14 21:03:35 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:03:35,116 - WARNING - Could not retrieve variants from source file in region 4:77957919-77960991. Error was invalid region `4:77957920-77960991`
[2016-04-15T04:03Z] 2016-04-14 21:03:35 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:03:35,936 - WARNING - Could not retrieve variants from source file in region 4:75248223-75248624. Error was invalid region `4:75248224-75248624`
[2016-04-15T04:03Z] 2016-04-14 21:03:36 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:03:36,474 - WARNING - Could not retrieve variants from source file in region 4:71704754-71705452. Error was invalid region `4:71704755-71705452`
[2016-04-15T04:03Z] 2016-04-14 21:03:38 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:03:38,200 - WARNING - Could not retrieve variants from source file in region 4:78986946-78987347. Error was invalid region `4:78986947-78987347`
[2016-04-15T04:03Z] 2016-04-14 21:03:38 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:03:38,759 - WARNING - Could not retrieve variants from source file in region 4:71346490-71346891. Error was invalid region `4:71346491-71346891`
[2016-04-15T04:03Z] 2016-04-14 21:03:40 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:03:40,687 - WARNING - Could not retrieve variants from source file in region 4:81966977-81967378. Error was invalid region `4:81966978-81967378`
[2016-04-15T04:03Z] 2016-04-14 21:03:40 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:03:40,891 - WARNING - Could not retrieve variants from source file in region 4:69681637-69688177. Error was invalid region `4:69681638-69688177`
[2016-04-15T04:03Z] 2016-04-14 21:03:41 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:03:41,188 - WARNING - Could not retrieve variants from source file in region 4:69094296-69095387. Error was invalid region `4:69094297-69095387`
[2016-04-15T04:03Z] 2016-04-14 21:03:41 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:03:41,221 - WARNING - Could not retrieve variants from source file in region 4:75937760-75938426. Error was invalid region `4:75937761-75938426`
[2016-04-15T04:03Z] 2016-04-14 21:03:41 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:03:41,420 - WARNING - Could not retrieve variants from source file in region 4:77026899-77065770. Error was invalid region `4:77026900-77065770`
[2016-04-15T04:03Z] 2016-04-14 21:03:48 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:03:48,680 - WARNING - Could not retrieve variants from source file in region 4:72934421-72934822. Error was invalid region `4:72934422-72934822`
[2016-04-15T04:03Z] 2016-04-14 21:03:50 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:03:50,355 - WARNING - Could not retrieve variants from source file in region 4:74318119-74318520. Error was invalid region `4:74318120-74318520`
[2016-04-15T04:03Z] 2016-04-14 21:03:51 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:03:51,289 - WARNING - Could not retrieve variants from source file in region 4:83581394-83582401. Error was invalid region `4:83581395-83582401`
[2016-04-15T04:03Z] 2016-04-14 21:03:52 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:03:52,142 - WARNING - Could not retrieve variants from source file in region 4:70346353-70355401. Error was invalid region `4:70346354-70355401`
[2016-04-15T04:03Z] 2016-04-14 21:03:52 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:03:52,156 - WARNING - Could not retrieve variants from source file in region 4:80329132-80329533. Error was invalid region `4:80329133-80329533`
[2016-04-15T04:03Z] 2016-04-14 21:03:53 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:03:53,272 - WARNING - Could not retrieve variants from source file in region 4:77659951-77675695. Error was invalid region `4:77659952-77675695`
[2016-04-15T04:03Z] 2016-04-14 21:03:53 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:03:53,400 - WARNING - Could not retrieve variants from source file in region 4:74863786-74864187. Error was invalid region `4:74863787-74864187`
[2016-04-15T04:03Z] 2016-04-14 21:03:53 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:03:53,614 - WARNING - Could not retrieve variants from source file in region 4:71657561-71657962. Error was invalid region `4:71657562-71657962`
[2016-04-15T04:03Z] 2016-04-14 21:03:53 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:03:53,761 - WARNING - Could not retrieve variants from source file in region 4:72934421-72934822. Error was invalid region `4:72934422-72934822`
[2016-04-15T04:03Z] 2016-04-14 21:03:54 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:03:54,314 - WARNING - Could not retrieve variants from source file in region 4:71275176-71275577. Error was invalid region `4:71275177-71275577`
[2016-04-15T04:03Z] 2016-04-14 21:03:55 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:03:55,214 - WARNING - Could not retrieve variants from source file in region 4:78830223-78830624. Error was invalid region `4:78830224-78830624`
[2016-04-15T04:03Z] 2016-04-14 21:03:55 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:03:55,333 - WARNING - Could not retrieve variants from source file in region 4:74318119-74318520. Error was invalid region `4:74318120-74318520`
[2016-04-15T04:03Z] 2016-04-14 21:03:57 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:03:57,106 - WARNING - Could not retrieve variants from source file in region 4:81884511-81884912. Error was invalid region `4:81884512-81884912`
[2016-04-15T04:03Z] 2016-04-14 21:03:58 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:03:58,681 - WARNING - Could not retrieve variants from source file in region 4:70346353-70355401. Error was invalid region `4:70346354-70355401`
[2016-04-15T04:03Z] 2016-04-14 21:03:59 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:03:59,083 - WARNING - Could not retrieve variants from source file in region 4:74863786-74864187. Error was invalid region `4:74863787-74864187`
[2016-04-15T04:03Z] 2016-04-14 21:03:59 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:03:59,446 - WARNING - Could not retrieve variants from source file in region 4:72934421-72934822. Error was invalid region `4:72934422-72934822`
[2016-04-15T04:03Z] 2016-04-14 21:03:59 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:03:59,652 - WARNING - Could not retrieve variants from source file in region 4:69512636-69536274. Error was invalid region `4:69512637-69536274`
[2016-04-15T04:03Z] 2016-04-14 21:03:59 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:03:59,691 - WARNING - Could not retrieve variants from source file in region 4:71657561-71657962. Error was invalid region `4:71657562-71657962`
[2016-04-15T04:03Z] 2016-04-14 21:03:59 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:03:59,818 - WARNING - Could not retrieve variants from source file in region 4:68995318-68995719. Error was invalid region `4:68995319-68995719`
[2016-04-15T04:04Z] 2016-04-14 21:04:00 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:04:00,146 - WARNING - Could not retrieve variants from source file in region 4:74318119-74318520. Error was invalid region `4:74318120-74318520`
[2016-04-15T04:04Z] 2016-04-14 21:04:01 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:04:01,814 - WARNING - Could not retrieve variants from source file in region 4:81884511-81884912. Error was invalid region `4:81884512-81884912`
[2016-04-15T04:04Z] 2016-04-14 21:04:02 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:04:02,750 - WARNING - Could not retrieve variants from source file in region 4:83581394-83582401. Error was invalid region `4:83581395-83582401`
[2016-04-15T04:04Z] 2016-04-14 21:04:03 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:04:03,877 - WARNING - Could not retrieve variants from source file in region 4:80329132-80329533. Error was invalid region `4:80329133-80329533`
[2016-04-15T04:04Z] 2016-04-14 21:04:05 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:04:05,849 - WARNING - Could not retrieve variants from source file in region 4:71657561-71657962. Error was invalid region `4:71657562-71657962`
[2016-04-15T04:04Z] 2016-04-14 21:04:05 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:04:05,955 - WARNING - Could not retrieve variants from source file in region 4:69512636-69536274. Error was invalid region `4:69512637-69536274`
[2016-04-15T04:04Z] 2016-04-14 21:04:05 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:04:05,960 - WARNING - Could not retrieve variants from source file in region 4:71275176-71275577. Error was invalid region `4:71275177-71275577`
[2016-04-15T04:04Z] 2016-04-14 21:04:06 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:04:06,342 - WARNING - Could not retrieve variants from source file in region 4:81884511-81884912. Error was invalid region `4:81884512-81884912`
[2016-04-15T04:04Z] 2016-04-14 21:04:11 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:04:11,745 - WARNING - Could not retrieve variants from source file in region 4:68995318-68995719. Error was invalid region `4:68995319-68995719`
[2016-04-15T04:04Z] 2016-04-14 21:04:12 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:04:12,122 - WARNING - Could not retrieve variants from source file in region 4:69512636-69536274. Error was invalid region `4:69512637-69536274`
[2016-04-15T04:04Z] 2016-04-14 21:04:13 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:04:13,806 - WARNING - Could not retrieve variants from source file in region 4:74285028-74285429. Error was invalid region `4:74285029-74285429`
[2016-04-15T04:04Z] 2016-04-14 21:04:15 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:04:15,361 - WARNING - Could not retrieve variants from source file in region 4:73990795-73991196. Error was invalid region `4:73990796-73991196`
[2016-04-15T04:04Z] 2016-04-14 21:04:18 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:04:18,319 - WARNING - Could not retrieve variants from source file in region 4:70146019-70160499. Error was invalid region `4:70146020-70160499`
[2016-04-15T04:04Z] 2016-04-14 21:04:19 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:04:19,374 - WARNING - Could not retrieve variants from source file in region 4:79831947-79841549. Error was invalid region `4:79831948-79841549`
[2016-04-15T04:04Z] 2016-04-14 21:04:19 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:04:19,723 - WARNING - Could not retrieve variants from source file in region 4:74285028-74285429. Error was invalid region `4:74285029-74285429`
[2016-04-15T04:04Z] 2016-04-14 21:04:20 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:04:20,843 - WARNING - Could not retrieve variants from source file in region 4:72413206-72426053. Error was invalid region `4:72413207-72426053`
[2016-04-15T04:04Z] 2016-04-14 21:04:20 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:04:20,993 - WARNING - Could not retrieve variants from source file in region 4:72618085-72618524. Error was invalid region `4:72618086-72618524`
[2016-04-15T04:04Z] 2016-04-14 21:04:21 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:04:21,433 - WARNING - Could not retrieve variants from source file in region 4:73990795-73991196. Error was invalid region `4:73990796-73991196`
[2016-04-15T04:04Z] 2016-04-14 21:04:21 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:04:21,845 - WARNING - Could not retrieve variants from source file in region 4:71232219-71232891. Error was invalid region `4:71232220-71232891`
[2016-04-15T04:04Z] 2016-04-14 21:04:22 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:04:22,262 - WARNING - Could not retrieve variants from source file in region 4:69417359-69433904. Error was invalid region `4:69417360-69433904`
[2016-04-15T04:04Z] 2016-04-14 21:04:22 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:04:22,581 - WARNING - Could not retrieve variants from source file in region 4:81529307-81529708. Error was invalid region `4:81529308-81529708`
[2016-04-15T04:04Z] 2016-04-14 21:04:23 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:04:23,391 - WARNING - Could not retrieve variants from source file in region 4:83347055-83350953. Error was invalid region `4:83347056-83350953`
[2016-04-15T04:04Z] 2016-04-14 21:04:24 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:04:24,096 - WARNING - Could not retrieve variants from source file in region 4:70146019-70160499. Error was invalid region `4:70146020-70160499`
[2016-04-15T04:04Z] 2016-04-14 21:04:25 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:04:25,422 - WARNING - Could not retrieve variants from source file in region 4:74285028-74285429. Error was invalid region `4:74285029-74285429`
[2016-04-15T04:04Z] 2016-04-14 21:04:26 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:04:26,295 - WARNING - Could not retrieve variants from source file in region 4:77631214-77631615. Error was invalid region `4:77631215-77631615`
[2016-04-15T04:04Z] 2016-04-14 21:04:26 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:04:26,853 - WARNING - Could not retrieve variants from source file in region 4:72413206-72426053. Error was invalid region `4:72413207-72426053`
[2016-04-15T04:04Z] 2016-04-14 21:04:29 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:04:29,120 - WARNING - Could not retrieve variants from source file in region 4:71232219-71232891. Error was invalid region `4:71232220-71232891`
[2016-04-15T04:04Z] 2016-04-14 21:04:29 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:04:29,143 - WARNING - Could not retrieve variants from source file in region 4:68812072-68812473. Error was invalid region `4:68812073-68812473`
[2016-04-15T04:04Z] 2016-04-14 21:04:29 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:04:29,843 - WARNING - Could not retrieve variants from source file in region 4:73990795-73991196. Error was invalid region `4:73990796-73991196`
[2016-04-15T04:04Z] 2016-04-14 21:04:30 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:04:30,077 - WARNING - Could not retrieve variants from source file in region 4:70146019-70160499. Error was invalid region `4:70146020-70160499`
[2016-04-15T04:04Z] 2016-04-14 21:04:30 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:04:30,234 - WARNING - Could not retrieve variants from source file in region 4:81529307-81529708. Error was invalid region `4:81529308-81529708`
[2016-04-15T04:04Z] 2016-04-14 21:04:30 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:04:30,572 - WARNING - Could not retrieve variants from source file in region 4:76793017-76809576. Error was invalid region `4:76793018-76809576`
[2016-04-15T04:04Z] 2016-04-14 21:04:30 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:04:30,614 - WARNING - Could not retrieve variants from source file in region 4:79831947-79841549. Error was invalid region `4:79831948-79841549`
[2016-04-15T04:04Z] 2016-04-14 21:04:33 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:04:33,439 - WARNING - Could not retrieve variants from source file in region 4:69337114-69337515. Error was invalid region `4:69337115-69337515`
[2016-04-15T04:04Z] 2016-04-14 21:04:36 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:04:36,056 - WARNING - Could not retrieve variants from source file in region 4:68812072-68812473. Error was invalid region `4:68812073-68812473`
[2016-04-15T04:04Z] 2016-04-14 21:04:36 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:04:36,476 - WARNING - Could not retrieve variants from source file in region 4:69417359-69433904. Error was invalid region `4:69417360-69433904`
[2016-04-15T04:04Z] 2016-04-14 21:04:36 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:04:36,636 - WARNING - Could not retrieve variants from source file in region 4:71232219-71232891. Error was invalid region `4:71232220-71232891`
[2016-04-15T04:04Z] 2016-04-14 21:04:37 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:04:37,788 - WARNING - Could not retrieve variants from source file in region 4:81529307-81529708. Error was invalid region `4:81529308-81529708`
[2016-04-15T04:04Z] 2016-04-14 21:04:38 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:04:38,603 - WARNING - Could not retrieve variants from source file in region 4:76793017-76809576. Error was invalid region `4:76793018-76809576`
[2016-04-15T04:04Z] 2016-04-14 21:04:41 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:04:41,338 - WARNING - Could not retrieve variants from source file in region 4:68812072-68812473. Error was invalid region `4:68812073-68812473`
[2016-04-15T04:04Z] 2016-04-14 21:04:44 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:04:44,810 - WARNING - Could not retrieve variants from source file in region 4:76793017-76809576. Error was invalid region `4:76793018-76809576`
[2016-04-15T04:04Z] 2016-04-14 21:04:46 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:04:46,676 - WARNING - Could not retrieve variants from source file in region 4:70079627-70080028. Error was invalid region `4:70079628-70080028`
[2016-04-15T04:04Z] 2016-04-14 21:04:47 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:04:47,211 - WARNING - Could not retrieve variants from source file in region 4:68780188-68784964. Error was invalid region `4:68780189-68784964`
[2016-04-15T04:04Z] 2016-04-14 21:04:47 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:04:47,363 - WARNING - Could not retrieve variants from source file in region 4:71108692-71115146. Error was invalid region `4:71108693-71115146`
[2016-04-15T04:04Z] 2016-04-14 21:04:47 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:04:47,937 - WARNING - Could not retrieve variants from source file in region 4:79791952-79792353. Error was invalid region `4:79791953-79792353`
[2016-04-15T04:04Z] 2016-04-14 21:04:47 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:04:47,948 - WARNING - Could not retrieve variants from source file in region 4:81124385-81124786. Error was invalid region `4:81124386-81124786`
[2016-04-15T04:04Z] 2016-04-14 21:04:48 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:04:48,582 - WARNING - Could not retrieve variants from source file in region 4:77305135-77305536. Error was invalid region `4:77305136-77305536`
[2016-04-15T04:04Z] 2016-04-14 21:04:50 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:04:50,816 - WARNING - Could not retrieve variants from source file in region 4:68780188-68784964. Error was invalid region `4:68780189-68784964`
[2016-04-15T04:04Z] 2016-04-14 21:04:50 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:04:50,871 - WARNING - Could not retrieve variants from source file in region 4:68562154-68562555. Error was invalid region `4:68562155-68562555`
[2016-04-15T04:04Z] 2016-04-14 21:04:51 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:04:51,399 - WARNING - Could not retrieve variants from source file in region 4:81124385-81124786. Error was invalid region `4:81124386-81124786`
[2016-04-15T04:04Z] 2016-04-14 21:04:51 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:04:51,421 - WARNING - Could not retrieve variants from source file in region 4:71201177-71202133. Error was invalid region `4:71201178-71202133`
[2016-04-15T04:04Z] 2016-04-14 21:04:51 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:04:51,522 - WARNING - Could not retrieve variants from source file in region 4:70079627-70080028. Error was invalid region `4:70079628-70080028`
[2016-04-15T04:04Z] 2016-04-14 21:04:52 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:04:52,133 - WARNING - Could not retrieve variants from source file in region 4:68780188-68784964. Error was invalid region `4:68780189-68784964`
[2016-04-15T04:04Z] 2016-04-14 21:04:52 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:04:52,744 - WARNING - Could not retrieve variants from source file in region 4:79791952-79792353. Error was invalid region `4:79791953-79792353`
[2016-04-15T04:04Z] 2016-04-14 21:04:53 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:04:53,474 - WARNING - Could not retrieve variants from source file in region 4:71023888-71024289. Error was invalid region `4:71023889-71024289`
[2016-04-15T04:04Z] 2016-04-14 21:04:56 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:04:56,227 - WARNING - Could not retrieve variants from source file in region 4:70079627-70080028. Error was invalid region `4:70079628-70080028`
[2016-04-15T04:04Z] 2016-04-14 21:04:57 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:04:57,687 - WARNING - Could not retrieve variants from source file in region 4:77305135-77305536. Error was invalid region `4:77305136-77305536`
[2016-04-15T04:04Z] 2016-04-14 21:04:58 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:04:58,294 - WARNING - Could not retrieve variants from source file in region 4:71062045-71068679. Error was invalid region `4:71062046-71068679`
[2016-04-15T04:04Z] 2016-04-14 21:04:58 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:04:58,294 - WARNING - Could not retrieve variants from source file in region 4:76489371-76489772. Error was invalid region `4:76489372-76489772`
[2016-04-15T04:05Z] 2016-04-14 21:05:00 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:05:00,401 - WARNING - Could not retrieve variants from source file in region 4:76489371-76489772. Error was invalid region `4:76489372-76489772`
[2016-04-15T04:05Z] 2016-04-14 21:05:03 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:05:03,138 - WARNING - Could not retrieve variants from source file in region 4:71023888-71024289. Error was invalid region `4:71023889-71024289`
[2016-04-15T04:05Z] 2016-04-14 21:05:03 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:05:03,250 - WARNING - Could not retrieve variants from source file in region 4:71062045-71068679. Error was invalid region `4:71062046-71068679`
[2016-04-15T04:05Z] 2016-04-14 21:05:05 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:05:05,599 - WARNING - Could not retrieve variants from source file in region 4:68497386-68500361. Error was invalid region `4:68497387-68500361`
[2016-04-15T04:05Z] 2016-04-14 21:05:05 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:05:05,772 - WARNING - Could not retrieve variants from source file in region 4:70807560-70807961. Error was invalid region `4:70807561-70807961`
[2016-04-15T04:05Z] 2016-04-14 21:05:06 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:05:06,031 - WARNING - Could not retrieve variants from source file in region 4:68534181-68534582. Error was invalid region `4:68534182-68534582`
[2016-04-15T04:05Z] 2016-04-14 21:05:09 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:05:09,001 - WARNING - Could not retrieve variants from source file in region 4:70504951-70513329. Error was invalid region `4:70504952-70513329`
[2016-04-15T04:05Z] 2016-04-14 21:05:09 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:05:09,157 - WARNING - Could not retrieve variants from source file in region 4:68497386-68500361. Error was invalid region `4:68497387-68500361`
[2016-04-15T04:05Z] 2016-04-14 21:05:09 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:05:09,766 - WARNING - Could not retrieve variants from source file in region 4:68442757-68447230. Error was invalid region `4:68442758-68447230`
[2016-04-15T04:05Z] 2016-04-14 21:05:10 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:05:10,365 - WARNING - Could not retrieve variants from source file in region 4:68534181-68534582. Error was invalid region `4:68534182-68534582`
[2016-04-15T04:05Z] 2016-04-14 21:05:12 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:05:12,630 - WARNING - Could not retrieve variants from source file in region 4:68374386-68384198. Error was invalid region `4:68374387-68384198`
[2016-04-15T04:05Z] ['bcbio-variation-recall', 'square', '-Xms750m', '-Xmx7280m', '-XX:+UseSerialGC', '-c', 16, '-r', u'4:83857134-99393738', '--caller', 'platypus', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/4/Batch1-4_83857133_99393738.vcf.gz', '/mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/4/Batch1-4_83857133_99393738.vcf-inputs.txt'] in region: 4:83857134-99393738
[2016-04-15T04:05Z] 2016-04-14 21:05:27 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:05:27,791 - WARNING - Could not retrieve variants from source file in region 4:99026926-99049783. Error was invalid region `4:99026927-99049783`
[2016-04-15T04:05Z] 2016-04-14 21:05:28 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:05:28,408 - WARNING - Could not retrieve variants from source file in region 4:96106111-96128059. Error was invalid region `4:96106112-96128059`
[2016-04-15T04:05Z] 2016-04-14 21:05:29 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:05:29,171 - WARNING - Could not retrieve variants from source file in region 4:87769718-87770119. Error was invalid region `4:87769719-87770119`
[2016-04-15T04:05Z] 2016-04-14 21:05:29 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:05:29,931 - WARNING - Could not retrieve variants from source file in region 4:96256405-96256863. Error was invalid region `4:96256406-96256863`
[2016-04-15T04:05Z] 2016-04-14 21:05:30 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:05:30,571 - WARNING - Could not retrieve variants from source file in region 4:88401405-88416413. Error was invalid region `4:88401406-88416413`
[2016-04-15T04:05Z] 2016-04-14 21:05:30 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:05:30,943 - WARNING - Could not retrieve variants from source file in region 4:88898730-88899131. Error was invalid region `4:88898731-88899131`
[2016-04-15T04:05Z] 2016-04-14 21:05:31 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:05:31,022 - WARNING - Could not retrieve variants from source file in region 4:95578377-95586917. Error was invalid region `4:95578378-95586917`
[2016-04-15T04:05Z] 2016-04-14 21:05:31 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:05:31,352 - WARNING - Could not retrieve variants from source file in region 4:88238082-88258673. Error was invalid region `4:88238083-88258673`
[2016-04-15T04:05Z] 2016-04-14 21:05:31 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:05:31,361 - WARNING - Could not retrieve variants from source file in region 4:88957351-88957752. Error was invalid region `4:88957352-88957752`
[2016-04-15T04:05Z] 2016-04-14 21:05:33 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:05:33,283 - WARNING - Could not retrieve variants from source file in region 4:99026926-99049783. Error was invalid region `4:99026927-99049783`
[2016-04-15T04:05Z] 2016-04-14 21:05:33 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:05:33,841 - WARNING - Could not retrieve variants from source file in region 4:96106111-96128059. Error was invalid region `4:96106112-96128059`
[2016-04-15T04:05Z] 2016-04-14 21:05:33 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:05:33,955 - WARNING - Could not retrieve variants from source file in region 4:85530422-85530823. Error was invalid region `4:85530423-85530823`
[2016-04-15T04:05Z] 2016-04-14 21:05:34 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:05:34,775 - WARNING - Could not retrieve variants from source file in region 4:87769718-87770119. Error was invalid region `4:87769719-87770119`
[2016-04-15T04:05Z] 2016-04-14 21:05:36 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:05:36,775 - WARNING - Could not retrieve variants from source file in region 4:96256405-96256863. Error was invalid region `4:96256406-96256863`
[2016-04-15T04:05Z] 2016-04-14 21:05:36 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:05:36,888 - WARNING - Could not retrieve variants from source file in region 4:89196610-89198065. Error was invalid region `4:89196611-89198065`
[2016-04-15T04:05Z] 2016-04-14 21:05:37 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:05:37,550 - WARNING - Could not retrieve variants from source file in region 4:89388863-89421276. Error was invalid region `4:89388864-89421276`
[2016-04-15T04:05Z] 2016-04-14 21:05:37 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:05:37,860 - WARNING - Could not retrieve variants from source file in region 4:94316552-94316953. Error was invalid region `4:94316553-94316953`
[2016-04-15T04:05Z] 2016-04-14 21:05:38 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:05:38,367 - WARNING - Could not retrieve variants from source file in region 4:88898730-88899131. Error was invalid region `4:88898731-88899131`
[2016-04-15T04:05Z] 2016-04-14 21:05:38 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:05:38,994 - WARNING - Could not retrieve variants from source file in region 4:99026926-99049783. Error was invalid region `4:99026927-99049783`
[2016-04-15T04:05Z] 2016-04-14 21:05:39 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:05:39,363 - WARNING - Could not retrieve variants from source file in region 4:87769718-87770119. Error was invalid region `4:87769719-87770119`
[2016-04-15T04:05Z] 2016-04-14 21:05:42 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:05:42,214 - WARNING - Could not retrieve variants from source file in region 4:96256405-96256863. Error was invalid region `4:96256406-96256863`
[2016-04-15T04:05Z] 2016-04-14 21:05:45 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:05:45,367 - WARNING - Could not retrieve variants from source file in region 4:89388863-89421276. Error was invalid region `4:89388864-89421276`
[2016-04-15T04:05Z] 2016-04-14 21:05:45 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:05:45,510 - WARNING - Could not retrieve variants from source file in region 4:88898730-88899131. Error was invalid region `4:88898731-88899131`
[2016-04-15T04:05Z] 2016-04-14 21:05:46 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:05:46,098 - WARNING - Could not retrieve variants from source file in region 4:88957351-88957752. Error was invalid region `4:88957352-88957752`
[2016-04-15T04:05Z] 2016-04-14 21:05:55 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:05:55,703 - WARNING - Could not retrieve variants from source file in region 4:98893226-98893666. Error was invalid region `4:98893227-98893666`
[2016-04-15T04:05Z] 2016-04-14 21:05:58 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:05:58,214 - WARNING - Could not retrieve variants from source file in region 4:88732320-88733101. Error was invalid region `4:88732321-88733101`
[2016-04-15T04:06Z] 2016-04-14 21:06:00 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:06:00,188 - WARNING - Could not retrieve variants from source file in region 4:98893226-98893666. Error was invalid region `4:98893227-98893666`
[2016-04-15T04:06Z] 2016-04-14 21:06:00 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:06:00,409 - WARNING - Could not retrieve variants from source file in region 4:88766797-88767198. Error was invalid region `4:88766798-88767198`
[2016-04-15T04:06Z] 2016-04-14 21:06:00 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:06:00,723 - WARNING - Could not retrieve variants from source file in region 4:88293676-88294077. Error was invalid region `4:88293677-88294077`
[2016-04-15T04:06Z] 2016-04-14 21:06:01 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:06:01,889 - WARNING - Could not retrieve variants from source file in region 4:89299890-89319486. Error was invalid region `4:89299891-89319486`
[2016-04-15T04:06Z] 2016-04-14 21:06:02 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:06:02,291 - WARNING - Could not retrieve variants from source file in region 4:87927993-87928394. Error was invalid region `4:87927994-87928394`
[2016-04-15T04:06Z] 2016-04-14 21:06:03 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:06:03,206 - WARNING - Could not retrieve variants from source file in region 4:84364540-84384000. Error was invalid region `4:84364541-84384000`
[2016-04-15T04:06Z] 2016-04-14 21:06:04 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:06:04,315 - WARNING - Could not retrieve variants from source file in region 4:98893226-98893666. Error was invalid region `4:98893227-98893666`
[2016-04-15T04:06Z] 2016-04-14 21:06:04 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:06:04,492 - WARNING - Could not retrieve variants from source file in region 4:88766797-88767198. Error was invalid region `4:88766798-88767198`
[2016-04-15T04:06Z] 2016-04-14 21:06:04 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:06:04,601 - WARNING - Could not retrieve variants from source file in region 4:88293676-88294077. Error was invalid region `4:88293677-88294077`
[2016-04-15T04:06Z] 2016-04-14 21:06:04 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:06:04,659 - WARNING - Could not retrieve variants from source file in region 4:87683820-87706696. Error was invalid region `4:87683821-87706696`
[2016-04-15T04:06Z] 2016-04-14 21:06:05 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:06:05,837 - WARNING - Could not retrieve variants from source file in region 4:90034475-90034876. Error was invalid region `4:90034476-90034876`
[2016-04-15T04:06Z] 2016-04-14 21:06:06 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:06:06,359 - WARNING - Could not retrieve variants from source file in region 4:87927993-87928394. Error was invalid region `4:87927994-87928394`
[2016-04-15T04:06Z] 2016-04-14 21:06:06 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:06:06,846 - WARNING - Could not retrieve variants from source file in region 4:88732320-88733101. Error was invalid region `4:88732321-88733101`
[2016-04-15T04:06Z] 2016-04-14 21:06:07 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:06:07,106 - WARNING - Could not retrieve variants from source file in region 4:91701509-91703090. Error was invalid region `4:91701510-91703090`
[2016-04-15T04:06Z] 2016-04-14 21:06:08 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:06:08,592 - WARNING - Could not retrieve variants from source file in region 4:88293676-88294077. Error was invalid region `4:88293677-88294077`
[2016-04-15T04:06Z] 2016-04-14 21:06:09 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:06:09,845 - WARNING - Could not retrieve variants from source file in region 4:90034475-90034876. Error was invalid region `4:90034476-90034876`
[2016-04-15T04:06Z] 2016-04-14 21:06:10 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:06:10,539 - WARNING - Could not retrieve variants from source file in region 4:87927993-87928394. Error was invalid region `4:87927994-87928394`
[2016-04-15T04:06Z] 2016-04-14 21:06:17 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:06:17,289 - WARNING - Could not retrieve variants from source file in region 4:85762174-85762575. Error was invalid region `4:85762175-85762575`
[2016-04-15T04:06Z] 2016-04-14 21:06:18 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:06:18,920 - WARNING - Could not retrieve variants from source file in region 4:88582924-88584350. Error was invalid region `4:88582925-88584350`
[2016-04-15T04:06Z] 2016-04-14 21:06:19 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:06:19,272 - WARNING - Could not retrieve variants from source file in region 4:89978070-89978471. Error was invalid region `4:89978071-89978471`
[2016-04-15T04:06Z] 2016-04-14 21:06:19 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:06:19,374 - WARNING - Could not retrieve variants from source file in region 4:87808814-87813683. Error was invalid region `4:87808815-87813683`
[2016-04-15T04:06Z] 2016-04-14 21:06:19 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:06:19,436 - WARNING - Could not retrieve variants from source file in region 4:84188639-84230809. Error was invalid region `4:84188640-84230809`
[2016-04-15T04:06Z] 2016-04-14 21:06:19 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:06:19,630 - WARNING - Could not retrieve variants from source file in region 4:83931476-83931877. Error was invalid region `4:83931477-83931877`
[2016-04-15T04:06Z] 2016-04-14 21:06:21 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:06:21,161 - WARNING - Could not retrieve variants from source file in region 4:85762174-85762575. Error was invalid region `4:85762175-85762575`
[2016-04-15T04:06Z] 2016-04-14 21:06:23 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:06:23,019 - WARNING - Could not retrieve variants from source file in region 4:89978070-89978471. Error was invalid region `4:89978071-89978471`
[2016-04-15T04:06Z] 2016-04-14 21:06:23 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:06:23,296 - WARNING - Could not retrieve variants from source file in region 4:85708581-85708982. Error was invalid region `4:85708582-85708982`
[2016-04-15T04:06Z] 2016-04-14 21:06:23 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:06:23,497 - WARNING - Could not retrieve variants from source file in region 4:84188639-84230809. Error was invalid region `4:84188640-84230809`
[2016-04-15T04:06Z] 2016-04-14 21:06:23 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:06:23,524 - WARNING - Could not retrieve variants from source file in region 4:83931476-83931877. Error was invalid region `4:83931477-83931877`
[2016-04-15T04:06Z] 2016-04-14 21:06:23 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:06:23,524 - WARNING - Could not retrieve variants from source file in region 4:89669944-89671911. Error was invalid region `4:89669945-89671911`
[2016-04-15T04:06Z] 2016-04-14 21:06:27 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:06:27,438 - WARNING - Could not retrieve variants from source file in region 4:83931476-83931877. Error was invalid region `4:83931477-83931877`
[2016-04-15T04:06Z] 2016-04-14 21:06:27 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:06:27,499 - WARNING - Could not retrieve variants from source file in region 4:89669944-89671911. Error was invalid region `4:89669945-89671911`
[2016-04-15T04:06Z] 2016-04-14 21:06:36 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:06:36,321 - WARNING - Could not retrieve variants from source file in region 4:89601089-89619027. Error was invalid region `4:89601090-89619027`
[2016-04-15T04:06Z] 2016-04-14 21:06:36 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:06:36,381 - WARNING - Could not retrieve variants from source file in region 4:83899832-83900233. Error was invalid region `4:83899833-83900233`
[2016-04-15T04:06Z] 2016-04-14 21:06:36 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:06:36,383 - WARNING - Could not retrieve variants from source file in region 4:83899832-83900233. Error was invalid region `4:83899833-83900233`
[2016-04-15T04:06Z] 2016-04-14 21:06:36 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:06:36,385 - WARNING - Could not retrieve variants from source file in region 4:83899832-83900233. Error was invalid region `4:83899833-83900233`
[2016-04-15T04:06Z] ['bcbio-variation-recall', 'square', '-Xms750m', '-Xmx7280m', '-XX:+UseSerialGC', '-c', 16, '-r', u'4:99397340-115544957', '--caller', 'platypus', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/4/Batch1-4_99397339_115544957.vcf.gz', '/mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/4/Batch1-4_99397339_115544957.vcf-inputs.txt'] in region: 4:99397340-115544957
[2016-04-15T04:06Z] 2016-04-14 21:06:52 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:06:52,560 - WARNING - Could not retrieve variants from source file in region 4:115544503-115544904. Error was invalid region `4:115544504-115544904`
[2016-04-15T04:06Z] 2016-04-14 21:06:53 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:06:53,006 - WARNING - Could not retrieve variants from source file in region 4:110772856-110791101. Error was invalid region `4:110772857-110791101`
[2016-04-15T04:06Z] 2016-04-14 21:06:53 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:06:53,782 - WARNING - Could not retrieve variants from source file in region 4:114066928-114067329. Error was invalid region `4:114066929-114067329`
[2016-04-15T04:06Z] 2016-04-14 21:06:53 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:06:53,823 - WARNING - Could not retrieve variants from source file in region 4:109745125-109770132. Error was invalid region `4:109745126-109770132`
[2016-04-15T04:06Z] 2016-04-14 21:06:53 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:06:53,836 - WARNING - Could not retrieve variants from source file in region 4:103225302-103228924. Error was invalid region `4:103225303-103228924`
[2016-04-15T04:06Z] 2016-04-14 21:06:54 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:06:54,077 - WARNING - Could not retrieve variants from source file in region 4:100140095-100140496. Error was invalid region `4:100140096-100140496`
[2016-04-15T04:06Z] 2016-04-14 21:06:54 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:06:54,641 - WARNING - Could not retrieve variants from source file in region 4:106473885-106474286. Error was invalid region `4:106473886-106474286`
[2016-04-15T04:06Z] 2016-04-14 21:06:54 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:06:54,645 - WARNING - Could not retrieve variants from source file in region 4:110638599-110639000. Error was invalid region `4:110638600-110639000`
[2016-04-15T04:06Z] 2016-04-14 21:06:54 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:06:54,904 - WARNING - Could not retrieve variants from source file in region 4:106317218-106317619. Error was invalid region `4:106317219-106317619`
[2016-04-15T04:06Z] 2016-04-14 21:06:58 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:06:58,054 - WARNING - Could not retrieve variants from source file in region 4:115544503-115544904. Error was invalid region `4:115544504-115544904`
[2016-04-15T04:06Z] 2016-04-14 21:06:58 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:06:58,749 - WARNING - Could not retrieve variants from source file in region 4:110772856-110791101. Error was invalid region `4:110772857-110791101`
[2016-04-15T04:07Z] 2016-04-14 21:07:02 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:07:02,079 - WARNING - Could not retrieve variants from source file in region 4:103225302-103228924. Error was invalid region `4:103225303-103228924`
[2016-04-15T04:07Z] 2016-04-14 21:07:02 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:07:02,138 - WARNING - Could not retrieve variants from source file in region 4:113351864-113362506. Error was invalid region `4:113351865-113362506`
[2016-04-15T04:07Z] 2016-04-14 21:07:02 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:07:02,563 - WARNING - Could not retrieve variants from source file in region 4:100140095-100140496. Error was invalid region `4:100140096-100140496`
[2016-04-15T04:07Z] 2016-04-14 21:07:02 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:07:02,674 - WARNING - Could not retrieve variants from source file in region 4:106580129-106580530. Error was invalid region `4:106580130-106580530`
[2016-04-15T04:07Z] 2016-04-14 21:07:02 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:07:02,855 - WARNING - Could not retrieve variants from source file in region 4:110638599-110639000. Error was invalid region `4:110638600-110639000`
[2016-04-15T04:07Z] 2016-04-14 21:07:02 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:07:02,983 - WARNING - Could not retrieve variants from source file in region 4:100784769-100785170. Error was invalid region `4:100784770-100785170`
[2016-04-15T04:07Z] 2016-04-14 21:07:03 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:07:03,234 - WARNING - Could not retrieve variants from source file in region 4:106473885-106474286. Error was invalid region `4:106473886-106474286`
[2016-04-15T04:07Z] 2016-04-14 21:07:03 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:07:03,301 - WARNING - Could not retrieve variants from source file in region 4:110384579-110384980. Error was invalid region `4:110384580-110384980`
[2016-04-15T04:07Z] 2016-04-14 21:07:03 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:07:03,659 - WARNING - Could not retrieve variants from source file in region 4:106317218-106317619. Error was invalid region `4:106317219-106317619`
[2016-04-15T04:07Z] 2016-04-14 21:07:03 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:07:03,802 - WARNING - Could not retrieve variants from source file in region 4:104006894-104013986. Error was invalid region `4:104006895-104013986`
[2016-04-15T04:07Z] 2016-04-14 21:07:03 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:07:03,980 - WARNING - Could not retrieve variants from source file in region 4:106291551-106292014. Error was invalid region `4:106291552-106292014`
[2016-04-15T04:07Z] 2016-04-14 21:07:04 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:07:04,167 - WARNING - Could not retrieve variants from source file in region 4:110772856-110791101. Error was invalid region `4:110772857-110791101`
[2016-04-15T04:07Z] 2016-04-14 21:07:04 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:07:04,177 - WARNING - Could not retrieve variants from source file in region 4:115544503-115544904. Error was invalid region `4:115544504-115544904`
[2016-04-15T04:07Z] 2016-04-14 21:07:05 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:07:05,955 - WARNING - Could not retrieve variants from source file in region 4:114066928-114067329. Error was invalid region `4:114066929-114067329`
[2016-04-15T04:07Z] 2016-04-14 21:07:08 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:07:08,234 - WARNING - Could not retrieve variants from source file in region 4:113351864-113362506. Error was invalid region `4:113351865-113362506`
[2016-04-15T04:07Z] 2016-04-14 21:07:09 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:07:09,361 - WARNING - Could not retrieve variants from source file in region 4:100140095-100140496. Error was invalid region `4:100140096-100140496`
[2016-04-15T04:07Z] 2016-04-14 21:07:09 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:07:09,430 - WARNING - Could not retrieve variants from source file in region 4:103225302-103228924. Error was invalid region `4:103225303-103228924`
[2016-04-15T04:07Z] 2016-04-14 21:07:09 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:07:09,825 - WARNING - Could not retrieve variants from source file in region 4:106580129-106580530. Error was invalid region `4:106580130-106580530`
[2016-04-15T04:07Z] 2016-04-14 21:07:10 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:07:10,532 - WARNING - Could not retrieve variants from source file in region 4:110638599-110639000. Error was invalid region `4:110638600-110639000`
[2016-04-15T04:07Z] 2016-04-14 21:07:10 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:07:10,672 - WARNING - Could not retrieve variants from source file in region 4:106473885-106474286. Error was invalid region `4:106473886-106474286`
[2016-04-15T04:07Z] 2016-04-14 21:07:10 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:07:10,800 - WARNING - Could not retrieve variants from source file in region 4:106317218-106317619. Error was invalid region `4:106317219-106317619`
[2016-04-15T04:07Z] 2016-04-14 21:07:11 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:07:11,063 - WARNING - Could not retrieve variants from source file in region 4:104006894-104013986. Error was invalid region `4:104006895-104013986`
[2016-04-15T04:07Z] 2016-04-14 21:07:22 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:07:22,497 - WARNING - Could not retrieve variants from source file in region 4:113539758-113540159. Error was invalid region `4:113539759-113540159`
[2016-04-15T04:07Z] 2016-04-14 21:07:23 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:07:23,300 - WARNING - Could not retrieve variants from source file in region 4:110737178-110737579. Error was invalid region `4:110737179-110737579`
[2016-04-15T04:07Z] 2016-04-14 21:07:25 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:07:25,401 - WARNING - Could not retrieve variants from source file in region 4:100045405-100063009. Error was invalid region `4:100045406-100063009`
[2016-04-15T04:07Z] 2016-04-14 21:07:26 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:07:26,933 - WARNING - Could not retrieve variants from source file in region 4:100348838-100349239. Error was invalid region `4:100348839-100349239`
[2016-04-15T04:07Z] 2016-04-14 21:07:28 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:07:28,365 - WARNING - Could not retrieve variants from source file in region 4:113539758-113540159. Error was invalid region `4:113539759-113540159`
[2016-04-15T04:07Z] 2016-04-14 21:07:28 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:07:28,519 - WARNING - Could not retrieve variants from source file in region 4:103910858-103911259. Error was invalid region `4:103910859-103911259`
[2016-04-15T04:07Z] 2016-04-14 21:07:28 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:07:28,896 - WARNING - Could not retrieve variants from source file in region 4:110737178-110737579. Error was invalid region `4:110737179-110737579`
[2016-04-15T04:07Z] 2016-04-14 21:07:28 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:07:28,937 - WARNING - Could not retrieve variants from source file in region 4:109841532-109863560. Error was invalid region `4:109841533-109863560`
[2016-04-15T04:07Z] 2016-04-14 21:07:29 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:07:29,546 - WARNING - Could not retrieve variants from source file in region 4:106196740-106197141. Error was invalid region `4:106196741-106197141`
[2016-04-15T04:07Z] 2016-04-14 21:07:29 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:07:29,614 - WARNING - Could not retrieve variants from source file in region 4:113303421-113303822. Error was invalid region `4:113303422-113303822`
[2016-04-15T04:07Z] 2016-04-14 21:07:29 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:07:29,620 - WARNING - Could not retrieve variants from source file in region 4:109670255-109670656. Error was invalid region `4:109670256-109670656`
[2016-04-15T04:07Z] 2016-04-14 21:07:30 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:07:30,349 - WARNING - Could not retrieve variants from source file in region 4:100045405-100063009. Error was invalid region `4:100045406-100063009`
[2016-04-15T04:07Z] 2016-04-14 21:07:34 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:07:34,427 - WARNING - Could not retrieve variants from source file in region 4:113539758-113540159. Error was invalid region `4:113539759-113540159`
[2016-04-15T04:07Z] 2016-04-14 21:07:35 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:07:35,058 - WARNING - Could not retrieve variants from source file in region 4:103910858-103911259. Error was invalid region `4:103910859-103911259`
[2016-04-15T04:07Z] 2016-04-14 21:07:36 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:07:36,222 - WARNING - Could not retrieve variants from source file in region 4:103748586-103749065. Error was invalid region `4:103748587-103749065`
[2016-04-15T04:07Z] 2016-04-14 21:07:36 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:07:36,225 - WARNING - Could not retrieve variants from source file in region 4:110603573-110605934. Error was invalid region `4:110603574-110605934`
[2016-04-15T04:07Z] 2016-04-14 21:07:36 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:07:36,233 - WARNING - Could not retrieve variants from source file in region 4:110737178-110737579. Error was invalid region `4:110737179-110737579`
[2016-04-15T04:07Z] 2016-04-14 21:07:36 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:07:36,750 - WARNING - Could not retrieve variants from source file in region 4:106196740-106197141. Error was invalid region `4:106196741-106197141`
[2016-04-15T04:07Z] 2016-04-14 21:07:37 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:07:37,130 - WARNING - Could not retrieve variants from source file in region 4:100045405-100063009. Error was invalid region `4:100045406-100063009`
[2016-04-15T04:07Z] 2016-04-14 21:07:40 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:07:40,535 - WARNING - Could not retrieve variants from source file in region 4:103910858-103911259. Error was invalid region `4:103910859-103911259`
[2016-04-15T04:07Z] 2016-04-14 21:07:43 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:07:43,666 - WARNING - Could not retrieve variants from source file in region 4:106196740-106197141. Error was invalid region `4:106196741-106197141`
[2016-04-15T04:07Z] 2016-04-14 21:07:52 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:07:52,814 - WARNING - Could not retrieve variants from source file in region 4:110678714-110679115. Error was invalid region `4:110678715-110679115`
[2016-04-15T04:07Z] 2016-04-14 21:07:54 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:07:54,458 - WARNING - Could not retrieve variants from source file in region 4:102964832-102965233. Error was invalid region `4:102964833-102965233`
[2016-04-15T04:07Z] 2016-04-14 21:07:54 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:07:54,543 - WARNING - Could not retrieve variants from source file in region 4:113435833-113436234. Error was invalid region `4:113435834-113436234`
[2016-04-15T04:07Z] 2016-04-14 21:07:54 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:07:54,954 - WARNING - Could not retrieve variants from source file in region 4:108930828-108931229. Error was invalid region `4:108930829-108931229`
[2016-04-15T04:07Z] 2016-04-14 21:07:55 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:07:55,048 - WARNING - Could not retrieve variants from source file in region 4:113198864-113199265. Error was invalid region `4:113198865-113199265`
[2016-04-15T04:07Z] 2016-04-14 21:07:55 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:07:55,437 - WARNING - Could not retrieve variants from source file in region 4:99849915-99850316. Error was invalid region `4:99849916-99850316`
[2016-04-15T04:07Z] 2016-04-14 21:07:55 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:07:55,545 - WARNING - Could not retrieve variants from source file in region 4:100234842-100239509. Error was invalid region `4:100234843-100239509`
[2016-04-15T04:07Z] 2016-04-14 21:07:55 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:07:55,666 - WARNING - Could not retrieve variants from source file in region 4:100265922-100268380. Error was invalid region `4:100265923-100268380`
[2016-04-15T04:07Z] 2016-04-14 21:07:56 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:07:56,315 - WARNING - Could not retrieve variants from source file in region 4:103822087-103822594. Error was invalid region `4:103822088-103822594`
[2016-04-15T04:07Z] 2016-04-14 21:07:56 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:07:56,667 - WARNING - Could not retrieve variants from source file in region 4:113468353-113468754. Error was invalid region `4:113468354-113468754`
[2016-04-15T04:07Z] 2016-04-14 21:07:57 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:07:57,227 - WARNING - Could not retrieve variants from source file in region 4:110678714-110679115. Error was invalid region `4:110678715-110679115`
[2016-04-15T04:07Z] 2016-04-14 21:07:59 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:07:59,172 - WARNING - Could not retrieve variants from source file in region 4:102964832-102965233. Error was invalid region `4:102964833-102965233`
[2016-04-15T04:08Z] 2016-04-14 21:08:00 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:08:00,131 - WARNING - Could not retrieve variants from source file in region 4:103611634-103612035. Error was invalid region `4:103611635-103612035`
[2016-04-15T04:08Z] 2016-04-14 21:08:00 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:08:00,410 - WARNING - Could not retrieve variants from source file in region 4:100265922-100268380. Error was invalid region `4:100265923-100268380`
[2016-04-15T04:08Z] 2016-04-14 21:08:01 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:08:01,139 - WARNING - Could not retrieve variants from source file in region 4:113198864-113199265. Error was invalid region `4:113198865-113199265`
[2016-04-15T04:08Z] 2016-04-14 21:08:01 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:08:01,179 - WARNING - Could not retrieve variants from source file in region 4:113435833-113436234. Error was invalid region `4:113435834-113436234`
[2016-04-15T04:08Z] 2016-04-14 21:08:01 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:08:01,263 - WARNING - Could not retrieve variants from source file in region 4:108930828-108931229. Error was invalid region `4:108930829-108931229`
[2016-04-15T04:08Z] 2016-04-14 21:08:01 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:08:01,448 - WARNING - Could not retrieve variants from source file in region 4:100234842-100239509. Error was invalid region `4:100234843-100239509`
[2016-04-15T04:08Z] 2016-04-14 21:08:01 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:08:01,779 - WARNING - Could not retrieve variants from source file in region 4:110678714-110679115. Error was invalid region `4:110678715-110679115`
[2016-04-15T04:08Z] 2016-04-14 21:08:03 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:08:03,629 - WARNING - Could not retrieve variants from source file in region 4:102964832-102965233. Error was invalid region `4:102964833-102965233`
[2016-04-15T04:08Z] 2016-04-14 21:08:03 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:08:03,836 - WARNING - Could not retrieve variants from source file in region 4:104061782-104082539. Error was invalid region `4:104061783-104082539`
[2016-04-15T04:08Z] 2016-04-14 21:08:05 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:08:05,091 - WARNING - Could not retrieve variants from source file in region 4:103611634-103612035. Error was invalid region `4:103611635-103612035`
[2016-04-15T04:08Z] 2016-04-14 21:08:05 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:08:05,454 - WARNING - Could not retrieve variants from source file in region 4:113198864-113199265. Error was invalid region `4:113198865-113199265`
[2016-04-15T04:08Z] 2016-04-14 21:08:05 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:08:05,861 - WARNING - Could not retrieve variants from source file in region 4:102839076-102839477. Error was invalid region `4:102839077-102839477`
[2016-04-15T04:08Z] 2016-04-14 21:08:06 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:08:06,547 - WARNING - Could not retrieve variants from source file in region 4:108930828-108931229. Error was invalid region `4:108930829-108931229`
[2016-04-15T04:08Z] 2016-04-14 21:08:06 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:08:06,955 - WARNING - Could not retrieve variants from source file in region 4:100234842-100239509. Error was invalid region `4:100234843-100239509`
[2016-04-15T04:08Z] 2016-04-14 21:08:06 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:08:06,980 - WARNING - Could not retrieve variants from source file in region 4:113435833-113436234. Error was invalid region `4:113435834-113436234`
[2016-04-15T04:08Z] 2016-04-14 21:08:08 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:08:08,310 - WARNING - Could not retrieve variants from source file in region 4:104061782-104082539. Error was invalid region `4:104061783-104082539`
[2016-04-15T04:08Z] 2016-04-14 21:08:10 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:08:10,468 - WARNING - Could not retrieve variants from source file in region 4:103611634-103612035. Error was invalid region `4:103611635-103612035`
[2016-04-15T04:08Z] 2016-04-14 21:08:10 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:08:10,688 - WARNING - Could not retrieve variants from source file in region 4:102839076-102839477. Error was invalid region `4:102839077-102839477`
[2016-04-15T04:08Z] 2016-04-14 21:08:15 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:08:15,267 - WARNING - Could not retrieve variants from source file in region 4:103789975-103790376. Error was invalid region `4:103789976-103790376`
[2016-04-15T04:08Z] 2016-04-14 21:08:15 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:08:15,905 - WARNING - Could not retrieve variants from source file in region 4:113066620-113067021. Error was invalid region `4:113066621-113067021`
[2016-04-15T04:08Z] 2016-04-14 21:08:17 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:08:17,016 - WARNING - Could not retrieve variants from source file in region 4:101367152-101367553. Error was invalid region `4:101367153-101367553`
[2016-04-15T04:08Z] 2016-04-14 21:08:18 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:08:18,802 - WARNING - Could not retrieve variants from source file in region 4:111397997-111409895. Error was invalid region `4:111397998-111409895`
[2016-04-15T04:08Z] 2016-04-14 21:08:19 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:08:19,941 - WARNING - Could not retrieve variants from source file in region 4:108640824-108641507. Error was invalid region `4:108640825-108641507`
[2016-04-15T04:08Z] 2016-04-14 21:08:20 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:08:20,642 - WARNING - Could not retrieve variants from source file in region 4:111543791-111544194. Error was invalid region `4:111543792-111544194`
[2016-04-15T04:08Z] 2016-04-14 21:08:21 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:08:21,244 - WARNING - Could not retrieve variants from source file in region 4:108575744-108576145. Error was invalid region `4:108575745-108576145`
[2016-04-15T04:08Z] 2016-04-14 21:08:21 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:08:21,298 - WARNING - Could not retrieve variants from source file in region 4:113066620-113067021. Error was invalid region `4:113066621-113067021`
[2016-04-15T04:08Z] 2016-04-14 21:08:21 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:08:21,756 - WARNING - Could not retrieve variants from source file in region 4:101367152-101367553. Error was invalid region `4:101367153-101367553`
[2016-04-15T04:08Z] 2016-04-14 21:08:21 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:08:21,808 - WARNING - Could not retrieve variants from source file in region 4:103555781-103561152. Error was invalid region `4:103555782-103561152`
[2016-04-15T04:08Z] 2016-04-14 21:08:21 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:08:21,820 - WARNING - Could not retrieve variants from source file in region 4:113066620-113067021. Error was invalid region `4:113066621-113067021`
[2016-04-15T04:08Z] 2016-04-14 21:08:22 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:08:22,982 - WARNING - Could not retrieve variants from source file in region 4:111397997-111409895. Error was invalid region `4:111397998-111409895`
[2016-04-15T04:08Z] 2016-04-14 21:08:24 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:08:24,126 - WARNING - Could not retrieve variants from source file in region 4:103499978-103514848. Error was invalid region `4:103499979-103514848`
[2016-04-15T04:08Z] 2016-04-14 21:08:24 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:08:24,223 - WARNING - Could not retrieve variants from source file in region 4:108640824-108641507. Error was invalid region `4:108640825-108641507`
[2016-04-15T04:08Z] 2016-04-14 21:08:26 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:08:26,135 - WARNING - Could not retrieve variants from source file in region 4:108575744-108576145. Error was invalid region `4:108575745-108576145`
[2016-04-15T04:08Z] 2016-04-14 21:08:26 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:08:26,722 - WARNING - Could not retrieve variants from source file in region 4:110900987-110914617. Error was invalid region `4:110900988-110914617`
[2016-04-15T04:08Z] 2016-04-14 21:08:27 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:08:27,235 - WARNING - Could not retrieve variants from source file in region 4:107133708-107168621. Error was invalid region `4:107133709-107168621`
[2016-04-15T04:08Z] 2016-04-14 21:08:27 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:08:27,252 - WARNING - Could not retrieve variants from source file in region 4:101367152-101367553. Error was invalid region `4:101367153-101367553`
[2016-04-15T04:08Z] 2016-04-14 21:08:27 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:08:27,274 - WARNING - Could not retrieve variants from source file in region 4:111397997-111409895. Error was invalid region `4:111397998-111409895`
[2016-04-15T04:08Z] 2016-04-14 21:08:28 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:08:28,884 - WARNING - Could not retrieve variants from source file in region 4:102750865-102751466. Error was invalid region `4:102750866-102751466`
[2016-04-15T04:08Z] 2016-04-14 21:08:28 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:08:28,885 - WARNING - Could not retrieve variants from source file in region 4:108640824-108641507. Error was invalid region `4:108640825-108641507`
[2016-04-15T04:08Z] 2016-04-14 21:08:31 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:08:31,901 - WARNING - Could not retrieve variants from source file in region 4:107133708-107168621. Error was invalid region `4:107133709-107168621`
[2016-04-15T04:08Z] 2016-04-14 21:08:33 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:08:33,217 - WARNING - Could not retrieve variants from source file in region 4:102750865-102751466. Error was invalid region `4:102750866-102751466`
[2016-04-15T04:08Z] 2016-04-14 21:08:35 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:08:35,052 - WARNING - Could not retrieve variants from source file in region 4:106859338-106861920. Error was invalid region `4:106859339-106861920`
[2016-04-15T04:08Z] 2016-04-14 21:08:35 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:08:35,366 - WARNING - Could not retrieve variants from source file in region 4:101108950-101109351. Error was invalid region `4:101108951-101109351`
[2016-04-15T04:08Z] 2016-04-14 21:08:35 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:08:35,497 - WARNING - Could not retrieve variants from source file in region 4:101108950-101109351. Error was invalid region `4:101108951-101109351`
[2016-04-15T04:08Z] 2016-04-14 21:08:37 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:08:37,722 - WARNING - Could not retrieve variants from source file in region 4:101108950-101109351. Error was invalid region `4:101108951-101109351`
[2016-04-15T04:08Z] 2016-04-14 21:08:38 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:08:38,058 - WARNING - Could not retrieve variants from source file in region 4:107279239-107279672. Error was invalid region `4:107279240-107279672`
[2016-04-15T04:08Z] 2016-04-14 21:08:41 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:08:41,035 - WARNING - Could not retrieve variants from source file in region 4:107279239-107279672. Error was invalid region `4:107279240-107279672`
[2016-04-15T04:08Z] ['bcbio-variation-recall', 'square', '-Xms750m', '-Xmx7280m', '-XX:+UseSerialGC', '-c', 16, '-r', u'4:115584858-134074404', '--caller', 'platypus', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/4/Batch1-4_115584857_134074404.vcf.gz', '/mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/4/Batch1-4_115584857_134074404.vcf-inputs.txt'] in region: 4:115584858-134074404
[2016-04-15T04:08Z] 2016-04-14 21:08:54 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:08:54,277 - WARNING - Could not retrieve variants from source file in region 4:134073847-134074248. Error was invalid region `4:134073848-134074248`
[2016-04-15T04:08Z] 2016-04-14 21:08:55 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:08:55,921 - WARNING - Could not retrieve variants from source file in region 4:120528116-120528517. Error was invalid region `4:120528117-120528517`
[2016-04-15T04:08Z] 2016-04-14 21:08:56 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:08:56,313 - WARNING - Could not retrieve variants from source file in region 4:128689725-128690126. Error was invalid region `4:128689726-128690126`
[2016-04-15T04:08Z] 2016-04-14 21:08:57 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:08:57,335 - WARNING - Could not retrieve variants from source file in region 4:121957348-121966997. Error was invalid region `4:121957349-121966997`
[2016-04-15T04:08Z] 2016-04-14 21:08:57 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:08:57,350 - WARNING - Could not retrieve variants from source file in region 4:129913134-129925167. Error was invalid region `4:129913135-129925167`
[2016-04-15T04:08Z] 2016-04-14 21:08:58 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:08:58,106 - WARNING - Could not retrieve variants from source file in region 4:130023673-130030842. Error was invalid region `4:130023674-130030842`
[2016-04-15T04:08Z] 2016-04-14 21:08:58 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:08:58,168 - WARNING - Could not retrieve variants from source file in region 4:128564789-128584770. Error was invalid region `4:128564790-128584770`
[2016-04-15T04:08Z] 2016-04-14 21:08:58 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:08:58,179 - WARNING - Could not retrieve variants from source file in region 4:122682796-122683197. Error was invalid region `4:122682797-122683197`
[2016-04-15T04:08Z] 2016-04-14 21:08:58 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:08:58,229 - WARNING - Could not retrieve variants from source file in region 4:129867069-129867470. Error was invalid region `4:129867070-129867470`
[2016-04-15T04:08Z] 2016-04-14 21:08:58 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:08:58,545 - WARNING - Could not retrieve variants from source file in region 4:120213599-120214220. Error was invalid region `4:120213600-120214220`
[2016-04-15T04:08Z] 2016-04-14 21:08:58 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:08:58,703 - WARNING - Could not retrieve variants from source file in region 4:122872508-122872909. Error was invalid region `4:122872509-122872909`
[2016-04-15T04:08Z] 2016-04-14 21:08:58 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:08:58,898 - WARNING - Could not retrieve variants from source file in region 4:129100432-129100833. Error was invalid region `4:129100433-129100833`
[2016-04-15T04:08Z] 2016-04-14 21:08:59 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:08:59,098 - WARNING - Could not retrieve variants from source file in region 4:134073847-134074248. Error was invalid region `4:134073848-134074248`
[2016-04-15T04:09Z] 2016-04-14 21:09:01 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:09:01,580 - WARNING - Could not retrieve variants from source file in region 4:120528116-120528517. Error was invalid region `4:120528117-120528517`
[2016-04-15T04:09Z] 2016-04-14 21:09:02 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:09:02,584 - WARNING - Could not retrieve variants from source file in region 4:124177796-124178197. Error was invalid region `4:124177797-124178197`
[2016-04-15T04:09Z] 2016-04-14 21:09:02 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:09:02,896 - WARNING - Could not retrieve variants from source file in region 4:128689725-128690126. Error was invalid region `4:128689726-128690126`
[2016-04-15T04:09Z] 2016-04-14 21:09:05 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:09:05,876 - WARNING - Could not retrieve variants from source file in region 4:128564789-128584770. Error was invalid region `4:128564790-128584770`
[2016-04-15T04:09Z] 2016-04-14 21:09:05 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:09:05,984 - WARNING - Could not retrieve variants from source file in region 4:128722831-128741900. Error was invalid region `4:128722832-128741900`
[2016-04-15T04:09Z] 2016-04-14 21:09:06 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:09:06,601 - WARNING - Could not retrieve variants from source file in region 4:129100432-129100833. Error was invalid region `4:129100433-129100833`
[2016-04-15T04:09Z] 2016-04-14 21:09:06 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:09:06,622 - WARNING - Could not retrieve variants from source file in region 4:128995429-129044360. Error was invalid region `4:128995430-129044360`
[2016-04-15T04:09Z] 2016-04-14 21:09:07 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:09:07,194 - WARNING - Could not retrieve variants from source file in region 4:134073847-134074248. Error was invalid region `4:134073848-134074248`
[2016-04-15T04:09Z] 2016-04-14 21:09:07 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:09:07,463 - WARNING - Could not retrieve variants from source file in region 4:129867069-129867470. Error was invalid region `4:129867070-129867470`
[2016-04-15T04:09Z] 2016-04-14 21:09:07 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:09:07,495 - WARNING - Could not retrieve variants from source file in region 4:122682796-122683197. Error was invalid region `4:122682797-122683197`
[2016-04-15T04:09Z] 2016-04-14 21:09:07 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:09:07,502 - WARNING - Could not retrieve variants from source file in region 4:120528116-120528517. Error was invalid region `4:120528117-120528517`
[2016-04-15T04:09Z] 2016-04-14 21:09:07 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:09:07,581 - WARNING - Could not retrieve variants from source file in region 4:128626670-128627071. Error was invalid region `4:128626671-128627071`
[2016-04-15T04:09Z] 2016-04-14 21:09:07 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:09:07,608 - WARNING - Could not retrieve variants from source file in region 4:122872508-122872909. Error was invalid region `4:122872509-122872909`
[2016-04-15T04:09Z] 2016-04-14 21:09:08 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:09:08,218 - WARNING - Could not retrieve variants from source file in region 4:128689725-128690126. Error was invalid region `4:128689726-128690126`
[2016-04-15T04:09Z] 2016-04-14 21:09:08 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:09:08,219 - WARNING - Could not retrieve variants from source file in region 4:124177796-124178197. Error was invalid region `4:124177797-124178197`
[2016-04-15T04:09Z] 2016-04-14 21:09:12 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:09:12,485 - WARNING - Could not retrieve variants from source file in region 4:128564789-128584770. Error was invalid region `4:128564790-128584770`
[2016-04-15T04:09Z] 2016-04-14 21:09:13 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:09:13,327 - WARNING - Could not retrieve variants from source file in region 4:128722831-128741900. Error was invalid region `4:128722832-128741900`
[2016-04-15T04:09Z] 2016-04-14 21:09:15 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:09:15,348 - WARNING - Could not retrieve variants from source file in region 4:128995429-129044360. Error was invalid region `4:128995430-129044360`
[2016-04-15T04:09Z] 2016-04-14 21:09:15 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:09:15,359 - WARNING - Could not retrieve variants from source file in region 4:129100432-129100833. Error was invalid region `4:129100433-129100833`
[2016-04-15T04:09Z] 2016-04-14 21:09:16 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:09:16,586 - WARNING - Could not retrieve variants from source file in region 4:129867069-129867470. Error was invalid region `4:129867070-129867470`
[2016-04-15T04:09Z] 2016-04-14 21:09:16 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:09:16,834 - WARNING - Could not retrieve variants from source file in region 4:122682796-122683197. Error was invalid region `4:122682797-122683197`
[2016-04-15T04:09Z] 2016-04-14 21:09:17 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:09:17,063 - WARNING - Could not retrieve variants from source file in region 4:122872508-122872909. Error was invalid region `4:122872509-122872909`
[2016-04-15T04:09Z] 2016-04-14 21:09:26 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:09:26,622 - WARNING - Could not retrieve variants from source file in region 4:121737838-121738239. Error was invalid region `4:121737839-121738239`
[2016-04-15T04:09Z] 2016-04-14 21:09:27 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:09:27,778 - WARNING - Could not retrieve variants from source file in region 4:120474648-120475049. Error was invalid region `4:120474649-120475049`
[2016-04-15T04:09Z] 2016-04-14 21:09:28 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:09:28,591 - WARNING - Could not retrieve variants from source file in region 4:121705990-121706391. Error was invalid region `4:121705991-121706391`
[2016-04-15T04:09Z] 2016-04-14 21:09:28 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:09:28,703 - WARNING - Could not retrieve variants from source file in region 4:120240027-120242092. Error was invalid region `4:120240028-120242092`
[2016-04-15T04:09Z] 2016-04-14 21:09:29 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:09:29,377 - WARNING - Could not retrieve variants from source file in region 4:123813508-123843906. Error was invalid region `4:123813509-123843906`
[2016-04-15T04:09Z] 2016-04-14 21:09:30 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:09:30,373 - WARNING - Could not retrieve variants from source file in region 4:120181513-120181914. Error was invalid region `4:120181514-120181914`
[2016-04-15T04:09Z] 2016-04-14 21:09:30 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:09:30,944 - WARNING - Could not retrieve variants from source file in region 4:128807008-128815154. Error was invalid region `4:128807009-128815154`
[2016-04-15T04:09Z] 2016-04-14 21:09:33 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:09:33,244 - WARNING - Could not retrieve variants from source file in region 4:123536752-123537153. Error was invalid region `4:123536753-123537153`
[2016-04-15T04:09Z] 2016-04-14 21:09:33 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:09:33,288 - WARNING - Could not retrieve variants from source file in region 4:122253803-122254204. Error was invalid region `4:122253804-122254204`
[2016-04-15T04:09Z] 2016-04-14 21:09:33 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:09:33,548 - WARNING - Could not retrieve variants from source file in region 4:120474648-120475049. Error was invalid region `4:120474649-120475049`
[2016-04-15T04:09Z] 2016-04-14 21:09:33 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:09:33,836 - WARNING - Could not retrieve variants from source file in region 4:129783838-129784239. Error was invalid region `4:129783839-129784239`
[2016-04-15T04:09Z] 2016-04-14 21:09:34 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:09:34,362 - WARNING - Could not retrieve variants from source file in region 4:123813508-123843906. Error was invalid region `4:123813509-123843906`
[2016-04-15T04:09Z] 2016-04-14 21:09:35 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:09:35,513 - WARNING - Could not retrieve variants from source file in region 4:128807008-128815154. Error was invalid region `4:128807009-128815154`
[2016-04-15T04:09Z] 2016-04-14 21:09:38 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:09:38,656 - WARNING - Could not retrieve variants from source file in region 4:123663993-123665109. Error was invalid region `4:123663994-123665109`
[2016-04-15T04:09Z] 2016-04-14 21:09:38 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:09:38,727 - WARNING - Could not retrieve variants from source file in region 4:122823841-122824242. Error was invalid region `4:122823842-122824242`
[2016-04-15T04:09Z] 2016-04-14 21:09:38 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:09:38,771 - WARNING - Could not retrieve variants from source file in region 4:122734931-122765342. Error was invalid region `4:122734932-122765342`
[2016-04-15T04:09Z] 2016-04-14 21:09:39 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:09:39,452 - WARNING - Could not retrieve variants from source file in region 4:123536752-123537153. Error was invalid region `4:123536753-123537153`
[2016-04-15T04:09Z] 2016-04-14 21:09:40 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:09:40,301 - WARNING - Could not retrieve variants from source file in region 4:120181513-120181914. Error was invalid region `4:120181514-120181914`
[2016-04-15T04:09Z] 2016-04-14 21:09:40 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:09:40,427 - WARNING - Could not retrieve variants from source file in region 4:128807008-128815154. Error was invalid region `4:128807009-128815154`
[2016-04-15T04:09Z] 2016-04-14 21:09:44 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:09:44,462 - WARNING - Could not retrieve variants from source file in region 4:122823841-122824242. Error was invalid region `4:122823842-122824242`
[2016-04-15T04:09Z] 2016-04-14 21:09:45 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:09:45,990 - WARNING - Could not retrieve variants from source file in region 4:122253803-122254204. Error was invalid region `4:122253804-122254204`
[2016-04-15T04:09Z] 2016-04-14 21:09:54 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:09:54,181 - WARNING - Could not retrieve variants from source file in region 4:126329578-126329979. Error was invalid region `4:126329579-126329979`
[2016-04-15T04:09Z] 2016-04-14 21:09:54 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:09:54,488 - WARNING - Could not retrieve variants from source file in region 4:126329578-126329979. Error was invalid region `4:126329579-126329979`
[2016-04-15T04:09Z] 2016-04-14 21:09:56 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:09:56,942 - WARNING - Could not retrieve variants from source file in region 4:119736585-119736986. Error was invalid region `4:119736586-119736986`
[2016-04-15T04:09Z] 2016-04-14 21:09:56 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:09:56,981 - WARNING - Could not retrieve variants from source file in region 4:126369661-126373979. Error was invalid region `4:126369662-126373979`
[2016-04-15T04:09Z] 2016-04-14 21:09:57 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:09:57,562 - WARNING - Could not retrieve variants from source file in region 4:123377271-123377672. Error was invalid region `4:123377272-123377672`
[2016-04-15T04:09Z] 2016-04-14 21:09:57 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:09:57,728 - WARNING - Could not retrieve variants from source file in region 4:122078073-122078474. Error was invalid region `4:122078074-122078474`
[2016-04-15T04:09Z] 2016-04-14 21:09:58 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:09:58,416 - WARNING - Could not retrieve variants from source file in region 4:126329578-126329979. Error was invalid region `4:126329579-126329979`
[2016-04-15T04:09Z] 2016-04-14 21:09:58 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:09:58,910 - WARNING - Could not retrieve variants from source file in region 4:126369661-126373979. Error was invalid region `4:126369662-126373979`
[2016-04-15T04:10Z] 2016-04-14 21:10:00 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:10:00,384 - WARNING - Could not retrieve variants from source file in region 4:119237137-119237538. Error was invalid region `4:119237138-119237538`
[2016-04-15T04:10Z] 2016-04-14 21:10:01 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:10:01,451 - WARNING - Could not retrieve variants from source file in region 4:123377271-123377672. Error was invalid region `4:123377272-123377672`
[2016-04-15T04:10Z] 2016-04-14 21:10:03 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:10:03,156 - WARNING - Could not retrieve variants from source file in region 4:123377271-123377672. Error was invalid region `4:123377272-123377672`
[2016-04-15T04:10Z] 2016-04-14 21:10:04 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:10:04,617 - WARNING - Could not retrieve variants from source file in region 4:119237137-119237538. Error was invalid region `4:119237138-119237538`
[2016-04-15T04:10Z] 2016-04-14 21:10:05 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:10:05,423 - WARNING - Could not retrieve variants from source file in region 4:119736585-119736986. Error was invalid region `4:119736586-119736986`
[2016-04-15T04:10Z] 2016-04-14 21:10:06 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:10:06,278 - WARNING - Could not retrieve variants from source file in region 4:123257537-123283355. Error was invalid region `4:123257538-123283355`
[2016-04-15T04:10Z] 2016-04-14 21:10:06 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:10:06,478 - WARNING - Could not retrieve variants from source file in region 4:125591476-125592630. Error was invalid region `4:125591477-125592630`
[2016-04-15T04:10Z] 2016-04-14 21:10:10 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:10:10,652 - WARNING - Could not retrieve variants from source file in region 4:119685836-119686237. Error was invalid region `4:119685837-119686237`
[2016-04-15T04:10Z] 2016-04-14 21:10:15 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:10:15,592 - WARNING - Could not retrieve variants from source file in region 4:119273501-119273902. Error was invalid region `4:119273502-119273902`
[2016-04-15T04:10Z] 2016-04-14 21:10:16 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:10:16,832 - WARNING - Could not retrieve variants from source file in region 4:115748794-115749195. Error was invalid region `4:115748795-115749195`
[2016-04-15T04:10Z] 2016-04-14 21:10:16 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:10:16,870 - WARNING - Could not retrieve variants from source file in region 4:118006096-118006497. Error was invalid region `4:118006097-118006497`
[2016-04-15T04:10Z] 2016-04-14 21:10:16 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:10:16,897 - WARNING - Could not retrieve variants from source file in region 4:115588750-115589492. Error was invalid region `4:115588751-115589492`
[2016-04-15T04:10Z] 2016-04-14 21:10:17 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:10:17,163 - WARNING - Could not retrieve variants from source file in region 4:119273501-119273902. Error was invalid region `4:119273502-119273902`
[2016-04-15T04:10Z] 2016-04-14 21:10:18 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:10:18,646 - WARNING - Could not retrieve variants from source file in region 4:119203010-119203411. Error was invalid region `4:119203011-119203411`
[2016-04-15T04:10Z] 2016-04-14 21:10:19 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:10:19,719 - WARNING - Could not retrieve variants from source file in region 4:119273501-119273902. Error was invalid region `4:119273502-119273902`
[2016-04-15T04:10Z] 2016-04-14 21:10:19 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:10:19,993 - WARNING - Could not retrieve variants from source file in region 4:119203010-119203411. Error was invalid region `4:119203011-119203411`
[2016-04-15T04:10Z] 2016-04-14 21:10:20 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:10:20,036 - WARNING - Could not retrieve variants from source file in region 4:115588750-115589492. Error was invalid region `4:115588751-115589492`
[2016-04-15T04:10Z] 2016-04-14 21:10:20 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:10:20,319 - WARNING - Could not retrieve variants from source file in region 4:119059078-119059479. Error was invalid region `4:119059079-119059479`
[2016-04-15T04:10Z] 2016-04-14 21:10:21 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:10:21,205 - WARNING - Could not retrieve variants from source file in region 4:115748794-115749195. Error was invalid region `4:115748795-115749195`
[2016-04-15T04:10Z] 2016-04-14 21:10:21 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:10:21,215 - WARNING - Could not retrieve variants from source file in region 4:118006096-118006497. Error was invalid region `4:118006097-118006497`
[2016-04-15T04:10Z] 2016-04-14 21:10:21 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:10:21,249 - WARNING - Could not retrieve variants from source file in region 4:115588750-115589492. Error was invalid region `4:115588751-115589492`
[2016-04-15T04:10Z] ['bcbio-variation-recall', 'square', '-Xms750m', '-Xmx7280m', '-XX:+UseSerialGC', '-c', 16, '-r', u'4:134075462-150351181', '--caller', 'platypus', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/4/Batch1-4_134075461_150351181.vcf.gz', '/mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/4/Batch1-4_134075461_150351181.vcf-inputs.txt'] in region: 4:134075462-150351181
[2016-04-15T04:10Z] 2016-04-14 21:10:39 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:10:39,397 - WARNING - Could not retrieve variants from source file in region 4:140810426-140811325. Error was invalid region `4:140810427-140811325`
[2016-04-15T04:10Z] 2016-04-14 21:10:39 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:10:39,507 - WARNING - Could not retrieve variants from source file in region 4:144442400-144467294. Error was invalid region `4:144442401-144467294`
[2016-04-15T04:10Z] 2016-04-14 21:10:40 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:10:40,531 - WARNING - Could not retrieve variants from source file in region 4:147430980-147431381. Error was invalid region `4:147430981-147431381`
[2016-04-15T04:10Z] 2016-04-14 21:10:40 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:10:40,667 - WARNING - Could not retrieve variants from source file in region 4:147560246-147560647. Error was invalid region `4:147560247-147560647`
[2016-04-15T04:10Z] 2016-04-14 21:10:40 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:10:40,704 - WARNING - Could not retrieve variants from source file in region 4:144918501-144921797. Error was invalid region `4:144918502-144921797`
[2016-04-15T04:10Z] 2016-04-14 21:10:41 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:10:41,032 - WARNING - Could not retrieve variants from source file in region 4:146653409-146653810. Error was invalid region `4:146653410-146653810`
[2016-04-15T04:10Z] 2016-04-14 21:10:41 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:10:41,227 - WARNING - Could not retrieve variants from source file in region 4:145041475-145041931. Error was invalid region `4:145041476-145041931`
[2016-04-15T04:10Z] 2016-04-14 21:10:41 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:10:41,553 - WARNING - Could not retrieve variants from source file in region 4:140651373-140651777. Error was invalid region `4:140651374-140651777`
[2016-04-15T04:10Z] 2016-04-14 21:10:41 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:10:41,576 - WARNING - Could not retrieve variants from source file in region 4:139100161-139100562. Error was invalid region `4:139100162-139100562`
[2016-04-15T04:10Z] 2016-04-14 21:10:41 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:10:41,596 - WARNING - Could not retrieve variants from source file in region 4:149356305-149366099. Error was invalid region `4:149356306-149366099`
[2016-04-15T04:10Z] 2016-04-14 21:10:41 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:10:41,834 - WARNING - Could not retrieve variants from source file in region 4:144801451-144801861. Error was invalid region `4:144801452-144801861`
[2016-04-15T04:10Z] 2016-04-14 21:10:42 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:10:42,176 - WARNING - Could not retrieve variants from source file in region 4:148463421-148463822. Error was invalid region `4:148463422-148463822`
[2016-04-15T04:10Z] 2016-04-14 21:10:42 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:10:42,190 - WARNING - Could not retrieve variants from source file in region 4:140005083-140005484. Error was invalid region `4:140005084-140005484`
[2016-04-15T04:10Z] 2016-04-14 21:10:42 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:10:42,212 - WARNING - Could not retrieve variants from source file in region 4:140449993-140450394. Error was invalid region `4:140449994-140450394`
[2016-04-15T04:10Z] 2016-04-14 21:10:45 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:10:45,190 - WARNING - Could not retrieve variants from source file in region 4:140810426-140811325. Error was invalid region `4:140810427-140811325`
[2016-04-15T04:10Z] 2016-04-14 21:10:45 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:10:45,685 - WARNING - Could not retrieve variants from source file in region 4:144442400-144467294. Error was invalid region `4:144442401-144467294`
[2016-04-15T04:10Z] 2016-04-14 21:10:48 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:10:48,439 - WARNING - Could not retrieve variants from source file in region 4:147560246-147560647. Error was invalid region `4:147560247-147560647`
[2016-04-15T04:10Z] 2016-04-14 21:10:49 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:10:49,179 - WARNING - Could not retrieve variants from source file in region 4:145041475-145041931. Error was invalid region `4:145041476-145041931`
[2016-04-15T04:10Z] 2016-04-14 21:10:49 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:10:49,668 - WARNING - Could not retrieve variants from source file in region 4:139100161-139100562. Error was invalid region `4:139100162-139100562`
[2016-04-15T04:10Z] 2016-04-14 21:10:49 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:10:49,854 - WARNING - Could not retrieve variants from source file in region 4:140005083-140005484. Error was invalid region `4:140005084-140005484`
[2016-04-15T04:10Z] 2016-04-14 21:10:50 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:10:50,320 - WARNING - Could not retrieve variants from source file in region 4:140651373-140651777. Error was invalid region `4:140651374-140651777`
[2016-04-15T04:10Z] 2016-04-14 21:10:50 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:10:50,372 - WARNING - Could not retrieve variants from source file in region 4:141589924-141600510. Error was invalid region `4:141589925-141600510`
[2016-04-15T04:10Z] 2016-04-14 21:10:53 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:10:53,101 - WARNING - Could not retrieve variants from source file in region 4:147430980-147431381. Error was invalid region `4:147430981-147431381`
[2016-04-15T04:10Z] 2016-04-14 21:10:55 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:10:55,130 - WARNING - Could not retrieve variants from source file in region 4:144918501-144921797. Error was invalid region `4:144918502-144921797`
[2016-04-15T04:10Z] 2016-04-14 21:10:55 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:10:55,168 - WARNING - Could not retrieve variants from source file in region 4:147560246-147560647. Error was invalid region `4:147560247-147560647`
[2016-04-15T04:10Z] 2016-04-14 21:10:56 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:10:56,073 - WARNING - Could not retrieve variants from source file in region 4:146653409-146653810. Error was invalid region `4:146653410-146653810`
[2016-04-15T04:10Z] 2016-04-14 21:10:56 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:10:56,494 - WARNING - Could not retrieve variants from source file in region 4:145041475-145041931. Error was invalid region `4:145041476-145041931`
[2016-04-15T04:10Z] 2016-04-14 21:10:56 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:10:56,630 - WARNING - Could not retrieve variants from source file in region 4:139100161-139100562. Error was invalid region `4:139100162-139100562`
[2016-04-15T04:10Z] 2016-04-14 21:10:57 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:10:57,584 - WARNING - Could not retrieve variants from source file in region 4:144801451-144801861. Error was invalid region `4:144801452-144801861`
[2016-04-15T04:10Z] 2016-04-14 21:10:57 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:10:57,957 - WARNING - Could not retrieve variants from source file in region 4:140005083-140005484. Error was invalid region `4:140005084-140005484`
[2016-04-15T04:10Z] 2016-04-14 21:10:58 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:10:58,308 - WARNING - Could not retrieve variants from source file in region 4:140449993-140450394. Error was invalid region `4:140449994-140450394`
[2016-04-15T04:10Z] 2016-04-14 21:10:58 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:10:58,688 - WARNING - Could not retrieve variants from source file in region 4:149356305-149366099. Error was invalid region `4:149356306-149366099`
[2016-04-15T04:10Z] 2016-04-14 21:10:58 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:10:58,695 - WARNING - Could not retrieve variants from source file in region 4:140651373-140651777. Error was invalid region `4:140651374-140651777`
[2016-04-15T04:11Z] 2016-04-14 21:11:07 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:11:07,577 - WARNING - Could not retrieve variants from source file in region 4:144135507-144135908. Error was invalid region `4:144135508-144135908`
[2016-04-15T04:11Z] 2016-04-14 21:11:08 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:11:08,420 - WARNING - Could not retrieve variants from source file in region 4:144616695-144621969. Error was invalid region `4:144616696-144621969`
[2016-04-15T04:11Z] 2016-04-14 21:11:09 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:11:09,578 - WARNING - Could not retrieve variants from source file in region 4:135120855-135121791. Error was invalid region `4:135120856-135121791`
[2016-04-15T04:11Z] 2016-04-14 21:11:10 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:11:10,283 - WARNING - Could not retrieve variants from source file in region 4:148944256-148944657. Error was invalid region `4:148944257-148944657`
[2016-04-15T04:11Z] 2016-04-14 21:11:10 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:11:10,297 - WARNING - Could not retrieve variants from source file in region 4:148944256-148944657. Error was invalid region `4:148944257-148944657`
[2016-04-15T04:11Z] 2016-04-14 21:11:12 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:11:12,555 - WARNING - Could not retrieve variants from source file in region 4:146076921-146080768. Error was invalid region `4:146076922-146080768`
[2016-04-15T04:11Z] 2016-04-14 21:11:13 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:11:13,399 - WARNING - Could not retrieve variants from source file in region 4:139140283-139140684. Error was invalid region `4:139140284-139140684`
[2016-04-15T04:11Z] 2016-04-14 21:11:13 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:11:13,839 - WARNING - Could not retrieve variants from source file in region 4:141543786-141544187. Error was invalid region `4:141543787-141544187`
[2016-04-15T04:11Z] 2016-04-14 21:11:13 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:11:13,924 - WARNING - Could not retrieve variants from source file in region 4:135120855-135121791. Error was invalid region `4:135120856-135121791`
[2016-04-15T04:11Z] 2016-04-14 21:11:14 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:11:14,468 - WARNING - Could not retrieve variants from source file in region 4:148944256-148944657. Error was invalid region `4:148944257-148944657`
[2016-04-15T04:11Z] 2016-04-14 21:11:17 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:11:17,263 - WARNING - Could not retrieve variants from source file in region 4:139140283-139140684. Error was invalid region `4:139140284-139140684`
[2016-04-15T04:11Z] 2016-04-14 21:11:17 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:11:17,315 - WARNING - Could not retrieve variants from source file in region 4:141483260-141489258. Error was invalid region `4:141483261-141489258`
[2016-04-15T04:11Z] 2016-04-14 21:11:17 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:11:17,348 - WARNING - Could not retrieve variants from source file in region 4:147824653-147825054. Error was invalid region `4:147824654-147825054`
[2016-04-15T04:11Z] 2016-04-14 21:11:17 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:11:17,478 - WARNING - Could not retrieve variants from source file in region 4:141543786-141544187. Error was invalid region `4:141543787-141544187`
[2016-04-15T04:11Z] 2016-04-14 21:11:17 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:11:17,542 - WARNING - Could not retrieve variants from source file in region 4:148559982-148560383. Error was invalid region `4:148559983-148560383`
[2016-04-15T04:11Z] 2016-04-14 21:11:17 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:11:17,731 - WARNING - Could not retrieve variants from source file in region 4:135120855-135121791. Error was invalid region `4:135120856-135121791`
[2016-04-15T04:11Z] 2016-04-14 21:11:18 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:11:18,065 - WARNING - Could not retrieve variants from source file in region 4:141543786-141544187. Error was invalid region `4:141543787-141544187`
[2016-04-15T04:11Z] 2016-04-14 21:11:21 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:11:21,398 - WARNING - Could not retrieve variants from source file in region 4:139140283-139140684. Error was invalid region `4:139140284-139140684`
[2016-04-15T04:11Z] 2016-04-14 21:11:24 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:11:24,099 - WARNING - Could not retrieve variants from source file in region 4:141294603-141295004. Error was invalid region `4:141294604-141295004`
[2016-04-15T04:11Z] 2016-04-14 21:11:25 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:11:25,929 - WARNING - Could not retrieve variants from source file in region 4:143323883-143324284. Error was invalid region `4:143323884-143324284`
[2016-04-15T04:11Z] ['bcbio-variation-recall', 'square', '-Xms750m', '-Xmx7280m', '-XX:+UseSerialGC', '-c', 16, '-r', u'4:150354548-165878648', '--caller', 'platypus', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/4/Batch1-4_150354547_165878648.vcf.gz', '/mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/4/Batch1-4_150354547_165878648.vcf-inputs.txt'] in region: 4:150354548-165878648
[2016-04-15T04:11Z] 2016-04-14 21:11:42 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:11:42,529 - WARNING - Could not retrieve variants from source file in region 4:155458983-155461303. Error was invalid region `4:155458984-155461303`
[2016-04-15T04:11Z] 2016-04-14 21:11:42 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:11:42,688 - WARNING - Could not retrieve variants from source file in region 4:153896147-153897960. Error was invalid region `4:153896148-153897960`
[2016-04-15T04:11Z] 2016-04-14 21:11:43 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:11:43,408 - WARNING - Could not retrieve variants from source file in region 4:157684037-157684438. Error was invalid region `4:157684038-157684438`
[2016-04-15T04:11Z] 2016-04-14 21:11:43 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:11:43,419 - WARNING - Could not retrieve variants from source file in region 4:159631780-159632181. Error was invalid region `4:159631781-159632181`
[2016-04-15T04:11Z] 2016-04-14 21:11:43 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:11:43,540 - WARNING - Could not retrieve variants from source file in region 4:159881268-159894495. Error was invalid region `4:159881269-159894495`
[2016-04-15T04:11Z] 2016-04-14 21:11:43 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:11:43,740 - WARNING - Could not retrieve variants from source file in region 4:164466613-164467014. Error was invalid region `4:164466614-164467014`
[2016-04-15T04:11Z] 2016-04-14 21:11:43 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:11:43,758 - WARNING - Could not retrieve variants from source file in region 4:156632180-156632581. Error was invalid region `4:156632181-156632581`
[2016-04-15T04:11Z] 2016-04-14 21:11:44 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:11:44,053 - WARNING - Could not retrieve variants from source file in region 4:152609615-152610016. Error was invalid region `4:152609616-152610016`
[2016-04-15T04:11Z] 2016-04-14 21:11:44 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:11:44,586 - WARNING - Could not retrieve variants from source file in region 4:160260185-160277466. Error was invalid region `4:160260186-160277466`
[2016-04-15T04:11Z] 2016-04-14 21:11:44 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:11:44,745 - WARNING - Could not retrieve variants from source file in region 4:155720063-155720464. Error was invalid region `4:155720064-155720464`
[2016-04-15T04:11Z] 2016-04-14 21:11:44 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:11:44,823 - WARNING - Could not retrieve variants from source file in region 4:152024115-152025463. Error was invalid region `4:152024116-152025463`
[2016-04-15T04:11Z] 2016-04-14 21:11:49 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:11:49,667 - WARNING - Could not retrieve variants from source file in region 4:155458983-155461303. Error was invalid region `4:155458984-155461303`
[2016-04-15T04:11Z] 2016-04-14 21:11:49 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:11:49,747 - WARNING - Could not retrieve variants from source file in region 4:155249078-155256395. Error was invalid region `4:155249079-155256395`
[2016-04-15T04:11Z] 2016-04-14 21:11:49 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:11:49,853 - WARNING - Could not retrieve variants from source file in region 4:153896147-153897960. Error was invalid region `4:153896148-153897960`
[2016-04-15T04:11Z] 2016-04-14 21:11:51 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:11:51,329 - WARNING - Could not retrieve variants from source file in region 4:157684037-157684438. Error was invalid region `4:157684038-157684438`
[2016-04-15T04:11Z] 2016-04-14 21:11:52 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:11:52,020 - WARNING - Could not retrieve variants from source file in region 4:159881268-159894495. Error was invalid region `4:159881269-159894495`
[2016-04-15T04:11Z] 2016-04-14 21:11:52 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:11:52,164 - WARNING - Could not retrieve variants from source file in region 4:165850477-165851935. Error was invalid region `4:165850478-165851935`
[2016-04-15T04:11Z] 2016-04-14 21:11:52 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:11:52,596 - WARNING - Could not retrieve variants from source file in region 4:164466613-164467014. Error was invalid region `4:164466614-164467014`
[2016-04-15T04:11Z] 2016-04-14 21:11:52 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:11:52,967 - WARNING - Could not retrieve variants from source file in region 4:156632180-156632581. Error was invalid region `4:156632181-156632581`
[2016-04-15T04:11Z] 2016-04-14 21:11:53 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:11:53,223 - WARNING - Could not retrieve variants from source file in region 4:154387386-154387787. Error was invalid region `4:154387387-154387787`
[2016-04-15T04:11Z] 2016-04-14 21:11:53 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:11:53,327 - WARNING - Could not retrieve variants from source file in region 4:164272492-164272893. Error was invalid region `4:164272493-164272893`
[2016-04-15T04:11Z] 2016-04-14 21:11:53 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:11:53,474 - WARNING - Could not retrieve variants from source file in region 4:152024115-152025463. Error was invalid region `4:152024116-152025463`
[2016-04-15T04:11Z] 2016-04-14 21:11:54 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:11:54,705 - WARNING - Could not retrieve variants from source file in region 4:155458983-155461303. Error was invalid region `4:155458984-155461303`
[2016-04-15T04:11Z] 2016-04-14 21:11:55 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:11:55,360 - WARNING - Could not retrieve variants from source file in region 4:153896147-153897960. Error was invalid region `4:153896148-153897960`
[2016-04-15T04:11Z] 2016-04-14 21:11:56 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:11:56,225 - WARNING - Could not retrieve variants from source file in region 4:159631780-159632181. Error was invalid region `4:159631781-159632181`
[2016-04-15T04:11Z] 2016-04-14 21:11:58 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:11:58,741 - WARNING - Could not retrieve variants from source file in region 4:159881268-159894495. Error was invalid region `4:159881269-159894495`
[2016-04-15T04:11Z] 2016-04-14 21:11:58 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:11:58,923 - WARNING - Could not retrieve variants from source file in region 4:164466613-164467014. Error was invalid region `4:164466614-164467014`
[2016-04-15T04:11Z] 2016-04-14 21:11:59 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:11:59,638 - WARNING - Could not retrieve variants from source file in region 4:155748408-155748810. Error was invalid region `4:155748409-155748810`
[2016-04-15T04:11Z] 2016-04-14 21:11:59 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:11:59,729 - WARNING - Could not retrieve variants from source file in region 4:154387386-154387787. Error was invalid region `4:154387387-154387787`
[2016-04-15T04:11Z] 2016-04-14 21:11:59 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:11:59,731 - WARNING - Could not retrieve variants from source file in region 4:152609615-152610016. Error was invalid region `4:152609616-152610016`
[2016-04-15T04:11Z] 2016-04-14 21:11:59 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:11:59,964 - WARNING - Could not retrieve variants from source file in region 4:156632180-156632581. Error was invalid region `4:156632181-156632581`
[2016-04-15T04:12Z] 2016-04-14 21:12:00 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:12:00,103 - WARNING - Could not retrieve variants from source file in region 4:152024115-152025463. Error was invalid region `4:152024116-152025463`
[2016-04-15T04:12Z] 2016-04-14 21:12:00 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:12:00,121 - WARNING - Could not retrieve variants from source file in region 4:160260185-160277466. Error was invalid region `4:160260186-160277466`
[2016-04-15T04:12Z] 2016-04-14 21:12:10 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:12:10,944 - WARNING - Could not retrieve variants from source file in region 4:155410611-155411294. Error was invalid region `4:155410612-155411294`
[2016-04-15T04:12Z] 2016-04-14 21:12:12 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:12:12,273 - WARNING - Could not retrieve variants from source file in region 4:153690631-153691032. Error was invalid region `4:153690632-153691032`
[2016-04-15T04:12Z] 2016-04-14 21:12:12 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:12:12,514 - WARNING - Could not retrieve variants from source file in region 4:154709643-154710046. Error was invalid region `4:154709644-154710046`
[2016-04-15T04:12Z] 2016-04-14 21:12:14 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:12:14,049 - WARNING - Could not retrieve variants from source file in region 4:159601465-159601866. Error was invalid region `4:159601466-159601866`
[2016-04-15T04:12Z] 2016-04-14 21:12:14 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:12:14,504 - WARNING - Could not retrieve variants from source file in region 4:156787129-156787530. Error was invalid region `4:156787130-156787530`
[2016-04-15T04:12Z] 2016-04-14 21:12:15 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:12:15,099 - WARNING - Could not retrieve variants from source file in region 4:164435054-164440771. Error was invalid region `4:164435055-164440771`
[2016-04-15T04:12Z] 2016-04-14 21:12:15 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:12:15,932 - WARNING - Could not retrieve variants from source file in region 4:165118441-165118986. Error was invalid region `4:165118442-165118986`
[2016-04-15T04:12Z] 2016-04-14 21:12:16 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:12:16,358 - WARNING - Could not retrieve variants from source file in region 4:155410611-155411294. Error was invalid region `4:155410612-155411294`
[2016-04-15T04:12Z] 2016-04-14 21:12:17 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:12:17,687 - WARNING - Could not retrieve variants from source file in region 4:155525759-155526160. Error was invalid region `4:155525760-155526160`
[2016-04-15T04:12Z] 2016-04-14 21:12:18 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:12:18,096 - WARNING - Could not retrieve variants from source file in region 4:154709643-154710046. Error was invalid region `4:154709644-154710046`
[2016-04-15T04:12Z] 2016-04-14 21:12:18 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:12:18,167 - WARNING - Could not retrieve variants from source file in region 4:151829613-151830014. Error was invalid region `4:151829614-151830014`
[2016-04-15T04:12Z] 2016-04-14 21:12:19 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:12:19,532 - WARNING - Could not retrieve variants from source file in region 4:159792419-159794078. Error was invalid region `4:159792420-159794078`
[2016-04-15T04:12Z] 2016-04-14 21:12:19 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:12:19,548 - WARNING - Could not retrieve variants from source file in region 4:159601465-159601866. Error was invalid region `4:159601466-159601866`
[2016-04-15T04:12Z] 2016-04-14 21:12:19 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:12:19,704 - WARNING - Could not retrieve variants from source file in region 4:156787129-156787530. Error was invalid region `4:156787130-156787530`
[2016-04-15T04:12Z] 2016-04-14 21:12:20 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:12:20,515 - WARNING - Could not retrieve variants from source file in region 4:164435054-164440771. Error was invalid region `4:164435055-164440771`
[2016-04-15T04:12Z] 2016-04-14 21:12:20 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:12:20,750 - WARNING - Could not retrieve variants from source file in region 4:165118441-165118986. Error was invalid region `4:165118442-165118986`
[2016-04-15T04:12Z] 2016-04-14 21:12:20 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:12:20,913 - WARNING - Could not retrieve variants from source file in region 4:155410611-155411294. Error was invalid region `4:155410612-155411294`
[2016-04-15T04:12Z] 2016-04-14 21:12:22 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:12:22,677 - WARNING - Could not retrieve variants from source file in region 4:164049705-164085615. Error was invalid region `4:164049706-164085615`
[2016-04-15T04:12Z] 2016-04-14 21:12:23 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:12:23,252 - WARNING - Could not retrieve variants from source file in region 4:155525759-155526160. Error was invalid region `4:155525760-155526160`
[2016-04-15T04:12Z] 2016-04-14 21:12:24 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:12:24,808 - WARNING - Could not retrieve variants from source file in region 4:156283001-156283402. Error was invalid region `4:156283002-156283402`
[2016-04-15T04:12Z] 2016-04-14 21:12:24 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:12:24,896 - WARNING - Could not retrieve variants from source file in region 4:159601465-159601866. Error was invalid region `4:159601466-159601866`
[2016-04-15T04:12Z] 2016-04-14 21:12:25 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:12:25,430 - WARNING - Could not retrieve variants from source file in region 4:156787129-156787530. Error was invalid region `4:156787130-156787530`
[2016-04-15T04:12Z] 2016-04-14 21:12:25 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:12:25,511 - WARNING - Could not retrieve variants from source file in region 4:165118441-165118986. Error was invalid region `4:165118442-165118986`
[2016-04-15T04:12Z] 2016-04-14 21:12:25 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:12:25,785 - WARNING - Could not retrieve variants from source file in region 4:164435054-164440771. Error was invalid region `4:164435055-164440771`
[2016-04-15T04:12Z] 2016-04-14 21:12:27 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:12:27,996 - WARNING - Could not retrieve variants from source file in region 4:155525759-155526160. Error was invalid region `4:155525760-155526160`
[2016-04-15T04:12Z] 2016-04-14 21:12:29 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:12:29,350 - WARNING - Could not retrieve variants from source file in region 4:151829613-151830014. Error was invalid region `4:151829614-151830014`
[2016-04-15T04:12Z] 2016-04-14 21:12:30 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:12:30,434 - WARNING - Could not retrieve variants from source file in region 4:156283001-156283402. Error was invalid region `4:156283002-156283402`
[2016-04-15T04:12Z] 2016-04-14 21:12:36 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:12:36,194 - WARNING - Could not retrieve variants from source file in region 4:153568128-153568624. Error was invalid region `4:153568129-153568624`
[2016-04-15T04:12Z] 2016-04-14 21:12:37 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:12:37,990 - WARNING - Could not retrieve variants from source file in region 4:155287324-155312601. Error was invalid region `4:155287325-155312601`
[2016-04-15T04:12Z] 2016-04-14 21:12:41 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:12:41,057 - WARNING - Could not retrieve variants from source file in region 4:162306789-162307250. Error was invalid region `4:162306790-162307250`
[2016-04-15T04:12Z] 2016-04-14 21:12:41 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:12:41,114 - WARNING - Could not retrieve variants from source file in region 4:154178486-154216900. Error was invalid region `4:154178487-154216900`
[2016-04-15T04:12Z] 2016-04-14 21:12:42 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:12:42,017 - WARNING - Could not retrieve variants from source file in region 4:153568128-153568624. Error was invalid region `4:153568129-153568624`
[2016-04-15T04:12Z] 2016-04-14 21:12:42 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:12:42,202 - WARNING - Could not retrieve variants from source file in region 4:164533491-164534237. Error was invalid region `4:164533492-164534237`
[2016-04-15T04:12Z] 2016-04-14 21:12:42 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:12:42,251 - WARNING - Could not retrieve variants from source file in region 4:156720887-156721388. Error was invalid region `4:156720888-156721388`
[2016-04-15T04:12Z] 2016-04-14 21:12:42 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:12:42,499 - WARNING - Could not retrieve variants from source file in region 4:152147230-152147631. Error was invalid region `4:152147231-152147631`
[2016-04-15T04:12Z] 2016-04-14 21:12:43 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:12:43,979 - WARNING - Could not retrieve variants from source file in region 4:156135465-156136217. Error was invalid region `4:156135466-156136217`
[2016-04-15T04:12Z] 2016-04-14 21:12:46 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:12:46,191 - WARNING - Could not retrieve variants from source file in region 4:164392906-164393307. Error was invalid region `4:164392907-164393307`
[2016-04-15T04:12Z] 2016-04-14 21:12:46 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:12:46,598 - WARNING - Could not retrieve variants from source file in region 4:153568128-153568624. Error was invalid region `4:153568129-153568624`
[2016-04-15T04:12Z] 2016-04-14 21:12:47 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:12:47,076 - WARNING - Could not retrieve variants from source file in region 4:159158466-159158867. Error was invalid region `4:159158467-159158867`
[2016-04-15T04:12Z] 2016-04-14 21:12:47 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:12:47,213 - WARNING - Could not retrieve variants from source file in region 4:152147230-152147631. Error was invalid region `4:152147231-152147631`
[2016-04-15T04:12Z] 2016-04-14 21:12:47 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:12:47,704 - WARNING - Could not retrieve variants from source file in region 4:151177129-151207317. Error was invalid region `4:151177130-151207317`
[2016-04-15T04:12Z] 2016-04-14 21:12:50 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:12:50,548 - WARNING - Could not retrieve variants from source file in region 4:154178486-154216900. Error was invalid region `4:154178487-154216900`
[2016-04-15T04:12Z] 2016-04-14 21:12:50 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:12:50,639 - WARNING - Could not retrieve variants from source file in region 4:164392906-164393307. Error was invalid region `4:164392907-164393307`
[2016-04-15T04:12Z] 2016-04-14 21:12:52 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:12:52,287 - WARNING - Could not retrieve variants from source file in region 4:154553762-154554163. Error was invalid region `4:154553763-154554163`
[2016-04-15T04:12Z] 2016-04-14 21:12:52 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:12:52,787 - WARNING - Could not retrieve variants from source file in region 4:150656392-150656793. Error was invalid region `4:150656393-150656793`
[2016-04-15T04:12Z] 2016-04-14 21:12:53 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:12:53,174 - WARNING - Could not retrieve variants from source file in region 4:152147230-152147631. Error was invalid region `4:152147231-152147631`
[2016-04-15T04:12Z] 2016-04-14 21:12:57 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:12:57,676 - WARNING - Could not retrieve variants from source file in region 4:150656392-150656793. Error was invalid region `4:150656393-150656793`
[2016-04-15T04:12Z] 2016-04-14 21:12:59 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:12:59,808 - WARNING - Could not retrieve variants from source file in region 4:159076615-159077016. Error was invalid region `4:159076616-159077016`
[2016-04-15T04:13Z] 2016-04-14 21:13:02 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:13:02,267 - WARNING - Could not retrieve variants from source file in region 4:159076615-159077016. Error was invalid region `4:159076616-159077016`
[2016-04-15T04:13Z] 2016-04-14 21:13:02 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:13:02,377 - WARNING - Could not retrieve variants from source file in region 4:150656392-150656793. Error was invalid region `4:150656393-150656793`
[2016-04-15T04:13Z] 2016-04-14 21:13:03 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:13:03,108 - WARNING - Could not retrieve variants from source file in region 4:158238619-158239020. Error was invalid region `4:158238620-158239020`
[2016-04-15T04:13Z] 2016-04-14 21:13:03 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:13:03,125 - WARNING - Could not retrieve variants from source file in region 4:154478011-154479620. Error was invalid region `4:154478012-154479620`
[2016-04-15T04:13Z] 2016-04-14 21:13:03 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:13:03,345 - WARNING - Could not retrieve variants from source file in region 4:159076615-159077016. Error was invalid region `4:159076616-159077016`
[2016-04-15T04:13Z] 2016-04-14 21:13:03 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:13:03,426 - WARNING - Could not retrieve variants from source file in region 4:158064827-158065228. Error was invalid region `4:158064828-158065228`
[2016-04-15T04:13Z] 2016-04-14 21:13:06 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:13:06,733 - WARNING - Could not retrieve variants from source file in region 4:158238619-158239020. Error was invalid region `4:158238620-158239020`
[2016-04-15T04:13Z] 2016-04-14 21:13:06 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:13:06,810 - WARNING - Could not retrieve variants from source file in region 4:154478011-154479620. Error was invalid region `4:154478012-154479620`
[2016-04-15T04:13Z] 2016-04-14 21:13:07 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:13:07,117 - WARNING - Could not retrieve variants from source file in region 4:158064827-158065228. Error was invalid region `4:158064828-158065228`
[2016-04-15T04:13Z] 2016-04-14 21:13:07 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:13:07,188 - WARNING - Could not retrieve variants from source file in region 4:158064827-158065228. Error was invalid region `4:158064828-158065228`
[2016-04-15T04:13Z] 2016-04-14 21:13:07 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:13:07,205 - WARNING - Could not retrieve variants from source file in region 4:158238619-158239020. Error was invalid region `4:158238620-158239020`
[2016-04-15T04:13Z] ['bcbio-variation-recall', 'square', '-Xms750m', '-Xmx7280m', '-XX:+UseSerialGC', '-c', 16, '-r', u'4:165889319-183245405', '--caller', 'platypus', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/4/Batch1-4_165889318_183245405.vcf.gz', '/mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/4/Batch1-4_165889318_183245405.vcf-inputs.txt'] in region: 4:165889319-183245405
[2016-04-15T04:13Z] 2016-04-14 21:13:23 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:13:23,167 - WARNING - Could not retrieve variants from source file in region 4:169083483-169086631. Error was invalid region `4:169083484-169086631`
[2016-04-15T04:13Z] 2016-04-14 21:13:23 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:13:23,461 - WARNING - Could not retrieve variants from source file in region 4:166405373-166405774. Error was invalid region `4:166405374-166405774`
[2016-04-15T04:13Z] 2016-04-14 21:13:24 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:13:24,536 - WARNING - Could not retrieve variants from source file in region 4:175442945-175443346. Error was invalid region `4:175442946-175443346`
[2016-04-15T04:13Z] 2016-04-14 21:13:24 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:13:24,668 - WARNING - Could not retrieve variants from source file in region 4:169432462-169433634. Error was invalid region `4:169432463-169433634`
[2016-04-15T04:13Z] 2016-04-14 21:13:24 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:13:24,889 - WARNING - Could not retrieve variants from source file in region 4:166140875-166141276. Error was invalid region `4:166140876-166141276`
[2016-04-15T04:13Z] 2016-04-14 21:13:25 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:13:25,073 - WARNING - Could not retrieve variants from source file in region 4:178359749-178360150. Error was invalid region `4:178359750-178360150`
[2016-04-15T04:13Z] 2016-04-14 21:13:25 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:13:25,087 - WARNING - Could not retrieve variants from source file in region 4:173232594-173232995. Error was invalid region `4:173232595-173232995`
[2016-04-15T04:13Z] 2016-04-14 21:13:25 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:13:25,162 - WARNING - Could not retrieve variants from source file in region 4:166231657-166232058. Error was invalid region `4:166231658-166232058`
[2016-04-15T04:13Z] 2016-04-14 21:13:25 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:13:25,500 - WARNING - Could not retrieve variants from source file in region 4:170476914-170477315. Error was invalid region `4:170476915-170477315`
[2016-04-15T04:13Z] 2016-04-14 21:13:25 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:13:25,575 - WARNING - Could not retrieve variants from source file in region 4:175598123-175598524. Error was invalid region `4:175598124-175598524`
[2016-04-15T04:13Z] 2016-04-14 21:13:25 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:13:25,666 - WARNING - Could not retrieve variants from source file in region 4:177604870-177605274. Error was invalid region `4:177604871-177605274`
[2016-04-15T04:13Z] 2016-04-14 21:13:26 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:13:26,279 - WARNING - Could not retrieve variants from source file in region 4:169909890-169931478. Error was invalid region `4:169909891-169931478`
[2016-04-15T04:13Z] 2016-04-14 21:13:29 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:13:29,170 - WARNING - Could not retrieve variants from source file in region 4:169083483-169086631. Error was invalid region `4:169083484-169086631`
[2016-04-15T04:13Z] 2016-04-14 21:13:31 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:13:31,374 - WARNING - Could not retrieve variants from source file in region 4:170923104-170923505. Error was invalid region `4:170923105-170923505`
[2016-04-15T04:13Z] 2016-04-14 21:13:33 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:13:33,143 - WARNING - Could not retrieve variants from source file in region 4:170634179-170679183. Error was invalid region `4:170634180-170679183`
[2016-04-15T04:13Z] 2016-04-14 21:13:33 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:13:33,677 - WARNING - Could not retrieve variants from source file in region 4:178359749-178360150. Error was invalid region `4:178359750-178360150`
[2016-04-15T04:13Z] 2016-04-14 21:13:34 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:13:34,154 - WARNING - Could not retrieve variants from source file in region 4:173232594-173232995. Error was invalid region `4:173232595-173232995`
[2016-04-15T04:13Z] 2016-04-14 21:13:34 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:13:34,193 - WARNING - Could not retrieve variants from source file in region 4:169909890-169931478. Error was invalid region `4:169909891-169931478`
[2016-04-15T04:13Z] 2016-04-14 21:13:34 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:13:34,481 - WARNING - Could not retrieve variants from source file in region 4:175598123-175598524. Error was invalid region `4:175598124-175598524`
[2016-04-15T04:13Z] 2016-04-14 21:13:34 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:13:34,772 - WARNING - Could not retrieve variants from source file in region 4:177604870-177605274. Error was invalid region `4:177604871-177605274`
[2016-04-15T04:13Z] 2016-04-14 21:13:34 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:13:34,885 - WARNING - Could not retrieve variants from source file in region 4:169083483-169086631. Error was invalid region `4:169083484-169086631`
[2016-04-15T04:13Z] 2016-04-14 21:13:34 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:13:34,921 - WARNING - Could not retrieve variants from source file in region 4:175183988-175184389. Error was invalid region `4:175183989-175184389`
[2016-04-15T04:13Z] 2016-04-14 21:13:34 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:13:34,940 - WARNING - Could not retrieve variants from source file in region 4:166405373-166405774. Error was invalid region `4:166405374-166405774`
[2016-04-15T04:13Z] 2016-04-14 21:13:36 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:13:36,734 - WARNING - Could not retrieve variants from source file in region 4:170923104-170923505. Error was invalid region `4:170923105-170923505`
[2016-04-15T04:13Z] 2016-04-14 21:13:38 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:13:38,953 - WARNING - Could not retrieve variants from source file in region 4:175442945-175443346. Error was invalid region `4:175442946-175443346`
[2016-04-15T04:13Z] 2016-04-14 21:13:40 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:13:40,405 - WARNING - Could not retrieve variants from source file in region 4:178359749-178360150. Error was invalid region `4:178359750-178360150`
[2016-04-15T04:13Z] 2016-04-14 21:13:41 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:13:41,245 - WARNING - Could not retrieve variants from source file in region 4:169432462-169433634. Error was invalid region `4:169432463-169433634`
[2016-04-15T04:13Z] 2016-04-14 21:13:42 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:13:42,142 - WARNING - Could not retrieve variants from source file in region 4:170476914-170477315. Error was invalid region `4:170476915-170477315`
[2016-04-15T04:13Z] 2016-04-14 21:13:42 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:13:42,902 - WARNING - Could not retrieve variants from source file in region 4:166231657-166232058. Error was invalid region `4:166231658-166232058`
[2016-04-15T04:13Z] 2016-04-14 21:13:42 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:13:42,917 - WARNING - Could not retrieve variants from source file in region 4:177604870-177605274. Error was invalid region `4:177604871-177605274`
[2016-04-15T04:13Z] 2016-04-14 21:13:43 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:13:43,063 - WARNING - Could not retrieve variants from source file in region 4:173232594-173232995. Error was invalid region `4:173232595-173232995`
[2016-04-15T04:13Z] 2016-04-14 21:13:43 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:13:43,440 - WARNING - Could not retrieve variants from source file in region 4:175598123-175598524. Error was invalid region `4:175598124-175598524`
[2016-04-15T04:13Z] 2016-04-14 21:13:50 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:13:50,702 - WARNING - Could not retrieve variants from source file in region 4:169799237-169799638. Error was invalid region `4:169799238-169799638`
[2016-04-15T04:13Z] 2016-04-14 21:13:53 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:13:53,747 - WARNING - Could not retrieve variants from source file in region 4:175563273-175563675. Error was invalid region `4:175563274-175563675`
[2016-04-15T04:13Z] 2016-04-14 21:13:54 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:13:54,660 - WARNING - Could not retrieve variants from source file in region 4:175563273-175563675. Error was invalid region `4:175563274-175563675`
[2016-04-15T04:13Z] 2016-04-14 21:13:54 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:13:54,688 - WARNING - Could not retrieve variants from source file in region 4:175225241-175241318. Error was invalid region `4:175225242-175241318`
[2016-04-15T04:13Z] 2016-04-14 21:13:54 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:13:54,692 - WARNING - Could not retrieve variants from source file in region 4:178230941-178231342. Error was invalid region `4:178230942-178231342`
[2016-04-15T04:13Z] 2016-04-14 21:13:55 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:13:55,444 - WARNING - Could not retrieve variants from source file in region 4:170581359-170581760. Error was invalid region `4:170581360-170581760`
[2016-04-15T04:13Z] 2016-04-14 21:13:55 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:13:55,890 - WARNING - Could not retrieve variants from source file in region 4:169799237-169799638. Error was invalid region `4:169799238-169799638`
[2016-04-15T04:13Z] 2016-04-14 21:13:57 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:13:57,586 - WARNING - Could not retrieve variants from source file in region 4:170398243-170398644. Error was invalid region `4:170398244-170398644`
[2016-04-15T04:13Z] 2016-04-14 21:13:58 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:13:58,586 - WARNING - Could not retrieve variants from source file in region 4:174089793-174090194. Error was invalid region `4:174089794-174090194`
[2016-04-15T04:13Z] 2016-04-14 21:13:59 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:13:59,407 - WARNING - Could not retrieve variants from source file in region 4:167012170-167012670. Error was invalid region `4:167012171-167012670`
[2016-04-15T04:13Z] 2016-04-14 21:13:59 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:13:59,417 - WARNING - Could not retrieve variants from source file in region 4:167655862-167675825. Error was invalid region `4:167655863-167675825`
[2016-04-15T04:13Z] 2016-04-14 21:13:59 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:13:59,755 - WARNING - Could not retrieve variants from source file in region 4:178230941-178231342. Error was invalid region `4:178230942-178231342`
[2016-04-15T04:14Z] 2016-04-14 21:14:00 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:14:00,551 - WARNING - Could not retrieve variants from source file in region 4:169799237-169799638. Error was invalid region `4:169799238-169799638`
[2016-04-15T04:14Z] 2016-04-14 21:14:01 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:14:01,320 - WARNING - Could not retrieve variants from source file in region 4:170581359-170581760. Error was invalid region `4:170581360-170581760`
[2016-04-15T04:14Z] 2016-04-14 21:14:01 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:14:01,348 - WARNING - Could not retrieve variants from source file in region 4:166021600-166022001. Error was invalid region `4:166021601-166022001`
[2016-04-15T04:14Z] 2016-04-14 21:14:01 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:14:01,988 - WARNING - Could not retrieve variants from source file in region 4:170398243-170398644. Error was invalid region `4:170398244-170398644`
[2016-04-15T04:14Z] 2016-04-14 21:14:02 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:14:02,946 - WARNING - Could not retrieve variants from source file in region 4:174089793-174090194. Error was invalid region `4:174089794-174090194`
[2016-04-15T04:14Z] 2016-04-14 21:14:03 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:14:03,924 - WARNING - Could not retrieve variants from source file in region 4:167012170-167012670. Error was invalid region `4:167012171-167012670`
[2016-04-15T04:14Z] 2016-04-14 21:14:04 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:14:04,451 - WARNING - Could not retrieve variants from source file in region 4:178230941-178231342. Error was invalid region `4:178230942-178231342`
[2016-04-15T04:14Z] 2016-04-14 21:14:06 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:14:06,498 - WARNING - Could not retrieve variants from source file in region 4:166021600-166022001. Error was invalid region `4:166021601-166022001`
[2016-04-15T04:14Z] 2016-04-14 21:14:06 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:14:06,516 - WARNING - Could not retrieve variants from source file in region 4:170581359-170581760. Error was invalid region `4:170581360-170581760`
[2016-04-15T04:14Z] 2016-04-14 21:14:07 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:14:07,647 - WARNING - Could not retrieve variants from source file in region 4:174089793-174090194. Error was invalid region `4:174089794-174090194`
[2016-04-15T04:14Z] 2016-04-14 21:14:08 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:14:08,624 - WARNING - Could not retrieve variants from source file in region 4:167012170-167012670. Error was invalid region `4:167012171-167012670`
[2016-04-15T04:14Z] 2016-04-14 21:14:11 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:14:11,324 - WARNING - Could not retrieve variants from source file in region 4:166951873-166952274. Error was invalid region `4:166951874-166952274`
[2016-04-15T04:14Z] 2016-04-14 21:14:12 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:14:12,383 - WARNING - Could not retrieve variants from source file in region 4:166951873-166952274. Error was invalid region `4:166951874-166952274`
[2016-04-15T04:14Z] 2016-04-14 21:14:13 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:14:13,267 - WARNING - Could not retrieve variants from source file in region 4:166951873-166952274. Error was invalid region `4:166951874-166952274`
[2016-04-15T04:14Z] 2016-04-14 21:14:13 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:14:13,872 - WARNING - Could not retrieve variants from source file in region 4:176733239-176733642. Error was invalid region `4:176733240-176733642`
[2016-04-15T04:14Z] 2016-04-14 21:14:16 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:14:16,431 - WARNING - Could not retrieve variants from source file in region 4:175687927-175688328. Error was invalid region `4:175687928-175688328`
[2016-04-15T04:14Z] 2016-04-14 21:14:16 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:14:16,731 - WARNING - Could not retrieve variants from source file in region 4:175687927-175688328. Error was invalid region `4:175687928-175688328`
[2016-04-15T04:14Z] ['bcbio-variation-recall', 'square', '-Xms750m', '-Xmx7280m', '-XX:+UseSerialGC', '-c', 16, '-r', u'4:183267804-191154276', '--caller', 'platypus', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/4/Batch1-4_183267803_191154276.vcf.gz', '/mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/4/Batch1-4_183267803_191154276.vcf-inputs.txt'] in region: 4:183267804-191154276
[2016-04-15T04:14Z] 2016-04-14 21:14:32 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:14:32,962 - WARNING - Could not retrieve variants from source file in region 4:187627581-187631179. Error was invalid region `4:187627582-187631179`
[2016-04-15T04:14Z] 2016-04-14 21:14:33 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:14:33,889 - WARNING - Could not retrieve variants from source file in region 4:186090607-186112301. Error was invalid region `4:186090608-186112301`
[2016-04-15T04:14Z] 2016-04-14 21:14:34 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:14:34,878 - WARNING - Could not retrieve variants from source file in region 4:184367347-184367751. Error was invalid region `4:184367348-184367751`
[2016-04-15T04:14Z] 2016-04-14 21:14:35 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:14:35,915 - WARNING - Could not retrieve variants from source file in region 4:186527961-186541491. Error was invalid region `4:186527962-186541491`
[2016-04-15T04:14Z] 2016-04-14 21:14:36 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:14:36,036 - WARNING - Could not retrieve variants from source file in region 4:184426176-184432172. Error was invalid region `4:184426177-184432172`
[2016-04-15T04:14Z] 2016-04-14 21:14:36 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:14:36,045 - WARNING - Could not retrieve variants from source file in region 4:187454740-187455162. Error was invalid region `4:187454741-187455162`
[2016-04-15T04:14Z] 2016-04-14 21:14:36 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:14:36,807 - WARNING - Could not retrieve variants from source file in region 4:189060825-189061296. Error was invalid region `4:189060826-189061296`
[2016-04-15T04:14Z] 2016-04-14 21:14:36 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:14:36,950 - WARNING - Could not retrieve variants from source file in region 4:186316033-186321257. Error was invalid region `4:186316034-186321257`
[2016-04-15T04:14Z] 2016-04-14 21:14:36 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:14:36,969 - WARNING - Could not retrieve variants from source file in region 4:185586954-185655382. Error was invalid region `4:185586955-185655382`
[2016-04-15T04:14Z] 2016-04-14 21:14:41 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:14:41,598 - WARNING - Could not retrieve variants from source file in region 4:184367347-184367751. Error was invalid region `4:184367348-184367751`
[2016-04-15T04:14Z] 2016-04-14 21:14:44 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:14:44,907 - WARNING - Could not retrieve variants from source file in region 4:189012469-189012918. Error was invalid region `4:189012470-189012918`
[2016-04-15T04:14Z] 2016-04-14 21:14:45 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:14:45,316 - WARNING - Could not retrieve variants from source file in region 4:189060825-189061296. Error was invalid region `4:189060826-189061296`
[2016-04-15T04:14Z] 2016-04-14 21:14:45 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:14:45,977 - WARNING - Could not retrieve variants from source file in region 4:186365970-186379561. Error was invalid region `4:186365971-186379561`
[2016-04-15T04:14Z] 2016-04-14 21:14:46 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:14:46,225 - WARNING - Could not retrieve variants from source file in region 4:183815477-183838293. Error was invalid region `4:183815478-183838293`
[2016-04-15T04:14Z] 2016-04-14 21:14:46 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:14:46,558 - WARNING - Could not retrieve variants from source file in region 4:184367347-184367751. Error was invalid region `4:184367348-184367751`
[2016-04-15T04:14Z] 2016-04-14 21:14:49 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:14:49,973 - WARNING - Could not retrieve variants from source file in region 4:186527961-186541491. Error was invalid region `4:186527962-186541491`
[2016-04-15T04:14Z] 2016-04-14 21:14:50 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:14:50,146 - WARNING - Could not retrieve variants from source file in region 4:187454740-187455162. Error was invalid region `4:187454741-187455162`
[2016-04-15T04:14Z] 2016-04-14 21:14:52 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:14:52,558 - WARNING - Could not retrieve variants from source file in region 4:184426176-184432172. Error was invalid region `4:184426177-184432172`
[2016-04-15T04:14Z] 2016-04-14 21:14:53 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:14:53,000 - WARNING - Could not retrieve variants from source file in region 4:189012469-189012918. Error was invalid region `4:189012470-189012918`
[2016-04-15T04:14Z] 2016-04-14 21:14:53 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:14:53,116 - WARNING - Could not retrieve variants from source file in region 4:186316033-186321257. Error was invalid region `4:186316034-186321257`
[2016-04-15T04:14Z] 2016-04-14 21:14:53 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:14:53,126 - WARNING - Could not retrieve variants from source file in region 4:189060825-189061296. Error was invalid region `4:189060826-189061296`
[2016-04-15T04:14Z] 2016-04-14 21:14:53 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:14:53,542 - WARNING - Could not retrieve variants from source file in region 4:186365970-186379561. Error was invalid region `4:186365971-186379561`
[2016-04-15T04:15Z] 2016-04-14 21:15:05 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:15:05,610 - WARNING - Could not retrieve variants from source file in region 4:184242748-184243718. Error was invalid region `4:184242749-184243718`
[2016-04-15T04:15Z] 2016-04-14 21:15:05 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:15:05,673 - WARNING - Could not retrieve variants from source file in region 4:187516669-187558083. Error was invalid region `4:187516670-187558083`
[2016-04-15T04:15Z] 2016-04-14 21:15:06 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:15:06,355 - WARNING - Could not retrieve variants from source file in region 4:185012176-185012588. Error was invalid region `4:185012177-185012588`
[2016-04-15T04:15Z] 2016-04-14 21:15:06 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:15:06,605 - WARNING - Could not retrieve variants from source file in region 4:186423426-186434862. Error was invalid region `4:186423427-186434862`
[2016-04-15T04:15Z] 2016-04-14 21:15:09 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:15:09,855 - WARNING - Could not retrieve variants from source file in region 4:184570504-184570905. Error was invalid region `4:184570505-184570905`
[2016-04-15T04:15Z] 2016-04-14 21:15:10 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:15:10,591 - WARNING - Could not retrieve variants from source file in region 4:185310007-185310408. Error was invalid region `4:185310008-185310408`
[2016-04-15T04:15Z] 2016-04-14 21:15:10 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:15:10,827 - WARNING - Could not retrieve variants from source file in region 4:184570504-184570905. Error was invalid region `4:184570505-184570905`
[2016-04-15T04:15Z] 2016-04-14 21:15:10 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:15:10,859 - WARNING - Could not retrieve variants from source file in region 4:184600390-184615307. Error was invalid region `4:184600391-184615307`
[2016-04-15T04:15Z] 2016-04-14 21:15:11 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:15:11,225 - WARNING - Could not retrieve variants from source file in region 4:183710121-183713820. Error was invalid region `4:183710122-183713820`
[2016-04-15T04:15Z] 2016-04-14 21:15:12 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:15:12,522 - WARNING - Could not retrieve variants from source file in region 4:184600390-184615307. Error was invalid region `4:184600391-184615307`
[2016-04-15T04:15Z] 2016-04-14 21:15:14 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:15:14,111 - WARNING - Could not retrieve variants from source file in region 4:184570504-184570905. Error was invalid region `4:184570505-184570905`
[2016-04-15T04:15Z] 2016-04-14 21:15:14 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:15:14,920 - WARNING - Could not retrieve variants from source file in region 4:185235089-185235490. Error was invalid region `4:185235090-185235490`
[2016-04-15T04:15Z] 2016-04-14 21:15:14 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:15:14,943 - WARNING - Could not retrieve variants from source file in region 4:185310007-185310408. Error was invalid region `4:185310008-185310408`
[2016-04-15T04:15Z] 2016-04-14 21:15:17 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:15:17,816 - WARNING - Could not retrieve variants from source file in region 4:185235089-185235490. Error was invalid region `4:185235090-185235490`
[2016-04-15T04:15Z] 2016-04-14 21:15:17 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:15:17,842 - WARNING - Could not retrieve variants from source file in region 4:185235089-185235490. Error was invalid region `4:185235090-185235490`
[2016-04-15T04:15Z] 2016-04-14 21:15:17 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:15:17,955 - WARNING - Could not retrieve variants from source file in region 4:183710121-183713820. Error was invalid region `4:183710122-183713820`
[2016-04-15T04:15Z] 2016-04-14 21:15:18 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:15:18,545 - WARNING - Could not retrieve variants from source file in region 4:184930435-184932278. Error was invalid region `4:184930436-184932278`
[2016-04-15T04:15Z] 2016-04-14 21:15:19 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:15:19,377 - WARNING - Could not retrieve variants from source file in region 4:184930435-184932278. Error was invalid region `4:184930436-184932278`
[2016-04-15T04:15Z] 2016-04-14 21:15:19 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:15:19,665 - WARNING - Could not retrieve variants from source file in region 4:183651964-183674887. Error was invalid region `4:183651965-183674887`
[2016-04-15T04:15Z] 2016-04-14 21:15:21 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:15:21,286 - WARNING - Could not retrieve variants from source file in region 4:183601636-183602037. Error was invalid region `4:183601637-183602037`
[2016-04-15T04:15Z] 2016-04-14 21:15:22 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:15:22,747 - WARNING - Could not retrieve variants from source file in region 4:183601636-183602037. Error was invalid region `4:183601637-183602037`
[2016-04-15T04:15Z] 2016-04-14 21:15:22 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:15:22,767 - WARNING - Could not retrieve variants from source file in region 4:183601636-183602037. Error was invalid region `4:183601637-183602037`
[2016-04-15T04:15Z] ['bcbio-variation-recall', 'square', '-Xms750m', '-Xmx7280m', '-XX:+UseSerialGC', '-c', 16, '-r', u'5:1-15580921', '--caller', 'platypus', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/5/Batch1-5_0_15580921.vcf.gz', '/mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/5/Batch1-5_0_15580921.vcf-inputs.txt'] in region: 5:1-15580921
[2016-04-15T04:15Z] 2016-04-14 21:15:39 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:15:39,153 - WARNING - Could not retrieve variants from source file in region 5:14397027-14420217. Error was invalid region `5:14397028-14420217`
[2016-04-15T04:15Z] 2016-04-14 21:15:39 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:15:39,661 - WARNING - Could not retrieve variants from source file in region 5:11396978-11397379. Error was invalid region `5:11396979-11397379`
[2016-04-15T04:15Z] 2016-04-14 21:15:39 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:15:39,849 - WARNING - Could not retrieve variants from source file in region 5:9629318-9629719. Error was invalid region `5:9629319-9629719`
[2016-04-15T04:15Z] 2016-04-14 21:15:40 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:15:40,054 - WARNING - Could not retrieve variants from source file in region 5:3600123-3600524. Error was invalid region `5:3600124-3600524`
[2016-04-15T04:15Z] 2016-04-14 21:15:40 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:15:40,326 - WARNING - Could not retrieve variants from source file in region 5:6448633-6449055. Error was invalid region `5:6448634-6449055`
[2016-04-15T04:15Z] 2016-04-14 21:15:40 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:15:40,370 - WARNING - Could not retrieve variants from source file in region 5:14368764-14369165. Error was invalid region `5:14368765-14369165`
[2016-04-15T04:15Z] 2016-04-14 21:15:40 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:15:40,463 - WARNING - Could not retrieve variants from source file in region 5:5460358-5463858. Error was invalid region `5:5460359-5463858`
[2016-04-15T04:15Z] 2016-04-14 21:15:40 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:15:40,497 - WARNING - Could not retrieve variants from source file in region 5:10564635-10565036. Error was invalid region `5:10564636-10565036`
[2016-04-15T04:15Z] 2016-04-14 21:15:43 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:15:43,572 - WARNING - Could not retrieve variants from source file in region 5:14610098-14610499. Error was invalid region `5:14610099-14610499`
[2016-04-15T04:15Z] 2016-04-14 21:15:47 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:15:47,485 - WARNING - Could not retrieve variants from source file in region 5:11588819-11589220. Error was invalid region `5:11588820-11589220`
[2016-04-15T04:15Z] 2016-04-14 21:15:48 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:15:48,385 - WARNING - Could not retrieve variants from source file in region 5:7520670-7521071. Error was invalid region `5:7520671-7521071`
[2016-04-15T04:15Z] 2016-04-14 21:15:48 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:15:48,418 - WARNING - Could not retrieve variants from source file in region 5:10564635-10565036. Error was invalid region `5:10564636-10565036`
[2016-04-15T04:15Z] 2016-04-14 21:15:48 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:15:48,814 - WARNING - Could not retrieve variants from source file in region 5:3600123-3600524. Error was invalid region `5:3600124-3600524`
[2016-04-15T04:15Z] 2016-04-14 21:15:48 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:15:48,934 - WARNING - Could not retrieve variants from source file in region 5:7866756-7897473. Error was invalid region `5:7866757-7897473`
[2016-04-15T04:15Z] 2016-04-14 21:15:49 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:15:49,240 - WARNING - Could not retrieve variants from source file in region 5:14610098-14610499. Error was invalid region `5:14610099-14610499`
[2016-04-15T04:15Z] 2016-04-14 21:15:52 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:15:52,967 - WARNING - Could not retrieve variants from source file in region 5:13788675-13866170. Error was invalid region `5:13788676-13866170`
[2016-04-15T04:15Z] 2016-04-14 21:15:56 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:15:56,482 - WARNING - Could not retrieve variants from source file in region 5:10564635-10565036. Error was invalid region `5:10564636-10565036`
[2016-04-15T04:15Z] 2016-04-14 21:15:56 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:15:56,807 - WARNING - Could not retrieve variants from source file in region 5:3600123-3600524. Error was invalid region `5:3600124-3600524`
[2016-04-15T04:15Z] 2016-04-14 21:15:56 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:15:56,820 - WARNING - Could not retrieve variants from source file in region 5:10239067-10282586. Error was invalid region `5:10239068-10282586`
[2016-04-15T04:16Z] 2016-04-14 21:16:07 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:16:07,891 - WARNING - Could not retrieve variants from source file in region 5:14581847-14582248. Error was invalid region `5:14581848-14582248`
[2016-04-15T04:16Z] 2016-04-14 21:16:13 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:16:13,935 - WARNING - Could not retrieve variants from source file in region 5:6748448-6748849. Error was invalid region `5:6748449-6748849`
[2016-04-15T04:16Z] 2016-04-14 21:16:14 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:16:14,362 - WARNING - Could not retrieve variants from source file in region 5:7802152-7802553. Error was invalid region `5:7802153-7802553`
[2016-04-15T04:16Z] 2016-04-14 21:16:14 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:16:14,373 - WARNING - Could not retrieve variants from source file in region 5:13894683-13944702. Error was invalid region `5:13894684-13944702`
[2016-04-15T04:16Z] 2016-04-14 21:16:14 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:16:14,688 - WARNING - Could not retrieve variants from source file in region 5:6632831-6656400. Error was invalid region `5:6632832-6656400`
[2016-04-15T04:16Z] 2016-04-14 21:16:14 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:16:14,867 - WARNING - Could not retrieve variants from source file in region 5:1521362-1521763. Error was invalid region `5:1521363-1521763`
[2016-04-15T04:16Z] 2016-04-14 21:16:14 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:16:14,953 - WARNING - Could not retrieve variants from source file in region 5:9044436-9044864. Error was invalid region `5:9044437-9044864`
[2016-04-15T04:16Z] 2016-04-14 21:16:14 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:16:14,969 - WARNING - Could not retrieve variants from source file in region 5:2749574-2755675. Error was invalid region `5:2749575-2755675`
[2016-04-15T04:16Z] 2016-04-14 21:16:15 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:16:15,319 - WARNING - Could not retrieve variants from source file in region 5:13754183-13763162. Error was invalid region `5:13754184-13763162`
[2016-04-15T04:16Z] 2016-04-14 21:16:15 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:16:15,364 - WARNING - Could not retrieve variants from source file in region 5:10637969-10650340. Error was invalid region `5:10637970-10650340`
[2016-04-15T04:16Z] 2016-04-14 21:16:20 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:16:20,272 - WARNING - Could not retrieve variants from source file in region 5:5200070-5209400. Error was invalid region `5:5200071-5209400`
[2016-04-15T04:16Z] 2016-04-14 21:16:20 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:16:20,718 - WARNING - Could not retrieve variants from source file in region 5:6632831-6656400. Error was invalid region `5:6632832-6656400`
[2016-04-15T04:16Z] 2016-04-14 21:16:20 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:16:20,822 - WARNING - Could not retrieve variants from source file in region 5:5140421-5146585. Error was invalid region `5:5140422-5146585`
[2016-04-15T04:16Z] 2016-04-14 21:16:21 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:16:21,158 - WARNING - Could not retrieve variants from source file in region 5:1057404-1081957. Error was invalid region `5:1057405-1081957`
[2016-04-15T04:16Z] 2016-04-14 21:16:21 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:16:21,245 - WARNING - Could not retrieve variants from source file in region 5:1521362-1521763. Error was invalid region `5:1521363-1521763`
[2016-04-15T04:16Z] 2016-04-14 21:16:21 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:16:21,422 - WARNING - Could not retrieve variants from source file in region 5:9122679-9154849. Error was invalid region `5:9122680-9154849`
[2016-04-15T04:16Z] 2016-04-14 21:16:23 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:16:23,045 - WARNING - Could not retrieve variants from source file in region 5:6748448-6748849. Error was invalid region `5:6748449-6748849`
[2016-04-15T04:16Z] 2016-04-14 21:16:25 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:16:25,578 - WARNING - Could not retrieve variants from source file in region 5:5200070-5209400. Error was invalid region `5:5200071-5209400`
[2016-04-15T04:16Z] 2016-04-14 21:16:26 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:16:26,047 - WARNING - Could not retrieve variants from source file in region 5:5140421-5146585. Error was invalid region `5:5140422-5146585`
[2016-04-15T04:16Z] 2016-04-14 21:16:26 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:16:26,578 - WARNING - Could not retrieve variants from source file in region 5:6632831-6656400. Error was invalid region `5:6632832-6656400`
[2016-04-15T04:16Z] 2016-04-14 21:16:27 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:16:27,093 - WARNING - Could not retrieve variants from source file in region 5:9044436-9044864. Error was invalid region `5:9044437-9044864`
[2016-04-15T04:16Z] 2016-04-14 21:16:29 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:16:29,333 - WARNING - Could not retrieve variants from source file in region 5:1411201-1411602. Error was invalid region `5:1411202-1411602`
[2016-04-15T04:16Z] 2016-04-14 21:16:31 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:16:31,962 - WARNING - Could not retrieve variants from source file in region 5:13701314-13719279. Error was invalid region `5:13701315-13719279`
[2016-04-15T04:16Z] 2016-04-14 21:16:32 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:16:32,167 - WARNING - Could not retrieve variants from source file in region 5:1411201-1411602. Error was invalid region `5:1411202-1411602`
[2016-04-15T04:16Z] 2016-04-14 21:16:32 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:16:32,889 - WARNING - Could not retrieve variants from source file in region 5:7743576-7743977. Error was invalid region `5:7743577-7743977`
[2016-04-15T04:16Z] 2016-04-14 21:16:33 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:16:33,761 - WARNING - Could not retrieve variants from source file in region 5:1411201-1411602. Error was invalid region `5:1411202-1411602`
[2016-04-15T04:16Z] 2016-04-14 21:16:36 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:16:36,262 - WARNING - Could not retrieve variants from source file in region 5:908377-914854. Error was invalid region `5:908378-914854`
[2016-04-15T04:16Z] 2016-04-14 21:16:36 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:16:36,429 - WARNING - Could not retrieve variants from source file in region 5:1318280-1318681. Error was invalid region `5:1318281-1318681`
[2016-04-15T04:16Z] 2016-04-14 21:16:36 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:16:36,480 - WARNING - Could not retrieve variants from source file in region 5:13701314-13719279. Error was invalid region `5:13701315-13719279`
[2016-04-15T04:16Z] 2016-04-14 21:16:36 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:16:36,521 - WARNING - Could not retrieve variants from source file in region 5:7743576-7743977. Error was invalid region `5:7743577-7743977`
[2016-04-15T04:16Z] 2016-04-14 21:16:37 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:16:37,544 - WARNING - Could not retrieve variants from source file in region 5:1318280-1318681. Error was invalid region `5:1318281-1318681`
[2016-04-15T04:16Z] 2016-04-14 21:16:40 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:16:40,482 - WARNING - Could not retrieve variants from source file in region 5:13701314-13719279. Error was invalid region `5:13701315-13719279`
[2016-04-15T04:16Z] 2016-04-14 21:16:43 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:16:43,348 - WARNING - Could not retrieve variants from source file in region 5:908377-914854. Error was invalid region `5:908378-914854`
[2016-04-15T04:16Z] 2016-04-14 21:16:44 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:16:44,099 - WARNING - Could not retrieve variants from source file in region 5:311267-311668. Error was invalid region `5:311268-311668`
[2016-04-15T04:16Z] 2016-04-14 21:16:44 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:16:44,654 - WARNING - Could not retrieve variants from source file in region 5:162994-181952. Error was invalid region `5:162995-181952`
[2016-04-15T04:16Z] 2016-04-14 21:16:44 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:16:44,947 - WARNING - Could not retrieve variants from source file in region 5:230900-231301. Error was invalid region `5:230901-231301`
[2016-04-15T04:16Z] 2016-04-14 21:16:45 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:16:45,227 - WARNING - Could not retrieve variants from source file in region 5:311267-311668. Error was invalid region `5:311268-311668`
[2016-04-15T04:16Z] 2016-04-14 21:16:45 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:16:45,302 - WARNING - Could not retrieve variants from source file in region 5:230900-231301. Error was invalid region `5:230901-231301`
[2016-04-15T04:16Z] 2016-04-14 21:16:47 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:16:47,247 - WARNING - Could not retrieve variants from source file in region 5:870408-870809. Error was invalid region `5:870409-870809`
[2016-04-15T04:16Z] 2016-04-14 21:16:47 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:16:47,759 - WARNING - Could not retrieve variants from source file in region 5:474893-483754. Error was invalid region `5:474894-483754`
[2016-04-15T04:16Z] 2016-04-14 21:16:48 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:16:48,265 - WARNING - Could not retrieve variants from source file in region 5:230900-231301. Error was invalid region `5:230901-231301`
[2016-04-15T04:16Z] 2016-04-14 21:16:48 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:16:48,879 - WARNING - Could not retrieve variants from source file in region 5:311267-311668. Error was invalid region `5:311268-311668`
[2016-04-15T04:16Z] 2016-04-14 21:16:51 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:16:51,059 - WARNING - Could not retrieve variants from source file in region 5:745095-767223. Error was invalid region `5:745096-767223`
[2016-04-15T04:16Z] 2016-04-14 21:16:51 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:16:51,465 - WARNING - Could not retrieve variants from source file in region 5:870408-870809. Error was invalid region `5:870409-870809`
[2016-04-15T04:16Z] 2016-04-14 21:16:51 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:16:51,964 - WARNING - Could not retrieve variants from source file in region 5:474893-483754. Error was invalid region `5:474894-483754`
[2016-04-15T04:16Z] 2016-04-14 21:16:56 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:16:56,535 - WARNING - Could not retrieve variants from source file in region 5:434511-434912. Error was invalid region `5:434512-434912`
[2016-04-15T04:16Z] 2016-04-14 21:16:56 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:16:56,536 - WARNING - Could not retrieve variants from source file in region 5:434511-434912. Error was invalid region `5:434512-434912`
[2016-04-15T04:16Z] 2016-04-14 21:16:56 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:16:56,538 - WARNING - Could not retrieve variants from source file in region 5:434511-434912. Error was invalid region `5:434512-434912`
[2016-04-15T04:17Z] ['bcbio-variation-recall', 'square', '-Xms750m', '-Xmx7280m', '-XX:+UseSerialGC', '-c', 16, '-r', u'5:15616092-31267808', '--caller', 'platypus', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/5/Batch1-5_15616091_31267808.vcf.gz', '/mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/5/Batch1-5_15616091_31267808.vcf-inputs.txt'] in region: 5:15616092-31267808
[2016-04-15T04:17Z] 2016-04-14 21:17:11 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:17:11,216 - WARNING - Could not retrieve variants from source file in region 5:22212421-22212822. Error was invalid region `5:22212422-22212822`
[2016-04-15T04:17Z] 2016-04-14 21:17:11 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:17:11,179 - WARNING - Could not retrieve variants from source file in region 5:21889627-21890028. Error was invalid region `5:21889628-21890028`
[2016-04-15T04:17Z] 2016-04-14 21:17:11 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:17:11,238 - WARNING - Could not retrieve variants from source file in region 5:22212421-22212822. Error was invalid region `5:22212422-22212822`
[2016-04-15T04:17Z] 2016-04-14 21:17:11 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:17:11,273 - WARNING - Could not retrieve variants from source file in region 5:21889627-21890028. Error was invalid region `5:21889628-21890028`
[2016-04-15T04:17Z] 2016-04-14 21:17:11 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:17:11,307 - WARNING - Could not retrieve variants from source file in region 5:21889627-21890028. Error was invalid region `5:21889628-21890028`
[2016-04-15T04:17Z] 2016-04-14 21:17:11 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:17:11,590 - WARNING - Could not retrieve variants from source file in region 5:16794705-16795106. Error was invalid region `5:16794706-16795106`
[2016-04-15T04:17Z] 2016-04-14 21:17:11 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:17:11,719 - WARNING - Could not retrieve variants from source file in region 5:16673764-16674165. Error was invalid region `5:16673765-16674165`
[2016-04-15T04:17Z] 2016-04-14 21:17:11 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:17:11,942 - WARNING - Could not retrieve variants from source file in region 5:16477989-16478390. Error was invalid region `5:16477990-16478390`
[2016-04-15T04:17Z] 2016-04-14 21:17:11 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:17:11,952 - WARNING - Could not retrieve variants from source file in region 5:19721279-19721680. Error was invalid region `5:19721280-19721680`
[2016-04-15T04:17Z] 2016-04-14 21:17:11 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:17:11,989 - WARNING - Could not retrieve variants from source file in region 5:19590963-19591364. Error was invalid region `5:19590964-19591364`
[2016-04-15T04:17Z] 2016-04-14 21:17:12 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:17:12,561 - WARNING - Could not retrieve variants from source file in region 5:16769062-16769463. Error was invalid region `5:16769063-16769463`
[2016-04-15T04:17Z] 2016-04-14 21:17:12 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:17:12,637 - WARNING - Could not retrieve variants from source file in region 5:21751839-21752246. Error was invalid region `5:21751840-21752246`
[2016-04-15T04:17Z] 2016-04-14 21:17:12 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:17:12,711 - WARNING - Could not retrieve variants from source file in region 5:16508618-16509102. Error was invalid region `5:16508619-16509102`
[2016-04-15T04:17Z] 2016-04-14 21:17:12 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:17:12,716 - WARNING - Could not retrieve variants from source file in region 5:16177652-16178053. Error was invalid region `5:16177653-16178053`
[2016-04-15T04:17Z] 2016-04-14 21:17:12 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:17:12,733 - WARNING - Could not retrieve variants from source file in region 5:16713254-16713655. Error was invalid region `5:16713255-16713655`
[2016-04-15T04:17Z] 2016-04-14 21:17:18 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:17:18,443 - WARNING - Could not retrieve variants from source file in region 5:22212421-22212822. Error was invalid region `5:22212422-22212822`
[2016-04-15T04:17Z] 2016-04-14 21:17:20 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:17:20,106 - WARNING - Could not retrieve variants from source file in region 5:16713254-16713655. Error was invalid region `5:16713255-16713655`
[2016-04-15T04:17Z] 2016-04-14 21:17:20 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:17:20,187 - WARNING - Could not retrieve variants from source file in region 5:16477989-16478390. Error was invalid region `5:16477990-16478390`
[2016-04-15T04:17Z] 2016-04-14 21:17:20 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:17:20,339 - WARNING - Could not retrieve variants from source file in region 5:16794705-16795106. Error was invalid region `5:16794706-16795106`
[2016-04-15T04:17Z] 2016-04-14 21:17:20 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:17:20,639 - WARNING - Could not retrieve variants from source file in region 5:16673764-16674165. Error was invalid region `5:16673765-16674165`
[2016-04-15T04:17Z] 2016-04-14 21:17:20 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:17:20,642 - WARNING - Could not retrieve variants from source file in region 5:22078373-22078774. Error was invalid region `5:22078374-22078774`
[2016-04-15T04:17Z] 2016-04-14 21:17:21 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:17:21,012 - WARNING - Could not retrieve variants from source file in region 5:19721279-19721680. Error was invalid region `5:19721280-19721680`
[2016-04-15T04:17Z] 2016-04-14 21:17:21 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:17:21,355 - WARNING - Could not retrieve variants from source file in region 5:16477989-16478390. Error was invalid region `5:16477990-16478390`
[2016-04-15T04:17Z] 2016-04-14 21:17:21 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:17:21,418 - WARNING - Could not retrieve variants from source file in region 5:16713254-16713655. Error was invalid region `5:16713255-16713655`
[2016-04-15T04:17Z] 2016-04-14 21:17:21 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:17:21,499 - WARNING - Could not retrieve variants from source file in region 5:21751839-21752246. Error was invalid region `5:21751840-21752246`
[2016-04-15T04:17Z] 2016-04-14 21:17:23 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:17:23,195 - WARNING - Could not retrieve variants from source file in region 5:16177652-16178053. Error was invalid region `5:16177653-16178053`
[2016-04-15T04:17Z] 2016-04-14 21:17:23 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:17:23,692 - WARNING - Could not retrieve variants from source file in region 5:16794705-16795106. Error was invalid region `5:16794706-16795106`
[2016-04-15T04:17Z] 2016-04-14 21:17:26 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:17:26,843 - WARNING - Could not retrieve variants from source file in region 5:16673764-16674165. Error was invalid region `5:16673765-16674165`
[2016-04-15T04:17Z] 2016-04-14 21:17:26 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:17:26,884 - WARNING - Could not retrieve variants from source file in region 5:22078373-22078774. Error was invalid region `5:22078374-22078774`
[2016-04-15T04:17Z] 2016-04-14 21:17:27 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:17:27,300 - WARNING - Could not retrieve variants from source file in region 5:19590963-19591364. Error was invalid region `5:19590964-19591364`
[2016-04-15T04:17Z] 2016-04-14 21:17:27 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:17:27,428 - WARNING - Could not retrieve variants from source file in region 5:19721279-19721680. Error was invalid region `5:19721280-19721680`
[2016-04-15T04:17Z] 2016-04-14 21:17:27 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:17:27,449 - WARNING - Could not retrieve variants from source file in region 5:21751839-21752246. Error was invalid region `5:21751840-21752246`
[2016-04-15T04:17Z] ['bcbio-variation-recall', 'square', '-Xms750m', '-Xmx7280m', '-XX:+UseSerialGC', '-c', 16, '-r', u'5:31294069-49695124', '--caller', 'platypus', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/5/Batch1-5_31294068_49695124.vcf.gz', '/mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/5/Batch1-5_31294068_49695124.vcf-inputs.txt'] in region: 5:31294069-49695124
[2016-04-15T04:17Z] 2016-04-14 21:17:44 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:17:44,261 - WARNING - Could not retrieve variants from source file in region 5:43609132-43609533. Error was invalid region `5:43609133-43609533`
[2016-04-15T04:17Z] 2016-04-14 21:17:46 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:17:46,273 - WARNING - Could not retrieve variants from source file in region 5:34757455-34757856. Error was invalid region `5:34757456-34757856`
[2016-04-15T04:17Z] 2016-04-14 21:17:46 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:17:46,307 - WARNING - Could not retrieve variants from source file in region 5:43492767-43509538. Error was invalid region `5:43492768-43509538`
[2016-04-15T04:17Z] 2016-04-14 21:17:46 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:17:46,962 - WARNING - Could not retrieve variants from source file in region 5:36608813-36609214. Error was invalid region `5:36608814-36609214`
[2016-04-15T04:17Z] 2016-04-14 21:17:46 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:17:46,981 - WARNING - Could not retrieve variants from source file in region 5:45695961-45696362. Error was invalid region `5:45695962-45696362`
[2016-04-15T04:17Z] 2016-04-14 21:17:47 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:17:47,029 - WARNING - Could not retrieve variants from source file in region 5:41154877-41159699. Error was invalid region `5:41154878-41159699`
[2016-04-15T04:17Z] 2016-04-14 21:17:47 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:17:47,984 - WARNING - Could not retrieve variants from source file in region 5:36182549-36183288. Error was invalid region `5:36182550-36183288`
[2016-04-15T04:17Z] 2016-04-14 21:17:49 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:17:49,065 - WARNING - Could not retrieve variants from source file in region 5:43609132-43609533. Error was invalid region `5:43609133-43609533`
[2016-04-15T04:17Z] 2016-04-14 21:17:51 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:17:51,042 - WARNING - Could not retrieve variants from source file in region 5:40852240-40853238. Error was invalid region `5:40852241-40853238`
[2016-04-15T04:17Z] 2016-04-14 21:17:51 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:17:51,046 - WARNING - Could not retrieve variants from source file in region 5:42699810-42719429. Error was invalid region `5:42699811-42719429`
[2016-04-15T04:17Z] 2016-04-14 21:17:52 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:17:52,705 - WARNING - Could not retrieve variants from source file in region 5:43492767-43509538. Error was invalid region `5:43492768-43509538`
[2016-04-15T04:17Z] 2016-04-14 21:17:54 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:17:54,147 - WARNING - Could not retrieve variants from source file in region 5:39119512-39141430. Error was invalid region `5:39119513-39141430`
[2016-04-15T04:17Z] 2016-04-14 21:17:55 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:17:55,115 - WARNING - Could not retrieve variants from source file in region 5:36608813-36609214. Error was invalid region `5:36608814-36609214`
[2016-04-15T04:17Z] 2016-04-14 21:17:55 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:17:55,596 - WARNING - Could not retrieve variants from source file in region 5:43245711-43246112. Error was invalid region `5:43245712-43246112`
[2016-04-15T04:17Z] 2016-04-14 21:17:55 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:17:55,666 - WARNING - Could not retrieve variants from source file in region 5:44808951-44809559. Error was invalid region `5:44808952-44809559`
[2016-04-15T04:17Z] 2016-04-14 21:17:55 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:17:55,976 - WARNING - Could not retrieve variants from source file in region 5:32233752-32248032. Error was invalid region `5:32233753-32248032`
[2016-04-15T04:17Z] 2016-04-14 21:17:56 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:17:56,066 - WARNING - Could not retrieve variants from source file in region 5:43556175-43556576. Error was invalid region `5:43556176-43556576`
[2016-04-15T04:17Z] 2016-04-14 21:17:56 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:17:56,073 - WARNING - Could not retrieve variants from source file in region 5:32786178-32786579. Error was invalid region `5:32786179-32786579`
[2016-04-15T04:17Z] 2016-04-14 21:17:56 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:17:56,519 - WARNING - Could not retrieve variants from source file in region 5:36182549-36183288. Error was invalid region `5:36182550-36183288`
[2016-04-15T04:17Z] 2016-04-14 21:17:56 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:17:56,522 - WARNING - Could not retrieve variants from source file in region 5:43609132-43609533. Error was invalid region `5:43609133-43609533`
[2016-04-15T04:17Z] 2016-04-14 21:17:56 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:17:56,697 - WARNING - Could not retrieve variants from source file in region 5:42699810-42719429. Error was invalid region `5:42699811-42719429`
[2016-04-15T04:17Z] 2016-04-14 21:17:57 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:17:57,577 - WARNING - Could not retrieve variants from source file in region 5:43492767-43509538. Error was invalid region `5:43492768-43509538`
[2016-04-15T04:18Z] 2016-04-14 21:18:00 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:18:00,128 - WARNING - Could not retrieve variants from source file in region 5:39119512-39141430. Error was invalid region `5:39119513-39141430`
[2016-04-15T04:18Z] 2016-04-14 21:18:03 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:18:03,369 - WARNING - Could not retrieve variants from source file in region 5:32233752-32248032. Error was invalid region `5:32233753-32248032`
[2016-04-15T04:18Z] 2016-04-14 21:18:03 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:18:03,438 - WARNING - Could not retrieve variants from source file in region 5:41154877-41159699. Error was invalid region `5:41154878-41159699`
[2016-04-15T04:18Z] 2016-04-14 21:18:03 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:18:03,891 - WARNING - Could not retrieve variants from source file in region 5:36608813-36609214. Error was invalid region `5:36608814-36609214`
[2016-04-15T04:18Z] 2016-04-14 21:18:13 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:18:13,143 - WARNING - Could not retrieve variants from source file in region 5:41917493-41917894. Error was invalid region `5:41917494-41917894`
[2016-04-15T04:18Z] 2016-04-14 21:18:15 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:18:15,798 - WARNING - Could not retrieve variants from source file in region 5:43296933-43297334. Error was invalid region `5:43296934-43297334`
[2016-04-15T04:18Z] 2016-04-14 21:18:16 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:18:16,548 - WARNING - Could not retrieve variants from source file in region 5:34687999-34688406. Error was invalid region `5:34688000-34688406`
[2016-04-15T04:18Z] 2016-04-14 21:18:17 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:18:17,159 - WARNING - Could not retrieve variants from source file in region 5:35807904-35808305. Error was invalid region `5:35807905-35808305`
[2016-04-15T04:18Z] 2016-04-14 21:18:17 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:18:17,169 - WARNING - Could not retrieve variants from source file in region 5:38950565-38955986. Error was invalid region `5:38950566-38955986`
[2016-04-15T04:18Z] 2016-04-14 21:18:17 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:18:17,938 - WARNING - Could not retrieve variants from source file in region 5:41917493-41917894. Error was invalid region `5:41917494-41917894`
[2016-04-15T04:18Z] 2016-04-14 21:18:18 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:18:18,163 - WARNING - Could not retrieve variants from source file in region 5:39311125-39311526. Error was invalid region `5:39311126-39311526`
[2016-04-15T04:18Z] 2016-04-14 21:18:18 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:18:18,605 - WARNING - Could not retrieve variants from source file in region 5:32057904-32093260. Error was invalid region `5:32057905-32093260`
[2016-04-15T04:18Z] 2016-04-14 21:18:19 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:18:19,938 - WARNING - Could not retrieve variants from source file in region 5:33946344-33954701. Error was invalid region `5:33946345-33954701`
[2016-04-15T04:18Z] 2016-04-14 21:18:20 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:18:20,357 - WARNING - Could not retrieve variants from source file in region 5:35965759-35966160. Error was invalid region `5:35965760-35966160`
[2016-04-15T04:18Z] 2016-04-14 21:18:20 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:18:20,859 - WARNING - Could not retrieve variants from source file in region 5:42801057-42801458. Error was invalid region `5:42801058-42801458`
[2016-04-15T04:18Z] 2016-04-14 21:18:21 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:18:21,360 - WARNING - Could not retrieve variants from source file in region 5:43161140-43161541. Error was invalid region `5:43161141-43161541`
[2016-04-15T04:18Z] 2016-04-14 21:18:21 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:18:21,584 - WARNING - Could not retrieve variants from source file in region 5:36269340-36269741. Error was invalid region `5:36269341-36269741`
[2016-04-15T04:18Z] 2016-04-14 21:18:22 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:18:22,382 - WARNING - Could not retrieve variants from source file in region 5:34687999-34688406. Error was invalid region `5:34688000-34688406`
[2016-04-15T04:18Z] 2016-04-14 21:18:23 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:18:23,796 - WARNING - Could not retrieve variants from source file in region 5:41917493-41917894. Error was invalid region `5:41917494-41917894`
[2016-04-15T04:18Z] 2016-04-14 21:18:23 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:18:23,903 - WARNING - Could not retrieve variants from source file in region 5:39311125-39311526. Error was invalid region `5:39311126-39311526`
[2016-04-15T04:18Z] 2016-04-14 21:18:24 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:18:24,251 - WARNING - Could not retrieve variants from source file in region 5:32711442-32713555. Error was invalid region `5:32711443-32713555`
[2016-04-15T04:18Z] 2016-04-14 21:18:25 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:18:25,137 - WARNING - Could not retrieve variants from source file in region 5:33946344-33954701. Error was invalid region `5:33946345-33954701`
[2016-04-15T04:18Z] 2016-04-14 21:18:26 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:18:26,426 - WARNING - Could not retrieve variants from source file in region 5:36269340-36269741. Error was invalid region `5:36269341-36269741`
[2016-04-15T04:18Z] 2016-04-14 21:18:27 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:18:27,793 - WARNING - Could not retrieve variants from source file in region 5:34687999-34688406. Error was invalid region `5:34688000-34688406`
[2016-04-15T04:18Z] 2016-04-14 21:18:28 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:18:28,284 - WARNING - Could not retrieve variants from source file in region 5:38950565-38955986. Error was invalid region `5:38950566-38955986`
[2016-04-15T04:18Z] 2016-04-14 21:18:30 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:18:30,422 - WARNING - Could not retrieve variants from source file in region 5:33946344-33954701. Error was invalid region `5:33946345-33954701`
[2016-04-15T04:18Z] 2016-04-14 21:18:31 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:18:31,024 - WARNING - Could not retrieve variants from source file in region 5:35965759-35966160. Error was invalid region `5:35965760-35966160`
[2016-04-15T04:18Z] 2016-04-14 21:18:31 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:18:31,712 - WARNING - Could not retrieve variants from source file in region 5:36269340-36269741. Error was invalid region `5:36269341-36269741`
[2016-04-15T04:18Z] 2016-04-14 21:18:36 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:18:36,824 - WARNING - Could not retrieve variants from source file in region 5:36219499-36219900. Error was invalid region `5:36219500-36219900`
[2016-04-15T04:18Z] 2016-04-14 21:18:38 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:18:38,366 - WARNING - Could not retrieve variants from source file in region 5:39219404-39219805. Error was invalid region `5:39219405-39219805`
[2016-04-15T04:18Z] 2016-04-14 21:18:41 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:18:41,522 - WARNING - Could not retrieve variants from source file in region 5:36219499-36219900. Error was invalid region `5:36219500-36219900`
[2016-04-15T04:18Z] 2016-04-14 21:18:42 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:18:42,822 - WARNING - Could not retrieve variants from source file in region 5:38881392-38923361. Error was invalid region `5:38881393-38923361`
[2016-04-15T04:18Z] 2016-04-14 21:18:43 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:18:43,219 - WARNING - Could not retrieve variants from source file in region 5:39219404-39219805. Error was invalid region `5:39219405-39219805`
[2016-04-15T04:18Z] 2016-04-14 21:18:43 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:18:43,297 - WARNING - Could not retrieve variants from source file in region 5:31515446-31553085. Error was invalid region `5:31515447-31553085`
[2016-04-15T04:18Z] 2016-04-14 21:18:43 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:18:43,330 - WARNING - Could not retrieve variants from source file in region 5:32403135-32403536. Error was invalid region `5:32403136-32403536`
[2016-04-15T04:18Z] 2016-04-14 21:18:44 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:18:44,462 - WARNING - Could not retrieve variants from source file in region 5:35910318-35910719. Error was invalid region `5:35910319-35910719`
[2016-04-15T04:18Z] 2016-04-14 21:18:48 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:18:48,055 - WARNING - Could not retrieve variants from source file in region 5:35641371-35711096. Error was invalid region `5:35641372-35711096`
[2016-04-15T04:18Z] 2016-04-14 21:18:48 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:18:48,449 - WARNING - Could not retrieve variants from source file in region 5:39219404-39219805. Error was invalid region `5:39219405-39219805`
[2016-04-15T04:18Z] 2016-04-14 21:18:48 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:18:48,501 - WARNING - Could not retrieve variants from source file in region 5:32403135-32403536. Error was invalid region `5:32403136-32403536`
[2016-04-15T04:18Z] 2016-04-14 21:18:48 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:18:48,878 - WARNING - Could not retrieve variants from source file in region 5:33989307-34008290. Error was invalid region `5:33989308-34008290`
[2016-04-15T04:18Z] 2016-04-14 21:18:48 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:18:48,885 - WARNING - Could not retrieve variants from source file in region 5:33534849-33549564. Error was invalid region `5:33534850-33549564`
[2016-04-15T04:18Z] 2016-04-14 21:18:49 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:18:49,840 - WARNING - Could not retrieve variants from source file in region 5:35910318-35910719. Error was invalid region `5:35910319-35910719`
[2016-04-15T04:18Z] 2016-04-14 21:18:50 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:18:50,687 - WARNING - Could not retrieve variants from source file in region 5:38485854-38486255. Error was invalid region `5:38485855-38486255`
[2016-04-15T04:18Z] 2016-04-14 21:18:52 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:18:52,879 - WARNING - Could not retrieve variants from source file in region 5:32403135-32403536. Error was invalid region `5:32403136-32403536`
[2016-04-15T04:18Z] 2016-04-14 21:18:53 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:18:53,960 - WARNING - Could not retrieve variants from source file in region 5:33534849-33549564. Error was invalid region `5:33534850-33549564`
[2016-04-15T04:18Z] 2016-04-14 21:18:55 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:18:55,210 - WARNING - Could not retrieve variants from source file in region 5:38485854-38486255. Error was invalid region `5:38485855-38486255`
[2016-04-15T04:18Z] 2016-04-14 21:18:58 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:18:58,018 - WARNING - Could not retrieve variants from source file in region 5:34998666-35039676. Error was invalid region `5:34998667-35039676`
[2016-04-15T04:19Z] 2016-04-14 21:19:01 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:19:01,452 - WARNING - Could not retrieve variants from source file in region 5:38370326-38370727. Error was invalid region `5:38370327-38370727`
[2016-04-15T04:19Z] 2016-04-14 21:19:02 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:19:02,180 - WARNING - Could not retrieve variants from source file in region 5:37364232-37364633. Error was invalid region `5:37364233-37364633`
[2016-04-15T04:19Z] 2016-04-14 21:19:02 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:19:02,858 - WARNING - Could not retrieve variants from source file in region 5:37364232-37364633. Error was invalid region `5:37364233-37364633`
[2016-04-15T04:19Z] 2016-04-14 21:19:05 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:19:05,091 - WARNING - Could not retrieve variants from source file in region 5:31302077-31318142. Error was invalid region `5:31302078-31318142`
[2016-04-15T04:19Z] 2016-04-14 21:19:05 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:19:05,198 - WARNING - Could not retrieve variants from source file in region 5:38370326-38370727. Error was invalid region `5:38370327-38370727`
[2016-04-15T04:19Z] 2016-04-14 21:19:05 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:19:05,531 - WARNING - Could not retrieve variants from source file in region 5:37364232-37364633. Error was invalid region `5:37364233-37364633`
[2016-04-15T04:19Z] 2016-04-14 21:19:05 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:19:05,656 - WARNING - Could not retrieve variants from source file in region 5:33461144-33461545. Error was invalid region `5:33461145-33461545`
[2016-04-15T04:19Z] 2016-04-14 21:19:06 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:19:06,171 - WARNING - Could not retrieve variants from source file in region 5:34807717-34841031. Error was invalid region `5:34807718-34841031`
[2016-04-15T04:19Z] 2016-04-14 21:19:08 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:19:08,139 - WARNING - Could not retrieve variants from source file in region 5:31302077-31318142. Error was invalid region `5:31302078-31318142`
[2016-04-15T04:19Z] 2016-04-14 21:19:08 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:19:08,746 - WARNING - Could not retrieve variants from source file in region 5:33461144-33461545. Error was invalid region `5:33461145-33461545`
[2016-04-15T04:19Z] 2016-04-14 21:19:08 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:19:08,918 - WARNING - Could not retrieve variants from source file in region 5:33461144-33461545. Error was invalid region `5:33461145-33461545`
[2016-04-15T04:19Z] 2016-04-14 21:19:09 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:19:09,405 - WARNING - Could not retrieve variants from source file in region 5:34807717-34841031. Error was invalid region `5:34807718-34841031`
[2016-04-15T04:19Z] 2016-04-14 21:19:11 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:19:11,525 - WARNING - Could not retrieve variants from source file in region 5:34807717-34841031. Error was invalid region `5:34807718-34841031`
[2016-04-15T04:19Z] 2016-04-14 21:19:11 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:19:11,735 - WARNING - Could not retrieve variants from source file in region 5:31302077-31318142. Error was invalid region `5:31302078-31318142`
[2016-04-15T04:19Z] ['bcbio-variation-recall', 'square', '-Xms750m', '-Xmx7280m', '-XX:+UseSerialGC', '-c', 16, '-r', u'5:49695693-65288736', '--caller', 'platypus', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/5/Batch1-5_49695692_65288736.vcf.gz', '/mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/5/Batch1-5_49695692_65288736.vcf-inputs.txt'] in region: 5:49695693-65288736
[2016-04-15T04:19Z] 2016-04-14 21:19:26 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:19:26,913 - WARNING - Could not retrieve variants from source file in region 5:52941872-52942387. Error was invalid region `5:52941873-52942387`
[2016-04-15T04:19Z] 2016-04-14 21:19:27 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:19:27,036 - WARNING - Could not retrieve variants from source file in region 5:58270283-58295572. Error was invalid region `5:58270284-58295572`
[2016-04-15T04:19Z] 2016-04-14 21:19:27 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:19:27,083 - WARNING - Could not retrieve variants from source file in region 5:63665237-63665638. Error was invalid region `5:63665238-63665638`
[2016-04-15T04:19Z] 2016-04-14 21:19:28 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:19:28,191 - WARNING - Could not retrieve variants from source file in region 5:60240931-60241332. Error was invalid region `5:60240932-60241332`
[2016-04-15T04:19Z] 2016-04-14 21:19:28 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:19:28,291 - WARNING - Could not retrieve variants from source file in region 5:61772324-61772725. Error was invalid region `5:61772325-61772725`
[2016-04-15T04:19Z] 2016-04-14 21:19:28 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:19:28,849 - WARNING - Could not retrieve variants from source file in region 5:61603993-61604394. Error was invalid region `5:61603994-61604394`
[2016-04-15T04:19Z] 2016-04-14 21:19:28 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:19:28,889 - WARNING - Could not retrieve variants from source file in region 5:65108004-65108405. Error was invalid region `5:65108005-65108405`
[2016-04-15T04:19Z] 2016-04-14 21:19:29 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:19:29,269 - WARNING - Could not retrieve variants from source file in region 5:52856293-52856694. Error was invalid region `5:52856294-52856694`
[2016-04-15T04:19Z] 2016-04-14 21:19:29 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:19:29,426 - WARNING - Could not retrieve variants from source file in region 5:58335081-58335482. Error was invalid region `5:58335082-58335482`
[2016-04-15T04:19Z] 2016-04-14 21:19:29 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:19:29,541 - WARNING - Could not retrieve variants from source file in region 5:55155191-55155592. Error was invalid region `5:55155192-55155592`
[2016-04-15T04:19Z] 2016-04-14 21:19:29 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:19:29,688 - WARNING - Could not retrieve variants from source file in region 5:64103503-64103904. Error was invalid region `5:64103504-64103904`
[2016-04-15T04:19Z] 2016-04-14 21:19:31 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:19:31,031 - WARNING - Could not retrieve variants from source file in region 5:58571406-58572105. Error was invalid region `5:58571407-58572105`
[2016-04-15T04:19Z] 2016-04-14 21:19:32 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:19:32,054 - WARNING - Could not retrieve variants from source file in region 5:52941872-52942387. Error was invalid region `5:52941873-52942387`
[2016-04-15T04:19Z] 2016-04-14 21:19:35 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:19:35,097 - WARNING - Could not retrieve variants from source file in region 5:60240931-60241332. Error was invalid region `5:60240932-60241332`
[2016-04-15T04:19Z] 2016-04-14 21:19:35 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:19:35,888 - WARNING - Could not retrieve variants from source file in region 5:61772324-61772725. Error was invalid region `5:61772325-61772725`
[2016-04-15T04:19Z] 2016-04-14 21:19:35 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:19:35,971 - WARNING - Could not retrieve variants from source file in region 5:52781386-52781787. Error was invalid region `5:52781387-52781787`
[2016-04-15T04:19Z] 2016-04-14 21:19:36 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:19:36,546 - WARNING - Could not retrieve variants from source file in region 5:65108004-65108405. Error was invalid region `5:65108005-65108405`
[2016-04-15T04:19Z] 2016-04-14 21:19:36 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:19:36,594 - WARNING - Could not retrieve variants from source file in region 5:52347158-52351603. Error was invalid region `5:52347159-52351603`
[2016-04-15T04:19Z] 2016-04-14 21:19:37 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:19:37,034 - WARNING - Could not retrieve variants from source file in region 5:52856293-52856694. Error was invalid region `5:52856294-52856694`
[2016-04-15T04:19Z] 2016-04-14 21:19:37 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:19:37,083 - WARNING - Could not retrieve variants from source file in region 5:53578104-53578505. Error was invalid region `5:53578105-53578505`
[2016-04-15T04:19Z] 2016-04-14 21:19:37 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:19:37,237 - WARNING - Could not retrieve variants from source file in region 5:55155191-55155592. Error was invalid region `5:55155192-55155592`
[2016-04-15T04:19Z] 2016-04-14 21:19:37 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:19:37,338 - WARNING - Could not retrieve variants from source file in region 5:64103503-64103904. Error was invalid region `5:64103504-64103904`
[2016-04-15T04:19Z] 2016-04-14 21:19:37 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:19:37,778 - WARNING - Could not retrieve variants from source file in region 5:58571406-58572105. Error was invalid region `5:58571407-58572105`
[2016-04-15T04:19Z] 2016-04-14 21:19:37 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:19:37,955 - WARNING - Could not retrieve variants from source file in region 5:52941872-52942387. Error was invalid region `5:52941873-52942387`
[2016-04-15T04:19Z] 2016-04-14 21:19:37 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:19:37,987 - WARNING - Could not retrieve variants from source file in region 5:58335081-58335482. Error was invalid region `5:58335082-58335482`
[2016-04-15T04:19Z] 2016-04-14 21:19:38 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:19:38,303 - WARNING - Could not retrieve variants from source file in region 5:63665237-63665638. Error was invalid region `5:63665238-63665638`
[2016-04-15T04:19Z] 2016-04-14 21:19:40 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:19:40,050 - WARNING - Could not retrieve variants from source file in region 5:60240931-60241332. Error was invalid region `5:60240932-60241332`
[2016-04-15T04:19Z] 2016-04-14 21:19:41 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:19:41,569 - WARNING - Could not retrieve variants from source file in region 5:61772324-61772725. Error was invalid region `5:61772325-61772725`
[2016-04-15T04:19Z] 2016-04-14 21:19:43 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:19:43,406 - WARNING - Could not retrieve variants from source file in region 5:65108004-65108405. Error was invalid region `5:65108005-65108405`
[2016-04-15T04:19Z] 2016-04-14 21:19:44 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:19:44,061 - WARNING - Could not retrieve variants from source file in region 5:61603993-61604394. Error was invalid region `5:61603994-61604394`
[2016-04-15T04:19Z] 2016-04-14 21:19:44 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:19:44,103 - WARNING - Could not retrieve variants from source file in region 5:52347158-52351603. Error was invalid region `5:52347159-52351603`
[2016-04-15T04:19Z] 2016-04-14 21:19:44 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:19:44,589 - WARNING - Could not retrieve variants from source file in region 5:55155191-55155592. Error was invalid region `5:55155192-55155592`
[2016-04-15T04:19Z] 2016-04-14 21:19:44 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:19:44,703 - WARNING - Could not retrieve variants from source file in region 5:53578104-53578505. Error was invalid region `5:53578105-53578505`
[2016-04-15T04:19Z] 2016-04-14 21:19:44 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:19:44,714 - WARNING - Could not retrieve variants from source file in region 5:52856293-52856694. Error was invalid region `5:52856294-52856694`
[2016-04-15T04:19Z] 2016-04-14 21:19:45 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:19:45,123 - WARNING - Could not retrieve variants from source file in region 5:58335081-58335482. Error was invalid region `5:58335082-58335482`
[2016-04-15T04:19Z] 2016-04-14 21:19:54 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:19:54,165 - WARNING - Could not retrieve variants from source file in region 5:63991262-63991663. Error was invalid region `5:63991263-63991663`
[2016-04-15T04:19Z] 2016-04-14 21:19:54 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:19:54,897 - WARNING - Could not retrieve variants from source file in region 5:61694168-61694569. Error was invalid region `5:61694169-61694569`
[2016-04-15T04:19Z] 2016-04-14 21:19:56 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:19:56,115 - WARNING - Could not retrieve variants from source file in region 5:61694168-61694569. Error was invalid region `5:61694169-61694569`
[2016-04-15T04:19Z] 2016-04-14 21:19:57 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:19:57,203 - WARNING - Could not retrieve variants from source file in region 5:52379066-52379467. Error was invalid region `5:52379067-52379467`
[2016-04-15T04:19Z] 2016-04-14 21:19:58 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:19:58,522 - WARNING - Could not retrieve variants from source file in region 5:63991262-63991663. Error was invalid region `5:63991263-63991663`
[2016-04-15T04:19Z] 2016-04-14 21:19:59 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:19:59,575 - WARNING - Could not retrieve variants from source file in region 5:61694168-61694569. Error was invalid region `5:61694169-61694569`
[2016-04-15T04:20Z] 2016-04-14 21:20:00 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:20:00,408 - WARNING - Could not retrieve variants from source file in region 5:52193076-52193477. Error was invalid region `5:52193077-52193477`
[2016-04-15T04:20Z] 2016-04-14 21:20:00 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:20:00,485 - WARNING - Could not retrieve variants from source file in region 5:54557072-54572353. Error was invalid region `5:54557073-54572353`
[2016-04-15T04:20Z] 2016-04-14 21:20:00 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:20:00,707 - WARNING - Could not retrieve variants from source file in region 5:56526572-56526973. Error was invalid region `5:56526573-56526973`
[2016-04-15T04:20Z] 2016-04-14 21:20:01 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:20:01,033 - WARNING - Could not retrieve variants from source file in region 5:60200454-60200855. Error was invalid region `5:60200455-60200855`
[2016-04-15T04:20Z] 2016-04-14 21:20:01 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:20:01,533 - WARNING - Could not retrieve variants from source file in region 5:55062553-55082664. Error was invalid region `5:55062554-55082664`
[2016-04-15T04:20Z] 2016-04-14 21:20:01 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:20:01,712 - WARNING - Could not retrieve variants from source file in region 5:52379066-52379467. Error was invalid region `5:52379067-52379467`
[2016-04-15T04:20Z] 2016-04-14 21:20:02 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:20:02,782 - WARNING - Could not retrieve variants from source file in region 5:64865194-64886736. Error was invalid region `5:64865195-64886736`
[2016-04-15T04:20Z] 2016-04-14 21:20:03 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:20:03,282 - WARNING - Could not retrieve variants from source file in region 5:63991262-63991663. Error was invalid region `5:63991263-63991663`
[2016-04-15T04:20Z] 2016-04-14 21:20:04 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:20:04,577 - WARNING - Could not retrieve variants from source file in region 5:52405166-52405567. Error was invalid region `5:52405167-52405567`
[2016-04-15T04:20Z] 2016-04-14 21:20:05 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:20:05,278 - WARNING - Could not retrieve variants from source file in region 5:56526572-56526973. Error was invalid region `5:56526573-56526973`
[2016-04-15T04:20Z] 2016-04-14 21:20:06 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:20:06,486 - WARNING - Could not retrieve variants from source file in region 5:54960398-54960877. Error was invalid region `5:54960399-54960877`
[2016-04-15T04:20Z] 2016-04-14 21:20:09 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:20:09,950 - WARNING - Could not retrieve variants from source file in region 5:52193076-52193477. Error was invalid region `5:52193077-52193477`
[2016-04-15T04:20Z] 2016-04-14 21:20:10 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:20:10,182 - WARNING - Could not retrieve variants from source file in region 5:56526572-56526973. Error was invalid region `5:56526573-56526973`
[2016-04-15T04:20Z] 2016-04-14 21:20:11 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:20:11,222 - WARNING - Could not retrieve variants from source file in region 5:60627942-60628604. Error was invalid region `5:60627943-60628604`
[2016-04-15T04:20Z] 2016-04-14 21:20:11 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:20:11,554 - WARNING - Could not retrieve variants from source file in region 5:54960398-54960877. Error was invalid region `5:54960399-54960877`
[2016-04-15T04:20Z] 2016-04-14 21:20:13 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:20:13,567 - WARNING - Could not retrieve variants from source file in region 5:54674085-54674486. Error was invalid region `5:54674086-54674486`
[2016-04-15T04:20Z] 2016-04-14 21:20:16 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:20:16,633 - WARNING - Could not retrieve variants from source file in region 5:63904857-63905258. Error was invalid region `5:63904858-63905258`
[2016-04-15T04:20Z] 2016-04-14 21:20:17 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:20:17,901 - WARNING - Could not retrieve variants from source file in region 5:52096678-52097079. Error was invalid region `5:52096679-52097079`
[2016-04-15T04:20Z] 2016-04-14 21:20:18 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:20:18,391 - WARNING - Could not retrieve variants from source file in region 5:64272807-64273208. Error was invalid region `5:64272808-64273208`
[2016-04-15T04:20Z] 2016-04-14 21:20:18 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:20:18,976 - WARNING - Could not retrieve variants from source file in region 5:60627942-60628604. Error was invalid region `5:60627943-60628604`
[2016-04-15T04:20Z] 2016-04-14 21:20:19 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:20:19,020 - WARNING - Could not retrieve variants from source file in region 5:56161576-56178407. Error was invalid region `5:56161577-56178407`
[2016-04-15T04:20Z] 2016-04-14 21:20:19 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:20:19,031 - WARNING - Could not retrieve variants from source file in region 5:54645200-54645601. Error was invalid region `5:54645201-54645601`
[2016-04-15T04:20Z] 2016-04-14 21:20:19 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:20:19,511 - WARNING - Could not retrieve variants from source file in region 5:58882120-58882521. Error was invalid region `5:58882121-58882521`
[2016-04-15T04:20Z] 2016-04-14 21:20:21 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:20:21,264 - WARNING - Could not retrieve variants from source file in region 5:63904857-63905258. Error was invalid region `5:63904858-63905258`
[2016-04-15T04:20Z] 2016-04-14 21:20:22 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:20:22,570 - WARNING - Could not retrieve variants from source file in region 5:52096678-52097079. Error was invalid region `5:52096679-52097079`
[2016-04-15T04:20Z] 2016-04-14 21:20:23 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:20:23,715 - WARNING - Could not retrieve variants from source file in region 5:52157163-52157564. Error was invalid region `5:52157164-52157564`
[2016-04-15T04:20Z] 2016-04-14 21:20:24 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:20:24,649 - WARNING - Could not retrieve variants from source file in region 5:58882120-58882521. Error was invalid region `5:58882121-58882521`
[2016-04-15T04:20Z] 2016-04-14 21:20:25 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:20:25,473 - WARNING - Could not retrieve variants from source file in region 5:63904857-63905258. Error was invalid region `5:63904858-63905258`
[2016-04-15T04:20Z] 2016-04-14 21:20:26 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:20:26,469 - WARNING - Could not retrieve variants from source file in region 5:52096678-52097079. Error was invalid region `5:52096679-52097079`
[2016-04-15T04:20Z] 2016-04-14 21:20:27 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:20:27,820 - WARNING - Could not retrieve variants from source file in region 5:64272807-64273208. Error was invalid region `5:64272808-64273208`
[2016-04-15T04:20Z] 2016-04-14 21:20:28 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:20:28,042 - WARNING - Could not retrieve variants from source file in region 5:52157163-52157564. Error was invalid region `5:52157164-52157564`
[2016-04-15T04:20Z] 2016-04-14 21:20:29 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:20:29,635 - WARNING - Could not retrieve variants from source file in region 5:54988371-54988772. Error was invalid region `5:54988372-54988772`
[2016-04-15T04:20Z] 2016-04-14 21:20:29 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:20:29,652 - WARNING - Could not retrieve variants from source file in region 5:54988371-54988772. Error was invalid region `5:54988372-54988772`
[2016-04-15T04:20Z] 2016-04-14 21:20:29 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:20:29,680 - WARNING - Could not retrieve variants from source file in region 5:56205862-56242964. Error was invalid region `5:56205863-56242964`
[2016-04-15T04:20Z] 2016-04-14 21:20:32 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:20:32,634 - WARNING - Could not retrieve variants from source file in region 5:52157163-52157564. Error was invalid region `5:52157164-52157564`
[2016-04-15T04:20Z] 2016-04-14 21:20:37 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:20:37,649 - WARNING - Could not retrieve variants from source file in region 5:55406741-55423414. Error was invalid region `5:55406742-55423414`
[2016-04-15T04:20Z] 2016-04-14 21:20:39 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:20:39,329 - WARNING - Could not retrieve variants from source file in region 5:54403746-54410310. Error was invalid region `5:54403747-54410310`
[2016-04-15T04:20Z] 2016-04-14 21:20:39 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:20:39,500 - WARNING - Could not retrieve variants from source file in region 5:56111540-56111941. Error was invalid region `5:56111541-56111941`
[2016-04-15T04:20Z] 2016-04-14 21:20:39 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:20:39,883 - WARNING - Could not retrieve variants from source file in region 5:50685294-50685695. Error was invalid region `5:50685295-50685695`
[2016-04-15T04:20Z] 2016-04-14 21:20:40 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:20:40,121 - WARNING - Could not retrieve variants from source file in region 5:50057518-50057919. Error was invalid region `5:50057519-50057919`
[2016-04-15T04:20Z] 2016-04-14 21:20:41 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:20:41,317 - WARNING - Could not retrieve variants from source file in region 5:56111540-56111941. Error was invalid region `5:56111541-56111941`
[2016-04-15T04:20Z] 2016-04-14 21:20:41 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:20:41,694 - WARNING - Could not retrieve variants from source file in region 5:53751690-53752178. Error was invalid region `5:53751691-53752178`
[2016-04-15T04:20Z] 2016-04-14 21:20:42 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:20:42,741 - WARNING - Could not retrieve variants from source file in region 5:54439255-54460151. Error was invalid region `5:54439256-54460151`
[2016-04-15T04:20Z] 2016-04-14 21:20:44 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:20:44,227 - WARNING - Could not retrieve variants from source file in region 5:50057518-50057919. Error was invalid region `5:50057519-50057919`
[2016-04-15T04:20Z] 2016-04-14 21:20:46 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:20:46,289 - WARNING - Could not retrieve variants from source file in region 5:53751690-53752178. Error was invalid region `5:53751691-53752178`
[2016-04-15T04:20Z] 2016-04-14 21:20:46 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:20:46,408 - WARNING - Could not retrieve variants from source file in region 5:54439255-54460151. Error was invalid region `5:54439256-54460151`
[2016-04-15T04:20Z] 2016-04-14 21:20:47 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:20:47,520 - WARNING - Could not retrieve variants from source file in region 5:54403746-54410310. Error was invalid region `5:54403747-54410310`
[2016-04-15T04:20Z] 2016-04-14 21:20:48 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:20:48,033 - WARNING - Could not retrieve variants from source file in region 5:50057518-50057919. Error was invalid region `5:50057519-50057919`
[2016-04-15T04:20Z] 2016-04-14 21:20:49 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:20:49,343 - WARNING - Could not retrieve variants from source file in region 5:53813619-53815685. Error was invalid region `5:53813620-53815685`
[2016-04-15T04:20Z] 2016-04-14 21:20:50 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:20:50,769 - WARNING - Could not retrieve variants from source file in region 5:49962526-49962927. Error was invalid region `5:49962527-49962927`
[2016-04-15T04:20Z] 2016-04-14 21:20:50 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:20:50,779 - WARNING - Could not retrieve variants from source file in region 5:49962526-49962927. Error was invalid region `5:49962527-49962927`
[2016-04-15T04:20Z] 2016-04-14 21:20:50 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:20:50,785 - WARNING - Could not retrieve variants from source file in region 5:49962526-49962927. Error was invalid region `5:49962527-49962927`
[2016-04-15T04:20Z] 2016-04-14 21:20:54 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:20:54,104 - WARNING - Could not retrieve variants from source file in region 5:53606084-53606485. Error was invalid region `5:53606085-53606485`
[2016-04-15T04:20Z] 2016-04-14 21:20:54 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:20:54,111 - WARNING - Could not retrieve variants from source file in region 5:53606084-53606485. Error was invalid region `5:53606085-53606485`
[2016-04-15T04:20Z] 2016-04-14 21:20:54 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:20:54,115 - WARNING - Could not retrieve variants from source file in region 5:53606084-53606485. Error was invalid region `5:53606085-53606485`
[2016-04-15T04:21Z] ['bcbio-variation-recall', 'square', '-Xms750m', '-Xmx7280m', '-XX:+UseSerialGC', '-c', 16, '-r', u'5:65290575-80809536', '--caller', 'platypus', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/5/Batch1-5_65290574_80809536.vcf.gz', '/mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/5/Batch1-5_65290574_80809536.vcf-inputs.txt'] in region: 5:65290575-80809536
[2016-04-15T04:21Z] 2016-04-14 21:21:10 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:21:10,536 - WARNING - Could not retrieve variants from source file in region 5:75427724-75428125. Error was invalid region `5:75427725-75428125`
[2016-04-15T04:21Z] 2016-04-14 21:21:11 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:21:11,334 - WARNING - Could not retrieve variants from source file in region 5:76349689-76373431. Error was invalid region `5:76349690-76373431`
[2016-04-15T04:21Z] 2016-04-14 21:21:11 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:21:11,380 - WARNING - Could not retrieve variants from source file in region 5:75923074-75961055. Error was invalid region `5:75923075-75961055`
[2016-04-15T04:21Z] 2016-04-14 21:21:11 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:21:11,853 - WARNING - Could not retrieve variants from source file in region 5:78317202-78373621. Error was invalid region `5:78317203-78373621`
[2016-04-15T04:21Z] 2016-04-14 21:21:12 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:21:12,155 - WARNING - Could not retrieve variants from source file in region 5:76171041-76171442. Error was invalid region `5:76171042-76171442`
[2016-04-15T04:21Z] 2016-04-14 21:21:12 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:21:12,255 - WARNING - Could not retrieve variants from source file in region 5:77745642-77746043. Error was invalid region `5:77745643-77746043`
[2016-04-15T04:21Z] 2016-04-14 21:21:12 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:21:12,328 - WARNING - Could not retrieve variants from source file in region 5:79095206-79095607. Error was invalid region `5:79095207-79095607`
[2016-04-15T04:21Z] 2016-04-14 21:21:12 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:21:12,494 - WARNING - Could not retrieve variants from source file in region 5:75700099-75700500. Error was invalid region `5:75700100-75700500`
[2016-04-15T04:21Z] 2016-04-14 21:21:12 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:21:12,506 - WARNING - Could not retrieve variants from source file in region 5:80736233-80736634. Error was invalid region `5:80736234-80736634`
[2016-04-15T04:21Z] 2016-04-14 21:21:15 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:21:15,417 - WARNING - Could not retrieve variants from source file in region 5:79615872-79617126. Error was invalid region `5:79615873-79617126`
[2016-04-15T04:21Z] 2016-04-14 21:21:15 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:21:15,701 - WARNING - Could not retrieve variants from source file in region 5:76704638-76734274. Error was invalid region `5:76704639-76734274`
[2016-04-15T04:21Z] 2016-04-14 21:21:17 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:21:17,058 - WARNING - Could not retrieve variants from source file in region 5:75427724-75428125. Error was invalid region `5:75427725-75428125`
[2016-04-15T04:21Z] 2016-04-14 21:21:17 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:21:17,106 - WARNING - Could not retrieve variants from source file in region 5:79950530-79966219. Error was invalid region `5:79950531-79966219`
[2016-04-15T04:21Z] 2016-04-14 21:21:19 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:21:19,443 - WARNING - Could not retrieve variants from source file in region 5:73981059-73985470. Error was invalid region `5:73981060-73985470`
[2016-04-15T04:21Z] 2016-04-14 21:21:19 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:21:19,479 - WARNING - Could not retrieve variants from source file in region 5:78573579-78610652. Error was invalid region `5:78573580-78610652`
[2016-04-15T04:21Z] 2016-04-14 21:21:20 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:21:20,276 - WARNING - Could not retrieve variants from source file in region 5:72183887-72192548. Error was invalid region `5:72183888-72192548`
[2016-04-15T04:21Z] 2016-04-14 21:21:20 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:21:20,294 - WARNING - Could not retrieve variants from source file in region 5:74921475-74921876. Error was invalid region `5:74921476-74921876`
[2016-04-15T04:21Z] 2016-04-14 21:21:20 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:21:20,456 - WARNING - Could not retrieve variants from source file in region 5:75923074-75961055. Error was invalid region `5:75923075-75961055`
[2016-04-15T04:21Z] 2016-04-14 21:21:20 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:21:20,723 - WARNING - Could not retrieve variants from source file in region 5:79095206-79095607. Error was invalid region `5:79095207-79095607`
[2016-04-15T04:21Z] 2016-04-14 21:21:20 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:21:20,917 - WARNING - Could not retrieve variants from source file in region 5:76171041-76171442. Error was invalid region `5:76171042-76171442`
[2016-04-15T04:21Z] 2016-04-14 21:21:21 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:21:21,147 - WARNING - Could not retrieve variants from source file in region 5:77745642-77746043. Error was invalid region `5:77745643-77746043`
[2016-04-15T04:21Z] 2016-04-14 21:21:21 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:21:21,374 - WARNING - Could not retrieve variants from source file in region 5:75700099-75700500. Error was invalid region `5:75700100-75700500`
[2016-04-15T04:21Z] 2016-04-14 21:21:21 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:21:21,676 - WARNING - Could not retrieve variants from source file in region 5:75427724-75428125. Error was invalid region `5:75427725-75428125`
[2016-04-15T04:21Z] 2016-04-14 21:21:26 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:21:26,741 - WARNING - Could not retrieve variants from source file in region 5:78573579-78610652. Error was invalid region `5:78573580-78610652`
[2016-04-15T04:21Z] 2016-04-14 21:21:29 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:21:29,831 - WARNING - Could not retrieve variants from source file in region 5:72183887-72192548. Error was invalid region `5:72183888-72192548`
[2016-04-15T04:21Z] 2016-04-14 21:21:29 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:21:29,940 - WARNING - Could not retrieve variants from source file in region 5:80736233-80736634. Error was invalid region `5:80736234-80736634`
[2016-04-15T04:21Z] 2016-04-14 21:21:30 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:21:30,246 - WARNING - Could not retrieve variants from source file in region 5:75923074-75961055. Error was invalid region `5:75923075-75961055`
[2016-04-15T04:21Z] 2016-04-14 21:21:30 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:21:30,263 - WARNING - Could not retrieve variants from source file in region 5:79095206-79095607. Error was invalid region `5:79095207-79095607`
[2016-04-15T04:21Z] 2016-04-14 21:21:30 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:21:30,404 - WARNING - Could not retrieve variants from source file in region 5:76171041-76171442. Error was invalid region `5:76171042-76171442`
[2016-04-15T04:21Z] 2016-04-14 21:21:30 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:21:30,540 - WARNING - Could not retrieve variants from source file in region 5:77745642-77746043. Error was invalid region `5:77745643-77746043`
[2016-04-15T04:21Z] 2016-04-14 21:21:30 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:21:30,544 - WARNING - Could not retrieve variants from source file in region 5:75700099-75700500. Error was invalid region `5:75700100-75700500`
[2016-04-15T04:21Z] 2016-04-14 21:21:42 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:21:42,428 - WARNING - Could not retrieve variants from source file in region 5:79855161-79855562. Error was invalid region `5:79855162-79855562`
[2016-04-15T04:21Z] 2016-04-14 21:21:44 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:21:44,005 - WARNING - Could not retrieve variants from source file in region 5:73930540-73931436. Error was invalid region `5:73930541-73931436`
[2016-04-15T04:21Z] 2016-04-14 21:21:45 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:21:45,177 - WARNING - Could not retrieve variants from source file in region 5:78532447-78532848. Error was invalid region `5:78532448-78532848`
[2016-04-15T04:21Z] 2016-04-14 21:21:46 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:21:46,050 - WARNING - Could not retrieve variants from source file in region 5:79435472-79439503. Error was invalid region `5:79435473-79439503`
[2016-04-15T04:21Z] 2016-04-14 21:21:47 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:21:47,815 - WARNING - Could not retrieve variants from source file in region 5:76128310-76129324. Error was invalid region `5:76128311-76129324`
[2016-04-15T04:21Z] 2016-04-14 21:21:47 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:21:47,822 - WARNING - Could not retrieve variants from source file in region 5:79815447-79815848. Error was invalid region `5:79815448-79815848`
[2016-04-15T04:21Z] 2016-04-14 21:21:47 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:21:47,940 - WARNING - Could not retrieve variants from source file in region 5:72143794-72144195. Error was invalid region `5:72143795-72144195`
[2016-04-15T04:21Z] 2016-04-14 21:21:48 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:21:48,107 - WARNING - Could not retrieve variants from source file in region 5:79855161-79855562. Error was invalid region `5:79855162-79855562`
[2016-04-15T04:21Z] 2016-04-14 21:21:48 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:21:48,537 - WARNING - Could not retrieve variants from source file in region 5:78181266-78181667. Error was invalid region `5:78181267-78181667`
[2016-04-15T04:21Z] 2016-04-14 21:21:48 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:21:48,821 - WARNING - Could not retrieve variants from source file in region 5:74964911-75003868. Error was invalid region `5:74964912-75003868`
[2016-04-15T04:21Z] 2016-04-14 21:21:48 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:21:48,878 - WARNING - Could not retrieve variants from source file in region 5:75884523-75884924. Error was invalid region `5:75884524-75884924`
[2016-04-15T04:21Z] 2016-04-14 21:21:49 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:21:49,401 - WARNING - Could not retrieve variants from source file in region 5:73930540-73931436. Error was invalid region `5:73930541-73931436`
[2016-04-15T04:21Z] 2016-04-14 21:21:50 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:21:50,569 - WARNING - Could not retrieve variants from source file in region 5:74877055-74877456. Error was invalid region `5:74877056-74877456`
[2016-04-15T04:21Z] 2016-04-14 21:21:52 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:21:52,921 - WARNING - Could not retrieve variants from source file in region 5:79815447-79815848. Error was invalid region `5:79815448-79815848`
[2016-04-15T04:21Z] 2016-04-14 21:21:53 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:21:53,294 - WARNING - Could not retrieve variants from source file in region 5:72143794-72144195. Error was invalid region `5:72143795-72144195`
[2016-04-15T04:21Z] 2016-04-14 21:21:54 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:21:54,133 - WARNING - Could not retrieve variants from source file in region 5:79855161-79855562. Error was invalid region `5:79855162-79855562`
[2016-04-15T04:21Z] 2016-04-14 21:21:54 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:21:54,226 - WARNING - Could not retrieve variants from source file in region 5:78181266-78181667. Error was invalid region `5:78181267-78181667`
[2016-04-15T04:21Z] 2016-04-14 21:21:54 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:21:54,814 - WARNING - Could not retrieve variants from source file in region 5:77472954-77473355. Error was invalid region `5:77472955-77473355`
[2016-04-15T04:21Z] 2016-04-14 21:21:54 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:21:54,892 - WARNING - Could not retrieve variants from source file in region 5:75884523-75884924. Error was invalid region `5:75884524-75884924`
[2016-04-15T04:21Z] 2016-04-14 21:21:55 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:21:55,246 - WARNING - Could not retrieve variants from source file in region 5:73930540-73931436. Error was invalid region `5:73930541-73931436`
[2016-04-15T04:21Z] 2016-04-14 21:21:57 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:21:57,254 - WARNING - Could not retrieve variants from source file in region 5:79815447-79815848. Error was invalid region `5:79815448-79815848`
[2016-04-15T04:21Z] 2016-04-14 21:21:57 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:21:57,842 - WARNING - Could not retrieve variants from source file in region 5:72143794-72144195. Error was invalid region `5:72143795-72144195`
[2016-04-15T04:21Z] 2016-04-14 21:21:58 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:21:58,354 - WARNING - Could not retrieve variants from source file in region 5:76128310-76129324. Error was invalid region `5:76128311-76129324`
[2016-04-15T04:21Z] 2016-04-14 21:21:59 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:21:59,634 - WARNING - Could not retrieve variants from source file in region 5:78181266-78181667. Error was invalid region `5:78181267-78181667`
[2016-04-15T04:22Z] 2016-04-14 21:22:00 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:22:00,440 - WARNING - Could not retrieve variants from source file in region 5:75884523-75884924. Error was invalid region `5:75884524-75884924`
[2016-04-15T04:22Z] 2016-04-14 21:22:01 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:22:01,859 - WARNING - Could not retrieve variants from source file in region 5:80600408-80604620. Error was invalid region `5:80600409-80604620`
[2016-04-15T04:22Z] 2016-04-14 21:22:01 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:22:01,943 - WARNING - Could not retrieve variants from source file in region 5:77472954-77473355. Error was invalid region `5:77472955-77473355`
[2016-04-15T04:22Z] 2016-04-14 21:22:03 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:22:03,303 - WARNING - Could not retrieve variants from source file in region 5:77411800-77425218. Error was invalid region `5:77411801-77425218`
[2016-04-15T04:22Z] 2016-04-14 21:22:08 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:22:08,149 - WARNING - Could not retrieve variants from source file in region 5:74491281-74491908. Error was invalid region `5:74491282-74491908`
[2016-04-15T04:22Z] 2016-04-14 21:22:08 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:22:08,857 - WARNING - Could not retrieve variants from source file in region 5:77411800-77425218. Error was invalid region `5:77411801-77425218`
[2016-04-15T04:22Z] 2016-04-14 21:22:08 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:22:08,869 - WARNING - Could not retrieve variants from source file in region 5:79732868-79745659. Error was invalid region `5:79732869-79745659`
[2016-04-15T04:22Z] 2016-04-14 21:22:09 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:22:09,684 - WARNING - Could not retrieve variants from source file in region 5:78421748-78422149. Error was invalid region `5:78421749-78422149`
[2016-04-15T04:22Z] 2016-04-14 21:22:12 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:22:12,022 - WARNING - Could not retrieve variants from source file in region 5:78421748-78422149. Error was invalid region `5:78421749-78422149`
[2016-04-15T04:22Z] 2016-04-14 21:22:13 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:22:13,529 - WARNING - Could not retrieve variants from source file in region 5:68715099-68715500. Error was invalid region `5:68715100-68715500`
[2016-04-15T04:22Z] 2016-04-14 21:22:14 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:22:14,259 - WARNING - Could not retrieve variants from source file in region 5:77411800-77425218. Error was invalid region `5:77411801-77425218`
[2016-04-15T04:22Z] 2016-04-14 21:22:14 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:22:14,693 - WARNING - Could not retrieve variants from source file in region 5:79732868-79745659. Error was invalid region `5:79732869-79745659`
[2016-04-15T04:22Z] 2016-04-14 21:22:15 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:22:15,213 - WARNING - Could not retrieve variants from source file in region 5:74324337-74325092. Error was invalid region `5:74324338-74325092`
[2016-04-15T04:22Z] 2016-04-14 21:22:15 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:22:15,317 - WARNING - Could not retrieve variants from source file in region 5:78421748-78422149. Error was invalid region `5:78421749-78422149`
[2016-04-15T04:22Z] 2016-04-14 21:22:15 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:22:15,958 - WARNING - Could not retrieve variants from source file in region 5:80409518-80409919. Error was invalid region `5:80409519-80409919`
[2016-04-15T04:22Z] 2016-04-14 21:22:16 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:22:16,179 - WARNING - Could not retrieve variants from source file in region 5:76987441-76987842. Error was invalid region `5:76987442-76987842`
[2016-04-15T04:22Z] 2016-04-14 21:22:16 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:22:16,612 - WARNING - Could not retrieve variants from source file in region 5:74806989-74807390. Error was invalid region `5:74806990-74807390`
[2016-04-15T04:22Z] 2016-04-14 21:22:17 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:22:17,069 - WARNING - Could not retrieve variants from source file in region 5:73207161-73207562. Error was invalid region `5:73207162-73207562`
[2016-04-15T04:22Z] 2016-04-14 21:22:19 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:22:19,077 - WARNING - Could not retrieve variants from source file in region 5:71755891-71757457. Error was invalid region `5:71755892-71757457`
[2016-04-15T04:22Z] 2016-04-14 21:22:19 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:22:19,784 - WARNING - Could not retrieve variants from source file in region 5:78111463-78135391. Error was invalid region `5:78111464-78135391`
[2016-04-15T04:22Z] 2016-04-14 21:22:21 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:22:21,023 - WARNING - Could not retrieve variants from source file in region 5:79732868-79745659. Error was invalid region `5:79732869-79745659`
[2016-04-15T04:22Z] 2016-04-14 21:22:21 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:22:21,115 - WARNING - Could not retrieve variants from source file in region 5:74400305-74400706. Error was invalid region `5:74400306-74400706`
[2016-04-15T04:22Z] 2016-04-14 21:22:21 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:22:21,643 - WARNING - Could not retrieve variants from source file in region 5:74324337-74325092. Error was invalid region `5:74324338-74325092`
[2016-04-15T04:22Z] 2016-04-14 21:22:21 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:22:21,931 - WARNING - Could not retrieve variants from source file in region 5:76987441-76987842. Error was invalid region `5:76987442-76987842`
[2016-04-15T04:22Z] 2016-04-14 21:22:22 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:22:22,168 - WARNING - Could not retrieve variants from source file in region 5:74806989-74807390. Error was invalid region `5:74806990-74807390`
[2016-04-15T04:22Z] 2016-04-14 21:22:22 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:22:22,236 - WARNING - Could not retrieve variants from source file in region 5:73207161-73207562. Error was invalid region `5:73207162-73207562`
[2016-04-15T04:22Z] 2016-04-14 21:22:27 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:22:27,256 - WARNING - Could not retrieve variants from source file in region 5:74324337-74325092. Error was invalid region `5:74324338-74325092`
[2016-04-15T04:22Z] 2016-04-14 21:22:27 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:22:27,264 - WARNING - Could not retrieve variants from source file in region 5:76987441-76987842. Error was invalid region `5:76987442-76987842`
[2016-04-15T04:22Z] 2016-04-14 21:22:27 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:22:27,780 - WARNING - Could not retrieve variants from source file in region 5:80409518-80409919. Error was invalid region `5:80409519-80409919`
[2016-04-15T04:22Z] 2016-04-14 21:22:28 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:22:28,871 - WARNING - Could not retrieve variants from source file in region 5:76926367-76926768. Error was invalid region `5:76926368-76926768`
[2016-04-15T04:22Z] 2016-04-14 21:22:30 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:22:30,139 - WARNING - Could not retrieve variants from source file in region 5:79282587-79282999. Error was invalid region `5:79282588-79282999`
[2016-04-15T04:22Z] 2016-04-14 21:22:30 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:22:30,977 - WARNING - Could not retrieve variants from source file in region 5:74681562-74681963. Error was invalid region `5:74681563-74681963`
[2016-04-15T04:22Z] 2016-04-14 21:22:33 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:22:33,639 - WARNING - Could not retrieve variants from source file in region 5:76926367-76926768. Error was invalid region `5:76926368-76926768`
[2016-04-15T04:22Z] 2016-04-14 21:22:33 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:22:33,966 - WARNING - Could not retrieve variants from source file in region 5:74442199-74443322. Error was invalid region `5:74442200-74443322`
[2016-04-15T04:22Z] 2016-04-14 21:22:36 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:22:36,690 - WARNING - Could not retrieve variants from source file in region 5:70944864-70945265. Error was invalid region `5:70944865-70945265`
[2016-04-15T04:22Z] 2016-04-14 21:22:37 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:22:37,265 - WARNING - Could not retrieve variants from source file in region 5:76926367-76926768. Error was invalid region `5:76926368-76926768`
[2016-04-15T04:22Z] 2016-04-14 21:22:38 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:22:38,005 - WARNING - Could not retrieve variants from source file in region 5:77784527-77784928. Error was invalid region `5:77784528-77784928`
[2016-04-15T04:22Z] 2016-04-14 21:22:38 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:22:38,100 - WARNING - Could not retrieve variants from source file in region 5:71490751-71495231. Error was invalid region `5:71490752-71495231`
[2016-04-15T04:22Z] 2016-04-14 21:22:38 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:22:38,449 - WARNING - Could not retrieve variants from source file in region 5:68616120-68616521. Error was invalid region `5:68616121-68616521`
[2016-04-15T04:22Z] 2016-04-14 21:22:40 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:22:40,113 - WARNING - Could not retrieve variants from source file in region 5:74017288-74070053. Error was invalid region `5:74017289-74070053`
[2016-04-15T04:22Z] 2016-04-14 21:22:41 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:22:41,833 - WARNING - Could not retrieve variants from source file in region 5:80149770-80169127. Error was invalid region `5:80149771-80169127`
[2016-04-15T04:22Z] 2016-04-14 21:22:42 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:22:42,195 - WARNING - Could not retrieve variants from source file in region 5:70944864-70945265. Error was invalid region `5:70944865-70945265`
[2016-04-15T04:22Z] 2016-04-14 21:22:42 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:22:42,909 - WARNING - Could not retrieve variants from source file in region 5:77784527-77784928. Error was invalid region `5:77784528-77784928`
[2016-04-15T04:22Z] 2016-04-14 21:22:42 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:22:42,963 - WARNING - Could not retrieve variants from source file in region 5:71490751-71495231. Error was invalid region `5:71490752-71495231`
[2016-04-15T04:22Z] 2016-04-14 21:22:43 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:22:43,159 - WARNING - Could not retrieve variants from source file in region 5:68616120-68616521. Error was invalid region `5:68616121-68616521`
[2016-04-15T04:22Z] 2016-04-14 21:22:43 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:22:43,325 - WARNING - Could not retrieve variants from source file in region 5:73142085-73164155. Error was invalid region `5:73142086-73164155`
[2016-04-15T04:22Z] 2016-04-14 21:22:45 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:22:45,077 - WARNING - Could not retrieve variants from source file in region 5:74017288-74070053. Error was invalid region `5:74017289-74070053`
[2016-04-15T04:22Z] 2016-04-14 21:22:45 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:22:45,366 - WARNING - Could not retrieve variants from source file in region 5:67522511-67522912. Error was invalid region `5:67522512-67522912`
[2016-04-15T04:22Z] 2016-04-14 21:22:46 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:22:46,441 - WARNING - Could not retrieve variants from source file in region 5:80149770-80169127. Error was invalid region `5:80149771-80169127`
[2016-04-15T04:22Z] 2016-04-14 21:22:46 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:22:46,709 - WARNING - Could not retrieve variants from source file in region 5:80149770-80169127. Error was invalid region `5:80149771-80169127`
[2016-04-15T04:22Z] 2016-04-14 21:22:46 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:22:46,771 - WARNING - Could not retrieve variants from source file in region 5:70944864-70945265. Error was invalid region `5:70944865-70945265`
[2016-04-15T04:22Z] 2016-04-14 21:22:47 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:22:47,708 - WARNING - Could not retrieve variants from source file in region 5:77784527-77784928. Error was invalid region `5:77784528-77784928`
[2016-04-15T04:22Z] 2016-04-14 21:22:47 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:22:47,943 - WARNING - Could not retrieve variants from source file in region 5:71490751-71495231. Error was invalid region `5:71490752-71495231`
[2016-04-15T04:22Z] 2016-04-14 21:22:47 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:22:47,952 - WARNING - Could not retrieve variants from source file in region 5:73142085-73164155. Error was invalid region `5:73142086-73164155`
[2016-04-15T04:22Z] 2016-04-14 21:22:48 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:22:48,009 - WARNING - Could not retrieve variants from source file in region 5:68616120-68616521. Error was invalid region `5:68616121-68616521`
[2016-04-15T04:22Z] 2016-04-14 21:22:50 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:22:50,160 - WARNING - Could not retrieve variants from source file in region 5:67522511-67522912. Error was invalid region `5:67522512-67522912`
[2016-04-15T04:22Z] 2016-04-14 21:22:50 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:22:50,804 - WARNING - Could not retrieve variants from source file in region 5:70800264-70807148. Error was invalid region `5:70800265-70807148`
[2016-04-15T04:22Z] 2016-04-14 21:22:50 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:22:50,815 - WARNING - Could not retrieve variants from source file in region 5:70751607-70752008. Error was invalid region `5:70751608-70752008`
[2016-04-15T04:22Z] 2016-04-14 21:22:54 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:22:54,280 - WARNING - Could not retrieve variants from source file in region 5:70800264-70807148. Error was invalid region `5:70800265-70807148`
[2016-04-15T04:22Z] 2016-04-14 21:22:55 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:22:55,229 - WARNING - Could not retrieve variants from source file in region 5:67522511-67522912. Error was invalid region `5:67522512-67522912`
[2016-04-15T04:22Z] 2016-04-14 21:22:56 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:22:56,612 - WARNING - Could not retrieve variants from source file in region 5:70800264-70807148. Error was invalid region `5:70800265-70807148`
[2016-04-15T04:22Z] 2016-04-14 21:22:56 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:22:56,648 - WARNING - Could not retrieve variants from source file in region 5:70751607-70752008. Error was invalid region `5:70751608-70752008`
[2016-04-15T04:22Z] 2016-04-14 21:22:56 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:22:56,673 - WARNING - Could not retrieve variants from source file in region 5:65892556-65892957. Error was invalid region `5:65892557-65892957`
[2016-04-15T04:22Z] 2016-04-14 21:22:58 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:22:58,546 - WARNING - Could not retrieve variants from source file in region 5:72742671-72743489. Error was invalid region `5:72742672-72743489`
[2016-04-15T04:22Z] 2016-04-14 21:22:59 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:22:59,490 - WARNING - Could not retrieve variants from source file in region 5:70837084-70858384. Error was invalid region `5:70837085-70858384`
[2016-04-15T04:23Z] 2016-04-14 21:23:00 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:23:00,701 - WARNING - Could not retrieve variants from source file in region 5:72874696-72875097. Error was invalid region `5:72874697-72875097`
[2016-04-15T04:23Z] 2016-04-14 21:23:00 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:23:00,750 - WARNING - Could not retrieve variants from source file in region 5:70751607-70752008. Error was invalid region `5:70751608-70752008`
[2016-04-15T04:23Z] 2016-04-14 21:23:03 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:23:03,201 - WARNING - Could not retrieve variants from source file in region 5:70837084-70858384. Error was invalid region `5:70837085-70858384`
[2016-04-15T04:23Z] 2016-04-14 21:23:04 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:23:04,166 - WARNING - Could not retrieve variants from source file in region 5:72874696-72875097. Error was invalid region `5:72874697-72875097`
[2016-04-15T04:23Z] 2016-04-14 21:23:05 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:23:05,949 - WARNING - Could not retrieve variants from source file in region 5:66459667-66480194. Error was invalid region `5:66459668-66480194`
[2016-04-15T04:23Z] 2016-04-14 21:23:06 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:23:06,556 - WARNING - Could not retrieve variants from source file in region 5:70837084-70858384. Error was invalid region `5:70837085-70858384`
[2016-04-15T04:23Z] 2016-04-14 21:23:07 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:23:07,311 - WARNING - Could not retrieve variants from source file in region 5:70308040-70308441. Error was invalid region `5:70308041-70308441`
[2016-04-15T04:23Z] 2016-04-14 21:23:07 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:23:07,643 - WARNING - Could not retrieve variants from source file in region 5:66459667-66480194. Error was invalid region `5:66459668-66480194`
[2016-04-15T04:23Z] 2016-04-14 21:23:07 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:23:07,693 - WARNING - Could not retrieve variants from source file in region 5:70308040-70308441. Error was invalid region `5:70308041-70308441`
[2016-04-15T04:23Z] 2016-04-14 21:23:09 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:23:09,492 - WARNING - Could not retrieve variants from source file in region 5:66459667-66480194. Error was invalid region `5:66459668-66480194`
[2016-04-15T04:23Z] 2016-04-14 21:23:10 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:23:10,782 - WARNING - Could not retrieve variants from source file in region 5:70308040-70308441. Error was invalid region `5:70308041-70308441`
[2016-04-15T04:23Z] 2016-04-14 21:23:13 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:23:13,912 - WARNING - Could not retrieve variants from source file in region 5:65452520-65453375. Error was invalid region `5:65452521-65453375`
[2016-04-15T04:23Z] 2016-04-14 21:23:17 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:23:17,185 - WARNING - Could not retrieve variants from source file in region 5:65316970-65321556. Error was invalid region `5:65316971-65321556`
[2016-04-15T04:23Z] 2016-04-14 21:23:17 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:23:17,213 - WARNING - Could not retrieve variants from source file in region 5:72419056-72419807. Error was invalid region `5:72419057-72419807`
[2016-04-15T04:23Z] 2016-04-14 21:23:17 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:23:17,450 - WARNING - Could not retrieve variants from source file in region 5:72348061-72348462. Error was invalid region `5:72348062-72348462`
[2016-04-15T04:23Z] 2016-04-14 21:23:19 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:23:19,209 - WARNING - Could not retrieve variants from source file in region 5:72348061-72348462. Error was invalid region `5:72348062-72348462`
[2016-04-15T04:23Z] ['bcbio-variation-recall', 'square', '-Xms750m', '-Xmx7280m', '-XX:+UseSerialGC', '-c', 16, '-r', u'5:80911292-96430739', '--caller', 'platypus', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/5/Batch1-5_80911291_96430739.vcf.gz', '/mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/5/Batch1-5_80911291_96430739.vcf-inputs.txt'] in region: 5:80911292-96430739
[2016-04-15T04:23Z] 2016-04-14 21:23:32 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:23:32,000 - WARNING - Could not retrieve variants from source file in region 5:96346067-96363649. Error was invalid region `5:96346068-96363649`
[2016-04-15T04:23Z] 2016-04-14 21:23:34 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:23:34,196 - WARNING - Could not retrieve variants from source file in region 5:94938982-94939383. Error was invalid region `5:94938983-94939383`
[2016-04-15T04:23Z] 2016-04-14 21:23:34 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:23:34,714 - WARNING - Could not retrieve variants from source file in region 5:94860907-94861308. Error was invalid region `5:94860908-94861308`
[2016-04-15T04:23Z] 2016-04-14 21:23:35 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:23:35,311 - WARNING - Could not retrieve variants from source file in region 5:95010978-95011379. Error was invalid region `5:95010979-95011379`
[2016-04-15T04:23Z] 2016-04-14 21:23:35 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:23:35,391 - WARNING - Could not retrieve variants from source file in region 5:94826444-94826845. Error was invalid region `5:94826445-94826845`
[2016-04-15T04:23Z] 2016-04-14 21:23:35 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:23:35,931 - WARNING - Could not retrieve variants from source file in region 5:93201630-93202031. Error was invalid region `5:93201631-93202031`
[2016-04-15T04:23Z] 2016-04-14 21:23:36 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:23:36,260 - WARNING - Could not retrieve variants from source file in region 5:96031358-96031759. Error was invalid region `5:96031359-96031759`
[2016-04-15T04:23Z] 2016-04-14 21:23:36 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:23:36,566 - WARNING - Could not retrieve variants from source file in region 5:95152102-95152503. Error was invalid region `5:95152103-95152503`
[2016-04-15T04:23Z] 2016-04-14 21:23:36 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:23:36,567 - WARNING - Could not retrieve variants from source file in region 5:95728687-95751975. Error was invalid region `5:95728688-95751975`
[2016-04-15T04:23Z] 2016-04-14 21:23:36 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:23:36,584 - WARNING - Could not retrieve variants from source file in region 5:94277918-94278319. Error was invalid region `5:94277919-94278319`
[2016-04-15T04:23Z] 2016-04-14 21:23:36 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:23:36,933 - WARNING - Could not retrieve variants from source file in region 5:95083920-95116149. Error was invalid region `5:95083921-95116149`
[2016-04-15T04:23Z] 2016-04-14 21:23:41 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:23:41,330 - WARNING - Could not retrieve variants from source file in region 5:89703430-89703831. Error was invalid region `5:89703431-89703831`
[2016-04-15T04:23Z] 2016-04-14 21:23:43 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:23:43,329 - WARNING - Could not retrieve variants from source file in region 5:96215469-96249305. Error was invalid region `5:96215470-96249305`
[2016-04-15T04:23Z] 2016-04-14 21:23:44 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:23:44,089 - WARNING - Could not retrieve variants from source file in region 5:93201630-93202031. Error was invalid region `5:93201631-93202031`
[2016-04-15T04:23Z] 2016-04-14 21:23:44 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:23:44,181 - WARNING - Could not retrieve variants from source file in region 5:95152102-95152503. Error was invalid region `5:95152103-95152503`
[2016-04-15T04:23Z] 2016-04-14 21:23:45 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:23:45,250 - WARNING - Could not retrieve variants from source file in region 5:95234139-95236649. Error was invalid region `5:95234140-95236649`
[2016-04-15T04:23Z] 2016-04-14 21:23:47 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:23:47,080 - WARNING - Could not retrieve variants from source file in region 5:95010978-95011379. Error was invalid region `5:95010979-95011379`
[2016-04-15T04:23Z] 2016-04-14 21:23:49 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:23:49,457 - WARNING - Could not retrieve variants from source file in region 5:96031358-96031759. Error was invalid region `5:96031359-96031759`
[2016-04-15T04:23Z] 2016-04-14 21:23:50 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:23:50,492 - WARNING - Could not retrieve variants from source file in region 5:93201630-93202031. Error was invalid region `5:93201631-93202031`
[2016-04-15T04:23Z] 2016-04-14 21:23:51 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:23:51,400 - WARNING - Could not retrieve variants from source file in region 5:95152102-95152503. Error was invalid region `5:95152103-95152503`
[2016-04-15T04:23Z] 2016-04-14 21:23:53 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:23:53,357 - WARNING - Could not retrieve variants from source file in region 5:95234139-95236649. Error was invalid region `5:95234140-95236649`
[2016-04-15T04:24Z] 2016-04-14 21:24:01 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:24:01,930 - WARNING - Could not retrieve variants from source file in region 5:88119868-88120269. Error was invalid region `5:88119869-88120269`
[2016-04-15T04:24Z] 2016-04-14 21:24:02 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:24:02,570 - WARNING - Could not retrieve variants from source file in region 5:93987321-93987722. Error was invalid region `5:93987322-93987722`
[2016-04-15T04:24Z] 2016-04-14 21:24:03 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:24:03,545 - WARNING - Could not retrieve variants from source file in region 5:90079609-90080010. Error was invalid region `5:90079610-90080010`
[2016-04-15T04:24Z] 2016-04-14 21:24:04 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:24:04,096 - WARNING - Could not retrieve variants from source file in region 5:86564784-86565185. Error was invalid region `5:86564785-86565185`
[2016-04-15T04:24Z] 2016-04-14 21:24:04 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:24:04,302 - WARNING - Could not retrieve variants from source file in region 5:82875589-82875990. Error was invalid region `5:82875590-82875990`
[2016-04-15T04:24Z] 2016-04-14 21:24:04 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:24:04,565 - WARNING - Could not retrieve variants from source file in region 5:93855426-93855827. Error was invalid region `5:93855427-93855827`
[2016-04-15T04:24Z] 2016-04-14 21:24:04 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:24:04,569 - WARNING - Could not retrieve variants from source file in region 5:93140657-93160161. Error was invalid region `5:93140658-93160161`
[2016-04-15T04:24Z] 2016-04-14 21:24:07 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:24:07,157 - WARNING - Could not retrieve variants from source file in region 5:93987321-93987722. Error was invalid region `5:93987322-93987722`
[2016-04-15T04:24Z] 2016-04-14 21:24:08 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:24:08,411 - WARNING - Could not retrieve variants from source file in region 5:81549005-81549430. Error was invalid region `5:81549006-81549430`
[2016-04-15T04:24Z] 2016-04-14 21:24:08 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:24:08,808 - WARNING - Could not retrieve variants from source file in region 5:90079609-90080010. Error was invalid region `5:90079610-90080010`
[2016-04-15T04:24Z] 2016-04-14 21:24:09 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:24:09,815 - WARNING - Could not retrieve variants from source file in region 5:82875589-82875990. Error was invalid region `5:82875590-82875990`
[2016-04-15T04:24Z] 2016-04-14 21:24:09 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:24:09,910 - WARNING - Could not retrieve variants from source file in region 5:86564784-86565185. Error was invalid region `5:86564785-86565185`
[2016-04-15T04:24Z] 2016-04-14 21:24:09 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:24:09,997 - WARNING - Could not retrieve variants from source file in region 5:93855426-93855827. Error was invalid region `5:93855427-93855827`
[2016-04-15T04:24Z] 2016-04-14 21:24:10 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:24:10,001 - WARNING - Could not retrieve variants from source file in region 5:93140657-93160161. Error was invalid region `5:93140658-93160161`
[2016-04-15T04:24Z] 2016-04-14 21:24:11 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:24:11,549 - WARNING - Could not retrieve variants from source file in region 5:94230147-94230548. Error was invalid region `5:94230148-94230548`
[2016-04-15T04:24Z] 2016-04-14 21:24:11 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:24:11,806 - WARNING - Could not retrieve variants from source file in region 5:88119868-88120269. Error was invalid region `5:88119869-88120269`
[2016-04-15T04:24Z] 2016-04-14 21:24:11 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:24:11,960 - WARNING - Could not retrieve variants from source file in region 5:82940062-82940463. Error was invalid region `5:82940063-82940463`
[2016-04-15T04:24Z] 2016-04-14 21:24:12 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:24:12,193 - WARNING - Could not retrieve variants from source file in region 5:93987321-93987722. Error was invalid region `5:93987322-93987722`
[2016-04-15T04:24Z] 2016-04-14 21:24:13 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:24:13,711 - WARNING - Could not retrieve variants from source file in region 5:89797898-89821174. Error was invalid region `5:89797899-89821174`
[2016-04-15T04:24Z] 2016-04-14 21:24:13 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:24:13,836 - WARNING - Could not retrieve variants from source file in region 5:81549005-81549430. Error was invalid region `5:81549006-81549430`
[2016-04-15T04:24Z] 2016-04-14 21:24:14 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:24:14,761 - WARNING - Could not retrieve variants from source file in region 5:90079609-90080010. Error was invalid region `5:90079610-90080010`
[2016-04-15T04:24Z] 2016-04-14 21:24:15 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:24:15,001 - WARNING - Could not retrieve variants from source file in region 5:93855426-93855827. Error was invalid region `5:93855427-93855827`
[2016-04-15T04:24Z] 2016-04-14 21:24:15 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:24:15,315 - WARNING - Could not retrieve variants from source file in region 5:82875589-82875990. Error was invalid region `5:82875590-82875990`
[2016-04-15T04:24Z] 2016-04-14 21:24:15 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:24:15,345 - WARNING - Could not retrieve variants from source file in region 5:86564784-86565185. Error was invalid region `5:86564785-86565185`
[2016-04-15T04:24Z] 2016-04-14 21:24:17 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:24:17,392 - WARNING - Could not retrieve variants from source file in region 5:82940062-82940463. Error was invalid region `5:82940063-82940463`
[2016-04-15T04:24Z] 2016-04-14 21:24:19 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:24:19,370 - WARNING - Could not retrieve variants from source file in region 5:81549005-81549430. Error was invalid region `5:81549006-81549430`
[2016-04-15T04:24Z] 2016-04-14 21:24:25 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:24:25,579 - WARNING - Could not retrieve variants from source file in region 5:87491334-87499039. Error was invalid region `5:87491335-87499039`
[2016-04-15T04:24Z] 2016-04-14 21:24:25 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:24:25,806 - WARNING - Could not retrieve variants from source file in region 5:93731774-93732175. Error was invalid region `5:93731775-93732175`
[2016-04-15T04:24Z] 2016-04-14 21:24:26 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:24:26,000 - WARNING - Could not retrieve variants from source file in region 5:93731774-93732175. Error was invalid region `5:93731775-93732175`
[2016-04-15T04:24Z] 2016-04-14 21:24:28 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:24:28,013 - WARNING - Could not retrieve variants from source file in region 5:87491334-87499039. Error was invalid region `5:87491335-87499039`
[2016-04-15T04:24Z] 2016-04-14 21:24:28 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:24:28,037 - WARNING - Could not retrieve variants from source file in region 5:87491334-87499039. Error was invalid region `5:87491335-87499039`
[2016-04-15T04:24Z] 2016-04-14 21:24:28 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:24:28,040 - WARNING - Could not retrieve variants from source file in region 5:93731774-93732175. Error was invalid region `5:93731775-93732175`
[2016-04-15T04:24Z] 2016-04-14 21:24:28 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:24:28,334 - WARNING - Could not retrieve variants from source file in region 5:90052078-90052562. Error was invalid region `5:90052079-90052562`
[2016-04-15T04:24Z] 2016-04-14 21:24:28 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:24:28,827 - WARNING - Could not retrieve variants from source file in region 5:90151378-90151779. Error was invalid region `5:90151379-90151779`
[2016-04-15T04:24Z] 2016-04-14 21:24:30 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:24:30,527 - WARNING - Could not retrieve variants from source file in region 5:89769517-89770189. Error was invalid region `5:89769518-89770189`
[2016-04-15T04:24Z] 2016-04-14 21:24:30 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:24:30,909 - WARNING - Could not retrieve variants from source file in region 5:86695063-86695464. Error was invalid region `5:86695064-86695464`
[2016-04-15T04:24Z] 2016-04-14 21:24:31 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:24:31,104 - WARNING - Could not retrieve variants from source file in region 5:90106897-90119514. Error was invalid region `5:90106898-90119514`
[2016-04-15T04:24Z] 2016-04-14 21:24:31 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:24:31,637 - WARNING - Could not retrieve variants from source file in region 5:90106897-90119514. Error was invalid region `5:90106898-90119514`
[2016-04-15T04:24Z] 2016-04-14 21:24:31 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:24:31,910 - WARNING - Could not retrieve variants from source file in region 5:86695063-86695464. Error was invalid region `5:86695064-86695464`
[2016-04-15T04:24Z] 2016-04-14 21:24:31 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:24:31,967 - WARNING - Could not retrieve variants from source file in region 5:90052078-90052562. Error was invalid region `5:90052079-90052562`
[2016-04-15T04:24Z] 2016-04-14 21:24:32 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:24:32,359 - WARNING - Could not retrieve variants from source file in region 5:90151378-90151779. Error was invalid region `5:90151379-90151779`
[2016-04-15T04:24Z] 2016-04-14 21:24:34 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:24:34,700 - WARNING - Could not retrieve variants from source file in region 5:90106897-90119514. Error was invalid region `5:90106898-90119514`
[2016-04-15T04:24Z] 2016-04-14 21:24:35 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:24:35,324 - WARNING - Could not retrieve variants from source file in region 5:90151378-90151779. Error was invalid region `5:90151379-90151779`
[2016-04-15T04:24Z] ['bcbio-variation-recall', 'square', '-Xms750m', '-Xmx7280m', '-XX:+UseSerialGC', '-c', 16, '-r', u'5:96432514-112043579', '--caller', 'platypus', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/5/Batch1-5_96432513_112043579.vcf.gz', '/mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/5/Batch1-5_96432513_112043579.vcf-inputs.txt'] in region: 5:96432514-112043579
[2016-04-15T04:24Z] 2016-04-14 21:24:49 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:24:49,285 - WARNING - Could not retrieve variants from source file in region 5:111610865-111611266. Error was invalid region `5:111610866-111611266`
[2016-04-15T04:24Z] 2016-04-14 21:24:50 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:24:50,803 - WARNING - Could not retrieve variants from source file in region 5:102512359-102520590. Error was invalid region `5:102512360-102520590`
[2016-04-15T04:24Z] 2016-04-14 21:24:52 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:24:52,205 - WARNING - Could not retrieve variants from source file in region 5:102433198-102433599. Error was invalid region `5:102433199-102433599`
[2016-04-15T04:24Z] 2016-04-14 21:24:52 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:24:52,359 - WARNING - Could not retrieve variants from source file in region 5:101631579-101631980. Error was invalid region `5:101631580-101631980`
[2016-04-15T04:24Z] 2016-04-14 21:24:53 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:24:53,614 - WARNING - Could not retrieve variants from source file in region 5:109960778-109974092. Error was invalid region `5:109960779-109974092`
[2016-04-15T04:24Z] 2016-04-14 21:24:53 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:24:53,843 - WARNING - Could not retrieve variants from source file in region 5:102345335-102345736. Error was invalid region `5:102345336-102345736`
[2016-04-15T04:24Z] 2016-04-14 21:24:56 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:24:56,373 - WARNING - Could not retrieve variants from source file in region 5:110819542-110836475. Error was invalid region `5:110819543-110836475`
[2016-04-15T04:24Z] 2016-04-14 21:24:59 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:24:59,557 - WARNING - Could not retrieve variants from source file in region 5:101774244-101774645. Error was invalid region `5:101774245-101774645`
[2016-04-15T04:24Z] 2016-04-14 21:24:59 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:24:59,620 - WARNING - Could not retrieve variants from source file in region 5:100220978-100221444. Error was invalid region `5:100220979-100221444`
[2016-04-15T04:25Z] 2016-04-14 21:25:00 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:25:00,849 - WARNING - Could not retrieve variants from source file in region 5:98191953-98199394. Error was invalid region `5:98191954-98199394`
[2016-04-15T04:25Z] 2016-04-14 21:25:01 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:25:01,157 - WARNING - Could not retrieve variants from source file in region 5:101631579-101631980. Error was invalid region `5:101631580-101631980`
[2016-04-15T04:25Z] 2016-04-14 21:25:01 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:25:01,201 - WARNING - Could not retrieve variants from source file in region 5:102891484-102895314. Error was invalid region `5:102891485-102895314`
[2016-04-15T04:25Z] 2016-04-14 21:25:01 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:25:01,832 - WARNING - Could not retrieve variants from source file in region 5:107197291-107215820. Error was invalid region `5:107197292-107215820`
[2016-04-15T04:25Z] 2016-04-14 21:25:02 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:25:02,196 - WARNING - Could not retrieve variants from source file in region 5:101724237-101748931. Error was invalid region `5:101724238-101748931`
[2016-04-15T04:25Z] 2016-04-14 21:25:02 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:25:02,256 - WARNING - Could not retrieve variants from source file in region 5:111610865-111611266. Error was invalid region `5:111610866-111611266`
[2016-04-15T04:25Z] 2016-04-14 21:25:06 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:25:06,870 - WARNING - Could not retrieve variants from source file in region 5:98191953-98199394. Error was invalid region `5:98191954-98199394`
[2016-04-15T04:25Z] 2016-04-14 21:25:07 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:25:07,635 - WARNING - Could not retrieve variants from source file in region 5:102891484-102895314. Error was invalid region `5:102891485-102895314`
[2016-04-15T04:25Z] 2016-04-14 21:25:08 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:25:08,026 - WARNING - Could not retrieve variants from source file in region 5:101631579-101631980. Error was invalid region `5:101631580-101631980`
[2016-04-15T04:25Z] 2016-04-14 21:25:09 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:25:09,613 - WARNING - Could not retrieve variants from source file in region 5:109110326-109117361. Error was invalid region `5:109110327-109117361`
[2016-04-15T04:25Z] 2016-04-14 21:25:19 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:25:19,359 - WARNING - Could not retrieve variants from source file in region 5:110408856-110409257. Error was invalid region `5:110408857-110409257`
[2016-04-15T04:25Z] 2016-04-14 21:25:19 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:25:19,726 - WARNING - Could not retrieve variants from source file in region 5:110408856-110409257. Error was invalid region `5:110408857-110409257`
[2016-04-15T04:25Z] 2016-04-14 21:25:20 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:25:20,165 - WARNING - Could not retrieve variants from source file in region 5:111504268-111545860. Error was invalid region `5:111504269-111545860`
[2016-04-15T04:25Z] 2016-04-14 21:25:20 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:25:20,278 - WARNING - Could not retrieve variants from source file in region 5:109181471-109191128. Error was invalid region `5:109181472-109191128`
[2016-04-15T04:25Z] 2016-04-14 21:25:20 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:25:20,469 - WARNING - Could not retrieve variants from source file in region 5:96498572-96513661. Error was invalid region `5:96498573-96513661`
[2016-04-15T04:25Z] 2016-04-14 21:25:20 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:25:20,655 - WARNING - Could not retrieve variants from source file in region 5:101574880-101575281. Error was invalid region `5:101574881-101575281`
[2016-04-15T04:25Z] 2016-04-14 21:25:20 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:25:20,696 - WARNING - Could not retrieve variants from source file in region 5:101574880-101575281. Error was invalid region `5:101574881-101575281`
[2016-04-15T04:25Z] 2016-04-14 21:25:21 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:25:21,113 - WARNING - Could not retrieve variants from source file in region 5:108713759-108714488. Error was invalid region `5:108713760-108714488`
[2016-04-15T04:25Z] 2016-04-14 21:25:23 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:25:23,159 - WARNING - Could not retrieve variants from source file in region 5:107633971-107635184. Error was invalid region `5:107633972-107635184`
[2016-04-15T04:25Z] 2016-04-14 21:25:23 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:25:23,449 - WARNING - Could not retrieve variants from source file in region 5:110408856-110409257. Error was invalid region `5:110408857-110409257`
[2016-04-15T04:25Z] 2016-04-14 21:25:23 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:25:23,727 - WARNING - Could not retrieve variants from source file in region 5:109181471-109191128. Error was invalid region `5:109181472-109191128`
[2016-04-15T04:25Z] 2016-04-14 21:25:24 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:25:24,313 - WARNING - Could not retrieve variants from source file in region 5:96498572-96513661. Error was invalid region `5:96498573-96513661`
[2016-04-15T04:25Z] 2016-04-14 21:25:24 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:25:24,320 - WARNING - Could not retrieve variants from source file in region 5:101574880-101575281. Error was invalid region `5:101574881-101575281`
[2016-04-15T04:25Z] 2016-04-14 21:25:24 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:25:24,356 - WARNING - Could not retrieve variants from source file in region 5:111504268-111545860. Error was invalid region `5:111504269-111545860`
[2016-04-15T04:25Z] 2016-04-14 21:25:24 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:25:24,614 - WARNING - Could not retrieve variants from source file in region 5:108713759-108714488. Error was invalid region `5:108713760-108714488`
[2016-04-15T04:25Z] 2016-04-14 21:25:26 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:25:26,655 - WARNING - Could not retrieve variants from source file in region 5:108713759-108714488. Error was invalid region `5:108713760-108714488`
[2016-04-15T04:25Z] 2016-04-14 21:25:27 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:25:27,597 - WARNING - Could not retrieve variants from source file in region 5:96498572-96513661. Error was invalid region `5:96498573-96513661`
[2016-04-15T04:25Z] 2016-04-14 21:25:27 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:25:27,684 - WARNING - Could not retrieve variants from source file in region 5:111504268-111545860. Error was invalid region `5:111504269-111545860`
[2016-04-15T04:25Z] 2016-04-14 21:25:32 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:25:32,221 - WARNING - Could not retrieve variants from source file in region 5:111092715-111093134. Error was invalid region `5:111092716-111093134`
[2016-04-15T04:25Z] ['bcbio-variation-recall', 'square', '-Xms750m', '-Xmx7280m', '-XX:+UseSerialGC', '-c', 16, '-r', u'5:112073556-127595521', '--caller', 'platypus', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/5/Batch1-5_112073555_127595521.vcf.gz', '/mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/5/Batch1-5_112073555_127595521.vcf-inputs.txt'] in region: 5:112073556-127595521
[2016-04-15T04:25Z] 2016-04-14 21:25:46 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:25:46,013 - WARNING - Could not retrieve variants from source file in region 5:126993038-126993453. Error was invalid region `5:126993039-126993453`
[2016-04-15T04:25Z] 2016-04-14 21:25:47 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:25:47,257 - WARNING - Could not retrieve variants from source file in region 5:122757956-122758357. Error was invalid region `5:122757957-122758357`
[2016-04-15T04:25Z] 2016-04-14 21:25:47 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:25:47,682 - WARNING - Could not retrieve variants from source file in region 5:122718525-122727216. Error was invalid region `5:122718526-122727216`
[2016-04-15T04:25Z] 2016-04-14 21:25:48 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:25:48,604 - WARNING - Could not retrieve variants from source file in region 5:114462144-114462545. Error was invalid region `5:114462145-114462545`
[2016-04-15T04:25Z] 2016-04-14 21:25:48 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:25:48,651 - WARNING - Could not retrieve variants from source file in region 5:112439730-112440131. Error was invalid region `5:112439731-112440131`
[2016-04-15T04:25Z] 2016-04-14 21:25:49 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:25:49,168 - WARNING - Could not retrieve variants from source file in region 5:115469562-115469963. Error was invalid region `5:115469563-115469963`
[2016-04-15T04:25Z] 2016-04-14 21:25:49 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:25:49,173 - WARNING - Could not retrieve variants from source file in region 5:118728742-118729143. Error was invalid region `5:118728743-118729143`
[2016-04-15T04:25Z] 2016-04-14 21:25:49 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:25:49,698 - WARNING - Could not retrieve variants from source file in region 5:112823787-112824238. Error was invalid region `5:112823788-112824238`
[2016-04-15T04:25Z] 2016-04-14 21:25:49 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:25:49,842 - WARNING - Could not retrieve variants from source file in region 5:113828910-113829311. Error was invalid region `5:113828911-113829311`
[2016-04-15T04:25Z] 2016-04-14 21:25:49 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:25:49,847 - WARNING - Could not retrieve variants from source file in region 5:118969749-118970150. Error was invalid region `5:118969750-118970150`
[2016-04-15T04:25Z] 2016-04-14 21:25:49 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:25:49,956 - WARNING - Could not retrieve variants from source file in region 5:121488295-121488696. Error was invalid region `5:121488296-121488696`
[2016-04-15T04:25Z] 2016-04-14 21:25:51 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:25:51,280 - WARNING - Could not retrieve variants from source file in region 5:126993038-126993453. Error was invalid region `5:126993039-126993453`
[2016-04-15T04:25Z] 2016-04-14 21:25:52 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:25:52,526 - WARNING - Could not retrieve variants from source file in region 5:123984552-123984953. Error was invalid region `5:123984553-123984953`
[2016-04-15T04:25Z] 2016-04-14 21:25:54 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:25:54,068 - WARNING - Could not retrieve variants from source file in region 5:122718525-122727216. Error was invalid region `5:122718526-122727216`
[2016-04-15T04:25Z] 2016-04-14 21:25:54 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:25:54,893 - WARNING - Could not retrieve variants from source file in region 5:125887504-125887905. Error was invalid region `5:125887505-125887905`
[2016-04-15T04:25Z] 2016-04-14 21:25:55 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:25:55,880 - WARNING - Could not retrieve variants from source file in region 5:112439730-112440131. Error was invalid region `5:112439731-112440131`
[2016-04-15T04:25Z] 2016-04-14 21:25:56 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:25:56,517 - WARNING - Could not retrieve variants from source file in region 5:118574351-118574752. Error was invalid region `5:118574352-118574752`
[2016-04-15T04:25Z] 2016-04-14 21:25:56 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:25:56,605 - WARNING - Could not retrieve variants from source file in region 5:114462144-114462545. Error was invalid region `5:114462145-114462545`
[2016-04-15T04:25Z] 2016-04-14 21:25:57 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:25:57,425 - WARNING - Could not retrieve variants from source file in region 5:118728742-118729143. Error was invalid region `5:118728743-118729143`
[2016-04-15T04:25Z] 2016-04-14 21:25:57 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:25:57,846 - WARNING - Could not retrieve variants from source file in region 5:113828910-113829311. Error was invalid region `5:113828911-113829311`
[2016-04-15T04:25Z] 2016-04-14 21:25:58 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:25:58,071 - WARNING - Could not retrieve variants from source file in region 5:115469562-115469963. Error was invalid region `5:115469563-115469963`
[2016-04-15T04:25Z] 2016-04-14 21:25:58 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:25:58,674 - WARNING - Could not retrieve variants from source file in region 5:123984552-123984953. Error was invalid region `5:123984553-123984953`
[2016-04-15T04:25Z] 2016-04-14 21:25:58 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:25:58,701 - WARNING - Could not retrieve variants from source file in region 5:126993038-126993453. Error was invalid region `5:126993039-126993453`
[2016-04-15T04:25Z] 2016-04-14 21:25:58 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:25:58,746 - WARNING - Could not retrieve variants from source file in region 5:122757956-122758357. Error was invalid region `5:122757957-122758357`
[2016-04-15T04:25Z] 2016-04-14 21:25:58 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:25:58,922 - WARNING - Could not retrieve variants from source file in region 5:122718525-122727216. Error was invalid region `5:122718526-122727216`
[2016-04-15T04:26Z] 2016-04-14 21:26:00 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:26:00,969 - WARNING - Could not retrieve variants from source file in region 5:112439730-112440131. Error was invalid region `5:112439731-112440131`
[2016-04-15T04:26Z] 2016-04-14 21:26:02 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:26:02,437 - WARNING - Could not retrieve variants from source file in region 5:114462144-114462545. Error was invalid region `5:114462145-114462545`
[2016-04-15T04:26Z] 2016-04-14 21:26:04 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:26:04,180 - WARNING - Could not retrieve variants from source file in region 5:112868482-112929203. Error was invalid region `5:112868483-112929203`
[2016-04-15T04:26Z] 2016-04-14 21:26:05 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:26:05,043 - WARNING - Could not retrieve variants from source file in region 5:118728742-118729143. Error was invalid region `5:118728743-118729143`
[2016-04-15T04:26Z] 2016-04-14 21:26:06 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:26:06,157 - WARNING - Could not retrieve variants from source file in region 5:113828910-113829311. Error was invalid region `5:113828911-113829311`
[2016-04-15T04:26Z] 2016-04-14 21:26:06 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:26:06,159 - WARNING - Could not retrieve variants from source file in region 5:115469562-115469963. Error was invalid region `5:115469563-115469963`
[2016-04-15T04:26Z] 2016-04-14 21:26:06 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:26:06,264 - WARNING - Could not retrieve variants from source file in region 5:118969749-118970150. Error was invalid region `5:118969750-118970150`
[2016-04-15T04:26Z] 2016-04-14 21:26:19 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:26:19,409 - WARNING - Could not retrieve variants from source file in region 5:112379078-112407052. Error was invalid region `5:112379079-112407052`
[2016-04-15T04:26Z] 2016-04-14 21:26:19 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:26:19,908 - WARNING - Could not retrieve variants from source file in region 5:125695929-125696330. Error was invalid region `5:125695930-125696330`
[2016-04-15T04:26Z] 2016-04-14 21:26:20 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:26:20,584 - WARNING - Could not retrieve variants from source file in region 5:113698333-113698821. Error was invalid region `5:113698334-113698821`
[2016-04-15T04:26Z] 2016-04-14 21:26:20 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:26:20,979 - WARNING - Could not retrieve variants from source file in region 5:112478793-112479194. Error was invalid region `5:112478794-112479194`
[2016-04-15T04:26Z] 2016-04-14 21:26:23 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:26:23,225 - WARNING - Could not retrieve variants from source file in region 5:115428123-115428571. Error was invalid region `5:115428124-115428571`
[2016-04-15T04:26Z] 2016-04-14 21:26:23 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:26:23,257 - WARNING - Could not retrieve variants from source file in region 5:122682137-122685917. Error was invalid region `5:122682138-122685917`
[2016-04-15T04:26Z] 2016-04-14 21:26:24 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:26:24,801 - WARNING - Could not retrieve variants from source file in region 5:115336651-115341828. Error was invalid region `5:115336652-115341828`
[2016-04-15T04:26Z] 2016-04-14 21:26:25 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:26:25,210 - WARNING - Could not retrieve variants from source file in region 5:121412679-121413398. Error was invalid region `5:121412680-121413398`
[2016-04-15T04:26Z] 2016-04-14 21:26:25 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:26:25,269 - WARNING - Could not retrieve variants from source file in region 5:126887358-126889560. Error was invalid region `5:126887359-126889560`
[2016-04-15T04:26Z] 2016-04-14 21:26:25 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:26:25,643 - WARNING - Could not retrieve variants from source file in region 5:125695929-125696330. Error was invalid region `5:125695930-125696330`
[2016-04-15T04:26Z] 2016-04-14 21:26:25 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:26:25,836 - WARNING - Could not retrieve variants from source file in region 5:112478793-112479194. Error was invalid region `5:112478794-112479194`
[2016-04-15T04:26Z] 2016-04-14 21:26:26 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:26:26,064 - WARNING - Could not retrieve variants from source file in region 5:113698333-113698821. Error was invalid region `5:113698334-113698821`
[2016-04-15T04:26Z] 2016-04-14 21:26:26 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:26:26,285 - WARNING - Could not retrieve variants from source file in region 5:118484593-118484994. Error was invalid region `5:118484594-118484994`
[2016-04-15T04:26Z] 2016-04-14 21:26:29 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:26:29,481 - WARNING - Could not retrieve variants from source file in region 5:115336651-115341828. Error was invalid region `5:115336652-115341828`
[2016-04-15T04:26Z] 2016-04-14 21:26:30 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:26:30,283 - WARNING - Could not retrieve variants from source file in region 5:118860727-118861903. Error was invalid region `5:118860728-118861903`
[2016-04-15T04:26Z] 2016-04-14 21:26:30 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:26:30,685 - WARNING - Could not retrieve variants from source file in region 5:125695929-125696330. Error was invalid region `5:125695930-125696330`
[2016-04-15T04:26Z] 2016-04-14 21:26:31 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:26:31,317 - WARNING - Could not retrieve variants from source file in region 5:112478793-112479194. Error was invalid region `5:112478794-112479194`
[2016-04-15T04:26Z] 2016-04-14 21:26:32 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:26:32,444 - WARNING - Could not retrieve variants from source file in region 5:115428123-115428571. Error was invalid region `5:115428124-115428571`
[2016-04-15T04:26Z] 2016-04-14 21:26:34 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:26:34,026 - WARNING - Could not retrieve variants from source file in region 5:115336651-115341828. Error was invalid region `5:115336652-115341828`
[2016-04-15T04:26Z] 2016-04-14 21:26:35 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:26:35,594 - WARNING - Could not retrieve variants from source file in region 5:118860727-118861903. Error was invalid region `5:118860728-118861903`
[2016-04-15T04:26Z] 2016-04-14 21:26:39 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:26:39,915 - WARNING - Could not retrieve variants from source file in region 5:115298167-115298708. Error was invalid region `5:115298168-115298708`
[2016-04-15T04:26Z] 2016-04-14 21:26:40 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:26:40,479 - WARNING - Could not retrieve variants from source file in region 5:115394415-115394816. Error was invalid region `5:115394416-115394816`
[2016-04-15T04:26Z] 2016-04-14 21:26:41 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:26:41,321 - WARNING - Could not retrieve variants from source file in region 5:115394415-115394816. Error was invalid region `5:115394416-115394816`
[2016-04-15T04:26Z] 2016-04-14 21:26:41 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:26:41,672 - WARNING - Could not retrieve variants from source file in region 5:115298167-115298708. Error was invalid region `5:115298168-115298708`
[2016-04-15T04:26Z] 2016-04-14 21:26:41 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:26:41,993 - WARNING - Could not retrieve variants from source file in region 5:112312465-112349260. Error was invalid region `5:112312466-112349260`
[2016-04-15T04:26Z] 2016-04-14 21:26:44 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:26:44,893 - WARNING - Could not retrieve variants from source file in region 5:115813515-115813916. Error was invalid region `5:115813516-115813916`
[2016-04-15T04:26Z] 2016-04-14 21:26:45 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:26:45,131 - WARNING - Could not retrieve variants from source file in region 5:115298167-115298708. Error was invalid region `5:115298168-115298708`
[2016-04-15T04:26Z] 2016-04-14 21:26:45 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:26:45,261 - WARNING - Could not retrieve variants from source file in region 5:112257697-112258098. Error was invalid region `5:112257698-112258098`
[2016-04-15T04:26Z] 2016-04-14 21:26:45 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:26:45,322 - WARNING - Could not retrieve variants from source file in region 5:115394415-115394816. Error was invalid region `5:115394416-115394816`
[2016-04-15T04:26Z] 2016-04-14 21:26:45 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:26:45,653 - WARNING - Could not retrieve variants from source file in region 5:122425621-122435817. Error was invalid region `5:122425622-122435817`
[2016-04-15T04:26Z] 2016-04-14 21:26:45 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:26:45,846 - WARNING - Could not retrieve variants from source file in region 5:120021608-120022009. Error was invalid region `5:120021609-120022009`
[2016-04-15T04:26Z] 2016-04-14 21:26:46 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:26:46,495 - WARNING - Could not retrieve variants from source file in region 5:112312465-112349260. Error was invalid region `5:112312466-112349260`
[2016-04-15T04:26Z] 2016-04-14 21:26:48 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:26:48,505 - WARNING - Could not retrieve variants from source file in region 5:118788258-118811723. Error was invalid region `5:118788259-118811723`
[2016-04-15T04:26Z] 2016-04-14 21:26:48 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:26:48,622 - WARNING - Could not retrieve variants from source file in region 5:115813515-115813916. Error was invalid region `5:115813516-115813916`
[2016-04-15T04:26Z] 2016-04-14 21:26:48 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:26:48,855 - WARNING - Could not retrieve variants from source file in region 5:115813515-115813916. Error was invalid region `5:115813516-115813916`
[2016-04-15T04:26Z] 2016-04-14 21:26:49 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:26:49,404 - WARNING - Could not retrieve variants from source file in region 5:112257697-112258098. Error was invalid region `5:112257698-112258098`
[2016-04-15T04:26Z] 2016-04-14 21:26:49 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:26:49,758 - WARNING - Could not retrieve variants from source file in region 5:120021608-120022009. Error was invalid region `5:120021609-120022009`
[2016-04-15T04:26Z] 2016-04-14 21:26:50 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:26:50,463 - WARNING - Could not retrieve variants from source file in region 5:112312465-112349260. Error was invalid region `5:112312466-112349260`
[2016-04-15T04:26Z] 2016-04-14 21:26:53 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:26:53,621 - WARNING - Could not retrieve variants from source file in region 5:112257697-112258098. Error was invalid region `5:112257698-112258098`
[2016-04-15T04:26Z] 2016-04-14 21:26:54 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:26:54,008 - WARNING - Could not retrieve variants from source file in region 5:120021608-120022009. Error was invalid region `5:120021609-120022009`
[2016-04-15T04:26Z] 2016-04-14 21:26:56 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:26:56,506 - WARNING - Could not retrieve variants from source file in region 5:112203085-112203487. Error was invalid region `5:112203086-112203487`
[2016-04-15T04:26Z] 2016-04-14 21:26:56 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:26:56,856 - WARNING - Could not retrieve variants from source file in region 5:126113331-126113732. Error was invalid region `5:126113332-126113732`
[2016-04-15T04:26Z] 2016-04-14 21:26:59 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:26:59,919 - WARNING - Could not retrieve variants from source file in region 5:125939198-125939599. Error was invalid region `5:125939199-125939599`
[2016-04-15T04:27Z] 2016-04-14 21:27:00 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:27:00,897 - WARNING - Could not retrieve variants from source file in region 5:126113331-126113732. Error was invalid region `5:126113332-126113732`
[2016-04-15T04:27Z] 2016-04-14 21:27:01 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:27:01,330 - WARNING - Could not retrieve variants from source file in region 5:122343659-122359830. Error was invalid region `5:122343660-122359830`
[2016-04-15T04:27Z] 2016-04-14 21:27:01 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:27:01,383 - WARNING - Could not retrieve variants from source file in region 5:122343659-122359830. Error was invalid region `5:122343660-122359830`
[2016-04-15T04:27Z] 2016-04-14 21:27:03 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:27:03,630 - WARNING - Could not retrieve variants from source file in region 5:122110961-122111400. Error was invalid region `5:122110962-122111400`
[2016-04-15T04:27Z] 2016-04-14 21:27:03 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:27:03,641 - WARNING - Could not retrieve variants from source file in region 5:121518098-121518499. Error was invalid region `5:121518099-121518499`
[2016-04-15T04:27Z] 2016-04-14 21:27:04 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:27:04,487 - WARNING - Could not retrieve variants from source file in region 5:121518098-121518499. Error was invalid region `5:121518099-121518499`
[2016-04-15T04:27Z] 2016-04-14 21:27:04 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:27:04,500 - WARNING - Could not retrieve variants from source file in region 5:125939198-125939599. Error was invalid region `5:125939199-125939599`
[2016-04-15T04:27Z] 2016-04-14 21:27:04 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:27:04,747 - WARNING - Could not retrieve variants from source file in region 5:122110961-122111400. Error was invalid region `5:122110962-122111400`
[2016-04-15T04:27Z] 2016-04-14 21:27:05 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:27:05,487 - WARNING - Could not retrieve variants from source file in region 5:122343659-122359830. Error was invalid region `5:122343660-122359830`
[2016-04-15T04:27Z] 2016-04-14 21:27:07 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:27:07,503 - WARNING - Could not retrieve variants from source file in region 5:121518098-121518499. Error was invalid region `5:121518099-121518499`
[2016-04-15T04:27Z] 2016-04-14 21:27:07 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:27:07,525 - WARNING - Could not retrieve variants from source file in region 5:112176545-112176946. Error was invalid region `5:112176546-112176946`
[2016-04-15T04:27Z] 2016-04-14 21:27:07 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:27:07,544 - WARNING - Could not retrieve variants from source file in region 5:122110961-122111400. Error was invalid region `5:122110962-122111400`
[2016-04-15T04:27Z] ['bcbio-variation-recall', 'square', '-Xms750m', '-Xmx7280m', '-XX:+UseSerialGC', '-c', 16, '-r', u'5:127597428-143191869', '--caller', 'platypus', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/5/Batch1-5_127597427_143191869.vcf.gz', '/mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/5/Batch1-5_127597427_143191869.vcf-inputs.txt'] in region: 5:127597428-143191869
[2016-04-15T04:27Z] 2016-04-14 21:27:22 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:27:22,962 - WARNING - Could not retrieve variants from source file in region 5:142782804-142784319. Error was invalid region `5:142782805-142784319`
[2016-04-15T04:27Z] 2016-04-14 21:27:24 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:27:24,853 - WARNING - Could not retrieve variants from source file in region 5:135692364-135692765. Error was invalid region `5:135692365-135692765`
[2016-04-15T04:27Z] 2016-04-14 21:27:24 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:27:24,948 - WARNING - Could not retrieve variants from source file in region 5:135275990-135287219. Error was invalid region `5:135275991-135287219`
[2016-04-15T04:27Z] 2016-04-14 21:27:25 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:27:25,683 - WARNING - Could not retrieve variants from source file in region 5:134782203-134782766. Error was invalid region `5:134782204-134782766`
[2016-04-15T04:27Z] 2016-04-14 21:27:25 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:27:25,723 - WARNING - Could not retrieve variants from source file in region 5:138266335-138268006. Error was invalid region `5:138266336-138268006`
[2016-04-15T04:27Z] 2016-04-14 21:27:25 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:27:25,835 - WARNING - Could not retrieve variants from source file in region 5:137027818-137028219. Error was invalid region `5:137027819-137028219`
[2016-04-15T04:27Z] 2016-04-14 21:27:26 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:27:26,234 - WARNING - Could not retrieve variants from source file in region 5:142421204-142421605. Error was invalid region `5:142421205-142421605`
[2016-04-15T04:27Z] 2016-04-14 21:27:26 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:27:26,282 - WARNING - Could not retrieve variants from source file in region 5:135177913-135178314. Error was invalid region `5:135177914-135178314`
[2016-04-15T04:27Z] 2016-04-14 21:27:26 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:27:26,586 - WARNING - Could not retrieve variants from source file in region 5:137206349-137206750. Error was invalid region `5:137206350-137206750`
[2016-04-15T04:27Z] 2016-04-14 21:27:26 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:27:26,628 - WARNING - Could not retrieve variants from source file in region 5:139740243-139745344. Error was invalid region `5:139740244-139745344`
[2016-04-15T04:27Z] 2016-04-14 21:27:26 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:27:26,691 - WARNING - Could not retrieve variants from source file in region 5:131995753-131996154. Error was invalid region `5:131995754-131996154`
[2016-04-15T04:27Z] 2016-04-14 21:27:28 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:27:28,055 - WARNING - Could not retrieve variants from source file in region 5:142782804-142784319. Error was invalid region `5:142782805-142784319`
[2016-04-15T04:27Z] 2016-04-14 21:27:30 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:27:30,811 - WARNING - Could not retrieve variants from source file in region 5:140856054-140871615. Error was invalid region `5:140856055-140871615`
[2016-04-15T04:27Z] 2016-04-14 21:27:32 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:27:32,209 - WARNING - Could not retrieve variants from source file in region 5:135275990-135287219. Error was invalid region `5:135275991-135287219`
[2016-04-15T04:27Z] 2016-04-14 21:27:33 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:27:33,520 - WARNING - Could not retrieve variants from source file in region 5:135382778-135392616. Error was invalid region `5:135382779-135392616`
[2016-04-15T04:27Z] 2016-04-14 21:27:34 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:27:34,595 - WARNING - Could not retrieve variants from source file in region 5:138266335-138268006. Error was invalid region `5:138266336-138268006`
[2016-04-15T04:27Z] 2016-04-14 21:27:34 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:27:34,804 - WARNING - Could not retrieve variants from source file in region 5:135177913-135178314. Error was invalid region `5:135177914-135178314`
[2016-04-15T04:27Z] 2016-04-14 21:27:34 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:27:34,914 - WARNING - Could not retrieve variants from source file in region 5:137027818-137028219. Error was invalid region `5:137027819-137028219`
[2016-04-15T04:27Z] 2016-04-14 21:27:34 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:27:34,934 - WARNING - Could not retrieve variants from source file in region 5:139740243-139745344. Error was invalid region `5:139740244-139745344`
[2016-04-15T04:27Z] 2016-04-14 21:27:35 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:27:35,212 - WARNING - Could not retrieve variants from source file in region 5:142782804-142784319. Error was invalid region `5:142782805-142784319`
[2016-04-15T04:27Z] 2016-04-14 21:27:35 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:27:35,377 - WARNING - Could not retrieve variants from source file in region 5:131995753-131996154. Error was invalid region `5:131995754-131996154`
[2016-04-15T04:27Z] 2016-04-14 21:27:35 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:27:35,474 - WARNING - Could not retrieve variants from source file in region 5:142421204-142421605. Error was invalid region `5:142421205-142421605`
[2016-04-15T04:27Z] 2016-04-14 21:27:35 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:27:35,575 - WARNING - Could not retrieve variants from source file in region 5:137206349-137206750. Error was invalid region `5:137206350-137206750`
[2016-04-15T04:27Z] 2016-04-14 21:27:36 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:27:36,987 - WARNING - Could not retrieve variants from source file in region 5:135692364-135692765. Error was invalid region `5:135692365-135692765`
[2016-04-15T04:27Z] 2016-04-14 21:27:37 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:27:37,287 - WARNING - Could not retrieve variants from source file in region 5:135275990-135287219. Error was invalid region `5:135275991-135287219`
[2016-04-15T04:27Z] 2016-04-14 21:27:41 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:27:41,809 - WARNING - Could not retrieve variants from source file in region 5:134782203-134782766. Error was invalid region `5:134782204-134782766`
[2016-04-15T04:27Z] 2016-04-14 21:27:42 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:27:42,539 - WARNING - Could not retrieve variants from source file in region 5:135177913-135178314. Error was invalid region `5:135177914-135178314`
[2016-04-15T04:27Z] 2016-04-14 21:27:43 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:27:43,054 - WARNING - Could not retrieve variants from source file in region 5:139740243-139745344. Error was invalid region `5:139740244-139745344`
[2016-04-15T04:27Z] 2016-04-14 21:27:43 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:27:43,194 - WARNING - Could not retrieve variants from source file in region 5:137027818-137028219. Error was invalid region `5:137027819-137028219`
[2016-04-15T04:27Z] 2016-04-14 21:27:43 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:27:43,556 - WARNING - Could not retrieve variants from source file in region 5:131995753-131996154. Error was invalid region `5:131995754-131996154`
[2016-04-15T04:27Z] 2016-04-14 21:27:43 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:27:43,628 - WARNING - Could not retrieve variants from source file in region 5:142421204-142421605. Error was invalid region `5:142421205-142421605`
[2016-04-15T04:27Z] 2016-04-14 21:27:44 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:27:44,103 - WARNING - Could not retrieve variants from source file in region 5:137206349-137206750. Error was invalid region `5:137206350-137206750`
[2016-04-15T04:27Z] 2016-04-14 21:27:55 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:27:55,505 - WARNING - Could not retrieve variants from source file in region 5:134907341-134907742. Error was invalid region `5:134907342-134907742`
[2016-04-15T04:27Z] 2016-04-14 21:27:55 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:27:55,571 - WARNING - Could not retrieve variants from source file in region 5:135512874-135513275. Error was invalid region `5:135512875-135513275`
[2016-04-15T04:27Z] 2016-04-14 21:27:56 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:27:56,058 - WARNING - Could not retrieve variants from source file in region 5:135512874-135513275. Error was invalid region `5:135512875-135513275`
[2016-04-15T04:27Z] 2016-04-14 21:27:57 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:27:57,391 - WARNING - Could not retrieve variants from source file in region 5:142661279-142674880. Error was invalid region `5:142661280-142674880`
[2016-04-15T04:27Z] 2016-04-14 21:27:59 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:27:59,013 - WARNING - Could not retrieve variants from source file in region 5:138147732-138148133. Error was invalid region `5:138147733-138148133`
[2016-04-15T04:27Z] 2016-04-14 21:27:59 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:27:59,402 - WARNING - Could not retrieve variants from source file in region 5:139653228-139653629. Error was invalid region `5:139653229-139653629`
[2016-04-15T04:28Z] 2016-04-14 21:28:00 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:28:00,106 - WARNING - Could not retrieve variants from source file in region 5:135512874-135513275. Error was invalid region `5:135512875-135513275`
[2016-04-15T04:28Z] 2016-04-14 21:28:00 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:28:00,445 - WARNING - Could not retrieve variants from source file in region 5:141391321-141391722. Error was invalid region `5:141391322-141391722`
[2016-04-15T04:28Z] 2016-04-14 21:28:00 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:28:00,587 - WARNING - Could not retrieve variants from source file in region 5:131821844-131822245. Error was invalid region `5:131821845-131822245`
[2016-04-15T04:28Z] 2016-04-14 21:28:01 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:28:01,308 - WARNING - Could not retrieve variants from source file in region 5:141242422-141244546. Error was invalid region `5:141242423-141244546`
[2016-04-15T04:28Z] 2016-04-14 21:28:03 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:28:03,557 - WARNING - Could not retrieve variants from source file in region 5:139653228-139653629. Error was invalid region `5:139653229-139653629`
[2016-04-15T04:28Z] 2016-04-14 21:28:04 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:28:04,513 - WARNING - Could not retrieve variants from source file in region 5:138772879-138773280. Error was invalid region `5:138772880-138773280`
[2016-04-15T04:28Z] 2016-04-14 21:28:04 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:28:04,534 - WARNING - Could not retrieve variants from source file in region 5:134907341-134907742. Error was invalid region `5:134907342-134907742`
[2016-04-15T04:28Z] 2016-04-14 21:28:04 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:28:04,879 - WARNING - Could not retrieve variants from source file in region 5:131821844-131822245. Error was invalid region `5:131821845-131822245`
[2016-04-15T04:28Z] 2016-04-14 21:28:07 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:28:07,830 - WARNING - Could not retrieve variants from source file in region 5:139653228-139653629. Error was invalid region `5:139653229-139653629`
[2016-04-15T04:28Z] 2016-04-14 21:28:08 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:28:08,502 - WARNING - Could not retrieve variants from source file in region 5:139573839-139574240. Error was invalid region `5:139573840-139574240`
[2016-04-15T04:28Z] 2016-04-14 21:28:09 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:28:09,151 - WARNING - Could not retrieve variants from source file in region 5:138772879-138773280. Error was invalid region `5:138772880-138773280`
[2016-04-15T04:28Z] 2016-04-14 21:28:09 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:28:09,974 - WARNING - Could not retrieve variants from source file in region 5:131821844-131822245. Error was invalid region `5:131821845-131822245`
[2016-04-15T04:28Z] 2016-04-14 21:28:12 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:28:12,519 - WARNING - Could not retrieve variants from source file in region 5:137667134-137667702. Error was invalid region `5:137667135-137667702`
[2016-04-15T04:28Z] 2016-04-14 21:28:13 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:28:13,085 - WARNING - Could not retrieve variants from source file in region 5:142593441-142593842. Error was invalid region `5:142593442-142593842`
[2016-04-15T04:28Z] 2016-04-14 21:28:13 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:28:13,728 - WARNING - Could not retrieve variants from source file in region 5:142593441-142593842. Error was invalid region `5:142593442-142593842`
[2016-04-15T04:28Z] 2016-04-14 21:28:13 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:28:13,907 - WARNING - Could not retrieve variants from source file in region 5:139573839-139574240. Error was invalid region `5:139573840-139574240`
[2016-04-15T04:28Z] 2016-04-14 21:28:14 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:28:14,814 - WARNING - Could not retrieve variants from source file in region 5:142482666-142483067. Error was invalid region `5:142482667-142483067`
[2016-04-15T04:28Z] 2016-04-14 21:28:18 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:28:18,008 - WARNING - Could not retrieve variants from source file in region 5:139573839-139574240. Error was invalid region `5:139573840-139574240`
[2016-04-15T04:28Z] 2016-04-14 21:28:19 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:28:19,192 - WARNING - Could not retrieve variants from source file in region 5:139217109-139228268. Error was invalid region `5:139217110-139228268`
[2016-04-15T04:28Z] 2016-04-14 21:28:19 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:28:19,482 - WARNING - Could not retrieve variants from source file in region 5:137667134-137667702. Error was invalid region `5:137667135-137667702`
[2016-04-15T04:28Z] 2016-04-14 21:28:19 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:28:19,796 - WARNING - Could not retrieve variants from source file in region 5:142593441-142593842. Error was invalid region `5:142593442-142593842`
[2016-04-15T04:28Z] 2016-04-14 21:28:20 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:28:20,646 - WARNING - Could not retrieve variants from source file in region 5:141014283-141060058. Error was invalid region `5:141014284-141060058`
[2016-04-15T04:28Z] 2016-04-14 21:28:20 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:28:20,769 - WARNING - Could not retrieve variants from source file in region 5:137891959-137902529. Error was invalid region `5:137891960-137902529`
[2016-04-15T04:28Z] 2016-04-14 21:28:21 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:28:21,276 - WARNING - Could not retrieve variants from source file in region 5:142482666-142483067. Error was invalid region `5:142482667-142483067`
[2016-04-15T04:28Z] 2016-04-14 21:28:24 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:28:24,183 - WARNING - Could not retrieve variants from source file in region 5:138642786-138643187. Error was invalid region `5:138642787-138643187`
[2016-04-15T04:28Z] 2016-04-14 21:28:24 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:28:24,263 - WARNING - Could not retrieve variants from source file in region 5:132652070-132652471. Error was invalid region `5:132652071-132652471`
[2016-04-15T04:28Z] 2016-04-14 21:28:24 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:28:24,520 - WARNING - Could not retrieve variants from source file in region 5:137667134-137667702. Error was invalid region `5:137667135-137667702`
[2016-04-15T04:28Z] 2016-04-14 21:28:24 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:28:24,834 - WARNING - Could not retrieve variants from source file in region 5:131705738-131721364. Error was invalid region `5:131705739-131721364`
[2016-04-15T04:28Z] 2016-04-14 21:28:26 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:28:26,773 - WARNING - Could not retrieve variants from source file in region 5:134223539-134223940. Error was invalid region `5:134223540-134223940`
[2016-04-15T04:28Z] 2016-04-14 21:28:26 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:28:26,867 - WARNING - Could not retrieve variants from source file in region 5:140682546-140683455. Error was invalid region `5:140682547-140683455`
[2016-04-15T04:28Z] 2016-04-14 21:28:26 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:28:26,899 - WARNING - Could not retrieve variants from source file in region 5:142482666-142483067. Error was invalid region `5:142482667-142483067`
[2016-04-15T04:28Z] 2016-04-14 21:28:26 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:28:26,922 - WARNING - Could not retrieve variants from source file in region 5:139217109-139228268. Error was invalid region `5:139217110-139228268`
[2016-04-15T04:28Z] 2016-04-14 21:28:29 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:28:29,102 - WARNING - Could not retrieve variants from source file in region 5:138642786-138643187. Error was invalid region `5:138642787-138643187`
[2016-04-15T04:28Z] 2016-04-14 21:28:29 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:28:29,380 - WARNING - Could not retrieve variants from source file in region 5:132652070-132652471. Error was invalid region `5:132652071-132652471`
[2016-04-15T04:28Z] 2016-04-14 21:28:29 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:28:29,527 - WARNING - Could not retrieve variants from source file in region 5:140346257-140347243. Error was invalid region `5:140346258-140347243`
[2016-04-15T04:28Z] 2016-04-14 21:28:29 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:28:29,672 - WARNING - Could not retrieve variants from source file in region 5:131705738-131721364. Error was invalid region `5:131705739-131721364`
[2016-04-15T04:28Z] 2016-04-14 21:28:30 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:28:30,165 - WARNING - Could not retrieve variants from source file in region 5:138713748-138732769. Error was invalid region `5:138713749-138732769`
[2016-04-15T04:28Z] 2016-04-14 21:28:31 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:28:31,803 - WARNING - Could not retrieve variants from source file in region 5:140682546-140683455. Error was invalid region `5:140682547-140683455`
[2016-04-15T04:28Z] 2016-04-14 21:28:33 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:28:33,601 - WARNING - Could not retrieve variants from source file in region 5:138642786-138643187. Error was invalid region `5:138642787-138643187`
[2016-04-15T04:28Z] 2016-04-14 21:28:34 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:28:34,353 - WARNING - Could not retrieve variants from source file in region 5:140346257-140347243. Error was invalid region `5:140346258-140347243`
[2016-04-15T04:28Z] 2016-04-14 21:28:34 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:28:34,423 - WARNING - Could not retrieve variants from source file in region 5:131705738-131721364. Error was invalid region `5:131705739-131721364`
[2016-04-15T04:28Z] 2016-04-14 21:28:37 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:28:37,471 - WARNING - Could not retrieve variants from source file in region 5:137475576-137525533. Error was invalid region `5:137475577-137525533`
[2016-04-15T04:28Z] 2016-04-14 21:28:39 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:28:39,831 - WARNING - Could not retrieve variants from source file in region 5:140346257-140347243. Error was invalid region `5:140346258-140347243`
[2016-04-15T04:28Z] 2016-04-14 21:28:41 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:28:41,076 - WARNING - Could not retrieve variants from source file in region 5:130766451-130766852. Error was invalid region `5:130766452-130766852`
[2016-04-15T04:28Z] 2016-04-14 21:28:41 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:28:41,079 - WARNING - Could not retrieve variants from source file in region 5:138456604-138457005. Error was invalid region `5:138456605-138457005`
[2016-04-15T04:28Z] 2016-04-14 21:28:41 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:28:41,509 - WARNING - Could not retrieve variants from source file in region 5:133861452-133861853. Error was invalid region `5:133861453-133861853`
[2016-04-15T04:28Z] 2016-04-14 21:28:41 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:28:41,513 - WARNING - Could not retrieve variants from source file in region 5:133861452-133861853. Error was invalid region `5:133861453-133861853`
[2016-04-15T04:28Z] 2016-04-14 21:28:41 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:28:41,913 - WARNING - Could not retrieve variants from source file in region 5:137844063-137849849. Error was invalid region `5:137844064-137849849`
[2016-04-15T04:28Z] 2016-04-14 21:28:43 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:28:43,131 - WARNING - Could not retrieve variants from source file in region 5:138456604-138457005. Error was invalid region `5:138456605-138457005`
[2016-04-15T04:28Z] 2016-04-14 21:28:46 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:28:46,292 - WARNING - Could not retrieve variants from source file in region 5:137708223-137754885. Error was invalid region `5:137708224-137754885`
[2016-04-15T04:28Z] 2016-04-14 21:28:46 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:28:46,754 - WARNING - Could not retrieve variants from source file in region 5:130766451-130766852. Error was invalid region `5:130766452-130766852`
[2016-04-15T04:28Z] 2016-04-14 21:28:46 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:28:46,985 - WARNING - Could not retrieve variants from source file in region 5:133861452-133861853. Error was invalid region `5:133861453-133861853`
[2016-04-15T04:28Z] 2016-04-14 21:28:47 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:28:47,820 - WARNING - Could not retrieve variants from source file in region 5:137475576-137525533. Error was invalid region `5:137475577-137525533`
[2016-04-15T04:28Z] 2016-04-14 21:28:48 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:28:48,001 - WARNING - Could not retrieve variants from source file in region 5:137426236-137426958. Error was invalid region `5:137426237-137426958`
[2016-04-15T04:28Z] 2016-04-14 21:28:48 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:28:48,245 - WARNING - Could not retrieve variants from source file in region 5:137844063-137849849. Error was invalid region `5:137844064-137849849`
[2016-04-15T04:28Z] 2016-04-14 21:28:48 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:28:48,290 - WARNING - Could not retrieve variants from source file in region 5:132232104-132232505. Error was invalid region `5:132232105-132232505`
[2016-04-15T04:28Z] 2016-04-14 21:28:50 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:28:50,854 - WARNING - Could not retrieve variants from source file in region 5:137708223-137754885. Error was invalid region `5:137708224-137754885`
[2016-04-15T04:28Z] 2016-04-14 21:28:50 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:28:50,903 - WARNING - Could not retrieve variants from source file in region 5:130766451-130766852. Error was invalid region `5:130766452-130766852`
[2016-04-15T04:28Z] 2016-04-14 21:28:52 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:28:52,260 - WARNING - Could not retrieve variants from source file in region 5:140307073-140309206. Error was invalid region `5:140307074-140309206`
[2016-04-15T04:28Z] 2016-04-14 21:28:52 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:28:52,501 - WARNING - Could not retrieve variants from source file in region 5:137426236-137426958. Error was invalid region `5:137426237-137426958`
[2016-04-15T04:28Z] 2016-04-14 21:28:52 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:28:52,536 - WARNING - Could not retrieve variants from source file in region 5:137844063-137849849. Error was invalid region `5:137844064-137849849`
[2016-04-15T04:28Z] 2016-04-14 21:28:52 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:28:52,836 - WARNING - Could not retrieve variants from source file in region 5:131662851-131676510. Error was invalid region `5:131662852-131676510`
[2016-04-15T04:28Z] 2016-04-14 21:28:52 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:28:52,850 - WARNING - Could not retrieve variants from source file in region 5:132232104-132232505. Error was invalid region `5:132232105-132232505`
[2016-04-15T04:28Z] 2016-04-14 21:28:54 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:28:54,828 - WARNING - Could not retrieve variants from source file in region 5:137708223-137754885. Error was invalid region `5:137708224-137754885`
[2016-04-15T04:28Z] 2016-04-14 21:28:56 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:28:56,642 - WARNING - Could not retrieve variants from source file in region 5:140307073-140309206. Error was invalid region `5:140307074-140309206`
[2016-04-15T04:28Z] 2016-04-14 21:28:59 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:28:59,041 - WARNING - Could not retrieve variants from source file in region 5:128863260-128863661. Error was invalid region `5:128863261-128863661`
[2016-04-15T04:28Z] 2016-04-14 21:28:59 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:28:59,066 - WARNING - Could not retrieve variants from source file in region 5:131601955-131607778. Error was invalid region `5:131601956-131607778`
[2016-04-15T04:28Z] 2016-04-14 21:28:59 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:28:59,340 - WARNING - Could not retrieve variants from source file in region 5:132197988-132198389. Error was invalid region `5:132197989-132198389`
[2016-04-15T04:28Z] 2016-04-14 21:28:59 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:28:59,343 - WARNING - Could not retrieve variants from source file in region 5:137347287-137347688. Error was invalid region `5:137347288-137347688`
[2016-04-15T04:29Z] 2016-04-14 21:29:00 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:29:00,953 - WARNING - Could not retrieve variants from source file in region 5:140307073-140309206. Error was invalid region `5:140307074-140309206`
[2016-04-15T04:29Z] 2016-04-14 21:29:03 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:29:03,230 - WARNING - Could not retrieve variants from source file in region 5:129520915-129521316. Error was invalid region `5:129520916-129521316`
[2016-04-15T04:29Z] 2016-04-14 21:29:03 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:29:03,527 - WARNING - Could not retrieve variants from source file in region 5:137347287-137347688. Error was invalid region `5:137347288-137347688`
[2016-04-15T04:29Z] 2016-04-14 21:29:03 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:29:03,528 - WARNING - Could not retrieve variants from source file in region 5:128863260-128863661. Error was invalid region `5:128863261-128863661`
[2016-04-15T04:29Z] 2016-04-14 21:29:03 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:29:03,729 - WARNING - Could not retrieve variants from source file in region 5:132197988-132198389. Error was invalid region `5:132197989-132198389`
[2016-04-15T04:29Z] 2016-04-14 21:29:06 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:29:06,936 - WARNING - Could not retrieve variants from source file in region 5:129337060-129337461. Error was invalid region `5:129337061-129337461`
[2016-04-15T04:29Z] 2016-04-14 21:29:07 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:29:07,241 - WARNING - Could not retrieve variants from source file in region 5:129520915-129521316. Error was invalid region `5:129520916-129521316`
[2016-04-15T04:29Z] 2016-04-14 21:29:07 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:29:07,722 - WARNING - Could not retrieve variants from source file in region 5:137347287-137347688. Error was invalid region `5:137347288-137347688`
[2016-04-15T04:29Z] 2016-04-14 21:29:07 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:29:07,903 - WARNING - Could not retrieve variants from source file in region 5:131601955-131607778. Error was invalid region `5:131601956-131607778`
[2016-04-15T04:29Z] 2016-04-14 21:29:08 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:29:08,151 - WARNING - Could not retrieve variants from source file in region 5:128863260-128863661. Error was invalid region `5:128863261-128863661`
[2016-04-15T04:29Z] 2016-04-14 21:29:08 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:29:08,192 - WARNING - Could not retrieve variants from source file in region 5:137244306-137272340. Error was invalid region `5:137244307-137272340`
[2016-04-15T04:29Z] 2016-04-14 21:29:08 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:29:08,192 - WARNING - Could not retrieve variants from source file in region 5:132197988-132198389. Error was invalid region `5:132197989-132198389`
[2016-04-15T04:29Z] 2016-04-14 21:29:09 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:29:09,385 - WARNING - Could not retrieve variants from source file in region 5:132149111-132161484. Error was invalid region `5:132149112-132161484`
[2016-04-15T04:29Z] 2016-04-14 21:29:09 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:29:09,544 - WARNING - Could not retrieve variants from source file in region 5:131324039-131347710. Error was invalid region `5:131324040-131347710`
[2016-04-15T04:29Z] 2016-04-14 21:29:11 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:29:11,101 - WARNING - Could not retrieve variants from source file in region 5:129337060-129337461. Error was invalid region `5:129337061-129337461`
[2016-04-15T04:29Z] 2016-04-14 21:29:11 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:29:11,157 - WARNING - Could not retrieve variants from source file in region 5:129520915-129521316. Error was invalid region `5:129520916-129521316`
[2016-04-15T04:29Z] 2016-04-14 21:29:12 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:29:12,726 - WARNING - Could not retrieve variants from source file in region 5:140021271-140052461. Error was invalid region `5:140021272-140052461`
[2016-04-15T04:29Z] 2016-04-14 21:29:13 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:29:13,852 - WARNING - Could not retrieve variants from source file in region 5:131324039-131347710. Error was invalid region `5:131324040-131347710`
[2016-04-15T04:29Z] 2016-04-14 21:29:15 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:29:15,257 - WARNING - Could not retrieve variants from source file in region 5:129337060-129337461. Error was invalid region `5:129337061-129337461`
[2016-04-15T04:29Z] 2016-04-14 21:29:17 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:29:17,029 - WARNING - Could not retrieve variants from source file in region 5:140021271-140052461. Error was invalid region `5:140021272-140052461`
[2016-04-15T04:29Z] 2016-04-14 21:29:19 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:29:19,385 - WARNING - Could not retrieve variants from source file in region 5:128430546-128430947. Error was invalid region `5:128430547-128430947`
[2016-04-15T04:29Z] 2016-04-14 21:29:19 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:29:19,602 - WARNING - Could not retrieve variants from source file in region 5:131396267-131411650. Error was invalid region `5:131396268-131411650`
[2016-04-15T04:29Z] 2016-04-14 21:29:19 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:29:19,938 - WARNING - Could not retrieve variants from source file in region 5:132098031-132098432. Error was invalid region `5:132098032-132098432`
[2016-04-15T04:29Z] 2016-04-14 21:29:20 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:29:20,702 - WARNING - Could not retrieve variants from source file in region 5:132098031-132098432. Error was invalid region `5:132098032-132098432`
[2016-04-15T04:29Z] 2016-04-14 21:29:20 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:29:20,829 - WARNING - Could not retrieve variants from source file in region 5:132098031-132098432. Error was invalid region `5:132098032-132098432`
[2016-04-15T04:29Z] 2016-04-14 21:29:20 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:29:20,873 - WARNING - Could not retrieve variants from source file in region 5:140021271-140052461. Error was invalid region `5:140021272-140052461`
[2016-04-15T04:29Z] 2016-04-14 21:29:21 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:29:21,062 - WARNING - Could not retrieve variants from source file in region 5:139931418-139941508. Error was invalid region `5:139931419-139941508`
[2016-04-15T04:29Z] 2016-04-14 21:29:22 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:29:22,793 - WARNING - Could not retrieve variants from source file in region 5:129240761-129241162. Error was invalid region `5:129240762-129241162`
[2016-04-15T04:29Z] 2016-04-14 21:29:22 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:29:22,846 - WARNING - Could not retrieve variants from source file in region 5:129240761-129241162. Error was invalid region `5:129240762-129241162`
[2016-04-15T04:29Z] 2016-04-14 21:29:23 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:29:23,762 - WARNING - Could not retrieve variants from source file in region 5:128430546-128430947. Error was invalid region `5:128430547-128430947`
[2016-04-15T04:29Z] 2016-04-14 21:29:24 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:29:24,520 - WARNING - Could not retrieve variants from source file in region 5:131066514-131066915. Error was invalid region `5:131066515-131066915`
[2016-04-15T04:29Z] 2016-04-14 21:29:25 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:29:25,254 - WARNING - Could not retrieve variants from source file in region 5:131396267-131411650. Error was invalid region `5:131396268-131411650`
[2016-04-15T04:29Z] 2016-04-14 21:29:25 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:29:25,650 - WARNING - Could not retrieve variants from source file in region 5:139931418-139941508. Error was invalid region `5:139931419-139941508`
[2016-04-15T04:29Z] 2016-04-14 21:29:25 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:29:25,738 - WARNING - Could not retrieve variants from source file in region 5:139931418-139941508. Error was invalid region `5:139931419-139941508`
[2016-04-15T04:29Z] 2016-04-14 21:29:25 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:29:25,898 - WARNING - Could not retrieve variants from source file in region 5:131066514-131066915. Error was invalid region `5:131066515-131066915`
[2016-04-15T04:29Z] 2016-04-14 21:29:27 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:29:27,089 - WARNING - Could not retrieve variants from source file in region 5:129240761-129241162. Error was invalid region `5:129240762-129241162`
[2016-04-15T04:29Z] 2016-04-14 21:29:27 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:29:27,945 - WARNING - Could not retrieve variants from source file in region 5:128430546-128430947. Error was invalid region `5:128430547-128430947`
[2016-04-15T04:29Z] 2016-04-14 21:29:28 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:29:28,662 - WARNING - Could not retrieve variants from source file in region 5:129039845-129040246. Error was invalid region `5:129039846-129040246`
[2016-04-15T04:29Z] 2016-04-14 21:29:28 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:29:28,972 - WARNING - Could not retrieve variants from source file in region 5:131066514-131066915. Error was invalid region `5:131066515-131066915`
[2016-04-15T04:29Z] 2016-04-14 21:29:29 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:29:29,169 - WARNING - Could not retrieve variants from source file in region 5:131007983-131008384. Error was invalid region `5:131007984-131008384`
[2016-04-15T04:29Z] 2016-04-14 21:29:29 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:29:29,661 - WARNING - Could not retrieve variants from source file in region 5:131007983-131008384. Error was invalid region `5:131007984-131008384`
[2016-04-15T04:29Z] 2016-04-14 21:29:32 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:29:32,819 - WARNING - Could not retrieve variants from source file in region 5:128301674-128302161. Error was invalid region `5:128301675-128302161`
[2016-04-15T04:29Z] 2016-04-14 21:29:33 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:29:33,288 - WARNING - Could not retrieve variants from source file in region 5:131007983-131008384. Error was invalid region `5:131007984-131008384`
[2016-04-15T04:29Z] 2016-04-14 21:29:33 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:29:33,488 - WARNING - Could not retrieve variants from source file in region 5:128301674-128302161. Error was invalid region `5:128301675-128302161`
[2016-04-15T04:29Z] 2016-04-14 21:29:33 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:29:33,840 - WARNING - Could not retrieve variants from source file in region 5:127684924-127685325. Error was invalid region `5:127684925-127685325`
[2016-04-15T04:29Z] 2016-04-14 21:29:36 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:29:36,442 - WARNING - Could not retrieve variants from source file in region 5:127684924-127685325. Error was invalid region `5:127684925-127685325`
[2016-04-15T04:29Z] 2016-04-14 21:29:36 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:29:36,443 - WARNING - Could not retrieve variants from source file in region 5:127684924-127685325. Error was invalid region `5:127684925-127685325`
[2016-04-15T04:29Z] 2016-04-14 21:29:36 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:29:36,762 - WARNING - Could not retrieve variants from source file in region 5:127597307-127614662. Error was invalid region `5:127597308-127614662`
[2016-04-15T04:29Z] ['bcbio-variation-recall', 'square', '-Xms750m', '-Xmx7280m', '-XX:+UseSerialGC', '-c', 16, '-r', u'5:143200045-158710347', '--caller', 'platypus', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/5/Batch1-5_143200044_158710347.vcf.gz', '/mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/5/Batch1-5_143200044_158710347.vcf-inputs.txt'] in region: 5:143200045-158710347
[2016-04-15T04:29Z] 2016-04-14 21:29:53 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:29:53,194 - WARNING - Could not retrieve variants from source file in region 5:156898479-156936554. Error was invalid region `5:156898480-156936554`
[2016-04-15T04:29Z] 2016-04-14 21:29:53 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:29:53,987 - WARNING - Could not retrieve variants from source file in region 5:157164751-157171176. Error was invalid region `5:157164752-157171176`
[2016-04-15T04:29Z] 2016-04-14 21:29:54 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:29:54,087 - WARNING - Could not retrieve variants from source file in region 5:145889817-145895086. Error was invalid region `5:145889818-145895086`
[2016-04-15T04:29Z] 2016-04-14 21:29:54 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:29:54,460 - WARNING - Could not retrieve variants from source file in region 5:148243262-148252287. Error was invalid region `5:148243263-148252287`
[2016-04-15T04:29Z] 2016-04-14 21:29:54 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:29:54,472 - WARNING - Could not retrieve variants from source file in region 5:148638851-148639252. Error was invalid region `5:148638852-148639252`
[2016-04-15T04:29Z] 2016-04-14 21:29:54 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:29:54,473 - WARNING - Could not retrieve variants from source file in region 5:150227755-150228156. Error was invalid region `5:150227756-150228156`
[2016-04-15T04:29Z] 2016-04-14 21:29:54 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:29:54,667 - WARNING - Could not retrieve variants from source file in region 5:150097672-150098073. Error was invalid region `5:150097673-150098073`
[2016-04-15T04:29Z] 2016-04-14 21:29:54 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:29:54,775 - WARNING - Could not retrieve variants from source file in region 5:149677607-149678041. Error was invalid region `5:149677608-149678041`
[2016-04-15T04:29Z] 2016-04-14 21:29:54 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:29:54,987 - WARNING - Could not retrieve variants from source file in region 5:147285802-147286244. Error was invalid region `5:147285803-147286244`
[2016-04-15T04:29Z] 2016-04-14 21:29:55 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:29:55,239 - WARNING - Could not retrieve variants from source file in region 5:156531525-156531926. Error was invalid region `5:156531526-156531926`
[2016-04-15T04:29Z] 2016-04-14 21:29:55 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:29:55,260 - WARNING - Could not retrieve variants from source file in region 5:147856021-147856447. Error was invalid region `5:147856022-147856447`
[2016-04-15T04:29Z] 2016-04-14 21:29:56 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:29:56,974 - WARNING - Could not retrieve variants from source file in region 5:146618995-146619396. Error was invalid region `5:146618996-146619396`
[2016-04-15T04:30Z] 2016-04-14 21:30:03 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:30:03,471 - WARNING - Could not retrieve variants from source file in region 5:148243262-148252287. Error was invalid region `5:148243263-148252287`
[2016-04-15T04:30Z] 2016-04-14 21:30:04 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:30:04,241 - WARNING - Could not retrieve variants from source file in region 5:146618995-146619396. Error was invalid region `5:146618996-146619396`
[2016-04-15T04:30Z] 2016-04-14 21:30:04 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:30:04,431 - WARNING - Could not retrieve variants from source file in region 5:148638851-148639252. Error was invalid region `5:148638852-148639252`
[2016-04-15T04:30Z] 2016-04-14 21:30:04 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:30:04,511 - WARNING - Could not retrieve variants from source file in region 5:156531525-156531926. Error was invalid region `5:156531526-156531926`
[2016-04-15T04:30Z] 2016-04-14 21:30:07 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:30:07,012 - WARNING - Could not retrieve variants from source file in region 5:157164751-157171176. Error was invalid region `5:157164752-157171176`
[2016-04-15T04:30Z] 2016-04-14 21:30:08 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:30:08,080 - WARNING - Could not retrieve variants from source file in region 5:148988911-149008711. Error was invalid region `5:148988912-149008711`
[2016-04-15T04:30Z] 2016-04-14 21:30:08 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:30:08,662 - WARNING - Could not retrieve variants from source file in region 5:150227755-150228156. Error was invalid region `5:150227756-150228156`
[2016-04-15T04:30Z] 2016-04-14 21:30:09 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:30:09,188 - WARNING - Could not retrieve variants from source file in region 5:149677607-149678041. Error was invalid region `5:149677608-149678041`
[2016-04-15T04:30Z] 2016-04-14 21:30:09 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:30:09,687 - WARNING - Could not retrieve variants from source file in region 5:145889817-145895086. Error was invalid region `5:145889818-145895086`
[2016-04-15T04:30Z] 2016-04-14 21:30:10 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:30:10,147 - WARNING - Could not retrieve variants from source file in region 5:150097672-150098073. Error was invalid region `5:150097673-150098073`
[2016-04-15T04:30Z] 2016-04-14 21:30:11 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:30:11,329 - WARNING - Could not retrieve variants from source file in region 5:148638851-148639252. Error was invalid region `5:148638852-148639252`
[2016-04-15T04:30Z] 2016-04-14 21:30:12 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:30:12,343 - WARNING - Could not retrieve variants from source file in region 5:147285802-147286244. Error was invalid region `5:147285803-147286244`
[2016-04-15T04:30Z] 2016-04-14 21:30:12 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:30:12,756 - WARNING - Could not retrieve variants from source file in region 5:156531525-156531926. Error was invalid region `5:156531526-156531926`
[2016-04-15T04:30Z] 2016-04-14 21:30:20 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:30:20,380 - WARNING - Could not retrieve variants from source file in region 5:146435369-146435770. Error was invalid region `5:146435370-146435770`
[2016-04-15T04:30Z] 2016-04-14 21:30:23 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:30:23,178 - WARNING - Could not retrieve variants from source file in region 5:150275576-150275977. Error was invalid region `5:150275577-150275977`
[2016-04-15T04:30Z] 2016-04-14 21:30:23 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:30:23,345 - WARNING - Could not retrieve variants from source file in region 5:157101948-157102375. Error was invalid region `5:157101949-157102375`
[2016-04-15T04:30Z] 2016-04-14 21:30:25 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:30:25,390 - WARNING - Could not retrieve variants from source file in region 5:151229342-151230001. Error was invalid region `5:151229343-151230001`
[2016-04-15T04:30Z] 2016-04-14 21:30:26 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:30:26,523 - WARNING - Could not retrieve variants from source file in region 5:150137826-150138227. Error was invalid region `5:150137827-150138227`
[2016-04-15T04:30Z] 2016-04-14 21:30:26 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:30:26,712 - WARNING - Could not retrieve variants from source file in region 5:150028428-150052148. Error was invalid region `5:150028429-150052148`
[2016-04-15T04:30Z] 2016-04-14 21:30:26 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:30:26,718 - WARNING - Could not retrieve variants from source file in region 5:146435369-146435770. Error was invalid region `5:146435370-146435770`
[2016-04-15T04:30Z] 2016-04-14 21:30:26 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:30:26,743 - WARNING - Could not retrieve variants from source file in region 5:149583089-149602798. Error was invalid region `5:149583090-149602798`
[2016-04-15T04:30Z] 2016-04-14 21:30:27 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:30:27,496 - WARNING - Could not retrieve variants from source file in region 5:158204214-158204615. Error was invalid region `5:158204215-158204615`
[2016-04-15T04:30Z] 2016-04-14 21:30:28 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:30:28,137 - WARNING - Could not retrieve variants from source file in region 5:148386314-148408291. Error was invalid region `5:148386315-148408291`
[2016-04-15T04:30Z] 2016-04-14 21:30:29 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:30:29,170 - WARNING - Could not retrieve variants from source file in region 5:157101948-157102375. Error was invalid region `5:157101949-157102375`
[2016-04-15T04:30Z] 2016-04-14 21:30:30 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:30:30,173 - WARNING - Could not retrieve variants from source file in region 5:147804909-147805310. Error was invalid region `5:147804910-147805310`
[2016-04-15T04:30Z] 2016-04-14 21:30:30 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:30:30,348 - WARNING - Could not retrieve variants from source file in region 5:148877587-148883824. Error was invalid region `5:148877588-148883824`
[2016-04-15T04:30Z] 2016-04-14 21:30:31 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:30:31,178 - WARNING - Could not retrieve variants from source file in region 5:145838424-145839019. Error was invalid region `5:145838425-145839019`
[2016-04-15T04:30Z] 2016-04-14 21:30:33 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:30:33,126 - WARNING - Could not retrieve variants from source file in region 5:146435369-146435770. Error was invalid region `5:146435370-146435770`
[2016-04-15T04:30Z] 2016-04-14 21:30:33 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:30:33,359 - WARNING - Could not retrieve variants from source file in region 5:149583089-149602798. Error was invalid region `5:149583090-149602798`
[2016-04-15T04:30Z] 2016-04-14 21:30:34 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:30:34,805 - WARNING - Could not retrieve variants from source file in region 5:150275576-150275977. Error was invalid region `5:150275577-150275977`
[2016-04-15T04:30Z] 2016-04-14 21:30:35 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:30:35,658 - WARNING - Could not retrieve variants from source file in region 5:148386314-148408291. Error was invalid region `5:148386315-148408291`
[2016-04-15T04:30Z] 2016-04-14 21:30:37 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:30:37,126 - WARNING - Could not retrieve variants from source file in region 5:157101948-157102375. Error was invalid region `5:157101949-157102375`
[2016-04-15T04:30Z] 2016-04-14 21:30:37 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:30:37,318 - WARNING - Could not retrieve variants from source file in region 5:145838424-145839019. Error was invalid region `5:145838425-145839019`
[2016-04-15T04:30Z] 2016-04-14 21:30:37 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:30:37,318 - WARNING - Could not retrieve variants from source file in region 5:148877587-148883824. Error was invalid region `5:148877588-148883824`
[2016-04-15T04:30Z] 2016-04-14 21:30:37 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:30:37,953 - WARNING - Could not retrieve variants from source file in region 5:150137826-150138227. Error was invalid region `5:150137827-150138227`
[2016-04-15T04:30Z] 2016-04-14 21:30:38 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:30:38,078 - WARNING - Could not retrieve variants from source file in region 5:151229342-151230001. Error was invalid region `5:151229343-151230001`
[2016-04-15T04:30Z] 2016-04-14 21:30:38 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:30:38,663 - WARNING - Could not retrieve variants from source file in region 5:150028428-150052148. Error was invalid region `5:150028429-150052148`
[2016-04-15T04:30Z] 2016-04-14 21:30:39 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:30:39,199 - WARNING - Could not retrieve variants from source file in region 5:149583089-149602798. Error was invalid region `5:149583090-149602798`
[2016-04-15T04:30Z] 2016-04-14 21:30:39 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:30:39,285 - WARNING - Could not retrieve variants from source file in region 5:158204214-158204615. Error was invalid region `5:158204215-158204615`
[2016-04-15T04:30Z] 2016-04-14 21:30:41 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:30:41,521 - WARNING - Could not retrieve variants from source file in region 5:148386314-148408291. Error was invalid region `5:148386315-148408291`
[2016-04-15T04:30Z] 2016-04-14 21:30:50 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:30:50,277 - WARNING - Could not retrieve variants from source file in region 5:156721652-156722053. Error was invalid region `5:156721653-156722053`
[2016-04-15T04:30Z] 2016-04-14 21:30:50 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:30:50,295 - WARNING - Could not retrieve variants from source file in region 5:146258079-146258480. Error was invalid region `5:146258080-146258480`
[2016-04-15T04:30Z] 2016-04-14 21:30:55 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:30:55,718 - WARNING - Could not retrieve variants from source file in region 5:148033680-148034230. Error was invalid region `5:148033681-148034230`
[2016-04-15T04:30Z] 2016-04-14 21:30:56 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:30:56,483 - WARNING - Could not retrieve variants from source file in region 5:147593286-147593687. Error was invalid region `5:147593287-147593687`
[2016-04-15T04:30Z] 2016-04-14 21:30:56 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:30:56,675 - WARNING - Could not retrieve variants from source file in region 5:156721652-156722053. Error was invalid region `5:156721653-156722053`
[2016-04-15T04:30Z] 2016-04-14 21:30:57 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:30:57,048 - WARNING - Could not retrieve variants from source file in region 5:149546617-149547018. Error was invalid region `5:149546618-149547018`
[2016-04-15T04:30Z] 2016-04-14 21:30:58 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:30:58,104 - WARNING - Could not retrieve variants from source file in region 5:147475175-147511056. Error was invalid region `5:147475176-147511056`
[2016-04-15T04:30Z] 2016-04-14 21:30:58 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:30:58,357 - WARNING - Could not retrieve variants from source file in region 5:145718554-145718955. Error was invalid region `5:145718555-145718955`
[2016-04-15T04:30Z] 2016-04-14 21:30:58 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:30:58,910 - WARNING - Could not retrieve variants from source file in region 5:156376492-156376893. Error was invalid region `5:156376493-156376893`
[2016-04-15T04:30Z] 2016-04-14 21:30:59 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:30:59,507 - WARNING - Could not retrieve variants from source file in region 5:148737433-148748092. Error was invalid region `5:148737434-148748092`
[2016-04-15T04:31Z] 2016-04-14 21:31:02 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:31:02,752 - WARNING - Could not retrieve variants from source file in region 5:147593286-147593687. Error was invalid region `5:147593287-147593687`
[2016-04-15T04:31Z] 2016-04-14 21:31:02 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:31:02,753 - WARNING - Could not retrieve variants from source file in region 5:149823574-149826716. Error was invalid region `5:149823575-149826716`
[2016-04-15T04:31Z] 2016-04-14 21:31:03 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:31:03,324 - WARNING - Could not retrieve variants from source file in region 5:156721652-156722053. Error was invalid region `5:156721653-156722053`
[2016-04-15T04:31Z] 2016-04-14 21:31:03 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:31:03,331 - WARNING - Could not retrieve variants from source file in region 5:149546617-149547018. Error was invalid region `5:149546618-149547018`
[2016-04-15T04:31Z] 2016-04-14 21:31:03 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:31:03,401 - WARNING - Could not retrieve variants from source file in region 5:147475175-147511056. Error was invalid region `5:147475176-147511056`
[2016-04-15T04:31Z] 2016-04-14 21:31:03 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:31:03,797 - WARNING - Could not retrieve variants from source file in region 5:156376492-156376893. Error was invalid region `5:156376493-156376893`
[2016-04-15T04:31Z] 2016-04-14 21:31:04 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:31:04,100 - WARNING - Could not retrieve variants from source file in region 5:148737433-148748092. Error was invalid region `5:148737434-148748092`
[2016-04-15T04:31Z] 2016-04-14 21:31:08 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:31:08,041 - WARNING - Could not retrieve variants from source file in region 5:156589374-156590545. Error was invalid region `5:156589375-156590545`
[2016-04-15T04:31Z] 2016-04-14 21:31:08 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:31:08,604 - WARNING - Could not retrieve variants from source file in region 5:147593286-147593687. Error was invalid region `5:147593287-147593687`
[2016-04-15T04:31Z] 2016-04-14 21:31:09 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:31:09,894 - WARNING - Could not retrieve variants from source file in region 5:149546617-149547018. Error was invalid region `5:149546618-149547018`
[2016-04-15T04:31Z] 2016-04-14 21:31:10 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:31:10,175 - WARNING - Could not retrieve variants from source file in region 5:147475175-147511056. Error was invalid region `5:147475176-147511056`
[2016-04-15T04:31Z] 2016-04-14 21:31:10 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:31:10,290 - WARNING - Could not retrieve variants from source file in region 5:156376492-156376893. Error was invalid region `5:156376493-156376893`
[2016-04-15T04:31Z] 2016-04-14 21:31:10 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:31:10,292 - WARNING - Could not retrieve variants from source file in region 5:149823574-149826716. Error was invalid region `5:149823575-149826716`
[2016-04-15T04:31Z] 2016-04-14 21:31:11 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:31:11,873 - WARNING - Could not retrieve variants from source file in region 5:145439436-145442393. Error was invalid region `5:145439437-145442393`
[2016-04-15T04:31Z] 2016-04-14 21:31:12 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:31:12,129 - WARNING - Could not retrieve variants from source file in region 5:150696236-150696730. Error was invalid region `5:150696237-150696730`
[2016-04-15T04:31Z] 2016-04-14 21:31:17 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:31:17,443 - WARNING - Could not retrieve variants from source file in region 5:145439436-145442393. Error was invalid region `5:145439437-145442393`
[2016-04-15T04:31Z] 2016-04-14 21:31:19 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:31:19,327 - WARNING - Could not retrieve variants from source file in region 5:149764027-149776545. Error was invalid region `5:149764028-149776545`
[2016-04-15T04:31Z] 2016-04-14 21:31:21 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:31:21,071 - WARNING - Could not retrieve variants from source file in region 5:145483492-145508488. Error was invalid region `5:145483493-145508488`
[2016-04-15T04:31Z] 2016-04-14 21:31:21 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:31:21,976 - WARNING - Could not retrieve variants from source file in region 5:150723595-150723996. Error was invalid region `5:150723596-150723996`
[2016-04-15T04:31Z] 2016-04-14 21:31:22 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:31:22,520 - WARNING - Could not retrieve variants from source file in region 5:150578363-150578764. Error was invalid region `5:150578364-150578764`
[2016-04-15T04:31Z] 2016-04-14 21:31:22 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:31:22,713 - WARNING - Could not retrieve variants from source file in region 5:149449921-149450322. Error was invalid region `5:149449922-149450322`
[2016-04-15T04:31Z] 2016-04-14 21:31:22 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:31:22,771 - WARNING - Could not retrieve variants from source file in region 5:155771368-155771769. Error was invalid region `5:155771369-155771769`
[2016-04-15T04:31Z] 2016-04-14 21:31:22 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:31:22,779 - WARNING - Could not retrieve variants from source file in region 5:154394947-154396695. Error was invalid region `5:154394948-154396695`
[2016-04-15T04:31Z] 2016-04-14 21:31:23 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:31:23,145 - WARNING - Could not retrieve variants from source file in region 5:145439436-145442393. Error was invalid region `5:145439437-145442393`
[2016-04-15T04:31Z] 2016-04-14 21:31:24 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:31:24,097 - WARNING - Could not retrieve variants from source file in region 5:149764027-149776545. Error was invalid region `5:149764028-149776545`
[2016-04-15T04:31Z] 2016-04-14 21:31:24 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:31:24,254 - WARNING - Could not retrieve variants from source file in region 5:149495184-149499862. Error was invalid region `5:149495185-149499862`
[2016-04-15T04:31Z] 2016-04-14 21:31:25 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:31:25,699 - WARNING - Could not retrieve variants from source file in region 5:145245874-145252567. Error was invalid region `5:145245875-145252567`
[2016-04-15T04:31Z] 2016-04-14 21:31:27 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:31:27,184 - WARNING - Could not retrieve variants from source file in region 5:150723595-150723996. Error was invalid region `5:150723596-150723996`
[2016-04-15T04:31Z] 2016-04-14 21:31:27 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:31:27,321 - WARNING - Could not retrieve variants from source file in region 5:155771368-155771769. Error was invalid region `5:155771369-155771769`
[2016-04-15T04:31Z] 2016-04-14 21:31:27 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:31:27,560 - WARNING - Could not retrieve variants from source file in region 5:149449921-149450322. Error was invalid region `5:149449922-149450322`
[2016-04-15T04:31Z] 2016-04-14 21:31:29 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:31:29,666 - WARNING - Could not retrieve variants from source file in region 5:143538455-143539975. Error was invalid region `5:143538456-143539975`
[2016-04-15T04:31Z] 2016-04-14 21:31:30 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:31:30,177 - WARNING - Could not retrieve variants from source file in region 5:145245874-145252567. Error was invalid region `5:145245875-145252567`
[2016-04-15T04:31Z] 2016-04-14 21:31:31 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:31:31,556 - WARNING - Could not retrieve variants from source file in region 5:150578363-150578764. Error was invalid region `5:150578364-150578764`
[2016-04-15T04:31Z] 2016-04-14 21:31:32 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:31:32,021 - WARNING - Could not retrieve variants from source file in region 5:154394947-154396695. Error was invalid region `5:154394948-154396695`
[2016-04-15T04:31Z] 2016-04-14 21:31:32 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:31:32,270 - WARNING - Could not retrieve variants from source file in region 5:149449921-149450322. Error was invalid region `5:149449922-149450322`
[2016-04-15T04:31Z] 2016-04-14 21:31:36 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:31:36,198 - WARNING - Could not retrieve variants from source file in region 5:145393153-145393554. Error was invalid region `5:145393154-145393554`
[2016-04-15T04:31Z] 2016-04-14 21:31:36 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:31:36,301 - WARNING - Could not retrieve variants from source file in region 5:150639198-150667206. Error was invalid region `5:150639199-150667206`
[2016-04-15T04:31Z] 2016-04-14 21:31:37 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:31:37,250 - WARNING - Could not retrieve variants from source file in region 5:150489179-150489580. Error was invalid region `5:150489180-150489580`
[2016-04-15T04:31Z] 2016-04-14 21:31:39 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:31:39,421 - WARNING - Could not retrieve variants from source file in region 5:150489179-150489580. Error was invalid region `5:150489180-150489580`
[2016-04-15T04:31Z] 2016-04-14 21:31:40 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:31:40,320 - WARNING - Could not retrieve variants from source file in region 5:145393153-145393554. Error was invalid region `5:145393154-145393554`
[2016-04-15T04:31Z] 2016-04-14 21:31:41 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:31:41,954 - WARNING - Could not retrieve variants from source file in region 5:150489179-150489580. Error was invalid region `5:150489180-150489580`
[2016-04-15T04:31Z] 2016-04-14 21:31:44 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:31:44,501 - WARNING - Could not retrieve variants from source file in region 5:145393153-145393554. Error was invalid region `5:145393154-145393554`
[2016-04-15T04:31Z] 2016-04-14 21:31:44 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:31:44,742 - WARNING - Could not retrieve variants from source file in region 5:154135175-154136206. Error was invalid region `5:154135176-154136206`
[2016-04-15T04:31Z] 2016-04-14 21:31:44 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:31:44,853 - WARNING - Could not retrieve variants from source file in region 5:154268691-154307162. Error was invalid region `5:154268692-154307162`
[2016-04-15T04:31Z] 2016-04-14 21:31:44 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:31:44,891 - WARNING - Could not retrieve variants from source file in region 5:149323561-149324096. Error was invalid region `5:149323562-149324096`
[2016-04-15T04:31Z] 2016-04-14 21:31:45 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:31:45,114 - WARNING - Could not retrieve variants from source file in region 5:149360666-149421692. Error was invalid region `5:149360667-149421692`
[2016-04-15T04:31Z] 2016-04-14 21:31:45 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:31:45,552 - WARNING - Could not retrieve variants from source file in region 5:154268691-154307162. Error was invalid region `5:154268692-154307162`
[2016-04-15T04:31Z] 2016-04-14 21:31:48 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:31:48,441 - WARNING - Could not retrieve variants from source file in region 5:154268691-154307162. Error was invalid region `5:154268692-154307162`
[2016-04-15T04:31Z] 2016-04-14 21:31:49 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:31:49,198 - WARNING - Could not retrieve variants from source file in region 5:149323561-149324096. Error was invalid region `5:149323562-149324096`
[2016-04-15T04:31Z] 2016-04-14 21:31:49 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:31:49,200 - WARNING - Could not retrieve variants from source file in region 5:154135175-154136206. Error was invalid region `5:154135176-154136206`
[2016-04-15T04:31Z] 2016-04-14 21:31:52 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:31:52,476 - WARNING - Could not retrieve variants from source file in region 5:153413179-153433160. Error was invalid region `5:153413180-153433160`
[2016-04-15T04:31Z] 2016-04-14 21:31:52 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:31:52,525 - WARNING - Could not retrieve variants from source file in region 5:153413179-153433160. Error was invalid region `5:153413180-153433160`
[2016-04-15T04:31Z] 2016-04-14 21:31:52 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:31:52,527 - WARNING - Could not retrieve variants from source file in region 5:153413179-153433160. Error was invalid region `5:153413180-153433160`
[2016-04-15T04:31Z] 2016-04-14 21:31:52 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:31:52,790 - WARNING - Could not retrieve variants from source file in region 5:149199832-149212990. Error was invalid region `5:149199833-149212990`
[2016-04-15T04:31Z] 2016-04-14 21:31:52 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:31:52,797 - WARNING - Could not retrieve variants from source file in region 5:149199832-149212990. Error was invalid region `5:149199833-149212990`
[2016-04-15T04:31Z] 2016-04-14 21:31:52 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:31:52,798 - WARNING - Could not retrieve variants from source file in region 5:149199832-149212990. Error was invalid region `5:149199833-149212990`
[2016-04-15T04:31Z] 2016-04-14 21:31:53 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:31:53,147 - WARNING - Could not retrieve variants from source file in region 5:153029749-153030150. Error was invalid region `5:153029750-153030150`
[2016-04-15T04:32Z] ['bcbio-variation-recall', 'square', '-Xms750m', '-Xmx7280m', '-XX:+UseSerialGC', '-c', 16, '-r', u'5:158711912-174870102', '--caller', 'platypus', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/5/Batch1-5_158711911_174870102.vcf.gz', '/mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/5/Batch1-5_158711911_174870102.vcf-inputs.txt'] in region: 5:158711912-174870102
[2016-04-15T04:32Z] 2016-04-14 21:32:09 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:32:09,289 - WARNING - Could not retrieve variants from source file in region 5:174868629-174869030. Error was invalid region `5:174868630-174869030`
[2016-04-15T04:32Z] 2016-04-14 21:32:11 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:32:11,399 - WARNING - Could not retrieve variants from source file in region 5:169931033-169931434. Error was invalid region `5:169931034-169931434`
[2016-04-15T04:32Z] 2016-04-14 21:32:11 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:32:11,436 - WARNING - Could not retrieve variants from source file in region 5:169533029-169535712. Error was invalid region `5:169533030-169535712`
[2016-04-15T04:32Z] 2016-04-14 21:32:11 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:32:11,872 - WARNING - Could not retrieve variants from source file in region 5:159659031-159659463. Error was invalid region `5:159659032-159659463`
[2016-04-15T04:32Z] 2016-04-14 21:32:11 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:32:11,924 - WARNING - Could not retrieve variants from source file in region 5:169310002-169310403. Error was invalid region `5:169310003-169310403`
[2016-04-15T04:32Z] 2016-04-14 21:32:12 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:32:12,146 - WARNING - Could not retrieve variants from source file in region 5:167488882-167489283. Error was invalid region `5:167488883-167489283`
[2016-04-15T04:32Z] 2016-04-14 21:32:12 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:32:12,328 - WARNING - Could not retrieve variants from source file in region 5:161118860-161128951. Error was invalid region `5:161118861-161128951`
[2016-04-15T04:32Z] 2016-04-14 21:32:12 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:32:12,943 - WARNING - Could not retrieve variants from source file in region 5:171481395-171481796. Error was invalid region `5:171481396-171481796`
[2016-04-15T04:32Z] 2016-04-14 21:32:12 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:32:12,994 - WARNING - Could not retrieve variants from source file in region 5:172196500-172196901. Error was invalid region `5:172196501-172196901`
[2016-04-15T04:32Z] 2016-04-14 21:32:13 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:32:13,334 - WARNING - Could not retrieve variants from source file in region 5:169021399-169031340. Error was invalid region `5:169021400-169031340`
[2016-04-15T04:32Z] 2016-04-14 21:32:13 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:32:13,516 - WARNING - Could not retrieve variants from source file in region 5:169661783-169695636. Error was invalid region `5:169661784-169695636`
[2016-04-15T04:32Z] 2016-04-14 21:32:14 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:32:14,893 - WARNING - Could not retrieve variants from source file in region 5:174868629-174869030. Error was invalid region `5:174868630-174869030`
[2016-04-15T04:32Z] 2016-04-14 21:32:15 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:32:15,821 - WARNING - Could not retrieve variants from source file in region 5:169435502-169461737. Error was invalid region `5:169435503-169461737`
[2016-04-15T04:32Z] 2016-04-14 21:32:19 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:32:19,018 - WARNING - Could not retrieve variants from source file in region 5:169931033-169931434. Error was invalid region `5:169931034-169931434`
[2016-04-15T04:32Z] 2016-04-14 21:32:20 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:32:20,848 - WARNING - Could not retrieve variants from source file in region 5:172196500-172196901. Error was invalid region `5:172196501-172196901`
[2016-04-15T04:32Z] 2016-04-14 21:32:21 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:32:21,118 - WARNING - Could not retrieve variants from source file in region 5:171481395-171481796. Error was invalid region `5:171481396-171481796`
[2016-04-15T04:32Z] 2016-04-14 21:32:21 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:32:21,357 - WARNING - Could not retrieve variants from source file in region 5:169021399-169031340. Error was invalid region `5:169021400-169031340`
[2016-04-15T04:32Z] 2016-04-14 21:32:21 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:32:21,381 - WARNING - Could not retrieve variants from source file in region 5:161118860-161128951. Error was invalid region `5:161118861-161128951`
[2016-04-15T04:32Z] 2016-04-14 21:32:21 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:32:21,875 - WARNING - Could not retrieve variants from source file in region 5:168175113-168180271. Error was invalid region `5:168175114-168180271`
[2016-04-15T04:32Z] 2016-04-14 21:32:21 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:32:21,892 - WARNING - Could not retrieve variants from source file in region 5:169267573-169268688. Error was invalid region `5:169267574-169268688`
[2016-04-15T04:32Z] 2016-04-14 21:32:22 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:32:22,022 - WARNING - Could not retrieve variants from source file in region 5:174868629-174869030. Error was invalid region `5:174868630-174869030`
[2016-04-15T04:32Z] 2016-04-14 21:32:22 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:32:22,331 - WARNING - Could not retrieve variants from source file in region 5:169435502-169461737. Error was invalid region `5:169435503-169461737`
[2016-04-15T04:32Z] 2016-04-14 21:32:23 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:32:23,813 - WARNING - Could not retrieve variants from source file in region 5:169533029-169535712. Error was invalid region `5:169533030-169535712`
[2016-04-15T04:32Z] 2016-04-14 21:32:24 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:32:24,654 - WARNING - Could not retrieve variants from source file in region 5:169126886-169129612. Error was invalid region `5:169126887-169129612`
[2016-04-15T04:32Z] 2016-04-14 21:32:24 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:32:24,728 - WARNING - Could not retrieve variants from source file in region 5:169931033-169931434. Error was invalid region `5:169931034-169931434`
[2016-04-15T04:32Z] 2016-04-14 21:32:26 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:32:26,192 - WARNING - Could not retrieve variants from source file in region 5:169310002-169310403. Error was invalid region `5:169310003-169310403`
[2016-04-15T04:32Z] 2016-04-14 21:32:27 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:32:27,505 - WARNING - Could not retrieve variants from source file in region 5:172196500-172196901. Error was invalid region `5:172196501-172196901`
[2016-04-15T04:32Z] 2016-04-14 21:32:29 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:32:29,204 - WARNING - Could not retrieve variants from source file in region 5:169267573-169268688. Error was invalid region `5:169267574-169268688`
[2016-04-15T04:32Z] 2016-04-14 21:32:29 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:32:29,408 - WARNING - Could not retrieve variants from source file in region 5:169661783-169695636. Error was invalid region `5:169661784-169695636`
[2016-04-15T04:32Z] 2016-04-14 21:32:38 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:32:38,591 - WARNING - Could not retrieve variants from source file in region 5:174155957-174156358. Error was invalid region `5:174155958-174156358`
[2016-04-15T04:32Z] 2016-04-14 21:32:39 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:32:39,156 - WARNING - Could not retrieve variants from source file in region 5:173416297-173416698. Error was invalid region `5:173416298-173416698`
[2016-04-15T04:32Z] 2016-04-14 21:32:40 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:32:40,985 - WARNING - Could not retrieve variants from source file in region 5:168212740-168233664. Error was invalid region `5:168212741-168233664`
[2016-04-15T04:32Z] 2016-04-14 21:32:41 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:32:41,842 - WARNING - Could not retrieve variants from source file in region 5:167181844-167182245. Error was invalid region `5:167181845-167182245`
[2016-04-15T04:32Z] 2016-04-14 21:32:42 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:32:42,469 - WARNING - Could not retrieve variants from source file in region 5:159545802-159546203. Error was invalid region `5:159545803-159546203`
[2016-04-15T04:32Z] 2016-04-14 21:32:43 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:32:43,406 - WARNING - Could not retrieve variants from source file in region 5:174155957-174156358. Error was invalid region `5:174155958-174156358`
[2016-04-15T04:32Z] 2016-04-14 21:32:43 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:32:43,776 - WARNING - Could not retrieve variants from source file in region 5:170626524-170626925. Error was invalid region `5:170626525-170626925`
[2016-04-15T04:32Z] 2016-04-14 21:32:44 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:32:44,516 - WARNING - Could not retrieve variants from source file in region 5:160143729-160144130. Error was invalid region `5:160143730-160144130`
[2016-04-15T04:32Z] 2016-04-14 21:32:44 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:32:44,731 - WARNING - Could not retrieve variants from source file in region 5:167674159-167689418. Error was invalid region `5:167674160-167689418`
[2016-04-15T04:32Z] 2016-04-14 21:32:44 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:32:44,968 - WARNING - Could not retrieve variants from source file in region 5:168212740-168233664. Error was invalid region `5:168212741-168233664`
[2016-04-15T04:32Z] 2016-04-14 21:32:45 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:32:45,122 - WARNING - Could not retrieve variants from source file in region 5:167645677-167646078. Error was invalid region `5:167645678-167646078`
[2016-04-15T04:32Z] 2016-04-14 21:32:46 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:32:46,088 - WARNING - Could not retrieve variants from source file in region 5:167181844-167182245. Error was invalid region `5:167181845-167182245`
[2016-04-15T04:32Z] 2016-04-14 21:32:46 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:32:46,492 - WARNING - Could not retrieve variants from source file in region 5:172113024-172113425. Error was invalid region `5:172113025-172113425`
[2016-04-15T04:32Z] 2016-04-14 21:32:47 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:32:47,799 - WARNING - Could not retrieve variants from source file in region 5:174155957-174156358. Error was invalid region `5:174155958-174156358`
[2016-04-15T04:32Z] 2016-04-14 21:32:48 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:32:48,567 - WARNING - Could not retrieve variants from source file in region 5:160143729-160144130. Error was invalid region `5:160143730-160144130`
[2016-04-15T04:32Z] 2016-04-14 21:32:49 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:32:49,448 - WARNING - Could not retrieve variants from source file in region 5:168098024-168098653. Error was invalid region `5:168098025-168098653`
[2016-04-15T04:32Z] 2016-04-14 21:32:50 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:32:50,548 - WARNING - Could not retrieve variants from source file in region 5:167181844-167182245. Error was invalid region `5:167181845-167182245`
[2016-04-15T04:32Z] 2016-04-14 21:32:50 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:32:50,736 - WARNING - Could not retrieve variants from source file in region 5:172113024-172113425. Error was invalid region `5:172113025-172113425`
[2016-04-15T04:32Z] 2016-04-14 21:32:53 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:32:53,472 - WARNING - Could not retrieve variants from source file in region 5:167645677-167646078. Error was invalid region `5:167645678-167646078`
[2016-04-15T04:32Z] 2016-04-14 21:32:53 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:32:53,590 - WARNING - Could not retrieve variants from source file in region 5:160143729-160144130. Error was invalid region `5:160143730-160144130`
[2016-04-15T04:32Z] 2016-04-14 21:32:53 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:32:53,721 - WARNING - Could not retrieve variants from source file in region 5:167674159-167689418. Error was invalid region `5:167674160-167689418`
[2016-04-15T04:32Z] 2016-04-14 21:32:53 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:32:53,810 - WARNING - Could not retrieve variants from source file in region 5:168098024-168098653. Error was invalid region `5:168098025-168098653`
[2016-04-15T04:32Z] 2016-04-14 21:32:58 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:32:58,586 - WARNING - Could not retrieve variants from source file in region 5:159374504-159374905. Error was invalid region `5:159374505-159374905`
[2016-04-15T04:32Z] 2016-04-14 21:32:59 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:32:59,701 - WARNING - Could not retrieve variants from source file in region 5:172752696-172753097. Error was invalid region `5:172752697-172753097`
[2016-04-15T04:33Z] 2016-04-14 21:33:00 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:33:00,809 - WARNING - Could not retrieve variants from source file in region 5:172661813-172662214. Error was invalid region `5:172661814-172662214`
[2016-04-15T04:33Z] 2016-04-14 21:33:04 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:33:04,820 - WARNING - Could not retrieve variants from source file in region 5:162890742-162909906. Error was invalid region `5:162890743-162909906`
[2016-04-15T04:33Z] 2016-04-14 21:33:05 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:33:05,698 - WARNING - Could not retrieve variants from source file in region 5:171849260-171849661. Error was invalid region `5:171849261-171849661`
[2016-04-15T04:33Z] 2016-04-14 21:33:06 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:33:06,076 - WARNING - Could not retrieve variants from source file in region 5:159344250-159344651. Error was invalid region `5:159344251-159344651`
[2016-04-15T04:33Z] 2016-04-14 21:33:06 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:33:06,174 - WARNING - Could not retrieve variants from source file in region 5:172661813-172662214. Error was invalid region `5:172661814-172662214`
[2016-04-15T04:33Z] 2016-04-14 21:33:07 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:33:07,175 - WARNING - Could not retrieve variants from source file in region 5:171660955-171661356. Error was invalid region `5:171660956-171661356`
[2016-04-15T04:33Z] 2016-04-14 21:33:07 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:33:07,706 - WARNING - Could not retrieve variants from source file in region 5:160097285-160097822. Error was invalid region `5:160097286-160097822`
[2016-04-15T04:33Z] 2016-04-14 21:33:09 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:33:09,233 - WARNING - Could not retrieve variants from source file in region 5:162940788-162941189. Error was invalid region `5:162940789-162941189`
[2016-04-15T04:33Z] 2016-04-14 21:33:10 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:33:10,165 - WARNING - Could not retrieve variants from source file in region 5:162890742-162909906. Error was invalid region `5:162890743-162909906`
[2016-04-15T04:33Z] 2016-04-14 21:33:11 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:33:11,165 - WARNING - Could not retrieve variants from source file in region 5:159517491-159519226. Error was invalid region `5:159517492-159519226`
[2016-04-15T04:33Z] 2016-04-14 21:33:11 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:33:11,453 - WARNING - Could not retrieve variants from source file in region 5:158750118-158750519. Error was invalid region `5:158750119-158750519`
[2016-04-15T04:33Z] 2016-04-14 21:33:11 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:33:11,770 - WARNING - Could not retrieve variants from source file in region 5:159344250-159344651. Error was invalid region `5:159344251-159344651`
[2016-04-15T04:33Z] 2016-04-14 21:33:12 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:33:12,224 - WARNING - Could not retrieve variants from source file in region 5:160097285-160097822. Error was invalid region `5:160097286-160097822`
[2016-04-15T04:33Z] 2016-04-14 21:33:13 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:33:13,562 - WARNING - Could not retrieve variants from source file in region 5:162940788-162941189. Error was invalid region `5:162940789-162941189`
[2016-04-15T04:33Z] 2016-04-14 21:33:16 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:33:16,026 - WARNING - Could not retrieve variants from source file in region 5:161528069-161528470. Error was invalid region `5:161528070-161528470`
[2016-04-15T04:33Z] 2016-04-14 21:33:17 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:33:17,526 - WARNING - Could not retrieve variants from source file in region 5:160097285-160097822. Error was invalid region `5:160097286-160097822`
[2016-04-15T04:33Z] 2016-04-14 21:33:19 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:33:19,142 - WARNING - Could not retrieve variants from source file in region 5:171533418-171533972. Error was invalid region `5:171533419-171533972`
[2016-04-15T04:33Z] 2016-04-14 21:33:20 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:33:20,709 - WARNING - Could not retrieve variants from source file in region 5:161528069-161528470. Error was invalid region `5:161528070-161528470`
[2016-04-15T04:33Z] 2016-04-14 21:33:21 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:33:21,910 - WARNING - Could not retrieve variants from source file in region 5:161281034-161281435. Error was invalid region `5:161281035-161281435`
[2016-04-15T04:33Z] 2016-04-14 21:33:23 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:33:23,100 - WARNING - Could not retrieve variants from source file in region 5:171533418-171533972. Error was invalid region `5:171533419-171533972`
[2016-04-15T04:33Z] 2016-04-14 21:33:24 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:33:24,641 - WARNING - Could not retrieve variants from source file in region 5:159992444-159992944. Error was invalid region `5:159992445-159992944`
[2016-04-15T04:33Z] 2016-04-14 21:33:24 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:33:24,948 - WARNING - Could not retrieve variants from source file in region 5:159992444-159992944. Error was invalid region `5:159992445-159992944`
[2016-04-15T04:33Z] 2016-04-14 21:33:27 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:33:27,918 - WARNING - Could not retrieve variants from source file in region 5:159835447-159835848. Error was invalid region `5:159835448-159835848`
[2016-04-15T04:33Z] 2016-04-14 21:33:28 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:33:28,394 - WARNING - Could not retrieve variants from source file in region 5:159835447-159835848. Error was invalid region `5:159835448-159835848`
[2016-04-15T04:33Z] 2016-04-14 21:33:28 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:33:28,394 - WARNING - Could not retrieve variants from source file in region 5:159835447-159835848. Error was invalid region `5:159835448-159835848`
[2016-04-15T04:33Z] 2016-04-14 21:33:29 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:33:29,710 - WARNING - Could not retrieve variants from source file in region 5:159686292-159686693. Error was invalid region `5:159686293-159686693`
[2016-04-15T04:33Z] 2016-04-14 21:33:29 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:33:29,714 - WARNING - Could not retrieve variants from source file in region 5:159686292-159686693. Error was invalid region `5:159686293-159686693`
[2016-04-15T04:33Z] ['bcbio-variation-recall', 'square', '-Xms750m', '-Xmx7280m', '-XX:+UseSerialGC', '-c', 16, '-r', u'5:174919107-180915260', '--caller', 'platypus', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/5/Batch1-5_174919106_180915260.vcf.gz', '/mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/5/Batch1-5_174919106_180915260.vcf-inputs.txt'] in region: 5:174919107-180915260
[2016-04-15T04:33Z] 2016-04-14 21:33:44 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:33:44,876 - WARNING - Could not retrieve variants from source file in region 5:180582393-180582794. Error was invalid region `5:180582394-180582794`
[2016-04-15T04:33Z] 2016-04-14 21:33:45 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:33:45,999 - WARNING - Could not retrieve variants from source file in region 5:180165930-180166651. Error was invalid region `5:180165931-180166651`
[2016-04-15T04:33Z] 2016-04-14 21:33:46 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:33:46,895 - WARNING - Could not retrieve variants from source file in region 5:180472287-180487031. Error was invalid region `5:180472288-180487031`
[2016-04-15T04:33Z] 2016-04-14 21:33:46 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:33:46,899 - WARNING - Could not retrieve variants from source file in region 5:180432205-180432606. Error was invalid region `5:180432206-180432606`
[2016-04-15T04:33Z] 2016-04-14 21:33:47 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:33:47,015 - WARNING - Could not retrieve variants from source file in region 5:176863308-176951466. Error was invalid region `5:176863309-176951466`
[2016-04-15T04:33Z] 2016-04-14 21:33:47 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:33:47,388 - WARNING - Could not retrieve variants from source file in region 5:179995900-179996301. Error was invalid region `5:179995901-179996301`
[2016-04-15T04:33Z] 2016-04-14 21:33:47 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:33:47,409 - WARNING - Could not retrieve variants from source file in region 5:177419756-177423098. Error was invalid region `5:177419757-177423098`
[2016-04-15T04:33Z] 2016-04-14 21:33:47 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:33:47,870 - WARNING - Could not retrieve variants from source file in region 5:180218457-180218858. Error was invalid region `5:180218458-180218858`
[2016-04-15T04:33Z] 2016-04-14 21:33:48 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:33:48,047 - WARNING - Could not retrieve variants from source file in region 5:179528913-179529314. Error was invalid region `5:179528914-179529314`
[2016-04-15T04:33Z] 2016-04-14 21:33:51 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:33:51,490 - WARNING - Could not retrieve variants from source file in region 5:180582393-180582794. Error was invalid region `5:180582394-180582794`
[2016-04-15T04:33Z] 2016-04-14 21:33:53 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:33:53,497 - WARNING - Could not retrieve variants from source file in region 5:178506858-178507280. Error was invalid region `5:178506859-178507280`
[2016-04-15T04:33Z] 2016-04-14 21:33:56 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:33:56,266 - WARNING - Could not retrieve variants from source file in region 5:178049233-178049634. Error was invalid region `5:178049234-178049634`
[2016-04-15T04:33Z] 2016-04-14 21:33:56 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:33:56,283 - WARNING - Could not retrieve variants from source file in region 5:177419756-177423098. Error was invalid region `5:177419757-177423098`
[2016-04-15T04:33Z] 2016-04-14 21:33:56 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:33:56,294 - WARNING - Could not retrieve variants from source file in region 5:179995900-179996301. Error was invalid region `5:179995901-179996301`
[2016-04-15T04:33Z] 2016-04-14 21:33:57 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:33:57,047 - WARNING - Could not retrieve variants from source file in region 5:180218457-180218858. Error was invalid region `5:180218458-180218858`
[2016-04-15T04:33Z] 2016-04-14 21:33:57 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:33:57,118 - WARNING - Could not retrieve variants from source file in region 5:178293848-178310636. Error was invalid region `5:178293849-178310636`
[2016-04-15T04:33Z] 2016-04-14 21:33:57 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:33:57,164 - WARNING - Could not retrieve variants from source file in region 5:180582393-180582794. Error was invalid region `5:180582394-180582794`
[2016-04-15T04:33Z] 2016-04-14 21:33:58 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:33:58,351 - WARNING - Could not retrieve variants from source file in region 5:178506858-178507280. Error was invalid region `5:178506859-178507280`
[2016-04-15T04:34Z] 2016-04-14 21:34:03 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:34:03,061 - WARNING - Could not retrieve variants from source file in region 5:179729308-179741017. Error was invalid region `5:179729309-179741017`
[2016-04-15T04:34Z] 2016-04-14 21:34:05 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:34:05,095 - WARNING - Could not retrieve variants from source file in region 5:179995900-179996301. Error was invalid region `5:179995901-179996301`
[2016-04-15T04:34Z] 2016-04-14 21:34:05 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:34:05,518 - WARNING - Could not retrieve variants from source file in region 5:177419756-177423098. Error was invalid region `5:177419757-177423098`
[2016-04-15T04:34Z] 2016-04-14 21:34:05 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:34:05,918 - WARNING - Could not retrieve variants from source file in region 5:179528913-179529314. Error was invalid region `5:179528914-179529314`
[2016-04-15T04:34Z] 2016-04-14 21:34:06 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:34:06,331 - WARNING - Could not retrieve variants from source file in region 5:178293848-178310636. Error was invalid region `5:178293849-178310636`
[2016-04-15T04:34Z] 2016-04-14 21:34:06 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:34:06,461 - WARNING - Could not retrieve variants from source file in region 5:180218457-180218858. Error was invalid region `5:180218458-180218858`
[2016-04-15T04:34Z] 2016-04-14 21:34:18 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:34:18,531 - WARNING - Could not retrieve variants from source file in region 5:180043177-180043578. Error was invalid region `5:180043178-180043578`
[2016-04-15T04:34Z] 2016-04-14 21:34:19 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:34:19,874 - WARNING - Could not retrieve variants from source file in region 5:179563224-179563625. Error was invalid region `5:179563225-179563625`
[2016-04-15T04:34Z] 2016-04-14 21:34:21 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:34:21,196 - WARNING - Could not retrieve variants from source file in region 5:180043177-180043578. Error was invalid region `5:180043178-180043578`
[2016-04-15T04:34Z] 2016-04-14 21:34:21 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:34:21,375 - WARNING - Could not retrieve variants from source file in region 5:177161680-177164234. Error was invalid region `5:177161681-177164234`
[2016-04-15T04:34Z] 2016-04-14 21:34:22 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:34:22,496 - WARNING - Could not retrieve variants from source file in region 5:179498384-179498848. Error was invalid region `5:179498385-179498848`
[2016-04-15T04:34Z] 2016-04-14 21:34:22 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:34:22,923 - WARNING - Could not retrieve variants from source file in region 5:178139231-178140280. Error was invalid region `5:178139232-178140280`
[2016-04-15T04:34Z] 2016-04-14 21:34:22 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:34:22,955 - WARNING - Could not retrieve variants from source file in region 5:180276191-180278583. Error was invalid region `5:180276192-180278583`
[2016-04-15T04:34Z] 2016-04-14 21:34:23 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:34:23,096 - WARNING - Could not retrieve variants from source file in region 5:176514384-176518974. Error was invalid region `5:176514385-176518974`
[2016-04-15T04:34Z] 2016-04-14 21:34:23 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:34:23,816 - WARNING - Could not retrieve variants from source file in region 5:179563224-179563625. Error was invalid region `5:179563225-179563625`
[2016-04-15T04:34Z] 2016-04-14 21:34:24 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:34:24,932 - WARNING - Could not retrieve variants from source file in region 5:177658672-177684095. Error was invalid region `5:177658673-177684095`
[2016-04-15T04:34Z] 2016-04-14 21:34:26 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:34:26,745 - WARNING - Could not retrieve variants from source file in region 5:176813035-176832016. Error was invalid region `5:176813036-176832016`
[2016-04-15T04:34Z] 2016-04-14 21:34:27 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:34:27,049 - WARNING - Could not retrieve variants from source file in region 5:176514384-176518974. Error was invalid region `5:176514385-176518974`
[2016-04-15T04:34Z] 2016-04-14 21:34:27 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:34:27,592 - WARNING - Could not retrieve variants from source file in region 5:179563224-179563625. Error was invalid region `5:179563225-179563625`
[2016-04-15T04:34Z] 2016-04-14 21:34:28 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:34:28,914 - WARNING - Could not retrieve variants from source file in region 5:177161680-177164234. Error was invalid region `5:177161681-177164234`
[2016-04-15T04:34Z] 2016-04-14 21:34:30 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:34:30,337 - WARNING - Could not retrieve variants from source file in region 5:179498384-179498848. Error was invalid region `5:179498385-179498848`
[2016-04-15T04:34Z] 2016-04-14 21:34:30 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:34:30,620 - WARNING - Could not retrieve variants from source file in region 5:176813035-176832016. Error was invalid region `5:176813036-176832016`
[2016-04-15T04:34Z] 2016-04-14 21:34:31 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:34:31,127 - WARNING - Could not retrieve variants from source file in region 5:176514384-176518974. Error was invalid region `5:176514385-176518974`
[2016-04-15T04:34Z] 2016-04-14 21:34:32 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:34:32,138 - WARNING - Could not retrieve variants from source file in region 5:175717005-175717406. Error was invalid region `5:175717006-175717406`
[2016-04-15T04:34Z] 2016-04-14 21:34:39 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:34:39,204 - WARNING - Could not retrieve variants from source file in region 5:175533374-175533775. Error was invalid region `5:175533375-175533775`
[2016-04-15T04:34Z] 2016-04-14 21:34:39 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:34:39,741 - WARNING - Could not retrieve variants from source file in region 5:179259942-179291035. Error was invalid region `5:179259943-179291035`
[2016-04-15T04:34Z] 2016-04-14 21:34:42 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:34:42,355 - WARNING - Could not retrieve variants from source file in region 5:175998035-176026337. Error was invalid region `5:175998036-176026337`
[2016-04-15T04:34Z] 2016-04-14 21:34:43 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:34:43,069 - WARNING - Could not retrieve variants from source file in region 5:176720987-176740473. Error was invalid region `5:176720988-176740473`
[2016-04-15T04:34Z] 2016-04-14 21:34:43 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:34:43,328 - WARNING - Could not retrieve variants from source file in region 5:176378363-176402591. Error was invalid region `5:176378364-176402591`
[2016-04-15T04:34Z] 2016-04-14 21:34:43 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:34:43,785 - WARNING - Could not retrieve variants from source file in region 5:175533374-175533775. Error was invalid region `5:175533375-175533775`
[2016-04-15T04:34Z] 2016-04-14 21:34:43 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:34:43,826 - WARNING - Could not retrieve variants from source file in region 5:174936982-174937383. Error was invalid region `5:174936983-174937383`
[2016-04-15T04:34Z] 2016-04-14 21:34:44 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:34:44,517 - WARNING - Could not retrieve variants from source file in region 5:179259942-179291035. Error was invalid region `5:179259943-179291035`
[2016-04-15T04:34Z] 2016-04-14 21:34:44 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:34:44,709 - WARNING - Could not retrieve variants from source file in region 5:176314248-176316749. Error was invalid region `5:176314249-176316749`
[2016-04-15T04:34Z] 2016-04-14 21:34:46 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:34:46,314 - WARNING - Could not retrieve variants from source file in region 5:177029625-177036154. Error was invalid region `5:177029626-177036154`
[2016-04-15T04:34Z] 2016-04-14 21:34:47 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:34:47,589 - WARNING - Could not retrieve variants from source file in region 5:176720987-176740473. Error was invalid region `5:176720988-176740473`
[2016-04-15T04:34Z] 2016-04-14 21:34:48 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:34:48,874 - WARNING - Could not retrieve variants from source file in region 5:179125187-179126280. Error was invalid region `5:179125188-179126280`
[2016-04-15T04:34Z] 2016-04-14 21:34:48 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:34:48,958 - WARNING - Could not retrieve variants from source file in region 5:179259942-179291035. Error was invalid region `5:179259943-179291035`
[2016-04-15T04:34Z] 2016-04-14 21:34:50 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:34:50,598 - WARNING - Could not retrieve variants from source file in region 5:177547036-177574751. Error was invalid region `5:177547037-177574751`
[2016-04-15T04:34Z] 2016-04-14 21:34:51 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:34:51,858 - WARNING - Could not retrieve variants from source file in region 5:176720987-176740473. Error was invalid region `5:176720988-176740473`
[2016-04-15T04:34Z] 2016-04-14 21:34:59 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:34:59,194 - WARNING - Could not retrieve variants from source file in region 5:179160191-179160592. Error was invalid region `5:179160192-179160592`
[2016-04-15T04:34Z] 2016-04-14 21:34:59 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:34:59,468 - WARNING - Could not retrieve variants from source file in region 5:175792394-175811284. Error was invalid region `5:175792395-175811284`
[2016-04-15T04:35Z] 2016-04-14 21:35:00 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:35:00,306 - WARNING - Could not retrieve variants from source file in region 5:179160191-179160592. Error was invalid region `5:179160192-179160592`
[2016-04-15T04:35Z] 2016-04-14 21:35:00 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:35:00,327 - WARNING - Could not retrieve variants from source file in region 5:175792394-175811284. Error was invalid region `5:175792395-175811284`
[2016-04-15T04:35Z] 2016-04-14 21:35:02 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:35:02,084 - WARNING - Could not retrieve variants from source file in region 5:178986767-179036623. Error was invalid region `5:178986768-179036623`
[2016-04-15T04:35Z] 2016-04-14 21:35:04 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:35:04,303 - WARNING - Could not retrieve variants from source file in region 5:178634336-178634873. Error was invalid region `5:178634337-178634873`
[2016-04-15T04:35Z] 2016-04-14 21:35:04 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:35:04,368 - WARNING - Could not retrieve variants from source file in region 5:178986767-179036623. Error was invalid region `5:178986768-179036623`
[2016-04-15T04:35Z] 2016-04-14 21:35:05 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:35:05,039 - WARNING - Could not retrieve variants from source file in region 5:178770770-178772449. Error was invalid region `5:178770771-178772449`
[2016-04-15T04:35Z] 2016-04-14 21:35:05 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:35:05,686 - WARNING - Could not retrieve variants from source file in region 5:178986767-179036623. Error was invalid region `5:178986768-179036623`
[2016-04-15T04:35Z] 2016-04-14 21:35:06 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:35:06,085 - WARNING - Could not retrieve variants from source file in region 5:178540764-178563157. Error was invalid region `5:178540765-178563157`
[2016-04-15T04:35Z] 2016-04-14 21:35:07 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:35:07,550 - WARNING - Could not retrieve variants from source file in region 5:178540764-178563157. Error was invalid region `5:178540765-178563157`
[2016-04-15T04:35Z] ['bcbio-variation-recall', 'square', '-Xms750m', '-Xmx7280m', '-XX:+UseSerialGC', '-c', 16, '-r', u'6:1-15509601', '--caller', 'platypus', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/6/Batch1-6_0_15509601.vcf.gz', '/mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/6/Batch1-6_0_15509601.vcf-inputs.txt'] in region: 6:1-15509601
[2016-04-15T04:35Z] 2016-04-14 21:35:23 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:35:23,515 - WARNING - Could not retrieve variants from source file in region 6:655932-656333. Error was invalid region `6:655933-656333`
[2016-04-15T04:35Z] 2016-04-14 21:35:24 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:35:24,389 - WARNING - Could not retrieve variants from source file in region 6:13206071-13206472. Error was invalid region `6:13206072-13206472`
[2016-04-15T04:35Z] 2016-04-14 21:35:24 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:35:24,562 - WARNING - Could not retrieve variants from source file in region 6:1390065-1391275. Error was invalid region `6:1390066-1391275`
[2016-04-15T04:35Z] 2016-04-14 21:35:24 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:35:24,704 - WARNING - Could not retrieve variants from source file in region 6:2623609-2624010. Error was invalid region `6:2623610-2624010`
[2016-04-15T04:35Z] 2016-04-14 21:35:25 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:35:25,003 - WARNING - Could not retrieve variants from source file in region 6:3154660-3155061. Error was invalid region `6:3154661-3155061`
[2016-04-15T04:35Z] 2016-04-14 21:35:25 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:35:25,360 - WARNING - Could not retrieve variants from source file in region 6:13469902-13470303. Error was invalid region `6:13469903-13470303`
[2016-04-15T04:35Z] 2016-04-14 21:35:25 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:35:25,761 - WARNING - Could not retrieve variants from source file in region 6:13801404-13814530. Error was invalid region `6:13801405-13814530`
[2016-04-15T04:35Z] 2016-04-14 21:35:25 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:35:25,774 - WARNING - Could not retrieve variants from source file in region 6:10398496-10412378. Error was invalid region `6:10398497-10412378`
[2016-04-15T04:35Z] 2016-04-14 21:35:29 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:35:29,173 - WARNING - Could not retrieve variants from source file in region 6:1742583-1742984. Error was invalid region `6:1742584-1742984`
[2016-04-15T04:35Z] 2016-04-14 21:35:30 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:35:30,678 - WARNING - Could not retrieve variants from source file in region 6:655932-656333. Error was invalid region `6:655933-656333`
[2016-04-15T04:35Z] 2016-04-14 21:35:33 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:35:33,600 - WARNING - Could not retrieve variants from source file in region 6:5260725-5261326. Error was invalid region `6:5260726-5261326`
[2016-04-15T04:35Z] 2016-04-14 21:35:34 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:35:34,437 - WARNING - Could not retrieve variants from source file in region 6:3154660-3155061. Error was invalid region `6:3154661-3155061`
[2016-04-15T04:35Z] 2016-04-14 21:35:34 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:35:34,460 - WARNING - Could not retrieve variants from source file in region 6:2680521-2680957. Error was invalid region `6:2680522-2680957`
[2016-04-15T04:35Z] 2016-04-14 21:35:34 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:35:34,520 - WARNING - Could not retrieve variants from source file in region 6:15496451-15496852. Error was invalid region `6:15496452-15496852`
[2016-04-15T04:35Z] 2016-04-14 21:35:34 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:35:34,597 - WARNING - Could not retrieve variants from source file in region 6:13469902-13470303. Error was invalid region `6:13469903-13470303`
[2016-04-15T04:35Z] 2016-04-14 21:35:34 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:35:34,814 - WARNING - Could not retrieve variants from source file in region 6:1742583-1742984. Error was invalid region `6:1742584-1742984`
[2016-04-15T04:35Z] 2016-04-14 21:35:34 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:35:34,913 - WARNING - Could not retrieve variants from source file in region 6:13711068-13711469. Error was invalid region `6:13711069-13711469`
[2016-04-15T04:35Z] 2016-04-14 21:35:35 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:35:35,240 - WARNING - Could not retrieve variants from source file in region 6:655932-656333. Error was invalid region `6:655933-656333`
[2016-04-15T04:35Z] 2016-04-14 21:35:36 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:35:36,852 - WARNING - Could not retrieve variants from source file in region 6:13206071-13206472. Error was invalid region `6:13206072-13206472`
[2016-04-15T04:35Z] 2016-04-14 21:35:37 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:35:37,908 - WARNING - Could not retrieve variants from source file in region 6:2959302-2971451. Error was invalid region `6:2959303-2971451`
[2016-04-15T04:35Z] 2016-04-14 21:35:40 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:35:40,099 - WARNING - Could not retrieve variants from source file in region 6:2623609-2624010. Error was invalid region `6:2623610-2624010`
[2016-04-15T04:35Z] 2016-04-14 21:35:41 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:35:41,989 - WARNING - Could not retrieve variants from source file in region 6:3154660-3155061. Error was invalid region `6:3154661-3155061`
[2016-04-15T04:35Z] 2016-04-14 21:35:42 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:35:42,582 - WARNING - Could not retrieve variants from source file in region 6:13469902-13470303. Error was invalid region `6:13469903-13470303`
[2016-04-15T04:35Z] 2016-04-14 21:35:42 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:35:42,728 - WARNING - Could not retrieve variants from source file in region 6:2680521-2680957. Error was invalid region `6:2680522-2680957`
[2016-04-15T04:35Z] 2016-04-14 21:35:43 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:35:43,270 - WARNING - Could not retrieve variants from source file in region 6:13711068-13711469. Error was invalid region `6:13711069-13711469`
[2016-04-15T04:35Z] 2016-04-14 21:35:51 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:35:51,566 - WARNING - Could not retrieve variants from source file in region 6:11005475-11005876. Error was invalid region `6:11005476-11005876`
[2016-04-15T04:35Z] 2016-04-14 21:35:53 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:35:53,436 - WARNING - Could not retrieve variants from source file in region 6:2749170-2784761. Error was invalid region `6:2749171-2784761`
[2016-04-15T04:35Z] 2016-04-14 21:35:54 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:35:54,335 - WARNING - Could not retrieve variants from source file in region 6:7393241-7393642. Error was invalid region `6:7393242-7393642`
[2016-04-15T04:35Z] 2016-04-14 21:35:54 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:35:54,959 - WARNING - Could not retrieve variants from source file in region 6:13407930-13408335. Error was invalid region `6:13407931-13408335`
[2016-04-15T04:35Z] 2016-04-14 21:35:56 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:35:56,313 - WARNING - Could not retrieve variants from source file in region 6:563934-564335. Error was invalid region `6:563935-564335`
[2016-04-15T04:35Z] 2016-04-14 21:35:58 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:35:58,103 - WARNING - Could not retrieve variants from source file in region 6:12294047-12296445. Error was invalid region `6:12294048-12296445`
[2016-04-15T04:35Z] 2016-04-14 21:35:58 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:35:58,314 - WARNING - Could not retrieve variants from source file in region 6:3076930-3077331. Error was invalid region `6:3076931-3077331`
[2016-04-15T04:35Z] 2016-04-14 21:35:59 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:35:59,159 - WARNING - Could not retrieve variants from source file in region 6:13295304-13297016. Error was invalid region `6:13295305-13297016`
[2016-04-15T04:35Z] 2016-04-14 21:35:59 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:35:59,791 - WARNING - Could not retrieve variants from source file in region 6:7393241-7393642. Error was invalid region `6:7393242-7393642`
[2016-04-15T04:35Z] 2016-04-14 21:35:59 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:35:59,832 - WARNING - Could not retrieve variants from source file in region 6:15247553-15247954. Error was invalid region `6:15247554-15247954`
[2016-04-15T04:36Z] 2016-04-14 21:36:00 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:36:00,297 - WARNING - Could not retrieve variants from source file in region 6:5186689-5187090. Error was invalid region `6:5186690-5187090`
[2016-04-15T04:36Z] 2016-04-14 21:36:00 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:36:00,319 - WARNING - Could not retrieve variants from source file in region 6:13407930-13408335. Error was invalid region `6:13407931-13408335`
[2016-04-15T04:36Z] 2016-04-14 21:36:01 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:36:01,442 - WARNING - Could not retrieve variants from source file in region 6:563934-564335. Error was invalid region `6:563935-564335`
[2016-04-15T04:36Z] 2016-04-14 21:36:01 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:36:01,470 - WARNING - Could not retrieve variants from source file in region 6:11005475-11005876. Error was invalid region `6:11005476-11005876`
[2016-04-15T04:36Z] 2016-04-14 21:36:01 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:36:01,666 - WARNING - Could not retrieve variants from source file in region 6:1312867-1314249. Error was invalid region `6:1312868-1314249`
[2016-04-15T04:36Z] 2016-04-14 21:36:02 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:36:02,457 - WARNING - Could not retrieve variants from source file in region 6:12294047-12296445. Error was invalid region `6:12294048-12296445`
[2016-04-15T04:36Z] 2016-04-14 21:36:03 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:36:03,066 - WARNING - Could not retrieve variants from source file in region 6:3076930-3077331. Error was invalid region `6:3076931-3077331`
[2016-04-15T04:36Z] 2016-04-14 21:36:04 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:36:04,770 - WARNING - Could not retrieve variants from source file in region 6:15468665-15469066. Error was invalid region `6:15468666-15469066`
[2016-04-15T04:36Z] 2016-04-14 21:36:04 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:36:04,884 - WARNING - Could not retrieve variants from source file in region 6:13295304-13297016. Error was invalid region `6:13295305-13297016`
[2016-04-15T04:36Z] 2016-04-14 21:36:05 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:36:05,090 - WARNING - Could not retrieve variants from source file in region 6:7393241-7393642. Error was invalid region `6:7393242-7393642`
[2016-04-15T04:36Z] 2016-04-14 21:36:05 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:36:05,383 - WARNING - Could not retrieve variants from source file in region 6:15247553-15247954. Error was invalid region `6:15247554-15247954`
[2016-04-15T04:36Z] 2016-04-14 21:36:05 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:36:05,416 - WARNING - Could not retrieve variants from source file in region 6:9933281-9933682. Error was invalid region `6:9933282-9933682`
[2016-04-15T04:36Z] 2016-04-14 21:36:06 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:36:06,081 - WARNING - Could not retrieve variants from source file in region 6:13407930-13408335. Error was invalid region `6:13407931-13408335`
[2016-04-15T04:36Z] 2016-04-14 21:36:07 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:36:07,632 - WARNING - Could not retrieve variants from source file in region 6:3076930-3077331. Error was invalid region `6:3076931-3077331`
[2016-04-15T04:36Z] 2016-04-14 21:36:09 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:36:09,341 - WARNING - Could not retrieve variants from source file in region 6:15468665-15469066. Error was invalid region `6:15468666-15469066`
[2016-04-15T04:36Z] 2016-04-14 21:36:09 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:36:09,716 - WARNING - Could not retrieve variants from source file in region 6:13295304-13297016. Error was invalid region `6:13295305-13297016`
[2016-04-15T04:36Z] 2016-04-14 21:36:10 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:36:10,865 - WARNING - Could not retrieve variants from source file in region 6:15247553-15247954. Error was invalid region `6:15247554-15247954`
[2016-04-15T04:36Z] 2016-04-14 21:36:17 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:36:17,471 - WARNING - Could not retrieve variants from source file in region 6:11538323-11538754. Error was invalid region `6:11538324-11538754`
[2016-04-15T04:36Z] 2016-04-14 21:36:17 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:36:17,811 - WARNING - Could not retrieve variants from source file in region 6:10955197-10964205. Error was invalid region `6:10955198-10964205`
[2016-04-15T04:36Z] 2016-04-14 21:36:20 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:36:20,366 - WARNING - Could not retrieve variants from source file in region 6:10891570-10906446. Error was invalid region `6:10891571-10906446`
[2016-04-15T04:36Z] 2016-04-14 21:36:20 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:36:20,609 - WARNING - Could not retrieve variants from source file in region 6:4891870-4892271. Error was invalid region `6:4891871-4892271`
[2016-04-15T04:36Z] 2016-04-14 21:36:21 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:36:21,206 - WARNING - Could not retrieve variants from source file in region 6:5085859-5109782. Error was invalid region `6:5085860-5109782`
[2016-04-15T04:36Z] 2016-04-14 21:36:22 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:36:22,028 - WARNING - Could not retrieve variants from source file in region 6:7310048-7310449. Error was invalid region `6:7310049-7310449`
[2016-04-15T04:36Z] 2016-04-14 21:36:22 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:36:22,108 - WARNING - Could not retrieve variants from source file in region 6:401253-401654. Error was invalid region `6:401254-401654`
[2016-04-15T04:36Z] 2016-04-14 21:36:22 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:36:22,923 - WARNING - Could not retrieve variants from source file in region 6:12120234-12125045. Error was invalid region `6:12120235-12125045`
[2016-04-15T04:36Z] 2016-04-14 21:36:23 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:36:23,807 - WARNING - Could not retrieve variants from source file in region 6:7211607-7247534. Error was invalid region `6:7211608-7247534`
[2016-04-15T04:36Z] 2016-04-14 21:36:25 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:36:25,157 - WARNING - Could not retrieve variants from source file in region 6:10891570-10906446. Error was invalid region `6:10891571-10906446`
[2016-04-15T04:36Z] 2016-04-14 21:36:26 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:36:26,727 - WARNING - Could not retrieve variants from source file in region 6:9705425-9705826. Error was invalid region `6:9705426-9705826`
[2016-04-15T04:36Z] 2016-04-14 21:36:28 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:36:28,336 - WARNING - Could not retrieve variants from source file in region 6:3003564-3019844. Error was invalid region `6:3003565-3019844`
[2016-04-15T04:36Z] 2016-04-14 21:36:28 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:36:28,385 - WARNING - Could not retrieve variants from source file in region 6:11538323-11538754. Error was invalid region `6:11538324-11538754`
[2016-04-15T04:36Z] 2016-04-14 21:36:29 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:36:29,225 - WARNING - Could not retrieve variants from source file in region 6:10955197-10964205. Error was invalid region `6:10955198-10964205`
[2016-04-15T04:36Z] 2016-04-14 21:36:29 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:36:29,931 - WARNING - Could not retrieve variants from source file in region 6:5999043-5999444. Error was invalid region `6:5999044-5999444`
[2016-04-15T04:36Z] 2016-04-14 21:36:30 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:36:30,372 - WARNING - Could not retrieve variants from source file in region 6:10891570-10906446. Error was invalid region `6:10891571-10906446`
[2016-04-15T04:36Z] 2016-04-14 21:36:33 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:36:33,692 - WARNING - Could not retrieve variants from source file in region 6:8435243-8435644. Error was invalid region `6:8435244-8435644`
[2016-04-15T04:36Z] 2016-04-14 21:36:36 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:36:36,095 - WARNING - Could not retrieve variants from source file in region 6:9705425-9705826. Error was invalid region `6:9705426-9705826`
[2016-04-15T04:36Z] 2016-04-14 21:36:39 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:36:39,278 - WARNING - Could not retrieve variants from source file in region 6:6151926-6175056. Error was invalid region `6:6151927-6175056`
[2016-04-15T04:36Z] 2016-04-14 21:36:39 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:36:39,744 - WARNING - Could not retrieve variants from source file in region 6:6151926-6175056. Error was invalid region `6:6151927-6175056`
[2016-04-15T04:36Z] 2016-04-14 21:36:43 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:36:43,576 - WARNING - Could not retrieve variants from source file in region 6:10728809-10731408. Error was invalid region `6:10728810-10731408`
[2016-04-15T04:36Z] 2016-04-14 21:36:43 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:36:43,692 - WARNING - Could not retrieve variants from source file in region 6:5368931-5369332. Error was invalid region `6:5368932-5369332`
[2016-04-15T04:36Z] 2016-04-14 21:36:43 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:36:43,780 - WARNING - Could not retrieve variants from source file in region 6:8435243-8435644. Error was invalid region `6:8435244-8435644`
[2016-04-15T04:36Z] 2016-04-14 21:36:43 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:36:43,823 - WARNING - Could not retrieve variants from source file in region 6:10764516-10764917. Error was invalid region `6:10764517-10764917`
[2016-04-15T04:36Z] 2016-04-14 21:36:43 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:36:43,878 - WARNING - Could not retrieve variants from source file in region 6:7862420-7862821. Error was invalid region `6:7862421-7862821`
[2016-04-15T04:36Z] 2016-04-14 21:36:47 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:36:47,679 - WARNING - Could not retrieve variants from source file in region 6:3727600-3739383. Error was invalid region `6:3727601-3739383`
[2016-04-15T04:36Z] 2016-04-14 21:36:47 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:36:47,689 - WARNING - Could not retrieve variants from source file in region 6:5368931-5369332. Error was invalid region `6:5368932-5369332`
[2016-04-15T04:36Z] 2016-04-14 21:36:47 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:36:47,711 - WARNING - Could not retrieve variants from source file in region 6:10728809-10731408. Error was invalid region `6:10728810-10731408`
[2016-04-15T04:36Z] 2016-04-14 21:36:47 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:36:47,883 - WARNING - Could not retrieve variants from source file in region 6:4031787-4131787. Error was invalid region `6:4031788-4131787`
[2016-04-15T04:36Z] 2016-04-14 21:36:47 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:36:47,887 - WARNING - Could not retrieve variants from source file in region 6:4131787-4134045. Error was invalid region `6:4131788-4134045`
[2016-04-15T04:36Z] 2016-04-14 21:36:47 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:36:47,985 - WARNING - Could not retrieve variants from source file in region 6:10764516-10764917. Error was invalid region `6:10764517-10764917`
[2016-04-15T04:36Z] 2016-04-14 21:36:48 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:36:48,123 - WARNING - Could not retrieve variants from source file in region 6:7862420-7862821. Error was invalid region `6:7862421-7862821`
[2016-04-15T04:36Z] 2016-04-14 21:36:48 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:36:48,156 - WARNING - Could not retrieve variants from source file in region 6:3264276-3287308. Error was invalid region `6:3264277-3287308`
[2016-04-15T04:36Z] 2016-04-14 21:36:50 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:36:50,283 - WARNING - Could not retrieve variants from source file in region 6:8102110-8102512. Error was invalid region `6:8102111-8102512`
[2016-04-15T04:36Z] 2016-04-14 21:36:51 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:36:51,148 - WARNING - Could not retrieve variants from source file in region 6:10728809-10731408. Error was invalid region `6:10728810-10731408`
[2016-04-15T04:36Z] 2016-04-14 21:36:51 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:36:51,442 - WARNING - Could not retrieve variants from source file in region 6:10764516-10764917. Error was invalid region `6:10764517-10764917`
[2016-04-15T04:36Z] 2016-04-14 21:36:51 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:36:51,483 - WARNING - Could not retrieve variants from source file in region 6:3264276-3287308. Error was invalid region `6:3264277-3287308`
[2016-04-15T04:36Z] 2016-04-14 21:36:51 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:36:51,687 - WARNING - Could not retrieve variants from source file in region 6:7862420-7862821. Error was invalid region `6:7862421-7862821`
[2016-04-15T04:36Z] 2016-04-14 21:36:54 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:36:54,363 - WARNING - Could not retrieve variants from source file in region 6:3264276-3287308. Error was invalid region `6:3264277-3287308`
[2016-04-15T04:36Z] 2016-04-14 21:36:57 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:36:57,576 - WARNING - Could not retrieve variants from source file in region 6:7727060-7727461. Error was invalid region `6:7727061-7727461`
[2016-04-15T04:36Z] 2016-04-14 21:36:57 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:36:57,607 - WARNING - Could not retrieve variants from source file in region 6:7727060-7727461. Error was invalid region `6:7727061-7727461`
[2016-04-15T04:36Z] 2016-04-14 21:36:57 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:36:57,696 - WARNING - Could not retrieve variants from source file in region 6:10556661-10587228. Error was invalid region `6:10556662-10587228`
[2016-04-15T04:36Z] 2016-04-14 21:36:58 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:36:58,096 - WARNING - Could not retrieve variants from source file in region 6:7727060-7727461. Error was invalid region `6:7727061-7727461`
[2016-04-15T04:37Z] ['bcbio-variation-recall', 'square', '-Xms750m', '-Xmx7280m', '-XX:+UseSerialGC', '-c', 16, '-r', u'6:15511527-31080332', '--caller', 'platypus', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/6/Batch1-6_15511526_31080332.vcf.gz', '/mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/6/Batch1-6_15511526_31080332.vcf-inputs.txt'] in region: 6:15511527-31080332
[2016-04-15T04:37Z] 2016-04-14 21:37:13 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:37:13,467 - WARNING - Could not retrieve variants from source file in region 6:26637513-26638693. Error was invalid region `6:26637514-26638693`
[2016-04-15T04:37Z] 2016-04-14 21:37:14 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:37:14,030 - WARNING - Could not retrieve variants from source file in region 6:18187880-18188281. Error was invalid region `6:18187881-18188281`
[2016-04-15T04:37Z] 2016-04-14 21:37:14 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:37:14,046 - WARNING - Could not retrieve variants from source file in region 6:29595669-29596082. Error was invalid region `6:29595670-29596082`
[2016-04-15T04:37Z] 2016-04-14 21:37:14 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:37:14,589 - WARNING - Could not retrieve variants from source file in region 6:24551453-24551919. Error was invalid region `6:24551454-24551919`
[2016-04-15T04:37Z] 2016-04-14 21:37:14 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:37:14,844 - WARNING - Could not retrieve variants from source file in region 6:22569978-22570435. Error was invalid region `6:22569979-22570435`
[2016-04-15T04:37Z] 2016-04-14 21:37:15 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:37:15,010 - WARNING - Could not retrieve variants from source file in region 6:30457521-30458254. Error was invalid region `6:30457522-30458254`
[2016-04-15T04:37Z] 2016-04-14 21:37:15 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:37:15,234 - WARNING - Could not retrieve variants from source file in region 6:16145114-16145515. Error was invalid region `6:16145115-16145515`
[2016-04-15T04:37Z] 2016-04-14 21:37:15 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:37:15,296 - WARNING - Could not retrieve variants from source file in region 6:31079025-31080206. Error was invalid region `6:31079026-31080206`
[2016-04-15T04:37Z] 2016-04-14 21:37:15 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:37:15,853 - WARNING - Could not retrieve variants from source file in region 6:21065239-21065640. Error was invalid region `6:21065240-21065640`
[2016-04-15T04:37Z] 2016-04-14 21:37:16 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:37:16,050 - WARNING - Could not retrieve variants from source file in region 6:25914642-25917169. Error was invalid region `6:25914643-25917169`
[2016-04-15T04:37Z] 2016-04-14 21:37:16 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:37:16,103 - WARNING - Could not retrieve variants from source file in region 6:26368068-26410080. Error was invalid region `6:26368069-26410080`
[2016-04-15T04:37Z] 2016-04-14 21:37:16 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:37:16,108 - WARNING - Could not retrieve variants from source file in region 6:17541113-17543492. Error was invalid region `6:17541114-17543492`
[2016-04-15T04:37Z] 2016-04-14 21:37:21 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:37:21,365 - WARNING - Could not retrieve variants from source file in region 6:29595669-29596082. Error was invalid region `6:29595670-29596082`
[2016-04-15T04:37Z] 2016-04-14 21:37:23 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:37:23,417 - WARNING - Could not retrieve variants from source file in region 6:28483271-28483672. Error was invalid region `6:28483272-28483672`
[2016-04-15T04:37Z] 2016-04-14 21:37:24 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:37:24,014 - WARNING - Could not retrieve variants from source file in region 6:30684475-30684876. Error was invalid region `6:30684476-30684876`
[2016-04-15T04:37Z] 2016-04-14 21:37:24 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:37:24,212 - WARNING - Could not retrieve variants from source file in region 6:22569978-22570435. Error was invalid region `6:22569979-22570435`
[2016-04-15T04:37Z] 2016-04-14 21:37:24 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:37:24,230 - WARNING - Could not retrieve variants from source file in region 6:30457521-30458254. Error was invalid region `6:30457522-30458254`
[2016-04-15T04:37Z] 2016-04-14 21:37:24 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:37:24,861 - WARNING - Could not retrieve variants from source file in region 6:16145114-16145515. Error was invalid region `6:16145115-16145515`
[2016-04-15T04:37Z] 2016-04-14 21:37:25 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:37:25,524 - WARNING - Could not retrieve variants from source file in region 6:25914642-25917169. Error was invalid region `6:25914643-25917169`
[2016-04-15T04:37Z] 2016-04-14 21:37:27 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:37:27,669 - WARNING - Could not retrieve variants from source file in region 6:24551453-24551919. Error was invalid region `6:24551454-24551919`
[2016-04-15T04:37Z] 2016-04-14 21:37:29 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:37:29,291 - WARNING - Could not retrieve variants from source file in region 6:28483271-28483672. Error was invalid region `6:28483272-28483672`
[2016-04-15T04:37Z] 2016-04-14 21:37:31 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:37:31,465 - WARNING - Could not retrieve variants from source file in region 6:22569978-22570435. Error was invalid region `6:22569979-22570435`
[2016-04-15T04:37Z] 2016-04-14 21:37:31 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:37:31,531 - WARNING - Could not retrieve variants from source file in region 6:30684475-30684876. Error was invalid region `6:30684476-30684876`
[2016-04-15T04:37Z] 2016-04-14 21:37:33 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:37:33,196 - WARNING - Could not retrieve variants from source file in region 6:26090968-26108472. Error was invalid region `6:26090969-26108472`
[2016-04-15T04:37Z] 2016-04-14 21:37:34 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:37:34,043 - WARNING - Could not retrieve variants from source file in region 6:16145114-16145515. Error was invalid region `6:16145115-16145515`
[2016-04-15T04:37Z] 2016-04-14 21:37:46 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:37:46,727 - WARNING - Could not retrieve variants from source file in region 6:28358109-28366341. Error was invalid region `6:28358110-28366341`
[2016-04-15T04:37Z] 2016-04-14 21:37:47 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:37:47,402 - WARNING - Could not retrieve variants from source file in region 6:30297318-30314757. Error was invalid region `6:30297319-30314757`
[2016-04-15T04:37Z] 2016-04-14 21:37:48 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:37:48,092 - WARNING - Could not retrieve variants from source file in region 6:30652570-30652971. Error was invalid region `6:30652571-30652971`
[2016-04-15T04:37Z] 2016-04-14 21:37:49 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:37:49,173 - WARNING - Could not retrieve variants from source file in region 6:29523465-29524147. Error was invalid region `6:29523466-29524147`
[2016-04-15T04:37Z] 2016-04-14 21:37:49 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:37:49,293 - WARNING - Could not retrieve variants from source file in region 6:26597122-26598378. Error was invalid region `6:26597123-26598378`
[2016-04-15T04:37Z] 2016-04-14 21:37:50 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:37:50,388 - WARNING - Could not retrieve variants from source file in region 6:30558266-30558667. Error was invalid region `6:30558267-30558667`
[2016-04-15T04:37Z] 2016-04-14 21:37:51 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:37:51,202 - WARNING - Could not retrieve variants from source file in region 6:25849409-25862656. Error was invalid region `6:25849410-25862656`
[2016-04-15T04:37Z] 2016-04-14 21:37:51 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:37:51,387 - WARNING - Could not retrieve variants from source file in region 6:18139003-18161753. Error was invalid region `6:18139004-18161753`
[2016-04-15T04:37Z] 2016-04-14 21:37:52 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:37:52,816 - WARNING - Could not retrieve variants from source file in region 6:21201282-21201683. Error was invalid region `6:21201283-21201683`
[2016-04-15T04:37Z] 2016-04-14 21:37:53 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:37:53,381 - WARNING - Could not retrieve variants from source file in region 6:28358109-28366341. Error was invalid region `6:28358110-28366341`
[2016-04-15T04:37Z] 2016-04-14 21:37:53 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:37:53,798 - WARNING - Could not retrieve variants from source file in region 6:30297318-30314757. Error was invalid region `6:30297319-30314757`
[2016-04-15T04:37Z] 2016-04-14 21:37:54 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:37:54,223 - WARNING - Could not retrieve variants from source file in region 6:30652570-30652971. Error was invalid region `6:30652571-30652971`
[2016-04-15T04:37Z] 2016-04-14 21:37:55 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:37:55,345 - WARNING - Could not retrieve variants from source file in region 6:26597122-26598378. Error was invalid region `6:26597123-26598378`
[2016-04-15T04:37Z] 2016-04-14 21:37:57 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:37:57,098 - WARNING - Could not retrieve variants from source file in region 6:26017331-26056739. Error was invalid region `6:26017332-26056739`
[2016-04-15T04:37Z] 2016-04-14 21:37:57 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:37:57,223 - WARNING - Could not retrieve variants from source file in region 6:24479902-24503780. Error was invalid region `6:24479903-24503780`
[2016-04-15T04:37Z] 2016-04-14 21:37:57 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:37:57,251 - WARNING - Could not retrieve variants from source file in region 6:30558266-30558667. Error was invalid region `6:30558267-30558667`
[2016-04-15T04:37Z] 2016-04-14 21:37:57 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:37:57,455 - WARNING - Could not retrieve variants from source file in region 6:17282204-17289735. Error was invalid region `6:17282205-17289735`
[2016-04-15T04:37Z] 2016-04-14 21:37:58 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:37:58,153 - WARNING - Could not retrieve variants from source file in region 6:18139003-18161753. Error was invalid region `6:18139004-18161753`
[2016-04-15T04:37Z] 2016-04-14 21:37:58 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:37:58,660 - WARNING - Could not retrieve variants from source file in region 6:21201282-21201683. Error was invalid region `6:21201283-21201683`
[2016-04-15T04:37Z] 2016-04-14 21:37:59 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:37:59,389 - WARNING - Could not retrieve variants from source file in region 6:30297318-30314757. Error was invalid region `6:30297319-30314757`
[2016-04-15T04:38Z] 2016-04-14 21:38:03 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:38:03,584 - WARNING - Could not retrieve variants from source file in region 6:30558266-30558667. Error was invalid region `6:30558267-30558667`
[2016-04-15T04:38Z] 2016-04-14 21:38:03 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:38:03,622 - WARNING - Could not retrieve variants from source file in region 6:17282204-17289735. Error was invalid region `6:17282205-17289735`
[2016-04-15T04:38Z] 2016-04-14 21:38:11 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:38:11,559 - WARNING - Could not retrieve variants from source file in region 6:29394715-29408718. Error was invalid region `6:29394716-29408718`
[2016-04-15T04:38Z] 2016-04-14 21:38:14 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:38:14,640 - WARNING - Could not retrieve variants from source file in region 6:18213777-18215493. Error was invalid region `6:18213778-18215493`
[2016-04-15T04:38Z] 2016-04-14 21:38:15 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:38:15,292 - WARNING - Could not retrieve variants from source file in region 6:28328180-28331318. Error was invalid region `6:28328181-28331318`
[2016-04-15T04:38Z] 2016-04-14 21:38:15 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:38:15,774 - WARNING - Could not retrieve variants from source file in region 6:30514832-30530435. Error was invalid region `6:30514833-30530435`
[2016-04-15T04:38Z] 2016-04-14 21:38:16 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:38:16,945 - WARNING - Could not retrieve variants from source file in region 6:26545421-26545822. Error was invalid region `6:26545422-26545822`
[2016-04-15T04:38Z] 2016-04-14 21:38:18 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:38:18,026 - WARNING - Could not retrieve variants from source file in region 6:17831208-17834403. Error was invalid region `6:17831209-17834403`
[2016-04-15T04:38Z] 2016-04-14 21:38:19 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:38:19,691 - WARNING - Could not retrieve variants from source file in region 6:28328180-28331318. Error was invalid region `6:28328181-28331318`
[2016-04-15T04:38Z] 2016-04-14 21:38:20 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:38:20,328 - WARNING - Could not retrieve variants from source file in region 6:30514832-30530435. Error was invalid region `6:30514833-30530435`
[2016-04-15T04:38Z] 2016-04-14 21:38:21 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:38:21,522 - WARNING - Could not retrieve variants from source file in region 6:25812939-25813340. Error was invalid region `6:25812940-25813340`
[2016-04-15T04:38Z] 2016-04-14 21:38:21 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:38:21,523 - WARNING - Could not retrieve variants from source file in region 6:25966857-25983967. Error was invalid region `6:25966858-25983967`
[2016-04-15T04:38Z] 2016-04-14 21:38:21 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:38:21,728 - WARNING - Could not retrieve variants from source file in region 6:29394715-29408718. Error was invalid region `6:29394716-29408718`
[2016-04-15T04:38Z] 2016-04-14 21:38:21 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:38:21,858 - WARNING - Could not retrieve variants from source file in region 6:26545421-26545822. Error was invalid region `6:26545422-26545822`
[2016-04-15T04:38Z] 2016-04-14 21:38:22 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:38:22,361 - WARNING - Could not retrieve variants from source file in region 6:17831208-17834403. Error was invalid region `6:17831209-17834403`
[2016-04-15T04:38Z] 2016-04-14 21:38:26 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:38:26,568 - WARNING - Could not retrieve variants from source file in region 6:25812939-25813340. Error was invalid region `6:25812940-25813340`
[2016-04-15T04:38Z] 2016-04-14 21:38:26 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:38:26,575 - WARNING - Could not retrieve variants from source file in region 6:30954034-30956119. Error was invalid region `6:30954035-30956119`
[2016-04-15T04:38Z] 2016-04-14 21:38:27 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:38:27,587 - WARNING - Could not retrieve variants from source file in region 6:30121394-30166456. Error was invalid region `6:30121395-30166456`
[2016-04-15T04:38Z] 2016-04-14 21:38:31 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:38:31,584 - WARNING - Could not retrieve variants from source file in region 6:25812939-25813340. Error was invalid region `6:25812940-25813340`
[2016-04-15T04:38Z] 2016-04-14 21:38:36 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:38:36,370 - WARNING - Could not retrieve variants from source file in region 6:24290992-24291393. Error was invalid region `6:24290993-24291393`
[2016-04-15T04:38Z] 2016-04-14 21:38:36 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:38:36,990 - WARNING - Could not retrieve variants from source file in region 6:26463363-26468850. Error was invalid region `6:26463364-26468850`
[2016-04-15T04:38Z] 2016-04-14 21:38:38 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:38:38,711 - WARNING - Could not retrieve variants from source file in region 6:26463363-26468850. Error was invalid region `6:26463364-26468850`
[2016-04-15T04:38Z] 2016-04-14 21:38:39 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:38:39,124 - WARNING - Could not retrieve variants from source file in region 6:29141421-29142254. Error was invalid region `6:29141422-29142254`
[2016-04-15T04:38Z] 2016-04-14 21:38:39 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:38:39,257 - WARNING - Could not retrieve variants from source file in region 6:28268613-28297503. Error was invalid region `6:28268614-28297503`
[2016-04-15T04:38Z] 2016-04-14 21:38:40 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:38:40,758 - WARNING - Could not retrieve variants from source file in region 6:29759600-29760563. Error was invalid region `6:29759601-29760563`
[2016-04-15T04:38Z] 2016-04-14 21:38:40 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:38:40,936 - WARNING - Could not retrieve variants from source file in region 6:29274275-29274676. Error was invalid region `6:29274276-29274676`
[2016-04-15T04:38Z] 2016-04-14 21:38:41 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:38:41,595 - WARNING - Could not retrieve variants from source file in region 6:26501686-26509572. Error was invalid region `6:26501687-26509572`
[2016-04-15T04:38Z] 2016-04-14 21:38:43 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:38:43,350 - WARNING - Could not retrieve variants from source file in region 6:30071119-30080686. Error was invalid region `6:30071120-30080686`
[2016-04-15T04:38Z] 2016-04-14 21:38:43 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:38:43,384 - WARNING - Could not retrieve variants from source file in region 6:29692800-29693201. Error was invalid region `6:29692801-29693201`
[2016-04-15T04:38Z] 2016-04-14 21:38:46 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:38:46,306 - WARNING - Could not retrieve variants from source file in region 6:28268613-28297503. Error was invalid region `6:28268614-28297503`
[2016-04-15T04:38Z] 2016-04-14 21:38:47 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:38:47,435 - WARNING - Could not retrieve variants from source file in region 6:25769138-25769539. Error was invalid region `6:25769139-25769539`
[2016-04-15T04:38Z] 2016-04-14 21:38:47 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:38:47,783 - WARNING - Could not retrieve variants from source file in region 6:29759600-29760563. Error was invalid region `6:29759601-29760563`
[2016-04-15T04:38Z] 2016-04-14 21:38:48 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:38:48,344 - WARNING - Could not retrieve variants from source file in region 6:29274275-29274676. Error was invalid region `6:29274276-29274676`
[2016-04-15T04:38Z] 2016-04-14 21:38:48 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:38:48,608 - WARNING - Could not retrieve variants from source file in region 6:30711594-30711995. Error was invalid region `6:30711595-30711995`
[2016-04-15T04:38Z] 2016-04-14 21:38:48 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:38:48,659 - WARNING - Could not retrieve variants from source file in region 6:30071119-30080686. Error was invalid region `6:30071120-30080686`
[2016-04-15T04:38Z] 2016-04-14 21:38:48 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:38:48,763 - WARNING - Could not retrieve variants from source file in region 6:29692800-29693201. Error was invalid region `6:29692801-29693201`
[2016-04-15T04:38Z] 2016-04-14 21:38:50 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:38:50,473 - WARNING - Could not retrieve variants from source file in region 6:29141421-29142254. Error was invalid region `6:29141422-29142254`
[2016-04-15T04:38Z] 2016-04-14 21:38:53 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:38:53,712 - WARNING - Could not retrieve variants from source file in region 6:25769138-25769539. Error was invalid region `6:25769139-25769539`
[2016-04-15T04:38Z] 2016-04-14 21:38:55 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:38:55,523 - WARNING - Could not retrieve variants from source file in region 6:30711594-30711995. Error was invalid region `6:30711595-30711995`
[2016-04-15T04:38Z] 2016-04-14 21:38:56 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:38:56,426 - WARNING - Could not retrieve variants from source file in region 6:29692800-29693201. Error was invalid region `6:29692801-29693201`
[2016-04-15T04:38Z] 2016-04-14 21:38:58 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:38:58,247 - WARNING - Could not retrieve variants from source file in region 6:29795425-29797886. Error was invalid region `6:29795426-29797886`
[2016-04-15T04:38Z] 2016-04-14 21:38:59 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:38:59,116 - WARNING - Could not retrieve variants from source file in region 6:25769138-25769539. Error was invalid region `6:25769139-25769539`
[2016-04-15T04:39Z] 2016-04-14 21:39:00 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:39:00,226 - WARNING - Could not retrieve variants from source file in region 6:29624790-29634202. Error was invalid region `6:29624791-29634202`
[2016-04-15T04:39Z] 2016-04-14 21:39:00 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:39:00,867 - WARNING - Could not retrieve variants from source file in region 6:30711594-30711995. Error was invalid region `6:30711595-30711995`
[2016-04-15T04:39Z] 2016-04-14 21:39:05 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:39:05,350 - WARNING - Could not retrieve variants from source file in region 6:25600757-25605281. Error was invalid region `6:25600758-25605281`
[2016-04-15T04:39Z] 2016-04-14 21:39:05 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:39:05,725 - WARNING - Could not retrieve variants from source file in region 6:29624790-29634202. Error was invalid region `6:29624791-29634202`
[2016-04-15T04:39Z] 2016-04-14 21:39:05 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:39:05,734 - WARNING - Could not retrieve variants from source file in region 6:28195310-28240122. Error was invalid region `6:28195311-28240122`
[2016-04-15T04:39Z] 2016-04-14 21:39:05 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:39:05,826 - WARNING - Could not retrieve variants from source file in region 6:29624790-29634202. Error was invalid region `6:29624791-29634202`
[2016-04-15T04:39Z] 2016-04-14 21:39:08 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:39:08,871 - WARNING - Could not retrieve variants from source file in region 6:24205025-24205426. Error was invalid region `6:24205026-24205426`
[2016-04-15T04:39Z] 2016-04-14 21:39:10 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:39:10,495 - WARNING - Could not retrieve variants from source file in region 6:25600757-25605281. Error was invalid region `6:25600758-25605281`
[2016-04-15T04:39Z] 2016-04-14 21:39:10 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:39:10,497 - WARNING - Could not retrieve variants from source file in region 6:28963037-28963438. Error was invalid region `6:28963038-28963438`
[2016-04-15T04:39Z] 2016-04-14 21:39:10 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:39:10,765 - WARNING - Could not retrieve variants from source file in region 6:28890965-28891366. Error was invalid region `6:28890966-28891366`
[2016-04-15T04:39Z] 2016-04-14 21:39:11 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:39:11,184 - WARNING - Could not retrieve variants from source file in region 6:30039138-30039539. Error was invalid region `6:30039139-30039539`
[2016-04-15T04:39Z] 2016-04-14 21:39:11 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:39:11,906 - WARNING - Could not retrieve variants from source file in region 6:29080133-29080640. Error was invalid region `6:29080134-29080640`
[2016-04-15T04:39Z] 2016-04-14 21:39:13 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:39:13,399 - WARNING - Could not retrieve variants from source file in region 6:24205025-24205426. Error was invalid region `6:24205026-24205426`
[2016-04-15T04:39Z] 2016-04-14 21:39:14 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:39:14,070 - WARNING - Could not retrieve variants from source file in region 6:30039138-30039539. Error was invalid region `6:30039139-30039539`
[2016-04-15T04:39Z] 2016-04-14 21:39:15 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:39:15,061 - WARNING - Could not retrieve variants from source file in region 6:25600757-25605281. Error was invalid region `6:25600758-25605281`
[2016-04-15T04:39Z] 2016-04-14 21:39:15 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:39:15,614 - WARNING - Could not retrieve variants from source file in region 6:28963037-28963438. Error was invalid region `6:28963038-28963438`
[2016-04-15T04:39Z] 2016-04-14 21:39:15 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:39:15,708 - WARNING - Could not retrieve variants from source file in region 6:28890965-28891366. Error was invalid region `6:28890966-28891366`
[2016-04-15T04:39Z] 2016-04-14 21:39:15 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:39:15,824 - WARNING - Could not retrieve variants from source file in region 6:28542213-28543454. Error was invalid region `6:28542214-28543454`
[2016-04-15T04:39Z] 2016-04-14 21:39:16 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:39:16,845 - WARNING - Could not retrieve variants from source file in region 6:29080133-29080640. Error was invalid region `6:29080134-29080640`
[2016-04-15T04:39Z] 2016-04-14 21:39:17 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:39:17,183 - WARNING - Could not retrieve variants from source file in region 6:25726410-25727707. Error was invalid region `6:25726411-25727707`
[2016-04-15T04:39Z] 2016-04-14 21:39:21 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:39:21,234 - WARNING - Could not retrieve variants from source file in region 6:28542213-28543454. Error was invalid region `6:28542214-28543454`
[2016-04-15T04:39Z] 2016-04-14 21:39:21 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:39:21,401 - WARNING - Could not retrieve variants from source file in region 6:25420133-25435948. Error was invalid region `6:25420134-25435948`
[2016-04-15T04:39Z] 2016-04-14 21:39:26 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:39:26,150 - WARNING - Could not retrieve variants from source file in region 6:24687554-24710296. Error was invalid region `6:24687555-24710296`
[2016-04-15T04:39Z] 2016-04-14 21:39:26 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:39:26,895 - WARNING - Could not retrieve variants from source file in region 6:24687554-24710296. Error was invalid region `6:24687555-24710296`
[2016-04-15T04:39Z] 2016-04-14 21:39:26 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:39:26,901 - WARNING - Could not retrieve variants from source file in region 6:25420133-25435948. Error was invalid region `6:25420134-25435948`
[2016-04-15T04:39Z] 2016-04-14 21:39:27 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:39:27,160 - WARNING - Could not retrieve variants from source file in region 6:24588673-24601501. Error was invalid region `6:24588674-24601501`
[2016-04-15T04:39Z] 2016-04-14 21:39:30 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:39:30,172 - WARNING - Could not retrieve variants from source file in region 6:28096982-28121088. Error was invalid region `6:28096983-28121088`
[2016-04-15T04:39Z] 2016-04-14 21:39:30 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:39:30,909 - WARNING - Could not retrieve variants from source file in region 6:24588673-24601501. Error was invalid region `6:24588674-24601501`
[2016-04-15T04:39Z] 2016-04-14 21:39:34 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:39:34,044 - WARNING - Could not retrieve variants from source file in region 6:28096982-28121088. Error was invalid region `6:28096983-28121088`
[2016-04-15T04:39Z] 2016-04-14 21:39:34 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:39:34,176 - WARNING - Could not retrieve variants from source file in region 6:27424974-27425375. Error was invalid region `6:27424975-27425375`
[2016-04-15T04:39Z] 2016-04-14 21:39:34 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:39:34,316 - WARNING - Could not retrieve variants from source file in region 6:27277191-27278210. Error was invalid region `6:27277192-27278210`
[2016-04-15T04:39Z] 2016-04-14 21:39:34 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:39:34,576 - WARNING - Could not retrieve variants from source file in region 6:27277191-27278210. Error was invalid region `6:27277192-27278210`
[2016-04-15T04:39Z] 2016-04-14 21:39:34 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:39:34,625 - WARNING - Could not retrieve variants from source file in region 6:27277191-27278210. Error was invalid region `6:27277192-27278210`
[2016-04-15T04:39Z] 2016-04-14 21:39:38 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:39:38,194 - WARNING - Could not retrieve variants from source file in region 6:27832963-27880172. Error was invalid region `6:27832964-27880172`
[2016-04-15T04:39Z] 2016-04-14 21:39:38 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:39:38,429 - WARNING - Could not retrieve variants from source file in region 6:27424974-27425375. Error was invalid region `6:27424975-27425375`
[2016-04-15T04:39Z] 2016-04-14 21:39:38 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:39:38,502 - WARNING - Could not retrieve variants from source file in region 6:27222853-27223269. Error was invalid region `6:27222854-27223269`
[2016-04-15T04:39Z] 2016-04-14 21:39:38 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:39:38,942 - WARNING - Could not retrieve variants from source file in region 6:27775463-27782346. Error was invalid region `6:27775464-27782346`
[2016-04-15T04:39Z] 2016-04-14 21:39:39 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:39:39,155 - WARNING - Could not retrieve variants from source file in region 6:27424974-27425375. Error was invalid region `6:27424975-27425375`
[2016-04-15T04:39Z] 2016-04-14 21:39:39 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:39:39,159 - WARNING - Could not retrieve variants from source file in region 6:27832963-27880172. Error was invalid region `6:27832964-27880172`
[2016-04-15T04:39Z] 2016-04-14 21:39:39 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:39:39,159 - WARNING - Could not retrieve variants from source file in region 6:27222853-27223269. Error was invalid region `6:27222854-27223269`
[2016-04-15T04:39Z] 2016-04-14 21:39:39 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:39:39,327 - WARNING - Could not retrieve variants from source file in region 6:27222853-27223269. Error was invalid region `6:27222854-27223269`
[2016-04-15T04:39Z] ['bcbio-variation-recall', 'square', '-Xms750m', '-Xmx7280m', '-XX:+UseSerialGC', '-c', 16, '-r', u'6:31083802-46593245', '--caller', 'platypus', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/6/Batch1-6_31083801_46593245.vcf.gz', '/mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/6/Batch1-6_31083801_46593245.vcf-inputs.txt'] in region: 6:31083802-46593245
[2016-04-15T04:39Z] 2016-04-14 21:39:57 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:39:57,291 - WARNING - Could not retrieve variants from source file in region 6:46047247-46047648. Error was invalid region `6:46047248-46047648`
[2016-04-15T04:39Z] 2016-04-14 21:39:58 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:39:58,334 - WARNING - Could not retrieve variants from source file in region 6:46550973-46551374. Error was invalid region `6:46550974-46551374`
[2016-04-15T04:39Z] 2016-04-14 21:39:58 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:39:58,435 - WARNING - Could not retrieve variants from source file in region 6:46293117-46293518. Error was invalid region `6:46293118-46293518`
[2016-04-15T04:39Z] 2016-04-14 21:39:59 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:39:59,461 - WARNING - Could not retrieve variants from source file in region 6:39324867-39325268. Error was invalid region `6:39324868-39325268`
[2016-04-15T04:40Z] 2016-04-14 21:40:03 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:40:03,664 - WARNING - Could not retrieve variants from source file in region 6:46047247-46047648. Error was invalid region `6:46047248-46047648`
[2016-04-15T04:40Z] 2016-04-14 21:40:04 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:40:04,646 - WARNING - Could not retrieve variants from source file in region 6:35476814-35479764. Error was invalid region `6:35476815-35479764`
[2016-04-15T04:40Z] 2016-04-14 21:40:06 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:40:06,360 - WARNING - Could not retrieve variants from source file in region 6:34985589-34985990. Error was invalid region `6:34985590-34985990`
[2016-04-15T04:40Z] 2016-04-14 21:40:06 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:40:06,644 - WARNING - Could not retrieve variants from source file in region 6:43109540-43109941. Error was invalid region `6:43109541-43109941`
[2016-04-15T04:40Z] 2016-04-14 21:40:06 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:40:06,926 - WARNING - Could not retrieve variants from source file in region 6:46293117-46293518. Error was invalid region `6:46293118-46293518`
[2016-04-15T04:40Z] 2016-04-14 21:40:07 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:40:07,836 - WARNING - Could not retrieve variants from source file in region 6:38120749-38121150. Error was invalid region `6:38120750-38121150`
[2016-04-15T04:40Z] 2016-04-14 21:40:07 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:40:07,995 - WARNING - Could not retrieve variants from source file in region 6:35260292-35285910. Error was invalid region `6:35260293-35285910`
[2016-04-15T04:40Z] 2016-04-14 21:40:08 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:40:08,217 - WARNING - Could not retrieve variants from source file in region 6:46047247-46047648. Error was invalid region `6:46047248-46047648`
[2016-04-15T04:40Z] 2016-04-14 21:40:09 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:40:09,789 - WARNING - Could not retrieve variants from source file in region 6:35476814-35479764. Error was invalid region `6:35476815-35479764`
[2016-04-15T04:40Z] 2016-04-14 21:40:12 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:40:12,952 - WARNING - Could not retrieve variants from source file in region 6:34985589-34985990. Error was invalid region `6:34985590-34985990`
[2016-04-15T04:40Z] 2016-04-14 21:40:14 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:40:14,372 - WARNING - Could not retrieve variants from source file in region 6:46293117-46293518. Error was invalid region `6:46293118-46293518`
[2016-04-15T04:40Z] 2016-04-14 21:40:15 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:40:15,340 - WARNING - Could not retrieve variants from source file in region 6:34803736-34857501. Error was invalid region `6:34803737-34857501`
[2016-04-15T04:40Z] 2016-04-14 21:40:15 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:40:15,487 - WARNING - Could not retrieve variants from source file in region 6:32782875-32825280. Error was invalid region `6:32782876-32825280`
[2016-04-15T04:40Z] 2016-04-14 21:40:15 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:40:15,685 - WARNING - Could not retrieve variants from source file in region 6:32333744-32337876. Error was invalid region `6:32333745-32337876`
[2016-04-15T04:40Z] 2016-04-14 21:40:15 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:40:15,891 - WARNING - Could not retrieve variants from source file in region 6:35260292-35285910. Error was invalid region `6:35260293-35285910`
[2016-04-15T04:40Z] 2016-04-14 21:40:26 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:40:26,595 - WARNING - Could not retrieve variants from source file in region 6:35423451-35437115. Error was invalid region `6:35423452-35437115`
[2016-04-15T04:40Z] 2016-04-14 21:40:27 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:40:27,639 - WARNING - Could not retrieve variants from source file in region 6:45879316-45888263. Error was invalid region `6:45879317-45888263`
[2016-04-15T04:40Z] 2016-04-14 21:40:28 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:40:28,962 - WARNING - Could not retrieve variants from source file in region 6:46107541-46136174. Error was invalid region `6:46107542-46136174`
[2016-04-15T04:40Z] 2016-04-14 21:40:29 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:40:29,673 - WARNING - Could not retrieve variants from source file in region 6:34949396-34949797. Error was invalid region `6:34949397-34949797`
[2016-04-15T04:40Z] 2016-04-14 21:40:31 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:40:31,548 - WARNING - Could not retrieve variants from source file in region 6:37623355-37623756. Error was invalid region `6:37623356-37623756`
[2016-04-15T04:40Z] 2016-04-14 21:40:31 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:40:31,615 - WARNING - Could not retrieve variants from source file in region 6:39281825-39290390. Error was invalid region `6:39281826-39290390`
[2016-04-15T04:40Z] 2016-04-14 21:40:31 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:40:31,752 - WARNING - Could not retrieve variants from source file in region 6:35423451-35437115. Error was invalid region `6:35423452-35437115`
[2016-04-15T04:40Z] 2016-04-14 21:40:33 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:40:33,464 - WARNING - Could not retrieve variants from source file in region 6:44081507-44081908. Error was invalid region `6:44081508-44081908`
[2016-04-15T04:40Z] 2016-04-14 21:40:34 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:40:34,001 - WARNING - Could not retrieve variants from source file in region 6:32298161-32307572. Error was invalid region `6:32298162-32307572`
[2016-04-15T04:40Z] 2016-04-14 21:40:34 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:40:34,696 - WARNING - Could not retrieve variants from source file in region 6:41691085-41708854. Error was invalid region `6:41691086-41708854`
[2016-04-15T04:40Z] 2016-04-14 21:40:34 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:40:34,782 - WARNING - Could not retrieve variants from source file in region 6:42989202-43044810. Error was invalid region `6:42989203-43044810`
[2016-04-15T04:40Z] 2016-04-14 21:40:35 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:40:35,193 - WARNING - Could not retrieve variants from source file in region 6:34949396-34949797. Error was invalid region `6:34949397-34949797`
[2016-04-15T04:40Z] 2016-04-14 21:40:35 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:40:35,515 - WARNING - Could not retrieve variants from source file in region 6:46107541-46136174. Error was invalid region `6:46107542-46136174`
[2016-04-15T04:40Z] 2016-04-14 21:40:36 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:40:36,584 - WARNING - Could not retrieve variants from source file in region 6:34212532-34216109. Error was invalid region `6:34212533-34216109`
[2016-04-15T04:40Z] 2016-04-14 21:40:37 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:40:37,648 - WARNING - Could not retrieve variants from source file in region 6:35423451-35437115. Error was invalid region `6:35423452-35437115`
[2016-04-15T04:40Z] 2016-04-14 21:40:37 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:40:37,752 - WARNING - Could not retrieve variants from source file in region 6:35027716-35058307. Error was invalid region `6:35027717-35058307`
[2016-04-15T04:40Z] 2016-04-14 21:40:37 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:40:37,857 - WARNING - Could not retrieve variants from source file in region 6:37623355-37623756. Error was invalid region `6:37623356-37623756`
[2016-04-15T04:40Z] 2016-04-14 21:40:39 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:40:39,175 - WARNING - Could not retrieve variants from source file in region 6:44081507-44081908. Error was invalid region `6:44081508-44081908`
[2016-04-15T04:40Z] 2016-04-14 21:40:39 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:40:39,198 - WARNING - Could not retrieve variants from source file in region 6:45879316-45888263. Error was invalid region `6:45879317-45888263`
[2016-04-15T04:40Z] 2016-04-14 21:40:41 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:40:41,006 - WARNING - Could not retrieve variants from source file in region 6:36824188-36824589. Error was invalid region `6:36824189-36824589`
[2016-04-15T04:40Z] 2016-04-14 21:40:41 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:40:41,025 - WARNING - Could not retrieve variants from source file in region 6:34949396-34949797. Error was invalid region `6:34949397-34949797`
[2016-04-15T04:40Z] 2016-04-14 21:40:41 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:40:41,386 - WARNING - Could not retrieve variants from source file in region 6:46107541-46136174. Error was invalid region `6:46107542-46136174`
[2016-04-15T04:40Z] 2016-04-14 21:40:42 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:40:42,361 - WARNING - Could not retrieve variants from source file in region 6:34212532-34216109. Error was invalid region `6:34212533-34216109`
[2016-04-15T04:40Z] 2016-04-14 21:40:43 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:40:43,233 - WARNING - Could not retrieve variants from source file in region 6:37623355-37623756. Error was invalid region `6:37623356-37623756`
[2016-04-15T04:40Z] 2016-04-14 21:40:43 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:40:43,804 - WARNING - Could not retrieve variants from source file in region 6:35027716-35058307. Error was invalid region `6:35027717-35058307`
[2016-04-15T04:40Z] 2016-04-14 21:40:44 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:40:44,774 - WARNING - Could not retrieve variants from source file in region 6:44081507-44081908. Error was invalid region `6:44081508-44081908`
[2016-04-15T04:40Z] 2016-04-14 21:40:52 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:40:52,442 - WARNING - Could not retrieve variants from source file in region 6:35365135-35391977. Error was invalid region `6:35365136-35391977`
[2016-04-15T04:40Z] 2016-04-14 21:40:54 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:40:54,670 - WARNING - Could not retrieve variants from source file in region 6:44320337-44329319. Error was invalid region `6:44320338-44329319`
[2016-04-15T04:40Z] 2016-04-14 21:40:55 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:40:55,262 - WARNING - Could not retrieve variants from source file in region 6:41652393-41659079. Error was invalid region `6:41652394-41659079`
[2016-04-15T04:40Z] 2016-04-14 21:40:55 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:40:55,814 - WARNING - Could not retrieve variants from source file in region 6:37249901-37252400. Error was invalid region `6:37249902-37252400`
[2016-04-15T04:40Z] 2016-04-14 21:40:57 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:40:57,758 - WARNING - Could not retrieve variants from source file in region 6:34067581-34101158. Error was invalid region `6:34067582-34101158`
[2016-04-15T04:40Z] 2016-04-14 21:40:58 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:40:58,102 - WARNING - Could not retrieve variants from source file in region 6:35365135-35391977. Error was invalid region `6:35365136-35391977`
[2016-04-15T04:40Z] 2016-04-14 21:40:58 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:40:58,816 - WARNING - Could not retrieve variants from source file in region 6:37447783-37448953. Error was invalid region `6:37447784-37448953`
[2016-04-15T04:40Z] 2016-04-14 21:40:59 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:40:59,570 - WARNING - Could not retrieve variants from source file in region 6:44320337-44329319. Error was invalid region `6:44320338-44329319`
[2016-04-15T04:41Z] 2016-04-14 21:41:01 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:41:01,393 - WARNING - Could not retrieve variants from source file in region 6:37249901-37252400. Error was invalid region `6:37249902-37252400`
[2016-04-15T04:41Z] 2016-04-14 21:41:01 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:41:01,593 - WARNING - Could not retrieve variants from source file in region 6:32261041-32261961. Error was invalid region `6:32261042-32261961`
[2016-04-15T04:41Z] 2016-04-14 21:41:02 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:41:02,335 - WARNING - Could not retrieve variants from source file in region 6:42931989-42946680. Error was invalid region `6:42931990-42946680`
[2016-04-15T04:41Z] 2016-04-14 21:41:04 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:41:04,000 - WARNING - Could not retrieve variants from source file in region 6:43399626-43406691. Error was invalid region `6:43399627-43406691`
[2016-04-15T04:41Z] 2016-04-14 21:41:04 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:41:04,559 - WARNING - Could not retrieve variants from source file in region 6:35365135-35391977. Error was invalid region `6:35365136-35391977`
[2016-04-15T04:41Z] 2016-04-14 21:41:04 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:41:04,635 - WARNING - Could not retrieve variants from source file in region 6:39076981-39077382. Error was invalid region `6:39076982-39077382`
[2016-04-15T04:41Z] 2016-04-14 21:41:05 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:41:05,158 - WARNING - Could not retrieve variants from source file in region 6:43492367-43496852. Error was invalid region `6:43492368-43496852`
[2016-04-15T04:41Z] 2016-04-14 21:41:05 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:41:05,257 - WARNING - Could not retrieve variants from source file in region 6:44320337-44329319. Error was invalid region `6:44320338-44329319`
[2016-04-15T04:41Z] 2016-04-14 21:41:06 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:41:06,882 - WARNING - Could not retrieve variants from source file in region 6:37249901-37252400. Error was invalid region `6:37249902-37252400`
[2016-04-15T04:41Z] 2016-04-14 21:41:07 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:41:07,343 - WARNING - Could not retrieve variants from source file in region 6:36795152-36795553. Error was invalid region `6:36795153-36795553`
[2016-04-15T04:41Z] 2016-04-14 21:41:10 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:41:10,746 - WARNING - Could not retrieve variants from source file in region 6:37447783-37448953. Error was invalid region `6:37447784-37448953`
[2016-04-15T04:41Z] 2016-04-14 21:41:13 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:41:13,175 - WARNING - Could not retrieve variants from source file in region 6:36795152-36795553. Error was invalid region `6:36795153-36795553`
[2016-04-15T04:41Z] 2016-04-14 21:41:21 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:41:21,458 - WARNING - Could not retrieve variants from source file in region 6:37185734-37186135. Error was invalid region `6:37185735-37186135`
[2016-04-15T04:41Z] 2016-04-14 21:41:26 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:41:26,481 - WARNING - Could not retrieve variants from source file in region 6:33754381-33769087. Error was invalid region `6:33754382-33769087`
[2016-04-15T04:41Z] 2016-04-14 21:41:26 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:41:26,548 - WARNING - Could not retrieve variants from source file in region 6:41533362-41545997. Error was invalid region `6:41533363-41545997`
[2016-04-15T04:41Z] 2016-04-14 21:41:27 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:41:27,238 - WARNING - Could not retrieve variants from source file in region 6:36686061-36733322. Error was invalid region `6:36686062-36733322`
[2016-04-15T04:41Z] 2016-04-14 21:41:28 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:41:28,317 - WARNING - Could not retrieve variants from source file in region 6:33690585-33696005. Error was invalid region `6:33690586-33696005`
[2016-04-15T04:41Z] 2016-04-14 21:41:29 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:41:29,742 - WARNING - Could not retrieve variants from source file in region 6:37348822-37349223. Error was invalid region `6:37348823-37349223`
[2016-04-15T04:41Z] 2016-04-14 21:41:31 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:41:31,595 - WARNING - Could not retrieve variants from source file in region 6:37185734-37186135. Error was invalid region `6:37185735-37186135`
[2016-04-15T04:41Z] 2016-04-14 21:41:34 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:41:34,406 - WARNING - Could not retrieve variants from source file in region 6:32121721-32191851. Error was invalid region `6:32121722-32191851`
[2016-04-15T04:41Z] 2016-04-14 21:41:34 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:41:34,695 - WARNING - Could not retrieve variants from source file in region 6:37348822-37349223. Error was invalid region `6:37348823-37349223`
[2016-04-15T04:41Z] 2016-04-14 21:41:35 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:41:35,537 - WARNING - Could not retrieve variants from source file in region 6:43306135-43336961. Error was invalid region `6:43306136-43336961`
[2016-04-15T04:41Z] 2016-04-14 21:41:45 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:41:45,841 - WARNING - Could not retrieve variants from source file in region 6:41309341-41318628. Error was invalid region `6:41309342-41318628`
[2016-04-15T04:41Z] 2016-04-14 21:41:45 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:41:45,948 - WARNING - Could not retrieve variants from source file in region 6:37138009-37138410. Error was invalid region `6:37138010-37138410`
[2016-04-15T04:41Z] 2016-04-14 21:41:47 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:41:47,917 - WARNING - Could not retrieve variants from source file in region 6:38957642-38980271. Error was invalid region `6:38957643-38980271`
[2016-04-15T04:41Z] 2016-04-14 21:41:48 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:41:48,555 - WARNING - Could not retrieve variants from source file in region 6:36976426-36988554. Error was invalid region `6:36976427-36988554`
[2016-04-15T04:41Z] 2016-04-14 21:41:49 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:41:49,888 - WARNING - Could not retrieve variants from source file in region 6:36645485-36645886. Error was invalid region `6:36645486-36645886`
[2016-04-15T04:41Z] 2016-04-14 21:41:50 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:41:50,005 - WARNING - Could not retrieve variants from source file in region 6:41309341-41318628. Error was invalid region `6:41309342-41318628`
[2016-04-15T04:41Z] 2016-04-14 21:41:50 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:41:50,380 - WARNING - Could not retrieve variants from source file in region 6:42850992-42851393. Error was invalid region `6:42850993-42851393`
[2016-04-15T04:41Z] 2016-04-14 21:41:52 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:41:52,109 - WARNING - Could not retrieve variants from source file in region 6:33545129-33545530. Error was invalid region `6:33545130-33545530`
[2016-04-15T04:41Z] 2016-04-14 21:41:52 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:41:52,711 - WARNING - Could not retrieve variants from source file in region 6:36976426-36988554. Error was invalid region `6:36976427-36988554`
[2016-04-15T04:41Z] 2016-04-14 21:41:53 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:41:53,567 - WARNING - Could not retrieve variants from source file in region 6:32975685-32976086. Error was invalid region `6:32975686-32976086`
[2016-04-15T04:41Z] 2016-04-14 21:41:54 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:41:54,187 - WARNING - Could not retrieve variants from source file in region 6:41309341-41318628. Error was invalid region `6:41309342-41318628`
[2016-04-15T04:41Z] 2016-04-14 21:41:54 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:41:54,333 - WARNING - Could not retrieve variants from source file in region 6:42850992-42851393. Error was invalid region `6:42850993-42851393`
[2016-04-15T04:41Z] 2016-04-14 21:41:55 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:41:55,957 - WARNING - Could not retrieve variants from source file in region 6:33545129-33545530. Error was invalid region `6:33545130-33545530`
[2016-04-15T04:41Z] 2016-04-14 21:41:57 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:41:57,496 - WARNING - Could not retrieve variants from source file in region 6:32975685-32976086. Error was invalid region `6:32975686-32976086`
[2016-04-15T04:42Z] 2016-04-14 21:42:06 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:42:06,708 - WARNING - Could not retrieve variants from source file in region 6:41247553-41247954. Error was invalid region `6:41247554-41247954`
[2016-04-15T04:42Z] 2016-04-14 21:42:08 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:42:08,991 - WARNING - Could not retrieve variants from source file in region 6:32410776-32411836. Error was invalid region `6:32410777-32411836`
[2016-04-15T04:42Z] 2016-04-14 21:42:09 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:42:09,022 - WARNING - Could not retrieve variants from source file in region 6:42600108-42600509. Error was invalid region `6:42600109-42600509`
[2016-04-15T04:42Z] 2016-04-14 21:42:09 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:42:09,659 - WARNING - Could not retrieve variants from source file in region 6:31838230-31864737. Error was invalid region `6:31838231-31864737`
[2016-04-15T04:42Z] 2016-04-14 21:42:09 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:42:09,720 - WARNING - Could not retrieve variants from source file in region 6:42531891-42532292. Error was invalid region `6:42531892-42532292`
[2016-04-15T04:42Z] 2016-04-14 21:42:11 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:42:11,291 - WARNING - Could not retrieve variants from source file in region 6:32410776-32411836. Error was invalid region `6:32410777-32411836`
[2016-04-15T04:42Z] 2016-04-14 21:42:11 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:42:11,883 - WARNING - Could not retrieve variants from source file in region 6:41247553-41247954. Error was invalid region `6:41247554-41247954`
[2016-04-15T04:42Z] 2016-04-14 21:42:15 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:42:15,822 - WARNING - Could not retrieve variants from source file in region 6:32410776-32411836. Error was invalid region `6:32410777-32411836`
[2016-04-15T04:42Z] 2016-04-14 21:42:15 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:42:15,857 - WARNING - Could not retrieve variants from source file in region 6:42600108-42600509. Error was invalid region `6:42600109-42600509`
[2016-04-15T04:42Z] 2016-04-14 21:42:16 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:42:16,041 - WARNING - Could not retrieve variants from source file in region 6:32904770-32905276. Error was invalid region `6:32904771-32905276`
[2016-04-15T04:42Z] 2016-04-14 21:42:16 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:42:16,594 - WARNING - Could not retrieve variants from source file in region 6:38750677-38850677. Error was invalid region `6:38750678-38850677`
[2016-04-15T04:42Z] 2016-04-14 21:42:16 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:42:16,599 - WARNING - Could not retrieve variants from source file in region 6:38850677-38851859. Error was invalid region `6:38850678-38851859`
[2016-04-15T04:42Z] 2016-04-14 21:42:16 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:42:16,738 - WARNING - Could not retrieve variants from source file in region 6:42531891-42532292. Error was invalid region `6:42531892-42532292`
[2016-04-15T04:42Z] 2016-04-14 21:42:16 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:42:16,834 - WARNING - Could not retrieve variants from source file in region 6:41162351-41166089. Error was invalid region `6:41162352-41166089`
[2016-04-15T04:42Z] 2016-04-14 21:42:17 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:42:17,051 - WARNING - Could not retrieve variants from source file in region 6:41247553-41247954. Error was invalid region `6:41247554-41247954`
[2016-04-15T04:42Z] 2016-04-14 21:42:18 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:42:18,746 - WARNING - Could not retrieve variants from source file in region 6:32940604-32946323. Error was invalid region `6:32940605-32946323`
[2016-04-15T04:42Z] 2016-04-14 21:42:20 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:42:20,590 - WARNING - Could not retrieve variants from source file in region 6:31964017-31964521. Error was invalid region `6:31964018-31964521`
[2016-04-15T04:42Z] 2016-04-14 21:42:21 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:42:21,057 - WARNING - Could not retrieve variants from source file in region 6:42600108-42600509. Error was invalid region `6:42600109-42600509`
[2016-04-15T04:42Z] 2016-04-14 21:42:22 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:42:22,281 - WARNING - Could not retrieve variants from source file in region 6:31838230-31864737. Error was invalid region `6:31838231-31864737`
[2016-04-15T04:42Z] 2016-04-14 21:42:22 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:42:22,349 - WARNING - Could not retrieve variants from source file in region 6:32904770-32905276. Error was invalid region `6:32904771-32905276`
[2016-04-15T04:42Z] 2016-04-14 21:42:22 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:42:22,362 - WARNING - Could not retrieve variants from source file in region 6:42531891-42532292. Error was invalid region `6:42531892-42532292`
[2016-04-15T04:42Z] 2016-04-14 21:42:22 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:42:22,971 - WARNING - Could not retrieve variants from source file in region 6:41162351-41166089. Error was invalid region `6:41162352-41166089`
[2016-04-15T04:42Z] 2016-04-14 21:42:22 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:42:22,990 - WARNING - Could not retrieve variants from source file in region 6:32363605-32371025. Error was invalid region `6:32363606-32371025`
[2016-04-15T04:42Z] 2016-04-14 21:42:30 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:42:30,289 - WARNING - Could not retrieve variants from source file in region 6:41196394-41198047. Error was invalid region `6:41196395-41198047`
[2016-04-15T04:42Z] 2016-04-14 21:42:30 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:42:30,774 - WARNING - Could not retrieve variants from source file in region 6:42627219-42627624. Error was invalid region `6:42627220-42627624`
[2016-04-15T04:42Z] 2016-04-14 21:42:33 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:42:33,278 - WARNING - Could not retrieve variants from source file in region 6:41196394-41198047. Error was invalid region `6:41196395-41198047`
[2016-04-15T04:42Z] 2016-04-14 21:42:35 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:42:35,007 - WARNING - Could not retrieve variants from source file in region 6:41196394-41198047. Error was invalid region `6:41196395-41198047`
[2016-04-15T04:42Z] 2016-04-14 21:42:35 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:42:35,554 - WARNING - Could not retrieve variants from source file in region 6:42627219-42627624. Error was invalid region `6:42627220-42627624`
[2016-04-15T04:42Z] 2016-04-14 21:42:35 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:42:35,614 - WARNING - Could not retrieve variants from source file in region 6:36260647-36287502. Error was invalid region `6:36260648-36287502`
[2016-04-15T04:42Z] 2016-04-14 21:42:37 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:42:37,159 - WARNING - Could not retrieve variants from source file in region 6:40360254-40360655. Error was invalid region `6:40360255-40360655`
[2016-04-15T04:42Z] 2016-04-14 21:42:37 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:42:37,363 - WARNING - Could not retrieve variants from source file in region 6:31762632-31785418. Error was invalid region `6:31762633-31785418`
[2016-04-15T04:42Z] 2016-04-14 21:42:37 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:42:37,584 - WARNING - Could not retrieve variants from source file in region 6:39851607-39865237. Error was invalid region `6:39851608-39865237`
[2016-04-15T04:42Z] 2016-04-14 21:42:37 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:42:37,967 - WARNING - Could not retrieve variants from source file in region 6:39895199-39895600. Error was invalid region `6:39895200-39895600`
[2016-04-15T04:42Z] 2016-04-14 21:42:39 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:42:39,436 - WARNING - Could not retrieve variants from source file in region 6:39895199-39895600. Error was invalid region `6:39895200-39895600`
[2016-04-15T04:42Z] 2016-04-14 21:42:40 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:42:40,412 - WARNING - Could not retrieve variants from source file in region 6:41028898-41029532. Error was invalid region `6:41028899-41029532`
[2016-04-15T04:42Z] 2016-04-14 21:42:40 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:42:40,458 - WARNING - Could not retrieve variants from source file in region 6:42627219-42627624. Error was invalid region `6:42627220-42627624`
[2016-04-15T04:42Z] 2016-04-14 21:42:42 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:42:42,766 - WARNING - Could not retrieve variants from source file in region 6:39851607-39865237. Error was invalid region `6:39851608-39865237`
[2016-04-15T04:42Z] 2016-04-14 21:42:43 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:42:43,370 - WARNING - Could not retrieve variants from source file in region 6:40360254-40360655. Error was invalid region `6:40360255-40360655`
[2016-04-15T04:42Z] 2016-04-14 21:42:43 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:42:43,479 - WARNING - Could not retrieve variants from source file in region 6:31902078-31936869. Error was invalid region `6:31902079-31936869`
[2016-04-15T04:42Z] 2016-04-14 21:42:43 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:42:43,603 - WARNING - Could not retrieve variants from source file in region 6:39895199-39895600. Error was invalid region `6:39895200-39895600`
[2016-04-15T04:42Z] 2016-04-14 21:42:47 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:42:47,837 - WARNING - Could not retrieve variants from source file in region 6:39851607-39865237. Error was invalid region `6:39851608-39865237`
[2016-04-15T04:42Z] 2016-04-14 21:42:48 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:42:48,464 - WARNING - Could not retrieve variants from source file in region 6:40360254-40360655. Error was invalid region `6:40360255-40360655`
[2016-04-15T04:42Z] 2016-04-14 21:42:48 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:42:48,570 - WARNING - Could not retrieve variants from source file in region 6:31902078-31936869. Error was invalid region `6:31902079-31936869`
[2016-04-15T04:42Z] 2016-04-14 21:42:48 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:42:48,631 - WARNING - Could not retrieve variants from source file in region 6:38650377-38650818. Error was invalid region `6:38650378-38650818`
[2016-04-15T04:42Z] 2016-04-14 21:42:53 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:42:53,207 - WARNING - Could not retrieve variants from source file in region 6:42018667-42019073. Error was invalid region `6:42018668-42019073`
[2016-04-15T04:42Z] 2016-04-14 21:42:57 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:42:57,981 - WARNING - Could not retrieve variants from source file in region 6:39507678-39508079. Error was invalid region `6:39507679-39508079`
[2016-04-15T04:42Z] 2016-04-14 21:42:58 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:42:58,169 - WARNING - Could not retrieve variants from source file in region 6:42018667-42019073. Error was invalid region `6:42018668-42019073`
[2016-04-15T04:42Z] 2016-04-14 21:42:59 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:42:59,478 - WARNING - Could not retrieve variants from source file in region 6:31473335-31557118. Error was invalid region `6:31473336-31557118`
[2016-04-15T04:43Z] 2016-04-14 21:43:01 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:43:01,553 - WARNING - Could not retrieve variants from source file in region 6:39507678-39508079. Error was invalid region `6:39507679-39508079`
[2016-04-15T04:43Z] 2016-04-14 21:43:01 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:43:01,556 - WARNING - Could not retrieve variants from source file in region 6:36168417-36168818. Error was invalid region `6:36168418-36168818`
[2016-04-15T04:43Z] 2016-04-14 21:43:03 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:43:03,136 - WARNING - Could not retrieve variants from source file in region 6:41894939-41903972. Error was invalid region `6:41894940-41903972`
[2016-04-15T04:43Z] 2016-04-14 21:43:11 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:43:11,666 - WARNING - Could not retrieve variants from source file in region 6:36098199-36098600. Error was invalid region `6:36098200-36098600`
[2016-04-15T04:43Z] 2016-04-14 21:43:11 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:43:11,704 - WARNING - Could not retrieve variants from source file in region 6:35802981-35803382. Error was invalid region `6:35802982-35803382`
[2016-04-15T04:43Z] 2016-04-14 21:43:11 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:43:11,989 - WARNING - Could not retrieve variants from source file in region 6:35802981-35803382. Error was invalid region `6:35802982-35803382`
[2016-04-15T04:43Z] 2016-04-14 21:43:12 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:43:12,022 - WARNING - Could not retrieve variants from source file in region 6:35802981-35803382. Error was invalid region `6:35802982-35803382`
[2016-04-15T04:43Z] 2016-04-14 21:43:12 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:43:12,113 - WARNING - Could not retrieve variants from source file in region 6:35705681-35706082. Error was invalid region `6:35705682-35706082`
[2016-04-15T04:43Z] 2016-04-14 21:43:13 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:43:13,536 - WARNING - Could not retrieve variants from source file in region 6:35705681-35706082. Error was invalid region `6:35705682-35706082`
[2016-04-15T04:43Z] 2016-04-14 21:43:15 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:43:15,580 - WARNING - Could not retrieve variants from source file in region 6:35923035-35923436. Error was invalid region `6:35923036-35923436`
[2016-04-15T04:43Z] 2016-04-14 21:43:15 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:43:15,633 - WARNING - Could not retrieve variants from source file in region 6:35755447-35755848. Error was invalid region `6:35755448-35755848`
[2016-04-15T04:43Z] 2016-04-14 21:43:15 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:43:15,744 - WARNING - Could not retrieve variants from source file in region 6:36098199-36098600. Error was invalid region `6:36098200-36098600`
[2016-04-15T04:43Z] 2016-04-14 21:43:16 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:43:16,586 - WARNING - Could not retrieve variants from source file in region 6:35705681-35706082. Error was invalid region `6:35705682-35706082`
[2016-04-15T04:43Z] 2016-04-14 21:43:19 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:43:19,200 - WARNING - Could not retrieve variants from source file in region 6:36098199-36098600. Error was invalid region `6:36098200-36098600`
[2016-04-15T04:43Z] 2016-04-14 21:43:19 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:43:19,248 - WARNING - Could not retrieve variants from source file in region 6:35755447-35755848. Error was invalid region `6:35755448-35755848`
[2016-04-15T04:43Z] 2016-04-14 21:43:19 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:43:19,514 - WARNING - Could not retrieve variants from source file in region 6:35755447-35755848. Error was invalid region `6:35755448-35755848`
[2016-04-15T04:43Z] ['bcbio-variation-recall', 'square', '-Xms750m', '-Xmx7280m', '-XX:+UseSerialGC', '-c', 16, '-r', u'6:46598700-62284307', '--caller', 'platypus', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/6/Batch1-6_46598699_62284307.vcf.gz', '/mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/6/Batch1-6_46598699_62284307.vcf-inputs.txt'] in region: 6:46598700-62284307
[2016-04-15T04:43Z] 2016-04-14 21:43:36 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:43:36,580 - WARNING - Could not retrieve variants from source file in region 6:49403071-49425711. Error was invalid region `6:49403072-49425711`
[2016-04-15T04:43Z] 2016-04-14 21:43:36 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:43:36,718 - WARNING - Could not retrieve variants from source file in region 6:46726289-46726690. Error was invalid region `6:46726290-46726690`
[2016-04-15T04:43Z] 2016-04-14 21:43:37 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:43:37,193 - WARNING - Could not retrieve variants from source file in region 6:46792964-46856290. Error was invalid region `6:46792965-46856290`
[2016-04-15T04:43Z] 2016-04-14 21:43:37 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:43:37,482 - WARNING - Could not retrieve variants from source file in region 6:51524198-51524599. Error was invalid region `6:51524199-51524599`
[2016-04-15T04:43Z] 2016-04-14 21:43:38 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:43:38,139 - WARNING - Could not retrieve variants from source file in region 6:62284036-62284437. Error was invalid region `6:62284037-62284437`
[2016-04-15T04:43Z] 2016-04-14 21:43:38 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:43:38,588 - WARNING - Could not retrieve variants from source file in region 6:47563481-47563882. Error was invalid region `6:47563482-47563882`
[2016-04-15T04:43Z] 2016-04-14 21:43:38 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:43:38,666 - WARNING - Could not retrieve variants from source file in region 6:51720627-51732997. Error was invalid region `6:51720628-51732997`
[2016-04-15T04:43Z] 2016-04-14 21:43:45 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:43:45,737 - WARNING - Could not retrieve variants from source file in region 6:49814168-49814569. Error was invalid region `6:49814169-49814569`
[2016-04-15T04:43Z] 2016-04-14 21:43:45 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:43:45,761 - WARNING - Could not retrieve variants from source file in region 6:51483750-51497693. Error was invalid region `6:51483751-51497693`
[2016-04-15T04:43Z] 2016-04-14 21:43:46 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:43:46,300 - WARNING - Could not retrieve variants from source file in region 6:46792964-46856290. Error was invalid region `6:46792965-46856290`
[2016-04-15T04:43Z] 2016-04-14 21:43:46 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:43:46,468 - WARNING - Could not retrieve variants from source file in region 6:51612966-51613367. Error was invalid region `6:51612967-51613367`
[2016-04-15T04:43Z] 2016-04-14 21:43:47 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:43:47,302 - WARNING - Could not retrieve variants from source file in region 6:52657341-52659152. Error was invalid region `6:52657342-52659152`
[2016-04-15T04:43Z] 2016-04-14 21:43:47 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:43:47,544 - WARNING - Could not retrieve variants from source file in region 6:47563481-47563882. Error was invalid region `6:47563482-47563882`
[2016-04-15T04:43Z] 2016-04-14 21:43:47 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:43:47,732 - WARNING - Could not retrieve variants from source file in region 6:62284036-62284437. Error was invalid region `6:62284037-62284437`
[2016-04-15T04:43Z] 2016-04-14 21:43:47 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:43:47,871 - WARNING - Could not retrieve variants from source file in region 6:51720627-51732997. Error was invalid region `6:51720628-51732997`
[2016-04-15T04:43Z] 2016-04-14 21:43:49 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:43:49,377 - WARNING - Could not retrieve variants from source file in region 6:49403071-49425711. Error was invalid region `6:49403072-49425711`
[2016-04-15T04:43Z] 2016-04-14 21:43:50 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:43:50,521 - WARNING - Could not retrieve variants from source file in region 6:51483750-51497693. Error was invalid region `6:51483751-51497693`
[2016-04-15T04:43Z] 2016-04-14 21:43:53 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:43:53,434 - WARNING - Could not retrieve variants from source file in region 6:51612966-51613367. Error was invalid region `6:51612967-51613367`
[2016-04-15T04:43Z] 2016-04-14 21:43:54 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:43:54,698 - WARNING - Could not retrieve variants from source file in region 6:52657341-52659152. Error was invalid region `6:52657342-52659152`
[2016-04-15T04:43Z] 2016-04-14 21:43:54 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:43:54,739 - WARNING - Could not retrieve variants from source file in region 6:47563481-47563882. Error was invalid region `6:47563482-47563882`
[2016-04-15T04:43Z] 2016-04-14 21:43:55 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:43:55,047 - WARNING - Could not retrieve variants from source file in region 6:62284036-62284437. Error was invalid region `6:62284037-62284437`
[2016-04-15T04:44Z] 2016-04-14 21:44:04 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:44:04,674 - WARNING - Could not retrieve variants from source file in region 6:47682393-47682794. Error was invalid region `6:47682394-47682794`
[2016-04-15T04:44Z] 2016-04-14 21:44:05 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:44:05,703 - WARNING - Could not retrieve variants from source file in region 6:46980147-46980548. Error was invalid region `6:46980148-46980548`
[2016-04-15T04:44Z] 2016-04-14 21:44:06 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:44:06,549 - WARNING - Could not retrieve variants from source file in region 6:46980147-46980548. Error was invalid region `6:46980148-46980548`
[2016-04-15T04:44Z] 2016-04-14 21:44:07 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:44:07,407 - WARNING - Could not retrieve variants from source file in region 6:46609694-46623888. Error was invalid region `6:46609695-46623888`
[2016-04-15T04:44Z] 2016-04-14 21:44:07 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:44:07,462 - WARNING - Could not retrieve variants from source file in region 6:49701228-49701713. Error was invalid region `6:49701229-49701713`
[2016-04-15T04:44Z] 2016-04-14 21:44:08 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:44:08,652 - WARNING - Could not retrieve variants from source file in region 6:52617520-52617921. Error was invalid region `6:52617521-52617921`
[2016-04-15T04:44Z] 2016-04-14 21:44:08 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:44:08,663 - WARNING - Could not retrieve variants from source file in region 6:51875039-51947427. Error was invalid region `6:51875040-51947427`
[2016-04-15T04:44Z] 2016-04-14 21:44:08 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:44:08,989 - WARNING - Could not retrieve variants from source file in region 6:47682393-47682794. Error was invalid region `6:47682394-47682794`
[2016-04-15T04:44Z] 2016-04-14 21:44:10 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:44:10,041 - WARNING - Could not retrieve variants from source file in region 6:52129273-52144411. Error was invalid region `6:52129274-52144411`
[2016-04-15T04:44Z] 2016-04-14 21:44:10 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:44:10,947 - WARNING - Could not retrieve variants from source file in region 6:49927905-49931973. Error was invalid region `6:49927906-49931973`
[2016-04-15T04:44Z] 2016-04-14 21:44:11 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:44:11,107 - WARNING - Could not retrieve variants from source file in region 6:55266414-55266815. Error was invalid region `6:55266415-55266815`
[2016-04-15T04:44Z] 2016-04-14 21:44:11 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:44:11,590 - WARNING - Could not retrieve variants from source file in region 6:49701228-49701713. Error was invalid region `6:49701229-49701713`
[2016-04-15T04:44Z] 2016-04-14 21:44:11 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:44:11,712 - WARNING - Could not retrieve variants from source file in region 6:51586560-51586961. Error was invalid region `6:51586561-51586961`
[2016-04-15T04:44Z] 2016-04-14 21:44:12 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:44:12,727 - WARNING - Could not retrieve variants from source file in region 6:52617520-52617921. Error was invalid region `6:52617521-52617921`
[2016-04-15T04:44Z] 2016-04-14 21:44:13 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:44:13,110 - WARNING - Could not retrieve variants from source file in region 6:47682393-47682794. Error was invalid region `6:47682394-47682794`
[2016-04-15T04:44Z] 2016-04-14 21:44:15 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:44:15,364 - WARNING - Could not retrieve variants from source file in region 6:55266414-55266815. Error was invalid region `6:55266415-55266815`
[2016-04-15T04:44Z] 2016-04-14 21:44:15 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:44:15,852 - WARNING - Could not retrieve variants from source file in region 6:49701228-49701713. Error was invalid region `6:49701229-49701713`
[2016-04-15T04:44Z] 2016-04-14 21:44:15 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:44:15,928 - WARNING - Could not retrieve variants from source file in region 6:51586560-51586961. Error was invalid region `6:51586561-51586961`
[2016-04-15T04:44Z] 2016-04-14 21:44:16 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:44:16,862 - WARNING - Could not retrieve variants from source file in region 6:52617520-52617921. Error was invalid region `6:52617521-52617921`
[2016-04-15T04:44Z] 2016-04-14 21:44:18 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:44:18,891 - WARNING - Could not retrieve variants from source file in region 6:57498733-57512868. Error was invalid region `6:57498734-57512868`
[2016-04-15T04:44Z] 2016-04-14 21:44:19 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:44:19,629 - WARNING - Could not retrieve variants from source file in region 6:55266414-55266815. Error was invalid region `6:55266415-55266815`
[2016-04-15T04:44Z] 2016-04-14 21:44:22 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:44:22,359 - WARNING - Could not retrieve variants from source file in region 6:56557133-56569294. Error was invalid region `6:56557134-56569294`
[2016-04-15T04:44Z] 2016-04-14 21:44:25 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:44:24,999 - WARNING - Could not retrieve variants from source file in region 6:49459767-49519104. Error was invalid region `6:49459768-49519104`
[2016-04-15T04:44Z] 2016-04-14 21:44:28 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:44:28,209 - WARNING - Could not retrieve variants from source file in region 6:57244569-57247172. Error was invalid region `6:57244570-57247172`
[2016-04-15T04:44Z] 2016-04-14 21:44:28 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:44:28,334 - WARNING - Could not retrieve variants from source file in region 6:54185936-54186337. Error was invalid region `6:54185937-54186337`
[2016-04-15T04:44Z] 2016-04-14 21:44:29 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:44:29,628 - WARNING - Could not retrieve variants from source file in region 6:53883632-53884033. Error was invalid region `6:53883633-53884033`
[2016-04-15T04:44Z] 2016-04-14 21:44:29 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:44:29,689 - WARNING - Could not retrieve variants from source file in region 6:54805477-54806679. Error was invalid region `6:54805478-54806679`
[2016-04-15T04:44Z] 2016-04-14 21:44:30 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:44:30,154 - WARNING - Could not retrieve variants from source file in region 6:49459767-49519104. Error was invalid region `6:49459768-49519104`
[2016-04-15T04:44Z] 2016-04-14 21:44:30 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:44:30,275 - WARNING - Could not retrieve variants from source file in region 6:56044367-56044768. Error was invalid region `6:56044368-56044768`
[2016-04-15T04:44Z] 2016-04-14 21:44:30 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:44:30,294 - WARNING - Could not retrieve variants from source file in region 6:54054475-54082328. Error was invalid region `6:54054476-54082328`
[2016-04-15T04:44Z] 2016-04-14 21:44:30 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:44:30,459 - WARNING - Could not retrieve variants from source file in region 6:52343688-52344089. Error was invalid region `6:52343689-52344089`
[2016-04-15T04:44Z] 2016-04-14 21:44:30 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:44:30,670 - WARNING - Could not retrieve variants from source file in region 6:54734911-54735312. Error was invalid region `6:54734912-54735312`
[2016-04-15T04:44Z] 2016-04-14 21:44:32 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:44:32,145 - WARNING - Could not retrieve variants from source file in region 6:57466964-57467365. Error was invalid region `6:57466965-57467365`
[2016-04-15T04:44Z] 2016-04-14 21:44:32 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:44:32,949 - WARNING - Could not retrieve variants from source file in region 6:57244569-57247172. Error was invalid region `6:57244570-57247172`
[2016-04-15T04:44Z] 2016-04-14 21:44:33 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:44:33,045 - WARNING - Could not retrieve variants from source file in region 6:54185936-54186337. Error was invalid region `6:54185937-54186337`
[2016-04-15T04:44Z] 2016-04-14 21:44:33 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:44:33,723 - WARNING - Could not retrieve variants from source file in region 6:55142126-55142547. Error was invalid region `6:55142127-55142547`
[2016-04-15T04:44Z] 2016-04-14 21:44:35 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:44:35,929 - WARNING - Could not retrieve variants from source file in region 6:56044367-56044768. Error was invalid region `6:56044368-56044768`
[2016-04-15T04:44Z] 2016-04-14 21:44:35 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:44:35,983 - WARNING - Could not retrieve variants from source file in region 6:52343688-52344089. Error was invalid region `6:52343689-52344089`
[2016-04-15T04:44Z] 2016-04-14 21:44:36 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:44:36,396 - WARNING - Could not retrieve variants from source file in region 6:54054475-54082328. Error was invalid region `6:54054476-54082328`
[2016-04-15T04:44Z] 2016-04-14 21:44:36 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:44:36,776 - WARNING - Could not retrieve variants from source file in region 6:54734911-54735312. Error was invalid region `6:54734912-54735312`
[2016-04-15T04:44Z] 2016-04-14 21:44:36 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:44:36,978 - WARNING - Could not retrieve variants from source file in region 6:57466964-57467365. Error was invalid region `6:57466965-57467365`
[2016-04-15T04:44Z] 2016-04-14 21:44:37 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:44:37,478 - WARNING - Could not retrieve variants from source file in region 6:57244569-57247172. Error was invalid region `6:57244570-57247172`
[2016-04-15T04:44Z] 2016-04-14 21:44:37 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:44:37,582 - WARNING - Could not retrieve variants from source file in region 6:54185936-54186337. Error was invalid region `6:54185937-54186337`
[2016-04-15T04:44Z] 2016-04-14 21:44:40 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:44:40,322 - WARNING - Could not retrieve variants from source file in region 6:54805477-54806679. Error was invalid region `6:54805478-54806679`
[2016-04-15T04:44Z] 2016-04-14 21:44:40 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:44:40,789 - WARNING - Could not retrieve variants from source file in region 6:56044367-56044768. Error was invalid region `6:56044368-56044768`
[2016-04-15T04:44Z] 2016-04-14 21:44:41 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:44:41,774 - WARNING - Could not retrieve variants from source file in region 6:54054475-54082328. Error was invalid region `6:54054476-54082328`
[2016-04-15T04:44Z] 2016-04-14 21:44:41 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:44:41,887 - WARNING - Could not retrieve variants from source file in region 6:56973890-56974292. Error was invalid region `6:56973891-56974292`
[2016-04-15T04:44Z] 2016-04-14 21:44:42 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:44:42,884 - WARNING - Could not retrieve variants from source file in region 6:54734911-54735312. Error was invalid region `6:54734912-54735312`
[2016-04-15T04:44Z] 2016-04-14 21:44:43 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:44:43,153 - WARNING - Could not retrieve variants from source file in region 6:57466964-57467365. Error was invalid region `6:57466965-57467365`
[2016-04-15T04:44Z] 2016-04-14 21:44:47 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:44:47,045 - WARNING - Could not retrieve variants from source file in region 6:56469108-56473815. Error was invalid region `6:56469109-56473815`
[2016-04-15T04:44Z] 2016-04-14 21:44:51 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:44:51,661 - WARNING - Could not retrieve variants from source file in region 6:52700932-52701333. Error was invalid region `6:52700933-52701333`
[2016-04-15T04:44Z] 2016-04-14 21:44:51 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:44:51,864 - WARNING - Could not retrieve variants from source file in region 6:52700932-52701333. Error was invalid region `6:52700933-52701333`
[2016-04-15T04:44Z] 2016-04-14 21:44:52 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:44:52,204 - WARNING - Could not retrieve variants from source file in region 6:52878426-52878827. Error was invalid region `6:52878427-52878827`
[2016-04-15T04:44Z] 2016-04-14 21:44:52 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:44:52,912 - WARNING - Could not retrieve variants from source file in region 6:53516665-53519795. Error was invalid region `6:53516666-53519795`
[2016-04-15T04:44Z] 2016-04-14 21:44:53 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:44:53,303 - WARNING - Could not retrieve variants from source file in region 6:56417071-56417735. Error was invalid region `6:56417072-56417735`
[2016-04-15T04:44Z] 2016-04-14 21:44:54 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:44:54,025 - WARNING - Could not retrieve variants from source file in region 6:55739342-55739743. Error was invalid region `6:55739343-55739743`
[2016-04-15T04:44Z] 2016-04-14 21:44:54 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:44:54,368 - WARNING - Could not retrieve variants from source file in region 6:55638817-55639218. Error was invalid region `6:55638818-55639218`
[2016-04-15T04:44Z] 2016-04-14 21:44:55 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:44:55,220 - WARNING - Could not retrieve variants from source file in region 6:55739342-55739743. Error was invalid region `6:55739343-55739743`
[2016-04-15T04:44Z] 2016-04-14 21:44:56 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:44:56,125 - WARNING - Could not retrieve variants from source file in region 6:52700932-52701333. Error was invalid region `6:52700933-52701333`
[2016-04-15T04:44Z] 2016-04-14 21:44:56 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:44:56,486 - WARNING - Could not retrieve variants from source file in region 6:53989315-54002421. Error was invalid region `6:53989316-54002421`
[2016-04-15T04:44Z] 2016-04-14 21:44:57 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:44:57,059 - WARNING - Could not retrieve variants from source file in region 6:54219115-54219516. Error was invalid region `6:54219116-54219516`
[2016-04-15T04:44Z] 2016-04-14 21:44:57 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:44:57,212 - WARNING - Could not retrieve variants from source file in region 6:56417071-56417735. Error was invalid region `6:56417072-56417735`
[2016-04-15T04:44Z] 2016-04-14 21:44:58 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:44:58,007 - WARNING - Could not retrieve variants from source file in region 6:55739342-55739743. Error was invalid region `6:55739343-55739743`
[2016-04-15T04:44Z] 2016-04-14 21:44:58 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:44:58,694 - WARNING - Could not retrieve variants from source file in region 6:56417071-56417735. Error was invalid region `6:56417072-56417735`
[2016-04-15T04:45Z] 2016-04-14 21:45:00 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:45:00,709 - WARNING - Could not retrieve variants from source file in region 6:55638817-55639218. Error was invalid region `6:55638818-55639218`
[2016-04-15T04:45Z] 2016-04-14 21:45:00 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:45:00,822 - WARNING - Could not retrieve variants from source file in region 6:54219115-54219516. Error was invalid region `6:54219116-54219516`
[2016-04-15T04:45Z] ['bcbio-variation-recall', 'square', '-Xms750m', '-Xmx7280m', '-XX:+UseSerialGC', '-c', 16, '-r', u'6:62390868-78173120', '--caller', 'platypus', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/6/Batch1-6_62390867_78173120.vcf.gz', '/mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/6/Batch1-6_62390867_78173120.vcf-inputs.txt'] in region: 6:62390868-78173120
[2016-04-15T04:45Z] 2016-04-14 21:45:15 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:45:15,911 - WARNING - Could not retrieve variants from source file in region 6:78172049-78173182. Error was invalid region `6:78172050-78173182`
[2016-04-15T04:45Z] 2016-04-14 21:45:17 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:45:17,204 - WARNING - Could not retrieve variants from source file in region 6:71665775-71666974. Error was invalid region `6:71665776-71666974`
[2016-04-15T04:45Z] 2016-04-14 21:45:17 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:45:17,364 - WARNING - Could not retrieve variants from source file in region 6:64694143-64694544. Error was invalid region `6:64694144-64694544`
[2016-04-15T04:45Z] 2016-04-14 21:45:17 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:45:17,508 - WARNING - Could not retrieve variants from source file in region 6:71236005-71236406. Error was invalid region `6:71236006-71236406`
[2016-04-15T04:45Z] 2016-04-14 21:45:17 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:45:17,829 - WARNING - Could not retrieve variants from source file in region 6:69666473-69666874. Error was invalid region `6:69666474-69666874`
[2016-04-15T04:45Z] 2016-04-14 21:45:17 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:45:17,925 - WARNING - Could not retrieve variants from source file in region 6:73904346-73904747. Error was invalid region `6:73904347-73904747`
[2016-04-15T04:45Z] 2016-04-14 21:45:17 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:45:17,948 - WARNING - Could not retrieve variants from source file in region 6:70961622-70984626. Error was invalid region `6:70961623-70984626`
[2016-04-15T04:45Z] 2016-04-14 21:45:18 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:45:18,167 - WARNING - Could not retrieve variants from source file in region 6:72889261-72892573. Error was invalid region `6:72889262-72892573`
[2016-04-15T04:45Z] 2016-04-14 21:45:18 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:45:18,413 - WARNING - Could not retrieve variants from source file in region 6:73331829-73332311. Error was invalid region `6:73331830-73332311`
[2016-04-15T04:45Z] 2016-04-14 21:45:18 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:45:18,534 - WARNING - Could not retrieve variants from source file in region 6:70866398-70866799. Error was invalid region `6:70866399-70866799`
[2016-04-15T04:45Z] 2016-04-14 21:45:18 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:45:18,889 - WARNING - Could not retrieve variants from source file in region 6:72970922-72972752. Error was invalid region `6:72970923-72972752`
[2016-04-15T04:45Z] 2016-04-14 21:45:19 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:45:19,051 - WARNING - Could not retrieve variants from source file in region 6:65622252-65622653. Error was invalid region `6:65622253-65622653`
[2016-04-15T04:45Z] 2016-04-14 21:45:21 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:45:21,624 - WARNING - Could not retrieve variants from source file in region 6:70407254-70407655. Error was invalid region `6:70407255-70407655`
[2016-04-15T04:45Z] 2016-04-14 21:45:24 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:45:24,347 - WARNING - Could not retrieve variants from source file in region 6:71377570-71377971. Error was invalid region `6:71377571-71377971`
[2016-04-15T04:45Z] 2016-04-14 21:45:26 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:45:26,170 - WARNING - Could not retrieve variants from source file in region 6:69666473-69666874. Error was invalid region `6:69666474-69666874`
[2016-04-15T04:45Z] 2016-04-14 21:45:27 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:45:27,223 - WARNING - Could not retrieve variants from source file in region 6:70407254-70407655. Error was invalid region `6:70407255-70407655`
[2016-04-15T04:45Z] 2016-04-14 21:45:27 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:45:27,322 - WARNING - Could not retrieve variants from source file in region 6:70866398-70866799. Error was invalid region `6:70866399-70866799`
[2016-04-15T04:45Z] 2016-04-14 21:45:27 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:45:27,349 - WARNING - Could not retrieve variants from source file in region 6:73331829-73332311. Error was invalid region `6:73331830-73332311`
[2016-04-15T04:45Z] 2016-04-14 21:45:27 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:45:27,392 - WARNING - Could not retrieve variants from source file in region 6:71546491-71569280. Error was invalid region `6:71546492-71569280`
[2016-04-15T04:45Z] 2016-04-14 21:45:27 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:45:27,398 - WARNING - Could not retrieve variants from source file in region 6:65622252-65622653. Error was invalid region `6:65622253-65622653`
[2016-04-15T04:45Z] 2016-04-14 21:45:27 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:45:27,871 - WARNING - Could not retrieve variants from source file in region 6:64694143-64694544. Error was invalid region `6:64694144-64694544`
[2016-04-15T04:45Z] 2016-04-14 21:45:28 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:45:28,507 - WARNING - Could not retrieve variants from source file in region 6:71236005-71236406. Error was invalid region `6:71236006-71236406`
[2016-04-15T04:45Z] 2016-04-14 21:45:29 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:45:29,131 - WARNING - Could not retrieve variants from source file in region 6:71377570-71377971. Error was invalid region `6:71377571-71377971`
[2016-04-15T04:45Z] 2016-04-14 21:45:30 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:45:30,868 - WARNING - Could not retrieve variants from source file in region 6:70961622-70984626. Error was invalid region `6:70961623-70984626`
[2016-04-15T04:45Z] 2016-04-14 21:45:32 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:45:32,861 - WARNING - Could not retrieve variants from source file in region 6:69666473-69666874. Error was invalid region `6:69666474-69666874`
[2016-04-15T04:45Z] 2016-04-14 21:45:34 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:45:34,630 - WARNING - Could not retrieve variants from source file in region 6:71546491-71569280. Error was invalid region `6:71546492-71569280`
[2016-04-15T04:45Z] 2016-04-14 21:45:35 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:45:35,116 - WARNING - Could not retrieve variants from source file in region 6:65622252-65622653. Error was invalid region `6:65622253-65622653`
[2016-04-15T04:45Z] 2016-04-14 21:45:35 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:45:35,601 - WARNING - Could not retrieve variants from source file in region 6:73331829-73332311. Error was invalid region `6:73331830-73332311`
[2016-04-15T04:45Z] 2016-04-14 21:45:43 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:45:43,719 - WARNING - Could not retrieve variants from source file in region 6:62886888-62887289. Error was invalid region `6:62886889-62887289`
[2016-04-15T04:45Z] 2016-04-14 21:45:45 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:45:45,199 - WARNING - Could not retrieve variants from source file in region 6:71123455-71123856. Error was invalid region `6:71123456-71123856`
[2016-04-15T04:45Z] 2016-04-14 21:45:45 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:45:45,686 - WARNING - Could not retrieve variants from source file in region 6:71269248-71289379. Error was invalid region `6:71269249-71289379`
[2016-04-15T04:45Z] 2016-04-14 21:45:46 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:45:46,110 - WARNING - Could not retrieve variants from source file in region 6:70916677-70917078. Error was invalid region `6:70916678-70917078`
[2016-04-15T04:45Z] 2016-04-14 21:45:47 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:45:47,103 - WARNING - Could not retrieve variants from source file in region 6:70916677-70917078. Error was invalid region `6:70916678-70917078`
[2016-04-15T04:45Z] 2016-04-14 21:45:47 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:45:47,731 - WARNING - Could not retrieve variants from source file in region 6:66112198-66115336. Error was invalid region `6:66112199-66115336`
[2016-04-15T04:45Z] 2016-04-14 21:45:48 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:45:48,247 - WARNING - Could not retrieve variants from source file in region 6:76640570-76660741. Error was invalid region `6:76640571-76660741`
[2016-04-15T04:45Z] 2016-04-14 21:45:48 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:45:48,312 - WARNING - Could not retrieve variants from source file in region 6:72922339-72922740. Error was invalid region `6:72922340-72922740`
[2016-04-15T04:45Z] 2016-04-14 21:45:48 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:45:48,547 - WARNING - Could not retrieve variants from source file in region 6:74073320-74079231. Error was invalid region `6:74073321-74079231`
[2016-04-15T04:45Z] 2016-04-14 21:45:48 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:45:48,754 - WARNING - Could not retrieve variants from source file in region 6:62886888-62887289. Error was invalid region `6:62886889-62887289`
[2016-04-15T04:45Z] 2016-04-14 21:45:51 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:45:51,055 - WARNING - Could not retrieve variants from source file in region 6:70916677-70917078. Error was invalid region `6:70916678-70917078`
[2016-04-15T04:45Z] 2016-04-14 21:45:53 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:45:53,180 - WARNING - Could not retrieve variants from source file in region 6:74073320-74079231. Error was invalid region `6:74073321-74079231`
[2016-04-15T04:45Z] 2016-04-14 21:45:53 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:45:53,824 - WARNING - Could not retrieve variants from source file in region 6:62886888-62887289. Error was invalid region `6:62886889-62887289`
[2016-04-15T04:45Z] 2016-04-14 21:45:55 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:45:55,351 - WARNING - Could not retrieve variants from source file in region 6:65300305-65301694. Error was invalid region `6:65300306-65301694`
[2016-04-15T04:45Z] 2016-04-14 21:45:55 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:45:55,604 - WARNING - Could not retrieve variants from source file in region 6:71123455-71123856. Error was invalid region `6:71123456-71123856`
[2016-04-15T04:45Z] 2016-04-14 21:45:55 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:45:55,937 - WARNING - Could not retrieve variants from source file in region 6:71269248-71289379. Error was invalid region `6:71269249-71289379`
[2016-04-15T04:45Z] 2016-04-14 21:45:56 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:45:56,023 - WARNING - Could not retrieve variants from source file in region 6:70041711-70071363. Error was invalid region `6:70041712-70071363`
[2016-04-15T04:45Z] 2016-04-14 21:45:56 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:45:56,071 - WARNING - Could not retrieve variants from source file in region 6:74493221-74533382. Error was invalid region `6:74493222-74533382`
[2016-04-15T04:45Z] 2016-04-14 21:45:57 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:45:57,911 - WARNING - Could not retrieve variants from source file in region 6:74073320-74079231. Error was invalid region `6:74073321-74079231`
[2016-04-15T04:46Z] 2016-04-14 21:46:05 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:46:05,915 - WARNING - Could not retrieve variants from source file in region 6:75797091-75797492. Error was invalid region `6:75797092-75797492`
[2016-04-15T04:46Z] 2016-04-14 21:46:06 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:46:06,632 - WARNING - Could not retrieve variants from source file in region 6:76368843-76369244. Error was invalid region `6:76368844-76369244`
[2016-04-15T04:46Z] 2016-04-14 21:46:07 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:46:07,053 - WARNING - Could not retrieve variants from source file in region 6:75797091-75797492. Error was invalid region `6:75797092-75797492`
[2016-04-15T04:46Z] 2016-04-14 21:46:07 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:46:07,184 - WARNING - Could not retrieve variants from source file in region 6:75797091-75797492. Error was invalid region `6:75797092-75797492`
[2016-04-15T04:46Z] 2016-04-14 21:46:07 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:46:07,250 - WARNING - Could not retrieve variants from source file in region 6:62442393-62442794. Error was invalid region `6:62442394-62442794`
[2016-04-15T04:46Z] 2016-04-14 21:46:09 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:46:09,142 - WARNING - Could not retrieve variants from source file in region 6:76017599-76018000. Error was invalid region `6:76017600-76018000`
[2016-04-15T04:46Z] 2016-04-14 21:46:09 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:46:09,454 - WARNING - Could not retrieve variants from source file in region 6:62442393-62442794. Error was invalid region `6:62442394-62442794`
[2016-04-15T04:46Z] 2016-04-14 21:46:10 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:46:10,000 - WARNING - Could not retrieve variants from source file in region 6:74353964-74354365. Error was invalid region `6:74353965-74354365`
[2016-04-15T04:46Z] 2016-04-14 21:46:10 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:46:10,160 - WARNING - Could not retrieve variants from source file in region 6:74466166-74466567. Error was invalid region `6:74466167-74466567`
[2016-04-15T04:46Z] 2016-04-14 21:46:10 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:46:10,162 - WARNING - Could not retrieve variants from source file in region 6:74466166-74466567. Error was invalid region `6:74466167-74466567`
[2016-04-15T04:46Z] 2016-04-14 21:46:11 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:46:11,088 - WARNING - Could not retrieve variants from source file in region 6:76368843-76369244. Error was invalid region `6:76368844-76369244`
[2016-04-15T04:46Z] 2016-04-14 21:46:11 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:46:11,539 - WARNING - Could not retrieve variants from source file in region 6:66005646-66006160. Error was invalid region `6:66005647-66006160`
[2016-04-15T04:46Z] 2016-04-14 21:46:11 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:46:11,580 - WARNING - Could not retrieve variants from source file in region 6:74466166-74466567. Error was invalid region `6:74466167-74466567`
[2016-04-15T04:46Z] 2016-04-14 21:46:11 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:46:11,585 - WARNING - Could not retrieve variants from source file in region 6:62442393-62442794. Error was invalid region `6:62442394-62442794`
[2016-04-15T04:46Z] 2016-04-14 21:46:14 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:46:14,098 - WARNING - Could not retrieve variants from source file in region 6:66005646-66006160. Error was invalid region `6:66005647-66006160`
[2016-04-15T04:46Z] 2016-04-14 21:46:14 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:46:14,762 - WARNING - Could not retrieve variants from source file in region 6:76368843-76369244. Error was invalid region `6:76368844-76369244`
[2016-04-15T04:46Z] 2016-04-14 21:46:15 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:46:15,260 - WARNING - Could not retrieve variants from source file in region 6:76017599-76018000. Error was invalid region `6:76017600-76018000`
[2016-04-15T04:46Z] ['bcbio-variation-recall', 'square', '-Xms750m', '-Xmx7280m', '-XX:+UseSerialGC', '-c', 16, '-r', u'6:78400389-93953258', '--caller', 'platypus', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/6/Batch1-6_78400388_93953258.vcf.gz', '/mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/6/Batch1-6_78400388_93953258.vcf-inputs.txt'] in region: 6:78400389-93953258
[2016-04-15T04:46Z] 2016-04-14 21:46:30 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:46:30,739 - WARNING - Could not retrieve variants from source file in region 6:84300786-84303532. Error was invalid region `6:84300787-84303532`
[2016-04-15T04:46Z] 2016-04-14 21:46:32 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:46:32,257 - WARNING - Could not retrieve variants from source file in region 6:90307774-90340636. Error was invalid region `6:90307775-90340636`
[2016-04-15T04:46Z] 2016-04-14 21:46:32 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:46:32,342 - WARNING - Could not retrieve variants from source file in region 6:90039459-90039860. Error was invalid region `6:90039460-90039860`
[2016-04-15T04:46Z] 2016-04-14 21:46:33 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:46:33,090 - WARNING - Could not retrieve variants from source file in region 6:83877285-83881930. Error was invalid region `6:83877286-83881930`
[2016-04-15T04:46Z] 2016-04-14 21:46:33 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:46:33,326 - WARNING - Could not retrieve variants from source file in region 6:90447881-90459644. Error was invalid region `6:90447882-90459644`
[2016-04-15T04:46Z] 2016-04-14 21:46:33 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:46:33,599 - WARNING - Could not retrieve variants from source file in region 6:90499291-90499692. Error was invalid region `6:90499292-90499692`
[2016-04-15T04:46Z] 2016-04-14 21:46:33 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:46:33,927 - WARNING - Could not retrieve variants from source file in region 6:90642147-90661766. Error was invalid region `6:90642148-90661766`
[2016-04-15T04:46Z] 2016-04-14 21:46:33 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:46:33,981 - WARNING - Could not retrieve variants from source file in region 6:90368169-90418452. Error was invalid region `6:90368170-90418452`
[2016-04-15T04:46Z] 2016-04-14 21:46:36 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:46:36,942 - WARNING - Could not retrieve variants from source file in region 6:84300786-84303532. Error was invalid region `6:84300787-84303532`
[2016-04-15T04:46Z] 2016-04-14 21:46:39 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:46:39,739 - WARNING - Could not retrieve variants from source file in region 6:90307774-90340636. Error was invalid region `6:90307775-90340636`
[2016-04-15T04:46Z] 2016-04-14 21:46:39 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:46:39,964 - WARNING - Could not retrieve variants from source file in region 6:91257638-91258039. Error was invalid region `6:91257639-91258039`
[2016-04-15T04:46Z] 2016-04-14 21:46:40 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:46:40,972 - WARNING - Could not retrieve variants from source file in region 6:90039459-90039860. Error was invalid region `6:90039460-90039860`
[2016-04-15T04:46Z] 2016-04-14 21:46:41 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:46:41,077 - WARNING - Could not retrieve variants from source file in region 6:89907662-89927156. Error was invalid region `6:89907663-89927156`
[2016-04-15T04:46Z] 2016-04-14 21:46:41 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:46:41,906 - WARNING - Could not retrieve variants from source file in region 6:84772634-84773035. Error was invalid region `6:84772635-84773035`
[2016-04-15T04:46Z] 2016-04-14 21:46:41 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:46:41,982 - WARNING - Could not retrieve variants from source file in region 6:82900600-82901001. Error was invalid region `6:82900601-82901001`
[2016-04-15T04:46Z] 2016-04-14 21:46:42 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:46:42,015 - WARNING - Could not retrieve variants from source file in region 6:80196637-80197038. Error was invalid region `6:80196638-80197038`
[2016-04-15T04:46Z] 2016-04-14 21:46:42 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:46:42,162 - WARNING - Could not retrieve variants from source file in region 6:84233620-84234334. Error was invalid region `6:84233621-84234334`
[2016-04-15T04:46Z] 2016-04-14 21:46:42 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:46:42,219 - WARNING - Could not retrieve variants from source file in region 6:83877285-83881930. Error was invalid region `6:83877286-83881930`
[2016-04-15T04:46Z] 2016-04-14 21:46:42 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:46:42,496 - WARNING - Could not retrieve variants from source file in region 6:90447881-90459644. Error was invalid region `6:90447882-90459644`
[2016-04-15T04:46Z] 2016-04-14 21:46:42 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:46:42,793 - WARNING - Could not retrieve variants from source file in region 6:90499291-90499692. Error was invalid region `6:90499292-90499692`
[2016-04-15T04:46Z] 2016-04-14 21:46:42 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:46:42,861 - WARNING - Could not retrieve variants from source file in region 6:90368169-90418452. Error was invalid region `6:90368170-90418452`
[2016-04-15T04:46Z] 2016-04-14 21:46:42 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:46:42,974 - WARNING - Could not retrieve variants from source file in region 6:84798974-84799375. Error was invalid region `6:84798975-84799375`
[2016-04-15T04:46Z] 2016-04-14 21:46:43 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:46:43,147 - WARNING - Could not retrieve variants from source file in region 6:84300786-84303532. Error was invalid region `6:84300787-84303532`
[2016-04-15T04:46Z] 2016-04-14 21:46:43 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:46:43,251 - WARNING - Could not retrieve variants from source file in region 6:90565031-90577919. Error was invalid region `6:90565032-90577919`
[2016-04-15T04:46Z] 2016-04-14 21:46:45 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:46:45,531 - WARNING - Could not retrieve variants from source file in region 6:91257638-91258039. Error was invalid region `6:91257639-91258039`
[2016-04-15T04:46Z] 2016-04-14 21:46:46 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:46:46,412 - WARNING - Could not retrieve variants from source file in region 6:90039459-90039860. Error was invalid region `6:90039460-90039860`
[2016-04-15T04:46Z] 2016-04-14 21:46:49 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:46:49,957 - WARNING - Could not retrieve variants from source file in region 6:84233620-84234334. Error was invalid region `6:84233621-84234334`
[2016-04-15T04:46Z] 2016-04-14 21:46:50 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:46:50,237 - WARNING - Could not retrieve variants from source file in region 6:83877285-83881930. Error was invalid region `6:83877286-83881930`
[2016-04-15T04:46Z] 2016-04-14 21:46:50 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:46:50,717 - WARNING - Could not retrieve variants from source file in region 6:80196637-80197038. Error was invalid region `6:80196638-80197038`
[2016-04-15T04:46Z] 2016-04-14 21:46:50 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:46:50,767 - WARNING - Could not retrieve variants from source file in region 6:90447881-90459644. Error was invalid region `6:90447882-90459644`
[2016-04-15T04:46Z] 2016-04-14 21:46:50 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:46:50,891 - WARNING - Could not retrieve variants from source file in region 6:90642147-90661766. Error was invalid region `6:90642148-90661766`
[2016-04-15T04:47Z] 2016-04-14 21:47:01 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:47:01,436 - WARNING - Could not retrieve variants from source file in region 6:89967287-89981603. Error was invalid region `6:89967288-89981603`
[2016-04-15T04:47Z] 2016-04-14 21:47:01 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:47:01,947 - WARNING - Could not retrieve variants from source file in region 6:83949050-83949451. Error was invalid region `6:83949051-83949451`
[2016-04-15T04:47Z] 2016-04-14 21:47:02 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:47:02,788 - WARNING - Could not retrieve variants from source file in region 6:83949050-83949451. Error was invalid region `6:83949051-83949451`
[2016-04-15T04:47Z] 2016-04-14 21:47:03 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:47:03,549 - WARNING - Could not retrieve variants from source file in region 6:89967287-89981603. Error was invalid region `6:89967288-89981603`
[2016-04-15T04:47Z] 2016-04-14 21:47:04 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:47:04,863 - WARNING - Could not retrieve variants from source file in region 6:88853424-88853825. Error was invalid region `6:88853425-88853825`
[2016-04-15T04:47Z] 2016-04-14 21:47:05 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:47:05,146 - WARNING - Could not retrieve variants from source file in region 6:83666834-83667235. Error was invalid region `6:83666835-83667235`
[2016-04-15T04:47Z] 2016-04-14 21:47:05 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:47:05,188 - WARNING - Could not retrieve variants from source file in region 6:82455652-82457337. Error was invalid region `6:82455653-82457337`
[2016-04-15T04:47Z] 2016-04-14 21:47:06 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:47:06,438 - WARNING - Could not retrieve variants from source file in region 6:89967287-89981603. Error was invalid region `6:89967288-89981603`
[2016-04-15T04:47Z] 2016-04-14 21:47:06 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:47:06,464 - WARNING - Could not retrieve variants from source file in region 6:83949050-83949451. Error was invalid region `6:83949051-83949451`
[2016-04-15T04:47Z] 2016-04-14 21:47:06 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:47:06,865 - WARNING - Could not retrieve variants from source file in region 6:83838462-83838863. Error was invalid region `6:83838463-83838863`
[2016-04-15T04:47Z] 2016-04-14 21:47:07 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:47:07,507 - WARNING - Could not retrieve variants from source file in region 6:83075703-83076104. Error was invalid region `6:83075704-83076104`
[2016-04-15T04:47Z] 2016-04-14 21:47:08 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:47:08,391 - WARNING - Could not retrieve variants from source file in region 6:81017165-81017601. Error was invalid region `6:81017166-81017601`
[2016-04-15T04:47Z] 2016-04-14 21:47:09 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:47:09,286 - WARNING - Could not retrieve variants from source file in region 6:88853424-88853825. Error was invalid region `6:88853425-88853825`
[2016-04-15T04:47Z] 2016-04-14 21:47:09 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:47:09,296 - WARNING - Could not retrieve variants from source file in region 6:83666834-83667235. Error was invalid region `6:83666835-83667235`
[2016-04-15T04:47Z] 2016-04-14 21:47:10 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:47:10,282 - WARNING - Could not retrieve variants from source file in region 6:83666834-83667235. Error was invalid region `6:83666835-83667235`
[2016-04-15T04:47Z] 2016-04-14 21:47:11 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:47:11,301 - WARNING - Could not retrieve variants from source file in region 6:83075703-83076104. Error was invalid region `6:83075704-83076104`
[2016-04-15T04:47Z] 2016-04-14 21:47:11 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:47:11,905 - WARNING - Could not retrieve variants from source file in region 6:82933098-82933499. Error was invalid region `6:82933099-82933499`
[2016-04-15T04:47Z] 2016-04-14 21:47:12 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:47:12,115 - WARNING - Could not retrieve variants from source file in region 6:81017165-81017601. Error was invalid region `6:81017166-81017601`
[2016-04-15T04:47Z] 2016-04-14 21:47:13 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:47:13,318 - WARNING - Could not retrieve variants from source file in region 6:88853424-88853825. Error was invalid region `6:88853425-88853825`
[2016-04-15T04:47Z] 2016-04-14 21:47:14 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:47:14,566 - WARNING - Could not retrieve variants from source file in region 6:83838462-83838863. Error was invalid region `6:83838463-83838863`
[2016-04-15T04:47Z] 2016-04-14 21:47:14 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:47:14,625 - WARNING - Could not retrieve variants from source file in region 6:83075703-83076104. Error was invalid region `6:83075704-83076104`
[2016-04-15T04:47Z] 2016-04-14 21:47:15 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:47:15,427 - WARNING - Could not retrieve variants from source file in region 6:79911248-79911894. Error was invalid region `6:79911249-79911894`
[2016-04-15T04:47Z] 2016-04-14 21:47:16 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:47:16,571 - WARNING - Could not retrieve variants from source file in region 6:81017165-81017601. Error was invalid region `6:81017166-81017601`
[2016-04-15T04:47Z] 2016-04-14 21:47:19 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:47:19,263 - WARNING - Could not retrieve variants from source file in region 6:88046589-88058114. Error was invalid region `6:88046590-88058114`
[2016-04-15T04:47Z] 2016-04-14 21:47:19 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:47:19,812 - WARNING - Could not retrieve variants from source file in region 6:79707789-79708190. Error was invalid region `6:79707790-79708190`
[2016-04-15T04:47Z] 2016-04-14 21:47:19 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:47:19,826 - WARNING - Could not retrieve variants from source file in region 6:80579827-80580228. Error was invalid region `6:80579828-80580228`
[2016-04-15T04:47Z] 2016-04-14 21:47:24 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:47:24,523 - WARNING - Could not retrieve variants from source file in region 6:79656351-79679767. Error was invalid region `6:79656352-79679767`
[2016-04-15T04:47Z] 2016-04-14 21:47:25 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:47:25,294 - WARNING - Could not retrieve variants from source file in region 6:80579827-80580228. Error was invalid region `6:80579828-80580228`
[2016-04-15T04:47Z] 2016-04-14 21:47:25 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:47:25,299 - WARNING - Could not retrieve variants from source file in region 6:80228324-80228731. Error was invalid region `6:80228325-80228731`
[2016-04-15T04:47Z] 2016-04-14 21:47:25 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:47:25,358 - WARNING - Could not retrieve variants from source file in region 6:80228324-80228731. Error was invalid region `6:80228325-80228731`
[2016-04-15T04:47Z] 2016-04-14 21:47:25 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:47:25,655 - WARNING - Could not retrieve variants from source file in region 6:80579827-80580228. Error was invalid region `6:80579828-80580228`
[2016-04-15T04:47Z] 2016-04-14 21:47:25 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:47:25,863 - WARNING - Could not retrieve variants from source file in region 6:79707789-79708190. Error was invalid region `6:79707790-79708190`
[2016-04-15T04:47Z] 2016-04-14 21:47:25 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:47:25,863 - WARNING - Could not retrieve variants from source file in region 6:79707789-79708190. Error was invalid region `6:79707790-79708190`
[2016-04-15T04:47Z] 2016-04-14 21:47:25 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:47:25,874 - WARNING - Could not retrieve variants from source file in region 6:88170591-88170992. Error was invalid region `6:88170592-88170992`
[2016-04-15T04:47Z] 2016-04-14 21:47:25 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:47:25,896 - WARNING - Could not retrieve variants from source file in region 6:88223953-88239456. Error was invalid region `6:88223954-88239456`
[2016-04-15T04:47Z] 2016-04-14 21:47:29 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:47:29,178 - WARNING - Could not retrieve variants from source file in region 6:88117532-88126613. Error was invalid region `6:88117533-88126613`
[2016-04-15T04:47Z] 2016-04-14 21:47:30 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:47:30,340 - WARNING - Could not retrieve variants from source file in region 6:88117532-88126613. Error was invalid region `6:88117533-88126613`
[2016-04-15T04:47Z] 2016-04-14 21:47:30 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:47:30,430 - WARNING - Could not retrieve variants from source file in region 6:79656351-79679767. Error was invalid region `6:79656352-79679767`
[2016-04-15T04:47Z] 2016-04-14 21:47:30 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:47:30,517 - WARNING - Could not retrieve variants from source file in region 6:88046589-88058114. Error was invalid region `6:88046590-88058114`
[2016-04-15T04:47Z] 2016-04-14 21:47:33 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:47:33,721 - WARNING - Could not retrieve variants from source file in region 6:88117532-88126613. Error was invalid region `6:88117533-88126613`
[2016-04-15T04:47Z] 2016-04-14 21:47:33 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:47:33,948 - WARNING - Could not retrieve variants from source file in region 6:79594886-79612990. Error was invalid region `6:79594887-79612990`
[2016-04-15T04:47Z] 2016-04-14 21:47:37 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:47:37,254 - WARNING - Could not retrieve variants from source file in region 6:86199022-86199423. Error was invalid region `6:86199023-86199423`
[2016-04-15T04:47Z] 2016-04-14 21:47:37 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:47:37,290 - WARNING - Could not retrieve variants from source file in region 6:85473547-85473948. Error was invalid region `6:85473548-85473948`
[2016-04-15T04:47Z] 2016-04-14 21:47:37 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:47:37,451 - WARNING - Could not retrieve variants from source file in region 6:79594886-79612990. Error was invalid region `6:79594887-79612990`
[2016-04-15T04:47Z] 2016-04-14 21:47:40 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:47:40,383 - WARNING - Could not retrieve variants from source file in region 6:86199022-86199423. Error was invalid region `6:86199023-86199423`
[2016-04-15T04:47Z] 2016-04-14 21:47:40 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:47:40,499 - WARNING - Could not retrieve variants from source file in region 6:87965317-87994762. Error was invalid region `6:87965318-87994762`
[2016-04-15T04:47Z] 2016-04-14 21:47:40 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:47:40,595 - WARNING - Could not retrieve variants from source file in region 6:85473547-85473948. Error was invalid region `6:85473548-85473948`
[2016-04-15T04:47Z] 2016-04-14 21:47:40 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:47:40,665 - WARNING - Could not retrieve variants from source file in region 6:84881218-84881619. Error was invalid region `6:84881219-84881619`
[2016-04-15T04:47Z] 2016-04-14 21:47:40 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:47:40,680 - WARNING - Could not retrieve variants from source file in region 6:86199022-86199423. Error was invalid region `6:86199023-86199423`
[2016-04-15T04:47Z] ['bcbio-variation-recall', 'square', '-Xms750m', '-Xmx7280m', '-XX:+UseSerialGC', '-c', 16, '-r', u'6:93955016-109466584', '--caller', 'platypus', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/6/Batch1-6_93955015_109466584.vcf.gz', '/mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/6/Batch1-6_93955015_109466584.vcf-inputs.txt'] in region: 6:93955016-109466584
[2016-04-15T04:47Z] 2016-04-14 21:47:58 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:47:58,592 - WARNING - Could not retrieve variants from source file in region 6:109330547-109330949. Error was invalid region `6:109330548-109330949`
[2016-04-15T04:48Z] 2016-04-14 21:48:00 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:48:00,934 - WARNING - Could not retrieve variants from source file in region 6:108977452-108977853. Error was invalid region `6:108977453-108977853`
[2016-04-15T04:48Z] 2016-04-14 21:48:01 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:48:01,442 - WARNING - Could not retrieve variants from source file in region 6:99283165-99283566. Error was invalid region `6:99283166-99283566`
[2016-04-15T04:48Z] 2016-04-14 21:48:01 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:48:01,504 - WARNING - Could not retrieve variants from source file in region 6:97052543-97063745. Error was invalid region `6:97052544-97063745`
[2016-04-15T04:48Z] 2016-04-14 21:48:01 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:48:01,839 - WARNING - Could not retrieve variants from source file in region 6:107942141-107956285. Error was invalid region `6:107942142-107956285`
[2016-04-15T04:48Z] 2016-04-14 21:48:02 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:48:02,188 - WARNING - Could not retrieve variants from source file in region 6:107391185-107391586. Error was invalid region `6:107391186-107391586`
[2016-04-15T04:48Z] 2016-04-14 21:48:02 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:48:02,264 - WARNING - Could not retrieve variants from source file in region 6:108233718-108234119. Error was invalid region `6:108233719-108234119`
[2016-04-15T04:48Z] 2016-04-14 21:48:02 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:48:02,274 - WARNING - Could not retrieve variants from source file in region 6:101165884-101166285. Error was invalid region `6:101165885-101166285`
[2016-04-15T04:48Z] 2016-04-14 21:48:02 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:48:02,293 - WARNING - Could not retrieve variants from source file in region 6:108067792-108068193. Error was invalid region `6:108067793-108068193`
[2016-04-15T04:48Z] 2016-04-14 21:48:04 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:48:04,679 - WARNING - Could not retrieve variants from source file in region 6:109330547-109330949. Error was invalid region `6:109330548-109330949`
[2016-04-15T04:48Z] 2016-04-14 21:48:07 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:48:07,834 - WARNING - Could not retrieve variants from source file in region 6:97612952-97626564. Error was invalid region `6:97612953-97626564`
[2016-04-15T04:48Z] 2016-04-14 21:48:08 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:48:08,497 - WARNING - Could not retrieve variants from source file in region 6:108977452-108977853. Error was invalid region `6:108977453-108977853`
[2016-04-15T04:48Z] 2016-04-14 21:48:09 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:48:09,432 - WARNING - Could not retrieve variants from source file in region 6:105198056-105198457. Error was invalid region `6:105198057-105198457`
[2016-04-15T04:48Z] 2016-04-14 21:48:10 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:48:10,445 - WARNING - Could not retrieve variants from source file in region 6:99283165-99283566. Error was invalid region `6:99283166-99283566`
[2016-04-15T04:48Z] 2016-04-14 21:48:10 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:48:10,530 - WARNING - Could not retrieve variants from source file in region 6:107942141-107956285. Error was invalid region `6:107942142-107956285`
[2016-04-15T04:48Z] 2016-04-14 21:48:11 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:48:11,175 - WARNING - Could not retrieve variants from source file in region 6:108067792-108068193. Error was invalid region `6:108067793-108068193`
[2016-04-15T04:48Z] 2016-04-14 21:48:11 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:48:11,527 - WARNING - Could not retrieve variants from source file in region 6:108233718-108234119. Error was invalid region `6:108233719-108234119`
[2016-04-15T04:48Z] 2016-04-14 21:48:11 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:48:11,637 - WARNING - Could not retrieve variants from source file in region 6:109330547-109330949. Error was invalid region `6:109330548-109330949`
[2016-04-15T04:48Z] 2016-04-14 21:48:11 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:48:11,663 - WARNING - Could not retrieve variants from source file in region 6:101165884-101166285. Error was invalid region `6:101165885-101166285`
[2016-04-15T04:48Z] 2016-04-14 21:48:11 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:48:11,798 - WARNING - Could not retrieve variants from source file in region 6:105725825-105726226. Error was invalid region `6:105725826-105726226`
[2016-04-15T04:48Z] 2016-04-14 21:48:12 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:48:12,057 - WARNING - Could not retrieve variants from source file in region 6:107076572-107088421. Error was invalid region `6:107076573-107088421`
[2016-04-15T04:48Z] 2016-04-14 21:48:13 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:48:13,174 - WARNING - Could not retrieve variants from source file in region 6:97612952-97626564. Error was invalid region `6:97612953-97626564`
[2016-04-15T04:48Z] 2016-04-14 21:48:13 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:48:13,704 - WARNING - Could not retrieve variants from source file in region 6:106547161-106555215. Error was invalid region `6:106547162-106555215`
[2016-04-15T04:48Z] 2016-04-14 21:48:13 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:48:13,743 - WARNING - Could not retrieve variants from source file in region 6:108977452-108977853. Error was invalid region `6:108977453-108977853`
[2016-04-15T04:48Z] 2016-04-14 21:48:16 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:48:16,906 - WARNING - Could not retrieve variants from source file in region 6:107942141-107956285. Error was invalid region `6:107942142-107956285`
[2016-04-15T04:48Z] 2016-04-14 21:48:17 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:48:17,038 - WARNING - Could not retrieve variants from source file in region 6:99283165-99283566. Error was invalid region `6:99283166-99283566`
[2016-04-15T04:48Z] 2016-04-14 21:48:17 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:48:17,501 - WARNING - Could not retrieve variants from source file in region 6:108067792-108068193. Error was invalid region `6:108067793-108068193`
[2016-04-15T04:48Z] 2016-04-14 21:48:17 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:48:17,744 - WARNING - Could not retrieve variants from source file in region 6:107391185-107391586. Error was invalid region `6:107391186-107391586`
[2016-04-15T04:48Z] 2016-04-14 21:48:17 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:48:17,965 - WARNING - Could not retrieve variants from source file in region 6:97052543-97063745. Error was invalid region `6:97052544-97063745`
[2016-04-15T04:48Z] 2016-04-14 21:48:18 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:48:18,000 - WARNING - Could not retrieve variants from source file in region 6:101165884-101166285. Error was invalid region `6:101165885-101166285`
[2016-04-15T04:48Z] 2016-04-14 21:48:18 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:48:18,054 - WARNING - Could not retrieve variants from source file in region 6:108233718-108234119. Error was invalid region `6:108233719-108234119`
[2016-04-15T04:48Z] 2016-04-14 21:48:29 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:48:29,768 - WARNING - Could not retrieve variants from source file in region 6:99956349-99956750. Error was invalid region `6:99956350-99956750`
[2016-04-15T04:48Z] 2016-04-14 21:48:31 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:48:31,687 - WARNING - Could not retrieve variants from source file in region 6:97338867-97339278. Error was invalid region `6:97338868-97339278`
[2016-04-15T04:48Z] 2016-04-14 21:48:32 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:48:32,147 - WARNING - Could not retrieve variants from source file in region 6:108499216-108499617. Error was invalid region `6:108499217-108499617`
[2016-04-15T04:48Z] 2016-04-14 21:48:33 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:48:33,005 - WARNING - Could not retrieve variants from source file in region 6:108026244-108041991. Error was invalid region `6:108026245-108041991`
[2016-04-15T04:48Z] 2016-04-14 21:48:33 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:48:33,434 - WARNING - Could not retrieve variants from source file in region 6:107113504-107113905. Error was invalid region `6:107113505-107113905`
[2016-04-15T04:48Z] 2016-04-14 21:48:34 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:48:34,462 - WARNING - Could not retrieve variants from source file in region 6:99956349-99956750. Error was invalid region `6:99956350-99956750`
[2016-04-15T04:48Z] 2016-04-14 21:48:36 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:48:36,247 - WARNING - Could not retrieve variants from source file in region 6:97338867-97339278. Error was invalid region `6:97338868-97339278`
[2016-04-15T04:48Z] 2016-04-14 21:48:36 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:48:36,600 - WARNING - Could not retrieve variants from source file in region 6:101094343-101094744. Error was invalid region `6:101094344-101094744`
[2016-04-15T04:48Z] 2016-04-14 21:48:36 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:48:36,750 - WARNING - Could not retrieve variants from source file in region 6:96999514-96999915. Error was invalid region `6:96999515-96999915`
[2016-04-15T04:48Z] 2016-04-14 21:48:37 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:48:37,138 - WARNING - Could not retrieve variants from source file in region 6:108677766-108678167. Error was invalid region `6:108677767-108678167`
[2016-04-15T04:48Z] 2016-04-14 21:48:37 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:48:37,170 - WARNING - Could not retrieve variants from source file in region 6:105821238-105821639. Error was invalid region `6:105821239-105821639`
[2016-04-15T04:48Z] 2016-04-14 21:48:38 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:48:38,206 - WARNING - Could not retrieve variants from source file in region 6:102483145-102503507. Error was invalid region `6:102483146-102503507`
[2016-04-15T04:48Z] 2016-04-14 21:48:38 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:48:38,304 - WARNING - Could not retrieve variants from source file in region 6:105624706-105625107. Error was invalid region `6:105624707-105625107`
[2016-04-15T04:48Z] 2016-04-14 21:48:38 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:48:38,304 - WARNING - Could not retrieve variants from source file in region 6:108026244-108041991. Error was invalid region `6:108026245-108041991`
[2016-04-15T04:48Z] 2016-04-14 21:48:38 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:48:38,651 - WARNING - Could not retrieve variants from source file in region 6:97676907-97677308. Error was invalid region `6:97676908-97677308`
[2016-04-15T04:48Z] 2016-04-14 21:48:38 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:48:38,887 - WARNING - Could not retrieve variants from source file in region 6:99956349-99956750. Error was invalid region `6:99956350-99956750`
[2016-04-15T04:48Z] 2016-04-14 21:48:41 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:48:41,074 - WARNING - Could not retrieve variants from source file in region 6:97338867-97339278. Error was invalid region `6:97338868-97339278`
[2016-04-15T04:48Z] 2016-04-14 21:48:41 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:48:41,324 - WARNING - Could not retrieve variants from source file in region 6:96999514-96999915. Error was invalid region `6:96999515-96999915`
[2016-04-15T04:48Z] 2016-04-14 21:48:41 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:48:41,991 - WARNING - Could not retrieve variants from source file in region 6:108677766-108678167. Error was invalid region `6:108677767-108678167`
[2016-04-15T04:48Z] 2016-04-14 21:48:42 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:48:42,044 - WARNING - Could not retrieve variants from source file in region 6:105821238-105821639. Error was invalid region `6:105821239-105821639`
[2016-04-15T04:48Z] 2016-04-14 21:48:43 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:48:43,513 - WARNING - Could not retrieve variants from source file in region 6:107113504-107113905. Error was invalid region `6:107113505-107113905`
[2016-04-15T04:48Z] 2016-04-14 21:48:43 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:48:43,925 - WARNING - Could not retrieve variants from source file in region 6:108026244-108041991. Error was invalid region `6:108026245-108041991`
[2016-04-15T04:48Z] 2016-04-14 21:48:44 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:48:44,052 - WARNING - Could not retrieve variants from source file in region 6:97676907-97677308. Error was invalid region `6:97676908-97677308`
[2016-04-15T04:48Z] 2016-04-14 21:48:46 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:48:46,119 - WARNING - Could not retrieve variants from source file in region 6:96999514-96999915. Error was invalid region `6:96999515-96999915`
[2016-04-15T04:48Z] 2016-04-14 21:48:52 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:48:52,657 - WARNING - Could not retrieve variants from source file in region 6:105769975-105776982. Error was invalid region `6:105769976-105776982`
[2016-04-15T04:48Z] 2016-04-14 21:48:55 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:48:55,084 - WARNING - Could not retrieve variants from source file in region 6:100957133-100966196. Error was invalid region `6:100957134-100966196`
[2016-04-15T04:48Z] 2016-04-14 21:48:55 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:48:55,479 - WARNING - Could not retrieve variants from source file in region 6:101306291-101306692. Error was invalid region `6:101306292-101306692`
[2016-04-15T04:48Z] 2016-04-14 21:48:57 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:48:57,320 - WARNING - Could not retrieve variants from source file in region 6:99817390-99842246. Error was invalid region `6:99817391-99842246`
[2016-04-15T04:48Z] 2016-04-14 21:48:57 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:48:57,364 - WARNING - Could not retrieve variants from source file in region 6:99771329-99771730. Error was invalid region `6:99771330-99771730`
[2016-04-15T04:48Z] 2016-04-14 21:48:57 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:48:57,370 - WARNING - Could not retrieve variants from source file in region 6:100868510-100868969. Error was invalid region `6:100868511-100868969`
[2016-04-15T04:48Z] 2016-04-14 21:48:58 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:48:58,156 - WARNING - Could not retrieve variants from source file in region 6:97247336-97247737. Error was invalid region `6:97247337-97247737`
[2016-04-15T04:48Z] 2016-04-14 21:48:58 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:48:58,814 - WARNING - Could not retrieve variants from source file in region 6:96651529-96651930. Error was invalid region `6:96651530-96651930`
[2016-04-15T04:49Z] 2016-04-14 21:49:01 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:49:01,277 - WARNING - Could not retrieve variants from source file in region 6:105232862-105233263. Error was invalid region `6:105232863-105233263`
[2016-04-15T04:49Z] 2016-04-14 21:49:01 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:49:01,505 - WARNING - Could not retrieve variants from source file in region 6:99346610-99347011. Error was invalid region `6:99346611-99347011`
[2016-04-15T04:49Z] 2016-04-14 21:49:02 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:49:02,214 - WARNING - Could not retrieve variants from source file in region 6:99771329-99771730. Error was invalid region `6:99771330-99771730`
[2016-04-15T04:49Z] 2016-04-14 21:49:02 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:49:02,459 - WARNING - Could not retrieve variants from source file in region 6:97247336-97247737. Error was invalid region `6:97247337-97247737`
[2016-04-15T04:49Z] 2016-04-14 21:49:03 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:49:03,091 - WARNING - Could not retrieve variants from source file in region 6:96651529-96651930. Error was invalid region `6:96651530-96651930`
[2016-04-15T04:49Z] 2016-04-14 21:49:05 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:49:05,780 - WARNING - Could not retrieve variants from source file in region 6:99346610-99347011. Error was invalid region `6:99346611-99347011`
[2016-04-15T04:49Z] 2016-04-14 21:49:05 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:49:05,915 - WARNING - Could not retrieve variants from source file in region 6:100868510-100868969. Error was invalid region `6:100868511-100868969`
[2016-04-15T04:49Z] 2016-04-14 21:49:06 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:49:06,327 - WARNING - Could not retrieve variants from source file in region 6:99346610-99347011. Error was invalid region `6:99346611-99347011`
[2016-04-15T04:49Z] 2016-04-14 21:49:06 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:49:06,395 - WARNING - Could not retrieve variants from source file in region 6:99771329-99771730. Error was invalid region `6:99771330-99771730`
[2016-04-15T04:49Z] 2016-04-14 21:49:07 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:49:07,474 - WARNING - Could not retrieve variants from source file in region 6:96651529-96651930. Error was invalid region `6:96651530-96651930`
[2016-04-15T04:49Z] 2016-04-14 21:49:08 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:49:08,053 - WARNING - Could not retrieve variants from source file in region 6:100061413-100061814. Error was invalid region `6:100061414-100061814`
[2016-04-15T04:49Z] 2016-04-14 21:49:13 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:49:13,823 - WARNING - Could not retrieve variants from source file in region 6:96034349-96054452. Error was invalid region `6:96034350-96054452`
[2016-04-15T04:49Z] 2016-04-14 21:49:14 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:49:14,145 - WARNING - Could not retrieve variants from source file in region 6:94067770-94068171. Error was invalid region `6:94067771-94068171`
[2016-04-15T04:49Z] 2016-04-14 21:49:14 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:49:14,243 - WARNING - Could not retrieve variants from source file in region 6:94067770-94068171. Error was invalid region `6:94067771-94068171`
[2016-04-15T04:49Z] 2016-04-14 21:49:14 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:49:14,767 - WARNING - Could not retrieve variants from source file in region 6:93967640-93982314. Error was invalid region `6:93967641-93982314`
[2016-04-15T04:49Z] 2016-04-14 21:49:14 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:49:14,785 - WARNING - Could not retrieve variants from source file in region 6:93967640-93982314. Error was invalid region `6:93967641-93982314`
[2016-04-15T04:49Z] 2016-04-14 21:49:14 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:49:14,992 - WARNING - Could not retrieve variants from source file in region 6:93967640-93982314. Error was invalid region `6:93967641-93982314`
[2016-04-15T04:49Z] ['bcbio-variation-recall', 'square', '-Xms750m', '-Xmx7280m', '-XX:+UseSerialGC', '-c', 16, '-r', u'6:109467961-124979532', '--caller', 'platypus', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/6/Batch1-6_109467960_124979532.vcf.gz', '/mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/6/Batch1-6_109467960_124979532.vcf-inputs.txt'] in region: 6:109467961-124979532
[2016-04-15T04:49Z] 2016-04-14 21:49:28 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:49:28,941 - WARNING - Could not retrieve variants from source file in region 6:117725237-117725768. Error was invalid region `6:117725238-117725768`
[2016-04-15T04:49Z] 2016-04-14 21:49:31 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:49:31,054 - WARNING - Could not retrieve variants from source file in region 6:119148938-119149339. Error was invalid region `6:119148939-119149339`
[2016-04-15T04:49Z] 2016-04-14 21:49:31 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:49:31,566 - WARNING - Could not retrieve variants from source file in region 6:114180998-114181399. Error was invalid region `6:114180999-114181399`
[2016-04-15T04:49Z] 2016-04-14 21:49:31 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:49:31,579 - WARNING - Could not retrieve variants from source file in region 6:119510730-119511131. Error was invalid region `6:119510731-119511131`
[2016-04-15T04:49Z] 2016-04-14 21:49:31 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:49:31,602 - WARNING - Could not retrieve variants from source file in region 6:117243049-117248408. Error was invalid region `6:117243050-117248408`
[2016-04-15T04:49Z] 2016-04-14 21:49:31 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:49:31,820 - WARNING - Could not retrieve variants from source file in region 6:117683610-117684011. Error was invalid region `6:117683611-117684011`
[2016-04-15T04:49Z] 2016-04-14 21:49:31 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:49:31,968 - WARNING - Could not retrieve variants from source file in region 6:122772908-122773309. Error was invalid region `6:122772909-122773309`
[2016-04-15T04:49Z] 2016-04-14 21:49:32 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:49:32,056 - WARNING - Could not retrieve variants from source file in region 6:119215191-119215592. Error was invalid region `6:119215192-119215592`
[2016-04-15T04:49Z] 2016-04-14 21:49:32 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:49:32,423 - WARNING - Could not retrieve variants from source file in region 6:112457179-112457580. Error was invalid region `6:112457180-112457580`
[2016-04-15T04:49Z] 2016-04-14 21:49:32 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:49:32,428 - WARNING - Could not retrieve variants from source file in region 6:116875216-116875694. Error was invalid region `6:116875217-116875694`
[2016-04-15T04:49Z] 2016-04-14 21:49:32 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:49:32,753 - WARNING - Could not retrieve variants from source file in region 6:123671986-123699232. Error was invalid region `6:123671987-123699232`
[2016-04-15T04:49Z] 2016-04-14 21:49:38 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:49:38,321 - WARNING - Could not retrieve variants from source file in region 6:119148938-119149339. Error was invalid region `6:119148939-119149339`
[2016-04-15T04:49Z] 2016-04-14 21:49:39 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:49:39,925 - WARNING - Could not retrieve variants from source file in region 6:123823249-123869797. Error was invalid region `6:123823250-123869797`
[2016-04-15T04:49Z] 2016-04-14 21:49:39 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:49:39,949 - WARNING - Could not retrieve variants from source file in region 6:121620397-121629357. Error was invalid region `6:121620398-121629357`
[2016-04-15T04:49Z] 2016-04-14 21:49:40 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:49:40,617 - WARNING - Could not retrieve variants from source file in region 6:119510730-119511131. Error was invalid region `6:119510731-119511131`
[2016-04-15T04:49Z] 2016-04-14 21:49:40 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:49:40,666 - WARNING - Could not retrieve variants from source file in region 6:119669495-119669896. Error was invalid region `6:119669496-119669896`
[2016-04-15T04:49Z] 2016-04-14 21:49:41 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:49:41,605 - WARNING - Could not retrieve variants from source file in region 6:110713572-110714198. Error was invalid region `6:110713573-110714198`
[2016-04-15T04:49Z] 2016-04-14 21:49:44 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:49:44,500 - WARNING - Could not retrieve variants from source file in region 6:119148938-119149339. Error was invalid region `6:119148939-119149339`
[2016-04-15T04:49Z] 2016-04-14 21:49:45 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:49:45,615 - WARNING - Could not retrieve variants from source file in region 6:123823249-123869797. Error was invalid region `6:123823250-123869797`
[2016-04-15T04:49Z] 2016-04-14 21:49:46 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:49:46,428 - WARNING - Could not retrieve variants from source file in region 6:121620397-121629357. Error was invalid region `6:121620398-121629357`
[2016-04-15T04:49Z] 2016-04-14 21:49:48 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:49:48,207 - WARNING - Could not retrieve variants from source file in region 6:119510730-119511131. Error was invalid region `6:119510731-119511131`
[2016-04-15T04:49Z] 2016-04-14 21:49:48 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:49:48,590 - WARNING - Could not retrieve variants from source file in region 6:122772908-122773309. Error was invalid region `6:122772909-122773309`
[2016-04-15T04:49Z] 2016-04-14 21:49:48 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:49:48,997 - WARNING - Could not retrieve variants from source file in region 6:119215191-119215592. Error was invalid region `6:119215192-119215592`
[2016-04-15T04:49Z] 2016-04-14 21:49:49 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:49:49,406 - WARNING - Could not retrieve variants from source file in region 6:116875216-116875694. Error was invalid region `6:116875217-116875694`
[2016-04-15T04:49Z] 2016-04-14 21:49:49 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:49:49,439 - WARNING - Could not retrieve variants from source file in region 6:110713572-110714198. Error was invalid region `6:110713573-110714198`
[2016-04-15T04:50Z] 2016-04-14 21:50:00 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:50:00,035 - WARNING - Could not retrieve variants from source file in region 6:117621973-117622423. Error was invalid region `6:117621974-117622423`
[2016-04-15T04:50Z] 2016-04-14 21:50:00 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:50:00,562 - WARNING - Could not retrieve variants from source file in region 6:118886750-118887493. Error was invalid region `6:118886751-118887493`
[2016-04-15T04:50Z] 2016-04-14 21:50:02 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:50:02,407 - WARNING - Could not retrieve variants from source file in region 6:121577159-121577560. Error was invalid region `6:121577160-121577560`
[2016-04-15T04:50Z] 2016-04-14 21:50:02 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:50:02,628 - WARNING - Could not retrieve variants from source file in region 6:111587055-111587501. Error was invalid region `6:111587056-111587501`
[2016-04-15T04:50Z] 2016-04-14 21:50:02 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:50:02,788 - WARNING - Could not retrieve variants from source file in region 6:112671400-112671801. Error was invalid region `6:112671401-112671801`
[2016-04-15T04:50Z] 2016-04-14 21:50:04 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:50:04,861 - WARNING - Could not retrieve variants from source file in region 6:117621973-117622423. Error was invalid region `6:117621974-117622423`
[2016-04-15T04:50Z] 2016-04-14 21:50:05 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:50:05,488 - WARNING - Could not retrieve variants from source file in region 6:118886750-118887493. Error was invalid region `6:118886751-118887493`
[2016-04-15T04:50Z] 2016-04-14 21:50:05 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:50:05,953 - WARNING - Could not retrieve variants from source file in region 6:117869280-117871082. Error was invalid region `6:117869281-117871082`
[2016-04-15T04:50Z] 2016-04-14 21:50:06 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:50:06,252 - WARNING - Could not retrieve variants from source file in region 6:112493661-112508960. Error was invalid region `6:112493662-112508960`
[2016-04-15T04:50Z] 2016-04-14 21:50:06 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:50:06,851 - WARNING - Could not retrieve variants from source file in region 6:116783179-116785040. Error was invalid region `6:116783180-116785040`
[2016-04-15T04:50Z] 2016-04-14 21:50:07 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:50:07,595 - WARNING - Could not retrieve variants from source file in region 6:110679202-110679603. Error was invalid region `6:110679203-110679603`
[2016-04-15T04:50Z] 2016-04-14 21:50:09 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:50:09,536 - WARNING - Could not retrieve variants from source file in region 6:112382182-112382583. Error was invalid region `6:112382183-112382583`
[2016-04-15T04:50Z] 2016-04-14 21:50:10 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:50:10,164 - WARNING - Could not retrieve variants from source file in region 6:118886750-118887493. Error was invalid region `6:118886751-118887493`
[2016-04-15T04:50Z] 2016-04-14 21:50:10 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:50:10,896 - WARNING - Could not retrieve variants from source file in region 6:117869280-117871082. Error was invalid region `6:117869281-117871082`
[2016-04-15T04:50Z] 2016-04-14 21:50:11 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:50:11,225 - WARNING - Could not retrieve variants from source file in region 6:112493661-112508960. Error was invalid region `6:112493662-112508960`
[2016-04-15T04:50Z] 2016-04-14 21:50:11 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:50:11,369 - WARNING - Could not retrieve variants from source file in region 6:117113442-117130894. Error was invalid region `6:117113443-117130894`
[2016-04-15T04:50Z] 2016-04-14 21:50:11 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:50:11,677 - WARNING - Could not retrieve variants from source file in region 6:121577159-121577560. Error was invalid region `6:121577160-121577560`
[2016-04-15T04:50Z] 2016-04-14 21:50:12 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:50:12,024 - WARNING - Could not retrieve variants from source file in region 6:112671400-112671801. Error was invalid region `6:112671401-112671801`
[2016-04-15T04:50Z] 2016-04-14 21:50:12 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:50:12,687 - WARNING - Could not retrieve variants from source file in region 6:111587055-111587501. Error was invalid region `6:111587056-111587501`
[2016-04-15T04:50Z] 2016-04-14 21:50:12 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:50:12,793 - WARNING - Could not retrieve variants from source file in region 6:110679202-110679603. Error was invalid region `6:110679203-110679603`
[2016-04-15T04:50Z] 2016-04-14 21:50:16 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:50:16,265 - WARNING - Could not retrieve variants from source file in region 6:117869280-117871082. Error was invalid region `6:117869281-117871082`
[2016-04-15T04:50Z] 2016-04-14 21:50:16 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:50:16,440 - WARNING - Could not retrieve variants from source file in region 6:112493661-112508960. Error was invalid region `6:112493662-112508960`
[2016-04-15T04:50Z] 2016-04-14 21:50:16 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:50:16,689 - WARNING - Could not retrieve variants from source file in region 6:116783179-116785040. Error was invalid region `6:116783180-116785040`
[2016-04-15T04:50Z] 2016-04-14 21:50:17 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:50:17,876 - WARNING - Could not retrieve variants from source file in region 6:116949148-116973372. Error was invalid region `6:116949149-116973372`
[2016-04-15T04:50Z] 2016-04-14 21:50:18 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:50:18,224 - WARNING - Could not retrieve variants from source file in region 6:110679202-110679603. Error was invalid region `6:110679203-110679603`
[2016-04-15T04:50Z] 2016-04-14 21:50:18 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:50:18,283 - WARNING - Could not retrieve variants from source file in region 6:116441259-116446766. Error was invalid region `6:116441260-116446766`
[2016-04-15T04:50Z] 2016-04-14 21:50:26 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:50:26,152 - WARNING - Could not retrieve variants from source file in region 6:116757346-116757747. Error was invalid region `6:116757347-116757747`
[2016-04-15T04:50Z] 2016-04-14 21:50:27 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:50:27,440 - WARNING - Could not retrieve variants from source file in region 6:114378759-114379160. Error was invalid region `6:114378760-114379160`
[2016-04-15T04:50Z] 2016-04-14 21:50:29 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:50:29,103 - WARNING - Could not retrieve variants from source file in region 6:116757346-116757747. Error was invalid region `6:116757347-116757747`
[2016-04-15T04:50Z] 2016-04-14 21:50:29 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:50:29,189 - WARNING - Could not retrieve variants from source file in region 6:111288730-111289131. Error was invalid region `6:111288731-111289131`
[2016-04-15T04:50Z] 2016-04-14 21:50:30 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:50:30,466 - WARNING - Could not retrieve variants from source file in region 6:116757346-116757747. Error was invalid region `6:116757347-116757747`
[2016-04-15T04:50Z] 2016-04-14 21:50:30 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:50:30,617 - WARNING - Could not retrieve variants from source file in region 6:111493742-111494143. Error was invalid region `6:111493743-111494143`
[2016-04-15T04:50Z] 2016-04-14 21:50:30 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:50:30,941 - WARNING - Could not retrieve variants from source file in region 6:111888329-111913452. Error was invalid region `6:111888330-111913452`
[2016-04-15T04:50Z] 2016-04-14 21:50:31 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:50:31,052 - WARNING - Could not retrieve variants from source file in region 6:110653489-110653890. Error was invalid region `6:110653490-110653890`
[2016-04-15T04:50Z] 2016-04-14 21:50:34 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:50:34,640 - WARNING - Could not retrieve variants from source file in region 6:110653489-110653890. Error was invalid region `6:110653490-110653890`
[2016-04-15T04:50Z] 2016-04-14 21:50:36 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:50:36,268 - WARNING - Could not retrieve variants from source file in region 6:111288730-111289131. Error was invalid region `6:111288731-111289131`
[2016-04-15T04:50Z] 2016-04-14 21:50:39 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:50:39,738 - WARNING - Could not retrieve variants from source file in region 6:110146092-110146493. Error was invalid region `6:110146093-110146493`
[2016-04-15T04:50Z] 2016-04-14 21:50:41 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:50:41,666 - WARNING - Could not retrieve variants from source file in region 6:110107306-110107707. Error was invalid region `6:110107307-110107707`
[2016-04-15T04:50Z] 2016-04-14 21:50:42 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:50:42,284 - WARNING - Could not retrieve variants from source file in region 6:110448531-110448932. Error was invalid region `6:110448532-110448932`
[2016-04-15T04:50Z] 2016-04-14 21:50:42 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:50:42,538 - WARNING - Could not retrieve variants from source file in region 6:110746315-110746735. Error was invalid region `6:110746316-110746735`
[2016-04-15T04:50Z] 2016-04-14 21:50:43 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:50:43,626 - WARNING - Could not retrieve variants from source file in region 6:109582975-109591623. Error was invalid region `6:109582976-109591623`
[2016-04-15T04:50Z] 2016-04-14 21:50:43 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:50:43,760 - WARNING - Could not retrieve variants from source file in region 6:110146092-110146493. Error was invalid region `6:110146093-110146493`
[2016-04-15T04:50Z] 2016-04-14 21:50:45 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:50:45,417 - WARNING - Could not retrieve variants from source file in region 6:110797352-110797802. Error was invalid region `6:110797353-110797802`
[2016-04-15T04:50Z] 2016-04-14 21:50:46 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:50:46,868 - WARNING - Could not retrieve variants from source file in region 6:109762389-109775626. Error was invalid region `6:109762390-109775626`
[2016-04-15T04:50Z] 2016-04-14 21:50:47 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:50:47,134 - WARNING - Could not retrieve variants from source file in region 6:109827505-109837419. Error was invalid region `6:109827506-109837419`
[2016-04-15T04:50Z] 2016-04-14 21:50:47 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:50:47,370 - WARNING - Could not retrieve variants from source file in region 6:109885264-109906522. Error was invalid region `6:109885265-109906522`
[2016-04-15T04:50Z] 2016-04-14 21:50:47 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:50:47,919 - WARNING - Could not retrieve variants from source file in region 6:110746315-110746735. Error was invalid region `6:110746316-110746735`
[2016-04-15T04:50Z] 2016-04-14 21:50:50 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:50:50,636 - WARNING - Could not retrieve variants from source file in region 6:110107306-110107707. Error was invalid region `6:110107307-110107707`
[2016-04-15T04:50Z] 2016-04-14 21:50:51 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:50:51,894 - WARNING - Could not retrieve variants from source file in region 6:110746315-110746735. Error was invalid region `6:110746316-110746735`
[2016-04-15T04:50Z] 2016-04-14 21:50:54 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:50:54,751 - WARNING - Could not retrieve variants from source file in region 6:109689470-109690097. Error was invalid region `6:109689471-109690097`
[2016-04-15T04:51Z] 2016-04-14 21:51:00 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:51:00,212 - WARNING - Could not retrieve variants from source file in region 6:109505529-109549027. Error was invalid region `6:109505530-109549027`
[2016-04-15T04:51Z] ['bcbio-variation-recall', 'square', '-Xms750m', '-Xmx7280m', '-XX:+UseSerialGC', '-c', 16, '-r', u'6:125112485-142397186', '--caller', 'platypus', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/6/Batch1-6_125112484_142397186.vcf.gz', '/mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/6/Batch1-6_125112484_142397186.vcf-inputs.txt'] in region: 6:125112485-142397186
[2016-04-15T04:51Z] 2016-04-14 21:51:15 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:51:15,817 - WARNING - Could not retrieve variants from source file in region 6:137112926-137113327. Error was invalid region `6:137112927-137113327`
[2016-04-15T04:51Z] 2016-04-14 21:51:15 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:51:15,890 - WARNING - Could not retrieve variants from source file in region 6:132271741-132272170. Error was invalid region `6:132271742-132272170`
[2016-04-15T04:51Z] 2016-04-14 21:51:16 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:51:16,699 - WARNING - Could not retrieve variants from source file in region 6:133070784-133077253. Error was invalid region `6:133070785-133077253`
[2016-04-15T04:51Z] 2016-04-14 21:51:16 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:51:16,934 - WARNING - Could not retrieve variants from source file in region 6:136681961-136682362. Error was invalid region `6:136681962-136682362`
[2016-04-15T04:51Z] 2016-04-14 21:51:17 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:51:17,077 - WARNING - Could not retrieve variants from source file in region 6:138753126-138754513. Error was invalid region `6:138753127-138754513`
[2016-04-15T04:51Z] 2016-04-14 21:51:17 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:51:17,916 - WARNING - Could not retrieve variants from source file in region 6:139487625-139488026. Error was invalid region `6:139487626-139488026`
[2016-04-15T04:51Z] 2016-04-14 21:51:18 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:51:18,049 - WARNING - Could not retrieve variants from source file in region 6:138584474-138584875. Error was invalid region `6:138584475-138584875`
[2016-04-15T04:51Z] 2016-04-14 21:51:18 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:51:18,145 - WARNING - Could not retrieve variants from source file in region 6:139456550-139456951. Error was invalid region `6:139456551-139456951`
[2016-04-15T04:51Z] 2016-04-14 21:51:18 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:51:18,170 - WARNING - Could not retrieve variants from source file in region 6:133849755-133851567. Error was invalid region `6:133849756-133851567`
[2016-04-15T04:51Z] 2016-04-14 21:51:19 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:51:19,516 - WARNING - Could not retrieve variants from source file in region 6:133015060-133035288. Error was invalid region `6:133015061-133035288`
[2016-04-15T04:51Z] 2016-04-14 21:51:22 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:51:22,415 - WARNING - Could not retrieve variants from source file in region 6:132271741-132272170. Error was invalid region `6:132271742-132272170`
[2016-04-15T04:51Z] 2016-04-14 21:51:22 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:51:22,442 - WARNING - Could not retrieve variants from source file in region 6:137112926-137113327. Error was invalid region `6:137112927-137113327`
[2016-04-15T04:51Z] 2016-04-14 21:51:23 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:51:23,647 - WARNING - Could not retrieve variants from source file in region 6:139563703-139576926. Error was invalid region `6:139563704-139576926`
[2016-04-15T04:51Z] 2016-04-14 21:51:23 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:51:23,675 - WARNING - Could not retrieve variants from source file in region 6:137026055-137026456. Error was invalid region `6:137026056-137026456`
[2016-04-15T04:51Z] 2016-04-14 21:51:25 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:51:25,377 - WARNING - Could not retrieve variants from source file in region 6:133070784-133077253. Error was invalid region `6:133070785-133077253`
[2016-04-15T04:51Z] 2016-04-14 21:51:25 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:51:25,450 - WARNING - Could not retrieve variants from source file in region 6:129370895-129381216. Error was invalid region `6:129370896-129381216`
[2016-04-15T04:51Z] 2016-04-14 21:51:25 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:51:25,710 - WARNING - Could not retrieve variants from source file in region 6:133789517-133789918. Error was invalid region `6:133789518-133789918`
[2016-04-15T04:51Z] 2016-04-14 21:51:25 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:51:25,724 - WARNING - Could not retrieve variants from source file in region 6:139197398-139197799. Error was invalid region `6:139197399-139197799`
[2016-04-15T04:51Z] 2016-04-14 21:51:25 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:51:25,791 - WARNING - Could not retrieve variants from source file in region 6:138753126-138754513. Error was invalid region `6:138753127-138754513`
[2016-04-15T04:51Z] 2016-04-14 21:51:26 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:51:26,209 - WARNING - Could not retrieve variants from source file in region 6:136681961-136682362. Error was invalid region `6:136681962-136682362`
[2016-04-15T04:51Z] 2016-04-14 21:51:26 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:51:26,264 - WARNING - Could not retrieve variants from source file in region 6:139487625-139488026. Error was invalid region `6:139487626-139488026`
[2016-04-15T04:51Z] 2016-04-14 21:51:26 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:51:26,411 - WARNING - Could not retrieve variants from source file in region 6:133849755-133851567. Error was invalid region `6:133849756-133851567`
[2016-04-15T04:51Z] 2016-04-14 21:51:26 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:51:26,520 - WARNING - Could not retrieve variants from source file in region 6:133015060-133035288. Error was invalid region `6:133015061-133035288`
[2016-04-15T04:51Z] 2016-04-14 21:51:27 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:51:27,401 - WARNING - Could not retrieve variants from source file in region 6:137112926-137113327. Error was invalid region `6:137112927-137113327`
[2016-04-15T04:51Z] 2016-04-14 21:51:27 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:51:27,606 - WARNING - Could not retrieve variants from source file in region 6:132271741-132272170. Error was invalid region `6:132271742-132272170`
[2016-04-15T04:51Z] 2016-04-14 21:51:28 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:51:28,669 - WARNING - Could not retrieve variants from source file in region 6:137026055-137026456. Error was invalid region `6:137026056-137026456`
[2016-04-15T04:51Z] 2016-04-14 21:51:31 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:51:31,439 - WARNING - Could not retrieve variants from source file in region 6:129370895-129381216. Error was invalid region `6:129370896-129381216`
[2016-04-15T04:51Z] 2016-04-14 21:51:31 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:51:31,693 - WARNING - Could not retrieve variants from source file in region 6:133070784-133077253. Error was invalid region `6:133070785-133077253`
[2016-04-15T04:51Z] 2016-04-14 21:51:32 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:51:32,831 - WARNING - Could not retrieve variants from source file in region 6:138753126-138754513. Error was invalid region `6:138753127-138754513`
[2016-04-15T04:51Z] 2016-04-14 21:51:32 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:51:32,992 - WARNING - Could not retrieve variants from source file in region 6:133789517-133789918. Error was invalid region `6:133789518-133789918`
[2016-04-15T04:51Z] 2016-04-14 21:51:33 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:51:33,138 - WARNING - Could not retrieve variants from source file in region 6:136681961-136682362. Error was invalid region `6:136681962-136682362`
[2016-04-15T04:51Z] 2016-04-14 21:51:33 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:51:33,470 - WARNING - Could not retrieve variants from source file in region 6:139487625-139488026. Error was invalid region `6:139487626-139488026`
[2016-04-15T04:51Z] 2016-04-14 21:51:33 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:51:33,591 - WARNING - Could not retrieve variants from source file in region 6:133849755-133851567. Error was invalid region `6:133849756-133851567`
[2016-04-15T04:51Z] 2016-04-14 21:51:33 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:51:33,811 - WARNING - Could not retrieve variants from source file in region 6:139456550-139456951. Error was invalid region `6:139456551-139456951`
[2016-04-15T04:51Z] 2016-04-14 21:51:43 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:51:43,567 - WARNING - Could not retrieve variants from source file in region 6:132966068-132966469. Error was invalid region `6:132966069-132966469`
[2016-04-15T04:51Z] 2016-04-14 21:51:44 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:51:44,990 - WARNING - Could not retrieve variants from source file in region 6:132966068-132966469. Error was invalid region `6:132966069-132966469`
[2016-04-15T04:51Z] 2016-04-14 21:51:46 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:51:46,667 - WARNING - Could not retrieve variants from source file in region 6:132061209-132061610. Error was invalid region `6:132061210-132061610`
[2016-04-15T04:51Z] 2016-04-14 21:51:47 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:51:47,715 - WARNING - Could not retrieve variants from source file in region 6:128403534-128403935. Error was invalid region `6:128403535-128403935`
[2016-04-15T04:51Z] 2016-04-14 21:51:47 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:51:47,761 - WARNING - Could not retrieve variants from source file in region 6:138614937-138615338. Error was invalid region `6:138614938-138615338`
[2016-04-15T04:51Z] 2016-04-14 21:51:48 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:51:48,985 - WARNING - Could not retrieve variants from source file in region 6:135623373-135624023. Error was invalid region `6:135623374-135624023`
[2016-04-15T04:51Z] 2016-04-14 21:51:49 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:51:49,024 - WARNING - Could not retrieve variants from source file in region 6:132910401-132910802. Error was invalid region `6:132910402-132910802`
[2016-04-15T04:51Z] 2016-04-14 21:51:49 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:51:49,951 - WARNING - Could not retrieve variants from source file in region 6:137245305-137245706. Error was invalid region `6:137245306-137245706`
[2016-04-15T04:51Z] 2016-04-14 21:51:50 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:51:50,631 - WARNING - Could not retrieve variants from source file in region 6:135813911-135814312. Error was invalid region `6:135813912-135814312`
[2016-04-15T04:51Z] 2016-04-14 21:51:51 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:51:51,544 - WARNING - Could not retrieve variants from source file in region 6:135358356-135358757. Error was invalid region `6:135358357-135358757`
[2016-04-15T04:51Z] 2016-04-14 21:51:51 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:51:51,814 - WARNING - Could not retrieve variants from source file in region 6:130761593-130761994. Error was invalid region `6:130761594-130761994`
[2016-04-15T04:51Z] 2016-04-14 21:51:52 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:51:52,816 - WARNING - Could not retrieve variants from source file in region 6:128403534-128403935. Error was invalid region `6:128403535-128403935`
[2016-04-15T04:51Z] 2016-04-14 21:51:53 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:51:53,731 - WARNING - Could not retrieve variants from source file in region 6:132910401-132910802. Error was invalid region `6:132910402-132910802`
[2016-04-15T04:51Z] 2016-04-14 21:51:53 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:51:53,980 - WARNING - Could not retrieve variants from source file in region 6:135623373-135624023. Error was invalid region `6:135623374-135624023`
[2016-04-15T04:51Z] 2016-04-14 21:51:54 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:51:54,175 - WARNING - Could not retrieve variants from source file in region 6:136358813-136359215. Error was invalid region `6:136358814-136359215`
[2016-04-15T04:51Z] 2016-04-14 21:51:54 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:51:54,353 - WARNING - Could not retrieve variants from source file in region 6:137323002-137326037. Error was invalid region `6:137323003-137326037`
[2016-04-15T04:51Z] 2016-04-14 21:51:55 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:51:55,073 - WARNING - Could not retrieve variants from source file in region 6:135813911-135814312. Error was invalid region `6:135813912-135814312`
[2016-04-15T04:51Z] 2016-04-14 21:51:55 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:51:55,369 - WARNING - Could not retrieve variants from source file in region 6:131995102-131995503. Error was invalid region `6:131995103-131995503`
[2016-04-15T04:51Z] 2016-04-14 21:51:56 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:51:56,201 - WARNING - Could not retrieve variants from source file in region 6:132061209-132061610. Error was invalid region `6:132061210-132061610`
[2016-04-15T04:51Z] 2016-04-14 21:51:58 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:51:58,457 - WARNING - Could not retrieve variants from source file in region 6:132910401-132910802. Error was invalid region `6:132910402-132910802`
[2016-04-15T04:51Z] 2016-04-14 21:51:58 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:51:58,578 - WARNING - Could not retrieve variants from source file in region 6:135623373-135624023. Error was invalid region `6:135623374-135624023`
[2016-04-15T04:51Z] 2016-04-14 21:51:59 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:51:59,233 - WARNING - Could not retrieve variants from source file in region 6:136358813-136359215. Error was invalid region `6:136358814-136359215`
[2016-04-15T04:51Z] 2016-04-14 21:51:59 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:51:59,523 - WARNING - Could not retrieve variants from source file in region 6:137245305-137245706. Error was invalid region `6:137245306-137245706`
[2016-04-15T04:51Z] 2016-04-14 21:51:59 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:51:59,929 - WARNING - Could not retrieve variants from source file in region 6:135813911-135814312. Error was invalid region `6:135813912-135814312`
[2016-04-15T04:52Z] 2016-04-14 21:52:00 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:52:00,244 - WARNING - Could not retrieve variants from source file in region 6:131995102-131995503. Error was invalid region `6:131995103-131995503`
[2016-04-15T04:52Z] 2016-04-14 21:52:00 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:52:00,911 - WARNING - Could not retrieve variants from source file in region 6:135358356-135358757. Error was invalid region `6:135358357-135358757`
[2016-04-15T04:52Z] 2016-04-14 21:52:06 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:52:06,067 - WARNING - Could not retrieve variants from source file in region 6:132859226-132875004. Error was invalid region `6:132859227-132875004`
[2016-04-15T04:52Z] 2016-04-14 21:52:11 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:52:11,247 - WARNING - Could not retrieve variants from source file in region 6:132030755-132031156. Error was invalid region `6:132030756-132031156`
[2016-04-15T04:52Z] 2016-04-14 21:52:11 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:52:11,965 - WARNING - Could not retrieve variants from source file in region 6:135287322-135287723. Error was invalid region `6:135287323-135287723`
[2016-04-15T04:52Z] 2016-04-14 21:52:12 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:52:12,666 - WARNING - Could not retrieve variants from source file in region 6:127768551-127794479. Error was invalid region `6:127768552-127794479`
[2016-04-15T04:52Z] 2016-04-14 21:52:12 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:52:12,988 - WARNING - Could not retrieve variants from source file in region 6:130373891-130381436. Error was invalid region `6:130373892-130381436`
[2016-04-15T04:52Z] 2016-04-14 21:52:13 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:52:13,982 - WARNING - Could not retrieve variants from source file in region 6:132030755-132031156. Error was invalid region `6:132030756-132031156`
[2016-04-15T04:52Z] 2016-04-14 21:52:14 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:52:14,203 - WARNING - Could not retrieve variants from source file in region 6:130686204-130687304. Error was invalid region `6:130686205-130687304`
[2016-04-15T04:52Z] 2016-04-14 21:52:14 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:52:14,232 - WARNING - Could not retrieve variants from source file in region 6:131900179-131914422. Error was invalid region `6:131900180-131914422`
[2016-04-15T04:52Z] 2016-04-14 21:52:14 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:52:14,574 - WARNING - Could not retrieve variants from source file in region 6:128321013-128321508. Error was invalid region `6:128321014-128321508`
[2016-04-15T04:52Z] 2016-04-14 21:52:15 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:52:15,243 - WARNING - Could not retrieve variants from source file in region 6:130373891-130381436. Error was invalid region `6:130373892-130381436`
[2016-04-15T04:52Z] 2016-04-14 21:52:17 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:52:17,036 - WARNING - Could not retrieve variants from source file in region 6:131148526-131148927. Error was invalid region `6:131148527-131148927`
[2016-04-15T04:52Z] 2016-04-14 21:52:17 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:52:17,073 - WARNING - Could not retrieve variants from source file in region 6:127768551-127794479. Error was invalid region `6:127768552-127794479`
[2016-04-15T04:52Z] 2016-04-14 21:52:17 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:52:17,155 - WARNING - Could not retrieve variants from source file in region 6:130152268-130154876. Error was invalid region `6:130152269-130154876`
[2016-04-15T04:52Z] 2016-04-14 21:52:17 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:52:17,238 - WARNING - Could not retrieve variants from source file in region 6:130373891-130381436. Error was invalid region `6:130373892-130381436`
[2016-04-15T04:52Z] 2016-04-14 21:52:19 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:52:19,018 - WARNING - Could not retrieve variants from source file in region 6:128321013-128321508. Error was invalid region `6:128321014-128321508`
[2016-04-15T04:52Z] 2016-04-14 21:52:20 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:52:20,174 - WARNING - Could not retrieve variants from source file in region 6:135287322-135287723. Error was invalid region `6:135287323-135287723`
[2016-04-15T04:52Z] 2016-04-14 21:52:21 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:52:21,626 - WARNING - Could not retrieve variants from source file in region 6:127768551-127794479. Error was invalid region `6:127768552-127794479`
[2016-04-15T04:52Z] 2016-04-14 21:52:21 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:52:21,642 - WARNING - Could not retrieve variants from source file in region 6:130152268-130154876. Error was invalid region `6:130152269-130154876`
[2016-04-15T04:52Z] 2016-04-14 21:52:21 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:52:21,675 - WARNING - Could not retrieve variants from source file in region 6:131148526-131148927. Error was invalid region `6:131148527-131148927`
[2016-04-15T04:52Z] 2016-04-14 21:52:22 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:52:22,267 - WARNING - Could not retrieve variants from source file in region 6:126210184-126210585. Error was invalid region `6:126210185-126210585`
[2016-04-15T04:52Z] 2016-04-14 21:52:23 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:52:23,880 - WARNING - Could not retrieve variants from source file in region 6:125475304-125475835. Error was invalid region `6:125475305-125475835`
[2016-04-15T04:52Z] 2016-04-14 21:52:25 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:52:25,519 - WARNING - Could not retrieve variants from source file in region 6:127476305-127476706. Error was invalid region `6:127476306-127476706`
[2016-04-15T04:52Z] 2016-04-14 21:52:27 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:52:27,458 - WARNING - Could not retrieve variants from source file in region 6:128134474-128134875. Error was invalid region `6:128134475-128134875`
[2016-04-15T04:52Z] 2016-04-14 21:52:27 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:52:27,871 - WARNING - Could not retrieve variants from source file in region 6:125475304-125475835. Error was invalid region `6:125475305-125475835`
[2016-04-15T04:52Z] 2016-04-14 21:52:30 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:52:30,032 - WARNING - Could not retrieve variants from source file in region 6:127476305-127476706. Error was invalid region `6:127476306-127476706`
[2016-04-15T04:52Z] 2016-04-14 21:52:30 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:52:30,047 - WARNING - Could not retrieve variants from source file in region 6:129807418-129807889. Error was invalid region `6:129807419-129807889`
[2016-04-15T04:52Z] 2016-04-14 21:52:31 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:52:31,635 - WARNING - Could not retrieve variants from source file in region 6:128040628-128041029. Error was invalid region `6:128040629-128041029`
[2016-04-15T04:52Z] 2016-04-14 21:52:31 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:52:31,922 - WARNING - Could not retrieve variants from source file in region 6:128134474-128134875. Error was invalid region `6:128134475-128134875`
[2016-04-15T04:52Z] 2016-04-14 21:52:32 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:52:32,657 - WARNING - Could not retrieve variants from source file in region 6:125284246-125284647. Error was invalid region `6:125284247-125284647`
[2016-04-15T04:52Z] 2016-04-14 21:52:32 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:52:32,717 - WARNING - Could not retrieve variants from source file in region 6:130031004-130031405. Error was invalid region `6:130031005-130031405`
[2016-04-15T04:52Z] 2016-04-14 21:52:32 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:52:32,735 - WARNING - Could not retrieve variants from source file in region 6:125475304-125475835. Error was invalid region `6:125475305-125475835`
[2016-04-15T04:52Z] 2016-04-14 21:52:34 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:52:34,878 - WARNING - Could not retrieve variants from source file in region 6:129807418-129807889. Error was invalid region `6:129807419-129807889`
[2016-04-15T04:52Z] 2016-04-14 21:52:34 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:52:34,886 - WARNING - Could not retrieve variants from source file in region 6:129722178-129722615. Error was invalid region `6:129722179-129722615`
[2016-04-15T04:52Z] 2016-04-14 21:52:35 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:52:35,000 - WARNING - Could not retrieve variants from source file in region 6:126080311-126080712. Error was invalid region `6:126080312-126080712`
[2016-04-15T04:52Z] 2016-04-14 21:52:35 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:52:35,351 - WARNING - Could not retrieve variants from source file in region 6:127836649-127837050. Error was invalid region `6:127836650-127837050`
[2016-04-15T04:52Z] 2016-04-14 21:52:35 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:52:35,858 - WARNING - Could not retrieve variants from source file in region 6:128040628-128041029. Error was invalid region `6:128040629-128041029`
[2016-04-15T04:52Z] 2016-04-14 21:52:37 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:52:37,510 - WARNING - Could not retrieve variants from source file in region 6:125284246-125284647. Error was invalid region `6:125284247-125284647`
[2016-04-15T04:52Z] 2016-04-14 21:52:37 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:52:37,550 - WARNING - Could not retrieve variants from source file in region 6:127836649-127837050. Error was invalid region `6:127836650-127837050`
[2016-04-15T04:52Z] 2016-04-14 21:52:37 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:52:37,781 - WARNING - Could not retrieve variants from source file in region 6:130031004-130031405. Error was invalid region `6:130031005-130031405`
[2016-04-15T04:52Z] 2016-04-14 21:52:38 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:52:38,463 - WARNING - Could not retrieve variants from source file in region 6:126332343-126332744. Error was invalid region `6:126332344-126332744`
[2016-04-15T04:52Z] 2016-04-14 21:52:39 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:52:39,502 - WARNING - Could not retrieve variants from source file in region 6:129807418-129807889. Error was invalid region `6:129807419-129807889`
[2016-04-15T04:52Z] 2016-04-14 21:52:39 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:52:39,922 - WARNING - Could not retrieve variants from source file in region 6:129722178-129722615. Error was invalid region `6:129722179-129722615`
[2016-04-15T04:52Z] 2016-04-14 21:52:40 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:52:40,310 - WARNING - Could not retrieve variants from source file in region 6:128040628-128041029. Error was invalid region `6:128040629-128041029`
[2016-04-15T04:52Z] 2016-04-14 21:52:41 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:52:41,682 - WARNING - Could not retrieve variants from source file in region 6:125284246-125284647. Error was invalid region `6:125284247-125284647`
[2016-04-15T04:52Z] 2016-04-14 21:52:41 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:52:41,878 - WARNING - Could not retrieve variants from source file in region 6:130031004-130031405. Error was invalid region `6:130031005-130031405`
[2016-04-15T04:52Z] 2016-04-14 21:52:43 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:52:43,635 - WARNING - Could not retrieve variants from source file in region 6:129722178-129722615. Error was invalid region `6:129722179-129722615`
[2016-04-15T04:52Z] ['bcbio-variation-recall', 'square', '-Xms750m', '-Xmx7280m', '-XX:+UseSerialGC', '-c', 16, '-r', u'6:142399692-157963777', '--caller', 'platypus', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/6/Batch1-6_142399691_157963777.vcf.gz', '/mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/6/Batch1-6_142399691_157963777.vcf-inputs.txt'] in region: 6:142399692-157963777
[2016-04-15T04:52Z] 2016-04-14 21:52:58 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:52:58,395 - WARNING - Could not retrieve variants from source file in region 6:150389907-150390853. Error was invalid region `6:150389908-150390853`
[2016-04-15T04:52Z] 2016-04-14 21:52:59 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:52:59,305 - WARNING - Could not retrieve variants from source file in region 6:150716485-150716886. Error was invalid region `6:150716486-150716886`
[2016-04-15T04:53Z] 2016-04-14 21:53:00 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:53:00,510 - WARNING - Could not retrieve variants from source file in region 6:142758420-142758821. Error was invalid region `6:142758421-142758821`
[2016-04-15T04:53Z] 2016-04-14 21:53:00 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:53:00,596 - WARNING - Could not retrieve variants from source file in region 6:152529049-152540468. Error was invalid region `6:152529050-152540468`
[2016-04-15T04:53Z] 2016-04-14 21:53:00 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:53:00,795 - WARNING - Could not retrieve variants from source file in region 6:151766611-151790058. Error was invalid region `6:151766612-151790058`
[2016-04-15T04:53Z] 2016-04-14 21:53:01 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:53:01,173 - WARNING - Could not retrieve variants from source file in region 6:150114534-150114935. Error was invalid region `6:150114535-150114935`
[2016-04-15T04:53Z] 2016-04-14 21:53:01 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:53:01,305 - WARNING - Could not retrieve variants from source file in region 6:151121704-151122105. Error was invalid region `6:151121705-151122105`
[2016-04-15T04:53Z] 2016-04-14 21:53:01 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:53:01,696 - WARNING - Could not retrieve variants from source file in region 6:150515639-150516481. Error was invalid region `6:150515640-150516481`
[2016-04-15T04:53Z] 2016-04-14 21:53:01 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:53:01,830 - WARNING - Could not retrieve variants from source file in region 6:150464145-150464546. Error was invalid region `6:150464146-150464546`
[2016-04-15T04:53Z] 2016-04-14 21:53:01 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:53:01,848 - WARNING - Could not retrieve variants from source file in region 6:143510306-143510707. Error was invalid region `6:143510307-143510707`
[2016-04-15T04:53Z] 2016-04-14 21:53:01 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:53:01,963 - WARNING - Could not retrieve variants from source file in region 6:146754929-146756032. Error was invalid region `6:146754930-146756032`
[2016-04-15T04:53Z] 2016-04-14 21:53:03 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:53:03,780 - WARNING - Could not retrieve variants from source file in region 6:150389907-150390853. Error was invalid region `6:150389908-150390853`
[2016-04-15T04:53Z] 2016-04-14 21:53:05 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:53:05,370 - WARNING - Could not retrieve variants from source file in region 6:150716485-150716886. Error was invalid region `6:150716486-150716886`
[2016-04-15T04:53Z] 2016-04-14 21:53:07 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:53:07,628 - WARNING - Could not retrieve variants from source file in region 6:142758420-142758821. Error was invalid region `6:142758421-142758821`
[2016-04-15T04:53Z] 2016-04-14 21:53:08 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:53:08,932 - WARNING - Could not retrieve variants from source file in region 6:157405719-157406120. Error was invalid region `6:157405720-157406120`
[2016-04-15T04:53Z] 2016-04-14 21:53:09 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:53:09,014 - WARNING - Could not retrieve variants from source file in region 6:153042824-153043225. Error was invalid region `6:153042825-153043225`
[2016-04-15T04:53Z] 2016-04-14 21:53:09 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:53:09,477 - WARNING - Could not retrieve variants from source file in region 6:152128866-152129498. Error was invalid region `6:152128867-152129498`
[2016-04-15T04:53Z] 2016-04-14 21:53:09 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:53:09,478 - WARNING - Could not retrieve variants from source file in region 6:151766611-151790058. Error was invalid region `6:151766612-151790058`
[2016-04-15T04:53Z] 2016-04-14 21:53:09 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:53:09,791 - WARNING - Could not retrieve variants from source file in region 6:150464145-150464546. Error was invalid region `6:150464146-150464546`
[2016-04-15T04:53Z] 2016-04-14 21:53:10 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:53:10,215 - WARNING - Could not retrieve variants from source file in region 6:150114534-150114935. Error was invalid region `6:150114535-150114935`
[2016-04-15T04:53Z] 2016-04-14 21:53:10 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:53:10,569 - WARNING - Could not retrieve variants from source file in region 6:150515639-150516481. Error was invalid region `6:150515640-150516481`
[2016-04-15T04:53Z] 2016-04-14 21:53:10 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:53:10,785 - WARNING - Could not retrieve variants from source file in region 6:150716485-150716886. Error was invalid region `6:150716486-150716886`
[2016-04-15T04:53Z] 2016-04-14 21:53:13 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:53:13,786 - WARNING - Could not retrieve variants from source file in region 6:142758420-142758821. Error was invalid region `6:142758421-142758821`
[2016-04-15T04:53Z] 2016-04-14 21:53:17 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:53:17,853 - WARNING - Could not retrieve variants from source file in region 6:152128866-152129498. Error was invalid region `6:152128867-152129498`
[2016-04-15T04:53Z] 2016-04-14 21:53:18 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:53:18,104 - WARNING - Could not retrieve variants from source file in region 6:150464145-150464546. Error was invalid region `6:150464146-150464546`
[2016-04-15T04:53Z] 2016-04-14 21:53:18 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:53:18,282 - WARNING - Could not retrieve variants from source file in region 6:143510306-143510707. Error was invalid region `6:143510307-143510707`
[2016-04-15T04:53Z] 2016-04-14 21:53:18 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:53:18,467 - WARNING - Could not retrieve variants from source file in region 6:151121704-151122105. Error was invalid region `6:151121705-151122105`
[2016-04-15T04:53Z] 2016-04-14 21:53:18 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:53:18,647 - WARNING - Could not retrieve variants from source file in region 6:150515639-150516481. Error was invalid region `6:150515640-150516481`
[2016-04-15T04:53Z] 2016-04-14 21:53:18 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:53:18,765 - WARNING - Could not retrieve variants from source file in region 6:150114534-150114935. Error was invalid region `6:150114535-150114935`
[2016-04-15T04:53Z] 2016-04-14 21:53:30 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:53:30,554 - WARNING - Could not retrieve variants from source file in region 6:150342021-150346722. Error was invalid region `6:150342022-150346722`
[2016-04-15T04:53Z] 2016-04-14 21:53:31 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:53:31,439 - WARNING - Could not retrieve variants from source file in region 6:142718590-142718991. Error was invalid region `6:142718591-142718991`
[2016-04-15T04:53Z] 2016-04-14 21:53:32 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:53:32,763 - WARNING - Could not retrieve variants from source file in region 6:152772053-152780123. Error was invalid region `6:152772054-152780123`
[2016-04-15T04:53Z] 2016-04-14 21:53:34 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:53:34,036 - WARNING - Could not retrieve variants from source file in region 6:144081398-144081799. Error was invalid region `6:144081399-144081799`
[2016-04-15T04:53Z] 2016-04-14 21:53:34 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:53:34,831 - WARNING - Could not retrieve variants from source file in region 6:150342021-150346722. Error was invalid region `6:150342022-150346722`
[2016-04-15T04:53Z] 2016-04-14 21:53:35 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:53:35,404 - WARNING - Could not retrieve variants from source file in region 6:151936466-151939371. Error was invalid region `6:151936467-151939371`
[2016-04-15T04:53Z] 2016-04-14 21:53:35 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:53:35,830 - WARNING - Could not retrieve variants from source file in region 6:143824893-143825294. Error was invalid region `6:143824894-143825294`
[2016-04-15T04:53Z] 2016-04-14 21:53:36 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:53:36,297 - WARNING - Could not retrieve variants from source file in region 6:150342021-150346722. Error was invalid region `6:150342022-150346722`
[2016-04-15T04:53Z] 2016-04-14 21:53:36 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:53:36,408 - WARNING - Could not retrieve variants from source file in region 6:142688758-142691739. Error was invalid region `6:142688759-142691739`
[2016-04-15T04:53Z] 2016-04-14 21:53:36 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:53:36,563 - WARNING - Could not retrieve variants from source file in region 6:146234433-146234834. Error was invalid region `6:146234434-146234834`
[2016-04-15T04:53Z] 2016-04-14 21:53:36 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:53:36,620 - WARNING - Could not retrieve variants from source file in region 6:142718590-142718991. Error was invalid region `6:142718591-142718991`
[2016-04-15T04:53Z] 2016-04-14 21:53:36 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:53:36,767 - WARNING - Could not retrieve variants from source file in region 6:144081398-144081799. Error was invalid region `6:144081399-144081799`
[2016-04-15T04:53Z] 2016-04-14 21:53:37 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:53:37,405 - WARNING - Could not retrieve variants from source file in region 6:150049050-150049451. Error was invalid region `6:150049051-150049451`
[2016-04-15T04:53Z] 2016-04-14 21:53:39 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:53:39,152 - WARNING - Could not retrieve variants from source file in region 6:157100049-157100450. Error was invalid region `6:157100050-157100450`
[2016-04-15T04:53Z] 2016-04-14 21:53:41 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:53:41,720 - WARNING - Could not retrieve variants from source file in region 6:143824893-143825294. Error was invalid region `6:143824894-143825294`
[2016-04-15T04:53Z] 2016-04-14 21:53:42 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:53:42,520 - WARNING - Could not retrieve variants from source file in region 6:150267316-150285399. Error was invalid region `6:150267317-150285399`
[2016-04-15T04:53Z] 2016-04-14 21:53:42 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:53:42,629 - WARNING - Could not retrieve variants from source file in region 6:146234433-146234834. Error was invalid region `6:146234434-146234834`
[2016-04-15T04:53Z] 2016-04-14 21:53:43 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:53:43,276 - WARNING - Could not retrieve variants from source file in region 6:142718590-142718991. Error was invalid region `6:142718591-142718991`
[2016-04-15T04:53Z] 2016-04-14 21:53:43 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:53:43,338 - WARNING - Could not retrieve variants from source file in region 6:142688758-142691739. Error was invalid region `6:142688759-142691739`
[2016-04-15T04:53Z] 2016-04-14 21:53:43 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:53:43,508 - WARNING - Could not retrieve variants from source file in region 6:144742804-144758989. Error was invalid region `6:144742805-144758989`
[2016-04-15T04:53Z] 2016-04-14 21:53:43 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:53:43,636 - WARNING - Could not retrieve variants from source file in region 6:152772053-152780123. Error was invalid region `6:152772054-152780123`
[2016-04-15T04:53Z] 2016-04-14 21:53:48 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:53:48,758 - WARNING - Could not retrieve variants from source file in region 6:146234433-146234834. Error was invalid region `6:146234434-146234834`
[2016-04-15T04:53Z] 2016-04-14 21:53:49 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:53:49,114 - WARNING - Could not retrieve variants from source file in region 6:151936466-151939371. Error was invalid region `6:151936467-151939371`
[2016-04-15T04:53Z] 2016-04-14 21:53:50 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:53:50,073 - WARNING - Could not retrieve variants from source file in region 6:144742804-144758989. Error was invalid region `6:144742805-144758989`
[2016-04-15T04:53Z] 2016-04-14 21:53:54 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:53:54,538 - WARNING - Could not retrieve variants from source file in region 6:155485343-155485744. Error was invalid region `6:155485344-155485744`
[2016-04-15T04:53Z] 2016-04-14 21:53:55 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:53:55,378 - WARNING - Could not retrieve variants from source file in region 6:150239119-150241019. Error was invalid region `6:150239120-150241019`
[2016-04-15T04:53Z] 2016-04-14 21:53:57 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:53:57,652 - WARNING - Could not retrieve variants from source file in region 6:150239119-150241019. Error was invalid region `6:150239120-150241019`
[2016-04-15T04:54Z] 2016-04-14 21:54:00 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:54:00,140 - WARNING - Could not retrieve variants from source file in region 6:151894294-151894695. Error was invalid region `6:151894295-151894695`
[2016-04-15T04:54Z] 2016-04-14 21:54:00 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:54:00,413 - WARNING - Could not retrieve variants from source file in region 6:151894294-151894695. Error was invalid region `6:151894295-151894695`
[2016-04-15T04:54Z] 2016-04-14 21:54:00 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:54:00,419 - WARNING - Could not retrieve variants from source file in region 6:155749824-155750225. Error was invalid region `6:155749825-155750225`
[2016-04-15T04:54Z] 2016-04-14 21:54:00 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:54:00,966 - WARNING - Could not retrieve variants from source file in region 6:155485343-155485744. Error was invalid region `6:155485344-155485744`
[2016-04-15T04:54Z] 2016-04-14 21:54:01 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:54:01,106 - WARNING - Could not retrieve variants from source file in region 6:151859103-151859504. Error was invalid region `6:151859104-151859504`
[2016-04-15T04:54Z] 2016-04-14 21:54:01 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:54:01,186 - WARNING - Could not retrieve variants from source file in region 6:151336528-151336929. Error was invalid region `6:151336529-151336929`
[2016-04-15T04:54Z] 2016-04-14 21:54:01 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:54:01,266 - WARNING - Could not retrieve variants from source file in region 6:152265311-152265712. Error was invalid region `6:152265312-152265712`
[2016-04-15T04:54Z] 2016-04-14 21:54:03 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:54:03,082 - WARNING - Could not retrieve variants from source file in region 6:146125582-146126609. Error was invalid region `6:146125583-146126609`
[2016-04-15T04:54Z] 2016-04-14 21:54:04 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:54:04,106 - WARNING - Could not retrieve variants from source file in region 6:149983005-150004969. Error was invalid region `6:149983006-150004969`
[2016-04-15T04:54Z] 2016-04-14 21:54:04 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:54:04,902 - WARNING - Could not retrieve variants from source file in region 6:145992119-145992521. Error was invalid region `6:145992120-145992521`
[2016-04-15T04:54Z] 2016-04-14 21:54:05 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:54:05,480 - WARNING - Could not retrieve variants from source file in region 6:151894294-151894695. Error was invalid region `6:151894295-151894695`
[2016-04-15T04:54Z] 2016-04-14 21:54:06 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:54:06,258 - WARNING - Could not retrieve variants from source file in region 6:155749824-155750225. Error was invalid region `6:155749825-155750225`
[2016-04-15T04:54Z] 2016-04-14 21:54:06 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:54:06,465 - WARNING - Could not retrieve variants from source file in region 6:153364889-153365290. Error was invalid region `6:153364890-153365290`
[2016-04-15T04:54Z] 2016-04-14 21:54:06 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:54:06,886 - WARNING - Could not retrieve variants from source file in region 6:151336528-151336929. Error was invalid region `6:151336529-151336929`
[2016-04-15T04:54Z] 2016-04-14 21:54:06 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:54:06,925 - WARNING - Could not retrieve variants from source file in region 6:155485343-155485744. Error was invalid region `6:155485344-155485744`
[2016-04-15T04:54Z] 2016-04-14 21:54:06 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:54:06,980 - WARNING - Could not retrieve variants from source file in region 6:151859103-151859504. Error was invalid region `6:151859104-151859504`
[2016-04-15T04:54Z] 2016-04-14 21:54:07 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:54:07,091 - WARNING - Could not retrieve variants from source file in region 6:152265311-152265712. Error was invalid region `6:152265312-152265712`
[2016-04-15T04:54Z] 2016-04-14 21:54:07 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:54:07,426 - WARNING - Could not retrieve variants from source file in region 6:146125582-146126609. Error was invalid region `6:146125583-146126609`
[2016-04-15T04:54Z] 2016-04-14 21:54:08 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:54:08,485 - WARNING - Could not retrieve variants from source file in region 6:149983005-150004969. Error was invalid region `6:149983006-150004969`
[2016-04-15T04:54Z] 2016-04-14 21:54:11 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:54:11,357 - WARNING - Could not retrieve variants from source file in region 6:153364889-153365290. Error was invalid region `6:153364890-153365290`
[2016-04-15T04:54Z] 2016-04-14 21:54:12 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:54:12,230 - WARNING - Could not retrieve variants from source file in region 6:151859103-151859504. Error was invalid region `6:151859104-151859504`
[2016-04-15T04:54Z] 2016-04-14 21:54:12 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:54:12,726 - WARNING - Could not retrieve variants from source file in region 6:152265311-152265712. Error was invalid region `6:152265312-152265712`
[2016-04-15T04:54Z] 2016-04-14 21:54:12 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:54:12,737 - WARNING - Could not retrieve variants from source file in region 6:151336528-151336929. Error was invalid region `6:151336529-151336929`
[2016-04-15T04:54Z] 2016-04-14 21:54:13 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:54:13,110 - WARNING - Could not retrieve variants from source file in region 6:149983005-150004969. Error was invalid region `6:149983006-150004969`
[2016-04-15T04:54Z] 2016-04-14 21:54:13 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:54:13,728 - WARNING - Could not retrieve variants from source file in region 6:145992119-145992521. Error was invalid region `6:145992120-145992521`
[2016-04-15T04:54Z] 2016-04-14 21:54:20 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:54:20,771 - WARNING - Could not retrieve variants from source file in region 6:152614989-152615390. Error was invalid region `6:152614990-152615390`
[2016-04-15T04:54Z] 2016-04-14 21:54:21 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:54:21,559 - WARNING - Could not retrieve variants from source file in region 6:152614989-152615390. Error was invalid region `6:152614990-152615390`
[2016-04-15T04:54Z] 2016-04-14 21:54:21 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:54:21,605 - WARNING - Could not retrieve variants from source file in region 6:152614989-152615390. Error was invalid region `6:152614990-152615390`
[2016-04-15T04:54Z] 2016-04-14 21:54:21 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:54:21,629 - WARNING - Could not retrieve variants from source file in region 6:153296159-153323996. Error was invalid region `6:153296160-153323996`
[2016-04-15T04:54Z] 2016-04-14 21:54:21 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:54:21,846 - WARNING - Could not retrieve variants from source file in region 6:145103004-145103405. Error was invalid region `6:145103005-145103405`
[2016-04-15T04:54Z] 2016-04-14 21:54:21 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:54:21,878 - WARNING - Could not retrieve variants from source file in region 6:152201664-152202065. Error was invalid region `6:152201665-152202065`
[2016-04-15T04:54Z] 2016-04-14 21:54:21 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:54:21,894 - WARNING - Could not retrieve variants from source file in region 6:152201664-152202065. Error was invalid region `6:152201665-152202065`
[2016-04-15T04:54Z] 2016-04-14 21:54:22 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:54:22,796 - WARNING - Could not retrieve variants from source file in region 6:155561549-155606515. Error was invalid region `6:155561550-155606515`
[2016-04-15T04:54Z] 2016-04-14 21:54:25 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:54:25,937 - WARNING - Could not retrieve variants from source file in region 6:153296159-153323996. Error was invalid region `6:153296160-153323996`
[2016-04-15T04:54Z] 2016-04-14 21:54:26 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:54:26,996 - WARNING - Could not retrieve variants from source file in region 6:149953770-149954171. Error was invalid region `6:149953771-149954171`
[2016-04-15T04:54Z] 2016-04-14 21:54:27 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:54:27,001 - WARNING - Could not retrieve variants from source file in region 6:146056265-146056871. Error was invalid region `6:146056266-146056871`
[2016-04-15T04:54Z] 2016-04-14 21:54:27 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:54:27,044 - WARNING - Could not retrieve variants from source file in region 6:146056265-146056871. Error was invalid region `6:146056266-146056871`
[2016-04-15T04:54Z] 2016-04-14 21:54:27 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:54:27,255 - WARNING - Could not retrieve variants from source file in region 6:152201664-152202065. Error was invalid region `6:152201665-152202065`
[2016-04-15T04:54Z] 2016-04-14 21:54:27 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:54:27,457 - WARNING - Could not retrieve variants from source file in region 6:145946869-145947270. Error was invalid region `6:145946870-145947270`
[2016-04-15T04:54Z] 2016-04-14 21:54:31 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:54:31,244 - WARNING - Could not retrieve variants from source file in region 6:149953770-149954171. Error was invalid region `6:149953771-149954171`
[2016-04-15T04:54Z] 2016-04-14 21:54:31 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:54:31,470 - WARNING - Could not retrieve variants from source file in region 6:146056265-146056871. Error was invalid region `6:146056266-146056871`
[2016-04-15T04:54Z] 2016-04-14 21:54:31 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:54:31,893 - WARNING - Could not retrieve variants from source file in region 6:145946869-145947270. Error was invalid region `6:145946870-145947270`
[2016-04-15T04:54Z] 2016-04-14 21:54:34 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:54:34,173 - WARNING - Could not retrieve variants from source file in region 6:145051383-145051784. Error was invalid region `6:145051384-145051784`
[2016-04-15T04:54Z] 2016-04-14 21:54:35 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:54:35,341 - WARNING - Could not retrieve variants from source file in region 6:149953770-149954171. Error was invalid region `6:149953771-149954171`
[2016-04-15T04:54Z] 2016-04-14 21:54:35 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:54:35,944 - WARNING - Could not retrieve variants from source file in region 6:145051383-145051784. Error was invalid region `6:145051384-145051784`
[2016-04-15T04:54Z] 2016-04-14 21:54:36 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:54:36,119 - WARNING - Could not retrieve variants from source file in region 6:145051383-145051784. Error was invalid region `6:145051384-145051784`
[2016-04-15T04:54Z] 2016-04-14 21:54:40 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:54:40,695 - WARNING - Could not retrieve variants from source file in region 6:147829862-147830402. Error was invalid region `6:147829863-147830402`
[2016-04-15T04:54Z] 2016-04-14 21:54:40 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:54:40,826 - WARNING - Could not retrieve variants from source file in region 6:147635202-147635603. Error was invalid region `6:147635203-147635603`
[2016-04-15T04:54Z] 2016-04-14 21:54:41 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:54:41,032 - WARNING - Could not retrieve variants from source file in region 6:147680148-147680549. Error was invalid region `6:147680149-147680549`
[2016-04-15T04:54Z] 2016-04-14 21:54:41 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:54:41,570 - WARNING - Could not retrieve variants from source file in region 6:147635202-147635603. Error was invalid region `6:147635203-147635603`
[2016-04-15T04:54Z] 2016-04-14 21:54:42 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:54:42,673 - WARNING - Could not retrieve variants from source file in region 6:147106630-147107031. Error was invalid region `6:147106631-147107031`
[2016-04-15T04:54Z] 2016-04-14 21:54:42 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:54:42,704 - WARNING - Could not retrieve variants from source file in region 6:148664031-148664432. Error was invalid region `6:148664032-148664432`
[2016-04-15T04:54Z] 2016-04-14 21:54:45 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:54:44,992 - WARNING - Could not retrieve variants from source file in region 6:147829862-147830402. Error was invalid region `6:147829863-147830402`
[2016-04-15T04:54Z] 2016-04-14 21:54:45 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:54:45,430 - WARNING - Could not retrieve variants from source file in region 6:147635202-147635603. Error was invalid region `6:147635203-147635603`
[2016-04-15T04:54Z] 2016-04-14 21:54:46 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:54:46,324 - WARNING - Could not retrieve variants from source file in region 6:147066882-147067283. Error was invalid region `6:147066883-147067283`
[2016-04-15T04:54Z] 2016-04-14 21:54:46 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:54:46,326 - WARNING - Could not retrieve variants from source file in region 6:147136033-147136434. Error was invalid region `6:147136034-147136434`
[2016-04-15T04:54Z] 2016-04-14 21:54:46 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:54:46,328 - WARNING - Could not retrieve variants from source file in region 6:147680148-147680549. Error was invalid region `6:147680149-147680549`
[2016-04-15T04:54Z] 2016-04-14 21:54:46 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:54:46,376 - WARNING - Could not retrieve variants from source file in region 6:147106630-147107031. Error was invalid region `6:147106631-147107031`
[2016-04-15T04:54Z] 2016-04-14 21:54:46 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:54:46,628 - WARNING - Could not retrieve variants from source file in region 6:147680148-147680549. Error was invalid region `6:147680149-147680549`
[2016-04-15T04:54Z] 2016-04-14 21:54:46 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:54:46,649 - WARNING - Could not retrieve variants from source file in region 6:149782884-149795712. Error was invalid region `6:149782885-149795712`
[2016-04-15T04:54Z] 2016-04-14 21:54:46 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:54:46,876 - WARNING - Could not retrieve variants from source file in region 6:148664031-148664432. Error was invalid region `6:148664032-148664432`
[2016-04-15T04:54Z] 2016-04-14 21:54:46 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:54:46,916 - WARNING - Could not retrieve variants from source file in region 6:147106630-147107031. Error was invalid region `6:147106631-147107031`
[2016-04-15T04:54Z] 2016-04-14 21:54:48 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:54:48,726 - WARNING - Could not retrieve variants from source file in region 6:149326268-149326669. Error was invalid region `6:149326269-149326669`
[2016-04-15T04:54Z] 2016-04-14 21:54:50 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:54:50,714 - WARNING - Could not retrieve variants from source file in region 6:146993234-146993635. Error was invalid region `6:146993235-146993635`
[2016-04-15T04:54Z] 2016-04-14 21:54:51 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:54:51,560 - WARNING - Could not retrieve variants from source file in region 6:147136033-147136434. Error was invalid region `6:147136034-147136434`
[2016-04-15T04:54Z] 2016-04-14 21:54:52 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:54:52,743 - WARNING - Could not retrieve variants from source file in region 6:147066882-147067283. Error was invalid region `6:147066883-147067283`
[2016-04-15T04:54Z] 2016-04-14 21:54:52 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:54:52,908 - WARNING - Could not retrieve variants from source file in region 6:147066882-147067283. Error was invalid region `6:147066883-147067283`
[2016-04-15T04:54Z] 2016-04-14 21:54:57 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:54:57,191 - WARNING - Could not retrieve variants from source file in region 6:149721479-149721880. Error was invalid region `6:149721480-149721880`
[2016-04-15T04:54Z] 2016-04-14 21:54:57 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:54:57,598 - WARNING - Could not retrieve variants from source file in region 6:146993234-146993635. Error was invalid region `6:146993235-146993635`
[2016-04-15T04:55Z] 2016-04-14 21:55:00 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:55:00,596 - WARNING - Could not retrieve variants from source file in region 6:149721479-149721880. Error was invalid region `6:149721480-149721880`
[2016-04-15T04:55Z] 2016-04-14 21:55:00 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:55:00,699 - WARNING - Could not retrieve variants from source file in region 6:149721479-149721880. Error was invalid region `6:149721480-149721880`
[2016-04-15T04:55Z] ['bcbio-variation-recall', 'square', '-Xms750m', '-Xmx7280m', '-XX:+UseSerialGC', '-c', 16, '-r', u'6:158013811-171115067', '--caller', 'platypus', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/6/Batch1-6_158013810_171115067.vcf.gz', '/mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/6/Batch1-6_158013810_171115067.vcf-inputs.txt'] in region: 6:158013811-171115067
[2016-04-15T04:55Z] 2016-04-14 21:55:17 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:55:17,079 - WARNING - Could not retrieve variants from source file in region 6:166826044-166826494. Error was invalid region `6:166826045-166826494`
[2016-04-15T04:55Z] 2016-04-14 21:55:17 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:55:17,800 - WARNING - Could not retrieve variants from source file in region 6:163516239-163522467. Error was invalid region `6:163516240-163522467`
[2016-04-15T04:55Z] 2016-04-14 21:55:18 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:55:18,252 - WARNING - Could not retrieve variants from source file in region 6:170627440-170632499. Error was invalid region `6:170627441-170632499`
[2016-04-15T04:55Z] 2016-04-14 21:55:18 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:55:18,837 - WARNING - Could not retrieve variants from source file in region 6:160857977-160858378. Error was invalid region `6:160857978-160858378`
[2016-04-15T04:55Z] 2016-04-14 21:55:19 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:55:19,024 - WARNING - Could not retrieve variants from source file in region 6:168999459-168999860. Error was invalid region `6:168999460-168999860`
[2016-04-15T04:55Z] 2016-04-14 21:55:19 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:55:19,051 - WARNING - Could not retrieve variants from source file in region 6:165703312-165715863. Error was invalid region `6:165703313-165715863`
[2016-04-15T04:55Z] 2016-04-14 21:55:19 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:55:19,072 - WARNING - Could not retrieve variants from source file in region 6:160953431-160969819. Error was invalid region `6:160953432-160969819`
[2016-04-15T04:55Z] 2016-04-14 21:55:19 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:55:19,619 - WARNING - Could not retrieve variants from source file in region 6:169648556-169648957. Error was invalid region `6:169648557-169648957`
[2016-04-15T04:55Z] 2016-04-14 21:55:22 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:55:22,901 - WARNING - Could not retrieve variants from source file in region 6:166826044-166826494. Error was invalid region `6:166826045-166826494`
[2016-04-15T04:55Z] 2016-04-14 21:55:25 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:55:25,930 - WARNING - Could not retrieve variants from source file in region 6:160645621-160679590. Error was invalid region `6:160645622-160679590`
[2016-04-15T04:55Z] 2016-04-14 21:55:27 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:55:27,662 - WARNING - Could not retrieve variants from source file in region 6:166862022-166873200. Error was invalid region `6:166862023-166873200`
[2016-04-15T04:55Z] 2016-04-14 21:55:28 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:55:28,171 - WARNING - Could not retrieve variants from source file in region 6:160328409-160328810. Error was invalid region `6:160328410-160328810`
[2016-04-15T04:55Z] 2016-04-14 21:55:28 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:55:28,473 - WARNING - Could not retrieve variants from source file in region 6:166826044-166826494. Error was invalid region `6:166826045-166826494`
[2016-04-15T04:55Z] 2016-04-14 21:55:35 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:55:35,257 - WARNING - Could not retrieve variants from source file in region 6:163984755-163990498. Error was invalid region `6:163984756-163990498`
[2016-04-15T04:55Z] 2016-04-14 21:55:35 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:55:35,754 - WARNING - Could not retrieve variants from source file in region 6:168999459-168999860. Error was invalid region `6:168999460-168999860`
[2016-04-15T04:55Z] 2016-04-14 21:55:47 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:55:47,693 - WARNING - Could not retrieve variants from source file in region 6:170162326-170176838. Error was invalid region `6:170162327-170176838`
[2016-04-15T04:55Z] 2016-04-14 21:55:48 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:55:48,743 - WARNING - Could not retrieve variants from source file in region 6:165895613-165896014. Error was invalid region `6:165895614-165896014`
[2016-04-15T04:55Z] 2016-04-14 21:55:50 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:55:50,596 - WARNING - Could not retrieve variants from source file in region 6:161807644-161808045. Error was invalid region `6:161807645-161808045`
[2016-04-15T04:55Z] 2016-04-14 21:55:51 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:55:51,400 - WARNING - Could not retrieve variants from source file in region 6:169621325-169622680. Error was invalid region `6:169621326-169622680`
[2016-04-15T04:55Z] 2016-04-14 21:55:52 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:55:52,837 - WARNING - Could not retrieve variants from source file in region 6:168695134-168709575. Error was invalid region `6:168695135-168709575`
[2016-04-15T04:55Z] 2016-04-14 21:55:53 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:55:53,852 - WARNING - Could not retrieve variants from source file in region 6:161469563-161469964. Error was invalid region `6:161469564-161469964`
[2016-04-15T04:55Z] 2016-04-14 21:55:54 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:55:54,779 - WARNING - Could not retrieve variants from source file in region 6:167342930-167344773. Error was invalid region `6:167342931-167344773`
[2016-04-15T04:55Z] 2016-04-14 21:55:55 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:55:55,537 - WARNING - Could not retrieve variants from source file in region 6:169621325-169622680. Error was invalid region `6:169621326-169622680`
[2016-04-15T04:55Z] 2016-04-14 21:55:55 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:55:55,820 - WARNING - Could not retrieve variants from source file in region 6:170162326-170176838. Error was invalid region `6:170162327-170176838`
[2016-04-15T04:55Z] 2016-04-14 21:55:56 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:55:56,363 - WARNING - Could not retrieve variants from source file in region 6:160769600-160770001. Error was invalid region `6:160769601-160770001`
[2016-04-15T04:55Z] 2016-04-14 21:55:57 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:55:57,753 - WARNING - Could not retrieve variants from source file in region 6:161469563-161469964. Error was invalid region `6:161469564-161469964`
[2016-04-15T04:55Z] 2016-04-14 21:55:59 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:55:59,853 - WARNING - Could not retrieve variants from source file in region 6:169621325-169622680. Error was invalid region `6:169621326-169622680`
[2016-04-15T04:56Z] 2016-04-14 21:56:02 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:56:02,024 - WARNING - Could not retrieve variants from source file in region 6:161469563-161469964. Error was invalid region `6:161469564-161469964`
[2016-04-15T04:56Z] 2016-04-14 21:56:02 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:56:02,126 - WARNING - Could not retrieve variants from source file in region 6:160196132-160225202. Error was invalid region `6:160196133-160225202`
[2016-04-15T04:56Z] 2016-04-14 21:56:09 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:56:09,736 - WARNING - Could not retrieve variants from source file in region 6:167040252-167040653. Error was invalid region `6:167040253-167040653`
[2016-04-15T04:56Z] 2016-04-14 21:56:09 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:56:09,796 - WARNING - Could not retrieve variants from source file in region 6:160494198-160505389. Error was invalid region `6:160494199-160505389`
[2016-04-15T04:56Z] 2016-04-14 21:56:12 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:56:12,535 - WARNING - Could not retrieve variants from source file in region 6:167271500-167271906. Error was invalid region `6:167271501-167271906`
[2016-04-15T04:56Z] 2016-04-14 21:56:13 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:56:13,086 - WARNING - Could not retrieve variants from source file in region 6:161519139-161519546. Error was invalid region `6:161519140-161519546`
[2016-04-15T04:56Z] 2016-04-14 21:56:13 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:56:13,088 - WARNING - Could not retrieve variants from source file in region 6:161131935-161174136. Error was invalid region `6:161131936-161174136`
[2016-04-15T04:56Z] 2016-04-14 21:56:13 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:56:13,107 - WARNING - Could not retrieve variants from source file in region 6:166911851-166912252. Error was invalid region `6:166911852-166912252`
[2016-04-15T04:56Z] 2016-04-14 21:56:14 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:56:14,504 - WARNING - Could not retrieve variants from source file in region 6:160494198-160505389. Error was invalid region `6:160494199-160505389`
[2016-04-15T04:56Z] 2016-04-14 21:56:14 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:56:14,691 - WARNING - Could not retrieve variants from source file in region 6:166952053-166952454. Error was invalid region `6:166952054-166952454`
[2016-04-15T04:56Z] 2016-04-14 21:56:14 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:56:14,746 - WARNING - Could not retrieve variants from source file in region 6:160169047-160169448. Error was invalid region `6:160169048-160169448`
[2016-04-15T04:56Z] 2016-04-14 21:56:17 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:56:17,140 - WARNING - Could not retrieve variants from source file in region 6:167271500-167271906. Error was invalid region `6:167271501-167271906`
[2016-04-15T04:56Z] 2016-04-14 21:56:17 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:56:17,784 - WARNING - Could not retrieve variants from source file in region 6:161005961-161032858. Error was invalid region `6:161005962-161032858`
[2016-04-15T04:56Z] 2016-04-14 21:56:17 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:56:17,803 - WARNING - Could not retrieve variants from source file in region 6:166952053-166952454. Error was invalid region `6:166952054-166952454`
[2016-04-15T04:56Z] 2016-04-14 21:56:18 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:56:18,780 - WARNING - Could not retrieve variants from source file in region 6:160494198-160505389. Error was invalid region `6:160494199-160505389`
[2016-04-15T04:56Z] 2016-04-14 21:56:18 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:56:18,820 - WARNING - Could not retrieve variants from source file in region 6:167040252-167040653. Error was invalid region `6:167040253-167040653`
[2016-04-15T04:56Z] 2016-04-14 21:56:21 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:56:21,513 - WARNING - Could not retrieve variants from source file in region 6:161131935-161174136. Error was invalid region `6:161131936-161174136`
[2016-04-15T04:56Z] 2016-04-14 21:56:21 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:56:21,859 - WARNING - Could not retrieve variants from source file in region 6:167271500-167271906. Error was invalid region `6:167271501-167271906`
[2016-04-15T04:56Z] 2016-04-14 21:56:22 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:56:22,654 - WARNING - Could not retrieve variants from source file in region 6:166911851-166912252. Error was invalid region `6:166911852-166912252`
[2016-04-15T04:56Z] 2016-04-14 21:56:22 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:56:22,720 - WARNING - Could not retrieve variants from source file in region 6:168351894-168365488. Error was invalid region `6:168351895-168365488`
[2016-04-15T04:56Z] 2016-04-14 21:56:24 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:56:24,051 - WARNING - Could not retrieve variants from source file in region 6:160169047-160169448. Error was invalid region `6:160169048-160169448`
[2016-04-15T04:56Z] 2016-04-14 21:56:27 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:56:27,050 - WARNING - Could not retrieve variants from source file in region 6:167728563-167754911. Error was invalid region `6:167728564-167754911`
[2016-04-15T04:56Z] 2016-04-14 21:56:30 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:56:30,795 - WARNING - Could not retrieve variants from source file in region 6:167728563-167754911. Error was invalid region `6:167728564-167754911`
[2016-04-15T04:56Z] 2016-04-14 21:56:34 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:56:34,954 - WARNING - Could not retrieve variants from source file in region 6:158571290-158571691. Error was invalid region `6:158571291-158571691`
[2016-04-15T04:56Z] 2016-04-14 21:56:35 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:56:35,175 - WARNING - Could not retrieve variants from source file in region 6:158869870-158870271. Error was invalid region `6:158869871-158870271`
[2016-04-15T04:56Z] 2016-04-14 21:56:35 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:56:35,296 - WARNING - Could not retrieve variants from source file in region 6:158330554-158330955. Error was invalid region `6:158330555-158330955`
[2016-04-15T04:56Z] 2016-04-14 21:56:38 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:56:38,903 - WARNING - Could not retrieve variants from source file in region 6:160113661-160114062. Error was invalid region `6:160113662-160114062`
[2016-04-15T04:56Z] 2016-04-14 21:56:39 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:56:39,193 - WARNING - Could not retrieve variants from source file in region 6:158293973-158294374. Error was invalid region `6:158293974-158294374`
[2016-04-15T04:56Z] 2016-04-14 21:56:39 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:56:39,520 - WARNING - Could not retrieve variants from source file in region 6:158571290-158571691. Error was invalid region `6:158571291-158571691`
[2016-04-15T04:56Z] 2016-04-14 21:56:39 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:56:39,794 - WARNING - Could not retrieve variants from source file in region 6:158869870-158870271. Error was invalid region `6:158869871-158870271`
[2016-04-15T04:56Z] 2016-04-14 21:56:39 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:56:39,845 - WARNING - Could not retrieve variants from source file in region 6:158330554-158330955. Error was invalid region `6:158330555-158330955`
[2016-04-15T04:56Z] 2016-04-14 21:56:40 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:56:40,388 - WARNING - Could not retrieve variants from source file in region 6:159590523-159590924. Error was invalid region `6:159590524-159590924`
[2016-04-15T04:56Z] 2016-04-14 21:56:40 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:56:40,841 - WARNING - Could not retrieve variants from source file in region 6:158293973-158294374. Error was invalid region `6:158293974-158294374`
[2016-04-15T04:56Z] 2016-04-14 21:56:43 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:56:43,158 - WARNING - Could not retrieve variants from source file in region 6:160113661-160114062. Error was invalid region `6:160113662-160114062`
[2016-04-15T04:56Z] 2016-04-14 21:56:43 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:56:43,856 - WARNING - Could not retrieve variants from source file in region 6:158571290-158571691. Error was invalid region `6:158571291-158571691`
[2016-04-15T04:56Z] 2016-04-14 21:56:44 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:56:44,288 - WARNING - Could not retrieve variants from source file in region 6:158734876-158735280. Error was invalid region `6:158734877-158735280`
[2016-04-15T04:56Z] 2016-04-14 21:56:44 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:56:44,296 - WARNING - Could not retrieve variants from source file in region 6:158869870-158870271. Error was invalid region `6:158869871-158870271`
[2016-04-15T04:56Z] 2016-04-14 21:56:44 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:56:44,516 - WARNING - Could not retrieve variants from source file in region 6:158330554-158330955. Error was invalid region `6:158330555-158330955`
[2016-04-15T04:56Z] 2016-04-14 21:56:44 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:56:44,632 - WARNING - Could not retrieve variants from source file in region 6:158734876-158735280. Error was invalid region `6:158734877-158735280`
[2016-04-15T04:56Z] 2016-04-14 21:56:45 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:56:45,462 - WARNING - Could not retrieve variants from source file in region 6:159178134-159185753. Error was invalid region `6:159178135-159185753`
[2016-04-15T04:56Z] 2016-04-14 21:56:47 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:56:47,629 - WARNING - Could not retrieve variants from source file in region 6:158734876-158735280. Error was invalid region `6:158734877-158735280`
[2016-04-15T04:56Z] 2016-04-14 21:56:51 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:56:51,288 - WARNING - Could not retrieve variants from source file in region 6:159650767-159672732. Error was invalid region `6:159650768-159672732`
[2016-04-15T04:56Z] ['bcbio-variation-recall', 'square', '-Xms750m', '-Xmx7280m', '-XX:+UseSerialGC', '-c', 16, '-r', u'7:1-15584548', '--caller', 'platypus', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/7/Batch1-7_0_15584548.vcf.gz', '/mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/7/Batch1-7_0_15584548.vcf-inputs.txt'] in region: 7:1-15584548
[2016-04-15T04:57Z] 2016-04-14 21:57:07 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:57:07,063 - WARNING - Could not retrieve variants from source file in region 7:2394535-2415268. Error was invalid region `7:2394536-2415268`
[2016-04-15T04:57Z] 2016-04-14 21:57:07 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:57:07,136 - WARNING - Could not retrieve variants from source file in region 7:3341179-3341580. Error was invalid region `7:3341180-3341580`
[2016-04-15T04:57Z] 2016-04-14 21:57:08 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:57:08,203 - WARNING - Could not retrieve variants from source file in region 7:11580910-11581324. Error was invalid region `7:11580911-11581324`
[2016-04-15T04:57Z] 2016-04-14 21:57:08 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:57:08,256 - WARNING - Could not retrieve variants from source file in region 7:1784063-1784464. Error was invalid region `7:1784064-1784464`
[2016-04-15T04:57Z] 2016-04-14 21:57:08 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:57:08,394 - WARNING - Could not retrieve variants from source file in region 7:14758062-14758463. Error was invalid region `7:14758063-14758463`
[2016-04-15T04:57Z] 2016-04-14 21:57:08 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:57:08,956 - WARNING - Could not retrieve variants from source file in region 7:6204788-6205189. Error was invalid region `7:6204789-6205189`
[2016-04-15T04:57Z] 2016-04-14 21:57:09 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:57:09,365 - WARNING - Could not retrieve variants from source file in region 7:2699476-2700179. Error was invalid region `7:2699477-2700179`
[2016-04-15T04:57Z] 2016-04-14 21:57:09 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:57:09,548 - WARNING - Could not retrieve variants from source file in region 7:5096747-5105323. Error was invalid region `7:5096748-5105323`
[2016-04-15T04:57Z] 2016-04-14 21:57:09 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:57:09,569 - WARNING - Could not retrieve variants from source file in region 7:12610240-12620994. Error was invalid region `7:12610241-12620994`
[2016-04-15T04:57Z] 2016-04-14 21:57:09 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:57:09,931 - WARNING - Could not retrieve variants from source file in region 7:6537610-6538011. Error was invalid region `7:6537611-6538011`
[2016-04-15T04:57Z] 2016-04-14 21:57:13 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:57:13,586 - WARNING - Could not retrieve variants from source file in region 7:7545480-7545881. Error was invalid region `7:7545481-7545881`
[2016-04-15T04:57Z] 2016-04-14 21:57:14 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:57:14,012 - WARNING - Could not retrieve variants from source file in region 7:3341179-3341580. Error was invalid region `7:3341180-3341580`
[2016-04-15T04:57Z] 2016-04-14 21:57:15 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:57:15,267 - WARNING - Could not retrieve variants from source file in region 7:1022802-1028638. Error was invalid region `7:1022803-1028638`
[2016-04-15T04:57Z] 2016-04-14 21:57:16 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:57:16,676 - WARNING - Could not retrieve variants from source file in region 7:14758062-14758463. Error was invalid region `7:14758063-14758463`
[2016-04-15T04:57Z] 2016-04-14 21:57:16 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:57:16,812 - WARNING - Could not retrieve variants from source file in region 7:6537610-6538011. Error was invalid region `7:6537611-6538011`
[2016-04-15T04:57Z] 2016-04-14 21:57:16 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:57:16,871 - WARNING - Could not retrieve variants from source file in region 7:8272016-8272417. Error was invalid region `7:8272017-8272417`
[2016-04-15T04:57Z] 2016-04-14 21:57:17 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:57:17,460 - WARNING - Could not retrieve variants from source file in region 7:618727-619128. Error was invalid region `7:618728-619128`
[2016-04-15T04:57Z] 2016-04-14 21:57:17 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:57:17,505 - WARNING - Could not retrieve variants from source file in region 7:6204788-6205189. Error was invalid region `7:6204789-6205189`
[2016-04-15T04:57Z] 2016-04-14 21:57:17 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:57:17,542 - WARNING - Could not retrieve variants from source file in region 7:4780303-4802219. Error was invalid region `7:4780304-4802219`
[2016-04-15T04:57Z] 2016-04-14 21:57:18 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:57:18,914 - WARNING - Could not retrieve variants from source file in region 7:3341179-3341580. Error was invalid region `7:3341180-3341580`
[2016-04-15T04:57Z] 2016-04-14 21:57:23 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:57:23,575 - WARNING - Could not retrieve variants from source file in region 7:14758062-14758463. Error was invalid region `7:14758063-14758463`
[2016-04-15T04:57Z] 2016-04-14 21:57:23 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:57:23,692 - WARNING - Could not retrieve variants from source file in region 7:6537610-6538011. Error was invalid region `7:6537611-6538011`
[2016-04-15T04:57Z] 2016-04-14 21:57:25 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:57:25,671 - WARNING - Could not retrieve variants from source file in region 7:618727-619128. Error was invalid region `7:618728-619128`
[2016-04-15T04:57Z] 2016-04-14 21:57:25 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:57:25,728 - WARNING - Could not retrieve variants from source file in region 7:6204788-6205189. Error was invalid region `7:6204789-6205189`
[2016-04-15T04:57Z] 2016-04-14 21:57:37 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:57:37,329 - WARNING - Could not retrieve variants from source file in region 7:1586451-1595258. Error was invalid region `7:1586452-1595258`
[2016-04-15T04:57Z] 2016-04-14 21:57:37 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:57:37,834 - WARNING - Could not retrieve variants from source file in region 7:2296795-2304176. Error was invalid region `7:2296796-2304176`
[2016-04-15T04:57Z] 2016-04-14 21:57:40 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:57:40,870 - WARNING - Could not retrieve variants from source file in region 7:6505690-6506091. Error was invalid region `7:6505691-6506091`
[2016-04-15T04:57Z] 2016-04-14 21:57:41 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:57:41,371 - WARNING - Could not retrieve variants from source file in region 7:4959596-4959997. Error was invalid region `7:4959597-4959997`
[2016-04-15T04:57Z] 2016-04-14 21:57:42 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:57:42,358 - WARNING - Could not retrieve variants from source file in region 7:14215711-14217863. Error was invalid region `7:14215712-14217863`
[2016-04-15T04:57Z] 2016-04-14 21:57:42 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:57:42,518 - WARNING - Could not retrieve variants from source file in region 7:8125753-8126154. Error was invalid region `7:8125754-8126154`
[2016-04-15T04:57Z] 2016-04-14 21:57:42 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:57:42,739 - WARNING - Could not retrieve variants from source file in region 7:11143819-11146473. Error was invalid region `7:11143820-11146473`
[2016-04-15T04:57Z] 2016-04-14 21:57:42 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:57:42,963 - WARNING - Could not retrieve variants from source file in region 7:1586451-1595258. Error was invalid region `7:1586452-1595258`
[2016-04-15T04:57Z] 2016-04-14 21:57:43 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:57:43,007 - WARNING - Could not retrieve variants from source file in region 7:590855-591256. Error was invalid region `7:590856-591256`
[2016-04-15T04:57Z] 2016-04-14 21:57:43 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:57:43,118 - WARNING - Could not retrieve variants from source file in region 7:2296795-2304176. Error was invalid region `7:2296796-2304176`
[2016-04-15T04:57Z] 2016-04-14 21:57:43 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:57:43,480 - WARNING - Could not retrieve variants from source file in region 7:925506-940371. Error was invalid region `7:925507-940371`
[2016-04-15T04:57Z] 2016-04-14 21:57:44 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:57:44,864 - WARNING - Could not retrieve variants from source file in region 7:7495524-7514425. Error was invalid region `7:7495525-7514425`
[2016-04-15T04:57Z] 2016-04-14 21:57:47 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:57:47,221 - WARNING - Could not retrieve variants from source file in region 7:6505690-6506091. Error was invalid region `7:6505691-6506091`
[2016-04-15T04:57Z] 2016-04-14 21:57:48 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:57:48,021 - WARNING - Could not retrieve variants from source file in region 7:4959596-4959997. Error was invalid region `7:4959597-4959997`
[2016-04-15T04:57Z] 2016-04-14 21:57:50 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:57:50,711 - WARNING - Could not retrieve variants from source file in region 7:1586451-1595258. Error was invalid region `7:1586452-1595258`
[2016-04-15T04:57Z] 2016-04-14 21:57:51 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:57:51,043 - WARNING - Could not retrieve variants from source file in region 7:8125753-8126154. Error was invalid region `7:8125754-8126154`
[2016-04-15T04:57Z] 2016-04-14 21:57:51 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:57:51,198 - WARNING - Could not retrieve variants from source file in region 7:2296795-2304176. Error was invalid region `7:2296796-2304176`
[2016-04-15T04:57Z] 2016-04-14 21:57:51 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:57:51,548 - WARNING - Could not retrieve variants from source file in region 7:925506-940371. Error was invalid region `7:925507-940371`
[2016-04-15T04:57Z] 2016-04-14 21:57:51 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:57:51,676 - WARNING - Could not retrieve variants from source file in region 7:2644308-2649894. Error was invalid region `7:2644309-2649894`
[2016-04-15T04:57Z] 2016-04-14 21:57:51 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:57:51,731 - WARNING - Could not retrieve variants from source file in region 7:6063072-6076013. Error was invalid region `7:6063073-6076013`
[2016-04-15T04:57Z] 2016-04-14 21:57:52 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:57:52,134 - WARNING - Could not retrieve variants from source file in region 7:6505690-6506091. Error was invalid region `7:6505691-6506091`
[2016-04-15T04:57Z] 2016-04-14 21:57:52 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:57:52,448 - WARNING - Could not retrieve variants from source file in region 7:4959596-4959997. Error was invalid region `7:4959597-4959997`
[2016-04-15T04:57Z] 2016-04-14 21:57:54 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:57:54,962 - WARNING - Could not retrieve variants from source file in region 7:2946250-2969870. Error was invalid region `7:2946251-2969870`
[2016-04-15T04:57Z] 2016-04-14 21:57:57 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:57:57,709 - WARNING - Could not retrieve variants from source file in region 7:8125753-8126154. Error was invalid region `7:8125754-8126154`
[2016-04-15T04:57Z] 2016-04-14 21:57:59 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:57:59,270 - WARNING - Could not retrieve variants from source file in region 7:6063072-6076013. Error was invalid region `7:6063073-6076013`
[2016-04-15T04:58Z] 2016-04-14 21:58:06 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:58:06,876 - WARNING - Could not retrieve variants from source file in region 7:1481708-1484762. Error was invalid region `7:1481709-1484762`
[2016-04-15T04:58Z] 2016-04-14 21:58:08 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:58:08,753 - WARNING - Could not retrieve variants from source file in region 7:2257401-2257802. Error was invalid region `7:2257402-2257802`
[2016-04-15T04:58Z] 2016-04-14 21:58:09 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:58:09,597 - WARNING - Could not retrieve variants from source file in region 7:6369983-6370596. Error was invalid region `7:6369984-6370596`
[2016-04-15T04:58Z] 2016-04-14 21:58:09 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:58:09,735 - WARNING - Could not retrieve variants from source file in region 7:2853799-2854200. Error was invalid region `7:2853800-2854200`
[2016-04-15T04:58Z] 2016-04-14 21:58:10 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:58:10,871 - WARNING - Could not retrieve variants from source file in region 7:11102469-11102870. Error was invalid region `7:11102470-11102870`
[2016-04-15T04:58Z] 2016-04-14 21:58:11 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:58:11,377 - WARNING - Could not retrieve variants from source file in region 7:1481708-1484762. Error was invalid region `7:1481709-1484762`
[2016-04-15T04:58Z] 2016-04-14 21:58:12 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:58:12,296 - WARNING - Could not retrieve variants from source file in region 7:14025555-14025956. Error was invalid region `7:14025556-14025956`
[2016-04-15T04:58Z] 2016-04-14 21:58:13 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:58:13,204 - WARNING - Could not retrieve variants from source file in region 7:540307-552236. Error was invalid region `7:540308-552236`
[2016-04-15T04:58Z] 2016-04-14 21:58:13 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:58:13,675 - WARNING - Could not retrieve variants from source file in region 7:7646440-7646877. Error was invalid region `7:7646441-7646877`
[2016-04-15T04:58Z] 2016-04-14 21:58:14 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:58:14,320 - WARNING - Could not retrieve variants from source file in region 7:2257401-2257802. Error was invalid region `7:2257402-2257802`
[2016-04-15T04:58Z] 2016-04-14 21:58:15 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:58:15,010 - WARNING - Could not retrieve variants from source file in region 7:12269206-12269607. Error was invalid region `7:12269207-12269607`
[2016-04-15T04:58Z] 2016-04-14 21:58:15 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:58:15,911 - WARNING - Could not retrieve variants from source file in region 7:2853799-2854200. Error was invalid region `7:2853800-2854200`
[2016-04-15T04:58Z] 2016-04-14 21:58:16 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:58:16,345 - WARNING - Could not retrieve variants from source file in region 7:4874209-4901575. Error was invalid region `7:4874210-4901575`
[2016-04-15T04:58Z] 2016-04-14 21:58:16 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:58:16,597 - WARNING - Could not retrieve variants from source file in region 7:1481708-1484762. Error was invalid region `7:1481709-1484762`
[2016-04-15T04:58Z] 2016-04-14 21:58:16 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:58:16,645 - WARNING - Could not retrieve variants from source file in region 7:6026564-6037170. Error was invalid region `7:6026565-6037170`
[2016-04-15T04:58Z] 2016-04-14 21:58:16 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:58:16,794 - WARNING - Could not retrieve variants from source file in region 7:2611667-2612068. Error was invalid region `7:2611668-2612068`
[2016-04-15T04:58Z] 2016-04-14 21:58:17 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:58:17,008 - WARNING - Could not retrieve variants from source file in region 7:14025555-14025956. Error was invalid region `7:14025556-14025956`
[2016-04-15T04:58Z] 2016-04-14 21:58:17 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:58:17,499 - WARNING - Could not retrieve variants from source file in region 7:6844363-6844764. Error was invalid region `7:6844364-6844764`
[2016-04-15T04:58Z] 2016-04-14 21:58:18 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:58:18,411 - WARNING - Could not retrieve variants from source file in region 7:7646440-7646877. Error was invalid region `7:7646441-7646877`
[2016-04-15T04:58Z] 2016-04-14 21:58:19 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:58:19,358 - WARNING - Could not retrieve variants from source file in region 7:2257401-2257802. Error was invalid region `7:2257402-2257802`
[2016-04-15T04:58Z] 2016-04-14 21:58:21 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:58:21,180 - WARNING - Could not retrieve variants from source file in region 7:12269206-12269607. Error was invalid region `7:12269207-12269607`
[2016-04-15T04:58Z] 2016-04-14 21:58:22 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:58:22,379 - WARNING - Could not retrieve variants from source file in region 7:6369983-6370596. Error was invalid region `7:6369984-6370596`
[2016-04-15T04:58Z] 2016-04-14 21:58:22 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:58:22,975 - WARNING - Could not retrieve variants from source file in region 7:14025555-14025956. Error was invalid region `7:14025556-14025956`
[2016-04-15T04:58Z] 2016-04-14 21:58:23 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:58:23,005 - WARNING - Could not retrieve variants from source file in region 7:2853799-2854200. Error was invalid region `7:2853800-2854200`
[2016-04-15T04:58Z] 2016-04-14 21:58:23 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:58:23,097 - WARNING - Could not retrieve variants from source file in region 7:2611667-2612068. Error was invalid region `7:2611668-2612068`
[2016-04-15T04:58Z] 2016-04-14 21:58:23 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:58:23,098 - WARNING - Could not retrieve variants from source file in region 7:6026564-6037170. Error was invalid region `7:6026565-6037170`
[2016-04-15T04:58Z] 2016-04-14 21:58:23 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:58:23,412 - WARNING - Could not retrieve variants from source file in region 7:7646440-7646877. Error was invalid region `7:7646441-7646877`
[2016-04-15T04:58Z] 2016-04-14 21:58:25 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:58:25,658 - WARNING - Could not retrieve variants from source file in region 7:12269206-12269607. Error was invalid region `7:12269207-12269607`
[2016-04-15T04:58Z] 2016-04-14 21:58:29 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:58:29,089 - WARNING - Could not retrieve variants from source file in region 7:2611667-2612068. Error was invalid region `7:2611668-2612068`
[2016-04-15T04:58Z] 2016-04-14 21:58:29 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:58:29,682 - WARNING - Could not retrieve variants from source file in region 7:6026564-6037170. Error was invalid region `7:6026565-6037170`
[2016-04-15T04:58Z] 2016-04-14 21:58:34 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:58:34,860 - WARNING - Could not retrieve variants from source file in region 7:1976246-1976647. Error was invalid region `7:1976247-1976647`
[2016-04-15T04:58Z] 2016-04-14 21:58:35 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:58:35,754 - WARNING - Could not retrieve variants from source file in region 7:1131183-1132343. Error was invalid region `7:1131184-1132343`
[2016-04-15T04:58Z] 2016-04-14 21:58:36 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:58:36,415 - WARNING - Could not retrieve variants from source file in region 7:6732104-6732505. Error was invalid region `7:6732105-6732505`
[2016-04-15T04:58Z] 2016-04-14 21:58:36 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:58:36,820 - WARNING - Could not retrieve variants from source file in region 7:11022349-11022754. Error was invalid region `7:11022350-11022754`
[2016-04-15T04:58Z] 2016-04-14 21:58:38 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:58:38,681 - WARNING - Could not retrieve variants from source file in region 7:4841259-4841660. Error was invalid region `7:4841260-4841660`
[2016-04-15T04:58Z] 2016-04-14 21:58:39 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:58:39,311 - WARNING - Could not retrieve variants from source file in region 7:11676166-11676567. Error was invalid region `7:11676167-11676567`
[2016-04-15T04:58Z] 2016-04-14 21:58:39 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:58:39,324 - WARNING - Could not retrieve variants from source file in region 7:330875-331617. Error was invalid region `7:330876-331617`
[2016-04-15T04:58Z] 2016-04-14 21:58:39 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:58:39,965 - WARNING - Could not retrieve variants from source file in region 7:1976246-1976647. Error was invalid region `7:1976247-1976647`
[2016-04-15T04:58Z] 2016-04-14 21:58:40 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:58:40,184 - WARNING - Could not retrieve variants from source file in region 7:13978598-13978999. Error was invalid region `7:13978599-13978999`
[2016-04-15T04:58Z] 2016-04-14 21:58:40 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:58:40,533 - WARNING - Could not retrieve variants from source file in region 7:1131183-1132343. Error was invalid region `7:1131184-1132343`
[2016-04-15T04:58Z] 2016-04-14 21:58:42 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:58:42,161 - WARNING - Could not retrieve variants from source file in region 7:2752276-2752677. Error was invalid region `7:2752277-2752677`
[2016-04-15T04:58Z] 2016-04-14 21:58:43 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:58:43,627 - WARNING - Could not retrieve variants from source file in region 7:4841259-4841660. Error was invalid region `7:4841260-4841660`
[2016-04-15T04:58Z] 2016-04-14 21:58:44 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:58:44,698 - WARNING - Could not retrieve variants from source file in region 7:7612828-7613229. Error was invalid region `7:7612829-7613229`
[2016-04-15T04:58Z] 2016-04-14 21:58:45 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:58:45,008 - WARNING - Could not retrieve variants from source file in region 7:330875-331617. Error was invalid region `7:330876-331617`
[2016-04-15T04:58Z] 2016-04-14 21:58:45 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:58:45,272 - WARNING - Could not retrieve variants from source file in region 7:1976246-1976647. Error was invalid region `7:1976247-1976647`
[2016-04-15T04:58Z] 2016-04-14 21:58:46 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:58:46,090 - WARNING - Could not retrieve variants from source file in region 7:13978598-13978999. Error was invalid region `7:13978599-13978999`
[2016-04-15T04:58Z] 2016-04-14 21:58:47 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:58:47,399 - WARNING - Could not retrieve variants from source file in region 7:11022349-11022754. Error was invalid region `7:11022350-11022754`
[2016-04-15T04:58Z] 2016-04-14 21:58:47 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:58:47,408 - WARNING - Could not retrieve variants from source file in region 7:4116454-4116855. Error was invalid region `7:4116455-4116855`
[2016-04-15T04:58Z] 2016-04-14 21:58:47 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:58:47,773 - WARNING - Could not retrieve variants from source file in region 7:4841259-4841660. Error was invalid region `7:4841260-4841660`
[2016-04-15T04:58Z] 2016-04-14 21:58:50 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:58:50,438 - WARNING - Could not retrieve variants from source file in region 7:330875-331617. Error was invalid region `7:330876-331617`
[2016-04-15T04:58Z] 2016-04-14 21:58:50 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:58:50,893 - WARNING - Could not retrieve variants from source file in region 7:13978598-13978999. Error was invalid region `7:13978599-13978999`
[2016-04-15T04:58Z] 2016-04-14 21:58:55 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:58:55,771 - WARNING - Could not retrieve variants from source file in region 7:5920358-5920759. Error was invalid region `7:5920359-5920759`
[2016-04-15T04:58Z] 2016-04-14 21:58:58 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:58:58,794 - WARNING - Could not retrieve variants from source file in region 7:1067695-1068376. Error was invalid region `7:1067696-1068376`
[2016-04-15T04:59Z] 2016-04-14 21:59:01 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:59:01,119 - WARNING - Could not retrieve variants from source file in region 7:7570883-7571284. Error was invalid region `7:7570884-7571284`
[2016-04-15T04:59Z] 2016-04-14 21:59:01 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:59:01,449 - WARNING - Could not retrieve variants from source file in region 7:4026733-4027134. Error was invalid region `7:4026734-4027134`
[2016-04-15T04:59Z] 2016-04-14 21:59:02 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:59:02,438 - WARNING - Could not retrieve variants from source file in region 7:2514577-2515729. Error was invalid region `7:2514578-2515729`
[2016-04-15T04:59Z] 2016-04-14 21:59:04 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:59:04,495 - WARNING - Could not retrieve variants from source file in region 7:5920358-5920759. Error was invalid region `7:5920359-5920759`
[2016-04-15T04:59Z] 2016-04-14 21:59:05 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:59:05,492 - WARNING - Could not retrieve variants from source file in region 7:7570883-7571284. Error was invalid region `7:7570884-7571284`
[2016-04-15T04:59Z] 2016-04-14 21:59:06 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:59:06,521 - WARNING - Could not retrieve variants from source file in region 7:5521257-5541847. Error was invalid region `7:5521258-5541847`
[2016-04-15T04:59Z] 2016-04-14 21:59:06 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:59:06,666 - WARNING - Could not retrieve variants from source file in region 7:5770189-5770590. Error was invalid region `7:5770190-5770590`
[2016-04-15T04:59Z] 2016-04-14 21:59:08 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:59:08,859 - WARNING - Could not retrieve variants from source file in region 7:7570883-7571284. Error was invalid region `7:7570884-7571284`
[2016-04-15T04:59Z] 2016-04-14 21:59:10 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:59:10,211 - WARNING - Could not retrieve variants from source file in region 7:5770189-5770590. Error was invalid region `7:5770190-5770590`
[2016-04-15T04:59Z] 2016-04-14 21:59:12 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:59:12,149 - WARNING - Could not retrieve variants from source file in region 7:5232670-5254417. Error was invalid region `7:5232671-5254417`
[2016-04-15T04:59Z] 2016-04-14 21:59:12 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:59:12,150 - WARNING - Could not retrieve variants from source file in region 7:5232670-5254417. Error was invalid region `7:5232671-5254417`
[2016-04-15T04:59Z] ['bcbio-variation-recall', 'square', '-Xms750m', '-Xmx7280m', '-XX:+UseSerialGC', '-c', 16, '-r', u'7:15599766-31117713', '--caller', 'platypus', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/7/Batch1-7_15599765_31117713.vcf.gz', '/mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/7/Batch1-7_15599765_31117713.vcf-inputs.txt'] in region: 7:15599766-31117713
[2016-04-15T04:59Z] 2016-04-14 21:59:28 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:59:28,071 - WARNING - Could not retrieve variants from source file in region 7:23871687-23872088. Error was invalid region `7:23871688-23872088`
[2016-04-15T04:59Z] 2016-04-14 21:59:28 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:59:28,130 - WARNING - Could not retrieve variants from source file in region 7:28995589-28997786. Error was invalid region `7:28995590-28997786`
[2016-04-15T04:59Z] 2016-04-14 21:59:28 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:59:28,684 - WARNING - Could not retrieve variants from source file in region 7:27582422-27582823. Error was invalid region `7:27582423-27582823`
[2016-04-15T04:59Z] 2016-04-14 21:59:30 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:59:30,263 - WARNING - Could not retrieve variants from source file in region 7:21582752-21584857. Error was invalid region `7:21582753-21584857`
[2016-04-15T04:59Z] 2016-04-14 21:59:30 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:59:30,325 - WARNING - Could not retrieve variants from source file in region 7:26685723-26686124. Error was invalid region `7:26685724-26686124`
[2016-04-15T04:59Z] 2016-04-14 21:59:30 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:59:30,736 - WARNING - Could not retrieve variants from source file in region 7:26403860-26404261. Error was invalid region `7:26403861-26404261`
[2016-04-15T04:59Z] 2016-04-14 21:59:30 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:59:30,946 - WARNING - Could not retrieve variants from source file in region 7:24324798-24329323. Error was invalid region `7:24324799-24329323`
[2016-04-15T04:59Z] 2016-04-14 21:59:31 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:59:31,067 - WARNING - Could not retrieve variants from source file in region 7:24758584-24758985. Error was invalid region `7:24758585-24758985`
[2016-04-15T04:59Z] 2016-04-14 21:59:32 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:59:32,929 - WARNING - Could not retrieve variants from source file in region 7:30029503-30029904. Error was invalid region `7:30029504-30029904`
[2016-04-15T04:59Z] 2016-04-14 21:59:33 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:59:33,330 - WARNING - Could not retrieve variants from source file in region 7:23871687-23872088. Error was invalid region `7:23871688-23872088`
[2016-04-15T04:59Z] 2016-04-14 21:59:36 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:59:36,352 - WARNING - Could not retrieve variants from source file in region 7:29923361-29923762. Error was invalid region `7:29923362-29923762`
[2016-04-15T04:59Z] 2016-04-14 21:59:37 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:59:37,046 - WARNING - Could not retrieve variants from source file in region 7:25174121-25208184. Error was invalid region `7:25174122-25208184`
[2016-04-15T04:59Z] 2016-04-14 21:59:37 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:59:37,572 - WARNING - Could not retrieve variants from source file in region 7:26403860-26404261. Error was invalid region `7:26403861-26404261`
[2016-04-15T04:59Z] 2016-04-14 21:59:37 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:59:37,597 - WARNING - Could not retrieve variants from source file in region 7:30113495-30122615. Error was invalid region `7:30113496-30122615`
[2016-04-15T04:59Z] 2016-04-14 21:59:38 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:59:38,357 - WARNING - Could not retrieve variants from source file in region 7:30830871-30831278. Error was invalid region `7:30830872-30831278`
[2016-04-15T04:59Z] 2016-04-14 21:59:38 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:59:38,449 - WARNING - Could not retrieve variants from source file in region 7:30491100-30508974. Error was invalid region `7:30491101-30508974`
[2016-04-15T04:59Z] 2016-04-14 21:59:42 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:59:42,228 - WARNING - Could not retrieve variants from source file in region 7:29923361-29923762. Error was invalid region `7:29923362-29923762`
[2016-04-15T04:59Z] 2016-04-14 21:59:44 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:59:44,507 - WARNING - Could not retrieve variants from source file in region 7:21582752-21584857. Error was invalid region `7:21582753-21584857`
[2016-04-15T04:59Z] 2016-04-14 21:59:44 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:59:44,543 - WARNING - Could not retrieve variants from source file in region 7:25174121-25208184. Error was invalid region `7:25174122-25208184`
[2016-04-15T04:59Z] 2016-04-14 21:59:45 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:59:45,505 - WARNING - Could not retrieve variants from source file in region 7:26403860-26404261. Error was invalid region `7:26403861-26404261`
[2016-04-15T04:59Z] 2016-04-14 21:59:45 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:59:45,849 - WARNING - Could not retrieve variants from source file in region 7:24758584-24758985. Error was invalid region `7:24758585-24758985`
[2016-04-15T04:59Z] 2016-04-14 21:59:46 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:59:46,449 - WARNING - Could not retrieve variants from source file in region 7:30491100-30508974. Error was invalid region `7:30491101-30508974`
[2016-04-15T04:59Z] 2016-04-14 21:59:56 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:59:56,301 - WARNING - Could not retrieve variants from source file in region 7:23793742-23794143. Error was invalid region `7:23793743-23794143`
[2016-04-15T04:59Z] 2016-04-14 21:59:57 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:59:57,326 - WARNING - Could not retrieve variants from source file in region 7:27826892-27827293. Error was invalid region `7:27826893-27827293`
[2016-04-15T04:59Z] 2016-04-14 21:59:57 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:59:57,905 - WARNING - Could not retrieve variants from source file in region 7:27826892-27827293. Error was invalid region `7:27826893-27827293`
[2016-04-15T04:59Z] 2016-04-14 21:59:57 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:59:57,975 - WARNING - Could not retrieve variants from source file in region 7:27702179-27702580. Error was invalid region `7:27702180-27702580`
[2016-04-15T04:59Z] 2016-04-14 21:59:58 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 21:59:58,389 - WARNING - Could not retrieve variants from source file in region 7:27702179-27702580. Error was invalid region `7:27702180-27702580`
[2016-04-15T05:00Z] 2016-04-14 22:00:00 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:00:00,289 - WARNING - Could not retrieve variants from source file in region 7:27826892-27827293. Error was invalid region `7:27826893-27827293`
[2016-04-15T05:00Z] 2016-04-14 22:00:01 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:00:01,027 - WARNING - Could not retrieve variants from source file in region 7:20824403-20824804. Error was invalid region `7:20824404-20824804`
[2016-04-15T05:00Z] 2016-04-14 22:00:01 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:00:01,526 - WARNING - Could not retrieve variants from source file in region 7:24873700-24874101. Error was invalid region `7:24873701-24874101`
[2016-04-15T05:00Z] 2016-04-14 22:00:02 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:00:02,651 - WARNING - Could not retrieve variants from source file in region 7:22769562-22771346. Error was invalid region `7:22769563-22771346`
[2016-04-15T05:00Z] 2016-04-14 22:00:05 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:00:05,744 - WARNING - Could not retrieve variants from source file in region 7:29771386-29771791. Error was invalid region `7:29771387-29771791`
[2016-04-15T05:00Z] 2016-04-14 22:00:05 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:00:05,770 - WARNING - Could not retrieve variants from source file in region 7:30174562-30174963. Error was invalid region `7:30174563-30174963`
[2016-04-15T05:00Z] 2016-04-14 22:00:05 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:00:05,822 - WARNING - Could not retrieve variants from source file in region 7:25266189-25268153. Error was invalid region `7:25266190-25268153`
[2016-04-15T05:00Z] 2016-04-14 22:00:06 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:00:06,138 - WARNING - Could not retrieve variants from source file in region 7:20824403-20824804. Error was invalid region `7:20824404-20824804`
[2016-04-15T05:00Z] 2016-04-14 22:00:06 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:00:06,219 - WARNING - Could not retrieve variants from source file in region 7:27168882-27196306. Error was invalid region `7:27168883-27196306`
[2016-04-15T05:00Z] 2016-04-14 22:00:06 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:00:06,265 - WARNING - Could not retrieve variants from source file in region 7:24873700-24874101. Error was invalid region `7:24873701-24874101`
[2016-04-15T05:00Z] 2016-04-14 22:00:09 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:00:09,869 - WARNING - Could not retrieve variants from source file in region 7:29519087-29523753. Error was invalid region `7:29519088-29523753`
[2016-04-15T05:00Z] 2016-04-14 22:00:11 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:00:11,826 - WARNING - Could not retrieve variants from source file in region 7:24873700-24874101. Error was invalid region `7:24873701-24874101`
[2016-04-15T05:00Z] 2016-04-14 22:00:11 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:00:11,826 - WARNING - Could not retrieve variants from source file in region 7:22769562-22771346. Error was invalid region `7:22769563-22771346`
[2016-04-15T05:00Z] 2016-04-14 22:00:14 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:00:14,268 - WARNING - Could not retrieve variants from source file in region 7:29519087-29523753. Error was invalid region `7:29519088-29523753`
[2016-04-15T05:00Z] 2016-04-14 22:00:15 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:00:15,259 - WARNING - Could not retrieve variants from source file in region 7:18993659-18994060. Error was invalid region `7:18993660-18994060`
[2016-04-15T05:00Z] 2016-04-14 22:00:16 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:00:16,731 - WARNING - Could not retrieve variants from source file in region 7:27134885-27135504. Error was invalid region `7:27134886-27135504`
[2016-04-15T05:00Z] 2016-04-14 22:00:18 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:00:18,765 - WARNING - Could not retrieve variants from source file in region 7:29519087-29523753. Error was invalid region `7:29519088-29523753`
[2016-04-15T05:00Z] 2016-04-14 22:00:20 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:00:20,104 - WARNING - Could not retrieve variants from source file in region 7:23728705-23751926. Error was invalid region `7:23728706-23751926`
[2016-04-15T05:00Z] 2016-04-14 22:00:20 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:00:20,114 - WARNING - Could not retrieve variants from source file in region 7:26765385-26765786. Error was invalid region `7:26765386-26765786`
[2016-04-15T05:00Z] 2016-04-14 22:00:21 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:00:21,139 - WARNING - Could not retrieve variants from source file in region 7:29605764-29606478. Error was invalid region `7:29605765-29606478`
[2016-04-15T05:00Z] 2016-04-14 22:00:21 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:00:21,833 - WARNING - Could not retrieve variants from source file in region 7:29605764-29606478. Error was invalid region `7:29605765-29606478`
[2016-04-15T05:00Z] 2016-04-14 22:00:22 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:00:22,071 - WARNING - Could not retrieve variants from source file in region 7:23357110-23357511. Error was invalid region `7:23357111-23357511`
[2016-04-15T05:00Z] 2016-04-14 22:00:22 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:00:22,167 - WARNING - Could not retrieve variants from source file in region 7:27134885-27135504. Error was invalid region `7:27134886-27135504`
[2016-04-15T05:00Z] 2016-04-14 22:00:25 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:00:25,260 - WARNING - Could not retrieve variants from source file in region 7:18993659-18994060. Error was invalid region `7:18993660-18994060`
[2016-04-15T05:00Z] 2016-04-14 22:00:25 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:00:25,816 - WARNING - Could not retrieve variants from source file in region 7:20698059-20707091. Error was invalid region `7:20698060-20707091`
[2016-04-15T05:00Z] 2016-04-14 22:00:26 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:00:26,183 - WARNING - Could not retrieve variants from source file in region 7:21855940-21856341. Error was invalid region `7:21855941-21856341`
[2016-04-15T05:00Z] 2016-04-14 22:00:26 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:00:26,458 - WARNING - Could not retrieve variants from source file in region 7:23357110-23357511. Error was invalid region `7:23357111-23357511`
[2016-04-15T05:00Z] 2016-04-14 22:00:28 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:00:28,834 - WARNING - Could not retrieve variants from source file in region 7:26765385-26765786. Error was invalid region `7:26765386-26765786`
[2016-04-15T05:00Z] 2016-04-14 22:00:31 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:00:31,087 - WARNING - Could not retrieve variants from source file in region 7:21855940-21856341. Error was invalid region `7:21855941-21856341`
[2016-04-15T05:00Z] 2016-04-14 22:00:31 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:00:31,298 - WARNING - Could not retrieve variants from source file in region 7:21765241-21779468. Error was invalid region `7:21765242-21779468`
[2016-04-15T05:00Z] 2016-04-14 22:00:31 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:00:31,298 - WARNING - Could not retrieve variants from source file in region 7:22532049-22533642. Error was invalid region `7:22532050-22533642`
[2016-04-15T05:00Z] 2016-04-14 22:00:31 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:00:31,803 - WARNING - Could not retrieve variants from source file in region 7:29439984-29440385. Error was invalid region `7:29439985-29440385`
[2016-04-15T05:00Z] 2016-04-14 22:00:31 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:00:31,899 - WARNING - Could not retrieve variants from source file in region 7:29152160-29160794. Error was invalid region `7:29152161-29160794`
[2016-04-15T05:00Z] 2016-04-14 22:00:35 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:00:35,132 - WARNING - Could not retrieve variants from source file in region 7:20698059-20707091. Error was invalid region `7:20698060-20707091`
[2016-04-15T05:00Z] 2016-04-14 22:00:36 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:00:36,507 - WARNING - Could not retrieve variants from source file in region 7:29439984-29440385. Error was invalid region `7:29439985-29440385`
[2016-04-15T05:00Z] 2016-04-14 22:00:36 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:00:36,581 - WARNING - Could not retrieve variants from source file in region 7:22532049-22533642. Error was invalid region `7:22532050-22533642`
[2016-04-15T05:00Z] 2016-04-14 22:00:38 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:00:38,199 - WARNING - Could not retrieve variants from source file in region 7:18066358-18066759. Error was invalid region `7:18066359-18066759`
[2016-04-15T05:00Z] 2016-04-14 22:00:40 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:00:40,675 - WARNING - Could not retrieve variants from source file in region 7:20180506-20198630. Error was invalid region `7:20180507-20198630`
[2016-04-15T05:00Z] 2016-04-14 22:00:41 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:00:41,786 - WARNING - Could not retrieve variants from source file in region 7:21765241-21779468. Error was invalid region `7:21765242-21779468`
[2016-04-15T05:00Z] 2016-04-14 22:00:42 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:00:42,357 - WARNING - Could not retrieve variants from source file in region 7:19184535-19184936. Error was invalid region `7:19184536-19184936`
[2016-04-15T05:00Z] 2016-04-14 22:00:42 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:00:42,507 - WARNING - Could not retrieve variants from source file in region 7:29069998-29070399. Error was invalid region `7:29069999-29070399`
[2016-04-15T05:00Z] 2016-04-14 22:00:42 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:00:42,697 - WARNING - Could not retrieve variants from source file in region 7:29152160-29160794. Error was invalid region `7:29152161-29160794`
[2016-04-15T05:00Z] 2016-04-14 22:00:43 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:00:43,494 - WARNING - Could not retrieve variants from source file in region 7:23296322-23313935. Error was invalid region `7:23296323-23313935`
[2016-04-15T05:00Z] 2016-04-14 22:00:44 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:00:44,378 - WARNING - Could not retrieve variants from source file in region 7:20418467-20421680. Error was invalid region `7:20418468-20421680`
[2016-04-15T05:00Z] 2016-04-14 22:00:45 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:00:45,430 - WARNING - Could not retrieve variants from source file in region 7:20180506-20198630. Error was invalid region `7:20180507-20198630`
[2016-04-15T05:00Z] 2016-04-14 22:00:46 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:00:46,922 - WARNING - Could not retrieve variants from source file in region 7:19184535-19184936. Error was invalid region `7:19184536-19184936`
[2016-04-15T05:00Z] 2016-04-14 22:00:47 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:00:47,290 - WARNING - Could not retrieve variants from source file in region 7:29069998-29070399. Error was invalid region `7:29069999-29070399`
[2016-04-15T05:00Z] 2016-04-14 22:00:47 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:00:47,419 - WARNING - Could not retrieve variants from source file in region 7:20418467-20421680. Error was invalid region `7:20418468-20421680`
[2016-04-15T05:00Z] 2016-04-14 22:00:47 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:00:47,791 - WARNING - Could not retrieve variants from source file in region 7:18066358-18066759. Error was invalid region `7:18066359-18066759`
[2016-04-15T05:00Z] 2016-04-14 22:00:48 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:00:48,064 - WARNING - Could not retrieve variants from source file in region 7:23296322-23313935. Error was invalid region `7:23296323-23313935`
[2016-04-15T05:00Z] 2016-04-14 22:00:49 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:00:49,789 - WARNING - Could not retrieve variants from source file in region 7:20180506-20198630. Error was invalid region `7:20180507-20198630`
[2016-04-15T05:00Z] 2016-04-14 22:00:50 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:00:50,910 - WARNING - Could not retrieve variants from source file in region 7:22201906-22202307. Error was invalid region `7:22201907-22202307`
[2016-04-15T05:00Z] 2016-04-14 22:00:51 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:00:51,144 - WARNING - Could not retrieve variants from source file in region 7:29069998-29070399. Error was invalid region `7:29069999-29070399`
[2016-04-15T05:00Z] 2016-04-14 22:00:52 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:00:52,370 - WARNING - Could not retrieve variants from source file in region 7:21628026-21659835. Error was invalid region `7:21628027-21659835`
[2016-04-15T05:00Z] 2016-04-14 22:00:55 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:00:55,225 - WARNING - Could not retrieve variants from source file in region 7:22201906-22202307. Error was invalid region `7:22201907-22202307`
[2016-04-15T05:00Z] 2016-04-14 22:00:56 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:00:56,489 - WARNING - Could not retrieve variants from source file in region 7:23145901-23164891. Error was invalid region `7:23145902-23164891`
[2016-04-15T05:00Z] 2016-04-14 22:00:57 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:00:57,712 - WARNING - Could not retrieve variants from source file in region 7:23145901-23164891. Error was invalid region `7:23145902-23164891`
[2016-04-15T05:00Z] 2016-04-14 22:00:57 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:00:57,849 - WARNING - Could not retrieve variants from source file in region 7:23145901-23164891. Error was invalid region `7:23145902-23164891`
[2016-04-15T05:00Z] 2016-04-14 22:00:58 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:00:58,432 - WARNING - Could not retrieve variants from source file in region 7:17854321-17879743. Error was invalid region `7:17854322-17879743`
[2016-04-15T05:00Z] 2016-04-14 22:00:59 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:00:59,243 - WARNING - Could not retrieve variants from source file in region 7:17854321-17879743. Error was invalid region `7:17854322-17879743`
[2016-04-15T05:01Z] 2016-04-14 22:01:01 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:01:01,611 - WARNING - Could not retrieve variants from source file in region 7:16655176-16655577. Error was invalid region `7:16655177-16655577`
[2016-04-15T05:01Z] 2016-04-14 22:01:02 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:01:02,205 - WARNING - Could not retrieve variants from source file in region 7:16445602-16461083. Error was invalid region `7:16445603-16461083`
[2016-04-15T05:01Z] 2016-04-14 22:01:02 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:01:02,271 - WARNING - Could not retrieve variants from source file in region 7:15725586-15725990. Error was invalid region `7:15725587-15725990`
[2016-04-15T05:01Z] 2016-04-14 22:01:02 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:01:02,289 - WARNING - Could not retrieve variants from source file in region 7:15725586-15725990. Error was invalid region `7:15725587-15725990`
[2016-04-15T05:01Z] 2016-04-14 22:01:02 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:01:02,378 - WARNING - Could not retrieve variants from source file in region 7:16655176-16655577. Error was invalid region `7:16655177-16655577`
[2016-04-15T05:01Z] 2016-04-14 22:01:03 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:01:03,501 - WARNING - Could not retrieve variants from source file in region 7:15725586-15725990. Error was invalid region `7:15725587-15725990`
[2016-04-15T05:01Z] 2016-04-14 22:01:03 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:01:03,547 - WARNING - Could not retrieve variants from source file in region 7:16445602-16461083. Error was invalid region `7:16445603-16461083`
[2016-04-15T05:01Z] 2016-04-14 22:01:06 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:01:06,539 - WARNING - Could not retrieve variants from source file in region 7:16815789-16834787. Error was invalid region `7:16815790-16834787`
[2016-04-15T05:01Z] 2016-04-14 22:01:06 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:01:06,619 - WARNING - Could not retrieve variants from source file in region 7:16815789-16834787. Error was invalid region `7:16815790-16834787`
[2016-04-15T05:01Z] 2016-04-14 22:01:07 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:01:07,122 - WARNING - Could not retrieve variants from source file in region 7:16566434-16566835. Error was invalid region `7:16566435-16566835`
[2016-04-15T05:01Z] ['bcbio-variation-recall', 'square', '-Xms750m', '-Xmx7280m', '-XX:+UseSerialGC', '-c', 16, '-r', u'7:31120228-47317818', '--caller', 'platypus', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/7/Batch1-7_31120227_47317818.vcf.gz', '/mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/7/Batch1-7_31120227_47317818.vcf-inputs.txt'] in region: 7:31120228-47317818
[2016-04-15T05:01Z] 2016-04-14 22:01:22 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:01:22,302 - WARNING - Could not retrieve variants from source file in region 7:45197222-45203405. Error was invalid region `7:45197223-45203405`
[2016-04-15T05:01Z] 2016-04-14 22:01:22 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:01:22,497 - WARNING - Could not retrieve variants from source file in region 7:44873771-44874172. Error was invalid region `7:44873772-44874172`
[2016-04-15T05:01Z] 2016-04-14 22:01:22 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:01:22,913 - WARNING - Could not retrieve variants from source file in region 7:45932458-45932859. Error was invalid region `7:45932459-45932859`
[2016-04-15T05:01Z] 2016-04-14 22:01:23 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:01:23,123 - WARNING - Could not retrieve variants from source file in region 7:42951304-42977281. Error was invalid region `7:42951305-42977281`
[2016-04-15T05:01Z] 2016-04-14 22:01:24 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:01:24,127 - WARNING - Could not retrieve variants from source file in region 7:36763461-36763862. Error was invalid region `7:36763462-36763862`
[2016-04-15T05:01Z] 2016-04-14 22:01:24 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:01:24,818 - WARNING - Could not retrieve variants from source file in region 7:37988378-37988779. Error was invalid region `7:37988379-37988779`
[2016-04-15T05:01Z] 2016-04-14 22:01:29 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:01:29,036 - WARNING - Could not retrieve variants from source file in region 7:45197222-45203405. Error was invalid region `7:45197223-45203405`
[2016-04-15T05:01Z] 2016-04-14 22:01:29 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:01:29,528 - WARNING - Could not retrieve variants from source file in region 7:45932458-45932859. Error was invalid region `7:45932459-45932859`
[2016-04-15T05:01Z] 2016-04-14 22:01:32 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:01:32,294 - WARNING - Could not retrieve variants from source file in region 7:44529982-44555596. Error was invalid region `7:44529983-44555596`
[2016-04-15T05:01Z] 2016-04-14 22:01:32 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:01:32,384 - WARNING - Could not retrieve variants from source file in region 7:38468484-38469229. Error was invalid region `7:38468485-38469229`
[2016-04-15T05:01Z] 2016-04-14 22:01:32 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:01:32,832 - WARNING - Could not retrieve variants from source file in region 7:32908971-32909372. Error was invalid region `7:32908972-32909372`
[2016-04-15T05:01Z] 2016-04-14 22:01:32 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:01:32,954 - WARNING - Could not retrieve variants from source file in region 7:36763461-36763862. Error was invalid region `7:36763462-36763862`
[2016-04-15T05:01Z] 2016-04-14 22:01:33 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:01:33,077 - WARNING - Could not retrieve variants from source file in region 7:34125209-34125610. Error was invalid region `7:34125210-34125610`
[2016-04-15T05:01Z] 2016-04-14 22:01:33 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:01:33,666 - WARNING - Could not retrieve variants from source file in region 7:37988378-37988779. Error was invalid region `7:37988379-37988779`
[2016-04-15T05:01Z] 2016-04-14 22:01:33 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:01:33,738 - WARNING - Could not retrieve variants from source file in region 7:44250988-44283067. Error was invalid region `7:44250989-44283067`
[2016-04-15T05:01Z] 2016-04-14 22:01:33 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:01:33,926 - WARNING - Could not retrieve variants from source file in region 7:44039413-44047256. Error was invalid region `7:44039414-44047256`
[2016-04-15T05:01Z] 2016-04-14 22:01:34 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:01:34,306 - WARNING - Could not retrieve variants from source file in region 7:44873771-44874172. Error was invalid region `7:44873772-44874172`
[2016-04-15T05:01Z] 2016-04-14 22:01:34 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:01:34,826 - WARNING - Could not retrieve variants from source file in region 7:45932458-45932859. Error was invalid region `7:45932459-45932859`
[2016-04-15T05:01Z] 2016-04-14 22:01:34 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:01:34,826 - WARNING - Could not retrieve variants from source file in region 7:45197222-45203405. Error was invalid region `7:45197223-45203405`
[2016-04-15T05:01Z] 2016-04-14 22:01:39 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:01:39,272 - WARNING - Could not retrieve variants from source file in region 7:36763461-36763862. Error was invalid region `7:36763462-36763862`
[2016-04-15T05:01Z] 2016-04-14 22:01:40 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:01:40,537 - WARNING - Could not retrieve variants from source file in region 7:44250988-44283067. Error was invalid region `7:44250989-44283067`
[2016-04-15T05:01Z] 2016-04-14 22:01:40 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:01:40,872 - WARNING - Could not retrieve variants from source file in region 7:37988378-37988779. Error was invalid region `7:37988379-37988779`
[2016-04-15T05:01Z] 2016-04-14 22:01:51 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:01:51,816 - WARNING - Could not retrieve variants from source file in region 7:45703760-45704161. Error was invalid region `7:45703761-45704161`
[2016-04-15T05:01Z] 2016-04-14 22:01:54 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:01:54,159 - WARNING - Could not retrieve variants from source file in region 7:34817902-34818303. Error was invalid region `7:34817903-34818303`
[2016-04-15T05:01Z] 2016-04-14 22:01:55 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:01:55,420 - WARNING - Could not retrieve variants from source file in region 7:36655824-36658130. Error was invalid region `7:36655825-36658130`
[2016-04-15T05:01Z] 2016-04-14 22:01:56 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:01:56,651 - WARNING - Could not retrieve variants from source file in region 7:45703760-45704161. Error was invalid region `7:45703761-45704161`
[2016-04-15T05:01Z] 2016-04-14 22:01:57 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:01:57,720 - WARNING - Could not retrieve variants from source file in region 7:44799965-44800366. Error was invalid region `7:44799966-44800366`
[2016-04-15T05:01Z] 2016-04-14 22:01:59 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:01:59,296 - WARNING - Could not retrieve variants from source file in region 7:34817902-34818303. Error was invalid region `7:34817903-34818303`
[2016-04-15T05:01Z] 2016-04-14 22:01:59 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:01:59,963 - WARNING - Could not retrieve variants from source file in region 7:43906302-43917464. Error was invalid region `7:43906303-43917464`
[2016-04-15T05:02Z] 2016-04-14 22:02:00 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:02:00,013 - WARNING - Could not retrieve variants from source file in region 7:32529725-32530126. Error was invalid region `7:32529726-32530126`
[2016-04-15T05:02Z] 2016-04-14 22:02:00 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:02:00,768 - WARNING - Could not retrieve variants from source file in region 7:38356638-38357039. Error was invalid region `7:38356639-38357039`
[2016-04-15T05:02Z] 2016-04-14 22:02:00 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:02:00,908 - WARNING - Could not retrieve variants from source file in region 7:42079554-42088422. Error was invalid region `7:42079555-42088422`
[2016-04-15T05:02Z] 2016-04-14 22:02:01 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:02:01,111 - WARNING - Could not retrieve variants from source file in region 7:44443911-44444312. Error was invalid region `7:44443912-44444312`
[2016-04-15T05:02Z] 2016-04-14 22:02:01 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:02:01,275 - WARNING - Could not retrieve variants from source file in region 7:45703760-45704161. Error was invalid region `7:45703761-45704161`
[2016-04-15T05:02Z] 2016-04-14 22:02:04 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:02:04,218 - WARNING - Could not retrieve variants from source file in region 7:45003852-45009913. Error was invalid region `7:45003853-45009913`
[2016-04-15T05:02Z] 2016-04-14 22:02:04 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:02:04,232 - WARNING - Could not retrieve variants from source file in region 7:33388502-33388903. Error was invalid region `7:33388503-33388903`
[2016-04-15T05:02Z] 2016-04-14 22:02:04 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:02:04,625 - WARNING - Could not retrieve variants from source file in region 7:33388502-33388903. Error was invalid region `7:33388503-33388903`
[2016-04-15T05:02Z] 2016-04-14 22:02:04 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:02:04,774 - WARNING - Could not retrieve variants from source file in region 7:34817902-34818303. Error was invalid region `7:34817903-34818303`
[2016-04-15T05:02Z] 2016-04-14 22:02:06 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:02:06,387 - WARNING - Could not retrieve variants from source file in region 7:32529725-32530126. Error was invalid region `7:32529726-32530126`
[2016-04-15T05:02Z] 2016-04-14 22:02:06 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:02:06,896 - WARNING - Could not retrieve variants from source file in region 7:42079554-42088422. Error was invalid region `7:42079555-42088422`
[2016-04-15T05:02Z] 2016-04-14 22:02:07 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:02:07,028 - WARNING - Could not retrieve variants from source file in region 7:38356638-38357039. Error was invalid region `7:38356639-38357039`
[2016-04-15T05:02Z] 2016-04-14 22:02:09 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:02:09,418 - WARNING - Could not retrieve variants from source file in region 7:45003852-45009913. Error was invalid region `7:45003853-45009913`
[2016-04-15T05:02Z] 2016-04-14 22:02:12 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:02:12,380 - WARNING - Could not retrieve variants from source file in region 7:32529725-32530126. Error was invalid region `7:32529726-32530126`
[2016-04-15T05:02Z] 2016-04-14 22:02:12 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:02:12,993 - WARNING - Could not retrieve variants from source file in region 7:43906302-43917464. Error was invalid region `7:43906303-43917464`
[2016-04-15T05:02Z] 2016-04-14 22:02:15 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:02:15,186 - WARNING - Could not retrieve variants from source file in region 7:34192551-34192952. Error was invalid region `7:34192552-34192952`
[2016-04-15T05:02Z] 2016-04-14 22:02:17 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:02:17,976 - WARNING - Could not retrieve variants from source file in region 7:38299516-38305332. Error was invalid region `7:38299517-38305332`
[2016-04-15T05:02Z] 2016-04-14 22:02:18 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:02:18,591 - WARNING - Could not retrieve variants from source file in region 7:44605887-44621026. Error was invalid region `7:44605888-44621026`
[2016-04-15T05:02Z] 2016-04-14 22:02:19 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:02:19,932 - WARNING - Could not retrieve variants from source file in region 7:34192551-34192952. Error was invalid region `7:34192552-34192952`
[2016-04-15T05:02Z] 2016-04-14 22:02:20 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:02:20,803 - WARNING - Could not retrieve variants from source file in region 7:36552445-36552980. Error was invalid region `7:36552446-36552980`
[2016-04-15T05:02Z] 2016-04-14 22:02:21 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:02:21,758 - WARNING - Could not retrieve variants from source file in region 7:37890056-37907494. Error was invalid region `7:37890057-37907494`
[2016-04-15T05:02Z] 2016-04-14 22:02:22 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:02:22,673 - WARNING - Could not retrieve variants from source file in region 7:42005467-42007570. Error was invalid region `7:42005468-42007570`
[2016-04-15T05:02Z] 2016-04-14 22:02:23 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:02:23,264 - WARNING - Could not retrieve variants from source file in region 7:44605887-44621026. Error was invalid region `7:44605888-44621026`
[2016-04-15T05:02Z] 2016-04-14 22:02:24 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:02:24,140 - WARNING - Could not retrieve variants from source file in region 7:32109904-32111107. Error was invalid region `7:32109905-32111107`
[2016-04-15T05:02Z] 2016-04-14 22:02:24 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:02:24,915 - WARNING - Could not retrieve variants from source file in region 7:34192551-34192952. Error was invalid region `7:34192552-34192952`
[2016-04-15T05:02Z] 2016-04-14 22:02:25 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:02:25,313 - WARNING - Could not retrieve variants from source file in region 7:36552445-36552980. Error was invalid region `7:36552446-36552980`
[2016-04-15T05:02Z] 2016-04-14 22:02:26 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:02:26,032 - WARNING - Could not retrieve variants from source file in region 7:32338126-32338936. Error was invalid region `7:32338127-32338936`
[2016-04-15T05:02Z] 2016-04-14 22:02:26 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:02:26,457 - WARNING - Could not retrieve variants from source file in region 7:31682242-31698103. Error was invalid region `7:31682243-31698103`
[2016-04-15T05:02Z] 2016-04-14 22:02:27 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:02:27,593 - WARNING - Could not retrieve variants from source file in region 7:44605887-44621026. Error was invalid region `7:44605888-44621026`
[2016-04-15T05:02Z] 2016-04-14 22:02:28 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:02:28,491 - WARNING - Could not retrieve variants from source file in region 7:32109904-32111107. Error was invalid region `7:32109905-32111107`
[2016-04-15T05:02Z] 2016-04-14 22:02:29 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:02:29,503 - WARNING - Could not retrieve variants from source file in region 7:37298589-37298990. Error was invalid region `7:37298590-37298990`
[2016-04-15T05:02Z] 2016-04-14 22:02:29 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:02:29,914 - WARNING - Could not retrieve variants from source file in region 7:36552445-36552980. Error was invalid region `7:36552446-36552980`
[2016-04-15T05:02Z] 2016-04-14 22:02:30 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:02:30,501 - WARNING - Could not retrieve variants from source file in region 7:32338126-32338936. Error was invalid region `7:32338127-32338936`
[2016-04-15T05:02Z] 2016-04-14 22:02:32 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:02:32,244 - WARNING - Could not retrieve variants from source file in region 7:42005467-42007570. Error was invalid region `7:42005468-42007570`
[2016-04-15T05:02Z] 2016-04-14 22:02:32 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:02:32,653 - WARNING - Could not retrieve variants from source file in region 7:40313954-40314433. Error was invalid region `7:40313955-40314433`
[2016-04-15T05:02Z] 2016-04-14 22:02:33 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:02:33,748 - WARNING - Could not retrieve variants from source file in region 7:32338126-32338936. Error was invalid region `7:32338127-32338936`
[2016-04-15T05:02Z] 2016-04-14 22:02:38 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:02:38,353 - WARNING - Could not retrieve variants from source file in region 7:32209214-32209649. Error was invalid region `7:32209215-32209649`
[2016-04-15T05:02Z] 2016-04-14 22:02:40 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:02:40,418 - WARNING - Could not retrieve variants from source file in region 7:43647668-43664470. Error was invalid region `7:43647669-43664470`
[2016-04-15T05:02Z] 2016-04-14 22:02:43 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:02:43,001 - WARNING - Could not retrieve variants from source file in region 7:32209214-32209649. Error was invalid region `7:32209215-32209649`
[2016-04-15T05:02Z] 2016-04-14 22:02:43 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:02:43,310 - WARNING - Could not retrieve variants from source file in region 7:36320610-36338939. Error was invalid region `7:36320611-36338939`
[2016-04-15T05:02Z] 2016-04-14 22:02:45 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:02:45,236 - WARNING - Could not retrieve variants from source file in region 7:40899756-40900157. Error was invalid region `7:40899757-40900157`
[2016-04-15T05:02Z] 2016-04-14 22:02:48 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:02:48,185 - WARNING - Could not retrieve variants from source file in region 7:36320610-36338939. Error was invalid region `7:36320611-36338939`
[2016-04-15T05:02Z] 2016-04-14 22:02:48 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:02:48,663 - WARNING - Could not retrieve variants from source file in region 7:43647668-43664470. Error was invalid region `7:43647669-43664470`
[2016-04-15T05:02Z] 2016-04-14 22:02:49 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:02:49,687 - WARNING - Could not retrieve variants from source file in region 7:40899756-40900157. Error was invalid region `7:40899757-40900157`
[2016-04-15T05:02Z] 2016-04-14 22:02:51 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:02:51,640 - WARNING - Could not retrieve variants from source file in region 7:43591621-43592022. Error was invalid region `7:43591622-43592022`
[2016-04-15T05:02Z] 2016-04-14 22:02:51 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:02:51,711 - WARNING - Could not retrieve variants from source file in region 7:40899756-40900157. Error was invalid region `7:40899757-40900157`
[2016-04-15T05:02Z] 2016-04-14 22:02:52 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:02:52,461 - WARNING - Could not retrieve variants from source file in region 7:35292982-35293383. Error was invalid region `7:35292983-35293383`
[2016-04-15T05:02Z] 2016-04-14 22:02:52 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:02:52,551 - WARNING - Could not retrieve variants from source file in region 7:40027273-40027674. Error was invalid region `7:40027274-40027674`
[2016-04-15T05:02Z] 2016-04-14 22:02:54 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:02:54,570 - WARNING - Could not retrieve variants from source file in region 7:43540676-43541077. Error was invalid region `7:43540677-43541077`
[2016-04-15T05:02Z] 2016-04-14 22:02:55 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:02:55,277 - WARNING - Could not retrieve variants from source file in region 7:40127556-40127957. Error was invalid region `7:40127557-40127957`
[2016-04-15T05:02Z] 2016-04-14 22:02:55 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:02:55,562 - WARNING - Could not retrieve variants from source file in region 7:43591621-43592022. Error was invalid region `7:43591622-43592022`
[2016-04-15T05:02Z] 2016-04-14 22:02:56 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:02:56,624 - WARNING - Could not retrieve variants from source file in region 7:40027273-40027674. Error was invalid region `7:40027274-40027674`
[2016-04-15T05:02Z] 2016-04-14 22:02:57 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:02:57,840 - WARNING - Could not retrieve variants from source file in region 7:40127556-40127957. Error was invalid region `7:40127557-40127957`
[2016-04-15T05:02Z] 2016-04-14 22:02:59 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:02:59,090 - WARNING - Could not retrieve variants from source file in region 7:35709631-35710032. Error was invalid region `7:35709632-35710032`
[2016-04-15T05:02Z] 2016-04-14 22:02:59 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:02:59,175 - WARNING - Could not retrieve variants from source file in region 7:35709631-35710032. Error was invalid region `7:35709632-35710032`
[2016-04-15T05:03Z] 2016-04-14 22:03:01 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:03:01,428 - WARNING - Could not retrieve variants from source file in region 7:35709631-35710032. Error was invalid region `7:35709632-35710032`
[2016-04-15T05:03Z] 2016-04-14 22:03:03 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:03:03,197 - WARNING - Could not retrieve variants from source file in region 7:39990470-39990871. Error was invalid region `7:39990471-39990871`
[2016-04-15T05:03Z] 2016-04-14 22:03:04 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:03:04,454 - WARNING - Could not retrieve variants from source file in region 7:39990470-39990871. Error was invalid region `7:39990471-39990871`
[2016-04-15T05:03Z] 2016-04-14 22:03:06 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:03:06,177 - WARNING - Could not retrieve variants from source file in region 7:34917529-34917930. Error was invalid region `7:34917530-34917930`
[2016-04-15T05:03Z] 2016-04-14 22:03:06 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:03:06,180 - WARNING - Could not retrieve variants from source file in region 7:34917529-34917930. Error was invalid region `7:34917530-34917930`
[2016-04-15T05:03Z] ['bcbio-variation-recall', 'square', '-Xms750m', '-Xmx7280m', '-XX:+UseSerialGC', '-c', 16, '-r', u'7:47319762-63093154', '--caller', 'platypus', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/7/Batch1-7_47319761_63093154.vcf.gz', '/mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/7/Batch1-7_47319761_63093154.vcf-inputs.txt'] in region: 7:47319762-63093154
[2016-04-15T05:03Z] 2016-04-14 22:03:23 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:03:23,250 - WARNING - Could not retrieve variants from source file in region 7:56007365-56007766. Error was invalid region `7:56007366-56007766`
[2016-04-15T05:03Z] 2016-04-14 22:03:23 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:03:23,340 - WARNING - Could not retrieve variants from source file in region 7:55433669-55434074. Error was invalid region `7:55433670-55434074`
[2016-04-15T05:03Z] 2016-04-14 22:03:23 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:03:23,398 - WARNING - Could not retrieve variants from source file in region 7:50560172-50560583. Error was invalid region `7:50560173-50560583`
[2016-04-15T05:03Z] 2016-04-14 22:03:23 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:03:23,682 - WARNING - Could not retrieve variants from source file in region 7:47568507-47568908. Error was invalid region `7:47568508-47568908`
[2016-04-15T05:03Z] 2016-04-14 22:03:24 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:03:24,089 - WARNING - Could not retrieve variants from source file in region 7:47913368-47930467. Error was invalid region `7:47913369-47930467`
[2016-04-15T05:03Z] 2016-04-14 22:03:24 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:03:24,336 - WARNING - Could not retrieve variants from source file in region 7:48004751-48005152. Error was invalid region `7:48004752-48005152`
[2016-04-15T05:03Z] 2016-04-14 22:03:24 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:03:24,457 - WARNING - Could not retrieve variants from source file in region 7:50672818-50673219. Error was invalid region `7:50672819-50673219`
[2016-04-15T05:03Z] 2016-04-14 22:03:24 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:03:24,458 - WARNING - Could not retrieve variants from source file in region 7:51287259-51287660. Error was invalid region `7:51287260-51287660`
[2016-04-15T05:03Z] 2016-04-14 22:03:27 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:03:27,198 - WARNING - Could not retrieve variants from source file in region 7:56126149-56149600. Error was invalid region `7:56126150-56149600`
[2016-04-15T05:03Z] 2016-04-14 22:03:27 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:03:27,282 - WARNING - Could not retrieve variants from source file in region 7:57528786-57529582. Error was invalid region `7:57528787-57529582`
[2016-04-15T05:03Z] 2016-04-14 22:03:28 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:03:28,848 - WARNING - Could not retrieve variants from source file in region 7:55459352-55459753. Error was invalid region `7:55459353-55459753`
[2016-04-15T05:03Z] 2016-04-14 22:03:31 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:03:31,620 - WARNING - Could not retrieve variants from source file in region 7:55214137-55269139. Error was invalid region `7:55214138-55269139`
[2016-04-15T05:03Z] 2016-04-14 22:03:32 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:03:32,067 - WARNING - Could not retrieve variants from source file in region 7:57008423-57008929. Error was invalid region `7:57008424-57008929`
[2016-04-15T05:03Z] 2016-04-14 22:03:32 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:03:32,992 - WARNING - Could not retrieve variants from source file in region 7:55620187-55620588. Error was invalid region `7:55620188-55620588`
[2016-04-15T05:03Z] 2016-04-14 22:03:33 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:03:33,015 - WARNING - Could not retrieve variants from source file in region 7:51287259-51287660. Error was invalid region `7:51287260-51287660`
[2016-04-15T05:03Z] 2016-04-14 22:03:33 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:03:33,131 - WARNING - Could not retrieve variants from source file in region 7:48004751-48005152. Error was invalid region `7:48004752-48005152`
[2016-04-15T05:03Z] 2016-04-14 22:03:33 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:03:33,263 - WARNING - Could not retrieve variants from source file in region 7:57528786-57529582. Error was invalid region `7:57528787-57529582`
[2016-04-15T05:03Z] 2016-04-14 22:03:33 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:03:33,280 - WARNING - Could not retrieve variants from source file in region 7:50672818-50673219. Error was invalid region `7:50672819-50673219`
[2016-04-15T05:03Z] 2016-04-14 22:03:34 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:03:34,699 - WARNING - Could not retrieve variants from source file in region 7:56007365-56007766. Error was invalid region `7:56007366-56007766`
[2016-04-15T05:03Z] 2016-04-14 22:03:36 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:03:36,376 - WARNING - Could not retrieve variants from source file in region 7:47568507-47568908. Error was invalid region `7:47568508-47568908`
[2016-04-15T05:03Z] 2016-04-14 22:03:37 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:03:37,416 - WARNING - Could not retrieve variants from source file in region 7:55214137-55269139. Error was invalid region `7:55214138-55269139`
[2016-04-15T05:03Z] 2016-04-14 22:03:39 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:03:39,360 - WARNING - Could not retrieve variants from source file in region 7:55620187-55620588. Error was invalid region `7:55620188-55620588`
[2016-04-15T05:03Z] 2016-04-14 22:03:40 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:03:40,179 - WARNING - Could not retrieve variants from source file in region 7:48004751-48005152. Error was invalid region `7:48004752-48005152`
[2016-04-15T05:03Z] 2016-04-14 22:03:40 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:03:40,359 - WARNING - Could not retrieve variants from source file in region 7:50672818-50673219. Error was invalid region `7:50672819-50673219`
[2016-04-15T05:03Z] 2016-04-14 22:03:40 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:03:40,738 - WARNING - Could not retrieve variants from source file in region 7:51287259-51287660. Error was invalid region `7:51287260-51287660`
[2016-04-15T05:03Z] 2016-04-14 22:03:50 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:03:50,385 - WARNING - Could not retrieve variants from source file in region 7:47407818-47409164. Error was invalid region `7:47407819-47409164`
[2016-04-15T05:03Z] 2016-04-14 22:03:50 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:03:50,828 - WARNING - Could not retrieve variants from source file in region 7:50741969-50742370. Error was invalid region `7:50741970-50742370`
[2016-04-15T05:03Z] 2016-04-14 22:03:52 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:03:52,914 - WARNING - Could not retrieve variants from source file in region 7:56878113-56879630. Error was invalid region `7:56878114-56879630`
[2016-04-15T05:03Z] 2016-04-14 22:03:53 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:03:53,318 - WARNING - Could not retrieve variants from source file in region 7:50611524-50611925. Error was invalid region `7:50611525-50611925`
[2016-04-15T05:03Z] 2016-04-14 22:03:54 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:03:54,444 - WARNING - Could not retrieve variants from source file in region 7:48545765-48546166. Error was invalid region `7:48545766-48546166`
[2016-04-15T05:03Z] 2016-04-14 22:03:54 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:03:54,449 - WARNING - Could not retrieve variants from source file in region 7:47968716-47971816. Error was invalid region `7:47968717-47971816`
[2016-04-15T05:03Z] 2016-04-14 22:03:54 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:03:54,751 - WARNING - Could not retrieve variants from source file in region 7:50741969-50742370. Error was invalid region `7:50741970-50742370`
[2016-04-15T05:03Z] 2016-04-14 22:03:55 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:03:55,307 - WARNING - Could not retrieve variants from source file in region 7:47323245-47343273. Error was invalid region `7:47323246-47343273`
[2016-04-15T05:03Z] 2016-04-14 22:03:57 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:03:57,156 - WARNING - Could not retrieve variants from source file in region 7:50611524-50611925. Error was invalid region `7:50611525-50611925`
[2016-04-15T05:03Z] 2016-04-14 22:03:58 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:03:58,229 - WARNING - Could not retrieve variants from source file in region 7:48545765-48546166. Error was invalid region `7:48545766-48546166`
[2016-04-15T05:03Z] 2016-04-14 22:03:58 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:03:58,457 - WARNING - Could not retrieve variants from source file in region 7:50741969-50742370. Error was invalid region `7:50741970-50742370`
[2016-04-15T05:03Z] 2016-04-14 22:03:58 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:03:58,457 - WARNING - Could not retrieve variants from source file in region 7:47968716-47971816. Error was invalid region `7:47968717-47971816`
[2016-04-15T05:03Z] 2016-04-14 22:03:59 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:03:59,003 - WARNING - Could not retrieve variants from source file in region 7:50173566-50181162. Error was invalid region `7:50173567-50181162`
[2016-04-15T05:03Z] 2016-04-14 22:03:59 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:03:59,310 - WARNING - Could not retrieve variants from source file in region 7:47323245-47343273. Error was invalid region `7:47323246-47343273`
[2016-04-15T05:04Z] 2016-04-14 22:04:01 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:04:01,037 - WARNING - Could not retrieve variants from source file in region 7:50611524-50611925. Error was invalid region `7:50611525-50611925`
[2016-04-15T05:04Z] 2016-04-14 22:04:01 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:04:01,998 - WARNING - Could not retrieve variants from source file in region 7:48545765-48546166. Error was invalid region `7:48545766-48546166`
[2016-04-15T05:04Z] 2016-04-14 22:04:07 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:04:07,044 - WARNING - Could not retrieve variants from source file in region 7:48080884-48092676. Error was invalid region `7:48080885-48092676`
[2016-04-15T05:04Z] 2016-04-14 22:04:09 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:04:09,763 - WARNING - Could not retrieve variants from source file in region 7:48428504-48450347. Error was invalid region `7:48428505-48450347`
[2016-04-15T05:04Z] 2016-04-14 22:04:09 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:04:09,764 - WARNING - Could not retrieve variants from source file in region 7:48428504-48450347. Error was invalid region `7:48428505-48450347`
[2016-04-15T05:04Z] 2016-04-14 22:04:10 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:04:10,199 - WARNING - Could not retrieve variants from source file in region 7:48666263-48666664. Error was invalid region `7:48666264-48666664`
[2016-04-15T05:04Z] 2016-04-14 22:04:10 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:04:10,206 - WARNING - Could not retrieve variants from source file in region 7:49815179-49815683. Error was invalid region `7:49815180-49815683`
[2016-04-15T05:04Z] 2016-04-14 22:04:10 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:04:10,259 - WARNING - Could not retrieve variants from source file in region 7:48666263-48666664. Error was invalid region `7:48666264-48666664`
[2016-04-15T05:04Z] ['bcbio-variation-recall', 'square', '-Xms750m', '-Xmx7280m', '-XX:+UseSerialGC', '-c', 16, '-r', u'7:63095910-78636522', '--caller', 'platypus', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/7/Batch1-7_63095909_78636522.vcf.gz', '/mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/7/Batch1-7_63095909_78636522.vcf-inputs.txt'] in region: 7:63095910-78636522
[2016-04-15T05:04Z] 2016-04-14 22:04:27 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:04:27,595 - WARNING - Could not retrieve variants from source file in region 7:63726782-63727183. Error was invalid region `7:63726783-63727183`
[2016-04-15T05:04Z] 2016-04-14 22:04:28 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:04:28,214 - WARNING - Could not retrieve variants from source file in region 7:76916608-76922680. Error was invalid region `7:76916609-76922680`
[2016-04-15T05:04Z] 2016-04-14 22:04:28 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:04:28,470 - WARNING - Could not retrieve variants from source file in region 7:77423363-77423764. Error was invalid region `7:77423364-77423764`
[2016-04-15T05:04Z] 2016-04-14 22:04:28 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:04:28,555 - WARNING - Could not retrieve variants from source file in region 7:72193653-72209718. Error was invalid region `7:72193654-72209718`
[2016-04-15T05:04Z] 2016-04-14 22:04:28 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:04:28,809 - WARNING - Could not retrieve variants from source file in region 7:70227809-70228329. Error was invalid region `7:70227810-70228329`
[2016-04-15T05:04Z] 2016-04-14 22:04:29 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:04:29,486 - WARNING - Could not retrieve variants from source file in region 7:73020090-73020491. Error was invalid region `7:73020091-73020491`
[2016-04-15T05:04Z] 2016-04-14 22:04:29 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:04:29,580 - WARNING - Could not retrieve variants from source file in region 7:66104952-66108345. Error was invalid region `7:66104953-66108345`
[2016-04-15T05:04Z] 2016-04-14 22:04:29 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:04:29,860 - WARNING - Could not retrieve variants from source file in region 7:74193457-74193858. Error was invalid region `7:74193458-74193858`
[2016-04-15T05:04Z] 2016-04-14 22:04:29 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:04:29,867 - WARNING - Could not retrieve variants from source file in region 7:72984937-72985338. Error was invalid region `7:72984938-72985338`
[2016-04-15T05:04Z] 2016-04-14 22:04:30 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:04:30,010 - WARNING - Could not retrieve variants from source file in region 7:63529745-63538039. Error was invalid region `7:63529746-63538039`
[2016-04-15T05:04Z] 2016-04-14 22:04:32 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:04:32,304 - WARNING - Could not retrieve variants from source file in region 7:64146804-64169209. Error was invalid region `7:64146805-64169209`
[2016-04-15T05:04Z] 2016-04-14 22:04:34 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:04:34,074 - WARNING - Could not retrieve variants from source file in region 7:63726782-63727183. Error was invalid region `7:63726783-63727183`
[2016-04-15T05:04Z] 2016-04-14 22:04:34 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:04:34,182 - WARNING - Could not retrieve variants from source file in region 7:73151433-73151834. Error was invalid region `7:73151434-73151834`
[2016-04-15T05:04Z] 2016-04-14 22:04:34 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:04:34,905 - WARNING - Could not retrieve variants from source file in region 7:76916608-76922680. Error was invalid region `7:76916609-76922680`
[2016-04-15T05:04Z] 2016-04-14 22:04:37 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:04:37,107 - WARNING - Could not retrieve variants from source file in region 7:78118898-78119299. Error was invalid region `7:78118899-78119299`
[2016-04-15T05:04Z] 2016-04-14 22:04:37 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:04:37,158 - WARNING - Could not retrieve variants from source file in region 7:72738350-72738953. Error was invalid region `7:72738351-72738953`
[2016-04-15T05:04Z] 2016-04-14 22:04:37 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:04:37,396 - WARNING - Could not retrieve variants from source file in region 7:73020090-73020491. Error was invalid region `7:73020091-73020491`
[2016-04-15T05:04Z] 2016-04-14 22:04:37 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:04:37,871 - WARNING - Could not retrieve variants from source file in region 7:63529745-63538039. Error was invalid region `7:63529746-63538039`
[2016-04-15T05:04Z] 2016-04-14 22:04:38 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:04:38,026 - WARNING - Could not retrieve variants from source file in region 7:74193457-74193858. Error was invalid region `7:74193458-74193858`
[2016-04-15T05:04Z] 2016-04-14 22:04:38 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:04:38,029 - WARNING - Could not retrieve variants from source file in region 7:73097027-73123113. Error was invalid region `7:73097028-73123113`
[2016-04-15T05:04Z] 2016-04-14 22:04:39 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:04:39,055 - WARNING - Could not retrieve variants from source file in region 7:73151433-73151834. Error was invalid region `7:73151434-73151834`
[2016-04-15T05:04Z] 2016-04-14 22:04:40 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:04:40,254 - WARNING - Could not retrieve variants from source file in region 7:76916608-76922680. Error was invalid region `7:76916609-76922680`
[2016-04-15T05:04Z] 2016-04-14 22:04:44 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:04:44,477 - WARNING - Could not retrieve variants from source file in region 7:72738350-72738953. Error was invalid region `7:72738351-72738953`
[2016-04-15T05:04Z] 2016-04-14 22:04:45 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:04:45,313 - WARNING - Could not retrieve variants from source file in region 7:78118898-78119299. Error was invalid region `7:78118899-78119299`
[2016-04-15T05:04Z] 2016-04-14 22:04:45 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:04:45,491 - WARNING - Could not retrieve variants from source file in region 7:73020090-73020491. Error was invalid region `7:73020091-73020491`
[2016-04-15T05:04Z] 2016-04-14 22:04:45 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:04:45,641 - WARNING - Could not retrieve variants from source file in region 7:63529745-63538039. Error was invalid region `7:63529746-63538039`
[2016-04-15T05:04Z] 2016-04-14 22:04:46 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:04:46,145 - WARNING - Could not retrieve variants from source file in region 7:74193457-74193858. Error was invalid region `7:74193458-74193858`
[2016-04-15T05:04Z] 2016-04-14 22:04:57 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:04:57,696 - WARNING - Could not retrieve variants from source file in region 7:76870902-76885959. Error was invalid region `7:76870903-76885959`
[2016-04-15T05:04Z] 2016-04-14 22:04:57 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:04:57,854 - WARNING - Could not retrieve variants from source file in region 7:77247610-77265330. Error was invalid region `7:77247611-77265330`
[2016-04-15T05:04Z] 2016-04-14 22:04:58 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:04:58,454 - WARNING - Could not retrieve variants from source file in region 7:66703117-66703518. Error was invalid region `7:66703118-66703518`
[2016-04-15T05:04Z] 2016-04-14 22:04:59 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:04:59,613 - WARNING - Could not retrieve variants from source file in region 7:65579627-65580028. Error was invalid region `7:65579628-65580028`
[2016-04-15T05:04Z] 2016-04-14 22:04:59 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:04:59,783 - WARNING - Could not retrieve variants from source file in region 7:72891543-72891944. Error was invalid region `7:72891544-72891944`
[2016-04-15T05:04Z] 2016-04-14 22:04:59 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:04:59,951 - WARNING - Could not retrieve variants from source file in region 7:72891543-72891944. Error was invalid region `7:72891544-72891944`
[2016-04-15T05:05Z] 2016-04-14 22:05:03 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:05:03,186 - WARNING - Could not retrieve variants from source file in region 7:77756369-77756914. Error was invalid region `7:77756370-77756914`
[2016-04-15T05:05Z] 2016-04-14 22:05:03 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:05:03,730 - WARNING - Could not retrieve variants from source file in region 7:75512851-75513252. Error was invalid region `7:75512852-75513252`
[2016-04-15T05:05Z] 2016-04-14 22:05:04 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:05:04,299 - WARNING - Could not retrieve variants from source file in region 7:74016412-74016813. Error was invalid region `7:74016413-74016813`
[2016-04-15T05:05Z] 2016-04-14 22:05:05 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:05:05,260 - WARNING - Could not retrieve variants from source file in region 7:77551916-77552317. Error was invalid region `7:77551917-77552317`
[2016-04-15T05:05Z] 2016-04-14 22:05:05 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:05:05,404 - WARNING - Could not retrieve variants from source file in region 7:72891543-72891944. Error was invalid region `7:72891544-72891944`
[2016-04-15T05:05Z] 2016-04-14 22:05:05 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:05:05,515 - WARNING - Could not retrieve variants from source file in region 7:72093746-72094147. Error was invalid region `7:72093747-72094147`
[2016-04-15T05:05Z] 2016-04-14 22:05:07 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:05:07,533 - WARNING - Could not retrieve variants from source file in region 7:63673270-63680289. Error was invalid region `7:63673271-63680289`
[2016-04-15T05:05Z] 2016-04-14 22:05:08 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:05:08,271 - WARNING - Could not retrieve variants from source file in region 7:63226068-63227465. Error was invalid region `7:63226069-63227465`
[2016-04-15T05:05Z] 2016-04-14 22:05:08 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:05:08,865 - WARNING - Could not retrieve variants from source file in region 7:75172059-75176490. Error was invalid region `7:75172060-75176490`
[2016-04-15T05:05Z] 2016-04-14 22:05:09 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:05:09,802 - WARNING - Could not retrieve variants from source file in region 7:77756369-77756914. Error was invalid region `7:77756370-77756914`
[2016-04-15T05:05Z] 2016-04-14 22:05:10 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:05:10,448 - WARNING - Could not retrieve variants from source file in region 7:75512851-75513252. Error was invalid region `7:75512852-75513252`
[2016-04-15T05:05Z] 2016-04-14 22:05:10 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:05:10,598 - WARNING - Could not retrieve variants from source file in region 7:65579627-65580028. Error was invalid region `7:65579628-65580028`
[2016-04-15T05:05Z] 2016-04-14 22:05:10 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:05:10,736 - WARNING - Could not retrieve variants from source file in region 7:74016412-74016813. Error was invalid region `7:74016413-74016813`
[2016-04-15T05:05Z] 2016-04-14 22:05:10 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:05:10,887 - WARNING - Could not retrieve variants from source file in region 7:77551916-77552317. Error was invalid region `7:77551917-77552317`
[2016-04-15T05:05Z] 2016-04-14 22:05:13 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:05:13,854 - WARNING - Could not retrieve variants from source file in region 7:75172059-75176490. Error was invalid region `7:75172060-75176490`
[2016-04-15T05:05Z] 2016-04-14 22:05:15 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:05:15,901 - WARNING - Could not retrieve variants from source file in region 7:75512851-75513252. Error was invalid region `7:75512852-75513252`
[2016-04-15T05:05Z] 2016-04-14 22:05:15 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:05:15,938 - WARNING - Could not retrieve variants from source file in region 7:77756369-77756914. Error was invalid region `7:77756370-77756914`
[2016-04-15T05:05Z] 2016-04-14 22:05:17 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:05:17,039 - WARNING - Could not retrieve variants from source file in region 7:77551916-77552317. Error was invalid region `7:77551917-77552317`
[2016-04-15T05:05Z] 2016-04-14 22:05:17 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:05:17,130 - WARNING - Could not retrieve variants from source file in region 7:74016412-74016813. Error was invalid region `7:74016413-74016813`
[2016-04-15T05:05Z] 2016-04-14 22:05:23 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:05:23,127 - WARNING - Could not retrieve variants from source file in region 7:63808656-63809057. Error was invalid region `7:63808657-63809057`
[2016-04-15T05:05Z] 2016-04-14 22:05:24 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:05:24,863 - WARNING - Could not retrieve variants from source file in region 7:76240574-76241078. Error was invalid region `7:76240575-76241078`
[2016-04-15T05:05Z] 2016-04-14 22:05:25 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:05:25,703 - WARNING - Could not retrieve variants from source file in region 7:77035181-77035582. Error was invalid region `7:77035182-77035582`
[2016-04-15T05:05Z] 2016-04-14 22:05:25 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:05:25,778 - WARNING - Could not retrieve variants from source file in region 7:70255365-70255784. Error was invalid region `7:70255366-70255784`
[2016-04-15T05:05Z] 2016-04-14 22:05:25 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:05:25,786 - WARNING - Could not retrieve variants from source file in region 7:65425683-65426084. Error was invalid region `7:65425684-65426084`
[2016-04-15T05:05Z] 2016-04-14 22:05:26 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:05:26,204 - WARNING - Could not retrieve variants from source file in region 7:66647946-66648389. Error was invalid region `7:66647947-66648389`
[2016-04-15T05:05Z] 2016-04-14 22:05:29 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:05:29,233 - WARNING - Could not retrieve variants from source file in region 7:76240574-76241078. Error was invalid region `7:76240575-76241078`
[2016-04-15T05:05Z] 2016-04-14 22:05:30 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:05:30,536 - WARNING - Could not retrieve variants from source file in region 7:77035181-77035582. Error was invalid region `7:77035182-77035582`
[2016-04-15T05:05Z] 2016-04-14 22:05:30 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:05:30,650 - WARNING - Could not retrieve variants from source file in region 7:65425683-65426084. Error was invalid region `7:65425684-65426084`
[2016-04-15T05:05Z] 2016-04-14 22:05:31 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:05:31,064 - WARNING - Could not retrieve variants from source file in region 7:76022818-76023219. Error was invalid region `7:76022819-76023219`
[2016-04-15T05:05Z] 2016-04-14 22:05:31 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:05:31,722 - WARNING - Could not retrieve variants from source file in region 7:76957370-77009450. Error was invalid region `7:76957371-77009450`
[2016-04-15T05:05Z] 2016-04-14 22:05:31 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:05:31,843 - WARNING - Could not retrieve variants from source file in region 7:76111624-76144750. Error was invalid region `7:76111625-76144750`
[2016-04-15T05:05Z] 2016-04-14 22:05:31 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:05:31,882 - WARNING - Could not retrieve variants from source file in region 7:73969330-73969731. Error was invalid region `7:73969331-73969731`
[2016-04-15T05:05Z] 2016-04-14 22:05:32 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:05:32,236 - WARNING - Could not retrieve variants from source file in region 7:75051113-75072203. Error was invalid region `7:75051114-75072203`
[2016-04-15T05:05Z] 2016-04-14 22:05:32 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:05:32,359 - WARNING - Could not retrieve variants from source file in region 7:75442519-75442920. Error was invalid region `7:75442520-75442920`
[2016-04-15T05:05Z] 2016-04-14 22:05:33 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:05:33,524 - WARNING - Could not retrieve variants from source file in region 7:76240574-76241078. Error was invalid region `7:76240575-76241078`
[2016-04-15T05:05Z] 2016-04-14 22:05:34 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:05:34,913 - WARNING - Could not retrieve variants from source file in region 7:77035181-77035582. Error was invalid region `7:77035182-77035582`
[2016-04-15T05:05Z] 2016-04-14 22:05:35 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:05:35,602 - WARNING - Could not retrieve variants from source file in region 7:65425683-65426084. Error was invalid region `7:65425684-65426084`
[2016-04-15T05:05Z] 2016-04-14 22:05:35 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:05:35,709 - WARNING - Could not retrieve variants from source file in region 7:76022818-76023219. Error was invalid region `7:76022819-76023219`
[2016-04-15T05:05Z] 2016-04-14 22:05:37 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:05:37,568 - WARNING - Could not retrieve variants from source file in region 7:75442519-75442920. Error was invalid region `7:75442520-75442920`
[2016-04-15T05:05Z] 2016-04-14 22:05:40 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:05:40,005 - WARNING - Could not retrieve variants from source file in region 7:76022818-76023219. Error was invalid region `7:76022819-76023219`
[2016-04-15T05:05Z] 2016-04-14 22:05:46 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:05:46,176 - WARNING - Could not retrieve variants from source file in region 7:76054161-76070001. Error was invalid region `7:76054162-76070001`
[2016-04-15T05:05Z] 2016-04-14 22:05:46 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:05:46,492 - WARNING - Could not retrieve variants from source file in region 7:76054161-76070001. Error was invalid region `7:76054162-76070001`
[2016-04-15T05:05Z] 2016-04-14 22:05:47 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:05:47,826 - WARNING - Could not retrieve variants from source file in region 7:66463727-66464128. Error was invalid region `7:66463728-66464128`
[2016-04-15T05:05Z] 2016-04-14 22:05:47 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:05:47,872 - WARNING - Could not retrieve variants from source file in region 7:64348529-64350061. Error was invalid region `7:64348530-64350061`
[2016-04-15T05:05Z] 2016-04-14 22:05:49 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:05:49,690 - WARNING - Could not retrieve variants from source file in region 7:76054161-76070001. Error was invalid region `7:76054162-76070001`
[2016-04-15T05:05Z] 2016-04-14 22:05:50 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:05:50,243 - WARNING - Could not retrieve variants from source file in region 7:75914723-75915124. Error was invalid region `7:75914724-75915124`
[2016-04-15T05:05Z] 2016-04-14 22:05:50 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:05:50,614 - WARNING - Could not retrieve variants from source file in region 7:64274292-64292181. Error was invalid region `7:64274293-64292181`
[2016-04-15T05:05Z] 2016-04-14 22:05:51 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:05:51,375 - WARNING - Could not retrieve variants from source file in region 7:64348529-64350061. Error was invalid region `7:64348530-64350061`
[2016-04-15T05:05Z] 2016-04-14 22:05:52 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:05:52,709 - WARNING - Could not retrieve variants from source file in region 7:73814538-73814939. Error was invalid region `7:73814539-73814939`
[2016-04-15T05:05Z] 2016-04-14 22:05:52 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:05:52,918 - WARNING - Could not retrieve variants from source file in region 7:74489275-74489676. Error was invalid region `7:74489276-74489676`
[2016-04-15T05:05Z] 2016-04-14 22:05:53 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:05:53,392 - WARNING - Could not retrieve variants from source file in region 7:74489275-74489676. Error was invalid region `7:74489276-74489676`
[2016-04-15T05:05Z] 2016-04-14 22:05:53 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:05:53,609 - WARNING - Could not retrieve variants from source file in region 7:75914723-75915124. Error was invalid region `7:75914724-75915124`
[2016-04-15T05:05Z] 2016-04-14 22:05:53 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:05:53,860 - WARNING - Could not retrieve variants from source file in region 7:64274292-64292181. Error was invalid region `7:64274293-64292181`
[2016-04-15T05:05Z] 2016-04-14 22:05:54 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:05:54,784 - WARNING - Could not retrieve variants from source file in region 7:64348529-64350061. Error was invalid region `7:64348530-64350061`
[2016-04-15T05:05Z] 2016-04-14 22:05:56 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:05:56,050 - WARNING - Could not retrieve variants from source file in region 7:75914723-75915124. Error was invalid region `7:75914724-75915124`
[2016-04-15T05:05Z] 2016-04-14 22:05:56 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:05:56,078 - WARNING - Could not retrieve variants from source file in region 7:73814538-73814939. Error was invalid region `7:73814539-73814939`
[2016-04-15T05:05Z] 2016-04-14 22:05:56 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:05:56,864 - WARNING - Could not retrieve variants from source file in region 7:64274292-64292181. Error was invalid region `7:64274293-64292181`
[2016-04-15T05:05Z] 2016-04-14 22:05:59 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:05:59,267 - WARNING - Could not retrieve variants from source file in region 7:73814538-73814939. Error was invalid region `7:73814539-73814939`
[2016-04-15T05:06Z] 2016-04-14 22:06:02 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:06:02,038 - WARNING - Could not retrieve variants from source file in region 7:64438456-64439891. Error was invalid region `7:64438457-64439891`
[2016-04-15T05:06Z] 2016-04-14 22:06:02 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:06:02,040 - WARNING - Could not retrieve variants from source file in region 7:64438456-64439891. Error was invalid region `7:64438457-64439891`
[2016-04-15T05:06Z] 2016-04-14 22:06:02 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:06:02,046 - WARNING - Could not retrieve variants from source file in region 7:64438456-64439891. Error was invalid region `7:64438457-64439891`
[2016-04-15T05:06Z] 2016-04-14 22:06:02 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:06:02,961 - WARNING - Could not retrieve variants from source file in region 7:73753039-73753440. Error was invalid region `7:73753040-73753440`
[2016-04-15T05:06Z] 2016-04-14 22:06:03 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:06:03,055 - WARNING - Could not retrieve variants from source file in region 7:73753039-73753440. Error was invalid region `7:73753040-73753440`
[2016-04-15T05:06Z] 2016-04-14 22:06:03 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:06:03,072 - WARNING - Could not retrieve variants from source file in region 7:73753039-73753440. Error was invalid region `7:73753040-73753440`
[2016-04-15T05:06Z] 2016-04-14 22:06:03 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:06:03,394 - WARNING - Could not retrieve variants from source file in region 7:73651532-73651933. Error was invalid region `7:73651533-73651933`
[2016-04-15T05:06Z] 2016-04-14 22:06:05 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:06:05,998 - WARNING - Could not retrieve variants from source file in region 7:73248954-73280210. Error was invalid region `7:73248955-73280210`
[2016-04-15T05:06Z] ['bcbio-variation-recall', 'square', '-Xms750m', '-Xmx7280m', '-XX:+UseSerialGC', '-c', 16, '-r', u'7:79082335-94740703', '--caller', 'platypus', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/7/Batch1-7_79082334_94740703.vcf.gz', '/mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/7/Batch1-7_79082334_94740703.vcf-inputs.txt'] in region: 7:79082335-94740703
[2016-04-15T05:06Z] 2016-04-14 22:06:21 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:06:20,985 - WARNING - Could not retrieve variants from source file in region 7:94180480-94180881. Error was invalid region `7:94180481-94180881`
[2016-04-15T05:06Z] 2016-04-14 22:06:21 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:06:21,868 - WARNING - Could not retrieve variants from source file in region 7:92354822-92355223. Error was invalid region `7:92354823-92355223`
[2016-04-15T05:06Z] 2016-04-14 22:06:22 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:06:22,777 - WARNING - Could not retrieve variants from source file in region 7:92076992-92077393. Error was invalid region `7:92076993-92077393`
[2016-04-15T05:06Z] 2016-04-14 22:06:23 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:06:23,076 - WARNING - Could not retrieve variants from source file in region 7:93621182-93623648. Error was invalid region `7:93621183-93623648`
[2016-04-15T05:06Z] 2016-04-14 22:06:23 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:06:23,187 - WARNING - Could not retrieve variants from source file in region 7:92164340-92166230. Error was invalid region `7:92164341-92166230`
[2016-04-15T05:06Z] 2016-04-14 22:06:23 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:06:23,372 - WARNING - Could not retrieve variants from source file in region 7:94030688-94056539. Error was invalid region `7:94030689-94056539`
[2016-04-15T05:06Z] 2016-04-14 22:06:23 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:06:23,593 - WARNING - Could not retrieve variants from source file in region 7:90338639-90339275. Error was invalid region `7:90338640-90339275`
[2016-04-15T05:06Z] 2016-04-14 22:06:23 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:06:23,954 - WARNING - Could not retrieve variants from source file in region 7:92970636-92985442. Error was invalid region `7:92970637-92985442`
[2016-04-15T05:06Z] 2016-04-14 22:06:24 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:06:24,026 - WARNING - Could not retrieve variants from source file in region 7:87913010-87913551. Error was invalid region `7:87913011-87913551`
[2016-04-15T05:06Z] 2016-04-14 22:06:25 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:06:25,884 - WARNING - Could not retrieve variants from source file in region 7:88964299-88964700. Error was invalid region `7:88964300-88964700`
[2016-04-15T05:06Z] 2016-04-14 22:06:30 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:06:30,042 - WARNING - Could not retrieve variants from source file in region 7:86826936-86827337. Error was invalid region `7:86826937-86827337`
[2016-04-15T05:06Z] 2016-04-14 22:06:30 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:06:30,183 - WARNING - Could not retrieve variants from source file in region 7:93621182-93623648. Error was invalid region `7:93621183-93623648`
[2016-04-15T05:06Z] 2016-04-14 22:06:31 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:06:31,937 - WARNING - Could not retrieve variants from source file in region 7:87913010-87913551. Error was invalid region `7:87913011-87913551`
[2016-04-15T05:06Z] 2016-04-14 22:06:32 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:06:32,567 - WARNING - Could not retrieve variants from source file in region 7:83029227-83037941. Error was invalid region `7:83029228-83037941`
[2016-04-15T05:06Z] 2016-04-14 22:06:32 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:06:32,936 - WARNING - Could not retrieve variants from source file in region 7:92970636-92985442. Error was invalid region `7:92970637-92985442`
[2016-04-15T05:06Z] 2016-04-14 22:06:33 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:06:33,512 - WARNING - Could not retrieve variants from source file in region 7:93116088-93116489. Error was invalid region `7:93116089-93116489`
[2016-04-15T05:06Z] 2016-04-14 22:06:33 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:06:33,520 - WARNING - Could not retrieve variants from source file in region 7:94180480-94180881. Error was invalid region `7:94180481-94180881`
[2016-04-15T05:06Z] 2016-04-14 22:06:33 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:06:33,655 - WARNING - Could not retrieve variants from source file in region 7:92354822-92355223. Error was invalid region `7:92354823-92355223`
[2016-04-15T05:06Z] 2016-04-14 22:06:33 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:06:33,709 - WARNING - Could not retrieve variants from source file in region 7:84769442-84787144. Error was invalid region `7:84769443-84787144`
[2016-04-15T05:06Z] 2016-04-14 22:06:35 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:06:35,128 - WARNING - Could not retrieve variants from source file in region 7:93621182-93623648. Error was invalid region `7:93621183-93623648`
[2016-04-15T05:06Z] 2016-04-14 22:06:35 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:06:35,419 - WARNING - Could not retrieve variants from source file in region 7:86826936-86827337. Error was invalid region `7:86826937-86827337`
[2016-04-15T05:06Z] 2016-04-14 22:06:35 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:06:35,425 - WARNING - Could not retrieve variants from source file in region 7:92076992-92077393. Error was invalid region `7:92076993-92077393`
[2016-04-15T05:06Z] 2016-04-14 22:06:36 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:06:36,365 - WARNING - Could not retrieve variants from source file in region 7:92164340-92166230. Error was invalid region `7:92164341-92166230`
[2016-04-15T05:06Z] 2016-04-14 22:06:36 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:06:36,722 - WARNING - Could not retrieve variants from source file in region 7:94030688-94056539. Error was invalid region `7:94030689-94056539`
[2016-04-15T05:06Z] 2016-04-14 22:06:38 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:06:38,522 - WARNING - Could not retrieve variants from source file in region 7:87913010-87913551. Error was invalid region `7:87913011-87913551`
[2016-04-15T05:06Z] 2016-04-14 22:06:39 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:06:39,210 - WARNING - Could not retrieve variants from source file in region 7:92970636-92985442. Error was invalid region `7:92970637-92985442`
[2016-04-15T05:06Z] 2016-04-14 22:06:48 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:06:48,980 - WARNING - Could not retrieve variants from source file in region 7:91691390-91743340. Error was invalid region `7:91691391-91743340`
[2016-04-15T05:06Z] 2016-04-14 22:06:50 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:06:50,356 - WARNING - Could not retrieve variants from source file in region 7:93055542-93055943. Error was invalid region `7:93055543-93055943`
[2016-04-15T05:06Z] 2016-04-14 22:06:50 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:06:50,827 - WARNING - Could not retrieve variants from source file in region 7:93055542-93055943. Error was invalid region `7:93055543-93055943`
[2016-04-15T05:06Z] 2016-04-14 22:06:51 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:06:51,125 - WARNING - Could not retrieve variants from source file in region 7:92027828-92028229. Error was invalid region `7:92027829-92028229`
[2016-04-15T05:06Z] 2016-04-14 22:06:51 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:06:51,468 - WARNING - Could not retrieve variants from source file in region 7:86795669-86800541. Error was invalid region `7:86795670-86800541`
[2016-04-15T05:06Z] 2016-04-14 22:06:53 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:06:53,104 - WARNING - Could not retrieve variants from source file in region 7:87564286-87564687. Error was invalid region `7:87564287-87564687`
[2016-04-15T05:06Z] 2016-04-14 22:06:53 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:06:53,604 - WARNING - Could not retrieve variants from source file in region 7:91691390-91743340. Error was invalid region `7:91691391-91743340`
[2016-04-15T05:06Z] 2016-04-14 22:06:55 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:06:55,478 - WARNING - Could not retrieve variants from source file in region 7:93055542-93055943. Error was invalid region `7:93055543-93055943`
[2016-04-15T05:06Z] 2016-04-14 22:06:57 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:06:57,047 - WARNING - Could not retrieve variants from source file in region 7:92131078-92131479. Error was invalid region `7:92131079-92131479`
[2016-04-15T05:06Z] 2016-04-14 22:06:57 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:06:57,052 - WARNING - Could not retrieve variants from source file in region 7:84628778-84644690. Error was invalid region `7:84628779-84644690`
[2016-04-15T05:06Z] 2016-04-14 22:06:57 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:06:57,204 - WARNING - Could not retrieve variants from source file in region 7:81371836-81381516. Error was invalid region `7:81371837-81381516`
[2016-04-15T05:06Z] 2016-04-14 22:06:57 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:06:57,525 - WARNING - Could not retrieve variants from source file in region 7:83590641-83591042. Error was invalid region `7:83590642-83591042`
[2016-04-15T05:06Z] 2016-04-14 22:06:58 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:06:58,011 - WARNING - Could not retrieve variants from source file in region 7:91691390-91743340. Error was invalid region `7:91691391-91743340`
[2016-04-15T05:06Z] 2016-04-14 22:06:58 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:06:58,678 - WARNING - Could not retrieve variants from source file in region 7:90042646-90043504. Error was invalid region `7:90042647-90043504`
[2016-04-15T05:07Z] 2016-04-14 22:07:01 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:07:01,392 - WARNING - Could not retrieve variants from source file in region 7:86795669-86800541. Error was invalid region `7:86795670-86800541`
[2016-04-15T05:07Z] 2016-04-14 22:07:02 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:07:02,115 - WARNING - Could not retrieve variants from source file in region 7:84628778-84644690. Error was invalid region `7:84628779-84644690`
[2016-04-15T05:07Z] 2016-04-14 22:07:02 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:07:02,130 - WARNING - Could not retrieve variants from source file in region 7:81371836-81381516. Error was invalid region `7:81371837-81381516`
[2016-04-15T05:07Z] 2016-04-14 22:07:02 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:07:02,392 - WARNING - Could not retrieve variants from source file in region 7:87190466-87190867. Error was invalid region `7:87190467-87190867`
[2016-04-15T05:07Z] 2016-04-14 22:07:02 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:07:02,439 - WARNING - Could not retrieve variants from source file in region 7:92131078-92131479. Error was invalid region `7:92131079-92131479`
[2016-04-15T05:07Z] 2016-04-14 22:07:02 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:07:02,617 - WARNING - Could not retrieve variants from source file in region 7:87564286-87564687. Error was invalid region `7:87564287-87564687`
[2016-04-15T05:07Z] 2016-04-14 22:07:02 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:07:02,620 - WARNING - Could not retrieve variants from source file in region 7:83590641-83591042. Error was invalid region `7:83590642-83591042`
[2016-04-15T05:07Z] 2016-04-14 22:07:08 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:07:08,464 - WARNING - Could not retrieve variants from source file in region 7:83590641-83591042. Error was invalid region `7:83590642-83591042`
[2016-04-15T05:07Z] 2016-04-14 22:07:09 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:07:09,395 - WARNING - Could not retrieve variants from source file in region 7:80374131-80387956. Error was invalid region `7:80374132-80387956`
[2016-04-15T05:07Z] 2016-04-14 22:07:09 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:07:09,436 - WARNING - Could not retrieve variants from source file in region 7:92734240-92734641. Error was invalid region `7:92734241-92734641`
[2016-04-15T05:07Z] 2016-04-14 22:07:09 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:07:09,472 - WARNING - Could not retrieve variants from source file in region 7:86468043-86468444. Error was invalid region `7:86468044-86468444`
[2016-04-15T05:07Z] 2016-04-14 22:07:11 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:07:11,203 - WARNING - Could not retrieve variants from source file in region 7:91630409-91652368. Error was invalid region `7:91630410-91652368`
[2016-04-15T05:07Z] 2016-04-14 22:07:14 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:07:14,557 - WARNING - Could not retrieve variants from source file in region 7:92734240-92734641. Error was invalid region `7:92734241-92734641`
[2016-04-15T05:07Z] 2016-04-14 22:07:15 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:07:15,283 - WARNING - Could not retrieve variants from source file in region 7:92734240-92734641. Error was invalid region `7:92734241-92734641`
[2016-04-15T05:07Z] 2016-04-14 22:07:15 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:07:15,455 - WARNING - Could not retrieve variants from source file in region 7:91779760-91780161. Error was invalid region `7:91779761-91780161`
[2016-04-15T05:07Z] 2016-04-14 22:07:15 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:07:15,765 - WARNING - Could not retrieve variants from source file in region 7:80548250-80548651. Error was invalid region `7:80548251-80548651`
[2016-04-15T05:07Z] 2016-04-14 22:07:20 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:07:20,082 - WARNING - Could not retrieve variants from source file in region 7:80374131-80387956. Error was invalid region `7:80374132-80387956`
[2016-04-15T05:07Z] 2016-04-14 22:07:20 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:07:20,229 - WARNING - Could not retrieve variants from source file in region 7:82581277-82581678. Error was invalid region `7:82581278-82581678`
[2016-04-15T05:07Z] 2016-04-14 22:07:21 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:07:21,002 - WARNING - Could not retrieve variants from source file in region 7:91779760-91780161. Error was invalid region `7:91779761-91780161`
[2016-04-15T05:07Z] 2016-04-14 22:07:21 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:07:21,061 - WARNING - Could not retrieve variants from source file in region 7:80548250-80548651. Error was invalid region `7:80548251-80548651`
[2016-04-15T05:07Z] 2016-04-14 22:07:21 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:07:21,845 - WARNING - Could not retrieve variants from source file in region 7:87229229-87229630. Error was invalid region `7:87229230-87229630`
[2016-04-15T05:07Z] 2016-04-14 22:07:21 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:07:21,870 - WARNING - Could not retrieve variants from source file in region 7:80303249-80303654. Error was invalid region `7:80303250-80303654`
[2016-04-15T05:07Z] 2016-04-14 22:07:22 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:07:22,592 - WARNING - Could not retrieve variants from source file in region 7:87138434-87160808. Error was invalid region `7:87138435-87160808`
[2016-04-15T05:07Z] 2016-04-14 22:07:24 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:07:24,783 - WARNING - Could not retrieve variants from source file in region 7:82581277-82581678. Error was invalid region `7:82581278-82581678`
[2016-04-15T05:07Z] 2016-04-14 22:07:25 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:07:25,704 - WARNING - Could not retrieve variants from source file in region 7:91779760-91780161. Error was invalid region `7:91779761-91780161`
[2016-04-15T05:07Z] 2016-04-14 22:07:26 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:07:26,255 - WARNING - Could not retrieve variants from source file in region 7:80548250-80548651. Error was invalid region `7:80548251-80548651`
[2016-04-15T05:07Z] 2016-04-14 22:07:26 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:07:26,843 - WARNING - Could not retrieve variants from source file in region 7:87229229-87229630. Error was invalid region `7:87229230-87229630`
[2016-04-15T05:07Z] 2016-04-14 22:07:27 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:07:27,303 - WARNING - Could not retrieve variants from source file in region 7:89981921-90000741. Error was invalid region `7:89981922-90000741`
[2016-04-15T05:07Z] 2016-04-14 22:07:28 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:07:28,225 - WARNING - Could not retrieve variants from source file in region 7:79841946-79842347. Error was invalid region `7:79841947-79842347`
[2016-04-15T05:07Z] 2016-04-14 22:07:29 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:07:29,158 - WARNING - Could not retrieve variants from source file in region 7:90894248-90894649. Error was invalid region `7:90894249-90894649`
[2016-04-15T05:07Z] 2016-04-14 22:07:29 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:07:29,865 - WARNING - Could not retrieve variants from source file in region 7:82581277-82581678. Error was invalid region `7:82581278-82581678`
[2016-04-15T05:07Z] 2016-04-14 22:07:30 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:07:30,347 - WARNING - Could not retrieve variants from source file in region 7:87138434-87160808. Error was invalid region `7:87138435-87160808`
[2016-04-15T05:07Z] 2016-04-14 22:07:30 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:07:30,694 - WARNING - Could not retrieve variants from source file in region 7:90894248-90894649. Error was invalid region `7:90894249-90894649`
[2016-04-15T05:07Z] 2016-04-14 22:07:32 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:07:32,704 - WARNING - Could not retrieve variants from source file in region 7:79841946-79842347. Error was invalid region `7:79841947-79842347`
[2016-04-15T05:07Z] 2016-04-14 22:07:33 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:07:33,694 - WARNING - Could not retrieve variants from source file in region 7:90894248-90894649. Error was invalid region `7:90894249-90894649`
[2016-04-15T05:07Z] 2016-04-14 22:07:38 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:07:38,793 - WARNING - Could not retrieve variants from source file in region 7:81588425-81588826. Error was invalid region `7:81588426-81588826`
[2016-04-15T05:07Z] 2016-04-14 22:07:38 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:07:38,819 - WARNING - Could not retrieve variants from source file in region 7:81588425-81588826. Error was invalid region `7:81588426-81588826`
[2016-04-15T05:07Z] 2016-04-14 22:07:38 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:07:38,902 - WARNING - Could not retrieve variants from source file in region 7:82072747-82073148. Error was invalid region `7:82072748-82073148`
[2016-04-15T05:07Z] 2016-04-14 22:07:39 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:07:39,988 - WARNING - Could not retrieve variants from source file in region 7:82072747-82073148. Error was invalid region `7:82072748-82073148`
[2016-04-15T05:07Z] 2016-04-14 22:07:40 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:07:40,270 - WARNING - Could not retrieve variants from source file in region 7:80418478-80418879. Error was invalid region `7:80418479-80418879`
[2016-04-15T05:07Z] 2016-04-14 22:07:40 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:07:40,294 - WARNING - Could not retrieve variants from source file in region 7:80418478-80418879. Error was invalid region `7:80418479-80418879`
[2016-04-15T05:07Z] 2016-04-14 22:07:40 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:07:40,919 - WARNING - Could not retrieve variants from source file in region 7:82072747-82073148. Error was invalid region `7:82072748-82073148`
[2016-04-15T05:07Z] ['bcbio-variation-recall', 'square', '-Xms750m', '-Xmx7280m', '-XX:+UseSerialGC', '-c', 16, '-r', u'7:94750024-110303777', '--caller', 'platypus', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/7/Batch1-7_94750023_110303777.vcf.gz', '/mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/7/Batch1-7_94750023_110303777.vcf-inputs.txt'] in region: 7:94750024-110303777
[2016-04-15T05:07Z] 2016-04-14 22:07:55 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:07:55,227 - WARNING - Could not retrieve variants from source file in region 7:101194213-101200917. Error was invalid region `7:101194214-101200917`
[2016-04-15T05:07Z] 2016-04-14 22:07:56 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:07:56,829 - WARNING - Could not retrieve variants from source file in region 7:100281557-100305054. Error was invalid region `7:100281558-100305054`
[2016-04-15T05:07Z] 2016-04-14 22:07:57 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:07:57,615 - WARNING - Could not retrieve variants from source file in region 7:106685237-106685638. Error was invalid region `7:106685238-106685638`
[2016-04-15T05:07Z] 2016-04-14 22:07:57 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:07:57,898 - WARNING - Could not retrieve variants from source file in region 7:97920412-97933791. Error was invalid region `7:97920413-97933791`
[2016-04-15T05:07Z] 2016-04-14 22:07:58 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:07:58,516 - WARNING - Could not retrieve variants from source file in region 7:101836938-101845041. Error was invalid region `7:101836939-101845041`
[2016-04-15T05:07Z] 2016-04-14 22:07:58 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:07:58,723 - WARNING - Could not retrieve variants from source file in region 7:101460246-101460647. Error was invalid region `7:101460247-101460647`
[2016-04-15T05:08Z] 2016-04-14 22:08:02 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:08:02,717 - WARNING - Could not retrieve variants from source file in region 7:102462425-102462826. Error was invalid region `7:102462426-102462826`
[2016-04-15T05:08Z] 2016-04-14 22:08:05 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:08:05,921 - WARNING - Could not retrieve variants from source file in region 7:102036334-102037067. Error was invalid region `7:102036335-102037067`
[2016-04-15T05:08Z] 2016-04-14 22:08:06 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:08:06,530 - WARNING - Could not retrieve variants from source file in region 7:104377103-104377504. Error was invalid region `7:104377104-104377504`
[2016-04-15T05:08Z] 2016-04-14 22:08:06 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:08:06,856 - WARNING - Could not retrieve variants from source file in region 7:97920412-97933791. Error was invalid region `7:97920413-97933791`
[2016-04-15T05:08Z] 2016-04-14 22:08:06 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:08:06,964 - WARNING - Could not retrieve variants from source file in region 7:100458584-100488848. Error was invalid region `7:100458585-100488848`
[2016-04-15T05:08Z] 2016-04-14 22:08:07 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:08:07,556 - WARNING - Could not retrieve variants from source file in region 7:108209412-108212543. Error was invalid region `7:108209413-108212543`
[2016-04-15T05:08Z] 2016-04-14 22:08:07 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:08:07,721 - WARNING - Could not retrieve variants from source file in region 7:101460246-101460647. Error was invalid region `7:101460247-101460647`
[2016-04-15T05:08Z] 2016-04-14 22:08:07 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:08:07,749 - WARNING - Could not retrieve variants from source file in region 7:100064508-100088830. Error was invalid region `7:100064509-100088830`
[2016-04-15T05:08Z] 2016-04-14 22:08:07 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:08:07,942 - WARNING - Could not retrieve variants from source file in region 7:100798063-100807029. Error was invalid region `7:100798064-100807029`
[2016-04-15T05:08Z] 2016-04-14 22:08:08 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:08:08,020 - WARNING - Could not retrieve variants from source file in region 7:101194213-101200917. Error was invalid region `7:101194214-101200917`
[2016-04-15T05:08Z] 2016-04-14 22:08:10 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:08:10,773 - WARNING - Could not retrieve variants from source file in region 7:105615195-105621702. Error was invalid region `7:105615196-105621702`
[2016-04-15T05:08Z] 2016-04-14 22:08:13 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:08:13,203 - WARNING - Could not retrieve variants from source file in region 7:104377103-104377504. Error was invalid region `7:104377104-104377504`
[2016-04-15T05:08Z] 2016-04-14 22:08:13 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:08:13,970 - WARNING - Could not retrieve variants from source file in region 7:97920412-97933791. Error was invalid region `7:97920413-97933791`
[2016-04-15T05:08Z] 2016-04-14 22:08:14 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:08:14,685 - WARNING - Could not retrieve variants from source file in region 7:108209412-108212543. Error was invalid region `7:108209413-108212543`
[2016-04-15T05:08Z] 2016-04-14 22:08:14 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:08:14,709 - WARNING - Could not retrieve variants from source file in region 7:101836938-101845041. Error was invalid region `7:101836939-101845041`
[2016-04-15T05:08Z] 2016-04-14 22:08:15 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:08:15,658 - WARNING - Could not retrieve variants from source file in region 7:100064508-100088830. Error was invalid region `7:100064509-100088830`
[2016-04-15T05:08Z] 2016-04-14 22:08:15 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:08:15,996 - WARNING - Could not retrieve variants from source file in region 7:100798063-100807029. Error was invalid region `7:100798064-100807029`
[2016-04-15T05:08Z] 2016-04-14 22:08:16 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:08:16,227 - WARNING - Could not retrieve variants from source file in region 7:101460246-101460647. Error was invalid region `7:101460247-101460647`
[2016-04-15T05:08Z] 2016-04-14 22:08:26 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:08:26,773 - WARNING - Could not retrieve variants from source file in region 7:101006165-101006572. Error was invalid region `7:101006166-101006572`
[2016-04-15T05:08Z] 2016-04-14 22:08:27 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:08:27,127 - WARNING - Could not retrieve variants from source file in region 7:105400804-105401205. Error was invalid region `7:105400805-105401205`
[2016-04-15T05:08Z] 2016-04-14 22:08:28 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:08:28,402 - WARNING - Could not retrieve variants from source file in region 7:106508767-106509177. Error was invalid region `7:106508768-106509177`
[2016-04-15T05:08Z] 2016-04-14 22:08:28 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:08:28,450 - WARNING - Could not retrieve variants from source file in region 7:103629592-103629993. Error was invalid region `7:103629593-103629993`
[2016-04-15T05:08Z] 2016-04-14 22:08:28 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:08:28,765 - WARNING - Could not retrieve variants from source file in region 7:100200852-100201253. Error was invalid region `7:100200853-100201253`
[2016-04-15T05:08Z] 2016-04-14 22:08:29 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:08:29,238 - WARNING - Could not retrieve variants from source file in region 7:97854182-97874184. Error was invalid region `7:97854183-97874184`
[2016-04-15T05:08Z] 2016-04-14 22:08:30 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:08:30,188 - WARNING - Could not retrieve variants from source file in region 7:101256622-101257023. Error was invalid region `7:101256623-101257023`
[2016-04-15T05:08Z] 2016-04-14 22:08:31 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:08:31,990 - WARNING - Could not retrieve variants from source file in region 7:101006165-101006572. Error was invalid region `7:101006166-101006572`
[2016-04-15T05:08Z] 2016-04-14 22:08:32 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:08:32,399 - WARNING - Could not retrieve variants from source file in region 7:105400804-105401205. Error was invalid region `7:105400805-105401205`
[2016-04-15T05:08Z] 2016-04-14 22:08:32 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:08:32,804 - WARNING - Could not retrieve variants from source file in region 7:100730973-100732019. Error was invalid region `7:100730974-100732019`
[2016-04-15T05:08Z] 2016-04-14 22:08:33 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:08:33,085 - WARNING - Could not retrieve variants from source file in region 7:106508767-106509177. Error was invalid region `7:106508768-106509177`
[2016-04-15T05:08Z] 2016-04-14 22:08:36 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:08:36,136 - WARNING - Could not retrieve variants from source file in region 7:107824678-107873006. Error was invalid region `7:107824679-107873006`
[2016-04-15T05:08Z] 2016-04-14 22:08:37 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:08:37,433 - WARNING - Could not retrieve variants from source file in region 7:101006165-101006572. Error was invalid region `7:101006166-101006572`
[2016-04-15T05:08Z] 2016-04-14 22:08:37 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:08:37,743 - WARNING - Could not retrieve variants from source file in region 7:105400804-105401205. Error was invalid region `7:105400805-105401205`
[2016-04-15T05:08Z] 2016-04-14 22:08:38 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:08:38,023 - WARNING - Could not retrieve variants from source file in region 7:99569183-99569584. Error was invalid region `7:99569184-99569584`
[2016-04-15T05:08Z] 2016-04-14 22:08:38 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:08:38,169 - WARNING - Could not retrieve variants from source file in region 7:106508767-106509177. Error was invalid region `7:106508768-106509177`
[2016-04-15T05:08Z] 2016-04-14 22:08:39 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:08:39,142 - WARNING - Could not retrieve variants from source file in region 7:103629592-103629993. Error was invalid region `7:103629593-103629993`
[2016-04-15T05:08Z] 2016-04-14 22:08:39 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:08:39,268 - WARNING - Could not retrieve variants from source file in region 7:100200852-100201253. Error was invalid region `7:100200853-100201253`
[2016-04-15T05:08Z] 2016-04-14 22:08:39 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:08:39,270 - WARNING - Could not retrieve variants from source file in region 7:97854182-97874184. Error was invalid region `7:97854183-97874184`
[2016-04-15T05:08Z] 2016-04-14 22:08:40 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:08:40,568 - WARNING - Could not retrieve variants from source file in region 7:101256622-101257023. Error was invalid region `7:101256623-101257023`
[2016-04-15T05:08Z] 2016-04-14 22:08:40 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:08:40,597 - WARNING - Could not retrieve variants from source file in region 7:107824678-107873006. Error was invalid region `7:107824679-107873006`
[2016-04-15T05:08Z] 2016-04-14 22:08:44 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:08:44,029 - WARNING - Could not retrieve variants from source file in region 7:99569183-99569584. Error was invalid region `7:99569184-99569584`
[2016-04-15T05:08Z] 2016-04-14 22:08:44 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:08:44,064 - WARNING - Could not retrieve variants from source file in region 7:100730973-100732019. Error was invalid region `7:100730974-100732019`
[2016-04-15T05:08Z] 2016-04-14 22:08:44 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:08:44,748 - WARNING - Could not retrieve variants from source file in region 7:100017243-100033579. Error was invalid region `7:100017244-100033579`
[2016-04-15T05:08Z] 2016-04-14 22:08:49 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:08:49,102 - WARNING - Could not retrieve variants from source file in region 7:102235558-102246584. Error was invalid region `7:102235559-102246584`
[2016-04-15T05:08Z] 2016-04-14 22:08:51 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:08:51,879 - WARNING - Could not retrieve variants from source file in region 7:100875561-100875962. Error was invalid region `7:100875562-100875962`
[2016-04-15T05:08Z] 2016-04-14 22:08:52 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:08:52,478 - WARNING - Could not retrieve variants from source file in region 7:105253874-105254275. Error was invalid region `7:105253875-105254275`
[2016-04-15T05:08Z] 2016-04-14 22:08:52 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:08:52,987 - WARNING - Could not retrieve variants from source file in region 7:105903693-105904094. Error was invalid region `7:105903694-105904094`
[2016-04-15T05:08Z] 2016-04-14 22:08:53 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:08:53,024 - WARNING - Could not retrieve variants from source file in region 7:99032306-99032707. Error was invalid region `7:99032307-99032707`
[2016-04-15T05:08Z] 2016-04-14 22:08:54 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:08:54,682 - WARNING - Could not retrieve variants from source file in region 7:100175262-100175663. Error was invalid region `7:100175263-100175663`
[2016-04-15T05:08Z] 2016-04-14 22:08:55 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:08:55,684 - WARNING - Could not retrieve variants from source file in region 7:97821904-97822400. Error was invalid region `7:97821905-97822400`
[2016-04-15T05:08Z] 2016-04-14 22:08:55 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:08:55,923 - WARNING - Could not retrieve variants from source file in region 7:103250950-103251351. Error was invalid region `7:103250951-103251351`
[2016-04-15T05:08Z] 2016-04-14 22:08:56 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:08:56,806 - WARNING - Could not retrieve variants from source file in region 7:99500688-99501101. Error was invalid region `7:99500689-99501101`
[2016-04-15T05:08Z] 2016-04-14 22:08:57 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:08:57,820 - WARNING - Could not retrieve variants from source file in region 7:99459045-99474617. Error was invalid region `7:99459046-99474617`
[2016-04-15T05:08Z] 2016-04-14 22:08:58 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:08:58,600 - WARNING - Could not retrieve variants from source file in region 7:105903693-105904094. Error was invalid region `7:105903694-105904094`
[2016-04-15T05:08Z] 2016-04-14 22:08:59 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:08:59,696 - WARNING - Could not retrieve variants from source file in region 7:100675765-100681952. Error was invalid region `7:100675766-100681952`
[2016-04-15T05:09Z] 2016-04-14 22:09:02 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:09:02,095 - WARNING - Could not retrieve variants from source file in region 7:97821904-97822400. Error was invalid region `7:97821905-97822400`
[2016-04-15T05:09Z] 2016-04-14 22:09:02 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:09:02,168 - WARNING - Could not retrieve variants from source file in region 7:99500688-99501101. Error was invalid region `7:99500689-99501101`
[2016-04-15T05:09Z] 2016-04-14 22:09:02 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:09:02,785 - WARNING - Could not retrieve variants from source file in region 7:107738671-107743854. Error was invalid region `7:107738672-107743854`
[2016-04-15T05:09Z] 2016-04-14 22:09:03 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:09:03,308 - WARNING - Could not retrieve variants from source file in region 7:105253874-105254275. Error was invalid region `7:105253875-105254275`
[2016-04-15T05:09Z] 2016-04-14 22:09:03 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:09:03,536 - WARNING - Could not retrieve variants from source file in region 7:100875561-100875962. Error was invalid region `7:100875562-100875962`
[2016-04-15T05:09Z] 2016-04-14 22:09:05 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:09:05,498 - WARNING - Could not retrieve variants from source file in region 7:100175262-100175663. Error was invalid region `7:100175263-100175663`
[2016-04-15T05:09Z] 2016-04-14 22:09:05 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:09:05,535 - WARNING - Could not retrieve variants from source file in region 7:99956917-99972024. Error was invalid region `7:99956918-99972024`
[2016-04-15T05:09Z] 2016-04-14 22:09:06 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:09:06,868 - WARNING - Could not retrieve variants from source file in region 7:103250950-103251351. Error was invalid region `7:103250951-103251351`
[2016-04-15T05:09Z] 2016-04-14 22:09:07 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:09:07,948 - WARNING - Could not retrieve variants from source file in region 7:99500688-99501101. Error was invalid region `7:99500689-99501101`
[2016-04-15T05:09Z] 2016-04-14 22:09:08 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:09:08,016 - WARNING - Could not retrieve variants from source file in region 7:97821904-97822400. Error was invalid region `7:97821905-97822400`
[2016-04-15T05:09Z] 2016-04-14 22:09:08 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:09:08,628 - WARNING - Could not retrieve variants from source file in region 7:107569306-107626960. Error was invalid region `7:107569307-107626960`
[2016-04-15T05:09Z] 2016-04-14 22:09:10 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:09:10,128 - WARNING - Could not retrieve variants from source file in region 7:99459045-99474617. Error was invalid region `7:99459046-99474617`
[2016-04-15T05:09Z] 2016-04-14 22:09:10 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:09:10,953 - WARNING - Could not retrieve variants from source file in region 7:99956917-99972024. Error was invalid region `7:99956918-99972024`
[2016-04-15T05:09Z] 2016-04-14 22:09:11 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:09:11,087 - WARNING - Could not retrieve variants from source file in region 7:100675765-100681952. Error was invalid region `7:100675766-100681952`
[2016-04-15T05:09Z] 2016-04-14 22:09:19 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:09:19,024 - WARNING - Could not retrieve variants from source file in region 7:100839190-100839591. Error was invalid region `7:100839191-100839591`
[2016-04-15T05:09Z] 2016-04-14 22:09:20 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:09:20,497 - WARNING - Could not retrieve variants from source file in region 7:102105355-102119512. Error was invalid region `7:102105356-102119512`
[2016-04-15T05:09Z] 2016-04-14 22:09:21 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:09:21,850 - WARNING - Could not retrieve variants from source file in region 7:95800609-95801010. Error was invalid region `7:95800610-95801010`
[2016-04-15T05:09Z] 2016-04-14 22:09:23 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:09:23,933 - WARNING - Could not retrieve variants from source file in region 7:105176830-105177231. Error was invalid region `7:105176831-105177231`
[2016-04-15T05:09Z] 2016-04-14 22:09:24 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:09:24,249 - WARNING - Could not retrieve variants from source file in region 7:97488358-97488759. Error was invalid region `7:97488359-97488759`
[2016-04-15T05:09Z] 2016-04-14 22:09:24 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:09:24,613 - WARNING - Could not retrieve variants from source file in region 7:107414208-107414609. Error was invalid region `7:107414209-107414609`
[2016-04-15T05:09Z] 2016-04-14 22:09:24 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:09:24,972 - WARNING - Could not retrieve variants from source file in region 7:107664293-107664695. Error was invalid region `7:107664294-107664695`
[2016-04-15T05:09Z] 2016-04-14 22:09:25 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:09:25,152 - WARNING - Could not retrieve variants from source file in region 7:99306474-99306875. Error was invalid region `7:99306475-99306875`
[2016-04-15T05:09Z] 2016-04-14 22:09:25 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:09:25,700 - WARNING - Could not retrieve variants from source file in region 7:105752480-105752881. Error was invalid region `7:105752481-105752881`
[2016-04-15T05:09Z] 2016-04-14 22:09:27 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:09:27,816 - WARNING - Could not retrieve variants from source file in region 7:99917205-99917606. Error was invalid region `7:99917206-99917606`
[2016-04-15T05:09Z] 2016-04-14 22:09:29 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:09:29,716 - WARNING - Could not retrieve variants from source file in region 7:100839190-100839591. Error was invalid region `7:100839191-100839591`
[2016-04-15T05:09Z] 2016-04-14 22:09:29 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:09:29,839 - WARNING - Could not retrieve variants from source file in region 7:107414208-107414609. Error was invalid region `7:107414209-107414609`
[2016-04-15T05:09Z] 2016-04-14 22:09:30 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:09:30,451 - WARNING - Could not retrieve variants from source file in region 7:99306474-99306875. Error was invalid region `7:99306475-99306875`
[2016-04-15T05:09Z] 2016-04-14 22:09:30 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:09:30,460 - WARNING - Could not retrieve variants from source file in region 7:105752480-105752881. Error was invalid region `7:105752481-105752881`
[2016-04-15T05:09Z] 2016-04-14 22:09:31 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:09:31,494 - WARNING - Could not retrieve variants from source file in region 7:107664293-107664695. Error was invalid region `7:107664294-107664695`
[2016-04-15T05:09Z] 2016-04-14 22:09:33 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:09:33,638 - WARNING - Could not retrieve variants from source file in region 7:99917205-99917606. Error was invalid region `7:99917206-99917606`
[2016-04-15T05:09Z] 2016-04-14 22:09:35 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:09:35,586 - WARNING - Could not retrieve variants from source file in region 7:99306474-99306875. Error was invalid region `7:99306475-99306875`
[2016-04-15T05:09Z] 2016-04-14 22:09:35 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:09:35,770 - WARNING - Could not retrieve variants from source file in region 7:97488358-97488759. Error was invalid region `7:97488359-97488759`
[2016-04-15T05:09Z] 2016-04-14 22:09:36 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:09:36,136 - WARNING - Could not retrieve variants from source file in region 7:107414208-107414609. Error was invalid region `7:107414209-107414609`
[2016-04-15T05:09Z] 2016-04-14 22:09:36 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:09:36,453 - WARNING - Could not retrieve variants from source file in region 7:95216183-95216584. Error was invalid region `7:95216184-95216584`
[2016-04-15T05:09Z] 2016-04-14 22:09:44 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:09:44,662 - WARNING - Could not retrieve variants from source file in region 7:105658240-105662880. Error was invalid region `7:105658241-105662880`
[2016-04-15T05:09Z] 2016-04-14 22:09:45 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:09:45,900 - WARNING - Could not retrieve variants from source file in region 7:105148472-105148873. Error was invalid region `7:105148473-105148873`
[2016-04-15T05:09Z] 2016-04-14 22:09:45 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:09:45,962 - WARNING - Could not retrieve variants from source file in region 7:107002595-107002996. Error was invalid region `7:107002596-107002996`
[2016-04-15T05:09Z] 2016-04-14 22:09:46 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:09:46,905 - WARNING - Could not retrieve variants from source file in region 7:103007738-103008139. Error was invalid region `7:103007739-103008139`
[2016-04-15T05:09Z] 2016-04-14 22:09:47 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:09:47,504 - WARNING - Could not retrieve variants from source file in region 7:98649840-98650241. Error was invalid region `7:98649841-98650241`
[2016-04-15T05:09Z] 2016-04-14 22:09:48 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:09:48,176 - WARNING - Could not retrieve variants from source file in region 7:95726803-95727204. Error was invalid region `7:95726804-95727204`
[2016-04-15T05:09Z] 2016-04-14 22:09:50 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:09:50,084 - WARNING - Could not retrieve variants from source file in region 7:96746981-96747382. Error was invalid region `7:96746982-96747382`
[2016-04-15T05:09Z] 2016-04-14 22:09:50 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:09:50,657 - WARNING - Could not retrieve variants from source file in region 7:98460613-98461014. Error was invalid region `7:98460614-98461014`
[2016-04-15T05:09Z] 2016-04-14 22:09:50 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:09:50,687 - WARNING - Could not retrieve variants from source file in region 7:98460613-98461014. Error was invalid region `7:98460614-98461014`
[2016-04-15T05:09Z] 2016-04-14 22:09:50 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:09:50,828 - WARNING - Could not retrieve variants from source file in region 7:107002595-107002996. Error was invalid region `7:107002596-107002996`
[2016-04-15T05:09Z] 2016-04-14 22:09:51 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:09:51,302 - WARNING - Could not retrieve variants from source file in region 7:106848744-106849375. Error was invalid region `7:106848745-106849375`
[2016-04-15T05:09Z] 2016-04-14 22:09:52 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:09:52,492 - WARNING - Could not retrieve variants from source file in region 7:103007738-103008139. Error was invalid region `7:103007739-103008139`
[2016-04-15T05:09Z] 2016-04-14 22:09:52 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:09:52,644 - WARNING - Could not retrieve variants from source file in region 7:98649840-98650241. Error was invalid region `7:98649841-98650241`
[2016-04-15T05:09Z] 2016-04-14 22:09:53 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:09:53,147 - WARNING - Could not retrieve variants from source file in region 7:95726803-95727204. Error was invalid region `7:95726804-95727204`
[2016-04-15T05:09Z] 2016-04-14 22:09:54 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:09:54,856 - WARNING - Could not retrieve variants from source file in region 7:106799786-106800187. Error was invalid region `7:106799787-106800187`
[2016-04-15T05:09Z] 2016-04-14 22:09:56 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:09:56,044 - WARNING - Could not retrieve variants from source file in region 7:98460613-98461014. Error was invalid region `7:98460614-98461014`
[2016-04-15T05:09Z] 2016-04-14 22:09:57 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:09:57,026 - WARNING - Could not retrieve variants from source file in region 7:107002595-107002996. Error was invalid region `7:107002596-107002996`
[2016-04-15T05:09Z] 2016-04-14 22:09:57 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:09:57,147 - WARNING - Could not retrieve variants from source file in region 7:106799786-106800187. Error was invalid region `7:106799787-106800187`
[2016-04-15T05:09Z] 2016-04-14 22:09:57 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:09:57,171 - WARNING - Could not retrieve variants from source file in region 7:96746981-96747382. Error was invalid region `7:96746982-96747382`
[2016-04-15T05:09Z] 2016-04-14 22:09:57 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:09:57,388 - WARNING - Could not retrieve variants from source file in region 7:106848744-106849375. Error was invalid region `7:106848745-106849375`
[2016-04-15T05:09Z] 2016-04-14 22:09:57 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:09:57,533 - WARNING - Could not retrieve variants from source file in region 7:103007738-103008139. Error was invalid region `7:103007739-103008139`
[2016-04-15T05:09Z] 2016-04-14 22:09:57 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:09:57,930 - WARNING - Could not retrieve variants from source file in region 7:95726803-95727204. Error was invalid region `7:95726804-95727204`
[2016-04-15T05:09Z] 2016-04-14 22:09:59 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:09:59,804 - WARNING - Could not retrieve variants from source file in region 7:106799786-106800187. Error was invalid region `7:106799787-106800187`
[2016-04-15T05:10Z] 2016-04-14 22:10:00 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:10:00,638 - WARNING - Could not retrieve variants from source file in region 7:95001344-95041206. Error was invalid region `7:95001345-95041206`
[2016-04-15T05:10Z] 2016-04-14 22:10:02 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:10:02,305 - WARNING - Could not retrieve variants from source file in region 7:95001344-95041206. Error was invalid region `7:95001345-95041206`
[2016-04-15T05:10Z] 2016-04-14 22:10:02 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:10:02,933 - WARNING - Could not retrieve variants from source file in region 7:95001344-95041206. Error was invalid region `7:95001345-95041206`
[2016-04-15T05:10Z] 2016-04-14 22:10:07 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:10:07,526 - WARNING - Could not retrieve variants from source file in region 7:94937235-94946274. Error was invalid region `7:94937236-94946274`
[2016-04-15T05:10Z] 2016-04-14 22:10:07 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:10:07,997 - WARNING - Could not retrieve variants from source file in region 7:102937909-102938310. Error was invalid region `7:102937910-102938310`
[2016-04-15T05:10Z] 2016-04-14 22:10:08 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:10:08,715 - WARNING - Could not retrieve variants from source file in region 7:102667790-102668191. Error was invalid region `7:102667791-102668191`
[2016-04-15T05:10Z] 2016-04-14 22:10:11 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:10:11,014 - WARNING - Could not retrieve variants from source file in region 7:102789284-102789685. Error was invalid region `7:102789285-102789685`
[2016-04-15T05:10Z] 2016-04-14 22:10:12 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:10:12,046 - WARNING - Could not retrieve variants from source file in region 7:102667790-102668191. Error was invalid region `7:102667791-102668191`
[2016-04-15T05:10Z] 2016-04-14 22:10:12 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:10:12,094 - WARNING - Could not retrieve variants from source file in region 7:102743682-102760701. Error was invalid region `7:102743683-102760701`
[2016-04-15T05:10Z] 2016-04-14 22:10:12 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:10:12,107 - WARNING - Could not retrieve variants from source file in region 7:102574709-102575192. Error was invalid region `7:102574710-102575192`
[2016-04-15T05:10Z] 2016-04-14 22:10:12 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:10:12,260 - WARNING - Could not retrieve variants from source file in region 7:102667790-102668191. Error was invalid region `7:102667791-102668191`
[2016-04-15T05:10Z] 2016-04-14 22:10:14 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:10:14,493 - WARNING - Could not retrieve variants from source file in region 7:102789284-102789685. Error was invalid region `7:102789285-102789685`
[2016-04-15T05:10Z] 2016-04-14 22:10:15 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:10:15,217 - WARNING - Could not retrieve variants from source file in region 7:102789284-102789685. Error was invalid region `7:102789285-102789685`
[2016-04-15T05:10Z] ['bcbio-variation-recall', 'square', '-Xms750m', '-Xmx7280m', '-XX:+UseSerialGC', '-c', 16, '-r', u'7:110526649-126079222', '--caller', 'platypus', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/7/Batch1-7_110526648_126079222.vcf.gz', '/mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/7/Batch1-7_110526648_126079222.vcf-inputs.txt'] in region: 7:110526649-126079222
[2016-04-15T05:10Z] 2016-04-14 22:10:29 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:10:29,433 - WARNING - Could not retrieve variants from source file in region 7:112724206-112724715. Error was invalid region `7:112724207-112724715`
[2016-04-15T05:10Z] 2016-04-14 22:10:31 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:10:31,395 - WARNING - Could not retrieve variants from source file in region 7:122303110-122303511. Error was invalid region `7:122303111-122303511`
[2016-04-15T05:10Z] 2016-04-14 22:10:31 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:10:31,402 - WARNING - Could not retrieve variants from source file in region 7:116528029-116528430. Error was invalid region `7:116528030-116528430`
[2016-04-15T05:10Z] 2016-04-14 22:10:31 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:10:31,536 - WARNING - Could not retrieve variants from source file in region 7:123151808-123152418. Error was invalid region `7:123151809-123152418`
[2016-04-15T05:10Z] 2016-04-14 22:10:32 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:10:32,249 - WARNING - Could not retrieve variants from source file in region 7:120969558-120979279. Error was invalid region `7:120969559-120979279`
[2016-04-15T05:10Z] 2016-04-14 22:10:32 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:10:32,529 - WARNING - Could not retrieve variants from source file in region 7:120428588-120428989. Error was invalid region `7:120428589-120428989`
[2016-04-15T05:10Z] 2016-04-14 22:10:32 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:10:32,570 - WARNING - Could not retrieve variants from source file in region 7:123301729-123302130. Error was invalid region `7:123301730-123302130`
[2016-04-15T05:10Z] 2016-04-14 22:10:35 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:10:35,510 - WARNING - Could not retrieve variants from source file in region 7:112724206-112724715. Error was invalid region `7:112724207-112724715`
[2016-04-15T05:10Z] 2016-04-14 22:10:37 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:10:37,605 - WARNING - Could not retrieve variants from source file in region 7:113518223-113519986. Error was invalid region `7:113518224-113519986`
[2016-04-15T05:10Z] 2016-04-14 22:10:37 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:10:37,703 - WARNING - Could not retrieve variants from source file in region 7:120876624-120877025. Error was invalid region `7:120876625-120877025`
[2016-04-15T05:10Z] 2016-04-14 22:10:39 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:10:39,565 - WARNING - Could not retrieve variants from source file in region 7:116528029-116528430. Error was invalid region `7:116528030-116528430`
[2016-04-15T05:10Z] 2016-04-14 22:10:40 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:10:40,178 - WARNING - Could not retrieve variants from source file in region 7:112091999-112113082. Error was invalid region `7:112092000-112113082`
[2016-04-15T05:10Z] 2016-04-14 22:10:40 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:10:40,338 - WARNING - Could not retrieve variants from source file in region 7:114654027-114654428. Error was invalid region `7:114654028-114654428`
[2016-04-15T05:10Z] 2016-04-14 22:10:40 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:10:40,749 - WARNING - Could not retrieve variants from source file in region 7:122768708-122769109. Error was invalid region `7:122768709-122769109`
[2016-04-15T05:10Z] 2016-04-14 22:10:40 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:10:40,814 - WARNING - Could not retrieve variants from source file in region 7:121513350-121513751. Error was invalid region `7:121513351-121513751`
[2016-04-15T05:10Z] 2016-04-14 22:10:40 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:10:40,896 - WARNING - Could not retrieve variants from source file in region 7:117024609-117025010. Error was invalid region `7:117024610-117025010`
[2016-04-15T05:10Z] 2016-04-14 22:10:40 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:10:40,988 - WARNING - Could not retrieve variants from source file in region 7:120969558-120979279. Error was invalid region `7:120969559-120979279`
[2016-04-15T05:10Z] 2016-04-14 22:10:41 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:10:41,475 - WARNING - Could not retrieve variants from source file in region 7:124386881-124405173. Error was invalid region `7:124386882-124405173`
[2016-04-15T05:10Z] 2016-04-14 22:10:41 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:10:41,505 - WARNING - Could not retrieve variants from source file in region 7:120428588-120428989. Error was invalid region `7:120428589-120428989`
[2016-04-15T05:10Z] 2016-04-14 22:10:41 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:10:41,506 - WARNING - Could not retrieve variants from source file in region 7:112724206-112724715. Error was invalid region `7:112724207-112724715`
[2016-04-15T05:10Z] 2016-04-14 22:10:45 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:10:45,035 - WARNING - Could not retrieve variants from source file in region 7:122303110-122303511. Error was invalid region `7:122303111-122303511`
[2016-04-15T05:10Z] 2016-04-14 22:10:45 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:10:45,797 - WARNING - Could not retrieve variants from source file in region 7:116528029-116528430. Error was invalid region `7:116528030-116528430`
[2016-04-15T05:10Z] 2016-04-14 22:10:48 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:10:48,160 - WARNING - Could not retrieve variants from source file in region 7:114654027-114654428. Error was invalid region `7:114654028-114654428`
[2016-04-15T05:10Z] 2016-04-14 22:10:49 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:10:49,177 - WARNING - Could not retrieve variants from source file in region 7:120969558-120979279. Error was invalid region `7:120969559-120979279`
[2016-04-15T05:10Z] 2016-04-14 22:10:49 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:10:49,597 - WARNING - Could not retrieve variants from source file in region 7:123301729-123302130. Error was invalid region `7:123301730-123302130`
[2016-04-15T05:10Z] 2016-04-14 22:10:49 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:10:49,773 - WARNING - Could not retrieve variants from source file in region 7:120428588-120428989. Error was invalid region `7:120428589-120428989`
[2016-04-15T05:11Z] 2016-04-14 22:11:00 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:11:00,686 - WARNING - Could not retrieve variants from source file in region 7:112424439-112424840. Error was invalid region `7:112424440-112424840`
[2016-04-15T05:11Z] 2016-04-14 22:11:02 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:11:02,116 - WARNING - Could not retrieve variants from source file in region 7:121653163-121653588. Error was invalid region `7:121653164-121653588`
[2016-04-15T05:11Z] 2016-04-14 22:11:02 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:11:02,855 - WARNING - Could not retrieve variants from source file in region 7:120739892-120776287. Error was invalid region `7:120739893-120776287`
[2016-04-15T05:11Z] 2016-04-14 22:11:03 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:11:03,375 - WARNING - Could not retrieve variants from source file in region 7:111368280-111368681. Error was invalid region `7:111368281-111368681`
[2016-04-15T05:11Z] 2016-04-14 22:11:04 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:11:04,311 - WARNING - Could not retrieve variants from source file in region 7:123096983-123120180. Error was invalid region `7:123096984-123120180`
[2016-04-15T05:11Z] 2016-04-14 22:11:06 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:11:06,115 - WARNING - Could not retrieve variants from source file in region 7:123256216-123269308. Error was invalid region `7:123256217-123269308`
[2016-04-15T05:11Z] 2016-04-14 22:11:07 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:11:07,096 - WARNING - Could not retrieve variants from source file in region 7:123672245-123672652. Error was invalid region `7:123672246-123672652`
[2016-04-15T05:11Z] 2016-04-14 22:11:07 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:11:07,413 - WARNING - Could not retrieve variants from source file in region 7:122634813-122635214. Error was invalid region `7:122634814-122635214`
[2016-04-15T05:11Z] 2016-04-14 22:11:08 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:11:08,103 - WARNING - Could not retrieve variants from source file in region 7:120739892-120776287. Error was invalid region `7:120739893-120776287`
[2016-04-15T05:11Z] 2016-04-14 22:11:08 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:11:08,222 - WARNING - Could not retrieve variants from source file in region 7:115608144-115608545. Error was invalid region `7:115608145-115608545`
[2016-04-15T05:11Z] 2016-04-14 22:11:08 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:11:08,938 - WARNING - Could not retrieve variants from source file in region 7:114619387-114619879. Error was invalid region `7:114619388-114619879`
[2016-04-15T05:11Z] 2016-04-14 22:11:09 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:11:09,469 - WARNING - Could not retrieve variants from source file in region 7:111980796-111981197. Error was invalid region `7:111980797-111981197`
[2016-04-15T05:11Z] 2016-04-14 22:11:09 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:11:09,805 - WARNING - Could not retrieve variants from source file in region 7:112424439-112424840. Error was invalid region `7:112424440-112424840`
[2016-04-15T05:11Z] 2016-04-14 22:11:12 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:11:12,494 - WARNING - Could not retrieve variants from source file in region 7:123672245-123672652. Error was invalid region `7:123672246-123672652`
[2016-04-15T05:11Z] 2016-04-14 22:11:12 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:11:12,521 - WARNING - Could not retrieve variants from source file in region 7:121653163-121653588. Error was invalid region `7:121653164-121653588`
[2016-04-15T05:11Z] 2016-04-14 22:11:13 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:11:13,087 - WARNING - Could not retrieve variants from source file in region 7:116140064-116165653. Error was invalid region `7:116140065-116165653`
[2016-04-15T05:11Z] 2016-04-14 22:11:13 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:11:13,211 - WARNING - Could not retrieve variants from source file in region 7:120739892-120776287. Error was invalid region `7:120739893-120776287`
[2016-04-15T05:11Z] 2016-04-14 22:11:13 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:11:13,979 - WARNING - Could not retrieve variants from source file in region 7:111368280-111368681. Error was invalid region `7:111368281-111368681`
[2016-04-15T05:11Z] 2016-04-14 22:11:14 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:11:14,212 - WARNING - Could not retrieve variants from source file in region 7:115608144-115608545. Error was invalid region `7:115608145-115608545`
[2016-04-15T05:11Z] 2016-04-14 22:11:14 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:11:14,443 - WARNING - Could not retrieve variants from source file in region 7:123096983-123120180. Error was invalid region `7:123096984-123120180`
[2016-04-15T05:11Z] 2016-04-14 22:11:14 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:11:14,811 - WARNING - Could not retrieve variants from source file in region 7:123256216-123269308. Error was invalid region `7:123256217-123269308`
[2016-04-15T05:11Z] 2016-04-14 22:11:16 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:11:16,259 - WARNING - Could not retrieve variants from source file in region 7:120596306-120596823. Error was invalid region `7:120596307-120596823`
[2016-04-15T05:11Z] 2016-04-14 22:11:16 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:11:16,909 - WARNING - Could not retrieve variants from source file in region 7:123672245-123672652. Error was invalid region `7:123672246-123672652`
[2016-04-15T05:11Z] 2016-04-14 22:11:18 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:11:18,276 - WARNING - Could not retrieve variants from source file in region 7:116140064-116165653. Error was invalid region `7:116140065-116165653`
[2016-04-15T05:11Z] 2016-04-14 22:11:18 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:11:18,449 - WARNING - Could not retrieve variants from source file in region 7:122634813-122635214. Error was invalid region `7:122634814-122635214`
[2016-04-15T05:11Z] 2016-04-14 22:11:19 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:11:19,984 - WARNING - Could not retrieve variants from source file in region 7:115608144-115608545. Error was invalid region `7:115608145-115608545`
[2016-04-15T05:11Z] 2016-04-14 22:11:23 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:11:23,215 - WARNING - Could not retrieve variants from source file in region 7:122809023-122809424. Error was invalid region `7:122809024-122809424`
[2016-04-15T05:11Z] 2016-04-14 22:11:23 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:11:23,736 - WARNING - Could not retrieve variants from source file in region 7:123593995-123594396. Error was invalid region `7:123593996-123594396`
[2016-04-15T05:11Z] 2016-04-14 22:11:25 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:11:25,114 - WARNING - Could not retrieve variants from source file in region 7:122809023-122809424. Error was invalid region `7:122809024-122809424`
[2016-04-15T05:11Z] 2016-04-14 22:11:25 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:11:25,637 - WARNING - Could not retrieve variants from source file in region 7:122809023-122809424. Error was invalid region `7:122809024-122809424`
[2016-04-15T05:11Z] 2016-04-14 22:11:26 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:11:26,011 - WARNING - Could not retrieve variants from source file in region 7:121616039-121616440. Error was invalid region `7:121616040-121616440`
[2016-04-15T05:11Z] 2016-04-14 22:11:27 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:11:27,716 - WARNING - Could not retrieve variants from source file in region 7:121616039-121616440. Error was invalid region `7:121616040-121616440`
[2016-04-15T05:11Z] 2016-04-14 22:11:28 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:11:28,527 - WARNING - Could not retrieve variants from source file in region 7:123593995-123594396. Error was invalid region `7:123593996-123594396`
[2016-04-15T05:11Z] 2016-04-14 22:11:28 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:11:28,530 - WARNING - Could not retrieve variants from source file in region 7:121616039-121616440. Error was invalid region `7:121616040-121616440`
[2016-04-15T05:11Z] 2016-04-14 22:11:29 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:11:29,455 - WARNING - Could not retrieve variants from source file in region 7:110602581-110602982. Error was invalid region `7:110602582-110602982`
[2016-04-15T05:11Z] 2016-04-14 22:11:29 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:11:29,694 - WARNING - Could not retrieve variants from source file in region 7:123388521-123388922. Error was invalid region `7:123388522-123388922`
[2016-04-15T05:11Z] 2016-04-14 22:11:32 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:11:32,842 - WARNING - Could not retrieve variants from source file in region 7:110602581-110602982. Error was invalid region `7:110602582-110602982`
[2016-04-15T05:11Z] 2016-04-14 22:11:33 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:11:33,644 - WARNING - Could not retrieve variants from source file in region 7:123388521-123388922. Error was invalid region `7:123388522-123388922`
[2016-04-15T05:11Z] 2016-04-14 22:11:33 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:11:33,645 - WARNING - Could not retrieve variants from source file in region 7:117234844-117235245. Error was invalid region `7:117234845-117235245`
[2016-04-15T05:11Z] 2016-04-14 22:11:33 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:11:33,682 - WARNING - Could not retrieve variants from source file in region 7:110602581-110602982. Error was invalid region `7:110602582-110602982`
[2016-04-15T05:11Z] ['bcbio-variation-recall', 'square', '-Xms750m', '-Xmx7280m', '-XX:+UseSerialGC', '-c', 16, '-r', u'7:126086125-141619620', '--caller', 'platypus', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/7/Batch1-7_126086124_141619620.vcf.gz', '/mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/7/Batch1-7_126086124_141619620.vcf-inputs.txt'] in region: 7:126086125-141619620
[2016-04-15T05:11Z] 2016-04-14 22:11:51 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:11:51,940 - WARNING - Could not retrieve variants from source file in region 7:129813527-129813928. Error was invalid region `7:129813528-129813928`
[2016-04-15T05:11Z] 2016-04-14 22:11:52 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:11:52,378 - WARNING - Could not retrieve variants from source file in region 7:129916304-130016304. Error was invalid region `7:129916305-130016304`
[2016-04-15T05:11Z] 2016-04-14 22:11:52 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:11:52,385 - WARNING - Could not retrieve variants from source file in region 7:130016304-130021678. Error was invalid region `7:130016305-130021678`
[2016-04-15T05:11Z] 2016-04-14 22:11:53 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:11:53,271 - WARNING - Could not retrieve variants from source file in region 7:138455777-138456178. Error was invalid region `7:138455778-138456178`
[2016-04-15T05:11Z] 2016-04-14 22:11:53 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:11:53,918 - WARNING - Could not retrieve variants from source file in region 7:137600479-137613106. Error was invalid region `7:137600480-137613106`
[2016-04-15T05:11Z] 2016-04-14 22:11:54 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:11:54,152 - WARNING - Could not retrieve variants from source file in region 7:136935766-136936167. Error was invalid region `7:136935767-136936167`
[2016-04-15T05:11Z] 2016-04-14 22:11:54 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:11:54,215 - WARNING - Could not retrieve variants from source file in region 7:128530065-128550871. Error was invalid region `7:128530066-128550871`
[2016-04-15T05:11Z] 2016-04-14 22:11:54 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:11:54,405 - WARNING - Could not retrieve variants from source file in region 7:128807521-128807976. Error was invalid region `7:128807522-128807976`
[2016-04-15T05:11Z] 2016-04-14 22:11:54 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:11:54,751 - WARNING - Could not retrieve variants from source file in region 7:133748953-133749354. Error was invalid region `7:133748954-133749354`
[2016-04-15T05:11Z] 2016-04-14 22:11:59 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:11:59,147 - WARNING - Could not retrieve variants from source file in region 7:135329479-135333362. Error was invalid region `7:135329480-135333362`
[2016-04-15T05:12Z] 2016-04-14 22:12:00 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:12:00,558 - WARNING - Could not retrieve variants from source file in region 7:129015300-129040343. Error was invalid region `7:129015301-129040343`
[2016-04-15T05:12Z] 2016-04-14 22:12:01 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:12:01,108 - WARNING - Could not retrieve variants from source file in region 7:138455777-138456178. Error was invalid region `7:138455778-138456178`
[2016-04-15T05:12Z] 2016-04-14 22:12:01 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:12:01,485 - WARNING - Could not retrieve variants from source file in region 7:138732246-138764423. Error was invalid region `7:138732247-138764423`
[2016-04-15T05:12Z] 2016-04-14 22:12:01 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:12:01,795 - WARNING - Could not retrieve variants from source file in region 7:134678042-134719741. Error was invalid region `7:134678043-134719741`
[2016-04-15T05:12Z] 2016-04-14 22:12:02 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:12:02,226 - WARNING - Could not retrieve variants from source file in region 7:140050880-140051281. Error was invalid region `7:140050881-140051281`
[2016-04-15T05:12Z] 2016-04-14 22:12:02 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:12:02,315 - WARNING - Could not retrieve variants from source file in region 7:137600479-137613106. Error was invalid region `7:137600480-137613106`
[2016-04-15T05:12Z] 2016-04-14 22:12:02 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:12:02,664 - WARNING - Could not retrieve variants from source file in region 7:139208521-139208922. Error was invalid region `7:139208522-139208922`
[2016-04-15T05:12Z] 2016-04-14 22:12:02 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:12:02,760 - WARNING - Could not retrieve variants from source file in region 7:141537524-141538280. Error was invalid region `7:141537525-141538280`
[2016-04-15T05:12Z] 2016-04-14 22:12:05 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:12:05,890 - WARNING - Could not retrieve variants from source file in region 7:129015300-129040343. Error was invalid region `7:129015301-129040343`
[2016-04-15T05:12Z] 2016-04-14 22:12:07 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:12:07,792 - WARNING - Could not retrieve variants from source file in region 7:138455777-138456178. Error was invalid region `7:138455778-138456178`
[2016-04-15T05:12Z] 2016-04-14 22:12:08 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:12:08,761 - WARNING - Could not retrieve variants from source file in region 7:134678042-134719741. Error was invalid region `7:134678043-134719741`
[2016-04-15T05:12Z] 2016-04-14 22:12:09 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:12:09,337 - WARNING - Could not retrieve variants from source file in region 7:128807521-128807976. Error was invalid region `7:128807522-128807976`
[2016-04-15T05:12Z] 2016-04-14 22:12:09 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:12:09,683 - WARNING - Could not retrieve variants from source file in region 7:136935766-136936167. Error was invalid region `7:136935767-136936167`
[2016-04-15T05:12Z] 2016-04-14 22:12:10 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:12:10,189 - WARNING - Could not retrieve variants from source file in region 7:129663285-129668936. Error was invalid region `7:129663286-129668936`
[2016-04-15T05:12Z] 2016-04-14 22:12:10 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:12:10,350 - WARNING - Could not retrieve variants from source file in region 7:137600479-137613106. Error was invalid region `7:137600480-137613106`
[2016-04-15T05:12Z] 2016-04-14 22:12:10 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:12:10,557 - WARNING - Could not retrieve variants from source file in region 7:133748953-133749354. Error was invalid region `7:133748954-133749354`
[2016-04-15T05:12Z] 2016-04-14 22:12:10 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:12:10,644 - WARNING - Could not retrieve variants from source file in region 7:141537524-141538280. Error was invalid region `7:141537525-141538280`
[2016-04-15T05:12Z] 2016-04-14 22:12:22 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:12:22,778 - WARNING - Could not retrieve variants from source file in region 7:129855626-129856027. Error was invalid region `7:129855627-129856027`
[2016-04-15T05:12Z] 2016-04-14 22:12:23 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:12:23,909 - WARNING - Could not retrieve variants from source file in region 7:128846117-128865320. Error was invalid region `7:128846118-128865320`
[2016-04-15T05:12Z] 2016-04-14 22:12:23 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:12:23,949 - WARNING - Could not retrieve variants from source file in region 7:138417507-138419100. Error was invalid region `7:138417508-138419100`
[2016-04-15T05:12Z] 2016-04-14 22:12:25 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:12:25,087 - WARNING - Could not retrieve variants from source file in region 7:138583629-138603106. Error was invalid region `7:138583630-138603106`
[2016-04-15T05:12Z] 2016-04-14 22:12:25 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:12:25,505 - WARNING - Could not retrieve variants from source file in region 7:128641015-128641416. Error was invalid region `7:128641016-128641416`
[2016-04-15T05:12Z] 2016-04-14 22:12:26 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:12:26,300 - WARNING - Could not retrieve variants from source file in region 7:135614529-135614930. Error was invalid region `7:135614530-135614930`
[2016-04-15T05:12Z] 2016-04-14 22:12:26 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:12:26,643 - WARNING - Could not retrieve variants from source file in region 7:133689518-133689919. Error was invalid region `7:133689519-133689919`
[2016-04-15T05:12Z] 2016-04-14 22:12:27 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:12:27,351 - WARNING - Could not retrieve variants from source file in region 7:139167723-139168253. Error was invalid region `7:139167724-139168253`
[2016-04-15T05:12Z] 2016-04-14 22:12:28 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:12:28,466 - WARNING - Could not retrieve variants from source file in region 7:135269444-135304463. Error was invalid region `7:135269445-135304463`
[2016-04-15T05:12Z] 2016-04-14 22:12:28 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:12:28,950 - WARNING - Could not retrieve variants from source file in region 7:139138660-139139061. Error was invalid region `7:139138661-139139061`
[2016-04-15T05:12Z] 2016-04-14 22:12:29 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:12:29,467 - WARNING - Could not retrieve variants from source file in region 7:129855626-129856027. Error was invalid region `7:129855627-129856027`
[2016-04-15T05:12Z] 2016-04-14 22:12:30 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:12:30,901 - WARNING - Could not retrieve variants from source file in region 7:138417507-138419100. Error was invalid region `7:138417508-138419100`
[2016-04-15T05:12Z] 2016-04-14 22:12:30 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:12:30,925 - WARNING - Could not retrieve variants from source file in region 7:139797220-139801967. Error was invalid region `7:139797221-139801967`
[2016-04-15T05:12Z] 2016-04-14 22:12:31 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:12:31,664 - WARNING - Could not retrieve variants from source file in region 7:134645108-134645509. Error was invalid region `7:134645109-134645509`
[2016-04-15T05:12Z] 2016-04-14 22:12:31 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:12:31,958 - WARNING - Could not retrieve variants from source file in region 7:141464554-141490428. Error was invalid region `7:141464555-141490428`
[2016-04-15T05:12Z] 2016-04-14 22:12:31 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:12:31,985 - WARNING - Could not retrieve variants from source file in region 7:135614529-135614930. Error was invalid region `7:135614530-135614930`
[2016-04-15T05:12Z] 2016-04-14 22:12:32 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:12:32,043 - WARNING - Could not retrieve variants from source file in region 7:128641015-128641416. Error was invalid region `7:128641016-128641416`
[2016-04-15T05:12Z] 2016-04-14 22:12:34 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:12:34,613 - WARNING - Could not retrieve variants from source file in region 7:135047492-135095460. Error was invalid region `7:135047493-135095460`
[2016-04-15T05:12Z] 2016-04-14 22:12:35 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:12:35,537 - WARNING - Could not retrieve variants from source file in region 7:129855626-129856027. Error was invalid region `7:129855627-129856027`
[2016-04-15T05:12Z] 2016-04-14 22:12:37 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:12:37,217 - WARNING - Could not retrieve variants from source file in region 7:128455556-128488056. Error was invalid region `7:128455557-128488056`
[2016-04-15T05:12Z] 2016-04-14 22:12:38 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:12:38,173 - WARNING - Could not retrieve variants from source file in region 7:134645108-134645509. Error was invalid region `7:134645109-134645509`
[2016-04-15T05:12Z] 2016-04-14 22:12:39 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:12:39,049 - WARNING - Could not retrieve variants from source file in region 7:138417507-138419100. Error was invalid region `7:138417508-138419100`
[2016-04-15T05:12Z] 2016-04-14 22:12:39 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:12:39,057 - WARNING - Could not retrieve variants from source file in region 7:138583629-138603106. Error was invalid region `7:138583630-138603106`
[2016-04-15T05:12Z] 2016-04-14 22:12:39 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:12:39,097 - WARNING - Could not retrieve variants from source file in region 7:141464554-141490428. Error was invalid region `7:141464555-141490428`
[2016-04-15T05:12Z] 2016-04-14 22:12:39 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:12:39,229 - WARNING - Could not retrieve variants from source file in region 7:135614529-135614930. Error was invalid region `7:135614530-135614930`
[2016-04-15T05:12Z] 2016-04-14 22:12:39 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:12:39,260 - WARNING - Could not retrieve variants from source file in region 7:128641015-128641416. Error was invalid region `7:128641016-128641416`
[2016-04-15T05:12Z] 2016-04-14 22:12:39 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:12:39,419 - WARNING - Could not retrieve variants from source file in region 7:139138660-139139061. Error was invalid region `7:139138661-139139061`
[2016-04-15T05:12Z] 2016-04-14 22:12:41 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:12:41,651 - WARNING - Could not retrieve variants from source file in region 7:137128619-137150885. Error was invalid region `7:137128620-137150885`
[2016-04-15T05:12Z] 2016-04-14 22:12:43 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:12:43,464 - WARNING - Could not retrieve variants from source file in region 7:139797220-139801967. Error was invalid region `7:139797221-139801967`
[2016-04-15T05:12Z] 2016-04-14 22:12:45 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:12:45,338 - WARNING - Could not retrieve variants from source file in region 7:141464554-141490428. Error was invalid region `7:141464555-141490428`
[2016-04-15T05:12Z] 2016-04-14 22:12:49 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:12:49,576 - WARNING - Could not retrieve variants from source file in region 7:134925200-134925601. Error was invalid region `7:134925201-134925601`
[2016-04-15T05:12Z] 2016-04-14 22:12:53 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:12:53,715 - WARNING - Could not retrieve variants from source file in region 7:132657469-132658274. Error was invalid region `7:132657470-132658274`
[2016-04-15T05:12Z] 2016-04-14 22:12:54 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:12:54,198 - WARNING - Could not retrieve variants from source file in region 7:134618499-134618900. Error was invalid region `7:134618500-134618900`
[2016-04-15T05:12Z] 2016-04-14 22:12:54 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:12:54,772 - WARNING - Could not retrieve variants from source file in region 7:128587140-128607574. Error was invalid region `7:128587141-128607574`
[2016-04-15T05:12Z] 2016-04-14 22:12:55 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:12:55,430 - WARNING - Could not retrieve variants from source file in region 7:134925200-134925601. Error was invalid region `7:134925201-134925601`
[2016-04-15T05:12Z] 2016-04-14 22:12:55 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:12:55,435 - WARNING - Could not retrieve variants from source file in region 7:138344841-138363957. Error was invalid region `7:138344842-138363957`
[2016-04-15T05:12Z] 2016-04-14 22:12:56 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:12:56,676 - WARNING - Could not retrieve variants from source file in region 7:139059753-139060154. Error was invalid region `7:139059754-139060154`
[2016-04-15T05:12Z] 2016-04-14 22:12:57 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:12:57,228 - WARNING - Could not retrieve variants from source file in region 7:139025941-139026342. Error was invalid region `7:139025942-139026342`
[2016-04-15T05:12Z] 2016-04-14 22:12:58 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:12:58,372 - WARNING - Could not retrieve variants from source file in region 7:139715434-139746983. Error was invalid region `7:139715435-139746983`
[2016-04-15T05:12Z] 2016-04-14 22:12:59 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:12:59,513 - WARNING - Could not retrieve variants from source file in region 7:141137249-141137650. Error was invalid region `7:141137250-141137650`
[2016-04-15T05:13Z] 2016-04-14 22:13:00 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:13:00,169 - WARNING - Could not retrieve variants from source file in region 7:128587140-128607574. Error was invalid region `7:128587141-128607574`
[2016-04-15T05:13Z] 2016-04-14 22:13:00 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:13:00,189 - WARNING - Could not retrieve variants from source file in region 7:134925200-134925601. Error was invalid region `7:134925201-134925601`
[2016-04-15T05:13Z] 2016-04-14 22:13:00 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:13:00,468 - WARNING - Could not retrieve variants from source file in region 7:134849002-134889331. Error was invalid region `7:134849003-134889331`
[2016-04-15T05:13Z] 2016-04-14 22:13:01 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:13:01,995 - WARNING - Could not retrieve variants from source file in region 7:138545785-138546186. Error was invalid region `7:138545786-138546186`
[2016-04-15T05:13Z] 2016-04-14 22:13:03 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:13:03,428 - WARNING - Could not retrieve variants from source file in region 7:132657469-132658274. Error was invalid region `7:132657470-132658274`
[2016-04-15T05:13Z] 2016-04-14 22:13:04 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:13:04,576 - WARNING - Could not retrieve variants from source file in region 7:141137249-141137650. Error was invalid region `7:141137250-141137650`
[2016-04-15T05:13Z] 2016-04-14 22:13:04 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:13:04,610 - WARNING - Could not retrieve variants from source file in region 7:128587140-128607574. Error was invalid region `7:128587141-128607574`
[2016-04-15T05:13Z] 2016-04-14 22:13:05 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:13:05,102 - WARNING - Could not retrieve variants from source file in region 7:138344841-138363957. Error was invalid region `7:138344842-138363957`
[2016-04-15T05:13Z] 2016-04-14 22:13:06 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:13:06,087 - WARNING - Could not retrieve variants from source file in region 7:139059753-139060154. Error was invalid region `7:139059754-139060154`
[2016-04-15T05:13Z] 2016-04-14 22:13:06 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:13:06,476 - WARNING - Could not retrieve variants from source file in region 7:138545785-138546186. Error was invalid region `7:138545786-138546186`
[2016-04-15T05:13Z] 2016-04-14 22:13:06 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:13:06,989 - WARNING - Could not retrieve variants from source file in region 7:139025941-139026342. Error was invalid region `7:139025942-139026342`
[2016-04-15T05:13Z] 2016-04-14 22:13:07 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:13:07,658 - WARNING - Could not retrieve variants from source file in region 7:139715434-139746983. Error was invalid region `7:139715435-139746983`
[2016-04-15T05:13Z] 2016-04-14 22:13:09 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:13:09,429 - WARNING - Could not retrieve variants from source file in region 7:141137249-141137650. Error was invalid region `7:141137250-141137650`
[2016-04-15T05:13Z] 2016-04-14 22:13:16 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:13:16,800 - WARNING - Could not retrieve variants from source file in region 7:134258064-134264476. Error was invalid region `7:134258065-134264476`
[2016-04-15T05:13Z] 2016-04-14 22:13:17 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:13:17,872 - WARNING - Could not retrieve variants from source file in region 7:132192084-132193139. Error was invalid region `7:132192085-132193139`
[2016-04-15T05:13Z] 2016-04-14 22:13:18 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:13:18,041 - WARNING - Could not retrieve variants from source file in region 7:139652985-139653386. Error was invalid region `7:139652986-139653386`
[2016-04-15T05:13Z] 2016-04-14 22:13:18 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:13:18,507 - WARNING - Could not retrieve variants from source file in region 7:134215192-134226017. Error was invalid region `7:134215193-134226017`
[2016-04-15T05:13Z] 2016-04-14 22:13:19 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:13:19,401 - WARNING - Could not retrieve variants from source file in region 7:138311911-138312312. Error was invalid region `7:138311912-138312312`
[2016-04-15T05:13Z] 2016-04-14 22:13:19 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:13:19,828 - WARNING - Could not retrieve variants from source file in region 7:139259827-139289127. Error was invalid region `7:139259828-139289127`
[2016-04-15T05:13Z] 2016-04-14 22:13:20 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:13:20,492 - WARNING - Could not retrieve variants from source file in region 7:138485885-138486286. Error was invalid region `7:138485886-138486286`
[2016-04-15T05:13Z] 2016-04-14 22:13:20 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:13:20,593 - WARNING - Could not retrieve variants from source file in region 7:131240818-131241219. Error was invalid region `7:131240819-131241219`
[2016-04-15T05:13Z] 2016-04-14 22:13:21 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:13:21,017 - WARNING - Could not retrieve variants from source file in region 7:127721296-127721697. Error was invalid region `7:127721297-127721697`
[2016-04-15T05:13Z] 2016-04-14 22:13:21 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:13:21,535 - WARNING - Could not retrieve variants from source file in region 7:130827488-130827889. Error was invalid region `7:130827489-130827889`
[2016-04-15T05:13Z] 2016-04-14 22:13:21 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:13:21,634 - WARNING - Could not retrieve variants from source file in region 7:134258064-134264476. Error was invalid region `7:134258065-134264476`
[2016-04-15T05:13Z] 2016-04-14 22:13:23 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:13:23,039 - WARNING - Could not retrieve variants from source file in region 7:128038344-128038745. Error was invalid region `7:128038345-128038745`
[2016-04-15T05:13Z] 2016-04-14 22:13:23 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:13:23,440 - WARNING - Could not retrieve variants from source file in region 7:139652985-139653386. Error was invalid region `7:139652986-139653386`
[2016-04-15T05:13Z] 2016-04-14 22:13:24 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:13:24,213 - WARNING - Could not retrieve variants from source file in region 7:138311911-138312312. Error was invalid region `7:138311912-138312312`
[2016-04-15T05:13Z] 2016-04-14 22:13:24 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:13:24,364 - WARNING - Could not retrieve variants from source file in region 7:128173509-128173910. Error was invalid region `7:128173510-128173910`
[2016-04-15T05:13Z] 2016-04-14 22:13:25 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:13:25,338 - WARNING - Could not retrieve variants from source file in region 7:138485885-138486286. Error was invalid region `7:138485886-138486286`
[2016-04-15T05:13Z] 2016-04-14 22:13:25 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:13:25,923 - WARNING - Could not retrieve variants from source file in region 7:127721296-127721697. Error was invalid region `7:127721297-127721697`
[2016-04-15T05:13Z] 2016-04-14 22:13:26 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:13:26,107 - WARNING - Could not retrieve variants from source file in region 7:131240818-131241219. Error was invalid region `7:131240819-131241219`
[2016-04-15T05:13Z] 2016-04-14 22:13:28 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:13:28,929 - WARNING - Could not retrieve variants from source file in region 7:140774256-140774657. Error was invalid region `7:140774257-140774657`
[2016-04-15T05:13Z] 2016-04-14 22:13:28 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:13:28,930 - WARNING - Could not retrieve variants from source file in region 7:139652985-139653386. Error was invalid region `7:139652986-139653386`
[2016-04-15T05:13Z] 2016-04-14 22:13:29 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:13:29,555 - WARNING - Could not retrieve variants from source file in region 7:138311911-138312312. Error was invalid region `7:138311912-138312312`
[2016-04-15T05:13Z] 2016-04-14 22:13:29 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:13:29,631 - WARNING - Could not retrieve variants from source file in region 7:128173509-128173910. Error was invalid region `7:128173510-128173910`
[2016-04-15T05:13Z] 2016-04-14 22:13:30 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:13:30,248 - WARNING - Could not retrieve variants from source file in region 7:138485885-138486286. Error was invalid region `7:138485886-138486286`
[2016-04-15T05:13Z] 2016-04-14 22:13:30 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:13:30,784 - WARNING - Could not retrieve variants from source file in region 7:127721296-127721697. Error was invalid region `7:127721297-127721697`
[2016-04-15T05:13Z] 2016-04-14 22:13:30 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:13:30,955 - WARNING - Could not retrieve variants from source file in region 7:131240818-131241219. Error was invalid region `7:131240819-131241219`
[2016-04-15T05:13Z] 2016-04-14 22:13:31 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:13:31,398 - WARNING - Could not retrieve variants from source file in region 7:130827488-130827889. Error was invalid region `7:130827489-130827889`
[2016-04-15T05:13Z] 2016-04-14 22:13:32 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:13:32,223 - WARNING - Could not retrieve variants from source file in region 7:128119303-128142055. Error was invalid region `7:128119304-128142055`
[2016-04-15T05:13Z] 2016-04-14 22:13:34 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:13:34,510 - WARNING - Could not retrieve variants from source file in region 7:140774256-140774657. Error was invalid region `7:140774257-140774657`
[2016-04-15T05:13Z] 2016-04-14 22:13:41 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:13:41,400 - WARNING - Could not retrieve variants from source file in region 7:133906458-133906859. Error was invalid region `7:133906459-133906859`
[2016-04-15T05:13Z] 2016-04-14 22:13:43 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:13:43,201 - WARNING - Could not retrieve variants from source file in region 7:138281144-138282096. Error was invalid region `7:138281145-138282096`
[2016-04-15T05:13Z] 2016-04-14 22:13:45 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:13:45,082 - WARNING - Could not retrieve variants from source file in region 7:133848046-133868697. Error was invalid region `7:133848047-133868697`
[2016-04-15T05:13Z] 2016-04-14 22:13:45 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:13:45,411 - WARNING - Could not retrieve variants from source file in region 7:127250696-127255475. Error was invalid region `7:127250697-127255475`
[2016-04-15T05:13Z] 2016-04-14 22:13:47 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:13:47,010 - WARNING - Could not retrieve variants from source file in region 7:127990922-127999811. Error was invalid region `7:127990923-127999811`
[2016-04-15T05:13Z] 2016-04-14 22:13:47 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:13:47,270 - WARNING - Could not retrieve variants from source file in region 7:138281144-138282096. Error was invalid region `7:138281145-138282096`
[2016-04-15T05:13Z] 2016-04-14 22:13:49 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:13:49,445 - WARNING - Could not retrieve variants from source file in region 7:133979584-133979985. Error was invalid region `7:133979585-133979985`
[2016-04-15T05:13Z] 2016-04-14 22:13:51 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:13:51,213 - WARNING - Could not retrieve variants from source file in region 7:138281144-138282096. Error was invalid region `7:138281145-138282096`
[2016-04-15T05:13Z] 2016-04-14 22:13:51 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:13:51,713 - WARNING - Could not retrieve variants from source file in region 7:127990922-127999811. Error was invalid region `7:127990923-127999811`
[2016-04-15T05:13Z] 2016-04-14 22:13:53 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:13:53,563 - WARNING - Could not retrieve variants from source file in region 7:130056901-130059612. Error was invalid region `7:130056902-130059612`
[2016-04-15T05:13Z] 2016-04-14 22:13:54 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:13:54,039 - WARNING - Could not retrieve variants from source file in region 7:133979584-133979985. Error was invalid region `7:133979585-133979985`
[2016-04-15T05:13Z] 2016-04-14 22:13:54 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:13:54,280 - WARNING - Could not retrieve variants from source file in region 7:131190485-131196149. Error was invalid region `7:131190486-131196149`
[2016-04-15T05:13Z] 2016-04-14 22:13:54 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:13:54,741 - WARNING - Could not retrieve variants from source file in region 7:127250696-127255475. Error was invalid region `7:127250697-127255475`
[2016-04-15T05:13Z] 2016-04-14 22:13:56 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:13:56,111 - WARNING - Could not retrieve variants from source file in region 7:140244349-140258190. Error was invalid region `7:140244350-140258190`
[2016-04-15T05:14Z] 2016-04-14 22:14:03 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:14:03,126 - WARNING - Could not retrieve variants from source file in region 7:133812009-133812410. Error was invalid region `7:133812010-133812410`
[2016-04-15T05:14Z] 2016-04-14 22:14:03 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:14:03,129 - WARNING - Could not retrieve variants from source file in region 7:133812009-133812410. Error was invalid region `7:133812010-133812410`
[2016-04-15T05:14Z] 2016-04-14 22:14:03 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:14:03,879 - WARNING - Could not retrieve variants from source file in region 7:140301520-140301921. Error was invalid region `7:140301521-140301921`
[2016-04-15T05:14Z] 2016-04-14 22:14:03 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:14:03,905 - WARNING - Could not retrieve variants from source file in region 7:140301520-140301921. Error was invalid region `7:140301521-140301921`
[2016-04-15T05:14Z] 2016-04-14 22:14:03 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:14:03,918 - WARNING - Could not retrieve variants from source file in region 7:140301520-140301921. Error was invalid region `7:140301521-140301921`
[2016-04-15T05:14Z] 2016-04-14 22:14:03 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:14:03,950 - WARNING - Could not retrieve variants from source file in region 7:140158640-140159041. Error was invalid region `7:140158641-140159041`
[2016-04-15T05:14Z] 2016-04-14 22:14:06 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:14:06,958 - WARNING - Could not retrieve variants from source file in region 7:127221946-127224476. Error was invalid region `7:127221947-127224476`
[2016-04-15T05:14Z] 2016-04-14 22:14:06 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:14:06,967 - WARNING - Could not retrieve variants from source file in region 7:140079876-140080277. Error was invalid region `7:140079877-140080277`
[2016-04-15T05:14Z] 2016-04-14 22:14:07 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:14:07,645 - WARNING - Could not retrieve variants from source file in region 7:140158640-140159041. Error was invalid region `7:140158641-140159041`
[2016-04-15T05:14Z] ['bcbio-variation-recall', 'square', '-Xms750m', '-Xmx7280m', '-XX:+UseSerialGC', '-c', 16, '-r', u'7:141629904-157151331', '--caller', 'platypus', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/7/Batch1-7_141629903_157151331.vcf.gz', '/mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/7/Batch1-7_141629903_157151331.vcf-inputs.txt'] in region: 7:141629904-157151331
[2016-04-15T05:14Z] 2016-04-14 22:14:23 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:14:23,577 - WARNING - Could not retrieve variants from source file in region 7:156999965-157000366. Error was invalid region `7:156999966-157000366`
[2016-04-15T05:14Z] 2016-04-14 22:14:24 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:14:24,425 - WARNING - Could not retrieve variants from source file in region 7:154737124-154737525. Error was invalid region `7:154737125-154737525`
[2016-04-15T05:14Z] 2016-04-14 22:14:24 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:14:24,664 - WARNING - Could not retrieve variants from source file in region 7:150033973-150037850. Error was invalid region `7:150033974-150037850`
[2016-04-15T05:14Z] 2016-04-14 22:14:24 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:14:24,773 - WARNING - Could not retrieve variants from source file in region 7:142835992-142836393. Error was invalid region `7:142835993-142836393`
[2016-04-15T05:14Z] 2016-04-14 22:14:25 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:14:25,383 - WARNING - Could not retrieve variants from source file in region 7:148106279-148106680. Error was invalid region `7:148106280-148106680`
[2016-04-15T05:14Z] 2016-04-14 22:14:25 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:14:25,629 - WARNING - Could not retrieve variants from source file in region 7:142626338-142650665. Error was invalid region `7:142626339-142650665`
[2016-04-15T05:14Z] 2016-04-14 22:14:26 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:14:26,103 - WARNING - Could not retrieve variants from source file in region 7:156974143-156974544. Error was invalid region `7:156974144-156974544`
[2016-04-15T05:14Z] 2016-04-14 22:14:26 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:14:26,271 - WARNING - Could not retrieve variants from source file in region 7:155251222-155255522. Error was invalid region `7:155251223-155255522`
[2016-04-15T05:14Z] 2016-04-14 22:14:26 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:14:26,369 - WARNING - Could not retrieve variants from source file in region 7:155503709-155504110. Error was invalid region `7:155503710-155504110`
[2016-04-15T05:14Z] 2016-04-14 22:14:29 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:14:29,778 - WARNING - Could not retrieve variants from source file in region 7:156999965-157000366. Error was invalid region `7:156999966-157000366`
[2016-04-15T05:14Z] 2016-04-14 22:14:30 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:14:30,183 - WARNING - Could not retrieve variants from source file in region 7:148920929-148937068. Error was invalid region `7:148920930-148937068`
[2016-04-15T05:14Z] 2016-04-14 22:14:30 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:14:30,737 - WARNING - Could not retrieve variants from source file in region 7:143579556-143582457. Error was invalid region `7:143579557-143582457`
[2016-04-15T05:14Z] 2016-04-14 22:14:30 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:14:30,785 - WARNING - Could not retrieve variants from source file in region 7:154737124-154737525. Error was invalid region `7:154737125-154737525`
[2016-04-15T05:14Z] 2016-04-14 22:14:32 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:14:32,820 - WARNING - Could not retrieve variants from source file in region 7:150033973-150037850. Error was invalid region `7:150033974-150037850`
[2016-04-15T05:14Z] 2016-04-14 22:14:33 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:14:33,989 - WARNING - Could not retrieve variants from source file in region 7:148106279-148106680. Error was invalid region `7:148106280-148106680`
[2016-04-15T05:14Z] 2016-04-14 22:14:34 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:14:34,113 - WARNING - Could not retrieve variants from source file in region 7:155251222-155255522. Error was invalid region `7:155251223-155255522`
[2016-04-15T05:14Z] 2016-04-14 22:14:34 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:14:34,303 - WARNING - Could not retrieve variants from source file in region 7:149426094-149427599. Error was invalid region `7:149426095-149427599`
[2016-04-15T05:14Z] 2016-04-14 22:14:34 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:14:34,311 - WARNING - Could not retrieve variants from source file in region 7:142749526-142750337. Error was invalid region `7:142749527-142750337`
[2016-04-15T05:14Z] 2016-04-14 22:14:34 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:14:34,613 - WARNING - Could not retrieve variants from source file in region 7:155503709-155504110. Error was invalid region `7:155503710-155504110`
[2016-04-15T05:14Z] 2016-04-14 22:14:34 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:14:34,790 - WARNING - Could not retrieve variants from source file in region 7:156999965-157000366. Error was invalid region `7:156999966-157000366`
[2016-04-15T05:14Z] 2016-04-14 22:14:36 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:14:36,025 - WARNING - Could not retrieve variants from source file in region 7:154737124-154737525. Error was invalid region `7:154737125-154737525`
[2016-04-15T05:14Z] 2016-04-14 22:14:36 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:14:36,344 - WARNING - Could not retrieve variants from source file in region 7:143579556-143582457. Error was invalid region `7:143579557-143582457`
[2016-04-15T05:14Z] 2016-04-14 22:14:41 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:14:41,496 - WARNING - Could not retrieve variants from source file in region 7:156974143-156974544. Error was invalid region `7:156974144-156974544`
[2016-04-15T05:14Z] 2016-04-14 22:14:41 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:14:41,726 - WARNING - Could not retrieve variants from source file in region 7:142626338-142650665. Error was invalid region `7:142626339-142650665`
[2016-04-15T05:14Z] 2016-04-14 22:14:41 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:14:41,913 - WARNING - Could not retrieve variants from source file in region 7:148106279-148106680. Error was invalid region `7:148106280-148106680`
[2016-04-15T05:14Z] 2016-04-14 22:14:42 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:14:42,129 - WARNING - Could not retrieve variants from source file in region 7:149426094-149427599. Error was invalid region `7:149426095-149427599`
[2016-04-15T05:14Z] 2016-04-14 22:14:42 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:14:42,170 - WARNING - Could not retrieve variants from source file in region 7:142749526-142750337. Error was invalid region `7:142749527-142750337`
[2016-04-15T05:14Z] 2016-04-14 22:14:42 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:14:42,573 - WARNING - Could not retrieve variants from source file in region 7:155503709-155504110. Error was invalid region `7:155503710-155504110`
[2016-04-15T05:14Z] 2016-04-14 22:14:53 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:14:53,152 - WARNING - Could not retrieve variants from source file in region 7:148848147-148851403. Error was invalid region `7:148848148-148851403`
[2016-04-15T05:14Z] 2016-04-14 22:14:53 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:14:53,771 - WARNING - Could not retrieve variants from source file in region 7:148800880-148801848. Error was invalid region `7:148800881-148801848`
[2016-04-15T05:14Z] 2016-04-14 22:14:56 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:14:56,064 - WARNING - Could not retrieve variants from source file in region 7:148848147-148851403. Error was invalid region `7:148848148-148851403`
[2016-04-15T05:14Z] 2016-04-14 22:14:57 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:14:57,295 - WARNING - Could not retrieve variants from source file in region 7:149129618-149153096. Error was invalid region `7:149129619-149153096`
[2016-04-15T05:14Z] 2016-04-14 22:14:57 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:14:57,947 - WARNING - Could not retrieve variants from source file in region 7:143269961-143270362. Error was invalid region `7:143269962-143270362`
[2016-04-15T05:14Z] 2016-04-14 22:14:58 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:14:58,219 - WARNING - Could not retrieve variants from source file in region 7:148848147-148851403. Error was invalid region `7:148848148-148851403`
[2016-04-15T05:14Z] 2016-04-14 22:14:58 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:14:58,599 - WARNING - Could not retrieve variants from source file in region 7:152841100-152841529. Error was invalid region `7:152841101-152841529`
[2016-04-15T05:15Z] 2016-04-14 22:15:00 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:15:00,251 - WARNING - Could not retrieve variants from source file in region 7:149193722-149194361. Error was invalid region `7:149193723-149194361`
[2016-04-15T05:15Z] 2016-04-14 22:15:01 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:15:01,777 - WARNING - Could not retrieve variants from source file in region 7:150864029-150935620. Error was invalid region `7:150864030-150935620`
[2016-04-15T05:15Z] 2016-04-14 22:15:02 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:15:02,733 - WARNING - Could not retrieve variants from source file in region 7:143269961-143270362. Error was invalid region `7:143269962-143270362`
[2016-04-15T05:15Z] 2016-04-14 22:15:05 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:15:05,370 - WARNING - Could not retrieve variants from source file in region 7:144094402-144107469. Error was invalid region `7:144094403-144107469`
[2016-04-15T05:15Z] 2016-04-14 22:15:05 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:15:05,963 - WARNING - Could not retrieve variants from source file in region 7:149193722-149194361. Error was invalid region `7:149193723-149194361`
[2016-04-15T05:15Z] 2016-04-14 22:15:06 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:15:06,067 - WARNING - Could not retrieve variants from source file in region 7:156742290-156762438. Error was invalid region `7:156742291-156762438`
[2016-04-15T05:15Z] 2016-04-14 22:15:07 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:15:07,815 - WARNING - Could not retrieve variants from source file in region 7:149983354-149983756. Error was invalid region `7:149983355-149983756`
[2016-04-15T05:15Z] 2016-04-14 22:15:08 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:15:08,917 - WARNING - Could not retrieve variants from source file in region 7:152841100-152841529. Error was invalid region `7:152841101-152841529`
[2016-04-15T05:15Z] 2016-04-14 22:15:11 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:15:11,142 - WARNING - Could not retrieve variants from source file in region 7:149193722-149194361. Error was invalid region `7:149193723-149194361`
[2016-04-15T05:15Z] 2016-04-14 22:15:13 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:15:13,950 - WARNING - Could not retrieve variants from source file in region 7:150439289-150440233. Error was invalid region `7:150439290-150440233`
[2016-04-15T05:15Z] 2016-04-14 22:15:19 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:15:19,119 - WARNING - Could not retrieve variants from source file in region 7:151970645-151971121. Error was invalid region `7:151970646-151971121`
[2016-04-15T05:15Z] 2016-04-14 22:15:20 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:15:20,742 - WARNING - Could not retrieve variants from source file in region 7:151970645-151971121. Error was invalid region `7:151970646-151971121`
[2016-04-15T05:15Z] 2016-04-14 22:15:21 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:15:21,192 - WARNING - Could not retrieve variants from source file in region 7:141672393-141673535. Error was invalid region `7:141672394-141673535`
[2016-04-15T05:15Z] 2016-04-14 22:15:21 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:15:21,733 - WARNING - Could not retrieve variants from source file in region 7:150812282-150812873. Error was invalid region `7:150812283-150812873`
[2016-04-15T05:15Z] 2016-04-14 22:15:22 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:15:22,156 - WARNING - Could not retrieve variants from source file in region 7:143175291-143175692. Error was invalid region `7:143175292-143175692`
[2016-04-15T05:15Z] 2016-04-14 22:15:23 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:15:23,403 - WARNING - Could not retrieve variants from source file in region 7:144060591-144061309. Error was invalid region `7:144060592-144061309`
[2016-04-15T05:15Z] 2016-04-14 22:15:23 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:15:23,482 - WARNING - Could not retrieve variants from source file in region 7:148973407-148979513. Error was invalid region `7:148973408-148979513`
[2016-04-15T05:15Z] 2016-04-14 22:15:23 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:15:23,931 - WARNING - Could not retrieve variants from source file in region 7:151970645-151971121. Error was invalid region `7:151970646-151971121`
[2016-04-15T05:15Z] 2016-04-14 22:15:26 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:15:26,558 - WARNING - Could not retrieve variants from source file in region 7:150812282-150812873. Error was invalid region `7:150812283-150812873`
[2016-04-15T05:15Z] 2016-04-14 22:15:26 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:15:26,804 - WARNING - Could not retrieve variants from source file in region 7:143175291-143175692. Error was invalid region `7:143175292-143175692`
[2016-04-15T05:15Z] 2016-04-14 22:15:29 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:15:29,335 - WARNING - Could not retrieve variants from source file in region 7:143882462-143882863. Error was invalid region `7:143882463-143882863`
[2016-04-15T05:15Z] 2016-04-14 22:15:30 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:15:30,297 - WARNING - Could not retrieve variants from source file in region 7:143882462-143882863. Error was invalid region `7:143882463-143882863`
[2016-04-15T05:15Z] 2016-04-14 22:15:30 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:15:30,545 - WARNING - Could not retrieve variants from source file in region 7:150812282-150812873. Error was invalid region `7:150812283-150812873`
[2016-04-15T05:15Z] 2016-04-14 22:15:31 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:15:31,128 - WARNING - Could not retrieve variants from source file in region 7:151667852-151680262. Error was invalid region `7:151667853-151680262`
[2016-04-15T05:15Z] 2016-04-14 22:15:35 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:15:35,718 - WARNING - Could not retrieve variants from source file in region 7:151433190-151433591. Error was invalid region `7:151433191-151433591`
[2016-04-15T05:15Z] 2016-04-14 22:15:36 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:15:36,481 - WARNING - Could not retrieve variants from source file in region 7:150389382-150390046. Error was invalid region `7:150389383-150390046`
[2016-04-15T05:15Z] 2016-04-14 22:15:37 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:15:37,446 - WARNING - Could not retrieve variants from source file in region 7:150269331-150269732. Error was invalid region `7:150269332-150269732`
[2016-04-15T05:15Z] 2016-04-14 22:15:37 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:15:37,808 - WARNING - Could not retrieve variants from source file in region 7:150324964-150325365. Error was invalid region `7:150324965-150325365`
[2016-04-15T05:15Z] 2016-04-14 22:15:40 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:15:40,149 - WARNING - Could not retrieve variants from source file in region 7:143043029-143043430. Error was invalid region `7:143043030-143043430`
[2016-04-15T05:15Z] 2016-04-14 22:15:41 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:15:41,982 - WARNING - Could not retrieve variants from source file in region 7:150269331-150269732. Error was invalid region `7:150269332-150269732`
[2016-04-15T05:15Z] 2016-04-14 22:15:43 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:15:43,043 - WARNING - Could not retrieve variants from source file in region 7:150324964-150325365. Error was invalid region `7:150324965-150325365`
[2016-04-15T05:15Z] 2016-04-14 22:15:43 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:15:43,162 - WARNING - Could not retrieve variants from source file in region 7:150553394-150557768. Error was invalid region `7:150553395-150557768`
[2016-04-15T05:15Z] 2016-04-14 22:15:43 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:15:43,208 - WARNING - Could not retrieve variants from source file in region 7:142988515-143017997. Error was invalid region `7:142988516-143017997`
[2016-04-15T05:15Z] 2016-04-14 22:15:43 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:15:43,261 - WARNING - Could not retrieve variants from source file in region 7:150490165-150501706. Error was invalid region `7:150490166-150501706`
[2016-04-15T05:15Z] 2016-04-14 22:15:43 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:15:43,483 - WARNING - Could not retrieve variants from source file in region 7:151433190-151433591. Error was invalid region `7:151433191-151433591`
[2016-04-15T05:15Z] 2016-04-14 22:15:43 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:15:43,551 - WARNING - Could not retrieve variants from source file in region 7:143079849-143106020. Error was invalid region `7:143079850-143106020`
[2016-04-15T05:15Z] 2016-04-14 22:15:45 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:15:45,608 - WARNING - Could not retrieve variants from source file in region 7:143141264-143141665. Error was invalid region `7:143141265-143141665`
[2016-04-15T05:15Z] 2016-04-14 22:15:45 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:15:45,624 - WARNING - Could not retrieve variants from source file in region 7:143043029-143043430. Error was invalid region `7:143043030-143043430`
[2016-04-15T05:15Z] 2016-04-14 22:15:45 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:15:45,678 - WARNING - Could not retrieve variants from source file in region 7:151254232-151257163. Error was invalid region `7:151254233-151257163`
[2016-04-15T05:15Z] 2016-04-14 22:15:46 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:15:46,665 - WARNING - Could not retrieve variants from source file in region 7:150269331-150269732. Error was invalid region `7:150269332-150269732`
[2016-04-15T05:15Z] 2016-04-14 22:15:48 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:15:48,592 - WARNING - Could not retrieve variants from source file in region 7:150324964-150325365. Error was invalid region `7:150324965-150325365`
[2016-04-15T05:15Z] 2016-04-14 22:15:49 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:15:49,171 - WARNING - Could not retrieve variants from source file in region 7:143079849-143106020. Error was invalid region `7:143079850-143106020`
[2016-04-15T05:15Z] 2016-04-14 22:15:49 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:15:49,261 - WARNING - Could not retrieve variants from source file in region 7:150647987-150648979. Error was invalid region `7:150647988-150648979`
[2016-04-15T05:15Z] 2016-04-14 22:15:50 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:15:50,468 - WARNING - Could not retrieve variants from source file in region 7:143141264-143141665. Error was invalid region `7:143141265-143141665`
[2016-04-15T05:15Z] 2016-04-14 22:15:50 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:15:50,891 - WARNING - Could not retrieve variants from source file in region 7:143043029-143043430. Error was invalid region `7:143043030-143043430`
[2016-04-15T05:15Z] 2016-04-14 22:15:50 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:15:50,935 - WARNING - Could not retrieve variants from source file in region 7:151254232-151257163. Error was invalid region `7:151254233-151257163`
[2016-04-15T05:15Z] 2016-04-14 22:15:53 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:15:53,503 - WARNING - Could not retrieve variants from source file in region 7:142988515-143017997. Error was invalid region `7:142988516-143017997`
[2016-04-15T05:15Z] 2016-04-14 22:15:58 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:15:58,088 - WARNING - Could not retrieve variants from source file in region 7:150217037-150217525. Error was invalid region `7:150217038-150217525`
[2016-04-15T05:15Z] 2016-04-14 22:15:58 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:15:58,591 - WARNING - Could not retrieve variants from source file in region 7:150217037-150217525. Error was invalid region `7:150217038-150217525`
[2016-04-15T05:15Z] 2016-04-14 22:15:58 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:15:58,591 - WARNING - Could not retrieve variants from source file in region 7:150217037-150217525. Error was invalid region `7:150217038-150217525`
[2016-04-15T05:15Z] 2016-04-14 22:15:59 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:15:59,952 - WARNING - Could not retrieve variants from source file in region 7:150163626-150171900. Error was invalid region `7:150163627-150171900`
[2016-04-15T05:16Z] 2016-04-14 22:16:00 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:16:00,803 - WARNING - Could not retrieve variants from source file in region 7:150068160-150095043. Error was invalid region `7:150068161-150095043`
[2016-04-15T05:16Z] ['bcbio-variation-recall', 'square', '-Xms750m', '-Xmx7280m', '-XX:+UseSerialGC', '-c', 16, '-r', u'7:157155855-159138663', '--caller', 'platypus', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/7/Batch1-7_157155854_159138663.vcf.gz', '/mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/7/Batch1-7_157155854_159138663.vcf-inputs.txt'] in region: 7:157155855-159138663
[2016-04-15T05:16Z] 2016-04-14 22:16:12 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:16:12,687 - WARNING - Could not retrieve variants from source file in region 7:158672265-158672809. Error was invalid region `7:158672266-158672809`
[2016-04-15T05:16Z] 2016-04-14 22:16:12 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:16:12,824 - WARNING - Could not retrieve variants from source file in region 7:158827115-158851424. Error was invalid region `7:158827116-158851424`
[2016-04-15T05:16Z] 2016-04-14 22:16:12 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:16:12,827 - WARNING - Could not retrieve variants from source file in region 7:158672265-158672809. Error was invalid region `7:158672266-158672809`
[2016-04-15T05:16Z] 2016-04-14 22:16:12 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:16:12,837 - WARNING - Could not retrieve variants from source file in region 7:158827115-158851424. Error was invalid region `7:158827116-158851424`
[2016-04-15T05:16Z] 2016-04-14 22:16:12 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:16:12,927 - WARNING - Could not retrieve variants from source file in region 7:158827115-158851424. Error was invalid region `7:158827116-158851424`
[2016-04-15T05:16Z] 2016-04-14 22:16:13 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:16:13,598 - WARNING - Could not retrieve variants from source file in region 7:158715008-158735003. Error was invalid region `7:158715009-158735003`
[2016-04-15T05:16Z] 2016-04-14 22:16:13 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:16:13,813 - WARNING - Could not retrieve variants from source file in region 7:157333200-157333601. Error was invalid region `7:157333201-157333601`
[2016-04-15T05:16Z] 2016-04-14 22:16:13 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:16:13,936 - WARNING - Could not retrieve variants from source file in region 7:157333200-157333601. Error was invalid region `7:157333201-157333601`
[2016-04-15T05:16Z] 2016-04-14 22:16:14 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:16:14,033 - WARNING - Could not retrieve variants from source file in region 7:157387743-157414254. Error was invalid region `7:157387744-157414254`
[2016-04-15T05:16Z] 2016-04-14 22:16:14 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:16:14,497 - WARNING - Could not retrieve variants from source file in region 7:157903327-157903728. Error was invalid region `7:157903328-157903728`
[2016-04-15T05:16Z] 2016-04-14 22:16:14 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:16:14,518 - WARNING - Could not retrieve variants from source file in region 7:157959425-157985339. Error was invalid region `7:157959426-157985339`
[2016-04-15T05:16Z] 2016-04-14 22:16:14 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:16:14,522 - WARNING - Could not retrieve variants from source file in region 7:157930908-157931334. Error was invalid region `7:157930909-157931334`
[2016-04-15T05:16Z] 2016-04-14 22:16:21 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:16:21,694 - WARNING - Could not retrieve variants from source file in region 7:157903327-157903728. Error was invalid region `7:157903328-157903728`
[2016-04-15T05:16Z] 2016-04-14 22:16:21 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:16:21,708 - WARNING - Could not retrieve variants from source file in region 7:157930908-157931334. Error was invalid region `7:157930909-157931334`
[2016-04-15T05:16Z] 2016-04-14 22:16:22 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:16:22,143 - WARNING - Could not retrieve variants from source file in region 7:157903327-157903728. Error was invalid region `7:157903328-157903728`
[2016-04-15T05:16Z] ['bcbio-variation-recall', 'square', '-Xms750m', '-Xmx7280m', '-XX:+UseSerialGC', '-c', 16, '-r', u'8:1-15517156', '--caller', 'platypus', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/8/Batch1-8_0_15517156.vcf.gz', '/mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/8/Batch1-8_0_15517156.vcf-inputs.txt'] in region: 8:1-15517156
[2016-04-15T05:16Z] 2016-04-14 22:16:39 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:16:39,955 - WARNING - Could not retrieve variants from source file in region 8:10382927-10396244. Error was invalid region `8:10382928-10396244`
[2016-04-15T05:16Z] 2016-04-14 22:16:39 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:16:39,943 - WARNING - Could not retrieve variants from source file in region 8:13356591-13357009. Error was invalid region `8:13356592-13357009`
[2016-04-15T05:16Z] 2016-04-14 22:16:40 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:16:40,368 - WARNING - Could not retrieve variants from source file in region 8:1728081-1728482. Error was invalid region `8:1728082-1728482`
[2016-04-15T05:16Z] 2016-04-14 22:16:40 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:16:40,853 - WARNING - Could not retrieve variants from source file in region 8:11188532-11189725. Error was invalid region `8:11188533-11189725`
[2016-04-15T05:16Z] 2016-04-14 22:16:40 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:16:40,861 - WARNING - Could not retrieve variants from source file in region 8:11640573-11706771. Error was invalid region `8:11640574-11706771`
[2016-04-15T05:16Z] 2016-04-14 22:16:41 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:16:41,062 - WARNING - Could not retrieve variants from source file in region 8:13424354-13425543. Error was invalid region `8:13424355-13425543`
[2016-04-15T05:16Z] 2016-04-14 22:16:41 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:16:41,144 - WARNING - Could not retrieve variants from source file in region 8:7308175-7308576. Error was invalid region `8:7308176-7308576`
[2016-04-15T05:16Z] 2016-04-14 22:16:41 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:16:41,284 - WARNING - Could not retrieve variants from source file in region 8:11406382-11414427. Error was invalid region `8:11406383-11414427`
[2016-04-15T05:16Z] 2016-04-14 22:16:47 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:16:47,025 - WARNING - Could not retrieve variants from source file in region 8:12990307-12990708. Error was invalid region `8:12990308-12990708`
[2016-04-15T05:16Z] 2016-04-14 22:16:48 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:16:48,608 - WARNING - Could not retrieve variants from source file in region 8:2820534-2832329. Error was invalid region `8:2820535-2832329`
[2016-04-15T05:16Z] 2016-04-14 22:16:49 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:16:49,024 - WARNING - Could not retrieve variants from source file in region 8:13356591-13357009. Error was invalid region `8:13356592-13357009`
[2016-04-15T05:16Z] 2016-04-14 22:16:49 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:16:49,167 - WARNING - Could not retrieve variants from source file in region 8:11970441-11970842. Error was invalid region `8:11970442-11970842`
[2016-04-15T05:16Z] 2016-04-14 22:16:49 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:16:49,490 - WARNING - Could not retrieve variants from source file in region 8:11406382-11414427. Error was invalid region `8:11406383-11414427`
[2016-04-15T05:16Z] 2016-04-14 22:16:49 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:16:49,512 - WARNING - Could not retrieve variants from source file in region 8:7308175-7308576. Error was invalid region `8:7308176-7308576`
[2016-04-15T05:16Z] 2016-04-14 22:16:49 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:16:49,918 - WARNING - Could not retrieve variants from source file in region 8:10622927-10623328. Error was invalid region `8:10622928-10623328`
[2016-04-15T05:16Z] 2016-04-14 22:16:50 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:16:50,082 - WARNING - Could not retrieve variants from source file in region 8:606611-623783. Error was invalid region `8:606612-623783`
[2016-04-15T05:16Z] 2016-04-14 22:16:50 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:16:50,104 - WARNING - Could not retrieve variants from source file in region 8:8747683-8750657. Error was invalid region `8:8747684-8750657`
[2016-04-15T05:16Z] 2016-04-14 22:16:50 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:16:50,582 - WARNING - Could not retrieve variants from source file in region 8:12042713-12043114. Error was invalid region `8:12042714-12043114`
[2016-04-15T05:16Z] 2016-04-14 22:16:52 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:16:52,125 - WARNING - Could not retrieve variants from source file in region 8:12990307-12990708. Error was invalid region `8:12990308-12990708`
[2016-04-15T05:16Z] 2016-04-14 22:16:54 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:16:54,396 - WARNING - Could not retrieve variants from source file in region 8:2820534-2832329. Error was invalid region `8:2820535-2832329`
[2016-04-15T05:16Z] 2016-04-14 22:16:55 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:16:55,387 - WARNING - Could not retrieve variants from source file in region 8:13356591-13357009. Error was invalid region `8:13356592-13357009`
[2016-04-15T05:16Z] 2016-04-14 22:16:56 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:16:56,126 - WARNING - Could not retrieve variants from source file in region 8:7308175-7308576. Error was invalid region `8:7308176-7308576`
[2016-04-15T05:16Z] 2016-04-14 22:16:56 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:16:56,898 - WARNING - Could not retrieve variants from source file in region 8:10622927-10623328. Error was invalid region `8:10622928-10623328`
[2016-04-15T05:16Z] 2016-04-14 22:16:57 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:16:57,065 - WARNING - Could not retrieve variants from source file in region 8:11406382-11414427. Error was invalid region `8:11406383-11414427`
[2016-04-15T05:16Z] 2016-04-14 22:16:57 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:16:57,110 - WARNING - Could not retrieve variants from source file in region 8:11970441-11970842. Error was invalid region `8:11970442-11970842`
[2016-04-15T05:16Z] 2016-04-14 22:16:57 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:16:57,258 - WARNING - Could not retrieve variants from source file in region 8:8747683-8750657. Error was invalid region `8:8747684-8750657`
[2016-04-15T05:17Z] 2016-04-14 22:17:09 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:17:09,900 - WARNING - Could not retrieve variants from source file in region 8:11831868-11832269. Error was invalid region `8:11831869-11832269`
[2016-04-15T05:17Z] 2016-04-14 22:17:09 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:17:09,923 - WARNING - Could not retrieve variants from source file in region 8:1616507-1616908. Error was invalid region `8:1616508-1616908`
[2016-04-15T05:17Z] 2016-04-14 22:17:10 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:17:10,214 - WARNING - Could not retrieve variants from source file in region 8:11831868-11832269. Error was invalid region `8:11831869-11832269`
[2016-04-15T05:17Z] 2016-04-14 22:17:11 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:17:11,151 - WARNING - Could not retrieve variants from source file in region 8:9564226-9578130. Error was invalid region `8:9564227-9578130`
[2016-04-15T05:17Z] 2016-04-14 22:17:11 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:17:11,289 - WARNING - Could not retrieve variants from source file in region 8:11301390-11303201. Error was invalid region `8:11301391-11303201`
[2016-04-15T05:17Z] 2016-04-14 22:17:12 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:17:12,503 - WARNING - Could not retrieve variants from source file in region 8:11156077-11162686. Error was invalid region `8:11156078-11162686`
[2016-04-15T05:17Z] 2016-04-14 22:17:12 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:17:12,594 - WARNING - Could not retrieve variants from source file in region 8:10583295-10583696. Error was invalid region `8:10583296-10583696`
[2016-04-15T05:17Z] 2016-04-14 22:17:13 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:17:13,168 - WARNING - Could not retrieve variants from source file in region 8:494447-494854. Error was invalid region `8:494448-494854`
[2016-04-15T05:17Z] 2016-04-14 22:17:13 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:17:13,448 - WARNING - Could not retrieve variants from source file in region 8:8654687-8655088. Error was invalid region `8:8654688-8655088`
[2016-04-15T05:17Z] 2016-04-14 22:17:13 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:17:13,822 - WARNING - Could not retrieve variants from source file in region 8:12957264-12958215. Error was invalid region `8:12957265-12958215`
[2016-04-15T05:17Z] 2016-04-14 22:17:14 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:17:14,073 - WARNING - Could not retrieve variants from source file in region 8:11537880-11550572. Error was invalid region `8:11537881-11550572`
[2016-04-15T05:17Z] 2016-04-14 22:17:15 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:17:15,691 - WARNING - Could not retrieve variants from source file in region 8:11831868-11832269. Error was invalid region `8:11831869-11832269`
[2016-04-15T05:17Z] 2016-04-14 22:17:15 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:17:15,694 - WARNING - Could not retrieve variants from source file in region 8:1616507-1616908. Error was invalid region `8:1616508-1616908`
[2016-04-15T05:17Z] 2016-04-14 22:17:16 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:17:16,041 - WARNING - Could not retrieve variants from source file in region 8:4494694-4495095. Error was invalid region `8:4494695-4495095`
[2016-04-15T05:17Z] 2016-04-14 22:17:16 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:17:16,337 - WARNING - Could not retrieve variants from source file in region 8:13162004-13162731. Error was invalid region `8:13162005-13162731`
[2016-04-15T05:17Z] 2016-04-14 22:17:17 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:17:17,918 - WARNING - Could not retrieve variants from source file in region 8:10583295-10583696. Error was invalid region `8:10583296-10583696`
[2016-04-15T05:17Z] 2016-04-14 22:17:18 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:17:18,749 - WARNING - Could not retrieve variants from source file in region 8:11537880-11550572. Error was invalid region `8:11537881-11550572`
[2016-04-15T05:17Z] 2016-04-14 22:17:19 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:17:19,019 - WARNING - Could not retrieve variants from source file in region 8:8654687-8655088. Error was invalid region `8:8654688-8655088`
[2016-04-15T05:17Z] 2016-04-14 22:17:21 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:17:21,252 - WARNING - Could not retrieve variants from source file in region 8:7215483-7215884. Error was invalid region `8:7215484-7215884`
[2016-04-15T05:17Z] 2016-04-14 22:17:21 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:17:21,731 - WARNING - Could not retrieve variants from source file in region 8:13162004-13162731. Error was invalid region `8:13162005-13162731`
[2016-04-15T05:17Z] 2016-04-14 22:17:22 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:17:22,392 - WARNING - Could not retrieve variants from source file in region 8:10583295-10583696. Error was invalid region `8:10583296-10583696`
[2016-04-15T05:17Z] 2016-04-14 22:17:23 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:17:23,684 - WARNING - Could not retrieve variants from source file in region 8:11537880-11550572. Error was invalid region `8:11537881-11550572`
[2016-04-15T05:17Z] 2016-04-14 22:17:23 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:17:23,844 - WARNING - Could not retrieve variants from source file in region 8:8654687-8655088. Error was invalid region `8:8654688-8655088`
[2016-04-15T05:17Z] 2016-04-14 22:17:34 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:17:34,717 - WARNING - Could not retrieve variants from source file in region 8:1950896-1951297. Error was invalid region `8:1950897-1951297`
[2016-04-15T05:17Z] 2016-04-14 22:17:35 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:17:35,727 - WARNING - Could not retrieve variants from source file in region 8:6912820-6913221. Error was invalid region `8:6912821-6913221`
[2016-04-15T05:17Z] 2016-04-14 22:17:36 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:17:36,440 - WARNING - Could not retrieve variants from source file in region 8:2040087-2054361. Error was invalid region `8:2040088-2054361`
[2016-04-15T05:17Z] 2016-04-14 22:17:37 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:17:37,145 - WARNING - Could not retrieve variants from source file in region 8:1513798-1514199. Error was invalid region `8:1513799-1514199`
[2016-04-15T05:17Z] 2016-04-14 22:17:37 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:17:37,165 - WARNING - Could not retrieve variants from source file in region 8:9413838-9414239. Error was invalid region `8:9413839-9414239`
[2016-04-15T05:17Z] 2016-04-14 22:17:37 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:17:37,259 - WARNING - Could not retrieve variants from source file in region 8:362981-363382. Error was invalid region `8:362982-363382`
[2016-04-15T05:17Z] 2016-04-14 22:17:37 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:17:37,848 - WARNING - Could not retrieve variants from source file in region 8:8231932-8235058. Error was invalid region `8:8231933-8235058`
[2016-04-15T05:17Z] 2016-04-14 22:17:38 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:17:38,085 - WARNING - Could not retrieve variants from source file in region 8:10530007-10530408. Error was invalid region `8:10530008-10530408`
[2016-04-15T05:17Z] 2016-04-14 22:17:40 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:17:40,014 - WARNING - Could not retrieve variants from source file in region 8:3350936-3351385. Error was invalid region `8:3350937-3351385`
[2016-04-15T05:17Z] 2016-04-14 22:17:41 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:17:41,020 - WARNING - Could not retrieve variants from source file in region 8:6912820-6913221. Error was invalid region `8:6912821-6913221`
[2016-04-15T05:17Z] 2016-04-14 22:17:42 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:17:42,074 - WARNING - Could not retrieve variants from source file in region 8:10689001-10692348. Error was invalid region `8:10689002-10692348`
[2016-04-15T05:17Z] 2016-04-14 22:17:42 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:17:42,894 - WARNING - Could not retrieve variants from source file in region 8:362981-363382. Error was invalid region `8:362982-363382`
[2016-04-15T05:17Z] 2016-04-14 22:17:43 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:17:43,794 - WARNING - Could not retrieve variants from source file in region 8:1513798-1514199. Error was invalid region `8:1513799-1514199`
[2016-04-15T05:17Z] 2016-04-14 22:17:44 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:17:44,042 - WARNING - Could not retrieve variants from source file in region 8:876901-877302. Error was invalid region `8:876902-877302`
[2016-04-15T05:17Z] 2016-04-14 22:17:44 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:17:44,401 - WARNING - Could not retrieve variants from source file in region 8:418533-442579. Error was invalid region `8:418534-442579`
[2016-04-15T05:17Z] 2016-04-14 22:17:44 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:17:44,424 - WARNING - Could not retrieve variants from source file in region 8:10530007-10530408. Error was invalid region `8:10530008-10530408`
[2016-04-15T05:17Z] 2016-04-14 22:17:46 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:17:46,140 - WARNING - Could not retrieve variants from source file in region 8:6912820-6913221. Error was invalid region `8:6912821-6913221`
[2016-04-15T05:17Z] 2016-04-14 22:17:46 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:17:46,169 - WARNING - Could not retrieve variants from source file in region 8:2040087-2054361. Error was invalid region `8:2040088-2054361`
[2016-04-15T05:17Z] 2016-04-14 22:17:48 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:17:48,143 - WARNING - Could not retrieve variants from source file in region 8:362981-363382. Error was invalid region `8:362982-363382`
[2016-04-15T05:17Z] 2016-04-14 22:17:50 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:17:50,345 - WARNING - Could not retrieve variants from source file in region 8:10530007-10530408. Error was invalid region `8:10530008-10530408`
[2016-04-15T05:17Z] 2016-04-14 22:17:50 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:17:50,346 - WARNING - Could not retrieve variants from source file in region 8:876901-877302. Error was invalid region `8:876902-877302`
[2016-04-15T05:17Z] 2016-04-14 22:17:51 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:17:51,080 - WARNING - Could not retrieve variants from source file in region 8:3253557-3265780. Error was invalid region `8:3253558-3265780`
[2016-04-15T05:17Z] 2016-04-14 22:17:53 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:17:53,149 - WARNING - Could not retrieve variants from source file in region 8:1904921-1922726. Error was invalid region `8:1904922-1922726`
[2016-04-15T05:17Z] 2016-04-14 22:17:59 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:17:59,803 - WARNING - Could not retrieve variants from source file in region 8:2965033-2965434. Error was invalid region `8:2965034-2965434`
[2016-04-15T05:18Z] 2016-04-14 22:18:01 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:18:01,036 - WARNING - Could not retrieve variants from source file in region 8:2965033-2965434. Error was invalid region `8:2965034-2965434`
[2016-04-15T05:18Z] 2016-04-14 22:18:01 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:18:01,052 - WARNING - Could not retrieve variants from source file in region 8:2965033-2965434. Error was invalid region `8:2965034-2965434`
[2016-04-15T05:18Z] 2016-04-14 22:18:02 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:18:02,165 - WARNING - Could not retrieve variants from source file in region 8:6793370-6793771. Error was invalid region `8:6793371-6793771`
[2016-04-15T05:18Z] 2016-04-14 22:18:02 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:18:02,268 - WARNING - Could not retrieve variants from source file in region 8:2909781-2910210. Error was invalid region `8:2909782-2910210`
[2016-04-15T05:18Z] 2016-04-14 22:18:02 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:18:02,291 - WARNING - Could not retrieve variants from source file in region 8:8860409-8869389. Error was invalid region `8:8860410-8869389`
[2016-04-15T05:18Z] 2016-04-14 22:18:02 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:18:02,681 - WARNING - Could not retrieve variants from source file in region 8:3200666-3201067. Error was invalid region `8:3200667-3201067`
[2016-04-15T05:18Z] 2016-04-14 22:18:02 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:18:02,708 - WARNING - Could not retrieve variants from source file in region 8:8176010-8176744. Error was invalid region `8:8176011-8176744`
[2016-04-15T05:18Z] 2016-04-14 22:18:05 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:18:05,545 - WARNING - Could not retrieve variants from source file in region 8:1833590-1833991. Error was invalid region `8:1833591-1833991`
[2016-04-15T05:18Z] 2016-04-14 22:18:05 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:18:05,607 - WARNING - Could not retrieve variants from source file in region 8:8860409-8869389. Error was invalid region `8:8860410-8869389`
[2016-04-15T05:18Z] 2016-04-14 22:18:06 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:18:06,260 - WARNING - Could not retrieve variants from source file in region 8:2909781-2910210. Error was invalid region `8:2909782-2910210`
[2016-04-15T05:18Z] 2016-04-14 22:18:06 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:18:06,377 - WARNING - Could not retrieve variants from source file in region 8:6793370-6793771. Error was invalid region `8:6793371-6793771`
[2016-04-15T05:18Z] 2016-04-14 22:18:06 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:18:06,745 - WARNING - Could not retrieve variants from source file in region 8:8860409-8869389. Error was invalid region `8:8860410-8869389`
[2016-04-15T05:18Z] 2016-04-14 22:18:08 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:18:08,974 - WARNING - Could not retrieve variants from source file in region 8:2909781-2910210. Error was invalid region `8:2909782-2910210`
[2016-04-15T05:18Z] 2016-04-14 22:18:09 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:18:09,004 - WARNING - Could not retrieve variants from source file in region 8:1806018-1806419. Error was invalid region `8:1806019-1806419`
[2016-04-15T05:18Z] 2016-04-14 22:18:09 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:18:09,284 - WARNING - Could not retrieve variants from source file in region 8:1833590-1833991. Error was invalid region `8:1833591-1833991`
[2016-04-15T05:18Z] 2016-04-14 22:18:10 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:18:10,483 - WARNING - Could not retrieve variants from source file in region 8:6793370-6793771. Error was invalid region `8:6793371-6793771`
[2016-04-15T05:18Z] 2016-04-14 22:18:10 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:18:10,655 - WARNING - Could not retrieve variants from source file in region 8:1806018-1806419. Error was invalid region `8:1806019-1806419`
[2016-04-15T05:18Z] 2016-04-14 22:18:10 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:18:10,799 - WARNING - Could not retrieve variants from source file in region 8:1806018-1806419. Error was invalid region `8:1806019-1806419`
[2016-04-15T05:18Z] 2016-04-14 22:18:17 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:18:17,742 - WARNING - Could not retrieve variants from source file in region 8:6669420-6693158. Error was invalid region `8:6669421-6693158`
[2016-04-15T05:18Z] 2016-04-14 22:18:17 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:18:17,745 - WARNING - Could not retrieve variants from source file in region 8:6338095-6338496. Error was invalid region `8:6338096-6338496`
[2016-04-15T05:18Z] 2016-04-14 22:18:18 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:18:18,124 - WARNING - Could not retrieve variants from source file in region 8:6371104-6390079. Error was invalid region `8:6371105-6390079`
[2016-04-15T05:18Z] 2016-04-14 22:18:18 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:18:18,165 - WARNING - Could not retrieve variants from source file in region 8:6338095-6338496. Error was invalid region `8:6338096-6338496`
[2016-04-15T05:18Z] ['bcbio-variation-recall', 'square', '-Xms750m', '-Xmx7280m', '-XX:+UseSerialGC', '-c', 16, '-r', u'8:15519665-31030618', '--caller', 'platypus', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/8/Batch1-8_15519664_31030618.vcf.gz', '/mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/8/Batch1-8_15519664_31030618.vcf-inputs.txt'] in region: 8:15519665-31030618
[2016-04-15T05:18Z] 2016-04-14 22:18:34 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:18:34,304 - WARNING - Could not retrieve variants from source file in region 8:19677704-19678105. Error was invalid region `8:19677705-19678105`
[2016-04-15T05:18Z] 2016-04-14 22:18:34 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:18:34,283 - WARNING - Could not retrieve variants from source file in region 8:22262110-22280053. Error was invalid region `8:22262111-22280053`
[2016-04-15T05:18Z] 2016-04-14 22:18:35 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:18:35,072 - WARNING - Could not retrieve variants from source file in region 8:30608765-30621030. Error was invalid region `8:30608766-30621030`
[2016-04-15T05:18Z] 2016-04-14 22:18:35 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:18:35,258 - WARNING - Could not retrieve variants from source file in region 8:29197461-29206164. Error was invalid region `8:29197462-29206164`
[2016-04-15T05:18Z] 2016-04-14 22:18:35 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:18:35,767 - WARNING - Could not retrieve variants from source file in region 8:28637821-28638222. Error was invalid region `8:28637822-28638222`
[2016-04-15T05:18Z] 2016-04-14 22:18:36 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:18:36,073 - WARNING - Could not retrieve variants from source file in region 8:30973746-31024844. Error was invalid region `8:30973747-31024844`
[2016-04-15T05:18Z] 2016-04-14 22:18:36 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:18:36,384 - WARNING - Could not retrieve variants from source file in region 8:30924346-30924747. Error was invalid region `8:30924347-30924747`
[2016-04-15T05:18Z] 2016-04-14 22:18:36 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:18:36,404 - WARNING - Could not retrieve variants from source file in region 8:27462270-27462671. Error was invalid region `8:27462271-27462671`
[2016-04-15T05:18Z] 2016-04-14 22:18:36 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:18:36,788 - WARNING - Could not retrieve variants from source file in region 8:27886692-27887093. Error was invalid region `8:27886693-27887093`
[2016-04-15T05:18Z] 2016-04-14 22:18:36 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:18:36,873 - WARNING - Could not retrieve variants from source file in region 8:25708056-25708457. Error was invalid region `8:25708057-25708457`
[2016-04-15T05:18Z] 2016-04-14 22:18:37 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:18:37,323 - WARNING - Could not retrieve variants from source file in region 8:27660855-27680171. Error was invalid region `8:27660856-27680171`
[2016-04-15T05:18Z] 2016-04-14 22:18:40 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:18:40,183 - WARNING - Could not retrieve variants from source file in region 8:22262110-22280053. Error was invalid region `8:22262111-22280053`
[2016-04-15T05:18Z] 2016-04-14 22:18:41 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:18:41,900 - WARNING - Could not retrieve variants from source file in region 8:30608765-30621030. Error was invalid region `8:30608766-30621030`
[2016-04-15T05:18Z] 2016-04-14 22:18:42 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:18:42,590 - WARNING - Could not retrieve variants from source file in region 8:28637821-28638222. Error was invalid region `8:28637822-28638222`
[2016-04-15T05:18Z] 2016-04-14 22:18:43 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:18:43,464 - WARNING - Could not retrieve variants from source file in region 8:30402606-30413832. Error was invalid region `8:30402607-30413832`
[2016-04-15T05:18Z] 2016-04-14 22:18:43 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:18:43,643 - WARNING - Could not retrieve variants from source file in region 8:25708056-25708457. Error was invalid region `8:25708057-25708457`
[2016-04-15T05:18Z] 2016-04-14 22:18:44 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:18:44,079 - WARNING - Could not retrieve variants from source file in region 8:27462270-27462671. Error was invalid region `8:27462271-27462671`
[2016-04-15T05:18Z] 2016-04-14 22:18:44 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:18:44,175 - WARNING - Could not retrieve variants from source file in region 8:23225348-23225749. Error was invalid region `8:23225349-23225749`
[2016-04-15T05:18Z] 2016-04-14 22:18:44 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:18:44,187 - WARNING - Could not retrieve variants from source file in region 8:30924346-30924747. Error was invalid region `8:30924347-30924747`
[2016-04-15T05:18Z] 2016-04-14 22:18:44 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:18:44,844 - WARNING - Could not retrieve variants from source file in region 8:27886692-27887093. Error was invalid region `8:27886693-27887093`
[2016-04-15T05:18Z] 2016-04-14 22:18:44 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:18:44,918 - WARNING - Could not retrieve variants from source file in region 8:27767020-27779735. Error was invalid region `8:27767021-27779735`
[2016-04-15T05:18Z] 2016-04-14 22:18:44 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:18:44,921 - WARNING - Could not retrieve variants from source file in region 8:29964183-29996446. Error was invalid region `8:29964184-29996446`
[2016-04-15T05:18Z] 2016-04-14 22:18:45 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:18:45,356 - WARNING - Could not retrieve variants from source file in region 8:22262110-22280053. Error was invalid region `8:22262111-22280053`
[2016-04-15T05:18Z] 2016-04-14 22:18:46 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:18:46,311 - WARNING - Could not retrieve variants from source file in region 8:30608765-30621030. Error was invalid region `8:30608766-30621030`
[2016-04-15T05:18Z] 2016-04-14 22:18:47 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:18:47,773 - WARNING - Could not retrieve variants from source file in region 8:28637821-28638222. Error was invalid region `8:28637822-28638222`
[2016-04-15T05:18Z] 2016-04-14 22:18:49 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:18:49,399 - WARNING - Could not retrieve variants from source file in region 8:25708056-25708457. Error was invalid region `8:25708057-25708457`
[2016-04-15T05:18Z] 2016-04-14 22:18:51 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:18:51,079 - WARNING - Could not retrieve variants from source file in region 8:27462270-27462671. Error was invalid region `8:27462271-27462671`
[2016-04-15T05:18Z] 2016-04-14 22:18:51 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:18:51,851 - WARNING - Could not retrieve variants from source file in region 8:30924346-30924747. Error was invalid region `8:30924347-30924747`
[2016-04-15T05:18Z] 2016-04-14 22:18:53 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:18:53,064 - WARNING - Could not retrieve variants from source file in region 8:27886692-27887093. Error was invalid region `8:27886693-27887093`
[2016-04-15T05:19Z] 2016-04-14 22:19:00 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:19:00,281 - WARNING - Could not retrieve variants from source file in region 8:19362557-19362958. Error was invalid region `8:19362558-19362958`
[2016-04-15T05:19Z] 2016-04-14 22:19:04 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:19:04,366 - WARNING - Could not retrieve variants from source file in region 8:28384501-28384902. Error was invalid region `8:28384502-28384902`
[2016-04-15T05:19Z] 2016-04-14 22:19:04 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:19:04,439 - WARNING - Could not retrieve variants from source file in region 8:29004882-29005283. Error was invalid region `8:29004883-29005283`
[2016-04-15T05:19Z] 2016-04-14 22:19:04 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:19:04,625 - WARNING - Could not retrieve variants from source file in region 8:24772447-24774873. Error was invalid region `8:24772448-24774873`
[2016-04-15T05:19Z] 2016-04-14 22:19:05 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:19:05,038 - WARNING - Could not retrieve variants from source file in region 8:22926102-22926503. Error was invalid region `8:22926103-22926503`
[2016-04-15T05:19Z] 2016-04-14 22:19:05 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:19:05,335 - WARNING - Could not retrieve variants from source file in region 8:27633853-27634254. Error was invalid region `8:27633854-27634254`
[2016-04-15T05:19Z] 2016-04-14 22:19:05 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:19:05,707 - WARNING - Could not retrieve variants from source file in region 8:19362557-19362958. Error was invalid region `8:19362558-19362958`
[2016-04-15T05:19Z] 2016-04-14 22:19:06 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:19:06,433 - WARNING - Could not retrieve variants from source file in region 8:28867235-28867636. Error was invalid region `8:28867236-28867636`
[2016-04-15T05:19Z] 2016-04-14 22:19:08 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:19:08,133 - WARNING - Could not retrieve variants from source file in region 8:27528235-27530665. Error was invalid region `8:27528236-27530665`
[2016-04-15T05:19Z] 2016-04-14 22:19:08 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:19:08,426 - WARNING - Could not retrieve variants from source file in region 8:29927089-29927511. Error was invalid region `8:29927090-29927511`
[2016-04-15T05:19Z] 2016-04-14 22:19:08 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:19:08,946 - WARNING - Could not retrieve variants from source file in region 8:22144945-22145346. Error was invalid region `8:22144946-22145346`
[2016-04-15T05:19Z] 2016-04-14 22:19:09 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:19:09,355 - WARNING - Could not retrieve variants from source file in region 8:28384501-28384902. Error was invalid region `8:28384502-28384902`
[2016-04-15T05:19Z] 2016-04-14 22:19:09 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:19:09,442 - WARNING - Could not retrieve variants from source file in region 8:29004882-29005283. Error was invalid region `8:29004883-29005283`
[2016-04-15T05:19Z] 2016-04-14 22:19:10 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:19:10,753 - WARNING - Could not retrieve variants from source file in region 8:25360712-25365084. Error was invalid region `8:25360713-25365084`
[2016-04-15T05:19Z] 2016-04-14 22:19:11 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:19:11,106 - WARNING - Could not retrieve variants from source file in region 8:19362557-19362958. Error was invalid region `8:19362558-19362958`
[2016-04-15T05:19Z] 2016-04-14 22:19:11 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:19:11,167 - WARNING - Could not retrieve variants from source file in region 8:27394155-27402154. Error was invalid region `8:27394156-27402154`
[2016-04-15T05:19Z] 2016-04-14 22:19:11 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:19:11,196 - WARNING - Could not retrieve variants from source file in region 8:28867235-28867636. Error was invalid region `8:28867236-28867636`
[2016-04-15T05:19Z] 2016-04-14 22:19:11 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:19:11,416 - WARNING - Could not retrieve variants from source file in region 8:23145884-23191131. Error was invalid region `8:23145885-23191131`
[2016-04-15T05:19Z] 2016-04-14 22:19:13 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:19:13,585 - WARNING - Could not retrieve variants from source file in region 8:29927089-29927511. Error was invalid region `8:29927090-29927511`
[2016-04-15T05:19Z] 2016-04-14 22:19:14 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:19:14,260 - WARNING - Could not retrieve variants from source file in region 8:28384501-28384902. Error was invalid region `8:28384502-28384902`
[2016-04-15T05:19Z] 2016-04-14 22:19:14 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:19:14,616 - WARNING - Could not retrieve variants from source file in region 8:29004882-29005283. Error was invalid region `8:29004883-29005283`
[2016-04-15T05:19Z] 2016-04-14 22:19:16 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:19:16,014 - WARNING - Could not retrieve variants from source file in region 8:22926102-22926503. Error was invalid region `8:22926103-22926503`
[2016-04-15T05:19Z] 2016-04-14 22:19:16 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:19:16,534 - WARNING - Could not retrieve variants from source file in region 8:28867235-28867636. Error was invalid region `8:28867236-28867636`
[2016-04-15T05:19Z] 2016-04-14 22:19:17 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:19:17,613 - WARNING - Could not retrieve variants from source file in region 8:27394155-27402154. Error was invalid region `8:27394156-27402154`
[2016-04-15T05:19Z] 2016-04-14 22:19:18 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:19:18,483 - WARNING - Could not retrieve variants from source file in region 8:29927089-29927511. Error was invalid region `8:29927090-29927511`
[2016-04-15T05:19Z] 2016-04-14 22:19:28 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:19:28,573 - WARNING - Could not retrieve variants from source file in region 8:28285963-28304959. Error was invalid region `8:28285964-28304959`
[2016-04-15T05:19Z] 2016-04-14 22:19:28 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:19:28,860 - WARNING - Could not retrieve variants from source file in region 8:22052179-22105692. Error was invalid region `8:22052180-22105692`
[2016-04-15T05:19Z] 2016-04-14 22:19:29 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:19:29,238 - WARNING - Could not retrieve variants from source file in region 8:24339468-24367223. Error was invalid region `8:24339469-24367223`
[2016-04-15T05:19Z] 2016-04-14 22:19:30 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:19:30,208 - WARNING - Could not retrieve variants from source file in region 8:19315875-19316276. Error was invalid region `8:19315876-19316276`
[2016-04-15T05:19Z] 2016-04-14 22:19:30 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:19:30,414 - WARNING - Could not retrieve variants from source file in region 8:22851885-22886210. Error was invalid region `8:22851886-22886210`
[2016-04-15T05:19Z] 2016-04-14 22:19:31 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:19:31,085 - WARNING - Could not retrieve variants from source file in region 8:24810853-24811255. Error was invalid region `8:24810854-24811255`
[2016-04-15T05:19Z] 2016-04-14 22:19:33 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:19:33,270 - WARNING - Could not retrieve variants from source file in region 8:24193053-24211521. Error was invalid region `8:24193054-24211521`
[2016-04-15T05:19Z] 2016-04-14 22:19:35 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:19:35,377 - WARNING - Could not retrieve variants from source file in region 8:25314649-25323967. Error was invalid region `8:25314650-25323967`
[2016-04-15T05:19Z] 2016-04-14 22:19:35 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:19:35,916 - WARNING - Could not retrieve variants from source file in region 8:19315875-19316276. Error was invalid region `8:19315876-19316276`
[2016-04-15T05:19Z] 2016-04-14 22:19:36 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:19:36,717 - WARNING - Could not retrieve variants from source file in region 8:22782060-22782461. Error was invalid region `8:22782061-22782461`
[2016-04-15T05:19Z] 2016-04-14 22:19:36 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:19:36,848 - WARNING - Could not retrieve variants from source file in region 8:24810853-24811255. Error was invalid region `8:24810854-24811255`
[2016-04-15T05:19Z] 2016-04-14 22:19:38 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:19:38,239 - WARNING - Could not retrieve variants from source file in region 8:27358294-27358695. Error was invalid region `8:27358295-27358695`
[2016-04-15T05:19Z] 2016-04-14 22:19:38 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:19:38,293 - WARNING - Could not retrieve variants from source file in region 8:23049081-23060446. Error was invalid region `8:23049082-23060446`
[2016-04-15T05:19Z] 2016-04-14 22:19:38 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:19:38,502 - WARNING - Could not retrieve variants from source file in region 8:24193053-24211521. Error was invalid region `8:24193054-24211521`
[2016-04-15T05:19Z] 2016-04-14 22:19:39 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:19:39,044 - WARNING - Could not retrieve variants from source file in region 8:22526348-22571208. Error was invalid region `8:22526349-22571208`
[2016-04-15T05:19Z] 2016-04-14 22:19:40 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:19:40,094 - WARNING - Could not retrieve variants from source file in region 8:28200283-28206465. Error was invalid region `8:28200284-28206465`
[2016-04-15T05:19Z] 2016-04-14 22:19:40 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:19:40,104 - WARNING - Could not retrieve variants from source file in region 8:28285963-28304959. Error was invalid region `8:28285964-28304959`
[2016-04-15T05:19Z] 2016-04-14 22:19:40 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:19:40,945 - WARNING - Could not retrieve variants from source file in region 8:24339468-24367223. Error was invalid region `8:24339469-24367223`
[2016-04-15T05:19Z] 2016-04-14 22:19:42 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:19:42,508 - WARNING - Could not retrieve variants from source file in region 8:24810853-24811255. Error was invalid region `8:24810854-24811255`
[2016-04-15T05:19Z] 2016-04-14 22:19:42 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:19:42,794 - WARNING - Could not retrieve variants from source file in region 8:22782060-22782461. Error was invalid region `8:22782061-22782461`
[2016-04-15T05:19Z] 2016-04-14 22:19:43 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:19:43,419 - WARNING - Could not retrieve variants from source file in region 8:27358294-27358695. Error was invalid region `8:27358295-27358695`
[2016-04-15T05:19Z] 2016-04-14 22:19:44 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:19:44,234 - WARNING - Could not retrieve variants from source file in region 8:24193053-24211521. Error was invalid region `8:24193054-24211521`
[2016-04-15T05:19Z] 2016-04-14 22:19:45 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:19:45,437 - WARNING - Could not retrieve variants from source file in region 8:28200283-28206465. Error was invalid region `8:28200284-28206465`
[2016-04-15T05:19Z] 2016-04-14 22:19:55 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:19:55,139 - WARNING - Could not retrieve variants from source file in region 8:27917846-27928039. Error was invalid region `8:27917847-27928039`
[2016-04-15T05:19Z] 2016-04-14 22:19:56 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:19:56,192 - WARNING - Could not retrieve variants from source file in region 8:19218555-19221890. Error was invalid region `8:19218556-19221890`
[2016-04-15T05:19Z] 2016-04-14 22:19:56 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:19:56,373 - WARNING - Could not retrieve variants from source file in region 8:24256259-24261716. Error was invalid region `8:24256260-24261716`
[2016-04-15T05:19Z] 2016-04-14 22:19:56 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:19:56,857 - WARNING - Could not retrieve variants from source file in region 8:23001777-23021536. Error was invalid region `8:23001778-23021536`
[2016-04-15T05:19Z] 2016-04-14 22:19:57 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:19:57,853 - WARNING - Could not retrieve variants from source file in region 8:27254917-27325012. Error was invalid region `8:27254918-27325012`
[2016-04-15T05:19Z] 2016-04-14 22:19:59 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:19:59,122 - WARNING - Could not retrieve variants from source file in region 8:23423458-23424419. Error was invalid region `8:23423459-23424419`
[2016-04-15T05:19Z] 2016-04-14 22:19:59 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:19:59,160 - WARNING - Could not retrieve variants from source file in region 8:22974114-22974640. Error was invalid region `8:22974115-22974640`
[2016-04-15T05:20Z] 2016-04-14 22:20:00 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:20:00,687 - WARNING - Could not retrieve variants from source file in region 8:22021722-22022123. Error was invalid region `8:22021723-22022123`
[2016-04-15T05:20Z] 2016-04-14 22:20:02 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:20:02,213 - WARNING - Could not retrieve variants from source file in region 8:22409191-22460291. Error was invalid region `8:22409192-22460291`
[2016-04-15T05:20Z] 2016-04-14 22:20:03 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:20:03,265 - WARNING - Could not retrieve variants from source file in region 8:22974114-22974640. Error was invalid region `8:22974115-22974640`
[2016-04-15T05:20Z] 2016-04-14 22:20:03 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:20:03,574 - WARNING - Could not retrieve variants from source file in region 8:21846375-21862741. Error was invalid region `8:21846376-21862741`
[2016-04-15T05:20Z] 2016-04-14 22:20:05 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:20:05,007 - WARNING - Could not retrieve variants from source file in region 8:24256259-24261716. Error was invalid region `8:24256260-24261716`
[2016-04-15T05:20Z] 2016-04-14 22:20:06 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:20:06,333 - WARNING - Could not retrieve variants from source file in region 8:22409191-22460291. Error was invalid region `8:22409192-22460291`
[2016-04-15T05:20Z] 2016-04-14 22:20:07 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:20:07,753 - WARNING - Could not retrieve variants from source file in region 8:22974114-22974640. Error was invalid region `8:22974115-22974640`
[2016-04-15T05:20Z] 2016-04-14 22:20:07 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:20:07,867 - WARNING - Could not retrieve variants from source file in region 8:21846375-21862741. Error was invalid region `8:21846376-21862741`
[2016-04-15T05:20Z] 2016-04-14 22:20:14 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:20:14,512 - WARNING - Could not retrieve variants from source file in region 8:27101068-27101469. Error was invalid region `8:27101069-27101469`
[2016-04-15T05:20Z] 2016-04-14 22:20:15 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:20:15,659 - WARNING - Could not retrieve variants from source file in region 8:19171329-19192522. Error was invalid region `8:19171330-19192522`
[2016-04-15T05:20Z] 2016-04-14 22:20:17 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:20:17,335 - WARNING - Could not retrieve variants from source file in region 8:19171329-19192522. Error was invalid region `8:19171330-19192522`
[2016-04-15T05:20Z] 2016-04-14 22:20:17 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:20:17,656 - WARNING - Could not retrieve variants from source file in region 8:18729606-18730008. Error was invalid region `8:18729607-18730008`
[2016-04-15T05:20Z] 2016-04-14 22:20:19 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:20:19,513 - WARNING - Could not retrieve variants from source file in region 8:26481560-26481961. Error was invalid region `8:26481561-26481961`
[2016-04-15T05:20Z] 2016-04-14 22:20:19 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:20:19,665 - WARNING - Could not retrieve variants from source file in region 8:20110430-20110831. Error was invalid region `8:20110431-20110831`
[2016-04-15T05:20Z] 2016-04-14 22:20:20 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:20:20,350 - WARNING - Could not retrieve variants from source file in region 8:21550589-21550990. Error was invalid region `8:21550590-21550990`
[2016-04-15T05:20Z] 2016-04-14 22:20:21 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:20:21,666 - WARNING - Could not retrieve variants from source file in region 8:21952015-21985135. Error was invalid region `8:21952016-21985135`
[2016-04-15T05:20Z] 2016-04-14 22:20:21 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:20:21,853 - WARNING - Could not retrieve variants from source file in region 8:18729606-18730008. Error was invalid region `8:18729607-18730008`
[2016-04-15T05:20Z] 2016-04-14 22:20:21 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:20:21,897 - WARNING - Could not retrieve variants from source file in region 8:21550589-21550990. Error was invalid region `8:21550590-21550990`
[2016-04-15T05:20Z] 2016-04-14 22:20:23 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:20:23,561 - WARNING - Could not retrieve variants from source file in region 8:26481560-26481961. Error was invalid region `8:26481561-26481961`
[2016-04-15T05:20Z] 2016-04-14 22:20:24 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:20:24,509 - WARNING - Could not retrieve variants from source file in region 8:21550589-21550990. Error was invalid region `8:21550590-21550990`
[2016-04-15T05:20Z] 2016-04-14 22:20:27 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:20:27,844 - WARNING - Could not retrieve variants from source file in region 8:26510581-26510982. Error was invalid region `8:26510582-26510982`
[2016-04-15T05:20Z] 2016-04-14 22:20:27 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:20:27,857 - WARNING - Could not retrieve variants from source file in region 8:26481560-26481961. Error was invalid region `8:26481561-26481961`
[2016-04-15T05:20Z] 2016-04-14 22:20:30 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:20:30,107 - WARNING - Could not retrieve variants from source file in region 8:20036502-20037017. Error was invalid region `8:20036503-20037017`
[2016-04-15T05:20Z] 2016-04-14 22:20:32 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:20:32,483 - WARNING - Could not retrieve variants from source file in region 8:26510581-26510982. Error was invalid region `8:26510582-26510982`
[2016-04-15T05:20Z] 2016-04-14 22:20:32 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:20:32,569 - WARNING - Could not retrieve variants from source file in region 8:17230433-17230834. Error was invalid region `8:17230434-17230834`
[2016-04-15T05:20Z] 2016-04-14 22:20:33 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:20:33,825 - WARNING - Could not retrieve variants from source file in region 8:17918723-17941858. Error was invalid region `8:17918724-17941858`
[2016-04-15T05:20Z] 2016-04-14 22:20:33 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:20:33,942 - WARNING - Could not retrieve variants from source file in region 8:18257584-18258506. Error was invalid region `8:18257585-18258506`
[2016-04-15T05:20Z] 2016-04-14 22:20:34 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:20:34,462 - WARNING - Could not retrieve variants from source file in region 8:20036502-20037017. Error was invalid region `8:20036503-20037017`
[2016-04-15T05:20Z] 2016-04-14 22:20:35 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:20:35,157 - WARNING - Could not retrieve variants from source file in region 8:26510581-26510982. Error was invalid region `8:26510582-26510982`
[2016-04-15T05:20Z] 2016-04-14 22:20:36 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:20:36,725 - WARNING - Could not retrieve variants from source file in region 8:17230433-17230834. Error was invalid region `8:17230434-17230834`
[2016-04-15T05:20Z] 2016-04-14 22:20:37 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:20:37,796 - WARNING - Could not retrieve variants from source file in region 8:17918723-17941858. Error was invalid region `8:17918724-17941858`
[2016-04-15T05:20Z] 2016-04-14 22:20:38 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:20:38,168 - WARNING - Could not retrieve variants from source file in region 8:18076796-18077197. Error was invalid region `8:18076797-18077197`
[2016-04-15T05:20Z] 2016-04-14 22:20:38 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:20:38,193 - WARNING - Could not retrieve variants from source file in region 8:19810615-19811016. Error was invalid region `8:19810616-19811016`
[2016-04-15T05:20Z] 2016-04-14 22:20:39 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:20:39,335 - WARNING - Could not retrieve variants from source file in region 8:26441266-26441667. Error was invalid region `8:26441267-26441667`
[2016-04-15T05:20Z] 2016-04-14 22:20:40 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:20:40,593 - WARNING - Could not retrieve variants from source file in region 8:17230433-17230834. Error was invalid region `8:17230434-17230834`
[2016-04-15T05:20Z] 2016-04-14 22:20:41 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:20:41,836 - WARNING - Could not retrieve variants from source file in region 8:17796171-17819762. Error was invalid region `8:17796172-17819762`
[2016-04-15T05:20Z] 2016-04-14 22:20:41 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:20:41,898 - WARNING - Could not retrieve variants from source file in region 8:18076796-18077197. Error was invalid region `8:18076797-18077197`
[2016-04-15T05:20Z] 2016-04-14 22:20:41 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:20:41,997 - WARNING - Could not retrieve variants from source file in region 8:19810615-19811016. Error was invalid region `8:19810616-19811016`
[2016-04-15T05:20Z] 2016-04-14 22:20:45 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:20:45,703 - WARNING - Could not retrieve variants from source file in region 8:18076796-18077197. Error was invalid region `8:18076797-18077197`
[2016-04-15T05:20Z] 2016-04-14 22:20:48 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:20:48,063 - WARNING - Could not retrieve variants from source file in region 8:17739327-17743210. Error was invalid region `8:17739328-17743210`
[2016-04-15T05:20Z] 2016-04-14 22:20:49 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:20:49,023 - WARNING - Could not retrieve variants from source file in region 8:17796171-17819762. Error was invalid region `8:17796172-17819762`
[2016-04-15T05:20Z] 2016-04-14 22:20:49 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:20:49,401 - WARNING - Could not retrieve variants from source file in region 8:17739327-17743210. Error was invalid region `8:17739328-17743210`
[2016-04-15T05:20Z] 2016-04-14 22:20:49 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:20:49,743 - WARNING - Could not retrieve variants from source file in region 8:26240435-26240836. Error was invalid region `8:26240436-26240836`
[2016-04-15T05:20Z] 2016-04-14 22:20:51 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:20:51,203 - WARNING - Could not retrieve variants from source file in region 8:17486071-17503621. Error was invalid region `8:17486072-17503621`
[2016-04-15T05:20Z] 2016-04-14 22:20:51 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:20:51,212 - WARNING - Could not retrieve variants from source file in region 8:17125557-17142255. Error was invalid region `8:17125558-17142255`
[2016-04-15T05:20Z] 2016-04-14 22:20:53 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:20:53,323 - WARNING - Could not retrieve variants from source file in region 8:17089353-17089759. Error was invalid region `8:17089354-17089759`
[2016-04-15T05:20Z] 2016-04-14 22:20:53 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:20:53,335 - WARNING - Could not retrieve variants from source file in region 8:16859187-16859630. Error was invalid region `8:16859188-16859630`
[2016-04-15T05:20Z] 2016-04-14 22:20:53 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:20:53,447 - WARNING - Could not retrieve variants from source file in region 8:17396169-17396605. Error was invalid region `8:17396170-17396605`
[2016-04-15T05:20Z] 2016-04-14 22:20:53 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:20:53,520 - WARNING - Could not retrieve variants from source file in region 8:17486071-17503621. Error was invalid region `8:17486072-17503621`
[2016-04-15T05:20Z] 2016-04-14 22:20:53 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:20:53,751 - WARNING - Could not retrieve variants from source file in region 8:17125557-17142255. Error was invalid region `8:17125558-17142255`
[2016-04-15T05:20Z] 2016-04-14 22:20:53 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:20:53,754 - WARNING - Could not retrieve variants from source file in region 8:26240435-26240836. Error was invalid region `8:26240436-26240836`
[2016-04-15T05:20Z] 2016-04-14 22:20:55 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:20:55,187 - WARNING - Could not retrieve variants from source file in region 8:17125557-17142255. Error was invalid region `8:17125558-17142255`
[2016-04-15T05:20Z] 2016-04-14 22:20:55 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:20:55,210 - WARNING - Could not retrieve variants from source file in region 8:17486071-17503621. Error was invalid region `8:17486072-17503621`
[2016-04-15T05:20Z] 2016-04-14 22:20:57 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:20:57,113 - WARNING - Could not retrieve variants from source file in region 8:17089353-17089759. Error was invalid region `8:17089354-17089759`
[2016-04-15T05:21Z] 2016-04-14 22:21:00 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:21:00,650 - WARNING - Could not retrieve variants from source file in region 8:17270576-17270977. Error was invalid region `8:17270577-17270977`
[2016-04-15T05:21Z] 2016-04-14 22:21:01 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:21:01,018 - WARNING - Could not retrieve variants from source file in region 8:17270576-17270977. Error was invalid region `8:17270577-17270977`
[2016-04-15T05:21Z] 2016-04-14 22:21:01 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:21:01,487 - WARNING - Could not retrieve variants from source file in region 8:17270576-17270977. Error was invalid region `8:17270577-17270977`
[2016-04-15T05:21Z] 2016-04-14 22:21:01 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:21:01,519 - WARNING - Could not retrieve variants from source file in region 8:15977852-15998335. Error was invalid region `8:15977853-15998335`
[2016-04-15T05:21Z] 2016-04-14 22:21:01 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:21:01,521 - WARNING - Could not retrieve variants from source file in region 8:15977852-15998335. Error was invalid region `8:15977853-15998335`
[2016-04-15T05:21Z] 2016-04-14 22:21:02 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:21:02,916 - WARNING - Could not retrieve variants from source file in region 8:15977852-15998335. Error was invalid region `8:15977853-15998335`
[2016-04-15T05:21Z] 2016-04-14 22:21:04 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:21:04,845 - WARNING - Could not retrieve variants from source file in region 8:15615478-15615879. Error was invalid region `8:15615479-15615879`
[2016-04-15T05:21Z] 2016-04-14 22:21:04 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:21:04,852 - WARNING - Could not retrieve variants from source file in region 8:15615478-15615879. Error was invalid region `8:15615479-15615879`
[2016-04-15T05:21Z] 2016-04-14 22:21:04 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:21:04,853 - WARNING - Could not retrieve variants from source file in region 8:15615478-15615879. Error was invalid region `8:15615479-15615879`
[2016-04-15T05:21Z] ['bcbio-variation-recall', 'square', '-Xms750m', '-Xmx7280m', '-XX:+UseSerialGC', '-c', 16, '-r', u'8:31496911-48001429', '--caller', 'platypus', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/8/Batch1-8_31496910_48001429.vcf.gz', '/mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/8/Batch1-8_31496910_48001429.vcf-inputs.txt'] in region: 8:31496911-48001429
[2016-04-15T05:21Z] 2016-04-14 22:21:19 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:21:19,882 - WARNING - Could not retrieve variants from source file in region 8:33355863-33370184. Error was invalid region `8:33355864-33370184`
[2016-04-15T05:21Z] 2016-04-14 22:21:21 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:21:21,105 - WARNING - Could not retrieve variants from source file in region 8:39495818-39496219. Error was invalid region `8:39495819-39496219`
[2016-04-15T05:21Z] 2016-04-14 22:21:21 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:21:21,753 - WARNING - Could not retrieve variants from source file in region 8:32453147-32453548. Error was invalid region `8:32453148-32453548`
[2016-04-15T05:21Z] 2016-04-14 22:21:21 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:21:21,947 - WARNING - Could not retrieve variants from source file in region 8:36788268-36788669. Error was invalid region `8:36788269-36788669`
[2016-04-15T05:21Z] 2016-04-14 22:21:22 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:21:22,248 - WARNING - Could not retrieve variants from source file in region 8:41791072-41798607. Error was invalid region `8:41791073-41798607`
[2016-04-15T05:21Z] 2016-04-14 22:21:22 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:21:22,439 - WARNING - Could not retrieve variants from source file in region 8:37985686-38006407. Error was invalid region `8:37985687-38006407`
[2016-04-15T05:21Z] 2016-04-14 22:21:22 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:21:22,555 - WARNING - Could not retrieve variants from source file in region 8:43048984-43054743. Error was invalid region `8:43048985-43054743`
[2016-04-15T05:21Z] 2016-04-14 22:21:22 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:21:22,930 - WARNING - Could not retrieve variants from source file in region 8:37619865-37620266. Error was invalid region `8:37619866-37620266`
[2016-04-15T05:21Z] 2016-04-14 22:21:23 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:21:23,143 - WARNING - Could not retrieve variants from source file in region 8:38126148-38126549. Error was invalid region `8:38126149-38126549`
[2016-04-15T05:21Z] 2016-04-14 22:21:23 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:21:23,375 - WARNING - Could not retrieve variants from source file in region 8:41166426-41166830. Error was invalid region `8:41166427-41166830`
[2016-04-15T05:21Z] 2016-04-14 22:21:23 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:21:23,421 - WARNING - Could not retrieve variants from source file in region 8:42044743-42045144. Error was invalid region `8:42044744-42045144`
[2016-04-15T05:21Z] 2016-04-14 22:21:24 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:21:24,691 - WARNING - Could not retrieve variants from source file in region 8:33355863-33370184. Error was invalid region `8:33355864-33370184`
[2016-04-15T05:21Z] 2016-04-14 22:21:28 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:21:28,636 - WARNING - Could not retrieve variants from source file in region 8:32453147-32453548. Error was invalid region `8:32453148-32453548`
[2016-04-15T05:21Z] 2016-04-14 22:21:30 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:21:30,263 - WARNING - Could not retrieve variants from source file in region 8:43048984-43054743. Error was invalid region `8:43048985-43054743`
[2016-04-15T05:21Z] 2016-04-14 22:21:31 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:21:31,299 - WARNING - Could not retrieve variants from source file in region 8:38176224-38176625. Error was invalid region `8:38176225-38176625`
[2016-04-15T05:21Z] 2016-04-14 22:21:31 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:21:31,432 - WARNING - Could not retrieve variants from source file in region 8:37619865-37620266. Error was invalid region `8:37619866-37620266`
[2016-04-15T05:21Z] 2016-04-14 22:21:32 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:21:32,293 - WARNING - Could not retrieve variants from source file in region 8:42044743-42045144. Error was invalid region `8:42044744-42045144`
[2016-04-15T05:21Z] 2016-04-14 22:21:32 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:21:32,392 - WARNING - Could not retrieve variants from source file in region 8:38614674-38615075. Error was invalid region `8:38614675-38615075`
[2016-04-15T05:21Z] 2016-04-14 22:21:33 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:21:33,005 - WARNING - Could not retrieve variants from source file in region 8:39080421-39091716. Error was invalid region `8:39080422-39091716`
[2016-04-15T05:21Z] 2016-04-14 22:21:33 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:21:33,197 - WARNING - Could not retrieve variants from source file in region 8:33355863-33370184. Error was invalid region `8:33355864-33370184`
[2016-04-15T05:21Z] 2016-04-14 22:21:33 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:21:33,235 - WARNING - Could not retrieve variants from source file in region 8:37593937-37594339. Error was invalid region `8:37593938-37594339`
[2016-04-15T05:21Z] 2016-04-14 22:21:33 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:21:33,247 - WARNING - Could not retrieve variants from source file in region 8:39495818-39496219. Error was invalid region `8:39495819-39496219`
[2016-04-15T05:21Z] 2016-04-14 22:21:33 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:21:33,637 - WARNING - Could not retrieve variants from source file in region 8:32453147-32453548. Error was invalid region `8:32453148-32453548`
[2016-04-15T05:21Z] 2016-04-14 22:21:35 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:21:35,100 - WARNING - Could not retrieve variants from source file in region 8:41791072-41798607. Error was invalid region `8:41791073-41798607`
[2016-04-15T05:21Z] 2016-04-14 22:21:35 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:21:35,642 - WARNING - Could not retrieve variants from source file in region 8:43048984-43054743. Error was invalid region `8:43048985-43054743`
[2016-04-15T05:21Z] 2016-04-14 22:21:37 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:21:37,674 - WARNING - Could not retrieve variants from source file in region 8:37619865-37620266. Error was invalid region `8:37619866-37620266`
[2016-04-15T05:21Z] 2016-04-14 22:21:40 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:21:40,025 - WARNING - Could not retrieve variants from source file in region 8:38614674-38615075. Error was invalid region `8:38614675-38615075`
[2016-04-15T05:21Z] 2016-04-14 22:21:40 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:21:40,667 - WARNING - Could not retrieve variants from source file in region 8:42044743-42045144. Error was invalid region `8:42044744-42045144`
[2016-04-15T05:21Z] 2016-04-14 22:21:40 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:21:40,874 - WARNING - Could not retrieve variants from source file in region 8:38126148-38126549. Error was invalid region `8:38126149-38126549`
[2016-04-15T05:21Z] 2016-04-14 22:21:40 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:21:40,910 - WARNING - Could not retrieve variants from source file in region 8:37593937-37594339. Error was invalid region `8:37593938-37594339`
[2016-04-15T05:21Z] 2016-04-14 22:21:40 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:21:40,951 - WARNING - Could not retrieve variants from source file in region 8:38677111-38696186. Error was invalid region `8:38677112-38696186`
[2016-04-15T05:21Z] 2016-04-14 22:21:50 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:21:50,036 - WARNING - Could not retrieve variants from source file in region 8:39468731-39469132. Error was invalid region `8:39468732-39469132`
[2016-04-15T05:21Z] 2016-04-14 22:21:52 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:21:52,757 - WARNING - Could not retrieve variants from source file in region 8:32405768-32406338. Error was invalid region `8:32405769-32406338`
[2016-04-15T05:21Z] 2016-04-14 22:21:53 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:21:53,114 - WARNING - Could not retrieve variants from source file in region 8:33415978-33416412. Error was invalid region `8:33415979-33416412`
[2016-04-15T05:21Z] 2016-04-14 22:21:54 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:21:54,543 - WARNING - Could not retrieve variants from source file in region 8:42231575-42231976. Error was invalid region `8:42231576-42231976`
[2016-04-15T05:21Z] 2016-04-14 22:21:54 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:21:54,585 - WARNING - Could not retrieve variants from source file in region 8:40644012-40644413. Error was invalid region `8:40644013-40644413`
[2016-04-15T05:21Z] 2016-04-14 22:21:55 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:21:55,066 - WARNING - Could not retrieve variants from source file in region 8:33415978-33416412. Error was invalid region `8:33415979-33416412`
[2016-04-15T05:21Z] 2016-04-14 22:21:55 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:21:55,128 - WARNING - Could not retrieve variants from source file in region 8:38965060-38965461. Error was invalid region `8:38965061-38965461`
[2016-04-15T05:21Z] 2016-04-14 22:21:55 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:21:55,265 - WARNING - Could not retrieve variants from source file in region 8:39468731-39469132. Error was invalid region `8:39468732-39469132`
[2016-04-15T05:21Z] 2016-04-14 22:21:56 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:21:56,085 - WARNING - Could not retrieve variants from source file in region 8:40010868-40011269. Error was invalid region `8:40010869-40011269`
[2016-04-15T05:21Z] 2016-04-14 22:21:57 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:21:57,887 - WARNING - Could not retrieve variants from source file in region 8:32405768-32406338. Error was invalid region `8:32405769-32406338`
[2016-04-15T05:21Z] 2016-04-14 22:21:57 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:21:57,985 - WARNING - Could not retrieve variants from source file in region 8:33415978-33416412. Error was invalid region `8:33415979-33416412`
[2016-04-15T05:21Z] 2016-04-14 22:21:59 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:21:59,924 - WARNING - Could not retrieve variants from source file in region 8:42186943-42187902. Error was invalid region `8:42186944-42187902`
[2016-04-15T05:22Z] 2016-04-14 22:22:00 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:22:00,730 - WARNING - Could not retrieve variants from source file in region 8:32504190-32504591. Error was invalid region `8:32504191-32504591`
[2016-04-15T05:22Z] 2016-04-14 22:22:01 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:22:01,314 - WARNING - Could not retrieve variants from source file in region 8:41905884-41906285. Error was invalid region `8:41905885-41906285`
[2016-04-15T05:22Z] 2016-04-14 22:22:01 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:22:01,732 - WARNING - Could not retrieve variants from source file in region 8:38095451-38095852. Error was invalid region `8:38095452-38095852`
[2016-04-15T05:22Z] 2016-04-14 22:22:01 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:22:01,807 - WARNING - Could not retrieve variants from source file in region 8:38965060-38965461. Error was invalid region `8:38965061-38965461`
[2016-04-15T05:22Z] 2016-04-14 22:22:01 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:22:01,984 - WARNING - Could not retrieve variants from source file in region 8:39468731-39469132. Error was invalid region `8:39468732-39469132`
[2016-04-15T05:22Z] 2016-04-14 22:22:02 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:22:02,042 - WARNING - Could not retrieve variants from source file in region 8:40010868-40011269. Error was invalid region `8:40010869-40011269`
[2016-04-15T05:22Z] 2016-04-14 22:22:02 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:22:02,407 - WARNING - Could not retrieve variants from source file in region 8:38826974-38854231. Error was invalid region `8:38826975-38854231`
[2016-04-15T05:22Z] 2016-04-14 22:22:02 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:22:02,719 - WARNING - Could not retrieve variants from source file in region 8:32405768-32406338. Error was invalid region `8:32405769-32406338`
[2016-04-15T05:22Z] 2016-04-14 22:22:03 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:22:03,230 - WARNING - Could not retrieve variants from source file in region 8:38644585-38645104. Error was invalid region `8:38644586-38645104`
[2016-04-15T05:22Z] 2016-04-14 22:22:04 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:22:04,141 - WARNING - Could not retrieve variants from source file in region 8:42186943-42187902. Error was invalid region `8:42186944-42187902`
[2016-04-15T05:22Z] 2016-04-14 22:22:06 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:22:06,495 - WARNING - Could not retrieve variants from source file in region 8:32504190-32504591. Error was invalid region `8:32504191-32504591`
[2016-04-15T05:22Z] 2016-04-14 22:22:07 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:22:07,414 - WARNING - Could not retrieve variants from source file in region 8:42231575-42231976. Error was invalid region `8:42231576-42231976`
[2016-04-15T05:22Z] 2016-04-14 22:22:07 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:22:07,771 - WARNING - Could not retrieve variants from source file in region 8:40644012-40644413. Error was invalid region `8:40644013-40644413`
[2016-04-15T05:22Z] 2016-04-14 22:22:08 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:22:08,896 - WARNING - Could not retrieve variants from source file in region 8:38965060-38965461. Error was invalid region `8:38965061-38965461`
[2016-04-15T05:22Z] 2016-04-14 22:22:09 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:22:09,867 - WARNING - Could not retrieve variants from source file in region 8:38644585-38645104. Error was invalid region `8:38644586-38645104`
[2016-04-15T05:22Z] 2016-04-14 22:22:09 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:22:09,877 - WARNING - Could not retrieve variants from source file in region 8:40010868-40011269. Error was invalid region `8:40010869-40011269`
[2016-04-15T05:22Z] 2016-04-14 22:22:10 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:22:10,243 - WARNING - Could not retrieve variants from source file in region 8:42186943-42187902. Error was invalid region `8:42186944-42187902`
[2016-04-15T05:22Z] 2016-04-14 22:22:10 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:22:10,345 - WARNING - Could not retrieve variants from source file in region 8:38826974-38854231. Error was invalid region `8:38826975-38854231`
[2016-04-15T05:22Z] 2016-04-14 22:22:11 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:22:11,558 - WARNING - Could not retrieve variants from source file in region 8:41905884-41906285. Error was invalid region `8:41905885-41906285`
[2016-04-15T05:22Z] 2016-04-14 22:22:15 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:22:15,598 - WARNING - Could not retrieve variants from source file in region 8:38095451-38095852. Error was invalid region `8:38095452-38095852`
[2016-04-15T05:22Z] 2016-04-14 22:22:17 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:22:17,911 - WARNING - Could not retrieve variants from source file in region 8:39862670-39873125. Error was invalid region `8:39862671-39873125`
[2016-04-15T05:22Z] 2016-04-14 22:22:18 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:22:18,526 - WARNING - Could not retrieve variants from source file in region 8:41525703-41526104. Error was invalid region `8:41525704-41526104`
[2016-04-15T05:22Z] 2016-04-14 22:22:20 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:22:20,012 - WARNING - Could not retrieve variants from source file in region 8:41525703-41526104. Error was invalid region `8:41525704-41526104`
[2016-04-15T05:22Z] 2016-04-14 22:22:20 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:22:20,348 - WARNING - Could not retrieve variants from source file in region 8:42155689-42156090. Error was invalid region `8:42155690-42156090`
[2016-04-15T05:22Z] 2016-04-14 22:22:20 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:22:20,564 - WARNING - Could not retrieve variants from source file in region 8:31497461-31497862. Error was invalid region `8:31497462-31497862`
[2016-04-15T05:22Z] 2016-04-14 22:22:23 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:22:23,076 - WARNING - Could not retrieve variants from source file in region 8:37698984-37699385. Error was invalid region `8:37698985-37699385`
[2016-04-15T05:22Z] 2016-04-14 22:22:23 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:22:23,241 - WARNING - Could not retrieve variants from source file in region 8:37698984-37699385. Error was invalid region `8:37698985-37699385`
[2016-04-15T05:22Z] 2016-04-14 22:22:24 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:22:24,011 - WARNING - Could not retrieve variants from source file in region 8:42155689-42156090. Error was invalid region `8:42155690-42156090`
[2016-04-15T05:22Z] ['bcbio-variation-recall', 'square', '-Xms750m', '-Xmx7280m', '-XX:+UseSerialGC', '-c', 16, '-r', u'8:48003023-63659688', '--caller', 'platypus', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/8/Batch1-8_48003022_63659688.vcf.gz', '/mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/8/Batch1-8_48003022_63659688.vcf-inputs.txt'] in region: 8:48003023-63659688
[2016-04-15T05:22Z] 2016-04-14 22:22:39 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:22:39,582 - WARNING - Could not retrieve variants from source file in region 8:48805605-48806006. Error was invalid region `8:48805606-48806006`
[2016-04-15T05:22Z] 2016-04-14 22:22:40 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:22:40,923 - WARNING - Could not retrieve variants from source file in region 8:61178363-61178764. Error was invalid region `8:61178364-61178764`
[2016-04-15T05:22Z] 2016-04-14 22:22:41 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:22:41,271 - WARNING - Could not retrieve variants from source file in region 8:51617044-51617445. Error was invalid region `8:51617045-51617445`
[2016-04-15T05:22Z] 2016-04-14 22:22:41 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:22:41,909 - WARNING - Could not retrieve variants from source file in region 8:49987019-49987991. Error was invalid region `8:49987020-49987991`
[2016-04-15T05:22Z] 2016-04-14 22:22:41 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:22:41,953 - WARNING - Could not retrieve variants from source file in region 8:63659399-63659800. Error was invalid region `8:63659400-63659800`
[2016-04-15T05:22Z] 2016-04-14 22:22:45 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:22:45,106 - WARNING - Could not retrieve variants from source file in region 8:48805605-48806006. Error was invalid region `8:48805606-48806006`
[2016-04-15T05:22Z] 2016-04-14 22:22:45 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:22:45,862 - WARNING - Could not retrieve variants from source file in region 8:52396030-52396431. Error was invalid region `8:52396031-52396431`
[2016-04-15T05:22Z] 2016-04-14 22:22:45 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:22:45,879 - WARNING - Could not retrieve variants from source file in region 8:52232276-52258619. Error was invalid region `8:52232277-52258619`
[2016-04-15T05:22Z] 2016-04-14 22:22:47 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:22:47,582 - WARNING - Could not retrieve variants from source file in region 8:61178363-61178764. Error was invalid region `8:61178364-61178764`
[2016-04-15T05:22Z] 2016-04-14 22:22:49 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:22:49,477 - WARNING - Could not retrieve variants from source file in region 8:55382571-55383038. Error was invalid region `8:55382572-55383038`
[2016-04-15T05:22Z] 2016-04-14 22:22:50 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:22:50,043 - WARNING - Could not retrieve variants from source file in region 8:59329227-59329628. Error was invalid region `8:59329228-59329628`
[2016-04-15T05:22Z] 2016-04-14 22:22:50 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:22:50,104 - WARNING - Could not retrieve variants from source file in region 8:56985603-56986004. Error was invalid region `8:56985604-56986004`
[2016-04-15T05:22Z] 2016-04-14 22:22:50 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:22:50,798 - WARNING - Could not retrieve variants from source file in region 8:57078722-57079123. Error was invalid region `8:57078723-57079123`
[2016-04-15T05:22Z] 2016-04-14 22:22:50 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:22:50,839 - WARNING - Could not retrieve variants from source file in region 8:48805605-48806006. Error was invalid region `8:48805606-48806006`
[2016-04-15T05:22Z] 2016-04-14 22:22:51 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:22:51,150 - WARNING - Could not retrieve variants from source file in region 8:63659399-63659800. Error was invalid region `8:63659400-63659800`
[2016-04-15T05:22Z] 2016-04-14 22:22:59 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:22:59,630 - WARNING - Could not retrieve variants from source file in region 8:63659399-63659800. Error was invalid region `8:63659400-63659800`
[2016-04-15T05:23Z] 2016-04-14 22:23:10 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:23:10,029 - WARNING - Could not retrieve variants from source file in region 8:53569469-53586896. Error was invalid region `8:53569470-53586896`
[2016-04-15T05:23Z] 2016-04-14 22:23:10 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:23:10,811 - WARNING - Could not retrieve variants from source file in region 8:48769635-48770036. Error was invalid region `8:48769636-48770036`
[2016-04-15T05:23Z] 2016-04-14 22:23:12 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:23:12,194 - WARNING - Could not retrieve variants from source file in region 8:59739227-59739628. Error was invalid region `8:59739228-59739628`
[2016-04-15T05:23Z] 2016-04-14 22:23:13 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:23:13,592 - WARNING - Could not retrieve variants from source file in region 8:51570961-51571362. Error was invalid region `8:51570962-51571362`
[2016-04-15T05:23Z] 2016-04-14 22:23:13 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:23:13,671 - WARNING - Could not retrieve variants from source file in region 8:48885225-48885626. Error was invalid region `8:48885226-48885626`
[2016-04-15T05:23Z] 2016-04-14 22:23:15 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:23:15,463 - WARNING - Could not retrieve variants from source file in region 8:62489123-62489524. Error was invalid region `8:62489124-62489524`
[2016-04-15T05:23Z] 2016-04-14 22:23:15 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:23:15,528 - WARNING - Could not retrieve variants from source file in region 8:56686013-56723747. Error was invalid region `8:56686014-56723747`
[2016-04-15T05:23Z] 2016-04-14 22:23:16 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:23:16,117 - WARNING - Could not retrieve variants from source file in region 8:57221861-57222326. Error was invalid region `8:57221862-57222326`
[2016-04-15T05:23Z] 2016-04-14 22:23:16 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:23:16,563 - WARNING - Could not retrieve variants from source file in region 8:52365989-52366490. Error was invalid region `8:52365990-52366490`
[2016-04-15T05:23Z] 2016-04-14 22:23:18 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:23:18,595 - WARNING - Could not retrieve variants from source file in region 8:48885225-48885626. Error was invalid region `8:48885226-48885626`
[2016-04-15T05:23Z] 2016-04-14 22:23:18 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:23:18,654 - WARNING - Could not retrieve variants from source file in region 8:55013736-55014137. Error was invalid region `8:55013737-55014137`
[2016-04-15T05:23Z] 2016-04-14 22:23:20 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:23:20,281 - WARNING - Could not retrieve variants from source file in region 8:48769635-48770036. Error was invalid region `8:48769636-48770036`
[2016-04-15T05:23Z] 2016-04-14 22:23:21 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:23:21,099 - WARNING - Could not retrieve variants from source file in region 8:52365989-52366490. Error was invalid region `8:52365990-52366490`
[2016-04-15T05:23Z] 2016-04-14 22:23:22 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:23:22,148 - WARNING - Could not retrieve variants from source file in region 8:59739227-59739628. Error was invalid region `8:59739228-59739628`
[2016-04-15T05:23Z] 2016-04-14 22:23:22 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:23:22,575 - WARNING - Could not retrieve variants from source file in region 8:48733260-48733661. Error was invalid region `8:48733261-48733661`
[2016-04-15T05:23Z] 2016-04-14 22:23:22 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:23:22,613 - WARNING - Could not retrieve variants from source file in region 8:48885225-48885626. Error was invalid region `8:48885226-48885626`
[2016-04-15T05:23Z] 2016-04-14 22:23:22 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:23:22,685 - WARNING - Could not retrieve variants from source file in region 8:51570961-51571362. Error was invalid region `8:51570962-51571362`
[2016-04-15T05:23Z] 2016-04-14 22:23:24 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:23:24,749 - WARNING - Could not retrieve variants from source file in region 8:62489123-62489524. Error was invalid region `8:62489124-62489524`
[2016-04-15T05:23Z] 2016-04-14 22:23:24 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:23:24,844 - WARNING - Could not retrieve variants from source file in region 8:56686013-56723747. Error was invalid region `8:56686014-56723747`
[2016-04-15T05:23Z] 2016-04-14 22:23:26 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:23:26,845 - WARNING - Could not retrieve variants from source file in region 8:52732839-52746343. Error was invalid region `8:52732840-52746343`
[2016-04-15T05:23Z] 2016-04-14 22:23:27 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:23:27,727 - WARNING - Could not retrieve variants from source file in region 8:48733260-48733661. Error was invalid region `8:48733261-48733661`
[2016-04-15T05:23Z] 2016-04-14 22:23:30 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:23:30,873 - WARNING - Could not retrieve variants from source file in region 8:55632551-55632952. Error was invalid region `8:55632552-55632952`
[2016-04-15T05:23Z] 2016-04-14 22:23:31 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:23:31,899 - WARNING - Could not retrieve variants from source file in region 8:55632551-55632952. Error was invalid region `8:55632552-55632952`
[2016-04-15T05:23Z] 2016-04-14 22:23:33 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:23:33,734 - WARNING - Could not retrieve variants from source file in region 8:59571645-59572046. Error was invalid region `8:59571646-59572046`
[2016-04-15T05:23Z] 2016-04-14 22:23:35 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:23:35,064 - WARNING - Could not retrieve variants from source file in region 8:59571645-59572046. Error was invalid region `8:59571646-59572046`
[2016-04-15T05:23Z] 2016-04-14 22:23:35 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:23:35,208 - WARNING - Could not retrieve variants from source file in region 8:55538846-55542730. Error was invalid region `8:55538847-55542730`
[2016-04-15T05:23Z] 2016-04-14 22:23:36 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:23:36,119 - WARNING - Could not retrieve variants from source file in region 8:59512123-59512524. Error was invalid region `8:59512124-59512524`
[2016-04-15T05:23Z] 2016-04-14 22:23:36 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:23:36,129 - WARNING - Could not retrieve variants from source file in region 8:59512123-59512524. Error was invalid region `8:59512124-59512524`
[2016-04-15T05:23Z] 2016-04-14 22:23:36 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:23:36,132 - WARNING - Could not retrieve variants from source file in region 8:59512123-59512524. Error was invalid region `8:59512124-59512524`
[2016-04-15T05:23Z] ['bcbio-variation-recall', 'square', '-Xms750m', '-Xmx7280m', '-XX:+UseSerialGC', '-c', 16, '-r', u'8:63775820-79510770', '--caller', 'platypus', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/8/Batch1-8_63775819_79510770.vcf.gz', '/mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/8/Batch1-8_63775819_79510770.vcf-inputs.txt'] in region: 8:63775820-79510770
[2016-04-15T05:23Z] 2016-04-14 22:23:50 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:23:50,624 - WARNING - Could not retrieve variants from source file in region 8:64098518-64098919. Error was invalid region `8:64098519-64098919`
[2016-04-15T05:23Z] 2016-04-14 22:23:52 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:23:52,502 - WARNING - Could not retrieve variants from source file in region 8:77617389-77617790. Error was invalid region `8:77617390-77617790`
[2016-04-15T05:23Z] 2016-04-14 22:23:52 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:23:52,598 - WARNING - Could not retrieve variants from source file in region 8:66525337-66525738. Error was invalid region `8:66525338-66525738`
[2016-04-15T05:23Z] 2016-04-14 22:23:52 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:23:52,827 - WARNING - Could not retrieve variants from source file in region 8:69143378-69143779. Error was invalid region `8:69143379-69143779`
[2016-04-15T05:23Z] 2016-04-14 22:23:53 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:23:53,501 - WARNING - Could not retrieve variants from source file in region 8:74462878-74463987. Error was invalid region `8:74462879-74463987`
[2016-04-15T05:23Z] 2016-04-14 22:23:53 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:23:53,545 - WARNING - Could not retrieve variants from source file in region 8:77745424-77766526. Error was invalid region `8:77745425-77766526`
[2016-04-15T05:23Z] 2016-04-14 22:23:54 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:23:54,251 - WARNING - Could not retrieve variants from source file in region 8:75262587-75274331. Error was invalid region `8:75262588-75274331`
[2016-04-15T05:23Z] 2016-04-14 22:23:54 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:23:54,702 - WARNING - Could not retrieve variants from source file in region 8:77895654-77896055. Error was invalid region `8:77895655-77896055`
[2016-04-15T05:23Z] 2016-04-14 22:23:54 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:23:54,750 - WARNING - Could not retrieve variants from source file in region 8:69445591-69445992. Error was invalid region `8:69445592-69445992`
[2016-04-15T05:23Z] 2016-04-14 22:23:54 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:23:54,753 - WARNING - Could not retrieve variants from source file in region 8:70744601-70745002. Error was invalid region `8:70744602-70745002`
[2016-04-15T05:23Z] 2016-04-14 22:23:55 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:23:55,309 - WARNING - Could not retrieve variants from source file in region 8:64098518-64098919. Error was invalid region `8:64098519-64098919`
[2016-04-15T05:23Z] 2016-04-14 22:23:56 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:23:56,575 - WARNING - Could not retrieve variants from source file in region 8:65527458-65527859. Error was invalid region `8:65527459-65527859`
[2016-04-15T05:23Z] 2016-04-14 22:23:57 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:23:57,118 - WARNING - Could not retrieve variants from source file in region 8:66620148-66620549. Error was invalid region `8:66620149-66620549`
[2016-04-15T05:23Z] 2016-04-14 22:23:59 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:23:59,277 - WARNING - Could not retrieve variants from source file in region 8:69143378-69143779. Error was invalid region `8:69143379-69143779`
[2016-04-15T05:24Z] 2016-04-14 22:24:00 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:24:00,850 - WARNING - Could not retrieve variants from source file in region 8:67576967-67592342. Error was invalid region `8:67576968-67592342`
[2016-04-15T05:24Z] 2016-04-14 22:24:01 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:24:01,458 - WARNING - Could not retrieve variants from source file in region 8:68396704-68397105. Error was invalid region `8:68396705-68397105`
[2016-04-15T05:24Z] 2016-04-14 22:24:01 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:24:01,667 - WARNING - Could not retrieve variants from source file in region 8:75262587-75274331. Error was invalid region `8:75262588-75274331`
[2016-04-15T05:24Z] 2016-04-14 22:24:01 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:24:01,937 - WARNING - Could not retrieve variants from source file in region 8:77895654-77896055. Error was invalid region `8:77895655-77896055`
[2016-04-15T05:24Z] 2016-04-14 22:24:02 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:24:02,124 - WARNING - Could not retrieve variants from source file in region 8:64098518-64098919. Error was invalid region `8:64098519-64098919`
[2016-04-15T05:24Z] 2016-04-14 22:24:02 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:24:02,423 - WARNING - Could not retrieve variants from source file in region 8:65527458-65527859. Error was invalid region `8:65527459-65527859`
[2016-04-15T05:24Z] 2016-04-14 22:24:02 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:24:02,436 - WARNING - Could not retrieve variants from source file in region 8:70744601-70745002. Error was invalid region `8:70744602-70745002`
[2016-04-15T05:24Z] 2016-04-14 22:24:02 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:24:02,509 - WARNING - Could not retrieve variants from source file in region 8:66620148-66620549. Error was invalid region `8:66620149-66620549`
[2016-04-15T05:24Z] 2016-04-14 22:24:03 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:24:03,172 - WARNING - Could not retrieve variants from source file in region 8:66525337-66525738. Error was invalid region `8:66525338-66525738`
[2016-04-15T05:24Z] 2016-04-14 22:24:04 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:24:04,599 - WARNING - Could not retrieve variants from source file in region 8:69143378-69143779. Error was invalid region `8:69143379-69143779`
[2016-04-15T05:24Z] 2016-04-14 22:24:06 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:24:06,996 - WARNING - Could not retrieve variants from source file in region 8:67576967-67592342. Error was invalid region `8:67576968-67592342`
[2016-04-15T05:24Z] 2016-04-14 22:24:07 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:24:07,398 - WARNING - Could not retrieve variants from source file in region 8:74462878-74463987. Error was invalid region `8:74462879-74463987`
[2016-04-15T05:24Z] 2016-04-14 22:24:08 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:24:08,093 - WARNING - Could not retrieve variants from source file in region 8:68396704-68397105. Error was invalid region `8:68396705-68397105`
[2016-04-15T05:24Z] 2016-04-14 22:24:09 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:24:09,018 - WARNING - Could not retrieve variants from source file in region 8:75262587-75274331. Error was invalid region `8:75262588-75274331`
[2016-04-15T05:24Z] 2016-04-14 22:24:09 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:24:09,548 - WARNING - Could not retrieve variants from source file in region 8:69445591-69445992. Error was invalid region `8:69445592-69445992`
[2016-04-15T05:24Z] 2016-04-14 22:24:09 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:24:09,676 - WARNING - Could not retrieve variants from source file in region 8:77745424-77766526. Error was invalid region `8:77745425-77766526`
[2016-04-15T05:24Z] 2016-04-14 22:24:09 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:24:09,823 - WARNING - Could not retrieve variants from source file in region 8:77895654-77896055. Error was invalid region `8:77895655-77896055`
[2016-04-15T05:24Z] 2016-04-14 22:24:10 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:24:10,478 - WARNING - Could not retrieve variants from source file in region 8:70744601-70745002. Error was invalid region `8:70744602-70745002`
[2016-04-15T05:24Z] 2016-04-14 22:24:20 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:24:20,399 - WARNING - Could not retrieve variants from source file in region 8:68967955-69020686. Error was invalid region `8:68967956-69020686`
[2016-04-15T05:24Z] 2016-04-14 22:24:21 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:24:21,093 - WARNING - Could not retrieve variants from source file in region 8:65493809-65494210. Error was invalid region `8:65493810-65494210`
[2016-04-15T05:24Z] 2016-04-14 22:24:21 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:24:21,107 - WARNING - Could not retrieve variants from source file in region 8:67813422-67813823. Error was invalid region `8:67813423-67813823`
[2016-04-15T05:24Z] 2016-04-14 22:24:22 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:24:22,076 - WARNING - Could not retrieve variants from source file in region 8:67351556-67380718. Error was invalid region `8:67351557-67380718`
[2016-04-15T05:24Z] 2016-04-14 22:24:23 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:24:23,003 - WARNING - Could not retrieve variants from source file in region 8:68066157-68066558. Error was invalid region `8:68066158-68066558`
[2016-04-15T05:24Z] 2016-04-14 22:24:23 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:24:23,120 - WARNING - Could not retrieve variants from source file in region 8:74527785-74528186. Error was invalid region `8:74527786-74528186`
[2016-04-15T05:24Z] 2016-04-14 22:24:23 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:24:23,987 - WARNING - Could not retrieve variants from source file in region 8:76452102-76468472. Error was invalid region `8:76452103-76468472`
[2016-04-15T05:24Z] 2016-04-14 22:24:24 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:24:24,073 - WARNING - Could not retrieve variants from source file in region 8:74888405-74917274. Error was invalid region `8:74888406-74917274`
[2016-04-15T05:24Z] 2016-04-14 22:24:24 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:24:24,461 - WARNING - Could not retrieve variants from source file in region 8:63775644-63776046. Error was invalid region `8:63775645-63776046`
[2016-04-15T05:24Z] 2016-04-14 22:24:25 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:24:25,949 - WARNING - Could not retrieve variants from source file in region 8:72935934-72936335. Error was invalid region `8:72935935-72936335`
[2016-04-15T05:24Z] 2016-04-14 22:24:26 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:24:26,807 - WARNING - Could not retrieve variants from source file in region 8:73981950-74005321. Error was invalid region `8:73981951-74005321`
[2016-04-15T05:24Z] 2016-04-14 22:24:27 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:24:27,063 - WARNING - Could not retrieve variants from source file in region 8:67813422-67813823. Error was invalid region `8:67813423-67813823`
[2016-04-15T05:24Z] 2016-04-14 22:24:27 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:24:27,239 - WARNING - Could not retrieve variants from source file in region 8:67351556-67380718. Error was invalid region `8:67351557-67380718`
[2016-04-15T05:24Z] 2016-04-14 22:24:27 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:24:27,623 - WARNING - Could not retrieve variants from source file in region 8:74527785-74528186. Error was invalid region `8:74527786-74528186`
[2016-04-15T05:24Z] 2016-04-14 22:24:28 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:24:28,909 - WARNING - Could not retrieve variants from source file in region 8:63775644-63776046. Error was invalid region `8:63775645-63776046`
[2016-04-15T05:24Z] 2016-04-14 22:24:31 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:24:31,376 - WARNING - Could not retrieve variants from source file in region 8:67813422-67813823. Error was invalid region `8:67813423-67813823`
[2016-04-15T05:24Z] 2016-04-14 22:24:31 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:24:31,569 - WARNING - Could not retrieve variants from source file in region 8:67351556-67380718. Error was invalid region `8:67351557-67380718`
[2016-04-15T05:24Z] 2016-04-14 22:24:31 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:24:31,644 - WARNING - Could not retrieve variants from source file in region 8:68066157-68066558. Error was invalid region `8:68066158-68066558`
[2016-04-15T05:24Z] 2016-04-14 22:24:31 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:24:31,705 - WARNING - Could not retrieve variants from source file in region 8:74527785-74528186. Error was invalid region `8:74527786-74528186`
[2016-04-15T05:24Z] 2016-04-14 22:24:36 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:24:36,382 - WARNING - Could not retrieve variants from source file in region 8:71646250-71646651. Error was invalid region `8:71646251-71646651`
[2016-04-15T05:24Z] 2016-04-14 22:24:36 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:24:36,900 - WARNING - Could not retrieve variants from source file in region 8:71646250-71646651. Error was invalid region `8:71646251-71646651`
[2016-04-15T05:24Z] 2016-04-14 22:24:38 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:24:38,077 - WARNING - Could not retrieve variants from source file in region 8:72965791-72987828. Error was invalid region `8:72965792-72987828`
[2016-04-15T05:24Z] 2016-04-14 22:24:38 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:24:38,653 - WARNING - Could not retrieve variants from source file in region 8:73849992-73850393. Error was invalid region `8:73849993-73850393`
[2016-04-15T05:24Z] 2016-04-14 22:24:38 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:24:38,810 - WARNING - Could not retrieve variants from source file in region 8:71593214-71593615. Error was invalid region `8:71593215-71593615`
[2016-04-15T05:24Z] 2016-04-14 22:24:40 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:24:40,272 - WARNING - Could not retrieve variants from source file in region 8:72965791-72987828. Error was invalid region `8:72965792-72987828`
[2016-04-15T05:24Z] 2016-04-14 22:24:40 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:24:40,642 - WARNING - Could not retrieve variants from source file in region 8:71593214-71593615. Error was invalid region `8:71593215-71593615`
[2016-04-15T05:24Z] 2016-04-14 22:24:40 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:24:40,645 - WARNING - Could not retrieve variants from source file in region 8:71593214-71593615. Error was invalid region `8:71593215-71593615`
[2016-04-15T05:24Z] 2016-04-14 22:24:41 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:24:41,013 - WARNING - Could not retrieve variants from source file in region 8:70964188-70967797. Error was invalid region `8:70964189-70967797`
[2016-04-15T05:24Z] 2016-04-14 22:24:42 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:24:42,520 - WARNING - Could not retrieve variants from source file in region 8:72965791-72987828. Error was invalid region `8:72965792-72987828`
[2016-04-15T05:24Z] 2016-04-14 22:24:42 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:24:42,985 - WARNING - Could not retrieve variants from source file in region 8:73849992-73850393. Error was invalid region `8:73849993-73850393`
[2016-04-15T05:24Z] 2016-04-14 22:24:44 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:24:44,596 - WARNING - Could not retrieve variants from source file in region 8:70964188-70967797. Error was invalid region `8:70964189-70967797`
[2016-04-15T05:24Z] 2016-04-14 22:24:44 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:24:44,688 - WARNING - Could not retrieve variants from source file in region 8:67786422-67786823. Error was invalid region `8:67786423-67786823`
[2016-04-15T05:24Z] 2016-04-14 22:24:44 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:24:44,771 - WARNING - Could not retrieve variants from source file in region 8:70964188-70967797. Error was invalid region `8:70964189-70967797`
[2016-04-15T05:24Z] 2016-04-14 22:24:46 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:24:46,094 - WARNING - Could not retrieve variants from source file in region 8:72111388-72129199. Error was invalid region `8:72111389-72129199`
[2016-04-15T05:24Z] 2016-04-14 22:24:46 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:24:46,125 - WARNING - Could not retrieve variants from source file in region 8:72111388-72129199. Error was invalid region `8:72111389-72129199`
[2016-04-15T05:24Z] 2016-04-14 22:24:48 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:24:48,300 - WARNING - Could not retrieve variants from source file in region 8:72111388-72129199. Error was invalid region `8:72111389-72129199`
[2016-04-15T05:24Z] ['bcbio-variation-recall', 'square', '-Xms750m', '-Xmx7280m', '-XX:+UseSerialGC', '-c', 16, '-r', u'8:79513977-95140568', '--caller', 'platypus', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/8/Batch1-8_79513976_95140568.vcf.gz', '/mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/8/Batch1-8_79513976_95140568.vcf-inputs.txt'] in region: 8:79513977-95140568
[2016-04-15T05:25Z] 2016-04-14 22:25:03 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:25:03,925 - WARNING - Could not retrieve variants from source file in region 8:94146445-94146846. Error was invalid region `8:94146446-94146846`
[2016-04-15T05:25Z] 2016-04-14 22:25:04 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:25:04,530 - WARNING - Could not retrieve variants from source file in region 8:94932629-94933611. Error was invalid region `8:94932630-94933611`
[2016-04-15T05:25Z] 2016-04-14 22:25:04 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:25:04,648 - WARNING - Could not retrieve variants from source file in region 8:94807954-94808355. Error was invalid region `8:94807955-94808355`
[2016-04-15T05:25Z] 2016-04-14 22:25:05 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:25:05,828 - WARNING - Could not retrieve variants from source file in region 8:86351786-86352187. Error was invalid region `8:86351787-86352187`
[2016-04-15T05:25Z] 2016-04-14 22:25:05 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:25:05,830 - WARNING - Could not retrieve variants from source file in region 8:82441483-82441884. Error was invalid region `8:82441484-82441884`
[2016-04-15T05:25Z] 2016-04-14 22:25:05 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:25:05,918 - WARNING - Could not retrieve variants from source file in region 8:86089497-86089977. Error was invalid region `8:86089498-86089977`
[2016-04-15T05:25Z] 2016-04-14 22:25:06 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:25:06,068 - WARNING - Could not retrieve variants from source file in region 8:92033291-92033692. Error was invalid region `8:92033292-92033692`
[2016-04-15T05:25Z] 2016-04-14 22:25:06 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:25:06,071 - WARNING - Could not retrieve variants from source file in region 8:94712923-94713324. Error was invalid region `8:94712924-94713324`
[2016-04-15T05:25Z] 2016-04-14 22:25:08 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:25:08,186 - WARNING - Could not retrieve variants from source file in region 8:87076309-87076710. Error was invalid region `8:87076310-87076710`
[2016-04-15T05:25Z] 2016-04-14 22:25:09 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:25:09,966 - WARNING - Could not retrieve variants from source file in region 8:94146445-94146846. Error was invalid region `8:94146446-94146846`
[2016-04-15T05:25Z] 2016-04-14 22:25:12 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:25:12,377 - WARNING - Could not retrieve variants from source file in region 8:94807954-94808355. Error was invalid region `8:94807955-94808355`
[2016-04-15T05:25Z] 2016-04-14 22:25:13 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:25:13,332 - WARNING - Could not retrieve variants from source file in region 8:92407235-92407636. Error was invalid region `8:92407236-92407636`
[2016-04-15T05:25Z] 2016-04-14 22:25:13 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:25:13,366 - WARNING - Could not retrieve variants from source file in region 8:92136517-92136918. Error was invalid region `8:92136518-92136918`
[2016-04-15T05:25Z] 2016-04-14 22:25:13 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:25:13,779 - WARNING - Could not retrieve variants from source file in region 8:81398969-81399370. Error was invalid region `8:81398970-81399370`
[2016-04-15T05:25Z] 2016-04-14 22:25:13 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:25:13,982 - WARNING - Could not retrieve variants from source file in region 8:80525738-80526139. Error was invalid region `8:80525739-80526139`
[2016-04-15T05:25Z] 2016-04-14 22:25:14 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:25:14,955 - WARNING - Could not retrieve variants from source file in region 8:87755565-87755966. Error was invalid region `8:87755566-87755966`
[2016-04-15T05:25Z] 2016-04-14 22:25:14 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:25:14,969 - WARNING - Could not retrieve variants from source file in region 8:86351786-86352187. Error was invalid region `8:86351787-86352187`
[2016-04-15T05:25Z] 2016-04-14 22:25:15 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:25:15,003 - WARNING - Could not retrieve variants from source file in region 8:94146445-94146846. Error was invalid region `8:94146446-94146846`
[2016-04-15T05:25Z] 2016-04-14 22:25:18 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:25:18,999 - WARNING - Could not retrieve variants from source file in region 8:94807954-94808355. Error was invalid region `8:94807955-94808355`
[2016-04-15T05:25Z] 2016-04-14 22:25:21 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:25:21,007 - WARNING - Could not retrieve variants from source file in region 8:92407235-92407636. Error was invalid region `8:92407236-92407636`
[2016-04-15T05:25Z] 2016-04-14 22:25:21 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:25:21,532 - WARNING - Could not retrieve variants from source file in region 8:81398969-81399370. Error was invalid region `8:81398970-81399370`
[2016-04-15T05:25Z] 2016-04-14 22:25:21 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:25:21,964 - WARNING - Could not retrieve variants from source file in region 8:94712923-94713324. Error was invalid region `8:94712924-94713324`
[2016-04-15T05:25Z] 2016-04-14 22:25:22 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:25:22,077 - WARNING - Could not retrieve variants from source file in region 8:80525738-80526139. Error was invalid region `8:80525739-80526139`
[2016-04-15T05:25Z] 2016-04-14 22:25:22 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:25:22,446 - WARNING - Could not retrieve variants from source file in region 8:82441483-82441884. Error was invalid region `8:82441484-82441884`
[2016-04-15T05:25Z] 2016-04-14 22:25:22 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:25:22,574 - WARNING - Could not retrieve variants from source file in region 8:86351786-86352187. Error was invalid region `8:86351787-86352187`
[2016-04-15T05:25Z] 2016-04-14 22:25:22 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:25:22,685 - WARNING - Could not retrieve variants from source file in region 8:87755565-87755966. Error was invalid region `8:87755566-87755966`
[2016-04-15T05:25Z] 2016-04-14 22:25:33 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:25:33,219 - WARNING - Could not retrieve variants from source file in region 8:86389192-86389593. Error was invalid region `8:86389193-86389593`
[2016-04-15T05:25Z] 2016-04-14 22:25:37 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:25:37,315 - WARNING - Could not retrieve variants from source file in region 8:87566982-87567383. Error was invalid region `8:87566983-87567383`
[2016-04-15T05:25Z] 2016-04-14 22:25:37 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:25:37,556 - WARNING - Could not retrieve variants from source file in region 8:86389192-86389593. Error was invalid region `8:86389193-86389593`
[2016-04-15T05:25Z] 2016-04-14 22:25:37 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:25:37,695 - WARNING - Could not retrieve variants from source file in region 8:82665265-82670961. Error was invalid region `8:82665266-82670961`
[2016-04-15T05:25Z] 2016-04-14 22:25:37 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:25:37,890 - WARNING - Could not retrieve variants from source file in region 8:87666040-87679493. Error was invalid region `8:87666041-87679493`
[2016-04-15T05:25Z] 2016-04-14 22:25:38 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:25:38,484 - WARNING - Could not retrieve variants from source file in region 8:86126616-86127017. Error was invalid region `8:86126617-86127017`
[2016-04-15T05:25Z] 2016-04-14 22:25:40 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:25:40,000 - WARNING - Could not retrieve variants from source file in region 8:92360365-92364290. Error was invalid region `8:92360366-92364290`
[2016-04-15T05:25Z] 2016-04-14 22:25:40 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:25:40,006 - WARNING - Could not retrieve variants from source file in region 8:90958211-90995209. Error was invalid region `8:90958212-90995209`
[2016-04-15T05:25Z] 2016-04-14 22:25:41 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:25:41,199 - WARNING - Could not retrieve variants from source file in region 8:87566982-87567383. Error was invalid region `8:87566983-87567383`
[2016-04-15T05:25Z] 2016-04-14 22:25:41 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:25:41,378 - WARNING - Could not retrieve variants from source file in region 8:86389192-86389593. Error was invalid region `8:86389193-86389593`
[2016-04-15T05:25Z] 2016-04-14 22:25:41 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:25:41,639 - WARNING - Could not retrieve variants from source file in region 8:79610499-79610900. Error was invalid region `8:79610500-79610900`
[2016-04-15T05:25Z] 2016-04-14 22:25:41 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:25:41,975 - WARNING - Could not retrieve variants from source file in region 8:87666040-87679493. Error was invalid region `8:87666041-87679493`
[2016-04-15T05:25Z] 2016-04-14 22:25:42 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:25:42,067 - WARNING - Could not retrieve variants from source file in region 8:82371334-82371735. Error was invalid region `8:82371335-82371735`
[2016-04-15T05:25Z] 2016-04-14 22:25:42 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:25:42,420 - WARNING - Could not retrieve variants from source file in region 8:82751868-82752269. Error was invalid region `8:82751869-82752269`
[2016-04-15T05:25Z] 2016-04-14 22:25:42 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:25:42,653 - WARNING - Could not retrieve variants from source file in region 8:86126616-86127017. Error was invalid region `8:86126617-86127017`
[2016-04-15T05:25Z] 2016-04-14 22:25:44 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:25:44,213 - WARNING - Could not retrieve variants from source file in region 8:92360365-92364290. Error was invalid region `8:92360366-92364290`
[2016-04-15T05:25Z] 2016-04-14 22:25:45 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:25:45,756 - WARNING - Could not retrieve variants from source file in region 8:79610499-79610900. Error was invalid region `8:79610500-79610900`
[2016-04-15T05:25Z] 2016-04-14 22:25:46 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:25:46,095 - WARNING - Could not retrieve variants from source file in region 8:87666040-87679493. Error was invalid region `8:87666041-87679493`
[2016-04-15T05:25Z] 2016-04-14 22:25:46 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:25:46,790 - WARNING - Could not retrieve variants from source file in region 8:86126616-86127017. Error was invalid region `8:86126617-86127017`
[2016-04-15T05:25Z] 2016-04-14 22:25:52 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:25:52,427 - WARNING - Could not retrieve variants from source file in region 8:87235062-87235463. Error was invalid region `8:87235063-87235463`
[2016-04-15T05:25Z] 2016-04-14 22:25:53 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:25:53,660 - WARNING - Could not retrieve variants from source file in region 8:87235062-87235463. Error was invalid region `8:87235063-87235463`
[2016-04-15T05:25Z] 2016-04-14 22:25:55 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:25:55,068 - WARNING - Could not retrieve variants from source file in region 8:81733516-81733917. Error was invalid region `8:81733517-81733917`
[2016-04-15T05:25Z] 2016-04-14 22:25:55 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:25:55,092 - WARNING - Could not retrieve variants from source file in region 8:81733516-81733917. Error was invalid region `8:81733517-81733917`
[2016-04-15T05:25Z] 2016-04-14 22:25:55 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:25:55,278 - WARNING - Could not retrieve variants from source file in region 8:82606571-82607338. Error was invalid region `8:82606572-82607338`
[2016-04-15T05:25Z] 2016-04-14 22:25:55 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:25:55,279 - WARNING - Could not retrieve variants from source file in region 8:81425985-81426386. Error was invalid region `8:81425986-81426386`
[2016-04-15T05:25Z] 2016-04-14 22:25:56 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:25:56,909 - WARNING - Could not retrieve variants from source file in region 8:81425985-81426386. Error was invalid region `8:81425986-81426386`
[2016-04-15T05:25Z] 2016-04-14 22:25:56 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:25:56,916 - WARNING - Could not retrieve variants from source file in region 8:82606571-82607338. Error was invalid region `8:82606572-82607338`
[2016-04-15T05:26Z] ['bcbio-variation-recall', 'square', '-Xms750m', '-Xmx7280m', '-XX:+UseSerialGC', '-c', 16, '-r', u'8:95142854-110655419', '--caller', 'platypus', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/8/Batch1-8_95142853_110655419.vcf.gz', '/mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/8/Batch1-8_95142853_110655419.vcf-inputs.txt'] in region: 8:95142854-110655419
[2016-04-15T05:26Z] 2016-04-14 22:26:14 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:26:14,055 - WARNING - Could not retrieve variants from source file in region 8:100133495-100133896. Error was invalid region `8:100133496-100133896`
[2016-04-15T05:26Z] 2016-04-14 22:26:14 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:26:14,924 - WARNING - Could not retrieve variants from source file in region 8:110655165-110655568. Error was invalid region `8:110655166-110655568`
[2016-04-15T05:26Z] 2016-04-14 22:26:15 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:26:15,142 - WARNING - Could not retrieve variants from source file in region 8:99205401-99208380. Error was invalid region `8:99205402-99208380`
[2016-04-15T05:26Z] 2016-04-14 22:26:15 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:26:15,185 - WARNING - Could not retrieve variants from source file in region 8:103250780-103276943. Error was invalid region `8:103250781-103276943`
[2016-04-15T05:26Z] 2016-04-14 22:26:15 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:26:15,201 - WARNING - Could not retrieve variants from source file in region 8:104394533-104394934. Error was invalid region `8:104394534-104394934`
[2016-04-15T05:26Z] 2016-04-14 22:26:15 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:26:15,622 - WARNING - Could not retrieve variants from source file in region 8:105261514-105264169. Error was invalid region `8:105261515-105264169`
[2016-04-15T05:26Z] 2016-04-14 22:26:16 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:26:16,028 - WARNING - Could not retrieve variants from source file in region 8:97243509-97243910. Error was invalid region `8:97243510-97243910`
[2016-04-15T05:26Z] 2016-04-14 22:26:16 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:26:16,155 - WARNING - Could not retrieve variants from source file in region 8:99101765-99115272. Error was invalid region `8:99101766-99115272`
[2016-04-15T05:26Z] 2016-04-14 22:26:16 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:26:16,363 - WARNING - Could not retrieve variants from source file in region 8:101585922-101609109. Error was invalid region `8:101585923-101609109`
[2016-04-15T05:26Z] 2016-04-14 22:26:16 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:26:16,585 - WARNING - Could not retrieve variants from source file in region 8:101152813-101153214. Error was invalid region `8:101152814-101153214`
[2016-04-15T05:26Z] 2016-04-14 22:26:20 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:26:20,700 - WARNING - Could not retrieve variants from source file in region 8:100133495-100133896. Error was invalid region `8:100133496-100133896`
[2016-04-15T05:26Z] 2016-04-14 22:26:23 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:26:23,243 - WARNING - Could not retrieve variants from source file in region 8:99205401-99208380. Error was invalid region `8:99205402-99208380`
[2016-04-15T05:26Z] 2016-04-14 22:26:23 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:26:23,659 - WARNING - Could not retrieve variants from source file in region 8:104394533-104394934. Error was invalid region `8:104394534-104394934`
[2016-04-15T05:26Z] 2016-04-14 22:26:25 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:26:25,200 - WARNING - Could not retrieve variants from source file in region 8:103665760-103666161. Error was invalid region `8:103665761-103666161`
[2016-04-15T05:26Z] 2016-04-14 22:26:25 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:26:25,243 - WARNING - Could not retrieve variants from source file in region 8:97243509-97243910. Error was invalid region `8:97243510-97243910`
[2016-04-15T05:26Z] 2016-04-14 22:26:25 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:26:25,402 - WARNING - Could not retrieve variants from source file in region 8:101152813-101153214. Error was invalid region `8:101152814-101153214`
[2016-04-15T05:26Z] 2016-04-14 22:26:25 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:26:25,892 - WARNING - Could not retrieve variants from source file in region 8:101962513-101962914. Error was invalid region `8:101962514-101962914`
[2016-04-15T05:26Z] 2016-04-14 22:26:25 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:26:25,898 - WARNING - Could not retrieve variants from source file in region 8:101585922-101609109. Error was invalid region `8:101585923-101609109`
[2016-04-15T05:26Z] 2016-04-14 22:26:26 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:26:26,134 - WARNING - Could not retrieve variants from source file in region 8:107782124-107782585. Error was invalid region `8:107782125-107782585`
[2016-04-15T05:26Z] 2016-04-14 22:26:26 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:26:26,160 - WARNING - Could not retrieve variants from source file in region 8:100133495-100133896. Error was invalid region `8:100133496-100133896`
[2016-04-15T05:26Z] 2016-04-14 22:26:26 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:26:26,172 - WARNING - Could not retrieve variants from source file in region 8:99152877-99170594. Error was invalid region `8:99152878-99170594`
[2016-04-15T05:26Z] 2016-04-14 22:26:28 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:26:28,760 - WARNING - Could not retrieve variants from source file in region 8:110655165-110655568. Error was invalid region `8:110655166-110655568`
[2016-04-15T05:26Z] 2016-04-14 22:26:29 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:26:29,693 - WARNING - Could not retrieve variants from source file in region 8:104394533-104394934. Error was invalid region `8:104394534-104394934`
[2016-04-15T05:26Z] 2016-04-14 22:26:32 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:26:32,761 - WARNING - Could not retrieve variants from source file in region 8:101152813-101153214. Error was invalid region `8:101152814-101153214`
[2016-04-15T05:26Z] 2016-04-14 22:26:32 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:26:32,808 - WARNING - Could not retrieve variants from source file in region 8:99101765-99115272. Error was invalid region `8:99101766-99115272`
[2016-04-15T05:26Z] 2016-04-14 22:26:33 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:26:33,004 - WARNING - Could not retrieve variants from source file in region 8:97243509-97243910. Error was invalid region `8:97243510-97243910`
[2016-04-15T05:26Z] 2016-04-14 22:26:33 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:26:33,246 - WARNING - Could not retrieve variants from source file in region 8:103665760-103666161. Error was invalid region `8:103665761-103666161`
[2016-04-15T05:26Z] 2016-04-14 22:26:33 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:26:33,539 - WARNING - Could not retrieve variants from source file in region 8:101585922-101609109. Error was invalid region `8:101585923-101609109`
[2016-04-15T05:26Z] 2016-04-14 22:26:33 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:26:33,718 - WARNING - Could not retrieve variants from source file in region 8:102702396-102704746. Error was invalid region `8:102702397-102704746`
[2016-04-15T05:26Z] 2016-04-14 22:26:44 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:26:44,812 - WARNING - Could not retrieve variants from source file in region 8:110410529-110477183. Error was invalid region `8:110410530-110477183`
[2016-04-15T05:26Z] 2016-04-14 22:26:45 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:26:45,646 - WARNING - Could not retrieve variants from source file in region 8:110587764-110588165. Error was invalid region `8:110587765-110588165`
[2016-04-15T05:26Z] 2016-04-14 22:26:46 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:26:46,288 - WARNING - Could not retrieve variants from source file in region 8:106813307-106815707. Error was invalid region `8:106813308-106815707`
[2016-04-15T05:26Z] 2016-04-14 22:26:48 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:26:48,743 - WARNING - Could not retrieve variants from source file in region 8:102216754-102217155. Error was invalid region `8:102216755-102217155`
[2016-04-15T05:26Z] 2016-04-14 22:26:50 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:26:50,394 - WARNING - Could not retrieve variants from source file in region 8:96069970-96070371. Error was invalid region `8:96069971-96070371`
[2016-04-15T05:26Z] 2016-04-14 22:26:51 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:26:51,446 - WARNING - Could not retrieve variants from source file in region 8:101724413-101724818. Error was invalid region `8:101724414-101724818`
[2016-04-15T05:26Z] 2016-04-14 22:26:51 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:26:51,627 - WARNING - Could not retrieve variants from source file in region 8:107754262-107754663. Error was invalid region `8:107754263-107754663`
[2016-04-15T05:26Z] 2016-04-14 22:26:51 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:26:51,759 - WARNING - Could not retrieve variants from source file in region 8:109254466-109255032. Error was invalid region `8:109254467-109255032`
[2016-04-15T05:26Z] 2016-04-14 22:26:51 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:26:51,766 - WARNING - Could not retrieve variants from source file in region 8:103572781-103573227. Error was invalid region `8:103572782-103573227`
[2016-04-15T05:26Z] 2016-04-14 22:26:52 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:26:52,822 - WARNING - Could not retrieve variants from source file in region 8:105235439-105235841. Error was invalid region `8:105235440-105235841`
[2016-04-15T05:26Z] 2016-04-14 22:26:53 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:26:53,275 - WARNING - Could not retrieve variants from source file in region 8:100844547-100844948. Error was invalid region `8:100844548-100844948`
[2016-04-15T05:26Z] 2016-04-14 22:26:55 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:26:55,038 - WARNING - Could not retrieve variants from source file in region 8:96069970-96070371. Error was invalid region `8:96069971-96070371`
[2016-04-15T05:26Z] 2016-04-14 22:26:55 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:26:55,663 - WARNING - Could not retrieve variants from source file in region 8:110587764-110588165. Error was invalid region `8:110587765-110588165`
[2016-04-15T05:26Z] 2016-04-14 22:26:57 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:26:57,102 - WARNING - Could not retrieve variants from source file in region 8:107754262-107754663. Error was invalid region `8:107754263-107754663`
[2016-04-15T05:26Z] 2016-04-14 22:26:57 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:26:57,816 - WARNING - Could not retrieve variants from source file in region 8:101533657-101534839. Error was invalid region `8:101533658-101534839`
[2016-04-15T05:26Z] 2016-04-14 22:26:58 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:26:58,166 - WARNING - Could not retrieve variants from source file in region 8:102216754-102217155. Error was invalid region `8:102216755-102217155`
[2016-04-15T05:26Z] 2016-04-14 22:26:58 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:26:58,244 - WARNING - Could not retrieve variants from source file in region 8:100844547-100844948. Error was invalid region `8:100844548-100844948`
[2016-04-15T05:26Z] 2016-04-14 22:26:59 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:26:59,693 - WARNING - Could not retrieve variants from source file in region 8:96069970-96070371. Error was invalid region `8:96069971-96070371`
[2016-04-15T05:27Z] 2016-04-14 22:27:02 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:27:02,512 - WARNING - Could not retrieve variants from source file in region 8:107754262-107754663. Error was invalid region `8:107754263-107754663`
[2016-04-15T05:27Z] 2016-04-14 22:27:03 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:27:03,201 - WARNING - Could not retrieve variants from source file in region 8:101533657-101534839. Error was invalid region `8:101533658-101534839`
[2016-04-15T05:27Z] 2016-04-14 22:27:09 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:27:09,927 - WARNING - Could not retrieve variants from source file in region 8:110535354-110535755. Error was invalid region `8:110535355-110535755`
[2016-04-15T05:27Z] 2016-04-14 22:27:10 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:27:10,156 - WARNING - Could not retrieve variants from source file in region 8:108970156-108970557. Error was invalid region `8:108970157-108970557`
[2016-04-15T05:27Z] 2016-04-14 22:27:12 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:27:12,380 - WARNING - Could not retrieve variants from source file in region 8:104152926-104153327. Error was invalid region `8:104152927-104153327`
[2016-04-15T05:27Z] 2016-04-14 22:27:12 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:27:12,936 - WARNING - Could not retrieve variants from source file in region 8:103307322-103307723. Error was invalid region `8:103307323-103307723`
[2016-04-15T05:27Z] 2016-04-14 22:27:13 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:27:13,505 - WARNING - Could not retrieve variants from source file in region 8:101647953-101648354. Error was invalid region `8:101647954-101648354`
[2016-04-15T05:27Z] 2016-04-14 22:27:14 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:27:14,226 - WARNING - Could not retrieve variants from source file in region 8:103307322-103307723. Error was invalid region `8:103307323-103307723`
[2016-04-15T05:27Z] 2016-04-14 22:27:14 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:27:14,311 - WARNING - Could not retrieve variants from source file in region 8:95877576-95888497. Error was invalid region `8:95877577-95888497`
[2016-04-15T05:27Z] 2016-04-14 22:27:14 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:27:14,720 - WARNING - Could not retrieve variants from source file in region 8:108970156-108970557. Error was invalid region `8:108970157-108970557`
[2016-04-15T05:27Z] 2016-04-14 22:27:15 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:27:15,416 - WARNING - Could not retrieve variants from source file in region 8:105478722-105479339. Error was invalid region `8:105478723-105479339`
[2016-04-15T05:27Z] 2016-04-14 22:27:16 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:27:16,612 - WARNING - Could not retrieve variants from source file in region 8:104427148-104432735. Error was invalid region `8:104427149-104432735`
[2016-04-15T05:27Z] 2016-04-14 22:27:17 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:27:17,602 - WARNING - Could not retrieve variants from source file in region 8:103307322-103307723. Error was invalid region `8:103307323-103307723`
[2016-04-15T05:27Z] 2016-04-14 22:27:18 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:27:18,473 - WARNING - Could not retrieve variants from source file in region 8:95877576-95888497. Error was invalid region `8:95877577-95888497`
[2016-04-15T05:27Z] 2016-04-14 22:27:18 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:27:18,823 - WARNING - Could not retrieve variants from source file in region 8:108970156-108970557. Error was invalid region `8:108970157-108970557`
[2016-04-15T05:27Z] 2016-04-14 22:27:20 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:27:20,581 - WARNING - Could not retrieve variants from source file in region 8:104427148-104432735. Error was invalid region `8:104427149-104432735`
[2016-04-15T05:27Z] 2016-04-14 22:27:21 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:27:21,925 - WARNING - Could not retrieve variants from source file in region 8:101647953-101648354. Error was invalid region `8:101647954-101648354`
[2016-04-15T05:27Z] 2016-04-14 22:27:22 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:27:22,528 - WARNING - Could not retrieve variants from source file in region 8:95877576-95888497. Error was invalid region `8:95877577-95888497`
[2016-04-15T05:27Z] 2016-04-14 22:27:30 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:27:30,014 - WARNING - Could not retrieve variants from source file in region 8:98289118-98290176. Error was invalid region `8:98289119-98290176`
[2016-04-15T05:27Z] 2016-04-14 22:27:30 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:27:30,090 - WARNING - Could not retrieve variants from source file in region 8:98787783-98788451. Error was invalid region `8:98787784-98788451`
[2016-04-15T05:27Z] 2016-04-14 22:27:33 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:27:33,677 - WARNING - Could not retrieve variants from source file in region 8:95523023-95547309. Error was invalid region `8:95523024-95547309`
[2016-04-15T05:27Z] 2016-04-14 22:27:34 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:27:34,753 - WARNING - Could not retrieve variants from source file in region 8:105368197-105368598. Error was invalid region `8:105368198-105368598`
[2016-04-15T05:27Z] 2016-04-14 22:27:36 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:27:36,872 - WARNING - Could not retrieve variants from source file in region 8:95655385-95690769. Error was invalid region `8:95655386-95690769`
[2016-04-15T05:27Z] 2016-04-14 22:27:37 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:27:37,886 - WARNING - Could not retrieve variants from source file in region 8:97605589-97614851. Error was invalid region `8:97605590-97614851`
[2016-04-15T05:27Z] 2016-04-14 22:27:40 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:27:40,161 - WARNING - Could not retrieve variants from source file in region 8:95655385-95690769. Error was invalid region `8:95655386-95690769`
[2016-04-15T05:27Z] ['bcbio-variation-recall', 'square', '-Xms750m', '-Xmx7280m', '-XX:+UseSerialGC', '-c', 16, '-r', u'8:110656865-126194498', '--caller', 'platypus', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/8/Batch1-8_110656864_126194498.vcf.gz', '/mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/8/Batch1-8_110656864_126194498.vcf-inputs.txt'] in region: 8:110656865-126194498
[2016-04-15T05:27Z] 2016-04-14 22:27:56 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:27:56,468 - WARNING - Could not retrieve variants from source file in region 8:125463039-125463734. Error was invalid region `8:125463040-125463734`
[2016-04-15T05:27Z] 2016-04-14 22:27:56 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:27:56,438 - WARNING - Could not retrieve variants from source file in region 8:120846977-120847378. Error was invalid region `8:120846978-120847378`
[2016-04-15T05:27Z] 2016-04-14 22:27:57 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:27:57,363 - WARNING - Could not retrieve variants from source file in region 8:125035577-125035978. Error was invalid region `8:125035578-125035978`
[2016-04-15T05:27Z] 2016-04-14 22:27:57 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:27:57,435 - WARNING - Could not retrieve variants from source file in region 8:125106990-125115610. Error was invalid region `8:125106991-125115610`
[2016-04-15T05:27Z] 2016-04-14 22:27:57 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:27:57,728 - WARNING - Could not retrieve variants from source file in region 8:121013559-121013960. Error was invalid region `8:121013560-121013960`
[2016-04-15T05:27Z] 2016-04-14 22:27:57 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:27:57,841 - WARNING - Could not retrieve variants from source file in region 8:124439963-124449656. Error was invalid region `8:124439964-124449656`
[2016-04-15T05:27Z] 2016-04-14 22:27:57 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:27:57,956 - WARNING - Could not retrieve variants from source file in region 8:124696656-124710919. Error was invalid region `8:124696657-124710919`
[2016-04-15T05:27Z] 2016-04-14 22:27:58 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:27:58,113 - WARNING - Could not retrieve variants from source file in region 8:121297945-121298346. Error was invalid region `8:121297946-121298346`
[2016-04-15T05:27Z] 2016-04-14 22:27:58 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:27:58,591 - WARNING - Could not retrieve variants from source file in region 8:120744082-120744483. Error was invalid region `8:120744083-120744483`
[2016-04-15T05:27Z] 2016-04-14 22:27:58 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:27:58,877 - WARNING - Could not retrieve variants from source file in region 8:120790093-120803827. Error was invalid region `8:120790094-120803827`
[2016-04-15T05:28Z] 2016-04-14 22:28:02 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:28:02,111 - WARNING - Could not retrieve variants from source file in region 8:120846977-120847378. Error was invalid region `8:120846978-120847378`
[2016-04-15T05:28Z] 2016-04-14 22:28:02 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:28:02,129 - WARNING - Could not retrieve variants from source file in region 8:125463039-125463734. Error was invalid region `8:125463040-125463734`
[2016-04-15T05:28Z] 2016-04-14 22:28:03 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:28:03,694 - WARNING - Could not retrieve variants from source file in region 8:125035577-125035978. Error was invalid region `8:125035578-125035978`
[2016-04-15T05:28Z] 2016-04-14 22:28:04 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:28:04,027 - WARNING - Could not retrieve variants from source file in region 8:125498087-125498737. Error was invalid region `8:125498088-125498737`
[2016-04-15T05:28Z] 2016-04-14 22:28:04 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:28:04,980 - WARNING - Could not retrieve variants from source file in region 8:124439963-124449656. Error was invalid region `8:124439964-124449656`
[2016-04-15T05:28Z] 2016-04-14 22:28:05 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:28:05,980 - WARNING - Could not retrieve variants from source file in region 8:121297945-121298346. Error was invalid region `8:121297946-121298346`
[2016-04-15T05:28Z] 2016-04-14 22:28:06 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:28:06,369 - WARNING - Could not retrieve variants from source file in region 8:119451862-119452263. Error was invalid region `8:119451863-119452263`
[2016-04-15T05:28Z] 2016-04-14 22:28:06 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:28:06,695 - WARNING - Could not retrieve variants from source file in region 8:121013559-121013960. Error was invalid region `8:121013560-121013960`
[2016-04-15T05:28Z] 2016-04-14 22:28:07 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:28:07,296 - WARNING - Could not retrieve variants from source file in region 8:120846977-120847378. Error was invalid region `8:120846978-120847378`
[2016-04-15T05:28Z] 2016-04-14 22:28:07 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:28:07,327 - WARNING - Could not retrieve variants from source file in region 8:125463039-125463734. Error was invalid region `8:125463040-125463734`
[2016-04-15T05:28Z] 2016-04-14 22:28:08 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:28:08,797 - WARNING - Could not retrieve variants from source file in region 8:125035577-125035978. Error was invalid region `8:125035578-125035978`
[2016-04-15T05:28Z] 2016-04-14 22:28:09 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:28:09,042 - WARNING - Could not retrieve variants from source file in region 8:125498087-125498737. Error was invalid region `8:125498088-125498737`
[2016-04-15T05:28Z] 2016-04-14 22:28:10 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:28:10,502 - WARNING - Could not retrieve variants from source file in region 8:124439963-124449656. Error was invalid region `8:124439964-124449656`
[2016-04-15T05:28Z] 2016-04-14 22:28:12 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:28:12,518 - WARNING - Could not retrieve variants from source file in region 8:124696656-124710919. Error was invalid region `8:124696657-124710919`
[2016-04-15T05:28Z] 2016-04-14 22:28:13 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:28:13,220 - WARNING - Could not retrieve variants from source file in region 8:120744082-120744483. Error was invalid region `8:120744083-120744483`
[2016-04-15T05:28Z] 2016-04-14 22:28:13 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:28:13,398 - WARNING - Could not retrieve variants from source file in region 8:120790093-120803827. Error was invalid region `8:120790094-120803827`
[2016-04-15T05:28Z] 2016-04-14 22:28:14 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:28:14,823 - WARNING - Could not retrieve variants from source file in region 8:121013559-121013960. Error was invalid region `8:121013560-121013960`
[2016-04-15T05:28Z] 2016-04-14 22:28:23 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:28:23,908 - WARNING - Could not retrieve variants from source file in region 8:125061684-125076779. Error was invalid region `8:125061685-125076779`
[2016-04-15T05:28Z] 2016-04-14 22:28:24 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:28:24,570 - WARNING - Could not retrieve variants from source file in region 8:124987267-124987668. Error was invalid region `8:124987268-124987668`
[2016-04-15T05:28Z] 2016-04-14 22:28:26 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:28:26,067 - WARNING - Could not retrieve variants from source file in region 8:125061684-125076779. Error was invalid region `8:125061685-125076779`
[2016-04-15T05:28Z] 2016-04-14 22:28:26 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:28:26,106 - WARNING - Could not retrieve variants from source file in region 8:121209858-121228869. Error was invalid region `8:121209859-121228869`
[2016-04-15T05:28Z] 2016-04-14 22:28:26 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:28:26,211 - WARNING - Could not retrieve variants from source file in region 8:124121587-124142679. Error was invalid region `8:124121588-124142679`
[2016-04-15T05:28Z] 2016-04-14 22:28:26 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:28:26,386 - WARNING - Could not retrieve variants from source file in region 8:120977278-120977679. Error was invalid region `8:120977279-120977679`
[2016-04-15T05:28Z] 2016-04-14 22:28:27 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:28:27,215 - WARNING - Could not retrieve variants from source file in region 8:121061668-121062069. Error was invalid region `8:121061669-121062069`
[2016-04-15T05:28Z] 2016-04-14 22:28:28 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:28:28,272 - WARNING - Could not retrieve variants from source file in region 8:120220564-120220966. Error was invalid region `8:120220565-120220966`
[2016-04-15T05:28Z] 2016-04-14 22:28:28 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:28:28,293 - WARNING - Could not retrieve variants from source file in region 8:121382837-121383272. Error was invalid region `8:121382838-121383272`
[2016-04-15T05:28Z] 2016-04-14 22:28:28 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:28:28,365 - WARNING - Could not retrieve variants from source file in region 8:125061684-125076779. Error was invalid region `8:125061685-125076779`
[2016-04-15T05:28Z] 2016-04-14 22:28:30 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:28:30,657 - WARNING - Could not retrieve variants from source file in region 8:124121587-124142679. Error was invalid region `8:124121588-124142679`
[2016-04-15T05:28Z] 2016-04-14 22:28:31 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:28:31,603 - WARNING - Could not retrieve variants from source file in region 8:120977278-120977679. Error was invalid region `8:120977279-120977679`
[2016-04-15T05:28Z] 2016-04-14 22:28:32 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:28:32,511 - WARNING - Could not retrieve variants from source file in region 8:123964742-123966349. Error was invalid region `8:123964743-123966349`
[2016-04-15T05:28Z] 2016-04-14 22:28:33 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:28:33,033 - WARNING - Could not retrieve variants from source file in region 8:120220564-120220966. Error was invalid region `8:120220565-120220966`
[2016-04-15T05:28Z] 2016-04-14 22:28:33 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:28:33,275 - WARNING - Could not retrieve variants from source file in region 8:120594591-120596213. Error was invalid region `8:120594592-120596213`
[2016-04-15T05:28Z] 2016-04-14 22:28:33 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:28:33,324 - WARNING - Could not retrieve variants from source file in region 8:121382837-121383272. Error was invalid region `8:121382838-121383272`
[2016-04-15T05:28Z] 2016-04-14 22:28:36 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:28:36,539 - WARNING - Could not retrieve variants from source file in region 8:121209858-121228869. Error was invalid region `8:121209859-121228869`
[2016-04-15T05:28Z] 2016-04-14 22:28:37 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:28:37,513 - WARNING - Could not retrieve variants from source file in region 8:121061668-121062069. Error was invalid region `8:121061669-121062069`
[2016-04-15T05:28Z] 2016-04-14 22:28:38 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:28:38,434 - WARNING - Could not retrieve variants from source file in region 8:120220564-120220966. Error was invalid region `8:120220565-120220966`
[2016-04-15T05:28Z] 2016-04-14 22:28:38 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:28:38,535 - WARNING - Could not retrieve variants from source file in region 8:121382837-121383272. Error was invalid region `8:121382838-121383272`
[2016-04-15T05:28Z] 2016-04-14 22:28:41 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:28:41,316 - WARNING - Could not retrieve variants from source file in region 8:124824615-124825016. Error was invalid region `8:124824616-124825016`
[2016-04-15T05:28Z] 2016-04-14 22:28:43 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:28:43,285 - WARNING - Could not retrieve variants from source file in region 8:124824615-124825016. Error was invalid region `8:124824616-124825016`
[2016-04-15T05:28Z] 2016-04-14 22:28:43 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:28:43,771 - WARNING - Could not retrieve variants from source file in region 8:119963841-119964242. Error was invalid region `8:119963842-119964242`
[2016-04-15T05:28Z] 2016-04-14 22:28:43 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:28:43,822 - WARNING - Could not retrieve variants from source file in region 8:117785120-117791923. Error was invalid region `8:117785121-117791923`
[2016-04-15T05:28Z] 2016-04-14 22:28:45 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:28:45,659 - WARNING - Could not retrieve variants from source file in region 8:124824615-124825016. Error was invalid region `8:124824616-124825016`
[2016-04-15T05:28Z] 2016-04-14 22:28:47 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:28:47,022 - WARNING - Could not retrieve variants from source file in region 8:119963841-119964242. Error was invalid region `8:119963842-119964242`
[2016-04-15T05:28Z] 2016-04-14 22:28:47 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:28:47,267 - WARNING - Could not retrieve variants from source file in region 8:117785120-117791923. Error was invalid region `8:117785121-117791923`
[2016-04-15T05:28Z] 2016-04-14 22:28:48 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:28:48,257 - WARNING - Could not retrieve variants from source file in region 8:119963841-119964242. Error was invalid region `8:119963842-119964242`
[2016-04-15T05:28Z] 2016-04-14 22:28:49 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:28:49,577 - WARNING - Could not retrieve variants from source file in region 8:118847571-118847972. Error was invalid region `8:118847572-118847972`
[2016-04-15T05:28Z] 2016-04-14 22:28:49 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:28:49,749 - WARNING - Could not retrieve variants from source file in region 8:118184572-118184973. Error was invalid region `8:118184573-118184973`
[2016-04-15T05:28Z] 2016-04-14 22:28:50 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:28:50,364 - WARNING - Could not retrieve variants from source file in region 8:116635661-116636132. Error was invalid region `8:116635662-116636132`
[2016-04-15T05:28Z] 2016-04-14 22:28:50 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:28:50,928 - WARNING - Could not retrieve variants from source file in region 8:113364485-113364886. Error was invalid region `8:113364486-113364886`
[2016-04-15T05:28Z] 2016-04-14 22:28:51 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:28:51,196 - WARNING - Could not retrieve variants from source file in region 8:113240877-113241278. Error was invalid region `8:113240878-113241278`
[2016-04-15T05:28Z] 2016-04-14 22:28:51 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:28:51,204 - WARNING - Could not retrieve variants from source file in region 8:114185792-114186193. Error was invalid region `8:114185793-114186193`
[2016-04-15T05:28Z] 2016-04-14 22:28:53 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:28:53,315 - WARNING - Could not retrieve variants from source file in region 8:118847571-118847972. Error was invalid region `8:118847572-118847972`
[2016-04-15T05:28Z] 2016-04-14 22:28:53 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:28:53,410 - WARNING - Could not retrieve variants from source file in region 8:113364485-113364886. Error was invalid region `8:113364486-113364886`
[2016-04-15T05:28Z] 2016-04-14 22:28:53 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:28:53,467 - WARNING - Could not retrieve variants from source file in region 8:118184572-118184973. Error was invalid region `8:118184573-118184973`
[2016-04-15T05:28Z] 2016-04-14 22:28:53 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:28:53,481 - WARNING - Could not retrieve variants from source file in region 8:113240877-113241278. Error was invalid region `8:113240878-113241278`
[2016-04-15T05:28Z] 2016-04-14 22:28:54 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:28:54,264 - WARNING - Could not retrieve variants from source file in region 8:116635661-116636132. Error was invalid region `8:116635662-116636132`
[2016-04-15T05:28Z] 2016-04-14 22:28:54 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:28:54,273 - WARNING - Could not retrieve variants from source file in region 8:114185792-114186193. Error was invalid region `8:114185793-114186193`
[2016-04-15T05:28Z] 2016-04-14 22:28:54 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:28:54,686 - WARNING - Could not retrieve variants from source file in region 8:116635661-116636132. Error was invalid region `8:116635662-116636132`
[2016-04-15T05:28Z] 2016-04-14 22:28:54 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:28:54,902 - WARNING - Could not retrieve variants from source file in region 8:113364485-113364886. Error was invalid region `8:113364486-113364886`
[2016-04-15T05:28Z] 2016-04-14 22:28:55 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:28:55,111 - WARNING - Could not retrieve variants from source file in region 8:113240877-113241278. Error was invalid region `8:113240878-113241278`
[2016-04-15T05:28Z] 2016-04-14 22:28:55 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:28:55,696 - WARNING - Could not retrieve variants from source file in region 8:118847571-118847972. Error was invalid region `8:118847572-118847972`
[2016-04-15T05:28Z] 2016-04-14 22:28:55 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:28:55,720 - WARNING - Could not retrieve variants from source file in region 8:118184572-118184973. Error was invalid region `8:118184573-118184973`
[2016-04-15T05:28Z] 2016-04-14 22:28:59 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:28:59,063 - WARNING - Could not retrieve variants from source file in region 8:117950557-117950958. Error was invalid region `8:117950558-117950958`
[2016-04-15T05:28Z] 2016-04-14 22:28:59 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:28:59,064 - WARNING - Could not retrieve variants from source file in region 8:117950557-117950958. Error was invalid region `8:117950558-117950958`
[2016-04-15T05:28Z] 2016-04-14 22:28:59 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:28:59,068 - WARNING - Could not retrieve variants from source file in region 8:117950557-117950958. Error was invalid region `8:117950558-117950958`
[2016-04-15T05:29Z] ['bcbio-variation-recall', 'square', '-Xms750m', '-Xmx7280m', '-XX:+UseSerialGC', '-c', 16, '-r', u'8:126369461-141889736', '--caller', 'platypus', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/8/Batch1-8_126369460_141889736.vcf.gz', '/mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/8/Batch1-8_126369460_141889736.vcf-inputs.txt'] in region: 8:126369461-141889736
[2016-04-15T05:29Z] 2016-04-14 22:29:15 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:29:15,406 - WARNING - Could not retrieve variants from source file in region 8:128427850-128429013. Error was invalid region `8:128427851-128429013`
[2016-04-15T05:29Z] 2016-04-14 22:29:16 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:29:16,104 - WARNING - Could not retrieve variants from source file in region 8:133975072-134014525. Error was invalid region `8:133975073-134014525`
[2016-04-15T05:29Z] 2016-04-14 22:29:17 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:29:17,040 - WARNING - Could not retrieve variants from source file in region 8:132982613-133082613. Error was invalid region `8:132982614-133082613`
[2016-04-15T05:29Z] 2016-04-14 22:29:17 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:29:17,052 - WARNING - Could not retrieve variants from source file in region 8:133082613-133108020. Error was invalid region `8:133082614-133108020`
[2016-04-15T05:29Z] 2016-04-14 22:29:18 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:29:18,152 - WARNING - Could not retrieve variants from source file in region 8:134473937-134488197. Error was invalid region `8:134473938-134488197`
[2016-04-15T05:29Z] 2016-04-14 22:29:18 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:29:18,231 - WARNING - Could not retrieve variants from source file in region 8:131921745-131922217. Error was invalid region `8:131921746-131922217`
[2016-04-15T05:29Z] 2016-04-14 22:29:18 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:29:18,247 - WARNING - Could not retrieve variants from source file in region 8:131124348-131124749. Error was invalid region `8:131124349-131124749`
[2016-04-15T05:29Z] 2016-04-14 22:29:18 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:29:18,247 - WARNING - Could not retrieve variants from source file in region 8:130760639-130761040. Error was invalid region `8:130760640-130761040`
[2016-04-15T05:29Z] 2016-04-14 22:29:19 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:29:19,002 - WARNING - Could not retrieve variants from source file in region 8:133759107-133759508. Error was invalid region `8:133759108-133759508`
[2016-04-15T05:29Z] 2016-04-14 22:29:19 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:29:19,439 - WARNING - Could not retrieve variants from source file in region 8:141780607-141781008. Error was invalid region `8:141780608-141781008`
[2016-04-15T05:29Z] 2016-04-14 22:29:21 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:29:21,241 - WARNING - Could not retrieve variants from source file in region 8:133975072-134014525. Error was invalid region `8:133975073-134014525`
[2016-04-15T05:29Z] 2016-04-14 22:29:21 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:29:21,260 - WARNING - Could not retrieve variants from source file in region 8:128427850-128429013. Error was invalid region `8:128427851-128429013`
[2016-04-15T05:29Z] 2016-04-14 22:29:24 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:29:24,515 - WARNING - Could not retrieve variants from source file in region 8:135612534-135615162. Error was invalid region `8:135612535-135615162`
[2016-04-15T05:29Z] 2016-04-14 22:29:24 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:29:24,520 - WARNING - Could not retrieve variants from source file in region 8:139697267-139701399. Error was invalid region `8:139697268-139701399`
[2016-04-15T05:29Z] 2016-04-14 22:29:25 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:29:25,623 - WARNING - Could not retrieve variants from source file in region 8:130864245-130864646. Error was invalid region `8:130864246-130864646`
[2016-04-15T05:29Z] 2016-04-14 22:29:25 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:29:25,671 - WARNING - Could not retrieve variants from source file in region 8:133637448-133637849. Error was invalid region `8:133637449-133637849`
[2016-04-15T05:29Z] 2016-04-14 22:29:26 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:29:26,053 - WARNING - Could not retrieve variants from source file in region 8:134473937-134488197. Error was invalid region `8:134473938-134488197`
[2016-04-15T05:29Z] 2016-04-14 22:29:26 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:29:26,261 - WARNING - Could not retrieve variants from source file in region 8:126443137-126444699. Error was invalid region `8:126443138-126444699`
[2016-04-15T05:29Z] 2016-04-14 22:29:26 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:29:26,302 - WARNING - Could not retrieve variants from source file in region 8:130760639-130761040. Error was invalid region `8:130760640-130761040`
[2016-04-15T05:29Z] 2016-04-14 22:29:26 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:29:26,525 - WARNING - Could not retrieve variants from source file in region 8:131921745-131922217. Error was invalid region `8:131921746-131922217`
[2016-04-15T05:29Z] 2016-04-14 22:29:27 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:29:27,034 - WARNING - Could not retrieve variants from source file in region 8:128427850-128429013. Error was invalid region `8:128427851-128429013`
[2016-04-15T05:29Z] 2016-04-14 22:29:27 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:29:27,079 - WARNING - Could not retrieve variants from source file in region 8:131124348-131124749. Error was invalid region `8:131124349-131124749`
[2016-04-15T05:29Z] 2016-04-14 22:29:27 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:29:27,093 - WARNING - Could not retrieve variants from source file in region 8:133975072-134014525. Error was invalid region `8:133975073-134014525`
[2016-04-15T05:29Z] 2016-04-14 22:29:33 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:29:33,365 - WARNING - Could not retrieve variants from source file in region 8:130864245-130864646. Error was invalid region `8:130864246-130864646`
[2016-04-15T05:29Z] 2016-04-14 22:29:34 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:29:34,540 - WARNING - Could not retrieve variants from source file in region 8:134473937-134488197. Error was invalid region `8:134473938-134488197`
[2016-04-15T05:29Z] 2016-04-14 22:29:34 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:29:34,939 - WARNING - Could not retrieve variants from source file in region 8:130760639-130761040. Error was invalid region `8:130760640-130761040`
[2016-04-15T05:29Z] 2016-04-14 22:29:35 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:29:35,322 - WARNING - Could not retrieve variants from source file in region 8:131921745-131922217. Error was invalid region `8:131921746-131922217`
[2016-04-15T05:29Z] 2016-04-14 22:29:35 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:29:35,323 - WARNING - Could not retrieve variants from source file in region 8:131124348-131124749. Error was invalid region `8:131124349-131124749`
[2016-04-15T05:29Z] 2016-04-14 22:29:46 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:29:46,720 - WARNING - Could not retrieve variants from source file in region 8:133900041-133931938. Error was invalid region `8:133900042-133931938`
[2016-04-15T05:29Z] 2016-04-14 22:29:47 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:29:47,382 - WARNING - Could not retrieve variants from source file in region 8:141551196-141568812. Error was invalid region `8:141551197-141568812`
[2016-04-15T05:29Z] 2016-04-14 22:29:48 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:29:48,882 - WARNING - Could not retrieve variants from source file in region 8:133900041-133931938. Error was invalid region `8:133900042-133931938`
[2016-04-15T05:29Z] 2016-04-14 22:29:49 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:29:49,097 - WARNING - Could not retrieve variants from source file in region 8:135521759-135522160. Error was invalid region `8:135521760-135522160`
[2016-04-15T05:29Z] 2016-04-14 22:29:49 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:29:49,479 - WARNING - Could not retrieve variants from source file in region 8:139647051-139647452. Error was invalid region `8:139647052-139647452`
[2016-04-15T05:29Z] 2016-04-14 22:29:50 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:29:50,547 - WARNING - Could not retrieve variants from source file in region 8:140630779-140631180. Error was invalid region `8:140630780-140631180`
[2016-04-15T05:29Z] 2016-04-14 22:29:50 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:29:50,658 - WARNING - Could not retrieve variants from source file in region 8:139163981-139165479. Error was invalid region `8:139163982-139165479`
[2016-04-15T05:29Z] 2016-04-14 22:29:51 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:29:51,120 - WARNING - Could not retrieve variants from source file in region 8:134239559-134239960. Error was invalid region `8:134239560-134239960`
[2016-04-15T05:29Z] 2016-04-14 22:29:51 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:29:51,644 - WARNING - Could not retrieve variants from source file in region 8:141460806-141468030. Error was invalid region `8:141460807-141468030`
[2016-04-15T05:29Z] 2016-04-14 22:29:54 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:29:54,194 - WARNING - Could not retrieve variants from source file in region 8:135521759-135522160. Error was invalid region `8:135521760-135522160`
[2016-04-15T05:29Z] 2016-04-14 22:29:54 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:29:54,271 - WARNING - Could not retrieve variants from source file in region 8:139647051-139647452. Error was invalid region `8:139647052-139647452`
[2016-04-15T05:29Z] 2016-04-14 22:29:54 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:29:54,284 - WARNING - Could not retrieve variants from source file in region 8:139163981-139165479. Error was invalid region `8:139163982-139165479`
[2016-04-15T05:29Z] 2016-04-14 22:29:54 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:29:54,520 - WARNING - Could not retrieve variants from source file in region 8:139647051-139647452. Error was invalid region `8:139647052-139647452`
[2016-04-15T05:29Z] 2016-04-14 22:29:54 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:29:54,731 - WARNING - Could not retrieve variants from source file in region 8:139823846-139839102. Error was invalid region `8:139823847-139839102`
[2016-04-15T05:29Z] 2016-04-14 22:29:54 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:29:54,733 - WARNING - Could not retrieve variants from source file in region 8:140630779-140631180. Error was invalid region `8:140630780-140631180`
[2016-04-15T05:29Z] 2016-04-14 22:29:55 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:29:55,353 - WARNING - Could not retrieve variants from source file in region 8:140630779-140631180. Error was invalid region `8:140630780-140631180`
[2016-04-15T05:29Z] 2016-04-14 22:29:55 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:29:55,356 - WARNING - Could not retrieve variants from source file in region 8:139163981-139165479. Error was invalid region `8:139163982-139165479`
[2016-04-15T05:29Z] 2016-04-14 22:29:55 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:29:55,853 - WARNING - Could not retrieve variants from source file in region 8:134239559-134239960. Error was invalid region `8:134239560-134239960`
[2016-04-15T05:29Z] 2016-04-14 22:29:57 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:29:57,935 - WARNING - Could not retrieve variants from source file in region 8:139749588-139749989. Error was invalid region `8:139749589-139749989`
[2016-04-15T05:29Z] 2016-04-14 22:29:58 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:29:58,263 - WARNING - Could not retrieve variants from source file in region 8:139823846-139839102. Error was invalid region `8:139823847-139839102`
[2016-04-15T05:29Z] 2016-04-14 22:29:58 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:29:58,391 - WARNING - Could not retrieve variants from source file in region 8:134239559-134239960. Error was invalid region `8:134239560-134239960`
[2016-04-15T05:29Z] 2016-04-14 22:29:59 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:29:59,656 - WARNING - Could not retrieve variants from source file in region 8:139749588-139749989. Error was invalid region `8:139749589-139749989`
[2016-04-15T05:30Z] ['bcbio-variation-recall', 'square', '-Xms750m', '-Xmx7280m', '-XX:+UseSerialGC', '-c', 16, '-r', u'8:141900642-146364022', '--caller', 'platypus', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/8/Batch1-8_141900641_146364022.vcf.gz', '/mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/8/Batch1-8_141900641_146364022.vcf-inputs.txt'] in region: 8:141900642-146364022
[2016-04-15T05:30Z] 2016-04-14 22:30:16 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:30:16,053 - WARNING - Could not retrieve variants from source file in region 8:146115156-146115557. Error was invalid region `8:146115157-146115557`
[2016-04-15T05:30Z] 2016-04-14 22:30:16 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:30:16,779 - WARNING - Could not retrieve variants from source file in region 8:145106727-145107985. Error was invalid region `8:145106728-145107985`
[2016-04-15T05:30Z] 2016-04-14 22:30:16 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:30:16,800 - WARNING - Could not retrieve variants from source file in region 8:144163699-144164100. Error was invalid region `8:144163700-144164100`
[2016-04-15T05:30Z] 2016-04-14 22:30:17 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:30:17,010 - WARNING - Could not retrieve variants from source file in region 8:144511742-144522576. Error was invalid region `8:144511743-144522576`
[2016-04-15T05:30Z] 2016-04-14 22:30:17 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:30:17,430 - WARNING - Could not retrieve variants from source file in region 8:146068383-146068784. Error was invalid region `8:146068384-146068784`
[2016-04-15T05:30Z] 2016-04-14 22:30:17 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:30:17,935 - WARNING - Could not retrieve variants from source file in region 8:146156036-146171627. Error was invalid region `8:146156037-146171627`
[2016-04-15T05:30Z] 2016-04-14 22:30:17 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:30:17,936 - WARNING - Could not retrieve variants from source file in region 8:144294972-144295373. Error was invalid region `8:144294973-144295373`
[2016-04-15T05:30Z] 2016-04-14 22:30:18 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:30:18,268 - WARNING - Could not retrieve variants from source file in region 8:144990317-145011394. Error was invalid region `8:144990318-145011394`
[2016-04-15T05:30Z] 2016-04-14 22:30:22 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:30:22,782 - WARNING - Could not retrieve variants from source file in region 8:146115156-146115557. Error was invalid region `8:146115157-146115557`
[2016-04-15T05:30Z] 2016-04-14 22:30:25 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:30:25,131 - WARNING - Could not retrieve variants from source file in region 8:144457535-144457936. Error was invalid region `8:144457536-144457936`
[2016-04-15T05:30Z] 2016-04-14 22:30:25 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:30:25,818 - WARNING - Could not retrieve variants from source file in region 8:145106727-145107985. Error was invalid region `8:145106728-145107985`
[2016-04-15T05:30Z] 2016-04-14 22:30:26 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:30:26,946 - WARNING - Could not retrieve variants from source file in region 8:146068383-146068784. Error was invalid region `8:146068384-146068784`
[2016-04-15T05:30Z] 2016-04-14 22:30:27 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:30:27,940 - WARNING - Could not retrieve variants from source file in region 8:146115156-146115557. Error was invalid region `8:146115157-146115557`
[2016-04-15T05:30Z] 2016-04-14 22:30:31 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:30:31,883 - WARNING - Could not retrieve variants from source file in region 8:144457535-144457936. Error was invalid region `8:144457536-144457936`
[2016-04-15T05:30Z] 2016-04-14 22:30:33 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:30:33,236 - WARNING - Could not retrieve variants from source file in region 8:145106727-145107985. Error was invalid region `8:145106728-145107985`
[2016-04-15T05:30Z] 2016-04-14 22:30:34 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:30:34,350 - WARNING - Could not retrieve variants from source file in region 8:144163699-144164100. Error was invalid region `8:144163700-144164100`
[2016-04-15T05:30Z] 2016-04-14 22:30:35 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:30:35,577 - WARNING - Could not retrieve variants from source file in region 8:146068383-146068784. Error was invalid region `8:146068384-146068784`
[2016-04-15T05:30Z] 2016-04-14 22:30:36 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:30:36,046 - WARNING - Could not retrieve variants from source file in region 8:146156036-146171627. Error was invalid region `8:146156037-146171627`
[2016-04-15T05:30Z] 2016-04-14 22:30:47 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:30:47,150 - WARNING - Could not retrieve variants from source file in region 8:145223077-145223478. Error was invalid region `8:145223078-145223478`
[2016-04-15T05:30Z] 2016-04-14 22:30:47 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:30:47,657 - WARNING - Could not retrieve variants from source file in region 8:144731815-144732608. Error was invalid region `8:144731816-144732608`
[2016-04-15T05:30Z] 2016-04-14 22:30:49 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:30:49,276 - WARNING - Could not retrieve variants from source file in region 8:144331801-144417241. Error was invalid region `8:144331802-144417241`
[2016-04-15T05:30Z] 2016-04-14 22:30:49 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:30:49,875 - WARNING - Could not retrieve variants from source file in region 8:145057372-145067076. Error was invalid region `8:145057373-145067076`
[2016-04-15T05:30Z] 2016-04-14 22:30:50 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:30:50,147 - WARNING - Could not retrieve variants from source file in region 8:143694564-143695334. Error was invalid region `8:143694565-143695334`
[2016-04-15T05:30Z] 2016-04-14 22:30:50 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:30:50,584 - WARNING - Could not retrieve variants from source file in region 8:144124398-144124799. Error was invalid region `8:144124399-144124799`
[2016-04-15T05:30Z] 2016-04-14 22:30:52 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:30:52,642 - WARNING - Could not retrieve variants from source file in region 8:145223077-145223478. Error was invalid region `8:145223078-145223478`
[2016-04-15T05:30Z] 2016-04-14 22:30:53 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:30:53,004 - WARNING - Could not retrieve variants from source file in region 8:143603207-143623649. Error was invalid region `8:143603208-143623649`
[2016-04-15T05:30Z] 2016-04-14 22:30:53 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:30:53,154 - WARNING - Could not retrieve variants from source file in region 8:144731815-144732608. Error was invalid region `8:144731816-144732608`
[2016-04-15T05:30Z] 2016-04-14 22:30:54 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:30:54,369 - WARNING - Could not retrieve variants from source file in region 8:145149890-145162013. Error was invalid region `8:145149891-145162013`
[2016-04-15T05:30Z] 2016-04-14 22:30:55 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:30:55,058 - WARNING - Could not retrieve variants from source file in region 8:143694564-143695334. Error was invalid region `8:143694565-143695334`
[2016-04-15T05:30Z] 2016-04-14 22:30:55 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:30:55,231 - WARNING - Could not retrieve variants from source file in region 8:144124398-144124799. Error was invalid region `8:144124399-144124799`
[2016-04-15T05:30Z] 2016-04-14 22:30:57 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:30:57,396 - WARNING - Could not retrieve variants from source file in region 8:145223077-145223478. Error was invalid region `8:145223078-145223478`
[2016-04-15T05:30Z] 2016-04-14 22:30:57 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:30:57,440 - WARNING - Could not retrieve variants from source file in region 8:144239648-144240447. Error was invalid region `8:144239649-144240447`
[2016-04-15T05:30Z] 2016-04-14 22:30:58 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:30:58,596 - WARNING - Could not retrieve variants from source file in region 8:143959039-143961195. Error was invalid region `8:143959040-143961195`
[2016-04-15T05:30Z] 2016-04-14 22:30:58 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:30:58,963 - WARNING - Could not retrieve variants from source file in region 8:145149890-145162013. Error was invalid region `8:145149891-145162013`
[2016-04-15T05:30Z] 2016-04-14 22:30:59 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:30:59,128 - WARNING - Could not retrieve variants from source file in region 8:145149890-145162013. Error was invalid region `8:145149891-145162013`
[2016-04-15T05:30Z] 2016-04-14 22:30:59 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:30:59,882 - WARNING - Could not retrieve variants from source file in region 8:143694564-143695334. Error was invalid region `8:143694565-143695334`
[2016-04-15T05:31Z] 2016-04-14 22:31:00 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:31:00,049 - WARNING - Could not retrieve variants from source file in region 8:144124398-144124799. Error was invalid region `8:144124399-144124799`
[2016-04-15T05:31Z] 2016-04-14 22:31:01 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:31:01,807 - WARNING - Could not retrieve variants from source file in region 8:144239648-144240447. Error was invalid region `8:144239649-144240447`
[2016-04-15T05:31Z] 2016-04-14 22:31:04 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:31:04,796 - WARNING - Could not retrieve variants from source file in region 8:144872200-144947008. Error was invalid region `8:144872201-144947008`
[2016-04-15T05:31Z] 2016-04-14 22:31:10 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:31:10,531 - WARNING - Could not retrieve variants from source file in region 8:143412925-143436224. Error was invalid region `8:143412926-143436224`
[2016-04-15T05:31Z] 2016-04-14 22:31:10 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:31:10,534 - WARNING - Could not retrieve variants from source file in region 8:143412925-143436224. Error was invalid region `8:143412926-143436224`
[2016-04-15T05:31Z] 2016-04-14 22:31:11 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:31:11,751 - WARNING - Could not retrieve variants from source file in region 8:142367124-142367749. Error was invalid region `8:142367125-142367749`
[2016-04-15T05:31Z] 2016-04-14 22:31:11 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:31:11,761 - WARNING - Could not retrieve variants from source file in region 8:142367124-142367749. Error was invalid region `8:142367125-142367749`
[2016-04-15T05:31Z] 2016-04-14 22:31:11 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:31:11,799 - WARNING - Could not retrieve variants from source file in region 8:142367124-142367749. Error was invalid region `8:142367125-142367749`
[2016-04-15T05:31Z] ['bcbio-variation-recall', 'square', '-Xms750m', '-Xmx7280m', '-XX:+UseSerialGC', '-c', 16, '-r', u'9:1-15510186', '--caller', 'platypus', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/9/Batch1-9_0_15510186.vcf.gz', '/mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/9/Batch1-9_0_15510186.vcf-inputs.txt'] in region: 9:1-15510186
[2016-04-15T05:31Z] 2016-04-14 22:31:28 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:31:28,890 - WARNING - Could not retrieve variants from source file in region 9:8389153-8389554. Error was invalid region `9:8389154-8389554`
[2016-04-15T05:31Z] 2016-04-14 22:31:28 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:31:28,935 - WARNING - Could not retrieve variants from source file in region 9:4117900-4118398. Error was invalid region `9:4117901-4118398`
[2016-04-15T05:31Z] 2016-04-14 22:31:29 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:31:29,531 - WARNING - Could not retrieve variants from source file in region 9:14313501-14313902. Error was invalid region `9:14313502-14313902`
[2016-04-15T05:31Z] 2016-04-14 22:31:29 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:31:29,870 - WARNING - Could not retrieve variants from source file in region 9:6505827-6506228. Error was invalid region `9:6505828-6506228`
[2016-04-15T05:31Z] 2016-04-14 22:31:29 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:31:29,882 - WARNING - Could not retrieve variants from source file in region 9:5968205-5969439. Error was invalid region `9:5968206-5969439`
[2016-04-15T05:31Z] 2016-04-14 22:31:30 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:31:30,100 - WARNING - Could not retrieve variants from source file in region 9:15459610-15472601. Error was invalid region `9:15459611-15472601`
[2016-04-15T05:31Z] 2016-04-14 22:31:30 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:31:30,504 - WARNING - Could not retrieve variants from source file in region 9:2073081-2073482. Error was invalid region `9:2073082-2073482`
[2016-04-15T05:31Z] 2016-04-14 22:31:30 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:31:30,504 - WARNING - Could not retrieve variants from source file in region 9:4662183-4662584. Error was invalid region `9:4662184-4662584`
[2016-04-15T05:31Z] 2016-04-14 22:31:30 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:31:30,509 - WARNING - Could not retrieve variants from source file in region 9:5381659-5382060. Error was invalid region `9:5381660-5382060`
[2016-04-15T05:31Z] 2016-04-14 22:31:33 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:31:33,222 - WARNING - Could not retrieve variants from source file in region 9:311913-334527. Error was invalid region `9:311914-334527`
[2016-04-15T05:31Z] 2016-04-14 22:31:36 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:31:36,515 - WARNING - Could not retrieve variants from source file in region 9:4117900-4118398. Error was invalid region `9:4117901-4118398`
[2016-04-15T05:31Z] 2016-04-14 22:31:37 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:31:37,446 - WARNING - Could not retrieve variants from source file in region 9:7103605-7104006. Error was invalid region `9:7103606-7104006`
[2016-04-15T05:31Z] 2016-04-14 22:31:37 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:31:37,627 - WARNING - Could not retrieve variants from source file in region 9:15214026-15214427. Error was invalid region `9:15214027-15214427`
[2016-04-15T05:31Z] 2016-04-14 22:31:38 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:31:38,047 - WARNING - Could not retrieve variants from source file in region 9:3246896-3247880. Error was invalid region `9:3246897-3247880`
[2016-04-15T05:31Z] 2016-04-14 22:31:38 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:31:38,086 - WARNING - Could not retrieve variants from source file in region 9:14313501-14313902. Error was invalid region `9:14313502-14313902`
[2016-04-15T05:31Z] 2016-04-14 22:31:38 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:31:38,432 - WARNING - Could not retrieve variants from source file in region 9:5968205-5969439. Error was invalid region `9:5968206-5969439`
[2016-04-15T05:31Z] 2016-04-14 22:31:38 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:31:38,470 - WARNING - Could not retrieve variants from source file in region 9:5381659-5382060. Error was invalid region `9:5381660-5382060`
[2016-04-15T05:31Z] 2016-04-14 22:31:38 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:31:38,769 - WARNING - Could not retrieve variants from source file in region 9:6505827-6506228. Error was invalid region `9:6505828-6506228`
[2016-04-15T05:31Z] 2016-04-14 22:31:41 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:31:41,869 - WARNING - Could not retrieve variants from source file in region 9:8389153-8389554. Error was invalid region `9:8389154-8389554`
[2016-04-15T05:31Z] 2016-04-14 22:31:44 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:31:44,598 - WARNING - Could not retrieve variants from source file in region 9:6924632-6925853. Error was invalid region `9:6924633-6925853`
[2016-04-15T05:31Z] 2016-04-14 22:31:45 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:31:45,836 - WARNING - Could not retrieve variants from source file in region 9:15214026-15214427. Error was invalid region `9:15214027-15214427`
[2016-04-15T05:31Z] 2016-04-14 22:31:45 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:31:45,855 - WARNING - Could not retrieve variants from source file in region 9:7103605-7104006. Error was invalid region `9:7103606-7104006`
[2016-04-15T05:31Z] 2016-04-14 22:31:46 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:31:46,706 - WARNING - Could not retrieve variants from source file in region 9:14313501-14313902. Error was invalid region `9:14313502-14313902`
[2016-04-15T05:31Z] 2016-04-14 22:31:46 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:31:46,755 - WARNING - Could not retrieve variants from source file in region 9:6505827-6506228. Error was invalid region `9:6505828-6506228`
[2016-04-15T05:31Z] 2016-04-14 22:31:46 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:31:46,850 - WARNING - Could not retrieve variants from source file in region 9:4662183-4662584. Error was invalid region `9:4662184-4662584`
[2016-04-15T05:31Z] 2016-04-14 22:31:47 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:31:47,030 - WARNING - Could not retrieve variants from source file in region 9:5381659-5382060. Error was invalid region `9:5381660-5382060`
[2016-04-15T05:31Z] 2016-04-14 22:31:47 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:31:47,057 - WARNING - Could not retrieve variants from source file in region 9:15459610-15472601. Error was invalid region `9:15459611-15472601`
[2016-04-15T05:31Z] 2016-04-14 22:31:47 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:31:47,200 - WARNING - Could not retrieve variants from source file in region 9:5968205-5969439. Error was invalid region `9:5968206-5969439`
[2016-04-15T05:31Z] 2016-04-14 22:31:58 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:31:58,027 - WARNING - Could not retrieve variants from source file in region 9:271427-286783. Error was invalid region `9:271428-286783`
[2016-04-15T05:32Z] 2016-04-14 22:32:00 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:32:00,363 - WARNING - Could not retrieve variants from source file in region 9:2648562-2648963. Error was invalid region `9:2648563-2648963`
[2016-04-15T05:32Z] 2016-04-14 22:32:00 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:32:00,434 - WARNING - Could not retrieve variants from source file in region 9:2811294-2828955. Error was invalid region `9:2811295-2828955`
[2016-04-15T05:32Z] 2016-04-14 22:32:01 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:32:01,706 - WARNING - Could not retrieve variants from source file in region 9:6757477-6757878. Error was invalid region `9:6757478-6757878`
[2016-04-15T05:32Z] 2016-04-14 22:32:03 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:32:03,777 - WARNING - Could not retrieve variants from source file in region 9:7799395-7799843. Error was invalid region `9:7799396-7799843`
[2016-04-15T05:32Z] 2016-04-14 22:32:04 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:32:04,611 - WARNING - Could not retrieve variants from source file in region 9:4622242-4625619. Error was invalid region `9:4622243-4625619`
[2016-04-15T05:32Z] 2016-04-14 22:32:05 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:32:05,775 - WARNING - Could not retrieve variants from source file in region 9:2811294-2828955. Error was invalid region `9:2811295-2828955`
[2016-04-15T05:32Z] 2016-04-14 22:32:05 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:32:05,777 - WARNING - Could not retrieve variants from source file in region 9:2648562-2648963. Error was invalid region `9:2648563-2648963`
[2016-04-15T05:32Z] 2016-04-14 22:32:05 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:32:05,934 - WARNING - Could not retrieve variants from source file in region 9:13111905-13112306. Error was invalid region `9:13111906-13112306`
[2016-04-15T05:32Z] 2016-04-14 22:32:06 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:32:06,250 - WARNING - Could not retrieve variants from source file in region 9:6328736-6331105. Error was invalid region `9:6328737-6331105`
[2016-04-15T05:32Z] 2016-04-14 22:32:06 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:32:06,745 - WARNING - Could not retrieve variants from source file in region 9:5335259-5335660. Error was invalid region `9:5335260-5335660`
[2016-04-15T05:32Z] 2016-04-14 22:32:06 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:32:06,754 - WARNING - Could not retrieve variants from source file in region 9:7076252-7076776. Error was invalid region `9:7076253-7076776`
[2016-04-15T05:32Z] 2016-04-14 22:32:06 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:32:06,878 - WARNING - Could not retrieve variants from source file in region 9:15187895-15188296. Error was invalid region `9:15187896-15188296`
[2016-04-15T05:32Z] 2016-04-14 22:32:10 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:32:10,850 - WARNING - Could not retrieve variants from source file in region 9:5832517-5832918. Error was invalid region `9:5832518-5832918`
[2016-04-15T05:32Z] 2016-04-14 22:32:11 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:32:11,343 - WARNING - Could not retrieve variants from source file in region 9:2648562-2648963. Error was invalid region `9:2648563-2648963`
[2016-04-15T05:32Z] 2016-04-14 22:32:11 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:32:11,525 - WARNING - Could not retrieve variants from source file in region 9:6328736-6331105. Error was invalid region `9:6328737-6331105`
[2016-04-15T05:32Z] 2016-04-14 22:32:11 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:32:11,649 - WARNING - Could not retrieve variants from source file in region 9:13111905-13112306. Error was invalid region `9:13111906-13112306`
[2016-04-15T05:32Z] 2016-04-14 22:32:12 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:32:12,110 - WARNING - Could not retrieve variants from source file in region 9:6757477-6757878. Error was invalid region `9:6757478-6757878`
[2016-04-15T05:32Z] 2016-04-14 22:32:12 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:32:12,357 - WARNING - Could not retrieve variants from source file in region 9:7076252-7076776. Error was invalid region `9:7076253-7076776`
[2016-04-15T05:32Z] 2016-04-14 22:32:12 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:32:12,398 - WARNING - Could not retrieve variants from source file in region 9:5335259-5335660. Error was invalid region `9:5335260-5335660`
[2016-04-15T05:32Z] 2016-04-14 22:32:12 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:32:12,419 - WARNING - Could not retrieve variants from source file in region 9:15187895-15188296. Error was invalid region `9:15187896-15188296`
[2016-04-15T05:32Z] 2016-04-14 22:32:13 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:32:13,488 - WARNING - Could not retrieve variants from source file in region 9:2039582-2040017. Error was invalid region `9:2039583-2040017`
[2016-04-15T05:32Z] 2016-04-14 22:32:13 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:32:13,657 - WARNING - Could not retrieve variants from source file in region 9:4622242-4625619. Error was invalid region `9:4622243-4625619`
[2016-04-15T05:32Z] 2016-04-14 22:32:16 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:32:16,320 - WARNING - Could not retrieve variants from source file in region 9:5832517-5832918. Error was invalid region `9:5832518-5832918`
[2016-04-15T05:32Z] 2016-04-14 22:32:17 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:32:17,376 - WARNING - Could not retrieve variants from source file in region 9:13111905-13112306. Error was invalid region `9:13111906-13112306`
[2016-04-15T05:32Z] 2016-04-14 22:32:18 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:32:18,098 - WARNING - Could not retrieve variants from source file in region 9:6328736-6331105. Error was invalid region `9:6328737-6331105`
[2016-04-15T05:32Z] 2016-04-14 22:32:18 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:32:18,193 - WARNING - Could not retrieve variants from source file in region 9:5335259-5335660. Error was invalid region `9:5335260-5335660`
[2016-04-15T05:32Z] 2016-04-14 22:32:26 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:32:26,966 - WARNING - Could not retrieve variants from source file in region 9:4564221-4576870. Error was invalid region `9:4564222-4576870`
[2016-04-15T05:32Z] 2016-04-14 22:32:27 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:32:27,172 - WARNING - Could not retrieve variants from source file in region 9:5557461-5557898. Error was invalid region `9:5557462-5557898`
[2016-04-15T05:32Z] 2016-04-14 22:32:28 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:32:28,223 - WARNING - Could not retrieve variants from source file in region 9:14662049-14662450. Error was invalid region `9:14662050-14662450`
[2016-04-15T05:32Z] 2016-04-14 22:32:28 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:32:28,902 - WARNING - Could not retrieve variants from source file in region 9:2115826-2116227. Error was invalid region `9:2115827-2116227`
[2016-04-15T05:32Z] 2016-04-14 22:32:29 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:32:29,419 - WARNING - Could not retrieve variants from source file in region 9:6610115-6610516. Error was invalid region `9:6610116-6610516`
[2016-04-15T05:32Z] 2016-04-14 22:32:30 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:32:30,666 - WARNING - Could not retrieve variants from source file in region 9:12775650-12777711. Error was invalid region `9:12775651-12777711`
[2016-04-15T05:32Z] 2016-04-14 22:32:31 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:32:31,057 - WARNING - Could not retrieve variants from source file in region 9:6253360-6253761. Error was invalid region `9:6253361-6253761`
[2016-04-15T05:32Z] 2016-04-14 22:32:31 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:32:31,876 - WARNING - Could not retrieve variants from source file in region 9:4564221-4576870. Error was invalid region `9:4564222-4576870`
[2016-04-15T05:32Z] 2016-04-14 22:32:32 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:32:32,294 - WARNING - Could not retrieve variants from source file in region 9:14662049-14662450. Error was invalid region `9:14662050-14662450`
[2016-04-15T05:32Z] 2016-04-14 22:32:33 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:32:33,328 - WARNING - Could not retrieve variants from source file in region 9:6610115-6610516. Error was invalid region `9:6610116-6610516`
[2016-04-15T05:32Z] 2016-04-14 22:32:34 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:32:34,936 - WARNING - Could not retrieve variants from source file in region 9:12775650-12777711. Error was invalid region `9:12775651-12777711`
[2016-04-15T05:32Z] 2016-04-14 22:32:35 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:32:35,130 - WARNING - Could not retrieve variants from source file in region 9:6253360-6253761. Error was invalid region `9:6253361-6253761`
[2016-04-15T05:32Z] 2016-04-14 22:32:36 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:32:36,628 - WARNING - Could not retrieve variants from source file in region 9:4564221-4576870. Error was invalid region `9:4564222-4576870`
[2016-04-15T05:32Z] 2016-04-14 22:32:36 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:32:36,692 - WARNING - Could not retrieve variants from source file in region 9:5081569-5081970. Error was invalid region `9:5081570-5081970`
[2016-04-15T05:32Z] 2016-04-14 22:32:36 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:32:36,874 - WARNING - Could not retrieve variants from source file in region 9:5557461-5557898. Error was invalid region `9:5557462-5557898`
[2016-04-15T05:32Z] 2016-04-14 22:32:39 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:32:39,259 - WARNING - Could not retrieve variants from source file in region 9:12775650-12777711. Error was invalid region `9:12775651-12777711`
[2016-04-15T05:32Z] 2016-04-14 22:32:39 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:32:39,813 - WARNING - Could not retrieve variants from source file in region 9:6253360-6253761. Error was invalid region `9:6253361-6253761`
[2016-04-15T05:32Z] 2016-04-14 22:32:41 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:32:41,604 - WARNING - Could not retrieve variants from source file in region 9:5081569-5081970. Error was invalid region `9:5081570-5081970`
[2016-04-15T05:32Z] 2016-04-14 22:32:45 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:32:45,061 - WARNING - Could not retrieve variants from source file in region 9:154584-172357. Error was invalid region `9:154585-172357`
[2016-04-15T05:32Z] 2016-04-14 22:32:45 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:32:45,974 - WARNING - Could not retrieve variants from source file in region 9:977101-991030. Error was invalid region `9:977102-991030`
[2016-04-15T05:32Z] 2016-04-14 22:32:46 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:32:46,965 - WARNING - Could not retrieve variants from source file in region 9:16913-17314. Error was invalid region `9:16914-17314`
[2016-04-15T05:32Z] 2016-04-14 22:32:51 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:32:51,367 - WARNING - Could not retrieve variants from source file in region 9:16913-17314. Error was invalid region `9:16914-17314`
[2016-04-15T05:32Z] ['bcbio-variation-recall', 'square', '-Xms750m', '-Xmx7280m', '-XX:+UseSerialGC', '-c', 16, '-r', u'9:15564087-32405601', '--caller', 'platypus', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/9/Batch1-9_15564086_32405601.vcf.gz', '/mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/9/Batch1-9_15564086_32405601.vcf-inputs.txt'] in region: 9:15564087-32405601
[2016-04-15T05:33Z] 2016-04-14 22:33:06 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:33:06,167 - WARNING - Could not retrieve variants from source file in region 9:20988215-20988616. Error was invalid region `9:20988216-20988616`
[2016-04-15T05:33Z] 2016-04-14 22:33:07 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:33:07,148 - WARNING - Could not retrieve variants from source file in region 9:20621690-20622091. Error was invalid region `9:20621691-20622091`
[2016-04-15T05:33Z] 2016-04-14 22:33:07 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:33:07,151 - WARNING - Could not retrieve variants from source file in region 9:19788465-19788866. Error was invalid region `9:19788466-19788866`
[2016-04-15T05:33Z] 2016-04-14 22:33:07 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:33:07,829 - WARNING - Could not retrieve variants from source file in region 9:19460982-19472191. Error was invalid region `9:19460983-19472191`
[2016-04-15T05:33Z] 2016-04-14 22:33:07 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:33:07,956 - WARNING - Could not retrieve variants from source file in region 9:19622057-19622458. Error was invalid region `9:19622058-19622458`
[2016-04-15T05:33Z] 2016-04-14 22:33:08 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:33:08,033 - WARNING - Could not retrieve variants from source file in region 9:26995576-27009290. Error was invalid region `9:26995577-27009290`
[2016-04-15T05:33Z] 2016-04-14 22:33:08 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:33:08,750 - WARNING - Could not retrieve variants from source file in region 9:21816547-21816948. Error was invalid region `9:21816548-21816948`
[2016-04-15T05:33Z] 2016-04-14 22:33:08 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:33:08,909 - WARNING - Could not retrieve variants from source file in region 9:27183252-27220256. Error was invalid region `9:27183253-27220256`
[2016-04-15T05:33Z] 2016-04-14 22:33:08 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:33:08,974 - WARNING - Could not retrieve variants from source file in region 9:20866763-20867164. Error was invalid region `9:20866764-20867164`
[2016-04-15T05:33Z] 2016-04-14 22:33:09 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:33:09,070 - WARNING - Could not retrieve variants from source file in region 9:21974806-21992113. Error was invalid region `9:21974807-21992113`
[2016-04-15T05:33Z] 2016-04-14 22:33:15 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:33:15,273 - WARNING - Could not retrieve variants from source file in region 9:19460982-19472191. Error was invalid region `9:19460983-19472191`
[2016-04-15T05:33Z] 2016-04-14 22:33:16 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:33:16,822 - WARNING - Could not retrieve variants from source file in region 9:27524520-27561655. Error was invalid region `9:27524521-27561655`
[2016-04-15T05:33Z] 2016-04-14 22:33:16 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:33:16,841 - WARNING - Could not retrieve variants from source file in region 9:21304592-21304993. Error was invalid region `9:21304593-21304993`
[2016-04-15T05:33Z] 2016-04-14 22:33:17 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:33:17,344 - WARNING - Could not retrieve variants from source file in region 9:19058425-19076863. Error was invalid region `9:19058426-19076863`
[2016-04-15T05:33Z] 2016-04-14 22:33:18 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:33:18,169 - WARNING - Could not retrieve variants from source file in region 9:21816547-21816948. Error was invalid region `9:21816548-21816948`
[2016-04-15T05:33Z] 2016-04-14 22:33:19 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:33:19,008 - WARNING - Could not retrieve variants from source file in region 9:18927999-18951085. Error was invalid region `9:18928000-18951085`
[2016-04-15T05:33Z] 2016-04-14 22:33:19 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:33:19,127 - WARNING - Could not retrieve variants from source file in region 9:27454924-27455775. Error was invalid region `9:27454925-27455775`
[2016-04-15T05:33Z] 2016-04-14 22:33:19 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:33:19,177 - WARNING - Could not retrieve variants from source file in region 9:20866763-20867164. Error was invalid region `9:20866764-20867164`
[2016-04-15T05:33Z] 2016-04-14 22:33:19 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:33:19,369 - WARNING - Could not retrieve variants from source file in region 9:18504705-18505106. Error was invalid region `9:18504706-18505106`
[2016-04-15T05:33Z] 2016-04-14 22:33:19 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:33:19,691 - WARNING - Could not retrieve variants from source file in region 9:19788465-19788866. Error was invalid region `9:19788466-19788866`
[2016-04-15T05:33Z] 2016-04-14 22:33:20 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:33:20,274 - WARNING - Could not retrieve variants from source file in region 9:19460982-19472191. Error was invalid region `9:19460983-19472191`
[2016-04-15T05:33Z] 2016-04-14 22:33:21 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:33:21,348 - WARNING - Could not retrieve variants from source file in region 9:26995576-27009290. Error was invalid region `9:26995577-27009290`
[2016-04-15T05:33Z] 2016-04-14 22:33:21 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:33:21,353 - WARNING - Could not retrieve variants from source file in region 9:19622057-19622458. Error was invalid region `9:19622058-19622458`
[2016-04-15T05:33Z] 2016-04-14 22:33:22 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:33:22,204 - WARNING - Could not retrieve variants from source file in region 9:21304592-21304993. Error was invalid region `9:21304593-21304993`
[2016-04-15T05:33Z] 2016-04-14 22:33:23 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:33:23,911 - WARNING - Could not retrieve variants from source file in region 9:27183252-27220256. Error was invalid region `9:27183253-27220256`
[2016-04-15T05:33Z] 2016-04-14 22:33:25 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:33:25,534 - WARNING - Could not retrieve variants from source file in region 9:21816547-21816948. Error was invalid region `9:21816548-21816948`
[2016-04-15T05:33Z] 2016-04-14 22:33:26 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:33:26,039 - WARNING - Could not retrieve variants from source file in region 9:27454924-27455775. Error was invalid region `9:27454925-27455775`
[2016-04-15T05:33Z] 2016-04-14 22:33:26 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:33:26,120 - WARNING - Could not retrieve variants from source file in region 9:21974806-21992113. Error was invalid region `9:21974807-21992113`
[2016-04-15T05:33Z] 2016-04-14 22:33:26 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:33:26,224 - WARNING - Could not retrieve variants from source file in region 9:20866763-20867164. Error was invalid region `9:20866764-20867164`
[2016-04-15T05:33Z] 2016-04-14 22:33:34 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:33:34,366 - WARNING - Could not retrieve variants from source file in region 9:20764659-20765060. Error was invalid region `9:20764660-20765060`
[2016-04-15T05:33Z] 2016-04-14 22:33:36 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:33:36,997 - WARNING - Could not retrieve variants from source file in region 9:19576738-19577139. Error was invalid region `9:19576739-19577139`
[2016-04-15T05:33Z] 2016-04-14 22:33:37 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:33:37,346 - WARNING - Could not retrieve variants from source file in region 9:26915714-26916115. Error was invalid region `9:26915715-26916115`
[2016-04-15T05:33Z] 2016-04-14 22:33:37 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:33:37,405 - WARNING - Could not retrieve variants from source file in region 9:19340834-19341235. Error was invalid region `9:19340835-19341235`
[2016-04-15T05:33Z] 2016-04-14 22:33:37 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:33:37,408 - WARNING - Could not retrieve variants from source file in region 9:18775599-18777612. Error was invalid region `9:18775600-18777612`
[2016-04-15T05:33Z] 2016-04-14 22:33:37 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:33:37,437 - WARNING - Could not retrieve variants from source file in region 9:20764659-20765060. Error was invalid region `9:20764660-20765060`
[2016-04-15T05:33Z] 2016-04-14 22:33:37 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:33:37,458 - WARNING - Could not retrieve variants from source file in region 9:19576738-19577139. Error was invalid region `9:19576739-19577139`
[2016-04-15T05:33Z] 2016-04-14 22:33:37 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:33:37,640 - WARNING - Could not retrieve variants from source file in region 9:27062510-27062911. Error was invalid region `9:27062511-27062911`
[2016-04-15T05:33Z] 2016-04-14 22:33:38 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:33:38,610 - WARNING - Could not retrieve variants from source file in region 9:20764659-20765060. Error was invalid region `9:20764660-20765060`
[2016-04-15T05:33Z] 2016-04-14 22:33:40 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:33:40,520 - WARNING - Could not retrieve variants from source file in region 9:20413573-20413974. Error was invalid region `9:20413574-20413974`
[2016-04-15T05:33Z] 2016-04-14 22:33:40 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:33:40,541 - WARNING - Could not retrieve variants from source file in region 9:21409184-21409585. Error was invalid region `9:21409185-21409585`
[2016-04-15T05:33Z] 2016-04-14 22:33:41 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:33:41,616 - WARNING - Could not retrieve variants from source file in region 9:19576738-19577139. Error was invalid region `9:19576739-19577139`
[2016-04-15T05:33Z] 2016-04-14 22:33:42 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:33:42,279 - WARNING - Could not retrieve variants from source file in region 9:18775599-18777612. Error was invalid region `9:18775600-18777612`
[2016-04-15T05:33Z] 2016-04-14 22:33:42 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:33:42,415 - WARNING - Could not retrieve variants from source file in region 9:21186910-21239637. Error was invalid region `9:21186911-21239637`
[2016-04-15T05:33Z] 2016-04-14 22:33:46 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:33:46,193 - WARNING - Could not retrieve variants from source file in region 9:26915714-26916115. Error was invalid region `9:26915715-26916115`
[2016-04-15T05:33Z] 2016-04-14 22:33:46 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:33:46,361 - WARNING - Could not retrieve variants from source file in region 9:27062510-27062911. Error was invalid region `9:27062511-27062911`
[2016-04-15T05:33Z] 2016-04-14 22:33:46 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:33:46,685 - WARNING - Could not retrieve variants from source file in region 9:18775599-18777612. Error was invalid region `9:18775600-18777612`
[2016-04-15T05:33Z] 2016-04-14 22:33:49 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:33:49,064 - WARNING - Could not retrieve variants from source file in region 9:21409184-21409585. Error was invalid region `9:21409185-21409585`
[2016-04-15T05:33Z] 2016-04-14 22:33:51 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:33:51,905 - WARNING - Could not retrieve variants from source file in region 9:17134904-17135305. Error was invalid region `9:17134905-17135305`
[2016-04-15T05:33Z] 2016-04-14 22:33:53 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:33:53,677 - WARNING - Could not retrieve variants from source file in region 9:15784349-15784750. Error was invalid region `9:15784350-15784750`
[2016-04-15T05:33Z] 2016-04-14 22:33:53 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:33:53,848 - WARNING - Could not retrieve variants from source file in region 9:25677487-25678312. Error was invalid region `9:25677488-25678312`
[2016-04-15T05:33Z] 2016-04-14 22:33:54 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:33:54,277 - WARNING - Could not retrieve variants from source file in region 9:15744330-15744731. Error was invalid region `9:15744331-15744731`
[2016-04-15T05:33Z] 2016-04-14 22:33:56 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:33:56,077 - WARNING - Could not retrieve variants from source file in region 9:25677487-25678312. Error was invalid region `9:25677488-25678312`
[2016-04-15T05:33Z] 2016-04-14 22:33:56 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:33:56,532 - WARNING - Could not retrieve variants from source file in region 9:21333043-21350810. Error was invalid region `9:21333044-21350810`
[2016-04-15T05:33Z] 2016-04-14 22:33:58 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:33:58,430 - WARNING - Could not retrieve variants from source file in region 9:15784349-15784750. Error was invalid region `9:15784350-15784750`
[2016-04-15T05:33Z] 2016-04-14 22:33:58 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:33:58,542 - WARNING - Could not retrieve variants from source file in region 9:25677487-25678312. Error was invalid region `9:25677488-25678312`
[2016-04-15T05:33Z] 2016-04-14 22:33:59 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:33:59,344 - WARNING - Could not retrieve variants from source file in region 9:15591161-15591562. Error was invalid region `9:15591162-15591562`
[2016-04-15T05:34Z] 2016-04-14 22:34:00 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:34:00,386 - WARNING - Could not retrieve variants from source file in region 9:17394325-17409556. Error was invalid region `9:17394326-17409556`
[2016-04-15T05:34Z] 2016-04-14 22:34:00 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:34:00,722 - WARNING - Could not retrieve variants from source file in region 9:17134904-17135305. Error was invalid region `9:17134905-17135305`
[2016-04-15T05:34Z] 2016-04-14 22:34:01 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:34:01,822 - WARNING - Could not retrieve variants from source file in region 9:17342172-17342573. Error was invalid region `9:17342173-17342573`
[2016-04-15T05:34Z] 2016-04-14 22:34:03 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:34:03,545 - WARNING - Could not retrieve variants from source file in region 9:24545302-24545960. Error was invalid region `9:24545303-24545960`
[2016-04-15T05:34Z] 2016-04-14 22:34:03 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:34:03,650 - WARNING - Could not retrieve variants from source file in region 9:15591161-15591562. Error was invalid region `9:15591162-15591562`
[2016-04-15T05:34Z] 2016-04-14 22:34:04 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:34:04,197 - WARNING - Could not retrieve variants from source file in region 9:17394325-17409556. Error was invalid region `9:17394326-17409556`
[2016-04-15T05:34Z] 2016-04-14 22:34:06 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:34:06,181 - WARNING - Could not retrieve variants from source file in region 9:17342172-17342573. Error was invalid region `9:17342173-17342573`
[2016-04-15T05:34Z] 2016-04-14 22:34:06 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:34:06,669 - WARNING - Could not retrieve variants from source file in region 9:15591161-15591562. Error was invalid region `9:15591162-15591562`
[2016-04-15T05:34Z] 2016-04-14 22:34:06 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:34:06,709 - WARNING - Could not retrieve variants from source file in region 9:17394325-17409556. Error was invalid region `9:17394326-17409556`
[2016-04-15T05:34Z] 2016-04-14 22:34:07 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:34:07,000 - WARNING - Could not retrieve variants from source file in region 9:16419308-16435904. Error was invalid region `9:16419309-16435904`
[2016-04-15T05:34Z] 2016-04-14 22:34:07 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:34:07,021 - WARNING - Could not retrieve variants from source file in region 9:22447444-22447845. Error was invalid region `9:22447445-22447845`
[2016-04-15T05:34Z] 2016-04-14 22:34:09 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:34:09,860 - WARNING - Could not retrieve variants from source file in region 9:17342172-17342573. Error was invalid region `9:17342173-17342573`
[2016-04-15T05:34Z] 2016-04-14 22:34:13 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:34:13,071 - WARNING - Could not retrieve variants from source file in region 9:17273520-17301903. Error was invalid region `9:17273521-17301903`
[2016-04-15T05:34Z] ['bcbio-variation-recall', 'square', '-Xms750m', '-Xmx7280m', '-XX:+UseSerialGC', '-c', 16, '-r', u'9:32407259-65506776', '--caller', 'platypus', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/9/Batch1-9_32407258_65506776.vcf.gz', '/mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/9/Batch1-9_32407258_65506776.vcf-inputs.txt'] in region: 9:32407259-65506776
[2016-04-15T05:34Z] 2016-04-14 22:34:25 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:34:25,595 - WARNING - Could not retrieve variants from source file in region 9:38395717-38396692. Error was invalid region `9:38395718-38396692`
[2016-04-15T05:34Z] 2016-04-14 22:34:26 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:34:26,003 - WARNING - Could not retrieve variants from source file in region 9:33442741-33447614. Error was invalid region `9:33442742-33447614`
[2016-04-15T05:34Z] 2016-04-14 22:34:27 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:34:27,409 - WARNING - Could not retrieve variants from source file in region 9:33750634-33751035. Error was invalid region `9:33750635-33751035`
[2016-04-15T05:34Z] 2016-04-14 22:34:28 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:34:28,160 - WARNING - Could not retrieve variants from source file in region 9:37781900-37784180. Error was invalid region `9:37781901-37784180`
[2016-04-15T05:34Z] 2016-04-14 22:34:28 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:34:28,862 - WARNING - Could not retrieve variants from source file in region 9:35043080-35043481. Error was invalid region `9:35043081-35043481`
[2016-04-15T05:34Z] 2016-04-14 22:34:28 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:34:28,911 - WARNING - Could not retrieve variants from source file in region 9:35792212-35833518. Error was invalid region `9:35792213-35833518`
[2016-04-15T05:34Z] 2016-04-14 22:34:29 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:34:29,433 - WARNING - Could not retrieve variants from source file in region 9:35071790-35108048. Error was invalid region `9:35071791-35108048`
[2016-04-15T05:34Z] 2016-04-14 22:34:29 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:34:29,888 - WARNING - Could not retrieve variants from source file in region 9:34310716-34311117. Error was invalid region `9:34310717-34311117`
[2016-04-15T05:34Z] 2016-04-14 22:34:29 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:34:29,902 - WARNING - Could not retrieve variants from source file in region 9:37729575-37745603. Error was invalid region `9:37729576-37745603`
[2016-04-15T05:34Z] 2016-04-14 22:34:30 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:34:30,083 - WARNING - Could not retrieve variants from source file in region 9:37974532-37974933. Error was invalid region `9:37974533-37974933`
[2016-04-15T05:34Z] 2016-04-14 22:34:30 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:34:30,159 - WARNING - Could not retrieve variants from source file in region 9:43849606-43861271. Error was invalid region `9:43849607-43861271`
[2016-04-15T05:34Z] 2016-04-14 22:34:30 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:34:30,482 - WARNING - Could not retrieve variants from source file in region 9:33442741-33447614. Error was invalid region `9:33442742-33447614`
[2016-04-15T05:34Z] 2016-04-14 22:34:31 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:34:31,852 - WARNING - Could not retrieve variants from source file in region 9:35606673-35608375. Error was invalid region `9:35606674-35608375`
[2016-04-15T05:34Z] 2016-04-14 22:34:35 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:34:35,782 - WARNING - Could not retrieve variants from source file in region 9:35043080-35043481. Error was invalid region `9:35043081-35043481`
[2016-04-15T05:34Z] 2016-04-14 22:34:37 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:34:37,345 - WARNING - Could not retrieve variants from source file in region 9:40702635-40703036. Error was invalid region `9:40702636-40703036`
[2016-04-15T05:34Z] 2016-04-14 22:34:37 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:34:37,815 - WARNING - Could not retrieve variants from source file in region 9:34310716-34311117. Error was invalid region `9:34310717-34311117`
[2016-04-15T05:34Z] 2016-04-14 22:34:38 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:34:38,224 - WARNING - Could not retrieve variants from source file in region 9:33442741-33447614. Error was invalid region `9:33442742-33447614`
[2016-04-15T05:34Z] 2016-04-14 22:34:38 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:34:38,640 - WARNING - Could not retrieve variants from source file in region 9:33750634-33751035. Error was invalid region `9:33750635-33751035`
[2016-04-15T05:34Z] 2016-04-14 22:34:38 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:34:38,730 - WARNING - Could not retrieve variants from source file in region 9:33927688-33941949. Error was invalid region `9:33927689-33941949`
[2016-04-15T05:34Z] 2016-04-14 22:34:41 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:34:41,480 - WARNING - Could not retrieve variants from source file in region 9:35792212-35833518. Error was invalid region `9:35792213-35833518`
[2016-04-15T05:34Z] 2016-04-14 22:34:41 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:34:41,666 - WARNING - Could not retrieve variants from source file in region 9:35043080-35043481. Error was invalid region `9:35043081-35043481`
[2016-04-15T05:34Z] 2016-04-14 22:34:45 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:34:45,826 - WARNING - Could not retrieve variants from source file in region 9:34310716-34311117. Error was invalid region `9:34310717-34311117`
[2016-04-15T05:34Z] 2016-04-14 22:34:45 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:34:45,964 - WARNING - Could not retrieve variants from source file in region 9:33927688-33941949. Error was invalid region `9:33927689-33941949`
[2016-04-15T05:34Z] 2016-04-14 22:34:54 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:34:54,336 - WARNING - Could not retrieve variants from source file in region 9:38068321-38068722. Error was invalid region `9:38068322-38068722`
[2016-04-15T05:34Z] 2016-04-14 22:34:55 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:34:55,549 - WARNING - Could not retrieve variants from source file in region 9:33386778-33387263. Error was invalid region `9:33386779-33387263`
[2016-04-15T05:34Z] 2016-04-14 22:34:56 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:34:56,591 - WARNING - Could not retrieve variants from source file in region 9:35546524-35562739. Error was invalid region `9:35546525-35562739`
[2016-04-15T05:34Z] 2016-04-14 22:34:56 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:34:56,645 - WARNING - Could not retrieve variants from source file in region 9:34500610-34501011. Error was invalid region `9:34500611-34501011`
[2016-04-15T05:34Z] 2016-04-14 22:34:57 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:34:57,127 - WARNING - Could not retrieve variants from source file in region 9:34972251-34972652. Error was invalid region `9:34972252-34972652`
[2016-04-15T05:34Z] 2016-04-14 22:34:58 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:34:58,304 - WARNING - Could not retrieve variants from source file in region 9:35749634-35753354. Error was invalid region `9:35749635-35753354`
[2016-04-15T05:34Z] 2016-04-14 22:34:58 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:34:58,538 - WARNING - Could not retrieve variants from source file in region 9:38615487-38615888. Error was invalid region `9:38615488-38615888`
[2016-04-15T05:34Z] 2016-04-14 22:34:58 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:34:58,830 - WARNING - Could not retrieve variants from source file in region 9:38068321-38068722. Error was invalid region `9:38068322-38068722`
[2016-04-15T05:35Z] 2016-04-14 22:35:00 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:35:00,619 - WARNING - Could not retrieve variants from source file in region 9:33386778-33387263. Error was invalid region `9:33386779-33387263`
[2016-04-15T05:35Z] 2016-04-14 22:35:01 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:35:01,721 - WARNING - Could not retrieve variants from source file in region 9:34500610-34501011. Error was invalid region `9:34500611-34501011`
[2016-04-15T05:35Z] 2016-04-14 22:35:02 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:35:02,001 - WARNING - Could not retrieve variants from source file in region 9:37692443-37692844. Error was invalid region `9:37692444-37692844`
[2016-04-15T05:35Z] 2016-04-14 22:35:02 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:35:02,061 - WARNING - Could not retrieve variants from source file in region 9:34972251-34972652. Error was invalid region `9:34972252-34972652`
[2016-04-15T05:35Z] 2016-04-14 22:35:03 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:35:03,356 - WARNING - Could not retrieve variants from source file in region 9:38068321-38068722. Error was invalid region `9:38068322-38068722`
[2016-04-15T05:35Z] 2016-04-14 22:35:04 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:35:04,755 - WARNING - Could not retrieve variants from source file in region 9:43816445-43822894. Error was invalid region `9:43816446-43822894`
[2016-04-15T05:35Z] 2016-04-14 22:35:05 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:35:05,010 - WARNING - Could not retrieve variants from source file in region 9:33386778-33387263. Error was invalid region `9:33386779-33387263`
[2016-04-15T05:35Z] 2016-04-14 22:35:06 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:35:06,813 - WARNING - Could not retrieve variants from source file in region 9:34500610-34501011. Error was invalid region `9:34500611-34501011`
[2016-04-15T05:35Z] 2016-04-14 22:35:06 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:35:06,853 - WARNING - Could not retrieve variants from source file in region 9:35546524-35562739. Error was invalid region `9:35546525-35562739`
[2016-04-15T05:35Z] 2016-04-14 22:35:07 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:35:07,892 - WARNING - Could not retrieve variants from source file in region 9:33796479-33798207. Error was invalid region `9:33796480-33798207`
[2016-04-15T05:35Z] 2016-04-14 22:35:08 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:35:08,588 - WARNING - Could not retrieve variants from source file in region 9:34622178-34628130. Error was invalid region `9:34622179-34628130`
[2016-04-15T05:35Z] 2016-04-14 22:35:11 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:35:11,074 - WARNING - Could not retrieve variants from source file in region 9:37692443-37692844. Error was invalid region `9:37692444-37692844`
[2016-04-15T05:35Z] 2016-04-14 22:35:11 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:35:11,437 - WARNING - Could not retrieve variants from source file in region 9:33796479-33798207. Error was invalid region `9:33796480-33798207`
[2016-04-15T05:35Z] 2016-04-14 22:35:21 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:35:21,145 - WARNING - Could not retrieve variants from source file in region 9:43737247-43737648. Error was invalid region `9:43737248-43737648`
[2016-04-15T05:35Z] 2016-04-14 22:35:22 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:35:22,115 - WARNING - Could not retrieve variants from source file in region 9:36674631-36675032. Error was invalid region `9:36674632-36675032`
[2016-04-15T05:35Z] 2016-04-14 22:35:22 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:35:22,130 - WARNING - Could not retrieve variants from source file in region 9:35295669-35296070. Error was invalid region `9:35295670-35296070`
[2016-04-15T05:35Z] 2016-04-14 22:35:22 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:35:22,844 - WARNING - Could not retrieve variants from source file in region 9:33240014-33264730. Error was invalid region `9:33240015-33264730`
[2016-04-15T05:35Z] 2016-04-14 22:35:24 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:35:24,579 - WARNING - Could not retrieve variants from source file in region 9:35385148-35398795. Error was invalid region `9:35385149-35398795`
[2016-04-15T05:35Z] 2016-04-14 22:35:25 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:35:25,142 - WARNING - Could not retrieve variants from source file in region 9:34016895-34017296. Error was invalid region `9:34016896-34017296`
[2016-04-15T05:35Z] 2016-04-14 22:35:26 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:35:26,034 - WARNING - Could not retrieve variants from source file in region 9:36674631-36675032. Error was invalid region `9:36674632-36675032`
[2016-04-15T05:35Z] 2016-04-14 22:35:26 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:35:26,580 - WARNING - Could not retrieve variants from source file in region 9:33240014-33264730. Error was invalid region `9:33240015-33264730`
[2016-04-15T05:35Z] 2016-04-14 22:35:27 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:35:27,170 - WARNING - Could not retrieve variants from source file in region 9:43737247-43737648. Error was invalid region `9:43737248-43737648`
[2016-04-15T05:35Z] 2016-04-14 22:35:27 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:35:27,755 - WARNING - Could not retrieve variants from source file in region 9:37592241-37592642. Error was invalid region `9:37592242-37592642`
[2016-04-15T05:35Z] 2016-04-14 22:35:28 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:35:28,606 - WARNING - Could not retrieve variants from source file in region 9:35385148-35398795. Error was invalid region `9:35385149-35398795`
[2016-04-15T05:35Z] 2016-04-14 22:35:29 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:35:29,971 - WARNING - Could not retrieve variants from source file in region 9:36674631-36675032. Error was invalid region `9:36674632-36675032`
[2016-04-15T05:35Z] 2016-04-14 22:35:32 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:35:32,358 - WARNING - Could not retrieve variants from source file in region 9:37592241-37592642. Error was invalid region `9:37592242-37592642`
[2016-04-15T05:35Z] 2016-04-14 22:35:32 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:35:32,943 - WARNING - Could not retrieve variants from source file in region 9:43625171-43627618. Error was invalid region `9:43625172-43627618`
[2016-04-15T05:35Z] 2016-04-14 22:35:33 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:35:33,172 - WARNING - Could not retrieve variants from source file in region 9:34016895-34017296. Error was invalid region `9:34016896-34017296`
[2016-04-15T05:35Z] 2016-04-14 22:35:34 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:35:34,503 - WARNING - Could not retrieve variants from source file in region 9:32784627-32785028. Error was invalid region `9:32784628-32785028`
[2016-04-15T05:35Z] 2016-04-14 22:35:35 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:35:35,281 - WARNING - Could not retrieve variants from source file in region 9:32459239-32459640. Error was invalid region `9:32459240-32459640`
[2016-04-15T05:35Z] 2016-04-14 22:35:36 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:35:36,556 - WARNING - Could not retrieve variants from source file in region 9:37537346-37537747. Error was invalid region `9:37537347-37537747`
[2016-04-15T05:35Z] 2016-04-14 22:35:37 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:35:37,182 - WARNING - Could not retrieve variants from source file in region 9:36087665-36108199. Error was invalid region `9:36087666-36108199`
[2016-04-15T05:35Z] 2016-04-14 22:35:37 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:35:37,761 - WARNING - Could not retrieve variants from source file in region 9:43625171-43627618. Error was invalid region `9:43625172-43627618`
[2016-04-15T05:35Z] 2016-04-14 22:35:41 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:35:41,130 - WARNING - Could not retrieve variants from source file in region 9:42368403-42368804. Error was invalid region `9:42368404-42368804`
[2016-04-15T05:35Z] 2016-04-14 22:35:42 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:35:42,151 - WARNING - Could not retrieve variants from source file in region 9:37537346-37537747. Error was invalid region `9:37537347-37537747`
[2016-04-15T05:35Z] 2016-04-14 22:35:43 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:35:43,220 - WARNING - Could not retrieve variants from source file in region 9:37537346-37537747. Error was invalid region `9:37537347-37537747`
[2016-04-15T05:35Z] 2016-04-14 22:35:43 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:35:43,345 - WARNING - Could not retrieve variants from source file in region 9:43625171-43627618. Error was invalid region `9:43625172-43627618`
[2016-04-15T05:35Z] 2016-04-14 22:35:43 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:35:43,541 - WARNING - Could not retrieve variants from source file in region 9:37486392-37503314. Error was invalid region `9:37486393-37503314`
[2016-04-15T05:35Z] 2016-04-14 22:35:43 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:35:43,557 - WARNING - Could not retrieve variants from source file in region 9:36400751-36401385. Error was invalid region `9:36400752-36401385`
[2016-04-15T05:35Z] 2016-04-14 22:35:48 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:35:48,883 - WARNING - Could not retrieve variants from source file in region 9:36400751-36401385. Error was invalid region `9:36400752-36401385`
[2016-04-15T05:35Z] 2016-04-14 22:35:49 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:35:49,228 - WARNING - Could not retrieve variants from source file in region 9:37486392-37503314. Error was invalid region `9:37486393-37503314`
[2016-04-15T05:35Z] 2016-04-14 22:35:49 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:35:49,276 - WARNING - Could not retrieve variants from source file in region 9:37429603-37441998. Error was invalid region `9:37429604-37441998`
[2016-04-15T05:35Z] 2016-04-14 22:35:52 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:35:52,836 - WARNING - Could not retrieve variants from source file in region 9:37486392-37503314. Error was invalid region `9:37486393-37503314`
[2016-04-15T05:35Z] 2016-04-14 22:35:53 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:35:53,065 - WARNING - Could not retrieve variants from source file in region 9:40773126-40784373. Error was invalid region `9:40773127-40784373`
[2016-04-15T05:35Z] 2016-04-14 22:35:53 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:35:53,756 - WARNING - Could not retrieve variants from source file in region 9:37429603-37441998. Error was invalid region `9:37429604-37441998`
[2016-04-15T05:35Z] 2016-04-14 22:35:53 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:35:53,758 - WARNING - Could not retrieve variants from source file in region 9:36400751-36401385. Error was invalid region `9:36400752-36401385`
[2016-04-15T05:35Z] 2016-04-14 22:35:56 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:35:56,759 - WARNING - Could not retrieve variants from source file in region 9:35906372-35906791. Error was invalid region `9:35906373-35906791`
[2016-04-15T05:35Z] 2016-04-14 22:35:57 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:35:57,112 - WARNING - Could not retrieve variants from source file in region 9:35957144-35958237. Error was invalid region `9:35957145-35958237`
[2016-04-15T05:36Z] 2016-04-14 22:36:00 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:36:00,458 - WARNING - Could not retrieve variants from source file in region 9:35869790-35870415. Error was invalid region `9:35869791-35870415`
[2016-04-15T05:36Z] 2016-04-14 22:36:03 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:36:03,296 - WARNING - Could not retrieve variants from source file in region 9:36840412-36840813. Error was invalid region `9:36840413-36840813`
[2016-04-15T05:36Z] 2016-04-14 22:36:04 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:36:04,357 - WARNING - Could not retrieve variants from source file in region 9:36840412-36840813. Error was invalid region `9:36840413-36840813`
[2016-04-15T05:36Z] 2016-04-14 22:36:04 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:36:04,767 - WARNING - Could not retrieve variants from source file in region 9:36840412-36840813. Error was invalid region `9:36840413-36840813`
[2016-04-15T05:36Z] ['bcbio-variation-recall', 'square', '-Xms750m', '-Xmx7280m', '-XX:+UseSerialGC', '-c', 16, '-r', u'9:65507206-82187750', '--caller', 'platypus', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/9/Batch1-9_65507205_82187750.vcf.gz', '/mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/9/Batch1-9_65507205_82187750.vcf-inputs.txt'] in region: 9:65507206-82187750
[2016-04-15T05:36Z] 2016-04-14 22:36:20 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:36:20,563 - WARNING - Could not retrieve variants from source file in region 9:82187539-82187940. Error was invalid region `9:82187540-82187940`
[2016-04-15T05:36Z] 2016-04-14 22:36:21 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:36:21,437 - WARNING - Could not retrieve variants from source file in region 9:79117540-79118519. Error was invalid region `9:79117541-79118519`
[2016-04-15T05:36Z] 2016-04-14 22:36:21 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:36:21,450 - WARNING - Could not retrieve variants from source file in region 9:73461126-73484111. Error was invalid region `9:73461127-73484111`
[2016-04-15T05:36Z] 2016-04-14 22:36:21 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:36:21,524 - WARNING - Could not retrieve variants from source file in region 9:79985846-79998071. Error was invalid region `9:79985847-79998071`
[2016-04-15T05:36Z] 2016-04-14 22:36:22 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:36:22,095 - WARNING - Could not retrieve variants from source file in region 9:80919545-80919946. Error was invalid region `9:80919546-80919946`
[2016-04-15T05:36Z] 2016-04-14 22:36:22 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:36:22,109 - WARNING - Could not retrieve variants from source file in region 9:73736109-73736510. Error was invalid region `9:73736110-73736510`
[2016-04-15T05:36Z] 2016-04-14 22:36:22 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:36:22,652 - WARNING - Could not retrieve variants from source file in region 9:75303442-75315628. Error was invalid region `9:75303443-75315628`
[2016-04-15T05:36Z] 2016-04-14 22:36:22 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:36:22,931 - WARNING - Could not retrieve variants from source file in region 9:72472620-72473021. Error was invalid region `9:72472621-72473021`
[2016-04-15T05:36Z] 2016-04-14 22:36:27 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:36:27,119 - WARNING - Could not retrieve variants from source file in region 9:82187539-82187940. Error was invalid region `9:82187540-82187940`
[2016-04-15T05:36Z] 2016-04-14 22:36:28 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:36:28,491 - WARNING - Could not retrieve variants from source file in region 9:80878938-80879339. Error was invalid region `9:80878939-80879339`
[2016-04-15T05:36Z] 2016-04-14 22:36:29 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:36:29,698 - WARNING - Could not retrieve variants from source file in region 9:71939220-71940389. Error was invalid region `9:71939221-71940389`
[2016-04-15T05:36Z] 2016-04-14 22:36:30 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:36:30,415 - WARNING - Could not retrieve variants from source file in region 9:79985846-79998071. Error was invalid region `9:79985847-79998071`
[2016-04-15T05:36Z] 2016-04-14 22:36:30 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:36:30,833 - WARNING - Could not retrieve variants from source file in region 9:73461126-73484111. Error was invalid region `9:73461127-73484111`
[2016-04-15T05:36Z] 2016-04-14 22:36:30 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:36:30,851 - WARNING - Could not retrieve variants from source file in region 9:69256605-69257023. Error was invalid region `9:69256606-69257023`
[2016-04-15T05:36Z] 2016-04-14 22:36:31 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:36:31,559 - WARNING - Could not retrieve variants from source file in region 9:74863238-74865267. Error was invalid region `9:74863239-74865267`
[2016-04-15T05:36Z] 2016-04-14 22:36:31 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:36:31,659 - WARNING - Could not retrieve variants from source file in region 9:80919545-80919946. Error was invalid region `9:80919546-80919946`
[2016-04-15T05:36Z] 2016-04-14 22:36:33 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:36:33,087 - WARNING - Could not retrieve variants from source file in region 9:82187539-82187940. Error was invalid region `9:82187540-82187940`
[2016-04-15T05:36Z] 2016-04-14 22:36:33 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:36:33,292 - WARNING - Could not retrieve variants from source file in region 9:80878938-80879339. Error was invalid region `9:80878939-80879339`
[2016-04-15T05:36Z] 2016-04-14 22:36:33 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:36:33,491 - WARNING - Could not retrieve variants from source file in region 9:79117540-79118519. Error was invalid region `9:79117541-79118519`
[2016-04-15T05:36Z] 2016-04-14 22:36:35 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:36:35,871 - WARNING - Could not retrieve variants from source file in region 9:79985846-79998071. Error was invalid region `9:79985847-79998071`
[2016-04-15T05:36Z] 2016-04-14 22:36:36 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:36:36,724 - WARNING - Could not retrieve variants from source file in region 9:73461126-73484111. Error was invalid region `9:73461127-73484111`
[2016-04-15T05:36Z] 2016-04-14 22:36:38 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:36:38,383 - WARNING - Could not retrieve variants from source file in region 9:80919545-80919946. Error was invalid region `9:80919546-80919946`
[2016-04-15T05:36Z] 2016-04-14 22:36:39 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:36:39,072 - WARNING - Could not retrieve variants from source file in region 9:74863238-74865267. Error was invalid region `9:74863239-74865267`
[2016-04-15T05:36Z] 2016-04-14 22:36:39 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:36:39,163 - WARNING - Could not retrieve variants from source file in region 9:72472620-72473021. Error was invalid region `9:72472621-72473021`
[2016-04-15T05:36Z] 2016-04-14 22:36:39 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:36:39,473 - WARNING - Could not retrieve variants from source file in region 9:75303442-75315628. Error was invalid region `9:75303443-75315628`
[2016-04-15T05:36Z] 2016-04-14 22:36:49 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:36:49,406 - WARNING - Could not retrieve variants from source file in region 9:80851139-80851717. Error was invalid region `9:80851140-80851717`
[2016-04-15T05:36Z] 2016-04-14 22:36:51 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:36:51,542 - WARNING - Could not retrieve variants from source file in region 9:78968848-78969249. Error was invalid region `9:78968849-78969249`
[2016-04-15T05:36Z] 2016-04-14 22:36:51 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:36:51,655 - WARNING - Could not retrieve variants from source file in region 9:79896944-79897345. Error was invalid region `9:79896945-79897345`
[2016-04-15T05:36Z] 2016-04-14 22:36:52 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:36:52,223 - WARNING - Could not retrieve variants from source file in region 9:69206713-69207114. Error was invalid region `9:69206714-69207114`
[2016-04-15T05:36Z] 2016-04-14 22:36:53 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:36:53,343 - WARNING - Could not retrieve variants from source file in region 9:71998180-71998581. Error was invalid region `9:71998181-71998581`
[2016-04-15T05:36Z] 2016-04-14 22:36:53 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:36:53,513 - WARNING - Could not retrieve variants from source file in region 9:80049087-80049488. Error was invalid region `9:80049088-80049488`
[2016-04-15T05:36Z] 2016-04-14 22:36:54 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:36:54,339 - WARNING - Could not retrieve variants from source file in region 9:74671508-74674353. Error was invalid region `9:74671509-74674353`
[2016-04-15T05:36Z] 2016-04-14 22:36:55 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:36:55,603 - WARNING - Could not retrieve variants from source file in region 9:74974925-74975326. Error was invalid region `9:74974926-74975326`
[2016-04-15T05:36Z] 2016-04-14 22:36:56 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:36:56,825 - WARNING - Could not retrieve variants from source file in region 9:73255343-73255744. Error was invalid region `9:73255344-73255744`
[2016-04-15T05:36Z] 2016-04-14 22:36:57 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:36:57,007 - WARNING - Could not retrieve variants from source file in region 9:69206713-69207114. Error was invalid region `9:69206714-69207114`
[2016-04-15T05:36Z] 2016-04-14 22:36:57 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:36:57,673 - WARNING - Could not retrieve variants from source file in region 9:71998180-71998581. Error was invalid region `9:71998181-71998581`
[2016-04-15T05:36Z] 2016-04-14 22:36:57 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:36:57,898 - WARNING - Could not retrieve variants from source file in region 9:80049087-80049488. Error was invalid region `9:80049088-80049488`
[2016-04-15T05:36Z] 2016-04-14 22:36:59 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:36:59,532 - WARNING - Could not retrieve variants from source file in region 9:80851139-80851717. Error was invalid region `9:80851140-80851717`
[2016-04-15T05:37Z] 2016-04-14 22:37:00 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:37:00,396 - WARNING - Could not retrieve variants from source file in region 9:74974925-74975326. Error was invalid region `9:74974926-74975326`
[2016-04-15T05:37Z] 2016-04-14 22:37:00 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:37:00,671 - WARNING - Could not retrieve variants from source file in region 9:72897223-72897630. Error was invalid region `9:72897224-72897630`
[2016-04-15T05:37Z] 2016-04-14 22:37:00 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:37:00,868 - WARNING - Could not retrieve variants from source file in region 9:78808118-78808519. Error was invalid region `9:78808119-78808519`
[2016-04-15T05:37Z] 2016-04-14 22:37:01 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:37:01,645 - WARNING - Could not retrieve variants from source file in region 9:73255343-73255744. Error was invalid region `9:73255344-73255744`
[2016-04-15T05:37Z] 2016-04-14 22:37:02 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:37:02,228 - WARNING - Could not retrieve variants from source file in region 9:69206713-69207114. Error was invalid region `9:69206714-69207114`
[2016-04-15T05:37Z] 2016-04-14 22:37:02 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:37:02,269 - WARNING - Could not retrieve variants from source file in region 9:71998180-71998581. Error was invalid region `9:71998181-71998581`
[2016-04-15T05:37Z] 2016-04-14 22:37:03 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:37:03,111 - WARNING - Could not retrieve variants from source file in region 9:74671508-74674353. Error was invalid region `9:74671509-74674353`
[2016-04-15T05:37Z] 2016-04-14 22:37:05 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:37:05,010 - WARNING - Could not retrieve variants from source file in region 9:74974925-74975326. Error was invalid region `9:74974926-74975326`
[2016-04-15T05:37Z] 2016-04-14 22:37:13 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:37:13,574 - WARNING - Could not retrieve variants from source file in region 9:71766382-71789294. Error was invalid region `9:71766383-71789294`
[2016-04-15T05:37Z] 2016-04-14 22:37:14 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:37:14,829 - WARNING - Could not retrieve variants from source file in region 9:77415073-77418992. Error was invalid region `9:77415074-77418992`
[2016-04-15T05:37Z] 2016-04-14 22:37:15 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:37:15,102 - WARNING - Could not retrieve variants from source file in region 9:67968247-67968666. Error was invalid region `9:67968248-67968666`
[2016-04-15T05:37Z] 2016-04-14 22:37:15 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:37:15,562 - WARNING - Could not retrieve variants from source file in region 9:77684479-77693615. Error was invalid region `9:77684480-77693615`
[2016-04-15T05:37Z] 2016-04-14 22:37:17 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:37:17,198 - WARNING - Could not retrieve variants from source file in region 9:71766382-71789294. Error was invalid region `9:71766383-71789294`
[2016-04-15T05:37Z] 2016-04-14 22:37:18 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:37:18,212 - WARNING - Could not retrieve variants from source file in region 9:72741036-72755321. Error was invalid region `9:72741037-72755321`
[2016-04-15T05:37Z] 2016-04-14 22:37:18 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:37:18,499 - WARNING - Could not retrieve variants from source file in region 9:75775024-75775425. Error was invalid region `9:75775025-75775425`
[2016-04-15T05:37Z] 2016-04-14 22:37:18 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:37:18,583 - WARNING - Could not retrieve variants from source file in region 9:70999104-70999505. Error was invalid region `9:70999105-70999505`
[2016-04-15T05:37Z] 2016-04-14 22:37:18 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:37:18,812 - WARNING - Could not retrieve variants from source file in region 9:74304809-74305210. Error was invalid region `9:74304810-74305210`
[2016-04-15T05:37Z] 2016-04-14 22:37:18 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:37:18,842 - WARNING - Could not retrieve variants from source file in region 9:77562876-77563277. Error was invalid region `9:77562877-77563277`
[2016-04-15T05:37Z] 2016-04-14 22:37:22 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:37:22,249 - WARNING - Could not retrieve variants from source file in region 9:70999104-70999505. Error was invalid region `9:70999105-70999505`
[2016-04-15T05:37Z] 2016-04-14 22:37:22 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:37:22,376 - WARNING - Could not retrieve variants from source file in region 9:77562876-77563277. Error was invalid region `9:77562877-77563277`
[2016-04-15T05:37Z] 2016-04-14 22:37:22 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:37:22,695 - WARNING - Could not retrieve variants from source file in region 9:77684479-77693615. Error was invalid region `9:77684480-77693615`
[2016-04-15T05:37Z] 2016-04-14 22:37:30 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:37:30,488 - WARNING - Could not retrieve variants from source file in region 9:77376422-77376837. Error was invalid region `9:77376423-77376837`
[2016-04-15T05:37Z] 2016-04-14 22:37:31 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:37:31,651 - WARNING - Could not retrieve variants from source file in region 9:75545671-75546072. Error was invalid region `9:75545672-75546072`
[2016-04-15T05:37Z] 2016-04-14 22:37:31 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:37:31,671 - WARNING - Could not retrieve variants from source file in region 9:75545671-75546072. Error was invalid region `9:75545672-75546072`
[2016-04-15T05:37Z] 2016-04-14 22:37:31 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:37:31,678 - WARNING - Could not retrieve variants from source file in region 9:75545671-75546072. Error was invalid region `9:75545672-75546072`
[2016-04-15T05:37Z] 2016-04-14 22:37:31 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:37:31,713 - WARNING - Could not retrieve variants from source file in region 9:75430865-75431266. Error was invalid region `9:75430866-75431266`
[2016-04-15T05:37Z] 2016-04-14 22:37:31 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:37:31,729 - WARNING - Could not retrieve variants from source file in region 9:75430865-75431266. Error was invalid region `9:75430866-75431266`
[2016-04-15T05:37Z] 2016-04-14 22:37:32 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:37:32,102 - WARNING - Could not retrieve variants from source file in region 9:77244951-77245352. Error was invalid region `9:77244952-77245352`
[2016-04-15T05:37Z] 2016-04-14 22:37:32 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:37:32,160 - WARNING - Could not retrieve variants from source file in region 9:77244951-77245352. Error was invalid region `9:77244952-77245352`
[2016-04-15T05:37Z] 2016-04-14 22:37:35 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:37:35,328 - WARNING - Could not retrieve variants from source file in region 9:77244951-77245352. Error was invalid region `9:77244952-77245352`
[2016-04-15T05:37Z] ['bcbio-variation-recall', 'square', '-Xms750m', '-Xmx7280m', '-XX:+UseSerialGC', '-c', 16, '-r', u'9:82188173-97717561', '--caller', 'platypus', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/9/Batch1-9_82188172_97717561.vcf.gz', '/mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/9/Batch1-9_82188172_97717561.vcf-inputs.txt'] in region: 9:82188173-97717561
[2016-04-15T05:37Z] 2016-04-14 22:37:51 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:37:51,560 - WARNING - Could not retrieve variants from source file in region 9:97221252-97221653. Error was invalid region `9:97221253-97221653`
[2016-04-15T05:37Z] 2016-04-14 22:37:52 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:37:52,363 - WARNING - Could not retrieve variants from source file in region 9:86503794-86518986. Error was invalid region `9:86503795-86518986`
[2016-04-15T05:37Z] 2016-04-14 22:37:52 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:37:52,525 - WARNING - Could not retrieve variants from source file in region 9:94830145-94830546. Error was invalid region `9:94830146-94830546`
[2016-04-15T05:37Z] 2016-04-14 22:37:52 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:37:52,631 - WARNING - Could not retrieve variants from source file in region 9:87491042-87491443. Error was invalid region `9:87491043-87491443`
[2016-04-15T05:37Z] 2016-04-14 22:37:52 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:37:52,932 - WARNING - Could not retrieve variants from source file in region 9:95569427-95570107. Error was invalid region `9:95569428-95570107`
[2016-04-15T05:37Z] 2016-04-14 22:37:53 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:37:53,277 - WARNING - Could not retrieve variants from source file in region 9:88356532-88357054. Error was invalid region `9:88356533-88357054`
[2016-04-15T05:37Z] 2016-04-14 22:37:53 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:37:53,356 - WARNING - Could not retrieve variants from source file in region 9:86464868-86474305. Error was invalid region `9:86464869-86474305`
[2016-04-15T05:37Z] 2016-04-14 22:37:53 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:37:53,360 - WARNING - Could not retrieve variants from source file in region 9:95219037-95285172. Error was invalid region `9:95219038-95285172`
[2016-04-15T05:37Z] 2016-04-14 22:37:53 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:37:53,835 - WARNING - Could not retrieve variants from source file in region 9:97055116-97081137. Error was invalid region `9:97055117-97081137`
[2016-04-15T05:37Z] 2016-04-14 22:37:53 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:37:53,837 - WARNING - Could not retrieve variants from source file in region 9:96015045-96021502. Error was invalid region `9:96015046-96021502`
[2016-04-15T05:37Z] 2016-04-14 22:37:58 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:37:58,691 - WARNING - Could not retrieve variants from source file in region 9:97221252-97221653. Error was invalid region `9:97221253-97221653`
[2016-04-15T05:37Z] 2016-04-14 22:37:59 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:37:59,492 - WARNING - Could not retrieve variants from source file in region 9:97349455-97369341. Error was invalid region `9:97349456-97369341`
[2016-04-15T05:38Z] 2016-04-14 22:38:00 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:38:00,481 - WARNING - Could not retrieve variants from source file in region 9:87491042-87491443. Error was invalid region `9:87491043-87491443`
[2016-04-15T05:38Z] 2016-04-14 22:38:01 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:38:01,440 - WARNING - Could not retrieve variants from source file in region 9:95569427-95570107. Error was invalid region `9:95569428-95570107`
[2016-04-15T05:38Z] 2016-04-14 22:38:02 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:38:02,451 - WARNING - Could not retrieve variants from source file in region 9:97055116-97081137. Error was invalid region `9:97055117-97081137`
[2016-04-15T05:38Z] 2016-04-14 22:38:03 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:38:03,103 - WARNING - Could not retrieve variants from source file in region 9:96015045-96021502. Error was invalid region `9:96015046-96021502`
[2016-04-15T05:38Z] 2016-04-14 22:38:03 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:38:03,157 - WARNING - Could not retrieve variants from source file in region 9:84547239-84547640. Error was invalid region `9:84547240-84547640`
[2016-04-15T05:38Z] 2016-04-14 22:38:03 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:38:03,621 - WARNING - Could not retrieve variants from source file in region 9:97221252-97221653. Error was invalid region `9:97221253-97221653`
[2016-04-15T05:38Z] 2016-04-14 22:38:05 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:38:05,845 - WARNING - Could not retrieve variants from source file in region 9:87491042-87491443. Error was invalid region `9:87491043-87491443`
[2016-04-15T05:38Z] 2016-04-14 22:38:07 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:38:07,037 - WARNING - Could not retrieve variants from source file in region 9:95569427-95570107. Error was invalid region `9:95569428-95570107`
[2016-04-15T05:38Z] 2016-04-14 22:38:08 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:38:08,791 - WARNING - Could not retrieve variants from source file in region 9:97055116-97081137. Error was invalid region `9:97055117-97081137`
[2016-04-15T05:38Z] 2016-04-14 22:38:10 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:38:10,451 - WARNING - Could not retrieve variants from source file in region 9:96015045-96021502. Error was invalid region `9:96015046-96021502`
[2016-04-15T05:38Z] 2016-04-14 22:38:20 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:38:20,401 - WARNING - Could not retrieve variants from source file in region 9:91792874-91793275. Error was invalid region `9:91792875-91793275`
[2016-04-15T05:38Z] 2016-04-14 22:38:21 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:38:21,990 - WARNING - Could not retrieve variants from source file in region 9:95067835-95068236. Error was invalid region `9:95067836-95068236`
[2016-04-15T05:38Z] 2016-04-14 22:38:22 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:38:22,519 - WARNING - Could not retrieve variants from source file in region 9:96714280-96714681. Error was invalid region `9:96714281-96714681`
[2016-04-15T05:38Z] 2016-04-14 22:38:23 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:38:23,665 - WARNING - Could not retrieve variants from source file in region 9:85859807-85863281. Error was invalid region `9:85859808-85863281`
[2016-04-15T05:38Z] 2016-04-14 22:38:24 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:38:24,403 - WARNING - Could not retrieve variants from source file in region 9:96407772-96439194. Error was invalid region `9:96407773-96439194`
[2016-04-15T05:38Z] 2016-04-14 22:38:25 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:38:25,283 - WARNING - Could not retrieve variants from source file in region 9:84266936-84267337. Error was invalid region `9:84266937-84267337`
[2016-04-15T05:38Z] 2016-04-14 22:38:25 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:38:25,453 - WARNING - Could not retrieve variants from source file in region 9:93640982-93641383. Error was invalid region `9:93640983-93641383`
[2016-04-15T05:38Z] 2016-04-14 22:38:25 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:38:25,454 - WARNING - Could not retrieve variants from source file in region 9:90588692-90589093. Error was invalid region `9:90588693-90589093`
[2016-04-15T05:38Z] 2016-04-14 22:38:26 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:38:26,148 - WARNING - Could not retrieve variants from source file in region 9:95873859-95887510. Error was invalid region `9:95873860-95887510`
[2016-04-15T05:38Z] 2016-04-14 22:38:28 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:38:28,199 - WARNING - Could not retrieve variants from source file in region 9:95475726-95477148. Error was invalid region `9:95475727-95477148`
[2016-04-15T05:38Z] 2016-04-14 22:38:29 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:38:29,167 - WARNING - Could not retrieve variants from source file in region 9:94486110-94495798. Error was invalid region `9:94486111-94495798`
[2016-04-15T05:38Z] 2016-04-14 22:38:30 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:38:30,599 - WARNING - Could not retrieve variants from source file in region 9:84266936-84267337. Error was invalid region `9:84266937-84267337`
[2016-04-15T05:38Z] 2016-04-14 22:38:31 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:38:31,125 - WARNING - Could not retrieve variants from source file in region 9:91792874-91793275. Error was invalid region `9:91792875-91793275`
[2016-04-15T05:38Z] 2016-04-14 22:38:31 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:38:31,843 - WARNING - Could not retrieve variants from source file in region 9:94985426-94985827. Error was invalid region `9:94985427-94985827`
[2016-04-15T05:38Z] 2016-04-14 22:38:32 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:38:32,107 - WARNING - Could not retrieve variants from source file in region 9:84205649-84206050. Error was invalid region `9:84205650-84206050`
[2016-04-15T05:38Z] 2016-04-14 22:38:32 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:38:32,233 - WARNING - Could not retrieve variants from source file in region 9:95873859-95887510. Error was invalid region `9:95873860-95887510`
[2016-04-15T05:38Z] 2016-04-14 22:38:32 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:38:32,505 - WARNING - Could not retrieve variants from source file in region 9:96097451-96097937. Error was invalid region `9:96097452-96097937`
[2016-04-15T05:38Z] 2016-04-14 22:38:32 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:38:32,546 - WARNING - Could not retrieve variants from source file in region 9:90588692-90589093. Error was invalid region `9:90588693-90589093`
[2016-04-15T05:38Z] 2016-04-14 22:38:32 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:38:32,942 - WARNING - Could not retrieve variants from source file in region 9:96714280-96714681. Error was invalid region `9:96714281-96714681`
[2016-04-15T05:38Z] 2016-04-14 22:38:34 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:38:34,159 - WARNING - Could not retrieve variants from source file in region 9:94486110-94495798. Error was invalid region `9:94486111-94495798`
[2016-04-15T05:38Z] 2016-04-14 22:38:34 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:38:34,985 - WARNING - Could not retrieve variants from source file in region 9:84266936-84267337. Error was invalid region `9:84266937-84267337`
[2016-04-15T05:38Z] 2016-04-14 22:38:37 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:38:37,513 - WARNING - Could not retrieve variants from source file in region 9:95873859-95887510. Error was invalid region `9:95873860-95887510`
[2016-04-15T05:38Z] 2016-04-14 22:38:37 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:38:37,827 - WARNING - Could not retrieve variants from source file in region 9:84205649-84206050. Error was invalid region `9:84205650-84206050`
[2016-04-15T05:38Z] 2016-04-14 22:38:38 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:38:38,283 - WARNING - Could not retrieve variants from source file in region 9:93640982-93641383. Error was invalid region `9:93640983-93641383`
[2016-04-15T05:38Z] 2016-04-14 22:38:38 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:38:38,372 - WARNING - Could not retrieve variants from source file in region 9:94985426-94985827. Error was invalid region `9:94985427-94985827`
[2016-04-15T05:38Z] 2016-04-14 22:38:38 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:38:38,749 - WARNING - Could not retrieve variants from source file in region 9:90588692-90589093. Error was invalid region `9:90588693-90589093`
[2016-04-15T05:38Z] 2016-04-14 22:38:45 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:38:45,913 - WARNING - Could not retrieve variants from source file in region 9:91725111-91725512. Error was invalid region `9:91725112-91725512`
[2016-04-15T05:38Z] 2016-04-14 22:38:48 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:38:48,554 - WARNING - Could not retrieve variants from source file in region 9:84607547-84607948. Error was invalid region `9:84607548-84607948`
[2016-04-15T05:38Z] 2016-04-14 22:38:49 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:38:49,370 - WARNING - Could not retrieve variants from source file in region 9:93980632-93981033. Error was invalid region `9:93980633-93981033`
[2016-04-15T05:38Z] 2016-04-14 22:38:49 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:38:49,986 - WARNING - Could not retrieve variants from source file in region 9:93606098-93606499. Error was invalid region `9:93606099-93606499`
[2016-04-15T05:38Z] 2016-04-14 22:38:50 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:38:50,648 - WARNING - Could not retrieve variants from source file in region 9:95780254-95780655. Error was invalid region `9:95780255-95780655`
[2016-04-15T05:38Z] 2016-04-14 22:38:51 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:38:51,100 - WARNING - Could not retrieve variants from source file in region 9:91656752-91657153. Error was invalid region `9:91656753-91657153`
[2016-04-15T05:38Z] 2016-04-14 22:38:52 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:38:52,981 - WARNING - Could not retrieve variants from source file in region 9:84607547-84607948. Error was invalid region `9:84607548-84607948`
[2016-04-15T05:38Z] 2016-04-14 22:38:53 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:38:53,164 - WARNING - Could not retrieve variants from source file in region 9:90500194-90503641. Error was invalid region `9:90500195-90503641`
[2016-04-15T05:38Z] 2016-04-14 22:38:53 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:38:53,320 - WARNING - Could not retrieve variants from source file in region 9:95362454-95362855. Error was invalid region `9:95362455-95362855`
[2016-04-15T05:38Z] 2016-04-14 22:38:54 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:38:54,080 - WARNING - Could not retrieve variants from source file in region 9:93980632-93981033. Error was invalid region `9:93980633-93981033`
[2016-04-15T05:38Z] 2016-04-14 22:38:54 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:38:54,145 - WARNING - Could not retrieve variants from source file in region 9:93980632-93981033. Error was invalid region `9:93980633-93981033`
[2016-04-15T05:38Z] 2016-04-14 22:38:54 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:38:54,420 - WARNING - Could not retrieve variants from source file in region 9:93606098-93606499. Error was invalid region `9:93606099-93606499`
[2016-04-15T05:38Z] 2016-04-14 22:38:55 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:38:55,016 - WARNING - Could not retrieve variants from source file in region 9:91725111-91725512. Error was invalid region `9:91725112-91725512`
[2016-04-15T05:38Z] 2016-04-14 22:38:55 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:38:55,024 - WARNING - Could not retrieve variants from source file in region 9:95780254-95780655. Error was invalid region `9:95780255-95780655`
[2016-04-15T05:38Z] 2016-04-14 22:38:55 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:38:55,328 - WARNING - Could not retrieve variants from source file in region 9:91656752-91657153. Error was invalid region `9:91656753-91657153`
[2016-04-15T05:38Z] 2016-04-14 22:38:55 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:38:55,699 - WARNING - Could not retrieve variants from source file in region 9:92003468-92020623. Error was invalid region `9:92003469-92020623`
[2016-04-15T05:38Z] 2016-04-14 22:38:57 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:38:57,183 - WARNING - Could not retrieve variants from source file in region 9:90500194-90503641. Error was invalid region `9:90500195-90503641`
[2016-04-15T05:38Z] 2016-04-14 22:38:57 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:38:57,871 - WARNING - Could not retrieve variants from source file in region 9:93606098-93606499. Error was invalid region `9:93606099-93606499`
[2016-04-15T05:38Z] 2016-04-14 22:38:57 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:38:57,894 - WARNING - Could not retrieve variants from source file in region 9:95780254-95780655. Error was invalid region `9:95780255-95780655`
[2016-04-15T05:38Z] 2016-04-14 22:38:59 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:38:59,784 - WARNING - Could not retrieve variants from source file in region 9:91656752-91657153. Error was invalid region `9:91656753-91657153`
[2016-04-15T05:39Z] 2016-04-14 22:39:00 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:39:00,078 - WARNING - Could not retrieve variants from source file in region 9:92003468-92020623. Error was invalid region `9:92003469-92020623`
[2016-04-15T05:39Z] 2016-04-14 22:39:01 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:39:01,493 - WARNING - Could not retrieve variants from source file in region 9:90500194-90503641. Error was invalid region `9:90500195-90503641`
[2016-04-15T05:39Z] 2016-04-14 22:39:02 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:39:02,368 - WARNING - Could not retrieve variants from source file in region 9:90264804-90265205. Error was invalid region `9:90264805-90265205`
[2016-04-15T05:39Z] 2016-04-14 22:39:04 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:39:04,956 - WARNING - Could not retrieve variants from source file in region 9:90320925-90322213. Error was invalid region `9:90320926-90322213`
[2016-04-15T05:39Z] 2016-04-14 22:39:05 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:39:05,761 - WARNING - Could not retrieve variants from source file in region 9:91262132-91262684. Error was invalid region `9:91262133-91262684`
[2016-04-15T05:39Z] 2016-04-14 22:39:05 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:39:05,764 - WARNING - Could not retrieve variants from source file in region 9:90264804-90265205. Error was invalid region `9:90264805-90265205`
[2016-04-15T05:39Z] 2016-04-14 22:39:05 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:39:05,998 - WARNING - Could not retrieve variants from source file in region 9:90264804-90265205. Error was invalid region `9:90264805-90265205`
[2016-04-15T05:39Z] 2016-04-14 22:39:08 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:39:08,618 - WARNING - Could not retrieve variants from source file in region 9:88937640-88960128. Error was invalid region `9:88937641-88960128`
[2016-04-15T05:39Z] 2016-04-14 22:39:08 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:39:08,628 - WARNING - Could not retrieve variants from source file in region 9:88937640-88960128. Error was invalid region `9:88937641-88960128`
[2016-04-15T05:39Z] 2016-04-14 22:39:10 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:39:10,501 - WARNING - Could not retrieve variants from source file in region 9:88649818-88650219. Error was invalid region `9:88649819-88650219`
[2016-04-15T05:39Z] ['bcbio-variation-recall', 'square', '-Xms750m', '-Xmx7280m', '-XX:+UseSerialGC', '-c', 16, '-r', u'9:97718190-113228306', '--caller', 'platypus', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/9/Batch1-9_97718189_113228306.vcf.gz', '/mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/9/Batch1-9_97718189_113228306.vcf-inputs.txt'] in region: 9:97718190-113228306
[2016-04-15T05:39Z] 2016-04-14 22:39:26 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:39:26,658 - WARNING - Could not retrieve variants from source file in region 9:104432662-104449288. Error was invalid region `9:104432663-104449288`
[2016-04-15T05:39Z] 2016-04-14 22:39:26 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:39:26,755 - WARNING - Could not retrieve variants from source file in region 9:99250252-99250653. Error was invalid region `9:99250253-99250653`
[2016-04-15T05:39Z] 2016-04-14 22:39:27 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:39:27,231 - WARNING - Could not retrieve variants from source file in region 9:112899150-112900656. Error was invalid region `9:112899151-112900656`
[2016-04-15T05:39Z] 2016-04-14 22:39:27 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:39:27,893 - WARNING - Could not retrieve variants from source file in region 9:98638077-98638478. Error was invalid region `9:98638078-98638478`
[2016-04-15T05:39Z] 2016-04-14 22:39:28 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:39:28,477 - WARNING - Could not retrieve variants from source file in region 9:111929209-111956789. Error was invalid region `9:111929210-111956789`
[2016-04-15T05:39Z] 2016-04-14 22:39:28 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:39:28,491 - WARNING - Could not retrieve variants from source file in region 9:98766650-98767051. Error was invalid region `9:98766651-98767051`
[2016-04-15T05:39Z] 2016-04-14 22:39:28 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:39:28,667 - WARNING - Could not retrieve variants from source file in region 9:113085021-113085722. Error was invalid region `9:113085022-113085722`
[2016-04-15T05:39Z] 2016-04-14 22:39:28 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:39:28,709 - WARNING - Could not retrieve variants from source file in region 9:98734459-98735081. Error was invalid region `9:98734460-98735081`
[2016-04-15T05:39Z] 2016-04-14 22:39:28 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:39:28,864 - WARNING - Could not retrieve variants from source file in region 9:99012066-99012718. Error was invalid region `9:99012067-99012718`
[2016-04-15T05:39Z] 2016-04-14 22:39:31 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:39:31,958 - WARNING - Could not retrieve variants from source file in region 9:107331293-107331694. Error was invalid region `9:107331294-107331694`
[2016-04-15T05:39Z] 2016-04-14 22:39:35 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:39:35,079 - WARNING - Could not retrieve variants from source file in region 9:98638077-98638478. Error was invalid region `9:98638078-98638478`
[2016-04-15T05:39Z] 2016-04-14 22:39:35 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:39:35,147 - WARNING - Could not retrieve variants from source file in region 9:100777573-100780944. Error was invalid region `9:100777574-100780944`
[2016-04-15T05:39Z] 2016-04-14 22:39:35 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:39:35,985 - WARNING - Could not retrieve variants from source file in region 9:103114582-103114983. Error was invalid region `9:103114583-103114983`
[2016-04-15T05:39Z] 2016-04-14 22:39:36 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:39:36,453 - WARNING - Could not retrieve variants from source file in region 9:111929209-111956789. Error was invalid region `9:111929210-111956789`
[2016-04-15T05:39Z] 2016-04-14 22:39:37 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:39:37,376 - WARNING - Could not retrieve variants from source file in region 9:107331293-107331694. Error was invalid region `9:107331294-107331694`
[2016-04-15T05:39Z] 2016-04-14 22:39:37 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:39:37,473 - WARNING - Could not retrieve variants from source file in region 9:99250252-99250653. Error was invalid region `9:99250253-99250653`
[2016-04-15T05:39Z] 2016-04-14 22:39:37 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:39:37,965 - WARNING - Could not retrieve variants from source file in region 9:104432662-104449288. Error was invalid region `9:104432663-104449288`
[2016-04-15T05:39Z] 2016-04-14 22:39:43 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:39:43,485 - WARNING - Could not retrieve variants from source file in region 9:103114582-103114983. Error was invalid region `9:103114583-103114983`
[2016-04-15T05:39Z] 2016-04-14 22:39:43 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:39:43,488 - WARNING - Could not retrieve variants from source file in region 9:111929209-111956789. Error was invalid region `9:111929210-111956789`
[2016-04-15T05:39Z] 2016-04-14 22:39:43 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:39:43,888 - WARNING - Could not retrieve variants from source file in region 9:98766650-98767051. Error was invalid region `9:98766651-98767051`
[2016-04-15T05:39Z] 2016-04-14 22:39:44 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:39:44,115 - WARNING - Could not retrieve variants from source file in region 9:98734459-98735081. Error was invalid region `9:98734460-98735081`
[2016-04-15T05:39Z] 2016-04-14 22:39:44 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:39:44,125 - WARNING - Could not retrieve variants from source file in region 9:99012066-99012718. Error was invalid region `9:99012067-99012718`
[2016-04-15T05:39Z] 2016-04-14 22:39:55 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:39:55,489 - WARNING - Could not retrieve variants from source file in region 9:104385500-104385902. Error was invalid region `9:104385501-104385902`
[2016-04-15T05:39Z] 2016-04-14 22:39:56 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:39:56,816 - WARNING - Could not retrieve variants from source file in region 9:99212698-99213099. Error was invalid region `9:99212699-99213099`
[2016-04-15T05:39Z] 2016-04-14 22:39:58 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:39:58,663 - WARNING - Could not retrieve variants from source file in region 9:108233996-108234484. Error was invalid region `9:108233997-108234484`
[2016-04-15T05:40Z] 2016-04-14 22:40:00 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:40:00,914 - WARNING - Could not retrieve variants from source file in region 9:111868674-111882357. Error was invalid region `9:111868675-111882357`
[2016-04-15T05:40Z] 2016-04-14 22:40:02 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:40:02,837 - WARNING - Could not retrieve variants from source file in region 9:112963293-112963892. Error was invalid region `9:112963294-112963892`
[2016-04-15T05:40Z] 2016-04-14 22:40:04 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:40:04,017 - WARNING - Could not retrieve variants from source file in region 9:98690926-98691327. Error was invalid region `9:98690927-98691327`
[2016-04-15T05:40Z] 2016-04-14 22:40:05 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:40:05,232 - WARNING - Could not retrieve variants from source file in region 9:101748023-101748546. Error was invalid region `9:101748024-101748546`
[2016-04-15T05:40Z] 2016-04-14 22:40:05 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:40:05,653 - WARNING - Could not retrieve variants from source file in region 9:107266385-107267542. Error was invalid region `9:107266386-107267542`
[2016-04-15T05:40Z] 2016-04-14 22:40:05 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:40:05,719 - WARNING - Could not retrieve variants from source file in region 9:101340090-101340491. Error was invalid region `9:101340091-101340491`
[2016-04-15T05:40Z] 2016-04-14 22:40:05 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:40:05,805 - WARNING - Could not retrieve variants from source file in region 9:113132010-113132411. Error was invalid region `9:113132011-113132411`
[2016-04-15T05:40Z] 2016-04-14 22:40:05 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:40:05,945 - WARNING - Could not retrieve variants from source file in region 9:98209383-98209784. Error was invalid region `9:98209384-98209784`
[2016-04-15T05:40Z] 2016-04-14 22:40:06 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:40:06,029 - WARNING - Could not retrieve variants from source file in region 9:112810802-112811221. Error was invalid region `9:112810803-112811221`
[2016-04-15T05:40Z] 2016-04-14 22:40:06 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:40:06,191 - WARNING - Could not retrieve variants from source file in region 9:104130258-104133818. Error was invalid region `9:104130259-104133818`
[2016-04-15T05:40Z] 2016-04-14 22:40:06 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:40:06,630 - WARNING - Could not retrieve variants from source file in region 9:104385500-104385902. Error was invalid region `9:104385501-104385902`
[2016-04-15T05:40Z] 2016-04-14 22:40:06 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:40:06,634 - WARNING - Could not retrieve variants from source file in region 9:99212698-99213099. Error was invalid region `9:99212699-99213099`
[2016-04-15T05:40Z] 2016-04-14 22:40:06 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:40:06,939 - WARNING - Could not retrieve variants from source file in region 9:103054730-103060576. Error was invalid region `9:103054731-103060576`
[2016-04-15T05:40Z] 2016-04-14 22:40:11 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:40:11,460 - WARNING - Could not retrieve variants from source file in region 9:106896598-106896999. Error was invalid region `9:106896599-106896999`
[2016-04-15T05:40Z] 2016-04-14 22:40:13 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:40:13,957 - WARNING - Could not retrieve variants from source file in region 9:101340090-101340491. Error was invalid region `9:101340091-101340491`
[2016-04-15T05:40Z] 2016-04-14 22:40:14 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:40:14,644 - WARNING - Could not retrieve variants from source file in region 9:112810802-112811221. Error was invalid region `9:112810803-112811221`
[2016-04-15T05:40Z] 2016-04-14 22:40:14 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:40:14,906 - WARNING - Could not retrieve variants from source file in region 9:100666720-100689883. Error was invalid region `9:100666721-100689883`
[2016-04-15T05:40Z] 2016-04-14 22:40:15 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:40:15,113 - WARNING - Could not retrieve variants from source file in region 9:98690926-98691327. Error was invalid region `9:98690927-98691327`
[2016-04-15T05:40Z] 2016-04-14 22:40:15 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:40:15,155 - WARNING - Could not retrieve variants from source file in region 9:112963293-112963892. Error was invalid region `9:112963294-112963892`
[2016-04-15T05:40Z] 2016-04-14 22:40:16 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:40:16,024 - WARNING - Could not retrieve variants from source file in region 9:106896598-106896999. Error was invalid region `9:106896599-106896999`
[2016-04-15T05:40Z] 2016-04-14 22:40:20 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:40:20,163 - WARNING - Could not retrieve variants from source file in region 9:101340090-101340491. Error was invalid region `9:101340091-101340491`
[2016-04-15T05:40Z] 2016-04-14 22:40:28 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:40:28,796 - WARNING - Could not retrieve variants from source file in region 9:104499364-104499765. Error was invalid region `9:104499365-104499765`
[2016-04-15T05:40Z] 2016-04-14 22:40:30 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:40:30,872 - WARNING - Could not retrieve variants from source file in region 9:111754797-111761603. Error was invalid region `9:111754798-111761603`
[2016-04-15T05:40Z] 2016-04-14 22:40:31 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:40:31,780 - WARNING - Could not retrieve variants from source file in region 9:104324334-104324735. Error was invalid region `9:104324335-104324735`
[2016-04-15T05:40Z] 2016-04-14 22:40:32 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:40:32,169 - WARNING - Could not retrieve variants from source file in region 9:101533009-101540700. Error was invalid region `9:101533010-101540700`
[2016-04-15T05:40Z] 2016-04-14 22:40:33 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:40:33,167 - WARNING - Could not retrieve variants from source file in region 9:104499364-104499765. Error was invalid region `9:104499365-104499765`
[2016-04-15T05:40Z] 2016-04-14 22:40:33 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:40:33,786 - WARNING - Could not retrieve variants from source file in region 9:100971137-100971538. Error was invalid region `9:100971138-100971538`
[2016-04-15T05:40Z] 2016-04-14 22:40:35 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:40:35,235 - WARNING - Could not retrieve variants from source file in region 9:103348423-103348824. Error was invalid region `9:103348424-103348824`
[2016-04-15T05:40Z] 2016-04-14 22:40:35 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:40:35,601 - WARNING - Could not retrieve variants from source file in region 9:97848879-97873625. Error was invalid region `9:97848880-97873625`
[2016-04-15T05:40Z] 2016-04-14 22:40:36 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:40:36,383 - WARNING - Could not retrieve variants from source file in region 9:103204366-103236043. Error was invalid region `9:103204367-103236043`
[2016-04-15T05:40Z] 2016-04-14 22:40:36 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:40:36,777 - WARNING - Could not retrieve variants from source file in region 9:102677378-102677779. Error was invalid region `9:102677379-102677779`
[2016-04-15T05:40Z] 2016-04-14 22:40:37 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:40:37,533 - WARNING - Could not retrieve variants from source file in region 9:112172463-112172864. Error was invalid region `9:112172464-112172864`
[2016-04-15T05:40Z] 2016-04-14 22:40:38 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:40:38,409 - WARNING - Could not retrieve variants from source file in region 9:104499364-104499765. Error was invalid region `9:104499365-104499765`
[2016-04-15T05:40Z] 2016-04-14 22:40:40 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:40:40,243 - WARNING - Could not retrieve variants from source file in region 9:103348423-103348824. Error was invalid region `9:103348424-103348824`
[2016-04-15T05:40Z] 2016-04-14 22:40:40 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:40:40,601 - WARNING - Could not retrieve variants from source file in region 9:97848879-97873625. Error was invalid region `9:97848880-97873625`
[2016-04-15T05:40Z] 2016-04-14 22:40:40 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:40:40,897 - WARNING - Could not retrieve variants from source file in region 9:103204366-103236043. Error was invalid region `9:103204367-103236043`
[2016-04-15T05:40Z] 2016-04-14 22:40:41 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:40:41,894 - WARNING - Could not retrieve variants from source file in region 9:100616372-100617211. Error was invalid region `9:100616373-100617211`
[2016-04-15T05:40Z] 2016-04-14 22:40:41 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:40:41,944 - WARNING - Could not retrieve variants from source file in region 9:101533009-101540700. Error was invalid region `9:101533010-101540700`
[2016-04-15T05:40Z] 2016-04-14 22:40:42 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:40:42,712 - WARNING - Could not retrieve variants from source file in region 9:112172463-112172864. Error was invalid region `9:112172464-112172864`
[2016-04-15T05:40Z] 2016-04-14 22:40:43 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:40:43,125 - WARNING - Could not retrieve variants from source file in region 9:100971137-100971538. Error was invalid region `9:100971138-100971538`
[2016-04-15T05:40Z] 2016-04-14 22:40:51 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:40:51,269 - WARNING - Could not retrieve variants from source file in region 9:107620656-107624219. Error was invalid region `9:107620657-107624219`
[2016-04-15T05:40Z] 2016-04-14 22:40:52 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:40:52,269 - WARNING - Could not retrieve variants from source file in region 9:100362371-100362772. Error was invalid region `9:100362372-100362772`
[2016-04-15T05:40Z] 2016-04-14 22:40:54 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:40:54,292 - WARNING - Could not retrieve variants from source file in region 9:100895232-100895633. Error was invalid region `9:100895233-100895633`
[2016-04-15T05:40Z] 2016-04-14 22:40:54 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:40:54,804 - WARNING - Could not retrieve variants from source file in region 9:111727459-111727860. Error was invalid region `9:111727460-111727860`
[2016-04-15T05:40Z] 2016-04-14 22:40:55 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:40:55,370 - WARNING - Could not retrieve variants from source file in region 9:104239110-104239511. Error was invalid region `9:104239111-104239511`
[2016-04-15T05:40Z] 2016-04-14 22:40:55 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:40:55,393 - WARNING - Could not retrieve variants from source file in region 9:101498353-101498754. Error was invalid region `9:101498354-101498754`
[2016-04-15T05:40Z] 2016-04-14 22:40:55 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:40:55,986 - WARNING - Could not retrieve variants from source file in region 9:100387908-100388387. Error was invalid region `9:100387909-100388387`
[2016-04-15T05:40Z] 2016-04-14 22:40:56 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:40:56,086 - WARNING - Could not retrieve variants from source file in region 9:107620656-107624219. Error was invalid region `9:107620657-107624219`
[2016-04-15T05:40Z] 2016-04-14 22:40:58 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:40:58,587 - WARNING - Could not retrieve variants from source file in region 9:100895232-100895633. Error was invalid region `9:100895233-100895633`
[2016-04-15T05:40Z] 2016-04-14 22:40:59 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:40:59,108 - WARNING - Could not retrieve variants from source file in region 9:100071517-100139351. Error was invalid region `9:100071518-100139351`
[2016-04-15T05:40Z] 2016-04-14 22:40:59 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:40:59,929 - WARNING - Could not retrieve variants from source file in region 9:101498353-101498754. Error was invalid region `9:101498354-101498754`
[2016-04-15T05:41Z] 2016-04-14 22:41:00 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:41:00,201 - WARNING - Could not retrieve variants from source file in region 9:104239110-104239511. Error was invalid region `9:104239111-104239511`
[2016-04-15T05:41Z] 2016-04-14 22:41:00 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:41:00,699 - WARNING - Could not retrieve variants from source file in region 9:100387908-100388387. Error was invalid region `9:100387909-100388387`
[2016-04-15T05:41Z] 2016-04-14 22:41:01 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:41:01,328 - WARNING - Could not retrieve variants from source file in region 9:100822873-100823325. Error was invalid region `9:100822874-100823325`
[2016-04-15T05:41Z] 2016-04-14 22:41:03 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:41:03,821 - WARNING - Could not retrieve variants from source file in region 9:100071517-100139351. Error was invalid region `9:100071518-100139351`
[2016-04-15T05:41Z] 2016-04-14 22:41:04 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:41:04,044 - WARNING - Could not retrieve variants from source file in region 9:102590716-102596511. Error was invalid region `9:102590717-102596511`
[2016-04-15T05:41Z] 2016-04-14 22:41:04 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:41:04,523 - WARNING - Could not retrieve variants from source file in region 9:101498353-101498754. Error was invalid region `9:101498354-101498754`
[2016-04-15T05:41Z] 2016-04-14 22:41:06 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:41:06,345 - WARNING - Could not retrieve variants from source file in region 9:100822873-100823325. Error was invalid region `9:100822874-100823325`
[2016-04-15T05:41Z] 2016-04-14 22:41:10 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:41:10,336 - WARNING - Could not retrieve variants from source file in region 9:107515003-107515404. Error was invalid region `9:107515004-107515404`
[2016-04-15T05:41Z] 2016-04-14 22:41:12 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:41:12,638 - WARNING - Could not retrieve variants from source file in region 9:107515003-107515404. Error was invalid region `9:107515004-107515404`
[2016-04-15T05:41Z] 2016-04-14 22:41:13 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:41:13,243 - WARNING - Could not retrieve variants from source file in region 9:107515003-107515404. Error was invalid region `9:107515004-107515404`
[2016-04-15T05:41Z] 2016-04-14 22:41:13 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:41:13,473 - WARNING - Could not retrieve variants from source file in region 9:100190569-100194596. Error was invalid region `9:100190570-100194596`
[2016-04-15T05:41Z] 2016-04-14 22:41:13 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:41:13,683 - WARNING - Could not retrieve variants from source file in region 9:107456552-107457722. Error was invalid region `9:107456553-107457722`
[2016-04-15T05:41Z] 2016-04-14 22:41:14 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:41:14,470 - WARNING - Could not retrieve variants from source file in region 9:99699274-99700402. Error was invalid region `9:99699275-99700402`
[2016-04-15T05:41Z] 2016-04-14 22:41:14 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:41:14,518 - WARNING - Could not retrieve variants from source file in region 9:100190569-100194596. Error was invalid region `9:100190570-100194596`
[2016-04-15T05:41Z] 2016-04-14 22:41:16 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:41:16,198 - WARNING - Could not retrieve variants from source file in region 9:109772934-109773335. Error was invalid region `9:109772935-109773335`
[2016-04-15T05:41Z] 2016-04-14 22:41:16 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:41:16,477 - WARNING - Could not retrieve variants from source file in region 9:110046921-110047322. Error was invalid region `9:110046922-110047322`
[2016-04-15T05:41Z] 2016-04-14 22:41:17 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:41:17,211 - WARNING - Could not retrieve variants from source file in region 9:100190569-100194596. Error was invalid region `9:100190570-100194596`
[2016-04-15T05:41Z] 2016-04-14 22:41:17 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:41:17,329 - WARNING - Could not retrieve variants from source file in region 9:107456552-107457722. Error was invalid region `9:107456553-107457722`
[2016-04-15T05:41Z] 2016-04-14 22:41:19 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:41:19,428 - WARNING - Could not retrieve variants from source file in region 9:109772934-109773335. Error was invalid region `9:109772935-109773335`
[2016-04-15T05:41Z] 2016-04-14 22:41:19 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:41:19,712 - WARNING - Could not retrieve variants from source file in region 9:110046921-110047322. Error was invalid region `9:110046922-110047322`
[2016-04-15T05:41Z] 2016-04-14 22:41:20 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:41:20,257 - WARNING - Could not retrieve variants from source file in region 9:110046921-110047322. Error was invalid region `9:110046922-110047322`
[2016-04-15T05:41Z] 2016-04-14 22:41:24 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:41:24,054 - WARNING - Could not retrieve variants from source file in region 9:109687192-109691866. Error was invalid region `9:109687193-109691866`
[2016-04-15T05:41Z] 2016-04-14 22:41:24 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:41:24,097 - WARNING - Could not retrieve variants from source file in region 9:109687192-109691866. Error was invalid region `9:109687193-109691866`
[2016-04-15T05:41Z] ['bcbio-variation-recall', 'square', '-Xms750m', '-Xmx7280m', '-XX:+UseSerialGC', '-c', 16, '-r', u'9:113231220-129089575', '--caller', 'platypus', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/9/Batch1-9_113231219_129089575.vcf.gz', '/mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/9/Batch1-9_113231219_129089575.vcf-inputs.txt'] in region: 9:113231220-129089575
[2016-04-15T05:41Z] 2016-04-14 22:41:41 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:41:41,217 - WARNING - Could not retrieve variants from source file in region 9:124751179-124751580. Error was invalid region `9:124751180-124751580`
[2016-04-15T05:41Z] 2016-04-14 22:41:41 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:41:41,264 - WARNING - Could not retrieve variants from source file in region 9:120053565-120053966. Error was invalid region `9:120053566-120053966`
[2016-04-15T05:41Z] 2016-04-14 22:41:41 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:41:41,829 - WARNING - Could not retrieve variants from source file in region 9:127020084-127020485. Error was invalid region `9:127020085-127020485`
[2016-04-15T05:41Z] 2016-04-14 22:41:42 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:41:42,058 - WARNING - Could not retrieve variants from source file in region 9:123290825-123291226. Error was invalid region `9:123290826-123291226`
[2016-04-15T05:41Z] 2016-04-14 22:41:42 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:41:42,433 - WARNING - Could not retrieve variants from source file in region 9:123671309-123671710. Error was invalid region `9:123671310-123671710`
[2016-04-15T05:41Z] 2016-04-14 22:41:42 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:41:42,626 - WARNING - Could not retrieve variants from source file in region 9:117552674-117553075. Error was invalid region `9:117552675-117553075`
[2016-04-15T05:41Z] 2016-04-14 22:41:42 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:41:42,631 - WARNING - Could not retrieve variants from source file in region 9:114521419-114521820. Error was invalid region `9:114521420-114521820`
[2016-04-15T05:41Z] 2016-04-14 22:41:44 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:41:44,635 - WARNING - Could not retrieve variants from source file in region 9:128305179-128305580. Error was invalid region `9:128305180-128305580`
[2016-04-15T05:41Z] 2016-04-14 22:41:45 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:41:45,782 - WARNING - Could not retrieve variants from source file in region 9:124499710-124522503. Error was invalid region `9:124499711-124522503`
[2016-04-15T05:41Z] 2016-04-14 22:41:48 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:41:48,661 - WARNING - Could not retrieve variants from source file in region 9:123850559-123860879. Error was invalid region `9:123850560-123860879`
[2016-04-15T05:41Z] 2016-04-14 22:41:49 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:41:49,117 - WARNING - Could not retrieve variants from source file in region 9:123903629-123917210. Error was invalid region `9:123903630-123917210`
[2016-04-15T05:41Z] 2016-04-14 22:41:49 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:41:49,181 - WARNING - Could not retrieve variants from source file in region 9:120053565-120053966. Error was invalid region `9:120053566-120053966`
[2016-04-15T05:41Z] 2016-04-14 22:41:49 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:41:49,917 - WARNING - Could not retrieve variants from source file in region 9:127818065-127818466. Error was invalid region `9:127818066-127818466`
[2016-04-15T05:41Z] 2016-04-14 22:41:50 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:41:50,371 - WARNING - Could not retrieve variants from source file in region 9:125288682-125289711. Error was invalid region `9:125288683-125289711`
[2016-04-15T05:41Z] 2016-04-14 22:41:50 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:41:50,856 - WARNING - Could not retrieve variants from source file in region 9:114521419-114521820. Error was invalid region `9:114521420-114521820`
[2016-04-15T05:41Z] 2016-04-14 22:41:50 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:41:50,923 - WARNING - Could not retrieve variants from source file in region 9:123671309-123671710. Error was invalid region `9:123671310-123671710`
[2016-04-15T05:41Z] 2016-04-14 22:41:51 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:41:51,276 - WARNING - Could not retrieve variants from source file in region 9:123768989-123780195. Error was invalid region `9:123768990-123780195`
[2016-04-15T05:41Z] 2016-04-14 22:41:51 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:41:51,393 - WARNING - Could not retrieve variants from source file in region 9:123290825-123291226. Error was invalid region `9:123290826-123291226`
[2016-04-15T05:41Z] 2016-04-14 22:41:51 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:41:51,484 - WARNING - Could not retrieve variants from source file in region 9:117552674-117553075. Error was invalid region `9:117552675-117553075`
[2016-04-15T05:41Z] 2016-04-14 22:41:51 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:41:51,484 - WARNING - Could not retrieve variants from source file in region 9:116279669-116299090. Error was invalid region `9:116279670-116299090`
[2016-04-15T05:41Z] 2016-04-14 22:41:51 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:41:51,939 - WARNING - Could not retrieve variants from source file in region 9:125133268-125144163. Error was invalid region `9:125133269-125144163`
[2016-04-15T05:41Z] 2016-04-14 22:41:51 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:41:51,947 - WARNING - Could not retrieve variants from source file in region 9:128305179-128305580. Error was invalid region `9:128305180-128305580`
[2016-04-15T05:41Z] 2016-04-14 22:41:53 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:41:53,867 - WARNING - Could not retrieve variants from source file in region 9:123850559-123860879. Error was invalid region `9:123850560-123860879`
[2016-04-15T05:41Z] 2016-04-14 22:41:54 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:41:54,577 - WARNING - Could not retrieve variants from source file in region 9:123903629-123917210. Error was invalid region `9:123903630-123917210`
[2016-04-15T05:41Z] 2016-04-14 22:41:54 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:41:54,649 - WARNING - Could not retrieve variants from source file in region 9:120053565-120053966. Error was invalid region `9:120053566-120053966`
[2016-04-15T05:41Z] 2016-04-14 22:41:55 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:41:55,973 - WARNING - Could not retrieve variants from source file in region 9:127818065-127818466. Error was invalid region `9:127818066-127818466`
[2016-04-15T05:41Z] 2016-04-14 22:41:57 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:41:57,131 - WARNING - Could not retrieve variants from source file in region 9:125288682-125289711. Error was invalid region `9:125288683-125289711`
[2016-04-15T05:41Z] 2016-04-14 22:41:58 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:41:58,012 - WARNING - Could not retrieve variants from source file in region 9:114521419-114521820. Error was invalid region `9:114521420-114521820`
[2016-04-15T05:41Z] 2016-04-14 22:41:58 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:41:58,041 - WARNING - Could not retrieve variants from source file in region 9:123768989-123780195. Error was invalid region `9:123768990-123780195`
[2016-04-15T05:41Z] 2016-04-14 22:41:58 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:41:58,111 - WARNING - Could not retrieve variants from source file in region 9:123671309-123671710. Error was invalid region `9:123671310-123671710`
[2016-04-15T05:41Z] 2016-04-14 22:41:58 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:41:58,604 - WARNING - Could not retrieve variants from source file in region 9:117552674-117553075. Error was invalid region `9:117552675-117553075`
[2016-04-15T05:41Z] 2016-04-14 22:41:58 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:41:58,708 - WARNING - Could not retrieve variants from source file in region 9:123290825-123291226. Error was invalid region `9:123290826-123291226`
[2016-04-15T05:42Z] 2016-04-14 22:42:07 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:42:07,994 - WARNING - Could not retrieve variants from source file in region 9:124102819-124103221. Error was invalid region `9:124102820-124103221`
[2016-04-15T05:42Z] 2016-04-14 22:42:08 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:42:08,822 - WARNING - Could not retrieve variants from source file in region 9:128246575-128246976. Error was invalid region `9:128246576-128246976`
[2016-04-15T05:42Z] 2016-04-14 22:42:11 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:42:11,259 - WARNING - Could not retrieve variants from source file in region 9:119770269-119770670. Error was invalid region `9:119770270-119770670`
[2016-04-15T05:42Z] 2016-04-14 22:42:13 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:42:13,373 - WARNING - Could not retrieve variants from source file in region 9:126783222-126783623. Error was invalid region `9:126783223-126783623`
[2016-04-15T05:42Z] 2016-04-14 22:42:14 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:42:14,018 - WARNING - Could not retrieve variants from source file in region 9:114454369-114490498. Error was invalid region `9:114454370-114490498`
[2016-04-15T05:42Z] 2016-04-14 22:42:14 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:42:14,409 - WARNING - Could not retrieve variants from source file in region 9:123631834-123639454. Error was invalid region `9:123631835-123639454`
[2016-04-15T05:42Z] 2016-04-14 22:42:14 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:42:14,438 - WARNING - Could not retrieve variants from source file in region 9:125239042-125239916. Error was invalid region `9:125239043-125239916`
[2016-04-15T05:42Z] 2016-04-14 22:42:15 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:42:15,085 - WARNING - Could not retrieve variants from source file in region 9:114174204-114174605. Error was invalid region `9:114174205-114174605`
[2016-04-15T05:42Z] 2016-04-14 22:42:15 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:42:15,368 - WARNING - Could not retrieve variants from source file in region 9:114415265-114415666. Error was invalid region `9:114415266-114415666`
[2016-04-15T05:42Z] 2016-04-14 22:42:15 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:42:15,797 - WARNING - Could not retrieve variants from source file in region 9:123170522-123170923. Error was invalid region `9:123170523-123170923`
[2016-04-15T05:42Z] 2016-04-14 22:42:15 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:42:15,968 - WARNING - Could not retrieve variants from source file in region 9:124983573-124983974. Error was invalid region `9:124983574-124983974`
[2016-04-15T05:42Z] 2016-04-14 22:42:16 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:42:16,188 - WARNING - Could not retrieve variants from source file in region 9:127616326-127674390. Error was invalid region `9:127616327-127674390`
[2016-04-15T05:42Z] 2016-04-14 22:42:17 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:42:17,599 - WARNING - Could not retrieve variants from source file in region 9:126783222-126783623. Error was invalid region `9:126783223-126783623`
[2016-04-15T05:42Z] 2016-04-14 22:42:19 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:42:19,888 - WARNING - Could not retrieve variants from source file in region 9:123631834-123639454. Error was invalid region `9:123631835-123639454`
[2016-04-15T05:42Z] 2016-04-14 22:42:21 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:42:21,430 - WARNING - Could not retrieve variants from source file in region 9:114174204-114174605. Error was invalid region `9:114174205-114174605`
[2016-04-15T05:42Z] 2016-04-14 22:42:22 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:42:22,511 - WARNING - Could not retrieve variants from source file in region 9:124983573-124983974. Error was invalid region `9:124983574-124983974`
[2016-04-15T05:42Z] 2016-04-14 22:42:22 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:42:22,630 - WARNING - Could not retrieve variants from source file in region 9:119770269-119770670. Error was invalid region `9:119770270-119770670`
[2016-04-15T05:42Z] 2016-04-14 22:42:22 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:42:22,733 - WARNING - Could not retrieve variants from source file in region 9:123170522-123170923. Error was invalid region `9:123170523-123170923`
[2016-04-15T05:42Z] 2016-04-14 22:42:23 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:42:23,171 - WARNING - Could not retrieve variants from source file in region 9:116222344-116222745. Error was invalid region `9:116222345-116222745`
[2016-04-15T05:42Z] 2016-04-14 22:42:23 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:42:23,258 - WARNING - Could not retrieve variants from source file in region 9:126783222-126783623. Error was invalid region `9:126783223-126783623`
[2016-04-15T05:42Z] 2016-04-14 22:42:23 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:42:23,552 - WARNING - Could not retrieve variants from source file in region 9:114454369-114490498. Error was invalid region `9:114454370-114490498`
[2016-04-15T05:42Z] 2016-04-14 22:42:24 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:42:24,585 - WARNING - Could not retrieve variants from source file in region 9:123631834-123639454. Error was invalid region `9:123631835-123639454`
[2016-04-15T05:42Z] 2016-04-14 22:42:26 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:42:26,467 - WARNING - Could not retrieve variants from source file in region 9:114174204-114174605. Error was invalid region `9:114174205-114174605`
[2016-04-15T05:42Z] 2016-04-14 22:42:27 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:42:27,069 - WARNING - Could not retrieve variants from source file in region 9:114415265-114415666. Error was invalid region `9:114415266-114415666`
[2016-04-15T05:42Z] 2016-04-14 22:42:28 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:42:28,062 - WARNING - Could not retrieve variants from source file in region 9:124983573-124983974. Error was invalid region `9:124983574-124983974`
[2016-04-15T05:42Z] 2016-04-14 22:42:28 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:42:28,969 - WARNING - Could not retrieve variants from source file in region 9:123170522-123170923. Error was invalid region `9:123170523-123170923`
[2016-04-15T05:42Z] 2016-04-14 22:42:29 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:42:29,625 - WARNING - Could not retrieve variants from source file in region 9:117428749-117433954. Error was invalid region `9:117428750-117433954`
[2016-04-15T05:42Z] 2016-04-14 22:42:29 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:42:29,929 - WARNING - Could not retrieve variants from source file in region 9:125885600-125886002. Error was invalid region `9:125885601-125886002`
[2016-04-15T05:42Z] 2016-04-14 22:42:31 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:42:31,090 - WARNING - Could not retrieve variants from source file in region 9:123582981-123583382. Error was invalid region `9:123582982-123583382`
[2016-04-15T05:42Z] 2016-04-14 22:42:31 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:42:31,465 - WARNING - Could not retrieve variants from source file in region 9:115818738-115819139. Error was invalid region `9:115818739-115819139`
[2016-04-15T05:42Z] 2016-04-14 22:42:37 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:42:37,459 - WARNING - Could not retrieve variants from source file in region 9:115818738-115819139. Error was invalid region `9:115818739-115819139`
[2016-04-15T05:42Z] 2016-04-14 22:42:37 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:42:37,484 - WARNING - Could not retrieve variants from source file in region 9:123582981-123583382. Error was invalid region `9:123582982-123583382`
[2016-04-15T05:42Z] 2016-04-14 22:42:40 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:42:40,257 - WARNING - Could not retrieve variants from source file in region 9:128074596-128074997. Error was invalid region `9:128074597-128074997`
[2016-04-15T05:42Z] 2016-04-14 22:42:41 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:42:41,111 - WARNING - Could not retrieve variants from source file in region 9:114359413-114359814. Error was invalid region `9:114359414-114359814`
[2016-04-15T05:42Z] 2016-04-14 22:42:41 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:42:41,284 - WARNING - Could not retrieve variants from source file in region 9:127566167-127566568. Error was invalid region `9:127566168-127566568`
[2016-04-15T05:42Z] 2016-04-14 22:42:43 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:42:43,204 - WARNING - Could not retrieve variants from source file in region 9:115818738-115819139. Error was invalid region `9:115818739-115819139`
[2016-04-15T05:42Z] 2016-04-14 22:42:43 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:42:43,255 - WARNING - Could not retrieve variants from source file in region 9:123582981-123583382. Error was invalid region `9:123582982-123583382`
[2016-04-15T05:42Z] 2016-04-14 22:42:43 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:42:43,813 - WARNING - Could not retrieve variants from source file in region 9:119738804-119739205. Error was invalid region `9:119738805-119739205`
[2016-04-15T05:42Z] 2016-04-14 22:42:44 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:42:44,651 - WARNING - Could not retrieve variants from source file in region 9:117165995-117188756. Error was invalid region `9:117165996-117188756`
[2016-04-15T05:42Z] 2016-04-14 22:42:45 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:42:45,597 - WARNING - Could not retrieve variants from source file in region 9:128074596-128074997. Error was invalid region `9:128074597-128074997`
[2016-04-15T05:42Z] 2016-04-14 22:42:45 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:42:45,615 - WARNING - Could not retrieve variants from source file in region 9:123549930-123550331. Error was invalid region `9:123549931-123550331`
[2016-04-15T05:42Z] 2016-04-14 22:42:45 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:42:45,897 - WARNING - Could not retrieve variants from source file in region 9:114359413-114359814. Error was invalid region `9:114359414-114359814`
[2016-04-15T05:42Z] 2016-04-14 22:42:46 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:42:46,192 - WARNING - Could not retrieve variants from source file in region 9:125675390-125675791. Error was invalid region `9:125675391-125675791`
[2016-04-15T05:42Z] 2016-04-14 22:42:46 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:42:46,943 - WARNING - Could not retrieve variants from source file in region 9:127566167-127566568. Error was invalid region `9:127566168-127566568`
[2016-04-15T05:42Z] 2016-04-14 22:42:47 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:42:47,576 - WARNING - Could not retrieve variants from source file in region 9:126175883-126176659. Error was invalid region `9:126175884-126176659`
[2016-04-15T05:42Z] 2016-04-14 22:42:48 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:42:48,525 - WARNING - Could not retrieve variants from source file in region 9:124914402-124938086. Error was invalid region `9:124914403-124938086`
[2016-04-15T05:42Z] 2016-04-14 22:42:48 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:42:48,891 - WARNING - Could not retrieve variants from source file in region 9:114090068-114090469. Error was invalid region `9:114090069-114090469`
[2016-04-15T05:42Z] 2016-04-14 22:42:50 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:42:50,529 - WARNING - Could not retrieve variants from source file in region 9:117165995-117188756. Error was invalid region `9:117165996-117188756`
[2016-04-15T05:42Z] 2016-04-14 22:42:51 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:42:51,025 - WARNING - Could not retrieve variants from source file in region 9:123549930-123550331. Error was invalid region `9:123549931-123550331`
[2016-04-15T05:42Z] 2016-04-14 22:42:51 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:42:51,059 - WARNING - Could not retrieve variants from source file in region 9:128074596-128074997. Error was invalid region `9:128074597-128074997`
[2016-04-15T05:42Z] 2016-04-14 22:42:51 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:42:51,644 - WARNING - Could not retrieve variants from source file in region 9:114359413-114359814. Error was invalid region `9:114359414-114359814`
[2016-04-15T05:42Z] 2016-04-14 22:42:52 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:42:52,317 - WARNING - Could not retrieve variants from source file in region 9:125675390-125675791. Error was invalid region `9:125675391-125675791`
[2016-04-15T05:42Z] 2016-04-14 22:42:52 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:42:52,378 - WARNING - Could not retrieve variants from source file in region 9:127566167-127566568. Error was invalid region `9:127566168-127566568`
[2016-04-15T05:42Z] 2016-04-14 22:42:53 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:42:53,992 - WARNING - Could not retrieve variants from source file in region 9:124914402-124938086. Error was invalid region `9:124914403-124938086`
[2016-04-15T05:42Z] 2016-04-14 22:42:54 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:42:54,890 - WARNING - Could not retrieve variants from source file in region 9:114090068-114090469. Error was invalid region `9:114090069-114090469`
[2016-04-15T05:42Z] 2016-04-14 22:42:55 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:42:55,800 - WARNING - Could not retrieve variants from source file in region 9:122045018-122045708. Error was invalid region `9:122045019-122045708`
[2016-04-15T05:42Z] 2016-04-14 22:42:56 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:42:56,819 - WARNING - Could not retrieve variants from source file in region 9:117165995-117188756. Error was invalid region `9:117165996-117188756`
[2016-04-15T05:42Z] 2016-04-14 22:42:58 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:42:58,440 - WARNING - Could not retrieve variants from source file in region 9:125675390-125675791. Error was invalid region `9:125675391-125675791`
[2016-04-15T05:42Z] 2016-04-14 22:42:59 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:42:59,612 - WARNING - Could not retrieve variants from source file in region 9:123476331-123476738. Error was invalid region `9:123476332-123476738`
[2016-04-15T05:43Z] 2016-04-14 22:43:02 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:43:02,377 - WARNING - Could not retrieve variants from source file in region 9:123476331-123476738. Error was invalid region `9:123476332-123476738`
[2016-04-15T05:43Z] 2016-04-14 22:43:03 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:43:03,517 - WARNING - Could not retrieve variants from source file in region 9:123476331-123476738. Error was invalid region `9:123476332-123476738`
[2016-04-15T05:43Z] 2016-04-14 22:43:05 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:43:05,718 - WARNING - Could not retrieve variants from source file in region 9:115652625-115653071. Error was invalid region `9:115652626-115653071`
[2016-04-15T05:43Z] 2016-04-14 22:43:08 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:43:08,087 - WARNING - Could not retrieve variants from source file in region 9:127176950-127177351. Error was invalid region `9:127176951-127177351`
[2016-04-15T05:43Z] 2016-04-14 22:43:10 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:43:10,623 - WARNING - Could not retrieve variants from source file in region 9:117002306-117002707. Error was invalid region `9:117002307-117002707`
[2016-04-15T05:43Z] 2016-04-14 22:43:11 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:43:11,012 - WARNING - Could not retrieve variants from source file in region 9:113457515-113457916. Error was invalid region `9:113457516-113457916`
[2016-04-15T05:43Z] 2016-04-14 22:43:11 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:43:11,129 - WARNING - Could not retrieve variants from source file in region 9:119491066-119495887. Error was invalid region `9:119491067-119495887`
[2016-04-15T05:43Z] 2016-04-14 22:43:11 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:43:11,336 - WARNING - Could not retrieve variants from source file in region 9:117085315-117124921. Error was invalid region `9:117085316-117124921`
[2016-04-15T05:43Z] 2016-04-14 22:43:11 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:43:11,780 - WARNING - Could not retrieve variants from source file in region 9:127995835-127996236. Error was invalid region `9:127995836-127996236`
[2016-04-15T05:43Z] 2016-04-14 22:43:11 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:43:11,970 - WARNING - Could not retrieve variants from source file in region 9:122000789-122001190. Error was invalid region `9:122000790-122001190`
[2016-04-15T05:43Z] 2016-04-14 22:43:12 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:43:12,559 - WARNING - Could not retrieve variants from source file in region 9:126125107-126144948. Error was invalid region `9:126125108-126144948`
[2016-04-15T05:43Z] 2016-04-14 22:43:14 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:43:14,346 - WARNING - Could not retrieve variants from source file in region 9:125486757-125513016. Error was invalid region `9:125486758-125513016`
[2016-04-15T05:43Z] 2016-04-14 22:43:14 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:43:14,843 - WARNING - Could not retrieve variants from source file in region 9:113261134-113275417. Error was invalid region `9:113261135-113275417`
[2016-04-15T05:43Z] 2016-04-14 22:43:14 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:43:14,991 - WARNING - Could not retrieve variants from source file in region 9:113637643-113638044. Error was invalid region `9:113637644-113638044`
[2016-04-15T05:43Z] 2016-04-14 22:43:15 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:43:15,629 - WARNING - Could not retrieve variants from source file in region 9:116044787-116082837. Error was invalid region `9:116044788-116082837`
[2016-04-15T05:43Z] 2016-04-14 22:43:16 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:43:16,188 - WARNING - Could not retrieve variants from source file in region 9:117002306-117002707. Error was invalid region `9:117002307-117002707`
[2016-04-15T05:43Z] 2016-04-14 22:43:16 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:43:16,275 - WARNING - Could not retrieve variants from source file in region 9:113457515-113457916. Error was invalid region `9:113457516-113457916`
[2016-04-15T05:43Z] 2016-04-14 22:43:17 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:43:17,234 - WARNING - Could not retrieve variants from source file in region 9:127995835-127996236. Error was invalid region `9:127995836-127996236`
[2016-04-15T05:43Z] 2016-04-14 22:43:18 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:43:18,939 - WARNING - Could not retrieve variants from source file in region 9:127176950-127177351. Error was invalid region `9:127176951-127177351`
[2016-04-15T05:43Z] 2016-04-14 22:43:20 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:43:20,380 - WARNING - Could not retrieve variants from source file in region 9:113637643-113638044. Error was invalid region `9:113637644-113638044`
[2016-04-15T05:43Z] 2016-04-14 22:43:22 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:43:22,244 - WARNING - Could not retrieve variants from source file in region 9:117002306-117002707. Error was invalid region `9:117002307-117002707`
[2016-04-15T05:43Z] 2016-04-14 22:43:22 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:43:22,284 - WARNING - Could not retrieve variants from source file in region 9:113457515-113457916. Error was invalid region `9:113457516-113457916`
[2016-04-15T05:43Z] 2016-04-14 22:43:24 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:43:24,379 - WARNING - Could not retrieve variants from source file in region 9:121929364-121929765. Error was invalid region `9:121929365-121929765`
[2016-04-15T05:43Z] 2016-04-14 22:43:24 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:43:24,825 - WARNING - Could not retrieve variants from source file in region 9:127951652-127952053. Error was invalid region `9:127951653-127952053`
[2016-04-15T05:43Z] 2016-04-14 22:43:28 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:43:28,429 - WARNING - Could not retrieve variants from source file in region 9:127951652-127952053. Error was invalid region `9:127951653-127952053`
[2016-04-15T05:43Z] 2016-04-14 22:43:30 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:43:30,121 - WARNING - Could not retrieve variants from source file in region 9:121929364-121929765. Error was invalid region `9:121929365-121929765`
[2016-04-15T05:43Z] 2016-04-14 22:43:31 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:43:31,863 - WARNING - Could not retrieve variants from source file in region 9:115566973-115601038. Error was invalid region `9:115566974-115601038`
[2016-04-15T05:43Z] 2016-04-14 22:43:34 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:43:34,065 - WARNING - Could not retrieve variants from source file in region 9:127101713-127102114. Error was invalid region `9:127101714-127102114`
[2016-04-15T05:43Z] 2016-04-14 22:43:34 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:43:34,087 - WARNING - Could not retrieve variants from source file in region 9:125920165-125920566. Error was invalid region `9:125920166-125920566`
[2016-04-15T05:43Z] 2016-04-14 22:43:36 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:43:36,776 - WARNING - Could not retrieve variants from source file in region 9:113233509-113233910. Error was invalid region `9:113233510-113233910`
[2016-04-15T05:43Z] 2016-04-14 22:43:37 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:43:37,606 - WARNING - Could not retrieve variants from source file in region 9:120475091-120475792. Error was invalid region `9:120475092-120475792`
[2016-04-15T05:43Z] 2016-04-14 22:43:37 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:43:37,649 - WARNING - Could not retrieve variants from source file in region 9:127101713-127102114. Error was invalid region `9:127101714-127102114`
[2016-04-15T05:43Z] 2016-04-14 22:43:38 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:43:38,824 - WARNING - Could not retrieve variants from source file in region 9:127101713-127102114. Error was invalid region `9:127101714-127102114`
[2016-04-15T05:43Z] 2016-04-14 22:43:38 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:43:38,866 - WARNING - Could not retrieve variants from source file in region 9:117032811-117044941. Error was invalid region `9:117032812-117044941`
[2016-04-15T05:43Z] 2016-04-14 22:43:39 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:43:39,356 - WARNING - Could not retrieve variants from source file in region 9:125920165-125920566. Error was invalid region `9:125920166-125920566`
[2016-04-15T05:43Z] 2016-04-14 22:43:39 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:43:39,635 - WARNING - Could not retrieve variants from source file in region 9:125423944-125424345. Error was invalid region `9:125423945-125424345`
[2016-04-15T05:43Z] 2016-04-14 22:43:40 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:43:40,299 - WARNING - Could not retrieve variants from source file in region 9:116967194-116967595. Error was invalid region `9:116967195-116967595`
[2016-04-15T05:43Z] 2016-04-14 22:43:41 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:43:41,958 - WARNING - Could not retrieve variants from source file in region 9:119106670-119107071. Error was invalid region `9:119106671-119107071`
[2016-04-15T05:43Z] 2016-04-14 22:43:42 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:43:42,227 - WARNING - Could not retrieve variants from source file in region 9:120475091-120475792. Error was invalid region `9:120475092-120475792`
[2016-04-15T05:43Z] 2016-04-14 22:43:43 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:43:43,663 - WARNING - Could not retrieve variants from source file in region 9:117032811-117044941. Error was invalid region `9:117032812-117044941`
[2016-04-15T05:43Z] 2016-04-14 22:43:43 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:43:43,973 - WARNING - Could not retrieve variants from source file in region 9:125920165-125920566. Error was invalid region `9:125920166-125920566`
[2016-04-15T05:43Z] 2016-04-14 22:43:45 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:43:45,970 - WARNING - Could not retrieve variants from source file in region 9:119106670-119107071. Error was invalid region `9:119106671-119107071`
[2016-04-15T05:43Z] 2016-04-14 22:43:47 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:43:47,546 - WARNING - Could not retrieve variants from source file in region 9:117032811-117044941. Error was invalid region `9:117032812-117044941`
[2016-04-15T05:43Z] 2016-04-14 22:43:48 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:43:48,016 - WARNING - Could not retrieve variants from source file in region 9:125423944-125424345. Error was invalid region `9:125423945-125424345`
[2016-04-15T05:43Z] 2016-04-14 22:43:50 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:43:50,291 - WARNING - Could not retrieve variants from source file in region 9:119106670-119107071. Error was invalid region `9:119106671-119107071`
[2016-04-15T05:43Z] 2016-04-14 22:43:51 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:43:51,516 - WARNING - Could not retrieve variants from source file in region 9:114803962-114804363. Error was invalid region `9:114803963-114804363`
[2016-04-15T05:43Z] 2016-04-14 22:43:53 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:43:53,534 - WARNING - Could not retrieve variants from source file in region 9:114982252-114986211. Error was invalid region `9:114982253-114986211`
[2016-04-15T05:43Z] 2016-04-14 22:43:54 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:43:54,387 - WARNING - Could not retrieve variants from source file in region 9:114694275-114694676. Error was invalid region `9:114694276-114694676`
[2016-04-15T05:43Z] 2016-04-14 22:43:56 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:43:56,970 - WARNING - Could not retrieve variants from source file in region 9:125376876-125391960. Error was invalid region `9:125376877-125391960`
[2016-04-15T05:43Z] 2016-04-14 22:43:58 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:43:58,258 - WARNING - Could not retrieve variants from source file in region 9:116856270-116856671. Error was invalid region `9:116856271-116856671`
[2016-04-15T05:43Z] 2016-04-14 22:43:58 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:43:58,291 - WARNING - Could not retrieve variants from source file in region 9:117835688-117853212. Error was invalid region `9:117835689-117853212`
[2016-04-15T05:43Z] 2016-04-14 22:43:58 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:43:58,562 - WARNING - Could not retrieve variants from source file in region 9:114803962-114804363. Error was invalid region `9:114803963-114804363`
[2016-04-15T05:43Z] 2016-04-14 22:43:59 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:43:59,102 - WARNING - Could not retrieve variants from source file in region 9:117792372-117808975. Error was invalid region `9:117792373-117808975`
[2016-04-15T05:44Z] 2016-04-14 22:44:01 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:44:01,296 - WARNING - Could not retrieve variants from source file in region 9:125376876-125391960. Error was invalid region `9:125376877-125391960`
[2016-04-15T05:44Z] 2016-04-14 22:44:01 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:44:01,364 - WARNING - Could not retrieve variants from source file in region 9:116929889-116940784. Error was invalid region `9:116929890-116940784`
[2016-04-15T05:44Z] 2016-04-14 22:44:02 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:44:02,470 - WARNING - Could not retrieve variants from source file in region 9:118949787-118950188. Error was invalid region `9:118949788-118950188`
[2016-04-15T05:44Z] 2016-04-14 22:44:02 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:44:02,887 - WARNING - Could not retrieve variants from source file in region 9:116856270-116856671. Error was invalid region `9:116856271-116856671`
[2016-04-15T05:44Z] 2016-04-14 22:44:03 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:44:03,410 - WARNING - Could not retrieve variants from source file in region 9:125376876-125391960. Error was invalid region `9:125376877-125391960`
[2016-04-15T05:44Z] 2016-04-14 22:44:03 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:44:03,594 - WARNING - Could not retrieve variants from source file in region 9:118163352-118163753. Error was invalid region `9:118163353-118163753`
[2016-04-15T05:44Z] 2016-04-14 22:44:03 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:44:03,712 - WARNING - Could not retrieve variants from source file in region 9:118949787-118950188. Error was invalid region `9:118949788-118950188`
[2016-04-15T05:44Z] 2016-04-14 22:44:05 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:44:05,152 - WARNING - Could not retrieve variants from source file in region 9:125315346-125330929. Error was invalid region `9:125315347-125330929`
[2016-04-15T05:44Z] 2016-04-14 22:44:07 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:44:07,949 - WARNING - Could not retrieve variants from source file in region 9:118163352-118163753. Error was invalid region `9:118163353-118163753`
[2016-04-15T05:44Z] 2016-04-14 22:44:09 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:44:09,228 - WARNING - Could not retrieve variants from source file in region 9:125315346-125330929. Error was invalid region `9:125315347-125330929`
[2016-04-15T05:44Z] 2016-04-14 22:44:11 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:44:11,173 - WARNING - Could not retrieve variants from source file in region 9:117663339-117668332. Error was invalid region `9:117663340-117668332`
[2016-04-15T05:44Z] 2016-04-14 22:44:11 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:44:11,289 - WARNING - Could not retrieve variants from source file in region 9:116790950-116791351. Error was invalid region `9:116790951-116791351`
[2016-04-15T05:44Z] 2016-04-14 22:44:11 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:44:11,751 - WARNING - Could not retrieve variants from source file in region 9:118163352-118163753. Error was invalid region `9:118163353-118163753`
[2016-04-15T05:44Z] 2016-04-14 22:44:12 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:44:12,107 - WARNING - Could not retrieve variants from source file in region 9:116790950-116791351. Error was invalid region `9:116790951-116791351`
[2016-04-15T05:44Z] 2016-04-14 22:44:12 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:44:12,116 - WARNING - Could not retrieve variants from source file in region 9:116790950-116791351. Error was invalid region `9:116790951-116791351`
[2016-04-15T05:44Z] 2016-04-14 22:44:14 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:44:14,830 - WARNING - Could not retrieve variants from source file in region 9:117663339-117668332. Error was invalid region `9:117663340-117668332`
[2016-04-15T05:44Z] ['bcbio-variation-recall', 'square', '-Xms750m', '-Xmx7280m', '-XX:+UseSerialGC', '-c', 16, '-r', u'9:129097485-141213431', '--caller', 'platypus', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/9/Batch1-9_129097484_141213431.vcf.gz', '/mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/9/Batch1-9_129097484_141213431.vcf-inputs.txt'] in region: 9:129097485-141213431
[2016-04-15T05:44Z] 2016-04-14 22:44:30 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:44:30,962 - WARNING - Could not retrieve variants from source file in region 9:138378645-138379192. Error was invalid region `9:138378646-138379192`
[2016-04-15T05:44Z] 2016-04-14 22:44:31 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:44:31,916 - WARNING - Could not retrieve variants from source file in region 9:130932162-130938851. Error was invalid region `9:130932163-130938851`
[2016-04-15T05:44Z] 2016-04-14 22:44:32 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:44:32,145 - WARNING - Could not retrieve variants from source file in region 9:135202618-135206650. Error was invalid region `9:135202619-135206650`
[2016-04-15T05:44Z] 2016-04-14 22:44:32 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:44:32,609 - WARNING - Could not retrieve variants from source file in region 9:131020171-131020988. Error was invalid region `9:131020172-131020988`
[2016-04-15T05:44Z] 2016-04-14 22:44:32 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:44:32,709 - WARNING - Could not retrieve variants from source file in region 9:131939808-131940209. Error was invalid region `9:131939809-131940209`
[2016-04-15T05:44Z] 2016-04-14 22:44:33 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:44:33,509 - WARNING - Could not retrieve variants from source file in region 9:130164782-130242356. Error was invalid region `9:130164783-130242356`
[2016-04-15T05:44Z] 2016-04-14 22:44:33 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:44:33,688 - WARNING - Could not retrieve variants from source file in region 9:133759895-133787415. Error was invalid region `9:133759896-133787415`
[2016-04-15T05:44Z] 2016-04-14 22:44:33 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:44:33,760 - WARNING - Could not retrieve variants from source file in region 9:130668067-130707271. Error was invalid region `9:130668068-130707271`
[2016-04-15T05:44Z] 2016-04-14 22:44:33 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:44:33,997 - WARNING - Could not retrieve variants from source file in region 9:131222330-131235511. Error was invalid region `9:131222331-131235511`
[2016-04-15T05:44Z] 2016-04-14 22:44:37 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:44:37,118 - WARNING - Could not retrieve variants from source file in region 9:138378645-138379192. Error was invalid region `9:138378646-138379192`
[2016-04-15T05:44Z] 2016-04-14 22:44:37 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:44:37,979 - WARNING - Could not retrieve variants from source file in region 9:131196484-131196894. Error was invalid region `9:131196485-131196894`
[2016-04-15T05:44Z] 2016-04-14 22:44:39 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:44:39,619 - WARNING - Could not retrieve variants from source file in region 9:135202618-135206650. Error was invalid region `9:135202619-135206650`
[2016-04-15T05:44Z] 2016-04-14 22:44:41 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:44:41,301 - WARNING - Could not retrieve variants from source file in region 9:132515036-132515437. Error was invalid region `9:132515037-132515437`
[2016-04-15T05:44Z] 2016-04-14 22:44:42 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:44:42,075 - WARNING - Could not retrieve variants from source file in region 9:131939808-131940209. Error was invalid region `9:131939809-131940209`
[2016-04-15T05:44Z] 2016-04-14 22:44:42 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:44:42,977 - WARNING - Could not retrieve variants from source file in region 9:130668067-130707271. Error was invalid region `9:130668068-130707271`
[2016-04-15T05:44Z] 2016-04-14 22:44:43 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:44:43,516 - WARNING - Could not retrieve variants from source file in region 9:130828828-130884943. Error was invalid region `9:130828829-130884943`
[2016-04-15T05:44Z] 2016-04-14 22:44:43 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:44:43,541 - WARNING - Could not retrieve variants from source file in region 9:131222330-131235511. Error was invalid region `9:131222331-131235511`
[2016-04-15T05:44Z] 2016-04-14 22:44:43 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:44:43,542 - WARNING - Could not retrieve variants from source file in region 9:138378645-138379192. Error was invalid region `9:138378646-138379192`
[2016-04-15T05:44Z] 2016-04-14 22:44:43 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:44:43,875 - WARNING - Could not retrieve variants from source file in region 9:131670246-131709587. Error was invalid region `9:131670247-131709587`
[2016-04-15T05:44Z] 2016-04-14 22:44:43 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:44:43,987 - WARNING - Could not retrieve variants from source file in region 9:135202618-135206650. Error was invalid region `9:135202619-135206650`
[2016-04-15T05:44Z] 2016-04-14 22:44:45 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:44:45,961 - WARNING - Could not retrieve variants from source file in region 9:131020171-131020988. Error was invalid region `9:131020172-131020988`
[2016-04-15T05:44Z] 2016-04-14 22:44:47 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:44:47,251 - WARNING - Could not retrieve variants from source file in region 9:132515036-132515437. Error was invalid region `9:132515037-132515437`
[2016-04-15T05:44Z] 2016-04-14 22:44:48 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:44:48,150 - WARNING - Could not retrieve variants from source file in region 9:131939808-131940209. Error was invalid region `9:131939809-131940209`
[2016-04-15T05:44Z] 2016-04-14 22:44:49 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:44:49,824 - WARNING - Could not retrieve variants from source file in region 9:130164782-130242356. Error was invalid region `9:130164783-130242356`
[2016-04-15T05:44Z] 2016-04-14 22:44:51 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:44:51,384 - WARNING - Could not retrieve variants from source file in region 9:130668067-130707271. Error was invalid region `9:130668068-130707271`
[2016-04-15T05:44Z] 2016-04-14 22:44:51 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:44:51,955 - WARNING - Could not retrieve variants from source file in region 9:131222330-131235511. Error was invalid region `9:131222331-131235511`
[2016-04-15T05:44Z] 2016-04-14 22:44:52 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:44:52,131 - WARNING - Could not retrieve variants from source file in region 9:130828828-130884943. Error was invalid region `9:130828829-130884943`
[2016-04-15T05:45Z] 2016-04-14 22:45:00 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:45:00,951 - WARNING - Could not retrieve variants from source file in region 9:131085162-131085563. Error was invalid region `9:131085163-131085563`
[2016-04-15T05:45Z] 2016-04-14 22:45:02 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:45:02,810 - WARNING - Could not retrieve variants from source file in region 9:130980726-130984945. Error was invalid region `9:130980727-130984945`
[2016-04-15T05:45Z] 2016-04-14 22:45:03 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:45:03,235 - WARNING - Could not retrieve variants from source file in region 9:138235820-138236402. Error was invalid region `9:138235821-138236402`
[2016-04-15T05:45Z] 2016-04-14 22:45:04 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:45:04,746 - WARNING - Could not retrieve variants from source file in region 9:135139690-135140210. Error was invalid region `9:135139691-135140210`
[2016-04-15T05:45Z] 2016-04-14 22:45:05 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:45:05,944 - WARNING - Could not retrieve variants from source file in region 9:131904966-131905367. Error was invalid region `9:131904967-131905367`
[2016-04-15T05:45Z] 2016-04-14 22:45:06 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:45:06,559 - WARNING - Could not retrieve variants from source file in region 9:133553782-133569390. Error was invalid region `9:133553783-133569390`
[2016-04-15T05:45Z] 2016-04-14 22:45:06 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:45:06,641 - WARNING - Could not retrieve variants from source file in region 9:131085162-131085563. Error was invalid region `9:131085163-131085563`
[2016-04-15T05:45Z] 2016-04-14 22:45:06 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:45:06,826 - WARNING - Could not retrieve variants from source file in region 9:131085162-131085563. Error was invalid region `9:131085163-131085563`
[2016-04-15T05:45Z] 2016-04-14 22:45:08 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:45:08,375 - WARNING - Could not retrieve variants from source file in region 9:131565343-131592383. Error was invalid region `9:131565344-131592383`
[2016-04-15T05:45Z] 2016-04-14 22:45:08 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:45:08,892 - WARNING - Could not retrieve variants from source file in region 9:138235820-138236402. Error was invalid region `9:138235821-138236402`
[2016-04-15T05:45Z] 2016-04-14 22:45:08 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:45:08,913 - WARNING - Could not retrieve variants from source file in region 9:141008665-141016452. Error was invalid region `9:141008666-141016452`
[2016-04-15T05:45Z] 2016-04-14 22:45:09 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:45:09,087 - WARNING - Could not retrieve variants from source file in region 9:130630428-130636510. Error was invalid region `9:130630429-130636510`
[2016-04-15T05:45Z] 2016-04-14 22:45:10 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:45:10,260 - WARNING - Could not retrieve variants from source file in region 9:131846746-131873828. Error was invalid region `9:131846747-131873828`
[2016-04-15T05:45Z] 2016-04-14 22:45:11 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:45:11,202 - WARNING - Could not retrieve variants from source file in region 9:132377689-132428400. Error was invalid region `9:132377690-132428400`
[2016-04-15T05:45Z] 2016-04-14 22:45:11 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:45:11,658 - WARNING - Could not retrieve variants from source file in region 9:131904966-131905367. Error was invalid region `9:131904967-131905367`
[2016-04-15T05:45Z] 2016-04-14 22:45:12 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:45:12,089 - WARNING - Could not retrieve variants from source file in region 9:129936809-129937210. Error was invalid region `9:129936810-129937210`
[2016-04-15T05:45Z] 2016-04-14 22:45:13 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:45:13,252 - WARNING - Could not retrieve variants from source file in region 9:130980726-130984945. Error was invalid region `9:130980727-130984945`
[2016-04-15T05:45Z] 2016-04-14 22:45:13 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:45:13,290 - WARNING - Could not retrieve variants from source file in region 9:131565343-131592383. Error was invalid region `9:131565344-131592383`
[2016-04-15T05:45Z] 2016-04-14 22:45:14 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:45:14,730 - WARNING - Could not retrieve variants from source file in region 9:138235820-138236402. Error was invalid region `9:138235821-138236402`
[2016-04-15T05:45Z] 2016-04-14 22:45:16 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:45:16,059 - WARNING - Could not retrieve variants from source file in region 9:135139690-135140210. Error was invalid region `9:135139691-135140210`
[2016-04-15T05:45Z] 2016-04-14 22:45:16 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:45:16,675 - WARNING - Could not retrieve variants from source file in region 9:131904966-131905367. Error was invalid region `9:131904967-131905367`
[2016-04-15T05:45Z] 2016-04-14 22:45:16 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:45:16,684 - WARNING - Could not retrieve variants from source file in region 9:133553782-133569390. Error was invalid region `9:133553783-133569390`
[2016-04-15T05:45Z] 2016-04-14 22:45:18 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:45:18,494 - WARNING - Could not retrieve variants from source file in region 9:141008665-141016452. Error was invalid region `9:141008666-141016452`
[2016-04-15T05:45Z] 2016-04-14 22:45:20 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:45:20,296 - WARNING - Could not retrieve variants from source file in region 9:130630428-130636510. Error was invalid region `9:130630429-130636510`
[2016-04-15T05:45Z] 2016-04-14 22:45:21 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:45:21,307 - WARNING - Could not retrieve variants from source file in region 9:140609831-140610232. Error was invalid region `9:140609832-140610232`
[2016-04-15T05:45Z] 2016-04-14 22:45:21 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:45:21,606 - WARNING - Could not retrieve variants from source file in region 9:131846746-131873828. Error was invalid region `9:131846747-131873828`
[2016-04-15T05:45Z] 2016-04-14 22:45:27 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:45:27,470 - WARNING - Could not retrieve variants from source file in region 9:131515336-131515737. Error was invalid region `9:131515337-131515737`
[2016-04-15T05:45Z] 2016-04-14 22:45:27 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:45:27,736 - WARNING - Could not retrieve variants from source file in region 9:131767457-131771695. Error was invalid region `9:131767458-131771695`
[2016-04-15T05:45Z] 2016-04-14 22:45:28 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:45:28,589 - WARNING - Could not retrieve variants from source file in region 9:132988498-132988899. Error was invalid region `9:132988499-132988899`
[2016-04-15T05:45Z] 2016-04-14 22:45:28 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:45:28,823 - WARNING - Could not retrieve variants from source file in region 9:138011441-138011842. Error was invalid region `9:138011442-138011842`
[2016-04-15T05:45Z] 2016-04-14 22:45:30 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:45:30,997 - WARNING - Could not retrieve variants from source file in region 9:134385225-134406261. Error was invalid region `9:134385226-134406261`
[2016-04-15T05:45Z] 2016-04-14 22:45:31 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:45:31,468 - WARNING - Could not retrieve variants from source file in region 9:135102043-135106154. Error was invalid region `9:135102044-135106154`
[2016-04-15T05:45Z] 2016-04-14 22:45:32 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:45:32,144 - WARNING - Could not retrieve variants from source file in region 9:129853988-129854389. Error was invalid region `9:129853989-129854389`
[2016-04-15T05:45Z] 2016-04-14 22:45:32 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:45:32,807 - WARNING - Could not retrieve variants from source file in region 9:131767457-131771695. Error was invalid region `9:131767458-131771695`
[2016-04-15T05:45Z] 2016-04-14 22:45:32 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:45:32,910 - WARNING - Could not retrieve variants from source file in region 9:131515336-131515737. Error was invalid region `9:131515337-131515737`
[2016-04-15T05:45Z] 2016-04-14 22:45:32 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:45:32,917 - WARNING - Could not retrieve variants from source file in region 9:131767457-131771695. Error was invalid region `9:131767458-131771695`
[2016-04-15T05:45Z] 2016-04-14 22:45:33 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:45:33,167 - WARNING - Could not retrieve variants from source file in region 9:132988498-132988899. Error was invalid region `9:132988499-132988899`
[2016-04-15T05:45Z] 2016-04-14 22:45:36 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:45:36,001 - WARNING - Could not retrieve variants from source file in region 9:134385225-134406261. Error was invalid region `9:134385226-134406261`
[2016-04-15T05:45Z] 2016-04-14 22:45:36 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:45:36,585 - WARNING - Could not retrieve variants from source file in region 9:132872475-132872876. Error was invalid region `9:132872476-132872876`
[2016-04-15T05:45Z] 2016-04-14 22:45:36 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:45:36,878 - WARNING - Could not retrieve variants from source file in region 9:135102043-135106154. Error was invalid region `9:135102044-135106154`
[2016-04-15T05:45Z] 2016-04-14 22:45:37 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:45:37,867 - WARNING - Could not retrieve variants from source file in region 9:139564457-139564858. Error was invalid region `9:139564458-139564858`
[2016-04-15T05:45Z] 2016-04-14 22:45:38 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:45:38,250 - WARNING - Could not retrieve variants from source file in region 9:140917970-140918371. Error was invalid region `9:140917971-140918371`
[2016-04-15T05:45Z] 2016-04-14 22:45:38 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:45:38,274 - WARNING - Could not retrieve variants from source file in region 9:131515336-131515737. Error was invalid region `9:131515337-131515737`
[2016-04-15T05:45Z] 2016-04-14 22:45:38 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:45:38,309 - WARNING - Could not retrieve variants from source file in region 9:132988498-132988899. Error was invalid region `9:132988499-132988899`
[2016-04-15T05:45Z] 2016-04-14 22:45:38 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:45:38,869 - WARNING - Could not retrieve variants from source file in region 9:130565056-130586878. Error was invalid region `9:130565057-130586878`
[2016-04-15T05:45Z] 2016-04-14 22:45:40 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:45:40,801 - WARNING - Could not retrieve variants from source file in region 9:134385225-134406261. Error was invalid region `9:134385226-134406261`
[2016-04-15T05:45Z] 2016-04-14 22:45:41 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:45:41,271 - WARNING - Could not retrieve variants from source file in region 9:132872475-132872876. Error was invalid region `9:132872476-132872876`
[2016-04-15T05:45Z] 2016-04-14 22:45:41 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:45:41,813 - WARNING - Could not retrieve variants from source file in region 9:135102043-135106154. Error was invalid region `9:135102044-135106154`
[2016-04-15T05:45Z] 2016-04-14 22:45:44 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:45:44,639 - WARNING - Could not retrieve variants from source file in region 9:140917970-140918371. Error was invalid region `9:140917971-140918371`
[2016-04-15T05:45Z] 2016-04-14 22:45:44 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:45:44,698 - WARNING - Could not retrieve variants from source file in region 9:140469389-140470309. Error was invalid region `9:140469390-140470309`
[2016-04-15T05:45Z] 2016-04-14 22:45:46 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:45:46,387 - WARNING - Could not retrieve variants from source file in region 9:132872475-132872876. Error was invalid region `9:132872476-132872876`
[2016-04-15T05:45Z] 2016-04-14 22:45:47 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:45:47,973 - WARNING - Could not retrieve variants from source file in region 9:138903460-138908440. Error was invalid region `9:138903461-138908440`
[2016-04-15T05:45Z] 2016-04-14 22:45:49 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:45:49,254 - WARNING - Could not retrieve variants from source file in region 9:135073666-135074067. Error was invalid region `9:135073667-135074067`
[2016-04-15T05:45Z] 2016-04-14 22:45:49 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:45:49,969 - WARNING - Could not retrieve variants from source file in region 9:139564457-139564858. Error was invalid region `9:139564458-139564858`
[2016-04-15T05:45Z] 2016-04-14 22:45:52 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:45:52,987 - WARNING - Could not retrieve variants from source file in region 9:131465491-131483939. Error was invalid region `9:131465492-131483939`
[2016-04-15T05:45Z] 2016-04-14 22:45:53 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:45:53,945 - WARNING - Could not retrieve variants from source file in region 9:137981916-137982317. Error was invalid region `9:137981917-137982317`
[2016-04-15T05:45Z] 2016-04-14 22:45:54 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:45:54,993 - WARNING - Could not retrieve variants from source file in region 9:135073666-135074067. Error was invalid region `9:135073667-135074067`
[2016-04-15T05:45Z] 2016-04-14 22:45:56 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:45:56,735 - WARNING - Could not retrieve variants from source file in region 9:135073666-135074067. Error was invalid region `9:135073667-135074067`
[2016-04-15T05:45Z] 2016-04-14 22:45:57 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:45:57,472 - WARNING - Could not retrieve variants from source file in region 9:134744015-134744416. Error was invalid region `9:134744016-134744416`
[2016-04-15T05:45Z] 2016-04-14 22:45:58 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:45:58,381 - WARNING - Could not retrieve variants from source file in region 9:131465491-131483939. Error was invalid region `9:131465492-131483939`
[2016-04-15T05:45Z] 2016-04-14 22:45:59 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:45:59,616 - WARNING - Could not retrieve variants from source file in region 9:138903460-138908440. Error was invalid region `9:138903461-138908440`
[2016-04-15T05:46Z] 2016-04-14 22:46:00 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:46:00,227 - WARNING - Could not retrieve variants from source file in region 9:137981916-137982317. Error was invalid region `9:137981917-137982317`
[2016-04-15T05:46Z] 2016-04-14 22:46:01 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:46:01,332 - WARNING - Could not retrieve variants from source file in region 9:131346007-131419018. Error was invalid region `9:131346008-131419018`
[2016-04-15T05:46Z] 2016-04-14 22:46:02 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:46:02,545 - WARNING - Could not retrieve variants from source file in region 9:134334377-134351533. Error was invalid region `9:134334378-134351533`
[2016-04-15T05:46Z] 2016-04-14 22:46:02 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:46:02,735 - WARNING - Could not retrieve variants from source file in region 9:140323162-140386120. Error was invalid region `9:140323163-140386120`
[2016-04-15T05:46Z] 2016-04-14 22:46:03 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:46:03,128 - WARNING - Could not retrieve variants from source file in region 9:134744015-134744416. Error was invalid region `9:134744016-134744416`
[2016-04-15T05:46Z] 2016-04-14 22:46:06 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:46:06,019 - WARNING - Could not retrieve variants from source file in region 9:131465491-131483939. Error was invalid region `9:131465492-131483939`
[2016-04-15T05:46Z] 2016-04-14 22:46:06 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:46:06,069 - WARNING - Could not retrieve variants from source file in region 9:129641662-129642063. Error was invalid region `9:129641663-129642063`
[2016-04-15T05:46Z] 2016-04-14 22:46:06 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:46:06,668 - WARNING - Could not retrieve variants from source file in region 9:130323274-130331456. Error was invalid region `9:130323275-130331456`
[2016-04-15T05:46Z] 2016-04-14 22:46:06 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:46:06,779 - WARNING - Could not retrieve variants from source file in region 9:137981916-137982317. Error was invalid region `9:137981917-137982317`
[2016-04-15T05:46Z] 2016-04-14 22:46:07 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:46:07,094 - WARNING - Could not retrieve variants from source file in region 9:129157791-129160073. Error was invalid region `9:129157792-129160073`
[2016-04-15T05:46Z] 2016-04-14 22:46:07 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:46:07,133 - WARNING - Could not retrieve variants from source file in region 9:140441615-140442016. Error was invalid region `9:140441616-140442016`
[2016-04-15T05:46Z] 2016-04-14 22:46:07 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:46:07,273 - WARNING - Could not retrieve variants from source file in region 9:134334377-134351533. Error was invalid region `9:134334378-134351533`
[2016-04-15T05:46Z] 2016-04-14 22:46:07 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:46:07,288 - WARNING - Could not retrieve variants from source file in region 9:131346007-131419018. Error was invalid region `9:131346008-131419018`
[2016-04-15T05:46Z] 2016-04-14 22:46:07 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:46:07,480 - WARNING - Could not retrieve variants from source file in region 9:134744015-134744416. Error was invalid region `9:134744016-134744416`
[2016-04-15T05:46Z] 2016-04-14 22:46:13 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:46:13,393 - WARNING - Could not retrieve variants from source file in region 9:129641662-129642063. Error was invalid region `9:129641663-129642063`
[2016-04-15T05:46Z] 2016-04-14 22:46:14 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:46:14,849 - WARNING - Could not retrieve variants from source file in region 9:140441615-140442016. Error was invalid region `9:140441616-140442016`
[2016-04-15T05:46Z] 2016-04-14 22:46:15 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:46:15,401 - WARNING - Could not retrieve variants from source file in region 9:131346007-131419018. Error was invalid region `9:131346008-131419018`
[2016-04-15T05:46Z] 2016-04-14 22:46:17 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:46:17,691 - WARNING - Could not retrieve variants from source file in region 9:134473444-134473845. Error was invalid region `9:134473445-134473845`
[2016-04-15T05:46Z] 2016-04-14 22:46:25 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:46:25,047 - WARNING - Could not retrieve variants from source file in region 9:134183168-134183693. Error was invalid region `9:134183169-134183693`
[2016-04-15T05:46Z] 2016-04-14 22:46:26 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:46:26,006 - WARNING - Could not retrieve variants from source file in region 9:131285744-131286145. Error was invalid region `9:131285745-131286145`
[2016-04-15T05:46Z] 2016-04-14 22:46:27 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:46:27,570 - WARNING - Could not retrieve variants from source file in region 9:138831356-138838330. Error was invalid region `9:138831357-138838330`
[2016-04-15T05:46Z] 2016-04-14 22:46:27 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:46:27,932 - WARNING - Could not retrieve variants from source file in region 9:129595684-129596085. Error was invalid region `9:129595685-129596085`
[2016-04-15T05:46Z] 2016-04-14 22:46:29 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:46:29,237 - WARNING - Could not retrieve variants from source file in region 9:137774944-137779281. Error was invalid region `9:137774945-137779281`
[2016-04-15T05:46Z] 2016-04-14 22:46:30 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:46:30,251 - WARNING - Could not retrieve variants from source file in region 9:138669050-138669451. Error was invalid region `9:138669051-138669451`
[2016-04-15T05:46Z] 2016-04-14 22:46:30 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:46:30,553 - WARNING - Could not retrieve variants from source file in region 9:129102629-129103030. Error was invalid region `9:129102630-129103030`
[2016-04-15T05:46Z] 2016-04-14 22:46:30 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:46:30,617 - WARNING - Could not retrieve variants from source file in region 9:134183168-134183693. Error was invalid region `9:134183169-134183693`
[2016-04-15T05:46Z] 2016-04-14 22:46:31 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:46:31,338 - WARNING - Could not retrieve variants from source file in region 9:130285899-130286300. Error was invalid region `9:130285900-130286300`
[2016-04-15T05:46Z] 2016-04-14 22:46:31 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:46:31,354 - WARNING - Could not retrieve variants from source file in region 9:140777095-140777496. Error was invalid region `9:140777096-140777496`
[2016-04-15T05:46Z] 2016-04-14 22:46:33 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:46:33,026 - WARNING - Could not retrieve variants from source file in region 9:129595684-129596085. Error was invalid region `9:129595685-129596085`
[2016-04-15T05:46Z] 2016-04-14 22:46:36 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:46:36,298 - WARNING - Could not retrieve variants from source file in region 9:138669050-138669451. Error was invalid region `9:138669051-138669451`
[2016-04-15T05:46Z] 2016-04-14 22:46:37 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:46:37,095 - WARNING - Could not retrieve variants from source file in region 9:134183168-134183693. Error was invalid region `9:134183169-134183693`
[2016-04-15T05:46Z] 2016-04-14 22:46:37 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:46:37,758 - WARNING - Could not retrieve variants from source file in region 9:140777095-140777496. Error was invalid region `9:140777096-140777496`
[2016-04-15T05:46Z] 2016-04-14 22:46:38 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:46:38,177 - WARNING - Could not retrieve variants from source file in region 9:134136304-134136867. Error was invalid region `9:134136305-134136867`
[2016-04-15T05:46Z] 2016-04-14 22:46:38 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:46:38,179 - WARNING - Could not retrieve variants from source file in region 9:138741866-138742267. Error was invalid region `9:138741867-138742267`
[2016-04-15T05:46Z] 2016-04-14 22:46:38 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:46:38,462 - WARNING - Could not retrieve variants from source file in region 9:129595684-129596085. Error was invalid region `9:129595685-129596085`
[2016-04-15T05:46Z] 2016-04-14 22:46:38 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:46:38,511 - WARNING - Could not retrieve variants from source file in region 9:130285899-130286300. Error was invalid region `9:130285900-130286300`
[2016-04-15T05:46Z] 2016-04-14 22:46:41 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:46:41,857 - WARNING - Could not retrieve variants from source file in region 9:138669050-138669451. Error was invalid region `9:138669051-138669451`
[2016-04-15T05:46Z] 2016-04-14 22:46:44 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:46:44,077 - WARNING - Could not retrieve variants from source file in region 9:140777095-140777496. Error was invalid region `9:140777096-140777496`
[2016-04-15T05:46Z] 2016-04-14 22:46:44 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:46:44,336 - WARNING - Could not retrieve variants from source file in region 9:138741866-138742267. Error was invalid region `9:138741867-138742267`
[2016-04-15T05:46Z] 2016-04-14 22:46:45 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:46:45,047 - WARNING - Could not retrieve variants from source file in region 9:134136304-134136867. Error was invalid region `9:134136305-134136867`
[2016-04-15T05:46Z] 2016-04-14 22:46:50 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:46:50,112 - WARNING - Could not retrieve variants from source file in region 9:137688490-137688891. Error was invalid region `9:137688491-137688891`
[2016-04-15T05:46Z] 2016-04-14 22:46:50 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:46:50,268 - WARNING - Could not retrieve variants from source file in region 9:134136304-134136867. Error was invalid region `9:134136305-134136867`
[2016-04-15T05:46Z] 2016-04-14 22:46:50 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:46:50,859 - WARNING - Could not retrieve variants from source file in region 9:134019875-134020282. Error was invalid region `9:134019876-134020282`
[2016-04-15T05:46Z] 2016-04-14 22:46:55 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:46:55,121 - WARNING - Could not retrieve variants from source file in region 9:138585987-138591456. Error was invalid region `9:138585988-138591456`
[2016-04-15T05:46Z] 2016-04-14 22:46:55 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:46:55,158 - WARNING - Could not retrieve variants from source file in region 9:137688490-137688891. Error was invalid region `9:137688491-137688891`
[2016-04-15T05:46Z] 2016-04-14 22:46:55 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:46:55,783 - WARNING - Could not retrieve variants from source file in region 9:136379679-136380080. Error was invalid region `9:136379680-136380080`
[2016-04-15T05:46Z] 2016-04-14 22:46:56 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:46:56,975 - WARNING - Could not retrieve variants from source file in region 9:140638250-140638651. Error was invalid region `9:140638251-140638651`
[2016-04-15T05:46Z] 2016-04-14 22:46:57 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:46:57,046 - WARNING - Could not retrieve variants from source file in region 9:137618984-137642844. Error was invalid region `9:137618985-137642844`
[2016-04-15T05:46Z] 2016-04-14 22:46:59 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:46:59,128 - WARNING - Could not retrieve variants from source file in region 9:134019875-134020282. Error was invalid region `9:134019876-134020282`
[2016-04-15T05:46Z] 2016-04-14 22:46:59 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:46:59,700 - WARNING - Could not retrieve variants from source file in region 9:138585987-138591456. Error was invalid region `9:138585988-138591456`
[2016-04-15T05:47Z] 2016-04-14 22:47:00 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:47:00,404 - WARNING - Could not retrieve variants from source file in region 9:136379679-136380080. Error was invalid region `9:136379680-136380080`
[2016-04-15T05:47Z] 2016-04-14 22:47:00 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:47:00,641 - WARNING - Could not retrieve variants from source file in region 9:138585987-138591456. Error was invalid region `9:138585988-138591456`
[2016-04-15T05:47Z] 2016-04-14 22:47:01 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:47:01,819 - WARNING - Could not retrieve variants from source file in region 9:138515908-138518200. Error was invalid region `9:138515909-138518200`
[2016-04-15T05:47Z] 2016-04-14 22:47:05 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:47:05,029 - WARNING - Could not retrieve variants from source file in region 9:136379679-136380080. Error was invalid region `9:136379680-136380080`
[2016-04-15T05:47Z] 2016-04-14 22:47:06 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:47:06,791 - WARNING - Could not retrieve variants from source file in region 9:138515908-138518200. Error was invalid region `9:138515909-138518200`
[2016-04-15T05:47Z] 2016-04-14 22:47:07 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:47:07,988 - WARNING - Could not retrieve variants from source file in region 9:133884609-133885010. Error was invalid region `9:133884610-133885010`
[2016-04-15T05:47Z] 2016-04-14 22:47:10 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:47:10,840 - WARNING - Could not retrieve variants from source file in region 9:133884609-133885010. Error was invalid region `9:133884610-133885010`
[2016-04-15T05:47Z] 2016-04-14 22:47:12 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:47:12,082 - WARNING - Could not retrieve variants from source file in region 9:137271107-137272011. Error was invalid region `9:137271108-137272011`
[2016-04-15T05:47Z] 2016-04-14 22:47:13 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:47:13,342 - WARNING - Could not retrieve variants from source file in region 9:138440314-138456513. Error was invalid region `9:138440315-138456513`
[2016-04-15T05:47Z] 2016-04-14 22:47:13 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:47:13,509 - WARNING - Could not retrieve variants from source file in region 9:135973868-136004960. Error was invalid region `9:135973869-136004960`
[2016-04-15T05:47Z] 2016-04-14 22:47:16 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:47:16,053 - WARNING - Could not retrieve variants from source file in region 9:137271107-137272011. Error was invalid region `9:137271108-137272011`
[2016-04-15T05:47Z] 2016-04-14 22:47:17 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:47:17,391 - WARNING - Could not retrieve variants from source file in region 9:138440314-138456513. Error was invalid region `9:138440315-138456513`
[2016-04-15T05:47Z] 2016-04-14 22:47:18 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:47:18,149 - WARNING - Could not retrieve variants from source file in region 9:136409448-136412486. Error was invalid region `9:136409449-136412486`
[2016-04-15T05:47Z] 2016-04-14 22:47:20 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:47:20,131 - WARNING - Could not retrieve variants from source file in region 9:137271107-137272011. Error was invalid region `9:137271108-137272011`
[2016-04-15T05:47Z] 2016-04-14 22:47:24 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:47:24,499 - WARNING - Could not retrieve variants from source file in region 9:136643697-136663118. Error was invalid region `9:136643698-136663118`
[2016-04-15T05:47Z] 2016-04-14 22:47:25 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:47:25,245 - WARNING - Could not retrieve variants from source file in region 9:135930524-135946789. Error was invalid region `9:135930525-135946789`
[2016-04-15T05:47Z] 2016-04-14 22:47:26 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:47:26,805 - WARNING - Could not retrieve variants from source file in region 9:135930524-135946789. Error was invalid region `9:135930525-135946789`
[2016-04-15T05:47Z] 2016-04-14 22:47:26 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:47:26,810 - WARNING - Could not retrieve variants from source file in region 9:135374553-135375088. Error was invalid region `9:135374554-135375088`
[2016-04-15T05:47Z] 2016-04-14 22:47:27 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:47:27,091 - WARNING - Could not retrieve variants from source file in region 9:135538596-135554756. Error was invalid region `9:135538597-135554756`
[2016-04-15T05:47Z] 2016-04-14 22:47:28 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:47:28,121 - WARNING - Could not retrieve variants from source file in region 9:135374553-135375088. Error was invalid region `9:135374554-135375088`
[2016-04-15T05:47Z] 2016-04-14 22:47:29 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:47:29,445 - WARNING - Could not retrieve variants from source file in region 9:135263362-135277197. Error was invalid region `9:135263363-135277197`
[2016-04-15T05:47Z] 2016-04-14 22:47:29 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:47:29,606 - WARNING - Could not retrieve variants from source file in region 9:135753799-135787094. Error was invalid region `9:135753800-135787094`
[2016-04-15T05:47Z] 2016-04-14 22:47:31 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:47:31,447 - WARNING - Could not retrieve variants from source file in region 9:135538596-135554756. Error was invalid region `9:135538597-135554756`
[2016-04-15T05:47Z] 2016-04-14 22:47:35 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:47:35,236 - WARNING - Could not retrieve variants from source file in region 9:135470203-135470604. Error was invalid region `9:135470204-135470604`
[2016-04-15T05:47Z] 2016-04-14 22:47:37 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:47:37,420 - WARNING - Could not retrieve variants from source file in region 9:135470203-135470604. Error was invalid region `9:135470204-135470604`
[2016-04-15T05:47Z] 2016-04-14 22:47:37 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:47:37,504 - WARNING - Could not retrieve variants from source file in region 9:136198648-136227450. Error was invalid region `9:136198649-136227450`
[2016-04-15T05:47Z] 2016-04-14 22:47:38 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:47:38,408 - WARNING - Could not retrieve variants from source file in region 9:136066483-136083770. Error was invalid region `9:136066484-136083770`
[2016-04-15T05:47Z] 2016-04-14 22:47:38 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:47:38,598 - WARNING - Could not retrieve variants from source file in region 9:135470203-135470604. Error was invalid region `9:135470204-135470604`
[2016-04-15T05:47Z] 2016-04-14 22:47:41 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:47:41,558 - WARNING - Could not retrieve variants from source file in region 9:136037531-136037932. Error was invalid region `9:136037532-136037932`
[2016-04-15T05:47Z] 2016-04-14 22:47:41 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:47:41,587 - WARNING - Could not retrieve variants from source file in region 9:136037531-136037932. Error was invalid region `9:136037532-136037932`
[2016-04-15T05:47Z] 2016-04-14 22:47:42 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:47:42,041 - WARNING - Could not retrieve variants from source file in region 9:136037531-136037932. Error was invalid region `9:136037532-136037932`
[2016-04-15T05:47Z] ['bcbio-variation-recall', 'square', '-Xms750m', '-Xmx7280m', '-XX:+UseSerialGC', '-c', 16, '-r', u'10:1-15559243', '--caller', 'platypus', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/10/Batch1-10_0_15559243.vcf.gz', '/mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/10/Batch1-10_0_15559243.vcf-inputs.txt'] in region: 10:1-15559243
[2016-04-15T05:47Z] 2016-04-14 22:47:58 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:47:58,193 - WARNING - Could not retrieve variants from source file in region 10:14590331-14614471. Error was invalid region `10:14590332-14614471`
[2016-04-15T05:47Z] 2016-04-14 22:47:59 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:47:59,306 - WARNING - Could not retrieve variants from source file in region 10:11299524-11299925. Error was invalid region `10:11299525-11299925`
[2016-04-15T05:47Z] 2016-04-14 22:47:59 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:47:59,346 - WARNING - Could not retrieve variants from source file in region 10:1717132-1717697. Error was invalid region `10:1717133-1717697`
[2016-04-15T05:47Z] 2016-04-14 22:47:59 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:47:59,615 - WARNING - Could not retrieve variants from source file in region 10:13481216-13494784. Error was invalid region `10:13481217-13494784`
[2016-04-15T05:47Z] 2016-04-14 22:47:59 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:47:59,761 - WARNING - Could not retrieve variants from source file in region 10:11504541-11505365. Error was invalid region `10:11504542-11505365`
[2016-04-15T05:48Z] 2016-04-14 22:48:00 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:48:00,450 - WARNING - Could not retrieve variants from source file in region 10:13633624-13653843. Error was invalid region `10:13633625-13653843`
[2016-04-15T05:48Z] 2016-04-14 22:48:00 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:48:00,627 - WARNING - Could not retrieve variants from source file in region 10:14816167-14816638. Error was invalid region `10:14816168-14816638`
[2016-04-15T05:48Z] 2016-04-14 22:48:00 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:48:00,654 - WARNING - Could not retrieve variants from source file in region 10:5540970-5541420. Error was invalid region `10:5540971-5541420`
[2016-04-15T05:48Z] 2016-04-14 22:48:00 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:48:00,772 - WARNING - Could not retrieve variants from source file in region 10:15255983-15256384. Error was invalid region `10:15255984-15256384`
[2016-04-15T05:48Z] 2016-04-14 22:48:00 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:48:00,876 - WARNING - Could not retrieve variants from source file in region 10:13932318-13933064. Error was invalid region `10:13932319-13933064`
[2016-04-15T05:48Z] 2016-04-14 22:48:01 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:48:01,008 - WARNING - Could not retrieve variants from source file in region 10:12191722-12209942. Error was invalid region `10:12191723-12209942`
[2016-04-15T05:48Z] 2016-04-14 22:48:01 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:48:01,042 - WARNING - Could not retrieve variants from source file in region 10:12867387-12867788. Error was invalid region `10:12867388-12867788`
[2016-04-15T05:48Z] 2016-04-14 22:48:04 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:48:04,167 - WARNING - Could not retrieve variants from source file in region 10:6520752-6527333. Error was invalid region `10:6520753-6527333`
[2016-04-15T05:48Z] 2016-04-14 22:48:04 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:48:04,223 - WARNING - Could not retrieve variants from source file in region 10:14590331-14614471. Error was invalid region `10:14590332-14614471`
[2016-04-15T05:48Z] 2016-04-14 22:48:05 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:48:05,252 - WARNING - Could not retrieve variants from source file in region 10:11911553-11912418. Error was invalid region `10:11911554-11912418`
[2016-04-15T05:48Z] 2016-04-14 22:48:06 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:48:06,041 - WARNING - Could not retrieve variants from source file in region 10:11784422-11806028. Error was invalid region `10:11784423-11806028`
[2016-04-15T05:48Z] 2016-04-14 22:48:06 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:48:06,702 - WARNING - Could not retrieve variants from source file in region 10:12046335-12071587. Error was invalid region `10:12046336-12071587`
[2016-04-15T05:48Z] 2016-04-14 22:48:06 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:48:06,866 - WARNING - Could not retrieve variants from source file in region 10:1717132-1717697. Error was invalid region `10:1717133-1717697`
[2016-04-15T05:48Z] 2016-04-14 22:48:07 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:48:07,385 - WARNING - Could not retrieve variants from source file in region 10:13481216-13494784. Error was invalid region `10:13481217-13494784`
[2016-04-15T05:48Z] 2016-04-14 22:48:07 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:48:07,774 - WARNING - Could not retrieve variants from source file in region 10:11504541-11505365. Error was invalid region `10:11504542-11505365`
[2016-04-15T05:48Z] 2016-04-14 22:48:07 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:48:07,795 - WARNING - Could not retrieve variants from source file in region 10:13932318-13933064. Error was invalid region `10:13932319-13933064`
[2016-04-15T05:48Z] 2016-04-14 22:48:08 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:48:08,316 - WARNING - Could not retrieve variants from source file in region 10:12191722-12209942. Error was invalid region `10:12191723-12209942`
[2016-04-15T05:48Z] 2016-04-14 22:48:08 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:48:08,378 - WARNING - Could not retrieve variants from source file in region 10:12867387-12867788. Error was invalid region `10:12867388-12867788`
[2016-04-15T05:48Z] 2016-04-14 22:48:08 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:48:08,386 - WARNING - Could not retrieve variants from source file in region 10:5540970-5541420. Error was invalid region `10:5540971-5541420`
[2016-04-15T05:48Z] 2016-04-14 22:48:08 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:48:08,405 - WARNING - Could not retrieve variants from source file in region 10:13633624-13653843. Error was invalid region `10:13633625-13653843`
[2016-04-15T05:48Z] 2016-04-14 22:48:10 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:48:10,299 - WARNING - Could not retrieve variants from source file in region 10:14590331-14614471. Error was invalid region `10:14590332-14614471`
[2016-04-15T05:48Z] 2016-04-14 22:48:10 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:48:10,882 - WARNING - Could not retrieve variants from source file in region 10:11911553-11912418. Error was invalid region `10:11911554-11912418`
[2016-04-15T05:48Z] 2016-04-14 22:48:11 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:48:11,974 - WARNING - Could not retrieve variants from source file in region 10:11299524-11299925. Error was invalid region `10:11299525-11299925`
[2016-04-15T05:48Z] 2016-04-14 22:48:14 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:48:14,069 - WARNING - Could not retrieve variants from source file in region 10:1717132-1717697. Error was invalid region `10:1717133-1717697`
[2016-04-15T05:48Z] 2016-04-14 22:48:14 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:48:14,630 - WARNING - Could not retrieve variants from source file in region 10:14816167-14816638. Error was invalid region `10:14816168-14816638`
[2016-04-15T05:48Z] 2016-04-14 22:48:14 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:48:14,911 - WARNING - Could not retrieve variants from source file in region 10:13481216-13494784. Error was invalid region `10:13481217-13494784`
[2016-04-15T05:48Z] 2016-04-14 22:48:15 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:48:15,047 - WARNING - Could not retrieve variants from source file in region 10:11504541-11505365. Error was invalid region `10:11504542-11505365`
[2016-04-15T05:48Z] 2016-04-14 22:48:15 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:48:15,118 - WARNING - Could not retrieve variants from source file in region 10:15255983-15256384. Error was invalid region `10:15255984-15256384`
[2016-04-15T05:48Z] 2016-04-14 22:48:15 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:48:15,285 - WARNING - Could not retrieve variants from source file in region 10:12191722-12209942. Error was invalid region `10:12191723-12209942`
[2016-04-15T05:48Z] 2016-04-14 22:48:15 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:48:15,319 - WARNING - Could not retrieve variants from source file in region 10:13932318-13933064. Error was invalid region `10:13932319-13933064`
[2016-04-15T05:48Z] 2016-04-14 22:48:15 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:48:15,514 - WARNING - Could not retrieve variants from source file in region 10:12867387-12867788. Error was invalid region `10:12867388-12867788`
[2016-04-15T05:48Z] 2016-04-14 22:48:15 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:48:15,531 - WARNING - Could not retrieve variants from source file in region 10:5540970-5541420. Error was invalid region `10:5540971-5541420`
[2016-04-15T05:48Z] 2016-04-14 22:48:29 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:48:29,871 - WARNING - Could not retrieve variants from source file in region 10:11046996-11047397. Error was invalid region `10:11046997-11047397`
[2016-04-15T05:48Z] 2016-04-14 22:48:30 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:48:30,640 - WARNING - Could not retrieve variants from source file in region 10:15057163-15057564. Error was invalid region `10:15057164-15057564`
[2016-04-15T05:48Z] 2016-04-14 22:48:32 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:48:32,296 - WARNING - Could not retrieve variants from source file in region 10:13375695-13376096. Error was invalid region `10:13375696-13376096`
[2016-04-15T05:48Z] 2016-04-14 22:48:33 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:48:33,597 - WARNING - Could not retrieve variants from source file in region 10:14013743-14014144. Error was invalid region `10:14013744-14014144`
[2016-04-15T05:48Z] 2016-04-14 22:48:33 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:48:33,737 - WARNING - Could not retrieve variants from source file in region 10:1046501-1046902. Error was invalid region `10:1046502-1046902`
[2016-04-15T05:48Z] 2016-04-14 22:48:33 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:48:33,752 - WARNING - Could not retrieve variants from source file in region 10:6244708-6268395. Error was invalid region `10:6244709-6268395`
[2016-04-15T05:48Z] 2016-04-14 22:48:33 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:48:33,833 - WARNING - Could not retrieve variants from source file in region 10:429757-460130. Error was invalid region `10:429758-460130`
[2016-04-15T05:48Z] 2016-04-14 22:48:33 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:48:33,873 - WARNING - Could not retrieve variants from source file in region 10:12110879-12150129. Error was invalid region `10:12110880-12150129`
[2016-04-15T05:48Z] 2016-04-14 22:48:34 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:48:34,266 - WARNING - Could not retrieve variants from source file in region 10:11046996-11047397. Error was invalid region `10:11046997-11047397`
[2016-04-15T05:48Z] 2016-04-14 22:48:34 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:48:34,733 - WARNING - Could not retrieve variants from source file in region 10:13522450-13545054. Error was invalid region `10:13522451-13545054`
[2016-04-15T05:48Z] 2016-04-14 22:48:34 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:48:34,931 - WARNING - Could not retrieve variants from source file in region 10:1230757-1231158. Error was invalid region `10:1230758-1231158`
[2016-04-15T05:48Z] 2016-04-14 22:48:36 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:48:36,053 - WARNING - Could not retrieve variants from source file in region 10:15145150-15146045. Error was invalid region `10:15145151-15146045`
[2016-04-15T05:48Z] 2016-04-14 22:48:38 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:48:38,459 - WARNING - Could not retrieve variants from source file in region 10:14941443-14941844. Error was invalid region `10:14941444-14941844`
[2016-04-15T05:48Z] 2016-04-14 22:48:38 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:48:38,940 - WARNING - Could not retrieve variants from source file in region 10:14013743-14014144. Error was invalid region `10:14013744-14014144`
[2016-04-15T05:48Z] 2016-04-14 22:48:39 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:48:39,535 - WARNING - Could not retrieve variants from source file in region 10:6244708-6268395. Error was invalid region `10:6244709-6268395`
[2016-04-15T05:48Z] 2016-04-14 22:48:40 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:48:40,099 - WARNING - Could not retrieve variants from source file in region 10:1046501-1046902. Error was invalid region `10:1046502-1046902`
[2016-04-15T05:48Z] 2016-04-14 22:48:40 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:48:40,150 - WARNING - Could not retrieve variants from source file in region 10:5488369-5495408. Error was invalid region `10:5488370-5495408`
[2016-04-15T05:48Z] 2016-04-14 22:48:40 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:48:40,199 - WARNING - Could not retrieve variants from source file in region 10:12110879-12150129. Error was invalid region `10:12110880-12150129`
[2016-04-15T05:48Z] 2016-04-14 22:48:40 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:48:40,428 - WARNING - Could not retrieve variants from source file in region 10:13522450-13545054. Error was invalid region `10:13522451-13545054`
[2016-04-15T05:48Z] 2016-04-14 22:48:40 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:48:40,655 - WARNING - Could not retrieve variants from source file in region 10:1230757-1231158. Error was invalid region `10:1230758-1231158`
[2016-04-15T05:48Z] 2016-04-14 22:48:40 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:48:40,702 - WARNING - Could not retrieve variants from source file in region 10:15145150-15146045. Error was invalid region `10:15145151-15146045`
[2016-04-15T05:48Z] 2016-04-14 22:48:41 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:48:41,605 - WARNING - Could not retrieve variants from source file in region 10:13375695-13376096. Error was invalid region `10:13375696-13376096`
[2016-04-15T05:48Z] 2016-04-14 22:48:44 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:48:44,951 - WARNING - Could not retrieve variants from source file in region 10:429757-460130. Error was invalid region `10:429758-460130`
[2016-04-15T05:48Z] 2016-04-14 22:48:45 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:48:45,015 - WARNING - Could not retrieve variants from source file in region 10:5488369-5495408. Error was invalid region `10:5488370-5495408`
[2016-04-15T05:48Z] 2016-04-14 22:48:45 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:48:45,033 - WARNING - Could not retrieve variants from source file in region 10:1046501-1046902. Error was invalid region `10:1046502-1046902`
[2016-04-15T05:48Z] 2016-04-14 22:48:45 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:48:45,523 - WARNING - Could not retrieve variants from source file in region 10:12110879-12150129. Error was invalid region `10:12110880-12150129`
[2016-04-15T05:48Z] 2016-04-14 22:48:45 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:48:45,875 - WARNING - Could not retrieve variants from source file in region 10:13522450-13545054. Error was invalid region `10:13522451-13545054`
[2016-04-15T05:48Z] 2016-04-14 22:48:54 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:48:54,019 - WARNING - Could not retrieve variants from source file in region 10:8006587-8007750. Error was invalid region `10:8006588-8007750`
[2016-04-15T05:48Z] 2016-04-14 22:48:55 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:48:55,849 - WARNING - Could not retrieve variants from source file in region 10:918821-919552. Error was invalid region `10:918822-919552`
[2016-04-15T05:48Z] 2016-04-14 22:48:57 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:48:57,539 - WARNING - Could not retrieve variants from source file in region 10:6188127-6188528. Error was invalid region `10:6188128-6188528`
[2016-04-15T05:48Z] 2016-04-14 22:48:58 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:48:58,483 - WARNING - Could not retrieve variants from source file in region 10:8006587-8007750. Error was invalid region `10:8006588-8007750`
[2016-04-15T05:48Z] 2016-04-14 22:48:58 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:48:58,549 - WARNING - Could not retrieve variants from source file in region 10:323072-323473. Error was invalid region `10:323073-323473`
[2016-04-15T05:48Z] 2016-04-14 22:48:58 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:48:58,991 - WARNING - Could not retrieve variants from source file in region 10:5415529-5437555. Error was invalid region `10:5415530-5437555`
[2016-04-15T05:49Z] 2016-04-14 22:49:01 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:49:01,027 - WARNING - Could not retrieve variants from source file in region 10:5567155-5567885. Error was invalid region `10:5567156-5567885`
[2016-04-15T05:49Z] 2016-04-14 22:49:01 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:49:01,105 - WARNING - Could not retrieve variants from source file in region 10:5781417-5828091. Error was invalid region `10:5781418-5828091`
[2016-04-15T05:49Z] 2016-04-14 22:49:02 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:49:02,417 - WARNING - Could not retrieve variants from source file in region 10:14974694-15008683. Error was invalid region `10:14974695-15008683`
[2016-04-15T05:49Z] 2016-04-14 22:49:02 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:49:02,806 - WARNING - Could not retrieve variants from source file in region 10:14884298-14888169. Error was invalid region `10:14884299-14888169`
[2016-04-15T05:49Z] 2016-04-14 22:49:03 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:49:03,405 - WARNING - Could not retrieve variants from source file in region 10:323072-323473. Error was invalid region `10:323073-323473`
[2016-04-15T05:49Z] 2016-04-14 22:49:03 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:49:03,547 - WARNING - Could not retrieve variants from source file in region 10:8006587-8007750. Error was invalid region `10:8006588-8007750`
[2016-04-15T05:49Z] 2016-04-14 22:49:05 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:49:05,622 - WARNING - Could not retrieve variants from source file in region 10:5567155-5567885. Error was invalid region `10:5567156-5567885`
[2016-04-15T05:49Z] 2016-04-14 22:49:09 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:49:09,012 - WARNING - Could not retrieve variants from source file in region 10:323072-323473. Error was invalid region `10:323073-323473`
[2016-04-15T05:49Z] 2016-04-14 22:49:11 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:49:11,334 - WARNING - Could not retrieve variants from source file in region 10:7679182-7679583. Error was invalid region `10:7679183-7679583`
[2016-04-15T05:49Z] 2016-04-14 22:49:12 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:49:12,360 - WARNING - Could not retrieve variants from source file in region 10:5567155-5567885. Error was invalid region `10:5567156-5567885`
[2016-04-15T05:49Z] 2016-04-14 22:49:14 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:49:14,242 - WARNING - Could not retrieve variants from source file in region 10:294742-295730. Error was invalid region `10:294743-295730`
[2016-04-15T05:49Z] 2016-04-14 22:49:14 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:49:14,724 - WARNING - Could not retrieve variants from source file in region 10:13275342-13275743. Error was invalid region `10:13275343-13275743`
[2016-04-15T05:49Z] 2016-04-14 22:49:17 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:49:17,341 - WARNING - Could not retrieve variants from source file in region 10:5919910-5936615. Error was invalid region `10:5919911-5936615`
[2016-04-15T05:49Z] 2016-04-14 22:49:17 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:49:17,342 - WARNING - Could not retrieve variants from source file in region 10:7679182-7679583. Error was invalid region `10:7679183-7679583`
[2016-04-15T05:49Z] 2016-04-14 22:49:19 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:49:19,114 - WARNING - Could not retrieve variants from source file in region 10:294742-295730. Error was invalid region `10:294743-295730`
[2016-04-15T05:49Z] 2016-04-14 22:49:19 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:49:19,197 - WARNING - Could not retrieve variants from source file in region 10:13275342-13275743. Error was invalid region `10:13275343-13275743`
[2016-04-15T05:49Z] 2016-04-14 22:49:21 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:49:21,571 - WARNING - Could not retrieve variants from source file in region 10:5919910-5936615. Error was invalid region `10:5919911-5936615`
[2016-04-15T05:49Z] 2016-04-14 22:49:22 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:49:22,244 - WARNING - Could not retrieve variants from source file in region 10:5241953-5260872. Error was invalid region `10:5241954-5260872`
[2016-04-15T05:49Z] 2016-04-14 22:49:22 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:49:22,614 - WARNING - Could not retrieve variants from source file in region 10:93392-94216. Error was invalid region `10:93393-94216`
[2016-04-15T05:49Z] 2016-04-14 22:49:22 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:49:22,810 - WARNING - Could not retrieve variants from source file in region 10:13165865-13166266. Error was invalid region `10:13165866-13166266`
[2016-04-15T05:49Z] 2016-04-14 22:49:23 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:49:23,018 - WARNING - Could not retrieve variants from source file in region 10:294742-295730. Error was invalid region `10:294743-295730`
[2016-04-15T05:49Z] 2016-04-14 22:49:23 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:49:23,648 - WARNING - Could not retrieve variants from source file in region 10:13275342-13275743. Error was invalid region `10:13275343-13275743`
[2016-04-15T05:49Z] 2016-04-14 22:49:25 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:49:25,605 - WARNING - Could not retrieve variants from source file in region 10:12940244-12940645. Error was invalid region `10:12940245-12940645`
[2016-04-15T05:49Z] 2016-04-14 22:49:27 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:49:27,451 - WARNING - Could not retrieve variants from source file in region 10:5014724-5015125. Error was invalid region `10:5014725-5015125`
[2016-04-15T05:49Z] 2016-04-14 22:49:27 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:49:27,476 - WARNING - Could not retrieve variants from source file in region 10:13165865-13166266. Error was invalid region `10:13165866-13166266`
[2016-04-15T05:49Z] 2016-04-14 22:49:29 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:49:29,865 - WARNING - Could not retrieve variants from source file in region 10:12940244-12940645. Error was invalid region `10:12940245-12940645`
[2016-04-15T05:49Z] 2016-04-14 22:49:29 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:49:29,935 - WARNING - Could not retrieve variants from source file in region 10:12940244-12940645. Error was invalid region `10:12940245-12940645`
[2016-04-15T05:49Z] 2016-04-14 22:49:30 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:49:30,923 - WARNING - Could not retrieve variants from source file in region 10:5241953-5260872. Error was invalid region `10:5241954-5260872`
[2016-04-15T05:49Z] 2016-04-14 22:49:32 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:49:32,192 - WARNING - Could not retrieve variants from source file in region 10:13165865-13166266. Error was invalid region `10:13165866-13166266`
[2016-04-15T05:49Z] 2016-04-14 22:49:36 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:49:36,328 - WARNING - Could not retrieve variants from source file in region 10:13230704-13234546. Error was invalid region `10:13230705-13234546`
[2016-04-15T05:49Z] ['bcbio-variation-recall', 'square', '-Xms750m', '-Xmx7280m', '-XX:+UseSerialGC', '-c', 16, '-r', u'10:15561289-31134502', '--caller', 'platypus', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/10/Batch1-10_15561288_31134502.vcf.gz', '/mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/10/Batch1-10_15561288_31134502.vcf-inputs.txt'] in region: 10:15561289-31134502
[2016-04-15T05:49Z] 2016-04-14 22:49:53 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:49:53,668 - WARNING - Could not retrieve variants from source file in region 10:28378547-28378948. Error was invalid region `10:28378548-28378948`
[2016-04-15T05:49Z] 2016-04-14 22:49:54 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:49:54,284 - WARNING - Could not retrieve variants from source file in region 10:24873158-24879977. Error was invalid region `10:24873159-24879977`
[2016-04-15T05:49Z] 2016-04-14 22:49:54 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:49:54,728 - WARNING - Could not retrieve variants from source file in region 10:27369472-27389387. Error was invalid region `10:27369473-27389387`
[2016-04-15T05:49Z] 2016-04-14 22:49:54 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:49:54,882 - WARNING - Could not retrieve variants from source file in region 10:23728648-23729049. Error was invalid region `10:23728649-23729049`
[2016-04-15T05:49Z] 2016-04-14 22:49:55 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:49:55,327 - WARNING - Could not retrieve variants from source file in region 10:26355695-26357938. Error was invalid region `10:26355696-26357938`
[2016-04-15T05:49Z] 2016-04-14 22:49:55 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:49:55,484 - WARNING - Could not retrieve variants from source file in region 10:26559360-26559761. Error was invalid region `10:26559361-26559761`
[2016-04-15T05:49Z] 2016-04-14 22:49:55 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:49:55,896 - WARNING - Could not retrieve variants from source file in region 10:19416970-19425894. Error was invalid region `10:19416971-19425894`
[2016-04-15T05:49Z] 2016-04-14 22:49:55 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:49:55,907 - WARNING - Could not retrieve variants from source file in region 10:25887969-25888370. Error was invalid region `10:25887970-25888370`
[2016-04-15T05:49Z] 2016-04-14 22:49:55 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:49:55,929 - WARNING - Could not retrieve variants from source file in region 10:26513257-26513658. Error was invalid region `10:26513258-26513658`
[2016-04-15T05:50Z] 2016-04-14 22:50:01 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:50:01,312 - WARNING - Could not retrieve variants from source file in region 10:28378547-28378948. Error was invalid region `10:28378548-28378948`
[2016-04-15T05:50Z] 2016-04-14 22:50:03 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:50:03,607 - WARNING - Could not retrieve variants from source file in region 10:31134003-31134404. Error was invalid region `10:31134004-31134404`
[2016-04-15T05:50Z] 2016-04-14 22:50:04 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:50:04,943 - WARNING - Could not retrieve variants from source file in region 10:25887969-25888370. Error was invalid region `10:25887970-25888370`
[2016-04-15T05:50Z] 2016-04-14 22:50:05 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:50:05,509 - WARNING - Could not retrieve variants from source file in region 10:26355695-26357938. Error was invalid region `10:26355696-26357938`
[2016-04-15T05:50Z] 2016-04-14 22:50:06 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:50:06,009 - WARNING - Could not retrieve variants from source file in region 10:29747010-29784262. Error was invalid region `10:29747011-29784262`
[2016-04-15T05:50Z] 2016-04-14 22:50:06 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:50:06,125 - WARNING - Could not retrieve variants from source file in region 10:19416970-19425894. Error was invalid region `10:19416971-19425894`
[2016-04-15T05:50Z] 2016-04-14 22:50:06 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:50:06,390 - WARNING - Could not retrieve variants from source file in region 10:28378547-28378948. Error was invalid region `10:28378548-28378948`
[2016-04-15T05:50Z] 2016-04-14 22:50:06 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:50:06,861 - WARNING - Could not retrieve variants from source file in region 10:24873158-24879977. Error was invalid region `10:24873159-24879977`
[2016-04-15T05:50Z] 2016-04-14 22:50:10 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:50:10,759 - WARNING - Could not retrieve variants from source file in region 10:25887969-25888370. Error was invalid region `10:25887970-25888370`
[2016-04-15T05:50Z] 2016-04-14 22:50:12 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:50:12,377 - WARNING - Could not retrieve variants from source file in region 10:23728648-23729049. Error was invalid region `10:23728649-23729049`
[2016-04-15T05:50Z] 2016-04-14 22:50:13 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:50:13,006 - WARNING - Could not retrieve variants from source file in region 10:19416970-19425894. Error was invalid region `10:19416971-19425894`
[2016-04-15T05:50Z] 2016-04-14 22:50:13 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:50:13,013 - WARNING - Could not retrieve variants from source file in region 10:29747010-29784262. Error was invalid region `10:29747011-29784262`
[2016-04-15T05:50Z] 2016-04-14 22:50:24 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:50:24,571 - WARNING - Could not retrieve variants from source file in region 10:24790182-24833327. Error was invalid region `10:24790183-24833327`
[2016-04-15T05:50Z] 2016-04-14 22:50:25 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:50:25,369 - WARNING - Could not retrieve variants from source file in region 10:30901545-30901946. Error was invalid region `10:30901546-30901946`
[2016-04-15T05:50Z] 2016-04-14 22:50:26 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:50:26,218 - WARNING - Could not retrieve variants from source file in region 10:23482424-23482825. Error was invalid region `10:23482425-23482825`
[2016-04-15T05:50Z] 2016-04-14 22:50:26 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:50:26,644 - WARNING - Could not retrieve variants from source file in region 10:26310259-26310696. Error was invalid region `10:26310260-26310696`
[2016-04-15T05:50Z] 2016-04-14 22:50:26 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:50:26,770 - WARNING - Could not retrieve variants from source file in region 10:17113352-17113753. Error was invalid region `10:17113353-17113753`
[2016-04-15T05:50Z] 2016-04-14 22:50:26 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:50:26,854 - WARNING - Could not retrieve variants from source file in region 10:28228654-28229055. Error was invalid region `10:28228655-28229055`
[2016-04-15T05:50Z] 2016-04-14 22:50:27 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:50:27,179 - WARNING - Could not retrieve variants from source file in region 10:25701130-25701531. Error was invalid region `10:25701131-25701531`
[2016-04-15T05:50Z] 2016-04-14 22:50:29 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:50:29,042 - WARNING - Could not retrieve variants from source file in region 10:28346373-28346819. Error was invalid region `10:28346374-28346819`
[2016-04-15T05:50Z] 2016-04-14 22:50:29 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:50:29,393 - WARNING - Could not retrieve variants from source file in region 10:23633355-23633756. Error was invalid region `10:23633356-23633756`
[2016-04-15T05:50Z] 2016-04-14 22:50:29 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:50:29,947 - WARNING - Could not retrieve variants from source file in region 10:30901545-30901946. Error was invalid region `10:30901546-30901946`
[2016-04-15T05:50Z] 2016-04-14 22:50:30 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:50:30,533 - WARNING - Could not retrieve variants from source file in region 10:29577873-29578274. Error was invalid region `10:29577874-29578274`
[2016-04-15T05:50Z] 2016-04-14 22:50:31 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:50:31,050 - WARNING - Could not retrieve variants from source file in region 10:23482424-23482825. Error was invalid region `10:23482425-23482825`
[2016-04-15T05:50Z] 2016-04-14 22:50:31 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:50:31,150 - WARNING - Could not retrieve variants from source file in region 10:23003015-23003416. Error was invalid region `10:23003016-23003416`
[2016-04-15T05:50Z] 2016-04-14 22:50:32 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:50:32,180 - WARNING - Could not retrieve variants from source file in region 10:28228654-28229055. Error was invalid region `10:28228655-28229055`
[2016-04-15T05:50Z] 2016-04-14 22:50:32 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:50:32,306 - WARNING - Could not retrieve variants from source file in region 10:25701130-25701531. Error was invalid region `10:25701131-25701531`
[2016-04-15T05:50Z] 2016-04-14 22:50:33 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:50:33,383 - WARNING - Could not retrieve variants from source file in region 10:28346373-28346819. Error was invalid region `10:28346374-28346819`
[2016-04-15T05:50Z] 2016-04-14 22:50:33 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:50:33,904 - WARNING - Could not retrieve variants from source file in region 10:23633355-23633756. Error was invalid region `10:23633356-23633756`
[2016-04-15T05:50Z] 2016-04-14 22:50:34 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:50:34,236 - WARNING - Could not retrieve variants from source file in region 10:30901545-30901946. Error was invalid region `10:30901546-30901946`
[2016-04-15T05:50Z] 2016-04-14 22:50:34 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:50:34,742 - WARNING - Could not retrieve variants from source file in region 10:29577873-29578274. Error was invalid region `10:29577874-29578274`
[2016-04-15T05:50Z] 2016-04-14 22:50:35 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:50:35,459 - WARNING - Could not retrieve variants from source file in region 10:23482424-23482825. Error was invalid region `10:23482425-23482825`
[2016-04-15T05:50Z] 2016-04-14 22:50:35 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:50:35,751 - WARNING - Could not retrieve variants from source file in region 10:23003015-23003416. Error was invalid region `10:23003016-23003416`
[2016-04-15T05:50Z] 2016-04-14 22:50:37 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:50:37,127 - WARNING - Could not retrieve variants from source file in region 10:28228654-28229055. Error was invalid region `10:28228655-28229055`
[2016-04-15T05:50Z] 2016-04-14 22:50:37 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:50:37,291 - WARNING - Could not retrieve variants from source file in region 10:17113352-17113753. Error was invalid region `10:17113353-17113753`
[2016-04-15T05:50Z] 2016-04-14 22:50:37 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:50:37,580 - WARNING - Could not retrieve variants from source file in region 10:18939946-18940987. Error was invalid region `10:18939947-18940987`
[2016-04-15T05:50Z] 2016-04-14 22:50:37 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:50:37,654 - WARNING - Could not retrieve variants from source file in region 10:25701130-25701531. Error was invalid region `10:25701131-25701531`
[2016-04-15T05:50Z] 2016-04-14 22:50:38 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:50:38,251 - WARNING - Could not retrieve variants from source file in region 10:23633355-23633756. Error was invalid region `10:23633356-23633756`
[2016-04-15T05:50Z] 2016-04-14 22:50:40 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:50:40,158 - WARNING - Could not retrieve variants from source file in region 10:23003015-23003416. Error was invalid region `10:23003016-23003416`
[2016-04-15T05:50Z] 2016-04-14 22:50:42 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:50:42,609 - WARNING - Could not retrieve variants from source file in region 10:18939946-18940987. Error was invalid region `10:18939947-18940987`
[2016-04-15T05:50Z] 2016-04-14 22:50:47 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:50:47,554 - WARNING - Could not retrieve variants from source file in region 10:24755412-24762655. Error was invalid region `10:24755413-24762655`
[2016-04-15T05:50Z] 2016-04-14 22:50:48 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:50:48,946 - WARNING - Could not retrieve variants from source file in region 10:30723382-30728291. Error was invalid region `10:30723383-30728291`
[2016-04-15T05:50Z] 2016-04-14 22:50:49 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:50:49,131 - WARNING - Could not retrieve variants from source file in region 10:23408067-23408468. Error was invalid region `10:23408068-23408468`
[2016-04-15T05:50Z] 2016-04-14 22:50:50 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:50:50,644 - WARNING - Could not retrieve variants from source file in region 10:25312478-25314008. Error was invalid region `10:25312479-25314008`
[2016-04-15T05:50Z] 2016-04-14 22:50:50 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:50:50,820 - WARNING - Could not retrieve variants from source file in region 10:20534122-20534523. Error was invalid region `10:20534123-20534523`
[2016-04-15T05:50Z] 2016-04-14 22:50:51 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:50:51,175 - WARNING - Could not retrieve variants from source file in region 10:17024292-17024805. Error was invalid region `10:17024293-17024805`
[2016-04-15T05:50Z] 2016-04-14 22:50:51 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:50:51,803 - WARNING - Could not retrieve variants from source file in region 10:24908475-24908876. Error was invalid region `10:24908476-24908876`
[2016-04-15T05:50Z] 2016-04-14 22:50:53 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:50:53,468 - WARNING - Could not retrieve variants from source file in region 10:24721735-24722136. Error was invalid region `10:24721736-24722136`
[2016-04-15T05:50Z] 2016-04-14 22:50:53 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:50:53,980 - WARNING - Could not retrieve variants from source file in region 10:23408067-23408468. Error was invalid region `10:23408068-23408468`
[2016-04-15T05:50Z] 2016-04-14 22:50:53 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:50:53,986 - WARNING - Could not retrieve variants from source file in region 10:22839417-22839818. Error was invalid region `10:22839418-22839818`
[2016-04-15T05:50Z] 2016-04-14 22:50:55 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:50:55,493 - WARNING - Could not retrieve variants from source file in region 10:20534122-20534523. Error was invalid region `10:20534123-20534523`
[2016-04-15T05:50Z] 2016-04-14 22:50:55 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:50:55,858 - WARNING - Could not retrieve variants from source file in region 10:30629015-30638257. Error was invalid region `10:30629016-30638257`
[2016-04-15T05:50Z] 2016-04-14 22:50:55 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:50:55,983 - WARNING - Could not retrieve variants from source file in region 10:17024292-17024805. Error was invalid region `10:17024293-17024805`
[2016-04-15T05:50Z] 2016-04-14 22:50:56 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:50:56,703 - WARNING - Could not retrieve variants from source file in region 10:18828160-18828825. Error was invalid region `10:18828161-18828825`
[2016-04-15T05:50Z] 2016-04-14 22:50:57 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:50:57,822 - WARNING - Could not retrieve variants from source file in region 10:23408067-23408468. Error was invalid region `10:23408068-23408468`
[2016-04-15T05:50Z] 2016-04-14 22:50:59 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:50:59,876 - WARNING - Could not retrieve variants from source file in region 10:20534122-20534523. Error was invalid region `10:20534123-20534523`
[2016-04-15T05:51Z] 2016-04-14 22:51:00 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:51:00,029 - WARNING - Could not retrieve variants from source file in region 10:25312478-25314008. Error was invalid region `10:25312479-25314008`
[2016-04-15T05:51Z] 2016-04-14 22:51:00 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:51:00,272 - WARNING - Could not retrieve variants from source file in region 10:17024292-17024805. Error was invalid region `10:17024293-17024805`
[2016-04-15T05:51Z] 2016-04-14 22:51:01 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:51:01,358 - WARNING - Could not retrieve variants from source file in region 10:24908475-24908876. Error was invalid region `10:24908476-24908876`
[2016-04-15T05:51Z] 2016-04-14 22:51:03 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:51:03,146 - WARNING - Could not retrieve variants from source file in region 10:18242093-18267179. Error was invalid region `10:18242094-18267179`
[2016-04-15T05:51Z] 2016-04-14 22:51:03 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:51:03,242 - WARNING - Could not retrieve variants from source file in region 10:22839417-22839818. Error was invalid region `10:22839418-22839818`
[2016-04-15T05:51Z] 2016-04-14 22:51:07 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:51:07,233 - WARNING - Could not retrieve variants from source file in region 10:19678286-19678687. Error was invalid region `10:19678287-19678687`
[2016-04-15T05:51Z] 2016-04-14 22:51:11 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:51:11,362 - WARNING - Could not retrieve variants from source file in region 10:15649487-15649888. Error was invalid region `10:15649488-15649888`
[2016-04-15T05:51Z] 2016-04-14 22:51:11 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:51:11,456 - WARNING - Could not retrieve variants from source file in region 10:16546847-16547248. Error was invalid region `10:16546848-16547248`
[2016-04-15T05:51Z] 2016-04-14 22:51:11 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:51:11,765 - WARNING - Could not retrieve variants from source file in region 10:19678286-19678687. Error was invalid region `10:19678287-19678687`
[2016-04-15T05:51Z] 2016-04-14 22:51:12 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:51:12,796 - WARNING - Could not retrieve variants from source file in region 10:18689375-18689828. Error was invalid region `10:18689376-18689828`
[2016-04-15T05:51Z] 2016-04-14 22:51:13 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:51:13,112 - WARNING - Could not retrieve variants from source file in region 10:20506207-20506608. Error was invalid region `10:20506208-20506608`
[2016-04-15T05:51Z] 2016-04-14 22:51:13 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:51:13,457 - WARNING - Could not retrieve variants from source file in region 10:22027178-22048520. Error was invalid region `10:22027179-22048520`
[2016-04-15T05:51Z] 2016-04-14 22:51:13 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:51:13,652 - WARNING - Could not retrieve variants from source file in region 10:16918786-16967776. Error was invalid region `10:16918787-16967776`
[2016-04-15T05:51Z] 2016-04-14 22:51:14 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:51:14,125 - WARNING - Could not retrieve variants from source file in region 10:22497998-22498939. Error was invalid region `10:22497999-22498939`
[2016-04-15T05:51Z] 2016-04-14 22:51:16 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:51:16,346 - WARNING - Could not retrieve variants from source file in region 10:16546847-16547248. Error was invalid region `10:16546848-16547248`
[2016-04-15T05:51Z] 2016-04-14 22:51:16 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:51:16,562 - WARNING - Could not retrieve variants from source file in region 10:18689375-18689828. Error was invalid region `10:18689376-18689828`
[2016-04-15T05:51Z] 2016-04-14 22:51:16 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:51:16,758 - WARNING - Could not retrieve variants from source file in region 10:15761559-15761964. Error was invalid region `10:15761560-15761964`
[2016-04-15T05:51Z] 2016-04-14 22:51:17 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:51:17,121 - WARNING - Could not retrieve variants from source file in region 10:19492491-19498468. Error was invalid region `10:19492492-19498468`
[2016-04-15T05:51Z] 2016-04-14 22:51:17 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:51:17,277 - WARNING - Could not retrieve variants from source file in region 10:17636098-17659339. Error was invalid region `10:17636099-17659339`
[2016-04-15T05:51Z] 2016-04-14 22:51:17 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:51:17,496 - WARNING - Could not retrieve variants from source file in region 10:19678286-19678687. Error was invalid region `10:19678287-19678687`
[2016-04-15T05:51Z] 2016-04-14 22:51:17 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:51:17,877 - WARNING - Could not retrieve variants from source file in region 10:20506207-20506608. Error was invalid region `10:20506208-20506608`
[2016-04-15T05:51Z] 2016-04-14 22:51:18 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:51:18,858 - WARNING - Could not retrieve variants from source file in region 10:22497998-22498939. Error was invalid region `10:22497999-22498939`
[2016-04-15T05:51Z] 2016-04-14 22:51:20 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:51:20,367 - WARNING - Could not retrieve variants from source file in region 10:15649487-15649888. Error was invalid region `10:15649488-15649888`
[2016-04-15T05:51Z] 2016-04-14 22:51:20 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:51:20,415 - WARNING - Could not retrieve variants from source file in region 10:17186236-17216746. Error was invalid region `10:17186237-17216746`
[2016-04-15T05:51Z] 2016-04-14 22:51:20 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:51:20,715 - WARNING - Could not retrieve variants from source file in region 10:16546847-16547248. Error was invalid region `10:16546848-16547248`
[2016-04-15T05:51Z] 2016-04-14 22:51:21 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:51:21,092 - WARNING - Could not retrieve variants from source file in region 10:15761559-15761964. Error was invalid region `10:15761560-15761964`
[2016-04-15T05:51Z] 2016-04-14 22:51:22 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:51:22,066 - WARNING - Could not retrieve variants from source file in region 10:20506207-20506608. Error was invalid region `10:20506208-20506608`
[2016-04-15T05:51Z] 2016-04-14 22:51:23 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:51:23,451 - WARNING - Could not retrieve variants from source file in region 10:16918786-16967776. Error was invalid region `10:16918787-16967776`
[2016-04-15T05:51Z] 2016-04-14 22:51:24 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:51:24,873 - WARNING - Could not retrieve variants from source file in region 10:16882307-16882708. Error was invalid region `10:16882308-16882708`
[2016-04-15T05:51Z] 2016-04-14 22:51:29 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:51:29,964 - WARNING - Could not retrieve variants from source file in region 10:19620196-19641225. Error was invalid region `10:19620197-19641225`
[2016-04-15T05:51Z] 2016-04-14 22:51:30 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:51:30,121 - WARNING - Could not retrieve variants from source file in region 10:16882307-16882708. Error was invalid region `10:16882308-16882708`
[2016-04-15T05:51Z] 2016-04-14 22:51:31 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:51:31,679 - WARNING - Could not retrieve variants from source file in region 10:16882307-16882708. Error was invalid region `10:16882308-16882708`
[2016-04-15T05:51Z] 2016-04-14 22:51:33 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:51:33,191 - WARNING - Could not retrieve variants from source file in region 10:17147310-17156341. Error was invalid region `10:17147311-17156341`
[2016-04-15T05:51Z] 2016-04-14 22:51:33 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:51:33,243 - WARNING - Could not retrieve variants from source file in region 10:15572839-15573240. Error was invalid region `10:15572840-15573240`
[2016-04-15T05:51Z] 2016-04-14 22:51:34 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:51:34,256 - WARNING - Could not retrieve variants from source file in region 10:17147310-17156341. Error was invalid region `10:17147311-17156341`
[2016-04-15T05:51Z] 2016-04-14 22:51:34 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:51:34,405 - WARNING - Could not retrieve variants from source file in region 10:15572839-15573240. Error was invalid region `10:15572840-15573240`
[2016-04-15T05:51Z] 2016-04-14 22:51:34 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:51:34,541 - WARNING - Could not retrieve variants from source file in region 10:19620196-19641225. Error was invalid region `10:19620197-19641225`
[2016-04-15T05:51Z] 2016-04-14 22:51:34 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:51:34,789 - WARNING - Could not retrieve variants from source file in region 10:19884053-19897020. Error was invalid region `10:19884054-19897020`
[2016-04-15T05:51Z] 2016-04-14 22:51:35 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:51:35,304 - WARNING - Could not retrieve variants from source file in region 10:19454504-19454905. Error was invalid region `10:19454505-19454905`
[2016-04-15T05:51Z] 2016-04-14 22:51:35 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:51:35,593 - WARNING - Could not retrieve variants from source file in region 10:21805255-21827986. Error was invalid region `10:21805256-21827986`
[2016-04-15T05:51Z] 2016-04-14 22:51:37 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:51:37,222 - WARNING - Could not retrieve variants from source file in region 10:17147310-17156341. Error was invalid region `10:17147311-17156341`
[2016-04-15T05:51Z] 2016-04-14 22:51:37 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:51:37,261 - WARNING - Could not retrieve variants from source file in region 10:15572839-15573240. Error was invalid region `10:15572840-15573240`
[2016-04-15T05:51Z] 2016-04-14 22:51:38 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:51:38,004 - WARNING - Could not retrieve variants from source file in region 10:19780252-19787608. Error was invalid region `10:19780253-19787608`
[2016-04-15T05:51Z] 2016-04-14 22:51:38 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:51:38,447 - WARNING - Could not retrieve variants from source file in region 10:21134071-21139579. Error was invalid region `10:21134072-21139579`
[2016-04-15T05:51Z] 2016-04-14 22:51:38 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:51:38,729 - WARNING - Could not retrieve variants from source file in region 10:19884053-19897020. Error was invalid region `10:19884054-19897020`
[2016-04-15T05:51Z] 2016-04-14 22:51:38 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:51:38,801 - WARNING - Could not retrieve variants from source file in region 10:19620196-19641225. Error was invalid region `10:19620197-19641225`
[2016-04-15T05:51Z] 2016-04-14 22:51:39 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:51:39,603 - WARNING - Could not retrieve variants from source file in region 10:21805255-21827986. Error was invalid region `10:21805256-21827986`
[2016-04-15T05:51Z] 2016-04-14 22:51:41 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:51:41,490 - WARNING - Could not retrieve variants from source file in region 10:19780252-19787608. Error was invalid region `10:19780253-19787608`
[2016-04-15T05:51Z] 2016-04-14 22:51:42 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:51:42,095 - WARNING - Could not retrieve variants from source file in region 10:19884053-19897020. Error was invalid region `10:19884054-19897020`
[2016-04-15T05:51Z] 2016-04-14 22:51:43 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:51:43,155 - WARNING - Could not retrieve variants from source file in region 10:21805255-21827986. Error was invalid region `10:21805256-21827986`
[2016-04-15T05:51Z] 2016-04-14 22:51:46 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:51:46,611 - WARNING - Could not retrieve variants from source file in region 10:21108166-21108567. Error was invalid region `10:21108167-21108567`
[2016-04-15T05:51Z] 2016-04-14 22:51:46 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:51:46,712 - WARNING - Could not retrieve variants from source file in region 10:21108166-21108567. Error was invalid region `10:21108167-21108567`
[2016-04-15T05:51Z] ['bcbio-variation-recall', 'square', '-Xms750m', '-Xmx7280m', '-XX:+UseSerialGC', '-c', 16, '-r', u'10:31137460-46960129', '--caller', 'platypus', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/10/Batch1-10_31137459_46960129.vcf.gz', '/mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/10/Batch1-10_31137459_46960129.vcf-inputs.txt'] in region: 10:31137460-46960129
[2016-04-15T05:52Z] 2016-04-14 22:52:02 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:52:02,041 - WARNING - Could not retrieve variants from source file in region 10:45953556-45959071. Error was invalid region `10:45953557-45959071`
[2016-04-15T05:52Z] 2016-04-14 22:52:02 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:52:02,843 - WARNING - Could not retrieve variants from source file in region 10:45430251-45430652. Error was invalid region `10:45430252-45430652`
[2016-04-15T05:52Z] 2016-04-14 22:52:04 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:52:04,222 - WARNING - Could not retrieve variants from source file in region 10:44103890-44104291. Error was invalid region `10:44103891-44104291`
[2016-04-15T05:52Z] 2016-04-14 22:52:04 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:52:04,650 - WARNING - Could not retrieve variants from source file in region 10:32745051-32745452. Error was invalid region `10:32745052-32745452`
[2016-04-15T05:52Z] 2016-04-14 22:52:05 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:52:05,477 - WARNING - Could not retrieve variants from source file in region 10:46245346-46245747. Error was invalid region `10:46245347-46245747`
[2016-04-15T05:52Z] 2016-04-14 22:52:05 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:52:05,492 - WARNING - Could not retrieve variants from source file in region 10:37890744-37891145. Error was invalid region `10:37890745-37891145`
[2016-04-15T05:52Z] 2016-04-14 22:52:06 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:52:06,011 - WARNING - Could not retrieve variants from source file in region 10:32974758-32975159. Error was invalid region `10:32974759-32975159`
[2016-04-15T05:52Z] 2016-04-14 22:52:06 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:52:06,156 - WARNING - Could not retrieve variants from source file in region 10:33510452-33510958. Error was invalid region `10:33510453-33510958`
[2016-04-15T05:52Z] 2016-04-14 22:52:06 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:52:06,568 - WARNING - Could not retrieve variants from source file in region 10:44052692-44059866. Error was invalid region `10:44052693-44059866`
[2016-04-15T05:52Z] 2016-04-14 22:52:06 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:52:06,793 - WARNING - Could not retrieve variants from source file in region 10:45953556-45959071. Error was invalid region `10:45953557-45959071`
[2016-04-15T05:52Z] 2016-04-14 22:52:11 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:52:11,151 - WARNING - Could not retrieve variants from source file in region 10:33209055-33214992. Error was invalid region `10:33209056-33214992`
[2016-04-15T05:52Z] 2016-04-14 22:52:12 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:52:12,412 - WARNING - Could not retrieve variants from source file in region 10:37890744-37891145. Error was invalid region `10:37890745-37891145`
[2016-04-15T05:52Z] 2016-04-14 22:52:13 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:52:13,342 - WARNING - Could not retrieve variants from source file in region 10:35896917-35897319. Error was invalid region `10:35896918-35897319`
[2016-04-15T05:52Z] 2016-04-14 22:52:13 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:52:13,428 - WARNING - Could not retrieve variants from source file in region 10:46245346-46245747. Error was invalid region `10:46245347-46245747`
[2016-04-15T05:52Z] 2016-04-14 22:52:13 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:52:13,934 - WARNING - Could not retrieve variants from source file in region 10:32579994-32580395. Error was invalid region `10:32579995-32580395`
[2016-04-15T05:52Z] 2016-04-14 22:52:14 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:52:14,036 - WARNING - Could not retrieve variants from source file in region 10:32974758-32975159. Error was invalid region `10:32974759-32975159`
[2016-04-15T05:52Z] 2016-04-14 22:52:14 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:52:14,153 - WARNING - Could not retrieve variants from source file in region 10:43650704-43704827. Error was invalid region `10:43650705-43704827`
[2016-04-15T05:52Z] 2016-04-14 22:52:14 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:52:14,553 - WARNING - Could not retrieve variants from source file in region 10:33510452-33510958. Error was invalid region `10:33510453-33510958`
[2016-04-15T05:52Z] 2016-04-14 22:52:14 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:52:14,595 - WARNING - Could not retrieve variants from source file in region 10:43595757-43623123. Error was invalid region `10:43595758-43623123`
[2016-04-15T05:52Z] 2016-04-14 22:52:14 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:52:14,644 - WARNING - Could not retrieve variants from source file in region 10:45430251-45430652. Error was invalid region `10:45430252-45430652`
[2016-04-15T05:52Z] 2016-04-14 22:52:14 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:52:14,656 - WARNING - Could not retrieve variants from source file in region 10:44052692-44059866. Error was invalid region `10:44052693-44059866`
[2016-04-15T05:52Z] 2016-04-14 22:52:14 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:52:14,932 - WARNING - Could not retrieve variants from source file in region 10:45953556-45959071. Error was invalid region `10:45953557-45959071`
[2016-04-15T05:52Z] 2016-04-14 22:52:15 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:52:15,123 - WARNING - Could not retrieve variants from source file in region 10:44103890-44104291. Error was invalid region `10:44103891-44104291`
[2016-04-15T05:52Z] 2016-04-14 22:52:15 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:52:15,720 - WARNING - Could not retrieve variants from source file in region 10:33209055-33214992. Error was invalid region `10:33209056-33214992`
[2016-04-15T05:52Z] 2016-04-14 22:52:19 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:52:19,880 - WARNING - Could not retrieve variants from source file in region 10:46245346-46245747. Error was invalid region `10:46245347-46245747`
[2016-04-15T05:52Z] 2016-04-14 22:52:20 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:52:20,304 - WARNING - Could not retrieve variants from source file in region 10:32579994-32580395. Error was invalid region `10:32579995-32580395`
[2016-04-15T05:52Z] 2016-04-14 22:52:21 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:52:21,850 - WARNING - Could not retrieve variants from source file in region 10:33510452-33510958. Error was invalid region `10:33510453-33510958`
[2016-04-15T05:52Z] 2016-04-14 22:52:22 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:52:22,046 - WARNING - Could not retrieve variants from source file in region 10:32974758-32975159. Error was invalid region `10:32974759-32975159`
[2016-04-15T05:52Z] 2016-04-14 22:52:33 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:52:33,261 - WARNING - Could not retrieve variants from source file in region 10:38118690-38119091. Error was invalid region `10:38118691-38119091`
[2016-04-15T05:52Z] 2016-04-14 22:52:33 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:52:33,971 - WARNING - Could not retrieve variants from source file in region 10:45869537-45869938. Error was invalid region `10:45869538-45869938`
[2016-04-15T05:52Z] 2016-04-14 22:52:35 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:52:35,175 - WARNING - Could not retrieve variants from source file in region 10:33123563-33143586. Error was invalid region `10:33123564-33143586`
[2016-04-15T05:52Z] 2016-04-14 22:52:35 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:52:35,344 - WARNING - Could not retrieve variants from source file in region 10:35772191-35772592. Error was invalid region `10:35772192-35772592`
[2016-04-15T05:52Z] 2016-04-14 22:52:35 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:52:35,667 - WARNING - Could not retrieve variants from source file in region 10:32635760-32636161. Error was invalid region `10:32635761-32636161`
[2016-04-15T05:52Z] 2016-04-14 22:52:35 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:52:35,775 - WARNING - Could not retrieve variants from source file in region 10:46143747-46144148. Error was invalid region `10:46143748-46144148`
[2016-04-15T05:52Z] 2016-04-14 22:52:35 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:52:35,799 - WARNING - Could not retrieve variants from source file in region 10:32120467-32141650. Error was invalid region `10:32120468-32141650`
[2016-04-15T05:52Z] 2016-04-14 22:52:37 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:52:37,387 - WARNING - Could not retrieve variants from source file in region 10:45479223-45499462. Error was invalid region `10:45479224-45499462`
[2016-04-15T05:52Z] 2016-04-14 22:52:37 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:52:37,438 - WARNING - Could not retrieve variants from source file in region 10:43089754-43090155. Error was invalid region `10:43089755-43090155`
[2016-04-15T05:52Z] 2016-04-14 22:52:37 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:52:37,872 - WARNING - Could not retrieve variants from source file in region 10:38118690-38119091. Error was invalid region `10:38118691-38119091`
[2016-04-15T05:52Z] 2016-04-14 22:52:38 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:52:38,876 - WARNING - Could not retrieve variants from source file in region 10:45869537-45869938. Error was invalid region `10:45869538-45869938`
[2016-04-15T05:52Z] 2016-04-14 22:52:40 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:52:40,197 - WARNING - Could not retrieve variants from source file in region 10:35772191-35772592. Error was invalid region `10:35772192-35772592`
[2016-04-15T05:52Z] 2016-04-14 22:52:40 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:52:40,713 - WARNING - Could not retrieve variants from source file in region 10:33468970-33474834. Error was invalid region `10:33468971-33474834`
[2016-04-15T05:52Z] 2016-04-14 22:52:40 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:52:40,714 - WARNING - Could not retrieve variants from source file in region 10:46143747-46144148. Error was invalid region `10:46143748-46144148`
[2016-04-15T05:52Z] 2016-04-14 22:52:40 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:52:40,775 - WARNING - Could not retrieve variants from source file in region 10:33123563-33143586. Error was invalid region `10:33123564-33143586`
[2016-04-15T05:52Z] 2016-04-14 22:52:40 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:52:40,794 - WARNING - Could not retrieve variants from source file in region 10:32635760-32636161. Error was invalid region `10:32635761-32636161`
[2016-04-15T05:52Z] 2016-04-14 22:52:41 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:52:41,516 - WARNING - Could not retrieve variants from source file in region 10:31137356-31146833. Error was invalid region `10:31137357-31146833`
[2016-04-15T05:52Z] 2016-04-14 22:52:42 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:52:42,223 - WARNING - Could not retrieve variants from source file in region 10:43089754-43090155. Error was invalid region `10:43089755-43090155`
[2016-04-15T05:52Z] 2016-04-14 22:52:44 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:52:44,963 - WARNING - Could not retrieve variants from source file in region 10:35772191-35772592. Error was invalid region `10:35772192-35772592`
[2016-04-15T05:52Z] 2016-04-14 22:52:45 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:52:45,338 - WARNING - Could not retrieve variants from source file in region 10:46143747-46144148. Error was invalid region `10:46143748-46144148`
[2016-04-15T05:52Z] 2016-04-14 22:52:45 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:52:45,625 - WARNING - Could not retrieve variants from source file in region 10:33123563-33143586. Error was invalid region `10:33123564-33143586`
[2016-04-15T05:52Z] 2016-04-14 22:52:45 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:52:45,633 - WARNING - Could not retrieve variants from source file in region 10:32635760-32636161. Error was invalid region `10:32635761-32636161`
[2016-04-15T05:52Z] 2016-04-14 22:52:46 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:52:46,961 - WARNING - Could not retrieve variants from source file in region 10:45479223-45499462. Error was invalid region `10:45479224-45499462`
[2016-04-15T05:52Z] 2016-04-14 22:52:47 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:52:47,551 - WARNING - Could not retrieve variants from source file in region 10:43089754-43090155. Error was invalid region `10:43089755-43090155`
[2016-04-15T05:52Z] 2016-04-14 22:52:57 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:52:57,046 - WARNING - Could not retrieve variants from source file in region 10:35484738-35485139. Error was invalid region `10:35484739-35485139`
[2016-04-15T05:52Z] 2016-04-14 22:52:58 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:52:58,031 - WARNING - Could not retrieve variants from source file in region 10:38405883-38407709. Error was invalid region `10:38405884-38407709`
[2016-04-15T05:52Z] 2016-04-14 22:52:58 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:52:58,248 - WARNING - Could not retrieve variants from source file in region 10:33018140-33018541. Error was invalid region `10:33018141-33018541`
[2016-04-15T05:52Z] 2016-04-14 22:52:58 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:52:58,286 - WARNING - Could not retrieve variants from source file in region 10:34620009-34634064. Error was invalid region `10:34620010-34634064`
[2016-04-15T05:52Z] 2016-04-14 22:52:58 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:52:58,674 - WARNING - Could not retrieve variants from source file in region 10:35302494-35321604. Error was invalid region `10:35302495-35321604`
[2016-04-15T05:52Z] 2016-04-14 22:52:59 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:52:59,651 - WARNING - Could not retrieve variants from source file in region 10:34408425-34408826. Error was invalid region `10:34408426-34408826`
[2016-04-15T05:52Z] 2016-04-14 22:52:59 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:52:59,721 - WARNING - Could not retrieve variants from source file in region 10:34558401-34558802. Error was invalid region `10:34558402-34558802`
[2016-04-15T05:52Z] 2016-04-14 22:52:59 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:52:59,895 - WARNING - Could not retrieve variants from source file in region 10:33623040-33623441. Error was invalid region `10:33623041-33623441`
[2016-04-15T05:53Z] 2016-04-14 22:53:01 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:53:01,015 - WARNING - Could not retrieve variants from source file in region 10:35484738-35485139. Error was invalid region `10:35484739-35485139`
[2016-04-15T05:53Z] 2016-04-14 22:53:01 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:53:01,784 - WARNING - Could not retrieve variants from source file in region 10:38405883-38407709. Error was invalid region `10:38405884-38407709`
[2016-04-15T05:53Z] 2016-04-14 22:53:02 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:53:02,201 - WARNING - Could not retrieve variants from source file in region 10:33018140-33018541. Error was invalid region `10:33018141-33018541`
[2016-04-15T05:53Z] 2016-04-14 22:53:02 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:53:02,498 - WARNING - Could not retrieve variants from source file in region 10:34671301-34688477. Error was invalid region `10:34671302-34688477`
[2016-04-15T05:53Z] 2016-04-14 22:53:02 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:53:02,506 - WARNING - Could not retrieve variants from source file in region 10:34620009-34634064. Error was invalid region `10:34620010-34634064`
[2016-04-15T05:53Z] 2016-04-14 22:53:02 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:53:02,850 - WARNING - Could not retrieve variants from source file in region 10:38344489-38346599. Error was invalid region `10:38344490-38346599`
[2016-04-15T05:53Z] 2016-04-14 22:53:03 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:53:03,595 - WARNING - Could not retrieve variants from source file in region 10:34408425-34408826. Error was invalid region `10:34408426-34408826`
[2016-04-15T05:53Z] 2016-04-14 22:53:05 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:53:05,050 - WARNING - Could not retrieve variants from source file in region 10:35484738-35485139. Error was invalid region `10:35484739-35485139`
[2016-04-15T05:53Z] 2016-04-14 22:53:05 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:53:05,745 - WARNING - Could not retrieve variants from source file in region 10:38405883-38407709. Error was invalid region `10:38405884-38407709`
[2016-04-15T05:53Z] 2016-04-14 22:53:06 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:53:06,248 - WARNING - Could not retrieve variants from source file in region 10:33018140-33018541. Error was invalid region `10:33018141-33018541`
[2016-04-15T05:53Z] 2016-04-14 22:53:06 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:53:06,730 - WARNING - Could not retrieve variants from source file in region 10:34620009-34634064. Error was invalid region `10:34620010-34634064`
[2016-04-15T05:53Z] 2016-04-14 22:53:06 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:53:06,749 - WARNING - Could not retrieve variants from source file in region 10:35302494-35321604. Error was invalid region `10:35302495-35321604`
[2016-04-15T05:53Z] 2016-04-14 22:53:07 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:53:07,014 - WARNING - Could not retrieve variants from source file in region 10:38344489-38346599. Error was invalid region `10:38344490-38346599`
[2016-04-15T05:53Z] 2016-04-14 22:53:07 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:53:07,808 - WARNING - Could not retrieve variants from source file in region 10:34408425-34408826. Error was invalid region `10:34408426-34408826`
[2016-04-15T05:53Z] 2016-04-14 22:53:14 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:53:14,790 - WARNING - Could not retrieve variants from source file in region 10:33552484-33552886. Error was invalid region `10:33552485-33552886`
[2016-04-15T05:53Z] ['bcbio-variation-recall', 'square', '-Xms750m', '-Xmx7280m', '-XX:+UseSerialGC', '-c', 16, '-r', u'10:46960411-62493077', '--caller', 'platypus', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/10/Batch1-10_46960410_62493077.vcf.gz', '/mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/10/Batch1-10_46960410_62493077.vcf-inputs.txt'] in region: 10:46960411-62493077
[2016-04-15T05:53Z] 2016-04-14 22:53:29 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:53:29,097 - WARNING - Could not retrieve variants from source file in region 10:52103496-52103897. Error was invalid region `10:52103497-52103897`
[2016-04-15T05:53Z] 2016-04-14 22:53:29 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:53:29,762 - WARNING - Could not retrieve variants from source file in region 10:51827723-51828124. Error was invalid region `10:51827724-51828124`
[2016-04-15T05:53Z] 2016-04-14 22:53:30 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:53:30,255 - WARNING - Could not retrieve variants from source file in region 10:61552481-61552964. Error was invalid region `10:61552482-61552964`
[2016-04-15T05:53Z] 2016-04-14 22:53:30 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:53:30,666 - WARNING - Could not retrieve variants from source file in region 10:61965414-61965815. Error was invalid region `10:61965415-61965815`
[2016-04-15T05:53Z] 2016-04-14 22:53:31 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:53:31,448 - WARNING - Could not retrieve variants from source file in region 10:53887659-53888060. Error was invalid region `10:53887660-53888060`
[2016-04-15T05:53Z] 2016-04-14 22:53:31 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:53:31,554 - WARNING - Could not retrieve variants from source file in region 10:61868505-61868906. Error was invalid region `10:61868506-61868906`
[2016-04-15T05:53Z] 2016-04-14 22:53:31 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:53:31,555 - WARNING - Could not retrieve variants from source file in region 10:57359486-57359887. Error was invalid region `10:57359487-57359887`
[2016-04-15T05:53Z] 2016-04-14 22:53:32 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:53:32,406 - WARNING - Could not retrieve variants from source file in region 10:49812706-49813107. Error was invalid region `10:49812707-49813107`
[2016-04-15T05:53Z] 2016-04-14 22:53:32 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:53:32,509 - WARNING - Could not retrieve variants from source file in region 10:61005033-61022493. Error was invalid region `10:61005034-61022493`
[2016-04-15T05:53Z] 2016-04-14 22:53:33 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:53:33,902 - WARNING - Could not retrieve variants from source file in region 10:52103496-52103897. Error was invalid region `10:52103497-52103897`
[2016-04-15T05:53Z] 2016-04-14 22:53:35 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:53:35,053 - WARNING - Could not retrieve variants from source file in region 10:51827723-51828124. Error was invalid region `10:51827724-51828124`
[2016-04-15T05:53Z] 2016-04-14 22:53:35 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:53:35,652 - WARNING - Could not retrieve variants from source file in region 10:61552481-61552964. Error was invalid region `10:61552482-61552964`
[2016-04-15T05:53Z] 2016-04-14 22:53:38 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:53:38,410 - WARNING - Could not retrieve variants from source file in region 10:53887659-53888060. Error was invalid region `10:53887660-53888060`
[2016-04-15T05:53Z] 2016-04-14 22:53:38 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:53:38,697 - WARNING - Could not retrieve variants from source file in region 10:61413286-61414201. Error was invalid region `10:61413287-61414201`
[2016-04-15T05:53Z] 2016-04-14 22:53:39 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:53:39,522 - WARNING - Could not retrieve variants from source file in region 10:57359486-57359887. Error was invalid region `10:57359487-57359887`
[2016-04-15T05:53Z] 2016-04-14 22:53:39 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:53:39,650 - WARNING - Could not retrieve variants from source file in region 10:62029723-62030124. Error was invalid region `10:62029724-62030124`
[2016-04-15T05:53Z] 2016-04-14 22:53:40 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:53:40,192 - WARNING - Could not retrieve variants from source file in region 10:60577182-60588743. Error was invalid region `10:60577183-60588743`
[2016-04-15T05:53Z] 2016-04-14 22:53:40 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:53:40,338 - WARNING - Could not retrieve variants from source file in region 10:49812706-49813107. Error was invalid region `10:49812707-49813107`
[2016-04-15T05:53Z] 2016-04-14 22:53:40 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:53:40,829 - WARNING - Could not retrieve variants from source file in region 10:52103496-52103897. Error was invalid region `10:52103497-52103897`
[2016-04-15T05:53Z] 2016-04-14 22:53:40 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:53:40,885 - WARNING - Could not retrieve variants from source file in region 10:50178039-50186605. Error was invalid region `10:50178040-50186605`
[2016-04-15T05:53Z] 2016-04-14 22:53:41 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:53:41,093 - WARNING - Could not retrieve variants from source file in region 10:60145131-60145532. Error was invalid region `10:60145132-60145532`
[2016-04-15T05:53Z] 2016-04-14 22:53:41 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:53:41,130 - WARNING - Could not retrieve variants from source file in region 10:51827723-51828124. Error was invalid region `10:51827724-51828124`
[2016-04-15T05:53Z] 2016-04-14 22:53:41 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:53:41,570 - WARNING - Could not retrieve variants from source file in region 10:61552481-61552964. Error was invalid region `10:61552482-61552964`
[2016-04-15T05:53Z] 2016-04-14 22:53:41 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:53:41,677 - WARNING - Could not retrieve variants from source file in region 10:61965414-61965815. Error was invalid region `10:61965415-61965815`
[2016-04-15T05:53Z] 2016-04-14 22:53:43 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:53:43,604 - WARNING - Could not retrieve variants from source file in region 10:53887659-53888060. Error was invalid region `10:53887660-53888060`
[2016-04-15T05:53Z] 2016-04-14 22:53:44 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:53:44,141 - WARNING - Could not retrieve variants from source file in region 10:61413286-61414201. Error was invalid region `10:61413287-61414201`
[2016-04-15T05:53Z] 2016-04-14 22:53:46 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:53:46,276 - WARNING - Could not retrieve variants from source file in region 10:61868505-61868906. Error was invalid region `10:61868506-61868906`
[2016-04-15T05:53Z] 2016-04-14 22:53:46 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:53:46,648 - WARNING - Could not retrieve variants from source file in region 10:62029723-62030124. Error was invalid region `10:62029724-62030124`
[2016-04-15T05:53Z] 2016-04-14 22:53:47 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:53:47,440 - WARNING - Could not retrieve variants from source file in region 10:60577182-60588743. Error was invalid region `10:60577183-60588743`
[2016-04-15T05:53Z] 2016-04-14 22:53:48 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:53:48,180 - WARNING - Could not retrieve variants from source file in region 10:50178039-50186605. Error was invalid region `10:50178040-50186605`
[2016-04-15T05:53Z] 2016-04-14 22:53:48 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:53:48,614 - WARNING - Could not retrieve variants from source file in region 10:49812706-49813107. Error was invalid region `10:49812707-49813107`
[2016-04-15T05:53Z] 2016-04-14 22:53:48 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:53:48,648 - WARNING - Could not retrieve variants from source file in region 10:51622936-51623337. Error was invalid region `10:51622937-51623337`
[2016-04-15T05:53Z] 2016-04-14 22:53:56 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:53:56,423 - WARNING - Could not retrieve variants from source file in region 10:52002769-52005343. Error was invalid region `10:52002770-52005343`
[2016-04-15T05:53Z] 2016-04-14 22:53:57 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:53:57,892 - WARNING - Could not retrieve variants from source file in region 10:51748098-51768866. Error was invalid region `10:51748099-51768866`
[2016-04-15T05:53Z] 2016-04-14 22:53:59 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:53:59,861 - WARNING - Could not retrieve variants from source file in region 10:61122057-61122458. Error was invalid region `10:61122058-61122458`
[2016-04-15T05:54Z] 2016-04-14 22:54:00 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:54:00,342 - WARNING - Could not retrieve variants from source file in region 10:53458787-53459188. Error was invalid region `10:53458788-53459188`
[2016-04-15T05:54Z] 2016-04-14 22:54:00 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:54:00,464 - WARNING - Could not retrieve variants from source file in region 10:61900145-61900546. Error was invalid region `10:61900146-61900546`
[2016-04-15T05:54Z] 2016-04-14 22:54:01 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:54:01,490 - WARNING - Could not retrieve variants from source file in region 10:56423757-56424158. Error was invalid region `10:56423758-56424158`
[2016-04-15T05:54Z] 2016-04-14 22:54:02 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:54:02,401 - WARNING - Could not retrieve variants from source file in region 10:51748098-51768866. Error was invalid region `10:51748099-51768866`
[2016-04-15T05:54Z] 2016-04-14 22:54:03 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:54:03,444 - WARNING - Could not retrieve variants from source file in region 10:58118419-58118820. Error was invalid region `10:58118420-58118820`
[2016-04-15T05:54Z] 2016-04-14 22:54:04 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:54:04,338 - WARNING - Could not retrieve variants from source file in region 10:61122057-61122458. Error was invalid region `10:61122058-61122458`
[2016-04-15T05:54Z] 2016-04-14 22:54:05 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:54:05,226 - WARNING - Could not retrieve variants from source file in region 10:61900145-61900546. Error was invalid region `10:61900146-61900546`
[2016-04-15T05:54Z] 2016-04-14 22:54:05 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:54:05,589 - WARNING - Could not retrieve variants from source file in region 10:56423757-56424158. Error was invalid region `10:56423758-56424158`
[2016-04-15T05:54Z] 2016-04-14 22:54:05 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:54:05,641 - WARNING - Could not retrieve variants from source file in region 10:52002769-52005343. Error was invalid region `10:52002770-52005343`
[2016-04-15T05:54Z] 2016-04-14 22:54:07 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:54:07,922 - WARNING - Could not retrieve variants from source file in region 10:58118419-58118820. Error was invalid region `10:58118420-58118820`
[2016-04-15T05:54Z] 2016-04-14 22:54:08 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:54:08,607 - WARNING - Could not retrieve variants from source file in region 10:50098528-50122371. Error was invalid region `10:50098529-50122371`
[2016-04-15T05:54Z] 2016-04-14 22:54:08 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:54:08,843 - WARNING - Could not retrieve variants from source file in region 10:61122057-61122458. Error was invalid region `10:61122058-61122458`
[2016-04-15T05:54Z] 2016-04-14 22:54:09 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:54:09,048 - WARNING - Could not retrieve variants from source file in region 10:49731930-49732331. Error was invalid region `10:49731931-49732331`
[2016-04-15T05:54Z] 2016-04-14 22:54:09 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:54:09,176 - WARNING - Could not retrieve variants from source file in region 10:47915680-47916081. Error was invalid region `10:47915681-47916081`
[2016-04-15T05:54Z] 2016-04-14 22:54:10 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:54:10,031 - WARNING - Could not retrieve variants from source file in region 10:51568167-51593544. Error was invalid region `10:51568168-51593544`
[2016-04-15T05:54Z] 2016-04-14 22:54:10 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:54:10,349 - WARNING - Could not retrieve variants from source file in region 10:61900145-61900546. Error was invalid region `10:61900146-61900546`
[2016-04-15T05:54Z] 2016-04-14 22:54:10 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:54:10,436 - WARNING - Could not retrieve variants from source file in region 10:56423757-56424158. Error was invalid region `10:56423758-56424158`
[2016-04-15T05:54Z] 2016-04-14 22:54:10 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:54:10,934 - WARNING - Could not retrieve variants from source file in region 10:50856441-50863337. Error was invalid region `10:50856442-50863337`
[2016-04-15T05:54Z] 2016-04-14 22:54:12 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:54:12,058 - WARNING - Could not retrieve variants from source file in region 10:58118419-58118820. Error was invalid region `10:58118420-58118820`
[2016-04-15T05:54Z] 2016-04-14 22:54:14 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:54:14,536 - WARNING - Could not retrieve variants from source file in region 10:51568167-51593544. Error was invalid region `10:51568168-51593544`
[2016-04-15T05:54Z] 2016-04-14 22:54:15 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:54:15,151 - WARNING - Could not retrieve variants from source file in region 10:52384274-52384675. Error was invalid region `10:52384275-52384675`
[2016-04-15T05:54Z] 2016-04-14 22:54:15 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:54:15,954 - WARNING - Could not retrieve variants from source file in region 10:50856441-50863337. Error was invalid region `10:50856442-50863337`
[2016-04-15T05:54Z] 2016-04-14 22:54:19 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:54:19,480 - WARNING - Could not retrieve variants from source file in region 10:52384274-52384675. Error was invalid region `10:52384275-52384675`
[2016-04-15T05:54Z] 2016-04-14 22:54:20 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:54:20,752 - WARNING - Could not retrieve variants from source file in region 10:50856441-50863337. Error was invalid region `10:50856442-50863337`
[2016-04-15T05:54Z] 2016-04-14 22:54:22 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:54:22,603 - WARNING - Could not retrieve variants from source file in region 10:55570136-55570537. Error was invalid region `10:55570137-55570537`
[2016-04-15T05:54Z] 2016-04-14 22:54:24 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:54:24,338 - WARNING - Could not retrieve variants from source file in region 10:61665675-61666076. Error was invalid region `10:61665676-61666076`
[2016-04-15T05:54Z] 2016-04-14 22:54:25 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:54:25,046 - WARNING - Could not retrieve variants from source file in region 10:49667584-49701842. Error was invalid region `10:49667585-49701842`
[2016-04-15T05:54Z] 2016-04-14 22:54:25 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:54:25,229 - WARNING - Could not retrieve variants from source file in region 10:47668496-47669467. Error was invalid region `10:47668497-47669467`
[2016-04-15T05:54Z] 2016-04-14 22:54:25 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:54:25,389 - WARNING - Could not retrieve variants from source file in region 10:47701091-47701492. Error was invalid region `10:47701092-47701492`
[2016-04-15T05:54Z] 2016-04-14 22:54:26 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:54:26,856 - WARNING - Could not retrieve variants from source file in region 10:49380788-49384166. Error was invalid region `10:49380789-49384166`
[2016-04-15T05:54Z] 2016-04-14 22:54:27 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:54:27,693 - WARNING - Could not retrieve variants from source file in region 10:51465341-51465742. Error was invalid region `10:51465342-51465742`
[2016-04-15T05:54Z] 2016-04-14 22:54:28 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:54:28,282 - WARNING - Could not retrieve variants from source file in region 10:55955274-55955800. Error was invalid region `10:55955275-55955800`
[2016-04-15T05:54Z] 2016-04-14 22:54:28 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:54:28,734 - WARNING - Could not retrieve variants from source file in region 10:61665675-61666076. Error was invalid region `10:61665676-61666076`
[2016-04-15T05:54Z] 2016-04-14 22:54:29 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:54:29,682 - WARNING - Could not retrieve variants from source file in region 10:49667584-49701842. Error was invalid region `10:49667585-49701842`
[2016-04-15T05:54Z] 2016-04-14 22:54:29 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:54:29,963 - WARNING - Could not retrieve variants from source file in region 10:47701091-47701492. Error was invalid region `10:47701092-47701492`
[2016-04-15T05:54Z] 2016-04-14 22:54:31 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:54:31,938 - WARNING - Could not retrieve variants from source file in region 10:51465341-51465742. Error was invalid region `10:51465342-51465742`
[2016-04-15T05:54Z] 2016-04-14 22:54:32 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:54:32,267 - WARNING - Could not retrieve variants from source file in region 10:46998683-47000429. Error was invalid region `10:46998684-47000429`
[2016-04-15T05:54Z] 2016-04-14 22:54:32 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:54:32,658 - WARNING - Could not retrieve variants from source file in region 10:55955274-55955800. Error was invalid region `10:55955275-55955800`
[2016-04-15T05:54Z] 2016-04-14 22:54:32 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:54:32,890 - WARNING - Could not retrieve variants from source file in region 10:61665675-61666076. Error was invalid region `10:61665676-61666076`
[2016-04-15T05:54Z] 2016-04-14 22:54:33 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:54:33,780 - WARNING - Could not retrieve variants from source file in region 10:49667584-49701842. Error was invalid region `10:49667585-49701842`
[2016-04-15T05:54Z] 2016-04-14 22:54:33 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:54:33,918 - WARNING - Could not retrieve variants from source file in region 10:47668496-47669467. Error was invalid region `10:47668497-47669467`
[2016-04-15T05:54Z] 2016-04-14 22:54:34 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:54:34,235 - WARNING - Could not retrieve variants from source file in region 10:47701091-47701492. Error was invalid region `10:47701092-47701492`
[2016-04-15T05:54Z] 2016-04-14 22:54:36 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:54:36,870 - WARNING - Could not retrieve variants from source file in region 10:51465341-51465742. Error was invalid region `10:51465342-51465742`
[2016-04-15T05:54Z] 2016-04-14 22:54:39 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:54:39,668 - WARNING - Could not retrieve variants from source file in region 10:51225296-51225697. Error was invalid region `10:51225297-51225697`
[2016-04-15T05:54Z] 2016-04-14 22:54:41 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:54:41,488 - WARNING - Could not retrieve variants from source file in region 10:46998683-47000429. Error was invalid region `10:46998684-47000429`
[2016-04-15T05:54Z] 2016-04-14 22:54:43 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:54:43,785 - WARNING - Could not retrieve variants from source file in region 10:51225296-51225697. Error was invalid region `10:51225297-51225697`
[2016-04-15T05:54Z] 2016-04-14 22:54:44 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:54:44,125 - WARNING - Could not retrieve variants from source file in region 10:54074546-54074947. Error was invalid region `10:54074547-54074947`
[2016-04-15T05:54Z] 2016-04-14 22:54:46 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:54:46,547 - WARNING - Could not retrieve variants from source file in region 10:54528055-54531425. Error was invalid region `10:54528056-54531425`
[2016-04-15T05:54Z] 2016-04-14 22:54:47 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:54:47,138 - WARNING - Could not retrieve variants from source file in region 10:54528055-54531425. Error was invalid region `10:54528056-54531425`
[2016-04-15T05:54Z] 2016-04-14 22:54:48 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:54:48,440 - WARNING - Could not retrieve variants from source file in region 10:54074546-54074947. Error was invalid region `10:54074547-54074947`
[2016-04-15T05:54Z] 2016-04-14 22:54:49 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:54:49,426 - WARNING - Could not retrieve variants from source file in region 10:50723473-50741066. Error was invalid region `10:50723474-50741066`
[2016-04-15T05:54Z] 2016-04-14 22:54:50 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:54:50,358 - WARNING - Could not retrieve variants from source file in region 10:54074546-54074947. Error was invalid region `10:54074547-54074947`
[2016-04-15T05:54Z] 2016-04-14 22:54:50 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:54:50,457 - WARNING - Could not retrieve variants from source file in region 10:50901727-50902874. Error was invalid region `10:50901728-50902874`
[2016-04-15T05:54Z] 2016-04-14 22:54:50 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:54:50,588 - WARNING - Could not retrieve variants from source file in region 10:50339543-50340152. Error was invalid region `10:50339544-50340152`
[2016-04-15T05:54Z] 2016-04-14 22:54:51 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:54:51,306 - WARNING - Could not retrieve variants from source file in region 10:50901727-50902874. Error was invalid region `10:50901728-50902874`
[2016-04-15T05:54Z] 2016-04-14 22:54:52 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:54:52,714 - WARNING - Could not retrieve variants from source file in region 10:50666894-50681223. Error was invalid region `10:50666895-50681223`
[2016-04-15T05:54Z] 2016-04-14 22:54:54 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:54:54,580 - WARNING - Could not retrieve variants from source file in region 10:50901727-50902874. Error was invalid region `10:50901728-50902874`
[2016-04-15T05:54Z] 2016-04-14 22:54:54 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:54:54,809 - WARNING - Could not retrieve variants from source file in region 10:50339543-50340152. Error was invalid region `10:50339544-50340152`
[2016-04-15T05:54Z] 2016-04-14 22:54:57 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:54:57,208 - WARNING - Could not retrieve variants from source file in region 10:46964807-46971378. Error was invalid region `10:46964808-46971378`
[2016-04-15T05:55Z] 2016-04-14 22:55:00 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:55:00,199 - WARNING - Could not retrieve variants from source file in region 10:50227574-50227975. Error was invalid region `10:50227575-50227975`
[2016-04-15T05:55Z] 2016-04-14 22:55:01 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:55:01,183 - WARNING - Could not retrieve variants from source file in region 10:50227574-50227975. Error was invalid region `10:50227575-50227975`
[2016-04-15T05:55Z] 2016-04-14 22:55:01 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:55:01,184 - WARNING - Could not retrieve variants from source file in region 10:50227574-50227975. Error was invalid region `10:50227575-50227975`
[2016-04-15T05:55Z] ['bcbio-variation-recall', 'square', '-Xms750m', '-Xmx7280m', '-XX:+UseSerialGC', '-c', 16, '-r', u'10:62539924-78084243', '--caller', 'platypus', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/10/Batch1-10_62539923_78084243.vcf.gz', '/mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/10/Batch1-10_62539923_78084243.vcf-inputs.txt'] in region: 10:62539924-78084243
[2016-04-15T05:55Z] 2016-04-14 22:55:15 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:55:15,048 - WARNING - Could not retrieve variants from source file in region 10:75936400-75936801. Error was invalid region `10:75936401-75936801`
[2016-04-15T05:55Z] 2016-04-14 22:55:15 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:55:15,719 - WARNING - Could not retrieve variants from source file in region 10:75864854-75871925. Error was invalid region `10:75864855-75871925`
[2016-04-15T05:55Z] 2016-04-14 22:55:16 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:55:16,521 - WARNING - Could not retrieve variants from source file in region 10:71060399-71060800. Error was invalid region `10:71060400-71060800`
[2016-04-15T05:55Z] 2016-04-14 22:55:16 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:55:16,614 - WARNING - Could not retrieve variants from source file in region 10:75672890-75673291. Error was invalid region `10:75672891-75673291`
[2016-04-15T05:55Z] 2016-04-14 22:55:17 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:55:17,351 - WARNING - Could not retrieve variants from source file in region 10:73767648-73768049. Error was invalid region `10:73767649-73768049`
[2016-04-15T05:55Z] 2016-04-14 22:55:17 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:55:17,499 - WARNING - Could not retrieve variants from source file in region 10:70405644-70406045. Error was invalid region `10:70405645-70406045`
[2016-04-15T05:55Z] 2016-04-14 22:55:17 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:55:17,944 - WARNING - Could not retrieve variants from source file in region 10:71331993-71332394. Error was invalid region `10:71331994-71332394`
[2016-04-15T05:55Z] 2016-04-14 22:55:18 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:55:18,108 - WARNING - Could not retrieve variants from source file in region 10:75558656-75576153. Error was invalid region `10:75558657-75576153`
[2016-04-15T05:55Z] 2016-04-14 22:55:18 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:55:18,563 - WARNING - Could not retrieve variants from source file in region 10:71873837-71876572. Error was invalid region `10:71873838-71876572`
[2016-04-15T05:55Z] 2016-04-14 22:55:18 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:55:18,627 - WARNING - Could not retrieve variants from source file in region 10:77542347-77542748. Error was invalid region `10:77542348-77542748`
[2016-04-15T05:55Z] 2016-04-14 22:55:20 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:55:20,156 - WARNING - Could not retrieve variants from source file in region 10:75936400-75936801. Error was invalid region `10:75936401-75936801`
[2016-04-15T05:55Z] 2016-04-14 22:55:21 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:55:21,355 - WARNING - Could not retrieve variants from source file in region 10:75864854-75871925. Error was invalid region `10:75864855-75871925`
[2016-04-15T05:55Z] 2016-04-14 22:55:21 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:55:21,755 - WARNING - Could not retrieve variants from source file in region 10:75672890-75673291. Error was invalid region `10:75672891-75673291`
[2016-04-15T05:55Z] 2016-04-14 22:55:22 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:55:22,181 - WARNING - Could not retrieve variants from source file in region 10:71060399-71060800. Error was invalid region `10:71060400-71060800`
[2016-04-15T05:55Z] 2016-04-14 22:55:24 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:55:24,571 - WARNING - Could not retrieve variants from source file in region 10:76854353-76868089. Error was invalid region `10:76854354-76868089`
[2016-04-15T05:55Z] 2016-04-14 22:55:24 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:55:24,576 - WARNING - Could not retrieve variants from source file in region 10:70405644-70406045. Error was invalid region `10:70405645-70406045`
[2016-04-15T05:55Z] 2016-04-14 22:55:25 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:55:25,069 - WARNING - Could not retrieve variants from source file in region 10:73767648-73768049. Error was invalid region `10:73767649-73768049`
[2016-04-15T05:55Z] 2016-04-14 22:55:25 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:55:25,094 - WARNING - Could not retrieve variants from source file in region 10:75558656-75576153. Error was invalid region `10:75558657-75576153`
[2016-04-15T05:55Z] 2016-04-14 22:55:25 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:55:25,779 - WARNING - Could not retrieve variants from source file in region 10:75441129-75441530. Error was invalid region `10:75441130-75441530`
[2016-04-15T05:55Z] 2016-04-14 22:55:25 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:55:25,887 - WARNING - Could not retrieve variants from source file in region 10:71142209-71168875. Error was invalid region `10:71142210-71168875`
[2016-04-15T05:55Z] 2016-04-14 22:55:25 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:55:25,937 - WARNING - Could not retrieve variants from source file in region 10:75936400-75936801. Error was invalid region `10:75936401-75936801`
[2016-04-15T05:55Z] 2016-04-14 22:55:26 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:55:26,008 - WARNING - Could not retrieve variants from source file in region 10:78083973-78084374. Error was invalid region `10:78083974-78084374`
[2016-04-15T05:55Z] 2016-04-14 22:55:26 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:55:26,389 - WARNING - Could not retrieve variants from source file in region 10:75864854-75871925. Error was invalid region `10:75864855-75871925`
[2016-04-15T05:55Z] 2016-04-14 22:55:26 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:55:26,505 - WARNING - Could not retrieve variants from source file in region 10:75672890-75673291. Error was invalid region `10:75672891-75673291`
[2016-04-15T05:55Z] 2016-04-14 22:55:26 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:55:26,781 - WARNING - Could not retrieve variants from source file in region 10:71060399-71060800. Error was invalid region `10:71060400-71060800`
[2016-04-15T05:55Z] 2016-04-14 22:55:29 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:55:29,740 - WARNING - Could not retrieve variants from source file in region 10:76927909-76928339. Error was invalid region `10:76927910-76928339`
[2016-04-15T05:55Z] 2016-04-14 22:55:31 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:55:31,400 - WARNING - Could not retrieve variants from source file in region 10:76854353-76868089. Error was invalid region `10:76854354-76868089`
[2016-04-15T05:55Z] 2016-04-14 22:55:31 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:55:31,940 - WARNING - Could not retrieve variants from source file in region 10:70405644-70406045. Error was invalid region `10:70405645-70406045`
[2016-04-15T05:55Z] 2016-04-14 22:55:32 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:55:32,983 - WARNING - Could not retrieve variants from source file in region 10:73767648-73768049. Error was invalid region `10:73767649-73768049`
[2016-04-15T05:55Z] 2016-04-14 22:55:33 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:55:33,565 - WARNING - Could not retrieve variants from source file in region 10:75558656-75576153. Error was invalid region `10:75558657-75576153`
[2016-04-15T05:55Z] 2016-04-14 22:55:33 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:55:33,665 - WARNING - Could not retrieve variants from source file in region 10:72604052-72648612. Error was invalid region `10:72604053-72648612`
[2016-04-15T05:55Z] 2016-04-14 22:55:34 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:55:34,058 - WARNING - Could not retrieve variants from source file in region 10:71331993-71332394. Error was invalid region `10:71331994-71332394`
[2016-04-15T05:55Z] 2016-04-14 22:55:34 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:55:34,411 - WARNING - Could not retrieve variants from source file in region 10:77542347-77542748. Error was invalid region `10:77542348-77542748`
[2016-04-15T05:55Z] 2016-04-14 22:55:46 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:55:46,361 - WARNING - Could not retrieve variants from source file in region 10:75632549-75632950. Error was invalid region `10:75632550-75632950`
[2016-04-15T05:55Z] 2016-04-14 22:55:46 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:55:46,421 - WARNING - Could not retrieve variants from source file in region 10:72289567-72289968. Error was invalid region `10:72289568-72289968`
[2016-04-15T05:55Z] 2016-04-14 22:55:47 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:55:47,213 - WARNING - Could not retrieve variants from source file in region 10:71018449-71026700. Error was invalid region `10:71018450-71026700`
[2016-04-15T05:55Z] 2016-04-14 22:55:48 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:55:48,077 - WARNING - Could not retrieve variants from source file in region 10:73270695-73271096. Error was invalid region `10:73270696-73271096`
[2016-04-15T05:55Z] 2016-04-14 22:55:49 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:55:49,301 - WARNING - Could not retrieve variants from source file in region 10:70332369-70332770. Error was invalid region `10:70332370-70332770`
[2016-04-15T05:55Z] 2016-04-14 22:55:50 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:55:50,046 - WARNING - Could not retrieve variants from source file in region 10:75523423-75523824. Error was invalid region `10:75523424-75523824`
[2016-04-15T05:55Z] 2016-04-14 22:55:50 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:55:50,962 - WARNING - Could not retrieve variants from source file in region 10:77160889-77161305. Error was invalid region `10:77160890-77161305`
[2016-04-15T05:55Z] 2016-04-14 22:55:51 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:55:51,721 - WARNING - Could not retrieve variants from source file in region 10:75632549-75632950. Error was invalid region `10:75632550-75632950`
[2016-04-15T05:55Z] 2016-04-14 22:55:51 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:55:51,975 - WARNING - Could not retrieve variants from source file in region 10:72289567-72289968. Error was invalid region `10:72289568-72289968`
[2016-04-15T05:55Z] 2016-04-14 22:55:52 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:55:52,322 - WARNING - Could not retrieve variants from source file in region 10:75405725-75410182. Error was invalid region `10:75405726-75410182`
[2016-04-15T05:55Z] 2016-04-14 22:55:52 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:55:52,626 - WARNING - Could not retrieve variants from source file in region 10:73270695-73271096. Error was invalid region `10:73270696-73271096`
[2016-04-15T05:55Z] 2016-04-14 22:55:53 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:55:53,227 - WARNING - Could not retrieve variants from source file in region 10:77806816-77807217. Error was invalid region `10:77806817-77807217`
[2016-04-15T05:55Z] 2016-04-14 22:55:54 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:55:54,410 - WARNING - Could not retrieve variants from source file in region 10:70332369-70332770. Error was invalid region `10:70332370-70332770`
[2016-04-15T05:55Z] 2016-04-14 22:55:57 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:55:57,162 - WARNING - Could not retrieve variants from source file in region 10:72289567-72289968. Error was invalid region `10:72289568-72289968`
[2016-04-15T05:55Z] 2016-04-14 22:55:57 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:55:57,332 - WARNING - Could not retrieve variants from source file in region 10:75632549-75632950. Error was invalid region `10:75632550-75632950`
[2016-04-15T05:55Z] 2016-04-14 22:55:57 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:55:57,906 - WARNING - Could not retrieve variants from source file in region 10:75405725-75410182. Error was invalid region `10:75405726-75410182`
[2016-04-15T05:55Z] 2016-04-14 22:55:58 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:55:58,194 - WARNING - Could not retrieve variants from source file in region 10:73270695-73271096. Error was invalid region `10:73270696-73271096`
[2016-04-15T05:55Z] 2016-04-14 22:55:58 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:55:58,902 - WARNING - Could not retrieve variants from source file in region 10:70332369-70332770. Error was invalid region `10:70332370-70332770`
[2016-04-15T05:56Z] 2016-04-14 22:56:01 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:56:01,772 - WARNING - Could not retrieve variants from source file in region 10:71097984-71103787. Error was invalid region `10:71097985-71103787`
[2016-04-15T05:56Z] 2016-04-14 22:56:11 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:56:11,744 - WARNING - Could not retrieve variants from source file in region 10:72179535-72195629. Error was invalid region `10:72179536-72195629`
[2016-04-15T05:56Z] 2016-04-14 22:56:11 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:56:11,793 - WARNING - Could not retrieve variants from source file in region 10:72060806-72083849. Error was invalid region `10:72060807-72083849`
[2016-04-15T05:56Z] 2016-04-14 22:56:13 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:56:13,438 - WARNING - Could not retrieve variants from source file in region 10:73111197-73122135. Error was invalid region `10:73111198-73122135`
[2016-04-15T05:56Z] 2016-04-14 22:56:13 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:56:13,964 - WARNING - Could not retrieve variants from source file in region 10:70166702-70167103. Error was invalid region `10:70166703-70167103`
[2016-04-15T05:56Z] 2016-04-14 22:56:14 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:56:14,030 - WARNING - Could not retrieve variants from source file in region 10:71968806-71969207. Error was invalid region `10:71968807-71969207`
[2016-04-15T05:56Z] 2016-04-14 22:56:14 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:56:14,260 - WARNING - Could not retrieve variants from source file in region 10:74094454-74094855. Error was invalid region `10:74094455-74094855`
[2016-04-15T05:56Z] 2016-04-14 22:56:14 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:56:14,822 - WARNING - Could not retrieve variants from source file in region 10:71904095-71906340. Error was invalid region `10:71904096-71906340`
[2016-04-15T05:56Z] 2016-04-14 22:56:16 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:56:16,118 - WARNING - Could not retrieve variants from source file in region 10:72179535-72195629. Error was invalid region `10:72179536-72195629`
[2016-04-15T05:56Z] 2016-04-14 22:56:17 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:56:17,578 - WARNING - Could not retrieve variants from source file in region 10:73892606-73893007. Error was invalid region `10:73892607-73893007`
[2016-04-15T05:56Z] 2016-04-14 22:56:18 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:56:18,329 - WARNING - Could not retrieve variants from source file in region 10:73082352-73082753. Error was invalid region `10:73082353-73082753`
[2016-04-15T05:56Z] 2016-04-14 22:56:18 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:56:18,733 - WARNING - Could not retrieve variants from source file in region 10:72323932-72326590. Error was invalid region `10:72323933-72326590`
[2016-04-15T05:56Z] 2016-04-14 22:56:19 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:56:19,553 - WARNING - Could not retrieve variants from source file in region 10:71562226-71562627. Error was invalid region `10:71562227-71562627`
[2016-04-15T05:56Z] 2016-04-14 22:56:20 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:56:20,391 - WARNING - Could not retrieve variants from source file in region 10:70166702-70167103. Error was invalid region `10:70166703-70167103`
[2016-04-15T05:56Z] 2016-04-14 22:56:20 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:56:20,562 - WARNING - Could not retrieve variants from source file in region 10:73111197-73122135. Error was invalid region `10:73111198-73122135`
[2016-04-15T05:56Z] 2016-04-14 22:56:20 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:56:20,727 - WARNING - Could not retrieve variants from source file in region 10:70968294-70992854. Error was invalid region `10:70968295-70992854`
[2016-04-15T05:56Z] 2016-04-14 22:56:21 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:56:21,024 - WARNING - Could not retrieve variants from source file in region 10:72358366-72358845. Error was invalid region `10:72358367-72358845`
[2016-04-15T05:56Z] 2016-04-14 22:56:21 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:56:21,153 - WARNING - Could not retrieve variants from source file in region 10:71904095-71906340. Error was invalid region `10:71904096-71906340`
[2016-04-15T05:56Z] 2016-04-14 22:56:21 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:56:21,370 - WARNING - Could not retrieve variants from source file in region 10:74094454-74094855. Error was invalid region `10:74094455-74094855`
[2016-04-15T05:56Z] 2016-04-14 22:56:21 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:56:21,550 - WARNING - Could not retrieve variants from source file in region 10:72179535-72195629. Error was invalid region `10:72179536-72195629`
[2016-04-15T05:56Z] 2016-04-14 22:56:23 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:56:23,478 - WARNING - Could not retrieve variants from source file in region 10:72323932-72326590. Error was invalid region `10:72323933-72326590`
[2016-04-15T05:56Z] 2016-04-14 22:56:24 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:56:24,212 - WARNING - Could not retrieve variants from source file in region 10:71562226-71562627. Error was invalid region `10:71562227-71562627`
[2016-04-15T05:56Z] 2016-04-14 22:56:26 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:56:26,400 - WARNING - Could not retrieve variants from source file in region 10:70166702-70167103. Error was invalid region `10:70166703-70167103`
[2016-04-15T05:56Z] 2016-04-14 22:56:26 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:56:26,409 - WARNING - Could not retrieve variants from source file in region 10:73111197-73122135. Error was invalid region `10:73111198-73122135`
[2016-04-15T05:56Z] 2016-04-14 22:56:27 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:56:27,177 - WARNING - Could not retrieve variants from source file in region 10:71904095-71906340. Error was invalid region `10:71904096-71906340`
[2016-04-15T05:56Z] 2016-04-14 22:56:27 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:56:27,243 - WARNING - Could not retrieve variants from source file in region 10:73044369-73051578. Error was invalid region `10:73044370-73051578`
[2016-04-15T05:56Z] 2016-04-14 22:56:27 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:56:27,465 - WARNING - Could not retrieve variants from source file in region 10:74094454-74094855. Error was invalid region `10:74094455-74094855`
[2016-04-15T05:56Z] 2016-04-14 22:56:28 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:56:28,982 - WARNING - Could not retrieve variants from source file in region 10:71562226-71562627. Error was invalid region `10:71562227-71562627`
[2016-04-15T05:56Z] 2016-04-14 22:56:39 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:56:39,406 - WARNING - Could not retrieve variants from source file in region 10:70105349-70105750. Error was invalid region `10:70105350-70105750`
[2016-04-15T05:56Z] 2016-04-14 22:56:40 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:56:40,917 - WARNING - Could not retrieve variants from source file in region 10:70856641-70857042. Error was invalid region `10:70856642-70857042`
[2016-04-15T05:56Z] 2016-04-14 22:56:41 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:56:41,777 - WARNING - Could not retrieve variants from source file in region 10:73846130-73846531. Error was invalid region `10:73846131-73846531`
[2016-04-15T05:56Z] 2016-04-14 22:56:43 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:56:43,635 - WARNING - Could not retrieve variants from source file in region 10:69829186-69829587. Error was invalid region `10:69829187-69829587`
[2016-04-15T05:56Z] 2016-04-14 22:56:43 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:56:43,920 - WARNING - Could not retrieve variants from source file in region 10:70105349-70105750. Error was invalid region `10:70105350-70105750`
[2016-04-15T05:56Z] 2016-04-14 22:56:44 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:56:44,790 - WARNING - Could not retrieve variants from source file in region 10:70856641-70857042. Error was invalid region `10:70856642-70857042`
[2016-04-15T05:56Z] 2016-04-14 22:56:46 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:56:46,346 - WARNING - Could not retrieve variants from source file in region 10:73846130-73846531. Error was invalid region `10:73846131-73846531`
[2016-04-15T05:56Z] 2016-04-14 22:56:46 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:56:46,854 - WARNING - Could not retrieve variants from source file in region 10:70748573-70748974. Error was invalid region `10:70748574-70748974`
[2016-04-15T05:56Z] 2016-04-14 22:56:47 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:56:47,247 - WARNING - Could not retrieve variants from source file in region 10:70641649-70642050. Error was invalid region `10:70641650-70642050`
[2016-04-15T05:56Z] 2016-04-14 22:56:47 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:56:47,450 - WARNING - Could not retrieve variants from source file in region 10:73377052-73377520. Error was invalid region `10:73377053-73377520`
[2016-04-15T05:56Z] 2016-04-14 22:56:47 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:56:47,465 - WARNING - Could not retrieve variants from source file in region 10:68138828-68139229. Error was invalid region `10:68138829-68139229`
[2016-04-15T05:56Z] 2016-04-14 22:56:47 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:56:47,884 - WARNING - Could not retrieve variants from source file in region 10:70043820-70052118. Error was invalid region `10:70043821-70052118`
[2016-04-15T05:56Z] 2016-04-14 22:56:48 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:56:48,106 - WARNING - Could not retrieve variants from source file in region 10:70696502-70722073. Error was invalid region `10:70696503-70722073`
[2016-04-15T05:56Z] 2016-04-14 22:56:48 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:56:48,779 - WARNING - Could not retrieve variants from source file in region 10:70105349-70105750. Error was invalid region `10:70105350-70105750`
[2016-04-15T05:56Z] 2016-04-14 22:56:48 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:56:48,891 - WARNING - Could not retrieve variants from source file in region 10:64159122-64161436. Error was invalid region `10:64159123-64161436`
[2016-04-15T05:56Z] 2016-04-14 22:56:48 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:56:48,940 - WARNING - Could not retrieve variants from source file in region 10:71390182-71392882. Error was invalid region `10:71390183-71392882`
[2016-04-15T05:56Z] 2016-04-14 22:56:49 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:56:49,233 - WARNING - Could not retrieve variants from source file in region 10:70587286-70587687. Error was invalid region `10:70587287-70587687`
[2016-04-15T05:56Z] 2016-04-14 22:56:49 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:56:49,321 - WARNING - Could not retrieve variants from source file in region 10:69829186-69829587. Error was invalid region `10:69829187-69829587`
[2016-04-15T05:56Z] 2016-04-14 22:56:49 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:56:49,336 - WARNING - Could not retrieve variants from source file in region 10:70856641-70857042. Error was invalid region `10:70856642-70857042`
[2016-04-15T05:56Z] 2016-04-14 22:56:50 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:56:50,706 - WARNING - Could not retrieve variants from source file in region 10:73846130-73846531. Error was invalid region `10:73846131-73846531`
[2016-04-15T05:56Z] 2016-04-14 22:56:51 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:56:51,396 - WARNING - Could not retrieve variants from source file in region 10:70748573-70748974. Error was invalid region `10:70748574-70748974`
[2016-04-15T05:56Z] 2016-04-14 22:56:52 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:56:52,422 - WARNING - Could not retrieve variants from source file in region 10:73377052-73377520. Error was invalid region `10:73377053-73377520`
[2016-04-15T05:56Z] 2016-04-14 22:56:54 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:56:54,046 - WARNING - Could not retrieve variants from source file in region 10:64159122-64161436. Error was invalid region `10:64159123-64161436`
[2016-04-15T05:56Z] 2016-04-14 22:56:54 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:56:54,070 - WARNING - Could not retrieve variants from source file in region 10:70587286-70587687. Error was invalid region `10:70587287-70587687`
[2016-04-15T05:56Z] 2016-04-14 22:56:54 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:56:54,186 - WARNING - Could not retrieve variants from source file in region 10:69829186-69829587. Error was invalid region `10:69829187-69829587`
[2016-04-15T05:57Z] 2016-04-14 22:57:03 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:57:03,346 - WARNING - Could not retrieve variants from source file in region 10:64564681-64573961. Error was invalid region `10:64564682-64573961`
[2016-04-15T05:57Z] 2016-04-14 22:57:04 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:57:04,788 - WARNING - Could not retrieve variants from source file in region 10:69773630-69774031. Error was invalid region `10:69773631-69774031`
[2016-04-15T05:57Z] 2016-04-14 22:57:06 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:57:06,701 - WARNING - Could not retrieve variants from source file in region 10:64564681-64573961. Error was invalid region `10:64564682-64573961`
[2016-04-15T05:57Z] 2016-04-14 22:57:06 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:57:06,804 - WARNING - Could not retrieve variants from source file in region 10:63829328-63829729. Error was invalid region `10:63829329-63829729`
[2016-04-15T05:57Z] 2016-04-14 22:57:06 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:57:06,808 - WARNING - Could not retrieve variants from source file in region 10:70502077-70521097. Error was invalid region `10:70502078-70521097`
[2016-04-15T05:57Z] 2016-04-14 22:57:08 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:57:08,235 - WARNING - Could not retrieve variants from source file in region 10:69773630-69774031. Error was invalid region `10:69773631-69774031`
[2016-04-15T05:57Z] 2016-04-14 22:57:09 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:57:09,928 - WARNING - Could not retrieve variants from source file in region 10:64564681-64573961. Error was invalid region `10:64564682-64573961`
[2016-04-15T05:57Z] 2016-04-14 22:57:10 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:57:10,282 - WARNING - Could not retrieve variants from source file in region 10:63829328-63829729. Error was invalid region `10:63829329-63829729`
[2016-04-15T05:57Z] 2016-04-14 22:57:12 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:57:12,008 - WARNING - Could not retrieve variants from source file in region 10:69773630-69774031. Error was invalid region `10:69773631-69774031`
[2016-04-15T05:57Z] 2016-04-14 22:57:19 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:57:19,795 - WARNING - Could not retrieve variants from source file in region 10:63520487-63520888. Error was invalid region `10:63520488-63520888`
[2016-04-15T05:57Z] 2016-04-14 22:57:19 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:57:19,954 - WARNING - Could not retrieve variants from source file in region 10:63520487-63520888. Error was invalid region `10:63520488-63520888`
[2016-04-15T05:57Z] 2016-04-14 22:57:20 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:57:20,226 - WARNING - Could not retrieve variants from source file in region 10:64414973-64415374. Error was invalid region `10:64414974-64415374`
[2016-04-15T05:57Z] 2016-04-14 22:57:20 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:57:20,276 - WARNING - Could not retrieve variants from source file in region 10:64414973-64415374. Error was invalid region `10:64414974-64415374`
[2016-04-15T05:57Z] 2016-04-14 22:57:20 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:57:20,311 - WARNING - Could not retrieve variants from source file in region 10:62545566-62546303. Error was invalid region `10:62545567-62546303`
[2016-04-15T05:57Z] 2016-04-14 22:57:20 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:57:20,335 - WARNING - Could not retrieve variants from source file in region 10:64414973-64415374. Error was invalid region `10:64414974-64415374`
[2016-04-15T05:57Z] 2016-04-14 22:57:20 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:57:20,349 - WARNING - Could not retrieve variants from source file in region 10:62545566-62546303. Error was invalid region `10:62545567-62546303`
[2016-04-15T05:57Z] ['bcbio-variation-recall', 'square', '-Xms750m', '-Xmx7280m', '-XX:+UseSerialGC', '-c', 16, '-r', u'10:78316967-93841258', '--caller', 'platypus', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/10/Batch1-10_78316966_93841258.vcf.gz', '/mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/10/Batch1-10_78316966_93841258.vcf-inputs.txt'] in region: 10:78316967-93841258
[2016-04-15T05:57Z] 2016-04-14 22:57:36 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:57:36,708 - WARNING - Could not retrieve variants from source file in region 10:93841016-93841417. Error was invalid region `10:93841017-93841417`
[2016-04-15T05:57Z] 2016-04-14 22:57:37 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:57:37,557 - WARNING - Could not retrieve variants from source file in region 10:88768042-88782274. Error was invalid region `10:88768043-88782274`
[2016-04-15T05:57Z] 2016-04-14 22:57:37 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:57:37,864 - WARNING - Could not retrieve variants from source file in region 10:85911821-85912222. Error was invalid region `10:85911822-85912222`
[2016-04-15T05:57Z] 2016-04-14 22:57:37 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:57:37,966 - WARNING - Could not retrieve variants from source file in region 10:80310425-80310826. Error was invalid region `10:80310426-80310826`
[2016-04-15T05:57Z] 2016-04-14 22:57:38 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:57:38,537 - WARNING - Could not retrieve variants from source file in region 10:88414358-88422341. Error was invalid region `10:88414359-88422341`
[2016-04-15T05:57Z] 2016-04-14 22:57:38 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:57:38,569 - WARNING - Could not retrieve variants from source file in region 10:91143318-91178190. Error was invalid region `10:91143319-91178190`
[2016-04-15T05:57Z] 2016-04-14 22:57:38 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:57:38,951 - WARNING - Could not retrieve variants from source file in region 10:90579933-90586009. Error was invalid region `10:90579934-90586009`
[2016-04-15T05:57Z] 2016-04-14 22:57:39 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:57:39,423 - WARNING - Could not retrieve variants from source file in region 10:88469836-88476577. Error was invalid region `10:88469837-88476577`
[2016-04-15T05:57Z] 2016-04-14 22:57:39 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:57:39,528 - WARNING - Could not retrieve variants from source file in region 10:88635568-88635969. Error was invalid region `10:88635569-88635969`
[2016-04-15T05:57Z] 2016-04-14 22:57:43 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:57:43,828 - WARNING - Could not retrieve variants from source file in region 10:93841016-93841417. Error was invalid region `10:93841017-93841417`
[2016-04-15T05:57Z] 2016-04-14 22:57:43 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:57:43,917 - WARNING - Could not retrieve variants from source file in region 10:82369008-82369409. Error was invalid region `10:82369009-82369409`
[2016-04-15T05:57Z] 2016-04-14 22:57:45 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:57:45,291 - WARNING - Could not retrieve variants from source file in region 10:88987904-88988305. Error was invalid region `10:88987905-88988305`
[2016-04-15T05:57Z] 2016-04-14 22:57:46 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:57:46,959 - WARNING - Could not retrieve variants from source file in region 10:80310425-80310826. Error was invalid region `10:80310426-80310826`
[2016-04-15T05:57Z] 2016-04-14 22:57:47 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:57:47,019 - WARNING - Could not retrieve variants from source file in region 10:88911630-88940152. Error was invalid region `10:88911631-88940152`
[2016-04-15T05:57Z] 2016-04-14 22:57:47 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:57:47,907 - WARNING - Could not retrieve variants from source file in region 10:90579933-90586009. Error was invalid region `10:90579934-90586009`
[2016-04-15T05:57Z] 2016-04-14 22:57:48 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:57:48,670 - WARNING - Could not retrieve variants from source file in region 10:93841016-93841417. Error was invalid region `10:93841017-93841417`
[2016-04-15T05:57Z] 2016-04-14 22:57:50 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:57:50,169 - WARNING - Could not retrieve variants from source file in region 10:88768042-88782274. Error was invalid region `10:88768043-88782274`
[2016-04-15T05:57Z] 2016-04-14 22:57:51 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:57:51,572 - WARNING - Could not retrieve variants from source file in region 10:85911821-85912222. Error was invalid region `10:85911822-85912222`
[2016-04-15T05:57Z] 2016-04-14 22:57:53 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:57:53,274 - WARNING - Could not retrieve variants from source file in region 10:80310425-80310826. Error was invalid region `10:80310426-80310826`
[2016-04-15T05:57Z] 2016-04-14 22:57:54 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:57:54,434 - WARNING - Could not retrieve variants from source file in region 10:88635568-88635969. Error was invalid region `10:88635569-88635969`
[2016-04-15T05:57Z] 2016-04-14 22:57:55 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:57:55,159 - WARNING - Could not retrieve variants from source file in region 10:91143318-91178190. Error was invalid region `10:91143319-91178190`
[2016-04-15T05:57Z] 2016-04-14 22:57:55 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:57:55,625 - WARNING - Could not retrieve variants from source file in region 10:88469836-88476577. Error was invalid region `10:88469837-88476577`
[2016-04-15T05:57Z] 2016-04-14 22:57:55 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:57:55,640 - WARNING - Could not retrieve variants from source file in region 10:90579933-90586009. Error was invalid region `10:90579934-90586009`
[2016-04-15T05:58Z] 2016-04-14 22:58:07 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:58:07,151 - WARNING - Could not retrieve variants from source file in region 10:88702139-88730502. Error was invalid region `10:88702140-88730502`
[2016-04-15T05:58Z] 2016-04-14 22:58:07 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:58:07,734 - WARNING - Could not retrieve variants from source file in region 10:88820578-88820979. Error was invalid region `10:88820579-88820979`
[2016-04-15T05:58Z] 2016-04-14 22:58:08 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:58:08,679 - WARNING - Could not retrieve variants from source file in region 10:84745045-84745446. Error was invalid region `10:84745046-84745446`
[2016-04-15T05:58Z] 2016-04-14 22:58:08 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:58:08,707 - WARNING - Could not retrieve variants from source file in region 10:79616394-79616795. Error was invalid region `10:79616395-79616795`
[2016-04-15T05:58Z] 2016-04-14 22:58:11 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:58:11,093 - WARNING - Could not retrieve variants from source file in region 10:82168586-82168987. Error was invalid region `10:82168587-82168987`
[2016-04-15T05:58Z] 2016-04-14 22:58:11 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:58:11,395 - WARNING - Could not retrieve variants from source file in region 10:93668197-93668598. Error was invalid region `10:93668198-93668598`
[2016-04-15T05:58Z] 2016-04-14 22:58:12 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:58:12,341 - WARNING - Could not retrieve variants from source file in region 10:88702139-88730502. Error was invalid region `10:88702140-88730502`
[2016-04-15T05:58Z] 2016-04-14 22:58:14 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:58:14,155 - WARNING - Could not retrieve variants from source file in region 10:79616394-79616795. Error was invalid region `10:79616395-79616795`
[2016-04-15T05:58Z] 2016-04-14 22:58:14 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:58:14,167 - WARNING - Could not retrieve variants from source file in region 10:84745045-84745446. Error was invalid region `10:84745046-84745446`
[2016-04-15T05:58Z] 2016-04-14 22:58:14 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:58:14,465 - WARNING - Could not retrieve variants from source file in region 10:88277246-88277647. Error was invalid region `10:88277247-88277647`
[2016-04-15T05:58Z] 2016-04-14 22:58:15 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:58:15,365 - WARNING - Could not retrieve variants from source file in region 10:91099419-91099820. Error was invalid region `10:91099420-91099820`
[2016-04-15T05:58Z] 2016-04-14 22:58:16 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:58:16,473 - WARNING - Could not retrieve variants from source file in region 10:93668197-93668598. Error was invalid region `10:93668198-93668598`
[2016-04-15T05:58Z] 2016-04-14 22:58:17 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:58:17,827 - WARNING - Could not retrieve variants from source file in region 10:88820578-88820979. Error was invalid region `10:88820579-88820979`
[2016-04-15T05:58Z] 2016-04-14 22:58:18 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:58:18,714 - WARNING - Could not retrieve variants from source file in region 10:79394097-79394519. Error was invalid region `10:79394098-79394519`
[2016-04-15T05:58Z] 2016-04-14 22:58:19 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:58:19,081 - WARNING - Could not retrieve variants from source file in region 10:79616394-79616795. Error was invalid region `10:79616395-79616795`
[2016-04-15T05:58Z] 2016-04-14 22:58:19 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:58:19,545 - WARNING - Could not retrieve variants from source file in region 10:81697607-81706514. Error was invalid region `10:81697608-81706514`
[2016-04-15T05:58Z] 2016-04-14 22:58:19 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:58:19,619 - WARNING - Could not retrieve variants from source file in region 10:88277246-88277647. Error was invalid region `10:88277247-88277647`
[2016-04-15T05:58Z] 2016-04-14 22:58:19 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:58:19,634 - WARNING - Could not retrieve variants from source file in region 10:90342626-90356788. Error was invalid region `10:90342627-90356788`
[2016-04-15T05:58Z] 2016-04-14 22:58:19 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:58:19,787 - WARNING - Could not retrieve variants from source file in region 10:91099419-91099820. Error was invalid region `10:91099420-91099820`
[2016-04-15T05:58Z] 2016-04-14 22:58:23 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:58:23,462 - WARNING - Could not retrieve variants from source file in region 10:81697607-81706514. Error was invalid region `10:81697608-81706514`
[2016-04-15T05:58Z] 2016-04-14 22:58:23 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:58:23,802 - WARNING - Could not retrieve variants from source file in region 10:79394097-79394519. Error was invalid region `10:79394098-79394519`
[2016-04-15T05:58Z] 2016-04-14 22:58:24 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:58:24,970 - WARNING - Could not retrieve variants from source file in region 10:88277246-88277647. Error was invalid region `10:88277247-88277647`
[2016-04-15T05:58Z] 2016-04-14 22:58:30 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:58:30,128 - WARNING - Could not retrieve variants from source file in region 10:93170039-93170440. Error was invalid region `10:93170040-93170440`
[2016-04-15T05:58Z] 2016-04-14 22:58:32 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:58:32,248 - WARNING - Could not retrieve variants from source file in region 10:91007128-91007550. Error was invalid region `10:91007129-91007550`
[2016-04-15T05:58Z] 2016-04-14 22:58:32 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:58:32,581 - WARNING - Could not retrieve variants from source file in region 10:82095757-82122983. Error was invalid region `10:82095758-82122983`
[2016-04-15T05:58Z] 2016-04-14 22:58:34 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:58:34,226 - WARNING - Could not retrieve variants from source file in region 10:81064739-81065140. Error was invalid region `10:81064740-81065140`
[2016-04-15T05:58Z] 2016-04-14 22:58:34 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:58:34,785 - WARNING - Could not retrieve variants from source file in region 10:82033383-82040242. Error was invalid region `10:82033384-82040242`
[2016-04-15T05:58Z] 2016-04-14 22:58:35 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:58:35,304 - WARNING - Could not retrieve variants from source file in region 10:93170039-93170440. Error was invalid region `10:93170040-93170440`
[2016-04-15T05:58Z] 2016-04-14 22:58:35 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:58:35,974 - WARNING - Could not retrieve variants from source file in region 10:91470623-91503850. Error was invalid region `10:91470624-91503850`
[2016-04-15T05:58Z] 2016-04-14 22:58:36 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:58:36,815 - WARNING - Could not retrieve variants from source file in region 10:91404237-91405234. Error was invalid region `10:91404238-91405234`
[2016-04-15T05:58Z] 2016-04-14 22:58:37 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:58:37,369 - WARNING - Could not retrieve variants from source file in region 10:82095757-82122983. Error was invalid region `10:82095758-82122983`
[2016-04-15T05:58Z] 2016-04-14 22:58:38 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:58:38,153 - WARNING - Could not retrieve variants from source file in region 10:78944379-78944780. Error was invalid region `10:78944380-78944780`
[2016-04-15T05:58Z] 2016-04-14 22:58:39 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:58:39,048 - WARNING - Could not retrieve variants from source file in region 10:79566421-79590700. Error was invalid region `10:79566422-79590700`
[2016-04-15T05:58Z] 2016-04-14 22:58:40 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:58:40,464 - WARNING - Could not retrieve variants from source file in region 10:91065738-91066959. Error was invalid region `10:91065739-91066959`
[2016-04-15T05:58Z] 2016-04-14 22:58:40 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:58:40,807 - WARNING - Could not retrieve variants from source file in region 10:90044134-90044979. Error was invalid region `10:90044135-90044979`
[2016-04-15T05:58Z] 2016-04-14 22:58:41 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:58:41,047 - WARNING - Could not retrieve variants from source file in region 10:82033383-82040242. Error was invalid region `10:82033384-82040242`
[2016-04-15T05:58Z] 2016-04-14 22:58:41 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:58:41,128 - WARNING - Could not retrieve variants from source file in region 10:88202857-88203258. Error was invalid region `10:88202858-88203258`
[2016-04-15T05:58Z] 2016-04-14 22:58:41 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:58:41,249 - WARNING - Could not retrieve variants from source file in region 10:93170039-93170440. Error was invalid region `10:93170040-93170440`
[2016-04-15T05:58Z] 2016-04-14 22:58:41 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:58:41,657 - WARNING - Could not retrieve variants from source file in region 10:91470623-91503850. Error was invalid region `10:91470624-91503850`
[2016-04-15T05:58Z] 2016-04-14 22:58:42 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:58:42,388 - WARNING - Could not retrieve variants from source file in region 10:90429441-90438397. Error was invalid region `10:90429442-90438397`
[2016-04-15T05:58Z] 2016-04-14 22:58:42 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:58:42,892 - WARNING - Could not retrieve variants from source file in region 10:78944379-78944780. Error was invalid region `10:78944380-78944780`
[2016-04-15T05:58Z] 2016-04-14 22:58:43 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:58:43,829 - WARNING - Could not retrieve variants from source file in region 10:91352755-91353156. Error was invalid region `10:91352756-91353156`
[2016-04-15T05:58Z] 2016-04-14 22:58:45 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:58:45,367 - WARNING - Could not retrieve variants from source file in region 10:91065738-91066959. Error was invalid region `10:91065739-91066959`
[2016-04-15T05:58Z] 2016-04-14 22:58:45 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:58:45,474 - WARNING - Could not retrieve variants from source file in region 10:90044134-90044979. Error was invalid region `10:90044135-90044979`
[2016-04-15T05:58Z] 2016-04-14 22:58:46 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:58:46,680 - WARNING - Could not retrieve variants from source file in region 10:88202857-88203258. Error was invalid region `10:88202858-88203258`
[2016-04-15T05:58Z] 2016-04-14 22:58:47 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:58:47,572 - WARNING - Could not retrieve variants from source file in region 10:90429441-90438397. Error was invalid region `10:90429442-90438397`
[2016-04-15T05:58Z] 2016-04-14 22:58:48 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:58:48,097 - WARNING - Could not retrieve variants from source file in region 10:78944379-78944780. Error was invalid region `10:78944380-78944780`
[2016-04-15T05:58Z] 2016-04-14 22:58:50 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:58:50,118 - WARNING - Could not retrieve variants from source file in region 10:90044134-90044979. Error was invalid region `10:90044135-90044979`
[2016-04-15T05:58Z] 2016-04-14 22:58:51 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:58:51,048 - WARNING - Could not retrieve variants from source file in region 10:88202857-88203258. Error was invalid region `10:88202858-88203258`
[2016-04-15T05:58Z] 2016-04-14 22:58:54 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:58:54,876 - WARNING - Could not retrieve variants from source file in region 10:90771618-90772019. Error was invalid region `10:90771619-90772019`
[2016-04-15T05:58Z] 2016-04-14 22:58:55 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:58:55,369 - WARNING - Could not retrieve variants from source file in region 10:87898518-87898919. Error was invalid region `10:87898519-87898919`
[2016-04-15T05:58Z] 2016-04-14 22:58:55 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:58:55,633 - WARNING - Could not retrieve variants from source file in region 10:90966335-90967186. Error was invalid region `10:90966336-90967186`
[2016-04-15T05:58Z] 2016-04-14 22:58:56 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:58:56,646 - WARNING - Could not retrieve variants from source file in region 10:78823326-78823976. Error was invalid region `10:78823327-78823976`
[2016-04-15T05:58Z] 2016-04-14 22:58:57 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:58:57,146 - WARNING - Could not retrieve variants from source file in region 10:78823326-78823976. Error was invalid region `10:78823327-78823976`
[2016-04-15T05:58Z] 2016-04-14 22:58:57 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:58:57,183 - WARNING - Could not retrieve variants from source file in region 10:90672836-90683314. Error was invalid region `10:90672837-90683314`
[2016-04-15T05:58Z] 2016-04-14 22:58:59 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:58:59,440 - WARNING - Could not retrieve variants from source file in region 10:90771618-90772019. Error was invalid region `10:90771619-90772019`
[2016-04-15T05:58Z] 2016-04-14 22:58:59 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:58:59,585 - WARNING - Could not retrieve variants from source file in region 10:89267746-89268147. Error was invalid region `10:89267747-89268147`
[2016-04-15T05:58Z] 2016-04-14 22:58:59 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:58:59,875 - WARNING - Could not retrieve variants from source file in region 10:90966335-90967186. Error was invalid region `10:90966336-90967186`
[2016-04-15T05:59Z] 2016-04-14 22:59:00 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:59:00,327 - WARNING - Could not retrieve variants from source file in region 10:78644856-78646726. Error was invalid region `10:78644857-78646726`
[2016-04-15T05:59Z] 2016-04-14 22:59:00 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:59:00,942 - WARNING - Could not retrieve variants from source file in region 10:86273038-86273439. Error was invalid region `10:86273039-86273439`
[2016-04-15T05:59Z] 2016-04-14 22:59:01 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:59:01,372 - WARNING - Could not retrieve variants from source file in region 10:78823326-78823976. Error was invalid region `10:78823327-78823976`
[2016-04-15T05:59Z] 2016-04-14 22:59:03 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:59:03,125 - WARNING - Could not retrieve variants from source file in region 10:89267746-89268147. Error was invalid region `10:89267747-89268147`
[2016-04-15T05:59Z] 2016-04-14 22:59:03 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:59:03,570 - WARNING - Could not retrieve variants from source file in region 10:89267746-89268147. Error was invalid region `10:89267747-89268147`
[2016-04-15T05:59Z] 2016-04-14 22:59:03 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:59:03,745 - WARNING - Could not retrieve variants from source file in region 10:90771618-90772019. Error was invalid region `10:90771619-90772019`
[2016-04-15T05:59Z] 2016-04-14 22:59:04 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:59:04,024 - WARNING - Could not retrieve variants from source file in region 10:78644856-78646726. Error was invalid region `10:78644857-78646726`
[2016-04-15T05:59Z] 2016-04-14 22:59:06 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:59:06,881 - WARNING - Could not retrieve variants from source file in region 10:86273038-86273439. Error was invalid region `10:86273039-86273439`
[2016-04-15T05:59Z] 2016-04-14 22:59:09 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:59:09,304 - WARNING - Could not retrieve variants from source file in region 10:86130848-86131249. Error was invalid region `10:86130849-86131249`
[2016-04-15T05:59Z] 2016-04-14 22:59:09 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:59:09,309 - WARNING - Could not retrieve variants from source file in region 10:86130848-86131249. Error was invalid region `10:86130849-86131249`
[2016-04-15T05:59Z] ['bcbio-variation-recall', 'square', '-Xms750m', '-Xmx7280m', '-XX:+UseSerialGC', '-c', 16, '-r', u'10:93851587-111625070', '--caller', 'platypus', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/10/Batch1-10_93851586_111625070.vcf.gz', '/mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/10/Batch1-10_93851586_111625070.vcf-inputs.txt'] in region: 10:93851587-111625070
[2016-04-15T05:59Z] 2016-04-14 22:59:24 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:59:24,709 - WARNING - Could not retrieve variants from source file in region 10:97731697-97772548. Error was invalid region `10:97731698-97772548`
[2016-04-15T05:59Z] 2016-04-14 22:59:24 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:59:24,784 - WARNING - Could not retrieve variants from source file in region 10:108338596-108338997. Error was invalid region `10:108338597-108338997`
[2016-04-15T05:59Z] 2016-04-14 22:59:25 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:59:25,596 - WARNING - Could not retrieve variants from source file in region 10:99625108-99625509. Error was invalid region `10:99625109-99625509`
[2016-04-15T05:59Z] 2016-04-14 22:59:25 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:59:25,738 - WARNING - Could not retrieve variants from source file in region 10:98924382-98924783. Error was invalid region `10:98924383-98924783`
[2016-04-15T05:59Z] 2016-04-14 22:59:26 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:59:26,002 - WARNING - Could not retrieve variants from source file in region 10:97990372-97990773. Error was invalid region `10:97990373-97990773`
[2016-04-15T05:59Z] 2016-04-14 22:59:26 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:59:26,466 - WARNING - Could not retrieve variants from source file in region 10:98380066-98386748. Error was invalid region `10:98380067-98386748`
[2016-04-15T05:59Z] 2016-04-14 22:59:26 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:59:26,600 - WARNING - Could not retrieve variants from source file in region 10:101639585-101658070. Error was invalid region `10:101639586-101658070`
[2016-04-15T05:59Z] 2016-04-14 22:59:26 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:59:26,706 - WARNING - Could not retrieve variants from source file in region 10:98077916-98078429. Error was invalid region `10:98077917-98078429`
[2016-04-15T05:59Z] 2016-04-14 22:59:27 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:59:27,483 - WARNING - Could not retrieve variants from source file in region 10:97175715-97192514. Error was invalid region `10:97175716-97192514`
[2016-04-15T05:59Z] 2016-04-14 22:59:27 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:59:27,503 - WARNING - Could not retrieve variants from source file in region 10:98346368-98346769. Error was invalid region `10:98346369-98346769`
[2016-04-15T05:59Z] 2016-04-14 22:59:30 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:59:30,414 - WARNING - Could not retrieve variants from source file in region 10:97731697-97772548. Error was invalid region `10:97731698-97772548`
[2016-04-15T05:59Z] 2016-04-14 22:59:33 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:59:33,063 - WARNING - Could not retrieve variants from source file in region 10:102672852-102684846. Error was invalid region `10:102672853-102684846`
[2016-04-15T05:59Z] 2016-04-14 22:59:33 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:59:33,819 - WARNING - Could not retrieve variants from source file in region 10:98803041-98809056. Error was invalid region `10:98803042-98809056`
[2016-04-15T05:59Z] 2016-04-14 22:59:33 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:59:33,887 - WARNING - Could not retrieve variants from source file in region 10:97990372-97990773. Error was invalid region `10:97990373-97990773`
[2016-04-15T05:59Z] 2016-04-14 22:59:34 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:59:34,408 - WARNING - Could not retrieve variants from source file in region 10:102056534-102056935. Error was invalid region `10:102056535-102056935`
[2016-04-15T05:59Z] 2016-04-14 22:59:34 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:59:34,445 - WARNING - Could not retrieve variants from source file in region 10:98380066-98386748. Error was invalid region `10:98380067-98386748`
[2016-04-15T05:59Z] 2016-04-14 22:59:34 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:59:34,661 - WARNING - Could not retrieve variants from source file in region 10:98077916-98078429. Error was invalid region `10:98077917-98078429`
[2016-04-15T05:59Z] 2016-04-14 22:59:35 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:59:35,312 - WARNING - Could not retrieve variants from source file in region 10:96997609-96998010. Error was invalid region `10:96997610-96998010`
[2016-04-15T05:59Z] 2016-04-14 22:59:35 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:59:35,460 - WARNING - Could not retrieve variants from source file in region 10:104378815-104379216. Error was invalid region `10:104378816-104379216`
[2016-04-15T05:59Z] 2016-04-14 22:59:35 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:59:35,537 - WARNING - Could not retrieve variants from source file in region 10:97731697-97772548. Error was invalid region `10:97731698-97772548`
[2016-04-15T05:59Z] 2016-04-14 22:59:35 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:59:35,658 - WARNING - Could not retrieve variants from source file in region 10:108338596-108338997. Error was invalid region `10:108338597-108338997`
[2016-04-15T05:59Z] 2016-04-14 22:59:36 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:59:36,328 - WARNING - Could not retrieve variants from source file in region 10:99625108-99625509. Error was invalid region `10:99625109-99625509`
[2016-04-15T05:59Z] 2016-04-14 22:59:38 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:59:38,593 - WARNING - Could not retrieve variants from source file in region 10:102672852-102684846. Error was invalid region `10:102672853-102684846`
[2016-04-15T05:59Z] 2016-04-14 22:59:40 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:59:40,145 - WARNING - Could not retrieve variants from source file in region 10:98803041-98809056. Error was invalid region `10:98803042-98809056`
[2016-04-15T05:59Z] 2016-04-14 22:59:40 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:59:40,335 - WARNING - Could not retrieve variants from source file in region 10:97990372-97990773. Error was invalid region `10:97990373-97990773`
[2016-04-15T05:59Z] 2016-04-14 22:59:41 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:59:41,483 - WARNING - Could not retrieve variants from source file in region 10:98380066-98386748. Error was invalid region `10:98380067-98386748`
[2016-04-15T05:59Z] 2016-04-14 22:59:42 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:59:42,380 - WARNING - Could not retrieve variants from source file in region 10:98346368-98346769. Error was invalid region `10:98346369-98346769`
[2016-04-15T05:59Z] 2016-04-14 22:59:42 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:59:42,539 - WARNING - Could not retrieve variants from source file in region 10:98077916-98078429. Error was invalid region `10:98077917-98078429`
[2016-04-15T05:59Z] 2016-04-14 22:59:42 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:59:42,674 - WARNING - Could not retrieve variants from source file in region 10:96997609-96998010. Error was invalid region `10:96997610-96998010`
[2016-04-15T05:59Z] 2016-04-14 22:59:42 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:59:42,754 - WARNING - Could not retrieve variants from source file in region 10:104378815-104379216. Error was invalid region `10:104378816-104379216`
[2016-04-15T05:59Z] 2016-04-14 22:59:52 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:59:52,646 - WARNING - Could not retrieve variants from source file in region 10:99531360-99531761. Error was invalid region `10:99531361-99531761`
[2016-04-15T05:59Z] 2016-04-14 22:59:53 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:59:53,728 - WARNING - Could not retrieve variants from source file in region 10:106907229-106907660. Error was invalid region `10:106907230-106907660`
[2016-04-15T05:59Z] 2016-04-14 22:59:54 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:59:54,204 - WARNING - Could not retrieve variants from source file in region 10:98469296-98469697. Error was invalid region `10:98469297-98469697`
[2016-04-15T05:59Z] 2016-04-14 22:59:54 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:59:54,802 - WARNING - Could not retrieve variants from source file in region 10:102568772-102569173. Error was invalid region `10:102568773-102569173`
[2016-04-15T05:59Z] 2016-04-14 22:59:56 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:59:56,381 - WARNING - Could not retrieve variants from source file in region 10:101964101-101978073. Error was invalid region `10:101964102-101978073`
[2016-04-15T05:59Z] 2016-04-14 22:59:56 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:59:56,593 - WARNING - Could not retrieve variants from source file in region 10:99531360-99531761. Error was invalid region `10:99531361-99531761`
[2016-04-15T05:59Z] 2016-04-14 22:59:57 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:59:57,404 - WARNING - Could not retrieve variants from source file in region 10:101603996-101604397. Error was invalid region `10:101603997-101604397`
[2016-04-15T05:59Z] 2016-04-14 22:59:57 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 22:59:57,716 - WARNING - Could not retrieve variants from source file in region 10:101829303-101829704. Error was invalid region `10:101829304-101829704`
[2016-04-15T06:00Z] 2016-04-14 23:00:00 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:00:00,735 - WARNING - Could not retrieve variants from source file in region 10:104210524-104236877. Error was invalid region `10:104210525-104236877`
[2016-04-15T06:00Z] 2016-04-14 23:00:00 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:00:00,977 - WARNING - Could not retrieve variants from source file in region 10:99531360-99531761. Error was invalid region `10:99531361-99531761`
[2016-04-15T06:00Z] 2016-04-14 23:00:03 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:00:03,032 - WARNING - Could not retrieve variants from source file in region 10:106907229-106907660. Error was invalid region `10:106907230-106907660`
[2016-04-15T06:00Z] 2016-04-14 23:00:03 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:00:03,495 - WARNING - Could not retrieve variants from source file in region 10:98469296-98469697. Error was invalid region `10:98469297-98469697`
[2016-04-15T06:00Z] 2016-04-14 23:00:04 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:00:04,590 - WARNING - Could not retrieve variants from source file in region 10:97141312-97144016. Error was invalid region `10:97141313-97144016`
[2016-04-15T06:00Z] 2016-04-14 23:00:14 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:00:14,254 - WARNING - Could not retrieve variants from source file in region 10:99498023-99504820. Error was invalid region `10:99498024-99504820`
[2016-04-15T06:00Z] 2016-04-14 23:00:17 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:00:17,652 - WARNING - Could not retrieve variants from source file in region 10:106073357-106075271. Error was invalid region `10:106073358-106075271`
[2016-04-15T06:00Z] 2016-04-14 23:00:17 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:00:17,849 - WARNING - Could not retrieve variants from source file in region 10:97105954-97106355. Error was invalid region `10:97105955-97106355`
[2016-04-15T06:00Z] 2016-04-14 23:00:17 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:00:17,928 - WARNING - Could not retrieve variants from source file in region 10:97365896-97388352. Error was invalid region `10:97365897-97388352`
[2016-04-15T06:00Z] 2016-04-14 23:00:18 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:00:18,470 - WARNING - Could not retrieve variants from source file in region 10:97105954-97106355. Error was invalid region `10:97105955-97106355`
[2016-04-15T06:00Z] 2016-04-14 23:00:19 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:00:19,536 - WARNING - Could not retrieve variants from source file in region 10:101802051-101802452. Error was invalid region `10:101802052-101802452`
[2016-04-15T06:00Z] 2016-04-14 23:00:19 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:00:19,654 - WARNING - Could not retrieve variants from source file in region 10:99498023-99504820. Error was invalid region `10:99498024-99504820`
[2016-04-15T06:00Z] 2016-04-14 23:00:20 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:00:20,015 - WARNING - Could not retrieve variants from source file in region 10:101544236-101544637. Error was invalid region `10:101544237-101544637`
[2016-04-15T06:00Z] 2016-04-14 23:00:20 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:00:20,855 - WARNING - Could not retrieve variants from source file in region 10:101911853-101912254. Error was invalid region `10:101911854-101912254`
[2016-04-15T06:00Z] 2016-04-14 23:00:21 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:00:21,426 - WARNING - Could not retrieve variants from source file in region 10:99005872-99019367. Error was invalid region `10:99005873-99019367`
[2016-04-15T06:00Z] 2016-04-14 23:00:21 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:00:21,976 - WARNING - Could not retrieve variants from source file in region 10:101715688-101716302. Error was invalid region `10:101715689-101716302`
[2016-04-15T06:00Z] 2016-04-14 23:00:22 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:00:22,689 - WARNING - Could not retrieve variants from source file in region 10:106073357-106075271. Error was invalid region `10:106073358-106075271`
[2016-04-15T06:00Z] 2016-04-14 23:00:23 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:00:23,356 - WARNING - Could not retrieve variants from source file in region 10:97105954-97106355. Error was invalid region `10:97105955-97106355`
[2016-04-15T06:00Z] 2016-04-14 23:00:24 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:00:24,649 - WARNING - Could not retrieve variants from source file in region 10:99498023-99504820. Error was invalid region `10:99498024-99504820`
[2016-04-15T06:00Z] 2016-04-14 23:00:24 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:00:24,658 - WARNING - Could not retrieve variants from source file in region 10:102222746-102269396. Error was invalid region `10:102222747-102269396`
[2016-04-15T06:00Z] 2016-04-14 23:00:24 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:00:24,935 - WARNING - Could not retrieve variants from source file in region 10:101544236-101544637. Error was invalid region `10:101544237-101544637`
[2016-04-15T06:00Z] 2016-04-14 23:00:25 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:00:25,573 - WARNING - Could not retrieve variants from source file in region 10:101911853-101912254. Error was invalid region `10:101911854-101912254`
[2016-04-15T06:00Z] 2016-04-14 23:00:25 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:00:25,841 - WARNING - Could not retrieve variants from source file in region 10:99005872-99019367. Error was invalid region `10:99005873-99019367`
[2016-04-15T06:00Z] 2016-04-14 23:00:28 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:00:28,219 - WARNING - Could not retrieve variants from source file in region 10:106073357-106075271. Error was invalid region `10:106073358-106075271`
[2016-04-15T06:00Z] 2016-04-14 23:00:29 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:00:29,542 - WARNING - Could not retrieve variants from source file in region 10:102222746-102269396. Error was invalid region `10:102222747-102269396`
[2016-04-15T06:00Z] 2016-04-14 23:00:29 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:00:29,872 - WARNING - Could not retrieve variants from source file in region 10:101544236-101544637. Error was invalid region `10:101544237-101544637`
[2016-04-15T06:00Z] 2016-04-14 23:00:30 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:00:30,531 - WARNING - Could not retrieve variants from source file in region 10:101911853-101912254. Error was invalid region `10:101911854-101912254`
[2016-04-15T06:00Z] 2016-04-14 23:00:31 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:00:31,130 - WARNING - Could not retrieve variants from source file in region 10:104136258-104175085. Error was invalid region `10:104136259-104175085`
[2016-04-15T06:00Z] 2016-04-14 23:00:36 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:00:36,008 - WARNING - Could not retrieve variants from source file in region 10:96740770-96748927. Error was invalid region `10:96740771-96748927`
[2016-04-15T06:00Z] 2016-04-14 23:00:42 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:00:42,706 - WARNING - Could not retrieve variants from source file in region 10:95891913-95892314. Error was invalid region `10:95891914-95892314`
[2016-04-15T06:00Z] 2016-04-14 23:00:45 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:00:45,384 - WARNING - Could not retrieve variants from source file in region 10:99393023-99393424. Error was invalid region `10:99393024-99393424`
[2016-04-15T06:00Z] 2016-04-14 23:00:47 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:00:47,584 - WARNING - Could not retrieve variants from source file in region 10:105657105-105660016. Error was invalid region `10:105657106-105660016`
[2016-04-15T06:00Z] 2016-04-14 23:00:48 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:00:48,947 - WARNING - Could not retrieve variants from source file in region 10:101419897-101420298. Error was invalid region `10:101419898-101420298`
[2016-04-15T06:00Z] 2016-04-14 23:00:49 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:00:49,317 - WARNING - Could not retrieve variants from source file in region 10:103555400-103555801. Error was invalid region `10:103555401-103555801`
[2016-04-15T06:00Z] 2016-04-14 23:00:50 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:00:50,041 - WARNING - Could not retrieve variants from source file in region 10:106022578-106022979. Error was invalid region `10:106022579-106022979`
[2016-04-15T06:00Z] 2016-04-14 23:00:50 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:00:50,866 - WARNING - Could not retrieve variants from source file in region 10:96492847-96493548. Error was invalid region `10:96492848-96493548`
[2016-04-15T06:00Z] 2016-04-14 23:00:50 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:00:50,891 - WARNING - Could not retrieve variants from source file in region 10:102116100-102116501. Error was invalid region `10:102116101-102116501`
[2016-04-15T06:00Z] 2016-04-14 23:00:51 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:00:51,668 - WARNING - Could not retrieve variants from source file in region 10:103991170-103991571. Error was invalid region `10:103991171-103991571`
[2016-04-15T06:00Z] 2016-04-14 23:00:51 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:00:51,993 - WARNING - Could not retrieve variants from source file in region 10:96602411-96602813. Error was invalid region `10:96602412-96602813`
[2016-04-15T06:00Z] 2016-04-14 23:00:53 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:00:53,414 - WARNING - Could not retrieve variants from source file in region 10:94695406-94714617. Error was invalid region `10:94695407-94714617`
[2016-04-15T06:00Z] 2016-04-14 23:00:53 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:00:53,453 - WARNING - Could not retrieve variants from source file in region 10:105657105-105660016. Error was invalid region `10:105657106-105660016`
[2016-04-15T06:00Z] 2016-04-14 23:00:54 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:00:54,988 - WARNING - Could not retrieve variants from source file in region 10:101419897-101420298. Error was invalid region `10:101419898-101420298`
[2016-04-15T06:00Z] 2016-04-14 23:00:56 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:00:56,737 - WARNING - Could not retrieve variants from source file in region 10:106022578-106022979. Error was invalid region `10:106022579-106022979`
[2016-04-15T06:00Z] 2016-04-14 23:00:56 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:00:56,901 - WARNING - Could not retrieve variants from source file in region 10:96492847-96493548. Error was invalid region `10:96492848-96493548`
[2016-04-15T06:00Z] 2016-04-14 23:00:57 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:00:57,335 - WARNING - Could not retrieve variants from source file in region 10:96602411-96602813. Error was invalid region `10:96602412-96602813`
[2016-04-15T06:00Z] 2016-04-14 23:00:58 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:00:58,524 - WARNING - Could not retrieve variants from source file in region 10:105657105-105660016. Error was invalid region `10:105657106-105660016`
[2016-04-15T06:01Z] 2016-04-14 23:01:03 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:01:03,038 - WARNING - Could not retrieve variants from source file in region 10:103991170-103991571. Error was invalid region `10:103991171-103991571`
[2016-04-15T06:01Z] 2016-04-14 23:01:10 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:01:10,312 - WARNING - Could not retrieve variants from source file in region 10:96104454-96115025. Error was invalid region `10:96104455-96115025`
[2016-04-15T06:01Z] 2016-04-14 23:01:10 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:01:10,345 - WARNING - Could not retrieve variants from source file in region 10:95791402-95791953. Error was invalid region `10:95791403-95791953`
[2016-04-15T06:01Z] 2016-04-14 23:01:10 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:01:10,927 - WARNING - Could not retrieve variants from source file in region 10:99337361-99350318. Error was invalid region `10:99337362-99350318`
[2016-04-15T06:01Z] 2016-04-14 23:01:11 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:01:11,127 - WARNING - Could not retrieve variants from source file in region 10:105793539-105824523. Error was invalid region `10:105793540-105824523`
[2016-04-15T06:01Z] 2016-04-14 23:01:11 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:01:11,750 - WARNING - Could not retrieve variants from source file in region 10:96313749-96314150. Error was invalid region `10:96313750-96314150`
[2016-04-15T06:01Z] 2016-04-14 23:01:13 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:01:13,792 - WARNING - Could not retrieve variants from source file in region 10:94594354-94594755. Error was invalid region `10:94594355-94594755`
[2016-04-15T06:01Z] 2016-04-14 23:01:13 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:01:13,941 - WARNING - Could not retrieve variants from source file in region 10:95552442-95552843. Error was invalid region `10:95552443-95552843`
[2016-04-15T06:01Z] 2016-04-14 23:01:14 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:01:14,821 - WARNING - Could not retrieve variants from source file in region 10:95072695-95073096. Error was invalid region `10:95072696-95073096`
[2016-04-15T06:01Z] 2016-04-14 23:01:17 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:01:17,197 - WARNING - Could not retrieve variants from source file in region 10:96104454-96115025. Error was invalid region `10:96104455-96115025`
[2016-04-15T06:01Z] 2016-04-14 23:01:17 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:01:17,219 - WARNING - Could not retrieve variants from source file in region 10:101292824-101295467. Error was invalid region `10:101292825-101295467`
[2016-04-15T06:01Z] 2016-04-14 23:01:17 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:01:17,417 - WARNING - Could not retrieve variants from source file in region 10:96313749-96314150. Error was invalid region `10:96313750-96314150`
[2016-04-15T06:01Z] 2016-04-14 23:01:17 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:01:17,792 - WARNING - Could not retrieve variants from source file in region 10:103874126-103899748. Error was invalid region `10:103874127-103899748`
[2016-04-15T06:01Z] 2016-04-14 23:01:18 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:01:18,360 - WARNING - Could not retrieve variants from source file in region 10:96162828-96163229. Error was invalid region `10:96162829-96163229`
[2016-04-15T06:01Z] 2016-04-14 23:01:19 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:01:19,014 - WARNING - Could not retrieve variants from source file in region 10:94594354-94594755. Error was invalid region `10:94594355-94594755`
[2016-04-15T06:01Z] 2016-04-14 23:01:19 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:01:19,039 - WARNING - Could not retrieve variants from source file in region 10:95552442-95552843. Error was invalid region `10:95552443-95552843`
[2016-04-15T06:01Z] 2016-04-14 23:01:19 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:01:19,299 - WARNING - Could not retrieve variants from source file in region 10:95072695-95073096. Error was invalid region `10:95072696-95073096`
[2016-04-15T06:01Z] 2016-04-14 23:01:21 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:01:21,702 - WARNING - Could not retrieve variants from source file in region 10:96104454-96115025. Error was invalid region `10:96104455-96115025`
[2016-04-15T06:01Z] 2016-04-14 23:01:23 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:01:23,645 - WARNING - Could not retrieve variants from source file in region 10:96313749-96314150. Error was invalid region `10:96313750-96314150`
[2016-04-15T06:01Z] 2016-04-14 23:01:23 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:01:23,699 - WARNING - Could not retrieve variants from source file in region 10:101292824-101295467. Error was invalid region `10:101292825-101295467`
[2016-04-15T06:01Z] 2016-04-14 23:01:24 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:01:24,252 - WARNING - Could not retrieve variants from source file in region 10:105344545-105373113. Error was invalid region `10:105344546-105373113`
[2016-04-15T06:01Z] 2016-04-14 23:01:24 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:01:24,642 - WARNING - Could not retrieve variants from source file in region 10:96162828-96163229. Error was invalid region `10:96162829-96163229`
[2016-04-15T06:01Z] 2016-04-14 23:01:24 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:01:24,684 - WARNING - Could not retrieve variants from source file in region 10:95552442-95552843. Error was invalid region `10:95552443-95552843`
[2016-04-15T06:01Z] 2016-04-14 23:01:24 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:01:24,865 - WARNING - Could not retrieve variants from source file in region 10:93999351-94000040. Error was invalid region `10:93999352-94000040`
[2016-04-15T06:01Z] 2016-04-14 23:01:24 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:01:24,869 - WARNING - Could not retrieve variants from source file in region 10:94594354-94594755. Error was invalid region `10:94594355-94594755`
[2016-04-15T06:01Z] 2016-04-14 23:01:24 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:01:24,951 - WARNING - Could not retrieve variants from source file in region 10:95072695-95073096. Error was invalid region `10:95072696-95073096`
[2016-04-15T06:01Z] 2016-04-14 23:01:30 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:01:30,784 - WARNING - Could not retrieve variants from source file in region 10:96162828-96163229. Error was invalid region `10:96162829-96163229`
[2016-04-15T06:01Z] 2016-04-14 23:01:35 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:01:35,737 - WARNING - Could not retrieve variants from source file in region 10:103285689-103286090. Error was invalid region `10:103285690-103286090`
[2016-04-15T06:01Z] 2016-04-14 23:01:37 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:01:37,406 - WARNING - Could not retrieve variants from source file in region 10:101090217-101090618. Error was invalid region `10:101090218-101090618`
[2016-04-15T06:01Z] 2016-04-14 23:01:40 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:01:40,435 - WARNING - Could not retrieve variants from source file in region 10:95441061-95460007. Error was invalid region `10:95441062-95460007`
[2016-04-15T06:01Z] 2016-04-14 23:01:40 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:01:40,694 - WARNING - Could not retrieve variants from source file in region 10:96039386-96039787. Error was invalid region `10:96039387-96039787`
[2016-04-15T06:01Z] 2016-04-14 23:01:41 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:01:41,787 - WARNING - Could not retrieve variants from source file in region 10:101090217-101090618. Error was invalid region `10:101090218-101090618`
[2016-04-15T06:01Z] 2016-04-14 23:01:43 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:01:43,761 - WARNING - Could not retrieve variants from source file in region 10:95930876-95931277. Error was invalid region `10:95930877-95931277`
[2016-04-15T06:01Z] 2016-04-14 23:01:43 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:01:43,797 - WARNING - Could not retrieve variants from source file in region 10:105110529-105128324. Error was invalid region `10:105110530-105128324`
[2016-04-15T06:01Z] 2016-04-14 23:01:44 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:01:44,666 - WARNING - Could not retrieve variants from source file in region 10:95360753-95395554. Error was invalid region `10:95360754-95395554`
[2016-04-15T06:01Z] 2016-04-14 23:01:44 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:01:44,677 - WARNING - Could not retrieve variants from source file in region 10:95930876-95931277. Error was invalid region `10:95930877-95931277`
[2016-04-15T06:01Z] 2016-04-14 23:01:45 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:01:45,327 - WARNING - Could not retrieve variants from source file in region 10:96039386-96039787. Error was invalid region `10:96039387-96039787`
[2016-04-15T06:01Z] 2016-04-14 23:01:46 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:01:46,430 - WARNING - Could not retrieve variants from source file in region 10:101090217-101090618. Error was invalid region `10:101090218-101090618`
[2016-04-15T06:01Z] 2016-04-14 23:01:47 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:01:47,454 - WARNING - Could not retrieve variants from source file in region 10:102824138-102849645. Error was invalid region `10:102824139-102849645`
[2016-04-15T06:01Z] 2016-04-14 23:01:48 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:01:48,034 - WARNING - Could not retrieve variants from source file in region 10:95930876-95931277. Error was invalid region `10:95930877-95931277`
[2016-04-15T06:01Z] 2016-04-14 23:01:48 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:01:48,417 - WARNING - Could not retrieve variants from source file in region 10:105110529-105128324. Error was invalid region `10:105110530-105128324`
[2016-04-15T06:01Z] 2016-04-14 23:01:50 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:01:50,077 - WARNING - Could not retrieve variants from source file in region 10:104572752-104573207. Error was invalid region `10:104572753-104573207`
[2016-04-15T06:01Z] 2016-04-14 23:01:56 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:01:56,117 - WARNING - Could not retrieve variants from source file in region 10:102797048-102798536. Error was invalid region `10:102797049-102798536`
[2016-04-15T06:01Z] 2016-04-14 23:01:57 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:01:57,883 - WARNING - Could not retrieve variants from source file in region 10:99695792-99696193. Error was invalid region `10:99695793-99696193`
[2016-04-15T06:01Z] 2016-04-14 23:01:57 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:01:57,895 - WARNING - Could not retrieve variants from source file in region 10:99695792-99696193. Error was invalid region `10:99695793-99696193`
[2016-04-15T06:02Z] ['bcbio-variation-recall', 'square', '-Xms750m', '-Xmx7280m', '-XX:+UseSerialGC', '-c', 16, '-r', u'10:111628372-127265443', '--caller', 'platypus', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/10/Batch1-10_111628371_127265443.vcf.gz', '/mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/10/Batch1-10_111628371_127265443.vcf-inputs.txt'] in region: 10:111628372-127265443
[2016-04-15T06:02Z] 2016-04-14 23:02:16 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:02:16,438 - WARNING - Could not retrieve variants from source file in region 10:118231149-118231553. Error was invalid region `10:118231150-118231553`
[2016-04-15T06:02Z] 2016-04-14 23:02:17 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:02:17,293 - WARNING - Could not retrieve variants from source file in region 10:122645165-122665948. Error was invalid region `10:122645166-122665948`
[2016-04-15T06:02Z] 2016-04-14 23:02:17 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:02:17,356 - WARNING - Could not retrieve variants from source file in region 10:126214557-126214958. Error was invalid region `10:126214558-126214958`
[2016-04-15T06:02Z] 2016-04-14 23:02:18 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:02:18,026 - WARNING - Could not retrieve variants from source file in region 10:118733351-118733752. Error was invalid region `10:118733352-118733752`
[2016-04-15T06:02Z] 2016-04-14 23:02:18 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:02:18,166 - WARNING - Could not retrieve variants from source file in region 10:116930890-116931291. Error was invalid region `10:116930891-116931291`
[2016-04-15T06:02Z] 2016-04-14 23:02:18 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:02:18,458 - WARNING - Could not retrieve variants from source file in region 10:116391780-116392181. Error was invalid region `10:116391781-116392181`
[2016-04-15T06:02Z] 2016-04-14 23:02:18 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:02:18,651 - WARNING - Could not retrieve variants from source file in region 10:127265163-127265564. Error was invalid region `10:127265164-127265564`
[2016-04-15T06:02Z] 2016-04-14 23:02:18 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:02:18,925 - WARNING - Could not retrieve variants from source file in region 10:117486552-117486953. Error was invalid region `10:117486553-117486953`
[2016-04-15T06:02Z] 2016-04-14 23:02:19 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:02:19,104 - WARNING - Could not retrieve variants from source file in region 10:118969135-118969536. Error was invalid region `10:118969136-118969536`
[2016-04-15T06:02Z] 2016-04-14 23:02:19 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:02:19,145 - WARNING - Could not retrieve variants from source file in region 10:124088825-124096251. Error was invalid region `10:124088826-124096251`
[2016-04-15T06:02Z] 2016-04-14 23:02:22 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:02:22,986 - WARNING - Could not retrieve variants from source file in region 10:118231149-118231553. Error was invalid region `10:118231150-118231553`
[2016-04-15T06:02Z] 2016-04-14 23:02:26 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:02:26,310 - WARNING - Could not retrieve variants from source file in region 10:124580348-124610217. Error was invalid region `10:124580349-124610217`
[2016-04-15T06:02Z] 2016-04-14 23:02:26 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:02:26,782 - WARNING - Could not retrieve variants from source file in region 10:118733351-118733752. Error was invalid region `10:118733352-118733752`
[2016-04-15T06:02Z] 2016-04-14 23:02:26 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:02:26,865 - WARNING - Could not retrieve variants from source file in region 10:116930890-116931291. Error was invalid region `10:116930891-116931291`
[2016-04-15T06:02Z] 2016-04-14 23:02:27 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:02:27,747 - WARNING - Could not retrieve variants from source file in region 10:127265163-127265564. Error was invalid region `10:127265164-127265564`
[2016-04-15T06:02Z] 2016-04-14 23:02:28 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:02:28,542 - WARNING - Could not retrieve variants from source file in region 10:112559413-112595909. Error was invalid region `10:112559414-112595909`
[2016-04-15T06:02Z] 2016-04-14 23:02:28 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:02:28,579 - WARNING - Could not retrieve variants from source file in region 10:117486552-117486953. Error was invalid region `10:117486553-117486953`
[2016-04-15T06:02Z] 2016-04-14 23:02:28 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:02:28,596 - WARNING - Could not retrieve variants from source file in region 10:119768340-119774767. Error was invalid region `10:119768341-119774767`
[2016-04-15T06:02Z] 2016-04-14 23:02:29 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:02:29,122 - WARNING - Could not retrieve variants from source file in region 10:116391780-116392181. Error was invalid region `10:116391781-116392181`
[2016-04-15T06:02Z] 2016-04-14 23:02:29 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:02:29,217 - WARNING - Could not retrieve variants from source file in region 10:118231149-118231553. Error was invalid region `10:118231150-118231553`
[2016-04-15T06:02Z] 2016-04-14 23:02:31 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:02:31,113 - WARNING - Could not retrieve variants from source file in region 10:126214557-126214958. Error was invalid region `10:126214558-126214958`
[2016-04-15T06:02Z] 2016-04-14 23:02:31 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:02:31,248 - WARNING - Could not retrieve variants from source file in region 10:124580348-124610217. Error was invalid region `10:124580349-124610217`
[2016-04-15T06:02Z] 2016-04-14 23:02:31 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:02:31,326 - WARNING - Could not retrieve variants from source file in region 10:122645165-122665948. Error was invalid region `10:122645166-122665948`
[2016-04-15T06:02Z] 2016-04-14 23:02:31 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:02:31,913 - WARNING - Could not retrieve variants from source file in region 10:118733351-118733752. Error was invalid region `10:118733352-118733752`
[2016-04-15T06:02Z] 2016-04-14 23:02:32 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:02:32,871 - WARNING - Could not retrieve variants from source file in region 10:116930890-116931291. Error was invalid region `10:116930891-116931291`
[2016-04-15T06:02Z] 2016-04-14 23:02:34 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:02:34,964 - WARNING - Could not retrieve variants from source file in region 10:118969135-118969536. Error was invalid region `10:118969136-118969536`
[2016-04-15T06:02Z] 2016-04-14 23:02:35 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:02:35,063 - WARNING - Could not retrieve variants from source file in region 10:112559413-112595909. Error was invalid region `10:112559414-112595909`
[2016-04-15T06:02Z] 2016-04-14 23:02:35 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:02:35,467 - WARNING - Could not retrieve variants from source file in region 10:124088825-124096251. Error was invalid region `10:124088826-124096251`
[2016-04-15T06:02Z] 2016-04-14 23:02:35 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:02:35,767 - WARNING - Could not retrieve variants from source file in region 10:127265163-127265564. Error was invalid region `10:127265164-127265564`
[2016-04-15T06:02Z] 2016-04-14 23:02:35 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:02:35,854 - WARNING - Could not retrieve variants from source file in region 10:116391780-116392181. Error was invalid region `10:116391781-116392181`
[2016-04-15T06:02Z] 2016-04-14 23:02:36 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:02:36,074 - WARNING - Could not retrieve variants from source file in region 10:117486552-117486953. Error was invalid region `10:117486553-117486953`
[2016-04-15T06:02Z] 2016-04-14 23:02:36 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:02:36,208 - WARNING - Could not retrieve variants from source file in region 10:119768340-119774767. Error was invalid region `10:119768341-119774767`
[2016-04-15T06:02Z] 2016-04-14 23:02:45 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:02:45,639 - WARNING - Could not retrieve variants from source file in region 10:114200144-114200545. Error was invalid region `10:114200145-114200545`
[2016-04-15T06:02Z] 2016-04-14 23:02:46 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:02:46,640 - WARNING - Could not retrieve variants from source file in region 10:126172652-126173053. Error was invalid region `10:126172653-126173053`
[2016-04-15T06:02Z] 2016-04-14 23:02:46 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:02:46,970 - WARNING - Could not retrieve variants from source file in region 10:118313054-118313455. Error was invalid region `10:118313055-118313455`
[2016-04-15T06:02Z] 2016-04-14 23:02:48 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:02:48,077 - WARNING - Could not retrieve variants from source file in region 10:118660779-118661180. Error was invalid region `10:118660780-118661180`
[2016-04-15T06:02Z] 2016-04-14 23:02:48 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:02:48,077 - WARNING - Could not retrieve variants from source file in region 10:122340645-122349159. Error was invalid region `10:122340646-122349159`
[2016-04-15T06:02Z] 2016-04-14 23:02:49 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:02:49,715 - WARNING - Could not retrieve variants from source file in region 10:124457241-124459329. Error was invalid region `10:124457242-124459329`
[2016-04-15T06:02Z] 2016-04-14 23:02:50 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:02:50,163 - WARNING - Could not retrieve variants from source file in region 10:116856332-116856733. Error was invalid region `10:116856333-116856733`
[2016-04-15T06:02Z] 2016-04-14 23:02:51 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:02:51,089 - WARNING - Could not retrieve variants from source file in region 10:118030204-118030605. Error was invalid region `10:118030205-118030605`
[2016-04-15T06:02Z] 2016-04-14 23:02:51 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:02:51,397 - WARNING - Could not retrieve variants from source file in region 10:114200144-114200545. Error was invalid region `10:114200145-114200545`
[2016-04-15T06:02Z] 2016-04-14 23:02:51 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:02:51,939 - WARNING - Could not retrieve variants from source file in region 10:118893020-118893421. Error was invalid region `10:118893021-118893421`
[2016-04-15T06:02Z] 2016-04-14 23:02:52 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:02:52,343 - WARNING - Could not retrieve variants from source file in region 10:112404091-112404492. Error was invalid region `10:112404092-112404492`
[2016-04-15T06:02Z] 2016-04-14 23:02:53 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:02:53,182 - WARNING - Could not retrieve variants from source file in region 10:126172652-126173053. Error was invalid region `10:126172653-126173053`
[2016-04-15T06:02Z] 2016-04-14 23:02:53 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:02:53,394 - WARNING - Could not retrieve variants from source file in region 10:123976031-123997166. Error was invalid region `10:123976032-123997166`
[2016-04-15T06:02Z] 2016-04-14 23:02:53 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:02:53,518 - WARNING - Could not retrieve variants from source file in region 10:125426201-125426755. Error was invalid region `10:125426202-125426755`
[2016-04-15T06:02Z] 2016-04-14 23:02:53 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:02:53,899 - WARNING - Could not retrieve variants from source file in region 10:118313054-118313455. Error was invalid region `10:118313055-118313455`
[2016-04-15T06:02Z] 2016-04-14 23:02:54 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:02:54,050 - WARNING - Could not retrieve variants from source file in region 10:118660779-118661180. Error was invalid region `10:118660780-118661180`
[2016-04-15T06:02Z] 2016-04-14 23:02:54 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:02:54,180 - WARNING - Could not retrieve variants from source file in region 10:122340645-122349159. Error was invalid region `10:122340646-122349159`
[2016-04-15T06:02Z] 2016-04-14 23:02:54 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:02:54,535 - WARNING - Could not retrieve variants from source file in region 10:126714503-126716536. Error was invalid region `10:126714504-126716536`
[2016-04-15T06:02Z] 2016-04-14 23:02:54 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:02:54,745 - WARNING - Could not retrieve variants from source file in region 10:117228583-117228984. Error was invalid region `10:117228584-117228984`
[2016-04-15T06:02Z] 2016-04-14 23:02:54 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:02:54,821 - WARNING - Could not retrieve variants from source file in region 10:116335035-116335436. Error was invalid region `10:116335036-116335436`
[2016-04-15T06:02Z] 2016-04-14 23:02:54 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:02:54,910 - WARNING - Could not retrieve variants from source file in region 10:124457241-124459329. Error was invalid region `10:124457242-124459329`
[2016-04-15T06:02Z] 2016-04-14 23:02:55 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:02:55,239 - WARNING - Could not retrieve variants from source file in region 10:116856332-116856733. Error was invalid region `10:116856333-116856733`
[2016-04-15T06:02Z] 2016-04-14 23:02:56 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:02:56,660 - WARNING - Could not retrieve variants from source file in region 10:114200144-114200545. Error was invalid region `10:114200145-114200545`
[2016-04-15T06:02Z] 2016-04-14 23:02:56 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:02:56,724 - WARNING - Could not retrieve variants from source file in region 10:118030204-118030605. Error was invalid region `10:118030205-118030605`
[2016-04-15T06:02Z] 2016-04-14 23:02:57 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:02:57,093 - WARNING - Could not retrieve variants from source file in region 10:118893020-118893421. Error was invalid region `10:118893021-118893421`
[2016-04-15T06:02Z] 2016-04-14 23:02:59 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:02:59,130 - WARNING - Could not retrieve variants from source file in region 10:126172652-126173053. Error was invalid region `10:126172653-126173053`
[2016-04-15T06:02Z] 2016-04-14 23:02:59 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:02:59,888 - WARNING - Could not retrieve variants from source file in region 10:125426201-125426755. Error was invalid region `10:125426202-125426755`
[2016-04-15T06:03Z] 2016-04-14 23:03:00 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:03:00,743 - WARNING - Could not retrieve variants from source file in region 10:118313054-118313455. Error was invalid region `10:118313055-118313455`
[2016-04-15T06:03Z] 2016-04-14 23:03:01 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:03:01,189 - WARNING - Could not retrieve variants from source file in region 10:118660779-118661180. Error was invalid region `10:118660780-118661180`
[2016-04-15T06:03Z] 2016-04-14 23:03:01 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:03:01,285 - WARNING - Could not retrieve variants from source file in region 10:119133757-119134248. Error was invalid region `10:119133758-119134248`
[2016-04-15T06:03Z] 2016-04-14 23:03:02 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:03:02,153 - WARNING - Could not retrieve variants from source file in region 10:124457241-124459329. Error was invalid region `10:124457242-124459329`
[2016-04-15T06:03Z] 2016-04-14 23:03:02 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:03:02,434 - WARNING - Could not retrieve variants from source file in region 10:122340645-122349159. Error was invalid region `10:122340646-122349159`
[2016-04-15T06:03Z] 2016-04-14 23:03:02 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:03:02,470 - WARNING - Could not retrieve variants from source file in region 10:116856332-116856733. Error was invalid region `10:116856333-116856733`
[2016-04-15T06:03Z] 2016-04-14 23:03:03 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:03:03,236 - WARNING - Could not retrieve variants from source file in region 10:118893020-118893421. Error was invalid region `10:118893021-118893421`
[2016-04-15T06:03Z] 2016-04-14 23:03:03 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:03:03,269 - WARNING - Could not retrieve variants from source file in region 10:117228583-117228984. Error was invalid region `10:117228584-117228984`
[2016-04-15T06:03Z] 2016-04-14 23:03:05 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:03:05,275 - WARNING - Could not retrieve variants from source file in region 10:125426201-125426755. Error was invalid region `10:125426202-125426755`
[2016-04-15T06:03Z] 2016-04-14 23:03:10 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:03:10,348 - WARNING - Could not retrieve variants from source file in region 10:117228583-117228984. Error was invalid region `10:117228584-117228984`
[2016-04-15T06:03Z] 2016-04-14 23:03:12 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:03:12,747 - WARNING - Could not retrieve variants from source file in region 10:114053335-114053736. Error was invalid region `10:114053336-114053736`
[2016-04-15T06:03Z] 2016-04-14 23:03:15 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:03:15,720 - WARNING - Could not retrieve variants from source file in region 10:126089223-126094662. Error was invalid region `10:126089224-126094662`
[2016-04-15T06:03Z] 2016-04-14 23:03:18 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:03:18,920 - WARNING - Could not retrieve variants from source file in region 10:122216651-122217052. Error was invalid region `10:122216652-122217052`
[2016-04-15T06:03Z] 2016-04-14 23:03:18 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:03:18,940 - WARNING - Could not retrieve variants from source file in region 10:117884739-117885140. Error was invalid region `10:117884740-117885140`
[2016-04-15T06:03Z] 2016-04-14 23:03:19 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:03:19,296 - WARNING - Could not retrieve variants from source file in region 10:124402466-124402867. Error was invalid region `10:124402467-124402867`
[2016-04-15T06:03Z] 2016-04-14 23:03:19 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:03:19,537 - WARNING - Could not retrieve variants from source file in region 10:118764618-118765019. Error was invalid region `10:118764619-118765019`
[2016-04-15T06:03Z] 2016-04-14 23:03:20 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:03:20,189 - WARNING - Could not retrieve variants from source file in region 10:123902922-123903323. Error was invalid region `10:123902923-123903323`
[2016-04-15T06:03Z] 2016-04-14 23:03:20 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:03:20,414 - WARNING - Could not retrieve variants from source file in region 10:126089223-126094662. Error was invalid region `10:126089224-126094662`
[2016-04-15T06:03Z] 2016-04-14 23:03:20 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:03:20,955 - WARNING - Could not retrieve variants from source file in region 10:124924191-124924676. Error was invalid region `10:124924192-124924676`
[2016-04-15T06:03Z] 2016-04-14 23:03:21 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:03:21,363 - WARNING - Could not retrieve variants from source file in region 10:118615899-118620649. Error was invalid region `10:118615900-118620649`
[2016-04-15T06:03Z] 2016-04-14 23:03:22 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:03:22,772 - WARNING - Could not retrieve variants from source file in region 10:116702214-116719733. Error was invalid region `10:116702215-116719733`
[2016-04-15T06:03Z] 2016-04-14 23:03:22 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:03:22,916 - WARNING - Could not retrieve variants from source file in region 10:114053335-114053736. Error was invalid region `10:114053336-114053736`
[2016-04-15T06:03Z] 2016-04-14 23:03:23 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:03:23,646 - WARNING - Could not retrieve variants from source file in region 10:116307293-116307694. Error was invalid region `10:116307294-116307694`
[2016-04-15T06:03Z] 2016-04-14 23:03:24 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:03:24,818 - WARNING - Could not retrieve variants from source file in region 10:117884739-117885140. Error was invalid region `10:117884740-117885140`
[2016-04-15T06:03Z] 2016-04-14 23:03:25 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:03:25,022 - WARNING - Could not retrieve variants from source file in region 10:118764618-118765019. Error was invalid region `10:118764619-118765019`
[2016-04-15T06:03Z] 2016-04-14 23:03:25 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:03:25,132 - WARNING - Could not retrieve variants from source file in region 10:117074964-117075365. Error was invalid region `10:117074965-117075365`
[2016-04-15T06:03Z] 2016-04-14 23:03:25 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:03:25,153 - WARNING - Could not retrieve variants from source file in region 10:112349211-112362060. Error was invalid region `10:112349212-112362060`
[2016-04-15T06:03Z] 2016-04-14 23:03:25 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:03:25,587 - WARNING - Could not retrieve variants from source file in region 10:126089223-126094662. Error was invalid region `10:126089224-126094662`
[2016-04-15T06:03Z] 2016-04-14 23:03:28 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:03:28,104 - WARNING - Could not retrieve variants from source file in region 10:116307293-116307694. Error was invalid region `10:116307294-116307694`
[2016-04-15T06:03Z] 2016-04-14 23:03:29 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:03:29,591 - WARNING - Could not retrieve variants from source file in region 10:122216651-122217052. Error was invalid region `10:122216652-122217052`
[2016-04-15T06:03Z] 2016-04-14 23:03:31 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:03:31,007 - WARNING - Could not retrieve variants from source file in region 10:118764618-118765019. Error was invalid region `10:118764619-118765019`
[2016-04-15T06:03Z] 2016-04-14 23:03:31 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:03:31,392 - WARNING - Could not retrieve variants from source file in region 10:117074964-117075365. Error was invalid region `10:117074965-117075365`
[2016-04-15T06:03Z] 2016-04-14 23:03:31 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:03:31,758 - WARNING - Could not retrieve variants from source file in region 10:124924191-124924676. Error was invalid region `10:124924192-124924676`
[2016-04-15T06:03Z] 2016-04-14 23:03:32 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:03:32,774 - WARNING - Could not retrieve variants from source file in region 10:116307293-116307694. Error was invalid region `10:116307294-116307694`
[2016-04-15T06:03Z] 2016-04-14 23:03:34 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:03:34,511 - WARNING - Could not retrieve variants from source file in region 10:117074964-117075365. Error was invalid region `10:117074965-117075365`
[2016-04-15T06:03Z] 2016-04-14 23:03:37 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:03:37,182 - WARNING - Could not retrieve variants from source file in region 10:113910510-113940519. Error was invalid region `10:113910511-113940519`
[2016-04-15T06:03Z] 2016-04-14 23:03:42 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:03:42,577 - WARNING - Could not retrieve variants from source file in region 10:113910510-113940519. Error was invalid region `10:113910511-113940519`
[2016-04-15T06:03Z] 2016-04-14 23:03:43 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:03:43,222 - WARNING - Could not retrieve variants from source file in region 10:121678802-121679203. Error was invalid region `10:121678803-121679203`
[2016-04-15T06:03Z] 2016-04-14 23:03:45 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:03:45,070 - WARNING - Could not retrieve variants from source file in region 10:118424507-118439396. Error was invalid region `10:118424508-118439396`
[2016-04-15T06:03Z] 2016-04-14 23:03:46 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:03:46,886 - WARNING - Could not retrieve variants from source file in region 10:115804845-115805246. Error was invalid region `10:115804846-115805246`
[2016-04-15T06:03Z] 2016-04-14 23:03:47 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:03:47,151 - WARNING - Could not retrieve variants from source file in region 10:118501844-118502245. Error was invalid region `10:118501845-118502245`
[2016-04-15T06:03Z] 2016-04-14 23:03:48 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:03:48,455 - WARNING - Could not retrieve variants from source file in region 10:123842312-123847545. Error was invalid region `10:123842313-123847545`
[2016-04-15T06:03Z] 2016-04-14 23:03:48 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:03:48,536 - WARNING - Could not retrieve variants from source file in region 10:124800642-124801043. Error was invalid region `10:124800643-124801043`
[2016-04-15T06:03Z] 2016-04-14 23:03:48 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:03:48,569 - WARNING - Could not retrieve variants from source file in region 10:124329499-124352144. Error was invalid region `10:124329500-124352144`
[2016-04-15T06:03Z] 2016-04-14 23:03:48 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:03:48,998 - WARNING - Could not retrieve variants from source file in region 10:113910510-113940519. Error was invalid region `10:113910511-113940519`
[2016-04-15T06:03Z] 2016-04-14 23:03:49 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:03:49,288 - WARNING - Could not retrieve variants from source file in region 10:121678802-121679203. Error was invalid region `10:121678803-121679203`
[2016-04-15T06:03Z] 2016-04-14 23:03:49 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:03:49,331 - WARNING - Could not retrieve variants from source file in region 10:121551370-121551771. Error was invalid region `10:121551371-121551771`
[2016-04-15T06:03Z] 2016-04-14 23:03:49 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:03:49,760 - WARNING - Could not retrieve variants from source file in region 10:125557367-125557769. Error was invalid region `10:125557368-125557769`
[2016-04-15T06:03Z] 2016-04-14 23:03:50 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:03:50,204 - WARNING - Could not retrieve variants from source file in region 10:112266560-112267013. Error was invalid region `10:112266561-112267013`
[2016-04-15T06:03Z] 2016-04-14 23:03:52 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:03:52,132 - WARNING - Could not retrieve variants from source file in region 10:115804845-115805246. Error was invalid region `10:115804846-115805246`
[2016-04-15T06:03Z] 2016-04-14 23:03:55 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:03:55,440 - WARNING - Could not retrieve variants from source file in region 10:126517778-126518179. Error was invalid region `10:126517779-126518179`
[2016-04-15T06:03Z] 2016-04-14 23:03:56 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:03:56,084 - WARNING - Could not retrieve variants from source file in region 10:124800642-124801043. Error was invalid region `10:124800643-124801043`
[2016-04-15T06:03Z] 2016-04-14 23:03:56 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:03:56,170 - WARNING - Could not retrieve variants from source file in region 10:125557367-125557769. Error was invalid region `10:125557368-125557769`
[2016-04-15T06:03Z] 2016-04-14 23:03:57 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:03:57,094 - WARNING - Could not retrieve variants from source file in region 10:121678802-121679203. Error was invalid region `10:121678803-121679203`
[2016-04-15T06:03Z] 2016-04-14 23:03:57 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:03:57,144 - WARNING - Could not retrieve variants from source file in region 10:118424507-118439396. Error was invalid region `10:118424508-118439396`
[2016-04-15T06:03Z] 2016-04-14 23:03:57 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:03:57,313 - WARNING - Could not retrieve variants from source file in region 10:115910717-115922964. Error was invalid region `10:115910718-115922964`
[2016-04-15T06:04Z] 2016-04-14 23:04:02 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:04:02,172 - WARNING - Could not retrieve variants from source file in region 10:126517778-126518179. Error was invalid region `10:126517779-126518179`
[2016-04-15T06:04Z] 2016-04-14 23:04:03 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:04:03,395 - WARNING - Could not retrieve variants from source file in region 10:121551370-121551771. Error was invalid region `10:121551371-121551771`
[2016-04-15T06:04Z] 2016-04-14 23:04:04 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:04:04,602 - WARNING - Could not retrieve variants from source file in region 10:124183521-124221466. Error was invalid region `10:124183522-124221466`
[2016-04-15T06:04Z] 2016-04-14 23:04:05 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:04:05,844 - WARNING - Could not retrieve variants from source file in region 10:112640842-112641243. Error was invalid region `10:112640843-112641243`
[2016-04-15T06:04Z] 2016-04-14 23:04:07 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:04:07,981 - WARNING - Could not retrieve variants from source file in region 10:126517778-126518179. Error was invalid region `10:126517779-126518179`
[2016-04-15T06:04Z] 2016-04-14 23:04:08 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:04:08,195 - WARNING - Could not retrieve variants from source file in region 10:115643829-115644230. Error was invalid region `10:115643830-115644230`
[2016-04-15T06:04Z] 2016-04-14 23:04:10 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:04:10,694 - WARNING - Could not retrieve variants from source file in region 10:112640842-112641243. Error was invalid region `10:112640843-112641243`
[2016-04-15T06:04Z] 2016-04-14 23:04:12 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:04:12,117 - WARNING - Could not retrieve variants from source file in region 10:124742581-124768773. Error was invalid region `10:124742582-124768773`
[2016-04-15T06:04Z] 2016-04-14 23:04:12 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:04:12,869 - WARNING - Could not retrieve variants from source file in region 10:124742581-124768773. Error was invalid region `10:124742582-124768773`
[2016-04-15T06:04Z] 2016-04-14 23:04:13 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:04:13,194 - WARNING - Could not retrieve variants from source file in region 10:111637590-111637991. Error was invalid region `10:111637591-111637991`
[2016-04-15T06:04Z] 2016-04-14 23:04:13 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:04:13,309 - WARNING - Could not retrieve variants from source file in region 10:115643829-115644230. Error was invalid region `10:115643830-115644230`
[2016-04-15T06:04Z] 2016-04-14 23:04:13 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:04:13,696 - WARNING - Could not retrieve variants from source file in region 10:121578829-121587467. Error was invalid region `10:121578830-121587467`
[2016-04-15T06:04Z] 2016-04-14 23:04:14 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:04:14,501 - WARNING - Could not retrieve variants from source file in region 10:115643829-115644230. Error was invalid region `10:115643830-115644230`
[2016-04-15T06:04Z] 2016-04-14 23:04:15 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:04:15,555 - WARNING - Could not retrieve variants from source file in region 10:112640842-112641243. Error was invalid region `10:112640843-112641243`
[2016-04-15T06:04Z] 2016-04-14 23:04:16 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:04:16,519 - WARNING - Could not retrieve variants from source file in region 10:111987749-111988150. Error was invalid region `10:111987750-111988150`
[2016-04-15T06:04Z] 2016-04-14 23:04:16 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:04:16,833 - WARNING - Could not retrieve variants from source file in region 10:124742581-124768773. Error was invalid region `10:124742582-124768773`
[2016-04-15T06:04Z] 2016-04-14 23:04:18 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:04:18,104 - WARNING - Could not retrieve variants from source file in region 10:121436151-121436552. Error was invalid region `10:121436152-121436552`
[2016-04-15T06:04Z] 2016-04-14 23:04:18 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:04:18,966 - WARNING - Could not retrieve variants from source file in region 10:115609704-115614930. Error was invalid region `10:115609705-115614930`
[2016-04-15T06:04Z] 2016-04-14 23:04:19 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:04:19,587 - WARNING - Could not retrieve variants from source file in region 10:115514909-115540601. Error was invalid region `10:115514910-115540601`
[2016-04-15T06:04Z] 2016-04-14 23:04:21 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:04:21,035 - WARNING - Could not retrieve variants from source file in region 10:111987749-111988150. Error was invalid region `10:111987750-111988150`
[2016-04-15T06:04Z] 2016-04-14 23:04:22 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:04:22,617 - WARNING - Could not retrieve variants from source file in region 10:121436151-121436552. Error was invalid region `10:121436152-121436552`
[2016-04-15T06:04Z] 2016-04-14 23:04:23 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:04:23,210 - WARNING - Could not retrieve variants from source file in region 10:121578829-121587467. Error was invalid region `10:121578830-121587467`
[2016-04-15T06:04Z] 2016-04-14 23:04:23 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:04:23,685 - WARNING - Could not retrieve variants from source file in region 10:123673128-123687047. Error was invalid region `10:123673129-123687047`
[2016-04-15T06:04Z] 2016-04-14 23:04:25 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:04:25,167 - WARNING - Could not retrieve variants from source file in region 10:126480170-126480571. Error was invalid region `10:126480171-126480571`
[2016-04-15T06:04Z] 2016-04-14 23:04:30 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:04:30,060 - WARNING - Could not retrieve variants from source file in region 10:120828758-120840851. Error was invalid region `10:120828759-120840851`
[2016-04-15T06:04Z] 2016-04-14 23:04:30 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:04:30,061 - WARNING - Could not retrieve variants from source file in region 10:120895816-120933514. Error was invalid region `10:120895817-120933514`
[2016-04-15T06:04Z] 2016-04-14 23:04:30 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:04:30,307 - WARNING - Could not retrieve variants from source file in region 10:115514909-115540601. Error was invalid region `10:115514910-115540601`
[2016-04-15T06:04Z] 2016-04-14 23:04:32 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:04:32,228 - WARNING - Could not retrieve variants from source file in region 10:120895816-120933514. Error was invalid region `10:120895817-120933514`
[2016-04-15T06:04Z] 2016-04-14 23:04:33 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:04:33,235 - WARNING - Could not retrieve variants from source file in region 10:123549480-123549881. Error was invalid region `10:123549481-123549881`
[2016-04-15T06:04Z] 2016-04-14 23:04:34 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:04:34,653 - WARNING - Could not retrieve variants from source file in region 10:121165777-121166179. Error was invalid region `10:121165778-121166179`
[2016-04-15T06:04Z] 2016-04-14 23:04:34 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:04:34,719 - WARNING - Could not retrieve variants from source file in region 10:120828758-120840851. Error was invalid region `10:120828759-120840851`
[2016-04-15T06:04Z] 2016-04-14 23:04:35 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:04:35,429 - WARNING - Could not retrieve variants from source file in region 10:121165777-121166179. Error was invalid region `10:121165778-121166179`
[2016-04-15T06:04Z] 2016-04-14 23:04:35 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:04:35,798 - WARNING - Could not retrieve variants from source file in region 10:123297947-123298348. Error was invalid region `10:123297948-123298348`
[2016-04-15T06:04Z] 2016-04-14 23:04:35 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:04:35,823 - WARNING - Could not retrieve variants from source file in region 10:120353699-120354100. Error was invalid region `10:120353700-120354100`
[2016-04-15T06:04Z] 2016-04-14 23:04:36 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:04:36,784 - WARNING - Could not retrieve variants from source file in region 10:123549480-123549881. Error was invalid region `10:123549481-123549881`
[2016-04-15T06:04Z] 2016-04-14 23:04:37 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:04:37,448 - WARNING - Could not retrieve variants from source file in region 10:123549480-123549881. Error was invalid region `10:123549481-123549881`
[2016-04-15T06:04Z] 2016-04-14 23:04:39 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:04:39,478 - WARNING - Could not retrieve variants from source file in region 10:120828758-120840851. Error was invalid region `10:120828759-120840851`
[2016-04-15T06:04Z] 2016-04-14 23:04:39 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:04:39,956 - WARNING - Could not retrieve variants from source file in region 10:123297947-123298348. Error was invalid region `10:123297948-123298348`
[2016-04-15T06:04Z] 2016-04-14 23:04:40 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:04:40,266 - WARNING - Could not retrieve variants from source file in region 10:120353699-120354100. Error was invalid region `10:120353700-120354100`
[2016-04-15T06:04Z] 2016-04-14 23:04:40 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:04:40,754 - WARNING - Could not retrieve variants from source file in region 10:123596043-123596444. Error was invalid region `10:123596044-123596444`
[2016-04-15T06:04Z] 2016-04-14 23:04:41 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:04:41,099 - WARNING - Could not retrieve variants from source file in region 10:123596043-123596444. Error was invalid region `10:123596044-123596444`
[2016-04-15T06:04Z] 2016-04-14 23:04:43 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:04:43,480 - WARNING - Could not retrieve variants from source file in region 10:123297947-123298348. Error was invalid region `10:123297948-123298348`
[2016-04-15T06:04Z] 2016-04-14 23:04:43 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:04:43,527 - WARNING - Could not retrieve variants from source file in region 10:120353699-120354100. Error was invalid region `10:120353700-120354100`
[2016-04-15T06:04Z] 2016-04-14 23:04:43 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:04:43,557 - WARNING - Could not retrieve variants from source file in region 10:123596043-123596444. Error was invalid region `10:123596044-123596444`
[2016-04-15T06:04Z] 2016-04-14 23:04:47 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:04:47,375 - WARNING - Could not retrieve variants from source file in region 10:123238901-123239302. Error was invalid region `10:123238902-123239302`
[2016-04-15T06:04Z] 2016-04-14 23:04:47 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:04:47,375 - WARNING - Could not retrieve variants from source file in region 10:123238901-123239302. Error was invalid region `10:123238902-123239302`
[2016-04-15T06:04Z] 2016-04-14 23:04:47 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:04:47,445 - WARNING - Could not retrieve variants from source file in region 10:123238901-123239302. Error was invalid region `10:123238902-123239302`
[2016-04-15T06:04Z] ['bcbio-variation-recall', 'square', '-Xms750m', '-Xmx7280m', '-XX:+UseSerialGC', '-c', 16, '-r', u'10:127328722-135534747', '--caller', 'platypus', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/10/Batch1-10_127328721_135534747.vcf.gz', '/mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/10/Batch1-10_127328721_135534747.vcf-inputs.txt'] in region: 10:127328722-135534747
[2016-04-15T06:05Z] 2016-04-14 23:05:04 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:05:04,024 - WARNING - Could not retrieve variants from source file in region 10:129690626-129691027. Error was invalid region `10:129690627-129691027`
[2016-04-15T06:05Z] 2016-04-14 23:05:04 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:05:04,395 - WARNING - Could not retrieve variants from source file in region 10:135340655-135351552. Error was invalid region `10:135340656-135351552`
[2016-04-15T06:05Z] 2016-04-14 23:05:05 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:05:05,194 - WARNING - Could not retrieve variants from source file in region 10:129160247-129160648. Error was invalid region `10:129160248-129160648`
[2016-04-15T06:05Z] 2016-04-14 23:05:05 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:05:05,260 - WARNING - Could not retrieve variants from source file in region 10:129350645-129351046. Error was invalid region `10:129350646-129351046`
[2016-04-15T06:05Z] 2016-04-14 23:05:05 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:05:05,269 - WARNING - Could not retrieve variants from source file in region 10:129245473-129249891. Error was invalid region `10:129245474-129249891`
[2016-04-15T06:05Z] 2016-04-14 23:05:05 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:05:05,639 - WARNING - Could not retrieve variants from source file in region 10:131265454-131265855. Error was invalid region `10:131265455-131265855`
[2016-04-15T06:05Z] 2016-04-14 23:05:05 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:05:05,811 - WARNING - Could not retrieve variants from source file in region 10:131964573-131964974. Error was invalid region `10:131964574-131964974`
[2016-04-15T06:05Z] 2016-04-14 23:05:09 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:05:09,484 - WARNING - Could not retrieve variants from source file in region 10:128018814-128019215. Error was invalid region `10:128018815-128019215`
[2016-04-15T06:05Z] 2016-04-14 23:05:11 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:05:11,385 - WARNING - Could not retrieve variants from source file in region 10:129216447-129216848. Error was invalid region `10:129216448-129216848`
[2016-04-15T06:05Z] 2016-04-14 23:05:14 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:05:14,019 - WARNING - Could not retrieve variants from source file in region 10:128974009-128974811. Error was invalid region `10:128974010-128974811`
[2016-04-15T06:05Z] 2016-04-14 23:05:14 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:05:14,080 - WARNING - Could not retrieve variants from source file in region 10:129845691-129871880. Error was invalid region `10:129845692-129871880`
[2016-04-15T06:05Z] 2016-04-14 23:05:14 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:05:14,291 - WARNING - Could not retrieve variants from source file in region 10:127661769-127683273. Error was invalid region `10:127661770-127683273`
[2016-04-15T06:05Z] 2016-04-14 23:05:14 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:05:14,564 - WARNING - Could not retrieve variants from source file in region 10:131265454-131265855. Error was invalid region `10:131265455-131265855`
[2016-04-15T06:05Z] 2016-04-14 23:05:14 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:05:14,911 - WARNING - Could not retrieve variants from source file in region 10:128018814-128019215. Error was invalid region `10:128018815-128019215`
[2016-04-15T06:05Z] 2016-04-14 23:05:15 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:05:15,035 - WARNING - Could not retrieve variants from source file in region 10:134598417-134647178. Error was invalid region `10:134598418-134647178`
[2016-04-15T06:05Z] 2016-04-14 23:05:15 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:05:15,855 - WARNING - Could not retrieve variants from source file in region 10:129690626-129691027. Error was invalid region `10:129690627-129691027`
[2016-04-15T06:05Z] 2016-04-14 23:05:15 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:05:15,879 - WARNING - Could not retrieve variants from source file in region 10:129216447-129216848. Error was invalid region `10:129216448-129216848`
[2016-04-15T06:05Z] 2016-04-14 23:05:20 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:05:20,789 - WARNING - Could not retrieve variants from source file in region 10:134973784-135051752. Error was invalid region `10:134973785-135051752`
[2016-04-15T06:05Z] 2016-04-14 23:05:23 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:05:23,545 - WARNING - Could not retrieve variants from source file in region 10:129350645-129351046. Error was invalid region `10:129350646-129351046`
[2016-04-15T06:05Z] 2016-04-14 23:05:23 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:05:23,634 - WARNING - Could not retrieve variants from source file in region 10:129160247-129160648. Error was invalid region `10:129160248-129160648`
[2016-04-15T06:05Z] 2016-04-14 23:05:23 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:05:23,989 - WARNING - Could not retrieve variants from source file in region 10:127661769-127683273. Error was invalid region `10:127661770-127683273`
[2016-04-15T06:05Z] 2016-04-14 23:05:23 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:05:23,991 - WARNING - Could not retrieve variants from source file in region 10:131265454-131265855. Error was invalid region `10:131265455-131265855`
[2016-04-15T06:05Z] 2016-04-14 23:05:36 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:05:36,134 - WARNING - Could not retrieve variants from source file in region 10:135233330-135237356. Error was invalid region `10:135233331-135237356`
[2016-04-15T06:05Z] 2016-04-14 23:05:36 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:05:36,676 - WARNING - Could not retrieve variants from source file in region 10:135233330-135237356. Error was invalid region `10:135233331-135237356`
[2016-04-15T06:05Z] 2016-04-14 23:05:36 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:05:36,852 - WARNING - Could not retrieve variants from source file in region 10:127530114-127530515. Error was invalid region `10:127530115-127530515`
[2016-04-15T06:05Z] 2016-04-14 23:05:36 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:05:36,976 - WARNING - Could not retrieve variants from source file in region 10:128925802-128926203. Error was invalid region `10:128925803-128926203`
[2016-04-15T06:05Z] 2016-04-14 23:05:39 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:05:39,314 - WARNING - Could not retrieve variants from source file in region 10:128830198-128830599. Error was invalid region `10:128830199-128830599`
[2016-04-15T06:05Z] 2016-04-14 23:05:39 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:05:39,378 - WARNING - Could not retrieve variants from source file in region 10:135165579-135205199. Error was invalid region `10:135165580-135205199`
[2016-04-15T06:05Z] 2016-04-14 23:05:39 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:05:39,462 - WARNING - Could not retrieve variants from source file in region 10:128192774-128213474. Error was invalid region `10:128192775-128213474`
[2016-04-15T06:05Z] 2016-04-14 23:05:40 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:05:40,004 - WARNING - Could not retrieve variants from source file in region 10:127462314-127491355. Error was invalid region `10:127462315-127491355`
[2016-04-15T06:05Z] 2016-04-14 23:05:40 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:05:40,298 - WARNING - Could not retrieve variants from source file in region 10:134540189-134540590. Error was invalid region `10:134540190-134540590`
[2016-04-15T06:05Z] 2016-04-14 23:05:41 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:05:41,557 - WARNING - Could not retrieve variants from source file in region 10:128925802-128926203. Error was invalid region `10:128925803-128926203`
[2016-04-15T06:05Z] 2016-04-14 23:05:43 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:05:43,988 - WARNING - Could not retrieve variants from source file in region 10:135165579-135205199. Error was invalid region `10:135165580-135205199`
[2016-04-15T06:05Z] 2016-04-14 23:05:44 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:05:44,296 - WARNING - Could not retrieve variants from source file in region 10:133918161-133918562. Error was invalid region `10:133918162-133918562`
[2016-04-15T06:05Z] 2016-04-14 23:05:45 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:05:45,242 - WARNING - Could not retrieve variants from source file in region 10:128830198-128830599. Error was invalid region `10:128830199-128830599`
[2016-04-15T06:05Z] 2016-04-14 23:05:45 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:05:45,983 - WARNING - Could not retrieve variants from source file in region 10:128925802-128926203. Error was invalid region `10:128925803-128926203`
[2016-04-15T06:05Z] 2016-04-14 23:05:48 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:05:48,366 - WARNING - Could not retrieve variants from source file in region 10:135165579-135205199. Error was invalid region `10:135165580-135205199`
[2016-04-15T06:05Z] 2016-04-14 23:05:48 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:05:48,545 - WARNING - Could not retrieve variants from source file in region 10:133918161-133918562. Error was invalid region `10:133918162-133918562`
[2016-04-15T06:05Z] 2016-04-14 23:05:49 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:05:49,276 - WARNING - Could not retrieve variants from source file in region 10:134540189-134540590. Error was invalid region `10:134540190-134540590`
[2016-04-15T06:05Z] 2016-04-14 23:05:56 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:05:56,823 - WARNING - Could not retrieve variants from source file in region 10:135082135-135106204. Error was invalid region `10:135082136-135106204`
[2016-04-15T06:05Z] 2016-04-14 23:05:57 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:05:57,673 - WARNING - Could not retrieve variants from source file in region 10:134721811-134748521. Error was invalid region `10:134721812-134748521`
[2016-04-15T06:05Z] 2016-04-14 23:05:57 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:05:57,674 - WARNING - Could not retrieve variants from source file in region 10:133948423-133981872. Error was invalid region `10:133948424-133981872`
[2016-04-15T06:05Z] 2016-04-14 23:05:57 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:05:57,746 - WARNING - Could not retrieve variants from source file in region 10:134721811-134748521. Error was invalid region `10:134721812-134748521`
[2016-04-15T06:05Z] 2016-04-14 23:05:57 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:05:57,898 - WARNING - Could not retrieve variants from source file in region 10:135082135-135106204. Error was invalid region `10:135082136-135106204`
[2016-04-15T06:05Z] 2016-04-14 23:05:58 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:05:58,231 - WARNING - Could not retrieve variants from source file in region 10:133948423-133981872. Error was invalid region `10:133948424-133981872`
[2016-04-15T06:05Z] 2016-04-14 23:05:58 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:05:58,373 - WARNING - Could not retrieve variants from source file in region 10:134721811-134748521. Error was invalid region `10:134721812-134748521`
[2016-04-15T06:06Z] 2016-04-14 23:06:01 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:06:01,374 - WARNING - Could not retrieve variants from source file in region 10:134682644-134683045. Error was invalid region `10:134682645-134683045`
[2016-04-15T06:06Z] 2016-04-14 23:06:02 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:06:02,592 - WARNING - Could not retrieve variants from source file in region 10:132079160-132079561. Error was invalid region `10:132079161-132079561`
[2016-04-15T06:06Z] 2016-04-14 23:06:03 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:06:03,308 - WARNING - Could not retrieve variants from source file in region 10:132079160-132079561. Error was invalid region `10:132079161-132079561`
[2016-04-15T06:06Z] 2016-04-14 23:06:03 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:06:03,314 - WARNING - Could not retrieve variants from source file in region 10:132079160-132079561. Error was invalid region `10:132079161-132079561`
[2016-04-15T06:06Z] 2016-04-14 23:06:03 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:06:03,404 - WARNING - Could not retrieve variants from source file in region 10:134218058-134218486. Error was invalid region `10:134218059-134218486`
[2016-04-15T06:06Z] 2016-04-14 23:06:03 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:06:03,439 - WARNING - Could not retrieve variants from source file in region 10:134121248-134180544. Error was invalid region `10:134121249-134180544`
[2016-04-15T06:06Z] 2016-04-14 23:06:05 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:06:05,633 - WARNING - Could not retrieve variants from source file in region 10:134218058-134218486. Error was invalid region `10:134218059-134218486`
[2016-04-15T06:06Z] 2016-04-14 23:06:05 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:06:05,647 - WARNING - Could not retrieve variants from source file in region 10:134682644-134683045. Error was invalid region `10:134682645-134683045`
[2016-04-15T06:06Z] 2016-04-14 23:06:05 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:06:05,853 - WARNING - Could not retrieve variants from source file in region 10:134682644-134683045. Error was invalid region `10:134682645-134683045`
[2016-04-15T06:06Z] ['bcbio-variation-recall', 'square', '-Xms750m', '-Xmx7280m', '-XX:+UseSerialGC', '-c', 16, '-r', u'11:1-15994658', '--caller', 'platypus', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/11/Batch1-11_0_15994658.vcf.gz', '/mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/11/Batch1-11_0_15994658.vcf-inputs.txt'] in region: 11:1-15994658
[2016-04-15T06:06Z] 2016-04-14 23:06:21 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:06:21,375 - WARNING - Could not retrieve variants from source file in region 11:15199746-15200147. Error was invalid region `11:15199747-15200147`
[2016-04-15T06:06Z] 2016-04-14 23:06:22 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:06:22,558 - WARNING - Could not retrieve variants from source file in region 11:5221434-5222015. Error was invalid region `11:5221435-5222015`
[2016-04-15T06:06Z] 2016-04-14 23:06:23 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:06:23,313 - WARNING - Could not retrieve variants from source file in region 11:8661879-8662706. Error was invalid region `11:8661880-8662706`
[2016-04-15T06:06Z] 2016-04-14 23:06:24 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:06:24,439 - WARNING - Could not retrieve variants from source file in region 11:9455163-9455564. Error was invalid region `11:9455164-9455564`
[2016-04-15T06:06Z] 2016-04-14 23:06:24 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:06:24,642 - WARNING - Could not retrieve variants from source file in region 11:6411724-6412125. Error was invalid region `11:6411725-6412125`
[2016-04-15T06:06Z] 2016-04-14 23:06:26 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:06:26,485 - WARNING - Could not retrieve variants from source file in region 11:15199746-15200147. Error was invalid region `11:15199747-15200147`
[2016-04-15T06:06Z] 2016-04-14 23:06:28 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:06:28,475 - WARNING - Could not retrieve variants from source file in region 11:7817327-7818503. Error was invalid region `11:7817328-7818503`
[2016-04-15T06:06Z] 2016-04-14 23:06:28 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:06:28,478 - WARNING - Could not retrieve variants from source file in region 11:5221434-5222015. Error was invalid region `11:5221435-5222015`
[2016-04-15T06:06Z] 2016-04-14 23:06:31 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:06:31,110 - WARNING - Could not retrieve variants from source file in region 11:13721749-13734745. Error was invalid region `11:13721750-13734745`
[2016-04-15T06:06Z] 2016-04-14 23:06:31 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:06:31,199 - WARNING - Could not retrieve variants from source file in region 11:8661879-8662706. Error was invalid region `11:8661880-8662706`
[2016-04-15T06:06Z] 2016-04-14 23:06:31 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:06:31,649 - WARNING - Could not retrieve variants from source file in region 11:4702954-4703952. Error was invalid region `11:4702955-4703952`
[2016-04-15T06:06Z] 2016-04-14 23:06:32 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:06:32,450 - WARNING - Could not retrieve variants from source file in region 11:6411724-6412125. Error was invalid region `11:6411725-6412125`
[2016-04-15T06:06Z] 2016-04-14 23:06:32 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:06:32,584 - WARNING - Could not retrieve variants from source file in region 11:15199746-15200147. Error was invalid region `11:15199747-15200147`
[2016-04-15T06:06Z] 2016-04-14 23:06:37 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:06:37,356 - WARNING - Could not retrieve variants from source file in region 11:13721749-13734745. Error was invalid region `11:13721750-13734745`
[2016-04-15T06:06Z] 2016-04-14 23:06:37 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:06:37,434 - WARNING - Could not retrieve variants from source file in region 11:8661879-8662706. Error was invalid region `11:8661880-8662706`
[2016-04-15T06:06Z] 2016-04-14 23:06:38 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:06:38,336 - WARNING - Could not retrieve variants from source file in region 11:4702954-4703952. Error was invalid region `11:4702955-4703952`
[2016-04-15T06:06Z] 2016-04-14 23:06:39 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:06:39,658 - WARNING - Could not retrieve variants from source file in region 11:6411724-6412125. Error was invalid region `11:6411725-6412125`
[2016-04-15T06:06Z] 2016-04-14 23:06:39 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:06:39,790 - WARNING - Could not retrieve variants from source file in region 11:9455163-9455564. Error was invalid region `11:9455164-9455564`
[2016-04-15T06:06Z] 2016-04-14 23:06:40 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:06:40,172 - WARNING - Could not retrieve variants from source file in region 11:6220958-6265432. Error was invalid region `11:6220959-6265432`
[2016-04-15T06:06Z] 2016-04-14 23:06:40 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:06:40,313 - WARNING - Could not retrieve variants from source file in region 11:12030232-12031500. Error was invalid region `11:12030233-12031500`
[2016-04-15T06:06Z] 2016-04-14 23:06:48 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:06:48,849 - WARNING - Could not retrieve variants from source file in region 11:14990153-14991729. Error was invalid region `11:14990154-14991729`
[2016-04-15T06:06Z] 2016-04-14 23:06:52 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:06:52,194 - WARNING - Could not retrieve variants from source file in region 11:7846997-7847662. Error was invalid region `11:7846998-7847662`
[2016-04-15T06:06Z] 2016-04-14 23:06:53 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:06:53,410 - WARNING - Could not retrieve variants from source file in region 11:8486099-8486500. Error was invalid region `11:8486100-8486500`
[2016-04-15T06:06Z] 2016-04-14 23:06:53 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:06:53,431 - WARNING - Could not retrieve variants from source file in region 11:13461246-13461647. Error was invalid region `11:13461247-13461647`
[2016-04-15T06:06Z] 2016-04-14 23:06:54 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:06:54,640 - WARNING - Could not retrieve variants from source file in region 11:9112791-9113201. Error was invalid region `11:9112792-9113201`
[2016-04-15T06:06Z] 2016-04-14 23:06:55 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:06:55,647 - WARNING - Could not retrieve variants from source file in region 11:5153050-5172976. Error was invalid region `11:5153051-5172976`
[2016-04-15T06:06Z] 2016-04-14 23:06:56 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:06:56,133 - WARNING - Could not retrieve variants from source file in region 11:7324264-7324774. Error was invalid region `11:7324265-7324774`
[2016-04-15T06:06Z] 2016-04-14 23:06:56 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:06:56,219 - WARNING - Could not retrieve variants from source file in region 11:6129626-6130027. Error was invalid region `11:6129627-6130027`
[2016-04-15T06:06Z] 2016-04-14 23:06:57 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:06:57,004 - WARNING - Could not retrieve variants from source file in region 11:11976417-11986251. Error was invalid region `11:11976418-11986251`
[2016-04-15T06:06Z] 2016-04-14 23:06:57 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:06:57,851 - WARNING - Could not retrieve variants from source file in region 11:9406138-9406539. Error was invalid region `11:9406139-9406539`
[2016-04-15T06:06Z] 2016-04-14 23:06:57 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:06:57,867 - WARNING - Could not retrieve variants from source file in region 11:7846997-7847662. Error was invalid region `11:7846998-7847662`
[2016-04-15T06:07Z] 2016-04-14 23:07:00 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:07:00,473 - WARNING - Could not retrieve variants from source file in region 11:3659782-3681709. Error was invalid region `11:3659783-3681709`
[2016-04-15T06:07Z] 2016-04-14 23:07:01 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:07:01,178 - WARNING - Could not retrieve variants from source file in region 11:5153050-5172976. Error was invalid region `11:5153051-5172976`
[2016-04-15T06:07Z] 2016-04-14 23:07:01 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:07:01,711 - WARNING - Could not retrieve variants from source file in region 11:6340314-6341874. Error was invalid region `11:6340315-6341874`
[2016-04-15T06:07Z] 2016-04-14 23:07:01 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:07:01,858 - WARNING - Could not retrieve variants from source file in region 11:7324264-7324774. Error was invalid region `11:7324265-7324774`
[2016-04-15T06:07Z] 2016-04-14 23:07:02 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:07:02,282 - WARNING - Could not retrieve variants from source file in region 11:6129626-6130027. Error was invalid region `11:6129627-6130027`
[2016-04-15T06:07Z] 2016-04-14 23:07:03 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:07:03,062 - WARNING - Could not retrieve variants from source file in region 11:9406138-9406539. Error was invalid region `11:9406139-9406539`
[2016-04-15T06:07Z] 2016-04-14 23:07:03 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:07:03,160 - WARNING - Could not retrieve variants from source file in region 11:7846997-7847662. Error was invalid region `11:7846998-7847662`
[2016-04-15T06:07Z] 2016-04-14 23:07:04 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:07:04,817 - WARNING - Could not retrieve variants from source file in region 11:8486099-8486500. Error was invalid region `11:8486100-8486500`
[2016-04-15T06:07Z] 2016-04-14 23:07:05 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:07:05,615 - WARNING - Could not retrieve variants from source file in region 11:13461246-13461647. Error was invalid region `11:13461247-13461647`
[2016-04-15T06:07Z] 2016-04-14 23:07:08 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:07:08,655 - WARNING - Could not retrieve variants from source file in region 11:6129626-6130027. Error was invalid region `11:6129627-6130027`
[2016-04-15T06:07Z] 2016-04-14 23:07:08 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:07:08,789 - WARNING - Could not retrieve variants from source file in region 11:9406138-9406539. Error was invalid region `11:9406139-9406539`
[2016-04-15T06:07Z] 2016-04-14 23:07:14 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:07:14,939 - WARNING - Could not retrieve variants from source file in region 11:14912920-14913765. Error was invalid region `11:14912921-14913765`
[2016-04-15T06:07Z] 2016-04-14 23:07:18 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:07:18,423 - WARNING - Could not retrieve variants from source file in region 11:6816567-6817065. Error was invalid region `11:6816568-6817065`
[2016-04-15T06:07Z] 2016-04-14 23:07:19 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:07:19,138 - WARNING - Could not retrieve variants from source file in region 11:14810551-14810952. Error was invalid region `11:14810552-14810952`
[2016-04-15T06:07Z] 2016-04-14 23:07:19 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:07:19,755 - WARNING - Could not retrieve variants from source file in region 11:8413879-8414281. Error was invalid region `11:8413880-8414281`
[2016-04-15T06:07Z] 2016-04-14 23:07:19 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:07:19,892 - WARNING - Could not retrieve variants from source file in region 11:4608331-4615698. Error was invalid region `11:4608332-4615698`
[2016-04-15T06:07Z] 2016-04-14 23:07:21 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:07:21,062 - WARNING - Could not retrieve variants from source file in region 11:14912920-14913765. Error was invalid region `11:14912921-14913765`
[2016-04-15T06:07Z] 2016-04-14 23:07:21 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:07:21,092 - WARNING - Could not retrieve variants from source file in region 11:13032300-13032701. Error was invalid region `11:13032301-13032701`
[2016-04-15T06:07Z] 2016-04-14 23:07:22 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:07:22,398 - WARNING - Could not retrieve variants from source file in region 11:3394683-3395084. Error was invalid region `11:3394684-3395084`
[2016-04-15T06:07Z] 2016-04-14 23:07:23 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:07:23,342 - WARNING - Could not retrieve variants from source file in region 11:11941554-11941955. Error was invalid region `11:11941555-11941955`
[2016-04-15T06:07Z] 2016-04-14 23:07:23 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:07:23,457 - WARNING - Could not retrieve variants from source file in region 11:6816567-6817065. Error was invalid region `11:6816568-6817065`
[2016-04-15T06:07Z] 2016-04-14 23:07:23 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:07:23,809 - WARNING - Could not retrieve variants from source file in region 11:9316519-9316920. Error was invalid region `11:9316520-9316920`
[2016-04-15T06:07Z] 2016-04-14 23:07:24 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:07:24,055 - WARNING - Could not retrieve variants from source file in region 11:14810551-14810952. Error was invalid region `11:14810552-14810952`
[2016-04-15T06:07Z] 2016-04-14 23:07:27 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:07:27,031 - WARNING - Could not retrieve variants from source file in region 11:14912920-14913765. Error was invalid region `11:14912921-14913765`
[2016-04-15T06:07Z] 2016-04-14 23:07:27 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:07:27,871 - WARNING - Could not retrieve variants from source file in region 11:13032300-13032701. Error was invalid region `11:13032301-13032701`
[2016-04-15T06:07Z] 2016-04-14 23:07:29 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:07:29,622 - WARNING - Could not retrieve variants from source file in region 11:3394683-3395084. Error was invalid region `11:3394684-3395084`
[2016-04-15T06:07Z] 2016-04-14 23:07:31 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:07:31,488 - WARNING - Could not retrieve variants from source file in region 11:6816567-6817065. Error was invalid region `11:6816568-6817065`
[2016-04-15T06:07Z] 2016-04-14 23:07:31 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:07:31,550 - WARNING - Could not retrieve variants from source file in region 11:14810551-14810952. Error was invalid region `11:14810552-14810952`
[2016-04-15T06:07Z] 2016-04-14 23:07:31 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:07:31,888 - WARNING - Could not retrieve variants from source file in region 11:8413879-8414281. Error was invalid region `11:8413880-8414281`
[2016-04-15T06:07Z] 2016-04-14 23:07:32 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:07:32,420 - WARNING - Could not retrieve variants from source file in region 11:13032300-13032701. Error was invalid region `11:13032301-13032701`
[2016-04-15T06:07Z] 2016-04-14 23:07:42 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:07:42,378 - WARNING - Could not retrieve variants from source file in region 11:14101282-14101683. Error was invalid region `11:14101283-14101683`
[2016-04-15T06:07Z] 2016-04-14 23:07:46 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:07:46,365 - WARNING - Could not retrieve variants from source file in region 11:5020205-5021245. Error was invalid region `11:5020206-5021245`
[2016-04-15T06:07Z] 2016-04-14 23:07:47 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:07:47,625 - WARNING - Could not retrieve variants from source file in region 11:14101282-14101683. Error was invalid region `11:14101283-14101683`
[2016-04-15T06:07Z] 2016-04-14 23:07:47 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:07:47,812 - WARNING - Could not retrieve variants from source file in region 11:6789083-6790296. Error was invalid region `11:6789084-6790296`
[2016-04-15T06:07Z] 2016-04-14 23:07:48 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:07:48,028 - WARNING - Could not retrieve variants from source file in region 11:14264705-14265106. Error was invalid region `11:14264706-14265106`
[2016-04-15T06:07Z] 2016-04-14 23:07:49 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:07:49,140 - WARNING - Could not retrieve variants from source file in region 11:12903232-12903633. Error was invalid region `11:12903233-12903633`
[2016-04-15T06:07Z] 2016-04-14 23:07:49 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:07:49,532 - WARNING - Could not retrieve variants from source file in region 11:8284770-8285314. Error was invalid region `11:8284771-8285314`
[2016-04-15T06:07Z] 2016-04-14 23:07:49 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:07:49,736 - WARNING - Could not retrieve variants from source file in region 11:4566500-4567375. Error was invalid region `11:4566501-4567375`
[2016-04-15T06:07Z] 2016-04-14 23:07:50 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:07:50,655 - WARNING - Could not retrieve variants from source file in region 11:11913374-11913775. Error was invalid region `11:11913375-11913775`
[2016-04-15T06:07Z] 2016-04-14 23:07:51 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:07:51,693 - WARNING - Could not retrieve variants from source file in region 11:8788014-8788415. Error was invalid region `11:8788015-8788415`
[2016-04-15T06:07Z] 2016-04-14 23:07:51 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:07:51,703 - WARNING - Could not retrieve variants from source file in region 11:3239348-3250174. Error was invalid region `11:3239349-3250174`
[2016-04-15T06:07Z] 2016-04-14 23:07:53 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:07:53,148 - WARNING - Could not retrieve variants from source file in region 11:14101282-14101683. Error was invalid region `11:14101283-14101683`
[2016-04-15T06:07Z] 2016-04-14 23:07:53 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:07:53,242 - WARNING - Could not retrieve variants from source file in region 11:6789083-6790296. Error was invalid region `11:6789084-6790296`
[2016-04-15T06:07Z] 2016-04-14 23:07:53 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:07:53,615 - WARNING - Could not retrieve variants from source file in region 11:9225275-9225676. Error was invalid region `11:9225276-9225676`
[2016-04-15T06:07Z] 2016-04-14 23:07:54 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:07:54,695 - WARNING - Could not retrieve variants from source file in region 11:4869438-4870488. Error was invalid region `11:4869439-4870488`
[2016-04-15T06:07Z] 2016-04-14 23:07:55 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:07:55,013 - WARNING - Could not retrieve variants from source file in region 11:12903232-12903633. Error was invalid region `11:12903233-12903633`
[2016-04-15T06:07Z] 2016-04-14 23:07:55 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:07:55,190 - WARNING - Could not retrieve variants from source file in region 11:5905837-5906481. Error was invalid region `11:5905838-5906481`
[2016-04-15T06:07Z] 2016-04-14 23:07:55 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:07:55,344 - WARNING - Could not retrieve variants from source file in region 11:8284770-8285314. Error was invalid region `11:8284771-8285314`
[2016-04-15T06:07Z] 2016-04-14 23:07:55 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:07:55,973 - WARNING - Could not retrieve variants from source file in region 11:11913374-11913775. Error was invalid region `11:11913375-11913775`
[2016-04-15T06:07Z] 2016-04-14 23:07:56 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:07:56,528 - WARNING - Could not retrieve variants from source file in region 11:8788014-8788415. Error was invalid region `11:8788015-8788415`
[2016-04-15T06:07Z] 2016-04-14 23:07:57 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:07:57,634 - WARNING - Could not retrieve variants from source file in region 11:6789083-6790296. Error was invalid region `11:6789084-6790296`
[2016-04-15T06:07Z] 2016-04-14 23:07:57 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:07:57,963 - WARNING - Could not retrieve variants from source file in region 11:14264705-14265106. Error was invalid region `11:14264706-14265106`
[2016-04-15T06:08Z] 2016-04-14 23:08:00 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:08:00,315 - WARNING - Could not retrieve variants from source file in region 11:12903232-12903633. Error was invalid region `11:12903233-12903633`
[2016-04-15T06:08Z] 2016-04-14 23:08:01 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:08:01,710 - WARNING - Could not retrieve variants from source file in region 11:8284770-8285314. Error was invalid region `11:8284771-8285314`
[2016-04-15T06:08Z] 2016-04-14 23:08:01 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:08:01,728 - WARNING - Could not retrieve variants from source file in region 11:8788014-8788415. Error was invalid region `11:8788015-8788415`
[2016-04-15T06:08Z] 2016-04-14 23:08:01 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:08:01,756 - WARNING - Could not retrieve variants from source file in region 11:5905837-5906481. Error was invalid region `11:5905838-5906481`
[2016-04-15T06:08Z] 2016-04-14 23:08:01 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:08:01,870 - WARNING - Could not retrieve variants from source file in region 11:11913374-11913775. Error was invalid region `11:11913375-11913775`
[2016-04-15T06:08Z] 2016-04-14 23:08:02 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:08:02,070 - WARNING - Could not retrieve variants from source file in region 11:3239348-3250174. Error was invalid region `11:3239349-3250174`
[2016-04-15T06:08Z] 2016-04-14 23:08:08 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:08:08,176 - WARNING - Could not retrieve variants from source file in region 11:13984372-13984773. Error was invalid region `11:13984373-13984773`
[2016-04-15T06:08Z] 2016-04-14 23:08:11 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:08:11,420 - WARNING - Could not retrieve variants from source file in region 11:4824667-4843115. Error was invalid region `11:4824668-4843115`
[2016-04-15T06:08Z] 2016-04-14 23:08:12 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:08:12,082 - WARNING - Could not retrieve variants from source file in region 11:4790900-4791301. Error was invalid region `11:4790901-4791301`
[2016-04-15T06:08Z] 2016-04-14 23:08:12 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:08:12,801 - WARNING - Could not retrieve variants from source file in region 11:13984372-13984773. Error was invalid region `11:13984373-13984773`
[2016-04-15T06:08Z] 2016-04-14 23:08:13 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:08:13,571 - WARNING - Could not retrieve variants from source file in region 11:12379738-12380139. Error was invalid region `11:12379739-12380139`
[2016-04-15T06:08Z] 2016-04-14 23:08:16 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:08:16,536 - WARNING - Could not retrieve variants from source file in region 11:8245970-8248672. Error was invalid region `11:8245971-8248672`
[2016-04-15T06:08Z] 2016-04-14 23:08:16 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:08:16,660 - WARNING - Could not retrieve variants from source file in region 11:5809097-5809936. Error was invalid region `11:5809098-5809936`
[2016-04-15T06:08Z] 2016-04-14 23:08:17 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:08:17,056 - WARNING - Could not retrieve variants from source file in region 11:4471289-4471690. Error was invalid region `11:4471290-4471690`
[2016-04-15T06:08Z] 2016-04-14 23:08:17 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:08:17,273 - WARNING - Could not retrieve variants from source file in region 11:8009030-8014669. Error was invalid region `11:8009031-8014669`
[2016-04-15T06:08Z] 2016-04-14 23:08:17 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:08:17,530 - WARNING - Could not retrieve variants from source file in region 11:4824667-4843115. Error was invalid region `11:4824668-4843115`
[2016-04-15T06:08Z] 2016-04-14 23:08:18 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:08:18,783 - WARNING - Could not retrieve variants from source file in region 11:4140921-4159656. Error was invalid region `11:4140922-4159656`
[2016-04-15T06:08Z] 2016-04-14 23:08:21 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:08:21,962 - WARNING - Could not retrieve variants from source file in region 11:5862321-5878169. Error was invalid region `11:5862322-5878169`
[2016-04-15T06:08Z] 2016-04-14 23:08:22 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:08:22,252 - WARNING - Could not retrieve variants from source file in region 11:11348458-11374473. Error was invalid region `11:11348459-11374473`
[2016-04-15T06:08Z] 2016-04-14 23:08:22 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:08:22,977 - WARNING - Could not retrieve variants from source file in region 11:12379738-12380139. Error was invalid region `11:12379739-12380139`
[2016-04-15T06:08Z] 2016-04-14 23:08:26 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:08:26,094 - WARNING - Could not retrieve variants from source file in region 11:8245970-8248672. Error was invalid region `11:8245971-8248672`
[2016-04-15T06:08Z] 2016-04-14 23:08:27 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:08:27,471 - WARNING - Could not retrieve variants from source file in region 11:5809097-5809936. Error was invalid region `11:5809098-5809936`
[2016-04-15T06:08Z] 2016-04-14 23:08:28 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:08:28,169 - WARNING - Could not retrieve variants from source file in region 11:8009030-8014669. Error was invalid region `11:8009031-8014669`
[2016-04-15T06:08Z] 2016-04-14 23:08:28 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:08:28,910 - WARNING - Could not retrieve variants from source file in region 11:12282086-12282487. Error was invalid region `11:12282087-12282487`
[2016-04-15T06:08Z] 2016-04-14 23:08:29 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:08:29,386 - WARNING - Could not retrieve variants from source file in region 11:3113979-3129217. Error was invalid region `11:3113980-3129217`
[2016-04-15T06:08Z] 2016-04-14 23:08:34 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:08:34,122 - WARNING - Could not retrieve variants from source file in region 11:5757574-5776813. Error was invalid region `11:5757575-5776813`
[2016-04-15T06:08Z] 2016-04-14 23:08:34 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:08:34,124 - WARNING - Could not retrieve variants from source file in region 11:12282086-12282487. Error was invalid region `11:12282087-12282487`
[2016-04-15T06:08Z] 2016-04-14 23:08:37 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:08:37,022 - WARNING - Could not retrieve variants from source file in region 11:12314975-12316579. Error was invalid region `11:12314976-12316579`
[2016-04-15T06:08Z] 2016-04-14 23:08:37 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:08:37,503 - WARNING - Could not retrieve variants from source file in region 11:5565819-5566679. Error was invalid region `11:5565820-5566679`
[2016-04-15T06:08Z] 2016-04-14 23:08:38 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:08:38,448 - WARNING - Could not retrieve variants from source file in region 11:12282086-12282487. Error was invalid region `11:12282087-12282487`
[2016-04-15T06:08Z] 2016-04-14 23:08:38 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:08:38,908 - WARNING - Could not retrieve variants from source file in region 11:4388694-4411661. Error was invalid region `11:4388695-4411661`
[2016-04-15T06:08Z] 2016-04-14 23:08:40 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:08:40,714 - WARNING - Could not retrieve variants from source file in region 11:8115488-8122281. Error was invalid region `11:8115489-8122281`
[2016-04-15T06:08Z] 2016-04-14 23:08:41 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:08:41,269 - WARNING - Could not retrieve variants from source file in region 11:12314975-12316579. Error was invalid region `11:12314976-12316579`
[2016-04-15T06:08Z] 2016-04-14 23:08:41 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:08:41,271 - WARNING - Could not retrieve variants from source file in region 11:4079889-4103714. Error was invalid region `11:4079890-4103714`
[2016-04-15T06:08Z] 2016-04-14 23:08:41 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:08:41,376 - WARNING - Could not retrieve variants from source file in region 11:5565819-5566679. Error was invalid region `11:5565820-5566679`
[2016-04-15T06:08Z] 2016-04-14 23:08:43 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:08:43,378 - WARNING - Could not retrieve variants from source file in region 11:11292489-11292890. Error was invalid region `11:11292490-11292890`
[2016-04-15T06:08Z] 2016-04-14 23:08:43 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:08:43,612 - WARNING - Could not retrieve variants from source file in region 11:12314975-12316579. Error was invalid region `11:12314976-12316579`
[2016-04-15T06:08Z] 2016-04-14 23:08:44 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:08:44,956 - WARNING - Could not retrieve variants from source file in region 11:7982386-7982787. Error was invalid region `11:7982387-7982787`
[2016-04-15T06:08Z] 2016-04-14 23:08:45 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:08:45,248 - WARNING - Could not retrieve variants from source file in region 11:5565819-5566679. Error was invalid region `11:5565820-5566679`
[2016-04-15T06:08Z] 2016-04-14 23:08:47 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:08:47,427 - WARNING - Could not retrieve variants from source file in region 11:11292489-11292890. Error was invalid region `11:11292490-11292890`
[2016-04-15T06:08Z] 2016-04-14 23:08:47 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:08:47,495 - WARNING - Could not retrieve variants from source file in region 11:5461780-5475787. Error was invalid region `11:5461781-5475787`
[2016-04-15T06:08Z] 2016-04-14 23:08:51 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:08:51,609 - WARNING - Could not retrieve variants from source file in region 11:10708983-10715314. Error was invalid region `11:10708984-10715314`
[2016-04-15T06:08Z] 2016-04-14 23:08:51 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:08:51,830 - WARNING - Could not retrieve variants from source file in region 11:5510073-5540275. Error was invalid region `11:5510074-5540275`
[2016-04-15T06:08Z] 2016-04-14 23:08:53 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:08:53,586 - WARNING - Could not retrieve variants from source file in region 11:12225658-12229845. Error was invalid region `11:12225659-12229845`
[2016-04-15T06:08Z] 2016-04-14 23:08:55 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:08:55,990 - WARNING - Could not retrieve variants from source file in region 11:10708983-10715314. Error was invalid region `11:10708984-10715314`
[2016-04-15T06:08Z] 2016-04-14 23:08:56 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:08:56,191 - WARNING - Could not retrieve variants from source file in region 11:5461780-5475787. Error was invalid region `11:5461781-5475787`
[2016-04-15T06:08Z] 2016-04-14 23:08:56 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:08:56,663 - WARNING - Could not retrieve variants from source file in region 11:10822139-10825283. Error was invalid region `11:10822140-10825283`
[2016-04-15T06:08Z] 2016-04-14 23:08:57 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:08:57,573 - WARNING - Could not retrieve variants from source file in region 11:5410723-5411770. Error was invalid region `11:5410724-5411770`
[2016-04-15T06:08Z] 2016-04-14 23:08:57 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:08:57,796 - WARNING - Could not retrieve variants from source file in region 11:10785931-10786332. Error was invalid region `11:10785932-10786332`
[2016-04-15T06:09Z] 2016-04-14 23:09:00 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:09:00,884 - WARNING - Could not retrieve variants from source file in region 11:10708983-10715314. Error was invalid region `11:10708984-10715314`
[2016-04-15T06:09Z] 2016-04-14 23:09:01 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:09:01,122 - WARNING - Could not retrieve variants from source file in region 11:10822139-10825283. Error was invalid region `11:10822140-10825283`
[2016-04-15T06:09Z] 2016-04-14 23:09:02 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:09:02,221 - WARNING - Could not retrieve variants from source file in region 11:5410723-5411770. Error was invalid region `11:5410724-5411770`
[2016-04-15T06:09Z] 2016-04-14 23:09:02 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:09:02,320 - WARNING - Could not retrieve variants from source file in region 11:10785931-10786332. Error was invalid region `11:10785932-10786332`
[2016-04-15T06:09Z] 2016-04-14 23:09:02 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:09:02,795 - WARNING - Could not retrieve variants from source file in region 11:2868977-2869378. Error was invalid region `11:2868978-2869378`
[2016-04-15T06:09Z] 2016-04-14 23:09:04 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:09:04,156 - WARNING - Could not retrieve variants from source file in region 11:5410723-5411770. Error was invalid region `11:5410724-5411770`
[2016-04-15T06:09Z] 2016-04-14 23:09:08 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:09:08,907 - WARNING - Could not retrieve variants from source file in region 11:1145633-1162643. Error was invalid region `11:1145634-1162643`
[2016-04-15T06:09Z] 2016-04-14 23:09:15 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:09:15,066 - WARNING - Could not retrieve variants from source file in region 11:5248032-5248433. Error was invalid region `11:5248033-5248433`
[2016-04-15T06:09Z] 2016-04-14 23:09:15 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:09:15,897 - WARNING - Could not retrieve variants from source file in region 11:10638366-10673929. Error was invalid region `11:10638367-10673929`
[2016-04-15T06:09Z] 2016-04-14 23:09:17 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:09:17,727 - WARNING - Could not retrieve variants from source file in region 11:985336-985737. Error was invalid region `11:985337-985737`
[2016-04-15T06:09Z] 2016-04-14 23:09:17 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:09:17,930 - WARNING - Could not retrieve variants from source file in region 11:10472028-10477103. Error was invalid region `11:10472029-10477103`
[2016-04-15T06:09Z] 2016-04-14 23:09:19 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:09:19,126 - WARNING - Could not retrieve variants from source file in region 11:5248032-5248433. Error was invalid region `11:5248033-5248433`
[2016-04-15T06:09Z] 2016-04-14 23:09:19 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:09:19,684 - WARNING - Could not retrieve variants from source file in region 11:10638366-10673929. Error was invalid region `11:10638367-10673929`
[2016-04-15T06:09Z] 2016-04-14 23:09:20 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:09:20,898 - WARNING - Could not retrieve variants from source file in region 11:1309745-1310146. Error was invalid region `11:1309746-1310146`
[2016-04-15T06:09Z] 2016-04-14 23:09:22 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:09:22,171 - WARNING - Could not retrieve variants from source file in region 11:985336-985737. Error was invalid region `11:985337-985737`
[2016-04-15T06:09Z] 2016-04-14 23:09:22 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:09:22,438 - WARNING - Could not retrieve variants from source file in region 11:10472028-10477103. Error was invalid region `11:10472029-10477103`
[2016-04-15T06:09Z] 2016-04-14 23:09:22 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:09:22,516 - WARNING - Could not retrieve variants from source file in region 11:1309745-1310146. Error was invalid region `11:1309746-1310146`
[2016-04-15T06:09Z] 2016-04-14 23:09:24 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:09:24,823 - WARNING - Could not retrieve variants from source file in region 11:1309745-1310146. Error was invalid region `11:1309746-1310146`
[2016-04-15T06:09Z] 2016-04-14 23:09:26 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:09:26,305 - WARNING - Could not retrieve variants from source file in region 11:985336-985737. Error was invalid region `11:985337-985737`
[2016-04-15T06:09Z] 2016-04-14 23:09:26 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:09:26,348 - WARNING - Could not retrieve variants from source file in region 11:2683041-2683442. Error was invalid region `11:2683042-2683442`
[2016-04-15T06:09Z] 2016-04-14 23:09:26 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:09:26,616 - WARNING - Could not retrieve variants from source file in region 11:1018163-1028001. Error was invalid region `11:1018164-1028001`
[2016-04-15T06:09Z] 2016-04-14 23:09:30 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:09:30,404 - WARNING - Could not retrieve variants from source file in region 11:2683041-2683442. Error was invalid region `11:2683042-2683442`
[2016-04-15T06:09Z] 2016-04-14 23:09:34 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:09:34,815 - WARNING - Could not retrieve variants from source file in region 11:9537693-9549332. Error was invalid region `11:9537694-9549332`
[2016-04-15T06:09Z] 2016-04-14 23:09:35 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:09:35,137 - WARNING - Could not retrieve variants from source file in region 11:9754010-9769752. Error was invalid region `11:9754011-9769752`
[2016-04-15T06:09Z] 2016-04-14 23:09:35 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:09:35,143 - WARNING - Could not retrieve variants from source file in region 11:10555378-10555779. Error was invalid region `11:10555379-10555779`
[2016-04-15T06:09Z] 2016-04-14 23:09:37 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:09:37,051 - WARNING - Could not retrieve variants from source file in region 11:2168803-2191141. Error was invalid region `11:2168804-2191141`
[2016-04-15T06:09Z] 2016-04-14 23:09:38 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:09:38,718 - WARNING - Could not retrieve variants from source file in region 11:902859-903260. Error was invalid region `11:902860-903260`
[2016-04-15T06:09Z] 2016-04-14 23:09:38 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:09:38,738 - WARNING - Could not retrieve variants from source file in region 11:9537693-9549332. Error was invalid region `11:9537694-9549332`
[2016-04-15T06:09Z] 2016-04-14 23:09:39 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:09:39,057 - WARNING - Could not retrieve variants from source file in region 11:1856962-1902958. Error was invalid region `11:1856963-1902958`
[2016-04-15T06:09Z] 2016-04-14 23:09:39 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:09:39,245 - WARNING - Could not retrieve variants from source file in region 11:9754010-9769752. Error was invalid region `11:9754011-9769752`
[2016-04-15T06:09Z] 2016-04-14 23:09:39 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:09:39,300 - WARNING - Could not retrieve variants from source file in region 11:10555378-10555779. Error was invalid region `11:10555379-10555779`
[2016-04-15T06:09Z] 2016-04-14 23:09:40 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:09:40,827 - WARNING - Could not retrieve variants from source file in region 11:2322811-2337202. Error was invalid region `11:2322812-2337202`
[2016-04-15T06:09Z] 2016-04-14 23:09:41 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:09:41,978 - WARNING - Could not retrieve variants from source file in region 11:902859-903260. Error was invalid region `11:902860-903260`
[2016-04-15T06:09Z] 2016-04-14 23:09:42 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:09:42,152 - WARNING - Could not retrieve variants from source file in region 11:2322811-2337202. Error was invalid region `11:2322812-2337202`
[2016-04-15T06:09Z] 2016-04-14 23:09:42 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:09:42,678 - WARNING - Could not retrieve variants from source file in region 11:9754010-9769752. Error was invalid region `11:9754011-9769752`
[2016-04-15T06:09Z] 2016-04-14 23:09:44 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:09:44,167 - WARNING - Could not retrieve variants from source file in region 11:2322811-2337202. Error was invalid region `11:2322812-2337202`
[2016-04-15T06:09Z] 2016-04-14 23:09:45 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:09:45,256 - WARNING - Could not retrieve variants from source file in region 11:902859-903260. Error was invalid region `11:902860-903260`
[2016-04-15T06:09Z] 2016-04-14 23:09:52 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:09:52,595 - WARNING - Could not retrieve variants from source file in region 11:1481719-1507921. Error was invalid region `11:1481720-1507921`
[2016-04-15T06:09Z] 2016-04-14 23:09:57 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:09:57,945 - WARNING - Could not retrieve variants from source file in region 11:498909-499310. Error was invalid region `11:498910-499310`
[2016-04-15T06:09Z] 2016-04-14 23:09:59 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:09:59,205 - WARNING - Could not retrieve variants from source file in region 11:1481719-1507921. Error was invalid region `11:1481720-1507921`
[2016-04-15T06:10Z] ['bcbio-variation-recall', 'square', '-Xms750m', '-Xmx7280m', '-XX:+UseSerialGC', '-c', 16, '-r', u'11:16007750-31531554', '--caller', 'platypus', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/11/Batch1-11_16007749_31531554.vcf.gz', '/mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/11/Batch1-11_16007749_31531554.vcf-inputs.txt'] in region: 11:16007750-31531554
[2016-04-15T06:10Z] 2016-04-14 23:10:21 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:10:21,823 - WARNING - Could not retrieve variants from source file in region 11:27114577-27114978. Error was invalid region `11:27114578-27114978`
[2016-04-15T06:10Z] 2016-04-14 23:10:21 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:10:21,814 - WARNING - Could not retrieve variants from source file in region 11:19167639-19192041. Error was invalid region `11:19167640-19192041`
[2016-04-15T06:10Z] 2016-04-14 23:10:23 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:10:23,392 - WARNING - Could not retrieve variants from source file in region 11:18579579-18579980. Error was invalid region `11:18579580-18579980`
[2016-04-15T06:10Z] 2016-04-14 23:10:23 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:10:23,692 - WARNING - Could not retrieve variants from source file in region 11:20385395-20404803. Error was invalid region `11:20385396-20404803`
[2016-04-15T06:10Z] 2016-04-14 23:10:23 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:10:23,965 - WARNING - Could not retrieve variants from source file in region 11:30473170-30473738. Error was invalid region `11:30473171-30473738`
[2016-04-15T06:10Z] 2016-04-14 23:10:24 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:10:24,488 - WARNING - Could not retrieve variants from source file in region 11:28109940-28135164. Error was invalid region `11:28109941-28135164`
[2016-04-15T06:10Z] 2016-04-14 23:10:24 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:10:24,850 - WARNING - Could not retrieve variants from source file in region 11:17035507-17035908. Error was invalid region `11:17035508-17035908`
[2016-04-15T06:10Z] 2016-04-14 23:10:25 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:10:25,347 - WARNING - Could not retrieve variants from source file in region 11:26568755-26587323. Error was invalid region `11:26568756-26587323`
[2016-04-15T06:10Z] 2016-04-14 23:10:28 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:10:28,548 - WARNING - Could not retrieve variants from source file in region 11:30352813-30353214. Error was invalid region `11:30352814-30353214`
[2016-04-15T06:10Z] 2016-04-14 23:10:30 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:10:30,031 - WARNING - Could not retrieve variants from source file in region 11:31327105-31327506. Error was invalid region `11:31327106-31327506`
[2016-04-15T06:10Z] 2016-04-14 23:10:31 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:10:31,708 - WARNING - Could not retrieve variants from source file in region 11:17980836-17981237. Error was invalid region `11:17980837-17981237`
[2016-04-15T06:10Z] 2016-04-14 23:10:32 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:10:32,321 - WARNING - Could not retrieve variants from source file in region 11:17035507-17035908. Error was invalid region `11:17035508-17035908`
[2016-04-15T06:10Z] 2016-04-14 23:10:32 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:10:32,375 - WARNING - Could not retrieve variants from source file in region 11:18252965-18291511. Error was invalid region `11:18252966-18291511`
[2016-04-15T06:10Z] 2016-04-14 23:10:32 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:10:32,463 - WARNING - Could not retrieve variants from source file in region 11:26568755-26587323. Error was invalid region `11:26568756-26587323`
[2016-04-15T06:10Z] 2016-04-14 23:10:32 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:10:32,568 - WARNING - Could not retrieve variants from source file in region 11:18727237-18764216. Error was invalid region `11:18727238-18764216`
[2016-04-15T06:10Z] 2016-04-14 23:10:33 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:10:33,313 - WARNING - Could not retrieve variants from source file in region 11:30352813-30353214. Error was invalid region `11:30352814-30353214`
[2016-04-15T06:10Z] 2016-04-14 23:10:39 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:10:39,864 - WARNING - Could not retrieve variants from source file in region 11:17980836-17981237. Error was invalid region `11:17980837-17981237`
[2016-04-15T06:10Z] 2016-04-14 23:10:40 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:10:40,330 - WARNING - Could not retrieve variants from source file in region 11:30473170-30473738. Error was invalid region `11:30473171-30473738`
[2016-04-15T06:10Z] 2016-04-14 23:10:40 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:10:40,689 - WARNING - Could not retrieve variants from source file in region 11:17035507-17035908. Error was invalid region `11:17035508-17035908`
[2016-04-15T06:10Z] 2016-04-14 23:10:52 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:10:52,012 - WARNING - Could not retrieve variants from source file in region 11:25098727-25099128. Error was invalid region `11:25098728-25099128`
[2016-04-15T06:10Z] 2016-04-14 23:10:55 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:10:55,329 - WARNING - Could not retrieve variants from source file in region 11:30254974-30255375. Error was invalid region `11:30254975-30255375`
[2016-04-15T06:10Z] 2016-04-14 23:10:55 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:10:55,425 - WARNING - Could not retrieve variants from source file in region 11:19077544-19078094. Error was invalid region `11:19077545-19078094`
[2016-04-15T06:10Z] 2016-04-14 23:10:55 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:10:55,452 - WARNING - Could not retrieve variants from source file in region 11:17408419-17452682. Error was invalid region `11:17408420-17452682`
[2016-04-15T06:10Z] 2016-04-14 23:10:56 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:10:56,230 - WARNING - Could not retrieve variants from source file in region 11:20178506-20178907. Error was invalid region `11:20178507-20178907`
[2016-04-15T06:10Z] 2016-04-14 23:10:56 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:10:56,278 - WARNING - Could not retrieve variants from source file in region 11:28057746-28058147. Error was invalid region `11:28057747-28058147`
[2016-04-15T06:10Z] 2016-04-14 23:10:56 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:10:56,282 - WARNING - Could not retrieve variants from source file in region 11:17796072-17809914. Error was invalid region `11:17796073-17809914`
[2016-04-15T06:10Z] 2016-04-14 23:10:57 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:10:57,084 - WARNING - Could not retrieve variants from source file in region 11:27076766-27077308. Error was invalid region `11:27076767-27077308`
[2016-04-15T06:10Z] 2016-04-14 23:10:57 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:10:57,189 - WARNING - Could not retrieve variants from source file in region 11:18467610-18487495. Error was invalid region `11:18467611-18487495`
[2016-04-15T06:10Z] 2016-04-14 23:10:57 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:10:57,475 - WARNING - Could not retrieve variants from source file in region 11:25098727-25099128. Error was invalid region `11:25098728-25099128`
[2016-04-15T06:10Z] 2016-04-14 23:10:57 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:10:57,684 - WARNING - Could not retrieve variants from source file in region 11:30920955-30921356. Error was invalid region `11:30920956-30921356`
[2016-04-15T06:10Z] 2016-04-14 23:10:58 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:10:58,087 - WARNING - Could not retrieve variants from source file in region 11:18158958-18159444. Error was invalid region `11:18158959-18159444`
[2016-04-15T06:10Z] 2016-04-14 23:10:58 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:10:58,257 - WARNING - Could not retrieve variants from source file in region 11:16837577-16848267. Error was invalid region `11:16837578-16848267`
[2016-04-15T06:11Z] 2016-04-14 23:11:01 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:11:01,186 - WARNING - Could not retrieve variants from source file in region 11:30254974-30255375. Error was invalid region `11:30254975-30255375`
[2016-04-15T06:11Z] 2016-04-14 23:11:03 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:11:03,794 - WARNING - Could not retrieve variants from source file in region 11:27076766-27077308. Error was invalid region `11:27076767-27077308`
[2016-04-15T06:11Z] 2016-04-14 23:11:03 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:11:03,804 - WARNING - Could not retrieve variants from source file in region 11:20178506-20178907. Error was invalid region `11:20178507-20178907`
[2016-04-15T06:11Z] 2016-04-14 23:11:04 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:11:04,396 - WARNING - Could not retrieve variants from source file in region 11:18467610-18487495. Error was invalid region `11:18467611-18487495`
[2016-04-15T06:11Z] 2016-04-14 23:11:04 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:11:04,464 - WARNING - Could not retrieve variants from source file in region 11:18158958-18159444. Error was invalid region `11:18158959-18159444`
[2016-04-15T06:11Z] 2016-04-14 23:11:05 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:11:05,367 - WARNING - Could not retrieve variants from source file in region 11:25098727-25099128. Error was invalid region `11:25098728-25099128`
[2016-04-15T06:11Z] 2016-04-14 23:11:05 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:11:05,948 - WARNING - Could not retrieve variants from source file in region 11:30254974-30255375. Error was invalid region `11:30254975-30255375`
[2016-04-15T06:11Z] 2016-04-14 23:11:12 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:11:12,556 - WARNING - Could not retrieve variants from source file in region 11:18158958-18159444. Error was invalid region `11:18158959-18159444`
[2016-04-15T06:11Z] 2016-04-14 23:11:13 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:11:13,446 - WARNING - Could not retrieve variants from source file in region 11:18467610-18487495. Error was invalid region `11:18467611-18487495`
[2016-04-15T06:11Z] 2016-04-14 23:11:13 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:11:13,950 - WARNING - Could not retrieve variants from source file in region 11:19955289-19970769. Error was invalid region `11:19955290-19970769`
[2016-04-15T06:11Z] 2016-04-14 23:11:21 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:11:21,240 - WARNING - Could not retrieve variants from source file in region 11:26733998-26734399. Error was invalid region `11:26733999-26734399`
[2016-04-15T06:11Z] 2016-04-14 23:11:26 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:11:26,992 - WARNING - Could not retrieve variants from source file in region 11:26733998-26734399. Error was invalid region `11:26733999-26734399`
[2016-04-15T06:11Z] 2016-04-14 23:11:27 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:11:27,731 - WARNING - Could not retrieve variants from source file in region 11:19853877-19854278. Error was invalid region `11:19853878-19854278`
[2016-04-15T06:11Z] 2016-04-14 23:11:28 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:11:28,860 - WARNING - Could not retrieve variants from source file in region 11:17333452-17351873. Error was invalid region `11:17333453-17351873`
[2016-04-15T06:11Z] 2016-04-14 23:11:29 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:11:29,397 - WARNING - Could not retrieve variants from source file in region 11:18327473-18327874. Error was invalid region `11:18327474-18327874`
[2016-04-15T06:11Z] 2016-04-14 23:11:30 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:11:30,819 - WARNING - Could not retrieve variants from source file in region 11:19901421-19901822. Error was invalid region `11:19901422-19901822`
[2016-04-15T06:11Z] 2016-04-14 23:11:31 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:11:31,674 - WARNING - Could not retrieve variants from source file in region 11:27148636-27149037. Error was invalid region `11:27148637-27149037`
[2016-04-15T06:11Z] 2016-04-14 23:11:31 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:11:31,839 - WARNING - Could not retrieve variants from source file in region 11:17663205-17663932. Error was invalid region `11:17663206-17663932`
[2016-04-15T06:11Z] 2016-04-14 23:11:31 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:11:31,974 - WARNING - Could not retrieve variants from source file in region 11:24912425-24914243. Error was invalid region `11:24912426-24914243`
[2016-04-15T06:11Z] 2016-04-14 23:11:32 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:11:32,391 - WARNING - Could not retrieve variants from source file in region 11:18422276-18424677. Error was invalid region `11:18422277-18424677`
[2016-04-15T06:11Z] 2016-04-14 23:11:32 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:11:32,420 - WARNING - Could not retrieve variants from source file in region 11:26733998-26734399. Error was invalid region `11:26733999-26734399`
[2016-04-15T06:11Z] 2016-04-14 23:11:32 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:11:32,822 - WARNING - Could not retrieve variants from source file in region 11:22214666-22215093. Error was invalid region `11:22214667-22215093`
[2016-04-15T06:11Z] 2016-04-14 23:11:33 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:11:33,140 - WARNING - Could not retrieve variants from source file in region 11:18108281-18127748. Error was invalid region `11:18108282-18127748`
[2016-04-15T06:11Z] 2016-04-14 23:11:36 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:11:36,829 - WARNING - Could not retrieve variants from source file in region 11:19901421-19901822. Error was invalid region `11:19901422-19901822`
[2016-04-15T06:11Z] 2016-04-14 23:11:37 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:11:37,771 - WARNING - Could not retrieve variants from source file in region 11:26656352-26705500. Error was invalid region `11:26656353-26705500`
[2016-04-15T06:11Z] 2016-04-14 23:11:38 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:11:38,334 - WARNING - Could not retrieve variants from source file in region 11:16807989-16808628. Error was invalid region `11:16807990-16808628`
[2016-04-15T06:11Z] 2016-04-14 23:11:38 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:11:38,905 - WARNING - Could not retrieve variants from source file in region 11:18422276-18424677. Error was invalid region `11:18422277-18424677`
[2016-04-15T06:11Z] 2016-04-14 23:11:39 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:11:39,307 - WARNING - Could not retrieve variants from source file in region 11:20098901-20129501. Error was invalid region `11:20098902-20129501`
[2016-04-15T06:11Z] 2016-04-14 23:11:39 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:11:39,333 - WARNING - Could not retrieve variants from source file in region 11:19853877-19854278. Error was invalid region `11:19853878-19854278`
[2016-04-15T06:11Z] 2016-04-14 23:11:39 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:11:39,792 - WARNING - Could not retrieve variants from source file in region 11:18327473-18327874. Error was invalid region `11:18327474-18327874`
[2016-04-15T06:11Z] 2016-04-14 23:11:39 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:11:39,848 - WARNING - Could not retrieve variants from source file in region 11:18108281-18127748. Error was invalid region `11:18108282-18127748`
[2016-04-15T06:11Z] 2016-04-14 23:11:40 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:11:40,995 - WARNING - Could not retrieve variants from source file in region 11:19901421-19901822. Error was invalid region `11:19901422-19901822`
[2016-04-15T06:11Z] 2016-04-14 23:11:41 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:11:41,658 - WARNING - Could not retrieve variants from source file in region 11:27362046-27390279. Error was invalid region `11:27362047-27390279`
[2016-04-15T06:11Z] 2016-04-14 23:11:43 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:11:43,903 - WARNING - Could not retrieve variants from source file in region 11:27148636-27149037. Error was invalid region `11:27148637-27149037`
[2016-04-15T06:11Z] 2016-04-14 23:11:50 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:11:50,634 - WARNING - Could not retrieve variants from source file in region 11:17171922-17191209. Error was invalid region `11:17171923-17191209`
[2016-04-15T06:11Z] 2016-04-14 23:11:50 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:11:50,882 - WARNING - Could not retrieve variants from source file in region 11:17171922-17191209. Error was invalid region `11:17171923-17191209`
[2016-04-15T06:11Z] 2016-04-14 23:11:53 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:11:53,232 - WARNING - Could not retrieve variants from source file in region 11:22880791-22881192. Error was invalid region `11:22880792-22881192`
[2016-04-15T06:11Z] 2016-04-14 23:11:54 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:11:54,196 - WARNING - Could not retrieve variants from source file in region 11:19251615-19252016. Error was invalid region `11:19251616-19252016`
[2016-04-15T06:11Z] 2016-04-14 23:11:54 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:11:54,835 - WARNING - Could not retrieve variants from source file in region 11:20065462-20067254. Error was invalid region `11:20065463-20067254`
[2016-04-15T06:11Z] 2016-04-14 23:11:54 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:11:54,876 - WARNING - Could not retrieve variants from source file in region 11:17171922-17191209. Error was invalid region `11:17171923-17191209`
[2016-04-15T06:11Z] 2016-04-14 23:11:55 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:11:55,289 - WARNING - Could not retrieve variants from source file in region 11:22696240-22696641. Error was invalid region `11:22696241-22696641`
[2016-04-15T06:11Z] 2016-04-14 23:11:55 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:11:55,385 - WARNING - Could not retrieve variants from source file in region 11:20805075-20805476. Error was invalid region `11:20805076-20805476`
[2016-04-15T06:11Z] 2016-04-14 23:11:55 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:11:55,461 - WARNING - Could not retrieve variants from source file in region 11:21581594-21581995. Error was invalid region `11:21581595-21581995`
[2016-04-15T06:11Z] 2016-04-14 23:11:55 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:11:55,928 - WARNING - Could not retrieve variants from source file in region 11:21392276-21392677. Error was invalid region `11:21392277-21392677`
[2016-04-15T06:11Z] 2016-04-14 23:11:56 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:11:56,866 - WARNING - Could not retrieve variants from source file in region 11:22880791-22881192. Error was invalid region `11:22880792-22881192`
[2016-04-15T06:11Z] 2016-04-14 23:11:57 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:11:57,718 - WARNING - Could not retrieve variants from source file in region 11:17627402-17632841. Error was invalid region `11:17627403-17632841`
[2016-04-15T06:11Z] 2016-04-14 23:11:58 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:11:58,727 - WARNING - Could not retrieve variants from source file in region 11:16117345-16133603. Error was invalid region `11:16117346-16133603`
[2016-04-15T06:11Z] 2016-04-14 23:11:58 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:11:58,747 - WARNING - Could not retrieve variants from source file in region 11:22696240-22696641. Error was invalid region `11:22696241-22696641`
[2016-04-15T06:11Z] 2016-04-14 23:11:59 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:11:59,182 - WARNING - Could not retrieve variants from source file in region 11:20805075-20805476. Error was invalid region `11:20805076-20805476`
[2016-04-15T06:11Z] 2016-04-14 23:11:59 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:11:59,246 - WARNING - Could not retrieve variants from source file in region 11:21581594-21581995. Error was invalid region `11:21581595-21581995`
[2016-04-15T06:12Z] 2016-04-14 23:12:00 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:12:00,953 - WARNING - Could not retrieve variants from source file in region 11:22880791-22881192. Error was invalid region `11:22880792-22881192`
[2016-04-15T06:12Z] 2016-04-14 23:12:01 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:12:01,969 - WARNING - Could not retrieve variants from source file in region 11:19251615-19252016. Error was invalid region `11:19251616-19252016`
[2016-04-15T06:12Z] 2016-04-14 23:12:02 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:12:02,266 - WARNING - Could not retrieve variants from source file in region 11:20959183-20959584. Error was invalid region `11:20959184-20959584`
[2016-04-15T06:12Z] 2016-04-14 23:12:03 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:12:03,131 - WARNING - Could not retrieve variants from source file in region 11:20065462-20067254. Error was invalid region `11:20065463-20067254`
[2016-04-15T06:12Z] 2016-04-14 23:12:03 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:12:03,133 - WARNING - Could not retrieve variants from source file in region 11:22696240-22696641. Error was invalid region `11:22696241-22696641`
[2016-04-15T06:12Z] 2016-04-14 23:12:03 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:12:03,285 - WARNING - Could not retrieve variants from source file in region 11:20805075-20805476. Error was invalid region `11:20805076-20805476`
[2016-04-15T06:12Z] 2016-04-14 23:12:03 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:12:03,336 - WARNING - Could not retrieve variants from source file in region 11:21581594-21581995. Error was invalid region `11:21581595-21581995`
[2016-04-15T06:12Z] 2016-04-14 23:12:09 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:12:09,312 - WARNING - Could not retrieve variants from source file in region 11:20959183-20959584. Error was invalid region `11:20959184-20959584`
[2016-04-15T06:12Z] 2016-04-14 23:12:11 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:12:11,512 - WARNING - Could not retrieve variants from source file in region 11:22271659-22272060. Error was invalid region `11:22271660-22272060`
[2016-04-15T06:12Z] 2016-04-14 23:12:11 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:12:11,520 - WARNING - Could not retrieve variants from source file in region 11:22271659-22272060. Error was invalid region `11:22271660-22272060`
[2016-04-15T06:12Z] 2016-04-14 23:12:11 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:12:11,523 - WARNING - Could not retrieve variants from source file in region 11:22271659-22272060. Error was invalid region `11:22271660-22272060`
[2016-04-15T06:12Z] 2016-04-14 23:12:12 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:12:12,678 - WARNING - Could not retrieve variants from source file in region 11:22242518-22242919. Error was invalid region `11:22242519-22242919`
[2016-04-15T06:12Z] 2016-04-14 23:12:12 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:12:12,702 - WARNING - Could not retrieve variants from source file in region 11:22242518-22242919. Error was invalid region `11:22242519-22242919`
[2016-04-15T06:12Z] 2016-04-14 23:12:13 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:12:13,057 - WARNING - Could not retrieve variants from source file in region 11:22646759-22647160. Error was invalid region `11:22646760-22647160`
[2016-04-15T06:12Z] 2016-04-14 23:12:13 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:12:13,139 - WARNING - Could not retrieve variants from source file in region 11:20622764-20639590. Error was invalid region `11:20622765-20639590`
[2016-04-15T06:12Z] 2016-04-14 23:12:13 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:12:13,284 - WARNING - Could not retrieve variants from source file in region 11:20529675-20530076. Error was invalid region `11:20529676-20530076`
[2016-04-15T06:12Z] 2016-04-14 23:12:15 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:12:15,378 - WARNING - Could not retrieve variants from source file in region 11:20529675-20530076. Error was invalid region `11:20529676-20530076`
[2016-04-15T06:12Z] 2016-04-14 23:12:16 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:12:16,758 - WARNING - Could not retrieve variants from source file in region 11:22242518-22242919. Error was invalid region `11:22242519-22242919`
[2016-04-15T06:12Z] 2016-04-14 23:12:17 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:12:17,366 - WARNING - Could not retrieve variants from source file in region 11:20622764-20639590. Error was invalid region `11:20622765-20639590`
[2016-04-15T06:12Z] 2016-04-14 23:12:17 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:12:17,523 - WARNING - Could not retrieve variants from source file in region 11:20529675-20530076. Error was invalid region `11:20529676-20530076`
[2016-04-15T06:12Z] ['bcbio-variation-recall', 'square', '-Xms750m', '-Xmx7280m', '-XX:+UseSerialGC', '-c', 16, '-r', u'11:31541603-47074069', '--caller', 'platypus', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/11/Batch1-11_31541602_47074069.vcf.gz', '/mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/11/Batch1-11_31541602_47074069.vcf-inputs.txt'] in region: 11:31541603-47074069
[2016-04-15T06:12Z] 2016-04-14 23:12:33 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:12:33,287 - WARNING - Could not retrieve variants from source file in region 11:45831746-45832222. Error was invalid region `11:45831747-45832222`
[2016-04-15T06:12Z] 2016-04-14 23:12:33 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:12:33,818 - WARNING - Could not retrieve variants from source file in region 11:44940617-44941018. Error was invalid region `11:44940618-44941018`
[2016-04-15T06:12Z] 2016-04-14 23:12:34 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:12:34,091 - WARNING - Could not retrieve variants from source file in region 11:45672050-45672451. Error was invalid region `11:45672051-45672451`
[2016-04-15T06:12Z] 2016-04-14 23:12:34 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:12:34,717 - WARNING - Could not retrieve variants from source file in region 11:44636622-44640458. Error was invalid region `11:44636623-44640458`
[2016-04-15T06:12Z] 2016-04-14 23:12:34 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:12:34,758 - WARNING - Could not retrieve variants from source file in region 11:46889954-46914788. Error was invalid region `11:46889955-46914788`
[2016-04-15T06:12Z] 2016-04-14 23:12:34 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:12:34,922 - WARNING - Could not retrieve variants from source file in region 11:46321446-46342449. Error was invalid region `11:46321447-46342449`
[2016-04-15T06:12Z] 2016-04-14 23:12:35 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:12:35,263 - WARNING - Could not retrieve variants from source file in region 11:32996594-32996995. Error was invalid region `11:32996595-32996995`
[2016-04-15T06:12Z] 2016-04-14 23:12:35 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:12:35,520 - WARNING - Could not retrieve variants from source file in region 11:36483997-36484398. Error was invalid region `11:36483998-36484398`
[2016-04-15T06:12Z] 2016-04-14 23:12:35 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:12:35,601 - WARNING - Could not retrieve variants from source file in region 11:45248161-45249504. Error was invalid region `11:45248162-45249504`
[2016-04-15T06:12Z] 2016-04-14 23:12:36 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:12:36,131 - WARNING - Could not retrieve variants from source file in region 11:35455850-35456343. Error was invalid region `11:35455851-35456343`
[2016-04-15T06:12Z] 2016-04-14 23:12:36 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:12:36,291 - WARNING - Could not retrieve variants from source file in region 11:44331098-44331699. Error was invalid region `11:44331099-44331699`
[2016-04-15T06:12Z] 2016-04-14 23:12:36 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:12:36,297 - WARNING - Could not retrieve variants from source file in region 11:43472535-43472936. Error was invalid region `11:43472536-43472936`
[2016-04-15T06:12Z] 2016-04-14 23:12:40 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:12:40,205 - WARNING - Could not retrieve variants from source file in region 11:45672050-45672451. Error was invalid region `11:45672051-45672451`
[2016-04-15T06:12Z] 2016-04-14 23:12:41 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:12:41,387 - WARNING - Could not retrieve variants from source file in region 11:46889954-46914788. Error was invalid region `11:46889955-46914788`
[2016-04-15T06:12Z] 2016-04-14 23:12:43 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:12:43,255 - WARNING - Could not retrieve variants from source file in region 11:45248161-45249504. Error was invalid region `11:45248162-45249504`
[2016-04-15T06:12Z] 2016-04-14 23:12:43 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:12:43,276 - WARNING - Could not retrieve variants from source file in region 11:36483997-36484398. Error was invalid region `11:36483998-36484398`
[2016-04-15T06:12Z] 2016-04-14 23:12:44 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:12:44,587 - WARNING - Could not retrieve variants from source file in region 11:45672050-45672451. Error was invalid region `11:45672051-45672451`
[2016-04-15T06:12Z] 2016-04-14 23:12:44 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:12:44,853 - WARNING - Could not retrieve variants from source file in region 11:44940617-44941018. Error was invalid region `11:44940618-44941018`
[2016-04-15T06:12Z] 2016-04-14 23:12:46 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:12:46,116 - WARNING - Could not retrieve variants from source file in region 11:46889954-46914788. Error was invalid region `11:46889955-46914788`
[2016-04-15T06:12Z] 2016-04-14 23:12:50 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:12:50,431 - WARNING - Could not retrieve variants from source file in region 11:46368916-46388123. Error was invalid region `11:46368917-46388123`
[2016-04-15T06:12Z] 2016-04-14 23:12:51 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:12:51,337 - WARNING - Could not retrieve variants from source file in region 11:45248161-45249504. Error was invalid region `11:45248162-45249504`
[2016-04-15T06:12Z] 2016-04-14 23:12:52 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:12:52,243 - WARNING - Could not retrieve variants from source file in region 11:35455850-35456343. Error was invalid region `11:35455851-35456343`
[2016-04-15T06:12Z] 2016-04-14 23:12:52 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:12:52,477 - WARNING - Could not retrieve variants from source file in region 11:36483997-36484398. Error was invalid region `11:36483998-36484398`
[2016-04-15T06:12Z] 2016-04-14 23:12:52 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:12:52,501 - WARNING - Could not retrieve variants from source file in region 11:32996594-32996995. Error was invalid region `11:32996595-32996995`
[2016-04-15T06:12Z] 2016-04-14 23:12:52 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:12:52,869 - WARNING - Could not retrieve variants from source file in region 11:44331098-44331699. Error was invalid region `11:44331099-44331699`
[2016-04-15T06:12Z] 2016-04-14 23:12:52 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:12:52,875 - WARNING - Could not retrieve variants from source file in region 11:46321446-46342449. Error was invalid region `11:46321447-46342449`
[2016-04-15T06:13Z] 2016-04-14 23:13:01 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:13:01,895 - WARNING - Could not retrieve variants from source file in region 11:46702709-46703110. Error was invalid region `11:46702710-46703110`
[2016-04-15T06:13Z] 2016-04-14 23:13:05 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:13:05,049 - WARNING - Could not retrieve variants from source file in region 11:46702709-46703110. Error was invalid region `11:46702710-46703110`
[2016-04-15T06:13Z] 2016-04-14 23:13:05 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:13:05,942 - WARNING - Could not retrieve variants from source file in region 11:36422581-36422982. Error was invalid region `11:36422582-36422982`
[2016-04-15T06:13Z] 2016-04-14 23:13:06 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:13:06,603 - WARNING - Could not retrieve variants from source file in region 11:46702709-46703110. Error was invalid region `11:46702710-46703110`
[2016-04-15T06:13Z] 2016-04-14 23:13:06 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:13:06,928 - WARNING - Could not retrieve variants from source file in region 11:35392390-35392791. Error was invalid region `11:35392391-35392791`
[2016-04-15T06:13Z] 2016-04-14 23:13:07 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:13:07,285 - WARNING - Could not retrieve variants from source file in region 11:36103017-36103418. Error was invalid region `11:36103018-36103418`
[2016-04-15T06:13Z] 2016-04-14 23:13:07 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:13:07,701 - WARNING - Could not retrieve variants from source file in region 11:32954133-32956810. Error was invalid region `11:32954134-32956810`
[2016-04-15T06:13Z] 2016-04-14 23:13:08 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:13:08,921 - WARNING - Could not retrieve variants from source file in region 11:33667122-33680561. Error was invalid region `11:33667123-33680561`
[2016-04-15T06:13Z] 2016-04-14 23:13:10 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:13:10,523 - WARNING - Could not retrieve variants from source file in region 11:34074200-34074601. Error was invalid region `11:34074201-34074601`
[2016-04-15T06:13Z] 2016-04-14 23:13:10 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:13:10,768 - WARNING - Could not retrieve variants from source file in region 11:34101089-34101490. Error was invalid region `11:34101090-34101490`
[2016-04-15T06:13Z] 2016-04-14 23:13:10 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:13:10,805 - WARNING - Could not retrieve variants from source file in region 11:32456087-32456884. Error was invalid region `11:32456088-32456884`
[2016-04-15T06:13Z] 2016-04-14 23:13:11 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:13:11,261 - WARNING - Could not retrieve variants from source file in region 11:36422581-36422982. Error was invalid region `11:36422582-36422982`
[2016-04-15T06:13Z] 2016-04-14 23:13:11 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:13:11,392 - WARNING - Could not retrieve variants from source file in region 11:34652913-34653314. Error was invalid region `11:34652914-34653314`
[2016-04-15T06:13Z] 2016-04-14 23:13:11 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:13:11,484 - WARNING - Could not retrieve variants from source file in region 11:34152728-34154831. Error was invalid region `11:34152729-34154831`
[2016-04-15T06:13Z] 2016-04-14 23:13:11 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:13:11,929 - WARNING - Could not retrieve variants from source file in region 11:35392390-35392791. Error was invalid region `11:35392391-35392791`
[2016-04-15T06:13Z] 2016-04-14 23:13:12 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:13:12,275 - WARNING - Could not retrieve variants from source file in region 11:36103017-36103418. Error was invalid region `11:36103018-36103418`
[2016-04-15T06:13Z] 2016-04-14 23:13:12 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:13:12,444 - WARNING - Could not retrieve variants from source file in region 11:32954133-32956810. Error was invalid region `11:32954134-32956810`
[2016-04-15T06:13Z] 2016-04-14 23:13:13 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:13:13,402 - WARNING - Could not retrieve variants from source file in region 11:40137332-40137733. Error was invalid region `11:40137333-40137733`
[2016-04-15T06:13Z] 2016-04-14 23:13:15 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:13:15,824 - WARNING - Could not retrieve variants from source file in region 11:34074200-34074601. Error was invalid region `11:34074201-34074601`
[2016-04-15T06:13Z] 2016-04-14 23:13:17 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:13:17,350 - WARNING - Could not retrieve variants from source file in region 11:36422581-36422982. Error was invalid region `11:36422582-36422982`
[2016-04-15T06:13Z] 2016-04-14 23:13:17 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:13:17,392 - WARNING - Could not retrieve variants from source file in region 11:34652913-34653314. Error was invalid region `11:34652914-34653314`
[2016-04-15T06:13Z] 2016-04-14 23:13:17 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:13:17,650 - WARNING - Could not retrieve variants from source file in region 11:44079999-44105171. Error was invalid region `11:44080000-44105171`
[2016-04-15T06:13Z] 2016-04-14 23:13:17 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:13:17,730 - WARNING - Could not retrieve variants from source file in region 11:34152728-34154831. Error was invalid region `11:34152729-34154831`
[2016-04-15T06:13Z] 2016-04-14 23:13:18 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:13:18,067 - WARNING - Could not retrieve variants from source file in region 11:35392390-35392791. Error was invalid region `11:35392391-35392791`
[2016-04-15T06:13Z] 2016-04-14 23:13:18 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:13:18,075 - WARNING - Could not retrieve variants from source file in region 11:32954133-32956810. Error was invalid region `11:32954134-32956810`
[2016-04-15T06:13Z] 2016-04-14 23:13:18 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:13:18,393 - WARNING - Could not retrieve variants from source file in region 11:33667122-33680561. Error was invalid region `11:33667123-33680561`
[2016-04-15T06:13Z] 2016-04-14 23:13:23 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:13:23,149 - WARNING - Could not retrieve variants from source file in region 11:43940391-43940834. Error was invalid region `11:43940392-43940834`
[2016-04-15T06:13Z] 2016-04-14 23:13:23 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:13:23,988 - WARNING - Could not retrieve variants from source file in region 11:32456087-32456884. Error was invalid region `11:32456088-32456884`
[2016-04-15T06:13Z] 2016-04-14 23:13:25 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:13:25,827 - WARNING - Could not retrieve variants from source file in region 11:44079999-44105171. Error was invalid region `11:44080000-44105171`
[2016-04-15T06:13Z] 2016-04-14 23:13:26 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:13:26,518 - WARNING - Could not retrieve variants from source file in region 11:34152728-34154831. Error was invalid region `11:34152729-34154831`
[2016-04-15T06:13Z] 2016-04-14 23:13:30 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:13:30,170 - WARNING - Could not retrieve variants from source file in region 11:32634885-32657456. Error was invalid region `11:32634886-32657456`
[2016-04-15T06:13Z] 2016-04-14 23:13:31 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:13:31,128 - WARNING - Could not retrieve variants from source file in region 11:32634885-32657456. Error was invalid region `11:32634886-32657456`
[2016-04-15T06:13Z] 2016-04-14 23:13:32 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:13:32,782 - WARNING - Could not retrieve variants from source file in region 11:43940391-43940834. Error was invalid region `11:43940392-43940834`
[2016-04-15T06:13Z] 2016-04-14 23:13:35 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:13:35,777 - WARNING - Could not retrieve variants from source file in region 11:34968901-34991917. Error was invalid region `11:34968902-34991917`
[2016-04-15T06:13Z] 2016-04-14 23:13:36 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:13:36,532 - WARNING - Could not retrieve variants from source file in region 11:33631212-33640294. Error was invalid region `11:33631213-33640294`
[2016-04-15T06:13Z] 2016-04-14 23:13:36 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:13:36,656 - WARNING - Could not retrieve variants from source file in region 11:33880805-33892239. Error was invalid region `11:33880806-33892239`
[2016-04-15T06:13Z] 2016-04-14 23:13:39 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:13:39,106 - WARNING - Could not retrieve variants from source file in region 11:33880805-33892239. Error was invalid region `11:33880806-33892239`
[2016-04-15T06:13Z] 2016-04-14 23:13:40 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:13:40,296 - WARNING - Could not retrieve variants from source file in region 11:32124767-32126151. Error was invalid region `11:32124768-32126151`
[2016-04-15T06:13Z] 2016-04-14 23:13:40 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:13:40,616 - WARNING - Could not retrieve variants from source file in region 11:31822643-31823044. Error was invalid region `11:31822644-31823044`
[2016-04-15T06:13Z] 2016-04-14 23:13:40 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:13:40,681 - WARNING - Could not retrieve variants from source file in region 11:34968901-34991917. Error was invalid region `11:34968902-34991917`
[2016-04-15T06:13Z] 2016-04-14 23:13:40 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:13:40,773 - WARNING - Could not retrieve variants from source file in region 11:43911154-43911555. Error was invalid region `11:43911155-43911555`
[2016-04-15T06:13Z] 2016-04-14 23:13:41 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:13:41,844 - WARNING - Could not retrieve variants from source file in region 11:32124767-32126151. Error was invalid region `11:32124768-32126151`
[2016-04-15T06:13Z] 2016-04-14 23:13:43 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:13:43,317 - WARNING - Could not retrieve variants from source file in region 11:43911154-43911555. Error was invalid region `11:43911155-43911555`
[2016-04-15T06:13Z] 2016-04-14 23:13:45 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:13:45,194 - WARNING - Could not retrieve variants from source file in region 11:43911154-43911555. Error was invalid region `11:43911155-43911555`
[2016-04-15T06:13Z] 2016-04-14 23:13:45 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:13:45,321 - WARNING - Could not retrieve variants from source file in region 11:33631212-33640294. Error was invalid region `11:33631213-33640294`
[2016-04-15T06:13Z] 2016-04-14 23:13:45 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:13:45,390 - WARNING - Could not retrieve variants from source file in region 11:43702319-43702805. Error was invalid region `11:43702320-43702805`
[2016-04-15T06:13Z] 2016-04-14 23:13:46 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:13:46,919 - WARNING - Could not retrieve variants from source file in region 11:31822643-31823044. Error was invalid region `11:31822644-31823044`
[2016-04-15T06:13Z] 2016-04-14 23:13:46 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:13:46,933 - WARNING - Could not retrieve variants from source file in region 11:34909715-34938500. Error was invalid region `11:34909716-34938500`
[2016-04-15T06:13Z] 2016-04-14 23:13:49 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:13:49,685 - WARNING - Could not retrieve variants from source file in region 11:43702319-43702805. Error was invalid region `11:43702320-43702805`
[2016-04-15T06:13Z] 2016-04-14 23:13:50 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:13:50,870 - WARNING - Could not retrieve variants from source file in region 11:33563912-33605150. Error was invalid region `11:33563913-33605150`
[2016-04-15T06:13Z] ['bcbio-variation-recall', 'square', '-Xms750m', '-Xmx7280m', '-XX:+UseSerialGC', '-c', 16, '-r', u'11:47158867-62678572', '--caller', 'platypus', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/11/Batch1-11_47158866_62678572.vcf.gz', '/mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/11/Batch1-11_47158866_62678572.vcf-inputs.txt'] in region: 11:47158867-62678572
[2016-04-15T06:14Z] 2016-04-14 23:14:09 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:14:09,417 - WARNING - Could not retrieve variants from source file in region 11:61895530-61913386. Error was invalid region `11:61895531-61913386`
[2016-04-15T06:14Z] 2016-04-14 23:14:10 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:14:10,045 - WARNING - Could not retrieve variants from source file in region 11:61106681-61116011. Error was invalid region `11:61106682-61116011`
[2016-04-15T06:14Z] 2016-04-14 23:14:10 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:14:10,444 - WARNING - Could not retrieve variants from source file in region 11:48145036-48189062. Error was invalid region `11:48145037-48189062`
[2016-04-15T06:14Z] 2016-04-14 23:14:10 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:14:10,606 - WARNING - Could not retrieve variants from source file in region 11:62039190-62039591. Error was invalid region `11:62039191-62039591`
[2016-04-15T06:14Z] 2016-04-14 23:14:10 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:14:10,833 - WARNING - Could not retrieve variants from source file in region 11:60230320-60230721. Error was invalid region `11:60230321-60230721`
[2016-04-15T06:14Z] 2016-04-14 23:14:10 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:14:10,942 - WARNING - Could not retrieve variants from source file in region 11:60531053-60539360. Error was invalid region `11:60531054-60539360`
[2016-04-15T06:14Z] 2016-04-14 23:14:11 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:14:11,658 - WARNING - Could not retrieve variants from source file in region 11:57381778-57382179. Error was invalid region `11:57381779-57382179`
[2016-04-15T06:14Z] 2016-04-14 23:14:15 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:14:15,128 - WARNING - Could not retrieve variants from source file in region 11:61895530-61913386. Error was invalid region `11:61895531-61913386`
[2016-04-15T06:14Z] 2016-04-14 23:14:18 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:14:18,729 - WARNING - Could not retrieve variants from source file in region 11:62039190-62039591. Error was invalid region `11:62039191-62039591`
[2016-04-15T06:14Z] 2016-04-14 23:14:19 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:14:19,878 - WARNING - Could not retrieve variants from source file in region 11:55371596-55371997. Error was invalid region `11:55371597-55371997`
[2016-04-15T06:14Z] 2016-04-14 23:14:20 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:14:20,264 - WARNING - Could not retrieve variants from source file in region 11:62010652-62011053. Error was invalid region `11:62010653-62011053`
[2016-04-15T06:14Z] 2016-04-14 23:14:20 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:14:20,287 - WARNING - Could not retrieve variants from source file in region 11:60102173-60102697. Error was invalid region `11:60102174-60102697`
[2016-04-15T06:14Z] 2016-04-14 23:14:20 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:14:20,322 - WARNING - Could not retrieve variants from source file in region 11:57381778-57382179. Error was invalid region `11:57381779-57382179`
[2016-04-15T06:14Z] 2016-04-14 23:14:20 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:14:20,766 - WARNING - Could not retrieve variants from source file in region 11:58892165-58892567. Error was invalid region `11:58892166-58892567`
[2016-04-15T06:14Z] 2016-04-14 23:14:20 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:14:20,801 - WARNING - Could not retrieve variants from source file in region 11:59480740-59481309. Error was invalid region `11:59480741-59481309`
[2016-04-15T06:14Z] 2016-04-14 23:14:20 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:14:20,840 - WARNING - Could not retrieve variants from source file in region 11:61291711-61300894. Error was invalid region `11:61291712-61300894`
[2016-04-15T06:14Z] 2016-04-14 23:14:20 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:14:20,879 - WARNING - Could not retrieve variants from source file in region 11:61895530-61913386. Error was invalid region `11:61895531-61913386`
[2016-04-15T06:14Z] 2016-04-14 23:14:24 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:14:24,261 - WARNING - Could not retrieve variants from source file in region 11:62039190-62039591. Error was invalid region `11:62039191-62039591`
[2016-04-15T06:14Z] 2016-04-14 23:14:26 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:14:26,843 - WARNING - Could not retrieve variants from source file in region 11:55371596-55371997. Error was invalid region `11:55371597-55371997`
[2016-04-15T06:14Z] 2016-04-14 23:14:27 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:14:27,269 - WARNING - Could not retrieve variants from source file in region 11:62010652-62011053. Error was invalid region `11:62010653-62011053`
[2016-04-15T06:14Z] 2016-04-14 23:14:27 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:14:27,593 - WARNING - Could not retrieve variants from source file in region 11:60102173-60102697. Error was invalid region `11:60102174-60102697`
[2016-04-15T06:14Z] 2016-04-14 23:14:27 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:14:27,633 - WARNING - Could not retrieve variants from source file in region 11:57381778-57382179. Error was invalid region `11:57381779-57382179`
[2016-04-15T06:14Z] 2016-04-14 23:14:39 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:14:39,341 - WARNING - Could not retrieve variants from source file in region 11:47834381-47834782. Error was invalid region `11:47834382-47834782`
[2016-04-15T06:14Z] 2016-04-14 23:14:41 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:14:41,299 - WARNING - Could not retrieve variants from source file in region 11:61658589-61687864. Error was invalid region `11:61658590-61687864`
[2016-04-15T06:14Z] 2016-04-14 23:14:43 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:14:43,324 - WARNING - Could not retrieve variants from source file in region 11:61538809-61539210. Error was invalid region `11:61538810-61539210`
[2016-04-15T06:14Z] 2016-04-14 23:14:43 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:14:43,575 - WARNING - Could not retrieve variants from source file in region 11:59836886-59837287. Error was invalid region `11:59836887-59837287`
[2016-04-15T06:14Z] 2016-04-14 23:14:44 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:14:44,165 - WARNING - Could not retrieve variants from source file in region 11:59422939-59423340. Error was invalid region `11:59422940-59423340`
[2016-04-15T06:14Z] 2016-04-14 23:14:44 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:14:44,502 - WARNING - Could not retrieve variants from source file in region 11:60970858-60971259. Error was invalid region `11:60970859-60971259`
[2016-04-15T06:14Z] 2016-04-14 23:14:44 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:14:44,838 - WARNING - Could not retrieve variants from source file in region 11:47834381-47834782. Error was invalid region `11:47834382-47834782`
[2016-04-15T06:14Z] 2016-04-14 23:14:45 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:14:45,289 - WARNING - Could not retrieve variants from source file in region 11:62554482-62567705. Error was invalid region `11:62554483-62567705`
[2016-04-15T06:14Z] 2016-04-14 23:14:45 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:14:45,322 - WARNING - Could not retrieve variants from source file in region 11:58477815-58478419. Error was invalid region `11:58477816-58478419`
[2016-04-15T06:14Z] 2016-04-14 23:14:46 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:14:46,831 - WARNING - Could not retrieve variants from source file in region 11:60264736-60291603. Error was invalid region `11:60264737-60291603`
[2016-04-15T06:14Z] 2016-04-14 23:14:48 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:14:48,696 - WARNING - Could not retrieve variants from source file in region 11:55322000-55340569. Error was invalid region `11:55322001-55340569`
[2016-04-15T06:14Z] 2016-04-14 23:14:50 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:14:50,559 - WARNING - Could not retrieve variants from source file in region 11:57313258-57313659. Error was invalid region `11:57313259-57313659`
[2016-04-15T06:14Z] 2016-04-14 23:14:51 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:14:51,100 - WARNING - Could not retrieve variants from source file in region 11:60970858-60971259. Error was invalid region `11:60970859-60971259`
[2016-04-15T06:14Z] 2016-04-14 23:14:51 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:14:51,144 - WARNING - Could not retrieve variants from source file in region 11:47834381-47834782. Error was invalid region `11:47834382-47834782`
[2016-04-15T06:14Z] 2016-04-14 23:14:51 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:14:51,934 - WARNING - Could not retrieve variants from source file in region 11:60049914-60073787. Error was invalid region `11:60049915-60073787`
[2016-04-15T06:14Z] 2016-04-14 23:14:52 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:14:52,054 - WARNING - Could not retrieve variants from source file in region 11:61249172-61257545. Error was invalid region `11:61249173-61257545`
[2016-04-15T06:14Z] 2016-04-14 23:14:52 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:14:52,216 - WARNING - Could not retrieve variants from source file in region 11:60264736-60291603. Error was invalid region `11:60264737-60291603`
[2016-04-15T06:14Z] 2016-04-14 23:14:53 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:14:53,393 - WARNING - Could not retrieve variants from source file in region 11:55322000-55340569. Error was invalid region `11:55322001-55340569`
[2016-04-15T06:14Z] 2016-04-14 23:14:54 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:14:54,787 - WARNING - Could not retrieve variants from source file in region 11:59836886-59837287. Error was invalid region `11:59836887-59837287`
[2016-04-15T06:14Z] 2016-04-14 23:14:55 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:14:55,345 - WARNING - Could not retrieve variants from source file in region 11:61538809-61539210. Error was invalid region `11:61538810-61539210`
[2016-04-15T06:14Z] 2016-04-14 23:14:56 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:14:56,646 - WARNING - Could not retrieve variants from source file in region 11:57313258-57313659. Error was invalid region `11:57313259-57313659`
[2016-04-15T06:14Z] 2016-04-14 23:14:57 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:14:57,239 - WARNING - Could not retrieve variants from source file in region 11:58477815-58478419. Error was invalid region `11:58477816-58478419`
[2016-04-15T06:14Z] 2016-04-14 23:14:58 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:14:58,023 - WARNING - Could not retrieve variants from source file in region 11:59422939-59423340. Error was invalid region `11:59422940-59423340`
[2016-04-15T06:15Z] 2016-04-14 23:15:04 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:15:04,483 - WARNING - Could not retrieve variants from source file in region 11:50002980-50003381. Error was invalid region `11:50002981-50003381`
[2016-04-15T06:15Z] 2016-04-14 23:15:06 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:15:06,270 - WARNING - Could not retrieve variants from source file in region 11:47751182-47753560. Error was invalid region `11:47751183-47753560`
[2016-04-15T06:15Z] 2016-04-14 23:15:06 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:15:06,702 - WARNING - Could not retrieve variants from source file in region 11:60609761-60638660. Error was invalid region `11:60609762-60638660`
[2016-04-15T06:15Z] 2016-04-14 23:15:09 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:15:09,790 - WARNING - Could not retrieve variants from source file in region 11:60892395-60899957. Error was invalid region `11:60892396-60899957`
[2016-04-15T06:15Z] 2016-04-14 23:15:09 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:15:09,945 - WARNING - Could not retrieve variants from source file in region 11:50002980-50003381. Error was invalid region `11:50002981-50003381`
[2016-04-15T06:15Z] 2016-04-14 23:15:09 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:15:09,989 - WARNING - Could not retrieve variants from source file in region 11:48510294-48510967. Error was invalid region `11:48510295-48510967`
[2016-04-15T06:15Z] 2016-04-14 23:15:10 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:15:10,508 - WARNING - Could not retrieve variants from source file in region 11:57268278-57268679. Error was invalid region `11:57268279-57268679`
[2016-04-15T06:15Z] 2016-04-14 23:15:11 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:15:11,301 - WARNING - Could not retrieve variants from source file in region 11:47751182-47753560. Error was invalid region `11:47751183-47753560`
[2016-04-15T06:15Z] 2016-04-14 23:15:12 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:15:12,825 - WARNING - Could not retrieve variants from source file in region 11:59271426-59271827. Error was invalid region `11:59271427-59271827`
[2016-04-15T06:15Z] 2016-04-14 23:15:15 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:15:15,089 - WARNING - Could not retrieve variants from source file in region 11:48510294-48510967. Error was invalid region `11:48510295-48510967`
[2016-04-15T06:15Z] 2016-04-14 23:15:15 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:15:15,242 - WARNING - Could not retrieve variants from source file in region 11:61165069-61204551. Error was invalid region `11:61165070-61204551`
[2016-04-15T06:15Z] 2016-04-14 23:15:15 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:15:15,246 - WARNING - Could not retrieve variants from source file in region 11:50002980-50003381. Error was invalid region `11:50002981-50003381`
[2016-04-15T06:15Z] 2016-04-14 23:15:15 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:15:15,859 - WARNING - Could not retrieve variants from source file in region 11:47751182-47753560. Error was invalid region `11:47751183-47753560`
[2016-04-15T06:15Z] 2016-04-14 23:15:17 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:15:17,127 - WARNING - Could not retrieve variants from source file in region 11:58378213-58378614. Error was invalid region `11:58378214-58378614`
[2016-04-15T06:15Z] 2016-04-14 23:15:19 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:15:19,491 - WARNING - Could not retrieve variants from source file in region 11:55110645-55136347. Error was invalid region `11:55110646-55136347`
[2016-04-15T06:15Z] 2016-04-14 23:15:20 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:15:20,566 - WARNING - Could not retrieve variants from source file in region 11:48510294-48510967. Error was invalid region `11:48510295-48510967`
[2016-04-15T06:15Z] 2016-04-14 23:15:20 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:15:20,665 - WARNING - Could not retrieve variants from source file in region 11:61165069-61204551. Error was invalid region `11:61165070-61204551`
[2016-04-15T06:15Z] 2016-04-14 23:15:21 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:15:21,181 - WARNING - Could not retrieve variants from source file in region 11:57268278-57268679. Error was invalid region `11:57268279-57268679`
[2016-04-15T06:15Z] 2016-04-14 23:15:22 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:15:22,776 - WARNING - Could not retrieve variants from source file in region 11:59271426-59271827. Error was invalid region `11:59271427-59271827`
[2016-04-15T06:15Z] 2016-04-14 23:15:25 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:15:25,514 - WARNING - Could not retrieve variants from source file in region 11:61165069-61204551. Error was invalid region `11:61165070-61204551`
[2016-04-15T06:15Z] 2016-04-14 23:15:30 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:15:30,033 - WARNING - Could not retrieve variants from source file in region 11:49974160-49974561. Error was invalid region `11:49974161-49974561`
[2016-04-15T06:15Z] 2016-04-14 23:15:31 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:15:31,008 - WARNING - Could not retrieve variants from source file in region 11:47701317-47701718. Error was invalid region `11:47701318-47701718`
[2016-04-15T06:15Z] 2016-04-14 23:15:31 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:15:31,565 - WARNING - Could not retrieve variants from source file in region 11:49055540-49080806. Error was invalid region `11:49055541-49080806`
[2016-04-15T06:15Z] 2016-04-14 23:15:32 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:15:32,578 - WARNING - Could not retrieve variants from source file in region 11:48285631-48286446. Error was invalid region `11:48285632-48286446`
[2016-04-15T06:15Z] 2016-04-14 23:15:32 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:15:32,909 - WARNING - Could not retrieve variants from source file in region 11:62380895-62381296. Error was invalid region `11:62380896-62381296`
[2016-04-15T06:15Z] 2016-04-14 23:15:33 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:15:33,430 - WARNING - Could not retrieve variants from source file in region 11:51515789-51516226. Error was invalid region `11:51515790-51516226`
[2016-04-15T06:15Z] 2016-04-14 23:15:35 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:15:35,324 - WARNING - Could not retrieve variants from source file in region 11:49974160-49974561. Error was invalid region `11:49974161-49974561`
[2016-04-15T06:15Z] 2016-04-14 23:15:35 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:15:35,682 - WARNING - Could not retrieve variants from source file in region 11:51411249-51412517. Error was invalid region `11:51411250-51412517`
[2016-04-15T06:15Z] 2016-04-14 23:15:36 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:15:36,813 - WARNING - Could not retrieve variants from source file in region 11:57235160-57235561. Error was invalid region `11:57235161-57235561`
[2016-04-15T06:15Z] 2016-04-14 23:15:37 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:15:37,368 - WARNING - Could not retrieve variants from source file in region 11:58317388-58318809. Error was invalid region `11:58317389-58318809`
[2016-04-15T06:15Z] 2016-04-14 23:15:37 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:15:37,446 - WARNING - Could not retrieve variants from source file in region 11:47701317-47701718. Error was invalid region `11:47701318-47701718`
[2016-04-15T06:15Z] 2016-04-14 23:15:38 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:15:38,014 - WARNING - Could not retrieve variants from source file in region 11:59189701-59225411. Error was invalid region `11:59189702-59225411`
[2016-04-15T06:15Z] 2016-04-14 23:15:38 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:15:38,479 - WARNING - Could not retrieve variants from source file in region 11:48285631-48286446. Error was invalid region `11:48285632-48286446`
[2016-04-15T06:15Z] 2016-04-14 23:15:38 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:15:38,497 - WARNING - Could not retrieve variants from source file in region 11:62433962-62458465. Error was invalid region `11:62433963-62458465`
[2016-04-15T06:15Z] 2016-04-14 23:15:38 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:15:38,551 - WARNING - Could not retrieve variants from source file in region 11:51515789-51516226. Error was invalid region `11:51515790-51516226`
[2016-04-15T06:15Z] 2016-04-14 23:15:38 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:15:38,709 - WARNING - Could not retrieve variants from source file in region 11:62380895-62381296. Error was invalid region `11:62380896-62381296`
[2016-04-15T06:15Z] 2016-04-14 23:15:39 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:15:39,792 - WARNING - Could not retrieve variants from source file in region 11:49974160-49974561. Error was invalid region `11:49974161-49974561`
[2016-04-15T06:15Z] 2016-04-14 23:15:43 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:15:43,266 - WARNING - Could not retrieve variants from source file in region 11:47701317-47701718. Error was invalid region `11:47701318-47701718`
[2016-04-15T06:15Z] 2016-04-14 23:15:43 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:15:43,839 - WARNING - Could not retrieve variants from source file in region 11:48285631-48286446. Error was invalid region `11:48285632-48286446`
[2016-04-15T06:15Z] 2016-04-14 23:15:44 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:15:44,693 - WARNING - Could not retrieve variants from source file in region 11:51411249-51412517. Error was invalid region `11:51411250-51412517`
[2016-04-15T06:15Z] 2016-04-14 23:15:44 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:15:44,915 - WARNING - Could not retrieve variants from source file in region 11:59189701-59225411. Error was invalid region `11:59189702-59225411`
[2016-04-15T06:15Z] 2016-04-14 23:15:45 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:15:45,144 - WARNING - Could not retrieve variants from source file in region 11:51515789-51516226. Error was invalid region `11:51515790-51516226`
[2016-04-15T06:15Z] 2016-04-14 23:15:45 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:15:45,342 - WARNING - Could not retrieve variants from source file in region 11:62380895-62381296. Error was invalid region `11:62380896-62381296`
[2016-04-15T06:15Z] 2016-04-14 23:15:47 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:15:47,257 - WARNING - Could not retrieve variants from source file in region 11:57235160-57235561. Error was invalid region `11:57235161-57235561`
[2016-04-15T06:15Z] 2016-04-14 23:15:53 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:15:53,522 - WARNING - Could not retrieve variants from source file in region 11:48238210-48239261. Error was invalid region `11:48238211-48239261`
[2016-04-15T06:15Z] 2016-04-14 23:15:57 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:15:57,107 - WARNING - Could not retrieve variants from source file in region 11:47640218-47640619. Error was invalid region `11:47640219-47640619`
[2016-04-15T06:15Z] 2016-04-14 23:15:58 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:15:58,965 - WARNING - Could not retrieve variants from source file in region 11:62292671-62298258. Error was invalid region `11:62292672-62298258`
[2016-04-15T06:15Z] 2016-04-14 23:15:59 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:15:59,564 - WARNING - Could not retrieve variants from source file in region 11:58034332-58034841. Error was invalid region `11:58034333-58034841`
[2016-04-15T06:16Z] 2016-04-14 23:16:00 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:16:00,885 - WARNING - Could not retrieve variants from source file in region 11:57146805-57158617. Error was invalid region `11:57146806-57158617`
[2016-04-15T06:16Z] 2016-04-14 23:16:01 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:16:01,292 - WARNING - Could not retrieve variants from source file in region 11:58978729-58979130. Error was invalid region `11:58978730-58979130`
[2016-04-15T06:16Z] 2016-04-14 23:16:01 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:16:01,324 - WARNING - Could not retrieve variants from source file in region 11:47609656-47610057. Error was invalid region `11:47609657-47610057`
[2016-04-15T06:16Z] 2016-04-14 23:16:01 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:16:01,622 - WARNING - Could not retrieve variants from source file in region 11:58125409-58126495. Error was invalid region `11:58125410-58126495`
[2016-04-15T06:16Z] 2016-04-14 23:16:01 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:16:01,627 - WARNING - Could not retrieve variants from source file in region 11:47640218-47640619. Error was invalid region `11:47640219-47640619`
[2016-04-15T06:16Z] 2016-04-14 23:16:04 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:16:04,603 - WARNING - Could not retrieve variants from source file in region 11:58169785-58207394. Error was invalid region `11:58169786-58207394`
[2016-04-15T06:16Z] 2016-04-14 23:16:04 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:16:04,728 - WARNING - Could not retrieve variants from source file in region 11:59132587-59132988. Error was invalid region `11:59132588-59132988`
[2016-04-15T06:16Z] 2016-04-14 23:16:04 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:16:04,762 - WARNING - Could not retrieve variants from source file in region 11:47460095-47469629. Error was invalid region `11:47460096-47469629`
[2016-04-15T06:16Z] 2016-04-14 23:16:05 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:16:05,980 - WARNING - Could not retrieve variants from source file in region 11:47609656-47610057. Error was invalid region `11:47609657-47610057`
[2016-04-15T06:16Z] 2016-04-14 23:16:06 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:16:06,231 - WARNING - Could not retrieve variants from source file in region 11:47640218-47640619. Error was invalid region `11:47640219-47640619`
[2016-04-15T06:16Z] 2016-04-14 23:16:09 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:16:09,293 - WARNING - Could not retrieve variants from source file in region 11:59132587-59132988. Error was invalid region `11:59132588-59132988`
[2016-04-15T06:16Z] 2016-04-14 23:16:11 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:16:11,145 - WARNING - Could not retrieve variants from source file in region 11:58919602-58940468. Error was invalid region `11:58919603-58940468`
[2016-04-15T06:16Z] 2016-04-14 23:16:11 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:16:11,198 - WARNING - Could not retrieve variants from source file in region 11:58978729-58979130. Error was invalid region `11:58978730-58979130`
[2016-04-15T06:16Z] 2016-04-14 23:16:11 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:16:11,353 - WARNING - Could not retrieve variants from source file in region 11:47609656-47610057. Error was invalid region `11:47609657-47610057`
[2016-04-15T06:16Z] 2016-04-14 23:16:11 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:16:11,989 - WARNING - Could not retrieve variants from source file in region 11:47330905-47331306. Error was invalid region `11:47330906-47331306`
[2016-04-15T06:16Z] 2016-04-14 23:16:16 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:16:16,547 - WARNING - Could not retrieve variants from source file in region 11:57563780-57571422. Error was invalid region `11:57563781-57571422`
[2016-04-15T06:16Z] 2016-04-14 23:16:17 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:16:17,014 - WARNING - Could not retrieve variants from source file in region 11:47330905-47331306. Error was invalid region `11:47330906-47331306`
[2016-04-15T06:16Z] 2016-04-14 23:16:17 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:16:17,604 - WARNING - Could not retrieve variants from source file in region 11:56309685-56310546. Error was invalid region `11:56309686-56310546`
[2016-04-15T06:16Z] 2016-04-14 23:16:20 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:16:20,754 - WARNING - Could not retrieve variants from source file in region 11:47515686-47516087. Error was invalid region `11:47515687-47516087`
[2016-04-15T06:16Z] 2016-04-14 23:16:21 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:16:21,387 - WARNING - Could not retrieve variants from source file in region 11:47515686-47516087. Error was invalid region `11:47515687-47516087`
[2016-04-15T06:16Z] 2016-04-14 23:16:21 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:16:21,829 - WARNING - Could not retrieve variants from source file in region 11:47238311-47238712. Error was invalid region `11:47238312-47238712`
[2016-04-15T06:16Z] 2016-04-14 23:16:21 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:16:21,898 - WARNING - Could not retrieve variants from source file in region 11:47330905-47331306. Error was invalid region `11:47330906-47331306`
[2016-04-15T06:16Z] 2016-04-14 23:16:22 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:16:22,215 - WARNING - Could not retrieve variants from source file in region 11:56309685-56310546. Error was invalid region `11:56309686-56310546`
[2016-04-15T06:16Z] 2016-04-14 23:16:22 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:16:22,342 - WARNING - Could not retrieve variants from source file in region 11:57798512-57799132. Error was invalid region `11:57798513-57799132`
[2016-04-15T06:16Z] 2016-04-14 23:16:22 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:16:22,535 - WARNING - Could not retrieve variants from source file in region 11:47431517-47431918. Error was invalid region `11:47431518-47431918`
[2016-04-15T06:16Z] 2016-04-14 23:16:25 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:16:25,182 - WARNING - Could not retrieve variants from source file in region 11:47515686-47516087. Error was invalid region `11:47515687-47516087`
[2016-04-15T06:16Z] 2016-04-14 23:16:26 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:16:26,268 - WARNING - Could not retrieve variants from source file in region 11:47238311-47238712. Error was invalid region `11:47238312-47238712`
[2016-04-15T06:16Z] 2016-04-14 23:16:26 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:16:26,291 - WARNING - Could not retrieve variants from source file in region 11:57563780-57571422. Error was invalid region `11:57563781-57571422`
[2016-04-15T06:16Z] 2016-04-14 23:16:26 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:16:26,621 - WARNING - Could not retrieve variants from source file in region 11:57798512-57799132. Error was invalid region `11:57798513-57799132`
[2016-04-15T06:16Z] 2016-04-14 23:16:27 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:16:26,991 - WARNING - Could not retrieve variants from source file in region 11:47431517-47431918. Error was invalid region `11:47431518-47431918`
[2016-04-15T06:16Z] 2016-04-14 23:16:31 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:16:31,236 - WARNING - Could not retrieve variants from source file in region 11:47431517-47431918. Error was invalid region `11:47431518-47431918`
[2016-04-15T06:16Z] 2016-04-14 23:16:31 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:16:31,250 - WARNING - Could not retrieve variants from source file in region 11:47238311-47238712. Error was invalid region `11:47238312-47238712`
[2016-04-15T06:16Z] 2016-04-14 23:16:31 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:16:31,274 - WARNING - Could not retrieve variants from source file in region 11:47357268-47357669. Error was invalid region `11:47357269-47357669`
[2016-04-15T06:16Z] 2016-04-14 23:16:35 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:16:35,560 - WARNING - Could not retrieve variants from source file in region 11:47298149-47303465. Error was invalid region `11:47298150-47303465`
[2016-04-15T06:16Z] 2016-04-14 23:16:36 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:16:36,191 - WARNING - Could not retrieve variants from source file in region 11:57463289-57472112. Error was invalid region `11:57463290-57472112`
[2016-04-15T06:16Z] 2016-04-14 23:16:37 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:16:37,617 - WARNING - Could not retrieve variants from source file in region 11:57520638-57529619. Error was invalid region `11:57520639-57529619`
[2016-04-15T06:16Z] 2016-04-14 23:16:38 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:16:38,910 - WARNING - Could not retrieve variants from source file in region 11:47357268-47357669. Error was invalid region `11:47357269-47357669`
[2016-04-15T06:16Z] 2016-04-14 23:16:38 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:16:38,922 - WARNING - Could not retrieve variants from source file in region 11:47182715-47188601. Error was invalid region `11:47182716-47188601`
[2016-04-15T06:16Z] 2016-04-14 23:16:39 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:16:39,305 - WARNING - Could not retrieve variants from source file in region 11:47298149-47303465. Error was invalid region `11:47298150-47303465`
[2016-04-15T06:16Z] 2016-04-14 23:16:39 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:16:39,851 - WARNING - Could not retrieve variants from source file in region 11:57463289-57472112. Error was invalid region `11:57463290-57472112`
[2016-04-15T06:16Z] 2016-04-14 23:16:41 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:16:41,240 - WARNING - Could not retrieve variants from source file in region 11:57520638-57529619. Error was invalid region `11:57520639-57529619`
[2016-04-15T06:16Z] 2016-04-14 23:16:43 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:16:43,136 - WARNING - Could not retrieve variants from source file in region 11:57463289-57472112. Error was invalid region `11:57463290-57472112`
[2016-04-15T06:16Z] 2016-04-14 23:16:43 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:16:43,405 - WARNING - Could not retrieve variants from source file in region 11:57004133-57004534. Error was invalid region `11:57004134-57004534`
[2016-04-15T06:16Z] 2016-04-14 23:16:48 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:16:48,890 - WARNING - Could not retrieve variants from source file in region 11:56510412-56510884. Error was invalid region `11:56510413-56510884`
[2016-04-15T06:16Z] 2016-04-14 23:16:49 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:16:49,662 - WARNING - Could not retrieve variants from source file in region 11:56431005-56431406. Error was invalid region `11:56431006-56431406`
[2016-04-15T06:16Z] 2016-04-14 23:16:49 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:16:49,875 - WARNING - Could not retrieve variants from source file in region 11:56379923-56380740. Error was invalid region `11:56379924-56380740`
[2016-04-15T06:16Z] 2016-04-14 23:16:50 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:16:50,116 - WARNING - Could not retrieve variants from source file in region 11:57428345-57428746. Error was invalid region `11:57428346-57428746`
[2016-04-15T06:16Z] 2016-04-14 23:16:51 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:16:51,023 - WARNING - Could not retrieve variants from source file in region 11:57004133-57004534. Error was invalid region `11:57004134-57004534`
[2016-04-15T06:16Z] 2016-04-14 23:16:52 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:16:52,825 - WARNING - Could not retrieve variants from source file in region 11:55999526-56058664. Error was invalid region `11:55999527-56058664`
[2016-04-15T06:16Z] 2016-04-14 23:16:53 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:16:53,336 - WARNING - Could not retrieve variants from source file in region 11:56431005-56431406. Error was invalid region `11:56431006-56431406`
[2016-04-15T06:16Z] 2016-04-14 23:16:56 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:16:56,042 - WARNING - Could not retrieve variants from source file in region 11:56510412-56510884. Error was invalid region `11:56510413-56510884`
[2016-04-15T06:16Z] 2016-04-14 23:16:56 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:16:56,255 - WARNING - Could not retrieve variants from source file in region 11:55999526-56058664. Error was invalid region `11:55999527-56058664`
[2016-04-15T06:16Z] 2016-04-14 23:16:56 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:16:56,802 - WARNING - Could not retrieve variants from source file in region 11:56431005-56431406. Error was invalid region `11:56431006-56431406`
[2016-04-15T06:17Z] 2016-04-14 23:17:01 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:17:01,899 - WARNING - Could not retrieve variants from source file in region 11:56949480-56955036. Error was invalid region `11:56949481-56955036`
[2016-04-15T06:17Z] 2016-04-14 23:17:04 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:17:04,169 - WARNING - Could not retrieve variants from source file in region 11:56756188-56756854. Error was invalid region `11:56756189-56756854`
[2016-04-15T06:17Z] 2016-04-14 23:17:04 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:17:04,520 - WARNING - Could not retrieve variants from source file in region 11:56085936-56086337. Error was invalid region `11:56085937-56086337`
[2016-04-15T06:17Z] 2016-04-14 23:17:04 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:17:04,931 - WARNING - Could not retrieve variants from source file in region 11:56085936-56086337. Error was invalid region `11:56085937-56086337`
[2016-04-15T06:17Z] 2016-04-14 23:17:05 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:17:05,382 - WARNING - Could not retrieve variants from source file in region 11:55797941-55799013. Error was invalid region `11:55797942-55799013`
[2016-04-15T06:17Z] 2016-04-14 23:17:05 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:17:05,649 - WARNING - Could not retrieve variants from source file in region 11:56756188-56756854. Error was invalid region `11:56756189-56756854`
[2016-04-15T06:17Z] 2016-04-14 23:17:05 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:17:05,711 - WARNING - Could not retrieve variants from source file in region 11:56085936-56086337. Error was invalid region `11:56085937-56086337`
[2016-04-15T06:17Z] 2016-04-14 23:17:05 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:17:05,722 - WARNING - Could not retrieve variants from source file in region 11:55797941-55799013. Error was invalid region `11:55797942-55799013`
[2016-04-15T06:17Z] 2016-04-14 23:17:06 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:17:06,007 - WARNING - Could not retrieve variants from source file in region 11:56949480-56955036. Error was invalid region `11:56949481-56955036`
[2016-04-15T06:17Z] 2016-04-14 23:17:07 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:17:07,968 - WARNING - Could not retrieve variants from source file in region 11:56756188-56756854. Error was invalid region `11:56756189-56756854`
[2016-04-15T06:17Z] 2016-04-14 23:17:09 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:17:09,792 - WARNING - Could not retrieve variants from source file in region 11:56949480-56955036. Error was invalid region `11:56949481-56955036`
[2016-04-15T06:17Z] 2016-04-14 23:17:13 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:17:13,324 - WARNING - Could not retrieve variants from source file in region 11:55432829-55433230. Error was invalid region `11:55432830-55433230`
[2016-04-15T06:17Z] 2016-04-14 23:17:13 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:17:13,379 - WARNING - Could not retrieve variants from source file in region 11:55432829-55433230. Error was invalid region `11:55432830-55433230`
[2016-04-15T06:17Z] 2016-04-14 23:17:13 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:17:13,401 - WARNING - Could not retrieve variants from source file in region 11:55432829-55433230. Error was invalid region `11:55432830-55433230`
[2016-04-15T06:17Z] ['bcbio-variation-recall', 'square', '-Xms750m', '-Xmx7280m', '-XX:+UseSerialGC', '-c', 16, '-r', u'11:62744266-78270665', '--caller', 'platypus', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/11/Batch1-11_62744265_78270665.vcf.gz', '/mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/11/Batch1-11_62744265_78270665.vcf-inputs.txt'] in region: 11:62744266-78270665
[2016-04-15T06:17Z] 2016-04-14 23:17:31 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:17:31,197 - WARNING - Could not retrieve variants from source file in region 11:76912425-76919668. Error was invalid region `11:76912426-76919668`
[2016-04-15T06:17Z] 2016-04-14 23:17:31 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:17:31,334 - WARNING - Could not retrieve variants from source file in region 11:69462699-69463100. Error was invalid region `11:69462700-69463100`
[2016-04-15T06:17Z] 2016-04-14 23:17:32 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:17:32,044 - WARNING - Could not retrieve variants from source file in region 11:74303630-74304031. Error was invalid region `11:74303631-74304031`
[2016-04-15T06:17Z] 2016-04-14 23:17:32 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:17:32,119 - WARNING - Could not retrieve variants from source file in region 11:76507481-76507882. Error was invalid region `11:76507482-76507882`
[2016-04-15T06:17Z] 2016-04-14 23:17:32 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:17:32,527 - WARNING - Could not retrieve variants from source file in region 11:66512079-66512480. Error was invalid region `11:66512080-66512480`
[2016-04-15T06:17Z] 2016-04-14 23:17:32 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:17:32,591 - WARNING - Could not retrieve variants from source file in region 11:71146366-71187957. Error was invalid region `11:71146367-71187957`
[2016-04-15T06:17Z] 2016-04-14 23:17:35 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:17:35,520 - WARNING - Could not retrieve variants from source file in region 11:76954577-76955023. Error was invalid region `11:76954578-76955023`
[2016-04-15T06:17Z] 2016-04-14 23:17:38 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:17:38,725 - WARNING - Could not retrieve variants from source file in region 11:68381007-68382260. Error was invalid region `11:68381008-68382260`
[2016-04-15T06:17Z] 2016-04-14 23:17:39 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:17:39,975 - WARNING - Could not retrieve variants from source file in region 11:67257612-67288784. Error was invalid region `11:67257613-67288784`
[2016-04-15T06:17Z] 2016-04-14 23:17:40 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:17:40,265 - WARNING - Could not retrieve variants from source file in region 11:74546694-74563267. Error was invalid region `11:74546695-74563267`
[2016-04-15T06:17Z] 2016-04-14 23:17:40 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:17:40,745 - WARNING - Could not retrieve variants from source file in region 11:73875105-73875506. Error was invalid region `11:73875106-73875506`
[2016-04-15T06:17Z] 2016-04-14 23:17:40 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:17:40,864 - WARNING - Could not retrieve variants from source file in region 11:74303630-74304031. Error was invalid region `11:74303631-74304031`
[2016-04-15T06:17Z] 2016-04-14 23:17:40 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:17:40,904 - WARNING - Could not retrieve variants from source file in region 11:65712996-65735364. Error was invalid region `11:65712997-65735364`
[2016-04-15T06:17Z] 2016-04-14 23:17:41 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:17:41,324 - WARNING - Could not retrieve variants from source file in region 11:76798793-76814300. Error was invalid region `11:76798794-76814300`
[2016-04-15T06:17Z] 2016-04-14 23:17:41 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:17:41,393 - WARNING - Could not retrieve variants from source file in region 11:71146366-71187957. Error was invalid region `11:71146367-71187957`
[2016-04-15T06:17Z] 2016-04-14 23:17:41 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:17:41,504 - WARNING - Could not retrieve variants from source file in region 11:66512079-66512480. Error was invalid region `11:66512080-66512480`
[2016-04-15T06:17Z] 2016-04-14 23:17:43 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:17:43,744 - WARNING - Could not retrieve variants from source file in region 11:68381007-68382260. Error was invalid region `11:68381008-68382260`
[2016-04-15T06:17Z] 2016-04-14 23:17:44 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:17:44,852 - WARNING - Could not retrieve variants from source file in region 11:69462699-69463100. Error was invalid region `11:69462700-69463100`
[2016-04-15T06:17Z] 2016-04-14 23:17:45 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:17:45,341 - WARNING - Could not retrieve variants from source file in region 11:67257612-67288784. Error was invalid region `11:67257613-67288784`
[2016-04-15T06:17Z] 2016-04-14 23:17:47 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:17:47,371 - WARNING - Could not retrieve variants from source file in region 11:73875105-73875506. Error was invalid region `11:73875106-73875506`
[2016-04-15T06:17Z] 2016-04-14 23:17:47 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:17:47,415 - WARNING - Could not retrieve variants from source file in region 11:74546694-74563267. Error was invalid region `11:74546695-74563267`
[2016-04-15T06:17Z] 2016-04-14 23:17:47 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:17:47,687 - WARNING - Could not retrieve variants from source file in region 11:74303630-74304031. Error was invalid region `11:74303631-74304031`
[2016-04-15T06:17Z] 2016-04-14 23:17:47 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:17:47,835 - WARNING - Could not retrieve variants from source file in region 11:66512079-66512480. Error was invalid region `11:66512080-66512480`
[2016-04-15T06:17Z] 2016-04-14 23:17:47 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:17:47,966 - WARNING - Could not retrieve variants from source file in region 11:76798793-76814300. Error was invalid region `11:76798794-76814300`
[2016-04-15T06:17Z] 2016-04-14 23:17:47 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:17:47,997 - WARNING - Could not retrieve variants from source file in region 11:65712996-65735364. Error was invalid region `11:65712997-65735364`
[2016-04-15T06:17Z] 2016-04-14 23:17:48 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:17:48,016 - WARNING - Could not retrieve variants from source file in region 11:71146366-71187957. Error was invalid region `11:71146367-71187957`
[2016-04-15T06:17Z] 2016-04-14 23:17:58 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:17:58,834 - WARNING - Could not retrieve variants from source file in region 11:77825109-77825510. Error was invalid region `11:77825110-77825510`
[2016-04-15T06:17Z] 2016-04-14 23:17:59 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:17:59,406 - WARNING - Could not retrieve variants from source file in region 11:70007100-70007582. Error was invalid region `11:70007101-70007582`
[2016-04-15T06:18Z] 2016-04-14 23:18:00 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:18:00,080 - WARNING - Could not retrieve variants from source file in region 11:76853572-76868562. Error was invalid region `11:76853573-76868562`
[2016-04-15T06:18Z] 2016-04-14 23:18:00 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:18:00,839 - WARNING - Could not retrieve variants from source file in region 11:72532358-72540822. Error was invalid region `11:72532359-72540822`
[2016-04-15T06:18Z] 2016-04-14 23:18:01 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:18:01,196 - WARNING - Could not retrieve variants from source file in region 11:68170802-68192880. Error was invalid region `11:68170803-68192880`
[2016-04-15T06:18Z] 2016-04-14 23:18:04 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:18:04,029 - WARNING - Could not retrieve variants from source file in region 11:77825109-77825510. Error was invalid region `11:77825110-77825510`
[2016-04-15T06:18Z] 2016-04-14 23:18:04 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:18:04,174 - WARNING - Could not retrieve variants from source file in region 11:70007100-70007582. Error was invalid region `11:70007101-70007582`
[2016-04-15T06:18Z] 2016-04-14 23:18:05 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:18:05,173 - WARNING - Could not retrieve variants from source file in region 11:76370581-76372608. Error was invalid region `11:76370582-76372608`
[2016-04-15T06:18Z] 2016-04-14 23:18:05 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:18:05,712 - WARNING - Could not retrieve variants from source file in region 11:74419146-74419568. Error was invalid region `11:74419147-74419568`
[2016-04-15T06:18Z] 2016-04-14 23:18:06 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:18:06,594 - WARNING - Could not retrieve variants from source file in region 11:74203097-74204917. Error was invalid region `11:74203098-74204917`
[2016-04-15T06:18Z] 2016-04-14 23:18:07 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:18:07,439 - WARNING - Could not retrieve variants from source file in region 11:72532358-72540822. Error was invalid region `11:72532359-72540822`
[2016-04-15T06:18Z] 2016-04-14 23:18:07 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:18:07,500 - WARNING - Could not retrieve variants from source file in region 11:68170802-68192880. Error was invalid region `11:68170803-68192880`
[2016-04-15T06:18Z] 2016-04-14 23:18:07 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:18:07,818 - WARNING - Could not retrieve variants from source file in region 11:66472063-66481823. Error was invalid region `11:66472064-66481823`
[2016-04-15T06:18Z] 2016-04-14 23:18:08 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:18:08,401 - WARNING - Could not retrieve variants from source file in region 11:77825109-77825510. Error was invalid region `11:77825110-77825510`
[2016-04-15T06:18Z] 2016-04-14 23:18:08 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:18:08,994 - WARNING - Could not retrieve variants from source file in region 11:70007100-70007582. Error was invalid region `11:70007101-70007582`
[2016-04-15T06:18Z] 2016-04-14 23:18:10 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:18:10,669 - WARNING - Could not retrieve variants from source file in region 11:74419146-74419568. Error was invalid region `11:74419147-74419568`
[2016-04-15T06:18Z] 2016-04-14 23:18:10 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:18:10,745 - WARNING - Could not retrieve variants from source file in region 11:73768342-73797107. Error was invalid region `11:73768343-73797107`
[2016-04-15T06:18Z] 2016-04-14 23:18:11 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:18:11,618 - WARNING - Could not retrieve variants from source file in region 11:70338330-70338731. Error was invalid region `11:70338331-70338731`
[2016-04-15T06:18Z] 2016-04-14 23:18:13 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:18:13,261 - WARNING - Could not retrieve variants from source file in region 11:68170802-68192880. Error was invalid region `11:68170803-68192880`
[2016-04-15T06:18Z] 2016-04-14 23:18:14 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:18:14,059 - WARNING - Could not retrieve variants from source file in region 11:72532358-72540822. Error was invalid region `11:72532359-72540822`
[2016-04-15T06:18Z] 2016-04-14 23:18:15 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:18:15,472 - WARNING - Could not retrieve variants from source file in region 11:74419146-74419568. Error was invalid region `11:74419147-74419568`
[2016-04-15T06:18Z] 2016-04-14 23:18:15 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:18:15,679 - WARNING - Could not retrieve variants from source file in region 11:73768342-73797107. Error was invalid region `11:73768343-73797107`
[2016-04-15T06:18Z] 2016-04-14 23:18:19 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:18:19,876 - WARNING - Could not retrieve variants from source file in region 11:76751330-76751794. Error was invalid region `11:76751331-76751794`
[2016-04-15T06:18Z] 2016-04-14 23:18:20 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:18:20,132 - WARNING - Could not retrieve variants from source file in region 11:66472063-66481823. Error was invalid region `11:66472064-66481823`
[2016-04-15T06:18Z] 2016-04-14 23:18:21 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:18:21,366 - WARNING - Could not retrieve variants from source file in region 11:65599445-65685415. Error was invalid region `11:65599446-65685415`
[2016-04-15T06:18Z] 2016-04-14 23:18:25 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:18:25,134 - WARNING - Could not retrieve variants from source file in region 11:77790442-77790845. Error was invalid region `11:77790443-77790845`
[2016-04-15T06:18Z] 2016-04-14 23:18:25 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:18:25,310 - WARNING - Could not retrieve variants from source file in region 11:69933874-69934275. Error was invalid region `11:69933875-69934275`
[2016-04-15T06:18Z] 2016-04-14 23:18:29 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:18:29,016 - WARNING - Could not retrieve variants from source file in region 11:76701395-76701796. Error was invalid region `11:76701396-76701796`
[2016-04-15T06:18Z] 2016-04-14 23:18:29 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:18:29,038 - WARNING - Could not retrieve variants from source file in region 11:67020855-67034456. Error was invalid region `11:67020856-67034456`
[2016-04-15T06:18Z] 2016-04-14 23:18:31 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:18:31,965 - WARNING - Could not retrieve variants from source file in region 11:77790442-77790845. Error was invalid region `11:77790443-77790845`
[2016-04-15T06:18Z] 2016-04-14 23:18:32 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:18:32,923 - WARNING - Could not retrieve variants from source file in region 11:76257004-76257405. Error was invalid region `11:76257005-76257405`
[2016-04-15T06:18Z] 2016-04-14 23:18:34 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:18:34,748 - WARNING - Could not retrieve variants from source file in region 11:76701395-76701796. Error was invalid region `11:76701396-76701796`
[2016-04-15T06:18Z] 2016-04-14 23:18:36 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:18:36,321 - WARNING - Could not retrieve variants from source file in region 11:76637440-76637870. Error was invalid region `11:76637441-76637870`
[2016-04-15T06:18Z] 2016-04-14 23:18:37 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:18:37,938 - WARNING - Could not retrieve variants from source file in region 11:67068648-67075339. Error was invalid region `11:67068649-67075339`
[2016-04-15T06:18Z] 2016-04-14 23:18:38 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:18:38,546 - WARNING - Could not retrieve variants from source file in region 11:77790442-77790845. Error was invalid region `11:77790443-77790845`
[2016-04-15T06:18Z] 2016-04-14 23:18:38 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:18:38,656 - WARNING - Could not retrieve variants from source file in region 11:69933874-69934275. Error was invalid region `11:69933875-69934275`
[2016-04-15T06:18Z] 2016-04-14 23:18:38 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:18:38,752 - WARNING - Could not retrieve variants from source file in region 11:74329404-74353561. Error was invalid region `11:74329405-74353561`
[2016-04-15T06:18Z] 2016-04-14 23:18:39 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:18:39,081 - WARNING - Could not retrieve variants from source file in region 11:74168200-74168601. Error was invalid region `11:74168201-74168601`
[2016-04-15T06:18Z] 2016-04-14 23:18:39 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:18:39,445 - WARNING - Could not retrieve variants from source file in region 11:70253264-70279956. Error was invalid region `11:70253265-70279956`
[2016-04-15T06:18Z] 2016-04-14 23:18:39 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:18:39,539 - WARNING - Could not retrieve variants from source file in region 11:76257004-76257405. Error was invalid region `11:76257005-76257405`
[2016-04-15T06:18Z] 2016-04-14 23:18:41 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:18:41,367 - WARNING - Could not retrieve variants from source file in region 11:67020855-67034456. Error was invalid region `11:67020856-67034456`
[2016-04-15T06:18Z] 2016-04-14 23:18:41 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:18:41,574 - WARNING - Could not retrieve variants from source file in region 11:76701395-76701796. Error was invalid region `11:76701396-76701796`
[2016-04-15T06:18Z] 2016-04-14 23:18:41 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:18:41,936 - WARNING - Could not retrieve variants from source file in region 11:76637440-76637870. Error was invalid region `11:76637441-76637870`
[2016-04-15T06:18Z] 2016-04-14 23:18:43 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:18:43,819 - WARNING - Could not retrieve variants from source file in region 11:65546646-65547523. Error was invalid region `11:65546647-65547523`
[2016-04-15T06:18Z] 2016-04-14 23:18:44 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:18:44,529 - WARNING - Could not retrieve variants from source file in region 11:67068648-67075339. Error was invalid region `11:67068649-67075339`
[2016-04-15T06:18Z] 2016-04-14 23:18:45 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:18:45,753 - WARNING - Could not retrieve variants from source file in region 11:74168200-74168601. Error was invalid region `11:74168201-74168601`
[2016-04-15T06:18Z] 2016-04-14 23:18:46 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:18:46,618 - WARNING - Could not retrieve variants from source file in region 11:73670434-73717444. Error was invalid region `11:73670435-73717444`
[2016-04-15T06:18Z] 2016-04-14 23:18:46 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:18:46,737 - WARNING - Could not retrieve variants from source file in region 11:76257004-76257405. Error was invalid region `11:76257005-76257405`
[2016-04-15T06:18Z] 2016-04-14 23:18:47 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:18:47,525 - WARNING - Could not retrieve variants from source file in region 11:76637440-76637870. Error was invalid region `11:76637441-76637870`
[2016-04-15T06:18Z] 2016-04-14 23:18:48 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:18:48,379 - WARNING - Could not retrieve variants from source file in region 11:65546646-65547523. Error was invalid region `11:65546647-65547523`
[2016-04-15T06:18Z] 2016-04-14 23:18:54 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:18:54,632 - WARNING - Could not retrieve variants from source file in region 11:77733998-77734399. Error was invalid region `11:77733999-77734399`
[2016-04-15T06:18Z] 2016-04-14 23:18:55 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:18:55,104 - WARNING - Could not retrieve variants from source file in region 11:69589345-69589746. Error was invalid region `11:69589346-69589746`
[2016-04-15T06:18Z] 2016-04-14 23:18:58 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:18:58,452 - WARNING - Could not retrieve variants from source file in region 11:66995392-66995793. Error was invalid region `11:66995393-66995793`
[2016-04-15T06:18Z] 2016-04-14 23:18:59 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:18:59,207 - WARNING - Could not retrieve variants from source file in region 11:66834041-66838155. Error was invalid region `11:66834042-66838155`
[2016-04-15T06:19Z] 2016-04-14 23:19:00 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:19:00,457 - WARNING - Could not retrieve variants from source file in region 11:77733998-77734399. Error was invalid region `11:77733999-77734399`
[2016-04-15T06:19Z] 2016-04-14 23:19:03 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:19:03,069 - WARNING - Could not retrieve variants from source file in region 11:75277417-75314978. Error was invalid region `11:75277418-75314978`
[2016-04-15T06:19Z] 2016-04-14 23:19:03 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:19:03,433 - WARNING - Could not retrieve variants from source file in region 11:66271931-66272332. Error was invalid region `11:66271932-66272332`
[2016-04-15T06:19Z] 2016-04-14 23:19:03 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:19:03,486 - WARNING - Could not retrieve variants from source file in region 11:73620326-73620727. Error was invalid region `11:73620327-73620727`
[2016-04-15T06:19Z] 2016-04-14 23:19:03 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:19:03,632 - WARNING - Could not retrieve variants from source file in region 11:66610434-66626424. Error was invalid region `11:66610435-66626424`
[2016-04-15T06:19Z] 2016-04-14 23:19:04 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:19:04,014 - WARNING - Could not retrieve variants from source file in region 11:68029804-68030363. Error was invalid region `11:68029805-68030363`
[2016-04-15T06:19Z] 2016-04-14 23:19:04 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:19:04,055 - WARNING - Could not retrieve variants from source file in region 11:66995392-66995793. Error was invalid region `11:66995393-66995793`
[2016-04-15T06:19Z] 2016-04-14 23:19:05 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:19:05,270 - WARNING - Could not retrieve variants from source file in region 11:77733998-77734399. Error was invalid region `11:77733999-77734399`
[2016-04-15T06:19Z] 2016-04-14 23:19:05 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:19:05,617 - WARNING - Could not retrieve variants from source file in region 11:69589345-69589746. Error was invalid region `11:69589346-69589746`
[2016-04-15T06:19Z] 2016-04-14 23:19:05 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:19:05,952 - WARNING - Could not retrieve variants from source file in region 11:74047532-74053737. Error was invalid region `11:74047533-74053737`
[2016-04-15T06:19Z] 2016-04-14 23:19:08 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:19:08,479 - WARNING - Could not retrieve variants from source file in region 11:75277417-75314978. Error was invalid region `11:75277418-75314978`
[2016-04-15T06:19Z] 2016-04-14 23:19:09 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:19:09,562 - WARNING - Could not retrieve variants from source file in region 11:66995392-66995793. Error was invalid region `11:66995393-66995793`
[2016-04-15T06:19Z] 2016-04-14 23:19:10 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:19:10,322 - WARNING - Could not retrieve variants from source file in region 11:70185114-70200719. Error was invalid region `11:70185115-70200719`
[2016-04-15T06:19Z] 2016-04-14 23:19:10 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:19:10,356 - WARNING - Could not retrieve variants from source file in region 11:75905447-75921817. Error was invalid region `11:75905448-75921817`
[2016-04-15T06:19Z] 2016-04-14 23:19:10 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:19:10,493 - WARNING - Could not retrieve variants from source file in region 11:66834041-66838155. Error was invalid region `11:66834042-66838155`
[2016-04-15T06:19Z] 2016-04-14 23:19:17 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:19:17,332 - WARNING - Could not retrieve variants from source file in region 11:73620326-73620727. Error was invalid region `11:73620327-73620727`
[2016-04-15T06:19Z] 2016-04-14 23:19:18 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:19:18,287 - WARNING - Could not retrieve variants from source file in region 11:75905447-75921817. Error was invalid region `11:75905448-75921817`
[2016-04-15T06:19Z] 2016-04-14 23:19:18 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:19:18,385 - WARNING - Could not retrieve variants from source file in region 11:70185114-70200719. Error was invalid region `11:70185115-70200719`
[2016-04-15T06:19Z] 2016-04-14 23:19:20 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:19:20,683 - WARNING - Could not retrieve variants from source file in region 11:74870673-74871074. Error was invalid region `11:74870674-74871074`
[2016-04-15T06:19Z] 2016-04-14 23:19:25 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:19:25,225 - WARNING - Could not retrieve variants from source file in region 11:77635671-77639701. Error was invalid region `11:77635672-77639701`
[2016-04-15T06:19Z] 2016-04-14 23:19:25 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:19:25,871 - WARNING - Could not retrieve variants from source file in region 11:67957307-67957708. Error was invalid region `11:67957308-67957708`
[2016-04-15T06:19Z] 2016-04-14 23:19:26 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:19:26,944 - WARNING - Could not retrieve variants from source file in region 11:71939627-71940028. Error was invalid region `11:71939628-71940028`
[2016-04-15T06:19Z] 2016-04-14 23:19:28 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:19:28,373 - WARNING - Could not retrieve variants from source file in region 11:75133554-75160765. Error was invalid region `11:75133555-75160765`
[2016-04-15T06:19Z] 2016-04-14 23:19:30 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:19:30,146 - WARNING - Could not retrieve variants from source file in region 11:66205958-66206359. Error was invalid region `11:66205959-66206359`
[2016-04-15T06:19Z] 2016-04-14 23:19:31 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:19:31,217 - WARNING - Could not retrieve variants from source file in region 11:77635671-77639701. Error was invalid region `11:77635672-77639701`
[2016-04-15T06:19Z] 2016-04-14 23:19:31 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:19:31,304 - WARNING - Could not retrieve variants from source file in region 11:77553427-77553828. Error was invalid region `11:77553428-77553828`
[2016-04-15T06:19Z] 2016-04-14 23:19:31 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:19:31,331 - WARNING - Could not retrieve variants from source file in region 11:74870673-74871074. Error was invalid region `11:74870674-74871074`
[2016-04-15T06:19Z] 2016-04-14 23:19:31 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:19:31,806 - WARNING - Could not retrieve variants from source file in region 11:67957307-67957708. Error was invalid region `11:67957308-67957708`
[2016-04-15T06:19Z] 2016-04-14 23:19:33 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:19:33,269 - WARNING - Could not retrieve variants from source file in region 11:73358452-73359287. Error was invalid region `11:73358453-73359287`
[2016-04-15T06:19Z] 2016-04-14 23:19:34 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:19:34,440 - WARNING - Could not retrieve variants from source file in region 11:68549129-68549530. Error was invalid region `11:68549130-68549530`
[2016-04-15T06:19Z] 2016-04-14 23:19:34 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:19:34,876 - WARNING - Could not retrieve variants from source file in region 11:75526270-75526672. Error was invalid region `11:75526271-75526672`
[2016-04-15T06:19Z] 2016-04-14 23:19:36 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:19:36,277 - WARNING - Could not retrieve variants from source file in region 11:73103624-73120843. Error was invalid region `11:73103625-73120843`
[2016-04-15T06:19Z] 2016-04-14 23:19:36 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:19:36,748 - WARNING - Could not retrieve variants from source file in region 11:77553427-77553828. Error was invalid region `11:77553428-77553828`
[2016-04-15T06:19Z] 2016-04-14 23:19:37 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:19:37,302 - WARNING - Could not retrieve variants from source file in region 11:67957307-67957708. Error was invalid region `11:67957308-67957708`
[2016-04-15T06:19Z] 2016-04-14 23:19:39 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:19:39,543 - WARNING - Could not retrieve variants from source file in region 11:73358452-73359287. Error was invalid region `11:73358453-73359287`
[2016-04-15T06:19Z] 2016-04-14 23:19:40 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:19:40,918 - WARNING - Could not retrieve variants from source file in region 11:65293608-65294009. Error was invalid region `11:65293609-65294009`
[2016-04-15T06:19Z] 2016-04-14 23:19:40 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:19:40,942 - WARNING - Could not retrieve variants from source file in region 11:68549129-68549530. Error was invalid region `11:68549130-68549530`
[2016-04-15T06:19Z] 2016-04-14 23:19:41 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:19:41,797 - WARNING - Could not retrieve variants from source file in region 11:77553427-77553828. Error was invalid region `11:77553428-77553828`
[2016-04-15T06:19Z] 2016-04-14 23:19:45 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:19:45,883 - WARNING - Could not retrieve variants from source file in region 11:73358452-73359287. Error was invalid region `11:73358453-73359287`
[2016-04-15T06:19Z] 2016-04-14 23:19:46 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:19:46,702 - WARNING - Could not retrieve variants from source file in region 11:74705485-74705886. Error was invalid region `11:74705486-74705886`
[2016-04-15T06:19Z] 2016-04-14 23:19:48 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:19:48,358 - WARNING - Could not retrieve variants from source file in region 11:65293608-65294009. Error was invalid region `11:65293609-65294009`
[2016-04-15T06:19Z] 2016-04-14 23:19:49 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:19:49,157 - WARNING - Could not retrieve variants from source file in region 11:77412640-77413041. Error was invalid region `11:77412641-77413041`
[2016-04-15T06:19Z] 2016-04-14 23:19:49 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:19:49,957 - WARNING - Could not retrieve variants from source file in region 11:75526270-75526672. Error was invalid region `11:75526271-75526672`
[2016-04-15T06:19Z] 2016-04-14 23:19:50 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:19:50,697 - WARNING - Could not retrieve variants from source file in region 11:68549129-68549530. Error was invalid region `11:68549130-68549530`
[2016-04-15T06:19Z] 2016-04-14 23:19:51 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:19:51,605 - WARNING - Could not retrieve variants from source file in region 11:74705485-74705886. Error was invalid region `11:74705486-74705886`
[2016-04-15T06:19Z] 2016-04-14 23:19:53 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:19:53,276 - WARNING - Could not retrieve variants from source file in region 11:67414281-67434059. Error was invalid region `11:67414282-67434059`
[2016-04-15T06:19Z] 2016-04-14 23:19:55 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:19:55,663 - WARNING - Could not retrieve variants from source file in region 11:77412640-77413041. Error was invalid region `11:77412641-77413041`
[2016-04-15T06:19Z] 2016-04-14 23:19:56 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:19:56,222 - WARNING - Could not retrieve variants from source file in region 11:71498380-71548734. Error was invalid region `11:71498381-71548734`
[2016-04-15T06:19Z] 2016-04-14 23:19:56 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:19:56,360 - WARNING - Could not retrieve variants from source file in region 11:77412640-77413041. Error was invalid region `11:77412641-77413041`
[2016-04-15T06:19Z] 2016-04-14 23:19:57 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:19:57,615 - WARNING - Could not retrieve variants from source file in region 11:74705485-74705886. Error was invalid region `11:74705486-74705886`
[2016-04-15T06:19Z] 2016-04-14 23:19:58 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:19:58,510 - WARNING - Could not retrieve variants from source file in region 11:67414281-67434059. Error was invalid region `11:67414282-67434059`
[2016-04-15T06:19Z] 2016-04-14 23:19:58 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:19:58,693 - WARNING - Could not retrieve variants from source file in region 11:66135058-66135459. Error was invalid region `11:66135059-66135459`
[2016-04-15T06:20Z] 2016-04-14 23:20:01 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:20:01,242 - WARNING - Could not retrieve variants from source file in region 11:72983148-72983549. Error was invalid region `11:72983149-72983549`
[2016-04-15T06:20Z] 2016-04-14 23:20:01 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:20:01,337 - WARNING - Could not retrieve variants from source file in region 11:67414281-67434059. Error was invalid region `11:67414282-67434059`
[2016-04-15T06:20Z] 2016-04-14 23:20:02 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:20:02,264 - WARNING - Could not retrieve variants from source file in region 11:65143864-65161319. Error was invalid region `11:65143865-65161319`
[2016-04-15T06:20Z] 2016-04-14 23:20:03 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:20:03,403 - WARNING - Could not retrieve variants from source file in region 11:74994141-75017856. Error was invalid region `11:74994142-75017856`
[2016-04-15T06:20Z] 2016-04-14 23:20:05 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:20:05,435 - WARNING - Could not retrieve variants from source file in region 11:75428747-75429148. Error was invalid region `11:75428748-75429148`
[2016-04-15T06:20Z] 2016-04-14 23:20:06 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:20:06,058 - WARNING - Could not retrieve variants from source file in region 11:75378463-75378864. Error was invalid region `11:75378464-75378864`
[2016-04-15T06:20Z] 2016-04-14 23:20:06 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:20:06,145 - WARNING - Could not retrieve variants from source file in region 11:71249175-71260355. Error was invalid region `11:71249176-71260355`
[2016-04-15T06:20Z] 2016-04-14 23:20:06 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:20:06,539 - WARNING - Could not retrieve variants from source file in region 11:71498380-71548734. Error was invalid region `11:71498381-71548734`
[2016-04-15T06:20Z] 2016-04-14 23:20:06 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:20:06,632 - WARNING - Could not retrieve variants from source file in region 11:65143864-65161319. Error was invalid region `11:65143865-65161319`
[2016-04-15T06:20Z] 2016-04-14 23:20:09 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:20:09,550 - WARNING - Could not retrieve variants from source file in region 11:75428747-75429148. Error was invalid region `11:75428748-75429148`
[2016-04-15T06:20Z] 2016-04-14 23:20:10 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:20:10,009 - WARNING - Could not retrieve variants from source file in region 11:74647825-74648226. Error was invalid region `11:74647826-74648226`
[2016-04-15T06:20Z] 2016-04-14 23:20:10 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:20:10,207 - WARNING - Could not retrieve variants from source file in region 11:74618054-74618455. Error was invalid region `11:74618055-74618455`
[2016-04-15T06:20Z] 2016-04-14 23:20:10 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:20:10,626 - WARNING - Could not retrieve variants from source file in region 11:75378463-75378864. Error was invalid region `11:75378464-75378864`
[2016-04-15T06:20Z] 2016-04-14 23:20:11 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:20:11,196 - WARNING - Could not retrieve variants from source file in region 11:65143864-65161319. Error was invalid region `11:65143865-65161319`
[2016-04-15T06:20Z] 2016-04-14 23:20:13 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:20:13,981 - WARNING - Could not retrieve variants from source file in region 11:75428747-75429148. Error was invalid region `11:75428748-75429148`
[2016-04-15T06:20Z] 2016-04-14 23:20:15 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:20:15,022 - WARNING - Could not retrieve variants from source file in region 11:65787455-65819851. Error was invalid region `11:65787456-65819851`
[2016-04-15T06:20Z] 2016-04-14 23:20:15 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:20:15,254 - WARNING - Could not retrieve variants from source file in region 11:75378463-75378864. Error was invalid region `11:75378464-75378864`
[2016-04-15T06:20Z] 2016-04-14 23:20:17 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:20:17,721 - WARNING - Could not retrieve variants from source file in region 11:74618054-74618455. Error was invalid region `11:74618055-74618455`
[2016-04-15T06:20Z] 2016-04-14 23:20:19 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:20:19,133 - WARNING - Could not retrieve variants from source file in region 11:74904151-74904552. Error was invalid region `11:74904152-74904552`
[2016-04-15T06:20Z] 2016-04-14 23:20:21 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:20:21,316 - WARNING - Could not retrieve variants from source file in region 11:74904151-74904552. Error was invalid region `11:74904152-74904552`
[2016-04-15T06:20Z] 2016-04-14 23:20:21 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:20:21,686 - WARNING - Could not retrieve variants from source file in region 11:74904151-74904552. Error was invalid region `11:74904152-74904552`
[2016-04-15T06:20Z] 2016-04-14 23:20:22 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:20:22,027 - WARNING - Could not retrieve variants from source file in region 11:64788983-64884242. Error was invalid region `11:64788984-64884242`
[2016-04-15T06:20Z] 2016-04-14 23:20:25 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:20:25,584 - WARNING - Could not retrieve variants from source file in region 11:64950759-64990231. Error was invalid region `11:64950760-64990231`
[2016-04-15T06:20Z] 2016-04-14 23:20:25 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:20:25,986 - WARNING - Could not retrieve variants from source file in region 11:64677082-64681009. Error was invalid region `11:64677083-64681009`
[2016-04-15T06:20Z] 2016-04-14 23:20:26 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:20:26,278 - WARNING - Could not retrieve variants from source file in region 11:64788983-64884242. Error was invalid region `11:64788984-64884242`
[2016-04-15T06:20Z] 2016-04-14 23:20:29 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:20:29,215 - WARNING - Could not retrieve variants from source file in region 11:64359075-64367515. Error was invalid region `11:64359076-64367515`
[2016-04-15T06:20Z] 2016-04-14 23:20:30 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:20:30,194 - WARNING - Could not retrieve variants from source file in region 11:64455864-64496547. Error was invalid region `11:64455865-64496547`
[2016-04-15T06:20Z] 2016-04-14 23:20:30 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:20:30,225 - WARNING - Could not retrieve variants from source file in region 11:64677082-64681009. Error was invalid region `11:64677083-64681009`
[2016-04-15T06:20Z] 2016-04-14 23:20:30 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:20:30,431 - WARNING - Could not retrieve variants from source file in region 11:64677082-64681009. Error was invalid region `11:64677083-64681009`
[2016-04-15T06:20Z] 2016-04-14 23:20:30 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:20:30,512 - WARNING - Could not retrieve variants from source file in region 11:64532857-64539825. Error was invalid region `11:64532858-64539825`
[2016-04-15T06:20Z] 2016-04-14 23:20:33 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:20:33,810 - WARNING - Could not retrieve variants from source file in region 11:64359075-64367515. Error was invalid region `11:64359076-64367515`
[2016-04-15T06:20Z] 2016-04-14 23:20:35 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:20:35,329 - WARNING - Could not retrieve variants from source file in region 11:64418689-64419090. Error was invalid region `11:64418690-64419090`
[2016-04-15T06:20Z] 2016-04-14 23:20:35 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:20:35,620 - WARNING - Could not retrieve variants from source file in region 11:63438625-63449315. Error was invalid region `11:63438626-63449315`
[2016-04-15T06:20Z] 2016-04-14 23:20:35 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:20:35,793 - WARNING - Could not retrieve variants from source file in region 11:64455864-64496547. Error was invalid region `11:64455865-64496547`
[2016-04-15T06:20Z] 2016-04-14 23:20:35 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:20:35,796 - WARNING - Could not retrieve variants from source file in region 11:64359075-64367515. Error was invalid region `11:64359076-64367515`
[2016-04-15T06:20Z] 2016-04-14 23:20:39 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:20:39,251 - WARNING - Could not retrieve variants from source file in region 11:64418689-64419090. Error was invalid region `11:64418690-64419090`
[2016-04-15T06:20Z] 2016-04-14 23:20:43 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:20:43,287 - WARNING - Could not retrieve variants from source file in region 11:64418689-64419090. Error was invalid region `11:64418690-64419090`
[2016-04-15T06:20Z] 2016-04-14 23:20:43 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:20:43,318 - WARNING - Could not retrieve variants from source file in region 11:63679158-63713507. Error was invalid region `11:63679159-63713507`
[2016-04-15T06:20Z] 2016-04-14 23:20:44 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:20:44,033 - WARNING - Could not retrieve variants from source file in region 11:63883774-63885894. Error was invalid region `11:63883775-63885894`
[2016-04-15T06:20Z] 2016-04-14 23:20:45 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:20:45,149 - WARNING - Could not retrieve variants from source file in region 11:62984657-62985058. Error was invalid region `11:62984658-62985058`
[2016-04-15T06:20Z] 2016-04-14 23:20:45 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:20:45,342 - WARNING - Could not retrieve variants from source file in region 11:62847242-62947242. Error was invalid region `11:62847243-62947242`
[2016-04-15T06:20Z] 2016-04-14 23:20:45 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:20:45,351 - WARNING - Could not retrieve variants from source file in region 11:63764091-63767376. Error was invalid region `11:63764092-63767376`
[2016-04-15T06:20Z] 2016-04-14 23:20:45 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:20:45,356 - WARNING - Could not retrieve variants from source file in region 11:62947242-62951411. Error was invalid region `11:62947243-62951411`
[2016-04-15T06:20Z] 2016-04-14 23:20:45 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:20:45,432 - WARNING - Could not retrieve variants from source file in region 11:63530964-63531365. Error was invalid region `11:63530965-63531365`
[2016-04-15T06:20Z] 2016-04-14 23:20:47 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:20:47,449 - WARNING - Could not retrieve variants from source file in region 11:63679158-63713507. Error was invalid region `11:63679159-63713507`
[2016-04-15T06:20Z] 2016-04-14 23:20:48 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:20:48,274 - WARNING - Could not retrieve variants from source file in region 11:63149459-63149860. Error was invalid region `11:63149460-63149860`
[2016-04-15T06:20Z] 2016-04-14 23:20:48 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:20:48,314 - WARNING - Could not retrieve variants from source file in region 11:63883774-63885894. Error was invalid region `11:63883775-63885894`
[2016-04-15T06:20Z] 2016-04-14 23:20:48 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:20:48,637 - WARNING - Could not retrieve variants from source file in region 11:63487175-63487576. Error was invalid region `11:63487176-63487576`
[2016-04-15T06:20Z] 2016-04-14 23:20:49 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:20:49,394 - WARNING - Could not retrieve variants from source file in region 11:62984657-62985058. Error was invalid region `11:62984658-62985058`
[2016-04-15T06:20Z] 2016-04-14 23:20:49 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:20:49,694 - WARNING - Could not retrieve variants from source file in region 11:62847242-62947242. Error was invalid region `11:62847243-62947242`
[2016-04-15T06:20Z] 2016-04-14 23:20:49 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:20:49,699 - WARNING - Could not retrieve variants from source file in region 11:62947242-62951411. Error was invalid region `11:62947243-62951411`
[2016-04-15T06:20Z] 2016-04-14 23:20:51 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:20:51,580 - WARNING - Could not retrieve variants from source file in region 11:62984657-62985058. Error was invalid region `11:62984658-62985058`
[2016-04-15T06:20Z] 2016-04-14 23:20:51 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:20:51,592 - WARNING - Could not retrieve variants from source file in region 11:63883774-63885894. Error was invalid region `11:63883775-63885894`
[2016-04-15T06:20Z] 2016-04-14 23:20:51 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:20:51,602 - WARNING - Could not retrieve variants from source file in region 11:63679158-63713507. Error was invalid region `11:63679159-63713507`
[2016-04-15T06:20Z] 2016-04-14 23:20:52 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:20:52,758 - WARNING - Could not retrieve variants from source file in region 11:63585593-63585994. Error was invalid region `11:63585594-63585994`
[2016-04-15T06:20Z] 2016-04-14 23:20:52 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:20:52,865 - WARNING - Could not retrieve variants from source file in region 11:63487175-63487576. Error was invalid region `11:63487176-63487576`
[2016-04-15T06:20Z] 2016-04-14 23:20:54 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:20:54,051 - WARNING - Could not retrieve variants from source file in region 11:62847242-62947242. Error was invalid region `11:62847243-62947242`
[2016-04-15T06:20Z] 2016-04-14 23:20:54 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:20:54,057 - WARNING - Could not retrieve variants from source file in region 11:62947242-62951411. Error was invalid region `11:62947243-62951411`
[2016-04-15T06:20Z] 2016-04-14 23:20:55 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:20:55,673 - WARNING - Could not retrieve variants from source file in region 11:63585593-63585994. Error was invalid region `11:63585594-63585994`
[2016-04-15T06:20Z] 2016-04-14 23:20:56 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:20:56,930 - WARNING - Could not retrieve variants from source file in region 11:63487175-63487576. Error was invalid region `11:63487176-63487576`
[2016-04-15T06:20Z] 2016-04-14 23:20:59 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:20:59,395 - WARNING - Could not retrieve variants from source file in region 11:63398406-63398807. Error was invalid region `11:63398407-63398807`
[2016-04-15T06:20Z] 2016-04-14 23:20:59 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:20:59,863 - WARNING - Could not retrieve variants from source file in region 11:63057714-63072500. Error was invalid region `11:63057715-63072500`
[2016-04-15T06:20Z] 2016-04-14 23:20:59 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:20:59,936 - WARNING - Could not retrieve variants from source file in region 11:63313433-63313834. Error was invalid region `11:63313434-63313834`
[2016-04-15T06:21Z] 2016-04-14 23:21:01 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:21:01,524 - WARNING - Could not retrieve variants from source file in region 11:63313433-63313834. Error was invalid region `11:63313434-63313834`
[2016-04-15T06:21Z] 2016-04-14 23:21:03 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:21:03,233 - WARNING - Could not retrieve variants from source file in region 11:63258205-63275753. Error was invalid region `11:63258206-63275753`
[2016-04-15T06:21Z] 2016-04-14 23:21:03 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:21:03,383 - WARNING - Could not retrieve variants from source file in region 11:63258205-63275753. Error was invalid region `11:63258206-63275753`
[2016-04-15T06:21Z] 2016-04-14 23:21:03 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:21:03,438 - WARNING - Could not retrieve variants from source file in region 11:63313433-63313834. Error was invalid region `11:63313434-63313834`
[2016-04-15T06:21Z] ['bcbio-variation-recall', 'square', '-Xms750m', '-Xmx7280m', '-XX:+UseSerialGC', '-c', 16, '-r', u'11:78277178-93796886', '--caller', 'platypus', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/11/Batch1-11_78277177_93796886.vcf.gz', '/mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/11/Batch1-11_78277177_93796886.vcf-inputs.txt'] in region: 11:78277178-93796886
[2016-04-15T06:21Z] 2016-04-14 23:21:20 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:21:20,318 - WARNING - Could not retrieve variants from source file in region 11:78443375-78443776. Error was invalid region `11:78443376-78443776`
[2016-04-15T06:21Z] 2016-04-14 23:21:20 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:21:20,648 - WARNING - Could not retrieve variants from source file in region 11:88911485-88911886. Error was invalid region `11:88911486-88911886`
[2016-04-15T06:21Z] 2016-04-14 23:21:21 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:21:21,126 - WARNING - Could not retrieve variants from source file in region 11:88241813-88242214. Error was invalid region `11:88241814-88242214`
[2016-04-15T06:21Z] 2016-04-14 23:21:21 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:21:21,976 - WARNING - Could not retrieve variants from source file in region 11:89531329-89531730. Error was invalid region `11:89531330-89531730`
[2016-04-15T06:21Z] 2016-04-14 23:21:22 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:21:22,040 - WARNING - Could not retrieve variants from source file in region 11:85725726-85726127. Error was invalid region `11:85725727-85726127`
[2016-04-15T06:21Z] 2016-04-14 23:21:22 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:21:22,046 - WARNING - Could not retrieve variants from source file in region 11:85968412-85968813. Error was invalid region `11:85968413-85968813`
[2016-04-15T06:21Z] 2016-04-14 23:21:28 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:21:28,384 - WARNING - Could not retrieve variants from source file in region 11:89901943-89902344. Error was invalid region `11:89901944-89902344`
[2016-04-15T06:21Z] 2016-04-14 23:21:28 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:21:28,458 - WARNING - Could not retrieve variants from source file in region 11:88911485-88911886. Error was invalid region `11:88911486-88911886`
[2016-04-15T06:21Z] 2016-04-14 23:21:28 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:21:28,562 - WARNING - Could not retrieve variants from source file in region 11:82643549-82645094. Error was invalid region `11:82643550-82645094`
[2016-04-15T06:21Z] 2016-04-14 23:21:29 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:21:29,098 - WARNING - Could not retrieve variants from source file in region 11:86153700-86161578. Error was invalid region `11:86153701-86161578`
[2016-04-15T06:21Z] 2016-04-14 23:21:29 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:21:29,125 - WARNING - Could not retrieve variants from source file in region 11:87906664-87908638. Error was invalid region `11:87906665-87908638`
[2016-04-15T06:21Z] 2016-04-14 23:21:29 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:21:29,148 - WARNING - Could not retrieve variants from source file in region 11:85725726-85726127. Error was invalid region `11:85725727-85726127`
[2016-04-15T06:21Z] 2016-04-14 23:21:29 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:21:29,790 - WARNING - Could not retrieve variants from source file in region 11:89531329-89531730. Error was invalid region `11:89531330-89531730`
[2016-04-15T06:21Z] 2016-04-14 23:21:30 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:21:30,087 - WARNING - Could not retrieve variants from source file in region 11:93400585-93425349. Error was invalid region `11:93400586-93425349`
[2016-04-15T06:21Z] 2016-04-14 23:21:30 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:21:30,125 - WARNING - Could not retrieve variants from source file in region 11:85968412-85968813. Error was invalid region `11:85968413-85968813`
[2016-04-15T06:21Z] 2016-04-14 23:21:30 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:21:30,132 - WARNING - Could not retrieve variants from source file in region 11:88241813-88242214. Error was invalid region `11:88241814-88242214`
[2016-04-15T06:21Z] 2016-04-14 23:21:30 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:21:30,159 - WARNING - Could not retrieve variants from source file in region 11:85435519-85456893. Error was invalid region `11:85435520-85456893`
[2016-04-15T06:21Z] 2016-04-14 23:21:35 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:21:35,088 - WARNING - Could not retrieve variants from source file in region 11:89901943-89902344. Error was invalid region `11:89901944-89902344`
[2016-04-15T06:21Z] 2016-04-14 23:21:35 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:21:35,510 - WARNING - Could not retrieve variants from source file in region 11:78443375-78443776. Error was invalid region `11:78443376-78443776`
[2016-04-15T06:21Z] 2016-04-14 23:21:36 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:21:36,819 - WARNING - Could not retrieve variants from source file in region 11:89774025-89774638. Error was invalid region `11:89774026-89774638`
[2016-04-15T06:21Z] 2016-04-14 23:21:38 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:21:38,049 - WARNING - Could not retrieve variants from source file in region 11:88241813-88242214. Error was invalid region `11:88241814-88242214`
[2016-04-15T06:21Z] 2016-04-14 23:21:38 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:21:38,624 - WARNING - Could not retrieve variants from source file in region 11:85435519-85456893. Error was invalid region `11:85435520-85456893`
[2016-04-15T06:21Z] 2016-04-14 23:21:39 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:21:39,227 - WARNING - Could not retrieve variants from source file in region 11:89531329-89531730. Error was invalid region `11:89531330-89531730`
[2016-04-15T06:21Z] 2016-04-14 23:21:39 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:21:39,232 - WARNING - Could not retrieve variants from source file in region 11:85725726-85726127. Error was invalid region `11:85725727-85726127`
[2016-04-15T06:21Z] 2016-04-14 23:21:49 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:21:49,392 - WARNING - Could not retrieve variants from source file in region 11:89133238-89133639. Error was invalid region `11:89133239-89133639`
[2016-04-15T06:21Z] 2016-04-14 23:21:51 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:21:51,491 - WARNING - Could not retrieve variants from source file in region 11:78372325-78372726. Error was invalid region `11:78372326-78372726`
[2016-04-15T06:21Z] 2016-04-14 23:21:52 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:21:52,092 - WARNING - Could not retrieve variants from source file in region 11:82550176-82550577. Error was invalid region `11:82550177-82550577`
[2016-04-15T06:21Z] 2016-04-14 23:21:54 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:21:54,633 - WARNING - Could not retrieve variants from source file in region 11:89133238-89133639. Error was invalid region `11:89133239-89133639`
[2016-04-15T06:21Z] 2016-04-14 23:21:55 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:21:55,147 - WARNING - Could not retrieve variants from source file in region 11:87013227-87032477. Error was invalid region `11:87013228-87032477`
[2016-04-15T06:21Z] 2016-04-14 23:21:55 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:21:55,535 - WARNING - Could not retrieve variants from source file in region 11:85691970-85692371. Error was invalid region `11:85691971-85692371`
[2016-04-15T06:21Z] 2016-04-14 23:21:55 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:21:55,552 - WARNING - Could not retrieve variants from source file in region 11:89868544-89868945. Error was invalid region `11:89868545-89868945`
[2016-04-15T06:21Z] 2016-04-14 23:21:55 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:21:55,653 - WARNING - Could not retrieve variants from source file in region 11:84633965-84634366. Error was invalid region `11:84633966-84634366`
[2016-04-15T06:21Z] 2016-04-14 23:21:56 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:21:56,209 - WARNING - Could not retrieve variants from source file in region 11:78372325-78372726. Error was invalid region `11:78372326-78372726`
[2016-04-15T06:21Z] 2016-04-14 23:21:56 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:21:56,523 - WARNING - Could not retrieve variants from source file in region 11:89443597-89443998. Error was invalid region `11:89443598-89443998`
[2016-04-15T06:21Z] 2016-04-14 23:21:57 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:21:57,227 - WARNING - Could not retrieve variants from source file in region 11:88026998-88045773. Error was invalid region `11:88026999-88045773`
[2016-04-15T06:21Z] 2016-04-14 23:21:58 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:21:58,959 - WARNING - Could not retrieve variants from source file in region 11:86098469-86123657. Error was invalid region `11:86098470-86123657`
[2016-04-15T06:21Z] 2016-04-14 23:21:59 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:21:59,378 - WARNING - Could not retrieve variants from source file in region 11:89133238-89133639. Error was invalid region `11:89133239-89133639`
[2016-04-15T06:22Z] 2016-04-14 23:22:00 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:22:00,350 - WARNING - Could not retrieve variants from source file in region 11:89868544-89868945. Error was invalid region `11:89868545-89868945`
[2016-04-15T06:22Z] 2016-04-14 23:22:00 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:22:00,367 - WARNING - Could not retrieve variants from source file in region 11:85691970-85692371. Error was invalid region `11:85691971-85692371`
[2016-04-15T06:22Z] 2016-04-14 23:22:01 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:22:01,088 - WARNING - Could not retrieve variants from source file in region 11:78372325-78372726. Error was invalid region `11:78372326-78372726`
[2016-04-15T06:22Z] 2016-04-14 23:22:01 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:22:01,713 - WARNING - Could not retrieve variants from source file in region 11:89443597-89443998. Error was invalid region `11:89443598-89443998`
[2016-04-15T06:22Z] 2016-04-14 23:22:02 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:22:02,178 - WARNING - Could not retrieve variants from source file in region 11:88026998-88045773. Error was invalid region `11:88026999-88045773`
[2016-04-15T06:22Z] 2016-04-14 23:22:05 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:22:05,036 - WARNING - Could not retrieve variants from source file in region 11:85691970-85692371. Error was invalid region `11:85691971-85692371`
[2016-04-15T06:22Z] 2016-04-14 23:22:06 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:22:06,349 - WARNING - Could not retrieve variants from source file in region 11:93211950-93214813. Error was invalid region `11:93211951-93214813`
[2016-04-15T06:22Z] 2016-04-14 23:22:11 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:22:11,455 - WARNING - Could not retrieve variants from source file in region 11:93129272-93141770. Error was invalid region `11:93129273-93141770`
[2016-04-15T06:22Z] 2016-04-14 23:22:14 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:22:14,176 - WARNING - Could not retrieve variants from source file in region 11:93129272-93141770. Error was invalid region `11:93129273-93141770`
[2016-04-15T06:22Z] 2016-04-14 23:22:14 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:22:14,196 - WARNING - Could not retrieve variants from source file in region 11:78277066-78279980. Error was invalid region `11:78277067-78279980`
[2016-04-15T06:22Z] 2016-04-14 23:22:14 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:22:14,741 - WARNING - Could not retrieve variants from source file in region 11:92531145-92534632. Error was invalid region `11:92531146-92534632`
[2016-04-15T06:22Z] 2016-04-14 23:22:15 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:22:15,922 - WARNING - Could not retrieve variants from source file in region 11:82443461-82443862. Error was invalid region `11:82443462-82443862`
[2016-04-15T06:22Z] 2016-04-14 23:22:16 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:22:16,187 - WARNING - Could not retrieve variants from source file in region 11:86511253-86511654. Error was invalid region `11:86511254-86511654`
[2016-04-15T06:22Z] 2016-04-14 23:22:16 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:22:16,209 - WARNING - Could not retrieve variants from source file in region 11:93129272-93141770. Error was invalid region `11:93129273-93141770`
[2016-04-15T06:22Z] 2016-04-14 23:22:17 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:22:17,967 - WARNING - Could not retrieve variants from source file in region 11:82924147-82924548. Error was invalid region `11:82924148-82924548`
[2016-04-15T06:22Z] 2016-04-14 23:22:18 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:22:18,560 - WARNING - Could not retrieve variants from source file in region 11:78277066-78279980. Error was invalid region `11:78277067-78279980`
[2016-04-15T06:22Z] 2016-04-14 23:22:19 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:22:19,369 - WARNING - Could not retrieve variants from source file in region 11:86665453-86665854. Error was invalid region `11:86665454-86665854`
[2016-04-15T06:22Z] 2016-04-14 23:22:19 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:22:19,468 - WARNING - Could not retrieve variants from source file in region 11:92531145-92534632. Error was invalid region `11:92531146-92534632`
[2016-04-15T06:22Z] 2016-04-14 23:22:19 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:22:19,794 - WARNING - Could not retrieve variants from source file in region 11:92087966-92088367. Error was invalid region `11:92087967-92088367`
[2016-04-15T06:22Z] 2016-04-14 23:22:20 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:22:20,299 - WARNING - Could not retrieve variants from source file in region 11:89935375-89935776. Error was invalid region `11:89935376-89935776`
[2016-04-15T06:22Z] 2016-04-14 23:22:22 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:22:22,052 - WARNING - Could not retrieve variants from source file in region 11:82924147-82924548. Error was invalid region `11:82924148-82924548`
[2016-04-15T06:22Z] 2016-04-14 23:22:22 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:22:22,061 - WARNING - Could not retrieve variants from source file in region 11:86267422-86267904. Error was invalid region `11:86267423-86267904`
[2016-04-15T06:22Z] 2016-04-14 23:22:22 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:22:22,680 - WARNING - Could not retrieve variants from source file in region 11:78277066-78279980. Error was invalid region `11:78277067-78279980`
[2016-04-15T06:22Z] 2016-04-14 23:22:23 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:22:23,598 - WARNING - Could not retrieve variants from source file in region 11:86665453-86665854. Error was invalid region `11:86665454-86665854`
[2016-04-15T06:22Z] 2016-04-14 23:22:23 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:22:23,607 - WARNING - Could not retrieve variants from source file in region 11:92531145-92534632. Error was invalid region `11:92531146-92534632`
[2016-04-15T06:22Z] 2016-04-14 23:22:23 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:22:23,976 - WARNING - Could not retrieve variants from source file in region 11:82443461-82443862. Error was invalid region `11:82443462-82443862`
[2016-04-15T06:22Z] 2016-04-14 23:22:23 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:22:23,977 - WARNING - Could not retrieve variants from source file in region 11:82959127-82997176. Error was invalid region `11:82959128-82997176`
[2016-04-15T06:22Z] 2016-04-14 23:22:24 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:22:24,726 - WARNING - Could not retrieve variants from source file in region 11:89935375-89935776. Error was invalid region `11:89935376-89935776`
[2016-04-15T06:22Z] 2016-04-14 23:22:24 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:22:24,909 - WARNING - Could not retrieve variants from source file in region 11:86267422-86267904. Error was invalid region `11:86267423-86267904`
[2016-04-15T06:22Z] 2016-04-14 23:22:25 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:22:25,958 - WARNING - Could not retrieve variants from source file in region 11:82924147-82924548. Error was invalid region `11:82924148-82924548`
[2016-04-15T06:22Z] ['bcbio-variation-recall', 'square', '-Xms750m', '-Xmx7280m', '-XX:+UseSerialGC', '-c', 16, '-r', u'11:93797497-109964158', '--caller', 'platypus', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/11/Batch1-11_93797496_109964158.vcf.gz', '/mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/11/Batch1-11_93797496_109964158.vcf-inputs.txt'] in region: 11:93797497-109964158
[2016-04-15T06:22Z] 2016-04-14 23:22:46 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:22:46,760 - WARNING - Could not retrieve variants from source file in region 11:94699296-94699697. Error was invalid region `11:94699297-94699697`
[2016-04-15T06:22Z] 2016-04-14 23:22:48 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:22:48,602 - WARNING - Could not retrieve variants from source file in region 11:106647011-106647412. Error was invalid region `11:106647012-106647412`
[2016-04-15T06:22Z] 2016-04-14 23:22:48 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:22:48,644 - WARNING - Could not retrieve variants from source file in region 11:105782443-105797831. Error was invalid region `11:105782444-105797831`
[2016-04-15T06:22Z] 2016-04-14 23:22:49 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:22:49,135 - WARNING - Could not retrieve variants from source file in region 11:109963878-109964279. Error was invalid region `11:109963879-109964279`
[2016-04-15T06:22Z] 2016-04-14 23:22:49 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:22:49,145 - WARNING - Could not retrieve variants from source file in region 11:106849189-106849590. Error was invalid region `11:106849190-106849590`
[2016-04-15T06:22Z] 2016-04-14 23:22:49 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:22:49,496 - WARNING - Could not retrieve variants from source file in region 11:103228816-103229217. Error was invalid region `11:103228817-103229217`
[2016-04-15T06:22Z] 2016-04-14 23:22:49 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:22:49,541 - WARNING - Could not retrieve variants from source file in region 11:104760889-104768288. Error was invalid region `11:104760890-104768288`
[2016-04-15T06:22Z] 2016-04-14 23:22:49 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:22:49,594 - WARNING - Could not retrieve variants from source file in region 11:103158067-103158468. Error was invalid region `11:103158068-103158468`
[2016-04-15T06:22Z] 2016-04-14 23:22:49 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:22:49,665 - WARNING - Could not retrieve variants from source file in region 11:107420319-107420720. Error was invalid region `11:107420320-107420720`
[2016-04-15T06:22Z] 2016-04-14 23:22:52 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:22:52,120 - WARNING - Could not retrieve variants from source file in region 11:94699296-94699697. Error was invalid region `11:94699297-94699697`
[2016-04-15T06:22Z] 2016-04-14 23:22:54 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:22:54,502 - WARNING - Could not retrieve variants from source file in region 11:103780244-103780645. Error was invalid region `11:103780245-103780645`
[2016-04-15T06:22Z] 2016-04-14 23:22:55 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:22:55,782 - WARNING - Could not retrieve variants from source file in region 11:106680919-106681320. Error was invalid region `11:106680920-106681320`
[2016-04-15T06:22Z] 2016-04-14 23:22:56 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:22:56,550 - WARNING - Could not retrieve variants from source file in region 11:106647011-106647412. Error was invalid region `11:106647012-106647412`
[2016-04-15T06:22Z] 2016-04-14 23:22:57 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:22:57,804 - WARNING - Could not retrieve variants from source file in region 11:107729350-107729805. Error was invalid region `11:107729351-107729805`
[2016-04-15T06:22Z] 2016-04-14 23:22:57 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:22:57,844 - WARNING - Could not retrieve variants from source file in region 11:101453981-101454382. Error was invalid region `11:101453982-101454382`
[2016-04-15T06:22Z] 2016-04-14 23:22:57 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:22:57,850 - WARNING - Could not retrieve variants from source file in region 11:103907745-103908925. Error was invalid region `11:103907746-103908925`
[2016-04-15T06:22Z] 2016-04-14 23:22:58 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:22:58,112 - WARNING - Could not retrieve variants from source file in region 11:106849189-106849590. Error was invalid region `11:106849190-106849590`
[2016-04-15T06:22Z] 2016-04-14 23:22:58 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:22:58,227 - WARNING - Could not retrieve variants from source file in region 11:109963878-109964279. Error was invalid region `11:109963879-109964279`
[2016-04-15T06:22Z] 2016-04-14 23:22:58 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:22:58,591 - WARNING - Could not retrieve variants from source file in region 11:95656900-95657301. Error was invalid region `11:95656901-95657301`
[2016-04-15T06:22Z] 2016-04-14 23:22:58 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:22:58,648 - WARNING - Could not retrieve variants from source file in region 11:103228816-103229217. Error was invalid region `11:103228817-103229217`
[2016-04-15T06:22Z] 2016-04-14 23:22:59 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:22:59,178 - WARNING - Could not retrieve variants from source file in region 11:107420319-107420720. Error was invalid region `11:107420320-107420720`
[2016-04-15T06:22Z] 2016-04-14 23:22:59 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:22:59,187 - WARNING - Could not retrieve variants from source file in region 11:104760889-104768288. Error was invalid region `11:104760890-104768288`
[2016-04-15T06:22Z] 2016-04-14 23:22:59 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:22:59,192 - WARNING - Could not retrieve variants from source file in region 11:94699296-94699697. Error was invalid region `11:94699297-94699697`
[2016-04-15T06:23Z] 2016-04-14 23:23:02 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:23:02,537 - WARNING - Could not retrieve variants from source file in region 11:106647011-106647412. Error was invalid region `11:106647012-106647412`
[2016-04-15T06:23Z] 2016-04-14 23:23:05 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:23:05,918 - WARNING - Could not retrieve variants from source file in region 11:103907745-103908925. Error was invalid region `11:103907746-103908925`
[2016-04-15T06:23Z] 2016-04-14 23:23:06 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:23:06,222 - WARNING - Could not retrieve variants from source file in region 11:106849189-106849590. Error was invalid region `11:106849190-106849590`
[2016-04-15T06:23Z] 2016-04-14 23:23:06 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:23:06,831 - WARNING - Could not retrieve variants from source file in region 11:109963878-109964279. Error was invalid region `11:109963879-109964279`
[2016-04-15T06:23Z] 2016-04-14 23:23:06 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:23:06,937 - WARNING - Could not retrieve variants from source file in region 11:103228816-103229217. Error was invalid region `11:103228817-103229217`
[2016-04-15T06:23Z] 2016-04-14 23:23:07 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:23:07,049 - WARNING - Could not retrieve variants from source file in region 11:95656900-95657301. Error was invalid region `11:95656901-95657301`
[2016-04-15T06:23Z] 2016-04-14 23:23:07 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:23:07,274 - WARNING - Could not retrieve variants from source file in region 11:104760889-104768288. Error was invalid region `11:104760890-104768288`
[2016-04-15T06:23Z] 2016-04-14 23:23:07 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:23:07,294 - WARNING - Could not retrieve variants from source file in region 11:107420319-107420720. Error was invalid region `11:107420320-107420720`
[2016-04-15T06:23Z] 2016-04-14 23:23:18 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:23:18,348 - WARNING - Could not retrieve variants from source file in region 11:107663420-107687185. Error was invalid region `11:107663421-107687185`
[2016-04-15T06:23Z] 2016-04-14 23:23:19 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:23:19,557 - WARNING - Could not retrieve variants from source file in region 11:94533162-94533563. Error was invalid region `11:94533163-94533563`
[2016-04-15T06:23Z] 2016-04-14 23:23:19 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:23:19,624 - WARNING - Could not retrieve variants from source file in region 11:102980113-102980514. Error was invalid region `11:102980114-102980514`
[2016-04-15T06:23Z] 2016-04-14 23:23:21 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:23:21,045 - WARNING - Could not retrieve variants from source file in region 11:107535547-107535948. Error was invalid region `11:107535548-107535948`
[2016-04-15T06:23Z] 2016-04-14 23:23:21 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:23:21,422 - WARNING - Could not retrieve variants from source file in region 11:104971046-104971447. Error was invalid region `11:104971047-104971447`
[2016-04-15T06:23Z] 2016-04-14 23:23:22 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:23:22,954 - WARNING - Could not retrieve variants from source file in region 11:101323559-101359940. Error was invalid region `11:101323560-101359940`
[2016-04-15T06:23Z] 2016-04-14 23:23:23 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:23:23,074 - WARNING - Could not retrieve variants from source file in region 11:94225596-94261470. Error was invalid region `11:94225597-94261470`
[2016-04-15T06:23Z] 2016-04-14 23:23:23 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:23:23,750 - WARNING - Could not retrieve variants from source file in region 11:103029305-103082780. Error was invalid region `11:103029306-103082780`
[2016-04-15T06:23Z] 2016-04-14 23:23:25 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:23:25,930 - WARNING - Could not retrieve variants from source file in region 11:107299420-107299821. Error was invalid region `11:107299421-107299821`
[2016-04-15T06:23Z] 2016-04-14 23:23:26 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:23:26,389 - WARNING - Could not retrieve variants from source file in region 11:108182956-108183357. Error was invalid region `11:108182957-108183357`
[2016-04-15T06:23Z] 2016-04-14 23:23:26 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:23:26,409 - WARNING - Could not retrieve variants from source file in region 11:94533162-94533563. Error was invalid region `11:94533163-94533563`
[2016-04-15T06:23Z] 2016-04-14 23:23:26 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:23:26,725 - WARNING - Could not retrieve variants from source file in region 11:102562489-102576565. Error was invalid region `11:102562490-102576565`
[2016-04-15T06:23Z] 2016-04-14 23:23:28 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:23:28,291 - WARNING - Could not retrieve variants from source file in region 11:94225596-94261470. Error was invalid region `11:94225597-94261470`
[2016-04-15T06:23Z] 2016-04-14 23:23:28 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:23:28,841 - WARNING - Could not retrieve variants from source file in region 11:103029305-103082780. Error was invalid region `11:103029306-103082780`
[2016-04-15T06:23Z] 2016-04-14 23:23:29 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:23:29,278 - WARNING - Could not retrieve variants from source file in region 11:108463998-108464552. Error was invalid region `11:108463999-108464552`
[2016-04-15T06:23Z] 2016-04-14 23:23:29 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:23:29,813 - WARNING - Could not retrieve variants from source file in region 11:95564048-95581116. Error was invalid region `11:95564049-95581116`
[2016-04-15T06:23Z] 2016-04-14 23:23:32 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:23:32,417 - WARNING - Could not retrieve variants from source file in region 11:94533162-94533563. Error was invalid region `11:94533163-94533563`
[2016-04-15T06:23Z] 2016-04-14 23:23:32 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:23:32,453 - WARNING - Could not retrieve variants from source file in region 11:108182956-108183357. Error was invalid region `11:108182957-108183357`
[2016-04-15T06:23Z] 2016-04-14 23:23:32 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:23:32,483 - WARNING - Could not retrieve variants from source file in region 11:102398382-102398783. Error was invalid region `11:102398383-102398783`
[2016-04-15T06:23Z] 2016-04-14 23:23:33 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:23:33,097 - WARNING - Could not retrieve variants from source file in region 11:107535547-107535948. Error was invalid region `11:107535548-107535948`
[2016-04-15T06:23Z] 2016-04-14 23:23:33 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:23:33,368 - WARNING - Could not retrieve variants from source file in region 11:94225596-94261470. Error was invalid region `11:94225597-94261470`
[2016-04-15T06:23Z] 2016-04-14 23:23:33 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:23:33,605 - WARNING - Could not retrieve variants from source file in region 11:103029305-103082780. Error was invalid region `11:103029306-103082780`
[2016-04-15T06:23Z] 2016-04-14 23:23:34 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:23:34,443 - WARNING - Could not retrieve variants from source file in region 11:95564048-95581116. Error was invalid region `11:95564049-95581116`
[2016-04-15T06:23Z] 2016-04-14 23:23:38 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:23:38,864 - WARNING - Could not retrieve variants from source file in region 11:102398382-102398783. Error was invalid region `11:102398383-102398783`
[2016-04-15T06:23Z] 2016-04-14 23:23:39 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:23:39,158 - WARNING - Could not retrieve variants from source file in region 11:108182956-108183357. Error was invalid region `11:108182957-108183357`
[2016-04-15T06:23Z] 2016-04-14 23:23:45 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:23:45,755 - WARNING - Could not retrieve variants from source file in region 11:102709214-102738986. Error was invalid region `11:102709215-102738986`
[2016-04-15T06:23Z] 2016-04-14 23:23:47 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:23:47,120 - WARNING - Could not retrieve variants from source file in region 11:94473923-94474324. Error was invalid region `11:94473924-94474324`
[2016-04-15T06:23Z] 2016-04-14 23:23:48 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:23:48,818 - WARNING - Could not retrieve variants from source file in region 11:104819116-104825839. Error was invalid region `11:104819117-104825839`
[2016-04-15T06:23Z] 2016-04-14 23:23:48 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:23:48,823 - WARNING - Could not retrieve variants from source file in region 11:102477166-102496188. Error was invalid region `11:102477167-102496188`
[2016-04-15T06:23Z] 2016-04-14 23:23:49 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:23:49,404 - WARNING - Could not retrieve variants from source file in region 11:95511849-95512250. Error was invalid region `11:95511850-95512250`
[2016-04-15T06:23Z] 2016-04-14 23:23:49 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:23:49,866 - WARNING - Could not retrieve variants from source file in region 11:94113255-94113656. Error was invalid region `11:94113256-94113656`
[2016-04-15T06:23Z] 2016-04-14 23:23:49 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:23:49,878 - WARNING - Could not retrieve variants from source file in region 11:107992135-107992536. Error was invalid region `11:107992136-107992536`
[2016-04-15T06:23Z] 2016-04-14 23:23:50 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:23:50,407 - WARNING - Could not retrieve variants from source file in region 11:106888397-106888798. Error was invalid region `11:106888398-106888798`
[2016-04-15T06:23Z] 2016-04-14 23:23:50 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:23:50,793 - WARNING - Could not retrieve variants from source file in region 11:108380124-108384397. Error was invalid region `11:108380125-108384397`
[2016-04-15T06:23Z] 2016-04-14 23:23:51 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:23:51,987 - WARNING - Could not retrieve variants from source file in region 11:108040273-108044281. Error was invalid region `11:108040274-108044281`
[2016-04-15T06:23Z] 2016-04-14 23:23:55 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:23:55,135 - WARNING - Could not retrieve variants from source file in region 11:107992135-107992536. Error was invalid region `11:107992136-107992536`
[2016-04-15T06:23Z] 2016-04-14 23:23:55 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:23:55,141 - WARNING - Could not retrieve variants from source file in region 11:94113255-94113656. Error was invalid region `11:94113256-94113656`
[2016-04-15T06:23Z] 2016-04-14 23:23:55 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:23:55,230 - WARNING - Could not retrieve variants from source file in region 11:95511849-95512250. Error was invalid region `11:95511850-95512250`
[2016-04-15T06:23Z] 2016-04-14 23:23:55 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:23:55,472 - WARNING - Could not retrieve variants from source file in region 11:102709214-102738986. Error was invalid region `11:102709215-102738986`
[2016-04-15T06:23Z] 2016-04-14 23:23:55 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:23:55,752 - WARNING - Could not retrieve variants from source file in region 11:108380124-108384397. Error was invalid region `11:108380125-108384397`
[2016-04-15T06:23Z] 2016-04-14 23:23:55 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:23:55,810 - WARNING - Could not retrieve variants from source file in region 11:106888397-106888798. Error was invalid region `11:106888398-106888798`
[2016-04-15T06:23Z] 2016-04-14 23:23:56 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:23:56,235 - WARNING - Could not retrieve variants from source file in region 11:94473923-94474324. Error was invalid region `11:94473924-94474324`
[2016-04-15T06:23Z] 2016-04-14 23:23:58 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:23:58,244 - WARNING - Could not retrieve variants from source file in region 11:104819116-104825839. Error was invalid region `11:104819117-104825839`
[2016-04-15T06:23Z] 2016-04-14 23:23:59 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:23:59,896 - WARNING - Could not retrieve variants from source file in region 11:107992135-107992536. Error was invalid region `11:107992136-107992536`
[2016-04-15T06:23Z] 2016-04-14 23:23:59 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:23:59,954 - WARNING - Could not retrieve variants from source file in region 11:94113255-94113656. Error was invalid region `11:94113256-94113656`
[2016-04-15T06:24Z] 2016-04-14 23:24:00 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:24:00,057 - WARNING - Could not retrieve variants from source file in region 11:95511849-95512250. Error was invalid region `11:95511850-95512250`
[2016-04-15T06:24Z] 2016-04-14 23:24:00 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:24:00,958 - WARNING - Could not retrieve variants from source file in region 11:106888397-106888798. Error was invalid region `11:106888398-106888798`
[2016-04-15T06:24Z] 2016-04-14 23:24:01 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:24:01,315 - WARNING - Could not retrieve variants from source file in region 11:108380124-108384397. Error was invalid region `11:108380125-108384397`
[2016-04-15T06:24Z] 2016-04-14 23:24:09 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:24:09,289 - WARNING - Could not retrieve variants from source file in region 11:100909780-100933602. Error was invalid region `11:100909781-100933602`
[2016-04-15T06:24Z] 2016-04-14 23:24:11 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:24:11,382 - WARNING - Could not retrieve variants from source file in region 11:94320026-94337410. Error was invalid region `11:94320027-94337410`
[2016-04-15T06:24Z] 2016-04-14 23:24:12 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:24:12,124 - WARNING - Could not retrieve variants from source file in region 11:101832267-101857948. Error was invalid region `11:101832268-101857948`
[2016-04-15T06:24Z] 2016-04-14 23:24:12 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:24:12,317 - WARNING - Could not retrieve variants from source file in region 11:101771037-101771438. Error was invalid region `11:101771038-101771438`
[2016-04-15T06:24Z] 2016-04-14 23:24:13 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:24:13,863 - WARNING - Could not retrieve variants from source file in region 11:107916876-107917277. Error was invalid region `11:107916877-107917277`
[2016-04-15T06:24Z] 2016-04-14 23:24:14 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:24:14,208 - WARNING - Could not retrieve variants from source file in region 11:93862282-93862683. Error was invalid region `11:93862283-93862683`
[2016-04-15T06:24Z] 2016-04-14 23:24:14 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:24:14,614 - WARNING - Could not retrieve variants from source file in region 11:94758848-94760322. Error was invalid region `11:94758849-94760322`
[2016-04-15T06:24Z] 2016-04-14 23:24:14 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:24:14,625 - WARNING - Could not retrieve variants from source file in region 11:100846725-100847240. Error was invalid region `11:100846726-100847240`
[2016-04-15T06:24Z] 2016-04-14 23:24:16 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:24:16,198 - WARNING - Could not retrieve variants from source file in region 11:101832267-101857948. Error was invalid region `11:101832268-101857948`
[2016-04-15T06:24Z] 2016-04-14 23:24:16 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:24:16,219 - WARNING - Could not retrieve variants from source file in region 11:101771037-101771438. Error was invalid region `11:101771038-101771438`
[2016-04-15T06:24Z] 2016-04-14 23:24:18 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:24:18,018 - WARNING - Could not retrieve variants from source file in region 11:107916876-107917277. Error was invalid region `11:107916877-107917277`
[2016-04-15T06:24Z] 2016-04-14 23:24:18 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:24:18,399 - WARNING - Could not retrieve variants from source file in region 11:93862282-93862683. Error was invalid region `11:93862283-93862683`
[2016-04-15T06:24Z] 2016-04-14 23:24:18 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:24:18,731 - WARNING - Could not retrieve variants from source file in region 11:100846725-100847240. Error was invalid region `11:100846726-100847240`
[2016-04-15T06:24Z] 2016-04-14 23:24:19 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:24:19,238 - WARNING - Could not retrieve variants from source file in region 11:94731548-94731949. Error was invalid region `11:94731549-94731949`
[2016-04-15T06:24Z] 2016-04-14 23:24:20 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:24:20,211 - WARNING - Could not retrieve variants from source file in region 11:101771037-101771438. Error was invalid region `11:101771038-101771438`
[2016-04-15T06:24Z] 2016-04-14 23:24:20 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:24:20,426 - WARNING - Could not retrieve variants from source file in region 11:101832267-101857948. Error was invalid region `11:101832268-101857948`
[2016-04-15T06:24Z] 2016-04-14 23:24:22 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:24:22,219 - WARNING - Could not retrieve variants from source file in region 11:107916876-107917277. Error was invalid region `11:107916877-107917277`
[2016-04-15T06:24Z] 2016-04-14 23:24:22 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:24:22,899 - WARNING - Could not retrieve variants from source file in region 11:93862282-93862683. Error was invalid region `11:93862283-93862683`
[2016-04-15T06:24Z] 2016-04-14 23:24:23 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:24:23,472 - WARNING - Could not retrieve variants from source file in region 11:94800691-94801092. Error was invalid region `11:94800692-94801092`
[2016-04-15T06:24Z] 2016-04-14 23:24:23 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:24:23,533 - WARNING - Could not retrieve variants from source file in region 11:94758848-94760322. Error was invalid region `11:94758849-94760322`
[2016-04-15T06:24Z] 2016-04-14 23:24:27 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:24:27,203 - WARNING - Could not retrieve variants from source file in region 11:93797408-93797809. Error was invalid region `11:93797409-93797809`
[2016-04-15T06:24Z] 2016-04-14 23:24:27 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:24:27,366 - WARNING - Could not retrieve variants from source file in region 11:99690075-99690618. Error was invalid region `11:99690076-99690618`
[2016-04-15T06:24Z] 2016-04-14 23:24:27 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:24:27,962 - WARNING - Could not retrieve variants from source file in region 11:94800691-94801092. Error was invalid region `11:94800692-94801092`
[2016-04-15T06:24Z] 2016-04-14 23:24:28 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:24:28,040 - WARNING - Could not retrieve variants from source file in region 11:94800691-94801092. Error was invalid region `11:94800692-94801092`
[2016-04-15T06:24Z] 2016-04-14 23:24:28 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:24:28,594 - WARNING - Could not retrieve variants from source file in region 11:93797408-93797809. Error was invalid region `11:93797409-93797809`
[2016-04-15T06:24Z] 2016-04-14 23:24:30 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:24:30,194 - WARNING - Could not retrieve variants from source file in region 11:93797408-93797809. Error was invalid region `11:93797409-93797809`
[2016-04-15T06:24Z] 2016-04-14 23:24:32 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:24:32,262 - WARNING - Could not retrieve variants from source file in region 11:95825586-95825987. Error was invalid region `11:95825587-95825987`
[2016-04-15T06:24Z] 2016-04-14 23:24:32 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:24:32,307 - WARNING - Could not retrieve variants from source file in region 11:95825586-95825987. Error was invalid region `11:95825587-95825987`
[2016-04-15T06:24Z] 2016-04-14 23:24:33 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:24:33,399 - WARNING - Could not retrieve variants from source file in region 11:95825586-95825987. Error was invalid region `11:95825587-95825987`
[2016-04-15T06:24Z] ['bcbio-variation-recall', 'square', '-Xms750m', '-Xmx7280m', '-XX:+UseSerialGC', '-c', 16, '-r', u'11:110001731-125514538', '--caller', 'platypus', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/11/Batch1-11_110001730_125514538.vcf.gz', '/mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/11/Batch1-11_110001730_125514538.vcf-inputs.txt'] in region: 11:110001731-125514538
[2016-04-15T06:24Z] 2016-04-14 23:24:49 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:24:49,815 - WARNING - Could not retrieve variants from source file in region 11:116691423-116701725. Error was invalid region `11:116691424-116701725`
[2016-04-15T06:24Z] 2016-04-14 23:24:49 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:24:49,924 - WARNING - Could not retrieve variants from source file in region 11:122738050-122738451. Error was invalid region `11:122738051-122738451`
[2016-04-15T06:24Z] 2016-04-14 23:24:50 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:24:50,409 - WARNING - Could not retrieve variants from source file in region 11:124179624-124189919. Error was invalid region `11:124179625-124189919`
[2016-04-15T06:24Z] 2016-04-14 23:24:50 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:24:50,597 - WARNING - Could not retrieve variants from source file in region 11:119004877-119005322. Error was invalid region `11:119004878-119005322`
[2016-04-15T06:24Z] 2016-04-14 23:24:50 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:24:50,763 - WARNING - Could not retrieve variants from source file in region 11:118219824-118221664. Error was invalid region `11:118219825-118221664`
[2016-04-15T06:24Z] 2016-04-14 23:24:51 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:24:51,111 - WARNING - Could not retrieve variants from source file in region 11:117222381-117227039. Error was invalid region `11:117222382-117227039`
[2016-04-15T06:24Z] 2016-04-14 23:24:51 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:24:51,364 - WARNING - Could not retrieve variants from source file in region 11:124440151-124440807. Error was invalid region `11:124440152-124440807`
[2016-04-15T06:24Z] 2016-04-14 23:24:51 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:24:51,367 - WARNING - Could not retrieve variants from source file in region 11:117160136-117164014. Error was invalid region `11:117160137-117164014`
[2016-04-15T06:24Z] 2016-04-14 23:24:54 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:24:54,080 - WARNING - Could not retrieve variants from source file in region 11:112020705-112021106. Error was invalid region `11:112020706-112021106`
[2016-04-15T06:24Z] 2016-04-14 23:24:56 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:24:56,402 - WARNING - Could not retrieve variants from source file in region 11:120099447-120111231. Error was invalid region `11:120099448-120111231`
[2016-04-15T06:24Z] 2016-04-14 23:24:58 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:24:58,061 - WARNING - Could not retrieve variants from source file in region 11:122738050-122738451. Error was invalid region `11:122738051-122738451`
[2016-04-15T06:24Z] 2016-04-14 23:24:58 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:24:58,717 - WARNING - Could not retrieve variants from source file in region 11:113848062-113856958. Error was invalid region `11:113848063-113856958`
[2016-04-15T06:24Z] 2016-04-14 23:24:59 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:24:59,095 - WARNING - Could not retrieve variants from source file in region 11:124545015-124545416. Error was invalid region `11:124545016-124545416`
[2016-04-15T06:24Z] 2016-04-14 23:24:59 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:24:59,112 - WARNING - Could not retrieve variants from source file in region 11:124440151-124440807. Error was invalid region `11:124440152-124440807`
[2016-04-15T06:24Z] 2016-04-14 23:24:59 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:24:59,323 - WARNING - Could not retrieve variants from source file in region 11:112020705-112021106. Error was invalid region `11:112020706-112021106`
[2016-04-15T06:25Z] 2016-04-14 23:25:04 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:25:04,233 - WARNING - Could not retrieve variants from source file in region 11:122738050-122738451. Error was invalid region `11:122738051-122738451`
[2016-04-15T06:25Z] 2016-04-14 23:25:05 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:25:05,661 - WARNING - Could not retrieve variants from source file in region 11:118219824-118221664. Error was invalid region `11:118219825-118221664`
[2016-04-15T06:25Z] 2016-04-14 23:25:06 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:25:06,144 - WARNING - Could not retrieve variants from source file in region 11:111845722-111853296. Error was invalid region `11:111845723-111853296`
[2016-04-15T06:25Z] 2016-04-14 23:25:06 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:25:06,145 - WARNING - Could not retrieve variants from source file in region 11:117222381-117227039. Error was invalid region `11:117222382-117227039`
[2016-04-15T06:25Z] 2016-04-14 23:25:06 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:25:06,583 - WARNING - Could not retrieve variants from source file in region 11:124545015-124545416. Error was invalid region `11:124545016-124545416`
[2016-04-15T06:25Z] 2016-04-14 23:25:06 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:25:06,781 - WARNING - Could not retrieve variants from source file in region 11:117160136-117164014. Error was invalid region `11:117160137-117164014`
[2016-04-15T06:25Z] 2016-04-14 23:25:06 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:25:06,815 - WARNING - Could not retrieve variants from source file in region 11:124440151-124440807. Error was invalid region `11:124440152-124440807`
[2016-04-15T06:25Z] 2016-04-14 23:25:06 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:25:06,981 - WARNING - Could not retrieve variants from source file in region 11:119004877-119005322. Error was invalid region `11:119004878-119005322`
[2016-04-15T06:25Z] 2016-04-14 23:25:16 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:25:16,762 - WARNING - Could not retrieve variants from source file in region 11:111420153-111420554. Error was invalid region `11:111420154-111420554`
[2016-04-15T06:25Z] 2016-04-14 23:25:18 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:25:18,337 - WARNING - Could not retrieve variants from source file in region 11:119998980-119999381. Error was invalid region `11:119998981-119999381`
[2016-04-15T06:25Z] 2016-04-14 23:25:21 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:25:21,191 - WARNING - Could not retrieve variants from source file in region 11:122646756-122665627. Error was invalid region `11:122646757-122665627`
[2016-04-15T06:25Z] 2016-04-14 23:25:21 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:25:21,878 - WARNING - Could not retrieve variants from source file in region 11:118074126-118111167. Error was invalid region `11:118074127-118111167`
[2016-04-15T06:25Z] 2016-04-14 23:25:22 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:25:22,418 - WARNING - Could not retrieve variants from source file in region 11:111420153-111420554. Error was invalid region `11:111420154-111420554`
[2016-04-15T06:25Z] 2016-04-14 23:25:24 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:25:24,574 - WARNING - Could not retrieve variants from source file in region 11:117109380-117109781. Error was invalid region `11:117109381-117109781`
[2016-04-15T06:25Z] 2016-04-14 23:25:24 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:25:24,935 - WARNING - Could not retrieve variants from source file in region 11:119998980-119999381. Error was invalid region `11:119998981-119999381`
[2016-04-15T06:25Z] 2016-04-14 23:25:25 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:25:25,005 - WARNING - Could not retrieve variants from source file in region 11:124481283-124481684. Error was invalid region `11:124481284-124481684`
[2016-04-15T06:25Z] 2016-04-14 23:25:25 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:25:25,217 - WARNING - Could not retrieve variants from source file in region 11:111169779-111179244. Error was invalid region `11:111169780-111179244`
[2016-04-15T06:25Z] 2016-04-14 23:25:25 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:25:25,577 - WARNING - Could not retrieve variants from source file in region 11:118885906-118967948. Error was invalid region `11:118885907-118967948`
[2016-04-15T06:25Z] 2016-04-14 23:25:25 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:25:25,738 - WARNING - Could not retrieve variants from source file in region 11:113802817-113803218. Error was invalid region `11:113802818-113803218`
[2016-04-15T06:25Z] 2016-04-14 23:25:26 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:25:26,175 - WARNING - Could not retrieve variants from source file in region 11:125452089-125452504. Error was invalid region `11:125452090-125452504`
[2016-04-15T06:25Z] 2016-04-14 23:25:26 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:25:26,652 - WARNING - Could not retrieve variants from source file in region 11:122646756-122665627. Error was invalid region `11:122646757-122665627`
[2016-04-15T06:25Z] 2016-04-14 23:25:26 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:25:26,967 - WARNING - Could not retrieve variants from source file in region 11:118074126-118111167. Error was invalid region `11:118074127-118111167`
[2016-04-15T06:25Z] 2016-04-14 23:25:27 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:25:27,335 - WARNING - Could not retrieve variants from source file in region 11:111420153-111420554. Error was invalid region `11:111420154-111420554`
[2016-04-15T06:25Z] 2016-04-14 23:25:32 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:25:32,640 - WARNING - Could not retrieve variants from source file in region 11:119998980-119999381. Error was invalid region `11:119998981-119999381`
[2016-04-15T06:25Z] 2016-04-14 23:25:33 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:25:33,170 - WARNING - Could not retrieve variants from source file in region 11:111169779-111179244. Error was invalid region `11:111169780-111179244`
[2016-04-15T06:25Z] 2016-04-14 23:25:33 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:25:33,727 - WARNING - Could not retrieve variants from source file in region 11:117039087-117046387. Error was invalid region `11:117039088-117046387`
[2016-04-15T06:25Z] 2016-04-14 23:25:33 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:25:33,996 - WARNING - Could not retrieve variants from source file in region 11:116633614-116634137. Error was invalid region `11:116633615-116634137`
[2016-04-15T06:25Z] 2016-04-14 23:25:33 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:25:33,996 - WARNING - Could not retrieve variants from source file in region 11:118074126-118111167. Error was invalid region `11:118074127-118111167`
[2016-04-15T06:25Z] 2016-04-14 23:25:34 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:25:34,039 - WARNING - Could not retrieve variants from source file in region 11:122646756-122665627. Error was invalid region `11:122646757-122665627`
[2016-04-15T06:25Z] 2016-04-14 23:25:39 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:25:39,617 - WARNING - Could not retrieve variants from source file in region 11:111169779-111179244. Error was invalid region `11:111169780-111179244`
[2016-04-15T06:25Z] 2016-04-14 23:25:40 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:25:40,015 - WARNING - Could not retrieve variants from source file in region 11:118885906-118967948. Error was invalid region `11:118885907-118967948`
[2016-04-15T06:25Z] 2016-04-14 23:25:40 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:25:40,751 - WARNING - Could not retrieve variants from source file in region 11:117039087-117046387. Error was invalid region `11:117039088-117046387`
[2016-04-15T06:25Z] 2016-04-14 23:25:48 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:25:48,602 - WARNING - Could not retrieve variants from source file in region 11:119510433-119545414. Error was invalid region `11:119510434-119545414`
[2016-04-15T06:25Z] 2016-04-14 23:25:52 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:25:52,167 - WARNING - Could not retrieve variants from source file in region 11:124006761-124016184. Error was invalid region `11:124006762-124016184`
[2016-04-15T06:25Z] 2016-04-14 23:25:53 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:25:53,034 - WARNING - Could not retrieve variants from source file in region 11:124266486-124267379. Error was invalid region `11:124266487-124267379`
[2016-04-15T06:25Z] 2016-04-14 23:25:53 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:25:53,321 - WARNING - Could not retrieve variants from source file in region 11:115374818-115375225. Error was invalid region `11:115374819-115375225`
[2016-04-15T06:25Z] 2016-04-14 23:25:53 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:25:53,415 - WARNING - Could not retrieve variants from source file in region 11:113669841-113679309. Error was invalid region `11:113669842-113679309`
[2016-04-15T06:25Z] 2016-04-14 23:25:54 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:25:54,088 - WARNING - Could not retrieve variants from source file in region 11:110447984-110452075. Error was invalid region `11:110447985-110452075`
[2016-04-15T06:25Z] 2016-04-14 23:25:54 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:25:54,222 - WARNING - Could not retrieve variants from source file in region 11:124948833-124972712. Error was invalid region `11:124948834-124972712`
[2016-04-15T06:25Z] 2016-04-14 23:25:55 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:25:55,051 - WARNING - Could not retrieve variants from source file in region 11:118828731-118829132. Error was invalid region `11:118828732-118829132`
[2016-04-15T06:25Z] 2016-04-14 23:25:57 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:25:57,809 - WARNING - Could not retrieve variants from source file in region 11:124266486-124267379. Error was invalid region `11:124266487-124267379`
[2016-04-15T06:25Z] 2016-04-14 23:25:57 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:25:57,915 - WARNING - Could not retrieve variants from source file in region 11:124006761-124016184. Error was invalid region `11:124006762-124016184`
[2016-04-15T06:25Z] 2016-04-14 23:25:58 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:25:58,986 - WARNING - Could not retrieve variants from source file in region 11:113669841-113679309. Error was invalid region `11:113669842-113679309`
[2016-04-15T06:25Z] 2016-04-14 23:25:59 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:25:59,415 - WARNING - Could not retrieve variants from source file in region 11:118015601-118016258. Error was invalid region `11:118015602-118016258`
[2016-04-15T06:26Z] 2016-04-14 23:26:01 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:26:01,116 - WARNING - Could not retrieve variants from source file in region 11:115044639-115045864. Error was invalid region `11:115044640-115045864`
[2016-04-15T06:26Z] 2016-04-14 23:26:02 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:26:02,983 - WARNING - Could not retrieve variants from source file in region 11:113193957-113194358. Error was invalid region `11:113193958-113194358`
[2016-04-15T06:26Z] 2016-04-14 23:26:03 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:26:03,038 - WARNING - Could not retrieve variants from source file in region 11:124006761-124016184. Error was invalid region `11:124006762-124016184`
[2016-04-15T06:26Z] 2016-04-14 23:26:04 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:26:04,222 - WARNING - Could not retrieve variants from source file in region 11:115374818-115375225. Error was invalid region `11:115374819-115375225`
[2016-04-15T06:26Z] 2016-04-14 23:26:04 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:26:04,465 - WARNING - Could not retrieve variants from source file in region 11:113669841-113679309. Error was invalid region `11:113669842-113679309`
[2016-04-15T06:26Z] 2016-04-14 23:26:05 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:26:05,293 - WARNING - Could not retrieve variants from source file in region 11:118828731-118829132. Error was invalid region `11:118828732-118829132`
[2016-04-15T06:26Z] 2016-04-14 23:26:06 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:26:06,666 - WARNING - Could not retrieve variants from source file in region 11:113560843-113571042. Error was invalid region `11:113560844-113571042`
[2016-04-15T06:26Z] 2016-04-14 23:26:13 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:26:13,166 - WARNING - Could not retrieve variants from source file in region 11:113193957-113194358. Error was invalid region `11:113193958-113194358`
[2016-04-15T06:26Z] 2016-04-14 23:26:13 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:26:13,361 - WARNING - Could not retrieve variants from source file in region 11:110035051-110036555. Error was invalid region `11:110035052-110036555`
[2016-04-15T06:26Z] 2016-04-14 23:26:14 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:26:14,483 - WARNING - Could not retrieve variants from source file in region 11:119180959-119252389. Error was invalid region `11:119180960-119252389`
[2016-04-15T06:26Z] 2016-04-14 23:26:14 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:26:14,841 - WARNING - Could not retrieve variants from source file in region 11:113560843-113571042. Error was invalid region `11:113560844-113571042`
[2016-04-15T06:26Z] 2016-04-14 23:26:15 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:26:15,478 - WARNING - Could not retrieve variants from source file in region 11:121367415-121367816. Error was invalid region `11:121367416-121367816`
[2016-04-15T06:26Z] 2016-04-14 23:26:16 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:26:16,213 - WARNING - Could not retrieve variants from source file in region 11:110035051-110036555. Error was invalid region `11:110035052-110036555`
[2016-04-15T06:26Z] 2016-04-14 23:26:20 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:26:20,913 - WARNING - Could not retrieve variants from source file in region 11:121367415-121367816. Error was invalid region `11:121367416-121367816`
[2016-04-15T06:26Z] 2016-04-14 23:26:22 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:26:22,949 - WARNING - Could not retrieve variants from source file in region 11:114568843-114576816. Error was invalid region `11:114568844-114576816`
[2016-04-15T06:26Z] 2016-04-14 23:26:23 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:26:23,096 - WARNING - Could not retrieve variants from source file in region 11:113238871-113283667. Error was invalid region `11:113238872-113283667`
[2016-04-15T06:26Z] 2016-04-14 23:26:25 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:26:25,711 - WARNING - Could not retrieve variants from source file in region 11:121367415-121367816. Error was invalid region `11:121367416-121367816`
[2016-04-15T06:26Z] 2016-04-14 23:26:27 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:26:27,157 - WARNING - Could not retrieve variants from source file in region 11:113134607-113136056. Error was invalid region `11:113134608-113136056`
[2016-04-15T06:26Z] 2016-04-14 23:26:34 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:26:34,579 - WARNING - Could not retrieve variants from source file in region 11:112832128-112832548. Error was invalid region `11:112832129-112832548`
[2016-04-15T06:26Z] 2016-04-14 23:26:34 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:26:34,626 - WARNING - Could not retrieve variants from source file in region 11:120745663-120746064. Error was invalid region `11:120745664-120746064`
[2016-04-15T06:26Z] 2016-04-14 23:26:34 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:26:34,786 - WARNING - Could not retrieve variants from source file in region 11:118501910-118534272. Error was invalid region `11:118501911-118534272`
[2016-04-15T06:26Z] 2016-04-14 23:26:37 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:26:37,259 - WARNING - Could not retrieve variants from source file in region 11:120775790-120776191. Error was invalid region `11:120775791-120776191`
[2016-04-15T06:26Z] 2016-04-14 23:26:38 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:26:38,952 - WARNING - Could not retrieve variants from source file in region 11:113103785-113104186. Error was invalid region `11:113103786-113104186`
[2016-04-15T06:26Z] 2016-04-14 23:26:39 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:26:39,591 - WARNING - Could not retrieve variants from source file in region 11:112832128-112832548. Error was invalid region `11:112832129-112832548`
[2016-04-15T06:26Z] 2016-04-14 23:26:44 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:26:44,244 - WARNING - Could not retrieve variants from source file in region 11:120339849-120340250. Error was invalid region `11:120339850-120340250`
[2016-04-15T06:26Z] 2016-04-14 23:26:44 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:26:44,363 - WARNING - Could not retrieve variants from source file in region 11:124653715-124654570. Error was invalid region `11:124653716-124654570`
[2016-04-15T06:26Z] 2016-04-14 23:26:45 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:26:45,028 - WARNING - Could not retrieve variants from source file in region 11:113103785-113104186. Error was invalid region `11:113103786-113104186`
[2016-04-15T06:26Z] 2016-04-14 23:26:45 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:26:45,157 - WARNING - Could not retrieve variants from source file in region 11:120745663-120746064. Error was invalid region `11:120745664-120746064`
[2016-04-15T06:26Z] 2016-04-14 23:26:45 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:26:45,323 - WARNING - Could not retrieve variants from source file in region 11:119031458-119064584. Error was invalid region `11:119031459-119064584`
[2016-04-15T06:26Z] 2016-04-14 23:26:46 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:26:46,548 - WARNING - Could not retrieve variants from source file in region 11:120775790-120776191. Error was invalid region `11:120775791-120776191`
[2016-04-15T06:26Z] 2016-04-14 23:26:47 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:26:47,227 - WARNING - Could not retrieve variants from source file in region 11:118399181-118405533. Error was invalid region `11:118399182-118405533`
[2016-04-15T06:26Z] 2016-04-14 23:26:50 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:26:50,063 - WARNING - Could not retrieve variants from source file in region 11:120339849-120340250. Error was invalid region `11:120339850-120340250`
[2016-04-15T06:26Z] 2016-04-14 23:26:50 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:26:50,514 - WARNING - Could not retrieve variants from source file in region 11:113103785-113104186. Error was invalid region `11:113103786-113104186`
[2016-04-15T06:26Z] 2016-04-14 23:26:55 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:26:55,117 - WARNING - Could not retrieve variants from source file in region 11:112122884-112123285. Error was invalid region `11:112122885-112123285`
[2016-04-15T06:26Z] 2016-04-14 23:26:58 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:26:58,982 - WARNING - Could not retrieve variants from source file in region 11:120175538-120208447. Error was invalid region `11:120175539-120208447`
[2016-04-15T06:26Z] 2016-04-14 23:26:59 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:26:59,683 - WARNING - Could not retrieve variants from source file in region 11:117403024-117403425. Error was invalid region `11:117403025-117403425`
[2016-04-15T06:26Z] 2016-04-14 23:26:59 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:26:59,690 - WARNING - Could not retrieve variants from source file in region 11:112122884-112123285. Error was invalid region `11:112122885-112123285`
[2016-04-15T06:26Z] 2016-04-14 23:26:59 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:26:59,915 - WARNING - Could not retrieve variants from source file in region 11:112122884-112123285. Error was invalid region `11:112122885-112123285`
[2016-04-15T06:27Z] 2016-04-14 23:27:00 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:27:00,869 - WARNING - Could not retrieve variants from source file in region 11:120175538-120208447. Error was invalid region `11:120175539-120208447`
[2016-04-15T06:27Z] 2016-04-14 23:27:03 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:27:03,516 - WARNING - Could not retrieve variants from source file in region 11:112065223-112088689. Error was invalid region `11:112065224-112088689`
[2016-04-15T06:27Z] 2016-04-14 23:27:04 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:27:04,622 - WARNING - Could not retrieve variants from source file in region 11:112065223-112088689. Error was invalid region `11:112065224-112088689`
[2016-04-15T06:27Z] 2016-04-14 23:27:07 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:27:07,471 - WARNING - Could not retrieve variants from source file in region 11:112065223-112088689. Error was invalid region `11:112065224-112088689`
[2016-04-15T06:27Z] 2016-04-14 23:27:08 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:27:08,562 - WARNING - Could not retrieve variants from source file in region 11:123477141-123481171. Error was invalid region `11:123477142-123481171`
[2016-04-15T06:27Z] 2016-04-14 23:27:09 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:27:09,045 - WARNING - Could not retrieve variants from source file in region 11:123477141-123481171. Error was invalid region `11:123477142-123481171`
[2016-04-15T06:27Z] 2016-04-14 23:27:11 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:27:11,999 - WARNING - Could not retrieve variants from source file in region 11:122928411-122929597. Error was invalid region `11:122928412-122929597`
[2016-04-15T06:27Z] 2016-04-14 23:27:12 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:27:12,161 - WARNING - Could not retrieve variants from source file in region 11:117376202-117376603. Error was invalid region `11:117376203-117376603`
[2016-04-15T06:27Z] 2016-04-14 23:27:15 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:27:15,613 - WARNING - Could not retrieve variants from source file in region 11:117335511-117342862. Error was invalid region `11:117335512-117342862`
[2016-04-15T06:27Z] 2016-04-14 23:27:16 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:27:16,670 - WARNING - Could not retrieve variants from source file in region 11:122928411-122929597. Error was invalid region `11:122928412-122929597`
[2016-04-15T06:27Z] 2016-04-14 23:27:16 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:27:16,700 - WARNING - Could not retrieve variants from source file in region 11:122795477-122795878. Error was invalid region `11:122795478-122795878`
[2016-04-15T06:27Z] 2016-04-14 23:27:19 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:27:19,816 - WARNING - Could not retrieve variants from source file in region 11:122795477-122795878. Error was invalid region `11:122795478-122795878`
[2016-04-15T06:27Z] ['bcbio-variation-recall', 'square', '-Xms750m', '-Xmx7280m', '-XX:+UseSerialGC', '-c', 16, '-r', u'11:125523641-135006516', '--caller', 'platypus', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/11/Batch1-11_125523640_135006516.vcf.gz', '/mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/11/Batch1-11_125523640_135006516.vcf-inputs.txt'] in region: 11:125523641-135006516
[2016-04-15T06:27Z] 2016-04-14 23:27:35 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:27:35,685 - WARNING - Could not retrieve variants from source file in region 11:128675081-128675482. Error was invalid region `11:128675082-128675482`
[2016-04-15T06:27Z] 2016-04-14 23:27:36 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:27:36,632 - WARNING - Could not retrieve variants from source file in region 11:130339101-130339502. Error was invalid region `11:130339102-130339502`
[2016-04-15T06:27Z] 2016-04-14 23:27:36 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:27:36,733 - WARNING - Could not retrieve variants from source file in region 11:134182164-134202226. Error was invalid region `11:134182165-134202226`
[2016-04-15T06:27Z] 2016-04-14 23:27:36 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:27:36,751 - WARNING - Could not retrieve variants from source file in region 11:134109713-134152165. Error was invalid region `11:134109714-134152165`
[2016-04-15T06:27Z] 2016-04-14 23:27:36 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:27:36,756 - WARNING - Could not retrieve variants from source file in region 11:133714311-133714712. Error was invalid region `11:133714312-133714712`
[2016-04-15T06:27Z] 2016-04-14 23:27:36 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:27:36,813 - WARNING - Could not retrieve variants from source file in region 11:128868028-128868429. Error was invalid region `11:128868029-128868429`
[2016-04-15T06:27Z] 2016-04-14 23:27:37 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:27:37,085 - WARNING - Could not retrieve variants from source file in region 11:132177352-132177823. Error was invalid region `11:132177353-132177823`
[2016-04-15T06:27Z] 2016-04-14 23:27:37 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:27:37,168 - WARNING - Could not retrieve variants from source file in region 11:129722342-129722743. Error was invalid region `11:129722343-129722743`
[2016-04-15T06:27Z] 2016-04-14 23:27:37 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:27:37,675 - WARNING - Could not retrieve variants from source file in region 11:130281277-130298310. Error was invalid region `11:130281278-130298310`
[2016-04-15T06:27Z] 2016-04-14 23:27:37 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:27:37,882 - WARNING - Could not retrieve variants from source file in region 11:129785383-129801233. Error was invalid region `11:129785384-129801233`
[2016-04-15T06:27Z] 2016-04-14 23:27:37 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:27:37,889 - WARNING - Could not retrieve variants from source file in region 11:133805374-133814381. Error was invalid region `11:133805375-133814381`
[2016-04-15T06:27Z] 2016-04-14 23:27:42 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:27:42,072 - WARNING - Could not retrieve variants from source file in region 11:132873433-132878373. Error was invalid region `11:132873434-132878373`
[2016-04-15T06:27Z] 2016-04-14 23:27:44 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:27:44,008 - WARNING - Could not retrieve variants from source file in region 11:130339101-130339502. Error was invalid region `11:130339102-130339502`
[2016-04-15T06:27Z] 2016-04-14 23:27:44 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:27:44,835 - WARNING - Could not retrieve variants from source file in region 11:134182164-134202226. Error was invalid region `11:134182165-134202226`
[2016-04-15T06:27Z] 2016-04-14 23:27:45 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:27:45,303 - WARNING - Could not retrieve variants from source file in region 11:128868028-128868429. Error was invalid region `11:128868029-128868429`
[2016-04-15T06:27Z] 2016-04-14 23:27:46 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:27:46,109 - WARNING - Could not retrieve variants from source file in region 11:126277992-126295007. Error was invalid region `11:126277993-126295007`
[2016-04-15T06:27Z] 2016-04-14 23:27:46 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:27:46,366 - WARNING - Could not retrieve variants from source file in region 11:128675081-128675482. Error was invalid region `11:128675082-128675482`
[2016-04-15T06:27Z] 2016-04-14 23:27:50 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:27:50,355 - WARNING - Could not retrieve variants from source file in region 11:130339101-130339502. Error was invalid region `11:130339102-130339502`
[2016-04-15T06:27Z] 2016-04-14 23:27:51 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:27:51,239 - WARNING - Could not retrieve variants from source file in region 11:134109713-134152165. Error was invalid region `11:134109714-134152165`
[2016-04-15T06:27Z] 2016-04-14 23:27:52 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:27:52,593 - WARNING - Could not retrieve variants from source file in region 11:134182164-134202226. Error was invalid region `11:134182165-134202226`
[2016-04-15T06:27Z] 2016-04-14 23:27:53 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:27:53,404 - WARNING - Could not retrieve variants from source file in region 11:128868028-128868429. Error was invalid region `11:128868029-128868429`
[2016-04-15T06:27Z] 2016-04-14 23:27:54 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:27:54,128 - WARNING - Could not retrieve variants from source file in region 11:125763535-125788868. Error was invalid region `11:125763536-125788868`
[2016-04-15T06:27Z] 2016-04-14 23:27:54 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:27:54,253 - WARNING - Could not retrieve variants from source file in region 11:129722342-129722743. Error was invalid region `11:129722343-129722743`
[2016-04-15T06:27Z] 2016-04-14 23:27:55 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:27:55,025 - WARNING - Could not retrieve variants from source file in region 11:126277992-126295007. Error was invalid region `11:126277993-126295007`
[2016-04-15T06:27Z] 2016-04-14 23:27:55 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:27:55,490 - WARNING - Could not retrieve variants from source file in region 11:130281277-130298310. Error was invalid region `11:130281278-130298310`
[2016-04-15T06:28Z] 2016-04-14 23:28:04 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:28:04,852 - WARNING - Could not retrieve variants from source file in region 11:130750431-130785494. Error was invalid region `11:130750432-130785494`
[2016-04-15T06:28Z] 2016-04-14 23:28:07 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:28:07,457 - WARNING - Could not retrieve variants from source file in region 11:129754433-129754834. Error was invalid region `11:129754434-129754834`
[2016-04-15T06:28Z] 2016-04-14 23:28:07 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:28:07,642 - WARNING - Could not retrieve variants from source file in region 11:129827489-129830986. Error was invalid region `11:129827490-129830986`
[2016-04-15T06:28Z] 2016-04-14 23:28:08 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:28:08,927 - WARNING - Could not retrieve variants from source file in region 11:129306437-129306838. Error was invalid region `11:129306438-129306838`
[2016-04-15T06:28Z] 2016-04-14 23:28:09 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:28:09,545 - WARNING - Could not retrieve variants from source file in region 11:125708082-125708483. Error was invalid region `11:125708083-125708483`
[2016-04-15T06:28Z] 2016-04-14 23:28:09 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:28:09,912 - WARNING - Could not retrieve variants from source file in region 11:128391726-128392127. Error was invalid region `11:128391727-128392127`
[2016-04-15T06:28Z] 2016-04-14 23:28:10 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:28:10,463 - WARNING - Could not retrieve variants from source file in region 11:125524984-125525385. Error was invalid region `11:125524985-125525385`
[2016-04-15T06:28Z] 2016-04-14 23:28:10 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:28:10,494 - WARNING - Could not retrieve variants from source file in region 11:125817188-125891459. Error was invalid region `11:125817189-125891459`
[2016-04-15T06:28Z] 2016-04-14 23:28:15 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:28:15,016 - WARNING - Could not retrieve variants from source file in region 11:126073981-126081593. Error was invalid region `11:126073982-126081593`
[2016-04-15T06:28Z] 2016-04-14 23:28:15 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:28:15,019 - WARNING - Could not retrieve variants from source file in region 11:130750431-130785494. Error was invalid region `11:130750432-130785494`
[2016-04-15T06:28Z] 2016-04-14 23:28:15 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:28:15,184 - WARNING - Could not retrieve variants from source file in region 11:125617395-125617800. Error was invalid region `11:125617396-125617800`
[2016-04-15T06:28Z] 2016-04-14 23:28:15 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:28:15,462 - WARNING - Could not retrieve variants from source file in region 11:128391726-128392127. Error was invalid region `11:128391727-128392127`
[2016-04-15T06:28Z] 2016-04-14 23:28:15 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:28:15,590 - WARNING - Could not retrieve variants from source file in region 11:133289978-133309379. Error was invalid region `11:133289979-133309379`
[2016-04-15T06:28Z] 2016-04-14 23:28:15 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:28:15,834 - WARNING - Could not retrieve variants from source file in region 11:125524984-125525385. Error was invalid region `11:125524985-125525385`
[2016-04-15T06:28Z] 2016-04-14 23:28:16 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:28:16,068 - WARNING - Could not retrieve variants from source file in region 11:129754433-129754834. Error was invalid region `11:129754434-129754834`
[2016-04-15T06:28Z] 2016-04-14 23:28:16 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:28:16,393 - WARNING - Could not retrieve variants from source file in region 11:129827489-129830986. Error was invalid region `11:129827490-129830986`
[2016-04-15T06:28Z] 2016-04-14 23:28:18 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:28:18,253 - WARNING - Could not retrieve variants from source file in region 11:125708082-125708483. Error was invalid region `11:125708083-125708483`
[2016-04-15T06:28Z] 2016-04-14 23:28:19 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:28:19,547 - WARNING - Could not retrieve variants from source file in region 11:126073981-126081593. Error was invalid region `11:126073982-126081593`
[2016-04-15T06:28Z] 2016-04-14 23:28:21 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:28:21,176 - WARNING - Could not retrieve variants from source file in region 11:125524984-125525385. Error was invalid region `11:125524985-125525385`
[2016-04-15T06:28Z] 2016-04-14 23:28:27 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:28:27,715 - WARNING - Could not retrieve variants from source file in region 11:126343016-126343417. Error was invalid region `11:126343017-126343417`
[2016-04-15T06:28Z] 2016-04-14 23:28:27 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:28:27,818 - WARNING - Could not retrieve variants from source file in region 11:128333292-128333693. Error was invalid region `11:128333293-128333693`
[2016-04-15T06:28Z] ['bcbio-variation-recall', 'square', '-Xms750m', '-Xmx7280m', '-XX:+UseSerialGC', '-c', 16, '-r', u'12:1-15637181', '--caller', 'platypus', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/12/Batch1-12_0_15637181.vcf.gz', '/mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/12/Batch1-12_0_15637181.vcf-inputs.txt'] in region: 12:1-15637181
[2016-04-15T06:28Z] 2016-04-14 23:28:43 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:28:43,489 - WARNING - Could not retrieve variants from source file in region 12:9994234-9994638. Error was invalid region `12:9994235-9994638`
[2016-04-15T06:28Z] 2016-04-14 23:28:43 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:28:43,825 - WARNING - Could not retrieve variants from source file in region 12:9554899-9555385. Error was invalid region `12:9554900-9555385`
[2016-04-15T06:28Z] 2016-04-14 23:28:45 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:28:45,261 - WARNING - Could not retrieve variants from source file in region 12:9822176-9845893. Error was invalid region `12:9822177-9845893`
[2016-04-15T06:28Z] 2016-04-14 23:28:45 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:28:45,366 - WARNING - Could not retrieve variants from source file in region 12:4919056-4919457. Error was invalid region `12:4919057-4919457`
[2016-04-15T06:28Z] 2016-04-14 23:28:45 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:28:45,687 - WARNING - Could not retrieve variants from source file in region 12:2224300-2224701. Error was invalid region `12:2224301-2224701`
[2016-04-15T06:28Z] 2016-04-14 23:28:46 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:28:46,222 - WARNING - Could not retrieve variants from source file in region 12:9750458-9750859. Error was invalid region `12:9750459-9750859`
[2016-04-15T06:28Z] 2016-04-14 23:28:46 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:28:46,679 - WARNING - Could not retrieve variants from source file in region 12:8277970-8278371. Error was invalid region `12:8277971-8278371`
[2016-04-15T06:28Z] 2016-04-14 23:28:46 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:28:46,690 - WARNING - Could not retrieve variants from source file in region 12:10763025-10783919. Error was invalid region `12:10763026-10783919`
[2016-04-15T06:28Z] 2016-04-14 23:28:47 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:28:47,801 - WARNING - Could not retrieve variants from source file in region 12:9994234-9994638. Error was invalid region `12:9994235-9994638`
[2016-04-15T06:28Z] 2016-04-14 23:28:47 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:28:47,890 - WARNING - Could not retrieve variants from source file in region 12:13061083-13061484. Error was invalid region `12:13061084-13061484`
[2016-04-15T06:28Z] 2016-04-14 23:28:48 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:28:48,392 - WARNING - Could not retrieve variants from source file in region 12:10041153-10069492. Error was invalid region `12:10041154-10069492`
[2016-04-15T06:28Z] 2016-04-14 23:28:49 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:28:49,613 - WARNING - Could not retrieve variants from source file in region 12:9248022-9254431. Error was invalid region `12:9248023-9254431`
[2016-04-15T06:28Z] 2016-04-14 23:28:52 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:28:52,939 - WARNING - Could not retrieve variants from source file in region 12:4919056-4919457. Error was invalid region `12:4919057-4919457`
[2016-04-15T06:28Z] 2016-04-14 23:28:53 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:28:53,793 - WARNING - Could not retrieve variants from source file in region 12:13061083-13061484. Error was invalid region `12:13061084-13061484`
[2016-04-15T06:28Z] 2016-04-14 23:28:54 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:28:54,366 - WARNING - Could not retrieve variants from source file in region 12:15081686-15103795. Error was invalid region `12:15081687-15103795`
[2016-04-15T06:28Z] 2016-04-14 23:28:54 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:28:54,511 - WARNING - Could not retrieve variants from source file in region 12:9994234-9994638. Error was invalid region `12:9994235-9994638`
[2016-04-15T06:28Z] 2016-04-14 23:28:54 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:28:54,529 - WARNING - Could not retrieve variants from source file in region 12:8277970-8278371. Error was invalid region `12:8277971-8278371`
[2016-04-15T06:28Z] 2016-04-14 23:28:54 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:28:54,612 - WARNING - Could not retrieve variants from source file in region 12:9554899-9555385. Error was invalid region `12:9554900-9555385`
[2016-04-15T06:29Z] 2016-04-14 23:29:01 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:29:01,436 - WARNING - Could not retrieve variants from source file in region 12:11243702-11245004. Error was invalid region `12:11243703-11245004`
[2016-04-15T06:29Z] 2016-04-14 23:29:02 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:29:02,043 - WARNING - Could not retrieve variants from source file in region 12:9688672-9697955. Error was invalid region `12:9688673-9697955`
[2016-04-15T06:29Z] 2016-04-14 23:29:02 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:29:02,180 - WARNING - Could not retrieve variants from source file in region 12:9750458-9750859. Error was invalid region `12:9750459-9750859`
[2016-04-15T06:29Z] 2016-04-14 23:29:03 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:29:03,460 - WARNING - Could not retrieve variants from source file in region 12:8277970-8278371. Error was invalid region `12:8277971-8278371`
[2016-04-15T06:29Z] 2016-04-14 23:29:12 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:29:12,697 - WARNING - Could not retrieve variants from source file in region 12:9142086-9161838. Error was invalid region `12:9142087-9161838`
[2016-04-15T06:29Z] 2016-04-14 23:29:13 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:29:13,628 - WARNING - Could not retrieve variants from source file in region 12:14648985-14656958. Error was invalid region `12:14648986-14656958`
[2016-04-15T06:29Z] 2016-04-14 23:29:15 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:29:15,315 - WARNING - Could not retrieve variants from source file in region 12:14829682-14830083. Error was invalid region `12:14829683-14830083`
[2016-04-15T06:29Z] 2016-04-14 23:29:16 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:29:16,894 - WARNING - Could not retrieve variants from source file in region 12:12966916-12967317. Error was invalid region `12:12966917-12967317`
[2016-04-15T06:29Z] 2016-04-14 23:29:19 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:29:19,003 - WARNING - Could not retrieve variants from source file in region 12:14720343-14720773. Error was invalid region `12:14720344-14720773`
[2016-04-15T06:29Z] 2016-04-14 23:29:19 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:29:19,025 - WARNING - Could not retrieve variants from source file in region 12:9142086-9161838. Error was invalid region `12:9142087-9161838`
[2016-04-15T06:29Z] 2016-04-14 23:29:19 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:29:19,888 - WARNING - Could not retrieve variants from source file in region 12:14793851-14794252. Error was invalid region `12:14793852-14794252`
[2016-04-15T06:29Z] 2016-04-14 23:29:19 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:29:19,987 - WARNING - Could not retrieve variants from source file in region 12:8925800-8929100. Error was invalid region `12:8925801-8929100`
[2016-04-15T06:29Z] 2016-04-14 23:29:21 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:29:21,107 - WARNING - Could not retrieve variants from source file in region 12:3046591-3049888. Error was invalid region `12:3046592-3049888`
[2016-04-15T06:29Z] 2016-04-14 23:29:21 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:29:21,506 - WARNING - Could not retrieve variants from source file in region 12:14829682-14830083. Error was invalid region `12:14829683-14830083`
[2016-04-15T06:29Z] 2016-04-14 23:29:22 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:29:22,203 - WARNING - Could not retrieve variants from source file in region 12:2062112-2062513. Error was invalid region `12:2062113-2062513`
[2016-04-15T06:29Z] 2016-04-14 23:29:22 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:29:22,221 - WARNING - Could not retrieve variants from source file in region 12:14976342-14994044. Error was invalid region `12:14976343-14994044`
[2016-04-15T06:29Z] 2016-04-14 23:29:22 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:29:22,867 - WARNING - Could not retrieve variants from source file in region 12:12966916-12967317. Error was invalid region `12:12966917-12967317`
[2016-04-15T06:29Z] 2016-04-14 23:29:24 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:29:24,147 - WARNING - Could not retrieve variants from source file in region 12:10373113-10374244. Error was invalid region `12:10373114-10374244`
[2016-04-15T06:29Z] 2016-04-14 23:29:24 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:29:24,239 - WARNING - Could not retrieve variants from source file in region 12:14720343-14720773. Error was invalid region `12:14720344-14720773`
[2016-04-15T06:29Z] 2016-04-14 23:29:24 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:29:24,788 - WARNING - Could not retrieve variants from source file in region 12:9142086-9161838. Error was invalid region `12:9142087-9161838`
[2016-04-15T06:29Z] 2016-04-14 23:29:26 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:29:26,243 - WARNING - Could not retrieve variants from source file in region 12:14793851-14794252. Error was invalid region `12:14793852-14794252`
[2016-04-15T06:29Z] 2016-04-14 23:29:27 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:29:27,042 - WARNING - Could not retrieve variants from source file in region 12:8925800-8929100. Error was invalid region `12:8925801-8929100`
[2016-04-15T06:29Z] 2016-04-14 23:29:27 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:29:27,609 - WARNING - Could not retrieve variants from source file in region 12:15034870-15036109. Error was invalid region `12:15034871-15036109`
[2016-04-15T06:29Z] 2016-04-14 23:29:28 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:29:28,517 - WARNING - Could not retrieve variants from source file in region 12:8073981-8074382. Error was invalid region `12:8073982-8074382`
[2016-04-15T06:29Z] 2016-04-14 23:29:28 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:29:28,699 - WARNING - Could not retrieve variants from source file in region 12:14829682-14830083. Error was invalid region `12:14829683-14830083`
[2016-04-15T06:29Z] 2016-04-14 23:29:28 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:29:28,897 - WARNING - Could not retrieve variants from source file in region 12:3046591-3049888. Error was invalid region `12:3046592-3049888`
[2016-04-15T06:29Z] 2016-04-14 23:29:29 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:29:29,241 - WARNING - Could not retrieve variants from source file in region 12:2062112-2062513. Error was invalid region `12:2062113-2062513`
[2016-04-15T06:29Z] 2016-04-14 23:29:29 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:29:29,277 - WARNING - Could not retrieve variants from source file in region 12:10560746-10603860. Error was invalid region `12:10560747-10603860`
[2016-04-15T06:29Z] 2016-04-14 23:29:29 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:29:29,474 - WARNING - Could not retrieve variants from source file in region 12:14976342-14994044. Error was invalid region `12:14976343-14994044`
[2016-04-15T06:29Z] 2016-04-14 23:29:29 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:29:29,779 - WARNING - Could not retrieve variants from source file in region 12:14720343-14720773. Error was invalid region `12:14720344-14720773`
[2016-04-15T06:29Z] 2016-04-14 23:29:31 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:29:31,125 - WARNING - Could not retrieve variants from source file in region 12:14793851-14794252. Error was invalid region `12:14793852-14794252`
[2016-04-15T06:29Z] 2016-04-14 23:29:31 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:29:31,508 - WARNING - Could not retrieve variants from source file in region 12:8925800-8929100. Error was invalid region `12:8925801-8929100`
[2016-04-15T06:29Z] 2016-04-14 23:29:38 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:29:38,273 - WARNING - Could not retrieve variants from source file in region 12:12869725-12870885. Error was invalid region `12:12869726-12870885`
[2016-04-15T06:29Z] 2016-04-14 23:29:42 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:29:42,675 - WARNING - Could not retrieve variants from source file in region 12:14577681-14587491. Error was invalid region `12:14577682-14587491`
[2016-04-15T06:29Z] 2016-04-14 23:29:44 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:29:44,138 - WARNING - Could not retrieve variants from source file in region 12:12869725-12870885. Error was invalid region `12:12869726-12870885`
[2016-04-15T06:29Z] 2016-04-14 23:29:45 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:29:45,823 - WARNING - Could not retrieve variants from source file in region 12:4671218-4671619. Error was invalid region `12:4671219-4671619`
[2016-04-15T06:29Z] 2016-04-14 23:29:45 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:29:45,894 - WARNING - Could not retrieve variants from source file in region 12:9070155-9087088. Error was invalid region `12:9070156-9087088`
[2016-04-15T06:29Z] 2016-04-14 23:29:45 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:29:45,940 - WARNING - Could not retrieve variants from source file in region 12:14688433-14688834. Error was invalid region `12:14688434-14688834`
[2016-04-15T06:29Z] 2016-04-14 23:29:46 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:29:46,534 - WARNING - Could not retrieve variants from source file in region 12:1995192-1995593. Error was invalid region `12:1995193-1995593`
[2016-04-15T06:29Z] 2016-04-14 23:29:46 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:29:46,565 - WARNING - Could not retrieve variants from source file in region 12:2788599-2791395. Error was invalid region `12:2788600-2791395`
[2016-04-15T06:29Z] 2016-04-14 23:29:47 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:29:47,297 - WARNING - Could not retrieve variants from source file in region 12:8757270-8757671. Error was invalid region `12:8757271-8757671`
[2016-04-15T06:29Z] 2016-04-14 23:29:47 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:29:47,429 - WARNING - Could not retrieve variants from source file in region 12:10525529-10532516. Error was invalid region `12:10525530-10532516`
[2016-04-15T06:29Z] 2016-04-14 23:29:48 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:29:48,081 - WARNING - Could not retrieve variants from source file in region 12:14577681-14587491. Error was invalid region `12:14577682-14587491`
[2016-04-15T06:29Z] 2016-04-14 23:29:48 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:29:48,572 - WARNING - Could not retrieve variants from source file in region 12:8023263-8043878. Error was invalid region `12:8023264-8043878`
[2016-04-15T06:29Z] 2016-04-14 23:29:48 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:29:48,650 - WARNING - Could not retrieve variants from source file in region 12:12869725-12870885. Error was invalid region `12:12869726-12870885`
[2016-04-15T06:29Z] 2016-04-14 23:29:49 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:29:49,584 - WARNING - Could not retrieve variants from source file in region 12:2967958-2997587. Error was invalid region `12:2967959-2997587`
[2016-04-15T06:29Z] 2016-04-14 23:29:49 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:29:49,937 - WARNING - Could not retrieve variants from source file in region 12:14923817-14924218. Error was invalid region `12:14923818-14924218`
[2016-04-15T06:29Z] 2016-04-14 23:29:51 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:29:51,071 - WARNING - Could not retrieve variants from source file in region 12:14688433-14688834. Error was invalid region `12:14688434-14688834`
[2016-04-15T06:29Z] 2016-04-14 23:29:51 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:29:51,111 - WARNING - Could not retrieve variants from source file in region 12:9070155-9087088. Error was invalid region `12:9070156-9087088`
[2016-04-15T06:29Z] 2016-04-14 23:29:51 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:29:51,782 - WARNING - Could not retrieve variants from source file in region 12:1995192-1995593. Error was invalid region `12:1995193-1995593`
[2016-04-15T06:29Z] 2016-04-14 23:29:52 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:29:52,612 - WARNING - Could not retrieve variants from source file in region 12:8757270-8757671. Error was invalid region `12:8757271-8757671`
[2016-04-15T06:29Z] 2016-04-14 23:29:53 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:29:53,207 - WARNING - Could not retrieve variants from source file in region 12:10525529-10532516. Error was invalid region `12:10525530-10532516`
[2016-04-15T06:29Z] 2016-04-14 23:29:53 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:29:53,897 - WARNING - Could not retrieve variants from source file in region 12:8023263-8043878. Error was invalid region `12:8023264-8043878`
[2016-04-15T06:29Z] 2016-04-14 23:29:54 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:29:54,287 - WARNING - Could not retrieve variants from source file in region 12:2967958-2997587. Error was invalid region `12:2967959-2997587`
[2016-04-15T06:29Z] 2016-04-14 23:29:54 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:29:54,895 - WARNING - Could not retrieve variants from source file in region 12:14923817-14924218. Error was invalid region `12:14923818-14924218`
[2016-04-15T06:29Z] 2016-04-14 23:29:55 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:29:55,324 - WARNING - Could not retrieve variants from source file in region 12:4671218-4671619. Error was invalid region `12:4671219-4671619`
[2016-04-15T06:29Z] 2016-04-14 23:29:55 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:29:55,472 - WARNING - Could not retrieve variants from source file in region 12:14688433-14688834. Error was invalid region `12:14688434-14688834`
[2016-04-15T06:29Z] 2016-04-14 23:29:56 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:29:56,587 - WARNING - Could not retrieve variants from source file in region 12:1995192-1995593. Error was invalid region `12:1995193-1995593`
[2016-04-15T06:29Z] 2016-04-14 23:29:58 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:29:58,331 - WARNING - Could not retrieve variants from source file in region 12:8757270-8757671. Error was invalid region `12:8757271-8757671`
[2016-04-15T06:29Z] 2016-04-14 23:29:58 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:29:58,980 - WARNING - Could not retrieve variants from source file in region 12:10525529-10532516. Error was invalid region `12:10525530-10532516`
[2016-04-15T06:29Z] 2016-04-14 23:29:59 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:29:59,231 - WARNING - Could not retrieve variants from source file in region 12:10251234-10278181. Error was invalid region `12:10251235-10278181`
[2016-04-15T06:30Z] 2016-04-14 23:30:02 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:30:02,940 - WARNING - Could not retrieve variants from source file in region 12:12814607-12815008. Error was invalid region `12:12814608-12815008`
[2016-04-15T06:30Z] 2016-04-14 23:30:05 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:30:05,759 - WARNING - Could not retrieve variants from source file in region 12:9004301-9021102. Error was invalid region `12:9004302-9021102`
[2016-04-15T06:30Z] 2016-04-14 23:30:08 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:30:08,272 - WARNING - Could not retrieve variants from source file in region 12:14018566-14019318. Error was invalid region `12:14018567-14019318`
[2016-04-15T06:30Z] 2016-04-14 23:30:08 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:30:08,761 - WARNING - Could not retrieve variants from source file in region 12:12814607-12815008. Error was invalid region `12:12814608-12815008`
[2016-04-15T06:30Z] 2016-04-14 23:30:09 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:30:09,452 - WARNING - Could not retrieve variants from source file in region 12:2936065-2936466. Error was invalid region `12:2936066-2936466`
[2016-04-15T06:30Z] 2016-04-14 23:30:11 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:30:11,140 - WARNING - Could not retrieve variants from source file in region 12:4387873-4388274. Error was invalid region `12:4387874-4388274`
[2016-04-15T06:30Z] 2016-04-14 23:30:12 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:30:12,409 - WARNING - Could not retrieve variants from source file in region 12:1902694-1903095. Error was invalid region `12:1902695-1903095`
[2016-04-15T06:30Z] 2016-04-14 23:30:12 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:30:12,450 - WARNING - Could not retrieve variants from source file in region 12:10461841-10462242. Error was invalid region `12:10461842-10462242`
[2016-04-15T06:30Z] 2016-04-14 23:30:12 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:30:12,533 - WARNING - Could not retrieve variants from source file in region 12:4553121-4554738. Error was invalid region `12:4553122-4554738`
[2016-04-15T06:30Z] 2016-04-14 23:30:13 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:30:13,839 - WARNING - Could not retrieve variants from source file in region 12:8667686-8668087. Error was invalid region `12:8667687-8668087`
[2016-04-15T06:30Z] 2016-04-14 23:30:13 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:30:13,946 - WARNING - Could not retrieve variants from source file in region 12:10206714-10207115. Error was invalid region `12:10206715-10207115`
[2016-04-15T06:30Z] 2016-04-14 23:30:14 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:30:14,085 - WARNING - Could not retrieve variants from source file in region 12:12814607-12815008. Error was invalid region `12:12814608-12815008`
[2016-04-15T06:30Z] 2016-04-14 23:30:14 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:30:14,712 - WARNING - Could not retrieve variants from source file in region 12:2936065-2936466. Error was invalid region `12:2936066-2936466`
[2016-04-15T06:30Z] 2016-04-14 23:30:14 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:30:14,803 - WARNING - Could not retrieve variants from source file in region 12:12239988-12248487. Error was invalid region `12:12239989-12248487`
[2016-04-15T06:30Z] 2016-04-14 23:30:16 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:30:16,597 - WARNING - Could not retrieve variants from source file in region 12:4387873-4388274. Error was invalid region `12:4387874-4388274`
[2016-04-15T06:30Z] 2016-04-14 23:30:18 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:30:18,266 - WARNING - Could not retrieve variants from source file in region 12:4553121-4554738. Error was invalid region `12:4553122-4554738`
[2016-04-15T06:30Z] 2016-04-14 23:30:18 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:30:18,707 - WARNING - Could not retrieve variants from source file in region 12:2720926-2721327. Error was invalid region `12:2720927-2721327`
[2016-04-15T06:30Z] 2016-04-14 23:30:18 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:30:18,709 - WARNING - Could not retrieve variants from source file in region 12:10461841-10462242. Error was invalid region `12:10461842-10462242`
[2016-04-15T06:30Z] 2016-04-14 23:30:20 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:30:20,362 - WARNING - Could not retrieve variants from source file in region 12:10206714-10207115. Error was invalid region `12:10206715-10207115`
[2016-04-15T06:30Z] 2016-04-14 23:30:20 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:30:20,971 - WARNING - Could not retrieve variants from source file in region 12:2936065-2936466. Error was invalid region `12:2936066-2936466`
[2016-04-15T06:30Z] 2016-04-14 23:30:22 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:30:22,056 - WARNING - Could not retrieve variants from source file in region 12:4387873-4388274. Error was invalid region `12:4387874-4388274`
[2016-04-15T06:30Z] 2016-04-14 23:30:23 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:30:23,535 - WARNING - Could not retrieve variants from source file in region 12:4553121-4554738. Error was invalid region `12:4553122-4554738`
[2016-04-15T06:30Z] 2016-04-14 23:30:24 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:30:24,345 - WARNING - Could not retrieve variants from source file in region 12:10461841-10462242. Error was invalid region `12:10461842-10462242`
[2016-04-15T06:30Z] 2016-04-14 23:30:26 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:30:26,607 - WARNING - Could not retrieve variants from source file in region 12:10206714-10207115. Error was invalid region `12:10206715-10207115`
[2016-04-15T06:30Z] 2016-04-14 23:30:29 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:30:29,300 - WARNING - Could not retrieve variants from source file in region 12:12630135-12633394. Error was invalid region `12:12630136-12633394`
[2016-04-15T06:30Z] 2016-04-14 23:30:36 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:30:36,339 - WARNING - Could not retrieve variants from source file in region 12:3787934-3788450. Error was invalid region `12:3787935-3788450`
[2016-04-15T06:30Z] 2016-04-14 23:30:38 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:30:38,872 - WARNING - Could not retrieve variants from source file in region 12:8327672-8330023. Error was invalid region `12:8327673-8330023`
[2016-04-15T06:30Z] 2016-04-14 23:30:39 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:30:39,489 - WARNING - Could not retrieve variants from source file in region 12:13764563-13764964. Error was invalid region `12:13764564-13764964`
[2016-04-15T06:30Z] 2016-04-14 23:30:39 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:30:39,654 - WARNING - Could not retrieve variants from source file in region 12:1739114-1739515. Error was invalid region `12:1739115-1739515`
[2016-04-15T06:30Z] 2016-04-14 23:30:39 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:30:39,715 - WARNING - Could not retrieve variants from source file in region 12:3701253-3701654. Error was invalid region `12:3701254-3701654`
[2016-04-15T06:30Z] 2016-04-14 23:30:40 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:30:40,120 - WARNING - Could not retrieve variants from source file in region 12:10137346-10170351. Error was invalid region `12:10137347-10170351`
[2016-04-15T06:30Z] 2016-04-14 23:30:40 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:30:40,277 - WARNING - Could not retrieve variants from source file in region 12:11991957-11992358. Error was invalid region `12:11991958-11992358`
[2016-04-15T06:30Z] 2016-04-14 23:30:40 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:30:40,640 - WARNING - Could not retrieve variants from source file in region 12:2905156-2905557. Error was invalid region `12:2905157-2905557`
[2016-04-15T06:30Z] 2016-04-14 23:30:41 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:30:41,180 - WARNING - Could not retrieve variants from source file in region 12:13366293-13366694. Error was invalid region `12:13366294-13366694`
[2016-04-15T06:30Z] 2016-04-14 23:30:41 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:30:41,947 - WARNING - Could not retrieve variants from source file in region 12:7893845-7918126. Error was invalid region `12:7893846-7918126`
[2016-04-15T06:30Z] 2016-04-14 23:30:44 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:30:44,714 - WARNING - Could not retrieve variants from source file in region 12:8327672-8330023. Error was invalid region `12:8327673-8330023`
[2016-04-15T06:30Z] 2016-04-14 23:30:45 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:30:45,465 - WARNING - Could not retrieve variants from source file in region 12:2694427-2694828. Error was invalid region `12:2694428-2694828`
[2016-04-15T06:30Z] 2016-04-14 23:30:46 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:30:46,391 - WARNING - Could not retrieve variants from source file in region 12:8374559-8383379. Error was invalid region `12:8374560-8383379`
[2016-04-15T06:30Z] 2016-04-14 23:30:46 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:30:46,425 - WARNING - Could not retrieve variants from source file in region 12:1739114-1739515. Error was invalid region `12:1739115-1739515`
[2016-04-15T06:30Z] 2016-04-14 23:30:46 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:30:46,856 - WARNING - Could not retrieve variants from source file in region 12:11991957-11992358. Error was invalid region `12:11991958-11992358`
[2016-04-15T06:30Z] 2016-04-14 23:30:47 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:30:47,103 - WARNING - Could not retrieve variants from source file in region 12:2905156-2905557. Error was invalid region `12:2905157-2905557`
[2016-04-15T06:30Z] 2016-04-14 23:30:47 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:30:47,119 - WARNING - Could not retrieve variants from source file in region 12:3787934-3788450. Error was invalid region `12:3787935-3788450`
[2016-04-15T06:30Z] 2016-04-14 23:30:47 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:30:47,384 - WARNING - Could not retrieve variants from source file in region 12:11091221-11091883. Error was invalid region `12:11091222-11091883`
[2016-04-15T06:30Z] 2016-04-14 23:30:52 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:30:52,472 - WARNING - Could not retrieve variants from source file in region 12:3701253-3701654. Error was invalid region `12:3701254-3701654`
[2016-04-15T06:30Z] 2016-04-14 23:30:52 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:30:52,721 - WARNING - Could not retrieve variants from source file in region 12:1739114-1739515. Error was invalid region `12:1739115-1739515`
[2016-04-15T06:30Z] 2016-04-14 23:30:54 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:30:54,109 - WARNING - Could not retrieve variants from source file in region 12:7893845-7918126. Error was invalid region `12:7893846-7918126`
[2016-04-15T06:30Z] 2016-04-14 23:30:54 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:30:54,410 - WARNING - Could not retrieve variants from source file in region 12:11091221-11091883. Error was invalid region `12:11091222-11091883`
[2016-04-15T06:30Z] 2016-04-14 23:30:56 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:30:56,378 - WARNING - Could not retrieve variants from source file in region 12:12483064-12510287. Error was invalid region `12:12483065-12510287`
[2016-04-15T06:31Z] 2016-04-14 23:31:01 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:31:01,493 - WARNING - Could not retrieve variants from source file in region 12:13214326-13221796. Error was invalid region `12:13214327-13221796`
[2016-04-15T06:31Z] 2016-04-14 23:31:01 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:31:01,901 - WARNING - Could not retrieve variants from source file in region 12:13102394-13102795. Error was invalid region `12:13102395-13102795`
[2016-04-15T06:31Z] 2016-04-14 23:31:02 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:31:02,797 - WARNING - Could not retrieve variants from source file in region 12:11545981-11546382. Error was invalid region `12:11545982-11546382`
[2016-04-15T06:31Z] 2016-04-14 23:31:04 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:31:04,511 - WARNING - Could not retrieve variants from source file in region 12:7585036-7586161. Error was invalid region `12:7585037-7586161`
[2016-04-15T06:31Z] 2016-04-14 23:31:05 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:31:05,890 - WARNING - Could not retrieve variants from source file in region 12:12483064-12510287. Error was invalid region `12:12483065-12510287`
[2016-04-15T06:31Z] 2016-04-14 23:31:06 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:31:06,319 - WARNING - Could not retrieve variants from source file in region 12:13214326-13221796. Error was invalid region `12:13214327-13221796`
[2016-04-15T06:31Z] 2016-04-14 23:31:07 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:31:07,640 - WARNING - Could not retrieve variants from source file in region 12:11060911-11061312. Error was invalid region `12:11060912-11061312`
[2016-04-15T06:31Z] 2016-04-14 23:31:07 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:31:07,716 - WARNING - Could not retrieve variants from source file in region 12:7803435-7805426. Error was invalid region `12:7803436-7805426`
[2016-04-15T06:31Z] 2016-04-14 23:31:07 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:31:07,964 - WARNING - Could not retrieve variants from source file in region 12:11545981-11546382. Error was invalid region `12:11545982-11546382`
[2016-04-15T06:31Z] 2016-04-14 23:31:08 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:31:08,174 - WARNING - Could not retrieve variants from source file in region 12:6344389-6345389. Error was invalid region `12:6344390-6345389`
[2016-04-15T06:31Z] 2016-04-14 23:31:08 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:31:08,277 - WARNING - Could not retrieve variants from source file in region 12:2557975-2558376. Error was invalid region `12:2557976-2558376`
[2016-04-15T06:31Z] 2016-04-14 23:31:09 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:31:09,165 - WARNING - Could not retrieve variants from source file in region 12:7585036-7586161. Error was invalid region `12:7585037-7586161`
[2016-04-15T06:31Z] 2016-04-14 23:31:11 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:31:11,009 - WARNING - Could not retrieve variants from source file in region 12:13214326-13221796. Error was invalid region `12:13214327-13221796`
[2016-04-15T06:31Z] 2016-04-14 23:31:12 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:31:12,145 - WARNING - Could not retrieve variants from source file in region 12:12333795-12337156. Error was invalid region `12:12333796-12337156`
[2016-04-15T06:31Z] 2016-04-14 23:31:12 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:31:12,387 - WARNING - Could not retrieve variants from source file in region 12:1702350-1702751. Error was invalid region `12:1702351-1702751`
[2016-04-15T06:31Z] 2016-04-14 23:31:13 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:31:13,088 - WARNING - Could not retrieve variants from source file in region 12:11545981-11546382. Error was invalid region `12:11545982-11546382`
[2016-04-15T06:31Z] 2016-04-14 23:31:13 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:31:13,106 - WARNING - Could not retrieve variants from source file in region 12:6344389-6345389. Error was invalid region `12:6344390-6345389`
[2016-04-15T06:31Z] 2016-04-14 23:31:17 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:31:17,288 - WARNING - Could not retrieve variants from source file in region 12:12333795-12337156. Error was invalid region `12:12333796-12337156`
[2016-04-15T06:31Z] 2016-04-14 23:31:17 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:31:17,710 - WARNING - Could not retrieve variants from source file in region 12:7803435-7805426. Error was invalid region `12:7803436-7805426`
[2016-04-15T06:31Z] 2016-04-14 23:31:17 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:31:17,963 - WARNING - Could not retrieve variants from source file in region 12:6344389-6345389. Error was invalid region `12:6344390-6345389`
[2016-04-15T06:31Z] 2016-04-14 23:31:18 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:31:18,402 - WARNING - Could not retrieve variants from source file in region 12:11060911-11061312. Error was invalid region `12:11060912-11061312`
[2016-04-15T06:31Z] 2016-04-14 23:31:19 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:31:19,066 - WARNING - Could not retrieve variants from source file in region 12:12301687-12302088. Error was invalid region `12:12301688-12302088`
[2016-04-15T06:31Z] 2016-04-14 23:31:20 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:31:20,344 - WARNING - Could not retrieve variants from source file in region 12:11461081-11463512. Error was invalid region `12:11461082-11463512`
[2016-04-15T06:31Z] 2016-04-14 23:31:24 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:31:24,709 - WARNING - Could not retrieve variants from source file in region 12:12301687-12302088. Error was invalid region `12:12301688-12302088`
[2016-04-15T06:31Z] 2016-04-14 23:31:26 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:31:26,358 - WARNING - Could not retrieve variants from source file in region 12:862778-863179. Error was invalid region `12:862779-863179`
[2016-04-15T06:31Z] 2016-04-14 23:31:26 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:31:26,484 - WARNING - Could not retrieve variants from source file in region 12:6619073-6640867. Error was invalid region `12:6619074-6640867`
[2016-04-15T06:31Z] 2016-04-14 23:31:26 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:31:26,494 - WARNING - Could not retrieve variants from source file in region 12:12301687-12302088. Error was invalid region `12:12301688-12302088`
[2016-04-15T06:31Z] 2016-04-14 23:31:27 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:31:27,382 - WARNING - Could not retrieve variants from source file in region 12:7528260-7551240. Error was invalid region `12:7528261-7551240`
[2016-04-15T06:31Z] 2016-04-14 23:31:28 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:31:28,034 - WARNING - Could not retrieve variants from source file in region 12:6839998-6840561. Error was invalid region `12:6839999-6840561`
[2016-04-15T06:31Z] 2016-04-14 23:31:31 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:31:31,174 - WARNING - Could not retrieve variants from source file in region 12:862778-863179. Error was invalid region `12:862779-863179`
[2016-04-15T06:31Z] 2016-04-14 23:31:31 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:31:31,215 - WARNING - Could not retrieve variants from source file in region 12:939091-939492. Error was invalid region `12:939092-939492`
[2016-04-15T06:31Z] 2016-04-14 23:31:32 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:31:32,307 - WARNING - Could not retrieve variants from source file in region 12:6839998-6840561. Error was invalid region `12:6839999-6840561`
[2016-04-15T06:31Z] 2016-04-14 23:31:35 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:31:35,609 - WARNING - Could not retrieve variants from source file in region 12:7635752-7655327. Error was invalid region `12:7635753-7655327`
[2016-04-15T06:31Z] 2016-04-14 23:31:35 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:31:35,732 - WARNING - Could not retrieve variants from source file in region 12:862778-863179. Error was invalid region `12:862779-863179`
[2016-04-15T06:31Z] 2016-04-14 23:31:35 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:31:35,773 - WARNING - Could not retrieve variants from source file in region 12:939091-939492. Error was invalid region `12:939092-939492`
[2016-04-15T06:31Z] 2016-04-14 23:31:36 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:31:36,196 - WARNING - Could not retrieve variants from source file in region 12:6127732-6172392. Error was invalid region `12:6127733-6172392`
[2016-04-15T06:31Z] 2016-04-14 23:31:36 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:31:36,490 - WARNING - Could not retrieve variants from source file in region 12:11034769-11035170. Error was invalid region `12:11034770-11035170`
[2016-04-15T06:31Z] 2016-04-14 23:31:38 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:31:38,799 - WARNING - Could not retrieve variants from source file in region 12:10954047-10999970. Error was invalid region `12:10954048-10999970`
[2016-04-15T06:31Z] 2016-04-14 23:31:40 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:31:40,390 - WARNING - Could not retrieve variants from source file in region 12:939091-939492. Error was invalid region `12:939092-939492`
[2016-04-15T06:31Z] 2016-04-14 23:31:48 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:31:48,002 - WARNING - Could not retrieve variants from source file in region 12:11420122-11421283. Error was invalid region `12:11420123-11421283`
[2016-04-15T06:31Z] 2016-04-14 23:31:48 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:31:48,042 - WARNING - Could not retrieve variants from source file in region 12:10954047-10999970. Error was invalid region `12:10954048-10999970`
[2016-04-15T06:31Z] 2016-04-14 23:31:49 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:31:49,168 - WARNING - Could not retrieve variants from source file in region 12:719452-719871. Error was invalid region `12:719453-719871`
[2016-04-15T06:31Z] 2016-04-14 23:31:49 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:31:49,646 - WARNING - Could not retrieve variants from source file in region 12:7463030-7463431. Error was invalid region `12:7463031-7463431`
[2016-04-15T06:31Z] 2016-04-14 23:31:49 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:31:49,740 - WARNING - Could not retrieve variants from source file in region 12:6776858-6777265. Error was invalid region `12:6776859-6777265`
[2016-04-15T06:31Z] 2016-04-14 23:31:52 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:31:52,293 - WARNING - Could not retrieve variants from source file in region 12:11420122-11421283. Error was invalid region `12:11420123-11421283`
[2016-04-15T06:31Z] 2016-04-14 23:31:53 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:31:53,118 - WARNING - Could not retrieve variants from source file in region 12:11285877-11286980. Error was invalid region `12:11285878-11286980`
[2016-04-15T06:31Z] 2016-04-14 23:31:53 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:31:53,518 - WARNING - Could not retrieve variants from source file in region 12:719452-719871. Error was invalid region `12:719453-719871`
[2016-04-15T06:31Z] 2016-04-14 23:31:54 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:31:54,188 - WARNING - Could not retrieve variants from source file in region 12:6776858-6777265. Error was invalid region `12:6776859-6777265`
[2016-04-15T06:31Z] 2016-04-14 23:31:54 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:31:54,251 - WARNING - Could not retrieve variants from source file in region 12:7463030-7463431. Error was invalid region `12:7463031-7463431`
[2016-04-15T06:31Z] 2016-04-14 23:31:54 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:31:54,624 - WARNING - Could not retrieve variants from source file in region 12:11323783-11339210. Error was invalid region `12:11323784-11339210`
[2016-04-15T06:31Z] 2016-04-14 23:31:55 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:31:55,824 - WARNING - Could not retrieve variants from source file in region 12:7342555-7342956. Error was invalid region `12:7342556-7342956`
[2016-04-15T06:31Z] 2016-04-14 23:31:57 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:31:57,708 - WARNING - Could not retrieve variants from source file in region 12:11285877-11286980. Error was invalid region `12:11285878-11286980`
[2016-04-15T06:31Z] 2016-04-14 23:31:57 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:31:57,755 - WARNING - Could not retrieve variants from source file in region 12:406081-427789. Error was invalid region `12:406082-427789`
[2016-04-15T06:31Z] 2016-04-14 23:31:58 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:31:58,367 - WARNING - Could not retrieve variants from source file in region 12:6090789-6094974. Error was invalid region `12:6090790-6094974`
[2016-04-15T06:31Z] 2016-04-14 23:31:58 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:31:58,690 - WARNING - Could not retrieve variants from source file in region 12:719452-719871. Error was invalid region `12:719453-719871`
[2016-04-15T06:31Z] 2016-04-14 23:31:59 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:31:59,039 - WARNING - Could not retrieve variants from source file in region 12:7463030-7463431. Error was invalid region `12:7463031-7463431`
[2016-04-15T06:31Z] 2016-04-14 23:31:59 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:31:59,123 - WARNING - Could not retrieve variants from source file in region 12:6776858-6777265. Error was invalid region `12:6776859-6777265`
[2016-04-15T06:31Z] 2016-04-14 23:31:59 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:31:59,456 - WARNING - Could not retrieve variants from source file in region 12:6554417-6575234. Error was invalid region `12:6554418-6575234`
[2016-04-15T06:31Z] 2016-04-14 23:31:59 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:31:59,923 - WARNING - Could not retrieve variants from source file in region 12:5916299-5916700. Error was invalid region `12:5916300-5916700`
[2016-04-15T06:32Z] 2016-04-14 23:32:02 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:32:02,235 - WARNING - Could not retrieve variants from source file in region 12:11285877-11286980. Error was invalid region `12:11285878-11286980`
[2016-04-15T06:32Z] 2016-04-14 23:32:02 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:32:02,761 - WARNING - Could not retrieve variants from source file in region 12:6090789-6094974. Error was invalid region `12:6090790-6094974`
[2016-04-15T06:32Z] 2016-04-14 23:32:05 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:32:05,334 - WARNING - Could not retrieve variants from source file in region 12:6030091-6054585. Error was invalid region `12:6030092-6054585`
[2016-04-15T06:32Z] 2016-04-14 23:32:10 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:32:10,633 - WARNING - Could not retrieve variants from source file in region 12:657193-675529. Error was invalid region `12:657194-675529`
[2016-04-15T06:32Z] 2016-04-14 23:32:12 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:32:12,130 - WARNING - Could not retrieve variants from source file in region 12:6707315-6711337. Error was invalid region `12:6707316-6711337`
[2016-04-15T06:32Z] 2016-04-14 23:32:12 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:32:12,151 - WARNING - Could not retrieve variants from source file in region 12:7170125-7170526. Error was invalid region `12:7170126-7170526`
[2016-04-15T06:32Z] 2016-04-14 23:32:14 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:32:14,151 - WARNING - Could not retrieve variants from source file in region 12:311738-319315. Error was invalid region `12:311739-319315`
[2016-04-15T06:32Z] 2016-04-14 23:32:14 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:32:14,381 - WARNING - Could not retrieve variants from source file in region 12:547472-547873. Error was invalid region `12:547473-547873`
[2016-04-15T06:32Z] 2016-04-14 23:32:16 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:32:16,764 - WARNING - Could not retrieve variants from source file in region 12:6484498-6495465. Error was invalid region `12:6484499-6495465`
[2016-04-15T06:32Z] 2016-04-14 23:32:17 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:32:17,172 - WARNING - Could not retrieve variants from source file in region 12:7170125-7170526. Error was invalid region `12:7170126-7170526`
[2016-04-15T06:32Z] 2016-04-14 23:32:18 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:32:18,798 - WARNING - Could not retrieve variants from source file in region 12:311738-319315. Error was invalid region `12:311739-319315`
[2016-04-15T06:32Z] 2016-04-14 23:32:18 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:32:18,854 - WARNING - Could not retrieve variants from source file in region 12:5603421-5603822. Error was invalid region `12:5603422-5603822`
[2016-04-15T06:32Z] 2016-04-14 23:32:18 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:32:18,877 - WARNING - Could not retrieve variants from source file in region 12:547472-547873. Error was invalid region `12:547473-547873`
[2016-04-15T06:32Z] 2016-04-14 23:32:18 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:32:18,914 - WARNING - Could not retrieve variants from source file in region 12:283810-284248. Error was invalid region `12:283811-284248`
[2016-04-15T06:32Z] 2016-04-14 23:32:19 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:32:19,640 - WARNING - Could not retrieve variants from source file in region 12:5674543-5674944. Error was invalid region `12:5674544-5674944`
[2016-04-15T06:32Z] 2016-04-14 23:32:21 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:32:21,169 - WARNING - Could not retrieve variants from source file in region 12:6484498-6495465. Error was invalid region `12:6484499-6495465`
[2016-04-15T06:32Z] 2016-04-14 23:32:21 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:32:21,319 - WARNING - Could not retrieve variants from source file in region 12:7021874-7086776. Error was invalid region `12:7021875-7086776`
[2016-04-15T06:32Z] 2016-04-14 23:32:21 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:32:21,399 - WARNING - Could not retrieve variants from source file in region 12:6707315-6711337. Error was invalid region `12:6707316-6711337`
[2016-04-15T06:32Z] 2016-04-14 23:32:23 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:32:23,461 - WARNING - Could not retrieve variants from source file in region 12:283810-284248. Error was invalid region `12:283811-284248`
[2016-04-15T06:32Z] 2016-04-14 23:32:23 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:32:23,481 - WARNING - Could not retrieve variants from source file in region 12:547472-547873. Error was invalid region `12:547473-547873`
[2016-04-15T06:32Z] 2016-04-14 23:32:23 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:32:23,944 - WARNING - Could not retrieve variants from source file in region 12:5674543-5674944. Error was invalid region `12:5674544-5674944`
[2016-04-15T06:32Z] 2016-04-14 23:32:31 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:32:31,970 - WARNING - Could not retrieve variants from source file in region 12:6421284-6457252. Error was invalid region `12:6421285-6457252`
[2016-04-15T06:32Z] 2016-04-14 23:32:31 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:32:31,985 - WARNING - Could not retrieve variants from source file in region 12:6421284-6457252. Error was invalid region `12:6421285-6457252`
[2016-04-15T06:32Z] 2016-04-14 23:32:32 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:32:32,006 - WARNING - Could not retrieve variants from source file in region 12:6421284-6457252. Error was invalid region `12:6421285-6457252`
[2016-04-15T06:32Z] 2016-04-14 23:32:33 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:32:33,560 - WARNING - Could not retrieve variants from source file in region 12:5154251-5154652. Error was invalid region `12:5154252-5154652`
[2016-04-15T06:32Z] 2016-04-14 23:32:33 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:32:33,564 - WARNING - Could not retrieve variants from source file in region 12:5154251-5154652. Error was invalid region `12:5154252-5154652`
[2016-04-15T06:32Z] 2016-04-14 23:32:34 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:32:34,008 - WARNING - Could not retrieve variants from source file in region 12:5021017-5022174. Error was invalid region `12:5021018-5022174`
[2016-04-15T06:32Z] 2016-04-14 23:32:35 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:32:35,326 - WARNING - Could not retrieve variants from source file in region 12:175928-176329. Error was invalid region `12:175929-176329`
[2016-04-15T06:32Z] 2016-04-14 23:32:35 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:32:35,355 - WARNING - Could not retrieve variants from source file in region 12:5021017-5022174. Error was invalid region `12:5021018-5022174`
[2016-04-15T06:32Z] 2016-04-14 23:32:36 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:32:36,726 - WARNING - Could not retrieve variants from source file in region 12:5154251-5154652. Error was invalid region `12:5154252-5154652`
[2016-04-15T06:32Z] 2016-04-14 23:32:37 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:32:37,038 - WARNING - Could not retrieve variants from source file in region 12:175928-176329. Error was invalid region `12:175929-176329`
[2016-04-15T06:32Z] 2016-04-14 23:32:37 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:32:37,184 - WARNING - Could not retrieve variants from source file in region 12:5021017-5022174. Error was invalid region `12:5021018-5022174`
[2016-04-15T06:32Z] ['bcbio-variation-recall', 'square', '-Xms750m', '-Xmx7280m', '-XX:+UseSerialGC', '-c', 16, '-r', u'12:15650179-31231471', '--caller', 'platypus', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/12/Batch1-12_15650178_31231471.vcf.gz', '/mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/12/Batch1-12_15650178_31231471.vcf-inputs.txt'] in region: 12:15650179-31231471
[2016-04-15T06:32Z] 2016-04-14 23:32:51 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:32:51,125 - WARNING - Could not retrieve variants from source file in region 12:25311278-25311679. Error was invalid region `12:25311279-25311679`
[2016-04-15T06:32Z] 2016-04-14 23:32:51 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:32:51,805 - WARNING - Could not retrieve variants from source file in region 12:24970755-24987319. Error was invalid region `12:24970756-24987319`
[2016-04-15T06:32Z] 2016-04-14 23:32:52 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:32:52,457 - WARNING - Could not retrieve variants from source file in region 12:28115846-28116301. Error was invalid region `12:28115847-28116301`
[2016-04-15T06:32Z] 2016-04-14 23:32:53 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:32:53,370 - WARNING - Could not retrieve variants from source file in region 12:29598081-29642763. Error was invalid region `12:29598082-29642763`
[2016-04-15T06:32Z] 2016-04-14 23:32:53 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:32:53,522 - WARNING - Could not retrieve variants from source file in region 12:28605215-28605616. Error was invalid region `12:28605216-28605616`
[2016-04-15T06:32Z] 2016-04-14 23:32:54 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:32:54,232 - WARNING - Could not retrieve variants from source file in region 12:22602585-22602986. Error was invalid region `12:22602586-22602986`
[2016-04-15T06:32Z] 2016-04-14 23:32:54 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:32:54,611 - WARNING - Could not retrieve variants from source file in region 12:22813825-22814226. Error was invalid region `12:22813826-22814226`
[2016-04-15T06:32Z] 2016-04-14 23:32:54 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:32:54,709 - WARNING - Could not retrieve variants from source file in region 12:22062904-22063305. Error was invalid region `12:22062905-22063305`
[2016-04-15T06:32Z] 2016-04-14 23:32:55 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:32:55,312 - WARNING - Could not retrieve variants from source file in region 12:29936402-29936803. Error was invalid region `12:29936403-29936803`
[2016-04-15T06:32Z] 2016-04-14 23:32:55 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:32:55,315 - WARNING - Could not retrieve variants from source file in region 12:26221947-26225594. Error was invalid region `12:26221948-26225594`
[2016-04-15T06:32Z] 2016-04-14 23:32:55 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:32:55,441 - WARNING - Could not retrieve variants from source file in region 12:31135267-31135769. Error was invalid region `12:31135268-31135769`
[2016-04-15T06:32Z] 2016-04-14 23:32:55 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:32:55,711 - WARNING - Could not retrieve variants from source file in region 12:27627594-27627995. Error was invalid region `12:27627595-27627995`
[2016-04-15T06:32Z] 2016-04-14 23:32:58 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:32:58,113 - WARNING - Could not retrieve variants from source file in region 12:30867791-30906548. Error was invalid region `12:30867792-30906548`
[2016-04-15T06:33Z] 2016-04-14 23:33:00 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:33:00,568 - WARNING - Could not retrieve variants from source file in region 12:22602585-22602986. Error was invalid region `12:22602586-22602986`
[2016-04-15T06:33Z] 2016-04-14 23:33:01 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:33:01,508 - WARNING - Could not retrieve variants from source file in region 12:22813825-22814226. Error was invalid region `12:22813826-22814226`
[2016-04-15T06:33Z] 2016-04-14 23:33:01 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:33:01,610 - WARNING - Could not retrieve variants from source file in region 12:22062904-22063305. Error was invalid region `12:22062905-22063305`
[2016-04-15T06:33Z] 2016-04-14 23:33:02 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:33:02,261 - WARNING - Could not retrieve variants from source file in region 12:27915507-27915908. Error was invalid region `12:27915508-27915908`
[2016-04-15T06:33Z] 2016-04-14 23:33:02 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:33:02,473 - WARNING - Could not retrieve variants from source file in region 12:27627594-27627995. Error was invalid region `12:27627595-27627995`
[2016-04-15T06:33Z] 2016-04-14 23:33:02 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:33:02,889 - WARNING - Could not retrieve variants from source file in region 12:31135267-31135769. Error was invalid region `12:31135268-31135769`
[2016-04-15T06:33Z] 2016-04-14 23:33:02 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:33:02,892 - WARNING - Could not retrieve variants from source file in region 12:29936402-29936803. Error was invalid region `12:29936403-29936803`
[2016-04-15T06:33Z] 2016-04-14 23:33:03 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:33:03,121 - WARNING - Could not retrieve variants from source file in region 12:25311278-25311679. Error was invalid region `12:25311279-25311679`
[2016-04-15T06:33Z] 2016-04-14 23:33:07 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:33:07,305 - WARNING - Could not retrieve variants from source file in region 12:28605215-28605616. Error was invalid region `12:28605216-28605616`
[2016-04-15T06:33Z] 2016-04-14 23:33:07 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:33:07,330 - WARNING - Could not retrieve variants from source file in region 12:22602585-22602986. Error was invalid region `12:22602586-22602986`
[2016-04-15T06:33Z] 2016-04-14 23:33:08 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:33:08,651 - WARNING - Could not retrieve variants from source file in region 12:22813825-22814226. Error was invalid region `12:22813826-22814226`
[2016-04-15T06:33Z] 2016-04-14 23:33:09 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:33:09,072 - WARNING - Could not retrieve variants from source file in region 12:22062904-22063305. Error was invalid region `12:22062905-22063305`
[2016-04-15T06:33Z] 2016-04-14 23:33:10 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:33:10,316 - WARNING - Could not retrieve variants from source file in region 12:27627594-27627995. Error was invalid region `12:27627595-27627995`
[2016-04-15T06:33Z] 2016-04-14 23:33:11 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:33:11,050 - WARNING - Could not retrieve variants from source file in region 12:29936402-29936803. Error was invalid region `12:29936403-29936803`
[2016-04-15T06:33Z] 2016-04-14 23:33:11 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:33:11,059 - WARNING - Could not retrieve variants from source file in region 12:31135267-31135769. Error was invalid region `12:31135268-31135769`
[2016-04-15T06:33Z] 2016-04-14 23:33:21 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:33:21,884 - WARNING - Could not retrieve variants from source file in region 12:27953056-27953457. Error was invalid region `12:27953057-27953457`
[2016-04-15T06:33Z] 2016-04-14 23:33:21 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:33:21,963 - WARNING - Could not retrieve variants from source file in region 12:26647881-26648282. Error was invalid region `12:26647882-26648282`
[2016-04-15T06:33Z] 2016-04-14 23:33:23 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:33:23,263 - WARNING - Could not retrieve variants from source file in region 12:29423249-29423650. Error was invalid region `12:29423250-29423650`
[2016-04-15T06:33Z] 2016-04-14 23:33:23 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:33:23,480 - WARNING - Could not retrieve variants from source file in region 12:30823760-30824161. Error was invalid region `12:30823761-30824161`
[2016-04-15T06:33Z] 2016-04-14 23:33:23 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:33:23,921 - WARNING - Could not retrieve variants from source file in region 12:22354710-22355111. Error was invalid region `12:22354711-22355111`
[2016-04-15T06:33Z] 2016-04-14 23:33:24 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:33:24,175 - WARNING - Could not retrieve variants from source file in region 12:21796818-21797219. Error was invalid region `12:21796819-21797219`
[2016-04-15T06:33Z] 2016-04-14 23:33:24 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:33:24,834 - WARNING - Could not retrieve variants from source file in region 12:28457407-28457808. Error was invalid region `12:28457408-28457808`
[2016-04-15T06:33Z] 2016-04-14 23:33:24 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:33:24,926 - WARNING - Could not retrieve variants from source file in region 12:27470655-27471056. Error was invalid region `12:27470656-27471056`
[2016-04-15T06:33Z] 2016-04-14 23:33:25 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:33:25,590 - WARNING - Could not retrieve variants from source file in region 12:25705923-25706324. Error was invalid region `12:25705924-25706324`
[2016-04-15T06:33Z] 2016-04-14 23:33:28 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:33:28,737 - WARNING - Could not retrieve variants from source file in region 12:25242384-25261925. Error was invalid region `12:25242385-25261925`
[2016-04-15T06:33Z] 2016-04-14 23:33:29 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:33:29,751 - WARNING - Could not retrieve variants from source file in region 12:29423249-29423650. Error was invalid region `12:29423250-29423650`
[2016-04-15T06:33Z] 2016-04-14 23:33:29 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:33:29,925 - WARNING - Could not retrieve variants from source file in region 12:30823760-30824161. Error was invalid region `12:30823761-30824161`
[2016-04-15T06:33Z] 2016-04-14 23:33:30 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:33:30,091 - WARNING - Could not retrieve variants from source file in region 12:21796818-21797219. Error was invalid region `12:21796819-21797219`
[2016-04-15T06:33Z] 2016-04-14 23:33:30 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:33:30,338 - WARNING - Could not retrieve variants from source file in region 12:21487333-21487734. Error was invalid region `12:21487334-21487734`
[2016-04-15T06:33Z] 2016-04-14 23:33:30 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:33:30,396 - WARNING - Could not retrieve variants from source file in region 12:27849584-27867917. Error was invalid region `12:27849585-27867917`
[2016-04-15T06:33Z] 2016-04-14 23:33:30 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:33:30,399 - WARNING - Could not retrieve variants from source file in region 12:22354710-22355111. Error was invalid region `12:22354711-22355111`
[2016-04-15T06:33Z] 2016-04-14 23:33:31 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:33:31,020 - WARNING - Could not retrieve variants from source file in region 12:28457407-28457808. Error was invalid region `12:28457408-28457808`
[2016-04-15T06:33Z] 2016-04-14 23:33:31 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:33:31,029 - WARNING - Could not retrieve variants from source file in region 12:27470655-27471056. Error was invalid region `12:27470656-27471056`
[2016-04-15T06:33Z] 2016-04-14 23:33:32 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:33:32,423 - WARNING - Could not retrieve variants from source file in region 12:26647881-26648282. Error was invalid region `12:26647882-26648282`
[2016-04-15T06:33Z] 2016-04-14 23:33:33 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:33:33,299 - WARNING - Could not retrieve variants from source file in region 12:25242384-25261925. Error was invalid region `12:25242385-25261925`
[2016-04-15T06:33Z] 2016-04-14 23:33:35 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:33:35,302 - WARNING - Could not retrieve variants from source file in region 12:29423249-29423650. Error was invalid region `12:29423250-29423650`
[2016-04-15T06:33Z] 2016-04-14 23:33:35 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:33:35,323 - WARNING - Could not retrieve variants from source file in region 12:21796818-21797219. Error was invalid region `12:21796819-21797219`
[2016-04-15T06:33Z] 2016-04-14 23:33:35 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:33:35,894 - WARNING - Could not retrieve variants from source file in region 12:22354710-22355111. Error was invalid region `12:22354711-22355111`
[2016-04-15T06:33Z] 2016-04-14 23:33:36 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:33:36,294 - WARNING - Could not retrieve variants from source file in region 12:28457407-28457808. Error was invalid region `12:28457408-28457808`
[2016-04-15T06:33Z] 2016-04-14 23:33:36 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:33:36,602 - WARNING - Could not retrieve variants from source file in region 12:27470655-27471056. Error was invalid region `12:27470656-27471056`
[2016-04-15T06:33Z] 2016-04-14 23:33:36 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:33:36,735 - WARNING - Could not retrieve variants from source file in region 12:25705923-25706324. Error was invalid region `12:25705924-25706324`
[2016-04-15T06:33Z] 2016-04-14 23:33:43 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:33:43,140 - WARNING - Could not retrieve variants from source file in region 12:25148544-25164556. Error was invalid region `12:25148545-25164556`
[2016-04-15T06:33Z] 2016-04-14 23:33:47 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:33:47,540 - WARNING - Could not retrieve variants from source file in region 12:26383623-26385801. Error was invalid region `12:26383624-26385801`
[2016-04-15T06:33Z] 2016-04-14 23:33:48 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:33:48,315 - WARNING - Could not retrieve variants from source file in region 12:21757603-21758004. Error was invalid region `12:21757604-21758004`
[2016-04-15T06:33Z] 2016-04-14 23:33:49 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:33:49,809 - WARNING - Could not retrieve variants from source file in region 12:27787810-27800936. Error was invalid region `12:27787811-27800936`
[2016-04-15T06:33Z] 2016-04-14 23:33:50 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:33:50,430 - WARNING - Could not retrieve variants from source file in region 12:27654687-27655088. Error was invalid region `12:27654688-27655088`
[2016-04-15T06:33Z] 2016-04-14 23:33:50 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:33:50,444 - WARNING - Could not retrieve variants from source file in region 12:27233989-27235571. Error was invalid region `12:27233990-27235571`
[2016-04-15T06:33Z] 2016-04-14 23:33:50 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:33:50,800 - WARNING - Could not retrieve variants from source file in region 12:18648846-18649247. Error was invalid region `12:18648847-18649247`
[2016-04-15T06:33Z] 2016-04-14 23:33:52 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:33:52,150 - WARNING - Could not retrieve variants from source file in region 12:25671548-25671949. Error was invalid region `12:25671549-25671949`
[2016-04-15T06:33Z] 2016-04-14 23:33:52 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:33:52,457 - WARNING - Could not retrieve variants from source file in region 12:21757603-21758004. Error was invalid region `12:21757604-21758004`
[2016-04-15T06:33Z] 2016-04-14 23:33:52 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:33:52,491 - WARNING - Could not retrieve variants from source file in region 12:20766348-20766749. Error was invalid region `12:20766349-20766749`
[2016-04-15T06:33Z] 2016-04-14 23:33:54 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:33:54,483 - WARNING - Could not retrieve variants from source file in region 12:27787810-27800936. Error was invalid region `12:27787811-27800936`
[2016-04-15T06:33Z] 2016-04-14 23:33:54 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:33:54,597 - WARNING - Could not retrieve variants from source file in region 12:21427741-21428264. Error was invalid region `12:21427742-21428264`
[2016-04-15T06:33Z] 2016-04-14 23:33:55 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:33:55,380 - WARNING - Could not retrieve variants from source file in region 12:27233989-27235571. Error was invalid region `12:27233990-27235571`
[2016-04-15T06:33Z] 2016-04-14 23:33:56 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:33:56,419 - WARNING - Could not retrieve variants from source file in region 12:27233989-27235571. Error was invalid region `12:27233990-27235571`
[2016-04-15T06:33Z] 2016-04-14 23:33:56 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:33:56,499 - WARNING - Could not retrieve variants from source file in region 12:20724777-20725178. Error was invalid region `12:20724778-20725178`
[2016-04-15T06:33Z] 2016-04-14 23:33:56 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:33:56,544 - WARNING - Could not retrieve variants from source file in region 12:18648846-18649247. Error was invalid region `12:18648847-18649247`
[2016-04-15T06:33Z] 2016-04-14 23:33:56 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:33:56,922 - WARNING - Could not retrieve variants from source file in region 12:27175429-27181989. Error was invalid region `12:27175430-27181989`
[2016-04-15T06:33Z] 2016-04-14 23:33:57 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:33:57,183 - WARNING - Could not retrieve variants from source file in region 12:21175924-21207579. Error was invalid region `12:21175925-21207579`
[2016-04-15T06:33Z] 2016-04-14 23:33:58 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:33:58,102 - WARNING - Could not retrieve variants from source file in region 12:25671548-25671949. Error was invalid region `12:25671549-25671949`
[2016-04-15T06:33Z] 2016-04-14 23:33:58 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:33:58,151 - WARNING - Could not retrieve variants from source file in region 12:21757603-21758004. Error was invalid region `12:21757604-21758004`
[2016-04-15T06:33Z] 2016-04-14 23:33:58 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:33:58,157 - WARNING - Could not retrieve variants from source file in region 12:20766348-20766749. Error was invalid region `12:20766349-20766749`
[2016-04-15T06:33Z] 2016-04-14 23:33:59 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:33:59,273 - WARNING - Could not retrieve variants from source file in region 12:27787810-27800936. Error was invalid region `12:27787811-27800936`
[2016-04-15T06:34Z] 2016-04-14 23:34:00 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:34:00,349 - WARNING - Could not retrieve variants from source file in region 12:21713191-21713592. Error was invalid region `12:21713192-21713592`
[2016-04-15T06:34Z] 2016-04-14 23:34:00 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:34:00,362 - WARNING - Could not retrieve variants from source file in region 12:27654687-27655088. Error was invalid region `12:27654688-27655088`
[2016-04-15T06:34Z] 2016-04-14 23:34:04 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:34:04,016 - WARNING - Could not retrieve variants from source file in region 12:18648846-18649247. Error was invalid region `12:18648847-18649247`
[2016-04-15T06:34Z] 2016-04-14 23:34:04 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:34:04,323 - WARNING - Could not retrieve variants from source file in region 12:27175429-27181989. Error was invalid region `12:27175430-27181989`
[2016-04-15T06:34Z] 2016-04-14 23:34:04 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:34:04,587 - WARNING - Could not retrieve variants from source file in region 12:20766348-20766749. Error was invalid region `12:20766349-20766749`
[2016-04-15T06:34Z] 2016-04-14 23:34:04 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:34:04,635 - WARNING - Could not retrieve variants from source file in region 12:25671548-25671949. Error was invalid region `12:25671549-25671949`
[2016-04-15T06:34Z] 2016-04-14 23:34:05 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:34:05,420 - WARNING - Could not retrieve variants from source file in region 12:21713191-21713592. Error was invalid region `12:21713192-21713592`
[2016-04-15T06:34Z] 2016-04-14 23:34:05 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:34:05,983 - WARNING - Could not retrieve variants from source file in region 12:16425445-16430474. Error was invalid region `12:16425446-16430474`
[2016-04-15T06:34Z] 2016-04-14 23:34:07 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:34:07,132 - WARNING - Could not retrieve variants from source file in region 12:20724777-20725178. Error was invalid region `12:20724778-20725178`
[2016-04-15T06:34Z] 2016-04-14 23:34:08 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:34:08,834 - WARNING - Could not retrieve variants from source file in region 12:21713191-21713592. Error was invalid region `12:21713192-21713592`
[2016-04-15T06:34Z] 2016-04-14 23:34:09 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:34:09,767 - WARNING - Could not retrieve variants from source file in region 12:27175429-27181989. Error was invalid region `12:27175430-27181989`
[2016-04-15T06:34Z] 2016-04-14 23:34:10 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:34:10,660 - WARNING - Could not retrieve variants from source file in region 12:26868078-26868512. Error was invalid region `12:26868079-26868512`
[2016-04-15T06:34Z] 2016-04-14 23:34:10 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:34:10,907 - WARNING - Could not retrieve variants from source file in region 12:16425445-16430474. Error was invalid region `12:16425446-16430474`
[2016-04-15T06:34Z] 2016-04-14 23:34:14 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:34:14,029 - WARNING - Could not retrieve variants from source file in region 12:26275344-26275745. Error was invalid region `12:26275345-26275745`
[2016-04-15T06:34Z] 2016-04-14 23:34:15 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:34:15,860 - WARNING - Could not retrieve variants from source file in region 12:16425445-16430474. Error was invalid region `12:16425446-16430474`
[2016-04-15T06:34Z] 2016-04-14 23:34:16 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:34:16,905 - WARNING - Could not retrieve variants from source file in region 12:19593305-19593706. Error was invalid region `12:19593306-19593706`
[2016-04-15T06:34Z] 2016-04-14 23:34:17 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:34:17,205 - WARNING - Could not retrieve variants from source file in region 12:18234045-18234446. Error was invalid region `12:18234046-18234446`
[2016-04-15T06:34Z] 2016-04-14 23:34:18 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:34:18,187 - WARNING - Could not retrieve variants from source file in region 12:26275344-26275745. Error was invalid region `12:26275345-26275745`
[2016-04-15T06:34Z] 2016-04-14 23:34:19 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:34:19,690 - WARNING - Could not retrieve variants from source file in region 12:20522041-20522442. Error was invalid region `12:20522042-20522442`
[2016-04-15T06:34Z] 2016-04-14 23:34:20 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:34:20,969 - WARNING - Could not retrieve variants from source file in region 12:27064021-27064422. Error was invalid region `12:27064022-27064422`
[2016-04-15T06:34Z] 2016-04-14 23:34:21 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:34:21,355 - WARNING - Could not retrieve variants from source file in region 12:18435187-18447071. Error was invalid region `12:18435188-18447071`
[2016-04-15T06:34Z] 2016-04-14 23:34:22 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:34:22,142 - WARNING - Could not retrieve variants from source file in region 12:26275344-26275745. Error was invalid region `12:26275345-26275745`
[2016-04-15T06:34Z] 2016-04-14 23:34:23 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:34:23,513 - WARNING - Could not retrieve variants from source file in region 12:25362254-25368652. Error was invalid region `12:25362255-25368652`
[2016-04-15T06:34Z] 2016-04-14 23:34:28 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:34:28,167 - WARNING - Could not retrieve variants from source file in region 12:27064021-27064422. Error was invalid region `12:27064022-27064422`
[2016-04-15T06:34Z] 2016-04-14 23:34:29 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:34:29,268 - WARNING - Could not retrieve variants from source file in region 12:16347097-16370018. Error was invalid region `12:16347098-16370018`
[2016-04-15T06:34Z] 2016-04-14 23:34:30 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:34:30,501 - WARNING - Could not retrieve variants from source file in region 12:16397466-16397948. Error was invalid region `12:16397467-16397948`
[2016-04-15T06:34Z] 2016-04-14 23:34:32 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:34:32,739 - WARNING - Could not retrieve variants from source file in region 12:16347097-16370018. Error was invalid region `12:16347098-16370018`
[2016-04-15T06:34Z] 2016-04-14 23:34:33 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:34:33,578 - WARNING - Could not retrieve variants from source file in region 12:15678909-15679310. Error was invalid region `12:15678910-15679310`
[2016-04-15T06:34Z] 2016-04-14 23:34:35 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:34:35,117 - WARNING - Could not retrieve variants from source file in region 12:15678909-15679310. Error was invalid region `12:15678910-15679310`
[2016-04-15T06:34Z] ['bcbio-variation-recall', 'square', '-Xms750m', '-Xmx7280m', '-XX:+UseSerialGC', '-c', 16, '-r', u'12:31236747-46754992', '--caller', 'platypus', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/12/Batch1-12_31236746_46754992.vcf.gz', '/mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/12/Batch1-12_31236746_46754992.vcf-inputs.txt'] in region: 12:31236747-46754992
[2016-04-15T06:34Z] 2016-04-14 23:34:49 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:34:49,241 - WARNING - Could not retrieve variants from source file in region 12:46385604-46386005. Error was invalid region `12:46385605-46386005`
[2016-04-15T06:34Z] 2016-04-14 23:34:51 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:34:51,006 - WARNING - Could not retrieve variants from source file in region 12:42503256-42503657. Error was invalid region `12:42503257-42503657`
[2016-04-15T06:34Z] 2016-04-14 23:34:51 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:34:51,099 - WARNING - Could not retrieve variants from source file in region 12:45823282-45826195. Error was invalid region `12:45823283-45826195`
[2016-04-15T06:34Z] 2016-04-14 23:34:52 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:34:52,236 - WARNING - Could not retrieve variants from source file in region 12:46321303-46321704. Error was invalid region `12:46321304-46321704`
[2016-04-15T06:34Z] 2016-04-14 23:34:53 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:34:53,378 - WARNING - Could not retrieve variants from source file in region 12:32133853-32138600. Error was invalid region `12:32133854-32138600`
[2016-04-15T06:34Z] 2016-04-14 23:34:53 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:34:53,451 - WARNING - Could not retrieve variants from source file in region 12:46589777-46590178. Error was invalid region `12:46589778-46590178`
[2016-04-15T06:34Z] 2016-04-14 23:34:53 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:34:53,767 - WARNING - Could not retrieve variants from source file in region 12:41365831-41366345. Error was invalid region `12:41365832-41366345`
[2016-04-15T06:34Z] 2016-04-14 23:34:59 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:34:59,359 - WARNING - Could not retrieve variants from source file in region 12:41312282-41337625. Error was invalid region `12:41312283-41337625`
[2016-04-15T06:34Z] 2016-04-14 23:34:59 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:34:59,444 - WARNING - Could not retrieve variants from source file in region 12:41966095-41966496. Error was invalid region `12:41966096-41966496`
[2016-04-15T06:35Z] 2016-04-14 23:35:00 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:35:00,532 - WARNING - Could not retrieve variants from source file in region 12:42627075-42629740. Error was invalid region `12:42627076-42629740`
[2016-04-15T06:35Z] 2016-04-14 23:35:00 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:35:00,682 - WARNING - Could not retrieve variants from source file in region 12:40688484-40716450. Error was invalid region `12:40688485-40716450`
[2016-04-15T06:35Z] 2016-04-14 23:35:01 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:35:01,122 - WARNING - Could not retrieve variants from source file in region 12:45724877-45725278. Error was invalid region `12:45724878-45725278`
[2016-04-15T06:35Z] 2016-04-14 23:35:01 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:35:01,195 - WARNING - Could not retrieve variants from source file in region 12:32763973-32777552. Error was invalid region `12:32763974-32777552`
[2016-04-15T06:35Z] 2016-04-14 23:35:02 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:35:02,002 - WARNING - Could not retrieve variants from source file in region 12:41365831-41366345. Error was invalid region `12:41365832-41366345`
[2016-04-15T06:35Z] 2016-04-14 23:35:08 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:35:08,145 - WARNING - Could not retrieve variants from source file in region 12:41365831-41366345. Error was invalid region `12:41365832-41366345`
[2016-04-15T06:35Z] 2016-04-14 23:35:16 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:35:16,836 - WARNING - Could not retrieve variants from source file in region 12:41582379-41582793. Error was invalid region `12:41582380-41582793`
[2016-04-15T06:35Z] 2016-04-14 23:35:18 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:35:18,737 - WARNING - Could not retrieve variants from source file in region 12:32654874-32655275. Error was invalid region `12:32654875-32655275`
[2016-04-15T06:35Z] 2016-04-14 23:35:20 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:35:20,003 - WARNING - Could not retrieve variants from source file in region 12:45409864-45430022. Error was invalid region `12:45409865-45430022`
[2016-04-15T06:35Z] 2016-04-14 23:35:20 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:35:20,367 - WARNING - Could not retrieve variants from source file in region 12:39087398-39087799. Error was invalid region `12:39087399-39087799`
[2016-04-15T06:35Z] 2016-04-14 23:35:21 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:35:21,116 - WARNING - Could not retrieve variants from source file in region 12:40618871-40631981. Error was invalid region `12:40618872-40631981`
[2016-04-15T06:35Z] 2016-04-14 23:35:21 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:35:21,186 - WARNING - Could not retrieve variants from source file in region 12:42554294-42554695. Error was invalid region `12:42554295-42554695`
[2016-04-15T06:35Z] 2016-04-14 23:35:21 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:35:21,493 - WARNING - Could not retrieve variants from source file in region 12:41582379-41582793. Error was invalid region `12:41582380-41582793`
[2016-04-15T06:35Z] 2016-04-14 23:35:21 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:35:21,521 - WARNING - Could not retrieve variants from source file in region 12:32735025-32735426. Error was invalid region `12:32735026-32735426`
[2016-04-15T06:35Z] 2016-04-14 23:35:23 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:35:23,373 - WARNING - Could not retrieve variants from source file in region 12:43860315-43860716. Error was invalid region `12:43860316-43860716`
[2016-04-15T06:35Z] 2016-04-14 23:35:24 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:35:24,383 - WARNING - Could not retrieve variants from source file in region 12:39087398-39087799. Error was invalid region `12:39087399-39087799`
[2016-04-15T06:35Z] 2016-04-14 23:35:25 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:35:25,230 - WARNING - Could not retrieve variants from source file in region 12:31944774-31945175. Error was invalid region `12:31944775-31945175`
[2016-04-15T06:35Z] 2016-04-14 23:35:25 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:35:25,407 - WARNING - Could not retrieve variants from source file in region 12:32735025-32735426. Error was invalid region `12:32735026-32735426`
[2016-04-15T06:35Z] 2016-04-14 23:35:25 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:35:25,420 - WARNING - Could not retrieve variants from source file in region 12:41582379-41582793. Error was invalid region `12:41582380-41582793`
[2016-04-15T06:35Z] 2016-04-14 23:35:26 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:35:26,281 - WARNING - Could not retrieve variants from source file in region 12:40742043-40758842. Error was invalid region `12:40742044-40758842`
[2016-04-15T06:35Z] 2016-04-14 23:35:27 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:35:27,051 - WARNING - Could not retrieve variants from source file in region 12:43860315-43860716. Error was invalid region `12:43860316-43860716`
[2016-04-15T06:35Z] 2016-04-14 23:35:28 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:35:28,090 - WARNING - Could not retrieve variants from source file in region 12:39087398-39087799. Error was invalid region `12:39087399-39087799`
[2016-04-15T06:35Z] 2016-04-14 23:35:29 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:35:29,198 - WARNING - Could not retrieve variants from source file in region 12:42554294-42554695. Error was invalid region `12:42554295-42554695`
[2016-04-15T06:35Z] 2016-04-14 23:35:29 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:35:29,210 - WARNING - Could not retrieve variants from source file in region 12:40618871-40631981. Error was invalid region `12:40618872-40631981`
[2016-04-15T06:35Z] 2016-04-14 23:35:29 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:35:29,265 - WARNING - Could not retrieve variants from source file in region 12:32735025-32735426. Error was invalid region `12:32735026-32735426`
[2016-04-15T06:35Z] 2016-04-14 23:35:30 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:35:30,786 - WARNING - Could not retrieve variants from source file in region 12:43860315-43860716. Error was invalid region `12:43860316-43860716`
[2016-04-15T06:35Z] 2016-04-14 23:35:37 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:35:37,580 - WARNING - Could not retrieve variants from source file in region 12:40085695-40086096. Error was invalid region `12:40085696-40086096`
[2016-04-15T06:35Z] 2016-04-14 23:35:38 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:35:38,455 - WARNING - Could not retrieve variants from source file in region 12:32552558-32552959. Error was invalid region `12:32552559-32552959`
[2016-04-15T06:35Z] 2016-04-14 23:35:39 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:35:39,659 - WARNING - Could not retrieve variants from source file in region 12:38711931-38715190. Error was invalid region `12:38711932-38715190`
[2016-04-15T06:35Z] 2016-04-14 23:35:42 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:35:42,224 - WARNING - Could not retrieve variants from source file in region 12:32481158-32492159. Error was invalid region `12:32481159-32492159`
[2016-04-15T06:35Z] 2016-04-14 23:35:42 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:35:42,538 - WARNING - Could not retrieve variants from source file in region 12:33535078-33535479. Error was invalid region `12:33535079-33535479`
[2016-04-15T06:35Z] 2016-04-14 23:35:43 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:35:43,870 - WARNING - Could not retrieve variants from source file in region 12:38711931-38715190. Error was invalid region `12:38711932-38715190`
[2016-04-15T06:35Z] 2016-04-14 23:35:45 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:35:45,550 - WARNING - Could not retrieve variants from source file in region 12:31648615-31649016. Error was invalid region `12:31648616-31649016`
[2016-04-15T06:35Z] 2016-04-14 23:35:46 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:35:46,455 - WARNING - Could not retrieve variants from source file in region 12:39299342-39299893. Error was invalid region `12:39299343-39299893`
[2016-04-15T06:35Z] 2016-04-14 23:35:46 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:35:46,591 - WARNING - Could not retrieve variants from source file in region 12:31867645-31868046. Error was invalid region `12:31867646-31868046`
[2016-04-15T06:35Z] 2016-04-14 23:35:47 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:35:47,493 - WARNING - Could not retrieve variants from source file in region 12:39299342-39299893. Error was invalid region `12:39299343-39299893`
[2016-04-15T06:35Z] 2016-04-14 23:35:47 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:35:47,550 - WARNING - Could not retrieve variants from source file in region 12:32908026-32908708. Error was invalid region `12:32908027-32908708`
[2016-04-15T06:35Z] 2016-04-14 23:35:47 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:35:47,896 - WARNING - Could not retrieve variants from source file in region 12:33535078-33535479. Error was invalid region `12:33535079-33535479`
[2016-04-15T06:35Z] 2016-04-14 23:35:48 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:35:48,341 - WARNING - Could not retrieve variants from source file in region 12:38711931-38715190. Error was invalid region `12:38711932-38715190`
[2016-04-15T06:35Z] 2016-04-14 23:35:50 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:35:50,004 - WARNING - Could not retrieve variants from source file in region 12:31648615-31649016. Error was invalid region `12:31648616-31649016`
[2016-04-15T06:35Z] 2016-04-14 23:35:51 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:35:51,834 - WARNING - Could not retrieve variants from source file in region 12:31648615-31649016. Error was invalid region `12:31648616-31649016`
[2016-04-15T06:35Z] ['bcbio-variation-recall', 'square', '-Xms750m', '-Xmx7280m', '-XX:+UseSerialGC', '-c', 16, '-r', u'12:46756067-62654284', '--caller', 'platypus', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/12/Batch1-12_46756066_62654284.vcf.gz', '/mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/12/Batch1-12_46756066_62654284.vcf-inputs.txt'] in region: 12:46756067-62654284
[2016-04-15T06:36Z] 2016-04-14 23:36:09 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:36:09,200 - WARNING - Could not retrieve variants from source file in region 12:53896773-53897174. Error was invalid region `12:53896774-53897174`
[2016-04-15T06:36Z] 2016-04-14 23:36:09 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:36:09,573 - WARNING - Could not retrieve variants from source file in region 12:56721849-56722250. Error was invalid region `12:56721850-56722250`
[2016-04-15T06:36Z] 2016-04-14 23:36:09 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:36:09,637 - WARNING - Could not retrieve variants from source file in region 12:56295523-56295924. Error was invalid region `12:56295524-56295924`
[2016-04-15T06:36Z] 2016-04-14 23:36:09 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:36:09,874 - WARNING - Could not retrieve variants from source file in region 12:60173145-60173546. Error was invalid region `12:60173146-60173546`
[2016-04-15T06:36Z] 2016-04-14 23:36:09 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:36:09,914 - WARNING - Could not retrieve variants from source file in region 12:57843500-57870345. Error was invalid region `12:57843501-57870345`
[2016-04-15T06:36Z] 2016-04-14 23:36:10 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:36:10,163 - WARNING - Could not retrieve variants from source file in region 12:56862675-56863076. Error was invalid region `12:56862676-56863076`
[2016-04-15T06:36Z] 2016-04-14 23:36:10 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:36:10,456 - WARNING - Could not retrieve variants from source file in region 12:54575247-54575990. Error was invalid region `12:54575248-54575990`
[2016-04-15T06:36Z] 2016-04-14 23:36:10 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:36:10,541 - WARNING - Could not retrieve variants from source file in region 12:58204072-58204473. Error was invalid region `12:58204073-58204473`
[2016-04-15T06:36Z] 2016-04-14 23:36:10 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:36:10,972 - WARNING - Could not retrieve variants from source file in region 12:56398243-56418868. Error was invalid region `12:56398244-56418868`
[2016-04-15T06:36Z] 2016-04-14 23:36:10 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:36:10,975 - WARNING - Could not retrieve variants from source file in region 12:54394286-54394687. Error was invalid region `12:54394287-54394687`
[2016-04-15T06:36Z] 2016-04-14 23:36:16 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:36:16,525 - WARNING - Could not retrieve variants from source file in region 12:54734078-54734479. Error was invalid region `12:54734079-54734479`
[2016-04-15T06:36Z] 2016-04-14 23:36:18 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:36:18,023 - WARNING - Could not retrieve variants from source file in region 12:56721849-56722250. Error was invalid region `12:56721850-56722250`
[2016-04-15T06:36Z] 2016-04-14 23:36:18 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:36:18,068 - WARNING - Could not retrieve variants from source file in region 12:55846412-55886484. Error was invalid region `12:55846413-55886484`
[2016-04-15T06:36Z] 2016-04-14 23:36:18 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:36:18,235 - WARNING - Could not retrieve variants from source file in region 12:56295523-56295924. Error was invalid region `12:56295524-56295924`
[2016-04-15T06:36Z] 2016-04-14 23:36:18 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:36:18,400 - WARNING - Could not retrieve variants from source file in region 12:60173145-60173546. Error was invalid region `12:60173146-60173546`
[2016-04-15T06:36Z] 2016-04-14 23:36:18 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:36:18,826 - WARNING - Could not retrieve variants from source file in region 12:55368034-55368558. Error was invalid region `12:55368035-55368558`
[2016-04-15T06:36Z] 2016-04-14 23:36:18 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:36:18,861 - WARNING - Could not retrieve variants from source file in region 12:58204072-58204473. Error was invalid region `12:58204073-58204473`
[2016-04-15T06:36Z] 2016-04-14 23:36:18 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:36:18,862 - WARNING - Could not retrieve variants from source file in region 12:50512068-50538815. Error was invalid region `12:50512069-50538815`
[2016-04-15T06:36Z] 2016-04-14 23:36:19 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:36:19,302 - WARNING - Could not retrieve variants from source file in region 12:54575247-54575990. Error was invalid region `12:54575248-54575990`
[2016-04-15T06:36Z] 2016-04-14 23:36:19 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:36:19,592 - WARNING - Could not retrieve variants from source file in region 12:53294170-53299025. Error was invalid region `12:53294171-53299025`
[2016-04-15T06:36Z] 2016-04-14 23:36:19 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:36:19,654 - WARNING - Could not retrieve variants from source file in region 12:54394286-54394687. Error was invalid region `12:54394287-54394687`
[2016-04-15T06:36Z] 2016-04-14 23:36:19 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:36:19,681 - WARNING - Could not retrieve variants from source file in region 12:56862675-56863076. Error was invalid region `12:56862676-56863076`
[2016-04-15T06:36Z] 2016-04-14 23:36:22 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:36:22,023 - WARNING - Could not retrieve variants from source file in region 12:53896773-53897174. Error was invalid region `12:53896774-53897174`
[2016-04-15T06:36Z] 2016-04-14 23:36:22 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:36:22,358 - WARNING - Could not retrieve variants from source file in region 12:54734078-54734479. Error was invalid region `12:54734079-54734479`
[2016-04-15T06:36Z] 2016-04-14 23:36:25 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:36:25,375 - WARNING - Could not retrieve variants from source file in region 12:56721849-56722250. Error was invalid region `12:56721850-56722250`
[2016-04-15T06:36Z] 2016-04-14 23:36:25 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:36:25,719 - WARNING - Could not retrieve variants from source file in region 12:60173145-60173546. Error was invalid region `12:60173146-60173546`
[2016-04-15T06:36Z] 2016-04-14 23:36:25 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:36:25,957 - WARNING - Could not retrieve variants from source file in region 12:56295523-56295924. Error was invalid region `12:56295524-56295924`
[2016-04-15T06:36Z] 2016-04-14 23:36:26 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:36:26,357 - WARNING - Could not retrieve variants from source file in region 12:58204072-58204473. Error was invalid region `12:58204073-58204473`
[2016-04-15T06:36Z] 2016-04-14 23:36:26 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:36:26,724 - WARNING - Could not retrieve variants from source file in region 12:55368034-55368558. Error was invalid region `12:55368035-55368558`
[2016-04-15T06:36Z] 2016-04-14 23:36:26 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:36:26,964 - WARNING - Could not retrieve variants from source file in region 12:56862675-56863076. Error was invalid region `12:56862676-56863076`
[2016-04-15T06:36Z] 2016-04-14 23:36:27 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:36:27,294 - WARNING - Could not retrieve variants from source file in region 12:54575247-54575990. Error was invalid region `12:54575248-54575990`
[2016-04-15T06:36Z] 2016-04-14 23:36:27 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:36:27,690 - WARNING - Could not retrieve variants from source file in region 12:54394286-54394687. Error was invalid region `12:54394287-54394687`
[2016-04-15T06:36Z] 2016-04-14 23:36:27 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:36:27,724 - WARNING - Could not retrieve variants from source file in region 12:50512068-50538815. Error was invalid region `12:50512069-50538815`
[2016-04-15T06:36Z] 2016-04-14 23:36:36 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:36:36,130 - WARNING - Could not retrieve variants from source file in region 12:56334896-56361066. Error was invalid region `12:56334897-56361066`
[2016-04-15T06:36Z] 2016-04-14 23:36:40 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:36:40,610 - WARNING - Could not retrieve variants from source file in region 12:53776960-53777361. Error was invalid region `12:53776961-53777361`
[2016-04-15T06:36Z] 2016-04-14 23:36:41 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:36:41,381 - WARNING - Could not retrieve variants from source file in region 12:56647700-56649791. Error was invalid region `12:56647701-56649791`
[2016-04-15T06:36Z] 2016-04-14 23:36:41 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:36:41,449 - WARNING - Could not retrieve variants from source file in region 12:56236320-56236721. Error was invalid region `12:56236321-56236721`
[2016-04-15T06:36Z] 2016-04-14 23:36:43 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:36:43,316 - WARNING - Could not retrieve variants from source file in region 12:57618998-57619552. Error was invalid region `12:57618999-57619552`
[2016-04-15T06:36Z] 2016-04-14 23:36:43 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:36:43,318 - WARNING - Could not retrieve variants from source file in region 12:55250401-55250802. Error was invalid region `12:55250402-55250802`
[2016-04-15T06:36Z] 2016-04-14 23:36:45 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:36:45,226 - WARNING - Could not retrieve variants from source file in region 12:54447895-54448296. Error was invalid region `12:54447896-54448296`
[2016-04-15T06:36Z] 2016-04-14 23:36:45 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:36:45,268 - WARNING - Could not retrieve variants from source file in region 12:50452497-50452898. Error was invalid region `12:50452498-50452898`
[2016-04-15T06:36Z] 2016-04-14 23:36:45 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:36:45,759 - WARNING - Could not retrieve variants from source file in region 12:54366850-54367251. Error was invalid region `12:54366851-54367251`
[2016-04-15T06:36Z] 2016-04-14 23:36:46 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:36:46,720 - WARNING - Could not retrieve variants from source file in region 12:59313037-59314126. Error was invalid region `12:59313038-59314126`
[2016-04-15T06:36Z] 2016-04-14 23:36:46 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:36:46,985 - WARNING - Could not retrieve variants from source file in region 12:56236320-56236721. Error was invalid region `12:56236321-56236721`
[2016-04-15T06:36Z] 2016-04-14 23:36:47 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:36:47,213 - WARNING - Could not retrieve variants from source file in region 12:56647700-56649791. Error was invalid region `12:56647701-56649791`
[2016-04-15T06:36Z] 2016-04-14 23:36:48 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:36:48,414 - WARNING - Could not retrieve variants from source file in region 12:55250401-55250802. Error was invalid region `12:55250402-55250802`
[2016-04-15T06:36Z] 2016-04-14 23:36:50 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:36:50,196 - WARNING - Could not retrieve variants from source file in region 12:58111978-58176804. Error was invalid region `12:58111979-58176804`
[2016-04-15T06:36Z] 2016-04-14 23:36:50 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:36:50,441 - WARNING - Could not retrieve variants from source file in region 12:56814442-56827884. Error was invalid region `12:56814443-56827884`
[2016-04-15T06:36Z] 2016-04-14 23:36:50 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:36:50,725 - WARNING - Could not retrieve variants from source file in region 12:50452497-50452898. Error was invalid region `12:50452498-50452898`
[2016-04-15T06:36Z] 2016-04-14 23:36:51 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:36:51,052 - WARNING - Could not retrieve variants from source file in region 12:54366850-54367251. Error was invalid region `12:54366851-54367251`
[2016-04-15T06:36Z] 2016-04-14 23:36:51 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:36:51,156 - WARNING - Could not retrieve variants from source file in region 12:53776960-53777361. Error was invalid region `12:53776961-53777361`
[2016-04-15T06:36Z] 2016-04-14 23:36:51 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:36:51,554 - WARNING - Could not retrieve variants from source file in region 12:56236320-56236721. Error was invalid region `12:56236321-56236721`
[2016-04-15T06:36Z] 2016-04-14 23:36:51 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:36:51,559 - WARNING - Could not retrieve variants from source file in region 12:56647700-56649791. Error was invalid region `12:56647701-56649791`
[2016-04-15T06:36Z] 2016-04-14 23:36:51 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:36:51,559 - WARNING - Could not retrieve variants from source file in region 12:59313037-59314126. Error was invalid region `12:59313038-59314126`
[2016-04-15T06:36Z] 2016-04-14 23:36:53 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:36:53,676 - WARNING - Could not retrieve variants from source file in region 12:55250401-55250802. Error was invalid region `12:55250402-55250802`
[2016-04-15T06:36Z] 2016-04-14 23:36:55 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:36:55,736 - WARNING - Could not retrieve variants from source file in region 12:58111978-58176804. Error was invalid region `12:58111979-58176804`
[2016-04-15T06:36Z] 2016-04-14 23:36:57 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:36:57,237 - WARNING - Could not retrieve variants from source file in region 12:53936667-53937068. Error was invalid region `12:53936668-53937068`
[2016-04-15T06:36Z] 2016-04-14 23:36:57 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:36:57,738 - WARNING - Could not retrieve variants from source file in region 12:56814442-56827884. Error was invalid region `12:56814443-56827884`
[2016-04-15T06:36Z] 2016-04-14 23:36:57 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:36:57,813 - WARNING - Could not retrieve variants from source file in region 12:54366850-54367251. Error was invalid region `12:54366851-54367251`
[2016-04-15T06:36Z] 2016-04-14 23:36:57 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:36:57,902 - WARNING - Could not retrieve variants from source file in region 12:50452497-50452898. Error was invalid region `12:50452498-50452898`
[2016-04-15T06:36Z] 2016-04-14 23:36:58 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:36:58,116 - WARNING - Could not retrieve variants from source file in region 12:56077529-56122894. Error was invalid region `12:56077530-56122894`
[2016-04-15T06:37Z] 2016-04-14 23:37:02 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:37:02,906 - WARNING - Could not retrieve variants from source file in region 12:53936667-53937068. Error was invalid region `12:53936668-53937068`
[2016-04-15T06:37Z] 2016-04-14 23:37:07 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:37:07,245 - WARNING - Could not retrieve variants from source file in region 12:56530943-56532199. Error was invalid region `12:56530944-56532199`
[2016-04-15T06:37Z] 2016-04-14 23:37:08 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:37:08,618 - WARNING - Could not retrieve variants from source file in region 12:55944908-55945309. Error was invalid region `12:55944909-55945309`
[2016-04-15T06:37Z] 2016-04-14 23:37:10 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:37:10,385 - WARNING - Could not retrieve variants from source file in region 12:57994532-58019662. Error was invalid region `12:57994533-58019662`
[2016-04-15T06:37Z] 2016-04-14 23:37:14 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:37:14,155 - WARNING - Could not retrieve variants from source file in region 12:55944908-55945309. Error was invalid region `12:55944909-55945309`
[2016-04-15T06:37Z] 2016-04-14 23:37:14 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:37:14,894 - WARNING - Could not retrieve variants from source file in region 12:55038493-55042308. Error was invalid region `12:55038494-55042308`
[2016-04-15T06:37Z] 2016-04-14 23:37:15 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:37:15,035 - WARNING - Could not retrieve variants from source file in region 12:56753783-56754184. Error was invalid region `12:56753784-56754184`
[2016-04-15T06:37Z] 2016-04-14 23:37:15 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:37:15,093 - WARNING - Could not retrieve variants from source file in region 12:55714195-55725880. Error was invalid region `12:55714196-55725880`
[2016-04-15T06:37Z] 2016-04-14 23:37:15 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:37:15,482 - WARNING - Could not retrieve variants from source file in region 12:58335415-58350821. Error was invalid region `12:58335416-58350821`
[2016-04-15T06:37Z] 2016-04-14 23:37:18 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:37:18,895 - WARNING - Could not retrieve variants from source file in region 12:55944908-55945309. Error was invalid region `12:55944909-55945309`
[2016-04-15T06:37Z] 2016-04-14 23:37:20 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:37:20,425 - WARNING - Could not retrieve variants from source file in region 12:55038493-55042308. Error was invalid region `12:55038494-55042308`
[2016-04-15T06:37Z] 2016-04-14 23:37:21 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:37:21,268 - WARNING - Could not retrieve variants from source file in region 12:54955113-54976027. Error was invalid region `12:54955114-54976027`
[2016-04-15T06:37Z] 2016-04-14 23:37:22 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:37:22,200 - WARNING - Could not retrieve variants from source file in region 12:53613806-53614207. Error was invalid region `12:53613807-53614207`
[2016-04-15T06:37Z] 2016-04-14 23:37:22 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:37:22,236 - WARNING - Could not retrieve variants from source file in region 12:50347867-50368203. Error was invalid region `12:50347868-50368203`
[2016-04-15T06:37Z] 2016-04-14 23:37:22 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:37:22,443 - WARNING - Could not retrieve variants from source file in region 12:58335415-58350821. Error was invalid region `12:58335416-58350821`
[2016-04-15T06:37Z] 2016-04-14 23:37:28 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:37:28,209 - WARNING - Could not retrieve variants from source file in region 12:53613806-53614207. Error was invalid region `12:53613807-53614207`
[2016-04-15T06:37Z] 2016-04-14 23:37:28 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:37:28,292 - WARNING - Could not retrieve variants from source file in region 12:50347867-50368203. Error was invalid region `12:50347868-50368203`
[2016-04-15T06:37Z] 2016-04-14 23:37:28 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:37:28,660 - WARNING - Could not retrieve variants from source file in region 12:49048527-49087846. Error was invalid region `12:49048528-49087846`
[2016-04-15T06:37Z] 2016-04-14 23:37:28 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:37:28,976 - WARNING - Could not retrieve variants from source file in region 12:57029815-57030216. Error was invalid region `12:57029816-57030216`
[2016-04-15T06:37Z] 2016-04-14 23:37:32 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:37:32,855 - WARNING - Could not retrieve variants from source file in region 12:53497191-53510123. Error was invalid region `12:53497192-53510123`
[2016-04-15T06:37Z] 2016-04-14 23:37:33 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:37:33,912 - WARNING - Could not retrieve variants from source file in region 12:57058398-57133330. Error was invalid region `12:57058399-57133330`
[2016-04-15T06:37Z] 2016-04-14 23:37:36 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:37:36,235 - WARNING - Could not retrieve variants from source file in region 12:57029815-57030216. Error was invalid region `12:57029816-57030216`
[2016-04-15T06:37Z] 2016-04-14 23:37:37 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:37:37,938 - WARNING - Could not retrieve variants from source file in region 12:55688056-55688457. Error was invalid region `12:55688057-55688457`
[2016-04-15T06:37Z] 2016-04-14 23:37:38 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:37:38,110 - WARNING - Could not retrieve variants from source file in region 12:53574279-53574680. Error was invalid region `12:53574280-53574680`
[2016-04-15T06:37Z] 2016-04-14 23:37:39 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:37:39,680 - WARNING - Could not retrieve variants from source file in region 12:53574279-53574680. Error was invalid region `12:53574280-53574680`
[2016-04-15T06:37Z] 2016-04-14 23:37:41 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:37:41,622 - WARNING - Could not retrieve variants from source file in region 12:54905604-54906005. Error was invalid region `12:54905605-54906005`
[2016-04-15T06:37Z] 2016-04-14 23:37:42 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:37:42,150 - WARNING - Could not retrieve variants from source file in region 12:57029815-57030216. Error was invalid region `12:57029816-57030216`
[2016-04-15T06:37Z] 2016-04-14 23:37:42 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:37:42,833 - WARNING - Could not retrieve variants from source file in region 12:48375357-48398270. Error was invalid region `12:48375358-48398270`
[2016-04-15T06:37Z] 2016-04-14 23:37:42 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:37:42,894 - WARNING - Could not retrieve variants from source file in region 12:54795199-54802770. Error was invalid region `12:54795200-54802770`
[2016-04-15T06:37Z] 2016-04-14 23:37:43 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:37:43,247 - WARNING - Could not retrieve variants from source file in region 12:56956002-56956403. Error was invalid region `12:56956003-56956403`
[2016-04-15T06:37Z] 2016-04-14 23:37:43 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:37:43,584 - WARNING - Could not retrieve variants from source file in region 12:55688056-55688457. Error was invalid region `12:55688057-55688457`
[2016-04-15T06:37Z] 2016-04-14 23:37:43 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:37:43,911 - WARNING - Could not retrieve variants from source file in region 12:50232285-50232971. Error was invalid region `12:50232286-50232971`
[2016-04-15T06:37Z] 2016-04-14 23:37:46 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:37:46,027 - WARNING - Could not retrieve variants from source file in region 12:54905604-54906005. Error was invalid region `12:54905605-54906005`
[2016-04-15T06:37Z] 2016-04-14 23:37:47 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:37:47,872 - WARNING - Could not retrieve variants from source file in region 12:48375357-48398270. Error was invalid region `12:48375358-48398270`
[2016-04-15T06:37Z] 2016-04-14 23:37:48 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:37:48,070 - WARNING - Could not retrieve variants from source file in region 12:56956002-56956403. Error was invalid region `12:56956003-56956403`
[2016-04-15T06:37Z] 2016-04-14 23:37:48 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:37:48,679 - WARNING - Could not retrieve variants from source file in region 12:55688056-55688457. Error was invalid region `12:55688057-55688457`
[2016-04-15T06:37Z] 2016-04-14 23:37:50 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:37:50,453 - WARNING - Could not retrieve variants from source file in region 12:54905604-54906005. Error was invalid region `12:54905605-54906005`
[2016-04-15T06:37Z] 2016-04-14 23:37:50 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:37:50,818 - WARNING - Could not retrieve variants from source file in region 12:56956002-56956403. Error was invalid region `12:56956003-56956403`
[2016-04-15T06:37Z] 2016-04-14 23:37:56 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:37:56,114 - WARNING - Could not retrieve variants from source file in region 12:48723573-48735499. Error was invalid region `12:48723574-48735499`
[2016-04-15T06:37Z] 2016-04-14 23:37:56 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:37:56,233 - WARNING - Could not retrieve variants from source file in region 12:53432878-53454383. Error was invalid region `12:53432879-53454383`
[2016-04-15T06:37Z] 2016-04-14 23:37:57 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:37:57,084 - WARNING - Could not retrieve variants from source file in region 12:52080754-52081155. Error was invalid region `12:52080755-52081155`
[2016-04-15T06:38Z] 2016-04-14 23:38:01 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:38:01,120 - WARNING - Could not retrieve variants from source file in region 12:48723573-48735499. Error was invalid region `12:48723574-48735499`
[2016-04-15T06:38Z] 2016-04-14 23:38:01 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:38:01,719 - WARNING - Could not retrieve variants from source file in region 12:55640864-55642110. Error was invalid region `12:55640865-55642110`
[2016-04-15T06:38Z] 2016-04-14 23:38:01 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:38:01,905 - WARNING - Could not retrieve variants from source file in region 12:52080754-52081155. Error was invalid region `12:52080755-52081155`
[2016-04-15T06:38Z] 2016-04-14 23:38:03 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:38:03,138 - WARNING - Could not retrieve variants from source file in region 12:55523375-55524504. Error was invalid region `12:55523376-55524504`
[2016-04-15T06:38Z] 2016-04-14 23:38:03 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:38:03,792 - WARNING - Could not retrieve variants from source file in region 12:51380021-51443134. Error was invalid region `12:51380022-51443134`
[2016-04-15T06:38Z] 2016-04-14 23:38:03 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:38:03,832 - WARNING - Could not retrieve variants from source file in region 12:48578114-48578632. Error was invalid region `12:48578115-48578632`
[2016-04-15T06:38Z] 2016-04-14 23:38:03 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:38:03,848 - WARNING - Could not retrieve variants from source file in region 12:51089523-51089924. Error was invalid region `12:51089524-51089924`
[2016-04-15T06:38Z] 2016-04-14 23:38:05 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:38:05,716 - WARNING - Could not retrieve variants from source file in region 12:48272684-48293906. Error was invalid region `12:48272685-48293906`
[2016-04-15T06:38Z] 2016-04-14 23:38:06 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:38:06,192 - WARNING - Could not retrieve variants from source file in region 12:54767601-54768002. Error was invalid region `12:54767602-54768002`
[2016-04-15T06:38Z] 2016-04-14 23:38:06 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:38:06,832 - WARNING - Could not retrieve variants from source file in region 12:48888383-48888879. Error was invalid region `12:48888384-48888879`
[2016-04-15T06:38Z] 2016-04-14 23:38:06 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:38:06,908 - WARNING - Could not retrieve variants from source file in region 12:53432878-53454383. Error was invalid region `12:53432879-53454383`
[2016-04-15T06:38Z] 2016-04-14 23:38:07 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:38:07,112 - WARNING - Could not retrieve variants from source file in region 12:48723573-48735499. Error was invalid region `12:48723574-48735499`
[2016-04-15T06:38Z] 2016-04-14 23:38:07 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:38:07,120 - WARNING - Could not retrieve variants from source file in region 12:52080754-52081155. Error was invalid region `12:52080755-52081155`
[2016-04-15T06:38Z] 2016-04-14 23:38:08 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:38:08,609 - WARNING - Could not retrieve variants from source file in region 12:51380021-51443134. Error was invalid region `12:51380022-51443134`
[2016-04-15T06:38Z] 2016-04-14 23:38:08 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:38:08,754 - WARNING - Could not retrieve variants from source file in region 12:48578114-48578632. Error was invalid region `12:48578115-48578632`
[2016-04-15T06:38Z] 2016-04-14 23:38:10 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:38:10,965 - WARNING - Could not retrieve variants from source file in region 12:54767601-54768002. Error was invalid region `12:54767602-54768002`
[2016-04-15T06:38Z] 2016-04-14 23:38:11 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:38:11,241 - WARNING - Could not retrieve variants from source file in region 12:49937602-49938003. Error was invalid region `12:49937603-49938003`
[2016-04-15T06:38Z] 2016-04-14 23:38:13 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:38:13,865 - WARNING - Could not retrieve variants from source file in region 12:48578114-48578632. Error was invalid region `12:48578115-48578632`
[2016-04-15T06:38Z] 2016-04-14 23:38:14 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:38:14,386 - WARNING - Could not retrieve variants from source file in region 12:51089523-51089924. Error was invalid region `12:51089524-51089924`
[2016-04-15T06:38Z] 2016-04-14 23:38:16 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:38:16,150 - WARNING - Could not retrieve variants from source file in region 12:49937602-49938003. Error was invalid region `12:49937603-49938003`
[2016-04-15T06:38Z] 2016-04-14 23:38:17 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:38:17,174 - WARNING - Could not retrieve variants from source file in region 12:48888383-48888879. Error was invalid region `12:48888384-48888879`
[2016-04-15T06:38Z] 2016-04-14 23:38:24 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:38:24,310 - WARNING - Could not retrieve variants from source file in region 12:48238546-48238947. Error was invalid region `12:48238547-48238947`
[2016-04-15T06:38Z] 2016-04-14 23:38:24 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:38:24,836 - WARNING - Could not retrieve variants from source file in region 12:51723387-51737752. Error was invalid region `12:51723388-51737752`
[2016-04-15T06:38Z] 2016-04-14 23:38:26 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:38:26,311 - WARNING - Could not retrieve variants from source file in region 12:51855948-51874346. Error was invalid region `12:51855949-51874346`
[2016-04-15T06:38Z] 2016-04-14 23:38:28 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:38:28,380 - WARNING - Could not retrieve variants from source file in region 12:49500187-49522795. Error was invalid region `12:49500188-49522795`
[2016-04-15T06:38Z] 2016-04-14 23:38:28 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:38:28,658 - WARNING - Could not retrieve variants from source file in region 12:50854984-50855385. Error was invalid region `12:50854985-50855385`
[2016-04-15T06:38Z] 2016-04-14 23:38:28 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:38:28,929 - WARNING - Could not retrieve variants from source file in region 12:51135064-51135465. Error was invalid region `12:51135065-51135465`
[2016-04-15T06:38Z] 2016-04-14 23:38:29 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:38:29,151 - WARNING - Could not retrieve variants from source file in region 12:48238546-48238947. Error was invalid region `12:48238547-48238947`
[2016-04-15T06:38Z] 2016-04-14 23:38:29 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:38:29,870 - WARNING - Could not retrieve variants from source file in region 12:51723387-51737752. Error was invalid region `12:51723388-51737752`
[2016-04-15T06:38Z] 2016-04-14 23:38:33 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:38:33,119 - WARNING - Could not retrieve variants from source file in region 12:50854984-50855385. Error was invalid region `12:50854985-50855385`
[2016-04-15T06:38Z] 2016-04-14 23:38:33 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:38:33,440 - WARNING - Could not retrieve variants from source file in region 12:51135064-51135465. Error was invalid region `12:51135065-51135465`
[2016-04-15T06:38Z] 2016-04-14 23:38:33 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:38:33,450 - WARNING - Could not retrieve variants from source file in region 12:52758017-52789135. Error was invalid region `12:52758018-52789135`
[2016-04-15T06:38Z] 2016-04-14 23:38:33 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:38:33,865 - WARNING - Could not retrieve variants from source file in region 12:48238546-48238947. Error was invalid region `12:48238547-48238947`
[2016-04-15T06:38Z] 2016-04-14 23:38:33 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:38:33,927 - WARNING - Could not retrieve variants from source file in region 12:49500187-49522795. Error was invalid region `12:49500188-49522795`
[2016-04-15T06:38Z] 2016-04-14 23:38:34 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:38:34,181 - WARNING - Could not retrieve variants from source file in region 12:51723387-51737752. Error was invalid region `12:51723388-51737752`
[2016-04-15T06:38Z] 2016-04-14 23:38:35 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:38:35,301 - WARNING - Could not retrieve variants from source file in region 12:51135064-51135465. Error was invalid region `12:51135065-51135465`
[2016-04-15T06:38Z] 2016-04-14 23:38:37 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:38:37,404 - WARNING - Could not retrieve variants from source file in region 12:49308073-49360337. Error was invalid region `12:49308074-49360337`
[2016-04-15T06:38Z] 2016-04-14 23:38:38 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:38:38,728 - WARNING - Could not retrieve variants from source file in region 12:52758017-52789135. Error was invalid region `12:52758018-52789135`
[2016-04-15T06:38Z] 2016-04-14 23:38:39 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:38:39,739 - WARNING - Could not retrieve variants from source file in region 12:50854984-50855385. Error was invalid region `12:50854985-50855385`
[2016-04-15T06:38Z] 2016-04-14 23:38:40 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:38:40,373 - WARNING - Could not retrieve variants from source file in region 12:49221411-49230225. Error was invalid region `12:49221412-49230225`
[2016-04-15T06:38Z] 2016-04-14 23:38:41 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:38:41,263 - WARNING - Could not retrieve variants from source file in region 12:48134353-48190234. Error was invalid region `12:48134354-48190234`
[2016-04-15T06:38Z] 2016-04-14 23:38:41 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:38:41,898 - WARNING - Could not retrieve variants from source file in region 12:49255587-49255988. Error was invalid region `12:49255588-49255988`
[2016-04-15T06:38Z] 2016-04-14 23:38:45 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:38:45,073 - WARNING - Could not retrieve variants from source file in region 12:51681692-51686021. Error was invalid region `12:51681693-51686021`
[2016-04-15T06:38Z] 2016-04-14 23:38:45 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:38:45,205 - WARNING - Could not retrieve variants from source file in region 12:51681692-51686021. Error was invalid region `12:51681693-51686021`
[2016-04-15T06:38Z] 2016-04-14 23:38:46 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:38:46,550 - WARNING - Could not retrieve variants from source file in region 12:49221411-49230225. Error was invalid region `12:49221412-49230225`
[2016-04-15T06:38Z] 2016-04-14 23:38:48 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:38:48,017 - WARNING - Could not retrieve variants from source file in region 12:49255587-49255988. Error was invalid region `12:49255588-49255988`
[2016-04-15T06:38Z] 2016-04-14 23:38:48 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:38:48,721 - WARNING - Could not retrieve variants from source file in region 12:51636048-51637094. Error was invalid region `12:51636049-51637094`
[2016-04-15T06:38Z] 2016-04-14 23:38:49 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:38:49,633 - WARNING - Could not retrieve variants from source file in region 12:51681692-51686021. Error was invalid region `12:51681693-51686021`
[2016-04-15T06:38Z] 2016-04-14 23:38:50 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:38:50,369 - WARNING - Could not retrieve variants from source file in region 12:47471228-47471629. Error was invalid region `12:47471229-47471629`
[2016-04-15T06:38Z] 2016-04-14 23:38:50 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:38:50,812 - WARNING - Could not retrieve variants from source file in region 12:49221411-49230225. Error was invalid region `12:49221412-49230225`
[2016-04-15T06:38Z] 2016-04-14 23:38:53 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:38:53,375 - WARNING - Could not retrieve variants from source file in region 12:51636048-51637094. Error was invalid region `12:51636049-51637094`
[2016-04-15T06:38Z] 2016-04-14 23:38:53 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:38:53,941 - WARNING - Could not retrieve variants from source file in region 12:50594736-50616536. Error was invalid region `12:50594737-50616536`
[2016-04-15T06:38Z] 2016-04-14 23:38:57 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:38:57,441 - WARNING - Could not retrieve variants from source file in region 12:52467463-52467887. Error was invalid region `12:52467464-52467887`
[2016-04-15T06:38Z] 2016-04-14 23:38:57 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:38:57,844 - WARNING - Could not retrieve variants from source file in region 12:51636048-51637094. Error was invalid region `12:51636049-51637094`
[2016-04-15T06:38Z] 2016-04-14 23:38:58 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:38:58,060 - WARNING - Could not retrieve variants from source file in region 12:49168587-49168988. Error was invalid region `12:49168588-49168988`
[2016-04-15T06:38Z] 2016-04-14 23:38:58 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:38:58,556 - WARNING - Could not retrieve variants from source file in region 12:49168587-49168988. Error was invalid region `12:49168588-49168988`
[2016-04-15T06:38Z] 2016-04-14 23:38:59 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:38:59,088 - WARNING - Could not retrieve variants from source file in region 12:47471228-47471629. Error was invalid region `12:47471229-47471629`
[2016-04-15T06:39Z] 2016-04-14 23:39:00 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:39:00,142 - WARNING - Could not retrieve variants from source file in region 12:47629157-47629558. Error was invalid region `12:47629158-47629558`
[2016-04-15T06:39Z] 2016-04-14 23:39:00 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:39:00,949 - WARNING - Could not retrieve variants from source file in region 12:52467463-52467887. Error was invalid region `12:52467464-52467887`
[2016-04-15T06:39Z] 2016-04-14 23:39:01 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:39:01,190 - WARNING - Could not retrieve variants from source file in region 12:50594736-50616536. Error was invalid region `12:50594737-50616536`
[2016-04-15T06:39Z] 2016-04-14 23:39:04 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:39:04,395 - WARNING - Could not retrieve variants from source file in region 12:47629157-47629558. Error was invalid region `12:47629158-47629558`
[2016-04-15T06:39Z] 2016-04-14 23:39:07 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:39:07,382 - WARNING - Could not retrieve variants from source file in region 12:52565111-52566237. Error was invalid region `12:52565112-52566237`
[2016-04-15T06:39Z] 2016-04-14 23:39:07 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:39:07,420 - WARNING - Could not retrieve variants from source file in region 12:52565111-52566237. Error was invalid region `12:52565112-52566237`
[2016-04-15T06:39Z] 2016-04-14 23:39:07 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:39:07,431 - WARNING - Could not retrieve variants from source file in region 12:52565111-52566237. Error was invalid region `12:52565112-52566237`
[2016-04-15T06:39Z] 2016-04-14 23:39:08 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:39:08,557 - WARNING - Could not retrieve variants from source file in region 12:47168687-47169088. Error was invalid region `12:47168688-47169088`
[2016-04-15T06:39Z] 2016-04-14 23:39:08 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:39:08,559 - WARNING - Could not retrieve variants from source file in region 12:47168687-47169088. Error was invalid region `12:47168688-47169088`
[2016-04-15T06:39Z] 2016-04-14 23:39:08 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:39:08,575 - WARNING - Could not retrieve variants from source file in region 12:47168687-47169088. Error was invalid region `12:47168688-47169088`
[2016-04-15T06:39Z] 2016-04-14 23:39:10 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:39:10,465 - WARNING - Could not retrieve variants from source file in region 12:52408662-52437681. Error was invalid region `12:52408663-52437681`
[2016-04-15T06:39Z] 2016-04-14 23:39:10 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:39:10,953 - WARNING - Could not retrieve variants from source file in region 12:52281849-52284858. Error was invalid region `12:52281850-52284858`
[2016-04-15T06:39Z] 2016-04-14 23:39:10 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:39:10,962 - WARNING - Could not retrieve variants from source file in region 12:52281849-52284858. Error was invalid region `12:52281850-52284858`
[2016-04-15T06:39Z] ['bcbio-variation-recall', 'square', '-Xms750m', '-Xmx7280m', '-XX:+UseSerialGC', '-c', 16, '-r', u'12:62687960-78225484', '--caller', 'platypus', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/12/Batch1-12_62687959_78225484.vcf.gz', '/mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/12/Batch1-12_62687959_78225484.vcf-inputs.txt'] in region: 12:62687960-78225484
[2016-04-15T06:39Z] 2016-04-14 23:39:27 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:39:27,722 - WARNING - Could not retrieve variants from source file in region 12:64472592-64472993. Error was invalid region `12:64472593-64472993`
[2016-04-15T06:39Z] 2016-04-14 23:39:28 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:39:28,566 - WARNING - Could not retrieve variants from source file in region 12:72416024-72416425. Error was invalid region `12:72416025-72416425`
[2016-04-15T06:39Z] 2016-04-14 23:39:28 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:39:28,599 - WARNING - Could not retrieve variants from source file in region 12:68708550-68725141. Error was invalid region `12:68708551-68725141`
[2016-04-15T06:39Z] 2016-04-14 23:39:28 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:39:28,618 - WARNING - Could not retrieve variants from source file in region 12:63543998-63544399. Error was invalid region `12:63543999-63544399`
[2016-04-15T06:39Z] 2016-04-14 23:39:28 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:39:28,658 - WARNING - Could not retrieve variants from source file in region 12:62729011-62749314. Error was invalid region `12:62729012-62749314`
[2016-04-15T06:39Z] 2016-04-14 23:39:28 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:39:28,910 - WARNING - Could not retrieve variants from source file in region 12:78225163-78225564. Error was invalid region `12:78225164-78225564`
[2016-04-15T06:39Z] 2016-04-14 23:39:29 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:39:29,187 - WARNING - Could not retrieve variants from source file in region 12:76424705-76454156. Error was invalid region `12:76424706-76454156`
[2016-04-15T06:39Z] 2016-04-14 23:39:29 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:39:29,203 - WARNING - Could not retrieve variants from source file in region 12:64519595-64519996. Error was invalid region `12:64519596-64519996`
[2016-04-15T06:39Z] 2016-04-14 23:39:29 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:39:29,893 - WARNING - Could not retrieve variants from source file in region 12:64712300-64712736. Error was invalid region `12:64712301-64712736`
[2016-04-15T06:39Z] 2016-04-14 23:39:29 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:39:29,901 - WARNING - Could not retrieve variants from source file in region 12:63954093-63954494. Error was invalid region `12:63954094-63954494`
[2016-04-15T06:39Z] 2016-04-14 23:39:31 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:39:31,975 - WARNING - Could not retrieve variants from source file in region 12:62926187-62928823. Error was invalid region `12:62926188-62928823`
[2016-04-15T06:39Z] 2016-04-14 23:39:33 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:39:33,702 - WARNING - Could not retrieve variants from source file in region 12:64472592-64472993. Error was invalid region `12:64472593-64472993`
[2016-04-15T06:39Z] 2016-04-14 23:39:36 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:39:36,322 - WARNING - Could not retrieve variants from source file in region 12:72416024-72416425. Error was invalid region `12:72416025-72416425`
[2016-04-15T06:39Z] 2016-04-14 23:39:37 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:39:37,277 - WARNING - Could not retrieve variants from source file in region 12:63543998-63544399. Error was invalid region `12:63543999-63544399`
[2016-04-15T06:39Z] 2016-04-14 23:39:37 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:39:37,441 - WARNING - Could not retrieve variants from source file in region 12:68708550-68725141. Error was invalid region `12:68708551-68725141`
[2016-04-15T06:39Z] 2016-04-14 23:39:38 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:39:38,034 - WARNING - Could not retrieve variants from source file in region 12:64519595-64519996. Error was invalid region `12:64519596-64519996`
[2016-04-15T06:39Z] 2016-04-14 23:39:38 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:39:38,068 - WARNING - Could not retrieve variants from source file in region 12:78225163-78225564. Error was invalid region `12:78225164-78225564`
[2016-04-15T06:39Z] 2016-04-14 23:39:38 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:39:38,108 - WARNING - Could not retrieve variants from source file in region 12:75816603-75817004. Error was invalid region `12:75816604-75817004`
[2016-04-15T06:39Z] 2016-04-14 23:39:38 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:39:38,285 - WARNING - Could not retrieve variants from source file in region 12:69967651-69995537. Error was invalid region `12:69967652-69995537`
[2016-04-15T06:39Z] 2016-04-14 23:39:38 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:39:38,764 - WARNING - Could not retrieve variants from source file in region 12:77191047-77191448. Error was invalid region `12:77191048-77191448`
[2016-04-15T06:39Z] 2016-04-14 23:39:38 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:39:38,949 - WARNING - Could not retrieve variants from source file in region 12:63954093-63954494. Error was invalid region `12:63954094-63954494`
[2016-04-15T06:39Z] 2016-04-14 23:39:38 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:39:38,953 - WARNING - Could not retrieve variants from source file in region 12:62926187-62928823. Error was invalid region `12:62926188-62928823`
[2016-04-15T06:39Z] 2016-04-14 23:39:38 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:39:38,956 - WARNING - Could not retrieve variants from source file in region 12:62777854-62785853. Error was invalid region `12:62777855-62785853`
[2016-04-15T06:39Z] 2016-04-14 23:39:39 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:39:39,051 - WARNING - Could not retrieve variants from source file in region 12:64712300-64712736. Error was invalid region `12:64712301-64712736`
[2016-04-15T06:39Z] 2016-04-14 23:39:39 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:39:39,298 - WARNING - Could not retrieve variants from source file in region 12:64472592-64472993. Error was invalid region `12:64472593-64472993`
[2016-04-15T06:39Z] 2016-04-14 23:39:42 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:39:42,669 - WARNING - Could not retrieve variants from source file in region 12:72416024-72416425. Error was invalid region `12:72416025-72416425`
[2016-04-15T06:39Z] 2016-04-14 23:39:44 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:39:44,061 - WARNING - Could not retrieve variants from source file in region 12:63543998-63544399. Error was invalid region `12:63543999-63544399`
[2016-04-15T06:39Z] 2016-04-14 23:39:46 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:39:46,139 - WARNING - Could not retrieve variants from source file in region 12:64519595-64519996. Error was invalid region `12:64519596-64519996`
[2016-04-15T06:39Z] 2016-04-14 23:39:47 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:39:47,166 - WARNING - Could not retrieve variants from source file in region 12:69967651-69995537. Error was invalid region `12:69967652-69995537`
[2016-04-15T06:39Z] 2016-04-14 23:39:47 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:39:47,649 - WARNING - Could not retrieve variants from source file in region 12:78225163-78225564. Error was invalid region `12:78225164-78225564`
[2016-04-15T06:39Z] 2016-04-14 23:39:47 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:39:47,688 - WARNING - Could not retrieve variants from source file in region 12:64712300-64712736. Error was invalid region `12:64712301-64712736`
[2016-04-15T06:39Z] 2016-04-14 23:39:58 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:39:58,547 - WARNING - Could not retrieve variants from source file in region 12:64061812-64062255. Error was invalid region `12:64061813-64062255`
[2016-04-15T06:39Z] 2016-04-14 23:39:59 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:39:59,086 - WARNING - Could not retrieve variants from source file in region 12:70329876-70351874. Error was invalid region `12:70329877-70351874`
[2016-04-15T06:39Z] 2016-04-14 23:39:59 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:39:59,772 - WARNING - Could not retrieve variants from source file in region 12:72356103-72373052. Error was invalid region `12:72356104-72373052`
[2016-04-15T06:40Z] 2016-04-14 23:40:01 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:40:01,708 - WARNING - Could not retrieve variants from source file in region 12:62958926-62959327. Error was invalid region `12:62958927-62959327`
[2016-04-15T06:40Z] 2016-04-14 23:40:03 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:40:03,873 - WARNING - Could not retrieve variants from source file in region 12:64061812-64062255. Error was invalid region `12:64061813-64062255`
[2016-04-15T06:40Z] 2016-04-14 23:40:04 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:40:04,282 - WARNING - Could not retrieve variants from source file in region 12:77419130-77449980. Error was invalid region `12:77419131-77449980`
[2016-04-15T06:40Z] 2016-04-14 23:40:04 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:40:04,489 - WARNING - Could not retrieve variants from source file in region 12:64668879-64669280. Error was invalid region `12:64668880-64669280`
[2016-04-15T06:40Z] 2016-04-14 23:40:04 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:40:04,626 - WARNING - Could not retrieve variants from source file in region 12:72356103-72373052. Error was invalid region `12:72356104-72373052`
[2016-04-15T06:40Z] 2016-04-14 23:40:04 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:40:04,967 - WARNING - Could not retrieve variants from source file in region 12:77256266-77256871. Error was invalid region `12:77256267-77256871`
[2016-04-15T06:40Z] 2016-04-14 23:40:05 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:40:05,003 - WARNING - Could not retrieve variants from source file in region 12:69646703-69647104. Error was invalid region `12:69646704-69647104`
[2016-04-15T06:40Z] 2016-04-14 23:40:05 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:40:05,707 - WARNING - Could not retrieve variants from source file in region 12:68051967-68052368. Error was invalid region `12:68051968-68052368`
[2016-04-15T06:40Z] 2016-04-14 23:40:06 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:40:06,195 - WARNING - Could not retrieve variants from source file in region 12:75434980-75437443. Error was invalid region `12:75434981-75437443`
[2016-04-15T06:40Z] 2016-04-14 23:40:08 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:40:08,127 - WARNING - Could not retrieve variants from source file in region 12:75763220-75785290. Error was invalid region `12:75763221-75785290`
[2016-04-15T06:40Z] 2016-04-14 23:40:08 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:40:08,717 - WARNING - Could not retrieve variants from source file in region 12:64061812-64062255. Error was invalid region `12:64061813-64062255`
[2016-04-15T06:40Z] 2016-04-14 23:40:09 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:40:09,020 - WARNING - Could not retrieve variants from source file in region 12:64668879-64669280. Error was invalid region `12:64668880-64669280`
[2016-04-15T06:40Z] 2016-04-14 23:40:09 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:40:09,477 - WARNING - Could not retrieve variants from source file in region 12:62883668-62884072. Error was invalid region `12:62883669-62884072`
[2016-04-15T06:40Z] 2016-04-14 23:40:09 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:40:09,510 - WARNING - Could not retrieve variants from source file in region 12:70329876-70351874. Error was invalid region `12:70329877-70351874`
[2016-04-15T06:40Z] 2016-04-14 23:40:09 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:40:09,599 - WARNING - Could not retrieve variants from source file in region 12:72356103-72373052. Error was invalid region `12:72356104-72373052`
[2016-04-15T06:40Z] 2016-04-14 23:40:09 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:40:09,692 - WARNING - Could not retrieve variants from source file in region 12:77256266-77256871. Error was invalid region `12:77256267-77256871`
[2016-04-15T06:40Z] 2016-04-14 23:40:10 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:40:10,478 - WARNING - Could not retrieve variants from source file in region 12:68051967-68052368. Error was invalid region `12:68051968-68052368`
[2016-04-15T06:40Z] 2016-04-14 23:40:11 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:40:11,017 - WARNING - Could not retrieve variants from source file in region 12:62958926-62959327. Error was invalid region `12:62958927-62959327`
[2016-04-15T06:40Z] 2016-04-14 23:40:11 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:40:11,222 - WARNING - Could not retrieve variants from source file in region 12:75900171-75900778. Error was invalid region `12:75900172-75900778`
[2016-04-15T06:40Z] 2016-04-14 23:40:14 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:40:14,039 - WARNING - Could not retrieve variants from source file in region 12:64668879-64669280. Error was invalid region `12:64668880-64669280`
[2016-04-15T06:40Z] 2016-04-14 23:40:14 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:40:14,687 - WARNING - Could not retrieve variants from source file in region 12:77256266-77256871. Error was invalid region `12:77256267-77256871`
[2016-04-15T06:40Z] 2016-04-14 23:40:24 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:40:24,057 - WARNING - Could not retrieve variants from source file in region 12:67706255-67706656. Error was invalid region `12:67706256-67706656`
[2016-04-15T06:40Z] 2016-04-14 23:40:25 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:40:25,116 - WARNING - Could not retrieve variants from source file in region 12:74931948-74932349. Error was invalid region `12:74931949-74932349`
[2016-04-15T06:40Z] 2016-04-14 23:40:25 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:40:25,353 - WARNING - Could not retrieve variants from source file in region 12:64587098-64609752. Error was invalid region `12:64587099-64609752`
[2016-04-15T06:40Z] 2016-04-14 23:40:25 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:40:25,424 - WARNING - Could not retrieve variants from source file in region 12:72976111-72976512. Error was invalid region `12:72976112-72976512`
[2016-04-15T06:40Z] 2016-04-14 23:40:27 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:40:27,382 - WARNING - Could not retrieve variants from source file in region 12:64875576-64875977. Error was invalid region `12:64875577-64875977`
[2016-04-15T06:40Z] 2016-04-14 23:40:28 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:40:28,213 - WARNING - Could not retrieve variants from source file in region 12:67706255-67706656. Error was invalid region `12:67706256-67706656`
[2016-04-15T06:40Z] 2016-04-14 23:40:29 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:40:29,177 - WARNING - Could not retrieve variants from source file in region 12:65223963-65224364. Error was invalid region `12:65223964-65224364`
[2016-04-15T06:40Z] 2016-04-14 23:40:29 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:40:29,245 - WARNING - Could not retrieve variants from source file in region 12:74931948-74932349. Error was invalid region `12:74931949-74932349`
[2016-04-15T06:40Z] 2016-04-14 23:40:31 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:40:31,222 - WARNING - Could not retrieve variants from source file in region 12:69252504-69260969. Error was invalid region `12:69252505-69260969`
[2016-04-15T06:40Z] 2016-04-14 23:40:32 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:40:32,111 - WARNING - Could not retrieve variants from source file in region 12:67706255-67706656. Error was invalid region `12:67706256-67706656`
[2016-04-15T06:40Z] 2016-04-14 23:40:33 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:40:33,293 - WARNING - Could not retrieve variants from source file in region 12:65223963-65224364. Error was invalid region `12:65223964-65224364`
[2016-04-15T06:40Z] 2016-04-14 23:40:33 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:40:33,512 - WARNING - Could not retrieve variants from source file in region 12:74931948-74932349. Error was invalid region `12:74931949-74932349`
[2016-04-15T06:40Z] 2016-04-14 23:40:35 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:40:35,317 - WARNING - Could not retrieve variants from source file in region 12:69252504-69260969. Error was invalid region `12:69252505-69260969`
[2016-04-15T06:40Z] 2016-04-14 23:40:35 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:40:35,780 - WARNING - Could not retrieve variants from source file in region 12:64875576-64875977. Error was invalid region `12:64875577-64875977`
[2016-04-15T06:40Z] 2016-04-14 23:40:38 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:40:38,682 - WARNING - Could not retrieve variants from source file in region 12:66308825-66309386. Error was invalid region `12:66308826-66309386`
[2016-04-15T06:40Z] 2016-04-14 23:40:43 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:40:43,273 - WARNING - Could not retrieve variants from source file in region 12:65514055-65514456. Error was invalid region `12:65514056-65514456`
[2016-04-15T06:40Z] 2016-04-14 23:40:44 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:40:44,263 - WARNING - Could not retrieve variants from source file in region 12:66696199-66699085. Error was invalid region `12:66696200-66699085`
[2016-04-15T06:40Z] 2016-04-14 23:40:44 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:40:44,371 - WARNING - Could not retrieve variants from source file in region 12:66785880-66786281. Error was invalid region `12:66785881-66786281`
[2016-04-15T06:40Z] 2016-04-14 23:40:44 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:40:44,794 - WARNING - Could not retrieve variants from source file in region 12:69082594-69127435. Error was invalid region `12:69082595-69127435`
[2016-04-15T06:40Z] 2016-04-14 23:40:45 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:40:45,678 - WARNING - Could not retrieve variants from source file in region 12:65146321-65150675. Error was invalid region `12:65146322-65150675`
[2016-04-15T06:40Z] 2016-04-14 23:40:46 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:40:46,980 - WARNING - Could not retrieve variants from source file in region 12:64746622-64747023. Error was invalid region `12:64746623-64747023`
[2016-04-15T06:40Z] 2016-04-14 23:40:47 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:40:47,038 - WARNING - Could not retrieve variants from source file in region 12:71139453-71139854. Error was invalid region `12:71139454-71139854`
[2016-04-15T06:40Z] 2016-04-14 23:40:47 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:40:47,090 - WARNING - Could not retrieve variants from source file in region 12:64746622-64747023. Error was invalid region `12:64746623-64747023`
[2016-04-15T06:40Z] 2016-04-14 23:40:47 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:40:47,100 - WARNING - Could not retrieve variants from source file in region 12:66696199-66699085. Error was invalid region `12:66696200-66699085`
[2016-04-15T06:40Z] 2016-04-14 23:40:47 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:40:47,278 - WARNING - Could not retrieve variants from source file in region 12:65514055-65514456. Error was invalid region `12:65514056-65514456`
[2016-04-15T06:40Z] 2016-04-14 23:40:48 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:40:48,015 - WARNING - Could not retrieve variants from source file in region 12:71950196-71960398. Error was invalid region `12:71950197-71960398`
[2016-04-15T06:40Z] 2016-04-14 23:40:48 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:40:48,448 - WARNING - Could not retrieve variants from source file in region 12:66696199-66699085. Error was invalid region `12:66696200-66699085`
[2016-04-15T06:40Z] 2016-04-14 23:40:48 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:40:48,926 - WARNING - Could not retrieve variants from source file in region 12:66785880-66786281. Error was invalid region `12:66785881-66786281`
[2016-04-15T06:40Z] 2016-04-14 23:40:49 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:40:49,803 - WARNING - Could not retrieve variants from source file in region 12:65146321-65150675. Error was invalid region `12:65146322-65150675`
[2016-04-15T06:40Z] 2016-04-14 23:40:51 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:40:51,378 - WARNING - Could not retrieve variants from source file in region 12:66591276-66605418. Error was invalid region `12:66591277-66605418`
[2016-04-15T06:40Z] 2016-04-14 23:40:51 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:40:51,390 - WARNING - Could not retrieve variants from source file in region 12:65514055-65514456. Error was invalid region `12:65514056-65514456`
[2016-04-15T06:40Z] 2016-04-14 23:40:51 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:40:51,634 - WARNING - Could not retrieve variants from source file in region 12:71522923-71533724. Error was invalid region `12:71522924-71533724`
[2016-04-15T06:40Z] 2016-04-14 23:40:51 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:40:51,639 - WARNING - Could not retrieve variants from source file in region 12:71139453-71139854. Error was invalid region `12:71139454-71139854`
[2016-04-15T06:40Z] 2016-04-14 23:40:52 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:40:52,195 - WARNING - Could not retrieve variants from source file in region 12:71950196-71960398. Error was invalid region `12:71950197-71960398`
[2016-04-15T06:40Z] 2016-04-14 23:40:52 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:40:52,685 - WARNING - Could not retrieve variants from source file in region 12:69082594-69127435. Error was invalid region `12:69082595-69127435`
[2016-04-15T06:40Z] 2016-04-14 23:40:53 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:40:53,499 - WARNING - Could not retrieve variants from source file in region 12:66785880-66786281. Error was invalid region `12:66785881-66786281`
[2016-04-15T06:40Z] 2016-04-14 23:40:53 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:40:53,742 - WARNING - Could not retrieve variants from source file in region 12:65146321-65150675. Error was invalid region `12:65146322-65150675`
[2016-04-15T06:40Z] 2016-04-14 23:40:55 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:40:55,270 - WARNING - Could not retrieve variants from source file in region 12:66591276-66605418. Error was invalid region `12:66591277-66605418`
[2016-04-15T06:40Z] 2016-04-14 23:40:55 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:40:55,545 - WARNING - Could not retrieve variants from source file in region 12:71139453-71139854. Error was invalid region `12:71139454-71139854`
[2016-04-15T06:41Z] ['bcbio-variation-recall', 'square', '-Xms750m', '-Xmx7280m', '-XX:+UseSerialGC', '-c', 16, '-r', u'12:78334099-93863131', '--caller', 'platypus', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/12/Batch1-12_78334098_93863131.vcf.gz', '/mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/12/Batch1-12_78334098_93863131.vcf-inputs.txt'] in region: 12:78334099-93863131
[2016-04-15T06:41Z] 2016-04-14 23:41:09 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:41:09,424 - WARNING - Could not retrieve variants from source file in region 12:88547066-88547467. Error was invalid region `12:88547067-88547467`
[2016-04-15T06:41Z] 2016-04-14 23:41:10 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:41:10,436 - WARNING - Could not retrieve variants from source file in region 12:93258454-93258855. Error was invalid region `12:93258455-93258855`
[2016-04-15T06:41Z] 2016-04-14 23:41:10 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:41:10,661 - WARNING - Could not retrieve variants from source file in region 12:81991790-81992191. Error was invalid region `12:81991791-81992191`
[2016-04-15T06:41Z] 2016-04-14 23:41:11 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:41:11,386 - WARNING - Could not retrieve variants from source file in region 12:80329033-80329434. Error was invalid region `12:80329034-80329434`
[2016-04-15T06:41Z] 2016-04-14 23:41:11 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:41:11,515 - WARNING - Could not retrieve variants from source file in region 12:78530768-78542889. Error was invalid region `12:78530769-78542889`
[2016-04-15T06:41Z] 2016-04-14 23:41:11 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:41:11,832 - WARNING - Could not retrieve variants from source file in region 12:78598680-78599081. Error was invalid region `12:78598681-78599081`
[2016-04-15T06:41Z] 2016-04-14 23:41:12 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:41:12,078 - WARNING - Could not retrieve variants from source file in region 12:86373010-86373411. Error was invalid region `12:86373011-86373411`
[2016-04-15T06:41Z] 2016-04-14 23:41:12 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:41:12,955 - WARNING - Could not retrieve variants from source file in region 12:79611163-79611564. Error was invalid region `12:79611164-79611564`
[2016-04-15T06:41Z] 2016-04-14 23:41:12 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:41:12,998 - WARNING - Could not retrieve variants from source file in region 12:92818271-92818976. Error was invalid region `12:92818272-92818976`
[2016-04-15T06:41Z] 2016-04-14 23:41:13 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:41:13,336 - WARNING - Could not retrieve variants from source file in region 12:80014696-80015097. Error was invalid region `12:80014697-80015097`
[2016-04-15T06:41Z] 2016-04-14 23:41:13 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:41:13,341 - WARNING - Could not retrieve variants from source file in region 12:88504867-88505268. Error was invalid region `12:88504868-88505268`
[2016-04-15T06:41Z] 2016-04-14 23:41:14 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:41:14,142 - WARNING - Could not retrieve variants from source file in region 12:88547066-88547467. Error was invalid region `12:88547067-88547467`
[2016-04-15T06:41Z] 2016-04-14 23:41:15 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:41:15,956 - WARNING - Could not retrieve variants from source file in region 12:93258454-93258855. Error was invalid region `12:93258455-93258855`
[2016-04-15T06:41Z] 2016-04-14 23:41:16 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:41:16,580 - WARNING - Could not retrieve variants from source file in region 12:81991790-81992191. Error was invalid region `12:81991791-81992191`
[2016-04-15T06:41Z] 2016-04-14 23:41:17 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:41:17,692 - WARNING - Could not retrieve variants from source file in region 12:80329033-80329434. Error was invalid region `12:80329034-80329434`
[2016-04-15T06:41Z] 2016-04-14 23:41:18 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:41:18,388 - WARNING - Could not retrieve variants from source file in region 12:78530768-78542889. Error was invalid region `12:78530769-78542889`
[2016-04-15T06:41Z] 2016-04-14 23:41:18 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:41:18,542 - WARNING - Could not retrieve variants from source file in region 12:80172918-80173319. Error was invalid region `12:80172919-80173319`
[2016-04-15T06:41Z] 2016-04-14 23:41:19 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:41:19,706 - WARNING - Could not retrieve variants from source file in region 12:78598680-78599081. Error was invalid region `12:78598681-78599081`
[2016-04-15T06:41Z] 2016-04-14 23:41:20 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:41:20,062 - WARNING - Could not retrieve variants from source file in region 12:85438288-85466913. Error was invalid region `12:85438289-85466913`
[2016-04-15T06:41Z] 2016-04-14 23:41:20 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:41:20,462 - WARNING - Could not retrieve variants from source file in region 12:79611163-79611564. Error was invalid region `12:79611164-79611564`
[2016-04-15T06:41Z] 2016-04-14 23:41:20 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:41:20,469 - WARNING - Could not retrieve variants from source file in region 12:93196211-93202991. Error was invalid region `12:93196212-93202991`
[2016-04-15T06:41Z] 2016-04-14 23:41:20 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:41:20,469 - WARNING - Could not retrieve variants from source file in region 12:78400673-78401074. Error was invalid region `12:78400674-78401074`
[2016-04-15T06:41Z] 2016-04-14 23:41:20 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:41:20,765 - WARNING - Could not retrieve variants from source file in region 12:80014696-80015097. Error was invalid region `12:80014697-80015097`
[2016-04-15T06:41Z] 2016-04-14 23:41:20 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:41:20,842 - WARNING - Could not retrieve variants from source file in region 12:88379577-88380284. Error was invalid region `12:88379578-88380284`
[2016-04-15T06:41Z] 2016-04-14 23:41:20 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:41:20,849 - WARNING - Could not retrieve variants from source file in region 12:88504867-88505268. Error was invalid region `12:88504868-88505268`
[2016-04-15T06:41Z] 2016-04-14 23:41:21 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:41:21,031 - WARNING - Could not retrieve variants from source file in region 12:88547066-88547467. Error was invalid region `12:88547067-88547467`
[2016-04-15T06:41Z] 2016-04-14 23:41:21 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:41:21,125 - WARNING - Could not retrieve variants from source file in region 12:93258454-93258855. Error was invalid region `12:93258455-93258855`
[2016-04-15T06:41Z] 2016-04-14 23:41:21 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:41:21,292 - WARNING - Could not retrieve variants from source file in region 12:81991790-81992191. Error was invalid region `12:81991791-81992191`
[2016-04-15T06:41Z] 2016-04-14 23:41:22 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:41:22,788 - WARNING - Could not retrieve variants from source file in region 12:80329033-80329434. Error was invalid region `12:80329034-80329434`
[2016-04-15T06:41Z] 2016-04-14 23:41:23 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:41:23,434 - WARNING - Could not retrieve variants from source file in region 12:78530768-78542889. Error was invalid region `12:78530769-78542889`
[2016-04-15T06:41Z] 2016-04-14 23:41:24 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:41:24,189 - WARNING - Could not retrieve variants from source file in region 12:80172918-80173319. Error was invalid region `12:80172919-80173319`
[2016-04-15T06:41Z] 2016-04-14 23:41:26 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:41:26,680 - WARNING - Could not retrieve variants from source file in region 12:78598680-78599081. Error was invalid region `12:78598681-78599081`
[2016-04-15T06:41Z] 2016-04-14 23:41:27 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:41:27,537 - WARNING - Could not retrieve variants from source file in region 12:79611163-79611564. Error was invalid region `12:79611164-79611564`
[2016-04-15T06:41Z] 2016-04-14 23:41:28 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:41:28,215 - WARNING - Could not retrieve variants from source file in region 12:93196211-93202991. Error was invalid region `12:93196212-93202991`
[2016-04-15T06:41Z] 2016-04-14 23:41:28 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:41:28,260 - WARNING - Could not retrieve variants from source file in region 12:80014696-80015097. Error was invalid region `12:80014697-80015097`
[2016-04-15T06:41Z] 2016-04-14 23:41:28 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:41:28,556 - WARNING - Could not retrieve variants from source file in region 12:92818271-92818976. Error was invalid region `12:92818272-92818976`
[2016-04-15T06:41Z] 2016-04-14 23:41:28 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:41:28,686 - WARNING - Could not retrieve variants from source file in region 12:88504867-88505268. Error was invalid region `12:88504868-88505268`
[2016-04-15T06:41Z] 2016-04-14 23:41:39 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:41:39,710 - WARNING - Could not retrieve variants from source file in region 12:88440465-88440866. Error was invalid region `12:88440466-88440866`
[2016-04-15T06:41Z] 2016-04-14 23:41:39 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:41:39,762 - WARNING - Could not retrieve variants from source file in region 12:93130992-93155725. Error was invalid region `12:93130993-93155725`
[2016-04-15T06:41Z] 2016-04-14 23:41:40 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:41:40,419 - WARNING - Could not retrieve variants from source file in region 12:81627027-81627428. Error was invalid region `12:81627028-81627428`
[2016-04-15T06:41Z] 2016-04-14 23:41:40 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:41:40,783 - WARNING - Could not retrieve variants from source file in region 12:80837964-80838754. Error was invalid region `12:80837965-80838754`
[2016-04-15T06:41Z] 2016-04-14 23:41:41 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:41:41,428 - WARNING - Could not retrieve variants from source file in region 12:86405431-86405832. Error was invalid region `12:86405432-86405832`
[2016-04-15T06:41Z] 2016-04-14 23:41:41 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:41:41,685 - WARNING - Could not retrieve variants from source file in region 12:88440465-88440866. Error was invalid region `12:88440466-88440866`
[2016-04-15T06:41Z] 2016-04-14 23:41:41 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:41:41,799 - WARNING - Could not retrieve variants from source file in region 12:78333968-78334384. Error was invalid region `12:78333969-78334384`
[2016-04-15T06:41Z] 2016-04-14 23:41:41 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:41:41,971 - WARNING - Could not retrieve variants from source file in region 12:85275895-85277798. Error was invalid region `12:85275896-85277798`
[2016-04-15T06:41Z] 2016-04-14 23:41:42 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:41:42,906 - WARNING - Could not retrieve variants from source file in region 12:82780465-82792977. Error was invalid region `12:82780466-82792977`
[2016-04-15T06:41Z] 2016-04-14 23:41:43 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:41:43,770 - WARNING - Could not retrieve variants from source file in region 12:93130992-93155725. Error was invalid region `12:93130993-93155725`
[2016-04-15T06:41Z] 2016-04-14 23:41:44 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:41:44,198 - WARNING - Could not retrieve variants from source file in region 12:91449779-91450180. Error was invalid region `12:91449780-91450180`
[2016-04-15T06:41Z] 2016-04-14 23:41:45 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:41:45,941 - WARNING - Could not retrieve variants from source file in region 12:85638434-85638836. Error was invalid region `12:85638435-85638836`
[2016-04-15T06:41Z] 2016-04-14 23:41:48 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:41:48,343 - WARNING - Could not retrieve variants from source file in region 12:91449779-91450180. Error was invalid region `12:91449780-91450180`
[2016-04-15T06:41Z] 2016-04-14 23:41:49 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:41:49,513 - WARNING - Could not retrieve variants from source file in region 12:86405431-86405832. Error was invalid region `12:86405432-86405832`
[2016-04-15T06:41Z] 2016-04-14 23:41:49 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:41:49,966 - WARNING - Could not retrieve variants from source file in region 12:85275895-85277798. Error was invalid region `12:85275896-85277798`
[2016-04-15T06:41Z] 2016-04-14 23:41:51 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:41:51,359 - WARNING - Could not retrieve variants from source file in region 12:91449779-91450180. Error was invalid region `12:91449780-91450180`
[2016-04-15T06:41Z] 2016-04-14 23:41:55 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:41:55,238 - WARNING - Could not retrieve variants from source file in region 12:89916600-89919518. Error was invalid region `12:89916601-89919518`
[2016-04-15T06:41Z] 2016-04-14 23:41:56 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:41:56,093 - WARNING - Could not retrieve variants from source file in region 12:89743012-89745667. Error was invalid region `12:89743013-89745667`
[2016-04-15T06:41Z] 2016-04-14 23:41:56 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:41:56,258 - WARNING - Could not retrieve variants from source file in region 12:80712209-80772003. Error was invalid region `12:80712210-80772003`
[2016-04-15T06:41Z] 2016-04-14 23:41:56 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:41:56,472 - WARNING - Could not retrieve variants from source file in region 12:80712209-80772003. Error was invalid region `12:80712210-80772003`
[2016-04-15T06:41Z] 2016-04-14 23:41:57 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:41:57,386 - WARNING - Could not retrieve variants from source file in region 12:80712209-80772003. Error was invalid region `12:80712210-80772003`
[2016-04-15T06:41Z] 2016-04-14 23:41:57 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:41:57,439 - WARNING - Could not retrieve variants from source file in region 12:89743012-89745667. Error was invalid region `12:89743013-89745667`
[2016-04-15T06:42Z] ['bcbio-variation-recall', 'square', '-Xms750m', '-Xmx7280m', '-XX:+UseSerialGC', '-c', 16, '-r', u'12:93870730-109490566', '--caller', 'platypus', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/12/Batch1-12_93870729_109490566.vcf.gz', '/mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/12/Batch1-12_93870729_109490566.vcf-inputs.txt'] in region: 12:93870730-109490566
[2016-04-15T06:42Z] 2016-04-14 23:42:13 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:42:13,083 - WARNING - Could not retrieve variants from source file in region 12:104046266-104086821. Error was invalid region `12:104046267-104086821`
[2016-04-15T06:42Z] 2016-04-14 23:42:14 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:42:14,391 - WARNING - Could not retrieve variants from source file in region 12:108618419-108618820. Error was invalid region `12:108618420-108618820`
[2016-04-15T06:42Z] 2016-04-14 23:42:14 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:42:14,503 - WARNING - Could not retrieve variants from source file in region 12:108685797-108686198. Error was invalid region `12:108685798-108686198`
[2016-04-15T06:42Z] 2016-04-14 23:42:15 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:42:15,140 - WARNING - Could not retrieve variants from source file in region 12:102108090-102117779. Error was invalid region `12:102108091-102117779`
[2016-04-15T06:42Z] 2016-04-14 23:42:16 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:42:16,398 - WARNING - Could not retrieve variants from source file in region 12:106994754-106995155. Error was invalid region `12:106994755-106995155`
[2016-04-15T06:42Z] 2016-04-14 23:42:16 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:42:16,435 - WARNING - Could not retrieve variants from source file in region 12:107712669-107713701. Error was invalid region `12:107712670-107713701`
[2016-04-15T06:42Z] 2016-04-14 23:42:16 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:42:16,441 - WARNING - Could not retrieve variants from source file in region 12:107394895-107395296. Error was invalid region `12:107394896-107395296`
[2016-04-15T06:42Z] 2016-04-14 23:42:16 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:42:16,478 - WARNING - Could not retrieve variants from source file in region 12:104680450-104709749. Error was invalid region `12:104680451-104709749`
[2016-04-15T06:42Z] 2016-04-14 23:42:20 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:42:20,738 - WARNING - Could not retrieve variants from source file in region 12:108685797-108686198. Error was invalid region `12:108685798-108686198`
[2016-04-15T06:42Z] 2016-04-14 23:42:23 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:42:23,821 - WARNING - Could not retrieve variants from source file in region 12:105198827-105199228. Error was invalid region `12:105198828-105199228`
[2016-04-15T06:42Z] 2016-04-14 23:42:23 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:42:23,834 - WARNING - Could not retrieve variants from source file in region 12:102108090-102117779. Error was invalid region `12:102108091-102117779`
[2016-04-15T06:42Z] 2016-04-14 23:42:24 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:42:24,138 - WARNING - Could not retrieve variants from source file in region 12:104645152-104645595. Error was invalid region `12:104645153-104645595`
[2016-04-15T06:42Z] 2016-04-14 23:42:24 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:42:24,254 - WARNING - Could not retrieve variants from source file in region 12:109182792-109183193. Error was invalid region `12:109182793-109183193`
[2016-04-15T06:42Z] 2016-04-14 23:42:24 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:42:24,443 - WARNING - Could not retrieve variants from source file in region 12:107394895-107395296. Error was invalid region `12:107394896-107395296`
[2016-04-15T06:42Z] 2016-04-14 23:42:25 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:42:25,212 - WARNING - Could not retrieve variants from source file in region 12:107712669-107713701. Error was invalid region `12:107712670-107713701`
[2016-04-15T06:42Z] 2016-04-14 23:42:25 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:42:25,252 - WARNING - Could not retrieve variants from source file in region 12:106994754-106995155. Error was invalid region `12:106994755-106995155`
[2016-04-15T06:42Z] 2016-04-14 23:42:25 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:42:25,378 - WARNING - Could not retrieve variants from source file in region 12:104680450-104709749. Error was invalid region `12:104680451-104709749`
[2016-04-15T06:42Z] 2016-04-14 23:42:25 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:42:25,596 - WARNING - Could not retrieve variants from source file in region 12:108618419-108618820. Error was invalid region `12:108618420-108618820`
[2016-04-15T06:42Z] 2016-04-14 23:42:25 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:42:25,714 - WARNING - Could not retrieve variants from source file in region 12:108685797-108686198. Error was invalid region `12:108685798-108686198`
[2016-04-15T06:42Z] 2016-04-14 23:42:26 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:42:26,862 - WARNING - Could not retrieve variants from source file in region 12:104373517-104373918. Error was invalid region `12:104373518-104373918`
[2016-04-15T06:42Z] 2016-04-14 23:42:29 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:42:29,889 - WARNING - Could not retrieve variants from source file in region 12:109017439-109017870. Error was invalid region `12:109017440-109017870`
[2016-04-15T06:42Z] 2016-04-14 23:42:29 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:42:29,893 - WARNING - Could not retrieve variants from source file in region 12:102108090-102117779. Error was invalid region `12:102108091-102117779`
[2016-04-15T06:42Z] 2016-04-14 23:42:32 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:42:32,026 - WARNING - Could not retrieve variants from source file in region 12:107394895-107395296. Error was invalid region `12:107394896-107395296`
[2016-04-15T06:42Z] 2016-04-14 23:42:32 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:42:32,971 - WARNING - Could not retrieve variants from source file in region 12:103237257-103249114. Error was invalid region `12:103237258-103249114`
[2016-04-15T06:42Z] 2016-04-14 23:42:34 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:42:34,041 - WARNING - Could not retrieve variants from source file in region 12:107712669-107713701. Error was invalid region `12:107712670-107713701`
[2016-04-15T06:42Z] 2016-04-14 23:42:34 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:42:34,089 - WARNING - Could not retrieve variants from source file in region 12:106994754-106995155. Error was invalid region `12:106994755-106995155`
[2016-04-15T06:42Z] 2016-04-14 23:42:34 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:42:34,131 - WARNING - Could not retrieve variants from source file in region 12:104680450-104709749. Error was invalid region `12:104680451-104709749`
[2016-04-15T06:42Z] 2016-04-14 23:42:41 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:42:41,968 - WARNING - Could not retrieve variants from source file in region 12:107078351-107090391. Error was invalid region `12:107078352-107090391`
[2016-04-15T06:42Z] 2016-04-14 23:42:42 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:42:42,830 - WARNING - Could not retrieve variants from source file in region 12:103871961-103872362. Error was invalid region `12:103871962-103872362`
[2016-04-15T06:42Z] 2016-04-14 23:42:42 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:42:42,900 - WARNING - Could not retrieve variants from source file in region 12:104340892-104341293. Error was invalid region `12:104340893-104341293`
[2016-04-15T06:42Z] 2016-04-14 23:42:43 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:42:43,524 - WARNING - Could not retrieve variants from source file in region 12:108011855-108012256. Error was invalid region `12:108011856-108012256`
[2016-04-15T06:42Z] 2016-04-14 23:42:44 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:42:44,391 - WARNING - Could not retrieve variants from source file in region 12:102063907-102079608. Error was invalid region `12:102063908-102079608`
[2016-04-15T06:42Z] 2016-04-14 23:42:44 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:42:44,401 - WARNING - Could not retrieve variants from source file in region 12:106641086-106641682. Error was invalid region `12:106641087-106641682`
[2016-04-15T06:42Z] 2016-04-14 23:42:46 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:42:46,542 - WARNING - Could not retrieve variants from source file in region 12:107078351-107090391. Error was invalid region `12:107078352-107090391`
[2016-04-15T06:42Z] 2016-04-14 23:42:48 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:42:48,187 - WARNING - Could not retrieve variants from source file in region 12:104340892-104341293. Error was invalid region `12:104340893-104341293`
[2016-04-15T06:42Z] 2016-04-14 23:42:48 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:42:48,222 - WARNING - Could not retrieve variants from source file in region 12:103871961-103872362. Error was invalid region `12:103871962-103872362`
[2016-04-15T06:42Z] 2016-04-14 23:42:48 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:42:48,590 - WARNING - Could not retrieve variants from source file in region 12:96974540-96974941. Error was invalid region `12:96974541-96974941`
[2016-04-15T06:42Z] 2016-04-14 23:42:48 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:42:48,645 - WARNING - Could not retrieve variants from source file in region 12:106848203-106848604. Error was invalid region `12:106848204-106848604`
[2016-04-15T06:42Z] 2016-04-14 23:42:48 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:42:48,976 - WARNING - Could not retrieve variants from source file in region 12:104408583-104408984. Error was invalid region `12:104408584-104408984`
[2016-04-15T06:42Z] 2016-04-14 23:42:49 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:42:49,025 - WARNING - Could not retrieve variants from source file in region 12:102063907-102079608. Error was invalid region `12:102063908-102079608`
[2016-04-15T06:42Z] 2016-04-14 23:42:49 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:42:49,131 - WARNING - Could not retrieve variants from source file in region 12:95906392-95927952. Error was invalid region `12:95906393-95927952`
[2016-04-15T06:42Z] 2016-04-14 23:42:51 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:42:51,189 - WARNING - Could not retrieve variants from source file in region 12:104186735-104209058. Error was invalid region `12:104186736-104209058`
[2016-04-15T06:42Z] 2016-04-14 23:42:52 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:42:52,645 - WARNING - Could not retrieve variants from source file in region 12:102813126-102813527. Error was invalid region `12:102813127-102813527`
[2016-04-15T06:42Z] 2016-04-14 23:42:52 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:42:52,702 - WARNING - Could not retrieve variants from source file in region 12:104340892-104341293. Error was invalid region `12:104340893-104341293`
[2016-04-15T06:42Z] 2016-04-14 23:42:52 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:42:52,727 - WARNING - Could not retrieve variants from source file in region 12:103871961-103872362. Error was invalid region `12:103871962-103872362`
[2016-04-15T06:42Z] 2016-04-14 23:42:53 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:42:53,351 - WARNING - Could not retrieve variants from source file in region 12:104408583-104408984. Error was invalid region `12:104408584-104408984`
[2016-04-15T06:42Z] 2016-04-14 23:42:53 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:42:53,815 - WARNING - Could not retrieve variants from source file in region 12:102063907-102079608. Error was invalid region `12:102063908-102079608`
[2016-04-15T06:42Z] 2016-04-14 23:42:57 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:42:57,073 - WARNING - Could not retrieve variants from source file in region 12:102813126-102813527. Error was invalid region `12:102813127-102813527`
[2016-04-15T06:42Z] 2016-04-14 23:42:58 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:42:58,485 - WARNING - Could not retrieve variants from source file in region 12:106848203-106848604. Error was invalid region `12:106848204-106848604`
[2016-04-15T06:42Z] 2016-04-14 23:42:59 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:42:59,870 - WARNING - Could not retrieve variants from source file in region 12:105541720-105568366. Error was invalid region `12:105541721-105568366`
[2016-04-15T06:43Z] 2016-04-14 23:43:00 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:43:00,711 - WARNING - Could not retrieve variants from source file in region 12:100451816-100452217. Error was invalid region `12:100451817-100452217`
[2016-04-15T06:43Z] 2016-04-14 23:43:00 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:43:00,804 - WARNING - Could not retrieve variants from source file in region 12:101683718-101693724. Error was invalid region `12:101683719-101693724`
[2016-04-15T06:43Z] 2016-04-14 23:43:05 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:43:05,690 - WARNING - Could not retrieve variants from source file in region 12:105541720-105568366. Error was invalid region `12:105541721-105568366`
[2016-04-15T06:43Z] 2016-04-14 23:43:06 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:43:06,428 - WARNING - Could not retrieve variants from source file in region 12:104152793-104153194. Error was invalid region `12:104152794-104153194`
[2016-04-15T06:43Z] 2016-04-14 23:43:08 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:43:08,735 - WARNING - Could not retrieve variants from source file in region 12:106751664-106752105. Error was invalid region `12:106751665-106752105`
[2016-04-15T06:43Z] 2016-04-14 23:43:08 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:43:08,873 - WARNING - Could not retrieve variants from source file in region 12:104123700-104124101. Error was invalid region `12:104123701-104124101`
[2016-04-15T06:43Z] 2016-04-14 23:43:09 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:43:09,172 - WARNING - Could not retrieve variants from source file in region 12:102517542-102517943. Error was invalid region `12:102517543-102517943`
[2016-04-15T06:43Z] 2016-04-14 23:43:09 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:43:09,438 - WARNING - Could not retrieve variants from source file in region 12:102036094-102036495. Error was invalid region `12:102036095-102036495`
[2016-04-15T06:43Z] 2016-04-14 23:43:11 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:43:11,235 - WARNING - Could not retrieve variants from source file in region 12:105541720-105568366. Error was invalid region `12:105541721-105568366`
[2016-04-15T06:43Z] 2016-04-14 23:43:11 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:43:11,265 - WARNING - Could not retrieve variants from source file in region 12:102224225-102224626. Error was invalid region `12:102224226-102224626`
[2016-04-15T06:43Z] 2016-04-14 23:43:11 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:43:11,959 - WARNING - Could not retrieve variants from source file in region 12:100451816-100452217. Error was invalid region `12:100451817-100452217`
[2016-04-15T06:43Z] 2016-04-14 23:43:12 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:43:12,592 - WARNING - Could not retrieve variants from source file in region 12:101683718-101693724. Error was invalid region `12:101683719-101693724`
[2016-04-15T06:43Z] 2016-04-14 23:43:12 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:43:12,601 - WARNING - Could not retrieve variants from source file in region 12:96927761-96928176. Error was invalid region `12:96927762-96928176`
[2016-04-15T06:43Z] 2016-04-14 23:43:13 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:43:13,292 - WARNING - Could not retrieve variants from source file in region 12:106704763-106723575. Error was invalid region `12:106704764-106723575`
[2016-04-15T06:43Z] 2016-04-14 23:43:13 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:43:13,777 - WARNING - Could not retrieve variants from source file in region 12:103695971-103696372. Error was invalid region `12:103695972-103696372`
[2016-04-15T06:43Z] 2016-04-14 23:43:13 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:43:13,933 - WARNING - Could not retrieve variants from source file in region 12:96640805-96641206. Error was invalid region `12:96640806-96641206`
[2016-04-15T06:43Z] 2016-04-14 23:43:14 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:43:14,895 - WARNING - Could not retrieve variants from source file in region 12:106751664-106752105. Error was invalid region `12:106751665-106752105`
[2016-04-15T06:43Z] 2016-04-14 23:43:15 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:43:15,353 - WARNING - Could not retrieve variants from source file in region 12:95693900-95694584. Error was invalid region `12:95693901-95694584`
[2016-04-15T06:43Z] 2016-04-14 23:43:15 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:43:15,665 - WARNING - Could not retrieve variants from source file in region 12:105600689-105601090. Error was invalid region `12:105600690-105601090`
[2016-04-15T06:43Z] 2016-04-14 23:43:16 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:43:16,229 - WARNING - Could not retrieve variants from source file in region 12:104152793-104153194. Error was invalid region `12:104152794-104153194`
[2016-04-15T06:43Z] 2016-04-14 23:43:16 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:43:16,642 - WARNING - Could not retrieve variants from source file in region 12:102224225-102224626. Error was invalid region `12:102224226-102224626`
[2016-04-15T06:43Z] 2016-04-14 23:43:17 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:43:17,575 - WARNING - Could not retrieve variants from source file in region 12:96927761-96928176. Error was invalid region `12:96927762-96928176`
[2016-04-15T06:43Z] 2016-04-14 23:43:17 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:43:17,921 - WARNING - Could not retrieve variants from source file in region 12:106704763-106723575. Error was invalid region `12:106704764-106723575`
[2016-04-15T06:43Z] 2016-04-14 23:43:19 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:43:19,205 - WARNING - Could not retrieve variants from source file in region 12:103695971-103696372. Error was invalid region `12:103695972-103696372`
[2016-04-15T06:43Z] 2016-04-14 23:43:21 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:43:21,040 - WARNING - Could not retrieve variants from source file in region 12:106751664-106752105. Error was invalid region `12:106751665-106752105`
[2016-04-15T06:43Z] 2016-04-14 23:43:21 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:43:21,542 - WARNING - Could not retrieve variants from source file in region 12:105600689-105601090. Error was invalid region `12:105600690-105601090`
[2016-04-15T06:43Z] 2016-04-14 23:43:22 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:43:22,398 - WARNING - Could not retrieve variants from source file in region 12:102224225-102224626. Error was invalid region `12:102224226-102224626`
[2016-04-15T06:43Z] 2016-04-14 23:43:22 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:43:22,656 - WARNING - Could not retrieve variants from source file in region 12:106704763-106723575. Error was invalid region `12:106704764-106723575`
[2016-04-15T06:43Z] 2016-04-14 23:43:27 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:43:27,564 - WARNING - Could not retrieve variants from source file in region 12:105433312-105434657. Error was invalid region `12:105433313-105434657`
[2016-04-15T06:43Z] 2016-04-14 23:43:28 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:43:28,271 - WARNING - Could not retrieve variants from source file in region 12:100041829-100042353. Error was invalid region `12:100041830-100042353`
[2016-04-15T06:43Z] 2016-04-14 23:43:28 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:43:28,536 - WARNING - Could not retrieve variants from source file in region 12:101551864-101574002. Error was invalid region `12:101551865-101574002`
[2016-04-15T06:43Z] 2016-04-14 23:43:33 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:43:33,318 - WARNING - Could not retrieve variants from source file in region 12:105433312-105434657. Error was invalid region `12:105433313-105434657`
[2016-04-15T06:43Z] 2016-04-14 23:43:34 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:43:34,321 - WARNING - Could not retrieve variants from source file in region 12:96374403-96374804. Error was invalid region `12:96374404-96374804`
[2016-04-15T06:43Z] 2016-04-14 23:43:35 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:43:35,639 - WARNING - Could not retrieve variants from source file in region 12:101520478-101520879. Error was invalid region `12:101520479-101520879`
[2016-04-15T06:43Z] 2016-04-14 23:43:35 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:43:35,704 - WARNING - Could not retrieve variants from source file in region 12:101732444-101751004. Error was invalid region `12:101732445-101751004`
[2016-04-15T06:43Z] 2016-04-14 23:43:36 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:43:36,455 - WARNING - Could not retrieve variants from source file in region 12:102158552-102158953. Error was invalid region `12:102158553-102158953`
[2016-04-15T06:43Z] 2016-04-14 23:43:36 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:43:36,846 - WARNING - Could not retrieve variants from source file in region 12:96883416-96883817. Error was invalid region `12:96883417-96883817`
[2016-04-15T06:43Z] 2016-04-14 23:43:38 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:43:38,244 - WARNING - Could not retrieve variants from source file in region 12:100041829-100042353. Error was invalid region `12:100041830-100042353`
[2016-04-15T06:43Z] 2016-04-14 23:43:38 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:43:38,245 - WARNING - Could not retrieve variants from source file in region 12:103351960-103352361. Error was invalid region `12:103351961-103352361`
[2016-04-15T06:43Z] 2016-04-14 23:43:38 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:43:38,265 - WARNING - Could not retrieve variants from source file in region 12:105433312-105434657. Error was invalid region `12:105433313-105434657`
[2016-04-15T06:43Z] 2016-04-14 23:43:38 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:43:38,402 - WARNING - Could not retrieve variants from source file in region 12:96374403-96374804. Error was invalid region `12:96374404-96374804`
[2016-04-15T06:43Z] 2016-04-14 23:43:39 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:43:39,367 - WARNING - Could not retrieve variants from source file in region 12:95659971-95660372. Error was invalid region `12:95659972-95660372`
[2016-04-15T06:43Z] 2016-04-14 23:43:40 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:43:40,503 - WARNING - Could not retrieve variants from source file in region 12:105379941-105380342. Error was invalid region `12:105379942-105380342`
[2016-04-15T06:43Z] 2016-04-14 23:43:40 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:43:40,865 - WARNING - Could not retrieve variants from source file in region 12:102158552-102158953. Error was invalid region `12:102158553-102158953`
[2016-04-15T06:43Z] 2016-04-14 23:43:42 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:43:42,756 - WARNING - Could not retrieve variants from source file in region 12:103351960-103352361. Error was invalid region `12:103351961-103352361`
[2016-04-15T06:43Z] 2016-04-14 23:43:42 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:43:42,934 - WARNING - Could not retrieve variants from source file in region 12:96374403-96374804. Error was invalid region `12:96374404-96374804`
[2016-04-15T06:43Z] 2016-04-14 23:43:45 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:43:45,369 - WARNING - Could not retrieve variants from source file in region 12:101732444-101751004. Error was invalid region `12:101732445-101751004`
[2016-04-15T06:43Z] 2016-04-14 23:43:45 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:43:45,590 - WARNING - Could not retrieve variants from source file in region 12:102158552-102158953. Error was invalid region `12:102158553-102158953`
[2016-04-15T06:43Z] 2016-04-14 23:43:50 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:43:50,305 - WARNING - Could not retrieve variants from source file in region 12:101017234-101018271. Error was invalid region `12:101017235-101018271`
[2016-04-15T06:43Z] 2016-04-14 23:43:50 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:43:50,688 - WARNING - Could not retrieve variants from source file in region 12:99640217-99640747. Error was invalid region `12:99640218-99640747`
[2016-04-15T06:43Z] 2016-04-14 23:43:55 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:43:55,074 - WARNING - Could not retrieve variants from source file in region 12:96131684-96132085. Error was invalid region `12:96131685-96132085`
[2016-04-15T06:43Z] 2016-04-14 23:43:56 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:43:56,223 - WARNING - Could not retrieve variants from source file in region 12:100631586-100657654. Error was invalid region `12:100631587-100657654`
[2016-04-15T06:43Z] 2016-04-14 23:43:57 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:43:57,576 - WARNING - Could not retrieve variants from source file in region 12:99018847-99020315. Error was invalid region `12:99018848-99020315`
[2016-04-15T06:43Z] 2016-04-14 23:43:57 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:43:57,607 - WARNING - Could not retrieve variants from source file in region 12:94673066-94673467. Error was invalid region `12:94673067-94673467`
[2016-04-15T06:43Z] 2016-04-14 23:43:58 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:43:58,473 - WARNING - Could not retrieve variants from source file in region 12:96077101-96077502. Error was invalid region `12:96077102-96077502`
[2016-04-15T06:43Z] 2016-04-14 23:43:58 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:43:58,941 - WARNING - Could not retrieve variants from source file in region 12:94620221-94645445. Error was invalid region `12:94620222-94645445`
[2016-04-15T06:43Z] 2016-04-14 23:43:59 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:43:59,565 - WARNING - Could not retrieve variants from source file in region 12:94543295-94543696. Error was invalid region `12:94543296-94543696`
[2016-04-15T06:43Z] 2016-04-14 23:43:59 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:43:59,680 - WARNING - Could not retrieve variants from source file in region 12:97254409-97254810. Error was invalid region `12:97254410-97254810`
[2016-04-15T06:44Z] 2016-04-14 23:44:00 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:44:00,170 - WARNING - Could not retrieve variants from source file in region 12:96131684-96132085. Error was invalid region `12:96131685-96132085`
[2016-04-15T06:44Z] 2016-04-14 23:44:03 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:44:03,681 - WARNING - Could not retrieve variants from source file in region 12:96077101-96077502. Error was invalid region `12:96077102-96077502`
[2016-04-15T06:44Z] 2016-04-14 23:44:04 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:44:04,799 - WARNING - Could not retrieve variants from source file in region 12:94543295-94543696. Error was invalid region `12:94543296-94543696`
[2016-04-15T06:44Z] 2016-04-14 23:44:05 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:44:05,244 - WARNING - Could not retrieve variants from source file in region 12:94673066-94673467. Error was invalid region `12:94673067-94673467`
[2016-04-15T06:44Z] 2016-04-14 23:44:05 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:44:05,439 - WARNING - Could not retrieve variants from source file in region 12:95531231-95531632. Error was invalid region `12:95531232-95531632`
[2016-04-15T06:44Z] 2016-04-14 23:44:05 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:44:05,495 - WARNING - Could not retrieve variants from source file in region 12:97254409-97254810. Error was invalid region `12:97254410-97254810`
[2016-04-15T06:44Z] 2016-04-14 23:44:07 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:44:07,991 - WARNING - Could not retrieve variants from source file in region 12:96077101-96077502. Error was invalid region `12:96077102-96077502`
[2016-04-15T06:44Z] 2016-04-14 23:44:10 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:44:10,071 - WARNING - Could not retrieve variants from source file in region 12:94543295-94543696. Error was invalid region `12:94543296-94543696`
[2016-04-15T06:44Z] 2016-04-14 23:44:10 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:44:10,498 - WARNING - Could not retrieve variants from source file in region 12:97254409-97254810. Error was invalid region `12:97254410-97254810`
[2016-04-15T06:44Z] 2016-04-14 23:44:10 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:44:10,520 - WARNING - Could not retrieve variants from source file in region 12:95531231-95531632. Error was invalid region `12:95531232-95531632`
[2016-04-15T06:44Z] 2016-04-14 23:44:15 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:44:15,082 - WARNING - Could not retrieve variants from source file in region 12:99288441-99288842. Error was invalid region `12:99288442-99288842`
[2016-04-15T06:44Z] 2016-04-14 23:44:17 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:44:17,516 - WARNING - Could not retrieve variants from source file in region 12:95043950-95044351. Error was invalid region `12:95043951-95044351`
[2016-04-15T06:44Z] 2016-04-14 23:44:17 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:44:17,551 - WARNING - Could not retrieve variants from source file in region 12:98928435-98928836. Error was invalid region `12:98928436-98928836`
[2016-04-15T06:44Z] 2016-04-14 23:44:18 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:44:18,354 - WARNING - Could not retrieve variants from source file in region 12:95043950-95044351. Error was invalid region `12:95043951-95044351`
[2016-04-15T06:44Z] 2016-04-14 23:44:18 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:44:18,753 - WARNING - Could not retrieve variants from source file in region 12:97133526-97136429. Error was invalid region `12:97133527-97136429`
[2016-04-15T06:44Z] 2016-04-14 23:44:18 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:44:18,803 - WARNING - Could not retrieve variants from source file in region 12:97133526-97136429. Error was invalid region `12:97133527-97136429`
[2016-04-15T06:44Z] 2016-04-14 23:44:18 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:44:18,819 - WARNING - Could not retrieve variants from source file in region 12:97133526-97136429. Error was invalid region `12:97133527-97136429`
[2016-04-15T06:44Z] 2016-04-14 23:44:18 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:44:18,848 - WARNING - Could not retrieve variants from source file in region 12:95043950-95044351. Error was invalid region `12:95043951-95044351`
[2016-04-15T06:44Z] 2016-04-14 23:44:19 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:44:19,237 - WARNING - Could not retrieve variants from source file in region 12:97098338-97102768. Error was invalid region `12:97098339-97102768`
[2016-04-15T06:44Z] 2016-04-14 23:44:21 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:44:21,097 - WARNING - Could not retrieve variants from source file in region 12:98928435-98928836. Error was invalid region `12:98928436-98928836`
[2016-04-15T06:44Z] 2016-04-14 23:44:22 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:44:22,578 - WARNING - Could not retrieve variants from source file in region 12:97098338-97102768. Error was invalid region `12:97098339-97102768`
[2016-04-15T06:44Z] 2016-04-14 23:44:22 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:44:22,622 - WARNING - Could not retrieve variants from source file in region 12:97098338-97102768. Error was invalid region `12:97098339-97102768`
[2016-04-15T06:44Z] ['bcbio-variation-recall', 'square', '-Xms750m', '-Xmx7280m', '-XX:+UseSerialGC', '-c', 16, '-r', u'12:109494487-125263132', '--caller', 'platypus', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/12/Batch1-12_109494486_125263132.vcf.gz', '/mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/12/Batch1-12_109494486_125263132.vcf-inputs.txt'] in region: 12:109494487-125263132
[2016-04-15T06:44Z] 2016-04-14 23:44:38 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:44:38,599 - WARNING - Could not retrieve variants from source file in region 12:109883163-109909344. Error was invalid region `12:109883164-109909344`
[2016-04-15T06:44Z] 2016-04-14 23:44:38 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:44:38,699 - WARNING - Could not retrieve variants from source file in region 12:109971826-110019528. Error was invalid region `12:109971827-110019528`
[2016-04-15T06:44Z] 2016-04-14 23:44:40 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:44:40,186 - WARNING - Could not retrieve variants from source file in region 12:110240627-110241028. Error was invalid region `12:110240628-110241028`
[2016-04-15T06:44Z] 2016-04-14 23:44:40 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:44:40,472 - WARNING - Could not retrieve variants from source file in region 12:117216930-117217331. Error was invalid region `12:117216931-117217331`
[2016-04-15T06:44Z] 2016-04-14 23:44:41 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:44:41,002 - WARNING - Could not retrieve variants from source file in region 12:120802316-120802717. Error was invalid region `12:120802317-120802717`
[2016-04-15T06:44Z] 2016-04-14 23:44:41 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:44:41,632 - WARNING - Could not retrieve variants from source file in region 12:122186057-122186507. Error was invalid region `12:122186058-122186507`
[2016-04-15T06:44Z] 2016-04-14 23:44:41 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:44:41,829 - WARNING - Could not retrieve variants from source file in region 12:123070007-123070408. Error was invalid region `12:123070008-123070408`
[2016-04-15T06:44Z] 2016-04-14 23:44:41 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:44:41,832 - WARNING - Could not retrieve variants from source file in region 12:110618024-110618425. Error was invalid region `12:110618025-110618425`
[2016-04-15T06:44Z] 2016-04-14 23:44:41 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:44:41,843 - WARNING - Could not retrieve variants from source file in region 12:110779896-110780297. Error was invalid region `12:110779897-110780297`
[2016-04-15T06:44Z] 2016-04-14 23:44:42 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:44:42,020 - WARNING - Could not retrieve variants from source file in region 12:118682540-118682941. Error was invalid region `12:118682541-118682941`
[2016-04-15T06:44Z] 2016-04-14 23:44:42 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:44:42,146 - WARNING - Could not retrieve variants from source file in region 12:124209121-124229619. Error was invalid region `12:124209122-124229619`
[2016-04-15T06:44Z] 2016-04-14 23:44:44 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:44:44,835 - WARNING - Could not retrieve variants from source file in region 12:109883163-109909344. Error was invalid region `12:109883164-109909344`
[2016-04-15T06:44Z] 2016-04-14 23:44:45 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:44:45,162 - WARNING - Could not retrieve variants from source file in region 12:109971826-110019528. Error was invalid region `12:109971827-110019528`
[2016-04-15T06:44Z] 2016-04-14 23:44:46 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:44:46,835 - WARNING - Could not retrieve variants from source file in region 12:110939080-110939481. Error was invalid region `12:110939081-110939481`
[2016-04-15T06:44Z] 2016-04-14 23:44:47 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:44:47,711 - WARNING - Could not retrieve variants from source file in region 12:110240627-110241028. Error was invalid region `12:110240628-110241028`
[2016-04-15T06:44Z] 2016-04-14 23:44:47 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:44:47,779 - WARNING - Could not retrieve variants from source file in region 12:124103838-124104876. Error was invalid region `12:124103839-124104876`
[2016-04-15T06:44Z] 2016-04-14 23:44:49 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:44:49,338 - WARNING - Could not retrieve variants from source file in region 12:117216930-117217331. Error was invalid region `12:117216931-117217331`
[2016-04-15T06:44Z] 2016-04-14 23:44:49 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:44:49,375 - WARNING - Could not retrieve variants from source file in region 12:122481668-122482069. Error was invalid region `12:122481669-122482069`
[2016-04-15T06:44Z] 2016-04-14 23:44:49 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:44:49,783 - WARNING - Could not retrieve variants from source file in region 12:122186057-122186507. Error was invalid region `12:122186058-122186507`
[2016-04-15T06:44Z] 2016-04-14 23:44:50 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:44:50,047 - WARNING - Could not retrieve variants from source file in region 12:124209121-124229619. Error was invalid region `12:124209122-124229619`
[2016-04-15T06:44Z] 2016-04-14 23:44:50 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:44:50,122 - WARNING - Could not retrieve variants from source file in region 12:123070007-123070408. Error was invalid region `12:123070008-123070408`
[2016-04-15T06:44Z] 2016-04-14 23:44:50 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:44:50,208 - WARNING - Could not retrieve variants from source file in region 12:109883163-109909344. Error was invalid region `12:109883164-109909344`
[2016-04-15T06:44Z] 2016-04-14 23:44:50 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:44:50,253 - WARNING - Could not retrieve variants from source file in region 12:109971826-110019528. Error was invalid region `12:109971827-110019528`
[2016-04-15T06:44Z] 2016-04-14 23:44:52 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:44:52,842 - WARNING - Could not retrieve variants from source file in region 12:124103838-124104876. Error was invalid region `12:124103839-124104876`
[2016-04-15T06:44Z] 2016-04-14 23:44:53 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:44:53,110 - WARNING - Could not retrieve variants from source file in region 12:110240627-110241028. Error was invalid region `12:110240628-110241028`
[2016-04-15T06:44Z] 2016-04-14 23:44:56 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:44:56,497 - WARNING - Could not retrieve variants from source file in region 12:117216930-117217331. Error was invalid region `12:117216931-117217331`
[2016-04-15T06:44Z] 2016-04-14 23:44:56 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:44:56,561 - WARNING - Could not retrieve variants from source file in region 12:122481668-122482069. Error was invalid region `12:122481669-122482069`
[2016-04-15T06:44Z] 2016-04-14 23:44:57 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:44:57,081 - WARNING - Could not retrieve variants from source file in region 12:122186057-122186507. Error was invalid region `12:122186058-122186507`
[2016-04-15T06:44Z] 2016-04-14 23:44:57 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:44:57,390 - WARNING - Could not retrieve variants from source file in region 12:123070007-123070408. Error was invalid region `12:123070008-123070408`
[2016-04-15T06:44Z] 2016-04-14 23:44:57 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:44:57,498 - WARNING - Could not retrieve variants from source file in region 12:124209121-124229619. Error was invalid region `12:124209122-124229619`
[2016-04-15T06:44Z] 2016-04-14 23:44:57 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:44:57,560 - WARNING - Could not retrieve variants from source file in region 12:124957416-124980023. Error was invalid region `12:124957417-124980023`
[2016-04-15T06:45Z] 2016-04-14 23:45:07 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:45:07,502 - WARNING - Could not retrieve variants from source file in region 12:109826423-109848757. Error was invalid region `12:109826424-109848757`
[2016-04-15T06:45Z] 2016-04-14 23:45:08 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:45:08,056 - WARNING - Could not retrieve variants from source file in region 12:109937323-109937724. Error was invalid region `12:109937324-109937724`
[2016-04-15T06:45Z] 2016-04-14 23:45:08 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:45:08,908 - WARNING - Could not retrieve variants from source file in region 12:124069002-124069403. Error was invalid region `12:124069003-124069403`
[2016-04-15T06:45Z] 2016-04-14 23:45:08 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:45:08,922 - WARNING - Could not retrieve variants from source file in region 12:109937323-109937724. Error was invalid region `12:109937324-109937724`
[2016-04-15T06:45Z] 2016-04-14 23:45:10 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:45:10,064 - WARNING - Could not retrieve variants from source file in region 12:124325766-124326167. Error was invalid region `12:124325767-124326167`
[2016-04-15T06:45Z] 2016-04-14 23:45:12 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:45:12,696 - WARNING - Could not retrieve variants from source file in region 12:117187696-117188097. Error was invalid region `12:117187697-117188097`
[2016-04-15T06:45Z] 2016-04-14 23:45:13 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:45:13,366 - WARNING - Could not retrieve variants from source file in region 12:122064562-122064969. Error was invalid region `12:122064563-122064969`
[2016-04-15T06:45Z] 2016-04-14 23:45:13 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:45:13,442 - WARNING - Could not retrieve variants from source file in region 12:109826423-109848757. Error was invalid region `12:109826424-109848757`
[2016-04-15T06:45Z] 2016-04-14 23:45:13 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:45:13,831 - WARNING - Could not retrieve variants from source file in region 12:123014494-123030978. Error was invalid region `12:123014495-123030978`
[2016-04-15T06:45Z] 2016-04-14 23:45:13 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:45:13,921 - WARNING - Could not retrieve variants from source file in region 12:109937323-109937724. Error was invalid region `12:109937324-109937724`
[2016-04-15T06:45Z] 2016-04-14 23:45:14 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:45:14,336 - WARNING - Could not retrieve variants from source file in region 12:109605519-109629647. Error was invalid region `12:109605520-109629647`
[2016-04-15T06:45Z] 2016-04-14 23:45:14 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:45:14,407 - WARNING - Could not retrieve variants from source file in region 12:124069002-124069403. Error was invalid region `12:124069003-124069403`
[2016-04-15T06:45Z] 2016-04-14 23:45:14 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:45:14,461 - WARNING - Could not retrieve variants from source file in region 12:124886847-124887248. Error was invalid region `12:124886848-124887248`
[2016-04-15T06:45Z] 2016-04-14 23:45:14 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:45:14,902 - WARNING - Could not retrieve variants from source file in region 12:124325766-124326167. Error was invalid region `12:124325767-124326167`
[2016-04-15T06:45Z] 2016-04-14 23:45:15 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:45:15,821 - WARNING - Could not retrieve variants from source file in region 12:122396184-122406102. Error was invalid region `12:122396185-122406102`
[2016-04-15T06:45Z] 2016-04-14 23:45:18 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:45:18,402 - WARNING - Could not retrieve variants from source file in region 12:122064562-122064969. Error was invalid region `12:122064563-122064969`
[2016-04-15T06:45Z] 2016-04-14 23:45:18 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:45:18,792 - WARNING - Could not retrieve variants from source file in region 12:109826423-109848757. Error was invalid region `12:109826424-109848757`
[2016-04-15T06:45Z] 2016-04-14 23:45:19 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:45:19,768 - WARNING - Could not retrieve variants from source file in region 12:124179206-124179607. Error was invalid region `12:124179207-124179607`
[2016-04-15T06:45Z] 2016-04-14 23:45:20 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:45:20,331 - WARNING - Could not retrieve variants from source file in region 12:124069002-124069403. Error was invalid region `12:124069003-124069403`
[2016-04-15T06:45Z] 2016-04-14 23:45:20 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:45:20,567 - WARNING - Could not retrieve variants from source file in region 12:124325766-124326167. Error was invalid region `12:124325767-124326167`
[2016-04-15T06:45Z] 2016-04-14 23:45:21 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:45:21,064 - WARNING - Could not retrieve variants from source file in region 12:120741171-120763027. Error was invalid region `12:120741172-120763027`
[2016-04-15T06:45Z] 2016-04-14 23:45:23 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:45:23,022 - WARNING - Could not retrieve variants from source file in region 12:122064562-122064969. Error was invalid region `12:122064563-122064969`
[2016-04-15T06:45Z] 2016-04-14 23:45:25 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:45:25,392 - WARNING - Could not retrieve variants from source file in region 12:124179206-124179607. Error was invalid region `12:124179207-124179607`
[2016-04-15T06:45Z] 2016-04-14 23:45:25 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:45:25,872 - WARNING - Could not retrieve variants from source file in region 12:109605519-109629647. Error was invalid region `12:109605520-109629647`
[2016-04-15T06:45Z] 2016-04-14 23:45:28 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:45:28,126 - WARNING - Could not retrieve variants from source file in region 12:123645592-123645993. Error was invalid region `12:123645593-123645993`
[2016-04-15T06:45Z] 2016-04-14 23:45:29 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:45:29,159 - WARNING - Could not retrieve variants from source file in region 12:109674818-109717887. Error was invalid region `12:109674819-109717887`
[2016-04-15T06:45Z] 2016-04-14 23:45:34 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:45:34,053 - WARNING - Could not retrieve variants from source file in region 12:123645592-123645993. Error was invalid region `12:123645593-123645993`
[2016-04-15T06:45Z] 2016-04-14 23:45:34 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:45:34,951 - WARNING - Could not retrieve variants from source file in region 12:109674818-109717887. Error was invalid region `12:109674819-109717887`
[2016-04-15T06:45Z] 2016-04-14 23:45:35 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:45:35,516 - WARNING - Could not retrieve variants from source file in region 12:109577524-109577925. Error was invalid region `12:109577525-109577925`
[2016-04-15T06:45Z] 2016-04-14 23:45:35 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:45:35,614 - WARNING - Could not retrieve variants from source file in region 12:124007862-124008263. Error was invalid region `12:124007863-124008263`
[2016-04-15T06:45Z] 2016-04-14 23:45:36 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:45:36,194 - WARNING - Could not retrieve variants from source file in region 12:120687724-120688125. Error was invalid region `12:120687725-120688125`
[2016-04-15T06:45Z] 2016-04-14 23:45:38 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:45:38,030 - WARNING - Could not retrieve variants from source file in region 12:121878448-121882038. Error was invalid region `12:121878449-121882038`
[2016-04-15T06:45Z] 2016-04-14 23:45:38 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:45:38,996 - WARNING - Could not retrieve variants from source file in region 12:123645592-123645993. Error was invalid region `12:123645593-123645993`
[2016-04-15T06:45Z] 2016-04-14 23:45:40 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:45:40,717 - WARNING - Could not retrieve variants from source file in region 12:124007862-124008263. Error was invalid region `12:124007863-124008263`
[2016-04-15T06:45Z] 2016-04-14 23:45:41 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:45:41,681 - WARNING - Could not retrieve variants from source file in region 12:120687724-120688125. Error was invalid region `12:120687725-120688125`
[2016-04-15T06:45Z] 2016-04-14 23:45:41 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:45:41,685 - WARNING - Could not retrieve variants from source file in region 12:109511045-109520959. Error was invalid region `12:109511046-109520959`
[2016-04-15T06:45Z] 2016-04-14 23:45:41 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:45:41,709 - WARNING - Could not retrieve variants from source file in region 12:118199075-118199476. Error was invalid region `12:118199076-118199476`
[2016-04-15T06:45Z] 2016-04-14 23:45:42 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:45:42,044 - WARNING - Could not retrieve variants from source file in region 12:124856407-124857223. Error was invalid region `12:124856408-124857223`
[2016-04-15T06:45Z] 2016-04-14 23:45:42 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:45:42,186 - WARNING - Could not retrieve variants from source file in region 12:122353585-122369952. Error was invalid region `12:122353586-122369952`
[2016-04-15T06:45Z] 2016-04-14 23:45:42 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:45:42,520 - WARNING - Could not retrieve variants from source file in region 12:114374676-114395841. Error was invalid region `12:114374677-114395841`
[2016-04-15T06:45Z] 2016-04-14 23:45:43 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:45:43,224 - WARNING - Could not retrieve variants from source file in region 12:121878448-121882038. Error was invalid region `12:121878449-121882038`
[2016-04-15T06:45Z] 2016-04-14 23:45:43 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:45:43,946 - WARNING - Could not retrieve variants from source file in region 12:122862022-122862423. Error was invalid region `12:122862023-122862423`
[2016-04-15T06:45Z] 2016-04-14 23:45:45 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:45:45,748 - WARNING - Could not retrieve variants from source file in region 12:124007862-124008263. Error was invalid region `12:124007863-124008263`
[2016-04-15T06:45Z] 2016-04-14 23:45:46 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:45:46,167 - WARNING - Could not retrieve variants from source file in region 12:109577524-109577925. Error was invalid region `12:109577525-109577925`
[2016-04-15T06:45Z] 2016-04-14 23:45:46 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:45:46,224 - WARNING - Could not retrieve variants from source file in region 12:118199075-118199476. Error was invalid region `12:118199076-118199476`
[2016-04-15T06:45Z] 2016-04-14 23:45:47 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:45:47,383 - WARNING - Could not retrieve variants from source file in region 12:124856407-124857223. Error was invalid region `12:124856408-124857223`
[2016-04-15T06:45Z] 2016-04-14 23:45:47 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:45:47,766 - WARNING - Could not retrieve variants from source file in region 12:121878448-121882038. Error was invalid region `12:121878449-121882038`
[2016-04-15T06:45Z] 2016-04-14 23:45:48 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:45:48,157 - WARNING - Could not retrieve variants from source file in region 12:122862022-122862423. Error was invalid region `12:122862023-122862423`
[2016-04-15T06:45Z] 2016-04-14 23:45:48 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:45:48,456 - WARNING - Could not retrieve variants from source file in region 12:124144184-124144585. Error was invalid region `12:124144185-124144585`
[2016-04-15T06:45Z] 2016-04-14 23:45:50 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:45:50,794 - WARNING - Could not retrieve variants from source file in region 12:118199075-118199476. Error was invalid region `12:118199076-118199476`
[2016-04-15T06:45Z] 2016-04-14 23:45:52 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:45:52,092 - WARNING - Could not retrieve variants from source file in region 12:123470375-123471284. Error was invalid region `12:123470376-123471284`
[2016-04-15T06:45Z] 2016-04-14 23:45:52 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:45:52,125 - WARNING - Could not retrieve variants from source file in region 12:109511045-109520959. Error was invalid region `12:109511046-109520959`
[2016-04-15T06:45Z] 2016-04-14 23:45:52 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:45:52,455 - WARNING - Could not retrieve variants from source file in region 12:124856407-124857223. Error was invalid region `12:124856408-124857223`
[2016-04-15T06:45Z] 2016-04-14 23:45:58 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:45:58,724 - WARNING - Could not retrieve variants from source file in region 12:123755373-123755782. Error was invalid region `12:123755374-123755782`
[2016-04-15T06:46Z] 2016-04-14 23:46:00 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:46:00,128 - WARNING - Could not retrieve variants from source file in region 12:120661766-120662167. Error was invalid region `12:120661767-120662167`
[2016-04-15T06:46Z] 2016-04-14 23:46:01 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:46:01,133 - WARNING - Could not retrieve variants from source file in region 12:122326601-122327002. Error was invalid region `12:122326602-122327002`
[2016-04-15T06:46Z] 2016-04-14 23:46:01 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:46:01,389 - WARNING - Could not retrieve variants from source file in region 12:121711866-121712267. Error was invalid region `12:121711867-121712267`
[2016-04-15T06:46Z] 2016-04-14 23:46:01 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:46:01,752 - WARNING - Could not retrieve variants from source file in region 12:123755373-123755782. Error was invalid region `12:123755374-123755782`
[2016-04-15T06:46Z] 2016-04-14 23:46:02 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:46:02,424 - WARNING - Could not retrieve variants from source file in region 12:122812292-122812693. Error was invalid region `12:122812293-122812693`
[2016-04-15T06:46Z] 2016-04-14 23:46:02 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:46:02,858 - WARNING - Could not retrieve variants from source file in region 12:123710624-123711025. Error was invalid region `12:123710625-123711025`
[2016-04-15T06:46Z] 2016-04-14 23:46:03 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:46:03,266 - WARNING - Could not retrieve variants from source file in region 12:118019904-118020305. Error was invalid region `12:118019905-118020305`
[2016-04-15T06:46Z] 2016-04-14 23:46:03 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:46:03,464 - WARNING - Could not retrieve variants from source file in region 12:123755373-123755782. Error was invalid region `12:123755374-123755782`
[2016-04-15T06:46Z] 2016-04-14 23:46:04 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:46:04,815 - WARNING - Could not retrieve variants from source file in region 12:120661766-120662167. Error was invalid region `12:120661767-120662167`
[2016-04-15T06:46Z] 2016-04-14 23:46:07 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:46:07,687 - WARNING - Could not retrieve variants from source file in region 12:122295124-122295525. Error was invalid region `12:122295125-122295525`
[2016-04-15T06:46Z] 2016-04-14 23:46:07 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:46:07,823 - WARNING - Could not retrieve variants from source file in region 12:124472360-124496506. Error was invalid region `12:124472361-124496506`
[2016-04-15T06:46Z] 2016-04-14 23:46:08 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:46:08,648 - WARNING - Could not retrieve variants from source file in region 12:122326601-122327002. Error was invalid region `12:122326602-122327002`
[2016-04-15T06:46Z] 2016-04-14 23:46:08 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:46:08,713 - WARNING - Could not retrieve variants from source file in region 12:121711866-121712267. Error was invalid region `12:121711867-121712267`
[2016-04-15T06:46Z] 2016-04-14 23:46:09 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:46:09,415 - WARNING - Could not retrieve variants from source file in region 12:122812292-122812693. Error was invalid region `12:122812293-122812693`
[2016-04-15T06:46Z] 2016-04-14 23:46:09 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:46:09,469 - WARNING - Could not retrieve variants from source file in region 12:114282285-114282686. Error was invalid region `12:114282286-114282686`
[2016-04-15T06:46Z] 2016-04-14 23:46:09 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:46:09,623 - WARNING - Could not retrieve variants from source file in region 12:123710624-123711025. Error was invalid region `12:123710625-123711025`
[2016-04-15T06:46Z] 2016-04-14 23:46:09 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:46:09,738 - WARNING - Could not retrieve variants from source file in region 12:120661766-120662167. Error was invalid region `12:120661767-120662167`
[2016-04-15T06:46Z] 2016-04-14 23:46:12 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:46:12,349 - WARNING - Could not retrieve variants from source file in region 12:122295124-122295525. Error was invalid region `12:122295125-122295525`
[2016-04-15T06:46Z] 2016-04-14 23:46:13 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:46:13,511 - WARNING - Could not retrieve variants from source file in region 12:122658281-122691928. Error was invalid region `12:122658282-122691928`
[2016-04-15T06:46Z] 2016-04-14 23:46:15 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:46:15,466 - WARNING - Could not retrieve variants from source file in region 12:123710624-123711025. Error was invalid region `12:123710625-123711025`
[2016-04-15T06:46Z] 2016-04-14 23:46:16 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:46:16,007 - WARNING - Could not retrieve variants from source file in region 12:122326601-122327002. Error was invalid region `12:122326602-122327002`
[2016-04-15T06:46Z] 2016-04-14 23:46:16 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:46:16,021 - WARNING - Could not retrieve variants from source file in region 12:121711866-121712267. Error was invalid region `12:121711867-121712267`
[2016-04-15T06:46Z] 2016-04-14 23:46:16 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:46:16,460 - WARNING - Could not retrieve variants from source file in region 12:112036542-112037190. Error was invalid region `12:112036543-112037190`
[2016-04-15T06:46Z] 2016-04-14 23:46:16 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:46:16,542 - WARNING - Could not retrieve variants from source file in region 12:122812292-122812693. Error was invalid region `12:122812293-122812693`
[2016-04-15T06:46Z] 2016-04-14 23:46:16 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:46:16,615 - WARNING - Could not retrieve variants from source file in region 12:114282285-114282686. Error was invalid region `12:114282286-114282686`
[2016-04-15T06:46Z] 2016-04-14 23:46:16 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:46:16,628 - WARNING - Could not retrieve variants from source file in region 12:118019904-118020305. Error was invalid region `12:118019905-118020305`
[2016-04-15T06:46Z] 2016-04-14 23:46:17 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:46:17,417 - WARNING - Could not retrieve variants from source file in region 12:122295124-122295525. Error was invalid region `12:122295125-122295525`
[2016-04-15T06:46Z] 2016-04-14 23:46:18 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:46:18,023 - WARNING - Could not retrieve variants from source file in region 12:122658281-122691928. Error was invalid region `12:122658282-122691928`
[2016-04-15T06:46Z] 2016-04-14 23:46:19 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:46:19,635 - WARNING - Could not retrieve variants from source file in region 12:123332854-123357201. Error was invalid region `12:123332855-123357201`
[2016-04-15T06:46Z] 2016-04-14 23:46:20 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:46:20,812 - WARNING - Could not retrieve variants from source file in region 12:117701503-117710436. Error was invalid region `12:117701504-117710436`
[2016-04-15T06:46Z] 2016-04-14 23:46:24 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:46:24,773 - WARNING - Could not retrieve variants from source file in region 12:123332854-123357201. Error was invalid region `12:123332855-123357201`
[2016-04-15T06:46Z] 2016-04-14 23:46:29 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:46:29,946 - WARNING - Could not retrieve variants from source file in region 12:123332854-123357201. Error was invalid region `12:123332855-123357201`
[2016-04-15T06:46Z] 2016-04-14 23:46:31 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:46:31,265 - WARNING - Could not retrieve variants from source file in region 12:123253587-123254046. Error was invalid region `12:123253588-123254046`
[2016-04-15T06:46Z] 2016-04-14 23:46:32 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:46:32,523 - WARNING - Could not retrieve variants from source file in region 12:113553270-113553671. Error was invalid region `12:113553271-113553671`
[2016-04-15T06:46Z] 2016-04-14 23:46:33 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:46:33,098 - WARNING - Could not retrieve variants from source file in region 12:122243694-122261646. Error was invalid region `12:122243695-122261646`
[2016-04-15T06:46Z] 2016-04-14 23:46:33 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:46:33,315 - WARNING - Could not retrieve variants from source file in region 12:121174688-121176869. Error was invalid region `12:121174689-121176869`
[2016-04-15T06:46Z] 2016-04-14 23:46:35 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:46:35,602 - WARNING - Could not retrieve variants from source file in region 12:122613998-122618756. Error was invalid region `12:122613999-122618756`
[2016-04-15T06:46Z] 2016-04-14 23:46:35 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:46:35,672 - WARNING - Could not retrieve variants from source file in region 12:123253587-123254046. Error was invalid region `12:123253588-123254046`
[2016-04-15T06:46Z] 2016-04-14 23:46:36 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:46:36,619 - WARNING - Could not retrieve variants from source file in region 12:111884397-111884798. Error was invalid region `12:111884398-111884798`
[2016-04-15T06:46Z] 2016-04-14 23:46:37 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:46:37,250 - WARNING - Could not retrieve variants from source file in region 12:113553270-113553671. Error was invalid region `12:113553271-113553671`
[2016-04-15T06:46Z] 2016-04-14 23:46:37 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:46:37,431 - WARNING - Could not retrieve variants from source file in region 12:117962550-117962951. Error was invalid region `12:117962551-117962951`
[2016-04-15T06:46Z] 2016-04-14 23:46:37 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:46:37,486 - WARNING - Could not retrieve variants from source file in region 12:113348659-113448478. Error was invalid region `12:113348660-113448478`
[2016-04-15T06:46Z] 2016-04-14 23:46:37 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:46:37,635 - WARNING - Could not retrieve variants from source file in region 12:122243694-122261646. Error was invalid region `12:122243695-122261646`
[2016-04-15T06:46Z] 2016-04-14 23:46:40 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:46:40,147 - WARNING - Could not retrieve variants from source file in region 12:122613998-122618756. Error was invalid region `12:122613999-122618756`
[2016-04-15T06:46Z] 2016-04-14 23:46:40 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:46:40,185 - WARNING - Could not retrieve variants from source file in region 12:123253587-123254046. Error was invalid region `12:123253588-123254046`
[2016-04-15T06:46Z] 2016-04-14 23:46:40 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:46:40,789 - WARNING - Could not retrieve variants from source file in region 12:111884397-111884798. Error was invalid region `12:111884398-111884798`
[2016-04-15T06:46Z] 2016-04-14 23:46:41 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:46:41,366 - WARNING - Could not retrieve variants from source file in region 12:113553270-113553671. Error was invalid region `12:113553271-113553671`
[2016-04-15T06:46Z] 2016-04-14 23:46:41 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:46:41,906 - WARNING - Could not retrieve variants from source file in region 12:117962550-117962951. Error was invalid region `12:117962551-117962951`
[2016-04-15T06:46Z] 2016-04-14 23:46:42 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:46:42,247 - WARNING - Could not retrieve variants from source file in region 12:113348659-113448478. Error was invalid region `12:113348660-113448478`
[2016-04-15T06:46Z] 2016-04-14 23:46:42 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:46:42,332 - WARNING - Could not retrieve variants from source file in region 12:122243694-122261646. Error was invalid region `12:122243695-122261646`
[2016-04-15T06:46Z] 2016-04-14 23:46:47 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:46:47,496 - WARNING - Could not retrieve variants from source file in region 12:123200036-123201127. Error was invalid region `12:123200037-123201127`
[2016-04-15T06:46Z] 2016-04-14 23:46:52 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:46:52,300 - WARNING - Could not retrieve variants from source file in region 12:123102710-123103111. Error was invalid region `12:123102711-123103111`
[2016-04-15T06:46Z] 2016-04-14 23:46:53 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:46:53,346 - WARNING - Could not retrieve variants from source file in region 12:111785871-111786272. Error was invalid region `12:111785872-111786272`
[2016-04-15T06:46Z] 2016-04-14 23:46:53 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:46:53,566 - WARNING - Could not retrieve variants from source file in region 12:120313742-120314143. Error was invalid region `12:120313743-120314143`
[2016-04-15T06:46Z] 2016-04-14 23:46:53 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:46:53,920 - WARNING - Could not retrieve variants from source file in region 12:117746999-117768344. Error was invalid region `12:117747000-117768344`
[2016-04-15T06:46Z] 2016-04-14 23:46:54 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:46:54,736 - WARNING - Could not retrieve variants from source file in region 12:121093090-121093825. Error was invalid region `12:121093091-121093825`
[2016-04-15T06:46Z] 2016-04-14 23:46:55 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:46:55,342 - WARNING - Could not retrieve variants from source file in region 12:121016960-121017361. Error was invalid region `12:121016961-121017361`
[2016-04-15T06:46Z] 2016-04-14 23:46:55 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:46:55,412 - WARNING - Could not retrieve variants from source file in region 12:117383109-117383510. Error was invalid region `12:117383110-117383510`
[2016-04-15T06:46Z] 2016-04-14 23:46:56 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:46:56,485 - WARNING - Could not retrieve variants from source file in region 12:123102710-123103111. Error was invalid region `12:123102711-123103111`
[2016-04-15T06:46Z] 2016-04-14 23:46:57 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:46:57,801 - WARNING - Could not retrieve variants from source file in region 12:123102710-123103111. Error was invalid region `12:123102711-123103111`
[2016-04-15T06:46Z] 2016-04-14 23:46:57 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:46:57,896 - WARNING - Could not retrieve variants from source file in region 12:117348803-117349204. Error was invalid region `12:117348804-117349204`
[2016-04-15T06:46Z] 2016-04-14 23:46:58 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:46:58,130 - WARNING - Could not retrieve variants from source file in region 12:111785871-111786272. Error was invalid region `12:111785872-111786272`
[2016-04-15T06:46Z] 2016-04-14 23:46:59 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:46:59,366 - WARNING - Could not retrieve variants from source file in region 12:121093090-121093825. Error was invalid region `12:121093091-121093825`
[2016-04-15T06:46Z] 2016-04-14 23:46:59 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:46:59,466 - WARNING - Could not retrieve variants from source file in region 12:111758245-111758646. Error was invalid region `12:111758246-111758646`
[2016-04-15T06:46Z] 2016-04-14 23:46:59 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:46:59,479 - WARNING - Could not retrieve variants from source file in region 12:121016960-121017361. Error was invalid region `12:121016961-121017361`
[2016-04-15T06:46Z] 2016-04-14 23:46:59 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:46:59,728 - WARNING - Could not retrieve variants from source file in region 12:117383109-117383510. Error was invalid region `12:117383110-117383510`
[2016-04-15T06:47Z] 2016-04-14 23:47:00 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:47:00,009 - WARNING - Could not retrieve variants from source file in region 12:117465646-117466047. Error was invalid region `12:117465647-117466047`
[2016-04-15T06:47Z] 2016-04-14 23:47:02 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:47:02,332 - WARNING - Could not retrieve variants from source file in region 12:117348803-117349204. Error was invalid region `12:117348804-117349204`
[2016-04-15T06:47Z] 2016-04-14 23:47:02 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:47:02,486 - WARNING - Could not retrieve variants from source file in region 12:111785871-111786272. Error was invalid region `12:111785872-111786272`
[2016-04-15T06:47Z] 2016-04-14 23:47:03 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:47:03,603 - WARNING - Could not retrieve variants from source file in region 12:121093090-121093825. Error was invalid region `12:121093091-121093825`
[2016-04-15T06:47Z] 2016-04-14 23:47:03 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:47:03,814 - WARNING - Could not retrieve variants from source file in region 12:117383109-117383510. Error was invalid region `12:117383110-117383510`
[2016-04-15T06:47Z] 2016-04-14 23:47:03 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:47:03,879 - WARNING - Could not retrieve variants from source file in region 12:121016960-121017361. Error was invalid region `12:121016961-121017361`
[2016-04-15T06:47Z] 2016-04-14 23:47:03 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:47:03,884 - WARNING - Could not retrieve variants from source file in region 12:111758245-111758646. Error was invalid region `12:111758246-111758646`
[2016-04-15T06:47Z] 2016-04-14 23:47:04 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:47:04,190 - WARNING - Could not retrieve variants from source file in region 12:117465646-117466047. Error was invalid region `12:117465647-117466047`
[2016-04-15T06:47Z] 2016-04-14 23:47:06 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:47:06,760 - WARNING - Could not retrieve variants from source file in region 12:117348803-117349204. Error was invalid region `12:117348804-117349204`
[2016-04-15T06:47Z] 2016-04-14 23:47:08 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:47:08,835 - WARNING - Could not retrieve variants from source file in region 12:117465646-117466047. Error was invalid region `12:117465647-117466047`
[2016-04-15T06:47Z] 2016-04-14 23:47:09 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:47:09,886 - WARNING - Could not retrieve variants from source file in region 12:120067350-120067751. Error was invalid region `12:120067351-120067751`
[2016-04-15T06:47Z] 2016-04-14 23:47:13 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:47:13,660 - WARNING - Could not retrieve variants from source file in region 12:120067350-120067751. Error was invalid region `12:120067351-120067751`
[2016-04-15T06:47Z] 2016-04-14 23:47:13 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:47:13,896 - WARNING - Could not retrieve variants from source file in region 12:120221996-120222397. Error was invalid region `12:120221997-120222397`
[2016-04-15T06:47Z] 2016-04-14 23:47:14 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:47:14,060 - WARNING - Could not retrieve variants from source file in region 12:120966710-120967111. Error was invalid region `12:120966711-120967111`
[2016-04-15T06:47Z] 2016-04-14 23:47:15 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:47:15,066 - WARNING - Could not retrieve variants from source file in region 12:117289944-117290372. Error was invalid region `12:117289945-117290372`
[2016-04-15T06:47Z] 2016-04-14 23:47:15 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:47:15,208 - WARNING - Could not retrieve variants from source file in region 12:110974679-110975080. Error was invalid region `12:110974680-110975080`
[2016-04-15T06:47Z] 2016-04-14 23:47:16 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:47:16,813 - WARNING - Could not retrieve variants from source file in region 12:120067350-120067751. Error was invalid region `12:120067351-120067751`
[2016-04-15T06:47Z] 2016-04-14 23:47:17 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:47:17,236 - WARNING - Could not retrieve variants from source file in region 12:120966710-120967111. Error was invalid region `12:120966711-120967111`
[2016-04-15T06:47Z] 2016-04-14 23:47:18 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:47:18,384 - WARNING - Could not retrieve variants from source file in region 12:117289944-117290372. Error was invalid region `12:117289945-117290372`
[2016-04-15T06:47Z] 2016-04-14 23:47:18 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:47:18,816 - WARNING - Could not retrieve variants from source file in region 12:120884117-120884518. Error was invalid region `12:120884118-120884518`
[2016-04-15T06:47Z] 2016-04-14 23:47:21 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:47:21,831 - WARNING - Could not retrieve variants from source file in region 12:117289944-117290372. Error was invalid region `12:117289945-117290372`
[2016-04-15T06:47Z] 2016-04-14 23:47:22 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:47:22,104 - WARNING - Could not retrieve variants from source file in region 12:120884117-120884518. Error was invalid region `12:120884118-120884518`
[2016-04-15T06:47Z] 2016-04-14 23:47:26 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:47:26,907 - WARNING - Could not retrieve variants from source file in region 12:119916689-119917090. Error was invalid region `12:119916690-119917090`
[2016-04-15T06:47Z] 2016-04-14 23:47:31 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:47:31,324 - WARNING - Could not retrieve variants from source file in region 12:119588751-119589152. Error was invalid region `12:119588752-119589152`
[2016-04-15T06:47Z] 2016-04-14 23:47:31 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:47:31,346 - WARNING - Could not retrieve variants from source file in region 12:119588751-119589152. Error was invalid region `12:119588752-119589152`
[2016-04-15T06:47Z] ['bcbio-variation-recall', 'square', '-Xms750m', '-Xmx7280m', '-XX:+UseSerialGC', '-c', 16, '-r', u'12:125267229-133851895', '--caller', 'platypus', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/12/Batch1-12_125267228_133851895.vcf.gz', '/mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/12/Batch1-12_125267228_133851895.vcf-inputs.txt'] in region: 12:125267229-133851895
[2016-04-15T06:47Z] 2016-04-14 23:47:45 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:47:45,427 - WARNING - Could not retrieve variants from source file in region 12:131306103-131306504. Error was invalid region `12:131306104-131306504`
[2016-04-15T06:47Z] 2016-04-14 23:47:48 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:47:48,262 - WARNING - Could not retrieve variants from source file in region 12:125434369-125478571. Error was invalid region `12:125434370-125478571`
[2016-04-15T06:47Z] 2016-04-14 23:47:48 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:47:48,287 - WARNING - Could not retrieve variants from source file in region 12:129559346-129559747. Error was invalid region `12:129559347-129559747`
[2016-04-15T06:47Z] 2016-04-14 23:47:48 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:47:48,924 - WARNING - Could not retrieve variants from source file in region 12:130991075-130991476. Error was invalid region `12:130991076-130991476`
[2016-04-15T06:47Z] 2016-04-14 23:47:48 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:47:48,950 - WARNING - Could not retrieve variants from source file in region 12:125549984-125561341. Error was invalid region `12:125549985-125561341`
[2016-04-15T06:47Z] 2016-04-14 23:47:49 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:47:49,211 - WARNING - Could not retrieve variants from source file in region 12:125396277-125398229. Error was invalid region `12:125396278-125398229`
[2016-04-15T06:47Z] 2016-04-14 23:47:49 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:47:49,355 - WARNING - Could not retrieve variants from source file in region 12:128899462-128900249. Error was invalid region `12:128899463-128900249`
[2016-04-15T06:47Z] 2016-04-14 23:47:49 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:47:49,435 - WARNING - Could not retrieve variants from source file in region 12:132680853-132688327. Error was invalid region `12:132680854-132688327`
[2016-04-15T06:47Z] 2016-04-14 23:47:49 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:47:49,872 - WARNING - Could not retrieve variants from source file in region 12:131306103-131306504. Error was invalid region `12:131306104-131306504`
[2016-04-15T06:47Z] 2016-04-14 23:47:52 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:47:52,301 - WARNING - Could not retrieve variants from source file in region 12:130838954-130839355. Error was invalid region `12:130838955-130839355`
[2016-04-15T06:47Z] 2016-04-14 23:47:55 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:47:55,756 - WARNING - Could not retrieve variants from source file in region 12:129153775-129154176. Error was invalid region `12:129153776-129154176`
[2016-04-15T06:47Z] 2016-04-14 23:47:55 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:47:55,892 - WARNING - Could not retrieve variants from source file in region 12:129559346-129559747. Error was invalid region `12:129559347-129559747`
[2016-04-15T06:47Z] 2016-04-14 23:47:56 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:47:56,349 - WARNING - Could not retrieve variants from source file in region 12:125833884-125834585. Error was invalid region `12:125833885-125834585`
[2016-04-15T06:47Z] 2016-04-14 23:47:57 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:47:57,146 - WARNING - Could not retrieve variants from source file in region 12:133682444-133682845. Error was invalid region `12:133682445-133682845`
[2016-04-15T06:47Z] 2016-04-14 23:47:57 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:47:57,465 - WARNING - Could not retrieve variants from source file in region 12:131306103-131306504. Error was invalid region `12:131306104-131306504`
[2016-04-15T06:47Z] 2016-04-14 23:47:57 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:47:57,786 - WARNING - Could not retrieve variants from source file in region 12:130991075-130991476. Error was invalid region `12:130991076-130991476`
[2016-04-15T06:47Z] 2016-04-14 23:47:58 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:47:58,249 - WARNING - Could not retrieve variants from source file in region 12:125396277-125398229. Error was invalid region `12:125396278-125398229`
[2016-04-15T06:47Z] 2016-04-14 23:47:58 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:47:58,405 - WARNING - Could not retrieve variants from source file in region 12:130838954-130839355. Error was invalid region `12:130838955-130839355`
[2016-04-15T06:47Z] 2016-04-14 23:47:58 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:47:58,723 - WARNING - Could not retrieve variants from source file in region 12:133357201-133384706. Error was invalid region `12:133357202-133384706`
[2016-04-15T06:48Z] 2016-04-14 23:48:00 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:48:00,035 - WARNING - Could not retrieve variants from source file in region 12:132312887-132326488. Error was invalid region `12:132312888-132326488`
[2016-04-15T06:48Z] 2016-04-14 23:48:01 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:48:01,445 - WARNING - Could not retrieve variants from source file in region 12:129559346-129559747. Error was invalid region `12:129559347-129559747`
[2016-04-15T06:48Z] 2016-04-14 23:48:01 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:48:01,987 - WARNING - Could not retrieve variants from source file in region 12:129153775-129154176. Error was invalid region `12:129153776-129154176`
[2016-04-15T06:48Z] 2016-04-14 23:48:03 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:48:03,421 - WARNING - Could not retrieve variants from source file in region 12:125833884-125834585. Error was invalid region `12:125833885-125834585`
[2016-04-15T06:48Z] 2016-04-14 23:48:04 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:48:04,337 - WARNING - Could not retrieve variants from source file in region 12:125549984-125561341. Error was invalid region `12:125549985-125561341`
[2016-04-15T06:48Z] 2016-04-14 23:48:05 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:48:05,268 - WARNING - Could not retrieve variants from source file in region 12:130991075-130991476. Error was invalid region `12:130991076-130991476`
[2016-04-15T06:48Z] 2016-04-14 23:48:05 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:48:05,794 - WARNING - Could not retrieve variants from source file in region 12:125396277-125398229. Error was invalid region `12:125396278-125398229`
[2016-04-15T06:48Z] 2016-04-14 23:48:15 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:48:15,006 - WARNING - Could not retrieve variants from source file in region 12:131276237-131276638. Error was invalid region `12:131276238-131276638`
[2016-04-15T06:48Z] 2016-04-14 23:48:16 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:48:16,829 - WARNING - Could not retrieve variants from source file in region 12:132237539-132271303. Error was invalid region `12:132237540-132271303`
[2016-04-15T06:48Z] 2016-04-14 23:48:18 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:48:18,001 - WARNING - Could not retrieve variants from source file in region 12:131276237-131276638. Error was invalid region `12:131276238-131276638`
[2016-04-15T06:48Z] 2016-04-14 23:48:19 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:48:19,345 - WARNING - Could not retrieve variants from source file in region 12:130648923-130649324. Error was invalid region `12:130648924-130649324`
[2016-04-15T06:48Z] 2016-04-14 23:48:19 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:48:19,503 - WARNING - Could not retrieve variants from source file in region 12:129278653-129293536. Error was invalid region `12:129278654-129293536`
[2016-04-15T06:48Z] 2016-04-14 23:48:19 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:48:19,671 - WARNING - Could not retrieve variants from source file in region 12:131276237-131276638. Error was invalid region `12:131276238-131276638`
[2016-04-15T06:48Z] 2016-04-14 23:48:21 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:48:21,042 - WARNING - Could not retrieve variants from source file in region 12:133253784-133331727. Error was invalid region `12:133253785-133331727`
[2016-04-15T06:48Z] 2016-04-14 23:48:21 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:48:21,502 - WARNING - Could not retrieve variants from source file in region 12:126136849-126137250. Error was invalid region `12:126136850-126137250`
[2016-04-15T06:48Z] 2016-04-14 23:48:24 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:48:24,157 - WARNING - Could not retrieve variants from source file in region 12:129181599-129190670. Error was invalid region `12:129181600-129190670`
[2016-04-15T06:48Z] 2016-04-14 23:48:24 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:48:24,170 - WARNING - Could not retrieve variants from source file in region 12:126068206-126068607. Error was invalid region `12:126068207-126068607`
[2016-04-15T06:48Z] 2016-04-14 23:48:25 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:48:25,880 - WARNING - Could not retrieve variants from source file in region 12:126068206-126068607. Error was invalid region `12:126068207-126068607`
[2016-04-15T06:48Z] 2016-04-14 23:48:26 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:48:26,194 - WARNING - Could not retrieve variants from source file in region 12:129278653-129293536. Error was invalid region `12:129278654-129293536`
[2016-04-15T06:48Z] 2016-04-14 23:48:26 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:48:26,286 - WARNING - Could not retrieve variants from source file in region 12:129028375-129028776. Error was invalid region `12:129028376-129028776`
[2016-04-15T06:48Z] 2016-04-14 23:48:26 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:48:26,286 - WARNING - Could not retrieve variants from source file in region 12:130648923-130649324. Error was invalid region `12:130648924-130649324`
[2016-04-15T06:48Z] 2016-04-14 23:48:27 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:48:27,390 - WARNING - Could not retrieve variants from source file in region 12:133732413-133732814. Error was invalid region `12:133732414-133732814`
[2016-04-15T06:48Z] 2016-04-14 23:48:27 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:48:27,578 - WARNING - Could not retrieve variants from source file in region 12:132237539-132271303. Error was invalid region `12:132237540-132271303`
[2016-04-15T06:48Z] 2016-04-14 23:48:27 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:48:27,580 - WARNING - Could not retrieve variants from source file in region 12:126136849-126137250. Error was invalid region `12:126136850-126137250`
[2016-04-15T06:48Z] 2016-04-14 23:48:29 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:48:29,866 - WARNING - Could not retrieve variants from source file in region 12:126068206-126068607. Error was invalid region `12:126068207-126068607`
[2016-04-15T06:48Z] 2016-04-14 23:48:34 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:48:34,635 - WARNING - Could not retrieve variants from source file in region 12:129278653-129293536. Error was invalid region `12:129278654-129293536`
[2016-04-15T06:48Z] 2016-04-14 23:48:35 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:48:35,638 - WARNING - Could not retrieve variants from source file in region 12:130884136-130884537. Error was invalid region `12:130884137-130884537`
[2016-04-15T06:48Z] 2016-04-14 23:48:41 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:48:41,207 - WARNING - Could not retrieve variants from source file in region 12:132508178-132508579. Error was invalid region `12:132508179-132508579`
[2016-04-15T06:48Z] 2016-04-14 23:48:42 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:48:42,590 - WARNING - Could not retrieve variants from source file in region 12:130884136-130884537. Error was invalid region `12:130884137-130884537`
[2016-04-15T06:48Z] 2016-04-14 23:48:44 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:48:44,395 - WARNING - Could not retrieve variants from source file in region 12:131620377-131622925. Error was invalid region `12:131620378-131622925`
[2016-04-15T06:48Z] 2016-04-14 23:48:45 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:48:45,327 - WARNING - Could not retrieve variants from source file in region 12:131620377-131622925. Error was invalid region `12:131620378-131622925`
[2016-04-15T06:48Z] 2016-04-14 23:48:46 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:48:46,092 - WARNING - Could not retrieve variants from source file in region 12:131590193-131590594. Error was invalid region `12:131590194-131590594`
[2016-04-15T06:48Z] 2016-04-14 23:48:47 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:48:47,526 - WARNING - Could not retrieve variants from source file in region 12:131620377-131622925. Error was invalid region `12:131620378-131622925`
[2016-04-15T06:48Z] 2016-04-14 23:48:47 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:48:47,621 - WARNING - Could not retrieve variants from source file in region 12:133159522-133212772. Error was invalid region `12:133159523-133212772`
[2016-04-15T06:48Z] 2016-04-14 23:48:47 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:48:47,654 - WARNING - Could not retrieve variants from source file in region 12:131590193-131590594. Error was invalid region `12:131590194-131590594`
[2016-04-15T06:48Z] 2016-04-14 23:48:49 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:48:49,935 - WARNING - Could not retrieve variants from source file in region 12:132396392-132403351. Error was invalid region `12:132396393-132403351`
[2016-04-15T06:48Z] 2016-04-14 23:48:51 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:48:51,148 - WARNING - Could not retrieve variants from source file in region 12:131466351-131466752. Error was invalid region `12:131466352-131466752`
[2016-04-15T06:48Z] 2016-04-14 23:48:51 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:48:51,772 - WARNING - Could not retrieve variants from source file in region 12:132981703-132982104. Error was invalid region `12:132981704-132982104`
[2016-04-15T06:48Z] 2016-04-14 23:48:53 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:48:53,223 - WARNING - Could not retrieve variants from source file in region 12:131466351-131466752. Error was invalid region `12:131466352-131466752`
[2016-04-15T06:48Z] 2016-04-14 23:48:55 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:48:55,120 - WARNING - Could not retrieve variants from source file in region 12:131466351-131466752. Error was invalid region `12:131466352-131466752`
[2016-04-15T06:48Z] 2016-04-14 23:48:56 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:48:56,305 - WARNING - Could not retrieve variants from source file in region 12:132981703-132982104. Error was invalid region `12:132981704-132982104`
[2016-04-15T06:49Z] ['bcbio-variation-recall', 'square', '-Xms750m', '-Xmx7280m', '-XX:+UseSerialGC', '-c', 16, '-r', u'13:1-19748299', '--caller', 'platypus', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/13/Batch1-13_0_19748299.vcf.gz', '/mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/13/Batch1-13_0_19748299.vcf-inputs.txt'] in region: 13:1-19748299
[2016-04-15T06:49Z] ['bcbio-variation-recall', 'square', '-Xms750m', '-Xmx7280m', '-XX:+UseSerialGC', '-c', 16, '-r', u'13:19751067-35517251', '--caller', 'platypus', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/13/Batch1-13_19751066_35517251.vcf.gz', '/mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/13/Batch1-13_19751066_35517251.vcf-inputs.txt'] in region: 13:19751067-35517251
[2016-04-15T06:49Z] 2016-04-14 23:49:13 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:49:13,926 - WARNING - Could not retrieve variants from source file in region 13:25378265-25378666. Error was invalid region `13:25378266-25378666`
[2016-04-15T06:49Z] 2016-04-14 23:49:13 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:49:13,973 - WARNING - Could not retrieve variants from source file in region 13:31480509-31481017. Error was invalid region `13:31480510-31481017`
[2016-04-15T06:49Z] 2016-04-14 23:49:14 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:49:14,090 - WARNING - Could not retrieve variants from source file in region 13:34013636-34014037. Error was invalid region `13:34013637-34014037`
[2016-04-15T06:49Z] 2016-04-14 23:49:14 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:49:14,474 - WARNING - Could not retrieve variants from source file in region 13:22275183-22275584. Error was invalid region `13:22275184-22275584`
[2016-04-15T06:49Z] 2016-04-14 23:49:14 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:49:14,668 - WARNING - Could not retrieve variants from source file in region 13:21422488-21440686. Error was invalid region `13:21422489-21440686`
[2016-04-15T06:49Z] 2016-04-14 23:49:14 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:49:14,791 - WARNING - Could not retrieve variants from source file in region 13:25875800-25876201. Error was invalid region `13:25875801-25876201`
[2016-04-15T06:49Z] 2016-04-14 23:49:15 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:49:15,392 - WARNING - Could not retrieve variants from source file in region 13:25115939-25116400. Error was invalid region `13:25115940-25116400`
[2016-04-15T06:49Z] 2016-04-14 23:49:15 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:49:15,517 - WARNING - Could not retrieve variants from source file in region 13:27250612-27257092. Error was invalid region `13:27250613-27257092`
[2016-04-15T06:49Z] 2016-04-14 23:49:16 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:49:16,188 - WARNING - Could not retrieve variants from source file in region 13:24734785-24735186. Error was invalid region `13:24734786-24735186`
[2016-04-15T06:49Z] 2016-04-14 23:49:20 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:49:20,807 - WARNING - Could not retrieve variants from source file in region 13:25378265-25378666. Error was invalid region `13:25378266-25378666`
[2016-04-15T06:49Z] 2016-04-14 23:49:22 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:49:22,586 - WARNING - Could not retrieve variants from source file in region 13:22275183-22275584. Error was invalid region `13:22275184-22275584`
[2016-04-15T06:49Z] 2016-04-14 23:49:23 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:49:23,186 - WARNING - Could not retrieve variants from source file in region 13:25875800-25876201. Error was invalid region `13:25875801-25876201`
[2016-04-15T06:49Z] 2016-04-14 23:49:23 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:49:23,340 - WARNING - Could not retrieve variants from source file in region 13:21422488-21440686. Error was invalid region `13:21422489-21440686`
[2016-04-15T06:49Z] 2016-04-14 23:49:25 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:49:25,102 - WARNING - Could not retrieve variants from source file in region 13:26273174-26273593. Error was invalid region `13:26273175-26273593`
[2016-04-15T06:49Z] 2016-04-14 23:49:25 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:49:25,445 - WARNING - Could not retrieve variants from source file in region 13:26042971-26043372. Error was invalid region `13:26042972-26043372`
[2016-04-15T06:49Z] 2016-04-14 23:49:25 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:49:25,508 - WARNING - Could not retrieve variants from source file in region 13:24734785-24735186. Error was invalid region `13:24734786-24735186`
[2016-04-15T06:49Z] 2016-04-14 23:49:25 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:49:25,809 - WARNING - Could not retrieve variants from source file in region 13:25378265-25378666. Error was invalid region `13:25378266-25378666`
[2016-04-15T06:49Z] 2016-04-14 23:49:25 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:49:25,849 - WARNING - Could not retrieve variants from source file in region 13:34013636-34014037. Error was invalid region `13:34013637-34014037`
[2016-04-15T06:49Z] 2016-04-14 23:49:25 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:49:25,863 - WARNING - Could not retrieve variants from source file in region 13:31480509-31481017. Error was invalid region `13:31480510-31481017`
[2016-04-15T06:49Z] 2016-04-14 23:49:27 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:49:27,587 - WARNING - Could not retrieve variants from source file in region 13:22275183-22275584. Error was invalid region `13:22275184-22275584`
[2016-04-15T06:49Z] 2016-04-14 23:49:28 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:49:28,478 - WARNING - Could not retrieve variants from source file in region 13:25875800-25876201. Error was invalid region `13:25875801-25876201`
[2016-04-15T06:49Z] 2016-04-14 23:49:29 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:49:29,369 - WARNING - Could not retrieve variants from source file in region 13:21422488-21440686. Error was invalid region `13:21422489-21440686`
[2016-04-15T06:49Z] 2016-04-14 23:49:32 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:49:32,090 - WARNING - Could not retrieve variants from source file in region 13:27250612-27257092. Error was invalid region `13:27250613-27257092`
[2016-04-15T06:49Z] 2016-04-14 23:49:32 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:49:32,827 - WARNING - Could not retrieve variants from source file in region 13:23898298-23912010. Error was invalid region `13:23898299-23912010`
[2016-04-15T06:49Z] 2016-04-14 23:49:44 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:49:44,621 - WARNING - Could not retrieve variants from source file in region 13:31231595-31233253. Error was invalid region `13:31231596-31233253`
[2016-04-15T06:49Z] 2016-04-14 23:49:46 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:49:46,580 - WARNING - Could not retrieve variants from source file in region 13:33691742-33704255. Error was invalid region `13:33691743-33704255`
[2016-04-15T06:49Z] 2016-04-14 23:49:47 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:49:47,792 - WARNING - Could not retrieve variants from source file in region 13:26148755-26149156. Error was invalid region `13:26148756-26149156`
[2016-04-15T06:49Z] 2016-04-14 23:49:48 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:49:48,932 - WARNING - Could not retrieve variants from source file in region 13:28882850-28883251. Error was invalid region `13:28882851-28883251`
[2016-04-15T06:49Z] 2016-04-14 23:49:49 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:49:49,720 - WARNING - Could not retrieve variants from source file in region 13:31231595-31233253. Error was invalid region `13:31231596-31233253`
[2016-04-15T06:49Z] 2016-04-14 23:49:50 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:49:50,274 - WARNING - Could not retrieve variants from source file in region 13:24167294-24167695. Error was invalid region `13:24167295-24167695`
[2016-04-15T06:49Z] 2016-04-14 23:49:50 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:49:50,917 - WARNING - Could not retrieve variants from source file in region 13:21861655-21862056. Error was invalid region `13:21861656-21862056`
[2016-04-15T06:49Z] 2016-04-14 23:49:51 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:49:51,729 - WARNING - Could not retrieve variants from source file in region 13:33691742-33704255. Error was invalid region `13:33691743-33704255`
[2016-04-15T06:49Z] 2016-04-14 23:49:52 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:49:52,101 - WARNING - Could not retrieve variants from source file in region 13:24465532-24471229. Error was invalid region `13:24465533-24471229`
[2016-04-15T06:49Z] 2016-04-14 23:49:53 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:49:53,078 - WARNING - Could not retrieve variants from source file in region 13:21374122-21374523. Error was invalid region `13:21374123-21374523`
[2016-04-15T06:49Z] 2016-04-14 23:49:53 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:49:53,251 - WARNING - Could not retrieve variants from source file in region 13:26148755-26149156. Error was invalid region `13:26148756-26149156`
[2016-04-15T06:49Z] 2016-04-14 23:49:53 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:49:53,768 - WARNING - Could not retrieve variants from source file in region 13:28882850-28883251. Error was invalid region `13:28882851-28883251`
[2016-04-15T06:49Z] 2016-04-14 23:49:53 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:49:53,991 - WARNING - Could not retrieve variants from source file in region 13:24797702-24798310. Error was invalid region `13:24797703-24798310`
[2016-04-15T06:49Z] 2016-04-14 23:49:55 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:49:55,622 - WARNING - Could not retrieve variants from source file in region 13:21861655-21862056. Error was invalid region `13:21861656-21862056`
[2016-04-15T06:49Z] 2016-04-14 23:49:56 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:49:56,543 - WARNING - Could not retrieve variants from source file in region 13:33691742-33704255. Error was invalid region `13:33691743-33704255`
[2016-04-15T06:49Z] 2016-04-14 23:49:57 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:49:57,062 - WARNING - Could not retrieve variants from source file in region 13:23808571-23824973. Error was invalid region `13:23808572-23824973`
[2016-04-15T06:49Z] 2016-04-14 23:49:57 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:49:57,938 - WARNING - Could not retrieve variants from source file in region 13:21374122-21374523. Error was invalid region `13:21374123-21374523`
[2016-04-15T06:49Z] 2016-04-14 23:49:58 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:49:58,461 - WARNING - Could not retrieve variants from source file in region 13:26148755-26149156. Error was invalid region `13:26148756-26149156`
[2016-04-15T06:49Z] 2016-04-14 23:49:58 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:49:58,567 - WARNING - Could not retrieve variants from source file in region 13:28882850-28883251. Error was invalid region `13:28882851-28883251`
[2016-04-15T06:50Z] 2016-04-14 23:50:01 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:50:01,702 - WARNING - Could not retrieve variants from source file in region 13:24465532-24471229. Error was invalid region `13:24465533-24471229`
[2016-04-15T06:50Z] 2016-04-14 23:50:07 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:50:07,290 - WARNING - Could not retrieve variants from source file in region 13:31036470-31040176. Error was invalid region `13:31036471-31040176`
[2016-04-15T06:50Z] 2016-04-14 23:50:08 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:50:08,589 - WARNING - Could not retrieve variants from source file in region 13:25418965-25487293. Error was invalid region `13:25418966-25487293`
[2016-04-15T06:50Z] 2016-04-14 23:50:10 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:50:10,157 - WARNING - Could not retrieve variants from source file in region 13:28239729-28240160. Error was invalid region `13:28239730-28240160`
[2016-04-15T06:50Z] 2016-04-14 23:50:11 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:50:11,874 - WARNING - Could not retrieve variants from source file in region 13:21277363-21277764. Error was invalid region `13:21277364-21277764`
[2016-04-15T06:50Z] 2016-04-14 23:50:12 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:50:12,537 - WARNING - Could not retrieve variants from source file in region 13:24411561-24436665. Error was invalid region `13:24411562-24436665`
[2016-04-15T06:50Z] 2016-04-14 23:50:13 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:50:13,418 - WARNING - Could not retrieve variants from source file in region 13:32776392-32785276. Error was invalid region `13:32776393-32785276`
[2016-04-15T06:50Z] 2016-04-14 23:50:13 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:50:13,432 - WARNING - Could not retrieve variants from source file in region 13:28674417-28674818. Error was invalid region `13:28674418-28674818`
[2016-04-15T06:50Z] 2016-04-14 23:50:14 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:50:14,697 - WARNING - Could not retrieve variants from source file in region 13:33627927-33636025. Error was invalid region `13:33627928-33636025`
[2016-04-15T06:50Z] 2016-04-14 23:50:14 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:50:14,751 - WARNING - Could not retrieve variants from source file in region 13:28239729-28240160. Error was invalid region `13:28239730-28240160`
[2016-04-15T06:50Z] 2016-04-14 23:50:14 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:50:14,915 - WARNING - Could not retrieve variants from source file in region 13:21619874-21620275. Error was invalid region `13:21619875-21620275`
[2016-04-15T06:50Z] 2016-04-14 23:50:14 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:50:14,961 - WARNING - Could not retrieve variants from source file in region 13:28143018-28143419. Error was invalid region `13:28143019-28143419`
[2016-04-15T06:50Z] 2016-04-14 23:50:16 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:50:16,353 - WARNING - Could not retrieve variants from source file in region 13:31036470-31040176. Error was invalid region `13:31036471-31040176`
[2016-04-15T06:50Z] 2016-04-14 23:50:16 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:50:16,812 - WARNING - Could not retrieve variants from source file in region 13:21277363-21277764. Error was invalid region `13:21277364-21277764`
[2016-04-15T06:50Z] 2016-04-14 23:50:17 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:50:17,623 - WARNING - Could not retrieve variants from source file in region 13:32776392-32785276. Error was invalid region `13:32776393-32785276`
[2016-04-15T06:50Z] 2016-04-14 23:50:18 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:50:18,433 - WARNING - Could not retrieve variants from source file in region 13:21000859-21006177. Error was invalid region `13:21000860-21006177`
[2016-04-15T06:50Z] 2016-04-14 23:50:19 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:50:19,578 - WARNING - Could not retrieve variants from source file in region 13:21619874-21620275. Error was invalid region `13:21619875-21620275`
[2016-04-15T06:50Z] 2016-04-14 23:50:19 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:50:19,821 - WARNING - Could not retrieve variants from source file in region 13:28143018-28143419. Error was invalid region `13:28143019-28143419`
[2016-04-15T06:50Z] 2016-04-14 23:50:21 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:50:21,025 - WARNING - Could not retrieve variants from source file in region 13:24411561-24436665. Error was invalid region `13:24411562-24436665`
[2016-04-15T06:50Z] 2016-04-14 23:50:21 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:50:21,323 - WARNING - Could not retrieve variants from source file in region 13:21277363-21277764. Error was invalid region `13:21277364-21277764`
[2016-04-15T06:50Z] 2016-04-14 23:50:21 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:50:21,774 - WARNING - Could not retrieve variants from source file in region 13:32776392-32785276. Error was invalid region `13:32776393-32785276`
[2016-04-15T06:50Z] 2016-04-14 23:50:22 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:50:22,744 - WARNING - Could not retrieve variants from source file in region 13:28674417-28674818. Error was invalid region `13:28674418-28674818`
[2016-04-15T06:50Z] 2016-04-14 23:50:23 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:50:23,048 - WARNING - Could not retrieve variants from source file in region 13:20277202-20277603. Error was invalid region `13:20277203-20277603`
[2016-04-15T06:50Z] 2016-04-14 23:50:24 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:50:24,298 - WARNING - Could not retrieve variants from source file in region 13:21619874-21620275. Error was invalid region `13:21619875-21620275`
[2016-04-15T06:50Z] 2016-04-14 23:50:24 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:50:24,688 - WARNING - Could not retrieve variants from source file in region 13:28143018-28143419. Error was invalid region `13:28143019-28143419`
[2016-04-15T06:50Z] 2016-04-14 23:50:27 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:50:27,706 - WARNING - Could not retrieve variants from source file in region 13:28197206-28197626. Error was invalid region `13:28197207-28197626`
[2016-04-15T06:50Z] 2016-04-14 23:50:28 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:50:28,260 - WARNING - Could not retrieve variants from source file in region 13:20277202-20277603. Error was invalid region `13:20277203-20277603`
[2016-04-15T06:50Z] 2016-04-14 23:50:29 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:50:29,589 - WARNING - Could not retrieve variants from source file in region 13:30091503-30092009. Error was invalid region `13:30091504-30092009`
[2016-04-15T06:50Z] 2016-04-14 23:50:33 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:50:33,526 - WARNING - Could not retrieve variants from source file in region 13:20277202-20277603. Error was invalid region `13:20277203-20277603`
[2016-04-15T06:50Z] 2016-04-14 23:50:33 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:50:33,751 - WARNING - Could not retrieve variants from source file in region 13:21562160-21563138. Error was invalid region `13:21562161-21563138`
[2016-04-15T06:50Z] 2016-04-14 23:50:34 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:50:34,340 - WARNING - Could not retrieve variants from source file in region 13:33590640-33591041. Error was invalid region `13:33590641-33591041`
[2016-04-15T06:50Z] 2016-04-14 23:50:34 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:50:34,997 - WARNING - Could not retrieve variants from source file in region 13:21204981-21205382. Error was invalid region `13:21204982-21205382`
[2016-04-15T06:50Z] 2016-04-14 23:50:35 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:50:35,665 - WARNING - Could not retrieve variants from source file in region 13:30091503-30092009. Error was invalid region `13:30091504-30092009`
[2016-04-15T06:50Z] 2016-04-14 23:50:35 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:50:35,672 - WARNING - Could not retrieve variants from source file in region 13:27845129-27845530. Error was invalid region `13:27845130-27845530`
[2016-04-15T06:50Z] 2016-04-14 23:50:35 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:50:35,729 - WARNING - Could not retrieve variants from source file in region 13:20000419-20000820. Error was invalid region `13:20000420-20000820`
[2016-04-15T06:50Z] 2016-04-14 23:50:36 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:50:36,781 - WARNING - Could not retrieve variants from source file in region 13:28624083-28636274. Error was invalid region `13:28624084-28636274`
[2016-04-15T06:50Z] 2016-04-14 23:50:37 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:50:37,669 - WARNING - Could not retrieve variants from source file in region 13:20716322-20716723. Error was invalid region `13:20716323-20716723`
[2016-04-15T06:50Z] 2016-04-14 23:50:39 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:50:39,318 - WARNING - Could not retrieve variants from source file in region 13:33590640-33591041. Error was invalid region `13:33590641-33591041`
[2016-04-15T06:50Z] 2016-04-14 23:50:39 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:50:39,980 - WARNING - Could not retrieve variants from source file in region 13:21204981-21205382. Error was invalid region `13:21204982-21205382`
[2016-04-15T06:50Z] 2016-04-14 23:50:40 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:50:40,169 - WARNING - Could not retrieve variants from source file in region 13:32747443-32747844. Error was invalid region `13:32747444-32747844`
[2016-04-15T06:50Z] 2016-04-14 23:50:40 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:50:40,837 - WARNING - Could not retrieve variants from source file in region 13:27845129-27845530. Error was invalid region `13:27845130-27845530`
[2016-04-15T06:50Z] 2016-04-14 23:50:40 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:50:40,841 - WARNING - Could not retrieve variants from source file in region 13:30091503-30092009. Error was invalid region `13:30091504-30092009`
[2016-04-15T06:50Z] 2016-04-14 23:50:41 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:50:41,030 - WARNING - Could not retrieve variants from source file in region 13:20000419-20000820. Error was invalid region `13:20000420-20000820`
[2016-04-15T06:50Z] 2016-04-14 23:50:41 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:50:41,412 - WARNING - Could not retrieve variants from source file in region 13:28624083-28636274. Error was invalid region `13:28624084-28636274`
[2016-04-15T06:50Z] 2016-04-14 23:50:42 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:50:42,603 - WARNING - Could not retrieve variants from source file in region 13:20716322-20716723. Error was invalid region `13:20716323-20716723`
[2016-04-15T06:50Z] 2016-04-14 23:50:43 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:50:43,344 - WARNING - Could not retrieve variants from source file in region 13:33590640-33591041. Error was invalid region `13:33590641-33591041`
[2016-04-15T06:50Z] 2016-04-14 23:50:44 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:50:44,235 - WARNING - Could not retrieve variants from source file in region 13:21204981-21205382. Error was invalid region `13:21204982-21205382`
[2016-04-15T06:50Z] 2016-04-14 23:50:44 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:50:44,563 - WARNING - Could not retrieve variants from source file in region 13:32747443-32747844. Error was invalid region `13:32747444-32747844`
[2016-04-15T06:50Z] 2016-04-14 23:50:44 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:50:44,838 - WARNING - Could not retrieve variants from source file in region 13:20000419-20000820. Error was invalid region `13:20000420-20000820`
[2016-04-15T06:50Z] 2016-04-14 23:50:45 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:50:45,380 - WARNING - Could not retrieve variants from source file in region 13:28624083-28636274. Error was invalid region `13:28624084-28636274`
[2016-04-15T06:50Z] 2016-04-14 23:50:45 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:50:45,717 - WARNING - Could not retrieve variants from source file in region 13:19751333-19751734. Error was invalid region `13:19751334-19751734`
[2016-04-15T06:50Z] 2016-04-14 23:50:46 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:50:46,514 - WARNING - Could not retrieve variants from source file in region 13:20716322-20716723. Error was invalid region `13:20716323-20716723`
[2016-04-15T06:50Z] 2016-04-14 23:50:50 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:50:50,510 - WARNING - Could not retrieve variants from source file in region 13:21063313-21086789. Error was invalid region `13:21063314-21086789`
[2016-04-15T06:50Z] 2016-04-14 23:50:50 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:50:50,641 - WARNING - Could not retrieve variants from source file in region 13:33232224-33232625. Error was invalid region `13:33232225-33232625`
[2016-04-15T06:50Z] 2016-04-14 23:50:53 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:50:53,101 - WARNING - Could not retrieve variants from source file in region 13:29898557-29898958. Error was invalid region `13:29898558-29898958`
[2016-04-15T06:50Z] 2016-04-14 23:50:54 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:50:54,192 - WARNING - Could not retrieve variants from source file in region 13:32981582-32986195. Error was invalid region `13:32981583-32986195`
[2016-04-15T06:50Z] 2016-04-14 23:50:54 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:50:54,702 - WARNING - Could not retrieve variants from source file in region 13:31821781-31822182. Error was invalid region `13:31821782-31822182`
[2016-04-15T06:50Z] 2016-04-14 23:50:54 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:50:54,842 - WARNING - Could not retrieve variants from source file in region 13:19751333-19751734. Error was invalid region `13:19751334-19751734`
[2016-04-15T06:50Z] 2016-04-14 23:50:54 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:50:54,968 - WARNING - Could not retrieve variants from source file in region 13:31891535-31891936. Error was invalid region `13:31891536-31891936`
[2016-04-15T06:50Z] 2016-04-14 23:50:55 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:50:55,659 - WARNING - Could not retrieve variants from source file in region 13:33232224-33232625. Error was invalid region `13:33232225-33232625`
[2016-04-15T06:50Z] 2016-04-14 23:50:56 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:50:56,082 - WARNING - Could not retrieve variants from source file in region 13:33091030-33091431. Error was invalid region `13:33091031-33091431`
[2016-04-15T06:50Z] 2016-04-14 23:50:58 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:50:58,162 - WARNING - Could not retrieve variants from source file in region 13:29898557-29898958. Error was invalid region `13:29898558-29898958`
[2016-04-15T06:50Z] 2016-04-14 23:50:58 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:50:58,433 - WARNING - Could not retrieve variants from source file in region 13:32675903-32676304. Error was invalid region `13:32675904-32676304`
[2016-04-15T06:50Z] 2016-04-14 23:50:59 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:50:59,339 - WARNING - Could not retrieve variants from source file in region 13:29274891-29275319. Error was invalid region `13:29274892-29275319`
[2016-04-15T06:50Z] 2016-04-14 23:50:59 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:50:59,357 - WARNING - Could not retrieve variants from source file in region 13:28366850-28367251. Error was invalid region `13:28366851-28367251`
[2016-04-15T06:50Z] 2016-04-14 23:50:59 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:50:59,488 - WARNING - Could not retrieve variants from source file in region 13:31821781-31822182. Error was invalid region `13:31821782-31822182`
[2016-04-15T06:50Z] 2016-04-14 23:50:59 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:50:59,734 - WARNING - Could not retrieve variants from source file in region 13:31891535-31891936. Error was invalid region `13:31891536-31891936`
[2016-04-15T06:50Z] 2016-04-14 23:50:59 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:50:59,767 - WARNING - Could not retrieve variants from source file in region 13:28537106-28562795. Error was invalid region `13:28537107-28562795`
[2016-04-15T06:51Z] 2016-04-14 23:51:00 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:51:00,502 - WARNING - Could not retrieve variants from source file in region 13:33232224-33232625. Error was invalid region `13:33232225-33232625`
[2016-04-15T06:51Z] 2016-04-14 23:51:00 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:51:00,601 - WARNING - Could not retrieve variants from source file in region 13:33091030-33091431. Error was invalid region `13:33091031-33091431`
[2016-04-15T06:51Z] 2016-04-14 23:51:02 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:51:02,308 - WARNING - Could not retrieve variants from source file in region 13:29898557-29898958. Error was invalid region `13:29898558-29898958`
[2016-04-15T06:51Z] 2016-04-14 23:51:02 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:51:02,617 - WARNING - Could not retrieve variants from source file in region 13:32675903-32676304. Error was invalid region `13:32675904-32676304`
[2016-04-15T06:51Z] 2016-04-14 23:51:04 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:51:04,491 - WARNING - Could not retrieve variants from source file in region 13:28366850-28367251. Error was invalid region `13:28366851-28367251`
[2016-04-15T06:51Z] 2016-04-14 23:51:04 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:51:04,574 - WARNING - Could not retrieve variants from source file in region 13:28366850-28367251. Error was invalid region `13:28366851-28367251`
[2016-04-15T06:51Z] 2016-04-14 23:51:04 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:51:04,579 - WARNING - Could not retrieve variants from source file in region 13:31821781-31822182. Error was invalid region `13:31821782-31822182`
[2016-04-15T06:51Z] 2016-04-14 23:51:04 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:51:04,632 - WARNING - Could not retrieve variants from source file in region 13:32675903-32676304. Error was invalid region `13:32675904-32676304`
[2016-04-15T06:51Z] 2016-04-14 23:51:04 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:51:04,836 - WARNING - Could not retrieve variants from source file in region 13:31891535-31891936. Error was invalid region `13:31891536-31891936`
[2016-04-15T06:51Z] 2016-04-14 23:51:04 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:51:04,950 - WARNING - Could not retrieve variants from source file in region 13:33091030-33091431. Error was invalid region `13:33091031-33091431`
[2016-04-15T06:51Z] 2016-04-14 23:51:10 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:51:10,938 - WARNING - Could not retrieve variants from source file in region 13:32360336-32360737. Error was invalid region `13:32360337-32360737`
[2016-04-15T06:51Z] 2016-04-14 23:51:14 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:51:14,029 - WARNING - Could not retrieve variants from source file in region 13:29040954-29041355. Error was invalid region `13:29040955-29041355`
[2016-04-15T06:51Z] 2016-04-14 23:51:15 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:51:15,505 - WARNING - Could not retrieve variants from source file in region 13:31725049-31729919. Error was invalid region `13:31725050-31729919`
[2016-04-15T06:51Z] 2016-04-14 23:51:17 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:51:17,598 - WARNING - Could not retrieve variants from source file in region 13:32811396-32811797. Error was invalid region `13:32811397-32811797`
[2016-04-15T06:51Z] 2016-04-14 23:51:17 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:51:17,646 - WARNING - Could not retrieve variants from source file in region 13:31725049-31729919. Error was invalid region `13:31725050-31729919`
[2016-04-15T06:51Z] 2016-04-14 23:51:18 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:51:18,365 - WARNING - Could not retrieve variants from source file in region 13:31848446-31848847. Error was invalid region `13:31848447-31848847`
[2016-04-15T06:51Z] 2016-04-14 23:51:18 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:51:18,393 - WARNING - Could not retrieve variants from source file in region 13:31530798-31531199. Error was invalid region `13:31530799-31531199`
[2016-04-15T06:51Z] 2016-04-14 23:51:19 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:51:19,571 - WARNING - Could not retrieve variants from source file in region 13:29674838-29675239. Error was invalid region `13:29674839-29675239`
[2016-04-15T06:51Z] 2016-04-14 23:51:21 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:51:21,341 - WARNING - Could not retrieve variants from source file in region 13:32811396-32811797. Error was invalid region `13:32811397-32811797`
[2016-04-15T06:51Z] 2016-04-14 23:51:21 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:51:21,503 - WARNING - Could not retrieve variants from source file in region 13:31848446-31848847. Error was invalid region `13:31848447-31848847`
[2016-04-15T06:51Z] 2016-04-14 23:51:22 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:51:22,140 - WARNING - Could not retrieve variants from source file in region 13:31530798-31531199. Error was invalid region `13:31530799-31531199`
[2016-04-15T06:51Z] 2016-04-14 23:51:24 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:51:24,839 - WARNING - Could not retrieve variants from source file in region 13:31530798-31531199. Error was invalid region `13:31530799-31531199`
[2016-04-15T06:51Z] ['bcbio-variation-recall', 'square', '-Xms750m', '-Xmx7280m', '-XX:+UseSerialGC', '-c', 16, '-r', u'13:35615070-51287376', '--caller', 'platypus', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/13/Batch1-13_35615069_51287376.vcf.gz', '/mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/13/Batch1-13_35615069_51287376.vcf-inputs.txt'] in region: 13:35615070-51287376
[2016-04-15T06:51Z] 2016-04-14 23:51:37 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:51:37,710 - WARNING - Could not retrieve variants from source file in region 13:41372733-41382901. Error was invalid region `13:41372734-41382901`
[2016-04-15T06:51Z] 2016-04-14 23:51:40 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:51:40,991 - WARNING - Could not retrieve variants from source file in region 13:38210894-38211295. Error was invalid region `13:38210895-38211295`
[2016-04-15T06:51Z] 2016-04-14 23:51:41 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:51:41,332 - WARNING - Could not retrieve variants from source file in region 13:50204814-50205215. Error was invalid region `13:50204815-50205215`
[2016-04-15T06:51Z] 2016-04-14 23:51:41 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:51:41,334 - WARNING - Could not retrieve variants from source file in region 13:50295904-50296305. Error was invalid region `13:50295905-50296305`
[2016-04-15T06:51Z] 2016-04-14 23:51:41 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:51:41,575 - WARNING - Could not retrieve variants from source file in region 13:49950931-49951383. Error was invalid region `13:49950932-49951383`
[2016-04-15T06:51Z] 2016-04-14 23:51:41 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:51:41,646 - WARNING - Could not retrieve variants from source file in region 13:46287934-46288335. Error was invalid region `13:46287935-46288335`
[2016-04-15T06:51Z] 2016-04-14 23:51:41 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:51:41,993 - WARNING - Could not retrieve variants from source file in region 13:48547256-48547657. Error was invalid region `13:48547257-48547657`
[2016-04-15T06:51Z] 2016-04-14 23:51:42 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:51:42,161 - WARNING - Could not retrieve variants from source file in region 13:46695060-46708481. Error was invalid region `13:46695061-46708481`
[2016-04-15T06:51Z] 2016-04-14 23:51:42 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:51:42,181 - WARNING - Could not retrieve variants from source file in region 13:43639634-43640035. Error was invalid region `13:43639635-43640035`
[2016-04-15T06:51Z] 2016-04-14 23:51:42 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:51:42,478 - WARNING - Could not retrieve variants from source file in region 13:44058068-44058469. Error was invalid region `13:44058069-44058469`
[2016-04-15T06:51Z] 2016-04-14 23:51:42 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:51:42,578 - WARNING - Could not retrieve variants from source file in region 13:43148335-43148755. Error was invalid region `13:43148336-43148755`
[2016-04-15T06:51Z] 2016-04-14 23:51:42 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:51:42,804 - WARNING - Could not retrieve variants from source file in region 13:41372733-41382901. Error was invalid region `13:41372734-41382901`
[2016-04-15T06:51Z] 2016-04-14 23:51:45 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:51:45,254 - WARNING - Could not retrieve variants from source file in region 13:42301184-42301585. Error was invalid region `13:42301185-42301585`
[2016-04-15T06:51Z] 2016-04-14 23:51:48 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:51:48,610 - WARNING - Could not retrieve variants from source file in region 13:45967929-45985773. Error was invalid region `13:45967930-45985773`
[2016-04-15T06:51Z] 2016-04-14 23:51:49 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:51:49,507 - WARNING - Could not retrieve variants from source file in region 13:50204814-50205215. Error was invalid region `13:50204815-50205215`
[2016-04-15T06:51Z] 2016-04-14 23:51:49 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:51:49,737 - WARNING - Could not retrieve variants from source file in region 13:50295904-50296305. Error was invalid region `13:50295905-50296305`
[2016-04-15T06:51Z] 2016-04-14 23:51:50 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:51:50,424 - WARNING - Could not retrieve variants from source file in region 13:48938886-48939287. Error was invalid region `13:48938887-48939287`
[2016-04-15T06:51Z] 2016-04-14 23:51:50 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:51:50,430 - WARNING - Could not retrieve variants from source file in region 13:49950931-49951383. Error was invalid region `13:49950932-49951383`
[2016-04-15T06:51Z] 2016-04-14 23:51:50 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:51:50,441 - WARNING - Could not retrieve variants from source file in region 13:46287934-46288335. Error was invalid region `13:46287935-46288335`
[2016-04-15T06:51Z] 2016-04-14 23:51:50 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:51:50,447 - WARNING - Could not retrieve variants from source file in region 13:48547256-48547657. Error was invalid region `13:48547257-48547657`
[2016-04-15T06:51Z] 2016-04-14 23:51:51 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:51:51,124 - WARNING - Could not retrieve variants from source file in region 13:44058068-44058469. Error was invalid region `13:44058069-44058469`
[2016-04-15T06:51Z] 2016-04-14 23:51:51 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:51:51,211 - WARNING - Could not retrieve variants from source file in region 13:46695060-46708481. Error was invalid region `13:46695061-46708481`
[2016-04-15T06:51Z] 2016-04-14 23:51:51 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:51:51,666 - WARNING - Could not retrieve variants from source file in region 13:41372733-41382901. Error was invalid region `13:41372734-41382901`
[2016-04-15T06:51Z] 2016-04-14 23:51:53 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:51:53,319 - WARNING - Could not retrieve variants from source file in region 13:45967929-45985773. Error was invalid region `13:45967930-45985773`
[2016-04-15T06:51Z] 2016-04-14 23:51:53 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:51:53,821 - WARNING - Could not retrieve variants from source file in region 13:50050409-50141552. Error was invalid region `13:50050410-50141552`
[2016-04-15T06:51Z] 2016-04-14 23:51:54 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:51:54,649 - WARNING - Could not retrieve variants from source file in region 13:50204814-50205215. Error was invalid region `13:50204815-50205215`
[2016-04-15T06:51Z] 2016-04-14 23:51:55 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:51:55,024 - WARNING - Could not retrieve variants from source file in region 13:50295904-50296305. Error was invalid region `13:50295905-50296305`
[2016-04-15T06:51Z] 2016-04-14 23:51:57 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:51:57,210 - WARNING - Could not retrieve variants from source file in region 13:48547256-48547657. Error was invalid region `13:48547257-48547657`
[2016-04-15T06:51Z] 2016-04-14 23:51:57 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:51:57,325 - WARNING - Could not retrieve variants from source file in region 13:49950931-49951383. Error was invalid region `13:49950932-49951383`
[2016-04-15T06:51Z] 2016-04-14 23:51:57 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:51:57,351 - WARNING - Could not retrieve variants from source file in region 13:48938886-48939287. Error was invalid region `13:48938887-48939287`
[2016-04-15T06:51Z] 2016-04-14 23:51:57 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:51:57,793 - WARNING - Could not retrieve variants from source file in region 13:44058068-44058469. Error was invalid region `13:44058069-44058469`
[2016-04-15T06:51Z] 2016-04-14 23:51:57 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:51:57,833 - WARNING - Could not retrieve variants from source file in region 13:46287934-46288335. Error was invalid region `13:46287935-46288335`
[2016-04-15T06:51Z] 2016-04-14 23:51:58 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:51:58,011 - WARNING - Could not retrieve variants from source file in region 13:46695060-46708481. Error was invalid region `13:46695061-46708481`
[2016-04-15T06:51Z] 2016-04-14 23:51:58 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:51:58,096 - WARNING - Could not retrieve variants from source file in region 13:43639634-43640035. Error was invalid region `13:43639635-43640035`
[2016-04-15T06:52Z] 2016-04-14 23:52:08 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:52:08,344 - WARNING - Could not retrieve variants from source file in region 13:42032361-42032762. Error was invalid region `13:42032362-42032762`
[2016-04-15T06:52Z] 2016-04-14 23:52:12 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:52:12,495 - WARNING - Could not retrieve variants from source file in region 13:49866111-49867059. Error was invalid region `13:49866112-49867059`
[2016-04-15T06:52Z] 2016-04-14 23:52:12 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:52:12,702 - WARNING - Could not retrieve variants from source file in region 13:45563253-45563654. Error was invalid region `13:45563254-45563654`
[2016-04-15T06:52Z] 2016-04-14 23:52:14 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:52:14,377 - WARNING - Could not retrieve variants from source file in region 13:42032361-42032762. Error was invalid region `13:42032362-42032762`
[2016-04-15T06:52Z] 2016-04-14 23:52:14 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:52:14,389 - WARNING - Could not retrieve variants from source file in region 13:47469729-47471014. Error was invalid region `13:47469730-47471014`
[2016-04-15T06:52Z] 2016-04-14 23:52:14 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:52:14,565 - WARNING - Could not retrieve variants from source file in region 13:48574996-48575398. Error was invalid region `13:48574997-48575398`
[2016-04-15T06:52Z] 2016-04-14 23:52:14 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:52:14,961 - WARNING - Could not retrieve variants from source file in region 13:37679057-37679458. Error was invalid region `13:37679058-37679458`
[2016-04-15T06:52Z] 2016-04-14 23:52:16 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:52:16,056 - WARNING - Could not retrieve variants from source file in region 13:44422871-44423278. Error was invalid region `13:44422872-44423278`
[2016-04-15T06:52Z] 2016-04-14 23:52:16 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:52:16,191 - WARNING - Could not retrieve variants from source file in region 13:45841291-45841692. Error was invalid region `13:45841292-45841692`
[2016-04-15T06:52Z] 2016-04-14 23:52:16 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:52:16,230 - WARNING - Could not retrieve variants from source file in region 13:46170398-46170927. Error was invalid region `13:46170399-46170927`
[2016-04-15T06:52Z] 2016-04-14 23:52:16 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:52:16,637 - WARNING - Could not retrieve variants from source file in region 13:46629733-46656859. Error was invalid region `13:46629734-46656859`
[2016-04-15T06:52Z] 2016-04-14 23:52:17 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:52:17,265 - WARNING - Could not retrieve variants from source file in region 13:49866111-49867059. Error was invalid region `13:49866112-49867059`
[2016-04-15T06:52Z] 2016-04-14 23:52:17 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:52:17,274 - WARNING - Could not retrieve variants from source file in region 13:45563253-45563654. Error was invalid region `13:45563254-45563654`
[2016-04-15T06:52Z] 2016-04-14 23:52:17 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:52:17,306 - WARNING - Could not retrieve variants from source file in region 13:43787947-43788348. Error was invalid region `13:43787948-43788348`
[2016-04-15T06:52Z] 2016-04-14 23:52:18 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:52:18,330 - WARNING - Could not retrieve variants from source file in region 13:36685927-36686328. Error was invalid region `13:36685928-36686328`
[2016-04-15T06:52Z] 2016-04-14 23:52:19 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:52:19,181 - WARNING - Could not retrieve variants from source file in region 13:47469729-47471014. Error was invalid region `13:47469730-47471014`
[2016-04-15T06:52Z] 2016-04-14 23:52:19 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:52:19,212 - WARNING - Could not retrieve variants from source file in region 13:42032361-42032762. Error was invalid region `13:42032362-42032762`
[2016-04-15T06:52Z] 2016-04-14 23:52:19 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:52:19,887 - WARNING - Could not retrieve variants from source file in region 13:48574996-48575398. Error was invalid region `13:48574997-48575398`
[2016-04-15T06:52Z] 2016-04-14 23:52:21 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:52:21,991 - WARNING - Could not retrieve variants from source file in region 13:45841291-45841692. Error was invalid region `13:45841292-45841692`
[2016-04-15T06:52Z] 2016-04-14 23:52:22 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:52:22,909 - WARNING - Could not retrieve variants from source file in region 13:43597654-43598055. Error was invalid region `13:43597655-43598055`
[2016-04-15T06:52Z] 2016-04-14 23:52:23 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:52:23,757 - WARNING - Could not retrieve variants from source file in region 13:40325099-40326475. Error was invalid region `13:40325100-40326475`
[2016-04-15T06:52Z] 2016-04-14 23:52:23 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:52:23,796 - WARNING - Could not retrieve variants from source file in region 13:43787947-43788348. Error was invalid region `13:43787948-43788348`
[2016-04-15T06:52Z] 2016-04-14 23:52:24 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:52:24,054 - WARNING - Could not retrieve variants from source file in region 13:42872508-42882810. Error was invalid region `13:42872509-42882810`
[2016-04-15T06:52Z] 2016-04-14 23:52:24 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:52:24,121 - WARNING - Could not retrieve variants from source file in region 13:36685927-36686328. Error was invalid region `13:36685928-36686328`
[2016-04-15T06:52Z] 2016-04-14 23:52:24 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:52:24,178 - WARNING - Could not retrieve variants from source file in region 13:45563253-45563654. Error was invalid region `13:45563254-45563654`
[2016-04-15T06:52Z] 2016-04-14 23:52:24 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:52:24,480 - WARNING - Could not retrieve variants from source file in region 13:47469729-47471014. Error was invalid region `13:47469730-47471014`
[2016-04-15T06:52Z] 2016-04-14 23:52:24 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:52:24,784 - WARNING - Could not retrieve variants from source file in region 13:48574996-48575398. Error was invalid region `13:48574997-48575398`
[2016-04-15T06:52Z] 2016-04-14 23:52:26 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:52:26,655 - WARNING - Could not retrieve variants from source file in region 13:44422871-44423278. Error was invalid region `13:44422872-44423278`
[2016-04-15T06:52Z] 2016-04-14 23:52:27 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:52:27,974 - WARNING - Could not retrieve variants from source file in region 13:46170398-46170927. Error was invalid region `13:46170399-46170927`
[2016-04-15T06:52Z] 2016-04-14 23:52:29 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:52:29,104 - WARNING - Could not retrieve variants from source file in region 13:43597654-43598055. Error was invalid region `13:43597655-43598055`
[2016-04-15T06:52Z] 2016-04-14 23:52:29 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:52:29,582 - WARNING - Could not retrieve variants from source file in region 13:46629733-46656859. Error was invalid region `13:46629734-46656859`
[2016-04-15T06:52Z] 2016-04-14 23:52:30 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:52:30,204 - WARNING - Could not retrieve variants from source file in region 13:43787947-43788348. Error was invalid region `13:43787948-43788348`
[2016-04-15T06:52Z] 2016-04-14 23:52:33 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:52:33,903 - WARNING - Could not retrieve variants from source file in region 13:41947009-41947413. Error was invalid region `13:41947010-41947413`
[2016-04-15T06:52Z] 2016-04-14 23:52:38 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:52:38,879 - WARNING - Could not retrieve variants from source file in region 13:41947009-41947413. Error was invalid region `13:41947010-41947413`
[2016-04-15T06:52Z] 2016-04-14 23:52:41 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:52:41,379 - WARNING - Could not retrieve variants from source file in region 13:43462211-43469401. Error was invalid region `13:43462212-43469401`
[2016-04-15T06:52Z] 2016-04-14 23:52:41 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:52:41,535 - WARNING - Could not retrieve variants from source file in region 13:37579928-37596591. Error was invalid region `13:37579929-37596591`
[2016-04-15T06:52Z] 2016-04-14 23:52:41 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:52:41,595 - WARNING - Could not retrieve variants from source file in region 13:45008554-45011534. Error was invalid region `13:45008555-45011534`
[2016-04-15T06:52Z] 2016-04-14 23:52:41 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:52:41,620 - WARNING - Could not retrieve variants from source file in region 13:36229662-36230063. Error was invalid region `13:36229663-36230063`
[2016-04-15T06:52Z] 2016-04-14 23:52:42 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:52:42,012 - WARNING - Could not retrieve variants from source file in region 13:47307898-47318087. Error was invalid region `13:47307899-47318087`
[2016-04-15T06:52Z] 2016-04-14 23:52:43 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:52:43,045 - WARNING - Could not retrieve variants from source file in region 13:41947009-41947413. Error was invalid region `13:41947010-41947413`
[2016-04-15T06:52Z] 2016-04-14 23:52:43 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:52:43,843 - WARNING - Could not retrieve variants from source file in region 13:36202058-36202459. Error was invalid region `13:36202059-36202459`
[2016-04-15T06:52Z] 2016-04-14 23:52:44 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:52:44,462 - WARNING - Could not retrieve variants from source file in region 13:41834533-41834934. Error was invalid region `13:41834534-41834934`
[2016-04-15T06:52Z] 2016-04-14 23:52:44 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:52:44,519 - WARNING - Could not retrieve variants from source file in region 13:40229680-40230147. Error was invalid region `13:40229681-40230147`
[2016-04-15T06:52Z] 2016-04-14 23:52:45 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:52:45,785 - WARNING - Could not retrieve variants from source file in region 13:46537546-46563125. Error was invalid region `13:46537547-46563125`
[2016-04-15T06:52Z] 2016-04-14 23:52:46 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:52:46,813 - WARNING - Could not retrieve variants from source file in region 13:42764353-42793669. Error was invalid region `13:42764354-42793669`
[2016-04-15T06:52Z] 2016-04-14 23:52:47 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:52:47,241 - WARNING - Could not retrieve variants from source file in region 13:37579928-37596591. Error was invalid region `13:37579929-37596591`
[2016-04-15T06:52Z] 2016-04-14 23:52:47 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:52:47,336 - WARNING - Could not retrieve variants from source file in region 13:36229662-36230063. Error was invalid region `13:36229663-36230063`
[2016-04-15T06:52Z] 2016-04-14 23:52:47 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:52:47,723 - WARNING - Could not retrieve variants from source file in region 13:47242985-47260244. Error was invalid region `13:47242986-47260244`
[2016-04-15T06:52Z] 2016-04-14 23:52:47 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:52:47,734 - WARNING - Could not retrieve variants from source file in region 13:36384820-36424888. Error was invalid region `13:36384821-36424888`
[2016-04-15T06:52Z] 2016-04-14 23:52:47 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:52:47,787 - WARNING - Could not retrieve variants from source file in region 13:47307898-47318087. Error was invalid region `13:47307899-47318087`
[2016-04-15T06:52Z] 2016-04-14 23:52:47 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:52:47,830 - WARNING - Could not retrieve variants from source file in region 13:46103724-46115921. Error was invalid region `13:46103725-46115921`
[2016-04-15T06:52Z] 2016-04-14 23:52:49 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:52:49,116 - WARNING - Could not retrieve variants from source file in region 13:36202058-36202459. Error was invalid region `13:36202059-36202459`
[2016-04-15T06:52Z] 2016-04-14 23:52:49 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:52:49,266 - WARNING - Could not retrieve variants from source file in region 13:41834533-41834934. Error was invalid region `13:41834534-41834934`
[2016-04-15T06:52Z] 2016-04-14 23:52:49 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:52:49,357 - WARNING - Could not retrieve variants from source file in region 13:40229680-40230147. Error was invalid region `13:40229681-40230147`
[2016-04-15T06:52Z] 2016-04-14 23:52:52 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:52:52,825 - WARNING - Could not retrieve variants from source file in region 13:36229662-36230063. Error was invalid region `13:36229663-36230063`
[2016-04-15T06:52Z] 2016-04-14 23:52:53 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:52:53,612 - WARNING - Could not retrieve variants from source file in region 13:46103724-46115921. Error was invalid region `13:46103725-46115921`
[2016-04-15T06:52Z] 2016-04-14 23:52:54 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:52:54,136 - WARNING - Could not retrieve variants from source file in region 13:36202058-36202459. Error was invalid region `13:36202059-36202459`
[2016-04-15T06:52Z] 2016-04-14 23:52:54 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:52:54,516 - WARNING - Could not retrieve variants from source file in region 13:41834533-41834934. Error was invalid region `13:41834534-41834934`
[2016-04-15T06:52Z] 2016-04-14 23:52:55 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:52:55,373 - WARNING - Could not retrieve variants from source file in region 13:46537546-46563125. Error was invalid region `13:46537547-46563125`
[2016-04-15T06:52Z] 2016-04-14 23:52:56 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:52:56,780 - WARNING - Could not retrieve variants from source file in region 13:41705284-41705685. Error was invalid region `13:41705285-41705685`
[2016-04-15T06:52Z] 2016-04-14 23:52:57 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:52:57,241 - WARNING - Could not retrieve variants from source file in region 13:41902728-41903129. Error was invalid region `13:41902729-41903129`
[2016-04-15T06:53Z] 2016-04-14 23:53:02 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:53:02,028 - WARNING - Could not retrieve variants from source file in region 13:41705284-41705685. Error was invalid region `13:41705285-41705685`
[2016-04-15T06:53Z] 2016-04-14 23:53:03 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:53:03,027 - WARNING - Could not retrieve variants from source file in region 13:41902728-41903129. Error was invalid region `13:41902729-41903129`
[2016-04-15T06:53Z] 2016-04-14 23:53:04 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:53:04,445 - WARNING - Could not retrieve variants from source file in region 13:37393307-37393708. Error was invalid region `13:37393308-37393708`
[2016-04-15T06:53Z] 2016-04-14 23:53:04 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:53:04,459 - WARNING - Could not retrieve variants from source file in region 13:41902728-41903129. Error was invalid region `13:41902729-41903129`
[2016-04-15T06:53Z] 2016-04-14 23:53:04 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:53:04,511 - WARNING - Could not retrieve variants from source file in region 13:39586132-39588079. Error was invalid region `13:39586133-39588079`
[2016-04-15T06:53Z] 2016-04-14 23:53:06 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:53:06,060 - WARNING - Could not retrieve variants from source file in region 13:41705284-41705685. Error was invalid region `13:41705285-41705685`
[2016-04-15T06:53Z] 2016-04-14 23:53:06 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:53:06,811 - WARNING - Could not retrieve variants from source file in region 13:37393307-37393708. Error was invalid region `13:37393308-37393708`
[2016-04-15T06:53Z] 2016-04-14 23:53:08 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:53:08,190 - WARNING - Could not retrieve variants from source file in region 13:41767127-41767531. Error was invalid region `13:41767128-41767531`
[2016-04-15T06:53Z] 2016-04-14 23:53:08 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:53:08,899 - WARNING - Could not retrieve variants from source file in region 13:39586132-39588079. Error was invalid region `13:39586133-39588079`
[2016-04-15T06:53Z] 2016-04-14 23:53:09 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:53:09,695 - WARNING - Could not retrieve variants from source file in region 13:46917258-46917659. Error was invalid region `13:46917259-46917659`
[2016-04-15T06:53Z] 2016-04-14 23:53:11 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:53:11,652 - WARNING - Could not retrieve variants from source file in region 13:46067382-46077571. Error was invalid region `13:46067383-46077571`
[2016-04-15T06:53Z] 2016-04-14 23:53:11 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:53:11,723 - WARNING - Could not retrieve variants from source file in region 13:46945946-46961490. Error was invalid region `13:46945947-46961490`
[2016-04-15T06:53Z] 2016-04-14 23:53:12 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:53:12,026 - WARNING - Could not retrieve variants from source file in region 13:46801759-46802367. Error was invalid region `13:46801760-46802367`
[2016-04-15T06:53Z] 2016-04-14 23:53:12 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:53:12,580 - WARNING - Could not retrieve variants from source file in region 13:41767127-41767531. Error was invalid region `13:41767128-41767531`
[2016-04-15T06:53Z] 2016-04-14 23:53:12 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:53:12,834 - WARNING - Could not retrieve variants from source file in region 13:41767127-41767531. Error was invalid region `13:41767128-41767531`
[2016-04-15T06:53Z] 2016-04-14 23:53:12 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:53:12,958 - WARNING - Could not retrieve variants from source file in region 13:46945946-46961490. Error was invalid region `13:46945947-46961490`
[2016-04-15T06:53Z] 2016-04-14 23:53:13 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:53:13,298 - WARNING - Could not retrieve variants from source file in region 13:39586132-39588079. Error was invalid region `13:39586133-39588079`
[2016-04-15T06:53Z] 2016-04-14 23:53:14 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:53:14,137 - WARNING - Could not retrieve variants from source file in region 13:46917258-46917659. Error was invalid region `13:46917259-46917659`
[2016-04-15T06:53Z] 2016-04-14 23:53:16 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:53:16,030 - WARNING - Could not retrieve variants from source file in region 13:46067382-46077571. Error was invalid region `13:46067383-46077571`
[2016-04-15T06:53Z] 2016-04-14 23:53:17 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:53:17,787 - WARNING - Could not retrieve variants from source file in region 13:41515075-41533242. Error was invalid region `13:41515076-41533242`
[2016-04-15T06:53Z] 2016-04-14 23:53:19 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:53:19,198 - WARNING - Could not retrieve variants from source file in region 13:39430103-39433796. Error was invalid region `13:39430104-39433796`
[2016-04-15T06:53Z] 2016-04-14 23:53:21 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:53:21,334 - WARNING - Could not retrieve variants from source file in region 13:41515075-41533242. Error was invalid region `13:41515076-41533242`
[2016-04-15T06:53Z] 2016-04-14 23:53:21 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:53:21,474 - WARNING - Could not retrieve variants from source file in region 13:38924052-38924453. Error was invalid region `13:38924053-38924453`
[2016-04-15T06:53Z] 2016-04-14 23:53:21 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:53:21,948 - WARNING - Could not retrieve variants from source file in region 13:41515075-41533242. Error was invalid region `13:41515076-41533242`
[2016-04-15T06:53Z] 2016-04-14 23:53:22 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:53:22,628 - WARNING - Could not retrieve variants from source file in region 13:38924052-38924453. Error was invalid region `13:38924053-38924453`
[2016-04-15T06:53Z] 2016-04-14 23:53:22 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:53:22,632 - WARNING - Could not retrieve variants from source file in region 13:38924052-38924453. Error was invalid region `13:38924053-38924453`
[2016-04-15T06:53Z] 2016-04-14 23:53:22 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:53:22,644 - WARNING - Could not retrieve variants from source file in region 13:39430103-39433796. Error was invalid region `13:39430104-39433796`
[2016-04-15T06:53Z] ['bcbio-variation-recall', 'square', '-Xms750m', '-Xmx7280m', '-XX:+UseSerialGC', '-c', 16, '-r', u'13:51396768-67205543', '--caller', 'platypus', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/13/Batch1-13_51396767_67205543.vcf.gz', '/mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/13/Batch1-13_51396767_67205543.vcf-inputs.txt'] in region: 13:51396768-67205543
[2016-04-15T06:53Z] 2016-04-14 23:53:38 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:53:38,602 - WARNING - Could not retrieve variants from source file in region 13:53216824-53217683. Error was invalid region `13:53216825-53217683`
[2016-04-15T06:53Z] 2016-04-14 23:53:39 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:53:39,335 - WARNING - Could not retrieve variants from source file in region 13:52602983-52603965. Error was invalid region `13:52602984-52603965`
[2016-04-15T06:53Z] 2016-04-14 23:53:39 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:53:39,572 - WARNING - Could not retrieve variants from source file in region 13:60587045-60587446. Error was invalid region `13:60587046-60587446`
[2016-04-15T06:53Z] 2016-04-14 23:53:39 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:53:39,752 - WARNING - Could not retrieve variants from source file in region 13:61986707-61987108. Error was invalid region `13:61986708-61987108`
[2016-04-15T06:53Z] 2016-04-14 23:53:39 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:53:39,881 - WARNING - Could not retrieve variants from source file in region 13:52971682-52972083. Error was invalid region `13:52971683-52972083`
[2016-04-15T06:53Z] 2016-04-14 23:53:39 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:53:39,950 - WARNING - Could not retrieve variants from source file in region 13:60240750-60241151. Error was invalid region `13:60240751-60241151`
[2016-04-15T06:53Z] 2016-04-14 23:53:40 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:53:40,107 - WARNING - Could not retrieve variants from source file in region 13:52024725-52025172. Error was invalid region `13:52024726-52025172`
[2016-04-15T06:53Z] 2016-04-14 23:53:40 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:53:40,179 - WARNING - Could not retrieve variants from source file in region 13:52515143-52548330. Error was invalid region `13:52515144-52548330`
[2016-04-15T06:53Z] 2016-04-14 23:53:45 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:53:45,987 - WARNING - Could not retrieve variants from source file in region 13:52709727-52718240. Error was invalid region `13:52709728-52718240`
[2016-04-15T06:53Z] 2016-04-14 23:53:46 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:53:46,524 - WARNING - Could not retrieve variants from source file in region 13:53024163-53036115. Error was invalid region `13:53024164-53036115`
[2016-04-15T06:53Z] 2016-04-14 23:53:47 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:53:47,414 - WARNING - Could not retrieve variants from source file in region 13:60240750-60241151. Error was invalid region `13:60240751-60241151`
[2016-04-15T06:53Z] 2016-04-14 23:53:48 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:53:48,305 - WARNING - Could not retrieve variants from source file in region 13:53608421-53608822. Error was invalid region `13:53608422-53608822`
[2016-04-15T06:53Z] 2016-04-14 23:53:48 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:53:48,376 - WARNING - Could not retrieve variants from source file in region 13:51397229-51397630. Error was invalid region `13:51397230-51397630`
[2016-04-15T06:53Z] 2016-04-14 23:53:48 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:53:48,384 - WARNING - Could not retrieve variants from source file in region 13:52709727-52718240. Error was invalid region `13:52709728-52718240`
[2016-04-15T06:53Z] 2016-04-14 23:53:49 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:53:49,368 - WARNING - Could not retrieve variants from source file in region 13:52439919-52440320. Error was invalid region `13:52439920-52440320`
[2016-04-15T06:53Z] 2016-04-14 23:53:49 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:53:49,371 - WARNING - Could not retrieve variants from source file in region 13:61102364-61102768. Error was invalid region `13:61102365-61102768`
[2016-04-15T06:53Z] 2016-04-14 23:53:49 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:53:49,418 - WARNING - Could not retrieve variants from source file in region 13:60587045-60587446. Error was invalid region `13:60587046-60587446`
[2016-04-15T06:53Z] 2016-04-14 23:53:49 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:53:49,515 - WARNING - Could not retrieve variants from source file in region 13:52971682-52972083. Error was invalid region `13:52971683-52972083`
[2016-04-15T06:53Z] 2016-04-14 23:53:49 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:53:49,532 - WARNING - Could not retrieve variants from source file in region 13:52024725-52025172. Error was invalid region `13:52024726-52025172`
[2016-04-15T06:53Z] 2016-04-14 23:53:55 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:53:55,783 - WARNING - Could not retrieve variants from source file in region 13:52602983-52603965. Error was invalid region `13:52602984-52603965`
[2016-04-15T06:53Z] 2016-04-14 23:53:55 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:53:55,926 - WARNING - Could not retrieve variants from source file in region 13:52971682-52972083. Error was invalid region `13:52971683-52972083`
[2016-04-15T06:53Z] 2016-04-14 23:53:56 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:53:56,030 - WARNING - Could not retrieve variants from source file in region 13:51397229-51397630. Error was invalid region `13:51397230-51397630`
[2016-04-15T06:53Z] 2016-04-14 23:53:56 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:53:56,473 - WARNING - Could not retrieve variants from source file in region 13:52515143-52548330. Error was invalid region `13:52515144-52548330`
[2016-04-15T06:53Z] 2016-04-14 23:53:56 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:53:56,492 - WARNING - Could not retrieve variants from source file in region 13:52024725-52025172. Error was invalid region `13:52024726-52025172`
[2016-04-15T06:54Z] ['bcbio-variation-recall', 'square', '-Xms750m', '-Xmx7280m', '-XX:+UseSerialGC', '-c', 16, '-r', u'13:67477636-84455642', '--caller', 'platypus', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/13/Batch1-13_67477635_84455642.vcf.gz', '/mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/13/Batch1-13_67477635_84455642.vcf-inputs.txt'] in region: 13:67477636-84455642
[2016-04-15T06:54Z] 2016-04-14 23:54:13 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:54:13,580 - WARNING - Could not retrieve variants from source file in region 13:80911314-80911715. Error was invalid region `13:80911315-80911715`
[2016-04-15T06:54Z] 2016-04-14 23:54:15 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:54:15,469 - WARNING - Could not retrieve variants from source file in region 13:78216662-78217063. Error was invalid region `13:78216663-78217063`
[2016-04-15T06:54Z] 2016-04-14 23:54:16 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:54:16,280 - WARNING - Could not retrieve variants from source file in region 13:76055609-76056010. Error was invalid region `13:76055610-76056010`
[2016-04-15T06:54Z] 2016-04-14 23:54:16 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:54:16,344 - WARNING - Could not retrieve variants from source file in region 13:77565947-77575173. Error was invalid region `13:77565948-77575173`
[2016-04-15T06:54Z] 2016-04-14 23:54:16 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:54:16,345 - WARNING - Could not retrieve variants from source file in region 13:78272059-78272460. Error was invalid region `13:78272060-78272460`
[2016-04-15T06:54Z] 2016-04-14 23:54:16 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:54:16,380 - WARNING - Could not retrieve variants from source file in region 13:78475102-78477864. Error was invalid region `13:78475103-78477864`
[2016-04-15T06:54Z] 2016-04-14 23:54:16 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:54:16,661 - WARNING - Could not retrieve variants from source file in region 13:77738453-77752082. Error was invalid region `13:77738454-77752082`
[2016-04-15T06:54Z] 2016-04-14 23:54:17 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:54:17,234 - WARNING - Could not retrieve variants from source file in region 13:75936308-75936709. Error was invalid region `13:75936309-75936709`
[2016-04-15T06:54Z] 2016-04-14 23:54:17 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:54:17,547 - WARNING - Could not retrieve variants from source file in region 13:78146090-78146491. Error was invalid region `13:78146091-78146491`
[2016-04-15T06:54Z] 2016-04-14 23:54:19 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:54:19,707 - WARNING - Could not retrieve variants from source file in region 13:76210531-76210932. Error was invalid region `13:76210532-76210932`
[2016-04-15T06:54Z] 2016-04-14 23:54:20 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:54:20,405 - WARNING - Could not retrieve variants from source file in region 13:77531150-77531551. Error was invalid region `13:77531151-77531551`
[2016-04-15T06:54Z] 2016-04-14 23:54:21 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:54:21,323 - WARNING - Could not retrieve variants from source file in region 13:78216662-78217063. Error was invalid region `13:78216663-78217063`
[2016-04-15T06:54Z] 2016-04-14 23:54:23 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:54:23,900 - WARNING - Could not retrieve variants from source file in region 13:78475102-78477864. Error was invalid region `13:78475103-78477864`
[2016-04-15T06:54Z] 2016-04-14 23:54:23 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:54:23,907 - WARNING - Could not retrieve variants from source file in region 13:76055609-76056010. Error was invalid region `13:76055610-76056010`
[2016-04-15T06:54Z] 2016-04-14 23:54:24 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:54:24,370 - WARNING - Could not retrieve variants from source file in region 13:78272059-78272460. Error was invalid region `13:78272060-78272460`
[2016-04-15T06:54Z] 2016-04-14 23:54:24 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:54:24,668 - WARNING - Could not retrieve variants from source file in region 13:75936308-75936709. Error was invalid region `13:75936309-75936709`
[2016-04-15T06:54Z] 2016-04-14 23:54:25 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:54:25,029 - WARNING - Could not retrieve variants from source file in region 13:70549695-70550096. Error was invalid region `13:70549696-70550096`
[2016-04-15T06:54Z] 2016-04-14 23:54:25 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:54:25,574 - WARNING - Could not retrieve variants from source file in region 13:78146090-78146491. Error was invalid region `13:78146091-78146491`
[2016-04-15T06:54Z] 2016-04-14 23:54:25 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:54:25,779 - WARNING - Could not retrieve variants from source file in region 13:80911314-80911715. Error was invalid region `13:80911315-80911715`
[2016-04-15T06:54Z] 2016-04-14 23:54:25 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:54:25,879 - WARNING - Could not retrieve variants from source file in region 13:76210531-76210932. Error was invalid region `13:76210532-76210932`
[2016-04-15T06:54Z] 2016-04-14 23:54:26 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:54:26,152 - WARNING - Could not retrieve variants from source file in region 13:75862905-75884406. Error was invalid region `13:75862906-75884406`
[2016-04-15T06:54Z] 2016-04-14 23:54:26 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:54:26,477 - WARNING - Could not retrieve variants from source file in region 13:78216662-78217063. Error was invalid region `13:78216663-78217063`
[2016-04-15T06:54Z] 2016-04-14 23:54:28 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:54:28,153 - WARNING - Could not retrieve variants from source file in region 13:77565947-77575173. Error was invalid region `13:77565948-77575173`
[2016-04-15T06:54Z] 2016-04-14 23:54:29 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:54:29,616 - WARNING - Could not retrieve variants from source file in region 13:78475102-78477864. Error was invalid region `13:78475103-78477864`
[2016-04-15T06:54Z] 2016-04-14 23:54:30 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:54:30,229 - WARNING - Could not retrieve variants from source file in region 13:78272059-78272460. Error was invalid region `13:78272060-78272460`
[2016-04-15T06:54Z] 2016-04-14 23:54:32 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:54:32,212 - WARNING - Could not retrieve variants from source file in region 13:70549695-70550096. Error was invalid region `13:70549696-70550096`
[2016-04-15T06:54Z] 2016-04-14 23:54:32 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:54:32,217 - WARNING - Could not retrieve variants from source file in region 13:75936308-75936709. Error was invalid region `13:75936309-75936709`
[2016-04-15T06:54Z] 2016-04-14 23:54:33 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:54:33,019 - WARNING - Could not retrieve variants from source file in region 13:76334607-76335299. Error was invalid region `13:76334608-76335299`
[2016-04-15T06:54Z] 2016-04-14 23:54:33 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:54:33,704 - WARNING - Could not retrieve variants from source file in region 13:78146090-78146491. Error was invalid region `13:78146091-78146491`
[2016-04-15T06:54Z] 2016-04-14 23:54:42 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:54:42,563 - WARNING - Could not retrieve variants from source file in region 13:74338893-74339294. Error was invalid region `13:74338894-74339294`
[2016-04-15T06:54Z] 2016-04-14 23:54:43 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:54:43,265 - WARNING - Could not retrieve variants from source file in region 13:74338893-74339294. Error was invalid region `13:74338894-74339294`
[2016-04-15T06:54Z] 2016-04-14 23:54:43 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:54:43,405 - WARNING - Could not retrieve variants from source file in region 13:70413080-70413481. Error was invalid region `13:70413081-70413481`
[2016-04-15T06:54Z] 2016-04-14 23:54:43 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:54:43,799 - WARNING - Could not retrieve variants from source file in region 13:70413080-70413481. Error was invalid region `13:70413081-70413481`
[2016-04-15T06:54Z] 2016-04-14 23:54:43 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:54:43,842 - WARNING - Could not retrieve variants from source file in region 13:70413080-70413481. Error was invalid region `13:70413081-70413481`
[2016-04-15T06:54Z] 2016-04-14 23:54:46 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:54:46,626 - WARNING - Could not retrieve variants from source file in region 13:72049101-72049502. Error was invalid region `13:72049102-72049502`
[2016-04-15T06:54Z] ['bcbio-variation-recall', 'square', '-Xms750m', '-Xmx7280m', '-XX:+UseSerialGC', '-c', 16, '-r', u'13:86368118-101881935', '--caller', 'platypus', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/13/Batch1-13_86368117_101881935.vcf.gz', '/mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/13/Batch1-13_86368117_101881935.vcf-inputs.txt'] in region: 13:86368118-101881935
[2016-04-15T06:55Z] 2016-04-14 23:55:02 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:55:02,974 - WARNING - Could not retrieve variants from source file in region 13:101881566-101881967. Error was invalid region `13:101881567-101881967`
[2016-04-15T06:55Z] 2016-04-14 23:55:03 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:55:03,043 - WARNING - Could not retrieve variants from source file in region 13:95714765-95727970. Error was invalid region `13:95714766-95727970`
[2016-04-15T06:55Z] 2016-04-14 23:55:03 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:55:03,937 - WARNING - Could not retrieve variants from source file in region 13:95816496-95816897. Error was invalid region `13:95816497-95816897`
[2016-04-15T06:55Z] 2016-04-14 23:55:04 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:55:04,936 - WARNING - Could not retrieve variants from source file in region 13:97639203-97639604. Error was invalid region `13:97639204-97639604`
[2016-04-15T06:55Z] 2016-04-14 23:55:04 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:55:04,957 - WARNING - Could not retrieve variants from source file in region 13:100518369-100518770. Error was invalid region `13:100518370-100518770`
[2016-04-15T06:55Z] 2016-04-14 23:55:05 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:55:05,032 - WARNING - Could not retrieve variants from source file in region 13:88329874-88330275. Error was invalid region `13:88329875-88330275`
[2016-04-15T06:55Z] 2016-04-14 23:55:05 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:55:05,380 - WARNING - Could not retrieve variants from source file in region 13:101287154-101287594. Error was invalid region `13:101287155-101287594`
[2016-04-15T06:55Z] 2016-04-14 23:55:05 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:55:05,392 - WARNING - Could not retrieve variants from source file in region 13:99667750-99668172. Error was invalid region `13:99667751-99668172`
[2016-04-15T06:55Z] 2016-04-14 23:55:05 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:55:05,769 - WARNING - Could not retrieve variants from source file in region 13:96293420-96293821. Error was invalid region `13:96293421-96293821`
[2016-04-15T06:55Z] 2016-04-14 23:55:06 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:55:06,125 - WARNING - Could not retrieve variants from source file in region 13:95858767-95861994. Error was invalid region `13:95858768-95861994`
[2016-04-15T06:55Z] 2016-04-14 23:55:09 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:55:09,436 - WARNING - Could not retrieve variants from source file in region 13:95714765-95727970. Error was invalid region `13:95714766-95727970`
[2016-04-15T06:55Z] 2016-04-14 23:55:11 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:55:11,136 - WARNING - Could not retrieve variants from source file in region 13:101327438-101328362. Error was invalid region `13:101327439-101328362`
[2016-04-15T06:55Z] 2016-04-14 23:55:12 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:55:12,511 - WARNING - Could not retrieve variants from source file in region 13:101287154-101287594. Error was invalid region `13:101287155-101287594`
[2016-04-15T06:55Z] 2016-04-14 23:55:13 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:55:13,565 - WARNING - Could not retrieve variants from source file in region 13:97639203-97639604. Error was invalid region `13:97639204-97639604`
[2016-04-15T06:55Z] 2016-04-14 23:55:13 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:55:13,812 - WARNING - Could not retrieve variants from source file in region 13:96539993-96555339. Error was invalid region `13:96539994-96555339`
[2016-04-15T06:55Z] 2016-04-14 23:55:13 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:55:13,888 - WARNING - Could not retrieve variants from source file in region 13:99194900-99195451. Error was invalid region `13:99194901-99195451`
[2016-04-15T06:55Z] 2016-04-14 23:55:13 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:55:13,896 - WARNING - Could not retrieve variants from source file in region 13:101720089-101736265. Error was invalid region `13:101720090-101736265`
[2016-04-15T06:55Z] 2016-04-14 23:55:14 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:55:14,159 - WARNING - Could not retrieve variants from source file in region 13:96506453-96506854. Error was invalid region `13:96506454-96506854`
[2016-04-15T06:55Z] 2016-04-14 23:55:14 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:55:14,383 - WARNING - Could not retrieve variants from source file in region 13:101881566-101881967. Error was invalid region `13:101881567-101881967`
[2016-04-15T06:55Z] 2016-04-14 23:55:14 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:55:14,400 - WARNING - Could not retrieve variants from source file in region 13:95858767-95861994. Error was invalid region `13:95858768-95861994`
[2016-04-15T06:55Z] 2016-04-14 23:55:14 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:55:14,773 - WARNING - Could not retrieve variants from source file in region 13:95714765-95727970. Error was invalid region `13:95714766-95727970`
[2016-04-15T06:55Z] 2016-04-14 23:55:15 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:55:15,958 - WARNING - Could not retrieve variants from source file in region 13:101327438-101328362. Error was invalid region `13:101327439-101328362`
[2016-04-15T06:55Z] 2016-04-14 23:55:19 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:55:19,253 - WARNING - Could not retrieve variants from source file in region 13:101287154-101287594. Error was invalid region `13:101287155-101287594`
[2016-04-15T06:55Z] 2016-04-14 23:55:19 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:55:19,553 - WARNING - Could not retrieve variants from source file in region 13:88329874-88330275. Error was invalid region `13:88329875-88330275`
[2016-04-15T06:55Z] 2016-04-14 23:55:21 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:55:21,828 - WARNING - Could not retrieve variants from source file in region 13:99667750-99668172. Error was invalid region `13:99667751-99668172`
[2016-04-15T06:55Z] 2016-04-14 23:55:21 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:55:21,891 - WARNING - Could not retrieve variants from source file in region 13:97639203-97639604. Error was invalid region `13:97639204-97639604`
[2016-04-15T06:55Z] 2016-04-14 23:55:22 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:55:22,331 - WARNING - Could not retrieve variants from source file in region 13:96293420-96293821. Error was invalid region `13:96293421-96293821`
[2016-04-15T06:55Z] 2016-04-14 23:55:23 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:55:23,082 - WARNING - Could not retrieve variants from source file in region 13:95858767-95861994. Error was invalid region `13:95858768-95861994`
[2016-04-15T06:55Z] 2016-04-14 23:55:32 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:55:32,891 - WARNING - Could not retrieve variants from source file in region 13:100887911-100888312. Error was invalid region `13:100887912-100888312`
[2016-04-15T06:55Z] 2016-04-14 23:55:33 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:55:33,766 - WARNING - Could not retrieve variants from source file in region 13:95264393-95264794. Error was invalid region `13:95264394-95264794`
[2016-04-15T06:55Z] 2016-04-14 23:55:34 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:55:34,730 - WARNING - Could not retrieve variants from source file in region 13:95264393-95264794. Error was invalid region `13:95264394-95264794`
[2016-04-15T06:55Z] 2016-04-14 23:55:36 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:55:36,327 - WARNING - Could not retrieve variants from source file in region 13:101143820-101144221. Error was invalid region `13:101143821-101144221`
[2016-04-15T06:55Z] 2016-04-14 23:55:36 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:55:36,486 - WARNING - Could not retrieve variants from source file in region 13:99947967-99948368. Error was invalid region `13:99947968-99948368`
[2016-04-15T06:55Z] 2016-04-14 23:55:36 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:55:36,819 - WARNING - Could not retrieve variants from source file in region 13:86368909-86369310. Error was invalid region `13:86368910-86369310`
[2016-04-15T06:55Z] 2016-04-14 23:55:37 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:55:37,260 - WARNING - Could not retrieve variants from source file in region 13:99575357-99575758. Error was invalid region `13:99575358-99575758`
[2016-04-15T06:55Z] 2016-04-14 23:55:39 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:55:39,192 - WARNING - Could not retrieve variants from source file in region 13:95264393-95264794. Error was invalid region `13:95264394-95264794`
[2016-04-15T06:55Z] 2016-04-14 23:55:39 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:55:39,763 - WARNING - Could not retrieve variants from source file in region 13:99457220-99476845. Error was invalid region `13:99457221-99476845`
[2016-04-15T06:55Z] 2016-04-14 23:55:40 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:55:40,236 - WARNING - Could not retrieve variants from source file in region 13:98896565-98897342. Error was invalid region `13:98896566-98897342`
[2016-04-15T06:55Z] 2016-04-14 23:55:40 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:55:40,373 - WARNING - Could not retrieve variants from source file in region 13:99089829-99112870. Error was invalid region `13:99089830-99112870`
[2016-04-15T06:55Z] 2016-04-14 23:55:41 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:55:41,859 - WARNING - Could not retrieve variants from source file in region 13:99947967-99948368. Error was invalid region `13:99947968-99948368`
[2016-04-15T06:55Z] 2016-04-14 23:55:41 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:55:41,861 - WARNING - Could not retrieve variants from source file in region 13:86368909-86369310. Error was invalid region `13:86368910-86369310`
[2016-04-15T06:55Z] 2016-04-14 23:55:42 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:55:42,106 - WARNING - Could not retrieve variants from source file in region 13:96638425-96638841. Error was invalid region `13:96638426-96638841`
[2016-04-15T06:55Z] 2016-04-14 23:55:43 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:55:43,737 - WARNING - Could not retrieve variants from source file in region 13:99907130-99907531. Error was invalid region `13:99907131-99907531`
[2016-04-15T06:55Z] 2016-04-14 23:55:44 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:55:44,930 - WARNING - Could not retrieve variants from source file in region 13:98896565-98897342. Error was invalid region `13:98896566-98897342`
[2016-04-15T06:55Z] 2016-04-14 23:55:46 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:55:46,353 - WARNING - Could not retrieve variants from source file in region 13:99947967-99948368. Error was invalid region `13:99947968-99948368`
[2016-04-15T06:55Z] 2016-04-14 23:55:46 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:55:46,814 - WARNING - Could not retrieve variants from source file in region 13:86368909-86369310. Error was invalid region `13:86368910-86369310`
[2016-04-15T06:55Z] 2016-04-14 23:55:47 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:55:47,391 - WARNING - Could not retrieve variants from source file in region 13:99575357-99575758. Error was invalid region `13:99575358-99575758`
[2016-04-15T06:55Z] 2016-04-14 23:55:48 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:55:48,055 - WARNING - Could not retrieve variants from source file in region 13:99907130-99907531. Error was invalid region `13:99907131-99907531`
[2016-04-15T06:55Z] 2016-04-14 23:55:49 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:55:49,935 - WARNING - Could not retrieve variants from source file in region 13:98896565-98897342. Error was invalid region `13:98896566-98897342`
[2016-04-15T06:55Z] 2016-04-14 23:55:52 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:55:52,029 - WARNING - Could not retrieve variants from source file in region 13:99853232-99853633. Error was invalid region `13:99853233-99853633`
[2016-04-15T06:55Z] 2016-04-14 23:55:52 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:55:52,032 - WARNING - Could not retrieve variants from source file in region 13:99853232-99853633. Error was invalid region `13:99853233-99853633`
[2016-04-15T06:55Z] 2016-04-14 23:55:53 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:55:53,962 - WARNING - Could not retrieve variants from source file in region 13:98828393-98829366. Error was invalid region `13:98828394-98829366`
[2016-04-15T06:55Z] 2016-04-14 23:55:54 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:55:54,296 - WARNING - Could not retrieve variants from source file in region 13:99340560-99356802. Error was invalid region `13:99340561-99356802`
[2016-04-15T06:55Z] 2016-04-14 23:55:54 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:55:54,354 - WARNING - Could not retrieve variants from source file in region 13:99853232-99853633. Error was invalid region `13:99853233-99853633`
[2016-04-15T06:55Z] 2016-04-14 23:55:57 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:55:57,044 - WARNING - Could not retrieve variants from source file in region 13:98828393-98829366. Error was invalid region `13:98828394-98829366`
[2016-04-15T06:56Z] ['bcbio-variation-recall', 'square', '-Xms750m', '-Xmx7280m', '-XX:+UseSerialGC', '-c', 16, '-r', u'13:101890106-115169878', '--caller', 'platypus', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/13/Batch1-13_101890105_115169878.vcf.gz', '/mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/13/Batch1-13_101890105_115169878.vcf-inputs.txt'] in region: 13:101890106-115169878
[2016-04-15T06:56Z] 2016-04-14 23:56:11 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:56:11,620 - WARNING - Could not retrieve variants from source file in region 13:114780553-114782969. Error was invalid region `13:114780554-114782969`
[2016-04-15T06:56Z] 2016-04-14 23:56:12 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:56:12,299 - WARNING - Could not retrieve variants from source file in region 13:113862590-113862991. Error was invalid region `13:113862591-113862991`
[2016-04-15T06:56Z] 2016-04-14 23:56:13 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:56:13,444 - WARNING - Could not retrieve variants from source file in region 13:109661148-109661549. Error was invalid region `13:109661149-109661549`
[2016-04-15T06:56Z] 2016-04-14 23:56:13 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:56:13,507 - WARNING - Could not retrieve variants from source file in region 13:111806034-111806435. Error was invalid region `13:111806035-111806435`
[2016-04-15T06:56Z] 2016-04-14 23:56:14 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:56:14,284 - WARNING - Could not retrieve variants from source file in region 13:108518233-108518634. Error was invalid region `13:108518234-108518634`
[2016-04-15T06:56Z] 2016-04-14 23:56:14 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:56:14,613 - WARNING - Could not retrieve variants from source file in region 13:115030503-115047495. Error was invalid region `13:115030504-115047495`
[2016-04-15T06:56Z] 2016-04-14 23:56:14 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:56:14,739 - WARNING - Could not retrieve variants from source file in region 13:113897109-113909529. Error was invalid region `13:113897110-113909529`
[2016-04-15T06:56Z] 2016-04-14 23:56:17 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:56:17,283 - WARNING - Could not retrieve variants from source file in region 13:111365694-111368506. Error was invalid region `13:111365695-111368506`
[2016-04-15T06:56Z] 2016-04-14 23:56:17 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:56:17,526 - WARNING - Could not retrieve variants from source file in region 13:113862590-113862991. Error was invalid region `13:113862591-113862991`
[2016-04-15T06:56Z] 2016-04-14 23:56:19 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:56:19,242 - WARNING - Could not retrieve variants from source file in region 13:111076986-111109915. Error was invalid region `13:111076987-111109915`
[2016-04-15T06:56Z] 2016-04-14 23:56:19 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:56:19,963 - WARNING - Could not retrieve variants from source file in region 13:114464080-114464481. Error was invalid region `13:114464081-114464481`
[2016-04-15T06:56Z] 2016-04-14 23:56:21 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:56:21,665 - WARNING - Could not retrieve variants from source file in region 13:114057501-114078748. Error was invalid region `13:114057502-114078748`
[2016-04-15T06:56Z] 2016-04-14 23:56:22 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:56:22,110 - WARNING - Could not retrieve variants from source file in region 13:113140138-113140539. Error was invalid region `13:113140139-113140539`
[2016-04-15T06:56Z] 2016-04-14 23:56:22 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:56:22,428 - WARNING - Could not retrieve variants from source file in region 13:110435020-110436422. Error was invalid region `13:110435021-110436422`
[2016-04-15T06:56Z] 2016-04-14 23:56:22 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:56:22,430 - WARNING - Could not retrieve variants from source file in region 13:113897109-113909529. Error was invalid region `13:113897110-113909529`
[2016-04-15T06:56Z] 2016-04-14 23:56:22 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:56:22,869 - WARNING - Could not retrieve variants from source file in region 13:111365694-111368506. Error was invalid region `13:111365695-111368506`
[2016-04-15T06:56Z] 2016-04-14 23:56:22 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:56:22,937 - WARNING - Could not retrieve variants from source file in region 13:113862590-113862991. Error was invalid region `13:113862591-113862991`
[2016-04-15T06:56Z] 2016-04-14 23:56:25 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:56:25,187 - WARNING - Could not retrieve variants from source file in region 13:109661148-109661549. Error was invalid region `13:109661149-109661549`
[2016-04-15T06:56Z] 2016-04-14 23:56:25 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:56:25,516 - WARNING - Could not retrieve variants from source file in region 13:114464080-114464481. Error was invalid region `13:114464081-114464481`
[2016-04-15T06:56Z] 2016-04-14 23:56:29 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:56:29,197 - WARNING - Could not retrieve variants from source file in region 13:108518233-108518634. Error was invalid region `13:108518234-108518634`
[2016-04-15T06:56Z] 2016-04-14 23:56:30 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:56:30,110 - WARNING - Could not retrieve variants from source file in region 13:115030503-115047495. Error was invalid region `13:115030504-115047495`
[2016-04-15T06:56Z] 2016-04-14 23:56:30 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:56:30,847 - WARNING - Could not retrieve variants from source file in region 13:113633585-113656406. Error was invalid region `13:113633586-113656406`
[2016-04-15T06:56Z] 2016-04-14 23:56:31 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:56:31,145 - WARNING - Could not retrieve variants from source file in region 13:110435020-110436422. Error was invalid region `13:110435021-110436422`
[2016-04-15T06:56Z] 2016-04-14 23:56:41 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:56:41,946 - WARNING - Could not retrieve variants from source file in region 13:114623669-114624070. Error was invalid region `13:114623670-114624070`
[2016-04-15T06:56Z] 2016-04-14 23:56:46 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:56:46,112 - WARNING - Could not retrieve variants from source file in region 13:114309015-114324187. Error was invalid region `13:114309016-114324187`
[2016-04-15T06:56Z] 2016-04-14 23:56:46 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:56:46,738 - WARNING - Could not retrieve variants from source file in region 13:107210630-107211031. Error was invalid region `13:107210631-107211031`
[2016-04-15T06:56Z] 2016-04-14 23:56:46 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:56:46,773 - WARNING - Could not retrieve variants from source file in region 13:115002094-115005125. Error was invalid region `13:115002095-115005125`
[2016-04-15T06:56Z] 2016-04-14 23:56:46 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:56:46,782 - WARNING - Could not retrieve variants from source file in region 13:111544901-111545388. Error was invalid region `13:111544902-111545388`
[2016-04-15T06:56Z] 2016-04-14 23:56:47 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:56:47,116 - WARNING - Could not retrieve variants from source file in region 13:114623669-114624070. Error was invalid region `13:114623670-114624070`
[2016-04-15T06:56Z] 2016-04-14 23:56:47 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:56:47,986 - WARNING - Could not retrieve variants from source file in region 13:113030463-113053660. Error was invalid region `13:113030464-113053660`
[2016-04-15T06:56Z] 2016-04-14 23:56:49 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:56:49,511 - WARNING - Could not retrieve variants from source file in region 13:114821742-114822143. Error was invalid region `13:114821743-114822143`
[2016-04-15T06:56Z] 2016-04-14 23:56:51 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:56:51,434 - WARNING - Could not retrieve variants from source file in region 13:113801526-113826290. Error was invalid region `13:113801527-113826290`
[2016-04-15T06:56Z] 2016-04-14 23:56:51 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:56:51,460 - WARNING - Could not retrieve variants from source file in region 13:110959145-110959546. Error was invalid region `13:110959146-110959546`
[2016-04-15T06:56Z] 2016-04-14 23:56:51 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:56:51,526 - WARNING - Could not retrieve variants from source file in region 13:114309015-114324187. Error was invalid region `13:114309016-114324187`
[2016-04-15T06:56Z] 2016-04-14 23:56:52 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:56:52,839 - WARNING - Could not retrieve variants from source file in region 13:111544901-111545388. Error was invalid region `13:111544902-111545388`
[2016-04-15T06:56Z] 2016-04-14 23:56:53 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:56:53,111 - WARNING - Could not retrieve variants from source file in region 13:109472522-109518768. Error was invalid region `13:109472523-109518768`
[2016-04-15T06:56Z] 2016-04-14 23:56:53 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:56:53,447 - WARNING - Could not retrieve variants from source file in region 13:107210630-107211031. Error was invalid region `13:107210631-107211031`
[2016-04-15T06:56Z] 2016-04-14 23:56:53 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:56:53,780 - WARNING - Could not retrieve variants from source file in region 13:114623669-114624070. Error was invalid region `13:114623670-114624070`
[2016-04-15T06:56Z] 2016-04-14 23:56:55 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:56:55,267 - WARNING - Could not retrieve variants from source file in region 13:111153847-111176709. Error was invalid region `13:111153848-111176709`
[2016-04-15T06:56Z] 2016-04-14 23:56:56 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:56:56,429 - WARNING - Could not retrieve variants from source file in region 13:114309015-114324187. Error was invalid region `13:114309016-114324187`
[2016-04-15T06:56Z] 2016-04-14 23:56:57 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:56:57,276 - WARNING - Could not retrieve variants from source file in region 13:111544901-111545388. Error was invalid region `13:111544902-111545388`
[2016-04-15T06:56Z] 2016-04-14 23:56:58 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:56:58,344 - WARNING - Could not retrieve variants from source file in region 13:115002094-115005125. Error was invalid region `13:115002095-115005125`
[2016-04-15T06:56Z] 2016-04-14 23:56:59 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:56:59,673 - WARNING - Could not retrieve variants from source file in region 13:107210630-107211031. Error was invalid region `13:107210631-107211031`
[2016-04-15T06:57Z] 2016-04-14 23:57:00 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:57:00,237 - WARNING - Could not retrieve variants from source file in region 13:114821742-114822143. Error was invalid region `13:114821743-114822143`
[2016-04-15T06:57Z] 2016-04-14 23:57:00 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:57:00,930 - WARNING - Could not retrieve variants from source file in region 13:109777292-109793910. Error was invalid region `13:109777293-109793910`
[2016-04-15T06:57Z] 2016-04-14 23:57:01 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:57:01,347 - WARNING - Could not retrieve variants from source file in region 13:111153847-111176709. Error was invalid region `13:111153848-111176709`
[2016-04-15T06:57Z] 2016-04-14 23:57:12 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:57:12,287 - WARNING - Could not retrieve variants from source file in region 13:113719140-113749835. Error was invalid region `13:113719141-113749835`
[2016-04-15T06:57Z] 2016-04-14 23:57:12 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:57:12,410 - WARNING - Could not retrieve variants from source file in region 13:110813498-110864415. Error was invalid region `13:110813499-110864415`
[2016-04-15T06:57Z] 2016-04-14 23:57:12 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:57:12,575 - WARNING - Could not retrieve variants from source file in region 13:113719140-113749835. Error was invalid region `13:113719141-113749835`
[2016-04-15T06:57Z] 2016-04-14 23:57:13 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:57:13,774 - WARNING - Could not retrieve variants from source file in region 13:111980326-111980727. Error was invalid region `13:111980327-111980727`
[2016-04-15T06:57Z] 2016-04-14 23:57:16 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:57:16,159 - WARNING - Could not retrieve variants from source file in region 13:109707616-109708017. Error was invalid region `13:109707617-109708017`
[2016-04-15T06:57Z] 2016-04-14 23:57:16 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:57:16,461 - WARNING - Could not retrieve variants from source file in region 13:106142024-106142425. Error was invalid region `13:106142025-106142425`
[2016-04-15T06:57Z] 2016-04-14 23:57:16 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:57:16,500 - WARNING - Could not retrieve variants from source file in region 13:113479602-113480010. Error was invalid region `13:113479603-113480010`
[2016-04-15T06:57Z] 2016-04-14 23:57:16 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:57:16,875 - WARNING - Could not retrieve variants from source file in region 13:111980326-111980727. Error was invalid region `13:111980327-111980727`
[2016-04-15T06:57Z] 2016-04-14 23:57:17 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:57:17,071 - WARNING - Could not retrieve variants from source file in region 13:108861702-108862103. Error was invalid region `13:108861703-108862103`
[2016-04-15T06:57Z] 2016-04-14 23:57:17 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:57:17,570 - WARNING - Could not retrieve variants from source file in region 13:107145252-107145800. Error was invalid region `13:107145253-107145800`
[2016-04-15T06:57Z] 2016-04-14 23:57:18 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:57:18,070 - WARNING - Could not retrieve variants from source file in region 13:111980326-111980727. Error was invalid region `13:111980327-111980727`
[2016-04-15T06:57Z] 2016-04-14 23:57:20 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:57:20,568 - WARNING - Could not retrieve variants from source file in region 13:109707616-109708017. Error was invalid region `13:109707617-109708017`
[2016-04-15T06:57Z] 2016-04-14 23:57:21 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:57:21,186 - WARNING - Could not retrieve variants from source file in region 13:102366614-102367015. Error was invalid region `13:102366615-102367015`
[2016-04-15T06:57Z] 2016-04-14 23:57:21 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:57:21,226 - WARNING - Could not retrieve variants from source file in region 13:113479602-113480010. Error was invalid region `13:113479603-113480010`
[2016-04-15T06:57Z] 2016-04-14 23:57:21 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:57:21,309 - WARNING - Could not retrieve variants from source file in region 13:108861702-108862103. Error was invalid region `13:108861703-108862103`
[2016-04-15T06:57Z] 2016-04-14 23:57:21 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:57:21,381 - WARNING - Could not retrieve variants from source file in region 13:107145252-107145800. Error was invalid region `13:107145253-107145800`
[2016-04-15T06:57Z] 2016-04-14 23:57:21 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:57:21,455 - WARNING - Could not retrieve variants from source file in region 13:113479602-113480010. Error was invalid region `13:113479603-113480010`
[2016-04-15T06:57Z] 2016-04-14 23:57:24 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:57:24,760 - WARNING - Could not retrieve variants from source file in region 13:106142024-106142425. Error was invalid region `13:106142025-106142425`
[2016-04-15T06:57Z] 2016-04-14 23:57:29 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:57:29,982 - WARNING - Could not retrieve variants from source file in region 13:103704833-103718498. Error was invalid region `13:103704834-103718498`
[2016-04-15T06:57Z] 2016-04-14 23:57:29 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:57:29,982 - WARNING - Could not retrieve variants from source file in region 13:103504306-103528120. Error was invalid region `13:103504307-103528120`
[2016-04-15T06:57Z] 2016-04-14 23:57:29 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:57:29,995 - WARNING - Could not retrieve variants from source file in region 13:103504306-103528120. Error was invalid region `13:103504307-103528120`
[2016-04-15T06:57Z] 2016-04-14 23:57:30 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:57:30,140 - WARNING - Could not retrieve variants from source file in region 13:103704833-103718498. Error was invalid region `13:103704834-103718498`
[2016-04-15T06:57Z] 2016-04-14 23:57:30 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:57:30,340 - WARNING - Could not retrieve variants from source file in region 13:103504306-103528120. Error was invalid region `13:103504307-103528120`
[2016-04-15T06:57Z] 2016-04-14 23:57:32 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:57:32,358 - WARNING - Could not retrieve variants from source file in region 13:102227661-102228062. Error was invalid region `13:102227662-102228062`
[2016-04-15T06:57Z] 2016-04-14 23:57:32 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:57:32,865 - WARNING - Could not retrieve variants from source file in region 13:103275175-103275576. Error was invalid region `13:103275176-103275576`
[2016-04-15T06:57Z] 2016-04-14 23:57:34 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:57:34,063 - WARNING - Could not retrieve variants from source file in region 13:102106065-102106466. Error was invalid region `13:102106066-102106466`
[2016-04-15T06:57Z] 2016-04-14 23:57:34 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:57:34,690 - WARNING - Could not retrieve variants from source file in region 13:103275175-103275576. Error was invalid region `13:103275176-103275576`
[2016-04-15T06:57Z] 2016-04-14 23:57:34 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:57:34,712 - WARNING - Could not retrieve variants from source file in region 13:103275175-103275576. Error was invalid region `13:103275176-103275576`
[2016-04-15T06:57Z] 2016-04-14 23:57:34 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:57:34,818 - WARNING - Could not retrieve variants from source file in region 13:102227661-102228062. Error was invalid region `13:102227662-102228062`
[2016-04-15T06:57Z] ['bcbio-variation-recall', 'square', '-Xms750m', '-Xmx7280m', '-XX:+UseSerialGC', '-c', 16, '-r', u'14:1-19378574', '--caller', 'platypus', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/14/Batch1-14_0_19378574.vcf.gz', '/mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/14/Batch1-14_0_19378574.vcf-inputs.txt'] in region: 14:1-19378574
[2016-04-15T06:57Z] 2016-04-14 23:57:48 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:57:48,383 - WARNING - Could not retrieve variants from source file in region 14:19377819-19378502. Error was invalid region `14:19377820-19378502`
[2016-04-15T06:57Z] ['bcbio-variation-recall', 'square', '-Xms750m', '-Xmx7280m', '-XX:+UseSerialGC', '-c', 16, '-r', u'14:19553417-35066851', '--caller', 'platypus', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/14/Batch1-14_19553416_35066851.vcf.gz', '/mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/14/Batch1-14_19553416_35066851.vcf-inputs.txt'] in region: 14:19553417-35066851
[2016-04-15T06:58Z] 2016-04-14 23:58:02 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:58:02,069 - WARNING - Could not retrieve variants from source file in region 14:23997802-23998203. Error was invalid region `14:23997803-23998203`
[2016-04-15T06:58Z] 2016-04-14 23:58:03 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:58:03,582 - WARNING - Could not retrieve variants from source file in region 14:23598741-23599142. Error was invalid region `14:23598742-23599142`
[2016-04-15T06:58Z] 2016-04-14 23:58:04 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:58:04,250 - WARNING - Could not retrieve variants from source file in region 14:35062101-35062502. Error was invalid region `14:35062102-35062502`
[2016-04-15T06:58Z] 2016-04-14 23:58:04 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:58:04,283 - WARNING - Could not retrieve variants from source file in region 14:20215778-20216488. Error was invalid region `14:20215779-20216488`
[2016-04-15T06:58Z] 2016-04-14 23:58:04 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:58:04,802 - WARNING - Could not retrieve variants from source file in region 14:20527996-20529233. Error was invalid region `14:20527997-20529233`
[2016-04-15T06:58Z] 2016-04-14 23:58:04 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:58:04,820 - WARNING - Could not retrieve variants from source file in region 14:21024408-21026963. Error was invalid region `14:21024409-21026963`
[2016-04-15T06:58Z] 2016-04-14 23:58:05 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:58:05,271 - WARNING - Could not retrieve variants from source file in region 14:20444279-20444680. Error was invalid region `14:20444280-20444680`
[2016-04-15T06:58Z] 2016-04-14 23:58:05 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:58:05,506 - WARNING - Could not retrieve variants from source file in region 14:33014803-33015204. Error was invalid region `14:33014804-33015204`
[2016-04-15T06:58Z] 2016-04-14 23:58:08 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:58:08,510 - WARNING - Could not retrieve variants from source file in region 14:21108698-21109916. Error was invalid region `14:21108699-21109916`
[2016-04-15T06:58Z] 2016-04-14 23:58:10 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:58:10,119 - WARNING - Could not retrieve variants from source file in region 14:31818836-31820103. Error was invalid region `14:31818837-31820103`
[2016-04-15T06:58Z] 2016-04-14 23:58:10 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:58:10,258 - WARNING - Could not retrieve variants from source file in region 14:23598741-23599142. Error was invalid region `14:23598742-23599142`
[2016-04-15T06:58Z] 2016-04-14 23:58:12 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:58:12,429 - WARNING - Could not retrieve variants from source file in region 14:35062101-35062502. Error was invalid region `14:35062102-35062502`
[2016-04-15T06:58Z] 2016-04-14 23:58:12 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:58:12,897 - WARNING - Could not retrieve variants from source file in region 14:20757593-20770226. Error was invalid region `14:20757594-20770226`
[2016-04-15T06:58Z] 2016-04-14 23:58:13 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:58:13,116 - WARNING - Could not retrieve variants from source file in region 14:33014803-33015204. Error was invalid region `14:33014804-33015204`
[2016-04-15T06:58Z] 2016-04-14 23:58:13 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:58:13,639 - WARNING - Could not retrieve variants from source file in region 14:24975076-24976764. Error was invalid region `14:24975077-24976764`
[2016-04-15T06:58Z] 2016-04-14 23:58:14 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:58:14,295 - WARNING - Could not retrieve variants from source file in region 14:20444279-20444680. Error was invalid region `14:20444280-20444680`
[2016-04-15T06:58Z] 2016-04-14 23:58:14 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:58:14,562 - WARNING - Could not retrieve variants from source file in region 14:23997802-23998203. Error was invalid region `14:23997803-23998203`
[2016-04-15T06:58Z] 2016-04-14 23:58:14 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:58:14,601 - WARNING - Could not retrieve variants from source file in region 14:24646195-24680067. Error was invalid region `14:24646196-24680067`
[2016-04-15T06:58Z] 2016-04-14 23:58:14 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:58:14,819 - WARNING - Could not retrieve variants from source file in region 14:31818836-31820103. Error was invalid region `14:31818837-31820103`
[2016-04-15T06:58Z] 2016-04-14 23:58:14 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:58:14,902 - WARNING - Could not retrieve variants from source file in region 14:23598741-23599142. Error was invalid region `14:23598742-23599142`
[2016-04-15T06:58Z] 2016-04-14 23:58:17 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:58:17,999 - WARNING - Could not retrieve variants from source file in region 14:35062101-35062502. Error was invalid region `14:35062102-35062502`
[2016-04-15T06:58Z] 2016-04-14 23:58:18 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:58:18,148 - WARNING - Could not retrieve variants from source file in region 14:20295552-20296200. Error was invalid region `14:20295553-20296200`
[2016-04-15T06:58Z] 2016-04-14 23:58:20 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:58:20,744 - WARNING - Could not retrieve variants from source file in region 14:33014803-33015204. Error was invalid region `14:33014804-33015204`
[2016-04-15T06:58Z] 2016-04-14 23:58:22 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:58:22,805 - WARNING - Could not retrieve variants from source file in region 14:20444279-20444680. Error was invalid region `14:20444280-20444680`
[2016-04-15T06:58Z] 2016-04-14 23:58:31 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:58:31,480 - WARNING - Could not retrieve variants from source file in region 14:31647030-31647638. Error was invalid region `14:31647031-31647638`
[2016-04-15T06:58Z] 2016-04-14 23:58:33 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:58:33,615 - WARNING - Could not retrieve variants from source file in region 14:23944294-23944704. Error was invalid region `14:23944295-23944704`
[2016-04-15T06:58Z] 2016-04-14 23:58:33 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:58:33,627 - WARNING - Could not retrieve variants from source file in region 14:23624372-23624773. Error was invalid region `14:23624373-23624773`
[2016-04-15T06:58Z] 2016-04-14 23:58:35 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:58:35,843 - WARNING - Could not retrieve variants from source file in region 14:32047006-32047407. Error was invalid region `14:32047007-32047407`
[2016-04-15T06:58Z] 2016-04-14 23:58:36 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:58:36,628 - WARNING - Could not retrieve variants from source file in region 14:20691977-20712042. Error was invalid region `14:20691978-20712042`
[2016-04-15T06:58Z] 2016-04-14 23:58:37 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:58:37,623 - WARNING - Could not retrieve variants from source file in region 14:31647030-31647638. Error was invalid region `14:31647031-31647638`
[2016-04-15T06:58Z] 2016-04-14 23:58:37 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:58:37,756 - WARNING - Could not retrieve variants from source file in region 14:20482260-20502310. Error was invalid region `14:20482261-20502310`
[2016-04-15T06:58Z] 2016-04-14 23:58:38 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:58:38,755 - WARNING - Could not retrieve variants from source file in region 14:34268956-34269965. Error was invalid region `14:34268957-34269965`
[2016-04-15T06:58Z] 2016-04-14 23:58:39 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:58:39,104 - WARNING - Could not retrieve variants from source file in region 14:23624372-23624773. Error was invalid region `14:23624373-23624773`
[2016-04-15T06:58Z] 2016-04-14 23:58:39 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:58:39,159 - WARNING - Could not retrieve variants from source file in region 14:23944294-23944704. Error was invalid region `14:23944295-23944704`
[2016-04-15T06:58Z] 2016-04-14 23:58:40 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:58:40,181 - WARNING - Could not retrieve variants from source file in region 14:20248617-20249366. Error was invalid region `14:20248618-20249366`
[2016-04-15T06:58Z] 2016-04-14 23:58:41 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:58:41,984 - WARNING - Could not retrieve variants from source file in region 14:32047006-32047407. Error was invalid region `14:32047007-32047407`
[2016-04-15T06:58Z] 2016-04-14 23:58:42 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:58:42,526 - WARNING - Could not retrieve variants from source file in region 14:24878274-24911164. Error was invalid region `14:24878275-24911164`
[2016-04-15T06:58Z] 2016-04-14 23:58:43 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:58:43,636 - WARNING - Could not retrieve variants from source file in region 14:20482260-20502310. Error was invalid region `14:20482261-20502310`
[2016-04-15T06:58Z] 2016-04-14 23:58:45 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:58:45,635 - WARNING - Could not retrieve variants from source file in region 14:23281899-23313113. Error was invalid region `14:23281900-23313113`
[2016-04-15T06:58Z] 2016-04-14 23:58:46 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:58:46,027 - WARNING - Could not retrieve variants from source file in region 14:23624372-23624773. Error was invalid region `14:23624373-23624773`
[2016-04-15T06:58Z] 2016-04-14 23:58:46 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:58:46,466 - WARNING - Could not retrieve variants from source file in region 14:23944294-23944704. Error was invalid region `14:23944295-23944704`
[2016-04-15T06:58Z] 2016-04-14 23:58:46 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:58:46,467 - WARNING - Could not retrieve variants from source file in region 14:20181291-20182129. Error was invalid region `14:20181292-20182129`
[2016-04-15T06:58Z] 2016-04-14 23:58:46 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:58:46,838 - WARNING - Could not retrieve variants from source file in region 14:32047006-32047407. Error was invalid region `14:32047007-32047407`
[2016-04-15T06:58Z] 2016-04-14 23:58:49 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:58:49,178 - WARNING - Could not retrieve variants from source file in region 14:20482260-20502310. Error was invalid region `14:20482261-20502310`
[2016-04-15T06:59Z] 2016-04-14 23:59:00 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:59:00,611 - WARNING - Could not retrieve variants from source file in region 14:31582169-31583702. Error was invalid region `14:31582170-31583702`
[2016-04-15T06:59Z] 2016-04-14 23:59:01 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:59:01,671 - WARNING - Could not retrieve variants from source file in region 14:33292532-33293721. Error was invalid region `14:33292533-33293721`
[2016-04-15T06:59Z] 2016-04-14 23:59:02 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:59:02,266 - WARNING - Could not retrieve variants from source file in region 14:19553553-19553954. Error was invalid region `14:19553554-19553954`
[2016-04-15T06:59Z] 2016-04-14 23:59:02 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:59:02,535 - WARNING - Could not retrieve variants from source file in region 14:20665579-20666365. Error was invalid region `14:20665580-20666365`
[2016-04-15T06:59Z] 2016-04-14 23:59:03 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:59:03,009 - WARNING - Could not retrieve variants from source file in region 14:30066718-30067119. Error was invalid region `14:30066719-30067119`
[2016-04-15T06:59Z] 2016-04-14 23:59:04 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:59:04,568 - WARNING - Could not retrieve variants from source file in region 14:20585831-20586622. Error was invalid region `14:20585832-20586622`
[2016-04-15T06:59Z] 2016-04-14 23:59:05 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:59:05,411 - WARNING - Could not retrieve variants from source file in region 14:23451501-23467854. Error was invalid region `14:23451502-23467854`
[2016-04-15T06:59Z] 2016-04-14 23:59:05 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:59:05,480 - WARNING - Could not retrieve variants from source file in region 14:31582169-31583702. Error was invalid region `14:31582170-31583702`
[2016-04-15T06:59Z] 2016-04-14 23:59:05 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:59:05,932 - WARNING - Could not retrieve variants from source file in region 14:23235597-23248302. Error was invalid region `14:23235598-23248302`
[2016-04-15T06:59Z] 2016-04-14 23:59:06 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:59:06,253 - WARNING - Could not retrieve variants from source file in region 14:33292532-33293721. Error was invalid region `14:33292533-33293721`
[2016-04-15T06:59Z] 2016-04-14 23:59:07 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:59:07,061 - WARNING - Could not retrieve variants from source file in region 14:19553553-19553954. Error was invalid region `14:19553554-19553954`
[2016-04-15T06:59Z] 2016-04-14 23:59:07 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:59:07,207 - WARNING - Could not retrieve variants from source file in region 14:20665579-20666365. Error was invalid region `14:20665580-20666365`
[2016-04-15T06:59Z] 2016-04-14 23:59:09 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:59:09,090 - WARNING - Could not retrieve variants from source file in region 14:31922304-31922705. Error was invalid region `14:31922305-31922705`
[2016-04-15T06:59Z] 2016-04-14 23:59:09 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:59:09,258 - WARNING - Could not retrieve variants from source file in region 14:20585831-20586622. Error was invalid region `14:20585832-20586622`
[2016-04-15T06:59Z] 2016-04-14 23:59:10 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:59:10,262 - WARNING - Could not retrieve variants from source file in region 14:23451501-23467854. Error was invalid region `14:23451502-23467854`
[2016-04-15T06:59Z] 2016-04-14 23:59:10 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:59:10,750 - WARNING - Could not retrieve variants from source file in region 14:33292532-33293721. Error was invalid region `14:33292533-33293721`
[2016-04-15T06:59Z] 2016-04-14 23:59:11 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:59:11,848 - WARNING - Could not retrieve variants from source file in region 14:20665579-20666365. Error was invalid region `14:20665580-20666365`
[2016-04-15T06:59Z] 2016-04-14 23:59:11 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:59:11,965 - WARNING - Could not retrieve variants from source file in region 14:19553553-19553954. Error was invalid region `14:19553554-19553954`
[2016-04-15T06:59Z] 2016-04-14 23:59:12 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:59:12,447 - WARNING - Could not retrieve variants from source file in region 14:30066718-30067119. Error was invalid region `14:30066719-30067119`
[2016-04-15T06:59Z] 2016-04-14 23:59:13 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:59:13,580 - WARNING - Could not retrieve variants from source file in region 14:31856169-31864675. Error was invalid region `14:31856170-31864675`
[2016-04-15T06:59Z] 2016-04-14 23:59:14 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:59:14,055 - WARNING - Could not retrieve variants from source file in region 14:20585831-20586622. Error was invalid region `14:20585832-20586622`
[2016-04-15T06:59Z] 2016-04-14 23:59:14 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:59:14,091 - WARNING - Could not retrieve variants from source file in region 14:24457951-24458352. Error was invalid region `14:24457952-24458352`
[2016-04-15T06:59Z] 2016-04-14 23:59:14 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:59:14,200 - WARNING - Could not retrieve variants from source file in region 14:31922304-31922705. Error was invalid region `14:31922305-31922705`
[2016-04-15T06:59Z] 2016-04-14 23:59:24 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:59:24,517 - WARNING - Could not retrieve variants from source file in region 14:33046177-33046578. Error was invalid region `14:33046178-33046578`
[2016-04-15T06:59Z] 2016-04-14 23:59:26 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:59:26,549 - WARNING - Could not retrieve variants from source file in region 14:21899420-21899821. Error was invalid region `14:21899421-21899821`
[2016-04-15T06:59Z] 2016-04-14 23:59:27 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:59:27,318 - WARNING - Could not retrieve variants from source file in region 14:27065852-27066253. Error was invalid region `14:27065853-27066253`
[2016-04-15T06:59Z] 2016-04-14 23:59:27 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:59:27,329 - WARNING - Could not retrieve variants from source file in region 14:23777163-23780067. Error was invalid region `14:23777164-23780067`
[2016-04-15T06:59Z] 2016-04-14 23:59:27 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:59:27,486 - WARNING - Could not retrieve variants from source file in region 14:21828918-21831609. Error was invalid region `14:21828919-21831609`
[2016-04-15T06:59Z] 2016-04-14 23:59:27 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:59:27,508 - WARNING - Could not retrieve variants from source file in region 14:21871442-21871843. Error was invalid region `14:21871443-21871843`
[2016-04-15T06:59Z] 2016-04-14 23:59:28 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:59:28,040 - WARNING - Could not retrieve variants from source file in region 14:22133205-22134208. Error was invalid region `14:22133206-22134208`
[2016-04-15T06:59Z] 2016-04-14 23:59:29 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:59:29,414 - WARNING - Could not retrieve variants from source file in region 14:21360005-21360406. Error was invalid region `14:21360006-21360406`
[2016-04-15T06:59Z] 2016-04-14 23:59:30 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:59:30,023 - WARNING - Could not retrieve variants from source file in region 14:33046177-33046578. Error was invalid region `14:33046178-33046578`
[2016-04-15T06:59Z] 2016-04-14 23:59:31 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:59:31,265 - WARNING - Could not retrieve variants from source file in region 14:23043791-23044194. Error was invalid region `14:23043792-23044194`
[2016-04-15T06:59Z] 2016-04-14 23:59:33 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:59:33,967 - WARNING - Could not retrieve variants from source file in region 14:27065852-27066253. Error was invalid region `14:27065853-27066253`
[2016-04-15T06:59Z] 2016-04-14 23:59:34 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:59:34,133 - WARNING - Could not retrieve variants from source file in region 14:21871442-21871843. Error was invalid region `14:21871443-21871843`
[2016-04-15T06:59Z] 2016-04-14 23:59:34 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:59:34,719 - WARNING - Could not retrieve variants from source file in region 14:21360005-21360406. Error was invalid region `14:21360006-21360406`
[2016-04-15T06:59Z] 2016-04-14 23:59:36 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:59:36,153 - WARNING - Could not retrieve variants from source file in region 14:33046177-33046578. Error was invalid region `14:33046178-33046578`
[2016-04-15T06:59Z] 2016-04-14 23:59:37 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:59:37,028 - WARNING - Could not retrieve variants from source file in region 14:21899420-21899821. Error was invalid region `14:21899421-21899821`
[2016-04-15T06:59Z] 2016-04-14 23:59:39 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:59:39,612 - WARNING - Could not retrieve variants from source file in region 14:21871442-21871843. Error was invalid region `14:21871443-21871843`
[2016-04-15T06:59Z] 2016-04-14 23:59:39 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:59:39,745 - WARNING - Could not retrieve variants from source file in region 14:27065852-27066253. Error was invalid region `14:27065853-27066253`
[2016-04-15T06:59Z] 2016-04-14 23:59:40 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:59:40,322 - WARNING - Could not retrieve variants from source file in region 14:21360005-21360406. Error was invalid region `14:21360006-21360406`
[2016-04-15T06:59Z] 2016-04-14 23:59:45 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:59:45,566 - WARNING - Could not retrieve variants from source file in region 14:26939121-26939664. Error was invalid region `14:26939122-26939664`
[2016-04-15T06:59Z] 2016-04-14 23:59:46 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:59:46,639 - WARNING - Could not retrieve variants from source file in region 14:21770470-21796974. Error was invalid region `14:21770471-21796974`
[2016-04-15T06:59Z] 2016-04-14 23:59:50 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:59:50,438 - WARNING - Could not retrieve variants from source file in region 14:26939121-26939664. Error was invalid region `14:26939122-26939664`
[2016-04-15T06:59Z] 2016-04-14 23:59:51 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:59:51,922 - WARNING - Could not retrieve variants from source file in region 14:26939121-26939664. Error was invalid region `14:26939122-26939664`
[2016-04-15T06:59Z] 2016-04-14 23:59:54 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:59:54,600 - WARNING - Could not retrieve variants from source file in region 14:22102163-22102629. Error was invalid region `14:22102164-22102629`
[2016-04-15T06:59Z] 2016-04-14 23:59:55 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:59:55,969 - WARNING - Could not retrieve variants from source file in region 14:21156625-21167766. Error was invalid region `14:21156626-21167766`
[2016-04-15T06:59Z] 2016-04-14 23:59:56 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:59:56,203 - WARNING - Could not retrieve variants from source file in region 14:22037999-22038849. Error was invalid region `14:22038000-22038849`
[2016-04-15T06:59Z] 2016-04-14 23:59:56 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:59:56,411 - WARNING - Could not retrieve variants from source file in region 14:25518700-25519101. Error was invalid region `14:25518701-25519101`
[2016-04-15T06:59Z] 2016-04-14 23:59:58 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:59:58,618 - WARNING - Could not retrieve variants from source file in region 14:25518700-25519101. Error was invalid region `14:25518701-25519101`
[2016-04-15T06:59Z] 2016-04-14 23:59:59 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-14 23:59:59,336 - WARNING - Could not retrieve variants from source file in region 14:25100071-25103604. Error was invalid region `14:25100072-25103604`
[2016-04-15T07:00Z] ['bcbio-variation-recall', 'square', '-Xms750m', '-Xmx7280m', '-XX:+UseSerialGC', '-c', 16, '-r', u'14:35072554-50583270', '--caller', 'platypus', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/14/Batch1-14_35072553_50583270.vcf.gz', '/mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/14/Batch1-14_35072553_50583270.vcf-inputs.txt'] in region: 14:35072554-50583270
[2016-04-15T07:00Z] 2016-04-15 00:00:19 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:00:19,008 - WARNING - Could not retrieve variants from source file in region 14:39870806-39871207. Error was invalid region `14:39870807-39871207`
[2016-04-15T07:00Z] 2016-04-15 00:00:19 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:00:19,042 - WARNING - Could not retrieve variants from source file in region 14:50195468-50195869. Error was invalid region `14:50195469-50195869`
[2016-04-15T07:00Z] 2016-04-15 00:00:20 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:00:20,023 - WARNING - Could not retrieve variants from source file in region 14:50298751-50299152. Error was invalid region `14:50298752-50299152`
[2016-04-15T07:00Z] 2016-04-15 00:00:20 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:00:20,416 - WARNING - Could not retrieve variants from source file in region 14:45540777-45541178. Error was invalid region `14:45540778-45541178`
[2016-04-15T07:00Z] 2016-04-15 00:00:20 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:00:20,416 - WARNING - Could not retrieve variants from source file in region 14:39777465-39777866. Error was invalid region `14:39777466-39777866`
[2016-04-15T07:00Z] 2016-04-15 00:00:21 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:00:21,552 - WARNING - Could not retrieve variants from source file in region 14:39817817-39818335. Error was invalid region `14:39817818-39818335`
[2016-04-15T07:00Z] 2016-04-15 00:00:21 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:00:21,585 - WARNING - Could not retrieve variants from source file in region 14:36789518-36789965. Error was invalid region `14:36789519-36789965`
[2016-04-15T07:00Z] 2016-04-15 00:00:25 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:00:25,888 - WARNING - Could not retrieve variants from source file in region 14:50195468-50195869. Error was invalid region `14:50195469-50195869`
[2016-04-15T07:00Z] 2016-04-15 00:00:26 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:00:26,199 - WARNING - Could not retrieve variants from source file in region 14:39870806-39871207. Error was invalid region `14:39870807-39871207`
[2016-04-15T07:00Z] 2016-04-15 00:00:27 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:00:27,360 - WARNING - Could not retrieve variants from source file in region 14:36211364-36211765. Error was invalid region `14:36211365-36211765`
[2016-04-15T07:00Z] 2016-04-15 00:00:28 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:00:28,699 - WARNING - Could not retrieve variants from source file in region 14:50298751-50299152. Error was invalid region `14:50298752-50299152`
[2016-04-15T07:00Z] 2016-04-15 00:00:28 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:00:28,749 - WARNING - Could not retrieve variants from source file in region 14:35761464-35782443. Error was invalid region `14:35761465-35782443`
[2016-04-15T07:00Z] 2016-04-15 00:00:29 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:00:29,054 - WARNING - Could not retrieve variants from source file in region 14:36152966-36153367. Error was invalid region `14:36152967-36153367`
[2016-04-15T07:00Z] 2016-04-15 00:00:29 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:00:29,353 - WARNING - Could not retrieve variants from source file in region 14:39777465-39777866. Error was invalid region `14:39777466-39777866`
[2016-04-15T07:00Z] 2016-04-15 00:00:29 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:00:29,579 - WARNING - Could not retrieve variants from source file in region 14:45605252-45606477. Error was invalid region `14:45605253-45606477`
[2016-04-15T07:00Z] 2016-04-15 00:00:29 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:00:29,612 - WARNING - Could not retrieve variants from source file in region 14:36789518-36789965. Error was invalid region `14:36789519-36789965`
[2016-04-15T07:00Z] 2016-04-15 00:00:29 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:00:29,975 - WARNING - Could not retrieve variants from source file in region 14:42360422-42364012. Error was invalid region `14:42360423-42364012`
[2016-04-15T07:00Z] 2016-04-15 00:00:30 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:00:30,097 - WARNING - Could not retrieve variants from source file in region 14:35546162-35546563. Error was invalid region `14:35546163-35546563`
[2016-04-15T07:00Z] 2016-04-15 00:00:30 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:00:30,578 - WARNING - Could not retrieve variants from source file in region 14:50195468-50195869. Error was invalid region `14:50195469-50195869`
[2016-04-15T07:00Z] 2016-04-15 00:00:30 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:00:30,617 - WARNING - Could not retrieve variants from source file in region 14:39870806-39871207. Error was invalid region `14:39870807-39871207`
[2016-04-15T07:00Z] 2016-04-15 00:00:33 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:00:33,287 - WARNING - Could not retrieve variants from source file in region 14:36211364-36211765. Error was invalid region `14:36211365-36211765`
[2016-04-15T07:00Z] 2016-04-15 00:00:36 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:00:36,487 - WARNING - Could not retrieve variants from source file in region 14:35761464-35782443. Error was invalid region `14:35761465-35782443`
[2016-04-15T07:00Z] 2016-04-15 00:00:37 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:00:37,175 - WARNING - Could not retrieve variants from source file in region 14:50298751-50299152. Error was invalid region `14:50298752-50299152`
[2016-04-15T07:00Z] 2016-04-15 00:00:37 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:00:37,562 - WARNING - Could not retrieve variants from source file in region 14:36152966-36153367. Error was invalid region `14:36152967-36153367`
[2016-04-15T07:00Z] 2016-04-15 00:00:37 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:00:37,945 - WARNING - Could not retrieve variants from source file in region 14:39777465-39777866. Error was invalid region `14:39777466-39777866`
[2016-04-15T07:00Z] 2016-04-15 00:00:38 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:00:38,219 - WARNING - Could not retrieve variants from source file in region 14:42360422-42364012. Error was invalid region `14:42360423-42364012`
[2016-04-15T07:00Z] 2016-04-15 00:00:38 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:00:38,285 - WARNING - Could not retrieve variants from source file in region 14:36789518-36789965. Error was invalid region `14:36789519-36789965`
[2016-04-15T07:00Z] 2016-04-15 00:00:48 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:00:48,537 - WARNING - Could not retrieve variants from source file in region 14:50131635-50132036. Error was invalid region `14:50131636-50132036`
[2016-04-15T07:00Z] 2016-04-15 00:00:53 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:00:53,360 - WARNING - Could not retrieve variants from source file in region 14:50251158-50251559. Error was invalid region `14:50251159-50251559`
[2016-04-15T07:00Z] 2016-04-15 00:00:53 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:00:53,479 - WARNING - Could not retrieve variants from source file in region 14:50131635-50132036. Error was invalid region `14:50131636-50132036`
[2016-04-15T07:00Z] 2016-04-15 00:00:54 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:00:54,157 - WARNING - Could not retrieve variants from source file in region 14:36003864-36004265. Error was invalid region `14:36003865-36004265`
[2016-04-15T07:00Z] 2016-04-15 00:00:55 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:00:55,380 - WARNING - Could not retrieve variants from source file in region 14:35872715-35873960. Error was invalid region `14:35872716-35873960`
[2016-04-15T07:00Z] 2016-04-15 00:00:55 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:00:55,409 - WARNING - Could not retrieve variants from source file in region 14:50068088-50101872. Error was invalid region `14:50068089-50101872`
[2016-04-15T07:00Z] 2016-04-15 00:00:55 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:00:55,854 - WARNING - Could not retrieve variants from source file in region 14:39644287-39650424. Error was invalid region `14:39644288-39650424`
[2016-04-15T07:00Z] 2016-04-15 00:00:56 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:00:56,374 - WARNING - Could not retrieve variants from source file in region 14:50472194-50472595. Error was invalid region `14:50472195-50472595`
[2016-04-15T07:00Z] 2016-04-15 00:00:56 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:00:56,724 - WARNING - Could not retrieve variants from source file in region 14:35592327-35592728. Error was invalid region `14:35592328-35592728`
[2016-04-15T07:00Z] 2016-04-15 00:00:58 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:00:58,069 - WARNING - Could not retrieve variants from source file in region 14:50251158-50251559. Error was invalid region `14:50251159-50251559`
[2016-04-15T07:00Z] 2016-04-15 00:00:58 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:00:58,141 - WARNING - Could not retrieve variants from source file in region 14:50131635-50132036. Error was invalid region `14:50131636-50132036`
[2016-04-15T07:00Z] 2016-04-15 00:00:58 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:00:58,447 - WARNING - Could not retrieve variants from source file in region 14:45432659-45433060. Error was invalid region `14:45432660-45433060`
[2016-04-15T07:00Z] 2016-04-15 00:00:58 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:00:58,502 - WARNING - Could not retrieve variants from source file in region 14:36003864-36004265. Error was invalid region `14:36003865-36004265`
[2016-04-15T07:01Z] 2016-04-15 00:01:01 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:01:01,291 - WARNING - Could not retrieve variants from source file in region 14:47613153-47613554. Error was invalid region `14:47613154-47613554`
[2016-04-15T07:01Z] 2016-04-15 00:01:01 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:01:01,414 - WARNING - Could not retrieve variants from source file in region 14:39644287-39650424. Error was invalid region `14:39644288-39650424`
[2016-04-15T07:01Z] 2016-04-15 00:01:01 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:01:01,783 - WARNING - Could not retrieve variants from source file in region 14:35592327-35592728. Error was invalid region `14:35592328-35592728`
[2016-04-15T07:01Z] 2016-04-15 00:01:01 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:01:01,836 - WARNING - Could not retrieve variants from source file in region 14:39900625-39901347. Error was invalid region `14:39900626-39901347`
[2016-04-15T07:01Z] 2016-04-15 00:01:02 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:01:02,130 - WARNING - Could not retrieve variants from source file in region 14:50251158-50251559. Error was invalid region `14:50251159-50251559`
[2016-04-15T07:01Z] 2016-04-15 00:01:03 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:01:03,070 - WARNING - Could not retrieve variants from source file in region 14:36003864-36004265. Error was invalid region `14:36003865-36004265`
[2016-04-15T07:01Z] 2016-04-15 00:01:04 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:01:04,904 - WARNING - Could not retrieve variants from source file in region 14:35872715-35873960. Error was invalid region `14:35872716-35873960`
[2016-04-15T07:01Z] 2016-04-15 00:01:05 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:01:05,974 - WARNING - Could not retrieve variants from source file in region 14:39644287-39650424. Error was invalid region `14:39644288-39650424`
[2016-04-15T07:01Z] 2016-04-15 00:01:12 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:01:12,279 - WARNING - Could not retrieve variants from source file in region 14:47528259-47528741. Error was invalid region `14:47528260-47528741`
[2016-04-15T07:01Z] 2016-04-15 00:01:12 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:01:12,924 - WARNING - Could not retrieve variants from source file in region 14:47528259-47528741. Error was invalid region `14:47528260-47528741`
[2016-04-15T07:01Z] 2016-04-15 00:01:14 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:01:14,463 - WARNING - Could not retrieve variants from source file in region 14:38265863-38278189. Error was invalid region `14:38265864-38278189`
[2016-04-15T07:01Z] 2016-04-15 00:01:15 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:01:15,044 - WARNING - Could not retrieve variants from source file in region 14:47528259-47528741. Error was invalid region `14:47528260-47528741`
[2016-04-15T07:01Z] 2016-04-15 00:01:15 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:01:15,350 - WARNING - Could not retrieve variants from source file in region 14:35222521-35243018. Error was invalid region `14:35222522-35243018`
[2016-04-15T07:01Z] 2016-04-15 00:01:18 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:01:18,627 - WARNING - Could not retrieve variants from source file in region 14:38193896-38194297. Error was invalid region `14:38193897-38194297`
[2016-04-15T07:01Z] 2016-04-15 00:01:19 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:01:19,938 - WARNING - Could not retrieve variants from source file in region 14:39544988-39556375. Error was invalid region `14:39544989-39556375`
[2016-04-15T07:01Z] 2016-04-15 00:01:20 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:01:20,839 - WARNING - Could not retrieve variants from source file in region 14:38679262-38679663. Error was invalid region `14:38679263-38679663`
[2016-04-15T07:01Z] 2016-04-15 00:01:21 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:01:21,703 - WARNING - Could not retrieve variants from source file in region 14:39544988-39556375. Error was invalid region `14:39544989-39556375`
[2016-04-15T07:01Z] 2016-04-15 00:01:22 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:01:22,184 - WARNING - Could not retrieve variants from source file in region 14:38060557-38061932. Error was invalid region `14:38060558-38061932`
[2016-04-15T07:01Z] 2016-04-15 00:01:22 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:01:22,303 - WARNING - Could not retrieve variants from source file in region 14:38679262-38679663. Error was invalid region `14:38679263-38679663`
[2016-04-15T07:01Z] 2016-04-15 00:01:28 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:01:28,394 - WARNING - Could not retrieve variants from source file in region 14:37050431-37050832. Error was invalid region `14:37050432-37050832`
[2016-04-15T07:01Z] ['bcbio-variation-recall', 'square', '-Xms750m', '-Xmx7280m', '-XX:+UseSerialGC', '-c', 16, '-r', u'14:50585062-66096324', '--caller', 'platypus', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/14/Batch1-14_50585061_66096324.vcf.gz', '/mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/14/Batch1-14_50585061_66096324.vcf-inputs.txt'] in region: 14:50585062-66096324
[2016-04-15T07:01Z] 2016-04-15 00:01:42 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:01:42,784 - WARNING - Could not retrieve variants from source file in region 14:53529458-53529859. Error was invalid region `14:53529459-53529859`
[2016-04-15T07:01Z] 2016-04-15 00:01:44 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:01:44,501 - WARNING - Could not retrieve variants from source file in region 14:66028235-66028636. Error was invalid region `14:66028236-66028636`
[2016-04-15T07:01Z] 2016-04-15 00:01:44 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:01:44,655 - WARNING - Could not retrieve variants from source file in region 14:58917243-58953936. Error was invalid region `14:58917244-58953936`
[2016-04-15T07:01Z] 2016-04-15 00:01:44 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:01:44,741 - WARNING - Could not retrieve variants from source file in region 14:61997015-61997416. Error was invalid region `14:61997016-61997416`
[2016-04-15T07:01Z] 2016-04-15 00:01:45 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:01:45,033 - WARNING - Could not retrieve variants from source file in region 14:65195583-65208216. Error was invalid region `14:65195584-65208216`
[2016-04-15T07:01Z] 2016-04-15 00:01:45 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:01:45,056 - WARNING - Could not retrieve variants from source file in region 14:64882169-64882570. Error was invalid region `14:64882170-64882570`
[2016-04-15T07:01Z] 2016-04-15 00:01:45 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:01:45,531 - WARNING - Could not retrieve variants from source file in region 14:51711881-51716657. Error was invalid region `14:51711882-51716657`
[2016-04-15T07:01Z] 2016-04-15 00:01:45 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:01:45,534 - WARNING - Could not retrieve variants from source file in region 14:64908634-64909035. Error was invalid region `14:64908635-64909035`
[2016-04-15T07:01Z] 2016-04-15 00:01:45 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:01:45,822 - WARNING - Could not retrieve variants from source file in region 14:63174405-63175150. Error was invalid region `14:63174406-63175150`
[2016-04-15T07:01Z] 2016-04-15 00:01:46 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:01:46,183 - WARNING - Could not retrieve variants from source file in region 14:60754482-60754883. Error was invalid region `14:60754483-60754883`
[2016-04-15T07:01Z] 2016-04-15 00:01:46 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:01:46,305 - WARNING - Could not retrieve variants from source file in region 14:64685914-64724241. Error was invalid region `14:64685915-64724241`
[2016-04-15T07:01Z] 2016-04-15 00:01:46 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:01:46,335 - WARNING - Could not retrieve variants from source file in region 14:52937044-52937445. Error was invalid region `14:52937045-52937445`
[2016-04-15T07:01Z] 2016-04-15 00:01:46 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:01:46,594 - WARNING - Could not retrieve variants from source file in region 14:61445756-61449518. Error was invalid region `14:61445757-61449518`
[2016-04-15T07:01Z] 2016-04-15 00:01:46 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:01:46,660 - WARNING - Could not retrieve variants from source file in region 14:64935509-64952245. Error was invalid region `14:64935510-64952245`
[2016-04-15T07:01Z] 2016-04-15 00:01:48 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:01:48,003 - WARNING - Could not retrieve variants from source file in region 14:53529458-53529859. Error was invalid region `14:53529459-53529859`
[2016-04-15T07:01Z] 2016-04-15 00:01:51 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:01:51,532 - WARNING - Could not retrieve variants from source file in region 14:66028235-66028636. Error was invalid region `14:66028236-66028636`
[2016-04-15T07:01Z] 2016-04-15 00:01:51 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:01:51,836 - WARNING - Could not retrieve variants from source file in region 14:58917243-58953936. Error was invalid region `14:58917244-58953936`
[2016-04-15T07:01Z] 2016-04-15 00:01:52 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:01:52,369 - WARNING - Could not retrieve variants from source file in region 14:61997015-61997416. Error was invalid region `14:61997016-61997416`
[2016-04-15T07:01Z] 2016-04-15 00:01:53 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:01:53,825 - WARNING - Could not retrieve variants from source file in region 14:64882169-64882570. Error was invalid region `14:64882170-64882570`
[2016-04-15T07:01Z] 2016-04-15 00:01:54 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:01:54,309 - WARNING - Could not retrieve variants from source file in region 14:63974703-63975104. Error was invalid region `14:63974704-63975104`
[2016-04-15T07:01Z] 2016-04-15 00:01:54 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:01:54,672 - WARNING - Could not retrieve variants from source file in region 14:64908634-64909035. Error was invalid region `14:64908635-64909035`
[2016-04-15T07:01Z] 2016-04-15 00:01:54 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:01:54,746 - WARNING - Could not retrieve variants from source file in region 14:65239105-65270581. Error was invalid region `14:65239106-65270581`
[2016-04-15T07:01Z] 2016-04-15 00:01:54 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:01:54,831 - WARNING - Could not retrieve variants from source file in region 14:61445756-61449518. Error was invalid region `14:61445757-61449518`
[2016-04-15T07:01Z] 2016-04-15 00:01:55 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:01:55,146 - WARNING - Could not retrieve variants from source file in region 14:52937044-52937445. Error was invalid region `14:52937045-52937445`
[2016-04-15T07:01Z] 2016-04-15 00:01:55 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:01:55,347 - WARNING - Could not retrieve variants from source file in region 14:60754482-60754883. Error was invalid region `14:60754483-60754883`
[2016-04-15T07:01Z] 2016-04-15 00:01:55 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:01:55,400 - WARNING - Could not retrieve variants from source file in region 14:64935509-64952245. Error was invalid region `14:64935510-64952245`
[2016-04-15T07:01Z] 2016-04-15 00:01:55 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:01:55,643 - WARNING - Could not retrieve variants from source file in region 14:53529458-53529859. Error was invalid region `14:53529459-53529859`
[2016-04-15T07:01Z] 2016-04-15 00:01:56 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:01:56,216 - WARNING - Could not retrieve variants from source file in region 14:66028235-66028636. Error was invalid region `14:66028236-66028636`
[2016-04-15T07:01Z] 2016-04-15 00:01:56 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:01:56,651 - WARNING - Could not retrieve variants from source file in region 14:58917243-58953936. Error was invalid region `14:58917244-58953936`
[2016-04-15T07:01Z] 2016-04-15 00:01:56 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:01:56,997 - WARNING - Could not retrieve variants from source file in region 14:61997015-61997416. Error was invalid region `14:61997016-61997416`
[2016-04-15T07:02Z] 2016-04-15 00:02:01 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:02:01,357 - WARNING - Could not retrieve variants from source file in region 14:63974703-63975104. Error was invalid region `14:63974704-63975104`
[2016-04-15T07:02Z] 2016-04-15 00:02:01 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:02:01,392 - WARNING - Could not retrieve variants from source file in region 14:64882169-64882570. Error was invalid region `14:64882170-64882570`
[2016-04-15T07:02Z] 2016-04-15 00:02:01 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:02:01,522 - WARNING - Could not retrieve variants from source file in region 14:64908634-64909035. Error was invalid region `14:64908635-64909035`
[2016-04-15T07:02Z] 2016-04-15 00:02:02 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:02:02,004 - WARNING - Could not retrieve variants from source file in region 14:52937044-52937445. Error was invalid region `14:52937045-52937445`
[2016-04-15T07:02Z] 2016-04-15 00:02:02 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:02:02,007 - WARNING - Could not retrieve variants from source file in region 14:63174405-63175150. Error was invalid region `14:63174406-63175150`
[2016-04-15T07:02Z] 2016-04-15 00:02:02 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:02:02,199 - WARNING - Could not retrieve variants from source file in region 14:64935509-64952245. Error was invalid region `14:64935510-64952245`
[2016-04-15T07:02Z] 2016-04-15 00:02:02 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:02:02,393 - WARNING - Could not retrieve variants from source file in region 14:61445756-61449518. Error was invalid region `14:61445757-61449518`
[2016-04-15T07:02Z] 2016-04-15 00:02:02 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:02:02,579 - WARNING - Could not retrieve variants from source file in region 14:60754482-60754883. Error was invalid region `14:60754483-60754883`
[2016-04-15T07:02Z] 2016-04-15 00:02:14 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:02:14,723 - WARNING - Could not retrieve variants from source file in region 14:58830931-58838891. Error was invalid region `14:58830932-58838891`
[2016-04-15T07:02Z] 2016-04-15 00:02:15 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:02:15,162 - WARNING - Could not retrieve variants from source file in region 14:53345167-53345568. Error was invalid region `14:53345168-53345568`
[2016-04-15T07:02Z] 2016-04-15 00:02:16 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:02:16,265 - WARNING - Could not retrieve variants from source file in region 14:51489381-51489782. Error was invalid region `14:51489382-51489782`
[2016-04-15T07:02Z] 2016-04-15 00:02:18 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:02:18,071 - WARNING - Could not retrieve variants from source file in region 14:64854830-64855231. Error was invalid region `14:64854831-64855231`
[2016-04-15T07:02Z] 2016-04-15 00:02:18 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:02:18,400 - WARNING - Could not retrieve variants from source file in region 14:63784196-63784597. Error was invalid region `14:63784197-63784597`
[2016-04-15T07:02Z] 2016-04-15 00:02:19 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:02:19,400 - WARNING - Could not retrieve variants from source file in region 14:52905870-52907543. Error was invalid region `14:52905871-52907543`
[2016-04-15T07:02Z] 2016-04-15 00:02:20 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:02:20,044 - WARNING - Could not retrieve variants from source file in region 14:61857758-61858159. Error was invalid region `14:61857759-61858159`
[2016-04-15T07:02Z] 2016-04-15 00:02:20 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:02:20,618 - WARNING - Could not retrieve variants from source file in region 14:53345167-53345568. Error was invalid region `14:53345168-53345568`
[2016-04-15T07:02Z] 2016-04-15 00:02:20 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:02:20,662 - WARNING - Could not retrieve variants from source file in region 14:61180446-61180847. Error was invalid region `14:61180447-61180847`
[2016-04-15T07:02Z] 2016-04-15 00:02:21 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:02:21,426 - WARNING - Could not retrieve variants from source file in region 14:60715805-60716206. Error was invalid region `14:60715806-60716206`
[2016-04-15T07:02Z] 2016-04-15 00:02:22 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:02:22,493 - WARNING - Could not retrieve variants from source file in region 14:64854830-64855231. Error was invalid region `14:64854831-64855231`
[2016-04-15T07:02Z] 2016-04-15 00:02:22 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:02:22,813 - WARNING - Could not retrieve variants from source file in region 14:63784196-63784597. Error was invalid region `14:63784197-63784597`
[2016-04-15T07:02Z] 2016-04-15 00:02:23 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:02:23,778 - WARNING - Could not retrieve variants from source file in region 14:52905870-52907543. Error was invalid region `14:52905871-52907543`
[2016-04-15T07:02Z] 2016-04-15 00:02:25 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:02:25,368 - WARNING - Could not retrieve variants from source file in region 14:58830931-58838891. Error was invalid region `14:58830932-58838891`
[2016-04-15T07:02Z] 2016-04-15 00:02:26 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:02:26,982 - WARNING - Could not retrieve variants from source file in region 14:61180446-61180847. Error was invalid region `14:61180447-61180847`
[2016-04-15T07:02Z] 2016-04-15 00:02:27 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:02:27,025 - WARNING - Could not retrieve variants from source file in region 14:51489381-51489782. Error was invalid region `14:51489382-51489782`
[2016-04-15T07:02Z] 2016-04-15 00:02:27 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:02:27,076 - WARNING - Could not retrieve variants from source file in region 14:53345167-53345568. Error was invalid region `14:53345168-53345568`
[2016-04-15T07:02Z] 2016-04-15 00:02:27 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:02:27,077 - WARNING - Could not retrieve variants from source file in region 14:56146146-56146547. Error was invalid region `14:56146147-56146547`
[2016-04-15T07:02Z] 2016-04-15 00:02:27 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:02:27,565 - WARNING - Could not retrieve variants from source file in region 14:60715805-60716206. Error was invalid region `14:60715806-60716206`
[2016-04-15T07:02Z] 2016-04-15 00:02:27 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:02:27,591 - WARNING - Could not retrieve variants from source file in region 14:63784196-63784597. Error was invalid region `14:63784197-63784597`
[2016-04-15T07:02Z] 2016-04-15 00:02:27 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:02:27,610 - WARNING - Could not retrieve variants from source file in region 14:64854830-64855231. Error was invalid region `14:64854831-64855231`
[2016-04-15T07:02Z] 2016-04-15 00:02:27 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:02:27,638 - WARNING - Could not retrieve variants from source file in region 14:62462555-62463404. Error was invalid region `14:62462556-62463404`
[2016-04-15T07:02Z] 2016-04-15 00:02:28 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:02:28,086 - WARNING - Could not retrieve variants from source file in region 14:52905870-52907543. Error was invalid region `14:52905871-52907543`
[2016-04-15T07:02Z] 2016-04-15 00:02:32 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:02:32,170 - WARNING - Could not retrieve variants from source file in region 14:61180446-61180847. Error was invalid region `14:61180447-61180847`
[2016-04-15T07:02Z] 2016-04-15 00:02:32 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:02:32,601 - WARNING - Could not retrieve variants from source file in region 14:56146146-56146547. Error was invalid region `14:56146147-56146547`
[2016-04-15T07:02Z] 2016-04-15 00:02:34 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:02:34,282 - WARNING - Could not retrieve variants from source file in region 14:60715805-60716206. Error was invalid region `14:60715806-60716206`
[2016-04-15T07:02Z] 2016-04-15 00:02:38 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:02:38,808 - WARNING - Could not retrieve variants from source file in region 14:61747433-61747834. Error was invalid region `14:61747434-61747834`
[2016-04-15T07:02Z] 2016-04-15 00:02:39 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:02:39,241 - WARNING - Could not retrieve variants from source file in region 14:58605579-58605980. Error was invalid region `14:58605580-58605980`
[2016-04-15T07:02Z] 2016-04-15 00:02:42 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:02:42,011 - WARNING - Could not retrieve variants from source file in region 14:51445350-51446406. Error was invalid region `14:51445351-51446406`
[2016-04-15T07:02Z] 2016-04-15 00:02:43 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:02:43,396 - WARNING - Could not retrieve variants from source file in region 14:62204816-62205251. Error was invalid region `14:62204817-62205251`
[2016-04-15T07:02Z] 2016-04-15 00:02:43 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:02:43,700 - WARNING - Could not retrieve variants from source file in region 14:52734897-52735298. Error was invalid region `14:52734898-52735298`
[2016-04-15T07:02Z] 2016-04-15 00:02:43 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:02:43,888 - WARNING - Could not retrieve variants from source file in region 14:60976326-60976727. Error was invalid region `14:60976327-60976727`
[2016-04-15T07:02Z] 2016-04-15 00:02:44 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:02:44,305 - WARNING - Could not retrieve variants from source file in region 14:61747433-61747834. Error was invalid region `14:61747434-61747834`
[2016-04-15T07:02Z] 2016-04-15 00:02:44 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:02:44,367 - WARNING - Could not retrieve variants from source file in region 14:58605579-58605980. Error was invalid region `14:58605580-58605980`
[2016-04-15T07:02Z] 2016-04-15 00:02:46 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:02:46,369 - WARNING - Could not retrieve variants from source file in region 14:60903546-60932942. Error was invalid region `14:60903547-60932942`
[2016-04-15T07:02Z] 2016-04-15 00:02:49 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:02:49,829 - WARNING - Could not retrieve variants from source file in region 14:51054387-51057917. Error was invalid region `14:51054388-51057917`
[2016-04-15T07:02Z] 2016-04-15 00:02:49 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:02:49,916 - WARNING - Could not retrieve variants from source file in region 14:60976326-60976727. Error was invalid region `14:60976327-60976727`
[2016-04-15T07:02Z] 2016-04-15 00:02:50 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:02:50,588 - WARNING - Could not retrieve variants from source file in region 14:61747433-61747834. Error was invalid region `14:61747434-61747834`
[2016-04-15T07:02Z] 2016-04-15 00:02:50 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:02:50,624 - WARNING - Could not retrieve variants from source file in region 14:64447565-64447966. Error was invalid region `14:64447566-64447966`
[2016-04-15T07:02Z] 2016-04-15 00:02:51 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:02:51,485 - WARNING - Could not retrieve variants from source file in region 14:58605579-58605980. Error was invalid region `14:58605580-58605980`
[2016-04-15T07:02Z] 2016-04-15 00:02:52 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:02:52,732 - WARNING - Could not retrieve variants from source file in region 14:51445350-51446406. Error was invalid region `14:51445351-51446406`
[2016-04-15T07:02Z] 2016-04-15 00:02:53 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:02:53,335 - WARNING - Could not retrieve variants from source file in region 14:60632035-60632436. Error was invalid region `14:60632036-60632436`
[2016-04-15T07:02Z] 2016-04-15 00:02:55 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:02:55,042 - WARNING - Could not retrieve variants from source file in region 14:60976326-60976727. Error was invalid region `14:60976327-60976727`
[2016-04-15T07:02Z] 2016-04-15 00:02:56 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:02:56,166 - WARNING - Could not retrieve variants from source file in region 14:52734897-52735298. Error was invalid region `14:52734898-52735298`
[2016-04-15T07:02Z] 2016-04-15 00:02:57 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:02:57,713 - WARNING - Could not retrieve variants from source file in region 14:50753781-50853781. Error was invalid region `14:50753782-50853781`
[2016-04-15T07:02Z] 2016-04-15 00:02:57 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:02:57,724 - WARNING - Could not retrieve variants from source file in region 14:50853781-50863183. Error was invalid region `14:50853782-50863183`
[2016-04-15T07:02Z] 2016-04-15 00:02:58 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:02:58,626 - WARNING - Could not retrieve variants from source file in region 14:60632035-60632436. Error was invalid region `14:60632036-60632436`
[2016-04-15T07:03Z] 2016-04-15 00:03:02 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:03:02,483 - WARNING - Could not retrieve variants from source file in region 14:51359012-51383622. Error was invalid region `14:51359013-51383622`
[2016-04-15T07:03Z] 2016-04-15 00:03:02 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:03:02,955 - WARNING - Could not retrieve variants from source file in region 14:61509713-61510114. Error was invalid region `14:61509714-61510114`
[2016-04-15T07:03Z] 2016-04-15 00:03:05 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:03:05,208 - WARNING - Could not retrieve variants from source file in region 14:58563483-58563884. Error was invalid region `14:58563484-58563884`
[2016-04-15T07:03Z] 2016-04-15 00:03:07 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:03:07,578 - WARNING - Could not retrieve variants from source file in region 14:61509713-61510114. Error was invalid region `14:61509714-61510114`
[2016-04-15T07:03Z] 2016-04-15 00:03:08 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:03:08,583 - WARNING - Could not retrieve variants from source file in region 14:61509713-61510114. Error was invalid region `14:61509714-61510114`
[2016-04-15T07:03Z] 2016-04-15 00:03:08 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:03:08,741 - WARNING - Could not retrieve variants from source file in region 14:50704120-50713869. Error was invalid region `14:50704121-50713869`
[2016-04-15T07:03Z] 2016-04-15 00:03:08 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:03:08,902 - WARNING - Could not retrieve variants from source file in region 14:53019733-53020134. Error was invalid region `14:53019734-53020134`
[2016-04-15T07:03Z] 2016-04-15 00:03:09 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:03:09,857 - WARNING - Could not retrieve variants from source file in region 14:58563483-58563884. Error was invalid region `14:58563484-58563884`
[2016-04-15T07:03Z] 2016-04-15 00:03:12 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:03:12,060 - WARNING - Could not retrieve variants from source file in region 14:60043211-60063662. Error was invalid region `14:60043212-60063662`
[2016-04-15T07:03Z] 2016-04-15 00:03:12 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:03:12,498 - WARNING - Could not retrieve variants from source file in region 14:55906961-55907362. Error was invalid region `14:55906962-55907362`
[2016-04-15T07:03Z] 2016-04-15 00:03:13 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:03:13,104 - WARNING - Could not retrieve variants from source file in region 14:50616667-50617068. Error was invalid region `14:50616668-50617068`
[2016-04-15T07:03Z] 2016-04-15 00:03:13 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:03:13,766 - WARNING - Could not retrieve variants from source file in region 14:53019733-53020134. Error was invalid region `14:53019734-53020134`
[2016-04-15T07:03Z] 2016-04-15 00:03:14 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:03:14,288 - WARNING - Could not retrieve variants from source file in region 14:58563483-58563884. Error was invalid region `14:58563484-58563884`
[2016-04-15T07:03Z] 2016-04-15 00:03:15 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:03:15,753 - WARNING - Could not retrieve variants from source file in region 14:55817497-55818896. Error was invalid region `14:55817498-55818896`
[2016-04-15T07:03Z] 2016-04-15 00:03:16 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:03:16,712 - WARNING - Could not retrieve variants from source file in region 14:52181870-52187156. Error was invalid region `14:52181871-52187156`
[2016-04-15T07:03Z] 2016-04-15 00:03:17 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:03:17,200 - WARNING - Could not retrieve variants from source file in region 14:60043211-60063662. Error was invalid region `14:60043212-60063662`
[2016-04-15T07:03Z] 2016-04-15 00:03:17 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:03:17,861 - WARNING - Could not retrieve variants from source file in region 14:55906961-55907362. Error was invalid region `14:55906962-55907362`
[2016-04-15T07:03Z] 2016-04-15 00:03:18 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:03:18,338 - WARNING - Could not retrieve variants from source file in region 14:53019733-53020134. Error was invalid region `14:53019734-53020134`
[2016-04-15T07:03Z] 2016-04-15 00:03:18 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:03:18,401 - WARNING - Could not retrieve variants from source file in region 14:60574328-60592077. Error was invalid region `14:60574329-60592077`
[2016-04-15T07:03Z] 2016-04-15 00:03:18 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:03:18,405 - WARNING - Could not retrieve variants from source file in region 14:50704120-50713869. Error was invalid region `14:50704121-50713869`
[2016-04-15T07:03Z] 2016-04-15 00:03:18 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:03:18,409 - WARNING - Could not retrieve variants from source file in region 14:50616667-50617068. Error was invalid region `14:50616668-50617068`
[2016-04-15T07:03Z] 2016-04-15 00:03:21 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:03:21,144 - WARNING - Could not retrieve variants from source file in region 14:52181870-52187156. Error was invalid region `14:52181871-52187156`
[2016-04-15T07:03Z] 2016-04-15 00:03:21 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:03:21,445 - WARNING - Could not retrieve variants from source file in region 14:60043211-60063662. Error was invalid region `14:60043212-60063662`
[2016-04-15T07:03Z] 2016-04-15 00:03:22 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:03:22,622 - WARNING - Could not retrieve variants from source file in region 14:55906961-55907362. Error was invalid region `14:55906962-55907362`
[2016-04-15T07:03Z] 2016-04-15 00:03:23 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:03:23,284 - WARNING - Could not retrieve variants from source file in region 14:50616667-50617068. Error was invalid region `14:50616668-50617068`
[2016-04-15T07:03Z] 2016-04-15 00:03:26 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:03:26,925 - WARNING - Could not retrieve variants from source file in region 14:57099648-57100049. Error was invalid region `14:57099649-57100049`
[2016-04-15T07:03Z] 2016-04-15 00:03:27 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:03:27,663 - WARNING - Could not retrieve variants from source file in region 14:55226892-55227293. Error was invalid region `14:55226893-55227293`
[2016-04-15T07:03Z] 2016-04-15 00:03:29 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:03:29,526 - WARNING - Could not retrieve variants from source file in region 14:57857983-57858384. Error was invalid region `14:57857984-57858384`
[2016-04-15T07:03Z] 2016-04-15 00:03:29 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:03:29,750 - WARNING - Could not retrieve variants from source file in region 14:57857983-57858384. Error was invalid region `14:57857984-57858384`
[2016-04-15T07:03Z] 2016-04-15 00:03:30 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:03:30,953 - WARNING - Could not retrieve variants from source file in region 14:57099648-57100049. Error was invalid region `14:57099649-57100049`
[2016-04-15T07:03Z] 2016-04-15 00:03:31 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:03:31,884 - WARNING - Could not retrieve variants from source file in region 14:55226892-55227293. Error was invalid region `14:55226893-55227293`
[2016-04-15T07:03Z] 2016-04-15 00:03:33 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:03:33,757 - WARNING - Could not retrieve variants from source file in region 14:54417311-54417712. Error was invalid region `14:54417312-54417712`
[2016-04-15T07:03Z] 2016-04-15 00:03:33 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:03:33,956 - WARNING - Could not retrieve variants from source file in region 14:59988113-60005034. Error was invalid region `14:59988114-60005034`
[2016-04-15T07:03Z] 2016-04-15 00:03:34 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:03:34,237 - WARNING - Could not retrieve variants from source file in region 14:54417311-54417712. Error was invalid region `14:54417312-54417712`
[2016-04-15T07:03Z] 2016-04-15 00:03:35 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:03:35,155 - WARNING - Could not retrieve variants from source file in region 14:57099648-57100049. Error was invalid region `14:57099649-57100049`
[2016-04-15T07:03Z] 2016-04-15 00:03:35 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:03:35,927 - WARNING - Could not retrieve variants from source file in region 14:59797024-59797425. Error was invalid region `14:59797025-59797425`
[2016-04-15T07:03Z] 2016-04-15 00:03:36 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:03:36,184 - WARNING - Could not retrieve variants from source file in region 14:53619252-53619734. Error was invalid region `14:53619253-53619734`
[2016-04-15T07:03Z] 2016-04-15 00:03:37 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:03:37,104 - WARNING - Could not retrieve variants from source file in region 14:55604724-55619501. Error was invalid region `14:55604725-55619501`
[2016-04-15T07:03Z] 2016-04-15 00:03:38 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:03:38,467 - WARNING - Could not retrieve variants from source file in region 14:54417311-54417712. Error was invalid region `14:54417312-54417712`
[2016-04-15T07:03Z] 2016-04-15 00:03:39 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:03:39,829 - WARNING - Could not retrieve variants from source file in region 14:55863919-55864336. Error was invalid region `14:55863920-55864336`
[2016-04-15T07:03Z] 2016-04-15 00:03:40 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:03:40,480 - WARNING - Could not retrieve variants from source file in region 14:59797024-59797425. Error was invalid region `14:59797025-59797425`
[2016-04-15T07:03Z] 2016-04-15 00:03:40 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:03:40,597 - WARNING - Could not retrieve variants from source file in region 14:53619252-53619734. Error was invalid region `14:53619253-53619734`
[2016-04-15T07:03Z] 2016-04-15 00:03:40 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:03:40,996 - WARNING - Could not retrieve variants from source file in region 14:57052300-57052701. Error was invalid region `14:57052301-57052701`
[2016-04-15T07:03Z] 2016-04-15 00:03:42 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:03:42,412 - WARNING - Could not retrieve variants from source file in region 14:57052300-57052701. Error was invalid region `14:57052301-57052701`
[2016-04-15T07:03Z] 2016-04-15 00:03:43 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:03:43,888 - WARNING - Could not retrieve variants from source file in region 14:59797024-59797425. Error was invalid region `14:59797025-59797425`
[2016-04-15T07:03Z] 2016-04-15 00:03:44 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:03:44,170 - WARNING - Could not retrieve variants from source file in region 14:53619252-53619734. Error was invalid region `14:53619253-53619734`
[2016-04-15T07:03Z] 2016-04-15 00:03:48 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:03:48,805 - WARNING - Could not retrieve variants from source file in region 14:59104977-59112922. Error was invalid region `14:59104978-59112922`
[2016-04-15T07:03Z] 2016-04-15 00:03:48 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:03:48,839 - WARNING - Could not retrieve variants from source file in region 14:59104977-59112922. Error was invalid region `14:59104978-59112922`
[2016-04-15T07:03Z] 2016-04-15 00:03:48 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:03:48,920 - WARNING - Could not retrieve variants from source file in region 14:59104977-59112922. Error was invalid region `14:59104978-59112922`
[2016-04-15T07:03Z] ['bcbio-variation-recall', 'square', '-Xms750m', '-Xmx7280m', '-XX:+UseSerialGC', '-c', 16, '-r', u'14:66135961-81646674', '--caller', 'platypus', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/14/Batch1-14_66135960_81646674.vcf.gz', '/mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/14/Batch1-14_66135960_81646674.vcf-inputs.txt'] in region: 14:66135961-81646674
[2016-04-15T07:04Z] 2016-04-15 00:04:05 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:04:05,224 - WARNING - Could not retrieve variants from source file in region 14:74753067-74766542. Error was invalid region `14:74753068-74766542`
[2016-04-15T07:04Z] 2016-04-15 00:04:06 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:04:06,067 - WARNING - Could not retrieve variants from source file in region 14:77332156-77332557. Error was invalid region `14:77332157-77332557`
[2016-04-15T07:04Z] 2016-04-15 00:04:06 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:04:06,108 - WARNING - Could not retrieve variants from source file in region 14:77788697-77794473. Error was invalid region `14:77788698-77794473`
[2016-04-15T07:04Z] 2016-04-15 00:04:06 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:04:06,132 - WARNING - Could not retrieve variants from source file in region 14:75078059-75078460. Error was invalid region `14:75078060-75078460`
[2016-04-15T07:04Z] 2016-04-15 00:04:06 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:04:06,390 - WARNING - Could not retrieve variants from source file in region 14:78390669-78391070. Error was invalid region `14:78390670-78391070`
[2016-04-15T07:04Z] 2016-04-15 00:04:06 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:04:06,753 - WARNING - Could not retrieve variants from source file in region 14:74875970-74876371. Error was invalid region `14:74875971-74876371`
[2016-04-15T07:04Z] 2016-04-15 00:04:06 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:04:06,754 - WARNING - Could not retrieve variants from source file in region 14:77880094-77880495. Error was invalid region `14:77880095-77880495`
[2016-04-15T07:04Z] 2016-04-15 00:04:06 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:04:06,921 - WARNING - Could not retrieve variants from source file in region 14:78140118-78140545. Error was invalid region `14:78140119-78140545`
[2016-04-15T07:04Z] 2016-04-15 00:04:07 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:04:07,548 - WARNING - Could not retrieve variants from source file in region 14:75513617-75538407. Error was invalid region `14:75513618-75538407`
[2016-04-15T07:04Z] 2016-04-15 00:04:07 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:04:07,683 - WARNING - Could not retrieve variants from source file in region 14:81610372-81610773. Error was invalid region `14:81610373-81610773`
[2016-04-15T07:04Z] 2016-04-15 00:04:07 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:04:07,730 - WARNING - Could not retrieve variants from source file in region 14:76905566-76905967. Error was invalid region `14:76905567-76905967`
[2016-04-15T07:04Z] 2016-04-15 00:04:14 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:04:14,217 - WARNING - Could not retrieve variants from source file in region 14:77624427-77643110. Error was invalid region `14:77624428-77643110`
[2016-04-15T07:04Z] 2016-04-15 00:04:14 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:04:14,458 - WARNING - Could not retrieve variants from source file in region 14:77332156-77332557. Error was invalid region `14:77332157-77332557`
[2016-04-15T07:04Z] 2016-04-15 00:04:15 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:04:15,385 - WARNING - Could not retrieve variants from source file in region 14:74946529-74946930. Error was invalid region `14:74946530-74946930`
[2016-04-15T07:04Z] 2016-04-15 00:04:15 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:04:15,567 - WARNING - Could not retrieve variants from source file in region 14:74875970-74876371. Error was invalid region `14:74875971-74876371`
[2016-04-15T07:04Z] 2016-04-15 00:04:16 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:04:16,206 - WARNING - Could not retrieve variants from source file in region 14:81610372-81610773. Error was invalid region `14:81610373-81610773`
[2016-04-15T07:04Z] 2016-04-15 00:04:20 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:04:20,591 - WARNING - Could not retrieve variants from source file in region 14:77624427-77643110. Error was invalid region `14:77624428-77643110`
[2016-04-15T07:04Z] 2016-04-15 00:04:21 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:04:21,639 - WARNING - Could not retrieve variants from source file in region 14:75078059-75078460. Error was invalid region `14:75078060-75078460`
[2016-04-15T07:04Z] 2016-04-15 00:04:21 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:04:21,694 - WARNING - Could not retrieve variants from source file in region 14:77332156-77332557. Error was invalid region `14:77332157-77332557`
[2016-04-15T07:04Z] 2016-04-15 00:04:24 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:04:24,665 - WARNING - Could not retrieve variants from source file in region 14:76905566-76905967. Error was invalid region `14:76905567-76905967`
[2016-04-15T07:04Z] 2016-04-15 00:04:24 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:04:24,699 - WARNING - Could not retrieve variants from source file in region 14:74875970-74876371. Error was invalid region `14:74875971-74876371`
[2016-04-15T07:04Z] 2016-04-15 00:04:24 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:04:24,984 - WARNING - Could not retrieve variants from source file in region 14:81610372-81610773. Error was invalid region `14:81610373-81610773`
[2016-04-15T07:04Z] 2016-04-15 00:04:25 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:04:25,006 - WARNING - Could not retrieve variants from source file in region 14:75513617-75538407. Error was invalid region `14:75513618-75538407`
[2016-04-15T07:04Z] 2016-04-15 00:04:37 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:04:37,331 - WARNING - Could not retrieve variants from source file in region 14:74711672-74712073. Error was invalid region `14:74711673-74712073`
[2016-04-15T07:04Z] 2016-04-15 00:04:38 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:04:38,994 - WARNING - Could not retrieve variants from source file in region 14:74711672-74712073. Error was invalid region `14:74711673-74712073`
[2016-04-15T07:04Z] 2016-04-15 00:04:39 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:04:39,535 - WARNING - Could not retrieve variants from source file in region 14:77236169-77236570. Error was invalid region `14:77236170-77236570`
[2016-04-15T07:04Z] 2016-04-15 00:04:39 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:04:39,584 - WARNING - Could not retrieve variants from source file in region 14:77744982-77752115. Error was invalid region `14:77744983-77752115`
[2016-04-15T07:04Z] 2016-04-15 00:04:41 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:04:41,019 - WARNING - Could not retrieve variants from source file in region 14:78174262-78197555. Error was invalid region `14:78174263-78197555`
[2016-04-15T07:04Z] 2016-04-15 00:04:41 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:04:41,261 - WARNING - Could not retrieve variants from source file in region 14:78028592-78028993. Error was invalid region `14:78028593-78028993`
[2016-04-15T07:04Z] 2016-04-15 00:04:42 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:04:42,418 - WARNING - Could not retrieve variants from source file in region 14:76644412-76644813. Error was invalid region `14:76644413-76644813`
[2016-04-15T07:04Z] 2016-04-15 00:04:42 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:04:42,968 - WARNING - Could not retrieve variants from source file in region 14:75483601-75484002. Error was invalid region `14:75483602-75484002`
[2016-04-15T07:04Z] 2016-04-15 00:04:43 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:04:43,033 - WARNING - Could not retrieve variants from source file in region 14:74711672-74712073. Error was invalid region `14:74711673-74712073`
[2016-04-15T07:04Z] 2016-04-15 00:04:44 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:04:44,350 - WARNING - Could not retrieve variants from source file in region 14:77236169-77236570. Error was invalid region `14:77236170-77236570`
[2016-04-15T07:04Z] 2016-04-15 00:04:44 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:04:44,585 - WARNING - Could not retrieve variants from source file in region 14:77744982-77752115. Error was invalid region `14:77744983-77752115`
[2016-04-15T07:04Z] 2016-04-15 00:04:45 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:04:45,954 - WARNING - Could not retrieve variants from source file in region 14:78028592-78028993. Error was invalid region `14:78028593-78028993`
[2016-04-15T07:04Z] 2016-04-15 00:04:47 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:04:47,612 - WARNING - Could not retrieve variants from source file in region 14:76644412-76644813. Error was invalid region `14:76644413-76644813`
[2016-04-15T07:04Z] 2016-04-15 00:04:47 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:04:47,802 - WARNING - Could not retrieve variants from source file in region 14:75483601-75484002. Error was invalid region `14:75483602-75484002`
[2016-04-15T07:04Z] 2016-04-15 00:04:49 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:04:49,059 - WARNING - Could not retrieve variants from source file in region 14:77236169-77236570. Error was invalid region `14:77236170-77236570`
[2016-04-15T07:04Z] 2016-04-15 00:04:49 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:04:49,219 - WARNING - Could not retrieve variants from source file in region 14:77744982-77752115. Error was invalid region `14:77744983-77752115`
[2016-04-15T07:04Z] 2016-04-15 00:04:50 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:04:50,619 - WARNING - Could not retrieve variants from source file in region 14:78028592-78028993. Error was invalid region `14:78028593-78028993`
[2016-04-15T07:04Z] 2016-04-15 00:04:51 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:04:51,586 - WARNING - Could not retrieve variants from source file in region 14:75483601-75484002. Error was invalid region `14:75483602-75484002`
[2016-04-15T07:04Z] 2016-04-15 00:04:52 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:04:52,111 - WARNING - Could not retrieve variants from source file in region 14:76644412-76644813. Error was invalid region `14:76644413-76644813`
[2016-04-15T07:04Z] 2016-04-15 00:04:54 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:04:54,073 - WARNING - Could not retrieve variants from source file in region 14:75248441-75279585. Error was invalid region `14:75248442-75279585`
[2016-04-15T07:04Z] 2016-04-15 00:04:56 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:04:56,726 - WARNING - Could not retrieve variants from source file in region 14:81251044-81259444. Error was invalid region `14:81251045-81259444`
[2016-04-15T07:04Z] 2016-04-15 00:04:56 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:04:56,782 - WARNING - Could not retrieve variants from source file in region 14:80669369-80669770. Error was invalid region `14:80669370-80669770`
[2016-04-15T07:05Z] 2016-04-15 00:05:00 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:05:00,794 - WARNING - Could not retrieve variants from source file in region 14:75142395-75142796. Error was invalid region `14:75142396-75142796`
[2016-04-15T07:05Z] 2016-04-15 00:05:01 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:05:01,347 - WARNING - Could not retrieve variants from source file in region 14:81251044-81259444. Error was invalid region `14:81251045-81259444`
[2016-04-15T07:05Z] 2016-04-15 00:05:01 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:05:01,591 - WARNING - Could not retrieve variants from source file in region 14:80669369-80669770. Error was invalid region `14:80669370-80669770`
[2016-04-15T07:05Z] 2016-04-15 00:05:03 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:05:03,627 - WARNING - Could not retrieve variants from source file in region 14:77925800-77951314. Error was invalid region `14:77925801-77951314`
[2016-04-15T07:05Z] 2016-04-15 00:05:05 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:05:05,444 - WARNING - Could not retrieve variants from source file in region 14:80669369-80669770. Error was invalid region `14:80669370-80669770`
[2016-04-15T07:05Z] 2016-04-15 00:05:05 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:05:05,672 - WARNING - Could not retrieve variants from source file in region 14:76957676-76965166. Error was invalid region `14:76957677-76965166`
[2016-04-15T07:05Z] 2016-04-15 00:05:07 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:05:07,360 - WARNING - Could not retrieve variants from source file in region 14:77925800-77951314. Error was invalid region `14:77925801-77951314`
[2016-04-15T07:05Z] 2016-04-15 00:05:08 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:05:08,838 - WARNING - Could not retrieve variants from source file in region 14:79181015-79181416. Error was invalid region `14:79181016-79181416`
[2016-04-15T07:05Z] 2016-04-15 00:05:08 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:05:08,967 - WARNING - Could not retrieve variants from source file in region 14:76524759-76543194. Error was invalid region `14:76524760-76543194`
[2016-04-15T07:05Z] 2016-04-15 00:05:09 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:05:09,267 - WARNING - Could not retrieve variants from source file in region 14:76957676-76965166. Error was invalid region `14:76957677-76965166`
[2016-04-15T07:05Z] 2016-04-15 00:05:11 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:05:11,105 - WARNING - Could not retrieve variants from source file in region 14:77925800-77951314. Error was invalid region `14:77925801-77951314`
[2016-04-15T07:05Z] 2016-04-15 00:05:12 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:05:12,777 - WARNING - Could not retrieve variants from source file in region 14:69702947-69704743. Error was invalid region `14:69702948-69704743`
[2016-04-15T07:05Z] 2016-04-15 00:05:12 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:05:12,788 - WARNING - Could not retrieve variants from source file in region 14:79181015-79181416. Error was invalid region `14:79181016-79181416`
[2016-04-15T07:05Z] 2016-04-15 00:05:12 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:05:12,787 - WARNING - Could not retrieve variants from source file in region 14:76524759-76543194. Error was invalid region `14:76524760-76543194`
[2016-04-15T07:05Z] 2016-04-15 00:05:14 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:05:14,918 - WARNING - Could not retrieve variants from source file in region 14:75904449-75912327. Error was invalid region `14:75904450-75912327`
[2016-04-15T07:05Z] 2016-04-15 00:05:15 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:05:15,155 - WARNING - Could not retrieve variants from source file in region 14:76156398-76156799. Error was invalid region `14:76156399-76156799`
[2016-04-15T07:05Z] 2016-04-15 00:05:16 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:05:16,721 - WARNING - Could not retrieve variants from source file in region 14:76045151-76046153. Error was invalid region `14:76045152-76046153`
[2016-04-15T07:05Z] 2016-04-15 00:05:22 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:05:22,950 - WARNING - Could not retrieve variants from source file in region 14:67849083-67878955. Error was invalid region `14:67849084-67878955`
[2016-04-15T07:05Z] 2016-04-15 00:05:23 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:05:23,419 - WARNING - Could not retrieve variants from source file in region 14:75746479-75746880. Error was invalid region `14:75746480-75746880`
[2016-04-15T07:05Z] 2016-04-15 00:05:24 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:05:24,905 - WARNING - Could not retrieve variants from source file in region 14:76156398-76156799. Error was invalid region `14:76156399-76156799`
[2016-04-15T07:05Z] 2016-04-15 00:05:24 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:05:24,957 - WARNING - Could not retrieve variants from source file in region 14:75904449-75912327. Error was invalid region `14:75904450-75912327`
[2016-04-15T07:05Z] 2016-04-15 00:05:26 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:05:26,818 - WARNING - Could not retrieve variants from source file in region 14:73302763-73303164. Error was invalid region `14:73302764-73303164`
[2016-04-15T07:05Z] 2016-04-15 00:05:27 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:05:27,181 - WARNING - Could not retrieve variants from source file in region 14:70633876-70634736. Error was invalid region `14:70633877-70634736`
[2016-04-15T07:05Z] 2016-04-15 00:05:28 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:05:28,368 - WARNING - Could not retrieve variants from source file in region 14:75746479-75746880. Error was invalid region `14:75746480-75746880`
[2016-04-15T07:05Z] 2016-04-15 00:05:28 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:05:28,704 - WARNING - Could not retrieve variants from source file in region 14:74340586-74340987. Error was invalid region `14:74340587-74340987`
[2016-04-15T07:05Z] 2016-04-15 00:05:28 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:05:28,978 - WARNING - Could not retrieve variants from source file in region 14:70171207-70171608. Error was invalid region `14:70171208-70171608`
[2016-04-15T07:05Z] 2016-04-15 00:05:31 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:05:31,822 - WARNING - Could not retrieve variants from source file in region 14:76329970-76330371. Error was invalid region `14:76329971-76330371`
[2016-04-15T07:05Z] 2016-04-15 00:05:32 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:05:32,447 - WARNING - Could not retrieve variants from source file in region 14:73302763-73303164. Error was invalid region `14:73302764-73303164`
[2016-04-15T07:05Z] 2016-04-15 00:05:32 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:05:32,599 - WARNING - Could not retrieve variants from source file in region 14:68234328-68265057. Error was invalid region `14:68234329-68265057`
[2016-04-15T07:05Z] 2016-04-15 00:05:32 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:05:32,719 - WARNING - Could not retrieve variants from source file in region 14:69521134-69522252. Error was invalid region `14:69521135-69522252`
[2016-04-15T07:05Z] 2016-04-15 00:05:33 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:05:33,062 - WARNING - Could not retrieve variants from source file in region 14:70489724-70490125. Error was invalid region `14:70489725-70490125`
[2016-04-15T07:05Z] 2016-04-15 00:05:33 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:05:33,262 - WARNING - Could not retrieve variants from source file in region 14:75746479-75746880. Error was invalid region `14:75746480-75746880`
[2016-04-15T07:05Z] 2016-04-15 00:05:33 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:05:33,391 - WARNING - Could not retrieve variants from source file in region 14:74340586-74340987. Error was invalid region `14:74340587-74340987`
[2016-04-15T07:05Z] 2016-04-15 00:05:37 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:05:37,333 - WARNING - Could not retrieve variants from source file in region 14:73302763-73303164. Error was invalid region `14:73302764-73303164`
[2016-04-15T07:05Z] 2016-04-15 00:05:38 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:05:38,350 - WARNING - Could not retrieve variants from source file in region 14:70633876-70634736. Error was invalid region `14:70633877-70634736`
[2016-04-15T07:05Z] 2016-04-15 00:05:38 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:05:38,640 - WARNING - Could not retrieve variants from source file in region 14:70171207-70171608. Error was invalid region `14:70171208-70171608`
[2016-04-15T07:05Z] 2016-04-15 00:05:38 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:05:38,643 - WARNING - Could not retrieve variants from source file in region 14:74340586-74340987. Error was invalid region `14:74340587-74340987`
[2016-04-15T07:05Z] 2016-04-15 00:05:38 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:05:38,652 - WARNING - Could not retrieve variants from source file in region 14:75573876-75601853. Error was invalid region `14:75573877-75601853`
[2016-04-15T07:05Z] 2016-04-15 00:05:40 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:05:40,431 - WARNING - Could not retrieve variants from source file in region 14:69259451-69263264. Error was invalid region `14:69259452-69263264`
[2016-04-15T07:05Z] 2016-04-15 00:05:42 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:05:42,225 - WARNING - Could not retrieve variants from source file in region 14:70489724-70490125. Error was invalid region `14:70489725-70490125`
[2016-04-15T07:05Z] 2016-04-15 00:05:47 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:05:47,018 - WARNING - Could not retrieve variants from source file in region 14:67664669-67690809. Error was invalid region `14:67664670-67690809`
[2016-04-15T07:05Z] 2016-04-15 00:05:48 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:05:48,848 - WARNING - Could not retrieve variants from source file in region 14:73219809-73220210. Error was invalid region `14:73219810-73220210`
[2016-04-15T07:05Z] 2016-04-15 00:05:48 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:05:48,924 - WARNING - Could not retrieve variants from source file in region 14:70263437-70263838. Error was invalid region `14:70263438-70263838`
[2016-04-15T07:05Z] 2016-04-15 00:05:49 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:05:49,971 - WARNING - Could not retrieve variants from source file in region 14:68193520-68193921. Error was invalid region `14:68193521-68193921`
[2016-04-15T07:05Z] 2016-04-15 00:05:51 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:05:51,159 - WARNING - Could not retrieve variants from source file in region 14:74196475-74206848. Error was invalid region `14:74196476-74206848`
[2016-04-15T07:05Z] 2016-04-15 00:05:53 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:05:53,551 - WARNING - Could not retrieve variants from source file in region 14:73219809-73220210. Error was invalid region `14:73219810-73220210`
[2016-04-15T07:05Z] 2016-04-15 00:05:55 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:05:55,479 - WARNING - Could not retrieve variants from source file in region 14:66135952-66136353. Error was invalid region `14:66135953-66136353`
[2016-04-15T07:05Z] 2016-04-15 00:05:55 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:05:55,997 - WARNING - Could not retrieve variants from source file in region 14:68193520-68193921. Error was invalid region `14:68193521-68193921`
[2016-04-15T07:05Z] 2016-04-15 00:05:55 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:05:55,999 - WARNING - Could not retrieve variants from source file in region 14:72055257-72055658. Error was invalid region `14:72055258-72055658`
[2016-04-15T07:05Z] 2016-04-15 00:05:56 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:05:56,612 - WARNING - Could not retrieve variants from source file in region 14:74196475-74206848. Error was invalid region `14:74196476-74206848`
[2016-04-15T07:05Z] 2016-04-15 00:05:57 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:05:57,286 - WARNING - Could not retrieve variants from source file in region 14:69061017-69062513. Error was invalid region `14:69061018-69062513`
[2016-04-15T07:05Z] 2016-04-15 00:05:58 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:05:58,395 - WARNING - Could not retrieve variants from source file in region 14:69006711-69029415. Error was invalid region `14:69006712-69029415`
[2016-04-15T07:05Z] 2016-04-15 00:05:58 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:05:58,947 - WARNING - Could not retrieve variants from source file in region 14:70263437-70263838. Error was invalid region `14:70263438-70263838`
[2016-04-15T07:05Z] 2016-04-15 00:05:59 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:05:59,022 - WARNING - Could not retrieve variants from source file in region 14:73219809-73220210. Error was invalid region `14:73219810-73220210`
[2016-04-15T07:05Z] 2016-04-15 00:05:59 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:05:59,092 - WARNING - Could not retrieve variants from source file in region 14:70236389-70236790. Error was invalid region `14:70236390-70236790`
[2016-04-15T07:06Z] 2016-04-15 00:06:00 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:06:00,979 - WARNING - Could not retrieve variants from source file in region 14:71199241-71199642. Error was invalid region `14:71199242-71199642`
[2016-04-15T07:06Z] 2016-04-15 00:06:00 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:06:00,981 - WARNING - Could not retrieve variants from source file in region 14:66135952-66136353. Error was invalid region `14:66135953-66136353`
[2016-04-15T07:06Z] 2016-04-15 00:06:02 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:06:02,242 - WARNING - Could not retrieve variants from source file in region 14:72055257-72055658. Error was invalid region `14:72055258-72055658`
[2016-04-15T07:06Z] 2016-04-15 00:06:02 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:06:02,995 - WARNING - Could not retrieve variants from source file in region 14:70038575-70040470. Error was invalid region `14:70038576-70040470`
[2016-04-15T07:06Z] 2016-04-15 00:06:03 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:06:03,020 - WARNING - Could not retrieve variants from source file in region 14:74196475-74206848. Error was invalid region `14:74196476-74206848`
[2016-04-15T07:06Z] 2016-04-15 00:06:03 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:06:03,278 - WARNING - Could not retrieve variants from source file in region 14:69061017-69062513. Error was invalid region `14:69061018-69062513`
[2016-04-15T07:06Z] 2016-04-15 00:06:03 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:06:03,638 - WARNING - Could not retrieve variants from source file in region 14:69006711-69029415. Error was invalid region `14:69006712-69029415`
[2016-04-15T07:06Z] 2016-04-15 00:06:05 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:06:05,229 - WARNING - Could not retrieve variants from source file in region 14:71199241-71199642. Error was invalid region `14:71199242-71199642`
[2016-04-15T07:06Z] 2016-04-15 00:06:07 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:06:07,677 - WARNING - Could not retrieve variants from source file in region 14:72055257-72055658. Error was invalid region `14:72055258-72055658`
[2016-04-15T07:06Z] 2016-04-15 00:06:14 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:06:14,791 - WARNING - Could not retrieve variants from source file in region 14:73716563-73735556. Error was invalid region `14:73716564-73735556`
[2016-04-15T07:06Z] 2016-04-15 00:06:15 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:06:15,823 - WARNING - Could not retrieve variants from source file in region 14:72116945-72117346. Error was invalid region `14:72116946-72117346`
[2016-04-15T07:06Z] 2016-04-15 00:06:18 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:06:18,174 - WARNING - Could not retrieve variants from source file in region 14:71444577-71444978. Error was invalid region `14:71444578-71444978`
[2016-04-15T07:06Z] 2016-04-15 00:06:19 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:06:19,079 - WARNING - Could not retrieve variants from source file in region 14:69993733-69994134. Error was invalid region `14:69993734-69994134`
[2016-04-15T07:06Z] 2016-04-15 00:06:19 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:06:19,849 - WARNING - Could not retrieve variants from source file in region 14:73957561-73969800. Error was invalid region `14:73957562-73969800`
[2016-04-15T07:06Z] 2016-04-15 00:06:20 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:06:20,161 - WARNING - Could not retrieve variants from source file in region 14:72944801-72945202. Error was invalid region `14:72944802-72945202`
[2016-04-15T07:06Z] 2016-04-15 00:06:20 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:06:20,774 - WARNING - Could not retrieve variants from source file in region 14:72116945-72117346. Error was invalid region `14:72116946-72117346`
[2016-04-15T07:06Z] 2016-04-15 00:06:20 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:06:20,898 - WARNING - Could not retrieve variants from source file in region 14:71374491-71374892. Error was invalid region `14:71374492-71374892`
[2016-04-15T07:06Z] 2016-04-15 00:06:23 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:06:23,541 - WARNING - Could not retrieve variants from source file in region 14:69966639-69967040. Error was invalid region `14:69966640-69967040`
[2016-04-15T07:06Z] 2016-04-15 00:06:24 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:06:24,128 - WARNING - Could not retrieve variants from source file in region 14:72116945-72117346. Error was invalid region `14:72116946-72117346`
[2016-04-15T07:06Z] 2016-04-15 00:06:24 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:06:24,609 - WARNING - Could not retrieve variants from source file in region 14:71137633-71138034. Error was invalid region `14:71137634-71138034`
[2016-04-15T07:06Z] 2016-04-15 00:06:25 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:06:25,172 - WARNING - Could not retrieve variants from source file in region 14:71374491-71374892. Error was invalid region `14:71374492-71374892`
[2016-04-15T07:06Z] 2016-04-15 00:06:27 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:06:27,850 - WARNING - Could not retrieve variants from source file in region 14:73358734-73359135. Error was invalid region `14:73358735-73359135`
[2016-04-15T07:06Z] 2016-04-15 00:06:28 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:06:28,325 - WARNING - Could not retrieve variants from source file in region 14:69993733-69994134. Error was invalid region `14:69993734-69994134`
[2016-04-15T07:06Z] 2016-04-15 00:06:28 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:06:28,528 - WARNING - Could not retrieve variants from source file in region 14:73358734-73359135. Error was invalid region `14:73358735-73359135`
[2016-04-15T07:06Z] 2016-04-15 00:06:29 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:06:29,277 - WARNING - Could not retrieve variants from source file in region 14:71374491-71374892. Error was invalid region `14:71374492-71374892`
[2016-04-15T07:06Z] 2016-04-15 00:06:31 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:06:31,790 - WARNING - Could not retrieve variants from source file in region 14:73358734-73359135. Error was invalid region `14:73358735-73359135`
[2016-04-15T07:06Z] 2016-04-15 00:06:32 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:06:32,118 - WARNING - Could not retrieve variants from source file in region 14:69794988-69795389. Error was invalid region `14:69794989-69795389`
[2016-04-15T07:06Z] 2016-04-15 00:06:34 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:06:34,992 - WARNING - Could not retrieve variants from source file in region 14:71108942-71109343. Error was invalid region `14:71108943-71109343`
[2016-04-15T07:06Z] 2016-04-15 00:06:35 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:06:35,272 - WARNING - Could not retrieve variants from source file in region 14:71108942-71109343. Error was invalid region `14:71108943-71109343`
[2016-04-15T07:06Z] 2016-04-15 00:06:35 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:06:35,625 - WARNING - Could not retrieve variants from source file in region 14:69794988-69795389. Error was invalid region `14:69794989-69795389`
[2016-04-15T07:06Z] ['bcbio-variation-recall', 'square', '-Xms750m', '-Xmx7280m', '-XX:+UseSerialGC', '-c', 16, '-r', u'14:81651875-97299968', '--caller', 'platypus', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/14/Batch1-14_81651874_97299968.vcf.gz', '/mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/14/Batch1-14_81651874_97299968.vcf-inputs.txt'] in region: 14:81651875-97299968
[2016-04-15T07:06Z] 2016-04-15 00:06:52 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:06:52,372 - WARNING - Could not retrieve variants from source file in region 14:91681710-91682111. Error was invalid region `14:91681711-91682111`
[2016-04-15T07:06Z] 2016-04-15 00:06:52 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:06:52,549 - WARNING - Could not retrieve variants from source file in region 14:97299642-97300043. Error was invalid region `14:97299643-97300043`
[2016-04-15T07:06Z] 2016-04-15 00:06:53 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:06:53,052 - WARNING - Could not retrieve variants from source file in region 14:91526203-91526604. Error was invalid region `14:91526204-91526604`
[2016-04-15T07:06Z] 2016-04-15 00:06:53 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:06:53,431 - WARNING - Could not retrieve variants from source file in region 14:91123364-91123765. Error was invalid region `14:91123365-91123765`
[2016-04-15T07:06Z] 2016-04-15 00:06:53 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:06:53,602 - WARNING - Could not retrieve variants from source file in region 14:92908862-92920561. Error was invalid region `14:92908863-92920561`
[2016-04-15T07:06Z] 2016-04-15 00:06:53 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:06:53,675 - WARNING - Could not retrieve variants from source file in region 14:93994743-94007265. Error was invalid region `14:93994744-94007265`
[2016-04-15T07:06Z] 2016-04-15 00:06:53 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:06:53,681 - WARNING - Could not retrieve variants from source file in region 14:96829079-96829480. Error was invalid region `14:96829080-96829480`
[2016-04-15T07:06Z] 2016-04-15 00:06:53 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:06:53,885 - WARNING - Could not retrieve variants from source file in region 14:93276443-93276844. Error was invalid region `14:93276444-93276844`
[2016-04-15T07:06Z] 2016-04-15 00:06:56 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:06:56,318 - WARNING - Could not retrieve variants from source file in region 14:94566464-94582320. Error was invalid region `14:94566465-94582320`
[2016-04-15T07:06Z] 2016-04-15 00:06:57 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:06:57,649 - WARNING - Could not retrieve variants from source file in region 14:92083793-92088206. Error was invalid region `14:92083794-92088206`
[2016-04-15T07:06Z] 2016-04-15 00:06:58 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:06:58,881 - WARNING - Could not retrieve variants from source file in region 14:91681710-91682111. Error was invalid region `14:91681711-91682111`
[2016-04-15T07:06Z] 2016-04-15 00:06:59 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:06:59,871 - WARNING - Could not retrieve variants from source file in region 14:94391488-94431068. Error was invalid region `14:94391489-94431068`
[2016-04-15T07:07Z] 2016-04-15 00:07:00 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:07:00,945 - WARNING - Could not retrieve variants from source file in region 14:96922541-96944997. Error was invalid region `14:96922542-96944997`
[2016-04-15T07:07Z] 2016-04-15 00:07:00 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:07:00,947 - WARNING - Could not retrieve variants from source file in region 14:92908862-92920561. Error was invalid region `14:92908863-92920561`
[2016-04-15T07:07Z] 2016-04-15 00:07:01 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:07:01,306 - WARNING - Could not retrieve variants from source file in region 14:96829079-96829480. Error was invalid region `14:96829080-96829480`
[2016-04-15T07:07Z] 2016-04-15 00:07:01 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:07:01,442 - WARNING - Could not retrieve variants from source file in region 14:93276443-93276844. Error was invalid region `14:93276444-93276844`
[2016-04-15T07:07Z] 2016-04-15 00:07:01 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:07:01,489 - WARNING - Could not retrieve variants from source file in region 14:93117827-93118859. Error was invalid region `14:93117828-93118859`
[2016-04-15T07:07Z] 2016-04-15 00:07:01 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:07:01,513 - WARNING - Could not retrieve variants from source file in region 14:97000129-97000530. Error was invalid region `14:97000130-97000530`
[2016-04-15T07:07Z] 2016-04-15 00:07:01 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:07:01,600 - WARNING - Could not retrieve variants from source file in region 14:94566464-94582320. Error was invalid region `14:94566465-94582320`
[2016-04-15T07:07Z] 2016-04-15 00:07:01 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:07:01,614 - WARNING - Could not retrieve variants from source file in region 14:93994743-94007265. Error was invalid region `14:93994744-94007265`
[2016-04-15T07:07Z] 2016-04-15 00:07:02 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:07:02,102 - WARNING - Could not retrieve variants from source file in region 14:92083793-92088206. Error was invalid region `14:92083794-92088206`
[2016-04-15T07:07Z] 2016-04-15 00:07:04 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:07:04,044 - WARNING - Could not retrieve variants from source file in region 14:91681710-91682111. Error was invalid region `14:91681711-91682111`
[2016-04-15T07:07Z] 2016-04-15 00:07:04 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:07:04,957 - WARNING - Could not retrieve variants from source file in region 14:97299642-97300043. Error was invalid region `14:97299643-97300043`
[2016-04-15T07:07Z] 2016-04-15 00:07:07 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:07:07,165 - WARNING - Could not retrieve variants from source file in region 14:94391488-94431068. Error was invalid region `14:94391489-94431068`
[2016-04-15T07:07Z] 2016-04-15 00:07:07 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:07:07,355 - WARNING - Could not retrieve variants from source file in region 14:95884112-95923860. Error was invalid region `14:95884113-95923860`
[2016-04-15T07:07Z] 2016-04-15 00:07:08 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:07:08,049 - WARNING - Could not retrieve variants from source file in region 14:91123364-91123765. Error was invalid region `14:91123365-91123765`
[2016-04-15T07:07Z] 2016-04-15 00:07:08 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:07:08,057 - WARNING - Could not retrieve variants from source file in region 14:96922541-96944997. Error was invalid region `14:96922542-96944997`
[2016-04-15T07:07Z] 2016-04-15 00:07:08 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:07:08,512 - WARNING - Could not retrieve variants from source file in region 14:92908862-92920561. Error was invalid region `14:92908863-92920561`
[2016-04-15T07:07Z] 2016-04-15 00:07:08 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:07:08,935 - WARNING - Could not retrieve variants from source file in region 14:93276443-93276844. Error was invalid region `14:93276444-93276844`
[2016-04-15T07:07Z] 2016-04-15 00:07:09 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:07:09,217 - WARNING - Could not retrieve variants from source file in region 14:93994743-94007265. Error was invalid region `14:93994744-94007265`
[2016-04-15T07:07Z] 2016-04-15 00:07:09 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:07:09,236 - WARNING - Could not retrieve variants from source file in region 14:96829079-96829480. Error was invalid region `14:96829080-96829480`
[2016-04-15T07:07Z] 2016-04-15 00:07:19 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:07:19,696 - WARNING - Could not retrieve variants from source file in region 14:91636184-91636722. Error was invalid region `14:91636185-91636722`
[2016-04-15T07:07Z] 2016-04-15 00:07:22 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:07:22,448 - WARNING - Could not retrieve variants from source file in region 14:94492656-94524406. Error was invalid region `14:94492657-94524406`
[2016-04-15T07:07Z] 2016-04-15 00:07:22 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:07:22,678 - WARNING - Could not retrieve variants from source file in region 14:92950847-92951390. Error was invalid region `14:92950848-92951390`
[2016-04-15T07:07Z] 2016-04-15 00:07:23 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:07:23,324 - WARNING - Could not retrieve variants from source file in region 14:94245438-94245842. Error was invalid region `14:94245439-94245842`
[2016-04-15T07:07Z] 2016-04-15 00:07:23 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:07:23,618 - WARNING - Could not retrieve variants from source file in region 14:91084127-91084528. Error was invalid region `14:91084128-91084528`
[2016-04-15T07:07Z] 2016-04-15 00:07:23 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:07:23,707 - WARNING - Could not retrieve variants from source file in region 14:92950847-92951390. Error was invalid region `14:92950848-92951390`
[2016-04-15T07:07Z] 2016-04-15 00:07:23 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:07:23,821 - WARNING - Could not retrieve variants from source file in region 14:91161651-91162052. Error was invalid region `14:91161652-91162052`
[2016-04-15T07:07Z] 2016-04-15 00:07:24 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:07:24,197 - WARNING - Could not retrieve variants from source file in region 14:91636184-91636722. Error was invalid region `14:91636185-91636722`
[2016-04-15T07:07Z] 2016-04-15 00:07:25 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:07:25,361 - WARNING - Could not retrieve variants from source file in region 14:92792044-92792445. Error was invalid region `14:92792045-92792445`
[2016-04-15T07:07Z] 2016-04-15 00:07:26 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:07:26,673 - WARNING - Could not retrieve variants from source file in region 14:93154326-93178381. Error was invalid region `14:93154327-93178381`
[2016-04-15T07:07Z] 2016-04-15 00:07:27 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:07:27,489 - WARNING - Could not retrieve variants from source file in region 14:93943787-93944188. Error was invalid region `14:93943788-93944188`
[2016-04-15T07:07Z] 2016-04-15 00:07:27 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:07:27,805 - WARNING - Could not retrieve variants from source file in region 14:96771748-96797914. Error was invalid region `14:96771749-96797914`
[2016-04-15T07:07Z] 2016-04-15 00:07:28 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:07:28,732 - WARNING - Could not retrieve variants from source file in region 14:91947832-91948233. Error was invalid region `14:91947833-91948233`
[2016-04-15T07:07Z] 2016-04-15 00:07:30 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:07:30,208 - WARNING - Could not retrieve variants from source file in region 14:95659536-95669564. Error was invalid region `14:95659537-95669564`
[2016-04-15T07:07Z] 2016-04-15 00:07:30 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:07:30,493 - WARNING - Could not retrieve variants from source file in region 14:91084127-91084528. Error was invalid region `14:91084128-91084528`
[2016-04-15T07:07Z] 2016-04-15 00:07:30 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:07:30,521 - WARNING - Could not retrieve variants from source file in region 14:91636184-91636722. Error was invalid region `14:91636185-91636722`
[2016-04-15T07:07Z] 2016-04-15 00:07:30 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:07:30,570 - WARNING - Could not retrieve variants from source file in region 14:94245438-94245842. Error was invalid region `14:94245439-94245842`
[2016-04-15T07:07Z] 2016-04-15 00:07:30 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:07:30,984 - WARNING - Could not retrieve variants from source file in region 14:92792044-92792445. Error was invalid region `14:92792045-92792445`
[2016-04-15T07:07Z] 2016-04-15 00:07:32 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:07:32,928 - WARNING - Could not retrieve variants from source file in region 14:96771748-96797914. Error was invalid region `14:96771749-96797914`
[2016-04-15T07:07Z] 2016-04-15 00:07:32 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:07:32,954 - WARNING - Could not retrieve variants from source file in region 14:93943787-93944188. Error was invalid region `14:93943788-93944188`
[2016-04-15T07:07Z] 2016-04-15 00:07:33 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:07:33,497 - WARNING - Could not retrieve variants from source file in region 14:91947832-91948233. Error was invalid region `14:91947833-91948233`
[2016-04-15T07:07Z] 2016-04-15 00:07:34 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:07:34,172 - WARNING - Could not retrieve variants from source file in region 14:91882918-91883319. Error was invalid region `14:91882919-91883319`
[2016-04-15T07:07Z] 2016-04-15 00:07:35 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:07:35,237 - WARNING - Could not retrieve variants from source file in region 14:96156976-96179154. Error was invalid region `14:96156977-96179154`
[2016-04-15T07:07Z] 2016-04-15 00:07:36 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:07:36,508 - WARNING - Could not retrieve variants from source file in region 14:91084127-91084528. Error was invalid region `14:91084128-91084528`
[2016-04-15T07:07Z] 2016-04-15 00:07:37 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:07:37,809 - WARNING - Could not retrieve variants from source file in region 14:94245438-94245842. Error was invalid region `14:94245439-94245842`
[2016-04-15T07:07Z] 2016-04-15 00:07:37 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:07:37,955 - WARNING - Could not retrieve variants from source file in region 14:91161651-91162052. Error was invalid region `14:91161652-91162052`
[2016-04-15T07:07Z] 2016-04-15 00:07:38 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:07:38,474 - WARNING - Could not retrieve variants from source file in region 14:92792044-92792445. Error was invalid region `14:92792045-92792445`
[2016-04-15T07:07Z] 2016-04-15 00:07:39 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:07:39,448 - WARNING - Could not retrieve variants from source file in region 14:96771748-96797914. Error was invalid region `14:96771749-96797914`
[2016-04-15T07:07Z] 2016-04-15 00:07:39 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:07:39,742 - WARNING - Could not retrieve variants from source file in region 14:93943787-93944188. Error was invalid region `14:93943788-93944188`
[2016-04-15T07:07Z] 2016-04-15 00:07:40 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:07:40,333 - WARNING - Could not retrieve variants from source file in region 14:94187621-94188022. Error was invalid region `14:94187622-94188022`
[2016-04-15T07:07Z] 2016-04-15 00:07:46 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:07:46,940 - WARNING - Could not retrieve variants from source file in region 14:94187621-94188022. Error was invalid region `14:94187622-94188022`
[2016-04-15T07:07Z] 2016-04-15 00:07:51 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:07:51,733 - WARNING - Could not retrieve variants from source file in region 14:95235993-95236394. Error was invalid region `14:95235994-95236394`
[2016-04-15T07:07Z] 2016-04-15 00:07:52 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:07:52,251 - WARNING - Could not retrieve variants from source file in region 14:94187621-94188022. Error was invalid region `14:94187622-94188022`
[2016-04-15T07:07Z] 2016-04-15 00:07:52 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:07:52,402 - WARNING - Could not retrieve variants from source file in region 14:90864336-90864798. Error was invalid region `14:90864337-90864798`
[2016-04-15T07:07Z] 2016-04-15 00:07:52 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:07:52,525 - WARNING - Could not retrieve variants from source file in region 14:94088376-94103792. Error was invalid region `14:94088377-94103792`
[2016-04-15T07:07Z] 2016-04-15 00:07:53 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:07:53,291 - WARNING - Could not retrieve variants from source file in region 14:92587791-92588192. Error was invalid region `14:92587792-92588192`
[2016-04-15T07:07Z] 2016-04-15 00:07:57 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:07:57,254 - WARNING - Could not retrieve variants from source file in region 14:90864336-90864798. Error was invalid region `14:90864337-90864798`
[2016-04-15T07:07Z] 2016-04-15 00:07:57 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:07:57,439 - WARNING - Could not retrieve variants from source file in region 14:94088376-94103792. Error was invalid region `14:94088377-94103792`
[2016-04-15T07:07Z] 2016-04-15 00:07:58 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:07:58,324 - WARNING - Could not retrieve variants from source file in region 14:93799010-93799411. Error was invalid region `14:93799011-93799411`
[2016-04-15T07:07Z] 2016-04-15 00:07:58 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:07:58,457 - WARNING - Could not retrieve variants from source file in region 14:92587791-92588192. Error was invalid region `14:92587792-92588192`
[2016-04-15T07:07Z] 2016-04-15 00:07:59 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:07:59,092 - WARNING - Could not retrieve variants from source file in region 14:94088376-94103792. Error was invalid region `14:94088377-94103792`
[2016-04-15T07:08Z] 2016-04-15 00:08:03 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:08:03,175 - WARNING - Could not retrieve variants from source file in region 14:90864336-90864798. Error was invalid region `14:90864337-90864798`
[2016-04-15T07:08Z] 2016-04-15 00:08:03 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:08:03,852 - WARNING - Could not retrieve variants from source file in region 14:94844632-94849391. Error was invalid region `14:94844633-94849391`
[2016-04-15T07:08Z] 2016-04-15 00:08:04 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:08:04,043 - WARNING - Could not retrieve variants from source file in region 14:92587791-92588192. Error was invalid region `14:92587792-92588192`
[2016-04-15T07:08Z] 2016-04-15 00:08:08 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:08:08,484 - WARNING - Could not retrieve variants from source file in region 14:94844632-94849391. Error was invalid region `14:94844633-94849391`
[2016-04-15T07:08Z] 2016-04-15 00:08:08 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:08:08,763 - WARNING - Could not retrieve variants from source file in region 14:92347469-92347870. Error was invalid region `14:92347470-92347870`
[2016-04-15T07:08Z] 2016-04-15 00:08:12 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:08:12,862 - WARNING - Could not retrieve variants from source file in region 14:92347469-92347870. Error was invalid region `14:92347470-92347870`
[2016-04-15T07:08Z] 2016-04-15 00:08:13 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:08:13,115 - WARNING - Could not retrieve variants from source file in region 14:92268404-92268805. Error was invalid region `14:92268405-92268805`
[2016-04-15T07:08Z] 2016-04-15 00:08:16 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:08:16,054 - WARNING - Could not retrieve variants from source file in region 14:92268404-92268805. Error was invalid region `14:92268405-92268805`
[2016-04-15T07:08Z] 2016-04-15 00:08:16 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:08:16,132 - WARNING - Could not retrieve variants from source file in region 14:92440855-92441256. Error was invalid region `14:92440856-92441256`
[2016-04-15T07:08Z] 2016-04-15 00:08:16 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:08:16,636 - WARNING - Could not retrieve variants from source file in region 14:90389903-90399097. Error was invalid region `14:90389904-90399097`
[2016-04-15T07:08Z] 2016-04-15 00:08:16 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:08:16,748 - WARNING - Could not retrieve variants from source file in region 14:88651751-88652579. Error was invalid region `14:88651752-88652579`
[2016-04-15T07:08Z] 2016-04-15 00:08:17 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:08:17,321 - WARNING - Could not retrieve variants from source file in region 14:92347469-92347870. Error was invalid region `14:92347470-92347870`
[2016-04-15T07:08Z] 2016-04-15 00:08:17 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:08:17,394 - WARNING - Could not retrieve variants from source file in region 14:92268404-92268805. Error was invalid region `14:92268405-92268805`
[2016-04-15T07:08Z] 2016-04-15 00:08:21 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:08:21,095 - WARNING - Could not retrieve variants from source file in region 14:92440855-92441256. Error was invalid region `14:92440856-92441256`
[2016-04-15T07:08Z] 2016-04-15 00:08:21 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:08:21,657 - WARNING - Could not retrieve variants from source file in region 14:89258666-89259067. Error was invalid region `14:89258667-89259067`
[2016-04-15T07:08Z] 2016-04-15 00:08:21 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:08:21,724 - WARNING - Could not retrieve variants from source file in region 14:89061087-89061488. Error was invalid region `14:89061088-89061488`
[2016-04-15T07:08Z] 2016-04-15 00:08:22 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:08:22,377 - WARNING - Could not retrieve variants from source file in region 14:90526747-90527148. Error was invalid region `14:90526748-90527148`
[2016-04-15T07:08Z] 2016-04-15 00:08:22 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:08:22,401 - WARNING - Could not retrieve variants from source file in region 14:90526747-90527148. Error was invalid region `14:90526748-90527148`
[2016-04-15T07:08Z] 2016-04-15 00:08:22 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:08:22,946 - WARNING - Could not retrieve variants from source file in region 14:90389903-90399097. Error was invalid region `14:90389904-90399097`
[2016-04-15T07:08Z] 2016-04-15 00:08:30 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:08:30,850 - WARNING - Could not retrieve variants from source file in region 14:86087845-86089505. Error was invalid region `14:86087846-86089505`
[2016-04-15T07:08Z] 2016-04-15 00:08:31 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:08:31,045 - WARNING - Could not retrieve variants from source file in region 14:88935714-88946812. Error was invalid region `14:88935715-88946812`
[2016-04-15T07:08Z] 2016-04-15 00:08:33 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:08:33,160 - WARNING - Could not retrieve variants from source file in region 14:88693514-88693915. Error was invalid region `14:88693515-88693915`
[2016-04-15T07:08Z] 2016-04-15 00:08:33 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:08:33,271 - WARNING - Could not retrieve variants from source file in region 14:81728077-81744926. Error was invalid region `14:81728078-81744926`
[2016-04-15T07:08Z] 2016-04-15 00:08:35 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:08:35,313 - WARNING - Could not retrieve variants from source file in region 14:86087845-86089505. Error was invalid region `14:86087846-86089505`
[2016-04-15T07:08Z] 2016-04-15 00:08:36 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:08:36,969 - WARNING - Could not retrieve variants from source file in region 14:88693514-88693915. Error was invalid region `14:88693515-88693915`
[2016-04-15T07:08Z] ['bcbio-variation-recall', 'square', '-Xms750m', '-Xmx7280m', '-XX:+UseSerialGC', '-c', 16, '-r', u'14:97304099-107349540', '--caller', 'platypus', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/14/Batch1-14_97304098_107349540.vcf.gz', '/mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/14/Batch1-14_97304098_107349540.vcf-inputs.txt'] in region: 14:97304099-107349540
[2016-04-15T07:08Z] 2016-04-15 00:08:51 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:08:51,957 - WARNING - Could not retrieve variants from source file in region 14:103934277-103934678. Error was invalid region `14:103934278-103934678`
[2016-04-15T07:08Z] 2016-04-15 00:08:54 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:08:54,527 - WARNING - Could not retrieve variants from source file in region 14:104464826-104465227. Error was invalid region `14:104464827-104465227`
[2016-04-15T07:08Z] 2016-04-15 00:08:54 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:08:54,889 - WARNING - Could not retrieve variants from source file in region 14:103566574-103602468. Error was invalid region `14:103566575-103602468`
[2016-04-15T07:08Z] 2016-04-15 00:08:55 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:08:55,629 - WARNING - Could not retrieve variants from source file in region 14:105459713-105478292. Error was invalid region `14:105459714-105478292`
[2016-04-15T07:08Z] 2016-04-15 00:08:56 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:08:56,516 - WARNING - Could not retrieve variants from source file in region 14:102322882-102323283. Error was invalid region `14:102322883-102323283`
[2016-04-15T07:08Z] 2016-04-15 00:08:56 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:08:56,665 - WARNING - Could not retrieve variants from source file in region 14:105520464-105520865. Error was invalid region `14:105520465-105520865`
[2016-04-15T07:08Z] 2016-04-15 00:08:57 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:08:57,182 - WARNING - Could not retrieve variants from source file in region 14:103934277-103934678. Error was invalid region `14:103934278-103934678`
[2016-04-15T07:08Z] 2016-04-15 00:08:59 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:08:59,706 - WARNING - Could not retrieve variants from source file in region 14:104464826-104465227. Error was invalid region `14:104464827-104465227`
[2016-04-15T07:09Z] 2016-04-15 00:09:01 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:09:01,950 - WARNING - Could not retrieve variants from source file in region 14:105916209-105962559. Error was invalid region `14:105916210-105962559`
[2016-04-15T07:09Z] 2016-04-15 00:09:02 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:09:02,710 - WARNING - Could not retrieve variants from source file in region 14:103523387-103523788. Error was invalid region `14:103523388-103523788`
[2016-04-15T07:09Z] 2016-04-15 00:09:03 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:09:03,744 - WARNING - Could not retrieve variants from source file in region 14:105995838-105996242. Error was invalid region `14:105995839-105996242`
[2016-04-15T07:09Z] 2016-04-15 00:09:03 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:09:03,783 - WARNING - Could not retrieve variants from source file in region 14:105459713-105478292. Error was invalid region `14:105459714-105478292`
[2016-04-15T07:09Z] 2016-04-15 00:09:03 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:09:03,913 - WARNING - Could not retrieve variants from source file in region 14:105714056-105714457. Error was invalid region `14:105714057-105714457`
[2016-04-15T07:09Z] 2016-04-15 00:09:04 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:09:04,341 - WARNING - Could not retrieve variants from source file in region 14:105520464-105520865. Error was invalid region `14:105520465-105520865`
[2016-04-15T07:09Z] 2016-04-15 00:09:04 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:09:04,841 - WARNING - Could not retrieve variants from source file in region 14:105267368-105268891. Error was invalid region `14:105267369-105268891`
[2016-04-15T07:09Z] 2016-04-15 00:09:05 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:09:05,178 - WARNING - Could not retrieve variants from source file in region 14:103934277-103934678. Error was invalid region `14:103934278-103934678`
[2016-04-15T07:09Z] 2016-04-15 00:09:05 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:09:05,243 - WARNING - Could not retrieve variants from source file in region 14:105344082-105354483. Error was invalid region `14:105344083-105354483`
[2016-04-15T07:09Z] 2016-04-15 00:09:05 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:09:05,264 - WARNING - Could not retrieve variants from source file in region 14:104464826-104465227. Error was invalid region `14:104464827-104465227`
[2016-04-15T07:09Z] 2016-04-15 00:09:07 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:09:07,384 - WARNING - Could not retrieve variants from source file in region 14:105916209-105962559. Error was invalid region `14:105916210-105962559`
[2016-04-15T07:09Z] 2016-04-15 00:09:08 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:09:08,782 - WARNING - Could not retrieve variants from source file in region 14:103523387-103523788. Error was invalid region `14:103523388-103523788`
[2016-04-15T07:09Z] 2016-04-15 00:09:09 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:09:09,735 - WARNING - Could not retrieve variants from source file in region 14:105995838-105996242. Error was invalid region `14:105995839-105996242`
[2016-04-15T07:09Z] 2016-04-15 00:09:11 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:09:11,027 - WARNING - Could not retrieve variants from source file in region 14:105714056-105714457. Error was invalid region `14:105714057-105714457`
[2016-04-15T07:09Z] 2016-04-15 00:09:11 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:09:11,299 - WARNING - Could not retrieve variants from source file in region 14:105459713-105478292. Error was invalid region `14:105459714-105478292`
[2016-04-15T07:09Z] 2016-04-15 00:09:11 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:09:11,515 - WARNING - Could not retrieve variants from source file in region 14:102322882-102323283. Error was invalid region `14:102322883-102323283`
[2016-04-15T07:09Z] 2016-04-15 00:09:11 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:09:11,929 - WARNING - Could not retrieve variants from source file in region 14:105267368-105268891. Error was invalid region `14:105267369-105268891`
[2016-04-15T07:09Z] 2016-04-15 00:09:13 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:09:13,198 - WARNING - Could not retrieve variants from source file in region 14:105520464-105520865. Error was invalid region `14:105520465-105520865`
[2016-04-15T07:09Z] 2016-04-15 00:09:22 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:09:22,908 - WARNING - Could not retrieve variants from source file in region 14:100794928-100809035. Error was invalid region `14:100794929-100809035`
[2016-04-15T07:09Z] 2016-04-15 00:09:23 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:09:23,637 - WARNING - Could not retrieve variants from source file in region 14:105221826-105238901. Error was invalid region `14:105221827-105238901`
[2016-04-15T07:09Z] 2016-04-15 00:09:24 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:09:24,720 - WARNING - Could not retrieve variants from source file in region 14:104429242-104429643. Error was invalid region `14:104429243-104429643`
[2016-04-15T07:09Z] 2016-04-15 00:09:26 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:09:26,692 - WARNING - Could not retrieve variants from source file in region 14:105054907-105070981. Error was invalid region `14:105054908-105070981`
[2016-04-15T07:09Z] 2016-04-15 00:09:27 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:09:27,760 - WARNING - Could not retrieve variants from source file in region 14:100794928-100809035. Error was invalid region `14:100794929-100809035`
[2016-04-15T07:09Z] 2016-04-15 00:09:28 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:09:28,449 - WARNING - Could not retrieve variants from source file in region 14:105221826-105238901. Error was invalid region `14:105221827-105238901`
[2016-04-15T07:09Z] 2016-04-15 00:09:29 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:09:29,021 - WARNING - Could not retrieve variants from source file in region 14:104574999-104577321. Error was invalid region `14:104575000-104577321`
[2016-04-15T07:09Z] 2016-04-15 00:09:29 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:09:29,126 - WARNING - Could not retrieve variants from source file in region 14:104429242-104429643. Error was invalid region `14:104429243-104429643`
[2016-04-15T07:09Z] 2016-04-15 00:09:29 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:09:29,993 - WARNING - Could not retrieve variants from source file in region 14:103410765-103411166. Error was invalid region `14:103410766-103411166`
[2016-04-15T07:09Z] 2016-04-15 00:09:30 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:09:30,826 - WARNING - Could not retrieve variants from source file in region 14:102275994-102276396. Error was invalid region `14:102275995-102276396`
[2016-04-15T07:09Z] 2016-04-15 00:09:32 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:09:32,468 - WARNING - Could not retrieve variants from source file in region 14:105609124-105642328. Error was invalid region `14:105609125-105642328`
[2016-04-15T07:09Z] 2016-04-15 00:09:32 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:09:32,488 - WARNING - Could not retrieve variants from source file in region 14:103059009-103059410. Error was invalid region `14:103059010-103059410`
[2016-04-15T07:09Z] 2016-04-15 00:09:32 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:09:32,507 - WARNING - Could not retrieve variants from source file in region 14:100794928-100809035. Error was invalid region `14:100794929-100809035`
[2016-04-15T07:09Z] 2016-04-15 00:09:33 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:09:33,997 - WARNING - Could not retrieve variants from source file in region 14:105221826-105238901. Error was invalid region `14:105221827-105238901`
[2016-04-15T07:09Z] 2016-04-15 00:09:34 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:09:34,025 - WARNING - Could not retrieve variants from source file in region 14:104429242-104429643. Error was invalid region `14:104429243-104429643`
[2016-04-15T07:09Z] 2016-04-15 00:09:34 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:09:34,312 - WARNING - Could not retrieve variants from source file in region 14:104574999-104577321. Error was invalid region `14:104575000-104577321`
[2016-04-15T07:09Z] 2016-04-15 00:09:35 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:09:35,082 - WARNING - Could not retrieve variants from source file in region 14:103440262-103440808. Error was invalid region `14:103440263-103440808`
[2016-04-15T07:09Z] 2016-04-15 00:09:37 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:09:37,515 - WARNING - Could not retrieve variants from source file in region 14:103059009-103059410. Error was invalid region `14:103059010-103059410`
[2016-04-15T07:09Z] 2016-04-15 00:09:39 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:09:39,693 - WARNING - Could not retrieve variants from source file in region 14:104574999-104577321. Error was invalid region `14:104575000-104577321`
[2016-04-15T07:09Z] 2016-04-15 00:09:45 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:09:45,291 - WARNING - Could not retrieve variants from source file in region 14:101346826-101350860. Error was invalid region `14:101346827-101350860`
[2016-04-15T07:09Z] 2016-04-15 00:09:45 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:09:45,386 - WARNING - Could not retrieve variants from source file in region 14:100069531-100069932. Error was invalid region `14:100069532-100069932`
[2016-04-15T07:09Z] 2016-04-15 00:09:45 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:09:45,822 - WARNING - Could not retrieve variants from source file in region 14:101198206-101200835. Error was invalid region `14:101198207-101200835`
[2016-04-15T07:09Z] 2016-04-15 00:09:45 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:09:45,956 - WARNING - Could not retrieve variants from source file in region 14:100615454-100626092. Error was invalid region `14:100615455-100626092`
[2016-04-15T07:09Z] 2016-04-15 00:09:48 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:09:48,930 - WARNING - Could not retrieve variants from source file in region 14:104500090-104500491. Error was invalid region `14:104500091-104500491`
[2016-04-15T07:09Z] 2016-04-15 00:09:49 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:09:49,504 - WARNING - Could not retrieve variants from source file in region 14:100069531-100069932. Error was invalid region `14:100069532-100069932`
[2016-04-15T07:09Z] 2016-04-15 00:09:50 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:09:50,220 - WARNING - Could not retrieve variants from source file in region 14:101198206-101200835. Error was invalid region `14:101198207-101200835`
[2016-04-15T07:09Z] 2016-04-15 00:09:51 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:09:51,708 - WARNING - Could not retrieve variants from source file in region 14:100996101-101005752. Error was invalid region `14:100996102-101005752`
[2016-04-15T07:09Z] 2016-04-15 00:09:52 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:09:52,219 - WARNING - Could not retrieve variants from source file in region 14:100842688-100848120. Error was invalid region `14:100842689-100848120`
[2016-04-15T07:09Z] 2016-04-15 00:09:52 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:09:52,888 - WARNING - Could not retrieve variants from source file in region 14:104193985-104205313. Error was invalid region `14:104193986-104205313`
[2016-04-15T07:09Z] 2016-04-15 00:09:53 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:09:53,487 - WARNING - Could not retrieve variants from source file in region 14:97321478-97321879. Error was invalid region `14:97321479-97321879`
[2016-04-15T07:09Z] 2016-04-15 00:09:53 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:09:53,613 - WARNING - Could not retrieve variants from source file in region 14:100069531-100069932. Error was invalid region `14:100069532-100069932`
[2016-04-15T07:09Z] 2016-04-15 00:09:55 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:09:55,796 - WARNING - Could not retrieve variants from source file in region 14:100996101-101005752. Error was invalid region `14:100996102-101005752`
[2016-04-15T07:09Z] 2016-04-15 00:09:56 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:09:56,446 - WARNING - Could not retrieve variants from source file in region 14:100842688-100848120. Error was invalid region `14:100842689-100848120`
[2016-04-15T07:09Z] 2016-04-15 00:09:57 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:09:57,574 - WARNING - Could not retrieve variants from source file in region 14:97321478-97321879. Error was invalid region `14:97321479-97321879`
[2016-04-15T07:10Z] 2016-04-15 00:10:04 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:10:04,922 - WARNING - Could not retrieve variants from source file in region 14:104028059-104029639. Error was invalid region `14:104028060-104029639`
[2016-04-15T07:10Z] 2016-04-15 00:10:05 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:10:05,239 - WARNING - Could not retrieve variants from source file in region 14:100380737-100381138. Error was invalid region `14:100380738-100381138`
[2016-04-15T07:10Z] 2016-04-15 00:10:06 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:10:06,567 - WARNING - Could not retrieve variants from source file in region 14:102550592-102568557. Error was invalid region `14:102550593-102568557`
[2016-04-15T07:10Z] 2016-04-15 00:10:06 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:10:06,646 - WARNING - Could not retrieve variants from source file in region 14:102378679-102379080. Error was invalid region `14:102378680-102379080`
[2016-04-15T07:10Z] 2016-04-15 00:10:07 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:10:07,307 - WARNING - Could not retrieve variants from source file in region 14:104028059-104029639. Error was invalid region `14:104028060-104029639`
[2016-04-15T07:10Z] 2016-04-15 00:10:10 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:10:10,007 - WARNING - Could not retrieve variants from source file in region 14:102550592-102568557. Error was invalid region `14:102550593-102568557`
[2016-04-15T07:10Z] 2016-04-15 00:10:10 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:10:10,025 - WARNING - Could not retrieve variants from source file in region 14:102378679-102379080. Error was invalid region `14:102378680-102379080`
[2016-04-15T07:10Z] 2016-04-15 00:10:10 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:10:10,438 - WARNING - Could not retrieve variants from source file in region 14:103986044-103996586. Error was invalid region `14:103986045-103996586`
[2016-04-15T07:10Z] 2016-04-15 00:10:11 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:10:11,100 - WARNING - Could not retrieve variants from source file in region 14:103986044-103996586. Error was invalid region `14:103986045-103996586`
[2016-04-15T07:10Z] 2016-04-15 00:10:11 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:10:11,129 - WARNING - Could not retrieve variants from source file in region 14:102550592-102568557. Error was invalid region `14:102550593-102568557`
[2016-04-15T07:10Z] ['bcbio-variation-recall', 'square', '-Xms750m', '-Xmx7280m', '-XX:+UseSerialGC', '-c', 16, '-r', u'15:1-20740485', '--caller', 'platypus', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/15/Batch1-15_0_20740485.vcf.gz', '/mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/15/Batch1-15_0_20740485.vcf-inputs.txt'] in region: 15:1-20740485
[2016-04-15T07:10Z] 2016-04-15 00:10:22 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:10:22,083 - WARNING - Could not retrieve variants from source file in region 15:20739674-20740442. Error was invalid region `15:20739675-20740442`
[2016-04-15T07:10Z] 2016-04-15 00:10:22 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:10:22,075 - WARNING - Could not retrieve variants from source file in region 15:20739674-20740442. Error was invalid region `15:20739675-20740442`
[2016-04-15T07:10Z] 2016-04-15 00:10:22 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:10:22,131 - WARNING - Could not retrieve variants from source file in region 15:20739674-20740442. Error was invalid region `15:20739675-20740442`
[2016-04-15T07:10Z] ['bcbio-variation-recall', 'square', '-Xms750m', '-Xmx7280m', '-XX:+UseSerialGC', '-c', 16, '-r', u'15:20741622-36872162', '--caller', 'platypus', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/15/Batch1-15_20741621_36872162.vcf.gz', '/mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/15/Batch1-15_20741621_36872162.vcf-inputs.txt'] in region: 15:20741622-36872162
[2016-04-15T07:10Z] 2016-04-15 00:10:38 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:10:38,577 - WARNING - Could not retrieve variants from source file in region 15:34112799-34137390. Error was invalid region `15:34112800-34137390`
[2016-04-15T07:10Z] 2016-04-15 00:10:38 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:10:38,896 - WARNING - Could not retrieve variants from source file in region 15:33871966-33872367. Error was invalid region `15:33871967-33872367`
[2016-04-15T07:10Z] 2016-04-15 00:10:39 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:10:39,224 - WARNING - Could not retrieve variants from source file in region 15:22527391-22527853. Error was invalid region `15:22527392-22527853`
[2016-04-15T07:10Z] 2016-04-15 00:10:39 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:10:39,389 - WARNING - Could not retrieve variants from source file in region 15:23811381-23811782. Error was invalid region `15:23811382-23811782`
[2016-04-15T07:10Z] 2016-04-15 00:10:39 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:10:39,395 - WARNING - Could not retrieve variants from source file in region 15:35148797-35149198. Error was invalid region `15:35148798-35149198`
[2016-04-15T07:10Z] 2016-04-15 00:10:39 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:10:39,616 - WARNING - Could not retrieve variants from source file in region 15:22921344-22969422. Error was invalid region `15:22921345-22969422`
[2016-04-15T07:10Z] 2016-04-15 00:10:39 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:10:39,635 - WARNING - Could not retrieve variants from source file in region 15:25924328-25926376. Error was invalid region `15:25924329-25926376`
[2016-04-15T07:10Z] 2016-04-15 00:10:40 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:10:40,055 - WARNING - Could not retrieve variants from source file in region 15:33357051-33381190. Error was invalid region `15:33357052-33381190`
[2016-04-15T07:10Z] 2016-04-15 00:10:40 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:10:40,211 - WARNING - Could not retrieve variants from source file in region 15:35812360-35813719. Error was invalid region `15:35812361-35813719`
[2016-04-15T07:10Z] 2016-04-15 00:10:40 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:10:40,212 - WARNING - Could not retrieve variants from source file in region 15:23052421-23052822. Error was invalid region `15:23052422-23052822`
[2016-04-15T07:10Z] 2016-04-15 00:10:40 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:10:40,245 - WARNING - Could not retrieve variants from source file in region 15:31294443-31294844. Error was invalid region `15:31294444-31294844`
[2016-04-15T07:10Z] 2016-04-15 00:10:43 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:10:43,734 - WARNING - Could not retrieve variants from source file in region 15:30008645-30018817. Error was invalid region `15:30008646-30018817`
[2016-04-15T07:10Z] 2016-04-15 00:10:44 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:10:44,786 - WARNING - Could not retrieve variants from source file in region 15:35045065-35045502. Error was invalid region `15:35045066-35045502`
[2016-04-15T07:10Z] 2016-04-15 00:10:46 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:10:46,120 - WARNING - Could not retrieve variants from source file in region 15:22368651-22383379. Error was invalid region `15:22368652-22383379`
[2016-04-15T07:10Z] 2016-04-15 00:10:46 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:10:46,149 - WARNING - Could not retrieve variants from source file in region 15:33871966-33872367. Error was invalid region `15:33871967-33872367`
[2016-04-15T07:10Z] 2016-04-15 00:10:47 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:10:47,799 - WARNING - Could not retrieve variants from source file in region 15:35148797-35149198. Error was invalid region `15:35148798-35149198`
[2016-04-15T07:10Z] 2016-04-15 00:10:48 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:10:48,224 - WARNING - Could not retrieve variants from source file in region 15:35664087-35664488. Error was invalid region `15:35664088-35664488`
[2016-04-15T07:10Z] 2016-04-15 00:10:48 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:10:48,494 - WARNING - Could not retrieve variants from source file in region 15:23052421-23052822. Error was invalid region `15:23052422-23052822`
[2016-04-15T07:10Z] 2016-04-15 00:10:48 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:10:48,806 - WARNING - Could not retrieve variants from source file in region 15:32459983-32460384. Error was invalid region `15:32459984-32460384`
[2016-04-15T07:10Z] 2016-04-15 00:10:48 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:10:48,812 - WARNING - Could not retrieve variants from source file in region 15:35812360-35813719. Error was invalid region `15:35812361-35813719`
[2016-04-15T07:10Z] 2016-04-15 00:10:49 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:10:49,130 - WARNING - Could not retrieve variants from source file in region 15:30008645-30018817. Error was invalid region `15:30008646-30018817`
[2016-04-15T07:10Z] 2016-04-15 00:10:49 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:10:49,580 - WARNING - Could not retrieve variants from source file in region 15:34112799-34137390. Error was invalid region `15:34112800-34137390`
[2016-04-15T07:10Z] 2016-04-15 00:10:52 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:10:52,103 - WARNING - Could not retrieve variants from source file in region 15:33871966-33872367. Error was invalid region `15:33871967-33872367`
[2016-04-15T07:10Z] 2016-04-15 00:10:54 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:10:54,158 - WARNING - Could not retrieve variants from source file in region 15:35148797-35149198. Error was invalid region `15:35148798-35149198`
[2016-04-15T07:10Z] 2016-04-15 00:10:55 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:10:55,177 - WARNING - Could not retrieve variants from source file in region 15:23811381-23811782. Error was invalid region `15:23811382-23811782`
[2016-04-15T07:10Z] 2016-04-15 00:10:56 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:10:56,089 - WARNING - Could not retrieve variants from source file in region 15:35664087-35664488. Error was invalid region `15:35664088-35664488`
[2016-04-15T07:10Z] 2016-04-15 00:10:56 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:10:56,123 - WARNING - Could not retrieve variants from source file in region 15:31294443-31294844. Error was invalid region `15:31294444-31294844`
[2016-04-15T07:10Z] 2016-04-15 00:10:56 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:10:56,734 - WARNING - Could not retrieve variants from source file in region 15:23052421-23052822. Error was invalid region `15:23052422-23052822`
[2016-04-15T07:10Z] 2016-04-15 00:10:56 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:10:56,745 - WARNING - Could not retrieve variants from source file in region 15:33357051-33381190. Error was invalid region `15:33357052-33381190`
[2016-04-15T07:10Z] 2016-04-15 00:10:56 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:10:56,874 - WARNING - Could not retrieve variants from source file in region 15:35812360-35813719. Error was invalid region `15:35812361-35813719`
[2016-04-15T07:11Z] 2016-04-15 00:11:07 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:11:07,514 - WARNING - Could not retrieve variants from source file in region 15:33446668-33447137. Error was invalid region `15:33446669-33447137`
[2016-04-15T07:11Z] 2016-04-15 00:11:08 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:11:08,518 - WARNING - Could not retrieve variants from source file in region 15:29544445-29544846. Error was invalid region `15:29544446-29544846`
[2016-04-15T07:11Z] 2016-04-15 00:11:09 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:11:09,386 - WARNING - Could not retrieve variants from source file in region 15:20743585-20743986. Error was invalid region `15:20743586-20743986`
[2016-04-15T07:11Z] 2016-04-15 00:11:10 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:11:10,432 - WARNING - Could not retrieve variants from source file in region 15:28358120-28358521. Error was invalid region `15:28358121-28358521`
[2016-04-15T07:11Z] 2016-04-15 00:11:11 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:11:11,047 - WARNING - Could not retrieve variants from source file in region 15:23021027-23021428. Error was invalid region `15:23021028-23021428`
[2016-04-15T07:11Z] 2016-04-15 00:11:12 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:11:12,282 - WARNING - Could not retrieve variants from source file in region 15:33446668-33447137. Error was invalid region `15:33446669-33447137`
[2016-04-15T07:11Z] 2016-04-15 00:11:14 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:11:14,409 - WARNING - Could not retrieve variants from source file in region 15:34610753-34611154. Error was invalid region `15:34610754-34611154`
[2016-04-15T07:11Z] 2016-04-15 00:11:14 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:11:14,607 - WARNING - Could not retrieve variants from source file in region 15:32983985-32984386. Error was invalid region `15:32983986-32984386`
[2016-04-15T07:11Z] 2016-04-15 00:11:15 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:11:15,169 - WARNING - Could not retrieve variants from source file in region 15:32322718-32323119. Error was invalid region `15:32322719-32323119`
[2016-04-15T07:11Z] 2016-04-15 00:11:15 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:11:15,202 - WARNING - Could not retrieve variants from source file in region 15:25652115-25652516. Error was invalid region `15:25652116-25652516`
[2016-04-15T07:11Z] 2016-04-15 00:11:15 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:11:15,565 - WARNING - Could not retrieve variants from source file in region 15:20743585-20743986. Error was invalid region `15:20743586-20743986`
[2016-04-15T07:11Z] 2016-04-15 00:11:16 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:11:16,919 - WARNING - Could not retrieve variants from source file in region 15:33446668-33447137. Error was invalid region `15:33446669-33447137`
[2016-04-15T07:11Z] 2016-04-15 00:11:17 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:11:17,170 - WARNING - Could not retrieve variants from source file in region 15:22840068-22840469. Error was invalid region `15:22840069-22840469`
[2016-04-15T07:11Z] 2016-04-15 00:11:17 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:11:17,640 - WARNING - Could not retrieve variants from source file in region 15:31266936-31267337. Error was invalid region `15:31266937-31267337`
[2016-04-15T07:11Z] 2016-04-15 00:11:18 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:11:18,649 - WARNING - Could not retrieve variants from source file in region 15:29544445-29544846. Error was invalid region `15:29544446-29544846`
[2016-04-15T07:11Z] 2016-04-15 00:11:20 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:11:20,066 - WARNING - Could not retrieve variants from source file in region 15:32983985-32984386. Error was invalid region `15:32983986-32984386`
[2016-04-15T07:11Z] 2016-04-15 00:11:22 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:11:22,553 - WARNING - Could not retrieve variants from source file in region 15:34640007-34673912. Error was invalid region `15:34640008-34673912`
[2016-04-15T07:11Z] 2016-04-15 00:11:22 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:11:22,787 - WARNING - Could not retrieve variants from source file in region 15:20743585-20743986. Error was invalid region `15:20743586-20743986`
[2016-04-15T07:11Z] 2016-04-15 00:11:23 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:11:23,078 - WARNING - Could not retrieve variants from source file in region 15:23021027-23021428. Error was invalid region `15:23021028-23021428`
[2016-04-15T07:11Z] 2016-04-15 00:11:23 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:11:23,450 - WARNING - Could not retrieve variants from source file in region 15:28358120-28358521. Error was invalid region `15:28358121-28358521`
[2016-04-15T07:11Z] 2016-04-15 00:11:23 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:11:23,524 - WARNING - Could not retrieve variants from source file in region 15:31266936-31267337. Error was invalid region `15:31266937-31267337`
[2016-04-15T07:11Z] 2016-04-15 00:11:24 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:11:24,646 - WARNING - Could not retrieve variants from source file in region 15:34610753-34611154. Error was invalid region `15:34610754-34611154`
[2016-04-15T07:11Z] 2016-04-15 00:11:24 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:11:24,686 - WARNING - Could not retrieve variants from source file in region 15:32983985-32984386. Error was invalid region `15:32983986-32984386`
[2016-04-15T07:11Z] 2016-04-15 00:11:27 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:11:27,716 - WARNING - Could not retrieve variants from source file in region 15:32322718-32323119. Error was invalid region `15:32322719-32323119`
[2016-04-15T07:11Z] 2016-04-15 00:11:38 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:11:38,443 - WARNING - Could not retrieve variants from source file in region 15:29415349-29421244. Error was invalid region `15:29415350-29421244`
[2016-04-15T07:11Z] 2016-04-15 00:11:39 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:11:39,054 - WARNING - Could not retrieve variants from source file in region 15:33954441-33954842. Error was invalid region `15:33954442-33954842`
[2016-04-15T07:11Z] 2016-04-15 00:11:39 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:11:39,391 - WARNING - Could not retrieve variants from source file in region 15:28211710-28235963. Error was invalid region `15:28211711-28235963`
[2016-04-15T07:11Z] 2016-04-15 00:11:39 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:11:39,601 - WARNING - Could not retrieve variants from source file in region 15:33905199-33905600. Error was invalid region `15:33905200-33905600`
[2016-04-15T07:11Z] 2016-04-15 00:11:40 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:11:40,427 - WARNING - Could not retrieve variants from source file in region 15:28414454-28422799. Error was invalid region `15:28414455-28422799`
[2016-04-15T07:11Z] 2016-04-15 00:11:40 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:11:40,436 - WARNING - Could not retrieve variants from source file in region 15:28502068-28517626. Error was invalid region `15:28502069-28517626`
[2016-04-15T07:11Z] 2016-04-15 00:11:41 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:11:41,334 - WARNING - Could not retrieve variants from source file in region 15:31775793-31794120. Error was invalid region `15:31775794-31794120`
[2016-04-15T07:11Z] 2016-04-15 00:11:44 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:11:44,433 - WARNING - Could not retrieve variants from source file in region 15:23579060-23579461. Error was invalid region `15:23579061-23579461`
[2016-04-15T07:11Z] 2016-04-15 00:11:45 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:11:45,983 - WARNING - Could not retrieve variants from source file in region 15:33954441-33954842. Error was invalid region `15:33954442-33954842`
[2016-04-15T07:11Z] 2016-04-15 00:11:46 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:11:46,441 - WARNING - Could not retrieve variants from source file in region 15:28211710-28235963. Error was invalid region `15:28211711-28235963`
[2016-04-15T07:11Z] 2016-04-15 00:11:46 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:11:46,525 - WARNING - Could not retrieve variants from source file in region 15:33905199-33905600. Error was invalid region `15:33905200-33905600`
[2016-04-15T07:11Z] 2016-04-15 00:11:46 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:11:46,585 - WARNING - Could not retrieve variants from source file in region 15:30814619-30815020. Error was invalid region `15:30814620-30815020`
[2016-04-15T07:11Z] 2016-04-15 00:11:47 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:11:47,325 - WARNING - Could not retrieve variants from source file in region 15:30905783-30906184. Error was invalid region `15:30905784-30906184`
[2016-04-15T07:11Z] 2016-04-15 00:11:47 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:11:47,358 - WARNING - Could not retrieve variants from source file in region 15:24921438-24923580. Error was invalid region `15:24921439-24923580`
[2016-04-15T07:11Z] 2016-04-15 00:11:47 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:11:47,445 - WARNING - Could not retrieve variants from source file in region 15:31775793-31794120. Error was invalid region `15:31775794-31794120`
[2016-04-15T07:11Z] 2016-04-15 00:11:47 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:11:47,479 - WARNING - Could not retrieve variants from source file in region 15:28502068-28517626. Error was invalid region `15:28502069-28517626`
[2016-04-15T07:11Z] 2016-04-15 00:11:47 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:11:47,703 - WARNING - Could not retrieve variants from source file in region 15:27182146-27193315. Error was invalid region `15:27182147-27193315`
[2016-04-15T07:11Z] 2016-04-15 00:11:48 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:11:48,828 - WARNING - Could not retrieve variants from source file in region 15:34528737-34551272. Error was invalid region `15:34528738-34551272`
[2016-04-15T07:11Z] 2016-04-15 00:11:51 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:11:51,186 - WARNING - Could not retrieve variants from source file in region 15:33954441-33954842. Error was invalid region `15:33954442-33954842`
[2016-04-15T07:11Z] 2016-04-15 00:11:53 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:11:53,286 - WARNING - Could not retrieve variants from source file in region 15:33905199-33905600. Error was invalid region `15:33905200-33905600`
[2016-04-15T07:11Z] 2016-04-15 00:11:53 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:11:53,423 - WARNING - Could not retrieve variants from source file in region 15:30814619-30815020. Error was invalid region `15:30814620-30815020`
[2016-04-15T07:11Z] 2016-04-15 00:11:53 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:11:53,434 - WARNING - Could not retrieve variants from source file in region 15:31775793-31794120. Error was invalid region `15:31775794-31794120`
[2016-04-15T07:11Z] 2016-04-15 00:11:53 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:11:53,702 - WARNING - Could not retrieve variants from source file in region 15:30905783-30906184. Error was invalid region `15:30905784-30906184`
[2016-04-15T07:11Z] 2016-04-15 00:11:53 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:11:53,762 - WARNING - Could not retrieve variants from source file in region 15:28414454-28422799. Error was invalid region `15:28414455-28422799`
[2016-04-15T07:11Z] 2016-04-15 00:11:53 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:11:53,859 - WARNING - Could not retrieve variants from source file in region 15:28502068-28517626. Error was invalid region `15:28502069-28517626`
[2016-04-15T07:12Z] 2016-04-15 00:12:06 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:12:06,815 - WARNING - Could not retrieve variants from source file in region 15:28467035-28467436. Error was invalid region `15:28467036-28467436`
[2016-04-15T07:12Z] 2016-04-15 00:12:09 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:12:09,317 - WARNING - Could not retrieve variants from source file in region 15:31619396-31619797. Error was invalid region `15:31619397-31619797`
[2016-04-15T07:12Z] 2016-04-15 00:12:09 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:12:09,547 - WARNING - Could not retrieve variants from source file in region 15:30260289-30260690. Error was invalid region `15:30260290-30260690`
[2016-04-15T07:12Z] 2016-04-15 00:12:09 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:12:09,635 - WARNING - Could not retrieve variants from source file in region 15:28386415-28386816. Error was invalid region `15:28386416-28386816`
[2016-04-15T07:12Z] 2016-04-15 00:12:10 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:12:10,310 - WARNING - Could not retrieve variants from source file in region 15:27017976-27018987. Error was invalid region `15:27017977-27018987`
[2016-04-15T07:12Z] 2016-04-15 00:12:11 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:12:11,116 - WARNING - Could not retrieve variants from source file in region 15:28386415-28386816. Error was invalid region `15:28386416-28386816`
[2016-04-15T07:12Z] 2016-04-15 00:12:11 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:12:11,284 - WARNING - Could not retrieve variants from source file in region 15:23891600-23892001. Error was invalid region `15:23891601-23892001`
[2016-04-15T07:12Z] 2016-04-15 00:12:12 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:12:12,191 - WARNING - Could not retrieve variants from source file in region 15:28089962-28096728. Error was invalid region `15:28089963-28096728`
[2016-04-15T07:12Z] 2016-04-15 00:12:13 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:12:13,456 - WARNING - Could not retrieve variants from source file in region 15:30260289-30260690. Error was invalid region `15:30260290-30260690`
[2016-04-15T07:12Z] 2016-04-15 00:12:13 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:12:13,848 - WARNING - Could not retrieve variants from source file in region 15:28386415-28386816. Error was invalid region `15:28386416-28386816`
[2016-04-15T07:12Z] 2016-04-15 00:12:14 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:12:14,155 - WARNING - Could not retrieve variants from source file in region 15:31452936-31453337. Error was invalid region `15:31452937-31453337`
[2016-04-15T07:12Z] 2016-04-15 00:12:14 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:12:14,156 - WARNING - Could not retrieve variants from source file in region 15:27017976-27018987. Error was invalid region `15:27017977-27018987`
[2016-04-15T07:12Z] 2016-04-15 00:12:15 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:12:15,317 - WARNING - Could not retrieve variants from source file in region 15:30384106-30384507. Error was invalid region `15:30384107-30384507`
[2016-04-15T07:12Z] 2016-04-15 00:12:16 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:12:16,996 - WARNING - Could not retrieve variants from source file in region 15:31619396-31619797. Error was invalid region `15:31619397-31619797`
[2016-04-15T07:12Z] 2016-04-15 00:12:17 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:12:17,767 - WARNING - Could not retrieve variants from source file in region 15:27017976-27018987. Error was invalid region `15:27017977-27018987`
[2016-04-15T07:12Z] 2016-04-15 00:12:17 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:12:17,855 - WARNING - Could not retrieve variants from source file in region 15:31452936-31453337. Error was invalid region `15:31452937-31453337`
[2016-04-15T07:12Z] 2016-04-15 00:12:22 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:12:22,638 - WARNING - Could not retrieve variants from source file in region 15:30053633-30054034. Error was invalid region `15:30053634-30054034`
[2016-04-15T07:12Z] 2016-04-15 00:12:22 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:12:22,664 - WARNING - Could not retrieve variants from source file in region 15:30053633-30054034. Error was invalid region `15:30053634-30054034`
[2016-04-15T07:12Z] 2016-04-15 00:12:24 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:12:24,873 - WARNING - Could not retrieve variants from source file in region 15:31515645-31521697. Error was invalid region `15:31515646-31521697`
[2016-04-15T07:12Z] 2016-04-15 00:12:24 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:12:24,929 - WARNING - Could not retrieve variants from source file in region 15:27772465-27772866. Error was invalid region `15:27772466-27772866`
[2016-04-15T07:12Z] 2016-04-15 00:12:24 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:12:24,971 - WARNING - Could not retrieve variants from source file in region 15:25961753-25962154. Error was invalid region `15:25961754-25962154`
[2016-04-15T07:12Z] 2016-04-15 00:12:25 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:12:25,361 - WARNING - Could not retrieve variants from source file in region 15:25961753-25962154. Error was invalid region `15:25961754-25962154`
[2016-04-15T07:12Z] 2016-04-15 00:12:26 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:12:26,303 - WARNING - Could not retrieve variants from source file in region 15:25961753-25962154. Error was invalid region `15:25961754-25962154`
[2016-04-15T07:12Z] 2016-04-15 00:12:28 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:12:28,080 - WARNING - Could not retrieve variants from source file in region 15:31515645-31521697. Error was invalid region `15:31515646-31521697`
[2016-04-15T07:12Z] 2016-04-15 00:12:28 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:12:28,124 - WARNING - Could not retrieve variants from source file in region 15:27772465-27772866. Error was invalid region `15:27772466-27772866`
[2016-04-15T07:12Z] 2016-04-15 00:12:29 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:12:29,290 - WARNING - Could not retrieve variants from source file in region 15:27772465-27772866. Error was invalid region `15:27772466-27772866`
[2016-04-15T07:12Z] ['bcbio-variation-recall', 'square', '-Xms750m', '-Xmx7280m', '-XX:+UseSerialGC', '-c', 16, '-r', u'15:36887087-52402170', '--caller', 'platypus', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/15/Batch1-15_36887086_52402170.vcf.gz', '/mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/15/Batch1-15_36887086_52402170.vcf-inputs.txt'] in region: 15:36887087-52402170
[2016-04-15T07:12Z] 2016-04-15 00:12:44 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:12:44,913 - WARNING - Could not retrieve variants from source file in region 15:51752140-51752541. Error was invalid region `15:51752141-51752541`
[2016-04-15T07:12Z] 2016-04-15 00:12:45 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:12:45,382 - WARNING - Could not retrieve variants from source file in region 15:51528901-51529302. Error was invalid region `15:51528902-51529302`
[2016-04-15T07:12Z] 2016-04-15 00:12:46 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:12:46,236 - WARNING - Could not retrieve variants from source file in region 15:52353287-52353688. Error was invalid region `15:52353288-52353688`
[2016-04-15T07:12Z] 2016-04-15 00:12:47 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:12:47,024 - WARNING - Could not retrieve variants from source file in region 15:49238573-49238974. Error was invalid region `15:49238574-49238974`
[2016-04-15T07:12Z] 2016-04-15 00:12:47 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:12:47,139 - WARNING - Could not retrieve variants from source file in region 15:40477620-40489041. Error was invalid region `15:40477621-40489041`
[2016-04-15T07:12Z] 2016-04-15 00:12:47 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:12:47,767 - WARNING - Could not retrieve variants from source file in region 15:40265588-40265989. Error was invalid region `15:40265589-40265989`
[2016-04-15T07:12Z] 2016-04-15 00:12:48 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:12:48,165 - WARNING - Could not retrieve variants from source file in region 15:41099688-41106116. Error was invalid region `15:41099689-41106116`
[2016-04-15T07:12Z] 2016-04-15 00:12:48 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:12:48,239 - WARNING - Could not retrieve variants from source file in region 15:51294621-51295022. Error was invalid region `15:51294622-51295022`
[2016-04-15T07:12Z] 2016-04-15 00:12:48 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:12:48,344 - WARNING - Could not retrieve variants from source file in region 15:50866871-50867272. Error was invalid region `15:50866872-50867272`
[2016-04-15T07:12Z] 2016-04-15 00:12:48 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:12:48,362 - WARNING - Could not retrieve variants from source file in region 15:43893522-43900343. Error was invalid region `15:43893523-43900343`
[2016-04-15T07:12Z] 2016-04-15 00:12:50 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:12:50,060 - WARNING - Could not retrieve variants from source file in region 15:51752140-51752541. Error was invalid region `15:51752141-51752541`
[2016-04-15T07:12Z] 2016-04-15 00:12:50 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:12:50,078 - WARNING - Could not retrieve variants from source file in region 15:45443922-45491272. Error was invalid region `15:45443923-45491272`
[2016-04-15T07:12Z] 2016-04-15 00:12:51 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:12:51,180 - WARNING - Could not retrieve variants from source file in region 15:51868162-51868563. Error was invalid region `15:51868163-51868563`
[2016-04-15T07:12Z] 2016-04-15 00:12:53 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:12:53,224 - WARNING - Could not retrieve variants from source file in region 15:49238573-49238974. Error was invalid region `15:49238574-49238974`
[2016-04-15T07:12Z] 2016-04-15 00:12:54 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:12:54,361 - WARNING - Could not retrieve variants from source file in region 15:40477620-40489041. Error was invalid region `15:40477621-40489041`
[2016-04-15T07:12Z] 2016-04-15 00:12:54 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:12:54,380 - WARNING - Could not retrieve variants from source file in region 15:39880066-39910621. Error was invalid region `15:39880067-39910621`
[2016-04-15T07:12Z] 2016-04-15 00:12:54 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:12:54,927 - WARNING - Could not retrieve variants from source file in region 15:51914451-51914968. Error was invalid region `15:51914452-51914968`
[2016-04-15T07:12Z] 2016-04-15 00:12:54 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:12:54,976 - WARNING - Could not retrieve variants from source file in region 15:41634376-41634778. Error was invalid region `15:41634377-41634778`
[2016-04-15T07:12Z] 2016-04-15 00:12:55 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:12:55,302 - WARNING - Could not retrieve variants from source file in region 15:51693602-51694003. Error was invalid region `15:51693603-51694003`
[2016-04-15T07:12Z] 2016-04-15 00:12:55 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:12:55,335 - WARNING - Could not retrieve variants from source file in region 15:40265588-40265989. Error was invalid region `15:40265589-40265989`
[2016-04-15T07:12Z] 2016-04-15 00:12:55 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:12:55,765 - WARNING - Could not retrieve variants from source file in region 15:51752140-51752541. Error was invalid region `15:51752141-51752541`
[2016-04-15T07:12Z] 2016-04-15 00:12:56 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:12:56,122 - WARNING - Could not retrieve variants from source file in region 15:51528901-51529302. Error was invalid region `15:51528902-51529302`
[2016-04-15T07:12Z] 2016-04-15 00:12:56 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:12:56,515 - WARNING - Could not retrieve variants from source file in region 15:52353287-52353688. Error was invalid region `15:52353288-52353688`
[2016-04-15T07:12Z] 2016-04-15 00:12:58 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:12:58,654 - WARNING - Could not retrieve variants from source file in region 15:49238573-49238974. Error was invalid region `15:49238574-49238974`
[2016-04-15T07:13Z] 2016-04-15 00:13:00 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:13:00,976 - WARNING - Could not retrieve variants from source file in region 15:40477620-40489041. Error was invalid region `15:40477621-40489041`
[2016-04-15T07:13Z] 2016-04-15 00:13:02 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:13:02,568 - WARNING - Could not retrieve variants from source file in region 15:41634376-41634778. Error was invalid region `15:41634377-41634778`
[2016-04-15T07:13Z] 2016-04-15 00:13:02 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:13:02,924 - WARNING - Could not retrieve variants from source file in region 15:51294621-51295022. Error was invalid region `15:51294622-51295022`
[2016-04-15T07:13Z] 2016-04-15 00:13:04 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:13:04,605 - WARNING - Could not retrieve variants from source file in region 15:40265588-40265989. Error was invalid region `15:40265589-40265989`
[2016-04-15T07:13Z] 2016-04-15 00:13:12 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:13:12,624 - WARNING - Could not retrieve variants from source file in region 15:45391864-45408604. Error was invalid region `15:45391865-45408604`
[2016-04-15T07:13Z] 2016-04-15 00:13:13 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:13:13,451 - WARNING - Could not retrieve variants from source file in region 15:51829601-51830002. Error was invalid region `15:51829602-51830002`
[2016-04-15T07:13Z] 2016-04-15 00:13:14 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:13:14,501 - WARNING - Could not retrieve variants from source file in region 15:49033116-49033518. Error was invalid region `15:49033117-49033518`
[2016-04-15T07:13Z] 2016-04-15 00:13:15 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:13:15,173 - WARNING - Could not retrieve variants from source file in region 15:40308648-40330754. Error was invalid region `15:40308649-40330754`
[2016-04-15T07:13Z] 2016-04-15 00:13:15 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:13:15,250 - WARNING - Could not retrieve variants from source file in region 15:51217150-51217551. Error was invalid region `15:51217151-51217551`
[2016-04-15T07:13Z] 2016-04-15 00:13:16 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:13:16,543 - WARNING - Could not retrieve variants from source file in region 15:38988604-38989005. Error was invalid region `15:38988605-38989005`
[2016-04-15T07:13Z] 2016-04-15 00:13:16 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:13:16,988 - WARNING - Could not retrieve variants from source file in region 15:38643363-38643764. Error was invalid region `15:38643364-38643764`
[2016-04-15T07:13Z] 2016-04-15 00:13:17 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:13:17,445 - WARNING - Could not retrieve variants from source file in region 15:40898432-40916427. Error was invalid region `15:40898433-40916427`
[2016-04-15T07:13Z] 2016-04-15 00:13:17 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:13:17,586 - WARNING - Could not retrieve variants from source file in region 15:45391864-45408604. Error was invalid region `15:45391865-45408604`
[2016-04-15T07:13Z] 2016-04-15 00:13:18 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:13:18,762 - WARNING - Could not retrieve variants from source file in region 15:51829601-51830002. Error was invalid region `15:51829602-51830002`
[2016-04-15T07:13Z] 2016-04-15 00:13:19 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:13:19,082 - WARNING - Could not retrieve variants from source file in region 15:40226284-40226685. Error was invalid region `15:40226285-40226685`
[2016-04-15T07:13Z] 2016-04-15 00:13:19 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:13:19,370 - WARNING - Could not retrieve variants from source file in region 15:41475998-41476787. Error was invalid region `15:41475999-41476787`
[2016-04-15T07:13Z] 2016-04-15 00:13:20 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:13:20,454 - WARNING - Could not retrieve variants from source file in region 15:38776595-38777005. Error was invalid region `15:38776596-38777005`
[2016-04-15T07:13Z] 2016-04-15 00:13:21 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:13:21,019 - WARNING - Could not retrieve variants from source file in region 15:51783609-51795362. Error was invalid region `15:51783610-51795362`
[2016-04-15T07:13Z] 2016-04-15 00:13:21 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:13:21,458 - WARNING - Could not retrieve variants from source file in region 15:38988604-38989005. Error was invalid region `15:38988605-38989005`
[2016-04-15T07:13Z] 2016-04-15 00:13:21 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:13:21,608 - WARNING - Could not retrieve variants from source file in region 15:38643363-38643764. Error was invalid region `15:38643364-38643764`
[2016-04-15T07:13Z] 2016-04-15 00:13:22 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:13:22,185 - WARNING - Could not retrieve variants from source file in region 15:45391864-45408604. Error was invalid region `15:45391865-45408604`
[2016-04-15T07:13Z] 2016-04-15 00:13:22 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:13:22,849 - WARNING - Could not retrieve variants from source file in region 15:50769309-50773945. Error was invalid region `15:50769310-50773945`
[2016-04-15T07:13Z] 2016-04-15 00:13:23 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:13:23,351 - WARNING - Could not retrieve variants from source file in region 15:40226284-40226685. Error was invalid region `15:40226285-40226685`
[2016-04-15T07:13Z] 2016-04-15 00:13:23 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:13:23,630 - WARNING - Could not retrieve variants from source file in region 15:51829601-51830002. Error was invalid region `15:51829602-51830002`
[2016-04-15T07:13Z] 2016-04-15 00:13:25 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:13:25,957 - WARNING - Could not retrieve variants from source file in region 15:40308648-40330754. Error was invalid region `15:40308649-40330754`
[2016-04-15T07:13Z] 2016-04-15 00:13:25 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:13:25,962 - WARNING - Could not retrieve variants from source file in region 15:43815727-43818269. Error was invalid region `15:43815728-43818269`
[2016-04-15T07:13Z] 2016-04-15 00:13:26 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:13:26,131 - WARNING - Could not retrieve variants from source file in region 15:51217150-51217551. Error was invalid region `15:51217151-51217551`
[2016-04-15T07:13Z] 2016-04-15 00:13:26 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:13:26,493 - WARNING - Could not retrieve variants from source file in region 15:38643363-38643764. Error was invalid region `15:38643364-38643764`
[2016-04-15T07:13Z] 2016-04-15 00:13:26 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:13:26,502 - WARNING - Could not retrieve variants from source file in region 15:38988604-38989005. Error was invalid region `15:38988605-38989005`
[2016-04-15T07:13Z] 2016-04-15 00:13:27 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:13:27,817 - WARNING - Could not retrieve variants from source file in region 15:40226284-40226685. Error was invalid region `15:40226285-40226685`
[2016-04-15T07:13Z] 2016-04-15 00:13:30 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:13:30,948 - WARNING - Could not retrieve variants from source file in region 15:38776595-38777005. Error was invalid region `15:38776596-38777005`
[2016-04-15T07:13Z] 2016-04-15 00:13:40 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:13:40,675 - WARNING - Could not retrieve variants from source file in region 15:50279451-50279852. Error was invalid region `15:50279452-50279852`
[2016-04-15T07:13Z] 2016-04-15 00:13:40 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:13:40,973 - WARNING - Could not retrieve variants from source file in region 15:40005561-40005962. Error was invalid region `15:40005562-40005962`
[2016-04-15T07:13Z] 2016-04-15 00:13:41 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:13:41,110 - WARNING - Could not retrieve variants from source file in region 15:42523854-42524255. Error was invalid region `15:42523855-42524255`
[2016-04-15T07:13Z] 2016-04-15 00:13:41 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:13:41,310 - WARNING - Could not retrieve variants from source file in region 15:38614314-38614715. Error was invalid region `15:38614315-38614715`
[2016-04-15T07:13Z] 2016-04-15 00:13:41 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:13:41,816 - WARNING - Could not retrieve variants from source file in region 15:45353019-45365914. Error was invalid region `15:45353020-45365914`
[2016-04-15T07:13Z] 2016-04-15 00:13:42 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:13:42,079 - WARNING - Could not retrieve variants from source file in region 15:41245465-41245866. Error was invalid region `15:41245466-41245866`
[2016-04-15T07:13Z] 2016-04-15 00:13:43 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:13:43,329 - WARNING - Could not retrieve variants from source file in region 15:48797096-48807827. Error was invalid region `15:48797097-48807827`
[2016-04-15T07:13Z] 2016-04-15 00:13:43 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:13:43,932 - WARNING - Could not retrieve variants from source file in region 15:41186779-41195547. Error was invalid region `15:41186780-41195547`
[2016-04-15T07:13Z] 2016-04-15 00:13:44 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:13:44,644 - WARNING - Could not retrieve variants from source file in region 15:48053018-48063266. Error was invalid region `15:48053019-48063266`
[2016-04-15T07:13Z] 2016-04-15 00:13:46 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:13:46,169 - WARNING - Could not retrieve variants from source file in region 15:38614314-38614715. Error was invalid region `15:38614315-38614715`
[2016-04-15T07:13Z] 2016-04-15 00:13:46 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:13:46,620 - WARNING - Could not retrieve variants from source file in region 15:41245465-41245866. Error was invalid region `15:41245466-41245866`
[2016-04-15T07:13Z] 2016-04-15 00:13:46 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:13:46,655 - WARNING - Could not retrieve variants from source file in region 15:42523854-42524255. Error was invalid region `15:42523855-42524255`
[2016-04-15T07:13Z] 2016-04-15 00:13:47 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:13:47,056 - WARNING - Could not retrieve variants from source file in region 15:50555333-50555734. Error was invalid region `15:50555334-50555734`
[2016-04-15T07:13Z] 2016-04-15 00:13:47 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:13:47,078 - WARNING - Could not retrieve variants from source file in region 15:40845091-40862254. Error was invalid region `15:40845092-40862254`
[2016-04-15T07:13Z] 2016-04-15 00:13:47 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:13:47,157 - WARNING - Could not retrieve variants from source file in region 15:36983751-36984152. Error was invalid region `15:36983752-36984152`
[2016-04-15T07:13Z] 2016-04-15 00:13:50 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:13:50,445 - WARNING - Could not retrieve variants from source file in region 15:40005561-40005962. Error was invalid region `15:40005562-40005962`
[2016-04-15T07:13Z] 2016-04-15 00:13:50 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:13:50,930 - WARNING - Could not retrieve variants from source file in region 15:38614314-38614715. Error was invalid region `15:38614315-38614715`
[2016-04-15T07:13Z] 2016-04-15 00:13:51 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:13:51,966 - WARNING - Could not retrieve variants from source file in region 15:41245465-41245866. Error was invalid region `15:41245466-41245866`
[2016-04-15T07:13Z] 2016-04-15 00:13:52 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:13:52,004 - WARNING - Could not retrieve variants from source file in region 15:42523854-42524255. Error was invalid region `15:42523855-42524255`
[2016-04-15T07:13Z] 2016-04-15 00:13:52 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:13:52,183 - WARNING - Could not retrieve variants from source file in region 15:50555333-50555734. Error was invalid region `15:50555334-50555734`
[2016-04-15T07:14Z] 2016-04-15 00:14:00 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:14:00,652 - WARNING - Could not retrieve variants from source file in region 15:48580502-48580903. Error was invalid region `15:48580503-48580903`
[2016-04-15T07:14Z] 2016-04-15 00:14:00 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:14:00,921 - WARNING - Could not retrieve variants from source file in region 15:45248910-45258548. Error was invalid region `15:45248911-45258548`
[2016-04-15T07:14Z] 2016-04-15 00:14:02 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:14:02,288 - WARNING - Could not retrieve variants from source file in region 15:45981106-45981507. Error was invalid region `15:45981107-45981507`
[2016-04-15T07:14Z] 2016-04-15 00:14:05 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:14:05,084 - WARNING - Could not retrieve variants from source file in region 15:48443488-48461117. Error was invalid region `15:48443489-48461117`
[2016-04-15T07:14Z] 2016-04-15 00:14:05 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:14:05,182 - WARNING - Could not retrieve variants from source file in region 15:50226102-50226503. Error was invalid region `15:50226103-50226503`
[2016-04-15T07:14Z] 2016-04-15 00:14:06 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:14:06,378 - WARNING - Could not retrieve variants from source file in region 15:41147952-41149351. Error was invalid region `15:41147953-41149351`
[2016-04-15T07:14Z] 2016-04-15 00:14:06 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:14:06,397 - WARNING - Could not retrieve variants from source file in region 15:42434043-42439566. Error was invalid region `15:42434044-42439566`
[2016-04-15T07:14Z] 2016-04-15 00:14:06 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:14:06,612 - WARNING - Could not retrieve variants from source file in region 15:48580502-48580903. Error was invalid region `15:48580503-48580903`
[2016-04-15T07:14Z] 2016-04-15 00:14:07 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:14:07,172 - WARNING - Could not retrieve variants from source file in region 15:45981106-45981507. Error was invalid region `15:45981107-45981507`
[2016-04-15T07:14Z] 2016-04-15 00:14:07 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:14:07,281 - WARNING - Could not retrieve variants from source file in region 15:49325078-49325479. Error was invalid region `15:49325079-49325479`
[2016-04-15T07:14Z] 2016-04-15 00:14:07 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:14:07,473 - WARNING - Could not retrieve variants from source file in region 15:44943546-44966579. Error was invalid region `15:44943547-44966579`
[2016-04-15T07:14Z] 2016-04-15 00:14:07 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:14:07,475 - WARNING - Could not retrieve variants from source file in region 15:45779599-45780000. Error was invalid region `15:45779600-45780000`
[2016-04-15T07:14Z] 2016-04-15 00:14:09 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:14:09,956 - WARNING - Could not retrieve variants from source file in region 15:50226102-50226503. Error was invalid region `15:50226103-50226503`
[2016-04-15T07:14Z] 2016-04-15 00:14:10 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:14:10,070 - WARNING - Could not retrieve variants from source file in region 15:48443488-48461117. Error was invalid region `15:48443489-48461117`
[2016-04-15T07:14Z] 2016-04-15 00:14:11 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:14:11,243 - WARNING - Could not retrieve variants from source file in region 15:45695171-45695885. Error was invalid region `15:45695172-45695885`
[2016-04-15T07:14Z] 2016-04-15 00:14:13 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:14:13,450 - WARNING - Could not retrieve variants from source file in region 15:48580502-48580903. Error was invalid region `15:48580503-48580903`
[2016-04-15T07:14Z] 2016-04-15 00:14:13 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:14:13,482 - WARNING - Could not retrieve variants from source file in region 15:45248910-45258548. Error was invalid region `15:45248911-45258548`
[2016-04-15T07:14Z] 2016-04-15 00:14:13 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:14:13,508 - WARNING - Could not retrieve variants from source file in region 15:40712137-40713681. Error was invalid region `15:40712138-40713681`
[2016-04-15T07:14Z] 2016-04-15 00:14:13 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:14:13,902 - WARNING - Could not retrieve variants from source file in region 15:45981106-45981507. Error was invalid region `15:45981107-45981507`
[2016-04-15T07:14Z] 2016-04-15 00:14:13 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:14:13,980 - WARNING - Could not retrieve variants from source file in region 15:43632338-43661992. Error was invalid region `15:43632339-43661992`
[2016-04-15T07:14Z] 2016-04-15 00:14:14 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:14:14,364 - WARNING - Could not retrieve variants from source file in region 15:45779599-45780000. Error was invalid region `15:45779600-45780000`
[2016-04-15T07:14Z] 2016-04-15 00:14:14 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:14:14,416 - WARNING - Could not retrieve variants from source file in region 15:49325078-49325479. Error was invalid region `15:49325079-49325479`
[2016-04-15T07:14Z] 2016-04-15 00:14:14 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:14:14,445 - WARNING - Could not retrieve variants from source file in region 15:44943546-44966579. Error was invalid region `15:44943547-44966579`
[2016-04-15T07:14Z] 2016-04-15 00:14:14 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:14:14,533 - WARNING - Could not retrieve variants from source file in region 15:50226102-50226503. Error was invalid region `15:50226103-50226503`
[2016-04-15T07:14Z] 2016-04-15 00:14:14 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:14:14,842 - WARNING - Could not retrieve variants from source file in region 15:48443488-48461117. Error was invalid region `15:48443489-48461117`
[2016-04-15T07:14Z] 2016-04-15 00:14:17 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:14:17,818 - WARNING - Could not retrieve variants from source file in region 15:42434043-42439566. Error was invalid region `15:42434044-42439566`
[2016-04-15T07:14Z] 2016-04-15 00:14:20 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:14:20,048 - WARNING - Could not retrieve variants from source file in region 15:40712137-40713681. Error was invalid region `15:40712138-40713681`
[2016-04-15T07:14Z] 2016-04-15 00:14:20 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:14:20,546 - WARNING - Could not retrieve variants from source file in region 15:50474555-50475090. Error was invalid region `15:50474556-50475090`
[2016-04-15T07:14Z] 2016-04-15 00:14:20 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:14:20,837 - WARNING - Could not retrieve variants from source file in region 15:45779599-45780000. Error was invalid region `15:45779600-45780000`
[2016-04-15T07:14Z] 2016-04-15 00:14:21 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:14:21,537 - WARNING - Could not retrieve variants from source file in region 15:44943546-44966579. Error was invalid region `15:44943547-44966579`
[2016-04-15T07:14Z] 2016-04-15 00:14:21 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:14:21,663 - WARNING - Could not retrieve variants from source file in region 15:49325078-49325479. Error was invalid region `15:49325079-49325479`
[2016-04-15T07:14Z] 2016-04-15 00:14:29 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:14:29,708 - WARNING - Could not retrieve variants from source file in region 15:50152372-50152773. Error was invalid region `15:50152373-50152773`
[2016-04-15T07:14Z] 2016-04-15 00:14:31 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:14:31,853 - WARNING - Could not retrieve variants from source file in region 15:42371541-42374000. Error was invalid region `15:42371542-42374000`
[2016-04-15T07:14Z] 2016-04-15 00:14:32 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:14:32,941 - WARNING - Could not retrieve variants from source file in region 15:45046923-45048841. Error was invalid region `15:45046924-45048841`
[2016-04-15T07:14Z] 2016-04-15 00:14:34 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:14:34,703 - WARNING - Could not retrieve variants from source file in region 15:49284631-49285191. Error was invalid region `15:49284632-49285191`
[2016-04-15T07:14Z] 2016-04-15 00:14:34 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:14:34,766 - WARNING - Could not retrieve variants from source file in region 15:50152372-50152773. Error was invalid region `15:50152373-50152773`
[2016-04-15T07:14Z] 2016-04-15 00:14:34 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:14:34,953 - WARNING - Could not retrieve variants from source file in region 15:50310924-50311338. Error was invalid region `15:50310925-50311338`
[2016-04-15T07:14Z] 2016-04-15 00:14:35 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:14:35,743 - WARNING - Could not retrieve variants from source file in region 15:44038688-44084895. Error was invalid region `15:44038689-44084895`
[2016-04-15T07:14Z] 2016-04-15 00:14:36 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:14:36,510 - WARNING - Could not retrieve variants from source file in region 15:43545517-43545918. Error was invalid region `15:43545518-43545918`
[2016-04-15T07:14Z] 2016-04-15 00:14:37 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:14:37,126 - WARNING - Could not retrieve variants from source file in region 15:45654116-45661868. Error was invalid region `15:45654117-45661868`
[2016-04-15T07:14Z] 2016-04-15 00:14:39 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:14:39,523 - WARNING - Could not retrieve variants from source file in region 15:50152372-50152773. Error was invalid region `15:50152373-50152773`
[2016-04-15T07:14Z] 2016-04-15 00:14:40 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:14:40,374 - WARNING - Could not retrieve variants from source file in region 15:44038688-44084895. Error was invalid region `15:44038689-44084895`
[2016-04-15T07:14Z] 2016-04-15 00:14:41 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:14:41,860 - WARNING - Could not retrieve variants from source file in region 15:44165157-44165558. Error was invalid region `15:44165158-44165558`
[2016-04-15T07:14Z] 2016-04-15 00:14:42 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:14:42,337 - WARNING - Could not retrieve variants from source file in region 15:43571179-43579756. Error was invalid region `15:43571180-43579756`
[2016-04-15T07:14Z] 2016-04-15 00:14:42 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:14:42,397 - WARNING - Could not retrieve variants from source file in region 15:42371541-42374000. Error was invalid region `15:42371542-42374000`
[2016-04-15T07:14Z] 2016-04-15 00:14:44 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:14:44,828 - WARNING - Could not retrieve variants from source file in region 15:44038688-44084895. Error was invalid region `15:44038689-44084895`
[2016-04-15T07:14Z] 2016-04-15 00:14:50 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:14:50,778 - WARNING - Could not retrieve variants from source file in region 15:44119102-44120749. Error was invalid region `15:44119103-44120749`
[2016-04-15T07:14Z] 2016-04-15 00:14:53 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:14:53,654 - WARNING - Could not retrieve variants from source file in region 15:44119102-44120749. Error was invalid region `15:44119103-44120749`
[2016-04-15T07:14Z] 2016-04-15 00:14:55 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:14:55,591 - WARNING - Could not retrieve variants from source file in region 15:44119102-44120749. Error was invalid region `15:44119103-44120749`
[2016-04-15T07:14Z] 2016-04-15 00:14:56 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:14:56,611 - WARNING - Could not retrieve variants from source file in region 15:42703894-42704295. Error was invalid region `15:42703895-42704295`
[2016-04-15T07:14Z] 2016-04-15 00:14:57 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:14:57,440 - WARNING - Could not retrieve variants from source file in region 15:43038033-43038434. Error was invalid region `15:43038034-43038434`
[2016-04-15T07:14Z] 2016-04-15 00:14:57 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:14:57,986 - WARNING - Could not retrieve variants from source file in region 15:42983562-42983963. Error was invalid region `15:42983563-42983963`
[2016-04-15T07:15Z] 2016-04-15 00:15:00 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:15:00,093 - WARNING - Could not retrieve variants from source file in region 15:41860279-41860680. Error was invalid region `15:41860280-41860680`
[2016-04-15T07:15Z] 2016-04-15 00:15:00 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:15:00,880 - WARNING - Could not retrieve variants from source file in region 15:42342607-42343014. Error was invalid region `15:42342608-42343014`
[2016-04-15T07:15Z] 2016-04-15 00:15:01 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:15:01,259 - WARNING - Could not retrieve variants from source file in region 15:42281508-42287796. Error was invalid region `15:42281509-42287796`
[2016-04-15T07:15Z] 2016-04-15 00:15:01 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:15:01,413 - WARNING - Could not retrieve variants from source file in region 15:42703894-42704295. Error was invalid region `15:42703895-42704295`
[2016-04-15T07:15Z] 2016-04-15 00:15:02 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:15:02,511 - WARNING - Could not retrieve variants from source file in region 15:43989319-43989722. Error was invalid region `15:43989320-43989722`
[2016-04-15T07:15Z] 2016-04-15 00:15:05 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:15:05,139 - WARNING - Could not retrieve variants from source file in region 15:42342607-42343014. Error was invalid region `15:42342608-42343014`
[2016-04-15T07:15Z] 2016-04-15 00:15:05 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:15:05,782 - WARNING - Could not retrieve variants from source file in region 15:42703894-42704295. Error was invalid region `15:42703895-42704295`
[2016-04-15T07:15Z] 2016-04-15 00:15:06 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:15:06,273 - WARNING - Could not retrieve variants from source file in region 15:41672173-41689422. Error was invalid region `15:41672174-41689422`
[2016-04-15T07:15Z] 2016-04-15 00:15:06 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:15:06,689 - WARNING - Could not retrieve variants from source file in region 15:43989319-43989722. Error was invalid region `15:43989320-43989722`
[2016-04-15T07:15Z] 2016-04-15 00:15:07 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:15:07,459 - WARNING - Could not retrieve variants from source file in region 15:43928129-43928530. Error was invalid region `15:43928130-43928530`
[2016-04-15T07:15Z] 2016-04-15 00:15:13 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:15:13,055 - WARNING - Could not retrieve variants from source file in region 15:42618320-42618721. Error was invalid region `15:42618321-42618721`
[2016-04-15T07:15Z] 2016-04-15 00:15:13 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:15:13,481 - WARNING - Could not retrieve variants from source file in region 15:42618320-42618721. Error was invalid region `15:42618321-42618721`
[2016-04-15T07:15Z] 2016-04-15 00:15:13 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:15:13,483 - WARNING - Could not retrieve variants from source file in region 15:43928129-43928530. Error was invalid region `15:43928130-43928530`
[2016-04-15T07:15Z] 2016-04-15 00:15:16 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:15:16,086 - WARNING - Could not retrieve variants from source file in region 15:42550138-42580138. Error was invalid region `15:42550139-42580138`
[2016-04-15T07:15Z] 2016-04-15 00:15:16 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:15:16,091 - WARNING - Could not retrieve variants from source file in region 15:42550138-42580138. Error was invalid region `15:42550139-42580138`
[2016-04-15T07:15Z] 2016-04-15 00:15:16 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:15:16,091 - WARNING - Could not retrieve variants from source file in region 15:42550138-42580138. Error was invalid region `15:42550139-42580138`
[2016-04-15T07:15Z] 2016-04-15 00:15:16 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:15:16,173 - WARNING - Could not retrieve variants from source file in region 15:41991104-41991505. Error was invalid region `15:41991105-41991505`
[2016-04-15T07:15Z] 2016-04-15 00:15:19 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:15:19,895 - WARNING - Could not retrieve variants from source file in region 15:41991104-41991505. Error was invalid region `15:41991105-41991505`
[2016-04-15T07:15Z] 2016-04-15 00:15:19 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:15:19,921 - WARNING - Could not retrieve variants from source file in region 15:41991104-41991505. Error was invalid region `15:41991105-41991505`
[2016-04-15T07:15Z] ['bcbio-variation-recall', 'square', '-Xms750m', '-Xmx7280m', '-XX:+UseSerialGC', '-c', 16, '-r', u'15:52404365-67923265', '--caller', 'platypus', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/15/Batch1-15_52404364_67923265.vcf.gz', '/mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/15/Batch1-15_52404364_67923265.vcf-inputs.txt'] in region: 15:52404365-67923265
[2016-04-15T07:15Z] 2016-04-15 00:15:34 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:15:34,480 - WARNING - Could not retrieve variants from source file in region 15:67767940-67768341. Error was invalid region `15:67767941-67768341`
[2016-04-15T07:15Z] 2016-04-15 00:15:35 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:15:35,359 - WARNING - Could not retrieve variants from source file in region 15:65903187-65903588. Error was invalid region `15:65903188-65903588`
[2016-04-15T07:15Z] 2016-04-15 00:15:35 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:15:35,908 - WARNING - Could not retrieve variants from source file in region 15:60884383-60884784. Error was invalid region `15:60884384-60884784`
[2016-04-15T07:15Z] 2016-04-15 00:15:36 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:15:36,471 - WARNING - Could not retrieve variants from source file in region 15:64418186-64418587. Error was invalid region `15:64418187-64418587`
[2016-04-15T07:15Z] 2016-04-15 00:15:36 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:15:36,475 - WARNING - Could not retrieve variants from source file in region 15:63594449-63594850. Error was invalid region `15:63594450-63594850`
[2016-04-15T07:15Z] 2016-04-15 00:15:36 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:15:36,987 - WARNING - Could not retrieve variants from source file in region 15:57967008-57967409. Error was invalid region `15:57967009-57967409`
[2016-04-15T07:15Z] 2016-04-15 00:15:37 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:15:37,232 - WARNING - Could not retrieve variants from source file in region 15:64962419-64962820. Error was invalid region `15:64962420-64962820`
[2016-04-15T07:15Z] 2016-04-15 00:15:37 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:15:37,310 - WARNING - Could not retrieve variants from source file in region 15:65994522-65994923. Error was invalid region `15:65994523-65994923`
[2016-04-15T07:15Z] 2016-04-15 00:15:37 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:15:37,348 - WARNING - Could not retrieve variants from source file in region 15:62990760-63009994. Error was invalid region `15:62990761-63009994`
[2016-04-15T07:15Z] 2016-04-15 00:15:37 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:15:37,836 - WARNING - Could not retrieve variants from source file in region 15:55931976-55932377. Error was invalid region `15:55931977-55932377`
[2016-04-15T07:15Z] 2016-04-15 00:15:37 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:15:37,837 - WARNING - Could not retrieve variants from source file in region 15:56207600-56208725. Error was invalid region `15:56207601-56208725`
[2016-04-15T07:15Z] 2016-04-15 00:15:37 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:15:37,910 - WARNING - Could not retrieve variants from source file in region 15:62259426-62259827. Error was invalid region `15:62259427-62259827`
[2016-04-15T07:15Z] 2016-04-15 00:15:39 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:15:39,464 - WARNING - Could not retrieve variants from source file in region 15:67767940-67768341. Error was invalid region `15:67767941-67768341`
[2016-04-15T07:15Z] 2016-04-15 00:15:39 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:15:39,599 - WARNING - Could not retrieve variants from source file in region 15:55488854-55489255. Error was invalid region `15:55488855-55489255`
[2016-04-15T07:15Z] 2016-04-15 00:15:40 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:15:40,056 - WARNING - Could not retrieve variants from source file in region 15:65903187-65903588. Error was invalid region `15:65903188-65903588`
[2016-04-15T07:15Z] 2016-04-15 00:15:43 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:15:43,269 - WARNING - Could not retrieve variants from source file in region 15:64418186-64418587. Error was invalid region `15:64418187-64418587`
[2016-04-15T07:15Z] 2016-04-15 00:15:43 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:15:43,968 - WARNING - Could not retrieve variants from source file in region 15:53957681-53958082. Error was invalid region `15:53957682-53958082`
[2016-04-15T07:15Z] 2016-04-15 00:15:43 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:15:43,980 - WARNING - Could not retrieve variants from source file in region 15:59180537-59180938. Error was invalid region `15:59180538-59180938`
[2016-04-15T07:15Z] 2016-04-15 00:15:44 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:15:44,351 - WARNING - Could not retrieve variants from source file in region 15:64962419-64962820. Error was invalid region `15:64962420-64962820`
[2016-04-15T07:15Z] 2016-04-15 00:15:45 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:15:45,297 - WARNING - Could not retrieve variants from source file in region 15:62259426-62259827. Error was invalid region `15:62259427-62259827`
[2016-04-15T07:15Z] 2016-04-15 00:15:45 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:15:45,448 - WARNING - Could not retrieve variants from source file in region 15:65621230-65624129. Error was invalid region `15:65621231-65624129`
[2016-04-15T07:15Z] 2016-04-15 00:15:45 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:15:45,507 - WARNING - Could not retrieve variants from source file in region 15:55931976-55932377. Error was invalid region `15:55931977-55932377`
[2016-04-15T07:15Z] 2016-04-15 00:15:45 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:15:45,523 - WARNING - Could not retrieve variants from source file in region 15:57967008-57967409. Error was invalid region `15:57967009-57967409`
[2016-04-15T07:15Z] 2016-04-15 00:15:45 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:15:45,533 - WARNING - Could not retrieve variants from source file in region 15:67767940-67768341. Error was invalid region `15:67767941-67768341`
[2016-04-15T07:15Z] 2016-04-15 00:15:45 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:15:45,997 - WARNING - Could not retrieve variants from source file in region 15:65903187-65903588. Error was invalid region `15:65903188-65903588`
[2016-04-15T07:15Z] 2016-04-15 00:15:46 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:15:46,020 - WARNING - Could not retrieve variants from source file in region 15:55488854-55489255. Error was invalid region `15:55488855-55489255`
[2016-04-15T07:15Z] 2016-04-15 00:15:46 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:15:46,137 - WARNING - Could not retrieve variants from source file in region 15:60884383-60884784. Error was invalid region `15:60884384-60884784`
[2016-04-15T07:15Z] 2016-04-15 00:15:49 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:15:49,303 - WARNING - Could not retrieve variants from source file in region 15:64418186-64418587. Error was invalid region `15:64418187-64418587`
[2016-04-15T07:15Z] 2016-04-15 00:15:49 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:15:49,471 - WARNING - Could not retrieve variants from source file in region 15:63594449-63594850. Error was invalid region `15:63594450-63594850`
[2016-04-15T07:15Z] 2016-04-15 00:15:50 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:15:50,760 - WARNING - Could not retrieve variants from source file in region 15:53957681-53958082. Error was invalid region `15:53957682-53958082`
[2016-04-15T07:15Z] 2016-04-15 00:15:53 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:15:53,947 - WARNING - Could not retrieve variants from source file in region 15:62990760-63009994. Error was invalid region `15:62990761-63009994`
[2016-04-15T07:15Z] 2016-04-15 00:15:54 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:15:54,269 - WARNING - Could not retrieve variants from source file in region 15:55931976-55932377. Error was invalid region `15:55931977-55932377`
[2016-04-15T07:15Z] 2016-04-15 00:15:54 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:15:54,353 - WARNING - Could not retrieve variants from source file in region 15:57967008-57967409. Error was invalid region `15:57967009-57967409`
[2016-04-15T07:15Z] 2016-04-15 00:15:54 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:15:54,684 - WARNING - Could not retrieve variants from source file in region 15:62259426-62259827. Error was invalid region `15:62259427-62259827`
[2016-04-15T07:16Z] 2016-04-15 00:16:02 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:16:02,504 - WARNING - Could not retrieve variants from source file in region 15:67692291-67692692. Error was invalid region `15:67692292-67692692`
[2016-04-15T07:16Z] 2016-04-15 00:16:05 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:16:05,151 - WARNING - Could not retrieve variants from source file in region 15:54918836-54919237. Error was invalid region `15:54918837-54919237`
[2016-04-15T07:16Z] 2016-04-15 00:16:05 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:16:05,901 - WARNING - Could not retrieve variants from source file in region 15:60789587-60789988. Error was invalid region `15:60789588-60789988`
[2016-04-15T07:16Z] 2016-04-15 00:16:05 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:16:05,992 - WARNING - Could not retrieve variants from source file in region 15:63413872-63433956. Error was invalid region `15:63413873-63433956`
[2016-04-15T07:16Z] 2016-04-15 00:16:08 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:16:08,088 - WARNING - Could not retrieve variants from source file in region 15:52901222-52902167. Error was invalid region `15:52901223-52902167`
[2016-04-15T07:16Z] 2016-04-15 00:16:08 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:16:08,100 - WARNING - Could not retrieve variants from source file in region 15:67692291-67692692. Error was invalid region `15:67692292-67692692`
[2016-04-15T07:16Z] 2016-04-15 00:16:08 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:16:08,608 - WARNING - Could not retrieve variants from source file in region 15:64914895-64915296. Error was invalid region `15:64914896-64915296`
[2016-04-15T07:16Z] 2016-04-15 00:16:09 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:16:09,473 - WARNING - Could not retrieve variants from source file in region 15:65856442-65856843. Error was invalid region `15:65856443-65856843`
[2016-04-15T07:16Z] 2016-04-15 00:16:10 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:16:10,381 - WARNING - Could not retrieve variants from source file in region 15:54918836-54919237. Error was invalid region `15:54918837-54919237`
[2016-04-15T07:16Z] 2016-04-15 00:16:12 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:16:12,176 - WARNING - Could not retrieve variants from source file in region 15:60789587-60789988. Error was invalid region `15:60789588-60789988`
[2016-04-15T07:16Z] 2016-04-15 00:16:12 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:16:12,194 - WARNING - Could not retrieve variants from source file in region 15:62202271-62223493. Error was invalid region `15:62202272-62223493`
[2016-04-15T07:16Z] 2016-04-15 00:16:13 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:16:13,521 - WARNING - Could not retrieve variants from source file in region 15:62456147-62456839. Error was invalid region `15:62456148-62456839`
[2016-04-15T07:16Z] 2016-04-15 00:16:13 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:16:13,971 - WARNING - Could not retrieve variants from source file in region 15:63413872-63433956. Error was invalid region `15:63413873-63433956`
[2016-04-15T07:16Z] 2016-04-15 00:16:14 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:16:14,417 - WARNING - Could not retrieve variants from source file in region 15:67692291-67692692. Error was invalid region `15:67692292-67692692`
[2016-04-15T07:16Z] 2016-04-15 00:16:14 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:16:14,495 - WARNING - Could not retrieve variants from source file in region 15:56152518-56153062. Error was invalid region `15:56152519-56153062`
[2016-04-15T07:16Z] 2016-04-15 00:16:14 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:16:14,801 - WARNING - Could not retrieve variants from source file in region 15:52901222-52902167. Error was invalid region `15:52901223-52902167`
[2016-04-15T07:16Z] 2016-04-15 00:16:14 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:16:14,831 - WARNING - Could not retrieve variants from source file in region 15:64914895-64915296. Error was invalid region `15:64914896-64915296`
[2016-04-15T07:16Z] 2016-04-15 00:16:14 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:16:14,842 - WARNING - Could not retrieve variants from source file in region 15:65856442-65856843. Error was invalid region `15:65856443-65856843`
[2016-04-15T07:16Z] 2016-04-15 00:16:15 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:16:15,112 - WARNING - Could not retrieve variants from source file in region 15:54918836-54919237. Error was invalid region `15:54918837-54919237`
[2016-04-15T07:16Z] 2016-04-15 00:16:17 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:16:17,216 - WARNING - Could not retrieve variants from source file in region 15:55789699-55790100. Error was invalid region `15:55789700-55790100`
[2016-04-15T07:16Z] 2016-04-15 00:16:18 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:16:18,172 - WARNING - Could not retrieve variants from source file in region 15:60789587-60789988. Error was invalid region `15:60789588-60789988`
[2016-04-15T07:16Z] 2016-04-15 00:16:20 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:16:20,294 - WARNING - Could not retrieve variants from source file in region 15:65488917-65494402. Error was invalid region `15:65488918-65494402`
[2016-04-15T07:16Z] 2016-04-15 00:16:20 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:16:20,801 - WARNING - Could not retrieve variants from source file in region 15:63413872-63433956. Error was invalid region `15:63413873-63433956`
[2016-04-15T07:16Z] 2016-04-15 00:16:20 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:16:20,851 - WARNING - Could not retrieve variants from source file in region 15:56152518-56153062. Error was invalid region `15:56152519-56153062`
[2016-04-15T07:16Z] 2016-04-15 00:16:21 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:16:21,137 - WARNING - Could not retrieve variants from source file in region 15:52901222-52902167. Error was invalid region `15:52901223-52902167`
[2016-04-15T07:16Z] 2016-04-15 00:16:21 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:16:21,195 - WARNING - Could not retrieve variants from source file in region 15:64914895-64915296. Error was invalid region `15:64914896-64915296`
[2016-04-15T07:16Z] 2016-04-15 00:16:22 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:16:22,136 - WARNING - Could not retrieve variants from source file in region 15:55789699-55790100. Error was invalid region `15:55789700-55790100`
[2016-04-15T07:16Z] 2016-04-15 00:16:22 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:16:22,791 - WARNING - Could not retrieve variants from source file in region 15:62202271-62223493. Error was invalid region `15:62202272-62223493`
[2016-04-15T07:16Z] 2016-04-15 00:16:27 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:16:27,496 - WARNING - Could not retrieve variants from source file in region 15:65488917-65494402. Error was invalid region `15:65488918-65494402`
[2016-04-15T07:16Z] 2016-04-15 00:16:32 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:16:32,254 - WARNING - Could not retrieve variants from source file in region 15:67528163-67528564. Error was invalid region `15:67528164-67528564`
[2016-04-15T07:16Z] 2016-04-15 00:16:32 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:16:32,282 - WARNING - Could not retrieve variants from source file in region 15:65667513-65703815. Error was invalid region `15:65667514-65703815`
[2016-04-15T07:16Z] 2016-04-15 00:16:32 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:16:32,292 - WARNING - Could not retrieve variants from source file in region 15:54841663-54847867. Error was invalid region `15:54841664-54847867`
[2016-04-15T07:16Z] 2016-04-15 00:16:34 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:16:34,741 - WARNING - Could not retrieve variants from source file in region 15:64214459-64215565. Error was invalid region `15:64214460-64215565`
[2016-04-15T07:16Z] 2016-04-15 00:16:38 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:16:38,418 - WARNING - Could not retrieve variants from source file in region 15:56126239-56126640. Error was invalid region `15:56126240-56126640`
[2016-04-15T07:16Z] 2016-04-15 00:16:38 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:16:38,733 - WARNING - Could not retrieve variants from source file in region 15:54841663-54847867. Error was invalid region `15:54841664-54847867`
[2016-04-15T07:16Z] 2016-04-15 00:16:38 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:16:38,767 - WARNING - Could not retrieve variants from source file in region 15:64737014-64737415. Error was invalid region `15:64737015-64737415`
[2016-04-15T07:16Z] 2016-04-15 00:16:39 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:16:39,406 - WARNING - Could not retrieve variants from source file in region 15:52664197-52689821. Error was invalid region `15:52664198-52689821`
[2016-04-15T07:16Z] 2016-04-15 00:16:39 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:16:39,703 - WARNING - Could not retrieve variants from source file in region 15:58471157-58476471. Error was invalid region `15:58471158-58476471`
[2016-04-15T07:16Z] 2016-04-15 00:16:39 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:16:39,853 - WARNING - Could not retrieve variants from source file in region 15:55758982-55759383. Error was invalid region `15:55758983-55759383`
[2016-04-15T07:16Z] 2016-04-15 00:16:39 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:16:39,905 - WARNING - Could not retrieve variants from source file in region 15:64214459-64215565. Error was invalid region `15:64214460-64215565`
[2016-04-15T07:16Z] 2016-04-15 00:16:44 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:16:44,469 - WARNING - Could not retrieve variants from source file in region 15:64737014-64737415. Error was invalid region `15:64737015-64737415`
[2016-04-15T07:16Z] 2016-04-15 00:16:44 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:16:44,673 - WARNING - Could not retrieve variants from source file in region 15:54841663-54847867. Error was invalid region `15:54841664-54847867`
[2016-04-15T07:16Z] 2016-04-15 00:16:45 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:16:45,042 - WARNING - Could not retrieve variants from source file in region 15:58471157-58476471. Error was invalid region `15:58471158-58476471`
[2016-04-15T07:16Z] 2016-04-15 00:16:45 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:16:45,359 - WARNING - Could not retrieve variants from source file in region 15:64214459-64215565. Error was invalid region `15:64214460-64215565`
[2016-04-15T07:16Z] 2016-04-15 00:16:45 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:16:45,840 - WARNING - Could not retrieve variants from source file in region 15:57731124-57731918. Error was invalid region `15:57731125-57731918`
[2016-04-15T07:16Z] 2016-04-15 00:16:47 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:16:47,429 - WARNING - Could not retrieve variants from source file in region 15:56126239-56126640. Error was invalid region `15:56126240-56126640`
[2016-04-15T07:16Z] 2016-04-15 00:16:49 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:16:49,390 - WARNING - Could not retrieve variants from source file in region 15:64737014-64737415. Error was invalid region `15:64737015-64737415`
[2016-04-15T07:16Z] 2016-04-15 00:16:51 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:16:51,170 - WARNING - Could not retrieve variants from source file in region 15:58471157-58476471. Error was invalid region `15:58471158-58476471`
[2016-04-15T07:16Z] 2016-04-15 00:16:51 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:16:51,717 - WARNING - Could not retrieve variants from source file in region 15:55758982-55759383. Error was invalid region `15:55758983-55759383`
[2016-04-15T07:16Z] 2016-04-15 00:16:51 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:16:51,932 - WARNING - Could not retrieve variants from source file in region 15:62156479-62159419. Error was invalid region `15:62156480-62159419`
[2016-04-15T07:16Z] 2016-04-15 00:16:52 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:16:52,321 - WARNING - Could not retrieve variants from source file in region 15:57731124-57731918. Error was invalid region `15:57731125-57731918`
[2016-04-15T07:16Z] 2016-04-15 00:16:53 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:16:53,850 - WARNING - Could not retrieve variants from source file in region 15:65235565-65242675. Error was invalid region `15:65235566-65242675`
[2016-04-15T07:16Z] 2016-04-15 00:16:53 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:16:53,917 - WARNING - Could not retrieve variants from source file in region 15:59784282-59784683. Error was invalid region `15:59784283-59784683`
[2016-04-15T07:16Z] 2016-04-15 00:16:58 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:16:58,178 - WARNING - Could not retrieve variants from source file in region 15:67457124-67457525. Error was invalid region `15:67457125-67457525`
[2016-04-15T07:16Z] 2016-04-15 00:16:59 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:16:59,327 - WARNING - Could not retrieve variants from source file in region 15:54306714-54307115. Error was invalid region `15:54306715-54307115`
[2016-04-15T07:17Z] 2016-04-15 00:17:00 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:17:00,083 - WARNING - Could not retrieve variants from source file in region 15:59784282-59784683. Error was invalid region `15:59784283-59784683`
[2016-04-15T07:17Z] 2016-04-15 00:17:00 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:17:00,995 - WARNING - Could not retrieve variants from source file in region 15:63892700-63988547. Error was invalid region `15:63892701-63988547`
[2016-04-15T07:17Z] 2016-04-15 00:17:01 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:17:01,574 - WARNING - Could not retrieve variants from source file in region 15:63130906-63131307. Error was invalid region `15:63130907-63131307`
[2016-04-15T07:17Z] 2016-04-15 00:17:02 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:17:02,496 - WARNING - Could not retrieve variants from source file in region 15:60685453-60690279. Error was invalid region `15:60685454-60690279`
[2016-04-15T07:17Z] 2016-04-15 00:17:03 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:17:03,125 - WARNING - Could not retrieve variants from source file in region 15:67457124-67457525. Error was invalid region `15:67457125-67457525`
[2016-04-15T07:17Z] 2016-04-15 00:17:04 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:17:04,346 - WARNING - Could not retrieve variants from source file in region 15:64710616-64711017. Error was invalid region `15:64710617-64711017`
[2016-04-15T07:17Z] 2016-04-15 00:17:04 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:17:04,469 - WARNING - Could not retrieve variants from source file in region 15:54306714-54307115. Error was invalid region `15:54306715-54307115`
[2016-04-15T07:17Z] 2016-04-15 00:17:06 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:17:06,158 - WARNING - Could not retrieve variants from source file in region 15:59784282-59784683. Error was invalid region `15:59784283-59784683`
[2016-04-15T07:17Z] 2016-04-15 00:17:07 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:17:07,496 - WARNING - Could not retrieve variants from source file in region 15:60685453-60690279. Error was invalid region `15:60685454-60690279`
[2016-04-15T07:17Z] 2016-04-15 00:17:08 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:17:08,464 - WARNING - Could not retrieve variants from source file in region 15:63130906-63131307. Error was invalid region `15:63130907-63131307`
[2016-04-15T07:17Z] 2016-04-15 00:17:09 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:17:09,196 - WARNING - Could not retrieve variants from source file in region 15:67457124-67457525. Error was invalid region `15:67457125-67457525`
[2016-04-15T07:17Z] 2016-04-15 00:17:09 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:17:09,655 - WARNING - Could not retrieve variants from source file in region 15:54306714-54307115. Error was invalid region `15:54306715-54307115`
[2016-04-15T07:17Z] 2016-04-15 00:17:12 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:17:12,379 - WARNING - Could not retrieve variants from source file in region 15:58255916-58256317. Error was invalid region `15:58255917-58256317`
[2016-04-15T07:17Z] 2016-04-15 00:17:13 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:17:13,773 - WARNING - Could not retrieve variants from source file in region 15:63892700-63988547. Error was invalid region `15:63892701-63988547`
[2016-04-15T07:17Z] 2016-04-15 00:17:14 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:17:14,968 - WARNING - Could not retrieve variants from source file in region 15:52517503-52568041. Error was invalid region `15:52517504-52568041`
[2016-04-15T07:17Z] 2016-04-15 00:17:16 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:17:16,021 - WARNING - Could not retrieve variants from source file in region 15:65108293-65116518. Error was invalid region `15:65108294-65116518`
[2016-04-15T07:17Z] 2016-04-15 00:17:16 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:17:16,191 - WARNING - Could not retrieve variants from source file in region 15:64710616-64711017. Error was invalid region `15:64710617-64711017`
[2016-04-15T07:17Z] 2016-04-15 00:17:17 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:17:17,218 - WARNING - Could not retrieve variants from source file in region 15:58255916-58256317. Error was invalid region `15:58255917-58256317`
[2016-04-15T07:17Z] 2016-04-15 00:17:17 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:17:17,516 - WARNING - Could not retrieve variants from source file in region 15:59963277-59981780. Error was invalid region `15:59963278-59981780`
[2016-04-15T07:17Z] 2016-04-15 00:17:23 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:17:23,199 - WARNING - Could not retrieve variants from source file in region 15:56923503-56993034. Error was invalid region `15:56923504-56993034`
[2016-04-15T07:17Z] 2016-04-15 00:17:23 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:17:23,310 - WARNING - Could not retrieve variants from source file in region 15:55969830-55972987. Error was invalid region `15:55969831-55972987`
[2016-04-15T07:17Z] 2016-04-15 00:17:23 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:17:23,831 - WARNING - Could not retrieve variants from source file in region 15:67417893-67418294. Error was invalid region `15:67417894-67418294`
[2016-04-15T07:17Z] 2016-04-15 00:17:25 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:17:25,692 - WARNING - Could not retrieve variants from source file in region 15:59498968-59510379. Error was invalid region `15:59498969-59510379`
[2016-04-15T07:17Z] 2016-04-15 00:17:27 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:17:27,953 - WARNING - Could not retrieve variants from source file in region 15:63834108-63834509. Error was invalid region `15:63834109-63834509`
[2016-04-15T07:17Z] 2016-04-15 00:17:29 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:17:29,235 - WARNING - Could not retrieve variants from source file in region 15:67417893-67418294. Error was invalid region `15:67417894-67418294`
[2016-04-15T07:17Z] 2016-04-15 00:17:29 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:17:29,388 - WARNING - Could not retrieve variants from source file in region 15:63047567-63047983. Error was invalid region `15:63047568-63047983`
[2016-04-15T07:17Z] 2016-04-15 00:17:29 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:17:29,956 - WARNING - Could not retrieve variants from source file in region 15:53994282-54009035. Error was invalid region `15:53994283-54009035`
[2016-04-15T07:17Z] 2016-04-15 00:17:30 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:17:30,815 - WARNING - Could not retrieve variants from source file in region 15:59498968-59510379. Error was invalid region `15:59498969-59510379`
[2016-04-15T07:17Z] 2016-04-15 00:17:33 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:17:33,385 - WARNING - Could not retrieve variants from source file in region 15:63834108-63834509. Error was invalid region `15:63834109-63834509`
[2016-04-15T07:17Z] 2016-04-15 00:17:33 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:17:33,422 - WARNING - Could not retrieve variants from source file in region 15:56386366-56388121. Error was invalid region `15:56386367-56388121`
[2016-04-15T07:17Z] 2016-04-15 00:17:33 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:17:33,779 - WARNING - Could not retrieve variants from source file in region 15:56386366-56388121. Error was invalid region `15:56386367-56388121`
[2016-04-15T07:17Z] 2016-04-15 00:17:33 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:17:33,876 - WARNING - Could not retrieve variants from source file in region 15:67417893-67418294. Error was invalid region `15:67417894-67418294`
[2016-04-15T07:17Z] 2016-04-15 00:17:35 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:17:35,857 - WARNING - Could not retrieve variants from source file in region 15:64508552-64508953. Error was invalid region `15:64508553-64508953`
[2016-04-15T07:17Z] 2016-04-15 00:17:38 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:17:38,346 - WARNING - Could not retrieve variants from source file in region 15:56386366-56388121. Error was invalid region `15:56386367-56388121`
[2016-04-15T07:17Z] 2016-04-15 00:17:38 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:17:38,863 - WARNING - Could not retrieve variants from source file in region 15:63834108-63834509. Error was invalid region `15:63834109-63834509`
[2016-04-15T07:17Z] 2016-04-15 00:17:38 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:17:38,949 - WARNING - Could not retrieve variants from source file in region 15:52404651-52405124. Error was invalid region `15:52404652-52405124`
[2016-04-15T07:17Z] 2016-04-15 00:17:38 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:17:38,986 - WARNING - Could not retrieve variants from source file in region 15:59453173-59453574. Error was invalid region `15:59453174-59453574`
[2016-04-15T07:17Z] 2016-04-15 00:17:40 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:17:40,279 - WARNING - Could not retrieve variants from source file in region 15:64508552-64508953. Error was invalid region `15:64508553-64508953`
[2016-04-15T07:17Z] 2016-04-15 00:17:43 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:17:43,525 - WARNING - Could not retrieve variants from source file in region 15:57999093-58001171. Error was invalid region `15:57999094-58001171`
[2016-04-15T07:17Z] 2016-04-15 00:17:44 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:17:44,591 - WARNING - Could not retrieve variants from source file in region 15:59225607-59226114. Error was invalid region `15:59225608-59226114`
[2016-04-15T07:17Z] 2016-04-15 00:17:47 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:17:47,221 - WARNING - Could not retrieve variants from source file in region 15:66821039-66821440. Error was invalid region `15:66821040-66821440`
[2016-04-15T07:17Z] 2016-04-15 00:17:47 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:17:47,520 - WARNING - Could not retrieve variants from source file in region 15:66821039-66821440. Error was invalid region `15:66821040-66821440`
[2016-04-15T07:17Z] 2016-04-15 00:17:48 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:17:48,488 - WARNING - Could not retrieve variants from source file in region 15:59322837-59368357. Error was invalid region `15:59322838-59368357`
[2016-04-15T07:17Z] 2016-04-15 00:17:52 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:17:52,312 - WARNING - Could not retrieve variants from source file in region 15:66586005-66586407. Error was invalid region `15:66586006-66586407`
[2016-04-15T07:17Z] 2016-04-15 00:17:52 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:17:52,325 - WARNING - Could not retrieve variants from source file in region 15:66586005-66586407. Error was invalid region `15:66586006-66586407`
[2016-04-15T07:17Z] 2016-04-15 00:17:52 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:17:52,346 - WARNING - Could not retrieve variants from source file in region 15:66586005-66586407. Error was invalid region `15:66586006-66586407`
[2016-04-15T07:17Z] 2016-04-15 00:17:55 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:17:55,001 - WARNING - Could not retrieve variants from source file in region 15:66257197-66274880. Error was invalid region `15:66257198-66274880`
[2016-04-15T07:17Z] 2016-04-15 00:17:55 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:17:55,005 - WARNING - Could not retrieve variants from source file in region 15:66257197-66274880. Error was invalid region `15:66257198-66274880`
[2016-04-15T07:17Z] 2016-04-15 00:17:55 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:17:55,005 - WARNING - Could not retrieve variants from source file in region 15:66257197-66274880. Error was invalid region `15:66257198-66274880`
[2016-04-15T07:18Z] ['bcbio-variation-recall', 'square', '-Xms750m', '-Xmx7280m', '-XX:+UseSerialGC', '-c', 16, '-r', u'15:67932891-83447639', '--caller', 'platypus', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/15/Batch1-15_67932890_83447639.vcf.gz', '/mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/15/Batch1-15_67932890_83447639.vcf-inputs.txt'] in region: 15:67932891-83447639
[2016-04-15T07:18Z] 2016-04-15 00:18:11 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:18:10,998 - WARNING - Could not retrieve variants from source file in region 15:80987601-80988002. Error was invalid region `15:80987602-80988002`
[2016-04-15T07:18Z] 2016-04-15 00:18:11 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:18:11,060 - WARNING - Could not retrieve variants from source file in region 15:80259803-80263596. Error was invalid region `15:80259804-80263596`
[2016-04-15T07:18Z] 2016-04-15 00:18:11 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:18:11,363 - WARNING - Could not retrieve variants from source file in region 15:82443728-82444627. Error was invalid region `15:82443729-82444627`
[2016-04-15T07:18Z] 2016-04-15 00:18:11 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:18:11,702 - WARNING - Could not retrieve variants from source file in region 15:73023726-73027668. Error was invalid region `15:73023727-73027668`
[2016-04-15T07:18Z] 2016-04-15 00:18:11 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:18:11,721 - WARNING - Could not retrieve variants from source file in region 15:75914538-75914939. Error was invalid region `15:75914539-75914939`
[2016-04-15T07:18Z] 2016-04-15 00:18:12 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:18:12,022 - WARNING - Could not retrieve variants from source file in region 15:71124882-71125394. Error was invalid region `15:71124883-71125394`
[2016-04-15T07:18Z] 2016-04-15 00:18:12 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:18:12,164 - WARNING - Could not retrieve variants from source file in region 15:77287279-77344983. Error was invalid region `15:77287280-77344983`
[2016-04-15T07:18Z] 2016-04-15 00:18:12 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:18:12,530 - WARNING - Could not retrieve variants from source file in region 15:75117701-75132149. Error was invalid region `15:75117702-75132149`
[2016-04-15T07:18Z] 2016-04-15 00:18:12 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:18:12,678 - WARNING - Could not retrieve variants from source file in region 15:69548127-69561708. Error was invalid region `15:69548128-69561708`
[2016-04-15T07:18Z] 2016-04-15 00:18:12 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:18:12,767 - WARNING - Could not retrieve variants from source file in region 15:78758466-78789678. Error was invalid region `15:78758467-78789678`
[2016-04-15T07:18Z] 2016-04-15 00:18:12 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:18:12,788 - WARNING - Could not retrieve variants from source file in region 15:81212397-81212798. Error was invalid region `15:81212398-81212798`
[2016-04-15T07:18Z] 2016-04-15 00:18:18 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:18:18,526 - WARNING - Could not retrieve variants from source file in region 15:80987601-80988002. Error was invalid region `15:80987602-80988002`
[2016-04-15T07:18Z] 2016-04-15 00:18:18 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:18:18,988 - WARNING - Could not retrieve variants from source file in region 15:74836105-74836506. Error was invalid region `15:74836106-74836506`
[2016-04-15T07:18Z] 2016-04-15 00:18:19 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:18:19,476 - WARNING - Could not retrieve variants from source file in region 15:80259803-80263596. Error was invalid region `15:80259804-80263596`
[2016-04-15T07:18Z] 2016-04-15 00:18:20 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:18:20,166 - WARNING - Could not retrieve variants from source file in region 15:82443728-82444627. Error was invalid region `15:82443729-82444627`
[2016-04-15T07:18Z] 2016-04-15 00:18:20 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:18:20,212 - WARNING - Could not retrieve variants from source file in region 15:74219371-74219772. Error was invalid region `15:74219372-74219772`
[2016-04-15T07:18Z] 2016-04-15 00:18:20 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:18:20,619 - WARNING - Could not retrieve variants from source file in region 15:75914538-75914939. Error was invalid region `15:75914539-75914939`
[2016-04-15T07:18Z] 2016-04-15 00:18:20 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:18:20,829 - WARNING - Could not retrieve variants from source file in region 15:83447420-83447821. Error was invalid region `15:83447421-83447821`
[2016-04-15T07:18Z] 2016-04-15 00:18:21 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:18:21,022 - WARNING - Could not retrieve variants from source file in region 15:73023726-73027668. Error was invalid region `15:73023727-73027668`
[2016-04-15T07:18Z] 2016-04-15 00:18:22 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:18:22,014 - WARNING - Could not retrieve variants from source file in region 15:71124882-71125394. Error was invalid region `15:71124883-71125394`
[2016-04-15T07:18Z] 2016-04-15 00:18:22 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:18:22,158 - WARNING - Could not retrieve variants from source file in region 15:81577928-81637474. Error was invalid region `15:81577929-81637474`
[2016-04-15T07:18Z] 2016-04-15 00:18:22 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:18:22,186 - WARNING - Could not retrieve variants from source file in region 15:81212397-81212798. Error was invalid region `15:81212398-81212798`
[2016-04-15T07:18Z] 2016-04-15 00:18:23 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:18:23,773 - WARNING - Could not retrieve variants from source file in region 15:80987601-80988002. Error was invalid region `15:80987602-80988002`
[2016-04-15T07:18Z] 2016-04-15 00:18:25 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:18:25,072 - WARNING - Could not retrieve variants from source file in region 15:80259803-80263596. Error was invalid region `15:80259804-80263596`
[2016-04-15T07:18Z] 2016-04-15 00:18:27 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:18:27,479 - WARNING - Could not retrieve variants from source file in region 15:75914538-75914939. Error was invalid region `15:75914539-75914939`
[2016-04-15T07:18Z] 2016-04-15 00:18:27 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:18:27,604 - WARNING - Could not retrieve variants from source file in region 15:73023726-73027668. Error was invalid region `15:73023727-73027668`
[2016-04-15T07:18Z] 2016-04-15 00:18:28 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:18:28,046 - WARNING - Could not retrieve variants from source file in region 15:83447420-83447821. Error was invalid region `15:83447421-83447821`
[2016-04-15T07:18Z] 2016-04-15 00:18:28 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:18:28,631 - WARNING - Could not retrieve variants from source file in region 15:69548127-69561708. Error was invalid region `15:69548128-69561708`
[2016-04-15T07:18Z] 2016-04-15 00:18:29 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:18:29,270 - WARNING - Could not retrieve variants from source file in region 15:77287279-77344983. Error was invalid region `15:77287280-77344983`
[2016-04-15T07:18Z] 2016-04-15 00:18:29 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:18:29,316 - WARNING - Could not retrieve variants from source file in region 15:71124882-71125394. Error was invalid region `15:71124883-71125394`
[2016-04-15T07:18Z] 2016-04-15 00:18:29 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:18:29,378 - WARNING - Could not retrieve variants from source file in region 15:78758466-78789678. Error was invalid region `15:78758467-78789678`
[2016-04-15T07:18Z] 2016-04-15 00:18:29 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:18:29,411 - WARNING - Could not retrieve variants from source file in region 15:81212397-81212798. Error was invalid region `15:81212398-81212798`
[2016-04-15T07:18Z] 2016-04-15 00:18:40 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:18:40,947 - WARNING - Could not retrieve variants from source file in region 15:80191132-80191533. Error was invalid region `15:80191133-80191533`
[2016-04-15T07:18Z] 2016-04-15 00:18:41 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:18:41,014 - WARNING - Could not retrieve variants from source file in region 15:80883814-80884215. Error was invalid region `15:80883815-80884215`
[2016-04-15T07:18Z] 2016-04-15 00:18:42 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:18:42,043 - WARNING - Could not retrieve variants from source file in region 15:80883814-80884215. Error was invalid region `15:80883815-80884215`
[2016-04-15T07:18Z] 2016-04-15 00:18:43 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:18:43,586 - WARNING - Could not retrieve variants from source file in region 15:74032572-74032973. Error was invalid region `15:74032573-74032973`
[2016-04-15T07:18Z] 2016-04-15 00:18:43 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:18:43,990 - WARNING - Could not retrieve variants from source file in region 15:72668328-72668729. Error was invalid region `15:72668329-72668729`
[2016-04-15T07:18Z] 2016-04-15 00:18:44 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:18:44,146 - WARNING - Could not retrieve variants from source file in region 15:83224485-83240483. Error was invalid region `15:83224486-83240483`
[2016-04-15T07:18Z] 2016-04-15 00:18:45 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:18:45,036 - WARNING - Could not retrieve variants from source file in region 15:74703718-74710165. Error was invalid region `15:74703719-74710165`
[2016-04-15T07:18Z] 2016-04-15 00:18:46 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:18:46,125 - WARNING - Could not retrieve variants from source file in region 15:77241297-77241732. Error was invalid region `15:77241298-77241732`
[2016-04-15T07:18Z] 2016-04-15 00:18:46 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:18:46,862 - WARNING - Could not retrieve variants from source file in region 15:80883814-80884215. Error was invalid region `15:80883815-80884215`
[2016-04-15T07:18Z] 2016-04-15 00:18:47 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:18:47,199 - WARNING - Could not retrieve variants from source file in region 15:75047215-75047616. Error was invalid region `15:75047216-75047616`
[2016-04-15T07:18Z] 2016-04-15 00:18:47 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:18:47,201 - WARNING - Could not retrieve variants from source file in region 15:80191132-80191533. Error was invalid region `15:80191133-80191533`
[2016-04-15T07:18Z] 2016-04-15 00:18:48 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:18:48,570 - WARNING - Could not retrieve variants from source file in region 15:74032572-74032973. Error was invalid region `15:74032573-74032973`
[2016-04-15T07:18Z] 2016-04-15 00:18:48 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:18:48,682 - WARNING - Could not retrieve variants from source file in region 15:81489128-81489529. Error was invalid region `15:81489129-81489529`
[2016-04-15T07:18Z] 2016-04-15 00:18:48 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:18:48,710 - WARNING - Could not retrieve variants from source file in region 15:75650625-75652171. Error was invalid region `15:75650626-75652171`
[2016-04-15T07:18Z] 2016-04-15 00:18:48 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:18:48,908 - WARNING - Could not retrieve variants from source file in region 15:72668328-72668729. Error was invalid region `15:72668329-72668729`
[2016-04-15T07:18Z] 2016-04-15 00:18:48 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:18:48,950 - WARNING - Could not retrieve variants from source file in region 15:83224485-83240483. Error was invalid region `15:83224486-83240483`
[2016-04-15T07:18Z] 2016-04-15 00:18:50 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:18:50,795 - WARNING - Could not retrieve variants from source file in region 15:69325370-69328416. Error was invalid region `15:69325371-69328416`
[2016-04-15T07:18Z] 2016-04-15 00:18:52 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:18:52,806 - WARNING - Could not retrieve variants from source file in region 15:70991714-70994473. Error was invalid region `15:70991715-70994473`
[2016-04-15T07:18Z] 2016-04-15 00:18:52 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:18:52,833 - WARNING - Could not retrieve variants from source file in region 15:74536189-74560966. Error was invalid region `15:74536190-74560966`
[2016-04-15T07:18Z] 2016-04-15 00:18:52 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:18:52,955 - WARNING - Could not retrieve variants from source file in region 15:78632619-78633020. Error was invalid region `15:78632620-78633020`
[2016-04-15T07:18Z] 2016-04-15 00:18:53 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:18:52,999 - WARNING - Could not retrieve variants from source file in region 15:75047215-75047616. Error was invalid region `15:75047216-75047616`
[2016-04-15T07:18Z] 2016-04-15 00:18:53 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:18:53,394 - WARNING - Could not retrieve variants from source file in region 15:74032572-74032973. Error was invalid region `15:74032573-74032973`
[2016-04-15T07:18Z] 2016-04-15 00:18:54 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:18:54,378 - WARNING - Could not retrieve variants from source file in region 15:83224485-83240483. Error was invalid region `15:83224486-83240483`
[2016-04-15T07:18Z] 2016-04-15 00:18:54 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:18:54,374 - WARNING - Could not retrieve variants from source file in region 15:72668328-72668729. Error was invalid region `15:72668329-72668729`
[2016-04-15T07:18Z] 2016-04-15 00:18:58 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:18:58,091 - WARNING - Could not retrieve variants from source file in region 15:78632619-78633020. Error was invalid region `15:78632620-78633020`
[2016-04-15T07:18Z] 2016-04-15 00:18:58 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:18:58,196 - WARNING - Could not retrieve variants from source file in region 15:70991714-70994473. Error was invalid region `15:70991715-70994473`
[2016-04-15T07:18Z] 2016-04-15 00:18:58 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:18:58,726 - WARNING - Could not retrieve variants from source file in region 15:75047215-75047616. Error was invalid region `15:75047216-75047616`
[2016-04-15T07:19Z] 2016-04-15 00:19:00 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:19:00,215 - WARNING - Could not retrieve variants from source file in region 15:75498337-75503337. Error was invalid region `15:75498338-75503337`
[2016-04-15T07:19Z] 2016-04-15 00:19:00 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:19:00,468 - WARNING - Could not retrieve variants from source file in region 15:74658104-74658505. Error was invalid region `15:74658105-74658505`
[2016-04-15T07:19Z] 2016-04-15 00:19:05 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:19:05,881 - WARNING - Could not retrieve variants from source file in region 15:74658104-74658505. Error was invalid region `15:74658105-74658505`
[2016-04-15T07:19Z] 2016-04-15 00:19:07 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:19:07,330 - WARNING - Could not retrieve variants from source file in region 15:75336518-75336919. Error was invalid region `15:75336519-75336919`
[2016-04-15T07:19Z] 2016-04-15 00:19:10 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:19:10,185 - WARNING - Could not retrieve variants from source file in region 15:72637584-72639082. Error was invalid region `15:72637585-72639082`
[2016-04-15T07:19Z] 2016-04-15 00:19:10 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:19:10,465 - WARNING - Could not retrieve variants from source file in region 15:73859277-73860045. Error was invalid region `15:73859278-73860045`
[2016-04-15T07:19Z] 2016-04-15 00:19:10 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:19:10,466 - WARNING - Could not retrieve variants from source file in region 15:82636850-82637269. Error was invalid region `15:82636851-82637269`
[2016-04-15T07:19Z] 2016-04-15 00:19:11 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:19:11,500 - WARNING - Could not retrieve variants from source file in region 15:77175947-77176348. Error was invalid region `15:77175948-77176348`
[2016-04-15T07:19Z] 2016-04-15 00:19:11 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:19:11,535 - WARNING - Could not retrieve variants from source file in region 15:75498337-75503337. Error was invalid region `15:75498338-75503337`
[2016-04-15T07:19Z] 2016-04-15 00:19:12 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:19:12,139 - WARNING - Could not retrieve variants from source file in region 15:74658104-74658505. Error was invalid region `15:74658105-74658505`
[2016-04-15T07:19Z] 2016-04-15 00:19:12 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:19:12,432 - WARNING - Could not retrieve variants from source file in region 15:80137349-80137750. Error was invalid region `15:80137350-80137750`
[2016-04-15T07:19Z] 2016-04-15 00:19:13 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:19:13,164 - WARNING - Could not retrieve variants from source file in region 15:75336518-75336919. Error was invalid region `15:75336519-75336919`
[2016-04-15T07:19Z] 2016-04-15 00:19:13 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:19:13,171 - WARNING - Could not retrieve variants from source file in region 15:70959857-70960258. Error was invalid region `15:70959858-70960258`
[2016-04-15T07:19Z] 2016-04-15 00:19:14 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:19:14,796 - WARNING - Could not retrieve variants from source file in region 15:78556794-78585296. Error was invalid region `15:78556795-78585296`
[2016-04-15T07:19Z] 2016-04-15 00:19:15 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:19:15,491 - WARNING - Could not retrieve variants from source file in region 15:72637584-72639082. Error was invalid region `15:72637585-72639082`
[2016-04-15T07:19Z] 2016-04-15 00:19:16 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:19:16,349 - WARNING - Could not retrieve variants from source file in region 15:82636850-82637269. Error was invalid region `15:82636851-82637269`
[2016-04-15T07:19Z] 2016-04-15 00:19:16 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:19:16,372 - WARNING - Could not retrieve variants from source file in region 15:69238234-69238635. Error was invalid region `15:69238235-69238635`
[2016-04-15T07:19Z] 2016-04-15 00:19:17 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:19:17,160 - WARNING - Could not retrieve variants from source file in region 15:77175947-77176348. Error was invalid region `15:77175948-77176348`
[2016-04-15T07:19Z] 2016-04-15 00:19:19 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:19:19,162 - WARNING - Could not retrieve variants from source file in region 15:70959857-70960258. Error was invalid region `15:70959858-70960258`
[2016-04-15T07:19Z] 2016-04-15 00:19:19 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:19:19,205 - WARNING - Could not retrieve variants from source file in region 15:75012776-75013177. Error was invalid region `15:75012777-75013177`
[2016-04-15T07:19Z] 2016-04-15 00:19:19 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:19:19,214 - WARNING - Could not retrieve variants from source file in region 15:75336518-75336919. Error was invalid region `15:75336519-75336919`
[2016-04-15T07:19Z] 2016-04-15 00:19:19 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:19:19,633 - WARNING - Could not retrieve variants from source file in region 15:78441558-78466317. Error was invalid region `15:78441559-78466317`
[2016-04-15T07:19Z] 2016-04-15 00:19:20 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:19:20,323 - WARNING - Could not retrieve variants from source file in region 15:74467585-74500428. Error was invalid region `15:74467586-74500428`
[2016-04-15T07:19Z] 2016-04-15 00:19:21 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:19:21,063 - WARNING - Could not retrieve variants from source file in region 15:78556794-78585296. Error was invalid region `15:78556795-78585296`
[2016-04-15T07:19Z] 2016-04-15 00:19:21 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:19:21,843 - WARNING - Could not retrieve variants from source file in region 15:72637584-72639082. Error was invalid region `15:72637585-72639082`
[2016-04-15T07:19Z] 2016-04-15 00:19:22 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:19:22,210 - WARNING - Could not retrieve variants from source file in region 15:82636850-82637269. Error was invalid region `15:82636851-82637269`
[2016-04-15T07:19Z] 2016-04-15 00:19:24 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:19:24,008 - WARNING - Could not retrieve variants from source file in region 15:70959857-70960258. Error was invalid region `15:70959858-70960258`
[2016-04-15T07:19Z] 2016-04-15 00:19:24 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:19:24,954 - WARNING - Could not retrieve variants from source file in region 15:78441558-78466317. Error was invalid region `15:78441559-78466317`
[2016-04-15T07:19Z] 2016-04-15 00:19:25 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:19:25,768 - WARNING - Could not retrieve variants from source file in region 15:74467585-74500428. Error was invalid region `15:74467586-74500428`
[2016-04-15T07:19Z] 2016-04-15 00:19:27 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:19:27,841 - WARNING - Could not retrieve variants from source file in region 15:75189719-75190120. Error was invalid region `15:75189720-75190120`
[2016-04-15T07:19Z] 2016-04-15 00:19:28 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:19:28,493 - WARNING - Could not retrieve variants from source file in region 15:78369589-78398336. Error was invalid region `15:78369590-78398336`
[2016-04-15T07:19Z] 2016-04-15 00:19:29 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:19:29,299 - WARNING - Could not retrieve variants from source file in region 15:75189719-75190120. Error was invalid region `15:75189720-75190120`
[2016-04-15T07:19Z] 2016-04-15 00:19:33 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:19:33,193 - WARNING - Could not retrieve variants from source file in region 15:75189719-75190120. Error was invalid region `15:75189720-75190120`
[2016-04-15T07:19Z] 2016-04-15 00:19:37 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:19:37,208 - WARNING - Could not retrieve variants from source file in region 15:77906934-77907974. Error was invalid region `15:77906935-77907974`
[2016-04-15T07:19Z] 2016-04-15 00:19:39 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:19:39,170 - WARNING - Could not retrieve variants from source file in region 15:76726254-76726655. Error was invalid region `15:76726255-76726655`
[2016-04-15T07:19Z] 2016-04-15 00:19:39 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:19:39,251 - WARNING - Could not retrieve variants from source file in region 15:82557823-82564181. Error was invalid region `15:82557824-82564181`
[2016-04-15T07:19Z] 2016-04-15 00:19:39 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:19:39,340 - WARNING - Could not retrieve variants from source file in region 15:72598403-72598804. Error was invalid region `15:72598404-72598804`
[2016-04-15T07:19Z] 2016-04-15 00:19:39 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:19:39,594 - WARNING - Could not retrieve variants from source file in region 15:70345415-70353158. Error was invalid region `15:70345416-70353158`
[2016-04-15T07:19Z] 2016-04-15 00:19:39 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:19:39,871 - WARNING - Could not retrieve variants from source file in region 15:72432372-72432773. Error was invalid region `15:72432373-72432773`
[2016-04-15T07:19Z] 2016-04-15 00:19:40 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:19:40,893 - WARNING - Could not retrieve variants from source file in region 15:74425199-74425695. Error was invalid region `15:74425200-74425695`
[2016-04-15T07:19Z] 2016-04-15 00:19:41 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:19:41,389 - WARNING - Could not retrieve variants from source file in region 15:73614623-73616068. Error was invalid region `15:73614624-73616068`
[2016-04-15T07:19Z] 2016-04-15 00:19:41 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:19:41,774 - WARNING - Could not retrieve variants from source file in region 15:77906934-77907974. Error was invalid region `15:77906935-77907974`
[2016-04-15T07:19Z] 2016-04-15 00:19:42 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:19:42,963 - WARNING - Could not retrieve variants from source file in region 15:68924229-68924630. Error was invalid region `15:68924230-68924630`
[2016-04-15T07:19Z] 2016-04-15 00:19:43 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:19:43,657 - WARNING - Could not retrieve variants from source file in region 15:76726254-76726655. Error was invalid region `15:76726255-76726655`
[2016-04-15T07:19Z] 2016-04-15 00:19:43 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:19:43,958 - WARNING - Could not retrieve variants from source file in region 15:82557823-82564181. Error was invalid region `15:82557824-82564181`
[2016-04-15T07:19Z] 2016-04-15 00:19:44 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:19:44,414 - WARNING - Could not retrieve variants from source file in region 15:72598403-72598804. Error was invalid region `15:72598404-72598804`
[2016-04-15T07:19Z] 2016-04-15 00:19:45 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:19:45,937 - WARNING - Could not retrieve variants from source file in region 15:72432372-72432773. Error was invalid region `15:72432373-72432773`
[2016-04-15T07:19Z] 2016-04-15 00:19:46 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:19:46,188 - WARNING - Could not retrieve variants from source file in region 15:79749050-79750497. Error was invalid region `15:79749051-79750497`
[2016-04-15T07:19Z] 2016-04-15 00:19:47 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:19:47,979 - WARNING - Could not retrieve variants from source file in region 15:73614623-73616068. Error was invalid region `15:73614624-73616068`
[2016-04-15T07:19Z] 2016-04-15 00:19:48 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:19:48,017 - WARNING - Could not retrieve variants from source file in region 15:77906934-77907974. Error was invalid region `15:77906935-77907974`
[2016-04-15T07:19Z] 2016-04-15 00:19:48 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:19:48,547 - WARNING - Could not retrieve variants from source file in region 15:71507478-71507879. Error was invalid region `15:71507479-71507879`
[2016-04-15T07:19Z] 2016-04-15 00:19:49 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:19:49,342 - WARNING - Could not retrieve variants from source file in region 15:72598403-72598804. Error was invalid region `15:72598404-72598804`
[2016-04-15T07:19Z] 2016-04-15 00:19:50 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:19:50,436 - WARNING - Could not retrieve variants from source file in region 15:82512218-82512619. Error was invalid region `15:82512219-82512619`
[2016-04-15T07:19Z] 2016-04-15 00:19:51 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:19:51,552 - WARNING - Could not retrieve variants from source file in region 15:70345415-70353158. Error was invalid region `15:70345416-70353158`
[2016-04-15T07:19Z] 2016-04-15 00:19:52 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:19:52,166 - WARNING - Could not retrieve variants from source file in region 15:72432372-72432773. Error was invalid region `15:72432373-72432773`
[2016-04-15T07:19Z] 2016-04-15 00:19:53 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:19:53,274 - WARNING - Could not retrieve variants from source file in region 15:74425199-74425695. Error was invalid region `15:74425200-74425695`
[2016-04-15T07:19Z] 2016-04-15 00:19:56 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:19:56,018 - WARNING - Could not retrieve variants from source file in region 15:77450753-77451154. Error was invalid region `15:77450754-77451154`
[2016-04-15T07:19Z] 2016-04-15 00:19:57 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:19:57,542 - WARNING - Could not retrieve variants from source file in region 15:82512218-82512619. Error was invalid region `15:82512219-82512619`
[2016-04-15T07:19Z] 2016-04-15 00:19:58 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:19:58,200 - WARNING - Could not retrieve variants from source file in region 15:79270653-79277701. Error was invalid region `15:79270654-79277701`
[2016-04-15T07:20Z] 2016-04-15 00:20:03 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:20:03,298 - WARNING - Could not retrieve variants from source file in region 15:79586150-79614608. Error was invalid region `15:79586151-79614608`
[2016-04-15T07:20Z] 2016-04-15 00:20:04 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:20:04,308 - WARNING - Could not retrieve variants from source file in region 15:79270653-79277701. Error was invalid region `15:79270654-79277701`
[2016-04-15T07:20Z] 2016-04-15 00:20:04 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:20:04,379 - WARNING - Could not retrieve variants from source file in region 15:68582964-68657770. Error was invalid region `15:68582965-68657770`
[2016-04-15T07:20Z] 2016-04-15 00:20:05 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:20:05,632 - WARNING - Could not retrieve variants from source file in region 15:72545572-72545973. Error was invalid region `15:72545573-72545973`
[2016-04-15T07:20Z] 2016-04-15 00:20:07 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:20:07,818 - WARNING - Could not retrieve variants from source file in region 15:72190862-72191456. Error was invalid region `15:72190863-72191456`
[2016-04-15T07:20Z] 2016-04-15 00:20:08 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:20:08,343 - WARNING - Could not retrieve variants from source file in region 15:69728738-69732926. Error was invalid region `15:69728739-69732926`
[2016-04-15T07:20Z] 2016-04-15 00:20:08 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:20:08,443 - WARNING - Could not retrieve variants from source file in region 15:74277584-74277985. Error was invalid region `15:74277585-74277985`
[2016-04-15T07:20Z] 2016-04-15 00:20:08 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:20:08,597 - WARNING - Could not retrieve variants from source file in region 15:73541302-73565071. Error was invalid region `15:73541303-73565071`
[2016-04-15T07:20Z] 2016-04-15 00:20:09 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:20:09,285 - WARNING - Could not retrieve variants from source file in region 15:79586150-79614608. Error was invalid region `15:79586151-79614608`
[2016-04-15T07:20Z] 2016-04-15 00:20:10 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:20:10,285 - WARNING - Could not retrieve variants from source file in region 15:74277584-74277985. Error was invalid region `15:74277585-74277985`
[2016-04-15T07:20Z] 2016-04-15 00:20:11 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:20:11,034 - WARNING - Could not retrieve variants from source file in region 15:79586150-79614608. Error was invalid region `15:79586151-79614608`
[2016-04-15T07:20Z] 2016-04-15 00:20:11 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:20:11,086 - WARNING - Could not retrieve variants from source file in region 15:76630092-76632491. Error was invalid region `15:76630093-76632491`
[2016-04-15T07:20Z] 2016-04-15 00:20:12 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:20:12,946 - WARNING - Could not retrieve variants from source file in region 15:72190862-72191456. Error was invalid region `15:72190863-72191456`
[2016-04-15T07:20Z] 2016-04-15 00:20:13 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:20:13,450 - WARNING - Could not retrieve variants from source file in region 15:74277584-74277985. Error was invalid region `15:74277585-74277985`
[2016-04-15T07:20Z] 2016-04-15 00:20:13 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:20:13,828 - WARNING - Could not retrieve variants from source file in region 15:71276269-71276673. Error was invalid region `15:71276270-71276673`
[2016-04-15T07:20Z] 2016-04-15 00:20:14 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:20:14,482 - WARNING - Could not retrieve variants from source file in region 15:73541302-73565071. Error was invalid region `15:73541303-73565071`
[2016-04-15T07:20Z] 2016-04-15 00:20:14 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:20:14,693 - WARNING - Could not retrieve variants from source file in region 15:77406903-77407304. Error was invalid region `15:77406904-77407304`
[2016-04-15T07:20Z] 2016-04-15 00:20:15 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:20:15,726 - WARNING - Could not retrieve variants from source file in region 15:68114288-68124855. Error was invalid region `15:68114289-68124855`
[2016-04-15T07:20Z] 2016-04-15 00:20:15 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:20:15,887 - WARNING - Could not retrieve variants from source file in region 15:77406903-77407304. Error was invalid region `15:77406904-77407304`
[2016-04-15T07:20Z] 2016-04-15 00:20:17 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:20:17,959 - WARNING - Could not retrieve variants from source file in region 15:72190862-72191456. Error was invalid region `15:72190863-72191456`
[2016-04-15T07:20Z] 2016-04-15 00:20:19 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:20:19,290 - WARNING - Could not retrieve variants from source file in region 15:69728738-69732926. Error was invalid region `15:69728739-69732926`
[2016-04-15T07:20Z] 2016-04-15 00:20:19 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:20:19,638 - WARNING - Could not retrieve variants from source file in region 15:77406903-77407304. Error was invalid region `15:77406904-77407304`
[2016-04-15T07:20Z] 2016-04-15 00:20:24 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:20:24,016 - WARNING - Could not retrieve variants from source file in region 15:79217479-79237514. Error was invalid region `15:79217480-79237514`
[2016-04-15T07:20Z] 2016-04-15 00:20:25 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:20:25,131 - WARNING - Could not retrieve variants from source file in region 15:68114288-68124855. Error was invalid region `15:68114289-68124855`
[2016-04-15T07:20Z] 2016-04-15 00:20:26 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:20:26,492 - WARNING - Could not retrieve variants from source file in region 15:73067023-73067424. Error was invalid region `15:73067024-73067424`
[2016-04-15T07:20Z] 2016-04-15 00:20:27 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:20:27,664 - WARNING - Could not retrieve variants from source file in region 15:73067023-73067424. Error was invalid region `15:73067024-73067424`
[2016-04-15T07:20Z] 2016-04-15 00:20:27 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:20:27,985 - WARNING - Could not retrieve variants from source file in region 15:79217479-79237514. Error was invalid region `15:79217480-79237514`
[2016-04-15T07:20Z] 2016-04-15 00:20:28 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:20:28,673 - WARNING - Could not retrieve variants from source file in region 15:76496021-76496530. Error was invalid region `15:76496022-76496530`
[2016-04-15T07:20Z] 2016-04-15 00:20:28 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:20:28,858 - WARNING - Could not retrieve variants from source file in region 15:72105717-72106119. Error was invalid region `15:72105718-72106119`
[2016-04-15T07:20Z] 2016-04-15 00:20:30 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:20:30,500 - WARNING - Could not retrieve variants from source file in region 15:73067023-73067424. Error was invalid region `15:73067024-73067424`
[2016-04-15T07:20Z] 2016-04-15 00:20:30 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:20:30,753 - WARNING - Could not retrieve variants from source file in region 15:69671643-69672044. Error was invalid region `15:69671644-69672044`
[2016-04-15T07:20Z] 2016-04-15 00:20:31 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:20:31,443 - WARNING - Could not retrieve variants from source file in region 15:76452265-76452666. Error was invalid region `15:76452266-76452666`
[2016-04-15T07:20Z] 2016-04-15 00:20:31 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:20:31,564 - WARNING - Could not retrieve variants from source file in region 15:78882714-78917589. Error was invalid region `15:78882715-78917589`
[2016-04-15T07:20Z] 2016-04-15 00:20:32 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:20:32,889 - WARNING - Could not retrieve variants from source file in region 15:72105717-72106119. Error was invalid region `15:72105718-72106119`
[2016-04-15T07:20Z] 2016-04-15 00:20:32 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:20:32,927 - WARNING - Could not retrieve variants from source file in region 15:76496021-76496530. Error was invalid region `15:76496022-76496530`
[2016-04-15T07:20Z] 2016-04-15 00:20:34 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:20:34,488 - WARNING - Could not retrieve variants from source file in region 15:71184436-71184837. Error was invalid region `15:71184437-71184837`
[2016-04-15T07:20Z] 2016-04-15 00:20:34 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:20:34,567 - WARNING - Could not retrieve variants from source file in region 15:72105717-72106119. Error was invalid region `15:72105718-72106119`
[2016-04-15T07:20Z] 2016-04-15 00:20:34 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:20:34,897 - WARNING - Could not retrieve variants from source file in region 15:69671643-69672044. Error was invalid region `15:69671644-69672044`
[2016-04-15T07:20Z] 2016-04-15 00:20:39 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:20:39,116 - WARNING - Could not retrieve variants from source file in region 15:69671643-69672044. Error was invalid region `15:69671644-69672044`
[2016-04-15T07:20Z] 2016-04-15 00:20:40 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:20:40,454 - WARNING - Could not retrieve variants from source file in region 15:76136557-76136958. Error was invalid region `15:76136558-76136958`
[2016-04-15T07:20Z] 2016-04-15 00:20:40 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:20:40,627 - WARNING - Could not retrieve variants from source file in region 15:79185687-79186088. Error was invalid region `15:79185688-79186088`
[2016-04-15T07:20Z] 2016-04-15 00:20:42 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:20:42,109 - WARNING - Could not retrieve variants from source file in region 15:76017241-76017642. Error was invalid region `15:76017242-76017642`
[2016-04-15T07:20Z] 2016-04-15 00:20:42 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:20:42,398 - WARNING - Could not retrieve variants from source file in region 15:71184436-71184837. Error was invalid region `15:71184437-71184837`
[2016-04-15T07:20Z] 2016-04-15 00:20:42 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:20:42,427 - WARNING - Could not retrieve variants from source file in region 15:76222624-76223025. Error was invalid region `15:76222625-76223025`
[2016-04-15T07:20Z] 2016-04-15 00:20:42 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:20:42,700 - WARNING - Could not retrieve variants from source file in region 15:79185687-79186088. Error was invalid region `15:79185688-79186088`
[2016-04-15T07:20Z] 2016-04-15 00:20:44 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:20:44,680 - WARNING - Could not retrieve variants from source file in region 15:78820932-78841410. Error was invalid region `15:78820933-78841410`
[2016-04-15T07:20Z] 2016-04-15 00:20:46 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:20:46,154 - WARNING - Could not retrieve variants from source file in region 15:76017241-76017642. Error was invalid region `15:76017242-76017642`
[2016-04-15T07:20Z] 2016-04-15 00:20:46 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:20:46,288 - WARNING - Could not retrieve variants from source file in region 15:76222624-76223025. Error was invalid region `15:76222625-76223025`
[2016-04-15T07:20Z] 2016-04-15 00:20:46 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:20:46,391 - WARNING - Could not retrieve variants from source file in region 15:76222624-76223025. Error was invalid region `15:76222625-76223025`
[2016-04-15T07:20Z] 2016-04-15 00:20:48 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:20:48,338 - WARNING - Could not retrieve variants from source file in region 15:78820932-78841410. Error was invalid region `15:78820933-78841410`
[2016-04-15T07:20Z] 2016-04-15 00:20:49 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:20:49,710 - WARNING - Could not retrieve variants from source file in region 15:76191591-76191992. Error was invalid region `15:76191592-76191992`
[2016-04-15T07:20Z] 2016-04-15 00:20:49 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:20:49,947 - WARNING - Could not retrieve variants from source file in region 15:76017241-76017642. Error was invalid region `15:76017242-76017642`
[2016-04-15T07:20Z] 2016-04-15 00:20:49 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:20:49,956 - WARNING - Could not retrieve variants from source file in region 15:76191591-76191992. Error was invalid region `15:76191592-76191992`
[2016-04-15T07:20Z] 2016-04-15 00:20:49 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:20:49,968 - WARNING - Could not retrieve variants from source file in region 15:76191591-76191992. Error was invalid region `15:76191592-76191992`
[2016-04-15T07:20Z] 2016-04-15 00:20:50 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:20:50,490 - WARNING - Could not retrieve variants from source file in region 15:75969124-75982618. Error was invalid region `15:75969125-75982618`
[2016-04-15T07:20Z] ['bcbio-variation-recall', 'square', '-Xms750m', '-Xmx7280m', '-XX:+UseSerialGC', '-c', 16, '-r', u'15:83448997-98982979', '--caller', 'platypus', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/15/Batch1-15_83448996_98982979.vcf.gz', '/mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/15/Batch1-15_83448996_98982979.vcf-inputs.txt'] in region: 15:83448997-98982979
[2016-04-15T07:21Z] 2016-04-15 00:21:04 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:21:04,905 - WARNING - Could not retrieve variants from source file in region 15:97327182-97327583. Error was invalid region `15:97327183-97327583`
[2016-04-15T07:21Z] 2016-04-15 00:21:05 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:21:05,910 - WARNING - Could not retrieve variants from source file in region 15:91010565-91010966. Error was invalid region `15:91010566-91010966`
[2016-04-15T07:21Z] 2016-04-15 00:21:06 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:21:06,561 - WARNING - Could not retrieve variants from source file in region 15:89169403-89195716. Error was invalid region `15:89169404-89195716`
[2016-04-15T07:21Z] 2016-04-15 00:21:07 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:21:07,102 - WARNING - Could not retrieve variants from source file in region 15:86623037-86623438. Error was invalid region `15:86623038-86623438`
[2016-04-15T07:21Z] 2016-04-15 00:21:07 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:21:07,752 - WARNING - Could not retrieve variants from source file in region 15:93198460-93198974. Error was invalid region `15:93198461-93198974`
[2016-04-15T07:21Z] 2016-04-15 00:21:08 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:21:08,608 - WARNING - Could not retrieve variants from source file in region 15:92637982-92647835. Error was invalid region `15:92637983-92647835`
[2016-04-15T07:21Z] 2016-04-15 00:21:08 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:21:08,829 - WARNING - Could not retrieve variants from source file in region 15:90319909-90320336. Error was invalid region `15:90319910-90320336`
[2016-04-15T07:21Z] 2016-04-15 00:21:08 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:21:08,924 - WARNING - Could not retrieve variants from source file in region 15:90125910-90138860. Error was invalid region `15:90125911-90138860`
[2016-04-15T07:21Z] 2016-04-15 00:21:11 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:21:11,781 - WARNING - Could not retrieve variants from source file in region 15:89169403-89195716. Error was invalid region `15:89169404-89195716`
[2016-04-15T07:21Z] 2016-04-15 00:21:13 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:21:13,156 - WARNING - Could not retrieve variants from source file in region 15:86623037-86623438. Error was invalid region `15:86623038-86623438`
[2016-04-15T07:21Z] 2016-04-15 00:21:14 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:21:14,524 - WARNING - Could not retrieve variants from source file in region 15:91337268-91354695. Error was invalid region `15:91337269-91354695`
[2016-04-15T07:21Z] 2016-04-15 00:21:15 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:21:15,458 - WARNING - Could not retrieve variants from source file in region 15:93198460-93198974. Error was invalid region `15:93198461-93198974`
[2016-04-15T07:21Z] 2016-04-15 00:21:15 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:21:15,461 - WARNING - Could not retrieve variants from source file in region 15:92397404-92397805. Error was invalid region `15:92397405-92397805`
[2016-04-15T07:21Z] 2016-04-15 00:21:16 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:21:16,264 - WARNING - Could not retrieve variants from source file in region 15:94945508-94946421. Error was invalid region `15:94945509-94946421`
[2016-04-15T07:21Z] 2016-04-15 00:21:16 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:21:16,859 - WARNING - Could not retrieve variants from source file in region 15:98503889-98514035. Error was invalid region `15:98503890-98514035`
[2016-04-15T07:21Z] 2016-04-15 00:21:17 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:21:17,189 - WARNING - Could not retrieve variants from source file in region 15:97327182-97327583. Error was invalid region `15:97327183-97327583`
[2016-04-15T07:21Z] 2016-04-15 00:21:17 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:21:17,881 - WARNING - Could not retrieve variants from source file in region 15:89169403-89195716. Error was invalid region `15:89169404-89195716`
[2016-04-15T07:21Z] 2016-04-15 00:21:17 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:21:17,882 - WARNING - Could not retrieve variants from source file in region 15:91010565-91010966. Error was invalid region `15:91010566-91010966`
[2016-04-15T07:21Z] 2016-04-15 00:21:17 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:21:17,887 - WARNING - Could not retrieve variants from source file in region 15:90125910-90138860. Error was invalid region `15:90125911-90138860`
[2016-04-15T07:21Z] 2016-04-15 00:21:18 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:21:18,285 - WARNING - Could not retrieve variants from source file in region 15:86623037-86623438. Error was invalid region `15:86623038-86623438`
[2016-04-15T07:21Z] 2016-04-15 00:21:20 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:21:20,640 - WARNING - Could not retrieve variants from source file in region 15:92397404-92397805. Error was invalid region `15:92397405-92397805`
[2016-04-15T07:21Z] 2016-04-15 00:21:20 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:21:20,651 - WARNING - Could not retrieve variants from source file in region 15:93198460-93198974. Error was invalid region `15:93198461-93198974`
[2016-04-15T07:21Z] 2016-04-15 00:21:22 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:21:22,316 - WARNING - Could not retrieve variants from source file in region 15:85429330-85449065. Error was invalid region `15:85429331-85449065`
[2016-04-15T07:21Z] 2016-04-15 00:21:22 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:21:22,335 - WARNING - Could not retrieve variants from source file in region 15:94945508-94946421. Error was invalid region `15:94945509-94946421`
[2016-04-15T07:21Z] 2016-04-15 00:21:26 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:21:26,040 - WARNING - Could not retrieve variants from source file in region 15:98503889-98514035. Error was invalid region `15:98503890-98514035`
[2016-04-15T07:21Z] 2016-04-15 00:21:26 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:21:26,092 - WARNING - Could not retrieve variants from source file in region 15:90125910-90138860. Error was invalid region `15:90125911-90138860`
[2016-04-15T07:21Z] 2016-04-15 00:21:34 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:21:34,294 - WARNING - Could not retrieve variants from source file in region 15:96874076-96876801. Error was invalid region `15:96874077-96876801`
[2016-04-15T07:21Z] 2016-04-15 00:21:36 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:21:36,737 - WARNING - Could not retrieve variants from source file in region 15:91185080-91185481. Error was invalid region `15:91185081-91185481`
[2016-04-15T07:21Z] 2016-04-15 00:21:36 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:21:36,863 - WARNING - Could not retrieve variants from source file in region 15:90897741-90903808. Error was invalid region `15:90897742-90903808`
[2016-04-15T07:21Z] 2016-04-15 00:21:36 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:21:36,919 - WARNING - Could not retrieve variants from source file in region 15:93015216-93015617. Error was invalid region `15:93015217-93015617`
[2016-04-15T07:21Z] 2016-04-15 00:21:37 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:21:37,763 - WARNING - Could not retrieve variants from source file in region 15:86287656-86288057. Error was invalid region `15:86287657-86288057`
[2016-04-15T07:21Z] 2016-04-15 00:21:38 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:21:38,868 - WARNING - Could not retrieve variants from source file in region 15:96874076-96876801. Error was invalid region `15:96874077-96876801`
[2016-04-15T07:21Z] 2016-04-15 00:21:39 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:21:39,272 - WARNING - Could not retrieve variants from source file in region 15:89055829-89056230. Error was invalid region `15:89055830-89056230`
[2016-04-15T07:21Z] 2016-04-15 00:21:41 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:21:41,207 - WARNING - Could not retrieve variants from source file in region 15:90293565-90294496. Error was invalid region `15:90293566-90294496`
[2016-04-15T07:21Z] 2016-04-15 00:21:41 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:21:41,811 - WARNING - Could not retrieve variants from source file in region 15:89803832-89804233. Error was invalid region `15:89803833-89804233`
[2016-04-15T07:21Z] 2016-04-15 00:21:42 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:21:42,034 - WARNING - Could not retrieve variants from source file in region 15:93015216-93015617. Error was invalid region `15:93015217-93015617`
[2016-04-15T07:21Z] 2016-04-15 00:21:42 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:21:42,585 - WARNING - Could not retrieve variants from source file in region 15:86287656-86288057. Error was invalid region `15:86287657-86288057`
[2016-04-15T07:21Z] 2016-04-15 00:21:46 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:21:46,371 - WARNING - Could not retrieve variants from source file in region 15:89803832-89804233. Error was invalid region `15:89803833-89804233`
[2016-04-15T07:21Z] 2016-04-15 00:21:47 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:21:47,233 - WARNING - Could not retrieve variants from source file in region 15:89836017-89877017. Error was invalid region `15:89836018-89877017`
[2016-04-15T07:21Z] 2016-04-15 00:21:48 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:21:48,595 - WARNING - Could not retrieve variants from source file in region 15:90768060-90809460. Error was invalid region `15:90768061-90809460`
[2016-04-15T07:21Z] 2016-04-15 00:21:50 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:21:50,875 - WARNING - Could not retrieve variants from source file in region 15:89803832-89804233. Error was invalid region `15:89803833-89804233`
[2016-04-15T07:21Z] 2016-04-15 00:21:52 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:21:52,215 - WARNING - Could not retrieve variants from source file in region 15:84539408-84539809. Error was invalid region `15:84539409-84539809`
[2016-04-15T07:21Z] 2016-04-15 00:21:54 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:21:54,494 - WARNING - Could not retrieve variants from source file in region 15:90349250-90349748. Error was invalid region `15:90349251-90349748`
[2016-04-15T07:21Z] 2016-04-15 00:21:57 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:21:57,864 - WARNING - Could not retrieve variants from source file in region 15:84539408-84539809. Error was invalid region `15:84539409-84539809`
[2016-04-15T07:21Z] 2016-04-15 00:21:57 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:21:57,882 - WARNING - Could not retrieve variants from source file in region 15:91083142-91083543. Error was invalid region `15:91083143-91083543`
[2016-04-15T07:21Z] 2016-04-15 00:21:59 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:21:59,295 - WARNING - Could not retrieve variants from source file in region 15:93510392-93588526. Error was invalid region `15:93510393-93588526`
[2016-04-15T07:21Z] 2016-04-15 00:21:59 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:21:59,329 - WARNING - Could not retrieve variants from source file in region 15:88679574-88679975. Error was invalid region `15:88679575-88679975`
[2016-04-15T07:22Z] 2016-04-15 00:22:02 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:22:02,709 - WARNING - Could not retrieve variants from source file in region 15:91083142-91083543. Error was invalid region `15:91083143-91083543`
[2016-04-15T07:22Z] 2016-04-15 00:22:02 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:22:02,755 - WARNING - Could not retrieve variants from source file in region 15:84539408-84539809. Error was invalid region `15:84539409-84539809`
[2016-04-15T07:22Z] 2016-04-15 00:22:03 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:22:03,713 - WARNING - Could not retrieve variants from source file in region 15:88679574-88679975. Error was invalid region `15:88679575-88679975`
[2016-04-15T07:22Z] 2016-04-15 00:22:06 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:22:06,592 - WARNING - Could not retrieve variants from source file in region 15:91083142-91083543. Error was invalid region `15:91083143-91083543`
[2016-04-15T07:22Z] 2016-04-15 00:22:07 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:22:07,736 - WARNING - Could not retrieve variants from source file in region 15:88679574-88679975. Error was invalid region `15:88679575-88679975`
[2016-04-15T07:22Z] 2016-04-15 00:22:07 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:22:07,798 - WARNING - Could not retrieve variants from source file in region 15:86162712-86163113. Error was invalid region `15:86162713-86163113`
[2016-04-15T07:22Z] 2016-04-15 00:22:11 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:22:11,692 - WARNING - Could not retrieve variants from source file in region 15:84909174-84909575. Error was invalid region `15:84909175-84909575`
[2016-04-15T07:22Z] 2016-04-15 00:22:12 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:22:12,011 - WARNING - Could not retrieve variants from source file in region 15:86162712-86163113. Error was invalid region `15:86162713-86163113`
[2016-04-15T07:22Z] 2016-04-15 00:22:13 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:22:13,068 - WARNING - Could not retrieve variants from source file in region 15:84706250-84706651. Error was invalid region `15:84706251-84706651`
[2016-04-15T07:22Z] 2016-04-15 00:22:13 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:22:13,086 - WARNING - Could not retrieve variants from source file in region 15:84639139-84651480. Error was invalid region `15:84639140-84651480`
[2016-04-15T07:22Z] 2016-04-15 00:22:15 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:22:15,741 - WARNING - Could not retrieve variants from source file in region 15:84581678-84582314. Error was invalid region `15:84581679-84582314`
[2016-04-15T07:22Z] 2016-04-15 00:22:15 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:22:15,923 - WARNING - Could not retrieve variants from source file in region 15:88575974-88576375. Error was invalid region `15:88575975-88576375`
[2016-04-15T07:22Z] 2016-04-15 00:22:16 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:22:16,253 - WARNING - Could not retrieve variants from source file in region 15:84488425-84488826. Error was invalid region `15:84488426-84488826`
[2016-04-15T07:22Z] 2016-04-15 00:22:16 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:22:16,492 - WARNING - Could not retrieve variants from source file in region 15:88575974-88576375. Error was invalid region `15:88575975-88576375`
[2016-04-15T07:22Z] 2016-04-15 00:22:17 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:22:17,210 - WARNING - Could not retrieve variants from source file in region 15:84639139-84651480. Error was invalid region `15:84639140-84651480`
[2016-04-15T07:22Z] 2016-04-15 00:22:18 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:22:18,573 - WARNING - Could not retrieve variants from source file in region 15:87217402-87217803. Error was invalid region `15:87217403-87217803`
[2016-04-15T07:22Z] 2016-04-15 00:22:20 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:22:20,485 - WARNING - Could not retrieve variants from source file in region 15:88575974-88576375. Error was invalid region `15:88575975-88576375`
[2016-04-15T07:22Z] 2016-04-15 00:22:20 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:22:20,531 - WARNING - Could not retrieve variants from source file in region 15:84488425-84488826. Error was invalid region `15:84488426-84488826`
[2016-04-15T07:22Z] 2016-04-15 00:22:21 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:22:21,578 - WARNING - Could not retrieve variants from source file in region 15:84581678-84582314. Error was invalid region `15:84581679-84582314`
[2016-04-15T07:22Z] 2016-04-15 00:22:22 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:22:22,894 - WARNING - Could not retrieve variants from source file in region 15:87217402-87217803. Error was invalid region `15:87217403-87217803`
[2016-04-15T07:22Z] 2016-04-15 00:22:25 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:22:25,407 - WARNING - Could not retrieve variants from source file in region 15:84488425-84488826. Error was invalid region `15:84488426-84488826`
[2016-04-15T07:22Z] 2016-04-15 00:22:25 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:22:25,472 - WARNING - Could not retrieve variants from source file in region 15:85525345-85525746. Error was invalid region `15:85525346-85525746`
[2016-04-15T07:22Z] 2016-04-15 00:22:26 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:22:26,156 - WARNING - Could not retrieve variants from source file in region 15:85476230-85478919. Error was invalid region `15:85476231-85478919`
[2016-04-15T07:22Z] 2016-04-15 00:22:27 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:22:27,185 - WARNING - Could not retrieve variants from source file in region 15:87217402-87217803. Error was invalid region `15:87217403-87217803`
[2016-04-15T07:22Z] 2016-04-15 00:22:30 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:22:30,085 - WARNING - Could not retrieve variants from source file in region 15:85525345-85525746. Error was invalid region `15:85525346-85525746`
[2016-04-15T07:22Z] 2016-04-15 00:22:30 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:22:30,091 - WARNING - Could not retrieve variants from source file in region 15:85476230-85478919. Error was invalid region `15:85476231-85478919`
[2016-04-15T07:22Z] 2016-04-15 00:22:32 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:22:32,967 - WARNING - Could not retrieve variants from source file in region 15:85788310-85788711. Error was invalid region `15:85788311-85788711`
[2016-04-15T07:22Z] 2016-04-15 00:22:33 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:22:33,230 - WARNING - Could not retrieve variants from source file in region 15:83951927-83952328. Error was invalid region `15:83951928-83952328`
[2016-04-15T07:22Z] 2016-04-15 00:22:34 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:22:34,041 - WARNING - Could not retrieve variants from source file in region 15:86799998-86815056. Error was invalid region `15:86799999-86815056`
[2016-04-15T07:22Z] 2016-04-15 00:22:34 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:22:34,050 - WARNING - Could not retrieve variants from source file in region 15:86799998-86815056. Error was invalid region `15:86799999-86815056`
[2016-04-15T07:22Z] 2016-04-15 00:22:37 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:22:37,152 - WARNING - Could not retrieve variants from source file in region 15:83620563-83620964. Error was invalid region `15:83620564-83620964`
[2016-04-15T07:22Z] 2016-04-15 00:22:37 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:22:37,325 - WARNING - Could not retrieve variants from source file in region 15:83951927-83952328. Error was invalid region `15:83951928-83952328`
[2016-04-15T07:22Z] 2016-04-15 00:22:39 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:22:39,412 - WARNING - Could not retrieve variants from source file in region 15:83677059-83680616. Error was invalid region `15:83677060-83680616`
[2016-04-15T07:22Z] ['bcbio-variation-recall', 'square', '-Xms750m', '-Xmx7280m', '-XX:+UseSerialGC', '-c', 16, '-r', u'15:98984300-102531392', '--caller', 'platypus', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/15/Batch1-15_98984299_102531392.vcf.gz', '/mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/15/Batch1-15_98984299_102531392.vcf-inputs.txt'] in region: 15:98984300-102531392
[2016-04-15T07:22Z] 2016-04-15 00:22:55 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:22:55,847 - WARNING - Could not retrieve variants from source file in region 15:102029386-102029875. Error was invalid region `15:102029387-102029875`
[2016-04-15T07:22Z] 2016-04-15 00:22:56 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:22:56,445 - WARNING - Could not retrieve variants from source file in region 15:100942751-100943152. Error was invalid region `15:100942752-100943152`
[2016-04-15T07:22Z] 2016-04-15 00:22:57 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:22:57,459 - WARNING - Could not retrieve variants from source file in region 15:100514403-100514804. Error was invalid region `15:100514404-100514804`
[2016-04-15T07:22Z] 2016-04-15 00:22:57 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:22:57,800 - WARNING - Could not retrieve variants from source file in region 15:102192291-102196376. Error was invalid region `15:102192292-102196376`
[2016-04-15T07:22Z] 2016-04-15 00:22:57 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:22:57,976 - WARNING - Could not retrieve variants from source file in region 15:101791148-101791795. Error was invalid region `15:101791149-101791795`
[2016-04-15T07:22Z] 2016-04-15 00:22:58 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:22:58,059 - WARNING - Could not retrieve variants from source file in region 15:100672026-100672427. Error was invalid region `15:100672027-100672427`
[2016-04-15T07:22Z] 2016-04-15 00:22:58 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:22:58,080 - WARNING - Could not retrieve variants from source file in region 15:99478014-99478415. Error was invalid region `15:99478015-99478415`
[2016-04-15T07:22Z] 2016-04-15 00:22:58 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:22:58,615 - WARNING - Could not retrieve variants from source file in region 15:100794152-100801888. Error was invalid region `15:100794153-100801888`
[2016-04-15T07:22Z] 2016-04-15 00:22:58 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:22:58,644 - WARNING - Could not retrieve variants from source file in region 15:101910339-101924736. Error was invalid region `15:101910340-101924736`
[2016-04-15T07:22Z] 2016-04-15 00:22:58 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:22:58,671 - WARNING - Could not retrieve variants from source file in region 15:99761830-99762231. Error was invalid region `15:99761831-99762231`
[2016-04-15T07:22Z] 2016-04-15 00:22:58 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:22:58,730 - WARNING - Could not retrieve variants from source file in region 15:99715141-99715542. Error was invalid region `15:99715142-99715542`
[2016-04-15T07:23Z] 2016-04-15 00:23:00 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:23:00,749 - WARNING - Could not retrieve variants from source file in region 15:102284464-102284865. Error was invalid region `15:102284465-102284865`
[2016-04-15T07:23Z] 2016-04-15 00:23:01 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:23:01,305 - WARNING - Could not retrieve variants from source file in region 15:102029386-102029875. Error was invalid region `15:102029387-102029875`
[2016-04-15T07:23Z] 2016-04-15 00:23:02 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:23:02,747 - WARNING - Could not retrieve variants from source file in region 15:100942751-100943152. Error was invalid region `15:100942752-100943152`
[2016-04-15T07:23Z] 2016-04-15 00:23:05 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:23:05,040 - WARNING - Could not retrieve variants from source file in region 15:100514403-100514804. Error was invalid region `15:100514404-100514804`
[2016-04-15T07:23Z] 2016-04-15 00:23:06 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:23:06,299 - WARNING - Could not retrieve variants from source file in region 15:102192291-102196376. Error was invalid region `15:102192292-102196376`
[2016-04-15T07:23Z] 2016-04-15 00:23:06 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:23:06,634 - WARNING - Could not retrieve variants from source file in region 15:100672026-100672427. Error was invalid region `15:100672027-100672427`
[2016-04-15T07:23Z] 2016-04-15 00:23:06 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:23:06,998 - WARNING - Could not retrieve variants from source file in region 15:99478014-99478415. Error was invalid region `15:99478015-99478415`
[2016-04-15T07:23Z] 2016-04-15 00:23:07 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:23:07,170 - WARNING - Could not retrieve variants from source file in region 15:99511582-99511983. Error was invalid region `15:99511583-99511983`
[2016-04-15T07:23Z] 2016-04-15 00:23:08 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:23:08,011 - WARNING - Could not retrieve variants from source file in region 15:99715141-99715542. Error was invalid region `15:99715142-99715542`
[2016-04-15T07:23Z] 2016-04-15 00:23:08 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:23:08,080 - WARNING - Could not retrieve variants from source file in region 15:100942751-100943152. Error was invalid region `15:100942752-100943152`
[2016-04-15T07:23Z] 2016-04-15 00:23:10 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:23:10,791 - WARNING - Could not retrieve variants from source file in region 15:100514403-100514804. Error was invalid region `15:100514404-100514804`
[2016-04-15T07:23Z] 2016-04-15 00:23:11 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:23:11,629 - WARNING - Could not retrieve variants from source file in region 15:99645602-99679845. Error was invalid region `15:99645603-99679845`
[2016-04-15T07:23Z] 2016-04-15 00:23:13 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:23:13,370 - WARNING - Could not retrieve variants from source file in region 15:102192291-102196376. Error was invalid region `15:102192292-102196376`
[2016-04-15T07:23Z] 2016-04-15 00:23:13 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:23:13,702 - WARNING - Could not retrieve variants from source file in region 15:101791148-101791795. Error was invalid region `15:101791149-101791795`
[2016-04-15T07:23Z] 2016-04-15 00:23:14 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:23:14,168 - WARNING - Could not retrieve variants from source file in region 15:100672026-100672427. Error was invalid region `15:100672027-100672427`
[2016-04-15T07:23Z] 2016-04-15 00:23:14 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:23:14,753 - WARNING - Could not retrieve variants from source file in region 15:99478014-99478415. Error was invalid region `15:99478015-99478415`
[2016-04-15T07:23Z] 2016-04-15 00:23:14 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:23:14,899 - WARNING - Could not retrieve variants from source file in region 15:101717469-101728571. Error was invalid region `15:101717470-101728571`
[2016-04-15T07:23Z] 2016-04-15 00:23:15 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:23:15,412 - WARNING - Could not retrieve variants from source file in region 15:99511582-99511983. Error was invalid region `15:99511583-99511983`
[2016-04-15T07:23Z] 2016-04-15 00:23:15 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:23:15,567 - WARNING - Could not retrieve variants from source file in region 15:99715141-99715542. Error was invalid region `15:99715142-99715542`
[2016-04-15T07:23Z] 2016-04-15 00:23:15 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:23:15,641 - WARNING - Could not retrieve variants from source file in region 15:100794152-100801888. Error was invalid region `15:100794153-100801888`
[2016-04-15T07:23Z] 2016-04-15 00:23:26 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:23:26,882 - WARNING - Could not retrieve variants from source file in region 15:101458465-101465105. Error was invalid region `15:101458466-101465105`
[2016-04-15T07:23Z] 2016-04-15 00:23:27 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:23:27,113 - WARNING - Could not retrieve variants from source file in region 15:101562582-101567737. Error was invalid region `15:101562583-101567737`
[2016-04-15T07:23Z] 2016-04-15 00:23:27 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:23:27,141 - WARNING - Could not retrieve variants from source file in region 15:98994870-98995271. Error was invalid region `15:98994871-98995271`
[2016-04-15T07:23Z] 2016-04-15 00:23:27 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:23:27,263 - WARNING - Could not retrieve variants from source file in region 15:98994870-98995271. Error was invalid region `15:98994871-98995271`
[2016-04-15T07:23Z] 2016-04-15 00:23:27 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:23:27,270 - WARNING - Could not retrieve variants from source file in region 15:98994870-98995271. Error was invalid region `15:98994871-98995271`
[2016-04-15T07:23Z] 2016-04-15 00:23:27 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:23:27,548 - WARNING - Could not retrieve variants from source file in region 15:101041685-101042086. Error was invalid region `15:101041686-101042086`
[2016-04-15T07:23Z] 2016-04-15 00:23:31 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:23:31,030 - WARNING - Could not retrieve variants from source file in region 15:101597989-101606380. Error was invalid region `15:101597990-101606380`
[2016-04-15T07:23Z] 2016-04-15 00:23:31 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:23:31,327 - WARNING - Could not retrieve variants from source file in region 15:101041685-101042086. Error was invalid region `15:101041686-101042086`
[2016-04-15T07:23Z] 2016-04-15 00:23:31 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:23:31,441 - WARNING - Could not retrieve variants from source file in region 15:101041685-101042086. Error was invalid region `15:101041686-101042086`
[2016-04-15T07:23Z] ['bcbio-variation-recall', 'square', '-Xms750m', '-Xmx7280m', '-XX:+UseSerialGC', '-c', 16, '-r', u'16:1-15528616', '--caller', 'platypus', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/16/Batch1-16_0_15528616.vcf.gz', '/mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/16/Batch1-16_0_15528616.vcf-inputs.txt'] in region: 16:1-15528616
[2016-04-15T07:23Z] 2016-04-15 00:23:47 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:23:47,945 - WARNING - Could not retrieve variants from source file in region 16:3490711-3491112. Error was invalid region `16:3490712-3491112`
[2016-04-15T07:23Z] 2016-04-15 00:23:48 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:23:48,523 - WARNING - Could not retrieve variants from source file in region 16:10837702-10838103. Error was invalid region `16:10837703-10838103`
[2016-04-15T07:23Z] 2016-04-15 00:23:49 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:23:49,429 - WARNING - Could not retrieve variants from source file in region 16:1129661-1130102. Error was invalid region `16:1129662-1130102`
[2016-04-15T07:23Z] 2016-04-15 00:23:49 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:23:49,906 - WARNING - Could not retrieve variants from source file in region 16:3434488-3452383. Error was invalid region `16:3434489-3452383`
[2016-04-15T07:23Z] 2016-04-15 00:23:50 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:23:50,010 - WARNING - Could not retrieve variants from source file in region 16:4164153-4165622. Error was invalid region `16:4164154-4165622`
[2016-04-15T07:23Z] 2016-04-15 00:23:50 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:23:50,125 - WARNING - Could not retrieve variants from source file in region 16:9943455-9943856. Error was invalid region `16:9943456-9943856`
[2016-04-15T07:23Z] 2016-04-15 00:23:52 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:23:52,327 - WARNING - Could not retrieve variants from source file in region 16:4475878-4519738. Error was invalid region `16:4475879-4519738`
[2016-04-15T07:23Z] 2016-04-15 00:23:53 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:23:53,861 - WARNING - Could not retrieve variants from source file in region 16:3490711-3491112. Error was invalid region `16:3490712-3491112`
[2016-04-15T07:23Z] 2016-04-15 00:23:56 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:23:56,248 - WARNING - Could not retrieve variants from source file in region 16:14028822-14042148. Error was invalid region `16:14028823-14042148`
[2016-04-15T07:23Z] 2016-04-15 00:23:57 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:23:57,589 - WARNING - Could not retrieve variants from source file in region 16:15178288-15178689. Error was invalid region `16:15178289-15178689`
[2016-04-15T07:23Z] 2016-04-15 00:23:57 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:23:57,793 - WARNING - Could not retrieve variants from source file in region 16:3364649-3365050. Error was invalid region `16:3364650-3365050`
[2016-04-15T07:23Z] 2016-04-15 00:23:58 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:23:58,281 - WARNING - Could not retrieve variants from source file in region 16:9943455-9943856. Error was invalid region `16:9943456-9943856`
[2016-04-15T07:23Z] 2016-04-15 00:23:58 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:23:58,885 - WARNING - Could not retrieve variants from source file in region 16:4475878-4519738. Error was invalid region `16:4475879-4519738`
[2016-04-15T07:23Z] 2016-04-15 00:23:58 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:23:58,973 - WARNING - Could not retrieve variants from source file in region 16:2367125-2367954. Error was invalid region `16:2367126-2367954`
[2016-04-15T07:23Z] 2016-04-15 00:23:59 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:23:59,150 - WARNING - Could not retrieve variants from source file in region 16:4164153-4165622. Error was invalid region `16:4164154-4165622`
[2016-04-15T07:23Z] 2016-04-15 00:23:59 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:23:59,324 - WARNING - Could not retrieve variants from source file in region 16:3490711-3491112. Error was invalid region `16:3490712-3491112`
[2016-04-15T07:24Z] 2016-04-15 00:24:01 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:24:01,651 - WARNING - Could not retrieve variants from source file in region 16:14028822-14042148. Error was invalid region `16:14028823-14042148`
[2016-04-15T07:24Z] 2016-04-15 00:24:03 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:24:03,864 - WARNING - Could not retrieve variants from source file in region 16:15178288-15178689. Error was invalid region `16:15178289-15178689`
[2016-04-15T07:24Z] 2016-04-15 00:24:06 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:24:06,144 - WARNING - Could not retrieve variants from source file in region 16:9943455-9943856. Error was invalid region `16:9943456-9943856`
[2016-04-15T07:24Z] 2016-04-15 00:24:06 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:24:06,261 - WARNING - Could not retrieve variants from source file in region 16:4164153-4165622. Error was invalid region `16:4164154-4165622`
[2016-04-15T07:24Z] 2016-04-15 00:24:06 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:24:06,554 - WARNING - Could not retrieve variants from source file in region 16:3434488-3452383. Error was invalid region `16:3434489-3452383`
[2016-04-15T07:24Z] 2016-04-15 00:24:06 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:24:06,960 - WARNING - Could not retrieve variants from source file in region 16:2367125-2367954. Error was invalid region `16:2367126-2367954`
[2016-04-15T07:24Z] 2016-04-15 00:24:16 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:24:16,901 - WARNING - Could not retrieve variants from source file in region 16:3405775-3406816. Error was invalid region `16:3405776-3406816`
[2016-04-15T07:24Z] 2016-04-15 00:24:19 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:24:19,315 - WARNING - Could not retrieve variants from source file in region 16:4430991-4445517. Error was invalid region `16:4430992-4445517`
[2016-04-15T07:24Z] 2016-04-15 00:24:20 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:24:20,500 - WARNING - Could not retrieve variants from source file in region 16:3293677-3299939. Error was invalid region `16:3293678-3299939`
[2016-04-15T07:24Z] 2016-04-15 00:24:21 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:24:21,497 - WARNING - Could not retrieve variants from source file in region 16:983792-1035144. Error was invalid region `16:983793-1035144`
[2016-04-15T07:24Z] 2016-04-15 00:24:21 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:24:21,615 - WARNING - Could not retrieve variants from source file in region 16:3405775-3406816. Error was invalid region `16:3405776-3406816`
[2016-04-15T07:24Z] 2016-04-15 00:24:22 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:24:22,428 - WARNING - Could not retrieve variants from source file in region 16:9915993-9916394. Error was invalid region `16:9915994-9916394`
[2016-04-15T07:24Z] 2016-04-15 00:24:23 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:24:23,662 - WARNING - Could not retrieve variants from source file in region 16:4016465-4033626. Error was invalid region `16:4016466-4033626`
[2016-04-15T07:24Z] 2016-04-15 00:24:25 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:24:25,442 - WARNING - Could not retrieve variants from source file in region 16:8619539-8619940. Error was invalid region `16:8619540-8619940`
[2016-04-15T07:24Z] 2016-04-15 00:24:27 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:24:27,100 - WARNING - Could not retrieve variants from source file in region 16:9915993-9916394. Error was invalid region `16:9915994-9916394`
[2016-04-15T07:24Z] 2016-04-15 00:24:28 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:24:28,221 - WARNING - Could not retrieve variants from source file in region 16:13002148-13005304. Error was invalid region `16:13002149-13005304`
[2016-04-15T07:24Z] 2016-04-15 00:24:28 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:24:28,726 - WARNING - Could not retrieve variants from source file in region 16:4016465-4033626. Error was invalid region `16:4016466-4033626`
[2016-04-15T07:24Z] 2016-04-15 00:24:28 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:24:28,828 - WARNING - Could not retrieve variants from source file in region 16:11969513-11981677. Error was invalid region `16:11969514-11981677`
[2016-04-15T07:24Z] 2016-04-15 00:24:31 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:24:31,447 - WARNING - Could not retrieve variants from source file in region 16:8619539-8619940. Error was invalid region `16:8619540-8619940`
[2016-04-15T07:24Z] 2016-04-15 00:24:32 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:24:32,962 - WARNING - Could not retrieve variants from source file in region 16:4430991-4445517. Error was invalid region `16:4430992-4445517`
[2016-04-15T07:24Z] 2016-04-15 00:24:33 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:24:33,021 - WARNING - Could not retrieve variants from source file in region 16:983792-1035144. Error was invalid region `16:983793-1035144`
[2016-04-15T07:24Z] 2016-04-15 00:24:33 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:24:33,585 - WARNING - Could not retrieve variants from source file in region 16:15095464-15134079. Error was invalid region `16:15095465-15134079`
[2016-04-15T07:24Z] 2016-04-15 00:24:33 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:24:33,601 - WARNING - Could not retrieve variants from source file in region 16:3016913-3027486. Error was invalid region `16:3016914-3027486`
[2016-04-15T07:24Z] 2016-04-15 00:24:33 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:24:33,777 - WARNING - Could not retrieve variants from source file in region 16:9915993-9916394. Error was invalid region `16:9915994-9916394`
[2016-04-15T07:24Z] 2016-04-15 00:24:33 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:24:33,937 - WARNING - Could not retrieve variants from source file in region 16:14968805-14976643. Error was invalid region `16:14968806-14976643`
[2016-04-15T07:24Z] 2016-04-15 00:24:35 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:24:35,759 - WARNING - Could not retrieve variants from source file in region 16:8619539-8619940. Error was invalid region `16:8619540-8619940`
[2016-04-15T07:24Z] 2016-04-15 00:24:36 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:24:36,152 - WARNING - Could not retrieve variants from source file in region 16:11540501-11556311. Error was invalid region `16:11540502-11556311`
[2016-04-15T07:24Z] 2016-04-15 00:24:41 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:24:41,794 - WARNING - Could not retrieve variants from source file in region 16:3254259-3255162. Error was invalid region `16:3254260-3255162`
[2016-04-15T07:24Z] 2016-04-15 00:24:42 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:24:42,816 - WARNING - Could not retrieve variants from source file in region 16:12758035-12759156. Error was invalid region `16:12758036-12759156`
[2016-04-15T07:24Z] 2016-04-15 00:24:45 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:24:45,784 - WARNING - Could not retrieve variants from source file in region 16:3254259-3255162. Error was invalid region `16:3254260-3255162`
[2016-04-15T07:24Z] 2016-04-15 00:24:48 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:24:48,813 - WARNING - Could not retrieve variants from source file in region 16:12758035-12759156. Error was invalid region `16:12758036-12759156`
[2016-04-15T07:24Z] 2016-04-15 00:24:48 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:24:48,868 - WARNING - Could not retrieve variants from source file in region 16:10631701-10632102. Error was invalid region `16:10631702-10632102`
[2016-04-15T07:24Z] 2016-04-15 00:24:48 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:24:48,948 - WARNING - Could not retrieve variants from source file in region 16:9030233-9030634. Error was invalid region `16:9030234-9030634`
[2016-04-15T07:24Z] 2016-04-15 00:24:49 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:24:49,901 - WARNING - Could not retrieve variants from source file in region 16:14742189-14742590. Error was invalid region `16:14742190-14742590`
[2016-04-15T07:24Z] 2016-04-15 00:24:49 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:24:49,976 - WARNING - Could not retrieve variants from source file in region 16:2987068-2987469. Error was invalid region `16:2987069-2987469`
[2016-04-15T07:24Z] 2016-04-15 00:24:50 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:24:50,226 - WARNING - Could not retrieve variants from source file in region 16:4386603-4387004. Error was invalid region `16:4386604-4387004`
[2016-04-15T07:24Z] 2016-04-15 00:24:51 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:24:51,127 - WARNING - Could not retrieve variants from source file in region 16:7759955-7760387. Error was invalid region `16:7759956-7760387`
[2016-04-15T07:24Z] 2016-04-15 00:24:51 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:24:51,642 - WARNING - Could not retrieve variants from source file in region 16:3707536-3724655. Error was invalid region `16:3707537-3724655`
[2016-04-15T07:24Z] 2016-04-15 00:24:51 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:24:51,831 - WARNING - Could not retrieve variants from source file in region 16:11940179-11940580. Error was invalid region `16:11940180-11940580`
[2016-04-15T07:24Z] 2016-04-15 00:24:52 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:24:52,515 - WARNING - Could not retrieve variants from source file in region 16:4855068-4861899. Error was invalid region `16:4855069-4861899`
[2016-04-15T07:24Z] 2016-04-15 00:24:53 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:24:53,546 - WARNING - Could not retrieve variants from source file in region 16:929500-929901. Error was invalid region `16:929501-929901`
[2016-04-15T07:24Z] 2016-04-15 00:24:53 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:24:53,994 - WARNING - Could not retrieve variants from source file in region 16:9030233-9030634. Error was invalid region `16:9030234-9030634`
[2016-04-15T07:24Z] 2016-04-15 00:24:54 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:24:54,013 - WARNING - Could not retrieve variants from source file in region 16:10631701-10632102. Error was invalid region `16:10631702-10632102`
[2016-04-15T07:24Z] 2016-04-15 00:24:54 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:24:54,097 - WARNING - Could not retrieve variants from source file in region 16:12758035-12759156. Error was invalid region `16:12758036-12759156`
[2016-04-15T07:24Z] 2016-04-15 00:24:55 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:24:55,196 - WARNING - Could not retrieve variants from source file in region 16:4386603-4387004. Error was invalid region `16:4386604-4387004`
[2016-04-15T07:24Z] 2016-04-15 00:24:56 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:24:56,699 - WARNING - Could not retrieve variants from source file in region 16:3707536-3724655. Error was invalid region `16:3707537-3724655`
[2016-04-15T07:24Z] 2016-04-15 00:24:57 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:24:57,259 - WARNING - Could not retrieve variants from source file in region 16:11940179-11940580. Error was invalid region `16:11940180-11940580`
[2016-04-15T07:24Z] 2016-04-15 00:24:58 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:24:58,629 - WARNING - Could not retrieve variants from source file in region 16:929500-929901. Error was invalid region `16:929501-929901`
[2016-04-15T07:25Z] 2016-04-15 00:25:00 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:25:00,632 - WARNING - Could not retrieve variants from source file in region 16:10631701-10632102. Error was invalid region `16:10631702-10632102`
[2016-04-15T07:25Z] 2016-04-15 00:25:00 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:25:00,787 - WARNING - Could not retrieve variants from source file in region 16:14742189-14742590. Error was invalid region `16:14742190-14742590`
[2016-04-15T07:25Z] 2016-04-15 00:25:01 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:25:01,168 - WARNING - Could not retrieve variants from source file in region 16:4386603-4387004. Error was invalid region `16:4386604-4387004`
[2016-04-15T07:25Z] 2016-04-15 00:25:01 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:25:01,215 - WARNING - Could not retrieve variants from source file in region 16:9030233-9030634. Error was invalid region `16:9030234-9030634`
[2016-04-15T07:25Z] 2016-04-15 00:25:02 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:25:02,675 - WARNING - Could not retrieve variants from source file in region 16:11940179-11940580. Error was invalid region `16:11940180-11940580`
[2016-04-15T07:25Z] 2016-04-15 00:25:05 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:25:05,774 - WARNING - Could not retrieve variants from source file in region 16:12662209-12666715. Error was invalid region `16:12662210-12666715`
[2016-04-15T07:25Z] 2016-04-15 00:25:07 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:25:07,998 - WARNING - Could not retrieve variants from source file in region 16:11477937-11487534. Error was invalid region `16:11477938-11487534`
[2016-04-15T07:25Z] 2016-04-15 00:25:09 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:25:09,546 - WARNING - Could not retrieve variants from source file in region 16:12145729-12163159. Error was invalid region `16:12145730-12163159`
[2016-04-15T07:25Z] 2016-04-15 00:25:17 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:25:17,306 - WARNING - Could not retrieve variants from source file in region 16:4310257-4310658. Error was invalid region `16:4310258-4310658`
[2016-04-15T07:25Z] 2016-04-15 00:25:17 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:25:17,820 - WARNING - Could not retrieve variants from source file in region 16:8952037-8960501. Error was invalid region `16:8952038-8960501`
[2016-04-15T07:25Z] 2016-04-15 00:25:18 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:25:18,098 - WARNING - Could not retrieve variants from source file in region 16:7354004-7354508. Error was invalid region `16:7354005-7354508`
[2016-04-15T07:25Z] 2016-04-15 00:25:19 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:25:19,044 - WARNING - Could not retrieve variants from source file in region 16:11769737-11773852. Error was invalid region `16:11769738-11773852`
[2016-04-15T07:25Z] 2016-04-15 00:25:19 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:25:19,875 - WARNING - Could not retrieve variants from source file in region 16:3638928-3656672. Error was invalid region `16:3638929-3656672`
[2016-04-15T07:25Z] 2016-04-15 00:25:19 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:25:19,963 - WARNING - Could not retrieve variants from source file in region 16:12145729-12163159. Error was invalid region `16:12145730-12163159`
[2016-04-15T07:25Z] 2016-04-15 00:25:21 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:25:21,266 - WARNING - Could not retrieve variants from source file in region 16:11836187-11852544. Error was invalid region `16:11836188-11852544`
[2016-04-15T07:25Z] 2016-04-15 00:25:22 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:25:22,193 - WARNING - Could not retrieve variants from source file in region 16:4310257-4310658. Error was invalid region `16:4310258-4310658`
[2016-04-15T07:25Z] 2016-04-15 00:25:24 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:25:24,029 - WARNING - Could not retrieve variants from source file in region 16:7354004-7354508. Error was invalid region `16:7354005-7354508`
[2016-04-15T07:25Z] 2016-04-15 00:25:24 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:25:24,709 - WARNING - Could not retrieve variants from source file in region 16:11769737-11773852. Error was invalid region `16:11769738-11773852`
[2016-04-15T07:25Z] 2016-04-15 00:25:25 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:25:25,828 - WARNING - Could not retrieve variants from source file in region 16:3638928-3656672. Error was invalid region `16:3638929-3656672`
[2016-04-15T07:25Z] 2016-04-15 00:25:26 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:25:26,089 - WARNING - Could not retrieve variants from source file in region 16:10565767-10576014. Error was invalid region `16:10565768-10576014`
[2016-04-15T07:25Z] 2016-04-15 00:25:26 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:25:26,235 - WARNING - Could not retrieve variants from source file in region 16:4790062-4815798. Error was invalid region `16:4790063-4815798`
[2016-04-15T07:25Z] 2016-04-15 00:25:26 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:25:26,560 - WARNING - Could not retrieve variants from source file in region 16:2512312-2512713. Error was invalid region `16:2512313-2512713`
[2016-04-15T07:25Z] 2016-04-15 00:25:26 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:25:26,858 - WARNING - Could not retrieve variants from source file in region 16:12059952-12060353. Error was invalid region `16:12059953-12060353`
[2016-04-15T07:25Z] 2016-04-15 00:25:27 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:25:27,908 - WARNING - Could not retrieve variants from source file in region 16:11439285-11444762. Error was invalid region `16:11439286-11444762`
[2016-04-15T07:25Z] 2016-04-15 00:25:27 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:25:27,976 - WARNING - Could not retrieve variants from source file in region 16:2812436-2822179. Error was invalid region `16:2812437-2822179`
[2016-04-15T07:25Z] 2016-04-15 00:25:29 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:25:29,150 - WARNING - Could not retrieve variants from source file in region 16:12059952-12060353. Error was invalid region `16:12059953-12060353`
[2016-04-15T07:25Z] 2016-04-15 00:25:29 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:25:29,330 - WARNING - Could not retrieve variants from source file in region 16:11769737-11773852. Error was invalid region `16:11769738-11773852`
[2016-04-15T07:25Z] 2016-04-15 00:25:30 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:25:30,657 - WARNING - Could not retrieve variants from source file in region 16:3638928-3656672. Error was invalid region `16:3638929-3656672`
[2016-04-15T07:25Z] 2016-04-15 00:25:33 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:25:33,739 - WARNING - Could not retrieve variants from source file in region 16:12059952-12060353. Error was invalid region `16:12059953-12060353`
[2016-04-15T07:25Z] 2016-04-15 00:25:38 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:25:38,673 - WARNING - Could not retrieve variants from source file in region 16:2512312-2512713. Error was invalid region `16:2512313-2512713`
[2016-04-15T07:25Z] 2016-04-15 00:25:39 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:25:39,797 - WARNING - Could not retrieve variants from source file in region 16:10524445-10524849. Error was invalid region `16:10524446-10524849`
[2016-04-15T07:25Z] 2016-04-15 00:25:40 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:25:40,914 - WARNING - Could not retrieve variants from source file in region 16:4245482-4245883. Error was invalid region `16:4245483-4245883`
[2016-04-15T07:25Z] 2016-04-15 00:25:43 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:25:43,447 - WARNING - Could not retrieve variants from source file in region 16:6533698-6534099. Error was invalid region `16:6533699-6534099`
[2016-04-15T07:25Z] 2016-04-15 00:25:44 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:25:44,239 - WARNING - Could not retrieve variants from source file in region 16:10524445-10524849. Error was invalid region `16:10524446-10524849`
[2016-04-15T07:25Z] 2016-04-15 00:25:45 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:25:45,306 - WARNING - Could not retrieve variants from source file in region 16:4245482-4245883. Error was invalid region `16:4245483-4245883`
[2016-04-15T07:25Z] 2016-04-15 00:25:46 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:25:46,488 - WARNING - Could not retrieve variants from source file in region 16:1961463-1962322. Error was invalid region `16:1961464-1962322`
[2016-04-15T07:25Z] 2016-04-15 00:25:47 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:25:47,739 - WARNING - Could not retrieve variants from source file in region 16:8839743-8844579. Error was invalid region `16:8839744-8844579`
[2016-04-15T07:25Z] 2016-04-15 00:25:47 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:25:47,882 - WARNING - Could not retrieve variants from source file in region 16:11647281-11647722. Error was invalid region `16:11647282-11647722`
[2016-04-15T07:25Z] 2016-04-15 00:25:48 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:25:48,274 - WARNING - Could not retrieve variants from source file in region 16:6069273-6069674. Error was invalid region `16:6069274-6069674`
[2016-04-15T07:25Z] 2016-04-15 00:25:49 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:25:49,027 - WARNING - Could not retrieve variants from source file in region 16:10524445-10524849. Error was invalid region `16:10524446-10524849`
[2016-04-15T07:25Z] 2016-04-15 00:25:49 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:25:49,817 - WARNING - Could not retrieve variants from source file in region 16:4245482-4245883. Error was invalid region `16:4245483-4245883`
[2016-04-15T07:25Z] 2016-04-15 00:25:52 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:25:52,743 - WARNING - Could not retrieve variants from source file in region 16:8839743-8844579. Error was invalid region `16:8839744-8844579`
[2016-04-15T07:25Z] 2016-04-15 00:25:53 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:25:53,571 - WARNING - Could not retrieve variants from source file in region 16:6533698-6534099. Error was invalid region `16:6533699-6534099`
[2016-04-15T07:25Z] 2016-04-15 00:25:57 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:25:57,347 - WARNING - Could not retrieve variants from source file in region 16:11362518-11375056. Error was invalid region `16:11362519-11375056`
[2016-04-15T07:25Z] 2016-04-15 00:25:59 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:25:59,459 - WARNING - Could not retrieve variants from source file in region 16:6069273-6069674. Error was invalid region `16:6069274-6069674`
[2016-04-15T07:26Z] 2016-04-15 00:26:02 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:26:02,630 - WARNING - Could not retrieve variants from source file in region 16:11154559-11154960. Error was invalid region `16:11154560-11154960`
[2016-04-15T07:26Z] 2016-04-15 00:26:03 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:26:03,716 - WARNING - Could not retrieve variants from source file in region 16:3533366-3535082. Error was invalid region `16:3533367-3535082`
[2016-04-15T07:26Z] 2016-04-15 00:26:03 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:26:03,750 - WARNING - Could not retrieve variants from source file in region 16:3533366-3535082. Error was invalid region `16:3533367-3535082`
[2016-04-15T07:26Z] 2016-04-15 00:26:06 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:26:06,533 - WARNING - Could not retrieve variants from source file in region 16:3533366-3535082. Error was invalid region `16:3533367-3535082`
[2016-04-15T07:26Z] 2016-04-15 00:26:07 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:26:07,038 - WARNING - Could not retrieve variants from source file in region 16:11154559-11154960. Error was invalid region `16:11154560-11154960`
[2016-04-15T07:26Z] 2016-04-15 00:26:07 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:26:07,838 - WARNING - Could not retrieve variants from source file in region 16:1917914-1918315. Error was invalid region `16:1917915-1918315`
[2016-04-15T07:26Z] 2016-04-15 00:26:10 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:26:10,814 - WARNING - Could not retrieve variants from source file in region 16:11154559-11154960. Error was invalid region `16:11154560-11154960`
[2016-04-15T07:26Z] 2016-04-15 00:26:11 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:26:11,918 - WARNING - Could not retrieve variants from source file in region 16:1917914-1918315. Error was invalid region `16:1917915-1918315`
[2016-04-15T07:26Z] 2016-04-15 00:26:13 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:26:13,451 - WARNING - Could not retrieve variants from source file in region 16:103306-142904. Error was invalid region `16:103307-142904`
[2016-04-15T07:26Z] 2016-04-15 00:26:13 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:26:13,821 - WARNING - Could not retrieve variants from source file in region 16:216209-239970. Error was invalid region `16:216210-239970`
[2016-04-15T07:26Z] 2016-04-15 00:26:14 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:26:14,237 - WARNING - Could not retrieve variants from source file in region 16:1917914-1918315. Error was invalid region `16:1917915-1918315`
[2016-04-15T07:26Z] 2016-04-15 00:26:14 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:26:14,278 - WARNING - Could not retrieve variants from source file in region 16:1664720-1665121. Error was invalid region `16:1664721-1665121`
[2016-04-15T07:26Z] 2016-04-15 00:26:15 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:26:15,846 - WARNING - Could not retrieve variants from source file in region 16:277247-279170. Error was invalid region `16:277248-279170`
[2016-04-15T07:26Z] 2016-04-15 00:26:22 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:26:22,159 - WARNING - Could not retrieve variants from source file in region 16:103306-142904. Error was invalid region `16:103307-142904`
[2016-04-15T07:26Z] 2016-04-15 00:26:22 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:26:22,348 - WARNING - Could not retrieve variants from source file in region 16:216209-239970. Error was invalid region `16:216210-239970`
[2016-04-15T07:26Z] 2016-04-15 00:26:23 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:26:23,696 - WARNING - Could not retrieve variants from source file in region 16:1706224-1706625. Error was invalid region `16:1706225-1706625`
[2016-04-15T07:26Z] 2016-04-15 00:26:26 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:26:26,300 - WARNING - Could not retrieve variants from source file in region 16:1706224-1706625. Error was invalid region `16:1706225-1706625`
[2016-04-15T07:26Z] 2016-04-15 00:26:27 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:26:27,692 - WARNING - Could not retrieve variants from source file in region 16:1706224-1706625. Error was invalid region `16:1706225-1706625`
[2016-04-15T07:26Z] ['bcbio-variation-recall', 'square', '-Xms750m', '-Xmx7280m', '-XX:+UseSerialGC', '-c', 16, '-r', u'16:15596123-31106473', '--caller', 'platypus', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/16/Batch1-16_15596122_31106473.vcf.gz', '/mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/16/Batch1-16_15596122_31106473.vcf-inputs.txt'] in region: 16:15596123-31106473
[2016-04-15T07:26Z] 2016-04-15 00:26:45 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:26:45,121 - WARNING - Could not retrieve variants from source file in region 16:28549297-28549698. Error was invalid region `16:28549298-28549698`
[2016-04-15T07:26Z] 2016-04-15 00:26:45 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:26:45,691 - WARNING - Could not retrieve variants from source file in region 16:20752912-20753313. Error was invalid region `16:20752913-20753313`
[2016-04-15T07:26Z] 2016-04-15 00:26:45 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:26:45,913 - WARNING - Could not retrieve variants from source file in region 16:23489500-23489901. Error was invalid region `16:23489501-23489901`
[2016-04-15T07:26Z] 2016-04-15 00:26:46 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:26:46,373 - WARNING - Could not retrieve variants from source file in region 16:20328474-20376945. Error was invalid region `16:20328475-20376945`
[2016-04-15T07:26Z] 2016-04-15 00:26:46 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:26:46,652 - WARNING - Could not retrieve variants from source file in region 16:25703934-25704335. Error was invalid region `16:25703935-25704335`
[2016-04-15T07:26Z] 2016-04-15 00:26:46 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:26:46,790 - WARNING - Could not retrieve variants from source file in region 16:24583195-24583596. Error was invalid region `16:24583196-24583596`
[2016-04-15T07:26Z] 2016-04-15 00:26:47 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:26:47,333 - WARNING - Could not retrieve variants from source file in region 16:21973901-21994601. Error was invalid region `16:21973902-21994601`
[2016-04-15T07:26Z] 2016-04-15 00:26:47 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:26:47,351 - WARNING - Could not retrieve variants from source file in region 16:19125589-19125990. Error was invalid region `16:19125590-19125990`
[2016-04-15T07:26Z] 2016-04-15 00:26:47 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:26:47,786 - WARNING - Could not retrieve variants from source file in region 16:31072698-31099772. Error was invalid region `16:31072699-31099772`
[2016-04-15T07:26Z] 2016-04-15 00:26:47 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:26:47,877 - WARNING - Could not retrieve variants from source file in region 16:29394341-29395643. Error was invalid region `16:29394342-29395643`
[2016-04-15T07:26Z] 2016-04-15 00:26:51 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:26:51,010 - WARNING - Could not retrieve variants from source file in region 16:20752912-20753313. Error was invalid region `16:20752913-20753313`
[2016-04-15T07:26Z] 2016-04-15 00:26:51 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:26:51,909 - WARNING - Could not retrieve variants from source file in region 16:23489500-23489901. Error was invalid region `16:23489501-23489901`
[2016-04-15T07:26Z] 2016-04-15 00:26:54 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:26:54,513 - WARNING - Could not retrieve variants from source file in region 16:25703934-25704335. Error was invalid region `16:25703935-25704335`
[2016-04-15T07:26Z] 2016-04-15 00:26:54 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:26:54,617 - WARNING - Could not retrieve variants from source file in region 16:19800002-19800403. Error was invalid region `16:19800003-19800403`
[2016-04-15T07:26Z] 2016-04-15 00:26:54 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:26:54,868 - WARNING - Could not retrieve variants from source file in region 16:20440842-20441274. Error was invalid region `16:20440843-20441274`
[2016-04-15T07:26Z] 2016-04-15 00:26:55 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:26:55,153 - WARNING - Could not retrieve variants from source file in region 16:29994711-30046953. Error was invalid region `16:29994712-30046953`
[2016-04-15T07:26Z] 2016-04-15 00:26:55 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:26:55,489 - WARNING - Could not retrieve variants from source file in region 16:25137078-25137575. Error was invalid region `16:25137079-25137575`
[2016-04-15T07:26Z] 2016-04-15 00:26:55 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:26:55,666 - WARNING - Could not retrieve variants from source file in region 16:30666156-30680845. Error was invalid region `16:30666157-30680845`
[2016-04-15T07:26Z] 2016-04-15 00:26:55 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:26:55,841 - WARNING - Could not retrieve variants from source file in region 16:21050998-21051399. Error was invalid region `16:21050999-21051399`
[2016-04-15T07:26Z] 2016-04-15 00:26:56 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:26:56,166 - WARNING - Could not retrieve variants from source file in region 16:20752912-20753313. Error was invalid region `16:20752913-20753313`
[2016-04-15T07:26Z] 2016-04-15 00:26:56 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:26:56,561 - WARNING - Could not retrieve variants from source file in region 16:23489500-23489901. Error was invalid region `16:23489501-23489901`
[2016-04-15T07:27Z] 2016-04-15 00:27:01 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:27:01,184 - WARNING - Could not retrieve variants from source file in region 16:25703934-25704335. Error was invalid region `16:25703935-25704335`
[2016-04-15T07:27Z] 2016-04-15 00:27:02 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:27:02,669 - WARNING - Could not retrieve variants from source file in region 16:20440842-20441274. Error was invalid region `16:20440843-20441274`
[2016-04-15T07:27Z] 2016-04-15 00:27:02 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:27:02,722 - WARNING - Could not retrieve variants from source file in region 16:24583195-24583596. Error was invalid region `16:24583196-24583596`
[2016-04-15T07:27Z] 2016-04-15 00:27:03 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:27:03,546 - WARNING - Could not retrieve variants from source file in region 16:29994711-30046953. Error was invalid region `16:29994712-30046953`
[2016-04-15T07:27Z] 2016-04-15 00:27:04 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:27:04,427 - WARNING - Could not retrieve variants from source file in region 16:21973901-21994601. Error was invalid region `16:21973902-21994601`
[2016-04-15T07:27Z] 2016-04-15 00:27:05 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:27:05,831 - WARNING - Could not retrieve variants from source file in region 16:31072698-31099772. Error was invalid region `16:31072699-31099772`
[2016-04-15T07:27Z] 2016-04-15 00:27:15 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:27:15,203 - WARNING - Could not retrieve variants from source file in region 16:23359988-23360389. Error was invalid region `16:23359989-23360389`
[2016-04-15T07:27Z] 2016-04-15 00:27:15 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:27:15,962 - WARNING - Could not retrieve variants from source file in region 16:20551864-20570851. Error was invalid region `16:20551865-20570851`
[2016-04-15T07:27Z] 2016-04-15 00:27:18 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:27:18,854 - WARNING - Could not retrieve variants from source file in region 16:20043119-20043520. Error was invalid region `16:20043120-20043520`
[2016-04-15T07:27Z] 2016-04-15 00:27:19 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:27:19,916 - WARNING - Could not retrieve variants from source file in region 16:29908222-29912992. Error was invalid region `16:29908223-29912992`
[2016-04-15T07:27Z] 2016-04-15 00:27:20 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:27:20,792 - WARNING - Could not retrieve variants from source file in region 16:23359988-23360389. Error was invalid region `16:23359989-23360389`
[2016-04-15T07:27Z] 2016-04-15 00:27:21 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:27:21,421 - WARNING - Could not retrieve variants from source file in region 16:30566536-30569539. Error was invalid region `16:30566537-30569539`
[2016-04-15T07:27Z] 2016-04-15 00:27:21 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:27:21,801 - WARNING - Could not retrieve variants from source file in region 16:20551864-20570851. Error was invalid region `16:20551865-20570851`
[2016-04-15T07:27Z] 2016-04-15 00:27:21 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:27:21,844 - WARNING - Could not retrieve variants from source file in region 16:28997786-28998187. Error was invalid region `16:28997787-28998187`
[2016-04-15T07:27Z] 2016-04-15 00:27:21 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:27:21,848 - WARNING - Could not retrieve variants from source file in region 16:21008479-21008880. Error was invalid region `16:21008480-21008880`
[2016-04-15T07:27Z] 2016-04-15 00:27:21 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:27:21,859 - WARNING - Could not retrieve variants from source file in region 16:19041384-19085488. Error was invalid region `16:19041385-19085488`
[2016-04-15T07:27Z] 2016-04-15 00:27:22 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:27:22,294 - WARNING - Could not retrieve variants from source file in region 16:30996660-31004359. Error was invalid region `16:30996661-31004359`
[2016-04-15T07:27Z] 2016-04-15 00:27:23 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:27:23,837 - WARNING - Could not retrieve variants from source file in region 16:19711506-19729206. Error was invalid region `16:19711507-19729206`
[2016-04-15T07:27Z] 2016-04-15 00:27:24 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:27:24,269 - WARNING - Could not retrieve variants from source file in region 16:20410277-20410737. Error was invalid region `16:20410278-20410737`
[2016-04-15T07:27Z] 2016-04-15 00:27:27 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:27:27,942 - WARNING - Could not retrieve variants from source file in region 16:30566536-30569539. Error was invalid region `16:30566537-30569539`
[2016-04-15T07:27Z] 2016-04-15 00:27:28 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:27:28,030 - WARNING - Could not retrieve variants from source file in region 16:21610593-21611140. Error was invalid region `16:21610594-21611140`
[2016-04-15T07:27Z] 2016-04-15 00:27:28 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:27:28,065 - WARNING - Could not retrieve variants from source file in region 16:29908222-29912992. Error was invalid region `16:29908223-29912992`
[2016-04-15T07:27Z] 2016-04-15 00:27:28 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:27:28,463 - WARNING - Could not retrieve variants from source file in region 16:23359988-23360389. Error was invalid region `16:23359989-23360389`
[2016-04-15T07:27Z] 2016-04-15 00:27:28 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:27:28,570 - WARNING - Could not retrieve variants from source file in region 16:20551864-20570851. Error was invalid region `16:20551865-20570851`
[2016-04-15T07:27Z] 2016-04-15 00:27:28 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:27:28,587 - WARNING - Could not retrieve variants from source file in region 16:21008479-21008880. Error was invalid region `16:21008480-21008880`
[2016-04-15T07:27Z] 2016-04-15 00:27:28 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:27:28,755 - WARNING - Could not retrieve variants from source file in region 16:30996660-31004359. Error was invalid region `16:30996661-31004359`
[2016-04-15T07:27Z] 2016-04-15 00:27:29 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:27:29,152 - WARNING - Could not retrieve variants from source file in region 16:20410277-20410737. Error was invalid region `16:20410278-20410737`
[2016-04-15T07:27Z] 2016-04-15 00:27:29 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:27:29,177 - WARNING - Could not retrieve variants from source file in region 16:19041384-19085488. Error was invalid region `16:19041385-19085488`
[2016-04-15T07:27Z] 2016-04-15 00:27:34 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:27:34,965 - WARNING - Could not retrieve variants from source file in region 16:29908222-29912992. Error was invalid region `16:29908223-29912992`
[2016-04-15T07:27Z] 2016-04-15 00:27:35 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:27:35,314 - WARNING - Could not retrieve variants from source file in region 16:28997786-28998187. Error was invalid region `16:28997787-28998187`
[2016-04-15T07:27Z] 2016-04-15 00:27:37 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:27:37,032 - WARNING - Could not retrieve variants from source file in region 16:30996660-31004359. Error was invalid region `16:30996661-31004359`
[2016-04-15T07:27Z] 2016-04-15 00:27:44 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:27:44,305 - WARNING - Could not retrieve variants from source file in region 16:30517830-30538609. Error was invalid region `16:30517831-30538609`
[2016-04-15T07:27Z] 2016-04-15 00:27:45 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:27:45,518 - WARNING - Could not retrieve variants from source file in region 16:23226576-23226977. Error was invalid region `16:23226577-23226977`
[2016-04-15T07:27Z] 2016-04-15 00:27:47 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:27:47,006 - WARNING - Could not retrieve variants from source file in region 16:19680335-19680736. Error was invalid region `16:19680336-19680736`
[2016-04-15T07:27Z] 2016-04-15 00:27:47 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:27:47,173 - WARNING - Could not retrieve variants from source file in region 16:24788211-24802515. Error was invalid region `16:24788212-24802515`
[2016-04-15T07:27Z] 2016-04-15 00:27:48 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:27:48,748 - WARNING - Could not retrieve variants from source file in region 16:19896363-19896764. Error was invalid region `16:19896364-19896764`
[2016-04-15T07:27Z] 2016-04-15 00:27:51 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:27:51,059 - WARNING - Could not retrieve variants from source file in region 16:21272380-21272781. Error was invalid region `16:21272381-21272781`
[2016-04-15T07:27Z] 2016-04-15 00:27:51 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:27:51,307 - WARNING - Could not retrieve variants from source file in region 16:29790653-29825316. Error was invalid region `16:29790654-29825316`
[2016-04-15T07:27Z] 2016-04-15 00:27:53 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:27:53,347 - WARNING - Could not retrieve variants from source file in region 16:24165919-24166320. Error was invalid region `16:24165920-24166320`
[2016-04-15T07:27Z] 2016-04-15 00:27:53 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:27:53,462 - WARNING - Could not retrieve variants from source file in region 16:30964729-30965130. Error was invalid region `16:30964730-30965130`
[2016-04-15T07:27Z] 2016-04-15 00:27:53 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:27:53,791 - WARNING - Could not retrieve variants from source file in region 16:20471239-20487694. Error was invalid region `16:20471240-20487694`
[2016-04-15T07:27Z] 2016-04-15 00:27:54 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:27:54,641 - WARNING - Could not retrieve variants from source file in region 16:30517830-30538609. Error was invalid region `16:30517831-30538609`
[2016-04-15T07:27Z] 2016-04-15 00:27:54 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:27:54,664 - WARNING - Could not retrieve variants from source file in region 16:28354142-28354543. Error was invalid region `16:28354143-28354543`
[2016-04-15T07:27Z] 2016-04-15 00:27:55 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:27:55,961 - WARNING - Could not retrieve variants from source file in region 16:28944185-28944890. Error was invalid region `16:28944186-28944890`
[2016-04-15T07:27Z] 2016-04-15 00:27:56 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:27:56,616 - WARNING - Could not retrieve variants from source file in region 16:29790653-29825316. Error was invalid region `16:29790654-29825316`
[2016-04-15T07:27Z] 2016-04-15 00:27:57 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:27:57,406 - WARNING - Could not retrieve variants from source file in region 16:20809856-20873957. Error was invalid region `16:20809857-20873957`
[2016-04-15T07:27Z] 2016-04-15 00:27:57 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:27:57,728 - WARNING - Could not retrieve variants from source file in region 16:18907218-18907619. Error was invalid region `16:18907219-18907619`
[2016-04-15T07:27Z] 2016-04-15 00:27:58 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:27:58,301 - WARNING - Could not retrieve variants from source file in region 16:19680335-19680736. Error was invalid region `16:19680336-19680736`
[2016-04-15T07:27Z] 2016-04-15 00:27:58 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:27:58,879 - WARNING - Could not retrieve variants from source file in region 16:30964729-30965130. Error was invalid region `16:30964730-30965130`
[2016-04-15T07:27Z] 2016-04-15 00:27:59 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:27:59,671 - WARNING - Could not retrieve variants from source file in region 16:20471239-20487694. Error was invalid region `16:20471240-20487694`
[2016-04-15T07:28Z] 2016-04-15 00:28:00 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:28:00,906 - WARNING - Could not retrieve variants from source file in region 16:21272380-21272781. Error was invalid region `16:21272381-21272781`
[2016-04-15T07:28Z] 2016-04-15 00:28:01 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:28:01,844 - WARNING - Could not retrieve variants from source file in region 16:29790653-29825316. Error was invalid region `16:29790654-29825316`
[2016-04-15T07:28Z] 2016-04-15 00:28:02 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:28:02,232 - WARNING - Could not retrieve variants from source file in region 16:20809856-20873957. Error was invalid region `16:20809857-20873957`
[2016-04-15T07:28Z] 2016-04-15 00:28:02 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:28:02,723 - WARNING - Could not retrieve variants from source file in region 16:18907218-18907619. Error was invalid region `16:18907219-18907619`
[2016-04-15T07:28Z] 2016-04-15 00:28:05 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:28:05,410 - WARNING - Could not retrieve variants from source file in region 16:30964729-30965130. Error was invalid region `16:30964730-30965130`
[2016-04-15T07:28Z] 2016-04-15 00:28:08 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:28:08,794 - WARNING - Could not retrieve variants from source file in region 16:23847364-23847765. Error was invalid region `16:23847365-23847765`
[2016-04-15T07:28Z] 2016-04-15 00:28:08 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:28:08,856 - WARNING - Could not retrieve variants from source file in region 16:23080423-23098612. Error was invalid region `16:23080424-23098612`
[2016-04-15T07:28Z] 2016-04-15 00:28:11 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:28:11,162 - WARNING - Could not retrieve variants from source file in region 16:23200550-23201038. Error was invalid region `16:23200551-23201038`
[2016-04-15T07:28Z] 2016-04-15 00:28:15 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:28:15,805 - WARNING - Could not retrieve variants from source file in region 16:19297008-19310282. Error was invalid region `16:19297009-19310282`
[2016-04-15T07:28Z] 2016-04-15 00:28:15 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:28:15,832 - WARNING - Could not retrieve variants from source file in region 16:28328705-28329106. Error was invalid region `16:28328706-28329106`
[2016-04-15T07:28Z] 2016-04-15 00:28:16 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:28:16,042 - WARNING - Could not retrieve variants from source file in region 16:29708139-29708540. Error was invalid region `16:29708140-29708540`
[2016-04-15T07:28Z] 2016-04-15 00:28:16 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:28:16,279 - WARNING - Could not retrieve variants from source file in region 16:30456518-30456919. Error was invalid region `16:30456519-30456919`
[2016-04-15T07:28Z] 2016-04-15 00:28:16 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:28:16,825 - WARNING - Could not retrieve variants from source file in region 16:23200550-23201038. Error was invalid region `16:23200551-23201038`
[2016-04-15T07:28Z] 2016-04-15 00:28:16 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:28:16,839 - WARNING - Could not retrieve variants from source file in region 16:21172350-21223131. Error was invalid region `16:21172351-21223131`
[2016-04-15T07:28Z] 2016-04-15 00:28:21 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:28:21,267 - WARNING - Could not retrieve variants from source file in region 16:30768281-30781018. Error was invalid region `16:30768282-30781018`
[2016-04-15T07:28Z] 2016-04-15 00:28:21 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:28:21,527 - WARNING - Could not retrieve variants from source file in region 16:23722069-23722470. Error was invalid region `16:23722070-23722470`
[2016-04-15T07:28Z] 2016-04-15 00:28:22 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:28:22,658 - WARNING - Could not retrieve variants from source file in region 16:23847364-23847765. Error was invalid region `16:23847365-23847765`
[2016-04-15T07:28Z] 2016-04-15 00:28:24 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:28:24,415 - WARNING - Could not retrieve variants from source file in region 16:29708139-29708540. Error was invalid region `16:29708140-29708540`
[2016-04-15T07:28Z] 2016-04-15 00:28:24 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:28:24,484 - WARNING - Could not retrieve variants from source file in region 16:30456518-30456919. Error was invalid region `16:30456519-30456919`
[2016-04-15T07:28Z] 2016-04-15 00:28:24 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:28:24,911 - WARNING - Could not retrieve variants from source file in region 16:19194919-19195320. Error was invalid region `16:19194920-19195320`
[2016-04-15T07:28Z] 2016-04-15 00:28:25 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:28:25,408 - WARNING - Could not retrieve variants from source file in region 16:29675717-29676118. Error was invalid region `16:29675718-29676118`
[2016-04-15T07:28Z] 2016-04-15 00:28:25 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:28:25,644 - WARNING - Could not retrieve variants from source file in region 16:28874911-28915717. Error was invalid region `16:28874912-28915717`
[2016-04-15T07:28Z] 2016-04-15 00:28:25 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:28:25,895 - WARNING - Could not retrieve variants from source file in region 16:23200550-23201038. Error was invalid region `16:23200551-23201038`
[2016-04-15T07:28Z] 2016-04-15 00:28:26 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:28:26,471 - WARNING - Could not retrieve variants from source file in region 16:30768281-30781018. Error was invalid region `16:30768282-30781018`
[2016-04-15T07:28Z] 2016-04-15 00:28:29 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:28:29,951 - WARNING - Could not retrieve variants from source file in region 16:19297008-19310282. Error was invalid region `16:19297009-19310282`
[2016-04-15T07:28Z] 2016-04-15 00:28:30 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:28:30,828 - WARNING - Could not retrieve variants from source file in region 16:29708139-29708540. Error was invalid region `16:29708140-29708540`
[2016-04-15T07:28Z] 2016-04-15 00:28:32 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:28:32,386 - WARNING - Could not retrieve variants from source file in region 16:19194919-19195320. Error was invalid region `16:19194920-19195320`
[2016-04-15T07:28Z] 2016-04-15 00:28:34 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:28:34,937 - WARNING - Could not retrieve variants from source file in region 16:28874911-28915717. Error was invalid region `16:28874912-28915717`
[2016-04-15T07:28Z] 2016-04-15 00:28:34 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:28:34,963 - WARNING - Could not retrieve variants from source file in region 16:30768281-30781018. Error was invalid region `16:30768282-30781018`
[2016-04-15T07:28Z] 2016-04-15 00:28:34 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:28:34,987 - WARNING - Could not retrieve variants from source file in region 16:18823168-18872240. Error was invalid region `16:18823169-18872240`
[2016-04-15T07:28Z] 2016-04-15 00:28:39 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:28:39,616 - WARNING - Could not retrieve variants from source file in region 16:23521432-23563691. Error was invalid region `16:23521433-23563691`
[2016-04-15T07:28Z] 2016-04-15 00:28:40 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:28:40,170 - WARNING - Could not retrieve variants from source file in region 16:28164698-28165099. Error was invalid region `16:28164699-28165099`
[2016-04-15T07:28Z] 2016-04-15 00:28:40 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:28:40,580 - WARNING - Could not retrieve variants from source file in region 16:30197940-30198341. Error was invalid region `16:30197941-30198341`
[2016-04-15T07:28Z] 2016-04-15 00:28:40 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:28:40,793 - WARNING - Could not retrieve variants from source file in region 16:22926300-22926701. Error was invalid region `16:22926301-22926701`
[2016-04-15T07:28Z] 2016-04-15 00:28:42 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:28:42,206 - WARNING - Could not retrieve variants from source file in region 16:30197940-30198341. Error was invalid region `16:30197941-30198341`
[2016-04-15T07:28Z] 2016-04-15 00:28:42 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:28:42,517 - WARNING - Could not retrieve variants from source file in region 16:30197940-30198341. Error was invalid region `16:30197941-30198341`
[2016-04-15T07:28Z] 2016-04-15 00:28:44 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:28:44,155 - WARNING - Could not retrieve variants from source file in region 16:23521432-23563691. Error was invalid region `16:23521433-23563691`
[2016-04-15T07:28Z] 2016-04-15 00:28:44 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:28:44,998 - WARNING - Could not retrieve variants from source file in region 16:28164698-28165099. Error was invalid region `16:28164699-28165099`
[2016-04-15T07:28Z] 2016-04-15 00:28:46 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:28:46,699 - WARNING - Could not retrieve variants from source file in region 16:17228157-17228558. Error was invalid region `16:17228158-17228558`
[2016-04-15T07:28Z] 2016-04-15 00:28:46 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:28:46,744 - WARNING - Could not retrieve variants from source file in region 16:28835469-28847056. Error was invalid region `16:28835470-28847056`
[2016-04-15T07:28Z] 2016-04-15 00:28:48 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:28:48,141 - WARNING - Could not retrieve variants from source file in region 16:30723859-30735153. Error was invalid region `16:30723860-30735153`
[2016-04-15T07:28Z] 2016-04-15 00:28:48 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:28:48,648 - WARNING - Could not retrieve variants from source file in region 16:23521432-23563691. Error was invalid region `16:23521433-23563691`
[2016-04-15T07:28Z] 2016-04-15 00:28:49 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:28:49,145 - WARNING - Could not retrieve variants from source file in region 16:28164698-28165099. Error was invalid region `16:28164699-28165099`
[2016-04-15T07:28Z] 2016-04-15 00:28:49 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:28:49,935 - WARNING - Could not retrieve variants from source file in region 16:22926300-22926701. Error was invalid region `16:22926301-22926701`
[2016-04-15T07:28Z] 2016-04-15 00:28:51 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:28:51,400 - WARNING - Could not retrieve variants from source file in region 16:23160027-23160428. Error was invalid region `16:23160028-23160428`
[2016-04-15T07:28Z] 2016-04-15 00:28:51 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:28:51,482 - WARNING - Could not retrieve variants from source file in region 16:17291993-17292394. Error was invalid region `16:17291994-17292394`
[2016-04-15T07:28Z] 2016-04-15 00:28:51 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:28:51,486 - WARNING - Could not retrieve variants from source file in region 16:17228157-17228558. Error was invalid region `16:17228158-17228558`
[2016-04-15T07:28Z] 2016-04-15 00:28:51 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:28:51,820 - WARNING - Could not retrieve variants from source file in region 16:17291993-17292394. Error was invalid region `16:17291994-17292394`
[2016-04-15T07:28Z] 2016-04-15 00:28:51 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:28:51,867 - WARNING - Could not retrieve variants from source file in region 16:22545686-22546087. Error was invalid region `16:22545687-22546087`
[2016-04-15T07:28Z] 2016-04-15 00:28:51 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:28:51,890 - WARNING - Could not retrieve variants from source file in region 16:28835469-28847056. Error was invalid region `16:28835470-28847056`
[2016-04-15T07:28Z] 2016-04-15 00:28:51 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:28:51,892 - WARNING - Could not retrieve variants from source file in region 16:28835469-28847056. Error was invalid region `16:28835470-28847056`
[2016-04-15T07:28Z] 2016-04-15 00:28:52 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:28:52,203 - WARNING - Could not retrieve variants from source file in region 16:30723859-30735153. Error was invalid region `16:30723860-30735153`
[2016-04-15T07:28Z] 2016-04-15 00:28:53 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:28:53,174 - WARNING - Could not retrieve variants from source file in region 16:21078482-21078883. Error was invalid region `16:21078483-21078883`
[2016-04-15T07:28Z] 2016-04-15 00:28:56 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:28:56,204 - WARNING - Could not retrieve variants from source file in region 16:17228157-17228558. Error was invalid region `16:17228158-17228558`
[2016-04-15T07:28Z] 2016-04-15 00:28:56 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:28:56,375 - WARNING - Could not retrieve variants from source file in region 16:22545686-22546087. Error was invalid region `16:22545687-22546087`
[2016-04-15T07:28Z] 2016-04-15 00:28:56 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:28:56,562 - WARNING - Could not retrieve variants from source file in region 16:30723859-30735153. Error was invalid region `16:30723860-30735153`
[2016-04-15T07:29Z] 2016-04-15 00:29:01 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:29:01,282 - WARNING - Could not retrieve variants from source file in region 16:27974276-27974677. Error was invalid region `16:27974277-27974677`
[2016-04-15T07:29Z] 2016-04-15 00:29:01 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:29:01,618 - WARNING - Could not retrieve variants from source file in region 16:27899189-27899590. Error was invalid region `16:27899190-27899590`
[2016-04-15T07:29Z] 2016-04-15 00:29:01 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:29:01,671 - WARNING - Could not retrieve variants from source file in region 16:27355992-27375117. Error was invalid region `16:27355993-27375117`
[2016-04-15T07:29Z] 2016-04-15 00:29:05 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:29:05,111 - WARNING - Could not retrieve variants from source file in region 16:22826128-22826529. Error was invalid region `16:22826129-22826529`
[2016-04-15T07:29Z] 2016-04-15 00:29:05 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:29:05,222 - WARNING - Could not retrieve variants from source file in region 16:27974276-27974677. Error was invalid region `16:27974277-27974677`
[2016-04-15T07:29Z] 2016-04-15 00:29:05 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:29:05,621 - WARNING - Could not retrieve variants from source file in region 16:27899189-27899590. Error was invalid region `16:27899190-27899590`
[2016-04-15T07:29Z] 2016-04-15 00:29:06 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:29:06,115 - WARNING - Could not retrieve variants from source file in region 16:27974276-27974677. Error was invalid region `16:27974277-27974677`
[2016-04-15T07:29Z] 2016-04-15 00:29:06 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:29:06,221 - WARNING - Could not retrieve variants from source file in region 16:27355992-27375117. Error was invalid region `16:27355993-27375117`
[2016-04-15T07:29Z] 2016-04-15 00:29:08 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:29:08,550 - WARNING - Could not retrieve variants from source file in region 16:27325053-27325454. Error was invalid region `16:27325054-27325454`
[2016-04-15T07:29Z] 2016-04-15 00:29:09 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:29:09,568 - WARNING - Could not retrieve variants from source file in region 16:22826128-22826529. Error was invalid region `16:22826129-22826529`
[2016-04-15T07:29Z] 2016-04-15 00:29:10 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:29:10,334 - WARNING - Could not retrieve variants from source file in region 16:27231529-27238300. Error was invalid region `16:27231530-27238300`
[2016-04-15T07:29Z] 2016-04-15 00:29:11 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:29:11,803 - WARNING - Could not retrieve variants from source file in region 16:16271146-16302776. Error was invalid region `16:16271147-16302776`
[2016-04-15T07:29Z] 2016-04-15 00:29:12 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:29:12,721 - WARNING - Could not retrieve variants from source file in region 16:27325053-27325454. Error was invalid region `16:27325054-27325454`
[2016-04-15T07:29Z] 2016-04-15 00:29:15 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:29:15,207 - WARNING - Could not retrieve variants from source file in region 16:22262303-22291860. Error was invalid region `16:22262304-22291860`
[2016-04-15T07:29Z] 2016-04-15 00:29:18 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:29:18,594 - WARNING - Could not retrieve variants from source file in region 16:27772690-27784687. Error was invalid region `16:27772691-27784687`
[2016-04-15T07:29Z] 2016-04-15 00:29:18 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:29:18,849 - WARNING - Could not retrieve variants from source file in region 16:27772690-27784687. Error was invalid region `16:27772691-27784687`
[2016-04-15T07:29Z] 2016-04-15 00:29:23 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:29:23,839 - WARNING - Could not retrieve variants from source file in region 16:15595931-15596332. Error was invalid region `16:15595932-15596332`
[2016-04-15T07:29Z] 2016-04-15 00:29:24 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:29:24,858 - WARNING - Could not retrieve variants from source file in region 16:15595931-15596332. Error was invalid region `16:15595932-15596332`
[2016-04-15T07:29Z] 2016-04-15 00:29:24 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:29:24,891 - WARNING - Could not retrieve variants from source file in region 16:15595931-15596332. Error was invalid region `16:15595932-15596332`
[2016-04-15T07:29Z] ['bcbio-variation-recall', 'square', '-Xms750m', '-Xmx7280m', '-XX:+UseSerialGC', '-c', 16, '-r', u'16:31120545-46629582', '--caller', 'platypus', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/16/Batch1-16_31120544_46629582.vcf.gz', '/mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/16/Batch1-16_31120544_46629582.vcf-inputs.txt'] in region: 16:31120545-46629582
[2016-04-15T07:29Z] 2016-04-15 00:29:38 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:29:38,417 - WARNING - Could not retrieve variants from source file in region 16:31926408-31926809. Error was invalid region `16:31926409-31926809`
[2016-04-15T07:29Z] 2016-04-15 00:29:38 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:29:38,617 - WARNING - Could not retrieve variants from source file in region 16:31926408-31926809. Error was invalid region `16:31926409-31926809`
[2016-04-15T07:29Z] 2016-04-15 00:29:38 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:29:38,667 - WARNING - Could not retrieve variants from source file in region 16:31230252-31230653. Error was invalid region `16:31230253-31230653`
[2016-04-15T07:29Z] 2016-04-15 00:29:39 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:29:39,165 - WARNING - Could not retrieve variants from source file in region 16:31195068-31195469. Error was invalid region `16:31195069-31195469`
[2016-04-15T07:29Z] 2016-04-15 00:29:39 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:29:39,169 - WARNING - Could not retrieve variants from source file in region 16:31230252-31230653. Error was invalid region `16:31230253-31230653`
[2016-04-15T07:29Z] 2016-04-15 00:29:39 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:29:39,192 - WARNING - Could not retrieve variants from source file in region 16:31926408-31926809. Error was invalid region `16:31926409-31926809`
[2016-04-15T07:29Z] 2016-04-15 00:29:39 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:29:39,265 - WARNING - Could not retrieve variants from source file in region 16:31230252-31230653. Error was invalid region `16:31230253-31230653`
[2016-04-15T07:29Z] 2016-04-15 00:29:39 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:29:39,733 - WARNING - Could not retrieve variants from source file in region 16:31422218-31422619. Error was invalid region `16:31422219-31422619`
[2016-04-15T07:29Z] 2016-04-15 00:29:39 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:29:39,914 - WARNING - Could not retrieve variants from source file in region 16:31470329-31476648. Error was invalid region `16:31470330-31476648`
[2016-04-15T07:29Z] 2016-04-15 00:29:40 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:29:40,185 - WARNING - Could not retrieve variants from source file in region 16:32264811-32265212. Error was invalid region `16:32264812-32265212`
[2016-04-15T07:29Z] 2016-04-15 00:29:40 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:29:40,218 - WARNING - Could not retrieve variants from source file in region 16:31121582-31154336. Error was invalid region `16:31121583-31154336`
[2016-04-15T07:29Z] 2016-04-15 00:29:46 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:29:46,842 - WARNING - Could not retrieve variants from source file in region 16:31765009-31765410. Error was invalid region `16:31765010-31765410`
[2016-04-15T07:29Z] 2016-04-15 00:29:46 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:29:46,993 - WARNING - Could not retrieve variants from source file in region 16:31422218-31422619. Error was invalid region `16:31422219-31422619`
[2016-04-15T07:29Z] 2016-04-15 00:29:47 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:29:47,399 - WARNING - Could not retrieve variants from source file in region 16:31470329-31476648. Error was invalid region `16:31470330-31476648`
[2016-04-15T07:29Z] 2016-04-15 00:29:48 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:29:48,824 - WARNING - Could not retrieve variants from source file in region 16:31422218-31422619. Error was invalid region `16:31422219-31422619`
[2016-04-15T07:29Z] 2016-04-15 00:29:48 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:29:48,949 - WARNING - Could not retrieve variants from source file in region 16:31470329-31476648. Error was invalid region `16:31470330-31476648`
[2016-04-15T07:29Z] 2016-04-15 00:29:49 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:29:49,951 - WARNING - Could not retrieve variants from source file in region 16:31195068-31195469. Error was invalid region `16:31195069-31195469`
[2016-04-15T07:29Z] 2016-04-15 00:29:50 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:29:50,063 - WARNING - Could not retrieve variants from source file in region 16:32264811-32265212. Error was invalid region `16:32264812-32265212`
[2016-04-15T07:29Z] 2016-04-15 00:29:50 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:29:50,119 - WARNING - Could not retrieve variants from source file in region 16:31121582-31154336. Error was invalid region `16:31121583-31154336`
[2016-04-15T07:29Z] 2016-04-15 00:29:50 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:29:50,175 - WARNING - Could not retrieve variants from source file in region 16:31195068-31195469. Error was invalid region `16:31195069-31195469`
[2016-04-15T07:29Z] 2016-04-15 00:29:51 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:29:51,737 - WARNING - Could not retrieve variants from source file in region 16:31121582-31154336. Error was invalid region `16:31121583-31154336`
[2016-04-15T07:29Z] ['bcbio-variation-recall', 'square', '-Xms750m', '-Xmx7280m', '-XX:+UseSerialGC', '-c', 16, '-r', u'16:46633743-64982002', '--caller', 'platypus', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/16/Batch1-16_46633742_64982002.vcf.gz', '/mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/16/Batch1-16_46633742_64982002.vcf-inputs.txt'] in region: 16:46633743-64982002
[2016-04-15T07:30Z] 2016-04-15 00:30:07 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:30:07,332 - WARNING - Could not retrieve variants from source file in region 16:48122371-48122772. Error was invalid region `16:48122372-48122772`
[2016-04-15T07:30Z] 2016-04-15 00:30:07 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:30:07,502 - WARNING - Could not retrieve variants from source file in region 16:58078954-58079355. Error was invalid region `16:58078955-58079355`
[2016-04-15T07:30Z] 2016-04-15 00:30:08 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:30:08,354 - WARNING - Could not retrieve variants from source file in region 16:46696073-46696474. Error was invalid region `16:46696074-46696474`
[2016-04-15T07:30Z] 2016-04-15 00:30:08 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:30:08,946 - WARNING - Could not retrieve variants from source file in region 16:53859928-53860329. Error was invalid region `16:53859929-53860329`
[2016-04-15T07:30Z] 2016-04-15 00:30:09 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:30:09,221 - WARNING - Could not retrieve variants from source file in region 16:57392522-57397639. Error was invalid region `16:57392523-57397639`
[2016-04-15T07:30Z] 2016-04-15 00:30:09 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:30:09,388 - WARNING - Could not retrieve variants from source file in region 16:56839228-56855686. Error was invalid region `16:56839229-56855686`
[2016-04-15T07:30Z] 2016-04-15 00:30:14 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:30:14,445 - WARNING - Could not retrieve variants from source file in region 16:48122371-48122772. Error was invalid region `16:48122372-48122772`
[2016-04-15T07:30Z] 2016-04-15 00:30:15 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:30:15,856 - WARNING - Could not retrieve variants from source file in region 16:57551877-57562994. Error was invalid region `16:57551878-57562994`
[2016-04-15T07:30Z] 2016-04-15 00:30:16 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:30:16,348 - WARNING - Could not retrieve variants from source file in region 16:50608795-50609197. Error was invalid region `16:50608796-50609197`
[2016-04-15T07:30Z] 2016-04-15 00:30:17 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:30:17,310 - WARNING - Could not retrieve variants from source file in region 16:50827307-50827708. Error was invalid region `16:50827308-50827708`
[2016-04-15T07:30Z] 2016-04-15 00:30:17 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:30:17,452 - WARNING - Could not retrieve variants from source file in region 16:46696073-46696474. Error was invalid region `16:46696074-46696474`
[2016-04-15T07:30Z] 2016-04-15 00:30:18 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:30:18,026 - WARNING - Could not retrieve variants from source file in region 16:50059351-50059752. Error was invalid region `16:50059352-50059752`
[2016-04-15T07:30Z] 2016-04-15 00:30:18 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:30:18,967 - WARNING - Could not retrieve variants from source file in region 16:48122371-48122772. Error was invalid region `16:48122372-48122772`
[2016-04-15T07:30Z] 2016-04-15 00:30:23 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:30:23,019 - WARNING - Could not retrieve variants from source file in region 16:50744413-50763968. Error was invalid region `16:50744414-50763968`
[2016-04-15T07:30Z] 2016-04-15 00:30:24 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:30:24,517 - WARNING - Could not retrieve variants from source file in region 16:46696073-46696474. Error was invalid region `16:46696074-46696474`
[2016-04-15T07:30Z] 2016-04-15 00:30:25 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:30:25,650 - WARNING - Could not retrieve variants from source file in region 16:64980607-64981008. Error was invalid region `16:64980608-64981008`
[2016-04-15T07:30Z] 2016-04-15 00:30:26 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:30:26,292 - WARNING - Could not retrieve variants from source file in region 16:53859928-53860329. Error was invalid region `16:53859929-53860329`
[2016-04-15T07:30Z] 2016-04-15 00:30:26 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:30:26,466 - WARNING - Could not retrieve variants from source file in region 16:56839228-56855686. Error was invalid region `16:56839229-56855686`
[2016-04-15T07:30Z] 2016-04-15 00:30:37 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:30:37,792 - WARNING - Could not retrieve variants from source file in region 16:46773788-46774189. Error was invalid region `16:46773789-46774189`
[2016-04-15T07:30Z] 2016-04-15 00:30:38 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:30:38,649 - WARNING - Could not retrieve variants from source file in region 16:57474476-57500092. Error was invalid region `16:57474477-57500092`
[2016-04-15T07:30Z] 2016-04-15 00:30:39 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:30:39,239 - WARNING - Could not retrieve variants from source file in region 16:57601581-57601982. Error was invalid region `16:57601582-57601982`
[2016-04-15T07:30Z] 2016-04-15 00:30:39 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:30:39,863 - WARNING - Could not retrieve variants from source file in region 16:50326450-50342848. Error was invalid region `16:50326451-50342848`
[2016-04-15T07:30Z] 2016-04-15 00:30:40 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:30:40,231 - WARNING - Could not retrieve variants from source file in region 16:46654999-46655400. Error was invalid region `16:46655000-46655400`
[2016-04-15T07:30Z] 2016-04-15 00:30:40 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:30:40,286 - WARNING - Could not retrieve variants from source file in region 16:50709512-50709913. Error was invalid region `16:50709513-50709913`
[2016-04-15T07:30Z] 2016-04-15 00:30:40 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:30:40,619 - WARNING - Could not retrieve variants from source file in region 16:55731624-55737846. Error was invalid region `16:55731625-55737846`
[2016-04-15T07:30Z] 2016-04-15 00:30:43 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:30:43,358 - WARNING - Could not retrieve variants from source file in region 16:46773788-46774189. Error was invalid region `16:46773789-46774189`
[2016-04-15T07:30Z] 2016-04-15 00:30:43 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:30:43,638 - WARNING - Could not retrieve variants from source file in region 16:49888099-49888659. Error was invalid region `16:49888100-49888659`
[2016-04-15T07:30Z] 2016-04-15 00:30:43 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:30:43,879 - WARNING - Could not retrieve variants from source file in region 16:57601581-57601982. Error was invalid region `16:57601582-57601982`
[2016-04-15T07:30Z] 2016-04-15 00:30:44 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:30:44,941 - WARNING - Could not retrieve variants from source file in region 16:50326450-50342848. Error was invalid region `16:50326451-50342848`
[2016-04-15T07:30Z] 2016-04-15 00:30:45 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:30:45,214 - WARNING - Could not retrieve variants from source file in region 16:57015881-57016282. Error was invalid region `16:57015882-57016282`
[2016-04-15T07:30Z] 2016-04-15 00:30:45 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:30:45,599 - WARNING - Could not retrieve variants from source file in region 16:46654999-46655400. Error was invalid region `16:46655000-46655400`
[2016-04-15T07:30Z] 2016-04-15 00:30:45 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:30:45,761 - WARNING - Could not retrieve variants from source file in region 16:50709512-50709913. Error was invalid region `16:50709513-50709913`
[2016-04-15T07:30Z] 2016-04-15 00:30:47 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:30:47,737 - WARNING - Could not retrieve variants from source file in region 16:57147063-57147464. Error was invalid region `16:57147064-57147464`
[2016-04-15T07:30Z] 2016-04-15 00:30:48 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:30:48,278 - WARNING - Could not retrieve variants from source file in region 16:46773788-46774189. Error was invalid region `16:46773789-46774189`
[2016-04-15T07:30Z] 2016-04-15 00:30:48 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:30:48,585 - WARNING - Could not retrieve variants from source file in region 16:57996721-58045659. Error was invalid region `16:57996722-58045659`
[2016-04-15T07:30Z] 2016-04-15 00:30:49 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:30:49,400 - WARNING - Could not retrieve variants from source file in region 16:57601581-57601982. Error was invalid region `16:57601582-57601982`
[2016-04-15T07:30Z] 2016-04-15 00:30:49 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:30:49,607 - WARNING - Could not retrieve variants from source file in region 16:56704227-56704628. Error was invalid region `16:56704228-56704628`
[2016-04-15T07:30Z] 2016-04-15 00:30:50 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:30:50,091 - WARNING - Could not retrieve variants from source file in region 16:53480799-53504911. Error was invalid region `16:53480800-53504911`
[2016-04-15T07:30Z] 2016-04-15 00:30:50 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:30:50,683 - WARNING - Could not retrieve variants from source file in region 16:50326450-50342848. Error was invalid region `16:50326451-50342848`
[2016-04-15T07:30Z] 2016-04-15 00:30:50 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:30:50,839 - WARNING - Could not retrieve variants from source file in region 16:50709512-50709913. Error was invalid region `16:50709513-50709913`
[2016-04-15T07:30Z] 2016-04-15 00:30:50 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:30:50,850 - WARNING - Could not retrieve variants from source file in region 16:57015881-57016282. Error was invalid region `16:57015882-57016282`
[2016-04-15T07:30Z] 2016-04-15 00:30:51 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:30:51,174 - WARNING - Could not retrieve variants from source file in region 16:46654999-46655400. Error was invalid region `16:46655000-46655400`
[2016-04-15T07:30Z] 2016-04-15 00:30:54 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:30:54,621 - WARNING - Could not retrieve variants from source file in region 16:56704227-56704628. Error was invalid region `16:56704228-56704628`
[2016-04-15T07:30Z] 2016-04-15 00:30:55 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:30:55,736 - WARNING - Could not retrieve variants from source file in region 16:53480799-53504911. Error was invalid region `16:53480800-53504911`
[2016-04-15T07:30Z] 2016-04-15 00:30:56 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:30:56,061 - WARNING - Could not retrieve variants from source file in region 16:57015881-57016282. Error was invalid region `16:57015882-57016282`
[2016-04-15T07:31Z] 2016-04-15 00:31:04 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:31:04,268 - WARNING - Could not retrieve variants from source file in region 16:53326649-53358629. Error was invalid region `16:53326650-53358629`
[2016-04-15T07:31Z] 2016-04-15 00:31:05 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:31:05,234 - WARNING - Could not retrieve variants from source file in region 16:53403992-53404393. Error was invalid region `16:53403993-53404393`
[2016-04-15T07:31Z] 2016-04-15 00:31:05 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:31:05,653 - WARNING - Could not retrieve variants from source file in region 16:48164566-48164967. Error was invalid region `16:48164567-48164967`
[2016-04-15T07:31Z] 2016-04-15 00:31:07 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:31:07,002 - WARNING - Could not retrieve variants from source file in region 16:50106383-50106784. Error was invalid region `16:50106384-50106784`
[2016-04-15T07:31Z] 2016-04-15 00:31:07 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:31:07,083 - WARNING - Could not retrieve variants from source file in region 16:55601177-55601578. Error was invalid region `16:55601178-55601578`
[2016-04-15T07:31Z] 2016-04-15 00:31:07 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:31:07,245 - WARNING - Could not retrieve variants from source file in region 16:55562255-55562656. Error was invalid region `16:55562256-55562656`
[2016-04-15T07:31Z] 2016-04-15 00:31:09 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:31:09,125 - WARNING - Could not retrieve variants from source file in region 16:53326649-53358629. Error was invalid region `16:53326650-53358629`
[2016-04-15T07:31Z] 2016-04-15 00:31:09 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:31:09,189 - WARNING - Could not retrieve variants from source file in region 16:56667071-56674018. Error was invalid region `16:56667072-56674018`
[2016-04-15T07:31Z] 2016-04-15 00:31:09 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:31:09,841 - WARNING - Could not retrieve variants from source file in region 16:53403992-53404393. Error was invalid region `16:53403993-53404393`
[2016-04-15T07:31Z] 2016-04-15 00:31:10 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:31:10,484 - WARNING - Could not retrieve variants from source file in region 16:48164566-48164967. Error was invalid region `16:48164567-48164967`
[2016-04-15T07:31Z] 2016-04-15 00:31:12 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:31:12,064 - WARNING - Could not retrieve variants from source file in region 16:50106383-50106784. Error was invalid region `16:50106384-50106784`
[2016-04-15T07:31Z] 2016-04-15 00:31:12 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:31:12,721 - WARNING - Could not retrieve variants from source file in region 16:55562255-55562656. Error was invalid region `16:55562256-55562656`
[2016-04-15T07:31Z] 2016-04-15 00:31:12 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:31:12,779 - WARNING - Could not retrieve variants from source file in region 16:55601177-55601578. Error was invalid region `16:55601178-55601578`
[2016-04-15T07:31Z] 2016-04-15 00:31:13 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:31:13,786 - WARNING - Could not retrieve variants from source file in region 16:56667071-56674018. Error was invalid region `16:56667072-56674018`
[2016-04-15T07:31Z] 2016-04-15 00:31:13 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:31:13,817 - WARNING - Could not retrieve variants from source file in region 16:53326649-53358629. Error was invalid region `16:53326650-53358629`
[2016-04-15T07:31Z] 2016-04-15 00:31:14 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:31:14,310 - WARNING - Could not retrieve variants from source file in region 16:53403992-53404393. Error was invalid region `16:53403993-53404393`
[2016-04-15T07:31Z] 2016-04-15 00:31:14 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:31:14,842 - WARNING - Could not retrieve variants from source file in region 16:48164566-48164967. Error was invalid region `16:48164567-48164967`
[2016-04-15T07:31Z] 2016-04-15 00:31:15 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:31:15,281 - WARNING - Could not retrieve variants from source file in region 16:56904376-56913703. Error was invalid region `16:56904377-56913703`
[2016-04-15T07:31Z] 2016-04-15 00:31:16 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:31:16,997 - WARNING - Could not retrieve variants from source file in region 16:50106383-50106784. Error was invalid region `16:50106384-50106784`
[2016-04-15T07:31Z] 2016-04-15 00:31:17 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:31:17,399 - WARNING - Could not retrieve variants from source file in region 16:55562255-55562656. Error was invalid region `16:55562256-55562656`
[2016-04-15T07:31Z] 2016-04-15 00:31:17 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:31:17,885 - WARNING - Could not retrieve variants from source file in region 16:56965800-56969338. Error was invalid region `16:56965801-56969338`
[2016-04-15T07:31Z] 2016-04-15 00:31:18 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:31:18,231 - WARNING - Could not retrieve variants from source file in region 16:60392432-60393594. Error was invalid region `16:60392433-60393594`
[2016-04-15T07:31Z] 2016-04-15 00:31:18 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:31:18,332 - WARNING - Could not retrieve variants from source file in region 16:56667071-56674018. Error was invalid region `16:56667072-56674018`
[2016-04-15T07:31Z] 2016-04-15 00:31:19 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:31:19,550 - WARNING - Could not retrieve variants from source file in region 16:56904376-56913703. Error was invalid region `16:56904377-56913703`
[2016-04-15T07:31Z] 2016-04-15 00:31:26 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:31:26,473 - WARNING - Could not retrieve variants from source file in region 16:54966885-54967320. Error was invalid region `16:54966886-54967320`
[2016-04-15T07:31Z] 2016-04-15 00:31:27 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:31:27,173 - WARNING - Could not retrieve variants from source file in region 16:53283755-53284156. Error was invalid region `16:53283756-53284156`
[2016-04-15T07:31Z] 2016-04-15 00:31:27 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:31:27,981 - WARNING - Could not retrieve variants from source file in region 16:56533593-56548691. Error was invalid region `16:56533594-56548691`
[2016-04-15T07:31Z] 2016-04-15 00:31:28 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:31:28,712 - WARNING - Could not retrieve variants from source file in region 16:52473052-52478405. Error was invalid region `16:52473053-52478405`
[2016-04-15T07:31Z] 2016-04-15 00:31:28 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:31:28,728 - WARNING - Could not retrieve variants from source file in region 16:58743243-58757873. Error was invalid region `16:58743244-58757873`
[2016-04-15T07:31Z] 2016-04-15 00:31:31 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:31:31,014 - WARNING - Could not retrieve variants from source file in region 16:54966885-54967320. Error was invalid region `16:54966886-54967320`
[2016-04-15T07:31Z] 2016-04-15 00:31:31 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:31:31,388 - WARNING - Could not retrieve variants from source file in region 16:56601509-56601912. Error was invalid region `16:56601510-56601912`
[2016-04-15T07:31Z] 2016-04-15 00:31:31 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:31:31,451 - WARNING - Could not retrieve variants from source file in region 16:53283755-53284156. Error was invalid region `16:53283756-53284156`
[2016-04-15T07:31Z] 2016-04-15 00:31:33 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:31:33,379 - WARNING - Could not retrieve variants from source file in region 16:58743243-58757873. Error was invalid region `16:58743244-58757873`
[2016-04-15T07:31Z] 2016-04-15 00:31:33 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:31:33,405 - WARNING - Could not retrieve variants from source file in region 16:52473052-52478405. Error was invalid region `16:52473053-52478405`
[2016-04-15T07:31Z] 2016-04-15 00:31:34 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:31:34,479 - WARNING - Could not retrieve variants from source file in region 16:55519324-55536953. Error was invalid region `16:55519325-55536953`
[2016-04-15T07:31Z] 2016-04-15 00:31:35 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:31:35,572 - WARNING - Could not retrieve variants from source file in region 16:55519324-55536953. Error was invalid region `16:55519325-55536953`
[2016-04-15T07:31Z] 2016-04-15 00:31:35 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:31:35,586 - WARNING - Could not retrieve variants from source file in region 16:56601509-56601912. Error was invalid region `16:56601510-56601912`
[2016-04-15T07:31Z] 2016-04-15 00:31:35 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:31:35,984 - WARNING - Could not retrieve variants from source file in region 16:53283755-53284156. Error was invalid region `16:53283756-53284156`
[2016-04-15T07:31Z] 2016-04-15 00:31:35 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:31:35,998 - WARNING - Could not retrieve variants from source file in region 16:58616773-58617174. Error was invalid region `16:58616774-58617174`
[2016-04-15T07:31Z] 2016-04-15 00:31:37 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:31:37,842 - WARNING - Could not retrieve variants from source file in region 16:58743243-58757873. Error was invalid region `16:58743244-58757873`
[2016-04-15T07:31Z] 2016-04-15 00:31:37 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:31:37,897 - WARNING - Could not retrieve variants from source file in region 16:54317961-54320387. Error was invalid region `16:54317962-54320387`
[2016-04-15T07:31Z] 2016-04-15 00:31:39 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:31:39,899 - WARNING - Could not retrieve variants from source file in region 16:56601509-56601912. Error was invalid region `16:56601510-56601912`
[2016-04-15T07:31Z] 2016-04-15 00:31:40 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:31:40,271 - WARNING - Could not retrieve variants from source file in region 16:58616773-58617174. Error was invalid region `16:58616774-58617174`
[2016-04-15T07:31Z] 2016-04-15 00:31:43 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:31:43,814 - WARNING - Could not retrieve variants from source file in region 16:56457493-56457894. Error was invalid region `16:56457494-56457894`
[2016-04-15T07:31Z] 2016-04-15 00:31:45 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:31:45,478 - WARNING - Could not retrieve variants from source file in region 16:56457493-56457894. Error was invalid region `16:56457494-56457894`
[2016-04-15T07:31Z] 2016-04-15 00:31:45 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:31:45,497 - WARNING - Could not retrieve variants from source file in region 16:56457493-56457894. Error was invalid region `16:56457494-56457894`
[2016-04-15T07:31Z] 2016-04-15 00:31:45 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:31:45,534 - WARNING - Could not retrieve variants from source file in region 16:56499921-56500366. Error was invalid region `16:56499922-56500366`
[2016-04-15T07:31Z] 2016-04-15 00:31:48 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:31:48,912 - WARNING - Could not retrieve variants from source file in region 16:58314222-58327836. Error was invalid region `16:58314223-58327836`
[2016-04-15T07:31Z] ['bcbio-variation-recall', 'square', '-Xms750m', '-Xmx7280m', '-XX:+UseSerialGC', '-c', 16, '-r', u'16:64982512-80574976', '--caller', 'platypus', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/16/Batch1-16_64982511_80574976.vcf.gz', '/mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/16/Batch1-16_64982511_80574976.vcf-inputs.txt'] in region: 16:64982512-80574976
[2016-04-15T07:32Z] 2016-04-15 00:32:04 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:32:04,652 - WARNING - Could not retrieve variants from source file in region 16:70395176-70395577. Error was invalid region `16:70395177-70395577`
[2016-04-15T07:32Z] 2016-04-15 00:32:05 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:32:05,197 - WARNING - Could not retrieve variants from source file in region 16:71317790-71319836. Error was invalid region `16:71317791-71319836`
[2016-04-15T07:32Z] 2016-04-15 00:32:06 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:32:06,261 - WARNING - Could not retrieve variants from source file in region 16:78420564-78420965. Error was invalid region `16:78420565-78420965`
[2016-04-15T07:32Z] 2016-04-15 00:32:06 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:32:06,432 - WARNING - Could not retrieve variants from source file in region 16:76532372-76532773. Error was invalid region `16:76532373-76532773`
[2016-04-15T07:32Z] 2016-04-15 00:32:06 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:32:06,433 - WARNING - Could not retrieve variants from source file in region 16:77389745-77390146. Error was invalid region `16:77389746-77390146`
[2016-04-15T07:32Z] 2016-04-15 00:32:07 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:32:07,003 - WARNING - Could not retrieve variants from source file in region 16:66792503-66812987. Error was invalid region `16:66792504-66812987`
[2016-04-15T07:32Z] 2016-04-15 00:32:07 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:32:07,167 - WARNING - Could not retrieve variants from source file in region 16:75633803-75646875. Error was invalid region `16:75633804-75646875`
[2016-04-15T07:32Z] 2016-04-15 00:32:07 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:32:07,596 - WARNING - Could not retrieve variants from source file in region 16:68056885-68057286. Error was invalid region `16:68056886-68057286`
[2016-04-15T07:32Z] 2016-04-15 00:32:07 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:32:07,652 - WARNING - Could not retrieve variants from source file in region 16:69963144-69988563. Error was invalid region `16:69963145-69988563`
[2016-04-15T07:32Z] 2016-04-15 00:32:08 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:32:08,468 - WARNING - Could not retrieve variants from source file in region 16:67263808-67268041. Error was invalid region `16:67263809-67268041`
[2016-04-15T07:32Z] 2016-04-15 00:32:10 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:32:10,323 - WARNING - Could not retrieve variants from source file in region 16:70395176-70395577. Error was invalid region `16:70395177-70395577`
[2016-04-15T07:32Z] 2016-04-15 00:32:10 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:32:10,925 - WARNING - Could not retrieve variants from source file in region 16:71317790-71319836. Error was invalid region `16:71317791-71319836`
[2016-04-15T07:32Z] 2016-04-15 00:32:13 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:32:13,629 - WARNING - Could not retrieve variants from source file in region 16:77389745-77390146. Error was invalid region `16:77389746-77390146`
[2016-04-15T07:32Z] 2016-04-15 00:32:13 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:32:13,692 - WARNING - Could not retrieve variants from source file in region 16:76532372-76532773. Error was invalid region `16:76532373-76532773`
[2016-04-15T07:32Z] 2016-04-15 00:32:14 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:32:14,502 - WARNING - Could not retrieve variants from source file in region 16:75237857-75238293. Error was invalid region `16:75237858-75238293`
[2016-04-15T07:32Z] 2016-04-15 00:32:14 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:32:14,596 - WARNING - Could not retrieve variants from source file in region 16:66792503-66812987. Error was invalid region `16:66792504-66812987`
[2016-04-15T07:32Z] 2016-04-15 00:32:15 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:32:15,211 - WARNING - Could not retrieve variants from source file in region 16:68056885-68057286. Error was invalid region `16:68056886-68057286`
[2016-04-15T07:32Z] 2016-04-15 00:32:16 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:32:16,248 - WARNING - Could not retrieve variants from source file in region 16:70395176-70395577. Error was invalid region `16:70395177-70395577`
[2016-04-15T07:32Z] 2016-04-15 00:32:16 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:32:16,398 - WARNING - Could not retrieve variants from source file in region 16:70286966-70303770. Error was invalid region `16:70286967-70303770`
[2016-04-15T07:32Z] 2016-04-15 00:32:16 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:32:16,429 - WARNING - Could not retrieve variants from source file in region 16:67263808-67268041. Error was invalid region `16:67263809-67268041`
[2016-04-15T07:32Z] 2016-04-15 00:32:16 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:32:16,542 - WARNING - Could not retrieve variants from source file in region 16:71317790-71319836. Error was invalid region `16:71317791-71319836`
[2016-04-15T07:32Z] 2016-04-15 00:32:16 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:32:16,856 - WARNING - Could not retrieve variants from source file in region 16:78420564-78420965. Error was invalid region `16:78420565-78420965`
[2016-04-15T07:32Z] 2016-04-15 00:32:19 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:32:19,406 - WARNING - Could not retrieve variants from source file in region 16:76532372-76532773. Error was invalid region `16:76532373-76532773`
[2016-04-15T07:32Z] 2016-04-15 00:32:19 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:32:19,577 - WARNING - Could not retrieve variants from source file in region 16:77389745-77390146. Error was invalid region `16:77389746-77390146`
[2016-04-15T07:32Z] 2016-04-15 00:32:21 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:32:21,201 - WARNING - Could not retrieve variants from source file in region 16:66792503-66812987. Error was invalid region `16:66792504-66812987`
[2016-04-15T07:32Z] 2016-04-15 00:32:21 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:32:21,892 - WARNING - Could not retrieve variants from source file in region 16:68056885-68057286. Error was invalid region `16:68056886-68057286`
[2016-04-15T07:32Z] 2016-04-15 00:32:22 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:32:22,259 - WARNING - Could not retrieve variants from source file in region 16:69963144-69988563. Error was invalid region `16:69963145-69988563`
[2016-04-15T07:32Z] 2016-04-15 00:32:23 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:32:23,692 - WARNING - Could not retrieve variants from source file in region 16:72991449-72994021. Error was invalid region `16:72991450-72994021`
[2016-04-15T07:32Z] 2016-04-15 00:32:33 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:32:33,534 - WARNING - Could not retrieve variants from source file in region 16:67233055-67233456. Error was invalid region `16:67233056-67233456`
[2016-04-15T07:32Z] 2016-04-15 00:32:34 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:32:34,737 - WARNING - Could not retrieve variants from source file in region 16:71264312-71264751. Error was invalid region `16:71264313-71264751`
[2016-04-15T07:32Z] 2016-04-15 00:32:35 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:32:35,353 - WARNING - Could not retrieve variants from source file in region 16:70722729-70726985. Error was invalid region `16:70722730-70726985`
[2016-04-15T07:32Z] 2016-04-15 00:32:35 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:32:35,562 - WARNING - Could not retrieve variants from source file in region 16:77769623-77776249. Error was invalid region `16:77769624-77776249`
[2016-04-15T07:32Z] 2016-04-15 00:32:36 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:32:36,905 - WARNING - Could not retrieve variants from source file in region 16:75200384-75200787. Error was invalid region `16:75200385-75200787`
[2016-04-15T07:32Z] 2016-04-15 00:32:37 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:32:37,887 - WARNING - Could not retrieve variants from source file in region 16:69782644-69783045. Error was invalid region `16:69782645-69783045`
[2016-04-15T07:32Z] 2016-04-15 00:32:38 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:32:38,032 - WARNING - Could not retrieve variants from source file in region 16:68025590-68025991. Error was invalid region `16:68025591-68025991`
[2016-04-15T07:32Z] 2016-04-15 00:32:38 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:32:38,626 - WARNING - Could not retrieve variants from source file in region 16:67233055-67233456. Error was invalid region `16:67233056-67233456`
[2016-04-15T07:32Z] 2016-04-15 00:32:40 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:32:40,346 - WARNING - Could not retrieve variants from source file in region 16:71264312-71264751. Error was invalid region `16:71264313-71264751`
[2016-04-15T07:32Z] 2016-04-15 00:32:40 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:32:40,528 - WARNING - Could not retrieve variants from source file in region 16:75563119-75590303. Error was invalid region `16:75563120-75590303`
[2016-04-15T07:32Z] 2016-04-15 00:32:42 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:32:42,593 - WARNING - Could not retrieve variants from source file in region 16:75200384-75200787. Error was invalid region `16:75200385-75200787`
[2016-04-15T07:32Z] 2016-04-15 00:32:42 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:32:42,909 - WARNING - Could not retrieve variants from source file in region 16:66651802-66654916. Error was invalid region `16:66651803-66654916`
[2016-04-15T07:32Z] 2016-04-15 00:32:43 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:32:43,274 - WARNING - Could not retrieve variants from source file in region 16:68025590-68025991. Error was invalid region `16:68025591-68025991`
[2016-04-15T07:32Z] 2016-04-15 00:32:43 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:32:43,279 - WARNING - Could not retrieve variants from source file in region 16:69782644-69783045. Error was invalid region `16:69782645-69783045`
[2016-04-15T07:32Z] 2016-04-15 00:32:43 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:32:43,553 - WARNING - Could not retrieve variants from source file in region 16:67233055-67233456. Error was invalid region `16:67233056-67233456`
[2016-04-15T07:32Z] 2016-04-15 00:32:44 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:32:44,593 - WARNING - Could not retrieve variants from source file in region 16:71264312-71264751. Error was invalid region `16:71264313-71264751`
[2016-04-15T07:32Z] 2016-04-15 00:32:46 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:32:46,345 - WARNING - Could not retrieve variants from source file in region 16:72827547-72832325. Error was invalid region `16:72827548-72832325`
[2016-04-15T07:32Z] 2016-04-15 00:32:46 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:32:46,441 - WARNING - Could not retrieve variants from source file in region 16:70722729-70726985. Error was invalid region `16:70722730-70726985`
[2016-04-15T07:32Z] 2016-04-15 00:32:49 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:32:49,472 - WARNING - Could not retrieve variants from source file in region 16:75200384-75200787. Error was invalid region `16:75200385-75200787`
[2016-04-15T07:32Z] 2016-04-15 00:32:49 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:32:49,650 - WARNING - Could not retrieve variants from source file in region 16:76482536-76486771. Error was invalid region `16:76482537-76486771`
[2016-04-15T07:32Z] 2016-04-15 00:32:49 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:32:49,714 - WARNING - Could not retrieve variants from source file in region 16:68025590-68025991. Error was invalid region `16:68025591-68025991`
[2016-04-15T07:32Z] 2016-04-15 00:32:49 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:32:49,766 - WARNING - Could not retrieve variants from source file in region 16:69782644-69783045. Error was invalid region `16:69782645-69783045`
[2016-04-15T07:32Z] 2016-04-15 00:32:50 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:32:50,093 - WARNING - Could not retrieve variants from source file in region 16:79245575-79246151. Error was invalid region `16:79245576-79246151`
[2016-04-15T07:32Z] 2016-04-15 00:32:50 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:32:50,843 - WARNING - Could not retrieve variants from source file in region 16:75563119-75590303. Error was invalid region `16:75563120-75590303`
[2016-04-15T07:32Z] 2016-04-15 00:32:51 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:32:51,228 - WARNING - Could not retrieve variants from source file in region 16:72827547-72832325. Error was invalid region `16:72827548-72832325`
[2016-04-15T07:32Z] 2016-04-15 00:32:59 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:32:59,709 - WARNING - Could not retrieve variants from source file in region 16:66998159-66998560. Error was invalid region `16:66998160-66998560`
[2016-04-15T07:33Z] 2016-04-15 00:33:00 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:33:00,369 - WARNING - Could not retrieve variants from source file in region 16:71163482-71163883. Error was invalid region `16:71163483-71163883`
[2016-04-15T07:33Z] 2016-04-15 00:33:02 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:33:02,275 - WARNING - Could not retrieve variants from source file in region 16:76311391-76311792. Error was invalid region `16:76311392-76311792`
[2016-04-15T07:33Z] 2016-04-15 00:33:03 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:33:03,921 - WARNING - Could not retrieve variants from source file in region 16:77228418-77246985. Error was invalid region `16:77228419-77246985`
[2016-04-15T07:33Z] 2016-04-15 00:33:04 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:33:04,498 - WARNING - Could not retrieve variants from source file in region 16:66613556-66613957. Error was invalid region `16:66613557-66613957`
[2016-04-15T07:33Z] 2016-04-15 00:33:06 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:33:06,255 - WARNING - Could not retrieve variants from source file in region 16:67979212-67979613. Error was invalid region `16:67979213-67979613`
[2016-04-15T07:33Z] 2016-04-15 00:33:06 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:33:06,540 - WARNING - Could not retrieve variants from source file in region 16:69143366-69143767. Error was invalid region `16:69143367-69143767`
[2016-04-15T07:33Z] 2016-04-15 00:33:07 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:33:07,204 - WARNING - Could not retrieve variants from source file in region 16:71163482-71163883. Error was invalid region `16:71163483-71163883`
[2016-04-15T07:33Z] 2016-04-15 00:33:07 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:33:07,258 - WARNING - Could not retrieve variants from source file in region 16:72110737-72157032. Error was invalid region `16:72110738-72157032`
[2016-04-15T07:33Z] 2016-04-15 00:33:07 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:33:07,774 - WARNING - Could not retrieve variants from source file in region 16:76311391-76311792. Error was invalid region `16:76311392-76311792`
[2016-04-15T07:33Z] 2016-04-15 00:33:07 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:33:07,898 - WARNING - Could not retrieve variants from source file in region 16:70680639-70691179. Error was invalid region `16:70680640-70691179`
[2016-04-15T07:33Z] 2016-04-15 00:33:08 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:33:08,331 - WARNING - Could not retrieve variants from source file in region 16:68857230-68857631. Error was invalid region `16:68857231-68857631`
[2016-04-15T07:33Z] 2016-04-15 00:33:08 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:33:08,343 - WARNING - Could not retrieve variants from source file in region 16:70602010-70602411. Error was invalid region `16:70602011-70602411`
[2016-04-15T07:33Z] 2016-04-15 00:33:10 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:33:10,908 - WARNING - Could not retrieve variants from source file in region 16:74919980-74920381. Error was invalid region `16:74919981-74920381`
[2016-04-15T07:33Z] 2016-04-15 00:33:13 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:33:13,151 - WARNING - Could not retrieve variants from source file in region 16:67979212-67979613. Error was invalid region `16:67979213-67979613`
[2016-04-15T07:33Z] 2016-04-15 00:33:14 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:33:14,501 - WARNING - Could not retrieve variants from source file in region 16:69143366-69143767. Error was invalid region `16:69143367-69143767`
[2016-04-15T07:33Z] 2016-04-15 00:33:14 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:33:14,687 - WARNING - Could not retrieve variants from source file in region 16:72110737-72157032. Error was invalid region `16:72110738-72157032`
[2016-04-15T07:33Z] 2016-04-15 00:33:14 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:33:14,738 - WARNING - Could not retrieve variants from source file in region 16:71163482-71163883. Error was invalid region `16:71163483-71163883`
[2016-04-15T07:33Z] 2016-04-15 00:33:15 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:33:15,316 - WARNING - Could not retrieve variants from source file in region 16:75675398-75675799. Error was invalid region `16:75675399-75675799`
[2016-04-15T07:33Z] 2016-04-15 00:33:15 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:33:15,316 - WARNING - Could not retrieve variants from source file in region 16:76311391-76311792. Error was invalid region `16:76311392-76311792`
[2016-04-15T07:33Z] 2016-04-15 00:33:15 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:33:15,369 - WARNING - Could not retrieve variants from source file in region 16:68857230-68857631. Error was invalid region `16:68857231-68857631`
[2016-04-15T07:33Z] 2016-04-15 00:33:15 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:33:15,612 - WARNING - Could not retrieve variants from source file in region 16:76586991-76587521. Error was invalid region `16:76586992-76587521`
[2016-04-15T07:33Z] 2016-04-15 00:33:15 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:33:15,891 - WARNING - Could not retrieve variants from source file in region 16:66613556-66613957. Error was invalid region `16:66613557-66613957`
[2016-04-15T07:33Z] 2016-04-15 00:33:16 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:33:16,057 - WARNING - Could not retrieve variants from source file in region 16:74919980-74920381. Error was invalid region `16:74919981-74920381`
[2016-04-15T07:33Z] 2016-04-15 00:33:16 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:33:16,074 - WARNING - Could not retrieve variants from source file in region 16:70680639-70691179. Error was invalid region `16:70680640-70691179`
[2016-04-15T07:33Z] 2016-04-15 00:33:17 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:33:17,562 - WARNING - Could not retrieve variants from source file in region 16:68344152-68344886. Error was invalid region `16:68344153-68344886`
[2016-04-15T07:33Z] 2016-04-15 00:33:18 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:33:18,247 - WARNING - Could not retrieve variants from source file in region 16:67979212-67979613. Error was invalid region `16:67979213-67979613`
[2016-04-15T07:33Z] 2016-04-15 00:33:20 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:33:20,696 - WARNING - Could not retrieve variants from source file in region 16:69143366-69143767. Error was invalid region `16:69143367-69143767`
[2016-04-15T07:33Z] 2016-04-15 00:33:21 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:33:21,952 - WARNING - Could not retrieve variants from source file in region 16:72110737-72157032. Error was invalid region `16:72110738-72157032`
[2016-04-15T07:33Z] 2016-04-15 00:33:22 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:33:22,749 - WARNING - Could not retrieve variants from source file in region 16:75675398-75675799. Error was invalid region `16:75675399-75675799`
[2016-04-15T07:33Z] 2016-04-15 00:33:23 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:33:23,456 - WARNING - Could not retrieve variants from source file in region 16:76586991-76587521. Error was invalid region `16:76586992-76587521`
[2016-04-15T07:33Z] 2016-04-15 00:33:23 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:33:23,542 - WARNING - Could not retrieve variants from source file in region 16:70602010-70602411. Error was invalid region `16:70602011-70602411`
[2016-04-15T07:33Z] 2016-04-15 00:33:23 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:33:23,599 - WARNING - Could not retrieve variants from source file in region 16:68857230-68857631. Error was invalid region `16:68857231-68857631`
[2016-04-15T07:33Z] 2016-04-15 00:33:31 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:33:31,009 - WARNING - Could not retrieve variants from source file in region 16:66861755-66862156. Error was invalid region `16:66861756-66862156`
[2016-04-15T07:33Z] 2016-04-15 00:33:31 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:33:31,307 - WARNING - Could not retrieve variants from source file in region 16:70954704-70972785. Error was invalid region `16:70954705-70972785`
[2016-04-15T07:33Z] 2016-04-15 00:33:33 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:33:33,730 - WARNING - Could not retrieve variants from source file in region 16:70546023-70569405. Error was invalid region `16:70546024-70569405`
[2016-04-15T07:33Z] 2016-04-15 00:33:34 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:33:34,861 - WARNING - Could not retrieve variants from source file in region 16:67691457-67691858. Error was invalid region `16:67691458-67691858`
[2016-04-15T07:33Z] 2016-04-15 00:33:34 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:33:34,987 - WARNING - Could not retrieve variants from source file in region 16:70954704-70972785. Error was invalid region `16:70954705-70972785`
[2016-04-15T07:33Z] 2016-04-15 00:33:35 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:33:35,282 - WARNING - Could not retrieve variants from source file in region 16:74808214-74808615. Error was invalid region `16:74808215-74808615`
[2016-04-15T07:33Z] 2016-04-15 00:33:36 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:33:36,193 - WARNING - Could not retrieve variants from source file in region 16:68713519-68729975. Error was invalid region `16:68713520-68729975`
[2016-04-15T07:33Z] 2016-04-15 00:33:36 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:33:36,549 - WARNING - Could not retrieve variants from source file in region 16:66861755-66862156. Error was invalid region `16:66861756-66862156`
[2016-04-15T07:33Z] 2016-04-15 00:33:36 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:33:36,674 - WARNING - Could not retrieve variants from source file in region 16:70954704-70972785. Error was invalid region `16:70954705-70972785`
[2016-04-15T07:33Z] 2016-04-15 00:33:36 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:33:36,801 - WARNING - Could not retrieve variants from source file in region 16:71950239-72049811. Error was invalid region `16:71950240-72049811`
[2016-04-15T07:33Z] 2016-04-15 00:33:37 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:33:37,641 - WARNING - Could not retrieve variants from source file in region 16:75327705-75328106. Error was invalid region `16:75327706-75328106`
[2016-04-15T07:33Z] 2016-04-15 00:33:38 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:33:38,268 - WARNING - Could not retrieve variants from source file in region 16:71772979-71773380. Error was invalid region `16:71772980-71773380`
[2016-04-15T07:33Z] 2016-04-15 00:33:38 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:33:38,789 - WARNING - Could not retrieve variants from source file in region 16:70546023-70569405. Error was invalid region `16:70546024-70569405`
[2016-04-15T07:33Z] 2016-04-15 00:33:39 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:33:39,600 - WARNING - Could not retrieve variants from source file in region 16:66420674-66432614. Error was invalid region `16:66420675-66432614`
[2016-04-15T07:33Z] 2016-04-15 00:33:39 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:33:39,810 - WARNING - Could not retrieve variants from source file in region 16:67691457-67691858. Error was invalid region `16:67691458-67691858`
[2016-04-15T07:33Z] 2016-04-15 00:33:41 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:33:41,181 - WARNING - Could not retrieve variants from source file in region 16:68713519-68729975. Error was invalid region `16:68713520-68729975`
[2016-04-15T07:33Z] 2016-04-15 00:33:41 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:33:41,493 - WARNING - Could not retrieve variants from source file in region 16:66861755-66862156. Error was invalid region `16:66861756-66862156`
[2016-04-15T07:33Z] 2016-04-15 00:33:42 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:33:42,426 - WARNING - Could not retrieve variants from source file in region 16:75327705-75328106. Error was invalid region `16:75327706-75328106`
[2016-04-15T07:33Z] 2016-04-15 00:33:44 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:33:44,578 - WARNING - Could not retrieve variants from source file in region 16:67691457-67691858. Error was invalid region `16:67691458-67691858`
[2016-04-15T07:33Z] 2016-04-15 00:33:44 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:33:44,910 - WARNING - Could not retrieve variants from source file in region 16:68269609-68270010. Error was invalid region `16:68269610-68270010`
[2016-04-15T07:33Z] 2016-04-15 00:33:45 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:33:45,286 - WARNING - Could not retrieve variants from source file in region 16:74808214-74808615. Error was invalid region `16:74808215-74808615`
[2016-04-15T07:33Z] 2016-04-15 00:33:45 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:33:45,964 - WARNING - Could not retrieve variants from source file in region 16:65021903-65022304. Error was invalid region `16:65021904-65022304`
[2016-04-15T07:33Z] 2016-04-15 00:33:46 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:33:46,042 - WARNING - Could not retrieve variants from source file in region 16:68713519-68729975. Error was invalid region `16:68713520-68729975`
[2016-04-15T07:33Z] 2016-04-15 00:33:46 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:33:46,533 - WARNING - Could not retrieve variants from source file in region 16:71950239-72049811. Error was invalid region `16:71950240-72049811`
[2016-04-15T07:33Z] 2016-04-15 00:33:47 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:33:47,347 - WARNING - Could not retrieve variants from source file in region 16:71772979-71773380. Error was invalid region `16:71772980-71773380`
[2016-04-15T07:33Z] 2016-04-15 00:33:47 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:33:47,456 - WARNING - Could not retrieve variants from source file in region 16:75327705-75328106. Error was invalid region `16:75327706-75328106`
[2016-04-15T07:33Z] 2016-04-15 00:33:47 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:33:47,767 - WARNING - Could not retrieve variants from source file in region 16:68269609-68270010. Error was invalid region `16:68269610-68270010`
[2016-04-15T07:33Z] 2016-04-15 00:33:50 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:33:50,337 - WARNING - Could not retrieve variants from source file in region 16:65021903-65022304. Error was invalid region `16:65021904-65022304`
[2016-04-15T07:33Z] 2016-04-15 00:33:52 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:33:52,586 - WARNING - Could not retrieve variants from source file in region 16:65021903-65022304. Error was invalid region `16:65021904-65022304`
[2016-04-15T07:33Z] 2016-04-15 00:33:56 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:33:56,788 - WARNING - Could not retrieve variants from source file in region 16:74537380-74537781. Error was invalid region `16:74537381-74537781`
[2016-04-15T07:33Z] 2016-04-15 00:33:58 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:33:58,018 - WARNING - Could not retrieve variants from source file in region 16:74451860-74452261. Error was invalid region `16:74451861-74452261`
[2016-04-15T07:33Z] 2016-04-15 00:33:58 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:33:58,116 - WARNING - Could not retrieve variants from source file in region 16:71710217-71712976. Error was invalid region `16:71710218-71712976`
[2016-04-15T07:34Z] 2016-04-15 00:34:00 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:34:00,014 - WARNING - Could not retrieve variants from source file in region 16:74485978-74486379. Error was invalid region `16:74485979-74486379`
[2016-04-15T07:34Z] 2016-04-15 00:34:00 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:34:00,076 - WARNING - Could not retrieve variants from source file in region 16:71483286-71509986. Error was invalid region `16:71483287-71509986`
[2016-04-15T07:34Z] 2016-04-15 00:34:00 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:34:00,551 - WARNING - Could not retrieve variants from source file in region 16:67327431-67327832. Error was invalid region `16:67327432-67327832`
[2016-04-15T07:34Z] 2016-04-15 00:34:00 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:34:00,559 - WARNING - Could not retrieve variants from source file in region 16:71710217-71712976. Error was invalid region `16:71710218-71712976`
[2016-04-15T07:34Z] 2016-04-15 00:34:00 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:34:00,611 - WARNING - Could not retrieve variants from source file in region 16:74537380-74537781. Error was invalid region `16:74537381-74537781`
[2016-04-15T07:34Z] 2016-04-15 00:34:04 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:34:04,288 - WARNING - Could not retrieve variants from source file in region 16:74537380-74537781. Error was invalid region `16:74537381-74537781`
[2016-04-15T07:34Z] 2016-04-15 00:34:04 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:34:04,313 - WARNING - Could not retrieve variants from source file in region 16:71483286-71509986. Error was invalid region `16:71483287-71509986`
[2016-04-15T07:34Z] 2016-04-15 00:34:04 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:34:04,709 - WARNING - Could not retrieve variants from source file in region 16:67327431-67327832. Error was invalid region `16:67327432-67327832`
[2016-04-15T07:34Z] 2016-04-15 00:34:05 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:34:05,764 - WARNING - Could not retrieve variants from source file in region 16:71483286-71509986. Error was invalid region `16:71483287-71509986`
[2016-04-15T07:34Z] 2016-04-15 00:34:08 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:34:08,201 - WARNING - Could not retrieve variants from source file in region 16:71411425-71411826. Error was invalid region `16:71411426-71411826`
[2016-04-15T07:34Z] 2016-04-15 00:34:08 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:34:08,712 - WARNING - Could not retrieve variants from source file in region 16:74421925-74425759. Error was invalid region `16:74421926-74425759`
[2016-04-15T07:34Z] 2016-04-15 00:34:11 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:34:11,499 - WARNING - Could not retrieve variants from source file in region 16:71411425-71411826. Error was invalid region `16:71411426-71411826`
[2016-04-15T07:34Z] ['bcbio-variation-recall', 'square', '-Xms750m', '-Xmx7280m', '-XX:+UseSerialGC', '-c', 16, '-r', u'16:80575259-90354753', '--caller', 'platypus', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/16/Batch1-16_80575258_90354753.vcf.gz', '/mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/16/Batch1-16_80575258_90354753.vcf-inputs.txt'] in region: 16:80575259-90354753
[2016-04-15T07:34Z] 2016-04-15 00:34:24 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:34:24,938 - WARNING - Could not retrieve variants from source file in region 16:89349827-89350368. Error was invalid region `16:89349828-89350368`
[2016-04-15T07:34Z] 2016-04-15 00:34:27 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:34:27,668 - WARNING - Could not retrieve variants from source file in region 16:87723627-87724028. Error was invalid region `16:87723628-87724028`
[2016-04-15T07:34Z] 2016-04-15 00:34:28 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:34:28,143 - WARNING - Could not retrieve variants from source file in region 16:81887941-81888342. Error was invalid region `16:81887942-81888342`
[2016-04-15T07:34Z] 2016-04-15 00:34:28 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:34:28,349 - WARNING - Could not retrieve variants from source file in region 16:83816808-83817209. Error was invalid region `16:83816809-83817209`
[2016-04-15T07:34Z] 2016-04-15 00:34:28 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:34:28,833 - WARNING - Could not retrieve variants from source file in region 16:88931063-88931464. Error was invalid region `16:88931064-88931464`
[2016-04-15T07:34Z] 2016-04-15 00:34:28 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:34:28,964 - WARNING - Could not retrieve variants from source file in region 16:82123586-82123987. Error was invalid region `16:82123587-82123987`
[2016-04-15T07:34Z] 2016-04-15 00:34:29 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:34:29,154 - WARNING - Could not retrieve variants from source file in region 16:88017598-88017999. Error was invalid region `16:88017599-88017999`
[2016-04-15T07:34Z] 2016-04-15 00:34:29 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:34:29,220 - WARNING - Could not retrieve variants from source file in region 16:90102624-90141545. Error was invalid region `16:90102625-90141545`
[2016-04-15T07:34Z] 2016-04-15 00:34:29 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:34:29,239 - WARNING - Could not retrieve variants from source file in region 16:85203667-85205445. Error was invalid region `16:85203668-85205445`
[2016-04-15T07:34Z] 2016-04-15 00:34:29 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:34:29,661 - WARNING - Could not retrieve variants from source file in region 16:89349827-89350368. Error was invalid region `16:89349828-89350368`
[2016-04-15T07:34Z] 2016-04-15 00:34:30 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:34:30,682 - WARNING - Could not retrieve variants from source file in region 16:88643794-88666451. Error was invalid region `16:88643795-88666451`
[2016-04-15T07:34Z] 2016-04-15 00:34:31 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:34:31,353 - WARNING - Could not retrieve variants from source file in region 16:87788653-87789054. Error was invalid region `16:87788654-87789054`
[2016-04-15T07:34Z] 2016-04-15 00:34:35 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:34:35,533 - WARNING - Could not retrieve variants from source file in region 16:87723627-87724028. Error was invalid region `16:87723628-87724028`
[2016-04-15T07:34Z] 2016-04-15 00:34:36 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:34:36,448 - WARNING - Could not retrieve variants from source file in region 16:84402064-84402465. Error was invalid region `16:84402065-84402465`
[2016-04-15T07:34Z] 2016-04-15 00:34:36 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:34:36,613 - WARNING - Could not retrieve variants from source file in region 16:83816808-83817209. Error was invalid region `16:83816809-83817209`
[2016-04-15T07:34Z] 2016-04-15 00:34:36 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:34:36,659 - WARNING - Could not retrieve variants from source file in region 16:89763052-89806537. Error was invalid region `16:89763053-89806537`
[2016-04-15T07:34Z] 2016-04-15 00:34:37 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:34:37,041 - WARNING - Could not retrieve variants from source file in region 16:82123586-82123987. Error was invalid region `16:82123587-82123987`
[2016-04-15T07:34Z] 2016-04-15 00:34:37 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:34:37,246 - WARNING - Could not retrieve variants from source file in region 16:89349827-89350368. Error was invalid region `16:89349828-89350368`
[2016-04-15T07:34Z] 2016-04-15 00:34:37 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:34:37,587 - WARNING - Could not retrieve variants from source file in region 16:88017598-88017999. Error was invalid region `16:88017599-88017999`
[2016-04-15T07:34Z] 2016-04-15 00:34:37 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:34:37,661 - WARNING - Could not retrieve variants from source file in region 16:88643794-88666451. Error was invalid region `16:88643795-88666451`
[2016-04-15T07:34Z] 2016-04-15 00:34:41 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:34:41,501 - WARNING - Could not retrieve variants from source file in region 16:87723627-87724028. Error was invalid region `16:87723628-87724028`
[2016-04-15T07:34Z] 2016-04-15 00:34:43 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:34:43,308 - WARNING - Could not retrieve variants from source file in region 16:84402064-84402465. Error was invalid region `16:84402065-84402465`
[2016-04-15T07:34Z] 2016-04-15 00:34:43 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:34:43,383 - WARNING - Could not retrieve variants from source file in region 16:83816808-83817209. Error was invalid region `16:83816809-83817209`
[2016-04-15T07:34Z] 2016-04-15 00:34:44 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:34:44,256 - WARNING - Could not retrieve variants from source file in region 16:88931063-88931464. Error was invalid region `16:88931064-88931464`
[2016-04-15T07:34Z] 2016-04-15 00:34:45 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:34:45,176 - WARNING - Could not retrieve variants from source file in region 16:90102624-90141545. Error was invalid region `16:90102625-90141545`
[2016-04-15T07:34Z] 2016-04-15 00:34:45 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:34:45,487 - WARNING - Could not retrieve variants from source file in region 16:82123586-82123987. Error was invalid region `16:82123587-82123987`
[2016-04-15T07:34Z] 2016-04-15 00:34:46 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:34:46,751 - WARNING - Could not retrieve variants from source file in region 16:88017598-88017999. Error was invalid region `16:88017599-88017999`
[2016-04-15T07:34Z] 2016-04-15 00:34:46 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:34:46,788 - WARNING - Could not retrieve variants from source file in region 16:85203667-85205445. Error was invalid region `16:85203668-85205445`
[2016-04-15T07:34Z] 2016-04-15 00:34:57 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:34:57,213 - WARNING - Could not retrieve variants from source file in region 16:81528742-81529143. Error was invalid region `16:81528743-81529143`
[2016-04-15T07:34Z] 2016-04-15 00:34:58 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:34:58,259 - WARNING - Could not retrieve variants from source file in region 16:81819557-81819958. Error was invalid region `16:81819558-81819958`
[2016-04-15T07:34Z] 2016-04-15 00:34:58 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:34:58,988 - WARNING - Could not retrieve variants from source file in region 16:83214269-83214670. Error was invalid region `16:83214270-83214670`
[2016-04-15T07:34Z] 2016-04-15 00:34:59 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:34:59,358 - WARNING - Could not retrieve variants from source file in region 16:84360322-84360723. Error was invalid region `16:84360323-84360723`
[2016-04-15T07:35Z] 2016-04-15 00:35:00 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:35:00,134 - WARNING - Could not retrieve variants from source file in region 16:89985880-89986307. Error was invalid region `16:89985881-89986307`
[2016-04-15T07:35Z] 2016-04-15 00:35:01 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:35:01,809 - WARNING - Could not retrieve variants from source file in region 16:82033599-82034000. Error was invalid region `16:82033600-82034000`
[2016-04-15T07:35Z] 2016-04-15 00:35:02 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:35:02,929 - WARNING - Could not retrieve variants from source file in region 16:81922570-81941509. Error was invalid region `16:81922571-81941509`
[2016-04-15T07:35Z] 2016-04-15 00:35:03 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:35:03,472 - WARNING - Could not retrieve variants from source file in region 16:81528742-81529143. Error was invalid region `16:81528743-81529143`
[2016-04-15T07:35Z] 2016-04-15 00:35:04 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:35:04,164 - WARNING - Could not retrieve variants from source file in region 16:88494736-88520260. Error was invalid region `16:88494737-88520260`
[2016-04-15T07:35Z] 2016-04-15 00:35:05 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:35:05,821 - WARNING - Could not retrieve variants from source file in region 16:83214269-83214670. Error was invalid region `16:83214270-83214670`
[2016-04-15T07:35Z] 2016-04-15 00:35:06 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:35:06,627 - WARNING - Could not retrieve variants from source file in region 16:88871934-88883631. Error was invalid region `16:88871935-88883631`
[2016-04-15T07:35Z] 2016-04-15 00:35:06 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:35:06,661 - WARNING - Could not retrieve variants from source file in region 16:81819557-81819958. Error was invalid region `16:81819558-81819958`
[2016-04-15T07:35Z] 2016-04-15 00:35:06 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:35:06,876 - WARNING - Could not retrieve variants from source file in region 16:87445152-87451497. Error was invalid region `16:87445153-87451497`
[2016-04-15T07:35Z] 2016-04-15 00:35:08 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:35:08,264 - WARNING - Could not retrieve variants from source file in region 16:81528742-81529143. Error was invalid region `16:81528743-81529143`
[2016-04-15T07:35Z] 2016-04-15 00:35:08 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:35:08,493 - WARNING - Could not retrieve variants from source file in region 16:88709617-88724537. Error was invalid region `16:88709618-88724537`
[2016-04-15T07:35Z] 2016-04-15 00:35:11 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:35:11,824 - WARNING - Could not retrieve variants from source file in region 16:83214269-83214670. Error was invalid region `16:83214270-83214670`
[2016-04-15T07:35Z] 2016-04-15 00:35:12 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:35:12,387 - WARNING - Could not retrieve variants from source file in region 16:84360322-84360723. Error was invalid region `16:84360323-84360723`
[2016-04-15T07:35Z] 2016-04-15 00:35:14 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:35:14,408 - WARNING - Could not retrieve variants from source file in region 16:81819557-81819958. Error was invalid region `16:81819558-81819958`
[2016-04-15T07:35Z] 2016-04-15 00:35:28 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:35:28,541 - WARNING - Could not retrieve variants from source file in region 16:82672836-82673237. Error was invalid region `16:82672837-82673237`
[2016-04-15T07:35Z] 2016-04-15 00:35:29 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:35:29,907 - WARNING - Could not retrieve variants from source file in region 16:88051950-88061340. Error was invalid region `16:88051951-88061340`
[2016-04-15T07:35Z] 2016-04-15 00:35:31 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:35:31,705 - WARNING - Could not retrieve variants from source file in region 16:89864892-89866233. Error was invalid region `16:89864893-89866233`
[2016-04-15T07:35Z] 2016-04-15 00:35:32 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:35:32,588 - WARNING - Could not retrieve variants from source file in region 16:81678940-81679341. Error was invalid region `16:81678941-81679341`
[2016-04-15T07:35Z] 2016-04-15 00:35:33 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:35:33,547 - WARNING - Could not retrieve variants from source file in region 16:89379725-89380126. Error was invalid region `16:89379726-89380126`
[2016-04-15T07:35Z] 2016-04-15 00:35:33 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:35:33,644 - WARNING - Could not retrieve variants from source file in region 16:81643876-81644277. Error was invalid region `16:81643877-81644277`
[2016-04-15T07:35Z] 2016-04-15 00:35:34 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:35:34,148 - WARNING - Could not retrieve variants from source file in region 16:82672836-82673237. Error was invalid region `16:82672837-82673237`
[2016-04-15T07:35Z] 2016-04-15 00:35:34 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:35:34,582 - WARNING - Could not retrieve variants from source file in region 16:89836112-89836513. Error was invalid region `16:89836113-89836513`
[2016-04-15T07:35Z] 2016-04-15 00:35:34 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:35:34,804 - WARNING - Could not retrieve variants from source file in region 16:87350504-87367915. Error was invalid region `16:87350505-87367915`
[2016-04-15T07:35Z] 2016-04-15 00:35:39 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:35:39,138 - WARNING - Could not retrieve variants from source file in region 16:89379725-89380126. Error was invalid region `16:89379726-89380126`
[2016-04-15T07:35Z] 2016-04-15 00:35:39 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:35:39,151 - WARNING - Could not retrieve variants from source file in region 16:85009759-85010160. Error was invalid region `16:85009760-85010160`
[2016-04-15T07:35Z] 2016-04-15 00:35:40 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:35:40,376 - WARNING - Could not retrieve variants from source file in region 16:82672836-82673237. Error was invalid region `16:82672837-82673237`
[2016-04-15T07:35Z] 2016-04-15 00:35:40 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:35:40,477 - WARNING - Could not retrieve variants from source file in region 16:84158037-84158438. Error was invalid region `16:84158038-84158438`
[2016-04-15T07:35Z] 2016-04-15 00:35:40 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:35:40,485 - WARNING - Could not retrieve variants from source file in region 16:89836112-89836513. Error was invalid region `16:89836113-89836513`
[2016-04-15T07:35Z] 2016-04-15 00:35:40 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:35:40,655 - WARNING - Could not retrieve variants from source file in region 16:82203531-82203958. Error was invalid region `16:82203532-82203958`
[2016-04-15T07:35Z] 2016-04-15 00:35:41 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:35:41,081 - WARNING - Could not retrieve variants from source file in region 16:89864892-89866233. Error was invalid region `16:89864893-89866233`
[2016-04-15T07:35Z] 2016-04-15 00:35:41 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:35:41,991 - WARNING - Could not retrieve variants from source file in region 16:81678940-81679341. Error was invalid region `16:81678941-81679341`
[2016-04-15T07:35Z] 2016-04-15 00:35:43 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:35:43,886 - WARNING - Could not retrieve variants from source file in region 16:85009759-85010160. Error was invalid region `16:85009760-85010160`
[2016-04-15T07:35Z] 2016-04-15 00:35:44 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:35:44,443 - WARNING - Could not retrieve variants from source file in region 16:89379725-89380126. Error was invalid region `16:89379726-89380126`
[2016-04-15T07:35Z] 2016-04-15 00:35:45 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:35:45,254 - WARNING - Could not retrieve variants from source file in region 16:81643876-81644277. Error was invalid region `16:81643877-81644277`
[2016-04-15T07:35Z] 2016-04-15 00:35:47 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:35:47,026 - WARNING - Could not retrieve variants from source file in region 16:89836112-89836513. Error was invalid region `16:89836113-89836513`
[2016-04-15T07:35Z] 2016-04-15 00:35:47 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:35:47,134 - WARNING - Could not retrieve variants from source file in region 16:84158037-84158438. Error was invalid region `16:84158038-84158438`
[2016-04-15T07:35Z] 2016-04-15 00:35:47 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:35:47,522 - WARNING - Could not retrieve variants from source file in region 16:82203531-82203958. Error was invalid region `16:82203532-82203958`
[2016-04-15T07:35Z] 2016-04-15 00:35:51 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:35:51,611 - WARNING - Could not retrieve variants from source file in region 16:85951812-85952213. Error was invalid region `16:85951813-85952213`
[2016-04-15T07:35Z] 2016-04-15 00:35:55 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:35:55,157 - WARNING - Could not retrieve variants from source file in region 16:81040281-81095553. Error was invalid region `16:81040282-81095553`
[2016-04-15T07:35Z] 2016-04-15 00:35:55 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:35:55,226 - WARNING - Could not retrieve variants from source file in region 16:89166883-89203263. Error was invalid region `16:89166884-89203263`
[2016-04-15T07:35Z] 2016-04-15 00:35:59 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:35:59,843 - WARNING - Could not retrieve variants from source file in region 16:80641865-80642266. Error was invalid region `16:80641866-80642266`
[2016-04-15T07:36Z] 2016-04-15 00:36:01 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:36:01,703 - WARNING - Could not retrieve variants from source file in region 16:85838442-85838843. Error was invalid region `16:85838443-85838843`
[2016-04-15T07:36Z] 2016-04-15 00:36:03 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:36:03,189 - WARNING - Could not retrieve variants from source file in region 16:84879253-84923049. Error was invalid region `16:84879254-84923049`
[2016-04-15T07:36Z] 2016-04-15 00:36:03 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:36:03,714 - WARNING - Could not retrieve variants from source file in region 16:80718668-80719069. Error was invalid region `16:80718669-80719069`
[2016-04-15T07:36Z] 2016-04-15 00:36:06 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:36:06,246 - WARNING - Could not retrieve variants from source file in region 16:85838442-85838843. Error was invalid region `16:85838443-85838843`
[2016-04-15T07:36Z] 2016-04-15 00:36:06 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:36:06,611 - WARNING - Could not retrieve variants from source file in region 16:84115182-84115673. Error was invalid region `16:84115183-84115673`
[2016-04-15T07:36Z] 2016-04-15 00:36:06 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:36:06,874 - WARNING - Could not retrieve variants from source file in region 16:80641865-80642266. Error was invalid region `16:80641866-80642266`
[2016-04-15T07:36Z] 2016-04-15 00:36:07 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:36:07,498 - WARNING - Could not retrieve variants from source file in region 16:80718668-80719069. Error was invalid region `16:80718669-80719069`
[2016-04-15T07:36Z] 2016-04-15 00:36:08 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:36:08,214 - WARNING - Could not retrieve variants from source file in region 16:86565615-86588845. Error was invalid region `16:86565616-86588845`
[2016-04-15T07:36Z] 2016-04-15 00:36:09 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:36:09,194 - WARNING - Could not retrieve variants from source file in region 16:85838442-85838843. Error was invalid region `16:85838443-85838843`
[2016-04-15T07:36Z] 2016-04-15 00:36:13 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:36:13,055 - WARNING - Could not retrieve variants from source file in region 16:83949343-83949744. Error was invalid region `16:83949344-83949744`
[2016-04-15T07:36Z] 2016-04-15 00:36:14 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:36:14,364 - WARNING - Could not retrieve variants from source file in region 16:85588740-85589141. Error was invalid region `16:85588741-85589141`
[2016-04-15T07:36Z] 2016-04-15 00:36:16 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:36:16,854 - WARNING - Could not retrieve variants from source file in region 16:83949343-83949744. Error was invalid region `16:83949344-83949744`
[2016-04-15T07:36Z] 2016-04-15 00:36:17 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:36:17,869 - WARNING - Could not retrieve variants from source file in region 16:85390868-85391301. Error was invalid region `16:85390869-85391301`
[2016-04-15T07:36Z] 2016-04-15 00:36:18 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:36:18,139 - WARNING - Could not retrieve variants from source file in region 16:85588740-85589141. Error was invalid region `16:85588741-85589141`
[2016-04-15T07:36Z] 2016-04-15 00:36:19 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:36:19,730 - WARNING - Could not retrieve variants from source file in region 16:84444138-84444539. Error was invalid region `16:84444139-84444539`
[2016-04-15T07:36Z] 2016-04-15 00:36:21 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:36:21,403 - WARNING - Could not retrieve variants from source file in region 16:85390868-85391301. Error was invalid region `16:85390869-85391301`
[2016-04-15T07:36Z] 2016-04-15 00:36:23 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:36:23,036 - WARNING - Could not retrieve variants from source file in region 16:84444138-84444539. Error was invalid region `16:84444139-84444539`
[2016-04-15T07:36Z] 2016-04-15 00:36:23 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:36:23,612 - WARNING - Could not retrieve variants from source file in region 16:84444138-84444539. Error was invalid region `16:84444139-84444539`
[2016-04-15T07:36Z] ['bcbio-variation-recall', 'square', '-Xms750m', '-Xmx7280m', '-XX:+UseSerialGC', '-c', 16, '-r', u'17:1-15511002', '--caller', 'platypus', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/17/Batch1-17_0_15511002.vcf.gz', '/mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/17/Batch1-17_0_15511002.vcf-inputs.txt'] in region: 17:1-15511002
[2016-04-15T07:36Z] 2016-04-15 00:36:40 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:36:40,281 - WARNING - Could not retrieve variants from source file in region 17:11582878-11583279. Error was invalid region `17:11582879-11583279`
[2016-04-15T07:36Z] 2016-04-15 00:36:40 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:36:40,293 - WARNING - Could not retrieve variants from source file in region 17:11511246-11550636. Error was invalid region `17:11511247-11550636`
[2016-04-15T07:36Z] 2016-04-15 00:36:40 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:36:40,808 - WARNING - Could not retrieve variants from source file in region 17:1173883-1183654. Error was invalid region `17:1173884-1183654`
[2016-04-15T07:36Z] 2016-04-15 00:36:40 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:36:40,957 - WARNING - Could not retrieve variants from source file in region 17:2929181-2930529. Error was invalid region `17:2929182-2930529`
[2016-04-15T07:36Z] 2016-04-15 00:36:41 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:36:41,125 - WARNING - Could not retrieve variants from source file in region 17:10296275-10318826. Error was invalid region `17:10296276-10318826`
[2016-04-15T07:36Z] 2016-04-15 00:36:41 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:36:41,341 - WARNING - Could not retrieve variants from source file in region 17:10535807-10544606. Error was invalid region `17:10535808-10544606`
[2016-04-15T07:36Z] 2016-04-15 00:36:41 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:36:41,621 - WARNING - Could not retrieve variants from source file in region 17:647975-655683. Error was invalid region `17:647976-655683`
[2016-04-15T07:36Z] 2016-04-15 00:36:41 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:36:41,714 - WARNING - Could not retrieve variants from source file in region 17:8791792-8792704. Error was invalid region `17:8791793-8792704`
[2016-04-15T07:36Z] 2016-04-15 00:36:41 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:36:41,834 - WARNING - Could not retrieve variants from source file in region 17:14248212-14248613. Error was invalid region `17:14248213-14248613`
[2016-04-15T07:36Z] 2016-04-15 00:36:48 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:36:48,290 - WARNING - Could not retrieve variants from source file in region 17:11582878-11583279. Error was invalid region `17:11582879-11583279`
[2016-04-15T07:36Z] 2016-04-15 00:36:49 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:36:49,383 - WARNING - Could not retrieve variants from source file in region 17:1173883-1183654. Error was invalid region `17:1173884-1183654`
[2016-04-15T07:36Z] 2016-04-15 00:36:50 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:36:50,135 - WARNING - Could not retrieve variants from source file in region 17:4390921-4391343. Error was invalid region `17:4390922-4391343`
[2016-04-15T07:36Z] 2016-04-15 00:36:50 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:36:50,139 - WARNING - Could not retrieve variants from source file in region 17:7606511-7630695. Error was invalid region `17:7606512-7630695`
[2016-04-15T07:36Z] 2016-04-15 00:36:50 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:36:50,687 - WARNING - Could not retrieve variants from source file in region 17:10535807-10544606. Error was invalid region `17:10535808-10544606`
[2016-04-15T07:36Z] 2016-04-15 00:36:50 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:36:50,731 - WARNING - Could not retrieve variants from source file in region 17:14248212-14248613. Error was invalid region `17:14248213-14248613`
[2016-04-15T07:36Z] 2016-04-15 00:36:50 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:36:50,883 - WARNING - Could not retrieve variants from source file in region 17:15492198-15511178. Error was invalid region `17:15492199-15511178`
[2016-04-15T07:36Z] 2016-04-15 00:36:50 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:36:50,908 - WARNING - Could not retrieve variants from source file in region 17:1990748-1991650. Error was invalid region `17:1990749-1991650`
[2016-04-15T07:36Z] 2016-04-15 00:36:50 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:36:50,988 - WARNING - Could not retrieve variants from source file in region 17:647975-655683. Error was invalid region `17:647976-655683`
[2016-04-15T07:36Z] 2016-04-15 00:36:53 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:36:53,483 - WARNING - Could not retrieve variants from source file in region 17:11582878-11583279. Error was invalid region `17:11582879-11583279`
[2016-04-15T07:36Z] 2016-04-15 00:36:56 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:36:56,049 - WARNING - Could not retrieve variants from source file in region 17:2929181-2930529. Error was invalid region `17:2929182-2930529`
[2016-04-15T07:36Z] 2016-04-15 00:36:56 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:36:56,068 - WARNING - Could not retrieve variants from source file in region 17:1173883-1183654. Error was invalid region `17:1173884-1183654`
[2016-04-15T07:36Z] 2016-04-15 00:36:57 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:36:57,461 - WARNING - Could not retrieve variants from source file in region 17:8791792-8792704. Error was invalid region `17:8791793-8792704`
[2016-04-15T07:36Z] 2016-04-15 00:36:58 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:36:58,331 - WARNING - Could not retrieve variants from source file in region 17:10535807-10544606. Error was invalid region `17:10535808-10544606`
[2016-04-15T07:36Z] 2016-04-15 00:36:58 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:36:58,358 - WARNING - Could not retrieve variants from source file in region 17:4390921-4391343. Error was invalid region `17:4390922-4391343`
[2016-04-15T07:36Z] 2016-04-15 00:36:58 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:36:58,665 - WARNING - Could not retrieve variants from source file in region 17:14248212-14248613. Error was invalid region `17:14248213-14248613`
[2016-04-15T07:36Z] 2016-04-15 00:36:58 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:36:58,671 - WARNING - Could not retrieve variants from source file in region 17:15492198-15511178. Error was invalid region `17:15492199-15511178`
[2016-04-15T07:36Z] 2016-04-15 00:36:58 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:36:58,728 - WARNING - Could not retrieve variants from source file in region 17:1990748-1991650. Error was invalid region `17:1990749-1991650`
[2016-04-15T07:36Z] 2016-04-15 00:36:58 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:36:58,795 - WARNING - Could not retrieve variants from source file in region 17:647975-655683. Error was invalid region `17:647976-655683`
[2016-04-15T07:37Z] 2016-04-15 00:37:09 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:37:09,692 - WARNING - Could not retrieve variants from source file in region 17:10614231-10633435. Error was invalid region `17:10614232-10633435`
[2016-04-15T07:37Z] 2016-04-15 00:37:10 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:37:10,504 - WARNING - Could not retrieve variants from source file in region 17:5485156-5485557. Error was invalid region `17:5485157-5485557`
[2016-04-15T07:37Z] 2016-04-15 00:37:12 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:37:12,130 - WARNING - Could not retrieve variants from source file in region 17:2868724-2883778. Error was invalid region `17:2868725-2883778`
[2016-04-15T07:37Z] 2016-04-15 00:37:12 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:37:12,216 - WARNING - Could not retrieve variants from source file in region 17:970202-970603. Error was invalid region `17:970203-970603`
[2016-04-15T07:37Z] 2016-04-15 00:37:13 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:37:13,146 - WARNING - Could not retrieve variants from source file in region 17:8700771-8725404. Error was invalid region `17:8700772-8725404`
[2016-04-15T07:37Z] 2016-04-15 00:37:15 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:37:15,146 - WARNING - Could not retrieve variants from source file in region 17:10448558-10451006. Error was invalid region `17:10448559-10451006`
[2016-04-15T07:37Z] 2016-04-15 00:37:15 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:37:15,637 - WARNING - Could not retrieve variants from source file in region 17:4337072-4352826. Error was invalid region `17:4337073-4352826`
[2016-04-15T07:37Z] 2016-04-15 00:37:15 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:37:15,665 - WARNING - Could not retrieve variants from source file in region 17:15340972-15341373. Error was invalid region `17:15340973-15341373`
[2016-04-15T07:37Z] 2016-04-15 00:37:15 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:37:15,711 - WARNING - Could not retrieve variants from source file in region 17:5485156-5485557. Error was invalid region `17:5485157-5485557`
[2016-04-15T07:37Z] 2016-04-15 00:37:16 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:37:16,248 - WARNING - Could not retrieve variants from source file in region 17:556274-556675. Error was invalid region `17:556275-556675`
[2016-04-15T07:37Z] 2016-04-15 00:37:16 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:37:16,642 - WARNING - Could not retrieve variants from source file in region 17:12656335-12656736. Error was invalid region `17:12656336-12656736`
[2016-04-15T07:37Z] 2016-04-15 00:37:17 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:37:17,413 - WARNING - Could not retrieve variants from source file in region 17:970202-970603. Error was invalid region `17:970203-970603`
[2016-04-15T07:37Z] 2016-04-15 00:37:17 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:37:17,890 - WARNING - Could not retrieve variants from source file in region 17:8700771-8725404. Error was invalid region `17:8700772-8725404`
[2016-04-15T07:37Z] 2016-04-15 00:37:18 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:37:18,833 - WARNING - Could not retrieve variants from source file in region 17:7557208-7579662. Error was invalid region `17:7557209-7579662`
[2016-04-15T07:37Z] 2016-04-15 00:37:20 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:37:20,561 - WARNING - Could not retrieve variants from source file in region 17:10448558-10451006. Error was invalid region `17:10448559-10451006`
[2016-04-15T07:37Z] 2016-04-15 00:37:21 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:37:21,138 - WARNING - Could not retrieve variants from source file in region 17:14138980-14140293. Error was invalid region `17:14138981-14140293`
[2016-04-15T07:37Z] 2016-04-15 00:37:21 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:37:21,769 - WARNING - Could not retrieve variants from source file in region 17:15340972-15341373. Error was invalid region `17:15340973-15341373`
[2016-04-15T07:37Z] 2016-04-15 00:37:21 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:37:21,769 - WARNING - Could not retrieve variants from source file in region 17:5485156-5485557. Error was invalid region `17:5485157-5485557`
[2016-04-15T07:37Z] 2016-04-15 00:37:22 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:37:22,792 - WARNING - Could not retrieve variants from source file in region 17:10614231-10633435. Error was invalid region `17:10614232-10633435`
[2016-04-15T07:37Z] 2016-04-15 00:37:22 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:37:22,924 - WARNING - Could not retrieve variants from source file in region 17:970202-970603. Error was invalid region `17:970203-970603`
[2016-04-15T07:37Z] 2016-04-15 00:37:22 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:37:22,949 - WARNING - Could not retrieve variants from source file in region 17:8700771-8725404. Error was invalid region `17:8700772-8725404`
[2016-04-15T07:37Z] 2016-04-15 00:37:25 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:37:25,199 - WARNING - Could not retrieve variants from source file in region 17:10448558-10451006. Error was invalid region `17:10448559-10451006`
[2016-04-15T07:37Z] 2016-04-15 00:37:28 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:37:28,776 - WARNING - Could not retrieve variants from source file in region 17:15340972-15341373. Error was invalid region `17:15340973-15341373`
[2016-04-15T07:37Z] 2016-04-15 00:37:28 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:37:28,980 - WARNING - Could not retrieve variants from source file in region 17:4337072-4352826. Error was invalid region `17:4337073-4352826`
[2016-04-15T07:37Z] 2016-04-15 00:37:36 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:37:36,158 - WARNING - Could not retrieve variants from source file in region 17:1359152-1387662. Error was invalid region `17:1359153-1387662`
[2016-04-15T07:37Z] 2016-04-15 00:37:38 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:37:38,910 - WARNING - Could not retrieve variants from source file in region 17:8658690-8659091. Error was invalid region `17:8658691-8659091`
[2016-04-15T07:37Z] 2016-04-15 00:37:40 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:37:40,451 - WARNING - Could not retrieve variants from source file in region 17:934687-935174. Error was invalid region `17:934688-935174`
[2016-04-15T07:37Z] 2016-04-15 00:37:40 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:37:40,486 - WARNING - Could not retrieve variants from source file in region 17:9846310-9846711. Error was invalid region `17:9846311-9846711`
[2016-04-15T07:37Z] 2016-04-15 00:37:40 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:37:40,786 - WARNING - Could not retrieve variants from source file in region 17:7530060-7530461. Error was invalid region `17:7530061-7530461`
[2016-04-15T07:37Z] 2016-04-15 00:37:41 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:37:41,236 - WARNING - Could not retrieve variants from source file in region 17:10403835-10416030. Error was invalid region `17:10403836-10416030`
[2016-04-15T07:37Z] 2016-04-15 00:37:41 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:37:41,672 - WARNING - Could not retrieve variants from source file in region 17:14085181-14095499. Error was invalid region `17:14085182-14095499`
[2016-04-15T07:37Z] 2016-04-15 00:37:45 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:37:45,215 - WARNING - Could not retrieve variants from source file in region 17:526696-527097. Error was invalid region `17:526697-527097`
[2016-04-15T07:37Z] 2016-04-15 00:37:46 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:37:46,963 - WARNING - Could not retrieve variants from source file in region 17:4088080-4090386. Error was invalid region `17:4088081-4090386`
[2016-04-15T07:37Z] 2016-04-15 00:37:48 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:37:48,375 - WARNING - Could not retrieve variants from source file in region 17:7530060-7530461. Error was invalid region `17:7530061-7530461`
[2016-04-15T07:37Z] 2016-04-15 00:37:48 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:37:48,502 - WARNING - Could not retrieve variants from source file in region 17:11833076-11835521. Error was invalid region `17:11833077-11835521`
[2016-04-15T07:37Z] 2016-04-15 00:37:48 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:37:48,754 - WARNING - Could not retrieve variants from source file in region 17:1359152-1387662. Error was invalid region `17:1359153-1387662`
[2016-04-15T07:37Z] 2016-04-15 00:37:49 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:37:49,251 - WARNING - Could not retrieve variants from source file in region 17:9846310-9846711. Error was invalid region `17:9846311-9846711`
[2016-04-15T07:37Z] 2016-04-15 00:37:49 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:37:49,783 - WARNING - Could not retrieve variants from source file in region 17:526696-527097. Error was invalid region `17:526697-527097`
[2016-04-15T07:37Z] 2016-04-15 00:37:49 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:37:49,804 - WARNING - Could not retrieve variants from source file in region 17:8658690-8659091. Error was invalid region `17:8658691-8659091`
[2016-04-15T07:37Z] 2016-04-15 00:37:54 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:37:54,088 - WARNING - Could not retrieve variants from source file in region 17:934687-935174. Error was invalid region `17:934688-935174`
[2016-04-15T07:37Z] 2016-04-15 00:37:55 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:37:55,920 - WARNING - Could not retrieve variants from source file in region 17:7530060-7530461. Error was invalid region `17:7530061-7530461`
[2016-04-15T07:37Z] 2016-04-15 00:37:56 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:37:56,139 - WARNING - Could not retrieve variants from source file in region 17:11833076-11835521. Error was invalid region `17:11833077-11835521`
[2016-04-15T07:37Z] 2016-04-15 00:37:56 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:37:56,489 - WARNING - Could not retrieve variants from source file in region 17:10403835-10416030. Error was invalid region `17:10403836-10416030`
[2016-04-15T07:37Z] 2016-04-15 00:37:57 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:37:57,000 - WARNING - Could not retrieve variants from source file in region 17:526696-527097. Error was invalid region `17:526697-527097`
[2016-04-15T07:38Z] 2016-04-15 00:38:05 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:38:05,593 - WARNING - Could not retrieve variants from source file in region 17:900228-900629. Error was invalid region `17:900229-900629`
[2016-04-15T07:38Z] 2016-04-15 00:38:08 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:38:08,301 - WARNING - Could not retrieve variants from source file in region 17:8416690-8424460. Error was invalid region `17:8416691-8424460`
[2016-04-15T07:38Z] 2016-04-15 00:38:10 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:38:10,615 - WARNING - Could not retrieve variants from source file in region 17:900228-900629. Error was invalid region `17:900229-900629`
[2016-04-15T07:38Z] 2016-04-15 00:38:11 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:38:11,598 - WARNING - Could not retrieve variants from source file in region 17:11786080-11787141. Error was invalid region `17:11786081-11787141`
[2016-04-15T07:38Z] 2016-04-15 00:38:12 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:38:12,106 - WARNING - Could not retrieve variants from source file in region 17:9792557-9793062. Error was invalid region `17:9792558-9793062`
[2016-04-15T07:38Z] 2016-04-15 00:38:13 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:38:13,351 - WARNING - Could not retrieve variants from source file in region 17:2323452-2323853. Error was invalid region `17:2323453-2323853`
[2016-04-15T07:38Z] 2016-04-15 00:38:13 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:38:13,792 - WARNING - Could not retrieve variants from source file in region 17:13972744-14005629. Error was invalid region `17:13972745-14005629`
[2016-04-15T07:38Z] 2016-04-15 00:38:14 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:38:14,269 - WARNING - Could not retrieve variants from source file in region 17:465564-465965. Error was invalid region `17:465565-465965`
[2016-04-15T07:38Z] 2016-04-15 00:38:14 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:38:14,519 - WARNING - Could not retrieve variants from source file in region 17:4792841-4802507. Error was invalid region `17:4792842-4802507`
[2016-04-15T07:38Z] 2016-04-15 00:38:14 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:38:14,879 - WARNING - Could not retrieve variants from source file in region 17:4045890-4046291. Error was invalid region `17:4045891-4046291`
[2016-04-15T07:38Z] 2016-04-15 00:38:18 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:38:18,211 - WARNING - Could not retrieve variants from source file in region 17:2323452-2323853. Error was invalid region `17:2323453-2323853`
[2016-04-15T07:38Z] 2016-04-15 00:38:19 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:38:19,438 - WARNING - Could not retrieve variants from source file in region 17:9585954-9586355. Error was invalid region `17:9585955-9586355`
[2016-04-15T07:38Z] 2016-04-15 00:38:19 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:38:19,541 - WARNING - Could not retrieve variants from source file in region 17:8416690-8424460. Error was invalid region `17:8416691-8424460`
[2016-04-15T07:38Z] 2016-04-15 00:38:20 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:38:20,850 - WARNING - Could not retrieve variants from source file in region 17:4045890-4046291. Error was invalid region `17:4045891-4046291`
[2016-04-15T07:38Z] 2016-04-15 00:38:24 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:38:24,661 - WARNING - Could not retrieve variants from source file in region 17:1731057-1733589. Error was invalid region `17:1731058-1733589`
[2016-04-15T07:38Z] 2016-04-15 00:38:24 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:38:24,879 - WARNING - Could not retrieve variants from source file in region 17:292708-293109. Error was invalid region `17:292709-293109`
[2016-04-15T07:38Z] 2016-04-15 00:38:25 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:38:25,435 - WARNING - Could not retrieve variants from source file in region 17:9585954-9586355. Error was invalid region `17:9585955-9586355`
[2016-04-15T07:38Z] 2016-04-15 00:38:26 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:38:26,750 - WARNING - Could not retrieve variants from source file in region 17:4575072-4578140. Error was invalid region `17:4575073-4578140`
[2016-04-15T07:38Z] 2016-04-15 00:38:26 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:38:26,888 - WARNING - Could not retrieve variants from source file in region 17:4045890-4046291. Error was invalid region `17:4045891-4046291`
[2016-04-15T07:38Z] 2016-04-15 00:38:27 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:38:27,242 - WARNING - Could not retrieve variants from source file in region 17:4792841-4802507. Error was invalid region `17:4792842-4802507`
[2016-04-15T07:38Z] 2016-04-15 00:38:30 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:38:30,212 - WARNING - Could not retrieve variants from source file in region 17:1731057-1733589. Error was invalid region `17:1731058-1733589`
[2016-04-15T07:38Z] 2016-04-15 00:38:32 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:38:32,231 - WARNING - Could not retrieve variants from source file in region 17:2266588-2268501. Error was invalid region `17:2266589-2268501`
[2016-04-15T07:38Z] 2016-04-15 00:38:33 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:38:33,589 - WARNING - Could not retrieve variants from source file in region 17:5280229-5295166. Error was invalid region `17:5280230-5295166`
[2016-04-15T07:38Z] 2016-04-15 00:38:34 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:38:34,470 - WARNING - Could not retrieve variants from source file in region 17:8274812-8296630. Error was invalid region `17:8274813-8296630`
[2016-04-15T07:38Z] 2016-04-15 00:38:35 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:38:35,860 - WARNING - Could not retrieve variants from source file in region 17:1731057-1733589. Error was invalid region `17:1731058-1733589`
[2016-04-15T07:38Z] 2016-04-15 00:38:37 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:38:37,371 - WARNING - Could not retrieve variants from source file in region 17:2266588-2268501. Error was invalid region `17:2266589-2268501`
[2016-04-15T07:38Z] 2016-04-15 00:38:37 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:38:37,767 - WARNING - Could not retrieve variants from source file in region 17:11757345-11757746. Error was invalid region `17:11757346-11757746`
[2016-04-15T07:38Z] 2016-04-15 00:38:38 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:38:38,970 - WARNING - Could not retrieve variants from source file in region 17:9471500-9471901. Error was invalid region `17:9471501-9471901`
[2016-04-15T07:38Z] 2016-04-15 00:38:40 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:38:40,304 - WARNING - Could not retrieve variants from source file in region 17:11725126-11725527. Error was invalid region `17:11725127-11725527`
[2016-04-15T07:38Z] 2016-04-15 00:38:41 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:38:41,030 - WARNING - Could not retrieve variants from source file in region 17:8274812-8296630. Error was invalid region `17:8274813-8296630`
[2016-04-15T07:38Z] 2016-04-15 00:38:41 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:38:41,325 - WARNING - Could not retrieve variants from source file in region 17:9515566-9515967. Error was invalid region `17:9515567-9515967`
[2016-04-15T07:38Z] 2016-04-15 00:38:45 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:38:45,067 - WARNING - Could not retrieve variants from source file in region 17:4008829-4016187. Error was invalid region `17:4008830-4016187`
[2016-04-15T07:38Z] 2016-04-15 00:38:45 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:38:45,716 - WARNING - Could not retrieve variants from source file in region 17:9471500-9471901. Error was invalid region `17:9471501-9471901`
[2016-04-15T07:38Z] 2016-04-15 00:38:47 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:38:47,006 - WARNING - Could not retrieve variants from source file in region 17:5280229-5295166. Error was invalid region `17:5280230-5295166`
[2016-04-15T07:38Z] 2016-04-15 00:38:47 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:38:47,340 - WARNING - Could not retrieve variants from source file in region 17:8274812-8296630. Error was invalid region `17:8274813-8296630`
[2016-04-15T07:38Z] 2016-04-15 00:38:47 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:38:47,374 - WARNING - Could not retrieve variants from source file in region 17:181263-183180. Error was invalid region `17:181264-183180`
[2016-04-15T07:38Z] 2016-04-15 00:38:47 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:38:47,584 - WARNING - Could not retrieve variants from source file in region 17:260088-260489. Error was invalid region `17:260089-260489`
[2016-04-15T07:38Z] 2016-04-15 00:38:47 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:38:47,948 - WARNING - Could not retrieve variants from source file in region 17:9515566-9515967. Error was invalid region `17:9515567-9515967`
[2016-04-15T07:38Z] 2016-04-15 00:38:48 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:38:48,399 - WARNING - Could not retrieve variants from source file in region 17:260088-260489. Error was invalid region `17:260089-260489`
[2016-04-15T07:38Z] 2016-04-15 00:38:48 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:38:48,799 - WARNING - Could not retrieve variants from source file in region 17:4536030-4536431. Error was invalid region `17:4536031-4536431`
[2016-04-15T07:38Z] 2016-04-15 00:38:49 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:38:49,225 - WARNING - Could not retrieve variants from source file in region 17:1578728-1585320. Error was invalid region `17:1578729-1585320`
[2016-04-15T07:38Z] 2016-04-15 00:38:51 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:38:51,470 - WARNING - Could not retrieve variants from source file in region 17:9471500-9471901. Error was invalid region `17:9471501-9471901`
[2016-04-15T07:38Z] 2016-04-15 00:38:53 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:38:53,475 - WARNING - Could not retrieve variants from source file in region 17:181263-183180. Error was invalid region `17:181264-183180`
[2016-04-15T07:38Z] 2016-04-15 00:38:54 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:38:54,346 - WARNING - Could not retrieve variants from source file in region 17:9515566-9515967. Error was invalid region `17:9515567-9515967`
[2016-04-15T07:39Z] 2016-04-15 00:39:03 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:39:03,519 - WARNING - Could not retrieve variants from source file in region 17:11648121-11651247. Error was invalid region `17:11648122-11651247`
[2016-04-15T07:39Z] 2016-04-15 00:39:05 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:39:05,246 - WARNING - Could not retrieve variants from source file in region 17:5904-6347. Error was invalid region `17:5905-6347`
[2016-04-15T07:39Z] 2016-04-15 00:39:05 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:39:05,936 - WARNING - Could not retrieve variants from source file in region 17:9395020-9395421. Error was invalid region `17:9395021-9395421`
[2016-04-15T07:39Z] 2016-04-15 00:39:07 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:39:07,788 - WARNING - Could not retrieve variants from source file in region 17:8092483-8192483. Error was invalid region `17:8092484-8192483`
[2016-04-15T07:39Z] 2016-04-15 00:39:07 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:39:07,817 - WARNING - Could not retrieve variants from source file in region 17:8192483-8248523. Error was invalid region `17:8192484-8248523`
[2016-04-15T07:39Z] 2016-04-15 00:39:08 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:39:08,127 - WARNING - Could not retrieve variants from source file in region 17:11648121-11651247. Error was invalid region `17:11648122-11651247`
[2016-04-15T07:39Z] 2016-04-15 00:39:09 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:39:09,172 - WARNING - Could not retrieve variants from source file in region 17:1538335-1542380. Error was invalid region `17:1538336-1542380`
[2016-04-15T07:39Z] 2016-04-15 00:39:09 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:39:09,457 - WARNING - Could not retrieve variants from source file in region 17:5904-6347. Error was invalid region `17:5905-6347`
[2016-04-15T07:39Z] 2016-04-15 00:39:10 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:39:10,473 - WARNING - Could not retrieve variants from source file in region 17:9395020-9395421. Error was invalid region `17:9395021-9395421`
[2016-04-15T07:39Z] 2016-04-15 00:39:10 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:39:10,579 - WARNING - Could not retrieve variants from source file in region 17:3916612-3981480. Error was invalid region `17:3916613-3981480`
[2016-04-15T07:39Z] 2016-04-15 00:39:11 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:39:11,637 - WARNING - Could not retrieve variants from source file in region 17:5116343-5126879. Error was invalid region `17:5116344-5126879`
[2016-04-15T07:39Z] 2016-04-15 00:39:12 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:39:12,127 - WARNING - Could not retrieve variants from source file in region 17:8092483-8192483. Error was invalid region `17:8092484-8192483`
[2016-04-15T07:39Z] 2016-04-15 00:39:12 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:39:12,159 - WARNING - Could not retrieve variants from source file in region 17:8192483-8248523. Error was invalid region `17:8192484-8248523`
[2016-04-15T07:39Z] 2016-04-15 00:39:12 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:39:12,306 - WARNING - Could not retrieve variants from source file in region 17:11648121-11651247. Error was invalid region `17:11648122-11651247`
[2016-04-15T07:39Z] 2016-04-15 00:39:13 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:39:13,708 - WARNING - Could not retrieve variants from source file in region 17:1538335-1542380. Error was invalid region `17:1538336-1542380`
[2016-04-15T07:39Z] 2016-04-15 00:39:13 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:39:13,712 - WARNING - Could not retrieve variants from source file in region 17:5904-6347. Error was invalid region `17:5905-6347`
[2016-04-15T07:39Z] 2016-04-15 00:39:13 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:39:13,942 - WARNING - Could not retrieve variants from source file in region 17:4495529-4498801. Error was invalid region `17:4495530-4498801`
[2016-04-15T07:39Z] 2016-04-15 00:39:15 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:39:15,012 - WARNING - Could not retrieve variants from source file in region 17:9395020-9395421. Error was invalid region `17:9395021-9395421`
[2016-04-15T07:39Z] 2016-04-15 00:39:21 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:39:21,658 - WARNING - Could not retrieve variants from source file in region 17:2091554-2091955. Error was invalid region `17:2091555-2091955`
[2016-04-15T07:39Z] 2016-04-15 00:39:23 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:39:23,539 - WARNING - Could not retrieve variants from source file in region 17:2091554-2091955. Error was invalid region `17:2091555-2091955`
[2016-04-15T07:39Z] 2016-04-15 00:39:24 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:39:24,347 - WARNING - Could not retrieve variants from source file in region 17:8021854-8066297. Error was invalid region `17:8021855-8066297`
[2016-04-15T07:39Z] 2016-04-15 00:39:24 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:39:24,522 - WARNING - Could not retrieve variants from source file in region 17:5042683-5087230. Error was invalid region `17:5042684-5087230`
[2016-04-15T07:39Z] 2016-04-15 00:39:26 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:39:26,000 - WARNING - Could not retrieve variants from source file in region 17:7011866-7018148. Error was invalid region `17:7011867-7018148`
[2016-04-15T07:39Z] 2016-04-15 00:39:27 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:39:27,031 - WARNING - Could not retrieve variants from source file in region 17:6364542-6407073. Error was invalid region `17:6364543-6407073`
[2016-04-15T07:39Z] 2016-04-15 00:39:27 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:39:27,152 - WARNING - Could not retrieve variants from source file in region 17:6716031-6716432. Error was invalid region `17:6716032-6716432`
[2016-04-15T07:39Z] 2016-04-15 00:39:27 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:39:27,749 - WARNING - Could not retrieve variants from source file in region 17:6441165-6441566. Error was invalid region `17:6441166-6441566`
[2016-04-15T07:39Z] 2016-04-15 00:39:28 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:39:28,480 - WARNING - Could not retrieve variants from source file in region 17:7984268-7984669. Error was invalid region `17:7984269-7984669`
[2016-04-15T07:39Z] 2016-04-15 00:39:30 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:39:30,011 - WARNING - Could not retrieve variants from source file in region 17:6978968-6981587. Error was invalid region `17:6978969-6981587`
[2016-04-15T07:39Z] 2016-04-15 00:39:30 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:39:30,927 - WARNING - Could not retrieve variants from source file in region 17:7011866-7018148. Error was invalid region `17:7011867-7018148`
[2016-04-15T07:39Z] 2016-04-15 00:39:32 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:39:32,354 - WARNING - Could not retrieve variants from source file in region 17:6716031-6716432. Error was invalid region `17:6716032-6716432`
[2016-04-15T07:39Z] 2016-04-15 00:39:33 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:39:33,365 - WARNING - Could not retrieve variants from source file in region 17:6441165-6441566. Error was invalid region `17:6441166-6441566`
[2016-04-15T07:39Z] 2016-04-15 00:39:33 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:39:33,940 - WARNING - Could not retrieve variants from source file in region 17:7984268-7984669. Error was invalid region `17:7984269-7984669`
[2016-04-15T07:39Z] 2016-04-15 00:39:35 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:39:35,166 - WARNING - Could not retrieve variants from source file in region 17:5042683-5087230. Error was invalid region `17:5042684-5087230`
[2016-04-15T07:39Z] 2016-04-15 00:39:35 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:39:35,264 - WARNING - Could not retrieve variants from source file in region 17:6978968-6981587. Error was invalid region `17:6978969-6981587`
[2016-04-15T07:39Z] 2016-04-15 00:39:38 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:39:38,858 - WARNING - Could not retrieve variants from source file in region 17:6328718-6337437. Error was invalid region `17:6328719-6337437`
[2016-04-15T07:39Z] 2016-04-15 00:39:39 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:39:39,178 - WARNING - Could not retrieve variants from source file in region 17:7984268-7984669. Error was invalid region `17:7984269-7984669`
[2016-04-15T07:39Z] 2016-04-15 00:39:40 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:39:40,504 - WARNING - Could not retrieve variants from source file in region 17:7788153-7788554. Error was invalid region `17:7788154-7788554`
[2016-04-15T07:39Z] 2016-04-15 00:39:42 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:39:42,845 - WARNING - Could not retrieve variants from source file in region 17:6328718-6337437. Error was invalid region `17:6328719-6337437`
[2016-04-15T07:39Z] 2016-04-15 00:39:42 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:39:42,934 - WARNING - Could not retrieve variants from source file in region 17:3768468-3789198. Error was invalid region `17:3768469-3789198`
[2016-04-15T07:39Z] 2016-04-15 00:39:48 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:39:48,382 - WARNING - Could not retrieve variants from source file in region 17:7942690-7952009. Error was invalid region `17:7942691-7952009`
[2016-04-15T07:39Z] 2016-04-15 00:39:51 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:39:51,659 - WARNING - Could not retrieve variants from source file in region 17:7832555-7849277. Error was invalid region `17:7832556-7849277`
[2016-04-15T07:39Z] 2016-04-15 00:39:52 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:39:52,605 - WARNING - Could not retrieve variants from source file in region 17:7832555-7849277. Error was invalid region `17:7832556-7849277`
[2016-04-15T07:39Z] 2016-04-15 00:39:56 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:39:56,075 - WARNING - Could not retrieve variants from source file in region 17:3559612-3594467. Error was invalid region `17:3559613-3594467`
[2016-04-15T07:39Z] 2016-04-15 00:39:56 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:39:56,593 - WARNING - Could not retrieve variants from source file in region 17:3100616-3119957. Error was invalid region `17:3100617-3119957`
[2016-04-15T07:40Z] 2016-04-15 00:40:02 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:40:02,483 - WARNING - Could not retrieve variants from source file in region 17:3627262-3657365. Error was invalid region `17:3627263-3657365`
[2016-04-15T07:40Z] 2016-04-15 00:40:03 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:40:03,982 - WARNING - Could not retrieve variants from source file in region 17:2965821-2966498. Error was invalid region `17:2965822-2966498`
[2016-04-15T07:40Z] 2016-04-15 00:40:04 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:40:04,102 - WARNING - Could not retrieve variants from source file in region 17:7722154-7722555. Error was invalid region `17:7722155-7722555`
[2016-04-15T07:40Z] 2016-04-15 00:40:04 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:40:04,847 - WARNING - Could not retrieve variants from source file in region 17:3559612-3594467. Error was invalid region `17:3559613-3594467`
[2016-04-15T07:40Z] 2016-04-15 00:40:07 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:40:07,326 - WARNING - Could not retrieve variants from source file in region 17:3195292-3195693. Error was invalid region `17:3195293-3195693`
[2016-04-15T07:40Z] 2016-04-15 00:40:07 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:40:07,646 - WARNING - Could not retrieve variants from source file in region 17:3492989-3514218. Error was invalid region `17:3492990-3514218`
[2016-04-15T07:40Z] 2016-04-15 00:40:08 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:40:08,318 - WARNING - Could not retrieve variants from source file in region 17:7722154-7722555. Error was invalid region `17:7722155-7722555`
[2016-04-15T07:40Z] 2016-04-15 00:40:11 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:40:11,232 - WARNING - Could not retrieve variants from source file in region 17:7673717-7682795. Error was invalid region `17:7673718-7682795`
[2016-04-15T07:40Z] 2016-04-15 00:40:11 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:40:11,284 - WARNING - Could not retrieve variants from source file in region 17:3195292-3195693. Error was invalid region `17:3195293-3195693`
[2016-04-15T07:40Z] 2016-04-15 00:40:11 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:40:11,322 - WARNING - Could not retrieve variants from source file in region 17:3195292-3195693. Error was invalid region `17:3195293-3195693`
[2016-04-15T07:40Z] 2016-04-15 00:40:11 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:40:11,610 - WARNING - Could not retrieve variants from source file in region 17:3492989-3514218. Error was invalid region `17:3492990-3514218`
[2016-04-15T07:40Z] 2016-04-15 00:40:12 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:40:12,353 - WARNING - Could not retrieve variants from source file in region 17:3492989-3514218. Error was invalid region `17:3492990-3514218`
[2016-04-15T07:40Z] ['bcbio-variation-recall', 'square', '-Xms750m', '-Xmx7280m', '-XX:+UseSerialGC', '-c', 16, '-r', u'17:15515956-31039213', '--caller', 'platypus', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/17/Batch1-17_15515955_31039213.vcf.gz', '/mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/17/Batch1-17_15515955_31039213.vcf-inputs.txt'] in region: 17:15515956-31039213
[2016-04-15T07:40Z] 2016-04-15 00:40:28 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:40:28,596 - WARNING - Could not retrieve variants from source file in region 17:19437128-19437529. Error was invalid region `17:19437129-19437529`
[2016-04-15T07:40Z] 2016-04-15 00:40:30 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:40:30,299 - WARNING - Could not retrieve variants from source file in region 17:28407665-28408066. Error was invalid region `17:28407666-28408066`
[2016-04-15T07:40Z] 2016-04-15 00:40:31 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:40:31,023 - WARNING - Could not retrieve variants from source file in region 17:30678316-30678717. Error was invalid region `17:30678317-30678717`
[2016-04-15T07:40Z] 2016-04-15 00:40:31 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:40:31,118 - WARNING - Could not retrieve variants from source file in region 17:28268606-28269007. Error was invalid region `17:28268607-28269007`
[2016-04-15T07:40Z] 2016-04-15 00:40:31 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:40:31,234 - WARNING - Could not retrieve variants from source file in region 17:19281617-19282018. Error was invalid region `17:19281618-19282018`
[2016-04-15T07:40Z] 2016-04-15 00:40:31 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:40:31,480 - WARNING - Could not retrieve variants from source file in region 17:27834927-27835328. Error was invalid region `17:27834928-27835328`
[2016-04-15T07:40Z] 2016-04-15 00:40:32 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:40:32,063 - WARNING - Could not retrieve variants from source file in region 17:20354625-20370972. Error was invalid region `17:20354626-20370972`
[2016-04-15T07:40Z] 2016-04-15 00:40:32 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:40:32,326 - WARNING - Could not retrieve variants from source file in region 17:17473642-17474394. Error was invalid region `17:17473643-17474394`
[2016-04-15T07:40Z] 2016-04-15 00:40:32 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:40:32,356 - WARNING - Could not retrieve variants from source file in region 17:16828948-16856068. Error was invalid region `17:16828949-16856068`
[2016-04-15T07:40Z] 2016-04-15 00:40:34 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:40:34,542 - WARNING - Could not retrieve variants from source file in region 17:19216327-19247265. Error was invalid region `17:19216328-19247265`
[2016-04-15T07:40Z] 2016-04-15 00:40:36 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:40:36,050 - WARNING - Could not retrieve variants from source file in region 17:29111157-29111558. Error was invalid region `17:29111158-29111558`
[2016-04-15T07:40Z] 2016-04-15 00:40:36 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:40:36,156 - WARNING - Could not retrieve variants from source file in region 17:28407665-28408066. Error was invalid region `17:28407666-28408066`
[2016-04-15T07:40Z] 2016-04-15 00:40:38 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:40:38,691 - WARNING - Could not retrieve variants from source file in region 17:27834927-27835328. Error was invalid region `17:27834928-27835328`
[2016-04-15T07:40Z] 2016-04-15 00:40:38 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:40:38,820 - WARNING - Could not retrieve variants from source file in region 17:19281617-19282018. Error was invalid region `17:19281618-19282018`
[2016-04-15T07:40Z] 2016-04-15 00:40:39 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:40:39,428 - WARNING - Could not retrieve variants from source file in region 17:17473642-17474394. Error was invalid region `17:17473643-17474394`
[2016-04-15T07:40Z] 2016-04-15 00:40:39 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:40:39,492 - WARNING - Could not retrieve variants from source file in region 17:19437128-19437529. Error was invalid region `17:19437129-19437529`
[2016-04-15T07:40Z] 2016-04-15 00:40:39 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:40:39,568 - WARNING - Could not retrieve variants from source file in region 17:18625106-18653335. Error was invalid region `17:18625107-18653335`
[2016-04-15T07:40Z] 2016-04-15 00:40:40 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:40:40,724 - WARNING - Could not retrieve variants from source file in region 17:29111157-29111558. Error was invalid region `17:29111158-29111558`
[2016-04-15T07:40Z] 2016-04-15 00:40:41 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:40:40,999 - WARNING - Could not retrieve variants from source file in region 17:28407665-28408066. Error was invalid region `17:28407666-28408066`
[2016-04-15T07:40Z] 2016-04-15 00:40:43 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:40:43,931 - WARNING - Could not retrieve variants from source file in region 17:28268606-28269007. Error was invalid region `17:28268607-28269007`
[2016-04-15T07:40Z] 2016-04-15 00:40:45 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:40:45,178 - WARNING - Could not retrieve variants from source file in region 17:27834927-27835328. Error was invalid region `17:27834928-27835328`
[2016-04-15T07:40Z] 2016-04-15 00:40:45 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:40:45,986 - WARNING - Could not retrieve variants from source file in region 17:19281617-19282018. Error was invalid region `17:19281618-19282018`
[2016-04-15T07:40Z] 2016-04-15 00:40:46 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:40:46,651 - WARNING - Could not retrieve variants from source file in region 17:18855275-18880458. Error was invalid region `17:18855276-18880458`
[2016-04-15T07:40Z] 2016-04-15 00:40:46 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:40:46,734 - WARNING - Could not retrieve variants from source file in region 17:17473642-17474394. Error was invalid region `17:17473643-17474394`
[2016-04-15T07:40Z] 2016-04-15 00:40:58 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:40:58,175 - WARNING - Could not retrieve variants from source file in region 17:17996998-17997399. Error was invalid region `17:17996999-17997399`
[2016-04-15T07:41Z] 2016-04-15 00:41:00 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:41:00,431 - WARNING - Could not retrieve variants from source file in region 17:27613466-27613867. Error was invalid region `17:27613467-27613867`
[2016-04-15T07:41Z] 2016-04-15 00:41:01 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:41:01,839 - WARNING - Could not retrieve variants from source file in region 17:16068129-16068533. Error was invalid region `17:16068130-16068533`
[2016-04-15T07:41Z] 2016-04-15 00:41:03 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:41:03,848 - WARNING - Could not retrieve variants from source file in region 17:26105721-26106122. Error was invalid region `17:26105722-26106122`
[2016-04-15T07:41Z] 2016-04-15 00:41:05 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:41:05,923 - WARNING - Could not retrieve variants from source file in region 17:17996998-17997399. Error was invalid region `17:17996999-17997399`
[2016-04-15T07:41Z] 2016-04-15 00:41:06 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:41:06,145 - WARNING - Could not retrieve variants from source file in region 17:17394400-17425821. Error was invalid region `17:17394401-17425821`
[2016-04-15T07:41Z] 2016-04-15 00:41:06 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:41:06,181 - WARNING - Could not retrieve variants from source file in region 17:30624994-30625395. Error was invalid region `17:30624995-30625395`
[2016-04-15T07:41Z] 2016-04-15 00:41:06 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:41:06,705 - WARNING - Could not retrieve variants from source file in region 17:27945128-27945529. Error was invalid region `17:27945129-27945529`
[2016-04-15T07:41Z] 2016-04-15 00:41:06 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:41:06,799 - WARNING - Could not retrieve variants from source file in region 17:27613466-27613867. Error was invalid region `17:27613467-27613867`
[2016-04-15T07:41Z] 2016-04-15 00:41:07 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:41:07,496 - WARNING - Could not retrieve variants from source file in region 17:20217164-20217565. Error was invalid region `17:20217165-20217565`
[2016-04-15T07:41Z] 2016-04-15 00:41:07 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:41:07,568 - WARNING - Could not retrieve variants from source file in region 17:28886923-28887324. Error was invalid region `17:28886924-28887324`
[2016-04-15T07:41Z] 2016-04-15 00:41:07 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:41:07,673 - WARNING - Could not retrieve variants from source file in region 17:18775689-18776090. Error was invalid region `17:18775690-18776090`
[2016-04-15T07:41Z] 2016-04-15 00:41:08 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:41:08,348 - WARNING - Could not retrieve variants from source file in region 17:18682188-18702410. Error was invalid region `17:18682189-18702410`
[2016-04-15T07:41Z] 2016-04-15 00:41:12 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:41:12,005 - WARNING - Could not retrieve variants from source file in region 17:18220463-18251079. Error was invalid region `17:18220464-18251079`
[2016-04-15T07:41Z] 2016-04-15 00:41:12 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:41:12,294 - WARNING - Could not retrieve variants from source file in region 17:17996998-17997399. Error was invalid region `17:17996999-17997399`
[2016-04-15T07:41Z] 2016-04-15 00:41:13 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:41:13,794 - WARNING - Could not retrieve variants from source file in region 17:30624994-30625395. Error was invalid region `17:30624995-30625395`
[2016-04-15T07:41Z] 2016-04-15 00:41:14 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:41:14,562 - WARNING - Could not retrieve variants from source file in region 17:27613466-27613867. Error was invalid region `17:27613467-27613867`
[2016-04-15T07:41Z] 2016-04-15 00:41:15 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:41:15,001 - WARNING - Could not retrieve variants from source file in region 17:17039350-17069295. Error was invalid region `17:17039351-17069295`
[2016-04-15T07:41Z] 2016-04-15 00:41:15 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:41:15,039 - WARNING - Could not retrieve variants from source file in region 17:16635769-16665181. Error was invalid region `17:16635770-16665181`
[2016-04-15T07:41Z] 2016-04-15 00:41:15 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:41:15,571 - WARNING - Could not retrieve variants from source file in region 17:27945128-27945529. Error was invalid region `17:27945129-27945529`
[2016-04-15T07:41Z] 2016-04-15 00:41:15 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:41:15,948 - WARNING - Could not retrieve variants from source file in region 17:18775689-18776090. Error was invalid region `17:18775690-18776090`
[2016-04-15T07:41Z] 2016-04-15 00:41:16 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:41:16,230 - WARNING - Could not retrieve variants from source file in region 17:28378010-28381331. Error was invalid region `17:28378011-28381331`
[2016-04-15T07:41Z] 2016-04-15 00:41:16 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:41:16,248 - WARNING - Could not retrieve variants from source file in region 17:28886923-28887324. Error was invalid region `17:28886924-28887324`
[2016-04-15T07:41Z] 2016-04-15 00:41:30 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:41:30,405 - WARNING - Could not retrieve variants from source file in region 17:17948264-17948665. Error was invalid region `17:17948265-17948665`
[2016-04-15T07:41Z] 2016-04-15 00:41:30 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:41:30,581 - WARNING - Could not retrieve variants from source file in region 17:30547935-30548336. Error was invalid region `17:30547936-30548336`
[2016-04-15T07:41Z] 2016-04-15 00:41:31 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:41:31,021 - WARNING - Could not retrieve variants from source file in region 17:27407564-27455379. Error was invalid region `17:27407565-27455379`
[2016-04-15T07:41Z] 2016-04-15 00:41:33 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:41:33,696 - WARNING - Could not retrieve variants from source file in region 17:15994677-15995078. Error was invalid region `17:15994678-15995078`
[2016-04-15T07:41Z] 2016-04-15 00:41:34 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:41:34,495 - WARNING - Could not retrieve variants from source file in region 17:18284051-18291749. Error was invalid region `17:18284052-18291749`
[2016-04-15T07:41Z] 2016-04-15 00:41:34 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:41:34,497 - WARNING - Could not retrieve variants from source file in region 17:25970431-25970832. Error was invalid region `17:25970432-25970832`
[2016-04-15T07:41Z] 2016-04-15 00:41:35 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:41:35,232 - WARNING - Could not retrieve variants from source file in region 17:28296116-28320438. Error was invalid region `17:28296117-28320438`
[2016-04-15T07:41Z] 2016-04-15 00:41:35 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:41:35,247 - WARNING - Could not retrieve variants from source file in region 17:28804785-28805186. Error was invalid region `17:28804786-28805186`
[2016-04-15T07:41Z] 2016-04-15 00:41:35 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:41:35,765 - WARNING - Could not retrieve variants from source file in region 17:17948264-17948665. Error was invalid region `17:17948265-17948665`
[2016-04-15T07:41Z] 2016-04-15 00:41:36 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:41:36,558 - WARNING - Could not retrieve variants from source file in region 17:17326152-17326795. Error was invalid region `17:17326153-17326795`
[2016-04-15T07:41Z] 2016-04-15 00:41:38 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:41:38,356 - WARNING - Could not retrieve variants from source file in region 17:16945862-16946263. Error was invalid region `17:16945863-16946263`
[2016-04-15T07:41Z] 2016-04-15 00:41:40 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:41:40,125 - WARNING - Could not retrieve variants from source file in region 17:15994677-15995078. Error was invalid region `17:15994678-15995078`
[2016-04-15T07:41Z] 2016-04-15 00:41:40 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:41:40,732 - WARNING - Could not retrieve variants from source file in region 17:25970431-25970832. Error was invalid region `17:25970432-25970832`
[2016-04-15T07:41Z] 2016-04-15 00:41:41 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:41:41,242 - WARNING - Could not retrieve variants from source file in region 17:28804785-28805186. Error was invalid region `17:28804786-28805186`
[2016-04-15T07:41Z] 2016-04-15 00:41:41 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:41:41,279 - WARNING - Could not retrieve variants from source file in region 17:18167186-18194131. Error was invalid region `17:18167187-18194131`
[2016-04-15T07:41Z] 2016-04-15 00:41:41 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:41:41,790 - WARNING - Could not retrieve variants from source file in region 17:30547935-30548336. Error was invalid region `17:30547936-30548336`
[2016-04-15T07:41Z] 2016-04-15 00:41:41 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:41:41,918 - WARNING - Could not retrieve variants from source file in region 17:28296116-28320438. Error was invalid region `17:28296117-28320438`
[2016-04-15T07:41Z] 2016-04-15 00:41:41 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:41:41,927 - WARNING - Could not retrieve variants from source file in region 17:17948264-17948665. Error was invalid region `17:17948265-17948665`
[2016-04-15T07:41Z] 2016-04-15 00:41:43 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:41:43,026 - WARNING - Could not retrieve variants from source file in region 17:16945862-16946263. Error was invalid region `17:16945863-16946263`
[2016-04-15T07:41Z] 2016-04-15 00:41:45 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:41:45,374 - WARNING - Could not retrieve variants from source file in region 17:15994677-15995078. Error was invalid region `17:15994678-15995078`
[2016-04-15T07:41Z] 2016-04-15 00:41:46 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:41:46,030 - WARNING - Could not retrieve variants from source file in region 17:16527305-16537397. Error was invalid region `17:16527306-16537397`
[2016-04-15T07:41Z] 2016-04-15 00:41:47 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:41:47,578 - WARNING - Could not retrieve variants from source file in region 17:25970431-25970832. Error was invalid region `17:25970432-25970832`
[2016-04-15T07:41Z] 2016-04-15 00:41:48 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:41:48,116 - WARNING - Could not retrieve variants from source file in region 17:17326152-17326795. Error was invalid region `17:17326153-17326795`
[2016-04-15T07:41Z] 2016-04-15 00:41:48 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:41:48,118 - WARNING - Could not retrieve variants from source file in region 17:18284051-18291749. Error was invalid region `17:18284052-18291749`
[2016-04-15T07:41Z] 2016-04-15 00:41:48 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:41:48,251 - WARNING - Could not retrieve variants from source file in region 17:28804785-28805186. Error was invalid region `17:28804786-28805186`
[2016-04-15T07:41Z] 2016-04-15 00:41:48 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:41:48,544 - WARNING - Could not retrieve variants from source file in region 17:28296116-28320438. Error was invalid region `17:28296117-28320438`
[2016-04-15T07:41Z] 2016-04-15 00:41:48 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:41:48,761 - WARNING - Could not retrieve variants from source file in region 17:16945862-16946263. Error was invalid region `17:16945863-16946263`
[2016-04-15T07:41Z] 2016-04-15 00:41:58 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:41:58,360 - WARNING - Could not retrieve variants from source file in region 17:30221791-30222192. Error was invalid region `17:30221792-30222192`
[2016-04-15T07:41Z] 2016-04-15 00:41:58 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:41:58,978 - WARNING - Could not retrieve variants from source file in region 17:27284232-27287041. Error was invalid region `17:27284233-27287041`
[2016-04-15T07:41Z] 2016-04-15 00:41:59 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:41:59,168 - WARNING - Could not retrieve variants from source file in region 17:17895879-17911204. Error was invalid region `17:17895880-17911204`
[2016-04-15T07:42Z] 2016-04-15 00:42:00 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:42:00,157 - WARNING - Could not retrieve variants from source file in region 17:18136930-18142083. Error was invalid region `17:18136931-18142083`
[2016-04-15T07:42Z] 2016-04-15 00:42:01 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:42:01,732 - WARNING - Could not retrieve variants from source file in region 17:27009538-27014673. Error was invalid region `17:27009539-27014673`
[2016-04-15T07:42Z] 2016-04-15 00:42:03 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:42:03,651 - WARNING - Could not retrieve variants from source file in region 17:30221791-30222192. Error was invalid region `17:30221792-30222192`
[2016-04-15T07:42Z] 2016-04-15 00:42:04 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:42:04,086 - WARNING - Could not retrieve variants from source file in region 17:30183646-30186082. Error was invalid region `17:30183647-30186082`
[2016-04-15T07:42Z] 2016-04-15 00:42:05 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:42:05,583 - WARNING - Could not retrieve variants from source file in region 17:15903391-15910052. Error was invalid region `17:15903392-15910052`
[2016-04-15T07:42Z] 2016-04-15 00:42:06 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:42:06,012 - WARNING - Could not retrieve variants from source file in region 17:20107562-20109379. Error was invalid region `17:20107563-20109379`
[2016-04-15T07:42Z] 2016-04-15 00:42:07 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:42:07,986 - WARNING - Could not retrieve variants from source file in region 17:28612237-28612638. Error was invalid region `17:28612238-28612638`
[2016-04-15T07:42Z] 2016-04-15 00:42:08 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:42:08,612 - WARNING - Could not retrieve variants from source file in region 17:25909639-25931908. Error was invalid region `17:25909640-25931908`
[2016-04-15T07:42Z] 2016-04-15 00:42:08 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:42:08,813 - WARNING - Could not retrieve variants from source file in region 17:30221791-30222192. Error was invalid region `17:30221792-30222192`
[2016-04-15T07:42Z] 2016-04-15 00:42:09 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:42:09,174 - WARNING - Could not retrieve variants from source file in region 17:30183646-30186082. Error was invalid region `17:30183647-30186082`
[2016-04-15T07:42Z] 2016-04-15 00:42:10 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:42:10,211 - WARNING - Could not retrieve variants from source file in region 17:17895879-17911204. Error was invalid region `17:17895880-17911204`
[2016-04-15T07:42Z] 2016-04-15 00:42:10 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:42:10,464 - WARNING - Could not retrieve variants from source file in region 17:16325757-16347122. Error was invalid region `17:16325758-16347122`
[2016-04-15T07:42Z] 2016-04-15 00:42:13 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:42:13,350 - WARNING - Could not retrieve variants from source file in region 17:28612237-28612638. Error was invalid region `17:28612238-28612638`
[2016-04-15T07:42Z] 2016-04-15 00:42:13 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:42:13,874 - WARNING - Could not retrieve variants from source file in region 17:25909639-25931908. Error was invalid region `17:25909640-25931908`
[2016-04-15T07:42Z] 2016-04-15 00:42:14 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:42:14,624 - WARNING - Could not retrieve variants from source file in region 17:30183646-30186082. Error was invalid region `17:30183647-30186082`
[2016-04-15T07:42Z] 2016-04-15 00:42:15 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:42:15,707 - WARNING - Could not retrieve variants from source file in region 17:16325757-16347122. Error was invalid region `17:16325758-16347122`
[2016-04-15T07:42Z] 2016-04-15 00:42:22 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:42:22,024 - WARNING - Could not retrieve variants from source file in region 17:20798908-20799309. Error was invalid region `17:20798909-20799309`
[2016-04-15T07:42Z] 2016-04-15 00:42:23 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:42:23,686 - WARNING - Could not retrieve variants from source file in region 17:28575865-28576266. Error was invalid region `17:28575866-28576266`
[2016-04-15T07:42Z] 2016-04-15 00:42:24 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:42:24,667 - WARNING - Could not retrieve variants from source file in region 17:20910993-20924713. Error was invalid region `17:20910994-20924713`
[2016-04-15T07:42Z] 2016-04-15 00:42:28 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:42:28,604 - WARNING - Could not retrieve variants from source file in region 17:26955119-26955520. Error was invalid region `17:26955120-26955520`
[2016-04-15T07:42Z] 2016-04-15 00:42:29 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:42:29,163 - WARNING - Could not retrieve variants from source file in region 17:28575865-28576266. Error was invalid region `17:28575866-28576266`
[2016-04-15T07:42Z] 2016-04-15 00:42:29 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:42:29,869 - WARNING - Could not retrieve variants from source file in region 17:28511767-28512168. Error was invalid region `17:28511768-28512168`
[2016-04-15T07:42Z] 2016-04-15 00:42:31 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:42:31,059 - WARNING - Could not retrieve variants from source file in region 17:29508564-29508965. Error was invalid region `17:29508565-29508965`
[2016-04-15T07:42Z] 2016-04-15 00:42:31 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:42:31,352 - WARNING - Could not retrieve variants from source file in region 17:28511767-28512168. Error was invalid region `17:28511768-28512168`
[2016-04-15T07:42Z] 2016-04-15 00:42:31 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:42:31,899 - WARNING - Could not retrieve variants from source file in region 17:15611284-15645479. Error was invalid region `17:15611285-15645479`
[2016-04-15T07:42Z] 2016-04-15 00:42:32 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:42:32,058 - WARNING - Could not retrieve variants from source file in region 17:16220280-16220681. Error was invalid region `17:16220281-16220681`
[2016-04-15T07:42Z] 2016-04-15 00:42:34 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:42:34,418 - WARNING - Could not retrieve variants from source file in region 17:20013591-20013992. Error was invalid region `17:20013592-20013992`
[2016-04-15T07:42Z] 2016-04-15 00:42:36 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:42:36,575 - WARNING - Could not retrieve variants from source file in region 17:26903717-26904118. Error was invalid region `17:26903718-26904118`
[2016-04-15T07:42Z] 2016-04-15 00:42:37 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:42:37,816 - WARNING - Could not retrieve variants from source file in region 17:29508564-29508965. Error was invalid region `17:29508565-29508965`
[2016-04-15T07:42Z] 2016-04-15 00:42:39 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:42:39,192 - WARNING - Could not retrieve variants from source file in region 17:16220280-16220681. Error was invalid region `17:16220281-16220681`
[2016-04-15T07:42Z] 2016-04-15 00:42:41 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:42:41,762 - WARNING - Could not retrieve variants from source file in region 17:20769651-20770056. Error was invalid region `17:20769652-20770056`
[2016-04-15T07:42Z] 2016-04-15 00:42:45 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:42:45,904 - WARNING - Could not retrieve variants from source file in region 17:26903717-26904118. Error was invalid region `17:26903718-26904118`
[2016-04-15T07:42Z] 2016-04-15 00:42:46 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:42:46,441 - WARNING - Could not retrieve variants from source file in region 17:20769651-20770056. Error was invalid region `17:20769652-20770056`
[2016-04-15T07:42Z] 2016-04-15 00:42:48 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:42:48,263 - WARNING - Could not retrieve variants from source file in region 17:29335211-29335612. Error was invalid region `17:29335212-29335612`
[2016-04-15T07:42Z] 2016-04-15 00:42:54 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:42:54,353 - WARNING - Could not retrieve variants from source file in region 17:29553274-29553675. Error was invalid region `17:29553275-29553675`
[2016-04-15T07:42Z] 2016-04-15 00:42:54 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:42:54,408 - WARNING - Could not retrieve variants from source file in region 17:15584045-15584446. Error was invalid region `17:15584046-15584446`
[2016-04-15T07:42Z] 2016-04-15 00:42:56 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:42:56,213 - WARNING - Could not retrieve variants from source file in region 17:21434349-21436771. Error was invalid region `17:21434350-21436771`
[2016-04-15T07:42Z] 2016-04-15 00:42:56 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:42:56,520 - WARNING - Could not retrieve variants from source file in region 17:29161292-29161693. Error was invalid region `17:29161293-29161693`
[2016-04-15T07:42Z] 2016-04-15 00:42:58 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:42:58,236 - WARNING - Could not retrieve variants from source file in region 17:26851391-26874504. Error was invalid region `17:26851392-26874504`
[2016-04-15T07:42Z] 2016-04-15 00:42:58 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:42:58,768 - WARNING - Could not retrieve variants from source file in region 17:29335211-29335612. Error was invalid region `17:29335212-29335612`
[2016-04-15T07:42Z] 2016-04-15 00:42:58 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:42:58,901 - WARNING - Could not retrieve variants from source file in region 17:15584045-15584446. Error was invalid region `17:15584046-15584446`
[2016-04-15T07:42Z] 2016-04-15 00:42:58 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:42:58,961 - WARNING - Could not retrieve variants from source file in region 17:19861247-19861648. Error was invalid region `17:19861248-19861648`
[2016-04-15T07:42Z] 2016-04-15 00:42:59 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:42:59,249 - WARNING - Could not retrieve variants from source file in region 17:21147309-21156720. Error was invalid region `17:21147310-21156720`
[2016-04-15T07:43Z] 2016-04-15 00:43:00 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:43:00,511 - WARNING - Could not retrieve variants from source file in region 17:21434349-21436771. Error was invalid region `17:21434350-21436771`
[2016-04-15T07:43Z] 2016-04-15 00:43:00 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:43:00,537 - WARNING - Could not retrieve variants from source file in region 17:21434349-21436771. Error was invalid region `17:21434350-21436771`
[2016-04-15T07:43Z] 2016-04-15 00:43:00 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:43:00,883 - WARNING - Could not retrieve variants from source file in region 17:29161292-29161693. Error was invalid region `17:29161293-29161693`
[2016-04-15T07:43Z] 2016-04-15 00:43:04 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:43:04,807 - WARNING - Could not retrieve variants from source file in region 17:26823945-26824346. Error was invalid region `17:26823946-26824346`
[2016-04-15T07:43Z] 2016-04-15 00:43:05 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:43:05,435 - WARNING - Could not retrieve variants from source file in region 17:29161292-29161693. Error was invalid region `17:29161293-29161693`
[2016-04-15T07:43Z] 2016-04-15 00:43:12 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:43:12,009 - WARNING - Could not retrieve variants from source file in region 17:19713529-19729685. Error was invalid region `17:19713530-19729685`
[2016-04-15T07:43Z] 2016-04-15 00:43:12 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:43:12,098 - WARNING - Could not retrieve variants from source file in region 17:19578662-19579063. Error was invalid region `17:19578663-19579063`
[2016-04-15T07:43Z] 2016-04-15 00:43:12 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:43:12,912 - WARNING - Could not retrieve variants from source file in region 17:19713529-19729685. Error was invalid region `17:19713530-19729685`
[2016-04-15T07:43Z] 2016-04-15 00:43:12 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:43:12,941 - WARNING - Could not retrieve variants from source file in region 17:19578662-19579063. Error was invalid region `17:19578663-19579063`
[2016-04-15T07:43Z] 2016-04-15 00:43:13 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:43:13,027 - WARNING - Could not retrieve variants from source file in region 17:19812330-19812731. Error was invalid region `17:19812331-19812731`
[2016-04-15T07:43Z] 2016-04-15 00:43:14 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:43:14,415 - WARNING - Could not retrieve variants from source file in region 17:19713529-19729685. Error was invalid region `17:19713530-19729685`
[2016-04-15T07:43Z] ['bcbio-variation-recall', 'square', '-Xms750m', '-Xmx7280m', '-XX:+UseSerialGC', '-c', 16, '-r', u'17:31048041-46607237', '--caller', 'platypus', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/17/Batch1-17_31048040_46607237.vcf.gz', '/mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/17/Batch1-17_31048040_46607237.vcf-inputs.txt'] in region: 17:31048041-46607237
[2016-04-15T07:43Z] 2016-04-15 00:43:28 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:43:28,902 - WARNING - Could not retrieve variants from source file in region 17:36292528-36292929. Error was invalid region `17:36292529-36292929`
[2016-04-15T07:43Z] 2016-04-15 00:43:30 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:43:30,183 - WARNING - Could not retrieve variants from source file in region 17:45911064-45917893. Error was invalid region `17:45911065-45917893`
[2016-04-15T07:43Z] 2016-04-15 00:43:30 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:43:30,253 - WARNING - Could not retrieve variants from source file in region 17:43545682-43553111. Error was invalid region `17:43545683-43553111`
[2016-04-15T07:43Z] 2016-04-15 00:43:30 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:43:30,310 - WARNING - Could not retrieve variants from source file in region 17:46606810-46607211. Error was invalid region `17:46606811-46607211`
[2016-04-15T07:43Z] 2016-04-15 00:43:30 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:43:30,948 - WARNING - Could not retrieve variants from source file in region 17:42475772-42476173. Error was invalid region `17:42475773-42476173`
[2016-04-15T07:43Z] 2016-04-15 00:43:30 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:43:30,967 - WARNING - Could not retrieve variants from source file in region 17:44144782-44160039. Error was invalid region `17:44144783-44160039`
[2016-04-15T07:43Z] 2016-04-15 00:43:31 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:43:31,073 - WARNING - Could not retrieve variants from source file in region 17:40913155-40913556. Error was invalid region `17:40913156-40913556`
[2016-04-15T07:43Z] 2016-04-15 00:43:31 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:43:31,903 - WARNING - Could not retrieve variants from source file in region 17:42164674-42165075. Error was invalid region `17:42164675-42165075`
[2016-04-15T07:43Z] 2016-04-15 00:43:32 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:43:32,035 - WARNING - Could not retrieve variants from source file in region 17:46178463-46178864. Error was invalid region `17:46178464-46178864`
[2016-04-15T07:43Z] 2016-04-15 00:43:32 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:43:32,555 - WARNING - Could not retrieve variants from source file in region 17:44828720-44829121. Error was invalid region `17:44828721-44829121`
[2016-04-15T07:43Z] 2016-04-15 00:43:32 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:43:32,589 - WARNING - Could not retrieve variants from source file in region 17:42925348-42927911. Error was invalid region `17:42925349-42927911`
[2016-04-15T07:43Z] 2016-04-15 00:43:33 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:43:33,562 - WARNING - Could not retrieve variants from source file in region 17:36292528-36292929. Error was invalid region `17:36292529-36292929`
[2016-04-15T07:43Z] 2016-04-15 00:43:36 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:43:36,190 - WARNING - Could not retrieve variants from source file in region 17:46606810-46607211. Error was invalid region `17:46606811-46607211`
[2016-04-15T07:43Z] 2016-04-15 00:43:38 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:43:38,126 - WARNING - Could not retrieve variants from source file in region 17:42475772-42476173. Error was invalid region `17:42475773-42476173`
[2016-04-15T07:43Z] 2016-04-15 00:43:38 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:43:38,741 - WARNING - Could not retrieve variants from source file in region 17:40125653-40126054. Error was invalid region `17:40125654-40126054`
[2016-04-15T07:43Z] 2016-04-15 00:43:39 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:43:39,180 - WARNING - Could not retrieve variants from source file in region 17:42164674-42165075. Error was invalid region `17:42164675-42165075`
[2016-04-15T07:43Z] 2016-04-15 00:43:39 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:43:39,902 - WARNING - Could not retrieve variants from source file in region 17:42925348-42927911. Error was invalid region `17:42925349-42927911`
[2016-04-15T07:43Z] 2016-04-15 00:43:40 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:43:40,736 - WARNING - Could not retrieve variants from source file in region 17:46178463-46178864. Error was invalid region `17:46178464-46178864`
[2016-04-15T07:43Z] 2016-04-15 00:43:40 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:43:40,830 - WARNING - Could not retrieve variants from source file in region 17:45911064-45917893. Error was invalid region `17:45911065-45917893`
[2016-04-15T07:43Z] 2016-04-15 00:43:41 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:43:41,110 - WARNING - Could not retrieve variants from source file in region 17:46606810-46607211. Error was invalid region `17:46606811-46607211`
[2016-04-15T07:43Z] 2016-04-15 00:43:43 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:43:43,208 - WARNING - Could not retrieve variants from source file in region 17:42475772-42476173. Error was invalid region `17:42475773-42476173`
[2016-04-15T07:43Z] 2016-04-15 00:43:46 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:43:46,838 - WARNING - Could not retrieve variants from source file in region 17:42164674-42165075. Error was invalid region `17:42164675-42165075`
[2016-04-15T07:43Z] 2016-04-15 00:43:47 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:43:47,490 - WARNING - Could not retrieve variants from source file in region 17:42925348-42927911. Error was invalid region `17:42925349-42927911`
[2016-04-15T07:43Z] 2016-04-15 00:43:47 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:43:47,921 - WARNING - Could not retrieve variants from source file in region 17:38121782-38137554. Error was invalid region `17:38121783-38137554`
[2016-04-15T07:43Z] 2016-04-15 00:43:55 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:43:55,933 - WARNING - Could not retrieve variants from source file in region 17:36080599-36081000. Error was invalid region `17:36080600-36081000`
[2016-04-15T07:43Z] 2016-04-15 00:43:58 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:43:58,086 - WARNING - Could not retrieve variants from source file in region 17:46473907-46474308. Error was invalid region `17:46473908-46474308`
[2016-04-15T07:43Z] 2016-04-15 00:43:58 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:43:58,141 - WARNING - Could not retrieve variants from source file in region 17:45885476-45885877. Error was invalid region `17:45885477-45885877`
[2016-04-15T07:43Z] 2016-04-15 00:43:59 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:43:59,256 - WARNING - Could not retrieve variants from source file in region 17:42391866-42398242. Error was invalid region `17:42391867-42398242`
[2016-04-15T07:44Z] 2016-04-15 00:44:00 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:44:00,146 - WARNING - Could not retrieve variants from source file in region 17:43502789-43507593. Error was invalid region `17:43502790-43507593`
[2016-04-15T07:44Z] 2016-04-15 00:44:02 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:44:02,092 - WARNING - Could not retrieve variants from source file in region 17:36080599-36081000. Error was invalid region `17:36080600-36081000`
[2016-04-15T07:44Z] 2016-04-15 00:44:03 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:44:03,839 - WARNING - Could not retrieve variants from source file in region 17:42030320-42030933. Error was invalid region `17:42030321-42030933`
[2016-04-15T07:44Z] 2016-04-15 00:44:03 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:44:03,999 - WARNING - Could not retrieve variants from source file in region 17:46473907-46474308. Error was invalid region `17:46473908-46474308`
[2016-04-15T07:44Z] 2016-04-15 00:44:04 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:44:04,281 - WARNING - Could not retrieve variants from source file in region 17:45885476-45885877. Error was invalid region `17:45885477-45885877`
[2016-04-15T07:44Z] 2016-04-15 00:44:04 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:44:04,812 - WARNING - Could not retrieve variants from source file in region 17:42391866-42398242. Error was invalid region `17:42391867-42398242`
[2016-04-15T07:44Z] 2016-04-15 00:44:04 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:44:04,883 - WARNING - Could not retrieve variants from source file in region 17:43907685-43924421. Error was invalid region `17:43907686-43924421`
[2016-04-15T07:44Z] 2016-04-15 00:44:05 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:44:05,592 - WARNING - Could not retrieve variants from source file in region 17:43108259-43111878. Error was invalid region `17:43108260-43111878`
[2016-04-15T07:44Z] 2016-04-15 00:44:06 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:44:06,357 - WARNING - Could not retrieve variants from source file in region 17:38061985-38064659. Error was invalid region `17:38061986-38064659`
[2016-04-15T07:44Z] 2016-04-15 00:44:08 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:44:08,390 - WARNING - Could not retrieve variants from source file in region 17:36080599-36081000. Error was invalid region `17:36080600-36081000`
[2016-04-15T07:44Z] 2016-04-15 00:44:10 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:44:10,151 - WARNING - Could not retrieve variants from source file in region 17:42030320-42030933. Error was invalid region `17:42030321-42030933`
[2016-04-15T07:44Z] 2016-04-15 00:44:10 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:44:10,897 - WARNING - Could not retrieve variants from source file in region 17:45885476-45885877. Error was invalid region `17:45885477-45885877`
[2016-04-15T07:44Z] 2016-04-15 00:44:11 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:44:11,251 - WARNING - Could not retrieve variants from source file in region 17:46473907-46474308. Error was invalid region `17:46473908-46474308`
[2016-04-15T07:44Z] 2016-04-15 00:44:12 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:44:12,036 - WARNING - Could not retrieve variants from source file in region 17:42391866-42398242. Error was invalid region `17:42391867-42398242`
[2016-04-15T07:44Z] 2016-04-15 00:44:13 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:44:13,030 - WARNING - Could not retrieve variants from source file in region 17:46114864-46136323. Error was invalid region `17:46114865-46136323`
[2016-04-15T07:44Z] 2016-04-15 00:44:13 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:44:13,408 - WARNING - Could not retrieve variants from source file in region 17:38061985-38064659. Error was invalid region `17:38061986-38064659`
[2016-04-15T07:44Z] 2016-04-15 00:44:15 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:44:15,504 - WARNING - Could not retrieve variants from source file in region 17:42030320-42030933. Error was invalid region `17:42030321-42030933`
[2016-04-15T07:44Z] 2016-04-15 00:44:19 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:44:19,605 - WARNING - Could not retrieve variants from source file in region 17:46114864-46136323. Error was invalid region `17:46114865-46136323`
[2016-04-15T07:44Z] 2016-04-15 00:44:20 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:44:20,111 - WARNING - Could not retrieve variants from source file in region 17:43108259-43111878. Error was invalid region `17:43108260-43111878`
[2016-04-15T07:44Z] 2016-04-15 00:44:20 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:44:20,249 - WARNING - Could not retrieve variants from source file in region 17:38061985-38064659. Error was invalid region `17:38061986-38064659`
[2016-04-15T07:44Z] 2016-04-15 00:44:25 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:44:25,400 - WARNING - Could not retrieve variants from source file in region 17:35984199-35988862. Error was invalid region `17:35984200-35988862`
[2016-04-15T07:44Z] 2016-04-15 00:44:27 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:44:27,160 - WARNING - Could not retrieve variants from source file in region 17:45785933-45786642. Error was invalid region `17:45785934-45786642`
[2016-04-15T07:44Z] 2016-04-15 00:44:28 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:44:28,790 - WARNING - Could not retrieve variants from source file in region 17:46261960-46262361. Error was invalid region `17:46261961-46262361`
[2016-04-15T07:44Z] 2016-04-15 00:44:30 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:44:30,625 - WARNING - Could not retrieve variants from source file in region 17:43474457-43474858. Error was invalid region `17:43474458-43474858`
[2016-04-15T07:44Z] 2016-04-15 00:44:30 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:44:30,900 - WARNING - Could not retrieve variants from source file in region 17:35984199-35988862. Error was invalid region `17:35984200-35988862`
[2016-04-15T07:44Z] 2016-04-15 00:44:32 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:44:32,074 - WARNING - Could not retrieve variants from source file in region 17:40766335-40766736. Error was invalid region `17:40766336-40766736`
[2016-04-15T07:44Z] 2016-04-15 00:44:32 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:44:32,104 - WARNING - Could not retrieve variants from source file in region 17:39333922-39346708. Error was invalid region `17:39333923-39346708`
[2016-04-15T07:44Z] 2016-04-15 00:44:34 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:44:34,393 - WARNING - Could not retrieve variants from source file in region 17:46261960-46262361. Error was invalid region `17:46261961-46262361`
[2016-04-15T07:44Z] 2016-04-15 00:44:36 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:44:36,843 - WARNING - Could not retrieve variants from source file in region 17:44248288-44249543. Error was invalid region `17:44248289-44249543`
[2016-04-15T07:44Z] 2016-04-15 00:44:38 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:44:38,373 - WARNING - Could not retrieve variants from source file in region 17:43318567-43364483. Error was invalid region `17:43318568-43364483`
[2016-04-15T07:44Z] 2016-04-15 00:44:39 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:44:39,298 - WARNING - Could not retrieve variants from source file in region 17:38024415-38031864. Error was invalid region `17:38024416-38031864`
[2016-04-15T07:44Z] 2016-04-15 00:44:39 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:44:39,309 - WARNING - Could not retrieve variants from source file in region 17:40766335-40766736. Error was invalid region `17:40766336-40766736`
[2016-04-15T07:44Z] 2016-04-15 00:44:40 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:44:40,474 - WARNING - Could not retrieve variants from source file in region 17:39967231-40011169. Error was invalid region `17:39967232-40011169`
[2016-04-15T07:44Z] 2016-04-15 00:44:43 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:44:43,975 - WARNING - Could not retrieve variants from source file in region 17:37243716-37262307. Error was invalid region `17:37243717-37262307`
[2016-04-15T07:44Z] 2016-04-15 00:44:44 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:44:44,365 - WARNING - Could not retrieve variants from source file in region 17:43318567-43364483. Error was invalid region `17:43318568-43364483`
[2016-04-15T07:44Z] 2016-04-15 00:44:44 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:44:44,860 - WARNING - Could not retrieve variants from source file in region 17:41891226-41985039. Error was invalid region `17:41891227-41985039`
[2016-04-15T07:44Z] 2016-04-15 00:44:46 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:44:46,145 - WARNING - Could not retrieve variants from source file in region 17:38024415-38031864. Error was invalid region `17:38024416-38031864`
[2016-04-15T07:44Z] 2016-04-15 00:44:46 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:44:46,179 - WARNING - Could not retrieve variants from source file in region 17:40766335-40766736. Error was invalid region `17:40766336-40766736`
[2016-04-15T07:44Z] 2016-04-15 00:44:47 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:44:47,654 - WARNING - Could not retrieve variants from source file in region 17:39333922-39346708. Error was invalid region `17:39333923-39346708`
[2016-04-15T07:44Z] 2016-04-15 00:44:49 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:44:49,389 - WARNING - Could not retrieve variants from source file in region 17:43318567-43364483. Error was invalid region `17:43318568-43364483`
[2016-04-15T07:44Z] 2016-04-15 00:44:52 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:44:52,301 - WARNING - Could not retrieve variants from source file in region 17:38024415-38031864. Error was invalid region `17:38024416-38031864`
[2016-04-15T07:44Z] 2016-04-15 00:44:57 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:44:57,162 - WARNING - Could not retrieve variants from source file in region 17:42225336-42287709. Error was invalid region `17:42225337-42287709`
[2016-04-15T07:44Z] 2016-04-15 00:44:59 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:44:59,476 - WARNING - Could not retrieve variants from source file in region 17:35937426-35956581. Error was invalid region `17:35937427-35956581`
[2016-04-15T07:44Z] 2016-04-15 00:44:59 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:44:59,782 - WARNING - Could not retrieve variants from source file in region 17:41601700-41604072. Error was invalid region `17:41601701-41604072`
[2016-04-15T07:45Z] 2016-04-15 00:45:01 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:45:01,367 - WARNING - Could not retrieve variants from source file in region 17:39871489-39926115. Error was invalid region `17:39871490-39926115`
[2016-04-15T07:45Z] 2016-04-15 00:45:04 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:45:04,048 - WARNING - Could not retrieve variants from source file in region 17:41361749-41362150. Error was invalid region `17:41361750-41362150`
[2016-04-15T07:45Z] 2016-04-15 00:45:08 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:45:08,530 - WARNING - Could not retrieve variants from source file in region 17:45438675-45490441. Error was invalid region `17:45438676-45490441`
[2016-04-15T07:45Z] 2016-04-15 00:45:08 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:45:08,616 - WARNING - Could not retrieve variants from source file in region 17:42953198-42953599. Error was invalid region `17:42953199-42953599`
[2016-04-15T07:45Z] 2016-04-15 00:45:08 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:45:08,910 - WARNING - Could not retrieve variants from source file in region 17:41601700-41604072. Error was invalid region `17:41601701-41604072`
[2016-04-15T07:45Z] 2016-04-15 00:45:13 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:45:13,145 - WARNING - Could not retrieve variants from source file in region 17:37400840-37401241. Error was invalid region `17:37400841-37401241`
[2016-04-15T07:45Z] 2016-04-15 00:45:13 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:45:13,231 - WARNING - Could not retrieve variants from source file in region 17:45368126-45369979. Error was invalid region `17:45368127-45369979`
[2016-04-15T07:45Z] 2016-04-15 00:45:13 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:45:13,238 - WARNING - Could not retrieve variants from source file in region 17:37052954-37101570. Error was invalid region `17:37052955-37101570`
[2016-04-15T07:45Z] 2016-04-15 00:45:13 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:45:13,660 - WARNING - Could not retrieve variants from source file in region 17:41361749-41362150. Error was invalid region `17:41361750-41362150`
[2016-04-15T07:45Z] 2016-04-15 00:45:18 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:45:18,667 - WARNING - Could not retrieve variants from source file in region 17:37400840-37401241. Error was invalid region `17:37400841-37401241`
[2016-04-15T07:45Z] 2016-04-15 00:45:18 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:45:18,780 - WARNING - Could not retrieve variants from source file in region 17:45368126-45369979. Error was invalid region `17:45368127-45369979`
[2016-04-15T07:45Z] 2016-04-15 00:45:22 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:45:22,128 - WARNING - Could not retrieve variants from source file in region 17:35895912-35902415. Error was invalid region `17:35895913-35902415`
[2016-04-15T07:45Z] 2016-04-15 00:45:22 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:45:22,888 - WARNING - Could not retrieve variants from source file in region 17:45000786-45019433. Error was invalid region `17:45000787-45019433`
[2016-04-15T07:45Z] 2016-04-15 00:45:22 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:45:22,977 - WARNING - Could not retrieve variants from source file in region 17:41165282-41174215. Error was invalid region `17:41165283-41174215`
[2016-04-15T07:45Z] 2016-04-15 00:45:24 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:45:24,775 - WARNING - Could not retrieve variants from source file in region 17:37400840-37401241. Error was invalid region `17:37400841-37401241`
[2016-04-15T07:45Z] 2016-04-15 00:45:25 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:45:25,008 - WARNING - Could not retrieve variants from source file in region 17:39535648-39537612. Error was invalid region `17:39535649-39537612`
[2016-04-15T07:45Z] 2016-04-15 00:45:25 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:45:25,222 - WARNING - Could not retrieve variants from source file in region 17:45368126-45369979. Error was invalid region `17:45368127-45369979`
[2016-04-15T07:45Z] 2016-04-15 00:45:27 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:45:27,163 - WARNING - Could not retrieve variants from source file in region 17:35895912-35902415. Error was invalid region `17:35895913-35902415`
[2016-04-15T07:45Z] 2016-04-15 00:45:27 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:45:27,186 - WARNING - Could not retrieve variants from source file in region 17:36997250-36997651. Error was invalid region `17:36997251-36997651`
[2016-04-15T07:45Z] 2016-04-15 00:45:27 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:45:27,760 - WARNING - Could not retrieve variants from source file in region 17:41222883-41245656. Error was invalid region `17:41222884-41245656`
[2016-04-15T07:45Z] 2016-04-15 00:45:31 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:45:31,439 - WARNING - Could not retrieve variants from source file in region 17:40383851-40384252. Error was invalid region `17:40383852-40384252`
[2016-04-15T07:45Z] 2016-04-15 00:45:32 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:45:32,028 - WARNING - Could not retrieve variants from source file in region 17:36622271-36666741. Error was invalid region `17:36622272-36666741`
[2016-04-15T07:45Z] 2016-04-15 00:45:32 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:45:32,102 - WARNING - Could not retrieve variants from source file in region 17:39723779-39767934. Error was invalid region `17:39723780-39767934`
[2016-04-15T07:45Z] 2016-04-15 00:45:33 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:45:33,801 - WARNING - Could not retrieve variants from source file in region 17:39134932-39135333. Error was invalid region `17:39134933-39135333`
[2016-04-15T07:45Z] 2016-04-15 00:45:33 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:45:33,873 - WARNING - Could not retrieve variants from source file in region 17:41165282-41174215. Error was invalid region `17:41165283-41174215`
[2016-04-15T07:45Z] 2016-04-15 00:45:36 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:45:36,312 - WARNING - Could not retrieve variants from source file in region 17:39535648-39537612. Error was invalid region `17:39535649-39537612`
[2016-04-15T07:45Z] 2016-04-15 00:45:36 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:45:36,372 - WARNING - Could not retrieve variants from source file in region 17:37561402-37561803. Error was invalid region `17:37561403-37561803`
[2016-04-15T07:45Z] 2016-04-15 00:45:37 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:45:37,087 - WARNING - Could not retrieve variants from source file in region 17:40383851-40384252. Error was invalid region `17:40383852-40384252`
[2016-04-15T07:45Z] 2016-04-15 00:45:37 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:45:37,914 - WARNING - Could not retrieve variants from source file in region 17:36622271-36666741. Error was invalid region `17:36622272-36666741`
[2016-04-15T07:45Z] 2016-04-15 00:45:38 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:45:38,574 - WARNING - Could not retrieve variants from source file in region 17:36997250-36997651. Error was invalid region `17:36997251-36997651`
[2016-04-15T07:45Z] 2016-04-15 00:45:39 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:45:39,534 - WARNING - Could not retrieve variants from source file in region 17:39134932-39135333. Error was invalid region `17:39134933-39135333`
[2016-04-15T07:45Z] 2016-04-15 00:45:39 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:45:39,621 - WARNING - Could not retrieve variants from source file in region 17:41222883-41245656. Error was invalid region `17:41222884-41245656`
[2016-04-15T07:45Z] 2016-04-15 00:45:39 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:45:39,864 - WARNING - Could not retrieve variants from source file in region 17:37318818-37319293. Error was invalid region `17:37318819-37319293`
[2016-04-15T07:45Z] 2016-04-15 00:45:41 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:45:41,814 - WARNING - Could not retrieve variants from source file in region 17:37561402-37561803. Error was invalid region `17:37561403-37561803`
[2016-04-15T07:45Z] 2016-04-15 00:45:42 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:45:42,455 - WARNING - Could not retrieve variants from source file in region 17:35771257-35771658. Error was invalid region `17:35771258-35771658`
[2016-04-15T07:45Z] 2016-04-15 00:45:48 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:45:48,220 - WARNING - Could not retrieve variants from source file in region 17:36707298-36707699. Error was invalid region `17:36707299-36707699`
[2016-04-15T07:45Z] 2016-04-15 00:45:48 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:45:48,269 - WARNING - Could not retrieve variants from source file in region 17:35771257-35771658. Error was invalid region `17:35771258-35771658`
[2016-04-15T07:45Z] 2016-04-15 00:45:49 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:45:49,084 - WARNING - Could not retrieve variants from source file in region 17:44949911-44950312. Error was invalid region `17:44949912-44950312`
[2016-04-15T07:45Z] 2016-04-15 00:45:50 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:45:50,447 - WARNING - Could not retrieve variants from source file in region 17:41116023-41133261. Error was invalid region `17:41116024-41133261`
[2016-04-15T07:45Z] 2016-04-15 00:45:50 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:45:50,525 - WARNING - Could not retrieve variants from source file in region 17:39502952-39503353. Error was invalid region `17:39502953-39503353`
[2016-04-15T07:45Z] 2016-04-15 00:45:53 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:45:53,333 - WARNING - Could not retrieve variants from source file in region 17:35771257-35771658. Error was invalid region `17:35771258-35771658`
[2016-04-15T07:45Z] 2016-04-15 00:45:53 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:45:53,939 - WARNING - Could not retrieve variants from source file in region 17:44949911-44950312. Error was invalid region `17:44949912-44950312`
[2016-04-15T07:45Z] 2016-04-15 00:45:55 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:45:55,544 - WARNING - Could not retrieve variants from source file in region 17:41116023-41133261. Error was invalid region `17:41116024-41133261`
[2016-04-15T07:45Z] 2016-04-15 00:45:55 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:45:55,620 - WARNING - Could not retrieve variants from source file in region 17:39502952-39503353. Error was invalid region `17:39502953-39503353`
[2016-04-15T07:45Z] 2016-04-15 00:45:55 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:45:55,727 - WARNING - Could not retrieve variants from source file in region 17:40336023-40336424. Error was invalid region `17:40336024-40336424`
[2016-04-15T07:45Z] 2016-04-15 00:45:57 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:45:57,335 - WARNING - Could not retrieve variants from source file in region 17:38855561-38859581. Error was invalid region `17:38855562-38859581`
[2016-04-15T07:45Z] 2016-04-15 00:45:58 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:45:58,859 - WARNING - Could not retrieve variants from source file in region 17:36707298-36707699. Error was invalid region `17:36707299-36707699`
[2016-04-15T07:45Z] 2016-04-15 00:45:58 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:45:58,918 - WARNING - Could not retrieve variants from source file in region 17:44949911-44950312. Error was invalid region `17:44949912-44950312`
[2016-04-15T07:45Z] 2016-04-15 00:45:59 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:45:59,020 - WARNING - Could not retrieve variants from source file in region 17:36861772-36909689. Error was invalid region `17:36861773-36909689`
[2016-04-15T07:45Z] 2016-04-15 00:45:59 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:45:59,477 - WARNING - Could not retrieve variants from source file in region 17:39081502-39084694. Error was invalid region `17:39081503-39084694`
[2016-04-15T07:46Z] 2016-04-15 00:46:00 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:46:00,535 - WARNING - Could not retrieve variants from source file in region 17:41116023-41133261. Error was invalid region `17:41116024-41133261`
[2016-04-15T07:46Z] 2016-04-15 00:46:05 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:46:05,760 - WARNING - Could not retrieve variants from source file in region 17:35696593-35696994. Error was invalid region `17:35696594-35696994`
[2016-04-15T07:46Z] 2016-04-15 00:46:08 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:46:08,055 - WARNING - Could not retrieve variants from source file in region 17:40266728-40267129. Error was invalid region `17:40266729-40267129`
[2016-04-15T07:46Z] 2016-04-15 00:46:09 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:46:09,609 - WARNING - Could not retrieve variants from source file in region 17:35696593-35696994. Error was invalid region `17:35696594-35696994`
[2016-04-15T07:46Z] 2016-04-15 00:46:09 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:46:09,651 - WARNING - Could not retrieve variants from source file in region 17:40266728-40267129. Error was invalid region `17:40266729-40267129`
[2016-04-15T07:46Z] 2016-04-15 00:46:12 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:46:12,829 - WARNING - Could not retrieve variants from source file in region 17:35478151-35478552. Error was invalid region `17:35478152-35478552`
[2016-04-15T07:46Z] 2016-04-15 00:46:13 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:46:13,469 - WARNING - Could not retrieve variants from source file in region 17:38599881-38600282. Error was invalid region `17:38599882-38600282`
[2016-04-15T07:46Z] 2016-04-15 00:46:17 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:46:17,254 - WARNING - Could not retrieve variants from source file in region 17:33503937-33504338. Error was invalid region `17:33503938-33504338`
[2016-04-15T07:46Z] 2016-04-15 00:46:17 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:46:17,282 - WARNING - Could not retrieve variants from source file in region 17:35478151-35478552. Error was invalid region `17:35478152-35478552`
[2016-04-15T07:46Z] 2016-04-15 00:46:17 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:46:17,607 - WARNING - Could not retrieve variants from source file in region 17:33801945-33814948. Error was invalid region `17:33801946-33814948`
[2016-04-15T07:46Z] 2016-04-15 00:46:17 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:46:17,623 - WARNING - Could not retrieve variants from source file in region 17:34942384-34942785. Error was invalid region `17:34942385-34942785`
[2016-04-15T07:46Z] 2016-04-15 00:46:17 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:46:17,928 - WARNING - Could not retrieve variants from source file in region 17:34746742-34747143. Error was invalid region `17:34746743-34747143`
[2016-04-15T07:46Z] 2016-04-15 00:46:18 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:46:18,122 - WARNING - Could not retrieve variants from source file in region 17:39023185-39023586. Error was invalid region `17:39023186-39023586`
[2016-04-15T07:46Z] 2016-04-15 00:46:18 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:46:18,365 - WARNING - Could not retrieve variants from source file in region 17:33998591-33998992. Error was invalid region `17:33998592-33998992`
[2016-04-15T07:46Z] 2016-04-15 00:46:18 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:46:18,545 - WARNING - Could not retrieve variants from source file in region 17:38599881-38600282. Error was invalid region `17:38599882-38600282`
[2016-04-15T07:46Z] 2016-04-15 00:46:19 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:46:19,099 - WARNING - Could not retrieve variants from source file in region 17:32612683-32613084. Error was invalid region `17:32612684-32613084`
[2016-04-15T07:46Z] 2016-04-15 00:46:23 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:46:23,716 - WARNING - Could not retrieve variants from source file in region 17:35478151-35478552. Error was invalid region `17:35478152-35478552`
[2016-04-15T07:46Z] 2016-04-15 00:46:23 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:46:23,763 - WARNING - Could not retrieve variants from source file in region 17:33503937-33504338. Error was invalid region `17:33503938-33504338`
[2016-04-15T07:46Z] 2016-04-15 00:46:23 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:46:23,810 - WARNING - Could not retrieve variants from source file in region 17:38519080-38519481. Error was invalid region `17:38519081-38519481`
[2016-04-15T07:46Z] 2016-04-15 00:46:24 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:46:24,159 - WARNING - Could not retrieve variants from source file in region 17:38599881-38600282. Error was invalid region `17:38599882-38600282`
[2016-04-15T07:46Z] 2016-04-15 00:46:24 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:46:24,378 - WARNING - Could not retrieve variants from source file in region 17:34746742-34747143. Error was invalid region `17:34746743-34747143`
[2016-04-15T07:46Z] 2016-04-15 00:46:24 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:46:24,519 - WARNING - Could not retrieve variants from source file in region 17:34942384-34942785. Error was invalid region `17:34942385-34942785`
[2016-04-15T07:46Z] 2016-04-15 00:46:24 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:46:24,814 - WARNING - Could not retrieve variants from source file in region 17:32612683-32613084. Error was invalid region `17:32612684-32613084`
[2016-04-15T07:46Z] 2016-04-15 00:46:24 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:46:24,978 - WARNING - Could not retrieve variants from source file in region 17:33998591-33998992. Error was invalid region `17:33998592-33998992`
[2016-04-15T07:46Z] 2016-04-15 00:46:26 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:46:26,336 - WARNING - Could not retrieve variants from source file in region 17:35346430-35346831. Error was invalid region `17:35346431-35346831`
[2016-04-15T07:46Z] 2016-04-15 00:46:32 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:46:32,109 - WARNING - Could not retrieve variants from source file in region 17:35346430-35346831. Error was invalid region `17:35346431-35346831`
[2016-04-15T07:46Z] 2016-04-15 00:46:35 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:46:35,277 - WARNING - Could not retrieve variants from source file in region 17:38519080-38519481. Error was invalid region `17:38519081-38519481`
[2016-04-15T07:46Z] 2016-04-15 00:46:38 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:46:38,705 - WARNING - Could not retrieve variants from source file in region 17:33430102-33469469. Error was invalid region `17:33430103-33469469`
[2016-04-15T07:46Z] 2016-04-15 00:46:39 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:46:39,528 - WARNING - Could not retrieve variants from source file in region 17:34431750-34432151. Error was invalid region `17:34431751-34432151`
[2016-04-15T07:46Z] 2016-04-15 00:46:41 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:46:41,628 - WARNING - Could not retrieve variants from source file in region 17:34868939-34872003. Error was invalid region `17:34868940-34872003`
[2016-04-15T07:46Z] 2016-04-15 00:46:44 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:46:44,740 - WARNING - Could not retrieve variants from source file in region 17:34431750-34432151. Error was invalid region `17:34431751-34432151`
[2016-04-15T07:46Z] 2016-04-15 00:46:44 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:46:44,957 - WARNING - Could not retrieve variants from source file in region 17:34868939-34872003. Error was invalid region `17:34868940-34872003`
[2016-04-15T07:46Z] 2016-04-15 00:46:45 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:46:45,017 - WARNING - Could not retrieve variants from source file in region 17:32583058-32583459. Error was invalid region `17:32583059-32583459`
[2016-04-15T07:46Z] 2016-04-15 00:46:45 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:46:45,405 - WARNING - Could not retrieve variants from source file in region 17:33592380-33592781. Error was invalid region `17:33592381-33592781`
[2016-04-15T07:46Z] 2016-04-15 00:46:46 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:46:46,317 - WARNING - Could not retrieve variants from source file in region 17:33592380-33592781. Error was invalid region `17:33592381-33592781`
[2016-04-15T07:46Z] 2016-04-15 00:46:48 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:46:48,122 - WARNING - Could not retrieve variants from source file in region 17:32483026-32483460. Error was invalid region `17:32483027-32483460`
[2016-04-15T07:46Z] 2016-04-15 00:46:49 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:46:49,218 - WARNING - Could not retrieve variants from source file in region 17:34431750-34432151. Error was invalid region `17:34431751-34432151`
[2016-04-15T07:46Z] 2016-04-15 00:46:49 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:46:49,452 - WARNING - Could not retrieve variants from source file in region 17:33592380-33592781. Error was invalid region `17:33592381-33592781`
[2016-04-15T07:46Z] 2016-04-15 00:46:51 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:46:51,735 - WARNING - Could not retrieve variants from source file in region 17:33329939-33330340. Error was invalid region `17:33329940-33330340`
[2016-04-15T07:46Z] 2016-04-15 00:46:52 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:46:52,888 - WARNING - Could not retrieve variants from source file in region 17:38328138-38328539. Error was invalid region `17:38328139-38328539`
[2016-04-15T07:46Z] 2016-04-15 00:46:53 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:46:53,093 - WARNING - Could not retrieve variants from source file in region 17:32583058-32583459. Error was invalid region `17:32583059-32583459`
[2016-04-15T07:46Z] 2016-04-15 00:46:55 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:46:55,213 - WARNING - Could not retrieve variants from source file in region 17:33329939-33330340. Error was invalid region `17:33329940-33330340`
[2016-04-15T07:46Z] 2016-04-15 00:46:55 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:46:55,706 - WARNING - Could not retrieve variants from source file in region 17:32483026-32483460. Error was invalid region `17:32483027-32483460`
[2016-04-15T07:46Z] 2016-04-15 00:46:56 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:46:56,450 - WARNING - Could not retrieve variants from source file in region 17:34328250-34341024. Error was invalid region `17:34328251-34341024`
[2016-04-15T07:46Z] 2016-04-15 00:46:57 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:46:57,638 - WARNING - Could not retrieve variants from source file in region 17:38246075-38246476. Error was invalid region `17:38246076-38246476`
[2016-04-15T07:47Z] 2016-04-15 00:47:00 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:47:00,159 - WARNING - Could not retrieve variants from source file in region 17:38172932-38182640. Error was invalid region `17:38172933-38182640`
[2016-04-15T07:47Z] 2016-04-15 00:47:01 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:47:01,271 - WARNING - Could not retrieve variants from source file in region 17:38246075-38246476. Error was invalid region `17:38246076-38246476`
[2016-04-15T07:47Z] 2016-04-15 00:47:03 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:47:03,226 - WARNING - Could not retrieve variants from source file in region 17:31618340-31619935. Error was invalid region `17:31618341-31619935`
[2016-04-15T07:47Z] ['bcbio-variation-recall', 'square', '-Xms750m', '-Xmx7280m', '-XX:+UseSerialGC', '-c', 16, '-r', u'17:46607690-62121560', '--caller', 'platypus', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/17/Batch1-17_46607689_62121560.vcf.gz', '/mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/17/Batch1-17_46607689_62121560.vcf-inputs.txt'] in region: 17:46607690-62121560
[2016-04-15T07:47Z] 2016-04-15 00:47:20 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:47:20,316 - WARNING - Could not retrieve variants from source file in region 17:60503681-60504111. Error was invalid region `17:60503682-60504111`
[2016-04-15T07:47Z] 2016-04-15 00:47:21 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:47:21,082 - WARNING - Could not retrieve variants from source file in region 17:59885645-59886046. Error was invalid region `17:59885646-59886046`
[2016-04-15T07:47Z] 2016-04-15 00:47:22 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:47:22,056 - WARNING - Could not retrieve variants from source file in region 17:48828173-48828574. Error was invalid region `17:48828174-48828574`
[2016-04-15T07:47Z] 2016-04-15 00:47:23 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:47:23,042 - WARNING - Could not retrieve variants from source file in region 17:57287243-57290573. Error was invalid region `17:57287244-57290573`
[2016-04-15T07:47Z] 2016-04-15 00:47:23 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:47:23,042 - WARNING - Could not retrieve variants from source file in region 17:59955215-59955616. Error was invalid region `17:59955216-59955616`
[2016-04-15T07:47Z] 2016-04-15 00:47:23 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:47:23,682 - WARNING - Could not retrieve variants from source file in region 17:62121269-62121670. Error was invalid region `17:62121270-62121670`
[2016-04-15T07:47Z] 2016-04-15 00:47:23 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:47:23,795 - WARNING - Could not retrieve variants from source file in region 17:60043673-60044074. Error was invalid region `17:60043674-60044074`
[2016-04-15T07:47Z] 2016-04-15 00:47:24 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:47:24,536 - WARNING - Could not retrieve variants from source file in region 17:59760785-59763655. Error was invalid region `17:59760786-59763655`
[2016-04-15T07:47Z] 2016-04-15 00:47:24 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:47:24,599 - WARNING - Could not retrieve variants from source file in region 17:47241393-47247169. Error was invalid region `17:47241394-47247169`
[2016-04-15T07:47Z] 2016-04-15 00:47:24 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:47:24,878 - WARNING - Could not retrieve variants from source file in region 17:60503681-60504111. Error was invalid region `17:60503682-60504111`
[2016-04-15T07:47Z] 2016-04-15 00:47:28 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:47:28,517 - WARNING - Could not retrieve variants from source file in region 17:56060004-56060405. Error was invalid region `17:56060005-56060405`
[2016-04-15T07:47Z] 2016-04-15 00:47:31 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:47:31,486 - WARNING - Could not retrieve variants from source file in region 17:61315061-61315462. Error was invalid region `17:61315062-61315462`
[2016-04-15T07:47Z] 2016-04-15 00:47:31 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:47:31,494 - WARNING - Could not retrieve variants from source file in region 17:59955215-59955616. Error was invalid region `17:59955216-59955616`
[2016-04-15T07:47Z] 2016-04-15 00:47:31 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:47:31,887 - WARNING - Could not retrieve variants from source file in region 17:62121269-62121670. Error was invalid region `17:62121270-62121670`
[2016-04-15T07:47Z] 2016-04-15 00:47:32 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:47:32,371 - WARNING - Could not retrieve variants from source file in region 17:60043673-60044074. Error was invalid region `17:60043674-60044074`
[2016-04-15T07:47Z] 2016-04-15 00:47:32 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:47:32,623 - WARNING - Could not retrieve variants from source file in region 17:59667742-59668211. Error was invalid region `17:59667743-59668211`
[2016-04-15T07:47Z] 2016-04-15 00:47:33 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:47:33,033 - WARNING - Could not retrieve variants from source file in region 17:47241393-47247169. Error was invalid region `17:47241394-47247169`
[2016-04-15T07:47Z] 2016-04-15 00:47:33 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:47:33,260 - WARNING - Could not retrieve variants from source file in region 17:59885645-59886046. Error was invalid region `17:59885646-59886046`
[2016-04-15T07:47Z] 2016-04-15 00:47:33 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:47:33,443 - WARNING - Could not retrieve variants from source file in region 17:61781120-61782174. Error was invalid region `17:61781121-61782174`
[2016-04-15T07:47Z] 2016-04-15 00:47:33 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:47:33,549 - WARNING - Could not retrieve variants from source file in region 17:59760785-59763655. Error was invalid region `17:59760786-59763655`
[2016-04-15T07:47Z] 2016-04-15 00:47:33 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:47:33,571 - WARNING - Could not retrieve variants from source file in region 17:60503681-60504111. Error was invalid region `17:60503682-60504111`
[2016-04-15T07:47Z] 2016-04-15 00:47:33 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:47:33,819 - WARNING - Could not retrieve variants from source file in region 17:56060004-56060405. Error was invalid region `17:56060005-56060405`
[2016-04-15T07:47Z] 2016-04-15 00:47:36 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:47:36,802 - WARNING - Could not retrieve variants from source file in region 17:57287243-57290573. Error was invalid region `17:57287244-57290573`
[2016-04-15T07:47Z] 2016-04-15 00:47:38 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:47:38,391 - WARNING - Could not retrieve variants from source file in region 17:59955215-59955616. Error was invalid region `17:59955216-59955616`
[2016-04-15T07:47Z] 2016-04-15 00:47:38 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:47:38,961 - WARNING - Could not retrieve variants from source file in region 17:62121269-62121670. Error was invalid region `17:62121270-62121670`
[2016-04-15T07:47Z] 2016-04-15 00:47:40 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:47:40,069 - WARNING - Could not retrieve variants from source file in region 17:60043673-60044074. Error was invalid region `17:60043674-60044074`
[2016-04-15T07:47Z] 2016-04-15 00:47:40 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:47:40,786 - WARNING - Could not retrieve variants from source file in region 17:58288210-58288611. Error was invalid region `17:58288211-58288611`
[2016-04-15T07:47Z] 2016-04-15 00:47:41 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:47:41,279 - WARNING - Could not retrieve variants from source file in region 17:47241393-47247169. Error was invalid region `17:47241394-47247169`
[2016-04-15T07:47Z] 2016-04-15 00:47:41 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:47:41,670 - WARNING - Could not retrieve variants from source file in region 17:59533657-59560875. Error was invalid region `17:59533658-59560875`
[2016-04-15T07:47Z] 2016-04-15 00:47:53 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:47:53,297 - WARNING - Could not retrieve variants from source file in region 17:57075893-57076294. Error was invalid region `17:57075894-57076294`
[2016-04-15T07:47Z] 2016-04-15 00:47:53 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:47:53,942 - WARNING - Could not retrieve variants from source file in region 17:48701589-48703942. Error was invalid region `17:48701590-48703942`
[2016-04-15T07:47Z] 2016-04-15 00:47:54 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:47:54,883 - WARNING - Could not retrieve variants from source file in region 17:56540056-56544470. Error was invalid region `17:56540057-56544470`
[2016-04-15T07:47Z] 2016-04-15 00:47:55 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:47:55,715 - WARNING - Could not retrieve variants from source file in region 17:55949853-55951227. Error was invalid region `17:55949854-55951227`
[2016-04-15T07:47Z] 2016-04-15 00:47:57 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:47:57,518 - WARNING - Could not retrieve variants from source file in region 17:58260487-58260888. Error was invalid region `17:58260488-58260888`
[2016-04-15T07:47Z] 2016-04-15 00:47:58 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:47:58,447 - WARNING - Could not retrieve variants from source file in region 17:59485344-59490083. Error was invalid region `17:59485345-59490083`
[2016-04-15T07:47Z] 2016-04-15 00:47:59 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:47:59,226 - WARNING - Could not retrieve variants from source file in region 17:47209955-47210696. Error was invalid region `17:47209956-47210696`
[2016-04-15T07:47Z] 2016-04-15 00:47:59 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:47:59,374 - WARNING - Could not retrieve variants from source file in region 17:58024013-58031602. Error was invalid region `17:58024014-58031602`
[2016-04-15T07:47Z] 2016-04-15 00:47:59 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:47:59,672 - WARNING - Could not retrieve variants from source file in region 17:60813416-60814463. Error was invalid region `17:60813417-60814463`
[2016-04-15T07:48Z] 2016-04-15 00:48:00 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:48:00,393 - WARNING - Could not retrieve variants from source file in region 17:61278018-61278419. Error was invalid region `17:61278019-61278419`
[2016-04-15T07:48Z] 2016-04-15 00:48:00 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:48:00,415 - WARNING - Could not retrieve variants from source file in region 17:48701589-48703942. Error was invalid region `17:48701590-48703942`
[2016-04-15T07:48Z] 2016-04-15 00:48:00 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:48:00,549 - WARNING - Could not retrieve variants from source file in region 17:61660678-61661080. Error was invalid region `17:61660679-61661080`
[2016-04-15T07:48Z] 2016-04-15 00:48:04 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:48:04,550 - WARNING - Could not retrieve variants from source file in region 17:59485344-59490083. Error was invalid region `17:59485345-59490083`
[2016-04-15T07:48Z] 2016-04-15 00:48:06 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:48:06,097 - WARNING - Could not retrieve variants from source file in region 17:56492589-56492990. Error was invalid region `17:56492590-56492990`
[2016-04-15T07:48Z] 2016-04-15 00:48:07 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:48:07,953 - WARNING - Could not retrieve variants from source file in region 17:60813416-60814463. Error was invalid region `17:60813417-60814463`
[2016-04-15T07:48Z] 2016-04-15 00:48:08 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:48:08,658 - WARNING - Could not retrieve variants from source file in region 17:61660678-61661080. Error was invalid region `17:61660679-61661080`
[2016-04-15T07:48Z] 2016-04-15 00:48:08 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:48:08,682 - WARNING - Could not retrieve variants from source file in region 17:61559712-61573951. Error was invalid region `17:61559713-61573951`
[2016-04-15T07:48Z] 2016-04-15 00:48:08 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:48:08,708 - WARNING - Could not retrieve variants from source file in region 17:56540056-56544470. Error was invalid region `17:56540057-56544470`
[2016-04-15T07:48Z] 2016-04-15 00:48:09 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:48:09,109 - WARNING - Could not retrieve variants from source file in region 17:48701589-48703942. Error was invalid region `17:48701590-48703942`
[2016-04-15T07:48Z] 2016-04-15 00:48:09 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:48:09,333 - WARNING - Could not retrieve variants from source file in region 17:58260487-58260888. Error was invalid region `17:58260488-58260888`
[2016-04-15T07:48Z] 2016-04-15 00:48:09 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:48:09,596 - WARNING - Could not retrieve variants from source file in region 17:59485344-59490083. Error was invalid region `17:59485345-59490083`
[2016-04-15T07:48Z] 2016-04-15 00:48:11 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:48:11,345 - WARNING - Could not retrieve variants from source file in region 17:56492589-56492990. Error was invalid region `17:56492590-56492990`
[2016-04-15T07:48Z] 2016-04-15 00:48:13 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:48:13,124 - WARNING - Could not retrieve variants from source file in region 17:58024013-58031602. Error was invalid region `17:58024014-58031602`
[2016-04-15T07:48Z] 2016-04-15 00:48:14 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:48:14,841 - WARNING - Could not retrieve variants from source file in region 17:60813416-60814463. Error was invalid region `17:60813417-60814463`
[2016-04-15T07:48Z] 2016-04-15 00:48:16 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:48:16,197 - WARNING - Could not retrieve variants from source file in region 17:61559712-61573951. Error was invalid region `17:61559713-61573951`
[2016-04-15T07:48Z] 2016-04-15 00:48:16 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:48:16,442 - WARNING - Could not retrieve variants from source file in region 17:61660678-61661080. Error was invalid region `17:61660679-61661080`
[2016-04-15T07:48Z] 2016-04-15 00:48:24 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:48:24,487 - WARNING - Could not retrieve variants from source file in region 17:55709169-55710540. Error was invalid region `17:55709170-55710540`
[2016-04-15T07:48Z] 2016-04-15 00:48:25 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:48:25,678 - WARNING - Could not retrieve variants from source file in region 17:56833246-56833647. Error was invalid region `17:56833247-56833647`
[2016-04-15T07:48Z] 2016-04-15 00:48:26 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:48:26,773 - WARNING - Could not retrieve variants from source file in region 17:60741706-60782662. Error was invalid region `17:60741707-60782662`
[2016-04-15T07:48Z] 2016-04-15 00:48:27 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:48:27,589 - WARNING - Could not retrieve variants from source file in region 17:57951762-57963727. Error was invalid region `17:57951763-57963727`
[2016-04-15T07:48Z] 2016-04-15 00:48:27 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:48:27,718 - WARNING - Could not retrieve variants from source file in region 17:47092041-47092500. Error was invalid region `17:47092042-47092500`
[2016-04-15T07:48Z] 2016-04-15 00:48:28 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:48:28,430 - WARNING - Could not retrieve variants from source file in region 17:59164034-59164435. Error was invalid region `17:59164035-59164435`
[2016-04-15T07:48Z] 2016-04-15 00:48:28 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:48:28,980 - WARNING - Could not retrieve variants from source file in region 17:55709169-55710540. Error was invalid region `17:55709170-55710540`
[2016-04-15T07:48Z] 2016-04-15 00:48:29 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:48:29,458 - WARNING - Could not retrieve variants from source file in region 17:60683292-60683693. Error was invalid region `17:60683293-60683693`
[2016-04-15T07:48Z] 2016-04-15 00:48:31 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:48:31,847 - WARNING - Could not retrieve variants from source file in region 17:56344656-56345057. Error was invalid region `17:56344657-56345057`
[2016-04-15T07:48Z] 2016-04-15 00:48:33 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:48:33,287 - WARNING - Could not retrieve variants from source file in region 17:47092041-47092500. Error was invalid region `17:47092042-47092500`
[2016-04-15T07:48Z] 2016-04-15 00:48:33 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:48:33,838 - WARNING - Could not retrieve variants from source file in region 17:57812520-57812921. Error was invalid region `17:57812521-57812921`
[2016-04-15T07:48Z] 2016-04-15 00:48:33 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:48:33,845 - WARNING - Could not retrieve variants from source file in region 17:61824456-61842598. Error was invalid region `17:61824457-61842598`
[2016-04-15T07:48Z] 2016-04-15 00:48:34 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:48:34,147 - WARNING - Could not retrieve variants from source file in region 17:60683292-60683693. Error was invalid region `17:60683293-60683693`
[2016-04-15T07:48Z] 2016-04-15 00:48:35 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:48:35,316 - WARNING - Could not retrieve variants from source file in region 17:61515201-61515602. Error was invalid region `17:61515202-61515602`
[2016-04-15T07:48Z] 2016-04-15 00:48:38 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:48:38,083 - WARNING - Could not retrieve variants from source file in region 17:57951762-57963727. Error was invalid region `17:57951763-57963727`
[2016-04-15T07:48Z] 2016-04-15 00:48:39 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:48:39,036 - WARNING - Could not retrieve variants from source file in region 17:47092041-47092500. Error was invalid region `17:47092042-47092500`
[2016-04-15T07:48Z] 2016-04-15 00:48:39 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:48:39,594 - WARNING - Could not retrieve variants from source file in region 17:57812520-57812921. Error was invalid region `17:57812521-57812921`
[2016-04-15T07:48Z] 2016-04-15 00:48:39 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:48:39,669 - WARNING - Could not retrieve variants from source file in region 17:61824456-61842598. Error was invalid region `17:61824457-61842598`
[2016-04-15T07:48Z] 2016-04-15 00:48:39 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:48:39,796 - WARNING - Could not retrieve variants from source file in region 17:60683292-60683693. Error was invalid region `17:60683293-60683693`
[2016-04-15T07:48Z] 2016-04-15 00:48:40 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:48:40,555 - WARNING - Could not retrieve variants from source file in region 17:56344656-56345057. Error was invalid region `17:56344657-56345057`
[2016-04-15T07:48Z] 2016-04-15 00:48:42 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:48:42,876 - WARNING - Could not retrieve variants from source file in region 17:55182992-55183906. Error was invalid region `17:55182993-55183906`
[2016-04-15T07:48Z] 2016-04-15 00:48:47 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:48:47,328 - WARNING - Could not retrieve variants from source file in region 17:55182992-55183906. Error was invalid region `17:55182993-55183906`
[2016-04-15T07:48Z] 2016-04-15 00:48:48 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:48:48,608 - WARNING - Could not retrieve variants from source file in region 17:56690637-56691038. Error was invalid region `17:56690638-56691038`
[2016-04-15T07:48Z] 2016-04-15 00:48:50 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:48:50,287 - WARNING - Could not retrieve variants from source file in region 17:56232823-56272580. Error was invalid region `17:56232824-56272580`
[2016-04-15T07:48Z] 2016-04-15 00:48:52 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:48:52,343 - WARNING - Could not retrieve variants from source file in region 17:55182992-55183906. Error was invalid region `17:55182993-55183906`
[2016-04-15T07:48Z] 2016-04-15 00:48:53 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:48:53,328 - WARNING - Could not retrieve variants from source file in region 17:47000040-47039322. Error was invalid region `17:47000041-47039322`
[2016-04-15T07:48Z] 2016-04-15 00:48:53 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:48:53,442 - WARNING - Could not retrieve variants from source file in region 17:58824356-58824757. Error was invalid region `17:58824357-58824757`
[2016-04-15T07:48Z] 2016-04-15 00:48:55 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:48:55,142 - WARNING - Could not retrieve variants from source file in region 17:53899966-53900367. Error was invalid region `17:53899967-53900367`
[2016-04-15T07:48Z] 2016-04-15 00:48:55 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:48:55,195 - WARNING - Could not retrieve variants from source file in region 17:48355757-48356450. Error was invalid region `17:48355758-48356450`
[2016-04-15T07:48Z] 2016-04-15 00:48:55 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:48:55,205 - WARNING - Could not retrieve variants from source file in region 17:48538824-48559749. Error was invalid region `17:48538825-48559749`
[2016-04-15T07:48Z] 2016-04-15 00:48:55 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:48:55,243 - WARNING - Could not retrieve variants from source file in region 17:47888641-47903571. Error was invalid region `17:47888642-47903571`
[2016-04-15T07:48Z] 2016-04-15 00:48:55 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:48:55,279 - WARNING - Could not retrieve variants from source file in region 17:56232823-56272580. Error was invalid region `17:56232824-56272580`
[2016-04-15T07:48Z] 2016-04-15 00:48:55 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:48:55,281 - WARNING - Could not retrieve variants from source file in region 17:58786414-58786815. Error was invalid region `17:58786415-58786815`
[2016-04-15T07:48Z] 2016-04-15 00:48:57 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:48:57,765 - WARNING - Could not retrieve variants from source file in region 17:47000040-47039322. Error was invalid region `17:47000041-47039322`
[2016-04-15T07:48Z] 2016-04-15 00:48:58 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:48:58,263 - WARNING - Could not retrieve variants from source file in region 17:58824356-58824757. Error was invalid region `17:58824357-58824757`
[2016-04-15T07:48Z] 2016-04-15 00:48:59 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:48:59,619 - WARNING - Could not retrieve variants from source file in region 17:46894166-46894567. Error was invalid region `17:46894167-46894567`
[2016-04-15T07:49Z] 2016-04-15 00:49:00 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:49:00,384 - WARNING - Could not retrieve variants from source file in region 17:58786414-58786815. Error was invalid region `17:58786415-58786815`
[2016-04-15T07:49Z] 2016-04-15 00:49:02 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:49:02,695 - WARNING - Could not retrieve variants from source file in region 17:47000040-47039322. Error was invalid region `17:47000041-47039322`
[2016-04-15T07:49Z] 2016-04-15 00:49:03 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:49:03,128 - WARNING - Could not retrieve variants from source file in region 17:58824356-58824757. Error was invalid region `17:58824357-58824757`
[2016-04-15T07:49Z] 2016-04-15 00:49:06 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:49:06,049 - WARNING - Could not retrieve variants from source file in region 17:55079260-55079661. Error was invalid region `17:55079261-55079661`
[2016-04-15T07:49Z] 2016-04-15 00:49:06 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:49:06,121 - WARNING - Could not retrieve variants from source file in region 17:47888641-47903571. Error was invalid region `17:47888642-47903571`
[2016-04-15T07:49Z] 2016-04-15 00:49:06 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:49:06,664 - WARNING - Could not retrieve variants from source file in region 17:58786414-58786815. Error was invalid region `17:58786415-58786815`
[2016-04-15T07:49Z] 2016-04-15 00:49:06 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:49:06,795 - WARNING - Could not retrieve variants from source file in region 17:48538824-48559749. Error was invalid region `17:48538825-48559749`
[2016-04-15T07:49Z] 2016-04-15 00:49:06 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:49:06,851 - WARNING - Could not retrieve variants from source file in region 17:53899966-53900367. Error was invalid region `17:53899967-53900367`
[2016-04-15T07:49Z] 2016-04-15 00:49:09 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:49:09,309 - WARNING - Could not retrieve variants from source file in region 17:54921283-54921684. Error was invalid region `17:54921284-54921684`
[2016-04-15T07:49Z] 2016-04-15 00:49:09 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:49:09,578 - WARNING - Could not retrieve variants from source file in region 17:55027639-55028040. Error was invalid region `17:55027640-55028040`
[2016-04-15T07:49Z] 2016-04-15 00:49:11 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:49:11,218 - WARNING - Could not retrieve variants from source file in region 17:55079260-55079661. Error was invalid region `17:55079261-55079661`
[2016-04-15T07:49Z] 2016-04-15 00:49:14 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:49:14,891 - WARNING - Could not retrieve variants from source file in region 17:54921283-54921684. Error was invalid region `17:54921284-54921684`
[2016-04-15T07:49Z] 2016-04-15 00:49:15 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:49:15,492 - WARNING - Could not retrieve variants from source file in region 17:55027639-55028040. Error was invalid region `17:55027640-55028040`
[2016-04-15T07:49Z] 2016-04-15 00:49:15 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:49:15,787 - WARNING - Could not retrieve variants from source file in region 17:54978583-54978984. Error was invalid region `17:54978584-54978984`
[2016-04-15T07:49Z] 2016-04-15 00:49:17 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:49:17,292 - WARNING - Could not retrieve variants from source file in region 17:46926404-46926805. Error was invalid region `17:46926405-46926805`
[2016-04-15T07:49Z] 2016-04-15 00:49:17 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:49:17,899 - WARNING - Could not retrieve variants from source file in region 17:55027639-55028040. Error was invalid region `17:55027640-55028040`
[2016-04-15T07:49Z] 2016-04-15 00:49:19 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:49:19,876 - WARNING - Could not retrieve variants from source file in region 17:54921283-54921684. Error was invalid region `17:54921284-54921684`
[2016-04-15T07:49Z] 2016-04-15 00:49:20 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:49:20,275 - WARNING - Could not retrieve variants from source file in region 17:54978583-54978984. Error was invalid region `17:54978584-54978984`
[2016-04-15T07:49Z] 2016-04-15 00:49:21 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:49:21,268 - WARNING - Could not retrieve variants from source file in region 17:53828467-53854331. Error was invalid region `17:53828468-53854331`
[2016-04-15T07:49Z] 2016-04-15 00:49:21 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:49:21,919 - WARNING - Could not retrieve variants from source file in region 17:46847153-46847554. Error was invalid region `17:46847154-46847554`
[2016-04-15T07:49Z] 2016-04-15 00:49:22 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:49:22,409 - WARNING - Could not retrieve variants from source file in region 17:53038443-53039673. Error was invalid region `17:53038444-53039673`
[2016-04-15T07:49Z] 2016-04-15 00:49:22 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:49:22,460 - WARNING - Could not retrieve variants from source file in region 17:46926404-46926805. Error was invalid region `17:46926405-46926805`
[2016-04-15T07:49Z] 2016-04-15 00:49:23 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:49:23,332 - WARNING - Could not retrieve variants from source file in region 17:47293695-47297487. Error was invalid region `17:47293696-47297487`
[2016-04-15T07:49Z] 2016-04-15 00:49:24 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:49:24,213 - WARNING - Could not retrieve variants from source file in region 17:47293695-47297487. Error was invalid region `17:47293696-47297487`
[2016-04-15T07:49Z] 2016-04-15 00:49:24 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:49:24,393 - WARNING - Could not retrieve variants from source file in region 17:54978583-54978984. Error was invalid region `17:54978584-54978984`
[2016-04-15T07:49Z] 2016-04-15 00:49:25 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:49:25,638 - WARNING - Could not retrieve variants from source file in region 17:48149175-48175098. Error was invalid region `17:48149176-48175098`
[2016-04-15T07:49Z] 2016-04-15 00:49:26 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:49:26,755 - WARNING - Could not retrieve variants from source file in region 17:46926404-46926805. Error was invalid region `17:46926405-46926805`
[2016-04-15T07:49Z] 2016-04-15 00:49:29 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:49:29,610 - WARNING - Could not retrieve variants from source file in region 17:48149175-48175098. Error was invalid region `17:48149176-48175098`
[2016-04-15T07:49Z] 2016-04-15 00:49:29 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:49:29,806 - WARNING - Could not retrieve variants from source file in region 17:53828467-53854331. Error was invalid region `17:53828468-53854331`
[2016-04-15T07:49Z] 2016-04-15 00:49:30 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:49:30,719 - WARNING - Could not retrieve variants from source file in region 17:49337782-49338447. Error was invalid region `17:49337783-49338447`
[2016-04-15T07:49Z] 2016-04-15 00:49:30 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:49:30,944 - WARNING - Could not retrieve variants from source file in region 17:54534423-54534824. Error was invalid region `17:54534424-54534824`
[2016-04-15T07:49Z] 2016-04-15 00:49:31 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:49:31,777 - WARNING - Could not retrieve variants from source file in region 17:54534423-54534824. Error was invalid region `17:54534424-54534824`
[2016-04-15T07:49Z] 2016-04-15 00:49:35 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:49:35,398 - WARNING - Could not retrieve variants from source file in region 17:54534423-54534824. Error was invalid region `17:54534424-54534824`
[2016-04-15T07:49Z] 2016-04-15 00:49:35 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:49:35,770 - WARNING - Could not retrieve variants from source file in region 17:49257735-49280296. Error was invalid region `17:49257736-49280296`
[2016-04-15T07:49Z] 2016-04-15 00:49:35 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:49:35,810 - WARNING - Could not retrieve variants from source file in region 17:53158281-53158682. Error was invalid region `17:53158282-53158682`
[2016-04-15T07:49Z] 2016-04-15 00:49:36 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:49:36,016 - WARNING - Could not retrieve variants from source file in region 17:54449827-54450324. Error was invalid region `17:54449828-54450324`
[2016-04-15T07:49Z] 2016-04-15 00:49:36 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:49:36,237 - WARNING - Could not retrieve variants from source file in region 17:46713860-46714261. Error was invalid region `17:46713861-46714261`
[2016-04-15T07:49Z] 2016-04-15 00:49:38 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:49:38,357 - WARNING - Could not retrieve variants from source file in region 17:46801797-46805780. Error was invalid region `17:46801798-46805780`
[2016-04-15T07:49Z] 2016-04-15 00:49:38 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:49:38,442 - WARNING - Could not retrieve variants from source file in region 17:51900518-51902442. Error was invalid region `17:51900519-51902442`
[2016-04-15T07:49Z] 2016-04-15 00:49:40 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:49:40,332 - WARNING - Could not retrieve variants from source file in region 17:54449827-54450324. Error was invalid region `17:54449828-54450324`
[2016-04-15T07:49Z] 2016-04-15 00:49:40 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:49:40,461 - WARNING - Could not retrieve variants from source file in region 17:46713860-46714261. Error was invalid region `17:46713861-46714261`
[2016-04-15T07:49Z] 2016-04-15 00:49:41 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:49:41,471 - WARNING - Could not retrieve variants from source file in region 17:53120809-53121210. Error was invalid region `17:53120810-53121210`
[2016-04-15T07:49Z] 2016-04-15 00:49:41 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:49:41,532 - WARNING - Could not retrieve variants from source file in region 17:48917122-48940612. Error was invalid region `17:48917123-48940612`
[2016-04-15T07:49Z] 2016-04-15 00:49:42 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:49:42,975 - WARNING - Could not retrieve variants from source file in region 17:54449827-54450324. Error was invalid region `17:54449828-54450324`
[2016-04-15T07:49Z] 2016-04-15 00:49:44 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:49:44,205 - WARNING - Could not retrieve variants from source file in region 17:46713860-46714261. Error was invalid region `17:46713861-46714261`
[2016-04-15T07:49Z] 2016-04-15 00:49:45 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:49:45,142 - WARNING - Could not retrieve variants from source file in region 17:48917122-48940612. Error was invalid region `17:48917123-48940612`
[2016-04-15T07:49Z] 2016-04-15 00:49:45 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:49:45,634 - WARNING - Could not retrieve variants from source file in region 17:51900518-51902442. Error was invalid region `17:51900519-51902442`
[2016-04-15T07:49Z] 2016-04-15 00:49:48 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:49:48,388 - WARNING - Could not retrieve variants from source file in region 17:48917122-48940612. Error was invalid region `17:48917123-48940612`
[2016-04-15T07:49Z] 2016-04-15 00:49:50 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:49:50,279 - WARNING - Could not retrieve variants from source file in region 17:53076588-53077176. Error was invalid region `17:53076589-53077176`
[2016-04-15T07:49Z] 2016-04-15 00:49:52 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:49:52,351 - WARNING - Could not retrieve variants from source file in region 17:46670309-46688446. Error was invalid region `17:46670310-46688446`
[2016-04-15T07:49Z] 2016-04-15 00:49:52 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:49:52,464 - WARNING - Could not retrieve variants from source file in region 17:46621484-46629783. Error was invalid region `17:46621485-46629783`
[2016-04-15T07:49Z] 2016-04-15 00:49:53 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:49:53,316 - WARNING - Could not retrieve variants from source file in region 17:53076588-53077176. Error was invalid region `17:53076589-53077176`
[2016-04-15T07:49Z] 2016-04-15 00:49:54 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:49:54,317 - WARNING - Could not retrieve variants from source file in region 17:53076588-53077176. Error was invalid region `17:53076589-53077176`
[2016-04-15T07:49Z] 2016-04-15 00:49:54 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:49:54,537 - WARNING - Could not retrieve variants from source file in region 17:49713089-49713490. Error was invalid region `17:49713090-49713490`
[2016-04-15T07:49Z] 2016-04-15 00:49:54 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:49:54,573 - WARNING - Could not retrieve variants from source file in region 17:46621484-46629783. Error was invalid region `17:46621485-46629783`
[2016-04-15T07:49Z] 2016-04-15 00:49:54 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:49:54,636 - WARNING - Could not retrieve variants from source file in region 17:46621484-46629783. Error was invalid region `17:46621485-46629783`
[2016-04-15T07:49Z] 2016-04-15 00:49:55 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:49:55,426 - WARNING - Could not retrieve variants from source file in region 17:49713089-49713490. Error was invalid region `17:49713090-49713490`
[2016-04-15T07:49Z] 2016-04-15 00:49:55 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:49:55,589 - WARNING - Could not retrieve variants from source file in region 17:46670309-46688446. Error was invalid region `17:46670310-46688446`
[2016-04-15T07:49Z] 2016-04-15 00:49:57 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:49:57,947 - WARNING - Could not retrieve variants from source file in region 17:46670309-46688446. Error was invalid region `17:46670310-46688446`
[2016-04-15T07:50Z] ['bcbio-variation-recall', 'square', '-Xms750m', '-Xmx7280m', '-XX:+UseSerialGC', '-c', 16, '-r', u'17:62122220-77705154', '--caller', 'platypus', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/17/Batch1-17_62122219_77705154.vcf.gz', '/mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/17/Batch1-17_62122219_77705154.vcf-inputs.txt'] in region: 17:62122220-77705154
[2016-04-15T07:50Z] 2016-04-15 00:50:12 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:50:12,045 - WARNING - Could not retrieve variants from source file in region 17:66985781-66986182. Error was invalid region `17:66985782-66986182`
[2016-04-15T07:50Z] 2016-04-15 00:50:13 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:50:13,070 - WARNING - Could not retrieve variants from source file in region 17:73127472-73127873. Error was invalid region `17:73127473-73127873`
[2016-04-15T07:50Z] 2016-04-15 00:50:13 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:50:13,260 - WARNING - Could not retrieve variants from source file in region 17:66448911-66449312. Error was invalid region `17:66448912-66449312`
[2016-04-15T07:50Z] 2016-04-15 00:50:14 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:50:14,253 - WARNING - Could not retrieve variants from source file in region 17:66244367-66267881. Error was invalid region `17:66244368-66267881`
[2016-04-15T07:50Z] 2016-04-15 00:50:14 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:50:14,805 - WARNING - Could not retrieve variants from source file in region 17:72245890-72249419. Error was invalid region `17:72245891-72249419`
[2016-04-15T07:50Z] 2016-04-15 00:50:15 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:50:15,316 - WARNING - Could not retrieve variants from source file in region 17:72773583-72785122. Error was invalid region `17:72773584-72785122`
[2016-04-15T07:50Z] 2016-04-15 00:50:16 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:50:16,480 - WARNING - Could not retrieve variants from source file in region 17:65211831-65212232. Error was invalid region `17:65211832-65212232`
[2016-04-15T07:50Z] 2016-04-15 00:50:16 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:50:16,514 - WARNING - Could not retrieve variants from source file in region 17:65052093-65052494. Error was invalid region `17:65052094-65052494`
[2016-04-15T07:50Z] 2016-04-15 00:50:16 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:50:16,518 - WARNING - Could not retrieve variants from source file in region 17:75400979-75401380. Error was invalid region `17:75400980-75401380`
[2016-04-15T07:50Z] 2016-04-15 00:50:17 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:50:17,275 - WARNING - Could not retrieve variants from source file in region 17:66985781-66986182. Error was invalid region `17:66985782-66986182`
[2016-04-15T07:50Z] 2016-04-15 00:50:18 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:50:18,083 - WARNING - Could not retrieve variants from source file in region 17:73127472-73127873. Error was invalid region `17:73127473-73127873`
[2016-04-15T07:50Z] 2016-04-15 00:50:19 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:50:19,059 - WARNING - Could not retrieve variants from source file in region 17:66448911-66449312. Error was invalid region `17:66448912-66449312`
[2016-04-15T07:50Z] 2016-04-15 00:50:21 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:50:21,238 - WARNING - Could not retrieve variants from source file in region 17:66244367-66267881. Error was invalid region `17:66244368-66267881`
[2016-04-15T07:50Z] 2016-04-15 00:50:21 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:50:21,827 - WARNING - Could not retrieve variants from source file in region 17:74056202-74077987. Error was invalid region `17:74056203-74077987`
[2016-04-15T07:50Z] 2016-04-15 00:50:22 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:50:22,126 - WARNING - Could not retrieve variants from source file in region 17:72773583-72785122. Error was invalid region `17:72773584-72785122`
[2016-04-15T07:50Z] 2016-04-15 00:50:23 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:50:23,445 - WARNING - Could not retrieve variants from source file in region 17:66985781-66986182. Error was invalid region `17:66985782-66986182`
[2016-04-15T07:50Z] 2016-04-15 00:50:23 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:50:23,802 - WARNING - Could not retrieve variants from source file in region 17:73127472-73127873. Error was invalid region `17:73127473-73127873`
[2016-04-15T07:50Z] 2016-04-15 00:50:24 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:50:24,073 - WARNING - Could not retrieve variants from source file in region 17:66448911-66449312. Error was invalid region `17:66448912-66449312`
[2016-04-15T07:50Z] 2016-04-15 00:50:26 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:50:26,223 - WARNING - Could not retrieve variants from source file in region 17:66244367-66267881. Error was invalid region `17:66244368-66267881`
[2016-04-15T07:50Z] 2016-04-15 00:50:27 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:50:27,219 - WARNING - Could not retrieve variants from source file in region 17:74056202-74077987. Error was invalid region `17:74056203-74077987`
[2016-04-15T07:50Z] 2016-04-15 00:50:27 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:50:27,240 - WARNING - Could not retrieve variants from source file in region 17:72245890-72249419. Error was invalid region `17:72245891-72249419`
[2016-04-15T07:50Z] 2016-04-15 00:50:29 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:50:29,445 - WARNING - Could not retrieve variants from source file in region 17:65211831-65212232. Error was invalid region `17:65211832-65212232`
[2016-04-15T07:50Z] 2016-04-15 00:50:30 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:50:30,502 - WARNING - Could not retrieve variants from source file in region 17:75400979-75401380. Error was invalid region `17:75400980-75401380`
[2016-04-15T07:50Z] 2016-04-15 00:50:30 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:50:30,517 - WARNING - Could not retrieve variants from source file in region 17:65052093-65052494. Error was invalid region `17:65052094-65052494`
[2016-04-15T07:50Z] 2016-04-15 00:50:40 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:50:40,695 - WARNING - Could not retrieve variants from source file in region 17:66364480-66364994. Error was invalid region `17:66364481-66364994`
[2016-04-15T07:50Z] 2016-04-15 00:50:43 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:50:43,240 - WARNING - Could not retrieve variants from source file in region 17:73089641-73101394. Error was invalid region `17:73089642-73101394`
[2016-04-15T07:50Z] 2016-04-15 00:50:43 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:50:43,543 - WARNING - Could not retrieve variants from source file in region 17:73997263-74014858. Error was invalid region `17:73997264-74014858`
[2016-04-15T07:50Z] 2016-04-15 00:50:43 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:50:43,625 - WARNING - Could not retrieve variants from source file in region 17:66202070-66202471. Error was invalid region `17:66202071-66202471`
[2016-04-15T07:50Z] 2016-04-15 00:50:44 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:50:44,054 - WARNING - Could not retrieve variants from source file in region 17:72691717-72701133. Error was invalid region `17:72691718-72701133`
[2016-04-15T07:50Z] 2016-04-15 00:50:45 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:50:45,247 - WARNING - Could not retrieve variants from source file in region 17:71746517-71747587. Error was invalid region `17:71746518-71747587`
[2016-04-15T07:50Z] 2016-04-15 00:50:45 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:50:45,604 - WARNING - Could not retrieve variants from source file in region 17:65104455-65105509. Error was invalid region `17:65104456-65105509`
[2016-04-15T07:50Z] 2016-04-15 00:50:46 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:50:46,573 - WARNING - Could not retrieve variants from source file in region 17:65014149-65014550. Error was invalid region `17:65014150-65014550`
[2016-04-15T07:50Z] 2016-04-15 00:50:47 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:50:47,912 - WARNING - Could not retrieve variants from source file in region 17:75369367-75372529. Error was invalid region `17:75369368-75372529`
[2016-04-15T07:50Z] 2016-04-15 00:50:47 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:50:47,981 - WARNING - Could not retrieve variants from source file in region 17:76395219-76395620. Error was invalid region `17:76395220-76395620`
[2016-04-15T07:50Z] 2016-04-15 00:50:48 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:50:48,451 - WARNING - Could not retrieve variants from source file in region 17:73089641-73101394. Error was invalid region `17:73089642-73101394`
[2016-04-15T07:50Z] 2016-04-15 00:50:49 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:50:49,384 - WARNING - Could not retrieve variants from source file in region 17:73997263-74014858. Error was invalid region `17:73997264-74014858`
[2016-04-15T07:50Z] 2016-04-15 00:50:49 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:50:49,545 - WARNING - Could not retrieve variants from source file in region 17:66202070-66202471. Error was invalid region `17:66202071-66202471`
[2016-04-15T07:50Z] 2016-04-15 00:50:49 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:50:49,600 - WARNING - Could not retrieve variants from source file in region 17:67210781-67215902. Error was invalid region `17:67210782-67215902`
[2016-04-15T07:50Z] 2016-04-15 00:50:50 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:50:50,352 - WARNING - Could not retrieve variants from source file in region 17:77039917-77042908. Error was invalid region `17:77039918-77042908`
[2016-04-15T07:50Z] 2016-04-15 00:50:50 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:50:50,357 - WARNING - Could not retrieve variants from source file in region 17:72691717-72701133. Error was invalid region `17:72691718-72701133`
[2016-04-15T07:50Z] 2016-04-15 00:50:52 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:50:52,349 - WARNING - Could not retrieve variants from source file in region 17:66364480-66364994. Error was invalid region `17:66364481-66364994`
[2016-04-15T07:50Z] 2016-04-15 00:50:52 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:50:52,931 - WARNING - Could not retrieve variants from source file in region 17:74524915-74525621. Error was invalid region `17:74524916-74525621`
[2016-04-15T07:50Z] 2016-04-15 00:50:53 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:50:53,170 - WARNING - Could not retrieve variants from source file in region 17:76395219-76395620. Error was invalid region `17:76395220-76395620`
[2016-04-15T07:50Z] 2016-04-15 00:50:53 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:50:53,378 - WARNING - Could not retrieve variants from source file in region 17:75369367-75372529. Error was invalid region `17:75369368-75372529`
[2016-04-15T07:50Z] 2016-04-15 00:50:54 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:50:54,741 - WARNING - Could not retrieve variants from source file in region 17:66202070-66202471. Error was invalid region `17:66202071-66202471`
[2016-04-15T07:50Z] 2016-04-15 00:50:54 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:50:54,839 - WARNING - Could not retrieve variants from source file in region 17:73997263-74014858. Error was invalid region `17:73997264-74014858`
[2016-04-15T07:50Z] 2016-04-15 00:50:55 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:50:55,816 - WARNING - Could not retrieve variants from source file in region 17:72691717-72701133. Error was invalid region `17:72691718-72701133`
[2016-04-15T07:50Z] 2016-04-15 00:50:56 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:50:56,345 - WARNING - Could not retrieve variants from source file in region 17:77039917-77042908. Error was invalid region `17:77039918-77042908`
[2016-04-15T07:50Z] 2016-04-15 00:50:57 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:50:57,007 - WARNING - Could not retrieve variants from source file in region 17:71746517-71747587. Error was invalid region `17:71746518-71747587`
[2016-04-15T07:50Z] 2016-04-15 00:50:58 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:50:58,193 - WARNING - Could not retrieve variants from source file in region 17:65014149-65014550. Error was invalid region `17:65014150-65014550`
[2016-04-15T07:50Z] 2016-04-15 00:50:58 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:50:58,875 - WARNING - Could not retrieve variants from source file in region 17:64023413-64025521. Error was invalid region `17:64023414-64025521`
[2016-04-15T07:50Z] 2016-04-15 00:50:59 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:50:59,313 - WARNING - Could not retrieve variants from source file in region 17:75369367-75372529. Error was invalid region `17:75369368-75372529`
[2016-04-15T07:50Z] 2016-04-15 00:50:59 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:50:59,910 - WARNING - Could not retrieve variants from source file in region 17:76395219-76395620. Error was invalid region `17:76395220-76395620`
[2016-04-15T07:51Z] 2016-04-15 00:51:00 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:51:00,743 - WARNING - Could not retrieve variants from source file in region 17:67210781-67215902. Error was invalid region `17:67210782-67215902`
[2016-04-15T07:51Z] 2016-04-15 00:51:08 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:51:08,121 - WARNING - Could not retrieve variants from source file in region 17:67178105-67178506. Error was invalid region `17:67178106-67178506`
[2016-04-15T07:51Z] 2016-04-15 00:51:08 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:51:08,150 - WARNING - Could not retrieve variants from source file in region 17:66039139-66039540. Error was invalid region `17:66039140-66039540`
[2016-04-15T07:51Z] 2016-04-15 00:51:09 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:51:09,288 - WARNING - Could not retrieve variants from source file in region 17:74474813-74476165. Error was invalid region `17:74474814-74476165`
[2016-04-15T07:51Z] 2016-04-15 00:51:10 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:51:10,191 - WARNING - Could not retrieve variants from source file in region 17:65977471-65989238. Error was invalid region `17:65977472-65989238`
[2016-04-15T07:51Z] 2016-04-15 00:51:11 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:51:11,461 - WARNING - Could not retrieve variants from source file in region 17:76970668-76973439. Error was invalid region `17:76970669-76973439`
[2016-04-15T07:51Z] 2016-04-15 00:51:11 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:51:11,612 - WARNING - Could not retrieve variants from source file in region 17:71503425-71503826. Error was invalid region `17:71503426-71503826`
[2016-04-15T07:51Z] 2016-04-15 00:51:12 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:51:12,903 - WARNING - Could not retrieve variants from source file in region 17:66596252-66596653. Error was invalid region `17:66596253-66596653`
[2016-04-15T07:51Z] 2016-04-15 00:51:13 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:51:13,558 - WARNING - Could not retrieve variants from source file in region 17:67178105-67178506. Error was invalid region `17:67178106-67178506`
[2016-04-15T07:51Z] 2016-04-15 00:51:13 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:51:13,833 - WARNING - Could not retrieve variants from source file in region 17:66039139-66039540. Error was invalid region `17:66039140-66039540`
[2016-04-15T07:51Z] 2016-04-15 00:51:13 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:51:13,933 - WARNING - Could not retrieve variants from source file in region 17:63533557-63554781. Error was invalid region `17:63533558-63554781`
[2016-04-15T07:51Z] 2016-04-15 00:51:15 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:51:15,017 - WARNING - Could not retrieve variants from source file in region 17:74474813-74476165. Error was invalid region `17:74474814-74476165`
[2016-04-15T07:51Z] 2016-04-15 00:51:16 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:51:16,116 - WARNING - Could not retrieve variants from source file in region 17:65977471-65989238. Error was invalid region `17:65977472-65989238`
[2016-04-15T07:51Z] 2016-04-15 00:51:16 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:51:16,395 - WARNING - Could not retrieve variants from source file in region 17:67056958-67126030. Error was invalid region `17:67056959-67126030`
[2016-04-15T07:51Z] 2016-04-15 00:51:16 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:51:16,977 - WARNING - Could not retrieve variants from source file in region 17:71503425-71503826. Error was invalid region `17:71503426-71503826`
[2016-04-15T07:51Z] 2016-04-15 00:51:17 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:51:17,706 - WARNING - Could not retrieve variants from source file in region 17:66596252-66596653. Error was invalid region `17:66596253-66596653`
[2016-04-15T07:51Z] 2016-04-15 00:51:18 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:51:18,888 - WARNING - Could not retrieve variants from source file in region 17:67178105-67178506. Error was invalid region `17:67178106-67178506`
[2016-04-15T07:51Z] 2016-04-15 00:51:19 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:51:19,425 - WARNING - Could not retrieve variants from source file in region 17:63533557-63554781. Error was invalid region `17:63533558-63554781`
[2016-04-15T07:51Z] 2016-04-15 00:51:19 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:51:19,427 - WARNING - Could not retrieve variants from source file in region 17:66039139-66039540. Error was invalid region `17:66039140-66039540`
[2016-04-15T07:51Z] 2016-04-15 00:51:21 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:51:21,304 - WARNING - Could not retrieve variants from source file in region 17:74474813-74476165. Error was invalid region `17:74474814-74476165`
[2016-04-15T07:51Z] 2016-04-15 00:51:21 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:51:21,562 - WARNING - Could not retrieve variants from source file in region 17:72999562-73016811. Error was invalid region `17:72999563-73016811`
[2016-04-15T07:51Z] 2016-04-15 00:51:22 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:51:22,900 - WARNING - Could not retrieve variants from source file in region 17:67056958-67126030. Error was invalid region `17:67056959-67126030`
[2016-04-15T07:51Z] 2016-04-15 00:51:23 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:51:23,395 - WARNING - Could not retrieve variants from source file in region 17:71503425-71503826. Error was invalid region `17:71503426-71503826`
[2016-04-15T07:51Z] 2016-04-15 00:51:23 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:51:23,490 - WARNING - Could not retrieve variants from source file in region 17:65977471-65989238. Error was invalid region `17:65977472-65989238`
[2016-04-15T07:51Z] 2016-04-15 00:51:24 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:51:24,699 - WARNING - Could not retrieve variants from source file in region 17:63533557-63554781. Error was invalid region `17:63533558-63554781`
[2016-04-15T07:51Z] 2016-04-15 00:51:28 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:51:28,423 - WARNING - Could not retrieve variants from source file in region 17:67056958-67126030. Error was invalid region `17:67056959-67126030`
[2016-04-15T07:51Z] 2016-04-15 00:51:33 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:51:33,694 - WARNING - Could not retrieve variants from source file in region 17:74381344-74387474. Error was invalid region `17:74381345-74387474`
[2016-04-15T07:51Z] 2016-04-15 00:51:33 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:51:33,912 - WARNING - Could not retrieve variants from source file in region 17:67023313-67031647. Error was invalid region `17:67023314-67031647`
[2016-04-15T07:51Z] 2016-04-15 00:51:34 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:51:34,753 - WARNING - Could not retrieve variants from source file in region 17:65739416-65739817. Error was invalid region `17:65739417-65739817`
[2016-04-15T07:51Z] 2016-04-15 00:51:36 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:51:36,021 - WARNING - Could not retrieve variants from source file in region 17:72926912-72952207. Error was invalid region `17:72926913-72952207`
[2016-04-15T07:51Z] 2016-04-15 00:51:40 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:51:40,299 - WARNING - Could not retrieve variants from source file in region 17:71468056-71468457. Error was invalid region `17:71468057-71468457`
[2016-04-15T07:51Z] 2016-04-15 00:51:40 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:51:40,640 - WARNING - Could not retrieve variants from source file in region 17:63189476-63189877. Error was invalid region `17:63189477-63189877`
[2016-04-15T07:51Z] 2016-04-15 00:51:40 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:51:40,828 - WARNING - Could not retrieve variants from source file in region 17:65739416-65739817. Error was invalid region `17:65739417-65739817`
[2016-04-15T07:51Z] 2016-04-15 00:51:40 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:51:40,886 - WARNING - Could not retrieve variants from source file in region 17:76887221-76887622. Error was invalid region `17:76887222-76887622`
[2016-04-15T07:51Z] 2016-04-15 00:51:41 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:51:41,471 - WARNING - Could not retrieve variants from source file in region 17:73789882-73836352. Error was invalid region `17:73789883-73836352`
[2016-04-15T07:51Z] 2016-04-15 00:51:46 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:51:46,224 - WARNING - Could not retrieve variants from source file in region 17:74381344-74387474. Error was invalid region `17:74381345-74387474`
[2016-04-15T07:51Z] 2016-04-15 00:51:47 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:51:47,077 - WARNING - Could not retrieve variants from source file in region 17:76082812-76094058. Error was invalid region `17:76082813-76094058`
[2016-04-15T07:51Z] 2016-04-15 00:51:47 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:51:47,517 - WARNING - Could not retrieve variants from source file in region 17:74920918-74942668. Error was invalid region `17:74920919-74942668`
[2016-04-15T07:51Z] 2016-04-15 00:51:48 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:51:48,138 - WARNING - Could not retrieve variants from source file in region 17:65739416-65739817. Error was invalid region `17:65739417-65739817`
[2016-04-15T07:51Z] 2016-04-15 00:51:48 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:51:48,177 - WARNING - Could not retrieve variants from source file in region 17:74729553-74733289. Error was invalid region `17:74729554-74733289`
[2016-04-15T07:51Z] 2016-04-15 00:51:51 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:51:51,980 - WARNING - Could not retrieve variants from source file in region 17:76082812-76094058. Error was invalid region `17:76082813-76094058`
[2016-04-15T07:51Z] 2016-04-15 00:51:54 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:51:54,591 - WARNING - Could not retrieve variants from source file in region 17:74729553-74733289. Error was invalid region `17:74729554-74733289`
[2016-04-15T07:51Z] 2016-04-15 00:51:55 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:51:55,120 - WARNING - Could not retrieve variants from source file in region 17:73688083-73688484. Error was invalid region `17:73688084-73688484`
[2016-04-15T07:52Z] 2016-04-15 00:52:01 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:52:01,232 - WARNING - Could not retrieve variants from source file in region 17:73688083-73688484. Error was invalid region `17:73688084-73688484`
[2016-04-15T07:52Z] 2016-04-15 00:52:01 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:52:01,319 - WARNING - Could not retrieve variants from source file in region 17:71232476-71241834. Error was invalid region `17:71232477-71241834`
[2016-04-15T07:52Z] 2016-04-15 00:52:03 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:52:03,180 - WARNING - Could not retrieve variants from source file in region 17:75494494-75494895. Error was invalid region `17:75494495-75494895`
[2016-04-15T07:52Z] 2016-04-15 00:52:06 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:52:06,004 - WARNING - Could not retrieve variants from source file in region 17:73688083-73688484. Error was invalid region `17:73688084-73688484`
[2016-04-15T07:52Z] 2016-04-15 00:52:06 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:52:06,731 - WARNING - Could not retrieve variants from source file in region 17:73625075-73647329. Error was invalid region `17:73625076-73647329`
[2016-04-15T07:52Z] 2016-04-15 00:52:06 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:52:06,735 - WARNING - Could not retrieve variants from source file in region 17:73551974-73570908. Error was invalid region `17:73551975-73570908`
[2016-04-15T07:52Z] 2016-04-15 00:52:06 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:52:06,759 - WARNING - Could not retrieve variants from source file in region 17:73488583-73519603. Error was invalid region `17:73488584-73519603`
[2016-04-15T07:52Z] 2016-04-15 00:52:07 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:52:07,262 - WARNING - Could not retrieve variants from source file in region 17:71386366-71426860. Error was invalid region `17:71386367-71426860`
[2016-04-15T07:52Z] 2016-04-15 00:52:07 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:52:07,860 - WARNING - Could not retrieve variants from source file in region 17:75494494-75494895. Error was invalid region `17:75494495-75494895`
[2016-04-15T07:52Z] 2016-04-15 00:52:08 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:52:08,135 - WARNING - Could not retrieve variants from source file in region 17:62923604-62924005. Error was invalid region `17:62923605-62924005`
[2016-04-15T07:52Z] 2016-04-15 00:52:08 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:52:08,890 - WARNING - Could not retrieve variants from source file in region 17:76778086-76817280. Error was invalid region `17:76778087-76817280`
[2016-04-15T07:52Z] 2016-04-15 00:52:09 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:52:09,919 - WARNING - Could not retrieve variants from source file in region 17:63049487-63049888. Error was invalid region `17:63049488-63049888`
[2016-04-15T07:52Z] 2016-04-15 00:52:12 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:52:12,398 - WARNING - Could not retrieve variants from source file in region 17:73625075-73647329. Error was invalid region `17:73625076-73647329`
[2016-04-15T07:52Z] 2016-04-15 00:52:12 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:52:12,697 - WARNING - Could not retrieve variants from source file in region 17:75494494-75494895. Error was invalid region `17:75494495-75494895`
[2016-04-15T07:52Z] 2016-04-15 00:52:15 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:52:15,780 - WARNING - Could not retrieve variants from source file in region 17:73625075-73647329. Error was invalid region `17:73625076-73647329`
[2016-04-15T07:52Z] 2016-04-15 00:52:17 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:52:17,388 - WARNING - Could not retrieve variants from source file in region 17:73551974-73570908. Error was invalid region `17:73551975-73570908`
[2016-04-15T07:52Z] 2016-04-15 00:52:19 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:52:19,390 - WARNING - Could not retrieve variants from source file in region 17:73488583-73519603. Error was invalid region `17:73488584-73519603`
[2016-04-15T07:52Z] 2016-04-15 00:52:19 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:52:19,574 - WARNING - Could not retrieve variants from source file in region 17:70943779-70944180. Error was invalid region `17:70943780-70944180`
[2016-04-15T07:52Z] 2016-04-15 00:52:20 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:52:20,324 - WARNING - Could not retrieve variants from source file in region 17:63049487-63049888. Error was invalid region `17:63049488-63049888`
[2016-04-15T07:52Z] 2016-04-15 00:52:24 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:52:24,984 - WARNING - Could not retrieve variants from source file in region 17:70943779-70944180. Error was invalid region `17:70943780-70944180`
[2016-04-15T07:52Z] 2016-04-15 00:52:25 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:52:25,929 - WARNING - Could not retrieve variants from source file in region 17:72301221-72308509. Error was invalid region `17:72301222-72308509`
[2016-04-15T07:52Z] 2016-04-15 00:52:27 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:52:27,749 - WARNING - Could not retrieve variants from source file in region 17:62532526-62532927. Error was invalid region `17:62532527-62532927`
[2016-04-15T07:52Z] 2016-04-15 00:52:28 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:52:28,853 - WARNING - Could not retrieve variants from source file in region 17:70943779-70944180. Error was invalid region `17:70943780-70944180`
[2016-04-15T07:52Z] 2016-04-15 00:52:29 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:52:29,844 - WARNING - Could not retrieve variants from source file in region 17:62399661-62401113. Error was invalid region `17:62399662-62401113`
[2016-04-15T07:52Z] 2016-04-15 00:52:31 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:52:31,140 - WARNING - Could not retrieve variants from source file in region 17:62532526-62532927. Error was invalid region `17:62532527-62532927`
[2016-04-15T07:52Z] 2016-04-15 00:52:32 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:52:32,579 - WARNING - Could not retrieve variants from source file in region 17:62399661-62401113. Error was invalid region `17:62399662-62401113`
[2016-04-15T07:52Z] 2016-04-15 00:52:35 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:52:35,731 - WARNING - Could not retrieve variants from source file in region 17:62270730-62271131. Error was invalid region `17:62270731-62271131`
[2016-04-15T07:52Z] 2016-04-15 00:52:35 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:52:35,899 - WARNING - Could not retrieve variants from source file in region 17:70118724-70119125. Error was invalid region `17:70118725-70119125`
[2016-04-15T07:52Z] 2016-04-15 00:52:35 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:52:35,945 - WARNING - Could not retrieve variants from source file in region 17:70118724-70119125. Error was invalid region `17:70118725-70119125`
[2016-04-15T07:52Z] 2016-04-15 00:52:38 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:52:38,348 - WARNING - Could not retrieve variants from source file in region 17:67512792-67513193. Error was invalid region `17:67512793-67513193`
[2016-04-15T07:52Z] 2016-04-15 00:52:39 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:52:39,333 - WARNING - Could not retrieve variants from source file in region 17:67512792-67513193. Error was invalid region `17:67512793-67513193`
[2016-04-15T07:52Z] 2016-04-15 00:52:39 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:52:39,333 - WARNING - Could not retrieve variants from source file in region 17:67512792-67513193. Error was invalid region `17:67512793-67513193`
[2016-04-15T07:52Z] 2016-04-15 00:52:39 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:52:39,334 - WARNING - Could not retrieve variants from source file in region 17:62270730-62271131. Error was invalid region `17:62270731-62271131`
[2016-04-15T07:52Z] 2016-04-15 00:52:42 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:52:42,297 - WARNING - Could not retrieve variants from source file in region 17:62125061-62141645. Error was invalid region `17:62125062-62141645`
[2016-04-15T07:52Z] ['bcbio-variation-recall', 'square', '-Xms750m', '-Xmx7280m', '-XX:+UseSerialGC', '-c', 16, '-r', u'17:77707306-81195210', '--caller', 'platypus', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/17/Batch1-17_77707305_81195210.vcf.gz', '/mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/17/Batch1-17_77707305_81195210.vcf-inputs.txt'] in region: 17:77707306-81195210
[2016-04-15T07:52Z] 2016-04-15 00:52:57 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:52:57,227 - WARNING - Could not retrieve variants from source file in region 17:81042828-81043229. Error was invalid region `17:81042829-81043229`
[2016-04-15T07:52Z] 2016-04-15 00:52:58 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:52:58,786 - WARNING - Could not retrieve variants from source file in region 17:80618869-80619270. Error was invalid region `17:80618870-80619270`
[2016-04-15T07:52Z] 2016-04-15 00:52:58 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:52:58,794 - WARNING - Could not retrieve variants from source file in region 17:78854012-78854413. Error was invalid region `17:78854013-78854413`
[2016-04-15T07:52Z] 2016-04-15 00:52:59 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:52:59,449 - WARNING - Could not retrieve variants from source file in region 17:79165925-79220414. Error was invalid region `17:79165926-79220414`
[2016-04-15T07:52Z] 2016-04-15 00:52:59 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:52:59,594 - WARNING - Could not retrieve variants from source file in region 17:78896376-78935387. Error was invalid region `17:78896377-78935387`
[2016-04-15T07:52Z] 2016-04-15 00:52:59 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:52:59,643 - WARNING - Could not retrieve variants from source file in region 17:80788254-80796861. Error was invalid region `17:80788255-80796861`
[2016-04-15T07:52Z] 2016-04-15 00:52:59 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:52:59,835 - WARNING - Could not retrieve variants from source file in region 17:81006176-81009826. Error was invalid region `17:81006177-81009826`
[2016-04-15T07:53Z] 2016-04-15 00:53:00 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:53:00,230 - WARNING - Could not retrieve variants from source file in region 17:80963891-80964292. Error was invalid region `17:80963892-80964292`
[2016-04-15T07:53Z] 2016-04-15 00:53:00 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:53:00,504 - WARNING - Could not retrieve variants from source file in region 17:78599351-78599752. Error was invalid region `17:78599352-78599752`
[2016-04-15T07:53Z] 2016-04-15 00:53:06 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:53:06,081 - WARNING - Could not retrieve variants from source file in region 17:80618869-80619270. Error was invalid region `17:80618870-80619270`
[2016-04-15T07:53Z] 2016-04-15 00:53:06 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:53:06,589 - WARNING - Could not retrieve variants from source file in region 17:78854012-78854413. Error was invalid region `17:78854013-78854413`
[2016-04-15T07:53Z] 2016-04-15 00:53:08 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:53:08,360 - WARNING - Could not retrieve variants from source file in region 17:80442511-80442912. Error was invalid region `17:80442512-80442912`
[2016-04-15T07:53Z] 2016-04-15 00:53:08 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:53:08,975 - WARNING - Could not retrieve variants from source file in region 17:80963891-80964292. Error was invalid region `17:80963892-80964292`
[2016-04-15T07:53Z] 2016-04-15 00:53:09 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:53:09,163 - WARNING - Could not retrieve variants from source file in region 17:79354131-79354532. Error was invalid region `17:79354132-79354532`
[2016-04-15T07:53Z] 2016-04-15 00:53:09 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:53:09,260 - WARNING - Could not retrieve variants from source file in region 17:78820118-78820564. Error was invalid region `17:78820119-78820564`
[2016-04-15T07:53Z] 2016-04-15 00:53:09 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:53:09,343 - WARNING - Could not retrieve variants from source file in region 17:78747511-78748172. Error was invalid region `17:78747512-78748172`
[2016-04-15T07:53Z] 2016-04-15 00:53:09 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:53:09,412 - WARNING - Could not retrieve variants from source file in region 17:81042828-81043229. Error was invalid region `17:81042829-81043229`
[2016-04-15T07:53Z] 2016-04-15 00:53:11 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:53:11,800 - WARNING - Could not retrieve variants from source file in region 17:80584883-80587766. Error was invalid region `17:80584884-80587766`
[2016-04-15T07:53Z] 2016-04-15 00:53:11 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:53:11,834 - WARNING - Could not retrieve variants from source file in region 17:80618869-80619270. Error was invalid region `17:80618870-80619270`
[2016-04-15T07:53Z] 2016-04-15 00:53:12 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:53:12,373 - WARNING - Could not retrieve variants from source file in region 17:78854012-78854413. Error was invalid region `17:78854013-78854413`
[2016-04-15T07:53Z] 2016-04-15 00:53:30 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:53:30,276 - WARNING - Could not retrieve variants from source file in region 17:78972115-78972611. Error was invalid region `17:78972116-78972611`
[2016-04-15T07:53Z] 2016-04-15 00:53:31 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:53:31,345 - WARNING - Could not retrieve variants from source file in region 17:80553827-80554228. Error was invalid region `17:80553828-80554228`
[2016-04-15T07:53Z] 2016-04-15 00:53:32 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:53:32,440 - WARNING - Could not retrieve variants from source file in region 17:78444447-78445892. Error was invalid region `17:78444448-78445892`
[2016-04-15T07:53Z] 2016-04-15 00:53:33 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:53:33,032 - WARNING - Could not retrieve variants from source file in region 17:78013513-78013914. Error was invalid region `17:78013514-78013914`
[2016-04-15T07:53Z] 2016-04-15 00:53:33 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:53:33,531 - WARNING - Could not retrieve variants from source file in region 17:78972115-78972611. Error was invalid region `17:78972116-78972611`
[2016-04-15T07:53Z] 2016-04-15 00:53:33 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:53:33,645 - WARNING - Could not retrieve variants from source file in region 17:80674432-80710287. Error was invalid region `17:80674433-80710287`
[2016-04-15T07:53Z] 2016-04-15 00:53:34 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:53:34,486 - WARNING - Could not retrieve variants from source file in region 17:78682545-78682946. Error was invalid region `17:78682546-78682946`
[2016-04-15T07:53Z] 2016-04-15 00:53:34 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:53:34,527 - WARNING - Could not retrieve variants from source file in region 17:80553827-80554228. Error was invalid region `17:80553828-80554228`
[2016-04-15T07:53Z] 2016-04-15 00:53:35 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:53:35,636 - WARNING - Could not retrieve variants from source file in region 17:78444447-78445892. Error was invalid region `17:78444448-78445892`
[2016-04-15T07:53Z] 2016-04-15 00:53:36 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:53:36,316 - WARNING - Could not retrieve variants from source file in region 17:78013513-78013914. Error was invalid region `17:78013514-78013914`
[2016-04-15T07:53Z] 2016-04-15 00:53:36 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:53:36,760 - WARNING - Could not retrieve variants from source file in region 17:78972115-78972611. Error was invalid region `17:78972116-78972611`
[2016-04-15T07:53Z] 2016-04-15 00:53:36 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:53:36,819 - WARNING - Could not retrieve variants from source file in region 17:80674432-80710287. Error was invalid region `17:80674433-80710287`
[2016-04-15T07:53Z] 2016-04-15 00:53:39 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:53:39,496 - WARNING - Could not retrieve variants from source file in region 17:78013513-78013914. Error was invalid region `17:78013514-78013914`
[2016-04-15T07:53Z] 2016-04-15 00:53:44 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:53:44,451 - WARNING - Could not retrieve variants from source file in region 17:80280654-80281055. Error was invalid region `17:80280655-80281055`
[2016-04-15T07:53Z] 2016-04-15 00:53:44 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:53:44,728 - WARNING - Could not retrieve variants from source file in region 17:80280654-80281055. Error was invalid region `17:80280655-80281055`
[2016-04-15T07:53Z] 2016-04-15 00:53:45 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:53:45,653 - WARNING - Could not retrieve variants from source file in region 17:80195371-80205903. Error was invalid region `17:80195372-80205903`
[2016-04-15T07:53Z] 2016-04-15 00:53:47 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:53:47,455 - WARNING - Could not retrieve variants from source file in region 17:80159355-80159855. Error was invalid region `17:80159356-80159855`
[2016-04-15T07:53Z] 2016-04-15 00:53:49 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:53:49,093 - WARNING - Could not retrieve variants from source file in region 17:79871918-79899685. Error was invalid region `17:79871919-79899685`
[2016-04-15T07:53Z] 2016-04-15 00:53:50 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:53:50,123 - WARNING - Could not retrieve variants from source file in region 17:78395523-78404096. Error was invalid region `17:78395524-78404096`
[2016-04-15T07:53Z] 2016-04-15 00:53:50 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:53:50,259 - WARNING - Could not retrieve variants from source file in region 17:80195371-80205903. Error was invalid region `17:80195372-80205903`
[2016-04-15T07:53Z] 2016-04-15 00:53:50 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:53:50,997 - WARNING - Could not retrieve variants from source file in region 17:77807706-77808107. Error was invalid region `17:77807707-77808107`
[2016-04-15T07:53Z] 2016-04-15 00:53:52 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:53:52,828 - WARNING - Could not retrieve variants from source file in region 17:77917607-77926681. Error was invalid region `17:77917608-77926681`
[2016-04-15T07:53Z] 2016-04-15 00:53:53 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:53:53,586 - WARNING - Could not retrieve variants from source file in region 17:80195371-80205903. Error was invalid region `17:80195372-80205903`
[2016-04-15T07:53Z] 2016-04-15 00:53:55 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:53:55,771 - WARNING - Could not retrieve variants from source file in region 17:80159355-80159855. Error was invalid region `17:80159356-80159855`
[2016-04-15T07:53Z] 2016-04-15 00:53:57 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:53:57,119 - WARNING - Could not retrieve variants from source file in region 17:77917607-77926681. Error was invalid region `17:77917608-77926681`
[2016-04-15T07:53Z] 2016-04-15 00:53:57 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:53:57,138 - WARNING - Could not retrieve variants from source file in region 17:79871918-79899685. Error was invalid region `17:79871919-79899685`
[2016-04-15T07:53Z] 2016-04-15 00:53:58 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:53:58,180 - WARNING - Could not retrieve variants from source file in region 17:77807706-77808107. Error was invalid region `17:77807707-77808107`
[2016-04-15T07:54Z] 2016-04-15 00:54:00 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:54:00,807 - WARNING - Could not retrieve variants from source file in region 17:77752980-77768844. Error was invalid region `17:77752981-77768844`
[2016-04-15T07:54Z] ['bcbio-variation-recall', 'square', '-Xms750m', '-Xmx7280m', '-XX:+UseSerialGC', '-c', 16, '-r', u'18:1-18531348', '--caller', 'platypus', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/18/Batch1-18_0_18531348.vcf.gz', '/mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/18/Batch1-18_0_18531348.vcf-inputs.txt'] in region: 18:1-18531348
[2016-04-15T07:54Z] 2016-04-15 00:54:23 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:54:22,992 - WARNING - Could not retrieve variants from source file in region 18:10759629-10760030. Error was invalid region `18:10759630-10760030`
[2016-04-15T07:54Z] 2016-04-15 00:54:25 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:54:25,357 - WARNING - Could not retrieve variants from source file in region 18:8386984-8387409. Error was invalid region `18:8386985-8387409`
[2016-04-15T07:54Z] 2016-04-15 00:54:25 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:54:25,856 - WARNING - Could not retrieve variants from source file in region 18:6943053-6943454. Error was invalid region `18:6943054-6943454`
[2016-04-15T07:54Z] 2016-04-15 00:54:26 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:54:26,282 - WARNING - Could not retrieve variants from source file in region 18:3581755-3582156. Error was invalid region `18:3581756-3582156`
[2016-04-15T07:54Z] 2016-04-15 00:54:26 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:54:26,847 - WARNING - Could not retrieve variants from source file in region 18:11609692-11610522. Error was invalid region `18:11609693-11610522`
[2016-04-15T07:54Z] 2016-04-15 00:54:27 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:54:27,009 - WARNING - Could not retrieve variants from source file in region 18:13611322-13612735. Error was invalid region `18:13611323-13612735`
[2016-04-15T07:54Z] 2016-04-15 00:54:27 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:54:27,396 - WARNING - Could not retrieve variants from source file in region 18:5956027-5956428. Error was invalid region `18:5956028-5956428`
[2016-04-15T07:54Z] 2016-04-15 00:54:27 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:54:27,440 - WARNING - Could not retrieve variants from source file in region 18:11998904-11999305. Error was invalid region `18:11998905-11999305`
[2016-04-15T07:54Z] 2016-04-15 00:54:27 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:54:27,882 - WARNING - Could not retrieve variants from source file in region 18:10759629-10760030. Error was invalid region `18:10759630-10760030`
[2016-04-15T07:54Z] 2016-04-15 00:54:29 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:54:29,443 - WARNING - Could not retrieve variants from source file in region 18:9255771-9256448. Error was invalid region `18:9255772-9256448`
[2016-04-15T07:54Z] 2016-04-15 00:54:29 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:54:29,474 - WARNING - Could not retrieve variants from source file in region 18:12325159-12351532. Error was invalid region `18:12325160-12351532`
[2016-04-15T07:54Z] 2016-04-15 00:54:30 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:54:30,662 - WARNING - Could not retrieve variants from source file in region 18:11880791-11881192. Error was invalid region `18:11880792-11881192`
[2016-04-15T07:54Z] 2016-04-15 00:54:33 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:54:33,735 - WARNING - Could not retrieve variants from source file in region 18:3581755-3582156. Error was invalid region `18:3581756-3582156`
[2016-04-15T07:54Z] 2016-04-15 00:54:34 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:54:34,455 - WARNING - Could not retrieve variants from source file in region 18:11609692-11610522. Error was invalid region `18:11609693-11610522`
[2016-04-15T07:54Z] 2016-04-15 00:54:34 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:54:34,649 - WARNING - Could not retrieve variants from source file in region 18:10759629-10760030. Error was invalid region `18:10759630-10760030`
[2016-04-15T07:54Z] 2016-04-15 00:54:35 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:54:35,146 - WARNING - Could not retrieve variants from source file in region 18:12325159-12351532. Error was invalid region `18:12325160-12351532`
[2016-04-15T07:54Z] 2016-04-15 00:54:35 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:54:35,256 - WARNING - Could not retrieve variants from source file in region 18:11880791-11881192. Error was invalid region `18:11880792-11881192`
[2016-04-15T07:54Z] 2016-04-15 00:54:35 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:54:35,398 - WARNING - Could not retrieve variants from source file in region 18:8386984-8387409. Error was invalid region `18:8386985-8387409`
[2016-04-15T07:54Z] 2016-04-15 00:54:39 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:54:39,592 - WARNING - Could not retrieve variants from source file in region 18:14848610-14852525. Error was invalid region `18:14848611-14852525`
[2016-04-15T07:54Z] 2016-04-15 00:54:40 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:54:40,606 - WARNING - Could not retrieve variants from source file in region 18:5956027-5956428. Error was invalid region `18:5956028-5956428`
[2016-04-15T07:54Z] 2016-04-15 00:54:41 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:54:41,160 - WARNING - Could not retrieve variants from source file in region 18:13611322-13612735. Error was invalid region `18:13611323-13612735`
[2016-04-15T07:54Z] 2016-04-15 00:54:41 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:54:41,577 - WARNING - Could not retrieve variants from source file in region 18:11998904-11999305. Error was invalid region `18:11998905-11999305`
[2016-04-15T07:54Z] 2016-04-15 00:54:42 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:54:42,104 - WARNING - Could not retrieve variants from source file in region 18:8825872-8831407. Error was invalid region `18:8825873-8831407`
[2016-04-15T07:54Z] 2016-04-15 00:54:42 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:54:42,464 - WARNING - Could not retrieve variants from source file in region 18:11609692-11610522. Error was invalid region `18:11609693-11610522`
[2016-04-15T07:54Z] 2016-04-15 00:54:43 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:54:43,337 - WARNING - Could not retrieve variants from source file in region 18:12983933-13001713. Error was invalid region `18:12983934-13001713`
[2016-04-15T07:54Z] 2016-04-15 00:54:51 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:54:51,496 - WARNING - Could not retrieve variants from source file in region 18:10454749-10488108. Error was invalid region `18:10454750-10488108`
[2016-04-15T07:54Z] 2016-04-15 00:54:53 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:54:53,396 - WARNING - Could not retrieve variants from source file in region 18:14532894-14543329. Error was invalid region `18:14532895-14543329`
[2016-04-15T07:54Z] 2016-04-15 00:54:54 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:54:54,050 - WARNING - Could not retrieve variants from source file in region 18:6889762-6912333. Error was invalid region `18:6889763-6912333`
[2016-04-15T07:54Z] 2016-04-15 00:54:54 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:54:54,249 - WARNING - Could not retrieve variants from source file in region 18:9117656-9118057. Error was invalid region `18:9117657-9118057`
[2016-04-15T07:54Z] 2016-04-15 00:54:55 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:54:55,414 - WARNING - Could not retrieve variants from source file in region 18:14779758-14780159. Error was invalid region `18:14779759-14780159`
[2016-04-15T07:54Z] 2016-04-15 00:54:55 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:54:55,787 - WARNING - Could not retrieve variants from source file in region 18:8113435-8113836. Error was invalid region `18:8113436-8113836`
[2016-04-15T07:54Z] 2016-04-15 00:54:56 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:54:56,039 - WARNING - Could not retrieve variants from source file in region 18:13095398-13116622. Error was invalid region `18:13095399-13116622`
[2016-04-15T07:54Z] 2016-04-15 00:54:56 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:54:56,574 - WARNING - Could not retrieve variants from source file in region 18:10786836-10787237. Error was invalid region `18:10786837-10787237`
[2016-04-15T07:54Z] 2016-04-15 00:54:58 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:54:58,978 - WARNING - Could not retrieve variants from source file in region 18:9117656-9118057. Error was invalid region `18:9117657-9118057`
[2016-04-15T07:54Z] 2016-04-15 00:54:59 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:54:59,123 - WARNING - Could not retrieve variants from source file in region 18:6889762-6912333. Error was invalid region `18:6889763-6912333`
[2016-04-15T07:55Z] 2016-04-15 00:55:00 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:55:00,706 - WARNING - Could not retrieve variants from source file in region 18:14779758-14780159. Error was invalid region `18:14779759-14780159`
[2016-04-15T07:55Z] 2016-04-15 00:55:01 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:55:01,014 - WARNING - Could not retrieve variants from source file in region 18:5410363-5416350. Error was invalid region `18:5410364-5416350`
[2016-04-15T07:55Z] 2016-04-15 00:55:01 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:55:01,457 - WARNING - Could not retrieve variants from source file in region 18:10454749-10488108. Error was invalid region `18:10454750-10488108`
[2016-04-15T07:55Z] 2016-04-15 00:55:01 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:55:01,471 - WARNING - Could not retrieve variants from source file in region 18:13095398-13116622. Error was invalid region `18:13095399-13116622`
[2016-04-15T07:55Z] 2016-04-15 00:55:01 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:55:01,604 - WARNING - Could not retrieve variants from source file in region 18:10786836-10787237. Error was invalid region `18:10786837-10787237`
[2016-04-15T07:55Z] 2016-04-15 00:55:03 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:55:03,473 - WARNING - Could not retrieve variants from source file in region 18:9117656-9118057. Error was invalid region `18:9117657-9118057`
[2016-04-15T07:55Z] 2016-04-15 00:55:03 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:55:03,477 - WARNING - Could not retrieve variants from source file in region 18:9570109-9570510. Error was invalid region `18:9570110-9570510`
[2016-04-15T07:55Z] 2016-04-15 00:55:04 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:55:04,084 - WARNING - Could not retrieve variants from source file in region 18:12792729-12793130. Error was invalid region `18:12792730-12793130`
[2016-04-15T07:55Z] 2016-04-15 00:55:05 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:55:05,287 - WARNING - Could not retrieve variants from source file in region 18:14779758-14780159. Error was invalid region `18:14779759-14780159`
[2016-04-15T07:55Z] 2016-04-15 00:55:06 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:55:06,863 - WARNING - Could not retrieve variants from source file in region 18:13095398-13116622. Error was invalid region `18:13095399-13116622`
[2016-04-15T07:55Z] 2016-04-15 00:55:07 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:55:07,143 - WARNING - Could not retrieve variants from source file in region 18:10786836-10787237. Error was invalid region `18:10786837-10787237`
[2016-04-15T07:55Z] 2016-04-15 00:55:08 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:55:08,636 - WARNING - Could not retrieve variants from source file in region 18:12792729-12793130. Error was invalid region `18:12792730-12793130`
[2016-04-15T07:55Z] 2016-04-15 00:55:16 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:55:16,103 - WARNING - Could not retrieve variants from source file in region 18:8705468-8706376. Error was invalid region `18:8705469-8706376`
[2016-04-15T07:55Z] 2016-04-15 00:55:18 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:55:18,390 - WARNING - Could not retrieve variants from source file in region 18:5291819-5292220. Error was invalid region `18:5291820-5292220`
[2016-04-15T07:55Z] 2016-04-15 00:55:18 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:55:18,535 - WARNING - Could not retrieve variants from source file in region 18:14105712-14106229. Error was invalid region `18:14105713-14106229`
[2016-04-15T07:55Z] 2016-04-15 00:55:18 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:55:18,919 - WARNING - Could not retrieve variants from source file in region 18:5291819-5292220. Error was invalid region `18:5291820-5292220`
[2016-04-15T07:55Z] 2016-04-15 00:55:19 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:55:19,239 - WARNING - Could not retrieve variants from source file in region 18:14752746-14753147. Error was invalid region `18:14752747-14753147`
[2016-04-15T07:55Z] 2016-04-15 00:55:21 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:55:21,034 - WARNING - Could not retrieve variants from source file in region 18:5196959-5197360. Error was invalid region `18:5196960-5197360`
[2016-04-15T07:55Z] 2016-04-15 00:55:21 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:55:21,059 - WARNING - Could not retrieve variants from source file in region 18:8069546-8070058. Error was invalid region `18:8069547-8070058`
[2016-04-15T07:55Z] 2016-04-15 00:55:21 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:55:21,156 - WARNING - Could not retrieve variants from source file in region 18:8705468-8706376. Error was invalid region `18:8705469-8706376`
[2016-04-15T07:55Z] 2016-04-15 00:55:21 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:55:21,773 - WARNING - Could not retrieve variants from source file in region 18:13056122-13069972. Error was invalid region `18:13056123-13069972`
[2016-04-15T07:55Z] 2016-04-15 00:55:23 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:55:23,000 - WARNING - Could not retrieve variants from source file in region 18:3276866-3277427. Error was invalid region `18:3276867-3277427`
[2016-04-15T07:55Z] 2016-04-15 00:55:23 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:55:23,088 - WARNING - Could not retrieve variants from source file in region 18:12718382-12718783. Error was invalid region `18:12718383-12718783`
[2016-04-15T07:55Z] 2016-04-15 00:55:24 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:55:24,236 - WARNING - Could not retrieve variants from source file in region 18:12657834-12658235. Error was invalid region `18:12657835-12658235`
[2016-04-15T07:55Z] 2016-04-15 00:55:24 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:55:24,499 - WARNING - Could not retrieve variants from source file in region 18:5291819-5292220. Error was invalid region `18:5291820-5292220`
[2016-04-15T07:55Z] 2016-04-15 00:55:24 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:55:24,593 - WARNING - Could not retrieve variants from source file in region 18:14752746-14753147. Error was invalid region `18:14752747-14753147`
[2016-04-15T07:55Z] 2016-04-15 00:55:27 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:55:27,223 - WARNING - Could not retrieve variants from source file in region 18:13056122-13069972. Error was invalid region `18:13056123-13069972`
[2016-04-15T07:55Z] 2016-04-15 00:55:27 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:55:27,360 - WARNING - Could not retrieve variants from source file in region 18:12718382-12718783. Error was invalid region `18:12718383-12718783`
[2016-04-15T07:55Z] 2016-04-15 00:55:27 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:55:27,886 - WARNING - Could not retrieve variants from source file in region 18:3276866-3277427. Error was invalid region `18:3276867-3277427`
[2016-04-15T07:55Z] 2016-04-15 00:55:29 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:55:29,270 - WARNING - Could not retrieve variants from source file in region 18:12657834-12658235. Error was invalid region `18:12657835-12658235`
[2016-04-15T07:55Z] 2016-04-15 00:55:29 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:55:29,753 - WARNING - Could not retrieve variants from source file in region 18:14752746-14753147. Error was invalid region `18:14752747-14753147`
[2016-04-15T07:55Z] 2016-04-15 00:55:29 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:55:29,959 - WARNING - Could not retrieve variants from source file in region 18:14105712-14106229. Error was invalid region `18:14105713-14106229`
[2016-04-15T07:55Z] 2016-04-15 00:55:30 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:55:30,416 - WARNING - Could not retrieve variants from source file in region 18:12657834-12658235. Error was invalid region `18:12657835-12658235`
[2016-04-15T07:55Z] 2016-04-15 00:55:31 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:55:31,830 - WARNING - Could not retrieve variants from source file in region 18:13056122-13069972. Error was invalid region `18:13056123-13069972`
[2016-04-15T07:55Z] 2016-04-15 00:55:32 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:55:32,124 - WARNING - Could not retrieve variants from source file in region 18:12718382-12718783. Error was invalid region `18:12718383-12718783`
[2016-04-15T07:55Z] 2016-04-15 00:55:32 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:55:32,355 - WARNING - Could not retrieve variants from source file in region 18:13760079-13762201. Error was invalid region `18:13760080-13762201`
[2016-04-15T07:55Z] 2016-04-15 00:55:37 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:55:37,486 - WARNING - Could not retrieve variants from source file in region 18:13760079-13762201. Error was invalid region `18:13760080-13762201`
[2016-04-15T07:55Z] 2016-04-15 00:55:40 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:55:40,982 - WARNING - Could not retrieve variants from source file in region 18:2616246-2616647. Error was invalid region `18:2616247-2616647`
[2016-04-15T07:55Z] 2016-04-15 00:55:43 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:55:43,918 - WARNING - Could not retrieve variants from source file in region 18:580412-580813. Error was invalid region `18:580413-580813`
[2016-04-15T07:55Z] 2016-04-15 00:55:44 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:55:44,010 - WARNING - Could not retrieve variants from source file in region 18:252348-252749. Error was invalid region `18:252349-252749`
[2016-04-15T07:55Z] 2016-04-15 00:55:44 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:55:44,011 - WARNING - Could not retrieve variants from source file in region 18:904555-909751. Error was invalid region `18:904556-909751`
[2016-04-15T07:55Z] 2016-04-15 00:55:44 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:55:44,399 - WARNING - Could not retrieve variants from source file in region 18:13641735-13642911. Error was invalid region `18:13641736-13642911`
[2016-04-15T07:55Z] 2016-04-15 00:55:44 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:55:44,436 - WARNING - Could not retrieve variants from source file in region 18:13641735-13642911. Error was invalid region `18:13641736-13642911`
[2016-04-15T07:55Z] 2016-04-15 00:55:45 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:55:45,756 - WARNING - Could not retrieve variants from source file in region 18:166608-167009. Error was invalid region `18:166609-167009`
[2016-04-15T07:55Z] 2016-04-15 00:55:46 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:55:46,455 - WARNING - Could not retrieve variants from source file in region 18:2656037-2656438. Error was invalid region `18:2656038-2656438`
[2016-04-15T07:55Z] 2016-04-15 00:55:46 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:55:46,515 - WARNING - Could not retrieve variants from source file in region 18:2705489-2770242. Error was invalid region `18:2705490-2770242`
[2016-04-15T07:55Z] 2016-04-15 00:55:46 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:55:46,551 - WARNING - Could not retrieve variants from source file in region 18:3067067-3075936. Error was invalid region `18:3067068-3075936`
[2016-04-15T07:55Z] 2016-04-15 00:55:48 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:55:48,449 - WARNING - Could not retrieve variants from source file in region 18:252348-252749. Error was invalid region `18:252349-252749`
[2016-04-15T07:55Z] 2016-04-15 00:55:48 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:55:48,874 - WARNING - Could not retrieve variants from source file in region 18:334531-335289. Error was invalid region `18:334532-335289`
[2016-04-15T07:55Z] 2016-04-15 00:55:48 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:55:48,917 - WARNING - Could not retrieve variants from source file in region 18:2656037-2656438. Error was invalid region `18:2656038-2656438`
[2016-04-15T07:55Z] 2016-04-15 00:55:49 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:55:49,885 - WARNING - Could not retrieve variants from source file in region 18:166608-167009. Error was invalid region `18:166609-167009`
[2016-04-15T07:55Z] 2016-04-15 00:55:50 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:55:50,103 - WARNING - Could not retrieve variants from source file in region 18:3164174-3189166. Error was invalid region `18:3164175-3189166`
[2016-04-15T07:55Z] 2016-04-15 00:55:51 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:55:51,145 - WARNING - Could not retrieve variants from source file in region 18:3067067-3075936. Error was invalid region `18:3067068-3075936`
[2016-04-15T07:55Z] 2016-04-15 00:55:52 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:55:52,987 - WARNING - Could not retrieve variants from source file in region 18:252348-252749. Error was invalid region `18:252349-252749`
[2016-04-15T07:55Z] 2016-04-15 00:55:53 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:55:53,065 - WARNING - Could not retrieve variants from source file in region 18:334531-335289. Error was invalid region `18:334532-335289`
[2016-04-15T07:55Z] 2016-04-15 00:55:53 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:55:53,233 - WARNING - Could not retrieve variants from source file in region 18:580412-580813. Error was invalid region `18:580413-580813`
[2016-04-15T07:55Z] 2016-04-15 00:55:55 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:55:55,428 - WARNING - Could not retrieve variants from source file in region 18:3067067-3075936. Error was invalid region `18:3067068-3075936`
[2016-04-15T07:56Z] 2016-04-15 00:56:00 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:56:00,066 - WARNING - Could not retrieve variants from source file in region 18:674109-724802. Error was invalid region `18:674110-724802`
[2016-04-15T07:56Z] ['bcbio-variation-recall', 'square', '-Xms750m', '-Xmx7280m', '-XX:+UseSerialGC', '-c', 16, '-r', u'18:18533539-34081962', '--caller', 'platypus', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/18/Batch1-18_18533538_34081962.vcf.gz', '/mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/18/Batch1-18_18533538_34081962.vcf-inputs.txt'] in region: 18:18533539-34081962
[2016-04-15T07:56Z] 2016-04-15 00:56:14 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:56:14,666 - WARNING - Could not retrieve variants from source file in region 18:29497362-29497763. Error was invalid region `18:29497363-29497763`
[2016-04-15T07:56Z] 2016-04-15 00:56:15 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:56:15,910 - WARNING - Could not retrieve variants from source file in region 18:21413658-21441907. Error was invalid region `18:21413659-21441907`
[2016-04-15T07:56Z] 2016-04-15 00:56:16 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:56:16,700 - WARNING - Could not retrieve variants from source file in region 18:21602358-21602759. Error was invalid region `18:21602359-21602759`
[2016-04-15T07:56Z] 2016-04-15 00:56:17 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:56:17,200 - WARNING - Could not retrieve variants from source file in region 18:19995520-19996995. Error was invalid region `18:19995521-19996995`
[2016-04-15T07:56Z] 2016-04-15 00:56:17 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:56:17,282 - WARNING - Could not retrieve variants from source file in region 18:19153283-19154333. Error was invalid region `18:19153284-19154333`
[2016-04-15T07:56Z] 2016-04-15 00:56:17 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:56:17,786 - WARNING - Could not retrieve variants from source file in region 18:22020332-22020733. Error was invalid region `18:22020333-22020733`
[2016-04-15T07:56Z] 2016-04-15 00:56:18 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:56:18,142 - WARNING - Could not retrieve variants from source file in region 18:30804545-30804946. Error was invalid region `18:30804546-30804946`
[2016-04-15T07:56Z] 2016-04-15 00:56:18 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:56:18,392 - WARNING - Could not retrieve variants from source file in region 18:21891764-21892165. Error was invalid region `18:21891765-21892165`
[2016-04-15T07:56Z] 2016-04-15 00:56:18 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:56:18,400 - WARNING - Could not retrieve variants from source file in region 18:29304669-29305458. Error was invalid region `18:29304670-29305458`
[2016-04-15T07:56Z] 2016-04-15 00:56:19 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:56:19,016 - WARNING - Could not retrieve variants from source file in region 18:29497362-29497763. Error was invalid region `18:29497363-29497763`
[2016-04-15T07:56Z] 2016-04-15 00:56:20 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:56:20,554 - WARNING - Could not retrieve variants from source file in region 18:29055424-29056305. Error was invalid region `18:29055425-29056305`
[2016-04-15T07:56Z] 2016-04-15 00:56:22 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:56:22,978 - WARNING - Could not retrieve variants from source file in region 18:21602358-21602759. Error was invalid region `18:21602359-21602759`
[2016-04-15T07:56Z] 2016-04-15 00:56:24 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:56:24,835 - WARNING - Could not retrieve variants from source file in region 18:20953509-20953910. Error was invalid region `18:20953510-20953910`
[2016-04-15T07:56Z] 2016-04-15 00:56:24 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:56:24,935 - WARNING - Could not retrieve variants from source file in region 18:19153283-19154333. Error was invalid region `18:19153284-19154333`
[2016-04-15T07:56Z] 2016-04-15 00:56:25 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:56:25,747 - WARNING - Could not retrieve variants from source file in region 18:33848370-33848771. Error was invalid region `18:33848371-33848771`
[2016-04-15T07:56Z] 2016-04-15 00:56:25 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:56:25,777 - WARNING - Could not retrieve variants from source file in region 18:22020332-22020733. Error was invalid region `18:22020333-22020733`
[2016-04-15T07:56Z] 2016-04-15 00:56:26 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:56:26,005 - WARNING - Could not retrieve variants from source file in region 18:29172654-29173055. Error was invalid region `18:29172655-29173055`
[2016-04-15T07:56Z] 2016-04-15 00:56:26 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:56:26,234 - WARNING - Could not retrieve variants from source file in region 18:30804545-30804946. Error was invalid region `18:30804546-30804946`
[2016-04-15T07:56Z] 2016-04-15 00:56:26 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:56:26,390 - WARNING - Could not retrieve variants from source file in region 18:21891764-21892165. Error was invalid region `18:21891765-21892165`
[2016-04-15T07:56Z] 2016-04-15 00:56:26 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:56:26,425 - WARNING - Could not retrieve variants from source file in region 18:29497362-29497763. Error was invalid region `18:29497363-29497763`
[2016-04-15T07:56Z] 2016-04-15 00:56:26 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:56:26,837 - WARNING - Could not retrieve variants from source file in region 18:21510823-21513958. Error was invalid region `18:21510824-21513958`
[2016-04-15T07:56Z] 2016-04-15 00:56:26 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:56:26,865 - WARNING - Could not retrieve variants from source file in region 18:29304669-29305458. Error was invalid region `18:29304670-29305458`
[2016-04-15T07:56Z] 2016-04-15 00:56:26 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:56:26,909 - WARNING - Could not retrieve variants from source file in region 18:21269493-21269894. Error was invalid region `18:21269494-21269894`
[2016-04-15T07:56Z] 2016-04-15 00:56:26 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:56:26,967 - WARNING - Could not retrieve variants from source file in region 18:29055424-29056305. Error was invalid region `18:29055425-29056305`
[2016-04-15T07:56Z] 2016-04-15 00:56:27 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:56:27,255 - WARNING - Could not retrieve variants from source file in region 18:21413658-21441907. Error was invalid region `18:21413659-21441907`
[2016-04-15T07:56Z] 2016-04-15 00:56:27 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:56:27,484 - WARNING - Could not retrieve variants from source file in region 18:21602358-21602759. Error was invalid region `18:21602359-21602759`
[2016-04-15T07:56Z] 2016-04-15 00:56:29 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:56:29,335 - WARNING - Could not retrieve variants from source file in region 18:19995520-19996995. Error was invalid region `18:19995521-19996995`
[2016-04-15T07:56Z] 2016-04-15 00:56:31 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:56:31,482 - WARNING - Could not retrieve variants from source file in region 18:20953509-20953910. Error was invalid region `18:20953510-20953910`
[2016-04-15T07:56Z] 2016-04-15 00:56:31 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:56:31,870 - WARNING - Could not retrieve variants from source file in region 18:19153283-19154333. Error was invalid region `18:19153284-19154333`
[2016-04-15T07:56Z] 2016-04-15 00:56:33 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:56:33,874 - WARNING - Could not retrieve variants from source file in region 18:33848370-33848771. Error was invalid region `18:33848371-33848771`
[2016-04-15T07:56Z] 2016-04-15 00:56:33 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:56:33,873 - WARNING - Could not retrieve variants from source file in region 18:22020332-22020733. Error was invalid region `18:22020333-22020733`
[2016-04-15T07:56Z] 2016-04-15 00:56:34 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:56:34,378 - WARNING - Could not retrieve variants from source file in region 18:30804545-30804946. Error was invalid region `18:30804546-30804946`
[2016-04-15T07:56Z] 2016-04-15 00:56:34 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:56:34,911 - WARNING - Could not retrieve variants from source file in region 18:21100029-21140622. Error was invalid region `18:21100030-21140622`
[2016-04-15T07:56Z] 2016-04-15 00:56:35 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:56:35,083 - WARNING - Could not retrieve variants from source file in region 18:21891764-21892165. Error was invalid region `18:21891765-21892165`
[2016-04-15T07:56Z] 2016-04-15 00:56:35 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:56:35,665 - WARNING - Could not retrieve variants from source file in region 18:29304669-29305458. Error was invalid region `18:29304670-29305458`
[2016-04-15T07:56Z] 2016-04-15 00:56:43 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:56:43,360 - WARNING - Could not retrieve variants from source file in region 18:29432413-29432814. Error was invalid region `18:29432414-29432814`
[2016-04-15T07:56Z] 2016-04-15 00:56:48 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:56:48,150 - WARNING - Could not retrieve variants from source file in region 18:23873252-23873653. Error was invalid region `18:23873253-23873653`
[2016-04-15T07:56Z] 2016-04-15 00:56:48 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:56:48,197 - WARNING - Could not retrieve variants from source file in region 18:21481022-21481423. Error was invalid region `18:21481023-21481423`
[2016-04-15T07:56Z] 2016-04-15 00:56:48 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:56:48,217 - WARNING - Could not retrieve variants from source file in region 18:25543176-25570418. Error was invalid region `18:25543177-25570418`
[2016-04-15T07:56Z] 2016-04-15 00:56:49 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:56:49,414 - WARNING - Could not retrieve variants from source file in region 18:33779610-33785375. Error was invalid region `18:33779611-33785375`
[2016-04-15T07:56Z] 2016-04-15 00:56:50 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:56:50,722 - WARNING - Could not retrieve variants from source file in region 18:24208939-24209340. Error was invalid region `18:24208940-24209340`
[2016-04-15T07:56Z] 2016-04-15 00:56:51 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:56:51,570 - WARNING - Could not retrieve variants from source file in region 18:21481022-21481423. Error was invalid region `18:21481023-21481423`
[2016-04-15T07:56Z] 2016-04-15 00:56:52 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:56:52,680 - WARNING - Could not retrieve variants from source file in region 18:25543176-25570418. Error was invalid region `18:25543177-25570418`
[2016-04-15T07:56Z] 2016-04-15 00:56:52 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:56:52,724 - WARNING - Could not retrieve variants from source file in region 18:23873252-23873653. Error was invalid region `18:23873253-23873653`
[2016-04-15T07:56Z] 2016-04-15 00:56:54 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:56:54,153 - WARNING - Could not retrieve variants from source file in region 18:21710110-21752556. Error was invalid region `18:21710111-21752556`
[2016-04-15T07:56Z] 2016-04-15 00:56:54 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:56:54,301 - WARNING - Could not retrieve variants from source file in region 18:29104487-29126860. Error was invalid region `18:29104488-29126860`
[2016-04-15T07:56Z] 2016-04-15 00:56:54 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:56:54,523 - WARNING - Could not retrieve variants from source file in region 18:30349480-30349881. Error was invalid region `18:30349481-30349881`
[2016-04-15T07:56Z] 2016-04-15 00:56:54 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:56:54,704 - WARNING - Could not retrieve variants from source file in region 18:24208939-24209340. Error was invalid region `18:24208940-24209340`
[2016-04-15T07:56Z] 2016-04-15 00:56:57 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:56:57,382 - WARNING - Could not retrieve variants from source file in region 18:23873252-23873653. Error was invalid region `18:23873253-23873653`
[2016-04-15T07:56Z] 2016-04-15 00:56:59 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:56:59,529 - WARNING - Could not retrieve variants from source file in region 18:24208939-24209340. Error was invalid region `18:24208940-24209340`
[2016-04-15T07:56Z] 2016-04-15 00:56:59 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:56:59,562 - WARNING - Could not retrieve variants from source file in region 18:33779610-33785375. Error was invalid region `18:33779611-33785375`
[2016-04-15T07:57Z] 2016-04-15 00:57:06 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:57:06,277 - WARNING - Could not retrieve variants from source file in region 18:30050145-30050546. Error was invalid region `18:30050146-30050546`
[2016-04-15T07:57Z] 2016-04-15 00:57:06 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:57:06,513 - WARNING - Could not retrieve variants from source file in region 18:32446086-32470481. Error was invalid region `18:32446087-32470481`
[2016-04-15T07:57Z] 2016-04-15 00:57:06 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:57:06,516 - WARNING - Could not retrieve variants from source file in region 18:29339699-29340100. Error was invalid region `18:29339700-29340100`
[2016-04-15T07:57Z] 2016-04-15 00:57:10 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:57:10,179 - WARNING - Could not retrieve variants from source file in region 18:29339699-29340100. Error was invalid region `18:29339700-29340100`
[2016-04-15T07:57Z] 2016-04-15 00:57:10 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:57:10,421 - WARNING - Could not retrieve variants from source file in region 18:33693909-33750236. Error was invalid region `18:33693910-33750236`
[2016-04-15T07:57Z] 2016-04-15 00:57:10 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:57:10,693 - WARNING - Could not retrieve variants from source file in region 18:24126797-24127198. Error was invalid region `18:24126798-24127198`
[2016-04-15T07:57Z] 2016-04-15 00:57:11 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:57:11,722 - WARNING - Could not retrieve variants from source file in region 18:32917433-32918829. Error was invalid region `18:32917434-32918829`
[2016-04-15T07:57Z] 2016-04-15 00:57:11 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:57:11,997 - WARNING - Could not retrieve variants from source file in region 18:23662166-23662567. Error was invalid region `18:23662167-23662567`
[2016-04-15T07:57Z] 2016-04-15 00:57:12 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:57:12,598 - WARNING - Could not retrieve variants from source file in region 18:29339699-29340100. Error was invalid region `18:29339700-29340100`
[2016-04-15T07:57Z] 2016-04-15 00:57:15 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:57:15,275 - WARNING - Could not retrieve variants from source file in region 18:33647043-33647444. Error was invalid region `18:33647044-33647444`
[2016-04-15T07:57Z] 2016-04-15 00:57:16 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:57:16,855 - WARNING - Could not retrieve variants from source file in region 18:33693909-33750236. Error was invalid region `18:33693910-33750236`
[2016-04-15T07:57Z] 2016-04-15 00:57:18 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:57:18,546 - WARNING - Could not retrieve variants from source file in region 18:32917433-32918829. Error was invalid region `18:32917434-32918829`
[2016-04-15T07:57Z] 2016-04-15 00:57:18 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:57:18,809 - WARNING - Could not retrieve variants from source file in region 18:22774974-22775375. Error was invalid region `18:22774975-22775375`
[2016-04-15T07:57Z] 2016-04-15 00:57:19 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:57:19,150 - WARNING - Could not retrieve variants from source file in region 18:32825877-32844246. Error was invalid region `18:32825878-32844246`
[2016-04-15T07:57Z] 2016-04-15 00:57:19 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:57:19,456 - WARNING - Could not retrieve variants from source file in region 18:31320018-31325124. Error was invalid region `18:31320019-31325124`
[2016-04-15T07:57Z] 2016-04-15 00:57:19 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:57:19,489 - WARNING - Could not retrieve variants from source file in region 18:32917433-32918829. Error was invalid region `18:32917434-32918829`
[2016-04-15T07:57Z] 2016-04-15 00:57:19 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:57:19,973 - WARNING - Could not retrieve variants from source file in region 18:33647043-33647444. Error was invalid region `18:33647044-33647444`
[2016-04-15T07:57Z] 2016-04-15 00:57:24 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:57:24,629 - WARNING - Could not retrieve variants from source file in region 18:32825877-32844246. Error was invalid region `18:32825878-32844246`
[2016-04-15T07:57Z] 2016-04-15 00:57:24 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:57:24,700 - WARNING - Could not retrieve variants from source file in region 18:23662166-23662567. Error was invalid region `18:23662167-23662567`
[2016-04-15T07:57Z] 2016-04-15 00:57:25 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:57:25,152 - WARNING - Could not retrieve variants from source file in region 18:31320018-31325124. Error was invalid region `18:31320019-31325124`
[2016-04-15T07:57Z] 2016-04-15 00:57:26 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:57:26,304 - WARNING - Could not retrieve variants from source file in region 18:33647043-33647444. Error was invalid region `18:33647044-33647444`
[2016-04-15T07:57Z] 2016-04-15 00:57:26 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:57:26,702 - WARNING - Could not retrieve variants from source file in region 18:29625474-29625875. Error was invalid region `18:29625475-29625875`
[2016-04-15T07:57Z] 2016-04-15 00:57:27 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:57:27,634 - WARNING - Could not retrieve variants from source file in region 18:30846684-30847085. Error was invalid region `18:30846685-30847085`
[2016-04-15T07:57Z] 2016-04-15 00:57:29 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:57:29,311 - WARNING - Could not retrieve variants from source file in region 18:30846684-30847085. Error was invalid region `18:30846685-30847085`
[2016-04-15T07:57Z] 2016-04-15 00:57:29 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:57:29,600 - WARNING - Could not retrieve variants from source file in region 18:29625474-29625875. Error was invalid region `18:29625475-29625875`
[2016-04-15T07:57Z] 2016-04-15 00:57:29 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:57:29,805 - WARNING - Could not retrieve variants from source file in region 18:30846684-30847085. Error was invalid region `18:30846685-30847085`
[2016-04-15T07:57Z] 2016-04-15 00:57:30 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:57:30,291 - WARNING - Could not retrieve variants from source file in region 18:25616240-25616641. Error was invalid region `18:25616241-25616641`
[2016-04-15T07:57Z] 2016-04-15 00:57:30 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:57:30,584 - WARNING - Could not retrieve variants from source file in region 18:33557255-33557656. Error was invalid region `18:33557256-33557656`
[2016-04-15T07:57Z] 2016-04-15 00:57:31 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:57:31,210 - WARNING - Could not retrieve variants from source file in region 18:29625474-29625875. Error was invalid region `18:29625475-29625875`
[2016-04-15T07:57Z] ['bcbio-variation-recall', 'square', '-Xms750m', '-Xmx7280m', '-XX:+UseSerialGC', '-c', 16, '-r', u'18:34092401-49867248', '--caller', 'platypus', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/18/Batch1-18_34092400_49867248.vcf.gz', '/mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/18/Batch1-18_34092400_49867248.vcf-inputs.txt'] in region: 18:34092401-49867248
[2016-04-15T07:57Z] 2016-04-15 00:57:51 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:57:51,112 - WARNING - Could not retrieve variants from source file in region 18:34310457-34324281. Error was invalid region `18:34310458-34324281`
[2016-04-15T07:57Z] 2016-04-15 00:57:51 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:57:51,113 - WARNING - Could not retrieve variants from source file in region 18:42456442-42457543. Error was invalid region `18:42456443-42457543`
[2016-04-15T07:57Z] 2016-04-15 00:57:51 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:57:51,372 - WARNING - Could not retrieve variants from source file in region 18:47088444-47094054. Error was invalid region `18:47088445-47094054`
[2016-04-15T07:57Z] 2016-04-15 00:57:51 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:57:51,717 - WARNING - Could not retrieve variants from source file in region 18:42532919-42533320. Error was invalid region `18:42532920-42533320`
[2016-04-15T07:57Z] 2016-04-15 00:57:51 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:57:51,923 - WARNING - Could not retrieve variants from source file in region 18:43677813-43678225. Error was invalid region `18:43677814-43678225`
[2016-04-15T07:57Z] 2016-04-15 00:57:52 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:57:52,005 - WARNING - Could not retrieve variants from source file in region 18:49867013-49867414. Error was invalid region `18:49867014-49867414`
[2016-04-15T07:57Z] 2016-04-15 00:57:52 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:57:52,023 - WARNING - Could not retrieve variants from source file in region 18:43916136-43916538. Error was invalid region `18:43916137-43916538`
[2016-04-15T07:57Z] 2016-04-15 00:57:54 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:57:54,323 - WARNING - Could not retrieve variants from source file in region 18:34647111-34664283. Error was invalid region `18:34647112-34664283`
[2016-04-15T07:57Z] 2016-04-15 00:57:55 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:57:55,783 - WARNING - Could not retrieve variants from source file in region 18:40323286-40323687. Error was invalid region `18:40323287-40323687`
[2016-04-15T07:57Z] 2016-04-15 00:57:57 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:57:57,666 - WARNING - Could not retrieve variants from source file in region 18:34802859-34805305. Error was invalid region `18:34802860-34805305`
[2016-04-15T07:57Z] 2016-04-15 00:57:58 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:57:58,490 - WARNING - Could not retrieve variants from source file in region 18:34232332-34232847. Error was invalid region `18:34232333-34232847`
[2016-04-15T07:57Z] 2016-04-15 00:57:59 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:57:59,325 - WARNING - Could not retrieve variants from source file in region 18:34310457-34324281. Error was invalid region `18:34310458-34324281`
[2016-04-15T07:58Z] 2016-04-15 00:58:00 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:58:00,120 - WARNING - Could not retrieve variants from source file in region 18:47088444-47094054. Error was invalid region `18:47088445-47094054`
[2016-04-15T07:58Z] 2016-04-15 00:58:00 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:58:00,342 - WARNING - Could not retrieve variants from source file in region 18:34850635-34854319. Error was invalid region `18:34850636-34854319`
[2016-04-15T07:58Z] 2016-04-15 00:58:00 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:58:00,642 - WARNING - Could not retrieve variants from source file in region 18:34273068-34273469. Error was invalid region `18:34273069-34273469`
[2016-04-15T07:58Z] 2016-04-15 00:58:00 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:58:00,876 - WARNING - Could not retrieve variants from source file in region 18:49867013-49867414. Error was invalid region `18:49867014-49867414`
[2016-04-15T07:58Z] 2016-04-15 00:58:01 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:58:01,087 - WARNING - Could not retrieve variants from source file in region 18:42532919-42533320. Error was invalid region `18:42532920-42533320`
[2016-04-15T07:58Z] 2016-04-15 00:58:01 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:58:01,093 - WARNING - Could not retrieve variants from source file in region 18:40323286-40323687. Error was invalid region `18:40323287-40323687`
[2016-04-15T07:58Z] 2016-04-15 00:58:05 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:58:05,161 - WARNING - Could not retrieve variants from source file in region 18:44126698-44140405. Error was invalid region `18:44126699-44140405`
[2016-04-15T07:58Z] 2016-04-15 00:58:07 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:58:07,142 - WARNING - Could not retrieve variants from source file in region 18:34310457-34324281. Error was invalid region `18:34310458-34324281`
[2016-04-15T07:58Z] 2016-04-15 00:58:08 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:58:08,670 - WARNING - Could not retrieve variants from source file in region 18:47088444-47094054. Error was invalid region `18:47088445-47094054`
[2016-04-15T07:58Z] 2016-04-15 00:58:08 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:58:08,780 - WARNING - Could not retrieve variants from source file in region 18:43677813-43678225. Error was invalid region `18:43677814-43678225`
[2016-04-15T07:58Z] 2016-04-15 00:58:08 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:58:08,924 - WARNING - Could not retrieve variants from source file in region 18:49867013-49867414. Error was invalid region `18:49867014-49867414`
[2016-04-15T07:58Z] 2016-04-15 00:58:09 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:58:09,095 - WARNING - Could not retrieve variants from source file in region 18:42532919-42533320. Error was invalid region `18:42532920-42533320`
[2016-04-15T07:58Z] 2016-04-15 00:58:20 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:58:20,182 - WARNING - Could not retrieve variants from source file in region 18:45663177-45663578. Error was invalid region `18:45663178-45663578`
[2016-04-15T07:58Z] 2016-04-15 00:58:20 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:58:20,456 - WARNING - Could not retrieve variants from source file in region 18:43833467-43833891. Error was invalid region `18:43833468-43833891`
[2016-04-15T07:58Z] 2016-04-15 00:58:22 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:58:22,287 - WARNING - Could not retrieve variants from source file in region 18:43307035-43331086. Error was invalid region `18:43307036-43331086`
[2016-04-15T07:58Z] 2016-04-15 00:58:23 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:58:23,463 - WARNING - Could not retrieve variants from source file in region 18:47908345-47908746. Error was invalid region `18:47908346-47908746`
[2016-04-15T07:58Z] 2016-04-15 00:58:25 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:58:25,288 - WARNING - Could not retrieve variants from source file in region 18:45663177-45663578. Error was invalid region `18:45663178-45663578`
[2016-04-15T07:58Z] 2016-04-15 00:58:25 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:58:25,944 - WARNING - Could not retrieve variants from source file in region 18:48723006-48723629. Error was invalid region `18:48723007-48723629`
[2016-04-15T07:58Z] 2016-04-15 00:58:26 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:58:26,285 - WARNING - Could not retrieve variants from source file in region 18:47563088-47563489. Error was invalid region `18:47563089-47563489`
[2016-04-15T07:58Z] 2016-04-15 00:58:26 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:58:26,291 - WARNING - Could not retrieve variants from source file in region 18:44636824-44637225. Error was invalid region `18:44636825-44637225`
[2016-04-15T07:58Z] 2016-04-15 00:58:26 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:58:26,937 - WARNING - Could not retrieve variants from source file in region 18:47510902-47511303. Error was invalid region `18:47510903-47511303`
[2016-04-15T07:58Z] 2016-04-15 00:58:27 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:58:27,743 - WARNING - Could not retrieve variants from source file in region 18:47908345-47908746. Error was invalid region `18:47908346-47908746`
[2016-04-15T07:58Z] 2016-04-15 00:58:28 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:58:28,871 - WARNING - Could not retrieve variants from source file in region 18:44560089-44586145. Error was invalid region `18:44560090-44586145`
[2016-04-15T07:58Z] 2016-04-15 00:58:30 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:58:30,072 - WARNING - Could not retrieve variants from source file in region 18:46735818-46736219. Error was invalid region `18:46735819-46736219`
[2016-04-15T07:58Z] 2016-04-15 00:58:30 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:58:30,502 - WARNING - Could not retrieve variants from source file in region 18:45663177-45663578. Error was invalid region `18:45663178-45663578`
[2016-04-15T07:58Z] 2016-04-15 00:58:31 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:58:31,094 - WARNING - Could not retrieve variants from source file in region 18:43833467-43833891. Error was invalid region `18:43833468-43833891`
[2016-04-15T07:58Z] 2016-04-15 00:58:31 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:58:31,684 - WARNING - Could not retrieve variants from source file in region 18:48723006-48723629. Error was invalid region `18:48723007-48723629`
[2016-04-15T07:58Z] 2016-04-15 00:58:32 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:58:32,109 - WARNING - Could not retrieve variants from source file in region 18:44636824-44637225. Error was invalid region `18:44636825-44637225`
[2016-04-15T07:58Z] 2016-04-15 00:58:32 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:58:32,281 - WARNING - Could not retrieve variants from source file in region 18:47563088-47563489. Error was invalid region `18:47563089-47563489`
[2016-04-15T07:58Z] 2016-04-15 00:58:32 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:58:32,763 - WARNING - Could not retrieve variants from source file in region 18:47908345-47908746. Error was invalid region `18:47908346-47908746`
[2016-04-15T07:58Z] 2016-04-15 00:58:33 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:58:33,702 - WARNING - Could not retrieve variants from source file in region 18:44560089-44586145. Error was invalid region `18:44560090-44586145`
[2016-04-15T07:58Z] 2016-04-15 00:58:34 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:58:34,391 - WARNING - Could not retrieve variants from source file in region 18:46735818-46736219. Error was invalid region `18:46735819-46736219`
[2016-04-15T07:58Z] 2016-04-15 00:58:37 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:58:37,289 - WARNING - Could not retrieve variants from source file in region 18:48723006-48723629. Error was invalid region `18:48723007-48723629`
[2016-04-15T07:58Z] 2016-04-15 00:58:37 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:58:37,392 - WARNING - Could not retrieve variants from source file in region 18:47563088-47563489. Error was invalid region `18:47563089-47563489`
[2016-04-15T07:58Z] 2016-04-15 00:58:38 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:58:38,206 - WARNING - Could not retrieve variants from source file in region 18:48327604-48346214. Error was invalid region `18:48327605-48346214`
[2016-04-15T07:58Z] 2016-04-15 00:58:44 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:58:44,468 - WARNING - Could not retrieve variants from source file in region 18:48190229-48190630. Error was invalid region `18:48190230-48190630`
[2016-04-15T07:58Z] 2016-04-15 00:58:44 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:58:44,866 - WARNING - Could not retrieve variants from source file in region 18:47455712-47456113. Error was invalid region `18:47455713-47456113`
[2016-04-15T07:58Z] 2016-04-15 00:58:47 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:58:47,557 - WARNING - Could not retrieve variants from source file in region 18:43245945-43262549. Error was invalid region `18:43245946-43262549`
[2016-04-15T07:58Z] 2016-04-15 00:58:47 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:58:47,609 - WARNING - Could not retrieve variants from source file in region 18:44396035-44398326. Error was invalid region `18:44396036-44398326`
[2016-04-15T07:58Z] 2016-04-15 00:58:48 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:58:48,010 - WARNING - Could not retrieve variants from source file in region 18:48190229-48190630. Error was invalid region `18:48190230-48190630`
[2016-04-15T07:58Z] 2016-04-15 00:58:48 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:58:48,229 - WARNING - Could not retrieve variants from source file in region 18:47455712-47456113. Error was invalid region `18:47455713-47456113`
[2016-04-15T07:58Z] 2016-04-15 00:58:48 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:58:48,357 - WARNING - Could not retrieve variants from source file in region 18:43245945-43262549. Error was invalid region `18:43245946-43262549`
[2016-04-15T07:58Z] 2016-04-15 00:58:49 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:58:49,188 - WARNING - Could not retrieve variants from source file in region 18:47455712-47456113. Error was invalid region `18:47455713-47456113`
[2016-04-15T07:58Z] 2016-04-15 00:58:49 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:58:49,208 - WARNING - Could not retrieve variants from source file in region 18:48190229-48190630. Error was invalid region `18:48190230-48190630`
[2016-04-15T07:58Z] 2016-04-15 00:58:49 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:58:49,590 - WARNING - Could not retrieve variants from source file in region 18:43206774-43207175. Error was invalid region `18:43206775-43207175`
[2016-04-15T07:58Z] 2016-04-15 00:58:51 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:58:51,141 - WARNING - Could not retrieve variants from source file in region 18:46284376-46284777. Error was invalid region `18:46284377-46284777`
[2016-04-15T07:58Z] 2016-04-15 00:58:51 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:58:51,442 - WARNING - Could not retrieve variants from source file in region 18:43245945-43262549. Error was invalid region `18:43245946-43262549`
[2016-04-15T07:58Z] 2016-04-15 00:58:52 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:58:52,185 - WARNING - Could not retrieve variants from source file in region 18:46343455-46343856. Error was invalid region `18:46343456-46343856`
[2016-04-15T07:58Z] 2016-04-15 00:58:52 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:58:52,888 - WARNING - Could not retrieve variants from source file in region 18:43206774-43207175. Error was invalid region `18:43206775-43207175`
[2016-04-15T07:58Z] 2016-04-15 00:58:54 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:58:54,346 - WARNING - Could not retrieve variants from source file in region 18:44171769-44181417. Error was invalid region `18:44171770-44181417`
[2016-04-15T07:58Z] 2016-04-15 00:58:54 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:58:54,464 - WARNING - Could not retrieve variants from source file in region 18:46284376-46284777. Error was invalid region `18:46284377-46284777`
[2016-04-15T07:58Z] 2016-04-15 00:58:55 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:58:55,426 - WARNING - Could not retrieve variants from source file in region 18:46343455-46343856. Error was invalid region `18:46343456-46343856`
[2016-04-15T07:58Z] 2016-04-15 00:58:55 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:58:55,774 - WARNING - Could not retrieve variants from source file in region 18:43206774-43207175. Error was invalid region `18:43206775-43207175`
[2016-04-15T07:58Z] 2016-04-15 00:58:55 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:58:55,786 - WARNING - Could not retrieve variants from source file in region 18:46284376-46284777. Error was invalid region `18:46284377-46284777`
[2016-04-15T07:59Z] ['bcbio-variation-recall', 'square', '-Xms750m', '-Xmx7280m', '-XX:+UseSerialGC', '-c', 16, '-r', u'18:50278424-66344430', '--caller', 'platypus', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/18/Batch1-18_50278423_66344430.vcf.gz', '/mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/18/Batch1-18_50278423_66344430.vcf-inputs.txt'] in region: 18:50278424-66344430
[2016-04-15T07:59Z] 2016-04-15 00:59:11 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:59:11,253 - WARNING - Could not retrieve variants from source file in region 18:56936184-56940497. Error was invalid region `18:56936185-56940497`
[2016-04-15T07:59Z] 2016-04-15 00:59:11 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:59:11,814 - WARNING - Could not retrieve variants from source file in region 18:52895320-52895721. Error was invalid region `18:52895321-52895721`
[2016-04-15T07:59Z] 2016-04-15 00:59:12 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:59:12,177 - WARNING - Could not retrieve variants from source file in region 18:60562087-60562488. Error was invalid region `18:60562088-60562488`
[2016-04-15T07:59Z] 2016-04-15 00:59:13 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:59:13,120 - WARNING - Could not retrieve variants from source file in region 18:60021550-60036273. Error was invalid region `18:60021551-60036273`
[2016-04-15T07:59Z] 2016-04-15 00:59:13 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:59:13,250 - WARNING - Could not retrieve variants from source file in region 18:56887296-56887697. Error was invalid region `18:56887297-56887697`
[2016-04-15T07:59Z] 2016-04-15 00:59:13 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:59:13,855 - WARNING - Could not retrieve variants from source file in region 18:65179618-65180019. Error was invalid region `18:65179619-65180019`
[2016-04-15T07:59Z] 2016-04-15 00:59:13 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:59:13,973 - WARNING - Could not retrieve variants from source file in region 18:63489167-63530206. Error was invalid region `18:63489168-63530206`
[2016-04-15T07:59Z] 2016-04-15 00:59:14 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:59:14,038 - WARNING - Could not retrieve variants from source file in region 18:59166330-59174949. Error was invalid region `18:59166331-59174949`
[2016-04-15T07:59Z] 2016-04-15 00:59:14 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:59:14,636 - WARNING - Could not retrieve variants from source file in region 18:56648545-56648946. Error was invalid region `18:56648546-56648946`
[2016-04-15T07:59Z] 2016-04-15 00:59:14 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:59:14,691 - WARNING - Could not retrieve variants from source file in region 18:57567488-57567889. Error was invalid region `18:57567489-57567889`
[2016-04-15T07:59Z] 2016-04-15 00:59:14 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:59:14,757 - WARNING - Could not retrieve variants from source file in region 18:61471312-61471713. Error was invalid region `18:61471313-61471713`
[2016-04-15T07:59Z] 2016-04-15 00:59:15 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:59:15,442 - WARNING - Could not retrieve variants from source file in region 18:59482991-59483704. Error was invalid region `18:59482992-59483704`
[2016-04-15T07:59Z] 2016-04-15 00:59:17 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:59:17,414 - WARNING - Could not retrieve variants from source file in region 18:60562087-60562488. Error was invalid region `18:60562088-60562488`
[2016-04-15T07:59Z] 2016-04-15 00:59:19 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:59:19,619 - WARNING - Could not retrieve variants from source file in region 18:56887296-56887697. Error was invalid region `18:56887297-56887697`
[2016-04-15T07:59Z] 2016-04-15 00:59:19 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:59:19,642 - WARNING - Could not retrieve variants from source file in region 18:60021550-60036273. Error was invalid region `18:60021551-60036273`
[2016-04-15T07:59Z] 2016-04-15 00:59:20 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:59:20,595 - WARNING - Could not retrieve variants from source file in region 18:57026225-57026626. Error was invalid region `18:57026226-57026626`
[2016-04-15T07:59Z] 2016-04-15 00:59:20 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:59:20,630 - WARNING - Could not retrieve variants from source file in region 18:64211040-64211441. Error was invalid region `18:64211041-64211441`
[2016-04-15T07:59Z] 2016-04-15 00:59:21 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:59:21,277 - WARNING - Could not retrieve variants from source file in region 18:54814814-54815215. Error was invalid region `18:54814815-54815215`
[2016-04-15T07:59Z] 2016-04-15 00:59:21 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:59:21,331 - WARNING - Could not retrieve variants from source file in region 18:65179618-65180019. Error was invalid region `18:65179619-65180019`
[2016-04-15T07:59Z] 2016-04-15 00:59:21 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:59:21,829 - WARNING - Could not retrieve variants from source file in region 18:63489167-63530206. Error was invalid region `18:63489168-63530206`
[2016-04-15T07:59Z] 2016-04-15 00:59:21 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:59:21,911 - WARNING - Could not retrieve variants from source file in region 18:59810352-59822033. Error was invalid region `18:59810353-59822033`
[2016-04-15T07:59Z] 2016-04-15 00:59:22 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:59:22,277 - WARNING - Could not retrieve variants from source file in region 18:57567488-57567889. Error was invalid region `18:57567489-57567889`
[2016-04-15T07:59Z] 2016-04-15 00:59:22 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:59:22,309 - WARNING - Could not retrieve variants from source file in region 18:59482991-59483704. Error was invalid region `18:59482992-59483704`
[2016-04-15T07:59Z] 2016-04-15 00:59:22 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:59:22,320 - WARNING - Could not retrieve variants from source file in region 18:56936184-56940497. Error was invalid region `18:56936185-56940497`
[2016-04-15T07:59Z] 2016-04-15 00:59:22 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:59:22,493 - WARNING - Could not retrieve variants from source file in region 18:60562087-60562488. Error was invalid region `18:60562088-60562488`
[2016-04-15T07:59Z] 2016-04-15 00:59:22 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:59:22,500 - WARNING - Could not retrieve variants from source file in region 18:52895320-52895721. Error was invalid region `18:52895321-52895721`
[2016-04-15T07:59Z] 2016-04-15 00:59:25 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:59:25,048 - WARNING - Could not retrieve variants from source file in region 18:56887296-56887697. Error was invalid region `18:56887297-56887697`
[2016-04-15T07:59Z] 2016-04-15 00:59:25 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:59:25,705 - WARNING - Could not retrieve variants from source file in region 18:60021550-60036273. Error was invalid region `18:60021551-60036273`
[2016-04-15T07:59Z] 2016-04-15 00:59:28 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:59:28,341 - WARNING - Could not retrieve variants from source file in region 18:57026225-57026626. Error was invalid region `18:57026226-57026626`
[2016-04-15T07:59Z] 2016-04-15 00:59:28 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:59:28,382 - WARNING - Could not retrieve variants from source file in region 18:64211040-64211441. Error was invalid region `18:64211041-64211441`
[2016-04-15T07:59Z] 2016-04-15 00:59:29 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:59:29,299 - WARNING - Could not retrieve variants from source file in region 18:54814814-54815215. Error was invalid region `18:54814815-54815215`
[2016-04-15T07:59Z] 2016-04-15 00:59:29 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:59:29,737 - WARNING - Could not retrieve variants from source file in region 18:65179618-65180019. Error was invalid region `18:65179619-65180019`
[2016-04-15T07:59Z] 2016-04-15 00:59:29 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:59:29,869 - WARNING - Could not retrieve variants from source file in region 18:59166330-59174949. Error was invalid region `18:59166331-59174949`
[2016-04-15T07:59Z] 2016-04-15 00:59:30 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:59:30,011 - WARNING - Could not retrieve variants from source file in region 18:56648545-56648946. Error was invalid region `18:56648546-56648946`
[2016-04-15T07:59Z] 2016-04-15 00:59:30 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:59:30,557 - WARNING - Could not retrieve variants from source file in region 18:63489167-63530206. Error was invalid region `18:63489168-63530206`
[2016-04-15T07:59Z] 2016-04-15 00:59:30 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:59:30,896 - WARNING - Could not retrieve variants from source file in region 18:57567488-57567889. Error was invalid region `18:57567489-57567889`
[2016-04-15T07:59Z] 2016-04-15 00:59:41 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:59:41,490 - WARNING - Could not retrieve variants from source file in region 18:52604977-52605469. Error was invalid region `18:52604978-52605469`
[2016-04-15T07:59Z] 2016-04-15 00:59:42 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:59:42,364 - WARNING - Could not retrieve variants from source file in region 18:58038400-58038801. Error was invalid region `18:58038401-58038801`
[2016-04-15T07:59Z] 2016-04-15 00:59:42 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:59:42,646 - WARNING - Could not retrieve variants from source file in region 18:51795746-51821205. Error was invalid region `18:51795747-51821205`
[2016-04-15T07:59Z] 2016-04-15 00:59:43 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:59:43,325 - WARNING - Could not retrieve variants from source file in region 18:64176154-64176555. Error was invalid region `18:64176155-64176555`
[2016-04-15T07:59Z] 2016-04-15 00:59:43 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:59:43,427 - WARNING - Could not retrieve variants from source file in region 18:60191217-60191618. Error was invalid region `18:60191218-60191618`
[2016-04-15T07:59Z] 2016-04-15 00:59:43 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:59:43,977 - WARNING - Could not retrieve variants from source file in region 18:54677224-54677625. Error was invalid region `18:54677225-54677625`
[2016-04-15T07:59Z] 2016-04-15 00:59:46 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:59:46,328 - WARNING - Could not retrieve variants from source file in region 18:56278814-56279215. Error was invalid region `18:56278815-56279215`
[2016-04-15T07:59Z] 2016-04-15 00:59:47 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:59:47,459 - WARNING - Could not retrieve variants from source file in region 18:50432391-50432792. Error was invalid region `18:50432392-50432792`
[2016-04-15T07:59Z] 2016-04-15 00:59:47 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:59:47,906 - WARNING - Could not retrieve variants from source file in region 18:59935931-59945163. Error was invalid region `18:59935932-59945163`
[2016-04-15T07:59Z] 2016-04-15 00:59:48 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:59:48,238 - WARNING - Could not retrieve variants from source file in region 18:59768164-59781990. Error was invalid region `18:59768165-59781990`
[2016-04-15T07:59Z] 2016-04-15 00:59:48 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:59:48,261 - WARNING - Could not retrieve variants from source file in region 18:54677224-54677625. Error was invalid region `18:54677225-54677625`
[2016-04-15T07:59Z] 2016-04-15 00:59:48 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:59:48,268 - WARNING - Could not retrieve variants from source file in region 18:64176154-64176555. Error was invalid region `18:64176155-64176555`
[2016-04-15T07:59Z] 2016-04-15 00:59:50 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:59:50,747 - WARNING - Could not retrieve variants from source file in region 18:56278814-56279215. Error was invalid region `18:56278815-56279215`
[2016-04-15T07:59Z] 2016-04-15 00:59:50 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:59:50,752 - WARNING - Could not retrieve variants from source file in region 18:61377368-61390760. Error was invalid region `18:61377369-61390760`
[2016-04-15T07:59Z] 2016-04-15 00:59:51 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:59:51,979 - WARNING - Could not retrieve variants from source file in region 18:50432391-50432792. Error was invalid region `18:50432392-50432792`
[2016-04-15T07:59Z] 2016-04-15 00:59:53 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:59:53,393 - WARNING - Could not retrieve variants from source file in region 18:60191217-60191618. Error was invalid region `18:60191218-60191618`
[2016-04-15T07:59Z] 2016-04-15 00:59:53 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:59:53,676 - WARNING - Could not retrieve variants from source file in region 18:54677224-54677625. Error was invalid region `18:54677225-54677625`
[2016-04-15T07:59Z] 2016-04-15 00:59:53 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:59:53,696 - WARNING - Could not retrieve variants from source file in region 18:59768164-59781990. Error was invalid region `18:59768165-59781990`
[2016-04-15T07:59Z] 2016-04-15 00:59:53 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:59:53,697 - WARNING - Could not retrieve variants from source file in region 18:64176154-64176555. Error was invalid region `18:64176155-64176555`
[2016-04-15T07:59Z] 2016-04-15 00:59:55 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:59:55,564 - WARNING - Could not retrieve variants from source file in region 18:56278814-56279215. Error was invalid region `18:56278815-56279215`
[2016-04-15T07:59Z] 2016-04-15 00:59:56 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:59:56,537 - WARNING - Could not retrieve variants from source file in region 18:50432391-50432792. Error was invalid region `18:50432392-50432792`
[2016-04-15T07:59Z] 2016-04-15 00:59:58 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 00:59:58,680 - WARNING - Could not retrieve variants from source file in region 18:59768164-59781990. Error was invalid region `18:59768165-59781990`
[2016-04-15T08:00Z] 2016-04-15 01:00:04 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:00:04,769 - WARNING - Could not retrieve variants from source file in region 18:61564183-61600574. Error was invalid region `18:61564184-61600574`
[2016-04-15T08:00Z] 2016-04-15 01:00:04 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:00:04,813 - WARNING - Could not retrieve variants from source file in region 18:54366929-54367330. Error was invalid region `18:54366930-54367330`
[2016-04-15T08:00Z] 2016-04-15 01:00:05 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:00:05,277 - WARNING - Could not retrieve variants from source file in region 18:52265097-52265498. Error was invalid region `18:52265098-52265498`
[2016-04-15T08:00Z] 2016-04-15 01:00:05 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:00:05,426 - WARNING - Could not retrieve variants from source file in region 18:51750373-51750774. Error was invalid region `18:51750374-51750774`
[2016-04-15T08:00Z] 2016-04-15 01:00:06 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:00:06,606 - WARNING - Could not retrieve variants from source file in region 18:53302890-53303291. Error was invalid region `18:53302891-53303291`
[2016-04-15T08:00Z] 2016-04-15 01:00:08 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:00:08,174 - WARNING - Could not retrieve variants from source file in region 18:50278475-50278876. Error was invalid region `18:50278476-50278876`
[2016-04-15T08:00Z] 2016-04-15 01:00:08 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:00:08,418 - WARNING - Could not retrieve variants from source file in region 18:53302890-53303291. Error was invalid region `18:53302891-53303291`
[2016-04-15T08:00Z] 2016-04-15 01:00:08 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:00:08,422 - WARNING - Could not retrieve variants from source file in region 18:54423645-54448968. Error was invalid region `18:54423646-54448968`
[2016-04-15T08:00Z] 2016-04-15 01:00:08 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:00:08,457 - WARNING - Could not retrieve variants from source file in region 18:54339607-54340008. Error was invalid region `18:54339608-54340008`
[2016-04-15T08:00Z] 2016-04-15 01:00:08 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:00:08,843 - WARNING - Could not retrieve variants from source file in region 18:56246231-56247790. Error was invalid region `18:56246232-56247790`
[2016-04-15T08:00Z] 2016-04-15 01:00:09 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:00:09,741 - WARNING - Could not retrieve variants from source file in region 18:54366929-54367330. Error was invalid region `18:54366930-54367330`
[2016-04-15T08:00Z] 2016-04-15 01:00:10 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:00:10,435 - WARNING - Could not retrieve variants from source file in region 18:52265097-52265498. Error was invalid region `18:52265098-52265498`
[2016-04-15T08:00Z] 2016-04-15 01:00:10 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:00:10,460 - WARNING - Could not retrieve variants from source file in region 18:51750373-51750774. Error was invalid region `18:51750374-51750774`
[2016-04-15T08:00Z] 2016-04-15 01:00:11 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:00:11,079 - WARNING - Could not retrieve variants from source file in region 18:53302890-53303291. Error was invalid region `18:53302891-53303291`
[2016-04-15T08:00Z] 2016-04-15 01:00:12 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:00:12,367 - WARNING - Could not retrieve variants from source file in region 18:53068414-53089710. Error was invalid region `18:53068415-53089710`
[2016-04-15T08:00Z] 2016-04-15 01:00:13 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:00:13,166 - WARNING - Could not retrieve variants from source file in region 18:54339607-54340008. Error was invalid region `18:54339608-54340008`
[2016-04-15T08:00Z] 2016-04-15 01:00:13 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:00:13,483 - WARNING - Could not retrieve variants from source file in region 18:61322784-61323185. Error was invalid region `18:61322785-61323185`
[2016-04-15T08:00Z] 2016-04-15 01:00:14 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:00:14,746 - WARNING - Could not retrieve variants from source file in region 18:54366929-54367330. Error was invalid region `18:54366930-54367330`
[2016-04-15T08:00Z] 2016-04-15 01:00:15 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:00:15,095 - WARNING - Could not retrieve variants from source file in region 18:52265097-52265498. Error was invalid region `18:52265098-52265498`
[2016-04-15T08:00Z] 2016-04-15 01:00:15 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:00:15,401 - WARNING - Could not retrieve variants from source file in region 18:51750373-51750774. Error was invalid region `18:51750374-51750774`
[2016-04-15T08:00Z] 2016-04-15 01:00:17 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:00:17,818 - WARNING - Could not retrieve variants from source file in region 18:54339607-54340008. Error was invalid region `18:54339608-54340008`
[2016-04-15T08:00Z] 2016-04-15 01:00:19 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:00:19,058 - WARNING - Could not retrieve variants from source file in region 18:56246231-56247790. Error was invalid region `18:56246232-56247790`
[2016-04-15T08:00Z] 2016-04-15 01:00:23 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:00:23,081 - WARNING - Could not retrieve variants from source file in region 18:55922578-55923595. Error was invalid region `18:55922579-55923595`
[2016-04-15T08:00Z] 2016-04-15 01:00:23 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:00:23,447 - WARNING - Could not retrieve variants from source file in region 18:61264087-61264658. Error was invalid region `18:61264088-61264658`
[2016-04-15T08:00Z] 2016-04-15 01:00:24 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:00:24,299 - WARNING - Could not retrieve variants from source file in region 18:55816580-55816981. Error was invalid region `18:55816581-55816981`
[2016-04-15T08:00Z] 2016-04-15 01:00:26 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:00:26,957 - WARNING - Could not retrieve variants from source file in region 18:55922578-55923595. Error was invalid region `18:55922579-55923595`
[2016-04-15T08:00Z] 2016-04-15 01:00:27 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:00:27,405 - WARNING - Could not retrieve variants from source file in region 18:61264087-61264658. Error was invalid region `18:61264088-61264658`
[2016-04-15T08:00Z] 2016-04-15 01:00:28 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:00:28,638 - WARNING - Could not retrieve variants from source file in region 18:55922578-55923595. Error was invalid region `18:55922579-55923595`
[2016-04-15T08:00Z] 2016-04-15 01:00:29 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:00:29,457 - WARNING - Could not retrieve variants from source file in region 18:55816580-55816981. Error was invalid region `18:55816581-55816981`
[2016-04-15T08:00Z] 2016-04-15 01:00:29 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:00:29,938 - WARNING - Could not retrieve variants from source file in region 18:55894870-55895271. Error was invalid region `18:55894871-55895271`
[2016-04-15T08:00Z] 2016-04-15 01:00:30 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:00:30,600 - WARNING - Could not retrieve variants from source file in region 18:61022580-61022981. Error was invalid region `18:61022581-61022981`
[2016-04-15T08:00Z] 2016-04-15 01:00:30 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:00:30,969 - WARNING - Could not retrieve variants from source file in region 18:55317465-55335556. Error was invalid region `18:55317466-55335556`
[2016-04-15T08:00Z] 2016-04-15 01:00:30 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:00:30,972 - WARNING - Could not retrieve variants from source file in region 18:61156395-61171115. Error was invalid region `18:61156396-61171115`
[2016-04-15T08:00Z] 2016-04-15 01:00:31 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:00:31,889 - WARNING - Could not retrieve variants from source file in region 18:61264087-61264658. Error was invalid region `18:61264088-61264658`
[2016-04-15T08:00Z] 2016-04-15 01:00:32 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:00:32,076 - WARNING - Could not retrieve variants from source file in region 18:56148888-56149289. Error was invalid region `18:56148889-56149289`
[2016-04-15T08:00Z] 2016-04-15 01:00:32 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:00:32,610 - WARNING - Could not retrieve variants from source file in region 18:55288865-55289266. Error was invalid region `18:55288866-55289266`
[2016-04-15T08:00Z] 2016-04-15 01:00:33 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:00:33,297 - WARNING - Could not retrieve variants from source file in region 18:56148888-56149289. Error was invalid region `18:56148889-56149289`
[2016-04-15T08:00Z] 2016-04-15 01:00:36 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:00:36,851 - WARNING - Could not retrieve variants from source file in region 18:61022580-61022981. Error was invalid region `18:61022581-61022981`
[2016-04-15T08:00Z] 2016-04-15 01:00:37 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:00:37,051 - WARNING - Could not retrieve variants from source file in region 18:55221437-55240695. Error was invalid region `18:55221438-55240695`
[2016-04-15T08:00Z] 2016-04-15 01:00:37 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:00:37,404 - WARNING - Could not retrieve variants from source file in region 18:56148888-56149289. Error was invalid region `18:56148889-56149289`
[2016-04-15T08:00Z] 2016-04-15 01:00:37 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:00:37,482 - WARNING - Could not retrieve variants from source file in region 18:55894870-55895271. Error was invalid region `18:55894871-55895271`
[2016-04-15T08:00Z] 2016-04-15 01:00:37 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:00:37,576 - WARNING - Could not retrieve variants from source file in region 18:55143555-55143956. Error was invalid region `18:55143556-55143956`
[2016-04-15T08:00Z] 2016-04-15 01:00:40 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:00:40,830 - WARNING - Could not retrieve variants from source file in region 18:61156395-61171115. Error was invalid region `18:61156396-61171115`
[2016-04-15T08:00Z] 2016-04-15 01:00:41 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:00:41,110 - WARNING - Could not retrieve variants from source file in region 18:61022580-61022981. Error was invalid region `18:61022581-61022981`
[2016-04-15T08:00Z] 2016-04-15 01:00:41 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:00:41,587 - WARNING - Could not retrieve variants from source file in region 18:55714411-55714812. Error was invalid region `18:55714412-55714812`
[2016-04-15T08:00Z] 2016-04-15 01:00:42 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:00:42,147 - WARNING - Could not retrieve variants from source file in region 18:55288865-55289266. Error was invalid region `18:55288866-55289266`
[2016-04-15T08:00Z] 2016-04-15 01:00:42 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:00:42,242 - WARNING - Could not retrieve variants from source file in region 18:55143555-55143956. Error was invalid region `18:55143556-55143956`
[2016-04-15T08:00Z] 2016-04-15 01:00:45 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:00:45,607 - WARNING - Could not retrieve variants from source file in region 18:55362321-55365042. Error was invalid region `18:55362322-55365042`
[2016-04-15T08:00Z] 2016-04-15 01:00:45 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:00:45,724 - WARNING - Could not retrieve variants from source file in region 18:55714411-55714812. Error was invalid region `18:55714412-55714812`
[2016-04-15T08:00Z] 2016-04-15 01:00:45 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:00:45,919 - WARNING - Could not retrieve variants from source file in region 18:55362321-55365042. Error was invalid region `18:55362322-55365042`
[2016-04-15T08:00Z] 2016-04-15 01:00:45 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:00:45,926 - WARNING - Could not retrieve variants from source file in region 18:55714411-55714812. Error was invalid region `18:55714412-55714812`
[2016-04-15T08:00Z] 2016-04-15 01:00:45 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:00:45,945 - WARNING - Could not retrieve variants from source file in region 18:55362321-55365042. Error was invalid region `18:55362322-55365042`
[2016-04-15T08:00Z] ['bcbio-variation-recall', 'square', '-Xms750m', '-Xmx7280m', '-XX:+UseSerialGC', '-c', 16, '-r', u'18:66346700-78077248', '--caller', 'platypus', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/18/Batch1-18_66346699_78077248.vcf.gz', '/mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/18/Batch1-18_66346699_78077248.vcf-inputs.txt'] in region: 18:66346700-78077248
[2016-04-15T08:01Z] 2016-04-15 01:01:00 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:01:00,691 - WARNING - Could not retrieve variants from source file in region 18:77805738-77806139. Error was invalid region `18:77805739-77806139`
[2016-04-15T08:01Z] 2016-04-15 01:01:02 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:01:02,041 - WARNING - Could not retrieve variants from source file in region 18:77472916-77473317. Error was invalid region `18:77472917-77473317`
[2016-04-15T08:01Z] 2016-04-15 01:01:02 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:01:02,836 - WARNING - Could not retrieve variants from source file in region 18:70209110-70209511. Error was invalid region `18:70209111-70209511`
[2016-04-15T08:01Z] 2016-04-15 01:01:04 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:01:04,235 - WARNING - Could not retrieve variants from source file in region 18:72342797-72347672. Error was invalid region `18:72342798-72347672`
[2016-04-15T08:01Z] 2016-04-15 01:01:04 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:01:04,630 - WARNING - Could not retrieve variants from source file in region 18:77066789-77067190. Error was invalid region `18:77066790-77067190`
[2016-04-15T08:01Z] 2016-04-15 01:01:04 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:01:04,785 - WARNING - Could not retrieve variants from source file in region 18:77727924-77746813. Error was invalid region `18:77727925-77746813`
[2016-04-15T08:01Z] 2016-04-15 01:01:04 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:01:04,901 - WARNING - Could not retrieve variants from source file in region 18:74154789-74155190. Error was invalid region `18:74154790-74155190`
[2016-04-15T08:01Z] 2016-04-15 01:01:05 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:01:05,205 - WARNING - Could not retrieve variants from source file in region 18:77513510-77513911. Error was invalid region `18:77513511-77513911`
[2016-04-15T08:01Z] 2016-04-15 01:01:05 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:01:05,210 - WARNING - Could not retrieve variants from source file in region 18:77894633-77895034. Error was invalid region `18:77894634-77895034`
[2016-04-15T08:01Z] 2016-04-15 01:01:05 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:01:05,249 - WARNING - Could not retrieve variants from source file in region 18:67718477-67718878. Error was invalid region `18:67718478-67718878`
[2016-04-15T08:01Z] 2016-04-15 01:01:05 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:01:05,308 - WARNING - Could not retrieve variants from source file in region 18:77623480-77623881. Error was invalid region `18:77623481-77623881`
[2016-04-15T08:01Z] 2016-04-15 01:01:05 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:01:05,351 - WARNING - Could not retrieve variants from source file in region 18:72021506-72021907. Error was invalid region `18:72021507-72021907`
[2016-04-15T08:01Z] 2016-04-15 01:01:05 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:01:05,642 - WARNING - Could not retrieve variants from source file in region 18:77805738-77806139. Error was invalid region `18:77805739-77806139`
[2016-04-15T08:01Z] 2016-04-15 01:01:07 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:01:07,407 - WARNING - Could not retrieve variants from source file in region 18:77472916-77473317. Error was invalid region `18:77472917-77473317`
[2016-04-15T08:01Z] 2016-04-15 01:01:08 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:01:08,864 - WARNING - Could not retrieve variants from source file in region 18:70209110-70209511. Error was invalid region `18:70209111-70209511`
[2016-04-15T08:01Z] 2016-04-15 01:01:11 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:01:11,534 - WARNING - Could not retrieve variants from source file in region 18:72103571-72114645. Error was invalid region `18:72103572-72114645`
[2016-04-15T08:01Z] 2016-04-15 01:01:12 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:01:12,604 - WARNING - Could not retrieve variants from source file in region 18:70501556-70501957. Error was invalid region `18:70501557-70501957`
[2016-04-15T08:01Z] 2016-04-15 01:01:13 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:01:13,363 - WARNING - Could not retrieve variants from source file in region 18:77439917-77440318. Error was invalid region `18:77439918-77440318`
[2016-04-15T08:01Z] 2016-04-15 01:01:13 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:01:13,439 - WARNING - Could not retrieve variants from source file in region 18:77727924-77746813. Error was invalid region `18:77727925-77746813`
[2016-04-15T08:01Z] 2016-04-15 01:01:14 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:01:14,110 - WARNING - Could not retrieve variants from source file in region 18:72021506-72021907. Error was invalid region `18:72021507-72021907`
[2016-04-15T08:01Z] 2016-04-15 01:01:14 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:01:14,147 - WARNING - Could not retrieve variants from source file in region 18:67718477-67718878. Error was invalid region `18:67718478-67718878`
[2016-04-15T08:01Z] 2016-04-15 01:01:14 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:01:14,165 - WARNING - Could not retrieve variants from source file in region 18:77513510-77513911. Error was invalid region `18:77513511-77513911`
[2016-04-15T08:01Z] 2016-04-15 01:01:14 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:01:14,614 - WARNING - Could not retrieve variants from source file in region 18:77472916-77473317. Error was invalid region `18:77472917-77473317`
[2016-04-15T08:01Z] 2016-04-15 01:01:14 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:01:14,703 - WARNING - Could not retrieve variants from source file in region 18:77894633-77895034. Error was invalid region `18:77894634-77895034`
[2016-04-15T08:01Z] 2016-04-15 01:01:14 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:01:14,704 - WARNING - Could not retrieve variants from source file in region 18:77805738-77806139. Error was invalid region `18:77805739-77806139`
[2016-04-15T08:01Z] 2016-04-15 01:01:14 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:01:14,798 - WARNING - Could not retrieve variants from source file in region 18:70209110-70209511. Error was invalid region `18:70209111-70209511`
[2016-04-15T08:01Z] 2016-04-15 01:01:17 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:01:17,615 - WARNING - Could not retrieve variants from source file in region 18:72103571-72114645. Error was invalid region `18:72103572-72114645`
[2016-04-15T08:01Z] 2016-04-15 01:01:19 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:01:19,021 - WARNING - Could not retrieve variants from source file in region 18:72342797-72347672. Error was invalid region `18:72342798-72347672`
[2016-04-15T08:01Z] 2016-04-15 01:01:21 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:01:21,268 - WARNING - Could not retrieve variants from source file in region 18:77727924-77746813. Error was invalid region `18:77727925-77746813`
[2016-04-15T08:01Z] 2016-04-15 01:01:21 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:01:21,525 - WARNING - Could not retrieve variants from source file in region 18:77513510-77513911. Error was invalid region `18:77513511-77513911`
[2016-04-15T08:01Z] 2016-04-15 01:01:21 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:01:21,944 - WARNING - Could not retrieve variants from source file in region 18:72021506-72021907. Error was invalid region `18:72021507-72021907`
[2016-04-15T08:01Z] 2016-04-15 01:01:21 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:01:21,990 - WARNING - Could not retrieve variants from source file in region 18:77894633-77895034. Error was invalid region `18:77894634-77895034`
[2016-04-15T08:01Z] 2016-04-15 01:01:22 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:01:22,203 - WARNING - Could not retrieve variants from source file in region 18:67718477-67718878. Error was invalid region `18:67718478-67718878`
[2016-04-15T08:01Z] 2016-04-15 01:01:31 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:01:31,437 - WARNING - Could not retrieve variants from source file in region 18:72914069-72917517. Error was invalid region `18:72914070-72917517`
[2016-04-15T08:01Z] 2016-04-15 01:01:32 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:01:32,979 - WARNING - Could not retrieve variants from source file in region 18:77170331-77171251. Error was invalid region `18:77170332-77171251`
[2016-04-15T08:01Z] 2016-04-15 01:01:34 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:01:34,326 - WARNING - Could not retrieve variants from source file in region 18:70532629-70533030. Error was invalid region `18:70532630-70533030`
[2016-04-15T08:01Z] 2016-04-15 01:01:34 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:01:34,444 - WARNING - Could not retrieve variants from source file in region 18:70417185-70417599. Error was invalid region `18:70417186-70417599`
[2016-04-15T08:01Z] 2016-04-15 01:01:34 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:01:34,889 - WARNING - Could not retrieve variants from source file in region 18:74090746-74091148. Error was invalid region `18:74090747-74091148`
[2016-04-15T08:01Z] 2016-04-15 01:01:35 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:01:35,329 - WARNING - Could not retrieve variants from source file in region 18:72223380-72234825. Error was invalid region `18:72223381-72234825`
[2016-04-15T08:01Z] 2016-04-15 01:01:36 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:01:36,090 - WARNING - Could not retrieve variants from source file in region 18:72914069-72917517. Error was invalid region `18:72914070-72917517`
[2016-04-15T08:01Z] 2016-04-15 01:01:36 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:01:36,778 - WARNING - Could not retrieve variants from source file in region 18:77170331-77171251. Error was invalid region `18:77170332-77171251`
[2016-04-15T08:01Z] 2016-04-15 01:01:38 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:01:38,193 - WARNING - Could not retrieve variants from source file in region 18:66541795-66542196. Error was invalid region `18:66541796-66542196`
[2016-04-15T08:01Z] 2016-04-15 01:01:38 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:01:38,956 - WARNING - Could not retrieve variants from source file in region 18:67992473-67992874. Error was invalid region `18:67992474-67992874`
[2016-04-15T08:01Z] 2016-04-15 01:01:39 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:01:39,189 - WARNING - Could not retrieve variants from source file in region 18:70532629-70533030. Error was invalid region `18:70532630-70533030`
[2016-04-15T08:01Z] 2016-04-15 01:01:39 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:01:39,342 - WARNING - Could not retrieve variants from source file in region 18:74090746-74091148. Error was invalid region `18:74090747-74091148`
[2016-04-15T08:01Z] 2016-04-15 01:01:40 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:01:40,580 - WARNING - Could not retrieve variants from source file in region 18:72914069-72917517. Error was invalid region `18:72914070-72917517`
[2016-04-15T08:01Z] 2016-04-15 01:01:41 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:01:41,962 - WARNING - Could not retrieve variants from source file in region 18:67344823-67365858. Error was invalid region `18:67344824-67365858`
[2016-04-15T08:01Z] 2016-04-15 01:01:43 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:01:43,589 - WARNING - Could not retrieve variants from source file in region 18:67992473-67992874. Error was invalid region `18:67992474-67992874`
[2016-04-15T08:01Z] 2016-04-15 01:01:44 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:01:44,017 - WARNING - Could not retrieve variants from source file in region 18:67344823-67365858. Error was invalid region `18:67344824-67365858`
[2016-04-15T08:01Z] 2016-04-15 01:01:44 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:01:44,055 - WARNING - Could not retrieve variants from source file in region 18:74090746-74091148. Error was invalid region `18:74090747-74091148`
[2016-04-15T08:01Z] 2016-04-15 01:01:44 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:01:44,333 - WARNING - Could not retrieve variants from source file in region 18:70417185-70417599. Error was invalid region `18:70417186-70417599`
[2016-04-15T08:01Z] 2016-04-15 01:01:44 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:01:44,356 - WARNING - Could not retrieve variants from source file in region 18:72223380-72234825. Error was invalid region `18:72223381-72234825`
[2016-04-15T08:01Z] 2016-04-15 01:01:47 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:01:47,989 - WARNING - Could not retrieve variants from source file in region 18:67531431-67534832. Error was invalid region `18:67531432-67534832`
[2016-04-15T08:01Z] 2016-04-15 01:01:51 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:01:51,995 - WARNING - Could not retrieve variants from source file in region 18:72775910-72776311. Error was invalid region `18:72775911-72776311`
[2016-04-15T08:01Z] 2016-04-15 01:01:52 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:01:52,149 - WARNING - Could not retrieve variants from source file in region 18:66503882-66504649. Error was invalid region `18:66503883-66504649`
[2016-04-15T08:01Z] 2016-04-15 01:01:53 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:01:53,023 - WARNING - Could not retrieve variants from source file in region 18:67855141-67871533. Error was invalid region `18:67855142-67871533`
[2016-04-15T08:01Z] 2016-04-15 01:01:53 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:01:53,192 - WARNING - Could not retrieve variants from source file in region 18:66503882-66504649. Error was invalid region `18:66503883-66504649`
[2016-04-15T08:01Z] 2016-04-15 01:01:53 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:01:53,690 - WARNING - Could not retrieve variants from source file in region 18:66503882-66504649. Error was invalid region `18:66503883-66504649`
[2016-04-15T08:01Z] 2016-04-15 01:01:53 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:01:53,696 - WARNING - Could not retrieve variants from source file in region 18:67855141-67871533. Error was invalid region `18:67855142-67871533`
[2016-04-15T08:01Z] 2016-04-15 01:01:56 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:01:56,192 - WARNING - Could not retrieve variants from source file in region 18:72775910-72776311. Error was invalid region `18:72775911-72776311`
[2016-04-15T08:01Z] 2016-04-15 01:01:57 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:01:57,463 - WARNING - Could not retrieve variants from source file in region 18:74962434-74980999. Error was invalid region `18:74962435-74980999`
[2016-04-15T08:01Z] 2016-04-15 01:01:57 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:01:57,836 - WARNING - Could not retrieve variants from source file in region 18:72516333-72516734. Error was invalid region `18:72516334-72516734`
[2016-04-15T08:01Z] 2016-04-15 01:01:58 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:01:58,054 - WARNING - Could not retrieve variants from source file in region 18:72775910-72776311. Error was invalid region `18:72775911-72776311`
[2016-04-15T08:01Z] 2016-04-15 01:01:58 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:01:58,096 - WARNING - Could not retrieve variants from source file in region 18:76829314-76829715. Error was invalid region `18:76829315-76829715`
[2016-04-15T08:01Z] 2016-04-15 01:01:59 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:01:59,165 - WARNING - Could not retrieve variants from source file in region 18:76753377-76754656. Error was invalid region `18:76753378-76754656`
[2016-04-15T08:02Z] 2016-04-15 01:02:00 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:02:00,893 - WARNING - Could not retrieve variants from source file in region 18:74962434-74980999. Error was invalid region `18:74962435-74980999`
[2016-04-15T08:02Z] 2016-04-15 01:02:01 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:02:01,101 - WARNING - Could not retrieve variants from source file in region 18:76829314-76829715. Error was invalid region `18:76829315-76829715`
[2016-04-15T08:02Z] 2016-04-15 01:02:01 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:02:01,555 - WARNING - Could not retrieve variants from source file in region 18:74962434-74980999. Error was invalid region `18:74962435-74980999`
[2016-04-15T08:02Z] 2016-04-15 01:02:01 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:02:01,763 - WARNING - Could not retrieve variants from source file in region 18:76753377-76754656. Error was invalid region `18:76753378-76754656`
[2016-04-15T08:02Z] 2016-04-15 01:02:01 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:02:01,776 - WARNING - Could not retrieve variants from source file in region 18:76753377-76754656. Error was invalid region `18:76753378-76754656`
[2016-04-15T08:02Z] 2016-04-15 01:02:06 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:02:06,264 - WARNING - Could not retrieve variants from source file in region 18:74580569-74627803. Error was invalid region `18:74580570-74627803`
[2016-04-15T08:02Z] 2016-04-15 01:02:11 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:02:11,455 - WARNING - Could not retrieve variants from source file in region 18:74202604-74208763. Error was invalid region `18:74202605-74208763`
[2016-04-15T08:02Z] ['bcbio-variation-recall', 'square', '-Xms750m', '-Xmx7280m', '-XX:+UseSerialGC', '-c', 16, '-r', u'19:1-15509577', '--caller', 'platypus', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/19/Batch1-19_0_15509577.vcf.gz', '/mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/19/Batch1-19_0_15509577.vcf-inputs.txt'] in region: 19:1-15509577
[2016-04-15T08:02Z] 2016-04-15 01:02:27 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:02:27,328 - WARNING - Could not retrieve variants from source file in region 19:13936174-13941787. Error was invalid region `19:13936175-13941787`
[2016-04-15T08:02Z] 2016-04-15 01:02:28 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:02:28,590 - WARNING - Could not retrieve variants from source file in region 19:12662107-12662508. Error was invalid region `19:12662108-12662508`
[2016-04-15T08:02Z] 2016-04-15 01:02:29 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:02:29,241 - WARNING - Could not retrieve variants from source file in region 19:11890792-11891193. Error was invalid region `19:11890793-11891193`
[2016-04-15T08:02Z] 2016-04-15 01:02:29 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:02:29,285 - WARNING - Could not retrieve variants from source file in region 19:14628939-14629340. Error was invalid region `19:14628940-14629340`
[2016-04-15T08:02Z] 2016-04-15 01:02:29 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:02:29,816 - WARNING - Could not retrieve variants from source file in region 19:10334452-10334853. Error was invalid region `19:10334453-10334853`
[2016-04-15T08:02Z] 2016-04-15 01:02:29 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:02:29,890 - WARNING - Could not retrieve variants from source file in region 19:15508151-15508552. Error was invalid region `19:15508152-15508552`
[2016-04-15T08:02Z] 2016-04-15 01:02:30 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:02:30,145 - WARNING - Could not retrieve variants from source file in region 19:14752114-14773068. Error was invalid region `19:14752115-14773068`
[2016-04-15T08:02Z] 2016-04-15 01:02:30 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:02:30,184 - WARNING - Could not retrieve variants from source file in region 19:14268588-14273831. Error was invalid region `19:14268589-14273831`
[2016-04-15T08:02Z] 2016-04-15 01:02:30 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:02:30,765 - WARNING - Could not retrieve variants from source file in region 19:14938405-14939123. Error was invalid region `19:14938406-14939123`
[2016-04-15T08:02Z] 2016-04-15 01:02:35 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:02:35,404 - WARNING - Could not retrieve variants from source file in region 19:12662107-12662508. Error was invalid region `19:12662108-12662508`
[2016-04-15T08:02Z] 2016-04-15 01:02:37 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:02:37,290 - WARNING - Could not retrieve variants from source file in region 19:11890792-11891193. Error was invalid region `19:11890793-11891193`
[2016-04-15T08:02Z] 2016-04-15 01:02:37 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:02:37,423 - WARNING - Could not retrieve variants from source file in region 19:15052209-15053173. Error was invalid region `19:15052210-15053173`
[2016-04-15T08:02Z] 2016-04-15 01:02:37 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:02:37,814 - WARNING - Could not retrieve variants from source file in region 19:14628939-14629340. Error was invalid region `19:14628940-14629340`
[2016-04-15T08:02Z] 2016-04-15 01:02:38 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:02:38,124 - WARNING - Could not retrieve variants from source file in region 19:15508151-15508552. Error was invalid region `19:15508152-15508552`
[2016-04-15T08:02Z] 2016-04-15 01:02:38 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:02:38,341 - WARNING - Could not retrieve variants from source file in region 19:10334452-10334853. Error was invalid region `19:10334453-10334853`
[2016-04-15T08:02Z] 2016-04-15 01:02:38 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:02:38,642 - WARNING - Could not retrieve variants from source file in region 19:9922012-9922413. Error was invalid region `19:9922013-9922413`
[2016-04-15T08:02Z] 2016-04-15 01:02:38 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:02:38,709 - WARNING - Could not retrieve variants from source file in region 19:13936174-13941787. Error was invalid region `19:13936175-13941787`
[2016-04-15T08:02Z] 2016-04-15 01:02:38 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:02:38,967 - WARNING - Could not retrieve variants from source file in region 19:14268588-14273831. Error was invalid region `19:14268589-14273831`
[2016-04-15T08:02Z] 2016-04-15 01:02:40 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:02:40,537 - WARNING - Could not retrieve variants from source file in region 19:12662107-12662508. Error was invalid region `19:12662108-12662508`
[2016-04-15T08:02Z] 2016-04-15 01:02:44 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:02:44,002 - WARNING - Could not retrieve variants from source file in region 19:11890792-11891193. Error was invalid region `19:11890793-11891193`
[2016-04-15T08:02Z] 2016-04-15 01:02:44 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:02:44,882 - WARNING - Could not retrieve variants from source file in region 19:14628939-14629340. Error was invalid region `19:14628940-14629340`
[2016-04-15T08:02Z] 2016-04-15 01:02:46 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:02:46,051 - WARNING - Could not retrieve variants from source file in region 19:15508151-15508552. Error was invalid region `19:15508152-15508552`
[2016-04-15T08:02Z] 2016-04-15 01:02:46 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:02:46,685 - WARNING - Could not retrieve variants from source file in region 19:14752114-14773068. Error was invalid region `19:14752115-14773068`
[2016-04-15T08:02Z] 2016-04-15 01:02:46 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:02:46,782 - WARNING - Could not retrieve variants from source file in region 19:10334452-10334853. Error was invalid region `19:10334453-10334853`
[2016-04-15T08:02Z] 2016-04-15 01:02:47 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:02:47,297 - WARNING - Could not retrieve variants from source file in region 19:14268588-14273831. Error was invalid region `19:14268589-14273831`
[2016-04-15T08:02Z] 2016-04-15 01:02:58 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:02:58,007 - WARNING - Could not retrieve variants from source file in region 19:12575838-12576239. Error was invalid region `19:12575839-12576239`
[2016-04-15T08:02Z] 2016-04-15 01:02:58 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:02:58,629 - WARNING - Could not retrieve variants from source file in region 19:13444997-13445398. Error was invalid region `19:13444998-13445398`
[2016-04-15T08:02Z] 2016-04-15 01:02:58 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:02:58,893 - WARNING - Could not retrieve variants from source file in region 19:8468126-8487074. Error was invalid region `19:8468127-8487074`
[2016-04-15T08:03Z] 2016-04-15 01:03:00 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:03:00,759 - WARNING - Could not retrieve variants from source file in region 19:15479156-15479557. Error was invalid region `19:15479157-15479557`
[2016-04-15T08:03Z] 2016-04-15 01:03:03 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:03:03,505 - WARNING - Could not retrieve variants from source file in region 19:10265101-10267267. Error was invalid region `19:10265102-10267267`
[2016-04-15T08:03Z] 2016-04-15 01:03:03 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:03:03,897 - WARNING - Could not retrieve variants from source file in region 19:9868067-9868594. Error was invalid region `19:9868068-9868594`
[2016-04-15T08:03Z] 2016-04-15 01:03:05 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:03:05,473 - WARNING - Could not retrieve variants from source file in region 19:13444997-13445398. Error was invalid region `19:13444998-13445398`
[2016-04-15T08:03Z] 2016-04-15 01:03:06 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:03:06,078 - WARNING - Could not retrieve variants from source file in region 19:10600231-10625257. Error was invalid region `19:10600232-10625257`
[2016-04-15T08:03Z] 2016-04-15 01:03:06 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:03:06,635 - WARNING - Could not retrieve variants from source file in region 19:11832624-11833025. Error was invalid region `19:11832625-11833025`
[2016-04-15T08:03Z] 2016-04-15 01:03:06 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:03:06,677 - WARNING - Could not retrieve variants from source file in region 19:14991432-14991833. Error was invalid region `19:14991433-14991833`
[2016-04-15T08:03Z] 2016-04-15 01:03:06 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:03:06,950 - WARNING - Could not retrieve variants from source file in region 19:15479156-15479557. Error was invalid region `19:15479157-15479557`
[2016-04-15T08:03Z] 2016-04-15 01:03:08 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:03:08,534 - WARNING - Could not retrieve variants from source file in region 19:9868067-9868594. Error was invalid region `19:9868068-9868594`
[2016-04-15T08:03Z] 2016-04-15 01:03:12 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:03:12,581 - WARNING - Could not retrieve variants from source file in region 19:12575838-12576239. Error was invalid region `19:12575839-12576239`
[2016-04-15T08:03Z] 2016-04-15 01:03:12 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:03:12,587 - WARNING - Could not retrieve variants from source file in region 19:13444997-13445398. Error was invalid region `19:13444998-13445398`
[2016-04-15T08:03Z] 2016-04-15 01:03:13 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:03:13,705 - WARNING - Could not retrieve variants from source file in region 19:14682593-14682994. Error was invalid region `19:14682594-14682994`
[2016-04-15T08:03Z] 2016-04-15 01:03:14 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:03:14,495 - WARNING - Could not retrieve variants from source file in region 19:8468126-8487074. Error was invalid region `19:8468127-8487074`
[2016-04-15T08:03Z] 2016-04-15 01:03:14 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:03:14,849 - WARNING - Could not retrieve variants from source file in region 19:15479156-15479557. Error was invalid region `19:15479157-15479557`
[2016-04-15T08:03Z] 2016-04-15 01:03:14 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:03:14,902 - WARNING - Could not retrieve variants from source file in region 19:11832624-11833025. Error was invalid region `19:11832625-11833025`
[2016-04-15T08:03Z] 2016-04-15 01:03:15 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:03:15,443 - WARNING - Could not retrieve variants from source file in region 19:9868067-9868594. Error was invalid region `19:9868068-9868594`
[2016-04-15T08:03Z] 2016-04-15 01:03:15 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:03:15,546 - WARNING - Could not retrieve variants from source file in region 19:10265101-10267267. Error was invalid region `19:10265102-10267267`
[2016-04-15T08:03Z] 2016-04-15 01:03:20 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:03:20,381 - WARNING - Could not retrieve variants from source file in region 19:14682593-14682994. Error was invalid region `19:14682594-14682994`
[2016-04-15T08:03Z] 2016-04-15 01:03:23 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:03:23,815 - WARNING - Could not retrieve variants from source file in region 19:14200685-14231520. Error was invalid region `19:14200686-14231520`
[2016-04-15T08:03Z] 2016-04-15 01:03:29 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:03:29,995 - WARNING - Could not retrieve variants from source file in region 19:12541321-12542962. Error was invalid region `19:12541322-12542962`
[2016-04-15T08:03Z] 2016-04-15 01:03:32 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:03:32,157 - WARNING - Could not retrieve variants from source file in region 19:14817337-14831945. Error was invalid region `19:14817338-14831945`
[2016-04-15T08:03Z] 2016-04-15 01:03:32 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:03:32,515 - WARNING - Could not retrieve variants from source file in region 19:7913763-7938496. Error was invalid region `19:7913764-7938496`
[2016-04-15T08:03Z] 2016-04-15 01:03:32 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:03:32,628 - WARNING - Could not retrieve variants from source file in region 19:8321735-8327094. Error was invalid region `19:8321736-8327094`
[2016-04-15T08:03Z] 2016-04-15 01:03:33 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:03:33,042 - WARNING - Could not retrieve variants from source file in region 19:8841347-8841748. Error was invalid region `19:8841348-8841748`
[2016-04-15T08:03Z] 2016-04-15 01:03:35 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:03:35,653 - WARNING - Could not retrieve variants from source file in region 19:10568308-10568709. Error was invalid region `19:10568309-10568709`
[2016-04-15T08:03Z] 2016-04-15 01:03:37 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:03:37,549 - WARNING - Could not retrieve variants from source file in region 19:15271560-15303415. Error was invalid region `19:15271561-15303415`
[2016-04-15T08:03Z] 2016-04-15 01:03:37 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:03:37,750 - WARNING - Could not retrieve variants from source file in region 19:9801229-9804614. Error was invalid region `19:9801230-9804614`
[2016-04-15T08:03Z] 2016-04-15 01:03:37 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:03:37,852 - WARNING - Could not retrieve variants from source file in region 19:8841347-8841748. Error was invalid region `19:8841348-8841748`
[2016-04-15T08:03Z] 2016-04-15 01:03:38 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:03:38,196 - WARNING - Could not retrieve variants from source file in region 19:10218313-10226446. Error was invalid region `19:10218314-10226446`
[2016-04-15T08:03Z] 2016-04-15 01:03:38 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:03:38,744 - WARNING - Could not retrieve variants from source file in region 19:12541321-12542962. Error was invalid region `19:12541322-12542962`
[2016-04-15T08:03Z] 2016-04-15 01:03:39 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:03:39,823 - WARNING - Could not retrieve variants from source file in region 19:10568308-10568709. Error was invalid region `19:10568309-10568709`
[2016-04-15T08:03Z] 2016-04-15 01:03:41 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:03:41,508 - WARNING - Could not retrieve variants from source file in region 19:14817337-14831945. Error was invalid region `19:14817338-14831945`
[2016-04-15T08:03Z] 2016-04-15 01:03:42 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:03:42,430 - WARNING - Could not retrieve variants from source file in region 19:15271560-15303415. Error was invalid region `19:15271561-15303415`
[2016-04-15T08:03Z] 2016-04-15 01:03:42 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:03:42,567 - WARNING - Could not retrieve variants from source file in region 19:8321735-8327094. Error was invalid region `19:8321736-8327094`
[2016-04-15T08:03Z] 2016-04-15 01:03:43 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:03:43,215 - WARNING - Could not retrieve variants from source file in region 19:8841347-8841748. Error was invalid region `19:8841348-8841748`
[2016-04-15T08:03Z] 2016-04-15 01:03:43 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:03:43,575 - WARNING - Could not retrieve variants from source file in region 19:10218313-10226446. Error was invalid region `19:10218314-10226446`
[2016-04-15T08:03Z] 2016-04-15 01:03:56 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:03:56,037 - WARNING - Could not retrieve variants from source file in region 19:9768714-9769115. Error was invalid region `19:9768715-9769115`
[2016-04-15T08:03Z] 2016-04-15 01:03:56 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:03:56,183 - WARNING - Could not retrieve variants from source file in region 19:9523974-9524375. Error was invalid region `19:9523975-9524375`
[2016-04-15T08:03Z] 2016-04-15 01:03:56 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:03:56,528 - WARNING - Could not retrieve variants from source file in region 19:7830836-7831818. Error was invalid region `19:7830837-7831818`
[2016-04-15T08:03Z] 2016-04-15 01:03:56 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:03:56,840 - WARNING - Could not retrieve variants from source file in region 19:15197813-15233771. Error was invalid region `19:15197814-15233771`
[2016-04-15T08:03Z] 2016-04-15 01:03:57 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:03:57,313 - WARNING - Could not retrieve variants from source file in region 19:9721190-9721591. Error was invalid region `19:9721191-9721591`
[2016-04-15T08:03Z] 2016-04-15 01:03:58 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:03:58,076 - WARNING - Could not retrieve variants from source file in region 19:8808162-8809132. Error was invalid region `19:8808163-8809132`
[2016-04-15T08:03Z] 2016-04-15 01:03:58 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:03:58,316 - WARNING - Could not retrieve variants from source file in region 19:14083550-14083951. Error was invalid region `19:14083551-14083951`
[2016-04-15T08:03Z] 2016-04-15 01:03:58 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:03:58,764 - WARNING - Could not retrieve variants from source file in region 19:11465105-11465506. Error was invalid region `19:11465106-11465506`
[2016-04-15T08:04Z] 2016-04-15 01:04:00 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:04:00,244 - WARNING - Could not retrieve variants from source file in region 19:10527455-10539727. Error was invalid region `19:10527456-10539727`
[2016-04-15T08:04Z] 2016-04-15 01:04:01 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:04:01,297 - WARNING - Could not retrieve variants from source file in region 19:9768714-9769115. Error was invalid region `19:9768715-9769115`
[2016-04-15T08:04Z] 2016-04-15 01:04:02 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:04:02,153 - WARNING - Could not retrieve variants from source file in region 19:7830836-7831818. Error was invalid region `19:7830837-7831818`
[2016-04-15T08:04Z] 2016-04-15 01:04:03 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:04:03,133 - WARNING - Could not retrieve variants from source file in region 19:9721190-9721591. Error was invalid region `19:9721191-9721591`
[2016-04-15T08:04Z] 2016-04-15 01:04:04 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:04:04,079 - WARNING - Could not retrieve variants from source file in region 19:8808162-8809132. Error was invalid region `19:8808163-8809132`
[2016-04-15T08:04Z] 2016-04-15 01:04:05 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:04:05,026 - WARNING - Could not retrieve variants from source file in region 19:11210701-11234131. Error was invalid region `19:11210702-11234131`
[2016-04-15T08:04Z] 2016-04-15 01:04:05 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:04:05,052 - WARNING - Could not retrieve variants from source file in region 19:14083550-14083951. Error was invalid region `19:14083551-14083951`
[2016-04-15T08:04Z] 2016-04-15 01:04:05 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:04:05,362 - WARNING - Could not retrieve variants from source file in region 19:11465105-11465506. Error was invalid region `19:11465106-11465506`
[2016-04-15T08:04Z] 2016-04-15 01:04:06 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:04:06,049 - WARNING - Could not retrieve variants from source file in region 19:9768714-9769115. Error was invalid region `19:9768715-9769115`
[2016-04-15T08:04Z] 2016-04-15 01:04:07 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:04:07,886 - WARNING - Could not retrieve variants from source file in region 19:9721190-9721591. Error was invalid region `19:9721191-9721591`
[2016-04-15T08:04Z] 2016-04-15 01:04:10 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:04:10,220 - WARNING - Could not retrieve variants from source file in region 19:8808162-8809132. Error was invalid region `19:8808163-8809132`
[2016-04-15T08:04Z] 2016-04-15 01:04:10 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:04:10,508 - WARNING - Could not retrieve variants from source file in region 19:14083550-14083951. Error was invalid region `19:14083551-14083951`
[2016-04-15T08:04Z] 2016-04-15 01:04:11 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:04:11,292 - WARNING - Could not retrieve variants from source file in region 19:11210701-11234131. Error was invalid region `19:11210702-11234131`
[2016-04-15T08:04Z] 2016-04-15 01:04:11 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:04:11,374 - WARNING - Could not retrieve variants from source file in region 19:11465105-11465506. Error was invalid region `19:11465106-11465506`
[2016-04-15T08:04Z] 2016-04-15 01:04:20 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:04:20,927 - WARNING - Could not retrieve variants from source file in region 19:12385637-12386038. Error was invalid region `19:12385638-12386038`
[2016-04-15T08:04Z] 2016-04-15 01:04:22 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:04:22,178 - WARNING - Could not retrieve variants from source file in region 19:11105397-11105798. Error was invalid region `19:11105398-11105798`
[2016-04-15T08:04Z] 2016-04-15 01:04:22 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:04:22,206 - WARNING - Could not retrieve variants from source file in region 19:15131119-15134116. Error was invalid region `19:15131120-15134116`
[2016-04-15T08:04Z] 2016-04-15 01:04:22 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:04:22,835 - WARNING - Could not retrieve variants from source file in region 19:7743610-7764558. Error was invalid region `19:7743611-7764558`
[2016-04-15T08:04Z] 2016-04-15 01:04:22 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:04:22,983 - WARNING - Could not retrieve variants from source file in region 19:13002189-13063815. Error was invalid region `19:13002190-13063815`
[2016-04-15T08:04Z] 2016-04-15 01:04:23 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:04:23,390 - WARNING - Could not retrieve variants from source file in region 19:9490603-9492560. Error was invalid region `19:9490604-9492560`
[2016-04-15T08:04Z] 2016-04-15 01:04:23 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:04:23,455 - WARNING - Could not retrieve variants from source file in region 19:13264187-13264739. Error was invalid region `19:13264188-13264739`
[2016-04-15T08:04Z] 2016-04-15 01:04:24 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:04:24,475 - WARNING - Could not retrieve variants from source file in region 19:8645575-8670166. Error was invalid region `19:8645576-8670166`
[2016-04-15T08:04Z] 2016-04-15 01:04:25 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:04:25,292 - WARNING - Could not retrieve variants from source file in region 19:12385637-12386038. Error was invalid region `19:12385638-12386038`
[2016-04-15T08:04Z] 2016-04-15 01:04:28 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:04:28,245 - WARNING - Could not retrieve variants from source file in region 19:11105397-11105798. Error was invalid region `19:11105398-11105798`
[2016-04-15T08:04Z] 2016-04-15 01:04:28 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:04:28,766 - WARNING - Could not retrieve variants from source file in region 19:11170628-11171029. Error was invalid region `19:11170629-11171029`
[2016-04-15T08:04Z] 2016-04-15 01:04:29 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:04:29,094 - WARNING - Could not retrieve variants from source file in region 19:4013111-4033652. Error was invalid region `19:4013112-4033652`
[2016-04-15T08:04Z] 2016-04-15 01:04:29 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:04:29,323 - WARNING - Could not retrieve variants from source file in region 19:11170628-11171029. Error was invalid region `19:11170629-11171029`
[2016-04-15T08:04Z] 2016-04-15 01:04:33 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:04:33,588 - WARNING - Could not retrieve variants from source file in region 19:11105397-11105798. Error was invalid region `19:11105398-11105798`
[2016-04-15T08:04Z] 2016-04-15 01:04:34 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:04:34,088 - WARNING - Could not retrieve variants from source file in region 19:11170628-11171029. Error was invalid region `19:11170629-11171029`
[2016-04-15T08:04Z] 2016-04-15 01:04:34 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:04:34,301 - WARNING - Could not retrieve variants from source file in region 19:4013111-4033652. Error was invalid region `19:4013112-4033652`
[2016-04-15T08:04Z] 2016-04-15 01:04:34 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:04:34,670 - WARNING - Could not retrieve variants from source file in region 19:15131119-15134116. Error was invalid region `19:15131120-15134116`
[2016-04-15T08:04Z] 2016-04-15 01:04:37 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:04:37,355 - WARNING - Could not retrieve variants from source file in region 19:12876753-12877154. Error was invalid region `19:12876754-12877154`
[2016-04-15T08:04Z] 2016-04-15 01:04:41 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:04:41,476 - WARNING - Could not retrieve variants from source file in region 19:12923768-12939982. Error was invalid region `19:12923769-12939982`
[2016-04-15T08:04Z] 2016-04-15 01:04:42 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:04:42,533 - WARNING - Could not retrieve variants from source file in region 19:12876753-12877154. Error was invalid region `19:12876754-12877154`
[2016-04-15T08:04Z] 2016-04-15 01:04:46 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:04:46,635 - WARNING - Could not retrieve variants from source file in region 19:12154588-12154989. Error was invalid region `19:12154589-12154989`
[2016-04-15T08:04Z] 2016-04-15 01:04:47 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:04:47,062 - WARNING - Could not retrieve variants from source file in region 19:12256147-12256548. Error was invalid region `19:12256148-12256548`
[2016-04-15T08:04Z] 2016-04-15 01:04:47 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:04:47,494 - WARNING - Could not retrieve variants from source file in region 19:12876753-12877154. Error was invalid region `19:12876754-12877154`
[2016-04-15T08:04Z] 2016-04-15 01:04:47 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:04:47,960 - WARNING - Could not retrieve variants from source file in region 19:10738428-10742360. Error was invalid region `19:10738429-10742360`
[2016-04-15T08:04Z] 2016-04-15 01:04:48 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:04:48,111 - WARNING - Could not retrieve variants from source file in region 19:10794419-10794820. Error was invalid region `19:10794420-10794820`
[2016-04-15T08:04Z] 2016-04-15 01:04:48 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:04:48,549 - WARNING - Could not retrieve variants from source file in region 19:9362132-9362633. Error was invalid region `19:9362133-9362633`
[2016-04-15T08:04Z] 2016-04-15 01:04:49 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:04:49,141 - WARNING - Could not retrieve variants from source file in region 19:12185937-12188097. Error was invalid region `19:12185938-12188097`
[2016-04-15T08:04Z] 2016-04-15 01:04:50 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:04:50,732 - WARNING - Could not retrieve variants from source file in region 19:9204096-9237732. Error was invalid region `19:9204097-9237732`
[2016-04-15T08:04Z] 2016-04-15 01:04:51 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:04:51,604 - WARNING - Could not retrieve variants from source file in region 19:12256147-12256548. Error was invalid region `19:12256148-12256548`
[2016-04-15T08:04Z] 2016-04-15 01:04:51 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:04:51,911 - WARNING - Could not retrieve variants from source file in region 19:7675158-7712467. Error was invalid region `19:7675159-7712467`
[2016-04-15T08:04Z] 2016-04-15 01:04:52 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:04:52,494 - WARNING - Could not retrieve variants from source file in region 19:3977275-3979598. Error was invalid region `19:3977276-3979598`
[2016-04-15T08:04Z] 2016-04-15 01:04:52 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:04:52,822 - WARNING - Could not retrieve variants from source file in region 19:10794419-10794820. Error was invalid region `19:10794420-10794820`
[2016-04-15T08:04Z] 2016-04-15 01:04:53 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:04:53,039 - WARNING - Could not retrieve variants from source file in region 19:10738428-10742360. Error was invalid region `19:10738429-10742360`
[2016-04-15T08:04Z] 2016-04-15 01:04:55 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:04:55,787 - WARNING - Could not retrieve variants from source file in region 19:12154588-12154989. Error was invalid region `19:12154589-12154989`
[2016-04-15T08:04Z] 2016-04-15 01:04:56 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:04:56,374 - WARNING - Could not retrieve variants from source file in region 19:7675158-7712467. Error was invalid region `19:7675159-7712467`
[2016-04-15T08:04Z] 2016-04-15 01:04:57 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:04:57,547 - WARNING - Could not retrieve variants from source file in region 19:10794419-10794820. Error was invalid region `19:10794420-10794820`
[2016-04-15T08:04Z] 2016-04-15 01:04:57 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:04:57,697 - WARNING - Could not retrieve variants from source file in region 19:10738428-10742360. Error was invalid region `19:10738429-10742360`
[2016-04-15T08:04Z] 2016-04-15 01:04:58 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:04:58,312 - WARNING - Could not retrieve variants from source file in region 19:2339738-2353340. Error was invalid region `19:2339739-2353340`
[2016-04-15T08:04Z] 2016-04-15 01:04:58 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:04:58,546 - WARNING - Could not retrieve variants from source file in region 19:12185937-12188097. Error was invalid region `19:12185938-12188097`
[2016-04-15T08:04Z] 2016-04-15 01:04:59 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:04:59,621 - WARNING - Could not retrieve variants from source file in region 19:12016847-12017248. Error was invalid region `19:12016848-12017248`
[2016-04-15T08:04Z] 2016-04-15 01:04:59 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:04:59,938 - WARNING - Could not retrieve variants from source file in region 19:12689530-12692191. Error was invalid region `19:12689531-12692191`
[2016-04-15T08:05Z] 2016-04-15 01:05:04 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:05:04,298 - WARNING - Could not retrieve variants from source file in region 19:12016847-12017248. Error was invalid region `19:12016848-12017248`
[2016-04-15T08:05Z] 2016-04-15 01:05:04 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:05:04,334 - WARNING - Could not retrieve variants from source file in region 19:12689530-12692191. Error was invalid region `19:12689531-12692191`
[2016-04-15T08:05Z] 2016-04-15 01:05:08 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:05:08,296 - WARNING - Could not retrieve variants from source file in region 19:11917814-11943887. Error was invalid region `19:11917815-11943887`
[2016-04-15T08:05Z] 2016-04-15 01:05:08 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:05:08,921 - WARNING - Could not retrieve variants from source file in region 19:12689530-12692191. Error was invalid region `19:12689531-12692191`
[2016-04-15T08:05Z] 2016-04-15 01:05:10 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:05:10,766 - WARNING - Could not retrieve variants from source file in region 19:538719-549868. Error was invalid region `19:538720-549868`
[2016-04-15T08:05Z] 2016-04-15 01:05:10 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:05:10,790 - WARNING - Could not retrieve variants from source file in region 19:3150027-3156092. Error was invalid region `19:3150028-3156092`
[2016-04-15T08:05Z] 2016-04-15 01:05:14 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:05:14,113 - WARNING - Could not retrieve variants from source file in region 19:7569071-7616093. Error was invalid region `19:7569072-7616093`
[2016-04-15T08:05Z] 2016-04-15 01:05:14 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:05:14,169 - WARNING - Could not retrieve variants from source file in region 19:3938436-3938837. Error was invalid region `19:3938437-3938837`
[2016-04-15T08:05Z] 2016-04-15 01:05:17 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:05:17,697 - WARNING - Could not retrieve variants from source file in region 19:372478-372879. Error was invalid region `19:372479-372879`
[2016-04-15T08:05Z] 2016-04-15 01:05:20 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:05:20,075 - WARNING - Could not retrieve variants from source file in region 19:538719-549868. Error was invalid region `19:538720-549868`
[2016-04-15T08:05Z] 2016-04-15 01:05:20 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:05:20,233 - WARNING - Could not retrieve variants from source file in region 19:3150027-3156092. Error was invalid region `19:3150028-3156092`
[2016-04-15T08:05Z] 2016-04-15 01:05:20 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:05:20,843 - WARNING - Could not retrieve variants from source file in region 19:343842-344489. Error was invalid region `19:343843-344489`
[2016-04-15T08:05Z] 2016-04-15 01:05:31 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:05:31,872 - WARNING - Could not retrieve variants from source file in region 19:7504458-7534040. Error was invalid region `19:7504459-7534040`
[2016-04-15T08:05Z] 2016-04-15 01:05:32 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:05:32,742 - WARNING - Could not retrieve variants from source file in region 19:7293687-7294088. Error was invalid region `19:7293688-7294088`
[2016-04-15T08:05Z] 2016-04-15 01:05:34 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:05:34,478 - WARNING - Could not retrieve variants from source file in region 19:920431-929943. Error was invalid region `19:920432-929943`
[2016-04-15T08:05Z] 2016-04-15 01:05:36 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:05:36,638 - WARNING - Could not retrieve variants from source file in region 19:5778306-5789755. Error was invalid region `19:5778307-5789755`
[2016-04-15T08:05Z] 2016-04-15 01:05:37 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:05:37,586 - WARNING - Could not retrieve variants from source file in region 19:282542-282943. Error was invalid region `19:282543-282943`
[2016-04-15T08:05Z] 2016-04-15 01:05:38 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:05:38,172 - WARNING - Could not retrieve variants from source file in region 19:7125086-7166566. Error was invalid region `19:7125087-7166566`
[2016-04-15T08:05Z] 2016-04-15 01:05:39 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:05:39,116 - WARNING - Could not retrieve variants from source file in region 19:2717045-2736081. Error was invalid region `19:2717046-2736081`
[2016-04-15T08:05Z] 2016-04-15 01:05:39 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:05:39,117 - WARNING - Could not retrieve variants from source file in region 19:7293687-7294088. Error was invalid region `19:7293688-7294088`
[2016-04-15T08:05Z] 2016-04-15 01:05:39 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:05:39,279 - WARNING - Could not retrieve variants from source file in region 19:3119028-3119429. Error was invalid region `19:3119029-3119429`
[2016-04-15T08:05Z] 2016-04-15 01:05:39 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:05:39,571 - WARNING - Could not retrieve variants from source file in region 19:498313-502090. Error was invalid region `19:498314-502090`
[2016-04-15T08:05Z] 2016-04-15 01:05:39 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:05:39,730 - WARNING - Could not retrieve variants from source file in region 19:920431-929943. Error was invalid region `19:920432-929943`
[2016-04-15T08:05Z] 2016-04-15 01:05:40 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:05:40,834 - WARNING - Could not retrieve variants from source file in region 19:2762374-2767382. Error was invalid region `19:2762375-2767382`
[2016-04-15T08:05Z] 2016-04-15 01:05:41 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:05:41,302 - WARNING - Could not retrieve variants from source file in region 19:5778306-5789755. Error was invalid region `19:5778307-5789755`
[2016-04-15T08:05Z] 2016-04-15 01:05:44 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:05:44,182 - WARNING - Could not retrieve variants from source file in region 19:7504458-7534040. Error was invalid region `19:7504459-7534040`
[2016-04-15T08:05Z] 2016-04-15 01:05:46 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:05:46,512 - WARNING - Could not retrieve variants from source file in region 19:920431-929943. Error was invalid region `19:920432-929943`
[2016-04-15T08:05Z] 2016-04-15 01:05:46 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:05:46,615 - WARNING - Could not retrieve variants from source file in region 19:7293687-7294088. Error was invalid region `19:7293688-7294088`
[2016-04-15T08:05Z] 2016-04-15 01:05:46 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:05:46,821 - WARNING - Could not retrieve variants from source file in region 19:2762374-2767382. Error was invalid region `19:2762375-2767382`
[2016-04-15T08:05Z] 2016-04-15 01:05:56 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:05:56,094 - WARNING - Could not retrieve variants from source file in region 19:7268227-7268628. Error was invalid region `19:7268228-7268628`
[2016-04-15T08:05Z] 2016-04-15 01:05:58 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:05:58,626 - WARNING - Could not retrieve variants from source file in region 19:7083418-7083819. Error was invalid region `19:7083419-7083819`
[2016-04-15T08:05Z] 2016-04-15 01:05:59 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:05:59,201 - WARNING - Could not retrieve variants from source file in region 19:2511827-2512341. Error was invalid region `19:2511828-2512341`
[2016-04-15T08:06Z] 2016-04-15 01:06:01 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:06:01,218 - WARNING - Could not retrieve variants from source file in region 19:5695935-5696336. Error was invalid region `19:5695936-5696336`
[2016-04-15T08:06Z] 2016-04-15 01:06:01 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:06:01,445 - WARNING - Could not retrieve variants from source file in region 19:7268227-7268628. Error was invalid region `19:7268228-7268628`
[2016-04-15T08:06Z] 2016-04-15 01:06:02 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:06:02,019 - WARNING - Could not retrieve variants from source file in region 19:3029349-3029750. Error was invalid region `19:3029350-3029750`
[2016-04-15T08:06Z] 2016-04-15 01:06:02 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:06:02,473 - WARNING - Could not retrieve variants from source file in region 19:2989486-2989887. Error was invalid region `19:2989487-2989887`
[2016-04-15T08:06Z] 2016-04-15 01:06:06 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:06:06,010 - WARNING - Could not retrieve variants from source file in region 19:5695935-5696336. Error was invalid region `19:5695936-5696336`
[2016-04-15T08:06Z] 2016-04-15 01:06:07 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:06:07,115 - WARNING - Could not retrieve variants from source file in region 19:1467473-1556154. Error was invalid region `19:1467474-1556154`
[2016-04-15T08:06Z] 2016-04-15 01:06:07 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:06:07,116 - WARNING - Could not retrieve variants from source file in region 19:3029349-3029750. Error was invalid region `19:3029350-3029750`
[2016-04-15T08:06Z] 2016-04-15 01:06:07 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:06:07,541 - WARNING - Could not retrieve variants from source file in region 19:2389661-2434080. Error was invalid region `19:2389662-2434080`
[2016-04-15T08:06Z] 2016-04-15 01:06:10 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:06:10,422 - WARNING - Could not retrieve variants from source file in region 19:5695935-5696336. Error was invalid region `19:5695936-5696336`
[2016-04-15T08:06Z] 2016-04-15 01:06:13 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:06:13,360 - WARNING - Could not retrieve variants from source file in region 19:2389661-2434080. Error was invalid region `19:2389662-2434080`
[2016-04-15T08:06Z] 2016-04-15 01:06:15 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:06:15,347 - WARNING - Could not retrieve variants from source file in region 19:4847502-4860127. Error was invalid region `19:4847503-4860127`
[2016-04-15T08:06Z] 2016-04-15 01:06:15 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:06:15,495 - WARNING - Could not retrieve variants from source file in region 19:6411619-6495926. Error was invalid region `19:6411620-6495926`
[2016-04-15T08:06Z] 2016-04-15 01:06:21 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:06:21,231 - WARNING - Could not retrieve variants from source file in region 19:6896272-6926568. Error was invalid region `19:6896273-6926568`
[2016-04-15T08:06Z] 2016-04-15 01:06:25 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:06:25,015 - WARNING - Could not retrieve variants from source file in region 19:4847502-4860127. Error was invalid region `19:4847503-4860127`
[2016-04-15T08:06Z] 2016-04-15 01:06:25 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:06:25,380 - WARNING - Could not retrieve variants from source file in region 19:2916975-2936813. Error was invalid region `19:2916976-2936813`
[2016-04-15T08:06Z] 2016-04-15 01:06:25 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:06:25,792 - WARNING - Could not retrieve variants from source file in region 19:6896272-6926568. Error was invalid region `19:6896273-6926568`
[2016-04-15T08:06Z] 2016-04-15 01:06:28 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:06:28,034 - WARNING - Could not retrieve variants from source file in region 19:4409545-4409946. Error was invalid region `19:4409546-4409946`
[2016-04-15T08:06Z] 2016-04-15 01:06:28 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:06:28,221 - WARNING - Could not retrieve variants from source file in region 19:5641450-5641851. Error was invalid region `19:5641451-5641851`
[2016-04-15T08:06Z] 2016-04-15 01:06:28 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:06:28,462 - WARNING - Could not retrieve variants from source file in region 19:3453806-3479054. Error was invalid region `19:3453807-3479054`
[2016-04-15T08:06Z] 2016-04-15 01:06:30 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:06:30,684 - WARNING - Could not retrieve variants from source file in region 19:6896272-6926568. Error was invalid region `19:6896273-6926568`
[2016-04-15T08:06Z] 2016-04-15 01:06:32 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:06:32,511 - WARNING - Could not retrieve variants from source file in region 19:3366351-3366752. Error was invalid region `19:3366352-3366752`
[2016-04-15T08:06Z] 2016-04-15 01:06:38 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:06:38,983 - WARNING - Could not retrieve variants from source file in region 19:6373538-6376021. Error was invalid region `19:6373539-6376021`
[2016-04-15T08:06Z] 2016-04-15 01:06:43 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:06:43,077 - WARNING - Could not retrieve variants from source file in region 19:4818167-4818568. Error was invalid region `19:4818168-4818568`
[2016-04-15T08:06Z] 2016-04-15 01:06:43 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:06:43,316 - WARNING - Could not retrieve variants from source file in region 19:3185874-3186275. Error was invalid region `19:3185875-3186275`
[2016-04-15T08:06Z] 2016-04-15 01:06:44 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:06:44,891 - WARNING - Could not retrieve variants from source file in region 19:4670025-4670503. Error was invalid region `19:4670026-4670503`
[2016-04-15T08:06Z] 2016-04-15 01:06:45 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:06:45,385 - WARNING - Could not retrieve variants from source file in region 19:6586057-6586458. Error was invalid region `19:6586058-6586458`
[2016-04-15T08:06Z] 2016-04-15 01:06:46 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:06:46,330 - WARNING - Could not retrieve variants from source file in region 19:3185874-3186275. Error was invalid region `19:3185875-3186275`
[2016-04-15T08:06Z] 2016-04-15 01:06:47 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:06:47,722 - WARNING - Could not retrieve variants from source file in region 19:4818167-4818568. Error was invalid region `19:4818168-4818568`
[2016-04-15T08:06Z] 2016-04-15 01:06:48 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:06:48,245 - WARNING - Could not retrieve variants from source file in region 19:3185874-3186275. Error was invalid region `19:3185875-3186275`
[2016-04-15T08:06Z] 2016-04-15 01:06:49 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:06:49,935 - WARNING - Could not retrieve variants from source file in region 19:5110583-5135582. Error was invalid region `19:5110584-5135582`
[2016-04-15T08:06Z] 2016-04-15 01:06:50 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:06:50,413 - WARNING - Could not retrieve variants from source file in region 19:5455400-5456640. Error was invalid region `19:5455401-5456640`
[2016-04-15T08:06Z] 2016-04-15 01:06:50 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:06:50,543 - WARNING - Could not retrieve variants from source file in region 19:6586057-6586458. Error was invalid region `19:6586058-6586458`
[2016-04-15T08:06Z] 2016-04-15 01:06:51 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:06:51,587 - WARNING - Could not retrieve variants from source file in region 19:5592558-5592959. Error was invalid region `19:5592559-5592959`
[2016-04-15T08:06Z] 2016-04-15 01:06:54 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:06:54,335 - WARNING - Could not retrieve variants from source file in region 19:4670025-4670503. Error was invalid region `19:4670026-4670503`
[2016-04-15T08:06Z] 2016-04-15 01:06:54 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:06:54,830 - WARNING - Could not retrieve variants from source file in region 19:6212164-6212565. Error was invalid region `19:6212165-6212565`
[2016-04-15T08:06Z] 2016-04-15 01:06:59 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:06:59,152 - WARNING - Could not retrieve variants from source file in region 19:6212164-6212565. Error was invalid region `19:6212165-6212565`
[2016-04-15T08:07Z] 2016-04-15 01:07:00 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:07:00,940 - WARNING - Could not retrieve variants from source file in region 19:4180625-4254565. Error was invalid region `19:4180626-4254565`
[2016-04-15T08:07Z] 2016-04-15 01:07:02 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:07:02,350 - WARNING - Could not retrieve variants from source file in region 19:6156272-6156700. Error was invalid region `19:6156273-6156700`
[2016-04-15T08:07Z] 2016-04-15 01:07:02 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:07:02,919 - WARNING - Could not retrieve variants from source file in region 19:5210571-5225992. Error was invalid region `19:5210572-5225992`
[2016-04-15T08:07Z] 2016-04-15 01:07:03 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:07:03,604 - WARNING - Could not retrieve variants from source file in region 19:6212164-6212565. Error was invalid region `19:6212165-6212565`
[2016-04-15T08:07Z] 2016-04-15 01:07:06 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:07:06,897 - WARNING - Could not retrieve variants from source file in region 19:5040967-5041368. Error was invalid region `19:5040968-5041368`
[2016-04-15T08:07Z] 2016-04-15 01:07:06 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:07:06,937 - WARNING - Could not retrieve variants from source file in region 19:6156272-6156700. Error was invalid region `19:6156273-6156700`
[2016-04-15T08:07Z] 2016-04-15 01:07:09 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:07:09,029 - WARNING - Could not retrieve variants from source file in region 19:6041848-6042249. Error was invalid region `19:6041849-6042249`
[2016-04-15T08:07Z] 2016-04-15 01:07:09 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:07:09,561 - WARNING - Could not retrieve variants from source file in region 19:4154699-4155100. Error was invalid region `19:4154700-4155100`
[2016-04-15T08:07Z] 2016-04-15 01:07:11 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:07:11,050 - WARNING - Could not retrieve variants from source file in region 19:5040967-5041368. Error was invalid region `19:5040968-5041368`
[2016-04-15T08:07Z] 2016-04-15 01:07:11 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:07:11,168 - WARNING - Could not retrieve variants from source file in region 19:6156272-6156700. Error was invalid region `19:6156273-6156700`
[2016-04-15T08:07Z] 2016-04-15 01:07:13 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:07:13,077 - WARNING - Could not retrieve variants from source file in region 19:6041848-6042249. Error was invalid region `19:6041849-6042249`
[2016-04-15T08:07Z] 2016-04-15 01:07:13 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:07:13,118 - WARNING - Could not retrieve variants from source file in region 19:4102238-4103066. Error was invalid region `19:4102239-4103066`
[2016-04-15T08:07Z] 2016-04-15 01:07:13 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:07:13,409 - WARNING - Could not retrieve variants from source file in region 19:4154699-4155100. Error was invalid region `19:4154700-4155100`
[2016-04-15T08:07Z] 2016-04-15 01:07:14 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:07:14,764 - WARNING - Could not retrieve variants from source file in region 19:5040967-5041368. Error was invalid region `19:5040968-5041368`
[2016-04-15T08:07Z] 2016-04-15 01:07:16 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:07:16,491 - WARNING - Could not retrieve variants from source file in region 19:6041848-6042249. Error was invalid region `19:6041849-6042249`
[2016-04-15T08:07Z] 2016-04-15 01:07:16 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:07:16,569 - WARNING - Could not retrieve variants from source file in region 19:4102238-4103066. Error was invalid region `19:4102239-4103066`
[2016-04-15T08:07Z] ['bcbio-variation-recall', 'square', '-Xms750m', '-Xmx7280m', '-XX:+UseSerialGC', '-c', 16, '-r', u'19:15510113-31025906', '--caller', 'platypus', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/19/Batch1-19_15510112_31025906.vcf.gz', '/mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/19/Batch1-19_15510112_31025906.vcf-inputs.txt'] in region: 19:15510113-31025906
[2016-04-15T08:07Z] 2016-04-15 01:07:32 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:07:32,645 - WARNING - Could not retrieve variants from source file in region 19:30935493-30935894. Error was invalid region `19:30935494-30935894`
[2016-04-15T08:07Z] 2016-04-15 01:07:34 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:07:34,150 - WARNING - Could not retrieve variants from source file in region 19:23328221-23329130. Error was invalid region `19:23328222-23329130`
[2016-04-15T08:07Z] 2016-04-15 01:07:34 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:07:34,172 - WARNING - Could not retrieve variants from source file in region 19:30499907-30500311. Error was invalid region `19:30499908-30500311`
[2016-04-15T08:07Z] 2016-04-15 01:07:34 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:07:34,711 - WARNING - Could not retrieve variants from source file in region 19:22846412-22847677. Error was invalid region `19:22846413-22847677`
[2016-04-15T08:07Z] 2016-04-15 01:07:34 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:07:34,919 - WARNING - Could not retrieve variants from source file in region 19:16024451-16045331. Error was invalid region `19:16024452-16045331`
[2016-04-15T08:07Z] 2016-04-15 01:07:35 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:07:35,168 - WARNING - Could not retrieve variants from source file in region 19:22498732-22499133. Error was invalid region `19:22498733-22499133`
[2016-04-15T08:07Z] 2016-04-15 01:07:35 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:07:35,334 - WARNING - Could not retrieve variants from source file in region 19:19369224-19413282. Error was invalid region `19:19369225-19413282`
[2016-04-15T08:07Z] 2016-04-15 01:07:35 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:07:35,384 - WARNING - Could not retrieve variants from source file in region 19:19825047-19825448. Error was invalid region `19:19825048-19825448`
[2016-04-15T08:07Z] 2016-04-15 01:07:35 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:07:35,607 - WARNING - Could not retrieve variants from source file in region 19:23836934-23837555. Error was invalid region `19:23836935-23837555`
[2016-04-15T08:07Z] 2016-04-15 01:07:36 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:07:36,004 - WARNING - Could not retrieve variants from source file in region 19:30020812-30021213. Error was invalid region `19:30020813-30021213`
[2016-04-15T08:07Z] 2016-04-15 01:07:36 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:07:36,016 - WARNING - Could not retrieve variants from source file in region 19:22154521-22157492. Error was invalid region `19:22154522-22157492`
[2016-04-15T08:07Z] 2016-04-15 01:07:36 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:07:36,144 - WARNING - Could not retrieve variants from source file in region 19:30314455-30314856. Error was invalid region `19:30314456-30314856`
[2016-04-15T08:07Z] 2016-04-15 01:07:39 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:07:39,361 - WARNING - Could not retrieve variants from source file in region 19:30499907-30500311. Error was invalid region `19:30499908-30500311`
[2016-04-15T08:07Z] 2016-04-15 01:07:40 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:07:40,465 - WARNING - Could not retrieve variants from source file in region 19:17163450-17171075. Error was invalid region `19:17163451-17171075`
[2016-04-15T08:07Z] 2016-04-15 01:07:41 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:07:41,737 - WARNING - Could not retrieve variants from source file in region 19:16024451-16045331. Error was invalid region `19:16024452-16045331`
[2016-04-15T08:07Z] 2016-04-15 01:07:42 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:07:42,549 - WARNING - Could not retrieve variants from source file in region 19:22498732-22499133. Error was invalid region `19:22498733-22499133`
[2016-04-15T08:07Z] 2016-04-15 01:07:43 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:07:43,824 - WARNING - Could not retrieve variants from source file in region 19:16339504-16339905. Error was invalid region `19:16339505-16339905`
[2016-04-15T08:07Z] 2016-04-15 01:07:44 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:07:44,333 - WARNING - Could not retrieve variants from source file in region 19:23836934-23837555. Error was invalid region `19:23836935-23837555`
[2016-04-15T08:07Z] 2016-04-15 01:07:44 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:07:44,547 - WARNING - Could not retrieve variants from source file in region 19:16790645-16791046. Error was invalid region `19:16790646-16791046`
[2016-04-15T08:07Z] 2016-04-15 01:07:44 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:07:44,567 - WARNING - Could not retrieve variants from source file in region 19:30314455-30314856. Error was invalid region `19:30314456-30314856`
[2016-04-15T08:07Z] 2016-04-15 01:07:44 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:07:44,942 - WARNING - Could not retrieve variants from source file in region 19:30499907-30500311. Error was invalid region `19:30499908-30500311`
[2016-04-15T08:07Z] 2016-04-15 01:07:46 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:07:46,455 - WARNING - Could not retrieve variants from source file in region 19:16024451-16045331. Error was invalid region `19:16024452-16045331`
[2016-04-15T08:07Z] 2016-04-15 01:07:47 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:07:47,648 - WARNING - Could not retrieve variants from source file in region 19:22498732-22499133. Error was invalid region `19:22498733-22499133`
[2016-04-15T08:07Z] 2016-04-15 01:07:51 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:07:51,780 - WARNING - Could not retrieve variants from source file in region 19:23836934-23837555. Error was invalid region `19:23836935-23837555`
[2016-04-15T08:07Z] 2016-04-15 01:07:52 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:07:52,030 - WARNING - Could not retrieve variants from source file in region 19:30314455-30314856. Error was invalid region `19:30314456-30314856`
[2016-04-15T08:08Z] 2016-04-15 01:08:06 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:08:06,172 - WARNING - Could not retrieve variants from source file in region 19:23158509-23159676. Error was invalid region `19:23158510-23159676`
[2016-04-15T08:08Z] 2016-04-15 01:08:06 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:08:06,185 - WARNING - Could not retrieve variants from source file in region 19:19307586-19307987. Error was invalid region `19:19307587-19307987`
[2016-04-15T08:08Z] 2016-04-15 01:08:06 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:08:06,248 - WARNING - Could not retrieve variants from source file in region 19:30193510-30193911. Error was invalid region `19:30193511-30193911`
[2016-04-15T08:08Z] 2016-04-15 01:08:06 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:08:06,530 - WARNING - Could not retrieve variants from source file in region 19:22363282-22376058. Error was invalid region `19:22363283-22376058`
[2016-04-15T08:08Z] 2016-04-15 01:08:07 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:08:07,246 - WARNING - Could not retrieve variants from source file in region 19:16267996-16268398. Error was invalid region `19:16267997-16268398`
[2016-04-15T08:08Z] 2016-04-15 01:08:07 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:08:07,864 - WARNING - Could not retrieve variants from source file in region 19:29703791-29704200. Error was invalid region `19:29703792-29704200`
[2016-04-15T08:08Z] 2016-04-15 01:08:09 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:08:09,511 - WARNING - Could not retrieve variants from source file in region 19:16665890-16666291. Error was invalid region `19:16665891-16666291`
[2016-04-15T08:08Z] 2016-04-15 01:08:09 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:08:09,536 - WARNING - Could not retrieve variants from source file in region 19:23542486-23545440. Error was invalid region `19:23542487-23545440`
[2016-04-15T08:08Z] 2016-04-15 01:08:09 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:08:09,610 - WARNING - Could not retrieve variants from source file in region 19:22575277-22575678. Error was invalid region `19:22575278-22575678`
[2016-04-15T08:08Z] 2016-04-15 01:08:10 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:08:10,981 - WARNING - Could not retrieve variants from source file in region 19:30156390-30156791. Error was invalid region `19:30156391-30156791`
[2016-04-15T08:08Z] 2016-04-15 01:08:12 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:08:12,256 - WARNING - Could not retrieve variants from source file in region 19:15838756-15853340. Error was invalid region `19:15838757-15853340`
[2016-04-15T08:08Z] 2016-04-15 01:08:14 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:08:14,747 - WARNING - Could not retrieve variants from source file in region 19:29703791-29704200. Error was invalid region `19:29703792-29704200`
[2016-04-15T08:08Z] 2016-04-15 01:08:14 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:08:14,932 - WARNING - Could not retrieve variants from source file in region 19:16267996-16268398. Error was invalid region `19:16267997-16268398`
[2016-04-15T08:08Z] 2016-04-15 01:08:15 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:08:15,307 - WARNING - Could not retrieve variants from source file in region 19:16665890-16666291. Error was invalid region `19:16665891-16666291`
[2016-04-15T08:08Z] 2016-04-15 01:08:15 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:08:15,325 - WARNING - Could not retrieve variants from source file in region 19:23542486-23545440. Error was invalid region `19:23542487-23545440`
[2016-04-15T08:08Z] 2016-04-15 01:08:16 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:08:16,175 - WARNING - Could not retrieve variants from source file in region 19:21948359-21948760. Error was invalid region `19:21948360-21948760`
[2016-04-15T08:08Z] 2016-04-15 01:08:17 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:08:17,924 - WARNING - Could not retrieve variants from source file in region 19:15838756-15853340. Error was invalid region `19:15838757-15853340`
[2016-04-15T08:08Z] 2016-04-15 01:08:20 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:08:20,303 - WARNING - Could not retrieve variants from source file in region 19:30193510-30193911. Error was invalid region `19:30193511-30193911`
[2016-04-15T08:08Z] 2016-04-15 01:08:22 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:08:22,240 - WARNING - Could not retrieve variants from source file in region 19:23158509-23159676. Error was invalid region `19:23158510-23159676`
[2016-04-15T08:08Z] 2016-04-15 01:08:22 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:08:22,242 - WARNING - Could not retrieve variants from source file in region 19:29703791-29704200. Error was invalid region `19:29703792-29704200`
[2016-04-15T08:08Z] 2016-04-15 01:08:22 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:08:22,591 - WARNING - Could not retrieve variants from source file in region 19:16267996-16268398. Error was invalid region `19:16267997-16268398`
[2016-04-15T08:08Z] 2016-04-15 01:08:22 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:08:22,985 - WARNING - Could not retrieve variants from source file in region 19:21948359-21948760. Error was invalid region `19:21948360-21948760`
[2016-04-15T08:08Z] 2016-04-15 01:08:23 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:08:23,148 - WARNING - Could not retrieve variants from source file in region 19:16665890-16666291. Error was invalid region `19:16665891-16666291`
[2016-04-15T08:08Z] 2016-04-15 01:08:23 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:08:23,202 - WARNING - Could not retrieve variants from source file in region 19:30156390-30156791. Error was invalid region `19:30156391-30156791`
[2016-04-15T08:08Z] 2016-04-15 01:08:23 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:08:23,391 - WARNING - Could not retrieve variants from source file in region 19:23542486-23545440. Error was invalid region `19:23542487-23545440`
[2016-04-15T08:08Z] 2016-04-15 01:08:34 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:08:34,520 - WARNING - Could not retrieve variants from source file in region 19:15726276-15808074. Error was invalid region `19:15726277-15808074`
[2016-04-15T08:08Z] 2016-04-15 01:08:34 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:08:34,660 - WARNING - Could not retrieve variants from source file in region 19:19212447-19231058. Error was invalid region `19:19212448-19231058`
[2016-04-15T08:08Z] 2016-04-15 01:08:34 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:08:34,988 - WARNING - Could not retrieve variants from source file in region 19:22271530-22271931. Error was invalid region `19:22271531-22271931`
[2016-04-15T08:08Z] 2016-04-15 01:08:36 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:08:36,214 - WARNING - Could not retrieve variants from source file in region 19:19650929-19656805. Error was invalid region `19:19650930-19656805`
[2016-04-15T08:08Z] 2016-04-15 01:08:37 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:08:37,518 - WARNING - Could not retrieve variants from source file in region 19:22939981-22952301. Error was invalid region `19:22939982-22952301`
[2016-04-15T08:08Z] 2016-04-15 01:08:38 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:08:38,882 - WARNING - Could not retrieve variants from source file in region 19:16238068-16238469. Error was invalid region `19:16238069-16238469`
[2016-04-15T08:08Z] 2016-04-15 01:08:40 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:08:40,779 - WARNING - Could not retrieve variants from source file in region 19:24115158-24115559. Error was invalid region `19:24115159-24115559`
[2016-04-15T08:08Z] 2016-04-15 01:08:41 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:08:41,813 - WARNING - Could not retrieve variants from source file in region 19:18774866-18778635. Error was invalid region `19:18774867-18778635`
[2016-04-15T08:08Z] 2016-04-15 01:08:42 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:08:42,400 - WARNING - Could not retrieve variants from source file in region 19:16976075-17025482. Error was invalid region `19:16976076-17025482`
[2016-04-15T08:08Z] 2016-04-15 01:08:43 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:08:43,576 - WARNING - Could not retrieve variants from source file in region 19:16238068-16238469. Error was invalid region `19:16238069-16238469`
[2016-04-15T08:08Z] 2016-04-15 01:08:44 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:08:44,969 - WARNING - Could not retrieve variants from source file in region 19:16591253-16634140. Error was invalid region `19:16591254-16634140`
[2016-04-15T08:08Z] 2016-04-15 01:08:45 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:08:45,449 - WARNING - Could not retrieve variants from source file in region 19:24115158-24115559. Error was invalid region `19:24115159-24115559`
[2016-04-15T08:08Z] 2016-04-15 01:08:46 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:08:46,607 - WARNING - Could not retrieve variants from source file in region 19:24015391-24016141. Error was invalid region `19:24015392-24016141`
[2016-04-15T08:08Z] 2016-04-15 01:08:47 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:08:47,925 - WARNING - Could not retrieve variants from source file in region 19:16238068-16238469. Error was invalid region `19:16238069-16238469`
[2016-04-15T08:08Z] 2016-04-15 01:08:50 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:08:50,352 - WARNING - Could not retrieve variants from source file in region 19:23926497-23928292. Error was invalid region `19:23926498-23928292`
[2016-04-15T08:08Z] 2016-04-15 01:08:52 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:08:52,122 - WARNING - Could not retrieve variants from source file in region 19:21909737-21910641. Error was invalid region `19:21909738-21910641`
[2016-04-15T08:08Z] 2016-04-15 01:08:52 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:08:52,719 - WARNING - Could not retrieve variants from source file in region 19:24015391-24016141. Error was invalid region `19:24015392-24016141`
[2016-04-15T08:08Z] 2016-04-15 01:08:54 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:08:54,642 - WARNING - Could not retrieve variants from source file in region 19:19164772-19165173. Error was invalid region `19:19164773-19165173`
[2016-04-15T08:08Z] 2016-04-15 01:08:56 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:08:56,474 - WARNING - Could not retrieve variants from source file in region 19:16512624-16513025. Error was invalid region `19:16512625-16513025`
[2016-04-15T08:08Z] 2016-04-15 01:08:56 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:08:56,489 - WARNING - Could not retrieve variants from source file in region 19:16899627-16900028. Error was invalid region `19:16899628-16900028`
[2016-04-15T08:08Z] 2016-04-15 01:08:59 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:08:59,659 - WARNING - Could not retrieve variants from source file in region 19:19164772-19165173. Error was invalid region `19:19164773-19165173`
[2016-04-15T08:08Z] 2016-04-15 01:08:59 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:08:59,966 - WARNING - Could not retrieve variants from source file in region 19:16512624-16513025. Error was invalid region `19:16512625-16513025`
[2016-04-15T08:09Z] 2016-04-15 01:09:01 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:09:01,150 - WARNING - Could not retrieve variants from source file in region 19:16512624-16513025. Error was invalid region `19:16512625-16513025`
[2016-04-15T08:09Z] 2016-04-15 01:09:01 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:09:01,223 - WARNING - Could not retrieve variants from source file in region 19:19606423-19625737. Error was invalid region `19:19606424-19625737`
[2016-04-15T08:09Z] 2016-04-15 01:09:01 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:09:01,639 - WARNING - Could not retrieve variants from source file in region 19:18726645-18727046. Error was invalid region `19:18726646-18727046`
[2016-04-15T08:09Z] 2016-04-15 01:09:01 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:09:01,642 - WARNING - Could not retrieve variants from source file in region 19:16899627-16900028. Error was invalid region `19:16899628-16900028`
[2016-04-15T08:09Z] 2016-04-15 01:09:01 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:09:01,674 - WARNING - Could not retrieve variants from source file in region 19:19136330-19136731. Error was invalid region `19:19136331-19136731`
[2016-04-15T08:09Z] 2016-04-15 01:09:02 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:09:02,504 - WARNING - Could not retrieve variants from source file in region 19:16186983-16187384. Error was invalid region `19:16186984-16187384`
[2016-04-15T08:09Z] 2016-04-15 01:09:02 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:09:02,509 - WARNING - Could not retrieve variants from source file in region 19:16436051-16436452. Error was invalid region `19:16436052-16436452`
[2016-04-15T08:09Z] 2016-04-15 01:09:06 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:09:06,349 - WARNING - Could not retrieve variants from source file in region 19:16899627-16900028. Error was invalid region `19:16899628-16900028`
[2016-04-15T08:09Z] 2016-04-15 01:09:06 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:09:06,687 - WARNING - Could not retrieve variants from source file in region 19:19136330-19136731. Error was invalid region `19:19136331-19136731`
[2016-04-15T08:09Z] 2016-04-15 01:09:06 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:09:06,918 - WARNING - Could not retrieve variants from source file in region 19:16436051-16436452. Error was invalid region `19:16436052-16436452`
[2016-04-15T08:09Z] 2016-04-15 01:09:07 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:09:07,340 - WARNING - Could not retrieve variants from source file in region 19:16129647-16131220. Error was invalid region `19:16129648-16131220`
[2016-04-15T08:09Z] 2016-04-15 01:09:09 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:09:09,176 - WARNING - Could not retrieve variants from source file in region 19:16436051-16436452. Error was invalid region `19:16436052-16436452`
[2016-04-15T08:09Z] 2016-04-15 01:09:11 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:09:11,535 - WARNING - Could not retrieve variants from source file in region 19:19136330-19136731. Error was invalid region `19:19136331-19136731`
[2016-04-15T08:09Z] 2016-04-15 01:09:12 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:09:12,150 - WARNING - Could not retrieve variants from source file in region 19:19105048-19105449. Error was invalid region `19:19105049-19105449`
[2016-04-15T08:09Z] 2016-04-15 01:09:13 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:09:13,508 - WARNING - Could not retrieve variants from source file in region 19:19446725-19449876. Error was invalid region `19:19446726-19449876`
[2016-04-15T08:09Z] 2016-04-15 01:09:16 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:09:16,144 - WARNING - Could not retrieve variants from source file in region 19:19446725-19449876. Error was invalid region `19:19446726-19449876`
[2016-04-15T08:09Z] 2016-04-15 01:09:18 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:09:18,394 - WARNING - Could not retrieve variants from source file in region 19:19446725-19449876. Error was invalid region `19:19446726-19449876`
[2016-04-15T08:09Z] 2016-04-15 01:09:20 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:09:20,928 - WARNING - Could not retrieve variants from source file in region 19:16841841-16873130. Error was invalid region `19:16841842-16873130`
[2016-04-15T08:09Z] 2016-04-15 01:09:22 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:09:22,333 - WARNING - Could not retrieve variants from source file in region 19:21299563-21300652. Error was invalid region `19:21299564-21300652`
[2016-04-15T08:09Z] 2016-04-15 01:09:22 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:09:22,736 - WARNING - Could not retrieve variants from source file in region 19:21590344-21607423. Error was invalid region `19:21590345-21607423`
[2016-04-15T08:09Z] 2016-04-15 01:09:24 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:09:24,286 - WARNING - Could not retrieve variants from source file in region 19:18679168-18700237. Error was invalid region `19:18679169-18700237`
[2016-04-15T08:09Z] 2016-04-15 01:09:25 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:09:25,467 - WARNING - Could not retrieve variants from source file in region 19:20806966-20828296. Error was invalid region `19:20806967-20828296`
[2016-04-15T08:09Z] 2016-04-15 01:09:25 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:09:25,687 - WARNING - Could not retrieve variants from source file in region 19:20806966-20828296. Error was invalid region `19:20806967-20828296`
[2016-04-15T08:09Z] 2016-04-15 01:09:26 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:09:26,320 - WARNING - Could not retrieve variants from source file in region 19:21299563-21300652. Error was invalid region `19:21299564-21300652`
[2016-04-15T08:09Z] 2016-04-15 01:09:28 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:09:28,830 - WARNING - Could not retrieve variants from source file in region 19:21719190-21719909. Error was invalid region `19:21719191-21719909`
[2016-04-15T08:09Z] 2016-04-15 01:09:28 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:09:28,863 - WARNING - Could not retrieve variants from source file in region 19:18679168-18700237. Error was invalid region `19:18679169-18700237`
[2016-04-15T08:09Z] 2016-04-15 01:09:29 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:09:29,387 - WARNING - Could not retrieve variants from source file in region 19:20721883-20722285. Error was invalid region `19:20721884-20722285`
[2016-04-15T08:09Z] 2016-04-15 01:09:30 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:09:30,058 - WARNING - Could not retrieve variants from source file in region 19:18112150-18112551. Error was invalid region `19:18112151-18112551`
[2016-04-15T08:09Z] 2016-04-15 01:09:30 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:09:30,953 - WARNING - Could not retrieve variants from source file in region 19:21299563-21300652. Error was invalid region `19:21299564-21300652`
[2016-04-15T08:09Z] 2016-04-15 01:09:31 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:09:31,837 - WARNING - Could not retrieve variants from source file in region 19:17513770-17514171. Error was invalid region `19:17513771-17514171`
[2016-04-15T08:09Z] 2016-04-15 01:09:36 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:09:36,907 - WARNING - Could not retrieve variants from source file in region 19:17513770-17514171. Error was invalid region `19:17513771-17514171`
[2016-04-15T08:09Z] 2016-04-15 01:09:39 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:09:39,340 - WARNING - Could not retrieve variants from source file in region 19:17922584-17945661. Error was invalid region `19:17922585-17945661`
[2016-04-15T08:09Z] 2016-04-15 01:09:39 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:09:39,571 - WARNING - Could not retrieve variants from source file in region 19:17547081-17559266. Error was invalid region `19:17547082-17559266`
[2016-04-15T08:09Z] 2016-04-15 01:09:39 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:09:39,904 - WARNING - Could not retrieve variants from source file in region 19:18112150-18112551. Error was invalid region `19:18112151-18112551`
[2016-04-15T08:09Z] 2016-04-15 01:09:41 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:09:41,213 - WARNING - Could not retrieve variants from source file in region 19:17513770-17514171. Error was invalid region `19:17513771-17514171`
[2016-04-15T08:09Z] 2016-04-15 01:09:44 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:09:44,327 - WARNING - Could not retrieve variants from source file in region 19:17547081-17559266. Error was invalid region `19:17547082-17559266`
[2016-04-15T08:09Z] 2016-04-15 01:09:44 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:09:44,508 - WARNING - Could not retrieve variants from source file in region 19:17830764-17838171. Error was invalid region `19:17830765-17838171`
[2016-04-15T08:09Z] 2016-04-15 01:09:44 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:09:44,766 - WARNING - Could not retrieve variants from source file in region 19:18529950-18546868. Error was invalid region `19:18529951-18546868`
[2016-04-15T08:09Z] 2016-04-15 01:09:47 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:09:47,818 - WARNING - Could not retrieve variants from source file in region 19:18047072-18047473. Error was invalid region `19:18047073-18047473`
[2016-04-15T08:09Z] 2016-04-15 01:09:48 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:09:48,775 - WARNING - Could not retrieve variants from source file in region 19:18047072-18047473. Error was invalid region `19:18047073-18047473`
[2016-04-15T08:09Z] 2016-04-15 01:09:49 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:09:49,187 - WARNING - Could not retrieve variants from source file in region 19:18529950-18546868. Error was invalid region `19:18529951-18546868`
[2016-04-15T08:09Z] 2016-04-15 01:09:56 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:09:56,733 - WARNING - Could not retrieve variants from source file in region 19:18496813-18503025. Error was invalid region `19:18496814-18503025`
[2016-04-15T08:09Z] 2016-04-15 01:09:56 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:09:56,807 - WARNING - Could not retrieve variants from source file in region 19:17273682-17338072. Error was invalid region `19:17273683-17338072`
[2016-04-15T08:10Z] 2016-04-15 01:10:00 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:10:00,190 - WARNING - Could not retrieve variants from source file in region 19:18170516-18197825. Error was invalid region `19:18170517-18197825`
[2016-04-15T08:10Z] ['bcbio-variation-recall', 'square', '-Xms750m', '-Xmx7280m', '-XX:+UseSerialGC', '-c', 16, '-r', u'19:31038850-46627578', '--caller', 'platypus', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/19/Batch1-19_31038849_46627578.vcf.gz', '/mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/19/Batch1-19_31038849_46627578.vcf-inputs.txt'] in region: 19:31038850-46627578
[2016-04-15T08:10Z] 2016-04-15 01:10:17 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:10:16,988 - WARNING - Could not retrieve variants from source file in region 19:45971750-45972151. Error was invalid region `19:45971751-45972151`
[2016-04-15T08:10Z] 2016-04-15 01:10:17 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:10:17,066 - WARNING - Could not retrieve variants from source file in region 19:40276452-40276853. Error was invalid region `19:40276453-40276853`
[2016-04-15T08:10Z] 2016-04-15 01:10:17 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:10:17,824 - WARNING - Could not retrieve variants from source file in region 19:46129788-46130189. Error was invalid region `19:46129789-46130189`
[2016-04-15T08:10Z] 2016-04-15 01:10:18 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:10:18,169 - WARNING - Could not retrieve variants from source file in region 19:46443528-46444076. Error was invalid region `19:46443529-46444076`
[2016-04-15T08:10Z] 2016-04-15 01:10:18 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:10:18,170 - WARNING - Could not retrieve variants from source file in region 19:37618512-37643112. Error was invalid region `19:37618513-37643112`
[2016-04-15T08:10Z] 2016-04-15 01:10:19 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:10:19,114 - WARNING - Could not retrieve variants from source file in region 19:46376006-46404769. Error was invalid region `19:46376007-46404769`
[2016-04-15T08:10Z] 2016-04-15 01:10:19 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:10:19,225 - WARNING - Could not retrieve variants from source file in region 19:37239067-37241331. Error was invalid region `19:37239068-37241331`
[2016-04-15T08:10Z] 2016-04-15 01:10:19 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:10:19,302 - WARNING - Could not retrieve variants from source file in region 19:41928441-41944427. Error was invalid region `19:41928442-41944427`
[2016-04-15T08:10Z] 2016-04-15 01:10:19 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:10:19,436 - WARNING - Could not retrieve variants from source file in region 19:34919641-34920042. Error was invalid region `19:34919642-34920042`
[2016-04-15T08:10Z] 2016-04-15 01:10:19 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:10:19,677 - WARNING - Could not retrieve variants from source file in region 19:46511337-46520216. Error was invalid region `19:46511338-46520216`
[2016-04-15T08:10Z] 2016-04-15 01:10:19 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:10:19,738 - WARNING - Could not retrieve variants from source file in region 19:44564770-44612421. Error was invalid region `19:44564771-44612421`
[2016-04-15T08:10Z] 2016-04-15 01:10:23 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:10:23,245 - WARNING - Could not retrieve variants from source file in region 19:45971750-45972151. Error was invalid region `19:45971751-45972151`
[2016-04-15T08:10Z] 2016-04-15 01:10:26 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:10:26,403 - WARNING - Could not retrieve variants from source file in region 19:46443528-46444076. Error was invalid region `19:46443529-46444076`
[2016-04-15T08:10Z] 2016-04-15 01:10:27 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:10:27,344 - WARNING - Could not retrieve variants from source file in region 19:34919641-34920042. Error was invalid region `19:34919642-34920042`
[2016-04-15T08:10Z] 2016-04-15 01:10:27 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:10:27,942 - WARNING - Could not retrieve variants from source file in region 19:44564770-44612421. Error was invalid region `19:44564771-44612421`
[2016-04-15T08:10Z] 2016-04-15 01:10:28 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:10:28,890 - WARNING - Could not retrieve variants from source file in region 19:36940411-36940950. Error was invalid region `19:36940412-36940950`
[2016-04-15T08:10Z] 2016-04-15 01:10:29 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:10:29,650 - WARNING - Could not retrieve variants from source file in region 19:45971750-45972151. Error was invalid region `19:45971751-45972151`
[2016-04-15T08:10Z] 2016-04-15 01:10:29 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:10:29,652 - WARNING - Could not retrieve variants from source file in region 19:37239067-37241331. Error was invalid region `19:37239068-37241331`
[2016-04-15T08:10Z] 2016-04-15 01:10:29 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:10:29,742 - WARNING - Could not retrieve variants from source file in region 19:46511337-46520216. Error was invalid region `19:46511338-46520216`
[2016-04-15T08:10Z] 2016-04-15 01:10:32 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:10:32,798 - WARNING - Could not retrieve variants from source file in region 19:46443528-46444076. Error was invalid region `19:46443529-46444076`
[2016-04-15T08:10Z] 2016-04-15 01:10:35 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:10:35,216 - WARNING - Could not retrieve variants from source file in region 19:46268691-46289699. Error was invalid region `19:46268692-46289699`
[2016-04-15T08:10Z] 2016-04-15 01:10:35 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:10:35,495 - WARNING - Could not retrieve variants from source file in region 19:34919641-34920042. Error was invalid region `19:34919642-34920042`
[2016-04-15T08:10Z] 2016-04-15 01:10:36 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:10:36,803 - WARNING - Could not retrieve variants from source file in region 19:46511337-46520216. Error was invalid region `19:46511338-46520216`
[2016-04-15T08:10Z] 2016-04-15 01:10:37 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:10:37,246 - WARNING - Could not retrieve variants from source file in region 19:44564770-44612421. Error was invalid region `19:44564771-44612421`
[2016-04-15T08:10Z] 2016-04-15 01:10:38 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:10:38,023 - WARNING - Could not retrieve variants from source file in region 19:37239067-37241331. Error was invalid region `19:37239068-37241331`
[2016-04-15T08:10Z] 2016-04-15 01:10:38 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:10:38,661 - WARNING - Could not retrieve variants from source file in region 19:41928441-41944427. Error was invalid region `19:41928442-41944427`
[2016-04-15T08:10Z] 2016-04-15 01:10:45 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:10:45,650 - WARNING - Could not retrieve variants from source file in region 19:40196400-40225836. Error was invalid region `19:40196401-40225836`
[2016-04-15T08:10Z] 2016-04-15 01:10:47 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:10:47,327 - WARNING - Could not retrieve variants from source file in region 19:46051704-46057271. Error was invalid region `19:46051705-46057271`
[2016-04-15T08:10Z] 2016-04-15 01:10:47 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:10:47,930 - WARNING - Could not retrieve variants from source file in region 19:45912278-45923843. Error was invalid region `19:45912279-45923843`
[2016-04-15T08:10Z] 2016-04-15 01:10:49 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:10:49,409 - WARNING - Could not retrieve variants from source file in region 19:37481940-37488689. Error was invalid region `19:37481941-37488689`
[2016-04-15T08:10Z] 2016-04-15 01:10:50 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:10:50,190 - WARNING - Could not retrieve variants from source file in region 19:38229613-38230910. Error was invalid region `19:38229614-38230910`
[2016-04-15T08:10Z] 2016-04-15 01:10:50 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:10:50,720 - WARNING - Could not retrieve variants from source file in region 19:34842277-34843951. Error was invalid region `19:34842278-34843951`
[2016-04-15T08:10Z] 2016-04-15 01:10:53 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:10:53,365 - WARNING - Could not retrieve variants from source file in region 19:46051704-46057271. Error was invalid region `19:46051705-46057271`
[2016-04-15T08:10Z] 2016-04-15 01:10:54 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:10:54,856 - WARNING - Could not retrieve variants from source file in region 19:36727154-36727555. Error was invalid region `19:36727155-36727555`
[2016-04-15T08:10Z] 2016-04-15 01:10:54 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:10:54,879 - WARNING - Could not retrieve variants from source file in region 19:46319204-46319605. Error was invalid region `19:46319205-46319605`
[2016-04-15T08:10Z] 2016-04-15 01:10:55 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:10:55,267 - WARNING - Could not retrieve variants from source file in region 19:41858710-41903410. Error was invalid region `19:41858711-41903410`
[2016-04-15T08:10Z] 2016-04-15 01:10:55 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:10:55,792 - WARNING - Could not retrieve variants from source file in region 19:44469978-44536189. Error was invalid region `19:44469979-44536189`
[2016-04-15T08:10Z] 2016-04-15 01:10:56 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:10:56,121 - WARNING - Could not retrieve variants from source file in region 19:38229613-38230910. Error was invalid region `19:38229614-38230910`
[2016-04-15T08:10Z] 2016-04-15 01:10:56 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:10:56,141 - WARNING - Could not retrieve variants from source file in region 19:44302413-44306672. Error was invalid region `19:44302414-44306672`
[2016-04-15T08:10Z] 2016-04-15 01:10:56 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:10:56,191 - WARNING - Could not retrieve variants from source file in region 19:40196400-40225836. Error was invalid region `19:40196401-40225836`
[2016-04-15T08:10Z] 2016-04-15 01:10:58 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:10:58,503 - WARNING - Could not retrieve variants from source file in region 19:46051704-46057271. Error was invalid region `19:46051705-46057271`
[2016-04-15T08:11Z] 2016-04-15 01:11:01 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:11:01,053 - WARNING - Could not retrieve variants from source file in region 19:36727154-36727555. Error was invalid region `19:36727155-36727555`
[2016-04-15T08:11Z] 2016-04-15 01:11:01 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:11:01,259 - WARNING - Could not retrieve variants from source file in region 19:41858710-41903410. Error was invalid region `19:41858711-41903410`
[2016-04-15T08:11Z] 2016-04-15 01:11:04 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:11:04,524 - WARNING - Could not retrieve variants from source file in region 19:38229613-38230910. Error was invalid region `19:38229614-38230910`
[2016-04-15T08:11Z] 2016-04-15 01:11:04 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:11:04,604 - WARNING - Could not retrieve variants from source file in region 19:44302413-44306672. Error was invalid region `19:44302414-44306672`
[2016-04-15T08:11Z] 2016-04-15 01:11:04 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:11:04,634 - WARNING - Could not retrieve variants from source file in region 19:45284055-45284456. Error was invalid region `19:45284056-45284456`
[2016-04-15T08:11Z] 2016-04-15 01:11:05 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:11:05,884 - WARNING - Could not retrieve variants from source file in region 19:36727154-36727555. Error was invalid region `19:36727155-36727555`
[2016-04-15T08:11Z] 2016-04-15 01:11:06 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:11:06,021 - WARNING - Could not retrieve variants from source file in region 19:41858710-41903410. Error was invalid region `19:41858711-41903410`
[2016-04-15T08:11Z] 2016-04-15 01:11:06 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:11:06,099 - WARNING - Could not retrieve variants from source file in region 19:46319204-46319605. Error was invalid region `19:46319205-46319605`
[2016-04-15T08:11Z] 2016-04-15 01:11:13 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:11:13,825 - WARNING - Could not retrieve variants from source file in region 19:40149086-40149487. Error was invalid region `19:40149087-40149487`
[2016-04-15T08:11Z] 2016-04-15 01:11:17 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:11:17,675 - WARNING - Could not retrieve variants from source file in region 19:43679199-43709846. Error was invalid region `19:43679200-43709846`
[2016-04-15T08:11Z] 2016-04-15 01:11:17 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:11:17,722 - WARNING - Could not retrieve variants from source file in region 19:37440900-37443815. Error was invalid region `19:37440901-37443815`
[2016-04-15T08:11Z] 2016-04-15 01:11:18 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:11:18,729 - WARNING - Could not retrieve variants from source file in region 19:40149086-40149487. Error was invalid region `19:40149087-40149487`
[2016-04-15T08:11Z] 2016-04-15 01:11:19 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:11:19,601 - WARNING - Could not retrieve variants from source file in region 19:38189229-38202706. Error was invalid region `19:38189230-38202706`
[2016-04-15T08:11Z] 2016-04-15 01:11:19 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:11:19,673 - WARNING - Could not retrieve variants from source file in region 19:34712443-34712995. Error was invalid region `19:34712444-34712995`
[2016-04-15T08:11Z] 2016-04-15 01:11:20 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:11:20,331 - WARNING - Could not retrieve variants from source file in region 19:44235306-44235725. Error was invalid region `19:44235307-44235725`
[2016-04-15T08:11Z] 2016-04-15 01:11:20 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:11:20,929 - WARNING - Could not retrieve variants from source file in region 19:36674094-36674495. Error was invalid region `19:36674095-36674495`
[2016-04-15T08:11Z] 2016-04-15 01:11:21 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:11:21,021 - WARNING - Could not retrieve variants from source file in region 19:41811519-41811920. Error was invalid region `19:41811520-41811920`
[2016-04-15T08:11Z] 2016-04-15 01:11:21 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:11:21,896 - WARNING - Could not retrieve variants from source file in region 19:45800807-45868499. Error was invalid region `19:45800808-45868499`
[2016-04-15T08:11Z] 2016-04-15 01:11:22 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:11:22,030 - WARNING - Could not retrieve variants from source file in region 19:44417364-44419220. Error was invalid region `19:44417365-44419220`
[2016-04-15T08:11Z] 2016-04-15 01:11:23 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:11:23,443 - WARNING - Could not retrieve variants from source file in region 19:40149086-40149487. Error was invalid region `19:40149087-40149487`
[2016-04-15T08:11Z] 2016-04-15 01:11:25 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:11:25,384 - WARNING - Could not retrieve variants from source file in region 19:38189229-38202706. Error was invalid region `19:38189230-38202706`
[2016-04-15T08:11Z] 2016-04-15 01:11:26 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:11:26,201 - WARNING - Could not retrieve variants from source file in region 19:41811519-41811920. Error was invalid region `19:41811520-41811920`
[2016-04-15T08:11Z] 2016-04-15 01:11:26 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:11:26,307 - WARNING - Could not retrieve variants from source file in region 19:45250945-45251346. Error was invalid region `19:45250946-45251346`
[2016-04-15T08:11Z] 2016-04-15 01:11:26 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:11:26,487 - WARNING - Could not retrieve variants from source file in region 19:36674094-36674495. Error was invalid region `19:36674095-36674495`
[2016-04-15T08:11Z] 2016-04-15 01:11:27 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:11:27,007 - WARNING - Could not retrieve variants from source file in region 19:45800807-45868499. Error was invalid region `19:45800808-45868499`
[2016-04-15T08:11Z] 2016-04-15 01:11:29 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:11:29,509 - WARNING - Could not retrieve variants from source file in region 19:44235306-44235725. Error was invalid region `19:44235307-44235725`
[2016-04-15T08:11Z] 2016-04-15 01:11:30 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:11:30,209 - WARNING - Could not retrieve variants from source file in region 19:38189229-38202706. Error was invalid region `19:38189230-38202706`
[2016-04-15T08:11Z] 2016-04-15 01:11:32 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:11:32,699 - WARNING - Could not retrieve variants from source file in region 19:37117091-37130609. Error was invalid region `19:37117092-37130609`
[2016-04-15T08:11Z] 2016-04-15 01:11:32 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:11:32,783 - WARNING - Could not retrieve variants from source file in region 19:41811519-41811920. Error was invalid region `19:41811520-41811920`
[2016-04-15T08:11Z] 2016-04-15 01:11:33 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:11:33,348 - WARNING - Could not retrieve variants from source file in region 19:45250945-45251346. Error was invalid region `19:45250946-45251346`
[2016-04-15T08:11Z] 2016-04-15 01:11:33 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:11:33,791 - WARNING - Could not retrieve variants from source file in region 19:44417364-44419220. Error was invalid region `19:44417365-44419220`
[2016-04-15T08:11Z] 2016-04-15 01:11:33 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:11:33,994 - WARNING - Could not retrieve variants from source file in region 19:40978429-40978830. Error was invalid region `19:40978430-40978830`
[2016-04-15T08:11Z] 2016-04-15 01:11:34 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:11:34,053 - WARNING - Could not retrieve variants from source file in region 19:44152889-44172378. Error was invalid region `19:44152890-44172378`
[2016-04-15T08:11Z] 2016-04-15 01:11:38 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:11:38,667 - WARNING - Could not retrieve variants from source file in region 19:37117091-37130609. Error was invalid region `19:37117092-37130609`
[2016-04-15T08:11Z] 2016-04-15 01:11:39 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:11:39,974 - WARNING - Could not retrieve variants from source file in region 19:40023097-40030844. Error was invalid region `19:40023098-40030844`
[2016-04-15T08:11Z] 2016-04-15 01:11:40 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:11:40,608 - WARNING - Could not retrieve variants from source file in region 19:45250945-45251346. Error was invalid region `19:45250946-45251346`
[2016-04-15T08:11Z] 2016-04-15 01:11:42 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:11:42,993 - WARNING - Could not retrieve variants from source file in region 19:40978429-40978830. Error was invalid region `19:40978430-40978830`
[2016-04-15T08:11Z] 2016-04-15 01:11:46 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:11:46,030 - WARNING - Could not retrieve variants from source file in region 19:37310133-37310534. Error was invalid region `19:37310134-37310534`
[2016-04-15T08:11Z] 2016-04-15 01:11:47 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:11:47,036 - WARNING - Could not retrieve variants from source file in region 19:38091721-38092122. Error was invalid region `19:38091722-38092122`
[2016-04-15T08:11Z] 2016-04-15 01:11:48 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:11:48,853 - WARNING - Could not retrieve variants from source file in region 19:41743650-41744051. Error was invalid region `19:41743651-41744051`
[2016-04-15T08:11Z] 2016-04-15 01:11:48 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:11:48,995 - WARNING - Could not retrieve variants from source file in region 19:40978429-40978830. Error was invalid region `19:40978430-40978830`
[2016-04-15T08:11Z] 2016-04-15 01:11:50 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:11:50,106 - WARNING - Could not retrieve variants from source file in region 19:45682613-45683014. Error was invalid region `19:45682614-45683014`
[2016-04-15T08:11Z] 2016-04-15 01:11:50 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:11:50,812 - WARNING - Could not retrieve variants from source file in region 19:43575694-43586854. Error was invalid region `19:43575695-43586854`
[2016-04-15T08:11Z] 2016-04-15 01:11:51 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:11:51,405 - WARNING - Could not retrieve variants from source file in region 19:34302069-34303239. Error was invalid region `19:34302070-34303239`
[2016-04-15T08:11Z] 2016-04-15 01:11:51 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:11:51,822 - WARNING - Could not retrieve variants from source file in region 19:40023097-40030844. Error was invalid region `19:40023098-40030844`
[2016-04-15T08:11Z] 2016-04-15 01:11:52 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:11:52,099 - WARNING - Could not retrieve variants from source file in region 19:37310133-37310534. Error was invalid region `19:37310134-37310534`
[2016-04-15T08:11Z] 2016-04-15 01:11:54 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:11:54,787 - WARNING - Could not retrieve variants from source file in region 19:41743650-41744051. Error was invalid region `19:41743651-41744051`
[2016-04-15T08:11Z] 2016-04-15 01:11:55 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:11:55,226 - WARNING - Could not retrieve variants from source file in region 19:45682613-45683014. Error was invalid region `19:45682614-45683014`
[2016-04-15T08:11Z] 2016-04-15 01:11:55 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:11:55,376 - WARNING - Could not retrieve variants from source file in region 19:45161827-45162228. Error was invalid region `19:45161828-45162228`
[2016-04-15T08:11Z] 2016-04-15 01:11:55 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:11:55,956 - WARNING - Could not retrieve variants from source file in region 19:34302069-34303239. Error was invalid region `19:34302070-34303239`
[2016-04-15T08:11Z] 2016-04-15 01:11:57 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:11:57,250 - WARNING - Could not retrieve variants from source file in region 19:37310133-37310534. Error was invalid region `19:37310134-37310534`
[2016-04-15T08:11Z] 2016-04-15 01:11:58 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:11:58,000 - WARNING - Could not retrieve variants from source file in region 19:43965453-43983930. Error was invalid region `19:43965454-43983930`
[2016-04-15T08:12Z] 2016-04-15 01:12:00 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:12:00,203 - WARNING - Could not retrieve variants from source file in region 19:41082657-41130032. Error was invalid region `19:41082658-41130032`
[2016-04-15T08:12Z] 2016-04-15 01:12:01 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:12:01,620 - WARNING - Could not retrieve variants from source file in region 19:37037881-37039259. Error was invalid region `19:37037882-37039259`
[2016-04-15T08:12Z] 2016-04-15 01:12:01 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:12:01,659 - WARNING - Could not retrieve variants from source file in region 19:41743650-41744051. Error was invalid region `19:41743651-41744051`
[2016-04-15T08:12Z] 2016-04-15 01:12:03 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:12:03,656 - WARNING - Could not retrieve variants from source file in region 19:45161827-45162228. Error was invalid region `19:45161828-45162228`
[2016-04-15T08:12Z] 2016-04-15 01:12:03 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:12:03,899 - WARNING - Could not retrieve variants from source file in region 19:45596424-45596825. Error was invalid region `19:45596425-45596825`
[2016-04-15T08:12Z] 2016-04-15 01:12:05 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:12:05,081 - WARNING - Could not retrieve variants from source file in region 19:40900654-40947941. Error was invalid region `19:40900655-40947941`
[2016-04-15T08:12Z] 2016-04-15 01:12:07 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:12:07,384 - WARNING - Could not retrieve variants from source file in region 19:37037881-37039259. Error was invalid region `19:37037882-37039259`
[2016-04-15T08:12Z] 2016-04-15 01:12:08 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:12:08,354 - WARNING - Could not retrieve variants from source file in region 19:39993259-39996217. Error was invalid region `19:39993260-39996217`
[2016-04-15T08:12Z] 2016-04-15 01:12:10 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:12:10,521 - WARNING - Could not retrieve variants from source file in region 19:45596424-45596825. Error was invalid region `19:45596425-45596825`
[2016-04-15T08:12Z] 2016-04-15 01:12:10 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:12:10,792 - WARNING - Could not retrieve variants from source file in region 19:43965453-43983930. Error was invalid region `19:43965454-43983930`
[2016-04-15T08:12Z] 2016-04-15 01:12:10 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:12:10,832 - WARNING - Could not retrieve variants from source file in region 19:45161827-45162228. Error was invalid region `19:45161828-45162228`
[2016-04-15T08:12Z] 2016-04-15 01:12:11 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:12:11,578 - WARNING - Could not retrieve variants from source file in region 19:40900654-40947941. Error was invalid region `19:40900655-40947941`
[2016-04-15T08:12Z] 2016-04-15 01:12:11 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:12:11,658 - WARNING - Could not retrieve variants from source file in region 19:41082657-41130032. Error was invalid region `19:41082658-41130032`
[2016-04-15T08:12Z] 2016-04-15 01:12:11 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:12:11,897 - WARNING - Could not retrieve variants from source file in region 19:43514308-43529217. Error was invalid region `19:43514309-43529217`
[2016-04-15T08:12Z] 2016-04-15 01:12:12 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:12:12,001 - WARNING - Could not retrieve variants from source file in region 19:45560852-45561253. Error was invalid region `19:45560853-45561253`
[2016-04-15T08:12Z] 2016-04-15 01:12:13 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:12:13,208 - WARNING - Could not retrieve variants from source file in region 19:37004727-37005128. Error was invalid region `19:37004728-37005128`
[2016-04-15T08:12Z] 2016-04-15 01:12:14 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:12:14,560 - WARNING - Could not retrieve variants from source file in region 19:38055401-38056764. Error was invalid region `19:38055402-38056764`
[2016-04-15T08:12Z] 2016-04-15 01:12:17 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:12:17,345 - WARNING - Could not retrieve variants from source file in region 19:37004727-37005128. Error was invalid region `19:37004728-37005128`
[2016-04-15T08:12Z] 2016-04-15 01:12:17 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:12:17,726 - WARNING - Could not retrieve variants from source file in region 19:40900654-40947941. Error was invalid region `19:40900655-40947941`
[2016-04-15T08:12Z] 2016-04-15 01:12:18 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:12:18,124 - WARNING - Could not retrieve variants from source file in region 19:45560852-45561253. Error was invalid region `19:45560853-45561253`
[2016-04-15T08:12Z] 2016-04-15 01:12:18 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:12:18,284 - WARNING - Could not retrieve variants from source file in region 19:41700282-41700683. Error was invalid region `19:41700283-41700683`
[2016-04-15T08:12Z] 2016-04-15 01:12:18 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:12:18,802 - WARNING - Could not retrieve variants from source file in region 19:43514308-43529217. Error was invalid region `19:43514309-43529217`
[2016-04-15T08:12Z] 2016-04-15 01:12:18 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:12:18,822 - WARNING - Could not retrieve variants from source file in region 19:37004727-37005128. Error was invalid region `19:37004728-37005128`
[2016-04-15T08:12Z] 2016-04-15 01:12:18 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:12:18,871 - WARNING - Could not retrieve variants from source file in region 19:34263661-34264062. Error was invalid region `19:34263662-34264062`
[2016-04-15T08:12Z] 2016-04-15 01:12:21 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:12:21,242 - WARNING - Could not retrieve variants from source file in region 19:45560852-45561253. Error was invalid region `19:45560853-45561253`
[2016-04-15T08:12Z] 2016-04-15 01:12:23 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:12:23,633 - WARNING - Could not retrieve variants from source file in region 19:41700282-41700683. Error was invalid region `19:41700283-41700683`
[2016-04-15T08:12Z] 2016-04-15 01:12:24 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:12:24,435 - WARNING - Could not retrieve variants from source file in region 19:43514308-43529217. Error was invalid region `19:43514309-43529217`
[2016-04-15T08:12Z] 2016-04-15 01:12:25 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:12:25,422 - WARNING - Could not retrieve variants from source file in region 19:45447825-45490826. Error was invalid region `19:45447826-45490826`
[2016-04-15T08:12Z] 2016-04-15 01:12:25 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:12:25,570 - WARNING - Could not retrieve variants from source file in region 19:36486234-36498605. Error was invalid region `19:36486235-36498605`
[2016-04-15T08:12Z] 2016-04-15 01:12:26 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:12:26,729 - WARNING - Could not retrieve variants from source file in region 19:44890486-44896760. Error was invalid region `19:44890487-44896760`
[2016-04-15T08:12Z] 2016-04-15 01:12:28 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:12:28,331 - WARNING - Could not retrieve variants from source file in region 19:41700282-41700683. Error was invalid region `19:41700283-41700683`
[2016-04-15T08:12Z] 2016-04-15 01:12:32 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:12:32,703 - WARNING - Could not retrieve variants from source file in region 19:36486234-36498605. Error was invalid region `19:36486235-36498605`
[2016-04-15T08:12Z] 2016-04-15 01:12:32 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:12:32,768 - WARNING - Could not retrieve variants from source file in region 19:41036280-41038764. Error was invalid region `19:41036281-41038764`
[2016-04-15T08:12Z] 2016-04-15 01:12:33 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:12:33,239 - WARNING - Could not retrieve variants from source file in region 19:45381823-45409357. Error was invalid region `19:45381824-45409357`
[2016-04-15T08:12Z] 2016-04-15 01:12:33 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:12:33,649 - WARNING - Could not retrieve variants from source file in region 19:40718865-40720269. Error was invalid region `19:40718866-40720269`
[2016-04-15T08:12Z] 2016-04-15 01:12:34 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:12:34,135 - WARNING - Could not retrieve variants from source file in region 19:44778194-44840979. Error was invalid region `19:44778195-44840979`
[2016-04-15T08:12Z] 2016-04-15 01:12:38 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:12:38,870 - WARNING - Could not retrieve variants from source file in region 19:36486234-36498605. Error was invalid region `19:36486235-36498605`
[2016-04-15T08:12Z] 2016-04-15 01:12:39 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:12:39,158 - WARNING - Could not retrieve variants from source file in region 19:41036280-41038764. Error was invalid region `19:41036281-41038764`
[2016-04-15T08:12Z] 2016-04-15 01:12:40 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:12:40,576 - WARNING - Could not retrieve variants from source file in region 19:38024060-38024461. Error was invalid region `19:38024061-38024461`
[2016-04-15T08:12Z] 2016-04-15 01:12:46 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:12:46,466 - WARNING - Could not retrieve variants from source file in region 19:40718865-40720269. Error was invalid region `19:40718866-40720269`
[2016-04-15T08:12Z] 2016-04-15 01:12:47 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:12:47,114 - WARNING - Could not retrieve variants from source file in region 19:33878626-33882412. Error was invalid region `19:33878627-33882412`
[2016-04-15T08:12Z] 2016-04-15 01:12:48 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:12:48,032 - WARNING - Could not retrieve variants from source file in region 19:43420240-43440038. Error was invalid region `19:43420241-43440038`
[2016-04-15T08:12Z] 2016-04-15 01:12:51 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:12:51,305 - WARNING - Could not retrieve variants from source file in region 19:38024060-38024461. Error was invalid region `19:38024061-38024461`
[2016-04-15T08:12Z] 2016-04-15 01:12:54 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:12:54,515 - WARNING - Could not retrieve variants from source file in region 19:41621896-41634170. Error was invalid region `19:41621897-41634170`
[2016-04-15T08:12Z] 2016-04-15 01:12:57 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:12:57,720 - WARNING - Could not retrieve variants from source file in region 19:37733560-37733961. Error was invalid region `19:37733561-37733961`
[2016-04-15T08:12Z] 2016-04-15 01:12:58 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:12:58,894 - WARNING - Could not retrieve variants from source file in region 19:41009771-41010172. Error was invalid region `19:41009772-41010172`
[2016-04-15T08:13Z] 2016-04-15 01:13:03 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:13:03,604 - WARNING - Could not retrieve variants from source file in region 19:33281713-33317611. Error was invalid region `19:33281714-33317611`
[2016-04-15T08:13Z] 2016-04-15 01:13:05 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:13:05,129 - WARNING - Could not retrieve variants from source file in region 19:41009771-41010172. Error was invalid region `19:41009772-41010172`
[2016-04-15T08:13Z] 2016-04-15 01:13:05 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:13:05,163 - WARNING - Could not retrieve variants from source file in region 19:39788904-39789305. Error was invalid region `19:39788905-39789305`
[2016-04-15T08:13Z] 2016-04-15 01:13:06 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:13:06,476 - WARNING - Could not retrieve variants from source file in region 19:33696497-33698481. Error was invalid region `19:33696498-33698481`
[2016-04-15T08:13Z] 2016-04-15 01:13:08 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:13:08,643 - WARNING - Could not retrieve variants from source file in region 19:37733560-37733961. Error was invalid region `19:37733561-37733961`
[2016-04-15T08:13Z] 2016-04-15 01:13:10 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:13:10,477 - WARNING - Could not retrieve variants from source file in region 19:39788904-39789305. Error was invalid region `19:39788905-39789305`
[2016-04-15T08:13Z] 2016-04-15 01:13:10 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:13:10,619 - WARNING - Could not retrieve variants from source file in region 19:37680737-37681138. Error was invalid region `19:37680738-37681138`
[2016-04-15T08:13Z] 2016-04-15 01:13:11 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:13:11,251 - WARNING - Could not retrieve variants from source file in region 19:33696497-33698481. Error was invalid region `19:33696498-33698481`
[2016-04-15T08:13Z] 2016-04-15 01:13:14 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:13:14,239 - WARNING - Could not retrieve variants from source file in region 19:42798838-42799239. Error was invalid region `19:42798839-42799239`
[2016-04-15T08:13Z] 2016-04-15 01:13:15 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:13:15,518 - WARNING - Could not retrieve variants from source file in region 19:33664977-33665524. Error was invalid region `19:33664978-33665524`
[2016-04-15T08:13Z] 2016-04-15 01:13:16 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:13:16,385 - WARNING - Could not retrieve variants from source file in region 19:33696497-33698481. Error was invalid region `19:33696498-33698481`
[2016-04-15T08:13Z] 2016-04-15 01:13:19 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:13:19,282 - WARNING - Could not retrieve variants from source file in region 19:40323755-40324156. Error was invalid region `19:40323756-40324156`
[2016-04-15T08:13Z] 2016-04-15 01:13:20 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:13:20,378 - WARNING - Could not retrieve variants from source file in region 19:36168703-36169104. Error was invalid region `19:36168704-36169104`
[2016-04-15T08:13Z] 2016-04-15 01:13:22 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:13:22,469 - WARNING - Could not retrieve variants from source file in region 19:41281271-41281672. Error was invalid region `19:41281272-41281672`
[2016-04-15T08:13Z] 2016-04-15 01:13:24 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:13:24,372 - WARNING - Could not retrieve variants from source file in region 19:42798838-42799239. Error was invalid region `19:42798839-42799239`
[2016-04-15T08:13Z] 2016-04-15 01:13:24 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:13:24,988 - WARNING - Could not retrieve variants from source file in region 19:36168703-36169104. Error was invalid region `19:36168704-36169104`
[2016-04-15T08:13Z] 2016-04-15 01:13:26 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:13:26,731 - WARNING - Could not retrieve variants from source file in region 19:32958958-32973267. Error was invalid region `19:32958959-32973267`
[2016-04-15T08:13Z] 2016-04-15 01:13:27 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:13:27,195 - WARNING - Could not retrieve variants from source file in region 19:33167244-33183542. Error was invalid region `19:33167245-33183542`
[2016-04-15T08:13Z] 2016-04-15 01:13:30 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:13:30,099 - WARNING - Could not retrieve variants from source file in region 19:36168703-36169104. Error was invalid region `19:36168704-36169104`
[2016-04-15T08:13Z] 2016-04-15 01:13:31 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:13:31,130 - WARNING - Could not retrieve variants from source file in region 19:43269488-43269895. Error was invalid region `19:43269489-43269895`
[2016-04-15T08:13Z] 2016-04-15 01:13:32 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:13:32,008 - WARNING - Could not retrieve variants from source file in region 19:32958958-32973267. Error was invalid region `19:32958959-32973267`
[2016-04-15T08:13Z] 2016-04-15 01:13:33 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:13:33,397 - WARNING - Could not retrieve variants from source file in region 19:39660066-39660467. Error was invalid region `19:39660067-39660467`
[2016-04-15T08:13Z] 2016-04-15 01:13:33 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:13:33,437 - WARNING - Could not retrieve variants from source file in region 19:39660066-39660467. Error was invalid region `19:39660067-39660467`
[2016-04-15T08:13Z] 2016-04-15 01:13:34 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:13:34,603 - WARNING - Could not retrieve variants from source file in region 19:39590744-39592328. Error was invalid region `19:39590745-39592328`
[2016-04-15T08:13Z] 2016-04-15 01:13:37 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:13:37,610 - WARNING - Could not retrieve variants from source file in region 19:42736056-42736457. Error was invalid region `19:42736057-42736457`
[2016-04-15T08:13Z] 2016-04-15 01:13:38 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:13:38,462 - WARNING - Could not retrieve variants from source file in region 19:43236858-43243438. Error was invalid region `19:43236859-43243438`
[2016-04-15T08:13Z] 2016-04-15 01:13:38 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:13:38,551 - WARNING - Could not retrieve variants from source file in region 19:33076762-33117856. Error was invalid region `19:33076763-33117856`
[2016-04-15T08:13Z] 2016-04-15 01:13:39 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:13:39,429 - WARNING - Could not retrieve variants from source file in region 19:33076762-33117856. Error was invalid region `19:33076763-33117856`
[2016-04-15T08:13Z] 2016-04-15 01:13:42 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:13:42,211 - WARNING - Could not retrieve variants from source file in region 19:32083485-32083886. Error was invalid region `19:32083486-32083886`
[2016-04-15T08:13Z] 2016-04-15 01:13:42 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:13:42,382 - WARNING - Could not retrieve variants from source file in region 19:32873487-32873888. Error was invalid region `19:32873488-32873888`
[2016-04-15T08:13Z] 2016-04-15 01:13:42 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:13:42,825 - WARNING - Could not retrieve variants from source file in region 19:42736056-42736457. Error was invalid region `19:42736057-42736457`
[2016-04-15T08:13Z] 2016-04-15 01:13:43 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:13:43,220 - WARNING - Could not retrieve variants from source file in region 19:33076762-33117856. Error was invalid region `19:33076763-33117856`
[2016-04-15T08:13Z] 2016-04-15 01:13:45 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:13:45,074 - WARNING - Could not retrieve variants from source file in region 19:32873487-32873888. Error was invalid region `19:32873488-32873888`
[2016-04-15T08:13Z] 2016-04-15 01:13:45 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:13:45,773 - WARNING - Could not retrieve variants from source file in region 19:32929858-32930259. Error was invalid region `19:32929859-32930259`
[2016-04-15T08:13Z] 2016-04-15 01:13:46 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:13:46,908 - WARNING - Could not retrieve variants from source file in region 19:35718727-35790693. Error was invalid region `19:35718728-35790693`
[2016-04-15T08:13Z] 2016-04-15 01:13:47 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:13:47,124 - WARNING - Could not retrieve variants from source file in region 19:32083485-32083886. Error was invalid region `19:32083486-32083886`
[2016-04-15T08:13Z] 2016-04-15 01:13:47 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:13:47,227 - WARNING - Could not retrieve variants from source file in region 19:32873487-32873888. Error was invalid region `19:32873488-32873888`
[2016-04-15T08:13Z] 2016-04-15 01:13:47 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:13:47,416 - WARNING - Could not retrieve variants from source file in region 19:42736056-42736457. Error was invalid region `19:42736057-42736457`
[2016-04-15T08:13Z] 2016-04-15 01:13:50 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:13:50,092 - WARNING - Could not retrieve variants from source file in region 19:32929858-32930259. Error was invalid region `19:32929859-32930259`
[2016-04-15T08:13Z] 2016-04-15 01:13:51 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:13:51,952 - WARNING - Could not retrieve variants from source file in region 19:32929858-32930259. Error was invalid region `19:32929859-32930259`
[2016-04-15T08:13Z] 2016-04-15 01:13:52 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:13:52,530 - WARNING - Could not retrieve variants from source file in region 19:32083485-32083886. Error was invalid region `19:32083486-32083886`
[2016-04-15T08:13Z] 2016-04-15 01:13:52 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:13:52,582 - WARNING - Could not retrieve variants from source file in region 19:35329763-35330164. Error was invalid region `19:35329764-35330164`
[2016-04-15T08:13Z] 2016-04-15 01:13:53 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:13:53,761 - WARNING - Could not retrieve variants from source file in region 19:38991305-39010243. Error was invalid region `19:38991306-39010243`
[2016-04-15T08:13Z] 2016-04-15 01:13:54 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:13:54,721 - WARNING - Could not retrieve variants from source file in region 19:39360386-39367301. Error was invalid region `19:39360387-39367301`
[2016-04-15T08:13Z] 2016-04-15 01:13:57 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:13:57,839 - WARNING - Could not retrieve variants from source file in region 19:35329763-35330164. Error was invalid region `19:35329764-35330164`
[2016-04-15T08:13Z] 2016-04-15 01:13:59 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:13:59,912 - WARNING - Could not retrieve variants from source file in region 19:42265678-42266079. Error was invalid region `19:42265679-42266079`
[2016-04-15T08:14Z] 2016-04-15 01:14:00 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:14:00,126 - WARNING - Could not retrieve variants from source file in region 19:31038784-31039185. Error was invalid region `19:31038785-31039185`
[2016-04-15T08:14Z] 2016-04-15 01:14:01 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:14:01,457 - WARNING - Could not retrieve variants from source file in region 19:42470839-42489706. Error was invalid region `19:42470840-42489706`
[2016-04-15T08:14Z] 2016-04-15 01:14:02 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:14:02,389 - WARNING - Could not retrieve variants from source file in region 19:35329763-35330164. Error was invalid region `19:35329764-35330164`
[2016-04-15T08:14Z] 2016-04-15 01:14:04 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:14:04,417 - WARNING - Could not retrieve variants from source file in region 19:39360386-39367301. Error was invalid region `19:39360387-39367301`
[2016-04-15T08:14Z] 2016-04-15 01:14:04 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:14:04,435 - WARNING - Could not retrieve variants from source file in region 19:42265678-42266079. Error was invalid region `19:42265679-42266079`
[2016-04-15T08:14Z] 2016-04-15 01:14:04 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:14:04,678 - WARNING - Could not retrieve variants from source file in region 19:31038784-31039185. Error was invalid region `19:31038785-31039185`
[2016-04-15T08:14Z] 2016-04-15 01:14:06 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:14:06,118 - WARNING - Could not retrieve variants from source file in region 19:42470839-42489706. Error was invalid region `19:42470840-42489706`
[2016-04-15T08:14Z] 2016-04-15 01:14:10 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:14:10,335 - WARNING - Could not retrieve variants from source file in region 19:42470839-42489706. Error was invalid region `19:42470840-42489706`
[2016-04-15T08:14Z] 2016-04-15 01:14:14 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:14:14,755 - WARNING - Could not retrieve variants from source file in region 19:35263168-35263569. Error was invalid region `19:35263169-35263569`
[2016-04-15T08:14Z] 2016-04-15 01:14:17 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:14:17,848 - WARNING - Could not retrieve variants from source file in region 19:38572683-38573084. Error was invalid region `19:38572684-38573084`
[2016-04-15T08:14Z] 2016-04-15 01:14:19 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:14:19,262 - WARNING - Could not retrieve variants from source file in region 19:42342108-42354819. Error was invalid region `19:42342109-42354819`
[2016-04-15T08:14Z] 2016-04-15 01:14:19 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:14:19,699 - WARNING - Could not retrieve variants from source file in region 19:35263168-35263569. Error was invalid region `19:35263169-35263569`
[2016-04-15T08:14Z] 2016-04-15 01:14:19 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:14:19,721 - WARNING - Could not retrieve variants from source file in region 19:38912553-38959870. Error was invalid region `19:38912554-38959870`
[2016-04-15T08:14Z] 2016-04-15 01:14:19 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:14:19,827 - WARNING - Could not retrieve variants from source file in region 19:38652751-38653152. Error was invalid region `19:38652752-38653152`
[2016-04-15T08:14Z] 2016-04-15 01:14:20 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:14:20,494 - WARNING - Could not retrieve variants from source file in region 19:42221396-42221797. Error was invalid region `19:42221397-42221797`
[2016-04-15T08:14Z] 2016-04-15 01:14:21 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:14:21,514 - WARNING - Could not retrieve variants from source file in region 19:42342108-42354819. Error was invalid region `19:42342109-42354819`
[2016-04-15T08:14Z] 2016-04-15 01:14:22 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:14:22,220 - WARNING - Could not retrieve variants from source file in region 19:42190648-42191049. Error was invalid region `19:42190649-42191049`
[2016-04-15T08:14Z] 2016-04-15 01:14:24 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:14:24,453 - WARNING - Could not retrieve variants from source file in region 19:38912553-38959870. Error was invalid region `19:38912554-38959870`
[2016-04-15T08:14Z] 2016-04-15 01:14:24 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:14:24,457 - WARNING - Could not retrieve variants from source file in region 19:38652751-38653152. Error was invalid region `19:38652752-38653152`
[2016-04-15T08:14Z] 2016-04-15 01:14:24 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:14:24,473 - WARNING - Could not retrieve variants from source file in region 19:35263168-35263569. Error was invalid region `19:35263169-35263569`
[2016-04-15T08:14Z] 2016-04-15 01:14:25 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:14:25,016 - WARNING - Could not retrieve variants from source file in region 19:42221396-42221797. Error was invalid region `19:42221397-42221797`
[2016-04-15T08:14Z] 2016-04-15 01:14:26 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:14:26,706 - WARNING - Could not retrieve variants from source file in region 19:35174997-35175965. Error was invalid region `19:35174998-35175965`
[2016-04-15T08:14Z] 2016-04-15 01:14:34 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:14:34,110 - WARNING - Could not retrieve variants from source file in region 19:42132103-42132504. Error was invalid region `19:42132104-42132504`
[2016-04-15T08:14Z] 2016-04-15 01:14:34 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:14:34,147 - WARNING - Could not retrieve variants from source file in region 19:35084266-35084667. Error was invalid region `19:35084267-35084667`
[2016-04-15T08:14Z] 2016-04-15 01:14:34 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:14:34,150 - WARNING - Could not retrieve variants from source file in region 19:42132103-42132504. Error was invalid region `19:42132104-42132504`
[2016-04-15T08:14Z] 2016-04-15 01:14:36 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:14:36,718 - WARNING - Could not retrieve variants from source file in region 19:42083638-42086063. Error was invalid region `19:42083639-42086063`
[2016-04-15T08:14Z] 2016-04-15 01:14:36 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:14:36,722 - WARNING - Could not retrieve variants from source file in region 19:42083638-42086063. Error was invalid region `19:42083639-42086063`
[2016-04-15T08:14Z] 2016-04-15 01:14:36 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:14:36,936 - WARNING - Could not retrieve variants from source file in region 19:34959768-34973666. Error was invalid region `19:34959769-34973666`
[2016-04-15T08:14Z] 2016-04-15 01:14:37 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:14:37,432 - WARNING - Could not retrieve variants from source file in region 19:34959768-34973666. Error was invalid region `19:34959769-34973666`
[2016-04-15T08:14Z] 2016-04-15 01:14:37 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:14:37,633 - WARNING - Could not retrieve variants from source file in region 19:34959768-34973666. Error was invalid region `19:34959769-34973666`
[2016-04-15T08:14Z] 2016-04-15 01:14:37 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:14:37,899 - WARNING - Could not retrieve variants from source file in region 19:42083638-42086063. Error was invalid region `19:42083639-42086063`
[2016-04-15T08:14Z] ['bcbio-variation-recall', 'square', '-Xms750m', '-Xmx7280m', '-XX:+UseSerialGC', '-c', 16, '-r', u'19:46627882-59128983', '--caller', 'platypus', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/19/Batch1-19_46627881_59128983.vcf.gz', '/mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/19/Batch1-19_46627881_59128983.vcf-inputs.txt'] in region: 19:46627882-59128983
[2016-04-15T08:14Z] 2016-04-15 01:14:54 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:14:54,975 - WARNING - Could not retrieve variants from source file in region 19:50720729-50726760. Error was invalid region `19:50720730-50726760`
[2016-04-15T08:14Z] 2016-04-15 01:14:55 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:14:55,424 - WARNING - Could not retrieve variants from source file in region 19:52803458-52825425. Error was invalid region `19:52803459-52825425`
[2016-04-15T08:14Z] 2016-04-15 01:14:55 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:14:55,724 - WARNING - Could not retrieve variants from source file in region 19:52032947-52033932. Error was invalid region `19:52032948-52033932`
[2016-04-15T08:14Z] 2016-04-15 01:14:55 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:14:55,753 - WARNING - Could not retrieve variants from source file in region 19:52327573-52327974. Error was invalid region `19:52327574-52327974`
[2016-04-15T08:14Z] 2016-04-15 01:14:56 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:14:56,157 - WARNING - Could not retrieve variants from source file in region 19:48800122-48806205. Error was invalid region `19:48800123-48806205`
[2016-04-15T08:14Z] 2016-04-15 01:14:56 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:14:56,161 - WARNING - Could not retrieve variants from source file in region 19:53383974-53384375. Error was invalid region `19:53383975-53384375`
[2016-04-15T08:14Z] 2016-04-15 01:14:56 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:14:56,534 - WARNING - Could not retrieve variants from source file in region 19:59082394-59082795. Error was invalid region `19:59082395-59082795`
[2016-04-15T08:14Z] 2016-04-15 01:14:56 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:14:56,666 - WARNING - Could not retrieve variants from source file in region 19:49438066-49438467. Error was invalid region `19:49438067-49438467`
[2016-04-15T08:15Z] 2016-04-15 01:15:00 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:15:00,654 - WARNING - Could not retrieve variants from source file in region 19:53911299-53912432. Error was invalid region `19:53911300-53912432`
[2016-04-15T08:15Z] 2016-04-15 01:15:02 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:15:02,661 - WARNING - Could not retrieve variants from source file in region 19:48484818-48495494. Error was invalid region `19:48484819-48495494`
[2016-04-15T08:15Z] 2016-04-15 01:15:03 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:15:03,797 - WARNING - Could not retrieve variants from source file in region 19:51359286-51363216. Error was invalid region `19:51359287-51363216`
[2016-04-15T08:15Z] 2016-04-15 01:15:04 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:15:04,517 - WARNING - Could not retrieve variants from source file in region 19:52803458-52825425. Error was invalid region `19:52803459-52825425`
[2016-04-15T08:15Z] 2016-04-15 01:15:05 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:15:05,044 - WARNING - Could not retrieve variants from source file in region 19:52032947-52033932. Error was invalid region `19:52032948-52033932`
[2016-04-15T08:15Z] 2016-04-15 01:15:05 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:15:05,339 - WARNING - Could not retrieve variants from source file in region 19:53383974-53384375. Error was invalid region `19:53383975-53384375`
[2016-04-15T08:15Z] 2016-04-15 01:15:05 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:15:05,711 - WARNING - Could not retrieve variants from source file in region 19:47979942-47980343. Error was invalid region `19:47979943-47980343`
[2016-04-15T08:15Z] 2016-04-15 01:15:08 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:15:08,034 - WARNING - Could not retrieve variants from source file in region 19:48484818-48495494. Error was invalid region `19:48484819-48495494`
[2016-04-15T08:15Z] 2016-04-15 01:15:11 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:15:11,242 - WARNING - Could not retrieve variants from source file in region 19:52803458-52825425. Error was invalid region `19:52803459-52825425`
[2016-04-15T08:15Z] 2016-04-15 01:15:12 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:15:12,515 - WARNING - Could not retrieve variants from source file in region 19:52327573-52327974. Error was invalid region `19:52327574-52327974`
[2016-04-15T08:15Z] 2016-04-15 01:15:13 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:15:13,215 - WARNING - Could not retrieve variants from source file in region 19:59082394-59082795. Error was invalid region `19:59082395-59082795`
[2016-04-15T08:15Z] 2016-04-15 01:15:13 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:15:13,269 - WARNING - Could not retrieve variants from source file in region 19:52032947-52033932. Error was invalid region `19:52032948-52033932`
[2016-04-15T08:15Z] 2016-04-15 01:15:13 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:15:13,349 - WARNING - Could not retrieve variants from source file in region 19:53383974-53384375. Error was invalid region `19:53383975-53384375`
[2016-04-15T08:15Z] 2016-04-15 01:15:13 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:15:13,487 - WARNING - Could not retrieve variants from source file in region 19:48800122-48806205. Error was invalid region `19:48800123-48806205`
[2016-04-15T08:15Z] 2016-04-15 01:15:13 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:15:13,597 - WARNING - Could not retrieve variants from source file in region 19:47979942-47980343. Error was invalid region `19:47979943-47980343`
[2016-04-15T08:15Z] 2016-04-15 01:15:25 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:15:25,270 - WARNING - Could not retrieve variants from source file in region 19:48389214-48389615. Error was invalid region `19:48389215-48389615`
[2016-04-15T08:15Z] 2016-04-15 01:15:25 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:15:25,601 - WARNING - Could not retrieve variants from source file in region 19:53856138-53856539. Error was invalid region `19:53856139-53856539`
[2016-04-15T08:15Z] 2016-04-15 01:15:28 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:15:28,670 - WARNING - Could not retrieve variants from source file in region 19:52728819-52729220. Error was invalid region `19:52728820-52729220`
[2016-04-15T08:15Z] 2016-04-15 01:15:28 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:15:28,943 - WARNING - Could not retrieve variants from source file in region 19:51656243-51656644. Error was invalid region `19:51656244-51656644`
[2016-04-15T08:15Z] 2016-04-15 01:15:30 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:15:30,364 - WARNING - Could not retrieve variants from source file in region 19:48389214-48389615. Error was invalid region `19:48389215-48389615`
[2016-04-15T08:15Z] 2016-04-15 01:15:30 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:15:30,430 - WARNING - Could not retrieve variants from source file in region 19:58982173-58992090. Error was invalid region `19:58982174-58992090`
[2016-04-15T08:15Z] 2016-04-15 01:15:31 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:15:31,313 - WARNING - Could not retrieve variants from source file in region 19:53856138-53856539. Error was invalid region `19:53856139-53856539`
[2016-04-15T08:15Z] 2016-04-15 01:15:32 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:15:32,254 - WARNING - Could not retrieve variants from source file in region 19:49407449-49407850. Error was invalid region `19:49407450-49407850`
[2016-04-15T08:15Z] 2016-04-15 01:15:35 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:15:35,207 - WARNING - Could not retrieve variants from source file in region 19:48697750-48737954. Error was invalid region `19:48697751-48737954`
[2016-04-15T08:15Z] 2016-04-15 01:15:35 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:15:35,231 - WARNING - Could not retrieve variants from source file in region 19:51656243-51656644. Error was invalid region `19:51656244-51656644`
[2016-04-15T08:15Z] 2016-04-15 01:15:35 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:15:35,644 - WARNING - Could not retrieve variants from source file in region 19:48389214-48389615. Error was invalid region `19:48389215-48389615`
[2016-04-15T08:15Z] 2016-04-15 01:15:36 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:15:36,019 - WARNING - Could not retrieve variants from source file in region 19:51983462-52004986. Error was invalid region `19:51983463-52004986`
[2016-04-15T08:15Z] 2016-04-15 01:15:36 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:15:36,658 - WARNING - Could not retrieve variants from source file in region 19:53856138-53856539. Error was invalid region `19:53856139-53856539`
[2016-04-15T08:15Z] 2016-04-15 01:15:37 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:15:37,588 - WARNING - Could not retrieve variants from source file in region 19:47223738-47224139. Error was invalid region `19:47223739-47224139`
[2016-04-15T08:15Z] 2016-04-15 01:15:38 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:15:38,731 - WARNING - Could not retrieve variants from source file in region 19:57293183-57293584. Error was invalid region `19:57293184-57293584`
[2016-04-15T08:15Z] 2016-04-15 01:15:41 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:15:41,085 - WARNING - Could not retrieve variants from source file in region 19:53343907-53357362. Error was invalid region `19:53343908-53357362`
[2016-04-15T08:15Z] 2016-04-15 01:15:42 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:15:42,116 - WARNING - Could not retrieve variants from source file in region 19:52728819-52729220. Error was invalid region `19:52728820-52729220`
[2016-04-15T08:15Z] 2016-04-15 01:15:42 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:15:42,731 - WARNING - Could not retrieve variants from source file in region 19:51656243-51656644. Error was invalid region `19:51656244-51656644`
[2016-04-15T08:15Z] 2016-04-15 01:15:42 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:15:42,731 - WARNING - Could not retrieve variants from source file in region 19:55238965-55287054. Error was invalid region `19:55238966-55287054`
[2016-04-15T08:15Z] 2016-04-15 01:15:42 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:15:42,798 - WARNING - Could not retrieve variants from source file in region 19:48697750-48737954. Error was invalid region `19:48697751-48737954`
[2016-04-15T08:15Z] 2016-04-15 01:15:43 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:15:43,154 - WARNING - Could not retrieve variants from source file in region 19:58982173-58992090. Error was invalid region `19:58982174-58992090`
[2016-04-15T08:15Z] 2016-04-15 01:15:43 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:15:43,159 - WARNING - Could not retrieve variants from source file in region 19:49407449-49407850. Error was invalid region `19:49407450-49407850`
[2016-04-15T08:15Z] 2016-04-15 01:15:43 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:15:43,296 - WARNING - Could not retrieve variants from source file in region 19:47223738-47224139. Error was invalid region `19:47223739-47224139`
[2016-04-15T08:15Z] 2016-04-15 01:15:43 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:15:43,519 - WARNING - Could not retrieve variants from source file in region 19:57293183-57293584. Error was invalid region `19:57293184-57293584`
[2016-04-15T08:15Z] 2016-04-15 01:15:52 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:15:52,603 - WARNING - Could not retrieve variants from source file in region 19:48697750-48737954. Error was invalid region `19:48697751-48737954`
[2016-04-15T08:15Z] 2016-04-15 01:15:54 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:15:54,331 - WARNING - Could not retrieve variants from source file in region 19:53792831-53793764. Error was invalid region `19:53792832-53793764`
[2016-04-15T08:16Z] 2016-04-15 01:16:00 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:16:00,199 - WARNING - Could not retrieve variants from source file in region 19:53792831-53793764. Error was invalid region `19:53792832-53793764`
[2016-04-15T08:16Z] 2016-04-15 01:16:02 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:16:02,050 - WARNING - Could not retrieve variants from source file in region 19:58907939-58946393. Error was invalid region `19:58907940-58946393`
[2016-04-15T08:16Z] 2016-04-15 01:16:02 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:16:02,081 - WARNING - Could not retrieve variants from source file in region 19:51228423-51228824. Error was invalid region `19:51228424-51228824`
[2016-04-15T08:16Z] 2016-04-15 01:16:02 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:16:02,147 - WARNING - Could not retrieve variants from source file in region 19:51584705-51630672. Error was invalid region `19:51584706-51630672`
[2016-04-15T08:16Z] 2016-04-15 01:16:02 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:16:02,461 - WARNING - Could not retrieve variants from source file in region 19:47177702-47178103. Error was invalid region `19:47177703-47178103`
[2016-04-15T08:16Z] 2016-04-15 01:16:02 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:16:02,689 - WARNING - Could not retrieve variants from source file in region 19:57175273-57176672. Error was invalid region `19:57175274-57176672`
[2016-04-15T08:16Z] 2016-04-15 01:16:02 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:16:02,710 - WARNING - Could not retrieve variants from source file in region 19:51920402-51920803. Error was invalid region `19:51920403-51920803`
[2016-04-15T08:16Z] 2016-04-15 01:16:02 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:16:02,897 - WARNING - Could not retrieve variants from source file in region 19:53302731-53304753. Error was invalid region `19:53302732-53304753`
[2016-04-15T08:16Z] 2016-04-15 01:16:03 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:16:03,632 - WARNING - Could not retrieve variants from source file in region 19:52659780-52660973. Error was invalid region `19:52659781-52660973`
[2016-04-15T08:16Z] 2016-04-15 01:16:06 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:16:06,420 - WARNING - Could not retrieve variants from source file in region 19:53792831-53793764. Error was invalid region `19:53792832-53793764`
[2016-04-15T08:16Z] 2016-04-15 01:16:08 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:16:08,843 - WARNING - Could not retrieve variants from source file in region 19:48654342-48654743. Error was invalid region `19:48654343-48654743`
[2016-04-15T08:16Z] 2016-04-15 01:16:09 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:16:09,227 - WARNING - Could not retrieve variants from source file in region 19:47822827-47824061. Error was invalid region `19:47822828-47824061`
[2016-04-15T08:16Z] 2016-04-15 01:16:09 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:16:09,559 - WARNING - Could not retrieve variants from source file in region 19:51228423-51228824. Error was invalid region `19:51228424-51228824`
[2016-04-15T08:16Z] 2016-04-15 01:16:10 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:16:10,417 - WARNING - Could not retrieve variants from source file in region 19:52217194-52223311. Error was invalid region `19:52217195-52223311`
[2016-04-15T08:16Z] 2016-04-15 01:16:10 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:16:10,574 - WARNING - Could not retrieve variants from source file in region 19:51920402-51920803. Error was invalid region `19:51920403-51920803`
[2016-04-15T08:16Z] 2016-04-15 01:16:10 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:16:10,598 - WARNING - Could not retrieve variants from source file in region 19:47177702-47178103. Error was invalid region `19:47177703-47178103`
[2016-04-15T08:16Z] 2016-04-15 01:16:10 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:16:10,755 - WARNING - Could not retrieve variants from source file in region 19:52659780-52660973. Error was invalid region `19:52659781-52660973`
[2016-04-15T08:16Z] 2016-04-15 01:16:11 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:16:11,277 - WARNING - Could not retrieve variants from source file in region 19:50139721-50193353. Error was invalid region `19:50139722-50193353`
[2016-04-15T08:16Z] 2016-04-15 01:16:14 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:16:14,976 - WARNING - Could not retrieve variants from source file in region 19:48654342-48654743. Error was invalid region `19:48654343-48654743`
[2016-04-15T08:16Z] 2016-04-15 01:16:16 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:16:16,610 - WARNING - Could not retrieve variants from source file in region 19:47822827-47824061. Error was invalid region `19:47822828-47824061`
[2016-04-15T08:16Z] 2016-04-15 01:16:18 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:16:18,227 - WARNING - Could not retrieve variants from source file in region 19:51228423-51228824. Error was invalid region `19:51228424-51228824`
[2016-04-15T08:16Z] 2016-04-15 01:16:18 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:16:18,672 - WARNING - Could not retrieve variants from source file in region 19:52217194-52223311. Error was invalid region `19:52217195-52223311`
[2016-04-15T08:16Z] 2016-04-15 01:16:19 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:16:19,056 - WARNING - Could not retrieve variants from source file in region 19:57175273-57176672. Error was invalid region `19:57175274-57176672`
[2016-04-15T08:16Z] 2016-04-15 01:16:19 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:16:19,348 - WARNING - Could not retrieve variants from source file in region 19:51920402-51920803. Error was invalid region `19:51920403-51920803`
[2016-04-15T08:16Z] 2016-04-15 01:16:19 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:16:19,392 - WARNING - Could not retrieve variants from source file in region 19:47177702-47178103. Error was invalid region `19:47177703-47178103`
[2016-04-15T08:16Z] 2016-04-15 01:16:21 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:16:21,761 - WARNING - Could not retrieve variants from source file in region 19:47822827-47824061. Error was invalid region `19:47822828-47824061`
[2016-04-15T08:16Z] 2016-04-15 01:16:33 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:16:33,674 - WARNING - Could not retrieve variants from source file in region 19:58864268-58880166. Error was invalid region `19:58864269-58880166`
[2016-04-15T08:16Z] 2016-04-15 01:16:34 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:16:34,990 - WARNING - Could not retrieve variants from source file in region 19:55143975-55144376. Error was invalid region `19:55143976-55144376`
[2016-04-15T08:16Z] 2016-04-15 01:16:37 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:16:37,253 - WARNING - Could not retrieve variants from source file in region 19:52618854-52619255. Error was invalid region `19:52618855-52619255`
[2016-04-15T08:16Z] 2016-04-15 01:16:38 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:16:38,507 - WARNING - Could not retrieve variants from source file in region 19:51835681-51871385. Error was invalid region `19:51835682-51871385`
[2016-04-15T08:16Z] 2016-04-15 01:16:39 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:16:39,536 - WARNING - Could not retrieve variants from source file in region 19:58864268-58880166. Error was invalid region `19:58864269-58880166`
[2016-04-15T08:16Z] 2016-04-15 01:16:40 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:16:40,994 - WARNING - Could not retrieve variants from source file in region 19:55143975-55144376. Error was invalid region `19:55143976-55144376`
[2016-04-15T08:16Z] 2016-04-15 01:16:42 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:16:42,909 - WARNING - Could not retrieve variants from source file in region 19:53270173-53270574. Error was invalid region `19:53270174-53270574`
[2016-04-15T08:16Z] 2016-04-15 01:16:43 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:16:43,968 - WARNING - Could not retrieve variants from source file in region 19:52618854-52619255. Error was invalid region `19:52618855-52619255`
[2016-04-15T08:16Z] 2016-04-15 01:16:44 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:16:44,857 - WARNING - Could not retrieve variants from source file in region 19:48598612-48622617. Error was invalid region `19:48598613-48622617`
[2016-04-15T08:16Z] 2016-04-15 01:16:45 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:16:45,014 - WARNING - Could not retrieve variants from source file in region 19:51835681-51871385. Error was invalid region `19:51835682-51871385`
[2016-04-15T08:16Z] 2016-04-15 01:16:46 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:16:46,091 - WARNING - Could not retrieve variants from source file in region 19:58864268-58880166. Error was invalid region `19:58864269-58880166`
[2016-04-15T08:16Z] 2016-04-15 01:16:46 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:16:46,993 - WARNING - Could not retrieve variants from source file in region 19:55143975-55144376. Error was invalid region `19:55143976-55144376`
[2016-04-15T08:16Z] 2016-04-15 01:16:48 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:16:48,152 - WARNING - Could not retrieve variants from source file in region 19:52130577-52149355. Error was invalid region `19:52130578-52149355`
[2016-04-15T08:16Z] 2016-04-15 01:16:49 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:16:49,564 - WARNING - Could not retrieve variants from source file in region 19:53270173-53270574. Error was invalid region `19:53270174-53270574`
[2016-04-15T08:16Z] 2016-04-15 01:16:51 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:16:51,094 - WARNING - Could not retrieve variants from source file in region 19:57064978-57093358. Error was invalid region `19:57064979-57093358`
[2016-04-15T08:16Z] 2016-04-15 01:16:51 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:16:51,668 - WARNING - Could not retrieve variants from source file in region 19:51480629-51538344. Error was invalid region `19:51480630-51538344`
[2016-04-15T08:16Z] 2016-04-15 01:16:52 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:16:52,180 - WARNING - Could not retrieve variants from source file in region 19:47123572-47137649. Error was invalid region `19:47123573-47137649`
[2016-04-15T08:16Z] 2016-04-15 01:16:58 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:16:58,573 - WARNING - Could not retrieve variants from source file in region 19:48034760-48035161. Error was invalid region `19:48034761-48035161`
[2016-04-15T08:17Z] 2016-04-15 01:17:00 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:17:00,436 - WARNING - Could not retrieve variants from source file in region 19:52089889-52090290. Error was invalid region `19:52089890-52090290`
[2016-04-15T08:17Z] 2016-04-15 01:17:02 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:17:02,213 - WARNING - Could not retrieve variants from source file in region 19:58773173-58806273. Error was invalid region `19:58773174-58806273`
[2016-04-15T08:17Z] 2016-04-15 01:17:03 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:17:03,976 - WARNING - Could not retrieve variants from source file in region 19:55086564-55110966. Error was invalid region `19:55086565-55110966`
[2016-04-15T08:17Z] 2016-04-15 01:17:05 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:17:05,295 - WARNING - Could not retrieve variants from source file in region 19:50059771-50060172. Error was invalid region `19:50059772-50060172`
[2016-04-15T08:17Z] 2016-04-15 01:17:05 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:17:05,926 - WARNING - Could not retrieve variants from source file in region 19:52089889-52090290. Error was invalid region `19:52089890-52090290`
[2016-04-15T08:17Z] 2016-04-15 01:17:06 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:17:06,012 - WARNING - Could not retrieve variants from source file in region 19:53209342-53209744. Error was invalid region `19:53209343-53209744`
[2016-04-15T08:17Z] 2016-04-15 01:17:07 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:17:07,047 - WARNING - Could not retrieve variants from source file in region 19:53644232-53669682. Error was invalid region `19:53644233-53669682`
[2016-04-15T08:17Z] 2016-04-15 01:17:07 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:17:07,866 - WARNING - Could not retrieve variants from source file in region 19:57019219-57036843. Error was invalid region `19:57019220-57036843`
[2016-04-15T08:17Z] 2016-04-15 01:17:07 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:17:07,993 - WARNING - Could not retrieve variants from source file in region 19:48525296-48544113. Error was invalid region `19:48525297-48544113`
[2016-04-15T08:17Z] 2016-04-15 01:17:08 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:17:08,325 - WARNING - Could not retrieve variants from source file in region 19:51411425-51452440. Error was invalid region `19:51411426-51452440`
[2016-04-15T08:17Z] 2016-04-15 01:17:09 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:17:09,020 - WARNING - Could not retrieve variants from source file in region 19:47700400-47700801. Error was invalid region `19:47700401-47700801`
[2016-04-15T08:17Z] 2016-04-15 01:17:09 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:17:09,087 - WARNING - Could not retrieve variants from source file in region 19:47079674-47080075. Error was invalid region `19:47079675-47080075`
[2016-04-15T08:17Z] 2016-04-15 01:17:10 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:17:10,103 - WARNING - Could not retrieve variants from source file in region 19:51015193-51021247. Error was invalid region `19:51015194-51021247`
[2016-04-15T08:17Z] 2016-04-15 01:17:10 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:17:10,611 - WARNING - Could not retrieve variants from source file in region 19:50059771-50060172. Error was invalid region `19:50059772-50060172`
[2016-04-15T08:17Z] 2016-04-15 01:17:13 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:17:13,097 - WARNING - Could not retrieve variants from source file in region 19:58773173-58806273. Error was invalid region `19:58773174-58806273`
[2016-04-15T08:17Z] 2016-04-15 01:17:16 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:17:16,183 - WARNING - Could not retrieve variants from source file in region 19:53209342-53209744. Error was invalid region `19:53209343-53209744`
[2016-04-15T08:17Z] 2016-04-15 01:17:16 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:17:16,716 - WARNING - Could not retrieve variants from source file in region 19:55086564-55110966. Error was invalid region `19:55086565-55110966`
[2016-04-15T08:17Z] 2016-04-15 01:17:18 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:17:18,249 - WARNING - Could not retrieve variants from source file in region 19:48525296-48544113. Error was invalid region `19:48525297-48544113`
[2016-04-15T08:17Z] 2016-04-15 01:17:18 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:17:18,934 - WARNING - Could not retrieve variants from source file in region 19:47079674-47080075. Error was invalid region `19:47079675-47080075`
[2016-04-15T08:17Z] 2016-04-15 01:17:21 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:17:21,692 - WARNING - Could not retrieve variants from source file in region 19:53612100-53612947. Error was invalid region `19:53612101-53612947`
[2016-04-15T08:17Z] 2016-04-15 01:17:21 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:17:21,725 - WARNING - Could not retrieve variants from source file in region 19:54600021-54600422. Error was invalid region `19:54600022-54600422`
[2016-04-15T08:17Z] 2016-04-15 01:17:23 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:17:23,659 - WARNING - Could not retrieve variants from source file in region 19:47585306-47585707. Error was invalid region `19:47585307-47585707`
[2016-04-15T08:17Z] 2016-04-15 01:17:26 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:17:26,879 - WARNING - Could not retrieve variants from source file in region 19:58718058-58718550. Error was invalid region `19:58718059-58718550`
[2016-04-15T08:17Z] 2016-04-15 01:17:27 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:17:27,734 - WARNING - Could not retrieve variants from source file in region 19:53612100-53612947. Error was invalid region `19:53612101-53612947`
[2016-04-15T08:17Z] 2016-04-15 01:17:27 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:17:27,740 - WARNING - Could not retrieve variants from source file in region 19:54600021-54600422. Error was invalid region `19:54600022-54600422`
[2016-04-15T08:17Z] 2016-04-15 01:17:28 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:17:28,598 - WARNING - Could not retrieve variants from source file in region 19:47585306-47585707. Error was invalid region `19:47585307-47585707`
[2016-04-15T08:17Z] 2016-04-15 01:17:30 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:17:30,114 - WARNING - Could not retrieve variants from source file in region 19:53116432-53117999. Error was invalid region `19:53116433-53117999`
[2016-04-15T08:17Z] 2016-04-15 01:17:32 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:17:32,012 - WARNING - Could not retrieve variants from source file in region 19:47615607-47634503. Error was invalid region `19:47615608-47634503`
[2016-04-15T08:17Z] 2016-04-15 01:17:32 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:17:32,773 - WARNING - Could not retrieve variants from source file in region 19:58718058-58718550. Error was invalid region `19:58718059-58718550`
[2016-04-15T08:17Z] 2016-04-15 01:17:33 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:17:33,392 - WARNING - Could not retrieve variants from source file in region 19:53612100-53612947. Error was invalid region `19:53612101-53612947`
[2016-04-15T08:17Z] 2016-04-15 01:17:34 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:17:34,037 - WARNING - Could not retrieve variants from source file in region 19:54600021-54600422. Error was invalid region `19:54600022-54600422`
[2016-04-15T08:17Z] 2016-04-15 01:17:34 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:17:34,236 - WARNING - Could not retrieve variants from source file in region 19:47585306-47585707. Error was invalid region `19:47585307-47585707`
[2016-04-15T08:17Z] 2016-04-15 01:17:34 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:17:34,750 - WARNING - Could not retrieve variants from source file in region 19:46996717-46998426. Error was invalid region `19:46996718-46998426`
[2016-04-15T08:17Z] 2016-04-15 01:17:35 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:17:35,280 - WARNING - Could not retrieve variants from source file in region 19:55019050-55019561. Error was invalid region `19:55019051-55019561`
[2016-04-15T08:17Z] 2016-04-15 01:17:36 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:17:36,444 - WARNING - Could not retrieve variants from source file in region 19:56539029-56565354. Error was invalid region `19:56539030-56565354`
[2016-04-15T08:17Z] 2016-04-15 01:17:37 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:17:37,025 - WARNING - Could not retrieve variants from source file in region 19:50862557-50882012. Error was invalid region `19:50862558-50882012`
[2016-04-15T08:17Z] 2016-04-15 01:17:37 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:17:37,800 - WARNING - Could not retrieve variants from source file in region 19:58718058-58718550. Error was invalid region `19:58718059-58718550`
[2016-04-15T08:17Z] 2016-04-15 01:17:40 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:17:40,648 - WARNING - Could not retrieve variants from source file in region 19:56935316-56952199. Error was invalid region `19:56935317-56952199`
[2016-04-15T08:17Z] 2016-04-15 01:17:41 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:17:41,008 - WARNING - Could not retrieve variants from source file in region 19:53116432-53117999. Error was invalid region `19:53116433-53117999`
[2016-04-15T08:17Z] 2016-04-15 01:17:41 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:17:41,381 - WARNING - Could not retrieve variants from source file in region 19:55019050-55019561. Error was invalid region `19:55019051-55019561`
[2016-04-15T08:17Z] 2016-04-15 01:17:42 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:17:42,480 - WARNING - Could not retrieve variants from source file in region 19:47615607-47634503. Error was invalid region `19:47615608-47634503`
[2016-04-15T08:17Z] 2016-04-15 01:17:42 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:17:42,768 - WARNING - Could not retrieve variants from source file in region 19:49001847-49002249. Error was invalid region `19:49001848-49002249`
[2016-04-15T08:17Z] 2016-04-15 01:17:48 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:17:48,341 - WARNING - Could not retrieve variants from source file in region 19:54544975-54561982. Error was invalid region `19:54544976-54561982`
[2016-04-15T08:17Z] 2016-04-15 01:17:49 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:17:49,669 - WARNING - Could not retrieve variants from source file in region 19:47543563-47548868. Error was invalid region `19:47543564-47548868`
[2016-04-15T08:17Z] 2016-04-15 01:17:55 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:17:55,652 - WARNING - Could not retrieve variants from source file in region 19:47543563-47548868. Error was invalid region `19:47543564-47548868`
[2016-04-15T08:17Z] 2016-04-15 01:17:55 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:17:55,764 - WARNING - Could not retrieve variants from source file in region 19:49815642-49841244. Error was invalid region `19:49815643-49841244`
[2016-04-15T08:17Z] 2016-04-15 01:17:57 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:17:57,571 - WARNING - Could not retrieve variants from source file in region 19:54965649-54974964. Error was invalid region `19:54965650-54974964`
[2016-04-15T08:17Z] 2016-04-15 01:17:57 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:17:57,835 - WARNING - Could not retrieve variants from source file in region 19:50831941-50832342. Error was invalid region `19:50831942-50832342`
[2016-04-15T08:18Z] 2016-04-15 01:18:00 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:18:00,240 - WARNING - Could not retrieve variants from source file in region 19:47342656-47343057. Error was invalid region `19:47342657-47343057`
[2016-04-15T08:18Z] 2016-04-15 01:18:00 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:18:00,553 - WARNING - Could not retrieve variants from source file in region 19:58609466-58620714. Error was invalid region `19:58609467-58620714`
[2016-04-15T08:18Z] 2016-04-15 01:18:00 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:18:00,601 - WARNING - Could not retrieve variants from source file in region 19:54544975-54561982. Error was invalid region `19:54544976-54561982`
[2016-04-15T08:18Z] 2016-04-15 01:18:01 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:18:01,246 - WARNING - Could not retrieve variants from source file in region 19:56733214-56739937. Error was invalid region `19:56733215-56739937`
[2016-04-15T08:18Z] 2016-04-15 01:18:01 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:18:01,383 - WARNING - Could not retrieve variants from source file in region 19:49815642-49841244. Error was invalid region `19:49815643-49841244`
[2016-04-15T08:18Z] 2016-04-15 01:18:01 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:18:01,709 - WARNING - Could not retrieve variants from source file in region 19:47543563-47548868. Error was invalid region `19:47543564-47548868`
[2016-04-15T08:18Z] 2016-04-15 01:18:01 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:18:01,876 - WARNING - Could not retrieve variants from source file in region 19:53056742-53086788. Error was invalid region `19:53056743-53086788`
[2016-04-15T08:18Z] 2016-04-15 01:18:01 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:18:01,989 - WARNING - Could not retrieve variants from source file in region 19:46893599-46915111. Error was invalid region `19:46893600-46915111`
[2016-04-15T08:18Z] 2016-04-15 01:18:02 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:18:02,162 - WARNING - Could not retrieve variants from source file in region 19:54965649-54974964. Error was invalid region `19:54965650-54974964`
[2016-04-15T08:18Z] 2016-04-15 01:18:02 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:18:02,239 - WARNING - Could not retrieve variants from source file in region 19:50831941-50832342. Error was invalid region `19:50831942-50832342`
[2016-04-15T08:18Z] 2016-04-15 01:18:09 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:18:09,815 - WARNING - Could not retrieve variants from source file in region 19:46893599-46915111. Error was invalid region `19:46893600-46915111`
[2016-04-15T08:18Z] 2016-04-15 01:18:09 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:18:09,976 - WARNING - Could not retrieve variants from source file in region 19:50831941-50832342. Error was invalid region `19:50831942-50832342`
[2016-04-15T08:18Z] 2016-04-15 01:18:10 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:18:10,426 - WARNING - Could not retrieve variants from source file in region 19:48945669-48949476. Error was invalid region `19:48945670-48949476`
[2016-04-15T08:18Z] 2016-04-15 01:18:10 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:18:10,623 - WARNING - Could not retrieve variants from source file in region 19:54965649-54974964. Error was invalid region `19:54965650-54974964`
[2016-04-15T08:18Z] 2016-04-15 01:18:10 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:18:10,643 - WARNING - Could not retrieve variants from source file in region 19:56459131-56499469. Error was invalid region `19:56459132-56499469`
[2016-04-15T08:18Z] 2016-04-15 01:18:11 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:18:11,280 - WARNING - Could not retrieve variants from source file in region 19:47342656-47343057. Error was invalid region `19:47342657-47343057`
[2016-04-15T08:18Z] 2016-04-15 01:18:12 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:18:12,374 - WARNING - Could not retrieve variants from source file in region 19:49611108-49658580. Error was invalid region `19:49611109-49658580`
[2016-04-15T08:18Z] 2016-04-15 01:18:14 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:18:14,491 - WARNING - Could not retrieve variants from source file in region 19:53453566-53454979. Error was invalid region `19:53453567-53454979`
[2016-04-15T08:18Z] 2016-04-15 01:18:16 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:18:16,257 - WARNING - Could not retrieve variants from source file in region 19:46893599-46915111. Error was invalid region `19:46893600-46915111`
[2016-04-15T08:18Z] 2016-04-15 01:18:21 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:18:21,940 - WARNING - Could not retrieve variants from source file in region 19:58549155-58578768. Error was invalid region `19:58549156-58578768`
[2016-04-15T08:18Z] 2016-04-15 01:18:22 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:18:22,705 - WARNING - Could not retrieve variants from source file in region 19:54501316-54501717. Error was invalid region `19:54501317-54501717`
[2016-04-15T08:18Z] 2016-04-15 01:18:23 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:18:23,927 - WARNING - Could not retrieve variants from source file in region 19:53453566-53454979. Error was invalid region `19:53453567-53454979`
[2016-04-15T08:18Z] 2016-04-15 01:18:27 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:18:27,585 - WARNING - Could not retrieve variants from source file in region 19:54385609-54395155. Error was invalid region `19:54385610-54395155`
[2016-04-15T08:18Z] 2016-04-15 01:18:28 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:18:28,236 - WARNING - Could not retrieve variants from source file in region 19:56693409-56704291. Error was invalid region `19:56693410-56704291`
[2016-04-15T08:18Z] 2016-04-15 01:18:30 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:18:30,459 - WARNING - Could not retrieve variants from source file in region 19:48863175-48863576. Error was invalid region `19:48863176-48863576`
[2016-04-15T08:18Z] 2016-04-15 01:18:30 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:18:30,477 - WARNING - Could not retrieve variants from source file in region 19:53014135-53015574. Error was invalid region `19:53014136-53015574`
[2016-04-15T08:18Z] 2016-04-15 01:18:31 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:18:31,685 - WARNING - Could not retrieve variants from source file in region 19:46856804-46857205. Error was invalid region `19:46856805-46857205`
[2016-04-15T08:18Z] 2016-04-15 01:18:33 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:18:33,640 - WARNING - Could not retrieve variants from source file in region 19:49468876-49485738. Error was invalid region `19:49468877-49485738`
[2016-04-15T08:18Z] 2016-04-15 01:18:35 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:18:35,549 - WARNING - Could not retrieve variants from source file in region 19:48863175-48863576. Error was invalid region `19:48863176-48863576`
[2016-04-15T08:18Z] 2016-04-15 01:18:35 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:18:35,932 - WARNING - Could not retrieve variants from source file in region 19:53014135-53015574. Error was invalid region `19:53014136-53015574`
[2016-04-15T08:18Z] 2016-04-15 01:18:36 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:18:36,584 - WARNING - Could not retrieve variants from source file in region 19:46856804-46857205. Error was invalid region `19:46856805-46857205`
[2016-04-15T08:18Z] 2016-04-15 01:18:40 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:18:40,638 - WARNING - Could not retrieve variants from source file in region 19:48863175-48863576. Error was invalid region `19:48863176-48863576`
[2016-04-15T08:18Z] 2016-04-15 01:18:42 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:18:42,101 - WARNING - Could not retrieve variants from source file in region 19:54445383-54445785. Error was invalid region `19:54445384-54445785`
[2016-04-15T08:18Z] 2016-04-15 01:18:47 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:18:47,070 - WARNING - Could not retrieve variants from source file in region 19:54445383-54445785. Error was invalid region `19:54445384-54445785`
[2016-04-15T08:18Z] 2016-04-15 01:18:48 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:18:48,237 - WARNING - Could not retrieve variants from source file in region 19:54445383-54445785. Error was invalid region `19:54445384-54445785`
[2016-04-15T08:18Z] 2016-04-15 01:18:49 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:18:49,473 - WARNING - Could not retrieve variants from source file in region 19:52938150-52942685. Error was invalid region `19:52938151-52942685`
[2016-04-15T08:18Z] 2016-04-15 01:18:49 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:18:49,696 - WARNING - Could not retrieve variants from source file in region 19:46733198-46733750. Error was invalid region `19:46733199-46733750`
[2016-04-15T08:18Z] 2016-04-15 01:18:51 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:18:51,177 - WARNING - Could not retrieve variants from source file in region 19:54307111-54327503. Error was invalid region `19:54307112-54327503`
[2016-04-15T08:18Z] 2016-04-15 01:18:52 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:18:52,756 - WARNING - Could not retrieve variants from source file in region 19:58385658-58386059. Error was invalid region `19:58385659-58386059`
[2016-04-15T08:18Z] 2016-04-15 01:18:53 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:18:53,059 - WARNING - Could not retrieve variants from source file in region 19:56599194-56599630. Error was invalid region `19:56599195-56599630`
[2016-04-15T08:18Z] 2016-04-15 01:18:53 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:18:53,198 - WARNING - Could not retrieve variants from source file in region 19:48836462-48836863. Error was invalid region `19:48836463-48836863`
[2016-04-15T08:18Z] 2016-04-15 01:18:54 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:18:54,314 - WARNING - Could not retrieve variants from source file in region 19:52938150-52942685. Error was invalid region `19:52938151-52942685`
[2016-04-15T08:18Z] 2016-04-15 01:18:57 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:18:57,549 - WARNING - Could not retrieve variants from source file in region 19:58385658-58386059. Error was invalid region `19:58385659-58386059`
[2016-04-15T08:18Z] 2016-04-15 01:18:58 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:18:58,897 - WARNING - Could not retrieve variants from source file in region 19:52938150-52942685. Error was invalid region `19:52938151-52942685`
[2016-04-15T08:19Z] 2016-04-15 01:19:01 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:19:01,856 - WARNING - Could not retrieve variants from source file in region 19:54079856-54080334. Error was invalid region `19:54079857-54080334`
[2016-04-15T08:19Z] 2016-04-15 01:19:02 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:19:02,121 - WARNING - Could not retrieve variants from source file in region 19:58385658-58386059. Error was invalid region `19:58385659-58386059`
[2016-04-15T08:19Z] 2016-04-15 01:19:03 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:19:03,010 - WARNING - Could not retrieve variants from source file in region 19:48836462-48836863. Error was invalid region `19:48836463-48836863`
[2016-04-15T08:19Z] 2016-04-15 01:19:08 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:19:08,521 - WARNING - Could not retrieve variants from source file in region 19:54079856-54080334. Error was invalid region `19:54079857-54080334`
[2016-04-15T08:19Z] 2016-04-15 01:19:08 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:19:08,548 - WARNING - Could not retrieve variants from source file in region 19:57864938-57869069. Error was invalid region `19:57864939-57869069`
[2016-04-15T08:19Z] 2016-04-15 01:19:13 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:19:13,330 - WARNING - Could not retrieve variants from source file in region 19:57864938-57869069. Error was invalid region `19:57864939-57869069`
[2016-04-15T08:19Z] 2016-04-15 01:19:15 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:19:15,896 - WARNING - Could not retrieve variants from source file in region 19:53989734-53995194. Error was invalid region `19:53989735-53995194`
[2016-04-15T08:19Z] 2016-04-15 01:19:16 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:19:16,124 - WARNING - Could not retrieve variants from source file in region 19:53952674-53959758. Error was invalid region `19:53952675-53959758`
[2016-04-15T08:19Z] 2016-04-15 01:19:16 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:19:16,139 - WARNING - Could not retrieve variants from source file in region 19:57802595-57803014. Error was invalid region `19:57802596-57803014`
[2016-04-15T08:19Z] 2016-04-15 01:19:16 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:19:16,312 - WARNING - Could not retrieve variants from source file in region 19:58117012-58117413. Error was invalid region `19:58117013-58117413`
[2016-04-15T08:19Z] 2016-04-15 01:19:17 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:19:17,964 - WARNING - Could not retrieve variants from source file in region 19:58290358-58290759. Error was invalid region `19:58290359-58290759`
[2016-04-15T08:19Z] 2016-04-15 01:19:19 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:19:19,585 - WARNING - Could not retrieve variants from source file in region 19:57640935-57650090. Error was invalid region `19:57640936-57650090`
[2016-04-15T08:19Z] 2016-04-15 01:19:20 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:19:20,487 - WARNING - Could not retrieve variants from source file in region 19:53952674-53959758. Error was invalid region `19:53952675-53959758`
[2016-04-15T08:19Z] 2016-04-15 01:19:20 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:19:20,635 - WARNING - Could not retrieve variants from source file in region 19:58117012-58117413. Error was invalid region `19:58117013-58117413`
[2016-04-15T08:19Z] 2016-04-15 01:19:21 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:19:21,676 - WARNING - Could not retrieve variants from source file in region 19:57802595-57803014. Error was invalid region `19:57802596-57803014`
[2016-04-15T08:19Z] 2016-04-15 01:19:22 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:19:22,256 - WARNING - Could not retrieve variants from source file in region 19:58117012-58117413. Error was invalid region `19:58117013-58117413`
[2016-04-15T08:19Z] 2016-04-15 01:19:22 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:19:22,414 - WARNING - Could not retrieve variants from source file in region 19:58290358-58290759. Error was invalid region `19:58290359-58290759`
[2016-04-15T08:19Z] 2016-04-15 01:19:22 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:19:22,462 - WARNING - Could not retrieve variants from source file in region 19:57722796-57765622. Error was invalid region `19:57722797-57765622`
[2016-04-15T08:19Z] 2016-04-15 01:19:24 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:19:24,602 - WARNING - Could not retrieve variants from source file in region 19:53952674-53959758. Error was invalid region `19:53952675-53959758`
[2016-04-15T08:19Z] 2016-04-15 01:19:25 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:19:25,789 - WARNING - Could not retrieve variants from source file in region 19:57640935-57650090. Error was invalid region `19:57640936-57650090`
[2016-04-15T08:19Z] 2016-04-15 01:19:25 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:19:25,948 - WARNING - Could not retrieve variants from source file in region 19:57722796-57765622. Error was invalid region `19:57722797-57765622`
[2016-04-15T08:19Z] 2016-04-15 01:19:28 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:19:28,968 - WARNING - Could not retrieve variants from source file in region 19:57837807-57839880. Error was invalid region `19:57837808-57839880`
[2016-04-15T08:19Z] ['bcbio-variation-recall', 'square', '-Xms750m', '-Xmx7280m', '-XX:+UseSerialGC', '-c', 16, '-r', u'20:1-15843471', '--caller', 'platypus', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/20/Batch1-20_0_15843471.vcf.gz', '/mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/20/Batch1-20_0_15843471.vcf-inputs.txt'] in region: 20:1-15843471
[2016-04-15T08:19Z] 2016-04-15 01:19:44 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:19:44,257 - WARNING - Could not retrieve variants from source file in region 20:13714173-13714574. Error was invalid region `20:13714174-13714574`
[2016-04-15T08:19Z] 2016-04-15 01:19:46 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:19:46,346 - WARNING - Could not retrieve variants from source file in region 20:15177309-15177815. Error was invalid region `20:15177310-15177815`
[2016-04-15T08:19Z] 2016-04-15 01:19:46 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:19:46,525 - WARNING - Could not retrieve variants from source file in region 20:4705507-4705908. Error was invalid region `20:4705508-4705908`
[2016-04-15T08:19Z] 2016-04-15 01:19:46 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:19:46,562 - WARNING - Could not retrieve variants from source file in region 20:10018882-10032603. Error was invalid region `20:10018883-10032603`
[2016-04-15T08:19Z] 2016-04-15 01:19:46 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:19:46,882 - WARNING - Could not retrieve variants from source file in region 20:1426182-1426583. Error was invalid region `20:1426183-1426583`
[2016-04-15T08:19Z] 2016-04-15 01:19:47 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:19:47,136 - WARNING - Could not retrieve variants from source file in region 20:168517-168918. Error was invalid region `20:168518-168918`
[2016-04-15T08:19Z] 2016-04-15 01:19:47 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:19:47,282 - WARNING - Could not retrieve variants from source file in region 20:590245-590733. Error was invalid region `20:590246-590733`
[2016-04-15T08:19Z] 2016-04-15 01:19:47 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:19:47,645 - WARNING - Could not retrieve variants from source file in region 20:825183-826611. Error was invalid region `20:825184-826611`
[2016-04-15T08:19Z] 2016-04-15 01:19:47 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:19:47,651 - WARNING - Could not retrieve variants from source file in region 20:2375051-2375452. Error was invalid region `20:2375052-2375452`
[2016-04-15T08:19Z] 2016-04-15 01:19:47 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:19:47,822 - WARNING - Could not retrieve variants from source file in region 20:5902856-5904230. Error was invalid region `20:5902857-5904230`
[2016-04-15T08:19Z] 2016-04-15 01:19:49 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:19:49,824 - WARNING - Could not retrieve variants from source file in region 20:5753368-5753769. Error was invalid region `20:5753369-5753769`
[2016-04-15T08:19Z] 2016-04-15 01:19:53 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:19:53,443 - WARNING - Could not retrieve variants from source file in region 20:15177309-15177815. Error was invalid region `20:15177310-15177815`
[2016-04-15T08:19Z] 2016-04-15 01:19:53 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:19:53,534 - WARNING - Could not retrieve variants from source file in region 20:4705507-4705908. Error was invalid region `20:4705508-4705908`
[2016-04-15T08:19Z] 2016-04-15 01:19:54 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:19:54,791 - WARNING - Could not retrieve variants from source file in region 20:168517-168918. Error was invalid region `20:168518-168918`
[2016-04-15T08:19Z] 2016-04-15 01:19:55 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:19:55,091 - WARNING - Could not retrieve variants from source file in region 20:590245-590733. Error was invalid region `20:590246-590733`
[2016-04-15T08:19Z] 2016-04-15 01:19:55 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:19:55,105 - WARNING - Could not retrieve variants from source file in region 20:13829926-13847610. Error was invalid region `20:13829927-13847610`
[2016-04-15T08:19Z] 2016-04-15 01:19:55 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:19:55,378 - WARNING - Could not retrieve variants from source file in region 20:5902856-5904230. Error was invalid region `20:5902857-5904230`
[2016-04-15T08:19Z] 2016-04-15 01:19:55 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:19:55,988 - WARNING - Could not retrieve variants from source file in region 20:2375051-2375452. Error was invalid region `20:2375052-2375452`
[2016-04-15T08:19Z] 2016-04-15 01:19:56 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:19:56,006 - WARNING - Could not retrieve variants from source file in region 20:1145925-1146326. Error was invalid region `20:1145926-1146326`
[2016-04-15T08:19Z] 2016-04-15 01:19:56 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:19:56,122 - WARNING - Could not retrieve variants from source file in region 20:5753368-5753769. Error was invalid region `20:5753369-5753769`
[2016-04-15T08:19Z] 2016-04-15 01:19:56 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:19:56,253 - WARNING - Could not retrieve variants from source file in region 20:3284915-3285330. Error was invalid region `20:3284916-3285330`
[2016-04-15T08:19Z] 2016-04-15 01:19:56 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:19:56,374 - WARNING - Could not retrieve variants from source file in region 20:238224-278880. Error was invalid region `20:238225-278880`
[2016-04-15T08:19Z] 2016-04-15 01:19:56 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:19:56,383 - WARNING - Could not retrieve variants from source file in region 20:13714173-13714574. Error was invalid region `20:13714174-13714574`
[2016-04-15T08:19Z] 2016-04-15 01:19:59 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:19:59,163 - WARNING - Could not retrieve variants from source file in region 20:15177309-15177815. Error was invalid region `20:15177310-15177815`
[2016-04-15T08:19Z] 2016-04-15 01:19:59 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:19:59,173 - WARNING - Could not retrieve variants from source file in region 20:4705507-4705908. Error was invalid region `20:4705508-4705908`
[2016-04-15T08:20Z] 2016-04-15 01:20:00 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:20:00,189 - WARNING - Could not retrieve variants from source file in region 20:1426182-1426583. Error was invalid region `20:1426183-1426583`
[2016-04-15T08:20Z] 2016-04-15 01:20:00 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:20:00,294 - WARNING - Could not retrieve variants from source file in region 20:10018882-10032603. Error was invalid region `20:10018883-10032603`
[2016-04-15T08:20Z] 2016-04-15 01:20:01 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:20:01,200 - WARNING - Could not retrieve variants from source file in region 20:168517-168918. Error was invalid region `20:168518-168918`
[2016-04-15T08:20Z] 2016-04-15 01:20:02 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:20:02,607 - WARNING - Could not retrieve variants from source file in region 20:590245-590733. Error was invalid region `20:590246-590733`
[2016-04-15T08:20Z] 2016-04-15 01:20:03 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:20:03,726 - WARNING - Could not retrieve variants from source file in region 20:5902856-5904230. Error was invalid region `20:5902857-5904230`
[2016-04-15T08:20Z] 2016-04-15 01:20:04 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:20:04,371 - WARNING - Could not retrieve variants from source file in region 20:2375051-2375452. Error was invalid region `20:2375052-2375452`
[2016-04-15T08:20Z] 2016-04-15 01:20:04 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:20:04,374 - WARNING - Could not retrieve variants from source file in region 20:3284915-3285330. Error was invalid region `20:3284916-3285330`
[2016-04-15T08:20Z] 2016-04-15 01:20:13 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:20:13,991 - WARNING - Could not retrieve variants from source file in region 20:5283045-5283566. Error was invalid region `20:5283046-5283566`
[2016-04-15T08:20Z] 2016-04-15 01:20:15 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:20:15,629 - WARNING - Could not retrieve variants from source file in region 20:13029553-13053225. Error was invalid region `20:13029554-13053225`
[2016-04-15T08:20Z] 2016-04-15 01:20:17 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:20:17,126 - WARNING - Could not retrieve variants from source file in region 20:4228524-4228925. Error was invalid region `20:4228525-4228925`
[2016-04-15T08:20Z] 2016-04-15 01:20:17 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:20:17,964 - WARNING - Could not retrieve variants from source file in region 20:125944-126502. Error was invalid region `20:125945-126502`
[2016-04-15T08:20Z] 2016-04-15 01:20:19 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:20:19,339 - WARNING - Could not retrieve variants from source file in region 20:1350461-1350899. Error was invalid region `20:1350462-1350899`
[2016-04-15T08:20Z] 2016-04-15 01:20:19 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:20:19,492 - WARNING - Could not retrieve variants from source file in region 20:371761-401395. Error was invalid region `20:371762-401395`
[2016-04-15T08:20Z] 2016-04-15 01:20:20 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:20:20,232 - WARNING - Could not retrieve variants from source file in region 20:5843601-5844002. Error was invalid region `20:5843602-5844002`
[2016-04-15T08:20Z] 2016-04-15 01:20:20 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:20:20,385 - WARNING - Could not retrieve variants from source file in region 20:13029553-13053225. Error was invalid region `20:13029554-13053225`
[2016-04-15T08:20Z] 2016-04-15 01:20:20 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:20:20,695 - WARNING - Could not retrieve variants from source file in region 20:741636-746387. Error was invalid region `20:741637-746387`
[2016-04-15T08:20Z] 2016-04-15 01:20:21 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:20:21,241 - WARNING - Could not retrieve variants from source file in region 20:13747230-13747631. Error was invalid region `20:13747231-13747631`
[2016-04-15T08:20Z] 2016-04-15 01:20:24 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:20:24,735 - WARNING - Could not retrieve variants from source file in region 20:209850-210251. Error was invalid region `20:209851-210251`
[2016-04-15T08:20Z] 2016-04-15 01:20:25 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:20:25,449 - WARNING - Could not retrieve variants from source file in region 20:9543411-9543812. Error was invalid region `20:9543412-9543812`
[2016-04-15T08:20Z] 2016-04-15 01:20:25 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:20:25,473 - WARNING - Could not retrieve variants from source file in region 20:5932897-5933298. Error was invalid region `20:5932898-5933298`
[2016-04-15T08:20Z] 2016-04-15 01:20:26 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:20:26,375 - WARNING - Could not retrieve variants from source file in region 20:1350461-1350899. Error was invalid region `20:1350462-1350899`
[2016-04-15T08:20Z] 2016-04-15 01:20:26 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:20:26,885 - WARNING - Could not retrieve variants from source file in region 20:14306685-14307143. Error was invalid region `20:14306686-14307143`
[2016-04-15T08:20Z] 2016-04-15 01:20:27 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:20:27,620 - WARNING - Could not retrieve variants from source file in region 20:5843601-5844002. Error was invalid region `20:5843602-5844002`
[2016-04-15T08:20Z] 2016-04-15 01:20:28 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:20:28,098 - WARNING - Could not retrieve variants from source file in region 20:13029553-13053225. Error was invalid region `20:13029554-13053225`
[2016-04-15T08:20Z] 2016-04-15 01:20:28 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:20:28,732 - WARNING - Could not retrieve variants from source file in region 20:1099312-1116109. Error was invalid region `20:1099313-1116109`
[2016-04-15T08:20Z] 2016-04-15 01:20:28 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:20:28,889 - WARNING - Could not retrieve variants from source file in region 20:13747230-13747631. Error was invalid region `20:13747231-13747631`
[2016-04-15T08:20Z] 2016-04-15 01:20:29 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:20:29,047 - WARNING - Could not retrieve variants from source file in region 20:4228524-4228925. Error was invalid region `20:4228525-4228925`
[2016-04-15T08:20Z] 2016-04-15 01:20:29 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:20:29,698 - WARNING - Could not retrieve variants from source file in region 20:125944-126502. Error was invalid region `20:125945-126502`
[2016-04-15T08:20Z] 2016-04-15 01:20:31 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:20:31,199 - WARNING - Could not retrieve variants from source file in region 20:5932897-5933298. Error was invalid region `20:5932898-5933298`
[2016-04-15T08:20Z] 2016-04-15 01:20:31 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:20:31,249 - WARNING - Could not retrieve variants from source file in region 20:9543411-9543812. Error was invalid region `20:9543412-9543812`
[2016-04-15T08:20Z] 2016-04-15 01:20:31 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:20:31,701 - WARNING - Could not retrieve variants from source file in region 20:371761-401395. Error was invalid region `20:371762-401395`
[2016-04-15T08:20Z] 2016-04-15 01:20:33 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:20:33,138 - WARNING - Could not retrieve variants from source file in region 20:14306685-14307143. Error was invalid region `20:14306686-14307143`
[2016-04-15T08:20Z] 2016-04-15 01:20:34 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:20:34,267 - WARNING - Could not retrieve variants from source file in region 20:5843601-5844002. Error was invalid region `20:5843602-5844002`
[2016-04-15T08:20Z] 2016-04-15 01:20:35 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:20:35,408 - WARNING - Could not retrieve variants from source file in region 20:1099312-1116109. Error was invalid region `20:1099313-1116109`
[2016-04-15T08:20Z] 2016-04-15 01:20:36 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:20:36,114 - WARNING - Could not retrieve variants from source file in region 20:13747230-13747631. Error was invalid region `20:13747231-13747631`
[2016-04-15T08:20Z] 2016-04-15 01:20:36 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:20:36,312 - WARNING - Could not retrieve variants from source file in region 20:2290122-2321295. Error was invalid region `20:2290123-2321295`
[2016-04-15T08:20Z] 2016-04-15 01:20:44 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:20:44,688 - WARNING - Could not retrieve variants from source file in region 20:5080608-5087129. Error was invalid region `20:5080609-5087129`
[2016-04-15T08:20Z] 2016-04-15 01:20:46 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:20:46,086 - WARNING - Could not retrieve variants from source file in region 20:9496505-9496906. Error was invalid region `20:9496506-9496906`
[2016-04-15T08:20Z] 2016-04-15 01:20:46 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:20:46,657 - WARNING - Could not retrieve variants from source file in region 20:76751-77203. Error was invalid region `20:76752-77203`
[2016-04-15T08:20Z] 2016-04-15 01:20:47 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:20:47,864 - WARNING - Could not retrieve variants from source file in region 20:4854471-4854872. Error was invalid region `20:4854472-4854872`
[2016-04-15T08:20Z] 2016-04-15 01:20:51 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:20:51,041 - WARNING - Could not retrieve variants from source file in region 20:944507-944908. Error was invalid region `20:944508-944908`
[2016-04-15T08:20Z] 2016-04-15 01:20:52 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:20:52,019 - WARNING - Could not retrieve variants from source file in region 20:76751-77203. Error was invalid region `20:76752-77203`
[2016-04-15T08:20Z] 2016-04-15 01:20:52 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:20:52,173 - WARNING - Could not retrieve variants from source file in region 20:3090637-3091038. Error was invalid region `20:3090638-3091038`
[2016-04-15T08:20Z] 2016-04-15 01:20:52 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:20:52,342 - WARNING - Could not retrieve variants from source file in region 20:9288311-9288712. Error was invalid region `20:9288312-9288712`
[2016-04-15T08:20Z] 2016-04-15 01:20:52 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:20:52,407 - WARNING - Could not retrieve variants from source file in region 20:10389211-10389612. Error was invalid region `20:10389212-10389612`
[2016-04-15T08:20Z] 2016-04-15 01:20:54 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:20:54,237 - WARNING - Could not retrieve variants from source file in region 20:8737523-8771012. Error was invalid region `20:8737524-8771012`
[2016-04-15T08:20Z] 2016-04-15 01:20:55 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:20:55,018 - WARNING - Could not retrieve variants from source file in region 20:9496505-9496906. Error was invalid region `20:9496506-9496906`
[2016-04-15T08:20Z] 2016-04-15 01:20:56 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:20:56,310 - WARNING - Could not retrieve variants from source file in region 20:2187732-2188353. Error was invalid region `20:2187733-2188353`
[2016-04-15T08:20Z] 2016-04-15 01:20:57 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:20:57,114 - WARNING - Could not retrieve variants from source file in region 20:3090637-3091038. Error was invalid region `20:3090638-3091038`
[2016-04-15T08:20Z] 2016-04-15 01:20:57 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:20:57,615 - WARNING - Could not retrieve variants from source file in region 20:4854471-4854872. Error was invalid region `20:4854472-4854872`
[2016-04-15T08:20Z] 2016-04-15 01:20:57 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:20:57,813 - WARNING - Could not retrieve variants from source file in region 20:9288311-9288712. Error was invalid region `20:9288312-9288712`
[2016-04-15T08:20Z] 2016-04-15 01:20:58 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:20:58,622 - WARNING - Could not retrieve variants from source file in region 20:8737523-8771012. Error was invalid region `20:8737524-8771012`
[2016-04-15T08:20Z] 2016-04-15 01:20:59 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:20:59,833 - WARNING - Could not retrieve variants from source file in region 20:944507-944908. Error was invalid region `20:944508-944908`
[2016-04-15T08:21Z] 2016-04-15 01:21:01 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:21:01,226 - WARNING - Could not retrieve variants from source file in region 20:2187732-2188353. Error was invalid region `20:2187733-2188353`
[2016-04-15T08:21Z] 2016-04-15 01:21:01 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:21:01,721 - WARNING - Could not retrieve variants from source file in region 20:3090637-3091038. Error was invalid region `20:3090638-3091038`
[2016-04-15T08:21Z] 2016-04-15 01:21:02 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:21:02,857 - WARNING - Could not retrieve variants from source file in region 20:9288311-9288712. Error was invalid region `20:9288312-9288712`
[2016-04-15T08:21Z] 2016-04-15 01:21:04 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:21:04,864 - WARNING - Could not retrieve variants from source file in region 20:1960923-1961349. Error was invalid region `20:1960924-1961349`
[2016-04-15T08:21Z] 2016-04-15 01:21:04 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:21:04,906 - WARNING - Could not retrieve variants from source file in region 20:6750823-6759305. Error was invalid region `20:6750824-6759305`
[2016-04-15T08:21Z] 2016-04-15 01:21:09 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:21:09,609 - WARNING - Could not retrieve variants from source file in region 20:6099877-6100278. Error was invalid region `20:6099878-6100278`
[2016-04-15T08:21Z] 2016-04-15 01:21:09 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:21:09,786 - WARNING - Could not retrieve variants from source file in region 20:6750823-6759305. Error was invalid region `20:6750824-6759305`
[2016-04-15T08:21Z] 2016-04-15 01:21:09 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:21:09,845 - WARNING - Could not retrieve variants from source file in region 20:6750823-6759305. Error was invalid region `20:6750824-6759305`
[2016-04-15T08:21Z] 2016-04-15 01:21:11 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:21:11,582 - WARNING - Could not retrieve variants from source file in region 20:3844718-3870314. Error was invalid region `20:3844719-3870314`
[2016-04-15T08:21Z] 2016-04-15 01:21:11 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:21:11,723 - WARNING - Could not retrieve variants from source file in region 20:7962830-7980580. Error was invalid region `20:7962831-7980580`
[2016-04-15T08:21Z] 2016-04-15 01:21:12 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:21:12,596 - WARNING - Could not retrieve variants from source file in region 20:854729-860616. Error was invalid region `20:854730-860616`
[2016-04-15T08:21Z] 2016-04-15 01:21:13 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:21:13,670 - WARNING - Could not retrieve variants from source file in region 20:6099877-6100278. Error was invalid region `20:6099878-6100278`
[2016-04-15T08:21Z] 2016-04-15 01:21:15 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:21:15,776 - WARNING - Could not retrieve variants from source file in region 20:6064499-6069913. Error was invalid region `20:6064500-6069913`
[2016-04-15T08:21Z] 2016-04-15 01:21:15 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:21:15,871 - WARNING - Could not retrieve variants from source file in region 20:2082556-2082957. Error was invalid region `20:2082557-2082957`
[2016-04-15T08:21Z] 2016-04-15 01:21:17 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:21:17,785 - WARNING - Could not retrieve variants from source file in region 20:6099877-6100278. Error was invalid region `20:6099878-6100278`
[2016-04-15T08:21Z] 2016-04-15 01:21:19 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:21:19,127 - WARNING - Could not retrieve variants from source file in region 20:2996286-2996687. Error was invalid region `20:2996287-2996687`
[2016-04-15T08:21Z] 2016-04-15 01:21:19 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:21:19,357 - WARNING - Could not retrieve variants from source file in region 20:1210436-1215004. Error was invalid region `20:1210437-1215004`
[2016-04-15T08:21Z] 2016-04-15 01:21:26 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:21:26,734 - WARNING - Could not retrieve variants from source file in region 20:1895889-1896290. Error was invalid region `20:1895890-1896290`
[2016-04-15T08:21Z] 2016-04-15 01:21:28 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:21:28,934 - WARNING - Could not retrieve variants from source file in region 20:3732422-3732823. Error was invalid region `20:3732423-3732823`
[2016-04-15T08:21Z] 2016-04-15 01:21:29 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:21:29,099 - WARNING - Could not retrieve variants from source file in region 20:3732422-3732823. Error was invalid region `20:3732423-3732823`
[2016-04-15T08:21Z] 2016-04-15 01:21:29 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:21:29,267 - WARNING - Could not retrieve variants from source file in region 20:1895889-1896290. Error was invalid region `20:1895890-1896290`
[2016-04-15T08:21Z] 2016-04-15 01:21:29 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:21:29,917 - WARNING - Could not retrieve variants from source file in region 20:1895889-1896290. Error was invalid region `20:1895890-1896290`
[2016-04-15T08:21Z] 2016-04-15 01:21:29 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:21:29,936 - WARNING - Could not retrieve variants from source file in region 20:3732422-3732823. Error was invalid region `20:3732423-3732823`
[2016-04-15T08:21Z] 2016-04-15 01:21:33 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:21:33,340 - WARNING - Could not retrieve variants from source file in region 20:2591021-2594053. Error was invalid region `20:2591022-2594053`
[2016-04-15T08:21Z] 2016-04-15 01:21:34 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:21:34,070 - WARNING - Could not retrieve variants from source file in region 20:3515713-3528325. Error was invalid region `20:3515714-3528325`
[2016-04-15T08:21Z] 2016-04-15 01:21:34 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:21:34,525 - WARNING - Could not retrieve variants from source file in region 20:2796804-2840963. Error was invalid region `20:2796805-2840963`
[2016-04-15T08:21Z] 2016-04-15 01:21:34 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:21:34,746 - WARNING - Could not retrieve variants from source file in region 20:2539176-2539577. Error was invalid region `20:2539177-2539577`
[2016-04-15T08:21Z] 2016-04-15 01:21:35 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:21:35,671 - WARNING - Could not retrieve variants from source file in region 20:2633725-2637261. Error was invalid region `20:2633726-2637261`
[2016-04-15T08:21Z] 2016-04-15 01:21:36 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:21:36,072 - WARNING - Could not retrieve variants from source file in region 20:3564461-3564862. Error was invalid region `20:3564462-3564862`
[2016-04-15T08:21Z] 2016-04-15 01:21:38 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:21:38,269 - WARNING - Could not retrieve variants from source file in region 20:3564461-3564862. Error was invalid region `20:3564462-3564862`
[2016-04-15T08:21Z] 2016-04-15 01:21:38 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:21:38,457 - WARNING - Could not retrieve variants from source file in region 20:1532384-1552647. Error was invalid region `20:1532385-1552647`
[2016-04-15T08:21Z] 2016-04-15 01:21:38 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:21:38,984 - WARNING - Could not retrieve variants from source file in region 20:2539176-2539577. Error was invalid region `20:2539177-2539577`
[2016-04-15T08:21Z] ['bcbio-variation-recall', 'square', '-Xms750m', '-Xmx7280m', '-XX:+UseSerialGC', '-c', 16, '-r', u'20:15866409-31376818', '--caller', 'platypus', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/20/Batch1-20_15866408_31376818.vcf.gz', '/mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/20/Batch1-20_15866408_31376818.vcf-inputs.txt'] in region: 20:15866409-31376818
[2016-04-15T08:21Z] 2016-04-15 01:21:58 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:21:58,742 - WARNING - Could not retrieve variants from source file in region 20:25398579-25398980. Error was invalid region `20:25398580-25398980`
[2016-04-15T08:21Z] 2016-04-15 01:21:59 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:21:59,052 - WARNING - Could not retrieve variants from source file in region 20:19970494-19970895. Error was invalid region `20:19970495-19970895`
[2016-04-15T08:21Z] 2016-04-15 01:21:59 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:21:59,762 - WARNING - Could not retrieve variants from source file in region 20:30795608-30796009. Error was invalid region `20:30795609-30796009`
[2016-04-15T08:21Z] 2016-04-15 01:21:59 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:21:59,781 - WARNING - Could not retrieve variants from source file in region 20:31367737-31368138. Error was invalid region `20:31367738-31368138`
[2016-04-15T08:21Z] 2016-04-15 01:21:59 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:21:59,784 - WARNING - Could not retrieve variants from source file in region 20:19560453-19560854. Error was invalid region `20:19560454-19560854`
[2016-04-15T08:22Z] 2016-04-15 01:22:00 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:22:00,870 - WARNING - Could not retrieve variants from source file in region 20:31123381-31123782. Error was invalid region `20:31123382-31123782`
[2016-04-15T08:22Z] 2016-04-15 01:22:01 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:22:01,468 - WARNING - Could not retrieve variants from source file in region 20:17639646-17640199. Error was invalid region `20:17639647-17640199`
[2016-04-15T08:22Z] 2016-04-15 01:22:01 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:22:01,476 - WARNING - Could not retrieve variants from source file in region 20:16486487-16493723. Error was invalid region `20:16486488-16493723`
[2016-04-15T08:22Z] 2016-04-15 01:22:01 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:22:01,516 - WARNING - Could not retrieve variants from source file in region 20:21106503-21106904. Error was invalid region `20:21106504-21106904`
[2016-04-15T08:22Z] 2016-04-15 01:22:06 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:22:06,374 - WARNING - Could not retrieve variants from source file in region 20:30795608-30796009. Error was invalid region `20:30795609-30796009`
[2016-04-15T08:22Z] 2016-04-15 01:22:07 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:22:07,658 - WARNING - Could not retrieve variants from source file in region 20:18611751-18613432. Error was invalid region `20:18611752-18613432`
[2016-04-15T08:22Z] 2016-04-15 01:22:08 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:22:08,551 - WARNING - Could not retrieve variants from source file in region 20:19560453-19560854. Error was invalid region `20:19560454-19560854`
[2016-04-15T08:22Z] 2016-04-15 01:22:08 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:22:08,562 - WARNING - Could not retrieve variants from source file in region 20:20144561-20153157. Error was invalid region `20:20144562-20153157`
[2016-04-15T08:22Z] 2016-04-15 01:22:08 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:22:08,583 - WARNING - Could not retrieve variants from source file in region 20:30584499-30584900. Error was invalid region `20:30584500-30584900`
[2016-04-15T08:22Z] 2016-04-15 01:22:08 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:22:08,614 - WARNING - Could not retrieve variants from source file in region 20:16486487-16493723. Error was invalid region `20:16486488-16493723`
[2016-04-15T08:22Z] 2016-04-15 01:22:09 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:22:09,232 - WARNING - Could not retrieve variants from source file in region 20:21106503-21106904. Error was invalid region `20:21106504-21106904`
[2016-04-15T08:22Z] 2016-04-15 01:22:09 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:22:09,408 - WARNING - Could not retrieve variants from source file in region 20:21284025-21284426. Error was invalid region `20:21284026-21284426`
[2016-04-15T08:22Z] 2016-04-15 01:22:09 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:22:09,572 - WARNING - Could not retrieve variants from source file in region 20:17639646-17640199. Error was invalid region `20:17639647-17640199`
[2016-04-15T08:22Z] 2016-04-15 01:22:10 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:22:10,084 - WARNING - Could not retrieve variants from source file in region 20:19970494-19970895. Error was invalid region `20:19970495-19970895`
[2016-04-15T08:22Z] 2016-04-15 01:22:11 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:22:11,329 - WARNING - Could not retrieve variants from source file in region 20:30795608-30796009. Error was invalid region `20:30795609-30796009`
[2016-04-15T08:22Z] 2016-04-15 01:22:13 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:22:13,169 - WARNING - Could not retrieve variants from source file in region 20:31367737-31368138. Error was invalid region `20:31367738-31368138`
[2016-04-15T08:22Z] 2016-04-15 01:22:16 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:22:16,089 - WARNING - Could not retrieve variants from source file in region 20:16486487-16493723. Error was invalid region `20:16486488-16493723`
[2016-04-15T08:22Z] 2016-04-15 01:22:17 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:22:17,349 - WARNING - Could not retrieve variants from source file in region 20:17639646-17640199. Error was invalid region `20:17639647-17640199`
[2016-04-15T08:22Z] 2016-04-15 01:22:17 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:22:17,747 - WARNING - Could not retrieve variants from source file in region 20:31123381-31123782. Error was invalid region `20:31123382-31123782`
[2016-04-15T08:22Z] 2016-04-15 01:22:18 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:22:18,170 - WARNING - Could not retrieve variants from source file in region 20:19560453-19560854. Error was invalid region `20:19560454-19560854`
[2016-04-15T08:22Z] 2016-04-15 01:22:18 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:22:18,175 - WARNING - Could not retrieve variants from source file in region 20:30584499-30584900. Error was invalid region `20:30584500-30584900`
[2016-04-15T08:22Z] 2016-04-15 01:22:18 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:22:18,361 - WARNING - Could not retrieve variants from source file in region 20:21106503-21106904. Error was invalid region `20:21106504-21106904`
[2016-04-15T08:22Z] 2016-04-15 01:22:28 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:22:28,152 - WARNING - Could not retrieve variants from source file in region 20:19634521-19634937. Error was invalid region `20:19634522-19634937`
[2016-04-15T08:22Z] 2016-04-15 01:22:29 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:22:29,153 - WARNING - Could not retrieve variants from source file in region 20:31291272-31291815. Error was invalid region `20:31291273-31291815`
[2016-04-15T08:22Z] 2016-04-15 01:22:31 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:22:31,525 - WARNING - Could not retrieve variants from source file in region 20:16410348-16410749. Error was invalid region `20:16410349-16410749`
[2016-04-15T08:22Z] 2016-04-15 01:22:33 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:22:33,305 - WARNING - Could not retrieve variants from source file in region 20:31022748-31024464. Error was invalid region `20:31022749-31024464`
[2016-04-15T08:22Z] 2016-04-15 01:22:33 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:22:33,658 - WARNING - Could not retrieve variants from source file in region 20:19634521-19634937. Error was invalid region `20:19634522-19634937`
[2016-04-15T08:22Z] 2016-04-15 01:22:34 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:22:34,950 - WARNING - Could not retrieve variants from source file in region 20:20493011-20493412. Error was invalid region `20:20493012-20493412`
[2016-04-15T08:22Z] 2016-04-15 01:22:35 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:22:35,727 - WARNING - Could not retrieve variants from source file in region 20:21185950-21186351. Error was invalid region `20:21185951-21186351`
[2016-04-15T08:22Z] 2016-04-15 01:22:35 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:22:35,794 - WARNING - Could not retrieve variants from source file in region 20:30436076-30457929. Error was invalid region `20:30436077-30457929`
[2016-04-15T08:22Z] 2016-04-15 01:22:36 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:22:36,475 - WARNING - Could not retrieve variants from source file in region 20:15967179-15967580. Error was invalid region `20:15967180-15967580`
[2016-04-15T08:22Z] 2016-04-15 01:22:36 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:22:36,549 - WARNING - Could not retrieve variants from source file in region 20:19261412-19261813. Error was invalid region `20:19261413-19261813`
[2016-04-15T08:22Z] 2016-04-15 01:22:36 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:22:36,837 - WARNING - Could not retrieve variants from source file in region 20:20032787-20033570. Error was invalid region `20:20032788-20033570`
[2016-04-15T08:22Z] 2016-04-15 01:22:36 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:22:36,941 - WARNING - Could not retrieve variants from source file in region 20:30064120-30070429. Error was invalid region `20:30064121-30070429`
[2016-04-15T08:22Z] 2016-04-15 01:22:38 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:22:38,544 - WARNING - Could not retrieve variants from source file in region 20:20079149-20079550. Error was invalid region `20:20079150-20079550`
[2016-04-15T08:22Z] 2016-04-15 01:22:39 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:22:39,384 - WARNING - Could not retrieve variants from source file in region 20:31022748-31024464. Error was invalid region `20:31022749-31024464`
[2016-04-15T08:22Z] 2016-04-15 01:22:39 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:22:39,763 - WARNING - Could not retrieve variants from source file in region 20:19634521-19634937. Error was invalid region `20:19634522-19634937`
[2016-04-15T08:22Z] 2016-04-15 01:22:41 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:22:41,381 - WARNING - Could not retrieve variants from source file in region 20:16728927-16729328. Error was invalid region `20:16728928-16729328`
[2016-04-15T08:22Z] 2016-04-15 01:22:41 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:22:41,671 - WARNING - Could not retrieve variants from source file in region 20:20493011-20493412. Error was invalid region `20:20493012-20493412`
[2016-04-15T08:22Z] 2016-04-15 01:22:42 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:22:42,223 - WARNING - Could not retrieve variants from source file in region 20:31291272-31291815. Error was invalid region `20:31291273-31291815`
[2016-04-15T08:22Z] 2016-04-15 01:22:42 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:22:42,706 - WARNING - Could not retrieve variants from source file in region 20:21185950-21186351. Error was invalid region `20:21185951-21186351`
[2016-04-15T08:22Z] 2016-04-15 01:22:43 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:22:43,608 - WARNING - Could not retrieve variants from source file in region 20:20032787-20033570. Error was invalid region `20:20032788-20033570`
[2016-04-15T08:22Z] 2016-04-15 01:22:43 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:22:43,782 - WARNING - Could not retrieve variants from source file in region 20:18513161-18523192. Error was invalid region `20:18513162-18523192`
[2016-04-15T08:22Z] 2016-04-15 01:22:44 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:22:44,449 - WARNING - Could not retrieve variants from source file in region 20:16410348-16410749. Error was invalid region `20:16410349-16410749`
[2016-04-15T08:22Z] 2016-04-15 01:22:44 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:22:44,529 - WARNING - Could not retrieve variants from source file in region 20:19261412-19261813. Error was invalid region `20:19261413-19261813`
[2016-04-15T08:22Z] 2016-04-15 01:22:44 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:22:44,923 - WARNING - Could not retrieve variants from source file in region 20:31022748-31024464. Error was invalid region `20:31022749-31024464`
[2016-04-15T08:22Z] 2016-04-15 01:22:46 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:22:46,582 - WARNING - Could not retrieve variants from source file in region 20:16728927-16729328. Error was invalid region `20:16728928-16729328`
[2016-04-15T08:22Z] 2016-04-15 01:22:46 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:22:46,606 - WARNING - Could not retrieve variants from source file in region 20:20493011-20493412. Error was invalid region `20:20493012-20493412`
[2016-04-15T08:22Z] 2016-04-15 01:22:48 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:22:48,743 - WARNING - Could not retrieve variants from source file in region 20:21185950-21186351. Error was invalid region `20:21185951-21186351`
[2016-04-15T08:22Z] 2016-04-15 01:22:50 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:22:50,070 - WARNING - Could not retrieve variants from source file in region 20:19261412-19261813. Error was invalid region `20:19261413-19261813`
[2016-04-15T08:22Z] 2016-04-15 01:22:51 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:22:51,185 - WARNING - Could not retrieve variants from source file in region 20:20032787-20033570. Error was invalid region `20:20032788-20033570`
[2016-04-15T08:22Z] 2016-04-15 01:22:51 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:22:51,736 - WARNING - Could not retrieve variants from source file in region 20:30064120-30070429. Error was invalid region `20:30064121-30070429`
[2016-04-15T08:22Z] 2016-04-15 01:22:53 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:22:53,182 - WARNING - Could not retrieve variants from source file in region 20:25177594-25195699. Error was invalid region `20:25177595-25195699`
[2016-04-15T08:22Z] 2016-04-15 01:22:57 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:22:57,125 - WARNING - Could not retrieve variants from source file in region 20:31238416-31238817. Error was invalid region `20:31238417-31238817`
[2016-04-15T08:22Z] 2016-04-15 01:22:57 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:22:57,746 - WARNING - Could not retrieve variants from source file in region 20:20006157-20006558. Error was invalid region `20:20006158-20006558`
[2016-04-15T08:23Z] 2016-04-15 01:23:01 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:23:01,179 - WARNING - Could not retrieve variants from source file in region 20:29521813-29524623. Error was invalid region `20:29521814-29524623`
[2016-04-15T08:23Z] 2016-04-15 01:23:01 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:23:01,238 - WARNING - Could not retrieve variants from source file in region 20:21142312-21143003. Error was invalid region `20:21142313-21143003`
[2016-04-15T08:23Z] 2016-04-15 01:23:01 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:23:01,733 - WARNING - Could not retrieve variants from source file in region 20:20303165-20303566. Error was invalid region `20:20303166-20303566`
[2016-04-15T08:23Z] 2016-04-15 01:23:01 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:23:01,946 - WARNING - Could not retrieve variants from source file in region 20:20232145-20232546. Error was invalid region `20:20232146-20232546`
[2016-04-15T08:23Z] 2016-04-15 01:23:02 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:23:02,061 - WARNING - Could not retrieve variants from source file in region 20:31238416-31238817. Error was invalid region `20:31238417-31238817`
[2016-04-15T08:23Z] 2016-04-15 01:23:03 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:23:03,921 - WARNING - Could not retrieve variants from source file in region 20:25177594-25195699. Error was invalid region `20:25177595-25195699`
[2016-04-15T08:23Z] 2016-04-15 01:23:04 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:23:04,684 - WARNING - Could not retrieve variants from source file in region 20:30369912-30370313. Error was invalid region `20:30369913-30370313`
[2016-04-15T08:23Z] 2016-04-15 01:23:04 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:23:04,739 - WARNING - Could not retrieve variants from source file in region 20:18287239-18296266. Error was invalid region `20:18287240-18296266`
[2016-04-15T08:23Z] 2016-04-15 01:23:05 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:23:05,954 - WARNING - Could not retrieve variants from source file in region 20:21142312-21143003. Error was invalid region `20:21142313-21143003`
[2016-04-15T08:23Z] 2016-04-15 01:23:06 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:23:06,781 - WARNING - Could not retrieve variants from source file in region 20:31238416-31238817. Error was invalid region `20:31238417-31238817`
[2016-04-15T08:23Z] 2016-04-15 01:23:07 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:23:07,631 - WARNING - Could not retrieve variants from source file in region 20:29976738-29977139. Error was invalid region `20:29976739-29977139`
[2016-04-15T08:23Z] 2016-04-15 01:23:08 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:23:08,868 - WARNING - Could not retrieve variants from source file in region 20:25433928-25477617. Error was invalid region `20:25433929-25477617`
[2016-04-15T08:23Z] 2016-04-15 01:23:09 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:23:09,508 - WARNING - Could not retrieve variants from source file in region 20:30369912-30370313. Error was invalid region `20:30369913-30370313`
[2016-04-15T08:23Z] 2016-04-15 01:23:10 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:23:10,133 - WARNING - Could not retrieve variants from source file in region 20:21142312-21143003. Error was invalid region `20:21142313-21143003`
[2016-04-15T08:23Z] 2016-04-15 01:23:11 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:23:11,548 - WARNING - Could not retrieve variants from source file in region 20:20232145-20232546. Error was invalid region `20:20232146-20232546`
[2016-04-15T08:23Z] 2016-04-15 01:23:15 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:23:15,494 - WARNING - Could not retrieve variants from source file in region 20:23729511-23731684. Error was invalid region `20:23729512-23731684`
[2016-04-15T08:23Z] 2016-04-15 01:23:15 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:23:15,942 - WARNING - Could not retrieve variants from source file in region 20:25059170-25059736. Error was invalid region `20:25059171-25059736`
[2016-04-15T08:23Z] 2016-04-15 01:23:16 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:23:16,881 - WARNING - Could not retrieve variants from source file in region 20:24939379-24939780. Error was invalid region `20:24939380-24939780`
[2016-04-15T08:23Z] 2016-04-15 01:23:18 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:23:18,525 - WARNING - Could not retrieve variants from source file in region 20:24939379-24939780. Error was invalid region `20:24939380-24939780`
[2016-04-15T08:23Z] 2016-04-15 01:23:19 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:23:19,431 - WARNING - Could not retrieve variants from source file in region 20:23859967-23860368. Error was invalid region `20:23859968-23860368`
[2016-04-15T08:23Z] 2016-04-15 01:23:20 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:23:20,299 - WARNING - Could not retrieve variants from source file in region 20:23859967-23860368. Error was invalid region `20:23859968-23860368`
[2016-04-15T08:23Z] 2016-04-15 01:23:20 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:23:20,352 - WARNING - Could not retrieve variants from source file in region 20:24939379-24939780. Error was invalid region `20:24939380-24939780`
[2016-04-15T08:23Z] 2016-04-15 01:23:20 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:23:20,743 - WARNING - Could not retrieve variants from source file in region 20:23729511-23731684. Error was invalid region `20:23729512-23731684`
[2016-04-15T08:23Z] 2016-04-15 01:23:22 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:23:22,972 - WARNING - Could not retrieve variants from source file in region 20:17942187-17942588. Error was invalid region `20:17942188-17942588`
[2016-04-15T08:23Z] 2016-04-15 01:23:23 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:23:23,880 - WARNING - Could not retrieve variants from source file in region 20:23859967-23860368. Error was invalid region `20:23859968-23860368`
[2016-04-15T08:23Z] 2016-04-15 01:23:24 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:23:24,150 - WARNING - Could not retrieve variants from source file in region 20:23420890-23432718. Error was invalid region `20:23420891-23432718`
[2016-04-15T08:23Z] 2016-04-15 01:23:24 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:23:24,156 - WARNING - Could not retrieve variants from source file in region 20:17680461-17716606. Error was invalid region `20:17680462-17716606`
[2016-04-15T08:23Z] 2016-04-15 01:23:24 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:23:24,619 - WARNING - Could not retrieve variants from source file in region 20:23345633-23346034. Error was invalid region `20:23345634-23346034`
[2016-04-15T08:23Z] 2016-04-15 01:23:24 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:23:24,633 - WARNING - Could not retrieve variants from source file in region 20:24973036-25011613. Error was invalid region `20:24973037-25011613`
[2016-04-15T08:23Z] 2016-04-15 01:23:24 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:23:24,862 - WARNING - Could not retrieve variants from source file in region 20:25059170-25059736. Error was invalid region `20:25059171-25059736`
[2016-04-15T08:23Z] 2016-04-15 01:23:24 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:23:24,865 - WARNING - Could not retrieve variants from source file in region 20:23729511-23731684. Error was invalid region `20:23729512-23731684`
[2016-04-15T08:23Z] 2016-04-15 01:23:25 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:23:25,329 - WARNING - Could not retrieve variants from source file in region 20:23064998-23065532. Error was invalid region `20:23064999-23065532`
[2016-04-15T08:23Z] 2016-04-15 01:23:27 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:23:27,499 - WARNING - Could not retrieve variants from source file in region 20:17942187-17942588. Error was invalid region `20:17942188-17942588`
[2016-04-15T08:23Z] 2016-04-15 01:23:29 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:23:29,285 - WARNING - Could not retrieve variants from source file in region 20:17680461-17716606. Error was invalid region `20:17680462-17716606`
[2016-04-15T08:23Z] 2016-04-15 01:23:29 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:23:29,293 - WARNING - Could not retrieve variants from source file in region 20:24973036-25011613. Error was invalid region `20:24973037-25011613`
[2016-04-15T08:23Z] 2016-04-15 01:23:29 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:23:29,871 - WARNING - Could not retrieve variants from source file in region 20:23064998-23065532. Error was invalid region `20:23064999-23065532`
[2016-04-15T08:23Z] 2016-04-15 01:23:31 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:23:31,736 - WARNING - Could not retrieve variants from source file in region 20:17942187-17942588. Error was invalid region `20:17942188-17942588`
[2016-04-15T08:23Z] 2016-04-15 01:23:32 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:23:32,181 - WARNING - Could not retrieve variants from source file in region 20:17680461-17716606. Error was invalid region `20:17680462-17716606`
[2016-04-15T08:23Z] 2016-04-15 01:23:33 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:23:33,802 - WARNING - Could not retrieve variants from source file in region 20:23064998-23065532. Error was invalid region `20:23064999-23065532`
[2016-04-15T08:23Z] 2016-04-15 01:23:37 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:23:37,223 - WARNING - Could not retrieve variants from source file in region 20:23618184-23618585. Error was invalid region `20:23618185-23618585`
[2016-04-15T08:23Z] 2016-04-15 01:23:37 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:23:37,227 - WARNING - Could not retrieve variants from source file in region 20:23618184-23618585. Error was invalid region `20:23618185-23618585`
[2016-04-15T08:23Z] 2016-04-15 01:23:37 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:23:37,533 - WARNING - Could not retrieve variants from source file in region 20:23618184-23618585. Error was invalid region `20:23618185-23618585`
[2016-04-15T08:23Z] 2016-04-15 01:23:37 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:23:37,813 - WARNING - Could not retrieve variants from source file in region 20:23583905-23586550. Error was invalid region `20:23583906-23586550`
[2016-04-15T08:23Z] 2016-04-15 01:23:37 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:23:37,979 - WARNING - Could not retrieve variants from source file in region 20:23583905-23586550. Error was invalid region `20:23583906-23586550`
[2016-04-15T08:23Z] 2016-04-15 01:23:38 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:23:38,055 - WARNING - Could not retrieve variants from source file in region 20:23472180-23472581. Error was invalid region `20:23472181-23472581`
[2016-04-15T08:23Z] 2016-04-15 01:23:40 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:23:40,085 - WARNING - Could not retrieve variants from source file in region 20:23472180-23472581. Error was invalid region `20:23472181-23472581`
[2016-04-15T08:23Z] 2016-04-15 01:23:40 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:23:40,239 - WARNING - Could not retrieve variants from source file in region 20:23583905-23586550. Error was invalid region `20:23583906-23586550`
[2016-04-15T08:23Z] 2016-04-15 01:23:40 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:23:40,307 - WARNING - Could not retrieve variants from source file in region 20:23016759-23028914. Error was invalid region `20:23016760-23028914`
[2016-04-15T08:23Z] 2016-04-15 01:23:40 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:23:40,308 - WARNING - Could not retrieve variants from source file in region 20:23472180-23472581. Error was invalid region `20:23472181-23472581`
[2016-04-15T08:23Z] ['bcbio-variation-recall', 'square', '-Xms750m', '-Xmx7280m', '-XX:+UseSerialGC', '-c', 16, '-r', u'20:31379407-47242465', '--caller', 'platypus', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/20/Batch1-20_31379406_47242465.vcf.gz', '/mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/20/Batch1-20_31379406_47242465.vcf-inputs.txt'] in region: 20:31379407-47242465
[2016-04-15T08:23Z] 2016-04-15 01:23:56 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:23:56,562 - WARNING - Could not retrieve variants from source file in region 20:35125423-35125824. Error was invalid region `20:35125424-35125824`
[2016-04-15T08:23Z] 2016-04-15 01:23:56 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:23:56,951 - WARNING - Could not retrieve variants from source file in region 20:46365360-46365761. Error was invalid region `20:46365361-46365761`
[2016-04-15T08:23Z] 2016-04-15 01:23:57 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:23:57,490 - WARNING - Could not retrieve variants from source file in region 20:36030728-36031129. Error was invalid region `20:36030729-36031129`
[2016-04-15T08:23Z] 2016-04-15 01:23:57 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:23:57,821 - WARNING - Could not retrieve variants from source file in region 20:39700804-39701205. Error was invalid region `20:39700805-39701205`
[2016-04-15T08:23Z] 2016-04-15 01:23:58 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:23:58,239 - WARNING - Could not retrieve variants from source file in region 20:33764421-33764822. Error was invalid region `20:33764422-33764822`
[2016-04-15T08:23Z] 2016-04-15 01:23:58 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:23:58,397 - WARNING - Could not retrieve variants from source file in region 20:44038363-44054539. Error was invalid region `20:44038364-44054539`
[2016-04-15T08:23Z] 2016-04-15 01:23:58 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:23:58,627 - WARNING - Could not retrieve variants from source file in region 20:35412623-35414958. Error was invalid region `20:35412624-35414958`
[2016-04-15T08:23Z] 2016-04-15 01:23:58 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:23:58,973 - WARNING - Could not retrieve variants from source file in region 20:32889493-32889894. Error was invalid region `20:32889494-32889894`
[2016-04-15T08:23Z] 2016-04-15 01:23:58 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:23:58,997 - WARNING - Could not retrieve variants from source file in region 20:32664653-32665054. Error was invalid region `20:32664654-32665054`
[2016-04-15T08:23Z] 2016-04-15 01:23:59 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:23:59,010 - WARNING - Could not retrieve variants from source file in region 20:34022176-34022577. Error was invalid region `20:34022177-34022577`
[2016-04-15T08:24Z] 2016-04-15 01:24:00 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:24:00,817 - WARNING - Could not retrieve variants from source file in region 20:36841545-36845928. Error was invalid region `20:36841546-36845928`
[2016-04-15T08:24Z] 2016-04-15 01:24:01 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:24:01,362 - WARNING - Could not retrieve variants from source file in region 20:33330477-33338395. Error was invalid region `20:33330478-33338395`
[2016-04-15T08:24Z] 2016-04-15 01:24:03 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:24:03,291 - WARNING - Could not retrieve variants from source file in region 20:46365360-46365761. Error was invalid region `20:46365361-46365761`
[2016-04-15T08:24Z] 2016-04-15 01:24:04 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:24:04,566 - WARNING - Could not retrieve variants from source file in region 20:32247952-32266324. Error was invalid region `20:32247953-32266324`
[2016-04-15T08:24Z] 2016-04-15 01:24:04 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:24:04,765 - WARNING - Could not retrieve variants from source file in region 20:33764421-33764822. Error was invalid region `20:33764422-33764822`
[2016-04-15T08:24Z] 2016-04-15 01:24:05 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:24:05,825 - WARNING - Could not retrieve variants from source file in region 20:39700804-39701205. Error was invalid region `20:39700805-39701205`
[2016-04-15T08:24Z] 2016-04-15 01:24:05 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:24:05,850 - WARNING - Could not retrieve variants from source file in region 20:36030728-36031129. Error was invalid region `20:36030729-36031129`
[2016-04-15T08:24Z] 2016-04-15 01:24:06 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:24:06,459 - WARNING - Could not retrieve variants from source file in region 20:32889493-32889894. Error was invalid region `20:32889494-32889894`
[2016-04-15T08:24Z] 2016-04-15 01:24:06 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:24:06,470 - WARNING - Could not retrieve variants from source file in region 20:32664653-32665054. Error was invalid region `20:32664654-32665054`
[2016-04-15T08:24Z] 2016-04-15 01:24:06 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:24:06,637 - WARNING - Could not retrieve variants from source file in region 20:35412623-35414958. Error was invalid region `20:35412624-35414958`
[2016-04-15T08:24Z] 2016-04-15 01:24:06 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:24:06,767 - WARNING - Could not retrieve variants from source file in region 20:33330477-33338395. Error was invalid region `20:33330478-33338395`
[2016-04-15T08:24Z] 2016-04-15 01:24:07 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:24:07,432 - WARNING - Could not retrieve variants from source file in region 20:46365360-46365761. Error was invalid region `20:46365361-46365761`
[2016-04-15T08:24Z] 2016-04-15 01:24:11 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:24:10,998 - WARNING - Could not retrieve variants from source file in region 20:33764421-33764822. Error was invalid region `20:33764422-33764822`
[2016-04-15T08:24Z] 2016-04-15 01:24:12 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:24:12,536 - WARNING - Could not retrieve variants from source file in region 20:36030728-36031129. Error was invalid region `20:36030729-36031129`
[2016-04-15T08:24Z] 2016-04-15 01:24:13 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:24:13,262 - WARNING - Could not retrieve variants from source file in region 20:39700804-39701205. Error was invalid region `20:39700805-39701205`
[2016-04-15T08:24Z] 2016-04-15 01:24:13 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:24:13,464 - WARNING - Could not retrieve variants from source file in region 20:34022176-34022577. Error was invalid region `20:34022177-34022577`
[2016-04-15T08:24Z] 2016-04-15 01:24:14 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:24:14,991 - WARNING - Could not retrieve variants from source file in region 20:32664653-32665054. Error was invalid region `20:32664654-32665054`
[2016-04-15T08:24Z] 2016-04-15 01:24:15 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:24:15,695 - WARNING - Could not retrieve variants from source file in region 20:35412623-35414958. Error was invalid region `20:35412624-35414958`
[2016-04-15T08:24Z] 2016-04-15 01:24:15 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:24:15,753 - WARNING - Could not retrieve variants from source file in region 20:32889493-32889894. Error was invalid region `20:32889494-32889894`
[2016-04-15T08:24Z] 2016-04-15 01:24:23 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:24:23,671 - WARNING - Could not retrieve variants from source file in region 20:36668663-36719921. Error was invalid region `20:36668664-36719921`
[2016-04-15T08:24Z] 2016-04-15 01:24:25 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:24:25,206 - WARNING - Could not retrieve variants from source file in region 20:36946637-36947038. Error was invalid region `20:36946638-36947038`
[2016-04-15T08:24Z] 2016-04-15 01:24:26 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:24:26,059 - WARNING - Could not retrieve variants from source file in region 20:35089643-35091010. Error was invalid region `20:35089644-35091010`
[2016-04-15T08:24Z] 2016-04-15 01:24:27 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:24:27,484 - WARNING - Could not retrieve variants from source file in region 20:33734694-33735095. Error was invalid region `20:33734695-33735095`
[2016-04-15T08:24Z] 2016-04-15 01:24:27 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:24:27,743 - WARNING - Could not retrieve variants from source file in region 20:35864843-35865244. Error was invalid region `20:35864844-35865244`
[2016-04-15T08:24Z] 2016-04-15 01:24:29 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:24:29,562 - WARNING - Could not retrieve variants from source file in region 20:33971703-33972104. Error was invalid region `20:33971704-33972104`
[2016-04-15T08:24Z] 2016-04-15 01:24:31 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:24:31,580 - WARNING - Could not retrieve variants from source file in region 20:36946637-36947038. Error was invalid region `20:36946638-36947038`
[2016-04-15T08:24Z] 2016-04-15 01:24:33 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:24:33,642 - WARNING - Could not retrieve variants from source file in region 20:33734694-33735095. Error was invalid region `20:33734695-33735095`
[2016-04-15T08:24Z] 2016-04-15 01:24:33 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:24:33,736 - WARNING - Could not retrieve variants from source file in region 20:32212479-32212880. Error was invalid region `20:32212480-32212880`
[2016-04-15T08:24Z] 2016-04-15 01:24:33 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:24:33,756 - WARNING - Could not retrieve variants from source file in region 20:35864843-35865244. Error was invalid region `20:35864844-35865244`
[2016-04-15T08:24Z] 2016-04-15 01:24:34 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:24:34,066 - WARNING - Could not retrieve variants from source file in region 20:32379052-32379453. Error was invalid region `20:32379053-32379453`
[2016-04-15T08:24Z] 2016-04-15 01:24:34 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:24:34,267 - WARNING - Could not retrieve variants from source file in region 20:45131454-45131855. Error was invalid region `20:45131455-45131855`
[2016-04-15T08:24Z] 2016-04-15 01:24:34 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:24:34,532 - WARNING - Could not retrieve variants from source file in region 20:33971703-33972104. Error was invalid region `20:33971704-33972104`
[2016-04-15T08:24Z] 2016-04-15 01:24:34 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:24:34,637 - WARNING - Could not retrieve variants from source file in region 20:36668663-36719921. Error was invalid region `20:36668664-36719921`
[2016-04-15T08:24Z] 2016-04-15 01:24:36 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:24:36,132 - WARNING - Could not retrieve variants from source file in region 20:43976780-44006126. Error was invalid region `20:43976781-44006126`
[2016-04-15T08:24Z] 2016-04-15 01:24:36 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:24:36,168 - WARNING - Could not retrieve variants from source file in region 20:36946637-36947038. Error was invalid region `20:36946638-36947038`
[2016-04-15T08:24Z] 2016-04-15 01:24:38 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:24:38,068 - WARNING - Could not retrieve variants from source file in region 20:32295330-32295731. Error was invalid region `20:32295331-32295731`
[2016-04-15T08:24Z] 2016-04-15 01:24:39 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:24:39,774 - WARNING - Could not retrieve variants from source file in region 20:32212479-32212880. Error was invalid region `20:32212480-32212880`
[2016-04-15T08:24Z] 2016-04-15 01:24:40 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:24:40,442 - WARNING - Could not retrieve variants from source file in region 20:37601032-37621242. Error was invalid region `20:37601033-37621242`
[2016-04-15T08:24Z] 2016-04-15 01:24:40 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:24:40,462 - WARNING - Could not retrieve variants from source file in region 20:31756776-31757177. Error was invalid region `20:31756777-31757177`
[2016-04-15T08:24Z] 2016-04-15 01:24:40 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:24:40,936 - WARNING - Could not retrieve variants from source file in region 20:32379052-32379453. Error was invalid region `20:32379053-32379453`
[2016-04-15T08:24Z] 2016-04-15 01:24:40 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:24:40,980 - WARNING - Could not retrieve variants from source file in region 20:33734694-33735095. Error was invalid region `20:33734695-33735095`
[2016-04-15T08:24Z] 2016-04-15 01:24:41 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:24:41,151 - WARNING - Could not retrieve variants from source file in region 20:33971703-33972104. Error was invalid region `20:33971704-33972104`
[2016-04-15T08:24Z] 2016-04-15 01:24:41 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:24:41,273 - WARNING - Could not retrieve variants from source file in region 20:35864843-35865244. Error was invalid region `20:35864844-35865244`
[2016-04-15T08:24Z] 2016-04-15 01:24:42 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:24:42,876 - WARNING - Could not retrieve variants from source file in region 20:32295330-32295731. Error was invalid region `20:32295331-32295731`
[2016-04-15T08:24Z] 2016-04-15 01:24:48 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:24:48,199 - WARNING - Could not retrieve variants from source file in region 20:32379052-32379453. Error was invalid region `20:32379053-32379453`
[2016-04-15T08:24Z] 2016-04-15 01:24:48 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:24:48,883 - WARNING - Could not retrieve variants from source file in region 20:42893419-42894093. Error was invalid region `20:42893420-42894093`
[2016-04-15T08:24Z] 2016-04-15 01:24:49 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:24:49,038 - WARNING - Could not retrieve variants from source file in region 20:33874509-33874910. Error was invalid region `20:33874510-33874910`
[2016-04-15T08:24Z] 2016-04-15 01:24:51 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:24:51,892 - WARNING - Could not retrieve variants from source file in region 20:45852826-45868042. Error was invalid region `20:45852827-45868042`
[2016-04-15T08:24Z] 2016-04-15 01:24:54 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:24:54,490 - WARNING - Could not retrieve variants from source file in region 20:42893419-42894093. Error was invalid region `20:42893420-42894093`
[2016-04-15T08:24Z] 2016-04-15 01:24:54 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:24:54,539 - WARNING - Could not retrieve variants from source file in region 20:33874509-33874910. Error was invalid region `20:33874510-33874910`
[2016-04-15T08:24Z] 2016-04-15 01:24:55 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:24:55,079 - WARNING - Could not retrieve variants from source file in region 20:31981638-31982039. Error was invalid region `20:31981639-31982039`
[2016-04-15T08:24Z] 2016-04-15 01:24:56 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:24:56,591 - WARNING - Could not retrieve variants from source file in region 20:33656915-33657316. Error was invalid region `20:33656916-33657316`
[2016-04-15T08:24Z] 2016-04-15 01:24:58 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:24:58,055 - WARNING - Could not retrieve variants from source file in region 20:44452486-44471206. Error was invalid region `20:44452487-44471206`
[2016-04-15T08:24Z] 2016-04-15 01:24:59 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:24:59,469 - WARNING - Could not retrieve variants from source file in region 20:42893419-42894093. Error was invalid region `20:42893420-42894093`
[2016-04-15T08:25Z] 2016-04-15 01:25:00 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:25:00,251 - WARNING - Could not retrieve variants from source file in region 20:31981638-31982039. Error was invalid region `20:31981639-31982039`
[2016-04-15T08:25Z] 2016-04-15 01:25:01 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:25:01,596 - WARNING - Could not retrieve variants from source file in region 20:44995971-45005620. Error was invalid region `20:44995972-45005620`
[2016-04-15T08:25Z] 2016-04-15 01:25:02 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:25:02,034 - WARNING - Could not retrieve variants from source file in region 20:37534454-37570915. Error was invalid region `20:37534455-37570915`
[2016-04-15T08:25Z] 2016-04-15 01:25:02 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:25:02,199 - WARNING - Could not retrieve variants from source file in region 20:45852826-45868042. Error was invalid region `20:45852827-45868042`
[2016-04-15T08:25Z] 2016-04-15 01:25:02 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:25:02,244 - WARNING - Could not retrieve variants from source file in region 20:33656915-33657316. Error was invalid region `20:33656916-33657316`
[2016-04-15T08:25Z] 2016-04-15 01:25:02 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:25:02,591 - WARNING - Could not retrieve variants from source file in region 20:35766126-35783684. Error was invalid region `20:35766127-35783684`
[2016-04-15T08:25Z] 2016-04-15 01:25:04 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:25:04,227 - WARNING - Could not retrieve variants from source file in region 20:31981638-31982039. Error was invalid region `20:31981639-31982039`
[2016-04-15T08:25Z] 2016-04-15 01:25:08 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:25:08,135 - WARNING - Could not retrieve variants from source file in region 20:37534454-37570915. Error was invalid region `20:37534455-37570915`
[2016-04-15T08:25Z] 2016-04-15 01:25:08 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:25:08,778 - WARNING - Could not retrieve variants from source file in region 20:33656915-33657316. Error was invalid region `20:33656916-33657316`
[2016-04-15T08:25Z] 2016-04-15 01:25:09 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:25:09,657 - WARNING - Could not retrieve variants from source file in region 20:31466323-31466724. Error was invalid region `20:31466324-31466724`
[2016-04-15T08:25Z] 2016-04-15 01:25:10 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:25:10,304 - WARNING - Could not retrieve variants from source file in region 20:37257379-37257780. Error was invalid region `20:37257380-37257780`
[2016-04-15T08:25Z] 2016-04-15 01:25:10 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:25:10,334 - WARNING - Could not retrieve variants from source file in region 20:35766126-35783684. Error was invalid region `20:35766127-35783684`
[2016-04-15T08:25Z] 2016-04-15 01:25:14 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:25:14,545 - WARNING - Could not retrieve variants from source file in region 20:45717743-45718144. Error was invalid region `20:45717744-45718144`
[2016-04-15T08:25Z] 2016-04-15 01:25:14 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:25:14,787 - WARNING - Could not retrieve variants from source file in region 20:42805508-42826569. Error was invalid region `20:42805509-42826569`
[2016-04-15T08:25Z] 2016-04-15 01:25:16 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:25:16,069 - WARNING - Could not retrieve variants from source file in region 20:33565269-33584479. Error was invalid region `20:33565270-33584479`
[2016-04-15T08:25Z] 2016-04-15 01:25:16 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:25:16,567 - WARNING - Could not retrieve variants from source file in region 20:31466323-31466724. Error was invalid region `20:31466324-31466724`
[2016-04-15T08:25Z] 2016-04-15 01:25:17 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:25:17,271 - WARNING - Could not retrieve variants from source file in region 20:45315575-45315976. Error was invalid region `20:45315576-45315976`
[2016-04-15T08:25Z] 2016-04-15 01:25:18 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:25:18,713 - WARNING - Could not retrieve variants from source file in region 20:42089300-42089701. Error was invalid region `20:42089301-42089701`
[2016-04-15T08:25Z] 2016-04-15 01:25:19 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:25:19,746 - WARNING - Could not retrieve variants from source file in region 20:45717743-45718144. Error was invalid region `20:45717744-45718144`
[2016-04-15T08:25Z] 2016-04-15 01:25:24 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:25:24,167 - WARNING - Could not retrieve variants from source file in region 20:44746771-44747172. Error was invalid region `20:44746772-44747172`
[2016-04-15T08:25Z] 2016-04-15 01:25:24 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:25:24,629 - WARNING - Could not retrieve variants from source file in region 20:42089300-42089701. Error was invalid region `20:42089301-42089701`
[2016-04-15T08:25Z] 2016-04-15 01:25:24 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:25:24,731 - WARNING - Could not retrieve variants from source file in region 20:33470483-33470884. Error was invalid region `20:33470484-33470884`
[2016-04-15T08:25Z] 2016-04-15 01:25:24 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:25:24,844 - WARNING - Could not retrieve variants from source file in region 20:43530023-43530424. Error was invalid region `20:43530024-43530424`
[2016-04-15T08:25Z] 2016-04-15 01:25:25 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:25:25,337 - WARNING - Could not retrieve variants from source file in region 20:44417432-44420872. Error was invalid region `20:44417433-44420872`
[2016-04-15T08:25Z] 2016-04-15 01:25:26 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:25:26,106 - WARNING - Could not retrieve variants from source file in region 20:31505081-31505482. Error was invalid region `20:31505082-31505482`
[2016-04-15T08:25Z] 2016-04-15 01:25:27 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:25:27,798 - WARNING - Could not retrieve variants from source file in region 20:35740583-35740984. Error was invalid region `20:35740584-35740984`
[2016-04-15T08:25Z] 2016-04-15 01:25:27 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:25:27,974 - WARNING - Could not retrieve variants from source file in region 20:37063424-37064251. Error was invalid region `20:37063425-37064251`
[2016-04-15T08:25Z] 2016-04-15 01:25:29 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:25:29,035 - WARNING - Could not retrieve variants from source file in region 20:45315575-45315976. Error was invalid region `20:45315576-45315976`
[2016-04-15T08:25Z] 2016-04-15 01:25:30 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:25:30,394 - WARNING - Could not retrieve variants from source file in region 20:44746771-44747172. Error was invalid region `20:44746772-44747172`
[2016-04-15T08:25Z] 2016-04-15 01:25:30 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:25:30,633 - WARNING - Could not retrieve variants from source file in region 20:37063424-37064251. Error was invalid region `20:37063425-37064251`
[2016-04-15T08:25Z] 2016-04-15 01:25:31 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:25:31,077 - WARNING - Could not retrieve variants from source file in region 20:33470483-33470884. Error was invalid region `20:33470484-33470884`
[2016-04-15T08:25Z] 2016-04-15 01:25:31 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:25:31,390 - WARNING - Could not retrieve variants from source file in region 20:43530023-43530424. Error was invalid region `20:43530024-43530424`
[2016-04-15T08:25Z] 2016-04-15 01:25:31 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:25:31,621 - WARNING - Could not retrieve variants from source file in region 20:42089300-42089701. Error was invalid region `20:42089301-42089701`
[2016-04-15T08:25Z] 2016-04-15 01:25:32 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:25:32,169 - WARNING - Could not retrieve variants from source file in region 20:44417432-44420872. Error was invalid region `20:44417433-44420872`
[2016-04-15T08:25Z] 2016-04-15 01:25:32 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:25:32,588 - WARNING - Could not retrieve variants from source file in region 20:31876470-31897744. Error was invalid region `20:31876471-31897744`
[2016-04-15T08:25Z] 2016-04-15 01:25:33 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:25:33,197 - WARNING - Could not retrieve variants from source file in region 20:31505081-31505482. Error was invalid region `20:31505082-31505482`
[2016-04-15T08:25Z] 2016-04-15 01:25:33 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:25:33,267 - WARNING - Could not retrieve variants from source file in region 20:31427424-31427825. Error was invalid region `20:31427425-31427825`
[2016-04-15T08:25Z] 2016-04-15 01:25:34 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:25:34,022 - WARNING - Could not retrieve variants from source file in region 20:33470483-33470884. Error was invalid region `20:33470484-33470884`
[2016-04-15T08:25Z] 2016-04-15 01:25:36 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:25:36,240 - WARNING - Could not retrieve variants from source file in region 20:43530023-43530424. Error was invalid region `20:43530024-43530424`
[2016-04-15T08:25Z] 2016-04-15 01:25:37 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:25:37,361 - WARNING - Could not retrieve variants from source file in region 20:44417432-44420872. Error was invalid region `20:44417433-44420872`
[2016-04-15T08:25Z] 2016-04-15 01:25:38 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:25:38,657 - WARNING - Could not retrieve variants from source file in region 20:31505081-31505482. Error was invalid region `20:31505082-31505482`
[2016-04-15T08:25Z] 2016-04-15 01:25:39 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:25:39,073 - WARNING - Could not retrieve variants from source file in region 20:35740583-35740984. Error was invalid region `20:35740584-35740984`
[2016-04-15T08:25Z] 2016-04-15 01:25:40 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:25:40,922 - WARNING - Could not retrieve variants from source file in region 20:42743243-42743644. Error was invalid region `20:42743244-42743644`
[2016-04-15T08:25Z] 2016-04-15 01:25:43 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:25:43,219 - WARNING - Could not retrieve variants from source file in region 20:43264716-43265117. Error was invalid region `20:43264717-43265117`
[2016-04-15T08:25Z] 2016-04-15 01:25:44 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:25:44,643 - WARNING - Could not retrieve variants from source file in region 20:43090718-43091119. Error was invalid region `20:43090719-43091119`
[2016-04-15T08:25Z] 2016-04-15 01:25:44 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:25:44,980 - WARNING - Could not retrieve variants from source file in region 20:35467502-35507732. Error was invalid region `20:35467503-35507732`
[2016-04-15T08:25Z] 2016-04-15 01:25:45 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:25:45,799 - WARNING - Could not retrieve variants from source file in region 20:41818078-41818479. Error was invalid region `20:41818079-41818479`
[2016-04-15T08:25Z] 2016-04-15 01:25:45 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:25:45,836 - WARNING - Could not retrieve variants from source file in region 20:42743243-42743644. Error was invalid region `20:42743244-42743644`
[2016-04-15T08:25Z] 2016-04-15 01:25:47 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:25:47,062 - WARNING - Could not retrieve variants from source file in region 20:31812712-31813113. Error was invalid region `20:31812713-31813113`
[2016-04-15T08:25Z] 2016-04-15 01:25:47 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:25:47,416 - WARNING - Could not retrieve variants from source file in region 20:43378559-43379644. Error was invalid region `20:43378560-43379644`
[2016-04-15T08:25Z] 2016-04-15 01:25:47 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:25:47,734 - WARNING - Could not retrieve variants from source file in region 20:43264716-43265117. Error was invalid region `20:43264717-43265117`
[2016-04-15T08:25Z] 2016-04-15 01:25:48 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:25:48,731 - WARNING - Could not retrieve variants from source file in region 20:44314398-44314799. Error was invalid region `20:44314399-44314799`
[2016-04-15T08:25Z] 2016-04-15 01:25:48 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:25:48,838 - WARNING - Could not retrieve variants from source file in region 20:31384590-31386639. Error was invalid region `20:31384591-31386639`
[2016-04-15T08:25Z] 2016-04-15 01:25:48 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:25:48,996 - WARNING - Could not retrieve variants from source file in region 20:43090718-43091119. Error was invalid region `20:43090719-43091119`
[2016-04-15T08:25Z] 2016-04-15 01:25:50 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:25:50,038 - WARNING - Could not retrieve variants from source file in region 20:41818078-41818479. Error was invalid region `20:41818079-41818479`
[2016-04-15T08:25Z] 2016-04-15 01:25:50 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:25:50,080 - WARNING - Could not retrieve variants from source file in region 20:42743243-42743644. Error was invalid region `20:42743244-42743644`
[2016-04-15T08:25Z] 2016-04-15 01:25:51 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:25:51,262 - WARNING - Could not retrieve variants from source file in region 20:31812712-31813113. Error was invalid region `20:31812713-31813113`
[2016-04-15T08:25Z] 2016-04-15 01:25:51 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:25:51,974 - WARNING - Could not retrieve variants from source file in region 20:43264716-43265117. Error was invalid region `20:43264717-43265117`
[2016-04-15T08:25Z] 2016-04-15 01:25:53 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:25:53,238 - WARNING - Could not retrieve variants from source file in region 20:44314398-44314799. Error was invalid region `20:44314399-44314799`
[2016-04-15T08:25Z] 2016-04-15 01:25:53 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:25:53,293 - WARNING - Could not retrieve variants from source file in region 20:43090718-43091119. Error was invalid region `20:43090719-43091119`
[2016-04-15T08:25Z] 2016-04-15 01:25:53 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:25:53,360 - WARNING - Could not retrieve variants from source file in region 20:44352409-44352810. Error was invalid region `20:44352410-44352810`
[2016-04-15T08:25Z] 2016-04-15 01:25:53 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:25:53,375 - WARNING - Could not retrieve variants from source file in region 20:31384590-31386639. Error was invalid region `20:31384591-31386639`
[2016-04-15T08:25Z] 2016-04-15 01:25:53 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:25:53,951 - WARNING - Could not retrieve variants from source file in region 20:41818078-41818479. Error was invalid region `20:41818079-41818479`
[2016-04-15T08:25Z] 2016-04-15 01:25:55 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:25:55,288 - WARNING - Could not retrieve variants from source file in region 20:31812712-31813113. Error was invalid region `20:31812713-31813113`
[2016-04-15T08:25Z] 2016-04-15 01:25:55 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:25:55,725 - WARNING - Could not retrieve variants from source file in region 20:43378559-43379644. Error was invalid region `20:43378560-43379644`
[2016-04-15T08:25Z] 2016-04-15 01:25:57 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:25:57,160 - WARNING - Could not retrieve variants from source file in region 20:44314398-44314799. Error was invalid region `20:44314399-44314799`
[2016-04-15T08:25Z] 2016-04-15 01:25:57 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:25:57,260 - WARNING - Could not retrieve variants from source file in region 20:44352409-44352810. Error was invalid region `20:44352410-44352810`
[2016-04-15T08:26Z] 2016-04-15 01:26:01 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:26:01,874 - WARNING - Could not retrieve variants from source file in region 20:42320670-42331647. Error was invalid region `20:42320671-42331647`
[2016-04-15T08:26Z] 2016-04-15 01:26:03 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:26:03,482 - WARNING - Could not retrieve variants from source file in region 20:43117806-43118207. Error was invalid region `20:43117807-43118207`
[2016-04-15T08:26Z] 2016-04-15 01:26:04 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:26:04,949 - WARNING - Could not retrieve variants from source file in region 20:41306389-41306790. Error was invalid region `20:41306390-41306790`
[2016-04-15T08:26Z] 2016-04-15 01:26:05 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:26:05,441 - WARNING - Could not retrieve variants from source file in region 20:40031818-40032499. Error was invalid region `20:40031819-40032499`
[2016-04-15T08:26Z] 2016-04-15 01:26:05 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:26:05,582 - WARNING - Could not retrieve variants from source file in region 20:42965652-42966215. Error was invalid region `20:42965653-42966215`
[2016-04-15T08:26Z] 2016-04-15 01:26:07 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:26:07,005 - WARNING - Could not retrieve variants from source file in region 20:42939539-42939940. Error was invalid region `20:42939540-42939940`
[2016-04-15T08:26Z] 2016-04-15 01:26:07 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:26:07,214 - WARNING - Could not retrieve variants from source file in region 20:44141120-44141521. Error was invalid region `20:44141121-44141521`
[2016-04-15T08:26Z] 2016-04-15 01:26:09 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:26:09,462 - WARNING - Could not retrieve variants from source file in region 20:44184164-44184565. Error was invalid region `20:44184165-44184565`
[2016-04-15T08:26Z] 2016-04-15 01:26:09 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:26:09,790 - WARNING - Could not retrieve variants from source file in region 20:42194778-42225304. Error was invalid region `20:42194779-42225304`
[2016-04-15T08:26Z] 2016-04-15 01:26:09 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:26:09,972 - WARNING - Could not retrieve variants from source file in region 20:42965652-42966215. Error was invalid region `20:42965653-42966215`
[2016-04-15T08:26Z] 2016-04-15 01:26:10 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:26:10,966 - WARNING - Could not retrieve variants from source file in region 20:39978787-39979188. Error was invalid region `20:39978788-39979188`
[2016-04-15T08:26Z] 2016-04-15 01:26:11 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:26:11,590 - WARNING - Could not retrieve variants from source file in region 20:44141120-44141521. Error was invalid region `20:44141121-44141521`
[2016-04-15T08:26Z] 2016-04-15 01:26:11 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:26:11,590 - WARNING - Could not retrieve variants from source file in region 20:42939539-42939940. Error was invalid region `20:42939540-42939940`
[2016-04-15T08:26Z] 2016-04-15 01:26:13 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:26:13,290 - WARNING - Could not retrieve variants from source file in region 20:41306389-41306790. Error was invalid region `20:41306390-41306790`
[2016-04-15T08:26Z] 2016-04-15 01:26:13 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:26:13,722 - WARNING - Could not retrieve variants from source file in region 20:42194778-42225304. Error was invalid region `20:42194779-42225304`
[2016-04-15T08:26Z] 2016-04-15 01:26:15 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:26:15,716 - WARNING - Could not retrieve variants from source file in region 20:44141120-44141521. Error was invalid region `20:44141121-44141521`
[2016-04-15T08:26Z] 2016-04-15 01:26:15 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:26:15,823 - WARNING - Could not retrieve variants from source file in region 20:42939539-42939940. Error was invalid region `20:42939540-42939940`
[2016-04-15T08:26Z] 2016-04-15 01:26:20 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:26:20,526 - WARNING - Could not retrieve variants from source file in region 20:39797254-39803004. Error was invalid region `20:39797255-39803004`
[2016-04-15T08:26Z] 2016-04-15 01:26:23 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:26:23,166 - WARNING - Could not retrieve variants from source file in region 20:44108293-44108694. Error was invalid region `20:44108294-44108694`
[2016-04-15T08:26Z] ['bcbio-variation-recall', 'square', '-Xms750m', '-Xmx7280m', '-XX:+UseSerialGC', '-c', 16, '-r', u'20:47244086-62830269', '--caller', 'platypus', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/20/Batch1-20_47244085_62830269.vcf.gz', '/mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/20/Batch1-20_47244085_62830269.vcf-inputs.txt'] in region: 20:47244086-62830269
[2016-04-15T08:26Z] 2016-04-15 01:26:38 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:26:38,434 - WARNING - Could not retrieve variants from source file in region 20:58251573-58251974. Error was invalid region `20:58251574-58251974`
[2016-04-15T08:26Z] 2016-04-15 01:26:39 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:26:39,409 - WARNING - Could not retrieve variants from source file in region 20:60774024-60791594. Error was invalid region `20:60774025-60791594`
[2016-04-15T08:26Z] 2016-04-15 01:26:40 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:26:40,482 - WARNING - Could not retrieve variants from source file in region 20:56793495-56803543. Error was invalid region `20:56793496-56803543`
[2016-04-15T08:26Z] 2016-04-15 01:26:41 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:26:41,007 - WARNING - Could not retrieve variants from source file in region 20:56186673-56190824. Error was invalid region `20:56186674-56190824`
[2016-04-15T08:26Z] 2016-04-15 01:26:41 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:26:41,037 - WARNING - Could not retrieve variants from source file in region 20:56136973-56139593. Error was invalid region `20:56136974-56139593`
[2016-04-15T08:26Z] 2016-04-15 01:26:41 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:26:41,068 - WARNING - Could not retrieve variants from source file in region 20:61834484-61834885. Error was invalid region `20:61834485-61834885`
[2016-04-15T08:26Z] 2016-04-15 01:26:45 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:26:45,267 - WARNING - Could not retrieve variants from source file in region 20:58251573-58251974. Error was invalid region `20:58251574-58251974`
[2016-04-15T08:26Z] 2016-04-15 01:26:47 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:26:47,694 - WARNING - Could not retrieve variants from source file in region 20:54823818-54824219. Error was invalid region `20:54823819-54824219`
[2016-04-15T08:26Z] 2016-04-15 01:26:47 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:26:47,823 - WARNING - Could not retrieve variants from source file in region 20:52645435-52645836. Error was invalid region `20:52645436-52645836`
[2016-04-15T08:26Z] 2016-04-15 01:26:48 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:26:48,577 - WARNING - Could not retrieve variants from source file in region 20:50235366-50235767. Error was invalid region `20:50235367-50235767`
[2016-04-15T08:26Z] 2016-04-15 01:26:48 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:26:48,887 - WARNING - Could not retrieve variants from source file in region 20:62038066-62038467. Error was invalid region `20:62038067-62038467`
[2016-04-15T08:26Z] 2016-04-15 01:26:48 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:26:48,924 - WARNING - Could not retrieve variants from source file in region 20:56227321-56227722. Error was invalid region `20:56227322-56227722`
[2016-04-15T08:26Z] 2016-04-15 01:26:49 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:26:49,428 - WARNING - Could not retrieve variants from source file in region 20:56136973-56139593. Error was invalid region `20:56136974-56139593`
[2016-04-15T08:26Z] 2016-04-15 01:26:49 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:26:49,499 - WARNING - Could not retrieve variants from source file in region 20:56186673-56190824. Error was invalid region `20:56186674-56190824`
[2016-04-15T08:26Z] 2016-04-15 01:26:49 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:26:49,782 - WARNING - Could not retrieve variants from source file in region 20:56793495-56803543. Error was invalid region `20:56793496-56803543`
[2016-04-15T08:26Z] 2016-04-15 01:26:49 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:26:49,957 - WARNING - Could not retrieve variants from source file in region 20:61834484-61834885. Error was invalid region `20:61834485-61834885`
[2016-04-15T08:26Z] 2016-04-15 01:26:50 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:26:50,194 - WARNING - Could not retrieve variants from source file in region 20:58251573-58251974. Error was invalid region `20:58251574-58251974`
[2016-04-15T08:26Z] 2016-04-15 01:26:53 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:26:53,863 - WARNING - Could not retrieve variants from source file in region 20:54823818-54824219. Error was invalid region `20:54823819-54824219`
[2016-04-15T08:26Z] 2016-04-15 01:26:53 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:26:53,886 - WARNING - Could not retrieve variants from source file in region 20:52645435-52645836. Error was invalid region `20:52645436-52645836`
[2016-04-15T08:26Z] 2016-04-15 01:26:56 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:26:56,097 - WARNING - Could not retrieve variants from source file in region 20:50235366-50235767. Error was invalid region `20:50235367-50235767`
[2016-04-15T08:26Z] 2016-04-15 01:26:56 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:26:56,506 - WARNING - Could not retrieve variants from source file in region 20:56227321-56227722. Error was invalid region `20:56227322-56227722`
[2016-04-15T08:26Z] 2016-04-15 01:26:56 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:26:56,889 - WARNING - Could not retrieve variants from source file in region 20:56186673-56190824. Error was invalid region `20:56186674-56190824`
[2016-04-15T08:26Z] 2016-04-15 01:26:57 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:26:57,240 - WARNING - Could not retrieve variants from source file in region 20:48522119-48525017. Error was invalid region `20:48522120-48525017`
[2016-04-15T08:26Z] 2016-04-15 01:26:57 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:26:57,753 - WARNING - Could not retrieve variants from source file in region 20:61834484-61834885. Error was invalid region `20:61834485-61834885`
[2016-04-15T08:27Z] 2016-04-15 01:27:08 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:27:08,086 - WARNING - Could not retrieve variants from source file in region 20:62582176-62599005. Error was invalid region `20:62582177-62599005`
[2016-04-15T08:27Z] 2016-04-15 01:27:08 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:27:08,100 - WARNING - Could not retrieve variants from source file in region 20:60713100-60713522. Error was invalid region `20:60713101-60713522`
[2016-04-15T08:27Z] 2016-04-15 01:27:09 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:27:09,909 - WARNING - Could not retrieve variants from source file in region 20:58179551-58204042. Error was invalid region `20:58179552-58204042`
[2016-04-15T08:27Z] 2016-04-15 01:27:10 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:27:10,912 - WARNING - Could not retrieve variants from source file in region 20:52775317-52786409. Error was invalid region `20:52775318-52786409`
[2016-04-15T08:27Z] 2016-04-15 01:27:12 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:27:12,000 - WARNING - Could not retrieve variants from source file in region 20:54940929-54961731. Error was invalid region `20:54940930-54961731`
[2016-04-15T08:27Z] 2016-04-15 01:27:13 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:27:13,453 - WARNING - Could not retrieve variants from source file in region 20:60713100-60713522. Error was invalid region `20:60713101-60713522`
[2016-04-15T08:27Z] 2016-04-15 01:27:14 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:27:14,525 - WARNING - Could not retrieve variants from source file in region 20:47849971-47886874. Error was invalid region `20:47849972-47886874`
[2016-04-15T08:27Z] 2016-04-15 01:27:15 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:27:15,047 - WARNING - Could not retrieve variants from source file in region 20:61577064-61594869. Error was invalid region `20:61577065-61594869`
[2016-04-15T08:27Z] 2016-04-15 01:27:15 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:27:15,135 - WARNING - Could not retrieve variants from source file in region 20:52561258-52561659. Error was invalid region `20:52561259-52561659`
[2016-04-15T08:27Z] 2016-04-15 01:27:15 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:27:15,166 - WARNING - Could not retrieve variants from source file in region 20:48491047-48491448. Error was invalid region `20:48491048-48491448`
[2016-04-15T08:27Z] 2016-04-15 01:27:15 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:27:15,489 - WARNING - Could not retrieve variants from source file in region 20:56533868-56534579. Error was invalid region `20:56533869-56534579`
[2016-04-15T08:27Z] 2016-04-15 01:27:15 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:27:15,977 - WARNING - Could not retrieve variants from source file in region 20:61867243-61951679. Error was invalid region `20:61867244-61951679`
[2016-04-15T08:27Z] 2016-04-15 01:27:15 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:27:15,985 - WARNING - Could not retrieve variants from source file in region 20:57564484-57572865. Error was invalid region `20:57564485-57572865`
[2016-04-15T08:27Z] 2016-04-15 01:27:16 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:27:16,342 - WARNING - Could not retrieve variants from source file in region 20:52775317-52786409. Error was invalid region `20:52775318-52786409`
[2016-04-15T08:27Z] 2016-04-15 01:27:16 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:27:16,399 - WARNING - Could not retrieve variants from source file in region 20:50091816-50092217. Error was invalid region `20:50091817-50092217`
[2016-04-15T08:27Z] 2016-04-15 01:27:16 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:27:16,589 - WARNING - Could not retrieve variants from source file in region 20:54940929-54961731. Error was invalid region `20:54940930-54961731`
[2016-04-15T08:27Z] 2016-04-15 01:27:19 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:27:19,805 - WARNING - Could not retrieve variants from source file in region 20:60713100-60713522. Error was invalid region `20:60713101-60713522`
[2016-04-15T08:27Z] 2016-04-15 01:27:21 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:27:21,250 - WARNING - Could not retrieve variants from source file in region 20:47849971-47886874. Error was invalid region `20:47849972-47886874`
[2016-04-15T08:27Z] 2016-04-15 01:27:21 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:27:21,562 - WARNING - Could not retrieve variants from source file in region 20:49411487-49411888. Error was invalid region `20:49411488-49411888`
[2016-04-15T08:27Z] 2016-04-15 01:27:21 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:27:21,720 - WARNING - Could not retrieve variants from source file in region 20:61577064-61594869. Error was invalid region `20:61577065-61594869`
[2016-04-15T08:27Z] 2016-04-15 01:27:22 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:27:22,262 - WARNING - Could not retrieve variants from source file in region 20:56533868-56534579. Error was invalid region `20:56533869-56534579`
[2016-04-15T08:27Z] 2016-04-15 01:27:22 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:27:22,454 - WARNING - Could not retrieve variants from source file in region 20:52561258-52561659. Error was invalid region `20:52561259-52561659`
[2016-04-15T08:27Z] 2016-04-15 01:27:22 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:27:22,608 - WARNING - Could not retrieve variants from source file in region 20:48491047-48491448. Error was invalid region `20:48491048-48491448`
[2016-04-15T08:27Z] 2016-04-15 01:27:23 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:27:23,492 - WARNING - Could not retrieve variants from source file in region 20:61980893-62005828. Error was invalid region `20:61980894-62005828`
[2016-04-15T08:27Z] 2016-04-15 01:27:23 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:27:23,629 - WARNING - Could not retrieve variants from source file in region 20:56072999-56099931. Error was invalid region `20:56073000-56099931`
[2016-04-15T08:27Z] 2016-04-15 01:27:27 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:27:27,390 - WARNING - Could not retrieve variants from source file in region 20:47849971-47886874. Error was invalid region `20:47849972-47886874`
[2016-04-15T08:27Z] 2016-04-15 01:27:27 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:27:27,522 - WARNING - Could not retrieve variants from source file in region 20:49411487-49411888. Error was invalid region `20:49411488-49411888`
[2016-04-15T08:27Z] 2016-04-15 01:27:27 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:27:27,532 - WARNING - Could not retrieve variants from source file in region 20:61577064-61594869. Error was invalid region `20:61577065-61594869`
[2016-04-15T08:27Z] 2016-04-15 01:27:28 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:27:28,918 - WARNING - Could not retrieve variants from source file in region 20:56533868-56534579. Error was invalid region `20:56533869-56534579`
[2016-04-15T08:27Z] 2016-04-15 01:27:30 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:27:30,033 - WARNING - Could not retrieve variants from source file in region 20:48491047-48491448. Error was invalid region `20:48491048-48491448`
[2016-04-15T08:27Z] 2016-04-15 01:27:31 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:27:31,091 - WARNING - Could not retrieve variants from source file in region 20:61867243-61951679. Error was invalid region `20:61867244-61951679`
[2016-04-15T08:27Z] 2016-04-15 01:27:36 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:27:36,349 - WARNING - Could not retrieve variants from source file in region 20:62521124-62521525. Error was invalid region `20:62521125-62521525`
[2016-04-15T08:27Z] 2016-04-15 01:27:39 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:27:39,544 - WARNING - Could not retrieve variants from source file in region 20:49620572-49621339. Error was invalid region `20:49620573-49621339`
[2016-04-15T08:27Z] 2016-04-15 01:27:40 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:27:40,387 - WARNING - Could not retrieve variants from source file in region 20:60639672-60640651. Error was invalid region `20:60639673-60640651`
[2016-04-15T08:27Z] 2016-04-15 01:27:43 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:27:43,437 - WARNING - Could not retrieve variants from source file in region 20:51870125-51871039. Error was invalid region `20:51870126-51871039`
[2016-04-15T08:27Z] 2016-04-15 01:27:43 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:27:43,651 - WARNING - Could not retrieve variants from source file in region 20:55803088-55803489. Error was invalid region `20:55803089-55803489`
[2016-04-15T08:27Z] 2016-04-15 01:27:44 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:27:44,320 - WARNING - Could not retrieve variants from source file in region 20:52674977-52675378. Error was invalid region `20:52674978-52675378`
[2016-04-15T08:27Z] 2016-04-15 01:27:44 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:27:44,420 - WARNING - Could not retrieve variants from source file in region 20:47775263-47775664. Error was invalid region `20:47775264-47775664`
[2016-04-15T08:27Z] 2016-04-15 01:27:44 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:27:44,583 - WARNING - Could not retrieve variants from source file in region 20:61512395-61537128. Error was invalid region `20:61512396-61537128`
[2016-04-15T08:27Z] 2016-04-15 01:27:44 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:27:44,774 - WARNING - Could not retrieve variants from source file in region 20:49620572-49621339. Error was invalid region `20:49620573-49621339`
[2016-04-15T08:27Z] 2016-04-15 01:27:44 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:27:44,858 - WARNING - Could not retrieve variants from source file in region 20:57829090-57829491. Error was invalid region `20:57829091-57829491`
[2016-04-15T08:27Z] 2016-04-15 01:27:45 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:27:45,177 - WARNING - Could not retrieve variants from source file in region 20:57464066-57478997. Error was invalid region `20:57464067-57478997`
[2016-04-15T08:27Z] 2016-04-15 01:27:45 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:27:45,213 - WARNING - Could not retrieve variants from source file in region 20:48252703-48259224. Error was invalid region `20:48252704-48259224`
[2016-04-15T08:27Z] 2016-04-15 01:27:45 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:27:45,739 - WARNING - Could not retrieve variants from source file in region 20:60639672-60640651. Error was invalid region `20:60639673-60640651`
[2016-04-15T08:27Z] 2016-04-15 01:27:45 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:27:45,898 - WARNING - Could not retrieve variants from source file in region 20:62521124-62521525. Error was invalid region `20:62521125-62521525`
[2016-04-15T08:27Z] 2016-04-15 01:27:46 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:27:46,030 - WARNING - Could not retrieve variants from source file in region 20:49507681-49508082. Error was invalid region `20:49507682-49508082`
[2016-04-15T08:27Z] 2016-04-15 01:27:49 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:27:49,482 - WARNING - Could not retrieve variants from source file in region 20:52674977-52675378. Error was invalid region `20:52674978-52675378`
[2016-04-15T08:27Z] 2016-04-15 01:27:51 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:27:51,121 - WARNING - Could not retrieve variants from source file in region 20:47775263-47775664. Error was invalid region `20:47775264-47775664`
[2016-04-15T08:27Z] 2016-04-15 01:27:51 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:27:51,233 - WARNING - Could not retrieve variants from source file in region 20:49620572-49621339. Error was invalid region `20:49620573-49621339`
[2016-04-15T08:27Z] 2016-04-15 01:27:51 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:27:51,330 - WARNING - Could not retrieve variants from source file in region 20:57829090-57829491. Error was invalid region `20:57829091-57829491`
[2016-04-15T08:27Z] 2016-04-15 01:27:51 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:27:51,574 - WARNING - Could not retrieve variants from source file in region 20:55209046-55209447. Error was invalid region `20:55209047-55209447`
[2016-04-15T08:27Z] 2016-04-15 01:27:51 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:27:51,872 - WARNING - Could not retrieve variants from source file in region 20:57464066-57478997. Error was invalid region `20:57464067-57478997`
[2016-04-15T08:27Z] 2016-04-15 01:27:52 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:27:52,351 - WARNING - Could not retrieve variants from source file in region 20:49507681-49508082. Error was invalid region `20:49507682-49508082`
[2016-04-15T08:27Z] 2016-04-15 01:27:53 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:27:53,229 - WARNING - Could not retrieve variants from source file in region 20:55803088-55803489. Error was invalid region `20:55803089-55803489`
[2016-04-15T08:27Z] 2016-04-15 01:27:56 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:27:56,307 - WARNING - Could not retrieve variants from source file in region 20:47775263-47775664. Error was invalid region `20:47775264-47775664`
[2016-04-15T08:27Z] 2016-04-15 01:27:58 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:27:58,014 - WARNING - Could not retrieve variants from source file in region 20:55209046-55209447. Error was invalid region `20:55209047-55209447`
[2016-04-15T08:27Z] 2016-04-15 01:27:58 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:27:58,961 - WARNING - Could not retrieve variants from source file in region 20:57464066-57478997. Error was invalid region `20:57464067-57478997`
[2016-04-15T08:28Z] 2016-04-15 01:28:00 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:28:00,141 - WARNING - Could not retrieve variants from source file in region 20:49507681-49508082. Error was invalid region `20:49507682-49508082`
[2016-04-15T08:28Z] 2016-04-15 01:28:03 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:28:03,341 - WARNING - Could not retrieve variants from source file in region 20:60572452-60572853. Error was invalid region `20:60572453-60572853`
[2016-04-15T08:28Z] 2016-04-15 01:28:06 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:28:06,153 - WARNING - Could not retrieve variants from source file in region 20:50287525-50287980. Error was invalid region `20:50287526-50287980`
[2016-04-15T08:28Z] 2016-04-15 01:28:08 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:28:08,054 - WARNING - Could not retrieve variants from source file in region 20:55070057-55111561. Error was invalid region `20:55070058-55111561`
[2016-04-15T08:28Z] 2016-04-15 01:28:08 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:28:08,152 - WARNING - Could not retrieve variants from source file in region 20:60572452-60572853. Error was invalid region `20:60572453-60572853`
[2016-04-15T08:28Z] 2016-04-15 01:28:09 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:28:09,916 - WARNING - Could not retrieve variants from source file in region 20:55070057-55111561. Error was invalid region `20:55070058-55111561`
[2016-04-15T08:28Z] 2016-04-15 01:28:10 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:28:10,984 - WARNING - Could not retrieve variants from source file in region 20:47630238-47630639. Error was invalid region `20:47630239-47630639`
[2016-04-15T08:28Z] 2016-04-15 01:28:11 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:28:11,634 - WARNING - Could not retrieve variants from source file in region 20:61443782-61468761. Error was invalid region `20:61443783-61468761`
[2016-04-15T08:28Z] 2016-04-15 01:28:11 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:28:11,705 - WARNING - Could not retrieve variants from source file in region 20:50287525-50287980. Error was invalid region `20:50287526-50287980`
[2016-04-15T08:28Z] 2016-04-15 01:28:11 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:28:11,714 - WARNING - Could not retrieve variants from source file in region 20:57766832-57769330. Error was invalid region `20:57766833-57769330`
[2016-04-15T08:28Z] 2016-04-15 01:28:12 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:28:12,975 - WARNING - Could not retrieve variants from source file in region 20:60572452-60572853. Error was invalid region `20:60572453-60572853`
[2016-04-15T08:28Z] 2016-04-15 01:28:14 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:28:14,677 - WARNING - Could not retrieve variants from source file in region 20:48807800-48808201. Error was invalid region `20:48807801-48808201`
[2016-04-15T08:28Z] 2016-04-15 01:28:16 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:28:16,928 - WARNING - Could not retrieve variants from source file in region 20:57766832-57769330. Error was invalid region `20:57766833-57769330`
[2016-04-15T08:28Z] 2016-04-15 01:28:16 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:28:16,937 - WARNING - Could not retrieve variants from source file in region 20:50287525-50287980. Error was invalid region `20:50287526-50287980`
[2016-04-15T08:28Z] 2016-04-15 01:28:18 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:28:18,615 - WARNING - Could not retrieve variants from source file in region 20:57416520-57416985. Error was invalid region `20:57416521-57416985`
[2016-04-15T08:28Z] 2016-04-15 01:28:19 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:28:19,550 - WARNING - Could not retrieve variants from source file in region 20:47991064-47991465. Error was invalid region `20:47991065-47991465`
[2016-04-15T08:28Z] 2016-04-15 01:28:19 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:28:19,638 - WARNING - Could not retrieve variants from source file in region 20:48807800-48808201. Error was invalid region `20:48807801-48808201`
[2016-04-15T08:28Z] 2016-04-15 01:28:19 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:28:19,780 - WARNING - Could not retrieve variants from source file in region 20:60485416-60512050. Error was invalid region `20:60485417-60512050`
[2016-04-15T08:28Z] 2016-04-15 01:28:20 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:28:20,396 - WARNING - Could not retrieve variants from source file in region 20:47630238-47630639. Error was invalid region `20:47630239-47630639`
[2016-04-15T08:28Z] 2016-04-15 01:28:25 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:28:25,410 - WARNING - Could not retrieve variants from source file in region 20:48807800-48808201. Error was invalid region `20:48807801-48808201`
[2016-04-15T08:28Z] 2016-04-15 01:28:26 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:28:26,141 - WARNING - Could not retrieve variants from source file in region 20:58576221-58576622. Error was invalid region `20:58576222-58576622`
[2016-04-15T08:28Z] 2016-04-15 01:28:28 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:28:28,517 - WARNING - Could not retrieve variants from source file in region 20:61303355-61303769. Error was invalid region `20:61303356-61303769`
[2016-04-15T08:28Z] 2016-04-15 01:28:30 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:28:30,399 - WARNING - Could not retrieve variants from source file in region 20:61386020-61386421. Error was invalid region `20:61386021-61386421`
[2016-04-15T08:28Z] 2016-04-15 01:28:31 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:28:31,006 - WARNING - Could not retrieve variants from source file in region 20:57598805-57599592. Error was invalid region `20:57598806-57599592`
[2016-04-15T08:28Z] 2016-04-15 01:28:31 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:28:31,107 - WARNING - Could not retrieve variants from source file in region 20:57045456-57045955. Error was invalid region `20:57045457-57045955`
[2016-04-15T08:28Z] 2016-04-15 01:28:31 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:28:31,578 - WARNING - Could not retrieve variants from source file in region 20:48712838-48770349. Error was invalid region `20:48712839-48770349`
[2016-04-15T08:28Z] 2016-04-15 01:28:34 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:28:34,182 - WARNING - Could not retrieve variants from source file in region 20:48712838-48770349. Error was invalid region `20:48712839-48770349`
[2016-04-15T08:28Z] 2016-04-15 01:28:35 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:28:35,977 - WARNING - Could not retrieve variants from source file in region 20:57045456-57045955. Error was invalid region `20:57045457-57045955`
[2016-04-15T08:28Z] 2016-04-15 01:28:38 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:28:38,042 - WARNING - Could not retrieve variants from source file in region 20:47305100-47305501. Error was invalid region `20:47305101-47305501`
[2016-04-15T08:28Z] 2016-04-15 01:28:38 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:28:38,062 - WARNING - Could not retrieve variants from source file in region 20:47244239-47273916. Error was invalid region `20:47244240-47273916`
[2016-04-15T08:28Z] 2016-04-15 01:28:41 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:28:41,275 - WARNING - Could not retrieve variants from source file in region 20:60347873-60348274. Error was invalid region `20:60347874-60348274`
[2016-04-15T08:28Z] 2016-04-15 01:28:42 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:28:42,018 - WARNING - Could not retrieve variants from source file in region 20:61039747-61048739. Error was invalid region `20:61039748-61048739`
[2016-04-15T08:28Z] 2016-04-15 01:28:42 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:28:42,779 - WARNING - Could not retrieve variants from source file in region 20:61162056-61168073. Error was invalid region `20:61162057-61168073`
[2016-04-15T08:28Z] 2016-04-15 01:28:46 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:28:46,047 - WARNING - Could not retrieve variants from source file in region 20:61162056-61168073. Error was invalid region `20:61162057-61168073`
[2016-04-15T08:28Z] 2016-04-15 01:28:46 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:28:46,558 - WARNING - Could not retrieve variants from source file in region 20:58514283-58514684. Error was invalid region `20:58514284-58514684`
[2016-04-15T08:28Z] 2016-04-15 01:28:46 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:28:46,632 - WARNING - Could not retrieve variants from source file in region 20:61162056-61168073. Error was invalid region `20:61162057-61168073`
[2016-04-15T08:28Z] 2016-04-15 01:28:50 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:28:50,147 - WARNING - Could not retrieve variants from source file in region 20:58514283-58514684. Error was invalid region `20:58514284-58514684`
[2016-04-15T08:28Z] 2016-04-15 01:28:50 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:28:50,312 - WARNING - Could not retrieve variants from source file in region 20:60966107-60986209. Error was invalid region `20:60966108-60986209`
[2016-04-15T08:28Z] 2016-04-15 01:28:50 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:28:50,667 - WARNING - Could not retrieve variants from source file in region 20:60881119-60937787. Error was invalid region `20:60881120-60937787`
[2016-04-15T08:28Z] 2016-04-15 01:28:52 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:28:52,232 - WARNING - Could not retrieve variants from source file in region 20:58466886-58467287. Error was invalid region `20:58466887-58467287`
[2016-04-15T08:28Z] 2016-04-15 01:28:52 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:28:52,284 - WARNING - Could not retrieve variants from source file in region 20:58466886-58467287. Error was invalid region `20:58466887-58467287`
[2016-04-15T08:28Z] ['bcbio-variation-recall', 'square', '-Xms750m', '-Xmx7280m', '-XX:+UseSerialGC', '-c', 16, '-r', u'20:62831245-63025520', '--caller', 'platypus', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/20/Batch1-20_62831244_63025520.vcf.gz', '/mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/20/Batch1-20_62831244_63025520.vcf-inputs.txt'] in region: 20:62831245-63025520
[2016-04-15T08:29Z] 2016-04-15 01:29:03 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:29:03,205 - WARNING - Could not retrieve variants from source file in region 20:62839499-62839900. Error was invalid region `20:62839500-62839900`
[2016-04-15T08:29Z] 2016-04-15 01:29:03 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:29:03,201 - WARNING - Could not retrieve variants from source file in region 20:62839499-62839900. Error was invalid region `20:62839500-62839900`
[2016-04-15T08:29Z] 2016-04-15 01:29:03 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:29:03,619 - WARNING - Could not retrieve variants from source file in region 20:62896454-62896855. Error was invalid region `20:62896455-62896855`
[2016-04-15T08:29Z] 2016-04-15 01:29:03 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:29:03,641 - WARNING - Could not retrieve variants from source file in region 20:62871021-62871422. Error was invalid region `20:62871022-62871422`
[2016-04-15T08:29Z] 2016-04-15 01:29:03 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:29:03,690 - WARNING - Could not retrieve variants from source file in region 20:62896454-62896855. Error was invalid region `20:62896455-62896855`
[2016-04-15T08:29Z] ['bcbio-variation-recall', 'square', '-Xms750m', '-Xmx7280m', '-XX:+UseSerialGC', '-c', 16, '-r', u'21:1-15517120', '--caller', 'platypus', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/21/Batch1-21_0_15517120.vcf.gz', '/mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/21/Batch1-21_0_15517120.vcf-inputs.txt'] in region: 21:1-15517120
[2016-04-15T08:29Z] 2016-04-15 01:29:15 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:29:15,178 - WARNING - Could not retrieve variants from source file in region 21:11039133-11058416. Error was invalid region `21:11039134-11058416`
[2016-04-15T08:29Z] 2016-04-15 01:29:15 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:29:15,404 - WARNING - Could not retrieve variants from source file in region 21:10910100-10920288. Error was invalid region `21:10910101-10920288`
[2016-04-15T08:29Z] 2016-04-15 01:29:15 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:29:15,518 - WARNING - Could not retrieve variants from source file in region 21:10910100-10920288. Error was invalid region `21:10910101-10920288`
[2016-04-15T08:29Z] 2016-04-15 01:29:15 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:29:15,616 - WARNING - Could not retrieve variants from source file in region 21:10910100-10920288. Error was invalid region `21:10910101-10920288`
[2016-04-15T08:29Z] 2016-04-15 01:29:15 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:29:15,675 - WARNING - Could not retrieve variants from source file in region 21:11097346-11098918. Error was invalid region `21:11097347-11098918`
[2016-04-15T08:29Z] 2016-04-15 01:29:16 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:29:16,997 - WARNING - Could not retrieve variants from source file in region 21:15481154-15481555. Error was invalid region `21:15481155-15481555`
[2016-04-15T08:29Z] 2016-04-15 01:29:17 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:29:17,067 - WARNING - Could not retrieve variants from source file in region 21:15481154-15481555. Error was invalid region `21:15481155-15481555`
[2016-04-15T08:29Z] 2016-04-15 01:29:17 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:29:17,097 - WARNING - Could not retrieve variants from source file in region 21:15481154-15481555. Error was invalid region `21:15481155-15481555`
[2016-04-15T08:29Z] 2016-04-15 01:29:17 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:29:17,777 - WARNING - Could not retrieve variants from source file in region 21:15516737-15517166. Error was invalid region `21:15516738-15517166`
[2016-04-15T08:29Z] 2016-04-15 01:29:17 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:29:17,899 - WARNING - Could not retrieve variants from source file in region 21:15516737-15517166. Error was invalid region `21:15516738-15517166`
[2016-04-15T08:29Z] ['bcbio-variation-recall', 'square', '-Xms750m', '-Xmx7280m', '-XX:+UseSerialGC', '-c', 16, '-r', u'21:15524894-31045484', '--caller', 'platypus', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/21/Batch1-21_15524893_31045484.vcf.gz', '/mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/21/Batch1-21_15524893_31045484.vcf-inputs.txt'] in region: 21:15524894-31045484
[2016-04-15T08:29Z] 2016-04-15 01:29:35 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:29:35,659 - WARNING - Could not retrieve variants from source file in region 21:15918366-15918767. Error was invalid region `21:15918367-15918767`
[2016-04-15T08:29Z] 2016-04-15 01:29:35 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:29:35,799 - WARNING - Could not retrieve variants from source file in region 21:30714565-30714966. Error was invalid region `21:30714566-30714966`
[2016-04-15T08:29Z] 2016-04-15 01:29:36 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:29:36,106 - WARNING - Could not retrieve variants from source file in region 21:19169007-19169408. Error was invalid region `21:19169008-19169408`
[2016-04-15T08:29Z] 2016-04-15 01:29:36 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:29:36,973 - WARNING - Could not retrieve variants from source file in region 21:19755829-19756230. Error was invalid region `21:19755830-19756230`
[2016-04-15T08:29Z] 2016-04-15 01:29:37 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:29:37,093 - WARNING - Could not retrieve variants from source file in region 21:19669907-19670308. Error was invalid region `21:19669908-19670308`
[2016-04-15T08:29Z] 2016-04-15 01:29:37 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:29:37,164 - WARNING - Could not retrieve variants from source file in region 21:26964937-26979140. Error was invalid region `21:26964938-26979140`
[2016-04-15T08:29Z] 2016-04-15 01:29:37 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:29:37,173 - WARNING - Could not retrieve variants from source file in region 21:22881040-22881441. Error was invalid region `21:22881041-22881441`
[2016-04-15T08:29Z] 2016-04-15 01:29:37 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:29:37,218 - WARNING - Could not retrieve variants from source file in region 21:30481160-30481906. Error was invalid region `21:30481161-30481906`
[2016-04-15T08:29Z] 2016-04-15 01:29:42 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:29:42,123 - WARNING - Could not retrieve variants from source file in region 21:15918366-15918767. Error was invalid region `21:15918367-15918767`
[2016-04-15T08:29Z] 2016-04-15 01:29:43 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:29:43,761 - WARNING - Could not retrieve variants from source file in region 21:19642074-19642475. Error was invalid region `21:19642075-19642475`
[2016-04-15T08:29Z] 2016-04-15 01:29:44 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:29:44,696 - WARNING - Could not retrieve variants from source file in region 21:19755829-19756230. Error was invalid region `21:19755830-19756230`
[2016-04-15T08:29Z] 2016-04-15 01:29:45 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:29:45,072 - WARNING - Could not retrieve variants from source file in region 21:19713610-19714011. Error was invalid region `21:19713611-19714011`
[2016-04-15T08:29Z] 2016-04-15 01:29:45 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:29:45,201 - WARNING - Could not retrieve variants from source file in region 21:26964937-26979140. Error was invalid region `21:26964938-26979140`
[2016-04-15T08:29Z] 2016-04-15 01:29:45 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:29:45,539 - WARNING - Could not retrieve variants from source file in region 21:19669907-19670308. Error was invalid region `21:19669908-19670308`
[2016-04-15T08:29Z] 2016-04-15 01:29:47 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:29:47,381 - WARNING - Could not retrieve variants from source file in region 21:15918366-15918767. Error was invalid region `21:15918367-15918767`
[2016-04-15T08:29Z] 2016-04-15 01:29:48 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:29:48,005 - WARNING - Could not retrieve variants from source file in region 21:15954317-15954850. Error was invalid region `21:15954318-15954850`
[2016-04-15T08:29Z] 2016-04-15 01:29:48 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:29:48,012 - WARNING - Could not retrieve variants from source file in region 21:15558135-15596962. Error was invalid region `21:15558136-15596962`
[2016-04-15T08:29Z] 2016-04-15 01:29:49 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:29:49,808 - WARNING - Could not retrieve variants from source file in region 21:19642074-19642475. Error was invalid region `21:19642075-19642475`
[2016-04-15T08:29Z] 2016-04-15 01:29:50 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:29:50,385 - WARNING - Could not retrieve variants from source file in region 21:19169007-19169408. Error was invalid region `21:19169008-19169408`
[2016-04-15T08:29Z] 2016-04-15 01:29:51 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:29:51,581 - WARNING - Could not retrieve variants from source file in region 21:19713610-19714011. Error was invalid region `21:19713611-19714011`
[2016-04-15T08:29Z] 2016-04-15 01:29:51 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:29:51,946 - WARNING - Could not retrieve variants from source file in region 21:19669907-19670308. Error was invalid region `21:19669908-19670308`
[2016-04-15T08:29Z] 2016-04-15 01:29:52 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:29:52,111 - WARNING - Could not retrieve variants from source file in region 21:26964937-26979140. Error was invalid region `21:26964938-26979140`
[2016-04-15T08:29Z] 2016-04-15 01:29:52 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:29:52,137 - WARNING - Could not retrieve variants from source file in region 21:19755829-19756230. Error was invalid region `21:19755830-19756230`
[2016-04-15T08:30Z] 2016-04-15 01:30:03 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:30:03,356 - WARNING - Could not retrieve variants from source file in region 21:30250344-30257758. Error was invalid region `21:30250345-30257758`
[2016-04-15T08:30Z] 2016-04-15 01:30:04 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:30:04,314 - WARNING - Could not retrieve variants from source file in region 21:30439124-30445964. Error was invalid region `21:30439125-30445964`
[2016-04-15T08:30Z] 2016-04-15 01:30:04 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:30:04,928 - WARNING - Could not retrieve variants from source file in region 21:28212549-28217368. Error was invalid region `21:28212550-28217368`
[2016-04-15T08:30Z] 2016-04-15 01:30:05 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:30:05,064 - WARNING - Could not retrieve variants from source file in region 21:22745976-22758166. Error was invalid region `21:22745977-22758166`
[2016-04-15T08:30Z] 2016-04-15 01:30:06 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:30:06,027 - WARNING - Could not retrieve variants from source file in region 21:27106445-27106846. Error was invalid region `21:27106446-27106846`
[2016-04-15T08:30Z] 2016-04-15 01:30:06 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:30:06,563 - WARNING - Could not retrieve variants from source file in region 21:27056039-27056440. Error was invalid region `21:27056040-27056440`
[2016-04-15T08:30Z] 2016-04-15 01:30:07 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:30:07,849 - WARNING - Could not retrieve variants from source file in region 21:30250344-30257758. Error was invalid region `21:30250345-30257758`
[2016-04-15T08:30Z] 2016-04-15 01:30:08 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:30:08,359 - WARNING - Could not retrieve variants from source file in region 21:28302144-28305402. Error was invalid region `21:28302145-28305402`
[2016-04-15T08:30Z] 2016-04-15 01:30:09 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:30:09,301 - WARNING - Could not retrieve variants from source file in region 21:22745976-22758166. Error was invalid region `21:22745977-22758166`
[2016-04-15T08:30Z] 2016-04-15 01:30:11 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:30:11,243 - WARNING - Could not retrieve variants from source file in region 21:30250344-30257758. Error was invalid region `21:30250345-30257758`
[2016-04-15T08:30Z] 2016-04-15 01:30:12 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:30:12,392 - WARNING - Could not retrieve variants from source file in region 21:28302144-28305402. Error was invalid region `21:28302145-28305402`
[2016-04-15T08:30Z] ['bcbio-variation-recall', 'square', '-Xms750m', '-Xmx7280m', '-XX:+UseSerialGC', '-c', 16, '-r', u'21:31062048-46591599', '--caller', 'platypus', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/21/Batch1-21_31062047_46591599.vcf.gz', '/mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/21/Batch1-21_31062047_46591599.vcf-inputs.txt'] in region: 21:31062048-46591599
[2016-04-15T08:30Z] 2016-04-15 01:30:28 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:30:28,119 - WARNING - Could not retrieve variants from source file in region 21:41032529-41032994. Error was invalid region `21:41032530-41032994`
[2016-04-15T08:30Z] 2016-04-15 01:30:30 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:30:30,012 - WARNING - Could not retrieve variants from source file in region 21:45844540-45844941. Error was invalid region `21:45844541-45844941`
[2016-04-15T08:30Z] 2016-04-15 01:30:30 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:30:30,067 - WARNING - Could not retrieve variants from source file in region 21:43639121-43640256. Error was invalid region `21:43639122-43640256`
[2016-04-15T08:30Z] 2016-04-15 01:30:30 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:30:30,107 - WARNING - Could not retrieve variants from source file in region 21:44480405-44480806. Error was invalid region `21:44480406-44480806`
[2016-04-15T08:30Z] 2016-04-15 01:30:30 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:30:30,199 - WARNING - Could not retrieve variants from source file in region 21:41137288-41137697. Error was invalid region `21:41137289-41137697`
[2016-04-15T08:30Z] 2016-04-15 01:30:30 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:30:30,545 - WARNING - Could not retrieve variants from source file in region 21:43985744-43996144. Error was invalid region `21:43985745-43996144`
[2016-04-15T08:30Z] 2016-04-15 01:30:30 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:30:30,978 - WARNING - Could not retrieve variants from source file in region 21:41165251-41165652. Error was invalid region `21:41165252-41165652`
[2016-04-15T08:30Z] 2016-04-15 01:30:31 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:30:31,533 - WARNING - Could not retrieve variants from source file in region 21:39870099-39870500. Error was invalid region `21:39870100-39870500`
[2016-04-15T08:30Z] 2016-04-15 01:30:31 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:30:31,538 - WARNING - Could not retrieve variants from source file in region 21:41465453-41465854. Error was invalid region `21:41465454-41465854`
[2016-04-15T08:30Z] 2016-04-15 01:30:31 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:30:31,598 - WARNING - Could not retrieve variants from source file in region 21:42812680-42845573. Error was invalid region `21:42812681-42845573`
[2016-04-15T08:30Z] 2016-04-15 01:30:32 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:30:32,874 - WARNING - Could not retrieve variants from source file in region 21:41032529-41032994. Error was invalid region `21:41032530-41032994`
[2016-04-15T08:30Z] 2016-04-15 01:30:33 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:30:33,562 - WARNING - Could not retrieve variants from source file in region 21:46396448-46396849. Error was invalid region `21:46396449-46396849`
[2016-04-15T08:30Z] 2016-04-15 01:30:36 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:30:36,171 - WARNING - Could not retrieve variants from source file in region 21:45844540-45844941. Error was invalid region `21:45844541-45844941`
[2016-04-15T08:30Z] 2016-04-15 01:30:37 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:30:37,422 - WARNING - Could not retrieve variants from source file in region 21:44480405-44480806. Error was invalid region `21:44480406-44480806`
[2016-04-15T08:30Z] 2016-04-15 01:30:37 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:30:37,887 - WARNING - Could not retrieve variants from source file in region 21:41137288-41137697. Error was invalid region `21:41137289-41137697`
[2016-04-15T08:30Z] 2016-04-15 01:30:37 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:30:37,900 - WARNING - Could not retrieve variants from source file in region 21:43639121-43640256. Error was invalid region `21:43639122-43640256`
[2016-04-15T08:30Z] 2016-04-15 01:30:38 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:30:38,579 - WARNING - Could not retrieve variants from source file in region 21:37661194-37664691. Error was invalid region `21:37661195-37664691`
[2016-04-15T08:30Z] 2016-04-15 01:30:39 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:30:39,202 - WARNING - Could not retrieve variants from source file in region 21:45217348-45217749. Error was invalid region `21:45217349-45217749`
[2016-04-15T08:30Z] 2016-04-15 01:30:39 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:30:39,509 - WARNING - Could not retrieve variants from source file in region 21:43985744-43996144. Error was invalid region `21:43985745-43996144`
[2016-04-15T08:30Z] 2016-04-15 01:30:39 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:30:39,528 - WARNING - Could not retrieve variants from source file in region 21:41165251-41165652. Error was invalid region `21:41165252-41165652`
[2016-04-15T08:30Z] 2016-04-15 01:30:39 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:30:39,943 - WARNING - Could not retrieve variants from source file in region 21:40651931-40670650. Error was invalid region `21:40651932-40670650`
[2016-04-15T08:30Z] 2016-04-15 01:30:40 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:30:40,399 - WARNING - Could not retrieve variants from source file in region 21:39870099-39870500. Error was invalid region `21:39870100-39870500`
[2016-04-15T08:30Z] 2016-04-15 01:30:40 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:30:40,412 - WARNING - Could not retrieve variants from source file in region 21:41032529-41032994. Error was invalid region `21:41032530-41032994`
[2016-04-15T08:30Z] 2016-04-15 01:30:40 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:30:40,468 - WARNING - Could not retrieve variants from source file in region 21:35169598-35169999. Error was invalid region `21:35169599-35169999`
[2016-04-15T08:30Z] 2016-04-15 01:30:41 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:30:41,000 - WARNING - Could not retrieve variants from source file in region 21:45844540-45844941. Error was invalid region `21:45844541-45844941`
[2016-04-15T08:30Z] 2016-04-15 01:30:42 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:30:42,817 - WARNING - Could not retrieve variants from source file in region 21:44480405-44480806. Error was invalid region `21:44480406-44480806`
[2016-04-15T08:30Z] 2016-04-15 01:30:43 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:30:43,269 - WARNING - Could not retrieve variants from source file in region 21:41137288-41137697. Error was invalid region `21:41137289-41137697`
[2016-04-15T08:30Z] 2016-04-15 01:30:43 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:30:43,332 - WARNING - Could not retrieve variants from source file in region 21:43639121-43640256. Error was invalid region `21:43639122-43640256`
[2016-04-15T08:30Z] 2016-04-15 01:30:47 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:30:47,254 - WARNING - Could not retrieve variants from source file in region 21:41165251-41165652. Error was invalid region `21:41165252-41165652`
[2016-04-15T08:30Z] 2016-04-15 01:30:47 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:30:47,292 - WARNING - Could not retrieve variants from source file in region 21:43985744-43996144. Error was invalid region `21:43985745-43996144`
[2016-04-15T08:30Z] 2016-04-15 01:30:47 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:30:47,458 - WARNING - Could not retrieve variants from source file in region 21:41465453-41465854. Error was invalid region `21:41465454-41465854`
[2016-04-15T08:30Z] 2016-04-15 01:30:49 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:30:49,053 - WARNING - Could not retrieve variants from source file in region 21:39870099-39870500. Error was invalid region `21:39870100-39870500`
[2016-04-15T08:30Z] 2016-04-15 01:30:49 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:30:49,285 - WARNING - Could not retrieve variants from source file in region 21:35169598-35169999. Error was invalid region `21:35169599-35169999`
[2016-04-15T08:30Z] 2016-04-15 01:30:49 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:30:49,427 - WARNING - Could not retrieve variants from source file in region 21:40651931-40670650. Error was invalid region `21:40651932-40670650`
[2016-04-15T08:30Z] 2016-04-15 01:30:58 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:30:58,262 - WARNING - Could not retrieve variants from source file in region 21:45811132-45811533. Error was invalid region `21:45811133-45811533`
[2016-04-15T08:30Z] 2016-04-15 01:30:59 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:30:59,511 - WARNING - Could not retrieve variants from source file in region 21:44430114-44430515. Error was invalid region `21:44430115-44430515`
[2016-04-15T08:30Z] 2016-04-15 01:30:59 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:30:59,565 - WARNING - Could not retrieve variants from source file in region 21:43326956-43328046. Error was invalid region `21:43326957-43328046`
[2016-04-15T08:31Z] 2016-04-15 01:31:01 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:31:01,905 - WARNING - Could not retrieve variants from source file in region 21:36080079-36080480. Error was invalid region `21:36080080-36080480`
[2016-04-15T08:31Z] 2016-04-15 01:31:02 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:31:02,546 - WARNING - Could not retrieve variants from source file in region 21:43895941-43906077. Error was invalid region `21:43895942-43906077`
[2016-04-15T08:31Z] 2016-04-15 01:31:03 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:31:03,238 - WARNING - Could not retrieve variants from source file in region 21:35821610-35822011. Error was invalid region `21:35821611-35822011`
[2016-04-15T08:31Z] 2016-04-15 01:31:04 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:31:04,435 - WARNING - Could not retrieve variants from source file in region 21:39751744-39753565. Error was invalid region `21:39751745-39753565`
[2016-04-15T08:31Z] 2016-04-15 01:31:05 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:31:05,067 - WARNING - Could not retrieve variants from source file in region 21:42717451-42717852. Error was invalid region `21:42717452-42717852`
[2016-04-15T08:31Z] 2016-04-15 01:31:05 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:31:05,982 - WARNING - Could not retrieve variants from source file in region 21:40871599-40883861. Error was invalid region `21:40871600-40883861`
[2016-04-15T08:31Z] 2016-04-15 01:31:06 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:31:06,402 - WARNING - Could not retrieve variants from source file in region 21:44430114-44430515. Error was invalid region `21:44430115-44430515`
[2016-04-15T08:31Z] 2016-04-15 01:31:07 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:31:07,234 - WARNING - Could not retrieve variants from source file in region 21:46191189-46191590. Error was invalid region `21:46191190-46191590`
[2016-04-15T08:31Z] 2016-04-15 01:31:08 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:31:08,464 - WARNING - Could not retrieve variants from source file in region 21:35821610-35822011. Error was invalid region `21:35821611-35822011`
[2016-04-15T08:31Z] 2016-04-15 01:31:10 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:31:10,820 - WARNING - Could not retrieve variants from source file in region 21:45811132-45811533. Error was invalid region `21:45811133-45811533`
[2016-04-15T08:31Z] 2016-04-15 01:31:11 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:31:11,348 - WARNING - Could not retrieve variants from source file in region 21:42717451-42717852. Error was invalid region `21:42717452-42717852`
[2016-04-15T08:31Z] 2016-04-15 01:31:13 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:31:13,052 - WARNING - Could not retrieve variants from source file in region 21:40871599-40883861. Error was invalid region `21:40871600-40883861`
[2016-04-15T08:31Z] 2016-04-15 01:31:13 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:31:13,534 - WARNING - Could not retrieve variants from source file in region 21:44430114-44430515. Error was invalid region `21:44430115-44430515`
[2016-04-15T08:31Z] 2016-04-15 01:31:13 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:31:13,861 - WARNING - Could not retrieve variants from source file in region 21:37609360-37634068. Error was invalid region `21:37609361-37634068`
[2016-04-15T08:31Z] 2016-04-15 01:31:13 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:31:13,935 - WARNING - Could not retrieve variants from source file in region 21:43895941-43906077. Error was invalid region `21:43895942-43906077`
[2016-04-15T08:31Z] 2016-04-15 01:31:13 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:31:13,937 - WARNING - Could not retrieve variants from source file in region 21:35821610-35822011. Error was invalid region `21:35821611-35822011`
[2016-04-15T08:31Z] 2016-04-15 01:31:16 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:31:16,727 - WARNING - Could not retrieve variants from source file in region 21:42717451-42717852. Error was invalid region `21:42717452-42717852`
[2016-04-15T08:31Z] 2016-04-15 01:31:19 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:31:19,339 - WARNING - Could not retrieve variants from source file in region 21:34896691-34945911. Error was invalid region `21:34896692-34945911`
[2016-04-15T08:31Z] 2016-04-15 01:31:30 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:31:30,677 - WARNING - Could not retrieve variants from source file in region 21:36041767-36042774. Error was invalid region `21:36041768-36042774`
[2016-04-15T08:31Z] 2016-04-15 01:31:31 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:31:31,739 - WARNING - Could not retrieve variants from source file in region 21:35467434-35475804. Error was invalid region `21:35467435-35475804`
[2016-04-15T08:31Z] 2016-04-15 01:31:33 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:31:33,328 - WARNING - Could not retrieve variants from source file in region 21:39671265-39671666. Error was invalid region `21:39671266-39671666`
[2016-04-15T08:31Z] 2016-04-15 01:31:34 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:31:34,120 - WARNING - Could not retrieve variants from source file in region 21:45095995-45107866. Error was invalid region `21:45095996-45107866`
[2016-04-15T08:31Z] 2016-04-15 01:31:34 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:31:34,990 - WARNING - Could not retrieve variants from source file in region 21:34787101-34787502. Error was invalid region `21:34787102-34787502`
[2016-04-15T08:31Z] 2016-04-15 01:31:36 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:31:36,756 - WARNING - Could not retrieve variants from source file in region 21:43852021-43863711. Error was invalid region `21:43852022-43863711`
[2016-04-15T08:31Z] 2016-04-15 01:31:38 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:31:38,115 - WARNING - Could not retrieve variants from source file in region 21:42622575-42622976. Error was invalid region `21:42622576-42622976`
[2016-04-15T08:31Z] 2016-04-15 01:31:41 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:31:41,135 - WARNING - Could not retrieve variants from source file in region 21:34787101-34787502. Error was invalid region `21:34787102-34787502`
[2016-04-15T08:31Z] 2016-04-15 01:31:42 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:31:42,971 - WARNING - Could not retrieve variants from source file in region 21:42622575-42622976. Error was invalid region `21:42622576-42622976`
[2016-04-15T08:31Z] 2016-04-15 01:31:47 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:31:47,037 - WARNING - Could not retrieve variants from source file in region 21:34787101-34787502. Error was invalid region `21:34787102-34787502`
[2016-04-15T08:31Z] 2016-04-15 01:31:49 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:31:49,060 - WARNING - Could not retrieve variants from source file in region 21:45646991-45670960. Error was invalid region `21:45646992-45670960`
[2016-04-15T08:31Z] 2016-04-15 01:31:57 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:31:57,750 - WARNING - Could not retrieve variants from source file in region 21:45603694-45604095. Error was invalid region `21:45603695-45604095`
[2016-04-15T08:31Z] 2016-04-15 01:31:58 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:31:58,749 - WARNING - Could not retrieve variants from source file in region 21:39086754-39087155. Error was invalid region `21:39086755-39087155`
[2016-04-15T08:31Z] 2016-04-15 01:31:59 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:31:59,054 - WARNING - Could not retrieve variants from source file in region 21:44180232-44189362. Error was invalid region `21:44180233-44189362`
[2016-04-15T08:31Z] 2016-04-15 01:31:59 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:31:59,983 - WARNING - Could not retrieve variants from source file in region 21:44837340-44846206. Error was invalid region `21:44837341-44846206`
[2016-04-15T08:32Z] 2016-04-15 01:32:02 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:32:02,537 - WARNING - Could not retrieve variants from source file in region 21:35237397-35260734. Error was invalid region `21:35237398-35260734`
[2016-04-15T08:32Z] 2016-04-15 01:32:02 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:32:02,570 - WARNING - Could not retrieve variants from source file in region 21:45603694-45604095. Error was invalid region `21:45603695-45604095`
[2016-04-15T08:32Z] 2016-04-15 01:32:03 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:32:03,513 - WARNING - Could not retrieve variants from source file in region 21:43770072-43770473. Error was invalid region `21:43770073-43770473`
[2016-04-15T08:32Z] 2016-04-15 01:32:03 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:32:03,551 - WARNING - Could not retrieve variants from source file in region 21:38877551-38877952. Error was invalid region `21:38877552-38877952`
[2016-04-15T08:32Z] 2016-04-15 01:32:04 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:32:04,003 - WARNING - Could not retrieve variants from source file in region 21:39086754-39087155. Error was invalid region `21:39086755-39087155`
[2016-04-15T08:32Z] 2016-04-15 01:32:05 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:32:05,534 - WARNING - Could not retrieve variants from source file in region 21:37415555-37444408. Error was invalid region `21:37415556-37444408`
[2016-04-15T08:32Z] 2016-04-15 01:32:07 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:32:07,963 - WARNING - Could not retrieve variants from source file in region 21:45603694-45604095. Error was invalid region `21:45603695-45604095`
[2016-04-15T08:32Z] 2016-04-15 01:32:08 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:32:08,645 - WARNING - Could not retrieve variants from source file in region 21:43770072-43770473. Error was invalid region `21:43770073-43770473`
[2016-04-15T08:32Z] 2016-04-15 01:32:09 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:32:09,398 - WARNING - Could not retrieve variants from source file in region 21:39086754-39087155. Error was invalid region `21:39086755-39087155`
[2016-04-15T08:32Z] 2016-04-15 01:32:09 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:32:09,399 - WARNING - Could not retrieve variants from source file in region 21:44144527-44144928. Error was invalid region `21:44144528-44144928`
[2016-04-15T08:32Z] 2016-04-15 01:32:10 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:32:10,429 - WARNING - Could not retrieve variants from source file in region 21:43795685-43824326. Error was invalid region `21:43795686-43824326`
[2016-04-15T08:32Z] 2016-04-15 01:32:13 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:32:13,826 - WARNING - Could not retrieve variants from source file in region 21:43770072-43770473. Error was invalid region `21:43770073-43770473`
[2016-04-15T08:32Z] 2016-04-15 01:32:14 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:32:14,712 - WARNING - Could not retrieve variants from source file in region 21:44144527-44144928. Error was invalid region `21:44144528-44144928`
[2016-04-15T08:32Z] 2016-04-15 01:32:16 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:32:16,838 - WARNING - Could not retrieve variants from source file in region 21:45482589-45565663. Error was invalid region `21:45482590-45565663`
[2016-04-15T08:32Z] 2016-04-15 01:32:18 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:32:18,280 - WARNING - Could not retrieve variants from source file in region 21:45482589-45565663. Error was invalid region `21:45482590-45565663`
[2016-04-15T08:32Z] 2016-04-15 01:32:21 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:32:21,011 - WARNING - Could not retrieve variants from source file in region 21:44589004-44589405. Error was invalid region `21:44589005-44589405`
[2016-04-15T08:32Z] 2016-04-15 01:32:21 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:32:21,612 - WARNING - Could not retrieve variants from source file in region 21:36259328-36260812. Error was invalid region `21:36259329-36260812`
[2016-04-15T08:32Z] 2016-04-15 01:32:22 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:32:22,943 - WARNING - Could not retrieve variants from source file in region 21:38997490-38997891. Error was invalid region `21:38997491-38997891`
[2016-04-15T08:32Z] 2016-04-15 01:32:24 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:32:24,803 - WARNING - Could not retrieve variants from source file in region 21:36193660-36194061. Error was invalid region `21:36193661-36194061`
[2016-04-15T08:32Z] 2016-04-15 01:32:25 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:32:25,671 - WARNING - Could not retrieve variants from source file in region 21:44589004-44589405. Error was invalid region `21:44589005-44589405`
[2016-04-15T08:32Z] 2016-04-15 01:32:27 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:32:27,277 - WARNING - Could not retrieve variants from source file in region 21:34442945-34443346. Error was invalid region `21:34442946-34443346`
[2016-04-15T08:32Z] 2016-04-15 01:32:27 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:32:27,395 - WARNING - Could not retrieve variants from source file in region 21:44589004-44589405. Error was invalid region `21:44589005-44589405`
[2016-04-15T08:32Z] 2016-04-15 01:32:27 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:32:27,847 - WARNING - Could not retrieve variants from source file in region 21:38997490-38997891. Error was invalid region `21:38997491-38997891`
[2016-04-15T08:32Z] 2016-04-15 01:32:27 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:32:27,885 - WARNING - Could not retrieve variants from source file in region 21:31869075-31869476. Error was invalid region `21:31869076-31869476`
[2016-04-15T08:32Z] 2016-04-15 01:32:28 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:32:28,057 - WARNING - Could not retrieve variants from source file in region 21:34399190-34399591. Error was invalid region `21:34399191-34399591`
[2016-04-15T08:32Z] 2016-04-15 01:32:29 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:32:29,128 - WARNING - Could not retrieve variants from source file in region 21:44109790-44110193. Error was invalid region `21:44109791-44110193`
[2016-04-15T08:32Z] 2016-04-15 01:32:29 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:32:29,432 - WARNING - Could not retrieve variants from source file in region 21:34442945-34443346. Error was invalid region `21:34442946-34443346`
[2016-04-15T08:32Z] 2016-04-15 01:32:29 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:32:29,627 - WARNING - Could not retrieve variants from source file in region 21:36193660-36194061. Error was invalid region `21:36193661-36194061`
[2016-04-15T08:32Z] 2016-04-15 01:32:32 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:32:32,179 - WARNING - Could not retrieve variants from source file in region 21:33367977-33371313. Error was invalid region `21:33367978-33371313`
[2016-04-15T08:32Z] 2016-04-15 01:32:32 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:32:32,532 - WARNING - Could not retrieve variants from source file in region 21:31869075-31869476. Error was invalid region `21:31869076-31869476`
[2016-04-15T08:32Z] 2016-04-15 01:32:33 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:32:33,238 - WARNING - Could not retrieve variants from source file in region 21:38444652-38455789. Error was invalid region `21:38444653-38455789`
[2016-04-15T08:32Z] 2016-04-15 01:32:33 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:32:33,255 - WARNING - Could not retrieve variants from source file in region 21:34399190-34399591. Error was invalid region `21:34399191-34399591`
[2016-04-15T08:32Z] 2016-04-15 01:32:33 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:32:33,352 - WARNING - Could not retrieve variants from source file in region 21:38997490-38997891. Error was invalid region `21:38997491-38997891`
[2016-04-15T08:32Z] 2016-04-15 01:32:34 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:32:34,177 - WARNING - Could not retrieve variants from source file in region 21:44109790-44110193. Error was invalid region `21:44109791-44110193`
[2016-04-15T08:32Z] 2016-04-15 01:32:34 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:32:34,373 - WARNING - Could not retrieve variants from source file in region 21:36193660-36194061. Error was invalid region `21:36193661-36194061`
[2016-04-15T08:32Z] 2016-04-15 01:32:36 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:32:36,295 - WARNING - Could not retrieve variants from source file in region 21:38308700-38320197. Error was invalid region `21:38308701-38320197`
[2016-04-15T08:32Z] 2016-04-15 01:32:37 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:32:37,905 - WARNING - Could not retrieve variants from source file in region 21:38444652-38455789. Error was invalid region `21:38444653-38455789`
[2016-04-15T08:32Z] 2016-04-15 01:32:38 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:32:38,215 - WARNING - Could not retrieve variants from source file in region 21:34399190-34399591. Error was invalid region `21:34399191-34399591`
[2016-04-15T08:32Z] 2016-04-15 01:32:40 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:32:40,350 - WARNING - Could not retrieve variants from source file in region 21:33950857-33956769. Error was invalid region `21:33950858-33956769`
[2016-04-15T08:32Z] 2016-04-15 01:32:42 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:32:42,567 - WARNING - Could not retrieve variants from source file in region 21:34165979-34166533. Error was invalid region `21:34165980-34166533`
[2016-04-15T08:32Z] 2016-04-15 01:32:42 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:32:42,662 - WARNING - Could not retrieve variants from source file in region 21:33950857-33956769. Error was invalid region `21:33950858-33956769`
[2016-04-15T08:32Z] 2016-04-15 01:32:43 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:32:43,430 - WARNING - Could not retrieve variants from source file in region 21:33950857-33956769. Error was invalid region `21:33950858-33956769`
[2016-04-15T08:32Z] 2016-04-15 01:32:45 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:32:45,413 - WARNING - Could not retrieve variants from source file in region 21:31709480-31709881. Error was invalid region `21:31709481-31709881`
[2016-04-15T08:32Z] 2016-04-15 01:32:47 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:32:47,086 - WARNING - Could not retrieve variants from source file in region 21:33886920-33887321. Error was invalid region `21:33886921-33887321`
[2016-04-15T08:32Z] 2016-04-15 01:32:47 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:32:47,668 - WARNING - Could not retrieve variants from source file in region 21:34165979-34166533. Error was invalid region `21:34165980-34166533`
[2016-04-15T08:32Z] 2016-04-15 01:32:47 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:32:47,938 - WARNING - Could not retrieve variants from source file in region 21:37833096-37833941. Error was invalid region `21:37833097-37833941`
[2016-04-15T08:32Z] 2016-04-15 01:32:47 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:32:47,942 - WARNING - Could not retrieve variants from source file in region 21:32201611-32202160. Error was invalid region `21:32201612-32202160`
[2016-04-15T08:32Z] 2016-04-15 01:32:48 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:32:48,258 - WARNING - Could not retrieve variants from source file in region 21:37833096-37833941. Error was invalid region `21:37833097-37833941`
[2016-04-15T08:32Z] 2016-04-15 01:32:48 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:32:48,560 - WARNING - Could not retrieve variants from source file in region 21:31973305-31973706. Error was invalid region `21:31973306-31973706`
[2016-04-15T08:32Z] 2016-04-15 01:32:50 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:32:50,103 - WARNING - Could not retrieve variants from source file in region 21:31802557-31812962. Error was invalid region `21:31802558-31812962`
[2016-04-15T08:32Z] 2016-04-15 01:32:51 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:32:51,791 - WARNING - Could not retrieve variants from source file in region 21:33886920-33887321. Error was invalid region `21:33886921-33887321`
[2016-04-15T08:32Z] 2016-04-15 01:32:52 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:32:52,800 - WARNING - Could not retrieve variants from source file in region 21:34165979-34166533. Error was invalid region `21:34165980-34166533`
[2016-04-15T08:32Z] 2016-04-15 01:32:53 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:32:53,266 - WARNING - Could not retrieve variants from source file in region 21:31913770-31914190. Error was invalid region `21:31913771-31914190`
[2016-04-15T08:32Z] 2016-04-15 01:32:53 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:32:53,354 - WARNING - Could not retrieve variants from source file in region 21:31655001-31661881. Error was invalid region `21:31655002-31661881`
[2016-04-15T08:32Z] 2016-04-15 01:32:53 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:32:53,860 - WARNING - Could not retrieve variants from source file in region 21:31709480-31709881. Error was invalid region `21:31709481-31709881`
[2016-04-15T08:32Z] 2016-04-15 01:32:53 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:32:53,919 - WARNING - Could not retrieve variants from source file in region 21:31973305-31973706. Error was invalid region `21:31973306-31973706`
[2016-04-15T08:32Z] 2016-04-15 01:32:54 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:32:54,035 - WARNING - Could not retrieve variants from source file in region 21:33044167-33074823. Error was invalid region `21:33044168-33074823`
[2016-04-15T08:32Z] 2016-04-15 01:32:55 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:32:55,043 - WARNING - Could not retrieve variants from source file in region 21:37741718-37760147. Error was invalid region `21:37741719-37760147`
[2016-04-15T08:32Z] 2016-04-15 01:32:55 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:32:55,049 - WARNING - Could not retrieve variants from source file in region 21:31802557-31812962. Error was invalid region `21:31802558-31812962`
[2016-04-15T08:32Z] 2016-04-15 01:32:55 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:32:55,661 - WARNING - Could not retrieve variants from source file in region 21:34003717-34011602. Error was invalid region `21:34003718-34011602`
[2016-04-15T08:32Z] 2016-04-15 01:32:56 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:32:56,129 - WARNING - Could not retrieve variants from source file in region 21:33886920-33887321. Error was invalid region `21:33886921-33887321`
[2016-04-15T08:32Z] 2016-04-15 01:32:58 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:32:58,709 - WARNING - Could not retrieve variants from source file in region 21:32201611-32202160. Error was invalid region `21:32201612-32202160`
[2016-04-15T08:32Z] 2016-04-15 01:32:58 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:32:58,751 - WARNING - Could not retrieve variants from source file in region 21:34003717-34011602. Error was invalid region `21:34003718-34011602`
[2016-04-15T08:32Z] 2016-04-15 01:32:58 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:32:58,866 - WARNING - Could not retrieve variants from source file in region 21:31913770-31914190. Error was invalid region `21:31913771-31914190`
[2016-04-15T08:32Z] 2016-04-15 01:32:59 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:32:59,256 - WARNING - Could not retrieve variants from source file in region 21:31973305-31973706. Error was invalid region `21:31973306-31973706`
[2016-04-15T08:32Z] 2016-04-15 01:32:59 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:32:59,342 - WARNING - Could not retrieve variants from source file in region 21:33044167-33074823. Error was invalid region `21:33044168-33074823`
[2016-04-15T08:33Z] 2016-04-15 01:33:07 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:33:07,804 - WARNING - Could not retrieve variants from source file in region 21:31587582-31587983. Error was invalid region `21:31587583-31587983`
[2016-04-15T08:33Z] 2016-04-15 01:33:09 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:33:09,783 - WARNING - Could not retrieve variants from source file in region 21:32492820-32493221. Error was invalid region `21:32492821-32493221`
[2016-04-15T08:33Z] ['bcbio-variation-recall', 'square', '-Xms750m', '-Xmx7280m', '-XX:+UseSerialGC', '-c', 16, '-r', u'21:46595645-48129895', '--caller', 'platypus', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/21/Batch1-21_46595644_48129895.vcf.gz', '/mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/21/Batch1-21_46595644_48129895.vcf-inputs.txt'] in region: 21:46595645-48129895
[2016-04-15T08:33Z] 2016-04-15 01:33:25 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:33:25,462 - WARNING - Could not retrieve variants from source file in region 21:47410720-47423826. Error was invalid region `21:47410721-47423826`
[2016-04-15T08:33Z] 2016-04-15 01:33:25 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:33:25,606 - WARNING - Could not retrieve variants from source file in region 21:47329141-47329542. Error was invalid region `21:47329142-47329542`
[2016-04-15T08:33Z] 2016-04-15 01:33:26 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:33:26,164 - WARNING - Could not retrieve variants from source file in region 21:48022019-48022420. Error was invalid region `21:48022020-48022420`
[2016-04-15T08:33Z] 2016-04-15 01:33:26 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:33:26,369 - WARNING - Could not retrieve variants from source file in region 21:48063265-48079653. Error was invalid region `21:48063266-48079653`
[2016-04-15T08:33Z] 2016-04-15 01:33:26 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:33:26,876 - WARNING - Could not retrieve variants from source file in region 21:46641757-46645180. Error was invalid region `21:46641758-46645180`
[2016-04-15T08:33Z] 2016-04-15 01:33:32 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:33:32,395 - WARNING - Could not retrieve variants from source file in region 21:47329141-47329542. Error was invalid region `21:47329142-47329542`
[2016-04-15T08:33Z] 2016-04-15 01:33:33 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:33:33,757 - WARNING - Could not retrieve variants from source file in region 21:47910312-47910713. Error was invalid region `21:47910313-47910713`
[2016-04-15T08:33Z] 2016-04-15 01:33:34 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:33:34,370 - WARNING - Could not retrieve variants from source file in region 21:48022019-48022420. Error was invalid region `21:48022020-48022420`
[2016-04-15T08:33Z] 2016-04-15 01:33:34 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:33:34,512 - WARNING - Could not retrieve variants from source file in region 21:47676500-47745093. Error was invalid region `21:47676501-47745093`
[2016-04-15T08:33Z] 2016-04-15 01:33:36 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:33:36,682 - WARNING - Could not retrieve variants from source file in region 21:47329141-47329542. Error was invalid region `21:47329142-47329542`
[2016-04-15T08:33Z] 2016-04-15 01:33:39 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:33:39,668 - WARNING - Could not retrieve variants from source file in region 21:48022019-48022420. Error was invalid region `21:48022020-48022420`
[2016-04-15T08:33Z] ['bcbio-variation-recall', 'square', '-Xms750m', '-Xmx7280m', '-XX:+UseSerialGC', '-c', 16, '-r', u'22:1-16258303', '--caller', 'platypus', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/22/Batch1-22_0_16258303.vcf.gz', '/mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/22/Batch1-22_0_16258303.vcf-inputs.txt'] in region: 22:1-16258303
[2016-04-15T08:33Z] ['bcbio-variation-recall', 'square', '-Xms750m', '-Xmx7280m', '-XX:+UseSerialGC', '-c', 16, '-r', u'22:16266929-31795711', '--caller', 'platypus', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/22/Batch1-22_16266928_31795711.vcf.gz', '/mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/22/Batch1-22_16266928_31795711.vcf-inputs.txt'] in region: 22:16266929-31795711
[2016-04-15T08:33Z] 2016-04-15 01:33:59 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:33:59,605 - WARNING - Could not retrieve variants from source file in region 22:29656178-29656621. Error was invalid region `22:29656179-29656621`
[2016-04-15T08:33Z] 2016-04-15 01:33:59 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:33:59,601 - WARNING - Could not retrieve variants from source file in region 22:24459227-24459628. Error was invalid region `22:24459228-24459628`
[2016-04-15T08:33Z] 2016-04-15 01:33:59 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:33:59,728 - WARNING - Could not retrieve variants from source file in region 22:28194722-28195123. Error was invalid region `22:28194723-28195123`
[2016-04-15T08:34Z] 2016-04-15 01:34:00 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:34:00,446 - WARNING - Could not retrieve variants from source file in region 22:27021246-27021647. Error was invalid region `22:27021247-27021647`
[2016-04-15T08:34Z] 2016-04-15 01:34:01 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:34:01,142 - WARNING - Could not retrieve variants from source file in region 22:18300029-18301883. Error was invalid region `22:18300030-18301883`
[2016-04-15T08:34Z] 2016-04-15 01:34:01 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:34:01,604 - WARNING - Could not retrieve variants from source file in region 22:19833715-19837765. Error was invalid region `22:19833716-19837765`
[2016-04-15T08:34Z] 2016-04-15 01:34:01 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:34:01,625 - WARNING - Could not retrieve variants from source file in region 22:31737225-31737626. Error was invalid region `22:31737226-31737626`
[2016-04-15T08:34Z] 2016-04-15 01:34:01 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:34:01,643 - WARNING - Could not retrieve variants from source file in region 22:22841995-22899424. Error was invalid region `22:22841996-22899424`
[2016-04-15T08:34Z] 2016-04-15 01:34:01 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:34:01,708 - WARNING - Could not retrieve variants from source file in region 22:30987650-31033110. Error was invalid region `22:30987651-31033110`
[2016-04-15T08:34Z] 2016-04-15 01:34:05 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:34:05,063 - WARNING - Could not retrieve variants from source file in region 22:29703914-29728076. Error was invalid region `22:29703915-29728076`
[2016-04-15T08:34Z] 2016-04-15 01:34:06 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:34:06,961 - WARNING - Could not retrieve variants from source file in region 22:24459227-24459628. Error was invalid region `22:24459228-24459628`
[2016-04-15T08:34Z] 2016-04-15 01:34:08 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:34:08,643 - WARNING - Could not retrieve variants from source file in region 22:26159078-26194235. Error was invalid region `22:26159079-26194235`
[2016-04-15T08:34Z] 2016-04-15 01:34:09 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:34:09,161 - WARNING - Could not retrieve variants from source file in region 22:27021246-27021647. Error was invalid region `22:27021247-27021647`
[2016-04-15T08:34Z] 2016-04-15 01:34:09 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:34:09,308 - WARNING - Could not retrieve variants from source file in region 22:26853694-26906279. Error was invalid region `22:26853695-26906279`
[2016-04-15T08:34Z] 2016-04-15 01:34:09 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:34:09,486 - WARNING - Could not retrieve variants from source file in region 22:23964071-23974390. Error was invalid region `22:23964072-23974390`
[2016-04-15T08:34Z] 2016-04-15 01:34:09 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:34:09,769 - WARNING - Could not retrieve variants from source file in region 22:30987650-31033110. Error was invalid region `22:30987651-31033110`
[2016-04-15T08:34Z] 2016-04-15 01:34:10 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:34:10,543 - WARNING - Could not retrieve variants from source file in region 22:18300029-18301883. Error was invalid region `22:18300030-18301883`
[2016-04-15T08:34Z] 2016-04-15 01:34:11 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:34:11,958 - WARNING - Could not retrieve variants from source file in region 22:24459227-24459628. Error was invalid region `22:24459228-24459628`
[2016-04-15T08:34Z] 2016-04-15 01:34:15 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:34:15,976 - WARNING - Could not retrieve variants from source file in region 22:27021246-27021647. Error was invalid region `22:27021247-27021647`
[2016-04-15T08:34Z] 2016-04-15 01:34:16 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:34:16,897 - WARNING - Could not retrieve variants from source file in region 22:19833715-19837765. Error was invalid region `22:19833716-19837765`
[2016-04-15T08:34Z] 2016-04-15 01:34:17 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:34:17,349 - WARNING - Could not retrieve variants from source file in region 22:23964071-23974390. Error was invalid region `22:23964072-23974390`
[2016-04-15T08:34Z] 2016-04-15 01:34:17 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:34:17,505 - WARNING - Could not retrieve variants from source file in region 22:30987650-31033110. Error was invalid region `22:30987651-31033110`
[2016-04-15T08:34Z] 2016-04-15 01:34:17 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:34:17,524 - WARNING - Could not retrieve variants from source file in region 22:29446400-29469320. Error was invalid region `22:29446401-29469320`
[2016-04-15T08:34Z] 2016-04-15 01:34:17 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:34:17,718 - WARNING - Could not retrieve variants from source file in region 22:18300029-18301883. Error was invalid region `22:18300030-18301883`
[2016-04-15T08:34Z] 2016-04-15 01:34:28 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:34:28,905 - WARNING - Could not retrieve variants from source file in region 22:29612270-29630527. Error was invalid region `22:29612271-29630527`
[2016-04-15T08:34Z] 2016-04-15 01:34:29 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:34:29,532 - WARNING - Could not retrieve variants from source file in region 22:26937116-26937517. Error was invalid region `22:26937117-26937517`
[2016-04-15T08:34Z] 2016-04-15 01:34:32 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:34:32,381 - WARNING - Could not retrieve variants from source file in region 22:19746871-19789731. Error was invalid region `22:19746872-19789731`
[2016-04-15T08:34Z] 2016-04-15 01:34:33 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:34:33,526 - WARNING - Could not retrieve variants from source file in region 22:24384008-24384409. Error was invalid region `22:24384009-24384409`
[2016-04-15T08:34Z] 2016-04-15 01:34:33 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:34:33,944 - WARNING - Could not retrieve variants from source file in region 22:31663631-31679300. Error was invalid region `22:31663632-31679300`
[2016-04-15T08:34Z] 2016-04-15 01:34:34 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:34:34,167 - WARNING - Could not retrieve variants from source file in region 22:26937116-26937517. Error was invalid region `22:26937117-26937517`
[2016-04-15T08:34Z] 2016-04-15 01:34:34 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:34:34,656 - WARNING - Could not retrieve variants from source file in region 22:22599169-22599895. Error was invalid region `22:22599170-22599895`
[2016-04-15T08:34Z] 2016-04-15 01:34:34 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:34:34,754 - WARNING - Could not retrieve variants from source file in region 22:29075483-29075884. Error was invalid region `22:29075484-29075884`
[2016-04-15T08:34Z] 2016-04-15 01:34:35 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:34:35,489 - WARNING - Could not retrieve variants from source file in region 22:25753020-25753421. Error was invalid region `22:25753021-25753421`
[2016-04-15T08:34Z] 2016-04-15 01:34:35 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:34:35,533 - WARNING - Could not retrieve variants from source file in region 22:26222243-26247646. Error was invalid region `22:26222244-26247646`
[2016-04-15T08:34Z] 2016-04-15 01:34:38 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:34:38,048 - WARNING - Could not retrieve variants from source file in region 22:29612270-29630527. Error was invalid region `22:29612271-29630527`
[2016-04-15T08:34Z] 2016-04-15 01:34:38 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:34:38,430 - WARNING - Could not retrieve variants from source file in region 22:31663631-31679300. Error was invalid region `22:31663632-31679300`
[2016-04-15T08:34Z] 2016-04-15 01:34:38 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:34:38,957 - WARNING - Could not retrieve variants from source file in region 22:26937116-26937517. Error was invalid region `22:26937117-26937517`
[2016-04-15T08:34Z] 2016-04-15 01:34:39 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:34:39,959 - WARNING - Could not retrieve variants from source file in region 22:25753020-25753421. Error was invalid region `22:25753021-25753421`
[2016-04-15T08:34Z] 2016-04-15 01:34:43 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:34:43,059 - WARNING - Could not retrieve variants from source file in region 22:31663631-31679300. Error was invalid region `22:31663632-31679300`
[2016-04-15T08:34Z] 2016-04-15 01:34:44 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:34:44,449 - WARNING - Could not retrieve variants from source file in region 22:23627158-23655274. Error was invalid region `22:23627159-23655274`
[2016-04-15T08:34Z] 2016-04-15 01:34:50 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:34:50,425 - WARNING - Could not retrieve variants from source file in region 22:24224444-24224849. Error was invalid region `22:24224445-24224849`
[2016-04-15T08:34Z] 2016-04-15 01:34:51 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:34:51,270 - WARNING - Could not retrieve variants from source file in region 22:31491084-31491522. Error was invalid region `22:31491085-31491522`
[2016-04-15T08:34Z] 2016-04-15 01:34:53 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:34:53,481 - WARNING - Could not retrieve variants from source file in region 22:23437980-23438381. Error was invalid region `22:23437981-23438381`
[2016-04-15T08:34Z] 2016-04-15 01:34:55 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:34:55,682 - WARNING - Could not retrieve variants from source file in region 22:24177300-24180112. Error was invalid region `22:24177301-24180112`
[2016-04-15T08:34Z] 2016-04-15 01:34:56 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:34:56,240 - WARNING - Could not retrieve variants from source file in region 22:24224444-24224849. Error was invalid region `22:24224445-24224849`
[2016-04-15T08:34Z] 2016-04-15 01:34:56 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:34:56,738 - WARNING - Could not retrieve variants from source file in region 22:31266335-31266736. Error was invalid region `22:31266336-31266736`
[2016-04-15T08:34Z] 2016-04-15 01:34:57 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:34:57,020 - WARNING - Could not retrieve variants from source file in region 22:19183884-19198086. Error was invalid region `22:19183885-19198086`
[2016-04-15T08:34Z] 2016-04-15 01:34:57 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:34:57,470 - WARNING - Could not retrieve variants from source file in region 22:31521384-31536323. Error was invalid region `22:31521385-31536323`
[2016-04-15T08:34Z] 2016-04-15 01:34:57 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:34:57,821 - WARNING - Could not retrieve variants from source file in region 22:25722039-25722440. Error was invalid region `22:25722040-25722440`
[2016-04-15T08:34Z] 2016-04-15 01:34:58 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:34:58,039 - WARNING - Could not retrieve variants from source file in region 22:18121308-18121709. Error was invalid region `22:18121309-18121709`
[2016-04-15T08:34Z] 2016-04-15 01:34:58 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:34:58,091 - WARNING - Could not retrieve variants from source file in region 22:23437980-23438381. Error was invalid region `22:23437981-23438381`
[2016-04-15T08:35Z] 2016-04-15 01:35:02 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:35:02,143 - WARNING - Could not retrieve variants from source file in region 22:19706034-19706435. Error was invalid region `22:19706035-19706435`
[2016-04-15T08:35Z] 2016-04-15 01:35:02 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:35:02,205 - WARNING - Could not retrieve variants from source file in region 22:24224444-24224849. Error was invalid region `22:24224445-24224849`
[2016-04-15T08:35Z] 2016-04-15 01:35:02 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:35:02,808 - WARNING - Could not retrieve variants from source file in region 22:31266335-31266736. Error was invalid region `22:31266336-31266736`
[2016-04-15T08:35Z] 2016-04-15 01:35:04 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:35:04,362 - WARNING - Could not retrieve variants from source file in region 22:25722039-25722440. Error was invalid region `22:25722040-25722440`
[2016-04-15T08:35Z] 2016-04-15 01:35:07 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:35:07,092 - WARNING - Could not retrieve variants from source file in region 22:19706034-19706435. Error was invalid region `22:19706035-19706435`
[2016-04-15T08:35Z] 2016-04-15 01:35:07 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:35:07,651 - WARNING - Could not retrieve variants from source file in region 22:31266335-31266736. Error was invalid region `22:31266336-31266736`
[2016-04-15T08:35Z] 2016-04-15 01:35:12 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:35:12,763 - WARNING - Could not retrieve variants from source file in region 22:29755677-29756078. Error was invalid region `22:29755678-29756078`
[2016-04-15T08:35Z] 2016-04-15 01:35:14 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:35:14,098 - WARNING - Could not retrieve variants from source file in region 22:22988600-22989471. Error was invalid region `22:22988601-22989471`
[2016-04-15T08:35Z] 2016-04-15 01:35:17 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:35:17,834 - WARNING - Could not retrieve variants from source file in region 22:29837326-29838015. Error was invalid region `22:29837327-29838015`
[2016-04-15T08:35Z] 2016-04-15 01:35:17 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:35:17,842 - WARNING - Could not retrieve variants from source file in region 22:23401654-23402055. Error was invalid region `22:23401655-23402055`
[2016-04-15T08:35Z] 2016-04-15 01:35:18 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:35:18,407 - WARNING - Could not retrieve variants from source file in region 22:29755677-29756078. Error was invalid region `22:29755678-29756078`
[2016-04-15T08:35Z] 2016-04-15 01:35:19 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:35:19,459 - WARNING - Could not retrieve variants from source file in region 22:25627393-25627794. Error was invalid region `22:25627394-25627794`
[2016-04-15T08:35Z] 2016-04-15 01:35:22 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:35:22,395 - WARNING - Could not retrieve variants from source file in region 22:23401654-23402055. Error was invalid region `22:23401655-23402055`
[2016-04-15T08:35Z] 2016-04-15 01:35:23 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:35:23,334 - WARNING - Could not retrieve variants from source file in region 22:31091094-31091495. Error was invalid region `22:31091095-31091495`
[2016-04-15T08:35Z] 2016-04-15 01:35:24 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:35:24,075 - WARNING - Could not retrieve variants from source file in region 22:18049470-18049871. Error was invalid region `22:18049471-18049871`
[2016-04-15T08:35Z] 2016-04-15 01:35:24 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:35:24,528 - WARNING - Could not retrieve variants from source file in region 22:29755677-29756078. Error was invalid region `22:29755678-29756078`
[2016-04-15T08:35Z] 2016-04-15 01:35:24 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:35:24,599 - WARNING - Could not retrieve variants from source file in region 22:24034077-24039037. Error was invalid region `22:24034078-24039037`
[2016-04-15T08:35Z] 2016-04-15 01:35:25 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:35:25,516 - WARNING - Could not retrieve variants from source file in region 22:19119334-19125573. Error was invalid region `22:19119335-19125573`
[2016-04-15T08:35Z] 2016-04-15 01:35:25 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:35:25,834 - WARNING - Could not retrieve variants from source file in region 22:22161915-22162316. Error was invalid region `22:22161916-22162316`
[2016-04-15T08:35Z] 2016-04-15 01:35:28 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:35:28,823 - WARNING - Could not retrieve variants from source file in region 22:18049470-18049871. Error was invalid region `22:18049471-18049871`
[2016-04-15T08:35Z] 2016-04-15 01:35:29 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:35:29,103 - WARNING - Could not retrieve variants from source file in region 22:24034077-24039037. Error was invalid region `22:24034078-24039037`
[2016-04-15T08:35Z] 2016-04-15 01:35:29 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:35:29,754 - WARNING - Could not retrieve variants from source file in region 22:19511714-19512582. Error was invalid region `22:19511715-19512582`
[2016-04-15T08:35Z] 2016-04-15 01:35:30 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:35:30,004 - WARNING - Could not retrieve variants from source file in region 22:19119334-19125573. Error was invalid region `22:19119335-19125573`
[2016-04-15T08:35Z] 2016-04-15 01:35:30 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:35:30,322 - WARNING - Could not retrieve variants from source file in region 22:22161915-22162316. Error was invalid region `22:22161916-22162316`
[2016-04-15T08:35Z] 2016-04-15 01:35:34 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:35:34,077 - WARNING - Could not retrieve variants from source file in region 22:18049470-18049871. Error was invalid region `22:18049471-18049871`
[2016-04-15T08:35Z] 2016-04-15 01:35:34 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:35:34,561 - WARNING - Could not retrieve variants from source file in region 22:19119334-19125573. Error was invalid region `22:19119335-19125573`
[2016-04-15T08:35Z] 2016-04-15 01:35:34 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:35:34,877 - WARNING - Could not retrieve variants from source file in region 22:22161915-22162316. Error was invalid region `22:22161916-22162316`
[2016-04-15T08:35Z] 2016-04-15 01:35:38 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:35:38,315 - WARNING - Could not retrieve variants from source file in region 22:18650471-18650872. Error was invalid region `22:18650472-18650872`
[2016-04-15T08:35Z] 2016-04-15 01:35:39 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:35:39,116 - WARNING - Could not retrieve variants from source file in region 22:25018944-25020678. Error was invalid region `22:25018945-25020678`
[2016-04-15T08:35Z] 2016-04-15 01:35:39 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:35:39,934 - WARNING - Could not retrieve variants from source file in region 22:21141089-21141490. Error was invalid region `22:21141090-21141490`
[2016-04-15T08:35Z] 2016-04-15 01:35:41 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:35:41,227 - WARNING - Could not retrieve variants from source file in region 22:25577477-25601386. Error was invalid region `22:25577478-25601386`
[2016-04-15T08:35Z] 2016-04-15 01:35:41 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:35:41,265 - WARNING - Could not retrieve variants from source file in region 22:20307045-20307446. Error was invalid region `22:20307046-20307446`
[2016-04-15T08:35Z] 2016-04-15 01:35:43 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:35:43,201 - WARNING - Could not retrieve variants from source file in region 22:18021393-18021794. Error was invalid region `22:18021394-18021794`
[2016-04-15T08:35Z] 2016-04-15 01:35:45 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:35:45,871 - WARNING - Could not retrieve variants from source file in region 22:18898209-18923935. Error was invalid region `22:18898210-18923935`
[2016-04-15T08:35Z] 2016-04-15 01:35:46 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:35:46,792 - WARNING - Could not retrieve variants from source file in region 22:20307045-20307446. Error was invalid region `22:20307046-20307446`
[2016-04-15T08:35Z] 2016-04-15 01:35:49 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:35:49,821 - WARNING - Could not retrieve variants from source file in region 22:18021393-18021794. Error was invalid region `22:18021394-18021794`
[2016-04-15T08:35Z] 2016-04-15 01:35:50 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:35:50,541 - WARNING - Could not retrieve variants from source file in region 22:19386422-19386823. Error was invalid region `22:19386423-19386823`
[2016-04-15T08:35Z] 2016-04-15 01:35:51 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:35:51,290 - WARNING - Could not retrieve variants from source file in region 22:19026402-19026803. Error was invalid region `22:19026403-19026803`
[2016-04-15T08:35Z] 2016-04-15 01:35:51 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:35:51,752 - WARNING - Could not retrieve variants from source file in region 22:21141089-21141490. Error was invalid region `22:21141090-21141490`
[2016-04-15T08:35Z] 2016-04-15 01:35:52 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:35:52,253 - WARNING - Could not retrieve variants from source file in region 22:25577477-25601386. Error was invalid region `22:25577478-25601386`
[2016-04-15T08:35Z] 2016-04-15 01:35:52 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:35:52,268 - WARNING - Could not retrieve variants from source file in region 22:20307045-20307446. Error was invalid region `22:20307046-20307446`
[2016-04-15T08:35Z] 2016-04-15 01:35:53 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:35:53,013 - WARNING - Could not retrieve variants from source file in region 22:17072272-17073256. Error was invalid region `22:17072273-17073256`
[2016-04-15T08:35Z] 2016-04-15 01:35:56 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:35:56,007 - WARNING - Could not retrieve variants from source file in region 22:18021393-18021794. Error was invalid region `22:18021394-18021794`
[2016-04-15T08:35Z] 2016-04-15 01:35:57 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:35:57,476 - WARNING - Could not retrieve variants from source file in region 22:19026402-19026803. Error was invalid region `22:19026403-19026803`
[2016-04-15T08:35Z] 2016-04-15 01:35:58 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:35:58,600 - WARNING - Could not retrieve variants from source file in region 22:17072272-17073256. Error was invalid region `22:17072273-17073256`
[2016-04-15T08:35Z] 2016-04-15 01:35:58 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:35:58,661 - WARNING - Could not retrieve variants from source file in region 22:22049572-22050959. Error was invalid region `22:22049573-22050959`
[2016-04-15T08:36Z] 2016-04-15 01:36:02 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:36:02,594 - WARNING - Could not retrieve variants from source file in region 22:19026402-19026803. Error was invalid region `22:19026403-19026803`
[2016-04-15T08:36Z] 2016-04-15 01:36:03 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:36:03,779 - WARNING - Could not retrieve variants from source file in region 22:17072272-17073256. Error was invalid region `22:17072273-17073256`
[2016-04-15T08:36Z] 2016-04-15 01:36:06 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:36:06,212 - WARNING - Could not retrieve variants from source file in region 22:21065434-21067087. Error was invalid region `22:21065435-21067087`
[2016-04-15T08:36Z] 2016-04-15 01:36:07 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:36:07,060 - WARNING - Could not retrieve variants from source file in region 22:24950875-24989110. Error was invalid region `22:24950876-24989110`
[2016-04-15T08:36Z] 2016-04-15 01:36:08 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:36:08,192 - WARNING - Could not retrieve variants from source file in region 22:24717639-24720443. Error was invalid region `22:24717640-24720443`
[2016-04-15T08:36Z] 2016-04-15 01:36:08 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:36:08,427 - WARNING - Could not retrieve variants from source file in region 22:24761256-24761657. Error was invalid region `22:24761257-24761657`
[2016-04-15T08:36Z] 2016-04-15 01:36:09 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:36:09,989 - WARNING - Could not retrieve variants from source file in region 22:17446780-17469239. Error was invalid region `22:17446781-17469239`
[2016-04-15T08:36Z] 2016-04-15 01:36:10 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:36:10,631 - WARNING - Could not retrieve variants from source file in region 22:17446780-17469239. Error was invalid region `22:17446781-17469239`
[2016-04-15T08:36Z] 2016-04-15 01:36:13 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:36:13,705 - WARNING - Could not retrieve variants from source file in region 22:16448839-16449240. Error was invalid region `22:16448840-16449240`
[2016-04-15T08:36Z] 2016-04-15 01:36:13 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:36:13,714 - WARNING - Could not retrieve variants from source file in region 22:24761256-24761657. Error was invalid region `22:24761257-24761657`
[2016-04-15T08:36Z] 2016-04-15 01:36:14 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:36:14,887 - WARNING - Could not retrieve variants from source file in region 22:17264913-17265314. Error was invalid region `22:17264914-17265314`
[2016-04-15T08:36Z] 2016-04-15 01:36:16 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:36:16,162 - WARNING - Could not retrieve variants from source file in region 22:24950875-24989110. Error was invalid region `22:24950876-24989110`
[2016-04-15T08:36Z] 2016-04-15 01:36:18 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:36:18,143 - WARNING - Could not retrieve variants from source file in region 22:16448839-16449240. Error was invalid region `22:16448840-16449240`
[2016-04-15T08:36Z] 2016-04-15 01:36:18 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:36:18,271 - WARNING - Could not retrieve variants from source file in region 22:24761256-24761657. Error was invalid region `22:24761257-24761657`
[2016-04-15T08:36Z] 2016-04-15 01:36:18 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:36:18,415 - WARNING - Could not retrieve variants from source file in region 22:24717639-24720443. Error was invalid region `22:24717640-24720443`
[2016-04-15T08:36Z] 2016-04-15 01:36:21 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:36:21,501 - WARNING - Could not retrieve variants from source file in region 22:16287640-16288041. Error was invalid region `22:16287641-16288041`
[2016-04-15T08:36Z] 2016-04-15 01:36:23 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:36:23,618 - WARNING - Could not retrieve variants from source file in region 22:20862435-20862836. Error was invalid region `22:20862436-20862836`
[2016-04-15T08:36Z] 2016-04-15 01:36:23 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:36:23,952 - WARNING - Could not retrieve variants from source file in region 22:20862435-20862836. Error was invalid region `22:20862436-20862836`
[2016-04-15T08:36Z] 2016-04-15 01:36:26 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:36:26,680 - WARNING - Could not retrieve variants from source file in region 22:21922059-21922646. Error was invalid region `22:21922060-21922646`
[2016-04-15T08:36Z] 2016-04-15 01:36:27 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:36:27,380 - WARNING - Could not retrieve variants from source file in region 22:20862435-20862836. Error was invalid region `22:20862436-20862836`
[2016-04-15T08:36Z] 2016-04-15 01:36:29 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:36:29,052 - WARNING - Could not retrieve variants from source file in region 22:24562729-24582231. Error was invalid region `22:24562730-24582231`
[2016-04-15T08:36Z] 2016-04-15 01:36:32 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:36:32,108 - WARNING - Could not retrieve variants from source file in region 22:20067718-20089461. Error was invalid region `22:20067719-20089461`
[2016-04-15T08:36Z] 2016-04-15 01:36:33 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:36:33,533 - WARNING - Could not retrieve variants from source file in region 22:21922059-21922646. Error was invalid region `22:21922060-21922646`
[2016-04-15T08:36Z] 2016-04-15 01:36:35 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:36:35,801 - WARNING - Could not retrieve variants from source file in region 22:20456849-20457394. Error was invalid region `22:20456850-20457394`
[2016-04-15T08:36Z] 2016-04-15 01:36:37 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:36:37,662 - WARNING - Could not retrieve variants from source file in region 22:20456849-20457394. Error was invalid region `22:20456850-20457394`
[2016-04-15T08:36Z] 2016-04-15 01:36:39 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:36:39,765 - WARNING - Could not retrieve variants from source file in region 22:20456849-20457394. Error was invalid region `22:20456850-20457394`
[2016-04-15T08:36Z] 2016-04-15 01:36:41 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:36:41,222 - WARNING - Could not retrieve variants from source file in region 22:21167576-21167977. Error was invalid region `22:21167577-21167977`
[2016-04-15T08:36Z] 2016-04-15 01:36:41 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:36:41,684 - WARNING - Could not retrieve variants from source file in region 22:21213205-21213606. Error was invalid region `22:21213206-21213606`
[2016-04-15T08:36Z] 2016-04-15 01:36:44 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:36:44,267 - WARNING - Could not retrieve variants from source file in region 22:21570085-21570787. Error was invalid region `22:21570086-21570787`
[2016-04-15T08:36Z] 2016-04-15 01:36:46 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:36:46,079 - WARNING - Could not retrieve variants from source file in region 22:21167576-21167977. Error was invalid region `22:21167577-21167977`
[2016-04-15T08:36Z] 2016-04-15 01:36:46 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:36:46,312 - WARNING - Could not retrieve variants from source file in region 22:21213205-21213606. Error was invalid region `22:21213206-21213606`
[2016-04-15T08:36Z] 2016-04-15 01:36:48 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:36:48,858 - WARNING - Could not retrieve variants from source file in region 22:19906888-19921193. Error was invalid region `22:19906889-19921193`
[2016-04-15T08:36Z] 2016-04-15 01:36:49 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:36:49,942 - WARNING - Could not retrieve variants from source file in region 22:19868007-19868408. Error was invalid region `22:19868008-19868408`
[2016-04-15T08:36Z] 2016-04-15 01:36:50 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:36:50,275 - WARNING - Could not retrieve variants from source file in region 22:19868007-19868408. Error was invalid region `22:19868008-19868408`
[2016-04-15T08:36Z] ['bcbio-variation-recall', 'square', '-Xms750m', '-Xmx7280m', '-XX:+UseSerialGC', '-c', 16, '-r', u'22:31796606-47308085', '--caller', 'platypus', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/22/Batch1-22_31796605_47308085.vcf.gz', '/mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/22/Batch1-22_31796605_47308085.vcf-inputs.txt'] in region: 22:31796606-47308085
[2016-04-15T08:37Z] 2016-04-15 01:37:06 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:37:06,470 - WARNING - Could not retrieve variants from source file in region 22:45683035-45691784. Error was invalid region `22:45683036-45691784`
[2016-04-15T08:37Z] 2016-04-15 01:37:06 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:37:06,918 - WARNING - Could not retrieve variants from source file in region 22:38008671-38013999. Error was invalid region `22:38008672-38013999`
[2016-04-15T08:37Z] 2016-04-15 01:37:07 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:37:07,026 - WARNING - Could not retrieve variants from source file in region 22:46929481-46932028. Error was invalid region `22:46929482-46932028`
[2016-04-15T08:37Z] 2016-04-15 01:37:07 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:37:07,321 - WARNING - Could not retrieve variants from source file in region 22:38822925-38823326. Error was invalid region `22:38822926-38823326`
[2016-04-15T08:37Z] 2016-04-15 01:37:07 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:37:07,729 - WARNING - Could not retrieve variants from source file in region 22:46652748-46677797. Error was invalid region `22:46652749-46677797`
[2016-04-15T08:37Z] 2016-04-15 01:37:08 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:37:08,498 - WARNING - Could not retrieve variants from source file in region 22:45608136-45608550. Error was invalid region `22:45608137-45608550`
[2016-04-15T08:37Z] 2016-04-15 01:37:09 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:37:09,019 - WARNING - Could not retrieve variants from source file in region 22:34022073-34022474. Error was invalid region `22:34022074-34022474`
[2016-04-15T08:37Z] 2016-04-15 01:37:09 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:37:09,114 - WARNING - Could not retrieve variants from source file in region 22:42089412-42089813. Error was invalid region `22:42089413-42089813`
[2016-04-15T08:37Z] 2016-04-15 01:37:09 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:37:09,129 - WARNING - Could not retrieve variants from source file in region 22:47189467-47189868. Error was invalid region `22:47189468-47189868`
[2016-04-15T08:37Z] 2016-04-15 01:37:11 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:37:11,236 - WARNING - Could not retrieve variants from source file in region 22:37524408-37531626. Error was invalid region `22:37524409-37531626`
[2016-04-15T08:37Z] 2016-04-15 01:37:15 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:37:15,578 - WARNING - Could not retrieve variants from source file in region 22:39966645-39967046. Error was invalid region `22:39966646-39967046`
[2016-04-15T08:37Z] 2016-04-15 01:37:16 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:37:16,284 - WARNING - Could not retrieve variants from source file in region 22:45608136-45608550. Error was invalid region `22:45608137-45608550`
[2016-04-15T08:37Z] 2016-04-15 01:37:16 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:37:16,683 - WARNING - Could not retrieve variants from source file in region 22:34022073-34022474. Error was invalid region `22:34022074-34022474`
[2016-04-15T08:37Z] 2016-04-15 01:37:16 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:37:16,755 - WARNING - Could not retrieve variants from source file in region 22:43435601-43466437. Error was invalid region `22:43435602-43466437`
[2016-04-15T08:37Z] 2016-04-15 01:37:17 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:37:17,424 - WARNING - Could not retrieve variants from source file in region 22:42089412-42089813. Error was invalid region `22:42089413-42089813`
[2016-04-15T08:37Z] 2016-04-15 01:37:17 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:37:17,539 - WARNING - Could not retrieve variants from source file in region 22:37524408-37531626. Error was invalid region `22:37524409-37531626`
[2016-04-15T08:37Z] 2016-04-15 01:37:17 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:37:17,542 - WARNING - Could not retrieve variants from source file in region 22:44222134-44223429. Error was invalid region `22:44222135-44223429`
[2016-04-15T08:37Z] 2016-04-15 01:37:17 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:37:17,622 - WARNING - Could not retrieve variants from source file in region 22:45683035-45691784. Error was invalid region `22:45683036-45691784`
[2016-04-15T08:37Z] 2016-04-15 01:37:18 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:37:18,150 - WARNING - Could not retrieve variants from source file in region 22:46929481-46932028. Error was invalid region `22:46929482-46932028`
[2016-04-15T08:37Z] 2016-04-15 01:37:18 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:37:18,187 - WARNING - Could not retrieve variants from source file in region 22:38008671-38013999. Error was invalid region `22:38008672-38013999`
[2016-04-15T08:37Z] 2016-04-15 01:37:22 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:37:22,882 - WARNING - Could not retrieve variants from source file in region 22:45608136-45608550. Error was invalid region `22:45608137-45608550`
[2016-04-15T08:37Z] 2016-04-15 01:37:25 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:37:25,104 - WARNING - Could not retrieve variants from source file in region 22:34022073-34022474. Error was invalid region `22:34022074-34022474`
[2016-04-15T08:37Z] 2016-04-15 01:37:25 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:37:25,244 - WARNING - Could not retrieve variants from source file in region 22:42782808-42794063. Error was invalid region `22:42782809-42794063`
[2016-04-15T08:37Z] 2016-04-15 01:37:25 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:37:25,428 - WARNING - Could not retrieve variants from source file in region 22:42089412-42089813. Error was invalid region `22:42089413-42089813`
[2016-04-15T08:37Z] 2016-04-15 01:37:36 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:37:36,474 - WARNING - Could not retrieve variants from source file in region 22:37964088-37964619. Error was invalid region `22:37964089-37964619`
[2016-04-15T08:37Z] 2016-04-15 01:37:38 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:37:38,144 - WARNING - Could not retrieve variants from source file in region 22:46829166-46829567. Error was invalid region `22:46829167-46829567`
[2016-04-15T08:37Z] 2016-04-15 01:37:38 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:37:38,316 - WARNING - Could not retrieve variants from source file in region 22:39917304-39917705. Error was invalid region `22:39917305-39917705`
[2016-04-15T08:37Z] 2016-04-15 01:37:38 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:37:38,754 - WARNING - Could not retrieve variants from source file in region 22:45197798-45198199. Error was invalid region `22:45197799-45198199`
[2016-04-15T08:37Z] 2016-04-15 01:37:38 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:37:38,767 - WARNING - Could not retrieve variants from source file in region 22:45197798-45198199. Error was invalid region `22:45197799-45198199`
[2016-04-15T08:37Z] 2016-04-15 01:37:38 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:37:38,956 - WARNING - Could not retrieve variants from source file in region 22:38615325-38617350. Error was invalid region `22:38615326-38617350`
[2016-04-15T08:37Z] 2016-04-15 01:37:39 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:37:39,268 - WARNING - Could not retrieve variants from source file in region 22:45075527-45075928. Error was invalid region `22:45075528-45075928`
[2016-04-15T08:37Z] 2016-04-15 01:37:39 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:37:39,542 - WARNING - Could not retrieve variants from source file in region 22:43278009-43289663. Error was invalid region `22:43278010-43289663`
[2016-04-15T08:37Z] 2016-04-15 01:37:39 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:37:39,876 - WARNING - Could not retrieve variants from source file in region 22:33253069-33253470. Error was invalid region `22:33253070-33253470`
[2016-04-15T08:37Z] 2016-04-15 01:37:41 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:37:41,077 - WARNING - Could not retrieve variants from source file in region 22:37964088-37964619. Error was invalid region `22:37964089-37964619`
[2016-04-15T08:37Z] 2016-04-15 01:37:43 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:37:43,925 - WARNING - Could not retrieve variants from source file in region 22:41984928-41985329. Error was invalid region `22:41984929-41985329`
[2016-04-15T08:37Z] 2016-04-15 01:37:44 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:37:44,090 - WARNING - Could not retrieve variants from source file in region 22:43088760-43090039. Error was invalid region `22:43088761-43090039`
[2016-04-15T08:37Z] 2016-04-15 01:37:45 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:37:45,729 - WARNING - Could not retrieve variants from source file in region 22:45197798-45198199. Error was invalid region `22:45197799-45198199`
[2016-04-15T08:37Z] 2016-04-15 01:37:46 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:37:46,161 - WARNING - Could not retrieve variants from source file in region 22:43278009-43289663. Error was invalid region `22:43278010-43289663`
[2016-04-15T08:37Z] 2016-04-15 01:37:46 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:37:46,445 - WARNING - Could not retrieve variants from source file in region 22:45075527-45075928. Error was invalid region `22:45075528-45075928`
[2016-04-15T08:37Z] 2016-04-15 01:37:46 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:37:46,509 - WARNING - Could not retrieve variants from source file in region 22:37453241-37485914. Error was invalid region `22:37453242-37485914`
[2016-04-15T08:37Z] 2016-04-15 01:37:46 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:37:46,993 - WARNING - Could not retrieve variants from source file in region 22:37964088-37964619. Error was invalid region `22:37964089-37964619`
[2016-04-15T08:37Z] 2016-04-15 01:37:49 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:37:49,551 - WARNING - Could not retrieve variants from source file in region 22:44112634-44131976. Error was invalid region `22:44112635-44131976`
[2016-04-15T08:37Z] 2016-04-15 01:37:49 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:37:49,758 - WARNING - Could not retrieve variants from source file in region 22:39917304-39917705. Error was invalid region `22:39917305-39917705`
[2016-04-15T08:37Z] 2016-04-15 01:37:50 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:37:50,719 - WARNING - Could not retrieve variants from source file in region 22:46829166-46829567. Error was invalid region `22:46829167-46829567`
[2016-04-15T08:37Z] 2016-04-15 01:37:50 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:37:50,892 - WARNING - Could not retrieve variants from source file in region 22:46449680-46450081. Error was invalid region `22:46449681-46450081`
[2016-04-15T08:37Z] 2016-04-15 01:37:52 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:37:52,801 - WARNING - Could not retrieve variants from source file in region 22:45075527-45075928. Error was invalid region `22:45075528-45075928`
[2016-04-15T08:37Z] 2016-04-15 01:37:52 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:37:52,873 - WARNING - Could not retrieve variants from source file in region 22:33253069-33253470. Error was invalid region `22:33253070-33253470`
[2016-04-15T08:37Z] 2016-04-15 01:37:53 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:37:53,565 - WARNING - Could not retrieve variants from source file in region 22:43278009-43289663. Error was invalid region `22:43278010-43289663`
[2016-04-15T08:38Z] 2016-04-15 01:38:03 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:38:03,448 - WARNING - Could not retrieve variants from source file in region 22:43194936-43223285. Error was invalid region `22:43194937-43223285`
[2016-04-15T08:38Z] 2016-04-15 01:38:03 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:38:03,473 - WARNING - Could not retrieve variants from source file in region 22:32445735-32446136. Error was invalid region `22:32445736-32446136`
[2016-04-15T08:38Z] 2016-04-15 01:38:04 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:38:04,338 - WARNING - Could not retrieve variants from source file in region 22:43010606-43032932. Error was invalid region `22:43010607-43032932`
[2016-04-15T08:38Z] 2016-04-15 01:38:04 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:38:04,949 - WARNING - Could not retrieve variants from source file in region 22:39825111-39829926. Error was invalid region `22:39825112-39829926`
[2016-04-15T08:38Z] 2016-04-15 01:38:05 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:38:05,011 - WARNING - Could not retrieve variants from source file in region 22:43194936-43223285. Error was invalid region `22:43194937-43223285`
[2016-04-15T08:38Z] 2016-04-15 01:38:05 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:38:05,594 - WARNING - Could not retrieve variants from source file in region 22:46760270-46760671. Error was invalid region `22:46760271-46760671`
[2016-04-15T08:38Z] 2016-04-15 01:38:07 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:38:07,454 - WARNING - Could not retrieve variants from source file in region 22:37397984-37398391. Error was invalid region `22:37397985-37398391`
[2016-04-15T08:38Z] 2016-04-15 01:38:08 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:38:08,565 - WARNING - Could not retrieve variants from source file in region 22:44681401-44681802. Error was invalid region `22:44681402-44681802`
[2016-04-15T08:38Z] 2016-04-15 01:38:09 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:38:09,788 - WARNING - Could not retrieve variants from source file in region 22:47016004-47016542. Error was invalid region `22:47016005-47016542`
[2016-04-15T08:38Z] 2016-04-15 01:38:10 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:38:10,621 - WARNING - Could not retrieve variants from source file in region 22:43194936-43223285. Error was invalid region `22:43194937-43223285`
[2016-04-15T08:38Z] 2016-04-15 01:38:10 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:38:10,864 - WARNING - Could not retrieve variants from source file in region 22:32871019-32871420. Error was invalid region `22:32871020-32871420`
[2016-04-15T08:38Z] 2016-04-15 01:38:11 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:38:11,378 - WARNING - Could not retrieve variants from source file in region 22:41911314-41911715. Error was invalid region `22:41911315-41911715`
[2016-04-15T08:38Z] 2016-04-15 01:38:11 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:38:11,731 - WARNING - Could not retrieve variants from source file in region 22:39825111-39829926. Error was invalid region `22:39825112-39829926`
[2016-04-15T08:38Z] 2016-04-15 01:38:12 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:38:12,118 - WARNING - Could not retrieve variants from source file in region 22:37397984-37398391. Error was invalid region `22:37397985-37398391`
[2016-04-15T08:38Z] 2016-04-15 01:38:12 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:38:12,794 - WARNING - Could not retrieve variants from source file in region 22:44681401-44681802. Error was invalid region `22:44681402-44681802`
[2016-04-15T08:38Z] 2016-04-15 01:38:15 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:38:15,564 - WARNING - Could not retrieve variants from source file in region 22:47016004-47016542. Error was invalid region `22:47016005-47016542`
[2016-04-15T08:38Z] 2016-04-15 01:38:17 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:38:17,307 - WARNING - Could not retrieve variants from source file in region 22:32871019-32871420. Error was invalid region `22:32871020-32871420`
[2016-04-15T08:38Z] 2016-04-15 01:38:17 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:38:17,641 - WARNING - Could not retrieve variants from source file in region 22:42523317-42526884. Error was invalid region `22:42523318-42526884`
[2016-04-15T08:38Z] 2016-04-15 01:38:18 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:38:18,607 - WARNING - Could not retrieve variants from source file in region 22:41911314-41911715. Error was invalid region `22:41911315-41911715`
[2016-04-15T08:38Z] 2016-04-15 01:38:18 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:38:18,665 - WARNING - Could not retrieve variants from source file in region 22:39825111-39829926. Error was invalid region `22:39825112-39829926`
[2016-04-15T08:38Z] 2016-04-15 01:38:19 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:38:19,316 - WARNING - Could not retrieve variants from source file in region 22:44681401-44681802. Error was invalid region `22:44681402-44681802`
[2016-04-15T08:38Z] 2016-04-15 01:38:19 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:38:19,406 - WARNING - Could not retrieve variants from source file in region 22:44083231-44083632. Error was invalid region `22:44083232-44083632`
[2016-04-15T08:38Z] 2016-04-15 01:38:19 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:38:19,738 - WARNING - Could not retrieve variants from source file in region 22:46320979-46323434. Error was invalid region `22:46320980-46323434`
[2016-04-15T08:38Z] 2016-04-15 01:38:20 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:38:20,428 - WARNING - Could not retrieve variants from source file in region 22:47016004-47016542. Error was invalid region `22:47016005-47016542`
[2016-04-15T08:38Z] 2016-04-15 01:38:21 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:38:21,631 - WARNING - Could not retrieve variants from source file in region 22:32871019-32871420. Error was invalid region `22:32871020-32871420`
[2016-04-15T08:38Z] 2016-04-15 01:38:24 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:38:24,460 - WARNING - Could not retrieve variants from source file in region 22:41911314-41911715. Error was invalid region `22:41911315-41911715`
[2016-04-15T08:38Z] 2016-04-15 01:38:26 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:38:26,721 - WARNING - Could not retrieve variants from source file in region 22:42967024-42982080. Error was invalid region `22:42967025-42982080`
[2016-04-15T08:38Z] 2016-04-15 01:38:27 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:38:27,608 - WARNING - Could not retrieve variants from source file in region 22:46722189-46722590. Error was invalid region `22:46722190-46722590`
[2016-04-15T08:38Z] 2016-04-15 01:38:29 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:38:29,673 - WARNING - Could not retrieve variants from source file in region 22:37326232-37334126. Error was invalid region `22:37326233-37334126`
[2016-04-15T08:38Z] 2016-04-15 01:38:30 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:38:30,806 - WARNING - Could not retrieve variants from source file in region 22:46722189-46722590. Error was invalid region `22:46722190-46722590`
[2016-04-15T08:38Z] 2016-04-15 01:38:32 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:38:32,953 - WARNING - Could not retrieve variants from source file in region 22:46722189-46722590. Error was invalid region `22:46722190-46722590`
[2016-04-15T08:38Z] 2016-04-15 01:38:34 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:38:34,348 - WARNING - Could not retrieve variants from source file in region 22:39774167-39778012. Error was invalid region `22:39774168-39778012`
[2016-04-15T08:38Z] 2016-04-15 01:38:37 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:38:37,279 - WARNING - Could not retrieve variants from source file in region 22:32795430-32812142. Error was invalid region `22:32795431-32812142`
[2016-04-15T08:38Z] 2016-04-15 01:38:37 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:38:37,411 - WARNING - Could not retrieve variants from source file in region 22:45923616-45924017. Error was invalid region `22:45923617-45924017`
[2016-04-15T08:38Z] 2016-04-15 01:38:38 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:38:38,007 - WARNING - Could not retrieve variants from source file in region 22:42967024-42982080. Error was invalid region `22:42967025-42982080`
[2016-04-15T08:38Z] 2016-04-15 01:38:38 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:38:38,854 - WARNING - Could not retrieve variants from source file in region 22:41832905-41833306. Error was invalid region `22:41832906-41833306`
[2016-04-15T08:38Z] 2016-04-15 01:38:39 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:38:39,336 - WARNING - Could not retrieve variants from source file in region 22:43976185-43976586. Error was invalid region `22:43976186-43976586`
[2016-04-15T08:38Z] 2016-04-15 01:38:39 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:38:39,459 - WARNING - Could not retrieve variants from source file in region 22:39774167-39778012. Error was invalid region `22:39774168-39778012`
[2016-04-15T08:38Z] 2016-04-15 01:38:40 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:38:40,217 - WARNING - Could not retrieve variants from source file in region 22:44577472-44602419. Error was invalid region `22:44577473-44602419`
[2016-04-15T08:38Z] 2016-04-15 01:38:40 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:38:40,953 - WARNING - Could not retrieve variants from source file in region 22:37326232-37334126. Error was invalid region `22:37326233-37334126`
[2016-04-15T08:38Z] 2016-04-15 01:38:43 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:38:43,274 - WARNING - Could not retrieve variants from source file in region 22:45923616-45924017. Error was invalid region `22:45923617-45924017`
[2016-04-15T08:38Z] 2016-04-15 01:38:43 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:38:43,675 - WARNING - Could not retrieve variants from source file in region 22:45923616-45924017. Error was invalid region `22:45923617-45924017`
[2016-04-15T08:38Z] 2016-04-15 01:38:43 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:38:43,677 - WARNING - Could not retrieve variants from source file in region 22:32795430-32812142. Error was invalid region `22:32795431-32812142`
[2016-04-15T08:38Z] 2016-04-15 01:38:44 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:38:44,439 - WARNING - Could not retrieve variants from source file in region 22:41832905-41833306. Error was invalid region `22:41832906-41833306`
[2016-04-15T08:38Z] 2016-04-15 01:38:44 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:38:44,960 - WARNING - Could not retrieve variants from source file in region 22:43976185-43976586. Error was invalid region `22:43976186-43976586`
[2016-04-15T08:38Z] 2016-04-15 01:38:45 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:38:45,146 - WARNING - Could not retrieve variants from source file in region 22:39774167-39778012. Error was invalid region `22:39774168-39778012`
[2016-04-15T08:38Z] 2016-04-15 01:38:45 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:38:45,168 - WARNING - Could not retrieve variants from source file in region 22:37769855-37771348. Error was invalid region `22:37769856-37771348`
[2016-04-15T08:38Z] 2016-04-15 01:38:45 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:38:45,505 - WARNING - Could not retrieve variants from source file in region 22:44577472-44602419. Error was invalid region `22:44577473-44602419`
[2016-04-15T08:38Z] 2016-04-15 01:38:46 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:38:46,604 - WARNING - Could not retrieve variants from source file in region 22:44489657-44490086. Error was invalid region `22:44489658-44490086`
[2016-04-15T08:38Z] 2016-04-15 01:38:46 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:38:46,884 - WARNING - Could not retrieve variants from source file in region 22:32108264-32112651. Error was invalid region `22:32108265-32112651`
[2016-04-15T08:38Z] 2016-04-15 01:38:50 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:38:50,354 - WARNING - Could not retrieve variants from source file in region 22:32795430-32812142. Error was invalid region `22:32795431-32812142`
[2016-04-15T08:38Z] 2016-04-15 01:38:50 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:38:50,894 - WARNING - Could not retrieve variants from source file in region 22:41832905-41833306. Error was invalid region `22:41832906-41833306`
[2016-04-15T08:38Z] 2016-04-15 01:38:52 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:38:52,267 - WARNING - Could not retrieve variants from source file in region 22:44489657-44490086. Error was invalid region `22:44489658-44490086`
[2016-04-15T08:38Z] 2016-04-15 01:38:52 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:38:52,448 - WARNING - Could not retrieve variants from source file in region 22:43976185-43976586. Error was invalid region `22:43976186-43976586`
[2016-04-15T08:38Z] 2016-04-15 01:38:55 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:38:55,712 - WARNING - Could not retrieve variants from source file in region 22:37271671-37272072. Error was invalid region `22:37271672-37272072`
[2016-04-15T08:38Z] 2016-04-15 01:38:57 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:38:57,527 - WARNING - Could not retrieve variants from source file in region 22:44489657-44490086. Error was invalid region `22:44489658-44490086`
[2016-04-15T08:38Z] 2016-04-15 01:38:59 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:38:59,299 - WARNING - Could not retrieve variants from source file in region 22:32754171-32756934. Error was invalid region `22:32754172-32756934`
[2016-04-15T08:39Z] 2016-04-15 01:39:00 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:39:00,985 - WARNING - Could not retrieve variants from source file in region 22:37699166-37699567. Error was invalid region `22:37699167-37699567`
[2016-04-15T08:39Z] 2016-04-15 01:39:01 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:39:01,103 - WARNING - Could not retrieve variants from source file in region 22:39714279-39714680. Error was invalid region `22:39714280-39714680`
[2016-04-15T08:39Z] 2016-04-15 01:39:01 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:39:01,358 - WARNING - Could not retrieve variants from source file in region 22:37607770-37608441. Error was invalid region `22:37607771-37608441`
[2016-04-15T08:39Z] 2016-04-15 01:39:02 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:39:02,169 - WARNING - Could not retrieve variants from source file in region 22:37271671-37272072. Error was invalid region `22:37271672-37272072`
[2016-04-15T08:39Z] 2016-04-15 01:39:03 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:39:03,623 - WARNING - Could not retrieve variants from source file in region 22:32239528-32239929. Error was invalid region `22:32239529-32239929`
[2016-04-15T08:39Z] 2016-04-15 01:39:04 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:39:04,094 - WARNING - Could not retrieve variants from source file in region 22:32754171-32756934. Error was invalid region `22:32754172-32756934`
[2016-04-15T08:39Z] 2016-04-15 01:39:04 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:39:04,530 - WARNING - Could not retrieve variants from source file in region 22:32545551-32555186. Error was invalid region `22:32545552-32555186`
[2016-04-15T08:39Z] 2016-04-15 01:39:07 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:39:07,234 - WARNING - Could not retrieve variants from source file in region 22:37607770-37608441. Error was invalid region `22:37607771-37608441`
[2016-04-15T08:39Z] 2016-04-15 01:39:07 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:39:07,339 - WARNING - Could not retrieve variants from source file in region 22:39714279-39714680. Error was invalid region `22:39714280-39714680`
[2016-04-15T08:39Z] 2016-04-15 01:39:07 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:39:07,347 - WARNING - Could not retrieve variants from source file in region 22:42422899-42423300. Error was invalid region `22:42422900-42423300`
[2016-04-15T08:39Z] 2016-04-15 01:39:07 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:39:07,450 - WARNING - Could not retrieve variants from source file in region 22:37699166-37699567. Error was invalid region `22:37699167-37699567`
[2016-04-15T08:39Z] 2016-04-15 01:39:08 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:39:08,527 - WARNING - Could not retrieve variants from source file in region 22:38273538-38273939. Error was invalid region `22:38273539-38273939`
[2016-04-15T08:39Z] 2016-04-15 01:39:09 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:39:09,151 - WARNING - Could not retrieve variants from source file in region 22:37271671-37272072. Error was invalid region `22:37271672-37272072`
[2016-04-15T08:39Z] 2016-04-15 01:39:09 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:39:09,219 - WARNING - Could not retrieve variants from source file in region 22:32754171-32756934. Error was invalid region `22:32754172-32756934`
[2016-04-15T08:39Z] 2016-04-15 01:39:11 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:39:11,665 - WARNING - Could not retrieve variants from source file in region 22:43807214-43831246. Error was invalid region `22:43807215-43831246`
[2016-04-15T08:39Z] 2016-04-15 01:39:11 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:39:11,826 - WARNING - Could not retrieve variants from source file in region 22:41783448-41783849. Error was invalid region `22:41783449-41783849`
[2016-04-15T08:39Z] 2016-04-15 01:39:12 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:39:12,033 - WARNING - Could not retrieve variants from source file in region 22:37699166-37699567. Error was invalid region `22:37699167-37699567`
[2016-04-15T08:39Z] 2016-04-15 01:39:12 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:39:12,652 - WARNING - Could not retrieve variants from source file in region 22:32081470-32081871. Error was invalid region `22:32081471-32081871`
[2016-04-15T08:39Z] 2016-04-15 01:39:12 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:39:12,727 - WARNING - Could not retrieve variants from source file in region 22:39714279-39714680. Error was invalid region `22:39714280-39714680`
[2016-04-15T08:39Z] 2016-04-15 01:39:12 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:39:12,894 - WARNING - Could not retrieve variants from source file in region 22:37607770-37608441. Error was invalid region `22:37607771-37608441`
[2016-04-15T08:39Z] 2016-04-15 01:39:13 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:39:13,989 - WARNING - Could not retrieve variants from source file in region 22:44324516-44342306. Error was invalid region `22:44324517-44342306`
[2016-04-15T08:39Z] 2016-04-15 01:39:25 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:39:25,058 - WARNING - Could not retrieve variants from source file in region 22:32624999-32625400. Error was invalid region `22:32625000-32625400`
[2016-04-15T08:39Z] 2016-04-15 01:39:25 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:39:25,147 - WARNING - Could not retrieve variants from source file in region 22:37168427-37168915. Error was invalid region `22:37168428-37168915`
[2016-04-15T08:39Z] 2016-04-15 01:39:25 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:39:25,191 - WARNING - Could not retrieve variants from source file in region 22:44367911-44420346. Error was invalid region `22:44367912-44420346`
[2016-04-15T08:39Z] 2016-04-15 01:39:25 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:39:25,387 - WARNING - Could not retrieve variants from source file in region 22:32205421-32205822. Error was invalid region `22:32205422-32205822`
[2016-04-15T08:39Z] 2016-04-15 01:39:26 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:39:26,254 - WARNING - Could not retrieve variants from source file in region 22:37637442-37637843. Error was invalid region `22:37637443-37637843`
[2016-04-15T08:39Z] 2016-04-15 01:39:30 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:39:30,186 - WARNING - Could not retrieve variants from source file in region 22:44282065-44287397. Error was invalid region `22:44282066-44287397`
[2016-04-15T08:39Z] 2016-04-15 01:39:30 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:39:30,452 - WARNING - Could not retrieve variants from source file in region 22:38203878-38221331. Error was invalid region `22:38203879-38221331`
[2016-04-15T08:39Z] 2016-04-15 01:39:30 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:39:30,459 - WARNING - Could not retrieve variants from source file in region 22:32487489-32506333. Error was invalid region `22:32487490-32506333`
[2016-04-15T08:39Z] 2016-04-15 01:39:31 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:39:31,353 - WARNING - Could not retrieve variants from source file in region 22:42159018-42159419. Error was invalid region `22:42159019-42159419`
[2016-04-15T08:39Z] 2016-04-15 01:39:31 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:39:31,856 - WARNING - Could not retrieve variants from source file in region 22:37168427-37168915. Error was invalid region `22:37168428-37168915`
[2016-04-15T08:39Z] 2016-04-15 01:39:31 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:39:31,914 - WARNING - Could not retrieve variants from source file in region 22:32205421-32205822. Error was invalid region `22:32205422-32205822`
[2016-04-15T08:39Z] 2016-04-15 01:39:32 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:39:32,307 - WARNING - Could not retrieve variants from source file in region 22:37581172-37581867. Error was invalid region `22:37581173-37581867`
[2016-04-15T08:39Z] 2016-04-15 01:39:33 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:39:33,256 - WARNING - Could not retrieve variants from source file in region 22:42390676-42393001. Error was invalid region `22:42390677-42393001`
[2016-04-15T08:39Z] 2016-04-15 01:39:38 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:39:38,212 - WARNING - Could not retrieve variants from source file in region 22:42159018-42159419. Error was invalid region `22:42159019-42159419`
[2016-04-15T08:39Z] 2016-04-15 01:39:38 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:39:38,281 - WARNING - Could not retrieve variants from source file in region 22:37637442-37637843. Error was invalid region `22:37637443-37637843`
[2016-04-15T08:39Z] 2016-04-15 01:39:38 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:39:38,680 - WARNING - Could not retrieve variants from source file in region 22:37168427-37168915. Error was invalid region `22:37168428-37168915`
[2016-04-15T08:39Z] 2016-04-15 01:39:38 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:39:38,714 - WARNING - Could not retrieve variants from source file in region 22:41609813-41652923. Error was invalid region `22:41609814-41652923`
[2016-04-15T08:39Z] 2016-04-15 01:39:44 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:39:44,299 - WARNING - Could not retrieve variants from source file in region 22:42159018-42159419. Error was invalid region `22:42159019-42159419`
[2016-04-15T08:39Z] 2016-04-15 01:39:45 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:39:45,586 - WARNING - Could not retrieve variants from source file in region 22:41609813-41652923. Error was invalid region `22:41609814-41652923`
[2016-04-15T08:39Z] 2016-04-15 01:39:51 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:39:51,581 - WARNING - Could not retrieve variants from source file in region 22:43558715-43577094. Error was invalid region `22:43558716-43577094`
[2016-04-15T08:39Z] 2016-04-15 01:39:52 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:39:52,389 - WARNING - Could not retrieve variants from source file in region 22:31837874-31838275. Error was invalid region `22:31837875-31838275`
[2016-04-15T08:39Z] 2016-04-15 01:39:52 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:39:52,523 - WARNING - Could not retrieve variants from source file in region 22:39476912-39498228. Error was invalid region `22:39476913-39498228`
[2016-04-15T08:39Z] 2016-04-15 01:39:53 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:39:53,762 - WARNING - Could not retrieve variants from source file in region 22:43529103-43529504. Error was invalid region `22:43529104-43529504`
[2016-04-15T08:39Z] 2016-04-15 01:39:53 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:39:53,903 - WARNING - Could not retrieve variants from source file in region 22:31837874-31838275. Error was invalid region `22:31837875-31838275`
[2016-04-15T08:39Z] 2016-04-15 01:39:55 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:39:55,792 - WARNING - Could not retrieve variants from source file in region 22:43558715-43577094. Error was invalid region `22:43558716-43577094`
[2016-04-15T08:39Z] 2016-04-15 01:39:57 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:39:57,195 - WARNING - Could not retrieve variants from source file in region 22:31837874-31838275. Error was invalid region `22:31837875-31838275`
[2016-04-15T08:39Z] 2016-04-15 01:39:57 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:39:57,332 - WARNING - Could not retrieve variants from source file in region 22:36877484-36902246. Error was invalid region `22:36877485-36902246`
[2016-04-15T08:39Z] 2016-04-15 01:39:58 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:39:58,387 - WARNING - Could not retrieve variants from source file in region 22:41075332-41075885. Error was invalid region `22:41075333-41075885`
[2016-04-15T08:39Z] 2016-04-15 01:39:58 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:39:58,571 - WARNING - Could not retrieve variants from source file in region 22:41550828-41551229. Error was invalid region `22:41550829-41551229`
[2016-04-15T08:39Z] 2016-04-15 01:39:58 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:39:58,611 - WARNING - Could not retrieve variants from source file in region 22:43529103-43529504. Error was invalid region `22:43529104-43529504`
[2016-04-15T08:40Z] 2016-04-15 01:40:01 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:40:01,164 - WARNING - Could not retrieve variants from source file in region 22:39476912-39498228. Error was invalid region `22:39476913-39498228`
[2016-04-15T08:40Z] 2016-04-15 01:40:01 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:40:01,228 - WARNING - Could not retrieve variants from source file in region 22:38119002-38142512. Error was invalid region `22:38119003-38142512`
[2016-04-15T08:40Z] 2016-04-15 01:40:01 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:40:01,340 - WARNING - Could not retrieve variants from source file in region 22:36877484-36902246. Error was invalid region `22:36877485-36902246`
[2016-04-15T08:40Z] 2016-04-15 01:40:02 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:40:02,120 - WARNING - Could not retrieve variants from source file in region 22:41075332-41075885. Error was invalid region `22:41075333-41075885`
[2016-04-15T08:40Z] 2016-04-15 01:40:02 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:40:02,511 - WARNING - Could not retrieve variants from source file in region 22:41222979-41223380. Error was invalid region `22:41222980-41223380`
[2016-04-15T08:40Z] 2016-04-15 01:40:02 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:40:02,597 - WARNING - Could not retrieve variants from source file in region 22:43529103-43529504. Error was invalid region `22:43529104-43529504`
[2016-04-15T08:40Z] 2016-04-15 01:40:02 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:40:02,633 - WARNING - Could not retrieve variants from source file in region 22:38046484-38052189. Error was invalid region `22:38046485-38052189`
[2016-04-15T08:40Z] 2016-04-15 01:40:06 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:40:06,210 - WARNING - Could not retrieve variants from source file in region 22:41075332-41075885. Error was invalid region `22:41075333-41075885`
[2016-04-15T08:40Z] 2016-04-15 01:40:06 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:40:06,678 - WARNING - Could not retrieve variants from source file in region 22:41222979-41223380. Error was invalid region `22:41222980-41223380`
[2016-04-15T08:40Z] 2016-04-15 01:40:06 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:40:06,985 - WARNING - Could not retrieve variants from source file in region 22:41550828-41551229. Error was invalid region `22:41550829-41551229`
[2016-04-15T08:40Z] 2016-04-15 01:40:08 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:40:08,815 - WARNING - Could not retrieve variants from source file in region 22:36006834-36007265. Error was invalid region `22:36006835-36007265`
[2016-04-15T08:40Z] 2016-04-15 01:40:10 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:40:10,916 - WARNING - Could not retrieve variants from source file in region 22:36006834-36007265. Error was invalid region `22:36006835-36007265`
[2016-04-15T08:40Z] 2016-04-15 01:40:13 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:40:13,220 - WARNING - Could not retrieve variants from source file in region 22:40417569-40418010. Error was invalid region `22:40417570-40418010`
[2016-04-15T08:40Z] 2016-04-15 01:40:13 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:40:13,612 - WARNING - Could not retrieve variants from source file in region 22:36006834-36007265. Error was invalid region `22:36006835-36007265`
[2016-04-15T08:40Z] 2016-04-15 01:40:15 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:40:15,419 - WARNING - Could not retrieve variants from source file in region 22:35462951-35481683. Error was invalid region `22:35462952-35481683`
[2016-04-15T08:40Z] 2016-04-15 01:40:15 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:40:15,772 - WARNING - Could not retrieve variants from source file in region 22:35947374-35947775. Error was invalid region `22:35947375-35947775`
[2016-04-15T08:40Z] 2016-04-15 01:40:17 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:40:17,465 - WARNING - Could not retrieve variants from source file in region 22:40417569-40418010. Error was invalid region `22:40417570-40418010`
[2016-04-15T08:40Z] 2016-04-15 01:40:18 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:40:18,349 - WARNING - Could not retrieve variants from source file in region 22:36586991-36598248. Error was invalid region `22:36586992-36598248`
[2016-04-15T08:40Z] 2016-04-15 01:40:18 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:40:18,998 - WARNING - Could not retrieve variants from source file in region 22:35660664-35661065. Error was invalid region `22:35660665-35661065`
[2016-04-15T08:40Z] 2016-04-15 01:40:19 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:40:19,034 - WARNING - Could not retrieve variants from source file in region 22:40696965-40697369. Error was invalid region `22:40696966-40697369`
[2016-04-15T08:40Z] 2016-04-15 01:40:20 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:40:20,173 - WARNING - Could not retrieve variants from source file in region 22:40551908-40552309. Error was invalid region `22:40551909-40552309`
[2016-04-15T08:40Z] 2016-04-15 01:40:22 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:40:22,850 - WARNING - Could not retrieve variants from source file in region 22:35660664-35661065. Error was invalid region `22:35660665-35661065`
[2016-04-15T08:40Z] 2016-04-15 01:40:23 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:40:23,127 - WARNING - Could not retrieve variants from source file in region 22:40696965-40697369. Error was invalid region `22:40696966-40697369`
[2016-04-15T08:40Z] 2016-04-15 01:40:24 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:40:24,406 - WARNING - Could not retrieve variants from source file in region 22:40551908-40552309. Error was invalid region `22:40551909-40552309`
[2016-04-15T08:40Z] 2016-04-15 01:40:29 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:40:29,291 - WARNING - Could not retrieve variants from source file in region 22:40322473-40322874. Error was invalid region `22:40322474-40322874`
[2016-04-15T08:40Z] 2016-04-15 01:40:31 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:40:31,255 - WARNING - Could not retrieve variants from source file in region 22:36424239-36424640. Error was invalid region `22:36424240-36424640`
[2016-04-15T08:40Z] 2016-04-15 01:40:32 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:40:32,289 - WARNING - Could not retrieve variants from source file in region 22:36537289-36557013. Error was invalid region `22:36537290-36557013`
[2016-04-15T08:40Z] 2016-04-15 01:40:32 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:40:32,821 - WARNING - Could not retrieve variants from source file in region 22:36424239-36424640. Error was invalid region `22:36424240-36424640`
[2016-04-15T08:40Z] 2016-04-15 01:40:32 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:40:32,919 - WARNING - Could not retrieve variants from source file in region 22:39133996-39147425. Error was invalid region `22:39133997-39147425`
[2016-04-15T08:40Z] 2016-04-15 01:40:33 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:40:33,935 - WARNING - Could not retrieve variants from source file in region 22:39381615-39388406. Error was invalid region `22:39381616-39388406`
[2016-04-15T08:40Z] 2016-04-15 01:40:34 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:40:34,378 - WARNING - Could not retrieve variants from source file in region 22:36537289-36557013. Error was invalid region `22:36537290-36557013`
[2016-04-15T08:40Z] 2016-04-15 01:40:35 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:40:35,101 - WARNING - Could not retrieve variants from source file in region 22:40161387-40161788. Error was invalid region `22:40161388-40161788`
[2016-04-15T08:40Z] 2016-04-15 01:40:35 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:40:35,418 - WARNING - Could not retrieve variants from source file in region 22:36424239-36424640. Error was invalid region `22:36424240-36424640`
[2016-04-15T08:40Z] 2016-04-15 01:40:41 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:40:41,203 - WARNING - Could not retrieve variants from source file in region 22:40054737-40075590. Error was invalid region `22:40054738-40075590`
[2016-04-15T08:40Z] 2016-04-15 01:40:43 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:40:43,338 - WARNING - Could not retrieve variants from source file in region 22:39178490-39178891. Error was invalid region `22:39178491-39178891`
[2016-04-15T08:40Z] 2016-04-15 01:40:43 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:40:43,763 - WARNING - Could not retrieve variants from source file in region 22:39218550-39222842. Error was invalid region `22:39218551-39222842`
[2016-04-15T08:40Z] 2016-04-15 01:40:44 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:40:44,420 - WARNING - Could not retrieve variants from source file in region 22:40054737-40075590. Error was invalid region `22:40054738-40075590`
[2016-04-15T08:40Z] 2016-04-15 01:40:46 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:40:46,666 - WARNING - Could not retrieve variants from source file in region 22:39178490-39178891. Error was invalid region `22:39178491-39178891`
[2016-04-15T08:40Z] 2016-04-15 01:40:47 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:40:47,712 - WARNING - Could not retrieve variants from source file in region 22:39096391-39096792. Error was invalid region `22:39096392-39096792`
[2016-04-15T08:40Z] 2016-04-15 01:40:47 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:40:47,764 - WARNING - Could not retrieve variants from source file in region 22:39068970-39069371. Error was invalid region `22:39068971-39069371`
[2016-04-15T08:40Z] ['bcbio-variation-recall', 'square', '-Xms750m', '-Xmx7280m', '-XX:+UseSerialGC', '-c', 16, '-r', u'22:47309230-51304566', '--caller', 'platypus', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/22/Batch1-22_47309229_51304566.vcf.gz', '/mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/22/Batch1-22_47309229_51304566.vcf-inputs.txt'] in region: 22:47309230-51304566
[2016-04-15T08:41Z] 2016-04-15 01:41:05 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:41:05,674 - WARNING - Could not retrieve variants from source file in region 22:51159587-51183445. Error was invalid region `22:51159588-51183445`
[2016-04-15T08:41Z] 2016-04-15 01:41:06 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:41:06,619 - WARNING - Could not retrieve variants from source file in region 22:51117369-51117770. Error was invalid region `22:51117370-51117770`
[2016-04-15T08:41Z] 2016-04-15 01:41:08 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:41:08,453 - WARNING - Could not retrieve variants from source file in region 22:50547036-50555876. Error was invalid region `22:50547037-50555876`
[2016-04-15T08:41Z] 2016-04-15 01:41:12 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:41:12,556 - WARNING - Could not retrieve variants from source file in region 22:51117369-51117770. Error was invalid region `22:51117370-51117770`
[2016-04-15T08:41Z] 2016-04-15 01:41:14 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:41:14,296 - WARNING - Could not retrieve variants from source file in region 22:50217176-50218489. Error was invalid region `22:50217177-50218489`
[2016-04-15T08:41Z] 2016-04-15 01:41:14 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:41:14,919 - WARNING - Could not retrieve variants from source file in region 22:50187642-50188043. Error was invalid region `22:50187643-50188043`
[2016-04-15T08:41Z] 2016-04-15 01:41:16 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:41:16,286 - WARNING - Could not retrieve variants from source file in region 22:48971906-48972307. Error was invalid region `22:48971907-48972307`
[2016-04-15T08:41Z] 2016-04-15 01:41:16 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:41:16,440 - WARNING - Could not retrieve variants from source file in region 22:50354608-50356883. Error was invalid region `22:50354609-50356883`
[2016-04-15T08:41Z] 2016-04-15 01:41:16 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:41:16,868 - WARNING - Could not retrieve variants from source file in region 22:50435269-50439384. Error was invalid region `22:50435270-50439384`
[2016-04-15T08:41Z] 2016-04-15 01:41:17 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:41:17,042 - WARNING - Could not retrieve variants from source file in region 22:51117369-51117770. Error was invalid region `22:51117370-51117770`
[2016-04-15T08:41Z] 2016-04-15 01:41:24 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:41:24,164 - WARNING - Could not retrieve variants from source file in region 22:48971906-48972307. Error was invalid region `22:48971907-48972307`
[2016-04-15T08:41Z] 2016-04-15 01:41:24 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:41:24,445 - WARNING - Could not retrieve variants from source file in region 22:50547036-50555876. Error was invalid region `22:50547037-50555876`
[2016-04-15T08:41Z] ['bcbio-variation-recall', 'square', '-Xms750m', '-Xmx7280m', '-XX:+UseSerialGC', '-c', 16, '-r', u'X:1-15509380', '--caller', 'platypus', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/X/Batch1-X_0_15509380.vcf.gz', '/mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/X/Batch1-X_0_15509380.vcf-inputs.txt'] in region: X:1-15509380
[2016-04-15T08:41Z] 2016-04-15 01:41:42 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:41:42,984 - WARNING - Could not retrieve variants from source file in region X:14626933-14627334. Error was invalid region `X:14626934-14627334`
[2016-04-15T08:41Z] 2016-04-15 01:41:43 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:41:43,262 - WARNING - Could not retrieve variants from source file in region X:10085463-10085864. Error was invalid region `X:10085464-10085864`
[2016-04-15T08:41Z] 2016-04-15 01:41:43 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:41:43,706 - WARNING - Could not retrieve variants from source file in region X:15332347-15332748. Error was invalid region `X:15332348-15332748`
[2016-04-15T08:41Z] 2016-04-15 01:41:43 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:41:43,830 - WARNING - Could not retrieve variants from source file in region X:9858887-9859288. Error was invalid region `X:9858888-9859288`
[2016-04-15T08:41Z] 2016-04-15 01:41:44 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:41:44,199 - WARNING - Could not retrieve variants from source file in region X:15415372-15415773. Error was invalid region `X:15415373-15415773`
[2016-04-15T08:41Z] 2016-04-15 01:41:44 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:41:44,252 - WARNING - Could not retrieve variants from source file in region X:9912541-9936034. Error was invalid region `X:9912542-9936034`
[2016-04-15T08:41Z] 2016-04-15 01:41:44 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:41:44,835 - WARNING - Could not retrieve variants from source file in region X:14032008-14044648. Error was invalid region `X:14032009-14044648`
[2016-04-15T08:41Z] 2016-04-15 01:41:45 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:41:45,085 - WARNING - Could not retrieve variants from source file in region X:2138975-2161319. Error was invalid region `X:2138976-2161319`
[2016-04-15T08:41Z] 2016-04-15 01:41:45 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:41:45,414 - WARNING - Could not retrieve variants from source file in region X:7811434-7812207. Error was invalid region `X:7811435-7812207`
[2016-04-15T08:41Z] 2016-04-15 01:41:45 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:41:45,693 - WARNING - Could not retrieve variants from source file in region X:6975541-6995628. Error was invalid region `X:6975542-6995628`
[2016-04-15T08:41Z] 2016-04-15 01:41:46 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:41:46,825 - WARNING - Could not retrieve variants from source file in region X:8137869-8138493. Error was invalid region `X:8137870-8138493`
[2016-04-15T08:41Z] 2016-04-15 01:41:48 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:41:48,310 - WARNING - Could not retrieve variants from source file in region X:14626933-14627334. Error was invalid region `X:14626934-14627334`
[2016-04-15T08:41Z] 2016-04-15 01:41:48 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:41:48,491 - WARNING - Could not retrieve variants from source file in region X:10085463-10085864. Error was invalid region `X:10085464-10085864`
[2016-04-15T08:41Z] 2016-04-15 01:41:49 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:41:49,364 - WARNING - Could not retrieve variants from source file in region X:11316531-11316932. Error was invalid region `X:11316532-11316932`
[2016-04-15T08:41Z] 2016-04-15 01:41:50 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:41:50,000 - WARNING - Could not retrieve variants from source file in region X:9858887-9859288. Error was invalid region `X:9858888-9859288`
[2016-04-15T08:41Z] 2016-04-15 01:41:51 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:41:51,327 - WARNING - Could not retrieve variants from source file in region X:2777774-2779760. Error was invalid region `X:2777775-2779760`
[2016-04-15T08:41Z] 2016-04-15 01:41:51 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:41:51,595 - WARNING - Could not retrieve variants from source file in region X:15415372-15415773. Error was invalid region `X:15415373-15415773`
[2016-04-15T08:41Z] 2016-04-15 01:41:51 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:41:51,742 - WARNING - Could not retrieve variants from source file in region X:11132859-11157725. Error was invalid region `X:11132860-11157725`
[2016-04-15T08:41Z] 2016-04-15 01:41:52 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:41:52,185 - WARNING - Could not retrieve variants from source file in region X:2138975-2161319. Error was invalid region `X:2138976-2161319`
[2016-04-15T08:41Z] 2016-04-15 01:41:54 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:41:54,176 - WARNING - Could not retrieve variants from source file in region X:15332347-15332748. Error was invalid region `X:15332348-15332748`
[2016-04-15T08:41Z] 2016-04-15 01:41:55 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:41:55,296 - WARNING - Could not retrieve variants from source file in region X:9858887-9859288. Error was invalid region `X:9858888-9859288`
[2016-04-15T08:41Z] 2016-04-15 01:41:57 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:41:57,952 - WARNING - Could not retrieve variants from source file in region X:14032008-14044648. Error was invalid region `X:14032009-14044648`
[2016-04-15T08:41Z] 2016-04-15 01:41:58 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:41:58,969 - WARNING - Could not retrieve variants from source file in region X:15415372-15415773. Error was invalid region `X:15415373-15415773`
[2016-04-15T08:42Z] 2016-04-15 01:42:09 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:42:09,510 - WARNING - Could not retrieve variants from source file in region X:13680904-13681869. Error was invalid region `X:13680905-13681869`
[2016-04-15T08:42Z] 2016-04-15 01:42:10 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:42:10,993 - WARNING - Could not retrieve variants from source file in region X:8503430-8505023. Error was invalid region `X:8503431-8505023`
[2016-04-15T08:42Z] 2016-04-15 01:42:12 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:42:12,257 - WARNING - Could not retrieve variants from source file in region X:7023467-7023868. Error was invalid region `X:7023468-7023868`
[2016-04-15T08:42Z] 2016-04-15 01:42:12 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:42:12,268 - WARNING - Could not retrieve variants from source file in region X:591484-592116. Error was invalid region `X:591485-592116`
[2016-04-15T08:42Z] 2016-04-15 01:42:12 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:42:12,579 - WARNING - Could not retrieve variants from source file in region X:1755193-1761951. Error was invalid region `X:1755194-1761951`
[2016-04-15T08:42Z] 2016-04-15 01:42:13 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:42:13,227 - WARNING - Could not retrieve variants from source file in region X:2658572-2658990. Error was invalid region `X:2658573-2658990`
[2016-04-15T08:42Z] 2016-04-15 01:42:14 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:42:14,538 - WARNING - Could not retrieve variants from source file in region X:2724549-2724950. Error was invalid region `X:2724550-2724950`
[2016-04-15T08:42Z] 2016-04-15 01:42:14 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:42:14,765 - WARNING - Could not retrieve variants from source file in region X:13752684-13753085. Error was invalid region `X:13752685-13753085`
[2016-04-15T08:42Z] 2016-04-15 01:42:15 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:42:15,686 - WARNING - Could not retrieve variants from source file in region X:8503430-8505023. Error was invalid region `X:8503431-8505023`
[2016-04-15T08:42Z] 2016-04-15 01:42:16 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:42:16,570 - WARNING - Could not retrieve variants from source file in region X:7023467-7023868. Error was invalid region `X:7023468-7023868`
[2016-04-15T08:42Z] 2016-04-15 01:42:17 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:42:17,724 - WARNING - Could not retrieve variants from source file in region X:294858-322447. Error was invalid region `X:294859-322447`
[2016-04-15T08:42Z] 2016-04-15 01:42:18 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:42:18,122 - WARNING - Could not retrieve variants from source file in region X:13680904-13681869. Error was invalid region `X:13680905-13681869`
[2016-04-15T08:42Z] 2016-04-15 01:42:18 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:42:18,559 - WARNING - Could not retrieve variants from source file in region X:2724549-2724950. Error was invalid region `X:2724550-2724950`
[2016-04-15T08:42Z] 2016-04-15 01:42:19 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:42:19,108 - WARNING - Could not retrieve variants from source file in region X:13752684-13753085. Error was invalid region `X:13752685-13753085`
[2016-04-15T08:42Z] 2016-04-15 01:42:20 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:42:20,778 - WARNING - Could not retrieve variants from source file in region X:591484-592116. Error was invalid region `X:591485-592116`
[2016-04-15T08:42Z] 2016-04-15 01:42:21 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:42:21,163 - WARNING - Could not retrieve variants from source file in region X:2658572-2658990. Error was invalid region `X:2658573-2658990`
[2016-04-15T08:42Z] 2016-04-15 01:42:22 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:42:22,796 - WARNING - Could not retrieve variants from source file in region X:2724549-2724950. Error was invalid region `X:2724550-2724950`
[2016-04-15T08:42Z] 2016-04-15 01:42:23 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:42:23,175 - WARNING - Could not retrieve variants from source file in region X:13752684-13753085. Error was invalid region `X:13752685-13753085`
[2016-04-15T08:42Z] 2016-04-15 01:42:24 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:42:24,104 - WARNING - Could not retrieve variants from source file in region X:5811319-5821976. Error was invalid region `X:5811320-5821976`
[2016-04-15T08:42Z] 2016-04-15 01:42:28 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:42:28,468 - WARNING - Could not retrieve variants from source file in region X:3228200-3241981. Error was invalid region `X:3228201-3241981`
[2016-04-15T08:42Z] 2016-04-15 01:42:28 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:42:28,776 - WARNING - Could not retrieve variants from source file in region X:3002476-3002877. Error was invalid region `X:3002477-3002877`
[2016-04-15T08:42Z] 2016-04-15 01:42:28 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:42:28,848 - WARNING - Could not retrieve variants from source file in region X:12809450-12809851. Error was invalid region `X:12809451-12809851`
[2016-04-15T08:42Z] 2016-04-15 01:42:30 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:42:30,312 - WARNING - Could not retrieve variants from source file in region X:3002476-3002877. Error was invalid region `X:3002477-3002877`
[2016-04-15T08:42Z] 2016-04-15 01:42:32 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:42:32,751 - WARNING - Could not retrieve variants from source file in region X:3228200-3241981. Error was invalid region `X:3228201-3241981`
[2016-04-15T08:42Z] 2016-04-15 01:42:34 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:42:34,370 - WARNING - Could not retrieve variants from source file in region X:2632271-2632672. Error was invalid region `X:2632272-2632672`
[2016-04-15T08:42Z] 2016-04-15 01:42:36 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:42:36,684 - WARNING - Could not retrieve variants from source file in region X:3630956-3631357. Error was invalid region `X:3630957-3631357`
[2016-04-15T08:42Z] 2016-04-15 01:42:36 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:42:36,972 - WARNING - Could not retrieve variants from source file in region X:2326571-2326972. Error was invalid region `X:2326572-2326972`
[2016-04-15T08:42Z] 2016-04-15 01:42:38 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:42:38,363 - WARNING - Could not retrieve variants from source file in region X:2326571-2326972. Error was invalid region `X:2326572-2326972`
[2016-04-15T08:42Z] 2016-04-15 01:42:38 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:42:38,390 - WARNING - Could not retrieve variants from source file in region X:3630956-3631357. Error was invalid region `X:3630957-3631357`
[2016-04-15T08:42Z] 2016-04-15 01:42:38 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:42:38,441 - WARNING - Could not retrieve variants from source file in region X:3592514-3592915. Error was invalid region `X:3592515-3592915`
[2016-04-15T08:42Z] 2016-04-15 01:42:39 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:42:39,813 - WARNING - Could not retrieve variants from source file in region X:3630956-3631357. Error was invalid region `X:3630957-3631357`
[2016-04-15T08:42Z] 2016-04-15 01:42:40 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:42:40,027 - WARNING - Could not retrieve variants from source file in region X:3592514-3592915. Error was invalid region `X:3592515-3592915`
[2016-04-15T08:42Z] 2016-04-15 01:42:42 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:42:42,358 - WARNING - Could not retrieve variants from source file in region X:3030192-3030593. Error was invalid region `X:3030193-3030593`
[2016-04-15T08:42Z] 2016-04-15 01:42:42 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:42:42,398 - WARNING - Could not retrieve variants from source file in region X:3592514-3592915. Error was invalid region `X:3592515-3592915`
[2016-04-15T08:42Z] ['bcbio-variation-recall', 'square', '-Xms750m', '-Xmx7280m', '-XX:+UseSerialGC', '-c', 16, '-r', u'X:15518900-31090070', '--caller', 'platypus', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/X/Batch1-X_15518899_31090070.vcf.gz', '/mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/X/Batch1-X_15518899_31090070.vcf-inputs.txt'] in region: X:15518900-31090070
[2016-04-15T08:42Z] 2016-04-15 01:42:57 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:42:57,892 - WARNING - Could not retrieve variants from source file in region X:23928278-23928679. Error was invalid region `X:23928279-23928679`
[2016-04-15T08:42Z] 2016-04-15 01:42:57 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:42:57,897 - WARNING - Could not retrieve variants from source file in region X:16887444-16887845. Error was invalid region `X:16887445-16887845`
[2016-04-15T08:42Z] 2016-04-15 01:42:58 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:42:58,313 - WARNING - Could not retrieve variants from source file in region X:24665062-24665463. Error was invalid region `X:24665063-24665463`
[2016-04-15T08:42Z] 2016-04-15 01:42:58 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:42:58,462 - WARNING - Could not retrieve variants from source file in region X:22012701-22013103. Error was invalid region `X:22012702-22013103`
[2016-04-15T08:42Z] 2016-04-15 01:42:58 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:42:58,717 - WARNING - Could not retrieve variants from source file in region X:17819166-17819567. Error was invalid region `X:17819167-17819567`
[2016-04-15T08:42Z] 2016-04-15 01:42:58 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:42:58,787 - WARNING - Could not retrieve variants from source file in region X:30577635-30578036. Error was invalid region `X:30577636-30578036`
[2016-04-15T08:42Z] 2016-04-15 01:42:59 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:42:59,072 - WARNING - Could not retrieve variants from source file in region X:16168256-16168867. Error was invalid region `X:16168257-16168867`
[2016-04-15T08:42Z] 2016-04-15 01:42:59 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:42:59,122 - WARNING - Could not retrieve variants from source file in region X:21861223-21861624. Error was invalid region `X:21861224-21861624`
[2016-04-15T08:42Z] 2016-04-15 01:42:59 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:42:59,364 - WARNING - Could not retrieve variants from source file in region X:15850329-15863466. Error was invalid region `X:15850330-15863466`
[2016-04-15T08:42Z] 2016-04-15 01:42:59 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:42:59,637 - WARNING - Could not retrieve variants from source file in region X:30236667-30261348. Error was invalid region `X:30236668-30261348`
[2016-04-15T08:43Z] 2016-04-15 01:43:00 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:43:00,173 - WARNING - Could not retrieve variants from source file in region X:30872391-30872792. Error was invalid region `X:30872392-30872792`
[2016-04-15T08:43Z] 2016-04-15 01:43:00 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:43:00,181 - WARNING - Could not retrieve variants from source file in region X:25031598-25031999. Error was invalid region `X:25031599-25031999`
[2016-04-15T08:43Z] 2016-04-15 01:43:00 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:43:00,304 - WARNING - Could not retrieve variants from source file in region X:18648818-18649219. Error was invalid region `X:18648819-18649219`
[2016-04-15T08:43Z] 2016-04-15 01:43:00 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:43:00,355 - WARNING - Could not retrieve variants from source file in region X:26212691-26213092. Error was invalid region `X:26212692-26213092`
[2016-04-15T08:43Z] 2016-04-15 01:43:05 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:43:05,952 - WARNING - Could not retrieve variants from source file in region X:24665062-24665463. Error was invalid region `X:24665063-24665463`
[2016-04-15T08:43Z] 2016-04-15 01:43:06 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:43:06,156 - WARNING - Could not retrieve variants from source file in region X:23928278-23928679. Error was invalid region `X:23928279-23928679`
[2016-04-15T08:43Z] 2016-04-15 01:43:06 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:43:06,695 - WARNING - Could not retrieve variants from source file in region X:16859417-16859818. Error was invalid region `X:16859418-16859818`
[2016-04-15T08:43Z] 2016-04-15 01:43:07 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:43:07,145 - WARNING - Could not retrieve variants from source file in region X:30577635-30578036. Error was invalid region `X:30577636-30578036`
[2016-04-15T08:43Z] 2016-04-15 01:43:07 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:43:07,181 - WARNING - Could not retrieve variants from source file in region X:17819166-17819567. Error was invalid region `X:17819167-17819567`
[2016-04-15T08:43Z] 2016-04-15 01:43:08 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:43:08,123 - WARNING - Could not retrieve variants from source file in region X:30872391-30872792. Error was invalid region `X:30872392-30872792`
[2016-04-15T08:43Z] 2016-04-15 01:43:08 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:43:08,139 - WARNING - Could not retrieve variants from source file in region X:21861223-21861624. Error was invalid region `X:21861224-21861624`
[2016-04-15T08:43Z] 2016-04-15 01:43:10 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:43:10,293 - WARNING - Could not retrieve variants from source file in region X:16887444-16887845. Error was invalid region `X:16887445-16887845`
[2016-04-15T08:43Z] 2016-04-15 01:43:10 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:43:10,678 - WARNING - Could not retrieve variants from source file in region X:22012701-22013103. Error was invalid region `X:22012702-22013103`
[2016-04-15T08:43Z] 2016-04-15 01:43:11 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:43:11,491 - WARNING - Could not retrieve variants from source file in region X:24665062-24665463. Error was invalid region `X:24665063-24665463`
[2016-04-15T08:43Z] 2016-04-15 01:43:12 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:43:12,944 - WARNING - Could not retrieve variants from source file in region X:23928278-23928679. Error was invalid region `X:23928279-23928679`
[2016-04-15T08:43Z] 2016-04-15 01:43:13 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:43:13,939 - WARNING - Could not retrieve variants from source file in region X:30577635-30578036. Error was invalid region `X:30577636-30578036`
[2016-04-15T08:43Z] 2016-04-15 01:43:15 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:43:15,056 - WARNING - Could not retrieve variants from source file in region X:15850329-15863466. Error was invalid region `X:15850330-15863466`
[2016-04-15T08:43Z] 2016-04-15 01:43:15 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:43:15,120 - WARNING - Could not retrieve variants from source file in region X:16168256-16168867. Error was invalid region `X:16168257-16168867`
[2016-04-15T08:43Z] 2016-04-15 01:43:15 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:43:15,894 - WARNING - Could not retrieve variants from source file in region X:30872391-30872792. Error was invalid region `X:30872392-30872792`
[2016-04-15T08:43Z] 2016-04-15 01:43:15 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:43:15,944 - WARNING - Could not retrieve variants from source file in region X:25031598-25031999. Error was invalid region `X:25031599-25031999`
[2016-04-15T08:43Z] 2016-04-15 01:43:16 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:43:16,024 - WARNING - Could not retrieve variants from source file in region X:17819166-17819567. Error was invalid region `X:17819167-17819567`
[2016-04-15T08:43Z] 2016-04-15 01:43:16 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:43:16,275 - WARNING - Could not retrieve variants from source file in region X:18648818-18649219. Error was invalid region `X:18648819-18649219`
[2016-04-15T08:43Z] 2016-04-15 01:43:24 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:43:24,886 - WARNING - Could not retrieve variants from source file in region X:21977849-21978250. Error was invalid region `X:21977850-21978250`
[2016-04-15T08:43Z] 2016-04-15 01:43:26 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:43:26,969 - WARNING - Could not retrieve variants from source file in region X:24073550-24073951. Error was invalid region `X:24073551-24073951`
[2016-04-15T08:43Z] 2016-04-15 01:43:27 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:43:27,209 - WARNING - Could not retrieve variants from source file in region X:24073550-24073951. Error was invalid region `X:24073551-24073951`
[2016-04-15T08:43Z] 2016-04-15 01:43:27 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:43:27,253 - WARNING - Could not retrieve variants from source file in region X:24073550-24073951. Error was invalid region `X:24073551-24073951`
[2016-04-15T08:43Z] 2016-04-15 01:43:27 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:43:27,655 - WARNING - Could not retrieve variants from source file in region X:21977849-21978250. Error was invalid region `X:21977850-21978250`
[2016-04-15T08:43Z] 2016-04-15 01:43:28 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:43:28,442 - WARNING - Could not retrieve variants from source file in region X:23398003-23398404. Error was invalid region `X:23398004-23398404`
[2016-04-15T08:43Z] 2016-04-15 01:43:28 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:43:28,588 - WARNING - Could not retrieve variants from source file in region X:23398003-23398404. Error was invalid region `X:23398004-23398404`
[2016-04-15T08:43Z] 2016-04-15 01:43:28 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:43:28,816 - WARNING - Could not retrieve variants from source file in region X:19482265-19482666. Error was invalid region `X:19482266-19482666`
[2016-04-15T08:43Z] 2016-04-15 01:43:30 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:43:30,079 - WARNING - Could not retrieve variants from source file in region X:19410012-19410413. Error was invalid region `X:19410013-19410413`
[2016-04-15T08:43Z] 2016-04-15 01:43:30 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:43:30,349 - WARNING - Could not retrieve variants from source file in region X:23019106-23019536. Error was invalid region `X:23019107-23019536`
[2016-04-15T08:43Z] 2016-04-15 01:43:31 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:43:31,404 - WARNING - Could not retrieve variants from source file in region X:19482265-19482666. Error was invalid region `X:19482266-19482666`
[2016-04-15T08:43Z] 2016-04-15 01:43:31 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:43:31,453 - WARNING - Could not retrieve variants from source file in region X:21901692-21902093. Error was invalid region `X:21901693-21902093`
[2016-04-15T08:43Z] 2016-04-15 01:43:31 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:43:31,862 - WARNING - Could not retrieve variants from source file in region X:19482265-19482666. Error was invalid region `X:19482266-19482666`
[2016-04-15T08:43Z] 2016-04-15 01:43:33 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:43:33,703 - WARNING - Could not retrieve variants from source file in region X:19410012-19410413. Error was invalid region `X:19410013-19410413`
[2016-04-15T08:43Z] 2016-04-15 01:43:35 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:43:35,005 - WARNING - Could not retrieve variants from source file in region X:21901692-21902093. Error was invalid region `X:21901693-21902093`
[2016-04-15T08:43Z] ['bcbio-variation-recall', 'square', '-Xms750m', '-Xmx7280m', '-XX:+UseSerialGC', '-c', 16, '-r', u'X:31139950-46696637', '--caller', 'platypus', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/X/Batch1-X_31139949_46696637.vcf.gz', '/mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/X/Batch1-X_31139949_46696637.vcf-inputs.txt'] in region: X:31139950-46696637
[2016-04-15T08:43Z] 2016-04-15 01:43:51 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:43:50,996 - WARNING - Could not retrieve variants from source file in region X:41587007-41587408. Error was invalid region `X:41587008-41587408`
[2016-04-15T08:43Z] 2016-04-15 01:43:51 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:43:51,163 - WARNING - Could not retrieve variants from source file in region X:37029214-37029615. Error was invalid region `X:37029215-37029615`
[2016-04-15T08:43Z] 2016-04-15 01:43:51 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:43:51,471 - WARNING - Could not retrieve variants from source file in region X:40506486-40507004. Error was invalid region `X:40506487-40507004`
[2016-04-15T08:43Z] 2016-04-15 01:43:51 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:43:51,589 - WARNING - Could not retrieve variants from source file in region X:43590825-43603581. Error was invalid region `X:43590826-43603581`
[2016-04-15T08:43Z] 2016-04-15 01:43:53 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:43:53,046 - WARNING - Could not retrieve variants from source file in region X:46618110-46618511. Error was invalid region `X:46618111-46618511`
[2016-04-15T08:43Z] 2016-04-15 01:43:53 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:43:53,054 - WARNING - Could not retrieve variants from source file in region X:37932675-37968058. Error was invalid region `X:37932676-37968058`
[2016-04-15T08:43Z] 2016-04-15 01:43:53 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:43:53,057 - WARNING - Could not retrieve variants from source file in region X:40572946-40573347. Error was invalid region `X:40572947-40573347`
[2016-04-15T08:43Z] 2016-04-15 01:43:53 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:43:53,153 - WARNING - Could not retrieve variants from source file in region X:46472615-46473016. Error was invalid region `X:46472616-46473016`
[2016-04-15T08:43Z] 2016-04-15 01:43:53 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:43:53,875 - WARNING - Could not retrieve variants from source file in region X:31893096-31893497. Error was invalid region `X:31893097-31893497`
[2016-04-15T08:43Z] 2016-04-15 01:43:54 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:43:54,034 - WARNING - Could not retrieve variants from source file in region X:37300192-37300593. Error was invalid region `X:37300193-37300593`
[2016-04-15T08:43Z] 2016-04-15 01:43:54 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:43:54,047 - WARNING - Could not retrieve variants from source file in region X:45021381-45023517. Error was invalid region `X:45021382-45023517`
[2016-04-15T08:43Z] 2016-04-15 01:43:57 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:43:57,158 - WARNING - Could not retrieve variants from source file in region X:38079764-38080168. Error was invalid region `X:38079765-38080168`
[2016-04-15T08:43Z] 2016-04-15 01:43:57 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:43:57,479 - WARNING - Could not retrieve variants from source file in region X:41587007-41587408. Error was invalid region `X:41587008-41587408`
[2016-04-15T08:43Z] 2016-04-15 01:43:59 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:43:59,548 - WARNING - Could not retrieve variants from source file in region X:43590825-43603581. Error was invalid region `X:43590826-43603581`
[2016-04-15T08:44Z] 2016-04-15 01:44:02 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:44:02,514 - WARNING - Could not retrieve variants from source file in region X:41193534-41193936. Error was invalid region `X:41193535-41193936`
[2016-04-15T08:44Z] 2016-04-15 01:44:02 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:44:02,559 - WARNING - Could not retrieve variants from source file in region X:37300192-37300593. Error was invalid region `X:37300193-37300593`
[2016-04-15T08:44Z] 2016-04-15 01:44:02 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:44:02,605 - WARNING - Could not retrieve variants from source file in region X:40572946-40573347. Error was invalid region `X:40572947-40573347`
[2016-04-15T08:44Z] 2016-04-15 01:44:02 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:44:02,981 - WARNING - Could not retrieve variants from source file in region X:31893096-31893497. Error was invalid region `X:31893097-31893497`
[2016-04-15T08:44Z] 2016-04-15 01:44:03 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:44:03,018 - WARNING - Could not retrieve variants from source file in region X:39932696-39933529. Error was invalid region `X:39932697-39933529`
[2016-04-15T08:44Z] 2016-04-15 01:44:03 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:44:03,254 - WARNING - Could not retrieve variants from source file in region X:41587007-41587408. Error was invalid region `X:41587008-41587408`
[2016-04-15T08:44Z] 2016-04-15 01:44:03 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:44:03,421 - WARNING - Could not retrieve variants from source file in region X:40506486-40507004. Error was invalid region `X:40506487-40507004`
[2016-04-15T08:44Z] 2016-04-15 01:44:04 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:44:04,140 - WARNING - Could not retrieve variants from source file in region X:43590825-43603581. Error was invalid region `X:43590826-43603581`
[2016-04-15T08:44Z] 2016-04-15 01:44:09 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:44:09,294 - WARNING - Could not retrieve variants from source file in region X:37300192-37300593. Error was invalid region `X:37300193-37300593`
[2016-04-15T08:44Z] 2016-04-15 01:44:10 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:44:10,458 - WARNING - Could not retrieve variants from source file in region X:40572946-40573347. Error was invalid region `X:40572947-40573347`
[2016-04-15T08:44Z] 2016-04-15 01:44:19 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:44:19,473 - WARNING - Could not retrieve variants from source file in region X:35820214-35821317. Error was invalid region `X:35820215-35821317`
[2016-04-15T08:44Z] 2016-04-15 01:44:19 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:44:19,474 - WARNING - Could not retrieve variants from source file in region X:32502983-32509815. Error was invalid region `X:32502984-32509815`
[2016-04-15T08:44Z] 2016-04-15 01:44:19 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:44:19,517 - WARNING - Could not retrieve variants from source file in region X:35820214-35821317. Error was invalid region `X:35820215-35821317`
[2016-04-15T08:44Z] 2016-04-15 01:44:20 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:44:20,815 - WARNING - Could not retrieve variants from source file in region X:31697425-31697826. Error was invalid region `X:31697426-31697826`
[2016-04-15T08:44Z] 2016-04-15 01:44:20 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:44:20,821 - WARNING - Could not retrieve variants from source file in region X:32380785-32381186. Error was invalid region `X:32380786-32381186`
[2016-04-15T08:44Z] 2016-04-15 01:44:21 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:44:21,123 - WARNING - Could not retrieve variants from source file in region X:31496139-31496540. Error was invalid region `X:31496140-31496540`
[2016-04-15T08:44Z] 2016-04-15 01:44:23 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:44:23,685 - WARNING - Could not retrieve variants from source file in region X:31496139-31496540. Error was invalid region `X:31496140-31496540`
[2016-04-15T08:44Z] 2016-04-15 01:44:23 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:44:23,762 - WARNING - Could not retrieve variants from source file in region X:31697425-31697826. Error was invalid region `X:31697426-31697826`
[2016-04-15T08:44Z] 2016-04-15 01:44:24 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:44:24,129 - WARNING - Could not retrieve variants from source file in region X:31496139-31496540. Error was invalid region `X:31496140-31496540`
[2016-04-15T08:44Z] ['bcbio-variation-recall', 'square', '-Xms750m', '-Xmx7280m', '-XX:+UseSerialGC', '-c', 16, '-r', u'X:46712911-62570698', '--caller', 'platypus', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/X/Batch1-X_46712910_62570698.vcf.gz', '/mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/X/Batch1-X_46712910_62570698.vcf-inputs.txt'] in region: X:46712911-62570698
[2016-04-15T08:44Z] 2016-04-15 01:44:38 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:44:38,733 - WARNING - Could not retrieve variants from source file in region X:57619437-57619838. Error was invalid region `X:57619438-57619838`
[2016-04-15T08:44Z] 2016-04-15 01:44:39 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:44:39,220 - WARNING - Could not retrieve variants from source file in region X:55116255-55116656. Error was invalid region `X:55116256-55116656`
[2016-04-15T08:44Z] 2016-04-15 01:44:39 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:44:39,447 - WARNING - Could not retrieve variants from source file in region X:48049455-48054930. Error was invalid region `X:48049456-48054930`
[2016-04-15T08:44Z] 2016-04-15 01:44:40 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:44:40,304 - WARNING - Could not retrieve variants from source file in region X:47917994-47918395. Error was invalid region `X:47917995-47918395`
[2016-04-15T08:44Z] 2016-04-15 01:44:40 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:44:40,976 - WARNING - Could not retrieve variants from source file in region X:50350463-50350948. Error was invalid region `X:50350464-50350948`
[2016-04-15T08:44Z] 2016-04-15 01:44:40 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:44:40,985 - WARNING - Could not retrieve variants from source file in region X:55514607-55515008. Error was invalid region `X:55514608-55515008`
[2016-04-15T08:44Z] 2016-04-15 01:44:41 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:44:41,383 - WARNING - Could not retrieve variants from source file in region X:50118874-50129559. Error was invalid region `X:50118875-50129559`
[2016-04-15T08:44Z] 2016-04-15 01:44:41 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:44:41,845 - WARNING - Could not retrieve variants from source file in region X:54209091-54209577. Error was invalid region `X:54209092-54209577`
[2016-04-15T08:44Z] 2016-04-15 01:44:42 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:44:42,054 - WARNING - Could not retrieve variants from source file in region X:51239084-51239499. Error was invalid region `X:51239085-51239499`
[2016-04-15T08:44Z] 2016-04-15 01:44:42 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:44:42,141 - WARNING - Could not retrieve variants from source file in region X:49179487-49179945. Error was invalid region `X:49179488-49179945`
[2016-04-15T08:44Z] 2016-04-15 01:44:42 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:44:42,165 - WARNING - Could not retrieve variants from source file in region X:51644537-51644938. Error was invalid region `X:51644538-51644938`
[2016-04-15T08:44Z] 2016-04-15 01:44:42 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:44:42,167 - WARNING - Could not retrieve variants from source file in region X:47444668-47466551. Error was invalid region `X:47444669-47466551`
[2016-04-15T08:44Z] 2016-04-15 01:44:43 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:44:43,483 - WARNING - Could not retrieve variants from source file in region X:57619437-57619838. Error was invalid region `X:57619438-57619838`
[2016-04-15T08:44Z] 2016-04-15 01:44:44 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:44:44,542 - WARNING - Could not retrieve variants from source file in region X:55116255-55116656. Error was invalid region `X:55116256-55116656`
[2016-04-15T08:44Z] 2016-04-15 01:44:45 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:44:45,175 - WARNING - Could not retrieve variants from source file in region X:48049455-48054930. Error was invalid region `X:48049456-48054930`
[2016-04-15T08:44Z] 2016-04-15 01:44:47 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:44:47,336 - WARNING - Could not retrieve variants from source file in region X:54951253-54951654. Error was invalid region `X:54951254-54951654`
[2016-04-15T08:44Z] 2016-04-15 01:44:48 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:44:48,398 - WARNING - Could not retrieve variants from source file in region X:49020841-49022890. Error was invalid region `X:49020842-49022890`
[2016-04-15T08:44Z] 2016-04-15 01:44:49 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:44:49,105 - WARNING - Could not retrieve variants from source file in region X:50350463-50350948. Error was invalid region `X:50350464-50350948`
[2016-04-15T08:44Z] 2016-04-15 01:44:49 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:44:49,489 - WARNING - Could not retrieve variants from source file in region X:49061531-49061932. Error was invalid region `X:49061532-49061932`
[2016-04-15T08:44Z] 2016-04-15 01:44:49 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:44:49,594 - WARNING - Could not retrieve variants from source file in region X:55514607-55515008. Error was invalid region `X:55514608-55515008`
[2016-04-15T08:44Z] 2016-04-15 01:44:49 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:44:49,858 - WARNING - Could not retrieve variants from source file in region X:51239084-51239499. Error was invalid region `X:51239085-51239499`
[2016-04-15T08:44Z] 2016-04-15 01:44:49 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:44:49,949 - WARNING - Could not retrieve variants from source file in region X:51644537-51644938. Error was invalid region `X:51644538-51644938`
[2016-04-15T08:44Z] 2016-04-15 01:44:50 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:44:50,191 - WARNING - Could not retrieve variants from source file in region X:57619437-57619838. Error was invalid region `X:57619438-57619838`
[2016-04-15T08:44Z] 2016-04-15 01:44:50 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:44:50,258 - WARNING - Could not retrieve variants from source file in region X:49179487-49179945. Error was invalid region `X:49179488-49179945`
[2016-04-15T08:44Z] 2016-04-15 01:44:50 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:44:50,327 - WARNING - Could not retrieve variants from source file in region X:55116255-55116656. Error was invalid region `X:55116256-55116656`
[2016-04-15T08:44Z] 2016-04-15 01:44:50 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:44:50,525 - WARNING - Could not retrieve variants from source file in region X:47444668-47466551. Error was invalid region `X:47444669-47466551`
[2016-04-15T08:44Z] 2016-04-15 01:44:50 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:44:50,601 - WARNING - Could not retrieve variants from source file in region X:48049455-48054930. Error was invalid region `X:48049456-48054930`
[2016-04-15T08:44Z] 2016-04-15 01:44:51 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:44:51,349 - WARNING - Could not retrieve variants from source file in region X:47917994-47918395. Error was invalid region `X:47917995-47918395`
[2016-04-15T08:44Z] 2016-04-15 01:44:55 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:44:55,982 - WARNING - Could not retrieve variants from source file in region X:50350463-50350948. Error was invalid region `X:50350464-50350948`
[2016-04-15T08:44Z] 2016-04-15 01:44:57 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:44:57,706 - WARNING - Could not retrieve variants from source file in region X:50118874-50129559. Error was invalid region `X:50118875-50129559`
[2016-04-15T08:44Z] 2016-04-15 01:44:57 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:44:57,855 - WARNING - Could not retrieve variants from source file in region X:55514607-55515008. Error was invalid region `X:55514608-55515008`
[2016-04-15T08:44Z] 2016-04-15 01:44:58 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:44:58,363 - WARNING - Could not retrieve variants from source file in region X:51239084-51239499. Error was invalid region `X:51239085-51239499`
[2016-04-15T08:44Z] 2016-04-15 01:44:58 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:44:58,479 - WARNING - Could not retrieve variants from source file in region X:49179487-49179945. Error was invalid region `X:49179488-49179945`
[2016-04-15T08:44Z] 2016-04-15 01:44:58 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:44:58,981 - WARNING - Could not retrieve variants from source file in region X:54209091-54209577. Error was invalid region `X:54209092-54209577`
[2016-04-15T08:45Z] 2016-04-15 01:45:09 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:45:09,007 - WARNING - Could not retrieve variants from source file in region X:48417915-48460504. Error was invalid region `X:48417916-48460504`
[2016-04-15T08:45Z] 2016-04-15 01:45:09 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:45:09,779 - WARNING - Could not retrieve variants from source file in region X:48887863-48888264. Error was invalid region `X:48887864-48888264`
[2016-04-15T08:45Z] 2016-04-15 01:45:10 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:45:10,302 - WARNING - Could not retrieve variants from source file in region X:57474921-57475322. Error was invalid region `X:57474922-57475322`
[2016-04-15T08:45Z] 2016-04-15 01:45:10 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:45:10,381 - WARNING - Could not retrieve variants from source file in region X:53457411-53457812. Error was invalid region `X:53457412-53457812`
[2016-04-15T08:45Z] 2016-04-15 01:45:10 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:45:10,979 - WARNING - Could not retrieve variants from source file in region X:54836150-54841927. Error was invalid region `X:54836151-54841927`
[2016-04-15T08:45Z] 2016-04-15 01:45:11 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:45:11,048 - WARNING - Could not retrieve variants from source file in region X:49369500-49369901. Error was invalid region `X:49369501-49369901`
[2016-04-15T08:45Z] 2016-04-15 01:45:11 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:45:11,679 - WARNING - Could not retrieve variants from source file in region X:47308281-47308682. Error was invalid region `X:47308282-47308682`
[2016-04-15T08:45Z] 2016-04-15 01:45:12 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:45:12,924 - WARNING - Could not retrieve variants from source file in region X:47057436-47062724. Error was invalid region `X:47057437-47062724`
[2016-04-15T08:45Z] 2016-04-15 01:45:15 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:45:15,347 - WARNING - Could not retrieve variants from source file in region X:53457411-53457812. Error was invalid region `X:53457412-53457812`
[2016-04-15T08:45Z] 2016-04-15 01:45:15 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:45:15,864 - WARNING - Could not retrieve variants from source file in region X:57474921-57475322. Error was invalid region `X:57474922-57475322`
[2016-04-15T08:45Z] 2016-04-15 01:45:16 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:45:16,718 - WARNING - Could not retrieve variants from source file in region X:54162749-54163150. Error was invalid region `X:54162750-54163150`
[2016-04-15T08:45Z] 2016-04-15 01:45:16 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:45:16,765 - WARNING - Could not retrieve variants from source file in region X:48814779-48847687. Error was invalid region `X:48814780-48847687`
[2016-04-15T08:45Z] 2016-04-15 01:45:16 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:45:16,807 - WARNING - Could not retrieve variants from source file in region X:49369500-49369901. Error was invalid region `X:49369501-49369901`
[2016-04-15T08:45Z] 2016-04-15 01:45:17 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:45:17,194 - WARNING - Could not retrieve variants from source file in region X:54111974-54112375. Error was invalid region `X:54111975-54112375`
[2016-04-15T08:45Z] 2016-04-15 01:45:18 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:45:18,055 - WARNING - Could not retrieve variants from source file in region X:54784192-54784593. Error was invalid region `X:54784193-54784593`
[2016-04-15T08:45Z] 2016-04-15 01:45:18 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:45:18,697 - WARNING - Could not retrieve variants from source file in region X:48887863-48888264. Error was invalid region `X:48887864-48888264`
[2016-04-15T08:45Z] 2016-04-15 01:45:20 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:45:20,861 - WARNING - Could not retrieve variants from source file in region X:57474921-57475322. Error was invalid region `X:57474922-57475322`
[2016-04-15T08:45Z] 2016-04-15 01:45:21 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:45:21,673 - WARNING - Could not retrieve variants from source file in region X:49369500-49369901. Error was invalid region `X:49369501-49369901`
[2016-04-15T08:45Z] 2016-04-15 01:45:23 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:45:23,122 - WARNING - Could not retrieve variants from source file in region X:47057436-47062724. Error was invalid region `X:47057437-47062724`
[2016-04-15T08:45Z] 2016-04-15 01:45:31 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:45:31,854 - WARNING - Could not retrieve variants from source file in region X:48316830-48317234. Error was invalid region `X:48316831-48317234`
[2016-04-15T08:45Z] 2016-04-15 01:45:32 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:45:32,436 - WARNING - Could not retrieve variants from source file in region X:53221832-53222233. Error was invalid region `X:53221833-53222233`
[2016-04-15T08:45Z] 2016-04-15 01:45:33 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:45:33,040 - WARNING - Could not retrieve variants from source file in region X:57404952-57405353. Error was invalid region `X:57404953-57405353`
[2016-04-15T08:45Z] 2016-04-15 01:45:34 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:45:34,122 - WARNING - Could not retrieve variants from source file in region X:53221832-53222233. Error was invalid region `X:53221833-53222233`
[2016-04-15T08:45Z] 2016-04-15 01:45:34 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:45:34,394 - WARNING - Could not retrieve variants from source file in region X:48116744-48125988. Error was invalid region `X:48116745-48125988`
[2016-04-15T08:45Z] 2016-04-15 01:45:34 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:45:34,477 - WARNING - Could not retrieve variants from source file in region X:52891442-52891843. Error was invalid region `X:52891443-52891843`
[2016-04-15T08:45Z] 2016-04-15 01:45:35 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:45:35,117 - WARNING - Could not retrieve variants from source file in region X:53641436-53641837. Error was invalid region `X:53641437-53641837`
[2016-04-15T08:45Z] 2016-04-15 01:45:36 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:45:36,745 - WARNING - Could not retrieve variants from source file in region X:52674305-52682166. Error was invalid region `X:52674306-52682166`
[2016-04-15T08:45Z] 2016-04-15 01:45:36 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:45:36,880 - WARNING - Could not retrieve variants from source file in region X:52825335-52825736. Error was invalid region `X:52825336-52825736`
[2016-04-15T08:45Z] 2016-04-15 01:45:37 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:45:37,265 - WARNING - Could not retrieve variants from source file in region X:53221832-53222233. Error was invalid region `X:53221833-53222233`
[2016-04-15T08:45Z] 2016-04-15 01:45:37 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:45:37,266 - WARNING - Could not retrieve variants from source file in region X:53563378-53563779. Error was invalid region `X:53563379-53563779`
[2016-04-15T08:45Z] 2016-04-15 01:45:37 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:45:37,457 - WARNING - Could not retrieve variants from source file in region X:57404952-57405353. Error was invalid region `X:57404953-57405353`
[2016-04-15T08:45Z] 2016-04-15 01:45:37 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:45:37,863 - WARNING - Could not retrieve variants from source file in region X:55650790-55651191. Error was invalid region `X:55650791-55651191`
[2016-04-15T08:45Z] 2016-04-15 01:45:39 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:45:39,431 - WARNING - Could not retrieve variants from source file in region X:53641436-53641837. Error was invalid region `X:53641437-53641837`
[2016-04-15T08:45Z] 2016-04-15 01:45:40 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:45:40,990 - WARNING - Could not retrieve variants from source file in region X:48116744-48125988. Error was invalid region `X:48116745-48125988`
[2016-04-15T08:45Z] 2016-04-15 01:45:41 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:45:41,538 - WARNING - Could not retrieve variants from source file in region X:52825335-52825736. Error was invalid region `X:52825336-52825736`
[2016-04-15T08:45Z] 2016-04-15 01:45:42 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:45:42,284 - WARNING - Could not retrieve variants from source file in region X:57404952-57405353. Error was invalid region `X:57404953-57405353`
[2016-04-15T08:45Z] 2016-04-15 01:45:42 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:45:42,309 - WARNING - Could not retrieve variants from source file in region X:53563378-53563779. Error was invalid region `X:53563379-53563779`
[2016-04-15T08:45Z] 2016-04-15 01:45:42 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:45:42,357 - WARNING - Could not retrieve variants from source file in region X:55650790-55651191. Error was invalid region `X:55650791-55651191`
[2016-04-15T08:45Z] 2016-04-15 01:45:43 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:45:43,562 - WARNING - Could not retrieve variants from source file in region X:52891442-52891843. Error was invalid region `X:52891443-52891843`
[2016-04-15T08:45Z] 2016-04-15 01:45:45 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:45:45,320 - WARNING - Could not retrieve variants from source file in region X:52825335-52825736. Error was invalid region `X:52825336-52825736`
[2016-04-15T08:45Z] 2016-04-15 01:45:45 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:45:45,790 - WARNING - Could not retrieve variants from source file in region X:53563378-53563779. Error was invalid region `X:53563379-53563779`
[2016-04-15T08:45Z] 2016-04-15 01:45:45 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:45:45,824 - WARNING - Could not retrieve variants from source file in region X:55650790-55651191. Error was invalid region `X:55650791-55651191`
[2016-04-15T08:45Z] ['bcbio-variation-recall', 'square', '-Xms750m', '-Xmx7280m', '-XX:+UseSerialGC', '-c', 16, '-r', u'X:62857908-78427545', '--caller', 'platypus', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/X/Batch1-X_62857907_78427545.vcf.gz', '/mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/X/Batch1-X_62857907_78427545.vcf-inputs.txt'] in region: X:62857908-78427545
[2016-04-15T08:46Z] 2016-04-15 01:46:00 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:46:00,957 - WARNING - Could not retrieve variants from source file in region X:69652551-69652952. Error was invalid region `X:69652552-69652952`
[2016-04-15T08:46Z] 2016-04-15 01:46:01 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:46:01,666 - WARNING - Could not retrieve variants from source file in region X:70146187-70148261. Error was invalid region `X:70146188-70148261`
[2016-04-15T08:46Z] 2016-04-15 01:46:03 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:46:03,306 - WARNING - Could not retrieve variants from source file in region X:70349736-70361341. Error was invalid region `X:70349737-70361341`
[2016-04-15T08:46Z] 2016-04-15 01:46:03 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:46:03,822 - WARNING - Could not retrieve variants from source file in region X:73641358-73641759. Error was invalid region `X:73641359-73641759`
[2016-04-15T08:46Z] 2016-04-15 01:46:04 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:46:04,380 - WARNING - Could not retrieve variants from source file in region X:71493480-71493881. Error was invalid region `X:71493481-71493881`
[2016-04-15T08:46Z] 2016-04-15 01:46:04 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:46:04,437 - WARNING - Could not retrieve variants from source file in region X:76937752-76938153. Error was invalid region `X:76937753-76938153`
[2016-04-15T08:46Z] 2016-04-15 01:46:04 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:46:04,692 - WARNING - Could not retrieve variants from source file in region X:77528106-77528507. Error was invalid region `X:77528107-77528507`
[2016-04-15T08:46Z] 2016-04-15 01:46:05 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:46:05,045 - WARNING - Could not retrieve variants from source file in region X:78426260-78427178. Error was invalid region `X:78426261-78427178`
[2016-04-15T08:46Z] 2016-04-15 01:46:05 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:46:05,202 - WARNING - Could not retrieve variants from source file in region X:71521656-71522057. Error was invalid region `X:71521657-71522057`
[2016-04-15T08:46Z] 2016-04-15 01:46:05 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:46:05,498 - WARNING - Could not retrieve variants from source file in region X:70323946-70324347. Error was invalid region `X:70323947-70324347`
[2016-04-15T08:46Z] 2016-04-15 01:46:05 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:46:05,510 - WARNING - Could not retrieve variants from source file in region X:67937064-67937465. Error was invalid region `X:67937065-67937465`
[2016-04-15T08:46Z] 2016-04-15 01:46:05 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:46:05,545 - WARNING - Could not retrieve variants from source file in region X:65382474-65382875. Error was invalid region `X:65382475-65382875`
[2016-04-15T08:46Z] 2016-04-15 01:46:05 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:46:05,730 - WARNING - Could not retrieve variants from source file in region X:69652551-69652952. Error was invalid region `X:69652552-69652952`
[2016-04-15T08:46Z] 2016-04-15 01:46:07 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:46:07,476 - WARNING - Could not retrieve variants from source file in region X:77268291-77268692. Error was invalid region `X:77268292-77268692`
[2016-04-15T08:46Z] 2016-04-15 01:46:08 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:46:08,832 - WARNING - Could not retrieve variants from source file in region X:71840503-71840904. Error was invalid region `X:71840504-71840904`
[2016-04-15T08:46Z] 2016-04-15 01:46:11 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:46:11,496 - WARNING - Could not retrieve variants from source file in region X:71493480-71493881. Error was invalid region `X:71493481-71493881`
[2016-04-15T08:46Z] 2016-04-15 01:46:13 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:46:13,166 - WARNING - Could not retrieve variants from source file in region X:78426260-78427178. Error was invalid region `X:78426261-78427178`
[2016-04-15T08:46Z] 2016-04-15 01:46:13 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:46:13,235 - WARNING - Could not retrieve variants from source file in region X:76937752-76938153. Error was invalid region `X:76937753-76938153`
[2016-04-15T08:46Z] 2016-04-15 01:46:13 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:46:13,448 - WARNING - Could not retrieve variants from source file in region X:71521656-71522057. Error was invalid region `X:71521657-71522057`
[2016-04-15T08:46Z] 2016-04-15 01:46:13 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:46:13,736 - WARNING - Could not retrieve variants from source file in region X:65382474-65382875. Error was invalid region `X:65382475-65382875`
[2016-04-15T08:46Z] 2016-04-15 01:46:13 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:46:13,781 - WARNING - Could not retrieve variants from source file in region X:69652551-69652952. Error was invalid region `X:69652552-69652952`
[2016-04-15T08:46Z] 2016-04-15 01:46:14 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:46:14,073 - WARNING - Could not retrieve variants from source file in region X:70349736-70361341. Error was invalid region `X:70349737-70361341`
[2016-04-15T08:46Z] 2016-04-15 01:46:16 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:46:16,694 - WARNING - Could not retrieve variants from source file in region X:71493480-71493881. Error was invalid region `X:71493481-71493881`
[2016-04-15T08:46Z] 2016-04-15 01:46:19 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:46:19,286 - WARNING - Could not retrieve variants from source file in region X:77528106-77528507. Error was invalid region `X:77528107-77528507`
[2016-04-15T08:46Z] 2016-04-15 01:46:20 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:46:20,181 - WARNING - Could not retrieve variants from source file in region X:70323946-70324347. Error was invalid region `X:70323947-70324347`
[2016-04-15T08:46Z] 2016-04-15 01:46:20 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:46:20,213 - WARNING - Could not retrieve variants from source file in region X:78426260-78427178. Error was invalid region `X:78426261-78427178`
[2016-04-15T08:46Z] 2016-04-15 01:46:20 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:46:20,603 - WARNING - Could not retrieve variants from source file in region X:65382474-65382875. Error was invalid region `X:65382475-65382875`
[2016-04-15T08:46Z] 2016-04-15 01:46:20 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:46:20,605 - WARNING - Could not retrieve variants from source file in region X:71521656-71522057. Error was invalid region `X:71521657-71522057`
[2016-04-15T08:46Z] 2016-04-15 01:46:20 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:46:20,692 - WARNING - Could not retrieve variants from source file in region X:67937064-67937465. Error was invalid region `X:67937065-67937465`
[2016-04-15T08:46Z] 2016-04-15 01:46:30 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:46:30,721 - WARNING - Could not retrieve variants from source file in region X:69510124-69510525. Error was invalid region `X:69510125-69510525`
[2016-04-15T08:46Z] 2016-04-15 01:46:31 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:46:31,790 - WARNING - Could not retrieve variants from source file in region X:77150681-77151082. Error was invalid region `X:77150682-77151082`
[2016-04-15T08:46Z] 2016-04-15 01:46:32 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:46:32,662 - WARNING - Could not retrieve variants from source file in region X:70468971-70469372. Error was invalid region `X:70468972-70469372`
[2016-04-15T08:46Z] 2016-04-15 01:46:33 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:46:33,542 - WARNING - Could not retrieve variants from source file in region X:74494259-74494673. Error was invalid region `X:74494260-74494673`
[2016-04-15T08:46Z] 2016-04-15 01:46:33 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:46:33,606 - WARNING - Could not retrieve variants from source file in region X:77298646-77299047. Error was invalid region `X:77298647-77299047`
[2016-04-15T08:46Z] 2016-04-15 01:46:33 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:46:33,867 - WARNING - Could not retrieve variants from source file in region X:69774306-69774707. Error was invalid region `X:69774307-69774707`
[2016-04-15T08:46Z] 2016-04-15 01:46:33 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:46:33,912 - WARNING - Could not retrieve variants from source file in region X:77298646-77299047. Error was invalid region `X:77298647-77299047`
[2016-04-15T08:46Z] 2016-04-15 01:46:35 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:46:35,298 - WARNING - Could not retrieve variants from source file in region X:69510124-69510525. Error was invalid region `X:69510125-69510525`
[2016-04-15T08:46Z] 2016-04-15 01:46:36 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:46:36,451 - WARNING - Could not retrieve variants from source file in region X:71130864-71131265. Error was invalid region `X:71130865-71131265`
[2016-04-15T08:46Z] 2016-04-15 01:46:36 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:46:36,574 - WARNING - Could not retrieve variants from source file in region X:70468971-70469372. Error was invalid region `X:70468972-70469372`
[2016-04-15T08:46Z] 2016-04-15 01:46:37 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:46:37,565 - WARNING - Could not retrieve variants from source file in region X:77298646-77299047. Error was invalid region `X:77298647-77299047`
[2016-04-15T08:46Z] 2016-04-15 01:46:37 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:46:37,577 - WARNING - Could not retrieve variants from source file in region X:65244760-65245161. Error was invalid region `X:65244761-65245161`
[2016-04-15T08:46Z] 2016-04-15 01:46:37 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:46:37,965 - WARNING - Could not retrieve variants from source file in region X:69774306-69774707. Error was invalid region `X:69774307-69774707`
[2016-04-15T08:46Z] 2016-04-15 01:46:38 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:46:38,038 - WARNING - Could not retrieve variants from source file in region X:74494259-74494673. Error was invalid region `X:74494260-74494673`
[2016-04-15T08:46Z] 2016-04-15 01:46:38 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:46:38,965 - WARNING - Could not retrieve variants from source file in region X:69510124-69510525. Error was invalid region `X:69510125-69510525`
[2016-04-15T08:46Z] 2016-04-15 01:46:40 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:46:40,455 - WARNING - Could not retrieve variants from source file in region X:70468971-70469372. Error was invalid region `X:70468972-70469372`
[2016-04-15T08:46Z] 2016-04-15 01:46:41 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:46:41,794 - WARNING - Could not retrieve variants from source file in region X:64950818-64951219. Error was invalid region `X:64950819-64951219`
[2016-04-15T08:46Z] 2016-04-15 01:46:41 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:46:41,842 - WARNING - Could not retrieve variants from source file in region X:74494259-74494673. Error was invalid region `X:74494260-74494673`
[2016-04-15T08:46Z] 2016-04-15 01:46:41 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:46:41,984 - WARNING - Could not retrieve variants from source file in region X:68725172-68725830. Error was invalid region `X:68725173-68725830`
[2016-04-15T08:46Z] 2016-04-15 01:46:42 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:46:42,015 - WARNING - Could not retrieve variants from source file in region X:69774306-69774707. Error was invalid region `X:69774307-69774707`
[2016-04-15T08:46Z] 2016-04-15 01:46:44 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:46:44,152 - WARNING - Could not retrieve variants from source file in region X:71130864-71131265. Error was invalid region `X:71130865-71131265`
[2016-04-15T08:46Z] 2016-04-15 01:46:45 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:46:45,768 - WARNING - Could not retrieve variants from source file in region X:65244760-65245161. Error was invalid region `X:65244761-65245161`
[2016-04-15T08:46Z] 2016-04-15 01:46:47 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:46:47,843 - WARNING - Could not retrieve variants from source file in region X:68725172-68725830. Error was invalid region `X:68725173-68725830`
[2016-04-15T08:46Z] 2016-04-15 01:46:50 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:46:50,124 - WARNING - Could not retrieve variants from source file in region X:68381053-68383026. Error was invalid region `X:68381054-68383026`
[2016-04-15T08:46Z] 2016-04-15 01:46:53 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:46:53,318 - WARNING - Could not retrieve variants from source file in region X:63488313-63488715. Error was invalid region `X:63488314-63488715`
[2016-04-15T08:46Z] 2016-04-15 01:46:53 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:46:53,777 - WARNING - Could not retrieve variants from source file in region X:65822396-65836031. Error was invalid region `X:65822397-65836031`
[2016-04-15T08:46Z] ['bcbio-variation-recall', 'square', '-Xms750m', '-Xmx7280m', '-XX:+UseSerialGC', '-c', 16, '-r', u'X:78616586-95940189', '--caller', 'platypus', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/X/Batch1-X_78616585_95940189.vcf.gz', '/mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/X/Batch1-X_78616585_95940189.vcf-inputs.txt'] in region: X:78616586-95940189
[2016-04-15T08:47Z] 2016-04-15 01:47:08 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:47:08,919 - WARNING - Could not retrieve variants from source file in region X:82763829-82764232. Error was invalid region `X:82763830-82764232`
[2016-04-15T08:47Z] 2016-04-15 01:47:09 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:47:09,020 - WARNING - Could not retrieve variants from source file in region X:82763829-82764232. Error was invalid region `X:82763830-82764232`
[2016-04-15T08:47Z] 2016-04-15 01:47:09 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:47:09,097 - WARNING - Could not retrieve variants from source file in region X:85218810-85224403. Error was invalid region `X:85218811-85224403`
[2016-04-15T08:47Z] 2016-04-15 01:47:09 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:47:09,102 - WARNING - Could not retrieve variants from source file in region X:82763829-82764232. Error was invalid region `X:82763830-82764232`
[2016-04-15T08:47Z] 2016-04-15 01:47:09 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:47:09,249 - WARNING - Could not retrieve variants from source file in region X:79943358-79943759. Error was invalid region `X:79943359-79943759`
[2016-04-15T08:47Z] 2016-04-15 01:47:09 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:47:09,707 - WARNING - Could not retrieve variants from source file in region X:89177462-89177863. Error was invalid region `X:89177463-89177863`
[2016-04-15T08:47Z] 2016-04-15 01:47:09 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:47:09,719 - WARNING - Could not retrieve variants from source file in region X:92927423-92927824. Error was invalid region `X:92927424-92927824`
[2016-04-15T08:47Z] 2016-04-15 01:47:09 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:47:09,856 - WARNING - Could not retrieve variants from source file in region X:84562924-84563325. Error was invalid region `X:84562925-84563325`
[2016-04-15T08:47Z] 2016-04-15 01:47:10 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:47:10,383 - WARNING - Could not retrieve variants from source file in region X:86921876-86922277. Error was invalid region `X:86921877-86922277`
[2016-04-15T08:47Z] 2016-04-15 01:47:10 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:47:10,746 - WARNING - Could not retrieve variants from source file in region X:84362929-84363330. Error was invalid region `X:84362930-84363330`
[2016-04-15T08:47Z] 2016-04-15 01:47:10 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:47:10,774 - WARNING - Could not retrieve variants from source file in region X:88008212-88008997. Error was invalid region `X:88008213-88008997`
[2016-04-15T08:47Z] 2016-04-15 01:47:10 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:47:10,776 - WARNING - Could not retrieve variants from source file in region X:79698153-79698783. Error was invalid region `X:79698154-79698783`
[2016-04-15T08:47Z] 2016-04-15 01:47:16 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:47:16,075 - WARNING - Could not retrieve variants from source file in region X:86877137-86887434. Error was invalid region `X:86877138-86887434`
[2016-04-15T08:47Z] 2016-04-15 01:47:18 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:47:18,746 - WARNING - Could not retrieve variants from source file in region X:86921876-86922277. Error was invalid region `X:86921877-86922277`
[2016-04-15T08:47Z] 2016-04-15 01:47:18 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:47:18,957 - WARNING - Could not retrieve variants from source file in region X:79943358-79943759. Error was invalid region `X:79943359-79943759`
[2016-04-15T08:47Z] 2016-04-15 01:47:19 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:47:19,278 - WARNING - Could not retrieve variants from source file in region X:92927423-92927824. Error was invalid region `X:92927424-92927824`
[2016-04-15T08:47Z] 2016-04-15 01:47:19 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:47:19,645 - WARNING - Could not retrieve variants from source file in region X:88008212-88008997. Error was invalid region `X:88008213-88008997`
[2016-04-15T08:47Z] 2016-04-15 01:47:19 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:47:19,706 - WARNING - Could not retrieve variants from source file in region X:89177462-89177863. Error was invalid region `X:89177463-89177863`
[2016-04-15T08:47Z] 2016-04-15 01:47:19 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:47:19,734 - WARNING - Could not retrieve variants from source file in region X:79698153-79698783. Error was invalid region `X:79698154-79698783`
[2016-04-15T08:47Z] 2016-04-15 01:47:22 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:47:22,396 - WARNING - Could not retrieve variants from source file in region X:84562924-84563325. Error was invalid region `X:84562925-84563325`
[2016-04-15T08:47Z] 2016-04-15 01:47:23 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:47:23,694 - WARNING - Could not retrieve variants from source file in region X:79943358-79943759. Error was invalid region `X:79943359-79943759`
[2016-04-15T08:47Z] 2016-04-15 01:47:25 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:47:25,185 - WARNING - Could not retrieve variants from source file in region X:92927423-92927824. Error was invalid region `X:92927424-92927824`
[2016-04-15T08:47Z] ['bcbio-variation-recall', 'square', '-Xms750m', '-Xmx7280m', '-XX:+UseSerialGC', '-c', 16, '-r', u'X:95990757-111698889', '--caller', 'platypus', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/X/Batch1-X_95990756_111698889.vcf.gz', '/mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/X/Batch1-X_95990756_111698889.vcf-inputs.txt'] in region: X:95990757-111698889
[2016-04-15T08:47Z] 2016-04-15 01:47:41 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:47:41,726 - WARNING - Could not retrieve variants from source file in region X:108708305-108708742. Error was invalid region `X:108708306-108708742`
[2016-04-15T08:47Z] 2016-04-15 01:47:41 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:47:41,924 - WARNING - Could not retrieve variants from source file in region X:103349517-103349918. Error was invalid region `X:103349518-103349918`
[2016-04-15T08:47Z] 2016-04-15 01:47:43 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:47:43,056 - WARNING - Could not retrieve variants from source file in region X:111697825-111698803. Error was invalid region `X:111697826-111698803`
[2016-04-15T08:47Z] 2016-04-15 01:47:43 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:47:43,231 - WARNING - Could not retrieve variants from source file in region X:105152790-105153191. Error was invalid region `X:105152791-105153191`
[2016-04-15T08:47Z] 2016-04-15 01:47:43 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:47:43,768 - WARNING - Could not retrieve variants from source file in region X:100870937-100871338. Error was invalid region `X:100870938-100871338`
[2016-04-15T08:47Z] 2016-04-15 01:47:44 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:47:44,166 - WARNING - Could not retrieve variants from source file in region X:106396191-106396645. Error was invalid region `X:106396192-106396645`
[2016-04-15T08:47Z] 2016-04-15 01:47:44 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:47:44,529 - WARNING - Could not retrieve variants from source file in region X:100270397-100270798. Error was invalid region `X:100270398-100270798`
[2016-04-15T08:47Z] 2016-04-15 01:47:44 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:47:44,766 - WARNING - Could not retrieve variants from source file in region X:109931645-109932046. Error was invalid region `X:109931646-109932046`
[2016-04-15T08:47Z] 2016-04-15 01:47:45 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:47:45,312 - WARNING - Could not retrieve variants from source file in region X:104464070-104464473. Error was invalid region `X:104464071-104464473`
[2016-04-15T08:47Z] 2016-04-15 01:47:45 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:47:45,730 - WARNING - Could not retrieve variants from source file in region X:99941494-99941895. Error was invalid region `X:99941495-99941895`
[2016-04-15T08:47Z] 2016-04-15 01:47:45 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:47:45,807 - WARNING - Could not retrieve variants from source file in region X:109418954-109419355. Error was invalid region `X:109418955-109419355`
[2016-04-15T08:47Z] 2016-04-15 01:47:45 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:47:45,874 - WARNING - Could not retrieve variants from source file in region X:103267654-103268055. Error was invalid region `X:103267655-103268055`
[2016-04-15T08:47Z] 2016-04-15 01:47:45 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:47:45,989 - WARNING - Could not retrieve variants from source file in region X:109694474-109694875. Error was invalid region `X:109694475-109694875`
[2016-04-15T08:47Z] 2016-04-15 01:47:48 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:47:48,676 - WARNING - Could not retrieve variants from source file in region X:105152790-105153191. Error was invalid region `X:105152791-105153191`
[2016-04-15T08:47Z] 2016-04-15 01:47:51 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:47:51,701 - WARNING - Could not retrieve variants from source file in region X:105449760-105450161. Error was invalid region `X:105449761-105450161`
[2016-04-15T08:47Z] 2016-04-15 01:47:52 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:47:52,622 - WARNING - Could not retrieve variants from source file in region X:105905037-105905438. Error was invalid region `X:105905038-105905438`
[2016-04-15T08:47Z] 2016-04-15 01:47:52 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:47:52,691 - WARNING - Could not retrieve variants from source file in region X:104464070-104464473. Error was invalid region `X:104464071-104464473`
[2016-04-15T08:47Z] 2016-04-15 01:47:52 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:47:52,708 - WARNING - Could not retrieve variants from source file in region X:107330631-107331032. Error was invalid region `X:107330632-107331032`
[2016-04-15T08:47Z] 2016-04-15 01:47:53 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:47:53,242 - WARNING - Could not retrieve variants from source file in region X:99941494-99941895. Error was invalid region `X:99941495-99941895`
[2016-04-15T08:47Z] 2016-04-15 01:47:53 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:47:53,500 - WARNING - Could not retrieve variants from source file in region X:103349517-103349918. Error was invalid region `X:103349518-103349918`
[2016-04-15T08:47Z] 2016-04-15 01:47:53 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:47:53,523 - WARNING - Could not retrieve variants from source file in region X:108708305-108708742. Error was invalid region `X:108708306-108708742`
[2016-04-15T08:47Z] 2016-04-15 01:47:53 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:47:53,641 - WARNING - Could not retrieve variants from source file in region X:111697825-111698803. Error was invalid region `X:111697826-111698803`
[2016-04-15T08:47Z] 2016-04-15 01:47:53 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:47:53,669 - WARNING - Could not retrieve variants from source file in region X:105152790-105153191. Error was invalid region `X:105152791-105153191`
[2016-04-15T08:47Z] 2016-04-15 01:47:55 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:47:55,050 - WARNING - Could not retrieve variants from source file in region X:106396191-106396645. Error was invalid region `X:106396192-106396645`
[2016-04-15T08:47Z] 2016-04-15 01:47:55 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:47:55,890 - WARNING - Could not retrieve variants from source file in region X:100270397-100270798. Error was invalid region `X:100270398-100270798`
[2016-04-15T08:47Z] 2016-04-15 01:47:57 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:47:57,687 - WARNING - Could not retrieve variants from source file in region X:109931645-109932046. Error was invalid region `X:109931646-109932046`
[2016-04-15T08:47Z] 2016-04-15 01:47:59 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:47:59,422 - WARNING - Could not retrieve variants from source file in region X:104464070-104464473. Error was invalid region `X:104464071-104464473`
[2016-04-15T08:48Z] 2016-04-15 01:48:00 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:48:00,477 - WARNING - Could not retrieve variants from source file in region X:99941494-99941895. Error was invalid region `X:99941495-99941895`
[2016-04-15T08:48Z] 2016-04-15 01:48:00 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:48:00,507 - WARNING - Could not retrieve variants from source file in region X:109694474-109694875. Error was invalid region `X:109694475-109694875`
[2016-04-15T08:48Z] 2016-04-15 01:48:00 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:48:00,658 - WARNING - Could not retrieve variants from source file in region X:103267654-103268055. Error was invalid region `X:103267655-103268055`
[2016-04-15T08:48Z] 2016-04-15 01:48:13 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:48:13,285 - WARNING - Could not retrieve variants from source file in region X:100547722-100548123. Error was invalid region `X:100547723-100548123`
[2016-04-15T08:48Z] 2016-04-15 01:48:13 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:48:13,757 - WARNING - Could not retrieve variants from source file in region X:100547722-100548123. Error was invalid region `X:100547723-100548123`
[2016-04-15T08:48Z] 2016-04-15 01:48:13 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:48:13,891 - WARNING - Could not retrieve variants from source file in region X:100242325-100243649. Error was invalid region `X:100242326-100243649`
[2016-04-15T08:48Z] 2016-04-15 01:48:14 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:48:14,376 - WARNING - Could not retrieve variants from source file in region X:106309690-106310091. Error was invalid region `X:106309691-106310091`
[2016-04-15T08:48Z] 2016-04-15 01:48:14 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:48:14,487 - WARNING - Could not retrieve variants from source file in region X:100507464-100507865. Error was invalid region `X:100507465-100507865`
[2016-04-15T08:48Z] 2016-04-15 01:48:15 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:48:15,324 - WARNING - Could not retrieve variants from source file in region X:99848806-99849207. Error was invalid region `X:99848807-99849207`
[2016-04-15T08:48Z] 2016-04-15 01:48:15 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:48:15,452 - WARNING - Could not retrieve variants from source file in region X:100395452-100395853. Error was invalid region `X:100395453-100395853`
[2016-04-15T08:48Z] 2016-04-15 01:48:15 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:48:15,468 - WARNING - Could not retrieve variants from source file in region X:107159080-107159481. Error was invalid region `X:107159081-107159481`
[2016-04-15T08:48Z] 2016-04-15 01:48:15 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:48:15,830 - WARNING - Could not retrieve variants from source file in region X:107976729-107979702. Error was invalid region `X:107976730-107979702`
[2016-04-15T08:48Z] 2016-04-15 01:48:17 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:48:17,318 - WARNING - Could not retrieve variants from source file in region X:99661758-99662159. Error was invalid region `X:99661759-99662159`
[2016-04-15T08:48Z] 2016-04-15 01:48:17 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:48:17,365 - WARNING - Could not retrieve variants from source file in region X:110969930-110970331. Error was invalid region `X:110969931-110970331`
[2016-04-15T08:48Z] 2016-04-15 01:48:17 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:48:17,371 - WARNING - Could not retrieve variants from source file in region X:102973298-102979676. Error was invalid region `X:102973299-102979676`
[2016-04-15T08:48Z] 2016-04-15 01:48:18 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:48:18,256 - WARNING - Could not retrieve variants from source file in region X:100547722-100548123. Error was invalid region `X:100547723-100548123`
[2016-04-15T08:48Z] 2016-04-15 01:48:21 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:48:21,183 - WARNING - Could not retrieve variants from source file in region X:99848806-99849207. Error was invalid region `X:99848807-99849207`
[2016-04-15T08:48Z] 2016-04-15 01:48:22 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:48:22,009 - WARNING - Could not retrieve variants from source file in region X:102973298-102979676. Error was invalid region `X:102973299-102979676`
[2016-04-15T08:48Z] 2016-04-15 01:48:22 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:48:22,727 - WARNING - Could not retrieve variants from source file in region X:107933009-107933410. Error was invalid region `X:107933010-107933410`
[2016-04-15T08:48Z] 2016-04-15 01:48:23 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:48:23,268 - WARNING - Could not retrieve variants from source file in region X:99848806-99849207. Error was invalid region `X:99848807-99849207`
[2016-04-15T08:48Z] 2016-04-15 01:48:23 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:48:23,403 - WARNING - Could not retrieve variants from source file in region X:100242325-100243649. Error was invalid region `X:100242326-100243649`
[2016-04-15T08:48Z] 2016-04-15 01:48:24 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:48:24,256 - WARNING - Could not retrieve variants from source file in region X:106309690-106310091. Error was invalid region `X:106309691-106310091`
[2016-04-15T08:48Z] 2016-04-15 01:48:24 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:48:24,541 - WARNING - Could not retrieve variants from source file in region X:100507464-100507865. Error was invalid region `X:100507465-100507865`
[2016-04-15T08:48Z] 2016-04-15 01:48:25 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:48:25,657 - WARNING - Could not retrieve variants from source file in region X:107159080-107159481. Error was invalid region `X:107159081-107159481`
[2016-04-15T08:48Z] 2016-04-15 01:48:26 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:48:26,027 - WARNING - Could not retrieve variants from source file in region X:100395452-100395853. Error was invalid region `X:100395453-100395853`
[2016-04-15T08:48Z] 2016-04-15 01:48:27 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:48:27,919 - WARNING - Could not retrieve variants from source file in region X:99661758-99662159. Error was invalid region `X:99661759-99662159`
[2016-04-15T08:48Z] 2016-04-15 01:48:32 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:48:32,197 - WARNING - Could not retrieve variants from source file in region X:106185740-106200392. Error was invalid region `X:106185741-106200392`
[2016-04-15T08:48Z] 2016-04-15 01:48:33 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:48:33,844 - WARNING - Could not retrieve variants from source file in region X:107870290-107870691. Error was invalid region `X:107870291-107870691`
[2016-04-15T08:48Z] 2016-04-15 01:48:37 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:48:37,952 - WARNING - Could not retrieve variants from source file in region X:101857939-101858340. Error was invalid region `X:101857940-101858340`
[2016-04-15T08:48Z] 2016-04-15 01:48:38 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:48:38,340 - WARNING - Could not retrieve variants from source file in region X:102840210-102842231. Error was invalid region `X:102840211-102842231`
[2016-04-15T08:48Z] 2016-04-15 01:48:39 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:48:39,884 - WARNING - Could not retrieve variants from source file in region X:101381794-101395970. Error was invalid region `X:101381795-101395970`
[2016-04-15T08:48Z] 2016-04-15 01:48:39 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:48:39,937 - WARNING - Could not retrieve variants from source file in region X:101090953-101097120. Error was invalid region `X:101090954-101097120`
[2016-04-15T08:48Z] 2016-04-15 01:48:40 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:48:40,024 - WARNING - Could not retrieve variants from source file in region X:102754931-102755741. Error was invalid region `X:102754932-102755741`
[2016-04-15T08:48Z] 2016-04-15 01:48:40 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:48:40,081 - WARNING - Could not retrieve variants from source file in region X:101138581-101138982. Error was invalid region `X:101138582-101138982`
[2016-04-15T08:48Z] 2016-04-15 01:48:41 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:48:41,908 - WARNING - Could not retrieve variants from source file in region X:101138581-101138982. Error was invalid region `X:101138582-101138982`
[2016-04-15T08:48Z] 2016-04-15 01:48:42 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:48:42,579 - WARNING - Could not retrieve variants from source file in region X:102840210-102842231. Error was invalid region `X:102840211-102842231`
[2016-04-15T08:48Z] 2016-04-15 01:48:44 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:48:44,266 - WARNING - Could not retrieve variants from source file in region X:101381794-101395970. Error was invalid region `X:101381795-101395970`
[2016-04-15T08:48Z] 2016-04-15 01:48:44 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:48:44,345 - WARNING - Could not retrieve variants from source file in region X:101138581-101138982. Error was invalid region `X:101138582-101138982`
[2016-04-15T08:48Z] 2016-04-15 01:48:45 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:48:45,880 - WARNING - Could not retrieve variants from source file in region X:102754931-102755741. Error was invalid region `X:102754932-102755741`
[2016-04-15T08:48Z] 2016-04-15 01:48:46 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:48:46,331 - WARNING - Could not retrieve variants from source file in region X:101381794-101395970. Error was invalid region `X:101381795-101395970`
[2016-04-15T08:48Z] 2016-04-15 01:48:46 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:48:46,617 - WARNING - Could not retrieve variants from source file in region X:102564372-102564773. Error was invalid region `X:102564373-102564773`
[2016-04-15T08:48Z] 2016-04-15 01:48:49 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:48:49,883 - WARNING - Could not retrieve variants from source file in region X:100910855-100911256. Error was invalid region `X:100910856-100911256`
[2016-04-15T08:48Z] 2016-04-15 01:48:49 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:48:49,884 - WARNING - Could not retrieve variants from source file in region X:100910855-100911256. Error was invalid region `X:100910856-100911256`
[2016-04-15T08:48Z] 2016-04-15 01:48:49 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:48:49,923 - WARNING - Could not retrieve variants from source file in region X:100910855-100911256. Error was invalid region `X:100910856-100911256`
[2016-04-15T08:48Z] ['bcbio-variation-recall', 'square', '-Xms750m', '-Xmx7280m', '-XX:+UseSerialGC', '-c', 16, '-r', u'X:111874648-128581278', '--caller', 'platypus', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/X/Batch1-X_111874647_128581278.vcf.gz', '/mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/X/Batch1-X_111874647_128581278.vcf-inputs.txt'] in region: X:111874648-128581278
[2016-04-15T08:49Z] 2016-04-15 01:49:04 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:49:04,954 - WARNING - Could not retrieve variants from source file in region X:118948997-118968381. Error was invalid region `X:118948998-118968381`
[2016-04-15T08:49Z] 2016-04-15 01:49:05 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:49:05,842 - WARNING - Could not retrieve variants from source file in region X:122537066-122537467. Error was invalid region `X:122537067-122537467`
[2016-04-15T08:49Z] 2016-04-15 01:49:06 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:49:06,366 - WARNING - Could not retrieve variants from source file in region X:119671849-119672250. Error was invalid region `X:119671850-119672250`
[2016-04-15T08:49Z] 2016-04-15 01:49:06 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:49:06,648 - WARNING - Could not retrieve variants from source file in region X:119387622-119388023. Error was invalid region `X:119387623-119388023`
[2016-04-15T08:49Z] 2016-04-15 01:49:06 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:49:06,980 - WARNING - Could not retrieve variants from source file in region X:120008768-120009169. Error was invalid region `X:120008769-120009169`
[2016-04-15T08:49Z] 2016-04-15 01:49:07 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:49:07,126 - WARNING - Could not retrieve variants from source file in region X:125955217-125955618. Error was invalid region `X:125955218-125955618`
[2016-04-15T08:49Z] 2016-04-15 01:49:07 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:49:07,305 - WARNING - Could not retrieve variants from source file in region X:118108574-118108975. Error was invalid region `X:118108575-118108975`
[2016-04-15T08:49Z] 2016-04-15 01:49:07 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:49:07,935 - WARNING - Could not retrieve variants from source file in region X:117106721-117107122. Error was invalid region `X:117106722-117107122`
[2016-04-15T08:49Z] 2016-04-15 01:49:08 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:49:08,303 - WARNING - Could not retrieve variants from source file in region X:119760418-119760819. Error was invalid region `X:119760419-119760819`
[2016-04-15T08:49Z] 2016-04-15 01:49:08 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:49:08,328 - WARNING - Could not retrieve variants from source file in region X:118219136-118222550. Error was invalid region `X:118219137-118222550`
[2016-04-15T08:49Z] 2016-04-15 01:49:08 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:49:08,374 - WARNING - Could not retrieve variants from source file in region X:118148018-118148419. Error was invalid region `X:118148019-118148419`
[2016-04-15T08:49Z] 2016-04-15 01:49:11 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:49:11,065 - WARNING - Could not retrieve variants from source file in region X:122537066-122537467. Error was invalid region `X:122537067-122537467`
[2016-04-15T08:49Z] 2016-04-15 01:49:12 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:49:12,529 - WARNING - Could not retrieve variants from source file in region X:119387622-119388023. Error was invalid region `X:119387623-119388023`
[2016-04-15T08:49Z] 2016-04-15 01:49:13 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:49:13,285 - WARNING - Could not retrieve variants from source file in region X:120008768-120009169. Error was invalid region `X:120008769-120009169`
[2016-04-15T08:49Z] 2016-04-15 01:49:14 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:49:14,191 - WARNING - Could not retrieve variants from source file in region X:125955217-125955618. Error was invalid region `X:125955218-125955618`
[2016-04-15T08:49Z] 2016-04-15 01:49:15 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:49:15,623 - WARNING - Could not retrieve variants from source file in region X:114874542-114874943. Error was invalid region `X:114874543-114874943`
[2016-04-15T08:49Z] 2016-04-15 01:49:15 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:49:15,935 - WARNING - Could not retrieve variants from source file in region X:118750851-118752502. Error was invalid region `X:118750852-118752502`
[2016-04-15T08:49Z] 2016-04-15 01:49:16 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:49:16,332 - WARNING - Could not retrieve variants from source file in region X:118148018-118148419. Error was invalid region `X:118148019-118148419`
[2016-04-15T08:49Z] 2016-04-15 01:49:16 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:49:16,392 - WARNING - Could not retrieve variants from source file in region X:117676698-117700331. Error was invalid region `X:117676699-117700331`
[2016-04-15T08:49Z] 2016-04-15 01:49:16 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:49:16,585 - WARNING - Could not retrieve variants from source file in region X:122537066-122537467. Error was invalid region `X:122537067-122537467`
[2016-04-15T08:49Z] 2016-04-15 01:49:16 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:49:16,667 - WARNING - Could not retrieve variants from source file in region X:118948997-118968381. Error was invalid region `X:118948998-118968381`
[2016-04-15T08:49Z] 2016-04-15 01:49:16 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:49:16,790 - WARNING - Could not retrieve variants from source file in region X:119671849-119672250. Error was invalid region `X:119671850-119672250`
[2016-04-15T08:49Z] 2016-04-15 01:49:17 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:49:17,295 - WARNING - Could not retrieve variants from source file in region X:119387622-119388023. Error was invalid region `X:119387623-119388023`
[2016-04-15T08:49Z] 2016-04-15 01:49:18 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:49:18,370 - WARNING - Could not retrieve variants from source file in region X:120008768-120009169. Error was invalid region `X:120008769-120009169`
[2016-04-15T08:49Z] 2016-04-15 01:49:22 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:49:22,255 - WARNING - Could not retrieve variants from source file in region X:118108574-118108975. Error was invalid region `X:118108575-118108975`
[2016-04-15T08:49Z] 2016-04-15 01:49:23 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:49:23,981 - WARNING - Could not retrieve variants from source file in region X:118219136-118222550. Error was invalid region `X:118219137-118222550`
[2016-04-15T08:49Z] 2016-04-15 01:49:24 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:49:24,024 - WARNING - Could not retrieve variants from source file in region X:118148018-118148419. Error was invalid region `X:118148019-118148419`
[2016-04-15T08:49Z] 2016-04-15 01:49:34 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:49:34,852 - WARNING - Could not retrieve variants from source file in region X:122336389-122338527. Error was invalid region `X:122336390-122338527`
[2016-04-15T08:49Z] 2016-04-15 01:49:36 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:49:36,929 - WARNING - Could not retrieve variants from source file in region X:125298479-125299657. Error was invalid region `X:125298480-125299657`
[2016-04-15T08:49Z] 2016-04-15 01:49:37 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:49:37,015 - WARNING - Could not retrieve variants from source file in region X:118725021-118725422. Error was invalid region `X:118725022-118725422`
[2016-04-15T08:49Z] 2016-04-15 01:49:38 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:49:38,034 - WARNING - Could not retrieve variants from source file in region X:118678153-118678554. Error was invalid region `X:118678154-118678554`
[2016-04-15T08:49Z] 2016-04-15 01:49:40 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:49:40,664 - WARNING - Could not retrieve variants from source file in region X:118281327-118281728. Error was invalid region `X:118281328-118281728`
[2016-04-15T08:49Z] 2016-04-15 01:49:40 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:49:40,742 - WARNING - Could not retrieve variants from source file in region X:118533155-118533613. Error was invalid region `X:118533156-118533613`
[2016-04-15T08:49Z] 2016-04-15 01:49:42 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:49:42,116 - WARNING - Could not retrieve variants from source file in region X:118678153-118678554. Error was invalid region `X:118678154-118678554`
[2016-04-15T08:49Z] 2016-04-15 01:49:43 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:49:43,626 - WARNING - Could not retrieve variants from source file in region X:122336389-122338527. Error was invalid region `X:122336390-122338527`
[2016-04-15T08:49Z] 2016-04-15 01:49:43 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:49:43,922 - WARNING - Could not retrieve variants from source file in region X:114424386-114427107. Error was invalid region `X:114424387-114427107`
[2016-04-15T08:49Z] 2016-04-15 01:49:44 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:49:44,815 - WARNING - Could not retrieve variants from source file in region X:118281327-118281728. Error was invalid region `X:118281328-118281728`
[2016-04-15T08:49Z] 2016-04-15 01:49:45 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:49:45,383 - WARNING - Could not retrieve variants from source file in region X:118281327-118281728. Error was invalid region `X:118281328-118281728`
[2016-04-15T08:49Z] 2016-04-15 01:49:46 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:49:46,391 - WARNING - Could not retrieve variants from source file in region X:118678153-118678554. Error was invalid region `X:118678154-118678554`
[2016-04-15T08:49Z] ['bcbio-variation-recall', 'square', '-Xms750m', '-Xmx7280m', '-XX:+UseSerialGC', '-c', 16, '-r', u'X:128582279-144329181', '--caller', 'platypus', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/X/Batch1-X_128582278_144329181.vcf.gz', '/mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/X/Batch1-X_128582278_144329181.vcf-inputs.txt'] in region: X:128582279-144329181
[2016-04-15T08:50Z] 2016-04-15 01:50:04 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:50:04,684 - WARNING - Could not retrieve variants from source file in region X:135426482-135431572. Error was invalid region `X:135426483-135431572`
[2016-04-15T08:50Z] 2016-04-15 01:50:04 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:50:04,743 - WARNING - Could not retrieve variants from source file in region X:139866266-139866667. Error was invalid region `X:139866267-139866667`
[2016-04-15T08:50Z] 2016-04-15 01:50:04 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:50:04,955 - WARNING - Could not retrieve variants from source file in region X:135741232-135741633. Error was invalid region `X:135741233-135741633`
[2016-04-15T08:50Z] 2016-04-15 01:50:05 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:50:05,508 - WARNING - Could not retrieve variants from source file in region X:138633069-138633470. Error was invalid region `X:138633070-138633470`
[2016-04-15T08:50Z] 2016-04-15 01:50:05 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:50:05,666 - WARNING - Could not retrieve variants from source file in region X:135849362-135850059. Error was invalid region `X:135849363-135850059`
[2016-04-15T08:50Z] 2016-04-15 01:50:05 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:50:05,876 - WARNING - Could not retrieve variants from source file in region X:135310574-135338502. Error was invalid region `X:135310575-135338502`
[2016-04-15T08:50Z] 2016-04-15 01:50:05 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:50:05,997 - WARNING - Could not retrieve variants from source file in region X:138679501-138679902. Error was invalid region `X:138679502-138679902`
[2016-04-15T08:50Z] 2016-04-15 01:50:06 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:50:06,267 - WARNING - Could not retrieve variants from source file in region X:137793212-137793843. Error was invalid region `X:137793213-137793843`
[2016-04-15T08:50Z] 2016-04-15 01:50:06 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:50:06,600 - WARNING - Could not retrieve variants from source file in region X:142967257-142967658. Error was invalid region `X:142967258-142967658`
[2016-04-15T08:50Z] 2016-04-15 01:50:06 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:50:06,722 - WARNING - Could not retrieve variants from source file in region X:135474209-135496588. Error was invalid region `X:135474210-135496588`
[2016-04-15T08:50Z] 2016-04-15 01:50:13 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:50:13,227 - WARNING - Could not retrieve variants from source file in region X:142596730-142597131. Error was invalid region `X:142596731-142597131`
[2016-04-15T08:50Z] 2016-04-15 01:50:14 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:50:14,878 - WARNING - Could not retrieve variants from source file in region X:132161462-132161863. Error was invalid region `X:132161463-132161863`
[2016-04-15T08:50Z] 2016-04-15 01:50:15 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:50:15,781 - WARNING - Could not retrieve variants from source file in region X:138679501-138679902. Error was invalid region `X:138679502-138679902`
[2016-04-15T08:50Z] 2016-04-15 01:50:16 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:50:16,844 - WARNING - Could not retrieve variants from source file in region X:137793212-137793843. Error was invalid region `X:137793213-137793843`
[2016-04-15T08:50Z] 2016-04-15 01:50:17 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:50:17,288 - WARNING - Could not retrieve variants from source file in region X:139866266-139866667. Error was invalid region `X:139866267-139866667`
[2016-04-15T08:50Z] 2016-04-15 01:50:20 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:50:20,261 - WARNING - Could not retrieve variants from source file in region X:135849362-135850059. Error was invalid region `X:135849363-135850059`
[2016-04-15T08:50Z] 2016-04-15 01:50:21 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:50:21,896 - WARNING - Could not retrieve variants from source file in region X:140785528-140785931. Error was invalid region `X:140785529-140785931`
[2016-04-15T08:50Z] 2016-04-15 01:50:23 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:50:23,240 - WARNING - Could not retrieve variants from source file in region X:140335531-140335932. Error was invalid region `X:140335532-140335932`
[2016-04-15T08:50Z] 2016-04-15 01:50:23 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:50:23,654 - WARNING - Could not retrieve variants from source file in region X:138679501-138679902. Error was invalid region `X:138679502-138679902`
[2016-04-15T08:50Z] 2016-04-15 01:50:24 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:50:24,255 - WARNING - Could not retrieve variants from source file in region X:135474209-135496588. Error was invalid region `X:135474210-135496588`
[2016-04-15T08:50Z] 2016-04-15 01:50:24 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:50:24,292 - WARNING - Could not retrieve variants from source file in region X:137793212-137793843. Error was invalid region `X:137793213-137793843`
[2016-04-15T08:50Z] 2016-04-15 01:50:24 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:50:24,588 - WARNING - Could not retrieve variants from source file in region X:138724514-138725032. Error was invalid region `X:138724515-138725032`
[2016-04-15T08:50Z] 2016-04-15 01:50:34 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:50:34,034 - WARNING - Could not retrieve variants from source file in region X:141290654-141291055. Error was invalid region `X:141290655-141291055`
[2016-04-15T08:50Z] 2016-04-15 01:50:35 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:50:35,117 - WARNING - Could not retrieve variants from source file in region X:134185786-134186187. Error was invalid region `X:134185787-134186187`
[2016-04-15T08:50Z] 2016-04-15 01:50:35 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:50:35,866 - WARNING - Could not retrieve variants from source file in region X:138896919-138897320. Error was invalid region `X:138896920-138897320`
[2016-04-15T08:50Z] 2016-04-15 01:50:37 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:50:37,500 - WARNING - Could not retrieve variants from source file in region X:138896919-138897320. Error was invalid region `X:138896920-138897320`
[2016-04-15T08:50Z] 2016-04-15 01:50:37 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:50:37,918 - WARNING - Could not retrieve variants from source file in region X:136113253-136113654. Error was invalid region `X:136113254-136113654`
[2016-04-15T08:50Z] 2016-04-15 01:50:38 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:50:38,630 - WARNING - Could not retrieve variants from source file in region X:134947823-134948224. Error was invalid region `X:134947824-134948224`
[2016-04-15T08:50Z] 2016-04-15 01:50:38 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:50:38,800 - WARNING - Could not retrieve variants from source file in region X:138773998-138774399. Error was invalid region `X:138773999-138774399`
[2016-04-15T08:50Z] 2016-04-15 01:50:39 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:50:39,202 - WARNING - Could not retrieve variants from source file in region X:134713644-134714045. Error was invalid region `X:134713645-134714045`
[2016-04-15T08:50Z] 2016-04-15 01:50:39 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:50:39,938 - WARNING - Could not retrieve variants from source file in region X:142795014-142795415. Error was invalid region `X:142795015-142795415`
[2016-04-15T08:50Z] 2016-04-15 01:50:40 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:50:40,035 - WARNING - Could not retrieve variants from source file in region X:134185786-134186187. Error was invalid region `X:134185787-134186187`
[2016-04-15T08:50Z] 2016-04-15 01:50:40 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:50:40,183 - WARNING - Could not retrieve variants from source file in region X:135122051-135122452. Error was invalid region `X:135122052-135122452`
[2016-04-15T08:50Z] 2016-04-15 01:50:40 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:50:40,943 - WARNING - Could not retrieve variants from source file in region X:138896919-138897320. Error was invalid region `X:138896920-138897320`
[2016-04-15T08:50Z] 2016-04-15 01:50:41 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:50:41,315 - WARNING - Could not retrieve variants from source file in region X:134420957-134421358. Error was invalid region `X:134420958-134421358`
[2016-04-15T08:50Z] 2016-04-15 01:50:42 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:50:42,895 - WARNING - Could not retrieve variants from source file in region X:130678256-130679034. Error was invalid region `X:130678257-130679034`
[2016-04-15T08:50Z] 2016-04-15 01:50:43 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:50:43,745 - WARNING - Could not retrieve variants from source file in region X:134947823-134948224. Error was invalid region `X:134947824-134948224`
[2016-04-15T08:50Z] 2016-04-15 01:50:44 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:50:44,128 - WARNING - Could not retrieve variants from source file in region X:138773998-138774399. Error was invalid region `X:138773999-138774399`
[2016-04-15T08:50Z] 2016-04-15 01:50:44 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:50:44,442 - WARNING - Could not retrieve variants from source file in region X:141290654-141291055. Error was invalid region `X:141290655-141291055`
[2016-04-15T08:50Z] 2016-04-15 01:50:45 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:50:45,072 - WARNING - Could not retrieve variants from source file in region X:142795014-142795415. Error was invalid region `X:142795015-142795415`
[2016-04-15T08:50Z] 2016-04-15 01:50:46 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:50:46,203 - WARNING - Could not retrieve variants from source file in region X:142795014-142795415. Error was invalid region `X:142795015-142795415`
[2016-04-15T08:50Z] 2016-04-15 01:50:46 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:50:46,447 - WARNING - Could not retrieve variants from source file in region X:134947823-134948224. Error was invalid region `X:134947824-134948224`
[2016-04-15T08:50Z] 2016-04-15 01:50:48 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:50:48,459 - WARNING - Could not retrieve variants from source file in region X:138773998-138774399. Error was invalid region `X:138773999-138774399`
[2016-04-15T08:50Z] 2016-04-15 01:50:49 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:50:49,067 - WARNING - Could not retrieve variants from source file in region X:134713644-134714045. Error was invalid region `X:134713645-134714045`
[2016-04-15T08:50Z] 2016-04-15 01:50:50 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:50:50,931 - WARNING - Could not retrieve variants from source file in region X:135122051-135122452. Error was invalid region `X:135122052-135122452`
[2016-04-15T08:50Z] 2016-04-15 01:50:55 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:50:55,486 - WARNING - Could not retrieve variants from source file in region X:133963057-133963458. Error was invalid region `X:133963058-133963458`
[2016-04-15T08:50Z] 2016-04-15 01:50:55 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:50:55,957 - WARNING - Could not retrieve variants from source file in region X:133379340-133379741. Error was invalid region `X:133379341-133379741`
[2016-04-15T08:50Z] 2016-04-15 01:50:56 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:50:56,352 - WARNING - Could not retrieve variants from source file in region X:134155693-134156311. Error was invalid region `X:134155694-134156311`
[2016-04-15T08:50Z] 2016-04-15 01:50:57 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:50:57,206 - WARNING - Could not retrieve variants from source file in region X:129498625-129499200. Error was invalid region `X:129498626-129499200`
[2016-04-15T08:51Z] 2016-04-15 01:51:00 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:51:00,043 - WARNING - Could not retrieve variants from source file in region X:129349084-129349485. Error was invalid region `X:129349085-129349485`
[2016-04-15T08:51Z] 2016-04-15 01:51:00 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:51:00,257 - WARNING - Could not retrieve variants from source file in region X:133963057-133963458. Error was invalid region `X:133963058-133963458`
[2016-04-15T08:51Z] 2016-04-15 01:51:00 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:51:00,653 - WARNING - Could not retrieve variants from source file in region X:133379340-133379741. Error was invalid region `X:133379341-133379741`
[2016-04-15T08:51Z] 2016-04-15 01:51:03 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:51:03,264 - WARNING - Could not retrieve variants from source file in region X:129472551-129472952. Error was invalid region `X:129472552-129472952`
[2016-04-15T08:51Z] 2016-04-15 01:51:03 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:51:03,874 - WARNING - Could not retrieve variants from source file in region X:133379340-133379741. Error was invalid region `X:133379341-133379741`
[2016-04-15T08:51Z] 2016-04-15 01:51:04 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:51:04,569 - WARNING - Could not retrieve variants from source file in region X:129200968-129201369. Error was invalid region `X:129200969-129201369`
[2016-04-15T08:51Z] 2016-04-15 01:51:05 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:51:05,378 - WARNING - Could not retrieve variants from source file in region X:129498625-129499200. Error was invalid region `X:129498626-129499200`
[2016-04-15T08:51Z] 2016-04-15 01:51:05 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:51:05,614 - WARNING - Could not retrieve variants from source file in region X:132437126-132439062. Error was invalid region `X:132437127-132439062`
[2016-04-15T08:51Z] 2016-04-15 01:51:07 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:51:07,148 - WARNING - Could not retrieve variants from source file in region X:129472551-129472952. Error was invalid region `X:129472552-129472952`
[2016-04-15T08:51Z] 2016-04-15 01:51:07 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:51:07,508 - WARNING - Could not retrieve variants from source file in region X:129146868-129150334. Error was invalid region `X:129146869-129150334`
[2016-04-15T08:51Z] 2016-04-15 01:51:09 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:51:09,377 - WARNING - Could not retrieve variants from source file in region X:132437126-132439062. Error was invalid region `X:132437127-132439062`
[2016-04-15T08:51Z] 2016-04-15 01:51:11 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:51:11,505 - WARNING - Could not retrieve variants from source file in region X:129283309-129283710. Error was invalid region `X:129283310-129283710`
[2016-04-15T08:51Z] 2016-04-15 01:51:14 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:51:14,031 - WARNING - Could not retrieve variants from source file in region X:129058671-129059072. Error was invalid region `X:129058672-129059072`
[2016-04-15T08:51Z] 2016-04-15 01:51:14 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:51:14,044 - WARNING - Could not retrieve variants from source file in region X:129058671-129059072. Error was invalid region `X:129058672-129059072`
[2016-04-15T08:51Z] ['bcbio-variation-recall', 'square', '-Xms750m', '-Xmx7280m', '-XX:+UseSerialGC', '-c', 16, '-r', u'X:144337191-155270560', '--caller', 'platypus', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/X/Batch1-X_144337190_155270560.vcf.gz', '/mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/X/Batch1-X_144337190_155270560.vcf-inputs.txt'] in region: X:144337191-155270560
[2016-04-15T08:51Z] 2016-04-15 01:51:28 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:51:28,438 - WARNING - Could not retrieve variants from source file in region X:152864266-152864703. Error was invalid region `X:152864267-152864703`
[2016-04-15T08:51Z] 2016-04-15 01:51:29 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:51:29,375 - WARNING - Could not retrieve variants from source file in region X:153994385-153994786. Error was invalid region `X:153994386-153994786`
[2016-04-15T08:51Z] 2016-04-15 01:51:29 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:51:29,482 - WARNING - Could not retrieve variants from source file in region X:152814878-152823918. Error was invalid region `X:152814879-152823918`
[2016-04-15T08:51Z] 2016-04-15 01:51:30 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:51:30,718 - WARNING - Could not retrieve variants from source file in region X:154019903-154020304. Error was invalid region `X:154019904-154020304`
[2016-04-15T08:51Z] 2016-04-15 01:51:31 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:51:31,123 - WARNING - Could not retrieve variants from source file in region X:149930895-149937594. Error was invalid region `X:149930896-149937594`
[2016-04-15T08:51Z] 2016-04-15 01:51:31 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:51:31,154 - WARNING - Could not retrieve variants from source file in region X:152771298-152771699. Error was invalid region `X:152771299-152771699`
[2016-04-15T08:51Z] 2016-04-15 01:51:31 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:51:31,394 - WARNING - Could not retrieve variants from source file in region X:148798012-148798413. Error was invalid region `X:148798013-148798413`
[2016-04-15T08:51Z] 2016-04-15 01:51:31 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:51:31,498 - WARNING - Could not retrieve variants from source file in region X:154456536-154456937. Error was invalid region `X:154456537-154456937`
[2016-04-15T08:51Z] 2016-04-15 01:51:31 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:51:31,693 - WARNING - Could not retrieve variants from source file in region X:155004069-155004470. Error was invalid region `X:155004070-155004470`
[2016-04-15T08:51Z] 2016-04-15 01:51:32 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:51:32,042 - WARNING - Could not retrieve variants from source file in region X:147014749-147026521. Error was invalid region `X:147014750-147026521`
[2016-04-15T08:51Z] 2016-04-15 01:51:32 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:51:32,086 - WARNING - Could not retrieve variants from source file in region X:144904041-144905072. Error was invalid region `X:144904042-144905072`
[2016-04-15T08:51Z] 2016-04-15 01:51:32 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:51:32,300 - WARNING - Could not retrieve variants from source file in region X:153149498-153176474. Error was invalid region `X:153149499-153176474`
[2016-04-15T08:51Z] 2016-04-15 01:51:33 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:51:33,062 - WARNING - Could not retrieve variants from source file in region X:152864266-152864703. Error was invalid region `X:152864267-152864703`
[2016-04-15T08:51Z] 2016-04-15 01:51:35 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:51:35,141 - WARNING - Could not retrieve variants from source file in region X:153994385-153994786. Error was invalid region `X:153994386-153994786`
[2016-04-15T08:51Z] 2016-04-15 01:51:36 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:51:36,062 - WARNING - Could not retrieve variants from source file in region X:151820996-151821467. Error was invalid region `X:151820997-151821467`
[2016-04-15T08:51Z] 2016-04-15 01:51:37 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:51:37,304 - WARNING - Could not retrieve variants from source file in region X:154019903-154020304. Error was invalid region `X:154019904-154020304`
[2016-04-15T08:51Z] 2016-04-15 01:51:39 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:51:39,166 - WARNING - Could not retrieve variants from source file in region X:152771298-152771699. Error was invalid region `X:152771299-152771699`
[2016-04-15T08:51Z] 2016-04-15 01:51:39 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:51:39,214 - WARNING - Could not retrieve variants from source file in region X:148626037-148628772. Error was invalid region `X:148626038-148628772`
[2016-04-15T08:51Z] 2016-04-15 01:51:39 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:51:39,666 - WARNING - Could not retrieve variants from source file in region X:148798012-148798413. Error was invalid region `X:148798013-148798413`
[2016-04-15T08:51Z] 2016-04-15 01:51:39 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:51:39,685 - WARNING - Could not retrieve variants from source file in region X:154456536-154456937. Error was invalid region `X:154456537-154456937`
[2016-04-15T08:51Z] 2016-04-15 01:51:39 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:51:39,827 - WARNING - Could not retrieve variants from source file in region X:155004069-155004470. Error was invalid region `X:155004070-155004470`
[2016-04-15T08:51Z] 2016-04-15 01:51:40 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:51:40,158 - WARNING - Could not retrieve variants from source file in region X:153761600-153762001. Error was invalid region `X:153761601-153762001`
[2016-04-15T08:51Z] 2016-04-15 01:51:40 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:51:40,418 - WARNING - Could not retrieve variants from source file in region X:152864266-152864703. Error was invalid region `X:152864267-152864703`
[2016-04-15T08:51Z] 2016-04-15 01:51:40 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:51:40,693 - WARNING - Could not retrieve variants from source file in region X:152814878-152823918. Error was invalid region `X:152814879-152823918`
[2016-04-15T08:51Z] 2016-04-15 01:51:40 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:51:40,700 - WARNING - Could not retrieve variants from source file in region X:148568351-148582739. Error was invalid region `X:148568352-148582739`
[2016-04-15T08:51Z] 2016-04-15 01:51:41 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:51:41,101 - WARNING - Could not retrieve variants from source file in region X:153994385-153994786. Error was invalid region `X:153994386-153994786`
[2016-04-15T08:51Z] 2016-04-15 01:51:41 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:51:41,939 - WARNING - Could not retrieve variants from source file in region X:154019903-154020304. Error was invalid region `X:154019904-154020304`
[2016-04-15T08:51Z] 2016-04-15 01:51:45 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:51:45,909 - WARNING - Could not retrieve variants from source file in region X:152771298-152771699. Error was invalid region `X:152771299-152771699`
[2016-04-15T08:51Z] 2016-04-15 01:51:48 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:51:48,275 - WARNING - Could not retrieve variants from source file in region X:148798012-148798413. Error was invalid region `X:148798013-148798413`
[2016-04-15T08:51Z] 2016-04-15 01:51:48 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:51:48,349 - WARNING - Could not retrieve variants from source file in region X:154456536-154456937. Error was invalid region `X:154456537-154456937`
[2016-04-15T08:51Z] 2016-04-15 01:51:49 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:51:49,241 - WARNING - Could not retrieve variants from source file in region X:155004069-155004470. Error was invalid region `X:155004070-155004470`
[2016-04-15T08:51Z] 2016-04-15 01:51:49 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:51:49,771 - WARNING - Could not retrieve variants from source file in region X:153149498-153176474. Error was invalid region `X:153149499-153176474`
[2016-04-15T08:52Z] 2016-04-15 01:52:00 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:52:00,523 - WARNING - Could not retrieve variants from source file in region X:151137968-151138369. Error was invalid region `X:151137969-151138369`
[2016-04-15T08:52Z] 2016-04-15 01:52:00 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:52:00,757 - WARNING - Could not retrieve variants from source file in region X:153418257-153422102. Error was invalid region `X:153418258-153422102`
[2016-04-15T08:52Z] 2016-04-15 01:52:01 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:52:01,107 - WARNING - Could not retrieve variants from source file in region X:150791292-150791702. Error was invalid region `X:150791293-150791702`
[2016-04-15T08:52Z] 2016-04-15 01:52:01 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:52:01,390 - WARNING - Could not retrieve variants from source file in region X:151303182-151303786. Error was invalid region `X:151303183-151303786`
[2016-04-15T08:52Z] 2016-04-15 01:52:02 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:52:02,841 - WARNING - Could not retrieve variants from source file in region X:151303182-151303786. Error was invalid region `X:151303183-151303786`
[2016-04-15T08:52Z] 2016-04-15 01:52:02 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:52:02,883 - WARNING - Could not retrieve variants from source file in region X:152612901-152613302. Error was invalid region `X:152612902-152613302`
[2016-04-15T08:52Z] 2016-04-15 01:52:03 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:52:03,292 - WARNING - Could not retrieve variants from source file in region X:150349660-150350061. Error was invalid region `X:150349661-150350061`
[2016-04-15T08:52Z] 2016-04-15 01:52:03 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:52:03,808 - WARNING - Could not retrieve variants from source file in region X:153628944-153657273. Error was invalid region `X:153628945-153657273`
[2016-04-15T08:52Z] 2016-04-15 01:52:04 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:52:04,857 - WARNING - Could not retrieve variants from source file in region X:149680328-149680744. Error was invalid region `X:149680329-149680744`
[2016-04-15T08:52Z] 2016-04-15 01:52:06 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:52:06,593 - WARNING - Could not retrieve variants from source file in region X:153031126-153073509. Error was invalid region `X:153031127-153073509`
[2016-04-15T08:52Z] 2016-04-15 01:52:06 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:52:06,636 - WARNING - Could not retrieve variants from source file in region X:151303182-151303786. Error was invalid region `X:151303183-151303786`
[2016-04-15T08:52Z] 2016-04-15 01:52:06 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:52:06,683 - WARNING - Could not retrieve variants from source file in region X:152226331-152226732. Error was invalid region `X:152226332-152226732`
[2016-04-15T08:52Z] 2016-04-15 01:52:07 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:52:07,810 - WARNING - Could not retrieve variants from source file in region X:150349660-150350061. Error was invalid region `X:150349661-150350061`
[2016-04-15T08:52Z] 2016-04-15 01:52:08 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:52:08,055 - WARNING - Could not retrieve variants from source file in region X:153628944-153657273. Error was invalid region `X:153628945-153657273`
[2016-04-15T08:52Z] 2016-04-15 01:52:09 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:52:09,449 - WARNING - Could not retrieve variants from source file in region X:149680328-149680744. Error was invalid region `X:149680329-149680744`
[2016-04-15T08:52Z] 2016-04-15 01:52:11 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:52:11,409 - WARNING - Could not retrieve variants from source file in region X:149638709-149642209. Error was invalid region `X:149638710-149642209`
[2016-04-15T08:52Z] 2016-04-15 01:52:11 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:52:11,474 - WARNING - Could not retrieve variants from source file in region X:152226331-152226732. Error was invalid region `X:152226332-152226732`
[2016-04-15T08:52Z] 2016-04-15 01:52:12 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:52:12,691 - WARNING - Could not retrieve variants from source file in region X:150349660-150350061. Error was invalid region `X:150349661-150350061`
[2016-04-15T08:52Z] 2016-04-15 01:52:12 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:52:12,726 - WARNING - Could not retrieve variants from source file in region X:153628944-153657273. Error was invalid region `X:153628945-153657273`
[2016-04-15T08:52Z] 2016-04-15 01:52:13 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:52:13,880 - WARNING - Could not retrieve variants from source file in region X:149680328-149680744. Error was invalid region `X:149680329-149680744`
[2016-04-15T08:52Z] 2016-04-15 01:52:15 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:52:15,897 - WARNING - Could not retrieve variants from source file in region X:151091915-151092843. Error was invalid region `X:151091916-151092843`
[2016-04-15T08:52Z] 2016-04-15 01:52:17 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:52:17,107 - WARNING - Could not retrieve variants from source file in region X:152226331-152226732. Error was invalid region `X:152226332-152226732`
[2016-04-15T08:52Z] 2016-04-15 01:52:25 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:52:25,048 - WARNING - Could not retrieve variants from source file in region X:153278618-153284673. Error was invalid region `X:153278619-153284673`
[2016-04-15T08:52Z] 2016-04-15 01:52:25 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:52:25,876 - WARNING - Could not retrieve variants from source file in region X:152018621-152034561. Error was invalid region `X:152018622-152034561`
[2016-04-15T08:52Z] 2016-04-15 01:52:26 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:52:26,310 - WARNING - Could not retrieve variants from source file in region X:153215628-153216029. Error was invalid region `X:153215629-153216029`
[2016-04-15T08:52Z] 2016-04-15 01:52:26 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:52:26,310 - WARNING - Could not retrieve variants from source file in region X:149013516-149013917. Error was invalid region `X:149013517-149013917`
[2016-04-15T08:52Z] 2016-04-15 01:52:26 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:52:26,400 - WARNING - Could not retrieve variants from source file in region X:149013516-149013917. Error was invalid region `X:149013517-149013917`
[2016-04-15T08:52Z] 2016-04-15 01:52:28 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:52:28,610 - WARNING - Could not retrieve variants from source file in region X:153278618-153284673. Error was invalid region `X:153278619-153284673`
[2016-04-15T08:52Z] 2016-04-15 01:52:29 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:52:29,214 - WARNING - Could not retrieve variants from source file in region X:149013516-149013917. Error was invalid region `X:149013517-149013917`
[2016-04-15T08:52Z] 2016-04-15 01:52:29 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:52:29,879 - WARNING - Could not retrieve variants from source file in region X:153215628-153216029. Error was invalid region `X:153215629-153216029`
[2016-04-15T08:52Z] 2016-04-15 01:52:30 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:52:30,913 - WARNING - Could not retrieve variants from source file in region X:153278618-153284673. Error was invalid region `X:153278619-153284673`
[2016-04-15T08:52Z] ['bcbio-variation-recall', 'square', '-Xms750m', '-Xmx7280m', '-XX:+UseSerialGC', '-c', 16, '-r', u'Y:1-15522993', '--caller', 'platypus', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/Y/Batch1-Y_0_15522993.vcf.gz', '/mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/Y/Batch1-Y_0_15522993.vcf-inputs.txt'] in region: Y:1-15522993
[2016-04-15T08:52Z] ['bcbio-variation-recall', 'square', '-Xms750m', '-Xmx7280m', '-XX:+UseSerialGC', '-c', 16, '-r', u'Y:15526615-59222281', '--caller', 'platypus', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/Y/Batch1-Y_15526614_59222281.vcf.gz', '/mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/Y/Batch1-Y_15526614_59222281.vcf-inputs.txt'] in region: Y:15526615-59222281
[2016-04-15T08:52Z] 2016-04-15 01:52:44 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:52:44,728 - WARNING - Could not retrieve variants from source file in region Y:21154112-21154759. Error was invalid region `Y:21154113-21154759`
[2016-04-15T08:52Z] 2016-04-15 01:52:44 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:52:44,777 - WARNING - Could not retrieve variants from source file in region Y:16952454-16952855. Error was invalid region `Y:16952455-16952855`
[2016-04-15T08:52Z] 2016-04-15 01:52:44 ihg-node-32 INFO [bcbio.run.itx] - 2016-04-15 01:52:44,873 - WARNING - Could not retrieve variants from source file in region Y:21154112-21154759. Error was invalid region `Y:21154113-21154759`
[2016-04-15T08:52Z] ['bcbio-variation-recall', 'square', '-Xms750m', '-Xmx7280m', '-XX:+UseSerialGC', '-c', 16, '-r', u'Y:59228292-59373566', '--caller', 'platypus', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/Y/Batch1-Y_59228291_59373566.vcf.gz', '/mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa', u'/mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/Y/Batch1-Y_59228291_59373566.vcf-inputs.txt'] in region: Y:59228292-59373566
[2016-04-15T08:52Z] multiprocessing: concat_variant_files
[2016-04-15T08:52Z] Resource requests: ; memory: 1.00; cores: 1
[2016-04-15T08:52Z] Configuring 16 jobs to run, using 1 cores each with 1.00g of memory reserved for each job
[2016-04-15T08:52Z] Concat variant files
[2016-04-15T08:52Z] INFO  01:52:56,413 HelpFormatter - -------------------------------------------------------
[2016-04-15T08:52Z] INFO  01:52:56,415 HelpFormatter - Program Name: org.broadinstitute.gatk.tools.CatVariants
[2016-04-15T08:52Z] INFO  01:52:56,419 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -V /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/gatk-haplotype-joint/Batch1/Batch1-joint-files.list -out /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/gatk-haplotype-joint/Batch1/tx/tmpk8zIyp/Batch1-joint.vcf.gz -assumeSorted
[2016-04-15T08:52Z] INFO  01:52:56,427 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T08:52Z] INFO  01:52:56,428 HelpFormatter - Date/Time: 2016/04/15 01:52:56
[2016-04-15T08:52Z] INFO  01:52:56,428 HelpFormatter - -------------------------------------------------------
[2016-04-15T08:52Z] INFO  01:52:56,428 HelpFormatter - -------------------------------------------------------
[2016-04-15T08:53Z] .........10.........20.........30.........40.........50.........60.........70.........80.........90.........100.........110.........120.........130.........140.........150.........160.........170.........180.........190.........200...
[2016-04-15T08:53Z] Resource requests: ; memory: 1.00; cores: 1
[2016-04-15T08:53Z] Configuring 16 jobs to run, using 1 cores each with 1.00g of memory reserved for each job
[2016-04-15T08:53Z] Concat variant files
[2016-04-15T08:53Z] INFO  01:53:08,854 HelpFormatter - -------------------------------------------------------
[2016-04-15T08:53Z] INFO  01:53:08,857 HelpFormatter - Program Name: org.broadinstitute.gatk.tools.CatVariants
[2016-04-15T08:53Z] INFO  01:53:08,861 HelpFormatter - Program Args: -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -V /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/Batch1-joint-files.list -out /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/tx/tmpPQKRUi/Batch1-joint.vcf.gz -assumeSorted
[2016-04-15T08:53Z] INFO  01:53:08,869 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T08:53Z] INFO  01:53:08,870 HelpFormatter - Date/Time: 2016/04/15 01:53:08
[2016-04-15T08:53Z] INFO  01:53:08,870 HelpFormatter - -------------------------------------------------------
[2016-04-15T08:53Z] INFO  01:53:08,870 HelpFormatter - -------------------------------------------------------
[2016-04-15T08:53Z] .........10.........20.........30.........40.........50.........60.........70.........80.........90.........100.........110.........120.........130.........140.........150.........160.........170.........180.........190.........
[2016-04-15T08:53Z] Timing: variant post-processing
[2016-04-15T08:53Z] multiprocessing: postprocess_variants
[2016-04-15T08:53Z] Finalizing variant calls: R14-18106_kapa-NGv3-PE100-NGv3, gatk-haplotype
[2016-04-15T08:53Z] Calculating variation effects for R14-18106_kapa-NGv3-PE100-NGv3, gatk-haplotype
[2016-04-15T08:53Z] snpEff effects : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T08:55Z] tabix index Batch1-joint-effects.vcf.gz
[2016-04-15T08:55Z] Filtering for R14-18106_kapa-NGv3-PE100-NGv3, gatk-haplotype
[2016-04-15T08:55Z] Subset to SNPs and indels
[2016-04-15T08:55Z] tabix index Batch1-joint-effects-snp.vcf.gz
[2016-04-15T08:55Z] Subset to SNPs and indels
[2016-04-15T08:55Z] tabix index Batch1-joint-effects-indel.vcf.gz
[2016-04-15T08:55Z] Skipping VQSR, using hard filers: we don't have whole genome input data
[2016-04-15T08:55Z] Hard filtering /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/gatk-haplotype-joint/Batch1/Batch1-joint-effects-snp.vcf.gz with QD < 2.0 || MQ < 30.0 || FS > 60.0 || MQRankSum < -12.5 || ReadPosRankSum < -8.0 : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T08:55Z] tabix index Batch1-joint-effects-snp-filterSNP.vcf.gz
[2016-04-15T08:55Z] Skipping VQSR, using hard filers: we don't have whole genome input data
[2016-04-15T08:55Z] Hard filtering /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/gatk-haplotype-joint/Batch1/Batch1-joint-effects-indel.vcf.gz with QD < 2.0 || ReadPosRankSum < -20.0 || FS > 200.0 : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T08:55Z] tabix index Batch1-joint-effects-indel-filterINDEL.vcf.gz
[2016-04-15T08:55Z] Resource requests: ; memory: 1.00; cores: 1
[2016-04-15T08:55Z] Configuring 2 jobs to run, using 1 cores each with 1.00g of memory reserved for each job
[2016-04-15T08:55Z] Combine variant files
[2016-04-15T08:55Z] INFO  01:55:20,630 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T08:55Z] INFO  01:55:20,631 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-65-g2434e49, Compiled 2015/10/09 18:46:40
[2016-04-15T08:55Z] INFO  01:55:20,632 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2016-04-15T08:55Z] INFO  01:55:20,632 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2016-04-15T08:55Z] INFO  01:55:20,635 HelpFormatter - Program Args: -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -T CombineVariants -R /mnt/speed/qc/sequencing/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa --out /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/gatk-haplotype-joint/Batch1/tx/tmpiHkTZJ/Batch1-joint-effects-combined.vcf.gz --variant:v0 /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/gatk-haplotype-joint/Batch1/Batch1-joint-effects-snp-filterSNP.vcf.gz --variant:v1 /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/gatk-haplotype-joint/Batch1/Batch1-joint-effects-indel-filterINDEL.vcf.gz --rod_priority_list v0,v1 --genotypemergeoption PRIORITIZE --suppressCommandLineHeader --setKey null -nt 4
[2016-04-15T08:55Z] INFO  01:55:20,642 HelpFormatter - Executing as sequencing@ihg-node-32 on Linux 2.6.32-504.1.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_91-b15.
[2016-04-15T08:55Z] INFO  01:55:20,642 HelpFormatter - Date/Time: 2016/04/15 01:55:20
[2016-04-15T08:55Z] INFO  01:55:20,642 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T08:55Z] INFO  01:55:20,642 HelpFormatter - ---------------------------------------------------------------------------------
[2016-04-15T08:55Z] INFO  01:55:20,714 GenomeAnalysisEngine - Strictness is SILENT
[2016-04-15T08:55Z] INFO  01:55:20,813 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
[2016-04-15T08:55Z] WARN  01:55:20,958 IndexDictionaryUtils - Track v0 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T08:55Z] WARN  01:55:20,958 IndexDictionaryUtils - Track v1 doesn't have a sequence dictionary built in, skipping dictionary validation
[2016-04-15T08:55Z] INFO  01:55:20,967 MicroScheduler - Running the GATK in parallel mode with 4 total threads, 1 CPU thread(s) for each of 4 data thread(s), of 16 processors available on this machine
[2016-04-15T08:55Z] INFO  01:55:21,026 GenomeAnalysisEngine - Preparing for traversal
[2016-04-15T08:55Z] INFO  01:55:21,044 GenomeAnalysisEngine - Done preparing for traversal
[2016-04-15T08:55Z] INFO  01:55:21,044 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
[2016-04-15T08:55Z] INFO  01:55:21,045 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining
[2016-04-15T08:55Z] INFO  01:55:21,045 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime
[2016-04-15T08:55Z] INFO  01:55:51,067 ProgressMeter -    11:133290189     30595.0    30.0 s      16.3 m       62.8%    47.0 s      17.0 s
[2016-04-15T08:56Z] INFO  01:56:06,364 ProgressMeter -            done     51184.0    45.0 s      14.8 m       98.6%    45.0 s       0.0 s
[2016-04-15T08:56Z] INFO  01:56:06,365 ProgressMeter - Total runtime 45.32 secs, 0.76 min, 0.01 hours
[2016-04-15T08:56Z] Remove stray NON_REF gVCF information from VCF output : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T08:56Z] tabix index Batch1-joint-effects-combined-gatkclean.vcf.gz
[2016-04-15T08:56Z] Prioritization for R14-18106_kapa-NGv3-PE100-NGv3, gatk-haplotype
[2016-04-15T08:56Z] Germline extraction for R14-18106_kapa-NGv3-PE100-NGv3, gatk-haplotype
[2016-04-15T08:56Z] Finalizing variant calls: R14-18106_kapa-NGv3-PE100-NGv3, platypus
[2016-04-15T08:56Z] Calculating variation effects for R14-18106_kapa-NGv3-PE100-NGv3, platypus
[2016-04-15T08:56Z] snpEff effects : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T08:57Z] tabix index Batch1-joint-effects.vcf.gz
[2016-04-15T08:57Z] Filtering for R14-18106_kapa-NGv3-PE100-NGv3, platypus
[2016-04-15T08:57Z] Hard filtering /mnt/speed/qc/sequencing/ihg-pipeline/MSC_3callers/joint/platypus-joint/Batch1/Batch1-joint-effects.vcf.gz with (FR[0] <= 0.5 && TC < 4 && %QUAL < 20) || (TC < 13 && %QUAL < 10) || (FR[0] > 0.5 && TC < 4 && %QUAL < 50) : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T08:57Z] tabix index Batch1-joint-effects-filter.vcf.gz
[2016-04-15T08:57Z] Prioritization for R14-18106_kapa-NGv3-PE100-NGv3, platypus
[2016-04-15T08:57Z] Germline extraction for R14-18106_kapa-NGv3-PE100-NGv3, platypus
[2016-04-15T08:57Z] Finalizing variant calls: R14-18106_kapa-NGv3-PE100-NGv3, gatk
[2016-04-15T08:57Z] Calculating variation effects for R14-18106_kapa-NGv3-PE100-NGv3, gatk
[2016-04-15T08:57Z] snpEff effects : R14-18106_kapa-NGv3-PE100-NGv3
[2016-04-15T08:59Z] tabix index R14-18106_kapa-NGv3-PE100-NGv3-effects.vcf.gz
[2016-04-15T08:59Z] Filtering for R14-18106_kapa-NGv3-PE100-NGv3, gatk
Traceback (most recent call last):
  File "/mnt/speed/qc/sequencing/bcbio/anaconda/bin/bcbio_nextgen.py", line 4, in <module>
    __import__('pkg_resources').run_script('bcbio-nextgen==0.9.7', 'bcbio_nextgen.py')
  File "/mnt/speed/qc/sequencing/bcbio/anaconda/lib/python2.7/site-packages/setuptools-20.2.2-py2.7.egg/pkg_resources/__init__.py", line 726, in run_script
    
  File "/mnt/speed/qc/sequencing/bcbio/anaconda/lib/python2.7/site-packages/setuptools-20.2.2-py2.7.egg/pkg_resources/__init__.py", line 1484, in run_script
    
  File "/mnt/speed/qc/sequencing/bcbio/anaconda/lib/python2.7/site-packages/bcbio_nextgen-0.9.7-py2.7.egg-info/scripts/bcbio_nextgen.py", line 226, in <module>
    main(**kwargs)
  File "/mnt/speed/qc/sequencing/bcbio/anaconda/lib/python2.7/site-packages/bcbio_nextgen-0.9.7-py2.7.egg-info/scripts/bcbio_nextgen.py", line 43, in main
    run_main(**kwargs)
  File "/mnt/speed/qc/sequencing/bcbio/anaconda/lib/python2.7/site-packages/bcbio/pipeline/main.py", line 39, in run_main
    fc_dir, run_info_yaml)
  File "/mnt/speed/qc/sequencing/bcbio/anaconda/lib/python2.7/site-packages/bcbio/pipeline/main.py", line 82, in _run_toplevel
    for xs in pipeline(config, run_info_yaml, parallel, dirs, samples):
  File "/mnt/speed/qc/sequencing/bcbio/anaconda/lib/python2.7/site-packages/bcbio/pipeline/main.py", line 161, in variant2pipeline
    samples = run_parallel("postprocess_variants", samples)
  File "/mnt/speed/qc/sequencing/bcbio/anaconda/lib/python2.7/site-packages/bcbio/distributed/multi.py", line 28, in run_parallel
    return run_multicore(fn, items, config, parallel=parallel)
  File "/mnt/speed/qc/sequencing/bcbio/anaconda/lib/python2.7/site-packages/bcbio/distributed/multi.py", line 86, in run_multicore
    for data in joblib.Parallel(parallel["num_jobs"])(joblib.delayed(fn)(x) for x in items):
  File "/mnt/speed/qc/sequencing/bcbio/anaconda/lib/python2.7/site-packages/joblib/parallel.py", line 804, in __call__
    while self.dispatch_one_batch(iterator):
  File "/mnt/speed/qc/sequencing/bcbio/anaconda/lib/python2.7/site-packages/joblib/parallel.py", line 662, in dispatch_one_batch
    self._dispatch(tasks)
  File "/mnt/speed/qc/sequencing/bcbio/anaconda/lib/python2.7/site-packages/joblib/parallel.py", line 570, in _dispatch
    job = ImmediateComputeBatch(batch)
  File "/mnt/speed/qc/sequencing/bcbio/anaconda/lib/python2.7/site-packages/joblib/parallel.py", line 183, in __init__
    self.results = batch()
  File "/mnt/speed/qc/sequencing/bcbio/anaconda/lib/python2.7/site-packages/joblib/parallel.py", line 72, in __call__
    return [func(*args, **kwargs) for func, args, kwargs in self.items]
  File "/mnt/speed/qc/sequencing/bcbio/anaconda/lib/python2.7/site-packages/bcbio/utils.py", line 51, in wrapper
    return apply(f, *args, **kwargs)
  File "/mnt/speed/qc/sequencing/bcbio/anaconda/lib/python2.7/site-packages/bcbio/distributed/multitasks.py", line 127, in postprocess_variants
    return variation.postprocess_variants(*args)
  File "/mnt/speed/qc/sequencing/bcbio/anaconda/lib/python2.7/site-packages/bcbio/pipeline/variation.py", line 32, in postprocess_variants
    orig_items = _get_orig_items(items)
  File "/mnt/speed/qc/sequencing/bcbio/anaconda/lib/python2.7/site-packages/bcbio/pipeline/variation.py", line 49, in _get_orig_items
    return vmulti.get_orig_items(data)
  File "/mnt/speed/qc/sequencing/bcbio/anaconda/lib/python2.7/site-packages/bcbio/variation/multi.py", line 213, in get_orig_items
    assert "group_orig" in base
AssertionError